From 5d7ce839a162fd16448689685840b2a3738024fe Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 22 Aug 2019 10:41:35 -0600
Subject: [PATCH 001/199] Fix memory leak

---
 python/lammps.py | 60 +++++++++++++++++++++++-------------------------
 1 file changed, 29 insertions(+), 31 deletions(-)

diff --git a/python/lammps.py b/python/lammps.py
index 36cf2d2fdd..e7062ba514 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -221,8 +221,8 @@ class lammps(object):
 
     # add way to insert Python callback for fix external
     self.callback = {}
-    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, c_void_p, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
-    self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, c_void_p]
+    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
+    self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, py_object]
     self.lib.lammps_set_fix_external_callback.restype = None
 
   # shut-down LAMMPS instance
@@ -357,26 +357,38 @@ class lammps(object):
           else:
             c_int_type = c_int
 
+          if dim == 1:
+            raw_ptr = self.lmp.extract_atom(name, 0)
+          else:
+            raw_ptr = self.lmp.extract_atom(name, 1)
+
+          return self.iarray(c_int_type, raw_ptr, nelem, dim)
+
+        def extract_atom_darray(self, name, nelem, dim=1):
+          if dim == 1:
+            raw_ptr = self.lmp.extract_atom(name, 2)
+          else:
+            raw_ptr = self.lmp.extract_atom(name, 3)
+
+          return self.darray(raw_ptr, nelem, dim)
+
+        def iarray(self, c_int_type, raw_ptr, nelem, dim=1):
           np_int_type = self._ctype_to_numpy_int(c_int_type)
 
           if dim == 1:
-            tmp = self.lmp.extract_atom(name, 0)
-            ptr = cast(tmp, POINTER(c_int_type * nelem))
+            ptr = cast(raw_ptr, POINTER(c_int_type * nelem))
           else:
-            tmp = self.lmp.extract_atom(name, 1)
-            ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
+            ptr = cast(raw_ptr[0], POINTER(c_int_type * nelem * dim))
 
           a = np.frombuffer(ptr.contents, dtype=np_int_type)
           a.shape = (nelem, dim)
           return a
 
-        def extract_atom_darray(self, name, nelem, dim=1):
+        def darray(self, raw_ptr, nelem, dim=1):
           if dim == 1:
-            tmp = self.lmp.extract_atom(name, 2)
-            ptr = cast(tmp, POINTER(c_double * nelem))
+            ptr = cast(raw_ptr, POINTER(c_double * nelem))
           else:
-            tmp = self.lmp.extract_atom(name, 3)
-            ptr = cast(tmp[0], POINTER(c_double * nelem * dim))
+            ptr = cast(raw_ptr[0], POINTER(c_double * nelem * dim))
 
           a = np.frombuffer(ptr.contents)
           a.shape = (nelem, dim)
@@ -617,28 +629,14 @@ class lammps(object):
             return np.int64
           return np.intc
 
-    def callback_wrapper(caller_ptr, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
-      if cast(caller_ptr,POINTER(py_object)).contents:
-        pyCallerObj = cast(caller_ptr,POINTER(py_object)).contents.value
-      else:
-        pyCallerObj = None
-
-      tptr = cast(tag_ptr, POINTER(self.c_tagint * nlocal))
-      tag = np.frombuffer(tptr.contents, dtype=_ctype_to_numpy_int(self.c_tagint))
-      tag.shape = (nlocal)
-
-      xptr = cast(x_ptr[0], POINTER(c_double * nlocal * 3))
-      x = np.frombuffer(xptr.contents)
-      x.shape = (nlocal, 3)
-
-      fptr = cast(fext_ptr[0], POINTER(c_double * nlocal * 3))
-      f = np.frombuffer(fptr.contents)
-      f.shape = (nlocal, 3)
-
-      callback(pyCallerObj, ntimestep, nlocal, tag, x, f)
+    def callback_wrapper(caller, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
+      tag = self.numpy.iarray(self.c_tagint, tag_ptr, nlocal, 1)
+      x   = self.numpy.darray(x_ptr, nlocal, 3)
+      f   = self.numpy.darray(fext_ptr, nlocal, 3)
+      callback(caller, ntimestep, nlocal, tag, x, f)
 
     cFunc   = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper)
-    cCaller = cast(pointer(py_object(caller)), c_void_p)
+    cCaller = caller
 
     self.callback[fix_name] = { 'function': cFunc, 'caller': caller }
 

From 3353bffb7211d5521f365ffacd491707b4a958a5 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 22 Aug 2019 10:45:24 -0600
Subject: [PATCH 002/199] Remove magic numbers and additional data types in
 extract_global

---
 python/lammps.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/python/lammps.py b/python/lammps.py
index e7062ba514..cd22a2bceb 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -32,6 +32,11 @@ import select
 import re
 import sys
 
+LAMMPS_INT    = 0
+LAMMPS_DOUBLE = 1
+LAMMPS_BIGINT = 2
+LAMMPS_TAGINT = 3
+
 def get_ctypes_int(size):
   if size == 4:
     return c_int32
@@ -283,10 +288,14 @@ class lammps(object):
 
   def extract_global(self,name,type):
     if name: name = name.encode()
-    if type == 0:
+    if type == LAMMPS_INT:
       self.lib.lammps_extract_global.restype = POINTER(c_int)
-    elif type == 1:
+    elif type == LAMMPS_DOUBLE:
       self.lib.lammps_extract_global.restype = POINTER(c_double)
+    elif type == LAMMPS_BIGINT:
+      self.lib.lammps_extract_global.restype = POINTER(self.c_bigint)
+    elif type == LAMMPS_TAGINT:
+      self.lib.lammps_extract_global.restype = POINTER(self.c_tagint)
     else: return None
     ptr = self.lib.lammps_extract_global(self.lmp,name)
     return ptr[0]

From 69854eab42de4c7cf12fbc01687462192668be38 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 12 Sep 2019 13:43:14 -0400
Subject: [PATCH 003/199] Expose Neighbor lists via library interface

---
 .../python/in.fix_python_invoke_neighlist     |  68 +++++++++
 python/lammps.py                              |  72 ++++++++++
 src/library.cpp                               | 133 ++++++++++++++++++
 src/library.h                                 |   6 +
 src/neigh_list.cpp                            |   3 +
 src/neigh_list.h                              |   4 +
 src/neighbor.cpp                              |   9 ++
 7 files changed, 295 insertions(+)
 create mode 100644 examples/python/in.fix_python_invoke_neighlist

diff --git a/examples/python/in.fix_python_invoke_neighlist b/examples/python/in.fix_python_invoke_neighlist
new file mode 100644
index 0000000000..36d4bffe67
--- /dev/null
+++ b/examples/python/in.fix_python_invoke_neighlist
@@ -0,0 +1,68 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 2 0 2 0 2
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.1 bin
+
+neigh_modify	every 20 delay 0 check no
+
+python         post_force_callback here """
+from __future__ import print_function
+from lammps import lammps
+
+def post_force_callback(lmp, v):
+  try:
+    L = lammps(ptr=lmp)
+    t = L.extract_global("ntimestep", 0)
+    print("### POST_FORCE ###", t)
+
+    #mylist = L.get_neighlist(0)
+    mylist = L.find_pair_neighlist("lj/cut", request=0)
+    print(mylist)
+    nlocal = L.extract_global("nlocal", 0)
+    nghost = L.extract_global("nghost", 0)
+    ntypes = L.extract_global("ntypes", 0)
+    mass = L.numpy.extract_atom_darray("mass", ntypes+1)
+    atype = L.numpy.extract_atom_iarray("type", nlocal+nghost)
+    x = L.numpy.extract_atom_darray("x", nlocal+nghost, dim=3)
+    v = L.numpy.extract_atom_darray("v", nlocal+nghost, dim=3)
+    f = L.numpy.extract_atom_darray("f", nlocal+nghost, dim=3)
+
+    for iatom, numneigh, neighs in mylist:
+      print("- {}".format(iatom), x[iatom], v[iatom], f[iatom], " : ",  numneigh, "Neighbors")
+      for jatom in neighs:
+        if jatom < nlocal:
+            print("    *  ", jatom, x[jatom], v[jatom], f[jatom])
+        else:
+            print("    * [GHOST]", jatom, x[jatom], v[jatom], f[jatom])
+  except Exception as e:
+    print(e)
+"""
+
+fix		1 all nve
+fix     3 all python/invoke 1 post_force post_force_callback
+
+#dump		id all atom 1 dump.melt
+
+#dump		2 all image 1 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+#dump		3 all movie 1 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3
+
+thermo		1
+run		1
diff --git a/python/lammps.py b/python/lammps.py
index cd22a2bceb..4772a34c8d 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -51,6 +51,31 @@ class MPIAbortException(Exception):
   def __str__(self):
     return repr(self.message)
 
+class NeighList:
+    def __init__(self, lmp, idx):
+        self.lmp = lmp
+        self.idx = idx
+
+    def __str__(self):
+        return "Neighbor List ({} atoms)".format(self.size)
+
+    def __repr__(self):
+        return self.__str__()
+
+    @property
+    def size(self):
+        return self.lmp.get_neighlist_size(self.idx)
+
+    def get(self, element):
+        iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)
+        return iatom, numneigh, neighbors
+
+    def __iter__(self):
+        inum = self.size
+
+        for ii in range(inum):
+            yield self.get(ii)
+
 class lammps(object):
 
   # detect if Python is using version of mpi4py that can pass a communicator
@@ -73,6 +98,7 @@ class lammps(object):
 
     modpath = dirname(abspath(getsourcefile(lambda:0)))
     self.lib = None
+    self.lmp = None
 
     # if a pointer to a LAMMPS object is handed in,
     # all symbols should already be available
@@ -137,6 +163,21 @@ class lammps(object):
       [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
     self.lib.lammps_scatter_atoms_subset.restype = None
 
+    self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int]
+    self.lib.lammps_find_pair_neighlist.restype  = c_int
+
+    self.lib.lammps_find_fix_neighlist.argtypes = [c_void_p, c_char_p, c_int]
+    self.lib.lammps_find_fix_neighlist.restype  = c_int
+
+    self.lib.lammps_find_compute_neighlist.argtypes = [c_void_p, c_char_p, c_int]
+    self.lib.lammps_find_compute_neighlist.restype  = c_int
+
+    self.lib.lammps_neighlist_num_elements.argtypes = [c_void_p, c_int]
+    self.lib.lammps_neighlist_num_elements.restype  = c_int
+
+    self.lib.lammps_neighlist_element_neighbors.argtypes = [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
+    self.lib.lammps_neighlist_element_neighbors.restype  = None
+
     # if no ptr provided, create an instance of LAMMPS
     #   don't know how to pass an MPI communicator from PyPar
     #   but we can pass an MPI communicator from mpi4py v2.0.0 and later
@@ -651,6 +692,37 @@ class lammps(object):
 
     self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller)
 
+  def get_neighlist(self, idx):
+    if idx < 0:
+        return None
+    return NeighList(self, idx)
+
+  def find_pair_neighlist(self, style, nsub=0, request=0):
+    style = style.encode()
+    idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, nsub, request)
+    return self.get_neighlist(idx)
+
+  def find_fix_neighlist(self, fixid, request=0):
+    fixid = fixid.encode()
+    idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request)
+    return self.get_neighlist(idx)
+
+  def find_compute_neighlist(self, computeid, request):
+    computeid = computeid.encode()
+    idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request)
+    return self.get_neighlist(idx)
+
+  def get_neighlist_size(self, idx):
+    return self.lib.lammps_neighlist_num_elements(self.lmp, idx)
+
+  def get_neighlist_element_neighbors(self, idx, element):
+    c_iatom = c_int()
+    c_numneigh = c_int()
+    c_neighbors = POINTER(c_int)()
+    self.lib.lammps_neighlist_element_neighbors(self.lmp, idx, element, byref(c_iatom), byref(c_numneigh), byref(c_neighbors))
+    neighbors = self.numpy.iarray(c_int, c_neighbors, c_numneigh.value, 1)
+    return c_iatom.value, c_numneigh.value, neighbors
+
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
diff --git a/src/library.cpp b/src/library.cpp
index 6f283ea4da..407ec454a9 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -38,6 +38,9 @@
 #include "force.h"
 #include "info.h"
 #include "fix_external.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
 
 #if defined(LAMMPS_EXCEPTIONS)
 #include "exceptions.h"
@@ -1727,3 +1730,133 @@ int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
 }
 
 #endif
+
+/* ----------------------------------------------------------------------
+   Find neighbor list index for pair style
+------------------------------------------------------------------------- */
+int lammps_find_pair_neighlist(void* ptr, char * style, int nsub, int request) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Pair* pair = lmp->force->pair_match(style, 1, nsub);
+
+  if (pair != NULL) {
+    // find neigh list
+    for (int i = 0; i < lmp->neighbor->nlist; i++) {
+      NeighList * list = lmp->neighbor->lists[i];
+      if (list->requestor_type != NeighList::PAIR || pair != list->requestor) continue;
+
+      if (list->index == request) {
+          return i;
+      }
+    }
+  }
+  return -1;
+}
+
+/* ----------------------------------------------------------------------
+   Find neighbor list index for compute with given fix ID
+   The request ID identifies which request it is in case of there are
+   multiple neighbor lists for this fix
+------------------------------------------------------------------------- */
+int lammps_find_fix_neighlist(void* ptr, char * id, int request) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Fix* fix = NULL;
+  const int nfix = lmp->modify->nfix;
+
+  // find fix with name
+  for (int ifix = 0; ifix < nfix; ifix++) {
+    if (strcmp(lmp->modify->fix[ifix]->id, id) == 0) {
+        fix = lmp->modify->fix[ifix];
+        break;
+    }
+  }
+
+  if (fix != NULL) {
+    // find neigh list
+    for (int i = 0; i < lmp->neighbor->nlist; i++) {
+      NeighList * list = lmp->neighbor->lists[i];
+      if (list->requestor_type != NeighList::FIX || fix != list->requestor) continue;
+
+      if (list->index == request) {
+          return i;
+      }
+    }
+  }
+  return -1;
+}
+
+/* ----------------------------------------------------------------------
+   Find neighbor list index for compute with given compute ID
+   The request ID identifies which request it is in case of there are
+   multiple neighbor lists for this compute
+------------------------------------------------------------------------- */
+
+int lammps_find_compute_neighlist(void* ptr, char * id, int request) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Compute* compute = NULL;
+  const int ncompute = lmp->modify->ncompute;
+
+  // find compute with name
+  for (int icompute = 0; icompute < ncompute; icompute++) {
+    if (strcmp(lmp->modify->compute[icompute]->id, id) == 0) {
+        compute = lmp->modify->compute[icompute];
+        break;
+    }
+  }
+
+  if (compute == NULL) {
+    // find neigh list
+    for (int i = 0; i < lmp->neighbor->nlist; i++) {
+      NeighList * list = lmp->neighbor->lists[i];
+      if (list->requestor_type != NeighList::COMPUTE || compute != list->requestor) continue;
+
+      if (list->index == request) {
+          return i;
+      }
+    }
+  }
+  return -1;
+}
+
+/* ----------------------------------------------------------------------
+   Return the number of entries in the neighbor list with given index
+------------------------------------------------------------------------- */
+
+int lammps_neighlist_num_elements(void * ptr, int idx) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Neighbor * neighbor = lmp->neighbor;
+
+  if(idx < 0 || idx >= neighbor->nlist) {
+    return -1;
+  }
+
+  NeighList * list = neighbor->lists[idx];
+  return list->inum;
+}
+
+/* ----------------------------------------------------------------------
+   Return atom index, number of neighbors and neighbor array for neighbor
+   list entry
+------------------------------------------------------------------------- */
+
+void lammps_neighlist_element_neighbors(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Neighbor * neighbor = lmp->neighbor;
+  *iatom = -1;
+  *numneigh = 0;
+  *neighbors = NULL;
+
+  if(idx < 0 || idx >= neighbor->nlist) {
+    return;
+  }
+
+  NeighList * list = neighbor->lists[idx];
+
+  if(element < 0 || element >= list->inum) {
+    return;
+  }
+
+  int i = list->ilist[element];
+  *iatom     = i;
+  *numneigh  = list->numneigh[i];
+  *neighbors = list->firstneigh[i];
+}
diff --git a/src/library.h b/src/library.h
index 59b68b9502..58fdbee160 100644
--- a/src/library.h
+++ b/src/library.h
@@ -75,6 +75,12 @@ int lammps_config_has_jpeg_support();
 int lammps_config_has_ffmpeg_support();
 int lammps_config_has_exceptions();
 
+int lammps_find_pair_neighlist(void* ptr, char * style, int nsub, int request);
+int lammps_find_fix_neighlist(void* ptr, char * id, int request);
+int lammps_find_compute_neighlist(void* ptr, char * id, int request);
+int lammps_neighlist_num_elements(void* ptr, int idx);
+void lammps_neighlist_element_neighbors(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);
+
 // lammps_create_atoms() takes tagint and imageint as args
 // ifdef insures they are compatible with rest of LAMMPS
 // caller must match to how LAMMPS library is built
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 31720cc78c..1c53b2f7a4 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -85,6 +85,9 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
   // USER-DPD package
 
   np = NULL;
+
+  requestor = NULL;
+  requestor_type = NeighList::NONE;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/neigh_list.h b/src/neigh_list.h
index aca11cd921..146a01e7b5 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -20,6 +20,10 @@ namespace LAMMPS_NS {
 
 class NeighList : protected Pointers {
  public:
+  enum RequestorType { NONE, PAIR, FIX, COMPUTE };
+  void *         requestor;        // object that made request
+  RequestorType  requestor_type;   // type of requestor
+
   int index;                   // index of which neigh list this is
                                // also indexes the request it came from
                                // and the npair list of NPair classes
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index d38aed08c0..acb22b9135 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -701,6 +701,15 @@ int Neighbor::init_pair()
       create_kokkos_list(i);
     else lists[i] = new NeighList(lmp);
     lists[i]->index = i;
+    lists[i]->requestor = requests[i]->requestor;
+
+    if(requests[i]->pair) {
+        lists[i]->requestor_type = NeighList::PAIR;
+    } else if(requests[i]->fix) {
+        lists[i]->requestor_type = NeighList::FIX;
+    } else if(requests[i]->compute) {
+        lists[i]->requestor_type = NeighList::COMPUTE;
+    }
 
     if (requests[i]->pair && i < nrequest_original) {
       Pair *pair = (Pair *) requests[i]->requestor;

From 34dbcf4f20ed969d63f172ed35cd7207caf0abdf Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 12 Sep 2019 13:53:29 -0400
Subject: [PATCH 004/199] Update example

---
 examples/python/in.fix_python_invoke_neighlist | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/examples/python/in.fix_python_invoke_neighlist b/examples/python/in.fix_python_invoke_neighlist
index 36d4bffe67..50f1d52c33 100644
--- a/examples/python/in.fix_python_invoke_neighlist
+++ b/examples/python/in.fix_python_invoke_neighlist
@@ -24,13 +24,17 @@ from lammps import lammps
 
 def post_force_callback(lmp, v):
   try:
+    import os
+    pid = os.getpid()
+    pid_prefix = "[{}] ".format(pid)
+
     L = lammps(ptr=lmp)
     t = L.extract_global("ntimestep", 0)
-    print("### POST_FORCE ###", t)
+    print(pid_prefix, "### POST_FORCE ###", t)
 
     #mylist = L.get_neighlist(0)
     mylist = L.find_pair_neighlist("lj/cut", request=0)
-    print(mylist)
+    print(pid_prefix, mylist)
     nlocal = L.extract_global("nlocal", 0)
     nghost = L.extract_global("nghost", 0)
     ntypes = L.extract_global("ntypes", 0)
@@ -41,18 +45,18 @@ def post_force_callback(lmp, v):
     f = L.numpy.extract_atom_darray("f", nlocal+nghost, dim=3)
 
     for iatom, numneigh, neighs in mylist:
-      print("- {}".format(iatom), x[iatom], v[iatom], f[iatom], " : ",  numneigh, "Neighbors")
+      print(pid_prefix, "- {}".format(iatom), x[iatom], v[iatom], f[iatom], " : ",  numneigh, "Neighbors")
       for jatom in neighs:
         if jatom < nlocal:
-            print("    *  ", jatom, x[jatom], v[jatom], f[jatom])
+            print(pid_prefix, "    *  ", jatom, x[jatom], v[jatom], f[jatom])
         else:
-            print("    * [GHOST]", jatom, x[jatom], v[jatom], f[jatom])
+            print(pid_prefix, "    * [GHOST]", jatom, x[jatom], v[jatom], f[jatom])
   except Exception as e:
     print(e)
 """
 
 fix		1 all nve
-fix     3 all python/invoke 1 post_force post_force_callback
+fix     3 all python/invoke 50 post_force post_force_callback
 
 #dump		id all atom 1 dump.melt
 
@@ -65,4 +69,4 @@ fix     3 all python/invoke 1 post_force post_force_callback
 #dump_modify	3 pad 3
 
 thermo		1
-run		1
+run		100

From fec98170868b9a79bd40fa52ee109660b39bde7c Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 12 Sep 2019 14:14:06 -0400
Subject: [PATCH 005/199] Add __getitem__ implementation for NeighList

---
 python/lammps.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/python/lammps.py b/python/lammps.py
index 4772a34c8d..99d0b026a5 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -70,6 +70,9 @@ class NeighList:
         iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)
         return iatom, numneigh, neighbors
 
+    def __getitem__(self, element):
+        return self.get(element)
+
     def __iter__(self):
         inum = self.size
 

From fb58eb5f2346f59aca391ae0ccff58584c26bec1 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 12 Sep 2019 14:37:18 -0400
Subject: [PATCH 006/199] Add __len__ implementation for NeighList

---
 python/lammps.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/python/lammps.py b/python/lammps.py
index 99d0b026a5..8e3628b0fb 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -72,6 +72,9 @@ class NeighList:
 
     def __getitem__(self, element):
         return self.get(element)
+    
+    def __len__(self):
+        return self.size
 
     def __iter__(self):
         inum = self.size

From 8bc54c96b048c5cc9a09028fa6c6843a3b46fc8d Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 12 Sep 2019 14:44:56 -0400
Subject: [PATCH 007/199] Add missing default

---
 python/lammps.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/lammps.py b/python/lammps.py
index 8e3628b0fb..e3a56a1f3d 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -713,7 +713,7 @@ class lammps(object):
     idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request)
     return self.get_neighlist(idx)
 
-  def find_compute_neighlist(self, computeid, request):
+  def find_compute_neighlist(self, computeid, request=0):
     computeid = computeid.encode()
     idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request)
     return self.get_neighlist(idx)

From 25c3a452f20a8ebd793d3ab5c717527e5f579047 Mon Sep 17 00:00:00 2001
From: Tongtong Shen <shen276@halstead-fe01.rcac.purdue.edu>
Date: Wed, 18 Sep 2019 17:29:45 -0400
Subject: [PATCH 008/199] Added New keywords rotation rx ry rz to fix_deposit

---
 src/MISC/fix_deposit.cpp | 27 ++++++++++++++++++++++-----
 src/MISC/fix_deposit.h   |  5 +++--
 2 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index c9d4958594..c56929d4b3 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "fix_deposit.h"
-#include <mpi.h>
 #include <cmath>
+#include <cstdlib>
 #include <cstring>
+#include "fix_deposit.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
@@ -418,9 +418,15 @@ void FixDeposit::pre_exchange()
       while (rng > molfrac[imol]) imol++;
       natom = onemols[imol]->natoms;
       if (dimension == 3) {
-        r[0] = random->uniform() - 0.5;
-        r[1] = random->uniform() - 0.5;
-        r[2] = random->uniform() - 0.5;
+        if (rflag == 1) {
+          r[0] = rx;
+          r[1] = ry;
+          r[2] = rz;
+        } else {
+          r[0] = random->uniform() - 0.5;
+          r[1] = random->uniform() - 0.5;
+          r[2] = random->uniform() - 0.5;
+        }
       } else {
         r[0] = r[1] = 0.0;
         r[2] = 1.0;
@@ -659,6 +665,10 @@ void FixDeposit::options(int narg, char **arg)
   xmid = ymid = zmid = 0.0;
   scaleflag = 1;
   targetflag = 0;
+  rflag = 0;
+  rx = 0.0;
+  ry = 0.0;
+  rz = 0.0;
 
   int iarg = 0;
   while (iarg < narg) {
@@ -766,6 +776,13 @@ void FixDeposit::options(int narg, char **arg)
       vzlo = force->numeric(FLERR,arg[iarg+1]);
       vzhi = force->numeric(FLERR,arg[iarg+2]);
       iarg += 3;
+    } else if (strcmp(arg[iarg],"rotation") == 0) {
+      if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
+      rflag = 1;
+      rx = force->numeric(FLERR,arg[iarg+1]);
+      ry = force->numeric(FLERR,arg[iarg+2]);
+      rz = force->numeric(FLERR,arg[iarg+3]);
+      iarg += 4;
     } else if (strcmp(arg[iarg],"units") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
       if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index e3104c890d..e9b08253b5 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -20,6 +20,7 @@ FixStyle(deposit,FixDeposit)
 #ifndef LMP_FIX_DEPOSIT_H
 #define LMP_FIX_DEPOSIT_H
 
+#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
@@ -38,9 +39,9 @@ class FixDeposit : public Fix {
  private:
   int ninsert,ntype,nfreq,seed;
   int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag;
-  int mode,rigidflag,shakeflag,idnext,distflag;
+  int mode,rigidflag,shakeflag,idnext,distflag,rflag;
   double lo,hi,deltasq,nearsq,rate,sigma;
-  double vxlo,vxhi,vylo,vyhi,vzlo,vzhi;
+  double vxlo,vxhi,vylo,vyhi,vzlo,vzhi,rx,ry,rz;
   double xlo,xhi,ylo,yhi,zlo,zhi,xmid,ymid,zmid;
   double tx,ty,tz;
   char *idregion;

From ff991c4c53b9fd2e70e00ea9efbb4ea0dcf63ae1 Mon Sep 17 00:00:00 2001
From: Tongtong Shen <shen276@halstead-fe03.rcac.purdue.edu>
Date: Tue, 24 Sep 2019 15:10:47 -0400
Subject: [PATCH 009/199] Added new keywords orientation rx ry rz to restrict
 random rotation

---
 src/MISC/fix_deposit.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index c56929d4b3..cb2b7e6531 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_deposit.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
@@ -776,7 +776,7 @@ void FixDeposit::options(int narg, char **arg)
       vzlo = force->numeric(FLERR,arg[iarg+1]);
       vzhi = force->numeric(FLERR,arg[iarg+2]);
       iarg += 3;
-    } else if (strcmp(arg[iarg],"rotation") == 0) {
+    } else if (strcmp(arg[iarg],"orientation") == 0) {
       if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
       rflag = 1;
       rx = force->numeric(FLERR,arg[iarg+1]);

From a705b635a51f2b244f1db577b47b96c84f8be57f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 25 Sep 2019 14:36:26 -0400
Subject: [PATCH 010/199] remove cstdio include

cstdio is implicitly included by pointers.h which is included by fix.h.
---
 src/MISC/fix_deposit.h | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index e9b08253b5..bc24dba2d2 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -20,7 +20,6 @@ FixStyle(deposit,FixDeposit)
 #ifndef LMP_FIX_DEPOSIT_H
 #define LMP_FIX_DEPOSIT_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {

From 227a82e19f5e24905cd03183751760ba34894ad5 Mon Sep 17 00:00:00 2001
From: Tongtong Shen <shen276@halstead-fe00.rcac.purdue.edu>
Date: Wed, 2 Oct 2019 15:47:10 -0400
Subject: [PATCH 011/199] an update to the documentation in
 doc/src/fix_deposit.txt describing the orientation rx ry rz to restrict
 random rotation

---
 doc/src/fix_deposit.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index 9ab125a55f..fb597b6374 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -57,7 +57,9 @@ keyword = {region} or {id} or {global} or {local} or {near} or {gaussian} or {at
     fix-ID = ID of "fix shake"_fix_shake.html command
   {units} value = {lattice} or {box}
     lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units :pre
+    box = the geometry is defined in simulation box units 
+  {orientation} value = rx ry rz
+    rx,ry,rz = axis of orientation vector :pre
 :ule
 
 [Examples:]

From 877329c1e4ef0495ba3fdbee909b28373a51c593 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 8 Oct 2019 16:35:50 +0200
Subject: [PATCH 012/199] rename rflag to orientflag to be consistent with
 documentation and more readable

---
 src/MISC/fix_deposit.cpp | 6 +++---
 src/MISC/fix_deposit.h   | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index cb2b7e6531..267bce9a02 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -418,7 +418,7 @@ void FixDeposit::pre_exchange()
       while (rng > molfrac[imol]) imol++;
       natom = onemols[imol]->natoms;
       if (dimension == 3) {
-        if (rflag == 1) {
+        if (orientflag == 1) {
           r[0] = rx;
           r[1] = ry;
           r[2] = rz;
@@ -665,7 +665,7 @@ void FixDeposit::options(int narg, char **arg)
   xmid = ymid = zmid = 0.0;
   scaleflag = 1;
   targetflag = 0;
-  rflag = 0;
+  orientflag = 0;
   rx = 0.0;
   ry = 0.0;
   rz = 0.0;
@@ -778,7 +778,7 @@ void FixDeposit::options(int narg, char **arg)
       iarg += 3;
     } else if (strcmp(arg[iarg],"orientation") == 0) {
       if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
-      rflag = 1;
+      orientflag = 1;
       rx = force->numeric(FLERR,arg[iarg+1]);
       ry = force->numeric(FLERR,arg[iarg+2]);
       rz = force->numeric(FLERR,arg[iarg+3]);
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index bc24dba2d2..92598862d2 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -38,7 +38,7 @@ class FixDeposit : public Fix {
  private:
   int ninsert,ntype,nfreq,seed;
   int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag;
-  int mode,rigidflag,shakeflag,idnext,distflag,rflag;
+  int mode,rigidflag,shakeflag,idnext,distflag,orientflag;
   double lo,hi,deltasq,nearsq,rate,sigma;
   double vxlo,vxhi,vylo,vyhi,vzlo,vzhi,rx,ry,rz;
   double xlo,xhi,ylo,yhi,zlo,zhi,xmid,ymid,zmid;

From 4743c0004f81e70a55bb4c1d0a14376e4e619d51 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Mon, 28 Oct 2019 15:34:52 -0600
Subject: [PATCH 013/199] Commit JT 102819 - corrected issue in Zeeman
 precession - improved documentation of Zeeman interaction

---
 doc/src/Eqs/fix_spin_zeeman.jpg               | Bin 0 -> 5896 bytes
 ...ce_spin_zeeman.tex => fix_spin_zeeman.tex} |   3 +-
 doc/src/Eqs/force_spin_zeeman.jpg             | Bin 6517 -> 0 bytes
 doc/src/JPG/zeeman_langevin.jpg               | Bin 0 -> 46268 bytes
 doc/src/fix_precession_spin.txt               |  33 ++++-
 src/SPIN/fix_precession_spin.cpp              | 114 +++++++++---------
 6 files changed, 90 insertions(+), 60 deletions(-)
 create mode 100644 doc/src/Eqs/fix_spin_zeeman.jpg
 rename doc/src/Eqs/{force_spin_zeeman.tex => fix_spin_zeeman.tex} (70%)
 delete mode 100644 doc/src/Eqs/force_spin_zeeman.jpg
 create mode 100644 doc/src/JPG/zeeman_langevin.jpg

diff --git a/doc/src/Eqs/fix_spin_zeeman.jpg b/doc/src/Eqs/fix_spin_zeeman.jpg
new file mode 100644
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diff --git a/doc/src/Eqs/force_spin_zeeman.tex b/doc/src/Eqs/fix_spin_zeeman.tex
similarity index 70%
rename from doc/src/Eqs/force_spin_zeeman.tex
rename to doc/src/Eqs/fix_spin_zeeman.tex
index d623ef85ae..79dd49526a 100644
--- a/doc/src/Eqs/force_spin_zeeman.tex
+++ b/doc/src/Eqs/fix_spin_zeeman.tex
@@ -5,7 +5,8 @@
 \begin{document}
 \begin{varwidth}{50in}
   \begin{equation}
-    \bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber 
+    \bm{H}_{Zeeman} = -g \sum_{i=0}^{N}\mu_{i}\, 
+    \vec{s}_{i} \cdot\vec{B}_{ext} \nonumber
   \end{equation}
 \end{varwidth}
 \end{document}
diff --git a/doc/src/Eqs/force_spin_zeeman.jpg b/doc/src/Eqs/force_spin_zeeman.jpg
deleted file mode 100644
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diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt
index 040a3086d3..152f717155 100644
--- a/doc/src/fix_precession_spin.txt
+++ b/doc/src/fix_precession_spin.txt
@@ -41,10 +41,37 @@ Style {zeeman} is used for the simulation of the interaction
 between the magnetic spins in the defined group and an external
 magnetic field:
 
-:c,image(Eqs/force_spin_zeeman.jpg)
+:c,image(Eqs/fix_spin_zeeman.jpg)
 
-with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T
-in metal units).
+with:
+
+Bext the external magnetic field (in T) :ulb,l
+g the Lande factor (hard-coded as g=2.0) :l
+si the unitary vector describing the orientation of spin i :l
+mui the atomic moment of spin i given as a multiple of the
+Bohr magneton muB (for example, mui ~ 2.2 in bulk iron).  :l
+:ule
+
+The field value in Tesla is multiplied by the gyromagnetic
+ratio, g*muB/hbar, converting it into a precession frequency in
+rad.THz (in metal units and with muB = 5.788 eV/T).
+
+As a comparison, the figure below displays the simulation of a
+single spin (of norm mui = 1.0) submitted to an external
+magnetic field of |Bext| = 10.0 Tesla (and oriented along the z
+axis). 
+The upper plot shows the average magnetization along the
+external magnetic field axis and the lower plot the Zeeman
+energy, both as a function of temperature.
+The reference result is provided by the plot of the Langevin 
+function for the same parameters.
+
+:c,image(JPG/zeeman_langevin.jpg)
+
+The temperature effects are accounted for by connecting the spin
+i to a thermal bath using a Langevin thermostat (see 
+"fix_langevin_spin"_fix_langevin_spin.html for the definition of 
+this thermostat).
 
 Style {anisotropy} is used to simulate an easy axis or an easy plane
 for the magnetic spins in the defined group:
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index 3296b28228..3b8817704d 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -173,9 +173,9 @@ int FixPrecessionSpin::setmask()
 
 void FixPrecessionSpin::init()
 {
-  const double hbar = force->hplanck/MY_2PI;    // eV/(rad.THz)
-  const double mub = 5.78901e-5;                // in eV/T
-  const double gyro = mub/hbar;                 // in rad.THz/T
+  const double hbar = force->hplanck/MY_2PI;	// eV/(rad.THz)
+  const double mub = 5.78901e-5;		// in eV/T
+  const double gyro = 2.0*mub/hbar;		// in rad.THz/T
 
   // convert field quantities to rad.THz
 
@@ -240,6 +240,7 @@ void FixPrecessionSpin::post_force(int /* vflag */)
   }
 
   int *mask = atom->mask;
+  double *emag = atom->emag;
   double **fm = atom->fm;
   double **sp = atom->sp;
   const int nlocal = atom->nlocal;
@@ -257,7 +258,7 @@ void FixPrecessionSpin::post_force(int /* vflag */)
 
       if (zeeman_flag) {          // compute Zeeman interaction
         compute_zeeman(i,fmi);
-        epreci -= hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
+        epreci -= 2.0*hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
       }
 
       if (aniso_flag) {           // compute magnetic anisotropy
@@ -271,6 +272,7 @@ void FixPrecessionSpin::post_force(int /* vflag */)
       }
 
       eprec += epreci;
+      emag[i] += epreci;
       fm[i][0] += fmi[0];
       fm[i][1] += fmi[1];
       fm[i][2] += fmi[2];
@@ -295,9 +297,9 @@ void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double f
 void FixPrecessionSpin::compute_zeeman(int i, double fmi[3])
 {
   double **sp = atom->sp;
-  fmi[0] += sp[i][3]*hx;
-  fmi[1] += sp[i][3]*hy;
-  fmi[2] += sp[i][3]*hz;
+  fmi[0] += 0.5*sp[i][3]*hx;
+  fmi[1] += 0.5*sp[i][3]*hy;
+  fmi[2] += 0.5*sp[i][3]*hz;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -305,9 +307,9 @@ void FixPrecessionSpin::compute_zeeman(int i, double fmi[3])
 void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3])
 {
   double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2];
-  fmi[0] += scalar*Kax;
-  fmi[1] += scalar*Kay;
-  fmi[2] += scalar*Kaz;
+  fmi[0] += 0.5*scalar*Kax;
+  fmi[1] += 0.5*scalar*Kay;
+  fmi[2] += 0.5*scalar*Kaz;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -316,52 +318,10 @@ double FixPrecessionSpin::compute_anisotropy_energy(double spi[3])
 {
   double energy = 0.0;
   double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2];
-  energy = Ka*scalar*scalar;
+  energy = 2.0*Ka*scalar*scalar;
   return energy; 
 }
 
-/* ---------------------------------------------------------------------- */
-
-void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
-{
-  if (ilevel == ilevel_respa) post_force(vflag);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPrecessionSpin::set_magneticprecession()
-{
-  if (zeeman_flag) {
-    hx = H_field*nhx;
-    hy = H_field*nhy;
-    hz = H_field*nhz;
-  }
-  if (aniso_flag) {
-    Kax = 2.0*Kah*nax;
-    Kay = 2.0*Kah*nay;
-    Kaz = 2.0*Kah*naz;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   compute cubic aniso energy of spin i
-------------------------------------------------------------------------- */
-
-double FixPrecessionSpin::compute_cubic_energy(double spi[3])
-{
-  double energy = 0.0;
-  double skx,sky,skz;
-
-  skx = spi[0]*nc1x+spi[1]*nc1y+spi[2]*nc1z;
-  sky = spi[0]*nc2x+spi[1]*nc2y+spi[2]*nc2z;
-  skz = spi[0]*nc3x+spi[1]*nc3y+spi[2]*nc3z;
-
-  energy = k1c*(skx*skx*sky*sky + sky*sky*skz*skz + skx*skx*skz*skz);
-  energy += k2c*skx*skx*sky*sky*skz*skz;
-
-  return energy;
-}
-
 /* ----------------------------------------------------------------------
    compute cubic anisotropy interaction for spin i
 ------------------------------------------------------------------------- */
@@ -396,9 +356,44 @@ void FixPrecessionSpin::compute_cubic(double spi[3], double fmi[3])
   sixy = k2ch*(nc1y*six1 + nc2y*six2 + nc3y*six3);
   sixz = k2ch*(nc1z*six1 + nc2z*six2 + nc3z*six3);
   
-  fmi[0] += fourx + sixx;
-  fmi[1] += foury + sixy;
-  fmi[2] += fourz + sixz;
+  fmi[0] += 0.5*(fourx + sixx);
+  fmi[1] += 0.5*(foury + sixy);
+  fmi[2] += 0.5*(fourz + sixz);
+}
+
+/* ----------------------------------------------------------------------
+   compute cubic aniso energy of spin i
+------------------------------------------------------------------------- */
+
+double FixPrecessionSpin::compute_cubic_energy(double spi[3])
+{
+  double energy = 0.0;
+  double skx,sky,skz;
+
+  skx = spi[0]*nc1x+spi[1]*nc1y+spi[2]*nc1z;
+  sky = spi[0]*nc2x+spi[1]*nc2y+spi[2]*nc2z;
+  skz = spi[0]*nc3x+spi[1]*nc3y+spi[2]*nc3z;
+
+  energy = k1c*(skx*skx*sky*sky + sky*sky*skz*skz + skx*skx*skz*skz);
+  energy += k2c*skx*skx*sky*sky*skz*skz;
+
+  return 2.0*energy;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPrecessionSpin::set_magneticprecession()
+{
+  if (zeeman_flag) {
+    hx = H_field*nhx;
+    hy = H_field*nhy;
+    hz = H_field*nhz;
+  }
+  if (aniso_flag) {
+    Kax = 2.0*Kah*nax;
+    Kay = 2.0*Kah*nay;
+    Kaz = 2.0*Kah*naz;
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -422,3 +417,10 @@ void FixPrecessionSpin::min_post_force(int vflag)
 {
   post_force(vflag);
 }
+
+/* ---------------------------------------------------------------------- */
+
+void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
+{
+  if (ilevel == ilevel_respa) post_force(vflag);
+}

From e119bffcca18464de95a9b0bb17b5e5f0181b0a5 Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Thu, 31 Oct 2019 01:15:53 -0500
Subject: [PATCH 014/199] Fixed bugs with kernel (re)compiling when the global
 device got cleared and then reinitialized

---
 lib/gpu/lal_base_atomic.cpp    | 5 ++++-
 lib/gpu/lal_base_charge.cpp    | 5 ++++-
 lib/gpu/lal_base_dipole.cpp    | 5 ++++-
 lib/gpu/lal_base_dpd.cpp       | 5 ++++-
 lib/gpu/lal_base_ellipsoid.cpp | 5 ++++-
 lib/gpu/lal_base_three.cpp     | 5 ++++-
 6 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/lib/gpu/lal_base_atomic.cpp b/lib/gpu/lal_base_atomic.cpp
index eb4dae636f..eb0eab87b6 100644
--- a/lib/gpu/lal_base_atomic.cpp
+++ b/lib/gpu/lal_base_atomic.cpp
@@ -26,15 +26,16 @@ BaseAtomicT::BaseAtomic() : _compiled(false), _max_bytes(0)  {
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
   pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseAtomicT::~BaseAtomic() {
   delete ans;
   delete nbor;
-  if (pair_program) delete pair_program;
   k_pair_fast.clear();
   k_pair.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -78,6 +79,8 @@ int BaseAtomicT::init_atomic(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
diff --git a/lib/gpu/lal_base_charge.cpp b/lib/gpu/lal_base_charge.cpp
index 17f30a7047..52e8ae2d89 100644
--- a/lib/gpu/lal_base_charge.cpp
+++ b/lib/gpu/lal_base_charge.cpp
@@ -26,15 +26,16 @@ BaseChargeT::BaseCharge() : _compiled(false), _max_bytes(0) {
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
   pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseChargeT::~BaseCharge() {
   delete ans;
   delete nbor;
-  if (pair_program) delete pair_program;
   k_pair_fast.clear();
   k_pair.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -78,6 +79,8 @@ int BaseChargeT::init_atomic(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
diff --git a/lib/gpu/lal_base_dipole.cpp b/lib/gpu/lal_base_dipole.cpp
index a4b0bf3c37..ed71029e68 100644
--- a/lib/gpu/lal_base_dipole.cpp
+++ b/lib/gpu/lal_base_dipole.cpp
@@ -26,15 +26,16 @@ BaseDipoleT::BaseDipole() : _compiled(false), _max_bytes(0) {
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
   pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseDipoleT::~BaseDipole() {
   delete ans;
   delete nbor;
-  if (pair_program) delete pair_program;
   k_pair_fast.clear();
   k_pair.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -79,6 +80,8 @@ int BaseDipoleT::init_atomic(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
diff --git a/lib/gpu/lal_base_dpd.cpp b/lib/gpu/lal_base_dpd.cpp
index bf4533ad1a..c0d7ad47bc 100644
--- a/lib/gpu/lal_base_dpd.cpp
+++ b/lib/gpu/lal_base_dpd.cpp
@@ -26,15 +26,16 @@ BaseDPDT::BaseDPD() : _compiled(false), _max_bytes(0) {
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
   pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseDPDT::~BaseDPD() {
   delete ans;
   delete nbor;
-  if (pair_program) delete pair_program;
   k_pair_fast.clear();
   k_pair.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -79,6 +80,8 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
diff --git a/lib/gpu/lal_base_ellipsoid.cpp b/lib/gpu/lal_base_ellipsoid.cpp
index dc32383264..abc8807a8b 100644
--- a/lib/gpu/lal_base_ellipsoid.cpp
+++ b/lib/gpu/lal_base_ellipsoid.cpp
@@ -36,6 +36,7 @@ BaseEllipsoidT::BaseEllipsoid() : _compiled(false), _max_bytes(0) {
   nbor_program=NULL;
   ellipsoid_program=NULL;
   lj_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
@@ -92,7 +93,9 @@ int BaseEllipsoidT::init_base(const int nlocal, const int nall,
                   max_nbors,cell_size,true,1);
   if (success!=0)
     return success;
-  
+
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
diff --git a/lib/gpu/lal_base_three.cpp b/lib/gpu/lal_base_three.cpp
index 1715fc3074..0b4dbdc89a 100644
--- a/lib/gpu/lal_base_three.cpp
+++ b/lib/gpu/lal_base_three.cpp
@@ -28,6 +28,7 @@ BaseThreeT::BaseThree() : _compiled(false), _max_bytes(0) {
   ans2=new Answer<numtyp,acctyp>();
   #endif
   pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
@@ -37,12 +38,12 @@ BaseThreeT::~BaseThree() {
   #ifdef THREE_CONCURRENT
   delete ans2;
   #endif
-  if (pair_program) delete pair_program;
   k_three_center.clear();
   k_three_end.clear();
   k_three_end_vatom.clear();
   k_pair.clear();
   k_short_nbor.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -94,6 +95,8 @@ int BaseThreeT::init_three(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 

From e6aa79101f3b3802aa5c5cb43574c67397ae394b Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 1 Nov 2019 10:54:12 +0000
Subject: [PATCH 015/199] Implemented and verified oxRNA2 model

---
 src/USER-CGDNA/bond_oxrna2_fene.cpp  |   49 +
 src/USER-CGDNA/bond_oxrna2_fene.h    |   65 ++
 src/USER-CGDNA/pair_oxdna2_dh.cpp    |    6 +-
 src/USER-CGDNA/pair_oxdna2_dh.h      |    3 +-
 src/USER-CGDNA/pair_oxdna_coaxstk.h  |    1 +
 src/USER-CGDNA/pair_oxrna2_dh.cpp    |   47 +
 src/USER-CGDNA/pair_oxrna2_dh.h      |   53 +
 src/USER-CGDNA/pair_oxrna2_excv.cpp  |   55 +
 src/USER-CGDNA/pair_oxrna2_excv.h    |   52 +
 src/USER-CGDNA/pair_oxrna2_hbond.cpp |   58 ++
 src/USER-CGDNA/pair_oxrna2_hbond.h   |   50 +
 src/USER-CGDNA/pair_oxrna2_stk.cpp   | 1435 ++++++++++++++++++++++++++
 src/USER-CGDNA/pair_oxrna2_stk.h     |   86 ++
 src/USER-CGDNA/pair_oxrna2_xstk.cpp  | 1079 +++++++++++++++++++
 src/USER-CGDNA/pair_oxrna2_xstk.h    |   85 ++
 15 files changed, 3120 insertions(+), 4 deletions(-)
 create mode 100644 src/USER-CGDNA/bond_oxrna2_fene.cpp
 create mode 100644 src/USER-CGDNA/bond_oxrna2_fene.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_dh.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_dh.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_excv.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_excv.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_hbond.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_hbond.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_stk.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_stk.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_xstk.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_xstk.h

diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/USER-CGDNA/bond_oxrna2_fene.cpp
new file mode 100644
index 0000000000..bdddccda87
--- /dev/null
+++ b/src/USER-CGDNA/bond_oxrna2_fene.cpp
@@ -0,0 +1,49 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdlib>
+#include "bond_oxrna2_fene.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+BondOxrna2Fene::BondOxrna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp)
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+BondOxrna2Fene::~BondOxrna2Fene()
+{
+
+}
+
+/* ----------------------------------------------------------------------
+    compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
+------------------------------------------------------------------------- */
+void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3],
+  double e3[3], double r[3])
+{
+  double d_cs_x=-0.4, d_cs_z=+0.2;
+
+  r[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
+  r[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
+  r[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
+
+}
diff --git a/src/USER-CGDNA/bond_oxrna2_fene.h b/src/USER-CGDNA/bond_oxrna2_fene.h
new file mode 100644
index 0000000000..585a253eb5
--- /dev/null
+++ b/src/USER-CGDNA/bond_oxrna2_fene.h
@@ -0,0 +1,65 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef BOND_CLASS
+
+BondStyle(oxrna2/fene,BondOxrna2Fene)
+
+#else
+
+#ifndef LMP_BOND_OXRNA2_FENE_H
+#define LMP_BOND_OXRNA2_FENE_H
+
+#include "bond_oxdna_fene.h"
+
+namespace LAMMPS_NS {
+
+class BondOxrna2Fene : public BondOxdnaFene {
+ public:
+  BondOxrna2Fene(class LAMMPS *);
+  virtual ~BondOxrna2Fene();
+  virtual void compute_interaction_sites(double *, double *, double *,
+    double *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+W: FENE bond too long: %ld %d %d %g
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up.
+
+E: Bad FENE bond
+
+Two atoms in a FENE bond have become so far apart that the bond cannot
+be computed.
+
+E: Incorrect args for bond coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+W: Use special bonds = 0,1,1 with bond style oxrna
+
+Most FENE models need this setting for the special_bonds command.
+
+W: FENE bond too long: %ld %g
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index 44413ee7f1..e698d8d906 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -64,7 +64,7 @@ PairOxdna2Dh::~PairOxdna2Dh()
     compute vector COM-sugar-phosphate backbone interaction site in oxDNA2
 ------------------------------------------------------------------------- */
 void PairOxdna2Dh::compute_interaction_sites(double e1[3],
-  double e2[3], double r[3])
+  double e2[3], double /*e3*/[3], double r[3])
 {
   double d_cs_x=-0.34, d_cs_y=+0.3408;
 
@@ -125,7 +125,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
     MathExtra::q_to_exyz(qa,ax,ay,az);
 
     // vector COM-backbone site a
-    compute_interaction_sites(ax,ay,ra_cs);
+    compute_interaction_sites(ax,ay,az,ra_cs);
 
     rtmp_s[0] = x[a][0] + ra_cs[0];
     rtmp_s[1] = x[a][1] + ra_cs[1];
@@ -145,7 +145,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
       MathExtra::q_to_exyz(qb,bx,by,bz);
 
       // vector COM-backbone site b
-      compute_interaction_sites(bx,by,rb_cs);
+      compute_interaction_sites(bx,by,bz,rb_cs);
 
       // vector backbone site b to a
       delr[0] = rtmp_s[0] - x[b][0] - rb_cs[0];
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/USER-CGDNA/pair_oxdna2_dh.h
index 7c907168e3..2a41524126 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.h
+++ b/src/USER-CGDNA/pair_oxdna2_dh.h
@@ -28,7 +28,8 @@ class PairOxdna2Dh : public Pair {
  public:
   PairOxdna2Dh(class LAMMPS *);
   virtual ~PairOxdna2Dh();
-  virtual void compute_interaction_sites(double *, double *, double *);
+  virtual void compute_interaction_sites(double *, double *, double *, 
+    double *);
   virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/USER-CGDNA/pair_oxdna_coaxstk.h
index e89e9bdbaa..79c8fa24ed 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.h
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.h
@@ -14,6 +14,7 @@
 #ifdef PAIR_CLASS
 
 PairStyle(oxdna/coaxstk,PairOxdnaCoaxstk)
+PairStyle(oxrna2/coaxstk,PairOxdnaCoaxstk)
 
 #else
 
diff --git a/src/USER-CGDNA/pair_oxrna2_dh.cpp b/src/USER-CGDNA/pair_oxrna2_dh.cpp
new file mode 100644
index 0000000000..045a6aa6bc
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_dh.cpp
@@ -0,0 +1,47 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include "pair_oxrna2_dh.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Dh::PairOxrna2Dh(LAMMPS *lmp) : PairOxdna2Dh(lmp)
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Dh::~PairOxrna2Dh()
+{
+
+}
+
+/* ----------------------------------------------------------------------
+    compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
+------------------------------------------------------------------------- */
+void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], 
+  double e3[3], double r[3])
+{
+  double d_cs_x=-0.4, d_cs_z=+0.2;
+
+  r[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
+  r[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
+  r[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
+
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_dh.h b/src/USER-CGDNA/pair_oxrna2_dh.h
new file mode 100644
index 0000000000..8ff4010113
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_dh.h
@@ -0,0 +1,53 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/dh,PairOxrna2Dh)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_DH_H
+#define LMP_PAIR_OXRNA2_DH_H
+
+#include "pair_oxdna2_dh.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Dh : public PairOxdna2Dh {
+ public:
+  PairOxrna2Dh(class LAMMPS *);
+  virtual ~PairOxrna2Dh();
+  virtual void compute_interaction_sites(double *, double *, double *,
+    double *);
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/USER-CGDNA/pair_oxrna2_excv.cpp
new file mode 100644
index 0000000000..3c0194d636
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_excv.cpp
@@ -0,0 +1,55 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_oxrna2_excv.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Excv::PairOxrna2Excv(LAMMPS *lmp) : PairOxdnaExcv(lmp)
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Excv::~PairOxrna2Excv()
+{
+
+}
+
+/* ----------------------------------------------------------------------
+    compute vector COM-excluded volume interaction sites in oxRNA2
+------------------------------------------------------------------------- */
+void PairOxrna2Excv::compute_interaction_sites(double e1[3], double /*e2*/[3],
+  double e3[3], double rs[3], double rb[3])
+{
+  double d_cs_x=-0.4, d_cs_z=+0.2, d_cb=+0.4;
+
+  rs[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
+  rs[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
+  rs[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
+
+  rb[0] = d_cb*e1[0];
+  rb[1] = d_cb*e1[1];
+  rb[2] = d_cb*e1[2];
+
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_excv.h b/src/USER-CGDNA/pair_oxrna2_excv.h
new file mode 100644
index 0000000000..2dfb356203
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_excv.h
@@ -0,0 +1,52 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/excv,PairOxrna2Excv)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_EXCV_H
+#define LMP_PAIR_OXRNA2_EXCV_H
+
+#include "pair_oxdna_excv.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Excv : public PairOxdnaExcv {
+ public:
+  PairOxrna2Excv(class LAMMPS *);
+  virtual ~PairOxrna2Excv();
+  virtual void compute_interaction_sites(double *, double *,
+    double *, double *, double *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.cpp b/src/USER-CGDNA/pair_oxrna2_hbond.cpp
new file mode 100644
index 0000000000..65f266ba36
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_hbond.cpp
@@ -0,0 +1,58 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include "pair_oxrna2_hbond.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp)
+{
+  single_enable = 0;
+  writedata = 1;
+
+  // sequence-specific base-pairing strength
+  // A:0 C:1 G:2 U:3, 5'- [i][j] -3'
+   
+  alpha_hb[0][0] = 1.00000;
+  alpha_hb[0][1] = 1.00000;
+  alpha_hb[0][2] = 1.00000;
+  alpha_hb[0][3] = 0.94253;
+
+  alpha_hb[1][0] = 1.00000;
+  alpha_hb[1][1] = 1.00000;
+  alpha_hb[1][2] = 1.22288;
+  alpha_hb[1][3] = 1.00000;
+
+  alpha_hb[2][0] = 1.00000;
+  alpha_hb[2][1] = 1.22288;
+  alpha_hb[2][2] = 1.00000;
+  alpha_hb[2][3] = 0.58655;
+
+  alpha_hb[3][0] = 0.94253;
+  alpha_hb[3][1] = 1.00000;
+  alpha_hb[3][2] = 0.58655;
+  alpha_hb[3][3] = 1.00000;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Hbond::~PairOxrna2Hbond()
+{
+
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.h b/src/USER-CGDNA/pair_oxrna2_hbond.h
new file mode 100644
index 0000000000..3386cc23ec
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_hbond.h
@@ -0,0 +1,50 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/hbond,PairOxrna2Hbond)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_HBOND_H
+#define LMP_PAIR_OXRNA2_HBOND_H
+
+#include "pair_oxdna_hbond.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Hbond : public PairOxdnaHbond {
+ public:
+  PairOxrna2Hbond(class LAMMPS *);
+  virtual ~PairOxrna2Hbond();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp
new file mode 100644
index 0000000000..5fd32099f3
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp
@@ -0,0 +1,1435 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_oxrna2_stk.h"
+#include "mf_oxdna.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "utils.h"
+#include "atom_vec_ellipsoid.h"
+#include "math_extra.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+using namespace MFOxdna;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp)
+{
+  single_enable = 0;
+  writedata = 1;
+
+  // sequence-specific stacking strength
+  // A:0 C:1 G:2 U:3, 5'- [i][j] -3'
+
+  eta_st[0][0] = 0.93851; 
+  eta_st[0][1] = 1.12901;
+  eta_st[0][2] = 1.15626;
+  eta_st[0][3] = 0.88850;
+
+  eta_st[1][0] = 0.86331;
+  eta_st[1][1] = 1.05060;
+  eta_st[1][2] = 0.90982;
+  eta_st[1][3] = 0.83252;
+
+  eta_st[2][0] = 0.99407;
+  eta_st[2][1] = 1.14333;
+  eta_st[2][2] = 1.06573;
+  eta_st[2][3] = 0.91705;
+
+  eta_st[3][0] = 0.98804;
+  eta_st[3][1] = 1.04949;
+  eta_st[3][2] = 1.12063;
+  eta_st[3][3] = 0.83818;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Stk::~PairOxrna2Stk()
+{
+  if (allocated) {
+
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(epsilon_st);
+    memory->destroy(a_st);
+    memory->destroy(cut_st_0);
+    memory->destroy(cut_st_c);
+    memory->destroy(cut_st_lo);
+    memory->destroy(cut_st_hi);
+    memory->destroy(cut_st_lc);
+    memory->destroy(cut_st_hc);
+    memory->destroy(b_st_lo);
+    memory->destroy(b_st_hi);
+    memory->destroy(shift_st);
+    memory->destroy(cutsq_st_hc);
+
+    memory->destroy(a_st5);
+    memory->destroy(theta_st5_0);
+    memory->destroy(dtheta_st5_ast);
+    memory->destroy(b_st5);
+    memory->destroy(dtheta_st5_c);
+
+    memory->destroy(a_st6);
+    memory->destroy(theta_st6_0);
+    memory->destroy(dtheta_st6_ast);
+    memory->destroy(b_st6);
+    memory->destroy(dtheta_st6_c);
+
+    memory->destroy(a_st9);
+    memory->destroy(theta_st9_0);
+    memory->destroy(dtheta_st9_ast);
+    memory->destroy(b_st9);
+    memory->destroy(dtheta_st9_c);
+
+    memory->destroy(a_st10);
+    memory->destroy(theta_st10_0);
+    memory->destroy(dtheta_st10_ast);
+    memory->destroy(b_st10);
+    memory->destroy(dtheta_st10_c);
+
+    memory->destroy(a_st1);
+    memory->destroy(cosphi_st1_ast);
+    memory->destroy(b_st1);
+    memory->destroy(cosphi_st1_c);
+    memory->destroy(a_st2);
+    memory->destroy(cosphi_st2_ast);
+    memory->destroy(b_st2);
+    memory->destroy(cosphi_st2_c);
+
+  }
+}
+
+/* ----------------------------------------------------------------------
+   tally energy and virial into global and per-atom accumulators
+
+   NOTE: Although this is a pair style interaction, the algorithm below
+   follows the virial incrementation of the bond style. This is because 
+   the bond topology is used in the main compute loop.
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::ev_tally_xyz(int i, int j, int nlocal, int newton_bond,
+                    double evdwl,
+                    double fx, double fy, double fz,
+                    double delx, double dely, double delz)
+{
+  double evdwlhalf,v[6];
+
+  if (eflag_either) {
+    if (eflag_global) {
+      if (newton_bond) eng_vdwl += evdwl;
+      else {
+        evdwlhalf = 0.5*evdwl;
+        if (i < nlocal) eng_vdwl += evdwlhalf;
+        if (j < nlocal) eng_vdwl += evdwlhalf;
+      }
+    }
+    if (eflag_atom) {
+      evdwlhalf = 0.5*evdwl;
+      if (newton_bond || i < nlocal) eatom[i] += evdwlhalf;
+      if (newton_bond || j < nlocal) eatom[j] += evdwlhalf;
+    }
+  }
+
+  if (vflag_either) {
+    v[0] = delx*fx;
+    v[1] = dely*fy;
+    v[2] = delz*fz;
+    v[3] = delx*fy;
+    v[4] = delx*fz;
+    v[5] = dely*fz;
+
+    if (vflag_global) {
+      if (newton_bond) {
+        virial[0] += v[0];
+        virial[1] += v[1];
+        virial[2] += v[2];
+        virial[3] += v[3];
+        virial[4] += v[4];
+        virial[5] += v[5];
+      } else {
+        if (i < nlocal) {
+          virial[0] += 0.5*v[0];
+          virial[1] += 0.5*v[1];
+          virial[2] += 0.5*v[2];
+          virial[3] += 0.5*v[3];
+          virial[4] += 0.5*v[4];
+          virial[5] += 0.5*v[5];
+        }
+        if (j < nlocal) {
+          virial[0] += 0.5*v[0];
+          virial[1] += 0.5*v[1];
+          virial[2] += 0.5*v[2];
+          virial[3] += 0.5*v[3];
+          virial[4] += 0.5*v[4];
+          virial[5] += 0.5*v[5];
+        }
+      }
+    }
+
+    if (vflag_atom) {
+      if (newton_bond || i < nlocal) {
+        vatom[i][0] += 0.5*v[0];
+        vatom[i][1] += 0.5*v[1];
+        vatom[i][2] += 0.5*v[2];
+        vatom[i][3] += 0.5*v[3];
+        vatom[i][4] += 0.5*v[4];
+        vatom[i][5] += 0.5*v[5];
+      }
+      if (newton_bond || j < nlocal) {
+        vatom[j][0] += 0.5*v[0];
+        vatom[j][1] += 0.5*v[1];
+        vatom[j][2] += 0.5*v[2];
+        vatom[j][3] += 0.5*v[3];
+        vatom[j][4] += 0.5*v[4];
+        vatom[j][5] += 0.5*v[5];
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   compute function for oxRNA2 pair interactions
+   s=sugar-phosphate backbone site, b=base site, st=stacking site
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::compute(int eflag, int vflag)
+{
+
+  double delf[3],delta[3],deltb[3]; // force, torque increment;
+  double evdwl,fpair,finc,tpair;
+  double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
+  double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
+  double theta5p,t5pdir[3],cost5p;
+  double theta6p,t6pdir[3],cost6p;
+  double theta9,t9dir[3],cost9;
+  double theta10,t10dir[3],cost10;
+  double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3];
+
+  // distances COM-backbone site, COM-3' and COM-5' stacking site
+  double d_cs_x=-0.4, d_cs_z=+0.2;
+  double d_cst_x_3p=+0.4, d_cst_y_3p=+0.1;
+  double d_cst_x_5p=+0.124906078525, d_cst_y_5p=-0.00866274917473;
+
+  // 3' and p5' auxiliary vectors
+  double  d3p_x=-0.462510,d3p_y=-0.528218,d3p_z=+0.712089;
+  double  d5p_x=-0.104402,d5p_y=-0.841783,d5p_z=+0.529624;
+  double aux3p[3], aux5p[3];
+
+  // vectors COM-backbone site, COM-stacking site in lab frame
+  double ra_cs[3],ra_cst[3];
+  double rb_cs[3],rb_cst[3];
+
+  // quaternions and Cartesian unit vectors in lab frame
+  double *qa,ax[3],ay[3],az[3];
+  double *qb,bx[3],by[3],bz[3];
+
+  double **x = atom->x;
+  double **f = atom->f;
+  double **torque = atom->torque;
+  int *type = atom->type;
+
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+
+  int **bondlist = neighbor->bondlist;
+  int nbondlist = neighbor->nbondlist;
+
+  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
+  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
+
+  int a,b,in,atype,btype;
+
+  double f1,f4t5,f4t6,f4t9,f4t10,f5c1,f5c2;
+  double df1,df4t5,df4t6,df4t9,df4t10,df5c1,df5c2;
+  double tptofp;
+
+  evdwl = 0.0;
+  ev_init(eflag,vflag);
+
+  // loop over stacking interaction neighbors using bond topology
+
+  for (in = 0; in < nbondlist; in++) {
+
+    a = bondlist[in][1];
+    b = bondlist[in][0];
+
+    qa=bonus[a].quat;
+    MathExtra::q_to_exyz(qa,ax,ay,az);
+    qb=bonus[b].quat;
+    MathExtra::q_to_exyz(qb,bx,by,bz);
+
+    // vector COM a - 3'-stacking site a
+    ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0];
+    ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1];
+    ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2];
+
+    // vector COM b - 5'-stacking site b
+    rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0];
+    rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1];
+    rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2];
+
+    // vector 5'-stacking site b to 3'-stacking site a
+    delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
+    delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
+    delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
+
+    // test for directionality of vector b to a
+    tptofp = MFOxdna::is_3pto5p(delr_st,bz);
+
+    // if b to a is 5' to 3' we need to swap roles of a and b
+    if (tptofp == -1) {
+
+      std::swap(a,b);
+      std::swap(ax,bx);
+      std::swap(ay,by);
+      std::swap(az,bz);
+
+    }
+
+    // a now in 5' direction, b in 3' direction
+    atype = type[a];
+    btype = type[b];
+
+    // calculate again
+    // vector COM a - 3'-stacking site a
+    ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0];
+    ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1];
+    ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2];
+
+    // vector COM b - 5'-stacking site b
+    rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0];
+    rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1];
+    rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2];
+
+    // vector 5'-stacking site b to 3'-stacking site a
+    delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
+    delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
+    delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
+
+    rsq_st = delr_st[0]*delr_st[0] + delr_st[1]*delr_st[1] + delr_st[2]*delr_st[2];
+    r_st = sqrt(rsq_st);
+    rinv_st = 1.0/r_st;
+
+    delr_st_norm[0] = delr_st[0] * rinv_st;
+    delr_st_norm[1] = delr_st[1] * rinv_st;
+    delr_st_norm[2] = delr_st[2] * rinv_st;
+
+    // vector COM a - backbone site a
+    ra_cs[0] = d_cs_x*ax[0] + d_cs_z*az[0];
+    ra_cs[1] = d_cs_x*ax[1] + d_cs_z*az[1];
+    ra_cs[2] = d_cs_x*ax[2] + d_cs_z*az[2];
+
+    // vector COM b - backbone site b
+    rb_cs[0] = d_cs_x*bx[0] + d_cs_z*bz[0];
+    rb_cs[1] = d_cs_x*bx[1] + d_cs_z*bz[1];
+    rb_cs[2] = d_cs_x*bx[2] + d_cs_z*bz[2];
+
+    // vector backbone site b to a
+    delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]);
+    delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]);
+    delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]);
+
+    rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2];
+    r_ss = sqrt(rsq_ss);
+    rinv_ss = 1.0/r_ss;
+
+    delr_ss_norm[0] = delr_ss[0] * rinv_ss;
+    delr_ss_norm[1] = delr_ss[1] * rinv_ss;
+    delr_ss_norm[2] = delr_ss[2] * rinv_ss;
+
+    f1 = F1(r_st, epsilon_st[atype][btype], a_st[atype][btype], cut_st_0[atype][btype],
+        cut_st_lc[atype][btype], cut_st_hc[atype][btype], cut_st_lo[atype][btype], cut_st_hi[atype][btype],
+        b_st_lo[atype][btype], b_st_hi[atype][btype], shift_st[atype][btype]);
+
+    // early rejection criterium
+    if (f1) {
+
+    // theta5 angle and correction
+    cost5p  = MathExtra::dot3(delr_st_norm,az);
+    if (cost5p >  1.0) cost5p =  1.0;
+    if (cost5p < -1.0) cost5p = -1.0;
+    theta5p = acos(cost5p);
+
+    f4t5 = F4(theta5p, a_st5[atype][btype], theta_st5_0[atype][btype], dtheta_st5_ast[atype][btype],
+        b_st5[atype][btype], dtheta_st5_c[atype][btype]);
+
+    // early rejection criterium
+    if (f4t5) {
+
+    cost6p = MathExtra::dot3(delr_st_norm,bz);
+    if (cost6p >  1.0) cost6p =  1.0;
+    if (cost6p < -1.0) cost6p = -1.0;
+    theta6p = acos(cost6p);
+
+    aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0]; 
+    aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1]; 
+    aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2]; 
+
+    aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0]; 
+    aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1]; 
+    aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2]; 
+
+    cost9 = MathExtra::dot3(delr_ss_norm,aux3p);
+    if (cost9 >  1.0) cost9 =  1.0;
+    if (cost9 < -1.0) cost9 = -1.0;
+    theta9 = acos(cost9);
+
+    cost10 = MathExtra::dot3(delr_ss_norm,aux5p);
+    if (cost10 >  1.0) cost10 =  1.0;
+    if (cost10 < -1.0) cost10 = -1.0;
+    theta10 = acos(cost10);
+
+    cosphi1 = MathExtra::dot3(delr_ss_norm,ay);
+    if (cosphi1 >  1.0) cosphi1 =  1.0;
+    if (cosphi1 < -1.0) cosphi1 = -1.0;
+
+    cosphi2 = MathExtra::dot3(delr_ss_norm,by);
+    if (cosphi2 >  1.0) cosphi2 =  1.0;
+    if (cosphi2 < -1.0) cosphi2 = -1.0;
+
+    f4t6 = F4(theta6p, a_st6[atype][btype], theta_st6_0[atype][btype], dtheta_st6_ast[atype][btype],
+        b_st6[atype][btype], dtheta_st6_c[atype][btype]);
+
+    f4t9 = F4(theta9, a_st9[atype][btype], theta_st9_0[atype][btype], dtheta_st9_ast[atype][btype],
+        b_st9[atype][btype], dtheta_st9_c[atype][btype]);
+
+    f4t10 = F4(theta10, a_st10[atype][btype], theta_st10_0[atype][btype], dtheta_st10_ast[atype][btype],
+        b_st10[atype][btype], dtheta_st10_c[atype][btype]);
+
+    f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
+        cosphi_st1_c[atype][btype]);
+
+    f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
+        cosphi_st2_c[atype][btype]);
+
+
+    evdwl = f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
+
+    // early rejection criterium
+    if (evdwl) {
+
+    df1 = DF1(r_st, epsilon_st[atype][btype], a_st[atype][btype], cut_st_0[atype][btype],
+        cut_st_lc[atype][btype], cut_st_hc[atype][btype], cut_st_lo[atype][btype], cut_st_hi[atype][btype],
+        b_st_lo[atype][btype], b_st_hi[atype][btype]);
+
+    df4t5 = DF4(theta5p, a_st5[atype][btype], theta_st5_0[atype][btype], dtheta_st5_ast[atype][btype],
+        b_st5[atype][btype], dtheta_st5_c[atype][btype])/sin(theta5p);
+
+    df4t6 = DF4(theta6p, a_st6[atype][btype], theta_st6_0[atype][btype], dtheta_st6_ast[atype][btype],
+        b_st6[atype][btype], dtheta_st6_c[atype][btype])/sin(theta6p);
+
+    df4t9 = DF4(theta9, a_st9[atype][btype], theta_st9_0[atype][btype], dtheta_st9_ast[atype][btype],
+        b_st9[atype][btype], dtheta_st9_c[atype][btype])/sin(theta9);
+
+    df4t10 = DF4(theta10, a_st10[atype][btype], theta_st10_0[atype][btype], dtheta_st10_ast[atype][btype],
+        b_st10[atype][btype], dtheta_st10_c[atype][btype])/sin(theta10);
+
+    df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
+        cosphi_st1_c[atype][btype]);
+
+    df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
+        cosphi_st2_c[atype][btype]);
+
+
+    // force, torque and virial contribution for forces between stacking sites
+
+    fpair = 0.0;
+
+    delf[0] = 0.0;
+    delf[1] = 0.0;
+    delf[2] = 0.0;
+
+    delta[0] = 0.0;
+    delta[1] = 0.0;
+    delta[2] = 0.0;
+
+    deltb[0] = 0.0;
+    deltb[1] = 0.0;
+    deltb[2] = 0.0;
+
+    // radial force
+    finc  = -df1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
+    fpair += finc;
+
+    delf[0] += delr_st[0] * finc;
+    delf[1] += delr_st[1] * finc;
+    delf[2] += delr_st[2] * finc;
+
+    // theta5p force
+    if (theta5p) {
+
+      finc   = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
+      fpair += finc;
+
+      delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc;
+      delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc;
+      delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc;
+
+    }
+
+    // theta6p force
+    if (theta6p) {
+
+      finc   = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
+      fpair += finc;
+
+      delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc;
+      delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc;
+      delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc;
+
+    }
+
+    // increment forces and torques
+
+    if (newton_bond || a < nlocal) {
+
+      f[a][0] += delf[0];
+      f[a][1] += delf[1];
+      f[a][2] += delf[2];
+
+      MathExtra::cross3(ra_cst,delf,delta);
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      f[b][0] -= delf[0];
+      f[b][1] -= delf[1];
+      f[b][2] -= delf[2];
+
+      MathExtra::cross3(rb_cst,delf,deltb);
+
+    }
+
+    if (newton_bond || a < nlocal) {
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      torque[b][0] -= deltb[0];
+      torque[b][1] -= deltb[1];
+      torque[b][2] -= deltb[2];
+
+    }
+
+    // increment energy and virial
+    // NOTE: The virial is calculated on the 'molecular' basis.
+    // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
+
+    if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl,
+        delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
+
+    // force, torque and virial contribution for forces between backbone sites
+
+    fpair = 0.0;
+
+    delf[0] = 0.0;
+    delf[1] = 0.0;
+    delf[2] = 0.0;
+
+    delta[0] = 0.0;
+    delta[1] = 0.0;
+    delta[2] = 0.0;
+
+    deltb[0] = 0.0;
+    deltb[1] = 0.0;
+    deltb[2] = 0.0;
+
+    // theta9 force
+    if (theta9) {
+
+      finc   = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2 * rinv_ss;
+      fpair += finc;
+
+      delf[0] += (delr_ss_norm[0]*cost9 - aux3p[0]) * finc;
+      delf[1] += (delr_ss_norm[1]*cost9 - aux3p[1]) * finc;
+      delf[2] += (delr_ss_norm[2]*cost9 - aux3p[2]) * finc;
+
+    }
+
+    // theta10 force
+    if (theta10) {
+
+      finc   = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2 * rinv_ss;
+      fpair += finc;
+
+      delf[0] += (delr_ss_norm[0]*cost10 - aux5p[0]) * finc;
+      delf[1] += (delr_ss_norm[1]*cost10 - aux5p[1]) * finc;
+      delf[2] += (delr_ss_norm[2]*cost10 - aux5p[2]) * finc;
+
+    }
+
+    // cosphi1 force
+    if (cosphi1) {
+
+      finc   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2 * rinv_ss;
+      fpair += finc;
+
+      delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc;
+      delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc;
+      delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc;
+
+    }
+
+    // cosphi2 force
+    if (cosphi2) {
+
+      finc   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2 * rinv_ss;
+      fpair += finc;
+
+      delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc;
+      delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc;
+      delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc;
+
+    }
+
+    // increment forces and torques
+
+    if (newton_bond || a < nlocal) {
+
+      f[a][0] += delf[0];
+      f[a][1] += delf[1];
+      f[a][2] += delf[2];
+
+      MathExtra::cross3(ra_cs,delf,delta);
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      f[b][0] -= delf[0];
+      f[b][1] -= delf[1];
+      f[b][2] -= delf[2];
+
+      MathExtra::cross3(rb_cs,delf,deltb);
+
+    }
+
+    if (newton_bond || a < nlocal) {
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      torque[b][0] -= deltb[0];
+      torque[b][1] -= deltb[1];
+      torque[b][2] -= deltb[2];
+
+    }
+
+    // increment virial only
+    if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0,
+        delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
+
+    // pure torques not expressible as r x f
+
+    delta[0] = 0.0;
+    delta[1] = 0.0;
+    delta[2] = 0.0;
+    deltb[0] = 0.0;
+    deltb[1] = 0.0;
+    deltb[2] = 0.0;
+
+    // theta5p torque
+    if (theta5p) {
+
+      tpair = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
+      MathExtra::cross3(delr_st_norm,az,t5pdir);
+
+      delta[0] += t5pdir[0] * tpair;
+      delta[1] += t5pdir[1] * tpair;
+      delta[2] += t5pdir[2] * tpair;
+
+    }
+
+    // theta6p torque
+    if (theta6p) {
+
+      tpair = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2;
+      MathExtra::cross3(delr_st_norm,bz,t6pdir);
+
+      deltb[0] -= t6pdir[0] * tpair;
+      deltb[1] -= t6pdir[1] * tpair;
+      deltb[2] -= t6pdir[2] * tpair;
+
+    }
+
+    // theta9 torque
+    if (theta9) {
+
+      tpair = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2;
+      MathExtra::cross3(delr_ss_norm,aux3p,t9dir);
+
+      delta[0] += t9dir[0] * tpair;
+      delta[1] += t9dir[1] * tpair;
+      delta[2] += t9dir[2] * tpair;
+
+    }
+
+    // theta10 torque
+    if (theta10) {
+
+      tpair = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2;
+      MathExtra::cross3(delr_ss_norm,aux5p,t10dir);
+
+      deltb[0] -= t10dir[0] * tpair;
+      deltb[1] -= t10dir[1] * tpair;
+      deltb[2] -= t10dir[2] * tpair;
+
+    }
+
+    // cosphi1 torque
+    if (cosphi1) {
+
+      tpair   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2;
+      MathExtra::cross3(delr_ss_norm,ay,cosphi1dir);
+
+      delta[0] += cosphi1dir[0] * tpair;
+      delta[1] += cosphi1dir[1] * tpair;
+      delta[2] += cosphi1dir[2] * tpair;
+
+    }
+
+    // cosphi2 torque
+    if (cosphi2) {
+
+      tpair   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2;
+      MathExtra::cross3(delr_ss_norm,by,cosphi2dir);
+
+      deltb[0] -= cosphi2dir[0] * tpair;
+      deltb[1] -= cosphi2dir[1] * tpair;
+      deltb[2] -= cosphi2dir[2] * tpair;
+
+    }
+
+    // increment torques
+    if (newton_bond || a < nlocal) {
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      torque[b][0] -= deltb[0];
+      torque[b][1] -= deltb[1];
+      torque[b][2] -= deltb[2];
+
+    }
+
+    }
+    }
+    }
+    // end early rejection criteria
+
+  }
+  // end stacking interaction
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+  memory->create(epsilon_st,n+1,n+1,"pair:epsilon_st");
+  memory->create(a_st,n+1,n+1,"pair:a_st");
+  memory->create(cut_st_0,n+1,n+1,"pair:cut_st_0");
+  memory->create(cut_st_c,n+1,n+1,"pair:cut_st_c");
+  memory->create(cut_st_lo,n+1,n+1,"pair:cut_st_lo");
+  memory->create(cut_st_hi,n+1,n+1,"pair:cut_st_hi");
+  memory->create(cut_st_lc,n+1,n+1,"pair:cut_st_lc");
+  memory->create(cut_st_hc,n+1,n+1,"pair:cut_st_hc");
+  memory->create(b_st_lo,n+1,n+1,"pair:b_st_lo");
+  memory->create(b_st_hi,n+1,n+1,"pair:b_st_hi");
+  memory->create(shift_st,n+1,n+1,"pair:shift_st");
+  memory->create(cutsq_st_hc,n+1,n+1,"pair:cutsq_st_hc");
+
+  memory->create(a_st5,n+1,n+1,"pair:a_st5");
+  memory->create(theta_st5_0,n+1,n+1,"pair:theta_st5_0");
+  memory->create(dtheta_st5_ast,n+1,n+1,"pair:dtheta_st5_ast");
+  memory->create(b_st5,n+1,n+1,"pair:b_st5");
+  memory->create(dtheta_st5_c,n+1,n+1,"pair:dtheta_st5_c");
+
+  memory->create(a_st6,n+1,n+1,"pair:a_st6");
+  memory->create(theta_st6_0,n+1,n+1,"pair:theta_st6_0");
+  memory->create(dtheta_st6_ast,n+1,n+1,"pair:dtheta_st6_ast");
+  memory->create(b_st6,n+1,n+1,"pair:b_st6");
+  memory->create(dtheta_st6_c,n+1,n+1,"pair:dtheta_st6_c");
+
+  memory->create(a_st9,n+1,n+1,"pair:a_st9");
+  memory->create(theta_st9_0,n+1,n+1,"pair:theta_st9_0");
+  memory->create(dtheta_st9_ast,n+1,n+1,"pair:dtheta_st9_ast");
+  memory->create(b_st9,n+1,n+1,"pair:b_st9");
+  memory->create(dtheta_st9_c,n+1,n+1,"pair:dtheta_st9_c");
+
+  memory->create(a_st10,n+1,n+1,"pair:a_st10");
+  memory->create(theta_st10_0,n+1,n+1,"pair:theta_st10_0");
+  memory->create(dtheta_st10_ast,n+1,n+1,"pair:dtheta_st10_ast");
+  memory->create(b_st10,n+1,n+1,"pair:b_st10");
+  memory->create(dtheta_st10_c,n+1,n+1,"pair:dtheta_st10_c");
+
+  memory->create(a_st1,n+1,n+1,"pair:a_st1");
+  memory->create(cosphi_st1_ast,n+1,n+1,"pair:cosphi_st1_ast");
+  memory->create(b_st1,n+1,n+1,"pair:b_st1");
+  memory->create(cosphi_st1_c,n+1,n+1,"pair:cosphi_st1_c");
+  memory->create(a_st2,n+1,n+1,"pair:a_st2");
+  memory->create(cosphi_st2_ast,n+1,n+1,"pair:cosphi_st2_ast");
+  memory->create(b_st2,n+1,n+1,"pair:b_st2");
+  memory->create(cosphi_st2_c,n+1,n+1,"pair:cosphi_st2_c");
+
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::settings(int narg, char **/*arg*/)
+{
+  if (narg != 0) error->all(FLERR,"Illegal pair_style command");
+
+}
+
+/* ----------------------------------------------------------------------
+   return temperature dependent oxRNA stacking strength
+------------------------------------------------------------------------- */
+
+double PairOxrna2Stk::stacking_strength(double xi_st, double kappa_st, double T)
+{
+  double eps;
+
+  eps = xi_st + kappa_st * T;
+
+  return eps;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::coeff(int narg, char **arg)
+{
+  int count;
+
+  if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+  // stacking interaction
+  count = 0;
+
+  double T, epsilon_st_one, xi_st_one, kappa_st_one, a_st_one, b_st_lo_one, b_st_hi_one;
+  double cut_st_0_one, cut_st_c_one, cut_st_lo_one, cut_st_hi_one;
+  double cut_st_lc_one, cut_st_hc_one, tmp, shift_st_one;
+
+  double a_st5_one, theta_st5_0_one, dtheta_st5_ast_one;
+  double b_st5_one, dtheta_st5_c_one;
+
+  double a_st6_one, theta_st6_0_one, dtheta_st6_ast_one;
+  double b_st6_one, dtheta_st6_c_one;
+
+  double a_st9_one, theta_st9_0_one, dtheta_st9_ast_one;
+  double b_st9_one, dtheta_st9_c_one;
+
+  double a_st10_one, theta_st10_0_one, dtheta_st10_ast_one;
+  double b_st10_one, dtheta_st10_c_one;
+
+  double a_st1_one, cosphi_st1_ast_one, b_st1_one, cosphi_st1_c_one;
+  double a_st2_one, cosphi_st2_ast_one, b_st2_one, cosphi_st2_c_one;
+
+  if (strcmp(arg[2], "seqav") != 0 && strcmp(arg[2], "seqdep") != 0) {
+    error->all(FLERR,"Incorrect setting, select seqav or seqdep in oxrna2/stk");
+  }
+  if (strcmp(arg[2],"seqav")  == 0) seqdepflag = 0;
+  if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1;
+
+  T = force->numeric(FLERR,arg[3]);
+  xi_st_one = force->numeric(FLERR,arg[4]);
+  kappa_st_one = force->numeric(FLERR,arg[5]);
+  epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T);
+
+  a_st_one = force->numeric(FLERR,arg[6]);
+  cut_st_0_one = force->numeric(FLERR,arg[7]);
+  cut_st_c_one = force->numeric(FLERR,arg[8]);
+  cut_st_lo_one = force->numeric(FLERR,arg[9]);
+  cut_st_hi_one = force->numeric(FLERR,arg[10]);
+
+  a_st5_one = force->numeric(FLERR,arg[11]);
+  theta_st5_0_one = force->numeric(FLERR,arg[12]);
+  dtheta_st5_ast_one = force->numeric(FLERR,arg[13]);
+  a_st6_one = force->numeric(FLERR,arg[14]);
+  theta_st6_0_one = force->numeric(FLERR,arg[15]);
+  dtheta_st6_ast_one = force->numeric(FLERR,arg[16]);
+
+  a_st9_one = force->numeric(FLERR,arg[17]);
+  theta_st9_0_one = force->numeric(FLERR,arg[18]);
+  dtheta_st9_ast_one = force->numeric(FLERR,arg[19]);
+  a_st10_one = force->numeric(FLERR,arg[20]);
+  theta_st10_0_one = force->numeric(FLERR,arg[21]);
+  dtheta_st10_ast_one = force->numeric(FLERR,arg[22]);
+
+  a_st1_one = force->numeric(FLERR,arg[23]);
+  cosphi_st1_ast_one = force->numeric(FLERR,arg[24]);
+  a_st2_one = force->numeric(FLERR,arg[25]);
+  cosphi_st2_ast_one = force->numeric(FLERR,arg[26]);
+
+  b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
+        2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
+        (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))/
+        (4*((1-exp(-a_st_one*(cut_st_lo_one -cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))-
+        (1-exp(-a_st_one*(cut_st_c_one -cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_c_one-cut_st_0_one)))));
+
+  cut_st_lc_one = cut_st_lo_one - a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
+        (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))/b_st_lo_one;
+
+  b_st_hi_one = 2*a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))*
+        2*a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))*
+        (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))/
+        (4*((1-exp(-a_st_one*(cut_st_hi_one -cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))-
+        (1-exp(-a_st_one*(cut_st_c_one -cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_c_one-cut_st_0_one)))));
+
+  cut_st_hc_one = cut_st_hi_one - a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))*
+        (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))/b_st_hi_one;
+
+  tmp = 1 - exp(-(cut_st_c_one-cut_st_0_one) * a_st_one);
+  shift_st_one = epsilon_st_one * tmp * tmp;
+
+  b_st5_one = a_st5_one*a_st5_one*dtheta_st5_ast_one*dtheta_st5_ast_one/(1-a_st5_one*dtheta_st5_ast_one*dtheta_st5_ast_one);
+  dtheta_st5_c_one = 1/(a_st5_one*dtheta_st5_ast_one);
+
+  b_st6_one = a_st6_one*a_st6_one*dtheta_st6_ast_one*dtheta_st6_ast_one/(1-a_st6_one*dtheta_st6_ast_one*dtheta_st6_ast_one);
+  dtheta_st6_c_one = 1/(a_st6_one*dtheta_st6_ast_one);
+
+  b_st9_one = a_st9_one*a_st9_one*dtheta_st9_ast_one*dtheta_st9_ast_one/(1-a_st9_one*dtheta_st9_ast_one*dtheta_st9_ast_one);
+  dtheta_st9_c_one = 1/(a_st9_one*dtheta_st9_ast_one);
+
+  b_st10_one = a_st10_one*a_st10_one*dtheta_st10_ast_one*dtheta_st10_ast_one/(1-a_st10_one*dtheta_st10_ast_one*dtheta_st10_ast_one);
+  dtheta_st10_c_one = 1/(a_st10_one*dtheta_st10_ast_one);
+
+  b_st1_one = a_st1_one*a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one/(1-a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one);
+  cosphi_st1_c_one=1/(a_st1_one*cosphi_st1_ast_one);
+
+  b_st2_one = a_st2_one*a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one/(1-a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one);
+  cosphi_st2_c_one=1/(a_st2_one*cosphi_st2_ast_one);
+
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+
+      epsilon_st[i][j] = epsilon_st_one;
+      if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1];
+      a_st[i][j] = a_st_one;
+      cut_st_0[i][j] = cut_st_0_one;
+      cut_st_c[i][j] = cut_st_c_one;
+      cut_st_lo[i][j] = cut_st_lo_one;
+      cut_st_hi[i][j] = cut_st_hi_one;
+      cut_st_lc[i][j] = cut_st_lc_one;
+      cut_st_hc[i][j] = cut_st_hc_one;
+      b_st_lo[i][j] = b_st_lo_one;
+      b_st_hi[i][j] = b_st_hi_one;
+      shift_st[i][j] = shift_st_one;
+      if (seqdepflag) shift_st[i][j] *= eta_st[i-1][j-1];
+
+      a_st5[i][j] = a_st5_one;
+      theta_st5_0[i][j] = theta_st5_0_one;
+      dtheta_st5_ast[i][j] = dtheta_st5_ast_one;
+      b_st5[i][j] = b_st5_one;
+      dtheta_st5_c[i][j] = dtheta_st5_c_one;
+
+      a_st6[i][j] = a_st6_one;
+      theta_st6_0[i][j] = theta_st6_0_one;
+      dtheta_st6_ast[i][j] = dtheta_st6_ast_one;
+      b_st6[i][j] = b_st6_one;
+      dtheta_st6_c[i][j] = dtheta_st6_c_one;
+
+      a_st9[i][j] = a_st9_one;
+      theta_st9_0[i][j] = theta_st9_0_one;
+      dtheta_st9_ast[i][j] = dtheta_st9_ast_one;
+      b_st9[i][j] = b_st9_one;
+      dtheta_st9_c[i][j] = dtheta_st9_c_one;
+
+      a_st10[i][j] = a_st10_one;
+      theta_st10_0[i][j] = theta_st10_0_one;
+      dtheta_st10_ast[i][j] = dtheta_st10_ast_one;
+      b_st10[i][j] = b_st10_one;
+      dtheta_st10_c[i][j] = dtheta_st10_c_one;
+
+      a_st1[i][j] = a_st1_one;
+      cosphi_st1_ast[i][j] = cosphi_st1_ast_one;
+      b_st1[i][j] = b_st1_one;
+      cosphi_st1_c[i][j] = cosphi_st1_c_one;
+
+      a_st2[i][j] = a_st2_one;
+      cosphi_st2_ast[i][j] = cosphi_st2_ast_one;
+      b_st2[i][j] = b_st2_one;
+      cosphi_st2_c[i][j] = cosphi_st2_c_one;
+
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
+
+}
+
+/* ----------------------------------------------------------------------
+   neighbor callback to inform pair style of neighbor list to use regular
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::init_list(int id, NeighList *ptr)
+{
+  if (id == 0) list = ptr;
+  if (id  > 0) error->all(FLERR,"Respa not supported");
+
+}
+
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairOxrna2Stk::init_one(int i, int j)
+{
+
+  if (setflag[i][j] == 0) {
+    error->all(FLERR,"Coefficient mixing not defined in oxRNA");
+  }
+  if (offset_flag) {
+    error->all(FLERR,"Offset not supported in oxRNA");
+  }
+
+  if (seqdepflag) {
+    epsilon_st[j][i] = epsilon_st[i][j]  / eta_st[i-1][j-1] * eta_st[j-1][i-1];
+  }
+  else {
+    epsilon_st[j][i] = epsilon_st[i][j];
+  }
+  a_st[j][i] = a_st[i][j];
+  b_st_lo[j][i] = b_st_lo[i][j];
+  b_st_hi[j][i] = b_st_hi[i][j];
+  cut_st_0[j][i] = cut_st_0[i][j];
+  cut_st_c[j][i] = cut_st_c[i][j];
+  cut_st_lo[j][i] = cut_st_lo[i][j];
+  cut_st_hi[j][i] = cut_st_hi[i][j];
+  cut_st_lc[j][i] = cut_st_lc[i][j];
+  cut_st_hc[j][i] = cut_st_hc[i][j];
+  if (seqdepflag) {
+    shift_st[j][i] = shift_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1];
+  }
+  else {
+    shift_st[j][i] = shift_st[i][j];
+  }
+
+  a_st5[j][i] = a_st5[i][j];
+  theta_st5_0[j][i] = theta_st5_0[i][j];
+  dtheta_st5_ast[j][i] = dtheta_st5_ast[i][j];
+  b_st5[j][i] = b_st5[i][j];
+  dtheta_st5_c[j][i] = dtheta_st5_c[i][j];
+
+  a_st6[j][i] = a_st6[i][j];
+  theta_st6_0[j][i] = theta_st6_0[i][j];
+  dtheta_st6_ast[j][i] = dtheta_st6_ast[i][j];
+  b_st6[j][i] = b_st6[i][j];
+  dtheta_st6_c[j][i] = dtheta_st6_c[i][j];
+
+  a_st9[j][i] = a_st9[i][j];
+  theta_st9_0[j][i] = theta_st9_0[i][j];
+  dtheta_st9_ast[j][i] = dtheta_st9_ast[i][j];
+  b_st9[j][i] = b_st9[i][j];
+  dtheta_st9_c[j][i] = dtheta_st9_c[i][j];
+
+  a_st10[j][i] = a_st10[i][j];
+  theta_st10_0[j][i] = theta_st10_0[i][j];
+  dtheta_st10_ast[j][i] = dtheta_st10_ast[i][j];
+  b_st10[j][i] = b_st10[i][j];
+  dtheta_st10_c[j][i] = dtheta_st10_c[i][j];
+
+  a_st1[j][i] = a_st1[i][j];
+  cosphi_st1_ast[j][i] = cosphi_st1_ast[i][j];
+  b_st1[j][i] = b_st1[i][j];
+  cosphi_st1_c[j][i] = cosphi_st1_c[i][j];
+
+  a_st2[j][i] = a_st2[i][j];
+  cosphi_st2_ast[j][i] = cosphi_st2_ast[i][j];
+  b_st2[j][i] = b_st2[i][j];
+  cosphi_st2_c[j][i] = cosphi_st2_c[i][j];
+
+  cutsq_st_hc[i][j] = cut_st_hc[i][j]*cut_st_hc[i][j];
+  cutsq_st_hc[j][i] = cutsq_st_hc[i][j];
+
+  // set the master list distance cutoff
+  return cut_st_hc[i][j];
+
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+      if (setflag[i][j]) {
+
+        fwrite(&epsilon_st[i][j],sizeof(double),1,fp);
+        fwrite(&a_st[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_0[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_c[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_lo[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_hi[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_lc[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_hc[i][j],sizeof(double),1,fp);
+        fwrite(&b_st_lo[i][j],sizeof(double),1,fp);
+        fwrite(&b_st_hi[i][j],sizeof(double),1,fp);
+        fwrite(&shift_st[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st5[i][j],sizeof(double),1,fp);
+        fwrite(&theta_st5_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st5_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st5[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st5_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st6[i][j],sizeof(double),1,fp);
+        fwrite(&theta_st6_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st6_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st6[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st6_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st9[i][j],sizeof(double),1,fp);
+        fwrite(&theta_st9_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st9_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st9[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st9_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st10[i][j],sizeof(double),1,fp);
+        fwrite(&theta_st10_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st10_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st10[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st10_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st1[i][j],sizeof(double),1,fp);
+        fwrite(&cosphi_st1_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st1[i][j],sizeof(double),1,fp);
+        fwrite(&cosphi_st1_c[i][j],sizeof(double),1,fp);
+        fwrite(&a_st2[i][j],sizeof(double),1,fp);
+        fwrite(&cosphi_st2_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st2[i][j],sizeof(double),1,fp);
+        fwrite(&cosphi_st2_c[i][j],sizeof(double),1,fp);
+
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+
+          utils::sfread(FLERR,&epsilon_st[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&a_st[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shift_st[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st5_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st5_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st5_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st6_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st6_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st6_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st9[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st9_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st9_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st9[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st9_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st10[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st10_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st10_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st10[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st10_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st1_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&a_st2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st2_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st2_c[i][j],sizeof(double),1,fp,NULL,error);
+
+        }
+
+        MPI_Bcast(&epsilon_st[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&a_st[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_c[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_lo[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_hi[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_lc[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_hc[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st_lo[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st_hi[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&shift_st[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st5[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_st5_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st5_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st5[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st5_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st6[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_st6_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st6_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st6[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st6_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st9[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_st9_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st9_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st9[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st9_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st10[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_st10_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st10_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st10[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st10_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st1[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cosphi_st1_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st1[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cosphi_st1_c[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&a_st2[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cosphi_st2_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st2[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cosphi_st2_c[i][j],1,MPI_DOUBLE,0,world);
+
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::write_restart_settings(FILE *fp)
+{
+  fwrite(&offset_flag,sizeof(int),1,fp);
+  fwrite(&mix_flag,sizeof(int),1,fp);
+  fwrite(&tail_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::read_restart_settings(FILE *fp)
+{
+  int me = comm->me;
+  if (me == 0) {
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+  }
+  MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d\
+         %g %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g\
+         %g %g %g %g\
+         \n",i,
+        epsilon_st[i][i],a_st[i][i],cut_st_0[i][i],cut_st_c[i][i],cut_st_lo[i][i],cut_st_hi[i][i],
+        cut_st_lc[i][i],cut_st_hc[i][i],b_st_lo[i][i],b_st_hi[i][i],shift_st[i][i],
+        a_st5[i][i],theta_st5_0[i][i],dtheta_st5_ast[i][i],b_st5[i][i],dtheta_st5_c[i][i],
+        a_st6[i][i],theta_st6_0[i][i],dtheta_st6_ast[i][i],b_st6[i][i],dtheta_st6_c[i][i],
+        a_st9[i][i],theta_st9_0[i][i],dtheta_st9_ast[i][i],b_st9[i][i],dtheta_st9_c[i][i],
+        a_st10[i][i],theta_st10_0[i][i],dtheta_st10_ast[i][i],b_st10[i][i],dtheta_st10_c[i][i],
+        a_st1[i][i],cosphi_st1_ast[i][i],b_st1[i][i], cosphi_st1_c[i][i],
+        a_st2[i][i],cosphi_st2_ast[i][i],b_st2[i][i], cosphi_st2_c[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d\
+         %g %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g\
+         %g %g %g %g\
+         \n",i,j,
+        epsilon_st[i][j],a_st[i][j],cut_st_0[i][j],cut_st_c[i][j],cut_st_lo[i][j],cut_st_hi[i][j],
+        cut_st_lc[i][j],cut_st_hc[i][j],b_st_lo[i][j],b_st_hi[i][j],shift_st[i][j],
+        a_st5[i][j],theta_st5_0[i][j],dtheta_st5_ast[i][j],b_st5[i][j],dtheta_st5_c[i][j],
+        a_st6[i][j],theta_st6_0[i][j],dtheta_st6_ast[i][j],b_st6[i][j],dtheta_st6_c[i][j],
+        a_st9[i][j],theta_st9_0[i][j],dtheta_st9_ast[i][j],b_st9[i][j],dtheta_st9_c[i][j],
+        a_st10[i][j],theta_st10_0[i][j],dtheta_st10_ast[i][j],b_st10[i][j],dtheta_st10_c[i][j],
+        a_st1[i][j],cosphi_st1_ast[i][j],b_st1[i][j],cosphi_st1_c[i][j],
+        a_st2[i][j],cosphi_st2_ast[i][j],b_st2[i][j],cosphi_st2_c[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairOxrna2Stk::extract(const char *str, int &dim)
+{
+  dim = 2;
+
+  if (strcmp(str,"epsilon_st") == 0) return (void *) epsilon_st;
+  if (strcmp(str,"a_st") == 0) return (void *) a_st;
+  if (strcmp(str,"cut_st_0") == 0) return (void *) cut_st_0;
+  if (strcmp(str,"cut_st_c") == 0) return (void *) cut_st_c;
+  if (strcmp(str,"cut_st_lo") == 0) return (void *) cut_st_lo;
+  if (strcmp(str,"cut_st_hi") == 0) return (void *) cut_st_hi;
+  if (strcmp(str,"cut_st_lc") == 0) return (void *) cut_st_lc;
+  if (strcmp(str,"cut_st_hc") == 0) return (void *) cut_st_hc;
+  if (strcmp(str,"b_st_lo") == 0) return (void *) b_st_lo;
+  if (strcmp(str,"b_st_hi") == 0) return (void *) b_st_hi;
+  if (strcmp(str,"shift_st") == 0) return (void *) shift_st;
+
+  if (strcmp(str,"a_st5") == 0) return (void *) a_st5;
+  if (strcmp(str,"theta_st5_0") == 0) return (void *) theta_st5_0;
+  if (strcmp(str,"dtheta_st5_ast") == 0) return (void *) dtheta_st5_ast;
+  if (strcmp(str,"b_st5") == 0) return (void *) b_st5;
+  if (strcmp(str,"dtheta_st5_c") == 0) return (void *) dtheta_st5_c;
+
+  if (strcmp(str,"a_st6") == 0) return (void *) a_st6;
+  if (strcmp(str,"theta_st6_0") == 0) return (void *) theta_st6_0;
+  if (strcmp(str,"dtheta_st6_ast") == 0) return (void *) dtheta_st6_ast;
+  if (strcmp(str,"b_st6") == 0) return (void *) b_st6;
+  if (strcmp(str,"dtheta_st6_c") == 0) return (void *) dtheta_st6_c;
+
+  if (strcmp(str,"a_st9") == 0) return (void *) a_st9;
+  if (strcmp(str,"theta_st9_0") == 0) return (void *) theta_st9_0;
+  if (strcmp(str,"dtheta_st9_ast") == 0) return (void *) dtheta_st9_ast;
+  if (strcmp(str,"b_st9") == 0) return (void *) b_st9;
+  if (strcmp(str,"dtheta_st9_c") == 0) return (void *) dtheta_st9_c;
+
+  if (strcmp(str,"a_st10") == 0) return (void *) a_st10;
+  if (strcmp(str,"theta_st10_0") == 0) return (void *) theta_st10_0;
+  if (strcmp(str,"dtheta_st10_ast") == 0) return (void *) dtheta_st10_ast;
+  if (strcmp(str,"b_st10") == 0) return (void *) b_st10;
+  if (strcmp(str,"dtheta_st10_c") == 0) return (void *) dtheta_st10_c;
+
+  if (strcmp(str,"a_st1") == 0) return (void *) a_st1;
+  if (strcmp(str,"cosphi_st1_ast") == 0) return (void *) cosphi_st1_ast;
+  if (strcmp(str,"b_st1") == 0) return (void *) b_st1;
+  if (strcmp(str,"cosphi_st1_c") == 0) return (void *) cosphi_st1_c;
+
+  if (strcmp(str,"a_st2") == 0) return (void *) a_st2;
+  if (strcmp(str,"cosphi_st2_ast") == 0) return (void *) cosphi_st2_ast;
+  if (strcmp(str,"b_st2") == 0) return (void *) b_st2;
+  if (strcmp(str,"cosphi_st2_c") == 0) return (void *) cosphi_st2_c;
+
+  return NULL;
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_stk.h b/src/USER-CGDNA/pair_oxrna2_stk.h
new file mode 100644
index 0000000000..519f7c0707
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_stk.h
@@ -0,0 +1,86 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/stk,PairOxrna2Stk)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_STK_H
+#define LMP_PAIR_OXRNA2_STK_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Stk : public Pair {
+ public:
+  PairOxrna2Stk(class LAMMPS *);
+  virtual ~PairOxrna2Stk();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  void init_list(int, class NeighList *);
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
+  void *extract(const char *, int &);
+
+ protected:
+  // stacking interaction
+  double eta_st[4][4];
+  double stacking_strength(double, double, double);
+  double **epsilon_st, **a_st, **cut_st_0, **cut_st_c;
+  double **cut_st_lo, **cut_st_hi;
+  double **cut_st_lc, **cut_st_hc, **b_st_lo, **b_st_hi, **shift_st;
+  double **cutsq_st_hc;
+  double **a_st5, **theta_st5_0, **dtheta_st5_ast;
+  double **b_st5, **dtheta_st5_c;
+  double **a_st6, **theta_st6_0, **dtheta_st6_ast;
+  double **b_st6, **dtheta_st6_c;
+  double **a_st9, **theta_st9_0, **dtheta_st9_ast;
+  double **b_st9, **dtheta_st9_c;
+  double **a_st10, **theta_st10_0, **dtheta_st10_ast;
+  double **b_st10, **dtheta_st10_c;
+  double **a_st1, **cosphi_st1_ast, **b_st1, **cosphi_st1_c;
+  double **a_st2, **cosphi_st2_ast, **b_st2, **cosphi_st2_c;
+
+  int seqdepflag;
+
+  virtual void allocate();
+  void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp
new file mode 100644
index 0000000000..f5207c53e7
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp
@@ -0,0 +1,1079 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include "pair_oxrna2_xstk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include "mf_oxdna.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "utils.h"
+#include "atom_vec_ellipsoid.h"
+#include "math_extra.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+using namespace MFOxdna;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Xstk::PairOxrna2Xstk(LAMMPS *lmp) : Pair(lmp)
+{
+  single_enable = 0;
+  writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Xstk::~PairOxrna2Xstk()
+{
+  if (allocated) {
+
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(k_xst);
+    memory->destroy(cut_xst_0);
+    memory->destroy(cut_xst_c);
+    memory->destroy(cut_xst_lo);
+    memory->destroy(cut_xst_hi);
+    memory->destroy(cut_xst_lc);
+    memory->destroy(cut_xst_hc);
+    memory->destroy(cutsq_xst_hc);
+    memory->destroy(b_xst_lo);
+    memory->destroy(b_xst_hi);
+
+    memory->destroy(a_xst1);
+    memory->destroy(theta_xst1_0);
+    memory->destroy(dtheta_xst1_ast);
+    memory->destroy(b_xst1);
+    memory->destroy(dtheta_xst1_c);
+
+    memory->destroy(a_xst2);
+    memory->destroy(theta_xst2_0);
+    memory->destroy(dtheta_xst2_ast);
+    memory->destroy(b_xst2);
+    memory->destroy(dtheta_xst2_c);
+
+    memory->destroy(a_xst3);
+    memory->destroy(theta_xst3_0);
+    memory->destroy(dtheta_xst3_ast);
+    memory->destroy(b_xst3);
+    memory->destroy(dtheta_xst3_c);
+
+    memory->destroy(a_xst7);
+    memory->destroy(theta_xst7_0);
+    memory->destroy(dtheta_xst7_ast);
+    memory->destroy(b_xst7);
+    memory->destroy(dtheta_xst7_c);
+
+    memory->destroy(a_xst8);
+    memory->destroy(theta_xst8_0);
+    memory->destroy(dtheta_xst8_ast);
+    memory->destroy(b_xst8);
+    memory->destroy(dtheta_xst8_c);
+
+  }
+}
+
+/* ----------------------------------------------------------------------
+   compute function for oxDNA pair interactions
+   hb=hydrogen bonding site
+
+   NOTE: The cross-stacking interaction takes place between hb sites
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::compute(int eflag, int vflag)
+{
+
+  double delf[3],delta[3],deltb[3]; // force, torque increment;
+  double evdwl,fpair,finc,tpair,factor_lj;
+  double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
+  double theta1,t1dir[3],cost1;
+  double theta2,t2dir[3],cost2;
+  double theta3,t3dir[3],cost3;
+  double theta4,theta4p,t4dir[3],cost4;
+  double theta7,theta7p,t7dir[3],cost7;
+  double theta8,theta8p,t8dir[3],cost8;
+
+  // distance COM-h-bonding site
+  double d_chb=+0.4;
+  // vectors COM-h-bonding site in lab frame
+  double ra_chb[3],rb_chb[3];
+
+  // quaternions and Cartesian unit vectors in lab frame
+  double *qa,ax[3],ay[3],az[3];
+  double *qb,bx[3],by[3],bz[3];
+
+  double **x = atom->x;
+  double **f = atom->f;
+  double **torque = atom->torque;
+  int *type = atom->type;
+
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+  int *alist,*blist,*numneigh,**firstneigh;
+  double *special_lj = force->special_lj;
+
+  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
+  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
+
+  int a,b,ia,ib,anum,bnum,atype,btype;
+
+  double f2,f4t1,f4t2,f4t3,f4t7,f4t8;
+  double df2,df4t1,df4t2,df4t3,df4t7,df4t8,rsint;
+
+  evdwl = 0.0;
+  ev_init(eflag,vflag);
+
+  anum = list->inum;
+  alist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over pair interaction neighbors of my atoms
+
+  for (ia = 0; ia < anum; ia++) {
+
+    a = alist[ia];
+    atype = type[a];
+
+    qa=bonus[a].quat;
+    MathExtra::q_to_exyz(qa,ax,ay,az);
+
+    ra_chb[0] = d_chb*ax[0];
+    ra_chb[1] = d_chb*ax[1];
+    ra_chb[2] = d_chb*ax[2];
+
+    blist = firstneigh[a];
+    bnum = numneigh[a];
+
+    for (ib = 0; ib < bnum; ib++) {
+
+      b = blist[ib];
+      factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
+      b &= NEIGHMASK;
+
+      btype = type[b];
+
+      qb=bonus[b].quat;
+      MathExtra::q_to_exyz(qb,bx,by,bz);
+
+      rb_chb[0] = d_chb*bx[0];
+      rb_chb[1] = d_chb*bx[1];
+      rb_chb[2] = d_chb*bx[2];
+
+      // vector h-bonding site b to a
+      delr_hb[0] = x[a][0] + ra_chb[0] - x[b][0] - rb_chb[0];
+      delr_hb[1] = x[a][1] + ra_chb[1] - x[b][1] - rb_chb[1];
+      delr_hb[2] = x[a][2] + ra_chb[2] - x[b][2] - rb_chb[2];
+
+      rsq_hb = delr_hb[0]*delr_hb[0] + delr_hb[1]*delr_hb[1] + delr_hb[2]*delr_hb[2];
+      r_hb = sqrt(rsq_hb);
+      rinv_hb = 1.0/r_hb;
+
+      delr_hb_norm[0] = delr_hb[0] * rinv_hb;
+      delr_hb_norm[1] = delr_hb[1] * rinv_hb;
+      delr_hb_norm[2] = delr_hb[2] * rinv_hb;
+
+      f2 = F2(r_hb, k_xst[atype][btype], cut_xst_0[atype][btype],
+           cut_xst_lc[atype][btype], cut_xst_hc[atype][btype], cut_xst_lo[atype][btype], cut_xst_hi[atype][btype],
+           b_xst_lo[atype][btype], b_xst_hi[atype][btype], cut_xst_c[atype][btype]);
+
+      // early rejection criterium
+      if (f2) {
+
+      cost1 = -1.0*MathExtra::dot3(ax,bx);
+      if (cost1 >  1.0) cost1 =  1.0;
+      if (cost1 < -1.0) cost1 = -1.0;
+      theta1 = acos(cost1);
+
+      f4t1 = F4(theta1, a_xst1[atype][btype], theta_xst1_0[atype][btype], dtheta_xst1_ast[atype][btype],
+             b_xst1[atype][btype], dtheta_xst1_c[atype][btype]);
+
+      // early rejection criterium
+      if (f4t1) {
+
+      cost2 = -1.0*MathExtra::dot3(ax,delr_hb_norm);
+      if (cost2 >  1.0) cost2 =  1.0;
+      if (cost2 < -1.0) cost2 = -1.0;
+      theta2 = acos(cost2);
+
+      f4t2 = F4(theta2, a_xst2[atype][btype], theta_xst2_0[atype][btype], dtheta_xst2_ast[atype][btype],
+             b_xst2[atype][btype], dtheta_xst2_c[atype][btype]);
+
+      // early rejection criterium
+      if (f4t2) {
+
+      cost3 = MathExtra::dot3(bx,delr_hb_norm);
+      if (cost3 >  1.0) cost3 =  1.0;
+      if (cost3 < -1.0) cost3 = -1.0;
+      theta3 = acos(cost3);
+
+      f4t3 = F4(theta3, a_xst3[atype][btype], theta_xst3_0[atype][btype], dtheta_xst3_ast[atype][btype],
+             b_xst3[atype][btype], dtheta_xst3_c[atype][btype]);
+
+      // early rejection criterium
+      if (f4t3) {
+
+      cost7 = -1.0*MathExtra::dot3(az,delr_hb_norm);
+      if (cost7 >  1.0) cost7 =  1.0;
+      if (cost7 < -1.0) cost7 = -1.0;
+      theta7 = acos(cost7);
+      theta7p = MY_PI - theta7;
+
+      f4t7 = F4(theta7, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype],
+             b_xst7[atype][btype], dtheta_xst7_c[atype][btype]) +
+             F4(theta7p, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype],
+             b_xst7[atype][btype], dtheta_xst7_c[atype][btype]);
+
+      // early rejection criterium
+      if (f4t7) {
+
+      cost8 = MathExtra::dot3(bz,delr_hb_norm);
+      if (cost8 >  1.0) cost8 =  1.0;
+      if (cost8 < -1.0) cost8 = -1.0;
+      theta8 = acos(cost8);
+      theta8p = MY_PI -theta8;
+
+      f4t8 = F4(theta8, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype],
+             b_xst8[atype][btype], dtheta_xst8_c[atype][btype]) +
+             F4(theta8p, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype],
+             b_xst8[atype][btype], dtheta_xst8_c[atype][btype]);
+
+
+      evdwl = f2 * f4t1 * f4t2 * f4t3 * f4t7 * f4t8 * factor_lj;
+
+
+      // early rejection criterium
+      if (evdwl) {
+
+      df2 = DF2(r_hb, k_xst[atype][btype], cut_xst_0[atype][btype],
+            cut_xst_lc[atype][btype], cut_xst_hc[atype][btype], cut_xst_lo[atype][btype], cut_xst_hi[atype][btype],
+            b_xst_lo[atype][btype], b_xst_hi[atype][btype]);
+
+      df4t1 = DF4(theta1, a_xst1[atype][btype], theta_xst1_0[atype][btype], dtheta_xst1_ast[atype][btype],
+              b_xst1[atype][btype], dtheta_xst1_c[atype][btype])/sin(theta1);
+
+      df4t2 = DF4(theta2, a_xst2[atype][btype], theta_xst2_0[atype][btype], dtheta_xst2_ast[atype][btype],
+              b_xst2[atype][btype], dtheta_xst2_c[atype][btype])/sin(theta2);
+
+      df4t3 = DF4(theta3, a_xst3[atype][btype], theta_xst3_0[atype][btype], dtheta_xst3_ast[atype][btype],
+              b_xst3[atype][btype], dtheta_xst3_c[atype][btype])/sin(theta3);
+
+      rsint = 1.0/sin(theta7);
+      df4t7 = DF4(theta7, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype],
+              b_xst7[atype][btype], dtheta_xst7_c[atype][btype])*rsint -
+              DF4(theta7p, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype],
+              b_xst7[atype][btype], dtheta_xst7_c[atype][btype])*rsint;
+
+      rsint = 1.0/sin(theta8);
+      df4t8 = DF4(theta8, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype],
+              b_xst8[atype][btype], dtheta_xst8_c[atype][btype])*rsint -
+              DF4(theta8p, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype],
+              b_xst8[atype][btype], dtheta_xst8_c[atype][btype])*rsint;
+
+      // force, torque and virial contribution for forces between h-bonding sites
+
+      fpair = 0.0;
+
+      delf[0] = 0.0;
+      delf[1] = 0.0;
+      delf[2] = 0.0;
+
+      delta[0] = 0.0;
+      delta[1] = 0.0;
+      delta[2] = 0.0;
+
+      deltb[0] = 0.0;
+      deltb[1] = 0.0;
+      deltb[2] = 0.0;
+
+      // radial force
+      finc  = -df2 * f4t1 * f4t2 * f4t3 * f4t7 * f4t8 * rinv_hb *factor_lj;
+      fpair += finc;
+
+      delf[0] += delr_hb[0] * finc;
+      delf[1] += delr_hb[1] * finc;
+      delf[2] += delr_hb[2] * finc;
+
+      // theta2 force
+      if (theta2) {
+
+        finc  = -f2 * f4t1 * df4t2 * f4t3 * f4t7 * f4t8 * rinv_hb * factor_lj;
+        fpair += finc;
+
+        delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc;
+        delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc;
+        delf[2] += (delr_hb_norm[2]*cost2 + ax[2]) * finc;
+
+      }
+
+      // theta3 force
+      if (theta3) {
+
+        finc  = -f2 * f4t1 * f4t2 * df4t3 * f4t7 * f4t8 * rinv_hb * factor_lj;
+        fpair += finc;
+
+        delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc;
+        delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc;
+        delf[2] += (delr_hb_norm[2]*cost3 - bx[2]) * finc;
+
+      }
+
+      // theta7 force
+      if (theta7) {
+
+        finc  = -f2 * f4t1 * f4t2 * f4t3 * df4t7 * f4t8 * rinv_hb * factor_lj;
+        fpair += finc;
+
+        delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc;
+        delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc;
+        delf[2] += (delr_hb_norm[2]*cost7 + az[2]) * finc;
+
+      }
+
+      // theta8 force
+      if (theta8) {
+
+        finc  = -f2 * f4t1 * f4t2 * f4t3 * f4t7 * df4t8 * rinv_hb * factor_lj;
+        fpair += finc;
+
+        delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc;
+        delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc;
+        delf[2] += (delr_hb_norm[2]*cost8 - bz[2]) * finc;
+
+      }
+
+      // increment forces and torques
+
+      f[a][0] += delf[0];
+      f[a][1] += delf[1];
+      f[a][2] += delf[2];
+
+      MathExtra::cross3(ra_chb,delf,delta);
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+      if (newton_pair || b < nlocal) {
+
+        f[b][0] -= delf[0];
+        f[b][1] -= delf[1];
+        f[b][2] -= delf[2];
+
+
+        MathExtra::cross3(rb_chb,delf,deltb);
+
+        torque[b][0] -= deltb[0];
+        torque[b][1] -= deltb[1];
+        torque[b][2] -= deltb[2];
+
+      }
+
+      // increment energy and virial
+      // NOTE: The virial is calculated on the 'molecular' basis.
+      // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
+
+      if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
+          delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
+
+      // pure torques not expressible as r x f
+
+      delta[0] = 0.0;
+      delta[1] = 0.0;
+      delta[2] = 0.0;
+      deltb[0] = 0.0;
+      deltb[1] = 0.0;
+      deltb[2] = 0.0;
+
+      // theta1 torque
+      if (theta1) {
+
+        tpair = -f2 * df4t1 * f4t2 * f4t3 * f4t7 * f4t8 * factor_lj;
+        MathExtra::cross3(ax,bx,t1dir);
+
+        delta[0] += t1dir[0]*tpair;
+        delta[1] += t1dir[1]*tpair;
+        delta[2] += t1dir[2]*tpair;
+
+        deltb[0] += t1dir[0]*tpair;
+        deltb[1] += t1dir[1]*tpair;
+        deltb[2] += t1dir[2]*tpair;
+
+      }
+
+      // theta2 torque
+      if (theta2) {
+
+        tpair = -f2 * f4t1 * df4t2 * f4t3 * f4t7 * f4t8 * factor_lj;
+        MathExtra::cross3(ax,delr_hb_norm,t2dir);
+
+        delta[0] += t2dir[0]*tpair;
+        delta[1] += t2dir[1]*tpair;
+        delta[2] += t2dir[2]*tpair;
+
+      }
+
+      // theta3 torque
+      if (theta3) {
+
+        tpair = -f2 * f4t1 * f4t2 * df4t3 * f4t7 * f4t8 * factor_lj;
+        MathExtra::cross3(bx,delr_hb_norm,t3dir);
+
+        deltb[0] += t3dir[0]*tpair;
+        deltb[1] += t3dir[1]*tpair;
+        deltb[2] += t3dir[2]*tpair;
+
+      }
+
+      // theta7 torque
+      if (theta7) {
+
+        tpair = -f2 * f4t1 * f4t2 * f4t3 * df4t7 * f4t8 * factor_lj;
+        MathExtra::cross3(az,delr_hb_norm,t7dir);
+
+        delta[0] += t7dir[0]*tpair;
+        delta[1] += t7dir[1]*tpair;
+        delta[2] += t7dir[2]*tpair;
+
+      }
+
+      // theta8 torque
+      if (theta8) {
+
+        tpair = -f2 * f4t1 * f4t2 * f4t3 * f4t7 * df4t8 * factor_lj;
+        MathExtra::cross3(bz,delr_hb_norm,t8dir);
+
+        deltb[0] += t8dir[0]*tpair;
+        deltb[1] += t8dir[1]*tpair;
+        deltb[2] += t8dir[2]*tpair;
+
+      }
+
+      // increment torques
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+      if (newton_pair || b < nlocal) {
+
+        torque[b][0] -= deltb[0];
+        torque[b][1] -= deltb[1];
+        torque[b][2] -= deltb[2];
+
+      }
+
+
+      }
+      }
+      }
+      }
+      }
+      }// end early rejection criteria
+
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+  memory->create(k_xst,n+1,n+1,"pair:k_xst");
+  memory->create(cut_xst_0,n+1,n+1,"pair:cut_xst_0");
+  memory->create(cut_xst_c,n+1,n+1,"pair:cut_xst_c");
+  memory->create(cut_xst_lo,n+1,n+1,"pair:cut_xst_lo");
+  memory->create(cut_xst_hi,n+1,n+1,"pair:cut_xst_hi");
+  memory->create(cut_xst_lc,n+1,n+1,"pair:cut_xst_lc");
+  memory->create(cut_xst_hc,n+1,n+1,"pair:cut_xst_hc");
+  memory->create(b_xst_lo,n+1,n+1,"pair:b_xst_lo");
+  memory->create(b_xst_hi,n+1,n+1,"pair:b_xst_hi");
+  memory->create(cutsq_xst_hc,n+1,n+1,"pair:cutsq_xst_hc");
+
+  memory->create(a_xst1,n+1,n+1,"pair:a_xst1");
+  memory->create(theta_xst1_0,n+1,n+1,"pair:theta_xst1_0");
+  memory->create(dtheta_xst1_ast,n+1,n+1,"pair:dtheta_xst1_ast");
+  memory->create(b_xst1,n+1,n+1,"pair:b_xst1");
+  memory->create(dtheta_xst1_c,n+1,n+1,"pair:dtheta_xst1_c");
+
+  memory->create(a_xst2,n+1,n+1,"pair:a_xst2");
+  memory->create(theta_xst2_0,n+1,n+1,"pair:theta_xst2_0");
+  memory->create(dtheta_xst2_ast,n+1,n+1,"pair:dtheta_xst2_ast");
+  memory->create(b_xst2,n+1,n+1,"pair:b_xst2");
+  memory->create(dtheta_xst2_c,n+1,n+1,"pair:dtheta_xst2_c");
+
+  memory->create(a_xst3,n+1,n+1,"pair:a_xst3");
+  memory->create(theta_xst3_0,n+1,n+1,"pair:theta_xst3_0");
+  memory->create(dtheta_xst3_ast,n+1,n+1,"pair:dtheta_xst3_ast");
+  memory->create(b_xst3,n+1,n+1,"pair:b_xst3");
+  memory->create(dtheta_xst3_c,n+1,n+1,"pair:dtheta_xst3_c");
+
+  memory->create(a_xst7,n+1,n+1,"pair:a_xst7");
+  memory->create(theta_xst7_0,n+1,n+1,"pair:theta_xst7_0");
+  memory->create(dtheta_xst7_ast,n+1,n+1,"pair:dtheta_xst7_ast");
+  memory->create(b_xst7,n+1,n+1,"pair:b_xst7");
+  memory->create(dtheta_xst7_c,n+1,n+1,"pair:dtheta_xst7_c");
+
+  memory->create(a_xst8,n+1,n+1,"pair:a_xst8");
+  memory->create(theta_xst8_0,n+1,n+1,"pair:theta_xst8_0");
+  memory->create(dtheta_xst8_ast,n+1,n+1,"pair:dtheta_xst8_ast");
+  memory->create(b_xst8,n+1,n+1,"pair:b_xst8");
+  memory->create(dtheta_xst8_c,n+1,n+1,"pair:dtheta_xst8_c");
+
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::settings(int narg, char **/*arg*/)
+{
+  if (narg != 0) error->all(FLERR,"Illegal pair_style command");
+
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::coeff(int narg, char **arg)
+{
+  int count;
+
+  if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+  // cross-stacking interaction
+  count = 0;
+
+  double k_xst_one, cut_xst_0_one, cut_xst_c_one, cut_xst_lo_one, cut_xst_hi_one;
+  double b_xst_lo_one, b_xst_hi_one, cut_xst_lc_one, cut_xst_hc_one;
+
+  double a_xst1_one, theta_xst1_0_one, dtheta_xst1_ast_one;
+  double b_xst1_one, dtheta_xst1_c_one;
+
+  double a_xst2_one, theta_xst2_0_one, dtheta_xst2_ast_one;
+  double b_xst2_one, dtheta_xst2_c_one;
+
+  double a_xst3_one, theta_xst3_0_one, dtheta_xst3_ast_one;
+  double b_xst3_one, dtheta_xst3_c_one;
+
+  double a_xst7_one, theta_xst7_0_one, dtheta_xst7_ast_one;
+  double b_xst7_one, dtheta_xst7_c_one;
+
+  double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one;
+  double b_xst8_one, dtheta_xst8_c_one;
+
+  k_xst_one = force->numeric(FLERR,arg[2]);
+  cut_xst_0_one = force->numeric(FLERR,arg[3]);
+  cut_xst_c_one = force->numeric(FLERR,arg[4]);
+  cut_xst_lo_one = force->numeric(FLERR,arg[5]);
+  cut_xst_hi_one = force->numeric(FLERR,arg[6]);
+
+  a_xst1_one = force->numeric(FLERR,arg[7]);
+  theta_xst1_0_one = force->numeric(FLERR,arg[8]);
+  dtheta_xst1_ast_one = force->numeric(FLERR,arg[9]);
+
+  a_xst2_one = force->numeric(FLERR,arg[10]);
+  theta_xst2_0_one = force->numeric(FLERR,arg[11]);
+  dtheta_xst2_ast_one = force->numeric(FLERR,arg[12]);
+
+  a_xst3_one = force->numeric(FLERR,arg[13]);
+  theta_xst3_0_one = force->numeric(FLERR,arg[14]);
+  dtheta_xst3_ast_one = force->numeric(FLERR,arg[15]);
+
+  a_xst7_one = force->numeric(FLERR,arg[16]);
+  theta_xst7_0_one = force->numeric(FLERR,arg[17]);
+  dtheta_xst7_ast_one = force->numeric(FLERR,arg[18]);
+
+  a_xst8_one = force->numeric(FLERR,arg[19]);
+  theta_xst8_0_one = force->numeric(FLERR,arg[20]);
+  dtheta_xst8_ast_one = force->numeric(FLERR,arg[21]);
+
+
+  b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/
+        (0.5 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one) -
+        k_xst_one * 0.5 * (cut_xst_0_one -cut_xst_c_one) * (cut_xst_0_one - cut_xst_c_one)/k_xst_one);
+
+  cut_xst_lc_one = cut_xst_lo_one - 0.5 * (cut_xst_lo_one - cut_xst_0_one)/b_xst_lo_one;;
+
+  b_xst_hi_one = 0.25 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one)/
+        (0.5 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one) -
+        k_xst_one * 0.5 * (cut_xst_0_one -cut_xst_c_one) * (cut_xst_0_one - cut_xst_c_one)/k_xst_one);
+
+  cut_xst_hc_one = cut_xst_hi_one - 0.5* (cut_xst_hi_one - cut_xst_0_one)/b_xst_hi_one;
+
+
+  b_xst1_one = a_xst1_one*a_xst1_one*dtheta_xst1_ast_one*dtheta_xst1_ast_one/(1-a_xst1_one*dtheta_xst1_ast_one*dtheta_xst1_ast_one);
+  dtheta_xst1_c_one = 1/(a_xst1_one*dtheta_xst1_ast_one);
+
+  b_xst2_one = a_xst2_one*a_xst2_one*dtheta_xst2_ast_one*dtheta_xst2_ast_one/(1-a_xst2_one*dtheta_xst2_ast_one*dtheta_xst2_ast_one);
+  dtheta_xst2_c_one = 1/(a_xst2_one*dtheta_xst2_ast_one);
+
+  b_xst3_one = a_xst3_one*a_xst3_one*dtheta_xst3_ast_one*dtheta_xst3_ast_one/(1-a_xst3_one*dtheta_xst3_ast_one*dtheta_xst3_ast_one);
+  dtheta_xst3_c_one = 1/(a_xst3_one*dtheta_xst3_ast_one);
+
+  b_xst7_one = a_xst7_one*a_xst7_one*dtheta_xst7_ast_one*dtheta_xst7_ast_one/(1-a_xst7_one*dtheta_xst7_ast_one*dtheta_xst7_ast_one);
+  dtheta_xst7_c_one = 1/(a_xst7_one*dtheta_xst7_ast_one);
+
+  b_xst8_one = a_xst8_one*a_xst8_one*dtheta_xst8_ast_one*dtheta_xst8_ast_one/(1-a_xst8_one*dtheta_xst8_ast_one*dtheta_xst8_ast_one);
+  dtheta_xst8_c_one = 1/(a_xst8_one*dtheta_xst8_ast_one);
+
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+
+      k_xst[i][j] = k_xst_one;
+      cut_xst_0[i][j] = cut_xst_0_one;
+      cut_xst_c[i][j] = cut_xst_c_one;
+      cut_xst_lo[i][j] = cut_xst_lo_one;
+      cut_xst_hi[i][j] = cut_xst_hi_one;
+      cut_xst_lc[i][j] = cut_xst_lc_one;
+      cut_xst_hc[i][j] = cut_xst_hc_one;
+      b_xst_lo[i][j] = b_xst_lo_one;
+      b_xst_hi[i][j] = b_xst_hi_one;
+
+      a_xst1[i][j] = a_xst1_one;
+      theta_xst1_0[i][j] = theta_xst1_0_one;
+      dtheta_xst1_ast[i][j] = dtheta_xst1_ast_one;
+      b_xst1[i][j] = b_xst1_one;
+      dtheta_xst1_c[i][j] = dtheta_xst1_c_one;
+
+      a_xst2[i][j] = a_xst2_one;
+      theta_xst2_0[i][j] = theta_xst2_0_one;
+      dtheta_xst2_ast[i][j] = dtheta_xst2_ast_one;
+      b_xst2[i][j] = b_xst2_one;
+      dtheta_xst2_c[i][j] = dtheta_xst2_c_one;
+
+      a_xst3[i][j] = a_xst3_one;
+      theta_xst3_0[i][j] = theta_xst3_0_one;
+      dtheta_xst3_ast[i][j] = dtheta_xst3_ast_one;
+      b_xst3[i][j] = b_xst3_one;
+      dtheta_xst3_c[i][j] = dtheta_xst3_c_one;
+
+      a_xst7[i][j] = a_xst7_one;
+      theta_xst7_0[i][j] = theta_xst7_0_one;
+      dtheta_xst7_ast[i][j] = dtheta_xst7_ast_one;
+      b_xst7[i][j] = b_xst7_one;
+      dtheta_xst7_c[i][j] = dtheta_xst7_c_one;
+
+      a_xst8[i][j] = a_xst8_one;
+      theta_xst8_0[i][j] = theta_xst8_0_one;
+      dtheta_xst8_ast[i][j] = dtheta_xst8_ast_one;
+      b_xst8[i][j] = b_xst8_one;
+      dtheta_xst8_c[i][j] = dtheta_xst8_c_one;
+
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk");
+
+}
+
+/* ----------------------------------------------------------------------
+   neighbor callback to inform pair style of neighbor list to use regular
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::init_list(int id, NeighList *ptr)
+{
+  if (id == 0) list = ptr;
+  if (id  > 0) error->all(FLERR,"Respa not supported");
+
+}
+
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairOxrna2Xstk::init_one(int i, int j)
+{
+
+  if (setflag[i][j] == 0) {
+    error->all(FLERR,"Coefficient mixing not defined in oxDNA");
+  }
+  if (offset_flag) {
+    error->all(FLERR,"Offset not supported in oxDNA");
+  }
+
+  k_xst[j][i] = k_xst[i][j];
+  cut_xst_0[j][i] = cut_xst_0[i][j];
+  cut_xst_c[j][i] = cut_xst_c[i][j];
+  cut_xst_lo[j][i] = cut_xst_lo[i][j];
+  cut_xst_hi[j][i] = cut_xst_hi[i][j];
+  b_xst_lo[j][i] = b_xst_lo[i][j];
+  b_xst_hi[j][i] = b_xst_hi[i][j];
+  cut_xst_lc[j][i] = cut_xst_lc[i][j];
+  cut_xst_hc[j][i] = cut_xst_hc[i][j];
+
+  a_xst1[j][i] = a_xst1[i][j];
+  theta_xst1_0[j][i] = theta_xst1_0[i][j];
+  dtheta_xst1_ast[j][i] = dtheta_xst1_ast[i][j];
+  b_xst1[j][i] = b_xst1[i][j];
+  dtheta_xst1_c[j][i] = dtheta_xst1_c[i][j];
+
+  a_xst2[j][i] = a_xst2[i][j];
+  theta_xst2_0[j][i] = theta_xst2_0[i][j];
+  dtheta_xst2_ast[j][i] = dtheta_xst2_ast[i][j];
+  b_xst2[j][i] = b_xst2[i][j];
+  dtheta_xst2_c[j][i] = dtheta_xst2_c[i][j];
+
+  a_xst3[j][i] = a_xst3[i][j];
+  theta_xst3_0[j][i] = theta_xst3_0[i][j];
+  dtheta_xst3_ast[j][i] = dtheta_xst3_ast[i][j];
+  b_xst3[j][i] = b_xst3[i][j];
+  dtheta_xst3_c[j][i] = dtheta_xst3_c[i][j];
+
+  a_xst7[j][i] = a_xst7[i][j];
+  theta_xst7_0[j][i] = theta_xst7_0[i][j];
+  dtheta_xst7_ast[j][i] = dtheta_xst7_ast[i][j];
+  b_xst7[j][i] = b_xst7[i][j];
+  dtheta_xst7_c[j][i] = dtheta_xst7_c[i][j];
+
+  a_xst8[j][i] = a_xst8[i][j];
+  theta_xst8_0[j][i] = theta_xst8_0[i][j];
+  dtheta_xst8_ast[j][i] = dtheta_xst8_ast[i][j];
+  b_xst8[j][i] = b_xst8[i][j];
+  dtheta_xst8_c[j][i] = dtheta_xst8_c[i][j];
+
+  cutsq_xst_hc[i][j] = cut_xst_hc[i][j]*cut_xst_hc[i][j];
+  cutsq_xst_hc[j][i] = cutsq_xst_hc[i][j];
+
+  // set the master list distance cutoff
+  return cut_xst_hc[i][j];
+
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+      if (setflag[i][j]) {
+
+        fwrite(&k_xst[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_0[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_c[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_lo[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_hi[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_lc[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_hc[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst_lo[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst_hi[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst1[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst1_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst1_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst1[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst1_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst2[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst2_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst2_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst2[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst2_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst3[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst3_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst3_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst3[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst3_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst7[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst7_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst7_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst7[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst7_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst8[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst8_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst8_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst8[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst8_c[i][j],sizeof(double),1,fp);
+
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+
+          utils::sfread(FLERR,&k_xst[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst_hi[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst1_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst1_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst2_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst2_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst2_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst3_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst3_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst3_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst7[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst7_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst7_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst7[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst7_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst8[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst8_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst8_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst8[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst8_c[i][j],sizeof(double),1,fp,NULL,error);
+
+        }
+
+        MPI_Bcast(&k_xst[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_c[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_lo[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_hi[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_lc[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_hc[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst_lo[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst_hi[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst1[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst1_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst1_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst1[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst1_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst2[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst2_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst2_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst2[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst2_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst3[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst3_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst3_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst3[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst3_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst7[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst7_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst7_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst7[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst7_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst8[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst8_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst8_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst8[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst8_c[i][j],1,MPI_DOUBLE,0,world);
+
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::write_restart_settings(FILE *fp)
+{
+  fwrite(&offset_flag,sizeof(int),1,fp);
+  fwrite(&mix_flag,sizeof(int),1,fp);
+  fwrite(&tail_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::read_restart_settings(FILE *fp)
+{
+  int me = comm->me;
+  if (me == 0) {
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+  }
+  MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d\
+         %g %g %g %g %g\
+         %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         \n",i,
+        k_xst[i][i],cut_xst_0[i][i],cut_xst_c[i][i],cut_xst_lo[i][i],cut_xst_hi[i][i],
+        cut_xst_lc[i][i],cut_xst_hc[i][i],b_xst_lo[i][i],b_xst_hi[i][i],
+        a_xst1[i][i],theta_xst1_0[i][i],dtheta_xst1_ast[i][i],b_xst1[i][i],dtheta_xst1_c[i][i],
+        a_xst2[i][i],theta_xst2_0[i][i],dtheta_xst2_ast[i][i],b_xst2[i][i],dtheta_xst2_c[i][i],
+        a_xst3[i][i],theta_xst3_0[i][i],dtheta_xst3_ast[i][i],b_xst3[i][i],dtheta_xst3_c[i][i],
+        a_xst7[i][i],theta_xst7_0[i][i],dtheta_xst7_ast[i][i],b_xst7[i][i],dtheta_xst7_c[i][i],
+        a_xst8[i][i],theta_xst8_0[i][i],dtheta_xst8_ast[i][i],b_xst8[i][i],dtheta_xst8_c[i][i]);
+
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d\
+         %g %g %g %g %g\
+         %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         \n",i,j,
+        k_xst[i][j],cut_xst_0[i][j],cut_xst_c[i][j],cut_xst_lo[i][j],cut_xst_hi[i][j],
+        cut_xst_lc[i][j],cut_xst_hc[i][j],b_xst_lo[i][j],b_xst_hi[i][j],
+        a_xst1[i][j],theta_xst1_0[i][j],dtheta_xst1_ast[i][j],b_xst1[i][j],dtheta_xst1_c[i][j],
+        a_xst2[i][j],theta_xst2_0[i][j],dtheta_xst2_ast[i][j],b_xst2[i][j],dtheta_xst2_c[i][j],
+        a_xst3[i][j],theta_xst3_0[i][j],dtheta_xst3_ast[i][j],b_xst3[i][j],dtheta_xst3_c[i][j],
+        a_xst7[i][j],theta_xst7_0[i][j],dtheta_xst7_ast[i][j],b_xst7[i][j],dtheta_xst7_c[i][j],
+        a_xst8[i][j],theta_xst8_0[i][j],dtheta_xst8_ast[i][j],b_xst8[i][j],dtheta_xst8_c[i][j]);
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairOxrna2Xstk::extract(const char *str, int &dim)
+{
+  dim = 2;
+
+  if (strcmp(str,"k_xst") == 0) return (void *) k_xst;
+  if (strcmp(str,"cut_xst_0") == 0) return (void *) cut_xst_0;
+  if (strcmp(str,"cut_xst_c") == 0) return (void *) cut_xst_c;
+  if (strcmp(str,"cut_xst_lo") == 0) return (void *) cut_xst_lo;
+  if (strcmp(str,"cut_xst_hi") == 0) return (void *) cut_xst_hi;
+  if (strcmp(str,"cut_xst_lc") == 0) return (void *) cut_xst_lc;
+  if (strcmp(str,"cut_xst_hc") == 0) return (void *) cut_xst_hc;
+  if (strcmp(str,"b_xst_lo") == 0) return (void *) b_xst_lo;
+  if (strcmp(str,"b_xst_hi") == 0) return (void *) b_xst_hi;
+
+  if (strcmp(str,"a_xst1") == 0) return (void *) a_xst1;
+  if (strcmp(str,"theta_xst1_0") == 0) return (void *) theta_xst1_0;
+  if (strcmp(str,"dtheta_xst1_ast") == 0) return (void *) dtheta_xst1_ast;
+  if (strcmp(str,"b_xst1") == 0) return (void *) b_xst1;
+  if (strcmp(str,"dtheta_xst1_c") == 0) return (void *) dtheta_xst1_c;
+
+  if (strcmp(str,"a_xst2") == 0) return (void *) a_xst2;
+  if (strcmp(str,"theta_xst2_0") == 0) return (void *) theta_xst2_0;
+  if (strcmp(str,"dtheta_xst2_ast") == 0) return (void *) dtheta_xst2_ast;
+  if (strcmp(str,"b_xst2") == 0) return (void *) b_xst2;
+  if (strcmp(str,"dtheta_xst2_c") == 0) return (void *) dtheta_xst2_c;
+
+  if (strcmp(str,"a_xst3") == 0) return (void *) a_xst3;
+  if (strcmp(str,"theta_xst3_0") == 0) return (void *) theta_xst3_0;
+  if (strcmp(str,"dtheta_xst3_ast") == 0) return (void *) dtheta_xst3_ast;
+  if (strcmp(str,"b_xst3") == 0) return (void *) b_xst3;
+  if (strcmp(str,"dtheta_xst3_c") == 0) return (void *) dtheta_xst3_c;
+
+  if (strcmp(str,"a_xst7") == 0) return (void *) a_xst7;
+  if (strcmp(str,"theta_xst7_0") == 0) return (void *) theta_xst7_0;
+  if (strcmp(str,"dtheta_xst7_ast") == 0) return (void *) dtheta_xst7_ast;
+  if (strcmp(str,"b_xst7") == 0) return (void *) b_xst7;
+  if (strcmp(str,"dtheta_xst7_c") == 0) return (void *) dtheta_xst7_c;
+
+  if (strcmp(str,"a_xst8") == 0) return (void *) a_xst8;
+  if (strcmp(str,"theta_xst8_0") == 0) return (void *) theta_xst8_0;
+  if (strcmp(str,"dtheta_xst8_ast") == 0) return (void *) dtheta_xst8_ast;
+  if (strcmp(str,"b_xst8") == 0) return (void *) b_xst8;
+  if (strcmp(str,"dtheta_xst8_c") == 0) return (void *) dtheta_xst8_c;
+
+  return NULL;
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.h b/src/USER-CGDNA/pair_oxrna2_xstk.h
new file mode 100644
index 0000000000..97e878c342
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_xstk.h
@@ -0,0 +1,85 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/xstk,PairOxrna2Xstk)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_XSTK_H
+#define LMP_PAIR_OXRNA2_XSTK_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Xstk : public Pair {
+ public:
+  PairOxrna2Xstk(class LAMMPS *);
+  virtual ~PairOxrna2Xstk();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  void init_list(int, class NeighList *);
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
+  void *extract(const char *, int &);
+
+ protected:
+  // cross-stacking interaction
+  double **k_xst, **cut_xst_0, **cut_xst_c, **cut_xst_lo, **cut_xst_hi;
+  double **cut_xst_lc, **cut_xst_hc, **b_xst_lo, **b_xst_hi;
+  double **cutsq_xst_hc;
+
+  double **a_xst1, **theta_xst1_0, **dtheta_xst1_ast;
+  double **b_xst1, **dtheta_xst1_c;
+
+  double **a_xst2, **theta_xst2_0, **dtheta_xst2_ast;
+  double **b_xst2, **dtheta_xst2_c;
+
+  double **a_xst3, **theta_xst3_0, **dtheta_xst3_ast;
+  double **b_xst3, **dtheta_xst3_c;
+
+  double **a_xst7, **theta_xst7_0, **dtheta_xst7_ast;
+  double **b_xst7, **dtheta_xst7_c;
+
+  double **a_xst8, **theta_xst8_0, **dtheta_xst8_ast;
+  double **b_xst8, **dtheta_xst8_c;
+
+  virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/

From d64bc2a1b791c149bbc59ed4c908aa6bbea511dd Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Mon, 4 Nov 2019 08:05:07 -0700
Subject: [PATCH 016/199] Commit JT 110419 - commit changes examples

---
 examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp | 6 +++---
 examples/SPIN/iron/in.spin.iron             | 5 +++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
index b9ede5f09c..8ea82a509b 100644
--- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
+++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
@@ -25,8 +25,8 @@ velocity 	all create 100 4928459 rot yes dist gaussian
 
 #pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
 pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy ../examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy Co
-#pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+# pair_coeff 	* * eam/alloy ../examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
 pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
 #pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652  
 
@@ -52,7 +52,7 @@ variable 	magnorm   equal c_out_mag[4]
 variable 	emag      equal c_out_mag[5]
 variable 	tmag      equal c_out_mag[6]
 
-thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo_style    custom step time v_magnorm v_emag temp press etotal
 thermo          10
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron
index 3468575493..fd504d2cfd 100644
--- a/examples/SPIN/iron/in.spin.iron
+++ b/examples/SPIN/iron/in.spin.iron
@@ -48,10 +48,11 @@ variable 	magnorm   equal c_out_mag[4]
 variable 	emag      equal c_out_mag[5]
 variable 	tmag      equal c_out_mag[6]
 
-thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe etotal
+thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe press etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+# dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z fx fy fz
 
 run 		50000

From 74e502eb637762f8d07d43eccfc7a1564aef68c7 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Mon, 4 Nov 2019 09:59:37 -0700
Subject: [PATCH 017/199] Commit2 JT 110419 - removed all tabs from spin
 package

---
 src/SPIN/atom_vec_spin.h          |  12 ++--
 src/SPIN/fix_neb_spin.h           |  24 +++----
 src/SPIN/fix_nve_spin.cpp         |   8 +--
 src/SPIN/fix_nve_spin.h           |  36 +++++-----
 src/SPIN/fix_precession_spin.cpp  |  14 ++--
 src/SPIN/fix_precession_spin.h    |  14 ++--
 src/SPIN/min_spin.cpp             |   6 +-
 src/SPIN/min_spin_cg.cpp          |  12 ++--
 src/SPIN/min_spin_cg.h            |  30 ++++-----
 src/SPIN/min_spin_lbfgs.cpp       |   8 +--
 src/SPIN/min_spin_lbfgs.h         |  32 ++++-----
 src/SPIN/neb_spin.cpp             | 108 +++++++++++++++---------------
 src/SPIN/pair_spin.h              |   4 +-
 src/SPIN/pair_spin_dipole_cut.cpp |  42 ++++++------
 src/SPIN/pair_spin_dipole_cut.h   |  14 ++--
 src/SPIN/pair_spin_dipole_long.h  |  14 ++--
 src/SPIN/pair_spin_dmi.h          |  10 +--
 src/SPIN/pair_spin_exchange.h     |   8 +--
 src/SPIN/pair_spin_magelec.h      |   8 +--
 src/SPIN/pair_spin_neel.h         |  12 ++--
 20 files changed, 208 insertions(+), 208 deletions(-)

diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h
index 1f1c34df52..a31e57bb48 100644
--- a/src/SPIN/atom_vec_spin.h
+++ b/src/SPIN/atom_vec_spin.h
@@ -67,13 +67,13 @@ class AtomVecSpin : public AtomVec {
   tagint *tag;
   int *type,*mask;
   imageint *image;
-  double **x,**v,**f;		// lattice quantities
+  double **x,**v,**f;           // lattice quantities
   
-  				// spin quantities
-  double **sp;			// sp[i][0-2] direction of the spin i
-				// sp[i][3] atomic magnetic moment of the spin i
-  double **fm;			// fm[i][0-2] direction of magnetic precession
-  double **fm_long;		// storage of long-range spin prec. components
+                                // spin quantities
+  double **sp;                  // sp[i][0-2] direction of the spin i
+                                // sp[i][3] atomic magnetic moment of the spin i
+  double **fm;                  // fm[i][0-2] direction of magnetic precession
+  double **fm_long;             // storage of long-range spin prec. components
 };
 
 }
diff --git a/src/SPIN/fix_neb_spin.h b/src/SPIN/fix_neb_spin.h
index 7ac83ddce7..9646684a3a 100644
--- a/src/SPIN/fix_neb_spin.h
+++ b/src/SPIN/fix_neb_spin.h
@@ -60,20 +60,20 @@ class FixNEBSpin : public Fix {
   double **spprev,**spnext,**fmnext;
   double **springF;
   double **tangent;
-  double **xsend,**xrecv;      	// coords to send/recv to/from other replica
-  double **fsend,**frecv;	// coords to send/recv to/from other replica
-  double **spsend,**sprecv;	// sp to send/recv to/from other replica
-  double **fmsend,**fmrecv;	// fm to send/recv to/from other replica
-  tagint *tagsend,*tagrecv;	// ditto for atom IDs
+  double **xsend,**xrecv;       // coords to send/recv to/from other replica
+  double **fsend,**frecv;       // coords to send/recv to/from other replica
+  double **spsend,**sprecv;     // sp to send/recv to/from other replica
+  double **fmsend,**fmrecv;     // fm to send/recv to/from other replica
+  tagint *tagsend,*tagrecv;     // ditto for atom IDs
 
-  				// info gathered from all procs in my replica
-  double **xsendall,**xrecvall;		// coords to send/recv to/from other replica
-  double **fsendall,**frecvall;		// force to send/recv to/from other replica
-  double **spsendall,**sprecvall;	// sp to send/recv to/from other replica
-  double **fmsendall,**fmrecvall;	// fm to send/recv to/from other replica
-  tagint *tagsendall,*tagrecvall;	// ditto for atom IDs
+                                // info gathered from all procs in my replica
+  double **xsendall,**xrecvall;         // coords to send/recv to/from other replica
+  double **fsendall,**frecvall;         // force to send/recv to/from other replica
+  double **spsendall,**sprecvall;       // sp to send/recv to/from other replica
+  double **fmsendall,**fmrecvall;       // fm to send/recv to/from other replica
+  tagint *tagsendall,*tagrecvall;       // ditto for atom IDs
 
-  int *counts,*displacements;		// used for MPI_Gather
+  int *counts,*displacements;           // used for MPI_Gather
 
   double geodesic_distance(double *, double *);
   void inter_replica_comm();
diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp
index 9b4f1916ae..87546ba9da 100644
--- a/src/SPIN/fix_nve_spin.cpp
+++ b/src/SPIN/fix_nve_spin.cpp
@@ -307,7 +307,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/)
           ComputeInteractionsSpin(i);
           AdvanceSingleSpin(i);
           i = forward_stacks[i];
-	}
+        }
       }
     }
     for (int j = nsectors-1; j >= 0; j--) {     // advance quarter s for nlocal
@@ -318,7 +318,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/)
           ComputeInteractionsSpin(i);
           AdvanceSingleSpin(i);
           i = backward_stacks[i];
-	}
+        }
       }
     }
   } else if (sector_flag == 0) {                // serial seq. update
@@ -360,7 +360,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/)
           ComputeInteractionsSpin(i);
           AdvanceSingleSpin(i);
           i = forward_stacks[i];
-	}
+        }
       }
     }
     for (int j = nsectors-1; j >= 0; j--) {     // advance quarter s for nlocal
@@ -371,7 +371,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/)
           ComputeInteractionsSpin(i);
           AdvanceSingleSpin(i);
           i = backward_stacks[i];
-	}
+        }
       }
     }
   } else if (sector_flag == 0) {                // serial seq. update
diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h
index 5871f721be..5aa6b8e4e4 100644
--- a/src/SPIN/fix_nve_spin.h
+++ b/src/SPIN/fix_nve_spin.h
@@ -34,30 +34,30 @@ friend class PairSpin;
   virtual void initial_integrate(int);
   virtual void final_integrate();
 
-  void ComputeInteractionsSpin(int);	// compute and advance single spin functions
+  void ComputeInteractionsSpin(int);    // compute and advance single spin functions
   void AdvanceSingleSpin(int);
 
-  void sectoring();			// sectoring operation functions
+  void sectoring();                     // sectoring operation functions
   int coords2sector(double *);
 
   void setup_pre_neighbor();
   void pre_neighbor();
 
-  int lattice_flag; 			// lattice_flag = 0 if spins only
-  					// lattice_flag = 1 if spin-lattice calc.
+  int lattice_flag;                     // lattice_flag = 0 if spins only
+                                        // lattice_flag = 1 if spin-lattice calc.
 
  protected:
-  int sector_flag;			// sector_flag = 0  if serial algorithm
-  					// sector_flag = 1  if parallel algorithm
+  int sector_flag;                      // sector_flag = 0  if serial algorithm
+                                        // sector_flag = 1  if parallel algorithm
 
-  double dtv, dtf, dts;			// velocity, force, and spin timesteps
+  double dtv, dtf, dts;                 // velocity, force, and spin timesteps
 
-  int nlocal_max;			// max value of nlocal (for size of lists)
+  int nlocal_max;                       // max value of nlocal (for size of lists)
 
-  int pair_spin_flag;			// magnetic pair flags
-  int long_spin_flag;			// magnetic long-range flag
-  int precession_spin_flag;		// magnetic precession flags
-  int maglangevin_flag;			// magnetic langevin flags
+  int pair_spin_flag;                   // magnetic pair flags
+  int long_spin_flag;                   // magnetic long-range flag
+  int precession_spin_flag;             // magnetic precession flags
+  int maglangevin_flag;                 // magnetic langevin flags
   int tdamp_flag, temp_flag;
   int setforce_spin_flag;
 
@@ -69,9 +69,9 @@ friend class PairSpin;
 
   // pointers to magnetic pair styles
 
-  int npairs, npairspin;		// # of pairs, and # of spin pairs
+  int npairs, npairspin;                // # of pairs, and # of spin pairs
   class Pair *pair;
-  class PairSpin **spin_pairs;		// vector of spin pairs
+  class PairSpin **spin_pairs;          // vector of spin pairs
 
   // sectoring variables
 
@@ -80,10 +80,10 @@ friend class PairSpin;
 
   // stacking variables for sectoring algorithm
 
-  int *stack_head;			// index of first atom in backward_stacks
-  int *stack_foot;			// index of first atom in forward_stacks
-  int *backward_stacks;			// index of next atom in backward stack
-  int *forward_stacks;			// index of next atom in forward stack
+  int *stack_head;                      // index of first atom in backward_stacks
+  int *stack_foot;                      // index of first atom in forward_stacks
+  int *backward_stacks;                 // index of next atom in backward stack
+  int *forward_stacks;                  // index of next atom in forward stack
 
 };
 
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index 3b8817704d..4294e5361a 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -173,9 +173,9 @@ int FixPrecessionSpin::setmask()
 
 void FixPrecessionSpin::init()
 {
-  const double hbar = force->hplanck/MY_2PI;	// eV/(rad.THz)
-  const double mub = 5.78901e-5;		// in eV/T
-  const double gyro = 2.0*mub/hbar;		// in rad.THz/T
+  const double hbar = force->hplanck/MY_2PI;    // eV/(rad.THz)
+  const double mub = 5.78901e-5;                // in eV/T
+  const double gyro = 2.0*mub/hbar;             // in rad.THz/T
 
   // convert field quantities to rad.THz
 
@@ -236,7 +236,7 @@ void FixPrecessionSpin::post_force(int /* vflag */)
   if (varflag != CONSTANT) {
     modify->clearstep_compute();
     modify->addstep_compute(update->ntimestep + 1);
-    set_magneticprecession();		// update mag. field if time-dep.
+    set_magneticprecession();           // update mag. field if time-dep.
   }
 
   int *mask = atom->mask;
@@ -266,9 +266,9 @@ void FixPrecessionSpin::post_force(int /* vflag */)
         epreci -= compute_anisotropy_energy(spi);
       }
 
-      if (cubic_flag) {		// compute cubic anisotropy
-	compute_cubic(spi,fmi);
-	epreci -= compute_cubic_energy(spi);
+      if (cubic_flag) {         // compute cubic anisotropy
+        compute_cubic(spi,fmi);
+        epreci -= compute_cubic_energy(spi);
       }
 
       eprec += epreci;
diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h
index 0037784a48..96d89e004e 100644
--- a/src/SPIN/fix_precession_spin.h
+++ b/src/SPIN/fix_precession_spin.h
@@ -54,7 +54,7 @@ class FixPrecessionSpin : public Fix {
   double compute_cubic_energy(double *);
  
  protected:
-  int style; 			// style of the magnetic precession
+  int style;                    // style of the magnetic precession
 
   double degree2rad;
   double hbar;
@@ -72,19 +72,19 @@ class FixPrecessionSpin : public Fix {
 
   double H_field;
   double nhx, nhy, nhz;
-  double hx, hy, hz; 		// temp. force variables
+  double hx, hy, hz;            // temp. force variables
 
   // magnetic anisotropy intensity and direction
 
-  double Ka;			// aniso const. in eV
-  double Kah;			// aniso const. in rad.THz
+  double Ka;                    // aniso const. in eV
+  double Kah;                   // aniso const. in rad.THz
   double nax, nay, naz;
-  double Kax, Kay, Kaz; 	// temp. force variables
+  double Kax, Kay, Kaz;         // temp. force variables
 
   // cubic anisotropy intensity
 
-  double k1c,k2c;		// cubic const. in eV
-  double k1ch,k2ch;		// cubic const. in rad.THz
+  double k1c,k2c;               // cubic const. in eV
+  double k1ch,k2ch;             // cubic const. in rad.THz
   double nc1x,nc1y,nc1z;
   double nc2x,nc2y,nc2z;
   double nc3x,nc3y,nc3z;
diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp
index 7315aca056..e39eb18744 100644
--- a/src/SPIN/min_spin.cpp
+++ b/src/SPIN/min_spin.cpp
@@ -165,9 +165,9 @@ int MinSpin::iterate(int maxiter)
 
     fmdotfm = fmsq = 0.0;
     if (update->ftol > 0.0) {
-      if (normstyle == MAX) fmsq = max_torque();	// max torque norm
-      else if (normstyle == INF) fmsq = inf_torque();	// inf torque norm
-      else if (normstyle == TWO) fmsq = total_torque();	// Euclidean torque 2-norm
+      if (normstyle == MAX) fmsq = max_torque();        // max torque norm
+      else if (normstyle == INF) fmsq = inf_torque();   // inf torque norm
+      else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm
       else error->all(FLERR,"Illegal min_modify command");
       fmdotfm = fmsq*fmsq;
       if (update->multireplica == 0) {
diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp
index 95bbcf437b..9c8c814bc4 100644
--- a/src/SPIN/min_spin_cg.cpp
+++ b/src/SPIN/min_spin_cg.cpp
@@ -270,9 +270,9 @@ int MinSpinCG::iterate(int maxiter)
 
     fmdotfm = fmsq = 0.0;
     if (update->ftol > 0.0) {
-      if (normstyle == MAX) fmsq = max_torque();	// max torque norm
-      else if (normstyle == INF) fmsq = inf_torque();	// inf torque norm
-      else if (normstyle == TWO) fmsq = total_torque();	// Euclidean torque 2-norm
+      if (normstyle == MAX) fmsq = max_torque();        // max torque norm
+      else if (normstyle == INF) fmsq = inf_torque();   // inf torque norm
+      else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm
       else error->all(FLERR,"Illegal min_modify command");
       fmdotfm = fmsq*fmsq;
       if (update->multireplica == 0) {
@@ -347,12 +347,12 @@ void MinSpinCG::calc_search_direction()
       factor = 0.0;
 
 
-  if (local_iter == 0 || local_iter % 5 == 0){ 	// steepest descent direction
+  if (local_iter == 0 || local_iter % 5 == 0){  // steepest descent direction
     for (int i = 0; i < 3 * nlocal; i++) {
       p_s[i] = -g_cur[i] * factor;
       g_old[i] = g_cur[i] * factor;
     }
-  } else { 				// conjugate direction
+  } else {                              // conjugate direction
     for (int i = 0; i < 3 * nlocal; i++) {
       g2old += g_old[i] * g_old[i];
       g2 += g_cur[i] * g_cur[i];
@@ -394,7 +394,7 @@ void MinSpinCG::advance_spins()
 {
   int nlocal = atom->nlocal;
   double **sp = atom->sp;
-  double rot_mat[9];	// exponential of matrix made of search direction
+  double rot_mat[9];    // exponential of matrix made of search direction
   double s_new[3];
 
   // loop on all spins on proc.
diff --git a/src/SPIN/min_spin_cg.h b/src/SPIN/min_spin_cg.h
index 0eed7a61e6..640721b8ef 100644
--- a/src/SPIN/min_spin_cg.h
+++ b/src/SPIN/min_spin_cg.h
@@ -35,21 +35,21 @@ class MinSpinCG: public Min {
   int iterate(int);
 
  private:
-  int local_iter;		// for neb
-  int nlocal_max;		// max value of nlocal (for size of lists)
-  int use_line_search;		// use line search or not.
-  int ireplica,nreplica;	// for neb
-  double dt;			// global timestep
-  double dts;			// spin timestep
-  double discrete_factor;	// factor for spin timestep evaluation
-  double der_e_cur;		// current derivative along search dir.
-  double der_e_pr;		// previous derivative along search dir.
-  double *spvec;		// variables for atomic dof, as 1d vector
-  double *fmvec;		// variables for atomic dof, as 1d vector
-  double *g_old;  		// gradient vector at previous step
-  double *g_cur;  		// current gradient vector
-  double *p_s;  		// search direction vector
-  double **sp_copy;		// copy of the spins
+  int local_iter;               // for neb
+  int nlocal_max;               // max value of nlocal (for size of lists)
+  int use_line_search;          // use line search or not.
+  int ireplica,nreplica;        // for neb
+  double dt;                    // global timestep
+  double dts;                   // spin timestep
+  double discrete_factor;       // factor for spin timestep evaluation
+  double der_e_cur;             // current derivative along search dir.
+  double der_e_pr;              // previous derivative along search dir.
+  double *spvec;                // variables for atomic dof, as 1d vector
+  double *fmvec;                // variables for atomic dof, as 1d vector
+  double *g_old;                // gradient vector at previous step
+  double *g_cur;                // current gradient vector
+  double *p_s;                  // search direction vector
+  double **sp_copy;             // copy of the spins
 
   void advance_spins();
   void calc_gradient();
diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp
index f86bdd5d48..a1ee010f3f 100644
--- a/src/SPIN/min_spin_lbfgs.cpp
+++ b/src/SPIN/min_spin_lbfgs.cpp
@@ -285,9 +285,9 @@ int MinSpinLBFGS::iterate(int maxiter)
 
     fmdotfm = fmsq = 0.0;
     if (update->ftol > 0.0) {
-      if (normstyle == MAX) fmsq = max_torque();	// max torque norm
-      else if (normstyle == INF) fmsq = inf_torque();	// inf torque norm
-      else if (normstyle == TWO) fmsq = total_torque();	// Euclidean torque 2-norm
+      if (normstyle == MAX) fmsq = max_torque();        // max torque norm
+      else if (normstyle == INF) fmsq = inf_torque();   // inf torque norm
+      else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm
       else error->all(FLERR,"Illegal min_modify command");
       fmdotfm = fmsq*fmsq;
       if (update->multireplica == 0) {
@@ -372,7 +372,7 @@ void MinSpinLBFGS::calc_search_direction()
     factor = 1.0;
   }
 
-  if (local_iter == 0){ 	// steepest descent direction
+  if (local_iter == 0){         // steepest descent direction
 
     //if no line search then calculate maximum rotation
     if (use_line_search == 0)
diff --git a/src/SPIN/min_spin_lbfgs.h b/src/SPIN/min_spin_lbfgs.h
index cead605b32..8b470b5d23 100644
--- a/src/SPIN/min_spin_lbfgs.h
+++ b/src/SPIN/min_spin_lbfgs.h
@@ -35,18 +35,18 @@ class MinSpinLBFGS: public Min {
   int iterate(int);
 
  private:
-  int local_iter;     		// for neb
-  int use_line_search; 		// use line search or not.
-  int nlocal_max;		// max value of nlocal (for size of lists)
-  int ireplica,nreplica; 	// for neb
-  double der_e_cur;		// current derivative along search dir.
-  double der_e_pr;    		// previous derivative along search dir.
+  int local_iter;               // for neb
+  int use_line_search;          // use line search or not.
+  int nlocal_max;               // max value of nlocal (for size of lists)
+  int ireplica,nreplica;        // for neb
+  double der_e_cur;             // current derivative along search dir.
+  double der_e_pr;              // previous derivative along search dir.
   double maxepsrot;
-  double *spvec;		// variables for atomic dof, as 1d vector
-  double *fmvec;		// variables for atomic dof, as 1d vector
-  double *g_old;  		// gradient vector at previous step
-  double *g_cur;  		// current gradient vector
-  double *p_s;  		// search direction vector
+  double *spvec;                // variables for atomic dof, as 1d vector
+  double *fmvec;                // variables for atomic dof, as 1d vector
+  double *g_old;                // gradient vector at previous step
+  double *g_cur;                // current gradient vector
+  double *p_s;                  // search direction vector
 
   void advance_spins();
   void calc_gradient();
@@ -58,11 +58,11 @@ class MinSpinLBFGS: public Min {
   int adescent(double, double);
   double maximum_rotation(double *);
 
-  double *rho;		// estimation of curvature
-  double **ds;		// change in rotation matrix between two iterations, da
-  double **dy;		// change in gradients between two iterations, dg
-  double **sp_copy;	// copy of the spins
-  int num_mem;		// number of stored steps
+  double *rho;          // estimation of curvature
+  double **ds;          // change in rotation matrix between two iterations, da
+  double **dy;          // change in gradients between two iterations, dg
+  double **sp_copy;     // copy of the spins
+  int num_mem;          // number of stored steps
   bigint last_negative;
 };
 
diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp
index 559fd1cb49..075850d1af 100644
--- a/src/SPIN/neb_spin.cpp
+++ b/src/SPIN/neb_spin.cpp
@@ -179,7 +179,7 @@ void NEBSpin::run()
 
   update->whichflag = 2;
   update->etol = etol;
-  update->ftol = ttol;		// update->ftol is a torque tolerance
+  update->ftol = ttol;          // update->ftol is a torque tolerance
   update->multireplica = 1;
 
   lmp->init();
@@ -214,7 +214,7 @@ void NEBSpin::run()
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT "
                 "RD1 PE1 RD2 PE2 ... RDN PEN "
-		"GradV0dottan DN0 ... GradVNdottan DNN\n");
+                "GradV0dottan DN0 ... GradVNdottan DNN\n");
       } else {
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
@@ -224,10 +224,10 @@ void NEBSpin::run()
 
     if (ulogfile) {
       if (verbose) {
-	fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
-	    "GradV0 GradV1 GradVc EBF EBR RDT "
-	    "RD1 PE1 RD2 PE2 ... RDN PEN "
-	    "GradV0dottan DN0 ... GradVNdottan DNN\n");
+        fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
+            "GradV0 GradV1 GradVc EBF EBR RDT "
+            "RD1 PE1 RD2 PE2 ... RDN PEN "
+            "GradV0dottan DN0 ... GradVNdottan DNN\n");
       } else {
         fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
@@ -301,7 +301,7 @@ void NEBSpin::run()
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT "
                 "RD1 PE1 RD2 PE2 ... RDN PEN "
-		"GradV0dottan DN0... GradVNdottan DNN\n");
+                "GradV0dottan DN0... GradVNdottan DNN\n");
       } else {
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc "
@@ -311,10 +311,10 @@ void NEBSpin::run()
     }
     if (ulogfile) {
       if (verbose) {
-	fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
-	    "GradV0 GradV1 GradVc EBF EBR RDT "
-	    "RD1 PE1 RD2 PE2 ... RDN PEN "
-	    "GradV0dottan DN0 ... GradVNdottan DNN\n");
+        fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
+            "GradV0 GradV1 GradVc EBF EBR RDT "
+            "RD1 PE1 RD2 PE2 ... RDN PEN "
+            "GradV0dottan DN0 ... GradVNdottan DNN\n");
       } else {
         fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc "
@@ -472,8 +472,8 @@ void NEBSpin::readfile(char *file, int flag)
       m = atom->map(tag);
       if (m >= 0 && m < nlocal) {
         ncount++;
-	musp = atof(values[1]);
-	xx = atof(values[2]);
+        musp = atof(values[1]);
+        xx = atof(values[2]);
         yy = atof(values[3]);
         zz = atof(values[4]);
         spx = atof(values[5]);
@@ -482,39 +482,39 @@ void NEBSpin::readfile(char *file, int flag)
 
         if (flag == 0) {
 
-	  spinit[0] = sp[m][0];
-	  spinit[1] = sp[m][1];
-	  spinit[2] = sp[m][2];
-	  spfinal[0] = spx;
-	  spfinal[1] = spy;
-	  spfinal[2] = spz;
+          spinit[0] = sp[m][0];
+          spinit[1] = sp[m][1];
+          spinit[2] = sp[m][2];
+          spfinal[0] = spx;
+          spfinal[1] = spy;
+          spfinal[2] = spz;
 
-	  // interpolate intermediate spin states
+          // interpolate intermediate spin states
 
-	  sp[m][3] = musp;
-	  if (fraction == 0.0) {
-	    sp[m][0] = spinit[0];
-	    sp[m][1] = spinit[1];
-	    sp[m][2] = spinit[2];
-	  } else if (fraction == 1.0) {
-	    sp[m][0] = spfinal[0];
-	    sp[m][1] = spfinal[1];
-	    sp[m][2] = spfinal[2];
-	  } else {
+          sp[m][3] = musp;
+          if (fraction == 0.0) {
+            sp[m][0] = spinit[0];
+            sp[m][1] = spinit[1];
+            sp[m][2] = spinit[2];
+          } else if (fraction == 1.0) {
+            sp[m][0] = spfinal[0];
+            sp[m][1] = spfinal[1];
+            sp[m][2] = spfinal[2];
+          } else {
             temp_flag = initial_rotation(spinit,spfinal,fraction);
             rot_flag = MAX(temp_flag,rot_flag);
-	    sp[m][0] = spfinal[0];
-	    sp[m][1] = spfinal[1];
-	    sp[m][2] = spfinal[2];
-	  }
+            sp[m][0] = spfinal[0];
+            sp[m][1] = spfinal[1];
+            sp[m][2] = spfinal[2];
+          }
         } else {
           sp[m][3] = musp;
-	  x[m][0] = xx;
+          x[m][0] = xx;
           x[m][1] = yy;
           x[m][2] = zz;
-	  sp[m][0] = spx;
-	  sp[m][1] = spy;
-	  sp[m][2] = spz;
+          sp[m][0] = spx;
+          sp[m][1] = spy;
+          sp[m][2] = spz;
         }
       }
 
@@ -602,24 +602,24 @@ int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction)
   // Rodrigues' formula breaks, needs to define another axis k
 
   if (knormsq == 0.0) {
-    if (sidotsf > 0.0) { 	// spins aligned and in same direction
+    if (sidotsf > 0.0) {        // spins aligned and in same direction
       return 0;
-    } else if (sidotsf < 0.0) {	// spins aligned and in opposite directions
+    } else if (sidotsf < 0.0) { // spins aligned and in opposite directions
 
       // defining a rotation axis
       // first guess, k = spi x [100]
       // second guess, k = spi x [010]
 
       if (spiy*spiy + spiz*spiz != 0.0) { // spin not along [100]
-	kx = 0.0;
-	ky = spiz;
-	kz = -spiy;
-	knormsq = ky*ky + kz*kz;
+        kx = 0.0;
+        ky = spiz;
+        kz = -spiy;
+        knormsq = ky*ky + kz*kz;
       } else if (spix*spix + spiz*spiz != 0.0) { // spin not along [010]
-	kx = -spiz;
-	ky = 0.0;
-	kz = spix;
-	knormsq = kx*kx + kz*kz;
+        kx = -spiz;
+        ky = 0.0;
+        kz = spix;
+        knormsq = kx*kx + kz*kz;
       } else error->all(FLERR,"Incorrect initial rotation operation");
       rot_flag = 1;
     }
@@ -822,9 +822,9 @@ void NEBSpin::print_status()
       for (int i = 0; i < nreplica; i++)
         fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
       if (verbose) {
-	for (int i = 0; i < nreplica-1; i++)
-	  fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]);
-	fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
+        for (int i = 0; i < nreplica-1; i++)
+          fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]);
+        fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
       }
       fprintf(uscreen,"\n");
     }
@@ -838,9 +838,9 @@ void NEBSpin::print_status()
       for (int i = 0; i < nreplica; i++)
         fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
       if (verbose) {
-	for (int i = 0; i < nreplica-1; i++)
-	  fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]);
-	fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
+        for (int i = 0; i < nreplica-1; i++)
+          fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]);
+        fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
       }
       fprintf(ulogfile,"\n");
       fflush(ulogfile);
diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h
index 0111814c72..34f12d8d59 100644
--- a/src/SPIN/pair_spin.h
+++ b/src/SPIN/pair_spin.h
@@ -33,8 +33,8 @@ friend class FixNVESpin;
   virtual void compute_single_pair(int, double *) {}
 
  protected:
-  double hbar;				// Planck constant (eV.ps.rad-1)
-  int lattice_flag;			// flag for mech force computation
+  double hbar;                          // Planck constant (eV.ps.rad-1)
+  int lattice_flag;                     // flag for mech force computation
 
   virtual void allocate() {}
 };
diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp
index 4ff90323f2..bae09689de 100644
--- a/src/SPIN/pair_spin_dipole_cut.cpp
+++ b/src/SPIN/pair_spin_dipole_cut.cpp
@@ -46,11 +46,11 @@ PairSpinDipoleCut::PairSpinDipoleCut(LAMMPS *lmp) : PairSpin(lmp)
 {
   spinflag = 1;
 
-  hbar = force->hplanck/MY_2PI;			      // eV/(rad.THz)
+  hbar = force->hplanck/MY_2PI;                       // eV/(rad.THz)
   mub = 9.274e-4;                             // in A.Ang^2
   mu_0 = 785.15;                              // in eV/Ang/A^2
   mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);   // in eV.Ang^3
-  //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);	// in eV
+  //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);   // in eV
   mub2mu0hbinv = mub2mu0 / hbar;              // in rad.THz
 }
 
@@ -178,7 +178,7 @@ void PairSpinDipoleCut::compute(int eflag, int vflag)
   double **x = atom->x;
   double **f = atom->f;
   double **fm = atom->fm;
-  double **sp = atom->sp;	
+  double **sp = atom->sp;       
 
   inum = list->inum;
   ilist = list->ilist;
@@ -228,36 +228,36 @@ void PairSpinDipoleCut::compute(int eflag, int vflag)
 
       if (rsq < local_cut2) {
         r2inv = 1.0/rsq;
-	r3inv = r2inv*rinv;
-	
-	compute_dipolar(i,j,eij,fmi,spi,spj,r3inv);
-	if (lattice_flag) compute_dipolar_mech(i,j,eij,fi,spi,spj,r2inv);
+        r3inv = r2inv*rinv;
+        
+        compute_dipolar(i,j,eij,fmi,spi,spj,r3inv);
+        if (lattice_flag) compute_dipolar_mech(i,j,eij,fi,spi,spj,r2inv);
       }
 
       // force accumulation
 
       f[i][0] += fi[0]; 
-      f[i][1] += fi[1];  	  
+      f[i][1] += fi[1];           
       f[i][2] += fi[2];
       fm[i][0] += fmi[0];
       fm[i][1] += fmi[1];
       fm[i][2] += fmi[2];
 
       if (newton_pair || j < nlocal) {
-	f[j][0] -= fi[0];	 
-        f[j][1] -= fi[1];	  	  
+        f[j][0] -= fi[0];        
+        f[j][1] -= fi[1];                 
         f[j][2] -= fi[2];
       }
 
       if (eflag) {
-	if (rsq <= local_cut2) {
-	  evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-	  evdwl *= hbar;
-	}
+        if (rsq <= local_cut2) {
+          evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
+          evdwl *= hbar;
+        }
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
-	  evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+          evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
 
     }
   }
@@ -277,7 +277,7 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3])
   int k,locflag;
   int *type = atom->type;  
   double **x = atom->x;
-  double **sp = atom->sp;	
+  double **sp = atom->sp;       
 
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
@@ -427,7 +427,7 @@ void PairSpinDipoleCut::write_restart(FILE *fp)
     for (j = i; j <= atom->ntypes; j++) {
       fwrite(&setflag[i][j],sizeof(int),1,fp);
       if (setflag[i][j]) {
-	fwrite(&cut_spin_long[i][j],sizeof(int),1,fp);
+        fwrite(&cut_spin_long[i][j],sizeof(int),1,fp);
       }
     }
   }
@@ -450,10 +450,10 @@ void PairSpinDipoleCut::read_restart(FILE *fp)
       if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
-	if (me == 0) {
-	  utils::sfread(FLERR,&cut_spin_long[i][j],sizeof(int),1,fp,NULL,error);
-	}
-	MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world);
+        if (me == 0) {
+          utils::sfread(FLERR,&cut_spin_long[i][j],sizeof(int),1,fp,NULL,error);
+        }
+        MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world);
       }
     }
   }
diff --git a/src/SPIN/pair_spin_dipole_cut.h b/src/SPIN/pair_spin_dipole_cut.h
index f9159a629f..33f62d1633 100644
--- a/src/SPIN/pair_spin_dipole_cut.h
+++ b/src/SPIN/pair_spin_dipole_cut.h
@@ -49,16 +49,16 @@ class PairSpinDipoleCut : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
   
-  double cut_spin_long_global;	// global long cutoff distance 
+  double cut_spin_long_global;  // global long cutoff distance 
 
  protected:
-  double hbar;			// reduced Planck's constant
-  double mub;			// Bohr's magneton
-  double mu_0;			// vacuum permeability
-  double mub2mu0;		// prefactor for mech force
-  double mub2mu0hbinv;		// prefactor for mag force
+  double hbar;                  // reduced Planck's constant
+  double mub;                   // Bohr's magneton
+  double mu_0;                  // vacuum permeability
+  double mub2mu0;               // prefactor for mech force
+  double mub2mu0hbinv;          // prefactor for mag force
 
-  double **cut_spin_long;	// cutoff distance long
+  double **cut_spin_long;       // cutoff distance long
 
   double g_ewald;
   int ewald_order;
diff --git a/src/SPIN/pair_spin_dipole_long.h b/src/SPIN/pair_spin_dipole_long.h
index 1997cbbc55..56fd4c7126 100644
--- a/src/SPIN/pair_spin_dipole_long.h
+++ b/src/SPIN/pair_spin_dipole_long.h
@@ -50,16 +50,16 @@ class PairSpinDipoleLong : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
   
-  double cut_spin_long_global;	// global long cutoff distance 
+  double cut_spin_long_global;  // global long cutoff distance 
 
  protected:
-  double hbar;	 		// reduced Planck's constant
-  double mub;			// Bohr's magneton
-  double mu_0;			// vacuum permeability
-  double mub2mu0;		// prefactor for mech force
-  double mub2mu0hbinv;		// prefactor for mag force
+  double hbar;                  // reduced Planck's constant
+  double mub;                   // Bohr's magneton
+  double mu_0;                  // vacuum permeability
+  double mub2mu0;               // prefactor for mech force
+  double mub2mu0hbinv;          // prefactor for mag force
 
-  double **cut_spin_long;	// cutoff distance long
+  double **cut_spin_long;       // cutoff distance long
 
   double g_ewald;
   int ewald_order;
diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h
index ac2aa387b3..01022623ec 100644
--- a/src/SPIN/pair_spin_dmi.h
+++ b/src/SPIN/pair_spin_dmi.h
@@ -44,13 +44,13 @@ class PairSpinDmi : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
-  double cut_spin_dmi_global;			// short range pair cutoff
+  double cut_spin_dmi_global;                   // short range pair cutoff
 
  protected:
-  double **DM;                     		// dmi coeff in eV
-  double **v_dmx, **v_dmy, **v_dmz;		// dmi direction
-  double **vmech_dmx, **vmech_dmy, **vmech_dmz;	// dmi mech direction
-  double **cut_spin_dmi;      			// cutoff distance dmi
+  double **DM;                                  // dmi coeff in eV
+  double **v_dmx, **v_dmy, **v_dmz;             // dmi direction
+  double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction
+  double **cut_spin_dmi;                        // cutoff distance dmi
 
   void allocate();
 };
diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h
index 5feb99210f..19eafeb5ca 100644
--- a/src/SPIN/pair_spin_exchange.h
+++ b/src/SPIN/pair_spin_exchange.h
@@ -44,13 +44,13 @@ class PairSpinExchange : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
-  double cut_spin_exchange_global;	// global exchange cutoff distance
+  double cut_spin_exchange_global;      // global exchange cutoff distance
 
  protected:
-  double **J1_mag;			// exchange coeffs in eV
-  double **J1_mech;			// mech exchange coeffs in
+  double **J1_mag;                      // exchange coeffs in eV
+  double **J1_mech;                     // mech exchange coeffs in
   double **J2, **J3;                    // J1 in eV, J2 adim, J3 in Ang
-  double **cut_spin_exchange;		// cutoff distance exchange
+  double **cut_spin_exchange;           // cutoff distance exchange
 
   void allocate();
 };
diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h
index b9e820b1d1..4df0078bea 100644
--- a/src/SPIN/pair_spin_magelec.h
+++ b/src/SPIN/pair_spin_magelec.h
@@ -44,12 +44,12 @@ class PairSpinMagelec : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
-  double cut_spin_magelec_global;	// global me cutoff
+  double cut_spin_magelec_global;       // global me cutoff
 
  protected:
-  double **ME, **ME_mech;		// magelec coeff in eV
-  double **v_mex, **v_mey, **v_mez;	// magelec direction
-  double **cut_spin_magelec;		// magelec cutoff distance
+  double **ME, **ME_mech;               // magelec coeff in eV
+  double **v_mex, **v_mey, **v_mez;     // magelec direction
+  double **cut_spin_magelec;            // magelec cutoff distance
 
   void allocate();
 };
diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h
index 796d8b53f0..5261a7f746 100644
--- a/src/SPIN/pair_spin_neel.h
+++ b/src/SPIN/pair_spin_neel.h
@@ -44,17 +44,17 @@ class PairSpinNeel : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
-  double cut_spin_neel_global;		// global neel cutoff distance
+  double cut_spin_neel_global;          // global neel cutoff distance
 
  protected:
 
   // pseudo-dipolar and pseudo-quadrupolar coeff.
 
-  double **g1, **g1_mech; 		// neel coeffs gij
-  double **g2, **g3; 			// g1 in eV, g2 adim, g3 in Ang
-  double **q1, **q1_mech; 		// neel coeffs qij
-  double **q2, **q3; 			// q1 in eV, q2 adim, q3 in Ang
-  double **cut_spin_neel;		// cutoff distance exchange
+  double **g1, **g1_mech;               // neel coeffs gij
+  double **g2, **g3;                    // g1 in eV, g2 adim, g3 in Ang
+  double **q1, **q1_mech;               // neel coeffs qij
+  double **q2, **q3;                    // q1 in eV, q2 adim, q3 in Ang
+  double **cut_spin_neel;               // cutoff distance exchange
 
   void allocate();
 };

From 816546d008cb2ccf83fb39e27dea4eb811e3b4e2 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Mon, 4 Nov 2019 17:38:32 -0700
Subject: [PATCH 018/199] Commit3 JT 110419 - comments in precession

---
 src/SPIN/compute_spin.cpp        |  2 +-
 src/SPIN/fix_langevin_spin.h     | 16 ++++++++--------
 src/SPIN/fix_precession_spin.cpp |  2 --
 src/SPIN/pair_spin_exchange.cpp  |  2 ++
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index 1f808eb1bd..9cd7f5473e 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -104,7 +104,7 @@ void ComputeSpin::compute_vector()
         mag[0] += sp[i][0];
         mag[1] += sp[i][1];
         mag[2] += sp[i][2];
-        magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
+        magenergy -= 2.0*(sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
         tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1];
         ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2];
         tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0];
diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h
index 5358438396..b581b70d34 100644
--- a/src/SPIN/fix_langevin_spin.h
+++ b/src/SPIN/fix_langevin_spin.h
@@ -32,17 +32,17 @@ class FixLangevinSpin : public Fix {
   void init();
   void setup(int);
   void post_force_respa(int, int, int);
-  void add_tdamping(double spi[3], double fmi[3]);	// add transverse damping
-  void add_temperature(double fmi[3]);			// add temperature
-  int tdamp_flag, ldamp_flag, temp_flag;		// damping and temperature flags
+  void add_tdamping(double spi[3], double fmi[3]);      // add transverse damping
+  void add_temperature(double fmi[3]);                  // add temperature
+  int tdamp_flag, ldamp_flag, temp_flag;                // damping and temperature flags
 
  protected:
   double *spi, *fmi;
-  double alpha_t;		// transverse mag. damping
-  double dts;        		// magnetic timestep
-  double temp;       		// spin bath temperature
-  double D,sigma;    		// bath intensity var.
-  double gil_factor; 		// gilbert's prefactor
+  double alpha_t;               // transverse mag. damping
+  double dts;                   // magnetic timestep
+  double temp;                  // spin bath temperature
+  double D,sigma;               // bath intensity var.
+  double gil_factor;            // gilbert's prefactor
 
   char *id_temp;
   class Compute *temperature;
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index 4294e5361a..3749b68d28 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -240,7 +240,6 @@ void FixPrecessionSpin::post_force(int /* vflag */)
   }
 
   int *mask = atom->mask;
-  double *emag = atom->emag;
   double **fm = atom->fm;
   double **sp = atom->sp;
   const int nlocal = atom->nlocal;
@@ -272,7 +271,6 @@ void FixPrecessionSpin::post_force(int /* vflag */)
       }
 
       eprec += epreci;
-      emag[i] += epreci;
       fm[i][0] += fmi[0];
       fm[i][1] += fmi[1];
       fm[i][2] += fmi[2];
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index ce5cf325c6..8150a7ab19 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -351,6 +351,8 @@ void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3],
   Jex *= (1.0-J2[itype][jtype]*ra);
   Jex *= exp(-ra);
 
+  printf("Exchange : %g %g \n",Jex,Jex*hbar);
+
   fmi[0] += 2.0*Jex*spj[0];
   fmi[1] += 2.0*Jex*spj[1];
   fmi[2] += 2.0*Jex*spj[2];

From f80c527b1791cb163eba508a3a22db26dadd365e Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Wed, 6 Nov 2019 14:15:25 -0700
Subject: [PATCH 019/199] Commit JT 100619 - modified precession and
 Langevin/spin

---
 src/SPIN/compute_spin.cpp        |  3 ++-
 src/SPIN/fix_langevin_spin.cpp   | 26 ++++++++++++++------------
 src/SPIN/fix_langevin_spin.h     | 10 +++++-----
 src/SPIN/fix_precession_spin.cpp | 12 ++++++++----
 4 files changed, 29 insertions(+), 22 deletions(-)

diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index 9cd7f5473e..6f1e72ef7e 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -104,7 +104,8 @@ void ComputeSpin::compute_vector()
         mag[0] += sp[i][0];
         mag[1] += sp[i][1];
         mag[2] += sp[i][2];
-        magenergy -= 2.0*(sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
+        // magenergy -= 2.0*(sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
+        magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
         tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1];
         ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2];
         tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0];
diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp
index ec9c98c4f8..e7bbacca6b 100644
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@@ -30,7 +30,8 @@
 #include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "random_park.h"
+// #include "random_park.h"
+#include "random_mars.h"
 #include "respa.h"
 #include "update.h"
 #include "utils.h"
@@ -74,7 +75,8 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
 
   // initialize Marsaglia RNG with processor-unique seed
 
-  random = new RanPark(lmp,seed + comm->me);
+  // random = new RanPark(lmp,seed + comm->me);
+  random = new RanMars(lmp,seed + comm->me);
 
 }
 
@@ -82,8 +84,6 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
 
 FixLangevinSpin::~FixLangevinSpin()
 {
-  memory->destroy(spi);
-  memory->destroy(fmi);
   delete random;
 }
 
@@ -113,15 +113,14 @@ void FixLangevinSpin::init()
   }
   if (flag_force >= flag_lang) error->all(FLERR,"Fix langevin/spin has to come after all other spin fixes");
 
-  memory->create(spi,3,"langevin:spi");
-  memory->create(fmi,3,"langevin:fmi");
-
   gil_factor = 1.0/(1.0+(alpha_t)*(alpha_t));
-  dts = update->dt;
+  dts = 0.25 * update->dt;
 
   double hbar = force->hplanck/MY_2PI;  // eV/(rad.THz)
   double kb = force->boltz;             // eV/K
-  D = (MY_2PI*alpha_t*gil_factor*kb*temp);
+  // D = (MY_2PI*alpha_t*gil_factor*kb*temp);
+  D = (1.0/MY_2PI)*(MY_2PI*alpha_t*gil_factor*kb*temp);
+  // D = (12.0/MY_2PI)*(MY_2PI*alpha_t*gil_factor*kb*temp);
   D /= (hbar*dts);
   sigma = sqrt(2.0*D);
 }
@@ -157,9 +156,12 @@ void FixLangevinSpin::add_tdamping(double spi[3], double fmi[3])
 void FixLangevinSpin::add_temperature(double fmi[3])
 {
 
-  double rx = sigma*(2.0*random->uniform() - 1.0);
-  double ry = sigma*(2.0*random->uniform() - 1.0);
-  double rz = sigma*(2.0*random->uniform() - 1.0);
+  // double rx = sigma*(2.0*random->uniform() - 1.0);
+  // double ry = sigma*(2.0*random->uniform() - 1.0);
+  // double rz = sigma*(2.0*random->uniform() - 1.0);
+  double rx = sigma*random->gaussian();
+  double ry = sigma*random->gaussian();
+  double rz = sigma*random->gaussian();
 
   // adding the random field
 
diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h
index b581b70d34..aabee7b37b 100644
--- a/src/SPIN/fix_langevin_spin.h
+++ b/src/SPIN/fix_langevin_spin.h
@@ -32,12 +32,11 @@ class FixLangevinSpin : public Fix {
   void init();
   void setup(int);
   void post_force_respa(int, int, int);
-  void add_tdamping(double spi[3], double fmi[3]);      // add transverse damping
-  void add_temperature(double fmi[3]);                  // add temperature
-  int tdamp_flag, ldamp_flag, temp_flag;                // damping and temperature flags
+  void add_tdamping(double *, double *);                 // add transverse damping
+  void add_temperature(double *);                        // add temperature
+  int tdamp_flag, ldamp_flag, temp_flag;                 // damping and temperature flags
 
  protected:
-  double *spi, *fmi;
   double alpha_t;               // transverse mag. damping
   double dts;                   // magnetic timestep
   double temp;                  // spin bath temperature
@@ -48,7 +47,8 @@ class FixLangevinSpin : public Fix {
   class Compute *temperature;
 
   int nlevels_respa;
-  class RanPark *random;
+  // class RanPark *random;
+  class RanMars *random;
   int seed;
 
 };
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index 3749b68d28..263118f5fb 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -257,7 +257,8 @@ void FixPrecessionSpin::post_force(int /* vflag */)
 
       if (zeeman_flag) {          // compute Zeeman interaction
         compute_zeeman(i,fmi);
-        epreci -= 2.0*hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
+        // epreci -= 2.0*hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
+        epreci -= hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
       }
 
       if (aniso_flag) {           // compute magnetic anisotropy
@@ -295,9 +296,12 @@ void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double f
 void FixPrecessionSpin::compute_zeeman(int i, double fmi[3])
 {
   double **sp = atom->sp;
-  fmi[0] += 0.5*sp[i][3]*hx;
-  fmi[1] += 0.5*sp[i][3]*hy;
-  fmi[2] += 0.5*sp[i][3]*hz;
+  // fmi[0] += 0.5*sp[i][3]*hx;
+  // fmi[1] += 0.5*sp[i][3]*hy;
+  // fmi[2] += 0.5*sp[i][3]*hz;
+  fmi[0] += sp[i][3]*hx;
+  fmi[1] += sp[i][3]*hy;
+  fmi[2] += sp[i][3]*hz;
 }
 
 /* ---------------------------------------------------------------------- */

From 64bdc59623640c8cc5f84cd1a3dfe29784d29919 Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Sun, 10 Nov 2019 02:38:58 +0300
Subject: [PATCH 020/199] Implement GPU pair style  lj/cut/tip4p/long/gpu

Source code, Makefiles and Install for GPU-accelerated TIP4P pair style.
It is implemented as a part of the standard GPU package.
The style is compatible with the standard  lj/cut/tip4p/long.
Also, this commit modifies "atom.h" just to
add a getter for variable 'max_same'.
---
 lib/gpu/Nvidia.makefile                |  18 +-
 lib/gpu/Opencl.makefile                |  15 +-
 lib/gpu/lal_lj_tip4p_long.cpp          | 241 ++++++++++++
 lib/gpu/lal_lj_tip4p_long.cu           | 518 +++++++++++++++++++++++++
 lib/gpu/lal_lj_tip4p_long.h            |  95 +++++
 lib/gpu/lal_lj_tip4p_long_ext.cpp      | 135 +++++++
 src/GPU/Install.sh                     |   2 +
 src/GPU/pair_lj_cut_tip4p_long_gpu.cpp | 234 +++++++++++
 src/GPU/pair_lj_cut_tip4p_long_gpu.h   |  32 ++
 src/atom.h                             |   1 +
 10 files changed, 1287 insertions(+), 4 deletions(-)
 create mode 100644 lib/gpu/lal_lj_tip4p_long.cpp
 create mode 100644 lib/gpu/lal_lj_tip4p_long.cu
 create mode 100644 lib/gpu/lal_lj_tip4p_long.h
 create mode 100644 lib/gpu/lal_lj_tip4p_long_ext.cpp
 create mode 100644 src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
 create mode 100644 src/GPU/pair_lj_cut_tip4p_long_gpu.h

diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile
index 233f43380f..65dcae7bdb 100644
--- a/lib/gpu/Nvidia.makefile
+++ b/lib/gpu/Nvidia.makefile
@@ -82,7 +82,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
        $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
        $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
        $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
-       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o
+       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
+       $(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
 
 CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
        $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \
@@ -143,7 +144,8 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
        $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \
        $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \
        $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \
-       $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h
+       $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h \
+       $(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long_cubin.h
 
 all: $(OBJ_DIR) $(GPU_LIB) $(EXECS)
 
@@ -297,6 +299,18 @@ $(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp $(OBJ_DIR)/lj_cubin.h $(OBJ_DI
 $(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
 	$(CUDR) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
 
+$(OBJ_DIR)/lj_tip4p_long.cubin: lal_lj_tip4p_long.cu lal_precision.h lal_preprocessor.h
+	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_tip4p_long.cu
+
+$(OBJ_DIR)/lj_tip4p_long_cubin.h: $(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long.cubin
+	$(BIN2C)  -c -n lj_tip4p_long $(OBJ_DIR)/lj_tip4p_long.cubin > $(OBJ_DIR)/lj_tip4p_long_cubin.h
+
+$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp  $(OBJ_DIR)/lj_tip4p_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o
+	$(CUDR) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
+	$(CUDR) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
+
 $(OBJ_DIR)/lj_coul.cubin: lal_lj_coul.cu lal_precision.h lal_preprocessor.h
 	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_coul.cu
 
diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile
index 86991a1e98..1b1932858b 100644
--- a/lib/gpu/Opencl.makefile
+++ b/lib/gpu/Opencl.makefile
@@ -71,7 +71,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \
        $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
        $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
        $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
-       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o
+       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
+       $(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
 
 KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
        $(OBJ_DIR)/neighbor_cpu_cl.h $(OBJ_DIR)/pppm_cl.h \
@@ -102,7 +103,8 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
        $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h \
        $(OBJ_DIR)/ufm_cl.h  $(OBJ_DIR)/dipole_long_lj_cl.h \
        $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/coul_long_cs_cl.h \
-       $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h
+       $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h \
+       $(OBJ_DIR)/lj_tip4p_long_cl.h
 
 
 OCL_EXECS = $(BIN_DIR)/ocl_get_devices
@@ -202,6 +204,15 @@ $(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp  $(OBJ_DIR)/lj_cl.h $(OBJ_DIR)
 $(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
 	$(OCL) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
 
+$(OBJ_DIR)/lj_tip4p_long_cl.h: lal_lj_tip4p_long.cu $(PRE1_H)
+	$(BSH) ./geryon/file_to_cstr.sh lj_tip4p_long $(PRE1_H) lal_lj_tip4p_long.cu $(OBJ_DIR)/lj_tip4p_long_cl.h;
+
+$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp  $(OBJ_DIR)/lj_tip4p_long_cl.h $(OBJ_DIR)/lj_tip4p_long_cl.h $(OBJ_DIR)/lal_base_atomic.o
+	$(OCL) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
+	$(OCL) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
+
 $(OBJ_DIR)/lj_coul_cl.h: lal_lj_coul.cu $(PRE1_H)
 	$(BSH) ./geryon/file_to_cstr.sh lj_coul $(PRE1_H) lal_lj_coul.cu $(OBJ_DIR)/lj_coul_cl.h;
 
diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
new file mode 100644
index 0000000000..9714e9bf91
--- /dev/null
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -0,0 +1,241 @@
+#if defined(USE_OPENCL)
+#include "lj_tip4p_long_cl.h"
+#elif defined(USE_CUDART)
+const char *lj_tip4p=0;
+#else
+#include "lj_tip4p_long_cubin.h"
+#endif
+
+#include "lal_lj_tip4p_long.h"
+#include <cassert>
+using namespace LAMMPS_AL;
+#define LJ_TIP4PLong_T LJ_TIP4PLong<numtyp, acctyp>
+
+extern Device<PRECISION,ACC_PRECISION> device;
+
+template <class numtyp, class acctyp>
+LJ_TIP4PLong<numtyp, acctyp>::LJ_TIP4PLong(): BaseCharge<numtyp,acctyp>(), _allocated(false) {
+}
+
+template <class numtyp, class acctyp>
+LJ_TIP4PLong<numtyp, acctyp>::~LJ_TIP4PLong() {
+  clear();
+}
+
+template <class numtyp, class acctyp>
+int LJ_TIP4PLong<numtyp, acctyp>::bytes_per_atom(const int max_nbors) const {
+  return this->bytes_per_atom_atomic(max_nbors);
+}
+
+template <class numtyp, class acctyp>
+int LJ_TIP4PLong<numtyp, acctyp>::init(const int ntypes,
+                          double **host_cutsq, double **host_lj1,
+                          double **host_lj2, double **host_lj3,
+                          double **host_lj4, double **host_offset,
+                          double *host_special_lj, const int nlocal,
+						  const int tH, const int tO,
+						  const double a, const double qd,
+                          const int nall, const int max_nbors,
+                          const int maxspecial, const double cell_size,
+                          const double gpu_split, FILE *_screen,
+						  double **host_cut_ljsq,
+						  const double host_cut_coulsq, const double host_cut_coulsqplus,
+						  double *host_special_coul, const double qqrd2e,
+						  const double g_ewald, int* tag,
+							 int *map_array, int map_size,
+							 int *sametag, int max_same) {
+  int success;
+  success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
+                            _screen,lj_tip4p_long,"k_lj_tip4p_long");
+  if (success!=0)
+    return success;
+  k_pair_distrib.set_function(*this->pair_program,"k_lj_tip4p_long_distrib");
+
+  TypeH = tH;
+  TypeO = tO;
+  alpha = a;
+  qdist = qd;
+
+  // If atom type constants fit in shared memory use fast kernel
+  int lj_types=ntypes;
+  shared_types=false;
+//  int max_shared_types=this->device->max_shared_types();
+//  if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
+//    lj_types=max_shared_types;
+//    shared_types=true;
+//  }
+  _lj_types=lj_types;
+
+  // Allocate a host write buffer for data initialization
+  UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
+                               UCL_WRITE_ONLY);
+
+  for (int i=0; i<lj_types*lj_types; i++)
+    host_write[i]=0.0;
+
+  lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+  this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2,
+                         host_cut_ljsq);
+
+  lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+  this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4,
+                         host_offset);
+
+  cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+  this->atom->type_pack1(ntypes,lj_types,cutsq,host_write,host_cutsq);
+
+  sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY);
+  for (int i=0; i<4; i++) {
+    host_write[i]=host_special_lj[i];
+    host_write[i+4]=host_special_coul[i];
+  }
+  ucl_copy(sp_lj,host_write,8,false);
+
+  force_comp.alloc(72*72, *(this->ucl_device), UCL_READ_WRITE);
+
+  _qqrd2e=qqrd2e;
+  _g_ewald=g_ewald;
+  cut_coulsq = host_cut_coulsq;
+  cut_coulsqplus = host_cut_coulsqplus;
+
+  hneight.alloc(nall*4,*(this->ucl_device), UCL_READ_WRITE);
+  m.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
+  ansO.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
+
+  // Allocate a host write buffer for data initialization
+  UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
+  this->tag.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
+  for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
+  ucl_copy(this->tag, host_tag_write, nall, false);
+
+  //if(max_same>host_tag_write.cols()) host_tag_write.resize(max_same);
+  this->atom_sametag.alloc(nall, *(this->ucl_device), UCL_READ_WRITE);
+  for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
+  ucl_copy(this->atom_sametag, host_tag_write, nall, false);
+
+  if(map_size>host_tag_write.cols()) host_tag_write.resize(map_size);
+  this->map_array.alloc(map_size,*(this->ucl_device), UCL_READ_WRITE);
+  for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
+  ucl_copy(this->map_array, host_tag_write, map_size, false);
+
+  _allocated=true;
+  this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+cutsq.row_bytes()+
+                   sp_lj.row_bytes() + hneight.row_bytes()+m.row_bytes()+
+				   this->tag.row_bytes()+this->atom_sametag.row_bytes() +
+				   this->map_array.row_bytes();
+  return 0;
+}
+
+
+template <class numtyp, class acctyp>
+void LJ_TIP4PLong<numtyp, acctyp>::clear() {
+  if (!_allocated)
+    return;
+  _allocated=false;
+
+  lj1.clear();
+  lj3.clear();
+  sp_lj.clear();
+  cutsq.clear();
+  hneight.clear();
+  m.clear();
+  tag.clear();
+  atom_sametag.clear();
+  map_array.clear();
+  ansO.clear();
+  force_comp.clear();
+
+  k_pair_distrib.clear();
+
+  this->clear_atomic();
+}
+
+template <class numtyp, class acctyp>
+double LJ_TIP4PLong<numtyp, acctyp>::host_memory_usage() const {
+  return this->host_memory_usage_atomic()+sizeof(LJ_TIP4PLong<numtyp,acctyp>);
+}
+
+// ---------------------------------------------------------------------------
+// Calculate energies, forces, and torques
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+void LJ_TIP4PLong<numtyp, acctyp>::loop(const bool _eflag, const bool _vflag) {
+  // Compute the block size and grid size to keep all cores busy
+  const int BX=this->block_size();
+  int eflag, vflag;
+  if (_eflag)
+    eflag=1;
+  else
+    eflag=0;
+
+  if (_vflag)
+    vflag=1;
+  else
+    vflag=0;
+
+  int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
+                               (BX/this->_threads_per_atom)));
+
+  int ainum=this->ans->inum();
+  int nbor_pitch=this->nbor->nbor_pitch();
+  this->time_pair.start();
+
+  this->k_pair.set_size(GX,BX);
+  if (vflag){
+	  this->ansO.resize(ainum*3);
+  } else {
+	  this->ansO.resize(ainum);
+  }
+  this->ansO.zero();
+  this->k_pair.run(&this->atom->x, &lj1, &lj3, &_lj_types, &sp_lj,
+          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+          &this->ans->force, &this->ans->engv, &eflag, &vflag,
+          &ainum, &nbor_pitch, &this->_threads_per_atom,
+			 &hneight, &m, &TypeO, &TypeH, &alpha,
+			 &this->atom->q, &cutsq, &_qqrd2e, &_g_ewald,
+			 &cut_coulsq, &cut_coulsqplus, &tag, &map_array,
+			 &atom_sametag, &this->ansO);
+  GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
+  this->k_pair_distrib.set_size(GX,BX);
+  this->k_pair_distrib.run(&this->atom->x, &this->ans->force, &this->ans->engv, &eflag, &vflag,
+                     &ainum, &nbor_pitch, &this->_threads_per_atom,
+					 &hneight, &m, &TypeO, &TypeH, &alpha,
+					 &this->atom->q,  &this->ansO);
+  this->time_pair.stop();
+}
+
+
+template <class numtyp, class acctyp>
+void LJ_TIP4PLong<numtyp, acctyp>::copy_relations_data(int **hn, double **newsite, int n,
+		int* tag, int *map_array, int map_size, int *sametag, int max_same, int ago){
+	int nall = n;
+	const int hn_sz = n*4; // matrix size = col size * col number
+	if(hn_sz > hneight.cols()){
+		hneight.resize(hn_sz+1);
+	}
+	if (ago == 0)
+		hneight.zero();
+	if(n > m.cols()){
+		m.resize(n+1);
+	}
+	m.zero();
+
+    UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
+    if(this->tag.cols() < nall) this->tag.resize(nall);
+    for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
+    ucl_copy(this->tag, host_tag_write, nall, false);
+
+    if(max_same>host_tag_write.cols()) host_tag_write.resize(max_same);
+    if(this->atom_sametag.cols() < nall) this->atom_sametag.resize(nall);
+    for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
+    ucl_copy(this->atom_sametag, host_tag_write, nall, false);
+
+    if(map_size>host_tag_write.cols()) host_tag_write.resize(map_size);
+    if(this->map_array.cols() < map_size) this->map_array.resize(map_size);
+    for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
+    ucl_copy(this->map_array, host_tag_write, map_size, false);
+
+    host_tag_write.clear();
+}
+
+template class LJ_TIP4PLong<PRECISION,ACC_PRECISION>;
diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
new file mode 100644
index 0000000000..7c6cec4473
--- /dev/null
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -0,0 +1,518 @@
+#ifdef NV_KERNEL
+
+#include "lal_aux_fun1.h"
+#ifndef _DOUBLE_DOUBLE
+texture<float4> pos_tex;
+texture<float> q_tex;
+#else
+texture<int4,1> pos_tex;
+texture<int2> q_tex;
+#endif
+
+#else
+#define pos_tex x_
+#define q_tex q_
+#endif
+
+ucl_inline int atom_mapping(const __global int *map, int glob){
+	return map[glob];
+}
+
+ucl_inline int closest_image(int i, int j, const __global int* sametag,
+		const __global numtyp4 *restrict x_)
+{
+  if (j < 0) return j;
+
+  numtyp4 xi; fetch4(xi,i,pos_tex); // = x[i];
+  numtyp4 xj; fetch4(xj,j,pos_tex);
+
+  int closest = j;
+  numtyp delx = xi.x - xj.x;
+  numtyp dely = xi.y - xj.y;
+  numtyp delz = xi.z - xj.z;
+  numtyp rsqmin = delx*delx + dely*dely + delz*delz;
+  numtyp rsq;
+
+  while (sametag[j] >= 0) {
+    j = sametag[j];
+    fetch4(xj,j,pos_tex);
+    delx = xi.x - xj.x;
+    dely = xi.y - xj.y;
+    delz = xi.z - xj.z;
+    rsq = delx*delx + dely*dely + delz*delz;
+    if (rsq < rsqmin) {
+      rsqmin = rsq;
+      closest = j;
+    }
+  }
+
+  return closest;
+}
+
+ucl_inline void compute_newsite(int iO, int  iH1, int  iH2,
+		__global numtyp4 *xM,
+		numtyp alpha, const __global numtyp4 *restrict x_){
+	numtyp4 xO;  fetch4(xO,iO,pos_tex);
+	numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+	numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+
+	numtyp delx1 = xH1.x - xO.x;
+	numtyp dely1 = xH1.y - xO.y;
+	numtyp delz1 = xH1.z - xO.z;
+
+	numtyp delx2 = xH2.x - xO.x;
+	numtyp dely2 = xH2.y - xO.y;
+	numtyp delz2 = xH2.z - xO.z;
+
+	numtyp ap = alpha * (numtyp)0.5;
+
+	(*xM).x = xO.x + ap * (delx1 + delx2);
+	(*xM).y = xO.y + ap * (dely1 + dely2);
+	(*xM).z = xO.z + ap * (delz1 + delz2);
+}
+
+__kernel void k_lj_tip4p_long_distrib(const __global numtyp4 *restrict x_,
+		__global acctyp4 *restrict ans,
+		__global acctyp *restrict engv,
+		const int eflag, const int vflag, const int inum,
+		const int nbor_pitch, const int t_per_atom,
+		__global int *restrict hneigh,
+		__global numtyp4 *restrict m,
+		const int typeO, const int typeH,
+		const numtyp alpha,
+		const __global numtyp *restrict q_, const __global acctyp4 *restrict ansO) {
+	int tid, ii, offset;
+	atom_info(t_per_atom,ii,tid,offset);
+	int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
+
+	acctyp4 f;
+	f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+
+	if (i<inum) {
+		numtyp4 ix; fetch4(ix,i,pos_tex);// = x_[i];
+		int itype = ix.w;
+		acctyp4 fM, vM;
+		acctyp eM;
+		if (itype == typeH) {
+			int iO = hneigh[i*4];
+			if (iO < inum) {
+				fM = ansO[iO];
+				f.x += fM.x * (acctyp)0.5 * alpha;
+				f.y += fM.y * (acctyp)0.5 * alpha;
+				f.z += fM.z * (acctyp)0.5 * alpha;
+				if (vflag > 0) {
+					vM = ansO[inum  +iO];
+					engv[inum*2 + i] += vM.x * (acctyp)0.5 * alpha;
+					engv[inum*3 + i] += vM.y * (acctyp)0.5 * alpha;
+					engv[inum*4 + i] += vM.z * (acctyp)0.5 * alpha;
+					vM = ansO[inum*2+iO];
+					engv[inum*5 + i] += vM.x * (acctyp)0.5 * alpha;
+					engv[inum*6 + i] += vM.y * (acctyp)0.5 * alpha;
+					engv[inum*7 + i] += vM.z * (acctyp)0.5 * alpha;
+				}
+			}
+		} else {
+			fM = ansO[i];
+			int iH1 = hneigh[i*4  ];
+			int iH2 = hneigh[i*4+1];
+			f.x += fM.x * (acctyp)(1 - alpha);
+			f.y += fM.y * (acctyp)(1 - alpha);
+			f.z += fM.z * (acctyp)(1 - alpha);
+			if (eflag > 0) {
+				eM = engv[i+inum];
+				engv[inum+i] = eM*(acctyp)(1 - alpha);
+				if (iH1 < inum) engv[inum+iH1] += eM * (acctyp)0.5 * alpha;
+				if (iH2 < inum) engv[inum+iH2] += eM * (acctyp)0.5 * alpha;
+			}
+			if (vflag > 0) {
+				vM = ansO[inum   + i];
+				engv[inum*2 + i] += vM.x * (acctyp)(1 - alpha);
+				engv[inum*3 + i] += vM.y * (acctyp)(1 - alpha);
+				engv[inum*4 + i] += vM.z * (acctyp)(1 - alpha);
+				vM = ansO[inum*2 + i];
+				engv[inum*5 + i] += vM.x * (acctyp)(1 - alpha);
+				engv[inum*6 + i] += vM.y * (acctyp)(1 - alpha);
+				engv[inum*7 + i] += vM.z * (acctyp)(1 - alpha);
+			}
+		}
+	    acctyp4 old=ans[i];
+	    old.x+=f.x;
+	    old.y+=f.y;
+	    old.z+=f.z;
+	    ans[i]=old;
+	} // if ii
+}
+
+__kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
+		const __global numtyp4 *restrict lj1,
+		const __global numtyp4 *restrict lj3,
+		const int lj_types,
+		const __global numtyp *restrict sp_lj,
+		const __global int * dev_nbor,
+		const __global int * dev_packed,
+		__global acctyp4 *restrict ans,
+		__global acctyp *restrict engv,
+		const int eflag, const int vflag, const int inum,
+		const int nbor_pitch, const int t_per_atom,
+		__global int *restrict hneigh,
+		__global numtyp4 *restrict m,
+		const int typeO, const int typeH,
+		const numtyp alpha,
+		const __global numtyp *restrict q_,
+		const __global numtyp *restrict cutsq,
+		const numtyp qqrd2e, const numtyp g_ewald,
+		const numtyp cut_coulsq, const numtyp cut_coulsqplus,
+		const __global int *restrict tag, const __global int *restrict map,
+		const __global int *restrict sametag, __global acctyp4 *restrict ansO) {
+	int tid, ii, offset;
+	atom_info(t_per_atom,ii,tid,offset);
+
+	acctyp energy = (acctyp)0;
+	acctyp e_coul = (acctyp)0;
+	acctyp4 f, fO;
+	f.x=(acctyp)0;  f.y=(acctyp)0;  f.z=(acctyp)0;
+	fO.x=(acctyp)0; fO.y=(acctyp)0; fO.z=(acctyp)0;
+	acctyp virial[6],vO[6];
+	for (int i=0; i<6; i++) {
+		virial[i]=(acctyp)0;
+		vO[i]=(acctyp)0;
+	}
+
+	if (ii<inum) {
+		int i, numj, nbor, nbor_end;
+		__local int n_stride;
+		nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
+				n_stride,nbor_end,nbor);
+
+		numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+		numtyp qtmp; fetch(qtmp,i,q_tex);
+		int itype = ix.w;
+		numtyp4 x1 = ix;
+
+		int non_local_oxy = 0;
+		int iH1, iH2, iO;
+
+		if(itype == typeO) {
+			iO  = i;
+			if (hneigh[i*4+2] != -1) {
+				iH1 = atom_mapping(map, tag[i] + 1);
+				iH2 = atom_mapping(map, tag[i] + 2);
+				// set iH1,iH2 to closest image to O
+				iH1 = closest_image(i, iH1, sametag, x_);
+				iH2 = closest_image(i, iH2, sametag, x_);
+				hneigh[  i*4  ] = iH1;
+				hneigh[  i*4+1] = iH2;
+				hneigh[  i*4+2] = -1;
+				hneigh[iH1*4  ] = i;
+				hneigh[iH1*4+1] += -1;
+				hneigh[iH1*4+2] = -1;
+				hneigh[iH2*4  ] = i;
+				hneigh[iH2*4+1] += -1;
+				hneigh[iH2*4+2] = -1;
+			} else {
+				iH1 = hneigh[i*4  ];
+				iH2 = hneigh[i*4+1];
+			}
+			if(m[iO].w == 0) {
+				compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
+				m[iO].w = qtmp;
+			}
+			x1 = m[iO];
+		} else {
+			if (hneigh[i*4+2] != -1) {
+				int iI, iH;
+				iI = atom_mapping(map,tag[i] - 1);
+				numtyp4 iIx; fetch4(iIx,iI,pos_tex); //x_[iI];
+				if (iIx.w == typeH) {
+					iO = atom_mapping(map,tag[i] - 2);
+					iO  = closest_image(i, iO, sametag, x_);
+					iH1 = closest_image(i, iI, sametag, x_);
+					iH2 = i;
+				} else if (iIx.w == typeO) {
+					iH = atom_mapping(map, tag[i] + 1);
+					iO  = closest_image(i,iI,sametag, x_);
+					iH1 = i;
+					iH2 = closest_image(i,iH,sametag, x_);
+				}
+
+				hneigh[iH1*4+0] = iO;
+				hneigh[iH1*4+1] += -1;
+				hneigh[iH1*4+2] = -1;
+
+				hneigh[iH2*4+0] = iO;
+				hneigh[iH2*4+1] += -1;
+				hneigh[iH2*4+2] = -1;
+
+				hneigh[iO*4+0] = iH1;
+				hneigh[iO*4+1] = iH2;
+				hneigh[iO*4+2] = -1;
+			} else {
+				iO  = hneigh[i *4  ];
+				iH1 = hneigh[iO*4  ];
+				iH2 = hneigh[iO*4+1];
+			}
+			if (iO >= inum) {
+				non_local_oxy = 1;
+				if(m[iO].w == 0) {
+					compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
+					numtyp qO; fetch(qO,iO,q_tex);
+					m[iO].w = qO;
+				}
+			}
+		}
+
+		for ( ; nbor<nbor_end; nbor+=n_stride) {
+			int j=dev_packed[nbor];
+
+			numtyp factor_lj,factor_coul;
+			factor_lj = sp_lj[sbmask(j)];
+			factor_coul = (numtyp)1.0-sp_lj[sbmask(j)+4];
+			j &= NEIGHMASK;
+
+			numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+			int jtype = jx.w;
+
+			// Compute r12
+			numtyp delx = ix.x-jx.x;
+			numtyp dely = ix.y-jx.y;
+			numtyp delz = ix.z-jx.z;
+			numtyp rsq = delx*delx+dely*dely+delz*delz;
+
+			int mtype = itype*lj_types+jtype;
+			if (rsq < lj1[mtype].z) { // cut_ljsq
+				numtyp r2inv = ucl_recip(rsq);
+				numtyp r6inv = r2inv*r2inv*r2inv;
+				numtyp forcelj = r6inv*(lj1[mtype].x*r6inv-lj1[mtype].y);
+				forcelj *= r2inv*factor_lj;
+
+				f.x += delx*forcelj;
+				f.y += dely*forcelj;
+				f.z += delz*forcelj;
+
+				if (eflag>0) {
+					numtyp e = r6inv * (lj3[mtype].x*r6inv-lj3[mtype].y);
+					energy += factor_lj * (e - lj3[mtype].z);
+				}
+		        if (vflag>0) {
+		          virial[0] += delx*delx*forcelj;
+		          virial[1] += dely*dely*forcelj;
+		          virial[2] += delz*delz*forcelj;
+		          virial[3] += delx*dely*forcelj;
+		          virial[4] += delx*delz*forcelj;
+		          virial[5] += dely*delz*forcelj;
+		        }
+			} // if LJ
+
+			if (rsq < cut_coulsqplus) { //cut_coulsqplus
+				int jH1, jH2, jO;
+				numtyp qj; fetch(qj,j,q_tex);
+				numtyp4 x2 = jx;
+				if(itype == typeO || jtype == typeO) {
+					if (jtype == typeO) {
+						jO = j;
+						if (hneigh[j*4+2] != -1) {
+							jH1 = atom_mapping(map,tag[j] + 1);
+							jH2 = atom_mapping(map,tag[j] + 2);
+							// set iH1,iH2 to closest image to O
+							jH1 = closest_image(j, jH1, sametag, x_);
+							jH2 = closest_image(j, jH2, sametag, x_);
+							hneigh[j*4  ] = jH1;
+							hneigh[j*4+1] = jH2;
+							hneigh[j*4+2] = -1;
+							hneigh[jH1*4  ] = j;
+							hneigh[jH1*4+1] += -1;
+							hneigh[jH1*4+2] = -1;
+							hneigh[jH2*4  ] = j;
+							hneigh[jH2*4+1] += -1;
+							hneigh[jH2*4+2] = -1;
+						} else {
+							jH1 = hneigh[j*4  ];
+							jH2 = hneigh[j*4+1];
+						}
+						if (m[j].w == 0) {
+							compute_newsite(j, jH1, jH2, &m[j], alpha, x_);
+							m[j].w = qj;
+						}
+						x2 = m[j];
+					}
+					delx = x1.x-x2.x;
+					dely = x1.y-x2.y;
+					delz = x1.z-x2.z;
+					rsq = delx*delx+dely*dely+delz*delz;
+				}
+				if (rsq < cut_coulsq) {
+					numtyp r2inv = ucl_recip(rsq);
+					numtyp r = ucl_rsqrt(r2inv);
+					numtyp grij = g_ewald * r;
+					numtyp expm2 = ucl_exp(-grij*grij);
+					numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
+					numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+
+					numtyp prefactor = qj;
+					prefactor *= qqrd2e*qtmp/r;
+					numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
+
+					if (itype == typeH) {
+						f.x += delx * force_coul;
+						f.y += dely * force_coul;
+						f.z += delz * force_coul;
+					} else {
+						fO.x += delx * force_coul;
+						fO.y += dely * force_coul;
+						fO.z += delz * force_coul;
+						fO.w += -1;
+					}
+					if (eflag>0) {
+						e_coul += prefactor*(_erfc-factor_coul);
+					}
+			        if (vflag>0) {
+			        	acctyp4 fd;
+			        	fd.x = delx*force_coul;
+			        	fd.y = dely*force_coul;
+			        	fd.z = delz*force_coul;
+			        	if (itype == typeH) {
+			        		if (jtype == typeH){
+								virial[0] += delx*fd.x;
+								virial[1] += dely*fd.y;
+								virial[2] += delz*fd.z;
+								virial[3] += delx*fd.y;
+								virial[4] += delx*fd.z;
+								virial[5] += dely*fd.z;
+			        		} else {
+								numtyp cO = 1 - alpha, cH = 0.5*alpha;
+								numtyp4 vdj;
+					        	numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
+								numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
+								numtyp4 xjO; fetch4(xjO,jO,pos_tex);
+								vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
+								vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
+								vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
+			        			virial[0] += (ix.x - vdj.x)*fd.x;
+			        			virial[1] += (ix.y - vdj.y)*fd.y;
+			        			virial[2] += (ix.z - vdj.z)*fd.z;
+			        			virial[3] += (ix.x - vdj.x)*fd.y;
+			        			virial[4] += (ix.x - vdj.x)*fd.z;
+			        			virial[5] += (ix.y - vdj.y)*fd.z;
+			        		}
+			        	} else {
+							numtyp cO = 1 - alpha, cH = 0.5*alpha;
+							numtyp4 vdi, vdj;
+							numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+							numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+							numtyp4 xO; fetch4(xO,iO,pos_tex);
+							vdi.x = xO.x*cO + xH1.x*cH + xH2.x*cH;
+							vdi.y = xO.y*cO + xH1.y*cH + xH2.y*cH;
+							vdi.z = xO.z*cO + xH1.z*cH + xH2.z*cH;
+			        		if (jtype != typeH){
+					        	numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
+								numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
+								numtyp4 xjO; fetch4(xjO,jO,pos_tex);
+								vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
+								vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
+								vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
+			        		} else vdj = jx;
+			        		vO[0] += 0.5*(vdi.x - vdj.x)*fd.x;
+			        		vO[1] += 0.5*(vdi.y - vdj.y)*fd.y;
+			        		vO[2] += 0.5*(vdi.z - vdj.z)*fd.z;
+			        		vO[3] += 0.5*(vdi.x - vdj.x)*fd.y;
+			        		vO[4] += 0.5*(vdi.x - vdj.x)*fd.z;
+			        		vO[5] += 0.5*(vdi.y - vdj.y)*fd.z;
+			        	}
+			        }
+				}
+				if (non_local_oxy == 1) {
+					if (iO == j) {
+						x2 = ix;
+						qj = qtmp;
+					}
+					numtyp4 x1m = m[iO];
+					delx = x1m.x-x2.x;
+					dely = x1m.y-x2.y;
+					delz = x1m.z-x2.z;
+					rsq = delx*delx+dely*dely+delz*delz;
+					if (rsq < cut_coulsq) {
+						numtyp r2inv = ucl_recip(rsq);
+						numtyp r = ucl_rsqrt(r2inv);
+						numtyp grij = g_ewald * r;
+						numtyp expm2 = ucl_exp(-grij*grij);
+						numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
+						numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+
+						numtyp prefactor = qj;
+						prefactor *= qqrd2e*x1m.w/r;
+						numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
+
+						numtyp cO = 1 - alpha, cH = 0.5*alpha;
+						numtyp4 fd;
+						fd.x = delx * force_coul * cH;
+						fd.y = dely * force_coul * cH;
+						fd.z = delz * force_coul * cH;
+
+						f.x += fd.x;
+						f.y += fd.y;
+						f.z += fd.z;
+
+						if (eflag>0) {
+							e_coul += prefactor*(_erfc-factor_coul) * (acctyp)0.5 * alpha;
+						}
+				        if (vflag>0) {
+				        	numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+							numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+							numtyp4 xO;  fetch4(xO,iO,pos_tex);
+
+							virial[0] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.x;
+							virial[1] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.y;
+							virial[2] += ((xO.z*cO + xH1.z*cH + xH2.z*cH) - x2.z) * fd.z;
+							virial[3] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.y;
+							virial[4] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.z;
+							virial[5] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.z;
+				        }
+					}
+				}
+			} // if cut_coulsqplus
+		} // for nbor
+		if (t_per_atom>1) {
+			__local acctyp red_acc[6][BLOCK_PAIR];
+			red_acc[0][tid]=fO.x;
+			red_acc[1][tid]=fO.y;
+			red_acc[2][tid]=fO.z;
+			red_acc[3][tid]=fO.w;
+			for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+				if (offset < s) {
+					for (int r=0; r<4; r++)
+						red_acc[r][tid] += red_acc[r][tid+s];
+				}
+			}
+			fO.x=red_acc[0][tid];
+			fO.y=red_acc[1][tid];
+			fO.z=red_acc[2][tid];
+			fO.w=red_acc[3][tid];
+			if (vflag>0) {
+				for (int r=0; r<6; r++) red_acc[r][tid]=vO[r];
+				for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+					if (offset < s) {
+						for (int r=0; r<6; r++)
+							red_acc[r][tid] += red_acc[r][tid+s];
+					}
+				}
+				for (int r=0; r<6; r++) vO[r]=red_acc[r][tid];
+			}
+		}
+		if(offset == 0) {
+			ansO[i] = fO;
+			if (vflag>0) {
+				ansO[inum   + i].x = vO[0];
+				ansO[inum   + i].y = vO[1];
+				ansO[inum   + i].z = vO[2];
+				ansO[inum*2 + i].x = vO[3];
+				ansO[inum*2 + i].y = vO[4];
+				ansO[inum*2 + i].z = vO[5];
+			}
+		}
+		store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
+				vflag,ans,engv);
+	} // if ii
+}
+
+
+__kernel void k_lj_tip4p_long_fast(){}
diff --git a/lib/gpu/lal_lj_tip4p_long.h b/lib/gpu/lal_lj_tip4p_long.h
new file mode 100644
index 0000000000..4bd6670aa8
--- /dev/null
+++ b/lib/gpu/lal_lj_tip4p_long.h
@@ -0,0 +1,95 @@
+#ifndef LAL_LJ_TIP4P_LONG_H
+#define LAL_LJ_TIP4P_LONG_H
+
+#include "lal_base_charge.h"
+
+namespace LAMMPS_AL {
+
+template <class numtyp, class acctyp>
+class LJ_TIP4PLong : public BaseCharge<numtyp, acctyp> {
+public:
+  LJ_TIP4PLong();
+  ~LJ_TIP4PLong();
+
+  /// Clear any previous data and set up for a new LAMMPS run
+  /** \param max_nbors initial number of rows in the neighbor matrix
+    * \param cell_size cutoff + skin
+    * \param gpu_split fraction of particles handled by device
+    *
+    * Returns:
+    * -  0 if successfull
+    * - -1 if fix gpu not found
+    * - -3 if there is an out of memory error
+    * - -4 if the GPU library was not compiled for GPU
+    * - -5 Double precision is not supported on card **/
+  int init(const int ntypes, double **host_cutsq,
+           double **host_lj1, double **host_lj2, double **host_lj3,
+           double **host_lj4, double **host_offset, double *host_special_lj,
+           const int nlocal, const int tH, const int tO,
+		   const double alpha, const double qdist,
+		   const int nall, const int max_nbors,
+           const int maxspecial, const double cell_size,
+           const double gpu_split, FILE *screen,
+		   double **host_cut_ljsq,
+		   const double host_cut_coulsq, const double host_cut_coulsqplus,
+		   double *host_special_coul, const double qqrd2e,
+		   const double g_ewald, int* tag,
+			 int *map_array, int map_size,
+			 int *sametag, int max_same);
+
+  /// Clear all host and device data
+  /** \note This is called at the beginning of the init() routine **/
+  void clear();
+
+  /// Returns memory usage on device per atom
+  int bytes_per_atom(const int max_nbors) const;
+
+  /// Total host memory used by library for pair style
+  double host_memory_usage() const;
+
+  /// Copy data which is easier to compute in LAMMPS_NS
+  void copy_relations_data(int **hn, double **m, int n,int* tag, int *map_array, int map_size,
+			 int *sametag, int max_same, int ago);
+
+  // --------------------------- TYPE DATA --------------------------
+
+  /// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq_vdw
+  UCL_D_Vec<numtyp4> lj1;
+  /// lj3.x = lj3, lj3.y = lj4, lj3.z = offset
+  UCL_D_Vec<numtyp4> lj3;
+  /// cutsq
+  UCL_D_Vec<numtyp> cutsq;
+  /// Special LJ values [0-3] and Special Coul values [4-7]
+  UCL_D_Vec<numtyp> sp_lj;
+
+  /// If atom type constants fit in shared memory, use fast kernels
+  bool shared_types;
+
+  /// Number of atom types
+  int _lj_types;
+
+  numtyp _qqrd2e, _g_ewald;
+  /// TIP4P water parameters
+  int TypeO, TypeH;
+  numtyp alpha, qdist;
+  numtyp cut_coulsq, cut_coulsqplus;
+
+  UCL_D_Vec<int> hneight;
+  UCL_D_Vec<numtyp4> m; // position and charge of virtual particle
+  UCL_D_Vec<acctyp4> ansO; // force applied to virtual particle
+  UCL_D_Vec<acctyp4> force_comp;
+
+  UCL_D_Vec<int> tag;
+  UCL_D_Vec<int> map_array;
+  UCL_D_Vec<int> atom_sametag;
+
+  UCL_Kernel k_pair_distrib;
+
+ private:
+  bool _allocated;
+  void loop(const bool _eflag, const bool _vflag);
+};
+
+}
+
+#endif
diff --git a/lib/gpu/lal_lj_tip4p_long_ext.cpp b/lib/gpu/lal_lj_tip4p_long_ext.cpp
new file mode 100644
index 0000000000..00698af82a
--- /dev/null
+++ b/lib/gpu/lal_lj_tip4p_long_ext.cpp
@@ -0,0 +1,135 @@
+#include <iostream>
+#include <cassert>
+#include <cmath>
+
+#include "lal_lj_tip4p_long.h"
+
+using namespace std;
+using namespace LAMMPS_AL;
+
+static LJ_TIP4PLong<PRECISION,ACC_PRECISION> LJTIP4PLMF;
+
+// ---------------------------------------------------------------------------
+// Allocate memory on host and device and copy constants to device
+// ---------------------------------------------------------------------------
+int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
+                 double **host_lj2, double **host_lj3, double **host_lj4,
+                 double **offset, double *special_lj, const int inum,
+				 const int tH, const int tO,
+				 const double alpha, const double qdist,
+                 const int nall, const int max_nbors,  const int maxspecial,
+                 const double cell_size, int &gpu_mode, FILE *screen,
+				 double **host_cut_ljsq,
+				 const double host_cut_coulsq, const double host_cut_coulsqplus,
+				 double *host_special_coul, const double qqrd2e,
+				 const double g_ewald, int* tag,
+				 int *map_array, int map_size,
+				 int *sametag, int max_same) {
+  LJTIP4PLMF.clear();
+  gpu_mode=LJTIP4PLMF.device->gpu_mode();
+  double gpu_split=LJTIP4PLMF.device->particle_split();
+  int first_gpu=LJTIP4PLMF.device->first_device();
+  int last_gpu=LJTIP4PLMF.device->last_device();
+  int world_me=LJTIP4PLMF.device->world_me();
+  int gpu_rank=LJTIP4PLMF.device->gpu_rank();
+  int procs_per_gpu=LJTIP4PLMF.device->procs_per_gpu();
+
+  LJTIP4PLMF.device->init_message(screen,"lj/cut/tip4p/long/gpu",first_gpu,last_gpu);
+
+  bool message=false;
+  if (LJTIP4PLMF.device->replica_me()==0 && screen)
+    message=true;
+
+  if (message) {
+    fprintf(screen,"Initializing Device and compiling on process 0...");
+    fflush(screen);
+  }
+
+  int init_ok=0;
+  if (world_me==0)
+    init_ok=LJTIP4PLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3,
+                       host_lj4, offset, special_lj, inum,
+					   tH, tO, alpha, qdist, nall, 300,
+                       maxspecial, cell_size, gpu_split, screen,
+					   host_cut_ljsq, host_cut_coulsq, host_cut_coulsqplus,
+					   host_special_coul, qqrd2e, g_ewald, tag,
+						 map_array, map_size,
+						 sametag, max_same);
+
+  LJTIP4PLMF.device->world_barrier();
+  if (message)
+    fprintf(screen,"Done.\n");
+
+  for (int i=0; i<procs_per_gpu; i++) {
+    if (message) {
+      if (last_gpu-first_gpu==0)
+        fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
+      else
+        fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
+                last_gpu,i);
+      fflush(screen);
+    }
+    if (gpu_rank==i && world_me!=0)
+      init_ok=LJTIP4PLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
+                         offset, special_lj, inum,
+						 tH, tO, alpha, qdist, nall, 300, maxspecial,
+                         cell_size, gpu_split, screen, host_cut_ljsq,
+	                     host_cut_coulsq, host_cut_coulsqplus,
+						 host_special_coul, qqrd2e, g_ewald,tag,
+						 map_array, map_size,
+						 sametag, max_same);
+
+    LJTIP4PLMF.device->gpu_barrier();
+    if (message)
+      fprintf(screen,"Done.\n");
+  }
+  if (message)
+    fprintf(screen,"\n");
+
+  if (init_ok==0)
+    LJTIP4PLMF.estimate_gpu_overhead();
+  return init_ok;
+}
+
+
+
+void ljtip4p_long_gpu_clear() {
+  LJTIP4PLMF.clear();
+}
+
+int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum_full,
+                        const int nall, double **host_x, int *host_type,
+                        double *sublo, double *subhi, tagint *tag, int **nspecial,
+                        tagint **special, const bool eflag, const bool vflag,
+                        const bool eatom, const bool vatom, int &host_start,
+                        int **ilist, int **jnum, const double cpu_time,
+                        bool &success, double *host_q, double *boxlo,
+                        double *prd) {
+  return LJTIP4PLMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
+                       subhi, tag, nspecial, special, eflag, vflag, eatom,
+                       vatom, host_start, ilist, jnum, cpu_time, success,
+					   host_q,boxlo, prd);
+}
+
+void ljtip4p_long_gpu_compute(const int ago, const int inum_full, const int nall,
+                     double **host_x, int *host_type, int *ilist, int *numj,
+                     int **firstneigh, const bool eflag, const bool vflag,
+                     const bool eatom, const bool vatom, int &host_start,
+                     const double cpu_time, bool &success,double *host_q,
+					 const int nlocal, double *boxlo, double *prd) {
+  LJTIP4PLMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
+                firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,host_q,
+				nlocal,boxlo,prd);
+}
+
+double ljtip4p_long_gpu_bytes() {
+  return LJTIP4PLMF.host_memory_usage();
+}
+
+void ljtip4p_long_copy_molecule_data(int **hn, double **m, int n, int* tag,
+		 int *map_array, int map_size,
+		 int *sametag, int max_same, int ago){
+	LJTIP4PLMF.copy_relations_data(hn, m, n, tag,map_array,map_size,sametag, max_same, ago);
+}
+
+
diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh
index 20429009db..f46c3b7fe0 100755
--- a/src/GPU/Install.sh
+++ b/src/GPU/Install.sh
@@ -143,6 +143,8 @@ action pair_ufm_gpu.cpp
 action pair_ufm_gpu.h
 action pair_lj_cut_dipole_long_gpu.cpp pair_lj_cut_dipole_long.cpp
 action pair_lj_cut_dipole_long_gpu.h pair_lj_cut_dipole_long.cpp
+action pair_lj_cut_tip4p_long_gpu.h
+action pair_lj_cut_tip4p_long_gpu.cpp
 
 # edit 2 Makefile.package files to include/exclude package info
 
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
new file mode 100644
index 0000000000..5e8e746c85
--- /dev/null
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -0,0 +1,234 @@
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_lj_cut_tip4p_long_gpu.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "integrate.h"
+#include "memory.h"
+#include "error.h"
+#include "neigh_request.h"
+#include "universe.h"
+#include "update.h"
+#include "domain.h"
+#include "kspace.h"
+#include "angle.h"
+#include "bond.h"
+#include "gpu_extra.h"
+
+#define EWALD_F   1.12837917
+#define EWALD_P   0.3275911
+#define A1        0.254829592
+#define A2       -0.284496736
+#define A3        1.421413741
+#define A4       -1.453152027
+#define A5        1.061405429
+
+using namespace LAMMPS_NS;
+
+// External functions from cuda library for atom decomposition
+
+int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
+                 double **host_lj2, double **host_lj3, double **host_lj4,
+                 double **offset, double *special_lj, const int nlocal,
+				 const int tH, const int tO, const double alpha, const double qdist,
+                 const int nall, const int max_nbors, const int maxspecial,
+                 const double cell_size, int &gpu_mode, FILE *screen,
+				 double **host_cut_ljsq, const double host_cut_coulsq,
+				 const double host_cut_coulsqplus,
+				 double *host_special_coul, const double qqrd2e,
+				 const double g_ewald, int* tag,
+				 int *map_array, int map_size,
+				 int *sametag, int max_same);
+void ljtip4p_long_gpu_clear();
+int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum,
+                         const int nall, double **host_x, int *host_type,
+                         double *sublo, double *subhi, tagint *tag, int **nspecial,
+                         tagint **special, const bool eflag, const bool vflag,
+                         const bool eatom, const bool vatom, int &host_start,
+                         int **ilist, int **jnum,
+                         const double cpu_time, bool &success, double *host_q,
+						 double *boxlo, double *prd);
+void ljtip4p_long_gpu_compute(const int ago, const int inum, const int nall,
+                     double **host_x, int *host_type, int *ilist, int *numj,
+                     int **firstneigh, const bool eflag, const bool vflag,
+                     const bool eatom, const bool vatom, int &host_start,
+                     const double cpu_time,
+                     bool &success, double *host_q, const int nlocal,
+                     double *boxlo, double *prd);
+double ljtip4p_long_gpu_bytes();
+void ljtip4p_long_copy_molecule_data(int **, double **, int, int* , int *, int, int *, int , int);
+
+/* ---------------------------------------------------------------------- */
+
+PairLJCutTIP4PLongGPU::PairLJCutTIP4PLongGPU(LAMMPS *lmp)
+: PairLJCutTIP4PLong(lmp), gpu_mode(GPU_FORCE)
+{
+  respa_enable = 0;
+  reinitflag = 0;
+  cpu_time = 0.0;
+  GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+}
+
+/* ----------------------------------------------------------------------
+   free all arrays
+------------------------------------------------------------------------- */
+
+PairLJCutTIP4PLongGPU::~PairLJCutTIP4PLongGPU()
+{
+	ljtip4p_long_gpu_clear();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJCutTIP4PLongGPU::compute(int eflag, int vflag)
+{
+
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  int nall = atom->nlocal + atom->nghost;
+  int inum, host_start;
+
+  ljtip4p_long_copy_molecule_data(hneigh, newsite, nall, atom->tag,
+			 atom->get_map_array(), atom->get_map_size(),
+			 atom->sametag, atom->get_max_same(), neighbor->ago);
+
+  bool success = true;
+  int *ilist, *numneigh, **firstneigh;
+  if (gpu_mode != GPU_FORCE) {
+    inum = atom->nlocal;
+    firstneigh = ljtip4p_long_gpu_compute_n(neighbor->ago, inum, nall,
+                                   atom->x, atom->type, domain->sublo,
+                                   domain->subhi, atom->tag, atom->nspecial,
+                                   atom->special, eflag, vflag, eflag_atom,
+                                   vflag_atom, host_start, &ilist, &numneigh,
+								   cpu_time, success, atom->q, domain->boxlo,
+								   domain->prd);
+  } else {
+    inum = list->inum;
+    ilist = list->ilist;
+    numneigh = list->numneigh;
+    firstneigh = list->firstneigh;
+    ljtip4p_long_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
+                    ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+                    vflag_atom, host_start, cpu_time, success, atom->q,
+					atom->nlocal, domain->boxlo, domain->prd);
+  }
+  if (!success)
+    error->one(FLERR,"Insufficient memory on accelerator");
+
+//  if (host_start<inum) {
+//    cpu_time = MPI_Wtime();
+//    cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
+//    cpu_time = MPI_Wtime() - cpu_time;
+//  }
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJCutTIP4PLongGPU::init_style()
+{
+
+  cut_respa = NULL;
+  if (atom->tag_enable == 0)
+    error->all(FLERR,"Pair style lj/cut/tip4p/long/gpu requires atom IDs");
+  if (!atom->q_flag)
+    error->all(FLERR,
+               "Pair style lj/cut/tip4p/long/gpu requires atom attribute q");
+  if (force->bond == NULL)
+    error->all(FLERR,"Must use a bond style with TIP4P potential");
+  if (force->angle == NULL)
+    error->all(FLERR,"Must use an angle style with TIP4P potential");
+
+  if (atom->map_style == 2)
+	  error->all(FLERR,"GPU-accelerated lj/cut/tip4p/long currently requires map style 'array' (atom_modify map array)");
+
+  //PairLJCutCoulLong::init_style();
+  // Repeat cutsq calculation because done after call to init_style
+  double maxcut = -1.0;
+  double cut;
+  for (int i = 1; i <= atom->ntypes; i++) {
+    for (int j = i; j <= atom->ntypes; j++) {
+      if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
+        cut = init_one(i,j);
+        cut *= cut;
+        if (cut > maxcut)
+          maxcut = cut;
+        cutsq[i][j] = cutsq[j][i] = cut;
+      } else
+        cutsq[i][j] = cutsq[j][i] = 0.0;
+    }
+  }
+  double cell_size = sqrt(maxcut) + neighbor->skin;
+
+  // insure use of KSpace long-range solver, set g_ewald
+  if (force->kspace == NULL)
+    error->all(FLERR,"Pair style requires a KSpace style");
+  g_ewald = force->kspace->g_ewald;
+
+  // setup force tables
+  if (ncoultablebits) init_tables(cut_coul,cut_respa);
+
+  int maxspecial=0;
+  if (atom->molecular)
+    maxspecial=atom->maxspecial;
+
+  // set alpha parameter
+  double theta = force->angle->equilibrium_angle(typeA);
+  double blen = force->bond->equilibrium_distance(typeB);
+  alpha = qdist / (cos(0.5*theta) * blen);
+
+  cut_coulsq = cut_coul * cut_coul;
+  double cut_coulsqplus = (cut_coul+qdist+blen) * (cut_coul+qdist+blen);
+  if (maxcut < cut_coulsqplus) {
+	  cell_size = (cut_coul+qdist+blen) + neighbor->skin;
+  }
+  if (comm->cutghostuser < cell_size) {
+    comm->cutghostuser = cell_size;
+    if (comm->me == 0)
+       error->warning(FLERR,"Increasing communication cutoff for TIP4P GPU style");
+  }
+
+  int success = ljtip4p_long_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
+                             offset, force->special_lj, atom->nlocal,
+							 typeH, typeO, alpha, qdist,
+                             atom->nlocal+atom->nghost, 300, maxspecial,
+                             cell_size, gpu_mode, screen, cut_ljsq,
+							 cut_coulsq, cut_coulsqplus,
+                             force->special_coul, force->qqrd2e,
+							 g_ewald,
+							 atom->tag,
+							 atom->get_map_array(), atom->get_map_size(),
+							 atom->sametag, atom->get_max_same());
+  GPU_EXTRA::check_flag(success,error,world);
+  if (gpu_mode == GPU_FORCE) {
+    int irequest = neighbor->request(this,instance_me);
+    neighbor->requests[irequest]->half = 0;
+    neighbor->requests[irequest]->full = 1;
+    neighbor->requests[irequest]->cut = 1;
+    neighbor->requests[irequest]->cutoff = cut_coul+qdist+blen + neighbor->skin;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairLJCutTIP4PLongGPU::memory_usage()
+{
+  double bytes = PairLJCutTIP4PLong::memory_usage();
+  return bytes + ljtip4p_long_gpu_bytes();
+}
+
+/* ---------------------------------------------------------------------- */
+
+//void PairLJCutTIP4PLongGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+//                               int *ilist, int *numneigh, int **firstneigh) {
+//	error->all(FLERR,"PairLJCutTIP4PLongGPU::cpu_compute not implemented");
+//}
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.h b/src/GPU/pair_lj_cut_tip4p_long_gpu.h
new file mode 100644
index 0000000000..23b96e201a
--- /dev/null
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.h
@@ -0,0 +1,32 @@
+#ifdef PAIR_CLASS
+
+PairStyle(lj/cut/tip4p/long/gpu,PairLJCutTIP4PLongGPU)
+
+#else
+
+#ifndef LMP_PAIR_LJ_TIP4P_LONG_GPU_H
+#define LMP_PAIR_LJ_TIP4P_LONG_GPU_H
+
+#include "pair_lj_cut_tip4p_long.h"
+
+namespace LAMMPS_NS {
+
+class PairLJCutTIP4PLongGPU : public PairLJCutTIP4PLong {
+ public:
+  PairLJCutTIP4PLongGPU(LAMMPS *lmp);
+  ~PairLJCutTIP4PLongGPU();
+//  void cpu_compute(int, int, int, int, int *, int *, int **);
+  void compute(int, int);
+  void init_style();
+  double memory_usage();
+
+ enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
+
+ private:
+  int gpu_mode;
+  double cpu_time;
+};
+
+}
+#endif
+#endif
diff --git a/src/atom.h b/src/atom.h
index 81f643c007..4c640f3252 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -287,6 +287,7 @@ class Atom : protected Pointers {
 
   inline int* get_map_array() {return map_array;};
   inline int get_map_size() {return map_tag_max+1;};
+  inline int get_max_same() {return max_same;};
   inline int get_map_maxarray() {return map_maxarray+1;};
 
   bigint memory_usage();

From f803ba56558aec87be6df267f2870b7637aaa5cb Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Tue, 12 Nov 2019 21:35:36 +0300
Subject: [PATCH 021/199] Add shfl_xor sum to kernel for ARCH>=300

---
 lib/gpu/lal_lj_tip4p_long.cu | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
index 7c6cec4473..1ea6de1d41 100644
--- a/lib/gpu/lal_lj_tip4p_long.cu
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -472,6 +472,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
 			} // if cut_coulsqplus
 		} // for nbor
 		if (t_per_atom>1) {
+#if (ARCH < 300)
 			__local acctyp red_acc[6][BLOCK_PAIR];
 			red_acc[0][tid]=fO.x;
 			red_acc[1][tid]=fO.y;
@@ -497,6 +498,20 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
 				}
 				for (int r=0; r<6; r++) vO[r]=red_acc[r][tid];
 			}
+#else
+			for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+				fO.x += shfl_xor(fO.x, s, t_per_atom);
+				fO.y += shfl_xor(fO.y, s, t_per_atom);
+				fO.z += shfl_xor(fO.z, s, t_per_atom);
+				fO.w += shfl_xor(fO.w, s, t_per_atom);
+			}
+			if (vflag>0) {
+				for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+						for (int r=0; r<6; r++)
+							vO[r] += shfl_xor(vO[r], s, t_per_atom);
+				}
+			}
+#endif
 		}
 		if(offset == 0) {
 			ansO[i] = fO;

From 7e92c2e0eea51310222c2cc7f8966bf5d1ce3f02 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 13 Nov 2019 14:30:13 -0500
Subject: [PATCH 022/199] Add more detailed code documentation

---
 src/library.cpp | 88 +++++++++++++++++++++++++++++++++++--------------
 src/library.h   |  2 +-
 2 files changed, 64 insertions(+), 26 deletions(-)

diff --git a/src/library.cpp b/src/library.cpp
index 407ec454a9..ee98e47aaa 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -1731,12 +1731,31 @@ int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
 
 #endif
 
-/* ----------------------------------------------------------------------
-   Find neighbor list index for pair style
-------------------------------------------------------------------------- */
-int lammps_find_pair_neighlist(void* ptr, char * style, int nsub, int request) {
+/*******************************************************************************
+ * Find neighbor list index of pair style neighbor list
+ *
+ * Try finding pair instance that matches style. If exact is set, the pair must
+ * match style exactly. If exact is 0, style must only be contained. If pair is
+ * of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style.
+ *
+ * Once the pair instance has been identified, multiple neighbor list requests
+ * may be found. Every neighbor list is uniquely identified by its request
+ * index. Thus, providing this request index ensures that the correct neighbor
+ * list index is returned.
+ *
+ * @param ptr      Pointer to LAMMPS instance
+ * @param style    String used to search for pair style instance
+ * @param exact    Flag to control whether style should match exactly or only
+ *                 must be contained in pair style name
+ * @param nsub     match nsub-th hybrid sub-style
+ * @param request  request index that specifies which neighbor list should be
+ *                 returned, in case there are multiple neighbor lists requests
+ *                 for the found pair style
+ * @return         return neighbor list index if found, otherwise -1
+ ******************************************************************************/
+int lammps_find_pair_neighlist(void* ptr, char * style, int exact, int nsub, int request) {
   LAMMPS *  lmp = (LAMMPS *) ptr;
-  Pair* pair = lmp->force->pair_match(style, 1, nsub);
+  Pair* pair = lmp->force->pair_match(style, exact, nsub);
 
   if (pair != NULL) {
     // find neigh list
@@ -1752,11 +1771,15 @@ int lammps_find_pair_neighlist(void* ptr, char * style, int nsub, int request) {
   return -1;
 }
 
-/* ----------------------------------------------------------------------
-   Find neighbor list index for compute with given fix ID
-   The request ID identifies which request it is in case of there are
-   multiple neighbor lists for this fix
-------------------------------------------------------------------------- */
+/*******************************************************************************
+ * Find neighbor list index of fix neighbor list
+ *
+ * @param ptr      Pointer to LAMMPS instance
+ * @param id       Identifier of fix instance
+ * @param request  request index that specifies which request should be returned,
+ *                 in case there are multiple neighbor lists for this fix
+ * @return         return neighbor list index if found, otherwise -1
+ ******************************************************************************/
 int lammps_find_fix_neighlist(void* ptr, char * id, int request) {
   LAMMPS *  lmp = (LAMMPS *) ptr;
   Fix* fix = NULL;
@@ -1784,12 +1807,15 @@ int lammps_find_fix_neighlist(void* ptr, char * id, int request) {
   return -1;
 }
 
-/* ----------------------------------------------------------------------
-   Find neighbor list index for compute with given compute ID
-   The request ID identifies which request it is in case of there are
-   multiple neighbor lists for this compute
-------------------------------------------------------------------------- */
-
+/*******************************************************************************
+ * Find neighbor list index of compute neighbor list
+ *
+ * @param ptr      Pointer to LAMMPS instance
+ * @param id       Identifier of fix instance
+ * @param request  request index that specifies which request should be returned,
+ *                 in case there are multiple neighbor lists for this fix
+ * @return         return neighbor list index if found, otherwise -1
+ ******************************************************************************/
 int lammps_find_compute_neighlist(void* ptr, char * id, int request) {
   LAMMPS *  lmp = (LAMMPS *) ptr;
   Compute* compute = NULL;
@@ -1817,10 +1843,14 @@ int lammps_find_compute_neighlist(void* ptr, char * id, int request) {
   return -1;
 }
 
-/* ----------------------------------------------------------------------
-   Return the number of entries in the neighbor list with given index
-------------------------------------------------------------------------- */
-
+/*******************************************************************************
+ * Return the number of entries in the neighbor list with given index
+ *
+ * @param ptr      Pointer to LAMMPS instance
+ * @param idx      neighbor list index
+ * @return         return number of entries in neighbor list, -1 if idx is
+ *                 not a valid index
+ ******************************************************************************/
 int lammps_neighlist_num_elements(void * ptr, int idx) {
   LAMMPS *  lmp = (LAMMPS *) ptr;
   Neighbor * neighbor = lmp->neighbor;
@@ -1833,11 +1863,19 @@ int lammps_neighlist_num_elements(void * ptr, int idx) {
   return list->inum;
 }
 
-/* ----------------------------------------------------------------------
-   Return atom index, number of neighbors and neighbor array for neighbor
-   list entry
-------------------------------------------------------------------------- */
-
+/*******************************************************************************
+ * Return atom local index, number of neighbors, and array of neighbor local
+ * atom indices of neighbor list entry
+ *
+ * @param ptr             Pointer to LAMMPS instance
+ * @param idx             neighbor list index
+ * @param element         neighbor list element index
+ * @param[out] iatom      atom local index in range [0, nlocal + nghost), -1 if
+                          invalid idx or element index
+ * @param[out] numneigh   number of neighbors of atom i or 0
+ * @param[out] neighbors  pointer to array of neighbor atom local indices or
+ *                        NULL
+ ******************************************************************************/
 void lammps_neighlist_element_neighbors(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors) {
   LAMMPS *  lmp = (LAMMPS *) ptr;
   Neighbor * neighbor = lmp->neighbor;
diff --git a/src/library.h b/src/library.h
index 3d67a46974..ce5e983f2f 100644
--- a/src/library.h
+++ b/src/library.h
@@ -78,7 +78,7 @@ int lammps_config_has_jpeg_support();
 int lammps_config_has_ffmpeg_support();
 int lammps_config_has_exceptions();
 
-int lammps_find_pair_neighlist(void* ptr, char * style, int nsub, int request);
+int lammps_find_pair_neighlist(void* ptr, char * style, int exact, int nsub, int request);
 int lammps_find_fix_neighlist(void* ptr, char * id, int request);
 int lammps_find_compute_neighlist(void* ptr, char * id, int request);
 int lammps_neighlist_num_elements(void* ptr, int idx);

From 28a9dc40cbf615b03f90e9cb3d629c779599a739 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 13 Nov 2019 15:53:25 -0500
Subject: [PATCH 023/199] Add docstring to new lammps.py methods

---
 python/lammps.py | 92 +++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 88 insertions(+), 4 deletions(-)

diff --git a/python/lammps.py b/python/lammps.py
index 665c8b43b8..e8fc240c75 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -52,6 +52,17 @@ class MPIAbortException(Exception):
     return repr(self.message)
 
 class NeighList:
+    """This is a wrapper class that exposes the contents of a neighbor list
+
+    It can be used like a regular Python list.
+
+    Internally it uses the lower-level LAMMPS C-library interface.
+
+    :param lmp: reference to instance of :class:`lammps`
+    :type  lmp: lammps
+    :param idx: neighbor list index
+    :type  idx: int
+    """
     def __init__(self, lmp, idx):
         self.lmp = lmp
         self.idx = idx
@@ -64,15 +75,24 @@ class NeighList:
 
     @property
     def size(self):
+        """
+        :return: number of elements in neighbor list
+        """
         return self.lmp.get_neighlist_size(self.idx)
 
     def get(self, element):
+        """
+        :return: tuple with atom local index, number of neighbors and array of neighbor local atom indices
+        :rtype:  (int, int, numpy.array)
+        """
         iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)
         return iatom, numneigh, neighbors
 
+    # the methods below implement the iterator interface, so NeighList can be used like a regular Python list
+
     def __getitem__(self, element):
         return self.get(element)
-    
+
     def __len__(self):
         return self.size
 
@@ -169,7 +189,7 @@ class lammps(object):
       [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
     self.lib.lammps_scatter_atoms_subset.restype = None
 
-    self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int]
+    self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int]
     self.lib.lammps_find_pair_neighlist.restype  = c_int
 
     self.lib.lammps_find_fix_neighlist.argtypes = [c_void_p, c_char_p, c_int]
@@ -699,29 +719,93 @@ class lammps(object):
     self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller)
 
   def get_neighlist(self, idx):
+    """Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index
+
+    :param idx: index of neighbor list
+    :type  idx: int
+    :return: an instance of :class:`NeighList` wrapping access to neighbor list data
+    :rtype:  NeighList
+    """
     if idx < 0:
         return None
     return NeighList(self, idx)
 
-  def find_pair_neighlist(self, style, nsub=0, request=0):
+  def find_pair_neighlist(self, style, exact=True, nsub=0, request=0):
+    """Find neighbor list index of pair style neighbor list
+
+    Try finding pair instance that matches style. If exact is set, the pair must
+    match style exactly. If exact is 0, style must only be contained. If pair is
+    of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style.
+
+    Once the pair instance has been identified, multiple neighbor list requests
+    may be found. Every neighbor list is uniquely identified by its request
+    index. Thus, providing this request index ensures that the correct neighbor
+    list index is returned.
+
+    :param style: name of pair style that should be searched for
+    :type  style: string
+    :param exact: controls whether style should match exactly or only must be contained in pair style name, defaults to True
+    :type  exact: bool, optional
+    :param nsub:  match nsub-th hybrid sub-style, defaults to 0
+    :type  nsub:  int, optional
+    :param request:   index of neighbor list request, in case there are more than one, defaults to 0
+    :type  request:   int, optional
+    :return: neighbor list index if found, otherwise -1
+    :rtype:  int
+     """
     style = style.encode()
-    idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, nsub, request)
+    exact = int(exact)
+    idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, request)
     return self.get_neighlist(idx)
 
   def find_fix_neighlist(self, fixid, request=0):
+    """Find neighbor list index of fix neighbor list
+
+    :param fixid: name of fix
+    :type  fixid: string
+    :param request:   index of neighbor list request, in case there are more than one, defaults to 0
+    :type  request:   int, optional
+    :return: neighbor list index if found, otherwise -1
+    :rtype:  int
+     """
     fixid = fixid.encode()
     idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request)
     return self.get_neighlist(idx)
 
   def find_compute_neighlist(self, computeid, request=0):
+    """Find neighbor list index of compute neighbor list
+
+    :param computeid: name of compute
+    :type  computeid: string
+    :param request:   index of neighbor list request, in case there are more than one, defaults to 0
+    :type  request:   int, optional
+    :return: neighbor list index if found, otherwise -1
+    :rtype:  int
+     """
     computeid = computeid.encode()
     idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request)
     return self.get_neighlist(idx)
 
   def get_neighlist_size(self, idx):
+    """Return the number of elements in neighbor list with the given index
+
+    :param idx: neighbor list index
+    :type  idx: int
+    :return: number of elements in neighbor list with index idx
+    :rtype:  int
+     """
     return self.lib.lammps_neighlist_num_elements(self.lmp, idx)
 
   def get_neighlist_element_neighbors(self, idx, element):
+    """Return data of neighbor list entry
+
+    :param element: neighbor list index
+    :type  element: int
+    :param element: neighbor list element index
+    :type  element: int
+    :return: tuple with atom local index, number of neighbors and array of neighbor local atom indices
+    :rtype:  (int, int, numpy.array)
+    """
     c_iatom = c_int()
     c_numneigh = c_int()
     c_neighbors = POINTER(c_int)()

From 62b3e790220d751dca64ff82c0fabb89adb7d3a0 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 13 Nov 2019 15:54:22 -0500
Subject: [PATCH 024/199] Add autodoc for lammps.lammps and lammps.NeighList

---
 doc/src/Python_library.rst      |  21 ++-
 doc/txt/Python_library.txt      | 256 --------------------------------
 doc/utils/sphinx-config/conf.py |   6 +-
 3 files changed, 20 insertions(+), 263 deletions(-)
 delete mode 100644 doc/txt/Python_library.txt

diff --git a/doc/src/Python_library.rst b/doc/src/Python_library.rst
index 8ad01e8a2b..e079df1a04 100644
--- a/doc/src/Python_library.rst
+++ b/doc/src/Python_library.rst
@@ -9,7 +9,7 @@ below assumes you have first imported the "lammps" module in your
 Python script, as follows:
 
 
-.. parsed-literal::
+.. code-block:: Python
 
    from lammps import lammps
 
@@ -23,7 +23,7 @@ The python/examples directory has Python scripts which show how Python
 can run LAMMPS, grab data, change it, and put it back into LAMMPS.
 
 
-.. parsed-literal::
+.. code-block:: Python
 
    lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
                             # 4 optional args are allowed: name, cmdargs, ptr, comm
@@ -100,7 +100,7 @@ can run LAMMPS, grab data, change it, and put it back into LAMMPS.
 The lines
 
 
-.. parsed-literal::
+.. code-block:: Python
 
    from lammps import lammps
    lmp = lammps()
@@ -117,7 +117,7 @@ prompt.
 If the ptr argument is set like this:
 
 
-.. parsed-literal::
+.. code-block:: Python
 
    lmp = lammps(ptr=lmpptr)
 
@@ -134,7 +134,7 @@ Note that you can create multiple LAMMPS objects in your Python
 script, and coordinate and run multiple simulations, e.g.
 
 
-.. parsed-literal::
+.. code-block:: Python
 
    from lammps import lammps
    lmp1 = lammps()
@@ -230,7 +230,7 @@ ctypes vector of ints or doubles, allocated and initialized something
 like this:
 
 
-.. parsed-literal::
+.. code-block:: Python
 
    from ctypes import \*
    natoms = lmp.get_natoms()
@@ -265,6 +265,15 @@ following steps:
   Python script.
 
 
+----------
+
+.. autoclass:: lammps.lammps
+   :members:
+   :no-undoc-members:
+
+.. autoclass:: lammps.NeighList
+   :members:
+   :no-undoc-members:
 
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
diff --git a/doc/txt/Python_library.txt b/doc/txt/Python_library.txt
deleted file mode 100644
index d9ddbe0cbb..0000000000
--- a/doc/txt/Python_library.txt
+++ /dev/null
@@ -1,256 +0,0 @@
-"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Python library interface :h3
-
-As described previously, the Python interface to LAMMPS consists of a
-Python "lammps" module, the source code for which is in
-python/lammps.py, which creates a "lammps" object, with a set of
-methods that can be invoked on that object.  The sample Python code
-below assumes you have first imported the "lammps" module in your
-Python script, as follows:
-
-from lammps import lammps :pre
-
-These are the methods defined by the lammps module.  If you look at
-the files src/library.cpp and src/library.h you will see they
-correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program, and which are described on the
-"Howto library"_Howto_library.html doc page.
-
-The python/examples directory has Python scripts which show how Python
-can run LAMMPS, grab data, change it, and put it back into LAMMPS.
-
-lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-                         # 4 optional args are allowed: name, cmdargs, ptr, comm
-lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
-lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
-lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
-lmp = lammps(name="g++",cmdargs=list)    # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre
-
-lmp.close()              # destroy a LAMMPS object :pre
-
-version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre
-
-lmp.file(file)           # run an entire input script, file = "in.lj"
-lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100"
-lmp.commands_list(cmdlist)     # invoke commands in cmdlist = ["run 10", "run 20"]
-lmp.commands_string(multicmd)  # invoke commands in multicmd = "run 10\nrun 20" :pre
-
-size = lmp.extract_setting(name)     # return data type info :pre
-
-xlo = lmp.extract_global(name,type)  # extract a global quantity
-                                     # name = "boxxlo", "nlocal", etc
-                                     # type = 0 = int
-                                     #        1 = double :pre
-
-boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box()  # extract box info :pre
-
-coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
-                                          # name = "x", "type", etc
-                                          # type = 0 = vector of ints
-                                          #        1 = array of ints
-                                          #        2 = vector of doubles
-                                          #        3 = array of doubles :pre
-
-eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
-v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
-                                          # id = ID of compute or fix
-                                          # style = 0 = global data
-                                          #         1 = per-atom data
-                                          #         2 = local data
-                                          # type = 0 = scalar
-                                          #        1 = vector
-                                          #        2 = array
-                                          # i,j = indices of value in global vector or array :pre
-
-var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
-                                             # name = name of variable
-                                             # group = group ID (ignored for equal-style variables)
-                                             # flag = 0 = equal-style variable
-                                             #        1 = atom-style variable :pre
-
-value = lmp.get_thermo(name)              # return current value of a thermo keyword
-natoms = lmp.get_natoms()                 # total # of atoms as int :pre
-
-flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
-lmp.reset_box(boxlo,boxhi,xy,yz,xz)       # reset the simulation box size :pre
-
-data = lmp.gather_atoms(name,type,count)  # return per-atom property of all atoms gathered into data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-data = lmp.gather_atoms_concat(name,type,count)  # ditto, but concatenated atom values from each proc (unordered)
-data = lmp.gather_atoms_subset(name,type,count,ndata,ids)  # ditto, but for subset of Ndata atoms with IDs :pre
-
-lmp.scatter_atoms(name,type,count,data)   # scatter per-atom property to all atoms from data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-                                          # count = # of per-atom values, 1 or 3, etc :pre
-lmp.scatter_atoms_subset(name,type,count,ndata,ids,data)  # ditto, but for subset of Ndata atoms with IDs :pre
-
-lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed)   # create N atoms with IDs, types, x, v, and image flags :pre
-
-:line
-
-The lines
-
-from lammps import lammps
-lmp = lammps() :pre
-
-create an instance of LAMMPS, wrapped in a Python class by the lammps
-Python module, and return an instance of the Python class as lmp.  It
-is used to make all subsequent calls to the LAMMPS library.
-
-Additional arguments to lammps() can be used to tell Python the name
-of the shared library to load or to pass arguments to the LAMMPS
-instance, the same as if LAMMPS were launched from a command-line
-prompt.
-
-If the ptr argument is set like this:
-
-lmp = lammps(ptr=lmpptr) :pre
-
-then lmpptr must be an argument passed to Python via the LAMMPS
-"python"_python.html command, when it is used to define a Python
-function that is invoked by the LAMMPS input script.  This mode of
-calling Python from LAMMPS is described in the "Python
-call"_Python_call.html doc page.  The variable lmpptr refers to the
-instance of LAMMPS that called the embedded Python interpreter.  Using
-it as an argument to lammps() allows the returned Python class
-instance "lmp" to make calls to that instance of LAMMPS.  See the
-"python"_python.html command doc page for examples using this syntax.
-
-Note that you can create multiple LAMMPS objects in your Python
-script, and coordinate and run multiple simulations, e.g.
-
-from lammps import lammps
-lmp1 = lammps()
-lmp2 = lammps()
-lmp1.file("in.file1")
-lmp2.file("in.file2") :pre
-
-The file(), command(), commands_list(), commands_string() methods
-allow an input script, a single command, or multiple commands to be
-invoked.
-
-The extract_setting(), extract_global(), extract_box(),
-extract_atom(), extract_compute(), extract_fix(), and
-extract_variable() methods return values or pointers to data
-structures internal to LAMMPS.
-
-For extract_global() see the src/library.cpp file for the list of
-valid names.  New names could easily be added.  A double or integer is
-returned.  You need to specify the appropriate data type via the type
-argument.
-
-For extract_atom(), a pointer to internal LAMMPS atom-based data is
-returned, which you can use via normal Python subscripting.  See the
-extract() method in the src/atom.cpp file for a list of valid names.
-Again, new names could easily be added if the property you want is not
-listed.  A pointer to a vector of doubles or integers, or a pointer to
-an array of doubles (double **) or integers (int **) is returned.  You
-need to specify the appropriate data type via the type argument.
-
-For extract_compute() and extract_fix(), the global, per-atom, or
-local data calculated by the compute or fix can be accessed.  What is
-returned depends on whether the compute or fix calculates a scalar or
-vector or array.  For a scalar, a single double value is returned.  If
-the compute or fix calculates a vector or array, a pointer to the
-internal LAMMPS data is returned, which you can use via normal Python
-subscripting.  The one exception is that for a fix that calculates a
-global vector or array, a single double value from the vector or array
-is returned, indexed by I (vector) or I and J (array).  I,J are
-zero-based indices.  The I,J arguments can be left out if not needed.
-See the "Howto output"_Howto_output.html doc page for a discussion of
-global, per-atom, and local data, and of scalar, vector, and array
-data types.  See the doc pages for individual "computes"_compute.html
-and "fixes"_fix.html for a description of what they calculate and
-store.
-
-For extract_variable(), an "equal-style or atom-style
-variable"_variable.html is evaluated and its result returned.
-
-For equal-style variables a single double value is returned and the
-group argument is ignored.  For atom-style variables, a vector of
-doubles is returned, one value per atom, which you can use via normal
-Python subscripting. The values will be zero for atoms not in the
-specified group.
-
-The get_thermo() method returns the current value of a thermo
-keyword as a float.
-
-The get_natoms() method returns the total number of atoms in the
-simulation, as an int.
-
-The set_variable() method sets an existing string-style variable to a
-new string value, so that subsequent LAMMPS commands can access the
-variable.
-
-The reset_box() method resets the size and shape of the simulation
-box, e.g. as part of restoring a previously extracted and saved state
-of a simulation.
-
-The gather methods collect peratom info of the requested type (atom
-coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each calling processor.  The scatter
-functions do the inverse.  They distribute a vector of peratom values,
-passed by all calling processors, to individual atoms, which may be
-owned by different processors.
-
-Note that the data returned by the gather methods,
-e.g. gather_atoms("x"), is different from the data structure returned
-by extract_atom("x") in four ways.  (1) Gather_atoms() returns a
-vector which you index as x\[i\]; extract_atom() returns an array
-which you index as x\[i\]\[j\].  (2) Gather_atoms() orders the atoms
-by atom ID while extract_atom() does not.  (3) Gather_atoms() returns
-a list of all atoms in the simulation; extract_atoms() returns just
-the atoms local to each processor.  (4) Finally, the gather_atoms()
-data structure is a copy of the atom coords stored internally in
-LAMMPS, whereas extract_atom() returns an array that effectively
-points directly to the internal data.  This means you can change
-values inside LAMMPS from Python by assigning a new values to the
-extract_atom() array.  To do this with the gather_atoms() vector, you
-need to change values in the vector, then invoke the scatter_atoms()
-method.
-
-For the scatter methods, the array of coordinates passed to must be a
-ctypes vector of ints or doubles, allocated and initialized something
-like this:
-
-from ctypes import *
-natoms = lmp.get_natoms()
-n3 = 3*natoms
-x = (n3*c_double)()
-x\[0\] = x coord of atom with ID 1
-x\[1\] = y coord of atom with ID 1
-x\[2\] = z coord of atom with ID 1
-x\[3\] = x coord of atom with ID 2
-...
-x\[n3-1\] = z coord of atom with ID natoms
-lmp.scatter_atoms("x",1,3,x) :pre
-
-Alternatively, you can just change values in the vector returned by
-the gather methods, since they are also ctypes vectors.
-
-:line
-
-As noted above, these Python class methods correspond one-to-one with
-the functions in the LAMMPS library interface in src/library.cpp and
-library.h.  This means you can extend the Python wrapper via the
-following steps:
-
-Add a new interface function to src/library.cpp and
-src/library.h. :ulb,l
-
-Rebuild LAMMPS as a shared library. :l
-
-Add a wrapper method to python/lammps.py for this interface
-function. :l
-
-You should now be able to invoke the new interface function from a
-Python script. :l
-:ule
diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py
index 70a96e1614..a002f5cdcb 100644
--- a/doc/utils/sphinx-config/conf.py
+++ b/doc/utils/sphinx-config/conf.py
@@ -30,7 +30,9 @@ import os
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.mathjax', 'sphinx.ext.imgmath'
+    'sphinx.ext.mathjax',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.autodoc',
 ]
 # 2017-12-07: commented out, since this package is broken with Sphinx 16.x
 #             yet we can no longer use Sphinx 15.x, since that breaks with
@@ -323,3 +325,5 @@ import LAMMPSLexer
 from sphinx.highlighting import lexers
 
 lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
+
+sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python'))

From 93bd2f4ab0cf50fd8dd25c6c4b645ab7ce19fb15 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Wed, 13 Nov 2019 20:46:28 -0700
Subject: [PATCH 025/199] Commit JT 111319 - addind 4 first benchmark examples
 (in examples/SPIN/benchmark) - corrected typo in examples (in dump commands)

---
 .../bench-spin-precession.in                  |    39 +
 .../llg_exchange.py                           |    72 +
 .../plot_precession.py                        |    44 +
 .../benchmarck_damped_exchange/res_lammps.dat |  3001 ++
 .../benchmarck_damped_exchange/res_llg.dat    | 30000 ++++++++++++++++
 .../run-bench-exchange.sh                     |    19 +
 .../benchmarck_damped_exchange/two_spins.data |    22 +
 .../bench-spin-precession.in                  |    48 +
 .../llg_precession.py                         |    51 +
 .../plot_precession.py                        |    39 +
 .../run-bench-prec.sh                         |    19 +
 .../bench-exchange-spin.template              |    41 +
 .../langevin-exchange.py                      |    34 +
 .../plot_exchange.py                          |    34 +
 .../run-bench-exchange.sh                     |    28 +
 .../bench-prec-spin.template                  |    46 +
 .../langevin.py                               |    27 +
 .../plot_precession.py                        |    37 +
 .../run-bench-prec.sh                         |    27 +
 examples/SPIN/bfo/in.spin.bfo                 |     2 +-
 examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc   |     4 +-
 examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp   |     3 +-
 examples/SPIN/iron/in.spin.iron               |     3 +-
 examples/SPIN/iron/in.spin.iron_cubic         |     2 +-
 examples/SPIN/nickel/in.spin.nickel           |     2 +-
 src/SPIN/fix_langevin_spin.cpp                |     3 +-
 src/SPIN/pair_spin_exchange.cpp               |    14 +-
 27 files changed, 33646 insertions(+), 15 deletions(-)
 create mode 100644 examples/SPIN/benchmark/benchmarck_damped_exchange/bench-spin-precession.in
 create mode 100755 examples/SPIN/benchmark/benchmarck_damped_exchange/llg_exchange.py
 create mode 100755 examples/SPIN/benchmark/benchmarck_damped_exchange/plot_precession.py
 create mode 100644 examples/SPIN/benchmark/benchmarck_damped_exchange/res_lammps.dat
 create mode 100644 examples/SPIN/benchmark/benchmarck_damped_exchange/res_llg.dat
 create mode 100755 examples/SPIN/benchmark/benchmarck_damped_exchange/run-bench-exchange.sh
 create mode 100644 examples/SPIN/benchmark/benchmarck_damped_exchange/two_spins.data
 create mode 100644 examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in
 create mode 100755 examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py
 create mode 100755 examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py
 create mode 100755 examples/SPIN/benchmark/benchmarck_damped_precession/run-bench-prec.sh
 create mode 100644 examples/SPIN/benchmark/benchmarck_langevin_exchange/bench-exchange-spin.template
 create mode 100755 examples/SPIN/benchmark/benchmarck_langevin_exchange/langevin-exchange.py
 create mode 100755 examples/SPIN/benchmark/benchmarck_langevin_exchange/plot_exchange.py
 create mode 100755 examples/SPIN/benchmark/benchmarck_langevin_exchange/run-bench-exchange.sh
 create mode 100644 examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template
 create mode 100755 examples/SPIN/benchmark/benchmarck_langevin_precession/langevin.py
 create mode 100755 examples/SPIN/benchmark/benchmarck_langevin_precession/plot_precession.py
 create mode 100755 examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh

diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/bench-spin-precession.in b/examples/SPIN/benchmark/benchmarck_damped_exchange/bench-spin-precession.in
new file mode 100644
index 0000000000..0ca49364d2
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_exchange/bench-spin-precession.in
@@ -0,0 +1,39 @@
+#LAMMPS in.run 
+ 
+units           metal
+atom_style      spin
+atom_modify     map array
+boundary        f f f 
+
+read_data	two_spins.data
+
+pair_style      spin/exchange 3.1
+pair_coeff	* * exchange 3.1 11.254 0.0 1.0
+
+group bead      type 1  
+ 
+variable        H equal 0.0
+variable        Kan equal 0.0
+variable        Temperature equal 0.0 
+variable        RUN equal 30000
+
+fix             1 all nve/spin lattice no
+fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
+fix_modify      2 energy yes
+fix             3 all langevin/spin ${Temperature} 0.01 12345
+
+compute		out_mag    all spin
+compute		out_pe     all pe
+
+variable	magx      equal c_out_mag[1]
+variable	magy      equal c_out_mag[2]
+variable	magz      equal c_out_mag[3]
+variable	magnorm   equal c_out_mag[4]
+variable	emag      equal c_out_mag[5]
+
+thermo_style    custom step time v_magx v_magy v_magz v_emag pe etotal
+thermo          10
+
+timestep	0.0001
+
+run             ${RUN}
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/llg_exchange.py b/examples/SPIN/benchmark/benchmarck_damped_exchange/llg_exchange.py
new file mode 100755
index 0000000000..a8639925f6
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_exchange/llg_exchange.py
@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+
+import numpy as np , pylab, tkinter
+import math
+import matplotlib.pyplot as plt
+import mpmath as mp
+
+hbar=0.658212           # Planck's constant (eV.fs/rad)
+J0=0.05                 # per-neighbor exchange interaction (eV)
+S1 = np.array([1.0, 0.0, 0.0])
+S2 = np.array([0.0, 1.0, 0.0])
+alpha=0.01              # damping coefficient
+pi=math.pi
+
+N=30000                 # number of timesteps
+dt=0.1                  # timestep (fs)
+
+# Rodrigues rotation formula
+def rotation_matrix(axis, theta):
+  """
+  Return the rotation matrix associated with counterclockwise
+  rotation about the given axis by theta radians
+  """
+  axis = np.asarray(axis)
+  a = math.cos(theta / 2.0)
+  b, c, d = -axis * math.sin(theta / 2.0)
+  aa, bb, cc, dd = a * a, b * b, c * c, d * d
+  bc, ad, ac, ab, bd, cd = b * c, a * d, a * c, a * b, b * d, c * d
+  return np.array([[aa + bb - cc - dd, 2 * (bc + ad), 2 * (bd - ac)],
+      [2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
+      [2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
+
+# calculating precession field of spin Sr
+def calc_rot_vector(Sr,Sf):
+  rot = (J0/hbar)*(Sf-alpha*np.cross(Sf,Sr))/(1.0+alpha**2)
+  return rot
+  
+# second-order ST decomposition as implemented in LAMMPS 
+for t in range (0,N):
+  # advance s1 by dt/4
+  wf1 = calc_rot_vector(S1,S2)
+  theta=dt*np.linalg.norm(wf1)*0.25
+  axis=wf1/np.linalg.norm(wf1)
+  S1 = np.dot(rotation_matrix(axis, theta), S1)
+  # advance s2 by dt/2
+  wf2 = calc_rot_vector(S2,S1)
+  theta=dt*np.linalg.norm(wf2)*0.5
+  axis=wf2/np.linalg.norm(wf2)
+  S2 = np.dot(rotation_matrix(axis, theta), S2)
+  # advance s1 by dt/2
+  wf1 = calc_rot_vector(S1,S2)
+  theta=dt*np.linalg.norm(wf1)*0.5
+  axis=wf1/np.linalg.norm(wf1)
+  S1 = np.dot(rotation_matrix(axis, theta), S1)
+  # advance s2 by dt/2
+  wf2 = calc_rot_vector(S2,S1)
+  theta=dt*np.linalg.norm(wf2)*0.5
+  axis=wf2/np.linalg.norm(wf2)
+  S2 = np.dot(rotation_matrix(axis, theta), S2)
+  # advance s1 by dt/4
+  wf1 = calc_rot_vector(S1,S2)
+  theta=dt*np.linalg.norm(wf1)*0.25
+  axis=wf1/np.linalg.norm(wf1)
+  S1 = np.dot(rotation_matrix(axis, theta), S1)
+  # calc. average magnetization
+  Sm = (S1+S2)*0.5
+  # calc. energy
+  # en = -hbar*(np.dot(S1,wf1)+np.dot(S2,wf2))
+  en = -2.0*J0*(np.dot(S1,S2))
+  # print res. in ps for comparison with LAMMPS
+  print(t*dt/1000.0,Sm[0],Sm[1],Sm[2],en)
+  # print(t*dt/1000.0,S1[0],S2[0],S1[1],S2[1],S1[2],S2[2],en)
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/plot_precession.py b/examples/SPIN/benchmark/benchmarck_damped_exchange/plot_precession.py
new file mode 100755
index 0000000000..6c8afca569
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_exchange/plot_precession.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+import sys, string, os
+
+
+argv = sys.argv
+if len(argv) != 3:
+  print("Syntax: ./plot_precession.py res_lammps.dat res_llg.dat")
+  sys.exit()
+
+lammps_file = sys.argv[1]
+llg_file = sys.argv[2]
+
+t_lmp,Sx_lmp,Sy_lmp,Sz_lmp,e_lmp = np.loadtxt(lammps_file,skiprows=0, usecols=(1,2,3,4,5),unpack=True)
+t_llg,Sx_llg,Sy_llg,Sz_llg,e_llg = np.loadtxt(llg_file,skiprows=0, usecols=(0,1,2,3,4),unpack=True)
+
+plt.figure()
+plt.subplot(411)
+plt.ylabel('Sx')
+plt.plot(t_lmp, Sx_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sx_llg, 'r--', label='LLG')
+
+plt.subplot(412)
+plt.ylabel('Sy')
+plt.plot(t_lmp, Sy_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sy_llg, 'r--', label='LLG')
+
+plt.subplot(413)
+plt.ylabel('Sz')
+plt.plot(t_lmp, Sz_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sz_llg, 'r--', label='LLG')
+
+plt.subplot(414)
+plt.ylabel('E (eV)')
+plt.plot(t_lmp, e_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, e_llg, 'r--', label='LLG')
+
+plt.xlabel('time (in ps)')
+plt.legend()
+plt.show()
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/res_lammps.dat b/examples/SPIN/benchmark/benchmarck_damped_exchange/res_lammps.dat
new file mode 100644
index 0000000000..aa331f50ea
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_exchange/res_lammps.dat
@@ -0,0 +1,3001 @@
+       0            0          0.5          0.5            0            0            0            0 
+      10        0.001   0.50037967   0.50037966 6.8386474e-08 -0.00015191886 -0.00015191886 -0.00015191886 
+      20        0.002   0.50075905   0.50075902 1.3603286e-07 -0.00030383701 -0.00030383701 -0.00030383701 
+      30        0.003   0.50113814   0.50113809 2.0215189e-07 -0.00045575377 -0.00045575377 -0.00045575377 
+      40        0.004   0.50151695   0.50151686 2.6596985e-07 -0.00060766842 -0.00060766842 -0.00060766842 
+      50        0.005   0.50189547   0.50189534 3.2673578e-07 -0.00075958028 -0.00075958028 -0.00075958028 
+      60        0.006    0.5022737   0.50227351 3.8373034e-07 -0.00091148862 -0.00091148862 -0.00091148862 
+      70        0.007   0.50265165   0.50265139 4.3627448e-07 -0.0010633928 -0.0010633928 -0.0010633928 
+      80        0.008   0.50302929   0.50302897 4.8373764e-07 -0.001215292 -0.001215292 -0.001215292 
+      90        0.009   0.50340665   0.50340624 5.2554551e-07 -0.0013671856 -0.0013671856 -0.0013671856 
+     100         0.01   0.50378371   0.50378322 5.6118711e-07 -0.001519073 -0.001519073 -0.001519073 
+     110        0.011   0.50416047   0.50415989 5.9022131e-07 -0.0016709533 -0.0016709533 -0.0016709533 
+     120        0.012   0.50453694   0.50453626 6.1228239e-07 -0.0018228259 -0.0018228259 -0.0018228259 
+     130        0.013    0.5049131   0.50491233 6.2708498e-07 -0.0019746901 -0.0019746901 -0.0019746901 
+     140        0.014   0.50528896   0.50528809 6.3442788e-07 -0.0021265452 -0.0021265452 -0.0021265452 
+     150        0.015   0.50566452   0.50566355 6.3419702e-07 -0.0022783904 -0.0022783904 -0.0022783904 
+     160        0.016   0.50603978   0.50603871 6.2636743e-07 -0.0024302252 -0.0024302252 -0.0024302252 
+     170        0.017   0.50641473   0.50641356 6.1100409e-07 -0.0025820488 -0.0025820488 -0.0025820488 
+     180        0.018   0.50678937   0.50678811 5.8826175e-07 -0.0027338604 -0.0027338604 -0.0027338604 
+     190        0.019    0.5071637   0.50716235 5.5838372e-07 -0.0028856595 -0.0028856595 -0.0028856595 
+     200         0.02   0.50753772   0.50753628 5.2169947e-07 -0.0030374452 -0.0030374452 -0.0030374452 
+     210        0.021   0.50791142   0.50790991 4.7862136e-07 -0.0031892169 -0.0031892169 -0.0031892169 
+     220        0.022   0.50828482   0.50828322 4.2964016e-07 -0.0033409739 -0.0033409739 -0.0033409739 
+     230        0.023   0.50865789   0.50865624 3.7531975e-07 -0.0034927156 -0.0034927156 -0.0034927156 
+     240        0.024   0.50903065   0.50902894 3.1629077e-07 -0.0036444411 -0.0036444411 -0.0036444411 
+     250        0.025   0.50940309   0.50940133 2.5324353e-07 -0.0037961498 -0.0037961498 -0.0037961498 
+     260        0.026   0.50977521   0.50977342 1.8692008e-07 -0.003947841 -0.003947841 -0.003947841 
+     270        0.027   0.51014701   0.51014519 1.1810555e-07 -0.0040995141 -0.0040995141 -0.0040995141 
+     280        0.028   0.51051849   0.51051665 4.7619044e-08 -0.0042511682 -0.0042511682 -0.0042511682 
+     290        0.029   0.51088964    0.5108878 -2.3696119e-08 -0.0044028027 -0.0044028027 -0.0044028027 
+     300         0.03   0.51126047   0.51125863 -9.4982408e-08 -0.004554417 -0.004554417 -0.004554417 
+     310        0.031   0.51163097   0.51162915 -1.653784e-07 -0.0047060103 -0.0047060103 -0.0047060103 
+     320        0.032   0.51200115   0.51199936 -2.3402922e-07 -0.0048575819 -0.0048575819 -0.0048575819 
+     330        0.033     0.512371   0.51236925 -3.0009692e-07 -0.0050091312 -0.0050091312 -0.0050091312 
+     340        0.034   0.51274052   0.51273882 -3.6277088e-07 -0.0051606574 -0.0051606574 -0.0051606574 
+     350        0.035   0.51310971   0.51310807 -4.2127775e-07 -0.0053121598 -0.0053121598 -0.0053121598 
+     360        0.036   0.51347857     0.513477 -4.7489123e-07 -0.0054636378 -0.0054636378 -0.0054636378 
+     370        0.037   0.51384711   0.51384561 -5.2294115e-07 -0.0056150906 -0.0056150906 -0.0056150906 
+     380        0.038   0.51421531   0.51421389 -5.6482212e-07 -0.0057665177 -0.0057665177 -0.0057665177 
+     390        0.039   0.51458318   0.51458185 -6.0000127e-07 -0.0059179181 -0.0059179181 -0.0059179181 
+     400         0.04   0.51495072   0.51494949 -6.2802531e-07 -0.0060692914 -0.0060692914 -0.0060692914 
+     410        0.041   0.51531793   0.51531679 -6.4852657e-07 -0.0062206367 -0.0062206367 -0.0062206367 
+     420        0.042   0.51568481   0.51568377 -6.6122807e-07 -0.0063719535 -0.0063719535 -0.0063719535 
+     430        0.043   0.51605135   0.51605041 -6.659475e-07 -0.0065232409 -0.0065232409 -0.0065232409 
+     440        0.044   0.51641756   0.51641673 -6.6260004e-07 -0.0066744984 -0.0066744984 -0.0066744984 
+     450        0.045   0.51678344   0.51678271 -6.5120005e-07 -0.0068257252 -0.0068257252 -0.0068257252 
+     460        0.046   0.51714898   0.51714835 -6.3186146e-07 -0.0069769206 -0.0069769206 -0.0069769206 
+     470        0.047   0.51751419   0.51751365 -6.0479702e-07 -0.007128084 -0.007128084 -0.007128084 
+     480        0.048   0.51787906   0.51787862 -5.7031623e-07 -0.0072792147 -0.0072792147 -0.0072792147 
+     490        0.049   0.51824361   0.51824324 -5.2882208e-07 -0.0074303119 -0.0074303119 -0.0074303119 
+     500         0.05   0.51860781   0.51860753 -4.8080667e-07 -0.0075813751 -0.0075813751 -0.0075813751 
+     510        0.051   0.51897168   0.51897147 -4.2684553e-07 -0.0077324034 -0.0077324034 -0.0077324034 
+     520        0.052   0.51933522   0.51933506 -3.6759103e-07 -0.0078833963 -0.0078833963 -0.0078833963 
+     530        0.053   0.51969841   0.51969831 -3.0376461e-07 -0.008034353 -0.008034353 -0.008034353 
+     540        0.054   0.52006127   0.52006121 -2.3614824e-07 -0.0081852728 -0.0081852728 -0.0081852728 
+     550        0.055    0.5204238   0.52042377 -1.6557495e-07 -0.0083361551 -0.0083361551 -0.0083361551 
+     560        0.056   0.52078598   0.52078597 -9.2918676e-08 -0.0084869992 -0.0084869992 -0.0084869992 
+     570        0.057   0.52114783   0.52114782 -1.9083552e-08 -0.0086378045 -0.0086378045 -0.0086378045 
+     580        0.058   0.52150933   0.52150932 5.5007325e-08 -0.0087885701 -0.0087885701 -0.0087885701 
+     590        0.059    0.5218705   0.52187047 1.2842339e-07 -0.0089392955 -0.0089392955 -0.0089392955 
+     600         0.06   0.52223132   0.52223127 2.0023832e-07  -0.00908998  -0.00908998  -0.00908998 
+     610        0.061    0.5225918   0.52259171 2.6954176e-07 -0.0092406228 -0.0092406228 -0.0092406228 
+     620        0.062   0.52295193   0.52295179 3.3545095e-07 -0.0093912234 -0.0093912234 -0.0093912234 
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+   29090        2.909   0.70705618   0.70705488 5.1194459e-09 -0.099968493 -0.099968493 -0.099968493 
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+   29230        2.923   0.70705831   0.70705702 -3.223323e-08   -0.0999697   -0.0999697   -0.0999697 
+   29240        2.924   0.70705845   0.70705717 -3.326215e-08 -0.099969784 -0.099969784 -0.099969784 
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+   29260        2.926   0.70705875   0.70705747 -3.3883892e-08 -0.099969952 -0.099969952 -0.099969952 
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+   29310        2.931   0.70705947   0.70705822 -2.7309908e-08 -0.099970367 -0.099970367 -0.099970367 
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+   29400         2.94   0.70706076   0.70705951 -1.039834e-09 -0.099971099 -0.099971099 -0.099971099 
+   29410        2.941    0.7070609   0.70705965 1.3889902e-09 -0.099971179 -0.099971179 -0.099971179 
+   29420        2.942   0.70706105   0.70705979 3.4852534e-09 -0.099971258 -0.099971258 -0.099971258 
+   29430        2.943   0.70706119   0.70705993 5.2017475e-09 -0.099971338 -0.099971338 -0.099971338 
+   29440        2.944   0.70706133   0.70706007 6.5001432e-09 -0.099971417 -0.099971417 -0.099971417 
+   29450        2.945   0.70706147   0.70706021 7.3518435e-09 -0.099971496 -0.099971496 -0.099971496 
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+   29470        2.947   0.70706176   0.70706048 7.652965e-09 -0.099971654 -0.099971654 -0.099971654 
+   29480        2.948    0.7070619   0.70706062 7.0983021e-09 -0.099971732 -0.099971732 -0.099971732 
+   29490        2.949   0.70706204   0.70706075 6.0888041e-09  -0.09997181  -0.09997181  -0.09997181 
+   29500         2.95   0.70706218   0.70706089 4.6490695e-09 -0.099971888 -0.099971888 -0.099971888 
+   29510        2.951   0.70706232   0.70706102 2.8135184e-09 -0.099971966 -0.099971966 -0.099971966 
+   29520        2.952   0.70706245   0.70706116 6.2557025e-10 -0.099972043 -0.099972043 -0.099972043 
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+   29550        2.955   0.70706287   0.70706156 -7.5062397e-09 -0.099972274 -0.099972274 -0.099972274 
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+   29650        2.965   0.70706419   0.70706291 -3.1716065e-08 -0.099973028 -0.099973028 -0.099973028 
+   29660        2.966   0.70706432   0.70706304 -3.2398677e-08 -0.099973103 -0.099973103 -0.099973103 
+   29670        2.967   0.70706445   0.70706317 -3.2627263e-08 -0.099973177 -0.099973177 -0.099973177 
+   29680        2.968   0.70706458    0.7070633 -3.2397941e-08  -0.09997325  -0.09997325  -0.09997325 
+   29690        2.969    0.7070647   0.70706344 -3.1717375e-08 -0.099973324 -0.099973324 -0.099973324 
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+   29740        2.974   0.70706534   0.70706409 -2.2474306e-08 -0.099973688 -0.099973688 -0.099973688 
+   29750        2.975   0.70706547   0.70706422 -1.9764448e-08  -0.09997376  -0.09997376  -0.09997376 
+   29760        2.976   0.70706559   0.70706435 -1.6901455e-08 -0.099973832 -0.099973832 -0.099973832 
+   29770        2.977   0.70706572   0.70706447 -1.3951642e-08 -0.099973904 -0.099973904 -0.099973904 
+   29780        2.978   0.70706585    0.7070646 -1.0983123e-08 -0.099973975 -0.099973975 -0.099973975 
+   29790        2.979   0.70706597   0.70706472 -8.0642345e-09 -0.099974047 -0.099974047 -0.099974047 
+   29800         2.98    0.7070661   0.70706485 -5.2619636e-09 -0.099974118 -0.099974118 -0.099974118 
+   29810        2.981   0.70706623   0.70706497 -2.6404129e-09 -0.099974189 -0.099974189 -0.099974189 
+   29820        2.982   0.70706635    0.7070651 -2.593337e-10 -0.099974259 -0.099974259 -0.099974259 
+   29830        2.983   0.70706648   0.70706522 1.8272352e-09  -0.09997433  -0.09997433  -0.09997433 
+   29840        2.984    0.7070666   0.70706534 3.5721929e-09   -0.0999744   -0.0999744   -0.0999744 
+   29850        2.985   0.70706673   0.70706547 4.9364389e-09  -0.09997447  -0.09997447  -0.09997447 
+   29860        2.986   0.70706685   0.70706559 5.889748e-09  -0.09997454  -0.09997454  -0.09997454 
+   29870        2.987   0.70706698   0.70706571 6.4114388e-09  -0.09997461  -0.09997461  -0.09997461 
+   29880        2.988    0.7070671   0.70706583 6.4908206e-09 -0.099974679 -0.099974679 -0.099974679 
+   29890        2.989   0.70706723   0.70706595 6.1274086e-09 -0.099974748 -0.099974748 -0.099974748 
+   29900         2.99   0.70706735   0.70706607 5.3309045e-09 -0.099974817 -0.099974817 -0.099974817 
+   29910        2.991   0.70706748   0.70706619 4.120942e-09 -0.099974886 -0.099974886 -0.099974886 
+   29920        2.992    0.7070676   0.70706631 2.5266059e-09 -0.099974954 -0.099974954 -0.099974954 
+   29930        2.993   0.70706772   0.70706643 5.8573349e-10 -0.099975023 -0.099975023 -0.099975023 
+   29940        2.994   0.70706784   0.70706655 -1.6559816e-09 -0.099975091 -0.099975091 -0.099975091 
+   29950        2.995   0.70706796   0.70706666 -4.1460645e-09 -0.099975159 -0.099975159 -0.099975159 
+   29960        2.996   0.70706808   0.70706678 -6.8264867e-09 -0.099975227 -0.099975227 -0.099975227 
+   29970        2.997    0.7070682    0.7070669 -9.6350175e-09 -0.099975294 -0.099975294 -0.099975294 
+   29980        2.998   0.70706832   0.70706702 -1.2506668e-08 -0.099975361 -0.099975361 -0.099975361 
+   29990        2.999   0.70706844   0.70706714 -1.5375195e-08 -0.099975428 -0.099975428 -0.099975428 
+   30000            3   0.70706856   0.70706726 -1.8174628e-08 -0.099975495 -0.099975495 -0.099975495 
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/res_llg.dat b/examples/SPIN/benchmark/benchmarck_damped_exchange/res_llg.dat
new file mode 100644
index 0000000000..6150a7db80
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_exchange/res_llg.dat
@@ -0,0 +1,30000 @@
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diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/run-bench-exchange.sh b/examples/SPIN/benchmark/benchmarck_damped_exchange/run-bench-exchange.sh
new file mode 100755
index 0000000000..15de8d350e
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_exchange/run-bench-exchange.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# clean old res
+rm res_*.dat
+
+# compute Lammps 
+./../../../../src/lmp_serial \
+  -in bench-spin-precession.in 
+in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
+en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
+in="$(echo "$in+1" | bc -l)"
+en="$(echo "$en-$in" | bc -l)"
+tail -n +$in log.lammps | head -n $en > res_lammps.dat
+
+# compute Langevin
+python3 -m llg_exchange.py > res_llg.dat
+
+# plot results
+python3 -m plot_precession.py res_lammps.dat res_llg.dat
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/two_spins.data b/examples/SPIN/benchmark/benchmarck_damped_exchange/two_spins.data
new file mode 100644
index 0000000000..013f813751
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_exchange/two_spins.data
@@ -0,0 +1,22 @@
+LAMMPS data file via write_data, version 19 Sep 2019, timestep = 0
+
+2 atoms
+1 atom types
+
+0.0 6.0 xlo xhi
+0.0 3.0 ylo yhi
+0.0 3.0 zlo zhi
+
+Masses
+
+1 1
+
+Atoms # spin
+
+1 1 2.0 0.0 0.0 0.0 1.0 0.0 0.0 0 0 0
+2 1 2.0 3.0 0.0 0.0 0.0 1.0 0.0 0 0 0
+
+Velocities
+
+1 0.0 0.0 0.0
+2 0.0 0.0 0.0
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in b/examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in
new file mode 100644
index 0000000000..37d1e3765a
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in
@@ -0,0 +1,48 @@
+#LAMMPS in.run 
+ 
+units           metal
+atom_style      spin
+atom_modify     map array
+boundary        p p p
+
+# read_data     singlespin.data
+
+lattice         sc 3.0
+region          box block 0.0 1.0 0.0 1.0 0.0 1.0
+create_box      1 box
+create_atoms    1 box
+
+mass            1 1.0
+set             type 1 spin 2.0 1.0 0.0 0.0
+
+# defines a pair/style for neighbor list, but do not use it
+pair_style      spin/exchange 4.0
+pair_coeff      * * exchange 1.0 0.0 0.0 1.0
+
+group bead      type 1  
+ 
+variable        H equal 10.0
+variable        Kan equal 0.0
+variable        Temperature equal 0.0 
+variable        RUN equal 100000
+
+fix             1 all nve/spin lattice no
+fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
+fix_modify      2 energy yes
+fix             3 all langevin/spin ${Temperature} 0.01 12345
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+
+thermo_style    custom step time v_magx v_magy v_magz v_emag pe etotal
+thermo          100
+
+timestep	0.0001
+
+run             ${RUN}
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py b/examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py
new file mode 100755
index 0000000000..edaa4f22cc
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+
+import numpy as np , pylab, tkinter
+import math
+import matplotlib.pyplot as plt
+import mpmath as mp
+
+mub=5.78901e-5          # Bohr magneton (eV/T)
+hbar=0.658212           # Planck's constant (eV.fs/rad)
+g=2.0                   # Lande factor (adim)
+gyro=g*mub/hbar         # gyromag ratio (rad/fs/T)
+alpha=0.01              # damping coefficient
+pi=math.pi
+
+Bnrm=10.0               # mag. field (T)
+Bext = np.array([0.0, 0.0, 1.0])
+Sn = 2.0                # spin norm (in # of muB)
+S = np.array([1.0, 0.0, 0.0])
+
+N=100000                # number of timesteps
+dt=0.1                  # timestep (fs)
+
+# Rodrigues rotation formula
+def rotation_matrix(axis, theta):
+  """
+  Return the rotation matrix associated with counterclockwise
+  rotation about the given axis by theta radians
+  """
+  axis = np.asarray(axis)
+  a = math.cos(theta / 2.0)
+  b, c, d = -axis * math.sin(theta / 2.0)
+  aa, bb, cc, dd = a * a, b * b, c * c, d * d
+  bc, ad, ac, ab, bd, cd = b * c, a * d, a * c, a * b, b * d, c * d
+  return np.array([[aa + bb - cc - dd, 2 * (bc + ad), 2 * (bd - ac)],
+      [2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
+      [2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
+
+# calc. precession field
+def calc_rot_vector(Fi,Sp):
+  rot = gyro*Sn*Bnrm*(Fi-alpha*np.cross(Fi,Sp))
+  return rot
+  
+# np.set_printoptions(precision=4)
+for t in range (0,N):
+  wf = calc_rot_vector(Bext,S)
+  theta=dt*np.linalg.norm(wf)
+  axis=wf/np.linalg.norm(wf)
+  S = np.dot(rotation_matrix(axis, theta), S)
+  # print res. in ps for comparison with LAMMPS
+  print(t*dt/1000.0,S[0],S[1],S[2])
+
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py b/examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py
new file mode 100755
index 0000000000..c15d6c0ff5
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py
@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+import sys, string, os
+
+
+argv = sys.argv
+if len(argv) != 3:
+  print("Syntax: ./plot_precession.py res_lammps.dat res_llg.dat")
+  sys.exit()
+
+lammps_file = sys.argv[1]
+llg_file = sys.argv[2]
+
+t_lmp,Sx_lmp,Sy_lmp,Sz_lmp = np.loadtxt(lammps_file, skiprows=0, usecols=(1,2,3,4),unpack=True)
+t_llg,Sx_llg,Sy_llg,Sz_llg = np.loadtxt(llg_file, skiprows=0, usecols=(0,1,2,3),unpack=True)
+
+plt.figure()
+plt.subplot(311)
+plt.ylabel('Sx')
+plt.plot(t_lmp, Sx_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sx_llg, 'r--', label='LLG')
+
+plt.subplot(312)
+plt.ylabel('Sy')
+plt.plot(t_lmp, Sy_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sy_llg, 'r--', label='LLG')
+
+plt.subplot(313)
+plt.ylabel('Sz')
+plt.plot(t_lmp, Sz_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sz_llg, 'r--', label='LLG')
+
+plt.xlabel('time (in ps)')
+plt.legend()
+plt.show()
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/run-bench-prec.sh b/examples/SPIN/benchmark/benchmarck_damped_precession/run-bench-prec.sh
new file mode 100755
index 0000000000..49ebc2ac4e
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_damped_precession/run-bench-prec.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# clean old res
+rm res_*.dat
+
+# compute Lammps 
+./../../../../src/lmp_serial \
+  -in bench-spin-precession.in 
+in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
+en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
+in="$(echo "$in+1" | bc -l)"
+en="$(echo "$en-$in" | bc -l)"
+tail -n +$in log.lammps | head -n $en > res_lammps.dat
+
+# compute Langevin
+python3 -m llg_precession.py > res_llg.dat
+
+# plot results
+python3 -m plot_precession.py res_lammps.dat res_llg.dat
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_exchange/bench-exchange-spin.template b/examples/SPIN/benchmark/benchmarck_langevin_exchange/bench-exchange-spin.template
new file mode 100644
index 0000000000..c4286e3597
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_langevin_exchange/bench-exchange-spin.template
@@ -0,0 +1,41 @@
+#LAMMPS in.run 
+ 
+units           metal
+atom_style      spin
+atom_modify     map array
+boundary        p p p
+
+lattice         sc 3.0
+region          box block 0.0 2.0 0.0 2.0 0.0 2.0
+create_box      1 box
+create_atoms    1 box
+
+mass            1 1.0
+set             type 1 spin 1.0 0.0 0.0 1.0
+
+# defines a pair/style for neighbor list, but do not use it
+pair_style      spin/exchange 3.1
+pair_coeff  	* * exchange 3.1 11.254 0.0 1.0
+
+variable        H equal 0.0
+variable        Kan equal 0.0
+variable        Temperature equal temperature
+variable        RUN equal 100000
+
+fix             1 all nve/spin lattice no
+fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
+fix             3 all langevin/spin ${Temperature} 0.01 12345
+
+thermo          500000
+thermo_style    custom step time temp vol 
+timestep        0.1
+
+compute         compute_spin all spin
+variable 	mag_energy equal c_compute_spin[5]
+variable 	AVEs equal c_compute_spin[4]
+
+fix 		avespin all ave/time 1 ${RUN} ${RUN} v_Temperature v_H v_Kan v_AVEs v_mag_energy file _av_spin
+
+run             ${RUN}
+
+shell           cat _av_spin
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_exchange/langevin-exchange.py b/examples/SPIN/benchmark/benchmarck_langevin_exchange/langevin-exchange.py
new file mode 100755
index 0000000000..d543f86cba
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_langevin_exchange/langevin-exchange.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+import mpmath as mp
+
+mub=5.78901e-5          # Bohr magneton (eV/T)
+kb=8.617333262145e-5    # Boltzman constant (eV/K)
+J0=0.05                 # per-neighbor exchange interaction (eV)
+z=6                     # number of NN (bcc)
+g=2.0                   # Lande factor (adim)
+Hz=10.0                # mag. field (T)
+
+#Definition of the Langevin function
+def func(sm,t):
+    return mp.coth(z*J0*sm/(kb*t))-1.0/(z*J0*sm/(kb*t))
+
+npoints=200
+tolerance=1e-5
+ti=0.01
+tf=2000.0
+sz=1.0
+szg=0.5
+for i in range (0,npoints):
+    temp=ti+i*(tf-ti)/npoints
+    count=0
+    sz=1.0
+    szg=0.5
+    while (abs(sz-szg)) >= tolerance:
+        sz=szg
+        szg=func(sz,temp)
+        count+=1
+    emag=-z*J0*sz*sz
+    print('%d %lf %lf %lf %lf' % (temp,szg,sz,emag,count))
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_exchange/plot_exchange.py b/examples/SPIN/benchmark/benchmarck_langevin_exchange/plot_exchange.py
new file mode 100755
index 0000000000..8fa6f55589
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_langevin_exchange/plot_exchange.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+import sys, string, os
+
+
+argv = sys.argv
+if len(argv) != 3:
+  print("Syntax: ./plot_precession.py res_lammps.dat res_langevin.dat")
+  sys.exit()
+
+lammps_file = sys.argv[1]
+langevin_file = sys.argv[2]
+
+T_lmp,S_lmp,E_lmp = np.loadtxt(lammps_file, skiprows=0, usecols=(0,2,3),unpack=True)
+T_lan,S_lan,E_lan = np.loadtxt(langevin_file, skiprows=0, usecols=(0,2,3),unpack=True)
+
+plt.figure()
+plt.subplot(211)
+plt.ylabel('<S>')
+plt.plot(T_lmp, S_lmp, 'b-', label='LAMMPS')
+plt.plot(T_lan, S_lan, 'r--', label='Langevin')
+
+plt.subplot(212)
+plt.ylabel('E (in eV)')
+plt.plot(T_lmp, E_lmp, 'b-', label='LAMMPS')
+plt.plot(T_lan, E_lan, 'r--', label='Langevin')
+
+plt.xlabel('T (in K)')
+plt.legend()
+plt.show()
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_exchange/run-bench-exchange.sh b/examples/SPIN/benchmark/benchmarck_langevin_exchange/run-bench-exchange.sh
new file mode 100755
index 0000000000..d631fdbc79
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_langevin_exchange/run-bench-exchange.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+# set initial and final temperature (K)
+tempi=0.0
+tempf=2000.0
+
+rm res_*.dat
+
+# run Lammps calculation
+N=20
+for (( i=0; i<$N; i++ ))
+do
+  temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)"
+  sed s/temperature/${temp}/g bench-exchange-spin.template > \
+    bench-exchange-spin.in
+  ../../../../src/lmp_serial \
+    -in bench-exchange-spin.in 
+  Hz="$(tail -n 1 _av_spin | awk -F " " '{print $3}')"
+  sm="$(tail -n 1 _av_spin | awk -F " " '{print $5}')"
+  en="$(tail -n 1 _av_spin | awk -F " " '{print $6}')"
+  echo $temp $Hz $sm $en >> res_lammps.dat
+done
+
+# run Langevin function calculation
+python3 -m langevin-exchange.py > res_langevin.dat
+
+# plot comparison
+python3 -m plot_exchange.py res_lammps.dat res_langevin.dat
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template b/examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template
new file mode 100644
index 0000000000..6e79fe9d25
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template
@@ -0,0 +1,46 @@
+#LAMMPS in.run 
+ 
+units           metal
+atom_style      spin
+atom_modify     map array
+boundary        p p p
+
+# read_data     singlespin.data
+
+lattice         sc 3.0
+region          box block 0.0 1.0 0.0 1.0 0.0 1.0
+create_box      1 box
+create_atoms    1 box
+
+mass            1 1.0
+set             type 1 spin 1.0 0.0 0.0 1.0
+
+# defines a pair/style for neighbor list, but do not use it
+pair_style      spin/exchange 4.0
+pair_coeff      * * exchange 1.0 0.0 0.0 1.0
+
+group bead      type 1  
+ 
+variable        H equal 10.0
+variable        Kan equal 0.0
+variable        Temperature equal temperature
+variable        RUN equal 1000000
+
+fix             1 all nve/spin lattice no
+fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
+fix_modify      2 energy yes
+fix             3 all langevin/spin ${Temperature} 0.01 12345
+
+compute         compute_spin all spin
+compute         outsp all property/atom spx spy spz sp
+compute         AVEsz all reduce ave c_outsp[3]
+
+thermo          50000
+thermo_style    custom step time temp vol pe c_compute_spin[5] etotal  
+
+variable        magnetic_energy equal c_compute_spin[5]
+
+fix             avespin all ave/time 1 ${RUN} ${RUN} v_Temperature v_H v_Kan c_AVEsz v_magnetic_energy file _av_spin
+
+timestep        0.1
+run             ${RUN}
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/langevin.py b/examples/SPIN/benchmark/benchmarck_langevin_precession/langevin.py
new file mode 100755
index 0000000000..7acb780143
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_langevin_precession/langevin.py
@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+
+#Program fitting the exchange interaction
+#Model curve: Bethe-Slater function
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+import mpmath as mp
+# from scipy.optimize import curve_fit
+# from decimal import *
+
+mub=5.78901e-5          # Bohr magneton (eV/T)
+kb=8.617333262145e-5    # Boltzman constant (eV/K)
+g=2.0                   # Lande factor (adim)
+
+Hz=10.0                # mag. field (T)
+
+#Definition of the Langevin function
+def func(t):
+    return mp.coth(g*mub*Hz/(kb*t))-1.0/(g*mub*Hz/(kb*t))
+
+npoints=200
+ti=0.01
+tf=20.0
+for i in range (0,npoints): 
+    temp=ti+i*(tf-ti)/npoints
+    print('%lf %lf %lf' % (temp,func(temp),-g*mub*Hz*func(temp)))
+
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/plot_precession.py b/examples/SPIN/benchmark/benchmarck_langevin_precession/plot_precession.py
new file mode 100755
index 0000000000..0141af56a0
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_langevin_precession/plot_precession.py
@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+
+#Program fitting the exchange interaction
+#Model curve: Bethe-Slater function
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+import sys, string, os
+
+
+argv = sys.argv
+if len(argv) != 3:
+  print("Syntax: ./plot_precession.py res_lammps.dat res_langevin.dat")
+  sys.exit()
+
+lammps_file = sys.argv[1]
+langevin_file = sys.argv[2]
+
+T_lmp,S_lmp,E_lmp = np.loadtxt(lammps_file, skiprows=0, usecols=(0,2,3),unpack=True)
+T_lan,S_lan,E_lan = np.loadtxt(langevin_file, skiprows=0, usecols=(0,1,2),unpack=True)
+
+plt.figure()
+plt.subplot(211)
+plt.ylabel('<Sz>')
+plt.plot(T_lmp, S_lmp, 'b-', label='LAMMPS')
+plt.plot(T_lan, S_lan, 'r--', label='Langevin')
+
+plt.subplot(212)
+plt.ylabel('E (in eV)')
+plt.plot(T_lmp, E_lmp, 'b-', label='LAMMPS')
+plt.plot(T_lan, E_lan, 'r--', label='Langevin')
+
+plt.xlabel('T (in K)')
+pylab.xlim([0,20.0])
+plt.legend()
+plt.show()
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh b/examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh
new file mode 100755
index 0000000000..ecbe7d2eff
--- /dev/null
+++ b/examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+tempi=0.0
+tempf=20.0
+
+rm res_*.dat
+
+# compute Lammps 
+N=20
+for (( i=0; i<$N; i++ ))
+do
+  temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)"
+  sed s/temperature/${temp}/g bench-prec-spin.template > \
+    bench-prec-spin.in
+  ./../../../../src/lmp_serial \
+    -in bench-prec-spin.in 
+  Hz="$(tail -n 1 _av_spin | awk -F " " '{print $3}')"
+  sz="$(tail -n 1 _av_spin | awk -F " " '{print $5}')"
+  en="$(tail -n 1 _av_spin | awk -F " " '{print $6}')"
+  echo $temp $Hz $sz $en >> res_lammps.dat
+done
+
+# compute Langevin
+python3 -m langevin.py > res_langevin.dat
+
+# plot results
+python3 -m plot_precession.py res_lammps.dat res_langevin.dat
diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo
index 2cd9200121..a32dde9dd7 100644
--- a/examples/SPIN/bfo/in.spin.bfo
+++ b/examples/SPIN/bfo/in.spin.bfo
@@ -51,6 +51,6 @@ thermo_style    custom step time v_magnorm pe ke v_emag temp etotal
 thermo          10
 
 compute outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
 run 		2000
diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
index 9193faa798..dd9ed890ee 100644
--- a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
+++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
@@ -57,7 +57,7 @@ variable 	tmag      equal c_out_mag[6]
 thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
 thermo          50
 
-#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+# compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+# dump 		1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
 run 		1000
diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
index 8ea82a509b..e5a49cd336 100644
--- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
+++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
@@ -25,7 +25,6 @@ velocity 	all create 100 4928459 rot yes dist gaussian
 
 #pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
 pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-# pair_coeff 	* * eam/alloy ../examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy Co
 pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
 pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
 #pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652  
@@ -56,6 +55,6 @@ thermo_style    custom step time v_magnorm v_emag temp press etotal
 thermo          10
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
 run 		20000
diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron
index fd504d2cfd..93485ee076 100644
--- a/examples/SPIN/iron/in.spin.iron
+++ b/examples/SPIN/iron/in.spin.iron
@@ -52,7 +52,6 @@ thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe press etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-# dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-dump 		1 all custom 100 dump_iron.lammpstrj type x y z fx fy fz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
 run 		50000
diff --git a/examples/SPIN/iron/in.spin.iron_cubic b/examples/SPIN/iron/in.spin.iron_cubic
index 859d9df0fa..349a6de3a0 100644
--- a/examples/SPIN/iron/in.spin.iron_cubic
+++ b/examples/SPIN/iron/in.spin.iron_cubic
@@ -52,7 +52,7 @@ thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
 run 		2000
 # min_style 	spin
diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel
index caa1c940ae..7096fda960 100644
--- a/examples/SPIN/nickel/in.spin.nickel
+++ b/examples/SPIN/nickel/in.spin.nickel
@@ -52,7 +52,7 @@ thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
 run 		2000
 
diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp
index e7bbacca6b..6b9ad517bb 100644
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@@ -119,7 +119,8 @@ void FixLangevinSpin::init()
   double hbar = force->hplanck/MY_2PI;  // eV/(rad.THz)
   double kb = force->boltz;             // eV/K
   // D = (MY_2PI*alpha_t*gil_factor*kb*temp);
-  D = (1.0/MY_2PI)*(MY_2PI*alpha_t*gil_factor*kb*temp);
+
+  D = (alpha_t*gil_factor*kb*temp);
   // D = (12.0/MY_2PI)*(MY_2PI*alpha_t*gil_factor*kb*temp);
   D /= (hbar*dts);
   sigma = sqrt(2.0*D);
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index 8150a7ab19..d547de6995 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -242,7 +242,8 @@ void PairSpinExchange::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        evdwl *= 0.5*hbar;
+        // evdwl *= 0.5*hbar;
+        evdwl *= hbar;
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
@@ -351,11 +352,14 @@ void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3],
   Jex *= (1.0-J2[itype][jtype]*ra);
   Jex *= exp(-ra);
 
-  printf("Exchange : %g %g \n",Jex,Jex*hbar);
+  // printf("Exchange : %g %g \n",Jex,Jex*hbar);
 
-  fmi[0] += 2.0*Jex*spj[0];
-  fmi[1] += 2.0*Jex*spj[1];
-  fmi[2] += 2.0*Jex*spj[2];
+  // fmi[0] += 2.0*Jex*spj[0];
+  // fmi[1] += 2.0*Jex*spj[1];
+  // fmi[2] += 2.0*Jex*spj[2];
+  fmi[0] += Jex*spj[0];
+  fmi[1] += Jex*spj[1];
+  fmi[2] += Jex*spj[2];
 }
 
 /* ----------------------------------------------------------------------

From 1df3a7173453216bd24ba476fcab3cc45950d1df Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 15:35:19 +0000
Subject: [PATCH 026/199] Updated documentation

---
 doc/src/bond_oxdna.rst                        |   75 +-
 doc/src/pair_oxdna.rst                        |   45 +-
 doc/src/pair_oxdna2.rst                       |   55 +-
 doc/src/pair_oxrna2.rst                       |  153 +++
 examples/USER/cgdna/README                    |   44 +-
 .../cgdna/examples/oxDNA2/duplex3/in.duplex3  |    2 +-
 .../oxDNA2/duplex3/log.07Aug19.duplex3.g++.1  |    2 +-
 .../oxDNA2/duplex3/log.07Aug19.duplex3.g++.4  |    2 +-
 .../examples/oxRNA2/duplex4/data.duplex4      |   96 ++
 .../cgdna/examples/oxRNA2/duplex4/in.duplex4  |   80 ++
 .../oxRNA2/duplex4/log.30Oct19.duplex4.g++.1  | 1174 +++++++++++++++++
 .../oxRNA2/duplex4/log.30Oct19.duplex4.g++.4  | 1174 +++++++++++++++++
 12 files changed, 2809 insertions(+), 93 deletions(-)
 create mode 100644 doc/src/pair_oxrna2.rst
 create mode 100644 examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4
 create mode 100644 examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4
 create mode 100644 examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1
 create mode 100644 examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4

diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst
index 51692f933b..36370ddf30 100644
--- a/doc/src/bond_oxdna.rst
+++ b/doc/src/bond_oxdna.rst
@@ -6,6 +6,9 @@ bond\_style oxdna/fene command
 bond\_style oxdna2/fene command
 ===============================
 
+bond\_style oxrna2/fene command
+===============================
+
 Syntax
 """"""
 
@@ -16,6 +19,8 @@ Syntax
 
    bond_style oxdna2/fene
 
+   bond_style oxrna2/fene
+
 Examples
 """"""""
 
@@ -28,18 +33,21 @@ Examples
    bond_style oxdna2/fene
    bond_coeff \* 2.0 0.25 0.7564
 
+   bond_style oxrna2/fene
+   bond_coeff \* 2.0 0.25 0.76107
+
 Description
 """""""""""
 
-The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
+The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential
 
 .. image:: Eqs/bond_oxdna_fene.jpg
    :align: center
 
 to define a modified finite extensible nonlinear elastic (FENE)
-potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
-phosphate backbone in the oxDNA force field for coarse-grained
-modelling of DNA.
+potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
+phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
+modelling of DNA/RNA.
 
 The following coefficients must be defined for the bond type via the
 :doc:`bond\_coeff <bond_coeff>` command as given in the above example, or
@@ -55,27 +63,36 @@ commands:
 
    The oxDNA bond style has to be used together with the
    corresponding oxDNA pair styles for excluded volume interaction
-   *oxdna/excv*\ , stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* and
+   *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
    coaxial stacking interaction *oxdna/coaxstk* as well as
    hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
    :doc:`pair\_style oxdna/excv <pair_oxdna>`). For the oxDNA2
-   :ref:`(Snodin) <oxdna2>` bond style the analogous pair styles and an
-   additional Debye-Hueckel pair style *oxdna2/dh* have to be defined.
+   :ref:`(Snodin) <Snodin0>` bond style the analogous pair styles 
+   *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
+   *oxdna2/hbond* and an additional Debye-Hueckel pair style 
+   *oxdna2/dh* have to be defined. The same applies to the oxRNA2
+   :ref:`(Sulc1) <Sulc01>` styles. 
    The coefficients in the above example have to be kept fixed and cannot
    be changed without reparameterizing the entire model.
 
-Example input and data files for DNA duplexes can be found in
-examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.  A simple python
-setup tool which creates single straight or helical DNA strands, DNA
-duplexes or arrays of DNA duplexes can be found in
+Example input and data files for DNA and RNA duplexes can be found in
+examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/.  A simple python
+setup tool which creates single straight or helical DNA strands, DNA/RNA
+duplexes or arrays of DNA/RNA duplexes can be found in
 examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich2>` and the relevant oxDNA articles in
-any publication that uses this implementation.  The article contains
-more information on the model, the structure of the input file, the
-setup tool and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found
+Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses 
+this implementation.  The article contains general information 
+on the model, its implementation and performance as well as the structure of 
+the data and input file. The preprint version of the article can be found
 `here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA/oxRNA publications. These are 
+:ref:`(Ouldridge) <Ouldridge0>` and 
+:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA, 
+:ref:`(Snodin) <Snodin0>` for oxDNA2, 
+:ref:`(Sulc1) <Sulc01>` for oxRNA2 
+and for sequence-specific hydrogen-bonding and stacking interactions 
+:ref:`(Sulc2) <Sulc02>`.
 
 
 ----------
@@ -92,35 +109,37 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`,
-:doc:`bond\_coeff <bond_coeff>`
+:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`, 
+:doc:`bond\_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
 **Default:** none
 
 
 ----------
 
+.. _Henrich0:
 
-.. _Henrich2:
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
+.. _Ouldridge-DPhil0:
 
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
-**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
-T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+.. _Ouldridge0:
 
-.. _oxdna\_fene:
+**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 
+.. _Snodin0:
 
+**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 
-**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
-J. Chem. Phys. 134, 085101 (2011).
+.. _Sulc01:
 
-.. _oxdna2:
+**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
 
+.. _Sulc02:
 
-
-**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
-J. Chem. Phys. 142, 234901 (2015).
+**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
 
 
 .. _lws: http://lammps.sandia.gov
diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst
index b40cf1f6cc..727f19c327 100644
--- a/doc/src/pair_oxdna.rst
+++ b/doc/src/pair_oxdna.rst
@@ -36,8 +36,8 @@ Syntax
      *oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
        seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
        T = temperature (oxDNA units, 0.1 = 300 K)
-       xi = temperature-independent coefficient in stacking strength
-       kappa = coefficient of linear temperature dependence in stacking strength
+       xi = 1.3448 (temperature-independent coefficient in stacking strength)
+       kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
      *oxdna/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
        seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
        eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
@@ -94,11 +94,15 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich1>` and the relevant oxDNA articles in any publication that uses this implementation.
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
-
+Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
+this implementation.  The article contains general information
+on the model, its implementation and performance as well as the structure of
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA publications
+:ref:`(Ouldridge) <Ouldridge1>`, 
+:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
+and :ref:`(Sulc) <Sulc1>`.
 
 ----------
 
@@ -114,39 +118,32 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`
-
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
+:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+ 
 **Default:** none
 
 
 ----------
 
-
 .. _Henrich1:
 
-
-
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
-.. _Sulc1:
-
-
-
-**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
 .. _Ouldridge-DPhil1:
 
-
-
-**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
 .. _Ouldridge1:
 
-
-
 **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 
+.. _Sulc1:
+
+**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst
index 4f64197f44..77052da666 100644
--- a/doc/src/pair_oxdna2.rst
+++ b/doc/src/pair_oxdna2.rst
@@ -39,15 +39,15 @@ Syntax
      *oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
        seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
        T = temperature (oxDNA units, 0.1 = 300 K)
-       xi = temperature-independent coefficient in stacking strength
-       kappa = coefficient of linear temperature dependence in stacking strength
+       xi = 1.3523 (temperature-independent coefficient in stacking strength)
+       kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
      *oxdna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
        seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
        eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
      *oxdna2/dh* args = T rhos qeff
        T = temperature (oxDNA units, 0.1 = 300 K)
        rhos = salt concentration (mole per litre)
-       qeff = effective charge (elementary charges)
+       qeff = 0.815 (effective charge in elementary charges)
 
 Examples
 """"""""
@@ -63,7 +63,7 @@ Examples
    pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
    pair_coeff \* \* oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
    pair_coeff \* \* oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
-   pair_coeff \* \* oxdna2/dh      0.1 1.0 0.815
+   pair_coeff \* \* oxdna2/dh      0.1 0.5 0.815
 
 Description
 """""""""""
@@ -83,7 +83,7 @@ The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,
 which themselves are constructed from a number of more basic potentials
 (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to :ref:`(Snodin) <Snodin>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
+We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
 and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
 
 .. note::
@@ -94,7 +94,7 @@ and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
    in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
    Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
    the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
-   after *oxdna2/dh* (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
+   after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat
    e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
    the temperature coefficients have to be matched to the one used in the fix.
 
@@ -102,11 +102,13 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich>` and the relevant oxDNA articles in any publication that uses this implementation.
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
-
+Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
+this implementation.  The article contains general information
+on the model, its implementation and performance as well as the structure of
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA2 publications
+:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
 
 ----------
 
@@ -122,43 +124,34 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
+:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
 **Default:** none
 
 
 ----------
 
-
-.. _Henrich:
-
-
+.. _Henrich2:
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
-.. _Sulc2:
-
-
-
-**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
-.. _Snodin:
-
-
+.. _Snodin2:
 
 **(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 
+.. _Sulc2:
+
+**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 .. _Ouldridge-DPhil2:
 
-
-
-**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
 .. _Ouldridge2:
 
-
-
 **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 
 
diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst
new file mode 100644
index 0000000000..469851eb5a
--- /dev/null
+++ b/doc/src/pair_oxrna2.rst
@@ -0,0 +1,153 @@
+.. index:: pair\_style oxrna2/excv
+
+pair\_style oxrna2/excv command
+===============================
+
+pair\_style oxrna2/stk command
+==============================
+
+pair\_style oxrna2/hbond command
+================================
+
+pair\_style oxrna2/xstk command
+===============================
+
+pair\_style oxrna2/coaxstk command
+==================================
+
+pair\_style oxrna2/dh command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style1
+
+   pair_coeff \* \* style2 args
+
+* style1 = *hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh*
+
+* style2 = *oxrna2/excv* or *oxrna2/stk* or *oxrna2/hbond* or *oxrna2/xstk* or *oxrna2/coaxstk* or *oxrna2/dh*
+* args = list of arguments for these particular styles
+
+
+.. parsed-literal::
+
+     *oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+       seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
+       T = temperature (oxDNA units, 0.1 = 300 K)
+       xi = 1.40206 (temperature-independent coefficient in stacking strength)
+       kappa = 2.77 (coefficient of linear temperature dependence in stacking strength)
+     *oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 
+       seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+       eps = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs)
+     *oxrna2/dh* args = T rhos qeff
+       T = temperature (oxDNA units, 0.1 = 300 K)
+       rhos = salt concentration (mole per litre)
+       qeff = 1.02455 (effective charge in elementary charges)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+   pair_coeff \* \* oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+   pair_coeff \* \* oxrna2/stk     seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+   pair_coeff \* \* oxrna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 1 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 2 3 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 3 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff \* \* oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
+   pair_coeff \* \* oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+   pair_coeff \* \* oxrna2/dh      0.1 0.5 1.02455
+
+Description
+"""""""""""
+
+The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
+excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-stacking *oxrna2/xstk*
+and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh*
+as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported :ref:`(Sulc) <Sulc2>`. Quasi-unique base-pairing between nucleotides can be achieved by using 
+more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
+This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
+up and down along the backbone.
+
+The exact functional form of the pair styles is rather complex.
+The individual potentials consist of products of modulation factors,
+which themselves are constructed from a number of more basic potentials
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
+We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
+and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
+
+.. note::
+
+   These pair styles have to be used together with the related oxDNA2 bond style
+   *oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of
+   :doc:`bond\_style oxrna2/fene <bond_oxdna>`). Most of the coefficients
+   in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
+   Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example),
+   the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients
+   after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat
+   e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+   the temperature coefficients have to be matched to the one used in the fix.
+
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
+A simple python setup tool which creates single straight or helical DNA strands,
+DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
+
+Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
+this implementation.  The article contains general information
+on the model, its implementation and performance as well as the structure of
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxRNA2 publications
+:ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+:doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+
+**Default:** none
+
+
+----------
+
+.. _Henrich3:
+
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
+.. _Sulc31:
+
+**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
+
+.. _Sulc32:
+
+**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README
index 8a9dc44359..a03490b630 100644
--- a/examples/USER/cgdna/README
+++ b/examples/USER/cgdna/README
@@ -1,8 +1,12 @@
 This directory contains example data and input files 
-and utility scripts for the oxDNA coarse-grained model 
-for DNA.
+as well as utility scripts for the oxDNA/oxDNA2/oxRNA2 
+coarse-grained model for DNA and RNA.
+
+/******************************************************************************/
+
+/examples/oxDNA/duplex1:
+/examples/oxDNA2/duplex1:
 
-/examples/duplex1:
 Input, data and log files for a DNA duplex (double-stranded DNA) 
 consisiting of 5 base pairs. The duplex contains two strands with 
 complementary base pairs. The topology is
@@ -11,7 +15,14 @@ A - C - G - T - A
 |   |   |   |   |
 T - G - C - A - T     
 
-/examples/duplex2:
+Note that in this example the stacking and hydrogen-bonding interactions 
+are sequence-averaged (cf. keyword 'seqav' in according pair styles).
+
+/******************************************************************************/
+
+/examples/oxDNA/duplex2:
+/examples/oxDNA2/duplex2:
+
 Input, data and log files for a nicked DNA duplex (double-stranded DNA) 
 consisiting of 8 base pairs. The duplex contains strands with 
 complementary base pairs, but the backbone on one side is not continuous: 
@@ -22,9 +33,15 @@ A - C - G - T - A - C - G - T
 |   |   |   |   |   |   |   |
 T - G - C - A   T - G - C - A
 
-/examples/duplex3:
-This is basically the duplex1 run with sequence-dependent stacking
-and hydrogen-bonding strengths enabled and both nucleotide mass and 
+Note that in this example the stacking and hydrogen-bonding interactions 
+are sequence-averaged (cf. keyword 'seqav' in according pair styles).
+
+/******************************************************************************/
+
+/examples/oxDNA2/duplex3:
+
+This is the duplex1 run with sequence-dependent stacking and
+hydrogen-bonding strengths enabled and both nucleotide mass and 
 moment of inertia set to the value of the standalone implementation 
 of oxDNA (M = I = 1). To achieve this, the masses can be set directly 
 in the input and data file, whereas the moment of inertia is set via 
@@ -33,6 +50,19 @@ The change of mass and moment of inertia allows direct comparision of
 e.g. trajectory data, energies or time-dependent observables on a per-timestep 
 basis until numerical noise causes deviations at later simulation times. 
 
+As mentioned above, the stacking and hydrogen-bonding interactions 
+are sequence-dependent (cf. keyword 'seqdep' in according pair styles).
+
+/******************************************************************************/
+
+/examples/oxRNA2/duplex4
+
+This is the duplex2 run with the oxRNA2 force field instead of the oxDNA or 
+oxDNA2 force field  and sequence-dependent stacking and hydrogen-bonding 
+strengths enabled.
+
+/******************************************************************************/
+
 /util:
 This directory contains a simple python setup tool which creates 
 single straight or helical DNA strands, DNA duplexes or arrays of DNA 
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
index fd75a6fc3f..033783dc15 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
@@ -1,4 +1,4 @@
-variable number	equal 1
+variable number	equal 3
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1
index 8f70e9ec96..9172c99492 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1
@@ -1,5 +1,5 @@
 LAMMPS (7 Aug 2019)
-variable number	equal 1
+variable number	equal 3
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4
index f110e20906..491f91e671 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4
@@ -1,5 +1,5 @@
 LAMMPS (7 Aug 2019)
-variable number	equal 1
+variable number	equal 3
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4
new file mode 100644
index 0000000000..72872d431a
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4
@@ -0,0 +1,96 @@
+# LAMMPS data file
+16 atoms
+16 ellipsoids
+13 bonds
+
+4 atom types
+1 bond types
+
+# System size
+-20.000000 20.000000 xlo xhi
+-20.000000 20.000000 ylo yhi
+-20.000000 20.000000 zlo zhi
+
+Masses
+
+1 3.1575
+2 3.1575
+3 3.1575
+4 3.1575
+
+# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
+Atoms
+
+1 1 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.860249842674776e-01 -3.518234140414736e-01  3.897628551303122e-01 1 1 1
+3 3 -1.874009511073395e-01 -5.699832309147915e-01  7.795257102606244e-01 1 1 1
+4 4  1.824198365552941e-01 -5.715968887521518e-01  1.169288565390937e+00 1 1 1
+5 1  4.829362784135484e-01 -3.560513319622209e-01  1.559051420521249e+00 1 1 1
+6 2  5.999771538385027e-01 -5.235921299024461e-03  1.948814275651561e+00 1 1 1
+7 3  4.890766774371325e-01  3.475687034056071e-01  2.338577130781873e+00 1 1 1
+8 4  1.923677943514057e-01  5.683261666476170e-01  2.728339985912185e+00 1 1 1
+9 1 -1.923677943514057e-01 -5.683261666476170e-01  2.728339985912185e+00 2 1 1
+10 2 -4.890766774371324e-01 -3.475687034056071e-01  2.338577130781873e+00 2 1 1
+11 3 -5.999771538385025e-01  5.235921299024461e-03  1.948814275651561e+00 2 1 1
+12 4 -4.829362784135481e-01  3.560513319622207e-01  1.559051420521249e+00 2 1 1
+13 1 -1.824198365552940e-01  5.715968887521514e-01  1.169288565390936e+00 2 1 1
+14 2  1.874009511073395e-01  5.699832309147912e-01  7.795257102606241e-01 2 1 1
+15 3  4.860249842674773e-01  3.518234140414733e-01  3.897628551303119e-01 2 1 1
+16 4  5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
+
+# Atom-ID, translational velocity, angular momentum
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+11  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+12  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+13  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+14  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+15  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+16  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.513258223252946e-01  0.000000000000000e+00  0.000000000000000e+00  3.081869234362515e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.100416404457962e-01  0.000000000000000e+00  0.000000000000000e+00  5.863723567357894e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.899012371043606e-01  0.000000000000000e+00  0.000000000000000e+00  8.074754054847398e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.123349185122326e-01  0.000000000000000e+00  0.000000000000000e+00  9.499720515246527e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  4.363309284746654e-03  0.000000000000000e+00  0.000000000000000e+00  9.999904807207346e-01
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -3.040330609254902e-01  0.000000000000000e+00  0.000000000000000e+00  9.526614812535865e-01
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.828323126827837e-01  0.000000000000000e+00  0.000000000000000e+00 -8.125924533816677e-01
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.125924533816681e-01  5.828323126827832e-01 -0.000000000000000e+00
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.526614812535864e-01  3.040330609254902e-01  0.000000000000000e+00
+11  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.999904807207346e-01 -4.363309284746654e-03  0.000000000000000e+00
+12  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.499720515246526e-01 -3.123349185122325e-01  0.000000000000000e+00
+13  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.074754054847402e-01 -5.899012371043603e-01  0.000000000000000e+00
+14  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.863723567357898e-01 -8.100416404457959e-01  0.000000000000000e+00
+15  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01  9.513258223252948e-01  0.000000000000000e+00
+16  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  2.775557561562893e-17  1.000000000000000e+00 -0.000000000000000e+00
+
+# Bond topology
+Bonds
+
+1  1  1  2
+2  1  2  3
+3  1  3  4
+4  1  4  5
+5  1  5  6
+6  1  6  7
+7  1  7  8
+8  1  9  10
+9  1  10  11
+10  1  11  12
+11  1  13  14
+12  1  14  15
+13  1  15  16
diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4
new file mode 100644
index 0000000000..ed2fafbe8b
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4
@@ -0,0 +1,80 @@
+variable number	equal 4
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex4
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxRNA2 bond interactions - FENE backbone
+bond_style oxrna2/fene
+bond_coeff * 2.0 0.25 0.761070781051
+
+# oxRNA2 pair interactions
+pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+
+pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxrna2/stk     seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 3 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 
+pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+pair_coeff * * oxrna2/dh      ${T} 0.5 1.02455
+
+# NVE ensemble
+#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all   nve/dot
+fix 1 all nve/asphere
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f"
+
+run 1000000
+
+#write_restart config.${number}.*
diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1 b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1
new file mode 100644
index 0000000000..d4c9fa3fcc
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1
@@ -0,0 +1,1174 @@
+LAMMPS (30 Oct 2019)
+variable number	equal 4
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex4
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 5.9e-05 secs
+  read_data CPU = 0.038375 secs
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxRNA2 bond interactions - FENE backbone
+bond_style oxrna2/fene
+bond_coeff * 2.0 0.25 0.761070781051
+
+# oxRNA2 pair interactions
+pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+
+pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxrna2/stk     seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/stk     seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 3 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
+pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+pair_coeff * * oxrna2/dh      ${T} 0.5 1.02455
+pair_coeff * * oxrna2/dh      0.1 0.5 1.02455
+
+# NVE ensemble
+#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all   nve/dot
+fix 1 all nve/asphere
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f"
+
+run 1000000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3015
+  ghost atom cutoff = 3.3015
+  binsize = 1.65075, bins = 25 25 25
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxrna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxrna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxrna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxrna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxrna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxrna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+0  ekin = 0 |  erot = 0 | epot = -13.282537590974 | etot = -13.282537590974
+Per MPI rank memory allocation (min/avg/max) = 2.951 | 2.951 | 2.951 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0  -0.84341458  0.013255977   -0.8301586 -2.0169485e-05 
+1000  ekin = 0.00448503054656468 |  erot = 0.00825381229611384 | epot = -13.2952764343122 | etot = -13.2825375914695
+2000  ekin = 0.0179027901180511 |  erot = 0.0327684151335467 | epot = -13.3332087967732 | etot = -13.2825375915216
+3000  ekin = 0.0401478317723584 |  erot = 0.0728240143066062 | epot = -13.3955094376815 | etot = -13.2825375916026
+4000  ekin = 0.0710654348932282 |  erot = 0.127292706283096 | epot = -13.4808957328808 | etot = -13.2825375917044
+5000  ekin = 0.110480309743662 |  erot = 0.194739074279834 | epot = -13.5877569758405 | etot = -13.282537591817
+6000  ekin = 0.158231230694432 |  erot = 0.273546913858903 | epot = -13.7143157364827 | etot = -13.2825375919294
+7000  ekin = 0.214206450831754 |  erot = 0.362058396901232 | epot = -13.8588024397642 | etot = -13.2825375920312
+8000  ekin = 0.278374111850069 |  erot = 0.458709556672181 | epot = -14.0196212606361 | etot = -13.2825375921138
+9000  ekin = 0.35080209403022 |  erot = 0.562145629088178 | epot = -14.1954853152903 | etot = -13.2825375921719
+10000  ekin = 0.431663021447766 |  erot = 0.671302139462136 | epot = -14.385502753114 | etot = -13.2825375922041
+11000  ekin = 0.521222365620265 |  erot = 0.78544264622411 | epot = -14.5892026040572 | etot = -13.2825375922128
+12000  ekin = 0.61981039873542 |  erot = 0.904150888366026 | epot = -14.8064988793055 | etot = -13.2825375922041
+13000  ekin = 0.72778153179885 |  erot = 1.02728222251243 | epot = -15.0376013464974 | etot = -13.2825375921861
+14000  ekin = 0.845466747659446 |  erot = 1.154885201864 | epot = -15.2828895416915 | etot = -13.2825375921681
+15000  ekin = 0.973515286429446 |  erot = 1.28640002432487 | epot = -15.5424529041413 | etot = -13.2825375933869
+16000  ekin = 1.12323013751098 |  erot = 1.40387495398598 | epot = -15.8096426839256 | etot = -13.2825375924286
+17000  ekin = 1.2976927283263 |  erot = 1.51347784068661 | epot = -16.0937081607397 | etot = -13.2825375917268
+18000  ekin = 1.48565191084531 |  erot = 1.63592970999661 | epot = -16.4041192134347 | etot = -13.2825375925928
+19000  ekin = 1.66750911163348 |  erot = 1.77940241938721 | epot = -16.7294491246368 | etot = -13.2825375936161
+20000  ekin = 1.84148924290423 |  erot = 1.93695511183687 | epot = -17.0609819484057 | etot = -13.2825375936646
+21000  ekin = 2.02307741366163 |  erot = 2.09844265792961 | epot = -17.4040576653939 | etot = -13.2825375938027
+22000  ekin = 2.21183606977224 |  erot = 2.26260708947302 | epot = -17.7569807531587 | etot = -13.2825375939134
+23000  ekin = 2.40735468792977 |  erot = 2.42817202047308 | epot = -18.1180643024997 | etot = -13.2825375940968
+24000  ekin = 2.60896890448861 |  erot = 2.59357882573853 | epot = -18.485085324508 | etot = -13.2825375942809
+25000  ekin = 2.81580135477345 |  erot = 2.75706655667055 | epot = -18.855405505957 | etot = -13.282537594513
+26000  ekin = 3.02680083558485 |  erot = 2.91667946897257 | epot = -19.2260178993271 | etot = -13.2825375947697
+27000  ekin = 3.24067707260308 |  erot = 3.07027299756498 | epot = -19.5934876652175 | etot = -13.2825375950495
+28000  ekin = 3.45601412953572 |  erot = 3.21560615188039 | epot = -19.9541578767293 | etot = -13.2825375953132
+29000  ekin = 3.6713683081319 |  erot = 3.35037905822946 | epot = -20.304284961999 | etot = -13.2825375956376
+30000  ekin = 3.88476027224393 |  erot = 3.47208481891837 | epot = -20.639382687185 | etot = -13.2825375960227
+31000  ekin = 4.09387957878895 |  erot = 3.57821385032035 | epot = -20.9546310254509 | etot = -13.2825375963416
+32000  ekin = 4.29662185345806 |  erot = 3.66648606531138 | epot = -21.2456455154186 | etot = -13.2825375966492
+33000  ekin = 4.49089153394062 |  erot = 3.73482555362569 | epot = -21.5082546845018 | etot = -13.2825375969355
+34000  ekin = 4.67464118182276 |  erot = 3.78142516888995 | epot = -21.738603947901 | etot = -13.2825375971883
+35000  ekin = 4.84586411782047 |  erot = 3.80480460777895 | epot = -21.9332063229962 | etot = -13.2825375973967
+36000  ekin = 5.00270940487365 |  erot = 3.8039453503275 | epot = -22.0891923527593 | etot = -13.2825375975582
+37000  ekin = 5.14355281474259 |  erot = 3.7783370953036 | epot = -22.204427507712 | etot = -13.2825375976658
+38000  ekin = 5.26699752588855 |  erot = 3.72801268545693 | epot = -22.2775478090594 | etot = -13.2825375977139
+39000  ekin = 5.37191151713863 |  erot = 3.65359747923659 | epot = -22.3080465940736 | etot = -13.2825375976984
+40000  ekin = 5.45746010972423 |  erot = 3.55633701588595 | epot = -22.2963347232305 | etot = -13.2825375976203
+41000  ekin = 5.52312188621308 |  erot = 3.43809872369854 | epot = -22.2437582073842 | etot = -13.2825375974726
+42000  ekin = 5.56872044211992 |  erot = 3.30135279333163 | epot = -22.1526108327155 | etot = -13.2825375972639
+43000  ekin = 5.59443660082917 |  erot = 3.14910305123731 | epot = -22.0260772490691 | etot = -13.2825375970026
+44000  ekin = 5.60078634437692 |  erot = 2.98477133565124 | epot = -21.8680952767294 | etot = -13.2825375967012
+45000  ekin = 5.58859564323333 |  erot = 2.81204277265316 | epot = -21.6831760122617 | etot = -13.2825375963752
+46000  ekin = 5.55896198288794 |  erot = 2.63469562167501 | epot = -21.4761952006007 | etot = -13.2825375960378
+47000  ekin = 5.51320424221946 |  erot = 2.45646420183046 | epot = -21.2522060397483 | etot = -13.2825375956984
+48000  ekin = 5.45280176988517 |  erot = 2.28095947573118 | epot = -21.0162988409769 | etot = -13.2825375953605
+49000  ekin = 5.37933239946638 |  erot = 2.11161440403257 | epot = -20.7734843985446 | etot = -13.2825375950457
+50000  ekin = 5.29440598595185 |  erot = 1.95156309993188 | epot = -20.5285066806346 | etot = -13.2825375947508
+51000  ekin = 5.19960275040233 |  erot = 1.8036634398305 | epot = -20.2858037847152 | etot = -13.2825375944824
+52000  ekin = 5.09244091535756 |  erot = 1.66034071449473 | epot = -20.0353192196127 | etot = -13.2825375897604
+53000  ekin = 5.00219098599272 |  erot = 1.54003539006211 | epot = -19.8247639698981 | etot = -13.2825375938433
+54000  ekin = 4.90058329526777 |  erot = 1.45132465506075 | epot = -19.6344455614683 | etot = -13.2825376111398
+55000  ekin = 4.70838087935139 |  erot = 1.38368494594893 | epot = -19.3746034336678 | etot = -13.2825376083675
+56000  ekin = 4.44064498303545 |  erot = 1.42525549496303 | epot = -19.1484380668508 | etot = -13.2825375888523
+57000  ekin = 4.28012764787285 |  erot = 1.59067222265512 | epot = -19.1533374833604 | etot = -13.2825376128325
+58000  ekin = 4.17606446205098 |  erot = 1.6926959141941 | epot = -19.1512979674148 | etot = -13.2825375911697
+59000  ekin = 4.0674801293444 |  erot = 1.75788112721294 | epot = -19.1078988477137 | etot = -13.2825375911564
+60000  ekin = 3.9544882347638 |  erot = 1.84391663061768 | epot = -19.0809424565336 | etot = -13.2825375911521
+61000  ekin = 3.83840387031284 |  erot = 1.95003019237208 | epot = -19.0709716537088 | etot = -13.2825375910239
+62000  ekin = 3.72130809963045 |  erot = 2.07501703895377 | epot = -19.0788627296237 | etot = -13.2825375910394
+63000  ekin = 3.60440089032981 |  erot = 2.21773397929798 | epot = -19.1046724606768 | etot = -13.282537591049
+64000  ekin = 3.48898621429844 |  erot = 2.37695650761985 | epot = -19.1484803129713 | etot = -13.282537591053
+65000  ekin = 3.37647880025293 |  erot = 2.55140907448467 | epot = -19.2104254657961 | etot = -13.2825375910585
+66000  ekin = 3.26833067403372 |  erot = 2.73974236805088 | epot = -19.2906106331593 | etot = -13.2825375910747
+67000  ekin = 3.16594788215578 |  erot = 2.94047174698236 | epot = -19.3889572202528 | etot = -13.2825375911146
+68000  ekin = 3.07060531612276 |  erot = 3.15188029478627 | epot = -19.5050232021015 | etot = -13.2825375911924
+69000  ekin = 2.98334905059819 |  erot = 3.37190853325577 | epot = -19.6377951751758 | etot = -13.2825375913219
+70000  ekin = 2.90492955397884 |  erot = 3.59802295152975 | epot = -19.7854900970223 | etot = -13.2825375915137
+71000  ekin = 2.83572376329218 |  erot = 3.8271560839742 | epot = -19.9454174390314 | etot = -13.282537591765
+72000  ekin = 2.77568510798997 |  erot = 4.05569348668259 | epot = -20.1139161867768 | etot = -13.2825375921043
+73000  ekin = 2.72437405649527 |  erot = 4.27929863267978 | epot = -20.2862102816556 | etot = -13.2825375924805
+74000  ekin = 2.6809894320095 |  erot = 4.4934031024691 | epot = -20.4569301273605 | etot = -13.2825375928819
+75000  ekin = 2.6444530940616 |  erot = 4.69339307186043 | epot = -20.6203837591939 | etot = -13.2825375932719
+76000  ekin = 2.61355415206022 |  erot = 4.87501053156087 | epot = -20.7711022772329 | etot = -13.2825375936118
+77000  ekin = 2.58710084062323 |  erot = 5.03478939172066 | epot = -20.9044278262183 | etot = -13.2825375938744
+78000  ekin = 2.56403853914049 |  erot = 5.17029283961051 | epot = -21.0168689727798 | etot = -13.2825375940288
+79000  ekin = 2.54361120788211 |  erot = 5.28037161018751 | epot = -21.1065204121487 | etot = -13.2825375940791
+80000  ekin = 2.52540527324247 |  erot = 5.36512720853065 | epot = -21.173070075803 | etot = -13.2825375940298
+81000  ekin = 2.50929384303298 |  erot = 5.42576598242971 | epot = -21.2175974194025 | etot = -13.2825375939398
+82000  ekin = 2.49524917644589 |  erot = 5.46414530531067 | epot = -21.2419320755728 | etot = -13.2825375938163
+83000  ekin = 2.4833426959312 |  erot = 5.48242032921998 | epot = -21.248300618845 | etot = -13.2825375936939
+84000  ekin = 2.47365997802594 |  erot = 5.48271691205541 | epot = -21.2389144836696 | etot = -13.2825375935882
+85000  ekin = 2.46626808184772 |  erot = 5.46691083838924 | epot = -21.2157165137399 | etot = -13.2825375935029
+86000  ekin = 2.46123154184243 |  erot = 5.43653398177485 | epot = -21.1803031170841 | etot = -13.2825375934668
+87000  ekin = 2.45852093879055 |  erot = 5.39265692383446 | epot = -21.1337154560121 | etot = -13.2825375933871
+88000  ekin = 2.45840646060175 |  erot = 5.33627030736198 | epot = -21.0772143612561 | etot = -13.2825375932924
+89000  ekin = 2.46146480126887 |  erot = 5.26838646846783 | epot = -21.0123888631742 | etot = -13.2825375934375
+90000  ekin = 2.4677317783594 |  erot = 5.18930366181446 | epot = -20.9395730335193 | etot = -13.2825375933455
+91000  ekin = 2.47726011905719 |  erot = 5.09951749277777 | epot = -20.8593152050595 | etot = -13.2825375932246
+92000  ekin = 2.49074261962909 |  erot = 5.00022791911595 | epot = -20.7735081318254 | etot = -13.2825375930803
+93000  ekin = 2.50902833057362 |  erot = 4.89281259013106 | epot = -20.6843785136292 | etot = -13.2825375929245
+94000  ekin = 2.53301288183075 |  erot = 4.77876912035546 | epot = -20.5943195949544 | etot = -13.2825375927682
+95000  ekin = 2.56354598704907 |  erot = 4.6596420581626 | epot = -20.5057256378352 | etot = -13.2825375926235
+96000  ekin = 2.60133194738611 |  erot = 4.53693642149354 | epot = -20.4208059613806 | etot = -13.2825375925009
+97000  ekin = 2.64684712537105 |  erot = 4.41204173729005 | epot = -20.3414264550665 | etot = -13.2825375924053
+98000  ekin = 2.70029551800324 |  erot = 4.28619503995162 | epot = -20.2690281502928 | etot = -13.2825375923379
+99000  ekin = 2.76159183076381 |  erot = 4.16048163754163 | epot = -20.2046110606006 | etot = -13.2825375922951
+100000  ekin = 2.83036874776579 |  erot = 4.03587523010376 | epot = -20.1487815701408 | etot = -13.2825375922712
+101000  ekin = 2.90599845693996 |  erot = 3.91330077540588 | epot = -20.1018368246064 | etot = -13.2825375922606
+102000  ekin = 2.98761606367604 |  erot = 3.79369343963812 | epot = -20.0638470955752 | etot = -13.2825375922611
+103000  ekin = 3.07413620026802 |  erot = 3.67802597580043 | epot = -20.0346997683418 | etot = -13.2825375922734
+104000  ekin = 3.16426099663645 |  erot = 3.56728973636564 | epot = -20.0140883253047 | etot = -13.2825375923026
+105000  ekin = 3.25648344622793 |  erot = 3.46242766269272 | epot = -20.0014487012763 | etot = -13.2825375923557
+106000  ekin = 3.34909407537355 |  erot = 3.36423261094161 | epot = -19.9958642787542 | etot = -13.282537592439
+107000  ekin = 3.4401993069765 |  erot = 3.27323316283015 | epot = -19.9959700623645 | etot = -13.2825375925578
+108000  ekin = 3.52775814523602 |  erot = 3.18959025645786 | epot = -19.999885994407 | etot = -13.2825375927131
+109000  ekin = 3.60964009104214 |  erot = 3.11302339299888 | epot = -20.0052010769433 | etot = -13.2825375929023
+110000  ekin = 3.68370388524509 |  erot = 3.04277828887564 | epot = -20.0090197672386 | etot = -13.2825375931179
+111000  ekin = 3.74789440567183 |  erot = 2.97764201100029 | epot = -20.0080740100205 | etot = -13.2825375933484
+112000  ekin = 3.80035415830428 |  erot = 2.91600823448521 | epot = -19.9988999863676 | etot = -13.2825375935781
+113000  ekin = 3.839544891464 |  erot = 2.8559933088984 | epot = -19.9780757941506 | etot = -13.2825375937882
+114000  ekin = 3.86437452036816 |  erot = 2.79560177874327 | epot = -19.9425138930678 | etot = -13.2825375939563
+115000  ekin = 3.87432139555448 |  erot = 2.7329343736024 | epot = -19.8897933632161 | etot = -13.2825375940592
+116000  ekin = 3.86954570193439 |  erot = 2.66642221950682 | epot = -19.8185055155168 | etot = -13.2825375940755
+117000  ekin = 3.85097050791378 |  erot = 2.59505981730843 | epot = -19.7285679191997 | etot = -13.2825375939775
+118000  ekin = 3.82031843896371 |  erot = 2.51866416069826 | epot = -19.6215201934448 | etot = -13.2825375937828
+119000  ekin = 3.78008379969918 |  erot = 2.43788144963878 | epot = -19.5005028428254 | etot = -13.2825375934874
+120000  ekin = 3.73339325084433 |  erot = 2.35417060362233 | epot = -19.3701014475786 | etot = -13.282537593112
+121000  ekin = 3.68379362023519 |  erot = 2.26974086129527 | epot = -19.23607207422 | etot = -13.2825375926895
+122000  ekin = 3.63497633455468 |  erot = 2.18733107351197 | epot = -19.1048450003258 | etot = -13.2825375922591
+123000  ekin = 3.59047168903067 |  erot = 2.10992442969337 | epot = -18.9829337105841 | etot = -13.2825375918601
+124000  ekin = 3.55336069064742 |  erot = 2.040449477976 | epot = -18.8763477601487 | etot = -13.2825375915253
+125000  ekin = 3.526052756485 |  erot = 1.98151529341996 | epot = -18.7901056411805 | etot = -13.2825375912756
+126000  ekin = 3.51088386083626 |  erot = 1.93492307727824 | epot = -18.728344529054 | etot = -13.2825375909395
+127000  ekin = 3.51016542665131 |  erot = 1.90135594382336 | epot = -18.6940589614221 | etot = -13.2825375909474
+128000  ekin = 3.52366007691459 |  erot = 1.88146923500262 | epot = -18.6876669021183 | etot = -13.2825375902011
+129000  ekin = 3.52804447871109 |  erot = 1.87939379818812 | epot = -18.6899759099344 | etot = -13.2825376330352
+130000  ekin = 3.39121727536937 |  erot = 1.95375354402963 | epot = -18.6275084102343 | etot = -13.2825375908353
+131000  ekin = 3.51597185423296 |  erot = 2.06600773707502 | epot = -18.8645172230933 | etot = -13.2825376317853
+132000  ekin = 3.65680948155273 |  erot = 2.09675964820427 | epot = -19.0361067214651 | etot = -13.2825375917081
+133000  ekin = 3.78260898444153 |  erot = 2.11778864665409 | epot = -19.1829352240667 | etot = -13.2825375929711
+134000  ekin = 3.90291219401782 |  erot = 2.13993246768634 | epot = -19.3253822549312 | etot = -13.282537593227
+135000  ekin = 4.0130725329214 |  erot = 2.16317596346888 | epot = -19.4587860898102 | etot = -13.2825375934199
+136000  ekin = 4.10942813981085 |  erot = 2.18779054238602 | epot = -19.579756275755 | etot = -13.2825375935581
+137000  ekin = 4.18918244084739 |  erot = 2.21413018926373 | epot = -19.6858502237401 | etot = -13.282537593629
+138000  ekin = 4.25055180725538 |  erot = 2.24252417705096 | epot = -19.7756135779486 | etot = -13.2825375936422
+139000  ekin = 4.29264193993076 |  erot = 2.27334414892611 | epot = -19.8485236824514 | etot = -13.2825375935945
+140000  ekin = 4.31542981069473 |  erot = 2.30704736065647 | epot = -19.9050147648392 | etot = -13.282537593488
+141000  ekin = 4.31969657449582 |  erot = 2.34420108979785 | epot = -19.9464352576258 | etot = -13.2825375933322
+142000  ekin = 4.30689625825181 |  erot = 2.38546661972145 | epot = -19.9749004711164 | etot = -13.2825375931432
+143000  ekin = 4.27897643633865 |  erot = 2.43154322469962 | epot = -19.9930572539778 | etot = -13.2825375929395
+144000  ekin = 4.23817759048809 |  erot = 2.4830525431645 | epot = -20.0037677263996 | etot = -13.282537592747
+145000  ekin = 4.18683687366757 |  erot = 2.54040585524226 | epot = -20.0097803214924 | etot = -13.2825375925826
+146000  ekin = 4.1272243777605 |  erot = 2.60369949546902 | epot = -20.0134614656897 | etot = -13.2825375924601
+147000  ekin = 4.06142641942193 |  erot = 2.67262771534946 | epot = -20.0165917271588 | etot = -13.2825375923874
+148000  ekin = 3.9912803569092 |  erot = 2.74643868481959 | epot = -20.0202566340943 | etot = -13.2825375923655
+149000  ekin = 3.91835859675027 |  erot = 2.82393987441759 | epot = -20.0248360635575 | etot = -13.2825375923896
+150000  ekin = 3.84399502540854 |  erot = 2.90355368904202 | epot = -20.0300863068999 | etot = -13.2825375924493
+151000  ekin = 3.76934462696646 |  erot = 2.98342057410476 | epot = -20.0353027936018 | etot = -13.2825375925305
+152000  ekin = 3.69546503896298 |  erot = 3.06154297168136 | epot = -20.0395456032602 | etot = -13.2825375926159
+153000  ekin = 3.62340677772839 |  erot = 3.13595781467703 | epot = -20.0419021850935 | etot = -13.2825375926881
+154000  ekin = 3.55429442921676 |  erot = 3.20491770297265 | epot = -20.0417497249216 | etot = -13.2825375927321
+155000  ekin = 3.48935808553585 |  erot = 3.26703376494699 | epot = -20.0389294432276 | etot = -13.2825375927448
+156000  ekin = 3.42995719397496 |  erot = 3.32146386703849 | epot = -20.0339586537003 | etot = -13.2825375926868
+157000  ekin = 3.37758377439356 |  erot = 3.36807693572793 | epot = -20.0281983027502 | etot = -13.2825375926288
+158000  ekin = 3.32977839475207 |  erot = 3.40502394976504 | epot = -20.0173399361875 | etot = -13.2825375916704
+159000  ekin = 3.28790229188226 |  erot = 3.43232801110884 | epot = -20.0027678906268 | etot = -13.2825375876357
+160000  ekin = 3.2827995172835 |  erot = 3.46457454882488 | epot = -20.0299116571487 | etot = -13.2825375910404
+161000  ekin = 3.29006841785848 |  erot = 3.48756894666501 | epot = -20.0601749524886 | etot = -13.2825375879651
+162000  ekin = 3.30320279765029 |  erot = 3.50064541816097 | epot = -20.0863858038423 | etot = -13.282537588031
+163000  ekin = 3.32680445360257 |  erot = 3.50703979240478 | epot = -20.1163818341648 | etot = -13.2825375881575
+164000  ekin = 3.35978204864574 |  erot = 3.50639799900046 | epot = -20.1487176359768 | etot = -13.2825375883306
+165000  ekin = 3.40052448161995 |  erot = 3.49807859199014 | epot = -20.1811406621343 | etot = -13.2825375885243
+166000  ekin = 3.44710440323596 |  erot = 3.48135096319306 | epot = -20.2109929551315 | etot = -13.2825375887025
+167000  ekin = 3.4975648313672 |  erot = 3.45565303648312 | epot = -20.2357554566791 | etot = -13.2825375888288
+168000  ekin = 3.55023572858497 |  erot = 3.42084325030349 | epot = -20.2536165677605 | etot = -13.282537588872
+169000  ekin = 3.60406985696843 |  erot = 3.37750569995077 | epot = -20.2641131456975 | etot = -13.2825375887783
+170000  ekin = 3.41798406778448 |  erot = 3.07782048145476 | epot = -19.7783420668553 | etot = -13.282537517616
+171000  ekin = 3.24552871157827 |  erot = 2.73637390316214 | epot = -19.2644400103087 | etot = -13.2825373955683
+172000  ekin = 3.78367855051371 |  erot = 3.0727453748938 | epot = -20.1389614956922 | etot = -13.2825375702847
+173000  ekin = 4.03457273059443 |  erot = 3.1833646910841 | epot = -20.5004749222031 | etot = -13.2825375005245
+174000  ekin = 4.14002439986023 |  erot = 3.16763893899922 | epot = -20.5902008391762 | etot = -13.2825375003167
+175000  ekin = 4.24061478727573 |  erot = 3.15086312051219 | epot = -20.6740154078953 | etot = -13.2825375001074
+176000  ekin = 4.33750550891641 |  erot = 3.1355261006119 | epot = -20.7555691095056 | etot = -13.2825374999773
+177000  ekin = 4.43118634626255 |  erot = 3.12342668205083 | epot = -20.8371505282964 | etot = -13.282537499983
+178000  ekin = 4.52112038535911 |  erot = 3.11516996838714 | epot = -20.9188278538863 | etot = -13.28253750014
+179000  ekin = 4.60569122910559 |  erot = 3.10997891303161 | epot = -20.9982076425525 | etot = -13.2825375004153
+180000  ekin = 4.68248742105205 |  erot = 3.10587534040976 | epot = -21.0709002621995 | etot = -13.2825375007377
+181000  ekin = 4.74885008880769 |  erot = 3.10016969122633 | epot = -21.1315572810546 | etot = -13.2825375010206
+182000  ekin = 4.80252004240904 |  erot = 3.09010778323153 | epot = -21.1751653268271 | etot = -13.2825375011865
+183000  ekin = 4.84185836209392 |  erot = 3.07355401450656 | epot = -21.1979498780501 | etot = -13.2825375014496
+184000  ekin = 4.86305938218274 |  erot = 3.04972947015758 | epot = -21.1953263537857 | etot = -13.2825375014454
+185000  ekin = 4.86484048379853 |  erot = 3.01830532387125 | epot = -21.165683308955 | etot = -13.2825375012852
+186000  ekin = 4.84781115921877 |  erot = 2.97987576045986 | epot = -21.1102244206817 | etot = -13.2825375010031
+187000  ekin = 4.8135776433552 |  erot = 2.93597501879465 | epot = -21.032090162799 | etot = -13.2825375006491
+188000  ekin = 4.76439584097176 |  erot = 2.8887503176203 | epot = -20.9356836588659 | etot = -13.2825375002739
+189000  ekin = 4.7028202134345 |  erot = 2.84056846871295 | epot = -20.8259261820664 | etot = -13.282537499919
+190000  ekin = 4.63141632940872 |  erot = 2.79367442377689 | epot = -20.7076282527969 | etot = -13.2825374996113
+191000  ekin = 4.55257205219687 |  erot = 2.74995133907398 | epot = -20.5850608906317 | etot = -13.2825374993609
+192000  ekin = 4.46841445137449 |  erot = 2.7108083514329 | epot = -20.4617603019722 | etot = -13.2825374991648
+193000  ekin = 4.38080987485702 |  erot = 2.67717312167301 | epot = -20.3405204955445 | etot = -13.2825374990145
+194000  ekin = 4.29140314493158 |  erot = 2.64952891334607 | epot = -20.2234695571822 | etot = -13.2825374989045
+195000  ekin = 4.20164846020147 |  erot = 2.62793199519283 | epot = -20.1121179542319 | etot = -13.2825374988376
+196000  ekin = 4.112799736886 |  erot = 2.6119729730638 | epot = -20.0073102087726 | etot = -13.2825374988228
+197000  ekin = 4.0258589719236 |  erot = 2.60069607327732 | epot = -19.9090925440707 | etot = -13.2825374988698
+198000  ekin = 3.94151021740635 |  erot = 2.59254113732139 | epot = -19.8165888537063 | etot = -13.2825374989786
+199000  ekin = 3.86008920571504 |  erot = 2.58539978552083 | epot = -19.728026490366 | etot = -13.2825374991301
+200000  ekin = 3.78163650515412 |  erot = 2.57685633277384 | epot = -19.6410303372136 | etot = -13.2825374992857
+201000  ekin = 3.70604145366868 |  erot = 2.56461316993842 | epot = -19.5531921230031 | etot = -13.282537499396
+202000  ekin = 3.63323784111708 |  erot = 2.54700321074533 | epot = -19.4627785512819 | etot = -13.2825374994195
+203000  ekin = 3.56337600429933 |  erot = 2.52342549129417 | epot = -19.3693389949301 | etot = -13.2825374993366
+204000  ekin = 3.49690618989364 |  erot = 2.49455276327499 | epot = -19.2739964523245 | etot = -13.2825374991559
+205000  ekin = 3.43455338767261 |  erot = 2.46224574346265 | epot = -19.1793366300441 | etot = -13.2825374989088
+206000  ekin = 3.37721205721374 |  erot = 2.42921548153353 | epot = -19.0889650373857 | etot = -13.2825374986384
+207000  ekin = 3.32580575275754 |  erot = 2.39854397251178 | epot = -19.0068872236571 | etot = -13.2825374983878
+208000  ekin = 3.28114891016496 |  erot = 2.37318814654829 | epot = -18.9368745549054 | etot = -13.2825374981921
+209000  ekin = 3.24383236356932 |  erot = 2.35556506548921 | epot = -18.8819349271337 | etot = -13.2825374980752
+210000  ekin = 3.21413821976281 |  erot = 2.34727297364745 | epot = -18.8439486914582 | etot = -13.282537498048
+211000  ekin = 3.19199204395966 |  erot = 2.34895966766644 | epot = -18.823489209736 | etot = -13.2825374981099
+212000  ekin = 3.17695628121177 |  erot = 2.360321472034 | epot = -18.819815251497 | etot = -13.2825374982512
+213000  ekin = 3.16826455951518 |  erot = 2.38020171954861 | epot = -18.8310037775187 | etot = -13.2825374984549
+214000  ekin = 3.16489343854634 |  erot = 2.4067605217501 | epot = -18.8541914589957 | etot = -13.2825374986993
+215000  ekin = 3.16566474352153 |  erot = 2.4376973804056 | epot = -18.8858996228856 | etot = -13.2825374989585
+216000  ekin = 3.16936807503256 |  erot = 2.47051711068081 | epot = -18.9224226849174 | etot = -13.282537499204
+217000  ekin = 3.16266988026838 |  erot = 2.47868467134127 | epot = -18.9238920507831 | etot = -13.2825374991734
+218000  ekin = 3.17835235865319 |  erot = 2.45704329444878 | epot = -18.9179331413792 | etot = -13.2825374882772
+219000  ekin = 3.26524817202019 |  erot = 2.48120766962855 | epot = -19.0289933444494 | etot = -13.2825375028007
+220000  ekin = 3.31083663795614 |  erot = 2.50602061547625 | epot = -19.0993947418608 | etot = -13.2825374884285
+221000  ekin = 3.33748530919716 |  erot = 2.52276996124467 | epot = -19.1427927588607 | etot = -13.2825374884189
+222000  ekin = 3.36243211589499 |  erot = 2.53668587910066 | epot = -19.181655483376 | etot = -13.2825374883803
+223000  ekin = 3.38541896904217 |  erot = 2.54888617169842 | epot = -19.2168426290796 | etot = -13.282537488339
+224000  ekin = 3.40625812507986 |  erot = 2.56049920868626 | epot = -19.2492948220809 | etot = -13.2825374883148
+225000  ekin = 3.42484722909618 |  erot = 2.57234499865719 | epot = -19.2797297160695 | etot = -13.2825374883162
+226000  ekin = 3.44121067431411 |  erot = 2.58472036633686 | epot = -19.3084685289968 | etot = -13.2825374883458
+227000  ekin = 3.45552721377379 |  erot = 2.59730386680743 | epot = -19.3353685689834 | etot = -13.2825374884022
+228000  ekin = 3.46810974282139 |  erot = 2.6091693120744 | epot = -19.3598165433777 | etot = -13.2825374884819
+229000  ekin = 3.4793267631311 |  erot = 2.61888809507087 | epot = -19.3807523467836 | etot = -13.2825374885816
+230000  ekin = 3.48948003513645 |  erot = 2.62469570471749 | epot = -19.3967132285507 | etot = -13.2825374886968
+231000  ekin = 3.49867242979377 |  erot = 2.62469374220078 | epot = -19.4059036608153 | etot = -13.2825374888207
+232000  ekin = 3.50671171842654 |  erot = 2.6170613032781 | epot = -19.4063105106474 | etot = -13.2825374889427
+233000  ekin = 3.51309701132125 |  erot = 2.60026316425572 | epot = -19.395897664621 | etot = -13.2825374890441
+234000  ekin = 3.51712117494327 |  erot = 2.5732608561 | epot = -19.3729195201406 | etot = -13.2825374890973
+235000  ekin = 3.51809173982137 |  erot = 2.53573892922866 | epot = -19.3363681581185 | etot = -13.2825374890685
+236000  ekin = 3.51562949139304 |  erot = 2.48833922691111 | epot = -19.2865062072295 | etot = -13.2825374889254
+237000  ekin = 3.50996386129235 |  erot = 2.43285732073676 | epot = -19.2253586706787 | etot = -13.2825374886496
+238000  ekin = 3.50212794781253 |  erot = 2.37232394343562 | epot = -19.1569893794952 | etot = -13.2825374882471
+239000  ekin = 3.49397580570111 |  erot = 2.31089750062538 | epot = -19.0874107940787 | etot = -13.2825374877522
+240000  ekin = 3.48799489984455 |  erot = 2.2535377170645 | epot = -19.0240701041318 | etot = -13.2825374872227
+241000  ekin = 3.4869474415209 |  erot = 2.2054938684223 | epot = -18.9749787966723 | etot = -13.2825374867291
+242000  ekin = 3.49341769740518 |  erot = 2.1716922310321 | epot = -18.9476474147781 | etot = -13.2825374863409
+243000  ekin = 3.50935803683834 |  erot = 2.15612557817114 | epot = -18.9480211011257 | etot = -13.2825374861162
+244000  ekin = 3.53571412218956 |  erot = 2.16133426987289 | epot = -18.979585878157 | etot = -13.2825374860946
+245000  ekin = 3.57218201231806 |  erot = 2.18803987534361 | epot = -19.0427593739549 | etot = -13.2825374862933
+246000  ekin = 3.61712090977309 |  erot = 2.23496626996945 | epot = -19.134624666449 | etot = -13.2825374867064
+247000  ekin = 3.66762313707197 |  erot = 2.29886938892499 | epot = -19.2490300133012 | etot = -13.2825374873042
+248000  ekin = 3.7197330409766 |  erot = 2.3747925366233 | epot = -19.377063065633 | etot = -13.2825374880331
+249000  ekin = 3.7687988475912 |  erot = 2.45655776432188 | epot = -19.5078941007305 | etot = -13.2825374888175
+250000  ekin = 3.80993596354031 |  erot = 2.53748030029899 | epot = -19.6299537534039 | etot = -13.2825374895646
+251000  ekin = 3.83856187827056 |  erot = 2.61124537605178 | epot = -19.7323447445001 | etot = -13.2825374901778
+252000  ekin = 3.85094160348732 |  erot = 2.67282602420842 | epot = -19.8063051182675 | etot = -13.2825374905717
+253000  ekin = 3.84466267221376 |  erot = 2.71927370140095 | epot = -19.8464738643054 | etot = -13.2825374906907
+254000  ekin = 3.81895334833665 |  erot = 2.75020964906229 | epot = -19.8517004879202 | etot = -13.2825374905212
+255000  ekin = 3.77477712370614 |  erot = 2.76789565653814 | epot = -19.8252102703408 | etot = -13.2825374900966
+256000  ekin = 3.71467746908406 |  erot = 2.77685421459328 | epot = -19.7740691731677 | etot = -13.2825374894904
+257000  ekin = 3.64239785971379 |  erot = 2.78310854270386 | epot = -19.7080438912194 | etot = -13.2825374888018
+258000  ekin = 3.56234912666851 |  erot = 2.79319020432263 | epot = -19.6380768191282 | etot = -13.2825374881371
+259000  ekin = 3.47902170398396 |  erot = 2.81309489223268 | epot = -19.5746540838083 | etot = -13.2825374875917
+260000  ekin = 3.39644765746004 |  erot = 2.84735592157315 | epot = -19.5263410662695 | etot = -13.2825374872363
+261000  ekin = 3.31779785755485 |  erot = 2.89836390677654 | epot = -19.4986992514401 | etot = -13.2825374871087
+262000  ekin = 3.24516405277549 |  erot = 2.96601202360082 | epot = -19.493713563585 | etot = -13.2825374872087
+263000  ekin = 3.17954694530476 |  erot = 3.04771661067519 | epot = -19.509801043485 | etot = -13.2825374875051
+264000  ekin = 3.12100159498054 |  erot = 3.13875568824872 | epot = -19.5422947711677 | etot = -13.2825374879384
+265000  ekin = 3.068909969511 |  erot = 3.23291804297596 | epot = -19.5843655009193 | etot = -13.2825374884324
+266000  ekin = 3.02230555156861 |  erot = 3.32335252530508 | epot = -19.6281955657834 | etot = -13.2825374889098
+267000  ekin = 2.98016989218859 |  erot = 3.40345614747457 | epot = -19.6661635289715 | etot = -13.2825374893083
+268000  ekin = 2.94163501488609 |  erot = 3.46763177350625 | epot = -19.6918042779853 | etot = -13.282537489593
+269000  ekin = 2.90604069318514 |  erot = 3.51175626238839 | epot = -19.7003344453578 | etot = -13.2825374897842
+270000  ekin = 2.87284037255906 |  erot = 3.53329819601916 | epot = -19.6886760584274 | etot = -13.2825374898492
+271000  ekin = 2.84156688817829 |  erot = 3.53141495904851 | epot = -19.6555193370576 | etot = -13.2825374898308
+272000  ekin = 2.81169493920539 |  erot = 3.50673144119823 | epot = -19.6009638701441 | etot = -13.2825374897405
+273000  ekin = 2.78262532285011 |  erot = 3.46115906465197 | epot = -19.5263218770821 | etot = -13.28253748958
+274000  ekin = 2.7538098130557 |  erot = 3.39781487150794 | epot = -19.4341621738894 | etot = -13.2825374893258
+275000  ekin = 2.72497357924299 |  erot = 3.32097131772016 | epot = -19.3284823859418 | etot = -13.2825374889787
+276000  ekin = 2.69631002934824 |  erot = 3.23585259467473 | epot = -19.2147001125792 | etot = -13.2825374885562
+277000  ekin = 2.66855210196767 |  erot = 3.14826501869249 | epot = -19.0993546087625 | etot = -13.2825374881024
+278000  ekin = 2.64286719085242 |  erot = 3.06403640806158 | epot = -18.9894410865919 | etot = -13.2825374876779
+279000  ekin = 2.6206102822317 |  erot = 2.98836162249344 | epot = -18.8915093920683 | etot = -13.2825374873432
+280000  ekin = 2.60303022005365 |  erot = 2.92520891289703 | epot = -18.810776620091 | etot = -13.2825374871403
+281000  ekin = 2.59103448458094 |  erot = 2.87693253510625 | epot = -18.7505045067693 | etot = -13.2825374870821
+282000  ekin = 2.58508390620569 |  erot = 2.84417540765416 | epot = -18.7117968010114 | etot = -13.2825374871516
+283000  ekin = 2.58523135936705 |  erot = 2.82606103956356 | epot = -18.6938298862415 | etot = -13.2825374873109
+284000  ekin = 2.59126091870015 |  erot = 2.82059473157549 | epot = -18.6943931377914 | etot = -13.2825374875157
+285000  ekin = 2.6028463107778 |  erot = 2.82514472713204 | epot = -18.7105285256397 | etot = -13.2825374877299
+286000  ekin = 2.61964775973889 |  erot = 2.83687342635821 | epot = -18.7390586740322 | etot = -13.2825374879351
+287000  ekin = 2.64167894317198 |  erot = 2.8528506609398 | epot = -18.777067092287 | etot = -13.2825374881753
+288000  ekin = 2.6687167813722 |  erot = 2.87022930110005 | epot = -18.8214835708729 | etot = -13.2825374884007
+289000  ekin = 2.69931643718217 |  erot = 2.88698660758031 | epot = -18.8688405333603 | etot = -13.2825374885979
+290000  ekin = 2.73194963658564 |  erot = 2.90163654912848 | epot = -18.91612367448 | etot = -13.2825374887658
+291000  ekin = 2.76502957907501 |  erot = 2.91324911168725 | epot = -18.9608161796579 | etot = -13.2825374888956
+292000  ekin = 2.79700561900648 |  erot = 2.92149576190988 | epot = -19.0010388698883 | etot = -13.282537488972
+293000  ekin = 2.82654239554718 |  erot = 2.92669002283955 | epot = -19.0357699073658 | etot = -13.2825374889791
+294000  ekin = 2.85272969462388 |  erot = 2.92951972788893 | epot = -19.0647869114596 | etot = -13.2825374889468
+295000  ekin = 2.87508597590098 |  erot = 2.9311082644765 | epot = -19.0887317291891 | etot = -13.2825374888116
+296000  ekin = 2.89378047526675 |  erot = 2.93349300132876 | epot = -19.1098109651873 | etot = -13.2825374885917
+297000  ekin = 2.90976516784938 |  erot = 2.93912517174385 | epot = -19.1314278279134 | etot = -13.2825374883201
+298000  ekin = 2.92469477926692 |  erot = 2.95047845944716 | epot = -19.1577107267524 | etot = -13.2825374880383
+299000  ekin = 2.94065805823336 |  erot = 2.96967690612592 | epot = -19.1928724521541 | etot = -13.2825374877948
+300000  ekin = 2.95980003469262 |  erot = 2.99812642992008 | epot = -19.2404639522493 | etot = -13.2825374876367
+301000  ekin = 2.98391272977048 |  erot = 3.03621252497702 | epot = -19.302662742346 | etot = -13.2825374875985
+302000  ekin = 3.01408971368422 |  erot = 3.08312901018064 | epot = -19.3797562115572 | etot = -13.2825374876923
+303000  ekin = 3.05053302665408 |  erot = 3.13689255668996 | epot = -19.4699630712472 | etot = -13.2825374879032
+304000  ekin = 3.08584972584671 |  erot = 3.19556015974062 | epot = -19.5639473752475 | etot = -13.2825374896602
+305000  ekin = 3.11890909070302 |  erot = 3.26281224727061 | epot = -19.6642588266132 | etot = -13.2825374886396
+306000  ekin = 3.16699270587545 |  erot = 3.33070506272287 | epot = -19.7802352601681 | etot = -13.2825374915697
+307000  ekin = 3.22023032257278 |  erot = 3.3799777181515 | epot = -19.8827455298064 | etot = -13.2825374890821
+308000  ekin = 3.27268739663165 |  erot = 3.41969099128438 | epot = -19.9749158771467 | etot = -13.2825374892307
+309000  ekin = 3.32280425481028 |  erot = 3.44976402097079 | epot = -20.0551057651176 | etot = -13.2825374893365
+310000  ekin = 3.36903652740728 |  erot = 3.46970323071463 | epot = -20.1212772475588 | etot = -13.2825374894369
+311000  ekin = 3.40972253534196 |  erot = 3.47940229944893 | epot = -20.1716623243582 | etot = -13.2825374895673
+312000  ekin = 3.44308129108907 |  erot = 3.47898447382754 | epot = -20.204603254423 | etot = -13.2825374895064
+313000  ekin = 3.46879202758663 |  erot = 3.47087869840748 | epot = -20.2222082156487 | etot = -13.2825374896546
+314000  ekin = 3.48565385463278 |  erot = 3.45582059749242 | epot = -20.2240119419355 | etot = -13.2825374898103
+315000  ekin = 3.4921631329082 |  erot = 3.43373104094955 | epot = -20.2084316637809 | etot = -13.2825374899231
+316000  ekin = 3.48736213303232 |  erot = 3.40482567255629 | epot = -20.1747252955269 | etot = -13.2825374899383
+317000  ekin = 3.46994132507374 |  erot = 3.36841330847356 | epot = -20.1208921250387 | etot = -13.2825374914914
+318000  ekin = 3.43614022048189 |  erot = 3.32066657788102 | epot = -20.0393442896713 | etot = -13.2825374913084
+319000  ekin = 3.38694293952315 |  erot = 3.2636491069797 | epot = -19.9331295374394 | etot = -13.2825374909366
+320000  ekin = 3.32506744212965 |  erot = 3.20113650606275 | epot = -19.8087414386365 | etot = -13.2825374904441
+321000  ekin = 3.25415482891539 |  erot = 3.13766117542953 | epot = -19.6743534942655 | etot = -13.2825374899206
+322000  ekin = 3.17813669787398 |  erot = 3.07780020747378 | epot = -19.5384743947986 | etot = -13.2825374894508
+323000  ekin = 3.10066688252112 |  erot = 3.02549088180775 | epot = -19.4086952534164 | etot = -13.2825374890875
+324000  ekin = 3.02479637479555 |  erot = 2.9835512249436 | epot = -19.2908850885836 | etot = -13.2825374888444
+325000  ekin = 2.95294332411579 |  erot = 2.95347420684863 | epot = -19.1889550196703 | etot = -13.2825374887059
+326000  ekin = 2.88706743998012 |  erot = 2.93544936652532 | epot = -19.1050542951527 | etot = -13.2825374886473
+327000  ekin = 2.82887581625042 |  erot = 2.92851219862423 | epot = -19.0399255035249 | etot = -13.2825374886502
+328000  ekin = 2.7799083006856 |  erot = 2.93074772300673 | epot = -18.9931935123989 | etot = -13.2825374887065
+329000  ekin = 2.74145002280429 |  erot = 2.93954016638564 | epot = -18.9635276780016 | etot = -13.2825374888116
+330000  ekin = 2.71432845550724 |  erot = 2.95189909643594 | epot = -18.9487650408976 | etot = -13.2825374889545
+331000  ekin = 2.69870867088015 |  erot = 2.96486608415783 | epot = -18.9461122441539 | etot = -13.2825374891159
+332000  ekin = 2.69398517733071 |  erot = 2.9759351218084 | epot = -18.9524577884139 | etot = -13.2825374892748
+333000  ekin = 2.69881348537833 |  erot = 2.98337443171614 | epot = -18.9647254065077 | etot = -13.2825374894133
+334000  ekin = 2.71127609678656 |  erot = 2.98637176000363 | epot = -18.9801853463082 | etot = -13.282537489518
+335000  ekin = 2.72916096430101 |  erot = 2.98501165510017 | epot = -18.9967101089767 | etot = -13.2825374895756
+336000  ekin = 2.75032164400955 |  erot = 2.98016551096549 | epot = -19.0130246445444 | etot = -13.2825374895694
+337000  ekin = 2.77304615866171 |  erot = 2.97336445321275 | epot = -19.0289481013653 | etot = -13.2825374894909
+338000  ekin = 2.79631213711555 |  erot = 2.96664518651948 | epot = -19.0454948129873 | etot = -13.2825374893522
+339000  ekin = 2.8198251309544 |  erot = 2.96230352229863 | epot = -19.0646661424453 | etot = -13.2825374891923
+340000  ekin = 2.84381599358249 |  erot = 2.96250923740561 | epot = -19.0888627200583 | etot = -13.2825374890702
+341000  ekin = 2.86861716322249 |  erot = 2.96879944354184 | epot = -19.1199540958278 | etot = -13.2825374890635
+342000  ekin = 2.8942330530754 |  erot = 2.98159830919509 | epot = -19.1583688514537 | etot = -13.2825374891832
+343000  ekin = 2.92230469127443 |  erot = 3.00151195978065 | epot = -19.2063541396099 | etot = -13.2825374885548
+344000  ekin = 2.95328542678957 |  erot = 3.02739469587516 | epot = -19.2632176118817 | etot = -13.282537489217
+345000  ekin = 2.98288076792584 |  erot = 3.05397730230856 | epot = -19.3193955601209 | etot = -13.2825374898865
+346000  ekin = 3.0068362280629 |  erot = 3.07579634903275 | epot = -19.3651700675335 | etot = -13.2825374904379
+347000  ekin = 3.021682039197 |  erot = 3.0883226978178 | epot = -19.3925422277954 | etot = -13.2825374907806
+348000  ekin = 3.02528371459214 |  erot = 3.08873432783574 | epot = -19.3965555333152 | etot = -13.2825374908873
+349000  ekin = 3.01708434471769 |  erot = 3.07610751269362 | epot = -19.3757293482008 | etot = -13.2825374907895
+350000  ekin = 2.99803087494402 |  erot = 3.05108999688533 | epot = -19.3316583623752 | etot = -13.2825374905459
+351000  ekin = 2.97033325354314 |  erot = 3.01539362128504 | epot = -19.268264365027 | etot = -13.2825374901988
+352000  ekin = 2.93755453890544 |  erot = 2.97175102427381 | epot = -19.1918430529999 | etot = -13.2825374898207
+353000  ekin = 2.90330530001813 |  erot = 2.92291261114237 | epot = -19.1087554005693 | etot = -13.2825374894088
+354000  ekin = 2.87126755833568 |  erot = 2.87170321125813 | epot = -19.0255082585641 | etot = -13.2825374889703
+355000  ekin = 2.84520639660643 |  erot = 2.82119115452776 | epot = -18.948935039652 | etot = -13.2825374885178
+356000  ekin = 2.8287863971603 |  erot = 2.7746321329023 | epot = -18.8859560181437 | etot = -13.2825374880811
+357000  ekin = 2.82589501110754 |  erot = 2.73507904234615 | epot = -18.8435115424282 | etot = -13.2825374889745
+358000  ekin = 2.83567543256197 |  erot = 2.6999034357179 | epot = -18.8181163574566 | etot = -13.2825374891768
+359000  ekin = 2.85413863003174 |  erot = 2.66477535390921 | epot = -18.8014514734662 | etot = -13.2825374895252
+360000  ekin = 2.87797108635824 |  erot = 2.62716069413401 | epot = -18.7876692705271 | etot = -13.2825374900349
+361000  ekin = 2.90295419334403 |  erot = 2.58324525246715 | epot = -18.7687369364404 | etot = -13.2825374906292
+362000  ekin = 2.92446718933308 |  erot = 2.52862237257544 | epot = -18.7356270530351 | etot = -13.2825374911266
+363000  ekin = 2.93848759933348 |  erot = 2.45989164640849 | epot = -18.680916737042 | etot = -13.2825374913
+364000  ekin = 2.94271150164586 |  erot = 2.37661313123214 | epot = -18.6018621239955 | etot = -13.2825374911175
+365000  ekin = 2.93600170081438 |  erot = 2.28250131433965 | epot = -18.5010405056253 | etot = -13.2825374904713
+366000  ekin = 2.91934189957478 |  erot = 2.18525996401368 | epot = -18.3871393531652 | etot = -13.2825374895768
+367000  ekin = 2.89548895825519 |  erot = 2.0946888564492 | epot = -18.2727153033882 | etot = -13.2825374886839
+368000  ekin = 2.86763306547926 |  erot = 2.02026878405327 | epot = -18.1704393375192 | etot = -13.2825374879867
+369000  ekin = 2.83845106986046 |  erot = 1.96931673436804 | epot = -18.0903052917965 | etot = -13.282537487568
+370000  ekin = 2.80963551309284 |  erot = 1.94618455936313 | epot = -18.0383575598705 | etot = -13.2825374874145
+371000  ekin = 2.78188668089849 |  erot = 1.95235490032645 | epot = -18.0167790686888 | etot = -13.2825374874639
+372000  ekin = 2.75518266190993 |  erot = 1.98699478725745 | epot = -18.0247149368147 | etot = -13.2825374876473
+373000  ekin = 2.7291288052834 |  erot = 2.04757125854604 | epot = -18.0592375517431 | etot = -13.2825374879136
+374000  ekin = 2.7032481730965 |  erot = 2.13030562163268 | epot = -18.1160912829679 | etot = -13.2825374882387
+375000  ekin = 2.67714701016873 |  erot = 2.23039820126271 | epot = -18.1900827000525 | etot = -13.282537488621
+376000  ekin = 2.65054772278943 |  erot = 2.34206662745006 | epot = -18.2751518393106 | etot = -13.2825374890711
+377000  ekin = 2.62322866602789 |  erot = 2.45852983339147 | epot = -18.3642959890092 | etot = -13.2825374895898
+378000  ekin = 2.59495135704074 |  erot = 2.57214449993232 | epot = -18.4496333471184 | etot = -13.2825374901453
+379000  ekin = 2.56546707826881 |  erot = 2.67491697597423 | epot = -18.522921544903 | etot = -13.2825374906599
+380000  ekin = 2.53466143096452 |  erot = 2.75950320018323 | epot = -18.5767021221686 | etot = -13.2825374910209
+381000  ekin = 2.50280930121905 |  erot = 2.82054519918234 | epot = -18.605891991525 | etot = -13.2825374911236
+382000  ekin = 2.47081272773286 |  erot = 2.85587907290837 | epot = -18.6092292915673 | etot = -13.2825374909261
+383000  ekin = 2.44026108011578 |  erot = 2.86702983653801 | epot = -18.5898284071325 | etot = -13.2825374904788
+384000  ekin = 2.41324034479873 |  erot = 2.85867137365971 | epot = -18.5544492083626 | etot = -13.2825374899041
+385000  ekin = 2.3919736779495 |  erot = 2.83724859058569 | epot = -18.5117597578745 | etot = -13.2825374893393
+386000  ekin = 2.37848037079693 |  erot = 2.80936838549168 | epot = -18.4703862451677 | etot = -13.2825374888791
+387000  ekin = 2.37440773877138 |  erot = 2.78057799551461 | epot = -18.4375232228406 | etot = -13.2825374885547
+388000  ekin = 2.38106033998944 |  erot = 2.75482980994152 | epot = -18.4184276382777 | etot = -13.2825374883468
+389000  ekin = 2.3995269472836 |  erot = 2.73455852133737 | epot = -18.4166229568386 | etot = -13.2825374882176
+390000  ekin = 2.43075796801538 |  erot = 2.72108399953604 | epot = -18.4343794556925 | etot = -13.2825374881411
+391000  ekin = 2.47547758104125 |  erot = 2.71503282252802 | epot = -18.4730478916894 | etot = -13.2825374881201
+392000  ekin = 2.53389941336301 |  erot = 2.71657607916961 | epot = -18.5330129807166 | etot = -13.282537488184
+393000  ekin = 2.60531467139514 |  erot = 2.72543162367145 | epot = -18.6132837834377 | etot = -13.2825374883712
+394000  ekin = 2.68770614221053 |  erot = 2.74072420161599 | epot = -18.710967832529 | etot = -13.2825374887024
+395000  ekin = 2.77757589910946 |  erot = 2.76089277951269 | epot = -18.821006167779 | etot = -13.2825374891568
+396000  ekin = 2.87012638573289 |  erot = 2.78383015196004 | epot = -18.9364940273591 | etot = -13.2825374896661
+397000  ekin = 2.95979968456986 |  erot = 2.80730760068458 | epot = -19.0496447753932 | etot = -13.2825374901387
+398000  ekin = 3.04101675292502 |  erot = 2.82953067572591 | epot = -19.1530849191498 | etot = -13.2825374904989
+399000  ekin = 3.10335323687934 |  erot = 2.84223393462917 | epot = -19.2281247208206 | etot = -13.2825375493121
+400000  ekin = 3.10435999781796 |  erot = 2.68059016642954 | epot = -19.0674876235022 | etot = -13.2825374592547
+401000  ekin = 3.39309095570315 |  erot = 2.63997900103007 | epot = -19.3156074940371 | etot = -13.2825375373039
+402000  ekin = 3.44106634979645 |  erot = 2.659790716706 | epot = -19.3833945765517 | etot = -13.2825375100493
+403000  ekin = 3.43207406397009 |  erot = 2.67998452069831 | epot = -19.394596094653 | etot = -13.2825375099846
+404000  ekin = 3.40426891789311 |  erot = 2.70237957195789 | epot = -19.3891859997632 | etot = -13.2825375099122
+405000  ekin = 3.3593347341666 |  erot = 2.72607645467142 | epot = -19.367948698657 | etot = -13.282537509819
+406000  ekin = 3.29966540905146 |  erot = 2.74995079993995 | epot = -19.3321537186901 | etot = -13.2825375096987
+407000  ekin = 3.2282311798008 |  erot = 2.77286165525633 | epot = -19.2836303446157 | etot = -13.2825375095586
+408000  ekin = 3.1483591073718 |  erot = 2.79373949027867 | epot = -19.2246361070933 | etot = -13.2825375094428
+409000  ekin = 3.06351542881959 |  erot = 2.81131469884056 | epot = -19.1573676369638 | etot = -13.2825375093037
+410000  ekin = 2.97699949579686 |  erot = 2.82462679197841 | epot = -19.0841637969767 | etot = -13.2825375092014
+411000  ekin = 2.89165449989684 |  erot = 2.83289882075493 | epot = -19.0070908297837 | etot = -13.2825375091319
+412000  ekin = 2.80978906687504 |  erot = 2.83549592230531 | epot = -18.9278224982521 | etot = -13.2825375090718
+413000  ekin = 2.73325536965585 |  erot = 2.83215388787228 | epot = -18.8479467665131 | etot = -13.282537508985
+414000  ekin = 2.66364879696115 |  erot = 2.82325639291671 | epot = -18.7694426987162 | etot = -13.2825375088383
+415000  ekin = 2.60253860597198 |  erot = 2.81004531899789 | epot = -18.6951214335864 | etot = -13.2825375086165
+416000  ekin = 2.55161661471215 |  erot = 2.7946463118532 | epot = -18.6288004349012 | etot = -13.2825375083358
+417000  ekin = 2.51265407611577 |  erot = 2.77984605489432 | epot = -18.5750376413434 | etot = -13.2825375103333
+418000  ekin = 2.47334604007925 |  erot = 2.77799997552572 | epot = -18.5338835235875 | etot = -13.2825375079825
+419000  ekin = 2.44559608969893 |  erot = 2.79655231012718 | epot = -18.5246859081463 | etot = -13.2825375083202
+420000  ekin = 2.44884495813904 |  erot = 2.81276776866598 | epot = -18.5441502345702 | etot = -13.2825375077651
+421000  ekin = 2.47134322854002 |  erot = 2.82756585669941 | epot = -18.5814465933144 | etot = -13.2825375080749
+422000  ekin = 2.50522487694504 |  erot = 2.84806830842347 | epot = -18.6358306938984 | etot = -13.2825375085299
+423000  ekin = 2.54673540365736 |  erot = 2.87162843047175 | epot = -18.7009013431671 | etot = -13.282537509038
+424000  ekin = 2.5915545267989 |  erot = 2.89540834353031 | epot = -18.7695003798181 | etot = -13.2825375094888
+425000  ekin = 2.63549518712503 |  erot = 2.9172494646209 | epot = -18.8352821615391 | etot = -13.2825375097932
+426000  ekin = 2.67515430284032 |  erot = 2.93632167691171 | epot = -18.8940134896611 | etot = -13.2825375099091
+427000  ekin = 2.70835356711895 |  erot = 2.95332774897864 | epot = -18.9442188259411 | etot = -13.2825375098435
+428000  ekin = 2.73429370857904 |  erot = 2.97029523905205 | epot = -18.9871264572657 | etot = -13.2825375096346
+429000  ekin = 2.75344687778548 |  erot = 2.99015713231241 | epot = -19.026141519429 | etot = -13.2825375093311
+430000  ekin = 2.76726512076715 |  erot = 3.01631311484004 | epot = -19.0661157445923 | etot = -13.2825375089851
+431000  ekin = 2.77776520584482 |  erot = 3.05220345439827 | epot = -19.1125061689064 | etot = -13.2825375086633
+432000  ekin = 2.78700254672782 |  erot = 3.10077153004471 | epot = -19.1703115852294 | etot = -13.2825375084569
+433000  ekin = 2.79644099946406 |  erot = 3.16368547122764 | epot = -19.2426639791689 | etot = -13.2825375084772
+434000  ekin = 2.8062952810192 |  erot = 3.24036053939458 | epot = -19.3291933292362 | etot = -13.2825375088224
+435000  ekin = 2.81503854863169 |  erot = 3.32707633256549 | epot = -19.4246523907207 | etot = -13.2825375095236
+436000  ekin = 2.81936003428183 |  erot = 3.41666372807462 | epot = -19.5185612728498 | etot = -13.2825375104934
+437000  ekin = 2.81480689571151 |  erot = 3.49920681099962 | epot = -19.5965512182294 | etot = -13.2825375115182
+438000  ekin = 2.79709037800121 |  erot = 3.56380823492809 | epot = -19.643436125261 | etot = -13.2825375123317
+439000  ekin = 2.76357573484572 |  erot = 3.60097663047473 | epot = -19.6470898780363 | etot = -13.2825375127159
+440000  ekin = 2.71419714341371 |  erot = 3.6047593537822 | epot = -19.6014940098261 | etot = -13.2825375126302
+441000  ekin = 2.65147586146338 |  erot = 3.57350682801194 | epot = -19.5075202016436 | etot = -13.2825375121683
+442000  ekin = 2.57978868207942 |  erot = 3.50949061111828 | epot = -19.3718168046656 | etot = -13.2825375114679
+443000  ekin = 2.50456558754104 |  erot = 3.4178674196423 | epot = -19.2049705178168 | etot = -13.2825375106335
+444000  ekin = 2.43185299049922 |  erot = 3.30558723792078 | epot = -19.0199777381447 | etot = -13.2825375097247
+445000  ekin = 2.36817510309063 |  erot = 3.18052048207573 | epot = -18.8312330939526 | etot = -13.2825375087862
+446000  ekin = 2.32036350430527 |  erot = 3.05081891044131 | epot = -18.6537199226123 | etot = -13.2825375078657
+447000  ekin = 2.29507009387958 |  erot = 2.92434156859069 | epot = -18.5019491695481 | etot = -13.2825375070778
+448000  ekin = 2.29792306265903 |  erot = 2.80795199471116 | epot = -18.3884125638822 | etot = -13.282537506512
+449000  ekin = 2.33256968728525 |  erot = 2.7069587718453 | epot = -18.3220659653954 | etot = -13.2825375062648
+450000  ekin = 2.39980570006764 |  erot = 2.6245346844449 | epot = -18.3068778909135 | etot = -13.282537506401
+451000  ekin = 2.49706752601175 |  erot = 2.56128240620743 | epot = -18.3408874391531 | etot = -13.2825375069339
+452000  ekin = 2.61842576959501 |  erot = 2.51510244034445 | epot = -18.4160657177213 | etot = -13.2825375077819
+453000  ekin = 2.75505822099958 |  erot = 2.48156991528656 | epot = -18.5191656452411 | etot = -13.2825375089549
+454000  ekin = 2.89583245290297 |  erot = 2.45420794646339 | epot = -18.6325779096657 | etot = -13.2825375102994
+455000  ekin = 3.02803920576056 |  erot = 2.42568753016163 | epot = -18.736264247583 | etot = -13.2825375116608
+456000  ekin = 3.13847091959985 |  erot = 2.38932191986942 | epot = -18.8103303522404 | etot = -13.2825375127711
+457000  ekin = 3.21547363215232 |  erot = 2.34093725374963 | epot = -18.83894839917 | etot = -13.2825375132681
+458000  ekin = 3.2519255085167 |  erot = 2.28077893487382 | epot = -18.8152419562951 | etot = -13.2825375129046
+459000  ekin = 3.24761130320326 |  erot = 2.21429904484092 | epot = -18.744447859815 | etot = -13.2825375117708
+460000  ekin = 3.20922400634736 |  erot = 2.15086461860742 | epot = -18.6426261352081 | etot = -13.2825375102533
+461000  ekin = 3.14796311215653 |  erot = 2.10092694607039 | epot = -18.5314275670048 | etot = -13.2825375087779
+462000  ekin = 3.07634336775073 |  erot = 2.07329933806439 | epot = -18.4321802134279 | etot = -13.2825375076128
+463000  ekin = 3.00570913413418 |  erot = 2.07367404520667 | epot = -18.3619206861977 | etot = -13.2825375068568
+464000  ekin = 2.9448582997097 |  erot = 2.10431183996111 | epot = -18.331707646191 | etot = -13.2825375065202
+465000  ekin = 2.89946798284609 |  erot = 2.16425406354561 | epot = -18.3462595529816 | etot = -13.2825375065899
+466000  ekin = 2.87195252749972 |  erot = 2.24955307487499 | epot = -18.4040431094255 | etot = -13.2825375070508
+467000  ekin = 2.86158324930207 |  erot = 2.3533892427293 | epot = -18.4975099999046 | etot = -13.2825375078732
+468000  ekin = 2.86493243611993 |  erot = 2.46640127706619 | epot = -18.6138712219846 | etot = -13.2825375087985
+469000  ekin = 2.87700241085747 |  erot = 2.57824581694139 | epot = -18.7377857379035 | etot = -13.2825375101046
+470000  ekin = 2.89115454215414 |  erot = 2.67606199010798 | epot = -18.8497540435902 | etot = -13.2825375113281
+471000  ekin = 2.90087699699085 |  erot = 2.74765202467846 | epot = -18.9310665338721 | etot = -13.2825375122028
+472000  ekin = 2.90129360656583 |  erot = 2.7844228810356 | epot = -18.9682540001117 | etot = -13.2825375125102
+473000  ekin = 2.89014262487726 |  erot = 2.78350866545128 | epot = -18.9561888025163 | etot = -13.2825375121877
+474000  ekin = 2.8679845551896 |  erot = 2.74843722225596 | epot = -18.8989592888163 | etot = -13.2825375113708
+475000  ekin = 2.83751222123126 |  erot = 2.68789202057427 | epot = -18.8079417521389 | etot = -13.2825375103333
+476000  ekin = 2.80225697256743 |  erot = 2.61311305367502 | epot = -18.6979075356038 | etot = -13.2825375093613
+477000  ekin = 2.76525060538535 |  erot = 2.53510543119006 | epot = -18.5828935452222 | etot = -13.2825375086468
+478000  ekin = 2.72814283271883 |  erot = 2.46266477167839 | epot = -18.4733451126463 | etot = -13.282537508249
+479000  ekin = 2.69099471858041 |  erot = 2.40160392945098 | epot = -18.375136156148 | etot = -13.2825375081166
+480000  ekin = 2.6526681049776 |  erot = 2.35496214915731 | epot = -18.2901677623243 | etot = -13.2825375081894
+481000  ekin = 2.611442355162 |  erot = 2.32364519373677 | epot = -18.2176250571627 | etot = -13.282537508264
+482000  ekin = 2.565776730153 |  erot = 2.30767778316155 | epot = -18.1559920216392 | etot = -13.2825375083247
+483000  ekin = 2.51481850308162 |  erot = 2.30660853349362 | epot = -18.1039645449013 | etot = -13.2825375083261
+484000  ekin = 2.45838132863017 |  erot = 2.3198450068296 | epot = -18.0607638434524 | etot = -13.2825375079926
+485000  ekin = 2.37536403481855 |  erot = 2.30798475223331 | epot = -17.9658863029946 | etot = -13.2825375159427
+486000  ekin = 2.31029787369058 |  erot = 2.27486987654653 | epot = -17.8677052455649 | etot = -13.2825374953278
+487000  ekin = 2.35903895728042 |  erot = 2.35840823831765 | epot = -17.9999847156837 | etot = -13.2825375200856
+488000  ekin = 2.35207405535098 |  erot = 2.45495770508831 | epot = -18.0895692764695 | etot = -13.2825375160302
+489000  ekin = 2.32025825397052 |  erot = 2.54616767539779 | epot = -18.1489634454364 | etot = -13.2825375160681
+490000  ekin = 2.29515153869984 |  erot = 2.64227715696153 | epot = -18.2199662119964 | etot = -13.282537516335
+491000  ekin = 2.27724499850078 |  erot = 2.73950547060331 | epot = -18.2992879857125 | etot = -13.2825375166084
+492000  ekin = 2.26670396937252 |  erot = 2.83351832936053 | epot = -18.3827598156682 | etot = -13.2825375169351
+493000  ekin = 2.26314468317306 |  erot = 2.91977614251813 | epot = -18.4654583429642 | etot = -13.282537517273
+494000  ekin = 2.26577113863215 |  erot = 2.99399214332928 | epot = -18.5423007995401 | etot = -13.2825375175787
+495000  ekin = 2.27355094493377 |  erot = 3.05259857144223 | epot = -18.6086870341908 | etot = -13.2825375178148
+496000  ekin = 2.28538641733465 |  erot = 3.09313022185941 | epot = -18.661054157153 | etot = -13.282537517959
+497000  ekin = 2.3002347482521 |  erot = 3.11444072103781 | epot = -18.6972129872905 | etot = -13.2825375180006
+498000  ekin = 2.31719365941364 |  erot = 3.11678508297333 | epot = -18.7165162603266 | etot = -13.2825375179397
+499000  ekin = 2.33554254163157 |  erot = 3.10178716717433 | epot = -18.7198672265901 | etot = -13.2825375177842
+500000  ekin = 2.31317350075609 |  erot = 3.05449093052383 | epot = -18.6502019679387 | etot = -13.2825375366588
+501000  ekin = 2.31231722963358 |  erot = 3.00810318070389 | epot = -18.6029579370661 | etot = -13.2825375267286
+502000  ekin = 2.38999638954889 |  erot = 2.98467042895374 | epot = -18.657204342138 | etot = -13.2825375236353
+503000  ekin = 2.41312387634462 |  erot = 2.93091691360098 | epot = -18.6265783132937 | etot = -13.2825375233481
+504000  ekin = 2.43600229238282 |  erot = 2.88130858484448 | epot = -18.5998484003617 | etot = -13.2825375231344
+505000  ekin = 2.45757791197103 |  erot = 2.84011866669662 | epot = -18.5802341017161 | etot = -13.2825375230484
+506000  ekin = 2.47627134224707 |  erot = 2.81025901810999 | epot = -18.5690678834978 | etot = -13.2825375231408
+507000  ekin = 2.48985246050729 |  erot = 2.79268587937519 | epot = -18.5650758633262 | etot = -13.2825375234437
+508000  ekin = 2.49542483825231 |  erot = 2.78597986942009 | epot = -18.5639422316207 | etot = -13.2825375239483
+509000  ekin = 2.48963204749862 |  erot = 2.78630577999958 | epot = -18.5584753520799 | etot = -13.2825375245818
+510000  ekin = 2.46917438876006 |  erot = 2.78796571286371 | epot = -18.5396776268285 | etot = -13.2825375252047
+511000  ekin = 2.43159454916956 |  erot = 2.78459744700141 | epot = -18.4987295218192 | etot = -13.2825375256482
+512000  ekin = 2.37609227914812 |  erot = 2.7707369794783 | epot = -18.4293667844085 | etot = -13.2825375257821
+513000  ekin = 2.30402039320529 |  erot = 2.74317280239451 | epot = -18.3297307211707 | etot = -13.2825375255709
+514000  ekin = 2.21884081240883 |  erot = 2.70155414867794 | epot = -18.2029324861636 | etot = -13.2825375250768
+515000  ekin = 2.12561338169144 |  erot = 2.64810551844221 | epot = -18.0562564245494 | etot = -13.2825375244158
+516000  ekin = 2.0302995856451 |  erot = 2.5867398599196 | epot = -17.8995769692659 | etot = -13.2825375237012
+517000  ekin = 1.93914577194817 |  erot = 2.52206054313542 | epot = -17.7437438380945 | etot = -13.2825375230109
+518000  ekin = 1.85826662411615 |  erot = 2.45858700715108 | epot = -17.5993911536592 | etot = -13.2825375223919
+519000  ekin = 1.79333215324367 |  erot = 2.40035341708211 | epot = -17.4762230921876 | etot = -13.2825375218619
+520000  ekin = 1.74929005168975 |  erot = 2.35078235676691 | epot = -17.3826099298929 | etot = -13.2825375214363
+521000  ekin = 1.73007209345073 |  erot = 2.31266171840817 | epot = -17.3252713329969 | etot = -13.282537521138
+522000  ekin = 1.73822781682595 |  erot = 2.2881155718937 | epot = -17.3088809097143 | etot = -13.2825375209947
+523000  ekin = 1.77456624772603 |  erot = 2.2785083458307 | epot = -17.3356121145903 | etot = -13.2825375210336
+524000  ekin = 1.83790458514344 |  erot = 2.28429322274723 | epot = -17.4047353291616 | etot = -13.2825375212709
+525000  ekin = 1.92500868748296 |  erot = 2.30484700359195 | epot = -17.5123932127819 | etot = -13.282537521707
+526000  ekin = 2.0307578025818 |  erot = 2.33833465322601 | epot = -17.651629978134 | etot = -13.2825375223262
+527000  ekin = 2.14850843905356 |  erot = 2.38164040104833 | epot = -17.8126863631983 | etot = -13.2825375230964
+528000  ekin = 2.27060096649051 |  erot = 2.43041424715665 | epot = -17.9835527376135 | etot = -13.2825375239663
+529000  ekin = 2.38896012863249 |  erot = 2.4793138751117 | epot = -18.1508115286032 | etot = -13.282537524859
+530000  ekin = 2.49576940535655 |  erot = 2.52254117021849 | epot = -18.3008481012414 | etot = -13.2825375256663
+531000  ekin = 2.58420744220974 |  erot = 2.55472238426385 | epot = -18.4214673527334 | etot = -13.2825375262598
+532000  ekin = 2.64918587017627 |  erot = 2.57201883162556 | epot = -18.5037422283274 | etot = -13.2825375265255
+533000  ekin = 2.68793333155572 |  erot = 2.57313230810709 | epot = -18.5436031660763 | etot = -13.2825375264134
+534000  ekin = 2.70021208216117 |  erot = 2.55975253147949 | epot = -18.542502139612 | etot = -13.2825375259714
+535000  ekin = 2.68802701634936 |  erot = 2.53615014862128 | epot = -18.5067146903044 | etot = -13.2825375253337
+536000  ekin = 2.65489019113449 |  erot = 2.50801671125187 | epot = -18.445444427055 | etot = -13.2825375246686
+537000  ekin = 2.60490332065097 |  erot = 2.48102333788784 | epot = -18.3684641826523 | etot = -13.2825375241135
+538000  ekin = 2.54198784537002 |  erot = 2.45965628961172 | epot = -18.2841816579271 | etot = -13.2825375229454
+539000  ekin = 2.47150013366557 |  erot = 2.44756195583901 | epot = -18.2015996124771 | etot = -13.2825375229725
+540000  ekin = 2.39647534126896 |  erot = 2.4452543590462 | epot = -18.1242672233716 | etot = -13.2825375230564
+541000  ekin = 2.31786635168338 |  erot = 2.45130088253407 | epot = -18.0517047573377 | etot = -13.2825375231202
+542000  ekin = 2.23702678132889 |  erot = 2.4642388816219 | epot = -17.983803186044 | etot = -13.2825375230932
+543000  ekin = 2.15612181951174 |  erot = 2.483136674149 | epot = -17.9217960165952 | etot = -13.2825375229345
+544000  ekin = 2.07836492819822 |  erot = 2.50789688708103 | epot = -17.8687993379301 | etot = -13.2825375226508
+545000  ekin = 2.00794258372951 |  erot = 2.53918840886296 | epot = -17.8296685148941 | etot = -13.2825375223016
+546000  ekin = 1.94957099412975 |  erot = 2.578008196098 | epot = -17.8101167122069 | etot = -13.2825375219791
+547000  ekin = 1.9077624243153 |  erot = 2.62501532097517 | epot = -17.8153152670783 | etot = -13.2825375217878
+548000  ekin = 1.88600984710573 |  erot = 2.67988146408135 | epot = -17.8484288329841 | etot = -13.282537521797
+549000  ekin = 1.88615242689691 |  erot = 2.74090375620349 | epot = -17.909593705124 | etot = -13.2825375220236
+550000  ekin = 1.90811801080135 |  erot = 2.80501593005898 | epot = -17.9956714632894 | etot = -13.282537522429
+551000  ekin = 1.95008337623402 |  erot = 2.86816804419082 | epot = -18.1007889433658 | etot = -13.2825375229409
+552000  ekin = 2.00893649351174 |  erot = 2.92590890426342 | epot = -18.2173829212562 | etot = -13.282537523481
+553000  ekin = 2.08084803911103 |  erot = 2.97396311008449 | epot = -18.3373486731828 | etot = -13.2825375239872
+554000  ekin = 2.16178844742615 |  erot = 3.00865361313796 | epot = -18.4529795849852 | etot = -13.2825375244211
+555000  ekin = 2.24792031030894 |  erot = 3.02713377648476 | epot = -18.5575916115531 | etot = -13.2825375247594
+556000  ekin = 2.3358895304738 |  erot = 3.02749801445229 | epot = -18.6459250699077 | etot = -13.2825375249816
+557000  ekin = 2.42273135018697 |  erot = 3.00799378133903 | epot = -18.7132626568713 | etot = -13.2825375253453
+558000  ekin = 2.50467530619079 |  erot = 2.96457109807151 | epot = -18.7517839296409 | etot = -13.2825375253786
+559000  ekin = 2.57989829547792 |  erot = 2.89795083547094 | epot = -18.7603866561117 | etot = -13.2825375251628
+560000  ekin = 2.64819333040997 |  erot = 2.8115011418383 | epot = -18.7422319969952 | etot = -13.282537524747
+561000  ekin = 2.71041014716014 |  erot = 2.71050571090859 | epot = -18.7034533823107 | etot = -13.282537524242
+562000  ekin = 2.76764108184349 |  erot = 2.60142670481719 | epot = -18.6516053104339 | etot = -13.2825375237732
+563000  ekin = 2.82041332178183 |  erot = 2.49094539995269 | epot = -18.5938962451522 | etot = -13.2825375234177
+564000  ekin = 2.86835957176528 |  erot = 2.38512022706598 | epot = -18.5360173220094 | etot = -13.2825375231781
+565000  ekin = 2.9105055625117 |  erot = 2.2888699309895 | epot = -18.4819130165188 | etot = -13.2825375230176
+566000  ekin = 2.9458361953691 |  erot = 2.20572382108587 | epot = -18.4340975393717 | etot = -13.2825375229167
+567000  ekin = 2.97364576057443 |  erot = 2.13764971279795 | epot = -18.3938329962642 | etot = -13.2825375228919
+568000  ekin = 2.99348659092395 |  erot = 2.08490808290625 | epot = -18.3609321968044 | etot = -13.2825375229742
+569000  ekin = 3.00487691648673 |  erot = 2.04604350391468 | epot = -18.3334579435673 | etot = -13.2825375231659
+570000  ekin = 3.00710556183365 |  erot = 2.01819764938775 | epot = -18.3078407346463 | etot = -13.2825375234249
+571000  ekin = 2.99930468668979 |  erot = 1.99774357915448 | epot = -18.2795857895248 | etot = -13.2825375236806
+572000  ekin = 2.98076231240025 |  erot = 1.98107714031761 | epot = -18.2443769765725 | etot = -13.2825375238547
+573000  ekin = 2.95134611356941 |  erot = 1.96535938854021 | epot = -18.1992430259928 | etot = -13.2825375238832
+574000  ekin = 2.91190615159568 |  erot = 1.94906161388935 | epot = -18.1435052892122 | etot = -13.2825375237272
+575000  ekin = 2.86455063786228 |  erot = 1.93223482555562 | epot = -18.0793229868005 | etot = -13.2825375233826
+576000  ekin = 2.81270724058511 |  erot = 1.91646454101314 | epot = -18.0117093044836 | etot = -13.2825375228853
+577000  ekin = 2.76090536133269 |  erot = 1.90450382048591 | epot = -17.9479467041287 | etot = -13.2825375223101
+578000  ekin = 2.71428886863997 |  erot = 1.89991544414445 | epot = -17.8967418344493 | etot = -13.2825375216648
+579000  ekin = 2.67747364116322 |  erot = 1.90598531717311 | epot = -17.8659964796474 | etot = -13.2825375213111
+580000  ekin = 2.65399321105106 |  erot = 1.92422800253716 | epot = -17.8607587347071 | etot = -13.2825375211188
+581000  ekin = 2.64614770794032 |  erot = 1.95489680825185 | epot = -17.8835820373323 | etot = -13.2825375211401
+582000  ekin = 2.65445309241879 |  erot = 1.99685469221747 | epot = -17.9338453060313 | etot = -13.2825375213951
+583000  ekin = 2.67733631615637 |  erot = 2.04763712314961 | epot = -18.0075109611623 | etot = -13.2825375218563
+584000  ekin = 2.71054840612045 |  erot = 2.10372916962355 | epot = -18.096815098413 | etot = -13.282537522669
+585000  ekin = 2.7473776369314 |  erot = 2.16073411837509 | epot = -18.1906492786902 | etot = -13.2825375233837
+586000  ekin = 2.78137869995175 |  erot = 2.21419390101714 | epot = -18.2781101249393 | etot = -13.2825375239704
+587000  ekin = 2.80697388616102 |  erot = 2.26053952383221 | epot = -18.3500509343302 | etot = -13.282537524337
+588000  ekin = 2.82026432882546 |  erot = 2.29760845660692 | epot = -18.4004103098989 | etot = -13.2825375244665
+589000  ekin = 2.81926713949848 |  erot = 2.32471340247678 | epot = -18.4265180663829 | etot = -13.2825375244076
+590000  ekin = 2.80363912226355 |  erot = 2.34232144628702 | epot = -18.4284980927864 | etot = -13.2825375242358
+591000  ekin = 2.77414618261205 |  erot = 2.35158565793045 | epot = -18.4082693645578 | etot = -13.2825375240153
+592000  ekin = 2.7321416208566 |  erot = 2.3539767270547 | epot = -18.3686558716927 | etot = -13.2825375237814
+593000  ekin = 2.67919893320834 |  erot = 2.35111989743036 | epot = -18.3128563541844 | etot = -13.2825375235457
+594000  ekin = 2.61691997595324 |  erot = 2.34478637080631 | epot = -18.2442438700672 | etot = -13.2825375233077
+595000  ekin = 2.54687226720393 |  erot = 2.33692048101831 | epot = -18.1663302712882 | etot = -13.282537523066
+596000  ekin = 2.47060065869688 |  erot = 2.32961421032747 | epot = -18.0827523918473 | etot = -13.2825375228229
+597000  ekin = 2.38967001339545 |  erot = 2.32500896596326 | epot = -17.9972165019425 | etot = -13.2825375225838
+598000  ekin = 2.30571268105541 |  erot = 2.32515834060355 | epot = -17.913408544013 | etot = -13.2825375223541
+599000  ekin = 2.22046028573514 |  erot = 2.33189649117281 | epot = -17.8348942990478 | etot = -13.2825375221398
+600000  ekin = 2.13574370513921 |  erot = 2.34673734055139 | epot = -17.7650185676378 | etot = -13.2825375219472
+601000  ekin = 2.05345123960456 |  erot = 2.37080533027377 | epot = -17.7067940916633 | etot = -13.282537521785
+602000  ekin = 1.97544542075628 |  erot = 2.40478648027266 | epot = -17.6627694226918 | etot = -13.2825375216629
+603000  ekin = 1.90345105222632 |  erot = 2.44889273151597 | epot = -17.6348813053331 | etot = -13.2825375215908
+604000  ekin = 1.83893895965995 |  erot = 2.50284547564257 | epot = -17.6243219568744 | etot = -13.2825375215719
+605000  ekin = 1.78304137675034 |  erot = 2.56590806862715 | epot = -17.6314869669817 | etot = -13.2825375216042
+606000  ekin = 1.73651700581096 |  erot = 2.63697396076247 | epot = -17.6560284882492 | etot = -13.2825375216757
+607000  ekin = 1.69978182244358 |  erot = 2.71471645477294 | epot = -17.6970357989852 | etot = -13.2825375217686
+608000  ekin = 1.67299629761026 |  erot = 2.79777529949349 | epot = -17.7533091189676 | etot = -13.2825375218638
+609000  ekin = 1.65617951207475 |  erot = 2.88492902620219 | epot = -17.8236460602245 | etot = -13.2825375219476
+610000  ekin = 1.64931072757095 |  erot = 2.97519911997342 | epot = -17.9070473695603 | etot = -13.282537522016
+611000  ekin = 1.65238727041245 |  erot = 3.06785620888426 | epot = -18.0027810013707 | etot = -13.282537522074
+612000  ekin = 1.66542824850629 |  erot = 3.16233835683711 | epot = -18.1103041274766 | etot = -13.2825375221332
+613000  ekin = 1.68843555876185 |  erot = 3.25812385015835 | epot = -18.229096931125 | etot = -13.2825375222048
+614000  ekin = 1.72133601897789 |  erot = 3.35460405549752 | epot = -18.3584775967737 | etot = -13.2825375222983
+615000  ekin = 1.7639238606995 |  erot = 3.45098117154084 | epot = -18.4974425546615 | etot = -13.2825375224212
+616000  ekin = 1.81580855367603 |  erot = 3.54618284196742 | epot = -18.6445289182257 | etot = -13.2825375225823
+617000  ekin = 1.87635766459386 |  erot = 3.63876572276478 | epot = -18.7976609101535 | etot = -13.2825375227949
+618000  ekin = 1.94461656677602 |  erot = 3.72678561689433 | epot = -18.9539397067471 | etot = -13.2825375230768
+619000  ekin = 2.01919440960516 |  erot = 3.80764382999315 | epot = -19.1093757630453 | etot = -13.282537523447
+620000  ekin = 2.09812821746402 |  erot = 3.87796751070656 | epot = -19.2586332520846 | etot = -13.282537523914
+621000  ekin = 2.17876896466308 |  erot = 3.93362434682925 | epot = -19.3949308359561 | etot = -13.2825375244638
+622000  ekin = 2.25776112958401 |  erot = 3.96997899351304 | epot = -19.5102776481477 | etot = -13.2825375250507
+623000  ekin = 2.33118920334088 |  erot = 3.98244070292824 | epot = -19.5961674318684 | etot = -13.2825375255993
+624000  ekin = 2.39492361725441 |  erot = 3.96722578250777 | epot = -19.6446869257843 | etot = -13.2825375260221
+625000  ekin = 2.44512221108716 |  erot = 3.9221202536408 | epot = -19.6497799909757 | etot = -13.2825375262478
+626000  ekin = 2.47876984854015 |  erot = 3.84697362699248 | epot = -19.6082810017757 | etot = -13.282537526243
+627000  ekin = 2.49411681806274 |  erot = 3.74375083232696 | epot = -19.5204051764073 | etot = -13.2825375260176
+628000  ekin = 2.49092177732992 |  erot = 3.61617309028914 | epot = -19.3896323932286 | etot = -13.2825375256095
+629000  ekin = 2.47048208798929 |  erot = 3.46915451618023 | epot = -19.2221741292344 | etot = -13.2825375250648
+630000  ekin = 2.43548970076025 |  erot = 3.30827690339842 | epot = -19.0263041285834 | etot = -13.2825375244248
+631000  ekin = 2.38975949010187 |  erot = 3.13944249310663 | epot = -18.8117395069329 | etot = -13.2825375237244
+632000  ekin = 2.33785618710456 |  erot = 2.96869689900809 | epot = -18.5890906091134 | etot = -13.2825375230008
+633000  ekin = 2.28462964554081 |  erot = 2.80211551079199 | epot = -18.3692826786328 | etot = -13.2825375223
+634000  ekin = 2.2346774623099 |  erot = 2.64563252181923 | epot = -18.1628475058086 | etot = -13.2825375216794
+635000  ekin = 2.15322765553028 |  erot = 2.4783509433522 | epot = -17.9141161496004 | etot = -13.2825375507179
+636000  ekin = 2.045499081381 |  erot = 2.31412508402215 | epot = -17.6421616868316 | etot = -13.2825375214284
+637000  ekin = 2.11104805172142 |  erot = 2.29419960724925 | epot = -17.6877852051452 | etot = -13.2825375461745
+638000  ekin = 2.16990019918255 |  erot = 2.26795673930499 | epot = -17.720394476478 | etot = -13.2825375379904
+639000  ekin = 2.15825321743049 |  erot = 2.17815663921299 | epot = -17.618947382429 | etot = -13.2825375257855
+640000  ekin = 2.18911467639275 |  erot = 2.15600946820072 | epot = -17.627661668601 | etot = -13.2825375240076
+641000  ekin = 2.26653815117271 |  erot = 2.22106973659358 | epot = -17.7701454239566 | etot = -13.2825375361904
+642000  ekin = 2.31444694707114 |  erot = 2.28426426133692 | epot = -17.881248736019 | etot = -13.282537527611
+643000  ekin = 2.32966846048322 |  erot = 2.3262511385741 | epot = -17.9384571271816 | etot = -13.2825375281243
+644000  ekin = 2.33971908597949 |  erot = 2.36941556707019 | epot = -17.9916721815437 | etot = -13.2825375284941
+645000  ekin = 2.34497836829283 |  erot = 2.40804261243074 | epot = -18.0355585093822 | etot = -13.2825375286587
+646000  ekin = 2.34716147904814 |  erot = 2.43809135035135 | epot = -18.0677903580053 | etot = -13.2825375286058
+647000  ekin = 2.3490135196742 |  erot = 2.45765540462488 | epot = -18.0892064526769 | etot = -13.2825375283778
+648000  ekin = 2.35429037946817 |  erot = 2.46814608860667 | epot = -18.1049739961949 | etot = -13.28253752812
+649000  ekin = 2.36637490458858 |  erot = 2.47306901786727 | epot = -18.1219814504981 | etot = -13.2825375280423
+650000  ekin = 2.38594651005796 |  erot = 2.47280388226564 | epot = -18.1412879203047 | etot = -13.2825375279811
+651000  ekin = 2.4129073237406 |  erot = 2.4679750054794 | epot = -18.163419857161 | etot = -13.282537527941
+652000  ekin = 2.44657292389676 |  erot = 2.45942209560756 | epot = -18.1885325474125 | etot = -13.2825375279081
+653000  ekin = 2.48591189111066 |  erot = 2.44818643115487 | epot = -18.2166358501265 | etot = -13.282537527861
+654000  ekin = 2.52980786333011 |  erot = 2.43558904341108 | epot = -18.2479344345246 | etot = -13.2825375277834
+655000  ekin = 2.57725720727345 |  erot = 2.42329690324718 | epot = -18.2830916381947 | etot = -13.2825375276741
+656000  ekin = 2.62745567851939 |  erot = 2.41329334478414 | epot = -18.3232865508506 | etot = -13.2825375275471
+657000  ekin = 2.67977157718863 |  erot = 2.40771681171411 | epot = -18.3700259163334 | etot = -13.2825375274306
+658000  ekin = 2.73363379212944 |  erot = 2.40858022047282 | epot = -18.4247515399622 | etot = -13.2825375273599
+659000  ekin = 2.78837854445156 |  erot = 2.41741767313059 | epot = -18.4883337449508 | etot = -13.2825375273687
+660000  ekin = 2.8431453631021 |  erot = 2.43497153575953 | epot = -18.5606544262937 | etot = -13.282537527432
+661000  ekin = 2.89550751705154 |  erot = 2.46002725134826 | epot = -18.6380722964866 | etot = -13.2825375280868
+662000  ekin = 2.93874528639294 |  erot = 2.48685588449209 | epot = -18.708138699583 | etot = -13.282537528698
+663000  ekin = 2.96871719420213 |  erot = 2.51022783061785 | epot = -18.7614825540622 | etot = -13.2825375292422
+664000  ekin = 2.98246138426592 |  erot = 2.52516926728115 | epot = -18.7901681811315 | etot = -13.2825375295844
+665000  ekin = 2.97884445496409 |  erot = 2.52787955702933 | epot = -18.7892615416111 | etot = -13.2825375296177
+666000  ekin = 2.95920183358837 |  erot = 2.5166150843606 | epot = -18.7583544472577 | etot = -13.2825375293087
+667000  ekin = 2.92742550364064 |  erot = 2.49210329863614 | epot = -18.7020663309941 | etot = -13.2825375287173
+668000  ekin = 2.88934250727334 |  erot = 2.45736670758744 | epot = -18.6292467428357 | etot = -13.2825375279749
+669000  ekin = 2.85155010055246 |  erot = 2.41708074188009 | epot = -18.5511683696627 | etot = -13.2825375272301
+670000  ekin = 2.82014314483841 |  erot = 2.37673699564913 | epot = -18.4794176670842 | etot = -13.2825375265966
+671000  ekin = 2.79977472973266 |  erot = 2.34183940288387 | epot = -18.4241516588856 | etot = -13.2825375262691
+672000  ekin = 2.7929325264564 |  erot = 2.3169522602719 | epot = -18.3924223127253 | etot = -13.282537525997
+673000  ekin = 2.80034442418812 |  erot = 2.30554472221923 | epot = -18.3884266723436 | etot = -13.2825375259362
+674000  ekin = 2.82129825266147 |  erot = 2.30955451996833 | epot = -18.4133902987243 | etot = -13.2825375260945
+675000  ekin = 2.85361934154458 |  erot = 2.32878748983352 | epot = -18.4649443578395 | etot = -13.2825375264614
+676000  ekin = 2.89394925003076 |  erot = 2.36084337721496 | epot = -18.5373301542345 | etot = -13.2825375269888
+677000  ekin = 2.93819888444081 |  erot = 2.40146056818827 | epot = -18.6221969802158 | etot = -13.2825375275867
+678000  ekin = 2.98219881053812 |  erot = 2.44527797803552 | epot = -18.7100143167158 | etot = -13.2825375281422
+679000  ekin = 3.02242735526952 |  erot = 2.48684948039664 | epot = -18.7918143642177 | etot = -13.2825375285515
+680000  ekin = 3.05660821688331 |  erot = 2.52163649392475 | epot = -18.860782239561 | etot = -13.282537528753
+681000  ekin = 3.08399348193173 |  erot = 2.54671087872184 | epot = -18.913241889389 | etot = -13.2825375287354
+682000  ekin = 3.10527370313695 |  erot = 2.56103519422108 | epot = -18.9488464258989 | etot = -13.2825375285409
+683000  ekin = 3.12217420792303 |  erot = 2.5653012869435 | epot = -18.9700130231063 | etot = -13.2825375282397
+684000  ekin = 3.13689854385765 |  erot = 2.56147023269689 | epot = -18.9809063044635 | etot = -13.282537527909
+685000  ekin = 3.15161752084921 |  erot = 2.55220833209368 | epot = -18.9863633805374 | etot = -13.2825375275945
+686000  ekin = 3.16825656296352 |  erot = 2.54047141966045 | epot = -18.9912655100342 | etot = -13.2825375274102
+687000  ekin = 3.18756268905896 |  erot = 2.5286150857463 | epot = -18.9987153021306 | etot = -13.2825375273253
+688000  ekin = 3.20935294731744 |  erot = 2.51834078650268 | epot = -19.010231261173 | etot = -13.2825375273529
+689000  ekin = 3.23260385768977 |  erot = 2.51058529366538 | epot = -19.0257266788501 | etot = -13.2825375274949
+690000  ekin = 3.25550449418191 |  erot = 2.50541094761942 | epot = -19.0434529695448 | etot = -13.2825375277435
+691000  ekin = 3.27559454465419 |  erot = 2.50196131508042 | epot = -19.0600933878108 | etot = -13.2825375280762
+692000  ekin = 3.29000453531072 |  erot = 2.49851988080605 | epot = -19.0710619445671 | etot = -13.2825375284504
+693000  ekin = 3.29579865375948 |  erot = 2.4927397485969 | epot = -19.0710759311631 | etot = -13.2825375288067
+694000  ekin = 3.290367420064 |  erot = 2.48207188558618 | epot = -19.0549768347317 | etot = -13.2825375290815
+695000  ekin = 3.27176421099226 |  erot = 2.46431581834491 | epot = -19.0186175585658 | etot = -13.2825375292286
+696000  ekin = 3.23887890264527 |  erot = 2.43812365839389 | epot = -18.9595400902738 | etot = -13.2825375292346
+697000  ekin = 3.19141377365438 |  erot = 2.40329594557291 | epot = -18.8772472483422 | etot = -13.2825375291149
+698000  ekin = 3.12971664160265 |  erot = 2.3607993405226 | epot = -18.7730535110309 | etot = -13.2825375289056
+699000  ekin = 3.05458980607575 |  erot = 2.31258576051436 | epot = -18.6497130952223 | etot = -13.2825375286322
+700000  ekin = 2.96718102277338 |  erot = 2.26139197222678 | epot = -18.5111105233092 | etot = -13.282537528309
+701000  ekin = 2.86896613270987 |  erot = 2.21057215475942 | epot = -18.3620758154114 | etot = -13.2825375279421
+702000  ekin = 2.76178671310755 |  erot = 2.16397434370647 | epot = -18.2082985843512 | etot = -13.2825375275372
+703000  ekin = 2.64787120281757 |  erot = 2.12574771765488 | epot = -18.0561564514672 | etot = -13.2825375309947
+704000  ekin = 2.52933762816201 |  erot = 2.08674637167894 | epot = -17.8986215285157 | etot = -13.2825375286748
+705000  ekin = 2.41679696488455 |  erot = 2.0566401236899 | epot = -17.7559746148443 | etot = -13.2825375262699
+706000  ekin = 2.30501007301267 |  erot = 2.06115876579317 | epot = -17.6487063632602 | etot = -13.2825375244543
+707000  ekin = 2.19269241312063 |  erot = 2.11375046401179 | epot = -17.5889804017709 | etot = -13.2825375246385
+708000  ekin = 2.09960598295589 |  erot = 2.19681319913428 | epot = -17.5789567090833 | etot = -13.2825375269932
+709000  ekin = 2.01320280572636 |  erot = 2.28016876669421 | epot = -17.5759090978068 | etot = -13.2825375253862
+710000  ekin = 1.93302644378252 |  erot = 2.3747322880584 | epot = -17.5902962577935 | etot = -13.2825375259526
+711000  ekin = 1.85957279021245 |  erot = 2.47358324949964 | epot = -17.6156935663468 | etot = -13.2825375266347
+712000  ekin = 1.79282630225992 |  erot = 2.56690430163368 | epot = -17.6422681311821 | etot = -13.2825375272885
+713000  ekin = 1.73341814837551 |  erot = 2.64462400363359 | epot = -17.660579679756 | etot = -13.2825375277469
+714000  ekin = 1.68328438218602 |  erot = 2.6981736471422 | epot = -17.6639955572078 | etot = -13.2825375278795
+715000  ekin = 1.64594117620278 |  erot = 2.72207244137003 | epot = -17.6505511452259 | etot = -13.2825375276531
+716000  ekin = 1.62610172677928 |  erot = 2.71479815184846 | epot = -17.6234374057783 | etot = -13.2825375271506
+717000  ekin = 1.62864489608611 |  erot = 2.67867233654835 | epot = -17.5898547591674 | etot = -13.2825375265329
+718000  ekin = 1.65730138294327 |  erot = 2.6189183930066 | epot = -17.5587573019149 | etot = -13.282537525965
+719000  ekin = 1.71360335043978 |  erot = 2.54235654261391 | epot = -17.5384974186061 | etot = -13.2825375255524
+720000  ekin = 1.79650653895858 |  erot = 2.45621436721656 | epot = -17.5352584314959 | etot = -13.2825375253208
+721000  ekin = 1.90273489837533 |  erot = 2.36731439674759 | epot = -17.5525868203611 | etot = -13.2825375252382
+722000  ekin = 2.02756635859999 |  erot = 2.28163864623686 | epot = -17.5917425300939 | etot = -13.2825375252571
+723000  ekin = 2.16566245404416 |  erot = 2.20411346317412 | epot = -17.6523134425647 | etot = -13.2825375253464
+724000  ekin = 2.31164907954197 |  erot = 2.13844446421075 | epot = -17.7326310692571 | etot = -13.2825375255043
+725000  ekin = 2.46036017261476 |  erot = 2.0869120442021 | epot = -17.8298097425667 | etot = -13.2825375257498
+726000  ekin = 2.6068349632846 |  erot = 2.05013619410202 | epot = -17.9395086834918 | etot = -13.2825375261052
+727000  ekin = 2.74622028370769 |  erot = 2.02690424048558 | epot = -18.0556620507673 | etot = -13.2825375265741
+728000  ekin = 2.87374866232265 |  erot = 2.01419303060157 | epot = -18.1704792200511 | etot = -13.2825375271269
+729000  ekin = 2.98490085153144 |  erot = 2.00751009684072 | epot = -18.2749484760646 | etot = -13.2825375276924
+730000  ekin = 3.07576690645469 |  erot = 2.00160558057494 | epot = -18.3599100152017 | etot = -13.2825375281721
+731000  ekin = 3.14351022556136 |  erot = 1.99146923005515 | epot = -18.4175169840844 | etot = -13.2825375284679
+732000  ekin = 3.18676307270908 |  erot = 1.9733775068131 | epot = -18.4426781080378 | etot = -13.2825375285156
+733000  ekin = 3.20579220143817 |  erot = 1.94568706577985 | epot = -18.4340167955229 | etot = -13.2825375283049
+734000  ekin = 3.20238921808403 |  erot = 1.9091725140226 | epot = -18.3940992599778 | etot = -13.2825375278711
+735000  ekin = 3.17951096478395 |  erot = 1.86680153214189 | epot = -18.3288500242332 | etot = -13.2825375273073
+736000  ekin = 3.1407386539016 |  erot = 1.82300587571906 | epot = -18.2462820563141 | etot = -13.2825375266935
+737000  ekin = 3.08984658439833 |  erot = 1.78292392999538 | epot = -18.1553080405002 | etot = -13.2825375261065
+738000  ekin = 3.03043228105068 |  erot = 1.7516193492114 | epot = -18.0645891558627 | etot = -13.2825375256006
+739000  ekin = 2.96566842761532 |  erot = 1.73346651074128 | epot = -17.9816724635652 | etot = -13.2825375252086
+740000  ekin = 2.89817088990248 |  erot = 1.73175552827542 | epot = -17.9124639431193 | etot = -13.2825375249414
+741000  ekin = 2.82995232215527 |  erot = 1.74850528578322 | epot = -17.8609951327411 | etot = -13.2825375248026
+742000  ekin = 2.76247533975977 |  erot = 1.78434362324901 | epot = -17.8293564878077 | etot = -13.2825375247989
+743000  ekin = 2.69668176522496 |  erot = 1.83847103615502 | epot = -17.8176903262763 | etot = -13.2825375248963
+744000  ekin = 2.63311444617166 |  erot = 1.90875045497562 | epot = -17.8244024262527 | etot = -13.2825375251054
+745000  ekin = 2.57196493518836 |  erot = 1.99171779916653 | epot = -17.8462202597747 | etot = -13.2825375254198
+746000  ekin = 2.5131159615418 |  erot = 2.08264215541026 | epot = -17.8782956427778 | etot = -13.2825375258257
+747000  ekin = 2.4562102402775 |  erot = 2.17571767167211 | epot = -17.9144654382424 | etot = -13.2825375262928
+748000  ekin = 2.4007641204688 |  erot = 2.2644524277425 | epot = -17.9477540749797 | etot = -13.2825375267684
+749000  ekin = 2.34635697391007 |  erot = 2.34231237519854 | epot = -17.9712068762851 | etot = -13.2825375271765
+750000  ekin = 2.29290375451717 |  erot = 2.40359513791455 | epot = -17.979036419863 | etot = -13.2825375274312
+751000  ekin = 2.24097207238015 |  erot = 2.44437862762129 | epot = -17.9678882274625 | etot = -13.2825375274611
+752000  ekin = 2.19206377657606 |  erot = 2.46328788077229 | epot = -17.937889184575 | etot = -13.2825375272267
+753000  ekin = 2.0191073671841 |  erot = 2.37844688220293 | epot = -17.6800917192494 | etot = -13.2825374698623
+754000  ekin = 2.03397419691681 |  erot = 2.38379927449377 | epot = -17.7003109683856 | etot = -13.282537496975
+755000  ekin = 2.10287082567493 |  erot = 2.42269050483285 | epot = -17.8080987746467 | etot = -13.2825374441389
+756000  ekin = 2.09556625439565 |  erot = 2.405750962181 | epot = -17.7838546600866 | etot = -13.2825374435099
+757000  ekin = 2.11013463581362 |  erot = 2.39174642164209 | epot = -17.7844185004694 | etot = -13.2825374430137
+758000  ekin = 2.14991880579705 |  erot = 2.38537981437436 | epot = -17.8178360628955 | etot = -13.2825374427241
+759000  ekin = 2.21691275063063 |  erot = 2.38948785825167 | epot = -17.8889380515667 | etot = -13.2825374426844
+760000  ekin = 2.31141054860375 |  erot = 2.40468264900161 | epot = -17.9986306405271 | etot = -13.2825374429218
+761000  ekin = 2.4317547235321 |  erot = 2.42917556854271 | epot = -18.14346773552 | etot = -13.2825374434452
+762000  ekin = 2.57423243233675 |  erot = 2.45878794777349 | epot = -18.3155578243444 | etot = -13.2825374442342
+763000  ekin = 2.73317609318437 |  erot = 2.48721280711223 | epot = -18.5029263455259 | etot = -13.2825374452293
+764000  ekin = 2.90131643265847 |  erot = 2.50663479921391 | epot = -18.6904886781953 | etot = -13.2825374463229
+765000  ekin = 3.07040159501002 |  erot = 2.50879317398454 | epot = -18.8617322163581 | etot = -13.2825374473636
+766000  ekin = 3.23203070978082 |  erot = 2.48644536574614 | epot = -19.0010135237083 | etot = -13.2825374481813
+767000  ekin = 3.37856609433327 |  erot = 2.43498274045147 | epot = -19.096086283418 | etot = -13.2825374486333
+768000  ekin = 3.50392633253189 |  erot = 2.35374465438907 | epot = -19.14020843557 | etot = -13.282537448649
+769000  ekin = 3.60408079934929 |  erot = 2.2465665844398 | epot = -19.1331848320412 | etot = -13.2825374482521
+770000  ekin = 3.67731902040089 |  erot = 2.12129310034524 | epot = -19.0811495682864 | etot = -13.2825374475402
+771000  ekin = 3.7250046645363 |  erot = 1.98803923032005 | epot = -18.9955813415612 | etot = -13.2825374467049
+772000  ekin = 3.73784328843035 |  erot = 1.84847100678562 | epot = -18.8688517433746 | etot = -13.2825374481586
+773000  ekin = 3.73518377757204 |  erot = 1.74399251359463 | epot = -18.7617137365844 | etot = -13.2825374454177
+774000  ekin = 3.73326270308357 |  erot = 1.69319142531066 | epot = -18.7089915825401 | etot = -13.2825374541459
+775000  ekin = 3.70600760956875 |  erot = 1.65662399761182 | epot = -18.6451690552018 | etot = -13.2825374480212
+776000  ekin = 3.66620955944038 |  erot = 1.65229490513874 | epot = -18.6010419124108 | etot = -13.2825374478317
+777000  ekin = 3.6164959066655 |  erot = 1.68124406400525 | epot = -18.5802774185067 | etot = -13.2825374478359
+778000  ekin = 3.5589217195722 |  erot = 1.74156460645431 | epot = -18.5830237740648 | etot = -13.2825374480383
+779000  ekin = 3.49505249793887 |  erot = 1.82861083484593 | epot = -18.6062007816394 | etot = -13.2825374488546
+780000  ekin = 3.4260605289351 |  erot = 1.93200454544541 | epot = -18.6406025240164 | etot = -13.2825374496359
+781000  ekin = 3.35141348649702 |  erot = 2.04005284529073 | epot = -18.6740037822594 | etot = -13.2825374504716
+782000  ekin = 3.27002343600189 |  erot = 2.14152553689654 | epot = -18.6940864240875 | etot = -13.2825374511891
+783000  ekin = 3.18141085606315 |  erot = 2.22636120778713 | epot = -18.6903095154617 | etot = -13.2825374516114
+784000  ekin = 3.08656488448361 |  erot = 2.28735807323151 | epot = -18.6564604093344 | etot = -13.2825374516193
+785000  ekin = 2.98843913984933 |  erot = 2.32136711553602 | epot = -18.592343706592 | etot = -13.2825374512067
+786000  ekin = 2.89178850735618 |  erot = 2.32954149828313 | epot = -18.5038674561269 | etot = -13.2825374504876
+787000  ekin = 2.80233070714568 |  erot = 2.31656731743012 | epot = -18.4014354742217 | etot = -13.2825374496459
+788000  ekin = 2.72556137455006 |  erot = 2.28924565768276 | epot = -18.2973444810906 | etot = -13.2825374488578
+789000  ekin = 2.66569850120894 |  erot = 2.25498711353627 | epot = -18.2032230629877 | etot = -13.2825374482425
+790000  ekin = 2.62507547495403 |  erot = 2.22062577794997 | epot = -18.1282387007584 | etot = -13.2825374478544
+791000  ekin = 2.60400664845757 |  erot = 2.19166523695208 | epot = -18.0782093331145 | etot = -13.2825374477048
+792000  ekin = 2.60095165826993 |  erot = 2.17186849883267 | epot = -18.0553576048892 | etot = -13.2825374477866
+793000  ekin = 2.61278727136947 |  erot = 2.1630579475058 | epot = -18.0583826669628 | etot = -13.2825374480875
+794000  ekin = 2.63509078750899 |  erot = 2.16503786010594 | epot = -18.0826660962031 | etot = -13.2825374485882
+795000  ekin = 2.66245645496094 |  erot = 2.17562900151097 | epot = -18.1206229057215 | etot = -13.2825374492496
+796000  ekin = 2.68895951797515 |  erot = 2.19088748039119 | epot = -18.1623844483558 | etot = -13.2825374499895
+797000  ekin = 2.70892452636473 |  erot = 2.20564060882902 | epot = -18.197102585859 | etot = -13.2825374506652
+798000  ekin = 2.7187387406754 |  erot = 2.21455364300775 | epot = -18.2158298332747 | etot = -13.2825374495916
+799000  ekin = 2.70000300099405 |  erot = 2.21050545408876 | epot = -18.193045904985 | etot = -13.2825374499022
+800000  ekin = 2.65392049001821 |  erot = 2.17300546938151 | epot = -18.109463378289 | etot = -13.2825374188892
+801000  ekin = 2.82505345096871 |  erot = 2.13616134701489 | epot = -18.2437522525054 | etot = -13.2825374545218
+802000  ekin = 2.90470228802172 |  erot = 2.10953657449614 | epot = -18.2967762799053 | etot = -13.2825374173874
+803000  ekin = 2.9677525986453 |  erot = 2.08137573444383 | epot = -18.3316657512964 | etot = -13.2825374182072
+804000  ekin = 3.01419864036155 |  erot = 2.05336319939514 | epot = -18.3500992581057 | etot = -13.282537418349
+805000  ekin = 3.03950260682403 |  erot = 2.02738087474037 | epot = -18.3494208999164 | etot = -13.282537418352
+806000  ekin = 3.04147612212525 |  erot = 2.00524180108709 | epot = -18.3292553414124 | etot = -13.2825374182001
+807000  ekin = 3.02009152418646 |  erot = 1.98876425940777 | epot = -18.2913932015099 | etot = -13.2825374179157
+808000  ekin = 2.97716861905469 |  erot = 1.9797928070483 | epot = -18.2394988436566 | etot = -13.2825374175536
+809000  ekin = 2.91576405317411 |  erot = 1.98007542202132 | epot = -18.1783768923745 | etot = -13.282537417179
+810000  ekin = 2.83951999241211 |  erot = 1.9910201414007 | epot = -18.1130775506578 | etot = -13.282537416845
+811000  ekin = 2.75216924413256 |  erot = 2.01344070631007 | epot = -18.0481473670229 | etot = -13.2825374165802
+812000  ekin = 2.65727213949033 |  erot = 2.04739495870437 | epot = -17.9872045145838 | etot = -13.2825374163891
+813000  ekin = 2.55815480063288 |  erot = 2.0921579466292 | epot = -17.9328501635216 | etot = -13.2825374162596
+814000  ekin = 2.45796623947603 |  erot = 2.14630993528002 | epot = -17.8868135909302 | etot = -13.2825374161741
+815000  ekin = 2.35976627429823 |  erot = 2.20788718833984 | epot = -17.8501908787554 | etot = -13.2825374161174
+816000  ekin = 2.26657575180629 |  erot = 2.27454135561794 | epot = -17.8236545235058 | etot = -13.2825374160815
+817000  ekin = 2.18134946662811 |  erot = 2.34367133400565 | epot = -17.807558216702 | etot = -13.2825374160682
+818000  ekin = 2.10686415591836 |  erot = 2.41251844102779 | epot = -17.8019200130316 | etot = -13.2825374160855
+819000  ekin = 2.04554497258418 |  erot = 2.47824070162555 | epot = -17.806323090351 | etot = -13.2825374161413
+820000  ekin = 1.99927680295696 |  erot = 2.53799486378974 | epot = -17.8198090829855 | etot = -13.2825374162388
+821000  ekin = 1.9692530805303 |  erot = 2.58905270210877 | epot = -17.8408431990125 | etot = -13.2825374163734
+822000  ekin = 1.95590272174924 |  erot = 2.62895986938386 | epot = -17.8674000076635 | etot = -13.2825374165304
+823000  ekin = 1.95890926788755 |  erot = 2.6557286058008 | epot = -17.8971752903778 | etot = -13.2825374166894
+824000  ekin = 1.97731046162633 |  erot = 2.66804286128345 | epot = -17.9278907397372 | etot = -13.2825374168275
+825000  ekin = 2.00964945342457 |  erot = 2.66544750451175 | epot = -17.9576343748594 | etot = -13.2825374169231
+826000  ekin = 2.05414423139186 |  erot = 2.64849047550104 | epot = -17.985172123854 | etot = -13.2825374169611
+827000  ekin = 2.10884212199665 |  erot = 2.61877894485958 | epot = -18.0101584837945 | etot = -13.2825374169382
+828000  ekin = 2.1717293569375 |  erot = 2.57890618314315 | epot = -18.0331729569469 | etot = -13.2825374168662
+829000  ekin = 2.24077304847179 |  erot = 2.53221651091816 | epot = -18.0555269761626 | etot = -13.2825374167726
+830000  ekin = 2.31389012743404 |  erot = 2.4824115756111 | epot = -18.0788391197418 | etot = -13.2825374166967
+831000  ekin = 2.38886546542343 |  erot = 2.43305573494131 | epot = -18.1044586170416 | etot = -13.2825374166768
+832000  ekin = 2.4632691578231 |  erot = 2.3870870487244 | epot = -18.1328936232866 | etot = -13.2825374167391
+833000  ekin = 2.5344365632194 |  erot = 2.34645691813147 | epot = -18.1634308982373 | etot = -13.2825374168864
+834000  ekin = 2.59956439019907 |  erot = 2.31199374777391 | epot = -18.1940955550686 | etot = -13.2825374170956
+835000  ekin = 2.65594315943653 |  erot = 2.28352232821168 | epot = -18.2220029049695 | etot = -13.2825374173213
+836000  ekin = 2.70130042683167 |  erot = 2.26019210697788 | epot = -18.244029951319 | etot = -13.2825374175095
+837000  ekin = 2.73418787962871 |  erot = 2.24090836893314 | epot = -18.2576336661722 | etot = -13.2825374176104
+838000  ekin = 2.75431729342696 |  erot = 2.22474076288568 | epot = -18.2615954739057 | etot = -13.2825374175931
+839000  ekin = 2.76274241629131 |  erot = 2.21121141093012 | epot = -18.256491244675 | etot = -13.2825374174536
+840000  ekin = 2.76179432989972 |  erot = 2.20041723303662 | epot = -18.2447489801545 | etot = -13.2825374172182
+841000  ekin = 2.75470877518085 |  erot = 2.19297958495076 | epot = -18.2302257770756 | etot = -13.2825374169439
+842000  ekin = 2.74495192528053 |  erot = 2.18982916449433 | epot = -18.2173185064846 | etot = -13.2825374167098
+843000  ekin = 2.73536701846579 |  erot = 2.19185320024881 | epot = -18.2097576353086 | etot = -13.282537416594
+844000  ekin = 2.72739699349177 |  erot = 2.1994851694244 | epot = -18.2094195795621 | etot = -13.2825374166459
+845000  ekin = 2.7206968024524 |  erot = 2.21238342751528 | epot = -18.2156176468218 | etot = -13.2825374168541
+846000  ekin = 2.71335246036253 |  erot = 2.22935500856137 | epot = -18.2252448860709 | etot = -13.282537417147
+847000  ekin = 2.70267547916117 |  erot = 2.24859000373239 | epot = -18.2338029003123 | etot = -13.2825374174188
+848000  ekin = 2.68627675195779 |  erot = 2.26812231144288 | epot = -18.236936480973 | etot = -13.2825374175723
+849000  ekin = 2.66300406671244 |  erot = 2.2863229263121 | epot = -18.2318644105805 | etot = -13.282537417556
+850000  ekin = 2.63341305523148 |  erot = 2.30223029747857 | epot = -18.2181807700874 | etot = -13.2825374173774
+851000  ekin = 2.59966043365591 |  erot = 2.3156167587262 | epot = -18.1978146094748 | etot = -13.2825374170927
+852000  ekin = 2.56493307993571 |  erot = 2.32681510713484 | epot = -18.1742856038479 | etot = -13.2825374167774
+853000  ekin = 2.53268459155754 |  erot = 2.33642702138572 | epot = -18.1516490294471 | etot = -13.2825374165038
+854000  ekin = 2.50591352797944 |  erot = 2.34503055123976 | epot = -18.1334814955374 | etot = -13.2825374163182
+855000  ekin = 2.4866740476675 |  erot = 2.35297873120409 | epot = -18.1221901951049 | etot = -13.2825374162333
+856000  ekin = 2.47592780860343 |  erot = 2.36034202539965 | epot = -18.1188072502362 | etot = -13.2825374162331
+857000  ekin = 2.47367803510516 |  erot = 2.36697109794411 | epot = -18.1231865493438 | etot = -13.2825374162946
+858000  ekin = 2.47922391681366 |  erot = 2.37260088210265 | epot = -18.1343622152926 | etot = -13.2825374163763
+859000  ekin = 2.49150776870147 |  erot = 2.37701215984104 | epot = -18.1510573449986 | etot = -13.282537416456
+860000  ekin = 2.50937686784747 |  erot = 2.38013993594023 | epot = -18.1720542203101 | etot = -13.2825374165224
+861000  ekin = 2.53170635996116 |  erot = 2.38211817150425 | epot = -18.1963619480387 | etot = -13.2825374165732
+862000  ekin = 2.55742566626407 |  erot = 2.38328933264109 | epot = -18.2232524155165 | etot = -13.2825374166114
+863000  ekin = 2.58549483187838 |  erot = 2.38419488482973 | epot = -18.252227133347 | etot = -13.2825374166389
+864000  ekin = 2.61488041066499 |  erot = 2.38555368834993 | epot = -18.2829715156728 | etot = -13.2825374166579
+865000  ekin = 2.64455846347095 |  erot = 2.38821849192421 | epot = -18.3153143720654 | etot = -13.2825374166702
+866000  ekin = 2.67354800424437 |  erot = 2.39309523344314 | epot = -18.3491806543665 | etot = -13.282537416679
+867000  ekin = 2.70096216988177 |  erot = 2.40101926554071 | epot = -18.3845188521138 | etot = -13.2825374166913
+868000  ekin = 2.72584498338572 |  erot = 2.41260829074957 | epot = -18.420990690944 | etot = -13.2825374168087
+869000  ekin = 2.74685098606623 |  erot = 2.42808376653873 | epot = -18.4574721694777 | etot = -13.2825374168728
+870000  ekin = 2.76334516398283 |  erot = 2.44707202879413 | epot = -18.4929546097441 | etot = -13.2825374169672
+871000  ekin = 2.77488977710316 |  erot = 2.46856883163597 | epot = -18.5259960258323 | etot = -13.2825374170932
+872000  ekin = 2.7811573123189 |  erot = 2.49101078851438 | epot = -18.5547055180778 | etot = -13.2825374172445
+873000  ekin = 2.78190152502928 |  erot = 2.51241399879738 | epot = -18.5768529412309 | etot = -13.2825374174043
+874000  ekin = 2.77696693725528 |  erot = 2.53063897161364 | epot = -18.5901433264131 | etot = -13.2825374175441
+875000  ekin = 2.76636320213146 |  erot = 2.54374754436265 | epot = -18.5926481641224 | etot = -13.2825374176283
+876000  ekin = 2.7504069828229 |  erot = 2.55039472310231 | epot = -18.5833391235459 | etot = -13.2825374176207
+877000  ekin = 2.72989722810813 |  erot = 2.55017286557422 | epot = -18.5626075111784 | etot = -13.2825374174961
+878000  ekin = 2.70625700294355 |  erot = 2.54382115071376 | epot = -18.5326155709077 | etot = -13.2825374172503
+879000  ekin = 2.68156506653427 |  erot = 2.5332421351554 | epot = -18.4973446185932 | etot = -13.2825374169036
+880000  ekin = 2.65843100554442 |  erot = 2.52132216836891 | epot = -18.4622905904093 | etot = -13.282537416496
+881000  ekin = 2.63972432922979 |  erot = 2.51160592366972 | epot = -18.4338676689779 | etot = -13.2825374160784
+882000  ekin = 2.62822235403347 |  erot = 2.50790034454678 | epot = -18.4186601142802 | etot = -13.2825374157
+883000  ekin = 2.62626662137136 |  erot = 2.51387422299541 | epot = -18.4226782597687 | etot = -13.2825374154019
+884000  ekin = 2.63550251772652 |  erot = 2.53269090787765 | epot = -18.4507308408175 | etot = -13.2825374152133
+885000  ekin = 2.65673814855014 |  erot = 2.56668643457077 | epot = -18.5059619982733 | etot = -13.2825374151524
+886000  ekin = 2.68991717237218 |  erot = 2.61709354768266 | epot = -18.5895481352837 | etot = -13.2825374152289
+887000  ekin = 2.734175532827 |  erot = 2.68381522130244 | epot = -18.700528169575 | etot = -13.2825374154455
+888000  ekin = 2.78795008719356 |  erot = 2.76526591136903 | epot = -18.8357534143588 | etot = -13.2825374157962
+889000  ekin = 2.8491201813508 |  erot = 2.85831710930318 | epot = -18.989974706918 | etot = -13.282537416264
+890000  ekin = 2.91517691868807 |  erot = 2.95839462643955 | epot = -19.1561089619448 | etot = -13.2825374168172
+891000  ekin = 2.98341767192295 |  erot = 3.0597676506775 | epot = -19.3257227400102 | etot = -13.2825374174098
+892000  ekin = 3.05115351644501 |  erot = 3.15603968258129 | epot = -19.4897306170114 | etot = -13.2825374179851
+893000  ekin = 3.11590367361418 |  erot = 3.24080526805507 | epot = -19.6392463601538 | etot = -13.2825374184846
+894000  ekin = 3.17554453075818 |  erot = 3.30838805788589 | epot = -19.7664700075009 | etot = -13.2825374188568
+895000  ekin = 3.22839008561766 |  erot = 3.35454380060236 | epot = -19.8654713052867 | etot = -13.2825374190666
+896000  ekin = 3.27319975165836 |  erot = 3.37700709394957 | epot = -19.9327442647079 | etot = -13.2825374191
+897000  ekin = 3.30912548499472 |  erot = 3.37578332995761 | epot = -19.9674462339186 | etot = -13.2825374189663
+898000  ekin = 3.33561719415195 |  erot = 3.35313099566656 | epot = -19.9712856085154 | etot = -13.2825374186968
+899000  ekin = 3.3523031028265 |  erot = 3.31323476596136 | epot = -19.9480752871285 | etot = -13.2825374183407
+900000  ekin = 3.35886034531518 |  erot = 3.26162723064569 | epot = -19.9030249939161 | etot = -13.2825374179552
+901000  ekin = 3.35489762759567 |  erot = 3.2044644832284 | epot = -19.8418995284194 | etot = -13.2825374175953
+902000  ekin = 3.33988398839342 |  erot = 3.14778460407791 | epot = -19.7702060097741 | etot = -13.2825374173028
+903000  ekin = 3.31316641909532 |  erot = 3.09687096103035 | epot = -19.6925747972223 | etot = -13.2825374170966
+904000  ekin = 3.27411465419852 |  erot = 3.05580881217869 | epot = -19.6124608833472 | etot = -13.2825374169699
+905000  ekin = 3.22240761869358 |  erot = 3.02727711490202 | epot = -19.5322221504879 | etot = -13.2825374168923
+906000  ekin = 3.15843123363071 |  erot = 3.01257047164431 | epot = -19.4535391220934 | etot = -13.2825374168184
+907000  ekin = 3.08369713046712 |  erot = 3.01180553644323 | epot = -19.3780400836148 | etot = -13.2825374167044
+908000  ekin = 3.00113487352882 |  erot = 3.02423547646297 | epot = -19.3079077665171 | etot = -13.2825374165253
+909000  ekin = 2.91509126964 |  erot = 3.04858097597399 | epot = -19.246209661904 | etot = -13.28253741629
+910000  ekin = 2.83091809249006 |  erot = 3.08328866196603 | epot = -19.1967441705011 | etot = -13.282537416045
+911000  ekin = 2.75416042802549 |  erot = 3.12665661766781 | epot = -19.1633544615573 | etot = -13.282537415864
+912000  ekin = 2.68982240197673 |  erot = 3.17670303509253 | epot = -19.1490628528293 | etot = -13.2825374157601
+913000  ekin = 2.64026279480142 |  erot = 3.23106967171228 | epot = -19.1538698824696 | etot = -13.2825374159559
+914000  ekin = 2.60494541586834 |  erot = 3.28757760350067 | epot = -19.1750604355173 | etot = -13.2825374161483
+915000  ekin = 2.58331294380949 |  erot = 3.34356245576663 | epot = -19.2094128163232 | etot = -13.282537416747
+916000  ekin = 2.572225278094 |  erot = 3.39542630003117 | epot = -19.250188995406 | etot = -13.2825374172809
+917000  ekin = 2.56717380000648 |  erot = 3.43991413165374 | epot = -19.2896253494389 | etot = -13.2825374177786
+918000  ekin = 2.56366862414259 |  erot = 3.47431911369141 | epot = -19.3205251559853 | etot = -13.2825374181513
+919000  ekin = 2.55808580528835 |  erot = 3.4968825160616 | epot = -19.337505739687 | etot = -13.2825374183371
+920000  ekin = 2.54828083604877 |  erot = 3.50706786620944 | epot = -19.3378861205732 | etot = -13.2825374183149
+921000  ekin = 2.5338583783986 |  erot = 3.5055796155901 | epot = -19.3219754120972 | etot = -13.2825374181085
+922000  ekin = 2.516060534879 |  erot = 3.49409623125511 | epot = -19.2926941839177 | etot = -13.2825374177836
+923000  ekin = 2.49728909023619 |  erot = 3.47476611514256 | epot = -19.2545926228132 | etot = -13.2825374174344
+924000  ekin = 2.48035717414061 |  erot = 3.44958564359935 | epot = -19.2124802348989 | etot = -13.282537417159
+925000  ekin = 2.46765713433988 |  erot = 3.41982437245358 | epot = -19.1700189238237 | etot = -13.2825374170303
+926000  ekin = 2.46048446299621 |  erot = 3.38566546870185 | epot = -19.1286873487718 | etot = -13.2825374170737
+927000  ekin = 2.45872404418899 |  erot = 3.34617863044022 | epot = -19.0874400918875 | etot = -13.2825374172583
+928000  ekin = 2.46097855235184 |  erot = 3.29964380866974 | epot = -19.043159778532 | etot = -13.2825374175104
+929000  ekin = 2.46505358100394 |  erot = 3.24413140303551 | epot = -18.99172240178 | etot = -13.2825374177406
+930000  ekin = 2.46859437790869 |  erot = 3.17816487222183 | epot = -18.9292966680023 | etot = -13.2825374178718
+931000  ekin = 2.46965047248253 |  erot = 3.10127887163483 | epot = -18.8534667619775 | etot = -13.2825374178601
+932000  ekin = 2.46701732520898 |  erot = 3.01434779059203 | epot = -18.7639025334928 | etot = -13.2825374176918
+933000  ekin = 2.46031519086868 |  erot = 2.91973998893973 | epot = -18.662592597222 | etot = -13.2825374174136
+934000  ekin = 2.44985996507097 |  erot = 2.82081794907183 | epot = -18.5532153312021 | etot = -13.2825374170593
+935000  ekin = 2.43642057973712 |  erot = 2.72162862891861 | epot = -18.4405866253331 | etot = -13.2825374166773
+936000  ekin = 2.42095423648383 |  erot = 2.62651830339036 | epot = -18.3300099561839 | etot = -13.2825374163097
+937000  ekin = 2.40438434874151 |  erot = 2.53973621394318 | epot = -18.2266579786711 | etot = -13.2825374159864
+938000  ekin = 2.38744919883856 |  erot = 2.46512923461683 | epot = -18.1351158491807 | etot = -13.2825374157253
+939000  ekin = 2.37062067030574 |  erot = 2.40593643917341 | epot = -18.0590945250148 | etot = -13.2825374155357
+940000  ekin = 2.35407564413747 |  erot = 2.36465978775718 | epot = -18.0012728473171 | etot = -13.2825374154225
+941000  ekin = 2.33770002379755 |  erot = 2.34297759096208 | epot = -17.9632150301481 | etot = -13.2825374153884
+942000  ekin = 2.32111004775224 |  erot = 2.34167204163274 | epot = -17.9453195048215 | etot = -13.2825374154365
+943000  ekin = 2.30368578996793 |  erot = 2.36056240830405 | epot = -17.9467856138391 | etot = -13.2825374155671
+944000  ekin = 2.28462216232314 |  erot = 2.39846175787113 | epot = -17.9656213359689 | etot = -13.2825374157746
+945000  ekin = 2.26300913007938 |  erot = 2.45319770726134 | epot = -17.9987442533843 | etot = -13.2825374160436
+946000  ekin = 2.23795189170117 |  erot = 2.52174524353285 | epot = -18.0422345515794 | etot = -13.2825374163454
+947000  ekin = 2.20873145116087 |  erot = 2.60050188059525 | epot = -18.091770748396 | etot = -13.2825374166398
+948000  ekin = 2.17498954714479 |  erot = 2.685690959925 | epot = -18.1432179239527 | etot = -13.2825374168829
+949000  ekin = 2.13690579554511 |  erot = 2.77382147697832 | epot = -18.1932646895605 | etot = -13.2825374170371
+950000  ekin = 2.09532426593736 |  erot = 2.86208909954954 | epot = -18.23995078257 | etot = -13.2825374170831
+951000  ekin = 2.05179335117992 |  erot = 2.94860198603871 | epot = -18.2829327542442 | etot = -13.2825374170256
+952000  ekin = 2.00850116862718 |  erot = 3.03236285097458 | epot = -18.3234014364934 | etot = -13.2825374168917
+953000  ekin = 1.96811370669122 |  erot = 3.11301524857533 | epot = -18.3636663719922 | etot = -13.2825374167257
+954000  ekin = 1.93354422355624 |  erot = 3.19043207917699 | epot = -18.4065137193093 | etot = -13.2825374165761
+955000  ekin = 1.907692996046 |  erot = 3.26426019428037 | epot = -18.4544906068132 | etot = -13.2825374164868
+956000  ekin = 1.89319483896647 |  erot = 3.33353105128001 | epot = -18.5092633067365 | etot = -13.28253741649
+957000  ekin = 1.89220136882553 |  erot = 3.39641763089531 | epot = -18.5711564163223 | etot = -13.2825374166015
+958000  ekin = 1.90621184477869 |  erot = 3.45018116396587 | epot = -18.6389304255644 | etot = -13.2825374168199
+959000  ekin = 1.93595602669004 |  erot = 3.49131884076761 | epot = -18.7098122845856 | etot = -13.2825374171279
+960000  ekin = 1.98132739841468 |  erot = 3.51589596637559 | epot = -18.7797607822856 | etot = -13.2825374174953
+961000  ekin = 2.04135467368814 |  erot = 3.5202262282781 | epot = -18.8441183198727 | etot = -13.2825374179065
+962000  ekin = 2.11395441204344 |  erot = 3.50134462359753 | epot = -18.8978364539492 | etot = -13.2825374183082
+963000  ekin = 2.19624676723989 |  erot = 3.45688460115197 | epot = -18.9356687870206 | etot = -13.2825374186287
+964000  ekin = 2.28502253674575 |  erot = 3.38607259828084 | epot = -18.9536325538576 | etot = -13.282537418831
+965000  ekin = 2.37703902148585 |  erot = 3.29004867798671 | epot = -18.9496251180009 | etot = -13.2825374185283
+966000  ekin = 2.47063968385215 |  erot = 3.17235139654337 | epot = -18.9255284988459 | etot = -13.2825374184504
+967000  ekin = 2.56372995555254 |  erot = 3.03797961239301 | epot = -18.8842469861485 | etot = -13.2825374182029
+968000  ekin = 2.65424152965125 |  erot = 2.89333165879526 | epot = -18.83011060625 | etot = -13.2825374178035
+969000  ekin = 2.74102205813625 |  erot = 2.74597895036798 | epot = -18.769538425812 | etot = -13.2825374173078
+970000  ekin = 2.82317857011101 |  erot = 2.60419008501349 | epot = -18.7099060720296 | etot = -13.2825374169051
+971000  ekin = 2.89946896083441 |  erot = 2.47604958426315 | epot = -18.658055961612 | etot = -13.2825374165144
+972000  ekin = 2.96927883277251 |  erot = 2.36783972346085 | epot = -18.6196559725141 | etot = -13.2825374162807
+973000  ekin = 3.03160430380023 |  erot = 2.28373901071249 | epot = -18.5978807307479 | etot = -13.2825374162352
+974000  ekin = 3.08487810119919 |  erot = 2.22552920056088 | epot = -18.5929447181232 | etot = -13.2825374163631
+975000  ekin = 3.12708218363217 |  erot = 2.1927093869337 | epot = -18.6023289871792 | etot = -13.2825374166133
+976000  ekin = 3.15606698430949 |  erot = 2.18294126831253 | epot = -18.6215456695412 | etot = -13.2825374169192
+977000  ekin = 3.16994500357178 |  erot = 2.19267118206454 | epot = -18.6451536028545 | etot = -13.2825374172182
+978000  ekin = 3.16742946522118 |  erot = 2.21776877494467 | epot = -18.6677356576302 | etot = -13.2825374174643
+979000  ekin = 3.14804045998247 |  erot = 2.25406876588806 | epot = -18.6846466435015 | etot = -13.282537417631
+980000  ekin = 3.11216367723466 |  erot = 2.29776911466814 | epot = -18.6924702096109 | etot = -13.2825374177081
+981000  ekin = 3.06099215360332 |  erot = 2.34569300138965 | epot = -18.6892225726894 | etot = -13.2825374176964
+982000  ekin = 2.99639965214887 |  erot = 2.39544433518914 | epot = -18.6743814049394 | etot = -13.2825374176014
+983000  ekin = 2.92078844513084 |  erot = 2.44547840887849 | epot = -18.6488042714436 | etot = -13.2825374174343
+984000  ekin = 2.83693459670618 |  erot = 2.4950891273926 | epot = -18.6145611413098 | etot = -13.282537417211
+985000  ekin = 2.74783420133486 |  erot = 2.54430433679905 | epot = -18.5746759550876 | etot = -13.2825374169537
+986000  ekin = 2.65654532109889 |  erot = 2.59369131660279 | epot = -18.5327740543913 | etot = -13.2825374166896
+987000  ekin = 2.56602544086508 |  erot = 2.64409904101799 | epot = -18.4926618983298 | etot = -13.2825374164468
+988000  ekin = 2.47897321649663 |  erot = 2.69638105882724 | epot = -18.4578916915741 | etot = -13.2825374162503
+989000  ekin = 2.39763961716918 |  erot = 2.75059396137744 | epot = -18.4307709947858 | etot = -13.2825374162392
+990000  ekin = 2.32368779821633 |  erot = 2.80603342998527 | epot = -18.4122586443938 | etot = -13.2825374161922
+991000  ekin = 2.2582530149192 |  erot = 2.86226671787586 | epot = -18.4030571490211 | etot = -13.282537416226
+992000  ekin = 2.20187988997662 |  erot = 2.91825634939035 | epot = -18.4026736557096 | etot = -13.2825374163427
+993000  ekin = 2.15452775947043 |  erot = 2.97231721293149 | epot = -18.4093823889398 | etot = -13.2825374165378
+994000  ekin = 2.11561176914432 |  erot = 3.02214023523714 | epot = -18.4202894211813 | etot = -13.2825374167998
+995000  ekin = 2.08408161375424 |  erot = 3.06489403643897 | epot = -18.4315130673008 | etot = -13.2825374171076
+996000  ekin = 2.05854312749319 |  erot = 3.09743221500535 | epot = -18.4385127599264 | etot = -13.2825374174279
+997000  ekin = 2.03742523569505 |  erot = 3.11662356420229 | epot = -18.4365862176148 | etot = -13.2825374177175
+998000  ekin = 2.01918449064732 |  erot = 3.11978989603429 | epot = -18.42151180461 | etot = -13.2825374179284
+999000  ekin = 2.00252382621622 |  erot = 3.10518925481745 | epot = -18.390250499052 | etot = -13.2825374180184
+1000000  ekin = 1.98658902577819 |  erot = 3.07244217845672 | epot = -18.3415686221954 | etot = -13.2825374179605
+ 1000000  0.088292846   -1.1874188  0.041070751   -1.0221862 -7.1515284e-05 
+Loop time of 31.7925 on 1 procs for 1000000 steps with 16 atoms
+
+Performance: 27176.198 tau/day, 31453.933 timesteps/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 28.401     | 28.401     | 28.401     |   0.0 | 89.33
+Bond    | 0.86019    | 0.86019    | 0.86019    |   0.0 |  2.71
+Neigh   | 0.00018    | 0.00018    | 0.00018    |   0.0 |  0.00
+Comm    | 0.16311    | 0.16311    | 0.16311    |   0.0 |  0.51
+Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
+Modify  | 2.1003     | 2.1003     | 2.1003     |   0.0 |  6.61
+Other   |            | 0.2673     |            |       |  0.84
+
+Nlocal:    16 ave 16 max 16 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    93 ave 93 max 93 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 93
+Ave neighs/atom = 5.8125
+Ave special neighs/atom = 3.75
+Neighbor list builds = 6
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:31
diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4
new file mode 100644
index 0000000000..8a3a723a1e
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4
@@ -0,0 +1,1174 @@
+LAMMPS (30 Oct 2019)
+variable number	equal 4
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex4
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000281 secs
+  read_data CPU = 0.003043 secs
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxRNA2 bond interactions - FENE backbone
+bond_style oxrna2/fene
+bond_coeff * 2.0 0.25 0.761070781051
+
+# oxRNA2 pair interactions
+pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+
+pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxrna2/stk     seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/stk     seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 3 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
+pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+pair_coeff * * oxrna2/dh      ${T} 0.5 1.02455
+pair_coeff * * oxrna2/dh      0.1 0.5 1.02455
+
+# NVE ensemble
+#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all   nve/dot
+fix 1 all nve/asphere
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f"
+
+run 1000000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3015
+  ghost atom cutoff = 3.3015
+  binsize = 1.65075, bins = 25 25 25
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxrna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxrna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxrna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxrna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxrna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxrna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+0  ekin = 0 |  erot = 0 | epot = -13.282537590974 | etot = -13.282537590974
+Per MPI rank memory allocation (min/avg/max) = 7.755 | 7.937 | 8.119 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0  -0.84341458  0.013255977   -0.8301586 -2.0169485e-05 
+1000  ekin = 0.00448503054655829 |  erot = 0.00825381229599554 | epot = -13.2952764343121 | etot = -13.2825375914696
+2000  ekin = 0.0179027901180383 |  erot = 0.0327684151333158 | epot = -13.333208796773 | etot = -13.2825375915216
+3000  ekin = 0.0401478317723388 |  erot = 0.0728240143062734 | epot = -13.3955094376812 | etot = -13.2825375916026
+4000  ekin = 0.0710654348932012 |  erot = 0.127292706282676 | epot = -13.4808957328803 | etot = -13.2825375917044
+5000  ekin = 0.110480309743627 |  erot = 0.194739074279345 | epot = -13.58775697584 | etot = -13.282537591817
+6000  ekin = 0.158231230694386 |  erot = 0.273546913858364 | epot = -13.7143157364821 | etot = -13.2825375919294
+7000  ekin = 0.214206450831694 |  erot = 0.362058396900661 | epot = -13.8588024397635 | etot = -13.2825375920312
+8000  ekin = 0.27837411184999 |  erot = 0.458709556671591 | epot = -14.0196212606354 | etot = -13.2825375921138
+9000  ekin = 0.350802094030117 |  erot = 0.562145629087582 | epot = -14.1954853152897 | etot = -13.282537592172
+10000  ekin = 0.431663021447632 |  erot = 0.671302139461542 | epot = -14.3855027531133 | etot = -13.2825375922041
+11000  ekin = 0.521222365620092 |  erot = 0.785442646223518 | epot = -14.5892026040564 | etot = -13.2825375922128
+12000  ekin = 0.619810398735201 |  erot = 0.90415088836544 | epot = -14.8064988793047 | etot = -13.2825375922041
+13000  ekin = 0.727781531798581 |  erot = 1.02728222251184 | epot = -15.0376013464965 | etot = -13.2825375921861
+14000  ekin = 0.845466747659119 |  erot = 1.15488520186341 | epot = -15.2828895416906 | etot = -13.2825375921681
+15000  ekin = 0.973515286429056 |  erot = 1.28640002432427 | epot = -15.5424529041403 | etot = -13.282537593387
+16000  ekin = 1.12323013751051 |  erot = 1.4038749539854 | epot = -15.8096426839246 | etot = -13.2825375924286
+17000  ekin = 1.29769272832575 |  erot = 1.51347784068601 | epot = -16.0937081607386 | etot = -13.2825375917268
+18000  ekin = 1.48565191084472 |  erot = 1.63592970999597 | epot = -16.4041192134335 | etot = -13.2825375925929
+19000  ekin = 1.66750911163292 |  erot = 1.77940241938649 | epot = -16.7294491246356 | etot = -13.2825375936162
+20000  ekin = 1.84148924290367 |  erot = 1.93695511183614 | epot = -17.0609819484045 | etot = -13.2825375936647
+21000  ekin = 2.02307741366106 |  erot = 2.09844265792887 | epot = -17.4040576653927 | etot = -13.2825375938028
+22000  ekin = 2.21183606977167 |  erot = 2.26260708947227 | epot = -17.7569807531574 | etot = -13.2825375939135
+23000  ekin = 2.40735468792923 |  erot = 2.42817202047232 | epot = -18.1180643024984 | etot = -13.2825375940969
+24000  ekin = 2.60896890448811 |  erot = 2.59357882573777 | epot = -18.4850853245068 | etot = -13.2825375942809
+25000  ekin = 2.815801354773 |  erot = 2.75706655666979 | epot = -18.8554055059558 | etot = -13.282537594513
+26000  ekin = 3.02680083558447 |  erot = 2.91667946897181 | epot = -19.2260178993261 | etot = -13.2825375947698
+27000  ekin = 3.24067707260278 |  erot = 3.07027299756425 | epot = -19.5934876652165 | etot = -13.2825375950495
+28000  ekin = 3.45601412953551 |  erot = 3.21560615187967 | epot = -19.9541578767284 | etot = -13.2825375953133
+29000  ekin = 3.67136830813179 |  erot = 3.35037905822876 | epot = -20.3042849619982 | etot = -13.2825375956377
+30000  ekin = 3.88476027224393 |  erot = 3.47208481891771 | epot = -20.6393826871844 | etot = -13.2825375960227
+31000  ekin = 4.09387957878907 |  erot = 3.57821385031972 | epot = -20.9546310254505 | etot = -13.2825375963417
+32000  ekin = 4.2966218534583 |  erot = 3.6664860653108 | epot = -21.2456455154184 | etot = -13.2825375966493
+33000  ekin = 4.49089153394099 |  erot = 3.73482555362516 | epot = -21.5082546845017 | etot = -13.2825375969356
+34000  ekin = 4.67464118182325 |  erot = 3.78142516888949 | epot = -21.7386039479011 | etot = -13.2825375971883
+35000  ekin = 4.84586411782109 |  erot = 3.80480460777856 | epot = -21.9332063229965 | etot = -13.2825375973968
+36000  ekin = 5.0027094048744 |  erot = 3.80394535032719 | epot = -22.0891923527598 | etot = -13.2825375975582
+37000  ekin = 5.14355281474345 |  erot = 3.77833709530338 | epot = -22.2044275077127 | etot = -13.2825375976659
+38000  ekin = 5.26699752588952 |  erot = 3.72801268545681 | epot = -22.2775478090603 | etot = -13.282537597714
+39000  ekin = 5.37191151713971 |  erot = 3.65359747923658 | epot = -22.3080465940747 | etot = -13.2825375976984
+40000  ekin = 5.45746010972539 |  erot = 3.55633701588603 | epot = -22.2963347232318 | etot = -13.2825375976204
+41000  ekin = 5.52312188621432 |  erot = 3.43809872369872 | epot = -22.2437582073857 | etot = -13.2825375974727
+42000  ekin = 5.56872044212123 |  erot = 3.3013527933319 | epot = -22.1526108327172 | etot = -13.2825375972641
+43000  ekin = 5.59443660083054 |  erot = 3.14910305123766 | epot = -22.0260772490709 | etot = -13.2825375970027
+44000  ekin = 5.60078634437832 |  erot = 2.98477133565166 | epot = -21.8680952767313 | etot = -13.2825375967014
+45000  ekin = 5.58859564323475 |  erot = 2.81204277265363 | epot = -21.6831760122637 | etot = -13.2825375963753
+46000  ekin = 5.55896198288938 |  erot = 2.6346956216755 | epot = -21.4761952006028 | etot = -13.2825375960379
+47000  ekin = 5.51320424222089 |  erot = 2.45646420183095 | epot = -21.2522060397504 | etot = -13.2825375956985
+48000  ekin = 5.45280176988658 |  erot = 2.28095947573165 | epot = -21.0162988409789 | etot = -13.2825375953606
+49000  ekin = 5.37933239946777 |  erot = 2.11161440403301 | epot = -20.7734843985466 | etot = -13.2825375950459
+50000  ekin = 5.29440598595322 |  erot = 1.95156309993227 | epot = -20.5285066806364 | etot = -13.2825375947509
+51000  ekin = 5.19960275040365 |  erot = 1.80366343983081 | epot = -20.2858037847169 | etot = -13.2825375944825
+52000  ekin = 5.09244091535893 |  erot = 1.66034071449528 | epot = -20.0353192196147 | etot = -13.2825375897605
+53000  ekin = 5.00219098599359 |  erot = 1.54003539006203 | epot = -19.8247639698989 | etot = -13.2825375938433
+54000  ekin = 4.9005832952689 |  erot = 1.45132465506065 | epot = -19.6344455614694 | etot = -13.2825376111398
+55000  ekin = 4.70838087935279 |  erot = 1.38368494594859 | epot = -19.374603433669 | etot = -13.2825376083676
+56000  ekin = 4.44064498303654 |  erot = 1.42525549496225 | epot = -19.1484380668512 | etot = -13.2825375888524
+57000  ekin = 4.28012764787381 |  erot = 1.59067222265449 | epot = -19.1533374833608 | etot = -13.2825376128325
+58000  ekin = 4.17606446205197 |  erot = 1.69269591419354 | epot = -19.1512979674153 | etot = -13.2825375911698
+59000  ekin = 4.06748012934537 |  erot = 1.75788112721229 | epot = -19.107898847714 | etot = -13.2825375911564
+60000  ekin = 3.95448823476477 |  erot = 1.84391663061692 | epot = -19.0809424565338 | etot = -13.2825375911521
+61000  ekin = 3.83840387031379 |  erot = 1.95003019237122 | epot = -19.0709716537089 | etot = -13.2825375910239
+62000  ekin = 3.72130809963139 |  erot = 2.0750170389528 | epot = -19.0788627296236 | etot = -13.2825375910394
+63000  ekin = 3.60440089033071 |  erot = 2.21773397929691 | epot = -19.1046724606766 | etot = -13.282537591049
+64000  ekin = 3.4889862142993 |  erot = 2.37695650761868 | epot = -19.148480312971 | etot = -13.282537591053
+65000  ekin = 3.37647880025376 |  erot = 2.55140907448341 | epot = -19.2104254657956 | etot = -13.2825375910584
+66000  ekin = 3.26833067403449 |  erot = 2.73974236804954 | epot = -19.2906106331586 | etot = -13.2825375910746
+67000  ekin = 3.16594788215649 |  erot = 2.94047174698095 | epot = -19.388957220252 | etot = -13.2825375911146
+68000  ekin = 3.0706053161234 |  erot = 3.15188029478479 | epot = -19.5050232021006 | etot = -13.2825375911924
+69000  ekin = 2.98334905059876 |  erot = 3.37190853325425 | epot = -19.6377951751748 | etot = -13.2825375913218
+70000  ekin = 2.90492955397934 |  erot = 3.59802295152821 | epot = -19.7854900970212 | etot = -13.2825375915136
+71000  ekin = 2.8357237632926 |  erot = 3.82715608397267 | epot = -19.9454174390302 | etot = -13.282537591765
+72000  ekin = 2.77568510799032 |  erot = 4.05569348668108 | epot = -20.1139161867756 | etot = -13.2825375921042
+73000  ekin = 2.72437405649554 |  erot = 4.27929863267833 | epot = -20.2862102816544 | etot = -13.2825375924805
+74000  ekin = 2.68098943200971 |  erot = 4.49340310246777 | epot = -20.4569301273593 | etot = -13.2825375928818
+75000  ekin = 2.64445309406174 |  erot = 4.69339307185924 | epot = -20.6203837591928 | etot = -13.2825375932718
+76000  ekin = 2.6135541520603 |  erot = 4.87501053155987 | epot = -20.7711022772319 | etot = -13.2825375936117
+77000  ekin = 2.58710084062325 |  erot = 5.03478939171986 | epot = -20.9044278262174 | etot = -13.2825375938743
+78000  ekin = 2.56403853914047 |  erot = 5.17029283960992 | epot = -21.0168689727791 | etot = -13.2825375940288
+79000  ekin = 2.54361120788205 |  erot = 5.28037161018718 | epot = -21.1065204121483 | etot = -13.2825375940791
+80000  ekin = 2.52540527324235 |  erot = 5.36512720853055 | epot = -21.1730700758027 | etot = -13.2825375940298
+81000  ekin = 2.50929384303282 |  erot = 5.42576598242984 | epot = -21.2175974194024 | etot = -13.2825375939398
+82000  ekin = 2.49524917644569 |  erot = 5.46414530531101 | epot = -21.2419320755729 | etot = -13.2825375938162
+83000  ekin = 2.48334269593095 |  erot = 5.4824203292205 | epot = -21.2483006188452 | etot = -13.2825375936938
+84000  ekin = 2.47365997802566 |  erot = 5.48271691205612 | epot = -21.2389144836699 | etot = -13.2825375935881
+85000  ekin = 2.46626808184741 |  erot = 5.46691083839012 | epot = -21.2157165137403 | etot = -13.2825375935028
+86000  ekin = 2.46123154184209 |  erot = 5.43653398177587 | epot = -21.1803031170847 | etot = -13.2825375934667
+87000  ekin = 2.45852093879021 |  erot = 5.39265692383558 | epot = -21.1337154560128 | etot = -13.282537593387
+88000  ekin = 2.45840646060141 |  erot = 5.33627030736318 | epot = -21.0772143612568 | etot = -13.2825375932922
+89000  ekin = 2.46146480126854 |  erot = 5.26838646846911 | epot = -21.012388863175 | etot = -13.2825375934373
+90000  ekin = 2.46773177835907 |  erot = 5.18930366181577 | epot = -20.9395730335201 | etot = -13.2825375933453
+91000  ekin = 2.47726011905689 |  erot = 5.09951749277907 | epot = -20.8593152050603 | etot = -13.2825375932243
+92000  ekin = 2.4907426196288 |  erot = 5.00022791911722 | epot = -20.7735081318261 | etot = -13.2825375930801
+93000  ekin = 2.50902833057334 |  erot = 4.89281259013229 | epot = -20.6843785136299 | etot = -13.2825375929243
+94000  ekin = 2.53301288183049 |  erot = 4.77876912035663 | epot = -20.5943195949551 | etot = -13.282537592768
+95000  ekin = 2.56354598704884 |  erot = 4.6596420581637 | epot = -20.5057256378358 | etot = -13.2825375926232
+96000  ekin = 2.60133194738592 |  erot = 4.53693642149458 | epot = -20.4208059613811 | etot = -13.2825375925006
+97000  ekin = 2.6468471253709 |  erot = 4.41204173729102 | epot = -20.341426455067 | etot = -13.2825375924051
+98000  ekin = 2.70029551800313 |  erot = 4.28619503995253 | epot = -20.2690281502933 | etot = -13.2825375923376
+99000  ekin = 2.76159183076374 |  erot = 4.1604816375425 | epot = -20.2046110606011 | etot = -13.2825375922949
+100000  ekin = 2.83036874776577 |  erot = 4.0358752301046 | epot = -20.1487815701413 | etot = -13.2825375922709
+101000  ekin = 2.90599845693998 |  erot = 3.9133007754067 | epot = -20.101836824607 | etot = -13.2825375922603
+102000  ekin = 2.98761606367611 |  erot = 3.79369343963891 | epot = -20.0638470955759 | etot = -13.2825375922608
+103000  ekin = 3.07413620026815 |  erot = 3.67802597580122 | epot = -20.0346997683425 | etot = -13.2825375922731
+104000  ekin = 3.16426099663664 |  erot = 3.5672897363664 | epot = -20.0140883253055 | etot = -13.2825375923024
+105000  ekin = 3.25648344622817 |  erot = 3.46242766269347 | epot = -20.0014487012771 | etot = -13.2825375923554
+106000  ekin = 3.34909407537385 |  erot = 3.36423261094233 | epot = -19.995864278755 | etot = -13.2825375924388
+107000  ekin = 3.44019930697686 |  erot = 3.27323316283083 | epot = -19.9959700623653 | etot = -13.2825375925576
+108000  ekin = 3.52775814523643 |  erot = 3.18959025645848 | epot = -19.9998859944077 | etot = -13.2825375927128
+109000  ekin = 3.6096400910426 |  erot = 3.11302339299944 | epot = -20.005201076944 | etot = -13.282537592902
+110000  ekin = 3.6837038852456 |  erot = 3.04277828887611 | epot = -20.0090197672392 | etot = -13.2825375931175
+111000  ekin = 3.74789440567239 |  erot = 2.97764201100065 | epot = -20.008074010021 | etot = -13.2825375933479
+112000  ekin = 3.80035415830488 |  erot = 2.91600823448545 | epot = -19.998899986368 | etot = -13.2825375935777
+113000  ekin = 3.83954489146462 |  erot = 2.8559933088985 | epot = -19.9780757941509 | etot = -13.2825375937878
+114000  ekin = 3.86437452036879 |  erot = 2.79560177874322 | epot = -19.9425138930679 | etot = -13.2825375939559
+115000  ekin = 3.87432139555512 |  erot = 2.7329343736022 | epot = -19.8897933632162 | etot = -13.2825375940589
+116000  ekin = 3.86954570193501 |  erot = 2.66642221950647 | epot = -19.8185055155167 | etot = -13.2825375940752
+117000  ekin = 3.85097050791437 |  erot = 2.59505981730791 | epot = -19.7285679191994 | etot = -13.2825375939772
+118000  ekin = 3.82031843896425 |  erot = 2.5186641606976 | epot = -19.6215201934443 | etot = -13.2825375937824
+119000  ekin = 3.78008379969966 |  erot = 2.43788144963801 | epot = -19.5005028428247 | etot = -13.282537593487
+120000  ekin = 3.73339325084474 |  erot = 2.35417060362146 | epot = -19.3701014475778 | etot = -13.2825375931116
+121000  ekin = 3.68379362023552 |  erot = 2.26974086129434 | epot = -19.2360720742189 | etot = -13.282537592689
+122000  ekin = 3.63497633455493 |  erot = 2.187331073511 | epot = -19.1048450003246 | etot = -13.2825375922586
+123000  ekin = 3.59047168903083 |  erot = 2.10992442969239 | epot = -18.9829337105828 | etot = -13.2825375918596
+124000  ekin = 3.55336069064751 |  erot = 2.04044947797503 | epot = -18.8763477601473 | etot = -13.2825375915248
+125000  ekin = 3.52605275648501 |  erot = 1.98151529341901 | epot = -18.7901056411792 | etot = -13.2825375912752
+126000  ekin = 3.51088386083619 |  erot = 1.93492307727733 | epot = -18.7283445290526 | etot = -13.2825375909391
+127000  ekin = 3.51016542665117 |  erot = 1.90135594382251 | epot = -18.6940589614207 | etot = -13.282537590947
+128000  ekin = 3.52366007691443 |  erot = 1.88146923500183 | epot = -18.6876669021169 | etot = -13.2825375902006
+129000  ekin = 3.52804447870926 |  erot = 1.87939379818771 | epot = -18.6899759099317 | etot = -13.2825376330347
+130000  ekin = 3.3912172753683 |  erot = 1.9537535440301 | epot = -18.6275084102333 | etot = -13.2825375908349
+131000  ekin = 3.51597185423426 |  erot = 2.06600773707507 | epot = -18.8645172230942 | etot = -13.2825376317848
+132000  ekin = 3.65680948155317 |  erot = 2.09675964820366 | epot = -19.0361067214645 | etot = -13.2825375917077
+133000  ekin = 3.7826089844419 |  erot = 2.11778864665351 | epot = -19.1829352240661 | etot = -13.2825375929707
+134000  ekin = 3.90291219401812 |  erot = 2.13993246768579 | epot = -19.3253822549305 | etot = -13.2825375932266
+135000  ekin = 4.01307253292161 |  erot = 2.16317596346837 | epot = -19.4587860898094 | etot = -13.2825375934194
+136000  ekin = 4.10942813981098 |  erot = 2.18779054238556 | epot = -19.5797562757542 | etot = -13.2825375935576
+137000  ekin = 4.18918244084745 |  erot = 2.21413018926333 | epot = -19.6858502237394 | etot = -13.2825375936286
+138000  ekin = 4.2505518072554 |  erot = 2.24252417705063 | epot = -19.7756135779478 | etot = -13.2825375936417
+139000  ekin = 4.29264193993074 |  erot = 2.27334414892585 | epot = -19.8485236824507 | etot = -13.2825375935941
+140000  ekin = 4.3154298106947 |  erot = 2.30704736065629 | epot = -19.9050147648385 | etot = -13.2825375934876
+141000  ekin = 4.31969657449578 |  erot = 2.34420108979774 | epot = -19.9464352576252 | etot = -13.2825375933317
+142000  ekin = 4.30689625825177 |  erot = 2.38546661972142 | epot = -19.9749004711159 | etot = -13.2825375931427
+143000  ekin = 4.27897643633862 |  erot = 2.43154322469966 | epot = -19.9930572539773 | etot = -13.282537592939
+144000  ekin = 4.23817759048806 |  erot = 2.48305254316461 | epot = -20.0037677263992 | etot = -13.2825375927466
+145000  ekin = 4.18683687366753 |  erot = 2.54040585524244 | epot = -20.009780321492 | etot = -13.2825375925821
+146000  ekin = 4.12722437776044 |  erot = 2.60369949546926 | epot = -20.0134614656893 | etot = -13.2825375924596
+147000  ekin = 4.06142641942185 |  erot = 2.67262771534978 | epot = -20.0165917271585 | etot = -13.2825375923869
+148000  ekin = 3.99128035690908 |  erot = 2.74643868481997 | epot = -20.020256634094 | etot = -13.282537592365
+149000  ekin = 3.91835859675011 |  erot = 2.82393987441806 | epot = -20.0248360635573 | etot = -13.2825375923891
+150000  ekin = 3.84399502540833 |  erot = 2.90355368904256 | epot = -20.0300863068997 | etot = -13.2825375924488
+151000  ekin = 3.76934462696621 |  erot = 2.98342057410539 | epot = -20.0353027936016 | etot = -13.28253759253
+152000  ekin = 3.69546503896268 |  erot = 3.06154297168208 | epot = -20.0395456032601 | etot = -13.2825375926153
+153000  ekin = 3.62340677772804 |  erot = 3.13595781467784 | epot = -20.0419021850934 | etot = -13.2825375926875
+154000  ekin = 3.55429442921638 |  erot = 3.20491770297356 | epot = -20.0417497249215 | etot = -13.2825375927316
+155000  ekin = 3.48935808553542 |  erot = 3.267033764948 | epot = -20.0389294432276 | etot = -13.2825375927442
+156000  ekin = 3.42995719397451 |  erot = 3.32146386703958 | epot = -20.0339586537004 | etot = -13.2825375926863
+157000  ekin = 3.37758377439308 |  erot = 3.3680769357291 | epot = -20.0281983027503 | etot = -13.2825375926282
+158000  ekin = 3.32977839475207 |  erot = 3.40502394976649 | epot = -20.0173399361884 | etot = -13.2825375916698
+159000  ekin = 3.28790229188182 |  erot = 3.43232801111001 | epot = -20.0027678906269 | etot = -13.2825375876351
+160000  ekin = 3.28279951728226 |  erot = 3.4645745488256 | epot = -20.0299116571476 | etot = -13.2825375910398
+161000  ekin = 3.29006841785755 |  erot = 3.48756894666592 | epot = -20.060174952488 | etot = -13.2825375879645
+162000  ekin = 3.30320279764929 |  erot = 3.5006454181618 | epot = -20.0863858038415 | etot = -13.2825375880305
+163000  ekin = 3.3268044536015 |  erot = 3.5070397924055 | epot = -20.1163818341639 | etot = -13.2825375881569
+164000  ekin = 3.35978204864461 |  erot = 3.50639799900104 | epot = -20.1487176359757 | etot = -13.2825375883301
+165000  ekin = 3.40052448161875 |  erot = 3.49807859199056 | epot = -20.181140662133 | etot = -13.2825375885237
+166000  ekin = 3.44710440323471 |  erot = 3.48135096319333 | epot = -20.2109929551299 | etot = -13.2825375887019
+167000  ekin = 3.49756483136592 |  erot = 3.45565303648324 | epot = -20.2357554566773 | etot = -13.2825375888282
+168000  ekin = 3.55023572858368 |  erot = 3.42084325030349 | epot = -20.2536165677586 | etot = -13.2825375888714
+169000  ekin = 3.60406985696714 |  erot = 3.37750569995069 | epot = -20.2641131456955 | etot = -13.2825375887777
+170000  ekin = 3.41798406778751 |  erot = 3.07782048145922 | epot = -19.778342066862 | etot = -13.2825375176153
+171000  ekin = 3.24552871157498 |  erot = 2.73637390316101 | epot = -19.2644400103033 | etot = -13.2825373955674
+172000  ekin = 3.78367855050775 |  erot = 3.07274537488996 | epot = -20.1389614956815 | etot = -13.2825375702838
+173000  ekin = 4.03457273059295 |  erot = 3.18336469108423 | epot = -20.5004749222008 | etot = -13.2825375005236
+174000  ekin = 4.14002439985893 |  erot = 3.16763893899956 | epot = -20.5902008391742 | etot = -13.2825375003158
+175000  ekin = 4.24061478727453 |  erot = 3.15086312051272 | epot = -20.6740154078936 | etot = -13.2825375001064
+176000  ekin = 4.33750550891526 |  erot = 3.13552610061259 | epot = -20.7555691095042 | etot = -13.2825374999763
+177000  ekin = 4.43118634626137 |  erot = 3.12342668205163 | epot = -20.8371505282951 | etot = -13.2825374999821
+178000  ekin = 4.52112038535783 |  erot = 3.11516996838801 | epot = -20.9188278538849 | etot = -13.282537500139
+179000  ekin = 4.60569122910417 |  erot = 3.10997891303252 | epot = -20.998207642551 | etot = -13.2825375004143
+180000  ekin = 4.68248742105047 |  erot = 3.1058753404107 | epot = -21.0709002621979 | etot = -13.2825375007368
+181000  ekin = 4.74885008880596 |  erot = 3.10016969122731 | epot = -21.1315572810529 | etot = -13.2825375010196
+182000  ekin = 4.8025200424072 |  erot = 3.09010778323257 | epot = -21.1751653268254 | etot = -13.2825375011856
+183000  ekin = 4.84185836209202 |  erot = 3.07355401450771 | epot = -21.1979498780484 | etot = -13.2825375014487
+184000  ekin = 4.86305938218088 |  erot = 3.04972947015888 | epot = -21.1953263537842 | etot = -13.2825375014444
+185000  ekin = 4.86484048379678 |  erot = 3.01830532387275 | epot = -21.1656833089538 | etot = -13.2825375012843
+186000  ekin = 4.84781115921716 |  erot = 2.97987576046156 | epot = -21.1102244206809 | etot = -13.2825375010021
+187000  ekin = 4.81357764335378 |  erot = 2.93597501879657 | epot = -21.0320901627985 | etot = -13.2825375006482
+188000  ekin = 4.76439584097053 |  erot = 2.8887503176224 | epot = -20.9356836588659 | etot = -13.282537500273
+189000  ekin = 4.70282021343345 |  erot = 2.84056846871519 | epot = -20.8259261820667 | etot = -13.282537499918
+190000  ekin = 4.63141632940784 |  erot = 2.79367442377921 | epot = -20.7076282527974 | etot = -13.2825374996104
+191000  ekin = 4.55257205219614 |  erot = 2.74995133907631 | epot = -20.5850608906324 | etot = -13.28253749936
+192000  ekin = 4.4684144513739 |  erot = 2.71080835143519 | epot = -20.461760301973 | etot = -13.2825374991639
+193000  ekin = 4.38080987485654 |  erot = 2.67717312167521 | epot = -20.3405204955454 | etot = -13.2825374990136
+194000  ekin = 4.29140314493119 |  erot = 2.64952891334815 | epot = -20.223469557183 | etot = -13.2825374989037
+195000  ekin = 4.20164846020117 |  erot = 2.62793199519477 | epot = -20.1121179542326 | etot = -13.2825374988367
+196000  ekin = 4.11279973688578 |  erot = 2.61197297306555 | epot = -20.0073102087732 | etot = -13.2825374988219
+197000  ekin = 4.02585897192346 |  erot = 2.6006960732789 | epot = -19.9090925440713 | etot = -13.2825374988689
+198000  ekin = 3.94151021740631 |  erot = 2.59254113732279 | epot = -19.8165888537068 | etot = -13.2825374989777
+199000  ekin = 3.8600892057151 |  erot = 2.58539978552207 | epot = -19.7280264903664 | etot = -13.2825374991292
+200000  ekin = 3.78163650515432 |  erot = 2.57685633277492 | epot = -19.641030337214 | etot = -13.2825374992847
+201000  ekin = 3.70604145366902 |  erot = 2.56461316993936 | epot = -19.5531921230034 | etot = -13.2825374993951
+202000  ekin = 3.63323784111755 |  erot = 2.54700321074615 | epot = -19.4627785512822 | etot = -13.2825374994185
+203000  ekin = 3.56337600429993 |  erot = 2.52342549129483 | epot = -19.3693389949304 | etot = -13.2825374993357
+204000  ekin = 3.49690618989434 |  erot = 2.49455276327548 | epot = -19.2739964523247 | etot = -13.2825374991549
+205000  ekin = 3.4345533876734 |  erot = 2.46224574346295 | epot = -19.1793366300441 | etot = -13.2825374989078
+206000  ekin = 3.37721205721461 |  erot = 2.42921548153362 | epot = -19.0889650373856 | etot = -13.2825374986374
+207000  ekin = 3.32580575275846 |  erot = 2.39854397251164 | epot = -19.0068872236569 | etot = -13.2825374983868
+208000  ekin = 3.28114891016592 |  erot = 2.3731881465479 | epot = -18.9368745549049 | etot = -13.2825374981911
+209000  ekin = 3.24383236357031 |  erot = 2.35556506548857 | epot = -18.881934927133 | etot = -13.2825374980741
+210000  ekin = 3.21413821976384 |  erot = 2.34727297364657 | epot = -18.8439486914573 | etot = -13.2825374980469
+211000  ekin = 3.1919920439607 |  erot = 2.34895966766535 | epot = -18.8234892097349 | etot = -13.2825374981088
+212000  ekin = 3.17695628121283 |  erot = 2.36032147203272 | epot = -18.8198152514957 | etot = -13.2825374982501
+213000  ekin = 3.16826455951627 |  erot = 2.3802017195472 | epot = -18.8310037775173 | etot = -13.2825374984538
+214000  ekin = 3.16489343854745 |  erot = 2.40676052174862 | epot = -18.8541914589943 | etot = -13.2825374986982
+215000  ekin = 3.16566474352266 |  erot = 2.43769738040411 | epot = -18.8858996228842 | etot = -13.2825374989574
+216000  ekin = 3.16936807503371 |  erot = 2.47051711067938 | epot = -18.922422684916 | etot = -13.2825374992029
+217000  ekin = 3.16266988026928 |  erot = 2.47868467133945 | epot = -18.9238920507811 | etot = -13.2825374991723
+218000  ekin = 3.17835235865462 |  erot = 2.45704329444748 | epot = -18.9179331413782 | etot = -13.2825374882761
+219000  ekin = 3.26524817202182 |  erot = 2.48120766962804 | epot = -19.0289933444494 | etot = -13.2825375027995
+220000  ekin = 3.3108366379572 |  erot = 2.50602061547593 | epot = -19.0993947418604 | etot = -13.2825374884273
+221000  ekin = 3.33748530919814 |  erot = 2.52276996124463 | epot = -19.1427927588605 | etot = -13.2825374884177
+222000  ekin = 3.36243211589585 |  erot = 2.53668587910087 | epot = -19.1816554833759 | etot = -13.2825374883791
+223000  ekin = 3.38541896904289 |  erot = 2.54888617169885 | epot = -19.2168426290795 | etot = -13.2825374883378
+224000  ekin = 3.40625812508042 |  erot = 2.56049920868685 | epot = -19.2492948220808 | etot = -13.2825374883136
+225000  ekin = 3.42484722909655 |  erot = 2.57234499865789 | epot = -19.2797297160694 | etot = -13.2825374883149
+226000  ekin = 3.44121067431426 |  erot = 2.5847203663376 | epot = -19.3084685289965 | etot = -13.2825374883446
+227000  ekin = 3.45552721377372 |  erot = 2.59730386680816 | epot = -19.3353685689828 | etot = -13.2825374884009
+228000  ekin = 3.46810974282108 |  erot = 2.60916931207508 | epot = -19.3598165433769 | etot = -13.2825374884807
+229000  ekin = 3.47932676313057 |  erot = 2.61888809507148 | epot = -19.3807523467825 | etot = -13.2825374885804
+230000  ekin = 3.48948003513572 |  erot = 2.62469570471801 | epot = -19.3967132285493 | etot = -13.2825374886956
+231000  ekin = 3.49867242979287 |  erot = 2.62469374220123 | epot = -19.4059036608136 | etot = -13.2825374888195
+232000  ekin = 3.50671171842553 |  erot = 2.61706130327851 | epot = -19.4063105106456 | etot = -13.2825374889415
+233000  ekin = 3.51309701132019 |  erot = 2.60026316425614 | epot = -19.3958976646192 | etot = -13.2825374890429
+234000  ekin = 3.51712117494225 |  erot = 2.57326085610047 | epot = -19.3729195201389 | etot = -13.2825374890961
+235000  ekin = 3.51809173982046 |  erot = 2.53573892922922 | epot = -19.336368158117 | etot = -13.2825374890673
+236000  ekin = 3.51562949139228 |  erot = 2.48833922691179 | epot = -19.2865062072283 | etot = -13.2825374889242
+237000  ekin = 3.50996386129181 |  erot = 2.43285732073755 | epot = -19.2253586706778 | etot = -13.2825374886484
+238000  ekin = 3.50212794781223 |  erot = 2.37232394343651 | epot = -19.1569893794947 | etot = -13.2825374882459
+239000  ekin = 3.49397580570105 |  erot = 2.3108975006263 | epot = -19.0874107940784 | etot = -13.282537487751
+240000  ekin = 3.48799489984471 |  erot = 2.25353771706539 | epot = -19.0240701041317 | etot = -13.2825374872216
+241000  ekin = 3.48694744152127 |  erot = 2.20549386842306 | epot = -18.9749787966723 | etot = -13.2825374867279
+242000  ekin = 3.4934176974057 |  erot = 2.17169223103266 | epot = -18.947647414778 | etot = -13.2825374863397
+243000  ekin = 3.50935803683896 |  erot = 2.15612557817141 | epot = -18.9480211011254 | etot = -13.282537486115
+244000  ekin = 3.53571412219025 |  erot = 2.16133426987283 | epot = -18.9795858781565 | etot = -13.2825374860934
+245000  ekin = 3.57218201231882 |  erot = 2.18803987534321 | epot = -19.0427593739541 | etot = -13.2825374862921
+246000  ekin = 3.61712090977394 |  erot = 2.23496626996872 | epot = -19.1346246664479 | etot = -13.2825374867053
+247000  ekin = 3.66762313707291 |  erot = 2.29886938892395 | epot = -19.2490300132999 | etot = -13.282537487303
+248000  ekin = 3.71973304097767 |  erot = 2.37479253662205 | epot = -19.3770630656317 | etot = -13.282537488032
+249000  ekin = 3.76879884759244 |  erot = 2.45655776432051 | epot = -19.5078941007293 | etot = -13.2825374888163
+250000  ekin = 3.80993596354176 |  erot = 2.5374803002976 | epot = -19.6299537534029 | etot = -13.2825374895636
+251000  ekin = 3.83856187827227 |  erot = 2.6112453760505 | epot = -19.7323447444996 | etot = -13.2825374901768
+252000  ekin = 3.85094160348931 |  erot = 2.67282602420732 | epot = -19.8063051182674 | etot = -13.2825374905708
+253000  ekin = 3.84466267221602 |  erot = 2.71927370140011 | epot = -19.8464738643058 | etot = -13.2825374906897
+254000  ekin = 3.81895334833917 |  erot = 2.75020964906172 | epot = -19.8517004879211 | etot = -13.2825374905202
+255000  ekin = 3.77477712370886 |  erot = 2.76789565653784 | epot = -19.8252102703423 | etot = -13.2825374900956
+256000  ekin = 3.71467746908689 |  erot = 2.7768542145932 | epot = -19.7740691731695 | etot = -13.2825374894894
+257000  ekin = 3.64239785971663 |  erot = 2.78310854270393 | epot = -19.7080438912214 | etot = -13.2825374888008
+258000  ekin = 3.56234912667125 |  erot = 2.79319020432275 | epot = -19.6380768191301 | etot = -13.2825374881361
+259000  ekin = 3.47902170398649 |  erot = 2.81309489223277 | epot = -19.5746540838101 | etot = -13.2825374875908
+260000  ekin = 3.39644765746229 |  erot = 2.84735592157313 | epot = -19.5263410662708 | etot = -13.2825374872354
+261000  ekin = 3.31779785755677 |  erot = 2.89836390677638 | epot = -19.4986992514409 | etot = -13.2825374871077
+262000  ekin = 3.24516405277705 |  erot = 2.96601202360051 | epot = -19.4937135635853 | etot = -13.2825374872077
+263000  ekin = 3.179546945306 |  erot = 3.04771661067476 | epot = -19.5098010434848 | etot = -13.2825374875041
+264000  ekin = 3.12100159498149 |  erot = 3.13875568824824 | epot = -19.5422947711671 | etot = -13.2825374879374
+265000  ekin = 3.06890996951173 |  erot = 3.23291804297549 | epot = -19.5843655009186 | etot = -13.2825374884314
+266000  ekin = 3.02230555156918 |  erot = 3.3233525253047 | epot = -19.6281955657826 | etot = -13.2825374889087
+267000  ekin = 2.98016989218907 |  erot = 3.40345614747432 | epot = -19.6661635289706 | etot = -13.2825374893072
+268000  ekin = 2.94163501488653 |  erot = 3.46763177350614 | epot = -19.6918042779846 | etot = -13.2825374895919
+269000  ekin = 2.90604069318559 |  erot = 3.5117562623884 | epot = -19.7003344453572 | etot = -13.2825374897832
+270000  ekin = 2.87284037255953 |  erot = 3.53329819601925 | epot = -19.688676058427 | etot = -13.2825374898482
+271000  ekin = 2.8415668881788 |  erot = 3.53141495904858 | epot = -19.6555193370572 | etot = -13.2825374898299
+272000  ekin = 2.81169493920591 |  erot = 3.50673144119824 | epot = -19.6009638701438 | etot = -13.2825374897396
+273000  ekin = 2.78262532285067 |  erot = 3.46115906465187 | epot = -19.5263218770816 | etot = -13.282537489579
+274000  ekin = 2.75380981305629 |  erot = 3.39781487150763 | epot = -19.4341621738888 | etot = -13.2825374893249
+275000  ekin = 2.7249735792436 |  erot = 3.32097131771962 | epot = -19.3284823859411 | etot = -13.2825374889778
+276000  ekin = 2.6963100293489 |  erot = 3.23585259467393 | epot = -19.2147001125781 | etot = -13.2825374885553
+277000  ekin = 2.66855210196835 |  erot = 3.14826501869141 | epot = -19.0993546087612 | etot = -13.2825374881014
+278000  ekin = 2.64286719085315 |  erot = 3.06403640806022 | epot = -18.9894410865903 | etot = -13.282537487677
+279000  ekin = 2.62061028223249 |  erot = 2.98836162249181 | epot = -18.8915093920665 | etot = -13.2825374873422
+280000  ekin = 2.60303022005452 |  erot = 2.92520891289514 | epot = -18.810776620089 | etot = -13.2825374871393
+281000  ekin = 2.59103448458187 |  erot = 2.87693253510413 | epot = -18.7505045067671 | etot = -13.2825374870811
+282000  ekin = 2.58508390620669 |  erot = 2.84417540765184 | epot = -18.7117968010092 | etot = -13.2825374871506
+283000  ekin = 2.58523135936813 |  erot = 2.82606103956109 | epot = -18.6938298862392 | etot = -13.2825374873099
+284000  ekin = 2.59126091870129 |  erot = 2.82059473157291 | epot = -18.6943931377889 | etot = -13.2825374875147
+285000  ekin = 2.60284631077899 |  erot = 2.82514472712939 | epot = -18.7105285256372 | etot = -13.2825374877289
+286000  ekin = 2.61964775974011 |  erot = 2.83687342635554 | epot = -18.7390586740297 | etot = -13.2825374879341
+287000  ekin = 2.6416789431732 |  erot = 2.85285066093716 | epot = -18.7770670922847 | etot = -13.2825374881743
+288000  ekin = 2.6687167813734 |  erot = 2.8702293010975 | epot = -18.8214835708707 | etot = -13.2825374883998
+289000  ekin = 2.69931643718338 |  erot = 2.88698660757789 | epot = -18.8688405333582 | etot = -13.282537488597
+290000  ekin = 2.73194963658688 |  erot = 2.90163654912622 | epot = -18.9161236744781 | etot = -13.282537488765
+291000  ekin = 2.76502957907631 |  erot = 2.91324911168519 | epot = -18.9608161796562 | etot = -13.2825374888947
+292000  ekin = 2.79700561900786 |  erot = 2.92149576190804 | epot = -19.0010388698871 | etot = -13.2825374889712
+293000  ekin = 2.82654239554868 |  erot = 2.92669002283791 | epot = -19.0357699073648 | etot = -13.2825374889783
+294000  ekin = 2.85272969462551 |  erot = 2.92951972788748 | epot = -19.064786911459 | etot = -13.282537488946
+295000  ekin = 2.87508597590273 |  erot = 2.9311082644752 | epot = -19.0887317291887 | etot = -13.2825374888108
+296000  ekin = 2.8937804752686 |  erot = 2.93349300132756 | epot = -19.1098109651871 | etot = -13.2825374885909
+297000  ekin = 2.90976516785128 |  erot = 2.93912517174271 | epot = -19.1314278279134 | etot = -13.2825374883194
+298000  ekin = 2.92469477926885 |  erot = 2.95047845944604 | epot = -19.1577107267523 | etot = -13.2825374880374
+299000  ekin = 2.94065805823525 |  erot = 2.96967690612477 | epot = -19.192872452154 | etot = -13.282537487794
+300000  ekin = 2.95980003469444 |  erot = 2.99812642991887 | epot = -19.2404639522491 | etot = -13.2825374876358
+301000  ekin = 2.9839127297722 |  erot = 3.03621252497576 | epot = -19.3026627423455 | etot = -13.2825374875976
+302000  ekin = 3.01408971368584 |  erot = 3.08312901017938 | epot = -19.3797562115566 | etot = -13.2825374876914
+303000  ekin = 3.05053302665562 |  erot = 3.13689255668877 | epot = -19.4699630712467 | etot = -13.2825374879023
+304000  ekin = 3.08584972584791 |  erot = 3.19556015973973 | epot = -19.563947375247 | etot = -13.2825374896594
+305000  ekin = 3.11890909070429 |  erot = 3.26281224727038 | epot = -19.6642588266134 | etot = -13.2825374886387
+306000  ekin = 3.16699270587699 |  erot = 3.33070506272307 | epot = -19.7802352601689 | etot = -13.2825374915688
+307000  ekin = 3.22023032257454 |  erot = 3.3799777181521 | epot = -19.8827455298078 | etot = -13.2825374890812
+308000  ekin = 3.2726873966337 |  erot = 3.41969099128558 | epot = -19.974915877149 | etot = -13.2825374892298
+309000  ekin = 3.32280425481262 |  erot = 3.44976402097258 | epot = -20.0551057651207 | etot = -13.2825374893356
+310000  ekin = 3.36903652740989 |  erot = 3.46970323071698 | epot = -20.1212772475628 | etot = -13.282537489436
+311000  ekin = 3.40972253534481 |  erot = 3.47940229945176 | epot = -20.1716623243629 | etot = -13.2825374895663
+312000  ekin = 3.44308129109209 |  erot = 3.47898447383071 | epot = -20.2046032544282 | etot = -13.2825374895054
+313000  ekin = 3.46879202758971 |  erot = 3.47087869841085 | epot = -20.2222082156542 | etot = -13.2825374896536
+314000  ekin = 3.48565385463582 |  erot = 3.45582059749585 | epot = -20.2240119419411 | etot = -13.2825374898094
+315000  ekin = 3.49216313291107 |  erot = 3.43373104095289 | epot = -20.2084316637861 | etot = -13.2825374899221
+316000  ekin = 3.4873621330349 |  erot = 3.4048256725594 | epot = -20.1747252955317 | etot = -13.2825374899373
+317000  ekin = 3.4699413250759 |  erot = 3.36841330847627 | epot = -20.1208921250426 | etot = -13.2825374914904
+318000  ekin = 3.43614022048349 |  erot = 3.32066657788322 | epot = -20.0393442896741 | etot = -13.2825374913073
+319000  ekin = 3.38694293952412 |  erot = 3.26364910698136 | epot = -19.933129537441 | etot = -13.2825374909355
+320000  ekin = 3.32506744212997 |  erot = 3.20113650606391 | epot = -19.8087414386369 | etot = -13.282537490443
+321000  ekin = 3.25415482891508 |  erot = 3.13766117543029 | epot = -19.6743534942649 | etot = -13.2825374899195
+322000  ekin = 3.17813669787313 |  erot = 3.07780020747427 | epot = -19.5384743947971 | etot = -13.2825374894497
+323000  ekin = 3.10066688251982 |  erot = 3.0254908818081 | epot = -19.4086952534143 | etot = -13.2825374890864
+324000  ekin = 3.02479637479388 |  erot = 2.98355122494391 | epot = -19.2908850885811 | etot = -13.2825374888433
+325000  ekin = 2.95294332411383 |  erot = 2.95347420684896 | epot = -19.1889550196676 | etot = -13.2825374887048
+326000  ekin = 2.88706743997792 |  erot = 2.93544936652566 | epot = -19.1050542951497 | etot = -13.2825374886462
+327000  ekin = 2.82887581624799 |  erot = 2.92851219862454 | epot = -19.0399255035216 | etot = -13.2825374886491
+328000  ekin = 2.77990830068301 |  erot = 2.93074772300687 | epot = -18.9931935123953 | etot = -13.2825374887054
+329000  ekin = 2.74145002280153 |  erot = 2.9395401663855 | epot = -18.9635276779975 | etot = -13.2825374888105
+330000  ekin = 2.71432845550434 |  erot = 2.95189909643542 | epot = -18.948765040893 | etot = -13.2825374889532
+331000  ekin = 2.69870867087714 |  erot = 2.96486608415688 | epot = -18.9461122441487 | etot = -13.2825374891147
+332000  ekin = 2.69398517732769 |  erot = 2.97593512180702 | epot = -18.9524577884083 | etot = -13.2825374892736
+333000  ekin = 2.69881348537541 |  erot = 2.98337443171444 | epot = -18.9647254065019 | etot = -13.282537489412
+334000  ekin = 2.71127609678388 |  erot = 2.98637176000176 | epot = -18.9801853463025 | etot = -13.2825374895168
+335000  ekin = 2.72916096429869 |  erot = 2.9850116550983 | epot = -18.9967101089713 | etot = -13.2825374895743
+336000  ekin = 2.75032164400772 |  erot = 2.98016551096382 | epot = -19.0130246445397 | etot = -13.2825374895682
+337000  ekin = 2.77304615866046 |  erot = 2.97336445321142 | epot = -19.0289481013616 | etot = -13.2825374894897
+338000  ekin = 2.79631213711493 |  erot = 2.96664518651861 | epot = -19.0454948129846 | etot = -13.2825374893511
+339000  ekin = 2.81982513095444 |  erot = 2.96230352229829 | epot = -19.0646661424439 | etot = -13.2825374891912
+340000  ekin = 2.84381599358321 |  erot = 2.96250923740585 | epot = -19.0888627200581 | etot = -13.282537489069
+341000  ekin = 2.86861716322387 |  erot = 2.96879944354266 | epot = -19.1199540958289 | etot = -13.2825374890623
+342000  ekin = 2.8942330530774 |  erot = 2.9815983091965 | epot = -19.1583688514559 | etot = -13.282537489182
+343000  ekin = 2.92230469127694 |  erot = 3.00151195978259 | epot = -19.2063541396131 | etot = -13.2825374885536
+344000  ekin = 2.95328542679254 |  erot = 3.02739469587761 | epot = -19.263217611886 | etot = -13.2825374892158
+345000  ekin = 2.98288076792924 |  erot = 3.0539773023115 | epot = -19.319395560126 | etot = -13.2825374898853
+346000  ekin = 3.00683622806662 |  erot = 3.07579634903604 | epot = -19.3651700675394 | etot = -13.2825374904367
+347000  ekin = 3.02168203920098 |  erot = 3.08832269782129 | epot = -19.3925422278017 | etot = -13.2825374907794
+348000  ekin = 3.02528371459624 |  erot = 3.08873432783917 | epot = -19.3965555333216 | etot = -13.2825374908862
+349000  ekin = 3.01708434472178 |  erot = 3.07610751269672 | epot = -19.3757293482069 | etot = -13.2825374907884
+350000  ekin = 2.99803087494797 |  erot = 3.05108999688778 | epot = -19.3316583623806 | etot = -13.2825374905448
+351000  ekin = 2.97033325354683 |  erot = 3.0153936212866 | epot = -19.2682643650312 | etot = -13.2825374901978
+352000  ekin = 2.9375545389088 |  erot = 2.97175102427437 | epot = -19.1918430530028 | etot = -13.2825374898196
+353000  ekin = 2.90330530002109 |  erot = 2.9229126111419 | epot = -19.1087554005707 | etot = -13.2825374894077
+354000  ekin = 2.87126755833817 |  erot = 2.8717032112567 | epot = -19.0255082585642 | etot = -13.2825374889693
+355000  ekin = 2.8452063966084 |  erot = 2.82119115452554 | epot = -18.9489350396508 | etot = -13.2825374885168
+356000  ekin = 2.8287863971617 |  erot = 2.77463213289955 | epot = -18.8859560181414 | etot = -13.2825374880802
+357000  ekin = 2.82589501110838 |  erot = 2.73507904234315 | epot = -18.8435115424251 | etot = -13.2825374889736
+358000  ekin = 2.83567543256236 |  erot = 2.69990343571512 | epot = -18.8181163574533 | etot = -13.2825374891758
+359000  ekin = 2.85413863003171 |  erot = 2.66477535390693 | epot = -18.8014514734629 | etot = -13.2825374895243
+360000  ekin = 2.87797108635789 |  erot = 2.62716069413247 | epot = -18.7876692705243 | etot = -13.2825374900339
+361000  ekin = 2.90295419334349 |  erot = 2.58324525246655 | epot = -18.7687369364383 | etot = -13.2825374906282
+362000  ekin = 2.92446718933245 |  erot = 2.52862237257584 | epot = -18.7356270530339 | etot = -13.2825374911256
+363000  ekin = 2.93848759933288 |  erot = 2.4598916464099 | epot = -18.6809167370418 | etot = -13.282537491299
+364000  ekin = 2.94271150164537 |  erot = 2.37661313123448 | epot = -18.6018621239963 | etot = -13.2825374911165
+365000  ekin = 2.93600170081407 |  erot = 2.28250131434272 | epot = -18.5010405056271 | etot = -13.2825374904703
+366000  ekin = 2.91934189957468 |  erot = 2.18525996401723 | epot = -18.3871393531676 | etot = -13.2825374895757
+367000  ekin = 2.89548895825523 |  erot = 2.09468885645295 | epot = -18.272715303391 | etot = -13.2825374886828
+368000  ekin = 2.86763306547941 |  erot = 2.02026878405696 | epot = -18.170439337522 | etot = -13.2825374879856
+369000  ekin = 2.83845106986062 |  erot = 1.96931673437145 | epot = -18.0903052917991 | etot = -13.282537487567
+370000  ekin = 2.80963551309293 |  erot = 1.9461845593661 | epot = -18.0383575598726 | etot = -13.2825374874135
+371000  ekin = 2.78188668089845 |  erot = 1.95235490032886 | epot = -18.0167790686903 | etot = -13.282537487463
+372000  ekin = 2.75518266190969 |  erot = 1.98699478725925 | epot = -18.0247149368153 | etot = -13.2825374876464
+373000  ekin = 2.72912880528294 |  erot = 2.04757125854723 | epot = -18.059237551743 | etot = -13.2825374879128
+374000  ekin = 2.7032481730958 |  erot = 2.13030562163336 | epot = -18.116091282967 | etot = -13.2825374882379
+375000  ekin = 2.67714701016783 |  erot = 2.230398201263 | epot = -18.190082700051 | etot = -13.2825374886202
+376000  ekin = 2.65054772278835 |  erot = 2.34206662745015 | epot = -18.2751518393088 | etot = -13.2825374890703
+377000  ekin = 2.6232286660267 |  erot = 2.4585298333916 | epot = -18.3642959890073 | etot = -13.282537489589
+378000  ekin = 2.59495135703951 |  erot = 2.57214449993273 | epot = -18.4496333471167 | etot = -13.2825374901445
+379000  ekin = 2.56546707826761 |  erot = 2.67491697597518 | epot = -18.5229215449019 | etot = -13.2825374906591
+380000  ekin = 2.5346614309634 |  erot = 2.75950320018496 | epot = -18.5767021221684 | etot = -13.28253749102
+381000  ekin = 2.50280930121805 |  erot = 2.820545199185 | epot = -18.6058919915259 | etot = -13.2825374911229
+382000  ekin = 2.470812727732 |  erot = 2.85587907291203 | epot = -18.6092292915694 | etot = -13.2825374909253
+383000  ekin = 2.44026108011508 |  erot = 2.86702983654261 | epot = -18.5898284071357 | etot = -13.282537490478
+384000  ekin = 2.41324034479816 |  erot = 2.85867137366513 | epot = -18.5544492083667 | etot = -13.2825374899034
+385000  ekin = 2.39197367794907 |  erot = 2.83724859059171 | epot = -18.5117597578793 | etot = -13.2825374893386
+386000  ekin = 2.37848037079664 |  erot = 2.80936838549805 | epot = -18.4703862451731 | etot = -13.2825374888784
+387000  ekin = 2.37440773877127 |  erot = 2.78057799552109 | epot = -18.4375232228463 | etot = -13.282537488554
+388000  ekin = 2.38106033998957 |  erot = 2.75482980994791 | epot = -18.4184276382837 | etot = -13.2825374883462
+389000  ekin = 2.39952694728403 |  erot = 2.73455852134344 | epot = -18.4166229568446 | etot = -13.2825374882171
+390000  ekin = 2.43075796801616 |  erot = 2.72108399954165 | epot = -18.4343794556986 | etot = -13.2825374881408
+391000  ekin = 2.47547758104241 |  erot = 2.71503282253302 | epot = -18.4730478916951 | etot = -13.2825374881197
+392000  ekin = 2.53389941336453 |  erot = 2.7165760791739 | epot = -18.5330129807221 | etot = -13.2825374881837
+393000  ekin = 2.60531467139695 |  erot = 2.72543162367493 | epot = -18.6132837834427 | etot = -13.2825374883708
+394000  ekin = 2.68770614221252 |  erot = 2.74072420161865 | epot = -18.7109678325333 | etot = -13.2825374887021
+395000  ekin = 2.77757589911151 |  erot = 2.76089277951452 | epot = -18.8210061677825 | etot = -13.2825374891565
+396000  ekin = 2.87012638573488 |  erot = 2.78383015196109 | epot = -18.9364940273617 | etot = -13.2825374896658
+397000  ekin = 2.95979968457167 |  erot = 2.80730760068494 | epot = -19.049644775395 | etot = -13.2825374901384
+398000  ekin = 3.04101675292653 |  erot = 2.82953067572568 | epot = -19.1530849191508 | etot = -13.2825374904986
+399000  ekin = 3.10335323688597 |  erot = 2.84223393463616 | epot = -19.228124720834 | etot = -13.2825375493118
+400000  ekin = 3.10435999780448 |  erot = 2.68059016645162 | epot = -19.0674876235106 | etot = -13.2825374592545
+401000  ekin = 3.39309095567053 |  erot = 2.6399790010433 | epot = -19.3156074940173 | etot = -13.2825375373034
+402000  ekin = 3.44106634978254 |  erot = 2.65979071672222 | epot = -19.3833945765536 | etot = -13.2825375100489
+403000  ekin = 3.43207406395648 |  erot = 2.67998452071647 | epot = -19.3945960946571 | etot = -13.2825375099842
+404000  ekin = 3.40426891788004 |  erot = 2.70237957197844 | epot = -19.3891859997704 | etot = -13.2825375099119
+405000  ekin = 3.35933473415418 |  erot = 2.72607645469475 | epot = -19.3679486986676 | etot = -13.2825375098187
+406000  ekin = 3.29966540903968 |  erot = 2.74995079996642 | epot = -19.3321537187046 | etot = -13.2825375096985
+407000  ekin = 3.22823117978945 |  erot = 2.77286165528619 | epot = -19.2836303446341 | etot = -13.2825375095584
+408000  ekin = 3.1483591073605 |  erot = 2.79373949031154 | epot = -19.2246361071148 | etot = -13.2825375094427
+409000  ekin = 3.06351542880808 |  erot = 2.81131469887469 | epot = -19.1573676369864 | etot = -13.2825375093037
+410000  ekin = 2.97699949578463 |  erot = 2.8246267920136 | epot = -19.0841637969997 | etot = -13.2825375092014
+411000  ekin = 2.89165449988321 |  erot = 2.83289882079081 | epot = -19.007090829806 | etot = -13.282537509132
+412000  ekin = 2.80978906685915 |  erot = 2.83549592234132 | epot = -18.9278224982724 | etot = -13.2825375090719
+413000  ekin = 2.73325536963672 |  erot = 2.83215388790773 | epot = -18.8479467665295 | etot = -13.2825375089851
+414000  ekin = 2.66364879693787 |  erot = 2.82325639295092 | epot = -18.7694426987271 | etot = -13.2825375088383
+415000  ekin = 2.60253860594386 |  erot = 2.81004531903034 | epot = -18.6951214335909 | etot = -13.2825375086167
+416000  ekin = 2.55161661467894 |  erot = 2.79464631188373 | epot = -18.6288004348987 | etot = -13.2825375083361
+417000  ekin = 2.51265407607916 |  erot = 2.77984605492258 | epot = -18.5750376413351 | etot = -13.2825375103333
+418000  ekin = 2.4733460400696 |  erot = 2.77799997552928 | epot = -18.5338835235814 | etot = -13.2825375079825
+419000  ekin = 2.44559608968299 |  erot = 2.79655231011318 | epot = -18.5246859081161 | etot = -13.2825375083199
+420000  ekin = 2.44884495810883 |  erot = 2.8127677686639 | epot = -18.5441502345376 | etot = -13.2825375077648
+421000  ekin = 2.47134322850907 |  erot = 2.8275658566971 | epot = -18.581446593281 | etot = -13.2825375080748
+422000  ekin = 2.50522487691509 |  erot = 2.84806830842189 | epot = -18.6358306938666 | etot = -13.2825375085297
+423000  ekin = 2.54673540362963 |  erot = 2.87162843047139 | epot = -18.7009013431387 | etot = -13.2825375090377
+424000  ekin = 2.59155452677409 |  erot = 2.89540834353099 | epot = -18.7695003797936 | etot = -13.2825375094885
+425000  ekin = 2.63549518710331 |  erot = 2.91724946462186 | epot = -18.8352821615182 | etot = -13.282537509793
+426000  ekin = 2.67515430282142 |  erot = 2.9363216769118 | epot = -18.8940134896421 | etot = -13.2825375099089
+427000  ekin = 2.70835356710237 |  erot = 2.95332774897657 | epot = -18.9442188259222 | etot = -13.2825375098433
+428000  ekin = 2.73429370856415 |  erot = 2.97029523904671 | epot = -18.9871264572452 | etot = -13.2825375096344
+429000  ekin = 2.75344687777166 |  erot = 2.99015713230311 | epot = -19.0261415194056 | etot = -13.2825375093308
+430000  ekin = 2.76726512075389 |  erot = 3.01631311482664 | epot = -19.0661157445654 | etot = -13.2825375089849
+431000  ekin = 2.77776520583174 |  erot = 3.05220345438128 | epot = -19.1125061688761 | etot = -13.282537508663
+432000  ekin = 2.78700254671475 |  erot = 3.10077153002521 | epot = -19.1703115851965 | etot = -13.2825375084566
+433000  ekin = 2.79644099945107 |  erot = 3.16368547120708 | epot = -19.2426639791351 | etot = -13.2825375084769
+434000  ekin = 2.80629528100655 |  erot = 3.24036053937453 | epot = -19.3291933292032 | etot = -13.2825375088222
+435000  ekin = 2.81503854861979 |  erot = 3.32707633254736 | epot = -19.4246523906905 | etot = -13.2825375095233
+436000  ekin = 2.81936003427121 |  erot = 3.41666372805949 | epot = -19.5185612728238 | etot = -13.2825375104931
+437000  ekin = 2.81480689570261 |  erot = 3.4992068109881 | epot = -19.5965512182087 | etot = -13.282537511518
+438000  ekin = 2.79709037799446 |  erot = 3.56380823491998 | epot = -19.6434361252458 | etot = -13.2825375123314
+439000  ekin = 2.76357573484127 |  erot = 3.60097663046949 | epot = -19.6470898780263 | etot = -13.2825375127155
+440000  ekin = 2.71419714341147 |  erot = 3.60475935377896 | epot = -19.6014940098203 | etot = -13.2825375126299
+441000  ekin = 2.65147586146302 |  erot = 3.5735068280095 | epot = -19.5075202016404 | etot = -13.2825375121679
+442000  ekin = 2.57978868208042 |  erot = 3.50949061111538 | epot = -19.3718168046633 | etot = -13.2825375114675
+443000  ekin = 2.5045655875428 |  erot = 3.41786741963772 | epot = -19.2049705178136 | etot = -13.2825375106331
+444000  ekin = 2.4318529905012 |  erot = 3.30558723791353 | epot = -19.0199777381389 | etot = -13.2825375097241
+445000  ekin = 2.36817510309247 |  erot = 3.18052048206526 | epot = -18.8312330939434 | etot = -13.2825375087857
+446000  ekin = 2.32036350430697 |  erot = 3.05081891042797 | epot = -18.6537199226 | etot = -13.2825375078651
+447000  ekin = 2.29507009388122 |  erot = 2.92434156857507 | epot = -18.5019491695335 | etot = -13.2825375070773
+448000  ekin = 2.29792306266074 |  erot = 2.80795199469404 | epot = -18.3884125638663 | etot = -13.2825375065115
+449000  ekin = 2.33256968728711 |  erot = 2.7069587718276 | epot = -18.3220659653791 | etot = -13.2825375062644
+450000  ekin = 2.39980570006952 |  erot = 2.62453468442755 | epot = -18.3068778908976 | etot = -13.2825375064006
+451000  ekin = 2.49706752601316 |  erot = 2.56128240619122 | epot = -18.340887439138 | etot = -13.2825375069336
+452000  ekin = 2.61842576959522 |  erot = 2.51510244033024 | epot = -18.4160657177069 | etot = -13.2825375077814
+453000  ekin = 2.75505822099767 |  erot = 2.4815699152751 | epot = -18.5191656452272 | etot = -13.2825375089544
+454000  ekin = 2.89583245289786 |  erot = 2.45420794645489 | epot = -18.6325779096516 | etot = -13.2825375102988
+455000  ekin = 3.02803920575135 |  erot = 2.42568753015633 | epot = -18.7362642475679 | etot = -13.2825375116602
+456000  ekin = 3.13847091958599 |  erot = 2.38932191986764 | epot = -18.8103303522241 | etot = -13.2825375127704
+457000  ekin = 3.21547363213364 |  erot = 2.34093725375183 | epot = -18.838948399153 | etot = -13.2825375132675
+458000  ekin = 3.2519255084935 |  erot = 2.28077893488055 | epot = -18.8152419562781 | etot = -13.282537512904
+459000  ekin = 3.24761130317629 |  erot = 2.2142990448528 | epot = -18.7444478597993 | etot = -13.2825375117702
+460000  ekin = 3.20922400631774 |  erot = 2.15086461862506 | epot = -18.6426261351955 | etot = -13.2825375102527
+461000  ekin = 3.14796311212567 |  erot = 2.10092694609436 | epot = -18.5314275669974 | etot = -13.2825375087774
+462000  ekin = 3.07634336772018 |  erot = 2.07329933809505 | epot = -18.4321802134275 | etot = -13.2825375076122
+463000  ekin = 3.00570913410551 |  erot = 2.0736740452441 | epot = -18.3619206862057 | etot = -13.2825375068561
+464000  ekin = 2.94485829968431 |  erot = 2.104311840005 | epot = -18.3317076462087 | etot = -13.2825375065194
+465000  ekin = 2.89946798282509 |  erot = 2.16425406359513 | epot = -18.3462595530094 | etot = -13.2825375065892
+466000  ekin = 2.87195252748384 |  erot = 2.24955307492882 | epot = -18.4040431094629 | etot = -13.2825375070502
+467000  ekin = 2.86158324929155 |  erot = 2.35338924278566 | epot = -18.4975099999498 | etot = -13.2825375078726
+468000  ekin = 2.86493243611462 |  erot = 2.46640127712313 | epot = -18.6138712220354 | etot = -13.2825375087976
+469000  ekin = 2.87700241085683 |  erot = 2.57824581699685 | epot = -18.7377857379574 | etot = -13.2825375101037
+470000  ekin = 2.89115454215717 |  erot = 2.6760619901597 | epot = -18.8497540436439 | etot = -13.2825375113271
+471000  ekin = 2.90087699699639 |  erot = 2.74765202472445 | epot = -18.9310665339225 | etot = -13.2825375122017
+472000  ekin = 2.90129360657261 |  erot = 2.78442288107442 | epot = -18.968254000156 | etot = -13.282537512509
+473000  ekin = 2.89014262488401 |  erot = 2.78350866548211 | epot = -18.9561888025525 | etot = -13.2825375121863
+474000  ekin = 2.86798455519513 |  erot = 2.74843722227868 | epot = -18.8989592888434 | etot = -13.2825375113696
+475000  ekin = 2.83751222123448 |  erot = 2.68789202058937 | epot = -18.8079417521561 | etot = -13.2825375103323
+476000  ekin = 2.80225697256735 |  erot = 2.6131130536835 | epot = -18.6979075356112 | etot = -13.2825375093603
+477000  ekin = 2.76525060538104 |  erot = 2.5351054311932 | epot = -18.5828935452201 | etot = -13.2825375086459
+478000  ekin = 2.72814283270942 |  erot = 2.46266477167759 | epot = -18.4733451126352 | etot = -13.2825375082482
+479000  ekin = 2.69099471856512 |  erot = 2.40160392944764 | epot = -18.3751361561287 | etot = -13.282537508116
+480000  ekin = 2.65266810495577 |  erot = 2.35496214915267 | epot = -18.2901677622972 | etot = -13.2825375081888
+481000  ekin = 2.61144235513308 |  erot = 2.32364519373199 | epot = -18.2176250571285 | etot = -13.2825375082635
+482000  ekin = 2.56577673011677 |  erot = 2.30767778315765 | epot = -18.1559920215987 | etot = -13.2825375083243
+483000  ekin = 2.51481850303814 |  erot = 2.3066085334913 | epot = -18.1039645448551 | etot = -13.2825375083257
+484000  ekin = 2.4583813285785 |  erot = 2.31984500682984 | epot = -18.0607638434006 | etot = -13.2825375079923
+485000  ekin = 2.37536403472682 |  erot = 2.30798475217265 | epot = -17.9658863028417 | etot = -13.2825375159423
+486000  ekin = 2.31029787366189 |  erot = 2.2748698765298 | epot = -17.8677052455195 | etot = -13.2825374953278
+487000  ekin = 2.35903895729104 |  erot = 2.35840823836807 | epot = -17.999984715744 | etot = -13.2825375200849
+488000  ekin = 2.35207405530543 |  erot = 2.45495770512307 | epot = -18.0895692764582 | etot = -13.2825375160297
+489000  ekin = 2.32025825392693 |  erot = 2.54616767543756 | epot = -18.1489634454321 | etot = -13.2825375160676
+490000  ekin = 2.29515153865843 |  erot = 2.64227715700559 | epot = -18.2199662119985 | etot = -13.2825375163345
+491000  ekin = 2.2772449984618 |  erot = 2.73950547065074 | epot = -18.2992879857204 | etot = -13.2825375166078
+492000  ekin = 2.26670396933619 |  erot = 2.83351832941017 | epot = -18.3827598156809 | etot = -13.2825375169346
+493000  ekin = 2.26314468313945 |  erot = 2.91977614256862 | epot = -18.4654583429805 | etot = -13.2825375172724
+494000  ekin = 2.26577113860128 |  erot = 2.99399214337922 | epot = -18.5423007995586 | etot = -13.2825375175781
+495000  ekin = 2.27355094490557 |  erot = 3.05259857148999 | epot = -18.6086870342097 | etot = -13.2825375178141
+496000  ekin = 2.28538641730899 |  erot = 3.09313022190335 | epot = -18.6610541571706 | etot = -13.2825375179582
+497000  ekin = 2.3002347482288 |  erot = 3.1144407210763 | epot = -18.6972129873049 | etot = -13.2825375179998
+498000  ekin = 2.3171936593925 |  erot = 3.11678508300488 | epot = -18.7165162603363 | etot = -13.2825375179389
+499000  ekin = 2.33554254161235 |  erot = 3.10178716719771 | epot = -18.7198672265934 | etot = -13.2825375177834
+500000  ekin = 2.31317350059265 |  erot = 3.05449093047628 | epot = -18.6502019677268 | etot = -13.2825375366579
+501000  ekin = 2.31231722972123 |  erot = 3.00810318076113 | epot = -18.6029579372101 | etot = -13.2825375267278
+502000  ekin = 2.3899963895355 |  erot = 2.98467042894116 | epot = -18.657204342111 | etot = -13.2825375236343
+503000  ekin = 2.41312387633379 |  erot = 2.93091691357846 | epot = -18.6265783132594 | etot = -13.2825375233471
+504000  ekin = 2.43600229237452 |  erot = 2.88130858481333 | epot = -18.5998484003212 | etot = -13.2825375231333
+505000  ekin = 2.45757791196529 |  erot = 2.8401186666586 | epot = -18.5802341016713 | etot = -13.2825375230474
+506000  ekin = 2.47627134224398 |  erot = 2.81025901806717 | epot = -18.5690678834509 | etot = -13.2825375231397
+507000  ekin = 2.48985246050699 |  erot = 2.79268587932984 | epot = -18.5650758632795 | etot = -13.2825375234427
+508000  ekin = 2.49542483825493 |  erot = 2.78597986937444 | epot = -18.5639422315766 | etot = -13.2825375239472
+509000  ekin = 2.48963204750428 |  erot = 2.78630577995571 | epot = -18.5584753520407 | etot = -13.2825375245807
+510000  ekin = 2.4691743887688 |  erot = 2.78796571282341 | epot = -18.5396776267959 | etot = -13.2825375252037
+511000  ekin = 2.43159454918128 |  erot = 2.78459744696608 | epot = -18.4987295217946 | etot = -13.2825375256472
+512000  ekin = 2.37609227916261 |  erot = 2.77073697944887 | epot = -18.4293667843926 | etot = -13.2825375257811
+513000  ekin = 2.30402039322225 |  erot = 2.74317280237148 | epot = -18.3297307211636 | etot = -13.2825375255699
+514000  ekin = 2.21884081242786 |  erot = 2.7015541486614 | epot = -18.2029324861651 | etot = -13.2825375250758
+515000  ekin = 2.12561338171218 |  erot = 2.64810551843191 | epot = -18.056256424559 | etot = -13.2825375244149
+516000  ekin = 2.03029958566718 |  erot = 2.58673985991495 | epot = -17.8995769692823 | etot = -13.2825375237002
+517000  ekin = 1.93914577197132 |  erot = 2.5220605431355 | epot = -17.7437438381168 | etot = -13.28253752301
+518000  ekin = 1.85826662413893 |  erot = 2.45858700715527 | epot = -17.5993911536849 | etot = -13.2825375223908
+519000  ekin = 1.79333215326611 |  erot = 2.40035341708905 | epot = -17.476223092216 | etot = -13.2825375218608
+520000  ekin = 1.74929005171215 |  erot = 2.35078235677519 | epot = -17.3826099299227 | etot = -13.2825375214353
+521000  ekin = 1.73007209347361 |  erot = 2.31266171841647 | epot = -17.3252713330271 | etot = -13.282537521137
+522000  ekin = 1.73822781685003 |  erot = 2.28811557190088 | epot = -17.3088809097447 | etot = -13.2825375209937
+523000  ekin = 1.77456624775216 |  erot = 2.27850834583591 | epot = -17.3356121146208 | etot = -13.2825375210327
+524000  ekin = 1.8379045851724 |  erot = 2.28429322274985 | epot = -17.4047353291923 | etot = -13.28253752127
+525000  ekin = 1.92500868751529 |  erot = 2.30484700359158 | epot = -17.5123932128129 | etot = -13.282537521706
+526000  ekin = 2.03075780261764 |  erot = 2.33833465322237 | epot = -17.6516299781653 | etot = -13.2825375223253
+527000  ekin = 2.14850843909257 |  erot = 2.38164040104111 | epot = -17.8126863632292 | etot = -13.2825375230955
+528000  ekin = 2.2706009665318 |  erot = 2.43041424714547 | epot = -17.9835527376429 | etot = -13.2825375239656
+529000  ekin = 2.38896012867467 |  erot = 2.47931387509597 | epot = -18.150811528629 | etot = -13.2825375248584
+530000  ekin = 2.4957694053979 |  erot = 2.52254117019752 | epot = -18.3008481012612 | etot = -13.2825375256658
+531000  ekin = 2.58420744224834 |  erot = 2.55472238423688 | epot = -18.4214673527446 | etot = -13.2825375262593
+532000  ekin = 2.64918587021021 |  erot = 2.57201883159204 | epot = -18.5037422283274 | etot = -13.2825375265252
+533000  ekin = 2.68793333158334 |  erot = 2.57313230806675 | epot = -18.5436031660632 | etot = -13.2825375264131
+534000  ekin = 2.7002120821811 |  erot = 2.55975253143246 | epot = -18.5425021395846 | etot = -13.2825375259711
+535000  ekin = 2.68802701636055 |  erot = 2.5361501485681 | epot = -18.5067146902622 | etot = -13.2825375253335
+536000  ekin = 2.65489019113613 |  erot = 2.50801671119336 | epot = -18.4454444269979 | etot = -13.2825375246684
+537000  ekin = 2.60490332064252 |  erot = 2.481023337825 | epot = -18.3684641825809 | etot = -13.2825375241133
+538000  ekin = 2.54198784535114 |  erot = 2.45965628954573 | epot = -18.2841816578421 | etot = -13.2825375229452
+539000  ekin = 2.47150013363699 |  erot = 2.44756195577151 | epot = -18.2015996123808 | etot = -13.2825375229723
+540000  ekin = 2.39647534123056 |  erot = 2.44525435897827 | epot = -18.124267223265 | etot = -13.2825375230561
+541000  ekin = 2.31786635163547 |  erot = 2.45130088246703 | epot = -18.0517047572224 | etot = -13.2825375231199
+542000  ekin = 2.23702678127242 |  erot = 2.46423888155736 | epot = -17.9838031859226 | etot = -13.2825375230928
+543000  ekin = 2.15612181944835 |  erot = 2.4831366740889 | epot = -17.9217960164714 | etot = -13.2825375229342
+544000  ekin = 2.07836492813028 |  erot = 2.50789688702757 | epot = -17.8687993378082 | etot = -13.2825375226504
+545000  ekin = 2.0079425836599 |  erot = 2.5391884088184 | epot = -17.8296685147796 | etot = -13.2825375223013
+546000  ekin = 1.94957099406152 |  erot = 2.57800819606447 | epot = -17.8101167121046 | etot = -13.2825375219786
+547000  ekin = 1.90776242425117 |  erot = 2.62501532095444 | epot = -17.8153152669927 | etot = -13.2825375217871
+548000  ekin = 1.88600984704774 |  erot = 2.67988146407457 | epot = -17.8484288329186 | etot = -13.2825375217963
+549000  ekin = 1.88615242684612 |  erot = 2.7409037562111 | epot = -17.90959370508 | etot = -13.2825375220228
+550000  ekin = 1.90811801075785 |  erot = 2.80501593008068 | epot = -17.9956714632668 | etot = -13.2825375224283
+551000  ekin = 1.95008337619707 |  erot = 2.8681680442257 | epot = -18.1007889433631 | etot = -13.2825375229403
+552000  ekin = 2.00893649348012 |  erot = 2.92590890431006 | epot = -18.2173829212704 | etot = -13.2825375234803
+553000  ekin = 2.08084803908336 |  erot = 2.97396311014114 | epot = -18.3373486732109 | etot = -13.2825375239864
+554000  ekin = 2.16178844740114 |  erot = 3.00865361320263 | epot = -18.452979585024 | etot = -13.2825375244202
+555000  ekin = 2.24792031028555 |  erot = 3.02713377655537 | epot = -18.5575916115995 | etot = -13.2825375247586
+556000  ekin = 2.3358895304513 |  erot = 3.02749801452678 | epot = -18.6459250699588 | etot = -13.2825375249808
+557000  ekin = 2.42273135016537 |  erot = 3.0079937814166 | epot = -18.7132626569264 | etot = -13.2825375253445
+558000  ekin = 2.50467530617043 |  erot = 2.96457109815147 | epot = -18.7517839296998 | etot = -13.2825375253779
+559000  ekin = 2.57989829545908 |  erot = 2.89795083555213 | epot = -18.7603866561733 | etot = -13.2825375251621
+560000  ekin = 2.64819333039288 |  erot = 2.81150114191978 | epot = -18.742231997059 | etot = -13.2825375247463
+561000  ekin = 2.7104101471449 |  erot = 2.71050571098959 | epot = -18.7034533823758 | etot = -13.2825375242413
+562000  ekin = 2.76764108182985 |  erot = 2.60142670489701 | epot = -18.6516053104994 | etot = -13.2825375237726
+563000  ekin = 2.8204133217691 |  erot = 2.4909454000306 | epot = -18.5938962452166 | etot = -13.2825375234169
+564000  ekin = 2.86835957175242 |  erot = 2.38512022714126 | epot = -18.536017322071 | etot = -13.2825375231773
+565000  ekin = 2.91050556249757 |  erot = 2.28886993106156 | epot = -18.481913016576 | etot = -13.2825375230169
+566000  ekin = 2.94583619535282 |  erot = 2.20572382115438 | epot = -18.4340975394231 | etot = -13.2825375229159
+567000  ekin = 2.97364576055568 |  erot = 2.13764971286302 | epot = -18.3938329963098 | etot = -13.2825375228911
+568000  ekin = 2.99348659090309 |  erot = 2.08490808296841 | epot = -18.360932196845 | etot = -13.2825375229735
+569000  ekin = 3.00487691646457 |  erot = 2.04604350397463 | epot = -18.3334579436043 | etot = -13.2825375231651
+570000  ekin = 3.00710556181106 |  erot = 2.01819764944608 | epot = -18.3078407346813 | etot = -13.2825375234241
+571000  ekin = 2.99930468666728 |  erot = 1.99774357921139 | epot = -18.2795857895585 | etot = -13.2825375236798
+572000  ekin = 2.98076231237764 |  erot = 1.98107714037278 | epot = -18.2443769766043 | etot = -13.2825375238539
+573000  ekin = 2.95134611354571 |  erot = 1.96535938859269 | epot = -18.1992430260208 | etot = -13.2825375238824
+574000  ekin = 2.91190615156914 |  erot = 1.94906161393782 | epot = -18.1435052892334 | etot = -13.2825375237264
+575000  ekin = 2.86455063783071 |  erot = 1.93223482559859 | epot = -18.079322986811 | etot = -13.2825375233817
+576000  ekin = 2.81270724054619 |  erot = 1.91646454104923 | epot = -18.0117093044799 | etot = -13.2825375228844
+577000  ekin = 2.76090536128439 |  erot = 1.9045038205141 | epot = -17.9479467041077 | etot = -13.2825375223092
+578000  ekin = 2.71428886858076 |  erot = 1.89991544416371 | epot = -17.8967418344083 | etot = -13.2825375216638
+579000  ekin = 2.67747364109253 |  erot = 1.90598531718256 | epot = -17.8659964795852 | etot = -13.2825375213101
+580000  ekin = 2.65399321096934 |  erot = 1.92422800253644 | epot = -17.8607587346238 | etot = -13.282537521118
+581000  ekin = 2.64614770784911 |  erot = 1.95489680824256 | epot = -17.883582037231 | etot = -13.2825375211393
+582000  ekin = 2.65445309232027 |  erot = 1.99685469220196 | epot = -17.9338453059165 | etot = -13.2825375213943
+583000  ekin = 2.67733631605306 |  erot = 2.04763712313085 | epot = -18.0075109610395 | etot = -13.2825375218556
+584000  ekin = 2.71054840601244 |  erot = 2.10372916960457 | epot = -18.0968150982853 | etot = -13.2825375226683
+585000  ekin = 2.74737763681928 |  erot = 2.16073411835811 | epot = -18.1906492785603 | etot = -13.282537523383
+586000  ekin = 2.7813786998355 |  erot = 2.21419390100359 | epot = -18.2781101248089 | etot = -13.2825375239698
+587000  ekin = 2.80697388603962 |  erot = 2.26053952382245 | epot = -18.3500509341984 | etot = -13.2825375243363
+588000  ekin = 2.82026432869703 |  erot = 2.29760845660022 | epot = -18.4004103097634 | etot = -13.2825375244661
+589000  ekin = 2.81926713936076 |  erot = 2.32471340247167 | epot = -18.4265180662398 | etot = -13.2825375244073
+590000  ekin = 2.80363912211435 |  erot = 2.34232144628174 | epot = -18.4284980926317 | etot = -13.2825375242356
+591000  ekin = 2.77414618244973 |  erot = 2.35158565792353 | epot = -18.4082693643883 | etot = -13.282537524015
+592000  ekin = 2.73214162068033 |  erot = 2.35397672704535 | epot = -18.3686558715069 | etot = -13.2825375237812
+593000  ekin = 2.67919893301821 |  erot = 2.35111989741865 | epot = -18.3128563539823 | etot = -13.2825375235455
+594000  ekin = 2.61691997575019 |  erot = 2.34478637079319 | epot = -18.2442438698508 | etot = -13.2825375233074
+595000  ekin = 2.54687226698967 |  erot = 2.33692048100541 | epot = -18.1663302710608 | etot = -13.2825375230657
+596000  ekin = 2.47060065847364 |  erot = 2.32961421031687 | epot = -18.0827523916134 | etot = -13.2825375228228
+597000  ekin = 2.38967001316585 |  erot = 2.32500896595718 | epot = -17.9972165017067 | etot = -13.2825375225837
+598000  ekin = 2.30571268082223 |  erot = 2.32515834060408 | epot = -17.9134085437803 | etot = -13.282537522354
+599000  ekin = 2.22046028550116 |  erot = 2.33189649118178 | epot = -17.8348942988225 | etot = -13.2825375221395
+600000  ekin = 2.13574370490705 |  erot = 2.34673734057022 | epot = -17.7650185674242 | etot = -13.2825375219469
+601000  ekin = 2.05345123937653 |  erot = 2.37080533030337 | epot = -17.7067940914646 | etot = -13.2825375217847
+602000  ekin = 1.97544542053429 |  erot = 2.40478648031343 | epot = -17.6627694225103 | etot = -13.2825375216626
+603000  ekin = 1.9034510520118 |  erot = 2.44889273156788 | epot = -17.6348813051703 | etot = -13.2825375215906
+604000  ekin = 1.83893895945378 |  erot = 2.50284547570514 | epot = -17.6243219567308 | etot = -13.2825375215719
+605000  ekin = 1.78304137655287 |  erot = 2.56590806869957 | epot = -17.6314869668566 | etot = -13.2825375216041
+606000  ekin = 1.736517005622 |  erot = 2.63697396084372 | epot = -17.6560284881414 | etot = -13.2825375216757
+607000  ekin = 1.69978182226254 |  erot = 2.71471645486191 | epot = -17.6970357988931 | etot = -13.2825375217686
+608000  ekin = 1.67299629743623 |  erot = 2.79777529958915 | epot = -17.7533091188892 | etot = -13.2825375218638
+609000  ekin = 1.65617951190665 |  erot = 2.88492902630375 | epot = -17.8236460601579 | etot = -13.2825375219475
+610000  ekin = 1.64931072740771 |  erot = 2.97519912008037 | epot = -17.9070473695038 | etot = -13.2825375220157
+611000  ekin = 1.65238727025306 |  erot = 3.06785620899647 | epot = -18.0027810013235 | etot = -13.2825375220739
+612000  ekin = 1.66542824834998 |  erot = 3.16233835695483 | epot = -18.1103041274379 | etot = -13.2825375221331
+613000  ekin = 1.68843555860806 |  erot = 3.25812385028217 | epot = -18.229096931095 | etot = -13.2825375222048
+614000  ekin = 1.72133601882631 |  erot = 3.35460405562833 | epot = -18.3584775967531 | etot = -13.2825375222984
+615000  ekin = 1.76392386055006 |  erot = 3.45098117167973 | epot = -18.4974425546512 | etot = -13.2825375224214
+616000  ekin = 1.81580855352879 |  erot = 3.54618284211553 | epot = -18.6445289182269 | etot = -13.2825375225826
+617000  ekin = 1.87635766444892 |  erot = 3.63876572292309 | epot = -18.7976609101672 | etot = -13.2825375227952
+618000  ekin = 1.94461656663335 |  erot = 3.72678561706335 | epot = -18.9539397067739 | etot = -13.2825375230772
+619000  ekin = 2.01919440946448 |  erot = 3.80764383017264 | epot = -19.1093757630845 | etot = -13.2825375234473
+620000  ekin = 2.09812821732459 |  erot = 3.87796751089518 | epot = -19.258633252134 | etot = -13.2825375239142
+621000  ekin = 2.17876896452369 |  erot = 3.9336243470245 | epot = -19.3949308360123 | etot = -13.2825375244641
+622000  ekin = 2.25776112944306 |  erot = 3.96997899371136 | epot = -19.5102776482054 | etot = -13.282537525051
+623000  ekin = 2.33118920319666 |  erot = 3.98244070312544 | epot = -19.5961674319216 | etot = -13.2825375255995
+624000  ekin = 2.39492361710553 |  erot = 3.96722578269959 | epot = -19.6446869258275 | etot = -13.2825375260223
+625000  ekin = 2.445122210933 |  erot = 3.92212025382369 | epot = -19.6497799910047 | etot = -13.282537526248
+626000  ekin = 2.47876984838125 |  erot = 3.84697362716387 | epot = -19.6082810017884 | etot = -13.2825375262432
+627000  ekin = 2.49411681790099 |  erot = 3.74375083248538 | epot = -19.5204051764041 | etot = -13.2825375260178
+628000  ekin = 2.49092177716844 |  erot = 3.61617309043397 | epot = -19.3896323932121 | etot = -13.2825375256096
+629000  ekin = 2.47048208783205 |  erot = 3.46915451631132 | epot = -19.2221741292085 | etot = -13.2825375250651
+630000  ekin = 2.43548970061162 |  erot = 3.30827690351569 | epot = -19.0263041285523 | etot = -13.282537524425
+631000  ekin = 2.38975948996613 |  erot = 3.13944249320995 | epot = -18.8117395069008 | etot = -13.2825375237248
+632000  ekin = 2.33785618698542 |  erot = 2.96869689909723 | epot = -18.5890906090837 | etot = -13.2825375230011
+633000  ekin = 2.28462964544115 |  erot = 2.80211551086663 | epot = -18.3692826786082 | etot = -13.2825375223005
+634000  ekin = 2.23467746223165 |  erot = 2.64563252187923 | epot = -18.1628475057907 | etot = -13.2825375216799
+635000  ekin = 2.15322765543132 |  erot = 2.47835094336846 | epot = -17.9141161495184 | etot = -13.2825375507186
+636000  ekin = 2.04549908133069 |  erot = 2.31412508405115 | epot = -17.6421616868109 | etot = -13.2825375214291
+637000  ekin = 2.11104805175097 |  erot = 2.29419960731515 | epot = -17.6877852052413 | etot = -13.2825375461752
+638000  ekin = 2.16990019917156 |  erot = 2.2679567393031 | epot = -17.7203944764658 | etot = -13.2825375379911
+639000  ekin = 2.15825321743296 |  erot = 2.17815663923705 | epot = -17.618947382456 | etot = -13.282537525786
+640000  ekin = 2.18911467644369 |  erot = 2.15600946831685 | epot = -17.627661668769 | etot = -13.2825375240084
+641000  ekin = 2.26653815123457 |  erot = 2.22106973674797 | epot = -17.7701454241734 | etot = -13.2825375361909
+642000  ekin = 2.3144469471055 |  erot = 2.28426426145084 | epot = -17.8812487361676 | etot = -13.2825375276113
+643000  ekin = 2.32966846054207 |  erot = 2.32625113868682 | epot = -17.9384571273534 | etot = -13.2825375281245
+644000  ekin = 2.33971908606118 |  erot = 2.36941556717976 | epot = -17.9916721817351 | etot = -13.2825375284942
+645000  ekin = 2.34497836839587 |  erot = 2.40804261253567 | epot = -18.0355585095904 | etot = -13.2825375286589
+646000  ekin = 2.34716147917123 |  erot = 2.43809135045114 | epot = -18.0677903582286 | etot = -13.2825375286062
+647000  ekin = 2.34901351981608 |  erot = 2.45765540472021 | epot = -18.0892064529145 | etot = -13.2825375283782
+648000  ekin = 2.35429037962735 |  erot = 2.46814608869922 | epot = -18.104973996447 | etot = -13.2825375281204
+649000  ekin = 2.36637490476275 |  erot = 2.47306901795835 | epot = -18.1219814507637 | etot = -13.2825375280426
+650000  ekin = 2.38594651024424 |  erot = 2.47280388235694 | epot = -18.1412879205825 | etot = -13.2825375279813
+651000  ekin = 2.41290732393566 |  erot = 2.46797500557286 | epot = -18.1634198574497 | etot = -13.2825375279412
+652000  ekin = 2.44657292409709 |  erot = 2.45942209570518 | epot = -18.1885325477104 | etot = -13.2825375279081
+653000  ekin = 2.48591189131261 |  erot = 2.44818643125859 | epot = -18.216635850432 | etot = -13.2825375278608
+654000  ekin = 2.52980786353021 |  erot = 2.43558904352257 | epot = -18.2479344348361 | etot = -13.2825375277833
+655000  ekin = 2.57725720746836 |  erot = 2.42329690336763 | epot = -18.2830916385098 | etot = -13.2825375276738
+656000  ekin = 2.62745567870598 |  erot = 2.41329334491405 | epot = -18.3232865511668 | etot = -13.2825375275468
+657000  ekin = 2.67977157736399 |  erot = 2.40771681185305 | epot = -18.3700259166474 | etot = -13.2825375274304
+658000  ekin = 2.73363379229086 |  erot = 2.40858022061921 | epot = -18.4247515402698 | etot = -13.2825375273597
+659000  ekin = 2.78837854459658 |  erot = 2.41741767328155 | epot = -18.4883337452466 | etot = -13.2825375273685
+660000  ekin = 2.84314536322858 |  erot = 2.43497153591091 | epot = -18.5606544265713 | etot = -13.2825375274319
+661000  ekin = 2.89550751715279 |  erot = 2.46002725149102 | epot = -18.6380722967303 | etot = -13.2825375280865
+662000  ekin = 2.93874528646413 |  erot = 2.48685588461621 | epot = -18.708138699778 | etot = -13.2825375286977
+663000  ekin = 2.9687171942415 |  erot = 2.51022783071497 | epot = -18.7614825541983 | etot = -13.2825375292419
+664000  ekin = 2.98246138427311 |  erot = 2.52516926734448 | epot = -18.7901681812018 | etot = -13.2825375295842
+665000  ekin = 2.97884445494023 |  erot = 2.52787955705445 | epot = -18.7892615416123 | etot = -13.2825375296177
+666000  ekin = 2.95920183353605 |  erot = 2.51661508434599 | epot = -18.7583544471906 | etot = -13.2825375293085
+667000  ekin = 2.92742550356365 |  erot = 2.49210329858316 | epot = -18.702066330864 | etot = -13.2825375287172
+668000  ekin = 2.88934250717656 |  erot = 2.45736670750009 | epot = -18.6292467426517 | etot = -13.282537527975
+669000  ekin = 2.85155010044156 |  erot = 2.41708074176435 | epot = -18.5511683694359 | etot = -13.28253752723
+670000  ekin = 2.82014314471955 |  erot = 2.37673699551223 | epot = -18.4794176668284 | etot = -13.2825375265966
+671000  ekin = 2.79977472961205 |  erot = 2.34183940273354 | epot = -18.4241516586146 | etot = -13.282537526269
+672000  ekin = 2.79293252634008 |  erot = 2.31695226011576 | epot = -18.3924223124527 | etot = -13.2825375259969
+673000  ekin = 2.80034442408037 |  erot = 2.30554472206325 | epot = -18.3884266720798 | etot = -13.2825375259361
+674000  ekin = 2.82129825256449 |  erot = 2.30955451981648 | epot = -18.4133902984753 | etot = -13.2825375260944
+675000  ekin = 2.85361934145821 |  erot = 2.32878748968739 | epot = -18.4649443576069 | etot = -13.2825375264613
+676000  ekin = 2.89394924995267 |  erot = 2.36084337707399 | epot = -18.5373301540152 | etot = -13.2825375269885
+677000  ekin = 2.93819888436731 |  erot = 2.40146056805032 | epot = -18.622196980004 | etot = -13.2825375275863
+678000  ekin = 2.98219881046511 |  erot = 2.44527797789796 | epot = -18.7100143165049 | etot = -13.2825375281419
+679000  ekin = 3.0224273551935 |  erot = 2.48684948025749 | epot = -18.7918143640021 | etot = -13.2825375285511
+680000  ekin = 3.05660821680256 |  erot = 2.52163649378434 | epot = -18.8607822393395 | etot = -13.2825375287526
+681000  ekin = 3.08399348184627 |  erot = 2.54671087858252 | epot = -18.913241889164 | etot = -13.2825375287352
+682000  ekin = 3.10527370304788 |  erot = 2.56103519408599 | epot = -18.9488464256748 | etot = -13.2825375285409
+683000  ekin = 3.12217420783238 |  erot = 2.56530128681684 | epot = -18.970013022889 | etot = -13.2825375282398
+684000  ekin = 3.13689854376774 |  erot = 2.56147023258304 | epot = -18.9809063042598 | etot = -13.282537527909
+685000  ekin = 3.1516175207619 |  erot = 2.55220833199615 | epot = -18.9863633803528 | etot = -13.2825375275947
+686000  ekin = 3.16825656288024 |  erot = 2.5404714195813 | epot = -18.9912655098718 | etot = -13.2825375274103
+687000  ekin = 3.18756268898112 |  erot = 2.52861508568613 | epot = -18.9987153019925 | etot = -13.2825375273252
+688000  ekin = 3.20935294724633 |  erot = 2.51834078646032 | epot = -19.0102312610592 | etot = -13.2825375273526
+689000  ekin = 3.232603857627 |  erot = 2.51058529363817 | epot = -19.0257266787599 | etot = -13.2825375274947
+690000  ekin = 3.25550449412986 |  erot = 2.50541094760363 | epot = -19.0434529694767 | etot = -13.2825375277432
+691000  ekin = 3.27559454461619 |  erot = 2.50196131507165 | epot = -19.0600933877637 | etot = -13.2825375280759
+692000  ekin = 3.29000453529088 |  erot = 2.49851988079962 | epot = -19.0710619445408 | etot = -13.2825375284503
+693000  ekin = 3.29579865376218 |  erot = 2.49273974858803 | epot = -19.0710759311567 | etot = -13.2825375288065
+694000  ekin = 3.29036742009323 |  erot = 2.48207188557003 | epot = -19.0549768347445 | etot = -13.2825375290813
+695000  ekin = 3.27176421105106 |  erot = 2.46431581831664 | epot = -19.018617558596 | etot = -13.2825375292283
+696000  ekin = 3.23887890273548 |  erot = 2.43812365834886 | epot = -18.9595400903186 | etot = -13.2825375292342
+697000  ekin = 3.19141377377666 |  erot = 2.40329594550704 | epot = -18.8772472483983 | etot = -13.2825375291146
+698000  ekin = 3.12971664175668 |  erot = 2.36079934043281 | epot = -18.7730535110947 | etot = -13.2825375289052
+699000  ekin = 3.05458980626054 |  erot = 2.31258576039904 | epot = -18.6497130952911 | etot = -13.2825375286315
+700000  ekin = 2.96718102298747 |  erot = 2.26139197208619 | epot = -18.511110523382 | etot = -13.2825375283083
+701000  ekin = 2.86896613295136 |  erot = 2.21057215459575 | epot = -18.3620758154883 | etot = -13.2825375279412
+702000  ekin = 2.76178671337415 |  erot = 2.16397434352371 | epot = -18.2082985844344 | etot = -13.2825375275365
+703000  ekin = 2.6478712031048 |  erot = 2.12574771744291 | epot = -18.0561564515416 | etot = -13.2825375309939
+704000  ekin = 2.52933762848166 |  erot = 2.08674637122766 | epot = -17.8986215283831 | etot = -13.2825375286737
+705000  ekin = 2.41679696536635 |  erot = 2.05664012325241 | epot = -17.7559746148874 | etot = -13.2825375262686
+706000  ekin = 2.30501007356423 |  erot = 2.0611587655127 | epot = -17.6487063635301 | etot = -13.2825375244532
+707000  ekin = 2.19269241365679 |  erot = 2.113750463821 | epot = -17.5889804021149 | etot = -13.2825375246371
+708000  ekin = 2.09960598348176 |  erot = 2.19681319891601 | epot = -17.57895670939 | etot = -13.2825375269922
+709000  ekin = 2.01320280623464 |  erot = 2.28016876647 | epot = -17.5759090980898 | etot = -13.2825375253852
+710000  ekin = 1.93302644427356 |  erot = 2.37473228784994 | epot = -17.5902962580752 | etot = -13.2825375259517
+711000  ekin = 1.85957279067715 |  erot = 2.47358324929754 | epot = -17.6156935666084 | etot = -13.2825375266337
+712000  ekin = 1.79282630268912 |  erot = 2.56690430142539 | epot = -17.642268131402 | etot = -13.2825375272875
+713000  ekin = 1.73341814876089 |  erot = 2.64462400340569 | epot = -17.6605796799123 | etot = -13.2825375277457
+714000  ekin = 1.68328438252143 |  erot = 2.69817364688335 | epot = -17.6639955572831 | etot = -13.2825375278783
+715000  ekin = 1.64594117648568 |  erot = 2.72207244107394 | epot = -17.6505511452113 | etot = -13.2825375276517
+716000  ekin = 1.62610172701181 |  erot = 2.71479815151566 | epot = -17.6234374056764 | etot = -13.282537527149
+717000  ekin = 1.62864489627545 |  erot = 2.67867233618631 | epot = -17.589854758993 | etot = -13.2825375265313
+718000  ekin = 1.65730138310094 |  erot = 2.6189183926284 | epot = -17.5587573016927 | etot = -13.2825375259634
+719000  ekin = 1.71360335058015 |  erot = 2.54235654223589 | epot = -17.5384974183669 | etot = -13.2825375255509
+720000  ekin = 1.79650653909672 |  erot = 2.45621436685583 | epot = -17.5352584312718 | etot = -13.2825375253192
+721000  ekin = 1.90273489852489 |  erot = 2.36731439641998 | epot = -17.5525868201814 | etot = -13.2825375252366
+722000  ekin = 2.02756635877135 |  erot = 2.28163864595547 | epot = -17.5917425299821 | etot = -13.2825375252553
+723000  ekin = 2.16566245424335 |  erot = 2.20411346294851 | epot = -17.6523134425365 | etot = -13.2825375253446
+724000  ekin = 2.31164907977026 |  erot = 2.13844446404667 | epot = -17.7326310693194 | etot = -13.2825375255025
+725000  ekin = 2.46036017286876 |  erot = 2.0869120441014 | epot = -17.8298097427178 | etot = -13.2825375257477
+726000  ekin = 2.60683496355671 |  erot = 2.05013619406281 | epot = -17.9395086837224 | etot = -13.2825375261029
+727000  ekin = 2.74622028398704 |  erot = 2.02690424050256 | epot = -18.0556620510616 | etot = -13.282537526572
+728000  ekin = 2.87374866259628 |  erot = 2.01419303066656 | epot = -18.1704792203877 | etot = -13.2825375271249
+729000  ekin = 2.98490085178579 |  erot = 2.00751009694371 | epot = -18.27494847642 | etot = -13.2825375276905
+730000  ekin = 3.07576690667731 |  erot = 2.00160558070566 | epot = -18.359910015553 | etot = -13.28253752817
+731000  ekin = 3.14351022574244 |  erot = 1.99146923020489 | epot = -18.4175169844133 | etot = -13.282537528466
+732000  ekin = 3.18676307284264 |  erot = 1.97337750697634 | epot = -18.4426781083327 | etot = -13.2825375285137
+733000  ekin = 3.20579220152253 |  erot = 1.9456870659553 | epot = -18.4340167957808 | etot = -13.282537528303
+734000  ekin = 3.20238921812918 |  erot = 1.90917251422492 | epot = -18.3940992602234 | etot = -13.2825375278693
+735000  ekin = 3.17951096479738 |  erot = 1.86680153237891 | epot = -18.3288500244819 | etot = -13.2825375273056
+736000  ekin = 3.14073865389039 |  erot = 1.8230058759971 | epot = -18.2462820565793 | etot = -13.2825375266918
+737000  ekin = 3.08984658437012 |  erot = 1.78292393032115 | epot = -18.1553080407961 | etot = -13.2825375261048
+738000  ekin = 3.03043228101277 |  erot = 1.75161934959083 | epot = -18.0645891562027 | etot = -13.2825375255991
+739000  ekin = 2.96566842757407 |  erot = 1.73346651117868 | epot = -17.9816724639599 | etot = -13.2825375252071
+740000  ekin = 2.89817088986259 |  erot = 1.73175552877345 | epot = -17.912463943576 | etot = -13.28253752494
+741000  ekin = 2.82995232211993 |  erot = 1.74850528634245 | epot = -17.8609951332633 | etot = -13.282537524801
+742000  ekin = 2.76247533972923 |  erot = 1.78434362386512 | epot = -17.8293564883915 | etot = -13.2825375247972
+743000  ekin = 2.69668176519633 |  erot = 1.83847103681881 | epot = -17.8176903269097 | etot = -13.2825375248946
+744000  ekin = 2.6331144461464 |  erot = 1.90875045568272 | epot = -17.8244024269328 | etot = -13.2825375251037
+745000  ekin = 2.5719649351672 |  erot = 1.99171779991018 | epot = -17.8462202604955 | etot = -13.2825375254181
+746000  ekin = 2.51311596152491 |  erot = 2.0826421561814 | epot = -17.8782956435303 | etot = -13.282537525824
+747000  ekin = 2.45621024026481 |  erot = 2.17571767245968 | epot = -17.9144654390156 | etot = -13.2825375262911
+748000  ekin = 2.4007641204603 |  erot = 2.26445242853415 | epot = -17.9477540757611 | etot = -13.2825375267666
+749000  ekin = 2.34635697390621 |  erot = 2.34231237598165 | epot = -17.9712068770626 | etot = -13.2825375271748
+750000  ekin = 2.29290375451926 |  erot = 2.40359513867759 | epot = -17.9790364206262 | etot = -13.2825375274293
+751000  ekin = 2.24097207239074 |  erot = 2.44437862835496 | epot = -17.9678882282051 | etot = -13.2825375274594
+752000  ekin = 2.19206377659927 |  erot = 2.46328788147024 | epot = -17.9378891852944 | etot = -13.2825375272249
+753000  ekin = 2.01910736680425 |  erot = 2.37844688257153 | epot = -17.6800917192355 | etot = -13.2825374698597
+754000  ekin = 2.03397419758721 |  erot = 2.38379927539831 | epot = -17.7003109699574 | etot = -13.2825374969719
+755000  ekin = 2.10287082583243 |  erot = 2.42269050537392 | epot = -17.808098775342 | etot = -13.2825374441357
+756000  ekin = 2.09556625459035 |  erot = 2.40575096267731 | epot = -17.7838546607744 | etot = -13.2825374435067
+757000  ekin = 2.11013463605079 |  erot = 2.39174642208689 | epot = -17.7844185011481 | etot = -13.2825374430104
+758000  ekin = 2.14991880608121 |  erot = 2.38537981475823 | epot = -17.8178360635602 | etot = -13.2825374427207
+759000  ekin = 2.21691275096553 |  erot = 2.38948785856312 | epot = -17.8889380522097 | etot = -13.2825374426811
+760000  ekin = 2.31141054899228 |  erot = 2.40468264922822 | epot = -17.9986306411391 | etot = -13.2825374429186
+761000  ekin = 2.43175472397619 |  erot = 2.42917556867249 | epot = -18.1434677360907 | etot = -13.282537443442
+762000  ekin = 2.57423243283704 |  erot = 2.45878794779634 | epot = -18.3155578248644 | etot = -13.2825374442311
+763000  ekin = 2.73317609373997 |  erot = 2.48721280702134 | epot = -18.5029263459876 | etot = -13.2825374452263
+764000  ekin = 2.90131643326679 |  erot = 2.50663479900723 | epot = -18.690488678594 | etot = -13.28253744632
+765000  ekin = 3.07040159566699 |  erot = 2.50879317366612 | epot = -18.8617322166939 | etot = -13.2825374473608
+766000  ekin = 3.23203071048149 |  erot = 2.48644536532744 | epot = -19.0010135239876 | etot = -13.2825374481786
+767000  ekin = 3.37856609507255 |  erot = 2.43498273995184 | epot = -19.0960862836549 | etot = -13.2825374486305
+768000  ekin = 3.50392633330507 |  erot = 2.35374465383522 | epot = -19.1402084357865 | etot = -13.2825374486462
+769000  ekin = 3.60408080015212 |  erot = 2.24656658386371 | epot = -19.1331848322651 | etot = -13.2825374482493
+770000  ekin = 3.67731902122504 |  erot = 2.12129309978206 | epot = -19.0811495685446 | etot = -13.2825374475374
+771000  ekin = 3.72500466537174 |  erot = 1.98803922980452 | epot = -18.9955813418785 | etot = -13.2825374467023
+772000  ekin = 3.73784328897891 |  erot = 1.84847100615872 | epot = -18.8688517432933 | etot = -13.2825374481557
+773000  ekin = 3.73518377850858 |  erot = 1.74399251375944 | epot = -18.761713737683 | etot = -13.2825374454149
+774000  ekin = 3.73326270400355 |  erot = 1.69319142559955 | epot = -18.7089915837464 | etot = -13.2825374541433
+775000  ekin = 3.70600761043796 |  erot = 1.6566239979388 | epot = -18.6451690563952 | etot = -13.2825374480184
+776000  ekin = 3.66620956029523 |  erot = 1.65229490555453 | epot = -18.6010419136787 | etot = -13.282537447829
+777000  ekin = 3.61649590749819 |  erot = 1.68124406448108 | epot = -18.5802774198126 | etot = -13.2825374478333
+778000  ekin = 3.55892172037955 |  erot = 1.74156460696009 | epot = -18.5830237753754 | etot = -13.2825374480357
+779000  ekin = 3.49505249872284 |  erot = 1.82861083535278 | epot = -18.6062007829277 | etot = -13.2825374488521
+780000  ekin = 3.42606052970244 |  erot = 1.93200454593087 | epot = -18.6406025252668 | etot = -13.2825374496335
+781000  ekin = 3.35141348725842 |  erot = 2.04005284573706 | epot = -18.6740037834645 | etot = -13.2825374504691
+782000  ekin = 3.2700234367696 |  erot = 2.14152553729048 | epot = -18.6940864252466 | etot = -13.2825374511865
+783000  ekin = 3.18141085684875 |  erot = 2.22636120811957 | epot = -18.690309516577 | etot = -13.2825374516087
+784000  ekin = 3.08656488529642 |  erot = 2.28735807349748 | epot = -18.6564604104105 | etot = -13.2825374516166
+785000  ekin = 2.98843914069599 |  erot = 2.32136711573499 | epot = -18.592343707635 | etot = -13.282537451204
+786000  ekin = 2.89178850824096 |  erot = 2.3295414984193 | epot = -18.5038674571453 | etot = -13.2825374504851
+787000  ekin = 2.8023307080712 |  erot = 2.31656731751225 | epot = -18.4014354752266 | etot = -13.2825374496432
+788000  ekin = 2.72556137551752 |  erot = 2.28924565772307 | epot = -18.2973444820957 | etot = -13.2825374488551
+789000  ekin = 2.6656985022175 |  erot = 2.25498711354848 | epot = -18.2032230640058 | etot = -13.2825374482399
+790000  ekin = 2.62507547599935 |  erot = 2.22062577794683 | epot = -18.1282387017979 | etot = -13.2825374478518
+791000  ekin = 2.60400664952963 |  erot = 2.19166523694291 | epot = -18.0782093341748 | etot = -13.2825374477022
+792000  ekin = 2.60095165935059 |  erot = 2.17186849882108 | epot = -18.0553576059557 | etot = -13.282537447784
+793000  ekin = 2.61278727243034 |  erot = 2.1630579474879 | epot = -18.0583826680031 | etot = -13.2825374480849
+794000  ekin = 2.63509078851047 |  erot = 2.16503786006958 | epot = -18.0826660971656 | etot = -13.2825374485855
+795000  ekin = 2.66245645585368 |  erot = 2.1756290014367 | epot = -18.1206229065374 | etot = -13.282537449247
+796000  ekin = 2.68895951870523 |  erot = 2.19088748025581 | epot = -18.1623844489478 | etot = -13.2825374499868
+797000  ekin = 2.70892452688332 |  erot = 2.2056406086122 | epot = -18.197102586158 | etot = -13.2825374506625
+798000  ekin = 2.71873874100197 |  erot = 2.21455364270924 | epot = -18.2158298332998 | etot = -13.2825374495886
+799000  ekin = 2.70000299973817 |  erot = 2.2105054534633 | epot = -18.1930459030985 | etot = -13.282537449897
+800000  ekin = 2.65392049094459 |  erot = 2.17300546859124 | epot = -18.1094633784201 | etot = -13.2825374188843
+801000  ekin = 2.82505345316557 |  erot = 2.13616134654269 | epot = -18.2437522542245 | etot = -13.2825374545162
+802000  ekin = 2.90470228885208 |  erot = 2.10953657420558 | epot = -18.2967762804394 | etot = -13.2825374173817
+803000  ekin = 2.96775259915972 |  erot = 2.08137573430732 | epot = -18.3316657516683 | etot = -13.2825374182013
+804000  ekin = 3.01419864043949 |  erot = 2.05336319944923 | epot = -18.3500992582319 | etot = -13.2825374183431
+805000  ekin = 3.03950260644552 |  erot = 2.02738087501351 | epot = -18.3494208998051 | etot = -13.2825374183461
+806000  ekin = 3.04147612131243 |  erot = 2.00524180159513 | epot = -18.3292553411016 | etot = -13.2825374181941
+807000  ekin = 3.02009152298814 |  erot = 1.98876426014739 | epot = -18.2913932010452 | etot = -13.2825374179097
+808000  ekin = 2.97716861753119 |  erot = 1.97979280799342 | epot = -18.2394988430722 | etot = -13.2825374175476
+809000  ekin = 2.91576405138726 |  erot = 1.98007542312432 | epot = -18.1783768916846 | etot = -13.282537417173
+810000  ekin = 2.83951999042134 |  erot = 1.99102014259852 | epot = -18.1130775498589 | etot = -13.282537416839
+811000  ekin = 2.75216924199515 |  erot = 2.01344070753323 | epot = -18.0481473661025 | etot = -13.2825374165741
+812000  ekin = 2.65727213726343 |  erot = 2.04739495988655 | epot = -17.987204513533 | etot = -13.282537416383
+813000  ekin = 2.55815479837528 |  erot = 2.09215794771562 | epot = -17.9328501623443 | etot = -13.2825374162534
+814000  ekin = 2.4579662372483 |  erot = 2.14630993623329 | epot = -17.8868135896497 | etot = -13.2825374161681
+815000  ekin = 2.35976627216073 |  erot = 2.20788718914275 | epot = -17.8501908774147 | etot = -13.2825374161112
+816000  ekin = 2.26657574981526 |  erot = 2.27454135627298 | epot = -17.8236545221636 | etot = -13.2825374160753
+817000  ekin = 2.18134946483051 |  erot = 2.3436713345316 | epot = -17.8075582154243 | etot = -13.2825374160622
+818000  ekin = 2.10686415434699 |  erot = 2.41251844145424 | epot = -17.8019200118806 | etot = -13.2825374160794
+819000  ekin = 2.04554497125477 |  erot = 2.47824070198672 | epot = -17.8063230893767 | etot = -13.2825374161352
+820000  ekin = 1.99927680186843 |  erot = 2.53799486411919 | epot = -17.8198090822204 | etot = -13.2825374162328
+821000  ekin = 1.96925307966866 |  erot = 2.58905270243613 | epot = -17.840843198472 | etot = -13.2825374163673
+822000  ekin = 1.95590272109404 |  erot = 2.62895986973405 | epot = -17.8674000073523 | etot = -13.2825374165242
+823000  ekin = 1.95890926741904 |  erot = 2.65572860619527 | epot = -17.8971752902976 | etot = -13.2825374166833
+824000  ekin = 1.977310461331 |  erot = 2.66804286174235 | epot = -17.9278907398948 | etot = -13.2825374168215
+825000  ekin = 2.00964945329754 |  erot = 2.66544750505568 | epot = -17.9576343752703 | etot = -13.2825374169171
+826000  ekin = 2.0541442314356 |  erot = 2.64849047615147 | epot = -17.9851721245422 | etot = -13.2825374169552
+827000  ekin = 2.10884212221679 |  erot = 2.61877894563757 | epot = -18.0101584847866 | etot = -13.2825374169322
+828000  ekin = 2.17172935733676 |  erot = 2.57890618406652 | epot = -18.0331729582634 | etot = -13.2825374168601
+829000  ekin = 2.24077304904372 |  erot = 2.5322165119978 | epot = -18.0555269778081 | etot = -13.2825374167666
+830000  ekin = 2.31389012815757 |  erot = 2.48241157684725 | epot = -18.0788391216955 | etot = -13.2825374166907
+831000  ekin = 2.38886546625953 |  erot = 2.43305573632076 | epot = -18.104458619251 | etot = -13.2825374166707
+832000  ekin = 2.46326915871406 |  erot = 2.38708705021977 | epot = -18.1328936256668 | etot = -13.282537416733
+833000  ekin = 2.53443656409172 |  erot = 2.34645691970375 | epot = -18.1634309006758 | etot = -13.2825374168804
+834000  ekin = 2.59956439097001 |  erot = 2.31199374937919 | epot = -18.1940955574388 | etot = -13.2825374170896
+835000  ekin = 2.65594316002407 |  erot = 2.28352232981187 | epot = -18.2220029071513 | etot = -13.2825374173153
+836000  ekin = 2.70130042716651 |  erot = 2.26019210855364 | epot = -18.2440299532235 | etot = -13.2825374175034
+837000  ekin = 2.73418787966583 |  erot = 2.24090837049561 | epot = -18.2576336677656 | etot = -13.2825374176041
+838000  ekin = 2.75431729315362 |  erot = 2.22474076448287 | epot = -18.2615954752233 | etot = -13.2825374175868
+839000  ekin = 2.76274241572831 |  erot = 2.21121141264461 | epot = -18.2564912458202 | etot = -13.2825374174473
+840000  ekin = 2.76179432909388 |  erot = 2.20041723497348 | epot = -18.2447489812793 | etot = -13.282537417212
+841000  ekin = 2.75470877418902 |  erot = 2.1929795872171 | epot = -18.2302257783439 | etot = -13.2825374169378
+842000  ekin = 2.74495192414829 |  erot = 2.18982916717498 | epot = -18.2173185080269 | etot = -13.2825374167036
+843000  ekin = 2.73536701720752 |  erot = 2.19185320338424 | epot = -18.2097576371796 | etot = -13.2825374165879
+844000  ekin = 2.72739699207957 |  erot = 2.19948517299773 | epot = -18.2094195817172 | etot = -13.2825374166399
+845000  ekin = 2.72069680081942 |  erot = 2.2123834314525 | epot = -18.2156176491199 | etot = -13.282537416848
+846000  ekin = 2.71335245842044 |  erot = 2.22935501274494 | epot = -18.2252448883063 | etot = -13.2825374171409
+847000  ekin = 2.70267547682563 |  erot = 2.24859000802352 | epot = -18.2338029022618 | etot = -13.2825374174127
+848000  ekin = 2.68627674917249 |  erot = 2.26812231570546 | epot = -18.2369364824441 | etot = -13.2825374175662
+849000  ekin = 2.66300406346419 |  erot = 2.28632293043157 | epot = -18.2318644114456 | etot = -13.2825374175499
+850000  ekin = 2.63341305155328 |  erot = 2.30223030137244 | epot = -18.218180770297 | etot = -13.2825374173713
+851000  ekin = 2.59966042962012 |  erot = 2.31561676234611 | epot = -18.1978146090528 | etot = -13.2825374170866
+852000  ekin = 2.5649330756416 |  erot = 2.32681511046273 | epot = -18.1742856028756 | etot = -13.2825374167712
+853000  ekin = 2.53268458711828 |  erot = 2.33642702442706 | epot = -18.1516490280431 | etot = -13.2825374164977
+854000  ekin = 2.50591352350999 |  erot = 2.34503055401556 | epot = -18.1334814938378 | etot = -13.2825374163123
+855000  ekin = 2.48667404327569 |  erot = 2.3529787337437 | epot = -18.1221901932468 | etot = -13.2825374162274
+856000  ekin = 2.47592780438371 |  erot = 2.3603420277346 | epot = -18.1188072483454 | etot = -13.2825374162271
+857000  ekin = 2.47367803113421 |  erot = 2.36697110010333 | epot = -18.1231865475261 | etot = -13.2825374162886
+858000  ekin = 2.47922391314762 |  erot = 2.37260088410896 | epot = -18.1343622136269 | etot = -13.2825374163703
+859000  ekin = 2.49150776537562 |  erot = 2.37701216170971 | epot = -18.1510573435355 | etot = -13.2825374164502
+860000  ekin = 2.50937686487663 |  erot = 2.38013993767848 | epot = -18.1720542190715 | etot = -13.2825374165164
+861000  ekin = 2.53170635734158 |  erot = 2.382118173112 | epot = -18.1963619470209 | etot = -13.2825374165673
+862000  ekin = 2.55742566397641 |  erot = 2.38328933411273 | epot = -18.2232524146946 | etot = -13.2825374166054
+863000  ekin = 2.58549482989182 |  erot = 2.38419488615669 | epot = -18.2522271326816 | etot = -13.2825374166331
+864000  ekin = 2.61488040894193 |  erot = 2.38555368952377 | epot = -18.2829715151176 | etot = -13.2825374166519
+865000  ekin = 2.64455846197211 |  erot = 2.38821849293994 | epot = -18.3153143715761 | etot = -13.282537416664
+866000  ekin = 2.67354800293375 |  erot = 2.39309523430222 | epot = -18.3491806539087 | etot = -13.2825374166727
+867000  ekin = 2.70096216873101 |  erot = 2.40101926625376 | epot = -18.3845188516697 | etot = -13.282537416685
+868000  ekin = 2.72584498237102 |  erot = 2.41260829133849 | epot = -18.4209906905118 | etot = -13.2825374168023
+869000  ekin = 2.74685098517846 |  erot = 2.42808376703703 | epot = -18.4574721690819 | etot = -13.2825374168664
+870000  ekin = 2.7633451632292 |  erot = 2.44707202924713 | epot = -18.492954609437 | etot = -13.2825374169607
+871000  ekin = 2.77488977650291 |  erot = 2.46856883210016 | epot = -18.52599602569 | etot = -13.2825374170869
+872000  ekin = 2.78115731189941 |  erot = 2.49101078905502 | epot = -18.5547055181929 | etot = -13.2825374172384
+873000  ekin = 2.78190152481948 |  erot = 2.51241399948397 | epot = -18.5768529417016 | etot = -13.2825374173982
+874000  ekin = 2.77696693727655 |  erot = 2.53063897251365 | epot = -18.5901433273283 | etot = -13.2825374175381
+875000  ekin = 2.76636320238677 |  erot = 2.54374754553387 | epot = -18.5926481655429 | etot = -13.2825374176222
+876000  ekin = 2.75040698328634 |  erot = 2.55039472458546 | epot = -18.5833391254864 | etot = -13.2825374176146
+877000  ekin = 2.72989722871737 |  erot = 2.55017286738757 | epot = -18.5626075135949 | etot = -13.28253741749
+878000  ekin = 2.70625700359845 |  erot = 2.54382115285145 | epot = -18.5326155736941 | etot = -13.2825374172442
+879000  ekin = 2.68156506710304 |  erot = 2.5332421375899 | epot = -18.4973446215902 | etot = -13.2825374168973
+880000  ekin = 2.65843100587721 |  erot = 2.52132217105652 | epot = -18.4622905934235 | etot = -13.2825374164897
+881000  ekin = 2.63972432917675 |  erot = 2.51160592655705 | epot = -18.4338676718058 | etot = -13.282537416072
+882000  ekin = 2.62822235346356 |  erot = 2.50790034757638 | epot = -18.4186601167335 | etot = -13.2825374156936
+883000  ekin = 2.62626662018779 |  erot = 2.51387422610971 | epot = -18.4226782616929 | etot = -13.2825374153954
+884000  ekin = 2.63550251587674 |  erot = 2.53269091102144 | epot = -18.4507308421049 | etot = -13.2825374152068
+885000  ekin = 2.65673814602945 |  erot = 2.56668643769325 | epot = -18.5059619988685 | etot = -13.2825374151458
+886000  ekin = 2.68991716922188 |  erot = 2.61709355073984 | epot = -18.5895481351839 | etot = -13.2825374152222
+887000  ekin = 2.73417552912835 |  erot = 2.6838152242605 | epot = -18.7005281688277 | etot = -13.2825374154388
+888000  ekin = 2.78795008305904 |  erot = 2.76526591420808 | epot = -18.8357534130565 | etot = -13.2825374157894
+889000  ekin = 2.84912017691373 |  erot = 2.85831711202064 | epot = -18.9899747051915 | etot = -13.2825374162572
+890000  ekin = 2.91517691409144 |  erot = 2.95839462905156 | epot = -19.1561089599533 | etot = -13.2825374168103
+891000  ekin = 2.98341766730812 |  erot = 3.05976765321724 | epot = -19.325722737928 | etot = -13.2825374174026
+892000  ekin = 3.05115351194122 |  erot = 3.15603968509377 | epot = -19.4897306150129 | etot = -13.2825374179779
+893000  ekin = 3.11590366932995 |  erot = 3.24080527058909 | epot = -19.6392463583964 | etot = -13.2825374184774
+894000  ekin = 3.17554452677574 |  erot = 3.30838806048503 | epot = -19.7664700061104 | etot = -13.2825374188496
+895000  ekin = 3.22839008199059 |  erot = 3.35454380329715 | epot = -19.8654713043472 | etot = -13.2825374190595
+896000  ekin = 3.27319974841242 |  erot = 3.37700709675264 | epot = -19.9327442642579 | etot = -13.2825374190928
+897000  ekin = 3.30912548213112 |  erot = 3.37578333286277 | epot = -19.967446233953 | etot = -13.2825374189591
+898000  ekin = 3.33561719165196 |  erot = 3.3531309986516 | epot = -19.9712856089931 | etot = -13.2825374186895
+899000  ekin = 3.35230310065721 |  erot = 3.31323476899373 | epot = -19.9480752879843 | etot = -13.2825374183334
+900000  ekin = 3.35886034343544 |  erot = 3.26162723368974 | epot = -19.9030249950731 | etot = -13.2825374179479
+901000  ekin = 3.35489762596209 |  erot = 3.20446448625264 | epot = -19.8418995298029 | etot = -13.2825374175882
+902000  ekin = 3.33988398696538 |  erot = 3.14778460706124 | epot = -19.7702060113224 | etot = -13.2825374172958
+903000  ekin = 3.31316641783821 |  erot = 3.09687096396604 | epot = -19.6925747988938 | etot = -13.2825374170895
+904000  ekin = 3.27411465308455 |  erot = 3.05580881507587 | epot = -19.6124608851232 | etot = -13.2825374169628
+905000  ekin = 3.22240761769978 |  erot = 3.02727711778411 | epot = -19.5322221523689 | etot = -13.282537416885
+906000  ekin = 3.15843123273498 |  erot = 3.01257047454492 | epot = -19.4535391240911 | etot = -13.2825374168112
+907000  ekin = 3.08369712964382 |  erot = 3.01180553940022 | epot = -19.3780400857413 | etot = -13.2825374166972
+908000  ekin = 3.00113487274611 |  erot = 3.02423547951158 | epot = -19.3079077687759 | etot = -13.2825374165182
+909000  ekin = 2.91509126886064 |  erot = 3.0485809791401 | epot = -19.2462096642835 | etot = -13.2825374162828
+910000  ekin = 2.83091809167562 |  erot = 3.08328866526031 | epot = -19.1967441729738 | etot = -13.2825374160379
+911000  ekin = 2.7541604271422 |  erot = 3.1266566210814 | epot = -19.1633544640806 | etot = -13.282537415857
+912000  ekin = 2.68982240100996 |  erot = 3.1767030385921 | epot = -19.1490628553551 | etot = -13.2825374157531
+913000  ekin = 2.64026279373643 |  erot = 3.23106967523778 | epot = -19.1538698849232 | etot = -13.282537415949
+914000  ekin = 2.60494541465082 |  erot = 3.28757760697213 | epot = -19.1750604377642 | etot = -13.2825374161413
+915000  ekin = 2.58331294239456 |  erot = 3.34356245911015 | epot = -19.2094128182448 | etot = -13.2825374167401
+916000  ekin = 2.57222527647779 |  erot = 3.39542630316431 | epot = -19.2501889969159 | etot = -13.2825374172738
+917000  ekin = 2.56717379817942 |  erot = 3.43991413449175 | epot = -19.2896253504428 | etot = -13.2825374177716
+918000  ekin = 2.56366862210109 |  erot = 3.47431911616615 | epot = -19.3205251564115 | etot = -13.2825374181443
+919000  ekin = 2.55808580304574 |  erot = 3.49688251813148 | epot = -19.3375057395072 | etot = -13.28253741833
+920000  ekin = 2.54828083364558 |  erot = 3.5070678678649 | epot = -19.3378861198184 | etot = -13.2825374183079
+921000  ekin = 2.53385837590705 |  erot = 3.50557961685233 | epot = -19.3219754108608 | etot = -13.2825374181014
+922000  ekin = 2.51606053239869 |  erot = 3.49409623216883 | epot = -19.2926941823441 | etot = -13.2825374177766
+923000  ekin = 2.49728908788132 |  erot = 3.47476611576438 | epot = -19.2545926210732 | etot = -13.2825374174275
+924000  ekin = 2.48035717202194 |  erot = 3.44958564398511 | epot = -19.2124802331591 | etot = -13.2825374171521
+925000  ekin = 2.46765713254659 |  erot = 3.41982437264767 | epot = -19.1700189222178 | etot = -13.2825374170235
+926000  ekin = 2.46048446158288 |  erot = 3.38566546873097 | epot = -19.1286873473806 | etot = -13.2825374170668
+927000  ekin = 2.45872404317125 |  erot = 3.34617863031278 | epot = -19.0874400907354 | etot = -13.2825374172514
+928000  ekin = 2.46097855171065 |  erot = 3.29964380838023 | epot = -19.0431597775946 | etot = -13.2825374175038
+929000  ekin = 2.46505358069594 |  erot = 3.24413140257229 | epot = -18.991722401002 | etot = -13.2825374177338
+930000  ekin = 2.46859437787823 |  erot = 3.17816487157566 | epot = -18.9292966673187 | etot = -13.2825374178649
+931000  ekin = 2.46965047267191 |  erot = 3.10127887080617 | epot = -18.8534667613313 | etot = -13.2825374178532
+932000  ekin = 2.4670173255647 |  erot = 3.01434778959557 | epot = -18.7639025328451 | etot = -13.2825374176848
+933000  ekin = 2.46031519134382 |  erot = 2.9197399878057 | epot = -18.6625925965562 | etot = -13.2825374174067
+934000  ekin = 2.44985996562476 |  erot = 2.82081794784481 | epot = -18.5532153305218 | etot = -13.2825374170523
+935000  ekin = 2.436420580333 |  erot = 2.72162862765433 | epot = -18.4405866246576 | etot = -13.2825374166703
+936000  ekin = 2.42095423708767 |  erot = 2.62651830215161 | epot = -18.3300099555418 | etot = -13.2825374163026
+937000  ekin = 2.40438434932027 |  erot = 2.53973621279557 | epot = -18.226657978095 | etot = -13.2825374159791
+938000  ekin = 2.38744919935998 |  erot = 2.4651292336249 | epot = -18.135115848703 | etot = -13.2825374157181
+939000  ekin = 2.37062067073867 |  erot = 2.40593643839711 | epot = -18.0590945246642 | etot = -13.2825374155285
+940000  ekin = 2.35407564445261 |  erot = 2.36465978724872 | epot = -18.0012728471164 | etot = -13.2825374154151
+941000  ekin = 2.33770002396805 |  erot = 2.3429775907629 | epot = -17.9632150301122 | etot = -13.2825374153812
+942000  ekin = 2.3211100477539 |  erot = 2.34167204177044 | epot = -17.9453195049536 | etot = -13.2825374154293
+943000  ekin = 2.30368578977883 |  erot = 2.36056240878928 | epot = -17.9467856141281 | etot = -13.28253741556
+944000  ekin = 2.28462216192276 |  erot = 2.39846175869457 | epot = -17.965621336385 | etot = -13.2825374157677
+945000  ekin = 2.2630091294477 |  erot = 2.45319770839139 | epot = -17.9987442538757 | etot = -13.2825374160366
+946000  ekin = 2.23795189081835 |  erot = 2.52174524491464 | epot = -18.0422345520714 | etot = -13.2825374163384
+947000  ekin = 2.20873145000821 |  erot = 2.60050188215201 | epot = -18.0917707487932 | etot = -13.282537416633
+948000  ekin = 2.17498954570766 |  erot = 2.68569096156255 | epot = -18.1432179241464 | etot = -13.2825374168762
+949000  ekin = 2.13690579381781 |  erot = 2.77382147859291 | epot = -18.1932646894412 | etot = -13.2825374170305
+950000  ekin = 2.09532426392926 |  erot = 2.86208910103834 | epot = -18.2399507820441 | etot = -13.2825374170765
+951000  ekin = 2.05179334892108 |  erot = 2.94860198731117 | epot = -18.2829327532513 | etot = -13.282537417019
+952000  ekin = 2.00850116617196 |  erot = 3.03236285196215 | epot = -18.3234014350193 | etot = -13.2825374168852
+953000  ekin = 1.96811370411823 |  erot = 3.11301524923778 | epot = -18.3636663700751 | etot = -13.2825374167191
+954000  ekin = 1.93354422096465 |  erot = 3.19043207950452 | epot = -18.4065137170385 | etot = -13.2825374165694
+955000  ekin = 1.90769299354898 |  erot = 3.26426019429227 | epot = -18.4544906043215 | etot = -13.2825374164802
+956000  ekin = 1.89319483668346 |  erot = 3.3335310510213 | epot = -18.5092633041882 | etot = -13.2825374164834
+957000  ekin = 1.89220136687493 |  erot = 3.39641763043281 | epot = -18.5711564139026 | etot = -13.2825374165948
+958000  ekin = 1.90621184327196 |  erot = 3.45018116338437 | epot = -18.6389304234696 | etot = -13.2825374168133
+959000  ekin = 1.93595602572738 |  erot = 3.49131884016615 | epot = -18.7098122830149 | etot = -13.2825374171214
+960000  ekin = 1.98132739808155 |  erot = 3.51589596586286 | epot = -18.7797607814332 | etot = -13.2825374174888
+961000  ekin = 2.04135467404736 |  erot = 3.52022622800403 | epot = -18.8441183199515 | etot = -13.2825374179001
+962000  ekin = 2.11395441310799 |  erot = 3.50134462367084 | epot = -18.8978364550807 | etot = -13.2825374183019
+963000  ekin = 2.19624676899701 |  erot = 3.45688460164827 | epot = -18.9356687892675 | etot = -13.2825374186222
+964000  ekin = 2.28502253915305 |  erot = 3.38607259923977 | epot = -18.9536325572173 | etot = -13.2825374188245
+965000  ekin = 2.37703902445876 |  erot = 3.290048679397 | epot = -18.9496251223776 | etot = -13.2825374185219
+966000  ekin = 2.47063968725093 |  erot = 3.1723513983338 | epot = -18.9255285040288 | etot = -13.2825374184441
+967000  ekin = 2.56372995923146 |  erot = 3.03797961445187 | epot = -18.8842469918799 | etot = -13.2825374181965
+968000  ekin = 2.65424153344269 |  erot = 2.89333166097639 | epot = -18.8301106122161 | etot = -13.282537417797
+969000  ekin = 2.74102206186552 |  erot = 2.74597895251273 | epot = -18.7695384316796 | etot = -13.2825374173014
+970000  ekin = 2.82317857356224 |  erot = 2.604190086995 | epot = -18.7099060774559 | etot = -13.2825374168987
+971000  ekin = 2.8994689638118 |  erot = 2.4760495859706 | epot = -18.6580559662902 | etot = -13.2825374165078
+972000  ekin = 2.9692788351105 |  erot = 2.36783972481189 | epot = -18.6196559761964 | etot = -13.282537416274
+973000  ekin = 3.03160430536472 |  erot = 2.2837390116559 | epot = -18.5978807332491 | etot = -13.2825374162285
+974000  ekin = 3.08487810189262 |  erot = 2.22552920107224 | epot = -18.5929447193212 | etot = -13.2825374163564
+975000  ekin = 3.12708218339791 |  erot = 2.19270938701088 | epot = -18.6023289870154 | etot = -13.2825374166067
+976000  ekin = 3.15606698313496 |  erot = 2.18294126797245 | epot = -18.6215456680199 | etot = -13.2825374169125
+977000  ekin = 3.16994500148915 |  erot = 2.19267118134068 | epot = -18.6451536000414 | etot = -13.2825374172116
+978000  ekin = 3.16742946230438 |  erot = 2.21776877388408 | epot = -18.6677356536463 | etot = -13.2825374174579
+979000  ekin = 3.14804045634032 |  erot = 2.25406876454721 | epot = -18.6846466385122 | etot = -13.2825374176247
+980000  ekin = 3.11216367300116 |  erot = 2.29776911310777 | epot = -18.6924702038109 | etot = -13.282537417702
+981000  ekin = 3.06099214892659 |  erot = 2.3456929996696 | epot = -18.6892225662862 | etot = -13.28253741769
+982000  ekin = 2.99639964718071 |  erot = 2.39544433336442 | epot = -18.6743813981403 | etot = -13.2825374175951
+983000  ekin = 2.92078844001815 |  erot = 2.44547840699747 | epot = -18.6488042644435 | etot = -13.2825374174279
+984000  ekin = 2.83693459158518 |  erot = 2.49508912549767 | epot = -18.6145611342876 | etot = -13.2825374172048
+985000  ekin = 2.74783419632812 |  erot = 2.5443043349293 | epot = -18.574675948205 | etot = -13.2825374169476
+986000  ekin = 2.65654531631453 |  erot = 2.59369131479764 | epot = -18.5327740477957 | etot = -13.2825374166835
+987000  ekin = 2.56602543639744 |  erot = 2.64409903932047 | epot = -18.4926618921587 | etot = -13.2825374164408
+988000  ekin = 2.47897321242724 |  erot = 2.69638105728562 | epot = -18.4578916859573 | etot = -13.2825374162445
+989000  ekin = 2.39763961356463 |  erot = 2.75059396001095 | epot = -18.4307709898088 | etot = -13.2825374162332
+990000  ekin = 2.32368779513216 |  erot = 2.8060334288419 | epot = -18.4122586401602 | etot = -13.2825374161862
+991000  ekin = 2.25825301239778 |  erot = 2.86226671700632 | epot = -18.403057145624 | etot = -13.2825374162199
+992000  ekin = 2.20187988804497 |  erot = 2.91825634883864 | epot = -18.40267365322 | etot = -13.2825374163364
+993000  ekin = 2.15452775813786 |  erot = 2.97231721272995 | epot = -18.4093823873994 | etot = -13.2825374165316
+994000  ekin = 2.1156117684003 |  erot = 3.02214023540268 | epot = -18.4202894205965 | etot = -13.2825374167935
+995000  ekin = 2.0840816135671 |  erot = 3.0648940369717 | epot = -18.4315130676401 | etot = -13.2825374171013
+996000  ekin = 2.05854312781033 |  erot = 3.09743221589021 | epot = -18.4385127611221 | etot = -13.2825374174216
+997000  ekin = 2.03742523644506 |  erot = 3.11662356541409 | epot = -18.4365862195703 | etot = -13.2825374177112
+998000  ekin = 2.0191844917443 |  erot = 3.11978989754515 | epot = -18.4215118072117 | etot = -13.2825374179223
+999000  ekin = 2.00252382756565 |  erot = 3.10518925660486 | epot = -18.3902505021827 | etot = -13.2825374180121
+1000000  ekin = 1.98658902728357 |  erot = 3.07244218051013 | epot = -18.341568625748 | etot = -13.2825374179543
+ 1000000  0.088292846   -1.1874188  0.041070751   -1.0221862 -7.1515284e-05 
+Loop time of 31.8631 on 4 procs for 1000000 steps with 16 atoms
+
+Performance: 27116.007 tau/day, 31384.268 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.7557     | 14.198     | 24.52      | 210.8 | 44.56
+Bond    | 0.22678    | 0.45105    | 0.74273    |  29.9 |  1.42
+Neigh   | 0.00012    | 0.00012675 | 0.00013    |   0.0 |  0.00
+Comm    | 2.6837     | 2.8338     | 3.0258     |   7.8 |  8.89
+Output  | 2e-05      | 2.75e-05   | 3e-05      |   0.0 |  0.00
+Modify  | 0.43472    | 0.8763     | 1.3871     |  38.7 |  2.75
+Other   |            | 13.5       |            |       | 42.38
+
+Nlocal:    4 ave 7 max 1 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:    10.5 ave 12 max 9 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    38.75 ave 63 max 11 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 155
+Ave neighs/atom = 9.6875
+Ave special neighs/atom = 3.75
+Neighbor list builds = 6
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:31

From cbbe449d07a051cb870efd9600e474d99f151623 Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 15:59:06 +0000
Subject: [PATCH 027/199] Updated README

---
 src/USER-CGDNA/README | 74 +++++++++++++++++++++++++------------------
 1 file changed, 44 insertions(+), 30 deletions(-)

diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README
index 48d6178d13..a57168e53e 100644
--- a/src/USER-CGDNA/README
+++ b/src/USER-CGDNA/README
@@ -2,12 +2,12 @@ This package contains a LAMMPS implementation of coarse-grained
 models of DNA, which can be used to model sequence-specific
 DNA strands.
 
-Please cite [1] and the relevant oxDNA articles in any publication 
-that uses this package.
+Please cite [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles 
+in any publication that uses this package.
 
-See the doc pages and [2,3,4] for the individual bond and pair styles. 
+See the doc pages and [2,3,4,5,6] for the individual bond and pair styles. 
 The packages contains also a new Langevin-type rigid-body integrator,
-which has also its own doc page and is explained in [5].
+which has also its own doc page and is explained in [7].
 
 [1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
 "Coarse-grained simulation of DNA using LAMMPS", 
@@ -17,24 +17,31 @@ Eur. Phys. J. E 41, 57 (2018).
 and thermodynamic properties of a coarse-grained DNA model",
 J. Chem. Phys. 134, 085101 (2011).
 
-[3] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA 
-self-assembly, DPhil. University of Oxford (2011).
+[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA 
+self-assembly", DPhil. University of Oxford (2011).
 
-[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
-Improved Structural Properties and Salt Dependence into a Coarse-Grained
-Model of DNA, J. Chem. Phys. 142, 234901 (2015).
+[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., "Introducing
+Improved structural properties and salt dependence into a coarse-grained
+model of DNA", J. Chem. Phys. 142, 234901 (2015).
 
-[5] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and 
+[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level 
+coarse-grained model of RNA", J. Chem. Phys. 140, 235102 (2014).
+
+[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent 
+thermodynamics of a coarse-grained DNA model",
+J. Chem. Phys. 137, 135101 (2012). 
+
+[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and 
 gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 
 144114 (2015).
 
 Example input and data files can be found in
-/examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. Python setup 
-tools which create single straight or helical DNA strands as
-well as DNA duplexes or arrays of duplexes can be found in
-/examples/USER/cgdna/util/. A technical report with more information
-on the models, the structure of the input and data file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA can be found
+/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. 
+Python setup tools which create single straight or helical DNA or RNA 
+strands as well as DNA or RNA duplexes or arrays of duplexes can be 
+found in /examples/USER/cgdna/util/. A technical report with more 
+general information on the model, its implementation and performance 
+as well as the structure of the data and input file can be found
 in /doc/src/PDF/USER-CGDNA.pdf.
 
 IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
@@ -54,34 +61,41 @@ oliver d o t henrich a t strath d o t ac d o t uk
 
 ** Bond styles provided by this package:
 
-bond_oxdna_fene.cpp:  backbone connectivity, a modified FENE potential
+bond_oxdna_fene.cpp:    backbone connectivity, 
+                        a modified FENE potential (see [2,3])
 
-bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3])
+bond_oxdna2_fene.cpp:   corresponding bond style in oxDNA2 (see [4])
+
+bond_oxrna2_fene.cpp:   corresponding bond style in oxRNA2 (see [5])
 
 ** Pair styles provided by this package:
 
-pair_oxdna_excv.cpp:  excluded volume interaction between the nucleotides
+pair_oxdna_excv.cpp:    excluded volume interaction between the nucleotides
 
-pair_oxdna_stk.cpp:  stacking interaction between consecutive nucleotides
-                     on the same strand
+pair_oxdna_stk.cpp:     stacking interaction between consecutive nucleotides
+                        on the same strand
 
-pair_oxdna_hbond.cpp:  hydrogen-bonding interaction between complementary
-                       nucleotides on different strands, e.g. A-T and C-G
+pair_oxdna_hbond.cpp:   hydrogen-bonding interaction between complementary
+                        nucleotides on different strands, e.g. A-T and C-G
 
-pair_oxdna_xstk.cpp:  cross-stacking interaction between nucleotides
+pair_oxdna_xstk.cpp:    cross-stacking interaction between nucleotides
 
-pair_oxdna_coaxstk.cpp:  coaxial stacking interaction between nucleotides
+pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
 
+pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: 
+                        corresponding pair styles in oxDNA2 (see [4])
 
-pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp:
-                     corresponding pair styles in oxDNA2 (see [3])
+pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp, 
+pair_oxrna2_xstk.cpp: 
+                        corresponding pair styles in oxDNA2 (see [5])
+
+pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp:  
+               Debye-Hueckel electrostatic interaction between backbone sites
 
-pair_oxdna2_dh.cpp:  Debye-Hueckel electrostatic interaction between backbone
-                     sites
 
 ** Fixes provided by this package:
 
 fix_nve_dotc_langevin.cpp:  fix for Langevin-type rigid body integrator "C"
-                            in above Ref. [3] 
+                            in above Ref. [7] 
 
 fix_nve_dot.cpp:  NVE-type rigid body integrator without noise

From cedcc6fc50902451bd00ee61b2b4069fee7937f4 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Fri, 15 Nov 2019 09:27:02 -0700
Subject: [PATCH 028/199] Commit JT 111519 - modified documentation spin
 (compute and exchange) - modified compute spin for Ts

---
 .../Eqs/pair_spin_exchange_interaction.jpg    | Bin 5940 -> 5554 bytes
 .../Eqs/pair_spin_exchange_interaction.tex    |   8 ++++++--
 doc/src/compute_spin.txt                      |  16 +++++++---------
 doc/src/pair_spin_exchange.txt                |   5 +++--
 src/SPIN/compute_spin.cpp                     |   3 ++-
 5 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.jpg b/doc/src/Eqs/pair_spin_exchange_interaction.jpg
index c70d8a6554003e37472d648c1944a13ee9d3f859..269be6c155cb006c07035f8b8f4f357ccb2eaf10 100644
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zlQmOTyHDPSq@RzaaE2Orp;-2W(7EDDpqRd3btt^a-&0;KJ2y-*+e7S3J{LEyM34>G
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zBGwfy!Em-Cj6lad@gY@r>uKExb<B`UA1CuAAK~<|)hga(PE<H$>FxXhu&y=G4WOt2
z1o17^8vh7I1Ks#R;p*hO2%WV74JN@hfjAwyRwOXbbo3*CRQeVhnN1k^N2N2Kjsh^T
dBLdy7%#T}Jskiwn4uu#PSWA?Yw3r@D{1@QG=?MS;

diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.tex b/doc/src/Eqs/pair_spin_exchange_interaction.tex
index f20b3e5740..8bb58e0885 100644
--- a/doc/src/Eqs/pair_spin_exchange_interaction.tex
+++ b/doc/src/Eqs/pair_spin_exchange_interaction.tex
@@ -1,11 +1,15 @@
 \documentclass[preview]{standalone}
 \usepackage{varwidth}
 \usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
 \begin{document}
 \begin{varwidth}{50in}
   \begin{equation}
-    \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
+    H_{ex} = 
+    -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j 
+    %&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F  
+  , \nonumber
   \end{equation}
 \end{varwidth}
 \end{document}
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index 0824a70dd0..dddbc856c4 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -24,17 +24,15 @@ compute out_mag all spin :pre
 Define a computation that calculates magnetic quantities for a system
 of atoms having spins.
 
-This compute calculates 6 magnetic quantities.
-
-The three first quantities are the x,y and z coordinates of the total
-magnetization.
-
-The fourth quantity is the norm of the total magnetization.
-
-The fifth quantity is the magnetic energy.
+This compute calculates the following 6 magnetic quantities:
 
+the three first quantities are the x,y and z coordinates of the total
+magnetization, :ulb,l
+the fourth quantity is the norm of the total magnetization, :l
+The fifth quantity is the magnetic energy (in eV), :l
 The sixth one is referred to as the spin temperature, according
-to the work of "(Nurdin)"_#Nurdin1.
+to the work of "(Nurdin)"_#Nurdin1. :l
+:ule
 
 The simplest way to output the results of the compute spin calculation
 is to define some of the quantities as variables, and to use the thermo and
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index 76a6d508d2..7bc6b5fef7 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -30,14 +30,15 @@ pairs of magnetic spins:
 :c,image(Eqs/pair_spin_exchange_interaction.jpg)
 
 where si and sj are two neighboring magnetic spins of two particles,
-rij = ri - rj is the inter-atomic distance between the two particles,
+rij = |ri - rj| is the inter-atomic distance between the two particles,
 and J(rij) is a function defining the intensity and the sign of the exchange
 interaction for different neighboring shells. This function is defined as:
 
 :c,image(Eqs/pair_spin_exchange_function.jpg)
 
 where a, b and d are the three constant coefficients defined in the associated
-"pair_coeff" command (see below for more explanations).
+"pair_coeff" command, and Rc is the radius cutoff associated to
+the pair interaction (see below for more explanations).
 
 The coefficients a, b, and d need to be fitted so that the function above matches with
 the value of the exchange interaction for the N neighbor shells taken into account.
diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index 6f1e72ef7e..7d7fb56e1c 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -129,7 +129,8 @@ void ComputeSpin::compute_vector()
   magtot[2] *= scale;
   magtot[3] = sqrt((magtot[0]*magtot[0])+(magtot[1]*magtot[1])+(magtot[2]*magtot[2]));
   spintemperature = hbar*tempnumtot;
-  spintemperature /= (kb*tempdenomtot);
+  // spintemperature /= (kb*tempdenomtot);
+  spintemperature /= (2.0*kb*tempdenomtot);
 
   vector[0] = magtot[0];
   vector[1] = magtot[1];

From f96520ffc65c8f624dc37424ffcd18978dc7e7db Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 17:49:17 +0000
Subject: [PATCH 029/199] Added unique base pairing

---
 examples/USER/cgdna/README                    |  17 +
 .../oxDNA2/unique_bp/data.duplex4.4type       | 130 +++
 .../oxDNA2/unique_bp/data.duplex4.8type       | 130 +++
 .../oxDNA2/unique_bp/generate_unique.py       | 828 ++++++++++++++++++
 .../oxDNA2/unique_bp/in.duplex4.4type         |  94 ++
 .../oxDNA2/unique_bp/in.duplex4.8type         |  94 ++
 .../unique_bp/log.07Aug19.duplex4.4type.g++1  | 232 +++++
 .../unique_bp/log.07Aug19.duplex4.4type.g++4  | 232 +++++
 .../unique_bp/log.07Aug19.duplex4.8type.g++1  | 274 ++++++
 .../unique_bp/log.07Aug19.duplex4.8type.g++4  | 274 ++++++
 10 files changed, 2305 insertions(+)
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1
 create mode 100644 examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4

diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README
index a03490b630..7cbf76fd5a 100644
--- a/examples/USER/cgdna/README
+++ b/examples/USER/cgdna/README
@@ -55,6 +55,23 @@ are sequence-dependent (cf. keyword 'seqdep' in according pair styles).
 
 /******************************************************************************/
 
+/examples/oxDNA2/unique_bp:
+
+This example uses atom types 1-8 to model a 13 base pair duplex.
+The nucleotide types are assigned as follows:
+A = 1,5; C = 2,6; G = 3,7; T = 4,8
+When a large number of atom types is used, this feature allows
+quasi-unique base pairing between two individual nucleotides.
+
+The topology is
+A   C   G   T   A   C   G   T   A   C   G   T   A
+1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 1 - 2 - 7 - 8 - 1
+|   |   |   |   |   |   |   |   |   |   |   |   |
+4 - 3 - 2 - 1 - 8 - 7 - 6 - 5 - 4 - 3 - 6 - 5 - 4
+T   G   C   A   T   G   C   A   T   G   C   A   T
+
+/******************************************************************************/
+
 /examples/oxRNA2/duplex4
 
 This is the duplex2 run with the oxRNA2 force field instead of the oxDNA or 
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type
new file mode 100644
index 0000000000..a8412eef07
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type
@@ -0,0 +1,130 @@
+# LAMMPS data file
+26 atoms
+26 ellipsoids
+24 bonds
+
+4 atom types
+1 bond types
+
+# System size
+-20.000000 20.000000 xlo xhi
+-20.000000 20.000000 ylo yhi
+-20.000000 20.000000 zlo zhi
+
+# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
+Atoms
+
+1 1 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.957432645895970e-01 -3.379920348381733e-01  3.897628551303122e-01 1 1 1
+3 3 -2.192046146198370e-01 -5.585242491865227e-01  7.795257102606244e-01 1 1 1
+4 4  1.335125603737887e-01 -5.849567473090943e-01  1.169288565390937e+00 1 1 1
+5 1  4.398311230978960e-01 -4.081036426625517e-01  1.559051420521249e+00 1 1 1
+6 2  5.932984957350773e-01 -8.942535970570469e-02  1.948814275651561e+00 1 1 1
+7 3  5.405813207414517e-01  2.603302434705350e-01  2.338577130781873e+00 1 1 1
+8 4  3.000000000000002e-01  5.196152422706634e-01  2.728339985912185e+00 1 1 1
+9 1 -4.483805615185452e-02  5.983222783087083e-01  3.118102841042497e+00 1 1 1
+10 2 -3.740938811152403e-01  4.690988894808181e-01  3.507865696172809e+00 1 1 1
+11 3 -5.733436834716847e-01  1.768531046465427e-01  3.897628551303121e+00 1 1 1
+12 4 -5.733436834716849e-01 -1.768531046465427e-01  4.287391406433434e+00 1 1 1
+13 1 -3.740938811152403e-01 -4.690988894808182e-01  4.677154261563746e+00 1 1 1
+14 4  3.740938811152403e-01  4.690988894808182e-01  4.677154261563746e+00 2 1 1
+15 1  5.733436834716849e-01  1.768531046465427e-01  4.287391406433434e+00 2 1 1
+16 2  5.733436834716849e-01 -1.768531046465426e-01  3.897628551303122e+00 2 1 1
+17 3  3.740938811152403e-01 -4.690988894808181e-01  3.507865696172810e+00 2 1 1
+18 4  4.483805615185462e-02 -5.983222783087085e-01  3.118102841042498e+00 2 1 1
+19 1 -3.000000000000003e-01 -5.196152422706636e-01  2.728339985912186e+00 2 1 1
+20 2 -5.405813207414519e-01 -2.603302434705351e-01  2.338577130781874e+00 2 1 1
+21 3 -5.932984957350776e-01  8.942535970570474e-02  1.948814275651561e+00 2 1 1
+22 4 -4.398311230978962e-01  4.081036426625520e-01  1.559051420521249e+00 2 1 1
+23 1 -1.335125603737888e-01  5.849567473090947e-01  1.169288565390937e+00 2 1 1
+24 2  2.192046146198373e-01  5.585242491865231e-01  7.795257102606246e-01 2 1 1
+25 3  4.957432645895974e-01  3.379920348381736e-01  3.897628551303123e-01 2 1 1
+26 4  6.000000000000006e-01  0.000000000000000e+00  1.110223024625157e-16 2 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+11  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+12  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+13  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+14  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+15  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+16  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+17  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+18  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+19  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+20  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+21  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+22  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+23  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+24  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+25  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+26  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.555728057861408e-01  0.000000000000000e+00  0.000000000000000e+00  2.947551744109042e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.262387743159949e-01  0.000000000000000e+00  0.000000000000000e+00  5.633200580636221e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  6.234898018587335e-01  0.000000000000000e+00  0.000000000000000e+00  7.818314824680299e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.653410243663950e-01  0.000000000000000e+00  0.000000000000000e+00  9.308737486442042e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  7.473009358642424e-02  0.000000000000000e+00  0.000000000000000e+00  9.972037971811802e-01
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -2.225209339563144e-01  0.000000000000000e+00  0.000000000000000e+00  9.749279121818237e-01
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -5.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00  8.660254037844387e-01
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  7.330518718298263e-01 -0.000000000000000e+00  0.000000000000000e+00 -6.801727377709196e-01
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.009688679024190e-01 -0.000000000000000e+00  0.000000000000000e+00 -4.338837391175581e-01
+11  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.888308262251286e-01 -0.000000000000000e+00  0.000000000000000e+00 -1.490422661761745e-01
+12  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.888308262251286e-01  0.000000000000000e+00  0.000000000000000e+00  1.490422661761745e-01
+13  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.009688679024190e-01  0.000000000000000e+00  0.000000000000000e+00  4.338837391175582e-01
+14  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00 -4.338837391175582e-01  9.009688679024190e-01  0.000000000000000e+00
+15  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01  9.888308262251286e-01  0.000000000000000e+00
+16  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  1.490422661761745e-01  9.888308262251286e-01 -0.000000000000000e+00
+17  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  4.338837391175581e-01  9.009688679024190e-01 -0.000000000000000e+00
+18  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  6.801727377709192e-01  7.330518718298267e-01  0.000000000000000e+00
+19  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.660254037844386e-01  5.000000000000001e-01  0.000000000000000e+00
+20  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.749279121818235e-01  2.225209339563145e-01  0.000000000000000e+00
+21  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.972037971811801e-01 -7.473009358642428e-02  0.000000000000000e+00
+22  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.308737486442041e-01 -3.653410243663952e-01  0.000000000000000e+00
+23  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  7.818314824680296e-01 -6.234898018587339e-01  0.000000000000000e+00
+24  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.633200580636215e-01 -8.262387743159952e-01  0.000000000000000e+00
+25  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01  9.555728057861407e-01  0.000000000000000e+00
+26  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  0.000000000000000e+00  1.000000000000000e+00 -0.000000000000000e+00
+
+# Bond topology
+Bonds
+
+1  1  1  2
+2  1  2  3
+3  1  3  4
+4  1  4  5
+5  1  5  6
+6  1  6  7
+7  1  7  8
+8  1  8  9
+9  1  9  10
+10  1  10  11
+11  1  11  12
+12  1  12  13
+13  1  14  15
+14  1  15  16
+15  1  16  17
+16  1  17  18
+17  1  18  19
+18  1  19  20
+19  1  20  21
+20  1  21  22
+21  1  22  23
+22  1  23  24
+23  1  24  25
+24  1  25  26
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type
new file mode 100644
index 0000000000..b4d622ac46
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type
@@ -0,0 +1,130 @@
+# LAMMPS data file
+26 atoms
+26 ellipsoids
+24 bonds
+
+8 atom types
+1 bond types
+
+# System size
+-20.000000 20.000000 xlo xhi
+-20.000000 20.000000 ylo yhi
+-20.000000 20.000000 zlo zhi
+
+# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
+Atoms
+
+1 1 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.957432645895970e-01 -3.379920348381733e-01  3.897628551303122e-01 1 1 1
+3 3 -2.192046146198370e-01 -5.585242491865227e-01  7.795257102606244e-01 1 1 1
+4 4  1.335125603737887e-01 -5.849567473090943e-01  1.169288565390937e+00 1 1 1
+5 5  4.398311230978960e-01 -4.081036426625517e-01  1.559051420521249e+00 1 1 1
+6 6  5.932984957350773e-01 -8.942535970570469e-02  1.948814275651561e+00 1 1 1
+7 7  5.405813207414517e-01  2.603302434705350e-01  2.338577130781873e+00 1 1 1
+8 8  3.000000000000002e-01  5.196152422706634e-01  2.728339985912185e+00 1 1 1
+9 1 -4.483805615185452e-02  5.983222783087083e-01  3.118102841042497e+00 1 1 1
+10 2 -3.740938811152403e-01  4.690988894808181e-01  3.507865696172809e+00 1 1 1
+11 7 -5.733436834716847e-01  1.768531046465427e-01  3.897628551303121e+00 1 1 1
+12 8 -5.733436834716849e-01 -1.768531046465427e-01  4.287391406433434e+00 1 1 1
+13 1 -3.740938811152403e-01 -4.690988894808182e-01  4.677154261563746e+00 1 1 1
+14 4  3.740938811152403e-01  4.690988894808182e-01  4.677154261563746e+00 2 1 1
+15 5  5.733436834716849e-01  1.768531046465427e-01  4.287391406433434e+00 2 1 1
+16 6  5.733436834716849e-01 -1.768531046465426e-01  3.897628551303122e+00 2 1 1
+17 3  3.740938811152403e-01 -4.690988894808181e-01  3.507865696172810e+00 2 1 1
+18 4  4.483805615185462e-02 -5.983222783087085e-01  3.118102841042498e+00 2 1 1
+19 5 -3.000000000000003e-01 -5.196152422706636e-01  2.728339985912186e+00 2 1 1
+20 6 -5.405813207414519e-01 -2.603302434705351e-01  2.338577130781874e+00 2 1 1
+21 7 -5.932984957350776e-01  8.942535970570474e-02  1.948814275651561e+00 2 1 1
+22 8 -4.398311230978962e-01  4.081036426625520e-01  1.559051420521249e+00 2 1 1
+23 1 -1.335125603737888e-01  5.849567473090947e-01  1.169288565390937e+00 2 1 1
+24 2  2.192046146198373e-01  5.585242491865231e-01  7.795257102606246e-01 2 1 1
+25 3  4.957432645895974e-01  3.379920348381736e-01  3.897628551303123e-01 2 1 1
+26 4  6.000000000000006e-01  0.000000000000000e+00  1.110223024625157e-16 2 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+11  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+12  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+13  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+14  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+15  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+16  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+17  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+18  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+19  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+20  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+21  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+22  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+23  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+24  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+25  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+26  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.555728057861408e-01  0.000000000000000e+00  0.000000000000000e+00  2.947551744109042e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.262387743159949e-01  0.000000000000000e+00  0.000000000000000e+00  5.633200580636221e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  6.234898018587335e-01  0.000000000000000e+00  0.000000000000000e+00  7.818314824680299e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.653410243663950e-01  0.000000000000000e+00  0.000000000000000e+00  9.308737486442042e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  7.473009358642424e-02  0.000000000000000e+00  0.000000000000000e+00  9.972037971811802e-01
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -2.225209339563144e-01  0.000000000000000e+00  0.000000000000000e+00  9.749279121818237e-01
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -5.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00  8.660254037844387e-01
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  7.330518718298263e-01 -0.000000000000000e+00  0.000000000000000e+00 -6.801727377709196e-01
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.009688679024190e-01 -0.000000000000000e+00  0.000000000000000e+00 -4.338837391175581e-01
+11  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.888308262251286e-01 -0.000000000000000e+00  0.000000000000000e+00 -1.490422661761745e-01
+12  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.888308262251286e-01  0.000000000000000e+00  0.000000000000000e+00  1.490422661761745e-01
+13  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.009688679024190e-01  0.000000000000000e+00  0.000000000000000e+00  4.338837391175582e-01
+14  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00 -4.338837391175582e-01  9.009688679024190e-01  0.000000000000000e+00
+15  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01  9.888308262251286e-01  0.000000000000000e+00
+16  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  1.490422661761745e-01  9.888308262251286e-01 -0.000000000000000e+00
+17  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  4.338837391175581e-01  9.009688679024190e-01 -0.000000000000000e+00
+18  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  6.801727377709192e-01  7.330518718298267e-01  0.000000000000000e+00
+19  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.660254037844386e-01  5.000000000000001e-01  0.000000000000000e+00
+20  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.749279121818235e-01  2.225209339563145e-01  0.000000000000000e+00
+21  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.972037971811801e-01 -7.473009358642428e-02  0.000000000000000e+00
+22  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.308737486442041e-01 -3.653410243663952e-01  0.000000000000000e+00
+23  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  7.818314824680296e-01 -6.234898018587339e-01  0.000000000000000e+00
+24  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.633200580636215e-01 -8.262387743159952e-01  0.000000000000000e+00
+25  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01  9.555728057861407e-01  0.000000000000000e+00
+26  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  0.000000000000000e+00  1.000000000000000e+00 -0.000000000000000e+00
+
+# Bond topology
+Bonds
+
+1  1  1  2
+2  1  2  3
+3  1  3  4
+4  1  4  5
+5  1  5  6
+6  1  6  7
+7  1  7  8
+8  1  8  9
+9  1  9  10
+10  1  10  11
+11  1  11  12
+12  1  12  13
+13  1  14  15
+14  1  15  16
+15  1  16  17
+16  1  17  18
+17  1  18  19
+18  1  19  20
+19  1  20  21
+20  1  21  22
+21  1  22  23
+22  1  23  24
+23  1  24  25
+24  1  25  26
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
new file mode 100644
index 0000000000..e5141bc47a
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
@@ -0,0 +1,828 @@
+#!/usr/bin/env python
+"""
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+"""
+"""
+Creates unique base-pairings to avoid asymmetrical H-bonds.  
+
+Modified to create the bead wall setup.
+N_BEADS is the number of beads along one direction, the final system will have N_BEADS^2 beads in the wall. N_BEADS should be set to be odd number.
+"""
+
+
+#Define number of base-pairs per turn for B-form DNA
+N = 10.5
+#Define distance between the big bead and the centre of mass of the last base-pair
+BEAD_OFFSET = 2.0
+WALL_PARTICLE_SIZE = 2.0
+N_BEADS = 11
+
+#Number of unique base type groups (1-4) ACGT counts as one group
+N_BASE_TYPES = 20
+
+
+"""
+Import basic modules
+"""
+import sys, os, timeit
+
+from timeit import default_timer as timer
+start_time = timer()
+"""
+Try to import numpy; if failed, import a local version mynumpy 
+which needs to be provided
+"""
+try:
+    import numpy as np
+except:
+    print("numpy not found. Exiting.", file=sys.stderr)
+    sys.exit(1)
+
+"""
+Check that the required arguments (box offset and size in simulation units 
+and the sequence file were provided
+"""
+try:
+    box_offset = float(sys.argv[1])
+    box_length = float(sys.argv[2])
+    infile = sys.argv[3]
+    if len(sys.argv) == 4:
+        topo = 'strand'
+        lk = 0
+    elif len(sys.argv) == 5:
+        topo = 'strand'
+        lk = int(sys.argv[4])
+           
+except:
+    print("Usage: %s <%s> <%s> <%s> <%s> " % (sys.argv[0], \
+	"box offset", "box length", "file with sequences", "[Lk]"), file=sys.stderr)
+    sys.exit(1)
+box = np.array ([box_length, box_length, box_length])
+
+"""
+Try to open the file and fail gracefully if file cannot be opened
+"""
+try:
+    inp = open (infile, 'r')
+    inp.close()
+except:
+    print("Could not open file '%s' for reading. \
+					      Aborting." % infile, file=sys.stderr)
+    sys.exit(2)
+
+# return parts of a string
+def partition(s, d):
+    if d in s:
+        sp = s.split(d, 1)
+        return sp[0], d, sp[1]
+    else:
+        return s, "", ""
+
+"""
+Define the model constants
+"""
+# set model constants
+PI = np.pi
+POS_BASE =  0.4
+POS_BACK = -0.4
+EXCL_RC1 =  0.711879214356
+EXCL_RC2 =  0.335388426126
+EXCL_RC3 =  0.52329943261
+
+"""
+Define auxillary variables for the construction of a helix
+"""
+# center of the double strand
+COM_CENTRE_DS = POS_BASE + 0.2
+
+# ideal rise between two consecutive nucleotides on the
+# same strand which are to be base paired in a duplex
+BASE_BASE = 0.3897628551303122
+
+# cutoff distance for overlap check
+RC2 = 16
+
+# squares of the excluded volume distances for overlap check
+RC2_BACK = EXCL_RC1**2
+RC2_BASE = EXCL_RC2**2
+RC2_BACK_BASE = EXCL_RC3**2
+
+# enumeration to translate from letters to numbers and vice versa
+number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
+base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
+                  'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
+
+# auxillary arrays
+positions = []
+a1s = []
+a3s = []
+quaternions = []
+
+newpositions = []
+newa1s = []
+newa3s = []
+
+basetype  = []
+strandnum = []
+
+bonds = []
+
+""" 
+Convert local body frame to quaternion DOF
+"""
+def exyz_to_quat (mya1, mya3):
+
+    mya2 = np.cross(mya3, mya1)
+    myquat = [1,0,0,0]
+
+    q0sq = 0.25 * (mya1[0] + mya2[1] + mya3[2] + 1.0)
+    q1sq = q0sq - 0.5 * (mya2[1] + mya3[2])
+    q2sq = q0sq - 0.5 * (mya1[0] + mya3[2])
+    q3sq = q0sq - 0.5 * (mya1[0] + mya2[1])
+
+    # some component must be greater than 1/4 since they sum to 1
+    # compute other components from it
+
+    if q0sq >= 0.25:
+        myquat[0] = np.sqrt(q0sq)
+        myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
+        myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
+        myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
+    elif q1sq >= 0.25:
+        myquat[1] = np.sqrt(q1sq)
+        myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
+        myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
+        myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
+    elif q2sq >= 0.25:
+        myquat[2] = np.sqrt(q2sq)
+        myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
+        myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
+        myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
+    elif q3sq >= 0.25:
+        myquat[3] = np.sqrt(q3sq)
+        myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
+        myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
+        myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
+
+    norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
+			  myquat[2]*myquat[2] + myquat[3]*myquat[3])
+    myquat[0] *= norm
+    myquat[1] *= norm
+    myquat[2] *= norm
+    myquat[3] *= norm
+
+    return np.array([myquat[0],myquat[1],myquat[2],myquat[3]])
+
+"""
+Adds a strand to the system by appending it to the array of previous strands
+"""
+def add_strands (mynewpositions, mynewa1s, mynewa3s):
+    overlap = False
+	
+    # This is a simple check for each of the particles where for previously 
+    # placed particles i we check whether it overlaps with any of the 
+    # newly created particles j
+
+    print("## Checking for overlaps", file=sys.stdout)
+
+    for i in range(len(positions)):
+
+        p = positions[i]
+        pa1 = a1s[i]
+
+        for j in range (len(mynewpositions)):
+
+            q = mynewpositions[j]
+            qa1 = mynewa1s[j]
+
+            # skip particles that are anyway too far away
+            dr = p - q
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) > RC2:
+                continue
+
+            # base site and backbone site of the two particles
+            p_pos_back = p + pa1 * POS_BACK
+            p_pos_base = p + pa1 * POS_BASE
+            q_pos_back = q + qa1 * POS_BACK
+            q_pos_base = q + qa1 * POS_BASE
+
+            # check for no overlap between the two backbone sites
+            dr = p_pos_back - q_pos_back
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK:
+                overlap = True
+
+            # check for no overlap between the two base sites
+            dr = p_pos_base -  q_pos_base
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BASE:
+                overlap = True
+
+            # check for no overlap between backbone site of particle p 
+            # with base site of particle q
+            dr = p_pos_back - q_pos_base
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK_BASE:
+                overlap = True
+
+            # check for no overlap between base site of particle p and 
+            # backbone site of particle q
+            dr = p_pos_base - q_pos_back
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK_BASE:
+                overlap = True
+
+            # exit if there is an overlap
+            if overlap:
+                return False
+
+    # append to the existing list if no overlap is found
+    if not overlap:
+
+        for p in mynewpositions:
+            positions.append(p)
+        for p in mynewa1s:
+            a1s.append (p)
+        for p in mynewa3s:
+            a3s.append (p)
+	# calculate quaternion from local body frame and append
+        for ia in range(len(mynewpositions)):
+            mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
+            quaternions.append(mynewquaternions)
+
+    return True
+
+"""
+Calculate angle of rotation site to site
+"""
+def get_angle(bp):
+   #n, minimal number of bases per turn
+   n = 10.5
+   found = False
+   while found == False:
+       turns = bp/n
+       diff = abs( turns - round(turns))
+       if diff < 0.03:
+           found = True
+           turns = round(turns)+lk
+           angle = (360*turns)/bp
+           angle = round (angle,2)
+           #angle =round( 360/n,2)
+       elif n > 11.5:
+           angle = 35.9
+           found = True
+       else:
+           n += 0.02
+   return angle
+
+
+def get_angle2(bp):
+    turns = bp/N + lk
+    angle = (360*turns)/bp
+    
+    return angle
+
+    
+
+"""
+Returns the rotation matrix defined by an axis and angle
+"""
+def get_rotation_matrix(axis, anglest, nbp=0):
+    # The argument anglest can be either an angle in radiants
+    # (accepted types are float, int or np.float64 or np.float64)
+    # or a tuple [angle, units] where angle is a number and
+    # units is a string. It tells the routine whether to use degrees,
+    # radiants (the default) or base pairs turns.
+    if not isinstance (anglest, (np.float64, np.float32, float, int)):
+        if len(anglest) > 1:
+            if anglest[1] in ["degrees", "deg", "o"]:
+                angle = (np.pi / 180.) * (anglest[0])
+            elif anglest[1] in ["bp"]:
+                if nbp == 0:
+                    angle = int(anglest[0]) * (np.pi / 180.) * (35.9)
+                else:    
+                    ang = get_angle2(nbp)
+                    angle = int(anglest[0]) * (np.pi / 180.) * (ang)
+            else:
+                angle = float(anglest[0])
+        else:
+            angle = float(anglest[0])
+    else:
+        angle = float(anglest) # in degrees (?)
+
+    axis = np.array(axis)
+    axis /= np.sqrt(np.dot(axis, axis))
+
+    ct = np.cos(angle)
+    st = np.sin(angle)
+    olc = 1. - ct
+    x, y, z = axis
+
+    return np.array([[olc*x*x+ct, olc*x*y-st*z, olc*x*z+st*y],
+                    [olc*x*y+st*z, olc*y*y+ct, olc*y*z-st*x],
+                    [olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
+
+"""
+Generates the position and orientation vectors of a 
+(single or double) strand from a sequence string
+"""
+def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
+	  dir=np.array([0, 0, 1]), perp=False, double=True, rot=0.):
+    # generate empty arrays
+    mynewpositions, mynewa1s, mynewa3s = [], [], []
+
+    # cast the provided start_pos array into a numpy array
+    start_pos = np.array(start_pos, dtype=float)
+
+    # overall direction of the helix
+    dir = np.array(dir, dtype=float)
+    #if sequence == None:
+    #    sequence = np.random.randint(1, 5, bp)
+
+    # the elseif here is most likely redundant 
+    #elif len(sequence) != bp:
+    #    n = bp - len(sequence)
+    #    sequence += np.random.randint(1, 5, n)
+    #    print("sequence is too short, adding %d random bases" % n, file=sys.stderr)
+
+    # normalize direction
+    dir_norm = np.sqrt(np.dot(dir,dir))
+    if dir_norm < 1e-10:
+        print("direction must be a valid vector,\
+                defaulting to (0, 0, 1)", file=sys.stderr)
+        dir = np.array([0, 0, 1])
+    else: dir /= dir_norm
+
+    # find a vector orthogonal to dir to act as helix direction,
+    # if not provided switch off random orientation
+    if perp is None or perp is False:
+        v1 = np.random.random_sample(3)
+        # comment in to suppress randomised base vector
+        v1 = [1,0,0]
+        v1 -= dir * (np.dot(dir, v1))
+        v1 /= np.sqrt(sum(v1*v1))
+    else:
+        v1 = perp;
+
+    # generate rotational matrix representing the overall rotation of the helix
+    R0 = get_rotation_matrix(dir, rot)
+	    
+    # rotation matrix corresponding to one step along the helix
+    R = get_rotation_matrix(dir, [1, "bp"],bp)
+
+    # set the vector a1 (backbone to base) to v1 
+    a1 = v1
+    
+    # apply the global rotation to a1 
+    a1 = np.dot(R0, a1)
+    
+    # set the position of the fist backbone site to start_pos
+    rb = np.array(start_pos)
+	    
+    # set a3 to the direction of the helix
+    a3 = dir
+
+    for i in range(bp):
+    # work out the position of the centre of mass of the nucleotide
+        rcom = rb - COM_CENTRE_DS * a1
+
+        # append to newpositions
+        mynewpositions.append(rcom)
+        mynewa1s.append(a1)
+        mynewa3s.append(a3)
+
+        # if we are not at the end of the helix, we work out a1 and rb for the 
+        # next nucleotide along the helix
+        if i != bp - 1:
+            a1 = np.dot(R, a1)
+            rb += a3 * BASE_BASE
+
+    # if we are working on a double strand, we do a cycle similar 
+    # to the previous one but backwards
+    if double == True:
+        a1 = -a1
+        a3 = -dir
+        R = R.transpose()
+        for i in range(bp):
+            rcom = rb - COM_CENTRE_DS * a1
+            mynewpositions.append (rcom)
+            mynewa1s.append (a1)
+            mynewa3s.append (a3)
+            a1 = np.dot(R, a1)
+            rb += a3 * BASE_BASE
+    
+  
+    #Calculate the positions of the bead wall
+    
+    last_base1 = mynewpositions[int( len(mynewpositions)/2 - 1) ]
+    last_base2 = mynewpositions[int( len(mynewpositions)/2) ]
+    mid_point =  (last_base1 + last_base2) / 2 
+    
+    NN = N_BEADS**2
+    p1 = [mid_point[0] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[1] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[2] + BEAD_OFFSET ]
+    for i in range(N_BEADS):
+        for j in range(N_BEADS):
+            position = [ p1[0] + 2*i*WALL_PARTICLE_SIZE, p1[1] + 2*j*WALL_PARTICLE_SIZE, p1[2]]
+            mynewa1s.append([1,0,0])
+            mynewa3s.append([1,0,0])
+            mynewpositions.append(position)
+
+    assert (len (mynewpositions) > 0)
+
+    return [mynewpositions, mynewa1s, mynewa3s]
+
+
+
+"""
+Main function for this script.
+Reads a text file with the following format:
+- Each line contains the sequence for a single strand (A,C,G,T)
+- Lines beginning with the keyword 'DOUBLE' produce double-stranded DNA
+
+Ex: Two ssDNA (single stranded DNA)
+ATATATA
+GCGCGCG
+
+Ex: Two strands, one double stranded, the other single stranded.
+DOUBLE AGGGCT
+CCTGTA
+
+"""
+
+def read_strands(filename):
+    try:
+        infile = open (filename)
+    except:
+        print("Could not open file '%s'. Aborting." % filename, file=sys.stderr)
+        sys.exit(2)
+
+    # This block works out the number of nucleotides and strands by reading 
+    # the number of non-empty lines in the input file and the number of letters,
+    # taking the possible DOUBLE keyword into account.
+    nstrands, nnucl, nbonds = 0, 0, 0
+    lines = infile.readlines()
+    for line in lines:
+        line = line.upper().strip()
+        if len(line) == 0:
+            continue
+        if line[:6] == 'DOUBLE':
+            line = line.split()[1]
+            length = len(line)
+            print("## Found duplex of %i base pairs" % length, file=sys.stdout)
+            nnucl += 2*length
+            nstrands += 2
+            nbonds+= 2*length
+            
+        else:
+            line = line.split()[0]
+            length = len(line)
+            print("## Found single strand of %i bases" % length, file=sys.stdout)
+            nnucl += length
+            nstrands += 1
+            if topo == 'ring':
+                nbonds =+ length
+            else:
+                nbonds += length+1
+    # rewind the sequence input file
+    infile.seek(0)
+
+    print("## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
+
+    # generate the data file in LAMMPS format
+    try:
+        out = open ("data.oxdna", "w")
+    except:
+        print("Could not open data file for writing. Aborting.", file=sys.stderr)
+        sys.exit(2)
+	
+    lines = infile.readlines()
+    nlines = len(lines)
+    i = 1
+    myns = 0
+    noffset = 1
+
+    for line in lines:
+        line = line.upper().strip()
+
+        # skip empty lines
+        if len(line) == 0: 
+            i += 1
+            continue
+
+	# block for duplexes: last argument of the generate function 
+	# is set to 'True'
+        if line[:6] == 'DOUBLE':
+            line = line.split()[1]
+            length = len(line)
+            seq = [(base_to_number[x]) for x in line]
+            seq = np.array(seq,dtype=int)
+            n_a, n_c, n_g, n_t = 0, 0, 0, 0
+            for s in range(seq.size):
+                if seq[s] == 1:
+                    n_a += 1
+                elif seq[s] == 2:
+                    n_c += 1
+                elif seq[s] ==3:
+                    n_g += 1
+                elif seq[s] == 4:
+                    n_t += 1
+            smallest_n_bases = n_c
+            if n_a < n_c:
+                smallest_n_bases = n_a
+            if smallest_n_bases > n_t:
+                smallest_n_bases = n_t
+            if smallest_n_bases > n_g:
+                smallest_n_bases = n_g
+             
+            if smallest_n_bases < N_BASE_TYPES:
+                print('## Not enough occurances of base types in the sequence for ' + str(N_BASE_TYPES))
+                print('## unique base types, switching to ' + str(smallest_n_bases) + ' unique types')
+            else:
+                smallest_n_bases = N_BASE_TYPES
+           
+            a, c, g, t = -3, -2, -1, 0
+            for s in range(seq.size):
+                if seq[s] == 1: 
+                    if a < (smallest_n_bases*4-3):
+                        a += 4
+                    else:
+                        a = 1
+                    seq[s] = a
+                
+                elif seq[s] == 2: 
+                    if c < (smallest_n_bases*4-2):
+                        c += 4
+                    else:
+                        c = 2
+                    seq[s] = c
+
+                elif seq[s] == 3:
+                    if g < (smallest_n_bases*4-1):
+                        g += 4
+                    else:
+                        g = 3
+                    seq[s] = g
+                elif seq[s] == 4:
+                    if t < (smallest_n_bases*4):
+                        t += 4
+                    else:
+                        t = 4
+                    seq[s] = t
+                
+
+
+            myns += 1
+
+            for b in range(length):
+                basetype.append(seq[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+     
+            
+            noffset += length 
+
+            # create the sequence of the second strand as made of 
+            # complementary bases
+            #seq2 = [5-s for s in seq]
+            seq2 = seq
+            for s in range(seq2.size):
+                if seq2[s]%4 == 1:
+                    seq2[s] += 3
+                elif seq2[s]%4 == 2:
+                    seq2[s] += 1
+                elif seq2[s]%4 == 3:
+                    seq2[s] -= 1
+                elif seq2[s]%4 == 0:
+                    seq2[s] -= 3    
+
+            #seq2.reverse()
+
+            myns += 1
+
+            for b in range(length):
+                basetype.append(seq2[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+
+                     
+            #create wall bead types
+            bead_type = 4*smallest_n_bases + 1
+            for i in range(N_BEADS**2):
+                
+                basetype.append(bead_type)
+                basetype.append(bead_type)
+                strandnum.append(bead_type)
+                strandnum.append(bead_type)
+            #bonds.append([length, noffset + length])
+            #bonds.append([length+1, noffset + length])
+
+            noffset += length
+
+            print("## Created duplex of %i bases" % (2*length), file=sys.stdout)
+
+            # generate random position of the first nucleotide
+            com = box_offset + np.random.random_sample(3) * box
+            # comment out to randomise
+            com = [0,0,0]
+
+            # generate the random direction of the helix 
+            axis = np.random.random_sample(3)
+            # comment out to randomise
+            axis = [0,0,1]
+            axis /= np.sqrt(np.dot(axis, axis))
+
+            # use the generate function defined above to create 
+            # the position and orientation vector of the strand
+            if topo == 'ring':
+                newpositions, newa1s, newa3s = generate_ring(len(line), \
+                      sequence=seq, dir=axis, start_pos=com, double=True)
+            else:
+                newpositions, newa1s, newa3s = generate_strand(len(line), \
+                    sequence=seq, dir=axis, start_pos=com, double=True)
+
+            # generate a new position for the strand until it does not overlap
+            # with anything already present
+            start = timer()
+            while not add_strands(newpositions, newa1s, newa3s):
+                com = box_offset + np.random.random_sample(3) * box
+                axis = np.random.random_sample(3)
+                axis /= np.sqrt(np.dot(axis, axis))
+                if topo == 'ring':
+                    newpositions, newa1s, newa3s = generate_ring(len(line), \
+                        sequence=seq, dir=axis, start_pos=com, double=True)
+                else:
+                    newpositions, newa1s, newa3s = generate_strand(len(line), \
+                        sequence=seq, dir=axis, start_pos=com, double=True)
+                print("## Trying %i" % i, file=sys.stdout)
+            end = timer()
+            print("## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
+                          (2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
+
+	# block for single strands: last argument of the generate function 
+	# is set to 'False'
+        else:
+            length = len(line)
+            seq = [(base_to_number[x]) for x in line]
+
+            myns += 1
+            for b in range(length):
+                basetype.append(seq[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+            if topo == 'ring':    
+                bondpair = [noffset, noffset + length-1]
+                bonds.append(bondpair)
+            noffset += length
+            
+
+	    # generate random position of the first nucleotide
+            com = box_offset + np.random.random_sample(3) * box
+            # comment out to randomise
+            com = [-30,0,0]
+
+            # generate the random direction of the helix 
+            axis = np.random.random_sample(3)
+            # comment out to randomise
+            axis = [0,0,1]
+            axis /= np.sqrt(np.dot(axis, axis))
+
+            print("## Created single strand of %i bases" % length, file=sys.stdout)
+            if topo == 'ring':    
+                newpositions, newa1s, newa3s = generate_ring(length, \
+		              sequence=seq, dir=axis, start_pos=com, double=False)
+            else:
+                newpositions, newa1s, newa3s = generate_strand(length, \
+		               sequence=seq, dir=axis, start_pos=com, double=False)
+            start = timer()
+            while not add_strands(newpositions, newa1s, newa3s):
+                com = box_offset + np.random.random_sample(3) * box
+                axis = np.random.random_sample(3)
+                axis /= np.sqrt(np.dot(axis, axis))
+                if topo == 'ring':
+                    newpositions, newa1s, newa3s = generate_ring(length, \
+                          sequence=seq, dir=axis, start_pos=com, double=False)
+
+                else:    
+                    newpositions, newa1s, newa3s = generate_strand(length, \
+                          sequence=seq, dir=axis, start_pos=com, double=False)
+                print("## Trying  %i" % (i), file=sys.stdout)
+            end = timer()
+            print("## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
+				      (length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
+
+        i += 1
+
+    # sanity check
+    #if not len(positions) == nnucl:
+    #    print(len(positions), nnucl)
+    #    raise AssertionError
+    nnucl = nnucl + (N_BEADS**2)
+    nbonds -= 4
+	
+    out.write('# LAMMPS data file\n')
+    out.write('%d atoms\n' % nnucl)
+    out.write('%d ellipsoids\n' % nnucl)
+    out.write('%d bonds\n' % nbonds)
+    out.write('\n')
+    out.write('%d atom types\n' %bead_type )
+    out.write('1 bond types\n')
+    out.write('\n')
+    out.write('# System size\n')
+    out.write('%f %f xlo xhi\n' % (box_offset,box_offset+box_length))
+    out.write('%f %f ylo yhi\n' % (box_offset,box_offset+box_length))
+    out.write('%f %f zlo zhi\n' % (0,box_length))
+
+    #out.write('\n')
+    #out.write('Masses\n')
+    #out.write('\n')
+    #out.write('1 3.1575\n')
+    #out.write('2 3.1575\n')
+    #out.write('3 3.1575\n')
+    #out.write('4 3.1575\n')
+    #out.write('5 3.1575\n')
+
+    # for each nucleotide print a line under the headers
+    # Atoms, Velocities, Ellipsoids and Bonds
+    out.write('\n')
+    out.write(\
+      '# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
+    out.write('Atoms\n')
+    out.write('\n')
+    
+    for i in range(nnucl):
+        out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
+                  % (i+1, basetype[i], \
+                     positions[i][0], positions[i][1], positions[i][2], \
+                     strandnum[i]))
+
+    out.write('\n')
+    out.write('# Atom-ID, translational, rotational velocity\n')
+    out.write('Velocities\n')
+    out.write('\n')
+
+    for i in range(nnucl):
+        out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
+                  % (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
+
+    out.write('\n')
+    out.write('# Atom-ID, shape, quaternion\n')
+    out.write('Ellipsoids\n')
+    out.write('\n')
+
+    for i in range(nnucl):
+        out.write(\
+    "%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n"  \
+      % (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
+	quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
+ 
+    out.write('\n')
+    out.write('# Bond topology\n')
+    out.write('Bonds\n')
+    out.write('\n')
+
+    for i in range(nbonds):
+        if i < nbonds-2:
+             out.write("%d  %d  %d  %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
+        #else:
+        
+        #out.write("%d  %d  %d  %d\n" % (i+1,2,bonds[i][0],bonds[i][1]))
+
+    out.close()
+
+    print("## Wrote data to 'data.oxdna'", file=sys.stdout)
+    print("## DONE", file=sys.stdout)
+
+# call the above main() function, which executes the program
+read_strands (infile)
+
+end_time=timer()
+runtime = end_time-start_time
+hours = runtime/3600
+minutes = (runtime-np.rint(hours)*3600)/60
+seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
+print("## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type
new file mode 100644
index 0000000000..0570cf042d
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type
@@ -0,0 +1,94 @@
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 4
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin 
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.4type
+mass * 3.1575
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene 
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype} 
+  variable basemod equal ${base}%4
+  if "${basemod} == 1" then &
+    "variable comp equal ${base}+3" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then &
+    "variable comp equal ${base}+1" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz 
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+
+#write_restart config.${number}.*
+
+
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type
new file mode 100644
index 0000000000..dae853a113
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type
@@ -0,0 +1,94 @@
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 8
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin 
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.8type
+mass * 3.1575
+
+group all type 1 8
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene 
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype} 
+  variable basemod equal ${base}%4
+  if "${basemod} == 1" then &
+    "variable comp equal ${base}+3" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then &
+    "variable comp equal ${base}+1" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz 
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+
+#write_restart config.${number}.*
+
+
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1
new file mode 100644
index 0000000000..d0195dd8e8
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1
@@ -0,0 +1,232 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 4
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.4type
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  26 atoms
+  reading velocities ...
+  26 velocities
+  26 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  24 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 6.2e-05 secs
+  read_data CPU = 0.001124 secs
+mass * 3.1575
+
+group all type 1 4
+26 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 1%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 1+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 2%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 2+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 3%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 4%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 10000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.63899
+  ghost atom cutoff = 5.63899
+  binsize = 2.81949, bins = 15 15 15
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.89 | 3.89 | 3.89 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
+10000  ekin = 1.01296379553452 |  erot = 1.38476360245491 | epot = -41.9785360036035 | etot = -39.5808086056141
+20000  ekin = 1.75607695499755 |  erot = 1.86620102096623 | epot = -41.9558496477913 | etot = -38.3335716718275
+30000  ekin = 2.25878673688255 |  erot = 2.60035907744906 | epot = -41.2869827431736 | etot = -36.427836928842
+40000  ekin = 2.11105717434601 |  erot = 3.16611217122795 | epot = -40.2762731426449 | etot = -34.999103797071
+50000  ekin = 3.05379083545185 |  erot = 2.45050275456902 | epot = -40.3032957287999 | etot = -34.799002138779
+60000  ekin = 3.05154113920288 |  erot = 2.52539576708931 | epot = -39.6800099891302 | etot = -34.103073082838
+70000  ekin = 3.23212209366503 |  erot = 3.28914763888578 | epot = -40.1240667487288 | etot = -33.602797016178
+80000  ekin = 2.82623224207568 |  erot = 2.91292948677805 | epot = -39.0983962904507 | etot = -33.3592345615969
+90000  ekin = 3.05995314905566 |  erot = 3.5429982411034 | epot = -39.1646070343971 | etot = -32.561655644238
+100000  ekin = 3.46139546969836 |  erot = 4.11704803295073 | epot = -38.5124679837256 | etot = -30.9340244810765
+  100000  0.092303879   -1.5243833  0.043134544   -1.3481182 6.862374e-06 
+Loop time of 7.99505 on 1 procs for 100000 steps with 26 atoms
+
+Performance: 108066.893 tau/day, 12507.742 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.2072     | 7.2072     | 7.2072     |   0.0 | 90.15
+Bond    | 0.14292    | 0.14292    | 0.14292    |   0.0 |  1.79
+Neigh   | 1.9e-05    | 1.9e-05    | 1.9e-05    |   0.0 |  0.00
+Comm    | 0.015676   | 0.015676   | 0.015676   |   0.0 |  0.20
+Output  | 0.001372   | 0.001372   | 0.001372   |   0.0 |  0.02
+Modify  | 0.61071    | 0.61071    | 0.61071    |   0.0 |  7.64
+Other   |            | 0.01714    |            |       |  0.21
+
+Nlocal:    26 ave 26 max 26 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    325 ave 325 max 325 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 325
+Ave neighs/atom = 12.5
+Ave special neighs/atom = 5.07692
+Neighbor list builds = 1
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+
+
+Total wall time: 0:00:07
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4
new file mode 100644
index 0000000000..a5647ccd77
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4
@@ -0,0 +1,232 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 4
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.4type
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  26 atoms
+  reading velocities ...
+  26 velocities
+  26 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  24 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000173 secs
+  read_data CPU = 0.00242 secs
+mass * 3.1575
+
+group all type 1 4
+26 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 1%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 1+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 2%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 2+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 3%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 4%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 10000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.63899
+  ghost atom cutoff = 5.63899
+  binsize = 2.81949, bins = 15 15 15
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.499 | 9.682 | 9.864 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
+10000  ekin = 1.20524984175817 |  erot = 1.2679122962101 | epot = -41.9183873815797 | etot = -39.4452252436114
+20000  ekin = 1.60856540355485 |  erot = 2.64140880508964 | epot = -41.0106168994545 | etot = -36.76064269081
+30000  ekin = 2.821101638199 |  erot = 3.06373823252434 | epot = -40.9348041675027 | etot = -35.0499642967793
+40000  ekin = 2.36296917392486 |  erot = 3.53353555114673 | epot = -39.5591676362755 | etot = -33.6626629112039
+50000  ekin = 2.93383938780818 |  erot = 3.39920211088179 | epot = -40.3602175538497 | etot = -34.0271760551597
+60000  ekin = 2.42811021532829 |  erot = 2.75130045540831 | epot = -39.3178531324554 | etot = -34.1384424617188
+70000  ekin = 2.7282200818863 |  erot = 3.76502037022117 | epot = -40.5673105068195 | etot = -34.074070054712
+80000  ekin = 2.90877851656705 |  erot = 2.43617899356904 | epot = -38.4099618426175 | etot = -33.0650043324814
+90000  ekin = 3.89203816080263 |  erot = 2.67194811393274 | epot = -39.1880466354802 | etot = -32.6240603607448
+100000  ekin = 3.98445325397832 |  erot = 2.77079124049636 | epot = -39.2805505658488 | etot = -32.5253060713741
+  100000   0.10625209   -1.5603519  0.049561514   -1.3575422 -1.7755557e-05 
+Loop time of 7.14827 on 4 procs for 100000 steps with 26 atoms
+
+Performance: 120868.376 tau/day, 13989.395 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.047776   | 3.0726     | 6.3143     | 172.8 | 42.98
+Bond    | 0.00736    | 0.056846   | 0.10864    |  20.7 |  0.80
+Neigh   | 1.9e-05    | 1.9e-05    | 1.9e-05    |   0.0 |  0.00
+Comm    | 0.30925    | 3.451      | 6.3739     | 157.5 | 48.28
+Output  | 0.000896   | 0.0010197  | 0.001301   |   0.5 |  0.01
+Modify  | 0.015512   | 0.18417    | 0.37845    |  39.4 |  2.58
+Other   |            | 0.3826     |            |       |  5.35
+
+Nlocal:    6.5 ave 13 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    19.5 ave 26 max 13 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    123.5 ave 247 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 494
+Ave neighs/atom = 19
+Ave special neighs/atom = 5.07692
+Neighbor list builds = 1
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+
+
+Total wall time: 0:00:07
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1
new file mode 100644
index 0000000000..c93943a4c7
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1
@@ -0,0 +1,274 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 8
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.8type
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  26 atoms
+  reading velocities ...
+  26 velocities
+  26 ellipsoids
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  24 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 6.5e-05 secs
+  read_data CPU = 0.001139 secs
+mass * 3.1575
+
+group all type 1 8
+26 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 1%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 1+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 2%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 2+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 3%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 4%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 5%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 5+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 5 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 5 8 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 6%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 6+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 6 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 6 7 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 7%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 8%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 10000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.63899
+  ghost atom cutoff = 4.63899
+  binsize = 2.31949, bins = 18 18 18
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.905 | 3.905 | 3.905 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
+10000  ekin = 1.0129637955345 |  erot = 1.38476360245492 | epot = -41.9785360036034 | etot = -39.580808605614
+20000  ekin = 1.75607695499755 |  erot = 1.86620102096618 | epot = -41.9558496477911 | etot = -38.3335716718274
+30000  ekin = 2.25878673688259 |  erot = 2.60035907744898 | epot = -41.2869827431736 | etot = -36.427836928842
+40000  ekin = 2.11105717434584 |  erot = 3.16611217122799 | epot = -40.2762731426449 | etot = -34.9991037970711
+50000  ekin = 3.05379083545187 |  erot = 2.45050275456888 | epot = -40.3032957287998 | etot = -34.7990021387791
+60000  ekin = 3.05154113920291 |  erot = 2.5253957670889 | epot = -39.6800099891299 | etot = -34.1030730828381
+70000  ekin = 3.23212209366464 |  erot = 3.28914763888543 | epot = -40.1240667487278 | etot = -33.6027970161777
+80000  ekin = 2.82623224207591 |  erot = 2.91292948677732 | epot = -39.0983962904496 | etot = -33.3592345615963
+90000  ekin = 3.05995314905694 |  erot = 3.54299824110274 | epot = -39.164607034397 | etot = -32.5616556442373
+100000  ekin = 3.46139546969892 |  erot = 4.11704803295143 | epot = -38.512467983727 | etot = -30.9340244810767
+  100000  0.092303879   -1.5243833  0.043134544   -1.3481182 6.862374e-06 
+Loop time of 7.94086 on 1 procs for 100000 steps with 26 atoms
+
+Performance: 108804.336 tau/day, 12593.094 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.1507     | 7.1507     | 7.1507     |   0.0 | 90.05
+Bond    | 0.14487    | 0.14487    | 0.14487    |   0.0 |  1.82
+Neigh   | 6.4e-05    | 6.4e-05    | 6.4e-05    |   0.0 |  0.00
+Comm    | 0.032259   | 0.032259   | 0.032259   |   0.0 |  0.41
+Output  | 0.003484   | 0.003484   | 0.003484   |   0.0 |  0.04
+Modify  | 0.59013    | 0.59013    | 0.59013    |   0.0 |  7.43
+Other   |            | 0.01934    |            |       |  0.24
+
+Nlocal:    26 ave 26 max 26 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    323 ave 323 max 323 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 323
+Ave neighs/atom = 12.4231
+Ave special neighs/atom = 5.07692
+Neighbor list builds = 4
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+
+
+Total wall time: 0:00:07
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4
new file mode 100644
index 0000000000..5cda079e9c
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4
@@ -0,0 +1,274 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 8
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.8type
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  26 atoms
+  reading velocities ...
+  26 velocities
+  26 ellipsoids
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  24 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000232 secs
+  read_data CPU = 0.002447 secs
+mass * 3.1575
+
+group all type 1 8
+26 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 1%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 1+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 2%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 2+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 3%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 4%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 5%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 5+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 5 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 5 8 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 6%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 6+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 6 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 6 7 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 7%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 8%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 10000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.63899
+  ghost atom cutoff = 4.63899
+  binsize = 2.31949, bins = 18 18 18
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.381 | 9.563 | 9.746 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
+10000  ekin = 1.20524984175816 |  erot = 1.26791229621008 | epot = -41.9183873815797 | etot = -39.4452252436115
+20000  ekin = 1.6085654035548 |  erot = 2.6414088050897 | epot = -41.0106168994546 | etot = -36.7606426908101
+30000  ekin = 2.82110163819891 |  erot = 3.06373823252419 | epot = -40.9348041675026 | etot = -35.0499642967795
+40000  ekin = 2.35553603700794 |  erot = 3.60405945883761 | epot = -39.5418687902286 | etot = -33.5822732943831
+50000  ekin = 3.06061403125833 |  erot = 3.35548669087246 | epot = -40.3236585928169 | etot = -33.9075578706861
+60000  ekin = 2.7347216991605 |  erot = 4.23926242244084 | epot = -39.5379959923263 | etot = -32.564011870725
+70000  ekin = 3.46562604991873 |  erot = 2.8521307045909 | epot = -38.7237000550356 | etot = -32.4059433005259
+80000  ekin = 3.17815543267806 |  erot = 3.11078099027451 | epot = -39.7525036398366 | etot = -33.463567216884
+90000  ekin = 3.51635117668857 |  erot = 2.58384069017333 | epot = -39.4762533092413 | etot = -33.3760614423795
+100000  ekin = 3.64218174280962 |  erot = 2.88607181210736 | epot = -37.6002449519119 | etot = -31.0719913969949
+  100000  0.097124846   -1.5164679  0.070304678   -1.3060794 -2.9111933e-05 
+Loop time of 5.64462 on 4 procs for 100000 steps with 26 atoms
+
+Performance: 153066.031 tau/day, 17715.976 timesteps/s
+99.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.069668   | 2.1601     | 4.2189     | 138.7 | 38.27
+Bond    | 0.008542   | 0.052544   | 0.095929   |  18.7 |  0.93
+Neigh   | 4.8e-05    | 5.6e-05    | 6.4e-05    |   0.0 |  0.00
+Comm    | 0.90402    | 3.1443     | 5.4155     | 124.9 | 55.70
+Output  | 0.001003   | 0.0011317  | 0.001468   |   0.6 |  0.02
+Modify  | 0.021098   | 0.20024    | 0.38154    |  39.2 |  3.55
+Other   |            | 0.0863     |            |       |  1.53
+
+Nlocal:    6.5 ave 13 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    17.5 ave 22 max 13 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    80.25 ave 167 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 321
+Ave neighs/atom = 12.3462
+Ave special neighs/atom = 5.07692
+Neighbor list builds = 3
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+
+
+Total wall time: 0:00:05

From 0346a3d6d189642a569741d06630835a4feb3c58 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Fri, 15 Nov 2019 10:53:39 -0700
Subject: [PATCH 030/199] Commit JT 111519 - add README file to the benchmark
 examples repo - removed comments from src/SPIN files

---
 examples/SPIN/README                          |    16 +-
 examples/SPIN/benchmark/README                |    47 +
 .../benchmarck_damped_exchange/res_lammps.dat |  3001 --
 .../benchmarck_damped_exchange/res_llg.dat    | 30000 ----------------
 .../bench-spin-precession.in                  |     5 +-
 .../llg_precession.py                         |     5 +-
 .../plot_precession.py                        |    16 +-
 .../bench-exchange-spin.template              |    41 -
 .../langevin-exchange.py                      |    34 -
 .../plot_exchange.py                          |    34 -
 .../run-bench-exchange.sh                     |    28 -
 .../bench-prec-spin.template                  |     4 +-
 .../run-bench-prec.sh                         |     6 +-
 src/SPIN/compute_spin.cpp                     |     2 -
 src/SPIN/fix_precession_spin.cpp              |    20 +-
 src/SPIN/pair_spin_exchange.cpp               |     6 -
 16 files changed, 86 insertions(+), 33179 deletions(-)
 create mode 100644 examples/SPIN/benchmark/README
 delete mode 100644 examples/SPIN/benchmark/benchmarck_damped_exchange/res_lammps.dat
 delete mode 100644 examples/SPIN/benchmark/benchmarck_damped_exchange/res_llg.dat
 delete mode 100644 examples/SPIN/benchmark/benchmarck_langevin_exchange/bench-exchange-spin.template
 delete mode 100755 examples/SPIN/benchmark/benchmarck_langevin_exchange/langevin-exchange.py
 delete mode 100755 examples/SPIN/benchmark/benchmarck_langevin_exchange/plot_exchange.py
 delete mode 100755 examples/SPIN/benchmark/benchmarck_langevin_exchange/run-bench-exchange.sh

diff --git a/examples/SPIN/README b/examples/SPIN/README
index 5ad252e7f2..affb1237f8 100644
--- a/examples/SPIN/README
+++ b/examples/SPIN/README
@@ -1,20 +1,24 @@
 This directory contains examples and applications of the SPIN package
 =====================================================================
 
+- the benchmark directory provides comparison between LAMMPS
+  results and a series of simple test problems (coded as python
+  scripts).
+
 - the iron, cobalt_hcp, cobalt_fcc and nickel directories provide 
-examples of spin-lattice calculations.
+  examples of spin-lattice calculations.
 
 - the bfo repository provides an example of spin dynamics calculation
-performed on a fixed lattice, and applied to the multiferroic 
-material bismuth-oxide. 
+  performed on a fixed lattice, and applied to the multiferroic 
+  material bismuth-oxide. 
 
 - the read_restart directory provides examples allowing to write or 
-read data files, and restart magneto-mechanical simulations.  
+  read data files, and restart magneto-mechanical simulations.  
 
 - vizualization of the dump files can be achieved using Ovito or 
-VMD. See the vmd repository for help vizualizing results with VMD. 
+  VMD. See the vmd repository for help vizualizing results with VMD. 
 
 ** Note, the aim of this repository is mainly to provide users with
 examples. Better values and tuning of the magnetic and mechanical 
-interactions can be achieved for more accurate materials 
+interactions can (have to...) be achieved for more accurate materials 
 simulations. **
diff --git a/examples/SPIN/benchmark/README b/examples/SPIN/benchmark/README
new file mode 100644
index 0000000000..5557e3d42b
--- /dev/null
+++ b/examples/SPIN/benchmark/README
@@ -0,0 +1,47 @@
+** The objective of the benchmark examples in this directory 
+   is the following twofold: 
+- verify the implementation of the LAMMPS' SPIN package by 
+  comparing its results to well-known analytic results, or 
+  to simple test problems,
+- provide users with simple comparisons, allowing them to 
+  better understand what is implemented in the code.
+
+The LAMMPS input file (bench-*) can be modified, as well as the
+associated python script, in order to try different comparisons.
+
+All scripts can be run by executing the shell script from its
+directory. Example:
+./run-bench-exchange.sh from the benchmarck_damped_exchange/
+directory. 
+
+** Below a brief description of the different benchmark 
+   problems:
+
+- benchmarck_damped_precession:
+  simulates the damped precession of a single spin in a magnetic
+  field. 
+  Run as: ./run-bench-prec.sh
+  Output: x, y and z components of the magnetization, and
+  magnetic energy.
+
+- benchmarck_damped_exchange:
+  simulates two spins interacting through the exchange
+  interaction. The parameters in the LAMMPS input script
+  (bench-spin-precession.in) are calibrated to match the
+  exchange definition in the python script (llg_exchange.py). 
+  Run as: ./run-bench-exchange.sh
+  Output: average magnetization resulting from the damped 
+  precession of the two interacting spins. Also plots the 
+  evolution of the magnetic energy.
+  
+- benchmarck_langevin_precession:
+  simulates a single spin in a magnetic field and in contact
+  with a thermal bath, and compares the statistical averages of 
+  the output to the analytical result of the Langevin function. 
+  Run as: ./run-bench-prec.sh
+  Output: statistical average of the z-component of the
+  magnetization (along the applied field) and of the magnetic
+  energy versus temperature. Comparison to the Langevin function
+  results (computed by the python script).
+  Note: This example is a reworked version of a test problem 
+  provided by Martin Kroger (ETHZ).  
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/res_lammps.dat b/examples/SPIN/benchmark/benchmarck_damped_exchange/res_lammps.dat
deleted file mode 100644
index aa331f50ea..0000000000
--- a/examples/SPIN/benchmark/benchmarck_damped_exchange/res_lammps.dat
+++ /dev/null
@@ -1,3001 +0,0 @@
-       0            0          0.5          0.5            0            0            0            0 
-      10        0.001   0.50037967   0.50037966 6.8386474e-08 -0.00015191886 -0.00015191886 -0.00015191886 
-      20        0.002   0.50075905   0.50075902 1.3603286e-07 -0.00030383701 -0.00030383701 -0.00030383701 
-      30        0.003   0.50113814   0.50113809 2.0215189e-07 -0.00045575377 -0.00045575377 -0.00045575377 
-      40        0.004   0.50151695   0.50151686 2.6596985e-07 -0.00060766842 -0.00060766842 -0.00060766842 
-      50        0.005   0.50189547   0.50189534 3.2673578e-07 -0.00075958028 -0.00075958028 -0.00075958028 
-      60        0.006    0.5022737   0.50227351 3.8373034e-07 -0.00091148862 -0.00091148862 -0.00091148862 
-      70        0.007   0.50265165   0.50265139 4.3627448e-07 -0.0010633928 -0.0010633928 -0.0010633928 
-      80        0.008   0.50302929   0.50302897 4.8373764e-07 -0.001215292 -0.001215292 -0.001215292 
-      90        0.009   0.50340665   0.50340624 5.2554551e-07 -0.0013671856 -0.0013671856 -0.0013671856 
-     100         0.01   0.50378371   0.50378322 5.6118711e-07 -0.001519073 -0.001519073 -0.001519073 
-     110        0.011   0.50416047   0.50415989 5.9022131e-07 -0.0016709533 -0.0016709533 -0.0016709533 
-     120        0.012   0.50453694   0.50453626 6.1228239e-07 -0.0018228259 -0.0018228259 -0.0018228259 
-     130        0.013    0.5049131   0.50491233 6.2708498e-07 -0.0019746901 -0.0019746901 -0.0019746901 
-     140        0.014   0.50528896   0.50528809 6.3442788e-07 -0.0021265452 -0.0021265452 -0.0021265452 
-     150        0.015   0.50566452   0.50566355 6.3419702e-07 -0.0022783904 -0.0022783904 -0.0022783904 
-     160        0.016   0.50603978   0.50603871 6.2636743e-07 -0.0024302252 -0.0024302252 -0.0024302252 
-     170        0.017   0.50641473   0.50641356 6.1100409e-07 -0.0025820488 -0.0025820488 -0.0025820488 
-     180        0.018   0.50678937   0.50678811 5.8826175e-07 -0.0027338604 -0.0027338604 -0.0027338604 
-     190        0.019    0.5071637   0.50716235 5.5838372e-07 -0.0028856595 -0.0028856595 -0.0028856595 
-     200         0.02   0.50753772   0.50753628 5.2169947e-07 -0.0030374452 -0.0030374452 -0.0030374452 
-     210        0.021   0.50791142   0.50790991 4.7862136e-07 -0.0031892169 -0.0031892169 -0.0031892169 
-     220        0.022   0.50828482   0.50828322 4.2964016e-07 -0.0033409739 -0.0033409739 -0.0033409739 
-     230        0.023   0.50865789   0.50865624 3.7531975e-07 -0.0034927156 -0.0034927156 -0.0034927156 
-     240        0.024   0.50903065   0.50902894 3.1629077e-07 -0.0036444411 -0.0036444411 -0.0036444411 
-     250        0.025   0.50940309   0.50940133 2.5324353e-07 -0.0037961498 -0.0037961498 -0.0037961498 
-     260        0.026   0.50977521   0.50977342 1.8692008e-07 -0.003947841 -0.003947841 -0.003947841 
-     270        0.027   0.51014701   0.51014519 1.1810555e-07 -0.0040995141 -0.0040995141 -0.0040995141 
-     280        0.028   0.51051849   0.51051665 4.7619044e-08 -0.0042511682 -0.0042511682 -0.0042511682 
-     290        0.029   0.51088964    0.5108878 -2.3696119e-08 -0.0044028027 -0.0044028027 -0.0044028027 
-     300         0.03   0.51126047   0.51125863 -9.4982408e-08 -0.004554417 -0.004554417 -0.004554417 
-     310        0.031   0.51163097   0.51162915 -1.653784e-07 -0.0047060103 -0.0047060103 -0.0047060103 
-     320        0.032   0.51200115   0.51199936 -2.3402922e-07 -0.0048575819 -0.0048575819 -0.0048575819 
-     330        0.033     0.512371   0.51236925 -3.0009692e-07 -0.0050091312 -0.0050091312 -0.0050091312 
-     340        0.034   0.51274052   0.51273882 -3.6277088e-07 -0.0051606574 -0.0051606574 -0.0051606574 
-     350        0.035   0.51310971   0.51310807 -4.2127775e-07 -0.0053121598 -0.0053121598 -0.0053121598 
-     360        0.036   0.51347857     0.513477 -4.7489123e-07 -0.0054636378 -0.0054636378 -0.0054636378 
-     370        0.037   0.51384711   0.51384561 -5.2294115e-07 -0.0056150906 -0.0056150906 -0.0056150906 
-     380        0.038   0.51421531   0.51421389 -5.6482212e-07 -0.0057665177 -0.0057665177 -0.0057665177 
-     390        0.039   0.51458318   0.51458185 -6.0000127e-07 -0.0059179181 -0.0059179181 -0.0059179181 
-     400         0.04   0.51495072   0.51494949 -6.2802531e-07 -0.0060692914 -0.0060692914 -0.0060692914 
-     410        0.041   0.51531793   0.51531679 -6.4852657e-07 -0.0062206367 -0.0062206367 -0.0062206367 
-     420        0.042   0.51568481   0.51568377 -6.6122807e-07 -0.0063719535 -0.0063719535 -0.0063719535 
-     430        0.043   0.51605135   0.51605041 -6.659475e-07 -0.0065232409 -0.0065232409 -0.0065232409 
-     440        0.044   0.51641756   0.51641673 -6.6260004e-07 -0.0066744984 -0.0066744984 -0.0066744984 
-     450        0.045   0.51678344   0.51678271 -6.5120005e-07 -0.0068257252 -0.0068257252 -0.0068257252 
-     460        0.046   0.51714898   0.51714835 -6.3186146e-07 -0.0069769206 -0.0069769206 -0.0069769206 
-     470        0.047   0.51751419   0.51751365 -6.0479702e-07 -0.007128084 -0.007128084 -0.007128084 
-     480        0.048   0.51787906   0.51787862 -5.7031623e-07 -0.0072792147 -0.0072792147 -0.0072792147 
-     490        0.049   0.51824361   0.51824324 -5.2882208e-07 -0.0074303119 -0.0074303119 -0.0074303119 
-     500         0.05   0.51860781   0.51860753 -4.8080667e-07 -0.0075813751 -0.0075813751 -0.0075813751 
-     510        0.051   0.51897168   0.51897147 -4.2684553e-07 -0.0077324034 -0.0077324034 -0.0077324034 
-     520        0.052   0.51933522   0.51933506 -3.6759103e-07 -0.0078833963 -0.0078833963 -0.0078833963 
-     530        0.053   0.51969841   0.51969831 -3.0376461e-07 -0.008034353 -0.008034353 -0.008034353 
-     540        0.054   0.52006127   0.52006121 -2.3614824e-07 -0.0081852728 -0.0081852728 -0.0081852728 
-     550        0.055    0.5204238   0.52042377 -1.6557495e-07 -0.0083361551 -0.0083361551 -0.0083361551 
-     560        0.056   0.52078598   0.52078597 -9.2918676e-08 -0.0084869992 -0.0084869992 -0.0084869992 
-     570        0.057   0.52114783   0.52114782 -1.9083552e-08 -0.0086378045 -0.0086378045 -0.0086378045 
-     580        0.058   0.52150933   0.52150932 5.5007325e-08 -0.0087885701 -0.0087885701 -0.0087885701 
-     590        0.059    0.5218705   0.52187047 1.2842339e-07 -0.0089392955 -0.0089392955 -0.0089392955 
-     600         0.06   0.52223132   0.52223127 2.0023832e-07  -0.00908998  -0.00908998  -0.00908998 
-     610        0.061    0.5225918   0.52259171 2.6954176e-07 -0.0092406228 -0.0092406228 -0.0092406228 
-     620        0.062   0.52295193   0.52295179 3.3545095e-07 -0.0093912234 -0.0093912234 -0.0093912234 
-     630        0.063   0.52331172   0.52331152 3.9712206e-07 -0.009541781 -0.009541781 -0.009541781 
-     640        0.064   0.52367116   0.52367089 4.5376114e-07 -0.0096922949 -0.0096922949 -0.0096922949 
-     650        0.065   0.52403026   0.52402991 5.046345e-07 -0.0098427645 -0.0098427645 -0.0098427645 
-     660        0.066   0.52438901   0.52438857 5.4907839e-07 -0.0099931892 -0.0099931892 -0.0099931892 
-     670        0.067    0.5247474   0.52474687 5.8650789e-07 -0.010143568 -0.010143568 -0.010143568 
-     680        0.068   0.52510544   0.52510482 6.1642481e-07 -0.010293901 -0.010293901 -0.010293901 
-     690        0.069   0.52546313   0.52546241 6.3842457e-07 -0.010444186 -0.010444186 -0.010444186 
-     700         0.07   0.52582047   0.52581964 6.5220194e-07 -0.010594424 -0.010594424 -0.010594424 
-     710        0.071   0.52617745   0.52617651 6.5755549e-07 -0.010744614 -0.010744614 -0.010744614 
-     720        0.072   0.52653407   0.52653302 6.5439079e-07 -0.010894754 -0.010894754 -0.010894754 
-     730        0.073   0.52689033   0.52688917 6.4272228e-07 -0.011044845 -0.011044845 -0.011044845 
-     740        0.074   0.52724622   0.52724497 6.2267365e-07 -0.011194886 -0.011194886 -0.011194886 
-     750        0.075   0.52760176    0.5276004 5.944769e-07 -0.011344875 -0.011344875 -0.011344875 
-     760        0.076   0.52795693   0.52795548   5.5847e-07 -0.011494813 -0.011494813 -0.011494813 
-     770        0.077   0.52831174    0.5283102 5.1509307e-07 -0.011644699 -0.011644699 -0.011644699 
-     780        0.078   0.52866618   0.52866456 4.6488335e-07 -0.011794531 -0.011794531 -0.011794531 
-     790        0.079   0.52902025   0.52901855 4.0846871e-07  -0.01194431  -0.01194431  -0.01194431 
-     800         0.08   0.52937395   0.52937219 3.465601e-07 -0.012094034 -0.012094034 -0.012094034 
-     810        0.081   0.52972728   0.52972547 2.7994273e-07 -0.012243703 -0.012243703 -0.012243703 
-     820        0.082   0.53008023   0.53007838 2.0946635e-07 -0.012393317 -0.012393317 -0.012393317 
-     830        0.083   0.53043282   0.53043093 1.3603449e-07 -0.012542874 -0.012542874 -0.012542874 
-     840        0.084   0.53078503   0.53078313 6.0593014e-08 -0.012692375 -0.012692375 -0.012692375 
-     850        0.085   0.53113686   0.53113495 -1.5881986e-08 -0.012841818 -0.012841818 -0.012841818 
-     860        0.086   0.53148832   0.53148642 -9.2396775e-08 -0.012991202 -0.012991202 -0.012991202 
-     870        0.087    0.5318394   0.53183752 -1.6795288e-07 -0.013140528 -0.013140528 -0.013140528 
-     880        0.088    0.5321901   0.53218825 -2.4156016e-07 -0.013289793 -0.013289793 -0.013289793 
-     890        0.089   0.53254043   0.53253862 -3.1224982e-07 -0.013438999 -0.013438999 -0.013438999 
-     900         0.09   0.53289037   0.53288862 -3.7908725e-07 -0.013588144 -0.013588144 -0.013588144 
-     910        0.091   0.53323994   0.53323825 -4.4118454e-07 -0.013737227 -0.013737227 -0.013737227 
-     920        0.092   0.53358913   0.53358751 -4.977124e-07 -0.013886248 -0.013886248 -0.013886248 
-     930        0.093   0.53393793    0.5339364 -5.4791141e-07 -0.014035206 -0.014035206 -0.014035206 
-     940        0.094   0.53428636   0.53428492 -5.9110247e-07   -0.0141841   -0.0141841   -0.0141841 
-     950        0.095   0.53463441   0.53463306 -6.2669617e-07 -0.014332931 -0.014332931 -0.014332931 
-     960        0.096   0.53498207   0.53498083 -6.5420112e-07 -0.014481696 -0.014481696 -0.014481696 
-     970        0.097   0.53532936   0.53532822 -6.7323096e-07 -0.014630397 -0.014630397 -0.014630397 
-     980        0.098   0.53567626   0.53567523 -6.8351008e-07 -0.014779031 -0.014779031 -0.014779031 
-     990        0.099   0.53602279   0.53602186 -6.8487786e-07 -0.014927598 -0.014927598 -0.014927598 
-    1000          0.1   0.53636893   0.53636812 -6.7729144e-07 -0.015076098 -0.015076098 -0.015076098 
-    1010        0.101   0.53671469   0.53671399 -6.6082695e-07  -0.01522453  -0.01522453  -0.01522453 
-    1020        0.102   0.53706008   0.53705947 -6.3567905e-07 -0.015372893 -0.015372893 -0.015372893 
-    1030        0.103   0.53740508   0.53740457 -6.0215905e-07 -0.015521187 -0.015521187 -0.015521187 
-    1040        0.104    0.5377497   0.53774928 -5.6069133e-07 -0.015669411 -0.015669411 -0.015669411 
-    1050        0.105   0.53809394   0.53809361 -5.1180824e-07 -0.015817565 -0.015817565 -0.015817565 
-    1060        0.106   0.53843779   0.53843754 -4.5614357e-07 -0.015965647 -0.015965647 -0.015965647 
-    1070        0.107   0.53878127   0.53878109 -3.9442456e-07 -0.016113658 -0.016113658 -0.016113658 
-    1080        0.108   0.53912436   0.53912424 -3.2746259e-07 -0.016261596 -0.016261596 -0.016261596 
-    1090        0.109   0.53946708     0.539467 -2.5614276e-07 -0.016409461 -0.016409461 -0.016409461 
-    1100         0.11   0.53980941   0.53980936 -1.8141231e-07 -0.016557252 -0.016557252 -0.016557252 
-    1110        0.111   0.54015135   0.54015133 -1.0426816e-07 -0.016704969 -0.016704969 -0.016704969 
-    1120        0.112   0.54049292   0.54049291 -2.5743734e-08 -0.016852611 -0.016852611 -0.016852611 
-    1130        0.113    0.5408341   0.54083408 5.3104867e-08 -0.017000178 -0.017000178 -0.017000178 
-    1140        0.114    0.5411749   0.54117486 1.3121303e-07 -0.017147668 -0.017147668 -0.017147668 
-    1150        0.115   0.54151531   0.54151524  2.07522e-07 -0.017295081 -0.017295081 -0.017295081 
-    1160        0.116   0.54185533   0.54185522 2.8099335e-07 -0.017442417 -0.017442417 -0.017442417 
-    1170        0.117   0.54219497   0.54219481 3.5062312e-07 -0.017589675 -0.017589675 -0.017589675 
-    1180        0.118   0.54253421   0.54253399 4.1545572e-07 -0.017736854 -0.017736854 -0.017736854 
-    1190        0.119   0.54287307   0.54287277 4.7459715e-07 -0.017883954 -0.017883954 -0.017883954 
-    1200         0.12   0.54321154   0.54321116 5.2722756e-07 -0.018030974 -0.018030974 -0.018030974 
-    1210        0.121   0.54354962   0.54354914 5.7261279e-07 -0.018177914 -0.018177914 -0.018177914 
-    1220        0.122    0.5438873   0.54388672 6.1011484e-07 -0.018324772 -0.018324772 -0.018324772 
-    1230        0.123   0.54422459   0.54422391 6.3920113e-07 -0.018471549 -0.018471549 -0.018471549 
-    1240        0.124   0.54456149   0.54456069 6.5945229e-07 -0.018618243 -0.018618243 -0.018618243 
-    1250        0.125   0.54489798   0.54489707 6.7056853e-07 -0.018764854 -0.018764854 -0.018764854 
-    1260        0.126   0.54523408   0.54523306 6.723743e-07 -0.018911382 -0.018911382 -0.018911382 
-    1270        0.127   0.54556978   0.54556864 6.6482138e-07 -0.019057825 -0.019057825 -0.019057825 
-    1280        0.128   0.54590507   0.54590383 6.4799014e-07 -0.019204184 -0.019204184 -0.019204184 
-    1290        0.129   0.54623997   0.54623861 6.2208909e-07 -0.019350458 -0.019350458 -0.019350458 
-    1300         0.13   0.54657445     0.546573 5.8745262e-07 -0.019496645 -0.019496645 -0.019496645 
-    1310        0.131   0.54690854   0.54690699 5.4453703e-07 -0.019642746 -0.019642746 -0.019642746 
-    1320        0.132   0.54724221   0.54724057 4.9391474e-07 -0.019788759 -0.019788759 -0.019788759 
-    1330        0.133   0.54757548   0.54757376  4.36267e-07 -0.019934685 -0.019934685 -0.019934685 
-    1340        0.134   0.54790834   0.54790655 3.7237494e-07 -0.020080523 -0.020080523 -0.020080523 
-    1350        0.135   0.54824079   0.54823894 3.0310917e-07 -0.020226271 -0.020226271 -0.020226271 
-    1360        0.136   0.54857283   0.54857093 2.2941816e-07  -0.02037193  -0.02037193  -0.02037193 
-    1370        0.137   0.54890445   0.54890252 1.5231537e-07 -0.020517499 -0.020517499 -0.020517499 
-    1380        0.138   0.54923567   0.54923371 7.2865429e-08 -0.020662978 -0.020662978 -0.020662978 
-    1390        0.139   0.54956646    0.5495645 -7.830451e-09 -0.020808364 -0.020808364 -0.020808364 
-    1400         0.14   0.54989685   0.54989489 -8.8649727e-08 -0.020953659 -0.020953659 -0.020953659 
-    1410        0.141   0.55022681   0.55022488 -1.6846411e-07 -0.021098862 -0.021098862 -0.021098862 
-    1420        0.142   0.55055637   0.55055446 -2.4615537e-07 -0.021243971 -0.021243971 -0.021243971 
-    1430        0.143    0.5508855   0.55088364 -3.2063102e-07 -0.021388987 -0.021388987 -0.021388987 
-    1440        0.144   0.55121422   0.55121242 -3.9083985e-07 -0.021533909 -0.021533909 -0.021533909 
-    1450        0.145   0.55154253   0.55154079 -4.5578686e-07 -0.021678736 -0.021678736 -0.021678736 
-    1460        0.146   0.55187041   0.55186876 -5.1454752e-07 -0.021823467 -0.021823467 -0.021823467 
-    1470        0.147   0.55219788   0.55219632 -5.6628117e-07 -0.021968102 -0.021968102 -0.021968102 
-    1480        0.148   0.55252494   0.55252347 -6.1024325e-07 -0.022112641 -0.022112641 -0.022112641 
-    1490        0.149   0.55285157   0.55285021 -6.4579628e-07 -0.022257083 -0.022257083 -0.022257083 
-    1500         0.15    0.5531778   0.55317654 -6.7241935e-07 -0.022401428 -0.022401428 -0.022401428 
-    1510        0.151    0.5535036   0.55350246 -6.8971607e-07 -0.022545674 -0.022545674 -0.022545674 
-    1520        0.152   0.55382899   0.55382796 -6.9742076e-07 -0.022689821 -0.022689821 -0.022689821 
-    1530        0.153   0.55415396   0.55415305 -6.9540277e-07 -0.022833869 -0.022833869 -0.022833869 
-    1540        0.154   0.55447852   0.55447772 -6.8366905e-07 -0.022977817 -0.022977817 -0.022977817 
-    1550        0.155   0.55480267   0.55480198 -6.623646e-07 -0.023121664 -0.023121664 -0.023121664 
-    1560        0.156    0.5551264   0.55512581 -6.3177108e-07 -0.023265411 -0.023265411 -0.023265411 
-    1570        0.157   0.55544971   0.55544923 -5.9230341e-07 -0.023409056 -0.023409056 -0.023409056 
-    1580        0.158   0.55577261   0.55577222 -5.4450444e-07 -0.023552599 -0.023552599 -0.023552599 
-    1590        0.159    0.5560951   0.55609479 -4.8903776e-07 -0.023696039 -0.023696039 -0.023696039 
-    1600         0.16   0.55641717   0.55641694 -4.2667879e-07 -0.023839376 -0.023839376 -0.023839376 
-    1610        0.161   0.55673883   0.55673866 -3.5830415e-07 -0.023982609 -0.023982609 -0.023982609 
-    1620        0.162   0.55706007   0.55705996 -2.8487954e-07 -0.024125737 -0.024125737 -0.024125737 
-    1630        0.163    0.5573809   0.55738083 -2.0744627e-07 -0.024268761 -0.024268761 -0.024268761 
-    1640        0.164   0.55770132   0.55770127 -1.2710666e-07  -0.02441168  -0.02441168  -0.02441168 
-    1650        0.165   0.55802132   0.55802129 -4.5008398e-08 -0.024554492 -0.024554492 -0.024554492 
-    1660        0.166   0.55834091   0.55834087 3.7671735e-08 -0.024697198 -0.024697198 -0.024697198 
-    1670        0.167   0.55866008   0.55866003 1.1974475e-07 -0.024839797 -0.024839797 -0.024839797 
-    1680        0.168   0.55897883   0.55897876 2.0002656e-07 -0.024982288 -0.024982288 -0.024982288 
-    1690        0.169   0.55929717   0.55929705 2.7735509e-07 -0.025124671 -0.025124671 -0.025124671 
-    1700         0.17   0.55961509   0.55961492 3.5060722e-07 -0.025266946 -0.025266946 -0.025266946 
-    1710        0.171    0.5599326   0.55993235 4.187152e-07 -0.025409111 -0.025409111 -0.025409111 
-    1720        0.172   0.56024968   0.56024936 4.8068242e-07 -0.025551167 -0.025551167 -0.025551167 
-    1730        0.173   0.56056635   0.56056593 5.3559812e-07 -0.025693112 -0.025693112 -0.025693112 
-    1740        0.174   0.56088259   0.56088208 5.8265107e-07 -0.025834947 -0.025834947 -0.025834947 
-    1750        0.175   0.56119841    0.5611978 6.2114175e-07  -0.02597667  -0.02597667  -0.02597667 
-    1760        0.176   0.56151381   0.56151308 6.5049306e-07 -0.026118282 -0.026118282 -0.026118282 
-    1770        0.177   0.56182878   0.56182794 6.7025922e-07 -0.026259781 -0.026259781 -0.026259781 
-    1780        0.178   0.56214333   0.56214237 6.8013288e-07 -0.026401167 -0.026401167 -0.026401167 
-    1790        0.179   0.56245744   0.56245637 6.7995015e-07  -0.02654244  -0.02654244  -0.02654244 
-    1800         0.18   0.56277113   0.56276994 6.6969368e-07 -0.026683599 -0.026683599 -0.026683599 
-    1810        0.181   0.56308439   0.56308308 6.4949344e-07 -0.026824644 -0.026824644 -0.026824644 
-    1820        0.182   0.56339722    0.5633958 6.1962549e-07 -0.026965574 -0.026965574 -0.026965574 
-    1830        0.183   0.56370962   0.56370809 5.8050855e-07 -0.027106388 -0.027106388 -0.027106388 
-    1840        0.184   0.56402158   0.56401996 5.326984e-07 -0.027247086 -0.027247086 -0.027247086 
-    1850        0.185   0.56433311    0.5643314 4.7688029e-07 -0.027387668 -0.027387668 -0.027387668 
-    1860        0.186    0.5646442   0.56464241 4.1385938e-07 -0.027528133 -0.027528133 -0.027528133 
-    1870        0.187   0.56495486     0.564953 3.445494e-07 -0.027668481 -0.027668481 -0.027668481 
-    1880        0.188   0.56526508   0.56526316 2.6995953e-07 -0.027808711 -0.027808711 -0.027808711 
-    1890        0.189   0.56557486    0.5655729 1.9117995e-07 -0.027948822 -0.027948822 -0.027948822 
-    1900         0.19    0.5658842   0.56588221 1.0936603e-07 -0.028088814 -0.028088814 -0.028088814 
-    1910        0.191    0.5661931    0.5661911 2.5721446e-08 -0.028228687 -0.028228687 -0.028228687 
-    1920        0.192   0.56650156   0.56649956 -5.8519431e-08  -0.02836844  -0.02836844  -0.02836844 
-    1930        0.193   0.56680958   0.56680759 -1.4210974e-07 -0.028508072 -0.028508072 -0.028508072 
-    1940        0.194   0.56711716    0.5671152 -2.2380861e-07 -0.028647584 -0.028647584 -0.028647584 
-    1950        0.195    0.5674243   0.56742238 -3.0239963e-07 -0.028786974 -0.028786974 -0.028786974 
-    1960        0.196   0.56773099   0.56772914 -3.7670909e-07 -0.028926242 -0.028926242 -0.028926242 
-    1970        0.197   0.56803725   0.56803546 -4.456236e-07 -0.029065388 -0.029065388 -0.029065388 
-    1980        0.198   0.56834306   0.56834136 -5.0810696e-07 -0.029204411 -0.029204411 -0.029204411 
-    1990        0.199   0.56864844   0.56864682 -5.6321599e-07 -0.029343311 -0.029343311 -0.029343311 
-    2000          0.2   0.56895337   0.56895185 -6.1011491e-07 -0.029482087 -0.029482087 -0.029482087 
-    2010        0.201   0.56925786   0.56925645 -6.4808837e-07 -0.029620739 -0.029620739 -0.029620739 
-    2020        0.202   0.56956192   0.56956062 -6.7655256e-07 -0.029759266 -0.029759266 -0.029759266 
-    2030        0.203   0.56986553   0.56986435 -6.9506456e-07 -0.029897668 -0.029897668 -0.029897668 
-    2040        0.204   0.57016871   0.57016765 -7.0332945e-07 -0.030035944 -0.030035944 -0.030035944 
-    2050        0.205   0.57047145    0.5704705 -7.0120542e-07 -0.030174094 -0.030174094 -0.030174094 
-    2060        0.206   0.57077375   0.57077292 -6.8870641e-07 -0.030312118 -0.030312118 -0.030312118 
-    2070        0.207   0.57107561    0.5710749 -6.6600254e-07 -0.030450014 -0.030450014 -0.030450014 
-    2080        0.208   0.57137704   0.57137644 -6.3341814e-07 -0.030587783 -0.030587783 -0.030587783 
-    2090        0.209   0.57167803   0.57167754 -5.9142746e-07 -0.030725424 -0.030725424 -0.030725424 
-    2100         0.21   0.57197859   0.57197819 -5.4064804e-07 -0.030862936 -0.030862936 -0.030862936 
-    2110        0.211   0.57227872    0.5722784 -4.8183194e-07  -0.03100032  -0.03100032  -0.03100032 
-    2120        0.212    0.5725784   0.57257817 -4.1585486e-07 -0.031137574 -0.031137574 -0.031137574 
-    2130        0.213   0.57287766   0.57287749 -3.4370333e-07 -0.031274698 -0.031274698 -0.031274698 
-    2140        0.214   0.57317648   0.57317636 -2.6646013e-07 -0.031411692 -0.031411692 -0.031411692 
-    2150        0.215   0.57347487   0.57347478 -1.8528826e-07 -0.031548556 -0.031548556 -0.031548556 
-    2160        0.216   0.57377282   0.57377276 -1.0141351e-07 -0.031685288 -0.031685288 -0.031685288 
-    2170        0.217   0.57407034   0.57407029 -1.6106051e-08 -0.031821889 -0.031821889 -0.031821889 
-    2180        0.218   0.57436743   0.57436736 6.9338743e-08 -0.031958358 -0.031958358 -0.031958358 
-    2190        0.219   0.57466408   0.57466399 1.5361998e-07 -0.032094694 -0.032094694 -0.032094694 
-    2200         0.22   0.57496029   0.57496017 2.3545107e-07 -0.032230897 -0.032230897 -0.032230897 
-    2210        0.221   0.57525608   0.57525591 3.1357945e-07 -0.032366967 -0.032366967 -0.032366967 
-    2220        0.222   0.57555142   0.57555119 3.8680589e-07 -0.032502904 -0.032502904 -0.032502904 
-    2230        0.223   0.57584633   0.57584602  4.54003e-07 -0.032638706 -0.032638706 -0.032638706 
-    2240        0.224    0.5761408   0.57614041 5.1413283e-07 -0.032774373 -0.032774373 -0.032774373 
-    2250        0.225   0.57643483   0.57643434 5.6626308e-07 -0.032909906 -0.032909906 -0.032909906 
-    2260        0.226   0.57672843   0.57672783 6.0958183e-07 -0.033045303 -0.033045303 -0.033045303 
-    2270        0.227   0.57702158   0.57702087 6.4341044e-07 -0.033180564 -0.033180564 -0.033180564 
-    2280        0.228    0.5773143   0.57731347 6.6721445e-07 -0.033315689 -0.033315689 -0.033315689 
-    2290        0.229   0.57760657   0.57760562 6.8061239e-07 -0.033450677 -0.033450677 -0.033450677 
-    2300         0.23   0.57789839   0.57789732 6.8338214e-07 -0.033585528 -0.033585528 -0.033585528 
-    2310        0.231   0.57818977   0.57818858 6.7546495e-07 -0.033720241 -0.033720241 -0.033720241 
-    2320        0.232   0.57848071    0.5784794 6.5696693e-07 -0.033854817 -0.033854817 -0.033854817 
-    2330        0.233    0.5787712   0.57876977 6.2815797e-07 -0.033989254 -0.033989254 -0.033989254 
-    2340        0.234   0.57906124    0.5790597 5.8946815e-07 -0.034123552 -0.034123552 -0.034123552 
-    2350        0.235   0.57935083   0.57934919 5.4148162e-07 -0.034257711 -0.034257711 -0.034257711 
-    2360        0.236   0.57963997   0.57963824 4.8492805e-07 -0.034391731 -0.034391731 -0.034391731 
-    2370        0.237   0.57992866   0.57992685 4.2067186e-07  -0.03452561  -0.03452561  -0.03452561 
-    2380        0.238    0.5802169   0.58021501 3.496992e-07  -0.03465935  -0.03465935  -0.03465935 
-    2390        0.239   0.58050468   0.58050274  2.73103e-07 -0.034792948 -0.034792948 -0.034792948 
-    2400         0.24   0.58079201   0.58079003 1.9206639e-07 -0.034926405 -0.034926405 -0.034926405 
-    2410        0.241   0.58107889   0.58107688 1.078445e-07 -0.035059721 -0.035059721 -0.035059721 
-    2420        0.242   0.58136532   0.58136329 2.1745102e-08 -0.035192895 -0.035192895 -0.035192895 
-    2430        0.243   0.58165129   0.58164926 -6.4891571e-08 -0.035325926 -0.035325926 -0.035325926 
-    2440        0.244    0.5819368   0.58193479 -1.5071374e-07 -0.035458815 -0.035458815 -0.035458815 
-    2450        0.245   0.58222186   0.58221988 -2.3437916e-07 -0.035591561 -0.035591561 -0.035591561 
-    2460        0.246   0.58250646   0.58250453 -3.145762e-07 -0.035724163 -0.035724163 -0.035724163 
-    2470        0.247   0.58279061   0.58278874 -3.900445e-07 -0.035856621 -0.035856621 -0.035856621 
-    2480        0.248   0.58307431   0.58307251 -4.5959495e-07 -0.035988935 -0.035988935 -0.035988935 
-    2490        0.249   0.58335755   0.58335584 -5.2212856e-07 -0.036121105 -0.036121105 -0.036121105 
-    2500         0.25   0.58364034   0.58363872 -5.7665408e-07 -0.036253129 -0.036253129 -0.036253129 
-    2510        0.251   0.58392268   0.58392116 -6.2230397e-07 -0.036385008 -0.036385008 -0.036385008 
-    2520        0.252   0.58420456   0.58420316 -6.583484e-07 -0.036516742 -0.036516742 -0.036516742 
-    2530        0.253     0.584486   0.58448471 -6.842073e-07 -0.036648329 -0.036648329 -0.036648329 
-    2540        0.254   0.58476698   0.58476581 -6.9945994e-07  -0.03677977  -0.03677977  -0.03677977 
-    2550        0.255   0.58504751   0.58504647 -7.0385209e-07 -0.036911064 -0.036911064 -0.036911064 
-    2560        0.256    0.5853276   0.58532668 -6.9730063e-07 -0.037042211 -0.037042211 -0.037042211 
-    2570        0.257   0.58560724   0.58560643 -6.7989533e-07  -0.03717321  -0.03717321  -0.03717321 
-    2580        0.258   0.58588642   0.58588574 -6.5189807e-07 -0.037304062 -0.037304062 -0.037304062 
-    2590        0.259   0.58616517   0.58616459 -6.1373914e-07 -0.037434765 -0.037434765 -0.037434765 
-    2600         0.26   0.58644347     0.586443 -5.66011e-07  -0.03756532  -0.03756532  -0.03756532 
-    2610        0.261   0.58672132   0.58672094 -5.0945935e-07 -0.037695726 -0.037695726 -0.037695726 
-    2620        0.262   0.58699873   0.58699843 -4.4497175e-07 -0.037825982 -0.037825982 -0.037825982 
-    2630        0.263    0.5872757   0.58727547 -3.7356393e-07 -0.037956089 -0.037956089 -0.037956089 
-    2640        0.264   0.58755222   0.58755205 -2.9636401e-07 -0.038086046 -0.038086046 -0.038086046 
-    2650        0.265    0.5878283   0.58782817 -2.1459483e-07 -0.038215852 -0.038215852 -0.038215852 
-    2660        0.266   0.58810394   0.58810384 -1.2955473e-07 -0.038345508 -0.038345508 -0.038345508 
-    2670        0.267   0.58837913   0.58837905 -4.2597042e-08 -0.038475013 -0.038475013 -0.038475013 
-    2680        0.268   0.58865388    0.5886538 4.489141e-08 -0.038604367 -0.038604367 -0.038604367 
-    2690        0.269    0.5889282   0.58892809 1.315124e-07 -0.038733569 -0.038733569 -0.038733569 
-    2700         0.27   0.58920206   0.58920193 2.1587867e-07 -0.038862619 -0.038862619 -0.038862619 
-    2710        0.271   0.58947549    0.5894753 2.9663624e-07 -0.038991516 -0.038991516 -0.038991516 
-    2720        0.272   0.58974847   0.58974823 3.724862e-07 -0.039120262 -0.039120262 -0.039120262 
-    2730        0.273   0.59002101   0.59002069 4.422058e-07 -0.039248854 -0.039248854 -0.039248854 
-    2740        0.274   0.59029311    0.5902927 5.0466829e-07 -0.039377293 -0.039377293 -0.039377293 
-    2750        0.275   0.59056476   0.59056425 5.5886139e-07 -0.039505578 -0.039505578 -0.039505578 
-    2760        0.276   0.59083596   0.59083534 6.0390391e-07 -0.039633709 -0.039633709 -0.039633709 
-    2770        0.277   0.59110672   0.59110599 6.3906037e-07 -0.039761687 -0.039761687 -0.039761687 
-    2780        0.278   0.59137702   0.59137617 6.6375325e-07 -0.039889509 -0.039889509 -0.039889509 
-    2790        0.279   0.59164688   0.59164591 6.7757286e-07 -0.040017177 -0.040017177 -0.040017177 
-    2800         0.28   0.59191629    0.5919152 6.8028436e-07  -0.04014469  -0.04014469  -0.04014469 
-    2810        0.281   0.59218525   0.59218403 6.7183215e-07 -0.040272047 -0.040272047 -0.040272047 
-    2820        0.282   0.59245376   0.59245242 6.5234123e-07 -0.040399248 -0.040399248 -0.040399248 
-    2830        0.283   0.59272182   0.59272035 6.221157e-07 -0.040526294 -0.040526294 -0.040526294 
-    2840        0.284   0.59298942   0.59298784 5.8163434e-07 -0.040653183 -0.040653183 -0.040653183 
-    2850        0.285   0.59325656   0.59325489 5.3154333e-07 -0.040779915 -0.040779915 -0.040779915 
-    2860        0.286   0.59352325   0.59352148 4.7264622e-07 -0.040906491 -0.040906491 -0.040906491 
-    2870        0.287   0.59378949   0.59378764 4.0589128e-07 -0.041032909 -0.041032909 -0.041032909 
-    2880        0.288   0.59405526   0.59405334 3.3235647e-07  -0.04115917  -0.04115917  -0.04115917 
-    2890        0.289   0.59432058   0.59431861 2.5323221e-07 -0.041285273 -0.041285273 -0.041285273 
-    2900         0.29   0.59458544   0.59458343 1.6980231e-07 -0.041411218 -0.041411218 -0.041411218 
-    2910        0.291   0.59484984   0.59484781 8.3423201e-08 -0.041537004 -0.041537004 -0.041537004 
-    2920        0.292   0.59511379   0.59511174 -4.4979772e-09 -0.041662632 -0.041662632 -0.041662632 
-    2930        0.293   0.59537727   0.59537523 -9.25263e-08 -0.041788101 -0.041788101 -0.041788101 
-    2940        0.294    0.5956403   0.59563828 -1.7922246e-07 -0.041913411 -0.041913411 -0.041913411 
-    2950        0.295   0.59590287   0.59590089 -2.6316634e-07 -0.042038561 -0.042038561 -0.042038561 
-    2960        0.296   0.59616498   0.59616305 -3.4298038e-07 -0.042163552 -0.042163552 -0.042163552 
-    2970        0.297   0.59642663   0.59642477 -4.1735227e-07 -0.042288382 -0.042288382 -0.042288382 
-    2980        0.298   0.59668783   0.59668604 -4.8505673e-07 -0.042413052 -0.042413052 -0.042413052 
-    2990        0.299   0.59694857   0.59694687 -5.4497585e-07 -0.042537562 -0.042537562 -0.042537562 
-    3000          0.3   0.59720885   0.59720726 -5.9611782e-07  -0.04266191  -0.04266191  -0.04266191 
-    3010        0.301   0.59746868    0.5974672 -6.3763354e-07 -0.042786098 -0.042786098 -0.042786098 
-    3020        0.302   0.59772805   0.59772669 -6.6883106e-07 -0.042910124 -0.042910124 -0.042910124 
-    3030        0.303   0.59798698   0.59798573 -6.8918737e-07 -0.043033989 -0.043033989 -0.043033989 
-    3040        0.304   0.59824545   0.59824433 -6.9835748e-07 -0.043157692 -0.043157692 -0.043157692 
-    3050        0.305   0.59850347   0.59850247 -6.9618058e-07 -0.043281233 -0.043281233 -0.043281233 
-    3060        0.306   0.59876104   0.59876017 -6.826832e-07 -0.043404611 -0.043404611 -0.043404611 
-    3070        0.307   0.59901816   0.59901741 -6.5807923e-07 -0.043527827 -0.043527827 -0.043527827 
-    3080        0.308   0.59927483    0.5992742 -6.2276684e-07  -0.04365088  -0.04365088  -0.04365088 
-    3090        0.309   0.59953106   0.59953053 -5.7732236e-07  -0.04377377  -0.04377377  -0.04377377 
-    3100         0.31   0.59978685   0.59978641 -5.2249119e-07 -0.043896496 -0.043896496 -0.043896496 
-    3110        0.311   0.60004219   0.60004184 -4.5917576e-07 -0.044019059 -0.044019059 -0.044019059 
-    3120        0.312   0.60029708   0.60029681 -3.8842101e-07 -0.044141458 -0.044141458 -0.044141458 
-    3130        0.313   0.60055153   0.60055132 -3.113973e-07 -0.044263693 -0.044263693 -0.044263693 
-    3140        0.314   0.60080554   0.60080538 -2.2938121e-07 -0.044385764 -0.044385764 -0.044385764 
-    3150        0.315   0.60105911   0.60105898 -1.4373457e-07  -0.04450767  -0.04450767  -0.04450767 
-    3160        0.316   0.60131224   0.60131212 -5.5881936e-08 -0.044629411 -0.044629411 -0.044629411 
-    3170        0.317   0.60156492   0.60156481 3.2713085e-08 -0.044750988 -0.044750988 -0.044750988 
-    3180        0.318   0.60181717   0.60181703 1.2057216e-07 -0.044872399 -0.044872399 -0.044872399 
-    3190        0.319   0.60206897    0.6020688 2.0622692e-07 -0.044993645 -0.044993645 -0.044993645 
-    3200         0.32   0.60232033   0.60232012 2.882436e-07 -0.045114725 -0.045114725 -0.045114725 
-    3210        0.321   0.60257125   0.60257097 3.6524711e-07 -0.045235639 -0.045235639 -0.045235639 
-    3220        0.322   0.60282173   0.60282137 4.3594424e-07 -0.045356388 -0.045356388 -0.045356388 
-    3230        0.323   0.60307176   0.60307132 4.9914554e-07 -0.045476969 -0.045476969 -0.045476969 
-    3240        0.324   0.60332135   0.60332081 5.537856e-07 -0.045597385 -0.045597385 -0.045597385 
-    3250        0.325    0.6035705   0.60356985 5.9894116e-07 -0.045717634 -0.045717634 -0.045717634 
-    3260        0.326   0.60381921   0.60381844 6.3384706e-07 -0.045837715 -0.045837715 -0.045837715 
-    3270        0.327   0.60406746   0.60406658 6.5790942e-07  -0.04595763  -0.04595763  -0.04595763 
-    3280        0.328   0.60431528   0.60431427 6.7071607e-07 -0.046077377 -0.046077377 -0.046077377 
-    3290        0.329   0.60456264    0.6045615 6.7204395e-07 -0.046196957 -0.046196957 -0.046196957 
-    3300         0.33   0.60480956    0.6048083 6.6186325e-07 -0.046316369 -0.046316369 -0.046316369 
-    3310        0.331   0.60505602   0.60505464 6.4033837e-07 -0.046435613 -0.046435613 -0.046435613 
-    3320        0.332   0.60530204   0.60530054 6.0782561e-07 -0.046554689 -0.046554689 -0.046554689 
-    3330        0.333   0.60554761     0.605546 5.6486753e-07 -0.046673597 -0.046673597 -0.046673597 
-    3340        0.334   0.60579272   0.60579101 5.1218422e-07 -0.046792336 -0.046792336 -0.046792336 
-    3350        0.335   0.60603738   0.60603558 4.5066146e-07 -0.046910906 -0.046910906 -0.046910906 
-    3360        0.336   0.60628159   0.60627971 3.8133609e-07 -0.047029308 -0.047029308 -0.047029308 
-    3370        0.337   0.60652535    0.6065234 3.0537872e-07  -0.04714754  -0.04714754  -0.04714754 
-    3380        0.338   0.60676865   0.60676665 2.2407417e-07 -0.047265604 -0.047265604 -0.047265604 
-    3390        0.339    0.6070115   0.60700946 1.3879984e-07 -0.047383497 -0.047383497 -0.047383497 
-    3400         0.34   0.60725389   0.60725184 5.1002519e-08 -0.047501222 -0.047501222 -0.047501222 
-    3410        0.341   0.60749583   0.60749377 -3.7826124e-08 -0.047618776 -0.047618776 -0.047618776 
-    3420        0.342   0.60773732   0.60773527 -1.2617486e-07  -0.04773616  -0.04773616  -0.04773616 
-    3430        0.343   0.60797835   0.60797633 -2.1253862e-07 -0.047853375 -0.047853375 -0.047853375 
-    3440        0.344   0.60821893   0.60821696 -2.9544421e-07 -0.047970419 -0.047970419 -0.047970419 
-    3450        0.345   0.60845905   0.60845714 -3.734755e-07 -0.048087292 -0.048087292 -0.048087292 
-    3460        0.346   0.60869873   0.60869689 -4.4529782e-07 -0.048203995 -0.048203995 -0.048203995 
-    3470        0.347   0.60893795    0.6089362 -5.0968088e-07 -0.048320527 -0.048320527 -0.048320527 
-    3480        0.348   0.60917672   0.60917507 -5.655201e-07 -0.048436888 -0.048436888 -0.048436888 
-    3490        0.349   0.60941504   0.60941349 -6.118558e-07 -0.048553078 -0.048553078 -0.048553078 
-    3500         0.35   0.60965292   0.60965148 -6.4788989e-07 -0.048669097 -0.048669097 -0.048669097 
-    3510        0.351   0.60989034   0.60988903 -6.7299997e-07 -0.048784944 -0.048784944 -0.048784944 
-    3520        0.352   0.61012732   0.61012613 -6.8675033e-07 -0.048900619 -0.048900619 -0.048900619 
-    3530        0.353   0.61036386    0.6103628 -6.8889983e-07 -0.049016123 -0.049016123 -0.049016123 
-    3540        0.354   0.61059995   0.61059901 -6.7940642e-07 -0.049131455 -0.049131455 -0.049131455 
-    3550        0.355    0.6108356   0.61083479 -6.5842829e-07 -0.049246615 -0.049246615 -0.049246615 
-    3560        0.356   0.61107081   0.61107011 -6.2632151e-07 -0.049361603 -0.049361603 -0.049361603 
-    3570        0.357   0.61130559     0.611305 -5.836343e-07 -0.049476418 -0.049476418 -0.049476418 
-    3580        0.358   0.61153992   0.61153943 -5.3109794e-07 -0.049591061 -0.049591061 -0.049591061 
-    3590        0.359   0.61177381   0.61177342 -4.6961453e-07 -0.049705531 -0.049705531 -0.049705531 
-    3600         0.36   0.61200727   0.61200695 -4.0024169e-07 -0.049819829 -0.049819829 -0.049819829 
-    3610        0.361    0.6122403   0.61224004 -3.241746e-07 -0.049933953 -0.049933953 -0.049933953 
-    3620        0.362   0.61247289   0.61247268 -2.4272558e-07 -0.050047905 -0.050047905 -0.050047905 
-    3630        0.363   0.61270504   0.61270487 -1.5730157e-07 -0.050161683 -0.050161683 -0.050161683 
-    3640        0.364   0.61293677   0.61293661 -6.937997e-08 -0.050275289 -0.050275289 -0.050275289 
-    3650        0.365   0.61316806    0.6131679 1.9516899e-08  -0.05038872  -0.05038872  -0.05038872 
-    3660        0.366   0.61339891   0.61339875 1.078481e-07 -0.050501979 -0.050501979 -0.050501979 
-    3670        0.367   0.61362934   0.61362914 1.9408082e-07 -0.050615063 -0.050615063 -0.050615063 
-    3680        0.368   0.61385933   0.61385909 2.7671704e-07 -0.050727974 -0.050727974 -0.050727974 
-    3690        0.369   0.61408889   0.61408858 3.543196e-07 -0.050840711 -0.050840711 -0.050840711 
-    3700         0.37   0.61431802   0.61431763 4.2553742e-07 -0.050953274 -0.050953274 -0.050953274 
-    3710        0.371   0.61454671   0.61454624 4.891291e-07 -0.051065662 -0.051065662 -0.051065662 
-    3720        0.372   0.61477497    0.6147744 5.4398482e-07 -0.051177877 -0.051177877 -0.051177877 
-    3730        0.373   0.61500279   0.61500212 5.8914589e-07 -0.051289917 -0.051289917 -0.051289917 
-    3740        0.374   0.61523018   0.61522939 6.2382182e-07 -0.051401782 -0.051401782 -0.051401782 
-    3750        0.375   0.61545714   0.61545622 6.4740433e-07 -0.051513473 -0.051513473 -0.051513473 
-    3760        0.376   0.61568366   0.61568261 6.5947843e-07  -0.05162499  -0.05162499  -0.05162499 
-    3770        0.377   0.61590974   0.61590857 6.598299e-07 -0.051736331 -0.051736331 -0.051736331 
-    3780        0.378   0.61613538   0.61613409 6.4844946e-07 -0.051847498 -0.051847498 -0.051847498 
-    3790        0.379   0.61636058   0.61635917 6.2553327e-07  -0.05195849  -0.05195849  -0.05195849 
-    3800         0.38   0.61658534   0.61658381 5.9147985e-07 -0.052069306 -0.052069306 -0.052069306 
-    3810        0.381   0.61680966   0.61680803 5.4688338e-07 -0.052179947 -0.052179947 -0.052179947 
-    3820        0.382   0.61703355   0.61703181 4.9252369e-07 -0.052290414 -0.052290414 -0.052290414 
-    3830        0.383   0.61725699   0.61725516 4.2935278e-07 -0.052400704 -0.052400704 -0.052400704 
-    3840        0.384   0.61747998   0.61747808 3.5847842e-07  -0.05251082  -0.05251082  -0.05251082 
-    3850        0.385   0.61770254   0.61770057 2.811449e-07 -0.052620759 -0.052620759 -0.052620759 
-    3860        0.386   0.61792465   0.61792263 1.9871133e-07 -0.052730523 -0.052730523 -0.052730523 
-    3870        0.387   0.61814632   0.61814427 1.126279e-07 -0.052840112 -0.052840112 -0.052840112 
-    3880        0.388   0.61836754   0.61836548 2.4410428e-08 -0.052949524 -0.052949524 -0.052949524 
-    3890        0.389   0.61858832   0.61858626 -6.4386247e-08 -0.053058761 -0.053058761 -0.053058761 
-    3900         0.39   0.61880866   0.61880662 -1.521957e-07 -0.053167821 -0.053167821 -0.053167821 
-    3910        0.391   0.61902856   0.61902656 -2.3746757e-07 -0.053276706 -0.053276706 -0.053276706 
-    3920        0.392   0.61924802   0.61924606 -3.1869499e-07 -0.053385414 -0.053385414 -0.053385414 
-    3930        0.393   0.61946703   0.61946514 -3.9444133e-07 -0.053493947 -0.053493947 -0.053493947 
-    3940        0.394   0.61968561    0.6196838 -4.6336578e-07 -0.053602303 -0.053602303 -0.053602303 
-    3950        0.395   0.61990374   0.61990202 -5.2424718e-07 -0.053710482 -0.053710482 -0.053710482 
-    3960        0.396   0.62012144   0.62011982 -5.7600597e-07 -0.053818486 -0.053818486 -0.053818486 
-    3970        0.397   0.62033871    0.6203372 -6.1772348e-07 -0.053926313 -0.053926313 -0.053926313 
-    3980        0.398   0.62055553   0.62055414 -6.486585e-07 -0.054033963 -0.054033963 -0.054033963 
-    3990        0.399   0.62077193   0.62077066 -6.6826077e-07 -0.054141436 -0.054141436 -0.054141436 
-    4000          0.4   0.62098789   0.62098674 -6.7618099e-07 -0.054248733 -0.054248733 -0.054248733 
-    4010        0.401   0.62120342    0.6212024 -6.7227739e-07 -0.054355854 -0.054355854 -0.054355854 
-    4020        0.402   0.62141852   0.62141762 -6.566185e-07 -0.054462797 -0.054462797 -0.054462797 
-    4030        0.403   0.62163319   0.62163242 -6.294823e-07 -0.054569564 -0.054569564 -0.054569564 
-    4040        0.404   0.62184744   0.62184677 -5.9135153e-07 -0.054676154 -0.054676154 -0.054676154 
-    4050        0.405   0.62206126    0.6220607 -5.4290537e-07 -0.054782567 -0.054782567 -0.054782567 
-    4060        0.406   0.62227466   0.62227419 -4.850076e-07 -0.054888803 -0.054888803 -0.054888803 
-    4070        0.407   0.62248763   0.62248725 -4.1869146e-07 -0.054994861 -0.054994861 -0.054994861 
-    4080        0.408   0.62270018   0.62269987 -3.4514137e-07 -0.055100743 -0.055100743 -0.055100743 
-    4090        0.409   0.62291232   0.62291206 -2.6567194e-07 -0.055206448 -0.055206448 -0.055206448 
-    4100         0.41   0.62312403   0.62312381 -1.8170469e-07 -0.055311975 -0.055311975 -0.055311975 
-    4110        0.411   0.62333532   0.62333513 -9.4742642e-08 -0.055417325 -0.055417325 -0.055417325 
-    4120        0.412    0.6235462   0.62354601 -6.3435298e-09 -0.055522499 -0.055522499 -0.055522499 
-    4130        0.413   0.62375665   0.62375645 8.1908081e-08 -0.055627494 -0.055627494 -0.055627494 
-    4140        0.414   0.62396669   0.62396646 1.6842921e-07 -0.055732313 -0.055732313 -0.055732313 
-    4150        0.415   0.62417631   0.62417604 2.5166689e-07 -0.055836954 -0.055836954 -0.055836954 
-    4160        0.416   0.62438551   0.62438518 3.3012615e-07 -0.055941417 -0.055941417 -0.055941417 
-    4170        0.417    0.6245943    0.6245939 4.0239694e-07 -0.056045704 -0.056045704 -0.056045704 
-    4180        0.418   0.62480266   0.62480218 4.6717967e-07 -0.056149812 -0.056149812 -0.056149812 
-    4190        0.419   0.62501061   0.62501003 5.2330875e-07 -0.056253744 -0.056253744 -0.056253744 
-    4200         0.42   0.62521814   0.62521745 5.6977374e-07 -0.056357498 -0.056357498 -0.056357498 
-    4210        0.421   0.62542525   0.62542444 6.057378e-07 -0.056461074 -0.056461074 -0.056461074 
-    4220        0.422   0.62563194   0.62563101 6.3055304e-07 -0.056564473 -0.056564473 -0.056564473 
-    4230        0.423    0.6258382   0.62583716 6.4377238e-07 -0.056667694 -0.056667694 -0.056667694 
-    4240        0.424   0.62604405   0.62604288 6.4515798e-07 -0.056770738 -0.056770738 -0.056770738 
-    4250        0.425   0.62624947   0.62624817 6.3468571e-07 -0.056873604 -0.056873604 -0.056873604 
-    4260        0.426   0.62645447   0.62645305 6.1254589e-07 -0.056976292 -0.056976292 -0.056976292 
-    4270        0.427   0.62665905   0.62665751 5.7914013e-07 -0.057078803 -0.057078803 -0.057078803 
-    4280        0.428    0.6268632   0.62686155 5.3507424e-07 -0.057181136 -0.057181136 -0.057181136 
-    4290        0.429   0.62706692   0.62706518 4.8114756e-07 -0.057283292 -0.057283292 -0.057283292 
-    4300         0.43   0.62727022   0.62726839 4.1833866e-07 -0.057385269 -0.057385269 -0.057385269 
-    4310        0.431    0.6274731   0.62747119 3.4778776e-07  -0.05748707  -0.05748707  -0.05748707 
-    4320        0.432   0.62767554   0.62767358 2.7077627e-07 -0.057588692 -0.057588692 -0.057588692 
-    4330        0.433   0.62787756   0.62787555 1.8870359e-07 -0.057690137 -0.057690137 -0.057690137 
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-    4350        0.435   0.62828033   0.62827827 1.5408826e-08 -0.057892494 -0.057892494 -0.057892494 
-    4360        0.436   0.62848107   0.62847902 -7.2660336e-08 -0.057993406 -0.057993406 -0.057993406 
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-    4390        0.439   0.62908074    0.6290788 -3.2346322e-07 -0.058295075 -0.058295075 -0.058295075 
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-    4410        0.441    0.6294784   0.62947661 -4.6445802e-07   -0.0584953   -0.0584953   -0.0584953 
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-    4450        0.445   0.63026869   0.63026731 -6.3911762e-07 -0.058893618 -0.058893618 -0.058893618 
-    4460        0.446   0.63046521   0.63046396 -6.5551459e-07 -0.058992754 -0.058992754 -0.058992754 
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-    4480        0.448   0.63085703   0.63085602 -6.5278946e-07 -0.059190493 -0.059190493 -0.059190493 
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-    4520        0.452   0.63163573   0.63163518 -5.1055337e-07  -0.05958384  -0.05958384  -0.05958384 
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-    4550        0.455   0.63221551   0.63221518 -3.0621194e-07 -0.059876988 -0.059876988 -0.059876988 
-    4560        0.456   0.63240796   0.63240768 -2.2556465e-07  -0.05997435  -0.05997435  -0.05997435 
-    4570        0.457   0.63260001   0.63259976 -1.4104413e-07 -0.060071534 -0.060071534 -0.060071534 
-    4580        0.458   0.63279166   0.63279143 -5.4210581e-08  -0.06016854  -0.06016854  -0.06016854 
-    4590        0.459   0.63298291   0.63298268 3.3332623e-08  -0.06026537  -0.06026537  -0.06026537 
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-    4610        0.461   0.63336422   0.63336393 2.0409657e-07 -0.060458498 -0.060458498 -0.060458498 
-    4620        0.462   0.63355427   0.63355394 2.8416203e-07 -0.060554796 -0.060554796 -0.060554796 
-    4630        0.463   0.63374393   0.63374353 3.5868507e-07 -0.060650918 -0.060650918 -0.060650918 
-    4640        0.464   0.63393318    0.6339327 4.2628804e-07 -0.060746862 -0.060746862 -0.060746862 
-    4650        0.465   0.63412204   0.63412147 4.8572121e-07 -0.060842629 -0.060842629 -0.060842629 
-    4660        0.466    0.6343105   0.63430983  5.35886e-07  -0.06093822  -0.06093822  -0.06093822 
-    4670        0.467   0.63449856   0.63449778 5.7585552e-07 -0.061033634 -0.061033634 -0.061033634 
-    4680        0.468   0.63468622   0.63468532 6.048919e-07  -0.06112887  -0.06112887  -0.06112887 
-    4690        0.469   0.63487347   0.63487245 6.2246016e-07 -0.061223931 -0.061223931 -0.061223931 
-    4700         0.47   0.63506033   0.63505918 6.2823833e-07 -0.061318814 -0.061318814 -0.061318814 
-    4710        0.471   0.63524678   0.63524551 6.2212359e-07 -0.061413521 -0.061413521 -0.061413521 
-    4720        0.472   0.63543283   0.63543144 6.0423435e-07 -0.061508051 -0.061508051 -0.061508051 
-    4730        0.473   0.63561847   0.63561697 5.7490826e-07 -0.061602405 -0.061602405 -0.061602405 
-    4740        0.474   0.63580371    0.6358021 5.3469601e-07 -0.061696582 -0.061696582 -0.061696582 
-    4750        0.475   0.63598855   0.63598684 4.8435128e-07 -0.061790583 -0.061790583 -0.061790583 
-    4760        0.476   0.63617298   0.63617118 4.2481683e-07 -0.061884408 -0.061884408 -0.061884408 
-    4770        0.477   0.63635701   0.63635512 3.5720699e-07 -0.061978056 -0.061978056 -0.061978056 
-    4780        0.478   0.63654062   0.63653868 2.8278703e-07 -0.062071529 -0.062071529 -0.062071529 
-    4790        0.479   0.63672384   0.63672184 2.0294959e-07 -0.062164825 -0.062164825 -0.062164825 
-    4800         0.48   0.63690664   0.63690461 1.1918874e-07 -0.062257945 -0.062257945 -0.062257945 
-    4810        0.481   0.63708904     0.637087 3.3072095e-08 -0.062350889 -0.062350889 -0.062350889 
-    4820        0.482   0.63727104   0.63726899 -5.3788471e-08 -0.062443657 -0.062443657 -0.062443657 
-    4830        0.483   0.63745263    0.6374506 -1.39767e-07 -0.062536249 -0.062536249 -0.062536249 
-    4840        0.484   0.63763381   0.63763182 -2.2325389e-07 -0.062628665 -0.062628665 -0.062628665 
-    4850        0.485   0.63781459   0.63781265 -3.0268612e-07 -0.062720906 -0.062720906 -0.062720906 
-    4860        0.486   0.63799497   0.63799309 -3.7657657e-07 -0.062812971 -0.062812971 -0.062812971 
-    4870        0.487   0.63817495   0.63817314 -4.4354199e-07 -0.062904861 -0.062904861 -0.062904861 
-    4880        0.488   0.63835452   0.63835281 -5.0232909e-07 -0.062996575 -0.062996575 -0.062996575 
-    4890        0.489    0.6385337   0.63853208 -5.5183811e-07 -0.063088114 -0.063088114 -0.063088114 
-    4900         0.49   0.63871248   0.63871097 -5.9114363e-07 -0.063179477 -0.063179477 -0.063179477 
-    4910        0.491   0.63889086   0.63888947 -6.1951209e-07 -0.063270665 -0.063270665 -0.063270665 
-    4920        0.492   0.63906885   0.63906758 -6.3641568e-07 -0.063361678 -0.063361678 -0.063361678 
-    4930        0.493   0.63924644    0.6392453 -6.4154246e-07 -0.063452516 -0.063452516 -0.063452516 
-    4940        0.494   0.63942365   0.63942262 -6.3480228e-07 -0.063543179 -0.063543179 -0.063543179 
-    4950        0.495   0.63960046   0.63959956 -6.1632869e-07 -0.063633667 -0.063633667 -0.063633667 
-    4960        0.496   0.63977689    0.6397761 -5.8647648e-07 -0.063723981 -0.063723981 -0.063723981 
-    4970        0.497   0.63995293   0.63995224 -5.4581515e-07 -0.063814119 -0.063814119 -0.063814119 
-    4980        0.498   0.64012859     0.640128 -4.9511825e-07 -0.063904083 -0.063904083 -0.063904083 
-    4990        0.499   0.64030386   0.64030336 -4.3534885e-07 -0.063993873 -0.063993873 -0.063993873 
-    5000          0.5   0.64047875   0.64047832 -3.6764149e-07 -0.064083488 -0.064083488 -0.064083488 
-    5010        0.501   0.64065325   0.64065289 -2.9328075e-07 -0.064172929 -0.064172929 -0.064172929 
-    5020        0.502   0.64082738   0.64082707 -2.1367704e-07 -0.064262195 -0.064262195 -0.064262195 
-    5030        0.503   0.64100113   0.64100085 -1.3033993e-07 -0.064351288 -0.064351288 -0.064351288 
-    5040        0.504    0.6411745   0.64117423 -4.4849648e-08 -0.064440206 -0.064440206 -0.064440206 
-    5050        0.505    0.6413475   0.64134722 4.1172909e-08  -0.06452895  -0.06452895  -0.06452895 
-    5060        0.506   0.64152011   0.64151982 1.2609686e-07 -0.064617521 -0.064617521 -0.064617521 
-    5070        0.507   0.64169236   0.64169202 2.0831228e-07 -0.064705918 -0.064705918 -0.064705918 
-    5080        0.508   0.64186422   0.64186384 2.8626081e-07 -0.064794141 -0.064794141 -0.064794141 
-    5090        0.509   0.64203571   0.64203526 3.5846527e-07 -0.064882191 -0.064882191 -0.064882191 
-    5100         0.51   0.64220682   0.64220629 4.2355775e-07 -0.064970067 -0.064970067 -0.064970067 
-    5110        0.511   0.64237755   0.64237693 4.8030571e-07  -0.06505777  -0.06505777  -0.06505777 
-    5120        0.512   0.64254791   0.64254719 5.2763546e-07   -0.0651453   -0.0651453   -0.0651453 
-    5130        0.513   0.64271789   0.64271705 5.6465267e-07 -0.065232657 -0.065232657 -0.065232657 
-    5140        0.514   0.64288749   0.64288654 5.906595e-07  -0.06531984  -0.06531984  -0.06531984 
-    5150        0.515   0.64305671   0.64305564 6.0516793e-07 -0.065406851 -0.065406851 -0.065406851 
-    5160        0.516   0.64322555   0.64322436 6.0790921e-07 -0.065493689 -0.065493689 -0.065493689 
-    5170        0.517   0.64339401    0.6433927 5.9883899e-07 -0.065580355 -0.065580355 -0.065580355 
-    5180        0.518   0.64356209   0.64356067 5.7813833e-07 -0.065666848 -0.065666848 -0.065666848 
-    5190        0.519   0.64372979   0.64372826 5.4621027e-07 -0.065753168 -0.065753168 -0.065753168 
-    5200         0.52   0.64389711   0.64389547 5.036722e-07 -0.065839316 -0.065839316 -0.065839316 
-    5210        0.521   0.64406405   0.64406231 4.5134419e-07 -0.065925292 -0.065925292 -0.065925292 
-    5220        0.522    0.6442306   0.64422878 3.9023331e-07 -0.066011096 -0.066011096 -0.066011096 
-    5230        0.523   0.64439677   0.64439488 3.2151444e-07 -0.066096729 -0.066096729 -0.066096729 
-    5240        0.524   0.64456256   0.64456061 2.4650783e-07 -0.066182189 -0.066182189 -0.066182189 
-    5250        0.525   0.64472797   0.64472597 1.6665388e-07 -0.066267477 -0.066267477 -0.066267477 
-    5260        0.526   0.64489299   0.64489096 8.3485522e-08 -0.066352594 -0.066352594 -0.066352594 
-    5270        0.527   0.64505763   0.64505559 -1.4011251e-09  -0.06643754  -0.06643754  -0.06643754 
-    5280        0.528   0.64522188   0.64521986 -8.6377351e-08 -0.066522314 -0.066522314 -0.066522314 
-    5290        0.529   0.64538576   0.64538376 -1.6981312e-07 -0.066606917 -0.066606917 -0.066606917 
-    5300         0.53   0.64554925   0.64554729 -2.5010835e-07 -0.066691349 -0.066691349 -0.066691349 
-    5310        0.531   0.64571237   0.64571046 -3.2572373e-07 -0.066775611 -0.066775611 -0.066775611 
-    5320        0.532    0.6458751   0.64587326 -3.9521022e-07 -0.066859701 -0.066859701 -0.066859701 
-    5330        0.533   0.64603746    0.6460357 -4.5723704e-07 -0.066943621 -0.066943621 -0.066943621 
-    5340        0.534   0.64619944   0.64619778 -5.1061726e-07  -0.06702737  -0.06702737  -0.06702737 
-    5350        0.535   0.64636105   0.64635948 -5.5433068e-07 -0.067110948 -0.067110948 -0.067110948 
-    5360        0.536   0.64652228   0.64652083 -5.8754354e-07 -0.067194357 -0.067194357 -0.067194357 
-    5370        0.537   0.64668314    0.6466818 -6.0962458e-07 -0.067277595 -0.067277595 -0.067277595 
-    5380        0.538   0.64684363   0.64684241 -6.2015733e-07 -0.067360664 -0.067360664 -0.067360664 
-    5390        0.539   0.64700376   0.64700266 -6.1894809e-07 -0.067443562 -0.067443562 -0.067443562 
-    5400         0.54   0.64716351   0.64716253 -6.0602979e-07 -0.067526291 -0.067526291 -0.067526291 
-    5410        0.541    0.6473229   0.64732204 -5.8166135e-07  -0.06760885  -0.06760885  -0.06760885 
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-    5430        0.543    0.6476406   0.64763994 -5.0070563e-07  -0.06777346  -0.06777346  -0.06777346 
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-    5450        0.545   0.64795685   0.64795636 -3.8237815e-07 -0.067937394 -0.067937394 -0.067937394 
-    5460        0.546   0.64811444   0.64811401 -3.119712e-07 -0.068019108 -0.068019108 -0.068019108 
-    5470        0.547   0.64827167    0.6482713 -2.3584813e-07 -0.068100653 -0.068100653 -0.068100653 
-    5480        0.548   0.64842855   0.64842821 -1.5548783e-07 -0.068182029 -0.068182029 -0.068182029 
-    5490        0.549   0.64858507   0.64858475 -7.2450737e-08 -0.068263237 -0.068263237 -0.068263237 
-    5500         0.55   0.64874124   0.64874092 1.1651408e-08 -0.068344276 -0.068344276 -0.068344276 
-    5510        0.551   0.64889706   0.64889673 9.5186848e-08 -0.068425148 -0.068425148 -0.068425148 
-    5520        0.552   0.64905252   0.64905216 1.7653547e-07 -0.068505851 -0.068505851 -0.068505851 
-    5530        0.553   0.64920763   0.64920722 2.5412026e-07 -0.068586387 -0.068586387 -0.068586387 
-    5540        0.554   0.64936239   0.64936192 3.2643798e-07 -0.068666755 -0.068666755 -0.068666755 
-    5550        0.555   0.64951679   0.64951625 3.9208836e-07 -0.068746955 -0.068746955 -0.068746955 
-    5560        0.556   0.64967085   0.64967022 4.4980134e-07 -0.068826988 -0.068826988 -0.068826988 
-    5570        0.557   0.64982455   0.64982382 4.984618e-07 -0.068906854 -0.068906854 -0.068906854 
-    5580        0.558   0.64997789   0.64997706 5.3713127e-07 -0.068986553 -0.068986553 -0.068986553 
-    5590        0.559   0.65013089   0.65012995 5.6506622e-07 -0.069066085 -0.069066085 -0.069066085 
-    5600         0.56   0.65028353   0.65028247 5.8173253e-07 -0.069145451 -0.069145451 -0.069145451 
-    5610        0.561   0.65043581   0.65043463 5.8681591e-07 -0.069224649 -0.069224649 -0.069224649 
-    5620        0.562   0.65058774   0.65058645 5.8022805e-07 -0.069303682 -0.069303682 -0.069303682 
-    5630        0.563   0.65073931    0.6507379 5.6210832e-07 -0.069382548 -0.069382548 -0.069382548 
-    5640        0.564   0.65089053   0.65088901 5.3282107e-07 -0.069461248 -0.069461248 -0.069461248 
-    5650        0.565   0.65104139   0.65103976 4.9294848e-07 -0.069539782 -0.069539782 -0.069539782 
-    5660        0.566   0.65119189   0.65119017 4.4327921e-07  -0.06961815  -0.06961815  -0.06961815 
-    5670        0.567   0.65134203   0.65134023 3.8479296e-07 -0.069696352 -0.069696352 -0.069696352 
-    5680        0.568   0.65149182   0.65148994 3.186413e-07  -0.06977439  -0.06977439  -0.06977439 
-    5690        0.569   0.65164124   0.65163931 2.4612515e-07 -0.069852262 -0.069852262 -0.069852262 
-    5700         0.57   0.65179031   0.65178833 1.6866929e-07 -0.069929968 -0.069929968 -0.069929968 
-    5710        0.571   0.65193902   0.65193702 8.7794446e-08  -0.07000751  -0.07000751  -0.07000751 
-    5720        0.572   0.65208737   0.65208536 5.0875238e-09 -0.070084887 -0.070084887 -0.070084887 
-    5730        0.573   0.65223537   0.65223336 -7.7829543e-08   -0.0701621   -0.0701621   -0.0701621 
-    5740        0.574   0.65238301   0.65238102 -1.5933158e-07 -0.070239148 -0.070239148 -0.070239148 
-    5750        0.575   0.65253029   0.65252834 -2.3782204e-07 -0.070316032 -0.070316032 -0.070316032 
-    5760        0.576   0.65267721   0.65267532 -3.1176438e-07 -0.070392751 -0.070392751 -0.070392751 
-    5770        0.577   0.65282379   0.65282196 -3.7971217e-07 -0.070469307 -0.070469307 -0.070469307 
-    5780        0.578   0.65297001   0.65296826 -4.4033753e-07 -0.070545699 -0.070545699 -0.070545699 
-    5790        0.579   0.65311588   0.65311422 -4.9245722e-07 -0.070621928 -0.070621928 -0.070621928 
-    5800         0.58   0.65326139   0.65325983 -5.3505586e-07 -0.070697993 -0.070697993 -0.070697993 
-    5810        0.581   0.65340657   0.65340511 -5.6730589e-07 -0.070773895 -0.070773895 -0.070773895 
-    5820        0.582   0.65355139   0.65355005 -5.8858382e-07 -0.070849633 -0.070849633 -0.070849633 
-    5830        0.583   0.65369587   0.65369464 -5.9848249e-07 -0.070925209 -0.070925209 -0.070925209 
-    5840        0.584      0.65384   0.65383889 -5.9681904e-07 -0.071000623 -0.071000623 -0.071000623 
-    5850        0.585    0.6539838    0.6539828 -5.8363849e-07 -0.071075873 -0.071075873 -0.071075873 
-    5860        0.586   0.65412725   0.65412637 -5.5921279e-07 -0.071150962 -0.071150962 -0.071150962 
-    5870        0.587   0.65427036   0.65426959 -5.2403544e-07 -0.071225888 -0.071225888 -0.071225888 
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-    7450        0.745   0.67298766   0.67298583 2.3108931e-07  -0.08116242  -0.08116242  -0.08116242 
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-    7470        0.747   0.67317977   0.67317787 9.572218e-08 -0.081265845 -0.081265845 -0.081265845 
-    7480        0.748   0.67327544   0.67327352 2.4147794e-08 -0.081317366 -0.081317366 -0.081317366 
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-    8120        0.812   0.67890121   0.67890063 -1.0440976e-07 -0.084360463 -0.084360463 -0.084360463 
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-    8140        0.814   0.67906206   0.67906149 3.043557e-08 -0.084447834 -0.084447834 -0.084447834 
-    8150        0.815   0.67914218   0.67914159 9.6993173e-08 -0.084491352 -0.084491352 -0.084491352 
-    8160        0.816   0.67922208   0.67922146 1.6108406e-07 -0.084534759 -0.084534759 -0.084534759 
-    8170        0.817   0.67930178   0.67930112 2.2135179e-07 -0.084578054 -0.084578054 -0.084578054 
-    8180        0.818   0.67938127   0.67938055 2.7652357e-07 -0.084621237 -0.084621237 -0.084621237 
-    8190        0.819   0.67946055   0.67945976 3.2543709e-07  -0.08466431  -0.08466431  -0.08466431 
-    8200         0.82   0.67953962   0.67953876 3.6706513e-07 -0.084707273 -0.084707273 -0.084707273 
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-    8240        0.824   0.67985382   0.67985261 4.4602016e-07  -0.08487802  -0.08487802  -0.08487802 
-    8250        0.825   0.67993184   0.67993054 4.4185622e-07 -0.084920432 -0.084920432 -0.084920432 
-    8260        0.826   0.68000966   0.68000826 4.2803707e-07 -0.084962736 -0.084962736 -0.084962736 
-    8270        0.827   0.68008726   0.68008577 4.0487627e-07  -0.08500493  -0.08500493  -0.08500493 
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-    8290        0.829   0.68024183   0.68024019 3.327646e-07 -0.085088991 -0.085088991 -0.085088991 
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-    8960        0.896   0.68496007   0.68495936 -1.975666e-07 -0.087665718 -0.087665718 -0.087665718 
-    8970        0.897   0.68502413   0.68502346 -1.4009717e-07 -0.087700831 -0.087700831 -0.087700831 
-    8980        0.898   0.68508802   0.68508737 -8.0005408e-08  -0.08773585  -0.08773585  -0.08773585 
-    8990        0.899   0.68515174   0.68515109 -1.8595382e-08 -0.087770776 -0.087770776 -0.087770776 
-    9000          0.9   0.68521529   0.68521464 4.2802966e-08 -0.087805609 -0.087805609 -0.087805609 
-    9010        0.901   0.68527867     0.685278 1.0286263e-07 -0.087840349 -0.087840349 -0.087840349 
-    9020        0.902   0.68534188   0.68534119 1.6028822e-07 -0.087874996 -0.087874996 -0.087874996 
-    9030        0.903   0.68540493   0.68540419 2.1384393e-07 -0.087909551 -0.087909551 -0.087909551 
-    9040        0.904   0.68546781   0.68546701 2.6238014e-07 -0.087944014 -0.087944014 -0.087944014 
-    9050        0.905   0.68553051   0.68552966 3.0485816e-07 -0.087978385 -0.087978385 -0.087978385 
-    9060        0.906   0.68559305   0.68559213 3.4037244e-07 -0.088012665 -0.088012665 -0.088012665 
-    9070        0.907   0.68565542   0.68565442   3.6817e-07 -0.088046852 -0.088046852 -0.088046852 
-    9080        0.908   0.68571762   0.68571654 3.8766636e-07 -0.088080949 -0.088080949 -0.088080949 
-    9090        0.909   0.68577965   0.68577848 3.9845796e-07 -0.088114954 -0.088114954 -0.088114954 
-    9100         0.91   0.68584151   0.68584025 4.0033051e-07 -0.088148868 -0.088148868 -0.088148868 
-    9110        0.911    0.6859032   0.68590186 3.9326329e-07 -0.088182692 -0.088182692 -0.088182692 
-    9120        0.912   0.68596471   0.68596329 3.7742924e-07 -0.088216425 -0.088216425 -0.088216425 
-    9130        0.913   0.68602606   0.68602455 3.5319086e-07 -0.088250067 -0.088250067 -0.088250067 
-    9140        0.914   0.68608723   0.68608565 3.2109199e-07  -0.08828362  -0.08828362  -0.08828362 
-    9150        0.915   0.68614823   0.68614659 2.8184568e-07 -0.088317083 -0.088317083 -0.088317083 
-    9160        0.916   0.68620905   0.68620735 2.3631841e-07 -0.088350456 -0.088350456 -0.088350456 
-    9170        0.917    0.6862697   0.68626796 1.8551105e-07  -0.08838374  -0.08838374  -0.08838374 
-    9180        0.918   0.68633018    0.6863284 1.3053687e-07 -0.088416934 -0.088416934 -0.088416934 
-    9190        0.919   0.68639049   0.68638868 7.2597189e-08 -0.088450039 -0.088450039 -0.088450039 
-    9200         0.92   0.68645062    0.6864488 1.2955167e-08 -0.088483056 -0.088483056 -0.088483056 
-    9210        0.921   0.68651058   0.68650876 -4.7091734e-08 -0.088515984 -0.088515984 -0.088515984 
-    9220        0.922   0.68657036   0.68656856 -1.0623996e-07 -0.088548823 -0.088548823 -0.088548823 
-    9230        0.923   0.68662998    0.6866282 -1.6320817e-07 -0.088581574 -0.088581574 -0.088581574 
-    9240        0.924   0.68668942   0.68668769 -2.1676499e-07 -0.088614237 -0.088614237 -0.088614237 
-    9250        0.925   0.68674869   0.68674701 -2.6575568e-07 -0.088646812 -0.088646812 -0.088646812 
-    9260        0.926   0.68680779   0.68680617 -3.0912704e-07   -0.0886793   -0.0886793   -0.0886793 
-    9270        0.927   0.68686673   0.68686517 -3.4595009e-07   -0.0887117   -0.0887117   -0.0887117 
-    9280        0.928    0.6869255   0.68692401 -3.7544002e-07 -0.088744013 -0.088744013 -0.088744013 
-    9290        0.929    0.6869841   0.68698269 -3.9697293e-07 -0.088776239 -0.088776239 -0.088776239 
-    9300         0.93   0.68704254   0.68704121 -4.1009912e-07 -0.088808378 -0.088808378 -0.088808378 
-    9310        0.931   0.68710081   0.68709956 -4.1455252e-07 -0.088840431 -0.088840431 -0.088840431 
-    9320        0.932   0.68715892   0.68715776 -4.1025607e-07 -0.088872397 -0.088872397 -0.088872397 
-    9330        0.933   0.68721687   0.68721579 -3.9732309e-07 -0.088904277 -0.088904277 -0.088904277 
-    9340        0.934   0.68727466   0.68727366 -3.7605442e-07 -0.088936071 -0.088936071 -0.088936071 
-    9350        0.935   0.68733229   0.68733137 -3.4693151e-07 -0.088967779 -0.088967779 -0.088967779 
-    9360        0.936   0.68738977   0.68738891 -3.1060559e-07 -0.088999401 -0.088999401 -0.088999401 
-    9370        0.937   0.68744709   0.68744628 -2.678832e-07 -0.089030938 -0.089030938 -0.089030938 
-    9380        0.938   0.68750426    0.6875035 -2.1970834e-07  -0.08906239  -0.08906239  -0.08906239 
-    9390        0.939   0.68756127   0.68756055 -1.671416e-07 -0.089093757 -0.089093757 -0.089093757 
-    9400         0.94   0.68761812   0.68761743 -1.1133694e-07 -0.089125039 -0.089125039 -0.089125039 
-    9410        0.941   0.68767483   0.68767415 -5.3516312e-08 -0.089156237 -0.089156237 -0.089156237 
-    9420        0.942   0.68773138    0.6877307 5.0570456e-09  -0.08918735  -0.08918735  -0.08918735 
-    9430        0.943   0.68778778   0.68778709 6.3106191e-08 -0.089218379 -0.089218379 -0.089218379 
-    9440        0.944   0.68784403   0.68784332 1.1936833e-07 -0.089249324 -0.089249324 -0.089249324 
-    9450        0.945   0.68790013   0.68789939 1.7262227e-07 -0.089280185 -0.089280185 -0.089280185 
-    9460        0.946   0.68795608   0.68795529  2.21715e-07 -0.089310962 -0.089310962 -0.089310962 
-    9470        0.947   0.68801188   0.68801103 2.6558658e-07 -0.089341657 -0.089341657 -0.089341657 
-    9480        0.948   0.68806752   0.68806662 3.0329316e-07 -0.089372267 -0.089372267 -0.089372267 
-    9490        0.949   0.68812302   0.68812204 3.3402726e-07 -0.089402795 -0.089402795 -0.089402795 
-    9500         0.95   0.68817836    0.6881773 3.5713511e-07  -0.08943324  -0.08943324  -0.08943324 
-    9510        0.951   0.68823355   0.68823241 3.721306e-07 -0.089463603 -0.089463603 -0.089463603 
-    9520        0.952   0.68828858   0.68828737 3.7870557e-07 -0.089493883 -0.089493883 -0.089493883 
-    9530        0.953   0.68834347   0.68834217 3.7673613e-07  -0.08952408  -0.08952408  -0.08952408 
-    9540        0.954   0.68839819   0.68839682 3.6628503e-07 -0.089554196 -0.089554196 -0.089554196 
-    9550        0.955   0.68845277   0.68845131 3.4759992e-07  -0.08958423  -0.08958423  -0.08958423 
-    9560        0.956   0.68850719   0.68850566 3.2110753e-07 -0.089614182 -0.089614182 -0.089614182 
-    9570        0.957   0.68856145   0.68855986 2.8740406e-07 -0.089644053 -0.089644053 -0.089644053 
-    9580        0.958   0.68861556   0.68861391 2.4724178e-07 -0.089673843 -0.089673843 -0.089673843 
-    9590        0.959   0.68866951   0.68866781 2.0151231e-07 -0.089703551 -0.089703551 -0.089703551 
-    9600         0.96    0.6887233   0.68872157 1.5122687e-07 -0.089733179 -0.089733179 -0.089733179 
-    9610        0.961   0.68877694   0.68877518 9.749396e-08 -0.089762726 -0.089762726 -0.089762726 
-    9620        0.962   0.68883043   0.68882864 4.1494944e-08 -0.089792192 -0.089792192 -0.089792192 
-    9630        0.963   0.68888376   0.68888197 -1.5541893e-08 -0.089821578 -0.089821578 -0.089821578 
-    9640        0.964   0.68893693   0.68893515 -7.2368278e-08 -0.089850884 -0.089850884 -0.089850884 
-    9650        0.965   0.68898995   0.68898818 -1.2774327e-07 -0.089880111 -0.089880111 -0.089880111 
-    9660        0.966   0.68904281   0.68904108 -1.8046035e-07 -0.089909257 -0.089909257 -0.089909257 
-    9670        0.967   0.68909552   0.68909383 -2.2937375e-07 -0.089938324 -0.089938324 -0.089938324 
-    9680        0.968   0.68914808   0.68914644 -2.7342333e-07 -0.089967312 -0.089967312 -0.089967312 
-    9690        0.969   0.68920048    0.6891989 -3.1165765e-07  -0.08999622  -0.08999622  -0.08999622 
-    9700         0.97   0.68925273   0.68925122 -3.4325447e-07  -0.09002505  -0.09002505  -0.09002505 
-    9710        0.971   0.68930484    0.6893034 -3.6753853e-07 -0.090053801 -0.090053801 -0.090053801 
-    9720        0.972    0.6893568   0.68935543 -3.8399599e-07 -0.090082473 -0.090082473 -0.090082473 
-    9730        0.973    0.6894086   0.68940732 -3.9228536e-07 -0.090111067 -0.090111067 -0.090111067 
-    9740        0.974   0.68946027   0.68945906 -3.9224459e-07 -0.090139582 -0.090139582 -0.090139582 
-    9750        0.975   0.68951179   0.68951066 -3.8389426e-07  -0.09016802  -0.09016802  -0.09016802 
-    9760        0.976   0.68956316   0.68956211 -3.6743677e-07  -0.09019638  -0.09019638  -0.09019638 
-    9770        0.977   0.68961439   0.68961341 -3.432515e-07 -0.090224662 -0.090224662 -0.090224662 
-    9780        0.978   0.68966548   0.68966457 -3.1188616e-07 -0.090252867 -0.090252867 -0.090252867 
-    9790        0.979   0.68971643   0.68971558 -2.7404444e-07 -0.090280995 -0.090280995 -0.090280995 
-    9800         0.98   0.68976724   0.68976644 -2.3057029e-07 -0.090309045 -0.090309045 -0.090309045 
-    9810        0.981   0.68981792   0.68981715 -1.8242913e-07 -0.090337019 -0.090337019 -0.090337019 
-    9820        0.982   0.68986845   0.68986772 -1.3068644e-07 -0.090364916 -0.090364916 -0.090364916 
-    9830        0.983   0.68991885   0.68991813 -7.6484243e-08 -0.090392736 -0.090392736 -0.090392736 
-    9840        0.984   0.68996912    0.6899684 -2.1015886e-08  -0.09042048  -0.09042048  -0.09042048 
-    9850        0.985   0.69001924   0.69001853 3.4500202e-08 -0.090448148 -0.090448148 -0.090448148 
-    9860        0.986   0.69006924    0.6900685 8.8847271e-08 -0.090475741 -0.090475741 -0.090475741 
-    9870        0.987   0.69011909   0.69011833 1.4083692e-07 -0.090503257 -0.090503257 -0.090503257 
-    9880        0.988   0.69016881   0.69016801 1.8933509e-07 -0.090530698 -0.090530698 -0.090530698 
-    9890        0.989    0.6902184   0.69021755 2.3328683e-07 -0.090558063 -0.090558063 -0.090558063 
-    9900         0.99   0.69026785   0.69026695 2.7173925e-07 -0.090585353 -0.090585353 -0.090585353 
-    9910        0.991   0.69031717    0.6903162 3.038622e-07 -0.090612569 -0.090612569 -0.090612569 
-    9920        0.992   0.69036635   0.69036531 3.2896626e-07 -0.090639709 -0.090639709 -0.090639709 
-    9930        0.993   0.69041539   0.69041428 3.4651751e-07 -0.090666775 -0.090666775 -0.090666775 
-    9940        0.994   0.69046429   0.69046311  3.56149e-07 -0.090693766 -0.090693766 -0.090693766 
-    9950        0.995   0.69051306    0.6905118 3.5766835e-07 -0.090720683 -0.090720683 -0.090720683 
-    9960        0.996   0.69056169   0.69056035 3.5106169e-07 -0.090747526 -0.090747526 -0.090747526 
-    9970        0.997   0.69061018   0.69060877 3.3649353e-07 -0.090774295 -0.090774295 -0.090774295 
-    9980        0.998   0.69065854   0.69065705 3.143028e-07  -0.09080099  -0.09080099  -0.09080099 
-    9990        0.999   0.69070675    0.6907052 2.8499502e-07 -0.090827612 -0.090827612 -0.090827612 
-   10000            1   0.69075483   0.69075321 2.4923086e-07  -0.09085416  -0.09085416  -0.09085416 
-   10010        1.001   0.69080276    0.6908011 2.0781127e-07 -0.090880635 -0.090880635 -0.090880635 
-   10020        1.002   0.69085056   0.69084885 1.6165961e-07 -0.090907037 -0.090907037 -0.090907037 
-   10030        1.003   0.69089821   0.69089648 1.118011e-07 -0.090933367 -0.090933367 -0.090933367 
-   10040        1.004   0.69094572   0.69094397 5.9340085e-08 -0.090959623 -0.090959623 -0.090959623 
-   10050        1.005    0.6909931   0.69099134 5.4355473e-09 -0.090985807 -0.090985807 -0.090985807 
-   10060        1.006   0.69104033   0.69103857 -4.8724427e-08 -0.091011919 -0.091011919 -0.091011919 
-   10070        1.007   0.69108743   0.69108568 -1.0194886e-07 -0.091037959 -0.091037959 -0.091037959 
-   10080        1.008   0.69113438   0.69113266 -1.5307005e-07 -0.091063927 -0.091063927 -0.091063927 
-   10090        1.009    0.6911812   0.69117952 -2.0096923e-07 -0.091089823 -0.091089823 -0.091089823 
-   10100         1.01   0.69122788   0.69122624 -2.4460104e-07 -0.091115648 -0.091115648 -0.091115648 
-   10110        1.011   0.69127443   0.69127284 -2.8301635e-07 -0.091141401 -0.091141401 -0.091141401 
-   10120        1.012   0.69132084   0.69131931 -3.1538295e-07 -0.091167083 -0.091167083 -0.091167083 
-   10130        1.013   0.69136711   0.69136565 -3.4100363e-07 -0.091192693 -0.091192693 -0.091192693 
-   10140        1.014   0.69141325   0.69141186 -3.5933117e-07 -0.091218233 -0.091218233 -0.091218233 
-   10150        1.015   0.69145926   0.69145794 -3.699801e-07 -0.091243703 -0.091243703 -0.091243703 
-   10160        1.016   0.69150514    0.6915039 -3.7273481e-07 -0.091269102 -0.091269102 -0.091269102 
-   10170        1.017   0.69155088   0.69154972 -3.6755394e-07  -0.09129443  -0.09129443  -0.09129443 
-   10180        1.018    0.6915965   0.69159541 -3.5457093e-07 -0.091319688 -0.091319688 -0.091319688 
-   10190        1.019   0.69164199   0.69164097 -3.3409064e-07 -0.091344877 -0.091344877 -0.091344877 
-   10200         1.02   0.69168736    0.6916864 -3.0658233e-07 -0.091369995 -0.091369995 -0.091369995 
-   10210        1.021   0.69173259   0.69173169 -2.7266894e-07 -0.091395044 -0.091395044 -0.091395044 
-   10220        1.022   0.69177771   0.69177686 -2.3311303e-07 -0.091420023 -0.091420023 -0.091420023 
-   10230        1.023    0.6918227   0.69182189 -1.8879967e-07 -0.091444933 -0.091444933 -0.091444933 
-   10240        1.024   0.69186757   0.69186679 -1.407167e-07 -0.091469774 -0.091469774 -0.091469774 
-   10250        1.025   0.69191231   0.69191155 -8.993269e-08 -0.091494546 -0.091494546 -0.091494546 
-   10260        1.026   0.69195693   0.69195619 -3.7573278e-08 -0.091519249 -0.091519249 -0.091519249 
-   10270        1.027   0.69200144   0.69200069 1.5203814e-08 -0.091543884 -0.091543884 -0.091543884 
-   10280        1.028   0.69204582   0.69204506 6.7234351e-08  -0.09156845  -0.09156845  -0.09156845 
-   10290        1.029   0.69209008   0.69208929 1.1737327e-07 -0.091592948 -0.091592948 -0.091592948 
-   10300         1.03   0.69213422    0.6921334 1.6451988e-07 -0.091617378 -0.091617378 -0.091617378 
-   10310        1.031   0.69217824   0.69217738 2.0764205e-07  -0.09164174  -0.09164174  -0.09164174 
-   10320        1.032   0.69222213   0.69222122 2.4579878e-07 -0.091666034 -0.091666034 -0.091666034 
-   10330        1.033   0.69226591   0.69226494 2.7816081e-07 -0.091690261 -0.091690261 -0.091690261 
-   10340        1.034   0.69230957   0.69230853 3.0402864e-07  -0.09171442  -0.09171442  -0.09171442 
-   10350        1.035    0.6923531     0.692352 3.2284766e-07 -0.091738512 -0.091738512 -0.091738512 
-   10360        1.036   0.69239651   0.69239534 3.3422007e-07 -0.091762537 -0.091762537 -0.091762537 
-   10370        1.037    0.6924398   0.69243855 3.3791336e-07 -0.091786495 -0.091786495 -0.091786495 
-   10380        1.038   0.69248296   0.69248164  3.33865e-07 -0.091810386 -0.091810386 -0.091810386 
-   10390        1.039   0.69252601   0.69252461 3.2218348e-07 -0.091834211 -0.091834211 -0.091834211 
-   10400         1.04   0.69256892   0.69256746 3.0314554e-07 -0.091857969 -0.091857969 -0.091857969 
-   10410        1.041   0.69261172   0.69261019 2.7718967e-07 -0.091881662 -0.091881662 -0.091881662 
-   10420        1.042   0.69265438    0.6926528 2.4490607e-07 -0.091905288 -0.091905288 -0.091905288 
-   10430        1.043   0.69269693    0.6926953 2.0702329e-07 -0.091928848 -0.091928848 -0.091928848 
-   10440        1.044   0.69273934   0.69273767 1.643918e-07 -0.091952342 -0.091952342 -0.091952342 
-   10450        1.045   0.69278164   0.69277993 1.1796495e-07 -0.091975771 -0.091975771 -0.091975771 
-   10460        1.046    0.6928238   0.69282208 6.8777704e-08 -0.091999135 -0.091999135 -0.091999135 
-   10470        1.047   0.69286584   0.69286411 1.7923524e-08 -0.092022433 -0.092022433 -0.092022433 
-   10480        1.048   0.69290776   0.69290602 -3.3469864e-08 -0.092045666 -0.092045666 -0.092045666 
-   10490        1.049   0.69294955   0.69294782 -8.4265498e-08 -0.092068835 -0.092068835 -0.092068835 
-   10500         1.05   0.69299121   0.69298951 -1.3334232e-07 -0.092091938 -0.092091938 -0.092091938 
-   10510        1.051   0.69303276   0.69303108 -1.7961993e-07 -0.092114977 -0.092114977 -0.092114977 
-   10520        1.052   0.69307417   0.69307254 -2.2208238e-07 -0.092137952 -0.092137952 -0.092137952 
-   10530        1.053   0.69311547   0.69311388 -2.5980046e-07 -0.092160863 -0.092160863 -0.092160863 
-   10540        1.054   0.69315664   0.69315511 -2.9195212e-07 -0.092183709 -0.092183709 -0.092183709 
-   10550        1.055    0.6931977   0.69319623 -3.1784032e-07 -0.092206492 -0.092206492 -0.092206492 
-   10560        1.056   0.69323863   0.69323723 -3.3690823e-07  -0.09222921  -0.09222921  -0.09222921 
-   10570        1.057   0.69327945   0.69327812 -3.4875121e-07 -0.092251865 -0.092251865 -0.092251865 
-   10580        1.058   0.69332014   0.69331888 -3.5312541e-07 -0.092274457 -0.092274457 -0.092274457 
-   10590        1.059   0.69336073   0.69335954 -3.4995279e-07 -0.092296986 -0.092296986 -0.092296986 
-   10600         1.06   0.69340119   0.69340007 -3.393225e-07 -0.092319451 -0.092319451 -0.092319451 
-   10610        1.061   0.69344154   0.69344049 -3.2148851e-07 -0.092341854 -0.092341854 -0.092341854 
-   10620        1.062   0.69348178   0.69348079 -2.9686361e-07 -0.092364193 -0.092364193 -0.092364193 
-   10630        1.063   0.69352191   0.69352097 -2.6600991e-07  -0.09238647  -0.09238647  -0.09238647 
-   10640        1.064   0.69356192   0.69356104 -2.2962607e-07 -0.092408685 -0.092408685 -0.092408685 
-   10650        1.065   0.69360183   0.69360098 -1.8853149e-07 -0.092430837 -0.092430837 -0.092430837 
-   10660        1.066   0.69364162   0.69364081 -1.4364793e-07 -0.092452928 -0.092452928 -0.092452928 
-   10670        1.067   0.69368131   0.69368052 -9.5978821e-08 -0.092474956 -0.092474956 -0.092474956 
-   10680        1.068   0.69372088   0.69372011 -4.6586875e-08 -0.092496922 -0.092496922 -0.092496922 
-   10690        1.069   0.69376035   0.69375958 3.4295913e-09 -0.092518827 -0.092518827 -0.092518827 
-   10700         1.07   0.69379971   0.69379893 5.2961074e-08  -0.09254067  -0.09254067  -0.09254067 
-   10710        1.071   0.69383897   0.69383816 1.0091149e-07 -0.092562452 -0.092562452 -0.092562452 
-   10720        1.072   0.69387811   0.69387728 1.4622244e-07 -0.092584173 -0.092584173 -0.092584173 
-   10730        1.073   0.69391715   0.69391628 1.8789655e-07 -0.092605833 -0.092605833 -0.092605833 
-   10740        1.074   0.69395608   0.69395516 2.2501949e-07 -0.092627432 -0.092627432 -0.092627432 
-   10750        1.075   0.69399491   0.69399393 2.5677998e-07  -0.09264897  -0.09264897  -0.09264897 
-   10760        1.076   0.69403362   0.69403259 2.824876e-07 -0.092670448 -0.092670448 -0.092670448 
-   10770        1.077   0.69407223   0.69407113 3.0158779e-07 -0.092691865 -0.092691865 -0.092691865 
-   10780        1.078   0.69411073   0.69410956 3.1367381e-07 -0.092713222 -0.092713222 -0.092713222 
-   10790        1.079   0.69414911   0.69414788 3.1849546e-07 -0.092734519 -0.092734519 -0.092734519 
-   10800         1.08   0.69418739   0.69418608 3.1596425e-07 -0.092755756 -0.092755756 -0.092755756 
-   10810        1.081   0.69422556   0.69422418 3.0615497e-07 -0.092776933 -0.092776933 -0.092776933 
-   10820        1.082   0.69426361   0.69426217 2.8930369e-07 -0.092798051 -0.092798051 -0.092798051 
-   10830        1.083   0.69430156   0.69430006 2.6580209e-07 -0.092819109 -0.092819109 -0.092819109 
-   10840        1.084   0.69433939   0.69433784 2.3618848e-07 -0.092840108 -0.092840108 -0.092840108 
-   10850        1.085   0.69437711   0.69437551 2.0113546e-07 -0.092861048 -0.092861048 -0.092861048 
-   10860        1.086   0.69441472   0.69441308 1.6143468e-07 -0.092881928 -0.092881928 -0.092881928 
-   10870        1.087   0.69445222   0.69445054 1.1797904e-07  -0.09290275  -0.09290275  -0.09290275 
-   10880        1.088    0.6944896    0.6944879 7.1742582e-08 -0.092923513 -0.092923513 -0.092923513 
-   10890        1.089   0.69452688   0.69452516 2.3758699e-08 -0.092944218 -0.092944218 -0.092944218 
-   10900         1.09   0.69456404   0.69456232 -2.4902945e-08 -0.092964864 -0.092964864 -0.092964864 
-   10910        1.091   0.69460108   0.69459938 -7.3160257e-08 -0.092985452 -0.092985452 -0.092985452 
-   10920        1.092   0.69463802   0.69463633 -1.1994277e-07 -0.093005982 -0.093005982 -0.093005982 
-   10930        1.093   0.69467485   0.69467319 -1.642154e-07 -0.093026454 -0.093026454 -0.093026454 
-   10940        1.094   0.69471156   0.69470994 -2.0500133e-07 -0.093046868 -0.093046868 -0.093046868 
-   10950        1.095   0.69474817   0.69474659 -2.4140361e-07 -0.093067225 -0.093067225 -0.093067225 
-   10960        1.096   0.69478466   0.69478314 -2.7262485e-07 -0.093087524 -0.093087524 -0.093087524 
-   10970        1.097   0.69482105   0.69481958 -2.9798474e-07 -0.093107766 -0.093107766 -0.093107766 
-   10980        1.098   0.69485733   0.69485593 -3.1693487e-07  -0.09312795  -0.09312795  -0.09312795 
-   10990        1.099   0.69489351   0.69489217 -3.2907063e-07 -0.093148078 -0.093148078 -0.093148078 
-   11000          1.1   0.69492958   0.69492831 -3.3413983e-07 -0.093168148 -0.093168148 -0.093168148 
-   11010        1.101   0.69496554   0.69496434 -3.3204797e-07 -0.093188162 -0.093188162 -0.093188162 
-   11020        1.102   0.69500141   0.69500027 -3.2285996e-07  -0.09320812  -0.09320812  -0.09320812 
-   11030        1.103   0.69503717   0.69503609 -3.0679831e-07  -0.09322802  -0.09322802  -0.09322802 
-   11040        1.104   0.69507283   0.69507181 -2.8423779e-07 -0.093247865 -0.093247865 -0.093247865 
-   11050        1.105   0.69510839   0.69510743 -2.5569675e-07 -0.093267653 -0.093267653 -0.093267653 
-   11060        1.106   0.69514385   0.69514293 -2.2182526e-07 -0.093287386 -0.093287386 -0.093287386 
-   11070        1.107   0.69517921   0.69517834 -1.8339032e-07 -0.093307062 -0.093307062 -0.093307062 
-   11080        1.108   0.69521447   0.69521363 -1.4125853e-07 -0.093326683 -0.093326683 -0.093326683 
-   11090        1.109   0.69524964   0.69524882 -9.6376583e-08 -0.093346248 -0.093346248 -0.093346248 
-   11100         1.11   0.69528471   0.69528391 -4.9750004e-08 -0.093365758 -0.093365758 -0.093365758 
-   11110        1.111   0.69531969   0.69531888 -2.4206371e-09 -0.093385213 -0.093385213 -0.093385213 
-   11120        1.112   0.69535457   0.69535375 4.4556621e-08 -0.093404612 -0.093404612 -0.093404612 
-   11130        1.113   0.69538935   0.69538852 9.0137329e-08 -0.093423957 -0.093423957 -0.093423957 
-   11140        1.114   0.69542404   0.69542318 1.3331072e-07 -0.093443247 -0.093443247 -0.093443247 
-   11150        1.115   0.69545863   0.69545774 1.7312213e-07 -0.093462482 -0.093462482 -0.093462482 
-   11160        1.116   0.69549313   0.69549219 2.0869409e-07 -0.093481662 -0.093481662 -0.093481662 
-   11170        1.117   0.69552753   0.69552654 2.3924572e-07 -0.093500788 -0.093500788 -0.093500788 
-   11180        1.118   0.69556183   0.69556079 2.6410983e-07  -0.09351986  -0.09351986  -0.09351986 
-   11190        1.119   0.69559604   0.69559493 2.8274756e-07 -0.093538877 -0.093538877 -0.093538877 
-   11200         1.12   0.69563015   0.69562898 2.9476002e-07 -0.093557841 -0.093557841 -0.093557841 
-   11210        1.121   0.69566416   0.69566293 2.9989688e-07 -0.093576751 -0.093576751 -0.093576751 
-   11220        1.122   0.69569807   0.69569677 2.9806158e-07 -0.093595607 -0.093595607 -0.093595607 
-   11230        1.123   0.69573189   0.69573053 2.8931308e-07  -0.09361441  -0.09361441  -0.09361441 
-   11240        1.124   0.69576561   0.69576418 2.7386421e-07 -0.093633159 -0.093633159 -0.093633159 
-   11250        1.125   0.69579923   0.69579774 2.5207657e-07 -0.093651855 -0.093651855 -0.093651855 
-   11260        1.126   0.69583274   0.69583121 2.2445205e-07 -0.093670497 -0.093670497 -0.093670497 
-   11270        1.127   0.69586616   0.69586458 1.9162136e-07 -0.093689087 -0.093689087 -0.093689087 
-   11280        1.128   0.69589948   0.69589786 1.5432967e-07 -0.093707624 -0.093707624 -0.093707624 
-   11290        1.129    0.6959327   0.69593104 1.1341969e-07 -0.093726108 -0.093726108 -0.093726108 
-   11300         1.13   0.69596581   0.69596414 6.9812661e-08  -0.09374454  -0.09374454  -0.09374454 
-   11310        1.131   0.69599883   0.69599714 2.4487635e-08 -0.093762919 -0.093762919 -0.093762919 
-   11320        1.132   0.69603175   0.69603006 -2.1540494e-08 -0.093781246 -0.093781246 -0.093781246 
-   11330        1.133   0.69606456   0.69606288 -6.7243707e-08 -0.093799521 -0.093799521 -0.093799521 
-   11340        1.134   0.69609728   0.69609561 -1.1160382e-07 -0.093817744 -0.093817744 -0.093817744 
-   11350        1.135    0.6961299   0.69612826 -1.5363517e-07 -0.093835915 -0.093835915 -0.093835915 
-   11360        1.136   0.69616241   0.69616081 -1.9240649e-07 -0.093854034 -0.093854034 -0.093854034 
-   11370        1.137   0.69619484   0.69619327 -2.2706161e-07 -0.093872101 -0.093872101 -0.093872101 
-   11380        1.138   0.69622716   0.69622564 -2.5683832e-07 -0.093890118 -0.093890118 -0.093890118 
-   11390        1.139   0.69625939   0.69625792 -2.8108514e-07 -0.093908082 -0.093908082 -0.093908082 
-   11400         1.14   0.69629152   0.69629011 -2.9927565e-07 -0.093925996 -0.093925996 -0.093925996 
-   11410        1.141   0.69632355   0.69632221 -3.1101987e-07 -0.093943859 -0.093943859 -0.093943859 
-   11420        1.142    0.6963555   0.69635422 -3.1607265e-07  -0.09396167  -0.09396167  -0.09396167 
-   11430        1.143   0.69638734   0.69638613 -3.143388e-07 -0.093979431 -0.093979431 -0.093979431 
-   11440        1.144    0.6964191   0.69641795 -3.0587483e-07 -0.093997141 -0.093997141 -0.093997141 
-   11450        1.145   0.69645077   0.69644968 -2.9088733e-07 -0.094014801 -0.094014801 -0.094014801 
-   11460        1.146   0.69648235   0.69648132 -2.6972799e-07  -0.09403241  -0.09403241  -0.09403241 
-   11470        1.147   0.69651384   0.69651286 -2.4288538e-07 -0.094049969 -0.094049969 -0.094049969 
-   11480        1.148   0.69654524    0.6965443 -2.1097374e-07 -0.094067478 -0.094067478 -0.094067478 
-   11490        1.149   0.69657655   0.69657565 -1.7471892e-07 -0.094084937 -0.094084937 -0.094084937 
-   11500         1.15   0.69660777   0.69660691 -1.3494192e-07 -0.094102347 -0.094102347 -0.094102347 
-   11510        1.151   0.69663891   0.69663807 -9.2540291e-08 -0.094119706 -0.094119706 -0.094119706 
-   11520        1.152   0.69666997   0.69666913 -4.8467946e-08 -0.094137016 -0.094137016 -0.094137016 
-   11530        1.153   0.69670094    0.6967001 -3.7136761e-09 -0.094154276 -0.094154276 -0.094154276 
-   11540        1.154   0.69673182   0.69673098 4.0721009e-08 -0.094171487 -0.094171487 -0.094171487 
-   11550        1.155   0.69676262   0.69676176 8.3844293e-08 -0.094188649 -0.094188649 -0.094188649 
-   11560        1.156   0.69679333   0.69679245 1.2469619e-07 -0.094205762 -0.094205762 -0.094205762 
-   11570        1.157   0.69682396   0.69682304 1.623699e-07 -0.094222826 -0.094222826 -0.094222826 
-   11580        1.158    0.6968545   0.69685355 1.9603199e-07 -0.094239841 -0.094239841 -0.094239841 
-   11590        1.159   0.69688496   0.69688396 2.2494077e-07 -0.094256808 -0.094256808 -0.094256808 
-   11600         1.16   0.69691533   0.69691428 2.484627e-07 -0.094273726 -0.094273726 -0.094273726 
-   11610        1.161   0.69694562   0.69694451 2.6608628e-07 -0.094290596 -0.094290596 -0.094290596 
-   11620        1.162   0.69697582   0.69697465 2.7743315e-07 -0.094307417 -0.094307417 -0.094307417 
-   11630        1.163   0.69700594    0.6970047 2.8226625e-07  -0.09432419  -0.09432419  -0.09432419 
-   11640        1.164   0.69703596   0.69703466 2.8049475e-07 -0.094340915 -0.094340915 -0.094340915 
-   11650        1.165    0.6970659   0.69706454 2.7217574e-07 -0.094357593 -0.094357593 -0.094357593 
-   11660        1.166   0.69709575   0.69709433 2.5751257e-07 -0.094374222 -0.094374222 -0.094374222 
-   11670        1.167   0.69712551   0.69712404 2.3684995e-07 -0.094390804 -0.094390804 -0.094390804 
-   11680        1.168   0.69715518   0.69715366 2.106659e-07 -0.094407339 -0.094407339 -0.094407339 
-   11690        1.169   0.69718477    0.6971832 1.7956068e-07 -0.094423826 -0.094423826 -0.094423826 
-   11700         1.17   0.69721426   0.69721266 1.4424311e-07 -0.094440266 -0.094440266 -0.094440266 
-   11710        1.171   0.69724367   0.69724203 1.0551442e-07 -0.094456659 -0.094456659 -0.094456659 
-   11720        1.172   0.69727298   0.69727133 6.4250108e-08 -0.094473004 -0.094473004 -0.094473004 
-   11730        1.173   0.69730221   0.69730054 2.1380133e-08 -0.094489303 -0.094489303 -0.094489303 
-   11740        1.174   0.69733134   0.69732967  -2.2132e-08 -0.094505556 -0.094505556 -0.094505556 
-   11750        1.175   0.69736039   0.69735873 -6.5310898e-08 -0.094521761 -0.094521761 -0.094521761 
-   11760        1.176   0.69738934    0.6973877 -1.0719114e-07  -0.09453792  -0.09453792  -0.09453792 
-   11770        1.177   0.69741821   0.69741659 -1.4683886e-07 -0.094554033 -0.094554033 -0.094554033 
-   11780        1.178   0.69744699    0.6974454 -1.8337258e-07   -0.0945701   -0.0945701   -0.0945701 
-   11790        1.179   0.69747568   0.69747414 -2.1598279e-07  -0.09458612  -0.09458612  -0.09458612 
-   11800         1.18   0.69750429   0.69750279 -2.4394994e-07 -0.094602095 -0.094602095 -0.094602095 
-   11810        1.181   0.69753281   0.69753136 -2.6666025e-07 -0.094618023 -0.094618023 -0.094618023 
-   11820        1.182   0.69756125   0.69755985 -2.8361928e-07 -0.094633906 -0.094633906 -0.094633906 
-   11830        1.183    0.6975896   0.69758826 -2.9446262e-07 -0.094649743 -0.094649743 -0.094649743 
-   11840        1.184   0.69761786   0.69761659 -2.9896379e-07 -0.094665535 -0.094665535 -0.094665535 
-   11850        1.185   0.69764605   0.69764483 -2.9703893e-07 -0.094681282 -0.094681282 -0.094681282 
-   11860        1.186   0.69767415     0.697673 -2.8874832e-07 -0.094696983 -0.094696983 -0.094696983 
-   11870        1.187   0.69770217   0.69770108 -2.742947e-07 -0.094712639 -0.094712639 -0.094712639 
-   11880        1.188   0.69773012   0.69772907 -2.5401833e-07  -0.09472825  -0.09472825  -0.09472825 
-   11890        1.189   0.69775798   0.69775698 -2.2838906e-07 -0.094743816 -0.094743816 -0.094743816 
-   11900         1.19   0.69778576   0.69778481 -1.9799542e-07 -0.094759338 -0.094759338 -0.094759338 
-   11910        1.191   0.69781347   0.69781255 -1.635312e-07 -0.094774815 -0.094774815 -0.094774815 
-   11920        1.192    0.6978411   0.69784021 -1.257796e-07 -0.094790247 -0.094790247 -0.094790247 
-   11930        1.193   0.69786866   0.69786778 -8.5595447e-08 -0.094805635 -0.094805635 -0.094805635 
-   11940        1.194   0.69789613   0.69789527 -4.3885875e-08 -0.094820979 -0.094820979 -0.094820979 
-   11950        1.195   0.69792354   0.69792268 -1.5898447e-09 -0.094836278 -0.094836278 -0.094836278 
-   11960        1.196   0.69795086      0.69795 4.0342983e-08 -0.094851534 -0.094851534 -0.094851534 
-   11970        1.197   0.69797812   0.69797723 8.097356e-08 -0.094866746 -0.094866746 -0.094866746 
-   11980        1.198   0.69800529   0.69800438 1.1939448e-07 -0.094881913 -0.094881913 -0.094881913 
-   11990        1.199   0.69803239   0.69803145 1.5475026e-07 -0.094897038 -0.094897038 -0.094897038 
-   12000          1.2   0.69805942   0.69805844 1.8625635e-07 -0.094912118 -0.094912118 -0.094912118 
-   12010        1.201   0.69808637   0.69808534 2.132166e-07 -0.094927155 -0.094927155 -0.094927155 
-   12020        1.202   0.69811324   0.69811217 2.3503862e-07 -0.094942149 -0.094942149 -0.094942149 
-   12030        1.203   0.69814004   0.69813891 2.512468e-07   -0.0949571   -0.0949571   -0.0949571 
-   12040        1.204   0.69816676   0.69816557 2.614927e-07 -0.094972008 -0.094972008 -0.094972008 
-   12050        1.205    0.6981934   0.69819216 2.6556253e-07 -0.094986872 -0.094986872 -0.094986872 
-   12060        1.206   0.69821997   0.69821866 2.6338162e-07 -0.095001694 -0.095001694 -0.095001694 
-   12070        1.207   0.69824646   0.69824509 2.550157e-07 -0.095016473 -0.095016473 -0.095016473 
-   12080        1.208   0.69827286   0.69827145 2.4066914e-07  -0.09503121  -0.09503121  -0.09503121 
-   12090        1.209   0.69829919   0.69829773 2.2067994e-07 -0.095045904 -0.095045904 -0.095045904 
-   12100         1.21   0.69832545   0.69832393 1.9551185e-07 -0.095060555 -0.095060555 -0.095060555 
-   12110        1.211   0.69835162   0.69835006 1.6574363e-07 -0.095075165 -0.095075165 -0.095075165 
-   12120        1.212   0.69837771   0.69837612 1.3205574e-07 -0.095089732 -0.095089732 -0.095089732 
-   12130        1.213   0.69840372    0.6984021 9.5214852e-08 -0.095104257 -0.095104257 -0.095104257 
-   12140        1.214   0.69842965   0.69842802 5.6056405e-08  -0.09511874  -0.09511874  -0.09511874 
-   12150        1.215    0.6984555   0.69845386 1.5465654e-08 -0.095133182 -0.095133182 -0.095133182 
-   12160        1.216   0.69848127   0.69847963 -2.5642312e-08 -0.095147582 -0.095147582 -0.095147582 
-   12170        1.217   0.69850697   0.69850533 -6.6343197e-08  -0.09516194  -0.09516194  -0.09516194 
-   12180        1.218   0.69853258   0.69853096 -1.0572428e-07 -0.095176257 -0.095176257 -0.095176257 
-   12190        1.219   0.69855811   0.69855651 -1.4290487e-07 -0.095190532 -0.095190532 -0.095190532 
-   12200         1.22   0.69858357     0.698582 -1.7705601e-07 -0.095204766 -0.095204766 -0.095204766 
-   12210        1.221   0.69860894   0.69860742 -2.0741899e-07 -0.095218959 -0.095218959 -0.095218959 
-   12220        1.222   0.69863424   0.69863276 -2.3332213e-07 -0.095233111 -0.095233111 -0.095233111 
-   12230        1.223   0.69865947   0.69865803 -2.5419574e-07 -0.095247223 -0.095247223 -0.095247223 
-   12240        1.224   0.69868461   0.69868323 -2.6958459e-07 -0.095261293 -0.095261293 -0.095261293 
-   12250        1.225   0.69870969   0.69870836 -2.7915786e-07 -0.095275323 -0.095275323 -0.095275323 
-   12260        1.226   0.69873469   0.69873342 -2.8271628e-07 -0.095289312 -0.095289312 -0.095289312 
-   12270        1.227   0.69875961    0.6987584 -2.8019621e-07 -0.095303261 -0.095303261 -0.095303261 
-   12280        1.228   0.69878446   0.69878331 -2.716708e-07 -0.095317169 -0.095317169 -0.095317169 
-   12290        1.229   0.69880924   0.69880814 -2.5734791e-07 -0.095331037 -0.095331037 -0.095331037 
-   12300         1.23   0.69883396    0.6988329 -2.3756517e-07 -0.095344865 -0.095344865 -0.095344865 
-   12310        1.231    0.6988586   0.69885759 -2.12782e-07 -0.095358653 -0.095358653 -0.095358653 
-   12320        1.232   0.69888317    0.6988822 -1.8356899e-07 -0.095372401 -0.095372401 -0.095372401 
-   12330        1.233   0.69890767   0.69890673 -1.5059482e-07  -0.09538611  -0.09538611  -0.09538611 
-   12340        1.234    0.6989321   0.69893119 -1.1461091e-07 -0.095399778 -0.095399778 -0.095399778 
-   12350        1.235   0.69895647   0.69895558 -7.6434352e-08 -0.095413407 -0.095413407 -0.095413407 
-   12360        1.236   0.69898077   0.69897988 -3.6929391e-08 -0.095426997 -0.095426997 -0.095426997 
-   12370        1.237     0.699005   0.69900412 3.0121756e-09 -0.095440547 -0.095440547 -0.095440547 
-   12380        1.238   0.69902917   0.69902827 4.2491092e-08 -0.095454059 -0.095454059 -0.095454059 
-   12390        1.239   0.69905327   0.69905236 8.0620895e-08 -0.095467531 -0.095467531 -0.095467531 
-   12400         1.24    0.6990773   0.69907636 1.1654781e-07 -0.095480963 -0.095480963 -0.095480963 
-   12410        1.241   0.69910126    0.6991003 1.4946989e-07 -0.095494357 -0.095494357 -0.095494357 
-   12420        1.242   0.69912516   0.69912416 1.7865487e-07 -0.095507713 -0.095507713 -0.095507713 
-   12430        1.243   0.69914899   0.69914795 2.0345652e-07 -0.095521029 -0.095521029 -0.095521029 
-   12440        1.244   0.69917276   0.69917166 2.2332892e-07 -0.095534307 -0.095534307 -0.095534307 
-   12450        1.245   0.69919645   0.69919531 2.3783848e-07 -0.095547546 -0.095547546 -0.095547546 
-   12460        1.246   0.69922008   0.69921888 2.4667342e-07 -0.095560748 -0.095560748 -0.095560748 
-   12470        1.247   0.69924364   0.69924238 2.4965047e-07  -0.09557391  -0.09557391  -0.09557391 
-   12480        1.248   0.69926713   0.69926582 2.4671863e-07 -0.095587035 -0.095587035 -0.095587035 
-   12490        1.249   0.69929055   0.69928918 2.3796002e-07 -0.095600121 -0.095600121 -0.095600121 
-   12500         1.25    0.6993139   0.69931248 2.2358765e-07  -0.09561317  -0.09561317  -0.09561317 
-   12510        1.251   0.69933718   0.69933572 2.0394029e-07 -0.095626181 -0.095626181 -0.095626181 
-   12520        1.252   0.69936039   0.69935888 1.7947455e-07 -0.095639154 -0.095639154 -0.095639154 
-   12530        1.253   0.69938353   0.69938198 1.5075424e-07 -0.095652089 -0.095652089 -0.095652089 
-   12540        1.254    0.6994066   0.69940502 1.1843746e-07 -0.095664987 -0.095664987 -0.095664987 
-   12550        1.255   0.69942959   0.69942799 8.3261482e-08 -0.095677847 -0.095677847 -0.095677847 
-   12560        1.256   0.69945252    0.6994509 4.6025993e-08  -0.09569067  -0.09569067  -0.09569067 
-   12570        1.257   0.69947537   0.69947375 7.5748999e-09 -0.095703456 -0.095703456 -0.095703456 
-   12580        1.258   0.69949816   0.69949653 -3.1222777e-08 -0.095716205 -0.095716205 -0.095716205 
-   12590        1.259   0.69952087   0.69951925 -6.9492541e-08 -0.095728916 -0.095728916 -0.095728916 
-   12600         1.26   0.69954351   0.69954191 -1.0637412e-07 -0.095741591 -0.095741591 -0.095741591 
-   12610        1.261   0.69956608    0.6995645 -1.4104082e-07 -0.095754229 -0.095754229 -0.095754229 
-   12620        1.262   0.69958858   0.69958703 -1.7271803e-07  -0.09576683  -0.09576683  -0.09576683 
-   12630        1.263   0.69961101    0.6996095 -2.0070054e-07 -0.095779394 -0.095779394 -0.095779394 
-   12640        1.264   0.69963337   0.69963191 -2.2436827e-07 -0.095791923 -0.095791923 -0.095791923 
-   12650        1.265   0.69965567   0.69965425 -2.4319998e-07 -0.095804414 -0.095804414 -0.095804414 
-   12660        1.266    0.6996779   0.69967653 -2.5678477e-07 -0.095816869 -0.095816869 -0.095816869 
-   12670        1.267   0.69970006   0.69969874 -2.6483105e-07 -0.095829289 -0.095829289 -0.095829289 
-   12680        1.268   0.69972215   0.69972089 -2.6717277e-07 -0.095841672 -0.095841672 -0.095841672 
-   12690        1.269   0.69974418   0.69974298 -2.6377289e-07 -0.095854019 -0.095854019 -0.095854019 
-   12700         1.27   0.69976615     0.699765 -2.5472381e-07  -0.09586633  -0.09586633  -0.09586633 
-   12710        1.271   0.69978805   0.69978695 -2.40245e-07 -0.095878605 -0.095878605 -0.095878605 
-   12720        1.272   0.69980989   0.69980883 -2.2067767e-07 -0.095890844 -0.095890844 -0.095890844 
-   12730        1.273   0.69983167   0.69983065 -1.964768e-07 -0.095903048 -0.095903048 -0.095903048 
-   12740        1.274   0.69985339   0.69985241 -1.682006e-07 -0.095915217 -0.095915217 -0.095915217 
-   12750        1.275   0.69987504   0.69987409 -1.3649759e-07  -0.09592735  -0.09592735  -0.09592735 
-   12760        1.276   0.69989664   0.69989571 -1.0209182e-07 -0.095939448 -0.095939448 -0.095939448 
-   12770        1.277   0.69991818   0.69991726 -6.5766278e-08  -0.09595151  -0.09595151  -0.09595151 
-   12780        1.278   0.69993965   0.69993874 -2.8345147e-08 -0.095963537 -0.095963537 -0.095963537 
-   12790        1.279   0.69996107   0.69996016 9.3249255e-09  -0.09597553  -0.09597553  -0.09597553 
-   12800         1.28   0.69998243   0.69998151 4.6393961e-08 -0.095987487 -0.095987487 -0.095987487 
-   12810        1.281   0.70000373   0.70000279 8.2027829e-08  -0.09599941  -0.09599941  -0.09599941 
-   12820        1.282   0.70002497   0.70002401 1.1542701e-07 -0.096011298 -0.096011298 -0.096011298 
-   12830        1.283   0.70004615   0.70004516 1.4584454e-07 -0.096023151 -0.096023151 -0.096023151 
-   12840        1.284   0.70006727   0.70006624 1.7260271e-07  -0.09603497  -0.09603497  -0.09603497 
-   12850        1.285   0.70008834   0.70008727 1.9510818e-07 -0.096046754 -0.096046754 -0.096046754 
-   12860        1.286   0.70010934   0.70010822 2.1286511e-07 -0.096058504 -0.096058504 -0.096058504 
-   12870        1.287   0.70013028   0.70012911 2.2548613e-07  -0.09607022  -0.09607022  -0.09607022 
-   12880        1.288   0.70015116   0.70014995 2.3270076e-07 -0.096081901 -0.096081901 -0.096081901 
-   12890        1.289   0.70017198   0.70017071 2.343612e-07 -0.096093549 -0.096093549 -0.096093549 
-   12900         1.29   0.70019274   0.70019142 2.3044536e-07 -0.096105162 -0.096105162 -0.096105162 
-   12910        1.291   0.70021344   0.70021207  2.21057e-07 -0.096116742 -0.096116742 -0.096116742 
-   12920        1.292   0.70023408   0.70023266 2.064231e-07 -0.096128288 -0.096128288 -0.096128288 
-   12930        1.293   0.70025465   0.70025318 1.8688835e-07   -0.0961398   -0.0961398   -0.0961398 
-   12940        1.294   0.70027516   0.70027366 1.6290711e-07 -0.096151279 -0.096151279 -0.096151279 
-   12950        1.295   0.70029561   0.70029407 1.3503284e-07 -0.096162724 -0.096162724 -0.096162724 
-   12960        1.296   0.70031599   0.70031442 1.0390534e-07 -0.096174135 -0.096174135 -0.096174135 
-   12970        1.297   0.70033631   0.70033472 7.0236124e-08 -0.096185514 -0.096185514 -0.096185514 
-   12980        1.298   0.70035657   0.70035497 3.4792111e-08 -0.096196859 -0.096196859 -0.096196859 
-   12990        1.299   0.70037676   0.70037515 -1.621789e-09 -0.096208171 -0.096208171 -0.096208171 
-   13000          1.3   0.70039689   0.70039529 -3.8180966e-08  -0.09621945  -0.09621945  -0.09621945 
-   13010        1.301   0.70041696   0.70041536 -7.405977e-08 -0.096230697 -0.096230697 -0.096230697 
-   13020        1.302   0.70043696   0.70043538 -1.0845016e-07  -0.09624191  -0.09624191  -0.09624191 
-   13030        1.303    0.7004569   0.70045535 -1.4057989e-07 -0.096253091 -0.096253091 -0.096253091 
-   13040        1.304   0.70047678   0.70047526 -1.6972986e-07 -0.096264239 -0.096264239 -0.096264239 
-   13050        1.305    0.7004966   0.70049511 -1.952502e-07 -0.096275354 -0.096275354 -0.096275354 
-   13060        1.306   0.70051635   0.70051491 -2.1657479e-07 -0.096286437 -0.096286437 -0.096286437 
-   13070        1.307   0.70053605   0.70053465 -2.3323376e-07 -0.096297487 -0.096297487 -0.096297487 
-   13080        1.308   0.70055569   0.70055434 -2.4486392e-07 -0.096308506 -0.096308506 -0.096308506 
-   13090        1.309   0.70057526   0.70057396 -2.5121661e-07 -0.096319492 -0.096319492 -0.096319492 
-   13100         1.31   0.70059478   0.70059353 -2.5216307e-07 -0.096330446 -0.096330446 -0.096330446 
-   13110        1.311   0.70061425   0.70061305 -2.4769696e-07 -0.096341368 -0.096341368 -0.096341368 
-   13120        1.312   0.70063365    0.7006325 -2.3793426e-07 -0.096352258 -0.096352258 -0.096352258 
-   13130        1.313     0.700653    0.7006519 -2.2311023e-07 -0.096363116 -0.096363116 -0.096363116 
-   13140        1.314   0.70067229   0.70067123 -2.0357386e-07 -0.096373942 -0.096373942 -0.096373942 
-   13150        1.315   0.70069153   0.70069051 -1.7977963e-07 -0.096384737 -0.096384737 -0.096384737 
-   13160        1.316   0.70071072   0.70070973 -1.5227697e-07   -0.0963955   -0.0963955   -0.0963955 
-   13170        1.317   0.70072985   0.70072888 -1.2169761e-07 -0.096406232 -0.096406232 -0.096406232 
-   13180        1.318   0.70074893   0.70074798 -8.8741043e-08 -0.096416932 -0.096416932 -0.096416932 
-   13190        1.319   0.70076795   0.70076702 -5.4158599e-08 -0.096427601 -0.096427601 -0.096427601 
-   13200         1.32   0.70078693     0.700786 -1.873627e-08 -0.096438239 -0.096438239 -0.096438239 
-   13210        1.321   0.70080585   0.70080492 1.6723116e-08 -0.096448846 -0.096448846 -0.096448846 
-   13220        1.322   0.70082472   0.70082377 5.1418091e-08 -0.096459421 -0.096459421 -0.096459421 
-   13230        1.323   0.70084353   0.70084257 8.4566661e-08 -0.096469966 -0.096469966 -0.096469966 
-   13240        1.324    0.7008623   0.70086131 1.1542392e-07  -0.09648048  -0.09648048  -0.09648048 
-   13250        1.325   0.70088101   0.70087999 1.4329881e-07 -0.096490963 -0.096490963 -0.096490963 
-   13260        1.326   0.70089967   0.70089862 1.6756957e-07 -0.096501415 -0.096501415 -0.096501415 
-   13270        1.327   0.70091828   0.70091718 1.8769761e-07 -0.096511837 -0.096511837 -0.096511837 
-   13280        1.328   0.70093683   0.70093569 2.032395e-07 -0.096522228 -0.096522228 -0.096522228 
-   13290        1.329   0.70095533   0.70095415 2.1385668e-07 -0.096532589 -0.096532589 -0.096532589 
-   13300         1.33   0.70097378   0.70097254 2.1932289e-07  -0.09654292  -0.09654292  -0.09654292 
-   13310        1.331   0.70099217   0.70099089 2.1952893e-07  -0.09655322  -0.09655322  -0.09655322 
-   13320        1.332   0.70101051   0.70100918 2.1448487e-07  -0.09656349  -0.09656349  -0.09656349 
-   13330        1.333   0.70102879   0.70102741 2.0431946e-07  -0.09657373  -0.09657373  -0.09657373 
-   13340        1.334   0.70104702    0.7010456 1.8927691e-07  -0.09658394  -0.09658394  -0.09658394 
-   13350        1.335   0.70106519   0.70106373 1.6971105e-07  -0.09659412  -0.09659412  -0.09659412 
-   13360        1.336   0.70108331   0.70108181 1.4607705e-07  -0.09660427  -0.09660427  -0.09660427 
-   13370        1.337   0.70110137   0.70109984 1.1892082e-07 -0.096614391 -0.096614391 -0.096614391 
-   13380        1.338   0.70111937   0.70111782 8.8866473e-08 -0.096624481 -0.096624481 -0.096624481 
-   13390        1.339   0.70113732   0.70113574 5.6601919e-08 -0.096634542 -0.096634542 -0.096634542 
-   13400         1.34   0.70115521   0.70115362 2.2863193e-08 -0.096644574 -0.096644574 -0.096644574 
-   13410        1.341   0.70117304   0.70117145 -1.1582356e-08 -0.096654576 -0.096654576 -0.096654576 
-   13420        1.342   0.70119082   0.70118924 -4.5953497e-08 -0.096664549 -0.096664549 -0.096664549 
-   13430        1.343   0.70120854   0.70120697 -7.947284e-08 -0.096674493 -0.096674493 -0.096674493 
-   13440        1.344   0.70122621   0.70122465 -1.1138441e-07 -0.096684408 -0.096684408 -0.096684408 
-   13450        1.345   0.70124382   0.70124229 -1.4097069e-07 -0.096694293 -0.096694293 -0.096694293 
-   13460        1.346   0.70126137   0.70125987 -1.6756876e-07 -0.096704149 -0.096704149 -0.096704149 
-   13470        1.347   0.70127887   0.70127741 -1.9058516e-07 -0.096713977 -0.096713977 -0.096713977 
-   13480        1.348   0.70129632   0.70129489 -2.095091e-07 -0.096723776 -0.096723776 -0.096723776 
-   13490        1.349   0.70131371   0.70131233 -2.2392384e-07 -0.096733546 -0.096733546 -0.096733546 
-   13500         1.35   0.70133105   0.70132971 -2.3351583e-07 -0.096743287 -0.096743287 -0.096743287 
-   13510        1.351   0.70134834   0.70134705 -2.3808155e-07 -0.096752999 -0.096752999 -0.096752999 
-   13520        1.352   0.70136557   0.70136433 -2.3753179e-07 -0.096762684 -0.096762684 -0.096762684 
-   13530        1.353   0.70138276   0.70138157 -2.318934e-07 -0.096772339 -0.096772339 -0.096772339 
-   13540        1.354   0.70139989   0.70139875 -2.2130834e-07 -0.096781967 -0.096781967 -0.096781967 
-   13550        1.355   0.70141698   0.70141588 -2.0603016e-07 -0.096791566 -0.096791566 -0.096791566 
-   13560        1.356   0.70143402   0.70143295 -1.8641795e-07 -0.096801137 -0.096801137 -0.096801137 
-   13570        1.357     0.701451   0.70144997 -1.6292792e-07 -0.096810679 -0.096810679 -0.096810679 
-   13580        1.358   0.70146795   0.70146695 -1.3610284e-07 -0.096820194 -0.096820194 -0.096820194 
-   13590        1.359   0.70148484   0.70148386 -1.0655946e-07 -0.096829681 -0.096829681 -0.096829681 
-   13600         1.36   0.70150169   0.70150073 -7.4974411e-08  -0.09683914  -0.09683914  -0.09683914 
-   13610        1.361   0.70151849   0.70151754 -4.2068642e-08 -0.096848571 -0.096848571 -0.096848571 
-   13620        1.362   0.70153524   0.70153429 -8.5910346e-09 -0.096857974 -0.096857974 -0.096857974 
-   13630        1.363   0.70155195     0.701551 2.4698661e-08  -0.09686735  -0.09686735  -0.09686735 
-   13640        1.364   0.70156861   0.70156765 5.7047056e-08 -0.096876699 -0.096876699 -0.096876699 
-   13650        1.365   0.70158523   0.70158424 8.7724172e-08 -0.096886019 -0.096886019 -0.096886019 
-   13660        1.366    0.7016018   0.70160079 1.1603991e-07 -0.096895313 -0.096895313 -0.096895313 
-   13670        1.367   0.70161833   0.70161728 1.4135956e-07 -0.096904579 -0.096904579 -0.096904579 
-   13680        1.368    0.7016348   0.70163373 1.6311807e-07 -0.096913817 -0.096913817 -0.096913817 
-   13690        1.369   0.70165123   0.70165012 1.808326e-07 -0.096923029 -0.096923029 -0.096923029 
-   13700         1.37   0.70166762   0.70166646 1.9411326e-07 -0.096932214 -0.096932214 -0.096932214 
-   13710        1.371   0.70168396   0.70168275 2.0267172e-07 -0.096941371 -0.096941371 -0.096941371 
-   13720        1.372   0.70170024   0.70169899 2.0632742e-07 -0.096950502 -0.096950502 -0.096950502 
-   13730        1.373   0.70171648   0.70171519 2.0501137e-07 -0.096959606 -0.096959606 -0.096959606 
-   13740        1.374   0.70173268   0.70173133 1.9876745e-07 -0.096968682 -0.096968682 -0.096968682 
-   13750        1.375   0.70174882   0.70174743 1.8775106e-07 -0.096977733 -0.096977733 -0.096977733 
-   13760        1.376   0.70176491   0.70176349 1.7222531e-07 -0.096986756 -0.096986756 -0.096986756 
-   13770        1.377   0.70178096   0.70177949 1.5255477e-07 -0.096995753 -0.096995753 -0.096995753 
-   13780        1.378   0.70179695   0.70179546 1.2919695e-07 -0.097004724 -0.097004724 -0.097004724 
-   13790        1.379    0.7018129   0.70181137 1.026916e-07 -0.097013668 -0.097013668 -0.097013668 
-   13800         1.38   0.70182879   0.70182725 7.3648346e-08 -0.097022586 -0.097022586 -0.097022586 
-   13810        1.381   0.70184464   0.70184308 4.273262e-08 -0.097031478 -0.097031478 -0.097031478 
-   13820        1.382   0.70186043   0.70185886 1.0650445e-08 -0.097040343 -0.097040343 -0.097040343 
-   13830        1.383   0.70187617    0.7018746 -2.1867685e-08 -0.097049182 -0.097049182 -0.097049182 
-   13840        1.384   0.70189187    0.7018903 -5.4083428e-08 -0.097057996 -0.097057996 -0.097057996 
-   13850        1.385   0.70190751   0.70190596 -8.5267357e-08 -0.097066783 -0.097066783 -0.097066783 
-   13860        1.386    0.7019231   0.70192157 -1.1471547e-07 -0.097075545 -0.097075545 -0.097075545 
-   13870        1.387   0.70193865   0.70193714 -1.4176509e-07  -0.09708428  -0.09708428  -0.09708428 
-   13880        1.388   0.70195414   0.70195267 -1.6580975e-07  -0.09709299  -0.09709299  -0.09709299 
-   13890        1.389   0.70196959   0.70196815 -1.8631284e-07 -0.097101674 -0.097101674 -0.097101674 
-   13900         1.39   0.70198499   0.70198359 -2.028195e-07 -0.097110333 -0.097110333 -0.097110333 
-   13910        1.391   0.70200034   0.70199898 -2.1496682e-07 -0.097118966 -0.097118966 -0.097118966 
-   13920        1.392   0.70201565   0.70201433 -2.2249171e-07 -0.097127574 -0.097127574 -0.097127574 
-   13930        1.393   0.70203091   0.70202964 -2.2523667e-07 -0.097136156 -0.097136156 -0.097136156 
-   13940        1.394   0.70204612   0.70204489 -2.2315301e-07 -0.097144713 -0.097144713 -0.097144713 
-   13950        1.395   0.70206129   0.70206011 -2.1630171e-07 -0.097153245 -0.097153245 -0.097153245 
-   13960        1.396   0.70207642   0.70207528 -2.048517e-07 -0.097161752 -0.097161752 -0.097161752 
-   13970        1.397    0.7020915    0.7020904 -1.8907575e-07 -0.097170234 -0.097170234 -0.097170234 
-   13980        1.398   0.70210654   0.70210547 -1.6934396e-07  -0.09717869  -0.09717869  -0.09717869 
-   13990        1.399   0.70212153    0.7021205 -1.4611516e-07 -0.097187122 -0.097187122 -0.097187122 
-   14000          1.4   0.70213649   0.70213548 -1.199262e-07 -0.097195529 -0.097195529 -0.097195529 
-   14010        1.401    0.7021514   0.70215041 -9.1379589e-08 -0.097203911 -0.097203911 -0.097203911 
-   14020        1.402   0.70216627   0.70216529 -6.1129618e-08 -0.097212268 -0.097212268 -0.097212268 
-   14030        1.403    0.7021811   0.70218013 -2.9867402e-08 -0.097220601 -0.097220601 -0.097220601 
-   14040        1.404   0.70219589   0.70219492 1.6949188e-09 -0.097228909 -0.097228909 -0.097228909 
-   14050        1.405   0.70221064   0.70220966 3.2840391e-08 -0.097237192 -0.097237192 -0.097237192 
-   14060        1.406   0.70222535   0.70222436 6.2863529e-08 -0.097245452 -0.097245452 -0.097245452 
-   14070        1.407   0.70224002   0.70223901 9.1086294e-08 -0.097253686 -0.097253686 -0.097253686 
-   14080        1.408   0.70225465   0.70225361 1.168734e-07 -0.097261897 -0.097261897 -0.097261897 
-   14090        1.409   0.70226923   0.70226817 1.3964662e-07 -0.097270083 -0.097270083 -0.097270083 
-   14100         1.41   0.70228378   0.70228268 1.5889773e-07 -0.097278245 -0.097278245 -0.097278245 
-   14110        1.411   0.70229828   0.70229714 1.7419988e-07 -0.097286383 -0.097286383 -0.097286383 
-   14120        1.412   0.70231275   0.70231157 1.8521704e-07 -0.097294497 -0.097294497 -0.097294497 
-   14130        1.413   0.70232717   0.70232594 1.9171137e-07 -0.097302587 -0.097302587 -0.097302587 
-   14140        1.414   0.70234155   0.70234028 1.9354835e-07 -0.097310653 -0.097310653 -0.097310653 
-   14150        1.415   0.70235588   0.70235457 1.9069957e-07 -0.097318695 -0.097318695 -0.097318695 
-   14160        1.416   0.70237017   0.70236882 1.8324303e-07 -0.097326714 -0.097326714 -0.097326714 
-   14170        1.417   0.70238442   0.70238303 1.7136113e-07 -0.097334709 -0.097334709 -0.097334709 
-   14180        1.418   0.70239863   0.70239719 1.5533621e-07  -0.09734268  -0.09734268  -0.09734268 
-   14190        1.419   0.70241279   0.70241132 1.3554388e-07 -0.097350628 -0.097350628 -0.097350628 
-   14200         1.42    0.7024269   0.70242541 1.1244419e-07 -0.097358552 -0.097358552 -0.097358552 
-   14210        1.421   0.70244098   0.70243946 8.657102e-08 -0.097366453 -0.097366453 -0.097366453 
-   14220        1.422     0.702455   0.70245347 5.8519701e-08 -0.097374331 -0.097374331 -0.097374331 
-   14230        1.423   0.70246899   0.70246744 2.8933347e-08 -0.097382185 -0.097382185 -0.097382185 
-   14240        1.424   0.70248292   0.70248137 -1.5118877e-09 -0.097390016 -0.097390016 -0.097390016 
-   14250        1.425   0.70249682   0.70249526 -3.2122246e-08 -0.097397824 -0.097397824 -0.097397824 
-   14260        1.426   0.70251067   0.70250912 -6.2202178e-08 -0.097405609 -0.097405609 -0.097405609 
-   14270        1.427   0.70252447   0.70252294 -9.1070138e-08  -0.09741337  -0.09741337  -0.09741337 
-   14280        1.428   0.70253823   0.70253672 -1.1807402e-07 -0.097421109 -0.097421109 -0.097421109 
-   14290        1.429   0.70255195   0.70255046 -1.4260591e-07 -0.097428825 -0.097428825 -0.097428825 
-   14300         1.43   0.70256562   0.70256416 -1.6411572e-07 -0.097436518 -0.097436518 -0.097436518 
-   14310        1.431   0.70257925   0.70257783 -1.8212358e-07 -0.097444189 -0.097444189 -0.097444189 
-   14320        1.432   0.70259284   0.70259145 -1.9623049e-07 -0.097451837 -0.097451837 -0.097451837 
-   14330        1.433   0.70260638   0.70260504 -2.061272e-07 -0.097459462 -0.097459462 -0.097459462 
-   14340        1.434   0.70261989   0.70261859 -2.1160096e-07 -0.097467064 -0.097467064 -0.097467064 
-   14350        1.435   0.70263335    0.7026321 -2.1254009e-07 -0.097474645 -0.097474645 -0.097474645 
-   14360        1.436   0.70264678   0.70264556 -2.0893625e-07 -0.097482202 -0.097482202 -0.097482202 
-   14370        1.437   0.70266016   0.70265899 -2.0088431e-07 -0.097489738 -0.097489738 -0.097489738 
-   14380        1.438   0.70267351   0.70267237 -1.8857993e-07 -0.097497251 -0.097497251 -0.097497251 
-   14390        1.439   0.70268682   0.70268572 -1.7231485e-07 -0.097504742 -0.097504742 -0.097504742 
-   14400         1.44   0.70270009   0.70269902 -1.5246993e-07  -0.09751221  -0.09751221  -0.09751221 
-   14410        1.441   0.70271332   0.70271228 -1.2950634e-07 -0.097519657 -0.097519657 -0.097519657 
-   14420        1.442   0.70272652    0.7027255 -1.0395477e-07 -0.097527081 -0.097527081 -0.097527081 
-   14430        1.443   0.70273968   0.70273867 -7.6403244e-08 -0.097534484 -0.097534484 -0.097534484 
-   14440        1.444    0.7027528   0.70275181 -4.7483544e-08 -0.097541865 -0.097541865 -0.097541865 
-   14450        1.445   0.70276589    0.7027649 -1.7856769e-08 -0.097549223 -0.097549223 -0.097549223 
-   14460        1.446   0.70277894   0.70277795 1.1801786e-08 -0.097556561 -0.097556561 -0.097556561 
-   14470        1.447   0.70279195   0.70279095 4.0818017e-08 -0.097563876 -0.097563876 -0.097563876 
-   14480        1.448   0.70280493   0.70280392 6.8534325e-08  -0.09757117  -0.09757117  -0.09757117 
-   14490        1.449   0.70281788   0.70281684 9.4324517e-08 -0.097578442 -0.097578442 -0.097578442 
-   14500         1.45   0.70283079   0.70282973 1.1760795e-07 -0.097585692 -0.097585692 -0.097585692 
-   14510        1.451   0.70284366   0.70284257 1.3786261e-07 -0.097592921 -0.097592921 -0.097592921 
-   14520        1.452    0.7028565   0.70285537 1.546368e-07 -0.097600129 -0.097600129 -0.097600129 
-   14530        1.453    0.7028693   0.70286813 1.6755921e-07 -0.097607315 -0.097607315 -0.097607315 
-   14540        1.454   0.70288206   0.70288086 1.7634715e-07  -0.09761448  -0.09761448  -0.09761448 
-   14550        1.455   0.70289478   0.70289354 1.8081273e-07 -0.097621624 -0.097621624 -0.097621624 
-   14560        1.456   0.70290747   0.70290619 1.8086683e-07 -0.097628747 -0.097628747 -0.097628747 
-   14570        1.457   0.70292012   0.70291879 1.7652089e-07 -0.097635848 -0.097635848 -0.097635848 
-   14580        1.458   0.70293273   0.70293137 1.6788635e-07 -0.097642929 -0.097642929 -0.097642929 
-   14590        1.459    0.7029453    0.7029439 1.5517184e-07 -0.097649989 -0.097649989 -0.097649989 
-   14600         1.46   0.70295784    0.7029564 1.3867815e-07 -0.097657027 -0.097657027 -0.097657027 
-   14610        1.461   0.70297033   0.70296887 1.1879117e-07 -0.097664045 -0.097664045 -0.097664045 
-   14620        1.462   0.70298279    0.7029813 9.5972821e-08 -0.097671042 -0.097671042 -0.097671042 
-   14630        1.463    0.7029952   0.70299369 7.0750397e-08 -0.097678018 -0.097678018 -0.097678018 
-   14640        1.464   0.70300758   0.70300605 4.3704347e-08 -0.097684974 -0.097684974 -0.097684974 
-   14650        1.465   0.70301991   0.70301838 1.5454946e-08 -0.097691909 -0.097691909 -0.097691909 
-   14660        1.466   0.70303221   0.70303067 -1.3351931e-08 -0.097698823 -0.097698823 -0.097698823 
-   14670        1.467   0.70304446   0.70304293 -4.2059562e-08 -0.097705717 -0.097705717 -0.097705717 
-   14680        1.468   0.70305668   0.70305516 -7.0015352e-08 -0.097712591 -0.097712591 -0.097712591 
-   14690        1.469   0.70306886   0.70306735 -9.658566e-08 -0.097719444 -0.097719444 -0.097719444 
-   14700         1.47     0.703081   0.70307951 -1.2117016e-07 -0.097726277 -0.097726277 -0.097726277 
-   14710        1.471    0.7030931   0.70309163 -1.432154e-07 -0.097733089 -0.097733089 -0.097733089 
-   14720        1.472   0.70310516   0.70310372 -1.6222726e-07 -0.097739882 -0.097739882 -0.097739882 
-   14730        1.473   0.70311718   0.70311578 -1.7778203e-07 -0.097746654 -0.097746654 -0.097746654 
-   14740        1.474   0.70312916    0.7031278 -1.8953585e-07 -0.097753406 -0.097753406 -0.097753406 
-   14750        1.475   0.70314111   0.70313979 -1.9723228e-07 -0.097760138 -0.097760138 -0.097760138 
-   14760        1.476   0.70315303   0.70315174 -2.0070795e-07  -0.09776685  -0.09776685  -0.09776685 
-   14770        1.477    0.7031649   0.70316366 -1.9989595e-07 -0.097773542 -0.097773542 -0.097773542 
-   14780        1.478   0.70317675   0.70317554 -1.9482712e-07 -0.097780215 -0.097780215 -0.097780215 
-   14790        1.479   0.70318855   0.70318739 -1.8562905e-07 -0.097786867 -0.097786867 -0.097786867 
-   14800         1.48   0.70320033    0.7031992 -1.7252294e-07   -0.0977935   -0.0977935   -0.0977935 
-   14810        1.481   0.70321206   0.70321097 -1.5581824e-07 -0.097800113 -0.097800113 -0.097800113 
-   14820        1.482   0.70322377    0.7032227 -1.3590543e-07 -0.097806707 -0.097806707 -0.097806707 
-   14830        1.483   0.70323545    0.7032344 -1.1324688e-07 -0.097813281 -0.097813281 -0.097813281 
-   14840        1.484   0.70324709   0.70324606 -8.8366093e-08 -0.097819835 -0.097819835 -0.097819835 
-   14850        1.485    0.7032587   0.70325768 -6.1835671e-08  -0.09782637  -0.09782637  -0.09782637 
-   14860        1.486   0.70327027   0.70326927 -3.4264114e-08 -0.097832886 -0.097832886 -0.097832886 
-   14870        1.487   0.70328182   0.70328081 -6.2818816e-09 -0.097839382 -0.097839382 -0.097839382 
-   14880        1.488   0.70329333   0.70329232 2.1473021e-08 -0.097845859 -0.097845859 -0.097845859 
-   14890        1.489   0.70330482    0.7033038 4.8369582e-08 -0.097852317 -0.097852317 -0.097852317 
-   14900         1.49   0.70331627   0.70331523 7.3798129e-08 -0.097858755 -0.097858755 -0.097858755 
-   14910        1.491   0.70332769   0.70332663 9.718414e-08 -0.097865175 -0.097865175 -0.097865175 
-   14920        1.492   0.70333908   0.70333799 1.1800123e-07 -0.097871575 -0.097871575 -0.097871575 
-   14930        1.493   0.70335043   0.70334932 1.3578298e-07 -0.097877956 -0.097877956 -0.097877956 
-   14940        1.494   0.70336176   0.70336061 1.501334e-07 -0.097884319 -0.097884319 -0.097884319 
-   14950        1.495   0.70337305   0.70337187 1.6073576e-07 -0.097890662 -0.097890662 -0.097890662 
-   14960        1.496   0.70338431   0.70338309 1.6735952e-07 -0.097896987 -0.097896987 -0.097896987 
-   14970        1.497   0.70339554   0.70339427 1.6986541e-07 -0.097903293 -0.097903293 -0.097903293 
-   14980        1.498   0.70340673   0.70340543 1.6820826e-07  -0.09790958  -0.09790958  -0.09790958 
-   14990        1.499   0.70341789   0.70341655 1.6243785e-07 -0.097915849 -0.097915849 -0.097915849 
-   15000          1.5   0.70342901   0.70342764 1.5269743e-07 -0.097922098 -0.097922098 -0.097922098 
-   15010        1.501    0.7034401   0.70343869 1.3922024e-07  -0.09792833  -0.09792833  -0.09792833 
-   15020        1.502   0.70345116   0.70344972 1.2232395e-07 -0.097934543 -0.097934543 -0.097934543 
-   15030        1.503   0.70346218   0.70346071 1.0240314e-07 -0.097940737 -0.097940737 -0.097940737 
-   15040        1.504   0.70347316   0.70347168 7.9920151e-08 -0.097946913 -0.097946913 -0.097946913 
-   15050        1.505   0.70348411   0.70348261 5.5394328e-08  -0.09795307  -0.09795307  -0.09795307 
-   15060        1.506   0.70349503   0.70349351 2.9390054e-08  -0.09795921  -0.09795921  -0.09795921 
-   15070        1.507   0.70350591   0.70350438 2.5037625e-09 -0.097965331 -0.097965331 -0.097965331 
-   15080        1.508   0.70351675   0.70351523 -2.4649737e-08 -0.097971434 -0.097971434 -0.097971434 
-   15090        1.509   0.70352756   0.70352604 -5.145131e-08 -0.097977518 -0.097977518 -0.097977518 
-   15100         1.51   0.70353833   0.70353683 -7.7291613e-08 -0.097983585 -0.097983585 -0.097983585 
-   15110        1.511   0.70354907   0.70354758 -1.0158494e-07 -0.097989633 -0.097989633 -0.097989633 
-   15120        1.512   0.70355978   0.70355831 -1.2378249e-07 -0.097995664 -0.097995664 -0.097995664 
-   15130        1.513   0.70357044     0.703569 -1.4338479e-07 -0.098001677 -0.098001677 -0.098001677 
-   15140        1.514   0.70358108   0.70357967 -1.5995288e-07 -0.098007671 -0.098007671 -0.098007671 
-   15150        1.515   0.70359168   0.70359031 -1.731182e-07 -0.098013648 -0.098013648 -0.098013648 
-   15160        1.516   0.70360225   0.70360091 -1.8259073e-07 -0.098019608 -0.098019608 -0.098019608 
-   15170        1.517   0.70361279   0.70361149 -1.8816541e-07 -0.098025549 -0.098025549 -0.098025549 
-   15180        1.518    0.7036233   0.70362203 -1.8972657e-07 -0.098031473 -0.098031473 -0.098031473 
-   15190        1.519   0.70363377   0.70363254 -1.8725029e-07 -0.098037379 -0.098037379 -0.098037379 
-   15200         1.52   0.70364421   0.70364302 -1.8080468e-07 -0.098043268 -0.098043268 -0.098043268 
-   15210        1.521   0.70365462   0.70365347 -1.7054811e-07 -0.098049139 -0.098049139 -0.098049139 
-   15220        1.522   0.70366501   0.70366388 -1.567253e-07 -0.098054992 -0.098054992 -0.098054992 
-   15230        1.523   0.70367536   0.70367426 -1.3966151e-07 -0.098060828 -0.098060828 -0.098060828 
-   15240        1.524   0.70368568   0.70368461 -1.1975493e-07 -0.098066647 -0.098066647 -0.098066647 
-   15250        1.525   0.70369598   0.70369493 -9.7467355e-08 -0.098072449 -0.098072449 -0.098072449 
-   15260        1.526   0.70370625   0.70370521 -7.3313509e-08 -0.098078233 -0.098078233 -0.098078233 
-   15270        1.527   0.70371649   0.70371546 -4.7849162e-08    -0.098084    -0.098084    -0.098084 
-   15280        1.528    0.7037267   0.70372568 -2.1658348e-08  -0.09808975  -0.09808975  -0.09808975 
-   15290        1.529   0.70373688   0.70373586 4.6600242e-09 -0.098095483 -0.098095483 -0.098095483 
-   15300         1.53   0.70374704   0.70374601 3.0505861e-08 -0.098101199 -0.098101199 -0.098101199 
-   15310        1.531   0.70375717   0.70375612 5.5291564e-08 -0.098106897 -0.098106897 -0.098106897 
-   15320        1.532   0.70376727   0.70376621 7.8455383e-08 -0.098112579 -0.098112579 -0.098112579 
-   15330        1.533   0.70377734   0.70377626 9.9474145e-08 -0.098118244 -0.098118244 -0.098118244 
-   15340        1.534   0.70378739   0.70378628 1.1787507e-07 -0.098123892 -0.098123892 -0.098123892 
-   15350        1.535    0.7037974   0.70379626 1.3324639e-07 -0.098129523 -0.098129523 -0.098129523 
-   15360        1.536   0.70380739   0.70380622 1.452466e-07 -0.098135137 -0.098135137 -0.098135137 
-   15370        1.537   0.70381735   0.70381614 1.5361197e-07 -0.098140735 -0.098140735 -0.098140735 
-   15380        1.538   0.70382728   0.70382604 1.581624e-07 -0.098146316 -0.098146316 -0.098146316 
-   15390        1.539   0.70383718    0.7038359 1.5880528e-07  -0.09815188  -0.09815188  -0.09815188 
-   15400         1.54   0.70384705   0.70384574 1.555373e-07 -0.098157428 -0.098157428 -0.098157428 
-   15410        1.541   0.70385689   0.70385554 1.4844432e-07 -0.098162959 -0.098162959 -0.098162959 
-   15420        1.542    0.7038667   0.70386532 1.3769916e-07 -0.098168474 -0.098168474 -0.098168474 
-   15430        1.543   0.70387648   0.70387507 1.2355736e-07 -0.098173973 -0.098173973 -0.098173973 
-   15440        1.544   0.70388623   0.70388479 1.0635119e-07 -0.098179455 -0.098179455 -0.098179455 
-   15450        1.545   0.70389595   0.70389449 8.6481803e-08  -0.09818492  -0.09818492  -0.09818492 
-   15460        1.546   0.70390564   0.70390415 6.4409912e-08  -0.09819037  -0.09819037  -0.09819037 
-   15470        1.547   0.70391529    0.7039138 4.0645117e-08 -0.098195803 -0.098195803 -0.098195803 
-   15480        1.548   0.70392492   0.70392341 1.5734144e-08  -0.09820122  -0.09820122  -0.09820122 
-   15490        1.549   0.70393451     0.703933 -9.7517264e-09 -0.098206621 -0.098206621 -0.098206621 
-   15500         1.55   0.70394407   0.70394256 -3.5229752e-08 -0.098212005 -0.098212005 -0.098212005 
-   15510        1.551    0.7039536    0.7039521 -6.0119051e-08 -0.098217374 -0.098217374 -0.098217374 
-   15520        1.552    0.7039631   0.70396161 -8.3853843e-08 -0.098222727 -0.098222727 -0.098222727 
-   15530        1.553   0.70397256    0.7039711 -1.058963e-07 -0.098228064 -0.098228064 -0.098228064 
-   15540        1.554     0.703982   0.70398056 -1.2574875e-07 -0.098233384 -0.098233384 -0.098233384 
-   15550        1.555   0.70399141   0.70398999 -1.4296488e-07 -0.098238689 -0.098238689 -0.098238689 
-   15560        1.556   0.70400079    0.7039994 -1.5715979e-07 -0.098243979 -0.098243979 -0.098243979 
-   15570        1.557   0.70401013   0.70400878 -1.6801858e-07 -0.098249252 -0.098249252 -0.098249252 
-   15580        1.558   0.70401945   0.70401813 -1.7530336e-07  -0.09825451  -0.09825451  -0.09825451 
-   15590        1.559   0.70402874   0.70402745 -1.7885842e-07 -0.098259752 -0.098259752 -0.098259752 
-   15600         1.56     0.704038   0.70403675 -1.7861355e-07 -0.098264978 -0.098264978 -0.098264978 
-   15610        1.561   0.70404724   0.70404602 -1.7458543e-07 -0.098270189 -0.098270189 -0.098270189 
-   15620        1.562   0.70405644   0.70405526 -1.6687696e-07 -0.098275384 -0.098275384 -0.098275384 
-   15630        1.563   0.70406562   0.70406447 -1.5567469e-07 -0.098280564 -0.098280564 -0.098280564 
-   15640        1.564   0.70407478   0.70407366 -1.4124432e-07 -0.098285728 -0.098285728 -0.098285728 
-   15650        1.565   0.70408391   0.70408281 -1.2392441e-07 -0.098290877 -0.098290877 -0.098290877 
-   15660        1.566   0.70409301   0.70409194 -1.0411845e-07 -0.098296011 -0.098296011 -0.098296011 
-   15670        1.567   0.70410209   0.70410103 -8.228546e-08 -0.098301129 -0.098301129 -0.098301129 
-   15680        1.568   0.70411114    0.7041101 -5.8929393e-08 -0.098306232 -0.098306232 -0.098306232 
-   15690        1.569   0.70412017   0.70411913 -3.4587472e-08  -0.09831132  -0.09831132  -0.09831132 
-   15700         1.57   0.70412918   0.70412814 -9.8178579e-09 -0.098316392 -0.098316392 -0.098316392 
-   15710        1.571   0.70413816   0.70413712 1.4813146e-08  -0.09832145  -0.09832145  -0.09832145 
-   15720        1.572   0.70414711   0.70414606 3.8744037e-08 -0.098326492 -0.098326492 -0.098326492 
-   15730        1.573   0.70415604   0.70415498 6.143091e-08  -0.09833152  -0.09833152  -0.09833152 
-   15740        1.574   0.70416495   0.70416387 8.2359818e-08 -0.098336532 -0.098336532 -0.098336532 
-   15750        1.575   0.70417383   0.70417273 1.0105841e-07 -0.098341529 -0.098341529 -0.098341529 
-   15760        1.576   0.70418269   0.70418156 1.1710658e-07 -0.098346512 -0.098346512 -0.098346512 
-   15770        1.577   0.70419153   0.70419036 1.3014592e-07 -0.098351479 -0.098351479 -0.098351479 
-   15780        1.578   0.70420033   0.70419914 1.3988771e-07 -0.098356432 -0.098356432 -0.098356432 
-   15790        1.579   0.70420912   0.70420789 1.461193e-07  -0.09836137  -0.09836137  -0.09836137 
-   15800         1.58   0.70421787   0.70421661 1.4870876e-07 -0.098366294 -0.098366294 -0.098366294 
-   15810        1.581    0.7042266   0.70422531 1.4760765e-07 -0.098371202 -0.098371202 -0.098371202 
-   15820        1.582   0.70423531   0.70423398 1.4285187e-07 -0.098376096 -0.098376096 -0.098376096 
-   15830        1.583   0.70424398   0.70424262 1.3456062e-07 -0.098380975 -0.098380975 -0.098380975 
-   15840        1.584   0.70425263   0.70425124 1.2293345e-07  -0.09838584  -0.09838584  -0.09838584 
-   15850        1.585   0.70426126   0.70425984 1.0824544e-07  -0.09839069  -0.09839069  -0.09839069 
-   15860        1.586   0.70426985   0.70426841 9.0840722e-08 -0.098395526 -0.098395526 -0.098395526 
-   15870        1.587   0.70427842   0.70427696 7.1124441e-08 -0.098400347 -0.098400347 -0.098400347 
-   15880        1.588   0.70428696   0.70428548 4.9553316e-08 -0.098405154 -0.098405154 -0.098405154 
-   15890        1.589   0.70429547   0.70429398 2.6625073e-08 -0.098409947 -0.098409947 -0.098409947 
-   15900         1.59   0.70430395   0.70430246 2.8669696e-09 -0.098414725 -0.098414725 -0.098414725 
-   15910        1.591   0.70431241   0.70431091 -2.1176328e-08 -0.098419489 -0.098419489 -0.098419489 
-   15920        1.592   0.70432084   0.70431935 -4.4955223e-08 -0.098424239 -0.098424239 -0.098424239 
-   15930        1.593   0.70432924   0.70432776 -6.792775e-08 -0.098428975 -0.098428975 -0.098428975 
-   15940        1.594   0.70433761   0.70433614 -8.9571923e-08 -0.098433696 -0.098433696 -0.098433696 
-   15950        1.595   0.70434595   0.70434451 -1.0939759e-07 -0.098438403 -0.098438403 -0.098438403 
-   15960        1.596   0.70435427   0.70435285 -1.2695754e-07 -0.098443097 -0.098443097 -0.098443097 
-   15970        1.597   0.70436256   0.70436116 -1.4185757e-07 -0.098447776 -0.098447776 -0.098447776 
-   15980        1.598   0.70437083   0.70436946 -1.5376534e-07 -0.098452441 -0.098452441 -0.098452441 
-   15990        1.599   0.70437907   0.70437773 -1.624178e-07 -0.098457093 -0.098457093 -0.098457093 
-   16000          1.6   0.70438728   0.70438597 -1.6762696e-07  -0.09846173  -0.09846173  -0.09846173 
-   16010        1.601   0.70439547    0.7043942 -1.6928399e-07 -0.098466354 -0.098466354 -0.098466354 
-   16020        1.602   0.70440363   0.70440239 -1.6736147e-07 -0.098470963 -0.098470963 -0.098470963 
-   16030        1.603   0.70441177   0.70441057 -1.6191378e-07 -0.098475559 -0.098475559 -0.098475559 
-   16040        1.604   0.70441989   0.70441871 -1.5307563e-07 -0.098480142 -0.098480142 -0.098480142 
-   16050        1.605   0.70442798   0.70442683 -1.4105875e-07  -0.09848471  -0.09848471  -0.09848471 
-   16060        1.606   0.70443605   0.70443493 -1.2614681e-07 -0.098489265 -0.098489265 -0.098489265 
-   16070        1.607    0.7044441     0.704443 -1.0868876e-07 -0.098493807 -0.098493807 -0.098493807 
-   16080        1.608   0.70445212   0.70445104 -8.9090701e-08 -0.098498334 -0.098498334 -0.098498334 
-   16090        1.609   0.70446013   0.70445906 -6.7806377e-08 -0.098502849 -0.098502849 -0.098502849 
-   16100         1.61   0.70446811   0.70446705 -4.5326735e-08 -0.098507349 -0.098507349 -0.098507349 
-   16110        1.611   0.70447607   0.70447502 -2.2168584e-08 -0.098511837 -0.098511837 -0.098511837 
-   16120        1.612   0.70448401   0.70448295 1.1372758e-09 -0.098516311 -0.098516311 -0.098516311 
-   16130        1.613   0.70449193   0.70449087 2.4058218e-08 -0.098520771 -0.098520771 -0.098520771 
-   16140        1.614   0.70449982   0.70449875 4.6071956e-08 -0.098525218 -0.098525218 -0.098525218 
-   16150        1.615    0.7045077   0.70450661 6.6678439e-08 -0.098529652 -0.098529652 -0.098529652 
-   16160        1.616   0.70451555   0.70451445 8.5411213e-08 -0.098534073 -0.098534073 -0.098534073 
-   16170        1.617   0.70452338   0.70452225 1.0184797e-07  -0.09853848  -0.09853848  -0.09853848 
-   16180        1.618   0.70453119   0.70453004 1.1562006e-07 -0.098542874 -0.098542874 -0.098542874 
-   16190        1.619   0.70453898    0.7045378 1.2642079e-07 -0.098547256 -0.098547256 -0.098547256 
-   16200         1.62   0.70454674   0.70454553 1.3401219e-07 -0.098551624 -0.098551624 -0.098551624 
-   16210        1.621   0.70455449   0.70455324 1.382303e-07 -0.098555978 -0.098555978 -0.098555978 
-   16220        1.622   0.70456221   0.70456093 1.3898867e-07  -0.09856032  -0.09856032  -0.09856032 
-   16230        1.623    0.7045699   0.70456859 1.3628015e-07 -0.098564649 -0.098564649 -0.098564649 
-   16240        1.624   0.70457758   0.70457623 1.3017678e-07 -0.098568965 -0.098568965 -0.098568965 
-   16250        1.625   0.70458522   0.70458385 1.2082792e-07 -0.098573268 -0.098573268 -0.098573268 
-   16260        1.626   0.70459285   0.70459145 1.0845664e-07 -0.098577559 -0.098577559 -0.098577559 
-   16270        1.627   0.70460045   0.70459903 9.3354414e-08 -0.098581836 -0.098581836 -0.098581836 
-   16280        1.628   0.70460803   0.70460658 7.5874224e-08 -0.098586101 -0.098586101 -0.098586101 
-   16290        1.629   0.70461558   0.70461412 5.6422355e-08 -0.098590352 -0.098590352 -0.098590352 
-   16300         1.63    0.7046231   0.70462163 3.5448945e-08 -0.098594591 -0.098594591 -0.098594591 
-   16310        1.631   0.70463061   0.70462913 1.3437578e-08 -0.098598818 -0.098598818 -0.098598818 
-   16320        1.632   0.70463808    0.7046366 -9.1058606e-09 -0.098603032 -0.098603032 -0.098603032 
-   16330        1.633   0.70464553   0.70464405 -3.1664807e-08 -0.098607233 -0.098607233 -0.098607233 
-   16340        1.634   0.70465296   0.70465149 -5.372385e-08 -0.098611421 -0.098611421 -0.098611421 
-   16350        1.635   0.70466036    0.7046589 -7.4780503e-08 -0.098615598 -0.098615598 -0.098615598 
-   16360        1.636   0.70466774    0.7046663 -9.4356646e-08 -0.098619761 -0.098619761 -0.098619761 
-   16370        1.637    0.7046751   0.70467367 -1.1200938e-07 -0.098623912 -0.098623912 -0.098623912 
-   16380        1.638   0.70468243   0.70468102 -1.2734106e-07 -0.098628051 -0.098628051 -0.098628051 
-   16390        1.639   0.70468973   0.70468836 -1.4000819e-07 -0.098632177 -0.098632177 -0.098632177 
-   16400         1.64   0.70469702   0.70469567 -1.4972922e-07 -0.098636291 -0.098636291 -0.098636291 
-   16410        1.641   0.70470428   0.70470296 -1.5629068e-07 -0.098640393 -0.098640393 -0.098640393 
-   16420        1.642   0.70471152   0.70471023 -1.5955195e-07 -0.098644482 -0.098644482 -0.098644482 
-   16430        1.643   0.70471873   0.70471748 -1.5944822e-07 -0.098648559 -0.098648559 -0.098648559 
-   16440        1.644   0.70472593    0.7047247 -1.5599177e-07 -0.098652624 -0.098652624 -0.098652624 
-   16450        1.645    0.7047331   0.70473191 -1.4927144e-07 -0.098656677 -0.098656677 -0.098656677 
-   16460        1.646   0.70474025   0.70473909 -1.3945041e-07 -0.098660718 -0.098660718 -0.098660718 
-   16470        1.647   0.70474739   0.70474624 -1.2676223e-07 -0.098664746 -0.098664746 -0.098664746 
-   16480        1.648    0.7047545   0.70475338 -1.115053e-07 -0.098668763 -0.098668763 -0.098668763 
-   16490        1.649   0.70476159   0.70476049 -9.4035824e-08 -0.098672767 -0.098672767 -0.098672767 
-   16500         1.65   0.70476867   0.70476758 -7.475956e-08  -0.09867676  -0.09867676  -0.09867676 
-   16510        1.651   0.70477572   0.70477465 -5.4122352e-08  -0.09868074  -0.09868074  -0.09868074 
-   16520        1.652   0.70478276   0.70478169 -3.259985e-08 -0.098684709 -0.098684709 -0.098684709 
-   16530        1.653   0.70478977   0.70478871 -1.0686544e-08 -0.098688666 -0.098688666 -0.098688666 
-   16540        1.654   0.70479677    0.7047957 1.111559e-08 -0.098692611 -0.098692611 -0.098692611 
-   16550        1.655   0.70480375   0.70480267 3.2308584e-08 -0.098696544 -0.098696544 -0.098696544 
-   16560        1.656   0.70481071   0.70480962 5.2409852e-08 -0.098700465 -0.098700465 -0.098700465 
-   16570        1.657   0.70481765   0.70481655 7.096317e-08 -0.098704374 -0.098704374 -0.098704374 
-   16580        1.658   0.70482458   0.70482345 8.7549031e-08 -0.098708272 -0.098708272 -0.098708272 
-   16590        1.659   0.70483148   0.70483033 1.0179413e-07 -0.098712158 -0.098712158 -0.098712158 
-   16600         1.66   0.70483837   0.70483719 1.1337974e-07 -0.098716033 -0.098716033 -0.098716033 
-   16610        1.661   0.70484523   0.70484403 1.2204889e-07 -0.098719896 -0.098719896 -0.098719896 
-   16620        1.662   0.70485208   0.70485084  1.27612e-07 -0.098723747 -0.098723747 -0.098723747 
-   16630        1.663    0.7048589   0.70485764 1.2995106e-07 -0.098727587 -0.098727587 -0.098727587 
-   16640        1.664    0.7048657   0.70486441 1.290221e-07 -0.098731415 -0.098731415 -0.098731415 
-   16650        1.665   0.70487249   0.70487117 1.2485598e-07 -0.098735232 -0.098735232 -0.098735232 
-   16660        1.666   0.70487925    0.7048779 1.1755749e-07 -0.098739038 -0.098739038 -0.098739038 
-   16670        1.667   0.70488599   0.70488461 1.0730269e-07 -0.098742832 -0.098742832 -0.098742832 
-   16680        1.668   0.70489271   0.70489131 9.4334741e-08 -0.098746614 -0.098746614 -0.098746614 
-   16690        1.669   0.70489941   0.70489799  7.89581e-08 -0.098750386 -0.098750386 -0.098750386 
-   16700         1.67   0.70490609   0.70490465 6.1531405e-08 -0.098754146 -0.098754146 -0.098754146 
-   16710        1.671   0.70491274   0.70491129 4.2459112e-08 -0.098757894 -0.098757894 -0.098757894 
-   16720        1.672   0.70491938   0.70491791 2.2182113e-08 -0.098761632 -0.098761632 -0.098761632 
-   16730        1.673   0.70492599   0.70492452 1.1675535e-09 -0.098765358 -0.098765358 -0.098765358 
-   16740        1.674   0.70493257    0.7049311 -2.0101928e-08 -0.098769073 -0.098769073 -0.098769073 
-   16750        1.675   0.70493914   0.70493767 -4.113928e-08 -0.098772777 -0.098772777 -0.098772777 
-   16760        1.676   0.70494568   0.70494423 -6.1464185e-08  -0.09877647  -0.09877647  -0.09877647 
-   16770        1.677   0.70495221   0.70495076 -8.0614024e-08 -0.098780152 -0.098780152 -0.098780152 
-   16780        1.678   0.70495871   0.70495728 -9.8154404e-08 -0.098783823 -0.098783823 -0.098783823 
-   16790        1.679   0.70496519   0.70496378 -1.1368901e-07 -0.098787483 -0.098787483 -0.098787483 
-   16800         1.68   0.70497165   0.70497026 -1.2686854e-07 -0.098791132 -0.098791132 -0.098791132 
-   16810        1.681   0.70497808   0.70497672 -1.3739859e-07  -0.09879477  -0.09879477  -0.09879477 
-   16820        1.682    0.7049845   0.70498317 -1.4504619e-07 -0.098798397 -0.098798397 -0.098798397 
-   16830        1.683    0.7049909    0.7049896 -1.4964497e-07 -0.098802013 -0.098802013 -0.098802013 
-   16840        1.684   0.70499728     0.704996 -1.5109878e-07 -0.098805618 -0.098805618 -0.098805618 
-   16850        1.685   0.70500363   0.70500239 -1.4938365e-07 -0.098809212 -0.098809212 -0.098809212 
-   16860        1.686   0.70500997   0.70500876 -1.4454818e-07 -0.098812796 -0.098812796 -0.098812796 
-   16870        1.687    0.7050163   0.70501511 -1.3671215e-07 -0.098816369 -0.098816369 -0.098816369 
-   16880        1.688    0.7050226   0.70502144 -1.2606364e-07 -0.098819931 -0.098819931 -0.098819931 
-   16890        1.689   0.70502888   0.70502775 -1.1285449e-07 -0.098823483 -0.098823483 -0.098823483 
-   16900         1.69   0.70503515   0.70503403 -9.7394347e-08 -0.098827024 -0.098827024 -0.098827024 
-   16910        1.691    0.7050414    0.7050403 -8.0043457e-08 -0.098830554 -0.098830554 -0.098830554 
-   16920        1.692   0.70504764   0.70504655 -6.1204235e-08 -0.098834074 -0.098834074 -0.098834074 
-   16930        1.693   0.70505386   0.70505277 -4.1311958e-08 -0.098837583 -0.098837583 -0.098837583 
-   16940        1.694   0.70506006   0.70505898 -2.0824711e-08 -0.098841082 -0.098841082 -0.098841082 
-   16950        1.695   0.70506624   0.70506516 -2.128402e-10  -0.09884457  -0.09884457  -0.09884457 
-   16960        1.696   0.70507241   0.70507132 2.0051838e-08 -0.098848048 -0.098848048 -0.098848048 
-   16970        1.697   0.70507856   0.70507747 3.9506835e-08 -0.098851515 -0.098851515 -0.098851515 
-   16980        1.698    0.7050847   0.70508359 5.7709542e-08 -0.098854972 -0.098854972 -0.098854972 
-   16990        1.699   0.70509082   0.70508969 7.4247296e-08 -0.098858418 -0.098858418 -0.098858418 
-   17000          1.7   0.70509692   0.70509577 8.8746729e-08 -0.098861854 -0.098861854 -0.098861854 
-   17010        1.701     0.705103   0.70510183 1.008822e-07  -0.09886528  -0.09886528  -0.09886528 
-   17020        1.702   0.70510907   0.70510788 1.103831e-07 -0.098868696 -0.098868696 -0.098868696 
-   17030        1.703   0.70511512    0.7051139 1.1703987e-07 -0.098872101 -0.098872101 -0.098872101 
-   17040        1.704   0.70512115    0.7051199 1.2070866e-07 -0.098875496 -0.098875496 -0.098875496 
-   17050        1.705   0.70512717   0.70512589 1.2131436e-07 -0.098878881 -0.098878881 -0.098878881 
-   17060        1.706   0.70513317   0.70513186 1.1885218e-07 -0.098882256 -0.098882256 -0.098882256 
-   17070        1.707   0.70513915   0.70513781 1.1338751e-07 -0.098885621 -0.098885621 -0.098885621 
-   17080        1.708    0.7051451   0.70514374 1.0505425e-07 -0.098888975 -0.098888975 -0.098888975 
-   17090        1.709   0.70515105   0.70514966 9.4051537e-08  -0.09889232  -0.09889232  -0.09889232 
-   17100         1.71   0.70515697   0.70515556 8.0638973e-08 -0.098895654 -0.098895654 -0.098895654 
-   17110        1.711   0.70516287   0.70516145 6.5130548e-08 -0.098898978 -0.098898978 -0.098898978 
-   17120        1.712   0.70516875   0.70516731 4.7887273e-08 -0.098902293 -0.098902293 -0.098902293 
-   17130        1.713   0.70517462   0.70517317 2.930879e-08 -0.098905597 -0.098905597 -0.098905597 
-   17140        1.714   0.70518046     0.705179 9.8241129e-09 -0.098908892 -0.098908892 -0.098908892 
-   17150        1.715   0.70518628   0.70518482 -1.0118272e-08 -0.098912177 -0.098912177 -0.098912177 
-   17160        1.716   0.70519209   0.70519063 -3.0060726e-08 -0.098915452 -0.098915452 -0.098915452 
-   17170        1.717   0.70519787   0.70519642 -4.9546956e-08 -0.098918717 -0.098918717 -0.098918717 
-   17180        1.718   0.70520364    0.7052022 -6.8132453e-08 -0.098921972 -0.098921972 -0.098921972 
-   17190        1.719   0.70520938   0.70520796 -8.5394625e-08 -0.098925217 -0.098925217 -0.098925217 
-   17200         1.72   0.70521511    0.7052137 -1.009424e-07 -0.098928453 -0.098928453 -0.098928453 
-   17210        1.721   0.70522082   0.70521943 -1.144251e-07 -0.098931679 -0.098931679 -0.098931679 
-   17220        1.722   0.70522651   0.70522514 -1.2554032e-07 -0.098934896 -0.098934896 -0.098934896 
-   17230        1.723   0.70523218   0.70523084 -1.3404073e-07 -0.098938102 -0.098938102 -0.098938102 
-   17240        1.724   0.70523783   0.70523652 -1.3973956e-07 -0.098941299 -0.098941299 -0.098941299 
-   17250        1.725   0.70524347   0.70524218 -1.4251469e-07 -0.098944487 -0.098944487 -0.098944487 
-   17260        1.726   0.70524909   0.70524783 -1.4231129e-07 -0.098947665 -0.098947665 -0.098947665 
-   17270        1.727   0.70525469   0.70525346 -1.3914283e-07 -0.098950833 -0.098950833 -0.098950833 
-   17280        1.728   0.70526027   0.70525907 -1.3309062e-07 -0.098953992 -0.098953992 -0.098953992 
-   17290        1.729   0.70526584   0.70526466 -1.243017e-07 -0.098957141 -0.098957141 -0.098957141 
-   17300         1.73    0.7052714   0.70527024 -1.1298532e-07 -0.098960281 -0.098960281 -0.098960281 
-   17310        1.731   0.70527694    0.7052758 -9.9407949e-08 -0.098963411 -0.098963411 -0.098963411 
-   17320        1.732   0.70528246   0.70528134 -8.3887032e-08 -0.098966533 -0.098966533 -0.098966533 
-   17330        1.733   0.70528797   0.70528686 -6.6783544e-08 -0.098969644 -0.098969644 -0.098969644 
-   17340        1.734   0.70529346   0.70529236 -4.8493623e-08 -0.098972747 -0.098972747 -0.098972747 
-   17350        1.735   0.70529894   0.70529785 -2.9439391e-08  -0.09897584  -0.09897584  -0.09897584 
-   17360        1.736   0.70530441   0.70530332 -1.0059218e-08 -0.098978923 -0.098978923 -0.098978923 
-   17370        1.737   0.70530986   0.70530876 9.2023572e-09 -0.098981998 -0.098981998 -0.098981998 
-   17380        1.738   0.70531529   0.70531419 2.7904822e-08 -0.098985063 -0.098985063 -0.098985063 
-   17390        1.739   0.70532071    0.7053196 4.5621759e-08 -0.098988119 -0.098988119 -0.098988119 
-   17400         1.74   0.70532612     0.705325 6.1950569e-08 -0.098991166 -0.098991166 -0.098991166 
-   17410        1.741   0.70533151   0.70533037 7.6521611e-08 -0.098994204 -0.098994204 -0.098994204 
-   17420        1.742   0.70533689   0.70533573 8.9006571e-08 -0.098997232 -0.098997232 -0.098997232 
-   17430        1.743   0.70534225   0.70534107 9.9125854e-08 -0.099000252 -0.099000252 -0.099000252 
-   17440        1.744    0.7053476   0.70534639 1.0665484e-07 -0.099003262 -0.099003262 -0.099003262 
-   17450        1.745   0.70535293    0.7053517 1.1142887e-07 -0.099006264 -0.099006264 -0.099006264 
-   17460        1.746   0.70535825   0.70535699 1.1334683e-07 -0.099009256 -0.099009256 -0.099009256 
-   17470        1.747   0.70536355   0.70536226 1.1237329e-07 -0.099012239 -0.099012239 -0.099012239 
-   17480        1.748   0.70536884   0.70536752 1.085391e-07 -0.099015214 -0.099015214 -0.099015214 
-   17490        1.749    0.7053741   0.70537276 1.0194053e-07 -0.099018179 -0.099018179 -0.099018179 
-   17500         1.75   0.70537936   0.70537799 9.2736828e-08 -0.099021136 -0.099021136 -0.099021136 
-   17510        1.751   0.70538459    0.7053832 8.1146424e-08 -0.099024084 -0.099024084 -0.099024084 
-   17520        1.752   0.70538981    0.7053884 6.7441735e-08 -0.099027023 -0.099027023 -0.099027023 
-   17530        1.753   0.70539501   0.70539358 5.1942781e-08 -0.099029953 -0.099029953 -0.099029953 
-   17540        1.754   0.70540019   0.70539875 3.500971e-08 -0.099032874 -0.099032874 -0.099032874 
-   17550        1.755   0.70540535   0.70540391 1.7034444e-08 -0.099035786 -0.099035786 -0.099035786 
-   17560        1.756    0.7054105   0.70540906 -1.5683958e-09  -0.09903869  -0.09903869  -0.09903869 
-   17570        1.757   0.70541563   0.70541419 -2.0371043e-08 -0.099041585 -0.099041585 -0.099041585 
-   17580        1.758   0.70542074    0.7054193 -3.894242e-08 -0.099044471 -0.099044471 -0.099044471 
-   17590        1.759   0.70542584    0.7054244 -5.685802e-08 -0.099047349 -0.099047349 -0.099047349 
-   17600         1.76   0.70543092   0.70542949 -7.3709601e-08 -0.099050218 -0.099050218 -0.099050218 
-   17610        1.761   0.70543598   0.70543457 -8.9114493e-08 -0.099053078 -0.099053078 -0.099053078 
-   17620        1.762   0.70544102   0.70543963 -1.0272428e-07  -0.09905593  -0.09905593  -0.09905593 
-   17630        1.763   0.70544605   0.70544468 -1.1423268e-07 -0.099058773 -0.099058773 -0.099058773 
-   17640        1.764   0.70545106   0.70544972 -1.2338242e-07 -0.099061607 -0.099061607 -0.099061607 
-   17650        1.765   0.70545606   0.70545474 -1.2997101e-07 -0.099064433 -0.099064433 -0.099064433 
-   17660        1.766   0.70546104   0.70545974 -1.3385519e-07 -0.099067251 -0.099067251 -0.099067251 
-   17670        1.767     0.705466   0.70546473 -1.3495407e-07  -0.09907006  -0.09907006  -0.09907006 
-   17680        1.768   0.70547095   0.70546971 -1.3325075e-07 -0.099072861 -0.099072861 -0.099072861 
-   17690        1.769   0.70547589   0.70547467 -1.2879257e-07 -0.099075653 -0.099075653 -0.099075653 
-   17700         1.77   0.70548081   0.70547961 -1.216898e-07 -0.099078437 -0.099078437 -0.099078437 
-   17710        1.771   0.70548571   0.70548454 -1.1211294e-07 -0.099081212 -0.099081212 -0.099081212 
-   17720        1.772   0.70549061   0.70548945 -1.0028866e-07  -0.09908398  -0.09908398  -0.09908398 
-   17730        1.773   0.70549549   0.70549435 -8.6494411e-08 -0.099086738 -0.099086738 -0.099086738 
-   17740        1.774   0.70550035   0.70549923 -7.1051936e-08 -0.099089489 -0.099089489 -0.099089489 
-   17750        1.775   0.70550521    0.7055041 -5.4319777e-08 -0.099092231 -0.099092231 -0.099092231 
-   17760        1.776   0.70551005   0.70550894 -3.6684948e-08 -0.099094965 -0.099094965 -0.099094965 
-   17770        1.777   0.70551488   0.70551377 -1.855399e-08 -0.099097691 -0.099097691 -0.099097691 
-   17780        1.778   0.70551969   0.70551859 -3.4360344e-10 -0.099100409 -0.099100409 -0.099100409 
-   17790        1.779   0.70552449   0.70552339 1.7528926e-08 -0.099103118 -0.099103118 -0.099103118 
-   17800         1.78   0.70552928   0.70552817 3.4655283e-08 -0.099105819 -0.099105819 -0.099105819 
-   17810        1.781   0.70553406   0.70553293 5.0645452e-08 -0.099108513 -0.099108513 -0.099108513 
-   17820        1.782   0.70553883   0.70553768 6.5136593e-08 -0.099111198 -0.099111198 -0.099111198 
-   17830        1.783   0.70554358   0.70554242 7.7801273e-08 -0.099113875 -0.099113875 -0.099113875 
-   17840        1.784   0.70554832   0.70554714 8.8354857e-08 -0.099116544 -0.099116544 -0.099116544 
-   17850        1.785   0.70555304   0.70555184 9.6561908e-08 -0.099119205 -0.099119205 -0.099119205 
-   17860        1.786   0.70555776   0.70555653 1.0224143e-07 -0.099121857 -0.099121857 -0.099121857 
-   17870        1.787   0.70556246    0.7055612 1.0527086e-07 -0.099124502 -0.099124502 -0.099124502 
-   17880        1.788   0.70556714   0.70556586 1.0558868e-07 -0.099127139 -0.099127139 -0.099127139 
-   17890        1.789   0.70557181    0.7055705 1.0319568e-07 -0.099129768 -0.099129768 -0.099129768 
-   17900         1.79   0.70557647   0.70557514 9.8154728e-08  -0.09913239  -0.09913239  -0.09913239 
-   17910        1.791   0.70558111   0.70557975 9.0589173e-08 -0.099135003 -0.099135003 -0.099135003 
-   17920        1.792   0.70558573   0.70558436 8.0679815e-08 -0.099137608 -0.099137608 -0.099137608 
-   17930        1.793   0.70559034   0.70558895 6.8660607e-08 -0.099140206 -0.099140206 -0.099140206 
-   17940        1.794   0.70559494   0.70559353 5.481314e-08 -0.099142796 -0.099142796 -0.099142796 
-   17950        1.795   0.70559952    0.7055981 3.9460048e-08 -0.099145378 -0.099145378 -0.099145378 
-   17960        1.796   0.70560409   0.70560266 2.2957502e-08 -0.099147952 -0.099147952 -0.099147952 
-   17970        1.797   0.70560864    0.7056072 5.6869442e-09 -0.099150518 -0.099150518 -0.099150518 
-   17980        1.798   0.70561317   0.70561173 -1.1953717e-08 -0.099153077 -0.099153077 -0.099153077 
-   17990        1.799   0.70561769   0.70561625 -2.9559276e-08 -0.099155628 -0.099155628 -0.099155628 
-   18000          1.8   0.70562219   0.70562076 -4.6726531e-08 -0.099158171 -0.099158171 -0.099158171 
-   18010        1.801   0.70562668   0.70562526 -6.3063516e-08 -0.099160707 -0.099160707 -0.099160707 
-   18020        1.802   0.70563115   0.70562974 -7.819845e-08 -0.099163235 -0.099163235 -0.099163235 
-   18030        1.803   0.70563561   0.70563422 -9.1788187e-08 -0.099165756 -0.099165756 -0.099165756 
-   18040        1.804   0.70564005   0.70563868 -1.03526e-07 -0.099168268 -0.099168268 -0.099168268 
-   18050        1.805   0.70564448   0.70564312 -1.131485e-07 -0.099170774 -0.099170774 -0.099170774 
-   18060        1.806   0.70564889   0.70564756 -1.2044154e-07 -0.099173272 -0.099173272 -0.099173272 
-   18070        1.807   0.70565329   0.70565198 -1.2524497e-07 -0.099175762 -0.099175762 -0.099175762 
-   18080        1.808   0.70565768   0.70565639 -1.2745617e-07 -0.099178245 -0.099178245 -0.099178245 
-   18090        1.809   0.70566205   0.70566079 -1.2703218e-07  -0.09918072  -0.09918072  -0.09918072 
-   18100         1.81   0.70566641   0.70566518 -1.2399058e-07 -0.099183188 -0.099183188 -0.099183188 
-   18110        1.811   0.70567076   0.70566955 -1.1840886e-07 -0.099185648 -0.099185648 -0.099185648 
-   18120        1.812   0.70567509    0.7056739 -1.1042245e-07 -0.099188101 -0.099188101 -0.099188101 
-   18130        1.813   0.70567941   0.70567824 -1.0022152e-07 -0.099190547 -0.099190547 -0.099190547 
-   18140        1.814   0.70568372   0.70568257 -8.8046375e-08 -0.099192985 -0.099192985 -0.099192985 
-   18150        1.815   0.70568802   0.70568688 -7.4181867e-08 -0.099195416 -0.099195416 -0.099195416 
-   18160        1.816   0.70569231   0.70569118 -5.8950699e-08  -0.09919784  -0.09919784  -0.09919784 
-   18170        1.817   0.70569659   0.70569547 -4.2705933e-08 -0.099200256 -0.099200256 -0.099200256 
-   18180        1.818   0.70570085   0.70569974 -2.5822808e-08 -0.099202665 -0.099202665 -0.099202665 
-   18190        1.819    0.7057051   0.70570399 -8.690076e-09 -0.099205067 -0.099205067 -0.099205067 
-   18200         1.82   0.70570935   0.70570823 8.2989437e-09 -0.099207462 -0.099207462 -0.099207462 
-   18210        1.821   0.70571358   0.70571246 2.4755394e-08 -0.099209849 -0.099209849 -0.099209849 
-   18220        1.822    0.7057178   0.70571667 4.0303774e-08 -0.099212229 -0.099212229 -0.099212229 
-   18230        1.823   0.70572201   0.70572087 5.4590506e-08 -0.099214602 -0.099214602 -0.099214602 
-   18240        1.824   0.70572621   0.70572505 6.7291973e-08 -0.099216968 -0.099216968 -0.099216968 
-   18250        1.825    0.7057304   0.70572922 7.8121845e-08 -0.099219327 -0.099219327 -0.099219327 
-   18260        1.826   0.70573457   0.70573337 8.683753e-08 -0.099221679 -0.099221679 -0.099221679 
-   18270        1.827   0.70573874   0.70573751 9.3245603e-08 -0.099224023 -0.099224023 -0.099224023 
-   18280        1.828   0.70574289   0.70574164 9.7206098e-08 -0.099226361 -0.099226361 -0.099226361 
-   18290        1.829   0.70574703   0.70574576 9.8635549e-08 -0.099228691 -0.099228691 -0.099228691 
-   18300         1.83   0.70575116   0.70574986 9.7508745e-08 -0.099231015 -0.099231015 -0.099231015 
-   18310        1.831   0.70575527   0.70575395 9.3859127e-08 -0.099233331 -0.099233331 -0.099233331 
-   18320        1.832   0.70575937   0.70575803 8.7777853e-08 -0.099235641 -0.099235641 -0.099235641 
-   18330        1.833   0.70576346    0.7057621 7.941154e-08 -0.099237943 -0.099237943 -0.099237943 
-   18340        1.834   0.70576754   0.70576616 6.8958732e-08 -0.099240239 -0.099240239 -0.099240239 
-   18350        1.835    0.7057716    0.7057702 5.6665204e-08 -0.099242528 -0.099242528 -0.099242528 
-   18360        1.836   0.70577565   0.70577424 4.2818186e-08 -0.099244809 -0.099244809 -0.099244809 
-   18370        1.837   0.70577968   0.70577826 2.7739657e-08 -0.099247084 -0.099247084 -0.099247084 
-   18380        1.838    0.7057837   0.70578228 1.1778865e-08 -0.099249353 -0.099249353 -0.099249353 
-   18390        1.839   0.70578771   0.70578628 -4.6957605e-09 -0.099251614 -0.099251614 -0.099251614 
-   18400         1.84    0.7057917   0.70579027 -2.1305108e-08 -0.099253868 -0.099253868 -0.099253868 
-   18410        1.841   0.70579568   0.70579425 -3.7668103e-08 -0.099256116 -0.099256116 -0.099256116 
-   18420        1.842   0.70579964   0.70579823 -5.3410454e-08 -0.099258357 -0.099258357 -0.099258357 
-   18430        1.843    0.7058036   0.70580219 -6.8173204e-08 -0.099260591 -0.099260591 -0.099260591 
-   18440        1.844   0.70580753   0.70580614 -8.1620914e-08 -0.099262818 -0.099262818 -0.099262818 
-   18450        1.845   0.70581146   0.70581008 -9.3449288e-08 -0.099265039 -0.099265039 -0.099265039 
-   18460        1.846   0.70581537   0.70581401 -1.0339205e-07 -0.099267253 -0.099267253 -0.099267253 
-   18470        1.847   0.70581927   0.70581793 -1.1122692e-07 -0.099269461 -0.099269461 -0.099269461 
-   18480        1.848   0.70582316   0.70582184 -1.1678063e-07 -0.099271661 -0.099271661 -0.099271661 
-   18490        1.849   0.70582703   0.70582574 -1.1993267e-07 -0.099273855 -0.099273855 -0.099273855 
-   18500         1.85   0.70583089   0.70582962 -1.2061797e-07 -0.099276043 -0.099276043 -0.099276043 
-   18510        1.851   0.70583474    0.7058335 -1.1882819e-07 -0.099278224 -0.099278224 -0.099278224 
-   18520        1.852   0.70583858   0.70583736 -1.1461174e-07 -0.099280398 -0.099280398 -0.099280398 
-   18530        1.853   0.70584241   0.70584121 -1.0807252e-07 -0.099282566 -0.099282566 -0.099282566 
-   18540        1.854   0.70584623   0.70584505 -9.9367345e-08 -0.099284727 -0.099284727 -0.099284727 
-   18550        1.855   0.70585004   0.70584887 -8.8702244e-08 -0.099286882 -0.099286882 -0.099286882 
-   18560        1.856   0.70585383   0.70585268 -7.6327541e-08  -0.09928903  -0.09928903  -0.09928903 
-   18570        1.857   0.70585762   0.70585648 -6.2532008e-08 -0.099291172 -0.099291172 -0.099291172 
-   18580        1.858    0.7058614   0.70586027 -4.7636131e-08 -0.099293307 -0.099293307 -0.099293307 
-   18590        1.859   0.70586517   0.70586404 -3.1984665e-08 -0.099295436 -0.099295436 -0.099295436 
-   18600         1.86   0.70586892    0.7058678 -1.593866e-08 -0.099297558 -0.099297558 -0.099297558 
-   18610        1.861   0.70587267   0.70587155 1.3286207e-10 -0.099299674 -0.099299674 -0.099299674 
-   18620        1.862   0.70587641   0.70587528 1.5861394e-08 -0.099301784 -0.099301784 -0.099301784 
-   18630        1.863   0.70588014     0.705879 3.0887388e-08 -0.099303888 -0.099303888 -0.099303888 
-   18640        1.864   0.70588386   0.70588271 4.4868472e-08 -0.099305985 -0.099305985 -0.099305985 
-   18650        1.865   0.70588757    0.7058864 5.7487246e-08 -0.099308075 -0.099308075 -0.099308075 
-   18660        1.866   0.70589127   0.70589009 6.8458489e-08  -0.09931016  -0.09931016  -0.09931016 
-   18670        1.867   0.70589495   0.70589376 7.7535597e-08 -0.099312238 -0.099312238 -0.099312238 
-   18680        1.868   0.70589863   0.70589742 8.4516128e-08  -0.09931431  -0.09931431  -0.09931431 
-   18690        1.869    0.7059023   0.70590106 8.9246306e-08 -0.099316375 -0.099316375 -0.099316375 
-   18700         1.87   0.70590596    0.7059047 9.1624407e-08 -0.099318435 -0.099318435 -0.099318435 
-   18710        1.871   0.70590961   0.70590832 9.1602936e-08 -0.099320488 -0.099320488 -0.099320488 
-   18720        1.872   0.70591324   0.70591194 8.9189552e-08 -0.099322535 -0.099322535 -0.099322535 
-   18730        1.873   0.70591687   0.70591554 8.4446732e-08 -0.099324576 -0.099324576 -0.099324576 
-   18740        1.874   0.70592048   0.70591913 7.7490175e-08  -0.09932661  -0.09932661  -0.09932661 
-   18750        1.875   0.70592408   0.70592272 6.848599e-08 -0.099328639 -0.099328639 -0.099328639 
-   18760        1.876   0.70592767   0.70592629 5.764674e-08 -0.099330661 -0.099330661 -0.099330661 
-   18770        1.877   0.70593125   0.70592985 4.522643e-08 -0.099332677 -0.099332677 -0.099332677 
-   18780        1.878   0.70593481   0.70593341 3.1514557e-08 -0.099334688 -0.099334688 -0.099334688 
-   18790        1.879   0.70593837   0.70593695 1.6829372e-08 -0.099336692 -0.099336692 -0.099336692 
-   18800         1.88   0.70594191   0.70594049 1.5104927e-09  -0.09933869  -0.09933869  -0.09933869 
-   18810        1.881   0.70594544   0.70594402 -1.4088944e-08 -0.099340682 -0.099340682 -0.099340682 
-   18820        1.882   0.70594895   0.70594753 -2.9610419e-08 -0.099342668 -0.099342668 -0.099342668 
-   18830        1.883   0.70595245   0.70595104 -4.4698272e-08 -0.099344648 -0.099344648 -0.099344648 
-   18840        1.884   0.70595595   0.70595454 -5.9007842e-08 -0.099346623 -0.099346623 -0.099346623 
-   18850        1.885   0.70595943   0.70595803 -7.2213343e-08 -0.099348591 -0.099348591 -0.099348591 
-   18860        1.886   0.70596289   0.70596152 -8.4015276e-08 -0.099350553 -0.099350553 -0.099350553 
-   18870        1.887   0.70596635   0.70596499 -9.4147216e-08  -0.09935251  -0.09935251  -0.09935251 
-   18880        1.888   0.70596979   0.70596845 -1.0238183e-07  -0.09935446  -0.09935446  -0.09935446 
-   18890        1.889   0.70597323    0.7059719 -1.0853597e-07 -0.099356405 -0.099356405 -0.099356405 
-   18900         1.89   0.70597665   0.70597535 -1.1247473e-07 -0.099358343 -0.099358343 -0.099358343 
-   18910        1.891   0.70598006   0.70597878 -1.1411442e-07 -0.099360276 -0.099360276 -0.099360276 
-   18920        1.892   0.70598346    0.7059822 -1.1342432e-07 -0.099362203 -0.099362203 -0.099362203 
-   18930        1.893   0.70598685   0.70598562 -1.1042722e-07 -0.099364125 -0.099364125 -0.099364125 
-   18940        1.894   0.70599023   0.70598902 -1.0519876e-07  -0.09936604  -0.09936604  -0.09936604 
-   18950        1.895   0.70599361   0.70599241 -9.7865496e-08  -0.09936795  -0.09936795  -0.09936795 
-   18960        1.896   0.70599697   0.70599579 -8.8601904e-08 -0.099369854 -0.099369854 -0.099369854 
-   18970        1.897   0.70600032   0.70599916 -7.7626193e-08 -0.099371752 -0.099371752 -0.099371752 
-   18980        1.898   0.70600367   0.70600251 -6.5195188e-08 -0.099373644 -0.099373644 -0.099373644 
-   18990        1.899     0.706007   0.70600586 -5.1598322e-08 -0.099375531 -0.099375531 -0.099375531 
-   19000          1.9   0.70601033   0.70600919 -3.71509e-08 -0.099377412 -0.099377412 -0.099377412 
-   19010        1.901   0.70601365   0.70601252 -2.2186797e-08 -0.099379288 -0.099379288 -0.099379288 
-   19020        1.902   0.70601696   0.70601583 -7.0507367e-09 -0.099381157 -0.099381157 -0.099381157 
-   19030        1.903   0.70602026   0.70601913 7.9096381e-09 -0.099383021 -0.099383021 -0.099383021 
-   19040        1.904   0.70602355   0.70602241 2.2351752e-08  -0.09938488  -0.09938488  -0.09938488 
-   19050        1.905   0.70602684   0.70602569 3.5945938e-08 -0.099386733 -0.099386733 -0.099386733 
-   19060        1.906   0.70603012   0.70602895 4.8382957e-08  -0.09938858  -0.09938858  -0.09938858 
-   19070        1.907   0.70603338   0.70603221 5.9381035e-08 -0.099390422 -0.099390422 -0.099390422 
-   19080        1.908   0.70603664   0.70603545 6.8692236e-08 -0.099392258 -0.099392258 -0.099392258 
-   19090        1.909   0.70603989   0.70603868 7.6108057e-08 -0.099394089 -0.099394089 -0.099394089 
-   19100         1.91   0.70604313    0.7060419 8.1464086e-08 -0.099395914 -0.099395914 -0.099395914 
-   19110        1.911   0.70604637   0.70604511 8.4643642e-08 -0.099397733 -0.099397733 -0.099397733 
-   19120        1.912   0.70604959   0.70604832 8.5580314e-08 -0.099399547 -0.099399547 -0.099399547 
-   19130        1.913    0.7060528   0.70605151 8.4259331e-08 -0.099401356 -0.099401356 -0.099401356 
-   19140        1.914     0.706056   0.70605469 8.0717747e-08 -0.099403159 -0.099403159 -0.099403159 
-   19150        1.915    0.7060592   0.70605786 7.5043437e-08 -0.099404957 -0.099404957 -0.099404957 
-   19160        1.916   0.70606238   0.70606103 6.7372934e-08 -0.099406749 -0.099406749 -0.099406749 
-   19170        1.917   0.70606555   0.70606418 5.7888148e-08 -0.099408536 -0.099408536 -0.099408536 
-   19180        1.918   0.70606871   0.70606733 4.6812058e-08 -0.099410318 -0.099410318 -0.099410318 
-   19190        1.919   0.70607186   0.70607047 3.4403481e-08 -0.099412094 -0.099412094 -0.099412094 
-   19200         1.92     0.706075    0.7060736 2.0951022e-08 -0.099413865 -0.099413865 -0.099413865 
-   19210        1.921   0.70607813   0.70607672 6.7663709e-09  -0.09941563  -0.09941563  -0.09941563 
-   19220        1.922   0.70608125   0.70607984 -7.8229194e-09 -0.099417391 -0.099417391 -0.099417391 
-   19230        1.923   0.70608435   0.70608294 -2.2480992e-08 -0.099419145 -0.099419145 -0.099419145 
-   19240        1.924   0.70608745   0.70608604 -3.6871415e-08 -0.099420895 -0.099420895 -0.099420895 
-   19250        1.925   0.70609053   0.70608913 -5.0664901e-08 -0.099422639 -0.099422639 -0.099422639 
-   19260        1.926   0.70609361   0.70609222 -6.3546837e-08 -0.099424378 -0.099424378 -0.099424378 
-   19270        1.927   0.70609667   0.70609529 -7.5224461e-08 -0.099426112 -0.099426112 -0.099426112 
-   19280        1.928   0.70609972   0.70609836 -8.543351e-08  -0.09942784  -0.09942784  -0.09942784 
-   19290        1.929   0.70610277   0.70610142 -9.3944199e-08 -0.099429564 -0.099429564 -0.099429564 
-   19300         1.93    0.7061058   0.70610447 -1.0056639e-07 -0.099431282 -0.099431282 -0.099431282 
-   19310        1.931   0.70610882   0.70610751 -1.0515382e-07 -0.099432995 -0.099432995 -0.099432995 
-   19320        1.932   0.70611183   0.70611055 -1.0760737e-07 -0.099434703 -0.099434703 -0.099434703 
-   19330        1.933   0.70611484   0.70611357 -1.0787713e-07 -0.099436405 -0.099436405 -0.099436405 
-   19340        1.934   0.70611783   0.70611659 -1.0596347e-07 -0.099438103 -0.099438103 -0.099438103 
-   19350        1.935   0.70612082   0.70611959 -1.0191683e-07 -0.099439795 -0.099439795 -0.099439795 
-   19360        1.936    0.7061238   0.70612259 -9.5836422e-08 -0.099441482 -0.099441482 -0.099441482 
-   19370        1.937   0.70612677   0.70612557 -8.7867838e-08 -0.099443164 -0.099443164 -0.099443164 
-   19380        1.938   0.70612973   0.70612855 -7.8199538e-08 -0.099444842 -0.099444842 -0.099444842 
-   19390        1.939   0.70613268   0.70613152 -6.7058418e-08 -0.099446514 -0.099446514 -0.099446514 
-   19400         1.94   0.70613563   0.70613447 -5.470448e-08 -0.099448181 -0.099448181 -0.099448181 
-   19410        1.941   0.70613857   0.70613742 -4.1424778e-08 -0.099449843 -0.099449843 -0.099449843 
-   19420        1.942    0.7061415   0.70614035 -2.7526741e-08 -0.099451499 -0.099451499 -0.099451499 
-   19430        1.943   0.70614442   0.70614328 -1.333107e-08 -0.099453151 -0.099453151 -0.099453151 
-   19440        1.944   0.70614734   0.70614619 8.3566774e-10 -0.099454798 -0.099454798 -0.099454798 
-   19450        1.945   0.70615024    0.7061491 1.4648542e-08  -0.09945644  -0.09945644  -0.09945644 
-   19460        1.946   0.70615315   0.70615199 2.7791714e-08 -0.099458077 -0.099458077 -0.099458077 
-   19470        1.947   0.70615604   0.70615488 3.9965652e-08 -0.099459709 -0.099459709 -0.099459709 
-   19480        1.948   0.70615893   0.70615775 5.0893959e-08 -0.099461337 -0.099461337 -0.099461337 
-   19490        1.949   0.70616181   0.70616061 6.032964e-08 -0.099462959 -0.099462959 -0.099462959 
-   19500         1.95   0.70616468   0.70616347 6.8060684e-08 -0.099464576 -0.099464576 -0.099464576 
-   19510        1.951   0.70616754   0.70616631 7.3914827e-08 -0.099466189 -0.099466189 -0.099466189 
-   19520        1.952    0.7061704   0.70616915 7.7763378e-08 -0.099467796 -0.099467796 -0.099467796 
-   19530        1.953   0.70617324   0.70617198 7.952405e-08 -0.099469399 -0.099469399 -0.099469399 
-   19540        1.954   0.70617608    0.7061748 7.9162704e-08 -0.099470997 -0.099470997 -0.099470997 
-   19550        1.955   0.70617891   0.70617761 7.6693992e-08  -0.09947259  -0.09947259  -0.09947259 
-   19560        1.956   0.70618173   0.70618041 7.2180872e-08 -0.099474178 -0.099474178 -0.099474178 
-   19570        1.957   0.70618454    0.7061832 6.5733024e-08 -0.099475762 -0.099475762 -0.099475762 
-   19580        1.958   0.70618735   0.70618599 5.7504189e-08 -0.099477341 -0.099477341 -0.099477341 
-   19590        1.959   0.70619014   0.70618877 4.7688515e-08 -0.099478915 -0.099478915 -0.099478915 
-   19600         1.96   0.70619292   0.70619154 3.6515978e-08 -0.099480484 -0.099480484 -0.099480484 
-   19610        1.961    0.7061957   0.70619431 2.4246999e-08 -0.099482048 -0.099482048 -0.099482048 
-   19620        1.962   0.70619846   0.70619706 1.1166379e-08 -0.099483608 -0.099483608 -0.099483608 
-   19630        1.963   0.70620122   0.70619981 -2.4233094e-09 -0.099485163 -0.099485163 -0.099485163 
-   19640        1.964   0.70620396   0.70620256 -1.6208717e-08 -0.099486713 -0.099486713 -0.099486713 
-   19650        1.965   0.70620669    0.7062053 -2.9872943e-08 -0.099488259 -0.099488259 -0.099488259 
-   19660        1.966   0.70620942   0.70620803 -4.3102813e-08   -0.0994898   -0.0994898   -0.0994898 
-   19670        1.967   0.70621214   0.70621075 -5.5596058e-08 -0.099491336 -0.099491336 -0.099491336 
-   19680        1.968   0.70621484   0.70621347 -6.7068215e-08 -0.099492868 -0.099492868 -0.099492868 
-   19690        1.969   0.70621754   0.70621617 -7.7259102e-08 -0.099494395 -0.099494395 -0.099494395 
-   19700         1.97   0.70622022   0.70621888 -8.5938718e-08 -0.099495918 -0.099495918 -0.099495918 
-   19710        1.971    0.7062229   0.70622157 -9.2912428e-08 -0.099497436 -0.099497436 -0.099497436 
-   19720        1.972   0.70622557   0.70622426 -9.8025326e-08 -0.099498949 -0.099498949 -0.099498949 
-   19730        1.973   0.70622823   0.70622694 -1.0116567e-07 -0.099500458 -0.099500458 -0.099500458 
-   19740        1.974   0.70623089   0.70622961 -1.0226731e-07 -0.099501962 -0.099501962 -0.099501962 
-   19750        1.975   0.70623353   0.70623228 -1.0131109e-07 -0.099503461 -0.099503461 -0.099503461 
-   19760        1.976   0.70623617   0.70623493 -9.8325127e-08 -0.099504956 -0.099504956 -0.099504956 
-   19770        1.977    0.7062388   0.70623758 -9.3384031e-08 -0.099506447 -0.099506447 -0.099506447 
-   19780        1.978   0.70624142   0.70624022 -8.660706e-08 -0.099507933 -0.099507933 -0.099507933 
-   19790        1.979   0.70624404   0.70624285 -7.8155241e-08 -0.099509415 -0.099509415 -0.099509415 
-   19800         1.98   0.70624664   0.70624547 -6.8227557e-08 -0.099510892 -0.099510892 -0.099510892 
-   19810        1.981   0.70624924   0.70624808 -5.7056261e-08 -0.099512365 -0.099512365 -0.099512365 
-   19820        1.982   0.70625184   0.70625068 -4.4901454e-08 -0.099513833 -0.099513833 -0.099513833 
-   19830        1.983   0.70625443   0.70625328 -3.2045025e-08 -0.099515297 -0.099515297 -0.099515297 
-   19840        1.984   0.70625701   0.70625586 -1.8784125e-08 -0.099516756 -0.099516756 -0.099516756 
-   19850        1.985   0.70625958   0.70625844 -5.4242937e-09 -0.099518211 -0.099518211 -0.099518211 
-   19860        1.986   0.70626215     0.706261 7.7275713e-09 -0.099519662 -0.099519662 -0.099519662 
-   19870        1.987   0.70626472   0.70626356 2.0370265e-08 -0.099521108 -0.099521108 -0.099521108 
-   19880        1.988   0.70626727   0.70626611 3.2215168e-08  -0.09952255  -0.09952255  -0.09952255 
-   19890        1.989   0.70626982   0.70626864 4.2992837e-08 -0.099523987 -0.099523987 -0.099523987 
-   19900         1.99   0.70627237   0.70627117 5.2459126e-08  -0.09952542  -0.09952542  -0.09952542 
-   19910        1.991    0.7062749    0.7062737 6.0400718e-08 -0.099526849 -0.099526849 -0.099526849 
-   19920        1.992   0.70627743   0.70627621 6.6639927e-08 -0.099528273 -0.099528273 -0.099528273 
-   19930        1.993   0.70627995   0.70627871 7.1038669e-08 -0.099529694 -0.099529694 -0.099529694 
-   19940        1.994   0.70628247   0.70628121 7.3501515e-08  -0.09953111  -0.09953111  -0.09953111 
-   19950        1.995   0.70628498    0.7062837 7.3977751e-08 -0.099532521 -0.099532521 -0.099532521 
-   19960        1.996   0.70628748   0.70628618 7.246241e-08 -0.099533929 -0.099533929 -0.099533929 
-   19970        1.997   0.70628997   0.70628865 6.8996248e-08 -0.099535332 -0.099535332 -0.099535332 
-   19980        1.998   0.70629245   0.70629112 6.3664676e-08 -0.099536731 -0.099536731 -0.099536731 
-   19990        1.999   0.70629493   0.70629358 5.6595659e-08 -0.099538125 -0.099538125 -0.099538125 
-   20000            2    0.7062974   0.70629604 4.7956659e-08 -0.099539516 -0.099539516 -0.099539516 
-   20010        2.001   0.70629986   0.70629848 3.7950669e-08 -0.099540902 -0.099540902 -0.099540902 
-   20020        2.002   0.70630231   0.70630093 2.681145e-08 -0.099542284 -0.099542284 -0.099542284 
-   20030        2.003   0.70630475   0.70630336 1.479807e-08 -0.099543662 -0.099543662 -0.099543662 
-   20040        2.004   0.70630718   0.70630579 2.1888892e-09 -0.099545036 -0.099545036 -0.099545036 
-   20050        2.005   0.70630961   0.70630821 -1.0724895e-08 -0.099546405 -0.099546405 -0.099546405 
-   20060        2.006   0.70631202   0.70631063 -2.3645964e-08 -0.099547771 -0.099547771 -0.099547771 
-   20070        2.007   0.70631443   0.70631304 -3.6277725e-08 -0.099549132 -0.099549132 -0.099549132 
-   20080        2.008   0.70631683   0.70631545 -4.8331111e-08 -0.099550489 -0.099550489 -0.099550489 
-   20090        2.009   0.70631922   0.70631785 -5.95312e-08 -0.099551842 -0.099551842 -0.099551842 
-   20100         2.01    0.7063216   0.70632024 -6.9623478e-08 -0.099553191 -0.099553191 -0.099553191 
-   20110        2.011   0.70632397   0.70632263 -7.8379623e-08 -0.099554536 -0.099554536 -0.099554536 
-   20120        2.012   0.70632634   0.70632501 -8.5602665e-08 -0.099555877 -0.099555877 -0.099555877 
-   20130        2.013    0.7063287   0.70632738 -9.1131414e-08 -0.099557214 -0.099557214 -0.099557214 
-   20140        2.014   0.70633105   0.70632975 -9.4844056e-08 -0.099558547 -0.099558547 -0.099558547 
-   20150        2.015   0.70633339   0.70633211 -9.6660828e-08 -0.099559875 -0.099559875 -0.099559875 
-   20160        2.016   0.70633573   0.70633446 -9.6545724e-08   -0.0995612   -0.0995612   -0.0995612 
-   20170        2.017   0.70633805   0.70633681 -9.4507189e-08 -0.099562521 -0.099562521 -0.099562521 
-   20180        2.018   0.70634038   0.70633915 -9.0597798e-08 -0.099563838 -0.099563838 -0.099563838 
-   20190        2.019   0.70634269   0.70634148 -8.4912909e-08  -0.09956515  -0.09956515  -0.09956515 
-   20200         2.02     0.706345    0.7063438 -7.7588353e-08 -0.099566459 -0.099566459 -0.099566459 
-   20210        2.021    0.7063473   0.70634612 -6.8797191e-08 -0.099567764 -0.099567764 -0.099567764 
-   20220        2.022    0.7063496   0.70634842 -5.8745631e-08 -0.099569065 -0.099569065 -0.099569065 
-   20230        2.023   0.70635189   0.70635072 -4.7668196e-08 -0.099570362 -0.099570362 -0.099570362 
-   20240        2.024   0.70635418   0.70635302 -3.5822255e-08 -0.099571655 -0.099571655 -0.099571655 
-   20250        2.025   0.70635646    0.7063553 -2.3482047e-08 -0.099572944 -0.099572944 -0.099572944 
-   20260        2.026   0.70635873   0.70635757 -1.0932334e-08  -0.09957423  -0.09957423  -0.09957423 
-   20270        2.027     0.706361   0.70635984 1.5381658e-09 -0.099575511 -0.099575511 -0.099575511 
-   20280        2.028   0.70636326    0.7063621 1.3643418e-08 -0.099576788 -0.099576788 -0.099576788 
-   20290        2.029   0.70636552   0.70636435 2.5106632e-08 -0.099578062 -0.099578062 -0.099578062 
-   20300         2.03   0.70636777   0.70636659 3.5666585e-08 -0.099579332 -0.099579332 -0.099579332 
-   20310        2.031   0.70637002   0.70636883 4.5083572e-08 -0.099580598 -0.099580598 -0.099580598 
-   20320        2.032   0.70637226   0.70637105 5.3144849e-08  -0.09958186  -0.09958186  -0.09958186 
-   20330        2.033   0.70637449   0.70637327 5.9669428e-08 -0.099583118 -0.099583118 -0.099583118 
-   20340        2.034   0.70637672   0.70637548 6.4512146e-08 -0.099584373 -0.099584373 -0.099584373 
-   20350        2.035   0.70637894   0.70637769 6.7566882e-08 -0.099585624 -0.099585624 -0.099585624 
-   20360        2.036   0.70638116   0.70637989 6.8768883e-08 -0.099586871 -0.099586871 -0.099586871 
-   20370        2.037   0.70638337   0.70638208 6.8096123e-08 -0.099588114 -0.099588114 -0.099588114 
-   20380        2.038   0.70638557   0.70638426 6.5569679e-08 -0.099589353 -0.099589353 -0.099589353 
-   20390        2.039   0.70638776   0.70638644 6.1253126e-08 -0.099590589 -0.099590589 -0.099590589 
-   20400         2.04   0.70638995   0.70638861 5.5250939e-08 -0.099591821 -0.099591821 -0.099591821 
-   20410        2.041   0.70639213   0.70639078 4.7705984e-08 -0.099593049 -0.099593049 -0.099593049 
-   20420        2.042    0.7063943   0.70639294 3.8796111e-08 -0.099594274 -0.099594274 -0.099594274 
-   20430        2.043   0.70639647    0.7063951 2.8729978e-08 -0.099595495 -0.099595495 -0.099595495 
-   20440        2.044   0.70639863   0.70639725 1.7742159e-08 -0.099596712 -0.099596712 -0.099596712 
-   20450        2.045   0.70640078   0.70639939 6.0876855e-09 -0.099597925 -0.099597925 -0.099597925 
-   20460        2.046   0.70640292   0.70640153 -5.9638709e-09 -0.099599135 -0.099599135 -0.099599135 
-   20470        2.047   0.70640505   0.70640367 -1.8134631e-08 -0.099600341 -0.099600341 -0.099600341 
-   20480        2.048   0.70640718    0.7064058 -3.0144812e-08 -0.099601544 -0.099601544 -0.099601544 
-   20490        2.049    0.7064093   0.70640792 -4.1719159e-08 -0.099602742 -0.099602742 -0.099602742 
-   20500         2.05   0.70641141   0.70641004 -5.2593248e-08 -0.099603938 -0.099603938 -0.099603938 
-   20510        2.051   0.70641351   0.70641215 -6.2519525e-08 -0.099605129 -0.099605129 -0.099605129 
-   20520        2.052   0.70641561   0.70641426 -7.1272944e-08 -0.099606317 -0.099606317 -0.099606317 
-   20530        2.053    0.7064177   0.70641636 -7.8656058e-08 -0.099607502 -0.099607502 -0.099607502 
-   20540        2.054   0.70641978   0.70641846 -8.4503476e-08 -0.099608683 -0.099608683 -0.099608683 
-   20550        2.055   0.70642186   0.70642055 -8.8685564e-08  -0.09960986  -0.09960986  -0.09960986 
-   20560        2.056   0.70642393   0.70642264 -9.1111311e-08 -0.099611034 -0.099611034 -0.099611034 
-   20570        2.057   0.70642599   0.70642472 -9.1730305e-08 -0.099612204 -0.099612204 -0.099612204 
-   20580        2.058   0.70642804   0.70642679 -9.0533768e-08  -0.09961337  -0.09961337  -0.09961337 
-   20590        2.059   0.70643009   0.70642885 -8.7554636e-08 -0.099614534 -0.099614534 -0.099614534 
-   20600         2.06   0.70643214   0.70643091 -8.2866671e-08 -0.099615693 -0.099615693 -0.099615693 
-   20610        2.061   0.70643418   0.70643297 -7.6582653e-08 -0.099616849 -0.099616849 -0.099616849 
-   20620        2.062   0.70643621   0.70643501 -6.8851668e-08 -0.099618002 -0.099618002 -0.099618002 
-   20630        2.063   0.70643824   0.70643705 -5.9855578e-08 -0.099619151 -0.099619151 -0.099619151 
-   20640        2.064   0.70644026   0.70643908 -4.9804747e-08 -0.099620297 -0.099620297 -0.099620297 
-   20650        2.065   0.70644228   0.70644111 -3.8933125e-08 -0.099621439 -0.099621439 -0.099621439 
-   20660        2.066   0.70644429   0.70644312 -2.7492808e-08 -0.099622578 -0.099622578 -0.099622578 
-   20670        2.067    0.7064463   0.70644513 -1.5748189e-08 -0.099623713 -0.099623713 -0.099623713 
-   20680        2.068    0.7064483   0.70644714 -3.969858e-09 -0.099624845 -0.099624845 -0.099624845 
-   20690        2.069    0.7064503   0.70644913 7.5716351e-09 -0.099625973 -0.099625973 -0.099625973 
-   20700         2.07   0.70645229   0.70645112 1.8611991e-08 -0.099627098 -0.099627098 -0.099627098 
-   20710        2.071   0.70645428    0.7064531 2.889921e-08  -0.09962822  -0.09962822  -0.09962822 
-   20720        2.072   0.70645627   0.70645507 3.8199345e-08 -0.099629338 -0.099629338 -0.099629338 
-   20730        2.073   0.70645824   0.70645704 4.6301814e-08 -0.099630453 -0.099630453 -0.099630453 
-   20740        2.074   0.70646022     0.706459 5.3024171e-08 -0.099631564 -0.099631564 -0.099631564 
-   20750        2.075   0.70646219   0.70646095 5.8216207e-08 -0.099632672 -0.099632672 -0.099632672 
-   20760        2.076   0.70646415    0.7064629 6.1763304e-08 -0.099633777 -0.099633777 -0.099633777 
-   20770        2.077   0.70646611   0.70646484 6.3588961e-08 -0.099634879 -0.099634879 -0.099634879 
-   20780        2.078   0.70646806   0.70646678 6.3656436e-08 -0.099635977 -0.099635977 -0.099635977 
-   20790        2.079      0.70647   0.70646871 6.1969469e-08 -0.099637072 -0.099637072 -0.099637072 
-   20800         2.08   0.70647194   0.70647063 5.8572077e-08 -0.099638163 -0.099638163 -0.099638163 
-   20810        2.081   0.70647387   0.70647255 5.354742e-08 -0.099639251 -0.099639251 -0.099639251 
-   20820        2.082    0.7064758   0.70647446 4.7015777e-08 -0.099640336 -0.099640336 -0.099640336 
-   20830        2.083   0.70647772   0.70647637 3.9131669e-08 -0.099641418 -0.099641418 -0.099641418 
-   20840        2.084   0.70647963   0.70647827 3.0080213e-08 -0.099642496 -0.099642496 -0.099642496 
-   20850        2.085   0.70648154   0.70648017 2.0072773e-08 -0.099643571 -0.099643571 -0.099643571 
-   20860        2.086   0.70648344   0.70648206 9.3420337e-09 -0.099644643 -0.099644643 -0.099644643 
-   20870        2.087   0.70648533   0.70648395 -1.8634114e-09 -0.099645712 -0.099645712 -0.099645712 
-   20880        2.088   0.70648722   0.70648584 -1.3284814e-08 -0.099646777 -0.099646777 -0.099646777 
-   20890        2.089    0.7064891   0.70648772 -2.4659244e-08 -0.099647839 -0.099647839 -0.099647839 
-   20900         2.09   0.70649097   0.70648959 -3.5725639e-08 -0.099648898 -0.099648898 -0.099648898 
-   20910        2.091   0.70649283   0.70649146 -4.6230798e-08 -0.099649954 -0.099649954 -0.099649954 
-   20920        2.092   0.70649469   0.70649333 -5.5935165e-08 -0.099651006 -0.099651006 -0.099651006 
-   20930        2.093   0.70649654   0.70649519 -6.4618297e-08 -0.099652056 -0.099652056 -0.099652056 
-   20940        2.094   0.70649839   0.70649705 -7.2083863e-08 -0.099653102 -0.099653102 -0.099653102 
-   20950        2.095   0.70650023    0.7064989 -7.8164087e-08 -0.099654145 -0.099654145 -0.099654145 
-   20960        2.096   0.70650206   0.70650075 -8.2723507e-08 -0.099655185 -0.099655185 -0.099655185 
-   20970        2.097   0.70650388   0.70650259 -8.5661997e-08 -0.099656221 -0.099656221 -0.099656221 
-   20980        2.098    0.7065057   0.70650443 -8.6916954e-08 -0.099657255 -0.099657255 -0.099657255 
-   20990        2.099   0.70650752   0.70650626 -8.6464627e-08 -0.099658285 -0.099658285 -0.099658285 
-   21000          2.1   0.70650933   0.70650808 -8.4320545e-08 -0.099659313 -0.099659313 -0.099659313 
-   21010        2.101   0.70651113    0.7065099 -8.0539042e-08 -0.099660337 -0.099660337 -0.099660337 
-   21020        2.102   0.70651293   0.70651172 -7.5211894e-08 -0.099661358 -0.099661358 -0.099661358 
-   21030        2.103   0.70651473   0.70651352 -6.8466096e-08 -0.099662376 -0.099662376 -0.099662376 
-   21040        2.104   0.70651652   0.70651533 -6.0460842e-08 -0.099663391 -0.099663391 -0.099663391 
-   21050        2.105   0.70651831   0.70651712 -5.1383775e-08 -0.099664403 -0.099664403 -0.099664403 
-   21060        2.106   0.70652009   0.70651891 -4.1446585e-08 -0.099665412 -0.099665412 -0.099665412 
-   21070        2.107   0.70652186   0.70652069 -3.0880082e-08 -0.099666418 -0.099666418 -0.099666418 
-   21080        2.108   0.70652364   0.70652247 -1.9928835e-08 -0.099667421 -0.099667421 -0.099667421 
-   21090        2.109   0.70652541   0.70652423 -8.845512e-09  -0.09966842  -0.09966842  -0.09966842 
-   21100         2.11   0.70652717     0.706526 2.1149427e-09 -0.099669417 -0.099669417 -0.099669417 
-   21110        2.111   0.70652893   0.70652775 1.2701175e-08 -0.099670411 -0.099670411 -0.099670411 
-   21120        2.112   0.70653069    0.7065295 2.267118e-08 -0.099671401 -0.099671401 -0.099671401 
-   21130        2.113   0.70653244   0.70653125 3.1797835e-08 -0.099672389 -0.099672389 -0.099672389 
-   21140        2.114   0.70653419   0.70653298 3.9874067e-08 -0.099673374 -0.099673374 -0.099673374 
-   21150        2.115   0.70653593   0.70653471 4.6717553e-08 -0.099674355 -0.099674355 -0.099674355 
-   21160        2.116   0.70653767   0.70653644 5.2174829e-08 -0.099675334 -0.099675334 -0.099675334 
-   21170        2.117    0.7065394   0.70653816 5.6124731e-08  -0.09967631  -0.09967631  -0.09967631 
-   21180        2.118   0.70654113   0.70653987 5.848108e-08 -0.099677283 -0.099677283 -0.099677283 
-   21190        2.119   0.70654285   0.70654158 5.9194556e-08 -0.099678253 -0.099678253 -0.099678253 
-   21200         2.12   0.70654457   0.70654328 5.825372e-08  -0.09967922  -0.09967922  -0.09967922 
-   21210        2.121   0.70654628   0.70654498 5.5685163e-08 -0.099680184 -0.099680184 -0.099680184 
-   21220        2.122   0.70654799   0.70654667 5.1552781e-08 -0.099681145 -0.099681145 -0.099681145 
-   21230        2.123   0.70654969   0.70654836 4.5956196e-08 -0.099682103 -0.099682103 -0.099682103 
-   21240        2.124   0.70655139   0.70655005 3.9028362e-08 -0.099683058 -0.099683058 -0.099683058 
-   21250        2.125   0.70655308   0.70655173 3.0932406e-08 -0.099684011 -0.099684011 -0.099684011 
-   21260        2.126   0.70655476    0.7065534 2.1857798e-08  -0.09968496  -0.09968496  -0.09968496 
-   21270        2.127   0.70655644   0.70655507 1.2015912e-08 -0.099685907 -0.099685907 -0.099685907 
-   21280        2.128   0.70655811   0.70655674 1.6351138e-09 -0.099686851 -0.099686851 -0.099686851 
-   21290        2.129   0.70655978   0.70655841 -9.0445433e-09 -0.099687792 -0.099687792 -0.099687792 
-   21300         2.13   0.70656144   0.70656007 -1.9776862e-08  -0.09968873  -0.09968873  -0.09968873 
-   21310        2.131   0.70656309   0.70656172 -3.0315175e-08 -0.099689665 -0.099689665 -0.099689665 
-   21320        2.132   0.70656474   0.70656337 -4.0418016e-08 -0.099690598 -0.099690598 -0.099690598 
-   21330        2.133   0.70656638   0.70656502 -4.9854645e-08 -0.099691527 -0.099691527 -0.099691527 
-   21340        2.134   0.70656802   0.70656667 -5.841032e-08 -0.099692454 -0.099692454 -0.099692454 
-   21350        2.135   0.70656965   0.70656831 -6.5891177e-08 -0.099693378 -0.099693378 -0.099693378 
-   21360        2.136   0.70657127   0.70656994 -7.2128628e-08 -0.099694299 -0.099694299 -0.099694299 
-   21370        2.137   0.70657289   0.70657157 -7.6983148e-08 -0.099695218 -0.099695218 -0.099695218 
-   21380        2.138    0.7065745    0.7065732 -8.03474e-08 -0.099696133 -0.099696133 -0.099696133 
-   21390        2.139   0.70657611   0.70657482 -8.2148598e-08 -0.099697046 -0.099697046 -0.099697046 
-   21400         2.14   0.70657771   0.70657644 -8.2350082e-08 -0.099697956 -0.099697956 -0.099697956 
-   21410        2.141   0.70657931   0.70657805 -8.0952044e-08 -0.099698864 -0.099698864 -0.099698864 
-   21420        2.142    0.7065809   0.70657966 -7.7991418e-08 -0.099699768 -0.099699768 -0.099699768 
-   21430        2.143   0.70658249   0.70658126 -7.3540919e-08  -0.09970067  -0.09970067  -0.09970067 
-   21440        2.144   0.70658407   0.70658286 -6.7707267e-08 -0.099701569 -0.099701569 -0.099701569 
-   21450        2.145   0.70658566   0.70658445 -6.062863e-08 -0.099702466 -0.099702466 -0.099702466 
-   21460        2.146   0.70658723   0.70658604 -5.247136e-08  -0.09970336  -0.09970336  -0.09970336 
-   21470        2.147    0.7065888   0.70658762 -4.3426085e-08 -0.099704251 -0.099704251 -0.099704251 
-   21480        2.148   0.70659037   0.70658919 -3.3703257e-08 -0.099705139 -0.099705139 -0.099705139 
-   21490        2.149   0.70659194   0.70659076 -2.3528257e-08 -0.099706025 -0.099706025 -0.099706025 
-   21500         2.15    0.7065935   0.70659232 -1.3136176e-08 -0.099706908 -0.099706908 -0.099706908 
-   21510        2.151   0.70659506   0.70659388 -2.7663851e-09 -0.099707788 -0.099707788 -0.099707788 
-   21520        2.152   0.70659661   0.70659543 7.3429794e-09 -0.099708665 -0.099708665 -0.099708665 
-   21530        2.153   0.70659816   0.70659698 1.6960479e-08  -0.09970954  -0.09970954  -0.09970954 
-   21540        2.154   0.70659971   0.70659852 2.5866671e-08 -0.099710413 -0.099710413 -0.099710413 
-   21550        2.155   0.70660125   0.70660005 3.3859113e-08 -0.099711282 -0.099711282 -0.099711282 
-   21560        2.156   0.70660279   0.70660158 4.075696e-08  -0.09971215  -0.09971215  -0.09971215 
-   21570        2.157   0.70660433    0.7066031 4.6405059e-08 -0.099713014 -0.099713014 -0.099713014 
-   21580        2.158   0.70660586   0.70660462 5.0677431e-08 -0.099713876 -0.099713876 -0.099713876 
-   21590        2.159   0.70660739   0.70660613 5.3480079e-08 -0.099714735 -0.099714735 -0.099714735 
-   21600         2.16   0.70660891   0.70660764 5.4753051e-08 -0.099715592 -0.099715592 -0.099715592 
-   21610        2.161   0.70661043   0.70660914 5.4471716e-08 -0.099716446 -0.099716446 -0.099716446 
-   21620        2.162   0.70661194   0.70661064 5.2647221e-08 -0.099717297 -0.099717297 -0.099717297 
-   21630        2.163   0.70661345   0.70661214 4.9326131e-08 -0.099718146 -0.099718146 -0.099718146 
-   21640        2.164   0.70661495   0.70661363 4.4589249e-08 -0.099718992 -0.099718992 -0.099718992 
-   21650        2.165   0.70661645   0.70661511 3.8549661e-08 -0.099719836 -0.099719836 -0.099719836 
-   21660        2.166   0.70661794    0.7066166 3.1350035e-08 -0.099720677 -0.099720677 -0.099720677 
-   21670        2.167   0.70661943   0.70661808 2.3159262e-08 -0.099721516 -0.099721516 -0.099721516 
-   21680        2.168   0.70662091   0.70661955 1.4168493e-08 -0.099722352 -0.099722352 -0.099722352 
-   21690        2.169   0.70662239   0.70662103 4.5866794e-09 -0.099723185 -0.099723185 -0.099723185 
-   21700         2.17   0.70662386   0.70662249 -5.3642766e-09 -0.099724016 -0.099724016 -0.099724016 
-   21710        2.171   0.70662533   0.70662396 -1.5454661e-08 -0.099724845 -0.099724845 -0.099724845 
-   21720        2.172   0.70662679   0.70662542 -2.545225e-08 -0.099725671 -0.099725671 -0.099725671 
-   21730        2.173   0.70662824   0.70662688 -3.5127648e-08 -0.099726495 -0.099726495 -0.099726495 
-   21740        2.174   0.70662969   0.70662834 -4.4259555e-08 -0.099727316 -0.099727316 -0.099727316 
-   21750        2.175   0.70663114   0.70662979 -5.263982e-08 -0.099728134 -0.099728134 -0.099728134 
-   21760        2.176   0.70663258   0.70663124 -6.007819e-08  -0.09972895  -0.09972895  -0.09972895 
-   21770        2.177   0.70663401   0.70663268 -6.640662e-08 -0.099729764 -0.099729764 -0.099729764 
-   21780        2.178   0.70663544   0.70663412 -7.1483074e-08 -0.099730575 -0.099730575 -0.099730575 
-   21790        2.179   0.70663686   0.70663556 -7.5194702e-08 -0.099731384 -0.099731384 -0.099731384 
-   21800         2.18   0.70663828   0.70663699 -7.7460351e-08  -0.09973219  -0.09973219  -0.09973219 
-   21810        2.181    0.7066397   0.70663842 -7.8232334e-08 -0.099732994 -0.099732994 -0.099732994 
-   21820        2.182   0.70664111   0.70663985 -7.7497419e-08 -0.099733795 -0.099733795 -0.099733795 
-   21830        2.183   0.70664251   0.70664127 -7.5277035e-08 -0.099734594 -0.099734594 -0.099734594 
-   21840        2.184   0.70664392   0.70664268 -7.1626675e-08 -0.099735391 -0.099735391 -0.099735391 
-   21850        2.185   0.70664531   0.70664409 -6.6634516e-08 -0.099736185 -0.099736185 -0.099736185 
-   21860        2.186   0.70664671    0.7066455 -6.0419295e-08 -0.099736976 -0.099736976 -0.099736976 
-   21870        2.187    0.7066481    0.7066469 -5.3127493e-08 -0.099737766 -0.099737766 -0.099737766 
-   21880        2.188   0.70664949   0.70664829 -4.4929882e-08 -0.099738553 -0.099738553 -0.099738553 
-   21890        2.189   0.70665087   0.70664969 -3.6017529e-08 -0.099739337 -0.099739337 -0.099739337 
-   21900         2.19   0.70665226   0.70665107 -2.6597349e-08 -0.099740119 -0.099740119 -0.099740119 
-   21910        2.191   0.70665363   0.70665245 -1.6887299e-08 -0.099740899 -0.099740899 -0.099740899 
-   21920        2.192   0.70665501   0.70665383 -7.1113393e-09 -0.099741677 -0.099741677 -0.099741677 
-   21930        2.193   0.70665638    0.7066552 2.5057297e-09 -0.099742452 -0.099742452 -0.099742452 
-   21940        2.194   0.70665775   0.70665656 1.1743436e-08 -0.099743224 -0.099743224 -0.099743224 
-   21950        2.195   0.70665912   0.70665792 2.0390686e-08 -0.099743995 -0.099743995 -0.099743995 
-   21960        2.196   0.70666048   0.70665928 2.8250591e-08 -0.099744763 -0.099744763 -0.099744763 
-   21970        2.197   0.70666184   0.70666063 3.5144941e-08 -0.099745529 -0.099745529 -0.099745529 
-   21980        2.198    0.7066632   0.70666197 4.0918251e-08 -0.099746292 -0.099746292 -0.099746292 
-   21990        2.199   0.70666455   0.70666331 4.5441257e-08 -0.099747053 -0.099747053 -0.099747053 
-   22000          2.2    0.7066659   0.70666465 4.8613813e-08 -0.099747812 -0.099747812 -0.099747812 
-   22010        2.201   0.70666724   0.70666598 5.0367102e-08 -0.099748569 -0.099748569 -0.099748569 
-   22020        2.202   0.70666858   0.70666731 5.0665122e-08 -0.099749323 -0.099749323 -0.099749323 
-   22030        2.203   0.70666992   0.70666863 4.9505415e-08 -0.099750075 -0.099750075 -0.099750075 
-   22040        2.204   0.70667125   0.70666995 4.6919025e-08 -0.099750825 -0.099750825 -0.099750825 
-   22050        2.205   0.70667258   0.70667126 4.2969679e-08 -0.099751572 -0.099751572 -0.099751572 
-   22060        2.206    0.7066739   0.70667258 3.7752229e-08 -0.099752317 -0.099752317 -0.099752317 
-   22070        2.207   0.70667522   0.70667389 3.1390377e-08  -0.09975306  -0.09975306  -0.09975306 
-   22080        2.208   0.70667654   0.70667519 2.4033745e-08 -0.099753801 -0.099753801 -0.099753801 
-   22090        2.209   0.70667785   0.70667649 1.5854363e-08 -0.099754539 -0.099754539 -0.099754539 
-   22100         2.21   0.70667915   0.70667779 7.0426432e-09 -0.099755275 -0.099755275 -0.099755275 
-   22110        2.211   0.70668045   0.70667909 -2.1970451e-09 -0.099756009 -0.099756009 -0.099756009 
-   22120        2.212   0.70668175   0.70668038 -1.1651116e-08 -0.099756741 -0.099756741 -0.099756741 
-   22130        2.213   0.70668304   0.70668168 -2.1101702e-08  -0.09975747  -0.09975747  -0.09975747 
-   22140        2.214   0.70668432   0.70668296 -3.0331671e-08 -0.099758198 -0.099758198 -0.099758198 
-   22150        2.215    0.7066856   0.70668425 -3.9129616e-08 -0.099758923 -0.099758923 -0.099758923 
-   22160        2.216   0.70668688   0.70668553 -4.7294692e-08 -0.099759646 -0.099759646 -0.099759646 
-   22170        2.217   0.70668815   0.70668681 -5.4641202e-08 -0.099760366 -0.099760366 -0.099760366 
-   22180        2.218   0.70668941   0.70668809 -6.1002816e-08 -0.099761085 -0.099761085 -0.099761085 
-   22190        2.219   0.70669068   0.70668936 -6.6236337e-08 -0.099761801 -0.099761801 -0.099761801 
-   22200         2.22   0.70669193   0.70669063 -7.0224917e-08 -0.099762515 -0.099762515 -0.099762515 
-   22210        2.221   0.70669319   0.70669189 -7.2880669e-08 -0.099763227 -0.099763227 -0.099763227 
-   22220        2.222   0.70669444   0.70669316 -7.4146593e-08 -0.099763937 -0.099763937 -0.099763937 
-   22230        2.223   0.70669568   0.70669441 -7.3997797e-08 -0.099764645 -0.099764645 -0.099764645 
-   22240        2.224   0.70669692   0.70669567 -7.2441969e-08 -0.099765351 -0.099765351 -0.099765351 
-   22250        2.225   0.70669816   0.70669692 -6.9519106e-08 -0.099766054 -0.099766054 -0.099766054 
-   22260        2.226    0.7066994   0.70669817 -6.5300494e-08 -0.099766755 -0.099766755 -0.099766755 
-   22270        2.227   0.70670063   0.70669941 -5.9886979e-08 -0.099767455 -0.099767455 -0.099767455 
-   22280        2.228   0.70670185   0.70670064 -5.3406557e-08 -0.099768152 -0.099768152 -0.099768152 
-   22290        2.229   0.70670308   0.70670188 -4.6011356e-08 -0.099768847 -0.099768847 -0.099768847 
-   22300         2.23    0.7067043   0.70670311 -3.7874064e-08  -0.09976954  -0.09976954  -0.09976954 
-   22310        2.231   0.70670552   0.70670433 -2.9183898e-08  -0.09977023  -0.09977023  -0.09977023 
-   22320        2.232   0.70670674   0.70670555 -2.0142212e-08 -0.099770919 -0.099770919 -0.099770919 
-   22330        2.233   0.70670795   0.70670676 -1.0957829e-08 -0.099771606 -0.099771606 -0.099771606 
-   22340        2.234   0.70670916   0.70670797 -1.8422197e-09  -0.09977229  -0.09977229  -0.09977229 
-   22350        2.235   0.70671037   0.70670918 6.9953612e-09 -0.099772972 -0.099772972 -0.099772972 
-   22360        2.236   0.70671158   0.70671038 1.5352679e-08 -0.099773653 -0.099773653 -0.099773653 
-   22370        2.237   0.70671278   0.70671158 2.3039146e-08 -0.099774331 -0.099774331 -0.099774331 
-   22380        2.238   0.70671398   0.70671277 2.9880161e-08 -0.099775007 -0.099775007 -0.099775007 
-   22390        2.239   0.70671518   0.70671396 3.572108e-08 -0.099775682 -0.099775682 -0.099775682 
-   22400         2.24   0.70671638   0.70671514 4.0430705e-08 -0.099776354 -0.099776354 -0.099776354 
-   22410        2.241   0.70671757   0.70671632 4.3904229e-08 -0.099777024 -0.099777024 -0.099777024 
-   22420        2.242   0.70671875    0.7067175 4.6065566e-08 -0.099777692 -0.099777692 -0.099777692 
-   22430        2.243   0.70671994   0.70671867 4.6869011e-08 -0.099778358 -0.099778358 -0.099778358 
-   22440        2.244   0.70672112   0.70671984 4.6300201e-08 -0.099779022 -0.099779022 -0.099779022 
-   22450        2.245    0.7067223     0.706721 4.4376349e-08 -0.099779684 -0.099779684 -0.099779684 
-   22460        2.246   0.70672347   0.70672216 4.1145753e-08 -0.099780344 -0.099780344 -0.099780344 
-   22470        2.247   0.70672464   0.70672332 3.6686596e-08 -0.099781002 -0.099781002 -0.099781002 
-   22480        2.248   0.70672581   0.70672448 3.1105053e-08 -0.099781658 -0.099781658 -0.099781658 
-   22490        2.249   0.70672697   0.70672563 2.4532774e-08 -0.099782313 -0.099782313 -0.099782313 
-   22500         2.25   0.70672812   0.70672678 1.7123777e-08 -0.099782965 -0.099782965 -0.099782965 
-   22510        2.251   0.70672928   0.70672792 9.0508418e-09 -0.099783615 -0.099783615 -0.099783615 
-   22520        2.252   0.70673042   0.70672907 5.0148589e-10 -0.099784263 -0.099784263 -0.099784263 
-   22530        2.253   0.70673157   0.70673021 -8.3263915e-09 -0.099784909 -0.099784909 -0.099784909 
-   22540        2.254   0.70673271   0.70673135 -1.7229088e-08 -0.099785553 -0.099785553 -0.099785553 
-   22550        2.255   0.70673384   0.70673249 -2.6001795e-08 -0.099786196 -0.099786196 -0.099786196 
-   22560        2.256   0.70673497   0.70673362 -3.444331e-08 -0.099786836 -0.099786836 -0.099786836 
-   22570        2.257    0.7067361   0.70673475 -4.2360648e-08 -0.099787474 -0.099787474 -0.099787474 
-   22580        2.258   0.70673722   0.70673588 -4.9573453e-08 -0.099788111 -0.099788111 -0.099788111 
-   22590        2.259   0.70673834   0.70673701 -5.59181e-08 -0.099788745 -0.099788745 -0.099788745 
-   22600         2.26   0.70673945   0.70673813 -6.125141e-08 -0.099789378 -0.099789378 -0.099789378 
-   22610        2.261   0.70674056   0.70673926 -6.5453878e-08 -0.099790009 -0.099790009 -0.099790009 
-   22620        2.262   0.70674167   0.70674037 -6.8432344e-08 -0.099790638 -0.099790638 -0.099790638 
-   22630        2.263   0.70674277   0.70674149 -7.0122059e-08 -0.099791264 -0.099791264 -0.099791264 
-   22640        2.264   0.70674387    0.7067426 -7.0488084e-08 -0.099791889 -0.099791889 -0.099791889 
-   22650        2.265   0.70674497   0.70674371 -6.9526007e-08 -0.099792513 -0.099792513 -0.099792513 
-   22660        2.266   0.70674606   0.70674481 -6.7261947e-08 -0.099793134 -0.099793134 -0.099793134 
-   22670        2.267   0.70674715   0.70674591 -6.3751866e-08 -0.099793753 -0.099793753 -0.099793753 
-   22680        2.268   0.70674824   0.70674701 -5.9080192e-08 -0.099794371 -0.099794371 -0.099794371 
-   22690        2.269   0.70674932   0.70674811 -5.3357793e-08 -0.099794986 -0.099794986 -0.099794986 
-   22700         2.27    0.7067504   0.70674919 -4.6719347e-08   -0.0997956   -0.0997956   -0.0997956 
-   22710        2.271   0.70675148   0.70675028 -3.932018e-08 -0.099796212 -0.099796212 -0.099796212 
-   22720        2.272   0.70675256   0.70675136 -3.133263e-08 -0.099796822 -0.099796822 -0.099796822 
-   22730        2.273   0.70675363   0.70675244 -2.2942037e-08  -0.09979743  -0.09979743  -0.09979743 
-   22740        2.274   0.70675471   0.70675351 -1.4342445e-08 -0.099798036 -0.099798036 -0.099798036 
-   22750        2.275   0.70675578   0.70675458 -5.7321139e-09 -0.099798641 -0.099798641 -0.099798641 
-   22760        2.276   0.70675684   0.70675565 2.6910464e-09 -0.099799243 -0.099799243 -0.099799243 
-   22770        2.277   0.70675791   0.70675671 1.0734025e-08 -0.099799844 -0.099799844 -0.099799844 
-   22780        2.278   0.70675897   0.70675776 1.8213131e-08 -0.099800443 -0.099800443 -0.099800443 
-   22790        2.279   0.70676003   0.70675881 2.4958185e-08 -0.099801041 -0.099801041 -0.099801041 
-   22800         2.28   0.70676109   0.70675986 3.0816393e-08 -0.099801636 -0.099801636 -0.099801636 
-   22810        2.281   0.70676214   0.70676091 3.5655801e-08  -0.09980223  -0.09980223  -0.09980223 
-   22820        2.282   0.70676319   0.70676195 3.9368268e-08 -0.099802821 -0.099802821 -0.099802821 
-   22830        2.283   0.70676424   0.70676299 4.187188e-08 -0.099803411 -0.099803411 -0.099803411 
-   22840        2.284   0.70676529   0.70676402 4.3112749e-08    -0.099804    -0.099804    -0.099804 
-   22850        2.285   0.70676633   0.70676505 4.3066173e-08 -0.099804586 -0.099804586 -0.099804586 
-   22860        2.286   0.70676737   0.70676608 4.1737109e-08 -0.099805171 -0.099805171 -0.099805171 
-   22870        2.287   0.70676841   0.70676711 3.9159976e-08 -0.099805754 -0.099805754 -0.099805754 
-   22880        2.288   0.70676944   0.70676813 3.5397772e-08 -0.099806335 -0.099806335 -0.099806335 
-   22890        2.289   0.70677047   0.70676915 3.054054e-08 -0.099806914 -0.099806914 -0.099806914 
-   22900         2.29    0.7067715   0.70677017 2.4703217e-08 -0.099807492 -0.099807492 -0.099807492 
-   22910        2.291   0.70677252   0.70677118 1.802292e-08 -0.099808068 -0.099808068 -0.099808068 
-   22920        2.292   0.70677354   0.70677219 1.0655723e-08 -0.099808642 -0.099808642 -0.099808642 
-   22930        2.293   0.70677455    0.7067732 2.7730173e-09 -0.099809214 -0.099809214 -0.099809214 
-   22940        2.294   0.70677556   0.70677421 -5.4424759e-09 -0.099809785 -0.099809785 -0.099809785 
-   22950        2.295   0.70677657   0.70677522 -1.3800939e-08 -0.099810354 -0.099810354 -0.099810354 
-   22960        2.296   0.70677757   0.70677622 -2.210984e-08 -0.099810921 -0.099810921 -0.099810921 
-   22970        2.297   0.70677857   0.70677722 -3.0178368e-08 -0.099811486 -0.099811486 -0.099811486 
-   22980        2.298   0.70677957   0.70677822 -3.7821814e-08  -0.09981205  -0.09981205  -0.09981205 
-   22990        2.299   0.70678056   0.70677922 -4.4865793e-08 -0.099812612 -0.099812612 -0.099812612 
-   23000          2.3   0.70678154   0.70678021 -5.1150227e-08 -0.099813172 -0.099813172 -0.099813172 
-   23010        2.301   0.70678253   0.70678121 -5.6532976e-08 -0.099813731 -0.099813731 -0.099813731 
-   23020        2.302   0.70678351    0.7067822 -6.0893052e-08 -0.099814288 -0.099814288 -0.099814288 
-   23030        2.303   0.70678448   0.70678318 -6.4133338e-08 -0.099814843 -0.099814843 -0.099814843 
-   23040        2.304   0.70678546   0.70678417 -6.6182745e-08 -0.099815397 -0.099815397 -0.099815397 
-   23050        2.305   0.70678643   0.70678515 -6.6997771e-08 -0.099815949 -0.099815949 -0.099815949 
-   23060        2.306    0.7067874   0.70678613 -6.6563413e-08 -0.099816499 -0.099816499 -0.099816499 
-   23070        2.307   0.70678836   0.70678711 -6.4893431e-08 -0.099817048 -0.099817048 -0.099817048 
-   23080        2.308   0.70678932   0.70678808 -6.2029939e-08 -0.099817595 -0.099817595 -0.099817595 
-   23090        2.309   0.70679028   0.70678905 -5.8042357e-08  -0.09981814  -0.09981814  -0.09981814 
-   23100         2.31   0.70679124   0.70679001 -5.3025731e-08 -0.099818684 -0.099818684 -0.099818684 
-   23110        2.311   0.70679219   0.70679098 -4.7098472e-08 -0.099819226 -0.099819226 -0.099819226 
-   23120        2.312   0.70679315   0.70679194 -4.039956e-08 -0.099819766 -0.099819766 -0.099819766 
-   23130        2.313    0.7067941   0.70679289 -3.3085295e-08 -0.099820305 -0.099820305 -0.099820305 
-   23140        2.314   0.70679504   0.70679384 -2.5325644e-08 -0.099820842 -0.099820842 -0.099820842 
-   23150        2.315   0.70679599   0.70679479 -1.7300302e-08 -0.099821377 -0.099821377 -0.099821377 
-   23160        2.316   0.70679693   0.70679573 -9.1945247e-09 -0.099821911 -0.099821911 -0.099821911 
-   23170        2.317   0.70679788   0.70679667 -1.1948586e-09 -0.099822443 -0.099822443 -0.099822443 
-   23180        2.318   0.70679882   0.70679761 6.5151521e-09 -0.099822974 -0.099822974 -0.099822974 
-   23190        2.319   0.70679975   0.70679854 1.3759175e-08 -0.099823503 -0.099823503 -0.099823503 
-   23200         2.32   0.70680069   0.70679947 2.037212e-08  -0.09982403  -0.09982403  -0.09982403 
-   23210        2.321   0.70680162    0.7068004 2.6203901e-08 -0.099824556 -0.099824556 -0.099824556 
-   23220        2.322   0.70680256   0.70680132 3.112284e-08  -0.09982508  -0.09982508  -0.09982508 
-   23230        2.323   0.70680348   0.70680224 3.5018635e-08 -0.099825603 -0.099825603 -0.099825603 
-   23240        2.324   0.70680441   0.70680316 3.7804836e-08 -0.099826124 -0.099826124 -0.099826124 
-   23250        2.325   0.70680534   0.70680407 3.9420758e-08 -0.099826643 -0.099826643 -0.099826643 
-   23260        2.326   0.70680626   0.70680498 3.9832795e-08 -0.099827161 -0.099827161 -0.099827161 
-   23270        2.327   0.70680718   0.70680589 3.9035115e-08 -0.099827677 -0.099827677 -0.099827677 
-   23280        2.328   0.70680809   0.70680679 3.7049709e-08 -0.099828192 -0.099828192 -0.099828192 
-   23290        2.329     0.706809    0.7068077 3.3925798e-08 -0.099828705 -0.099828705 -0.099828705 
-   23300         2.33   0.70680991    0.7068086 2.9738627e-08 -0.099829217 -0.099829217 -0.099829217 
-   23310        2.331   0.70681082   0.70680949 2.4587649e-08 -0.099829727 -0.099829727 -0.099829727 
-   23320        2.332   0.70681172   0.70681039 1.8594173e-08 -0.099830235 -0.099830235 -0.099830235 
-   23330        2.333   0.70681262   0.70681128 1.1898502e-08 -0.099830742 -0.099830742 -0.099830742 
-   23340        2.334   0.70681352   0.70681218 4.6566595e-09 -0.099831248 -0.099831248 -0.099831248 
-   23350        2.335   0.70681441   0.70681306 -2.9632507e-09 -0.099831752 -0.099831752 -0.099831752 
-   23360        2.336    0.7068153   0.70681395 -1.0784942e-08 -0.099832254 -0.099832254 -0.099832254 
-   23370        2.337   0.70681619   0.70681484 -1.8628022e-08 -0.099832755 -0.099832755 -0.099832755 
-   23380        2.338   0.70681707   0.70681572 -2.6312152e-08 -0.099833254 -0.099833254 -0.099833254 
-   23390        2.339   0.70681795   0.70681661 -3.3661192e-08 -0.099833752 -0.099833752 -0.099833752 
-   23400         2.34   0.70681882   0.70681749 -4.0507233e-08 -0.099834249 -0.099834249 -0.099834249 
-   23410        2.341   0.70681969   0.70681836 -4.669444e-08 -0.099834743 -0.099834743 -0.099834743 
-   23420        2.342   0.70682056   0.70681924 -5.2082587e-08 -0.099835237 -0.099835237 -0.099835237 
-   23430        2.343   0.70682143   0.70682012 -5.6550242e-08 -0.099835729 -0.099835729 -0.099835729 
-   23440        2.344   0.70682229   0.70682099 -5.9997496e-08 -0.099836219 -0.099836219 -0.099836219 
-   23450        2.345   0.70682315   0.70682186 -6.2348197e-08 -0.099836708 -0.099836708 -0.099836708 
-   23460        2.346   0.70682401   0.70682272 -6.3551627e-08 -0.099837195 -0.099837195 -0.099837195 
-   23470        2.347   0.70682486   0.70682359 -6.3583594e-08 -0.099837681 -0.099837681 -0.099837681 
-   23480        2.348   0.70682571   0.70682445 -6.2446904e-08 -0.099838165 -0.099838165 -0.099838165 
-   23490        2.349   0.70682656   0.70682531 -6.0171218e-08 -0.099838648 -0.099838648 -0.099838648 
-   23500         2.35   0.70682741   0.70682617 -5.6812289e-08  -0.09983913  -0.09983913  -0.09983913 
-   23510        2.351   0.70682825   0.70682702 -5.2450599e-08  -0.09983961  -0.09983961  -0.09983961 
-   23520        2.352   0.70682909   0.70682787 -4.7189438e-08 -0.099840089 -0.099840089 -0.099840089 
-   23530        2.353   0.70682993   0.70682872 -4.115246e-08 -0.099840566 -0.099840566 -0.099840566 
-   23540        2.354   0.70683077   0.70682956 -3.4480775e-08 -0.099841041 -0.099841041 -0.099841041 
-   23550        2.355   0.70683161    0.7068304 -2.732966e-08 -0.099841516 -0.099841516 -0.099841516 
-   23560        2.356   0.70683244   0.70683124 -1.9864941e-08 -0.099841988 -0.099841988 -0.099841988 
-   23570        2.357   0.70683328   0.70683207 -1.2259152e-08  -0.09984246  -0.09984246  -0.09984246 
-   23580        2.358   0.70683411    0.7068329 -4.6875496e-09  -0.09984293  -0.09984293  -0.09984293 
-   23590        2.359   0.70683494   0.70683373 2.675926e-09 -0.099843398 -0.099843398 -0.099843398 
-   23600         2.36   0.70683577   0.70683456 9.6626439e-09 -0.099843865 -0.099843865 -0.099843865 
-   23610        2.361   0.70683659   0.70683538 1.6113143e-08 -0.099844331 -0.099844331 -0.099844331 
-   23620        2.362   0.70683742   0.70683619 2.188077e-08 -0.099844795 -0.099844795 -0.099844795 
-   23630        2.363   0.70683824   0.70683701 2.6835011e-08 -0.099845258 -0.099845258 -0.099845258 
-   23640        2.364   0.70683906   0.70683782 3.0864443e-08  -0.09984572  -0.09984572  -0.09984572 
-   23650        2.365   0.70683988   0.70683863 3.387924e-08  -0.09984618  -0.09984618  -0.09984618 
-   23660        2.366    0.7068407   0.70683944 3.5813168e-08 -0.099846639 -0.099846639 -0.099846639 
-   23670        2.367   0.70684151   0.70684024 3.6625041e-08 -0.099847096 -0.099847096 -0.099847096 
-   23680        2.368   0.70684232   0.70684104 3.6299589e-08 -0.099847552 -0.099847552 -0.099847552 
-   23690        2.369   0.70684313   0.70684184 3.484773e-08 -0.099848006 -0.099848006 -0.099848006 
-   23700         2.37   0.70684394   0.70684263 3.2306245e-08 -0.099848459 -0.099848459 -0.099848459 
-   23710        2.371   0.70684474   0.70684343 2.8736849e-08 -0.099848911 -0.099848911 -0.099848911 
-   23720        2.372   0.70684554   0.70684422  2.42247e-08 -0.099849362 -0.099849362 -0.099849362 
-   23730        2.373   0.70684634   0.70684501 1.8876368e-08 -0.099849811 -0.099849811 -0.099849811 
-   23740        2.374   0.70684713    0.7068458 1.2817326e-08 -0.099850258 -0.099850258 -0.099850258 
-   23750        2.375   0.70684793   0.70684659 6.1890013e-09 -0.099850705 -0.099850705 -0.099850705 
-   23760        2.376   0.70684871   0.70684737 -8.5451703e-10  -0.09985115  -0.09985115  -0.09985115 
-   23770        2.377    0.7068495   0.70684816 -8.1500628e-09 -0.099851593 -0.099851593 -0.099851593 
-   23780        2.378   0.70685028   0.70684894 -1.5529169e-08 -0.099852036 -0.099852036 -0.099852036 
-   23790        2.379   0.70685106   0.70684972 -2.2821957e-08 -0.099852477 -0.099852477 -0.099852477 
-   23800         2.38   0.70685184    0.7068505 -2.9861045e-08 -0.099852916 -0.099852916 -0.099852916 
-   23810        2.381   0.70685261   0.70685128 -3.6485391e-08 -0.099853355 -0.099853355 -0.099853355 
-   23820        2.382   0.70685338   0.70685205 -4.254397e-08 -0.099853791 -0.099853791 -0.099853791 
-   23830        2.383   0.70685415   0.70685283 -4.7899223e-08 -0.099854227 -0.099854227 -0.099854227 
-   23840        2.384   0.70685491    0.7068536 -5.2430172e-08 -0.099854661 -0.099854661 -0.099854661 
-   23850        2.385   0.70685567   0.70685437 -5.6035154e-08 -0.099855094 -0.099855094 -0.099855094 
-   23860        2.386   0.70685643   0.70685514 -5.8634099e-08 -0.099855526 -0.099855526 -0.099855526 
-   23870        2.387   0.70685719    0.7068559 -6.0170307e-08 -0.099855956 -0.099855956 -0.099855956 
-   23880        2.388   0.70685794   0.70685667 -6.0611676e-08 -0.099856386 -0.099856386 -0.099856386 
-   23890        2.389   0.70685869   0.70685743 -5.9951373e-08 -0.099856813 -0.099856813 -0.099856813 
-   23900         2.39   0.70685944   0.70685819 -5.8207909e-08  -0.09985724  -0.09985724  -0.09985724 
-   23910        2.391   0.70686019   0.70685894 -5.5424637e-08 -0.099857665 -0.099857665 -0.099857665 
-   23920        2.392   0.70686093    0.7068597 -5.1668687e-08 -0.099858089 -0.099858089 -0.099858089 
-   23930        2.393   0.70686168   0.70686045 -4.702934e-08 -0.099858511 -0.099858511 -0.099858511 
-   23940        2.394   0.70686242    0.7068612 -4.1615921e-08 -0.099858933 -0.099858933 -0.099858933 
-   23950        2.395   0.70686316   0.70686194 -3.5555213e-08 -0.099859353 -0.099859353 -0.099859353 
-   23960        2.396    0.7068639   0.70686269 -2.8988501e-08 -0.099859772 -0.099859772 -0.099859772 
-   23970        2.397   0.70686463   0.70686342 -2.2068273e-08 -0.099860189 -0.099860189 -0.099860189 
-   23980        2.398   0.70686537   0.70686416 -1.4954682e-08 -0.099860605 -0.099860605 -0.099860605 
-   23990        2.399    0.7068661    0.7068649 -7.8118434e-09  -0.09986102  -0.09986102  -0.09986102 
-   24000          2.4   0.70686684   0.70686563 -8.0404842e-10 -0.099861434 -0.099861434 -0.099861434 
-   24010        2.401   0.70686757   0.70686635 5.9080126e-09 -0.099861847 -0.099861847 -0.099861847 
-   24020        2.402    0.7068683   0.70686708 1.2170934e-08 -0.099862258 -0.099862258 -0.099862258 
-   24030        2.403   0.70686902    0.7068678 1.7842097e-08 -0.099862668 -0.099862668 -0.099862668 
-   24040        2.404   0.70686975   0.70686852 2.2792921e-08 -0.099863077 -0.099863077 -0.099863077 
-   24050        2.405   0.70687048   0.70686924 2.6911771e-08 -0.099863484 -0.099863484 -0.099863484 
-   24060        2.406    0.7068712   0.70686995 3.0106476e-08  -0.09986389  -0.09986389  -0.09986389 
-   24070        2.407   0.70687192   0.70687066 3.2306389e-08 -0.099864295 -0.099864295 -0.099864295 
-   24080        2.408   0.70687264   0.70687137 3.3463945e-08 -0.099864699 -0.099864699 -0.099864699 
-   24090        2.409   0.70687336   0.70687208 3.3555687e-08 -0.099865102 -0.099865102 -0.099865102 
-   24100         2.41   0.70687407   0.70687278 3.2582728e-08 -0.099865503 -0.099865503 -0.099865503 
-   24110        2.411   0.70687478   0.70687349 3.0570656e-08 -0.099865903 -0.099865903 -0.099865903 
-   24120        2.412   0.70687549   0.70687419 2.756887e-08 -0.099866302 -0.099866302 -0.099866302 
-   24130        2.413    0.7068762   0.70687489 2.3649372e-08   -0.0998667   -0.0998667   -0.0998667 
-   24140        2.414   0.70687691   0.70687558 1.8905042e-08 -0.099867096 -0.099867096 -0.099867096 
-   24150        2.415   0.70687761   0.70687628 1.3447443e-08 -0.099867492 -0.099867492 -0.099867492 
-   24160        2.416   0.70687831   0.70687697 7.4041986e-09 -0.099867886 -0.099867886 -0.099867886 
-   24170        2.417     0.706879   0.70687767 9.1600922e-10 -0.099868279 -0.099868279 -0.099868279 
-   24180        2.418    0.7068797   0.70687836 -5.866621e-09 -0.099868671 -0.099868671 -0.099868671 
-   24190        2.419   0.70688039   0.70687905 -1.2786874e-08 -0.099869061 -0.099869061 -0.099869061 
-   24200         2.42   0.70688108   0.70687974 -1.9685241e-08  -0.09986945  -0.09986945  -0.09986945 
-   24210        2.421   0.70688176   0.70688043 -2.6403201e-08 -0.099869839 -0.099869839 -0.099869839 
-   24220        2.422   0.70688244   0.70688111 -3.2786856e-08 -0.099870226 -0.099870226 -0.099870226 
-   24230        2.423   0.70688312    0.7068818 -3.8690462e-08 -0.099870611 -0.099870611 -0.099870611 
-   24240        2.424    0.7068838   0.70688248 -4.3979751e-08 -0.099870996 -0.099870996 -0.099870996 
-   24250        2.425   0.70688448   0.70688316 -4.8534982e-08  -0.09987138  -0.09987138  -0.09987138 
-   24260        2.426   0.70688515   0.70688384 -5.2253654e-08 -0.099871762 -0.099871762 -0.099871762 
-   24270        2.427   0.70688582   0.70688452 -5.5052807e-08 -0.099872143 -0.099872143 -0.099872143 
-   24280        2.428   0.70688648    0.7068852 -5.6870872e-08 -0.099872523 -0.099872523 -0.099872523 
-   24290        2.429   0.70688715   0.70688587 -5.7669019e-08 -0.099872902 -0.099872902 -0.099872902 
-   24300         2.43   0.70688781   0.70688654 -5.7431987e-08  -0.09987328  -0.09987328  -0.09987328 
-   24310        2.431   0.70688847   0.70688722 -5.6168356e-08 -0.099873656 -0.099873656 -0.099873656 
-   24320        2.432   0.70688913   0.70688788 -5.3910283e-08 -0.099874032 -0.099874032 -0.099874032 
-   24330        2.433   0.70688979   0.70688855 -5.071269e-08 -0.099874406 -0.099874406 -0.099874406 
-   24340        2.434   0.70689045   0.70688921 -4.6651932e-08 -0.099874779 -0.099874779 -0.099874779 
-   24350        2.435    0.7068911   0.70688987 -4.1823977e-08 -0.099875151 -0.099875151 -0.099875151 
-   24360        2.436   0.70689175   0.70689053 -3.6342143e-08 -0.099875522 -0.099875522 -0.099875522 
-   24370        2.437   0.70689241   0.70689119 -3.0334435e-08 -0.099875892 -0.099875892 -0.099875892 
-   24380        2.438   0.70689306   0.70689184 -2.3940563e-08 -0.099876261 -0.099876261 -0.099876261 
-   24390        2.439   0.70689371   0.70689249 -1.730869e-08 -0.099876628 -0.099876628 -0.099876628 
-   24400         2.44   0.70689435   0.70689314 -1.0592007e-08 -0.099876995 -0.099876995 -0.099876995 
-   24410        2.441     0.706895   0.70689379 -3.945187e-09  -0.09987736  -0.09987736  -0.09987736 
-   24420        2.442   0.70689565   0.70689443 2.4791681e-09 -0.099877724 -0.099877724 -0.099877724 
-   24430        2.443   0.70689629   0.70689507 8.5340334e-09 -0.099878087 -0.099878087 -0.099878087 
-   24440        2.444   0.70689693   0.70689571 1.4081323e-08 -0.099878449 -0.099878449 -0.099878449 
-   24450        2.445   0.70689757   0.70689634 1.8995038e-08  -0.09987881  -0.09987881  -0.09987881 
-   24460        2.446   0.70689821   0.70689698 2.3164127e-08  -0.09987917  -0.09987917  -0.09987917 
-   24470        2.447   0.70689885   0.70689761 2.6494993e-08 -0.099879529 -0.099879529 -0.099879529 
-   24480        2.448   0.70689949   0.70689823 2.8913594e-08 -0.099879887 -0.099879887 -0.099879887 
-   24490        2.449   0.70690012   0.70689886 3.0367085e-08 -0.099880243 -0.099880243 -0.099880243 
-   24500         2.45   0.70690076   0.70689948 3.0824969e-08 -0.099880599 -0.099880599 -0.099880599 
-   24510        2.451   0.70690139   0.70690011 3.0279732e-08 -0.099880953 -0.099880953 -0.099880953 
-   24520        2.452   0.70690202   0.70690073 2.8746944e-08 -0.099881306 -0.099881306 -0.099881306 
-   24530        2.453   0.70690265   0.70690134 2.6264834e-08 -0.099881659 -0.099881659 -0.099881659 
-   24540        2.454   0.70690327   0.70690196 2.2893339e-08  -0.09988201  -0.09988201  -0.09988201 
-   24550        2.455   0.70690389   0.70690258 1.8712663e-08  -0.09988236  -0.09988236  -0.09988236 
-   24560        2.456   0.70690451   0.70690319 1.3821372e-08 -0.099882709 -0.099882709 -0.099882709 
-   24570        2.457   0.70690513    0.7069038 8.3340722e-09 -0.099883057 -0.099883057 -0.099883057 
-   24580        2.458   0.70690575   0.70690442 2.3787239e-09 -0.099883404 -0.099883404 -0.099883404 
-   24590        2.459   0.70690636   0.70690503 -3.9063373e-09  -0.09988375  -0.09988375  -0.09988375 
-   24600         2.46   0.70690697   0.70690564 -1.0375614e-08 -0.099884095 -0.099884095 -0.099884095 
-   24610        2.461   0.70690758   0.70690624 -1.6879814e-08 -0.099884439 -0.099884439 -0.099884439 
-   24620        2.462   0.70690818   0.70690685 -2.3269292e-08 -0.099884781 -0.099884781 -0.099884781 
-   24630        2.463   0.70690879   0.70690746 -2.9397496e-08 -0.099885123 -0.099885123 -0.099885123 
-   24640        2.464   0.70690939   0.70690806 -3.512432e-08 -0.099885464 -0.099885464 -0.099885464 
-   24650        2.465   0.70690998   0.70690866 -4.0319315e-08 -0.099885803 -0.099885803 -0.099885803 
-   24660        2.466   0.70691058   0.70690927 -4.486465e-08 -0.099886142 -0.099886142 -0.099886142 
-   24670        2.467   0.70691117   0.70690987 -4.8657787e-08  -0.09988648  -0.09988648  -0.09988648 
-   24680        2.468   0.70691176   0.70691047 -5.1613796e-08 -0.099886816 -0.099886816 -0.099886816 
-   24690        2.469   0.70691235   0.70691106 -5.3667247e-08 -0.099887152 -0.099887152 -0.099887152 
-   24700         2.47   0.70691294   0.70691166 -5.4773659e-08 -0.099887486 -0.099887486 -0.099887486 
-   24710        2.471   0.70691353   0.70691225 -5.4910461e-08  -0.09988782  -0.09988782  -0.09988782 
-   24720        2.472   0.70691411   0.70691285 -5.4077443e-08 -0.099888152 -0.099888152 -0.099888152 
-   24730        2.473   0.70691469   0.70691344 -5.2296692e-08 -0.099888484 -0.099888484 -0.099888484 
-   24740        2.474   0.70691527   0.70691403 -4.9612019e-08 -0.099888814 -0.099888814 -0.099888814 
-   24750        2.475   0.70691585   0.70691461 -4.6087884e-08 -0.099889144 -0.099889144 -0.099889144 
-   24760        2.476   0.70691643    0.7069152 -4.1807855e-08 -0.099889472 -0.099889472 -0.099889472 
-   24770        2.477     0.706917   0.70691578 -3.6872624e-08   -0.0998898   -0.0998898   -0.0998898 
-   24780        2.478   0.70691758   0.70691636 -3.1397643e-08 -0.099890126 -0.099890126 -0.099890126 
-   24790        2.479   0.70691815   0.70691694 -2.5510426e-08 -0.099890452 -0.099890452 -0.099890452 
-   24800         2.48   0.70691873   0.70691751 -1.9347578e-08 -0.099890777 -0.099890777 -0.099890777 
-   24810        2.481    0.7069193   0.70691808 -1.3051629e-08   -0.0998911   -0.0998911   -0.0998911 
-   24820        2.482   0.70691987   0.70691865 -6.767737e-09 -0.099891423 -0.099891423 -0.099891423 
-   24830        2.483   0.70692044   0.70691922 -6.4034447e-10 -0.099891744 -0.099891744 -0.099891744 
-   24840        2.484   0.70692101   0.70691979 5.1901416e-09 -0.099892065 -0.099892065 -0.099892065 
-   24850        2.485   0.70692158   0.70692035 1.0590565e-08 -0.099892385 -0.099892385 -0.099892385 
-   24860        2.486   0.70692214   0.70692091 1.5438062e-08 -0.099892703 -0.099892703 -0.099892703 
-   24870        2.487   0.70692271   0.70692147 1.962285e-08 -0.099893021 -0.099893021 -0.099893021 
-   24880        2.488   0.70692327   0.70692202 2.305072e-08 -0.099893338 -0.099893338 -0.099893338 
-   24890        2.489   0.70692383   0.70692258 2.5645147e-08 -0.099893654 -0.099893654 -0.099893654 
-   24900         2.49   0.70692439   0.70692313 2.7349003e-08 -0.099893968 -0.099893968 -0.099893968 
-   24910        2.491   0.70692495   0.70692368 2.8125808e-08 -0.099894282 -0.099894282 -0.099894282 
-   24920        2.492   0.70692551   0.70692423 2.7960507e-08 -0.099894595 -0.099894595 -0.099894595 
-   24930        2.493   0.70692607   0.70692478 2.6859752e-08 -0.099894907 -0.099894907 -0.099894907 
-   24940        2.494   0.70692662   0.70692532 2.4851683e-08 -0.099895218 -0.099895218 -0.099895218 
-   24950        2.495   0.70692717   0.70692587 2.1985217e-08 -0.099895528 -0.099895528 -0.099895528 
-   24960        2.496   0.70692772   0.70692641 1.8328859e-08 -0.099895838 -0.099895838 -0.099895838 
-   24970        2.497   0.70692827   0.70692695 1.3969067e-08 -0.099896146 -0.099896146 -0.099896146 
-   24980        2.498   0.70692882   0.70692749 9.0082126e-09 -0.099896453 -0.099896453 -0.099896453 
-   24990        2.499   0.70692936   0.70692803 3.5621776e-09 -0.099896759 -0.099896759 -0.099896759 
-   25000          2.5    0.7069299   0.70692857 -2.242352e-09 -0.099897065 -0.099897065 -0.099897065 
-   25010        2.501   0.70693044   0.70692911 -8.2708303e-09 -0.099897369 -0.099897369 -0.099897369 
-   25020        2.502   0.70693098   0.70692965 -1.438397e-08 -0.099897673 -0.099897673 -0.099897673 
-   25030        2.503   0.70693151   0.70693018 -2.0440957e-08 -0.099897976 -0.099897976 -0.099897976 
-   25040        2.504   0.70693205   0.70693072 -2.6302696e-08 -0.099898277 -0.099898277 -0.099898277 
-   25050        2.505   0.70693258   0.70693125 -3.1835002e-08 -0.099898578 -0.099898578 -0.099898578 
-   25060        2.506    0.7069331   0.70693178 -3.6911669e-08 -0.099898878 -0.099898878 -0.099898878 
-   25070        2.507   0.70693363   0.70693232 -4.1417351e-08 -0.099899177 -0.099899177 -0.099899177 
-   25080        2.508   0.70693415   0.70693285 -4.5250177e-08 -0.099899475 -0.099899475 -0.099899475 
-   25090        2.509   0.70693468   0.70693338 -4.8324058e-08 -0.099899772 -0.099899772 -0.099899772 
-   25100         2.51    0.7069352    0.7069339 -5.0570614e-08 -0.099900069 -0.099900069 -0.099900069 
-   25110        2.511   0.70693571   0.70693443 -5.1940696e-08 -0.099900364 -0.099900364 -0.099900364 
-   25120        2.512   0.70693623   0.70693495 -5.2405453e-08 -0.099900659 -0.099900659 -0.099900659 
-   25130        2.513   0.70693675   0.70693548 -5.1956942e-08 -0.099900952 -0.099900952 -0.099900952 
-   25140        2.514   0.70693726     0.706936 -5.0608239e-08 -0.099901245 -0.099901245 -0.099901245 
-   25150        2.515   0.70693777   0.70693652 -4.8393082e-08 -0.099901537 -0.099901537 -0.099901537 
-   25160        2.516   0.70693828   0.70693704 -4.5365025e-08 -0.099901828 -0.099901828 -0.099901828 
-   25170        2.517   0.70693879   0.70693755 -4.1596156e-08 -0.099902118 -0.099902118 -0.099902118 
-   25180        2.518    0.7069393   0.70693807 -3.7175374e-08 -0.099902407 -0.099902407 -0.099902407 
-   25190        2.519   0.70693981   0.70693858 -3.2206301e-08 -0.099902695 -0.099902695 -0.099902695 
-   25200         2.52   0.70694031   0.70693909 -2.6804852e-08 -0.099902983 -0.099902983 -0.099902983 
-   25210        2.521   0.70694082    0.7069396 -2.1096532e-08 -0.099903269 -0.099903269 -0.099903269 
-   25220        2.522   0.70694132    0.7069401 -1.5213525e-08 -0.099903555 -0.099903555 -0.099903555 
-   25230        2.523   0.70694183   0.70694061 -9.2916271e-09  -0.09990384  -0.09990384  -0.09990384 
-   25240        2.524   0.70694233   0.70694111 -3.4671218e-09 -0.099904124 -0.099904124 -0.099904124 
-   25250        2.525   0.70694283   0.70694161 2.1263612e-09 -0.099904407 -0.099904407 -0.099904407 
-   25260        2.526   0.70694333   0.70694211 7.3609082e-09 -0.099904689 -0.099904689 -0.099904689 
-   25270        2.527   0.70694383    0.7069426 1.2117246e-08 -0.099904971 -0.099904971 -0.099904971 
-   25280        2.528   0.70694433   0.70694309 1.6287457e-08 -0.099905251 -0.099905251 -0.099905251 
-   25290        2.529   0.70694483   0.70694359 1.9777428e-08 -0.099905531 -0.099905531 -0.099905531 
-   25300         2.53   0.70694533   0.70694407 2.2508973e-08  -0.09990581  -0.09990581  -0.09990581 
-   25310        2.531   0.70694582   0.70694456 2.4421578e-08 -0.099906088 -0.099906088 -0.099906088 
-   25320        2.532   0.70694632   0.70694505 2.5473747e-08 -0.099906365 -0.099906365 -0.099906365 
-   25330        2.533   0.70694681   0.70694553 2.564389e-08 -0.099906641 -0.099906641 -0.099906641 
-   25340        2.534    0.7069473   0.70694602 2.4930766e-08 -0.099906917 -0.099906917 -0.099906917 
-   25350        2.535   0.70694779    0.7069465 2.3353447e-08 -0.099907191 -0.099907191 -0.099907191 
-   25360        2.536   0.70694828   0.70694698 2.0950816e-08 -0.099907465 -0.099907465 -0.099907465 
-   25370        2.537   0.70694876   0.70694746 1.7780618e-08 -0.099907738 -0.099907738 -0.099907738 
-   25380        2.538   0.70694925   0.70694794 1.3918071e-08  -0.09990801  -0.09990801  -0.09990801 
-   25390        2.539   0.70694973   0.70694841 9.4540864e-09 -0.099908281 -0.099908281 -0.099908281 
-   25400         2.54   0.70695021   0.70694889 4.4931285e-09 -0.099908552 -0.099908552 -0.099908552 
-   25410        2.541   0.70695069   0.70694936 -8.4922654e-10 -0.099908822 -0.099908822 -0.099908822 
-   25420        2.542   0.70695117   0.70694984 -6.4489828e-09 -0.099909091 -0.099909091 -0.099909091 
-   25430        2.543   0.70695164   0.70695031 -1.2176601e-08 -0.099909359 -0.099909359 -0.099909359 
-   25440        2.544   0.70695211   0.70695078 -1.7899994e-08 -0.099909626 -0.099909626 -0.099909626 
-   25450        2.545   0.70695258   0.70695126 -2.348757e-08 -0.099909892 -0.099909892 -0.099909892 
-   25460        2.546   0.70695305   0.70695173 -2.8811262e-08 -0.099910158 -0.099910158 -0.099910158 
-   25470        2.547   0.70695352    0.7069522 -3.3749454e-08 -0.099910423 -0.099910423 -0.099910423 
-   25480        2.548   0.70695398   0.70695267 -3.8189766e-08 -0.099910687 -0.099910687 -0.099910687 
-   25490        2.549   0.70695444   0.70695314 -4.2031604e-08  -0.09991095  -0.09991095  -0.09991095 
-   25500         2.55    0.7069549    0.7069536 -4.5188441e-08 -0.099911212 -0.099911212 -0.099911212 
-   25510        2.551   0.70695536   0.70695407 -4.7589763e-08 -0.099911474 -0.099911474 -0.099911474 
-   25520        2.552   0.70695582   0.70695453 -4.9182641e-08 -0.099911735 -0.099911735 -0.099911735 
-   25530        2.553   0.70695628     0.706955 -4.9932896e-08 -0.099911995 -0.099911995 -0.099911995 
-   25540        2.554   0.70695673   0.70695546 -4.9825829e-08 -0.099912254 -0.099912254 -0.099912254 
-   25550        2.555   0.70695718   0.70695592 -4.8866497e-08 -0.099912513 -0.099912513 -0.099912513 
-   25560        2.556   0.70695764   0.70695638 -4.7079541e-08  -0.09991277  -0.09991277  -0.09991277 
-   25570        2.557   0.70695809   0.70695684 -4.4508558e-08 -0.099913027 -0.099913027 -0.099913027 
-   25580        2.558   0.70695854    0.7069573 -4.1215038e-08 -0.099913283 -0.099913283 -0.099913283 
-   25590        2.559   0.70695899   0.70695775 -3.7276903e-08 -0.099913539 -0.099913539 -0.099913539 
-   25600         2.56   0.70695943    0.7069582 -3.278666e-08 -0.099913793 -0.099913793 -0.099913793 
-   25610        2.561   0.70695988   0.70695865 -2.7849232e-08 -0.099914047 -0.099914047 -0.099914047 
-   25620        2.562   0.70696033    0.7069591 -2.2579507e-08   -0.0999143   -0.0999143   -0.0999143 
-   25630        2.563   0.70696077   0.70695955 -1.7099665e-08 -0.099914552 -0.099914552 -0.099914552 
-   25640        2.564   0.70696122   0.70695999 -1.1536349e-08 -0.099914804 -0.099914804 -0.099914804 
-   25650        2.565   0.70696166   0.70696044 -6.0177391e-09 -0.099915055 -0.099915055 -0.099915055 
-   25660        2.566    0.7069621   0.70696088 -6.7059702e-10 -0.099915305 -0.099915305 -0.099915305 
-   25670        2.567   0.70696254   0.70696132 4.3826405e-09 -0.099915554 -0.099915554 -0.099915554 
-   25680        2.568   0.70696299   0.70696175 9.026666e-09 -0.099915802 -0.099915802 -0.099915802 
-   25690        2.569   0.70696343   0.70696219 1.3155931e-08  -0.09991605  -0.09991605  -0.09991605 
-   25700         2.57   0.70696387   0.70696262 1.6677042e-08 -0.099916297 -0.099916297 -0.099916297 
-   25710        2.571   0.70696431   0.70696305 1.9510875e-08 -0.099916543 -0.099916543 -0.099916543 
-   25720        2.572   0.70696474   0.70696348 2.1594347e-08 -0.099916789 -0.099916789 -0.099916789 
-   25730        2.573   0.70696518   0.70696391 2.2881822e-08 -0.099917033 -0.099917033 -0.099917033 
-   25740        2.574   0.70696561   0.70696434 2.3346104e-08 -0.099917277 -0.099917277 -0.099917277 
-   25750        2.575   0.70696605   0.70696477 2.297901e-08  -0.09991752  -0.09991752  -0.09991752 
-   25760        2.576   0.70696648   0.70696519 2.1791499e-08 -0.099917763 -0.099917763 -0.099917763 
-   25770        2.577   0.70696691   0.70696562 1.9813363e-08 -0.099918005 -0.099918005 -0.099918005 
-   25780        2.578   0.70696734   0.70696604 1.7092482e-08 -0.099918246 -0.099918246 -0.099918246 
-   25790        2.579   0.70696777   0.70696646 1.3693673e-08 -0.099918486 -0.099918486 -0.099918486 
-   25800         2.58    0.7069682   0.70696688 9.6971429e-09 -0.099918726 -0.099918726 -0.099918726 
-   25810        2.581   0.70696862    0.7069673 5.1966028e-09 -0.099918964 -0.099918964 -0.099918964 
-   25820        2.582   0.70696904   0.70696772 2.9706868e-10 -0.099919203 -0.099919203 -0.099919203 
-   25830        2.583   0.70696946   0.70696814 -4.8875861e-09  -0.09991944  -0.09991944  -0.09991944 
-   25840        2.584   0.70696988   0.70696856 -1.0237277e-08 -0.099919677 -0.099919677 -0.099919677 
-   25850        2.585    0.7069703   0.70696898 -1.5628487e-08 -0.099919913 -0.099919913 -0.099919913 
-   25860        2.586   0.70697072   0.70696939 -2.093712e-08 -0.099920148 -0.099920148 -0.099920148 
-   25870        2.587   0.70697113   0.70696981 -2.6041352e-08 -0.099920382 -0.099920382 -0.099920382 
-   25880        2.588   0.70697154   0.70697022 -3.0824431e-08 -0.099920616 -0.099920616 -0.099920616 
-   25890        2.589   0.70697195   0.70697064 -3.5177341e-08 -0.099920849 -0.099920849 -0.099920849 
-   25900         2.59   0.70697236   0.70697105 -3.9001289e-08 -0.099921082 -0.099921082 -0.099921082 
-   25910        2.591   0.70697277   0.70697146 -4.2209945e-08 -0.099921313 -0.099921313 -0.099921313 
-   25920        2.592   0.70697317   0.70697188 -4.4731387e-08 -0.099921544 -0.099921544 -0.099921544 
-   25930        2.593   0.70697357   0.70697229 -4.6509718e-08 -0.099921775 -0.099921775 -0.099921775 
-   25940        2.594   0.70697398    0.7069727 -4.7506293e-08 -0.099922004 -0.099922004 -0.099922004 
-   25950        2.595   0.70697438    0.7069731 -4.7700565e-08 -0.099922233 -0.099922233 -0.099922233 
-   25960        2.596   0.70697478   0.70697351 -4.7090496e-08 -0.099922462 -0.099922462 -0.099922462 
-   25970        2.597   0.70697518   0.70697392 -4.569255e-08 -0.099922689 -0.099922689 -0.099922689 
-   25980        2.598   0.70697557   0.70697432 -4.3541262e-08 -0.099922916 -0.099922916 -0.099922916 
-   25990        2.599   0.70697597   0.70697472 -4.0688383e-08 -0.099923142 -0.099923142 -0.099923142 
-   26000          2.6   0.70697637   0.70697513 -3.7201641e-08 -0.099923367 -0.099923367 -0.099923367 
-   26010        2.601   0.70697676   0.70697553 -3.3163136e-08 -0.099923592 -0.099923592 -0.099923592 
-   26020        2.602   0.70697716   0.70697592 -2.8667406e-08 -0.099923816 -0.099923816 -0.099923816 
-   26030        2.603   0.70697755   0.70697632 -2.3819219e-08  -0.09992404  -0.09992404  -0.09992404 
-   26040        2.604   0.70697794   0.70697672 -1.873113e-08 -0.099924262 -0.099924262 -0.099924262 
-   26050        2.605   0.70697833   0.70697711 -1.3520869e-08 -0.099924485 -0.099924485 -0.099924485 
-   26060        2.606   0.70697873    0.7069775 -8.3086186e-09 -0.099924706 -0.099924706 -0.099924706 
-   26070        2.607   0.70697912   0.70697789 -3.2142456e-09 -0.099924927 -0.099924927 -0.099924927 
-   26080        2.608   0.70697951   0.70697828 1.6454587e-09 -0.099925147 -0.099925147 -0.099925147 
-   26090        2.609    0.7069799   0.70697866 6.1594525e-09 -0.099925366 -0.099925366 -0.099925366 
-   26100         2.61   0.70698029   0.70697905 1.022498e-08 -0.099925585 -0.099925585 -0.099925585 
-   26110        2.611   0.70698067   0.70697943 1.374991e-08 -0.099925803 -0.099925803 -0.099925803 
-   26120        2.612   0.70698106   0.70697981 1.665482e-08  -0.09992602  -0.09992602  -0.09992602 
-   26130        2.613   0.70698145   0.70698019 1.8874789e-08 -0.099926237 -0.099926237 -0.099926237 
-   26140        2.614   0.70698183   0.70698057 2.0360839e-08 -0.099926453 -0.099926453 -0.099926453 
-   26150        2.615   0.70698222   0.70698095 2.1081022e-08 -0.099926668 -0.099926668 -0.099926668 
-   26160        2.616    0.7069826   0.70698132 2.1021096e-08 -0.099926883 -0.099926883 -0.099926883 
-   26170        2.617   0.70698298    0.7069817 2.0184801e-08 -0.099927097 -0.099927097 -0.099927097 
-   26180        2.618   0.70698336   0.70698207 1.8593721e-08 -0.099927311 -0.099927311 -0.099927311 
-   26190        2.619   0.70698374   0.70698245 1.6286729e-08 -0.099927524 -0.099927524 -0.099927524 
-   26200         2.62   0.70698412   0.70698282 1.3319047e-08 -0.099927736 -0.099927736 -0.099927736 
-   26210        2.621    0.7069845   0.70698319 9.7609198e-09 -0.099927947 -0.099927947 -0.099927947 
-   26220        2.622   0.70698487   0.70698356 5.695959e-09 -0.099928158 -0.099928158 -0.099928158 
-   26230        2.623   0.70698525   0.70698393 1.2191777e-09 -0.099928368 -0.099928368 -0.099928368 
-   26240        2.624   0.70698562    0.7069843 -3.5652283e-09 -0.099928578 -0.099928578 -0.099928578 
-   26250        2.625   0.70698599   0.70698467 -8.5463044e-09 -0.099928787 -0.099928787 -0.099928787 
-   26260        2.626   0.70698636   0.70698504 -1.360891e-08 -0.099928995 -0.099928995 -0.099928995 
-   26270        2.627   0.70698672    0.7069854 -1.8636377e-08 -0.099929203 -0.099929203 -0.099929203 
-   26280        2.628   0.70698709   0.70698577 -2.3513199e-08  -0.09992941  -0.09992941  -0.09992941 
-   26290        2.629   0.70698745   0.70698614 -2.8127686e-08 -0.099929617 -0.099929617 -0.099929617 
-   26300         2.63   0.70698782    0.7069865 -3.2374515e-08 -0.099929823 -0.099929823 -0.099929823 
-   26310        2.631   0.70698818   0.70698687 -3.615714e-08 -0.099930028 -0.099930028 -0.099930028 
-   26320        2.632   0.70698854   0.70698723 -3.938998e-08 -0.099930232 -0.099930232 -0.099930232 
-   26330        2.633   0.70698889    0.7069876 -4.2000359e-08 -0.099930436 -0.099930436 -0.099930436 
-   26340        2.634   0.70698925   0.70698796 -4.3930131e-08  -0.09993064  -0.09993064  -0.09993064 
-   26350        2.635    0.7069896   0.70698832 -4.5136983e-08 -0.099930842 -0.099930842 -0.099930842 
-   26360        2.636   0.70698996   0.70698868 -4.5595349e-08 -0.099931044 -0.099931044 -0.099931044 
-   26370        2.637   0.70699031   0.70698904 -4.5296959e-08 -0.099931246 -0.099931246 -0.099931246 
-   26380        2.638   0.70699066    0.7069894 -4.4250965e-08 -0.099931447 -0.099931447 -0.099931447 
-   26390        2.639   0.70699101   0.70698976 -4.2483687e-08 -0.099931647 -0.099931647 -0.099931647 
-   26400         2.64   0.70699136   0.70699011 -4.0037951e-08 -0.099931847 -0.099931847 -0.099931847 
-   26410        2.641   0.70699171   0.70699047 -3.6972056e-08 -0.099932046 -0.099932046 -0.099932046 
-   26420        2.642   0.70699206   0.70699082 -3.3358386e-08 -0.099932244 -0.099932244 -0.099932244 
-   26430        2.643   0.70699241   0.70699117 -2.9281703e-08 -0.099932442 -0.099932442 -0.099932442 
-   26440        2.644   0.70699276   0.70699152 -2.4837158e-08 -0.099932639 -0.099932639 -0.099932639 
-   26450        2.645    0.7069931   0.70699187 -2.0128076e-08 -0.099932836 -0.099932836 -0.099932836 
-   26460        2.646   0.70699345   0.70699222 -1.5263551e-08 -0.099933032 -0.099933032 -0.099933032 
-   26470        2.647   0.70699379   0.70699257 -1.0355922e-08 -0.099933228 -0.099933228 -0.099933228 
-   26480        2.648   0.70699414   0.70699291 -5.5181785e-09 -0.099933423 -0.099933423 -0.099933423 
-   26490        2.649   0.70699448   0.70699325 -8.6136106e-10 -0.099933617 -0.099933617 -0.099933617 
-   26500         2.65   0.70699483   0.70699359 3.507987e-09 -0.099933811 -0.099933811 -0.099933811 
-   26510        2.651   0.70699517   0.70699393 7.4902557e-09 -0.099934004 -0.099934004 -0.099934004 
-   26520        2.652   0.70699551   0.70699427 1.0995039e-08 -0.099934196 -0.099934196 -0.099934196 
-   26530        2.653   0.70699586   0.70699461 1.3943183e-08 -0.099934388 -0.099934388 -0.099934388 
-   26540        2.654    0.7069962   0.70699494 1.6268578e-08 -0.099934579 -0.099934579 -0.099934579 
-   26550        2.655   0.70699654   0.70699528 1.7919633e-08  -0.09993477  -0.09993477  -0.09993477 
-   26560        2.656   0.70699688   0.70699561 1.8860422e-08  -0.09993496  -0.09993496  -0.09993496 
-   26570        2.657   0.70699722   0.70699594 1.9071461e-08  -0.09993515  -0.09993515  -0.09993515 
-   26580        2.658   0.70699755   0.70699627 1.8550109e-08 -0.099935339 -0.099935339 -0.099935339 
-   26590        2.659   0.70699789    0.7069966 1.7310572e-08 -0.099935528 -0.099935528 -0.099935528 
-   26600         2.66   0.70699823   0.70699693 1.5383533e-08 -0.099935716 -0.099935716 -0.099935716 
-   26610        2.661   0.70699856   0.70699726 1.281539e-08 -0.099935903 -0.099935903 -0.099935903 
-   26620        2.662   0.70699889   0.70699759 9.6671452e-09  -0.09993609  -0.09993609  -0.09993609 
-   26630        2.663   0.70699922   0.70699791 6.0129553e-09 -0.099936276 -0.099936276 -0.099936276 
-   26640        2.664   0.70699955   0.70699824 1.9383889e-09 -0.099936461 -0.099936461 -0.099936461 
-   26650        2.665   0.70699988   0.70699857 -2.4615778e-09 -0.099936647 -0.099936647 -0.099936647 
-   26660        2.666   0.70700021   0.70699889 -7.0847727e-09 -0.099936831 -0.099936831 -0.099936831 
-   26670        2.667   0.70700054   0.70699922 -1.18242e-08 -0.099937015 -0.099937015 -0.099937015 
-   26680        2.668   0.70700086   0.70699954 -1.6570514e-08 -0.099937198 -0.099937198 -0.099937198 
-   26690        2.669   0.70700118   0.70699987 -2.1214544e-08 -0.099937381 -0.099937381 -0.099937381 
-   26700         2.67    0.7070015   0.70700019 -2.5649799e-08 -0.099937564 -0.099937564 -0.099937564 
-   26710        2.671   0.70700182   0.70700051 -2.9774915e-08 -0.099937745 -0.099937745 -0.099937745 
-   26720        2.672   0.70700214   0.70700083 -3.3495964e-08 -0.099937926 -0.099937926 -0.099937926 
-   26730        2.673   0.70700246   0.70700116 -3.6728598e-08 -0.099938107 -0.099938107 -0.099938107 
-   26740        2.674   0.70700277   0.70700148 -3.9399956e-08 -0.099938287 -0.099938287 -0.099938287 
-   26750        2.675   0.70700309    0.7070018 -4.1450304e-08 -0.099938467 -0.099938467 -0.099938467 
-   26760        2.676    0.7070034   0.70700212 -4.2834371e-08 -0.099938646 -0.099938646 -0.099938646 
-   26770        2.677   0.70700371   0.70700244 -4.3522347e-08 -0.099938824 -0.099938824 -0.099938824 
-   26780        2.678   0.70700403   0.70700275 -4.3500519e-08 -0.099939002 -0.099939002 -0.099939002 
-   26790        2.679   0.70700434   0.70700307 -4.2771539e-08 -0.099939179 -0.099939179 -0.099939179 
-   26800         2.68   0.70700465   0.70700339 -4.1354316e-08 -0.099939356 -0.099939356 -0.099939356 
-   26810        2.681   0.70700495    0.7070037 -3.9283528e-08 -0.099939533 -0.099939533 -0.099939533 
-   26820        2.682   0.70700526   0.70700401 -3.6608776e-08 -0.099939708 -0.099939708 -0.099939708 
-   26830        2.683   0.70700557   0.70700433 -3.3393404e-08 -0.099939884 -0.099939884 -0.099939884 
-   26840        2.684   0.70700588   0.70700464 -2.9712994e-08 -0.099940058 -0.099940058 -0.099940058 
-   26850        2.685   0.70700618   0.70700495 -2.5653597e-08 -0.099940232 -0.099940232 -0.099940232 
-   26860        2.686   0.70700649   0.70700526 -2.1309716e-08 -0.099940406 -0.099940406 -0.099940406 
-   26870        2.687   0.70700679   0.70700556 -1.6782111e-08 -0.099940579 -0.099940579 -0.099940579 
-   26880        2.688    0.7070071   0.70700587 -1.2175464e-08 -0.099940752 -0.099940752 -0.099940752 
-   26890        2.689    0.7070074   0.70700617 -7.5959545e-09 -0.099940924 -0.099940924 -0.099940924 
-   26900         2.69   0.70700771   0.70700647 -3.1488182e-09 -0.099941095 -0.099941095 -0.099941095 
-   26910        2.691   0.70700801   0.70700677 1.0640726e-09 -0.099941266 -0.099941266 -0.099941266 
-   26920        2.692   0.70700831   0.70700707 4.9465414e-09 -0.099941437 -0.099941437 -0.099941437 
-   26930        2.693   0.70700862   0.70700737 8.4103017e-09 -0.099941607 -0.099941607 -0.099941607 
-   26940        2.694   0.70700892   0.70700767 1.1376964e-08 -0.099941776 -0.099941776 -0.099941776 
-   26950        2.695   0.70700922   0.70700797 1.3779808e-08 -0.099941945 -0.099941945 -0.099941945 
-   26960        2.696   0.70700952   0.70700826 1.5565283e-08 -0.099942114 -0.099942114 -0.099942114 
-   26970        2.697   0.70700982   0.70700855 1.6694197e-08 -0.099942282 -0.099942282 -0.099942282 
-   26980        2.698   0.70701012   0.70700885 1.7142578e-08 -0.099942449 -0.099942449 -0.099942449 
-   26990        2.699   0.70701042   0.70700914 1.6902175e-08 -0.099942616 -0.099942616 -0.099942616 
-   27000          2.7   0.70701072   0.70700943 1.5980604e-08 -0.099942783 -0.099942783 -0.099942783 
-   27010        2.701   0.70701101   0.70700972 1.4401123e-08 -0.099942948 -0.099942948 -0.099942948 
-   27020        2.702   0.70701131   0.70701001 1.220205e-08 -0.099943114 -0.099943114 -0.099943114 
-   27030        2.703    0.7070116    0.7070103 9.435837e-09 -0.099943279 -0.099943279 -0.099943279 
-   27040        2.704    0.7070119   0.70701059 6.1678181e-09 -0.099943443 -0.099943443 -0.099943443 
-   27050        2.705   0.70701219   0.70701088 2.4746714e-09 -0.099943607 -0.099943607 -0.099943607 
-   27060        2.706   0.70701248   0.70701116 -1.5573806e-09  -0.09994377  -0.09994377  -0.09994377 
-   27070        2.707   0.70701277   0.70701145 -5.8345826e-09 -0.099943933 -0.099943933 -0.099943933 
-   27080        2.708   0.70701305   0.70701174 -1.0257825e-08 -0.099944096 -0.099944096 -0.099944096 
-   27090        2.709   0.70701334   0.70701202 -1.4724941e-08 -0.099944258 -0.099944258 -0.099944258 
-   27100         2.71   0.70701363   0.70701231 -1.9133063e-08 -0.099944419 -0.099944419 -0.099944419 
-   27110        2.711   0.70701391    0.7070126 -2.3380992e-08  -0.09994458  -0.09994458  -0.09994458 
-   27120        2.712   0.70701419   0.70701288 -2.737152e-08 -0.099944741 -0.099944741 -0.099944741 
-   27130        2.713   0.70701447   0.70701317 -3.1013653e-08 -0.099944901 -0.099944901 -0.099944901 
-   27140        2.714   0.70701475   0.70701345 -3.4224685e-08  -0.09994506  -0.09994506  -0.09994506 
-   27150        2.715   0.70701503   0.70701373 -3.6932076e-08 -0.099945219 -0.099945219 -0.099945219 
-   27160        2.716   0.70701531   0.70701402 -3.9075088e-08 -0.099945378 -0.099945378 -0.099945378 
-   27170        2.717   0.70701558    0.7070143 -4.0606144e-08 -0.099945536 -0.099945536 -0.099945536 
-   27180        2.718   0.70701586   0.70701458 -4.149189e-08 -0.099945693 -0.099945693 -0.099945693 
-   27190        2.719   0.70701613   0.70701486 -4.171391e-08  -0.09994585  -0.09994585  -0.09994585 
-   27200         2.72   0.70701641   0.70701514 -4.1269108e-08 -0.099946007 -0.099946007 -0.099946007 
-   27210        2.721   0.70701668   0.70701542 -4.0169737e-08 -0.099946163 -0.099946163 -0.099946163 
-   27220        2.722   0.70701695    0.7070157 -3.8443063e-08 -0.099946319 -0.099946319 -0.099946319 
-   27230        2.723   0.70701723   0.70701597 -3.6130697e-08 -0.099946474 -0.099946474 -0.099946474 
-   27240        2.724    0.7070175   0.70701625 -3.3287594e-08 -0.099946629 -0.099946629 -0.099946629 
-   27250        2.725   0.70701777   0.70701653 -2.998075e-08 -0.099946783 -0.099946783 -0.099946783 
-   27260        2.726   0.70701804    0.7070168 -2.628762e-08 -0.099946937 -0.099946937 -0.099946937 
-   27270        2.727   0.70701831   0.70701707 -2.2294312e-08  -0.09994709  -0.09994709  -0.09994709 
-   27280        2.728   0.70701858   0.70701734 -1.8093574e-08 -0.099947243 -0.099947243 -0.099947243 
-   27290        2.729   0.70701885   0.70701761 -1.3782643e-08 -0.099947395 -0.099947395 -0.099947395 
-   27300         2.73   0.70701912   0.70701788 -9.4609994e-09 -0.099947547 -0.099947547 -0.099947547 
-   27310        2.731   0.70701938   0.70701815 -5.2280646e-09 -0.099947699 -0.099947699 -0.099947699 
-   27320        2.732   0.70701965   0.70701841 -1.1809204e-09  -0.09994785  -0.09994785  -0.09994785 
-   27330        2.733   0.70701992   0.70701868 2.5879185e-09    -0.099948    -0.099948    -0.099948 
-   27340        2.734   0.70702019   0.70701894 5.9926183e-09  -0.09994815  -0.09994815  -0.09994815 
-   27350        2.735   0.70702045    0.7070192 8.9559802e-09   -0.0999483   -0.0999483   -0.0999483 
-   27360        2.736   0.70702072   0.70701947 1.1411189e-08 -0.099948449 -0.099948449 -0.099948449 
-   27370        2.737   0.70702099   0.70701973 1.3303318e-08 -0.099948598 -0.099948598 -0.099948598 
-   27380        2.738   0.70702125   0.70701998 1.4590559e-08 -0.099948746 -0.099948746 -0.099948746 
-   27390        2.739   0.70702151   0.70702024 1.524514e-08 -0.099948894 -0.099948894 -0.099948894 
-   27400         2.74   0.70702178    0.7070205 1.5253923e-08 -0.099949041 -0.099949041 -0.099949041 
-   27410        2.741   0.70702204   0.70702076 1.4618664e-08 -0.099949188 -0.099949188 -0.099949188 
-   27420        2.742    0.7070223   0.70702101 1.3355924e-08 -0.099949335 -0.099949335 -0.099949335 
-   27430        2.743   0.70702256   0.70702127 1.1496647e-08 -0.099949481 -0.099949481 -0.099949481 
-   27440        2.744   0.70702282   0.70702152 9.0853996e-09 -0.099949626 -0.099949626 -0.099949626 
-   27450        2.745   0.70702308   0.70702178 6.1793106e-09 -0.099949771 -0.099949771 -0.099949771 
-   27460        2.746   0.70702334   0.70702203 2.8467151e-09 -0.099949916 -0.099949916 -0.099949916 
-   27470        2.747    0.7070236   0.70702229 -8.3444954e-10  -0.09995006  -0.09995006  -0.09995006 
-   27480        2.748   0.70702385   0.70702254 -4.7784655e-09 -0.099950204 -0.099950204 -0.099950204 
-   27490        2.749   0.70702411   0.70702279 -8.8938295e-09 -0.099950348 -0.099950348 -0.099950348 
-   27500         2.75   0.70702436   0.70702305 -1.3085375e-08 -0.099950491 -0.099950491 -0.099950491 
-   27510        2.751   0.70702461    0.7070233 -1.7256471e-08 -0.099950633 -0.099950633 -0.099950633 
-   27520        2.752   0.70702486   0.70702355 -2.131125e-08 -0.099950775 -0.099950775 -0.099950775 
-   27530        2.753   0.70702511    0.7070238 -2.5156811e-08 -0.099950917 -0.099950917 -0.099950917 
-   27540        2.754   0.70702536   0.70702405 -2.8705344e-08 -0.099951058 -0.099951058 -0.099951058 
-   27550        2.755   0.70702561    0.7070243 -3.187614e-08 -0.099951199 -0.099951199 -0.099951199 
-   27560        2.756   0.70702585   0.70702455 -3.4597417e-08 -0.099951339 -0.099951339 -0.099951339 
-   27570        2.757    0.7070261    0.7070248 -3.6807954e-08 -0.099951479 -0.099951479 -0.099951479 
-   27580        2.758   0.70702634   0.70702505 -3.8458458e-08 -0.099951619 -0.099951619 -0.099951619 
-   27590        2.759   0.70702658    0.7070253 -3.9512667e-08 -0.099951758 -0.099951758 -0.099951758 
-   27600         2.76   0.70702683   0.70702555 -3.9948144e-08 -0.099951897 -0.099951897 -0.099951897 
-   27610        2.761   0.70702707    0.7070258 -3.9756748e-08 -0.099952035 -0.099952035 -0.099952035 
-   27620        2.762   0.70702731   0.70702604 -3.8944781e-08 -0.099952173 -0.099952173 -0.099952173 
-   27630        2.763   0.70702755   0.70702629 -3.7532797e-08  -0.09995231  -0.09995231  -0.09995231 
-   27640        2.764   0.70702779   0.70702653 -3.5555091e-08 -0.099952447 -0.099952447 -0.099952447 
-   27650        2.765   0.70702803   0.70702678 -3.3058861e-08 -0.099952584 -0.099952584 -0.099952584 
-   27660        2.766   0.70702827   0.70702702 -3.010309e-08  -0.09995272  -0.09995272  -0.09995272 
-   27670        2.767    0.7070285   0.70702726 -2.6757149e-08 -0.099952856 -0.099952856 -0.099952856 
-   27680        2.768   0.70702874    0.7070275 -2.3099175e-08 -0.099952991 -0.099952991 -0.099952991 
-   27690        2.769   0.70702898   0.70702774 -1.9214242e-08 -0.099953126 -0.099953126 -0.099953126 
-   27700         2.77   0.70702922   0.70702798 -1.5192388e-08 -0.099953261 -0.099953261 -0.099953261 
-   27710        2.771   0.70702946   0.70702822 -1.1126526e-08 -0.099953395 -0.099953395 -0.099953395 
-   27720        2.772   0.70702969   0.70702845 -7.1102999e-09 -0.099953529 -0.099953529 -0.099953529 
-   27730        2.773   0.70702993   0.70702869 -3.235929e-09 -0.099953662 -0.099953662 -0.099953662 
-   27740        2.774   0.70703016   0.70702892 4.0791023e-10 -0.099953795 -0.099953795 -0.099953795 
-   27750        2.775    0.7070304   0.70702916 3.7381119e-09 -0.099953927 -0.099953927 -0.099953927 
-   27760        2.776   0.70703064   0.70702939 6.6790351e-09 -0.099954059 -0.099954059 -0.099954059 
-   27770        2.777   0.70703087   0.70702962 9.1642213e-09 -0.099954191 -0.099954191 -0.099954191 
-   27780        2.778   0.70703111   0.70702985 1.1137895e-08 -0.099954322 -0.099954322 -0.099954322 
-   27790        2.779   0.70703134   0.70703008 1.2556213e-08 -0.099954453 -0.099954453 -0.099954453 
-   27800         2.78   0.70703157    0.7070303 1.338824e-08 -0.099954584 -0.099954584 -0.099954584 
-   27810        2.781   0.70703181   0.70703053 1.3616615e-08 -0.099954714 -0.099954714 -0.099954714 
-   27820        2.782   0.70703204   0.70703076 1.3237917e-08 -0.099954844 -0.099954844 -0.099954844 
-   27830        2.783   0.70703227   0.70703098 1.2262695e-08 -0.099954973 -0.099954973 -0.099954973 
-   27840        2.784    0.7070325   0.70703121 1.0715186e-08 -0.099955102 -0.099955102 -0.099955102 
-   27850        2.785   0.70703273   0.70703143 8.6327161e-09 -0.099955231 -0.099955231 -0.099955231 
-   27860        2.786   0.70703296   0.70703166 6.0648015e-09 -0.099955359 -0.099955359 -0.099955359 
-   27870        2.787   0.70703319   0.70703188 3.0719735e-09 -0.099955487 -0.099955487 -0.099955487 
-   27880        2.788   0.70703341   0.70703211 -2.7564735e-10 -0.099955614 -0.099955614 -0.099955614 
-   27890        2.789   0.70703364   0.70703233 -3.8999933e-09 -0.099955741 -0.099955741 -0.099955741 
-   27900         2.79   0.70703386   0.70703255 -7.7168685e-09 -0.099955868 -0.099955868 -0.099955868 
-   27910        2.791   0.70703409   0.70703278 -1.1637904e-08 -0.099955994 -0.099955994 -0.099955994 
-   27920        2.792   0.70703431     0.707033 -1.5572604e-08  -0.09995612  -0.09995612  -0.09995612 
-   27930        2.793   0.70703453   0.70703322 -1.9430432e-08 -0.099956245 -0.099956245 -0.099956245 
-   27940        2.794   0.70703475   0.70703344 -2.3122893e-08  -0.09995637  -0.09995637  -0.09995637 
-   27950        2.795   0.70703497   0.70703366 -2.6565565e-08 -0.099956495 -0.099956495 -0.099956495 
-   27960        2.796   0.70703519   0.70703389 -2.9680026e-08 -0.099956619 -0.099956619 -0.099956619 
-   27970        2.797   0.70703541   0.70703411 -3.2395641e-08 -0.099956743 -0.099956743 -0.099956743 
-   27980        2.798   0.70703562   0.70703433 -3.465116e-08 -0.099956867 -0.099956867 -0.099956867 
-   27990        2.799   0.70703584   0.70703455 -3.6396105e-08  -0.09995699  -0.09995699  -0.09995699 
-   28000          2.8   0.70703605   0.70703477 -3.7591888e-08 -0.099957113 -0.099957113 -0.099957113 
-   28010        2.801   0.70703627   0.70703499 -3.8212674e-08 -0.099957235 -0.099957235 -0.099957235 
-   28020        2.802   0.70703648   0.70703521 -3.8245927e-08 -0.099957357 -0.099957357 -0.099957357 
-   28030        2.803   0.70703669   0.70703542 -3.7692663e-08 -0.099957479 -0.099957479 -0.099957479 
-   28040        2.804    0.7070369   0.70703564 -3.6567386e-08   -0.0999576   -0.0999576   -0.0999576 
-   28050        2.805   0.70703711   0.70703586 -3.4897709e-08 -0.099957721 -0.099957721 -0.099957721 
-   28060        2.806   0.70703733   0.70703607 -3.2723685e-08 -0.099957842 -0.099957842 -0.099957842 
-   28070        2.807   0.70703754   0.70703629 -3.0096843e-08 -0.099957962 -0.099957962 -0.099957962 
-   28080        2.808   0.70703775    0.7070365 -2.7078973e-08 -0.099958082 -0.099958082 -0.099958082 
-   28090        2.809   0.70703796   0.70703671 -2.374067e-08 -0.099958202 -0.099958202 -0.099958202 
-   28100         2.81   0.70703817   0.70703693 -2.0159683e-08 -0.099958321 -0.099958321 -0.099958321 
-   28110        2.811   0.70703838   0.70703714 -1.641911e-08  -0.09995844  -0.09995844  -0.09995844 
-   28120        2.812   0.70703858   0.70703735 -1.2605466e-08 -0.099958558 -0.099958558 -0.099958558 
-   28130        2.813   0.70703879   0.70703755 -8.8066839e-09 -0.099958676 -0.099958676 -0.099958676 
-   28140        2.814     0.707039   0.70703776 -5.1100898e-09 -0.099958794 -0.099958794 -0.099958794 
-   28150        2.815   0.70703921   0.70703797 -1.6003939e-09 -0.099958911 -0.099958911 -0.099958911 
-   28160        2.816   0.70703942   0.70703817 1.6422488e-09 -0.099959028 -0.099959028 -0.099959028 
-   28170        2.817   0.70703963   0.70703838 4.5440682e-09 -0.099959145 -0.099959145 -0.099959145 
-   28180        2.818   0.70703983   0.70703858 7.0393568e-09 -0.099959261 -0.099959261 -0.099959261 
-   28190        2.819   0.70704004   0.70703878 9.071956e-09 -0.099959377 -0.099959377 -0.099959377 
-   28200         2.82   0.70704025   0.70703899 1.0596519e-08 -0.099959493 -0.099959493 -0.099959493 
-   28210        2.821   0.70704046   0.70703919 1.1579522e-08 -0.099959608 -0.099959608 -0.099959608 
-   28220        2.822   0.70704066   0.70703939 1.1999998e-08 -0.099959723 -0.099959723 -0.099959723 
-   28230        2.823   0.70704087   0.70703959 1.184998e-08 -0.099959837 -0.099959837 -0.099959837 
-   28240        2.824   0.70704107   0.70703979 1.1134648e-08 -0.099959951 -0.099959951 -0.099959951 
-   28250        2.825   0.70704127   0.70703999 9.8721685e-09 -0.099960065 -0.099960065 -0.099960065 
-   28260        2.826   0.70704148   0.70704018 8.0932366e-09 -0.099960179 -0.099960179 -0.099960179 
-   28270        2.827   0.70704168   0.70704038 5.8403326e-09 -0.099960292 -0.099960292 -0.099960292 
-   28280        2.828   0.70704188   0.70704058 3.1667092e-09 -0.099960405 -0.099960405 -0.099960405 
-   28290        2.829   0.70704208   0.70704078 1.3513454e-10 -0.099960517 -0.099960517 -0.099960517 
-   28300         2.83   0.70704228   0.70704097 -3.183581e-09 -0.099960629 -0.099960629 -0.099960629 
-   28310        2.831   0.70704248   0.70704117 -6.7122374e-09 -0.099960741 -0.099960741 -0.099960741 
-   28320        2.832   0.70704268   0.70704137 -1.036904e-08 -0.099960853 -0.099960853 -0.099960853 
-   28330        2.833   0.70704287   0.70704156 -1.4069495e-08 -0.099960964 -0.099960964 -0.099960964 
-   28340        2.834   0.70704307   0.70704176 -1.7728359e-08 -0.099961074 -0.099961074 -0.099961074 
-   28350        2.835   0.70704326   0.70704196 -2.1261607e-08 -0.099961185 -0.099961185 -0.099961185 
-   28360        2.836   0.70704346   0.70704215 -2.4588354e-08 -0.099961295 -0.099961295 -0.099961295 
-   28370        2.837   0.70704365   0.70704235 -2.7632713e-08 -0.099961405 -0.099961405 -0.099961405 
-   28380        2.838   0.70704384   0.70704254 -3.0325519e-08 -0.099961514 -0.099961514 -0.099961514 
-   28390        2.839   0.70704403   0.70704274 -3.2605904e-08 -0.099961623 -0.099961623 -0.099961623 
-   28400         2.84   0.70704422   0.70704293 -3.442267e-08 -0.099961732 -0.099961732 -0.099961732 
-   28410        2.841   0.70704441   0.70704313 -3.5735436e-08 -0.099961841 -0.099961841 -0.099961841 
-   28420        2.842    0.7070446   0.70704332 -3.6515538e-08 -0.099961949 -0.099961949 -0.099961949 
-   28430        2.843   0.70704479   0.70704351 -3.6746647e-08 -0.099962056 -0.099962056 -0.099962056 
-   28440        2.844   0.70704498   0.70704371 -3.6425114e-08 -0.099962164 -0.099962164 -0.099962164 
-   28450        2.845   0.70704516    0.7070439 -3.5560007e-08 -0.099962271 -0.099962271 -0.099962271 
-   28460        2.846   0.70704535   0.70704409 -3.4172873e-08 -0.099962378 -0.099962378 -0.099962378 
-   28470        2.847   0.70704553   0.70704428 -3.2297198e-08 -0.099962484 -0.099962484 -0.099962484 
-   28480        2.848   0.70704572   0.70704447 -2.9977604e-08  -0.09996259  -0.09996259  -0.09996259 
-   28490        2.849   0.70704591   0.70704466 -2.7268788e-08 -0.099962696 -0.099962696 -0.099962696 
-   28500         2.85   0.70704609   0.70704485 -2.4234231e-08 -0.099962802 -0.099962802 -0.099962802 
-   28510        2.851   0.70704628   0.70704503 -2.0944717e-08 -0.099962907 -0.099962907 -0.099962907 
-   28520        2.852   0.70704646   0.70704522 -1.7476677e-08 -0.099963012 -0.099963012 -0.099963012 
-   28530        2.853   0.70704665    0.7070454 -1.3910418e-08 -0.099963117 -0.099963117 -0.099963117 
-   28540        2.854   0.70704683   0.70704559 -1.0328262e-08 -0.099963221 -0.099963221 -0.099963221 
-   28550        2.855   0.70704701   0.70704577 -6.8126461e-09 -0.099963325 -0.099963325 -0.099963325 
-   28560        2.856    0.7070472   0.70704595 -3.4442292e-09 -0.099963428 -0.099963428 -0.099963428 
-   28570        2.857   0.70704738   0.70704614 -3.0003878e-10 -0.099963532 -0.099963532 -0.099963532 
-   28580        2.858   0.70704757   0.70704632 2.5482883e-09 -0.099963635 -0.099963635 -0.099963635 
-   28590        2.859   0.70704775    0.7070465 5.036137e-09 -0.099963737 -0.099963737 -0.099963737 
-   28600         2.86   0.70704793   0.70704667 7.1073792e-09  -0.09996384  -0.09996384  -0.09996384 
-   28610        2.861   0.70704811   0.70704685 8.715639e-09 -0.099963942 -0.099963942 -0.099963942 
-   28620        2.862    0.7070483   0.70704703 9.8253296e-09 -0.099964043 -0.099964043 -0.099964043 
-   28630        2.863   0.70704848   0.70704721 1.0412439e-08 -0.099964145 -0.099964145 -0.099964145 
-   28640        2.864   0.70704866   0.70704738 1.0465049e-08 -0.099964246 -0.099964246 -0.099964246 
-   28650        2.865   0.70704884   0.70704756 9.9835685e-09 -0.099964347 -0.099964347 -0.099964347 
-   28660        2.866   0.70704902   0.70704773 8.9806913e-09 -0.099964447 -0.099964447 -0.099964447 
-   28670        2.867    0.7070492   0.70704791 7.4810643e-09 -0.099964548 -0.099964548 -0.099964548 
-   28680        2.868   0.70704938   0.70704808 5.5206852e-09 -0.099964647 -0.099964647 -0.099964647 
-   28690        2.869   0.70704956   0.70704826 3.1460399e-09 -0.099964747 -0.099964747 -0.099964747 
-   28700         2.87   0.70704973   0.70704843 4.1300166e-10 -0.099964846 -0.099964846 -0.099964846 
-   28710        2.871   0.70704991   0.70704861 -2.6144825e-09 -0.099964945 -0.099964945 -0.099964945 
-   28720        2.872   0.70705009   0.70704878 -5.8658871e-09 -0.099965044 -0.099965044 -0.099965044 
-   28730        2.873   0.70705026   0.70704895 -9.2657502e-09 -0.099965142 -0.099965142 -0.099965142 
-   28740        2.874   0.70705043   0.70704913 -1.2735424e-08 -0.099965241 -0.099965241 -0.099965241 
-   28750        2.875   0.70705061    0.7070493 -1.6194893e-08 -0.099965338 -0.099965338 -0.099965338 
-   28760        2.876   0.70705078   0.70704947 -1.956462e-08 -0.099965436 -0.099965436 -0.099965436 
-   28770        2.877   0.70705095   0.70704964 -2.2767372e-08 -0.099965533 -0.099965533 -0.099965533 
-   28780        2.878   0.70705112   0.70704982 -2.572999e-08  -0.09996563  -0.09996563  -0.09996563 
-   28790        2.879   0.70705129   0.70704999 -2.8385063e-08 -0.099965727 -0.099965727 -0.099965727 
-   28800         2.88   0.70705146   0.70705016 -3.0672454e-08 -0.099965823 -0.099965823 -0.099965823 
-   28810        2.881   0.70705162   0.70705033 -3.2540668e-08 -0.099965919 -0.099965919 -0.099965919 
-   28820        2.882   0.70705179   0.70705051 -3.3948006e-08 -0.099966015 -0.099966015 -0.099966015 
-   28830        2.883   0.70705196   0.70705068 -3.4863495e-08  -0.09996611  -0.09996611  -0.09996611 
-   28840        2.884   0.70705212   0.70705085 -3.5267571e-08 -0.099966205 -0.099966205 -0.099966205 
-   28850        2.885   0.70705229   0.70705102 -3.515249e-08   -0.0999663   -0.0999663   -0.0999663 
-   28860        2.886   0.70705245   0.70705119 -3.4522473e-08 -0.099966395 -0.099966395 -0.099966395 
-   28870        2.887   0.70705262   0.70705136 -3.3393572e-08 -0.099966489 -0.099966489 -0.099966489 
-   28880        2.888   0.70705278   0.70705152 -3.1793265e-08 -0.099966583 -0.099966583 -0.099966583 
-   28890        2.889   0.70705295   0.70705169 -2.9759789e-08 -0.099966677 -0.099966677 -0.099966677 
-   28900         2.89   0.70705311   0.70705186 -2.7341227e-08  -0.09996677  -0.09996677  -0.09996677 
-   28910        2.891   0.70705327   0.70705202 -2.4594376e-08 -0.099966863 -0.099966863 -0.099966863 
-   28920        2.892   0.70705344   0.70705219 -2.158341e-08 -0.099966956 -0.099966956 -0.099966956 
-   28930        2.893    0.7070536   0.70705235 -1.8378384e-08 -0.099967049 -0.099967049 -0.099967049 
-   28940        2.894   0.70705376   0.70705252 -1.5053602e-08 -0.099967141 -0.099967141 -0.099967141 
-   28950        2.895   0.70705392   0.70705268 -1.1685901e-08 -0.099967233 -0.099967233 -0.099967233 
-   28960        2.896   0.70705409   0.70705284 -8.3528678e-09 -0.099967325 -0.099967325 -0.099967325 
-   28970        2.897   0.70705425     0.707053 -5.1310606e-09 -0.099967417 -0.099967417 -0.099967417 
-   28980        2.898   0.70705441   0.70705316 -2.094245e-09 -0.099967508 -0.099967508 -0.099967508 
-   28990        2.899   0.70705457   0.70705332 6.8829132e-10 -0.099967599 -0.099967599 -0.099967599 
-   29000          2.9   0.70705474   0.70705348 3.1533193e-09 -0.099967689 -0.099967689 -0.099967689 
-   29010        2.901    0.7070549   0.70705364 5.2451044e-09  -0.09996778  -0.09996778  -0.09996778 
-   29020        2.902   0.70705506    0.7070538 6.916666e-09  -0.09996787  -0.09996787  -0.09996787 
-   29030        2.903   0.70705522   0.70705395 8.1308311e-09  -0.09996796  -0.09996796  -0.09996796 
-   29040        2.904   0.70705538   0.70705411 8.8610599e-09 -0.099968049 -0.099968049 -0.099968049 
-   29050        2.905   0.70705554   0.70705427 9.0920237e-09 -0.099968139 -0.099968139 -0.099968139 
-   29060        2.906    0.7070557   0.70705442 8.8199241e-09 -0.099968228 -0.099968228 -0.099968228 
-   29070        2.907   0.70705586   0.70705458 8.0525445e-09 -0.099968316 -0.099968316 -0.099968316 
-   29080        2.908   0.70705602   0.70705473 6.8090367e-09 -0.099968405 -0.099968405 -0.099968405 
-   29090        2.909   0.70705618   0.70705488 5.1194459e-09 -0.099968493 -0.099968493 -0.099968493 
-   29100         2.91   0.70705633   0.70705504 3.0239861e-09 -0.099968581 -0.099968581 -0.099968581 
-   29110        2.911   0.70705649   0.70705519 5.720847e-10 -0.099968669 -0.099968669 -0.099968669 
-   29120        2.912   0.70705665   0.70705534 -2.1787821e-09 -0.099968756 -0.099968756 -0.099968756 
-   29130        2.913    0.7070568    0.7070555 -5.1644361e-09 -0.099968843 -0.099968843 -0.099968843 
-   29140        2.914   0.70705695   0.70705565 -8.3154934e-09  -0.09996893  -0.09996893  -0.09996893 
-   29150        2.915   0.70705711    0.7070558 -1.1558976e-08 -0.099969017 -0.099969017 -0.099969017 
-   29160        2.916   0.70705726   0.70705596 -1.4820001e-08 -0.099969103 -0.099969103 -0.099969103 
-   29170        2.917   0.70705741   0.70705611 -1.802351e-08 -0.099969189 -0.099969189 -0.099969189 
-   29180        2.918   0.70705756   0.70705626 -2.1095993e-08 -0.099969275 -0.099969275 -0.099969275 
-   29190        2.919   0.70705771   0.70705641 -2.396718e-08  -0.09996936  -0.09996936  -0.09996936 
-   29200         2.92   0.70705786   0.70705657 -2.657164e-08 -0.099969446 -0.099969446 -0.099969446 
-   29210        2.921   0.70705801   0.70705672 -2.8850278e-08 -0.099969531 -0.099969531 -0.099969531 
-   29220        2.922   0.70705816   0.70705687 -3.0751671e-08 -0.099969616 -0.099969616 -0.099969616 
-   29230        2.923   0.70705831   0.70705702 -3.223323e-08   -0.0999697   -0.0999697   -0.0999697 
-   29240        2.924   0.70705845   0.70705717 -3.326215e-08 -0.099969784 -0.099969784 -0.099969784 
-   29250        2.925    0.7070586   0.70705732 -3.3816138e-08 -0.099969868 -0.099969868 -0.099969868 
-   29260        2.926   0.70705875   0.70705747 -3.3883892e-08 -0.099969952 -0.099969952 -0.099969952 
-   29270        2.927   0.70705889   0.70705762 -3.3465328e-08 -0.099970036 -0.099970036 -0.099970036 
-   29280        2.928   0.70705904   0.70705777 -3.2571548e-08 -0.099970119 -0.099970119 -0.099970119 
-   29290        2.929   0.70705918   0.70705792 -3.1224549e-08 -0.099970202 -0.099970202 -0.099970202 
-   29300         2.93   0.70705933   0.70705807 -2.945669e-08 -0.099970285 -0.099970285 -0.099970285 
-   29310        2.931   0.70705947   0.70705822 -2.7309908e-08 -0.099970367 -0.099970367 -0.099970367 
-   29320        2.932   0.70705961   0.70705836 -2.4834729e-08  -0.09997045  -0.09997045  -0.09997045 
-   29330        2.933   0.70705976   0.70705851 -2.2089082e-08 -0.099970532 -0.099970532 -0.099970532 
-   29340        2.934    0.7070599   0.70705866 -1.9136938e-08 -0.099970613 -0.099970613 -0.099970613 
-   29350        2.935   0.70706005    0.7070588 -1.6046826e-08 -0.099970695 -0.099970695 -0.099970695 
-   29360        2.936   0.70706019   0.70705894 -1.2890239e-08 -0.099970776 -0.099970776 -0.099970776 
-   29370        2.937   0.70706033   0.70705909 -9.7399839e-09 -0.099970857 -0.099970857 -0.099970857 
-   29380        2.938   0.70706048   0.70705923  -6.6685e-09 -0.099970938 -0.099970938 -0.099970938 
-   29390        2.939   0.70706062   0.70705937 -3.7461955e-09 -0.099971018 -0.099971018 -0.099971018 
-   29400         2.94   0.70706076   0.70705951 -1.039834e-09 -0.099971099 -0.099971099 -0.099971099 
-   29410        2.941    0.7070609   0.70705965 1.3889902e-09 -0.099971179 -0.099971179 -0.099971179 
-   29420        2.942   0.70706105   0.70705979 3.4852534e-09 -0.099971258 -0.099971258 -0.099971258 
-   29430        2.943   0.70706119   0.70705993 5.2017475e-09 -0.099971338 -0.099971338 -0.099971338 
-   29440        2.944   0.70706133   0.70706007 6.5001432e-09 -0.099971417 -0.099971417 -0.099971417 
-   29450        2.945   0.70706147   0.70706021 7.3518435e-09 -0.099971496 -0.099971496 -0.099971496 
-   29460        2.946   0.70706162   0.70706034 7.7386129e-09 -0.099971575 -0.099971575 -0.099971575 
-   29470        2.947   0.70706176   0.70706048 7.652965e-09 -0.099971654 -0.099971654 -0.099971654 
-   29480        2.948    0.7070619   0.70706062 7.0983021e-09 -0.099971732 -0.099971732 -0.099971732 
-   29490        2.949   0.70706204   0.70706075 6.0888041e-09  -0.09997181  -0.09997181  -0.09997181 
-   29500         2.95   0.70706218   0.70706089 4.6490695e-09 -0.099971888 -0.099971888 -0.099971888 
-   29510        2.951   0.70706232   0.70706102 2.8135184e-09 -0.099971966 -0.099971966 -0.099971966 
-   29520        2.952   0.70706245   0.70706116 6.2557025e-10 -0.099972043 -0.099972043 -0.099972043 
-   29530        2.953   0.70706259   0.70706129 -1.8633811e-09  -0.09997212  -0.09997212  -0.09997212 
-   29540        2.954   0.70706273   0.70706143 -4.5951746e-09 -0.099972197 -0.099972197 -0.099972197 
-   29550        2.955   0.70706287   0.70706156 -7.5062397e-09 -0.099972274 -0.099972274 -0.099972274 
-   29560        2.956     0.707063    0.7070617 -1.0529075e-08 -0.099972351 -0.099972351 -0.099972351 
-   29570        2.957   0.70706314   0.70706183 -1.3593813e-08 -0.099972427 -0.099972427 -0.099972427 
-   29580        2.958   0.70706327   0.70706197 -1.6629835e-08 -0.099972503 -0.099972503 -0.099972503 
-   29590        2.959    0.7070634    0.7070621 -1.9567396e-08 -0.099972579 -0.099972579 -0.099972579 
-   29600         2.96   0.70706354   0.70706224 -2.2339227e-08 -0.099972654 -0.099972654 -0.099972654 
-   29610        2.961   0.70706367   0.70706237 -2.4882075e-08 -0.099972729 -0.099972729 -0.099972729 
-   29620        2.962    0.7070638   0.70706251 -2.7138147e-08 -0.099972805 -0.099972805 -0.099972805 
-   29630        2.963   0.70706393   0.70706264 -2.9056419e-08 -0.099972879 -0.099972879 -0.099972879 
-   29640        2.964   0.70706406   0.70706277 -3.0593794e-08 -0.099972954 -0.099972954 -0.099972954 
-   29650        2.965   0.70706419   0.70706291 -3.1716065e-08 -0.099973028 -0.099973028 -0.099973028 
-   29660        2.966   0.70706432   0.70706304 -3.2398677e-08 -0.099973103 -0.099973103 -0.099973103 
-   29670        2.967   0.70706445   0.70706317 -3.2627263e-08 -0.099973177 -0.099973177 -0.099973177 
-   29680        2.968   0.70706458    0.7070633 -3.2397941e-08  -0.09997325  -0.09997325  -0.09997325 
-   29690        2.969    0.7070647   0.70706344 -3.1717375e-08 -0.099973324 -0.099973324 -0.099973324 
-   29700         2.97   0.70706483   0.70706357 -3.0602587e-08 -0.099973397 -0.099973397 -0.099973397 
-   29710        2.971   0.70706496    0.7070637 -2.9080536e-08  -0.09997347  -0.09997347  -0.09997347 
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-   29730        2.973   0.70706521   0.70706396 -2.4968041e-08 -0.099973616 -0.099973616 -0.099973616 
-   29740        2.974   0.70706534   0.70706409 -2.2474306e-08 -0.099973688 -0.099973688 -0.099973688 
-   29750        2.975   0.70706547   0.70706422 -1.9764448e-08  -0.09997376  -0.09997376  -0.09997376 
-   29760        2.976   0.70706559   0.70706435 -1.6901455e-08 -0.099973832 -0.099973832 -0.099973832 
-   29770        2.977   0.70706572   0.70706447 -1.3951642e-08 -0.099973904 -0.099973904 -0.099973904 
-   29780        2.978   0.70706585    0.7070646 -1.0983123e-08 -0.099973975 -0.099973975 -0.099973975 
-   29790        2.979   0.70706597   0.70706472 -8.0642345e-09 -0.099974047 -0.099974047 -0.099974047 
-   29800         2.98    0.7070661   0.70706485 -5.2619636e-09 -0.099974118 -0.099974118 -0.099974118 
-   29810        2.981   0.70706623   0.70706497 -2.6404129e-09 -0.099974189 -0.099974189 -0.099974189 
-   29820        2.982   0.70706635    0.7070651 -2.593337e-10 -0.099974259 -0.099974259 -0.099974259 
-   29830        2.983   0.70706648   0.70706522 1.8272352e-09  -0.09997433  -0.09997433  -0.09997433 
-   29840        2.984    0.7070666   0.70706534 3.5721929e-09   -0.0999744   -0.0999744   -0.0999744 
-   29850        2.985   0.70706673   0.70706547 4.9364389e-09  -0.09997447  -0.09997447  -0.09997447 
-   29860        2.986   0.70706685   0.70706559 5.889748e-09  -0.09997454  -0.09997454  -0.09997454 
-   29870        2.987   0.70706698   0.70706571 6.4114388e-09  -0.09997461  -0.09997461  -0.09997461 
-   29880        2.988    0.7070671   0.70706583 6.4908206e-09 -0.099974679 -0.099974679 -0.099974679 
-   29890        2.989   0.70706723   0.70706595 6.1274086e-09 -0.099974748 -0.099974748 -0.099974748 
-   29900         2.99   0.70706735   0.70706607 5.3309045e-09 -0.099974817 -0.099974817 -0.099974817 
-   29910        2.991   0.70706748   0.70706619 4.120942e-09 -0.099974886 -0.099974886 -0.099974886 
-   29920        2.992    0.7070676   0.70706631 2.5266059e-09 -0.099974954 -0.099974954 -0.099974954 
-   29930        2.993   0.70706772   0.70706643 5.8573349e-10 -0.099975023 -0.099975023 -0.099975023 
-   29940        2.994   0.70706784   0.70706655 -1.6559816e-09 -0.099975091 -0.099975091 -0.099975091 
-   29950        2.995   0.70706796   0.70706666 -4.1460645e-09 -0.099975159 -0.099975159 -0.099975159 
-   29960        2.996   0.70706808   0.70706678 -6.8264867e-09 -0.099975227 -0.099975227 -0.099975227 
-   29970        2.997    0.7070682    0.7070669 -9.6350175e-09 -0.099975294 -0.099975294 -0.099975294 
-   29980        2.998   0.70706832   0.70706702 -1.2506668e-08 -0.099975361 -0.099975361 -0.099975361 
-   29990        2.999   0.70706844   0.70706714 -1.5375195e-08 -0.099975428 -0.099975428 -0.099975428 
-   30000            3   0.70706856   0.70706726 -1.8174628e-08 -0.099975495 -0.099975495 -0.099975495 
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/res_llg.dat b/examples/SPIN/benchmark/benchmarck_damped_exchange/res_llg.dat
deleted file mode 100644
index 6150a7db80..0000000000
--- a/examples/SPIN/benchmark/benchmarck_damped_exchange/res_llg.dat
+++ /dev/null
@@ -1,30000 +0,0 @@
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-2.992 0.7070675960902895 0.707066283654185 -6.969975935820771e-09 -0.09997746298434619
-2.9921 0.7070676085754625 0.7070662953730658 -7.369717808236587e-09 -0.0999774698299009
-2.9922000000000004 0.7070676210525642 0.7070663070926658 -7.777582089647794e-09 -0.09997747667337648
-2.9923 0.7070676335215103 0.7070663188130728 -8.19347220452904e-09 -0.09997748351477365
-2.9924 0.7070676459822163 0.7070663305343727 -8.617289758497404e-09 -0.099977490354093
-2.9925 0.7070676584345996 0.7070663422566503 -9.048934550455467e-09 -0.09997749719133514
-2.9926000000000004 0.7070676708785786 0.7070663539799895 -9.488304609020504e-09 -0.0999775040265007
-2.9927 0.7070676833140725 0.7070663657044735 -9.935296212473799e-09 -0.09997751085959032
-2.9928000000000003 0.7070676957410023 0.707066377430184 -1.0389803906975248e-08 -0.0999775176906047
-2.9929 0.7070677081592891 0.7070663891572011 -1.0851720542125187e-08 -0.09997752451954436
-2.993 0.707067720568856 0.7070664008856042 -1.1320937287877947e-08 -0.09997753134640995
-2.9931000000000005 0.7070677329696273 0.7070664126154715 -1.1797343660996384e-08 -0.09997753817120211
-2.9932000000000003 0.7070677453615284 0.7070664243468804 -1.2280827555409546e-08 -0.0999775449939216
-2.9933 0.7070677577444853 0.7070664360799064 -1.2771275265197751e-08 -0.09997755181456891
-2.9934000000000003 0.7070677701184257 0.7070664478146238 -1.326857151191449e-08 -0.09997755863314466
-2.9935 0.707067782483279 0.7070664595511058 -1.3772599472341995e-08 -0.09997756544964953
-2.9936000000000003 0.7070677948389752 0.7070664712894246 -1.4283240805813141e-08 -0.09997757226408412
-2.9937000000000005 0.7070678071854463 0.7070664830296509 -1.4800375681099653e-08 -0.09997757907644911
-2.9938000000000002 0.7070678195226248 0.7070664947718539 -1.532388280503505e-08 -0.0999775858867451
-2.9939 0.7070678318504446 0.7070665065161015 -1.5853639450270213e-08 -0.09997759269497271
-2.994 0.7070678441688417 0.7070665182624605 -1.6389521486498415e-08 -0.09997759950113255
-2.9941000000000004 0.707067856477753 0.7070665300109965 -1.6931403404307765e-08 -0.09997760630522533
-2.9942 0.7070678687771165 0.7070665417617732 -1.7479158352911445e-08 -0.09997761310725156
-2.9943 0.7070678810668716 0.7070665535148534 -1.803265816183175e-08 -0.09997761990721192
-2.9944 0.7070678933469596 0.7070665652702982 -1.8591773373426157e-08 -0.09997762670510707
-2.9945 0.7070679056173229 0.7070665770281674 -1.915637327541339e-08 -0.09997763350093757
-2.9946 0.7070679178779053 0.7070665887885195 -1.9726325927327953e-08 -0.09997764029470411
-2.9947000000000004 0.707067930128652 0.7070666005514114 -2.0301498198684043e-08 -0.09997764708640729
-2.9948 0.7070679423695099 0.7070666123168985 -2.0881755788924872e-08 -0.09997765387604773
-2.9949 0.7070679546004267 0.7070666240850347 -2.1466963269056033e-08 -0.09997766066362604
-2.995 0.7070679668213526 0.707066635855873 -2.2056984106365307e-08 -0.0999776674491429
-2.9951000000000003 0.7070679790322385 0.7070666476294643 -2.2651680701285537e-08 -0.0999776742325989
-2.9952 0.7070679912330367 0.7070666594058583 -2.3250914416451246e-08 -0.09997768101399465
-2.9953000000000003 0.7070680034237018 0.7070666711851028 -2.385454560835734e-08 -0.09997768779333081
-2.9954 0.7070680156041891 0.707066682967245 -2.4462433663788308e-08 -0.099977694570608
-2.9955 0.7070680277744559 0.7070666947523294 -2.507443702757378e-08 -0.09997770134582688
-2.9956000000000005 0.7070680399344609 0.7070667065403998 -2.5690413239451426e-08 -0.09997770811898801
-2.9957000000000003 0.707068052084164 0.7070667183314983 -2.631021896355723e-08 -0.09997771489009204
-2.9958 0.7070680642235272 0.7070667301256649 -2.6933710027456786e-08 -0.09997772165913955
-2.9959000000000002 0.7070680763525139 0.7070667419229392 -2.7560741449033505e-08 -0.09997772842613128
-2.996 0.7070680884710888 0.7070667537233579 -2.8191167474435688e-08 -0.09997773519106778
-2.9961 0.7070681005792183 0.7070667655269569 -2.882484161125312e-08 -0.09997774195394965
-2.9962000000000004 0.7070681126768705 0.7070667773337705 -2.9461616660826292e-08 -0.0999777487147775
-2.9963 0.7070681247640149 0.7070667891438313 -3.010134475532611e-08 -0.099977755473552
-2.9964 0.7070681368406233 0.7070668009571701 -3.074387738876208e-08 -0.09997776223027383
-2.9965 0.707068148906668 0.7070668127738164 -3.138906545449571e-08 -0.0999777689849435
-2.9966000000000004 0.7070681609621237 0.7070668245937979 -3.2036759278850774e-08 -0.09997777573756168
-2.9967 0.7070681730069659 0.7070668364171409 -3.268680865298884e-08 -0.099977782488129
-2.9968000000000004 0.7070681850411729 0.7070668482438696 -3.333906287237426e-08 -0.09997778923664606
-2.9969 0.7070681970647239 0.707066860074007 -3.399337076734864e-08 -0.09997779598311349
-2.997 0.7070682090775997 0.7070668719075747 -3.464958074281266e-08 -0.09997780272753197
-2.9971000000000005 0.7070682210797827 0.707066883744592 -3.530754081010161e-08 -0.09997780946990202
-2.9972000000000003 0.7070682330712572 0.7070668955850772 -3.5967098622330385e-08 -0.09997781621022434
-2.9973 0.7070682450520094 0.7070669074290468 -3.662810150952163e-08 -0.09997782294849959
-2.9974000000000003 0.7070682570220264 0.7070669192765151 -3.7290396515685456e-08 -0.09997782968472832
-2.9975 0.7070682689812974 0.7070669311274951 -3.7953830433839174e-08 -0.09997783641891111
-2.9976000000000003 0.7070682809298132 0.7070669429819982 -3.8618249838316514e-08 -0.09997784315104866
-2.9977000000000005 0.7070682928675661 0.707066954840035 -3.928350112477469e-08 -0.09997784988114158
-2.9978000000000002 0.7070683047945503 0.7070669667016127 -3.994943054179889e-08 -0.09997785660919047
-2.9979 0.7070683167107616 0.7070669785667383 -4.0615884230367234e-08 -0.09997786333519597
-2.998 0.7070683286161972 0.7070669904354163 -4.1282708255455276e-08 -0.09997787005915867
-2.9981000000000004 0.7070683405108561 0.7070670023076497 -4.1949748644335436e-08 -0.09997787678107918
-2.9982 0.7070683523947392 0.7070670141834405 -4.261685141998398e-08 -0.09997788350095818
-2.9983 0.7070683642678489 0.7070670260627885 -4.3283862638919686e-08 -0.09997789021879627
-2.9984 0.7070683761301888 0.7070670379456915 -4.3950628424854754e-08 -0.09997789693459402
-2.9985 0.7070683879817645 0.7070670498321463 -4.461699500501559e-08 -0.09997790364835207
-2.9986 0.707068399822584 0.7070670617221477 -4.528280874460688e-08 -0.09997791036007109
-2.9987000000000004 0.7070684116526558 0.7070670736156892 -4.5947916185219446e-08 -0.09997791706975169
-2.9988 0.7070684234719904 0.7070670855127621 -4.661216407541831e-08 -0.09997792377739441
-2.9989 0.7070684352805999 0.7070670974133564 -4.7275399410126335e-08 -0.09997793048299992
-2.999 0.7070684470784985 0.7070671093174604 -4.793746946347554e-08 -0.09997793718656883
-2.9991000000000003 0.7070684588657018 0.7070671212250612 -4.859822182602235e-08 -0.09997794388810183
-2.9992 0.7070684706422268 0.7070671331361436 -4.925750443814103e-08 -0.0999779505875995
-2.9993000000000003 0.7070684824080922 0.7070671450506907 -4.9915165624067614e-08 -0.09997795728506242
-2.9994 0.7070684941633181 0.7070671569686846 -5.0571054130551726e-08 -0.09997796398049118
-2.9995 0.7070685059079269 0.7070671688901053 -5.122501915797318e-08 -0.09997797067388645
-2.9996000000000005 0.7070685176419423 0.7070671808149316 -5.187691039612065e-08 -0.09997797736524888
-2.9997000000000003 0.7070685293653893 0.7070671927431402 -5.252657805931982e-08 -0.09997798405457903
-2.9998 0.707068541078295 0.7070672046747066 -5.317387292156153e-08 -0.09997799074187752
-2.9999000000000002 0.7070685527806873 0.7070672166096044 -5.381864634675104e-08 -0.09997799742714493
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in b/examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in
index 37d1e3765a..ed8a5caeaf 100644
--- a/examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in
+++ b/examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in
@@ -15,7 +15,6 @@ create_atoms    1 box
 mass            1 1.0
 set             type 1 spin 2.0 1.0 0.0 0.0
 
-# defines a pair/style for neighbor list, but do not use it
 pair_style      spin/exchange 4.0
 pair_coeff      * * exchange 1.0 0.0 0.0 1.0
 
@@ -24,7 +23,7 @@ group bead      type 1
 variable        H equal 10.0
 variable        Kan equal 0.0
 variable        Temperature equal 0.0 
-variable        RUN equal 100000
+variable        Nsteps equal 500000
 
 fix             1 all nve/spin lattice no
 fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
@@ -45,4 +44,4 @@ thermo          100
 
 timestep	0.0001
 
-run             ${RUN}
+run             ${Nsteps}
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py b/examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py
index edaa4f22cc..e8a46f389a 100755
--- a/examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py
+++ b/examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py
@@ -17,7 +17,7 @@ Bext = np.array([0.0, 0.0, 1.0])
 Sn = 2.0                # spin norm (in # of muB)
 S = np.array([1.0, 0.0, 0.0])
 
-N=100000                # number of timesteps
+N=500000                # number of timesteps
 dt=0.1                  # timestep (fs)
 
 # Rodrigues rotation formula
@@ -46,6 +46,7 @@ for t in range (0,N):
   theta=dt*np.linalg.norm(wf)
   axis=wf/np.linalg.norm(wf)
   S = np.dot(rotation_matrix(axis, theta), S)
+  en = -hbar*gyro*Sn*Bnrm*np.dot(S,Bext)
   # print res. in ps for comparison with LAMMPS
-  print(t*dt/1000.0,S[0],S[1],S[2])
+  print(t*dt/1000.0,S[0],S[1],S[2],en)
 
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py b/examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py
index c15d6c0ff5..9c07f1cefa 100755
--- a/examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py
+++ b/examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py
@@ -15,25 +15,31 @@ if len(argv) != 3:
 lammps_file = sys.argv[1]
 llg_file = sys.argv[2]
 
-t_lmp,Sx_lmp,Sy_lmp,Sz_lmp = np.loadtxt(lammps_file, skiprows=0, usecols=(1,2,3,4),unpack=True)
-t_llg,Sx_llg,Sy_llg,Sz_llg = np.loadtxt(llg_file, skiprows=0, usecols=(0,1,2,3),unpack=True)
+t_lmp,Sx_lmp,Sy_lmp,Sz_lmp,en_lmp = np.loadtxt(lammps_file,
+        skiprows=0, usecols=(1,2,3,4,5),unpack=True)
+t_llg,Sx_llg,Sy_llg,Sz_llg,en_llg = np.loadtxt(llg_file, skiprows=0, usecols=(0,1,2,3,4),unpack=True)
 
 plt.figure()
-plt.subplot(311)
+plt.subplot(411)
 plt.ylabel('Sx')
 plt.plot(t_lmp, Sx_lmp, 'b-', label='LAMMPS')
 plt.plot(t_llg, Sx_llg, 'r--', label='LLG')
 
-plt.subplot(312)
+plt.subplot(412)
 plt.ylabel('Sy')
 plt.plot(t_lmp, Sy_lmp, 'b-', label='LAMMPS')
 plt.plot(t_llg, Sy_llg, 'r--', label='LLG')
 
-plt.subplot(313)
+plt.subplot(413)
 plt.ylabel('Sz')
 plt.plot(t_lmp, Sz_lmp, 'b-', label='LAMMPS')
 plt.plot(t_llg, Sz_llg, 'r--', label='LLG')
 
+plt.subplot(414)
+plt.ylabel('En (eV)')
+plt.plot(t_lmp, en_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, en_llg, 'r--', label='LLG')
+
 plt.xlabel('time (in ps)')
 plt.legend()
 plt.show()
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_exchange/bench-exchange-spin.template b/examples/SPIN/benchmark/benchmarck_langevin_exchange/bench-exchange-spin.template
deleted file mode 100644
index c4286e3597..0000000000
--- a/examples/SPIN/benchmark/benchmarck_langevin_exchange/bench-exchange-spin.template
+++ /dev/null
@@ -1,41 +0,0 @@
-#LAMMPS in.run 
- 
-units           metal
-atom_style      spin
-atom_modify     map array
-boundary        p p p
-
-lattice         sc 3.0
-region          box block 0.0 2.0 0.0 2.0 0.0 2.0
-create_box      1 box
-create_atoms    1 box
-
-mass            1 1.0
-set             type 1 spin 1.0 0.0 0.0 1.0
-
-# defines a pair/style for neighbor list, but do not use it
-pair_style      spin/exchange 3.1
-pair_coeff  	* * exchange 3.1 11.254 0.0 1.0
-
-variable        H equal 0.0
-variable        Kan equal 0.0
-variable        Temperature equal temperature
-variable        RUN equal 100000
-
-fix             1 all nve/spin lattice no
-fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
-fix             3 all langevin/spin ${Temperature} 0.01 12345
-
-thermo          500000
-thermo_style    custom step time temp vol 
-timestep        0.1
-
-compute         compute_spin all spin
-variable 	mag_energy equal c_compute_spin[5]
-variable 	AVEs equal c_compute_spin[4]
-
-fix 		avespin all ave/time 1 ${RUN} ${RUN} v_Temperature v_H v_Kan v_AVEs v_mag_energy file _av_spin
-
-run             ${RUN}
-
-shell           cat _av_spin
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_exchange/langevin-exchange.py b/examples/SPIN/benchmark/benchmarck_langevin_exchange/langevin-exchange.py
deleted file mode 100755
index d543f86cba..0000000000
--- a/examples/SPIN/benchmark/benchmarck_langevin_exchange/langevin-exchange.py
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env python3
-
-import numpy as np, pylab, tkinter
-import matplotlib.pyplot as plt
-import mpmath as mp
-
-mub=5.78901e-5          # Bohr magneton (eV/T)
-kb=8.617333262145e-5    # Boltzman constant (eV/K)
-J0=0.05                 # per-neighbor exchange interaction (eV)
-z=6                     # number of NN (bcc)
-g=2.0                   # Lande factor (adim)
-Hz=10.0                # mag. field (T)
-
-#Definition of the Langevin function
-def func(sm,t):
-    return mp.coth(z*J0*sm/(kb*t))-1.0/(z*J0*sm/(kb*t))
-
-npoints=200
-tolerance=1e-5
-ti=0.01
-tf=2000.0
-sz=1.0
-szg=0.5
-for i in range (0,npoints):
-    temp=ti+i*(tf-ti)/npoints
-    count=0
-    sz=1.0
-    szg=0.5
-    while (abs(sz-szg)) >= tolerance:
-        sz=szg
-        szg=func(sz,temp)
-        count+=1
-    emag=-z*J0*sz*sz
-    print('%d %lf %lf %lf %lf' % (temp,szg,sz,emag,count))
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_exchange/plot_exchange.py b/examples/SPIN/benchmark/benchmarck_langevin_exchange/plot_exchange.py
deleted file mode 100755
index 8fa6f55589..0000000000
--- a/examples/SPIN/benchmark/benchmarck_langevin_exchange/plot_exchange.py
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env python3
-
-import numpy as np, pylab, tkinter
-import matplotlib.pyplot as plt
-from scipy.optimize import curve_fit
-from decimal import *
-import sys, string, os
-
-
-argv = sys.argv
-if len(argv) != 3:
-  print("Syntax: ./plot_precession.py res_lammps.dat res_langevin.dat")
-  sys.exit()
-
-lammps_file = sys.argv[1]
-langevin_file = sys.argv[2]
-
-T_lmp,S_lmp,E_lmp = np.loadtxt(lammps_file, skiprows=0, usecols=(0,2,3),unpack=True)
-T_lan,S_lan,E_lan = np.loadtxt(langevin_file, skiprows=0, usecols=(0,2,3),unpack=True)
-
-plt.figure()
-plt.subplot(211)
-plt.ylabel('<S>')
-plt.plot(T_lmp, S_lmp, 'b-', label='LAMMPS')
-plt.plot(T_lan, S_lan, 'r--', label='Langevin')
-
-plt.subplot(212)
-plt.ylabel('E (in eV)')
-plt.plot(T_lmp, E_lmp, 'b-', label='LAMMPS')
-plt.plot(T_lan, E_lan, 'r--', label='Langevin')
-
-plt.xlabel('T (in K)')
-plt.legend()
-plt.show()
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_exchange/run-bench-exchange.sh b/examples/SPIN/benchmark/benchmarck_langevin_exchange/run-bench-exchange.sh
deleted file mode 100755
index d631fdbc79..0000000000
--- a/examples/SPIN/benchmark/benchmarck_langevin_exchange/run-bench-exchange.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-
-# set initial and final temperature (K)
-tempi=0.0
-tempf=2000.0
-
-rm res_*.dat
-
-# run Lammps calculation
-N=20
-for (( i=0; i<$N; i++ ))
-do
-  temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)"
-  sed s/temperature/${temp}/g bench-exchange-spin.template > \
-    bench-exchange-spin.in
-  ../../../../src/lmp_serial \
-    -in bench-exchange-spin.in 
-  Hz="$(tail -n 1 _av_spin | awk -F " " '{print $3}')"
-  sm="$(tail -n 1 _av_spin | awk -F " " '{print $5}')"
-  en="$(tail -n 1 _av_spin | awk -F " " '{print $6}')"
-  echo $temp $Hz $sm $en >> res_lammps.dat
-done
-
-# run Langevin function calculation
-python3 -m langevin-exchange.py > res_langevin.dat
-
-# plot comparison
-python3 -m plot_exchange.py res_lammps.dat res_langevin.dat
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template b/examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template
index 6e79fe9d25..52f6a105ea 100644
--- a/examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template
+++ b/examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template
@@ -33,14 +33,14 @@ fix             3 all langevin/spin ${Temperature} 0.01 12345
 
 compute         compute_spin all spin
 compute         outsp all property/atom spx spy spz sp
-compute         AVEsz all reduce ave c_outsp[3]
+compute         magsz all reduce ave c_outsp[3]
 
 thermo          50000
 thermo_style    custom step time temp vol pe c_compute_spin[5] etotal  
 
 variable        magnetic_energy equal c_compute_spin[5]
 
-fix             avespin all ave/time 1 ${RUN} ${RUN} v_Temperature v_H v_Kan c_AVEsz v_magnetic_energy file _av_spin
+fix             avespin all ave/time 1 ${RUN} ${RUN} v_Temperature v_H v_Kan c_magsz v_magnetic_energy file average_spin
 
 timestep        0.1
 run             ${RUN}
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh b/examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh
index ecbe7d2eff..98fceeca95 100755
--- a/examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh
+++ b/examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh
@@ -14,9 +14,9 @@ do
     bench-prec-spin.in
   ./../../../../src/lmp_serial \
     -in bench-prec-spin.in 
-  Hz="$(tail -n 1 _av_spin | awk -F " " '{print $3}')"
-  sz="$(tail -n 1 _av_spin | awk -F " " '{print $5}')"
-  en="$(tail -n 1 _av_spin | awk -F " " '{print $6}')"
+  Hz="$(tail -n 1 average_spin | awk -F " " '{print $3}')"
+  sz="$(tail -n 1 average_spin | awk -F " " '{print $5}')"
+  en="$(tail -n 1 average_spin | awk -F " " '{print $6}')"
   echo $temp $Hz $sz $en >> res_lammps.dat
 done
 
diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index 7d7fb56e1c..7ee2b5bcfc 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -104,7 +104,6 @@ void ComputeSpin::compute_vector()
         mag[0] += sp[i][0];
         mag[1] += sp[i][1];
         mag[2] += sp[i][2];
-        // magenergy -= 2.0*(sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
         magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
         tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1];
         ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2];
@@ -129,7 +128,6 @@ void ComputeSpin::compute_vector()
   magtot[2] *= scale;
   magtot[3] = sqrt((magtot[0]*magtot[0])+(magtot[1]*magtot[1])+(magtot[2]*magtot[2]));
   spintemperature = hbar*tempnumtot;
-  // spintemperature /= (kb*tempdenomtot);
   spintemperature /= (2.0*kb*tempdenomtot);
 
   vector[0] = magtot[0];
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index 263118f5fb..93f8ef9d32 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -257,7 +257,6 @@ void FixPrecessionSpin::post_force(int /* vflag */)
 
       if (zeeman_flag) {          // compute Zeeman interaction
         compute_zeeman(i,fmi);
-        // epreci -= 2.0*hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
         epreci -= hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
       }
 
@@ -296,9 +295,6 @@ void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double f
 void FixPrecessionSpin::compute_zeeman(int i, double fmi[3])
 {
   double **sp = atom->sp;
-  // fmi[0] += 0.5*sp[i][3]*hx;
-  // fmi[1] += 0.5*sp[i][3]*hy;
-  // fmi[2] += 0.5*sp[i][3]*hz;
   fmi[0] += sp[i][3]*hx;
   fmi[1] += sp[i][3]*hy;
   fmi[2] += sp[i][3]*hz;
@@ -309,9 +305,9 @@ void FixPrecessionSpin::compute_zeeman(int i, double fmi[3])
 void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3])
 {
   double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2];
-  fmi[0] += 0.5*scalar*Kax;
-  fmi[1] += 0.5*scalar*Kay;
-  fmi[2] += 0.5*scalar*Kaz;
+  fmi[0] += scalar*Kax;
+  fmi[1] += scalar*Kay;
+  fmi[2] += scalar*Kaz;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -320,7 +316,7 @@ double FixPrecessionSpin::compute_anisotropy_energy(double spi[3])
 {
   double energy = 0.0;
   double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2];
-  energy = 2.0*Ka*scalar*scalar;
+  energy = Ka*scalar*scalar;
   return energy; 
 }
 
@@ -358,9 +354,9 @@ void FixPrecessionSpin::compute_cubic(double spi[3], double fmi[3])
   sixy = k2ch*(nc1y*six1 + nc2y*six2 + nc3y*six3);
   sixz = k2ch*(nc1z*six1 + nc2z*six2 + nc3z*six3);
   
-  fmi[0] += 0.5*(fourx + sixx);
-  fmi[1] += 0.5*(foury + sixy);
-  fmi[2] += 0.5*(fourz + sixz);
+  fmi[0] += (fourx + sixx);
+  fmi[1] += (foury + sixy);
+  fmi[2] += (fourz + sixz);
 }
 
 /* ----------------------------------------------------------------------
@@ -379,7 +375,7 @@ double FixPrecessionSpin::compute_cubic_energy(double spi[3])
   energy = k1c*(skx*skx*sky*sky + sky*sky*skz*skz + skx*skx*skz*skz);
   energy += k2c*skx*skx*sky*sky*skz*skz;
 
-  return 2.0*energy;
+  return energy;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index d547de6995..2aa8b99f32 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -242,7 +242,6 @@ void PairSpinExchange::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        // evdwl *= 0.5*hbar;
         evdwl *= hbar;
       } else evdwl = 0.0;
 
@@ -352,11 +351,6 @@ void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3],
   Jex *= (1.0-J2[itype][jtype]*ra);
   Jex *= exp(-ra);
 
-  // printf("Exchange : %g %g \n",Jex,Jex*hbar);
-
-  // fmi[0] += 2.0*Jex*spj[0];
-  // fmi[1] += 2.0*Jex*spj[1];
-  // fmi[2] += 2.0*Jex*spj[2];
   fmi[0] += Jex*spj[0];
   fmi[1] += Jex*spj[1];
   fmi[2] += Jex*spj[2];

From 31ac2f3bd13ccc510c21e72b9620be8ebc976679 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Fri, 15 Nov 2019 11:42:04 -0700
Subject: [PATCH 031/199] Commit2 JT 151119 - adding doc exceptions to
 false-positives

---
 doc/utils/sphinx-config/false_positives.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 5b3020c7d1..8bc437bd48 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -212,6 +212,7 @@ Berne
 Bertotti
 Bessarab
 Beutler
+Bext
 bgq
 Bh
 Biersack
@@ -1041,6 +1042,7 @@ Gunsteren
 Gunzenmuller
 Guo
 gw
+gyromagnetic
 gz
 gzipped
 Haak
@@ -1060,6 +1062,7 @@ Haswell
 Haugk
 Hayoun
 Hayre
+hbar
 hbcut
 hbn
 hbnewflag
@@ -1401,6 +1404,7 @@ Lammps
 LAMMPS
 lammpsplot
 Lamoureux
+Lande
 Landron
 langevin
 Langevin
@@ -1772,6 +1776,7 @@ mtk
 Mtotal
 muB
 Muccioli
+mui
 Mukherjee
 Mulders
 multi

From f4491011d0d12733d6763b0dfa2c5ee4edb26695 Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 18:54:37 +0000
Subject: [PATCH 032/199] Modified README

---
 examples/USER/cgdna/README | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README
index 7cbf76fd5a..49b7cd1f84 100644
--- a/examples/USER/cgdna/README
+++ b/examples/USER/cgdna/README
@@ -1,6 +1,6 @@
 This directory contains example data and input files 
 as well as utility scripts for the oxDNA/oxDNA2/oxRNA2 
-coarse-grained model for DNA and RNA.
+coarse-grained model of DNA and RNA.
 
 /******************************************************************************/
 
@@ -40,15 +40,14 @@ are sequence-averaged (cf. keyword 'seqav' in according pair styles).
 
 /examples/oxDNA2/duplex3:
 
-This is the duplex1 run with sequence-dependent stacking and
-hydrogen-bonding strengths enabled and both nucleotide mass and 
-moment of inertia set to the value of the standalone implementation 
-of oxDNA (M = I = 1). To achieve this, the masses can be set directly 
-in the input and data file, whereas the moment of inertia is set via 
-the diameter of the ellipsoid in the data file and has a value of 3.16227766.
+This example uses the duplex1 with sequence-dependent stacking and
+hydrogen-bonding interactions and both nucleotide mass and 
+moment of inertia set to the value used in the standalone implementation 
+of oxDNA (M = I = 1). The masses can be set directly in the input and 
+data file, whereas the moment of inertia is set via the diameter of the 
+ellipsoid in the data file and has a value of 3.16227766.
 The change of mass and moment of inertia allows direct comparision of 
-e.g. trajectory data, energies or time-dependent observables on a per-timestep 
-basis until numerical noise causes deviations at later simulation times. 
+trajectory data or time-dependent observables on a per-timestep basis. 
 
 As mentioned above, the stacking and hydrogen-bonding interactions 
 are sequence-dependent (cf. keyword 'seqdep' in according pair styles).
@@ -60,8 +59,6 @@ are sequence-dependent (cf. keyword 'seqdep' in according pair styles).
 This example uses atom types 1-8 to model a 13 base pair duplex.
 The nucleotide types are assigned as follows:
 A = 1,5; C = 2,6; G = 3,7; T = 4,8
-When a large number of atom types is used, this feature allows
-quasi-unique base pairing between two individual nucleotides.
 
 The topology is
 A   C   G   T   A   C   G   T   A   C   G   T   A
@@ -70,13 +67,16 @@ A   C   G   T   A   C   G   T   A   C   G   T   A
 4 - 3 - 2 - 1 - 8 - 7 - 6 - 5 - 4 - 3 - 6 - 5 - 4
 T   G   C   A   T   G   C   A   T   G   C   A   T
 
+With a large (32 or 64) number of atom types quasi-unique base pairing 
+between two individual nucleotides can be established.
+
 /******************************************************************************/
 
 /examples/oxRNA2/duplex4
 
-This is the duplex2 run with the oxRNA2 force field instead of the oxDNA or 
-oxDNA2 force field  and sequence-dependent stacking and hydrogen-bonding 
-strengths enabled.
+This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or 
+oxDNA2 force field. Sequence-dependent stacking and hydrogen-bonding 
+strengths enabled (cf. keyword 'seqdep' in according pair styles).
 
 /******************************************************************************/
 

From 5ddac24161943cc04ac1a6a1ffb68d3a541d56b8 Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 19:27:48 +0000
Subject: [PATCH 033/199] Modified README

---
 src/USER-CGDNA/{README => README.md} | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)
 rename src/USER-CGDNA/{README => README.md} (95%)

diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README.md
similarity index 95%
rename from src/USER-CGDNA/README
rename to src/USER-CGDNA/README.md
index a57168e53e..138638525e 100644
--- a/src/USER-CGDNA/README
+++ b/src/USER-CGDNA/README.md
@@ -2,7 +2,11 @@ This package contains a LAMMPS implementation of coarse-grained
 models of DNA, which can be used to model sequence-specific
 DNA strands.
 
-Please cite [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles 
+Please cite 
+
+[![DOI](https://zenodo.org/badge/132764768.svg)](https://zenodo.org/badge/latestdoi/132764768)
+
+as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles 
 in any publication that uses this package.
 
 See the doc pages and [2,3,4,5,6] for the individual bond and pair styles. 

From 2c2b7cf20bd85a315e175534354cbb507573541f Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 21:19:33 +0000
Subject: [PATCH 034/199] Corrected linking error

---
 doc/src/pair_oxrna2.rst | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst
index 469851eb5a..c9d8314682 100644
--- a/doc/src/pair_oxrna2.rst
+++ b/doc/src/pair_oxrna2.rst
@@ -75,7 +75,7 @@ excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-
 and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh*
 as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on
 opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported :ref:`(Sulc) <Sulc2>`. Quasi-unique base-pairing between nucleotides can be achieved by using 
+are supported :ref:`(Sulc2) <Sulc32>`. Quasi-unique base-pairing between nucleotides can be achieved by using 
 more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
 This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
 up and down along the backbone.
@@ -84,8 +84,8 @@ The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,
 which themselves are constructed from a number of more basic potentials
 (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
-and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
+We refer to :ref:`(Sulc1) <Sulc31>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil3>`
+and  :ref:`(Ouldridge) <Ouldridge3>` for a detailed description of the oxRNA2 force field.
 
 .. note::
 
@@ -103,7 +103,7 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
+Please cite :ref:`(Henrich) <Henrich3>` in any publication that uses
 this implementation.  The article contains general information
 on the model, its implementation and performance as well as the structure of
 the data and input file. The preprint version of the article can be found
@@ -147,6 +147,14 @@ Related commands
 
 **(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
 
+.. _Ouldridge-DPhil3:
+
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+.. _Ouldridge3:
+
+**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+
 
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html

From 2d6e84edd74bcf23ce569d04a37561eb1c0f6204 Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 21:45:33 +0000
Subject: [PATCH 035/199] Fixed anchor errors

---
 doc/src/bond_oxdna.rst            | 75 ++++++++++++-------------------
 doc/src/fix_nve_dot.rst           | 16 +++----
 doc/src/fix_nve_dotc_langevin.rst | 21 ++++-----
 doc/src/pair_oxdna.rst            | 45 ++++++++++---------
 doc/src/pair_oxdna2.rst           | 53 ++++++++++++----------
 5 files changed, 96 insertions(+), 114 deletions(-)

diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst
index 36370ddf30..51692f933b 100644
--- a/doc/src/bond_oxdna.rst
+++ b/doc/src/bond_oxdna.rst
@@ -6,9 +6,6 @@ bond\_style oxdna/fene command
 bond\_style oxdna2/fene command
 ===============================
 
-bond\_style oxrna2/fene command
-===============================
-
 Syntax
 """"""
 
@@ -19,8 +16,6 @@ Syntax
 
    bond_style oxdna2/fene
 
-   bond_style oxrna2/fene
-
 Examples
 """"""""
 
@@ -33,21 +28,18 @@ Examples
    bond_style oxdna2/fene
    bond_coeff \* 2.0 0.25 0.7564
 
-   bond_style oxrna2/fene
-   bond_coeff \* 2.0 0.25 0.76107
-
 Description
 """""""""""
 
-The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential
+The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
 
 .. image:: Eqs/bond_oxdna_fene.jpg
    :align: center
 
 to define a modified finite extensible nonlinear elastic (FENE)
-potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
-phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
-modelling of DNA/RNA.
+potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
+phosphate backbone in the oxDNA force field for coarse-grained
+modelling of DNA.
 
 The following coefficients must be defined for the bond type via the
 :doc:`bond\_coeff <bond_coeff>` command as given in the above example, or
@@ -63,36 +55,27 @@ commands:
 
    The oxDNA bond style has to be used together with the
    corresponding oxDNA pair styles for excluded volume interaction
-   *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
+   *oxdna/excv*\ , stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* and
    coaxial stacking interaction *oxdna/coaxstk* as well as
    hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
    :doc:`pair\_style oxdna/excv <pair_oxdna>`). For the oxDNA2
-   :ref:`(Snodin) <Snodin0>` bond style the analogous pair styles 
-   *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
-   *oxdna2/hbond* and an additional Debye-Hueckel pair style 
-   *oxdna2/dh* have to be defined. The same applies to the oxRNA2
-   :ref:`(Sulc1) <Sulc01>` styles. 
+   :ref:`(Snodin) <oxdna2>` bond style the analogous pair styles and an
+   additional Debye-Hueckel pair style *oxdna2/dh* have to be defined.
    The coefficients in the above example have to be kept fixed and cannot
    be changed without reparameterizing the entire model.
 
-Example input and data files for DNA and RNA duplexes can be found in
-examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/.  A simple python
-setup tool which creates single straight or helical DNA strands, DNA/RNA
-duplexes or arrays of DNA/RNA duplexes can be found in
+Example input and data files for DNA duplexes can be found in
+examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.  A simple python
+setup tool which creates single straight or helical DNA strands, DNA
+duplexes or arrays of DNA duplexes can be found in
 examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses 
-this implementation.  The article contains general information 
-on the model, its implementation and performance as well as the structure of 
-the data and input file. The preprint version of the article can be found
+Please cite :ref:`(Henrich) <Henrich2>` and the relevant oxDNA articles in
+any publication that uses this implementation.  The article contains
+more information on the model, the structure of the input file, the
+setup tool and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found
 `here <PDF/USER-CGDNA.pdf>`_.
-Please cite also the relevant oxDNA/oxRNA publications. These are 
-:ref:`(Ouldridge) <Ouldridge0>` and 
-:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA, 
-:ref:`(Snodin) <Snodin0>` for oxDNA2, 
-:ref:`(Sulc1) <Sulc01>` for oxRNA2 
-and for sequence-specific hydrogen-bonding and stacking interactions 
-:ref:`(Sulc2) <Sulc02>`.
 
 
 ----------
@@ -109,37 +92,35 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`, 
-:doc:`bond\_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`,
+:doc:`bond\_coeff <bond_coeff>`
 
 **Default:** none
 
 
 ----------
 
-.. _Henrich0:
 
-**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+.. _Henrich2:
 
-.. _Ouldridge-DPhil0:
 
-**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
-.. _Ouldridge0:
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
+T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
-**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+.. _oxdna\_fene:
 
-.. _Snodin0:
 
-**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 
-.. _Sulc01:
+**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
+J. Chem. Phys. 134, 085101 (2011).
 
-**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
+.. _oxdna2:
 
-.. _Sulc02:
 
-**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
+**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
+J. Chem. Phys. 142, 234901 (2015).
 
 
 .. _lws: http://lammps.sandia.gov
diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst
index 33d9f61b49..5fc6a46ab5 100644
--- a/doc/src/fix_nve_dot.rst
+++ b/doc/src/fix_nve_dot.rst
@@ -26,11 +26,11 @@ Examples
 Description
 """""""""""
 
-Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack1>`
+Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack4>`
 to a group of atoms, but without Langevin dynamics.
 This command performs Molecular dynamics (MD)
 via a velocity-Verlet algorithm and an evolution operator that rotates
-the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller1>`.
+the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller4>`.
 
 This command is the equivalent of the :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 without damping and noise and can be used to determine the stability range
@@ -40,7 +40,7 @@ The command is equivalent to the :doc:`fix nve <fix_nve>`.
 The particles are always considered to have a finite size.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
-Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich3>`.
+Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich4>`.
 The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
 
 
@@ -66,19 +66,15 @@ Related commands
 ----------
 
 
-.. _Davidchack1:
-
-
-
-.. _Miller1:
+.. _Davidchack4:
 
 **(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 
-
-.. _Henrich3:
+.. _Miller4:
 
 **(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 
+.. _Henrich4:
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst
index 408aaf919e..3143db968f 100644
--- a/doc/src/fix_nve_dotc_langevin.rst
+++ b/doc/src/fix_nve_dotc_langevin.rst
@@ -38,14 +38,14 @@ Description
 """""""""""
 
 Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
-as described in :ref:`(Davidchack) <Davidchack2>`
+as described in :ref:`(Davidchack) <Davidchack5>`
 to a group of atoms, which models an interaction with an implicit background
 solvent.  This command performs Brownian dynamics (BD)
 via a technique that splits the integration into a deterministic Hamiltonian
 part and the Ornstein-Uhlenbeck process for noise and damping.
 The quaternion degrees of freedom are updated though an evolution
 operator which performs a rotation in quaternion space, preserves
-the quaternion norm and is akin to :ref:`(Miller) <Miller2>`.
+the quaternion norm and is akin to :ref:`(Miller) <Miller5>`.
 
 In terms of syntax this command has been closely modelled on the
 :doc:`fix langevin <fix_langevin>` and its *angmom* option. But it combines
@@ -86,7 +86,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
 temperature, m is the mass of the particle, dt is the timestep size,
 and damp is the damping factor.  Random numbers are used to randomize
 the direction and magnitude of this force as described in
-:ref:`(Dunweg) <Dunweg3>`, where a uniform random number is used (instead of
+:ref:`(Dunweg) <Dunweg5>`, where a uniform random number is used (instead of
 a Gaussian random number) for speed.
 
 
@@ -128,7 +128,7 @@ The scale factor after the *angmom* keyword gives the ratio of the rotational to
 the translational friction coefficient.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich4>`.
+Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
 The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
 
 
@@ -154,24 +154,19 @@ Related commands
 ----------
 
 
-.. _Davidchack2:
-
-
-
-.. _Miller2:
+.. _Davidchack5:
 
 **(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 
-
-.. _Dunweg3:
+.. _Miller5:
 
 **(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 
-
-.. _Henrich4:
+.. _Dunweg5:
 
 **(Dunweg)** B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
 
+.. _Henrich5:
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst
index 727f19c327..b40cf1f6cc 100644
--- a/doc/src/pair_oxdna.rst
+++ b/doc/src/pair_oxdna.rst
@@ -36,8 +36,8 @@ Syntax
      *oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
        seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
        T = temperature (oxDNA units, 0.1 = 300 K)
-       xi = 1.3448 (temperature-independent coefficient in stacking strength)
-       kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
+       xi = temperature-independent coefficient in stacking strength
+       kappa = coefficient of linear temperature dependence in stacking strength
      *oxdna/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
        seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
        eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
@@ -94,15 +94,11 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
-this implementation.  The article contains general information
-on the model, its implementation and performance as well as the structure of
-the data and input file. The preprint version of the article can be found
-`here <PDF/USER-CGDNA.pdf>`_.
-Please cite also the relevant oxDNA publications
-:ref:`(Ouldridge) <Ouldridge1>`, 
-:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
-and :ref:`(Sulc) <Sulc1>`.
+Please cite :ref:`(Henrich) <Henrich1>` and the relevant oxDNA articles in any publication that uses this implementation.
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
+
 
 ----------
 
@@ -118,32 +114,39 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
-:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
-:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
- 
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`
+
 **Default:** none
 
 
 ----------
 
+
 .. _Henrich1:
 
+
+
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
+.. _Sulc1:
+
+
+
+**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 .. _Ouldridge-DPhil1:
 
-**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+
+**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
 .. _Ouldridge1:
 
+
+
 **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 
-.. _Sulc1:
-
-**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
 
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst
index 77052da666..4f64197f44 100644
--- a/doc/src/pair_oxdna2.rst
+++ b/doc/src/pair_oxdna2.rst
@@ -39,15 +39,15 @@ Syntax
      *oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
        seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
        T = temperature (oxDNA units, 0.1 = 300 K)
-       xi = 1.3523 (temperature-independent coefficient in stacking strength)
-       kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
+       xi = temperature-independent coefficient in stacking strength
+       kappa = coefficient of linear temperature dependence in stacking strength
      *oxdna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
        seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
        eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
      *oxdna2/dh* args = T rhos qeff
        T = temperature (oxDNA units, 0.1 = 300 K)
        rhos = salt concentration (mole per litre)
-       qeff = 0.815 (effective charge in elementary charges)
+       qeff = effective charge (elementary charges)
 
 Examples
 """"""""
@@ -63,7 +63,7 @@ Examples
    pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
    pair_coeff \* \* oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
    pair_coeff \* \* oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
-   pair_coeff \* \* oxdna2/dh      0.1 0.5 0.815
+   pair_coeff \* \* oxdna2/dh      0.1 1.0 0.815
 
 Description
 """""""""""
@@ -83,7 +83,7 @@ The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,
 which themselves are constructed from a number of more basic potentials
 (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
+We refer to :ref:`(Snodin) <Snodin>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
 and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
 
 .. note::
@@ -94,7 +94,7 @@ and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
    in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
    Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
    the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
-   after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat
+   after *oxdna2/dh* (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
    e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
    the temperature coefficients have to be matched to the one used in the fix.
 
@@ -102,13 +102,11 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
-this implementation.  The article contains general information
-on the model, its implementation and performance as well as the structure of
-the data and input file. The preprint version of the article can be found
-`here <PDF/USER-CGDNA.pdf>`_.
-Please cite also the relevant oxDNA2 publications
-:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
+Please cite :ref:`(Henrich) <Henrich>` and the relevant oxDNA articles in any publication that uses this implementation.
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
+
 
 ----------
 
@@ -124,34 +122,43 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
-:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
-:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`
 
 **Default:** none
 
 
 ----------
 
-.. _Henrich2:
+
+.. _Henrich:
+
+
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
-.. _Snodin2:
-
-**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
-
 .. _Sulc2:
 
+
+
 **(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
 
+.. _Snodin:
+
+
+
+**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
+
 .. _Ouldridge-DPhil2:
 
-**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+
+**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
 .. _Ouldridge2:
 
+
+
 **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 
 

From 4fa86e6ee833ba7c9964b2ddc5f40aeec191c673 Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 21:59:21 +0000
Subject: [PATCH 036/199] Revert "Fixed anchor errors"

This reverts commit 2d6e84edd74bcf23ce569d04a37561eb1c0f6204.
---
 doc/src/bond_oxdna.rst            | 75 +++++++++++++++++++------------
 doc/src/fix_nve_dot.rst           | 16 ++++---
 doc/src/fix_nve_dotc_langevin.rst | 21 +++++----
 doc/src/pair_oxdna.rst            | 45 +++++++++----------
 doc/src/pair_oxdna2.rst           | 55 ++++++++++-------------
 5 files changed, 115 insertions(+), 97 deletions(-)

diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst
index 51692f933b..36370ddf30 100644
--- a/doc/src/bond_oxdna.rst
+++ b/doc/src/bond_oxdna.rst
@@ -6,6 +6,9 @@ bond\_style oxdna/fene command
 bond\_style oxdna2/fene command
 ===============================
 
+bond\_style oxrna2/fene command
+===============================
+
 Syntax
 """"""
 
@@ -16,6 +19,8 @@ Syntax
 
    bond_style oxdna2/fene
 
+   bond_style oxrna2/fene
+
 Examples
 """"""""
 
@@ -28,18 +33,21 @@ Examples
    bond_style oxdna2/fene
    bond_coeff \* 2.0 0.25 0.7564
 
+   bond_style oxrna2/fene
+   bond_coeff \* 2.0 0.25 0.76107
+
 Description
 """""""""""
 
-The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
+The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential
 
 .. image:: Eqs/bond_oxdna_fene.jpg
    :align: center
 
 to define a modified finite extensible nonlinear elastic (FENE)
-potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
-phosphate backbone in the oxDNA force field for coarse-grained
-modelling of DNA.
+potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
+phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
+modelling of DNA/RNA.
 
 The following coefficients must be defined for the bond type via the
 :doc:`bond\_coeff <bond_coeff>` command as given in the above example, or
@@ -55,27 +63,36 @@ commands:
 
    The oxDNA bond style has to be used together with the
    corresponding oxDNA pair styles for excluded volume interaction
-   *oxdna/excv*\ , stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* and
+   *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
    coaxial stacking interaction *oxdna/coaxstk* as well as
    hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
    :doc:`pair\_style oxdna/excv <pair_oxdna>`). For the oxDNA2
-   :ref:`(Snodin) <oxdna2>` bond style the analogous pair styles and an
-   additional Debye-Hueckel pair style *oxdna2/dh* have to be defined.
+   :ref:`(Snodin) <Snodin0>` bond style the analogous pair styles 
+   *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
+   *oxdna2/hbond* and an additional Debye-Hueckel pair style 
+   *oxdna2/dh* have to be defined. The same applies to the oxRNA2
+   :ref:`(Sulc1) <Sulc01>` styles. 
    The coefficients in the above example have to be kept fixed and cannot
    be changed without reparameterizing the entire model.
 
-Example input and data files for DNA duplexes can be found in
-examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.  A simple python
-setup tool which creates single straight or helical DNA strands, DNA
-duplexes or arrays of DNA duplexes can be found in
+Example input and data files for DNA and RNA duplexes can be found in
+examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/.  A simple python
+setup tool which creates single straight or helical DNA strands, DNA/RNA
+duplexes or arrays of DNA/RNA duplexes can be found in
 examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich2>` and the relevant oxDNA articles in
-any publication that uses this implementation.  The article contains
-more information on the model, the structure of the input file, the
-setup tool and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found
+Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses 
+this implementation.  The article contains general information 
+on the model, its implementation and performance as well as the structure of 
+the data and input file. The preprint version of the article can be found
 `here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA/oxRNA publications. These are 
+:ref:`(Ouldridge) <Ouldridge0>` and 
+:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA, 
+:ref:`(Snodin) <Snodin0>` for oxDNA2, 
+:ref:`(Sulc1) <Sulc01>` for oxRNA2 
+and for sequence-specific hydrogen-bonding and stacking interactions 
+:ref:`(Sulc2) <Sulc02>`.
 
 
 ----------
@@ -92,35 +109,37 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`,
-:doc:`bond\_coeff <bond_coeff>`
+:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`, 
+:doc:`bond\_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
 **Default:** none
 
 
 ----------
 
+.. _Henrich0:
 
-.. _Henrich2:
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
+.. _Ouldridge-DPhil0:
 
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
-**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
-T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+.. _Ouldridge0:
 
-.. _oxdna\_fene:
+**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 
+.. _Snodin0:
 
+**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 
-**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
-J. Chem. Phys. 134, 085101 (2011).
+.. _Sulc01:
 
-.. _oxdna2:
+**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
 
+.. _Sulc02:
 
-
-**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
-J. Chem. Phys. 142, 234901 (2015).
+**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
 
 
 .. _lws: http://lammps.sandia.gov
diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst
index 5fc6a46ab5..33d9f61b49 100644
--- a/doc/src/fix_nve_dot.rst
+++ b/doc/src/fix_nve_dot.rst
@@ -26,11 +26,11 @@ Examples
 Description
 """""""""""
 
-Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack4>`
+Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack1>`
 to a group of atoms, but without Langevin dynamics.
 This command performs Molecular dynamics (MD)
 via a velocity-Verlet algorithm and an evolution operator that rotates
-the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller4>`.
+the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller1>`.
 
 This command is the equivalent of the :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 without damping and noise and can be used to determine the stability range
@@ -40,7 +40,7 @@ The command is equivalent to the :doc:`fix nve <fix_nve>`.
 The particles are always considered to have a finite size.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
-Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich4>`.
+Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich3>`.
 The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
 
 
@@ -66,15 +66,19 @@ Related commands
 ----------
 
 
-.. _Davidchack4:
+.. _Davidchack1:
+
+
+
+.. _Miller1:
 
 **(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 
-.. _Miller4:
+
+.. _Henrich3:
 
 **(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 
-.. _Henrich4:
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst
index 3143db968f..408aaf919e 100644
--- a/doc/src/fix_nve_dotc_langevin.rst
+++ b/doc/src/fix_nve_dotc_langevin.rst
@@ -38,14 +38,14 @@ Description
 """""""""""
 
 Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
-as described in :ref:`(Davidchack) <Davidchack5>`
+as described in :ref:`(Davidchack) <Davidchack2>`
 to a group of atoms, which models an interaction with an implicit background
 solvent.  This command performs Brownian dynamics (BD)
 via a technique that splits the integration into a deterministic Hamiltonian
 part and the Ornstein-Uhlenbeck process for noise and damping.
 The quaternion degrees of freedom are updated though an evolution
 operator which performs a rotation in quaternion space, preserves
-the quaternion norm and is akin to :ref:`(Miller) <Miller5>`.
+the quaternion norm and is akin to :ref:`(Miller) <Miller2>`.
 
 In terms of syntax this command has been closely modelled on the
 :doc:`fix langevin <fix_langevin>` and its *angmom* option. But it combines
@@ -86,7 +86,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
 temperature, m is the mass of the particle, dt is the timestep size,
 and damp is the damping factor.  Random numbers are used to randomize
 the direction and magnitude of this force as described in
-:ref:`(Dunweg) <Dunweg5>`, where a uniform random number is used (instead of
+:ref:`(Dunweg) <Dunweg3>`, where a uniform random number is used (instead of
 a Gaussian random number) for speed.
 
 
@@ -128,7 +128,7 @@ The scale factor after the *angmom* keyword gives the ratio of the rotational to
 the translational friction coefficient.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
+Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich4>`.
 The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
 
 
@@ -154,19 +154,24 @@ Related commands
 ----------
 
 
-.. _Davidchack5:
+.. _Davidchack2:
+
+
+
+.. _Miller2:
 
 **(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 
-.. _Miller5:
+
+.. _Dunweg3:
 
 **(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 
-.. _Dunweg5:
+
+.. _Henrich4:
 
 **(Dunweg)** B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
 
-.. _Henrich5:
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst
index b40cf1f6cc..727f19c327 100644
--- a/doc/src/pair_oxdna.rst
+++ b/doc/src/pair_oxdna.rst
@@ -36,8 +36,8 @@ Syntax
      *oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
        seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
        T = temperature (oxDNA units, 0.1 = 300 K)
-       xi = temperature-independent coefficient in stacking strength
-       kappa = coefficient of linear temperature dependence in stacking strength
+       xi = 1.3448 (temperature-independent coefficient in stacking strength)
+       kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
      *oxdna/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
        seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
        eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
@@ -94,11 +94,15 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich1>` and the relevant oxDNA articles in any publication that uses this implementation.
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
-
+Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
+this implementation.  The article contains general information
+on the model, its implementation and performance as well as the structure of
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA publications
+:ref:`(Ouldridge) <Ouldridge1>`, 
+:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
+and :ref:`(Sulc) <Sulc1>`.
 
 ----------
 
@@ -114,39 +118,32 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`
-
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
+:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+ 
 **Default:** none
 
 
 ----------
 
-
 .. _Henrich1:
 
-
-
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
-.. _Sulc1:
-
-
-
-**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
 .. _Ouldridge-DPhil1:
 
-
-
-**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
 .. _Ouldridge1:
 
-
-
 **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 
+.. _Sulc1:
+
+**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst
index 4f64197f44..77052da666 100644
--- a/doc/src/pair_oxdna2.rst
+++ b/doc/src/pair_oxdna2.rst
@@ -39,15 +39,15 @@ Syntax
      *oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
        seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
        T = temperature (oxDNA units, 0.1 = 300 K)
-       xi = temperature-independent coefficient in stacking strength
-       kappa = coefficient of linear temperature dependence in stacking strength
+       xi = 1.3523 (temperature-independent coefficient in stacking strength)
+       kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
      *oxdna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
        seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
        eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
      *oxdna2/dh* args = T rhos qeff
        T = temperature (oxDNA units, 0.1 = 300 K)
        rhos = salt concentration (mole per litre)
-       qeff = effective charge (elementary charges)
+       qeff = 0.815 (effective charge in elementary charges)
 
 Examples
 """"""""
@@ -63,7 +63,7 @@ Examples
    pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
    pair_coeff \* \* oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
    pair_coeff \* \* oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
-   pair_coeff \* \* oxdna2/dh      0.1 1.0 0.815
+   pair_coeff \* \* oxdna2/dh      0.1 0.5 0.815
 
 Description
 """""""""""
@@ -83,7 +83,7 @@ The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,
 which themselves are constructed from a number of more basic potentials
 (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to :ref:`(Snodin) <Snodin>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
+We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
 and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
 
 .. note::
@@ -94,7 +94,7 @@ and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
    in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
    Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
    the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
-   after *oxdna2/dh* (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
+   after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat
    e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
    the temperature coefficients have to be matched to the one used in the fix.
 
@@ -102,11 +102,13 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 
-Please cite :ref:`(Henrich) <Henrich>` and the relevant oxDNA articles in any publication that uses this implementation.
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
-
+Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
+this implementation.  The article contains general information
+on the model, its implementation and performance as well as the structure of
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA2 publications
+:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
 
 ----------
 
@@ -122,43 +124,34 @@ USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 Related commands
 """"""""""""""""
 
-:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
+:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
 **Default:** none
 
 
 ----------
 
-
-.. _Henrich:
-
-
+.. _Henrich2:
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
-.. _Sulc2:
-
-
-
-**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
-.. _Snodin:
-
-
+.. _Snodin2:
 
 **(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 
+.. _Sulc2:
+
+**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 .. _Ouldridge-DPhil2:
 
-
-
-**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 
 .. _Ouldridge2:
 
-
-
 **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 
 

From 06c7464a20b6ceaefb01da2b77372b7618072643 Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Fri, 15 Nov 2019 22:05:12 +0000
Subject: [PATCH 037/199] Fixed anchor error

---
 doc/src/fix_nve_dot.rst           | 16 ++++++----------
 doc/src/fix_nve_dotc_langevin.rst | 21 ++++++++-------------
 2 files changed, 14 insertions(+), 23 deletions(-)

diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst
index 33d9f61b49..5fc6a46ab5 100644
--- a/doc/src/fix_nve_dot.rst
+++ b/doc/src/fix_nve_dot.rst
@@ -26,11 +26,11 @@ Examples
 Description
 """""""""""
 
-Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack1>`
+Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack4>`
 to a group of atoms, but without Langevin dynamics.
 This command performs Molecular dynamics (MD)
 via a velocity-Verlet algorithm and an evolution operator that rotates
-the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller1>`.
+the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller4>`.
 
 This command is the equivalent of the :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 without damping and noise and can be used to determine the stability range
@@ -40,7 +40,7 @@ The command is equivalent to the :doc:`fix nve <fix_nve>`.
 The particles are always considered to have a finite size.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
-Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich3>`.
+Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich4>`.
 The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
 
 
@@ -66,19 +66,15 @@ Related commands
 ----------
 
 
-.. _Davidchack1:
-
-
-
-.. _Miller1:
+.. _Davidchack4:
 
 **(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 
-
-.. _Henrich3:
+.. _Miller4:
 
 **(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 
+.. _Henrich4:
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst
index 408aaf919e..3143db968f 100644
--- a/doc/src/fix_nve_dotc_langevin.rst
+++ b/doc/src/fix_nve_dotc_langevin.rst
@@ -38,14 +38,14 @@ Description
 """""""""""
 
 Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
-as described in :ref:`(Davidchack) <Davidchack2>`
+as described in :ref:`(Davidchack) <Davidchack5>`
 to a group of atoms, which models an interaction with an implicit background
 solvent.  This command performs Brownian dynamics (BD)
 via a technique that splits the integration into a deterministic Hamiltonian
 part and the Ornstein-Uhlenbeck process for noise and damping.
 The quaternion degrees of freedom are updated though an evolution
 operator which performs a rotation in quaternion space, preserves
-the quaternion norm and is akin to :ref:`(Miller) <Miller2>`.
+the quaternion norm and is akin to :ref:`(Miller) <Miller5>`.
 
 In terms of syntax this command has been closely modelled on the
 :doc:`fix langevin <fix_langevin>` and its *angmom* option. But it combines
@@ -86,7 +86,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
 temperature, m is the mass of the particle, dt is the timestep size,
 and damp is the damping factor.  Random numbers are used to randomize
 the direction and magnitude of this force as described in
-:ref:`(Dunweg) <Dunweg3>`, where a uniform random number is used (instead of
+:ref:`(Dunweg) <Dunweg5>`, where a uniform random number is used (instead of
 a Gaussian random number) for speed.
 
 
@@ -128,7 +128,7 @@ The scale factor after the *angmom* keyword gives the ratio of the rotational to
 the translational friction coefficient.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich4>`.
+Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
 The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
 
 
@@ -154,24 +154,19 @@ Related commands
 ----------
 
 
-.. _Davidchack2:
-
-
-
-.. _Miller2:
+.. _Davidchack5:
 
 **(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 
-
-.. _Dunweg3:
+.. _Miller5:
 
 **(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 
-
-.. _Henrich4:
+.. _Dunweg5:
 
 **(Dunweg)** B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
 
+.. _Henrich5:
 
 **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 

From 58bbbc3d8b3e68c0fab028e9dace05d218af491b Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Fri, 15 Nov 2019 18:00:25 -0700
Subject: [PATCH 038/199] Started on ComputeSnap

---
 src/SNAP/compute_snap.cpp | 377 ++++++++++++++++++++++++++++++++++++++
 src/SNAP/compute_snap.h   |  77 ++++++++
 2 files changed, 454 insertions(+)
 create mode 100644 src/SNAP/compute_snap.cpp
 create mode 100644 src/SNAP/compute_snap.h

diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
new file mode 100644
index 0000000000..31b50e1902
--- /dev/null
+++ b/src/SNAP/compute_snap.cpp
@@ -0,0 +1,377 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "compute_snap.h"
+#include <cstring>
+#include <cstdlib>
+#include "sna.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "force.h"
+#include "pair.h"
+#include "comm.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snap(NULL),
+  radelem(NULL), wjelem(NULL)
+{
+  double rfac0, rmin0;
+  int twojmax, switchflag, bzeroflag;
+  radelem = NULL;
+  wjelem = NULL;
+
+  int ntypes = atom->ntypes;
+  int nargmin = 6+2*ntypes;
+
+  if (narg < nargmin) error->all(FLERR,"Illegal compute snap command");
+
+  // default values
+
+  rmin0 = 0.0;
+  switchflag = 1;
+  bzeroflag = 1;
+  quadraticflag = 0;
+
+  // process required arguments
+
+  memory->create(radelem,ntypes+1,"snap:radelem"); // offset by 1 to match up with types
+  memory->create(wjelem,ntypes+1,"snap:wjelem");
+  rcutfac = atof(arg[3]);
+  rfac0 = atof(arg[4]);
+  twojmax = atoi(arg[5]);
+  for(int i = 0; i < ntypes; i++)
+    radelem[i+1] = atof(arg[6+i]);
+  for(int i = 0; i < ntypes; i++)
+    wjelem[i+1] = atof(arg[6+ntypes+i]);
+
+  // construct cutsq
+
+  double cut;
+  cutmax = 0.0;
+  memory->create(cutsq,ntypes+1,ntypes+1,"snap:cutsq");
+  for(int i = 1; i <= ntypes; i++) {
+    cut = 2.0*radelem[i]*rcutfac;
+    if (cut > cutmax) cutmax = cut;
+    cutsq[i][i] = cut*cut;
+    for(int j = i+1; j <= ntypes; j++) {
+      cut = (radelem[i]+radelem[j])*rcutfac;
+      cutsq[i][j] = cutsq[j][i] = cut*cut;
+    }
+  }
+
+  // process optional args
+
+  int iarg = nargmin;
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"rmin0") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      rmin0 = atof(arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"bzeroflag") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      bzeroflag = atoi(arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"switchflag") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      switchflag = atoi(arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      quadraticflag = atoi(arg[iarg+1]);
+      iarg += 2;
+    } else error->all(FLERR,"Illegal compute snap command");
+  }
+
+  snaptr = new SNA(lmp,rfac0,twojmax,
+                   rmin0,switchflag,bzeroflag);
+
+  ncoeff = snaptr->ncoeff;
+  nperdim = ncoeff;
+  if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
+  yoffset = nperdim;
+  zoffset = 2*nperdim;
+  size_peratom_cols = 3*nperdim*atom->ntypes;
+  comm_reverse = size_peratom_cols;
+
+  nmax = 0;
+  snap = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeSnap::~ComputeSnap()
+{
+  memory->destroy(snap);
+  memory->destroy(radelem);
+  memory->destroy(wjelem);
+  memory->destroy(cutsq);
+  delete snaptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeSnap::init()
+{
+  if (force->pair == NULL)
+    error->all(FLERR,"Compute snap requires a pair style be defined");
+
+  if (cutmax > force->pair->cutforce)
+    error->all(FLERR,"Compute snap cutoff is longer than pairwise cutoff");
+
+  // need an occasional full neighbor list
+
+  int irequest = neighbor->request(this,instance_me);
+  neighbor->requests[irequest]->pair = 0;
+  neighbor->requests[irequest]->compute = 1;
+  neighbor->requests[irequest]->half = 0;
+  neighbor->requests[irequest]->full = 1;
+  neighbor->requests[irequest]->occasional = 1;
+
+  int count = 0;
+  for (int i = 0; i < modify->ncompute; i++)
+    if (strcmp(modify->compute[i]->style,"snap") == 0) count++;
+  if (count > 1 && comm->me == 0)
+    error->warning(FLERR,"More than one compute snap");
+  snaptr->init();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeSnap::init_list(int /*id*/, NeighList *ptr)
+{
+  list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeSnap::compute()
+{
+  int ntotal = atom->nlocal + atom->nghost;
+
+  invoked_peratom = update->ntimestep;
+
+  // grow snap array if necessary
+
+  if (atom->nmax > nmax) {
+    memory->destroy(snap);
+    nmax = atom->nmax;
+    memory->create(snap,nmax,size_peratom_cols,
+                   "snap:snap");
+    array = snap;
+  }
+
+  // clear local array
+
+  for (int i = 0; i < ntotal; i++)
+    for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++) {
+      snap[i][icoeff] = 0.0;
+    }
+
+  // invoke full neighbor list (will copy or build if necessary)
+
+  neighbor->build_one(list);
+
+  const int inum = list->inum;
+  const int* const ilist = list->ilist;
+  const int* const numneigh = list->numneigh;
+  int** const firstneigh = list->firstneigh;
+  int * const type = atom->type;
+
+  // compute sna derivatives for each atom in group
+  // use full neighbor list to count atoms less than cutoff
+
+  double** const x = atom->x;
+  const int* const mask = atom->mask;
+
+  for (int ii = 0; ii < inum; ii++) {
+    const int i = ilist[ii];
+    if (mask[i] & groupbit) {
+
+      const double xtmp = x[i][0];
+      const double ytmp = x[i][1];
+      const double ztmp = x[i][2];
+      const int itype = type[i];
+      const double radi = radelem[itype];
+      const int* const jlist = firstneigh[i];
+      const int jnum = numneigh[i];
+
+      // const int typeoffset = threencoeff*(atom->type[i]-1);
+      // const int quadraticoffset = threencoeff*atom->ntypes +
+      //   threencoeffq*(atom->type[i]-1);
+      const int typeoffset = 3*nperdim*(atom->type[i]-1);
+
+      // insure rij, inside, and typej  are of size jnum
+
+      snaptr->grow_rij(jnum);
+
+      // rij[][3] = displacements between atom I and those neighbors
+      // inside = indices of neighbors of I within cutoff
+      // typej = types of neighbors of I within cutoff
+      // note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi
+
+      int ninside = 0;
+      for (int jj = 0; jj < jnum; jj++) {
+        int j = jlist[jj];
+        j &= NEIGHMASK;
+
+        const double delx = x[j][0] - xtmp;
+        const double dely = x[j][1] - ytmp;
+        const double delz = x[j][2] - ztmp;
+        const double rsq = delx*delx + dely*dely + delz*delz;
+        int jtype = type[j];
+        if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
+          snaptr->rij[ninside][0] = delx;
+          snaptr->rij[ninside][1] = dely;
+          snaptr->rij[ninside][2] = delz;
+          snaptr->inside[ninside] = j;
+          snaptr->wj[ninside] = wjelem[jtype];
+          snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
+          ninside++;
+        }
+      }
+
+      snaptr->compute_ui(ninside);
+      snaptr->compute_zi();
+      if (quadraticflag) {
+        snaptr->compute_bi();
+      }
+
+      for (int jj = 0; jj < ninside; jj++) {
+        const int j = snaptr->inside[jj];
+        snaptr->compute_duidrj(snaptr->rij[jj],
+                                    snaptr->wj[jj],
+                                    snaptr->rcutij[jj],jj);
+        snaptr->compute_dbidrj();
+
+        // Accumulate -dBi/dRi, -dBi/dRj
+
+        double *snapi = snap[i]+typeoffset;
+        double *snapj = snap[j]+typeoffset;
+
+        for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+          snapi[icoeff] += snaptr->dblist[icoeff][0];
+          snapi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
+          snapi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
+          snapj[icoeff] -= snaptr->dblist[icoeff][0];
+          snapj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
+          snapj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
+        }
+
+        if (quadraticflag) {
+          const int quadraticoffset = ncoeff;
+          snapi += quadraticoffset;
+          snapj += quadraticoffset;
+          int ncount = 0;
+          for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+            double bi = snaptr->blist[icoeff];
+            double bix = snaptr->dblist[icoeff][0];
+            double biy = snaptr->dblist[icoeff][1];
+            double biz = snaptr->dblist[icoeff][2];
+
+            // diagonal elements of quadratic matrix
+
+            double dbxtmp = bi*bix;
+            double dbytmp = bi*biy;
+            double dbztmp = bi*biz;
+
+            snapi[ncount] +=         dbxtmp;
+            snapi[ncount+yoffset] += dbytmp;
+            snapi[ncount+zoffset] += dbztmp;
+            snapj[ncount] -=         dbxtmp;
+            snapj[ncount+yoffset] -= dbytmp;
+            snapj[ncount+zoffset] -= dbztmp;
+            ncount++;
+
+            // upper-triangular elements of quadratic matrix
+
+            for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
+              double dbxtmp = bi*snaptr->dblist[jcoeff][0]
+                + bix*snaptr->blist[jcoeff];
+              double dbytmp = bi*snaptr->dblist[jcoeff][1]
+                + biy*snaptr->blist[jcoeff];
+              double dbztmp = bi*snaptr->dblist[jcoeff][2]
+                + biz*snaptr->blist[jcoeff];
+
+              snapi[ncount] +=         dbxtmp;
+              snapi[ncount+yoffset] += dbytmp;
+              snapi[ncount+zoffset] += dbztmp;
+              snapj[ncount] -=         dbxtmp;
+              snapj[ncount+yoffset] -= dbytmp;
+              snapj[ncount+zoffset] -= dbztmp;
+              ncount++;
+            }
+          }
+        }
+      }
+    }
+  }
+
+  // communicate snap contributions between neighbor procs
+
+  comm->reverse_comm_compute(this);
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+int ComputeSnap::pack_reverse_comm(int n, int first, double *buf)
+{
+  int i,m,last,icoeff;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++)
+    for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
+      buf[m++] = snap[i][icoeff];
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeSnap::unpack_reverse_comm(int n, int *list, double *buf)
+{
+  int i,j,m,icoeff;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
+      snap[j][icoeff] += buf[m++];
+  }
+}
+
+/* ----------------------------------------------------------------------
+   memory usage
+------------------------------------------------------------------------- */
+
+double ComputeSnap::memory_usage()
+{
+
+  double bytes = nmax*size_peratom_cols * sizeof(double); // snap
+  bytes += snaptr->memory_usage();                        // SNA object
+
+  return bytes;
+}
diff --git a/src/SNAP/compute_snap.h b/src/SNAP/compute_snap.h
new file mode 100644
index 0000000000..9fa998981a
--- /dev/null
+++ b/src/SNAP/compute_snap.h
@@ -0,0 +1,77 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(snap,ComputeSnap)
+
+#else
+
+#ifndef LMP_COMPUTE_SNAP_H
+#define LMP_COMPUTE_SNAP_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeSnap : public Compute {
+ public:
+  ComputeSnap(class LAMMPS *, int, char **);
+  ~ComputeSnap();
+  void init();
+  void init_list(int, class NeighList *);
+  void compute();
+  int pack_reverse_comm(int, int, double *);
+  void unpack_reverse_comm(int, int *, double *);
+  double memory_usage();
+
+ private:
+  int nmax;
+  int ncoeff, nperdim, yoffset, zoffset;
+  double **cutsq;
+  class NeighList *list;
+  double **snap;
+  double rcutfac;
+  double *radelem;
+  double *wjelem;
+  class SNA* snaptr;
+  double cutmax;
+  int quadraticflag;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Compute snap requires a pair style be defined
+
+Self-explanatory.
+
+E: Compute snap cutoff is longer than pairwise cutoff
+
+UNDOCUMENTED
+
+W: More than one compute snad/atom
+
+Self-explanatory.
+
+*/

From ffc443c957644acc463a8c0d332af22bd653f778 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Fri, 15 Nov 2019 18:34:44 -0700
Subject: [PATCH 039/199] Started on ComputeSnap

---
 src/SNAP/compute_snap.cpp | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 31b50e1902..c636ee8841 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -10,7 +10,17 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
+/* IDEAS
 
+-Need to define a local array for snad on local and ghost atoms, in addition
+a local vector of (1+6)*size_array_cols scalars.  
+-Reverse communicate local array
+-MPI Allreduce on vector 
+-Copy vector and array into output array
+-size_array_cols = ncoeff
+-size_array_rows = total number of atoms
+-Boom!
+ */
 #include "compute_snap.h"
 #include <cstring>
 #include <cstdlib>
@@ -113,7 +123,8 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
   if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
   yoffset = nperdim;
   zoffset = 2*nperdim;
-  size_peratom_cols = 3*nperdim*atom->ntypes;
+  size_array_rows = total number of atoms
+  size_array_cols = 3*nperdim*atom->ntypes;
   comm_reverse = size_peratom_cols;
 
   nmax = 0;
@@ -178,7 +189,7 @@ void ComputeSnap::compute()
   if (atom->nmax > nmax) {
     memory->destroy(snap);
     nmax = atom->nmax;
-    memory->create(snap,nmax,size_peratom_cols,
+    memory->create(snap,size_array_rows,size_array_cols,
                    "snap:snap");
     array = snap;
   }

From 3861b3cbbb32f143f85e1668bb3fac774c4f7bd6 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Sat, 16 Nov 2019 18:20:08 -0700
Subject: [PATCH 040/199] ComputeSnap is working with, matching results
 FitSNAP3 A matrix

---
 src/SNAP/compute_snap.cpp | 302 ++++++++++++++++++++++++++++++--------
 src/SNAP/compute_snap.h   |   9 +-
 2 files changed, 250 insertions(+), 61 deletions(-)

diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index c636ee8841..5c472861ec 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -12,14 +12,16 @@
 ------------------------------------------------------------------------- */
 /* IDEAS
 
--Need to define a local array for snad on local and ghost atoms, in addition
-a local vector of (1+6)*size_array_cols scalars.  
--Reverse communicate local array
--MPI Allreduce on vector 
--Copy vector and array into output array
--size_array_cols = ncoeff
--size_array_rows = total number of atoms
--Boom!
+-DONE: Need to define a local peratom array for snad and snad on local and ghost atoms
+-DONE: Reverse communicate local peratom array
+-DONE: Copy peratom array into output array
+-DONE: size_array_cols = nperdim (ncoeff [+quadratic])
+-DONE: size_array_rows = 1 + total number of atoms + 6
+-DONE: size_peratom = (3+6)*nperdim*ntypes
+INCOMPLETE: Mappy from local to global
+INCOMPLETE: modify->find_compute() 
+INCOMPLETE: eliminate local peratom array for viral, replace with fdotr 
+
  */
 #include "compute_snap.h"
 #include <cstring>
@@ -39,10 +41,16 @@ a local vector of (1+6)*size_array_cols scalars.
 
 using namespace LAMMPS_NS;
 
+enum{SCALAR,VECTOR,ARRAY};
+
 ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snap(NULL),
-  radelem(NULL), wjelem(NULL)
+  radelem(NULL), wjelem(NULL), snap_peratom(NULL)
 {
+
+  array_flag = 1;
+  extarray = 0;
+
   double rfac0, rmin0;
   int twojmax, switchflag, bzeroflag;
   radelem = NULL;
@@ -123,12 +131,15 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
   if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
   yoffset = nperdim;
   zoffset = 2*nperdim;
-  size_array_rows = total number of atoms
-  size_array_cols = 3*nperdim*atom->ntypes;
-  comm_reverse = size_peratom_cols;
+  virialoffset = 3*nperdim;
+  natoms = atom->natoms;
+  size_array_rows = 1+3*natoms+6;
+  size_array_cols = nperdim*atom->ntypes+1; // extra col for reference potential
+  ndims_peratom = 9;
+  size_peratom = ndims_peratom*nperdim*atom->ntypes; // local atom force and virial data
+  comm_reverse = size_peratom;
 
   nmax = 0;
-  snap = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -136,6 +147,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
 ComputeSnap::~ComputeSnap()
 {
   memory->destroy(snap);
+  memory->destroy(snap_peratom);
   memory->destroy(radelem);
   memory->destroy(wjelem);
   memory->destroy(cutsq);
@@ -167,8 +179,36 @@ void ComputeSnap::init()
   if (count > 1 && comm->me == 0)
     error->warning(FLERR,"More than one compute snap");
   snaptr->init();
+
+  // allocate memory for global array
+
+  //  printf("allocate memory for global array rows = %d cols = %d\n",
+  //         size_array_rows,size_array_cols);
+  memory->create(snap,size_array_rows,size_array_cols,
+                 "snap:snap");
+  array = snap;
+
+  // INCOMPLETE: modify->find_compute() 
+  // was called 223960 times by snappy Ta example
+  // that is over 600 times per config?
+  // how is this possible???
+
+  // find compute for reference energy
+
+  char *id_pe = (char *) "thermo_pe";
+  int ipe = modify->find_compute(id_pe);
+  c_pe = modify->compute[ipe];
+
+  // add compute for reference virial tensor
+
+  char *id_virial = (char *) "snap_press";
+  int ivirial = modify->find_compute(id_virial);
+  if (ivirial == -1)
+    error->all(FLERR,"compute snap requires that compute snap_press exists!");
+  c_virial = modify->compute[ivirial];
 }
 
+
 /* ---------------------------------------------------------------------- */
 
 void ComputeSnap::init_list(int /*id*/, NeighList *ptr)
@@ -178,27 +218,34 @@ void ComputeSnap::init_list(int /*id*/, NeighList *ptr)
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeSnap::compute()
+void ComputeSnap::compute_array()
 {
   int ntotal = atom->nlocal + atom->nghost;
 
-  invoked_peratom = update->ntimestep;
+  invoked_array = update->ntimestep;
 
-  // grow snap array if necessary
+  //  printf("Invoking compute snap on timestep %d\n",invoked_array);
+
+  // grow snap_peratom array if necessary
 
   if (atom->nmax > nmax) {
-    memory->destroy(snap);
+    memory->destroy(snap_peratom);
     nmax = atom->nmax;
-    memory->create(snap,size_array_rows,size_array_cols,
-                   "snap:snap");
-    array = snap;
+    memory->create(snap_peratom,nmax,size_peratom,
+                   "snap:snap_peratom");
   }
 
-  // clear local array
+  // clear global array
+  // only need to zero out first row
+
+  for (int icoeff = 0; icoeff < size_array_cols; icoeff++)
+    snap[0][icoeff] = 0.0;
+
+  // clear peratom array
 
   for (int i = 0; i < ntotal; i++)
-    for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++) {
-      snap[i][icoeff] = 0.0;
+    for (int icoeff = 0; icoeff < size_peratom; icoeff++) {
+      snap_peratom[i][icoeff] = 0.0;
     }
 
   // invoke full neighbor list (will copy or build if necessary)
@@ -228,11 +275,7 @@ void ComputeSnap::compute()
       const double radi = radelem[itype];
       const int* const jlist = firstneigh[i];
       const int jnum = numneigh[i];
-
-      // const int typeoffset = threencoeff*(atom->type[i]-1);
-      // const int quadraticoffset = threencoeff*atom->ntypes +
-      //   threencoeffq*(atom->type[i]-1);
-      const int typeoffset = 3*nperdim*(atom->type[i]-1);
+      const int typeoffset = ndims_peratom*nperdim*(atom->type[i]-1);
 
       // insure rij, inside, and typej  are of size jnum
 
@@ -266,9 +309,9 @@ void ComputeSnap::compute()
 
       snaptr->compute_ui(ninside);
       snaptr->compute_zi();
-      if (quadraticflag) {
-        snaptr->compute_bi();
-      }
+      //      if (quadraticflag) {
+      snaptr->compute_bi();
+      //      }
 
       for (int jj = 0; jj < ninside; jj++) {
         const int j = snaptr->inside[jj];
@@ -279,22 +322,39 @@ void ComputeSnap::compute()
 
         // Accumulate -dBi/dRi, -dBi/dRj
 
-        double *snapi = snap[i]+typeoffset;
-        double *snapj = snap[j]+typeoffset;
+        double *snadi = snap_peratom[i]+typeoffset;
+        double *snadj = snap_peratom[j]+typeoffset;
+        double *snavi = snadi+virialoffset;
+        double *snavj = snadj+virialoffset;
 
         for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
-          snapi[icoeff] += snaptr->dblist[icoeff][0];
-          snapi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
-          snapi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
-          snapj[icoeff] -= snaptr->dblist[icoeff][0];
-          snapj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
-          snapj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
+          snadi[icoeff] += snaptr->dblist[icoeff][0];
+          snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
+          snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
+          snadj[icoeff] -= snaptr->dblist[icoeff][0];
+          snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
+          snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
+
+          snavi[icoeff]           += snaptr->dblist[icoeff][0]*xtmp;
+          snavi[icoeff+nperdim]   += snaptr->dblist[icoeff][1]*ytmp;
+          snavi[icoeff+2*nperdim] += snaptr->dblist[icoeff][2]*ztmp;
+          snavi[icoeff+3*nperdim] += snaptr->dblist[icoeff][1]*ztmp;
+          snavi[icoeff+4*nperdim] += snaptr->dblist[icoeff][0]*ztmp;
+          snavi[icoeff+5*nperdim] += snaptr->dblist[icoeff][0]*ytmp;
+          snavj[icoeff]           -= snaptr->dblist[icoeff][0]*x[j][0];
+          snavj[icoeff+nperdim]   -= snaptr->dblist[icoeff][1]*x[j][1];
+          snavj[icoeff+2*nperdim] -= snaptr->dblist[icoeff][2]*x[j][2];
+          snavj[icoeff+3*nperdim] -= snaptr->dblist[icoeff][1]*x[j][2];
+          snavj[icoeff+4*nperdim] -= snaptr->dblist[icoeff][0]*x[j][2];
+          snavj[icoeff+5*nperdim] -= snaptr->dblist[icoeff][0]*x[j][1];
         }
 
         if (quadraticflag) {
           const int quadraticoffset = ncoeff;
-          snapi += quadraticoffset;
-          snapj += quadraticoffset;
+          snadi += quadraticoffset;
+          snadj += quadraticoffset;
+          snavi += quadraticoffset;
+          snavj += quadraticoffset;
           int ncount = 0;
           for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
             double bi = snaptr->blist[icoeff];
@@ -308,12 +368,26 @@ void ComputeSnap::compute()
             double dbytmp = bi*biy;
             double dbztmp = bi*biz;
 
-            snapi[ncount] +=         dbxtmp;
-            snapi[ncount+yoffset] += dbytmp;
-            snapi[ncount+zoffset] += dbztmp;
-            snapj[ncount] -=         dbxtmp;
-            snapj[ncount+yoffset] -= dbytmp;
-            snapj[ncount+zoffset] -= dbztmp;
+            snadi[ncount] +=         dbxtmp;
+            snadi[ncount+yoffset] += dbytmp;
+            snadi[ncount+zoffset] += dbztmp;
+            snadj[ncount] -=         dbxtmp;
+            snadj[ncount+yoffset] -= dbytmp;
+            snadj[ncount+zoffset] -= dbztmp;
+
+            snavi[ncount] +=           dbxtmp*xtmp;
+            snavi[ncount+nperdim] +=   dbytmp*ytmp;
+            snavi[ncount+2*nperdim] += dbztmp*ztmp;
+            snavi[ncount+3*nperdim] += dbytmp*ztmp;
+            snavi[ncount+4*nperdim] += dbxtmp*ztmp;
+            snavi[ncount+5*nperdim] += dbxtmp*ytmp;
+            snavj[ncount] -=            dbxtmp*x[j][0];
+            snavj[ncount+nperdim] -=    dbytmp*x[j][1];
+            snavj[ncount+2*nperdim] -=  dbztmp*x[j][2];
+            snavj[ncount+3*nperdim] -=  dbytmp*x[j][2];
+            snavj[ncount+4*nperdim] -=  dbxtmp*x[j][2];
+            snavj[ncount+5*nperdim] -=  dbxtmp*x[j][1];
+
             ncount++;
 
             // upper-triangular elements of quadratic matrix
@@ -326,24 +400,132 @@ void ComputeSnap::compute()
               double dbztmp = bi*snaptr->dblist[jcoeff][2]
                 + biz*snaptr->blist[jcoeff];
 
-              snapi[ncount] +=         dbxtmp;
-              snapi[ncount+yoffset] += dbytmp;
-              snapi[ncount+zoffset] += dbztmp;
-              snapj[ncount] -=         dbxtmp;
-              snapj[ncount+yoffset] -= dbytmp;
-              snapj[ncount+zoffset] -= dbztmp;
+              snadi[ncount] +=         dbxtmp;
+              snadi[ncount+yoffset] += dbytmp;
+              snadi[ncount+zoffset] += dbztmp;
+              snadj[ncount] -=         dbxtmp;
+              snadj[ncount+yoffset] -= dbytmp;
+              snadj[ncount+zoffset] -= dbztmp;
+
+              snavi[ncount] +=           dbxtmp*xtmp;
+              snavi[ncount+nperdim] +=   dbytmp*ytmp;
+              snavi[ncount+2*nperdim] += dbztmp*ztmp;
+              snavi[ncount+3*nperdim] += dbytmp*ztmp;
+              snavi[ncount+4*nperdim] += dbxtmp*ztmp;
+              snavi[ncount+5*nperdim] += dbxtmp*ytmp;
+              snavj[ncount] -=           dbxtmp*x[j][0];
+              snavj[ncount+nperdim] -=   dbytmp*x[j][1];
+              snavj[ncount+2*nperdim] -= dbztmp*x[j][2];
+              snavj[ncount+3*nperdim] -= dbytmp*x[j][2];
+              snavj[ncount+4*nperdim] -= dbxtmp*x[j][2];
+              snavj[ncount+5*nperdim] -= dbxtmp*x[j][1];
+
               ncount++;
             }
           }
         }
       }
+
+      // Accumulate Bi
+      
+      // linear contributions
+
+      for (int icoeff = 0; icoeff < ncoeff; icoeff++)
+        snap[0][icoeff] += snaptr->blist[icoeff];
+
+      // quadratic contributions
+
+      if (quadraticflag) {
+        for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+          double bveci = snaptr->blist[icoeff];
+          snap[0][icoeff] += 0.5*bveci*bveci;
+          for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
+            double bvecj = snaptr->blist[jcoeff];
+            snap[0][icoeff] += bveci*bvecj;
+          }
+        }
+      }
     }
   }
 
+  // INCOMPLETE
+  // can get rid of virial from snap_peratom by doing
+  // equivalent of Pair::virial_fdotr_compute()
+  // before reverse communicate of snap_peratom
+
   // communicate snap contributions between neighbor procs
 
   comm->reverse_comm_compute(this);
 
+  // construct global array
+
+  for (int itype = 0; itype < atom->ntypes; itype++) {
+    const int typeoffset = 3*nperdim*itype;
+    for (int icoeff = 0; icoeff < nperdim; icoeff++) {
+
+      // assign force rows
+      // INCOMPLETE ignore local-global mapping for now
+
+      int irow = 1;
+      for (int i = 0; i < atom->nlocal; i++) {
+        double *snadi = snap_peratom[i]+typeoffset;
+        snap[irow++][icoeff+typeoffset] = snadi[icoeff];
+        snap[irow++][icoeff+typeoffset] = snadi[icoeff+yoffset];
+        snap[irow++][icoeff+typeoffset] = snadi[icoeff+zoffset];
+
+      }
+
+      // assign virial row
+
+      int irow0 = irow;
+      snap[irow++][icoeff+typeoffset] = 0.0; 
+      snap[irow++][icoeff+typeoffset] = 0.0; 
+      snap[irow++][icoeff+typeoffset] = 0.0; 
+      snap[irow++][icoeff+typeoffset] = 0.0; 
+      snap[irow++][icoeff+typeoffset] = 0.0; 
+      snap[irow++][icoeff+typeoffset] = 0.0;
+
+      for (int i = 0; i < atom->nlocal; i++) {
+        double *snavi = snap_peratom[i]+typeoffset+virialoffset;
+        irow = irow0;
+        snap[irow++][icoeff+typeoffset] += snavi[icoeff];
+        snap[irow++][icoeff+typeoffset] += snavi[icoeff+1*nperdim];
+        snap[irow++][icoeff+typeoffset] += snavi[icoeff+2*nperdim];
+        snap[irow++][icoeff+typeoffset] += snavi[icoeff+3*nperdim];
+        snap[irow++][icoeff+typeoffset] += snavi[icoeff+4*nperdim];
+        snap[irow++][icoeff+typeoffset] += snavi[icoeff+5*nperdim];
+      }
+
+    }
+  }
+
+  // assign energy row
+
+  int icol = size_array_cols-1;
+  int irow = 0;
+  double reference_energy = c_pe->compute_scalar();
+  snap[irow++][icol] = reference_energy; 
+
+  // assign force rows
+  // INCOMPLETE ignore local-global mapping for now
+
+  for (int i = 0; i < atom->nlocal; i++) {
+    snap[irow++][icol] = atom->f[i][0];
+    snap[irow++][icol] = atom->f[i][1];
+    snap[irow++][icol] = atom->f[i][2];
+  }
+
+  // assign virial row
+  // switch to Voigt notation
+
+  c_virial->compute_vector();
+  snap[irow++][icol] = c_virial->vector[0]; 
+  snap[irow++][icol] = c_virial->vector[1]; 
+  snap[irow++][icol] = c_virial->vector[2]; 
+  snap[irow++][icol] = c_virial->vector[5]; 
+  snap[irow++][icol] = c_virial->vector[4]; 
+  snap[irow++][icol] = c_virial->vector[3]; 
+
 }
 
 /* ---------------------------------------------------------------------- */
@@ -355,8 +537,8 @@ int ComputeSnap::pack_reverse_comm(int n, int first, double *buf)
   m = 0;
   last = first + n;
   for (i = first; i < last; i++)
-    for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
-      buf[m++] = snap[i][icoeff];
+    for (icoeff = 0; icoeff < size_peratom; icoeff++)
+      buf[m++] = snap_peratom[i][icoeff];
   return m;
 }
 
@@ -369,8 +551,8 @@ void ComputeSnap::unpack_reverse_comm(int n, int *list, double *buf)
   m = 0;
   for (i = 0; i < n; i++) {
     j = list[i];
-    for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
-      snap[j][icoeff] += buf[m++];
+    for (icoeff = 0; icoeff < size_peratom; icoeff++)
+      snap_peratom[j][icoeff] += buf[m++];
   }
 }
 
@@ -381,8 +563,10 @@ void ComputeSnap::unpack_reverse_comm(int n, int *list, double *buf)
 double ComputeSnap::memory_usage()
 {
 
-  double bytes = nmax*size_peratom_cols * sizeof(double); // snap
-  bytes += snaptr->memory_usage();                        // SNA object
+  double bytes = size_array_rows*size_array_cols * 
+    sizeof(double);                                     // snap
+  bytes += nmax*size_peratom * sizeof(double);          // snap_peratom
+  bytes += snaptr->memory_usage();                      // SNA object
 
   return bytes;
 }
diff --git a/src/SNAP/compute_snap.h b/src/SNAP/compute_snap.h
index 9fa998981a..970c79c67e 100644
--- a/src/SNAP/compute_snap.h
+++ b/src/SNAP/compute_snap.h
@@ -30,23 +30,28 @@ class ComputeSnap : public Compute {
   ~ComputeSnap();
   void init();
   void init_list(int, class NeighList *);
-  void compute();
+  void compute_array();
   int pack_reverse_comm(int, int, double *);
   void unpack_reverse_comm(int, int *, double *);
   double memory_usage();
 
  private:
-  int nmax;
+  int natoms, nmax, size_peratom;
   int ncoeff, nperdim, yoffset, zoffset;
+  int virialoffset, ndims_peratom;
   double **cutsq;
   class NeighList *list;
   double **snap;
+  double **snap_peratom;
   double rcutfac;
   double *radelem;
   double *wjelem;
   class SNA* snaptr;
   double cutmax;
   int quadraticflag;
+
+  Compute *c_pe;
+  Compute *c_virial;
 };
 
 }

From 7f448a02b1fa3d6c201a8701c653c0c9af6d2cd7 Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Sun, 17 Nov 2019 22:01:29 +0300
Subject: [PATCH 041/199] Add examples/water

---
 examples/water/data.spce  | 9029 +++++++++++++++++++++++++++++++++++++
 examples/water/data_file  |   19 +
 examples/water/in_massive |   80 +
 3 files changed, 9128 insertions(+)
 create mode 100644 examples/water/data.spce
 create mode 100644 examples/water/data_file
 create mode 100644 examples/water/in_massive

diff --git a/examples/water/data.spce b/examples/water/data.spce
new file mode 100644
index 0000000000..1e8a4a0913
--- /dev/null
+++ b/examples/water/data.spce
@@ -0,0 +1,9029 @@
+LAMMPS Atom File
+
+         4500 atoms
+         3000 bonds
+         1500 angles
+            0 dihedrals
+            0 impropers
+
+        2 atom types
+        1 bond types
+        1 angle types
+
+     0.02645   35.53280  xlo xhi
+     0.02645   35.53280  ylo yhi
+     0.02641   35.47360  zlo zhi
+
+Masses
+
+	1	15.9994
+	2	1.00794
+
+Atoms
+
+      1    1  1 -0.8472   12.12456   28.09298   22.27452  0  1  0
+      2    1  2  0.4236   12.53683   28.75606   22.89928  0  1  0
+      3    1  2  0.4236   11.49482   28.56390   21.65678  0  1  0
+      4    2  1 -0.8472    1.17079   29.37777   23.72984  1 -1  0
+      5    2  2  0.4236    1.91804   29.48483   23.07399  1 -1  0
+      6    2  2  0.4236    0.40074   28.91964   23.28586  1 -1  0
+      7    3  1 -0.8472   29.68313   14.73733   21.62793 -1  0  0
+      8    3  2  0.4236   30.54284   14.93741   21.15800 -1  0  0
+      9    3  2  0.4236   29.73135   15.07344   22.56848 -1  0  0
+     10    4  1 -0.8472   10.87272    7.00153   35.10920  0  1  0
+     11    4  2  0.4236   11.11057    6.21663   34.53712  0  1  0
+     12    4  2  0.4236    9.95658    7.32301   34.86983  0  1  0
+     13    5  1 -0.8472    9.46588    6.43648   19.79899  0  1  0
+     14    5  2  0.4236    9.04840    6.32936   18.89668  0  1  0
+     15    5  2  0.4236   10.31722    5.91326   19.83657  0  1  0
+     16    6  1 -0.8472    3.17905   29.69801   22.11922  0  0  0
+     17    6  2  0.4236    3.19240   30.63289   21.76465  0  0  0
+     18    6  2  0.4236    3.38651   29.05797   21.37944  0  0  0
+     19    7  1 -0.8472   23.38618   11.29979   30.78238  0  0  0
+     20    7  2  0.4236   23.69882   10.46688   31.23897  0  0  0
+     21    7  2  0.4236   24.17354   11.79208   30.41132  0  0  0
+     22    8  1 -0.8472   11.03761   10.46106   30.14741  0  1  0
+     23    8  2  0.4236   10.94682   11.45112   30.25464  0  1  0
+     24    8  2  0.4236   11.60678   10.09680   30.88450  0  1  0
+     25    9  1 -0.8472   26.24001   25.40937   21.06754  0  0  0
+     26    9  2  0.4236   25.67045   26.09258   21.52442  0  0  0
+     27    9  2  0.4236   26.22311   25.56759   20.08030  0  0  0
+     28   10  1 -0.8472   10.84087   35.33915   19.78347  0 -1  0
+     29   10  2  0.4236   10.20697    0.54421   19.48018  0  0  0
+     30   10  2  0.4236   11.06253   34.74012   19.01405  0 -1  0
+     31   11  1 -0.8472   20.07383    4.95885   33.62365  0  1  0
+     32   11  2  0.4236   19.77359    5.87080   33.90322  0  1  0
+     33   11  2  0.4236   20.68149    4.57954   34.32139  0  1  0
+     34   12  1 -0.8472   12.43897   28.56656   17.39837  0  0  0
+     35   12  2  0.4236   12.80348   27.99505   18.13354  0  0  0
+     36   12  2  0.4236   11.63887   28.12177   16.99597  0  0  0
+     37   13  1 -0.8472   14.80338    7.14199    1.42116  0  0  0
+     38   13  2  0.4236   14.86001    6.68442    0.53382  0  0  0
+     39   13  2  0.4236   14.13589    6.67036    1.99737  0  0  0
+     40   14  1 -0.8472   15.87968   22.18330   24.13468  1 -1  0
+     41   14  2  0.4236   15.97100   22.71526   23.29285  1 -1  0
+     42   14  2  0.4236   16.69618   22.30846   24.69826  1 -1  0
+     43   15  1 -0.8472   13.29194   18.30473   12.37157  1  0  0
+     44   15  2  0.4236   12.55838   18.63231   12.96701  1  0  0
+     45   15  2  0.4236   13.24823   18.78335   11.49467  1  0  0
+     46   16  1 -0.8472   20.27409   23.94157   15.50212  0  0  0
+     47   16  2  0.4236   20.17851   24.67734   14.83167  0  0  0
+     48   16  2  0.4236   20.62006   23.12024   15.04857  0  0  0
+     49   17  1 -0.8472   30.10203   10.78182   14.24321  1  0  0
+     50   17  2  0.4236   29.40171   11.00523   13.56532  1  0  0
+     51   17  2  0.4236   29.70120   10.21329   14.96159  1  0  0
+     52   18  1 -0.8472   19.71525   12.98975   25.40578  0  0  0
+     53   18  2  0.4236   20.21522   13.35852   26.18938  0  0  0
+     54   18  2  0.4236   18.75253   12.87297   25.64962  0  0  0
+     55   19  1 -0.8472    4.22362   18.99305   32.62946  1  0  0
+     56   19  2  0.4236    4.05067   18.17865   32.07556  1  0  0
+     57   19  2  0.4236    3.38513   19.53353   32.69833  1  0  0
+     58   20  1 -0.8472   17.67279   30.86798   34.86933  1 -1  0
+     59   20  2  0.4236   17.18866   31.74218   34.90528  1 -1  0
+     60   20  2  0.4236   18.18607   30.80612   34.01339  1 -1  0
+     61   21  1 -0.8472    7.49194   27.84024   34.65598  0  0  0
+     62   21  2  0.4236    7.36412   27.37987   33.77752  0  0  0
+     63   21  2  0.4236    7.83650   27.18529   35.32848  0  0  0
+     64   22  1 -0.8472    9.58199    8.75878   28.38767  0  0  0
+     65   22  2  0.4236    8.89931    8.96106   27.68557  0  0  0
+     66   22  2  0.4236    9.61451    9.50981   29.04713  0  0  0
+     67   23  1 -0.8472   18.15447    7.97877    4.02967  1  0  0
+     68   23  2  0.4236   17.65379    8.02465    3.16529  1  0  0
+     69   23  2  0.4236   17.56073    7.59903    4.73904  1  0  0
+     70   24  1 -0.8472   13.45467   10.30195   21.94603  0  0  0
+     71   24  2  0.4236   14.12655   11.01716   21.75366  0  0  0
+     72   24  2  0.4236   13.15542   10.37304   22.89754  0  0  0
+     73   25  1 -0.8472   28.77370    1.83495    6.23711  0  0  0
+     74   25  2  0.4236   29.55410    1.23316    6.06742  0  0  0
+     75   25  2  0.4236   28.43863    1.69170    7.16831  0  0  0
+     76   26  1 -0.8472   21.17410    3.00906    4.56251  0  1  0
+     77   26  2  0.4236   21.00772    2.96011    5.54734  0  1  0
+     78   26  2  0.4236   21.17488    3.96581    4.27178  0  1  0
+     79   27  1 -0.8472   15.86257   20.77629   10.34675  1 -1  0
+     80   27  2  0.4236   15.84751   19.99231   10.96732  1 -1  0
+     81   27  2  0.4236   15.76759   20.45695    9.40393  1 -1  0
+     82   28  1 -0.8472   19.37283    6.41248   28.33230  0  0  0
+     83   28  2  0.4236   19.86925    6.14505   27.50645  0  0  0
+     84   28  2  0.4236   19.23659    7.40311   28.33322  0  0  0
+     85   29  1 -0.8472   19.69874   26.80111   22.56675 -1 -1  0
+     86   29  2  0.4236   20.51873   26.54536   22.05471 -1 -1  0
+     87   29  2  0.4236   19.52519   26.12131   23.27927 -1 -1  0
+     88   30  1 -0.8472   10.44934    1.95847    4.23874  1  1  0
+     89   30  2  0.4236   10.99436    1.49085    4.93460  1  1  0
+     90   30  2  0.4236   10.84502    2.85816    4.05448  1  1  0
+     91   31  1 -0.8472    6.35411   29.19722   23.17920  0  0  0
+     92   31  2  0.4236    5.50252   29.65394   23.43641  0  0  0
+     93   31  2  0.4236    7.01350   29.87731   22.85887  0  0  0
+     94   32  1 -0.8472   27.70305   33.63868    1.45545  0  0  0
+     95   32  2  0.4236   27.45511   34.56848    1.72731  0  0  0
+     96   32  2  0.4236   28.23820   33.21008    2.18338  0  0  0
+     97   33  1 -0.8472   34.54150   25.90721   10.97268  0  0  0
+     98   33  2  0.4236   34.26945   25.07242   10.49403  0  0  0
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+   1321   1   3962   3961   3963
+   1322   1   3965   3964   3966
+   1323   1   3968   3967   3969
+   1324   1   3971   3970   3972
+   1325   1   3974   3973   3975
+   1326   1   3977   3976   3978
+   1327   1   3980   3979   3981
+   1328   1   3983   3982   3984
+   1329   1   3986   3985   3987
+   1330   1   3989   3988   3990
+   1331   1   3992   3991   3993
+   1332   1   3995   3994   3996
+   1333   1   3998   3997   3999
+   1334   1   4001   4000   4002
+   1335   1   4004   4003   4005
+   1336   1   4007   4006   4008
+   1337   1   4010   4009   4011
+   1338   1   4013   4012   4014
+   1339   1   4016   4015   4017
+   1340   1   4019   4018   4020
+   1341   1   4022   4021   4023
+   1342   1   4025   4024   4026
+   1343   1   4028   4027   4029
+   1344   1   4031   4030   4032
+   1345   1   4034   4033   4035
+   1346   1   4037   4036   4038
+   1347   1   4040   4039   4041
+   1348   1   4043   4042   4044
+   1349   1   4046   4045   4047
+   1350   1   4049   4048   4050
+   1351   1   4052   4051   4053
+   1352   1   4055   4054   4056
+   1353   1   4058   4057   4059
+   1354   1   4061   4060   4062
+   1355   1   4064   4063   4065
+   1356   1   4067   4066   4068
+   1357   1   4070   4069   4071
+   1358   1   4073   4072   4074
+   1359   1   4076   4075   4077
+   1360   1   4079   4078   4080
+   1361   1   4082   4081   4083
+   1362   1   4085   4084   4086
+   1363   1   4088   4087   4089
+   1364   1   4091   4090   4092
+   1365   1   4094   4093   4095
+   1366   1   4097   4096   4098
+   1367   1   4100   4099   4101
+   1368   1   4103   4102   4104
+   1369   1   4106   4105   4107
+   1370   1   4109   4108   4110
+   1371   1   4112   4111   4113
+   1372   1   4115   4114   4116
+   1373   1   4118   4117   4119
+   1374   1   4121   4120   4122
+   1375   1   4124   4123   4125
+   1376   1   4127   4126   4128
+   1377   1   4130   4129   4131
+   1378   1   4133   4132   4134
+   1379   1   4136   4135   4137
+   1380   1   4139   4138   4140
+   1381   1   4142   4141   4143
+   1382   1   4145   4144   4146
+   1383   1   4148   4147   4149
+   1384   1   4151   4150   4152
+   1385   1   4154   4153   4155
+   1386   1   4157   4156   4158
+   1387   1   4160   4159   4161
+   1388   1   4163   4162   4164
+   1389   1   4166   4165   4167
+   1390   1   4169   4168   4170
+   1391   1   4172   4171   4173
+   1392   1   4175   4174   4176
+   1393   1   4178   4177   4179
+   1394   1   4181   4180   4182
+   1395   1   4184   4183   4185
+   1396   1   4187   4186   4188
+   1397   1   4190   4189   4191
+   1398   1   4193   4192   4194
+   1399   1   4196   4195   4197
+   1400   1   4199   4198   4200
+   1401   1   4202   4201   4203
+   1402   1   4205   4204   4206
+   1403   1   4208   4207   4209
+   1404   1   4211   4210   4212
+   1405   1   4214   4213   4215
+   1406   1   4217   4216   4218
+   1407   1   4220   4219   4221
+   1408   1   4223   4222   4224
+   1409   1   4226   4225   4227
+   1410   1   4229   4228   4230
+   1411   1   4232   4231   4233
+   1412   1   4235   4234   4236
+   1413   1   4238   4237   4239
+   1414   1   4241   4240   4242
+   1415   1   4244   4243   4245
+   1416   1   4247   4246   4248
+   1417   1   4250   4249   4251
+   1418   1   4253   4252   4254
+   1419   1   4256   4255   4257
+   1420   1   4259   4258   4260
+   1421   1   4262   4261   4263
+   1422   1   4265   4264   4266
+   1423   1   4268   4267   4269
+   1424   1   4271   4270   4272
+   1425   1   4274   4273   4275
+   1426   1   4277   4276   4278
+   1427   1   4280   4279   4281
+   1428   1   4283   4282   4284
+   1429   1   4286   4285   4287
+   1430   1   4289   4288   4290
+   1431   1   4292   4291   4293
+   1432   1   4295   4294   4296
+   1433   1   4298   4297   4299
+   1434   1   4301   4300   4302
+   1435   1   4304   4303   4305
+   1436   1   4307   4306   4308
+   1437   1   4310   4309   4311
+   1438   1   4313   4312   4314
+   1439   1   4316   4315   4317
+   1440   1   4319   4318   4320
+   1441   1   4322   4321   4323
+   1442   1   4325   4324   4326
+   1443   1   4328   4327   4329
+   1444   1   4331   4330   4332
+   1445   1   4334   4333   4335
+   1446   1   4337   4336   4338
+   1447   1   4340   4339   4341
+   1448   1   4343   4342   4344
+   1449   1   4346   4345   4347
+   1450   1   4349   4348   4350
+   1451   1   4352   4351   4353
+   1452   1   4355   4354   4356
+   1453   1   4358   4357   4359
+   1454   1   4361   4360   4362
+   1455   1   4364   4363   4365
+   1456   1   4367   4366   4368
+   1457   1   4370   4369   4371
+   1458   1   4373   4372   4374
+   1459   1   4376   4375   4377
+   1460   1   4379   4378   4380
+   1461   1   4382   4381   4383
+   1462   1   4385   4384   4386
+   1463   1   4388   4387   4389
+   1464   1   4391   4390   4392
+   1465   1   4394   4393   4395
+   1466   1   4397   4396   4398
+   1467   1   4400   4399   4401
+   1468   1   4403   4402   4404
+   1469   1   4406   4405   4407
+   1470   1   4409   4408   4410
+   1471   1   4412   4411   4413
+   1472   1   4415   4414   4416
+   1473   1   4418   4417   4419
+   1474   1   4421   4420   4422
+   1475   1   4424   4423   4425
+   1476   1   4427   4426   4428
+   1477   1   4430   4429   4431
+   1478   1   4433   4432   4434
+   1479   1   4436   4435   4437
+   1480   1   4439   4438   4440
+   1481   1   4442   4441   4443
+   1482   1   4445   4444   4446
+   1483   1   4448   4447   4449
+   1484   1   4451   4450   4452
+   1485   1   4454   4453   4455
+   1486   1   4457   4456   4458
+   1487   1   4460   4459   4461
+   1488   1   4463   4462   4464
+   1489   1   4466   4465   4467
+   1490   1   4469   4468   4470
+   1491   1   4472   4471   4473
+   1492   1   4475   4474   4476
+   1493   1   4478   4477   4479
+   1494   1   4481   4480   4482
+   1495   1   4484   4483   4485
+   1496   1   4487   4486   4488
+   1497   1   4490   4489   4491
+   1498   1   4493   4492   4494
+   1499   1   4496   4495   4497
+   1500   1   4499   4498   4500
diff --git a/examples/water/data_file b/examples/water/data_file
new file mode 100644
index 0000000000..2f9d10f9d9
--- /dev/null
+++ b/examples/water/data_file
@@ -0,0 +1,19 @@
+#  data
+
+3 atoms
+
+1 atom types
+
+-10 10 xlo xhi
+-10 10 ylo yhi
+-10 10 zlo zhi
+
+Masses
+
+1 1.00794
+
+Atoms
+
+1 1 0 0 0
+2 1 1.5 0 0
+3 1 0 1.5 0
diff --git a/examples/water/in_massive b/examples/water/in_massive
new file mode 100644
index 0000000000..22d4e0c661
--- /dev/null
+++ b/examples/water/in_massive
@@ -0,0 +1,80 @@
+#LAMMPS input file
+#All informations can be find on http://lammps.sandia.gov/
+
+#choose the system of unit (real, metal, SI...)
+units           real
+
+#define the boundary conditions, periodic here
+boundary        p p p
+
+#define the atom style, bond style and angle style
+atom_style      full
+bond_style      harmonic
+angle_style     harmonic
+atom_modify	map array
+
+#comm_modify cutoff 15
+#atom_modify first water
+#neigh_modify cluster yes
+
+#choose the interaction between water molecules:
+pair_style		lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 
+pair_modify		table 0
+#water model is TIP4P/2005
+#water molecules less than 1nm from each other interact via a cut lennard jones potential 
+#water molecules interact via coulomb interactions calculated in real or conjugate space depending on the distance separating molecules
+
+#define the long-range solver (here for long range coulombic interaction)
+suffix off
+newton on
+kspace_style	pppm/tip4p 1.0e-5
+suffix on
+
+#neighbor 5.0 bin
+#neigh_modify	every 1 check yes
+
+#import the initial position of atoms, the coordinates of the box, etc
+read_data	data.spce
+replicate 2 2 2
+
+#define the pair coeff for LJ interaction
+pair_coeff      * * 0.0 0.0
+pair_coeff      1 1 0.1852 3.1589
+
+#define the coef for water molecule (distances between O-H and angle between H-O-H atoms)
+bond_coeff      1 0.0 0.9572
+angle_coeff     1 0.0 104.52
+
+#define groups
+group		water type 1 2
+
+#maintain the water molecule rigid
+fix             1 water shake 1.0e-4 200 0 b 1 a 1
+
+#udate position and velocity each timesteps using constant NVE integration
+fix		2 water nve
+
+#apply Langevin thermostat on water molecules
+#fix             3 water langevin 300.0 300.0 100.0 123
+
+#choose how often you want thermodynamic info to be print during the computation
+thermo          1000
+thermo_modify   flush yes
+thermo_style custom step etotal ke pe temp  evdwl ecoul elong press
+#thermo_modify  format float "%.15g"
+#give an initial random velocity to water molecule (corresponding to a temperature equal to 300K)
+velocity		water create 300 123
+
+#print the position of atoms to visualise it with VMD for example
+#dump			4 all atom 1 dump.lammpstrj
+#dump_modify		4 flush yes
+
+#if $(is_active(package,gpu)) &
+# then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz"&
+# else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+
+#choose the timestep, 2fs is a common choice
+timestep		1
+
+#run during 50000 timestep (0.1 ns)
+run		50000

From ca8d1ac2ff54a5826d9acbe175619e14a50673de Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Sun, 17 Nov 2019 22:02:56 +0300
Subject: [PATCH 042/199] Simplify tip4p GPU memory resize using 'resize_ib'

---
 lib/gpu/lal_lj_tip4p_long.cpp | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
index 9714e9bf91..7e2b8ecc72 100644
--- a/lib/gpu/lal_lj_tip4p_long.cpp
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -182,11 +182,12 @@ void LJ_TIP4PLong<numtyp, acctyp>::loop(const bool _eflag, const bool _vflag) {
 
   this->k_pair.set_size(GX,BX);
   if (vflag){
-	  this->ansO.resize(ainum*3);
+	  this->ansO.resize_ib(ainum*3);
   } else {
-	  this->ansO.resize(ainum);
+	  this->ansO.resize_ib(ainum);
   }
   this->ansO.zero();
+  this->device->gpu->sync();
   this->k_pair.run(&this->atom->x, &lj1, &lj3, &_lj_types, &sp_lj,
           &this->nbor->dev_nbor, &this->_nbor_data->begin(),
           &this->ans->force, &this->ans->engv, &eflag, &vflag,
@@ -210,28 +211,24 @@ void LJ_TIP4PLong<numtyp, acctyp>::copy_relations_data(int **hn, double **newsit
 		int* tag, int *map_array, int map_size, int *sametag, int max_same, int ago){
 	int nall = n;
 	const int hn_sz = n*4; // matrix size = col size * col number
-	if(hn_sz > hneight.cols()){
-		hneight.resize(hn_sz+1);
-	}
+	hneight.resize_ib(hn_sz+1);
 	if (ago == 0)
 		hneight.zero();
-	if(n > m.cols()){
-		m.resize(n+1);
-	}
+	m.resize_ib(n+1);
 	m.zero();
 
     UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
-    if(this->tag.cols() < nall) this->tag.resize(nall);
+    this->tag.resize_ib(nall);
     for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
     ucl_copy(this->tag, host_tag_write, nall, false);
 
     if(max_same>host_tag_write.cols()) host_tag_write.resize(max_same);
-    if(this->atom_sametag.cols() < nall) this->atom_sametag.resize(nall);
+    this->atom_sametag.resize_ib(nall);
     for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
     ucl_copy(this->atom_sametag, host_tag_write, nall, false);
 
     if(map_size>host_tag_write.cols()) host_tag_write.resize(map_size);
-    if(this->map_array.cols() < map_size) this->map_array.resize(map_size);
+    this->map_array.resize_ib(map_size);
     for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
     ucl_copy(this->map_array, host_tag_write, map_size, false);
 

From 4febc7f794dd797aac0c77aec96fc09219b2b9bb Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Sun, 17 Nov 2019 22:22:56 +0300
Subject: [PATCH 043/199] Add copyright and fix style

---
 doc/src/pair_lj.rst                    |   3 +
 lib/gpu/lal_lj_tip4p_long.cpp          | 121 ++--
 lib/gpu/lal_lj_tip4p_long.cu           | 900 +++++++++++++------------
 lib/gpu/lal_lj_tip4p_long.h            |  35 +-
 lib/gpu/lal_lj_tip4p_long_ext.cpp      |  83 ++-
 src/GPU/pair_lj_cut_tip4p_long_gpu.cpp | 113 ++--
 src/GPU/pair_lj_cut_tip4p_long_gpu.h   |  18 +-
 7 files changed, 684 insertions(+), 589 deletions(-)

diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst
index 18bba57c1a..54140a9faf 100644
--- a/doc/src/pair_lj.rst
+++ b/doc/src/pair_lj.rst
@@ -102,6 +102,9 @@ pair\_style lj/cut/tip4p/long/omp command
 pair\_style lj/cut/tip4p/long/opt command
 =========================================
 
+pair\_style lj/cut/tip4p/long/gpu command
+=====================================
+
 Syntax
 """"""
 
diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
index 7e2b8ecc72..9b20aea638 100644
--- a/lib/gpu/lal_lj_tip4p_long.cpp
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -1,3 +1,18 @@
+/**************************************************************************
+                               lj_tip4p_long.cpp
+                             -------------------
+                              V. Nikolskiy (HSE)
+
+  Class for acceleration of the lj/tip4p/long pair style
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : thevsevak@gmail.com
+***************************************************************************/
+
 #if defined(USE_OPENCL)
 #include "lj_tip4p_long_cl.h"
 #elif defined(USE_CUDART)
@@ -29,21 +44,21 @@ int LJ_TIP4PLong<numtyp, acctyp>::bytes_per_atom(const int max_nbors) const {
 
 template <class numtyp, class acctyp>
 int LJ_TIP4PLong<numtyp, acctyp>::init(const int ntypes,
-                          double **host_cutsq, double **host_lj1,
-                          double **host_lj2, double **host_lj3,
-                          double **host_lj4, double **host_offset,
-                          double *host_special_lj, const int nlocal,
-						  const int tH, const int tO,
-						  const double a, const double qd,
-                          const int nall, const int max_nbors,
-                          const int maxspecial, const double cell_size,
-                          const double gpu_split, FILE *_screen,
-						  double **host_cut_ljsq,
-						  const double host_cut_coulsq, const double host_cut_coulsqplus,
-						  double *host_special_coul, const double qqrd2e,
-						  const double g_ewald, int* tag,
-							 int *map_array, int map_size,
-							 int *sametag, int max_same) {
+    double **host_cutsq, double **host_lj1,
+    double **host_lj2, double **host_lj3,
+    double **host_lj4, double **host_offset,
+    double *host_special_lj, const int nlocal,
+    const int tH, const int tO,
+    const double a, const double qd,
+    const int nall, const int max_nbors,
+    const int maxspecial, const double cell_size,
+    const double gpu_split, FILE *_screen,
+    double **host_cut_ljsq,
+    const double host_cut_coulsq, const double host_cut_coulsqplus,
+    double *host_special_coul, const double qqrd2e,
+    const double g_ewald, int* tag,
+    int *map_array, int map_size,
+    int *sametag, int max_same) {
   int success;
   success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
                             _screen,lj_tip4p_long,"k_lj_tip4p_long");
@@ -91,7 +106,7 @@ int LJ_TIP4PLong<numtyp, acctyp>::init(const int ntypes,
   }
   ucl_copy(sp_lj,host_write,8,false);
 
-  force_comp.alloc(72*72, *(this->ucl_device), UCL_READ_WRITE);
+  //force_comp.alloc(72*72, *(this->ucl_device), UCL_READ_WRITE);
 
   _qqrd2e=qqrd2e;
   _g_ewald=g_ewald;
@@ -103,26 +118,26 @@ int LJ_TIP4PLong<numtyp, acctyp>::init(const int ntypes,
   ansO.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
 
   // Allocate a host write buffer for data initialization
-  UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
-  this->tag.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
+  UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_READ_WRITE);
+  this->tag.alloc(nall,*(this->ucl_device), UCL_READ_ONLY);
   for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
   ucl_copy(this->tag, host_tag_write, nall, false);
 
   //if(max_same>host_tag_write.cols()) host_tag_write.resize(max_same);
-  this->atom_sametag.alloc(nall, *(this->ucl_device), UCL_READ_WRITE);
+  this->atom_sametag.alloc(nall, *(this->ucl_device), UCL_READ_ONLY);
   for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
   ucl_copy(this->atom_sametag, host_tag_write, nall, false);
 
-  if(map_size>host_tag_write.cols()) host_tag_write.resize(map_size);
-  this->map_array.alloc(map_size,*(this->ucl_device), UCL_READ_WRITE);
+  host_tag_write.resize_ib(map_size);
+  this->map_array.alloc(map_size,*(this->ucl_device), UCL_READ_ONLY);
   for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
   ucl_copy(this->map_array, host_tag_write, map_size, false);
 
   _allocated=true;
   this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+cutsq.row_bytes()+
-                   sp_lj.row_bytes() + hneight.row_bytes()+m.row_bytes()+
-				   this->tag.row_bytes()+this->atom_sametag.row_bytes() +
-				   this->map_array.row_bytes();
+      sp_lj.row_bytes() + hneight.row_bytes()+m.row_bytes()+
+      this->tag.row_bytes()+this->atom_sametag.row_bytes() +
+      this->map_array.row_bytes();
   return 0;
 }
 
@@ -143,7 +158,7 @@ void LJ_TIP4PLong<numtyp, acctyp>::clear() {
   atom_sametag.clear();
   map_array.clear();
   ansO.clear();
-  force_comp.clear();
+  //force_comp.clear();
 
   k_pair_distrib.clear();
 
@@ -192,47 +207,47 @@ void LJ_TIP4PLong<numtyp, acctyp>::loop(const bool _eflag, const bool _vflag) {
           &this->nbor->dev_nbor, &this->_nbor_data->begin(),
           &this->ans->force, &this->ans->engv, &eflag, &vflag,
           &ainum, &nbor_pitch, &this->_threads_per_atom,
-			 &hneight, &m, &TypeO, &TypeH, &alpha,
-			 &this->atom->q, &cutsq, &_qqrd2e, &_g_ewald,
-			 &cut_coulsq, &cut_coulsqplus, &tag, &map_array,
-			 &atom_sametag, &this->ansO);
+          &hneight, &m, &TypeO, &TypeH, &alpha,
+          &this->atom->q, &cutsq, &_qqrd2e, &_g_ewald,
+          &cut_coulsq, &cut_coulsqplus, &tag, &map_array,
+          &atom_sametag, &this->ansO);
   GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
   this->k_pair_distrib.set_size(GX,BX);
   this->k_pair_distrib.run(&this->atom->x, &this->ans->force, &this->ans->engv, &eflag, &vflag,
-                     &ainum, &nbor_pitch, &this->_threads_per_atom,
-					 &hneight, &m, &TypeO, &TypeH, &alpha,
-					 &this->atom->q,  &this->ansO);
+      &ainum, &nbor_pitch, &this->_threads_per_atom,
+      &hneight, &m, &TypeO, &TypeH, &alpha,
+      &this->atom->q,  &this->ansO);
   this->time_pair.stop();
 }
 
 
 template <class numtyp, class acctyp>
 void LJ_TIP4PLong<numtyp, acctyp>::copy_relations_data(int **hn, double **newsite, int n,
-		int* tag, int *map_array, int map_size, int *sametag, int max_same, int ago){
-	int nall = n;
-	const int hn_sz = n*4; // matrix size = col size * col number
-	hneight.resize_ib(hn_sz+1);
-	if (ago == 0)
-		hneight.zero();
-	m.resize_ib(n+1);
-	m.zero();
+    int* tag, int *map_array, int map_size, int *sametag, int max_same, int ago){
+  int nall = n;
+  const int hn_sz = n*4; // matrix size = col size * col number
+  hneight.resize_ib(hn_sz);
+  if (ago == 0)
+    hneight.zero();
+  m.resize_ib(n);
+  m.zero();
 
-    UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
-    this->tag.resize_ib(nall);
-    for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
-    ucl_copy(this->tag, host_tag_write, nall, false);
+  UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
+  this->tag.resize_ib(nall);
+  for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
+  ucl_copy(this->tag, host_tag_write, nall, false);
 
-    if(max_same>host_tag_write.cols()) host_tag_write.resize(max_same);
-    this->atom_sametag.resize_ib(nall);
-    for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
-    ucl_copy(this->atom_sametag, host_tag_write, nall, false);
+  host_tag_write.resize_ib(max_same);
+  this->atom_sametag.resize_ib(nall);
+  for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
+  ucl_copy(this->atom_sametag, host_tag_write, nall, false);
 
-    if(map_size>host_tag_write.cols()) host_tag_write.resize(map_size);
-    this->map_array.resize_ib(map_size);
-    for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
-    ucl_copy(this->map_array, host_tag_write, map_size, false);
+  host_tag_write.resize_ib(map_size);
+  this->map_array.resize_ib(map_size);
+  for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
+  ucl_copy(this->map_array, host_tag_write, map_size, false);
 
-    host_tag_write.clear();
+  host_tag_write.clear();
 }
 
 template class LJ_TIP4PLong<PRECISION,ACC_PRECISION>;
diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
index 1ea6de1d41..2301cb39a7 100644
--- a/lib/gpu/lal_lj_tip4p_long.cu
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -1,3 +1,18 @@
+// **************************************************************************
+//                               lj_tip4p_long.cu
+//                             -------------------
+//                              V. Nikolskiy (HSE)
+//
+//  Device code for acceleration of the lj/tip4p/long pair style
+//
+// __________________________________________________________________________
+//    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+//    begin                :
+//    email                : thevsevak@gmail.com
+// ***************************************************************************/
+
 #ifdef NV_KERNEL
 
 #include "lal_aux_fun1.h"
@@ -14,6 +29,8 @@ texture<int2> q_tex;
 #define q_tex q_
 #endif
 
+#include <float.h>
+
 ucl_inline int atom_mapping(const __global int *map, int glob){
 	return map[glob];
 }
@@ -50,484 +67,487 @@ ucl_inline int closest_image(int i, int j, const __global int* sametag,
 }
 
 ucl_inline void compute_newsite(int iO, int  iH1, int  iH2,
-		__global numtyp4 *xM,
-		numtyp alpha, const __global numtyp4 *restrict x_){
-	numtyp4 xO;  fetch4(xO,iO,pos_tex);
-	numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
-	numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+    __global numtyp4 *xM,
+    numtyp alpha, const __global numtyp4 *restrict x_){
+  numtyp4 xO;  fetch4(xO,iO,pos_tex);
+  numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+  numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
 
-	numtyp delx1 = xH1.x - xO.x;
-	numtyp dely1 = xH1.y - xO.y;
-	numtyp delz1 = xH1.z - xO.z;
+  numtyp delx1 = xH1.x - xO.x;
+  numtyp dely1 = xH1.y - xO.y;
+  numtyp delz1 = xH1.z - xO.z;
 
-	numtyp delx2 = xH2.x - xO.x;
-	numtyp dely2 = xH2.y - xO.y;
-	numtyp delz2 = xH2.z - xO.z;
+  numtyp delx2 = xH2.x - xO.x;
+  numtyp dely2 = xH2.y - xO.y;
+  numtyp delz2 = xH2.z - xO.z;
 
-	numtyp ap = alpha * (numtyp)0.5;
+  numtyp ap = alpha * (numtyp)0.5;
 
-	(*xM).x = xO.x + ap * (delx1 + delx2);
-	(*xM).y = xO.y + ap * (dely1 + dely2);
-	(*xM).z = xO.z + ap * (delz1 + delz2);
+  (*xM).x = xO.x + ap * (delx1 + delx2);
+  (*xM).y = xO.y + ap * (dely1 + dely2);
+  (*xM).z = xO.z + ap * (delz1 + delz2);
 }
 
 __kernel void k_lj_tip4p_long_distrib(const __global numtyp4 *restrict x_,
-		__global acctyp4 *restrict ans,
-		__global acctyp *restrict engv,
-		const int eflag, const int vflag, const int inum,
-		const int nbor_pitch, const int t_per_atom,
-		__global int *restrict hneigh,
-		__global numtyp4 *restrict m,
-		const int typeO, const int typeH,
-		const numtyp alpha,
-		const __global numtyp *restrict q_, const __global acctyp4 *restrict ansO) {
-	int tid, ii, offset;
-	atom_info(t_per_atom,ii,tid,offset);
-	int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
+    __global acctyp4 *restrict ans,
+    __global acctyp *restrict engv,
+    const int eflag, const int vflag, const int inum,
+    const int nbor_pitch, const int t_per_atom,
+    __global int *restrict hneigh,
+    __global numtyp4 *restrict m,
+    const int typeO, const int typeH,
+    const numtyp alpha,
+    const __global numtyp *restrict q_, const __global acctyp4 *restrict ansO) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+  int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
 
-	acctyp4 f;
-	f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
 
-	if (i<inum) {
-		numtyp4 ix; fetch4(ix,i,pos_tex);// = x_[i];
-		int itype = ix.w;
-		acctyp4 fM, vM;
-		acctyp eM;
-		if (itype == typeH) {
-			int iO = hneigh[i*4];
-			if (iO < inum) {
-				fM = ansO[iO];
-				f.x += fM.x * (acctyp)0.5 * alpha;
-				f.y += fM.y * (acctyp)0.5 * alpha;
-				f.z += fM.z * (acctyp)0.5 * alpha;
-				if (vflag > 0) {
-					vM = ansO[inum  +iO];
-					engv[inum*2 + i] += vM.x * (acctyp)0.5 * alpha;
-					engv[inum*3 + i] += vM.y * (acctyp)0.5 * alpha;
-					engv[inum*4 + i] += vM.z * (acctyp)0.5 * alpha;
-					vM = ansO[inum*2+iO];
-					engv[inum*5 + i] += vM.x * (acctyp)0.5 * alpha;
-					engv[inum*6 + i] += vM.y * (acctyp)0.5 * alpha;
-					engv[inum*7 + i] += vM.z * (acctyp)0.5 * alpha;
-				}
-			}
-		} else {
-			fM = ansO[i];
-			int iH1 = hneigh[i*4  ];
-			int iH2 = hneigh[i*4+1];
-			f.x += fM.x * (acctyp)(1 - alpha);
-			f.y += fM.y * (acctyp)(1 - alpha);
-			f.z += fM.z * (acctyp)(1 - alpha);
-			if (eflag > 0) {
-				eM = engv[i+inum];
-				engv[inum+i] = eM*(acctyp)(1 - alpha);
-				if (iH1 < inum) engv[inum+iH1] += eM * (acctyp)0.5 * alpha;
-				if (iH2 < inum) engv[inum+iH2] += eM * (acctyp)0.5 * alpha;
-			}
-			if (vflag > 0) {
-				vM = ansO[inum   + i];
-				engv[inum*2 + i] += vM.x * (acctyp)(1 - alpha);
-				engv[inum*3 + i] += vM.y * (acctyp)(1 - alpha);
-				engv[inum*4 + i] += vM.z * (acctyp)(1 - alpha);
-				vM = ansO[inum*2 + i];
-				engv[inum*5 + i] += vM.x * (acctyp)(1 - alpha);
-				engv[inum*6 + i] += vM.y * (acctyp)(1 - alpha);
-				engv[inum*7 + i] += vM.z * (acctyp)(1 - alpha);
-			}
-		}
-	    acctyp4 old=ans[i];
-	    old.x+=f.x;
-	    old.y+=f.y;
-	    old.z+=f.z;
-	    ans[i]=old;
-	} // if ii
+  if (i<inum) {
+    numtyp4 ix; fetch4(ix,i,pos_tex);// = x_[i];
+    int itype = ix.w;
+    acctyp4 fM, vM;
+    acctyp eM;
+    if (itype == typeH) {
+      int iO = hneigh[i*4];
+      if (iO < inum) {
+        fM = ansO[iO];
+        f.x += fM.x * (acctyp)0.5 * alpha;
+        f.y += fM.y * (acctyp)0.5 * alpha;
+        f.z += fM.z * (acctyp)0.5 * alpha;
+        if (vflag > 0) {
+          vM = ansO[inum  +iO];
+          engv[inum*2 + i] += vM.x * (acctyp)0.5 * alpha;
+          engv[inum*3 + i] += vM.y * (acctyp)0.5 * alpha;
+          engv[inum*4 + i] += vM.z * (acctyp)0.5 * alpha;
+          vM = ansO[inum*2+iO];
+          engv[inum*5 + i] += vM.x * (acctyp)0.5 * alpha;
+          engv[inum*6 + i] += vM.y * (acctyp)0.5 * alpha;
+          engv[inum*7 + i] += vM.z * (acctyp)0.5 * alpha;
+        }
+      }
+    } else {
+      fM = ansO[i];
+      int iH1 = hneigh[i*4  ];
+      int iH2 = hneigh[i*4+1];
+      f.x += fM.x * (acctyp)(1 - alpha);
+      f.y += fM.y * (acctyp)(1 - alpha);
+      f.z += fM.z * (acctyp)(1 - alpha);
+      if (eflag > 0) {
+        eM = engv[i+inum];
+        engv[inum+i] = eM*(acctyp)(1 - alpha);
+        if (iH1 < inum) engv[inum+iH1] += eM * (acctyp)0.5 * alpha;
+        if (iH2 < inum) engv[inum+iH2] += eM * (acctyp)0.5 * alpha;
+      }
+      if (vflag > 0) {
+        vM = ansO[inum   + i];
+        engv[inum*2 + i] += vM.x * (acctyp)(1 - alpha);
+        engv[inum*3 + i] += vM.y * (acctyp)(1 - alpha);
+        engv[inum*4 + i] += vM.z * (acctyp)(1 - alpha);
+        vM = ansO[inum*2 + i];
+        engv[inum*5 + i] += vM.x * (acctyp)(1 - alpha);
+        engv[inum*6 + i] += vM.y * (acctyp)(1 - alpha);
+        engv[inum*7 + i] += vM.z * (acctyp)(1 - alpha);
+      }
+    }
+    acctyp4 old=ans[i];
+    old.x+=f.x;
+    old.y+=f.y;
+    old.z+=f.z;
+    ans[i]=old;
+  } // if ii
 }
 
 __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
-		const __global numtyp4 *restrict lj1,
-		const __global numtyp4 *restrict lj3,
-		const int lj_types,
-		const __global numtyp *restrict sp_lj,
-		const __global int * dev_nbor,
-		const __global int * dev_packed,
-		__global acctyp4 *restrict ans,
-		__global acctyp *restrict engv,
-		const int eflag, const int vflag, const int inum,
-		const int nbor_pitch, const int t_per_atom,
-		__global int *restrict hneigh,
-		__global numtyp4 *restrict m,
-		const int typeO, const int typeH,
-		const numtyp alpha,
-		const __global numtyp *restrict q_,
-		const __global numtyp *restrict cutsq,
-		const numtyp qqrd2e, const numtyp g_ewald,
-		const numtyp cut_coulsq, const numtyp cut_coulsqplus,
-		const __global int *restrict tag, const __global int *restrict map,
-		const __global int *restrict sametag, __global acctyp4 *restrict ansO) {
-	int tid, ii, offset;
-	atom_info(t_per_atom,ii,tid,offset);
+    const __global numtyp4 *restrict lj1,
+    const __global numtyp4 *restrict lj3,
+    const int lj_types,
+    const __global numtyp *restrict sp_lj,
+    const __global int * dev_nbor,
+    const __global int * dev_packed,
+    __global acctyp4 *restrict ans,
+    __global acctyp *restrict engv,
+    const int eflag, const int vflag, const int inum,
+    const int nbor_pitch, const int t_per_atom,
+    __global int *restrict hneigh,
+    __global numtyp4 *restrict m,
+    const int typeO, const int typeH,
+    const numtyp alpha,
+    const __global numtyp *restrict q_,
+    const __global numtyp *restrict cutsq,
+    const numtyp qqrd2e, const numtyp g_ewald,
+    const numtyp cut_coulsq, const numtyp cut_coulsqplus,
+    const __global int *restrict tag, const __global int *restrict map,
+    const __global int *restrict sametag, __global acctyp4 *restrict ansO) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
 
-	acctyp energy = (acctyp)0;
-	acctyp e_coul = (acctyp)0;
-	acctyp4 f, fO;
-	f.x=(acctyp)0;  f.y=(acctyp)0;  f.z=(acctyp)0;
-	fO.x=(acctyp)0; fO.y=(acctyp)0; fO.z=(acctyp)0;
-	acctyp virial[6],vO[6];
-	for (int i=0; i<6; i++) {
-		virial[i]=(acctyp)0;
-		vO[i]=(acctyp)0;
-	}
+  acctyp energy = (acctyp)0;
+  acctyp e_coul = (acctyp)0;
+  acctyp4 f, fO;
+  f.x=(acctyp)0;  f.y=(acctyp)0;  f.z=(acctyp)0;
+  fO.x=(acctyp)0; fO.y=(acctyp)0; fO.z=(acctyp)0;
+  acctyp virial[6],vO[6];
+  for (int i=0; i<6; i++) {
+    virial[i]=(acctyp)0;
+    vO[i]=(acctyp)0;
+  }
 
-	if (ii<inum) {
-		int i, numj, nbor, nbor_end;
-		__local int n_stride;
-		nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
-				n_stride,nbor_end,nbor);
+  if (ii<inum) {
+    int i, numj, nbor, nbor_end;
+    __local int n_stride;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
+        n_stride,nbor_end,nbor);
 
-		numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
-		numtyp qtmp; fetch(qtmp,i,q_tex);
-		int itype = ix.w;
-		numtyp4 x1 = ix;
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    numtyp qtmp; fetch(qtmp,i,q_tex);
+    int itype = ix.w;
+    numtyp4 x1 = ix;
 
-		int non_local_oxy = 0;
-		int iH1, iH2, iO;
+    int non_local_oxy = 0;
+    int iH1, iH2, iO;
 
-		if(itype == typeO) {
-			iO  = i;
-			if (hneigh[i*4+2] != -1) {
-				iH1 = atom_mapping(map, tag[i] + 1);
-				iH2 = atom_mapping(map, tag[i] + 2);
-				// set iH1,iH2 to closest image to O
-				iH1 = closest_image(i, iH1, sametag, x_);
-				iH2 = closest_image(i, iH2, sametag, x_);
-				hneigh[  i*4  ] = iH1;
-				hneigh[  i*4+1] = iH2;
-				hneigh[  i*4+2] = -1;
-				hneigh[iH1*4  ] = i;
-				hneigh[iH1*4+1] += -1;
-				hneigh[iH1*4+2] = -1;
-				hneigh[iH2*4  ] = i;
-				hneigh[iH2*4+1] += -1;
-				hneigh[iH2*4+2] = -1;
-			} else {
-				iH1 = hneigh[i*4  ];
-				iH2 = hneigh[i*4+1];
-			}
-			if(m[iO].w == 0) {
-				compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
-				m[iO].w = qtmp;
-			}
-			x1 = m[iO];
-		} else {
-			if (hneigh[i*4+2] != -1) {
-				int iI, iH;
-				iI = atom_mapping(map,tag[i] - 1);
-				numtyp4 iIx; fetch4(iIx,iI,pos_tex); //x_[iI];
-				if (iIx.w == typeH) {
-					iO = atom_mapping(map,tag[i] - 2);
-					iO  = closest_image(i, iO, sametag, x_);
-					iH1 = closest_image(i, iI, sametag, x_);
-					iH2 = i;
-				} else if (iIx.w == typeO) {
-					iH = atom_mapping(map, tag[i] + 1);
-					iO  = closest_image(i,iI,sametag, x_);
-					iH1 = i;
-					iH2 = closest_image(i,iH,sametag, x_);
-				}
+    if(itype == typeO) {
+      iO  = i;
+      if (hneigh[i*4+2] != -1) {
+        iH1 = atom_mapping(map, tag[i] + 1);
+        iH2 = atom_mapping(map, tag[i] + 2);
+        // set iH1,iH2 to closest image to O
+        iH1 = closest_image(i, iH1, sametag, x_);
+        iH2 = closest_image(i, iH2, sametag, x_);
+        hneigh[  i*4  ] = iH1;
+        hneigh[  i*4+1] = iH2;
+        hneigh[  i*4+2] = -1;
+        hneigh[iH1*4  ] = i;
+        hneigh[iH1*4+1] += -1;
+        hneigh[iH1*4+2] = -1;
+        hneigh[iH2*4  ] = i;
+        hneigh[iH2*4+1] += -1;
+        hneigh[iH2*4+2] = -1;
+      } else {
+        iH1 = hneigh[i*4  ];
+        iH2 = hneigh[i*4+1];
+      }
+      if(fabs(m[iO].w) <= FLT_EPSILON) {
+        compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
+        m[iO].w = qtmp;
+      }
+      x1 = m[iO];
+    } else {
+      if (hneigh[i*4+2] != -1) {
+        int iI, iH;
+        iI = atom_mapping(map,tag[i] - 1);
+        numtyp4 iIx; fetch4(iIx,iI,pos_tex); //x_[iI];
+        if ((int)iIx.w == typeH) {
+          iO = atom_mapping(map,tag[i] - 2);
+          iO  = closest_image(i, iO, sametag, x_);
+          iH1 = closest_image(i, iI, sametag, x_);
+          iH2 = i;
+        } else { //if ((int)iIx.w == typeO)
+          iH = atom_mapping(map, tag[i] + 1);
+          iO  = closest_image(i,iI,sametag, x_);
+          iH1 = i;
+          iH2 = closest_image(i,iH,sametag, x_);
+        }
 
-				hneigh[iH1*4+0] = iO;
-				hneigh[iH1*4+1] += -1;
-				hneigh[iH1*4+2] = -1;
+        hneigh[iH1*4+0] = iO;
+        hneigh[iH1*4+1] += -1;
+        hneigh[iH1*4+2] = -1;
 
-				hneigh[iH2*4+0] = iO;
-				hneigh[iH2*4+1] += -1;
-				hneigh[iH2*4+2] = -1;
+        hneigh[iH2*4+0] = iO;
+        hneigh[iH2*4+1] += -1;
+        hneigh[iH2*4+2] = -1;
 
-				hneigh[iO*4+0] = iH1;
-				hneigh[iO*4+1] = iH2;
-				hneigh[iO*4+2] = -1;
-			} else {
-				iO  = hneigh[i *4  ];
-				iH1 = hneigh[iO*4  ];
-				iH2 = hneigh[iO*4+1];
-			}
-			if (iO >= inum) {
-				non_local_oxy = 1;
-				if(m[iO].w == 0) {
-					compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
-					numtyp qO; fetch(qO,iO,q_tex);
-					m[iO].w = qO;
-				}
-			}
-		}
+        hneigh[iO*4+0] = iH1;
+        hneigh[iO*4+1] = iH2;
+        hneigh[iO*4+2] = -1;
+      } else {
+        iO  = hneigh[i *4  ];
+        iH1 = hneigh[iO*4  ];
+        iH2 = hneigh[iO*4+1];
+      }
+      if (iO >= inum) {
+        non_local_oxy = 1;
+        if(fabs(m[iO].w) <= FLT_EPSILON) {
+          compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
+          numtyp qO; fetch(qO,iO,q_tex);
+          m[iO].w = qO;
+        }
+      }
+    }
 
-		for ( ; nbor<nbor_end; nbor+=n_stride) {
-			int j=dev_packed[nbor];
+    for ( ; nbor<nbor_end; nbor+=n_stride) {
+      int j=dev_packed[nbor];
 
-			numtyp factor_lj,factor_coul;
-			factor_lj = sp_lj[sbmask(j)];
-			factor_coul = (numtyp)1.0-sp_lj[sbmask(j)+4];
-			j &= NEIGHMASK;
+      numtyp factor_lj,factor_coul;
+      factor_lj = sp_lj[sbmask(j)];
+      factor_coul = (numtyp)1.0-sp_lj[sbmask(j)+4];
+      j &= NEIGHMASK;
 
-			numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
-			int jtype = jx.w;
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype = jx.w;
 
-			// Compute r12
-			numtyp delx = ix.x-jx.x;
-			numtyp dely = ix.y-jx.y;
-			numtyp delz = ix.z-jx.z;
-			numtyp rsq = delx*delx+dely*dely+delz*delz;
+      // Compute r12
+      numtyp delx = ix.x-jx.x;
+      numtyp dely = ix.y-jx.y;
+      numtyp delz = ix.z-jx.z;
+      numtyp rsq = delx*delx+dely*dely+delz*delz;
 
-			int mtype = itype*lj_types+jtype;
-			if (rsq < lj1[mtype].z) { // cut_ljsq
-				numtyp r2inv = ucl_recip(rsq);
-				numtyp r6inv = r2inv*r2inv*r2inv;
-				numtyp forcelj = r6inv*(lj1[mtype].x*r6inv-lj1[mtype].y);
-				forcelj *= r2inv*factor_lj;
+      int mtype = itype*lj_types+jtype;
+      if (rsq < lj1[mtype].z) { // cut_ljsq
+        numtyp r2inv = ucl_recip(rsq);
+        numtyp r6inv = r2inv*r2inv*r2inv;
+        numtyp forcelj = r6inv*(lj1[mtype].x*r6inv-lj1[mtype].y);
+        forcelj *= r2inv*factor_lj;
 
-				f.x += delx*forcelj;
-				f.y += dely*forcelj;
-				f.z += delz*forcelj;
+        f.x += delx*forcelj;
+        f.y += dely*forcelj;
+        f.z += delz*forcelj;
 
-				if (eflag>0) {
-					numtyp e = r6inv * (lj3[mtype].x*r6inv-lj3[mtype].y);
-					energy += factor_lj * (e - lj3[mtype].z);
-				}
-		        if (vflag>0) {
-		          virial[0] += delx*delx*forcelj;
-		          virial[1] += dely*dely*forcelj;
-		          virial[2] += delz*delz*forcelj;
-		          virial[3] += delx*dely*forcelj;
-		          virial[4] += delx*delz*forcelj;
-		          virial[5] += dely*delz*forcelj;
-		        }
-			} // if LJ
+        if (eflag>0) {
+          numtyp e = r6inv * (lj3[mtype].x*r6inv-lj3[mtype].y);
+          energy += factor_lj * (e - lj3[mtype].z);
+        }
+        if (vflag>0) {
+          virial[0] += delx*delx*forcelj;
+          virial[1] += dely*dely*forcelj;
+          virial[2] += delz*delz*forcelj;
+          virial[3] += delx*dely*forcelj;
+          virial[4] += delx*delz*forcelj;
+          virial[5] += dely*delz*forcelj;
+        }
+      } // if LJ
 
-			if (rsq < cut_coulsqplus) { //cut_coulsqplus
-				int jH1, jH2, jO;
-				numtyp qj; fetch(qj,j,q_tex);
-				numtyp4 x2 = jx;
-				if(itype == typeO || jtype == typeO) {
-					if (jtype == typeO) {
-						jO = j;
-						if (hneigh[j*4+2] != -1) {
-							jH1 = atom_mapping(map,tag[j] + 1);
-							jH2 = atom_mapping(map,tag[j] + 2);
-							// set iH1,iH2 to closest image to O
-							jH1 = closest_image(j, jH1, sametag, x_);
-							jH2 = closest_image(j, jH2, sametag, x_);
-							hneigh[j*4  ] = jH1;
-							hneigh[j*4+1] = jH2;
-							hneigh[j*4+2] = -1;
-							hneigh[jH1*4  ] = j;
-							hneigh[jH1*4+1] += -1;
-							hneigh[jH1*4+2] = -1;
-							hneigh[jH2*4  ] = j;
-							hneigh[jH2*4+1] += -1;
-							hneigh[jH2*4+2] = -1;
-						} else {
-							jH1 = hneigh[j*4  ];
-							jH2 = hneigh[j*4+1];
-						}
-						if (m[j].w == 0) {
-							compute_newsite(j, jH1, jH2, &m[j], alpha, x_);
-							m[j].w = qj;
-						}
-						x2 = m[j];
-					}
-					delx = x1.x-x2.x;
-					dely = x1.y-x2.y;
-					delz = x1.z-x2.z;
-					rsq = delx*delx+dely*dely+delz*delz;
-				}
-				if (rsq < cut_coulsq) {
-					numtyp r2inv = ucl_recip(rsq);
-					numtyp r = ucl_rsqrt(r2inv);
-					numtyp grij = g_ewald * r;
-					numtyp expm2 = ucl_exp(-grij*grij);
-					numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
-					numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+      if (rsq < cut_coulsqplus) { //cut_coulsqplus
+        int jH1, jH2, jO;
+        numtyp qj; fetch(qj,j,q_tex);
+        numtyp4 x2 = jx;
+        if(itype == typeO || jtype == typeO) {
+          if (jtype == typeO) {
+            jO = j;
+            if (hneigh[j*4+2] != -1) {
+              jH1 = atom_mapping(map,tag[j] + 1);
+              jH2 = atom_mapping(map,tag[j] + 2);
+              // set iH1,iH2 to closest image to O
+              jH1 = closest_image(j, jH1, sametag, x_);
+              jH2 = closest_image(j, jH2, sametag, x_);
+              hneigh[j*4  ] = jH1;
+              hneigh[j*4+1] = jH2;
+              hneigh[j*4+2] = -1;
+              hneigh[jH1*4  ] = j;
+              hneigh[jH1*4+1] += -1;
+              hneigh[jH1*4+2] = -1;
+              hneigh[jH2*4  ] = j;
+              hneigh[jH2*4+1] += -1;
+              hneigh[jH2*4+2] = -1;
+            } else {
+              jH1 = hneigh[j*4  ];
+              jH2 = hneigh[j*4+1];
+            }
+            if (fabs(m[j].w) <= FLT_EPSILON) {
+              compute_newsite(j, jH1, jH2, &m[j], alpha, x_);
+              m[j].w = qj;
+            }
+            x2 = m[j];
+          }
+          delx = x1.x-x2.x;
+          dely = x1.y-x2.y;
+          delz = x1.z-x2.z;
+          rsq = delx*delx+dely*dely+delz*delz;
+        }
+        if (rsq < cut_coulsq) {
+          numtyp r2inv = ucl_recip(rsq);
+          numtyp r = ucl_rsqrt(r2inv);
+          numtyp grij = g_ewald * r;
+          numtyp expm2 = ucl_exp(-grij*grij);
+          numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
+          numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
 
-					numtyp prefactor = qj;
-					prefactor *= qqrd2e*qtmp/r;
-					numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
+          numtyp prefactor = qj;
+          prefactor *= qqrd2e*qtmp/r;
+          numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
 
-					if (itype == typeH) {
-						f.x += delx * force_coul;
-						f.y += dely * force_coul;
-						f.z += delz * force_coul;
-					} else {
-						fO.x += delx * force_coul;
-						fO.y += dely * force_coul;
-						fO.z += delz * force_coul;
-						fO.w += -1;
-					}
-					if (eflag>0) {
-						e_coul += prefactor*(_erfc-factor_coul);
-					}
-			        if (vflag>0) {
-			        	acctyp4 fd;
-			        	fd.x = delx*force_coul;
-			        	fd.y = dely*force_coul;
-			        	fd.z = delz*force_coul;
-			        	if (itype == typeH) {
-			        		if (jtype == typeH){
-								virial[0] += delx*fd.x;
-								virial[1] += dely*fd.y;
-								virial[2] += delz*fd.z;
-								virial[3] += delx*fd.y;
-								virial[4] += delx*fd.z;
-								virial[5] += dely*fd.z;
-			        		} else {
-								numtyp cO = 1 - alpha, cH = 0.5*alpha;
-								numtyp4 vdj;
-					        	numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
-								numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
-								numtyp4 xjO; fetch4(xjO,jO,pos_tex);
-								vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
-								vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
-								vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
-			        			virial[0] += (ix.x - vdj.x)*fd.x;
-			        			virial[1] += (ix.y - vdj.y)*fd.y;
-			        			virial[2] += (ix.z - vdj.z)*fd.z;
-			        			virial[3] += (ix.x - vdj.x)*fd.y;
-			        			virial[4] += (ix.x - vdj.x)*fd.z;
-			        			virial[5] += (ix.y - vdj.y)*fd.z;
-			        		}
-			        	} else {
-							numtyp cO = 1 - alpha, cH = 0.5*alpha;
-							numtyp4 vdi, vdj;
-							numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
-							numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
-							numtyp4 xO; fetch4(xO,iO,pos_tex);
-							vdi.x = xO.x*cO + xH1.x*cH + xH2.x*cH;
-							vdi.y = xO.y*cO + xH1.y*cH + xH2.y*cH;
-							vdi.z = xO.z*cO + xH1.z*cH + xH2.z*cH;
-			        		if (jtype != typeH){
-					        	numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
-								numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
-								numtyp4 xjO; fetch4(xjO,jO,pos_tex);
-								vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
-								vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
-								vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
-			        		} else vdj = jx;
-			        		vO[0] += 0.5*(vdi.x - vdj.x)*fd.x;
-			        		vO[1] += 0.5*(vdi.y - vdj.y)*fd.y;
-			        		vO[2] += 0.5*(vdi.z - vdj.z)*fd.z;
-			        		vO[3] += 0.5*(vdi.x - vdj.x)*fd.y;
-			        		vO[4] += 0.5*(vdi.x - vdj.x)*fd.z;
-			        		vO[5] += 0.5*(vdi.y - vdj.y)*fd.z;
-			        	}
-			        }
-				}
-				if (non_local_oxy == 1) {
-					if (iO == j) {
-						x2 = ix;
-						qj = qtmp;
-					}
-					numtyp4 x1m = m[iO];
-					delx = x1m.x-x2.x;
-					dely = x1m.y-x2.y;
-					delz = x1m.z-x2.z;
-					rsq = delx*delx+dely*dely+delz*delz;
-					if (rsq < cut_coulsq) {
-						numtyp r2inv = ucl_recip(rsq);
-						numtyp r = ucl_rsqrt(r2inv);
-						numtyp grij = g_ewald * r;
-						numtyp expm2 = ucl_exp(-grij*grij);
-						numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
-						numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+          if (itype == typeH) {
+            f.x += delx * force_coul;
+            f.y += dely * force_coul;
+            f.z += delz * force_coul;
+            f.w += 0;
+          } else {
+            fO.x += delx * force_coul;
+            fO.y += dely * force_coul;
+            fO.z += delz * force_coul;
+            fO.w += 0;
+          }
+          if (eflag>0) {
+            e_coul += prefactor*(_erfc-factor_coul);
+          }
+          if (vflag>0) {
+            acctyp4 fd;
+            fd.x = delx*force_coul;
+            fd.y = dely*force_coul;
+            fd.z = delz*force_coul;
+            if (itype == typeH) {
+              if (jtype == typeH){
+                virial[0] += delx*fd.x;
+                virial[1] += dely*fd.y;
+                virial[2] += delz*fd.z;
+                virial[3] += delx*fd.y;
+                virial[4] += delx*fd.z;
+                virial[5] += dely*fd.z;
+              } else {
+                numtyp cO = 1 - alpha, cH = 0.5*alpha;
+                numtyp4 vdj;
+                numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
+                numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
+                numtyp4 xjO; fetch4(xjO,jO,pos_tex);
+                vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
+                vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
+                vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
+                vdj.w = vdj.w;
+                virial[0] += (ix.x - vdj.x)*fd.x;
+                virial[1] += (ix.y - vdj.y)*fd.y;
+                virial[2] += (ix.z - vdj.z)*fd.z;
+                virial[3] += (ix.x - vdj.x)*fd.y;
+                virial[4] += (ix.x - vdj.x)*fd.z;
+                virial[5] += (ix.y - vdj.y)*fd.z;
+              }
+            } else {
+              numtyp cO = 1 - alpha, cH = 0.5*alpha;
+              numtyp4 vdi, vdj;
+              numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+              numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+              numtyp4 xO; fetch4(xO,iO,pos_tex);
+              vdi.x = xO.x*cO + xH1.x*cH + xH2.x*cH;
+              vdi.y = xO.y*cO + xH1.y*cH + xH2.y*cH;
+              vdi.z = xO.z*cO + xH1.z*cH + xH2.z*cH;
+              vdi.w = vdi.w;
+              if (jtype != typeH){
+                numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
+                numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
+                numtyp4 xjO; fetch4(xjO,jO,pos_tex);
+                vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
+                vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
+                vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
+                vdj.w = vdj.w;
+              } else vdj = jx;
+              vO[0] += 0.5*(vdi.x - vdj.x)*fd.x;
+              vO[1] += 0.5*(vdi.y - vdj.y)*fd.y;
+              vO[2] += 0.5*(vdi.z - vdj.z)*fd.z;
+              vO[3] += 0.5*(vdi.x - vdj.x)*fd.y;
+              vO[4] += 0.5*(vdi.x - vdj.x)*fd.z;
+              vO[5] += 0.5*(vdi.y - vdj.y)*fd.z;
+            }
+          }
+        }
+        if (non_local_oxy == 1) {
+          if (iO == j) {
+            x2 = ix;
+            qj = qtmp;
+          }
+          numtyp4 x1m = m[iO];
+          delx = x1m.x-x2.x;
+          dely = x1m.y-x2.y;
+          delz = x1m.z-x2.z;
+          rsq = delx*delx+dely*dely+delz*delz;
+          if (rsq < cut_coulsq) {
+            numtyp r2inv = ucl_recip(rsq);
+            numtyp r = ucl_rsqrt(r2inv);
+            numtyp grij = g_ewald * r;
+            numtyp expm2 = ucl_exp(-grij*grij);
+            numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
+            numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
 
-						numtyp prefactor = qj;
-						prefactor *= qqrd2e*x1m.w/r;
-						numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
+            numtyp prefactor = qj;
+            prefactor *= qqrd2e*x1m.w/r;
+            numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
 
-						numtyp cO = 1 - alpha, cH = 0.5*alpha;
-						numtyp4 fd;
-						fd.x = delx * force_coul * cH;
-						fd.y = dely * force_coul * cH;
-						fd.z = delz * force_coul * cH;
+            numtyp cO = 1 - alpha, cH = 0.5*alpha;
+            numtyp4 fd;
+            fd.x = delx * force_coul * cH;
+            fd.y = dely * force_coul * cH;
+            fd.z = delz * force_coul * cH;
 
-						f.x += fd.x;
-						f.y += fd.y;
-						f.z += fd.z;
+            f.x += fd.x;
+            f.y += fd.y;
+            f.z += fd.z;
 
-						if (eflag>0) {
-							e_coul += prefactor*(_erfc-factor_coul) * (acctyp)0.5 * alpha;
-						}
-				        if (vflag>0) {
-				        	numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
-							numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
-							numtyp4 xO;  fetch4(xO,iO,pos_tex);
+            if (eflag>0) {
+              e_coul += prefactor*(_erfc-factor_coul) * (acctyp)0.5 * alpha;
+            }
+            if (vflag>0) {
+              numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+              numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+              numtyp4 xO;  fetch4(xO,iO,pos_tex);
 
-							virial[0] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.x;
-							virial[1] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.y;
-							virial[2] += ((xO.z*cO + xH1.z*cH + xH2.z*cH) - x2.z) * fd.z;
-							virial[3] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.y;
-							virial[4] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.z;
-							virial[5] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.z;
-				        }
-					}
-				}
-			} // if cut_coulsqplus
-		} // for nbor
-		if (t_per_atom>1) {
+              virial[0] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.x;
+              virial[1] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.y;
+              virial[2] += ((xO.z*cO + xH1.z*cH + xH2.z*cH) - x2.z) * fd.z;
+              virial[3] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.y;
+              virial[4] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.z;
+              virial[5] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.z;
+            }
+          }
+        }
+      } // if cut_coulsqplus
+    } // for nbor
+    if (t_per_atom>1) {
 #if (ARCH < 300)
-			__local acctyp red_acc[6][BLOCK_PAIR];
-			red_acc[0][tid]=fO.x;
-			red_acc[1][tid]=fO.y;
-			red_acc[2][tid]=fO.z;
-			red_acc[3][tid]=fO.w;
-			for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
-				if (offset < s) {
-					for (int r=0; r<4; r++)
-						red_acc[r][tid] += red_acc[r][tid+s];
-				}
-			}
-			fO.x=red_acc[0][tid];
-			fO.y=red_acc[1][tid];
-			fO.z=red_acc[2][tid];
-			fO.w=red_acc[3][tid];
-			if (vflag>0) {
-				for (int r=0; r<6; r++) red_acc[r][tid]=vO[r];
-				for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
-					if (offset < s) {
-						for (int r=0; r<6; r++)
-							red_acc[r][tid] += red_acc[r][tid+s];
-					}
-				}
-				for (int r=0; r<6; r++) vO[r]=red_acc[r][tid];
-			}
+      __local acctyp red_acc[6][BLOCK_PAIR];
+      red_acc[0][tid]=fO.x;
+      red_acc[1][tid]=fO.y;
+      red_acc[2][tid]=fO.z;
+      red_acc[3][tid]=fO.w;
+      for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+        if (offset < s) {
+          for (int r=0; r<4; r++)
+            red_acc[r][tid] += red_acc[r][tid+s];
+        }
+      }
+      fO.x=red_acc[0][tid];
+      fO.y=red_acc[1][tid];
+      fO.z=red_acc[2][tid];
+      fO.w=red_acc[3][tid];
+      if (vflag>0) {
+        for (int r=0; r<6; r++) red_acc[r][tid]=vO[r];
+        for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+          if (offset < s) {
+            for (int r=0; r<6; r++)
+              red_acc[r][tid] += red_acc[r][tid+s];
+          }
+        }
+        for (int r=0; r<6; r++) vO[r]=red_acc[r][tid];
+      }
 #else
-			for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
-				fO.x += shfl_xor(fO.x, s, t_per_atom);
-				fO.y += shfl_xor(fO.y, s, t_per_atom);
-				fO.z += shfl_xor(fO.z, s, t_per_atom);
-				fO.w += shfl_xor(fO.w, s, t_per_atom);
-			}
-			if (vflag>0) {
-				for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
-						for (int r=0; r<6; r++)
-							vO[r] += shfl_xor(vO[r], s, t_per_atom);
-				}
-			}
+      for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+        fO.x += shfl_xor(fO.x, s, t_per_atom);
+        fO.y += shfl_xor(fO.y, s, t_per_atom);
+        fO.z += shfl_xor(fO.z, s, t_per_atom);
+        fO.w += shfl_xor(fO.w, s, t_per_atom);
+      }
+      if (vflag>0) {
+        for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+          for (int r=0; r<6; r++)
+            vO[r] += shfl_xor(vO[r], s, t_per_atom);
+        }
+      }
 #endif
-		}
-		if(offset == 0) {
-			ansO[i] = fO;
-			if (vflag>0) {
-				ansO[inum   + i].x = vO[0];
-				ansO[inum   + i].y = vO[1];
-				ansO[inum   + i].z = vO[2];
-				ansO[inum*2 + i].x = vO[3];
-				ansO[inum*2 + i].y = vO[4];
-				ansO[inum*2 + i].z = vO[5];
-			}
-		}
-		store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
-				vflag,ans,engv);
-	} // if ii
+    }
+    if(offset == 0) {
+      ansO[i] = fO;
+      if (vflag>0) {
+        ansO[inum   + i].x = vO[0];
+        ansO[inum   + i].y = vO[1];
+        ansO[inum   + i].z = vO[2];
+        ansO[inum*2 + i].x = vO[3];
+        ansO[inum*2 + i].y = vO[4];
+        ansO[inum*2 + i].z = vO[5];
+      }
+    }
+    store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
+        vflag,ans,engv);
+  } // if ii
 }
 
-
 __kernel void k_lj_tip4p_long_fast(){}
diff --git a/lib/gpu/lal_lj_tip4p_long.h b/lib/gpu/lal_lj_tip4p_long.h
index 4bd6670aa8..57df235467 100644
--- a/lib/gpu/lal_lj_tip4p_long.h
+++ b/lib/gpu/lal_lj_tip4p_long.h
@@ -1,3 +1,18 @@
+/**************************************************************************
+                               lj_tip4p_long.h
+                             -------------------
+                              V. Nikolskiy (HSE)
+
+  Class for acceleration of the lj/tip4p/long pair style
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : thevsevak@gmail.com
+***************************************************************************/
+
 #ifndef LAL_LJ_TIP4P_LONG_H
 #define LAL_LJ_TIP4P_LONG_H
 
@@ -26,16 +41,16 @@ public:
            double **host_lj1, double **host_lj2, double **host_lj3,
            double **host_lj4, double **host_offset, double *host_special_lj,
            const int nlocal, const int tH, const int tO,
-		   const double alpha, const double qdist,
-		   const int nall, const int max_nbors,
+           const double alpha, const double qdist,
+           const int nall, const int max_nbors,
            const int maxspecial, const double cell_size,
            const double gpu_split, FILE *screen,
-		   double **host_cut_ljsq,
-		   const double host_cut_coulsq, const double host_cut_coulsqplus,
-		   double *host_special_coul, const double qqrd2e,
-		   const double g_ewald, int* tag,
-			 int *map_array, int map_size,
-			 int *sametag, int max_same);
+           double **host_cut_ljsq,
+           const double host_cut_coulsq, const double host_cut_coulsqplus,
+           double *host_special_coul, const double qqrd2e,
+           const double g_ewald, int* tag,
+           int *map_array, int map_size,
+           int *sametag, int max_same);
 
   /// Clear all host and device data
   /** \note This is called at the beginning of the init() routine **/
@@ -49,7 +64,7 @@ public:
 
   /// Copy data which is easier to compute in LAMMPS_NS
   void copy_relations_data(int **hn, double **m, int n,int* tag, int *map_array, int map_size,
-			 int *sametag, int max_same, int ago);
+      int *sametag, int max_same, int ago);
 
   // --------------------------- TYPE DATA --------------------------
 
@@ -77,7 +92,7 @@ public:
   UCL_D_Vec<int> hneight;
   UCL_D_Vec<numtyp4> m; // position and charge of virtual particle
   UCL_D_Vec<acctyp4> ansO; // force applied to virtual particle
-  UCL_D_Vec<acctyp4> force_comp;
+  // UCL_D_Vec<acctyp4> force_comp;
 
   UCL_D_Vec<int> tag;
   UCL_D_Vec<int> map_array;
diff --git a/lib/gpu/lal_lj_tip4p_long_ext.cpp b/lib/gpu/lal_lj_tip4p_long_ext.cpp
index 00698af82a..7ddd8f03b6 100644
--- a/lib/gpu/lal_lj_tip4p_long_ext.cpp
+++ b/lib/gpu/lal_lj_tip4p_long_ext.cpp
@@ -1,3 +1,18 @@
+/***************************************************************************
+                            lj_tip4p_long_ext.cpp
+                             -------------------
+                              V. Nikolskiy (HSE)
+
+  Functions for LAMMPS access to lj/tip4p/long acceleration functions
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : thevsevak@gmail.com
+ ***************************************************************************/
+
 #include <iostream>
 #include <cassert>
 #include <cmath>
@@ -13,18 +28,18 @@ static LJ_TIP4PLong<PRECISION,ACC_PRECISION> LJTIP4PLMF;
 // Allocate memory on host and device and copy constants to device
 // ---------------------------------------------------------------------------
 int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
-                 double **host_lj2, double **host_lj3, double **host_lj4,
-                 double **offset, double *special_lj, const int inum,
-				 const int tH, const int tO,
-				 const double alpha, const double qdist,
-                 const int nall, const int max_nbors,  const int maxspecial,
-                 const double cell_size, int &gpu_mode, FILE *screen,
-				 double **host_cut_ljsq,
-				 const double host_cut_coulsq, const double host_cut_coulsqplus,
-				 double *host_special_coul, const double qqrd2e,
-				 const double g_ewald, int* tag,
-				 int *map_array, int map_size,
-				 int *sametag, int max_same) {
+    double **host_lj2, double **host_lj3, double **host_lj4,
+    double **offset, double *special_lj, const int inum,
+    const int tH, const int tO,
+    const double alpha, const double qdist,
+    const int nall, const int max_nbors,  const int maxspecial,
+    const double cell_size, int &gpu_mode, FILE *screen,
+    double **host_cut_ljsq,
+    const double host_cut_coulsq, const double host_cut_coulsqplus,
+    double *host_special_coul, const double qqrd2e,
+    const double g_ewald, int* tag,
+    int *map_array, int map_size,
+    int *sametag, int max_same) {
   LJTIP4PLMF.clear();
   gpu_mode=LJTIP4PLMF.device->gpu_mode();
   double gpu_split=LJTIP4PLMF.device->particle_split();
@@ -48,13 +63,13 @@ int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
   int init_ok=0;
   if (world_me==0)
     init_ok=LJTIP4PLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3,
-                       host_lj4, offset, special_lj, inum,
-					   tH, tO, alpha, qdist, nall, 300,
-                       maxspecial, cell_size, gpu_split, screen,
-					   host_cut_ljsq, host_cut_coulsq, host_cut_coulsqplus,
-					   host_special_coul, qqrd2e, g_ewald, tag,
-						 map_array, map_size,
-						 sametag, max_same);
+        host_lj4, offset, special_lj, inum,
+        tH, tO, alpha, qdist, nall, 300,
+        maxspecial, cell_size, gpu_split, screen,
+        host_cut_ljsq, host_cut_coulsq, host_cut_coulsqplus,
+        host_special_coul, qqrd2e, g_ewald, tag,
+        map_array, map_size,
+        sametag, max_same);
 
   LJTIP4PLMF.device->world_barrier();
   if (message)
@@ -71,13 +86,13 @@ int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
     }
     if (gpu_rank==i && world_me!=0)
       init_ok=LJTIP4PLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
-                         offset, special_lj, inum,
-						 tH, tO, alpha, qdist, nall, 300, maxspecial,
-                         cell_size, gpu_split, screen, host_cut_ljsq,
-	                     host_cut_coulsq, host_cut_coulsqplus,
-						 host_special_coul, qqrd2e, g_ewald,tag,
-						 map_array, map_size,
-						 sametag, max_same);
+          offset, special_lj, inum,
+          tH, tO, alpha, qdist, nall, 300, maxspecial,
+          cell_size, gpu_split, screen, host_cut_ljsq,
+          host_cut_coulsq, host_cut_coulsqplus,
+          host_special_coul, qqrd2e, g_ewald,tag,
+          map_array, map_size,
+          sametag, max_same);
 
     LJTIP4PLMF.device->gpu_barrier();
     if (message)
@@ -91,8 +106,6 @@ int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
   return init_ok;
 }
 
-
-
 void ljtip4p_long_gpu_clear() {
   LJTIP4PLMF.clear();
 }
@@ -108,7 +121,7 @@ int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum_full,
   return LJTIP4PLMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
                        subhi, tag, nspecial, special, eflag, vflag, eatom,
                        vatom, host_start, ilist, jnum, cpu_time, success,
-					   host_q,boxlo, prd);
+                       host_q,boxlo, prd);
 }
 
 void ljtip4p_long_gpu_compute(const int ago, const int inum_full, const int nall,
@@ -116,10 +129,10 @@ void ljtip4p_long_gpu_compute(const int ago, const int inum_full, const int nall
                      int **firstneigh, const bool eflag, const bool vflag,
                      const bool eatom, const bool vatom, int &host_start,
                      const double cpu_time, bool &success,double *host_q,
-					 const int nlocal, double *boxlo, double *prd) {
+                     const int nlocal, double *boxlo, double *prd) {
   LJTIP4PLMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
-                firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,host_q,
-				nlocal,boxlo,prd);
+      firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,host_q,
+      nlocal,boxlo,prd);
 }
 
 double ljtip4p_long_gpu_bytes() {
@@ -127,9 +140,9 @@ double ljtip4p_long_gpu_bytes() {
 }
 
 void ljtip4p_long_copy_molecule_data(int **hn, double **m, int n, int* tag,
-		 int *map_array, int map_size,
-		 int *sametag, int max_same, int ago){
-	LJTIP4PLMF.copy_relations_data(hn, m, n, tag,map_array,map_size,sametag, max_same, ago);
+    int *map_array, int map_size,
+    int *sametag, int max_same, int ago){
+  LJTIP4PLMF.copy_relations_data(hn, m, n, tag,map_array,map_size,sametag, max_same, ago);
 }
 
 
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
index 5e8e746c85..244da6a146 100644
--- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -1,3 +1,20 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Vsevolod Nikolskiy (HSE)
+------------------------------------------------------------------------- */
+
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
@@ -34,35 +51,35 @@ using namespace LAMMPS_NS;
 // External functions from cuda library for atom decomposition
 
 int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
-                 double **host_lj2, double **host_lj3, double **host_lj4,
-                 double **offset, double *special_lj, const int nlocal,
-				 const int tH, const int tO, const double alpha, const double qdist,
-                 const int nall, const int max_nbors, const int maxspecial,
-                 const double cell_size, int &gpu_mode, FILE *screen,
-				 double **host_cut_ljsq, const double host_cut_coulsq,
-				 const double host_cut_coulsqplus,
-				 double *host_special_coul, const double qqrd2e,
-				 const double g_ewald, int* tag,
-				 int *map_array, int map_size,
-				 int *sametag, int max_same);
+    double **host_lj2, double **host_lj3, double **host_lj4,
+    double **offset, double *special_lj, const int nlocal,
+    const int tH, const int tO, const double alpha, const double qdist,
+    const int nall, const int max_nbors, const int maxspecial,
+    const double cell_size, int &gpu_mode, FILE *screen,
+    double **host_cut_ljsq, const double host_cut_coulsq,
+    const double host_cut_coulsqplus, double *host_special_coul,
+    const double qqrd2e, const double g_ewald, int* tag,
+    int *map_array, int map_size,
+    int *sametag, int max_same);
 void ljtip4p_long_gpu_clear();
 int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum,
-                         const int nall, double **host_x, int *host_type,
-                         double *sublo, double *subhi, tagint *tag, int **nspecial,
-                         tagint **special, const bool eflag, const bool vflag,
-                         const bool eatom, const bool vatom, int &host_start,
-                         int **ilist, int **jnum,
-                         const double cpu_time, bool &success, double *host_q,
-						 double *boxlo, double *prd);
+    const int nall, double **host_x, int *host_type,
+    double *sublo, double *subhi, tagint *tag, int **nspecial,
+    tagint **special, const bool eflag, const bool vflag,
+    const bool eatom, const bool vatom, int &host_start,
+    int **ilist, int **jnum,
+    const double cpu_time, bool &success, double *host_q,
+    double *boxlo, double *prd);
 void ljtip4p_long_gpu_compute(const int ago, const int inum, const int nall,
-                     double **host_x, int *host_type, int *ilist, int *numj,
-                     int **firstneigh, const bool eflag, const bool vflag,
-                     const bool eatom, const bool vatom, int &host_start,
-                     const double cpu_time,
-                     bool &success, double *host_q, const int nlocal,
-                     double *boxlo, double *prd);
+    double **host_x, int *host_type, int *ilist, int *numj,
+    int **firstneigh, const bool eflag, const bool vflag,
+    const bool eatom, const bool vatom, int &host_start,
+    const double cpu_time,
+    bool &success, double *host_q, const int nlocal,
+    double *boxlo, double *prd);
 double ljtip4p_long_gpu_bytes();
-void ljtip4p_long_copy_molecule_data(int **, double **, int, int* , int *, int, int *, int , int);
+void ljtip4p_long_copy_molecule_data(int **, double **, int, int* , int *,
+		int, int *, int , int);
 
 /* ---------------------------------------------------------------------- */
 
@@ -81,7 +98,7 @@ PairLJCutTIP4PLongGPU::PairLJCutTIP4PLongGPU(LAMMPS *lmp)
 
 PairLJCutTIP4PLongGPU::~PairLJCutTIP4PLongGPU()
 {
-	ljtip4p_long_gpu_clear();
+  ljtip4p_long_gpu_clear();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -96,29 +113,29 @@ void PairLJCutTIP4PLongGPU::compute(int eflag, int vflag)
   int inum, host_start;
 
   ljtip4p_long_copy_molecule_data(hneigh, newsite, nall, atom->tag,
-			 atom->get_map_array(), atom->get_map_size(),
-			 atom->sametag, atom->get_max_same(), neighbor->ago);
+      atom->get_map_array(), atom->get_map_size(),
+      atom->sametag, atom->get_max_same(), neighbor->ago);
 
   bool success = true;
   int *ilist, *numneigh, **firstneigh;
   if (gpu_mode != GPU_FORCE) {
     inum = atom->nlocal;
     firstneigh = ljtip4p_long_gpu_compute_n(neighbor->ago, inum, nall,
-                                   atom->x, atom->type, domain->sublo,
-                                   domain->subhi, atom->tag, atom->nspecial,
-                                   atom->special, eflag, vflag, eflag_atom,
-                                   vflag_atom, host_start, &ilist, &numneigh,
-								   cpu_time, success, atom->q, domain->boxlo,
-								   domain->prd);
+        atom->x, atom->type, domain->sublo,
+        domain->subhi, atom->tag, atom->nspecial,
+        atom->special, eflag, vflag, eflag_atom,
+        vflag_atom, host_start, &ilist, &numneigh,
+        cpu_time, success, atom->q, domain->boxlo,
+        domain->prd);
   } else {
     inum = list->inum;
     ilist = list->ilist;
     numneigh = list->numneigh;
     firstneigh = list->firstneigh;
     ljtip4p_long_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
-                    ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
-                    vflag_atom, host_start, cpu_time, success, atom->q,
-					atom->nlocal, domain->boxlo, domain->prd);
+        ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+        vflag_atom, host_start, cpu_time, success, atom->q,
+        atom->nlocal, domain->boxlo, domain->prd);
   }
   if (!success)
     error->one(FLERR,"Insufficient memory on accelerator");
@@ -149,7 +166,8 @@ void PairLJCutTIP4PLongGPU::init_style()
     error->all(FLERR,"Must use an angle style with TIP4P potential");
 
   if (atom->map_style == 2)
-	  error->all(FLERR,"GPU-accelerated lj/cut/tip4p/long currently requires map style 'array' (atom_modify map array)");
+    error->all(FLERR,"GPU-accelerated lj/cut/tip4p/long currently"
+        " requires map style 'array' (atom_modify map array)");
 
   //PairLJCutCoulLong::init_style();
   // Repeat cutsq calculation because done after call to init_style
@@ -189,25 +207,24 @@ void PairLJCutTIP4PLongGPU::init_style()
   cut_coulsq = cut_coul * cut_coul;
   double cut_coulsqplus = (cut_coul+qdist+blen) * (cut_coul+qdist+blen);
   if (maxcut < cut_coulsqplus) {
-	  cell_size = (cut_coul+qdist+blen) + neighbor->skin;
+    cell_size = (cut_coul+qdist+blen) + neighbor->skin;
   }
   if (comm->cutghostuser < cell_size) {
     comm->cutghostuser = cell_size;
     if (comm->me == 0)
-       error->warning(FLERR,"Increasing communication cutoff for TIP4P GPU style");
+      error->warning(FLERR,"Increasing communication cutoff for TIP4P GPU style");
   }
 
   int success = ljtip4p_long_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
                              offset, force->special_lj, atom->nlocal,
-							 typeH, typeO, alpha, qdist,
+                             typeH, typeO, alpha, qdist,
                              atom->nlocal+atom->nghost, 300, maxspecial,
                              cell_size, gpu_mode, screen, cut_ljsq,
-							 cut_coulsq, cut_coulsqplus,
+                             cut_coulsq, cut_coulsqplus,
                              force->special_coul, force->qqrd2e,
-							 g_ewald,
-							 atom->tag,
-							 atom->get_map_array(), atom->get_map_size(),
-							 atom->sametag, atom->get_max_same());
+                             g_ewald,
+                             atom->tag, atom->get_map_array(), atom->get_map_size(),
+                             atom->sametag, atom->get_max_same());
   GPU_EXTRA::check_flag(success,error,world);
   if (gpu_mode == GPU_FORCE) {
     int irequest = neighbor->request(this,instance_me);
@@ -228,7 +245,3 @@ double PairLJCutTIP4PLongGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-//void PairLJCutTIP4PLongGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-//                               int *ilist, int *numneigh, int **firstneigh) {
-//	error->all(FLERR,"PairLJCutTIP4PLongGPU::cpu_compute not implemented");
-//}
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.h b/src/GPU/pair_lj_cut_tip4p_long_gpu.h
index 23b96e201a..e7ba93afb2 100644
--- a/src/GPU/pair_lj_cut_tip4p_long_gpu.h
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.h
@@ -1,3 +1,20 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Vsevolod Nikolskiy (HSE)
+------------------------------------------------------------------------- */
+
 #ifdef PAIR_CLASS
 
 PairStyle(lj/cut/tip4p/long/gpu,PairLJCutTIP4PLongGPU)
@@ -15,7 +32,6 @@ class PairLJCutTIP4PLongGPU : public PairLJCutTIP4PLong {
  public:
   PairLJCutTIP4PLongGPU(LAMMPS *lmp);
   ~PairLJCutTIP4PLongGPU();
-//  void cpu_compute(int, int, int, int, int *, int *, int **);
   void compute(int, int);
   void init_style();
   double memory_usage();

From 2fea49741f66b1d3c2d3e3d6303be596513bd695 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Sun, 17 Nov 2019 16:50:16 -0700
Subject: [PATCH 044/199] Fixed some problems with type offsets

---
 src/SNAP/compute_snap.cpp | 188 +++++++++++++++++---------------------
 src/SNAP/compute_snap.h   |   4 +-
 2 files changed, 88 insertions(+), 104 deletions(-)

diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 5c472861ec..904d75a8e3 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -20,7 +20,7 @@
 -DONE: size_peratom = (3+6)*nperdim*ntypes
 INCOMPLETE: Mappy from local to global
 INCOMPLETE: modify->find_compute() 
-INCOMPLETE: eliminate local peratom array for viral, replace with fdotr 
+DONE: eliminate local peratom array for viral, replace with fdotr 
 
  */
 #include "compute_snap.h"
@@ -129,14 +129,15 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
   ncoeff = snaptr->ncoeff;
   nperdim = ncoeff;
   if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
+  ndims_force = 3;
+  ndims_virial = 6;
   yoffset = nperdim;
   zoffset = 2*nperdim;
-  virialoffset = 3*nperdim;
   natoms = atom->natoms;
-  size_array_rows = 1+3*natoms+6;
-  size_array_cols = nperdim*atom->ntypes+1; // extra col for reference potential
-  ndims_peratom = 9;
-  size_peratom = ndims_peratom*nperdim*atom->ntypes; // local atom force and virial data
+  size_array_rows = 1+ndims_force*natoms+ndims_virial;
+  size_array_cols = nperdim*atom->ntypes+1;
+  ndims_peratom = ndims_force;
+  size_peratom = ndims_peratom*nperdim*atom->ntypes;
   comm_reverse = size_peratom;
 
   nmax = 0;
@@ -182,8 +183,6 @@ void ComputeSnap::init()
 
   // allocate memory for global array
 
-  //  printf("allocate memory for global array rows = %d cols = %d\n",
-  //         size_array_rows,size_array_cols);
   memory->create(snap,size_array_rows,size_array_cols,
                  "snap:snap");
   array = snap;
@@ -197,6 +196,8 @@ void ComputeSnap::init()
 
   char *id_pe = (char *) "thermo_pe";
   int ipe = modify->find_compute(id_pe);
+  if (ipe == -1)
+    error->all(FLERR,"compute thermo_pe does not exist.");
   c_pe = modify->compute[ipe];
 
   // add compute for reference virial tensor
@@ -204,7 +205,7 @@ void ComputeSnap::init()
   char *id_virial = (char *) "snap_press";
   int ivirial = modify->find_compute(id_virial);
   if (ivirial == -1)
-    error->all(FLERR,"compute snap requires that compute snap_press exists!");
+    error->all(FLERR,"compute snap requires that compute snap_press exists.");
   c_virial = modify->compute[ivirial];
 }
 
@@ -224,8 +225,6 @@ void ComputeSnap::compute_array()
 
   invoked_array = update->ntimestep;
 
-  //  printf("Invoking compute snap on timestep %d\n",invoked_array);
-
   // grow snap_peratom array if necessary
 
   if (atom->nmax > nmax) {
@@ -236,12 +235,12 @@ void ComputeSnap::compute_array()
   }
 
   // clear global array
-  // only need to zero out first row
+  // only need to zero out first row of bispectrum 
 
-  for (int icoeff = 0; icoeff < size_array_cols; icoeff++)
+  for (int icoeff = 0; icoeff < size_array_cols-1; icoeff++)
     snap[0][icoeff] = 0.0;
 
-  // clear peratom array
+  // clear local peratom array
 
   for (int i = 0; i < ntotal; i++)
     for (int icoeff = 0; icoeff < size_peratom; icoeff++) {
@@ -275,7 +274,8 @@ void ComputeSnap::compute_array()
       const double radi = radelem[itype];
       const int* const jlist = firstneigh[i];
       const int jnum = numneigh[i];
-      const int typeoffset = ndims_peratom*nperdim*(atom->type[i]-1);
+      const int typeoffset_local = ndims_peratom*nperdim*(itype-1);
+      const int typeoffset_global = nperdim*(itype-1);
 
       // insure rij, inside, and typej  are of size jnum
 
@@ -309,9 +309,7 @@ void ComputeSnap::compute_array()
 
       snaptr->compute_ui(ninside);
       snaptr->compute_zi();
-      //      if (quadraticflag) {
       snaptr->compute_bi();
-      //      }
 
       for (int jj = 0; jj < ninside; jj++) {
         const int j = snaptr->inside[jj];
@@ -322,10 +320,8 @@ void ComputeSnap::compute_array()
 
         // Accumulate -dBi/dRi, -dBi/dRj
 
-        double *snadi = snap_peratom[i]+typeoffset;
-        double *snadj = snap_peratom[j]+typeoffset;
-        double *snavi = snadi+virialoffset;
-        double *snavj = snadj+virialoffset;
+        double *snadi = snap_peratom[i]+typeoffset_local;
+        double *snadj = snap_peratom[j]+typeoffset_local;
 
         for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
           snadi[icoeff] += snaptr->dblist[icoeff][0];
@@ -334,27 +330,12 @@ void ComputeSnap::compute_array()
           snadj[icoeff] -= snaptr->dblist[icoeff][0];
           snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
           snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
-
-          snavi[icoeff]           += snaptr->dblist[icoeff][0]*xtmp;
-          snavi[icoeff+nperdim]   += snaptr->dblist[icoeff][1]*ytmp;
-          snavi[icoeff+2*nperdim] += snaptr->dblist[icoeff][2]*ztmp;
-          snavi[icoeff+3*nperdim] += snaptr->dblist[icoeff][1]*ztmp;
-          snavi[icoeff+4*nperdim] += snaptr->dblist[icoeff][0]*ztmp;
-          snavi[icoeff+5*nperdim] += snaptr->dblist[icoeff][0]*ytmp;
-          snavj[icoeff]           -= snaptr->dblist[icoeff][0]*x[j][0];
-          snavj[icoeff+nperdim]   -= snaptr->dblist[icoeff][1]*x[j][1];
-          snavj[icoeff+2*nperdim] -= snaptr->dblist[icoeff][2]*x[j][2];
-          snavj[icoeff+3*nperdim] -= snaptr->dblist[icoeff][1]*x[j][2];
-          snavj[icoeff+4*nperdim] -= snaptr->dblist[icoeff][0]*x[j][2];
-          snavj[icoeff+5*nperdim] -= snaptr->dblist[icoeff][0]*x[j][1];
         }
 
         if (quadraticflag) {
           const int quadraticoffset = ncoeff;
           snadi += quadraticoffset;
           snadj += quadraticoffset;
-          snavi += quadraticoffset;
-          snavj += quadraticoffset;
           int ncount = 0;
           for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
             double bi = snaptr->blist[icoeff];
@@ -375,19 +356,6 @@ void ComputeSnap::compute_array()
             snadj[ncount+yoffset] -= dbytmp;
             snadj[ncount+zoffset] -= dbztmp;
 
-            snavi[ncount] +=           dbxtmp*xtmp;
-            snavi[ncount+nperdim] +=   dbytmp*ytmp;
-            snavi[ncount+2*nperdim] += dbztmp*ztmp;
-            snavi[ncount+3*nperdim] += dbytmp*ztmp;
-            snavi[ncount+4*nperdim] += dbxtmp*ztmp;
-            snavi[ncount+5*nperdim] += dbxtmp*ytmp;
-            snavj[ncount] -=            dbxtmp*x[j][0];
-            snavj[ncount+nperdim] -=    dbytmp*x[j][1];
-            snavj[ncount+2*nperdim] -=  dbztmp*x[j][2];
-            snavj[ncount+3*nperdim] -=  dbytmp*x[j][2];
-            snavj[ncount+4*nperdim] -=  dbxtmp*x[j][2];
-            snavj[ncount+5*nperdim] -=  dbxtmp*x[j][1];
-
             ncount++;
 
             // upper-triangular elements of quadratic matrix
@@ -407,22 +375,10 @@ void ComputeSnap::compute_array()
               snadj[ncount+yoffset] -= dbytmp;
               snadj[ncount+zoffset] -= dbztmp;
 
-              snavi[ncount] +=           dbxtmp*xtmp;
-              snavi[ncount+nperdim] +=   dbytmp*ytmp;
-              snavi[ncount+2*nperdim] += dbztmp*ztmp;
-              snavi[ncount+3*nperdim] += dbytmp*ztmp;
-              snavi[ncount+4*nperdim] += dbxtmp*ztmp;
-              snavi[ncount+5*nperdim] += dbxtmp*ytmp;
-              snavj[ncount] -=           dbxtmp*x[j][0];
-              snavj[ncount+nperdim] -=   dbytmp*x[j][1];
-              snavj[ncount+2*nperdim] -= dbztmp*x[j][2];
-              snavj[ncount+3*nperdim] -= dbytmp*x[j][2];
-              snavj[ncount+4*nperdim] -= dbxtmp*x[j][2];
-              snavj[ncount+5*nperdim] -= dbxtmp*x[j][1];
-
               ncount++;
             }
           }
+
         }
       }
 
@@ -448,65 +404,39 @@ void ComputeSnap::compute_array()
     }
   }
 
-  // INCOMPLETE
-  // can get rid of virial from snap_peratom by doing
-  // equivalent of Pair::virial_fdotr_compute()
-  // before reverse communicate of snap_peratom
+  // accumulate virial contributions before reverse compute
 
-  // communicate snap contributions between neighbor procs
+  dbdotr_compute();
+
+  // communicate local peratom contributions between neighbor procs
 
   comm->reverse_comm_compute(this);
 
-  // construct global array
+  // copy peratom data to global array
+  // INCOMPLETE ignore local-global mapping for now
 
   for (int itype = 0; itype < atom->ntypes; itype++) {
-    const int typeoffset = 3*nperdim*itype;
+    const int typeoffset_local = ndims_peratom*nperdim*itype;
+    const int typeoffset_global = nperdim*itype;
     for (int icoeff = 0; icoeff < nperdim; icoeff++) {
-
-      // assign force rows
-      // INCOMPLETE ignore local-global mapping for now
-
       int irow = 1;
       for (int i = 0; i < atom->nlocal; i++) {
-        double *snadi = snap_peratom[i]+typeoffset;
-        snap[irow++][icoeff+typeoffset] = snadi[icoeff];
-        snap[irow++][icoeff+typeoffset] = snadi[icoeff+yoffset];
-        snap[irow++][icoeff+typeoffset] = snadi[icoeff+zoffset];
-
+        double *snadi = snap_peratom[i]+typeoffset_local;
+        snap[irow++][icoeff+typeoffset_global] = snadi[icoeff];
+        snap[irow++][icoeff+typeoffset_global] = snadi[icoeff+yoffset];
+        snap[irow++][icoeff+typeoffset_global] = snadi[icoeff+zoffset];
       }
-
-      // assign virial row
-
-      int irow0 = irow;
-      snap[irow++][icoeff+typeoffset] = 0.0; 
-      snap[irow++][icoeff+typeoffset] = 0.0; 
-      snap[irow++][icoeff+typeoffset] = 0.0; 
-      snap[irow++][icoeff+typeoffset] = 0.0; 
-      snap[irow++][icoeff+typeoffset] = 0.0; 
-      snap[irow++][icoeff+typeoffset] = 0.0;
-
-      for (int i = 0; i < atom->nlocal; i++) {
-        double *snavi = snap_peratom[i]+typeoffset+virialoffset;
-        irow = irow0;
-        snap[irow++][icoeff+typeoffset] += snavi[icoeff];
-        snap[irow++][icoeff+typeoffset] += snavi[icoeff+1*nperdim];
-        snap[irow++][icoeff+typeoffset] += snavi[icoeff+2*nperdim];
-        snap[irow++][icoeff+typeoffset] += snavi[icoeff+3*nperdim];
-        snap[irow++][icoeff+typeoffset] += snavi[icoeff+4*nperdim];
-        snap[irow++][icoeff+typeoffset] += snavi[icoeff+5*nperdim];
-      }
-
     }
   }
 
-  // assign energy row
+  // assign energy to last column
 
   int icol = size_array_cols-1;
   int irow = 0;
   double reference_energy = c_pe->compute_scalar();
   snap[irow++][icol] = reference_energy; 
 
-  // assign force rows
+  // assign forces to last column
   // INCOMPLETE ignore local-global mapping for now
 
   for (int i = 0; i < atom->nlocal; i++) {
@@ -515,7 +445,7 @@ void ComputeSnap::compute_array()
     snap[irow++][icol] = atom->f[i][2];
   }
 
-  // assign virial row
+  // assign virial stress to last column
   // switch to Voigt notation
 
   c_virial->compute_vector();
@@ -556,6 +486,58 @@ void ComputeSnap::unpack_reverse_comm(int n, int *list, double *buf)
   }
 }
 
+/* ----------------------------------------------------------------------
+   compute global virial contributions via summing dB dot r over 
+   own & ghost atoms, before reverse comm.
+------------------------------------------------------------------------- */
+
+void ComputeSnap::dbdotr_compute()
+{
+  double **x = atom->x;
+  int irow0 = 1+ndims_peratom*natoms;
+
+  // zero virial entries
+
+  for (int itype = 0; itype < atom->ntypes; itype++) {
+    const int typeoffset_global = nperdim*itype;
+    for (int icoeff = 0; icoeff < size_array_cols-1; icoeff++) {
+      int irow = irow0;
+      snap[irow++][icoeff+typeoffset_global] = 0.0;
+      snap[irow++][icoeff+typeoffset_global] = 0.0;
+      snap[irow++][icoeff+typeoffset_global] = 0.0;
+      snap[irow++][icoeff+typeoffset_global] = 0.0;
+      snap[irow++][icoeff+typeoffset_global] = 0.0;
+      snap[irow++][icoeff+typeoffset_global] = 0.0;
+    }
+  }
+
+  // sum over force on all particles including ghosts
+
+  int nall = atom->nlocal + atom->nghost;
+  for (int i = 0; i < nall; i++)
+    for (int itype = 0; itype < atom->ntypes; itype++) {
+      const int typeoffset_local = ndims_peratom*nperdim*itype;
+      const int typeoffset_global = nperdim*itype;
+      double *snadi = snap_peratom[i]+typeoffset_local;
+      for (int icoeff = 0; icoeff < nperdim; icoeff++) {
+        double dbdx = snadi[icoeff];
+        double dbdy = snadi[icoeff+yoffset];
+        double dbdz = snadi[icoeff+zoffset];
+        int irow = irow0;
+
+        // RHS is xi*dSum(b_j, j in itype)/dxi
+        // dSum(bj)/dxi is in first ntypes*3*nperdim elements of row snap_peratom[i]
+        // LHS is Sum(RHS, i), each row of length ntypes*nperdim
+        snap[irow++][icoeff+typeoffset_global] += dbdx*x[i][0];
+        snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][1];
+        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][2];
+        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][1];
+        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][0];
+        snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][0];
+      }
+    }
+}
+
 /* ----------------------------------------------------------------------
    memory usage
 ------------------------------------------------------------------------- */
diff --git a/src/SNAP/compute_snap.h b/src/SNAP/compute_snap.h
index 970c79c67e..671300faae 100644
--- a/src/SNAP/compute_snap.h
+++ b/src/SNAP/compute_snap.h
@@ -38,7 +38,7 @@ class ComputeSnap : public Compute {
  private:
   int natoms, nmax, size_peratom;
   int ncoeff, nperdim, yoffset, zoffset;
-  int virialoffset, ndims_peratom;
+  int ndims_peratom, ndims_force, ndims_virial;
   double **cutsq;
   class NeighList *list;
   double **snap;
@@ -52,6 +52,8 @@ class ComputeSnap : public Compute {
 
   Compute *c_pe;
   Compute *c_virial;
+
+  void dbdotr_compute();
 };
 
 }

From 7cfd5ce634e48d2704f08a2cecfaffd871f378f7 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Sun, 17 Nov 2019 17:01:12 -0700
Subject: [PATCH 045/199] Fixed another problem with typeoffsets

---
 src/SNAP/compute_snap.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 904d75a8e3..2a535d5a2b 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -494,13 +494,13 @@ void ComputeSnap::unpack_reverse_comm(int n, int *list, double *buf)
 void ComputeSnap::dbdotr_compute()
 {
   double **x = atom->x;
-  int irow0 = 1+ndims_peratom*natoms;
+  int irow0 = 1+ndims_force*natoms;
 
   // zero virial entries
 
   for (int itype = 0; itype < atom->ntypes; itype++) {
     const int typeoffset_global = nperdim*itype;
-    for (int icoeff = 0; icoeff < size_array_cols-1; icoeff++) {
+    for (int icoeff = 0; icoeff < nperdim; icoeff++) {
       int irow = irow0;
       snap[irow++][icoeff+typeoffset_global] = 0.0;
       snap[irow++][icoeff+typeoffset_global] = 0.0;

From c504d93e3ce583f42698538b12939722579955fd Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Sun, 17 Nov 2019 19:23:14 -0700
Subject: [PATCH 046/199] Found an error in energy row that only affected
 ntypes > 1

---
 src/SNAP/compute_snap.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 2a535d5a2b..2442e33641 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -387,17 +387,17 @@ void ComputeSnap::compute_array()
       // linear contributions
 
       for (int icoeff = 0; icoeff < ncoeff; icoeff++)
-        snap[0][icoeff] += snaptr->blist[icoeff];
+        snap[0][icoeff+typeoffset_global] += snaptr->blist[icoeff];
 
       // quadratic contributions
 
       if (quadraticflag) {
         for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
           double bveci = snaptr->blist[icoeff];
-          snap[0][icoeff] += 0.5*bveci*bveci;
+          snap[0][icoeff+typeoffset_global] += 0.5*bveci*bveci;
           for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
             double bvecj = snaptr->blist[jcoeff];
-            snap[0][icoeff] += bveci*bvecj;
+            snap[0][icoeff+typeoffset_global] += bveci*bvecj;
           }
         }
       }

From 11961084ce8089b9f75f84aba7e011b4c485e6dc Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Mon, 18 Nov 2019 21:35:32 -0700
Subject: [PATCH 047/199] Made compute snap fully parallel

---
 examples/snap/in.snap.compute |  94 +++++++++++++++++++++++
 src/SNAP/compute_snap.cpp     | 140 +++++++++++++---------------------
 src/SNAP/compute_snap.h       |   6 +-
 3 files changed, 147 insertions(+), 93 deletions(-)
 create mode 100644 examples/snap/in.snap.compute

diff --git a/examples/snap/in.snap.compute b/examples/snap/in.snap.compute
new file mode 100644
index 0000000000..9d0739f327
--- /dev/null
+++ b/examples/snap/in.snap.compute
@@ -0,0 +1,94 @@
+# Demonstrate bispectrum computes
+
+# Initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+#variable 	a equal 3.316
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	ny equal ${nrep}
+variable 	nz equal ${nrep}
+
+boundary	p p p
+
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	2 box
+create_atoms	2 box
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+
+
+# Setup dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_coeff 	* *
+
+# Setup reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_coeff 	* * ${zblz} ${zblz}
+
+# set up old-style per-atom computes
+
+compute 	b all sna/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+group 		snapgroup2 type 2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+
+# set up new-style global compute
+
+compute 	snap all snap ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	snap_press all pressure NULL virial
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(B_{000}^i, all i of type 2) 
+#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dr_j), all i of type 2), all j) 
+#                followed by counterparts from compute snap
+
+thermo_style	custom &
+		pe            pxy            c_bsum2[1]   c_vbsum[60] &
+       		c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] 
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 2442e33641..72fce3b01b 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -45,7 +45,7 @@ enum{SCALAR,VECTOR,ARRAY};
 
 ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snap(NULL),
-  radelem(NULL), wjelem(NULL), snap_peratom(NULL)
+  radelem(NULL), wjelem(NULL), snap_peratom(NULL), snapall(NULL)
 {
 
   array_flag = 1;
@@ -136,9 +136,10 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
   natoms = atom->natoms;
   size_array_rows = 1+ndims_force*natoms+ndims_virial;
   size_array_cols = nperdim*atom->ntypes+1;
+  lastcol = size_array_cols-1;
+
   ndims_peratom = ndims_force;
   size_peratom = ndims_peratom*nperdim*atom->ntypes;
-  comm_reverse = size_peratom;
 
   nmax = 0;
 }
@@ -148,6 +149,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
 ComputeSnap::~ComputeSnap()
 {
   memory->destroy(snap);
+  memory->destroy(snapall);
   memory->destroy(snap_peratom);
   memory->destroy(radelem);
   memory->destroy(wjelem);
@@ -185,7 +187,9 @@ void ComputeSnap::init()
 
   memory->create(snap,size_array_rows,size_array_cols,
                  "snap:snap");
-  array = snap;
+  memory->create(snapall,size_array_rows,size_array_cols,
+                 "snap:snapall");
+  array = snapall;
 
   // INCOMPLETE: modify->find_compute() 
   // was called 223960 times by snappy Ta example
@@ -235,10 +239,10 @@ void ComputeSnap::compute_array()
   }
 
   // clear global array
-  // only need to zero out first row of bispectrum 
 
-  for (int icoeff = 0; icoeff < size_array_cols-1; icoeff++)
-    snap[0][icoeff] = 0.0;
+  for (int irow = 0; irow < size_array_rows; irow++)
+    for (int icoeff = 0; icoeff < size_array_cols; icoeff++)
+      snap[irow][icoeff] = 0.0;
 
   // clear local peratom array
 
@@ -318,7 +322,7 @@ void ComputeSnap::compute_array()
                                     snaptr->rcutij[jj],jj);
         snaptr->compute_dbidrj();
 
-        // Accumulate -dBi/dRi, -dBi/dRj
+        // Accumulate dBi/dRi, -dBi/dRj
 
         double *snadi = snap_peratom[i]+typeoffset_local;
         double *snadj = snap_peratom[j]+typeoffset_local;
@@ -404,91 +408,65 @@ void ComputeSnap::compute_array()
     }
   }
 
-  // accumulate virial contributions before reverse compute
-
-  dbdotr_compute();
-
-  // communicate local peratom contributions between neighbor procs
-
-  comm->reverse_comm_compute(this);
-
-  // copy peratom data to global array
-  // INCOMPLETE ignore local-global mapping for now
+  // accumulate bispectrum force contributions to global array
 
   for (int itype = 0; itype < atom->ntypes; itype++) {
     const int typeoffset_local = ndims_peratom*nperdim*itype;
     const int typeoffset_global = nperdim*itype;
     for (int icoeff = 0; icoeff < nperdim; icoeff++) {
       int irow = 1;
-      for (int i = 0; i < atom->nlocal; i++) {
+      for (int i = 0; i < ntotal; i++) {
         double *snadi = snap_peratom[i]+typeoffset_local;
-        snap[irow++][icoeff+typeoffset_global] = snadi[icoeff];
-        snap[irow++][icoeff+typeoffset_global] = snadi[icoeff+yoffset];
-        snap[irow++][icoeff+typeoffset_global] = snadi[icoeff+zoffset];
+        int iglobal = atom->tag[i];
+        int irow = 3*(iglobal-1)+1;
+        snap[irow][icoeff+typeoffset_global] += snadi[icoeff];
+        snap[irow+1][icoeff+typeoffset_global] += snadi[icoeff+yoffset];
+        snap[irow+2][icoeff+typeoffset_global] += snadi[icoeff+zoffset];
       }
     }
   }
 
-  // assign energy to last column
-
-  int icol = size_array_cols-1;
-  int irow = 0;
-  double reference_energy = c_pe->compute_scalar();
-  snap[irow++][icol] = reference_energy; 
-
-  // assign forces to last column
-  // INCOMPLETE ignore local-global mapping for now
+ // accumulate forces to global array
 
   for (int i = 0; i < atom->nlocal; i++) {
-    snap[irow++][icol] = atom->f[i][0];
-    snap[irow++][icol] = atom->f[i][1];
-    snap[irow++][icol] = atom->f[i][2];
+    int iglobal = atom->tag[i];
+    int irow = 3*(iglobal-1)+1;
+    snap[irow][lastcol] = atom->f[i][0];
+    snap[irow+1][lastcol] = atom->f[i][1];
+    snap[irow+2][lastcol] = atom->f[i][2];
   }
 
+  // accumulate bispectrum virial contributions to global array
+
+  dbdotr_compute();
+
+  // sum up over all processes
+
+  MPI_Allreduce(&snap[0][0],&snapall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
+
+  // assign energy to last column
+
+  int irow = 0;
+  double reference_energy = c_pe->compute_scalar();
+  snapall[irow++][lastcol] = reference_energy; 
+
   // assign virial stress to last column
   // switch to Voigt notation
 
   c_virial->compute_vector();
-  snap[irow++][icol] = c_virial->vector[0]; 
-  snap[irow++][icol] = c_virial->vector[1]; 
-  snap[irow++][icol] = c_virial->vector[2]; 
-  snap[irow++][icol] = c_virial->vector[5]; 
-  snap[irow++][icol] = c_virial->vector[4]; 
-  snap[irow++][icol] = c_virial->vector[3]; 
+  irow += 3*natoms;
+  snapall[irow++][lastcol] = c_virial->vector[0]; 
+  snapall[irow++][lastcol] = c_virial->vector[1]; 
+  snapall[irow++][lastcol] = c_virial->vector[2]; 
+  snapall[irow++][lastcol] = c_virial->vector[5]; 
+  snapall[irow++][lastcol] = c_virial->vector[4]; 
+  snapall[irow++][lastcol] = c_virial->vector[3]; 
 
 }
 
-/* ---------------------------------------------------------------------- */
-
-int ComputeSnap::pack_reverse_comm(int n, int first, double *buf)
-{
-  int i,m,last,icoeff;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++)
-    for (icoeff = 0; icoeff < size_peratom; icoeff++)
-      buf[m++] = snap_peratom[i][icoeff];
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void ComputeSnap::unpack_reverse_comm(int n, int *list, double *buf)
-{
-  int i,j,m,icoeff;
-
-  m = 0;
-  for (i = 0; i < n; i++) {
-    j = list[i];
-    for (icoeff = 0; icoeff < size_peratom; icoeff++)
-      snap_peratom[j][icoeff] += buf[m++];
-  }
-}
-
 /* ----------------------------------------------------------------------
-   compute global virial contributions via summing dB dot r over 
-   own & ghost atoms, before reverse comm.
+   compute global virial contributions via summing r_i.dB^j/dr_i over 
+   own & ghost atoms
 ------------------------------------------------------------------------- */
 
 void ComputeSnap::dbdotr_compute()
@@ -496,22 +474,8 @@ void ComputeSnap::dbdotr_compute()
   double **x = atom->x;
   int irow0 = 1+ndims_force*natoms;
 
-  // zero virial entries
-
-  for (int itype = 0; itype < atom->ntypes; itype++) {
-    const int typeoffset_global = nperdim*itype;
-    for (int icoeff = 0; icoeff < nperdim; icoeff++) {
-      int irow = irow0;
-      snap[irow++][icoeff+typeoffset_global] = 0.0;
-      snap[irow++][icoeff+typeoffset_global] = 0.0;
-      snap[irow++][icoeff+typeoffset_global] = 0.0;
-      snap[irow++][icoeff+typeoffset_global] = 0.0;
-      snap[irow++][icoeff+typeoffset_global] = 0.0;
-      snap[irow++][icoeff+typeoffset_global] = 0.0;
-    }
-  }
-
-  // sum over force on all particles including ghosts
+  // sum over bispectrum contributions to forces
+  // on all particles including ghosts
 
   int nall = atom->nlocal + atom->nghost;
   for (int i = 0; i < nall; i++)
@@ -524,10 +488,6 @@ void ComputeSnap::dbdotr_compute()
         double dbdy = snadi[icoeff+yoffset];
         double dbdz = snadi[icoeff+zoffset];
         int irow = irow0;
-
-        // RHS is xi*dSum(b_j, j in itype)/dxi
-        // dSum(bj)/dxi is in first ntypes*3*nperdim elements of row snap_peratom[i]
-        // LHS is Sum(RHS, i), each row of length ntypes*nperdim
         snap[irow++][icoeff+typeoffset_global] += dbdx*x[i][0];
         snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][1];
         snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][2];
@@ -547,6 +507,8 @@ double ComputeSnap::memory_usage()
 
   double bytes = size_array_rows*size_array_cols * 
     sizeof(double);                                     // snap
+  bytes += size_array_rows*size_array_cols * 
+    sizeof(double);                                     // snapall
   bytes += nmax*size_peratom * sizeof(double);          // snap_peratom
   bytes += snaptr->memory_usage();                      // SNA object
 
diff --git a/src/SNAP/compute_snap.h b/src/SNAP/compute_snap.h
index 671300faae..4f30b7c507 100644
--- a/src/SNAP/compute_snap.h
+++ b/src/SNAP/compute_snap.h
@@ -31,17 +31,15 @@ class ComputeSnap : public Compute {
   void init();
   void init_list(int, class NeighList *);
   void compute_array();
-  int pack_reverse_comm(int, int, double *);
-  void unpack_reverse_comm(int, int *, double *);
   double memory_usage();
 
  private:
-  int natoms, nmax, size_peratom;
+  int natoms, nmax, size_peratom, lastcol;
   int ncoeff, nperdim, yoffset, zoffset;
   int ndims_peratom, ndims_force, ndims_virial;
   double **cutsq;
   class NeighList *list;
-  double **snap;
+  double **snap, **snapall;
   double **snap_peratom;
   double rcutfac;
   double *radelem;

From 59af51ca91e0f4c1d8a56199380d47e44ff0f33a Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Mon, 18 Nov 2019 23:51:08 -0700
Subject: [PATCH 048/199] Added code to create pressure compute snap_press
 behind the scenes

---
 examples/snap/in.snap.compute |  1 -
 src/SNAP/compute_snap.cpp     | 11 +++++++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/examples/snap/in.snap.compute b/examples/snap/in.snap.compute
index 9d0739f327..f6038ff37a 100644
--- a/examples/snap/in.snap.compute
+++ b/examples/snap/in.snap.compute
@@ -70,7 +70,6 @@ compute		vbsum all reduce sum c_vb[*]
 # set up new-style global compute
 
 compute 	snap all snap ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
-compute 	snap_press all pressure NULL virial
 fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
 
 thermo 		100
diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 72fce3b01b..80f731dcf3 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -207,10 +207,21 @@ void ComputeSnap::init()
   // add compute for reference virial tensor
 
   char *id_virial = (char *) "snap_press";
+
+  char **newarg = new char*[5];
+  newarg[0] = id_virial;
+  newarg[1] = (char *) "all";
+  newarg[2] = (char *) "pressure";
+  newarg[3] = (char *) "NULL";
+  newarg[4] = (char *) "virial";
+  modify->add_compute(5,newarg);
+  delete [] newarg;
+
   int ivirial = modify->find_compute(id_virial);
   if (ivirial == -1)
     error->all(FLERR,"compute snap requires that compute snap_press exists.");
   c_virial = modify->compute[ivirial];
+
 }
 
 

From b092a9fffa2d5dc88adf8250453cdbda1b036235 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Tue, 19 Nov 2019 00:00:04 -0700
Subject: [PATCH 049/199] Added code to create pressure compute snap_press
 behind the scenes

---
 src/SNAP/compute_snap.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 80f731dcf3..1a34c8cbc5 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -207,7 +207,6 @@ void ComputeSnap::init()
   // add compute for reference virial tensor
 
   char *id_virial = (char *) "snap_press";
-
   char **newarg = new char*[5];
   newarg[0] = id_virial;
   newarg[1] = (char *) "all";
@@ -219,7 +218,7 @@ void ComputeSnap::init()
 
   int ivirial = modify->find_compute(id_virial);
   if (ivirial == -1)
-    error->all(FLERR,"compute snap requires that compute snap_press exists.");
+    error->all(FLERR,"compute snap_press does not exist.");
   c_virial = modify->compute[ivirial];
 
 }

From 921d0794bbc00b7058286037acb59445d3fdaa3d Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Tue, 19 Nov 2019 00:12:57 -0700
Subject: [PATCH 050/199] Finished documentation and example

---
 doc/txt/compute_sna_atom.txt  | 52 ++++++++++++++++++++++++++++++++---
 examples/snap/in.snap.compute | 21 +++++++-------
 2 files changed, 59 insertions(+), 14 deletions(-)

diff --git a/doc/txt/compute_sna_atom.txt b/doc/txt/compute_sna_atom.txt
index eab32d8757..0639116b93 100644
--- a/doc/txt/compute_sna_atom.txt
+++ b/doc/txt/compute_sna_atom.txt
@@ -9,12 +9,14 @@
 compute sna/atom command :h3
 compute snad/atom command :h3
 compute snav/atom command :h3
+compute snap command :h3
 
 [Syntax:]
 
 compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
 compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
+compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... 
+compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
 
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 sna/atom = style name of this compute command :l
@@ -41,12 +43,17 @@ keyword = {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
 
 compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
 compute db all sna/atom 1.4 0.95 6 2.0 1.0
-compute vb all sna/atom 1.4 0.95 6 2.0 1.0 :pre
+compute vb all sna/atom 1.4 0.95 6 2.0 1.0
+compute snap all snap 1.4 0.95 6 2.0 1.0 :pre
 
 [Description:]
 
-Define a computation that calculates a set of bispectrum components
-for each atom in a group.
+Define a computation that calculates a set of quantities related to the
+bispectrum components of the atoms in a group. These computes are
+used primarily for calculating the dependence of energy, force, and
+stress components on the linear coefficients in the 
+"snap pair_style"_pair_snap.html, which is useful when training a
+SNAP potential to match target data.
 
 Bispectrum components of an atom are order parameters characterizing
 the radial and angular distribution of neighbor atoms. The detailed
@@ -130,6 +137,26 @@ Again, the sum is over all atoms {i'} of atom type {I}.  For each atom
 virial components, each atom type, and each bispectrum component.  See
 section below on output for a detailed explanation.
 
+Compute {snap} calculates a global array contains information related
+to all three of the preceding per-atom computes {sna/atom}, {snad/atom},
+and {snav/atom}. The first row of the array contains the summation of 
+{sna/atom} over all atoms, but broken out by type. The last six rows
+of the array contain the summation of {snav/atom} over all atoms, broken
+out by type. In between these are 3*N rows containing the same values
+computed by {snad/atom} (these are already summed over all atoms and
+broken out by type). The element in the last column of each row contains
+the corresponding contribution to potential energy, force, or stress. 
+These quantities correspond to the user-specified refence potential
+that must be subtracted from the target data when fitting SNAP.
+The potential energy calculation uses the built in compute {thermo_pe}.
+The stess calculation requires that a compute called {snap_press}
+be defined using the following command:
+
+compute snap_press all pressure NULL virial :pre
+
+See section below on output for a detailed explanation of the data
+layout in the global array.
+
 The value of all bispectrum components will be zero for atoms not in
 the group. Neighbor atoms not in the group do not contribute to the
 bispectrum of atoms in the group.
@@ -214,10 +241,27 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
 notation.  Each of these sub-blocks contains one column for each
 bispectrum component, the same as for compute {sna/atom}
 
+Compute {snap} evaluates a global array. 
+The columns are arranged into
+{ntypes} blocks, listed in order of atom type {I}. Each block
+contains one column for each bispectrum component, the same as for compute
+{sna/atom}. A final column contains the corresponding energy, force component
+on an atom, and virial stress component. The rows of the array appear 
+in the following order:
+
+   1 row: {sna/atom} quantities summed for all atoms of type {I}
+   3*N rows: {snad/atom} quantities, with derivatives w.r.t x, y, and z 
+coordinate of atom {i} appearing in consecutive rows. The atoms
+are sorted based on atom ID.
+   6 rows: {snav/atom} quantities summed for all atoms of type {I} :ul
+
 For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
 arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
 are 30, 90, and 180, respectively. With {quadratic} value=1,
 the numbers of columns are 930, 2790, and 5580, respectively.
+The number of columns in the global array generated by {snap}
+are 31, and 931, respectively, while the number of rows is
+1+3*{N} +6, where {N} is the total number of atoms.
 
 If the {quadratic} keyword value is set to 1, then additional
 columns are generated, corresponding to
diff --git a/examples/snap/in.snap.compute b/examples/snap/in.snap.compute
index f6038ff37a..8955500e0e 100644
--- a/examples/snap/in.snap.compute
+++ b/examples/snap/in.snap.compute
@@ -1,6 +1,6 @@
 # Demonstrate bispectrum computes
 
-# Initialize simulation
+# initialize simulation
 
 variable 	nsteps index 0
 variable 	nrep equal 1
@@ -35,14 +35,15 @@ variable 	radelem1 equal 2.3
 variable 	radelem2 equal 2.0
 variable	wj1 equal 1.0
 variable	wj2 equal 0.96
+variable 	snap_options string &
+"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0"
 
-
-# Setup dummy potential to satisfy cutoff
+# set up dummy potential to satisfy cutoff
 
 pair_style 	zero ${rcutfac}
 pair_coeff 	* *
 
-# Setup reference potential
+# set up reference potential
 
 variable 	zblcutinner equal 4
 variable 	zblcutouter equal 4.8
@@ -50,11 +51,11 @@ variable 	zblz equal 73
 pair_style 	zbl ${zblcutinner} ${zblcutouter}
 pair_coeff 	* * ${zblz} ${zblz}
 
-# set up old-style per-atom computes
+# set up per-atom computes
 
-compute 	b all sna/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
-compute 	vb all snav/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
-compute 	db all snad/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	b all sna/atom ${snap_options}
+compute 	vb all snav/atom ${snap_options}
+compute 	db all snad/atom ${snap_options}
 
 # perform sums over atoms
 
@@ -67,9 +68,9 @@ compute         bsum2 snapgroup2 reduce sum c_b[*]
 compute		vbsum all reduce sum c_vb[*]
 # fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
 
-# set up new-style global compute
+# set up compute snap generating global array
 
-compute 	snap all snap ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	snap all snap ${snap_options}
 fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
 
 thermo 		100

From 920a217ee19710cffc2cacb23b016588bb2d091b Mon Sep 17 00:00:00 2001
From: "Aidan P. Thompson" <athomps@sandia.gov>
Date: Tue, 19 Nov 2019 00:47:29 -0700
Subject: [PATCH 051/199] Fixed some formatting issues

---
 doc/src/compute_sna_atom.rst | 54 ++++++++++++++++++++++++++++++++++--
 doc/txt/compute_sna_atom.txt | 19 ++++++-------
 2 files changed, 60 insertions(+), 13 deletions(-)

diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst
index 882fdbb0a0..1119c21996 100644
--- a/doc/src/compute_sna_atom.rst
+++ b/doc/src/compute_sna_atom.rst
@@ -9,6 +9,9 @@ compute snad/atom command
 compute snav/atom command
 =========================
 
+compute snap command
+====================
+
 Syntax
 """"""
 
@@ -17,7 +20,8 @@ Syntax
 
    compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
    compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-   compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+   compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... 
+   compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * sna/atom = style name of this compute command
@@ -53,12 +57,17 @@ Examples
    compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
    compute db all sna/atom 1.4 0.95 6 2.0 1.0
    compute vb all sna/atom 1.4 0.95 6 2.0 1.0
+   compute snap all snap 1.4 0.95 6 2.0 1.0
 
 Description
 """""""""""
 
-Define a computation that calculates a set of bispectrum components
-for each atom in a group.
+Define a computation that calculates a set of quantities related to the
+bispectrum components of the atoms in a group. These computes are
+used primarily for calculating the dependence of energy, force, and
+stress components on the linear coefficients in the 
+:doc:`snap pair\_style <pair_snap>`, which is useful when training a
+SNAP potential to match target data.
 
 Bispectrum components of an atom are order parameters characterizing
 the radial and angular distribution of neighbor atoms. The detailed
@@ -148,6 +157,30 @@ Again, the sum is over all atoms *i'* of atom type *I*\ .  For each atom
 virial components, each atom type, and each bispectrum component.  See
 section below on output for a detailed explanation.
 
+Compute *snap* calculates a global array contains information related
+to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
+and *snav/atom*\ . The first row of the array contains the summation of 
+*sna/atom* over all atoms, but broken out by type. The last six rows
+of the array contain the summation of *snav/atom* over all atoms, broken
+out by type. In between these are 3\*\ *N* rows containing the same values
+computed by *snad/atom* (these are already summed over all atoms and
+broken out by type). The element in the last column of each row contains
+the potential energy, force, or stress, according to the row.
+These quantities correspond to the user-specified refence potential
+that must be subtracted from the target data when fitting SNAP.
+The potential energy calculation uses the built in compute *thermo\_pe*.
+The stress calculation uses a compute called *snap\_press* that is
+automatically created behind the scenes, according to the following
+command:
+
+
+.. parsed-literal::
+
+   compute snap_press all pressure NULL virial
+
+See section below on output for a detailed explanation of the data
+layout in the global array.
+
 The value of all bispectrum components will be zero for atoms not in
 the group. Neighbor atoms not in the group do not contribute to the
 bispectrum of atoms in the group.
@@ -239,10 +272,25 @@ block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
 notation.  Each of these sub-blocks contains one column for each
 bispectrum component, the same as for compute *sna/atom*
 
+Compute *snap* evaluates a global array. 
+The columns are arranged into
+*ntypes* blocks, listed in order of atom type *I*\ . Each block
+contains one column for each bispectrum component, the same as for compute
+*sna/atom*\ . A final column contains the corresponding energy, force component
+on an atom, or virial stress component. The rows of the array appear 
+in the following order:
+
+* 1 row: *sna/atom* quantities summed for all atoms of type *I*
+* 3\*\ *N* rows: *snad/atom* quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
+* 6 rows: *snav/atom* quantities summed for all atoms of type *I*
+
 For example, if *K* =30 and ntypes=1, the number of columns in the per-atom
 arrays generated by *sna/atom*\ , *snad/atom*\ , and *snav/atom*
 are 30, 90, and 180, respectively. With *quadratic* value=1,
 the numbers of columns are 930, 2790, and 5580, respectively.
+The number of columns in the global array generated by *snap*
+are 31, and 931, respectively, while the number of rows is
+1+3\*\ *N*\ +6, where *N* is the total number of atoms.
 
 If the *quadratic* keyword value is set to 1, then additional
 columns are generated, corresponding to
diff --git a/doc/txt/compute_sna_atom.txt b/doc/txt/compute_sna_atom.txt
index 0639116b93..05a0bee923 100644
--- a/doc/txt/compute_sna_atom.txt
+++ b/doc/txt/compute_sna_atom.txt
@@ -138,19 +138,20 @@ virial components, each atom type, and each bispectrum component.  See
 section below on output for a detailed explanation.
 
 Compute {snap} calculates a global array contains information related
-to all three of the preceding per-atom computes {sna/atom}, {snad/atom},
+to all three of the above per-atom computes {sna/atom}, {snad/atom},
 and {snav/atom}. The first row of the array contains the summation of 
 {sna/atom} over all atoms, but broken out by type. The last six rows
 of the array contain the summation of {snav/atom} over all atoms, broken
-out by type. In between these are 3*N rows containing the same values
+out by type. In between these are 3*{N} rows containing the same values
 computed by {snad/atom} (these are already summed over all atoms and
 broken out by type). The element in the last column of each row contains
-the corresponding contribution to potential energy, force, or stress. 
+the potential energy, force, or stress, according to the row.
 These quantities correspond to the user-specified refence potential
 that must be subtracted from the target data when fitting SNAP.
 The potential energy calculation uses the built in compute {thermo_pe}.
-The stess calculation requires that a compute called {snap_press}
-be defined using the following command:
+The stress calculation uses a compute called {snap_press} that is
+automatically created behind the scenes, according to the following
+command:
 
 compute snap_press all pressure NULL virial :pre
 
@@ -246,13 +247,11 @@ The columns are arranged into
 {ntypes} blocks, listed in order of atom type {I}. Each block
 contains one column for each bispectrum component, the same as for compute
 {sna/atom}. A final column contains the corresponding energy, force component
-on an atom, and virial stress component. The rows of the array appear 
+on an atom, or virial stress component. The rows of the array appear 
 in the following order:
 
    1 row: {sna/atom} quantities summed for all atoms of type {I}
-   3*N rows: {snad/atom} quantities, with derivatives w.r.t x, y, and z 
-coordinate of atom {i} appearing in consecutive rows. The atoms
-are sorted based on atom ID.
+   3*{N} rows: {snad/atom} quantities, with derivatives w.r.t. x, y, and z coordinate of atom {i} appearing in consecutive rows. The atoms are sorted based on atom ID.
    6 rows: {snav/atom} quantities summed for all atoms of type {I} :ul
 
 For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
@@ -261,7 +260,7 @@ are 30, 90, and 180, respectively. With {quadratic} value=1,
 the numbers of columns are 930, 2790, and 5580, respectively.
 The number of columns in the global array generated by {snap}
 are 31, and 931, respectively, while the number of rows is
-1+3*{N} +6, where {N} is the total number of atoms.
+1+3*{N}+6, where {N} is the total number of atoms.
 
 If the {quadratic} keyword value is set to 1, then additional
 columns are generated, corresponding to

From 897ffef242e513a3a42e9faac4279e380377cdea Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Tue, 19 Nov 2019 00:50:57 -0700
Subject: [PATCH 052/199] Fixed some formatting issues

---
 doc/src/compute_sna_atom.rst | 54 ++++++++++++++++++++++++++++++++++--
 doc/txt/compute_sna_atom.txt | 19 ++++++-------
 2 files changed, 60 insertions(+), 13 deletions(-)

diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst
index 882fdbb0a0..1119c21996 100644
--- a/doc/src/compute_sna_atom.rst
+++ b/doc/src/compute_sna_atom.rst
@@ -9,6 +9,9 @@ compute snad/atom command
 compute snav/atom command
 =========================
 
+compute snap command
+====================
+
 Syntax
 """"""
 
@@ -17,7 +20,8 @@ Syntax
 
    compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
    compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-   compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+   compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... 
+   compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * sna/atom = style name of this compute command
@@ -53,12 +57,17 @@ Examples
    compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
    compute db all sna/atom 1.4 0.95 6 2.0 1.0
    compute vb all sna/atom 1.4 0.95 6 2.0 1.0
+   compute snap all snap 1.4 0.95 6 2.0 1.0
 
 Description
 """""""""""
 
-Define a computation that calculates a set of bispectrum components
-for each atom in a group.
+Define a computation that calculates a set of quantities related to the
+bispectrum components of the atoms in a group. These computes are
+used primarily for calculating the dependence of energy, force, and
+stress components on the linear coefficients in the 
+:doc:`snap pair\_style <pair_snap>`, which is useful when training a
+SNAP potential to match target data.
 
 Bispectrum components of an atom are order parameters characterizing
 the radial and angular distribution of neighbor atoms. The detailed
@@ -148,6 +157,30 @@ Again, the sum is over all atoms *i'* of atom type *I*\ .  For each atom
 virial components, each atom type, and each bispectrum component.  See
 section below on output for a detailed explanation.
 
+Compute *snap* calculates a global array contains information related
+to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
+and *snav/atom*\ . The first row of the array contains the summation of 
+*sna/atom* over all atoms, but broken out by type. The last six rows
+of the array contain the summation of *snav/atom* over all atoms, broken
+out by type. In between these are 3\*\ *N* rows containing the same values
+computed by *snad/atom* (these are already summed over all atoms and
+broken out by type). The element in the last column of each row contains
+the potential energy, force, or stress, according to the row.
+These quantities correspond to the user-specified refence potential
+that must be subtracted from the target data when fitting SNAP.
+The potential energy calculation uses the built in compute *thermo\_pe*.
+The stress calculation uses a compute called *snap\_press* that is
+automatically created behind the scenes, according to the following
+command:
+
+
+.. parsed-literal::
+
+   compute snap_press all pressure NULL virial
+
+See section below on output for a detailed explanation of the data
+layout in the global array.
+
 The value of all bispectrum components will be zero for atoms not in
 the group. Neighbor atoms not in the group do not contribute to the
 bispectrum of atoms in the group.
@@ -239,10 +272,25 @@ block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
 notation.  Each of these sub-blocks contains one column for each
 bispectrum component, the same as for compute *sna/atom*
 
+Compute *snap* evaluates a global array. 
+The columns are arranged into
+*ntypes* blocks, listed in order of atom type *I*\ . Each block
+contains one column for each bispectrum component, the same as for compute
+*sna/atom*\ . A final column contains the corresponding energy, force component
+on an atom, or virial stress component. The rows of the array appear 
+in the following order:
+
+* 1 row: *sna/atom* quantities summed for all atoms of type *I*
+* 3\*\ *N* rows: *snad/atom* quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
+* 6 rows: *snav/atom* quantities summed for all atoms of type *I*
+
 For example, if *K* =30 and ntypes=1, the number of columns in the per-atom
 arrays generated by *sna/atom*\ , *snad/atom*\ , and *snav/atom*
 are 30, 90, and 180, respectively. With *quadratic* value=1,
 the numbers of columns are 930, 2790, and 5580, respectively.
+The number of columns in the global array generated by *snap*
+are 31, and 931, respectively, while the number of rows is
+1+3\*\ *N*\ +6, where *N* is the total number of atoms.
 
 If the *quadratic* keyword value is set to 1, then additional
 columns are generated, corresponding to
diff --git a/doc/txt/compute_sna_atom.txt b/doc/txt/compute_sna_atom.txt
index 0639116b93..05a0bee923 100644
--- a/doc/txt/compute_sna_atom.txt
+++ b/doc/txt/compute_sna_atom.txt
@@ -138,19 +138,20 @@ virial components, each atom type, and each bispectrum component.  See
 section below on output for a detailed explanation.
 
 Compute {snap} calculates a global array contains information related
-to all three of the preceding per-atom computes {sna/atom}, {snad/atom},
+to all three of the above per-atom computes {sna/atom}, {snad/atom},
 and {snav/atom}. The first row of the array contains the summation of 
 {sna/atom} over all atoms, but broken out by type. The last six rows
 of the array contain the summation of {snav/atom} over all atoms, broken
-out by type. In between these are 3*N rows containing the same values
+out by type. In between these are 3*{N} rows containing the same values
 computed by {snad/atom} (these are already summed over all atoms and
 broken out by type). The element in the last column of each row contains
-the corresponding contribution to potential energy, force, or stress. 
+the potential energy, force, or stress, according to the row.
 These quantities correspond to the user-specified refence potential
 that must be subtracted from the target data when fitting SNAP.
 The potential energy calculation uses the built in compute {thermo_pe}.
-The stess calculation requires that a compute called {snap_press}
-be defined using the following command:
+The stress calculation uses a compute called {snap_press} that is
+automatically created behind the scenes, according to the following
+command:
 
 compute snap_press all pressure NULL virial :pre
 
@@ -246,13 +247,11 @@ The columns are arranged into
 {ntypes} blocks, listed in order of atom type {I}. Each block
 contains one column for each bispectrum component, the same as for compute
 {sna/atom}. A final column contains the corresponding energy, force component
-on an atom, and virial stress component. The rows of the array appear 
+on an atom, or virial stress component. The rows of the array appear 
 in the following order:
 
    1 row: {sna/atom} quantities summed for all atoms of type {I}
-   3*N rows: {snad/atom} quantities, with derivatives w.r.t x, y, and z 
-coordinate of atom {i} appearing in consecutive rows. The atoms
-are sorted based on atom ID.
+   3*{N} rows: {snad/atom} quantities, with derivatives w.r.t. x, y, and z coordinate of atom {i} appearing in consecutive rows. The atoms are sorted based on atom ID.
    6 rows: {snav/atom} quantities summed for all atoms of type {I} :ul
 
 For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
@@ -261,7 +260,7 @@ are 30, 90, and 180, respectively. With {quadratic} value=1,
 the numbers of columns are 930, 2790, and 5580, respectively.
 The number of columns in the global array generated by {snap}
 are 31, and 931, respectively, while the number of rows is
-1+3*{N} +6, where {N} is the total number of atoms.
+1+3*{N}+6, where {N} is the total number of atoms.
 
 If the {quadratic} keyword value is set to 1, then additional
 columns are generated, corresponding to

From b109fd1687cef27de0f6a6c8053eaa7d51359a01 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Tue, 19 Nov 2019 12:50:52 -0700
Subject: [PATCH 053/199] Commit JT 111919 - modified named of tests, from
 benchmark to validation

---
 examples/SPIN/read_restart/in.spin.restart                      | 2 +-
 examples/SPIN/{benchmark => validation}/README                  | 0
 .../validation_damped_exchange}/bench-spin-precession.in        | 0
 .../validation_damped_exchange}/llg_exchange.py                 | 0
 .../validation_damped_exchange}/plot_precession.py              | 0
 .../validation_damped_exchange}/run-bench-exchange.sh           | 0
 .../validation_damped_exchange}/two_spins.data                  | 0
 .../validation_damped_precession}/bench-spin-precession.in      | 0
 .../validation_damped_precession}/llg_precession.py             | 0
 .../validation_damped_precession}/plot_precession.py            | 0
 .../validation_damped_precession}/run-bench-prec.sh             | 0
 .../validation_langevin_precession}/bench-prec-spin.template    | 0
 .../validation_langevin_precession}/langevin.py                 | 0
 .../validation_langevin_precession}/plot_precession.py          | 0
 .../validation_langevin_precession}/run-bench-prec.sh           | 0
 15 files changed, 1 insertion(+), 1 deletion(-)
 rename examples/SPIN/{benchmark => validation}/README (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_exchange => validation/validation_damped_exchange}/bench-spin-precession.in (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_exchange => validation/validation_damped_exchange}/llg_exchange.py (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_exchange => validation/validation_damped_exchange}/plot_precession.py (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_exchange => validation/validation_damped_exchange}/run-bench-exchange.sh (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_exchange => validation/validation_damped_exchange}/two_spins.data (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_precession => validation/validation_damped_precession}/bench-spin-precession.in (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_precession => validation/validation_damped_precession}/llg_precession.py (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_precession => validation/validation_damped_precession}/plot_precession.py (100%)
 rename examples/SPIN/{benchmark/benchmarck_damped_precession => validation/validation_damped_precession}/run-bench-prec.sh (100%)
 rename examples/SPIN/{benchmark/benchmarck_langevin_precession => validation/validation_langevin_precession}/bench-prec-spin.template (100%)
 rename examples/SPIN/{benchmark/benchmarck_langevin_precession => validation/validation_langevin_precession}/langevin.py (100%)
 rename examples/SPIN/{benchmark/benchmarck_langevin_precession => validation/validation_langevin_precession}/plot_precession.py (100%)
 rename examples/SPIN/{benchmark/benchmarck_langevin_precession => validation/validation_langevin_precession}/run-bench-prec.sh (100%)

diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart
index ccce25b254..ad6f337890 100644
--- a/examples/SPIN/read_restart/in.spin.restart
+++ b/examples/SPIN/read_restart/in.spin.restart
@@ -44,6 +44,6 @@ thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
 thermo_modify   format float %20.15g
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
 run 		100
diff --git a/examples/SPIN/benchmark/README b/examples/SPIN/validation/README
similarity index 100%
rename from examples/SPIN/benchmark/README
rename to examples/SPIN/validation/README
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/bench-spin-precession.in b/examples/SPIN/validation/validation_damped_exchange/bench-spin-precession.in
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_exchange/bench-spin-precession.in
rename to examples/SPIN/validation/validation_damped_exchange/bench-spin-precession.in
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/llg_exchange.py b/examples/SPIN/validation/validation_damped_exchange/llg_exchange.py
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_exchange/llg_exchange.py
rename to examples/SPIN/validation/validation_damped_exchange/llg_exchange.py
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/plot_precession.py b/examples/SPIN/validation/validation_damped_exchange/plot_precession.py
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_exchange/plot_precession.py
rename to examples/SPIN/validation/validation_damped_exchange/plot_precession.py
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/run-bench-exchange.sh b/examples/SPIN/validation/validation_damped_exchange/run-bench-exchange.sh
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_exchange/run-bench-exchange.sh
rename to examples/SPIN/validation/validation_damped_exchange/run-bench-exchange.sh
diff --git a/examples/SPIN/benchmark/benchmarck_damped_exchange/two_spins.data b/examples/SPIN/validation/validation_damped_exchange/two_spins.data
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_exchange/two_spins.data
rename to examples/SPIN/validation/validation_damped_exchange/two_spins.data
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in b/examples/SPIN/validation/validation_damped_precession/bench-spin-precession.in
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_precession/bench-spin-precession.in
rename to examples/SPIN/validation/validation_damped_precession/bench-spin-precession.in
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py b/examples/SPIN/validation/validation_damped_precession/llg_precession.py
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_precession/llg_precession.py
rename to examples/SPIN/validation/validation_damped_precession/llg_precession.py
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py b/examples/SPIN/validation/validation_damped_precession/plot_precession.py
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_precession/plot_precession.py
rename to examples/SPIN/validation/validation_damped_precession/plot_precession.py
diff --git a/examples/SPIN/benchmark/benchmarck_damped_precession/run-bench-prec.sh b/examples/SPIN/validation/validation_damped_precession/run-bench-prec.sh
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_damped_precession/run-bench-prec.sh
rename to examples/SPIN/validation/validation_damped_precession/run-bench-prec.sh
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template b/examples/SPIN/validation/validation_langevin_precession/bench-prec-spin.template
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_langevin_precession/bench-prec-spin.template
rename to examples/SPIN/validation/validation_langevin_precession/bench-prec-spin.template
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/langevin.py b/examples/SPIN/validation/validation_langevin_precession/langevin.py
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_langevin_precession/langevin.py
rename to examples/SPIN/validation/validation_langevin_precession/langevin.py
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/plot_precession.py b/examples/SPIN/validation/validation_langevin_precession/plot_precession.py
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_langevin_precession/plot_precession.py
rename to examples/SPIN/validation/validation_langevin_precession/plot_precession.py
diff --git a/examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh b/examples/SPIN/validation/validation_langevin_precession/run-bench-prec.sh
similarity index 100%
rename from examples/SPIN/benchmark/benchmarck_langevin_precession/run-bench-prec.sh
rename to examples/SPIN/validation/validation_langevin_precession/run-bench-prec.sh

From a0c51b40b9da8746242b02dc92a94fa6caa48014 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Tue, 19 Nov 2019 12:54:30 -0700
Subject: [PATCH 054/199] Commit2 JT 111919 - renaming validation directory

---
 examples/SPIN/{validation => test_problems}/README                | 0
 .../validation_damped_exchange/bench-spin-precession.in           | 0
 .../validation_damped_exchange/llg_exchange.py                    | 0
 .../validation_damped_exchange/plot_precession.py                 | 0
 .../validation_damped_exchange/run-bench-exchange.sh              | 0
 .../validation_damped_exchange/two_spins.data                     | 0
 .../validation_damped_precession/bench-spin-precession.in         | 0
 .../validation_damped_precession/llg_precession.py                | 0
 .../validation_damped_precession/plot_precession.py               | 0
 .../validation_damped_precession/run-bench-prec.sh                | 0
 .../validation_langevin_precession/bench-prec-spin.template       | 0
 .../validation_langevin_precession/langevin.py                    | 0
 .../validation_langevin_precession/plot_precession.py             | 0
 .../validation_langevin_precession/run-bench-prec.sh              | 0
 14 files changed, 0 insertions(+), 0 deletions(-)
 rename examples/SPIN/{validation => test_problems}/README (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_exchange/bench-spin-precession.in (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_exchange/llg_exchange.py (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_exchange/plot_precession.py (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_exchange/run-bench-exchange.sh (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_exchange/two_spins.data (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_precession/bench-spin-precession.in (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_precession/llg_precession.py (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_precession/plot_precession.py (100%)
 rename examples/SPIN/{validation => test_problems}/validation_damped_precession/run-bench-prec.sh (100%)
 rename examples/SPIN/{validation => test_problems}/validation_langevin_precession/bench-prec-spin.template (100%)
 rename examples/SPIN/{validation => test_problems}/validation_langevin_precession/langevin.py (100%)
 rename examples/SPIN/{validation => test_problems}/validation_langevin_precession/plot_precession.py (100%)
 rename examples/SPIN/{validation => test_problems}/validation_langevin_precession/run-bench-prec.sh (100%)

diff --git a/examples/SPIN/validation/README b/examples/SPIN/test_problems/README
similarity index 100%
rename from examples/SPIN/validation/README
rename to examples/SPIN/test_problems/README
diff --git a/examples/SPIN/validation/validation_damped_exchange/bench-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/bench-spin-precession.in
similarity index 100%
rename from examples/SPIN/validation/validation_damped_exchange/bench-spin-precession.in
rename to examples/SPIN/test_problems/validation_damped_exchange/bench-spin-precession.in
diff --git a/examples/SPIN/validation/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
similarity index 100%
rename from examples/SPIN/validation/validation_damped_exchange/llg_exchange.py
rename to examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
diff --git a/examples/SPIN/validation/validation_damped_exchange/plot_precession.py b/examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py
similarity index 100%
rename from examples/SPIN/validation/validation_damped_exchange/plot_precession.py
rename to examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py
diff --git a/examples/SPIN/validation/validation_damped_exchange/run-bench-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-bench-exchange.sh
similarity index 100%
rename from examples/SPIN/validation/validation_damped_exchange/run-bench-exchange.sh
rename to examples/SPIN/test_problems/validation_damped_exchange/run-bench-exchange.sh
diff --git a/examples/SPIN/validation/validation_damped_exchange/two_spins.data b/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data
similarity index 100%
rename from examples/SPIN/validation/validation_damped_exchange/two_spins.data
rename to examples/SPIN/test_problems/validation_damped_exchange/two_spins.data
diff --git a/examples/SPIN/validation/validation_damped_precession/bench-spin-precession.in b/examples/SPIN/test_problems/validation_damped_precession/bench-spin-precession.in
similarity index 100%
rename from examples/SPIN/validation/validation_damped_precession/bench-spin-precession.in
rename to examples/SPIN/test_problems/validation_damped_precession/bench-spin-precession.in
diff --git a/examples/SPIN/validation/validation_damped_precession/llg_precession.py b/examples/SPIN/test_problems/validation_damped_precession/llg_precession.py
similarity index 100%
rename from examples/SPIN/validation/validation_damped_precession/llg_precession.py
rename to examples/SPIN/test_problems/validation_damped_precession/llg_precession.py
diff --git a/examples/SPIN/validation/validation_damped_precession/plot_precession.py b/examples/SPIN/test_problems/validation_damped_precession/plot_precession.py
similarity index 100%
rename from examples/SPIN/validation/validation_damped_precession/plot_precession.py
rename to examples/SPIN/test_problems/validation_damped_precession/plot_precession.py
diff --git a/examples/SPIN/validation/validation_damped_precession/run-bench-prec.sh b/examples/SPIN/test_problems/validation_damped_precession/run-bench-prec.sh
similarity index 100%
rename from examples/SPIN/validation/validation_damped_precession/run-bench-prec.sh
rename to examples/SPIN/test_problems/validation_damped_precession/run-bench-prec.sh
diff --git a/examples/SPIN/validation/validation_langevin_precession/bench-prec-spin.template b/examples/SPIN/test_problems/validation_langevin_precession/bench-prec-spin.template
similarity index 100%
rename from examples/SPIN/validation/validation_langevin_precession/bench-prec-spin.template
rename to examples/SPIN/test_problems/validation_langevin_precession/bench-prec-spin.template
diff --git a/examples/SPIN/validation/validation_langevin_precession/langevin.py b/examples/SPIN/test_problems/validation_langevin_precession/langevin.py
similarity index 100%
rename from examples/SPIN/validation/validation_langevin_precession/langevin.py
rename to examples/SPIN/test_problems/validation_langevin_precession/langevin.py
diff --git a/examples/SPIN/validation/validation_langevin_precession/plot_precession.py b/examples/SPIN/test_problems/validation_langevin_precession/plot_precession.py
similarity index 100%
rename from examples/SPIN/validation/validation_langevin_precession/plot_precession.py
rename to examples/SPIN/test_problems/validation_langevin_precession/plot_precession.py
diff --git a/examples/SPIN/validation/validation_langevin_precession/run-bench-prec.sh b/examples/SPIN/test_problems/validation_langevin_precession/run-bench-prec.sh
similarity index 100%
rename from examples/SPIN/validation/validation_langevin_precession/run-bench-prec.sh
rename to examples/SPIN/test_problems/validation_langevin_precession/run-bench-prec.sh

From 3dc8b7b6e574dc424e8c750b3ca261f79e22c9b3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 19 Nov 2019 15:30:30 -0500
Subject: [PATCH 055/199] update rst files with changes to .txt versions

---
 doc/src/compute_spin.rst        | 16 +++++++---------
 doc/src/fix_precession_spin.rst | 34 ++++++++++++++++++++++++++++++---
 doc/src/pair_spin_exchange.rst  |  5 +++--
 3 files changed, 41 insertions(+), 14 deletions(-)

diff --git a/doc/src/compute_spin.rst b/doc/src/compute_spin.rst
index 4dd3103d78..7538746911 100644
--- a/doc/src/compute_spin.rst
+++ b/doc/src/compute_spin.rst
@@ -28,17 +28,15 @@ Description
 Define a computation that calculates magnetic quantities for a system
 of atoms having spins.
 
-This compute calculates 6 magnetic quantities.
+This compute calculates the following 6 magnetic quantities:
 
-The three first quantities are the x,y and z coordinates of the total
-magnetization.
+* the three first quantities are the x,y and z coordinates of the total
+  magnetization,
+* the fourth quantity is the norm of the total magnetization,
+* The fifth quantity is the magnetic energy (in eV),
+* The sixth one is referred to as the spin temperature, according
+  to the work of :ref:`(Nurdin) <Nurdin1>`.
 
-The fourth quantity is the norm of the total magnetization.
-
-The fifth quantity is the magnetic energy.
-
-The sixth one is referred to as the spin temperature, according
-to the work of :ref:`(Nurdin) <Nurdin1>`.
 
 The simplest way to output the results of the compute spin calculation
 is to define some of the quantities as variables, and to use the thermo and
diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst
index f2b99fa4a2..e47b9bd855 100644
--- a/doc/src/fix_precession_spin.rst
+++ b/doc/src/fix_precession_spin.rst
@@ -53,11 +53,39 @@ Style *zeeman* is used for the simulation of the interaction
 between the magnetic spins in the defined group and an external
 magnetic field:
 
-.. image:: Eqs/force_spin_zeeman.jpg
+.. image:: Eqs/fix_spin_zeeman.jpg
    :align: center
 
-with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T
-in metal units).
+with:
+
+* Bext the external magnetic field (in T)
+* g the Lande factor (hard-coded as g=2.0)
+* si the unitary vector describing the orientation of spin i
+* mui the atomic moment of spin i given as a multiple of the
+  Bohr magneton muB (for example, mui ~ 2.2 in bulk iron).
+
+
+The field value in Tesla is multiplied by the gyromagnetic
+ratio, g\*muB/hbar, converting it into a precession frequency in
+rad.THz (in metal units and with muB = 5.788 eV/T).
+
+As a comparison, the figure below displays the simulation of a
+single spin (of norm mui = 1.0) submitted to an external
+magnetic field of \|Bext\| = 10.0 Tesla (and oriented along the z
+axis). 
+The upper plot shows the average magnetization along the
+external magnetic field axis and the lower plot the Zeeman
+energy, both as a function of temperature.
+The reference result is provided by the plot of the Langevin 
+function for the same parameters.
+
+.. image:: JPG/zeeman_langevin.jpg
+   :align: center
+
+The temperature effects are accounted for by connecting the spin
+i to a thermal bath using a Langevin thermostat (see 
+:doc:`fix\_langevin\_spin <fix_langevin_spin>` for the definition of 
+this thermostat).
 
 Style *anisotropy* is used to simulate an easy axis or an easy plane
 for the magnetic spins in the defined group:
diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst
index 44533b69a0..5f7a630c60 100644
--- a/doc/src/pair_spin_exchange.rst
+++ b/doc/src/pair_spin_exchange.rst
@@ -34,7 +34,7 @@ pairs of magnetic spins:
    :align: center
 
 where si and sj are two neighboring magnetic spins of two particles,
-rij = ri - rj is the inter-atomic distance between the two particles,
+rij = \|ri - rj\| is the inter-atomic distance between the two particles,
 and J(rij) is a function defining the intensity and the sign of the exchange
 interaction for different neighboring shells. This function is defined as:
 
@@ -42,7 +42,8 @@ interaction for different neighboring shells. This function is defined as:
    :align: center
 
 where a, b and d are the three constant coefficients defined in the associated
-"pair\_coeff" command (see below for more explanations).
+"pair\_coeff" command, and Rc is the radius cutoff associated to
+the pair interaction (see below for more explanations).
 
 The coefficients a, b, and d need to be fitted so that the function above matches with
 the value of the exchange interaction for the N neighbor shells taken into account.

From 2a943241ae39ffa4504c26faedec3ff594c93852 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 19 Nov 2019 15:33:44 -0500
Subject: [PATCH 056/199] update doc/src/.gitignore

---
 doc/src/.gitignore | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/doc/src/.gitignore b/doc/src/.gitignore
index be126ab4aa..e0b9693457 100644
--- a/doc/src/.gitignore
+++ b/doc/src/.gitignore
@@ -1,2 +1,3 @@
-Eqs
-JPG
+/Eqs
+/JPG
+/false_positives.txt

From 280d0defec658c06530a6d64bab730ad129ab1fc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 19 Nov 2019 15:35:31 -0500
Subject: [PATCH 057/199] whitespace cleanup

---
 src/SPIN/fix_precession_spin.cpp | 2 +-
 src/SPIN/pair_spin_dipole_long.h | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index d06d70bc8c..2d55de33ea 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -353,7 +353,7 @@ void FixPrecessionSpin::compute_cubic(double spi[3], double fmi[3])
   sixx = k2ch*(nc1x*six1 + nc2x*six2 + nc3x*six3);
   sixy = k2ch*(nc1y*six1 + nc2y*six2 + nc3y*six3);
   sixz = k2ch*(nc1z*six1 + nc2z*six2 + nc3z*six3);
-  
+
   fmi[0] += (fourx + sixx);
   fmi[1] += (foury + sixy);
   fmi[2] += (fourz + sixz);
diff --git a/src/SPIN/pair_spin_dipole_long.h b/src/SPIN/pair_spin_dipole_long.h
index 61ae427e26..1ec30cdb93 100644
--- a/src/SPIN/pair_spin_dipole_long.h
+++ b/src/SPIN/pair_spin_dipole_long.h
@@ -49,8 +49,8 @@ class PairSpinDipoleLong : public PairSpin {
   void read_restart(FILE *);
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
-  
-  double cut_spin_long_global;  // global long cutoff distance 
+
+  double cut_spin_long_global;  // global long cutoff distance
 
  protected:
   double hbar;                  // reduced Planck's constant

From b4ba356f7b7a4c83d813b95c9e4ce4aa521665a5 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Tue, 19 Nov 2019 15:50:56 -0700
Subject: [PATCH 058/199] Commit JT 111919 - generated fresh log. files in
 examples - corrected some of the examples

---
 examples/SPIN/bfo/in.spin.bfo                 |    5 +-
 examples/SPIN/bfo/log.11May18.spin.bfo.g++.1  |  212 -
 examples/SPIN/bfo/log.11May18.spin.bfo.g++.4  |  212 -
 examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1  |  167 +
 examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4  |  167 +
 .../log.11May18.spin.cobalt_fcc.g++.1         |  142 -
 .../log.11May18.spin.cobalt_fcc.g++.4         |  142 -
 .../log.19Nov19.spin.cobalt_fcc.g++.1         |  142 +
 .../log.19Nov19.spin.cobalt_fcc.g++.4         |  142 +
 examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp   |    2 +-
 .../log.11May18.spin.cobalt_hcp.g++.1         |  318 -
 .../log.11May18.spin.cobalt_hcp.g++.4         |  318 -
 .../log.19Nov19.spin.cobalt_hcp.g++.1         |  219 +
 .../log.19Nov19.spin.cobalt_hcp.g++.4         |  219 +
 .../SPIN/dipole_spin/in.spin.iron_dipole_cut  |    4 +-
 .../dipole_spin/in.spin.iron_dipole_ewald     |    4 +-
 .../SPIN/dipole_spin/in.spin.iron_dipole_pppm |    4 +-
 .../log.19Nov19.spin.iron_dipole_cut.g++.1    |  125 +
 .../log.19Nov19.spin.iron_dipole_cut.g++.4    |  125 +
 .../log.19Nov19.spin.iron_dipole_ewald.g++.1  |  135 +
 .../log.19Nov19.spin.iron_dipole_ewald.g++.4  |  135 +
 .../log.19Nov19.spin.iron_dipole_pppm.g++.1   |  137 +
 .../log.19Nov19.spin.iron_dipole_pppm.g++.4   |  137 +
 examples/SPIN/iron/in.spin.iron               |    6 +-
 examples/SPIN/iron/in.spin.iron_cubic         |    2 +-
 .../SPIN/iron/log.19Nov19.spin.iron.g++.1     |  136 +
 .../SPIN/iron/log.19Nov19.spin.iron.g++.4     |  136 +
 ...++.1 => log.19Nov19.spin.iron_cubic.g++.1} |   66 +-
 ...++.4 => log.19Nov19.spin.iron_cubic.g++.4} |   76 +-
 .../SPIN/iron/log.30Apr19.spin.iron.g++.1     | 1117 ---
 .../SPIN/iron/log.30Apr19.spin.iron.g++.4     | 1117 ---
 examples/SPIN/nickel/in.spin.nickel           |   67 +-
 examples/SPIN/nickel/in.spin.nickel_cubic     |    4 +-
 .../SPIN/nickel/log.19Nov19.spin.nickel.g++.1 |  136 +
 .../SPIN/nickel/log.19Nov19.spin.nickel.g++.4 |  136 +
 ....1 => log.19Nov19.spin.nickel_cubic.g++.1} |  106 +-
 ....4 => log.19Nov19.spin.nickel_cubic.g++.4} |  118 +-
 .../SPIN/nickel/log.30Apr19.spin.nickel.g++.1 |  159 -
 .../SPIN/nickel/log.30Apr19.spin.nickel.g++.4 |  159 -
 .../read_restart/Co_PurjaPun_2012.eam.alloy   | 6007 ++++++++++++++++-
 examples/SPIN/read_restart/in.spin.restart    |    2 +-
 .../log.11May18.spin.read_data.g++.4          |  112 -
 .../log.11May18.spin.restart.g++.4            |  118 -
 ...g++.1 => log.19Nov19.spin.read_data.g++.1} |   53 +-
 .../log.19Nov19.spin.read_data.g++.4          |  113 +
 ...t.g++.1 => log.19Nov19.spin.restart.g++.1} |   50 +-
 .../log.19Nov19.spin.restart.g++.4            |  118 +
 ...1 => log.19Nov19.spin.write_restart.g++.1} |   48 +-
 ...4 => log.19Nov19.spin.write_restart.g++.4} |   48 +-
 examples/SPIN/run_spin_examples.sh            |  120 +
 .../{in.spinmin.setforce => in.spin.setforce} |    8 +-
 .../log.19Nov19.spin.setforce.g++.1           |  141 +
 .../log.19Nov19.spin.setforce.g++.4           |  141 +
 .../{in.spinmin.bfo => in.spin.bfo_min}       |    2 +-
 .../{in.spinmin_cg.bfo => in.spin.bfo_min_cg} |    4 +-
 ...pinmin_lbfgs.bfo => in.spin.bfo_min_lbfgs} |    2 +-
 .../{in.spinmin.iron => in.spin.iron_min}     |    4 +-
 .../spinmin/log.19Nov19.spin.bfo_min.g++.1    |  148 +
 .../spinmin/log.19Nov19.spin.bfo_min.g++.4    |  148 +
 .../spinmin/log.19Nov19.spin.bfo_min_cg.g++.1 |  141 +
 .../spinmin/log.19Nov19.spin.bfo_min_cg.g++.4 |  141 +
 .../log.19Nov19.spin.bfo_min_lbfgs.g++.1      |  139 +
 .../log.19Nov19.spin.bfo_min_lbfgs.g++.4      |  139 +
 .../spinmin/log.19Nov19.spin.iron_min.g++.1   |  126 +
 .../spinmin/log.19Nov19.spin.iron_min.g++.4   |  126 +
 65 files changed, 10439 insertions(+), 4514 deletions(-)
 delete mode 100644 examples/SPIN/bfo/log.11May18.spin.bfo.g++.1
 delete mode 100644 examples/SPIN/bfo/log.11May18.spin.bfo.g++.4
 create mode 100644 examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1
 create mode 100644 examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4
 delete mode 100644 examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1
 delete mode 100644 examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4
 create mode 100644 examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1
 create mode 100644 examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4
 delete mode 100644 examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1
 delete mode 100644 examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4
 create mode 100644 examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1
 create mode 100644 examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4
 create mode 100644 examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1
 create mode 100644 examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4
 create mode 100644 examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1
 create mode 100644 examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4
 create mode 100644 examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1
 create mode 100644 examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4
 create mode 100644 examples/SPIN/iron/log.19Nov19.spin.iron.g++.1
 create mode 100644 examples/SPIN/iron/log.19Nov19.spin.iron.g++.4
 rename examples/SPIN/iron/{log.30Apr19.spin.iron_cubic.g++.1 => log.19Nov19.spin.iron_cubic.g++.1} (59%)
 rename examples/SPIN/iron/{log.30Apr19.spin.iron_cubic.g++.4 => log.19Nov19.spin.iron_cubic.g++.4} (58%)
 delete mode 100644 examples/SPIN/iron/log.30Apr19.spin.iron.g++.1
 delete mode 100644 examples/SPIN/iron/log.30Apr19.spin.iron.g++.4
 create mode 100644 examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1
 create mode 100644 examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4
 rename examples/SPIN/nickel/{log.30Apr19.spin.nickel_cubic.g++.1 => log.19Nov19.spin.nickel_cubic.g++.1} (54%)
 rename examples/SPIN/nickel/{log.30Apr19.spin.nickel_cubic.g++.4 => log.19Nov19.spin.nickel_cubic.g++.4} (52%)
 delete mode 100644 examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1
 delete mode 100644 examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4
 mode change 120000 => 100644 examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
 delete mode 100644 examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4
 delete mode 100644 examples/SPIN/read_restart/log.11May18.spin.restart.g++.4
 rename examples/SPIN/read_restart/{log.11May18.spin.read_data.g++.1 => log.19Nov19.spin.read_data.g++.1} (50%)
 create mode 100644 examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4
 rename examples/SPIN/read_restart/{log.11May18.spin.restart.g++.1 => log.19Nov19.spin.restart.g++.1} (54%)
 create mode 100644 examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4
 rename examples/SPIN/read_restart/{log.11May18.spin.write_restart.g++.1 => log.19Nov19.spin.write_restart.g++.1} (64%)
 rename examples/SPIN/read_restart/{log.11May18.spin.write_restart.g++.4 => log.19Nov19.spin.write_restart.g++.4} (64%)
 create mode 100755 examples/SPIN/run_spin_examples.sh
 rename examples/SPIN/setforce_spin/{in.spinmin.setforce => in.spin.setforce} (86%)
 create mode 100644 examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1
 create mode 100644 examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4
 rename examples/SPIN/spinmin/{in.spinmin.bfo => in.spin.bfo_min} (97%)
 rename examples/SPIN/spinmin/{in.spinmin_cg.bfo => in.spin.bfo_min_cg} (94%)
 rename examples/SPIN/spinmin/{in.spinmin_lbfgs.bfo => in.spin.bfo_min_lbfgs} (97%)
 rename examples/SPIN/spinmin/{in.spinmin.iron => in.spin.iron_min} (94%)
 create mode 100644 examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1
 create mode 100644 examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4
 create mode 100644 examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1
 create mode 100644 examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4
 create mode 100644 examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1
 create mode 100644 examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4
 create mode 100644 examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1
 create mode 100644 examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4

diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo
index a32dde9dd7..b97f7e2d61 100644
--- a/examples/SPIN/bfo/in.spin.bfo
+++ b/examples/SPIN/bfo/in.spin.bfo
@@ -1,9 +1,7 @@
 # layer sc iron atoms (in the [001] plane) in bismuth oxide 
 
-clear 
 units 		metal
 atom_style 	spin
-
 dimension 	3
 boundary 	p p f
 
@@ -18,7 +16,6 @@ create_atoms 	1 box
 # setting mass, mag. moments, and interactions for bfo
 
 mass		1 1.0
-
 set 		group all spin/random 11 2.50
 
 #pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
@@ -53,4 +50,4 @@ thermo          10
 compute outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		500
diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1
deleted file mode 100644
index 8e9eb82d1f..0000000000
--- a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1
+++ /dev/null
@@ -1,212 +0,0 @@
-LAMMPS (11 May 2018)
-# layer sc iron atoms (in the [001] plane) in bismuth oxide
-
-clear
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p f
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	sc 3.96
-Lattice spacing in x,y,z = 3.96 3.96 3.96
-region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 5780 atoms
-  Time spent = 0.0013566 secs
-
-# setting mass, mag. moments, and interactions for bfo
-
-mass		1 1.0
-
-set 		group all spin/random 11 2.50
-  5780 settings made for spin/random
-
-pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
-pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
-pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.1 21
-fix 		3 all nve/spin lattice no
-
-timestep	0.0002
-
-compute 	out_mag	 all compute/spin
-compute 	out_pe	 all pe
-compute 	out_ke	 all ke
-compute 	out_temp all temp
-
-variable 	magz	 equal c_out_mag[3]
-variable 	magnorm	 equal c_out_mag[4]
-variable 	emag	 equal c_out_mag[5]
-variable 	tmag	 equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          50
-
-compute outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		5000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.1
-  ghost atom cutoff = 6.1
-  binsize = 3.05, bins = 45 45 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair spin/magelec, perpetual, copy from (1)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes
-Step Time v_magnorm v_emag Temp TotEng 
-       0            0  0.010071723  -0.13298298            0  -0.12034311 
-      50         0.01 0.0098643821   -1.3898985            0   -1.3772103 
-     100         0.02 0.0096526211   -2.6381677            0   -2.6254222 
-     150         0.03 0.0094342235   -3.8784006            0   -3.8656019 
-     200         0.04 0.0092074832    -5.111441            0   -5.0986001 
-     250         0.05 0.0089713115   -6.3380611            0   -6.3251904 
-     300         0.06 0.0087256081   -7.5587787            0   -7.5458894 
-     350         0.07 0.0084715548   -8.7738491            0   -8.7609521 
-     400         0.08  0.008211486   -9.9833855            0   -9.9704932 
-     450         0.09 0.0079483243    -11.18751            0   -11.174637 
-     500          0.1 0.0076849713   -12.386462            0    -12.37362 
-     550         0.11  0.007424064   -13.580633            0   -13.567832 
-     600         0.12 0.0071680699   -14.770519            0   -14.757759 
-     650         0.13 0.0069192726   -15.956579            0   -15.943853 
-     700         0.14 0.0066793495   -17.139049            0   -17.126343 
-     750         0.15 0.0064488038   -18.317803            0   -18.305099 
-     800         0.16 0.0062267571   -19.492336            0   -19.479616 
-     850         0.17 0.0060112235   -20.661925            0   -20.649176 
-     900         0.18 0.0057995251   -21.825931            0   -21.813141 
-     950         0.19 0.0055886511    -22.98413            0   -22.971297 
-    1000          0.2 0.0053757923   -24.136967            0   -24.124095 
-    1050         0.21 0.0051592263   -25.285621            0   -25.272717 
-    1100         0.22 0.0049391661   -26.431928            0   -26.419004 
-    1150         0.23 0.0047179149   -27.578212            0   -27.565281 
-    1200         0.24 0.0044991004   -28.727051            0   -28.714128 
-    1250         0.25 0.0042864034   -29.880967            0   -29.868062 
-    1300         0.26 0.0040824475   -31.042054            0   -31.029173 
-    1350         0.27 0.0038883007    -32.21165            0   -32.198795 
-    1400         0.28 0.0037036595   -33.390159            0   -33.377326 
-    1450         0.29 0.0035274815   -34.577121            0   -34.564302 
-    1500          0.3 0.0033587207   -35.771483            0   -35.758672 
-    1550         0.31 0.0031969501   -36.971996            0    -36.95919 
-    1600         0.32 0.0030429081   -38.177601            0   -38.164801 
-    1650         0.33 0.0028989804   -39.387757            0   -39.374962 
-    1700         0.34 0.0027692024   -40.602665            0   -40.589873 
-    1750         0.35 0.0026581403   -41.823341            0    -41.81054 
-    1800         0.36 0.0025686991    -43.05145            0   -43.038628 
-    1850         0.37  0.002500124   -44.288966            0   -44.276111 
-    1900         0.38 0.0024477804   -45.537752            0    -45.52486 
-    1950         0.39 0.0024050049   -46.799255            0   -46.786336 
-    2000          0.4 0.0023657031   -48.074388            0   -48.061466 
-    2050         0.41 0.0023260844   -49.363587            0   -49.350695 
-    2100         0.42 0.0022848329   -50.666866            0   -50.654039 
-    2150         0.43 0.0022419759   -51.983781            0   -51.971055 
-    2200         0.44 0.0021972506    -53.31336            0   -53.300764 
-    2250         0.45 0.0021488322   -54.654121            0   -54.641676 
-    2300         0.46 0.0020929483   -56.004207            0   -55.991918 
-    2350         0.47 0.0020244601   -57.361586            0   -57.349442 
-    2400         0.48  0.001938225    -58.72428            0   -58.712247 
-    2450         0.49 0.0018309419    -60.09064            0   -60.078671 
-    2500          0.5 0.0017030436   -61.459658            0   -61.447705 
-    2550         0.51 0.0015599449   -62.831213            0   -62.819237 
-    2600         0.52 0.0014117554   -64.206088            0   -64.194074 
-    2650         0.53 0.0012709942   -65.585701            0   -65.573657 
-    2700         0.54 0.0011490452   -66.971565            0   -66.959515 
-    2750         0.55  0.001053009   -68.364663            0   -68.352635 
-    2800         0.56 0.00098415327   -69.765002            0   -69.753017 
-    2850         0.57 0.00093809306   -71.171532            0   -71.159598 
-    2900         0.58 0.00090656933    -72.58234            0   -72.570459 
-    2950         0.59 0.00088069677   -73.994931            0   -73.983099 
-    3000          0.6 0.00085472643   -75.406507            0    -75.39472 
-    3050         0.61 0.00082842902   -76.814319            0   -76.802575 
-    3100         0.62 0.00080642618   -78.216074            0   -78.204373 
-    3150         0.63 0.00079463972   -79.610246            0   -79.598589 
-    3200         0.64 0.0007962304   -80.996103            0   -80.984494 
-    3250         0.65 0.00080980411    -82.37346            0   -82.361903 
-    3300         0.66 0.00083070982   -83.742356            0   -83.730855 
-    3350         0.67 0.00085389185   -85.102808            0   -85.091374 
-    3400         0.68 0.00087624091   -86.454619            0   -86.443259 
-    3450         0.69 0.00089741986   -87.797089            0   -87.785814 
-    3500          0.7 0.00091910796    -89.12875            0   -89.117567 
-    3550         0.71 0.00094318459   -90.447312            0   -90.436232 
-    3600         0.72 0.00096989367   -91.750008            0   -91.739046 
-    3650         0.73 0.00099713096   -93.034224            0   -93.023402 
-    3700         0.74 0.0010212995   -94.298186            0   -94.287529 
-    3750         0.75 0.0010391164     -95.5414            0   -95.530926 
-    3800         0.76 0.0010491462   -96.764626            0   -96.754338 
-    3850         0.77 0.0010521238   -97.969346            0    -97.95923 
-    3900         0.78 0.0010500324   -99.156875            0   -99.146899 
-    3950         0.79 0.0010447043   -100.32743            0   -100.31756 
-    4000          0.8 0.0010368986    -101.4796            0   -101.46978 
-    4050         0.81 0.0010263632   -102.61044            0   -102.60064 
-    4100         0.82 0.0010126933   -103.71619            0   -103.70639 
-    4150         0.83 0.00099631895   -104.79338            0   -104.78358 
-    4200         0.84 0.0009789075    -105.8398            0   -105.82998 
-    4250         0.85 0.00096287608   -106.85496            0   -106.84515 
-    4300         0.86 0.00095034023   -107.84011            0   -107.83029 
-    4350         0.87 0.00094219078    -108.7976            0   -108.78778 
-    4400         0.88 0.00093779428   -109.73016            0   -109.72031 
-    4450         0.89 0.0009354459   -110.63996            0   -110.63008 
-    4500          0.9 0.00093342614   -111.52805            0   -111.51812 
-    4550         0.91 0.0009311077   -112.39417            0   -112.38416 
-    4600         0.92 0.00092926689   -113.23706            0   -113.22697 
-    4650         0.93 0.00092921566   -114.05512            0   -114.04495 
-    4700         0.94 0.00093142598   -114.84701            0   -114.83675 
-    4750         0.95 0.00093479851   -115.61197            0   -115.60164 
-    4800         0.96 0.0009369799    -116.3499            0   -116.33951 
-    4850         0.97 0.00093516768   -117.06128            0   -117.05084 
-    4900         0.98 0.00092684411   -117.74695            0   -117.73645 
-    4950         0.99 0.00091046222   -118.40798            0   -118.39742 
-    5000            1 0.00088619957   -119.04554            0   -119.03492 
-Loop time of 128.304 on 1 procs for 5000 steps with 5780 atoms
-
-Performance: 0.673 ns/day, 35.640 hours/ns, 38.970 timesteps/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 24.227     | 24.227     | 24.227     |   0.0 | 18.88
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.081048   | 0.081048   | 0.081048   |   0.0 |  0.06
-Output  | 39.796     | 39.796     | 39.796     |   0.0 | 31.02
-Modify  | 64.112     | 64.112     | 64.112     |   0.0 | 49.97
-Other   |            | 0.08788    |            |       |  0.07
-
-Nlocal:    5780 ave 5780 max 5780 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1065 ave 1065 max 1065 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  92480 ave 92480 max 92480 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 92480
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:02:08
diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4
deleted file mode 100644
index c0f96b8195..0000000000
--- a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4
+++ /dev/null
@@ -1,212 +0,0 @@
-LAMMPS (11 May 2018)
-# layer sc iron atoms (in the [001] plane) in bismuth oxide
-
-clear
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p f
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	sc 3.96
-Lattice spacing in x,y,z = 3.96 3.96 3.96
-region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
-  2 by 2 by 1 MPI processor grid
-create_atoms 	1 box
-Created 5780 atoms
-  Time spent = 0.000355959 secs
-
-# setting mass, mag. moments, and interactions for bfo
-
-mass		1 1.0
-
-set 		group all spin/random 11 2.50
-  5780 settings made for spin/random
-
-pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
-pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
-pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.1 21
-fix 		3 all nve/spin lattice no
-
-timestep	0.0002
-
-compute 	out_mag	 all compute/spin
-compute 	out_pe	 all pe
-compute 	out_ke	 all ke
-compute 	out_temp all temp
-
-variable 	magz	 equal c_out_mag[3]
-variable 	magnorm	 equal c_out_mag[4]
-variable 	emag	 equal c_out_mag[5]
-variable 	tmag	 equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          50
-
-compute outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		5000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.1
-  ghost atom cutoff = 6.1
-  binsize = 3.05, bins = 45 45 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair spin/magelec, perpetual, copy from (1)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 6.862 | 6.862 | 6.862 Mbytes
-Step Time v_magnorm v_emag Temp TotEng 
-       0            0  0.010071723  -0.13298298            0  -0.12034311 
-      50         0.01 0.0098643821   -1.3898985            0   -1.3772103 
-     100         0.02  0.009652621   -2.6381677            0   -2.6254222 
-     150         0.03 0.0094342234   -3.8784007            0   -3.8656019 
-     200         0.04  0.009207483   -5.1114411            0   -5.0986001 
-     250         0.05 0.0089713114   -6.3380611            0   -6.3251904 
-     300         0.06 0.0087256079   -7.5587787            0   -7.5458894 
-     350         0.07 0.0084715546   -8.7738491            0   -8.7609521 
-     400         0.08 0.0082114858   -9.9833855            0   -9.9704932 
-     450         0.09 0.0079483242    -11.18751            0   -11.174637 
-     500          0.1 0.0076849711   -12.386462            0    -12.37362 
-     550         0.11 0.0074240638   -13.580633            0   -13.567832 
-     600         0.12 0.0071680697   -14.770519            0   -14.757759 
-     650         0.13 0.0069192724   -15.956579            0   -15.943853 
-     700         0.14 0.0066793493   -17.139049            0   -17.126343 
-     750         0.15 0.0064488035   -18.317803            0   -18.305099 
-     800         0.16 0.0062267569   -19.492336            0   -19.479616 
-     850         0.17 0.0060112233   -20.661925            0   -20.649176 
-     900         0.18  0.005799525   -21.825931            0   -21.813141 
-     950         0.19 0.0055886511    -22.98413            0   -22.971297 
-    1000          0.2 0.0053757923   -24.136967            0   -24.124095 
-    1050         0.21 0.0051592265   -25.285621            0   -25.272717 
-    1100         0.22 0.0049391664   -26.431928            0   -26.419004 
-    1150         0.23 0.0047179153   -27.578212            0   -27.565281 
-    1200         0.24 0.0044991009   -28.727051            0   -28.714128 
-    1250         0.25 0.0042864039   -29.880967            0   -29.868062 
-    1300         0.26  0.004082448   -31.042054            0   -31.029174 
-    1350         0.27 0.0038883012    -32.21165            0   -32.198795 
-    1400         0.28 0.0037036599   -33.390159            0   -33.377326 
-    1450         0.29 0.0035274817   -34.577121            0   -34.564302 
-    1500          0.3 0.0033587208   -35.771483            0   -35.758672 
-    1550         0.31 0.0031969501   -36.971996            0    -36.95919 
-    1600         0.32 0.0030429079   -38.177601            0   -38.164801 
-    1650         0.33 0.0028989801   -39.387757            0   -39.374962 
-    1700         0.34 0.0027692022   -40.602666            0   -40.589873 
-    1750         0.35 0.0026581401   -41.823341            0    -41.81054 
-    1800         0.36  0.002568699    -43.05145            0   -43.038628 
-    1850         0.37 0.0025001242   -44.288966            0   -44.276111 
-    1900         0.38 0.0024477808   -45.537752            0    -45.52486 
-    1950         0.39 0.0024050056   -46.799255            0   -46.786336 
-    2000          0.4  0.002365704   -48.074388            0   -48.061466 
-    2050         0.41 0.0023260854   -49.363587            0   -49.350695 
-    2100         0.42  0.002284834   -50.666866            0   -50.654039 
-    2150         0.43 0.0022419771   -51.983781            0   -51.971055 
-    2200         0.44 0.0021972518    -53.31336            0   -53.300764 
-    2250         0.45 0.0021488333   -54.654121            0   -54.641676 
-    2300         0.46 0.0020929494   -56.004207            0   -55.991918 
-    2350         0.47 0.0020244612   -57.361586            0   -57.349441 
-    2400         0.48 0.0019382262    -58.72428            0   -58.712247 
-    2450         0.49  0.001830943   -60.090639            0   -60.078671 
-    2500          0.5 0.0017030446   -61.459658            0   -61.447704 
-    2550         0.51 0.0015599459   -62.831213            0   -62.819237 
-    2600         0.52 0.0014117562   -64.206088            0   -64.194074 
-    2650         0.53  0.001270995     -65.5857            0   -65.573657 
-    2700         0.54  0.001149046   -66.971565            0   -66.959515 
-    2750         0.55 0.0010530098   -68.364663            0   -68.352635 
-    2800         0.56 0.00098415418   -69.765002            0   -69.753017 
-    2850         0.57 0.00093809402   -71.171532            0   -71.159598 
-    2900         0.58 0.00090657031    -72.58234            0   -72.570459 
-    2950         0.59 0.00088069773   -73.994931            0   -73.983099 
-    3000          0.6 0.00085472731   -75.406507            0    -75.39472 
-    3050         0.61 0.00082842975   -76.814319            0   -76.802575 
-    3100         0.62 0.00080642669   -78.216074            0   -78.204373 
-    3150         0.63   0.00079464   -79.610246            0    -79.59859 
-    3200         0.64 0.00079623049   -80.996103            0   -80.984494 
-    3250         0.65 0.00080980416   -82.373461            0   -82.361903 
-    3300         0.66 0.00083070997   -83.742356            0   -83.730856 
-    3350         0.67 0.00085389223   -85.102809            0   -85.091374 
-    3400         0.68 0.00087624159   -86.454619            0    -86.44326 
-    3450         0.69 0.00089742086    -87.79709            0   -87.785815 
-    3500          0.7 0.00091910931    -89.12875            0   -89.117568 
-    3550         0.71 0.00094318635   -90.447312            0   -90.436233 
-    3600         0.72 0.00096989594   -91.750008            0   -91.739047 
-    3650         0.73 0.00099713386   -93.034224            0   -93.023403 
-    3700         0.74 0.0010213031   -94.298186            0   -94.287529 
-    3750         0.75 0.0010391209   -95.541401            0   -95.530926 
-    3800         0.76 0.0010491514   -96.764626            0   -96.754339 
-    3850         0.77 0.0010521296   -97.969347            0   -97.959231 
-    3900         0.78 0.0010500386   -99.156876            0   -99.146899 
-    3950         0.79 0.0010447106   -100.32743            0   -100.31756 
-    4000          0.8 0.0010369046    -101.4796            0   -101.46978 
-    4050         0.81 0.0010263688   -102.61044            0   -102.60064 
-    4100         0.82 0.0010126985   -103.71619            0   -103.70639 
-    4150         0.83 0.00099632366   -104.79338            0   -104.78358 
-    4200         0.84 0.00097891183    -105.8398            0   -105.82998 
-    4250         0.85 0.00096288003   -106.85496            0   -106.84515 
-    4300         0.86 0.00095034371   -107.84011            0   -107.83029 
-    4350         0.87 0.00094219371    -108.7976            0   -108.78778 
-    4400         0.88 0.00093779663   -109.73016            0   -109.72031 
-    4450         0.89 0.00093544766   -110.63996            0   -110.63008 
-    4500          0.9 0.00093342739   -111.52805            0   -111.51812 
-    4550         0.91 0.00093110855   -112.39417            0   -112.38416 
-    4600         0.92 0.00092926746   -113.23706            0   -113.22697 
-    4650         0.93 0.00092921608   -114.05512            0   -114.04495 
-    4700         0.94 0.0009314263   -114.84701            0   -114.83675 
-    4750         0.95 0.0009347987   -115.61197            0   -115.60164 
-    4800         0.96 0.00093697985    -116.3499            0   -116.33951 
-    4850         0.97 0.00093516726   -117.06128            0   -117.05084 
-    4900         0.98 0.00092684316   -117.74695            0   -117.73645 
-    4950         0.99 0.00091046061   -118.40798            0   -118.39742 
-    5000            1 0.00088619727   -119.04554            0   -119.03492 
-Loop time of 37.142 on 4 procs for 5000 steps with 5780 atoms
-
-Performance: 2.326 ns/day, 10.317 hours/ns, 134.619 timesteps/s
-98.7% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 6.2804     | 6.3487     | 6.4569     |   2.7 | 17.09
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.15385    | 0.27957    | 0.36215    |  14.6 |  0.75
-Output  | 10.573     | 10.784     | 10.994     |   4.8 | 29.03
-Modify  | 19.48      | 19.707     | 19.925     |   3.7 | 53.06
-Other   |            | 0.02255    |            |       |  0.06
-
-Nlocal:    1445 ave 1445 max 1445 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    555 ave 555 max 555 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  23120 ave 23120 max 23120 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 92480
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:37
diff --git a/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1 b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1
new file mode 100644
index 0000000000..e7eb5cea59
--- /dev/null
+++ b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1
@@ -0,0 +1,167 @@
+LAMMPS (30 Oct 2019)
+# layer sc iron atoms (in the [001] plane) in bismuth oxide
+
+units 		metal
+atom_style 	spin
+dimension 	3
+boundary 	p p f
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00234604 secs
+
+# setting mass, mag. moments, and interactions for bfo
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+#pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice frozen
+
+timestep	0.0002
+
+compute 	out_mag	 all spin
+compute 	out_pe	 all pe
+compute 	out_ke	 all ke
+compute 	out_temp all temp
+
+variable 	magz	 equal c_out_mag[3]
+variable 	magnorm	 equal c_out_mag[4]
+variable 	emag	 equal c_out_mag[5]
+variable 	tmag	 equal c_out_mag[6]
+
+#thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo_style    custom step time v_magnorm pe ke v_emag temp etotal
+thermo          10
+
+compute outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		500
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.154 | 8.154 | 8.154 Mbytes
+Step Time v_magnorm PotEng KinEng v_emag Temp TotEng 
+       0            0  0.010071723  -0.11868622            0  -0.12966919            0  -0.11868622 
+      10        0.002  0.010030399  -0.37068593            0  -0.38171598            0  -0.37068593 
+      20        0.004 0.0099889925   -0.6223216            0   -0.6334048            0   -0.6223216 
+      30        0.006 0.0099474775  -0.87359358            0  -0.88473539            0  -0.87359358 
+      40        0.008 0.0099058307   -1.1245034            0   -1.1357086            0   -1.1245034 
+      50         0.01 0.0098640297   -1.3750538            0   -1.3863265            0   -1.3750538 
+      60        0.012 0.0098220536   -1.6252482            0   -1.6365919            0   -1.6252482 
+      70        0.014 0.0097798824   -1.8750914            0   -1.8865086            0   -1.8750914 
+      80        0.016 0.0097374974   -2.1245886            0   -2.1360814            0   -2.1245886 
+      90        0.018 0.0096948809   -2.3737458            0   -2.3853154            0   -2.3737458 
+     100         0.02  0.009652016   -2.6225698            0   -2.6342168            0   -2.6225698 
+     110        0.022 0.0096088867   -2.8710677            0   -2.8827919            0   -2.8710677 
+     120        0.024 0.0095654777   -3.1192468            0   -3.1310475            0   -3.1192468 
+     130        0.026 0.0095217747    -3.367115            0   -3.3789906            0    -3.367115 
+     140        0.028 0.0094777639     -3.61468            0   -3.6266285            0     -3.61468 
+     150         0.03 0.0094334324   -3.8619496            0   -3.8739683            0   -3.8619496 
+     160        0.032 0.0093887681   -4.1089316            0   -4.1210173            0   -4.1089316 
+     170        0.034 0.0093437598   -4.3556334            0   -4.3677824            0   -4.3556334 
+     180        0.036 0.0092983974   -4.6020625            0   -4.6142704            0   -4.6020625 
+     190        0.038 0.0092526719   -4.8482255            0   -4.8604877            0   -4.8482255 
+     200         0.04 0.0092065757   -5.0941291            0   -5.1064403            0   -5.0941291 
+     210        0.042 0.0091601026   -5.3397792            0   -5.3521339            0   -5.3397792 
+     220        0.044 0.0091132479   -5.5851813            0   -5.5975736            0   -5.5851813 
+     230        0.046  0.009066009   -5.8303404            0    -5.842764            0   -5.8303404 
+     240        0.048 0.0090183848   -6.0752609            0   -6.0877092            0   -6.0752609 
+     250         0.05 0.0089703766   -6.3199467            0   -6.3324129            0   -6.3199467 
+     260        0.052 0.0089219875   -6.5644011            0   -6.5768782            0   -6.5644011 
+     270        0.054  0.008873223    -6.808627            0   -6.8211078            0    -6.808627 
+     280        0.056 0.0088240907   -7.0526266            0   -7.0651038            0   -7.0526266 
+     290        0.058 0.0087746007    -7.296402            0   -7.3088682            0    -7.296402 
+     300         0.06 0.0087247649   -7.5399545            0   -7.5524024            0   -7.5399545 
+     310        0.062 0.0086745977   -7.7832854            0   -7.7957077            0   -7.7832854 
+     320        0.064 0.0086241151   -8.0263956            0    -8.038785            0   -8.0263956 
+     330        0.066 0.0085733351   -8.2692858            0    -8.281635            0   -8.2692858 
+     340        0.068 0.0085222773   -8.5119564            0   -8.5242586            0   -8.5119564 
+     350         0.07 0.0084709628   -8.7544078            0   -8.7666562            0   -8.7544078 
+     360        0.072 0.0084194137   -8.9966403            0   -9.0088285            0   -8.9966403 
+     370        0.074 0.0083676531   -9.2386543            0   -9.2507761            0   -9.2386543 
+     380        0.076 0.0083157047   -9.4804501            0   -9.4924997            0   -9.4804501 
+     390        0.078 0.0082635926   -9.7220281            0   -9.7340001            0   -9.7220281 
+     400         0.08 0.0082113413   -9.9633888            0   -9.9752784            0   -9.9633888 
+     410        0.082 0.0081589748   -10.204533            0   -10.216336            0   -10.204533 
+     420        0.084 0.0081065174   -10.445462            0   -10.457173            0   -10.445462 
+     430        0.086 0.0080539926   -10.686176            0   -10.697793            0   -10.686176 
+     440        0.088 0.0080014236   -10.926676            0   -10.938197            0   -10.926676 
+     450         0.09  0.007948833   -11.166966            0   -11.178387            0   -11.166966 
+     460        0.092 0.0078962428   -11.407045            0   -11.418366            0   -11.407045 
+     470        0.094 0.0078436745   -11.646917            0   -11.658136            0   -11.646917 
+     480        0.096 0.0077911488   -11.886583            0     -11.8977            0   -11.886583 
+     490        0.098 0.0077386861   -12.126047            0   -12.137063            0   -12.126047 
+     500          0.1 0.0076863063   -12.365311            0   -12.376226            0   -12.365311 
+Loop time of 19.2298 on 1 procs for 500 steps with 5780 atoms
+
+Performance: 0.449 ns/day, 53.416 hours/ns, 26.001 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.2712     | 5.2712     | 5.2712     |   0.0 | 27.41
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.039467   | 0.039467   | 0.039467   |   0.0 |  0.21
+Output  | 0.060013   | 0.060013   | 0.060013   |   0.0 |  0.31
+Modify  | 13.82      | 13.82      | 13.82      |   0.0 | 71.87
+Other   |            | 0.03928    |            |       |  0.20
+
+Nlocal:    5780 ave 5780 max 5780 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1065 ave 1065 max 1065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  92480 ave 92480 max 92480 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:19
diff --git a/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4 b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4
new file mode 100644
index 0000000000..8e3990787a
--- /dev/null
+++ b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4
@@ -0,0 +1,167 @@
+LAMMPS (30 Oct 2019)
+# layer sc iron atoms (in the [001] plane) in bismuth oxide
+
+units 		metal
+atom_style 	spin
+dimension 	3
+boundary 	p p f
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.000843048 secs
+
+# setting mass, mag. moments, and interactions for bfo
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+#pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice frozen
+
+timestep	0.0002
+
+compute 	out_mag	 all spin
+compute 	out_pe	 all pe
+compute 	out_ke	 all ke
+compute 	out_temp all temp
+
+variable 	magz	 equal c_out_mag[3]
+variable 	magnorm	 equal c_out_mag[4]
+variable 	emag	 equal c_out_mag[5]
+variable 	tmag	 equal c_out_mag[6]
+
+#thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo_style    custom step time v_magnorm pe ke v_emag temp etotal
+thermo          10
+
+compute outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		500
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.744 | 7.744 | 7.744 Mbytes
+Step Time v_magnorm PotEng KinEng v_emag Temp TotEng 
+       0            0  0.010071723  -0.11868622            0  -0.12966919            0  -0.11868622 
+      10        0.002  0.010030399  -0.37068593            0  -0.38171598            0  -0.37068593 
+      20        0.004 0.0099889925   -0.6223216            0   -0.6334048            0   -0.6223216 
+      30        0.006 0.0099474775  -0.87359359            0   -0.8847354            0  -0.87359359 
+      40        0.008 0.0099058307   -1.1245034            0   -1.1357086            0   -1.1245034 
+      50         0.01 0.0098640297   -1.3750538            0   -1.3863265            0   -1.3750538 
+      60        0.012 0.0098220535   -1.6252482            0   -1.6365919            0   -1.6252482 
+      70        0.014 0.0097798823   -1.8750914            0   -1.8865086            0   -1.8750914 
+      80        0.016 0.0097374973   -2.1245886            0   -2.1360814            0   -2.1245886 
+      90        0.018 0.0096948808   -2.3737458            0   -2.3853155            0   -2.3737458 
+     100         0.02 0.0096520159   -2.6225698            0   -2.6342168            0   -2.6225698 
+     110        0.022 0.0096088866   -2.8710677            0   -2.8827919            0   -2.8710677 
+     120        0.024 0.0095654776   -3.1192469            0   -3.1310475            0   -3.1192469 
+     130        0.026 0.0095217746    -3.367115            0   -3.3789906            0    -3.367115 
+     140        0.028 0.0094777638     -3.61468            0   -3.6266285            0     -3.61468 
+     150         0.03 0.0094334323   -3.8619496            0   -3.8739683            0   -3.8619496 
+     160        0.032 0.0093887679   -4.1089316            0   -4.1210173            0   -4.1089316 
+     170        0.034 0.0093437596   -4.3556335            0   -4.3677824            0   -4.3556335 
+     180        0.036 0.0092983972   -4.6020625            0   -4.6142704            0   -4.6020625 
+     190        0.038 0.0092526717   -4.8482255            0   -4.8604877            0   -4.8482255 
+     200         0.04 0.0092065755   -5.0941291            0   -5.1064403            0   -5.0941291 
+     210        0.042 0.0091601024   -5.3397792            0   -5.3521339            0   -5.3397792 
+     220        0.044 0.0091132478   -5.5851813            0   -5.5975736            0   -5.5851813 
+     230        0.046 0.0090660089   -5.8303404            0    -5.842764            0   -5.8303404 
+     240        0.048 0.0090183847   -6.0752609            0   -6.0877092            0   -6.0752609 
+     250         0.05 0.0089703764   -6.3199467            0   -6.3324129            0   -6.3199467 
+     260        0.052 0.0089219873   -6.5644011            0   -6.5768782            0   -6.5644011 
+     270        0.054 0.0088732228    -6.808627            0   -6.8211078            0    -6.808627 
+     280        0.056 0.0088240906   -7.0526266            0   -7.0651038            0   -7.0526266 
+     290        0.058 0.0087746006    -7.296402            0   -7.3088682            0    -7.296402 
+     300         0.06 0.0087247648   -7.5399545            0   -7.5524024            0   -7.5399545 
+     310        0.062 0.0086745976   -7.7832854            0   -7.7957077            0   -7.7832854 
+     320        0.064 0.0086241149   -8.0263956            0    -8.038785            0   -8.0263956 
+     330        0.066  0.008573335   -8.2692858            0    -8.281635            0   -8.2692858 
+     340        0.068 0.0085222772   -8.5119564            0   -8.5242586            0   -8.5119564 
+     350         0.07 0.0084709627   -8.7544078            0   -8.7666562            0   -8.7544078 
+     360        0.072 0.0084194136   -8.9966403            0   -9.0088285            0   -8.9966403 
+     370        0.074  0.008367653   -9.2386543            0   -9.2507761            0   -9.2386543 
+     380        0.076 0.0083157046   -9.4804501            0   -9.4924997            0   -9.4804501 
+     390        0.078 0.0082635925   -9.7220281            0   -9.7340001            0   -9.7220281 
+     400         0.08 0.0082113412   -9.9633888            0   -9.9752784            0   -9.9633888 
+     410        0.082 0.0081589747   -10.204533            0   -10.216336            0   -10.204533 
+     420        0.084 0.0081065173   -10.445462            0   -10.457173            0   -10.445462 
+     430        0.086 0.0080539925   -10.686176            0   -10.697793            0   -10.686176 
+     440        0.088 0.0080014235   -10.926676            0   -10.938197            0   -10.926676 
+     450         0.09 0.0079488329   -11.166966            0   -11.178387            0   -11.166966 
+     460        0.092 0.0078962427   -11.407045            0   -11.418366            0   -11.407045 
+     470        0.094 0.0078436743   -11.646917            0   -11.658136            0   -11.646917 
+     480        0.096 0.0077911486   -11.886583            0     -11.8977            0   -11.886583 
+     490        0.098  0.007738686   -12.126047            0   -12.137063            0   -12.126047 
+     500          0.1 0.0076863062   -12.365311            0   -12.376226            0   -12.365311 
+Loop time of 5.69323 on 4 procs for 500 steps with 5780 atoms
+
+Performance: 1.518 ns/day, 15.815 hours/ns, 87.824 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.2634     | 1.2866     | 1.3017     |   1.3 | 22.60
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.17396    | 0.18913    | 0.21531    |   3.6 |  3.32
+Output  | 0.020815   | 0.021116   | 0.021569   |   0.2 |  0.37
+Modify  | 4.1846     | 4.1875     | 4.1896     |   0.1 | 73.55
+Other   |            | 0.008815   |            |       |  0.15
+
+Nlocal:    1445 ave 1445 max 1445 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    555 ave 555 max 555 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  23120 ave 23120 max 23120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:05
diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1
deleted file mode 100644
index d832b0001a..0000000000
--- a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1
+++ /dev/null
@@ -1,142 +0,0 @@
-LAMMPS (11 May 2018)
-# fcc cobalt in a 3d periodic box
-
-clear
-units		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice fcc 	3.54
-Lattice spacing in x,y,z = 3.54 3.54 3.54
-region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  Time spent = 0.000651121 secs
-
-# setting mass, mag. moments, and interactions for fcc cobalt
-
-mass		1 58.93
-
-#set 		group all spin/random 31 1.72
-set 		group all spin 1.72 0.0 0.0 1.0
-  500 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix_modify 	1 energy yes
-
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-thermo_style	custom f_1
-
-variable 	magx      equal c_out_mag[1]
-variable 	magy      equal c_out_mag[2]
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
-thermo          50
-
-#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		1000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.59954
-  ghost atom cutoff = 6.59954
-  binsize = 3.29977, bins = 6 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes
-Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
-       0            0  0.049785486            0            0            1   -187.94116    100.00543   -2372.4636 
-      50        0.005  0.049785486            0            0            1   -187.94112    95.094679   -2372.4636 
-     100         0.01  0.049785486            0            0            1   -187.94071    81.578321   -2372.4636 
-     150        0.015  0.049785486            0            0            1   -187.93912    62.802727   -2372.4636 
-     200         0.02  0.049785486            0            0            1   -187.93551     43.35108   -2372.4636 
-     250        0.025  0.049785486            0            0            1   -187.92942    27.749821   -2372.4636 
-     300         0.03  0.049785486            0            0            1   -187.92118    19.149389   -2372.4636 
-     350        0.035  0.049785486            0            0            1   -187.91199    18.453387   -2372.4636 
-     400         0.04  0.049785486            0            0            1   -187.90364    24.249423   -2372.4636 
-     450        0.045  0.049785486            0            0            1   -187.89806    33.548008   -2372.4636 
-     500         0.05  0.049785486            0            0            1   -187.89668    42.973172   -2372.4636 
-     550        0.055  0.049785486            0            0            1       -187.9    49.902539   -2372.4636 
-     600         0.06  0.049785486            0            0            1   -187.90735    53.166772   -2372.4636 
-     650        0.065  0.049785486            0            0            1   -187.91706    53.153416   -2372.4636 
-     700         0.07  0.049785486            0            0            1   -187.92692    51.377187   -2372.4636 
-     750        0.075  0.049785486            0            0            1    -187.9348    49.725449   -2372.4636 
-     800         0.08  0.049785486            0            0            1   -187.93921    49.663576   -2372.4636 
-     850        0.085  0.049785486            0            0            1   -187.93974    51.681567   -2372.4636 
-     900         0.09  0.049785486            0            0            1     -187.937    55.166554   -2372.4636 
-     950        0.095  0.049785486            0            0            1   -187.93239    58.718232   -2372.4636 
-    1000          0.1  0.049785486            0            0            1   -187.92755     60.75567   -2372.4636 
-Loop time of 4.1303 on 1 procs for 1000 steps with 500 atoms
-
-Performance: 2.092 ns/day, 11.473 hours/ns, 242.113 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.142      | 2.142      | 2.142      |   0.0 | 51.86
-Neigh   | 0.0094573  | 0.0094573  | 0.0094573  |   0.0 |  0.23
-Comm    | 0.023293   | 0.023293   | 0.023293   |   0.0 |  0.56
-Output  | 0.00031972 | 0.00031972 | 0.00031972 |   0.0 |  0.01
-Modify  | 1.9488     | 1.9488     | 1.9488     |   0.0 | 47.18
-Other   |            | 0.006488   |            |       |  0.16
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1956 ave 1956 max 1956 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    24065 ave 24065 max 24065 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  48130 ave 48130 max 48130 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 48130
-Ave neighs/atom = 96.26
-Neighbor list builds = 6
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:04
diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4
deleted file mode 100644
index 358d7cfc7a..0000000000
--- a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4
+++ /dev/null
@@ -1,142 +0,0 @@
-LAMMPS (11 May 2018)
-# fcc cobalt in a 3d periodic box
-
-clear
-units		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice fcc 	3.54
-Lattice spacing in x,y,z = 3.54 3.54 3.54
-region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  Time spent = 0.000240088 secs
-
-# setting mass, mag. moments, and interactions for fcc cobalt
-
-mass		1 58.93
-
-#set 		group all spin/random 31 1.72
-set 		group all spin 1.72 0.0 0.0 1.0
-  500 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix_modify 	1 energy yes
-
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-thermo_style	custom f_1
-
-variable 	magx      equal c_out_mag[1]
-variable 	magy      equal c_out_mag[2]
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
-thermo          50
-
-#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		1000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.59954
-  ghost atom cutoff = 6.59954
-  binsize = 3.29977, bins = 6 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.163 | 5.163 | 5.163 Mbytes
-Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
-       0            0  0.049785486            0            0            1   -187.94116    100.00543   -2372.4636 
-      50        0.005  0.049785486            0            0            1   -187.94101    95.174807   -2372.4636 
-     100         0.01  0.049785486            0            0            1   -187.94029    81.854304   -2372.4636 
-     150        0.015  0.049785486            0            0            1   -187.93834    63.270938   -2372.4636 
-     200         0.02  0.049785486            0            0            1   -187.93446    43.867262   -2372.4636 
-     250        0.025  0.049785486            0            0            1   -187.92831    28.075261   -2372.4636 
-     300         0.03  0.049785486            0            0            1   -187.92031    19.046222   -2372.4636 
-     350        0.035  0.049785486            0            0            1   -187.91161     17.79071   -2372.4636 
-     400         0.04  0.049785486            0            0            1    -187.9039    23.079994   -2372.4636 
-     450        0.045  0.049785486            0            0            1   -187.89895    32.127316   -2372.4636 
-     500         0.05  0.049785486            0            0            1   -187.89801    41.709644   -2372.4636 
-     550        0.055  0.049785486            0            0            1   -187.90146    49.246292   -2372.4636 
-     600         0.06  0.049785486            0            0            1   -187.90859    53.465535   -2372.4636 
-     650        0.065  0.049785486            0            0            1   -187.91778    54.522857   -2372.4636 
-     700         0.07  0.049785486            0            0            1    -187.9269    53.635521   -2372.4636 
-     750        0.075  0.049785486            0            0            1   -187.93396    52.419678   -2372.4636 
-     800         0.08  0.049785486            0            0            1    -187.9376    52.176558   -2372.4636 
-     850        0.085  0.049785486            0            0            1   -187.93744    53.380592   -2372.4636 
-     900         0.09  0.049785486            0            0            1   -187.93412    55.551378   -2372.4636 
-     950        0.095  0.049785486            0            0            1   -187.92902    57.540047   -2372.4636 
-    1000          0.1  0.049785486            0            0            1   -187.92378    58.088674   -2372.4636 
-Loop time of 1.71411 on 4 procs for 1000 steps with 500 atoms
-
-Performance: 5.041 ns/day, 4.761 hours/ns, 583.392 timesteps/s
-97.7% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.54717    | 0.57392    | 0.58784    |   2.1 | 33.48
-Neigh   | 0.0023484  | 0.0025793  | 0.0026793  |   0.3 |  0.15
-Comm    | 0.058548   | 0.073335   | 0.10006    |   5.9 |  4.28
-Output  | 0.00042272 | 0.00079203 | 0.0018559  |   0.0 |  0.05
-Modify  | 1.0577     | 1.0611     | 1.0625     |   0.2 | 61.90
-Other   |            | 0.00239    |            |       |  0.14
-
-Nlocal:    125 ave 133 max 116 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Nghost:    1099 ave 1108 max 1091 min
-Histogram: 1 0 0 0 2 0 0 0 0 1
-Neighs:    6032.5 ave 6417 max 5489 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-FullNghs:  12065 ave 13062 max 10970 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-
-Total # of neighbors = 48260
-Ave neighs/atom = 96.52
-Neighbor list builds = 6
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01
diff --git a/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1 b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1
new file mode 100644
index 0000000000..fb95d9ab48
--- /dev/null
+++ b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1
@@ -0,0 +1,142 @@
+LAMMPS (30 Oct 2019)
+# fcc cobalt in a 3d periodic box
+
+clear
+units		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice fcc 	3.54
+Lattice spacing in x,y,z = 3.54 3.54 3.54
+region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  create_atoms CPU = 0.00110412 secs
+
+# setting mass, mag. moments, and interactions for fcc cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+  500 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+thermo_style	custom f_1
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
+thermo          50
+
+# compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+# dump 		1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.718 | 5.718 | 5.718 Mbytes
+Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
+       0            0 -0.099570972            0            0            1   -188.09051    100.00543   -2372.6129 
+      50        0.005 -0.099570972            0            0            1   -188.09048    95.094679   -2372.6129 
+     100         0.01 -0.099570972            0            0            1   -188.09007    81.578321   -2372.6129 
+     150        0.015 -0.099570972            0            0            1   -188.08848    62.802727   -2372.6129 
+     200         0.02 -0.099570972            0            0            1   -188.08487     43.35108   -2372.6129 
+     250        0.025 -0.099570972            0            0            1   -188.07877    27.749821   -2372.6129 
+     300         0.03 -0.099570972            0            0            1   -188.07054    19.149389   -2372.6129 
+     350        0.035 -0.099570972            0            0            1   -188.06135    18.453387   -2372.6129 
+     400         0.04 -0.099570972            0            0            1     -188.053    24.249423   -2372.6129 
+     450        0.045 -0.099570972            0            0            1   -188.04742    33.548008   -2372.6129 
+     500         0.05 -0.099570972            0            0            1   -188.04604    42.973172   -2372.6129 
+     550        0.055 -0.099570972            0            0            1   -188.04935    49.902539   -2372.6129 
+     600         0.06 -0.099570972            0            0            1    -188.0567    53.166772   -2372.6129 
+     650        0.065 -0.099570972            0            0            1   -188.06642    53.153416   -2372.6129 
+     700         0.07 -0.099570972            0            0            1   -188.07628    51.377187   -2372.6129 
+     750        0.075 -0.099570972            0            0            1   -188.08415    49.725449   -2372.6129 
+     800         0.08 -0.099570972            0            0            1   -188.08857    49.663576   -2372.6129 
+     850        0.085 -0.099570972            0            0            1    -188.0891    51.681567   -2372.6129 
+     900         0.09 -0.099570972            0            0            1   -188.08636    55.166554   -2372.6129 
+     950        0.095 -0.099570972            0            0            1   -188.08174    58.718232   -2372.6129 
+    1000          0.1 -0.099570972            0            0            1    -188.0769     60.75567   -2372.6129 
+Loop time of 5.66302 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 1.526 ns/day, 15.731 hours/ns, 176.584 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.8546     | 2.8546     | 2.8546     |   0.0 | 50.41
+Neigh   | 0.012496   | 0.012496   | 0.012496   |   0.0 |  0.22
+Comm    | 0.041981   | 0.041981   | 0.041981   |   0.0 |  0.74
+Output  | 0.0014014  | 0.0014014  | 0.0014014  |   0.0 |  0.02
+Modify  | 2.7441     | 2.7441     | 2.7441     |   0.0 | 48.46
+Other   |            | 0.008486   |            |       |  0.15
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    24065 ave 24065 max 24065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  48130 ave 48130 max 48130 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 48130
+Ave neighs/atom = 96.26
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:05
diff --git a/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4 b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4
new file mode 100644
index 0000000000..6d8e74f37f
--- /dev/null
+++ b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4
@@ -0,0 +1,142 @@
+LAMMPS (30 Oct 2019)
+# fcc cobalt in a 3d periodic box
+
+clear
+units		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice fcc 	3.54
+Lattice spacing in x,y,z = 3.54 3.54 3.54
+region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  create_atoms CPU = 0.00073719 secs
+
+# setting mass, mag. moments, and interactions for fcc cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+  500 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+thermo_style	custom f_1
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
+thermo          50
+
+# compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+# dump 		1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.664 | 5.664 | 5.664 Mbytes
+Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
+       0            0 -0.099570972            0            0            1   -188.09051    100.00543   -2372.6129 
+      50        0.005 -0.099570972            0            0            1   -188.09036    95.174807   -2372.6129 
+     100         0.01 -0.099570972            0            0            1   -188.08965    81.854304   -2372.6129 
+     150        0.015 -0.099570972            0            0            1    -188.0877    63.270938   -2372.6129 
+     200         0.02 -0.099570972            0            0            1   -188.08381    43.867262   -2372.6129 
+     250        0.025 -0.099570972            0            0            1   -188.07767    28.075261   -2372.6129 
+     300         0.03 -0.099570972            0            0            1   -188.06966    19.046222   -2372.6129 
+     350        0.035 -0.099570972            0            0            1   -188.06096     17.79071   -2372.6129 
+     400         0.04 -0.099570972            0            0            1   -188.05326    23.079994   -2372.6129 
+     450        0.045 -0.099570972            0            0            1   -188.04831    32.127316   -2372.6129 
+     500         0.05 -0.099570972            0            0            1   -188.04737    41.709644   -2372.6129 
+     550        0.055 -0.099570972            0            0            1   -188.05082    49.246292   -2372.6129 
+     600         0.06 -0.099570972            0            0            1   -188.05795    53.465535   -2372.6129 
+     650        0.065 -0.099570972            0            0            1   -188.06713    54.522857   -2372.6129 
+     700         0.07 -0.099570972            0            0            1   -188.07626    53.635521   -2372.6129 
+     750        0.075 -0.099570972            0            0            1   -188.08332    52.419678   -2372.6129 
+     800         0.08 -0.099570972            0            0            1   -188.08696    52.176558   -2372.6129 
+     850        0.085 -0.099570972            0            0            1    -188.0868    53.380592   -2372.6129 
+     900         0.09 -0.099570972            0            0            1   -188.08348    55.551378   -2372.6129 
+     950        0.095 -0.099570972            0            0            1   -188.07838    57.540047   -2372.6129 
+    1000          0.1 -0.099570972            0            0            1   -188.07314    58.088674   -2372.6129 
+Loop time of 3.36398 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 2.568 ns/day, 9.344 hours/ns, 297.267 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.67186    | 0.78327    | 0.87877    |   8.5 | 23.28
+Neigh   | 0.0027554  | 0.0033352  | 0.0038562  |   0.7 |  0.10
+Comm    | 0.20661    | 0.30174    | 0.41594    |  14.1 |  8.97
+Output  | 0.0007627  | 0.00084305 | 0.0010374  |   0.0 |  0.03
+Modify  | 2.2674     | 2.2712     | 2.2779     |   0.3 | 67.52
+Other   |            | 0.003571   |            |       |  0.11
+
+Nlocal:    125 ave 133 max 116 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:    1099 ave 1108 max 1091 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Neighs:    6032.5 ave 6417 max 5489 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+FullNghs:  12065 ave 13062 max 10970 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+
+Total # of neighbors = 48260
+Ave neighs/atom = 96.52
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
index e5a49cd336..dd114202cb 100644
--- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
+++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
@@ -57,4 +57,4 @@ thermo          10
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		20000
+run 		1000
diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1
deleted file mode 100644
index 4bb513de18..0000000000
--- a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1
+++ /dev/null
@@ -1,318 +0,0 @@
-LAMMPS (11 May 2018)
-# hcp cobalt in a 3d periodic box
-
-clear
-units	 	metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	hcp 2.5071
-Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  Time spent = 0.000801802 secs
-
-# setting mass, mag. moments, and interactions for hcp cobalt
-
-mass		1 58.93
-
-#set 		group all spin/random 31 1.72
-set 		group all spin 1.72 0.0 0.0 1.0
-  500 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
-
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-fix 		3 all nve/spin lattice yes
-
-timestep	0.0001
-
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          10
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.59954
-  ghost atom cutoff = 6.59954
-  binsize = 3.29977, bins = 4 7 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes
-Step Time v_magnorm v_emag Temp TotEng 
-       0            0            1   -187.29499    100.00543   -2375.8943 
-      10        0.001            1   -187.29714    99.845593   -2375.8943 
-      20        0.002            1   -187.30356    99.367234   -2375.8943 
-      30        0.003            1   -187.31419    98.573996   -2375.8943 
-      40        0.004            1   -187.32896    97.472027   -2375.8943 
-      50        0.005            1   -187.34772    96.069944   -2375.8943 
-      60        0.006            1   -187.37032    94.378764   -2375.8943 
-      70        0.007            1   -187.39656    92.411827   -2375.8943 
-      80        0.008            1    -187.4262    90.184697   -2375.8943 
-      90        0.009            1     -187.459    87.715037   -2375.8943 
-     100         0.01            1   -187.49466    85.022479   -2375.8943 
-     110        0.011            1   -187.53289    82.128462   -2375.8943 
-     120        0.012            1   -187.57334     79.05606   -2375.8943 
-     130        0.013            1   -187.61568     75.82979   -2375.8943 
-     140        0.014            1   -187.65953    72.475403   -2375.8943 
-     150        0.015            1   -187.70453    69.019658   -2375.8943 
-     160        0.016            1   -187.75028    65.490086   -2375.8943 
-     170        0.017            1   -187.79642    61.914735   -2375.8943 
-     180        0.018            1   -187.84254    58.321911   -2375.8943 
-     190        0.019            1   -187.88828    54.739907   -2375.8943 
-     200         0.02            1   -187.93324    51.196728   -2375.8943 
-     210        0.021            1   -187.97708    47.719812   -2375.8943 
-     220        0.022            1   -188.01947    44.335762   -2375.8943 
-     230        0.023            1   -188.06003     41.07007   -2375.8943 
-     240        0.024            1   -188.09853    37.946852   -2375.8944 
-     250        0.025            1   -188.13457    34.988599   -2375.8944 
-     260        0.026            1   -188.16795    32.215943   -2375.8944 
-     270        0.027            1   -188.19851    29.647465   -2375.8944 
-     280        0.028            1   -188.22593    27.299481   -2375.8944 
-     290        0.029            1   -188.25011    25.185896   -2375.8944 
-     300         0.03            1   -188.27095    23.318075   -2375.8945 
-     310        0.031            1    -188.2883     21.70475   -2375.8945 
-     320        0.032            1   -188.30213     20.35194   -2375.8945 
-     330        0.033            1   -188.31251    19.262946   -2375.8945 
-     340        0.034            1   -188.31928    18.438347   -2375.8945 
-     350        0.035            1   -188.32258    17.876036   -2375.8945 
-     360        0.036            1   -188.32249    17.571322   -2375.8945 
-     370        0.037            1   -188.31913    17.517032   -2375.8945 
-     380        0.038            1   -188.31264    17.703653   -2375.8945 
-     390        0.039            1   -188.30321    18.119513   -2375.8945 
-     400         0.04            1   -188.29102    18.750969   -2375.8945 
-     410        0.041            1    -188.2763    19.582631   -2375.8945 
-     420        0.042            1   -188.25929    20.597597   -2375.8945 
-     430        0.043            1   -188.24025    21.777699   -2375.8945 
-     440        0.044            1   -188.21945    23.103765   -2375.8945 
-     450        0.045            1   -188.19719    24.555878   -2375.8946 
-     460        0.046            1   -188.17368    26.113643   -2375.8946 
-     470        0.047            1    -188.1493    27.756439   -2375.8946 
-     480        0.048            1   -188.12429    29.463677   -2375.8946 
-     490        0.049            1   -188.09895     31.21504   -2375.8946 
-     500         0.05            1   -188.07354    32.990713   -2375.8946 
-     510        0.051            1   -188.04832    34.771601   -2375.8945 
-     520        0.052            1   -188.02358    36.539517   -2375.8945 
-     530        0.053            1   -187.99951     38.27736   -2375.8945 
-     540        0.054            1   -187.97636    39.969275   -2375.8945 
-     550        0.055            1   -187.95437    41.600775   -2375.8945 
-     560        0.056            1   -187.93364    43.158863   -2375.8944 
-     570        0.057            1    -187.9144    44.632119   -2375.8944 
-     580        0.058            1   -187.89669    46.010765   -2375.8944 
-     590        0.059            1   -187.88074    47.286714   -2375.8944 
-     600         0.06            1   -187.86658    48.453573   -2375.8944 
-     610        0.061            1   -187.85422    49.506668   -2375.8943 
-     620        0.062            1   -187.84377    50.443021   -2375.8943 
-     630        0.063            1    -187.8352    51.261297   -2375.8943 
-     640        0.064            1    -187.8285    51.961764   -2375.8943 
-     650        0.065            1    -187.8236     52.54622   -2375.8943 
-     660        0.066            1    -187.8205    53.017899   -2375.8943 
-     670        0.067            1   -187.81909    53.381374   -2375.8943 
-     680        0.068            1   -187.81926     53.64244   -2375.8943 
-     690        0.069            1   -187.82092    53.807997   -2375.8943 
-     700         0.07            1   -187.82391    53.885909   -2375.8943 
-     710        0.071            1   -187.82814    53.884865   -2375.8943 
-     720        0.072            1   -187.83339    53.814238   -2375.8943 
-     730        0.073            1   -187.83952     53.68392   -2375.8943 
-     740        0.074            1   -187.84635    53.504185   -2375.8943 
-     750        0.075            1   -187.85375    53.285525   -2375.8943 
-     760        0.076            1   -187.86153    53.038494   -2375.8943 
-     770        0.077            1   -187.86952    52.773567   -2375.8943 
-     780        0.078            1   -187.87758    52.500994   -2375.8943 
-     790        0.079            1   -187.88549    52.230655   -2375.8943 
-     800         0.08            1   -187.89313    51.971933   -2375.8943 
-     810        0.081            1   -187.90035    51.733593   -2375.8943 
-     820        0.082            1   -187.90702    51.523671   -2375.8943 
-     830        0.083            1   -187.91302    51.349376   -2375.8943 
-     840        0.084            1   -187.91824    51.217006   -2375.8943 
-     850        0.085            1    -187.9226    51.131875   -2375.8943 
-     860        0.086            1   -187.92602    51.098259   -2375.8943 
-     870        0.087            1   -187.92844    51.119356   -2375.8943 
-     880        0.088            1   -187.92979    51.197261   -2375.8943 
-     890        0.089            1   -187.93011    51.332955   -2375.8943 
-     900         0.09            1   -187.92937    51.526314   -2375.8943 
-     910        0.091            1   -187.92757     51.77613   -2375.8943 
-     920        0.092            1   -187.92475    52.080145   -2375.8943 
-     930        0.093            1   -187.92096    52.435106   -2375.8943 
-     940        0.094            1   -187.91624    52.836825   -2375.8943 
-     950        0.095            1   -187.91068    53.280251   -2375.8943 
-     960        0.096            1   -187.90435    53.759559   -2375.8943 
-     970        0.097            1   -187.89734    54.268246   -2375.8943 
-     980        0.098            1   -187.88981    54.799223   -2375.8943 
-     990        0.099            1   -187.88185    55.344928   -2375.8943 
-    1000          0.1            1   -187.87357    55.897438   -2375.8943 
-    1010        0.101            1   -187.86511    56.448585   -2375.8943 
-    1020        0.102            1    -187.8566    56.990069   -2375.8943 
-    1030        0.103            1   -187.84817    57.513575   -2375.8943 
-    1040        0.104            1   -187.83995    58.010887   -2375.8943 
-    1050        0.105            1   -187.83208    58.474004   -2375.8943 
-    1060        0.106            1    -187.8247     58.89524   -2375.8943 
-    1070        0.107            1   -187.81789    59.267328   -2375.8943 
-    1080        0.108            1   -187.81177    59.583518   -2375.8943 
-    1090        0.109            1   -187.80646    59.837665   -2375.8943 
-    1100         0.11            1   -187.80204    60.024306   -2375.8943 
-    1110        0.111            1   -187.79861    60.138734   -2375.8943 
-    1120        0.112            1   -187.79625    60.177056   -2375.8943 
-    1130        0.113            1   -187.79497    60.136244   -2375.8943 
-    1140        0.114            1   -187.79485    60.014176   -2375.8943 
-    1150        0.115            1    -187.7959    59.809665   -2375.8943 
-    1160        0.116            1   -187.79811     59.52248   -2375.8943 
-    1170        0.117            1   -187.80157    59.153353   -2375.8943 
-    1180        0.118            1   -187.80618    58.703971   -2375.8943 
-    1190        0.119            1   -187.81193    58.176956   -2375.8943 
-    1200         0.12            1   -187.81879    57.575849   -2375.8943 
-    1210        0.121            1   -187.82668    56.905072   -2375.8943 
-    1220        0.122            1   -187.83554    56.169878   -2375.8943 
-    1230        0.123            1   -187.84528    55.376297   -2375.8943 
-    1240        0.124            1   -187.85581     54.53107   -2375.8943 
-    1250        0.125            1   -187.86702    53.641573   -2375.8943 
-    1260        0.126            1    -187.8788    52.715739   -2375.8943 
-    1270        0.127            1   -187.89103    51.761969   -2375.8943 
-    1280        0.128            1   -187.90358    50.789036   -2375.8943 
-    1290        0.129            1   -187.91632    49.805988   -2375.8943 
-    1300         0.13            1   -187.92911    48.822045   -2375.8943 
-    1310        0.131            1   -187.94182    47.846491   -2375.8943 
-    1320        0.132            1   -187.95428    46.888574   -2375.8943 
-    1330        0.133            1   -187.96643    45.957394   -2375.8943 
-    1340        0.134            1    -187.9781    45.061794   -2375.8943 
-    1350        0.135            1    -187.9892    44.210263   -2375.8943 
-    1360        0.136            1   -187.99955    43.410832   -2375.8943 
-    1370        0.137            1   -188.00907    42.670979   -2375.8943 
-    1380        0.138            1   -188.01767    41.997547   -2375.8943 
-    1390        0.139            1   -188.02525    41.396655   -2375.8943 
-    1400         0.14            1   -188.03177    40.873631   -2375.8944 
-    1410        0.141            1   -188.03711    40.432952   -2375.8944 
-    1420        0.142            1   -188.04124    40.078172   -2375.8944 
-    1430        0.143            1   -188.04413    39.811902   -2375.8944 
-    1440        0.144            1   -188.04575    39.635775   -2375.8944 
-    1450        0.145            1   -188.04607    39.550435   -2375.8943 
-    1460        0.146            1   -188.04515    39.555512   -2375.8943 
-    1470        0.147            1   -188.04298    39.649651   -2375.8943 
-    1480        0.148            1   -188.03961    39.830523   -2375.8943 
-    1490        0.149            1   -188.03508    40.094865   -2375.8943 
-    1500         0.15            1   -188.02944    40.438519   -2375.8943 
-    1510        0.151            1   -188.02275    40.856491   -2375.8943 
-    1520        0.152            1   -188.01515    41.343019   -2375.8943 
-    1530        0.153            1   -188.00671    41.891643   -2375.8943 
-    1540        0.154            1   -187.99753    42.495295   -2375.8943 
-    1550        0.155            1   -187.98772     43.14639   -2375.8943 
-    1560        0.156            1    -187.9774    43.836918   -2375.8943 
-    1570        0.157            1    -187.9667    44.558553   -2375.8943 
-    1580        0.158            1   -187.95576    45.302751   -2375.8943 
-    1590        0.159            1   -187.94466    46.060862   -2375.8943 
-    1600         0.16            1   -187.93356    46.824226   -2375.8943 
-    1610        0.161            1   -187.92257    47.584289   -2375.8943 
-    1620        0.162            1   -187.91183    48.332703   -2375.8943 
-    1630        0.163            1   -187.90145    49.061422   -2375.8943 
-    1640        0.164            1   -187.89155    49.762798   -2375.8943 
-    1650        0.165            1   -187.88222    50.429671   -2375.8943 
-    1660        0.166            1   -187.87357    51.055445   -2375.8943 
-    1670        0.167            1   -187.86569    51.634167   -2375.8943 
-    1680        0.168            1   -187.85864    52.160588   -2375.8943 
-    1690        0.169            1   -187.85249    52.630219   -2375.8943 
-    1700         0.17            1    -187.8473    53.039377   -2375.8943 
-    1710        0.171            1   -187.84311    53.385221   -2375.8943 
-    1720        0.172            1   -187.83994    53.665778   -2375.8943 
-    1730        0.173            1   -187.83781    53.879954   -2375.8943 
-    1740        0.174            1   -187.83671    54.027539   -2375.8943 
-    1750        0.175            1   -187.83663    54.109201   -2375.8943 
-    1760        0.176            1   -187.83753    54.126472   -2375.8943 
-    1770        0.177            1   -187.83941    54.081708   -2375.8943 
-    1780        0.178            1    -187.8422     53.97806   -2375.8943 
-    1790        0.179            1   -187.84584    53.819424   -2375.8943 
-    1800         0.18            1   -187.85025    53.610389   -2375.8943 
-    1810        0.181            1   -187.85535    53.356163   -2375.8943 
-    1820        0.182            1   -187.86105     53.06251   -2375.8943 
-    1830        0.183            1   -187.86723    52.735671   -2375.8943 
-    1840        0.184            1   -187.87384    52.382262   -2375.8943 
-    1850        0.185            1   -187.88075    52.009201   -2375.8943 
-    1860        0.186            1   -187.88784    51.623613   -2375.8943 
-    1870        0.187            1   -187.89501    51.232726   -2375.8943 
-    1880        0.188            1   -187.90214    50.843782   -2375.8943 
-    1890        0.189            1   -187.90912    50.463929   -2375.8943 
-    1900         0.19            1   -187.91585    50.100133   -2375.8943 
-    1910        0.191            1   -187.92222    49.759075   -2375.8943 
-    1920        0.192            1   -187.92814    49.447064   -2375.8943 
-    1930        0.193            1   -187.93351    49.169949   -2375.8943 
-    1940        0.194            1   -187.93826    48.933036   -2375.8943 
-    1950        0.195            1   -187.94232    48.741013   -2375.8943 
-    1960        0.196            1   -187.94561    48.597888   -2375.8943 
-    1970        0.197            1   -187.94809    48.506926   -2375.8943 
-    1980        0.198            1   -187.94972    48.470605   -2375.8943 
-    1990        0.199            1   -187.95047    48.490576   -2375.8943 
-    2000          0.2            1   -187.95033    48.567643   -2375.8943 
-Loop time of 10.5391 on 1 procs for 2000 steps with 500 atoms
-
-Performance: 1.640 ns/day, 14.638 hours/ns, 189.770 timesteps/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 4.9958     | 4.9958     | 4.9958     |   0.0 | 47.40
-Neigh   | 0.020741   | 0.020741   | 0.020741   |   0.0 |  0.20
-Comm    | 0.05899    | 0.05899    | 0.05899    |   0.0 |  0.56
-Output  | 1.1598     | 1.1598     | 1.1598     |   0.0 | 11.00
-Modify  | 4.2885     | 4.2885     | 4.2885     |   0.0 | 40.69
-Other   |            | 0.01522    |            |       |  0.14
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2444 ave 2444 max 2444 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    27041 ave 27041 max 27041 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  54082 ave 54082 max 54082 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 54082
-Ave neighs/atom = 108.164
-Neighbor list builds = 12
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:10
diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4
deleted file mode 100644
index 4e7e6b1b97..0000000000
--- a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4
+++ /dev/null
@@ -1,318 +0,0 @@
-LAMMPS (11 May 2018)
-# hcp cobalt in a 3d periodic box
-
-clear
-units	 	metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	hcp 2.5071
-Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  Time spent = 0.000241518 secs
-
-# setting mass, mag. moments, and interactions for hcp cobalt
-
-mass		1 58.93
-
-#set 		group all spin/random 31 1.72
-set 		group all spin 1.72 0.0 0.0 1.0
-  500 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
-
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-fix 		3 all nve/spin lattice yes
-
-timestep	0.0001
-
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          10
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.59954
-  ghost atom cutoff = 6.59954
-  binsize = 3.29977, bins = 4 7 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.314 | 7.314 Mbytes
-Step Time v_magnorm v_emag Temp TotEng 
-       0            0            1   -187.29499    100.00543   -2375.8943 
-      10        0.001            1   -187.29721    99.841045   -2375.8943 
-      20        0.002            1   -187.30385    99.349208   -2375.8943 
-      30        0.003            1   -187.31485    98.533905   -2375.8943 
-      40        0.004            1   -187.33011    97.401749   -2375.8943 
-      50        0.005            1   -187.34949    95.961938   -2375.8943 
-      60        0.006            1   -187.37283     94.22618   -2375.8943 
-      70        0.007            1   -187.39992    92.208606   -2375.8943 
-      80        0.008            1   -187.43051     89.92566   -2375.8943 
-      90        0.009            1   -187.46434     87.39597   -2375.8943 
-     100         0.01            1    -187.5011    84.640195   -2375.8943 
-     110        0.011            1   -187.54047    81.680862   -2375.8943 
-     120        0.012            1    -187.5821    78.542172   -2375.8943 
-     130        0.013            1   -187.62564    75.249797   -2375.8943 
-     140        0.014            1   -187.67069    71.830656   -2375.8943 
-     150        0.015            1   -187.71686    68.312673   -2375.8943 
-     160        0.016            1   -187.76377    64.724523   -2375.8943 
-     170        0.017            1   -187.81099    61.095365   -2375.8943 
-     180        0.018            1   -187.85814    57.454566   -2375.8943 
-     190        0.019            1   -187.90481    53.831412   -2375.8943 
-     200         0.02            1   -187.95061    50.254822   -2375.8943 
-     210        0.021            1   -187.99517    46.753056   -2375.8943 
-     220        0.022            1   -188.03812    43.353428   -2375.8943 
-     230        0.023            1   -188.07913    40.082023   -2375.8943 
-     240        0.024            1   -188.11787    36.963429   -2375.8943 
-     250        0.025            1   -188.15409    34.020481   -2375.8943 
-     260        0.026            1    -188.1875     31.27403   -2375.8943 
-     270        0.027            1   -188.21782     28.74271   -2375.8943 
-     280        0.028            1    -188.2449     26.44276   -2375.8943 
-     290        0.029            1   -188.26857    24.387875   -2375.8943 
-     300         0.03            1   -188.28877    22.589076   -2375.8944 
-     310        0.031            1   -188.30529    21.054615   -2375.8944 
-     320        0.032            1   -188.31814    19.789913   -2375.8944 
-     330        0.033            1    -188.3273    18.797563   -2375.8944 
-     340        0.034            1   -188.33284    18.077336   -2375.8944 
-     350        0.035            1   -188.33478    17.626237   -2375.8945 
-     360        0.036            1   -188.33319    17.438611   -2375.8945 
-     370        0.037            1   -188.32824    17.506247   -2375.8945 
-     380        0.038            1   -188.32007    17.818564   -2375.8945 
-     390        0.039            1   -188.30888    18.362769   -2375.8945 
-     400         0.04            1    -188.2949    19.124086   -2375.8945 
-     410        0.041            1   -188.27837    20.085983   -2375.8945 
-     420        0.042            1   -188.25957    21.230423   -2375.8945 
-     430        0.043            1   -188.23868    22.538112   -2375.8945 
-     440        0.044            1   -188.21604    23.988778   -2375.8945 
-     450        0.045            1   -188.19195    25.561447   -2375.8945 
-     460        0.046            1   -188.16672    27.234703   -2375.8945 
-     470        0.047            1   -188.14064    28.986964   -2375.8946 
-     480        0.048            1   -188.11402    30.796738   -2375.8946 
-     490        0.049            1   -188.08713    32.642869   -2375.8945 
-     500         0.05            1   -188.06032    34.504776   -2375.8945 
-     510        0.051            1   -188.03383    36.362662   -2375.8945 
-     520        0.052            1   -188.00793    38.197721   -2375.8945 
-     530        0.053            1   -187.98284    39.992314   -2375.8945 
-     540        0.054            1   -187.95884    41.730127   -2375.8945 
-     550        0.055            1   -187.93612    43.396298   -2375.8945 
-     560        0.056            1   -187.91489     44.97754   -2375.8945 
-     570        0.057            1   -187.89524    46.462224   -2375.8945 
-     580        0.058            1   -187.87735    47.840443   -2375.8945 
-     590        0.059            1    -187.8613    49.104064   -2375.8945 
-     600         0.06            1   -187.84719    50.246744   -2375.8945 
-     610        0.061            1   -187.83509     51.26393   -2375.8944 
-     620        0.062            1   -187.82506    52.152839   -2375.8944 
-     630        0.063            1   -187.81706    52.912413   -2375.8944 
-     640        0.064            1   -187.81109    53.543272   -2375.8944 
-     650        0.065            1   -187.80708    54.047636   -2375.8944 
-     660        0.066            1   -187.80499    54.429234   -2375.8944 
-     670        0.067            1    -187.8047    54.693202   -2375.8944 
-     680        0.068            1   -187.80613    54.845965   -2375.8944 
-     690        0.069            1   -187.80914    54.895106   -2375.8944 
-     700         0.07            1   -187.81356    54.849238   -2375.8944 
-     710        0.071            1   -187.81923     54.71786   -2375.8943 
-     720        0.072            1   -187.82608    54.511181   -2375.8943 
-     730        0.073            1   -187.83388    54.239987   -2375.8943 
-     740        0.074            1   -187.84244     53.91548   -2375.8943 
-     750        0.075            1   -187.85158    53.549112   -2375.8943 
-     760        0.076            1   -187.86112    53.152433   -2375.8943 
-     770        0.077            1   -187.87086    52.736925   -2375.8943 
-     780        0.078            1   -187.88063    52.313858   -2375.8943 
-     790        0.079            1   -187.89026    51.894138   -2375.8943 
-     800         0.08            1   -187.89958    51.488169   -2375.8943 
-     810        0.081            1   -187.90842    51.105725   -2375.8943 
-     820        0.082            1   -187.91663    50.755829   -2375.8943 
-     830        0.083            1   -187.92411    50.446651   -2375.8943 
-     840        0.084            1   -187.93071    50.185404   -2375.8943 
-     850        0.085            1   -187.93637    49.978262   -2375.8943 
-     860        0.086            1   -187.94099    49.830307   -2375.8943 
-     870        0.087            1    -187.9445    49.745473   -2375.8943 
-     880        0.088            1   -187.94685    49.726517   -2375.8943 
-     890        0.089            1   -187.94802    49.774999   -2375.8943 
-     900         0.09            1   -187.94799    49.891282   -2375.8943 
-     910        0.091            1   -187.94678    50.074549   -2375.8943 
-     920        0.092            1   -187.94441    50.322833   -2375.8943 
-     930        0.093            1   -187.94093    50.633063   -2375.8943 
-     940        0.094            1   -187.93639    51.001126   -2375.8943 
-     950        0.095            1   -187.93089    51.421938   -2375.8943 
-     960        0.096            1    -187.9245    51.889531   -2375.8943 
-     970        0.097            1   -187.91733    52.397148   -2375.8943 
-     980        0.098            1    -187.9095    52.937345   -2375.8943 
-     990        0.099            1   -187.90113    53.502108   -2375.8943 
-    1000          0.1            1   -187.89236    54.082966   -2375.8943 
-    1010        0.101            1   -187.88332    54.671115   -2375.8943 
-    1020        0.102            1   -187.87415    55.257545   -2375.8943 
-    1030        0.103            1   -187.86501    55.833162   -2375.8943 
-    1040        0.104            1   -187.85602    56.388915   -2375.8943 
-    1050        0.105            1   -187.84734    56.915918   -2375.8943 
-    1060        0.106            1   -187.83909    57.405575   -2375.8943 
-    1070        0.107            1   -187.83143    57.849686   -2375.8943 
-    1080        0.108            1   -187.82446    58.240564   -2375.8943 
-    1090        0.109            1    -187.8183    58.571132   -2375.8943 
-    1100         0.11            1   -187.81306    58.835016   -2375.8943 
-    1110        0.111            1   -187.80883    59.026633   -2375.8943 
-    1120        0.112            1    -187.8057    59.141258   -2375.8943 
-    1130        0.113            1   -187.80372     59.17509   -2375.8943 
-    1140        0.114            1   -187.80295    59.125305   -2375.8943 
-    1150        0.115            1   -187.80341    58.990092   -2375.8943 
-    1160        0.116            1   -187.80515     58.76868   -2375.8943 
-    1170        0.117            1   -187.80814    58.461352   -2375.8943 
-    1180        0.118            1   -187.81244    58.069457   -2375.8943 
-    1190        0.119            1   -187.81794    57.595377   -2375.8944 
-    1200         0.12            1   -187.82458    57.042514   -2375.8944 
-    1210        0.121            1   -187.83233    56.415256   -2375.8944 
-    1220        0.122            1   -187.84112    55.718931   -2375.8944 
-    1230        0.123            1   -187.85086    54.959744   -2375.8944 
-    1240        0.124            1   -187.86145    54.144707   -2375.8944 
-    1250        0.125            1   -187.87277    53.281562   -2375.8944 
-    1260        0.126            1   -187.88471    52.378686   -2375.8944 
-    1270        0.127            1   -187.89713       51.445   -2375.8944 
-    1280        0.128            1    -187.9099    50.489858   -2375.8944 
-    1290        0.129            1   -187.92288    49.522943   -2375.8944 
-    1300         0.13            1   -187.93591    48.554147   -2375.8944 
-    1310        0.131            1   -187.94886    47.593456   -2375.8944 
-    1320        0.132            1   -187.96157    46.650829   -2375.8944 
-    1330        0.133            1   -187.97391    45.736073   -2375.8944 
-    1340        0.134            1   -187.98573    44.858733   -2375.8944 
-    1350        0.135            1   -187.99691    44.027964   -2375.8944 
-    1360        0.136            1   -188.00731    43.252426   -2375.8944 
-    1370        0.137            1   -188.01678    42.540178   -2375.8943 
-    1380        0.138            1   -188.02529    41.898568   -2375.8943 
-    1390        0.139            1    -188.0327    41.334152   -2375.8943 
-    1400         0.14            1   -188.03894    40.852606   -2375.8943 
-    1410        0.141            1   -188.04396     40.45866   -2375.8944 
-    1420        0.142            1   -188.04768    40.156041   -2375.8944 
-    1430        0.143            1   -188.05007    39.947416   -2375.8944 
-    1440        0.144            1   -188.05107    39.834367   -2375.8944 
-    1450        0.145            1    -188.0507    39.817378   -2375.8944 
-    1460        0.146            1   -188.04898    39.895828   -2375.8944 
-    1470        0.147            1   -188.04595    40.068005   -2375.8945 
-    1480        0.148            1   -188.04164    40.331129   -2375.8945 
-    1490        0.149            1   -188.03603    40.681394   -2375.8945 
-    1500         0.15            1   -188.02929    41.114003   -2375.8945 
-    1510        0.151            1   -188.02148    41.623259   -2375.8945 
-    1520        0.152            1    -188.0127     42.20263   -2375.8945 
-    1530        0.153            1   -188.00302    42.844846   -2375.8945 
-    1540        0.154            1   -187.99255    43.541977   -2375.8945 
-    1550        0.155            1   -187.98148    44.285554   -2375.8945 
-    1560        0.156            1   -187.96989    45.066666   -2375.8945 
-    1570        0.157            1   -187.95793    45.876084   -2375.8945 
-    1580        0.158            1   -187.94574    46.704378   -2375.8945 
-    1590        0.159            1   -187.93346    47.542032   -2375.8945 
-    1600         0.16            1   -187.92122    48.379564   -2375.8945 
-    1610        0.161            1   -187.90916    49.207642   -2375.8945 
-    1620        0.162            1   -187.89742      50.0172   -2375.8945 
-    1630        0.163            1   -187.88613    50.799541   -2375.8945 
-    1640        0.164            1   -187.87536    51.546446   -2375.8944 
-    1650        0.165            1   -187.86531    52.250265   -2375.8944 
-    1660        0.166            1   -187.85604    52.904001   -2375.8944 
-    1670        0.167            1   -187.84765    53.501394   -2375.8944 
-    1680        0.168            1   -187.84021    54.036987   -2375.8944 
-    1690        0.169            1   -187.83379    54.506178   -2375.8944 
-    1700         0.17            1   -187.82846    54.905273   -2375.8944 
-    1710        0.171            1   -187.82424    55.231514   -2375.8944 
-    1720        0.172            1   -187.82117    55.483104   -2375.8944 
-    1730        0.173            1   -187.81922    55.659221   -2375.8944 
-    1740        0.174            1   -187.81843    55.760007   -2375.8944 
-    1750        0.175            1   -187.81881    55.786556   -2375.8944 
-    1760        0.176            1   -187.82029    55.740888   -2375.8944 
-    1770        0.177            1   -187.82284    55.625916   -2375.8944 
-    1780        0.178            1   -187.82639    55.445397   -2375.8944 
-    1790        0.179            1   -187.83088    55.203871   -2375.8944 
-    1800         0.18            1   -187.83623    54.906597   -2375.8944 
-    1810        0.181            1   -187.84235    54.559471   -2375.8944 
-    1820        0.182            1   -187.84913    54.168949   -2375.8944 
-    1830        0.183            1   -187.85646    53.741952   -2375.8943 
-    1840        0.184            1   -187.86424     53.28578   -2375.8943 
-    1850        0.185            1   -187.87239    52.807988   -2375.8943 
-    1860        0.186            1   -187.88077      52.3163   -2375.8943 
-    1870        0.187            1   -187.88925     51.81851   -2375.8943 
-    1880        0.188            1   -187.89772    51.322368   -2375.8943 
-    1890        0.189            1   -187.90605    50.835483   -2375.8943 
-    1900         0.19            1   -187.91415    50.365218   -2375.8943 
-    1910        0.191            1   -187.92189      49.9186   -2375.8943 
-    1920        0.192            1   -187.92917    49.502222   -2375.8943 
-    1930        0.193            1   -187.93591    49.122167   -2375.8943 
-    1940        0.194            1   -187.94198    48.783928   -2375.8943 
-    1950        0.195            1   -187.94737    48.492348   -2375.8943 
-    1960        0.196            1   -187.95199     48.25154   -2375.8943 
-    1970        0.197            1   -187.95576    48.064862   -2375.8943 
-    1980        0.198            1   -187.95866    47.934875   -2375.8943 
-    1990        0.199            1   -187.96065    47.863314   -2375.8943 
-    2000          0.2            1   -187.96171    47.851079   -2375.8943 
-Loop time of 4.40076 on 4 procs for 2000 steps with 500 atoms
-
-Performance: 3.927 ns/day, 6.112 hours/ns, 454.467 timesteps/s
-96.2% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.2934     | 1.3683     | 1.432      |   4.2 | 31.09
-Neigh   | 0.005039   | 0.0053418  | 0.0054908  |   0.2 |  0.12
-Comm    | 0.12642    | 0.1922     | 0.26891    |  11.6 |  4.37
-Output  | 0.39256    | 0.40875    | 0.43431    |   2.5 |  9.29
-Modify  | 2.395      | 2.4202     | 2.4352     |   1.0 | 54.99
-Other   |            | 0.006007   |            |       |  0.14
-
-Nlocal:    125 ave 130 max 122 min
-Histogram: 1 1 0 1 0 0 0 0 0 1
-Nghost:    1324 ave 1330 max 1316 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Neighs:    6747 ave 6959 max 6652 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-FullNghs:  13494 ave 14060 max 13186 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-
-Total # of neighbors = 53976
-Ave neighs/atom = 107.952
-Neighbor list builds = 12
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:04
diff --git a/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1 b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1
new file mode 100644
index 0000000000..c534241f34
--- /dev/null
+++ b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1
@@ -0,0 +1,219 @@
+LAMMPS (30 Oct 2019)
+# hcp cobalt in a 3d periodic box
+
+clear
+units	 	metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000491858 secs
+
+# setting mass, mag. moments, and interactions for hcp cobalt
+
+mass		1 58.93
+
+set 		group all spin/random 31 1.72
+  500 settings made for spin/random
+#set 		group all spin 1.72 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
+#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 		1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
+#fix 		2 all langevin/spin 0.0 0.0 21
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice moving
+
+timestep	0.0001
+
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp press etotal
+thermo          10
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 4 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.902 | 7.902 | 7.902 Mbytes
+Step Time v_magnorm v_emag Temp Press TotEng 
+       0            0  0.076558814   -5.1073764    100.00543   -552.75983   -2190.3478 
+      10        0.001  0.074494403   -6.2746901    100.01038   -1571.7966   -2191.5266 
+      20        0.002  0.072366265   -7.4280779    99.885587   -2535.9845   -2192.6673 
+      30        0.003  0.070127018   -8.5667999    99.611653   -3445.9872   -2193.7707 
+      40        0.004  0.067755946   -9.6899272    99.164813   -4302.5715   -2194.8376 
+      50        0.005  0.065261592    -10.79648    98.520535   -5107.2841   -2195.8697 
+      60        0.006  0.062676613   -11.885341    97.657148   -5862.7198   -2196.8696 
+      70        0.007  0.060046709   -12.955115    96.558718   -6572.0571   -2197.8404 
+      80        0.008  0.057417313   -14.004096    95.216748   -7238.1396   -2198.7846 
+      90        0.009  0.054822275   -15.030416    93.630634   -7862.5226   -2199.7028 
+     100         0.01  0.052277835   -16.032345     91.80711   -8445.2646   -2200.5936 
+     110        0.011  0.049783153   -17.008652    89.759163   -8985.5937   -2201.4546 
+     120        0.012  0.047326373   -17.958895    87.504922   -9483.1141   -2202.2836 
+     130        0.013  0.044893289   -18.883574    85.066818   -9938.8838     -2203.08 
+     140        0.014  0.042474822   -19.784052    82.471014   -10355.911   -2203.8457 
+     150        0.015  0.040070404   -20.662271    79.746901   -10739.081   -2204.5843 
+     160        0.016  0.037686856   -21.520294    76.926428   -11094.793   -2205.3015 
+     170        0.017  0.035334961   -22.359822    74.043181   -11430.247   -2206.0035 
+     180        0.018  0.033026799   -23.181822    71.131269   -11752.268   -2206.6955 
+     190        0.019  0.030775544   -23.986406    68.224204   -12065.774   -2207.3807 
+     200         0.02  0.028597121   -24.773013    65.353995   -12372.712   -2208.0582 
+     210        0.021  0.026511775   -25.540835     62.55053   -12672.055   -2208.7235 
+     220        0.022   0.02454383   -26.289327    59.841288   -12961.112   -2209.3704 
+     230        0.023   0.02271918   -27.018625    57.251361   -13237.544   -2209.9931 
+     240        0.024  0.021061271   -27.729714     54.80373   -13501.028   -2210.5885 
+     250        0.025  0.019587072    -28.42449    52.519717   -13754.325   -2211.1572 
+     260        0.026  0.018304494   -29.105398    50.419388   -14002.718   -2211.7031 
+     270        0.027  0.017211977   -29.775134    48.521812   -14253.089   -2212.2321 
+     280        0.028  0.016300002   -30.436204    46.845075   -14512.437   -2212.7508 
+     290        0.029  0.015553519   -31.090499    45.405985    -14786.53   -2213.2644 
+     300         0.03  0.014954102   -31.739026    44.219544   -15079.165   -2213.7764 
+     310        0.031  0.014481189   -32.381585    43.298175   -15391.531   -2214.2875 
+     320        0.032  0.014112494   -33.016984    42.650874   -15722.828   -2214.7966 
+     330        0.033  0.013824206   -33.643289    42.282535   -16070.874   -2215.3011 
+     340        0.034  0.013591568   -34.258323     42.19365   -16433.065   -2215.7983 
+     350        0.035  0.013390035   -34.860184    42.380506   -16807.186    -2216.286 
+     360        0.036   0.01319679   -35.447655    42.835832   -17191.816    -2216.763 
+     370        0.037  0.012992271   -36.020512    43.549656   -17586.676   -2217.2292 
+     380        0.038  0.012761486   -36.579332    44.510078   -17991.857   -2217.6857 
+     390        0.039  0.012494918   -37.125414    45.703757   -18407.738   -2218.1336 
+     400         0.04    0.0121888   -37.660321    47.115967   -18834.276   -2218.5743 
+     410        0.041  0.011844474   -38.185489    48.730291   -19270.674   -2219.0083 
+     420        0.042  0.011466715    -38.70192    50.528119   -19715.276   -2219.4355 
+     430        0.043  0.011061388    -39.21005    52.488204    -20165.66   -2219.8551 
+     440        0.044  0.010633241   -39.709778    54.586528   -20618.997    -2220.266 
+     450        0.045  0.010184696   -40.200724     56.79654   -21072.538   -2220.6671 
+     460        0.046 0.0097161044   -40.682449    59.089699   -21523.873   -2221.0575 
+     470        0.047 0.0092271788   -41.154614    61.436133   -21970.922   -2221.4371 
+     480        0.048 0.0087187266   -41.617256    63.805414    -22412.32   -2221.8064 
+     490        0.049 0.0081937768   -42.070708    66.167399   -22847.061   -2222.1664 
+     500         0.05 0.0076576327    -42.51563    68.493235   -23274.619   -2222.5187 
+     510        0.051 0.0071170477   -42.952841    70.756444   -23694.559   -2222.8652 
+     520        0.052  0.006579078   -43.383338    72.933996   -24106.717   -2223.2075 
+     530        0.053  0.006050144   -43.807962    75.007131   -24510.338   -2223.5467 
+     540        0.054 0.0055354475   -44.227552    76.961803   -24904.495   -2223.8833 
+     550        0.055 0.0050386503    -44.64268    78.788647   -25287.341   -2224.2166 
+     560        0.056 0.0045617699   -45.053996      80.4825    -25657.11   -2224.5456 
+     570        0.057 0.0041054334   -45.461923    82.041527   -26011.443   -2224.8688 
+     580        0.058  0.003669689   -45.866895    83.466142   -26348.265   -2225.1846 
+     590        0.059 0.0032553824   -46.269219    84.757926   -26665.834    -2225.492 
+     600         0.06 0.0028655752   -46.669125    85.918711    -26963.24   -2225.7906 
+     610        0.061 0.0025060765   -47.066641        86.95   -27240.331   -2226.0806 
+     620        0.062 0.0021839971   -47.461566    87.852838   -27497.728   -2226.3626 
+     630        0.063 0.0019039581   -47.853462    88.628142   -27736.503   -2226.6376 
+     640        0.064 0.0016633855   -48.241747    89.277364    -27957.91   -2226.9064 
+     650        0.065 0.0014502904   -48.625803    89.803307    -28163.11   -2227.1692 
+     660        0.066 0.0012463786   -49.005026    90.210807   -28352.881   -2227.4258 
+     670        0.067 0.0010345087   -49.378935    90.507107   -28527.721   -2227.6754 
+     680        0.068 0.00080788134   -49.747325    90.701795   -28688.395   -2227.9175 
+     690        0.069  0.000586442   -50.110227     90.80636   -28836.094   -2228.1522 
+     700         0.07 0.00046855102   -50.467799    90.833539   -28972.361   -2228.3797 
+     710        0.071 0.00061091693    -50.82044    90.796649    -29099.44   -2228.6011 
+     720        0.072 0.00094960177   -51.168606    90.709122   -29219.676   -2228.8175 
+     730        0.073 0.0013742455   -51.512913    90.584346   -29335.643   -2229.0301 
+     740        0.074 0.0018397629   -51.853957    90.435783   -29449.521   -2229.2396 
+     750        0.075 0.0023216474   -52.192407    90.277231   -29563.316   -2229.4468 
+     760        0.076 0.0028000512   -52.528883    90.123061   -29678.726   -2229.6522 
+     770        0.077 0.0032569295   -52.863859     89.98824   -29797.079   -2229.8564 
+     780        0.078 0.0036765431   -53.197843    89.888047   -29919.964     -2230.06 
+     790        0.079 0.0040467094   -53.530921    89.837568   -30048.271   -2230.2638 
+     800         0.08 0.0043597837   -53.862938    89.850978   -30182.622   -2230.4682 
+     810        0.081 0.0046129296   -54.193489    89.940884   -30323.293   -2230.6737 
+     820        0.082 0.0048076151   -54.522077    90.117797   -30470.468   -2230.8804 
+     830        0.083  0.004948533    -54.84813    90.389814   -30624.056   -2231.0884 
+     840        0.084 0.0050423324   -55.171024    90.762454   -30783.658   -2231.2974 
+     850        0.085 0.0050965581   -55.490357    91.238681   -30949.141   -2231.5072 
+     860        0.086 0.0051190641   -55.805904    91.818973     -31120.5   -2231.7177 
+     870        0.087 0.0051180301   -56.117429    92.501449   -31297.412   -2231.9286 
+     880        0.088 0.0051024116   -56.424751    93.281992   -31479.436   -2232.1393 
+     890        0.089  0.005082454   -56.727832    94.154367   -31666.293   -2232.3495 
+     900         0.09 0.0050697645   -57.026442    95.110386   -31857.043   -2232.5582 
+     910        0.091 0.0050765431   -57.320291    96.140056   -32050.436   -2232.7645 
+     920        0.092 0.0051139309   -57.609075    97.231838   -32245.079   -2232.9672 
+     930        0.093 0.0051899535    -57.89236    98.372982   -32439.141   -2233.1648 
+     940        0.094 0.0053078572   -58.169742     99.54995   -32630.727   -2233.3559 
+     950        0.095 0.0054654923    -58.44083    100.74893   -32817.882   -2233.5392 
+     960        0.096 0.0056558757   -58.705483    101.95638   -32999.116   -2233.7136 
+     970        0.097 0.0058685513   -58.963698    103.15953   -33173.159   -2233.8785 
+     980        0.098 0.0060912487   -59.215624    104.34681   -33338.961   -2234.0336 
+     990        0.099 0.0063114886   -59.461806    105.50819   -33496.345   -2234.1794 
+    1000          0.1 0.0065179843   -59.702883    106.63524   -33645.259   -2234.3168 
+Loop time of 5.86376 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 1.473 ns/day, 16.288 hours/ns, 170.539 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9866     | 2.9866     | 2.9866     |   0.0 | 50.93
+Neigh   | 0.016013   | 0.016013   | 0.016013   |   0.0 |  0.27
+Comm    | 0.046018   | 0.046018   | 0.046018   |   0.0 |  0.78
+Output  | 0.011075   | 0.011075   | 0.011075   |   0.0 |  0.19
+Modify  | 2.7957     | 2.7957     | 2.7957     |   0.0 | 47.68
+Other   |            | 0.008332   |            |       |  0.14
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2442 ave 2442 max 2442 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    27581 ave 27581 max 27581 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  55162 ave 55162 max 55162 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 55162
+Ave neighs/atom = 110.324
+Neighbor list builds = 7
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:05
diff --git a/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4 b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4
new file mode 100644
index 0000000000..21adab3f19
--- /dev/null
+++ b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4
@@ -0,0 +1,219 @@
+LAMMPS (30 Oct 2019)
+# hcp cobalt in a 3d periodic box
+
+clear
+units	 	metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000671148 secs
+
+# setting mass, mag. moments, and interactions for hcp cobalt
+
+mass		1 58.93
+
+set 		group all spin/random 31 1.72
+  500 settings made for spin/random
+#set 		group all spin 1.72 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
+#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 		1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
+#fix 		2 all langevin/spin 0.0 0.0 21
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice moving
+
+timestep	0.0001
+
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp press etotal
+thermo          10
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 4 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.814 | 7.814 | 7.815 Mbytes
+Step Time v_magnorm v_emag Temp Press TotEng 
+       0            0  0.076558814   -5.1073764    100.00543   -552.75983   -2190.3478 
+      10        0.001  0.074494512   -6.2728301    99.980769   -1570.0726   -2191.5261 
+      20        0.002  0.072367013   -7.4259977    99.847801   -2531.5119   -2192.6655 
+      30        0.003  0.070129365    -8.566306    99.586282   -3438.1309   -2193.7672 
+      40        0.004  0.067761178   -9.6929189    99.171132    -4291.017   -2194.8323 
+      50        0.005  0.065270916     -10.8048    98.575397   -5091.9111   -2195.8628 
+      60        0.006  0.062690557   -11.900573    97.773618   -5843.4528   -2196.8612 
+      70        0.007  0.060064592   -12.978381    96.745047    -6548.726   -2197.8306 
+      80        0.008   0.05743694   -14.035923    95.476292   -7210.2954    -2198.773 
+      90        0.009  0.054839883    -15.07074    93.963026   -7829.4252    -2199.689 
+     100         0.01  0.052288504    -16.08066    92.210482   -8405.9983   -2200.5773 
+     110        0.011  0.049782155   -17.064251    90.232741   -8939.3051   -2201.4357 
+     120        0.012  0.047311759   -18.021135    88.051042   -9429.1353   -2202.2626 
+     130        0.013  0.044869196   -18.952065    85.691573   -9876.5628   -2203.0575 
+     140        0.014  0.042453961   -19.858739     83.18315   -10284.249   -2203.8215 
+     150        0.015  0.040074171   -20.743348    80.555177   -10656.417   -2204.5569 
+     160        0.016  0.037742459      -21.608    77.836156   -10998.818   -2205.2677 
+     170        0.017  0.035470168   -22.454209    75.052994   -11318.525   -2205.9587 
+     180        0.018  0.033263447   -23.282658    72.231211   -11623.118   -2206.6354 
+     190        0.019  0.031122821   -24.093311    69.395936   -11919.248   -2207.3023 
+     200         0.02  0.029045634    -24.88579    66.573223   -12211.306   -2207.9613 
+     210        0.021  0.027029857   -25.659817    63.791041   -12500.812   -2208.6115 
+     220        0.022  0.025077742   -26.415541    61.079413   -12787.018   -2209.2498 
+     230        0.023  0.023198048   -27.153652    58.469604   -13068.277   -2209.8722 
+     240        0.024   0.02140599   -27.875313    55.992687   -13343.621   -2210.4756 
+     250        0.025  0.019720922   -28.581973    53.678031    -13613.86   -2211.0588 
+     260        0.026  0.018162738   -29.275283    51.552191    -13882.15   -2211.6232 
+     270        0.027  0.016748514   -29.956802    49.638467   -14153.137   -2212.1718 
+     280        0.028   0.01549075   -30.628043    47.957071   -14432.246   -2212.7087 
+     290        0.029  0.014397611   -31.290177    46.525552   -14724.005   -2213.2371 
+     300         0.03  0.013474315   -31.943984    45.359085   -15031.315    -2213.759 
+     310        0.031  0.012723957   -32.589853     44.47023   -15355.595    -2214.275 
+     320        0.032  0.012146358   -33.227585    43.868153   -15696.845   -2214.7851 
+     330        0.033  0.011734827   -33.856656    43.557623   -16054.887    -2215.289 
+     340        0.034  0.011472508   -34.476313    43.538346    -16429.77   -2215.7871 
+     350        0.035  0.011330772   -35.085716    43.805034   -16821.627   -2216.2802 
+     360        0.036  0.011271169   -35.684147    44.348312    -17230.21   -2216.7687 
+     370        0.037   0.01125027   -36.271215    45.156046   -17654.485   -2217.2524 
+     380        0.038  0.011225354   -36.847053    46.214576   -18092.623   -2217.7301 
+     390        0.039  0.011159026   -37.412284    47.509345   -18542.156   -2218.2003 
+     400         0.04  0.011022073   -37.967916    49.024843   -19000.554   -2218.6614 
+     410        0.041   0.01079477   -38.515123    50.744046   -19465.713   -2219.1128 
+     420        0.042  0.010467095   -39.054921    52.647653   -19935.873   -2219.5544 
+     430        0.043  0.010038219   -39.588034    54.713405   -20409.666   -2219.9869 
+     440        0.044 0.0095155267   -40.114703    56.915658   -20885.556   -2220.4109 
+     450        0.045 0.0089134996   -40.634722    59.225397   -21361.621   -2220.8268 
+     460        0.046 0.0082528918   -41.147681    61.610799   -21835.762   -2221.2347 
+     470        0.047 0.0075606723   -41.653088    64.038349   -22305.687   -2221.6343 
+     480        0.048 0.0068707613   -42.150486    66.474377   -22768.948   -2222.0253 
+     490        0.049 0.0062249854   -42.639704    68.886721   -23223.418   -2222.4076 
+     500         0.05 0.0056723593   -43.120772     71.24617   -23667.077   -2222.7814 
+     510        0.051   0.00526312    -43.59404    73.527392   -24098.459    -2223.147 
+     520        0.052 0.0050342241   -44.059917    75.709206   -24516.163   -2223.5051 
+     530        0.053 0.0049906301   -44.518898    77.774314   -24919.192   -2223.8564 
+     540        0.054 0.0050976586   -44.971364    79.708763   -25306.611   -2224.2014 
+     550        0.055 0.0052941974   -45.417577    81.501347    -25677.67   -2224.5405 
+     560        0.056 0.0055157717   -45.857628    83.143173   -26031.673   -2224.8736 
+     570        0.057 0.0057113414   -46.291426    84.627457   -26367.904   -2225.2003 
+     580        0.058 0.0058493207   -46.718709    85.949497     -26685.6     -2225.52 
+     590        0.059 0.0059162201   -47.139052     87.10679   -26984.124   -2225.8316 
+     600         0.06 0.0059118584   -47.551892    88.099176   -27263.145   -2226.1347 
+     610        0.061  0.005843747   -47.956571    88.928929   -27522.773   -2226.4287 
+     620        0.062 0.0057222223   -48.352422    89.600763   -27763.549   -2226.7139 
+     630        0.063 0.0055570967   -48.738876     90.12173   -27986.321   -2226.9905 
+     640        0.064 0.0053558993   -49.115723    90.501081   -28192.238   -2227.2593 
+     650        0.065 0.0051233209   -49.483122    90.750056     -28382.3   -2227.5205 
+     660        0.066 0.0048614512   -49.841791    90.881635   -28557.623   -2227.7746 
+     670        0.067 0.0045706003   -50.192974    90.910245   -28719.422   -2228.0219 
+     680        0.068 0.0042506564   -50.538196    90.851397   -28868.809   -2228.2627 
+     690        0.069 0.0039028575   -50.879364    90.721317   -29007.619   -2228.4973 
+     700         0.07 0.0035319814   -51.218193    90.536521   -29137.623   -2228.7265 
+     710        0.071 0.0031491486   -51.556251    90.313501   -29261.193   -2228.9511 
+     720        0.072 0.0027758205   -51.894643    90.068503   -29380.924   -2229.1724 
+     730        0.073  0.002449449   -52.233987    89.817462   -29499.606   -2229.3917 
+     740        0.074 0.0022276613   -52.574465     89.57612   -29620.196   -2229.6103 
+     750        0.075 0.0021767124   -52.915641    89.360246   -29744.882    -2229.829 
+     760        0.076 0.0023310362   -53.256843    89.185838   -29875.573   -2230.0485 
+     770        0.077 0.0026637349   -53.597197    89.069228   -30013.477   -2230.2685 
+     780        0.078 0.0031129938    -53.93565    89.026943   -30158.812   -2230.4882 
+     790        0.079 0.0036204667   -54.271339    89.075322   -30311.602   -2230.7066 
+     800         0.08 0.0041448552   -54.603455    89.229912   -30471.244   -2230.9226 
+     810        0.081 0.0046613106   -54.931421    89.504766   -30636.938   -2231.1352 
+     820        0.082 0.0051580947   -55.255056    89.911726   -30808.087   -2231.3434 
+     830        0.083 0.0056329652   -55.574491    90.459766   -30984.153   -2231.5469 
+     840        0.084 0.0060893356   -55.890024    91.154456   -31164.372   -2231.7452 
+     850        0.085 0.0065324419   -56.202052    91.997528   -31347.792   -2231.9379 
+     860        0.086 0.0069661977   -56.511206    92.986622   -31533.977   -2232.1249 
+     870        0.087 0.0073913051   -56.817814    94.115192    -31721.92    -2232.306 
+     880        0.088 0.0078048547   -57.122061    95.372548   -31910.795   -2232.4809 
+     890        0.089  0.008201165   -57.423984    96.744135   -32100.108     -2232.65 
+     900         0.09 0.0085732702   -57.723377    98.212046   -32289.532   -2232.8136 
+     910        0.091 0.0089144724   -58.019938    99.755667   -32479.154   -2232.9728 
+     920        0.092 0.0092194916   -58.313266    101.35254   -32669.227   -2233.1285 
+     930        0.093 0.0094849872   -58.602956    102.97932   -32860.091   -2233.2822 
+     940        0.094 0.0097093572   -58.888668    104.61271   -33051.981   -2233.4348 
+     950        0.095 0.0098920175   -59.169925    106.23045   -33244.279   -2233.5871 
+     960        0.096   0.01003244    -59.44662    107.81212   -33436.562   -2233.7396 
+     970        0.097  0.010129313   -59.718668    109.33976   -33627.714   -2233.8925 
+     980        0.098  0.010180127   -59.986126    110.79823   -33816.218   -2234.0455 
+     990        0.099  0.010181304    -60.24929    112.17528   -34000.522   -2234.1984 
+    1000          0.1   0.01012881   -60.508632    113.46137   -34179.052   -2234.3508 
+Loop time of 4.82687 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 1.790 ns/day, 13.408 hours/ns, 207.173 timesteps/s
+97.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.1741     | 1.3056     | 1.4605     |  11.5 | 27.05
+Neigh   | 0.0042465  | 0.0048378  | 0.0051758  |   0.5 |  0.10
+Comm    | 0.31356    | 0.406      | 0.47906    |  11.6 |  8.41
+Output  | 0.0090122  | 0.0094153  | 0.010493   |   0.6 |  0.20
+Modify  | 3.0298     | 3.0936     | 3.1534     |   3.4 | 64.09
+Other   |            | 0.007349   |            |       |  0.15
+
+Nlocal:    125 ave 136 max 119 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+Nghost:    1324 ave 1331 max 1310 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Neighs:    6897.25 ave 7552 max 6604 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+FullNghs:  13794.5 ave 15117 max 13164 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 55178
+Ave neighs/atom = 110.356
+Neighbor list builds = 7
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut b/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut
index 34f7fea0d3..9c256338a2 100644
--- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut
+++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut
@@ -11,7 +11,7 @@ boundary 	p p p
 atom_modify 	map array 
 
 lattice 	bcc 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -56,4 +56,4 @@ thermo          50
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		100
diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald b/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald
index f694bc5ddc..560fcbb650 100644
--- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald
+++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald
@@ -11,7 +11,7 @@ boundary 	p p p
 atom_modify 	map array 
 
 lattice 	bcc 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -58,4 +58,4 @@ thermo          50
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		100
diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm b/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm
index 4175038ade..28d79e3d3e 100644
--- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm
+++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm
@@ -11,7 +11,7 @@ boundary 	p p p
 atom_modify 	map array 
 
 lattice 	bcc 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -59,4 +59,4 @@ thermo          50
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		100
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1
new file mode 100644
index 0000000000..9c4b9e6877
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1
@@ -0,0 +1,125 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00068903 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/cut 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff      * * spin/dipole/cut 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/cut, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 13.4 | 13.4 | 13.4 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 1.0737264e-35   -768.37511   -15560.055   -15515.394 
+      50        0.005           -1 -2.7722752e-10 -2.1828666e-10            1 6.8846921e-09   -768.35793   -15558.423   -15515.394 
+     100         0.01           -1 -2.0983066e-09 -1.7330951e-09            1 1.0038885e-08   -768.30868    -15553.81   -15515.394 
+Loop time of 9.81833 on 1 procs for 100 steps with 3456 atoms
+
+Performance: 0.088 ns/day, 272.731 hours/ns, 10.185 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.5684     | 4.5684     | 4.5684     |   0.0 | 46.53
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.022333   | 0.022333   | 0.022333   |   0.0 |  0.23
+Output  | 0.0062339  | 0.0062339  | 0.0062339  |   0.0 |  0.06
+Modify  | 5.2097     | 5.2097     | 5.2097     |   0.0 | 53.06
+Other   |            | 0.01171    |            |       |  0.12
+
+Nlocal:    3456 ave 3456 max 3456 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7289 ave 7289 max 7289 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    290304 ave 290304 max 290304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  580608 ave 580608 max 580608 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:09
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4
new file mode 100644
index 0000000000..6bd13bff4b
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4
@@ -0,0 +1,125 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00121498 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/cut 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff      * * spin/dipole/cut 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/cut, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.217 | 9.217 | 9.217 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 1.0737264e-35   -768.37511   -15560.055   -15515.394 
+      50        0.005           -1 9.6204015e-11 -3.3767807e-10            1 6.6905249e-09   -768.35767   -15558.438   -15515.394 
+     100         0.01           -1 7.8881609e-10 -2.7017321e-09            1 9.8111281e-09   -768.30769   -15553.868   -15515.394 
+Loop time of 4.21054 on 4 procs for 100 steps with 3456 atoms
+
+Performance: 0.205 ns/day, 116.959 hours/ns, 23.750 timesteps/s
+97.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.5515     | 1.5909     | 1.6287     |   2.8 | 37.78
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.1219     | 0.15371    | 0.18852    |   8.1 |  3.65
+Output  | 0.0032659  | 0.0032846  | 0.0033138  |   0.0 |  0.08
+Modify  | 2.4491     | 2.4549     | 2.4589     |   0.3 | 58.30
+Other   |            | 0.007701   |            |       |  0.18
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    3785 ave 3785 max 3785 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    72576 ave 72576 max 72576 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  145152 ave 145152 max 145152 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1
new file mode 100644
index 0000000000..9bd3b04a06
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1
@@ -0,0 +1,135 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.000730038 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/long 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff	* * spin/dipole/long 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+kspace_style 	ewald/dipole/spin 1.0e-4
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+EwaldDipoleSpin initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.324623
+  estimated absolute RMS force accuracy = 9.55526e-84
+  estimated relative force accuracy = 6.63576e-85
+  KSpace vectors: actual max1d max3d = 2084 10 4630
+                  kxmax kymax kzmax  = 10 10 10
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/long, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 30.07 | 30.07 | 30.07 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 2.5872886e-37   -767.88567   -15559.577   -15514.916 
+      50        0.005           -1 4.3660916e-09 -2.1918692e-09            1 5.3480999e-10   -767.86847   -15557.945   -15514.916 
+     100         0.01           -1 9.9854966e-09 -4.2823677e-09            1 2.3267629e-09   -767.81917   -15553.332   -15514.916 
+Loop time of 30.1001 on 1 procs for 100 steps with 3456 atoms
+
+Performance: 0.029 ns/day, 836.115 hours/ns, 3.322 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.6659     | 5.6659     | 5.6659     |   0.0 | 18.82
+Kspace  | 12.686     | 12.686     | 12.686     |   0.0 | 42.14
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.022781   | 0.022781   | 0.022781   |   0.0 |  0.08
+Output  | 0.00965    | 0.00965    | 0.00965    |   0.0 |  0.03
+Modify  | 11.705     | 11.705     | 11.705     |   0.0 | 38.89
+Other   |            | 0.01108    |            |       |  0.04
+
+Nlocal:    3456 ave 3456 max 3456 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7289 ave 7289 max 7289 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    290304 ave 290304 max 290304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  580608 ave 580608 max 580608 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:30
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4
new file mode 100644
index 0000000000..4989210d1d
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4
@@ -0,0 +1,135 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00238299 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/long 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff	* * spin/dipole/long 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+kspace_style 	ewald/dipole/spin 1.0e-4
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+EwaldDipoleSpin initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.324623
+  estimated absolute RMS force accuracy = 9.29828e-84
+  estimated relative force accuracy = 6.4573e-85
+  KSpace vectors: actual max1d max3d = 2084 10 4630
+                  kxmax kymax kzmax  = 10 10 10
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/long, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 25.89 | 25.89 | 25.89 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 3.5107565e-37   -767.88567   -15559.577   -15514.916 
+      50        0.005           -1 4.3196063e-09 -2.1966927e-09            1 5.1719577e-10   -767.86822    -15557.96   -15514.916 
+     100         0.01           -1 9.7636593e-09 -4.3236953e-09            1 2.2443181e-09   -767.81819    -15553.39   -15514.916 
+Loop time of 11.709 on 4 procs for 100 steps with 3456 atoms
+
+Performance: 0.074 ns/day, 325.251 hours/ns, 8.540 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.7524     | 1.9105     | 2.0593     |   9.8 | 16.32
+Kspace  | 4.1375     | 4.4309     | 4.7029     |  12.3 | 37.84
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.063121   | 0.47268    | 0.94431    |  59.7 |  4.04
+Output  | 0.0032601  | 0.0033116  | 0.0033839  |   0.1 |  0.03
+Modify  | 4.8621     | 4.8828     | 4.9008     |   0.8 | 41.70
+Other   |            | 0.008918   |            |       |  0.08
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    3785 ave 3785 max 3785 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    72576 ave 72576 max 72576 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  145152 ave 145152 max 145152 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:11
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1
new file mode 100644
index 0000000000..5984976c8d
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1
@@ -0,0 +1,137 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.000930071 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/long 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff	* * spin/dipole/long 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+kspace_style 	pppm/dipole/spin 1.0e-4
+kspace_modify 	compute yes
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+PPPMDipoleSpin initialization ...
+  G vector (1/distance) = 0.329367
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00175808
+  estimated relative force accuracy = 0.000122092
+  using double precision FFTs
+  3d grid and FFT values/proc = 15625 8000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/long, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 16.27 | 16.27 | 16.27 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 3.7996771e-37   -767.89759    -15559.59   -15514.929 
+      50        0.005           -1 3.6585337e-09 -1.9445403e-09            1 5.1405121e-10   -767.88039   -15557.958   -15514.929 
+     100         0.01           -1 7.3585728e-09 -3.8640878e-09            1 2.0194927e-09   -767.83109   -15553.345   -15514.929 
+Loop time of 18.493 on 1 procs for 100 steps with 3456 atoms
+
+Performance: 0.047 ns/day, 513.694 hours/ns, 5.407 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.7715     | 5.7715     | 5.7715     |   0.0 | 31.21
+Kspace  | 0.82553    | 0.82553    | 0.82553    |   0.0 |  4.46
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.022319   | 0.022319   | 0.022319   |   0.0 |  0.12
+Output  | 0.0066397  | 0.0066397  | 0.0066397  |   0.0 |  0.04
+Modify  | 11.857     | 11.857     | 11.857     |   0.0 | 64.12
+Other   |            | 0.009629   |            |       |  0.05
+
+Nlocal:    3456 ave 3456 max 3456 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7289 ave 7289 max 7289 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    290304 ave 290304 max 290304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  580608 ave 580608 max 580608 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:19
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4
new file mode 100644
index 0000000000..154e39958d
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4
@@ -0,0 +1,137 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00089097 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/long 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff	* * spin/dipole/long 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+kspace_style 	pppm/dipole/spin 1.0e-4
+kspace_modify 	compute yes
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+PPPMDipoleSpin initialization ...
+  G vector (1/distance) = 0.329367
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00175808
+  estimated relative force accuracy = 0.000122092
+  using double precision FFTs
+  3d grid and FFT values/proc = 5625 2000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/long, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 10.42 | 10.42 | 10.42 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 2.3173191e-37   -767.89759    -15559.59   -15514.929 
+      50        0.005           -1 3.6593054e-09 -1.9379563e-09            1 4.9747018e-10   -767.88014   -15557.972   -15514.929 
+     100         0.01           -1 7.3731919e-09 -3.8151563e-09            1 1.9544299e-09    -767.8301   -15553.402   -15514.929 
+Loop time of 6.23322 on 4 procs for 100 steps with 3456 atoms
+
+Performance: 0.139 ns/day, 173.145 hours/ns, 16.043 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.6633     | 1.6906     | 1.7152     |   1.4 | 27.12
+Kspace  | 0.38875    | 0.41372    | 0.44184    |   3.0 |  6.64
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.05118    | 0.053267   | 0.054998   |   0.6 |  0.85
+Output  | 0.0070119  | 0.0070257  | 0.0070462  |   0.0 |  0.11
+Modify  | 4.0616     | 4.0629     | 4.0646     |   0.1 | 65.18
+Other   |            | 0.005713   |            |       |  0.09
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    3785 ave 3785 max 3785 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    72576 ave 72576 max 72576 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  145152 ave 145152 max 145152 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:06
diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron
index 93485ee076..d60e6b86f5 100644
--- a/examples/SPIN/iron/in.spin.iron
+++ b/examples/SPIN/iron/in.spin.iron
@@ -19,8 +19,8 @@ create_atoms 	1 box
 
 mass		1 55.845
 
-#set 		group all spin/random 31 2.2
-set 		group all spin 2.2 0.0 0.0 1.0
+set 		group all spin/random 31 2.2
+# set 		group all spin 2.2 0.0 0.0 1.0
 velocity 	all create 100 4928459 rot yes dist gaussian
 
 pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
@@ -54,4 +54,4 @@ thermo          50
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		50000
+run 		1000
diff --git a/examples/SPIN/iron/in.spin.iron_cubic b/examples/SPIN/iron/in.spin.iron_cubic
index 349a6de3a0..30a3e0e97c 100644
--- a/examples/SPIN/iron/in.spin.iron_cubic
+++ b/examples/SPIN/iron/in.spin.iron_cubic
@@ -54,7 +54,7 @@ thermo          50
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		1000
 # min_style 	spin
 # min_modify	alpha_damp 1.0 discrete_factor 10
 # minimize 	1.0e-16 1.0e-16 10000 10000
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1 b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1
new file mode 100644
index 0000000000..cee42d433b
--- /dev/null
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1
@@ -0,0 +1,136 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.000509977 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+
+set 		group all spin/random 31 2.2
+  250 settings made for spin/random
+# set 		group all spin 2.2 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe press etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.77337
+  ghost atom cutoff = 5.77337
+  binsize = 2.88668, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.82 | 7.82 | 7.82 Mbytes
+Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng Press TotEng 
+       0            0  0.076456975    4554.5462    100.00358  -0.85791269    3.2186929   -1070.8579    394.43342   -1067.6392 
+      50        0.005  0.076456974     4658.383    96.663685  -0.86504718    3.1111957   -1070.7504    709.50826   -1067.6392 
+     100         0.01  0.076456983    4744.1872    86.965803  -0.88035771    2.7990619   -1070.4383    1466.6938   -1067.6392 
+     150        0.015  0.076456973    4794.5283    72.421197   -0.8996913    2.3309324   -1069.9702    2534.3867   -1067.6392 
+     200         0.02  0.076456944    4707.6548    55.633188    -0.921682    1.7905973   -1069.4298     3732.183   -1067.6392 
+     250        0.025  0.076456953    4439.4697    39.802206  -0.94649004    1.2810649   -1068.9203    4831.5559   -1067.6392 
+     300         0.03  0.076457027    4101.6694    27.882295  -0.97253854    0.8974133   -1068.5366    5612.0928   -1067.6392 
+     350        0.035  0.076457103    3860.1545    21.776538  -0.99708692   0.70089477   -1068.3401    5906.3057   -1067.6392 
+     400         0.04  0.076457117    3765.5341    21.857102   -1.0190244   0.70348778   -1068.3427    5682.0053   -1067.6392 
+     450        0.045  0.076457072    3739.9037    26.959407   -1.0389343   0.86770942   -1068.5069    5066.5077   -1067.6392 
+     500         0.05  0.076457001    3730.8342     34.92521   -1.0582008     1.124095   -1068.7633    4279.2424   -1067.6392 
+     550        0.055  0.076456962    3698.0556    43.405912   -1.0785156     1.397053   -1069.0363    3533.4153   -1067.6392 
+     600         0.06  0.076456997     3560.947    50.544844    -1.102048     1.626825   -1069.2661    2975.8479   -1067.6392 
+     650        0.065  0.076457079    3341.7402    55.261218   -1.1296588    1.7786252   -1069.4179    2683.3023   -1067.6392 
+     700         0.07  0.076457136    3156.8448     57.25083   -1.1595102    1.8426624   -1069.4819    2640.5967   -1067.6392 
+     750        0.075  0.076457132    3099.5181    56.934336   -1.1893875    1.8324758   -1069.4717    2778.3261   -1067.6392 
+     800         0.08  0.076457116    3132.9985    55.266343   -1.2181223    1.7787901    -1069.418    3020.1175   -1067.6392 
+     850        0.085  0.076457116    3163.2943    53.376453   -1.2443326    1.7179626   -1069.3572    3287.9042   -1067.6392 
+     900         0.09  0.076457121     3168.063    52.279557   -1.2676425    1.6826581   -1069.3219    3504.7334   -1067.6392 
+     950        0.095  0.076457122    3144.2102    52.667743   -1.2902335    1.6951522   -1069.3344    3622.1382   -1067.6392 
+    1000          0.1  0.076457135    3061.0811    54.684094    -1.314147      1.76005   -1069.3993    3625.2935   -1067.6392 
+Loop time of 2.06841 on 1 procs for 1000 steps with 250 atoms
+
+Performance: 4.177 ns/day, 5.746 hours/ns, 483.464 timesteps/s
+99.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.96898    | 0.96898    | 0.96898    |   0.0 | 46.85
+Neigh   | 0.005435   | 0.005435   | 0.005435   |   0.0 |  0.26
+Comm    | 0.028027   | 0.028027   | 0.028027   |   0.0 |  1.36
+Output  | 0.0051067  | 0.0051067  | 0.0051067  |   0.0 |  0.25
+Modify  | 1.0569     | 1.0569     | 1.0569     |   0.0 | 51.10
+Other   |            | 0.003989   |            |       |  0.19
+
+Nlocal:    250 ave 250 max 250 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1399 ave 1399 max 1399 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    7855 ave 7855 max 7855 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  15710 ave 15710 max 15710 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15710
+Ave neighs/atom = 62.84
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4 b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4
new file mode 100644
index 0000000000..63ddc9d4fe
--- /dev/null
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4
@@ -0,0 +1,136 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.000626087 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+
+set 		group all spin/random 31 2.2
+  250 settings made for spin/random
+# set 		group all spin 2.2 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe press etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.77337
+  ghost atom cutoff = 5.77337
+  binsize = 2.88668, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.766 | 7.766 | 7.766 Mbytes
+Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng Press TotEng 
+       0            0  0.076456975    4554.5462    100.00358  -0.85791269    3.2186929   -1070.8579    394.43342   -1067.6392 
+      50        0.005  0.076456995    4701.2004    96.298333  -0.85659448    3.0994366   -1070.7387    714.37866   -1067.6392 
+     100         0.01  0.076457028    4794.5923    86.330828  -0.87003341    2.7786247   -1070.4179    1484.2951   -1067.6392 
+     150        0.015  0.076457074    4836.9634    71.603402  -0.89006992    2.3046111   -1069.9438    2551.9258   -1067.6392 
+     200         0.02  0.076457106    4754.5574    54.648817  -0.91124541    1.7589146   -1069.3981    3731.1494   -1067.6392 
+     250        0.025  0.076457128     4502.135    38.599515  -0.93187522    1.2423553   -1068.8816     4804.619   -1067.6392 
+     300         0.03  0.076457157    4176.7186    26.383018  -0.95082226    0.8491579   -1068.4884    5563.3287   -1067.6392 
+     350        0.035  0.076457207    3955.5658     20.01039  -0.96826468   0.64404992   -1068.2833    5839.6479   -1067.6392 
+     400         0.04  0.076457243    3887.9746    20.097682  -0.98706373   0.64685949   -1068.2861    5601.1255   -1067.6392 
+     450        0.045  0.076457231    3868.5613    25.687511   -1.0095684   0.82677249    -1068.466    4974.0031   -1067.6392 
+     500         0.05  0.076457204    3838.4905    34.604697   -1.0349855     1.113779    -1068.753    4157.1837   -1067.6392 
+     550        0.055  0.076457196    3775.1404    44.251809   -1.0609123    1.4242788   -1069.0635       3357.1   -1067.6392 
+     600         0.06  0.076457188    3604.8828    52.475202   -1.0880854    1.6889551   -1069.3282    2752.0424   -1067.6392 
+     650        0.065   0.07645718    3345.5894    57.926479   -1.1179657    1.8644087   -1069.5036    2467.7403   -1067.6392 
+     700         0.07  0.076457185    3138.2001    60.030548   -1.1469999    1.9321298   -1069.5714    2510.1752   -1067.6392 
+     750        0.075   0.07645719    3074.9626    59.122504   -1.1721939    1.9029037   -1069.5421    2788.7489   -1067.6392 
+     800         0.08  0.076457195    3103.5294    56.349146   -1.1949365     1.813641   -1069.4529    3192.5158   -1067.6392 
+     850        0.085  0.076457199    3164.2317    53.154464   -1.2164642    1.7108177     -1069.35     3602.931   -1067.6392 
+     900         0.09  0.076457199    3228.1358    50.837416   -1.2366018    1.6362417   -1069.2755    3917.0758   -1067.6392 
+     950        0.095  0.076457222    3247.5532    50.234549   -1.2539657    1.6168379   -1069.2561    4059.9275   -1067.6392 
+    1000          0.1  0.076457266    3208.3875    51.592727   -1.2671834    1.6605519   -1069.2998    4001.4995   -1067.6392 
+Loop time of 2.27244 on 4 procs for 1000 steps with 250 atoms
+
+Performance: 3.802 ns/day, 6.312 hours/ns, 440.055 timesteps/s
+97.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.33296    | 0.37066    | 0.40364    |   4.3 | 16.31
+Neigh   | 0.0013368  | 0.0025837  | 0.0056586  |   3.5 |  0.11
+Comm    | 0.12627    | 0.16094    | 0.20183    |   7.1 |  7.08
+Output  | 0.0033641  | 0.003438   | 0.0036473  |   0.2 |  0.15
+Modify  | 1.7249     | 1.7261     | 1.7272     |   0.1 | 75.96
+Other   |            | 0.008682   |            |       |  0.38
+
+Nlocal:    62.5 ave 66 max 60 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost:    844 ave 857 max 829 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs:    1962.5 ave 2096 max 1855 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+FullNghs:  3925 ave 4139 max 3766 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 15700
+Ave neighs/atom = 62.8
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1 b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1
similarity index 59%
rename from examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1
rename to examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1
index ee1e71131e..26fdfb0004 100644
--- a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1
@@ -1,9 +1,7 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
+LAMMPS (30 Oct 2019)
 # bcc iron in a 3d periodic box
 
 clear
-  using 1 OpenMP thread(s) per MPI task
 units 		metal
 atom_style 	spin
 
@@ -21,7 +19,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.0527296 secs
+  create_atoms CPU = 0.000481129 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -40,7 +38,7 @@ fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -61,9 +59,9 @@ thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		1000
 Neighbor list info ...
   update every 10 steps, delay 20 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -81,7 +79,7 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.82 | 7.82 | 7.82 Mbytes
 Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
        0            0           -1            0            0            1            0    -55.58269   -1125.5827    -1122.364 
       50        0.005           -1            0            0            1            0   -55.581417   -1125.4672    -1122.364 
@@ -104,53 +102,33 @@ Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng
      900         0.09           -1            0            0            1            0    -55.55913   -1123.8714    -1122.364 
      950        0.095           -1            0            0            1            0   -55.560111   -1123.8726    -1122.364 
     1000          0.1           -1            0            0            1            0   -55.560705   -1123.9215    -1122.364 
-    1050        0.105           -1            0            0            1            0   -55.560979   -1124.0049    -1122.364 
-    1100         0.11           -1            0            0            1            0   -55.561005   -1124.0998    -1122.364 
-    1150        0.115           -1            0            0            1            0   -55.560847   -1124.1802    -1122.364 
-    1200         0.12           -1            0            0            1            0   -55.560562   -1124.2247    -1122.364 
-    1250        0.125           -1            0            0            1            0   -55.560199   -1124.2224    -1122.364 
-    1300         0.13           -1            0            0            1            0   -55.559804   -1124.1752    -1122.364 
-    1350        0.135           -1            0            0            1            0   -55.559416   -1124.0977    -1122.364 
-    1400         0.14           -1            0            0            1            0   -55.559073   -1124.0124    -1122.364 
-    1450        0.145           -1            0            0            1            0   -55.558803   -1123.9437    -1122.364 
-    1500         0.15           -1            0            0            1            0   -55.558617   -1123.9107    -1122.364 
-    1550        0.155           -1            0            0            1            0   -55.558503   -1123.9224    -1122.364 
-    1600         0.16           -1            0            0            1            0   -55.558425   -1123.9749    -1122.364 
-    1650        0.165           -1            0            0            1            0   -55.558323   -1124.0529    -1122.364 
-    1700         0.17           -1            0            0            1            0   -55.558122   -1124.1331    -1122.364 
-    1750        0.175           -1            0            0            1            0   -55.557751   -1124.1899    -1122.364 
-    1800         0.18           -1            0            0            1            0   -55.557157   -1124.2023    -1122.364 
-    1850        0.185           -1            0            0            1            0   -55.556326   -1124.1592    -1122.364 
-    1900         0.19           -1            0            0            1            0   -55.555301   -1124.0633    -1122.364 
-    1950        0.195           -1            0            0            1            0   -55.554178   -1123.9313    -1122.364 
-    2000          0.2           -1            0            0            1            0   -55.553099   -1123.7904    -1122.364 
-Loop time of 254.052 on 1 procs for 2000 steps with 250 atoms
+Loop time of 1.95614 on 1 procs for 1000 steps with 250 atoms
 
-Performance: 0.068 ns/day, 352.850 hours/ns, 7.872 timesteps/s
-99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 4.417 ns/day, 5.434 hours/ns, 511.211 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 60.584     | 60.584     | 60.584     |   0.0 | 23.85
-Neigh   | 0.34793    | 0.34793    | 0.34793    |   0.0 |  0.14
-Comm    | 1.9994     | 1.9994     | 1.9994     |   0.0 |  0.79
-Output  | 126.24     | 126.24     | 126.24     |   0.0 | 49.69
-Modify  | 64.475     | 64.475     | 64.475     |   0.0 | 25.38
-Other   |            | 0.4024     |            |       |  0.16
+Pair    | 0.90008    | 0.90008    | 0.90008    |   0.0 | 46.01
+Neigh   | 0.005214   | 0.005214   | 0.005214   |   0.0 |  0.27
+Comm    | 0.026026   | 0.026026   | 0.026026   |   0.0 |  1.33
+Output  | 0.0045307  | 0.0045307  | 0.0045307  |   0.0 |  0.23
+Modify  | 1.0168     | 1.0168     | 1.0168     |   0.0 | 51.98
+Other   |            | 0.003449   |            |       |  0.18
 
 Nlocal:    250 ave 250 max 250 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1419 ave 1419 max 1419 min
+Nghost:    1415 ave 1415 max 1415 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    7878 ave 7878 max 7878 min
+Neighs:    7873 ave 7873 max 7873 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  15756 ave 15756 max 15756 min
+FullNghs:  15746 ave 15746 max 15746 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 15756
-Ave neighs/atom = 63.024
-Neighbor list builds = 12
+Total # of neighbors = 15746
+Ave neighs/atom = 62.984
+Neighbor list builds = 6
 Dangerous builds = 0
 # min_style 	spin
 # min_modify	alpha_damp 1.0 discrete_factor 10
@@ -158,4 +136,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:04:16
+Total wall time: 0:00:01
diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4 b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
similarity index 58%
rename from examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4
rename to examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
index 677805d26a..2c911cb9bb 100644
--- a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
@@ -1,9 +1,7 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
+LAMMPS (30 Oct 2019)
 # bcc iron in a 3d periodic box
 
 clear
-  using 1 OpenMP thread(s) per MPI task
 units 		metal
 atom_style 	spin
 
@@ -21,7 +19,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.000627756 secs
+  create_atoms CPU = 0.000656843 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -40,7 +38,7 @@ fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -61,9 +59,9 @@ thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		1000
 Neighbor list info ...
   update every 10 steps, delay 20 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -81,7 +79,7 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.766 | 7.766 | 7.766 Mbytes
 Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
        0            0           -1            0            0            1            0    -55.58269   -1125.5827    -1122.364 
       50        0.005           -1            0            0            1            0   -55.581457   -1125.4635    -1122.364 
@@ -104,53 +102,33 @@ Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng
      900         0.09           -1            0            0            1            0   -55.560147   -1123.8404    -1122.364 
      950        0.095           -1            0            0            1            0   -55.560992   -1123.8312    -1122.364 
     1000          0.1           -1            0            0            1            0   -55.561635   -1123.8853    -1122.364 
-    1050        0.105           -1            0            0            1            0   -55.562156   -1123.9898    -1122.364 
-    1100         0.11           -1            0            0            1            0   -55.562594   -1124.1174    -1122.364 
-    1150        0.115           -1            0            0            1            0   -55.562944   -1124.2349    -1122.364 
-    1200         0.12           -1            0            0            1            0   -55.563163   -1124.3115    -1122.364 
-    1250        0.125           -1            0            0            1            0   -55.563193   -1124.3273    -1122.364 
-    1300         0.13           -1            0            0            1            0   -55.562982   -1124.2776    -1122.364 
-    1350        0.135           -1            0            0            1            0   -55.562513   -1124.1744    -1122.364 
-    1400         0.14           -1            0            0            1            0   -55.561812   -1124.0433    -1122.364 
-    1450        0.145           -1            0            0            1            0   -55.560956   -1123.9169    -1122.364 
-    1500         0.15           -1            0            0            1            0   -55.560057   -1123.8268    -1122.364 
-    1550        0.155           -1            0            0            1            0   -55.559235   -1123.7951    -1122.364 
-    1600         0.16           -1            0            0            1            0    -55.55859   -1123.8282    -1122.364 
-    1650        0.165           -1            0            0            1            0   -55.558174   -1123.9155    -1122.364 
-    1700         0.17           -1            0            0            1            0   -55.557974   -1124.0311    -1122.364 
-    1750        0.175           -1            0            0            1            0   -55.557913   -1124.1409    -1122.364 
-    1800         0.18           -1            0            0            1            0    -55.55788    -1124.212    -1122.364 
-    1850        0.185           -1            0            0            1            0   -55.557753   -1124.2208    -1122.364 
-    1900         0.19           -1            0            0            1            0   -55.557448   -1124.1596    -1122.364 
-    1950        0.195           -1            0            0            1            0   -55.556942   -1124.0384    -1122.364 
-    2000          0.2           -1            0            0            1            0   -55.556288    -1123.883    -1122.364 
-Loop time of 4.39485 on 4 procs for 2000 steps with 250 atoms
+Loop time of 2.38457 on 4 procs for 1000 steps with 250 atoms
 
-Performance: 3.932 ns/day, 6.104 hours/ns, 455.078 timesteps/s
-98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 3.623 ns/day, 6.624 hours/ns, 419.362 timesteps/s
+97.2% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.64527    | 0.6695     | 0.71114    |   3.3 | 15.23
-Neigh   | 0.0032711  | 0.0034365  | 0.0036387  |   0.3 |  0.08
-Comm    | 0.14872    | 0.19108    | 0.21485    |   6.1 |  4.35
-Output  | 0.40622    | 0.43119    | 0.45149    |   2.5 |  9.81
-Modify  | 3.0688     | 3.0921     | 3.1179     |   1.0 | 70.36
-Other   |            | 0.007548   |            |       |  0.17
+Pair    | 0.32773    | 0.36909    | 0.41504    |   6.0 | 15.48
+Neigh   | 0.0014782  | 0.0015869  | 0.001724   |   0.2 |  0.07
+Comm    | 0.14716    | 0.19316    | 0.23754    |   8.4 |  8.10
+Output  | 0.0030437  | 0.0032653  | 0.0035224  |   0.3 |  0.14
+Modify  | 1.8109     | 1.8139     | 1.8175     |   0.2 | 76.07
+Other   |            | 0.003611   |            |       |  0.15
 
-Nlocal:    62.5 ave 67 max 57 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost:    850.5 ave 856 max 847 min
-Histogram: 1 0 1 1 0 0 0 0 0 1
-Neighs:    1968.75 ave 2101 max 1792 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-FullNghs:  3937.5 ave 4217 max 3583 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
+Nlocal:    62.5 ave 66 max 60 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost:    848.25 ave 861 max 834 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    1962.75 ave 2087 max 1870 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+FullNghs:  3925.5 ave 4138 max 3776 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
 
-Total # of neighbors = 15750
-Ave neighs/atom = 63
-Neighbor list builds = 12
+Total # of neighbors = 15702
+Ave neighs/atom = 62.808
+Neighbor list builds = 6
 Dangerous builds = 0
 # min_style 	spin
 # min_modify	alpha_damp 1.0 discrete_factor 10
@@ -158,4 +136,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:04
+Total wall time: 0:00:02
diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1 b/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1
deleted file mode 100644
index f02c43e28c..0000000000
--- a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1
+++ /dev/null
@@ -1,1117 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# bcc iron in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	bcc 2.8665
-Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 250 atoms
-  create_atoms CPU = 0.00074935 secs
-
-# setting mass, mag. moments, and interactions for bcc iron
-
-mass		1 55.845
-
-set 		group all spin/random 31 2.2
-  250 settings made for spin/random
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
-pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
-pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		50000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.77337
-  ghost atom cutoff = 5.77337
-  binsize = 2.88668, bins = 5 5 5
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes
-Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng 
-       0            0  0.076456975    9109.0924    100.00358  -0.85791269    3.2186929   -1070.8579   -1067.6392 
-      50        0.005  0.076456974    9316.7659    96.663685  -0.86504718    3.1111957   -1070.7504   -1067.6392 
-     100         0.01  0.076456983    9488.3743    86.965803  -0.88035771    2.7990619   -1070.4383   -1067.6392 
-     150        0.015  0.076456973    9589.0566    72.421197   -0.8996913    2.3309324   -1069.9702   -1067.6392 
-     200         0.02  0.076456944    9415.3095    55.633188    -0.921682    1.7905973   -1069.4298   -1067.6392 
-     250        0.025  0.076456953    8878.9394    39.802206  -0.94649004    1.2810649   -1068.9203   -1067.6392 
-     300         0.03  0.076457027    8203.3388    27.882295  -0.97253854    0.8974133   -1068.5366   -1067.6392 
-     350        0.035  0.076457103     7720.309    21.776538  -0.99708692   0.70089477   -1068.3401   -1067.6392 
-     400         0.04  0.076457117    7531.0683    21.857102   -1.0190244   0.70348778   -1068.3427   -1067.6392 
-     450        0.045  0.076457072    7479.8073    26.959407   -1.0389343   0.86770942   -1068.5069   -1067.6392 
-     500         0.05  0.076457001    7461.6683     34.92521   -1.0582008     1.124095   -1068.7633   -1067.6392 
-     550        0.055  0.076456962    7396.1112    43.405912   -1.0785156     1.397053   -1069.0363   -1067.6392 
-     600         0.06  0.076456997     7121.894    50.544844    -1.102048     1.626825   -1069.2661   -1067.6392 
-     650        0.065  0.076457079    6683.4805    55.261218   -1.1296588    1.7786252   -1069.4179   -1067.6392 
-     700         0.07  0.076457136    6313.6896     57.25083   -1.1595102    1.8426624   -1069.4819   -1067.6392 
-     750        0.075  0.076457132    6199.0363    56.934336   -1.1893875    1.8324758   -1069.4717   -1067.6392 
-     800         0.08  0.076457116     6265.997    55.266343   -1.2181223    1.7787901    -1069.418   -1067.6392 
-     850        0.085  0.076457116    6326.5886    53.376453   -1.2443326    1.7179626   -1069.3572   -1067.6392 
-     900         0.09  0.076457121    6336.1261    52.279557   -1.2676425    1.6826581   -1069.3219   -1067.6392 
-     950        0.095  0.076457122    6288.4204    52.667743   -1.2902335    1.6951522   -1069.3344   -1067.6392 
-    1000          0.1  0.076457135    6122.1622    54.684094    -1.314147      1.76005   -1069.3993   -1067.6392 
-    1050        0.105  0.076457155    5830.2219    57.880399   -1.3392396    1.8629256   -1069.5022   -1067.6392 
-    1100         0.11  0.076457162    5477.4214    61.505616   -1.3662331     1.979606   -1069.6188   -1067.6392 
-    1150        0.115  0.076457195    5194.1423    64.810972   -1.3984474    2.0859914   -1069.7252   -1067.6392 
-    1200         0.12  0.076457219    5096.2484    67.147472    -1.438326    2.1611935   -1069.8004   -1067.6392 
-    1250        0.125  0.076457214    5180.7444    67.957533   -1.4822383    2.1872659   -1069.8265   -1067.6392 
-    1300         0.13  0.076457208    5332.4483     66.96652   -1.5226303    2.1553694   -1069.7946   -1067.6392 
-    1350        0.135  0.076457225    5441.1287    64.471602   -1.5553539    2.0750686   -1069.7143   -1067.6392 
-    1400         0.14  0.076457244    5466.8622    61.292592   -1.5804721    1.9727496    -1069.612   -1067.6392 
-    1450        0.145   0.07645724     5403.309    58.518161   -1.6006864    1.8834524   -1069.5227   -1067.6392 
-    1500         0.15  0.076457224    5275.2171      57.1713   -1.6196756    1.8401027   -1069.4793   -1067.6392 
-    1550        0.155  0.076457217    5122.7481    57.878063   -1.6407322    1.8628504   -1069.5021   -1067.6392 
-    1600         0.16  0.076457217    4968.5049    60.639452   -1.6657935    1.9517278    -1069.591   -1067.6392 
-    1650        0.165  0.076457208    4850.1861    64.668839    -1.690847    2.0814168   -1069.7206   -1067.6392 
-    1700         0.17  0.076457217    4809.0194    68.693586   -1.7087416    2.2109564   -1069.8502   -1067.6392 
-    1750        0.175  0.076457274    4835.8611    71.611033   -1.7188587    2.3048567   -1069.9441   -1067.6392 
-    1800         0.18  0.076457318    4929.7428    72.815077   -1.7280248    2.3436098   -1069.9828   -1067.6392 
-    1850        0.185  0.076457279    5036.6365    72.102335   -1.7426092    2.3206696   -1069.9599   -1067.6392 
-    1900         0.19  0.076457222    5116.2436    69.579977   -1.7638235    2.2394856   -1069.8787   -1067.6392 
-    1950        0.195  0.076457228    5207.2334    65.715745   -1.7895824    2.1151122   -1069.7543   -1067.6392 
-    2000          0.2  0.076457288    5216.0413    61.340972   -1.8174915    1.9743068   -1069.6135   -1067.6392 
-    2050        0.205  0.076457267    5023.1601    57.468628   -1.8456914    1.8496724   -1069.4889   -1067.6392 
-    2100         0.21  0.076457198    4748.7818    55.033266   -1.8742291    1.7712884   -1069.4105   -1067.6392 
-    2150        0.215  0.076457199    4558.1302    54.573806   -1.9035225    1.7565003   -1069.3957   -1067.6392 
-    2200         0.22  0.076457185    4483.1644    56.074241   -1.9322669     1.804793    -1069.444   -1067.6392 
-    2250        0.225  0.076457114    4430.1583      59.0552   -1.9577399    1.9007374     -1069.54   -1067.6392 
-    2300         0.23  0.076457092    4353.7973    62.874849   -1.9801275    2.0236758   -1069.6629   -1067.6392 
-    2350        0.235  0.076457145    4303.5275    66.892738   -2.0022129    2.1529947   -1069.7922   -1067.6392 
-    2400         0.24  0.076457171    4258.6889    70.426826   -2.0233072    2.2667421    -1069.906   -1067.6392 
-    2450        0.245  0.076457169    4178.5775    72.910422   -2.0405304    2.3466785   -1069.9859   -1067.6392 
-    2500         0.25   0.07645717     4114.786    74.106367   -2.0531755    2.3851709   -1070.0244   -1067.6392 
-    2550        0.255  0.076457136    4067.5017    74.169349   -2.0634674    2.3871981   -1070.0264   -1067.6392 
-    2600         0.26  0.076457099    4045.3324    73.586199   -2.0755814    2.3684289   -1070.0077   -1067.6392 
-    2650        0.265  0.076457099     4137.898    72.914235   -2.0913646    2.3468012    -1069.986   -1067.6392 
-    2700         0.27  0.076457106     4332.063    72.583192   -2.1091075    2.3361464   -1069.9754   -1067.6392 
-    2750        0.275   0.07645709    4465.1953    72.814559    -2.125099    2.3435931   -1069.9828   -1067.6392 
-    2800         0.28  0.076457051    4516.5192    73.652154   -2.1371914    2.3705517   -1070.0098   -1067.6392 
-    2850        0.285  0.076457019    4555.5962    75.060211   -2.1489378    2.4158711   -1070.0551   -1067.6392 
-    2900         0.29  0.076457069    4544.2734    76.844795   -2.1667679    2.4733094   -1070.1125   -1067.6392 
-    2950        0.295  0.076457172    4460.2109     78.48171   -2.1924421    2.5259948   -1070.1652   -1067.6392 
-    3000          0.3  0.076457219    4323.2746     79.20682   -2.2209955     2.549333   -1070.1886   -1067.6392 
-    3050        0.305  0.076457213     4155.688    78.543529   -2.2505299    2.5279844   -1070.1672   -1067.6392 
-    3100         0.31  0.076457203    3969.6188    76.554785   -2.2858382    2.4639752   -1070.1032   -1067.6392 
-    3150        0.315  0.076457187     3761.432    73.396149   -2.3245055     2.362312   -1070.0015   -1067.6392 
-    3200         0.32  0.076457142    3602.8035    69.313196   -2.3577056     2.230899   -1069.8701   -1067.6392 
-    3250        0.325  0.076457116     3505.707    65.032482   -2.3836874    2.0931209   -1069.7324   -1067.6392 
-    3300         0.33   0.07645716    3424.8795    61.551539   -2.4057167    1.9810841   -1069.6203   -1067.6392 
-    3350        0.335  0.076457236    3335.9672    59.709703   -2.4251844    1.9218031    -1069.561   -1067.6392 
-    3400         0.34  0.076457298    3238.0186    60.026953   -2.4425501    1.9320141   -1069.5712   -1067.6392 
-    3450        0.345  0.076457297    3185.0674    62.613739   -2.4593531    2.0152718   -1069.6545   -1067.6392 
-    3500         0.35   0.07645723    3197.4087    67.011871   -2.4756907    2.1568291   -1069.7961   -1067.6392 
-    3550        0.355  0.076457177    3216.1428    72.316209   -2.4911379    2.3275533   -1069.9668   -1067.6392 
-    3600         0.36  0.076457165    3241.0326    77.550071   -2.5083858    2.4960092   -1070.1352   -1067.6392 
-    3650        0.365  0.076457168    3309.6874    81.877688   -2.5306273    2.6352969   -1070.2745   -1067.6392 
-    3700         0.37   0.07645718     3350.748    84.764646   -2.5595247    2.7282159   -1070.3674   -1067.6392 
-    3750        0.375   0.07645721     3368.085    86.031781   -2.5938559    2.7689996   -1070.4082   -1067.6392 
-    3800         0.38  0.076457208    3425.3173    85.733048   -2.6266899    2.7593847   -1070.3986   -1067.6392 
-    3850        0.385  0.076457165    3420.4429    84.240647   -2.6514805    2.7113506   -1070.3506   -1067.6392 
-    3900         0.39  0.076457146    3323.0403    82.320886   -2.6700966    2.6495616   -1070.2888   -1067.6392 
-    3950        0.395  0.076457179    3273.2625    80.780607   -2.6892405    2.5999865   -1070.2392   -1067.6392 
-    4000          0.4  0.076457229    3313.2671     79.92769    -2.709641    2.5725347   -1070.2118   -1067.6392 
-    4050        0.405  0.076457272    3381.1117    79.663389   -2.7291493     2.564028   -1070.2033   -1067.6392 
-    4100         0.41   0.07645731    3373.3005    79.895158   -2.7514856    2.5714877   -1070.2107   -1067.6392 
-    4150        0.415  0.076457296    3279.6989    80.402828   -2.7788004    2.5878274   -1070.2271   -1067.6392 
-    4200         0.42  0.076457251    3197.0478    80.770336   -2.8064773     2.599656   -1070.2389   -1067.6392 
-    4250        0.425  0.076457243    3160.9065    80.756747   -2.8307967    2.5992186   -1070.2385   -1067.6392 
-    4300         0.43  0.076457282    3173.9599    80.446488    -2.852192    2.5892326   -1070.2285   -1067.6392 
-    4350        0.435  0.076457289    3185.8003    80.110494   -2.8726607    2.5784184   -1070.2177   -1067.6392 
-    4400         0.44  0.076457262    3166.3054    80.045036   -2.8936787    2.5763116   -1070.2155   -1067.6392 
-    4450        0.445  0.076457226    3177.4332    80.500194   -2.9171408    2.5909612   -1070.2302   -1067.6392 
-    4500         0.45  0.076457174    3238.8362    81.573722   -2.9447352    2.6255135   -1070.2647   -1067.6392 
-    4550        0.455   0.07645714    3277.7104    83.104228    -2.975052    2.6747741    -1070.314   -1067.6392 
-    4600         0.46  0.076457157    3224.8571    84.845474   -3.0065552    2.7308174     -1070.37   -1067.6392 
-    4650        0.465  0.076457215    3112.9952    86.608217     -3.03972    2.7875527   -1070.4268   -1067.6392 
-    4700         0.47  0.076457254     3001.141     88.18732    -3.074928    2.8383773   -1070.4776   -1067.6392 
-    4750        0.475  0.076457235    2904.0735    89.204263   -3.1082127    2.8711084   -1070.5103   -1067.6392 
-    4800         0.48  0.076457195    2832.0276     89.24571    -3.134302    2.8724424   -1070.5117   -1067.6392 
-    4850        0.485  0.076457172    2833.7453    88.206351   -3.1541802    2.8389899   -1070.4782   -1067.6392 
-    4900         0.49  0.076457184     2941.993    86.310712   -3.1725372    2.7779773   -1070.4172   -1067.6392 
-    4950        0.495  0.076457228    3082.4825    84.029047   -3.1931038    2.7045401   -1070.3438   -1067.6392 
-    5000          0.5   0.07645727    3155.7096     81.99875   -3.2175967    2.6391934   -1070.2784   -1067.6392 
-    5050        0.505  0.076457297    3162.1875     80.72053   -3.2420202    2.5980529   -1070.2373   -1067.6392 
-    5100         0.51  0.076457279    3133.3889    80.483768   -3.2606472    2.5904325   -1070.2297   -1067.6392 
-    5150        0.515  0.076457223    3144.6361    81.566513   -3.2759117    2.6252815   -1070.2645   -1067.6392 
-    5200         0.52  0.076457166    3156.8183    84.062018   -3.2944729    2.7056013   -1070.3448   -1067.6392 
-    5250        0.525  0.076457128    3059.9886    87.694328   -3.3209415      2.82251   -1070.4617   -1067.6392 
-    5300         0.53  0.076457126    2891.6506    91.782947   -3.3547324    2.9541054   -1070.5933   -1067.6392 
-    5350        0.535  0.076457151    2751.9452    95.417928   -3.3914125    3.0711001   -1070.7103   -1067.6392 
-    5400         0.54   0.07645725    2681.0266    97.845096    -3.427665    3.1492204   -1070.7885   -1067.6392 
-    5450        0.545  0.076457325    2657.0872    98.736021   -3.4632111    3.1778955   -1070.8171   -1067.6392 
-    5500         0.55  0.076457263    2653.1919    98.075728   -3.4957627    3.1566434   -1070.7959   -1067.6392 
-    5550        0.555  0.076457185    2644.2052    96.114965   -3.5208827    3.0935347   -1070.7328   -1067.6392 
-    5600         0.56  0.076457195    2622.4173     93.52581   -3.5389264    3.0102008   -1070.6494   -1067.6392 
-    5650        0.565   0.07645725     2616.385    91.264371   -3.5558734    2.9374146   -1070.5766   -1067.6392 
-    5700         0.57  0.076457256     2608.245    90.135398   -3.5771375    2.9010777   -1070.5403   -1067.6392 
-    5750        0.575  0.076457193    2573.2163    90.456889   -3.6030063    2.9114252   -1070.5507   -1067.6392 
-    5800         0.58  0.076457145    2565.3319    92.099497   -3.6318266    2.9642938   -1070.6035   -1067.6392 
-    5850        0.585  0.076457161    2566.2757    94.625315   -3.6627042    3.0455892   -1070.6848   -1067.6392 
-    5900         0.59  0.076457186    2564.6803    97.321385   -3.6927592    3.1323643   -1070.7716   -1067.6392 
-    5950        0.595  0.076457195    2570.6302    99.384974   -3.7170024    3.1987825    -1070.838   -1067.6392 
-    6000          0.6  0.076457206    2556.8451     100.3814   -3.7363623    3.2308531   -1070.8701   -1067.6392 
-    6050        0.605  0.076457195    2521.7968    100.35236   -3.7587516    3.2299187   -1070.8692   -1067.6392 
-    6100         0.61  0.076457175    2476.1834    99.370379   -3.7869326    3.1983128   -1070.8375   -1067.6392 
-    6150        0.615  0.076457178    2397.2793     97.46598   -3.8168635    3.1370182   -1070.7763   -1067.6392 
-    6200         0.62   0.07645713    2286.8537    94.931722   -3.8450244    3.0554511   -1070.6947   -1067.6392 
-    6250        0.625  0.076457116    2250.5276    92.438472   -3.8722444    2.9752039   -1070.6144   -1067.6392 
-    6300         0.63  0.076457156    2338.5273    90.714367   -3.9006127    2.9197123   -1070.5589   -1067.6392 
-    6350        0.635   0.07645717    2433.0191    90.142302   -3.9291161       2.9013   -1070.5405   -1067.6392 
-    6400         0.64  0.076457159    2467.5427    90.771124   -3.9562695    2.9215391   -1070.5608   -1067.6392 
-    6450        0.645  0.076457107    2475.8649    92.488037   -3.9828137    2.9767993    -1070.616   -1067.6392 
-    6500         0.65    0.0764571    2489.7445    95.127495   -4.0122155    3.0617523    -1070.701   -1067.6392 
-    6550        0.655  0.076457169    2500.4772    98.171784   -4.0419204    3.1597351    -1070.799   -1067.6392 
-    6600         0.66  0.076457208    2530.8002    100.74954   -4.0632043    3.2427022   -1070.8819   -1067.6392 
-    6650        0.665  0.076457205    2539.1451     102.2625   -4.0743218    3.2913979   -1070.9306   -1067.6392 
-    6700         0.67  0.076457193    2456.6604    102.74354   -4.0834224    3.3068807   -1070.9461   -1067.6392 
-    6750        0.675  0.076457138    2387.6116    102.56283   -4.0973681    3.3010644   -1070.9403   -1067.6392 
-    6800         0.68  0.076457109     2401.109    102.04322   -4.1140004    3.2843402   -1070.9236   -1067.6392 
-    6850        0.685  0.076457149     2426.903    101.49411   -4.1282038    3.2666667   -1070.9059   -1067.6392 
-    6900         0.69  0.076457185    2389.4414    101.35418   -4.1401788    3.2621629   -1070.9014   -1067.6392 
-    6950        0.695  0.076457175    2323.8548    101.97407   -4.1517576    3.2821145   -1070.9213   -1067.6392 
-    7000          0.7  0.076457145    2273.8774    103.46341   -4.1630759    3.3300502   -1070.9693   -1067.6392 
-    7050        0.705  0.076457126     2231.652      105.807   -4.1769876    3.4054803   -1071.0447   -1067.6392 
-    7100         0.71  0.076457114    2185.0532    108.81826   -4.1989101    3.5024002   -1071.1416   -1067.6392 
-    7150        0.715  0.076457137    2139.1143    111.85634   -4.2283255    3.6001832   -1071.2394   -1067.6392 
-    7200         0.72  0.076457149    2101.4939    113.84909   -4.2559584    3.6643212   -1071.3036   -1067.6392 
-    7250        0.725   0.07645712    2118.2862    113.94356   -4.2760809    3.6673619   -1071.3066   -1067.6392 
-    7300         0.73  0.076457121    2191.9037    111.95148   -4.2925005    3.6032452   -1071.2425   -1067.6392 
-    7350        0.735  0.076457137    2227.2391     108.2126   -4.3103519    3.4829066   -1071.1221   -1067.6392 
-    7400         0.74  0.076457111     2182.826     103.4321   -4.3300063    3.3290426   -1070.9683   -1067.6392 
-    7450        0.745  0.076457109    2101.7168    98.840049   -4.3541992    3.1812437   -1070.8205   -1067.6392 
-    7500         0.75  0.076457149    2036.3108    95.828239    -4.386682    3.0843062   -1070.7235   -1067.6392 
-    7550        0.755  0.076457161    1994.4837    95.142177   -4.4221587    3.0622248   -1070.7015   -1067.6392 
-    7600         0.76  0.076457127    1970.6785    96.747859   -4.4522387    3.1139049   -1070.7531   -1067.6392 
-    7650        0.765  0.076457086    1993.9417    100.15534   -4.4763203    3.2235774   -1070.8628   -1067.6392 
-    7700         0.77  0.076457048    2073.7836    104.50424   -4.4979798    3.3635502   -1071.0028   -1067.6392 
-    7750        0.775  0.076457026    2168.4033    108.65953   -4.5168753    3.4972912   -1071.1365   -1067.6392 
-    7800         0.78   0.07645702    2217.6427    111.71942   -4.5326251    3.5957762    -1071.235   -1067.6392 
-    7850        0.785  0.076457017    2202.5357    113.33023   -4.5487958    3.6476215   -1071.2869   -1067.6392 
-    7900         0.79  0.076457015     2164.601    113.51362   -4.5690254     3.653524   -1071.2928   -1067.6392 
-    7950        0.795  0.076457037    2131.6906    112.46493   -4.5932729    3.6197711    -1071.259   -1067.6392 
-    8000          0.8  0.076457042    2076.7626    110.60384   -4.6198371    3.5598705   -1071.1991   -1067.6392 
-    8050        0.805   0.07645706    2008.3681    108.69863   -4.6506123    3.4985496   -1071.1378   -1067.6392 
-    8100         0.81  0.076457078    1991.1056    107.59889   -4.6874954    3.4631539   -1071.1024   -1067.6392 
-    8150        0.815  0.076457081     2030.108    107.96066   -4.7301631    3.4747976    -1071.114   -1067.6392 
-    8200         0.82   0.07645709    2053.0781    110.00158   -4.7752612    3.5404861   -1071.1797   -1067.6392 
-    8250        0.825  0.076457092    2080.7633    113.42163   -4.8192627     3.650563   -1071.2898   -1067.6392 
-    8300         0.83  0.076457092    2136.3278      117.426   -4.8602394    3.7794468   -1071.4187   -1067.6392 
-    8350        0.835  0.076457128    2143.1741    120.76905   -4.8928022    3.8870456   -1071.5263   -1067.6392 
-    8400         0.84  0.076457182    2096.2614    122.36127   -4.9132303    3.9382923   -1071.5775   -1067.6392 
-    8450        0.845  0.076457199    2045.0508    121.81432   -4.9242986    3.9206885   -1071.5599   -1067.6392 
-    8500         0.85  0.076457148      1988.55    119.39197   -4.9305717    3.8427231    -1071.482   -1067.6392 
-    8550        0.855  0.076457089    1927.6698    115.82938   -4.9366606    3.7280586   -1071.3673   -1067.6392 
-    8600         0.86    0.0764571    1904.9377    112.15467   -4.9485473    3.6097852    -1071.249   -1067.6392 
-    8650        0.865  0.076457183    1942.1657    109.35829   -4.9712735    3.5197814    -1071.159   -1067.6392 
-    8700         0.87  0.076457275    1995.7079    107.97044   -5.0032067    3.4751123   -1071.1143   -1067.6392 
-    8750        0.875  0.076457274    2021.2979    107.91844   -5.0351272    3.4734386   -1071.1127   -1067.6392 
-    8800         0.88  0.076457159    2019.7716    108.89001   -5.0595657    3.5047095   -1071.1439   -1067.6392 
-    8850        0.885  0.076457056    1997.5026    110.65412   -5.0764543    3.5614886   -1071.2007   -1067.6392 
-    8900         0.89  0.076457086    1958.2352    113.01816   -5.0898539    3.6375771   -1071.2768   -1067.6392 
-    8950        0.895  0.076457184    1948.1688    115.69887   -5.1049282     3.723858   -1071.3631   -1067.6392 
-    9000          0.9  0.076457251    1946.4034     118.2422    -5.125187    3.8057169   -1071.4449   -1067.6392 
-    9050        0.905  0.076457271    1929.5103    120.07623   -5.1485984    3.8647467    -1071.504   -1067.6392 
-    9100         0.91  0.076457223    1920.5823    120.83551   -5.1696144    3.8891848   -1071.5284   -1067.6392 
-    9150        0.915   0.07645719    1947.9739    120.53164   -5.1820234    3.8794043   -1071.5186   -1067.6392 
-    9200         0.92  0.076457191    2021.9322     119.4904   -5.1820769    3.8458913   -1071.4851   -1067.6392 
-    9250        0.925  0.076457189    2120.5676    118.28073   -5.1733083    3.8069571   -1071.4462   -1067.6392 
-    9300         0.93  0.076457202    2218.9759    117.51293   -5.1649043    3.7822448   -1071.4215   -1067.6392 
-    9350        0.935   0.07645722    2256.6996    117.52636    -5.163384    3.7826772   -1071.4219   -1067.6392 
-    9400         0.94  0.076457192    2219.8074    118.22843   -5.1666597    3.8052737   -1071.4445   -1067.6392 
-    9450        0.945  0.076457133    2130.6686    119.30164   -5.1680994    3.8398158    -1071.479   -1067.6392 
-    9500         0.95  0.076457125    2013.4271    120.65247   -5.1678977    3.8832933   -1071.5225   -1067.6392 
-    9550        0.955  0.076457169    1923.3398    122.44923   -5.1747845    3.9411236   -1071.5804   -1067.6392 
-    9600         0.96  0.076457205    1913.1904    124.48108   -5.1900088    4.0065202   -1071.6458   -1067.6392 
-    9650        0.965  0.076457203    1960.3017    126.09586   -5.2054982    4.0584932   -1071.6977   -1067.6392 
-    9700         0.97    0.0764572    1993.4886    126.91655   -5.2204458    4.0849076   -1071.7241   -1067.6392 
-    9750        0.975  0.076457237    2016.3395    126.88895   -5.2391789    4.0840193   -1071.7233   -1067.6392 
-    9800         0.98  0.076457278    2059.2841     125.9798   -5.2613642    4.0547577    -1071.694   -1067.6392 
-    9850        0.985  0.076457268    2076.0892    124.30551   -5.2849423    4.0008692   -1071.6401   -1067.6392 
-    9900         0.99  0.076457232    2054.9566    122.26397   -5.3097299    3.9351607   -1071.5744   -1067.6392 
-    9950        0.995  0.076457211    2050.2277    120.49535   -5.3384666    3.8782362   -1071.5175   -1067.6392 
-   10000            1  0.076457247    2069.6559    119.63397    -5.374562    3.8505122   -1071.4897   -1067.6392 
-   10050        1.005  0.076457306    2079.8366    119.92165   -5.4169176    3.8597712    -1071.499   -1067.6392 
-   10100         1.01  0.076457317    2051.4213     121.0737   -5.4602428     3.896851   -1071.5361   -1067.6392 
-   10150        1.015  0.076457329    2026.2947    122.36851   -5.4975255    3.9385254   -1071.5778   -1067.6392 
-   10200         1.02  0.076457353    2042.1162    122.97997   -5.5239278    3.9582059   -1071.5974   -1067.6392 
-   10250        1.025  0.076457364    2059.2177    122.42397   -5.5402625    3.9403105   -1071.5795   -1067.6392 
-   10300         1.03  0.076457332    2037.1418    120.82131   -5.5531843    3.8887277    -1071.528   -1067.6392 
-   10350        1.035  0.076457305    1953.9125    118.75093   -5.5690263    3.8220908   -1071.4613   -1067.6392 
-   10400         1.04  0.076457265    1845.8999    116.97821   -5.5872522    3.7650343   -1071.4043   -1067.6392 
-   10450        1.045  0.076457218    1789.9704    116.44416   -5.6054265    3.7478455   -1071.3871   -1067.6392 
-   10500         1.05  0.076457227    1790.1722    117.85441   -5.6201726    3.7932355   -1071.4325   -1067.6392 
-   10550        1.055  0.076457265    1792.8951    121.26237   -5.6302348    3.9029234   -1071.5422   -1067.6392 
-   10600         1.06  0.076457285    1801.2253    126.08926   -5.6408443    4.0582808   -1071.6975   -1067.6392 
-   10650        1.065  0.076457276     1848.312    131.30844   -5.6585268    4.2262642   -1071.8655   -1067.6392 
-   10700         1.07  0.076457228     1899.189    135.63605      -5.6833    4.3655515   -1072.0048   -1067.6392 
-   10750        1.075  0.076457196    1933.4466    137.94816   -5.7116789    4.4399687   -1072.0792   -1067.6392 
-   10800         1.08  0.076457209    1952.1407    137.53149   -5.7380474    4.4265577   -1072.0658   -1067.6392 
-   10850        1.085  0.076457232    1956.2467    134.36784   -5.7597709    4.3247333    -1071.964   -1067.6392 
-   10900         1.09  0.076457254    1935.3183    129.23046   -5.7778262    4.1593827   -1071.7986   -1067.6392 
-   10950        1.095   0.07645725    1894.1382    123.56602   -5.7940915    3.9770683   -1071.6163   -1067.6392 
-   11000          1.1  0.076457202    1869.9315    119.13104   -5.8115801    3.8343249   -1071.4736   -1067.6392 
-   11050        1.105  0.076457157    1872.2105     117.1706   -5.8302554    3.7712266   -1071.4105   -1067.6392 
-   11100         1.11  0.076457121    1910.0087    117.93509   -5.8479403    3.7958325   -1071.4351   -1067.6392 
-   11150        1.115  0.076457111    1974.5822     120.8604   -5.8628947    3.8899857   -1071.5292   -1067.6392 
-   11200         1.12  0.076457152    2017.5386    125.16424   -5.8764671    4.0285084   -1071.6677   -1067.6392 
-   11250        1.125  0.076457215    2006.1464    130.14791   -5.8926588    4.1889116   -1071.8281   -1067.6392 
-   11300         1.13  0.076457208    1981.6806    134.97307   -5.9111129     4.344213   -1071.9834   -1067.6392 
-   11350        1.135  0.076457154    1955.8911    138.78712   -5.9293384    4.4669713   -1072.1062   -1067.6392 
-   11400         1.14  0.076457103     1903.025    141.01634   -5.9477992    4.5387205    -1072.178   -1067.6392 
-   11450        1.145  0.076457082    1861.8231    141.41934   -5.9709229    4.5516912   -1072.1909   -1067.6392 
-   11500         1.15  0.076457105       1864.1    139.85754    -5.999873    4.5014233   -1072.1407   -1067.6392 
-   11550        1.155  0.076457135     1864.553    136.29668   -6.0269465    4.3868144    -1072.026   -1067.6392 
-   11600         1.16  0.076457167    1838.5238    131.42789   -6.0482365    4.2301086   -1071.8693   -1067.6392 
-   11650        1.165  0.076457207    1805.0176    126.80497   -6.0718009    4.0813163   -1071.7205   -1067.6392 
-   11700         1.17  0.076457247    1735.2577    124.00212   -6.1059505    3.9911044   -1071.6303   -1067.6392 
-   11750        1.175  0.076457255    1641.4793    123.80317   -6.1481291     3.984701   -1071.6239   -1067.6392 
-   11800         1.18  0.076457236    1596.2043      126.199   -6.1904504    4.0618126    -1071.701   -1067.6392 
-   11850        1.185  0.076457229    1622.0725    130.64719   -6.2272702    4.2049812   -1071.8442   -1067.6392 
-   11900         1.19  0.076457283    1669.7039    136.11282   -6.2551373    4.3808969   -1072.0201   -1067.6392 
-   11950        1.195  0.076457361    1687.4469    141.27818   -6.2753897    4.5471478   -1072.1864   -1067.6392 
-   12000          1.2  0.076457336     1685.355     144.8526    -6.294312    4.6621933   -1072.3014   -1067.6392 
-   12050        1.205  0.076457364    1684.0235    145.75585   -6.3137437     4.691265   -1072.3305   -1067.6392 
-   12100         1.21  0.076457364    1695.7222    143.63233   -6.3312278    4.6229181   -1072.2622   -1067.6392 
-   12150        1.215  0.076457301    1744.0573    139.27223   -6.3471908    4.4825848   -1072.1218   -1067.6392 
-   12200         1.22  0.076457264    1815.5391    134.28007   -6.3640171    4.3219083   -1071.9611   -1067.6392 
-   12250        1.225  0.076457306    1839.4868     130.2409    -6.378914    4.1919044   -1071.8311   -1067.6392 
-   12300         1.23  0.076457381    1791.3388    128.29684   -6.3893167    4.1293333   -1071.7686   -1067.6392 
-   12350        1.235  0.076457382     1713.284    129.07652   -6.4002273     4.154428   -1071.7937   -1067.6392 
-   12400         1.24  0.076457352    1639.3792    132.52697   -6.4176635    4.2654835   -1071.9047   -1067.6392 
-   12450        1.245  0.076457344    1579.8725    137.81757   -6.4424211    4.4357656    -1072.075   -1067.6392 
-   12500         1.25  0.076457303    1557.3644    143.52235   -6.4729454    4.6193783   -1072.2586   -1067.6392 
-   12550        1.255  0.076457277    1618.5087    148.11444   -6.5082137    4.7671782   -1072.4064   -1067.6392 
-   12600         1.26  0.076457326    1720.3013     150.5465   -6.5476118     4.845456   -1072.4847   -1067.6392 
-   12650        1.265  0.076457391    1778.5404    150.56002   -6.5906298    4.8458912   -1072.4851   -1067.6392 
-   12700         1.27  0.076457351    1788.5951    148.56554   -6.6347601    4.7816972   -1072.4209   -1067.6392 
-   12750        1.275  0.076457269    1779.1884    145.24576   -6.6730452    4.6748475   -1072.3141   -1067.6392 
-   12800         1.28   0.07645728    1758.2949    141.40165    -6.701303    4.5511219   -1072.1904   -1067.6392 
-   12850        1.285  0.076457312    1712.5641     137.9123   -6.7240908    4.4388145    -1072.078   -1067.6392 
-   12900         1.29  0.076457327    1668.6646    135.42155   -6.7444763    4.3586478   -1071.9979   -1067.6392 
-   12950        1.295  0.076457332    1653.7008    134.40911   -6.7622343    4.3260615   -1071.9653   -1067.6392 
-   13000          1.3  0.076457334    1678.1215     135.3964   -6.7808215    4.3578383   -1071.9971   -1067.6392 
-   13050        1.305  0.076457316    1709.6866    138.43433   -6.7994699    4.4556163   -1072.0948   -1067.6392 
-   13100         1.31  0.076457256    1719.9198    142.81982   -6.8124215    4.5967668    -1072.236   -1067.6392 
-   13150        1.315  0.076457227    1716.5741    147.42301   -6.8192217     4.744924   -1072.3842   -1067.6392 
-   13200         1.32  0.076457238    1743.2587    150.89049   -6.8222296    4.8565276   -1072.4958   -1067.6392 
-   13250        1.325  0.076457261    1793.7636    151.98662   -6.8200794    4.8918073    -1072.531   -1067.6392 
-   13300         1.33   0.07645729    1825.2569    150.42643   -6.8140605    4.8415915   -1072.4808   -1067.6392 
-   13350        1.335  0.076457252     1838.476    147.28172   -6.8146446    4.7403765   -1072.3796   -1067.6392 
-   13400         1.34  0.076457169    1838.3398    144.11825   -6.8303357    4.6385577   -1072.2778   -1067.6392 
-   13450        1.345  0.076457222    1801.0039    141.93725   -6.8583491    4.5683605   -1072.2076   -1067.6392 
-   13500         1.35  0.076457347     1755.582    140.99498     -6.89022    4.5380327   -1072.1773   -1067.6392 
-   13550        1.355  0.076457427    1733.1918    141.21311   -6.9214427    4.5450535   -1072.1843   -1067.6392 
-   13600         1.36  0.076457431    1712.5682    142.19629   -6.9465697    4.5766981   -1072.2159   -1067.6392 
-   13650        1.365  0.076457399     1717.694     143.5117   -6.9629204    4.6190353   -1072.2583   -1067.6392 
-   13700         1.37  0.076457334    1770.8346    145.13001   -6.9802142     4.671122   -1072.3104   -1067.6392 
-   13750        1.375  0.076457247    1825.1073    146.95312   -7.0064861    4.7298002    -1072.369   -1067.6392 
-   13800         1.38  0.076457256    1824.3539    148.48573   -7.0381068    4.7791285   -1072.4184   -1067.6392 
-   13850        1.385  0.076457313    1782.7326    149.20301   -7.0651441    4.8022147   -1072.4414   -1067.6392 
-   13900         1.39  0.076457295    1750.9167    149.18894   -7.0840385    4.8017618    -1072.441   -1067.6392 
-   13950        1.395  0.076457288    1760.1963    149.12388   -7.1020342    4.7996679   -1072.4389   -1067.6392 
-   14000          1.4  0.076457265    1776.4309    149.46795   -7.1245024    4.8107421     -1072.45   -1067.6392 
-   14050        1.405  0.076457201    1795.0829    150.25585   -7.1514213    4.8361011   -1072.4753   -1067.6392 
-   14100         1.41  0.076457229    1812.6337    151.48841   -7.1831839    4.8757722    -1072.515   -1067.6392 
-   14150        1.415  0.076457297    1801.8728    153.13675   -7.2174201     4.928825   -1072.5681   -1067.6392 
-   14200         1.42  0.076457305    1773.4672    155.06508   -7.2481606    4.9908901   -1072.6301   -1067.6392 
-   14250        1.425  0.076457282    1738.9317    157.04135   -7.2698182    5.0544977   -1072.6937   -1067.6392 
-   14300         1.43  0.076457306    1716.5389    158.77479   -7.2837833    5.1102898   -1072.7495   -1067.6392 
-   14350        1.435   0.07645735    1720.7949     159.7069   -7.2945528    5.1402904   -1072.7795   -1067.6392 
-   14400         1.44  0.076457333    1748.7885    159.02986   -7.3011362    5.1184995   -1072.7577   -1067.6392 
-   14450        1.445  0.076457295    1742.8885    156.42679   -7.3047662    5.0347176    -1072.674   -1067.6392 
-   14500         1.45  0.076457256    1670.5068    152.24569   -7.3102428    4.9001455   -1072.5394   -1067.6392 
-   14550        1.455  0.076457265    1584.5241    147.05373    -7.318176    4.7330384   -1072.3723   -1067.6392 
-   14600         1.46  0.076457287    1529.9826    141.71242   -7.3290619    4.5611241   -1072.2004   -1067.6392 
-   14650        1.465  0.076457308    1510.2873    137.60969   -7.3489824    4.4290747   -1072.0683   -1067.6392 
-   14700         1.47  0.076457333    1517.9737    136.06432   -7.3778607    4.3793359   -1072.0186   -1067.6392 
-   14750        1.475  0.076457349    1536.5785     137.7444   -7.4074887    4.4334105   -1072.0726   -1067.6392 
-   14800         1.48  0.076457332     1570.427    142.60265    -7.435251     4.589777    -1072.229   -1067.6392 
-   14850        1.485  0.076457277    1605.5273    149.55383   -7.4584362     4.813506   -1072.4527   -1067.6392 
-   14900         1.49  0.076457286    1619.5816    156.68247   -7.4687128     5.042947   -1072.6822   -1067.6392 
-   14950        1.495  0.076457352    1628.8798    162.48759   -7.4692532    5.2297891    -1072.869   -1067.6392 
-   15000          1.5  0.076457367    1645.2779    166.28468   -7.4710214    5.3520015   -1072.9912   -1067.6392 
-   15050        1.505  0.076457354    1659.3085    168.01268   -7.4835147    5.4076185   -1073.0469   -1067.6392 
-   15100         1.51  0.076457322    1657.5151     167.8691   -7.5090057    5.4029973   -1073.0422   -1067.6392 
-   15150        1.515  0.076457334    1619.1825    165.90116   -7.5343027    5.3396576   -1072.9789   -1067.6392 
-   15200         1.52  0.076457345     1564.833    162.54809   -7.5475534    5.2317363    -1072.871   -1067.6392 
-   15250        1.525  0.076457333    1526.2301     158.9992   -7.5544031    5.1175126   -1072.7567   -1067.6392 
-   15300         1.53  0.076457299    1516.6129    156.42636   -7.5677145    5.0347037   -1072.6739   -1067.6392 
-   15350        1.535   0.07645727    1514.4631    155.10745   -7.5910984    4.9922537   -1072.6315   -1067.6392 
-   15400         1.54  0.076457295    1489.0219    154.49939   -7.6168589    4.9726826   -1072.6119   -1067.6392 
-   15450        1.545  0.076457307      1454.98    154.09722   -7.6374985    4.9597386    -1072.599   -1067.6392 
-   15500         1.55  0.076457289    1465.2041    153.94567   -7.6532363    4.9548609   -1072.5941   -1067.6392 
-   15550        1.555  0.076457258    1507.1468     154.2404   -7.6663203     4.964347   -1072.6036   -1067.6392 
-   15600         1.56  0.076457196    1529.3808    154.91397   -7.6776911    4.9860264   -1072.6253   -1067.6392 
-   15650        1.565  0.076457177    1523.9817     156.0119    -7.695343     5.021364   -1072.6606   -1067.6392 
-   15700         1.57  0.076457193    1522.7643    157.82491   -7.7296805    5.0797172   -1072.7189   -1067.6392 
-   15750        1.575  0.076457243    1494.5697      160.297   -7.7768073    5.1592832   -1072.7985   -1067.6392 
-   15800         1.58  0.076457287    1432.4424    162.81609   -7.8203339    5.2403621   -1072.8796   -1067.6392 
-   15850        1.585   0.07645733    1402.4977    164.59576   -7.8451116    5.2976423   -1072.9369   -1067.6392 
-   15900         1.59  0.076457402     1416.812    165.26647   -7.8504137    5.3192297   -1072.9585   -1067.6392 
-   15950        1.595  0.076457391    1434.0052    165.00555   -7.8513437    5.3108318   -1072.9501   -1067.6392 
-   16000          1.6   0.07645732     1448.028     163.9183   -7.8607479    5.2758378   -1072.9151   -1067.6392 
-   16050        1.605  0.076457324    1476.1802    161.67871   -7.8741051    5.2037547    -1072.843   -1067.6392 
-   16100         1.61  0.076457365    1517.1195      158.257   -7.8821118    5.0936245   -1072.7329   -1067.6392 
-   16150        1.615   0.07645732    1551.8013    154.48554   -7.8845021    4.9722371   -1072.6115   -1067.6392 
-   16200         1.62  0.076457224    1563.4592    151.61692   -7.8867696    4.8799081   -1072.5191   -1067.6392 
-   16250        1.625  0.076457231    1568.8982    150.52413   -7.8928325    4.8447358    -1072.484   -1067.6392 
-   16300         1.63  0.076457315    1587.8208    151.31592   -7.9028799    4.8702203   -1072.5095   -1067.6392 
-   16350        1.635  0.076457401    1587.1658    153.58503   -7.9155357    4.9432533   -1072.5825   -1067.6392 
-   16400         1.64    0.0764574    1564.8466    156.97281   -7.9329671    5.0522917   -1072.6915   -1067.6392 
-   16450        1.645  0.076457324    1559.9515    161.25392   -7.9569659    5.1900827   -1072.8293   -1067.6392 
-   16500         1.65   0.07645729    1572.1491    166.16033   -7.9871415    5.3479991   -1072.9872   -1067.6392 
-   16550        1.655  0.076457319    1587.1041    171.09675   -8.0223182    5.5068818   -1073.1461   -1067.6392 
-   16600         1.66  0.076457367    1611.2738    175.10798   -8.0612322    5.6359861   -1073.2752   -1067.6392 
-   16650        1.665  0.076457363     1645.197    177.28144    -8.100579    5.7059409   -1073.3452   -1067.6392 
-   16700         1.67  0.076457373     1687.596    177.10275   -8.1330656    5.7001896   -1073.3394   -1067.6392 
-   16750        1.675  0.076457406    1741.0657    174.63626   -8.1549243    5.6208035     -1073.26   -1067.6392 
-   16800         1.68  0.076457428    1770.5295     170.6939   -8.1775588    5.4939157   -1073.1331   -1067.6392 
-   16850        1.685  0.076457412    1764.9164    166.35555   -8.2116214    5.3542824   -1072.9935   -1067.6392 
-   16900         1.69  0.076457377    1753.4555    162.46345     -8.24703    5.2290123   -1072.8682   -1067.6392 
-   16950        1.695  0.076457382    1737.3044    159.85392   -8.2679658    5.1450224   -1072.7843   -1067.6392 
-   17000          1.7  0.076457397    1698.4267    159.38372   -8.2771546    5.1298887   -1072.7691   -1067.6392 
-   17050        1.705  0.076457398    1648.5432    161.02257   -8.2829365    5.1826363   -1072.8219   -1067.6392 
-   17100         1.71  0.076457362    1597.8104    163.90303   -8.2883924    5.2753461   -1072.9146   -1067.6392 
-   17150        1.715  0.076457407    1581.3305    167.13768   -8.2982879    5.3794559   -1073.0187   -1067.6392 
-   17200         1.72  0.076457416    1615.3538    169.91691   -8.3147181    5.4689075   -1073.1081   -1067.6392 
-   17250        1.725  0.076457317     1640.517    171.76528   -8.3382653    5.5283989   -1073.1676   -1067.6392 
-   17300         1.73  0.076457279    1642.0824    172.72393   -8.3672834    5.5592538   -1073.1985   -1067.6392 
-   17350        1.735  0.076457358    1654.7782    173.20812   -8.3956352    5.5748377   -1073.2141   -1067.6392 
-   17400         1.74  0.076457387    1690.9444    174.02756   -8.4250034    5.6012122   -1073.2404   -1067.6392 
-   17450        1.745  0.076457318    1700.9667    175.61591   -8.4582001    5.6523344   -1073.2916   -1067.6392 
-   17500         1.75  0.076457288    1647.3737    177.46686   -8.4919066    5.7119087   -1073.3511   -1067.6392 
-   17550        1.755  0.076457298    1540.9506    178.64086   -8.5244634    5.7496947   -1073.3889   -1067.6392 
-   17600         1.76  0.076457329    1446.6813    178.43003    -8.554886    5.7429089   -1073.3821   -1067.6392 
-   17650        1.765  0.076457379    1412.0895    176.95558   -8.5854884    5.6954528   -1073.3347   -1067.6392 
-   17700         1.77  0.076457349     1414.559     175.0213   -8.6219735    5.6331963   -1073.2724   -1067.6392 
-   17750        1.775  0.076457246    1413.6264    173.04798   -8.6573217    5.5696835   -1073.2089   -1067.6392 
-   17800         1.78  0.076457222     1399.031    170.80066    -8.673405    5.4973518   -1073.1366   -1067.6392 
-   17850        1.785  0.076457257    1402.9589    168.32364   -8.6692442     5.417627   -1073.0569   -1067.6392 
-   17900         1.79  0.076457292    1421.4914    166.26754    -8.667908    5.3514498   -1072.9907   -1067.6392 
-   17950        1.795   0.07645729    1459.6161    165.06532   -8.6883597    5.3127556    -1072.952   -1067.6392 
-   18000          1.8   0.07645728    1526.0272     164.4467    -8.724083    5.2928448   -1072.9321   -1067.6392 
-   18050        1.805  0.076457285     1579.053    164.14599   -8.7580049     5.283166   -1072.9224   -1067.6392 
-   18100         1.81  0.076457295    1585.8299    164.68311   -8.7876471    5.3004537   -1072.9397   -1067.6392 
-   18150        1.815  0.076457311    1571.4213    167.11719     -8.82749    5.3787965    -1073.018   -1067.6392 
-   18200         1.82  0.076457253    1566.7735    171.84493   -8.8828984    5.5309623   -1073.1702   -1067.6392 
-   18250        1.825  0.076457211    1565.9409    178.03402   -8.9379169    5.7301632   -1073.3694   -1067.6392 
-   18300         1.83  0.076457261    1564.3982    184.19934    -8.977693    5.9285986   -1073.5678   -1067.6392 
-   18350        1.835   0.07645725    1565.4674    188.93147   -9.0068361    6.0809061   -1073.7201   -1067.6392 
-   18400         1.84  0.076457214    1575.9469    191.19229   -9.0319747    6.1536724   -1073.7929   -1067.6392 
-   18450        1.845  0.076457289    1591.7212    190.75232   -9.0530056    6.1395115   -1073.7787   -1067.6392 
-   18500         1.85  0.076457356    1602.2968    188.42238   -9.0750081    6.0645207   -1073.7038   -1067.6392 
-   18550        1.855  0.076457289     1601.939    185.22419   -9.1006094    5.9615844   -1073.6008   -1067.6392 
-   18600         1.86  0.076457199    1571.9204    181.88092   -9.1245655    5.8539786   -1073.4932   -1067.6392 
-   18650        1.865  0.076457174    1547.9534    179.20735   -9.1468721    5.7679277   -1073.4072   -1067.6392 
-   18700         1.87  0.076457165    1552.3316    177.96057   -9.1713552    5.7277992    -1073.367   -1067.6392 
-   18750        1.875  0.076457197    1553.5318     178.2992   -9.1953424    5.7386981   -1073.3779   -1067.6392 
-   18800         1.88  0.076457184    1502.7768    179.82752   -9.2133625    5.7878883   -1073.4271   -1067.6392 
-   18850        1.885  0.076457121     1411.167    181.98955    -9.226772     5.857475   -1073.4967   -1067.6392 
-   18900         1.89   0.07645718    1331.5599    184.25555    -9.244306    5.9304078   -1073.5696   -1067.6392 
-   18950        1.895  0.076457306    1300.8838    185.96704    -9.269864    5.9854936   -1073.6247   -1067.6392 
-   19000          1.9  0.076457332    1341.3268    186.45142   -9.2968684    6.0010837   -1073.6403   -1067.6392 
-   19050        1.905  0.076457294    1418.9495    185.73025   -9.3201217    5.9778722   -1073.6171   -1067.6392 
-   19100         1.91  0.076457261    1469.3348    184.71078   -9.3405594    5.9450597   -1073.5843   -1067.6392 
-   19150        1.915   0.07645726    1494.8858    184.40838   -9.3593456    5.9353267   -1073.5746   -1067.6392 
-   19200         1.92  0.076457302    1535.9214    185.12696   -9.3754395     5.958455   -1073.5977   -1067.6392 
-   19250        1.925  0.076457322    1578.5937     186.7022   -9.3955891    6.0091552   -1073.6484   -1067.6392 
-   19300         1.93   0.07645736    1578.7452    188.80101   -9.4323472     6.076707   -1073.7159   -1067.6392 
-   19350        1.935  0.076457464    1549.5413    190.55677   -9.4860328    6.1332175   -1073.7725   -1067.6392 
-   19400         1.94  0.076457401    1518.0105     190.8838    -9.545051    6.1437434    -1073.783   -1067.6392 
-   19450        1.945  0.076457226    1476.9524    189.41845   -9.6005799    6.0965799   -1073.7358   -1067.6392 
-   19500         1.95  0.076457236    1453.8032     186.8834   -9.6531215    6.0149872   -1073.6542   -1067.6392 
-   19550        1.955  0.076457309    1436.5876    184.62159   -9.7075641     5.942189   -1073.5814   -1067.6392 
-   19600         1.96  0.076457314    1395.5458    183.83049   -9.7642712    5.9167271    -1073.556   -1067.6392 
-   19650        1.965  0.076457309     1342.194    185.07394   -9.8173107    5.9567485    -1073.596   -1067.6392 
-   19700         1.97  0.076457382    1296.9221    188.42121    -9.866389    6.0644829   -1073.7037   -1067.6392 
-   19750        1.975  0.076457367    1284.6809    193.29911   -9.9107399    6.2214817   -1073.8607   -1067.6392 
-   19800         1.98  0.076457239    1277.2922    198.66316    -9.946204    6.3941279   -1074.0334   -1067.6392 
-   19850        1.985  0.076457182    1240.7957    203.40147   -9.9754722    6.5466343   -1074.1859   -1067.6392 
-   19900         1.99   0.07645726    1203.1195    206.12078   -10.001353    6.6341571   -1074.2734   -1067.6392 
-   19950        1.995  0.076457363    1202.7274    205.68644   -10.025039    6.6201776   -1074.2594   -1067.6392 
-   20000            2  0.076457341     1220.191    202.20273   -10.047292    6.5080517   -1074.1473   -1067.6392 
-   20050        2.005  0.076457241    1219.9293    197.12841   -10.066398    6.3447308    -1073.984   -1067.6392 
-   20100         2.01  0.076457168    1194.4117    192.23758   -10.079101    6.1873157   -1073.8265   -1067.6392 
-   20150        2.015  0.076457198    1169.6328    188.78101   -10.085348    6.0760632   -1073.7153   -1067.6392 
-   20200         2.02  0.076457237    1170.2112    187.39597   -10.084836    6.0314848   -1073.6707   -1067.6392 
-   20250        2.025  0.076457263    1178.3781    188.35798   -10.080252    6.0624476   -1073.7017   -1067.6392 
-   20300         2.03  0.076457263    1193.5136    191.43468   -10.076517    6.1614738   -1073.8007   -1067.6392 
-   20350        2.035  0.076457217     1217.151    195.69411   -10.073155    6.2985667   -1073.9378   -1067.6392 
-   20400         2.04  0.076457203    1235.3327     200.1109   -10.073615    6.4407245     -1074.08   -1067.6392 
-   20450        2.045  0.076457254    1242.9155    203.63993   -10.081258    6.5543091   -1074.1935   -1067.6392 
-   20500         2.05  0.076457271    1241.9055     205.2779   -10.095394    6.6070286   -1074.2463   -1067.6392 
-   20550        2.055  0.076457271    1221.6949    204.56884   -10.116586    6.5842068   -1074.2234   -1067.6392 
-   20600         2.06  0.076457294    1226.6359    201.68982   -10.144389    6.4915433   -1074.1308   -1067.6392 
-   20650        2.065   0.07645732    1283.4482    197.23304   -10.174916    6.3480985   -1073.9873   -1067.6392 
-   20700         2.07  0.076457316      1329.13    192.42022   -10.208859    6.1931942   -1073.8324   -1067.6392 
-   20750        2.075  0.076457251    1326.0056    189.01786   -10.251588    6.0836867   -1073.7229   -1067.6392 
-   20800         2.08  0.076457224    1289.0675    188.31447   -10.298492    6.0610474   -1073.7003   -1067.6392 
-   20850        2.085  0.076457272    1261.4039    190.77218   -10.344257    6.1401507   -1073.7794   -1067.6392 
-   20900         2.09  0.076457341    1274.4048    195.96512   -10.390177    6.3072895   -1073.9465   -1067.6392 
-   20950        2.095  0.076457382    1294.6179    202.31796    -10.42989    6.5117606    -1074.151   -1067.6392 
-   21000          2.1  0.076457336    1271.5204    207.81694   -10.451365    6.6887496    -1074.328   -1067.6392 
-   21050        2.105  0.076457218    1224.8924    211.49094   -10.462946    6.8070002   -1074.4462   -1067.6392 
-   21100         2.11  0.076457179    1197.0124    213.27369   -10.482662    6.8643792   -1074.5036   -1067.6392 
-   21150        2.115  0.076457232    1200.2169    213.01628   -10.509071    6.8560942   -1074.4953   -1067.6392 
-   21200         2.12  0.076457334    1233.3373    211.01674   -10.539776    6.7917377    -1074.431   -1067.6392 
-   21250        2.125  0.076457324    1292.2293    208.23361   -10.582784    6.7021603   -1074.3414   -1067.6392 
-   21300         2.13  0.076457234    1353.0348    205.33718   -10.632972    6.6089366   -1074.2482   -1067.6392 
-   21350        2.135  0.076457274    1390.9107    202.43255   -10.667402    6.5154488   -1074.1547   -1067.6392 
-   21400         2.14  0.076457309    1398.7408    199.69704   -10.670157    6.4274041   -1074.0666   -1067.6392 
-   21450        2.145  0.076457306    1400.5231    197.71241   -10.646924    6.3635274   -1074.0028   -1067.6392 
-   21500         2.15  0.076457319    1422.7259    197.36253   -10.618311    6.3522661   -1073.9915   -1067.6392 
-   21550        2.155  0.076457297    1434.7766    199.14128   -10.598724    6.4095165   -1074.0487   -1067.6392 
-   21600         2.16  0.076457278    1429.5442    202.52793   -10.589548    6.5185185   -1074.1577   -1067.6392 
-   21650        2.165  0.076457295     1420.497     206.1935   -10.591701     6.636498   -1074.2757   -1067.6392 
-   21700         2.17  0.076457276    1378.0825    208.36958   -10.599065    6.7065365   -1074.3458   -1067.6392 
-   21750        2.175  0.076457297    1325.5891    208.06821   -10.604715    6.6968368   -1074.3361   -1067.6392 
-   21800         2.18  0.076457341    1286.1379    205.87017   -10.612217    6.6260911   -1074.2653   -1067.6392 
-   21850        2.185  0.076457343    1249.4394    203.00417   -10.618963    6.5338467   -1074.1731   -1067.6392 
-   21900         2.19  0.076457342    1219.6068    200.92404   -10.618829    6.4668963   -1074.1061   -1067.6392 
-   21950        2.195  0.076457255    1203.2091    201.06239   -10.615316    6.4713491   -1074.1106   -1067.6392 
-   22000          2.2  0.076457157    1207.2707    203.83245   -10.616122    6.5605055   -1074.1997   -1067.6392 
-   22050        2.205  0.076457174    1213.7955    208.32753   -10.627885    6.7051832   -1074.3444   -1067.6392 
-   22100         2.21  0.076457305    1217.4318    212.84143   -10.652913    6.8504667   -1074.4897   -1067.6392 
-   22150        2.215  0.076457345    1210.5327     215.5321   -10.688094    6.9370678   -1074.5763   -1067.6392 
-   22200         2.22  0.076457215    1195.2458    215.20969    -10.73343    6.9266909   -1074.5659   -1067.6392 
-   22250        2.225  0.076457077    1182.8507    211.73156   -10.788326    6.8147447    -1074.454   -1067.6392 
-   22300         2.23  0.076457075    1161.1546    206.13732   -10.841515    6.6346895   -1074.2739   -1067.6392 
-   22350        2.235  0.076457134    1136.2879    200.67718   -10.880177    6.4589508   -1074.0982   -1067.6392 
-   22400         2.24   0.07645722    1141.1588    197.90394   -10.902196     6.369692   -1074.0089   -1067.6392 
-   22450        2.245   0.07645725    1183.4596    199.22083   -10.913175     6.412077   -1074.0513   -1067.6392 
-   22500         2.25  0.076457199    1229.4238    204.41082   -10.921755    6.5791208   -1074.2184   -1067.6392 
-   22550        2.255  0.076457171     1264.902    212.14836   -10.939819    6.8281595   -1074.4674   -1067.6392 
-   22600         2.26  0.076457158    1287.9026    220.33991   -10.971089     7.091811    -1074.731   -1067.6392 
-   22650        2.265  0.076457207    1311.4828     226.7258   -11.007167    7.2973458   -1074.9366   -1067.6392 
-   22700         2.27  0.076457319    1353.9253    229.84218   -11.040634    7.3976489   -1075.0369   -1067.6392 
-   22750        2.275  0.076457274    1390.1174    229.24441   -11.068644    7.3784091   -1075.0176   -1067.6392 
-   22800         2.28  0.076457156    1387.0664    225.36499   -11.095325    7.2535471   -1074.8928   -1067.6392 
-   22850        2.285  0.076457176    1360.9519    219.18675   -11.130488    7.0546956   -1074.6939   -1067.6392 
-   22900         2.29  0.076457316     1344.359    211.76274   -11.174978    6.8157482    -1074.455   -1067.6392 
-   22950        2.295   0.07645732    1299.3984    204.35647   -11.214963    6.5773717   -1074.2166   -1067.6392 
-   23000          2.3  0.076457162    1231.7571    198.93484     -11.2383    6.4028722   -1074.0421   -1067.6392 
-   23050        2.305   0.07645712    1199.0791    197.45133   -11.245595    6.3551243   -1073.9944   -1067.6392 
-   23100         2.31  0.076457206    1194.5403    200.36018   -11.246069    6.4487479    -1074.088   -1067.6392 
-   23150        2.315   0.07645717    1213.0855    206.27572   -11.249945    6.6391441   -1074.2784   -1067.6392 
-   23200         2.32  0.076457149    1247.0389    212.62317    -11.25317    6.8434419   -1074.4827   -1067.6392 
-   23250        2.325  0.076457232    1252.9771    217.14066   -11.243809    6.9888406   -1074.6281   -1067.6392 
-   23300         2.33  0.076457298    1246.3963     219.5467   -11.230203    7.0662811   -1074.7055   -1067.6392 
-   23350        2.335  0.076457347    1263.8532    220.90621   -11.226826    7.1100378   -1074.7493   -1067.6392 
-   23400         2.34  0.076457343    1278.9193    222.02245   -11.231757    7.1459649   -1074.7852   -1067.6392 
-   23450        2.345  0.076457298    1271.4615    223.28544   -11.242585    7.1866153   -1074.8258   -1067.6392 
-   23500         2.35  0.076457216    1263.4764    224.76526   -11.261772    7.2342444   -1074.8735   -1067.6392 
-   23550        2.355  0.076457156    1269.5953    225.95356   -11.284145    7.2724905   -1074.9117   -1067.6392 
-   23600         2.36  0.076457239     1268.359    226.26773   -11.305282    7.2826025   -1074.9218   -1067.6392 
-   23650        2.365  0.076457257    1265.5906    225.69913     -11.3327    7.2643016   -1074.9035   -1067.6392 
-   23700         2.37  0.076457123    1275.7614    224.53597   -11.374051    7.2268646   -1074.8661   -1067.6392 
-   23750        2.375  0.076457085    1287.3169    222.75095   -11.424079    7.1694122   -1074.8086   -1067.6392 
-   23800         2.38  0.076457174    1303.4659    219.83945   -11.467156    7.0757035   -1074.7149   -1067.6392 
-   23850        2.385  0.076457349    1312.2776     215.4104   -11.491657    6.9331509   -1074.5724   -1067.6392 
-   23900         2.39  0.076457447    1300.2196    210.22181   -11.505842     6.766152   -1074.4054   -1067.6392 
-   23950        2.395  0.076457318    1285.3883    205.91466   -11.523034    6.6275231   -1074.2668   -1067.6392 
-   24000          2.4  0.076457215    1271.3069    203.89116   -11.544141    6.5623954   -1074.2016   -1067.6392 
-   24050        2.405   0.07645717    1275.6297    204.82158   -11.568504    6.5923414   -1074.2316   -1067.6392 
-   24100         2.41  0.076457155    1308.5278    208.28691   -11.593169     6.703876   -1074.3431   -1067.6392 
-   24150        2.415  0.076457173    1320.3939    213.14435   -11.610405    6.8602164   -1074.4994   -1067.6392 
-   24200         2.42  0.076457286    1290.2677    218.34701   -11.616172    7.0276681   -1074.6669   -1067.6392 
-   24250        2.425   0.07645742    1266.5534    223.16759   -11.612622     7.182822   -1074.8221   -1067.6392 
-   24300         2.43  0.076457424    1263.1458    227.14553   -11.607449     7.310855   -1074.9501   -1067.6392 
-   24350        2.435  0.076457322    1278.3394    229.88879   -11.606753    7.3991491   -1075.0384   -1067.6392 
-   24400         2.44  0.076457217    1299.8856    231.18375    -11.60862    7.4408286   -1075.0801   -1067.6392 
-   24450        2.445  0.076457261    1314.6037    231.51695   -11.609751    7.4515526   -1075.0908   -1067.6392 
-   24500         2.45  0.076457395    1306.5195    231.80528   -11.609243    7.4608328   -1075.1001   -1067.6392 
-   24550        2.455  0.076457379    1284.1202    232.64324    -11.61431    7.4878034    -1075.127   -1067.6392 
-   24600         2.46  0.076457237    1266.9925    233.34522   -11.628582     7.510397   -1075.1496   -1067.6392 
-   24650        2.465  0.076457198    1282.9995    232.39636   -11.648257    7.4798573   -1075.1191   -1067.6392 
-   24700         2.47   0.07645726     1305.414    229.20359   -11.674265    7.3770956   -1075.0163   -1067.6392 
-   24750        2.475   0.07645732    1301.6393    224.60137   -11.703977    7.2289695   -1074.8682   -1067.6392 
-   24800         2.48  0.076457337    1286.6037    220.28411   -11.728511     7.090015   -1074.7292   -1067.6392 
-   24850        2.485  0.076457248    1285.2636    217.75575   -11.741746    7.0086378   -1074.6479   -1067.6392 
-   24900         2.49  0.076457211    1273.3347    217.15842   -11.738866    6.9894122   -1074.6286   -1067.6392 
-   24950        2.495  0.076457314    1254.4627    217.67065   -11.724117    7.0058988   -1074.6451   -1067.6392 
-   25000          2.5   0.07645736    1252.7349     218.6929   -11.717307    7.0388007    -1074.678   -1067.6392 
-   25050        2.505  0.076457303    1253.3725     220.1096   -11.733758    7.0843985   -1074.7236   -1067.6392 
-   25100         2.51  0.076457303    1226.6085    221.88399   -11.763112    7.1415083   -1074.7807   -1067.6392 
-   25150        2.515  0.076457323    1179.7816    224.12648   -11.787319    7.2136847   -1074.8529   -1067.6392 
-   25200         2.52  0.076457341    1147.9357    227.17475   -11.806595    7.3117955    -1074.951   -1067.6392 
-   25250        2.525  0.076457289    1122.8538    230.61744   -11.827081    7.4226013   -1075.0618   -1067.6392 
-   25300         2.53  0.076457275    1123.0584    232.62891   -11.840179     7.487342   -1075.1266   -1067.6392 
-   25350        2.535  0.076457325    1135.7283    231.67931   -11.840266    7.4567784    -1075.096   -1067.6392 
-   25400         2.54  0.076457369    1132.9884    228.34818   -11.841402    7.3495632   -1074.9888   -1067.6392 
-   25450        2.545  0.076457373    1126.8396    224.33046   -11.849704    7.2202499   -1074.8595   -1067.6392 
-   25500         2.55  0.076457345    1138.9754    220.94924   -11.854541    7.1114227   -1074.7507   -1067.6392 
-   25550        2.555  0.076457293    1161.4091    218.97947    -11.85351    7.0480242   -1074.6873   -1067.6392 
-   25600         2.56  0.076457314    1174.3492    218.77523   -11.860158    7.0414507   -1074.6807   -1067.6392 
-   25650        2.565   0.07645744    1168.4635    220.04213   -11.881157    7.0822266   -1074.7215   -1067.6392 
-   25700         2.57  0.076457455    1176.9925    222.26325   -11.910611     7.153715   -1074.7929   -1067.6392 
-   25750        2.575  0.076457341    1184.7961    225.03857   -11.939316    7.2430409   -1074.8823   -1067.6392 
-   25800         2.58  0.076457304    1154.7511    227.79451   -11.960291    7.3317431    -1074.971   -1067.6392 
-   25850        2.585  0.076457382    1114.3611    229.90007    -11.97576    7.3995122   -1075.0387   -1067.6392 
-   25900         2.59  0.076457443    1085.8869    230.83015   -11.989347    7.4294476   -1075.0687   -1067.6392 
-   25950        2.595  0.076457402    1078.3201    230.19636   -12.002061    7.4090485   -1075.0483   -1067.6392 
-   26000          2.6  0.076457319    1095.9541    227.61221   -12.008597    7.3258755   -1074.9651   -1067.6392 
-   26050        2.605  0.076457291    1140.9903    223.50282   -12.008527    7.1936117   -1074.8328   -1067.6392 
-   26100         2.61  0.076457385     1178.622    219.76032   -12.018995    7.0731563   -1074.7124   -1067.6392 
-   26150        2.615  0.076457448    1173.4374    218.06955   -12.044671    7.0187377    -1074.658   -1067.6392 
-   26200         2.62  0.076457408    1151.1453    218.96082   -12.075861    7.0474238   -1074.6867   -1067.6392 
-   26250        2.625  0.076457383    1155.4138    222.06391   -12.101821    7.1472992   -1074.7865   -1067.6392 
-   26300         2.63  0.076457372    1194.7964    226.66949   -12.116261    7.2955333   -1074.9348   -1067.6392 
-   26350        2.635  0.076457363    1223.2766    232.21329   -12.127208    7.4739649   -1075.1132   -1067.6392 
-   26400         2.64  0.076457354    1223.9805    237.61275   -12.140513    7.6477507    -1075.287   -1067.6392 
-   26450        2.645  0.076457281     1218.086    241.25999    -12.14955    7.7651401   -1075.4044   -1067.6392 
-   26500         2.65   0.07645724    1226.9905    242.22464   -12.151248    7.7961882   -1075.4354   -1067.6392 
-   26550        2.655  0.076457293    1247.8203     240.6035   -12.151475    7.7440104   -1075.3832   -1067.6392 
-   26600         2.66  0.076457269    1242.9798    237.04434   -12.161376    7.6294559   -1075.2687   -1067.6392 
-   26650        2.665  0.076457162    1205.6877    232.19203   -12.183196    7.4732806   -1075.1125   -1067.6392 
-   26700         2.67   0.07645716    1172.6996    227.25303   -12.214748    7.3143152   -1074.9535   -1067.6392 
-   26750        2.675  0.076457262    1153.9255    224.05517   -12.256042    7.2113895   -1074.8506   -1067.6392 
-   26800         2.68  0.076457311    1136.0414    223.48738   -12.295525    7.1931146   -1074.8323   -1067.6392 
-   26850        2.685  0.076457307    1118.9445    225.12955   -12.319088    7.2459693   -1074.8852   -1067.6392 
-   26900         2.69  0.076457308    1108.0624     228.2382   -12.325255    7.3460238   -1074.9853   -1067.6392 
-   26950        2.695  0.076457378    1116.2269    232.45212   -12.323702    7.4816518   -1075.1209   -1067.6392 
-   27000          2.7   0.07645739    1134.9488    237.58432   -12.328662    7.6468358   -1075.2861   -1067.6392 
-   27050        2.705   0.07645735    1138.9878    242.69968   -12.344967    7.8114775   -1075.4507   -1067.6392 
-   27100         2.71   0.07645736    1129.3313    246.18245   -12.366079    7.9235733   -1075.5628   -1067.6392 
-   27150        2.715  0.076457354    1124.2775    246.92127   -12.384885    7.9473528   -1075.5866   -1067.6392 
-   27200         2.72  0.076457305     1108.739    245.14655   -12.403913    7.8902318   -1075.5295   -1067.6392 
-   27250        2.725  0.076457306    1108.6304    241.74994   -12.427874    7.7809096   -1075.4201   -1067.6392 
-   27300         2.73  0.076457366    1145.8269    237.40384   -12.453673     7.641027   -1075.2803   -1067.6392 
-   27350        2.735  0.076457346    1182.0337    232.72259   -12.475581    7.4903572   -1075.1296   -1067.6392 
-   27400         2.74  0.076457288    1197.1644    228.48145   -12.490327    7.3538529   -1074.9931   -1067.6392 
-   27450        2.745  0.076457272    1211.3793    225.74198    -12.50044    7.2656808   -1074.9049   -1067.6392 
-   27500         2.75  0.076457331    1258.8799    225.52316   -12.511305    7.2586379   -1074.8979   -1067.6392 
-   27550        2.755  0.076457388    1308.0524    227.54337   -12.522462    7.3236601   -1074.9629   -1067.6392 
-   27600         2.76  0.076457348     1328.121    230.14115   -12.523762    7.4072716   -1075.0465   -1067.6392 
-   27650        2.765  0.076457243    1340.2612    232.32442   -12.510293    7.4775417   -1075.1168   -1067.6392 
-   27700         2.77  0.076457161    1351.5963     234.3197   -12.488706    7.5417616    -1075.181   -1067.6392 
-   27750        2.775  0.076457282    1357.7982    236.12334   -12.460757    7.5998128    -1075.239   -1067.6392 
-   27800         2.78  0.076457422    1361.4651    237.29306   -12.430447    7.6374614   -1075.2767   -1067.6392 
-   27850        2.785  0.076457378    1361.9438    237.41071   -12.408369    7.6412479   -1075.2805   -1067.6392 
-   27900         2.79  0.076457207    1354.0021    236.45794   -12.402868    7.6105824   -1075.2498   -1067.6392 
-   27950        2.795  0.076457167    1330.2965    235.02473   -12.414971    7.5644534   -1075.2037   -1067.6392 
-   28000          2.8  0.076457251    1299.3048     233.7726    -12.43317    7.5241524   -1075.1634   -1067.6392 
-   28050        2.805  0.076457269    1277.0133    233.28243   -12.448406    7.5083761   -1075.1476   -1067.6392 
-   28100         2.81  0.076457225    1251.8497     234.0353   -12.464212    7.5326077   -1075.1718   -1067.6392 
-   28150        2.815  0.076457297    1208.4966    235.64084   -12.477803    7.5842833   -1075.2235   -1067.6392 
-   28200         2.82  0.076457399    1198.6158    237.16084   -12.484054    7.6332057   -1075.2724   -1067.6392 
-   28250        2.825  0.076457406    1239.4401     237.9696   -12.486107    7.6592361   -1075.2985   -1067.6392 
-   28300         2.83  0.076457357    1293.9124     237.8743   -12.489779    7.6561691   -1075.2954   -1067.6392 
-   28350        2.835  0.076457319    1312.3301    237.34832    -12.50409      7.63924   -1075.2785   -1067.6392 
-   28400         2.84  0.076457322    1285.5505    237.14016   -12.527163    7.6325402   -1075.2718   -1067.6392 
-   28450        2.845  0.076457378    1245.9557    237.75445   -12.548289    7.6523114   -1075.2915   -1067.6392 
-   28500         2.85  0.076457388    1235.3861    238.91062   -12.557157    7.6895238   -1075.3288   -1067.6392 
-   28550        2.855  0.076457337    1268.9513    240.25184   -12.560084    7.7326918   -1075.3719   -1067.6392 
-   28600         2.86  0.076457363    1304.4221    241.87684   -12.576878    7.7849937   -1075.4242   -1067.6392 
-   28650        2.865  0.076457362    1297.8936    243.05258    -12.60596    7.8228358   -1075.4621   -1067.6392 
-   28700         2.87  0.076457347    1249.8912    242.36176   -12.630048    7.8006014   -1075.4398   -1067.6392 
-   28750        2.875  0.076457391    1211.5737    239.53884   -12.648513    7.7097434    -1075.349   -1067.6392 
-   28800         2.88  0.076457383    1202.6703    235.69511   -12.669768      7.58603   -1075.2253   -1067.6392 
-   28850        2.885   0.07645729    1216.8735    232.20584   -12.686867    7.4737252    -1075.113   -1067.6392 
-   28900         2.89  0.076457246    1241.5924    230.54911   -12.693862    7.4204019   -1075.0596   -1067.6392 
-   28950        2.895  0.076457286     1240.767    231.97347   -12.701097    7.4662461   -1075.1055   -1067.6392 
-   29000          2.9  0.076457358    1217.5962    236.18629   -12.716277    7.6018392   -1075.2411   -1067.6392 
-   29050        2.905  0.076457432    1196.6203    241.17448    -12.73636    7.7623879   -1075.4016   -1067.6392 
-   29100         2.91  0.076457522    1195.7297     244.6264   -12.752906    7.8734904   -1075.5127   -1067.6392 
-   29150        2.915  0.076457557    1231.0931    245.54928   -12.765411    7.9031941   -1075.5424   -1067.6392 
-   29200         2.92   0.07645753    1267.4904    244.15127   -12.781472    7.8581982   -1075.4974   -1067.6392 
-   29250        2.925  0.076457521    1284.1755     240.9389   -12.800258    7.7548054    -1075.394   -1067.6392 
-   29300         2.93  0.076457564    1286.0387    237.25035   -12.821281    7.6360866   -1075.2753   -1067.6392 
-   29350        2.935  0.076457553    1256.2955    235.11519   -12.847909    7.5673647   -1075.2066   -1067.6392 
-   29400         2.94  0.076457534    1204.4184     235.8746   -12.878902     7.591807    -1075.231   -1067.6392 
-   29450        2.945  0.076457502    1156.6997    239.23804   -12.906804     7.700062   -1075.3393   -1067.6392 
-   29500         2.95  0.076457485    1116.1408    243.69565   -12.924534    7.8435336   -1075.4828   -1067.6392 
-   29550        2.955  0.076457504    1105.9977    247.90665   -12.938831     7.979068   -1075.6183   -1067.6392 
-   29600         2.96  0.076457547    1114.6315    250.84823   -12.956708    8.0737448    -1075.713   -1067.6392 
-   29650        2.965   0.07645753    1139.9431    251.55972   -12.974842    8.0966448   -1075.7359   -1067.6392 
-   29700         2.97  0.076457492    1194.9224    249.83103   -12.990073    8.0410056   -1075.6802   -1067.6392 
-   29750        2.975  0.076457443     1239.364     246.6967   -13.001472    7.9401246   -1075.5794   -1067.6392 
-   29800         2.98  0.076457457    1252.6783    243.80542   -13.010513    7.8470666   -1075.4863   -1067.6392 
-   29850        2.985  0.076457512    1240.1645    241.74022   -13.018373    7.7805965   -1075.4198   -1067.6392 
-   29900         2.99  0.076457565    1223.7615    239.43409   -13.020593    7.7063721   -1075.3456   -1067.6392 
-   29950        2.995  0.076457595    1204.1487    235.75951   -13.015055    7.5881027   -1075.2273   -1067.6392 
-   30000            3  0.076457625    1186.3894     230.7717   -13.002308    7.4275663   -1075.0668   -1067.6392 
-   30050        3.005  0.076457551    1196.5894    226.06185   -12.988551     7.275976   -1074.9152   -1067.6392 
-   30100         3.01  0.076457433    1233.2652    224.05561    -12.98272    7.2114038   -1074.8506   -1067.6392 
-   30150        3.015  0.076457506    1263.4065     226.5763   -12.989178    7.2925339   -1074.9318   -1067.6392 
-   30200         3.02  0.076457597    1273.2272    233.82971   -13.003426    7.5259905   -1075.1652   -1067.6392 
-   30250        3.025  0.076457526    1276.9473    244.40258   -13.018097    7.8662868   -1075.5055   -1067.6392 
-   30300         3.03  0.076457432    1275.5446    255.93782   -13.034602    8.2375574   -1075.8768   -1067.6392 
-   30350        3.035  0.076457464    1250.8783    265.87839   -13.057824    8.5575024   -1076.1967   -1067.6392 
-   30400         3.04  0.076457427    1235.9551    272.00442   -13.083661    8.7546732   -1076.3939   -1067.6392 
-   30450        3.045  0.076457316    1235.5042    273.37792   -13.111283    8.7988804   -1076.4381   -1067.6392 
-   30500         3.05   0.07645726    1230.6233    270.64686   -13.146707    8.7109792   -1076.3502   -1067.6392 
-   30550        3.055  0.076457233    1224.1115     265.0222   -13.182314    8.5299452   -1076.1692   -1067.6392 
-   30600         3.06  0.076457361    1212.3027    257.68391   -13.202367    8.2937568    -1075.933   -1067.6392 
-   30650        3.065  0.076457487    1190.0178    249.77024   -13.201564    8.0390489   -1075.6783   -1067.6392 
-   30700         3.07  0.076457394    1161.8109    242.31657   -13.191293    7.7991468   -1075.4384   -1067.6392 
-   30750        3.075  0.076457252    1158.6855    236.08427    -13.18911    7.5985553   -1075.2378   -1067.6392 
-   30800         3.08  0.076457183    1168.5206    231.60347   -13.197075    7.4543374   -1075.0936   -1067.6392 
-   30850        3.085  0.076457279    1158.9328    229.71585   -13.209643    7.3935831   -1075.0328   -1067.6392 
-   30900         3.09  0.076457454    1136.1168    231.05928   -13.230895    7.4368221   -1075.0761   -1067.6392 
-   30950        3.095  0.076457365    1140.4629    234.79871   -13.261019    7.5571786   -1075.1964   -1067.6392 
-   31000          3.1  0.076457233    1151.4718    238.95885     -13.2835     7.691076   -1075.3303   -1067.6392 
-   31050        3.105  0.076457249    1136.0165    241.99628   -13.285479    7.7888381   -1075.4281   -1067.6392 
-   31100         3.11  0.076457312    1095.4919     243.6173   -13.274528     7.841012   -1075.4802   -1067.6392 
-   31150        3.115  0.076457361    1043.3403    244.60685   -13.261288    7.8728613   -1075.5121   -1067.6392 
-   31200         3.12  0.076457255    1000.1386    246.53553   -13.250369    7.9349374   -1075.5742   -1067.6392 
-   31250        3.125  0.076457166    991.81643    250.55835    -13.24872    8.0644151   -1075.7036   -1067.6392 
-   31300         3.13  0.076457166    1022.1079     256.4075   -13.267835    8.2526743   -1075.8919   -1067.6392 
-   31350        3.135  0.076457189    1054.9092    262.76827   -13.305663    8.4574006   -1076.0966   -1067.6392 
-   31400         3.14   0.07645724    1060.5815    267.85735   -13.342713    8.6211968   -1076.2604   -1067.6392 
-   31450        3.145  0.076457287    1049.3579    269.97994    -13.36678    8.6895138   -1076.3287   -1067.6392 
-   31500         3.15  0.076457292    1020.7582     268.2573   -13.386937    8.6340694   -1076.2733   -1067.6392 
-   31550        3.155  0.076457309    996.86817    262.55532   -13.414409    8.4505467   -1076.0898   -1067.6392 
-   31600         3.16  0.076457265     988.4472    253.14804    -13.44617    8.1477662    -1075.787   -1067.6392 
-   31650        3.165   0.07645717    975.20678     241.3533   -13.472839    7.7681433   -1075.4074   -1067.6392 
-   31700         3.17  0.076457122    978.08946    230.12225   -13.489241    7.4066632   -1075.0459   -1067.6392 
-   31750        3.175  0.076457159     994.1906    223.24272     -13.4961    7.1852402   -1074.8245   -1067.6392 
-   31800         3.18  0.076457198    1011.9808    223.61603   -13.502125    7.1972556   -1074.8365   -1067.6392 
-   31850        3.185  0.076457197    1043.2929    231.32793   -13.514524    7.4454691   -1075.0847   -1067.6392 
-   31900         3.19  0.076457211    1073.2125    243.48614   -13.529663    7.8367904    -1075.476   -1067.6392 
-   31950        3.195  0.076457283     1089.512    255.96547   -13.531619    8.2384474   -1075.8777   -1067.6392 
-   32000          3.2  0.076457346    1091.1766    265.64481   -13.515072    8.5499844   -1076.1892   -1067.6392 
-   32050        3.205  0.076457238    1107.4466    271.60773   -13.502747    8.7419056   -1076.3811   -1067.6392 
-   32100         3.21  0.076457153    1117.8805    274.08365    -13.50656    8.8215948   -1076.4608   -1067.6392 
-   32150        3.215  0.076457122    1123.2092    273.86962   -13.522054    8.8147064   -1076.4539   -1067.6392 
-   32200         3.22  0.076457105    1152.6197    271.95614   -13.543888    8.7531194   -1076.3924   -1067.6392 
-   32250        3.225  0.076457164    1168.3769    268.86435   -13.563301    8.6536078   -1076.2928   -1067.6392 
-   32300         3.23  0.076457237    1158.6589    265.10575   -13.580865    8.5326342   -1076.1719   -1067.6392 
-   32350        3.235  0.076457159    1152.9881    261.29815   -13.605255    8.4100836   -1076.0493   -1067.6392 
-   32400         3.24   0.07645703    1164.2634    257.27542   -13.625646     8.280609   -1075.9198   -1067.6392 
-   32450        3.245  0.076457057    1173.0337    252.87376   -13.637472    8.1389381   -1075.7782   -1067.6392 
-   32500         3.25  0.076457171    1170.4615    248.34575   -13.651248    7.9932007   -1075.6324   -1067.6392 
-   32550        3.255  0.076457164    1172.6715    244.01198   -13.667945    7.8537149   -1075.4929   -1067.6392 
-   32600         3.26  0.076457072    1178.0602    240.61161   -13.683594    7.7442715   -1075.3835   -1067.6392 
-   32650        3.265  0.076457132    1164.2276    239.08635   -13.693266    7.6951799   -1075.3344   -1067.6392 
-   32700         3.27   0.07645721    1135.6536      239.997   -13.697188    7.7244896   -1075.3637   -1067.6392 
-   32750        3.275   0.07645717    1122.6725    242.77278   -13.697307    7.8138302   -1075.4531   -1067.6392 
-   32800         3.28  0.076457087    1124.7984    246.08264   -13.698507    7.9203608   -1075.5596   -1067.6392 
-   32850        3.285  0.076457071    1132.9874     248.8912    -13.71026    8.0107565     -1075.65   -1067.6392 
-   32900         3.29  0.076457146    1144.7957    250.92712   -13.736297    8.0762841   -1075.7155   -1067.6392 
-   32950        3.295   0.07645721    1152.7642    252.46291   -13.764351    8.1257148   -1075.7649   -1067.6392 
-   33000          3.3  0.076457168    1146.2857    254.10358   -13.779597    8.1785209   -1075.8178   -1067.6392 
-   33050        3.305  0.076457077    1145.5084     256.8303   -13.789612    8.2662826   -1075.9055   -1067.6392 
-   33100         3.31  0.076457096    1154.4041    261.13865   -13.808552      8.40495   -1076.0442   -1067.6392 
-   33150        3.315   0.07645715    1125.5641     266.3904   -13.833889    8.5739819   -1076.2132   -1067.6392 
-   33200         3.32   0.07645715    1093.2946     271.0557   -13.855364     8.724138   -1076.3634   -1067.6392 
-   33250        3.325  0.076457145    1095.5775    273.48025   -13.872191    8.8021741   -1076.4414   -1067.6392 
-   33300         3.33  0.076457162    1100.9708    272.81497   -13.884719    8.7807615     -1076.42   -1067.6392 
-   33350        3.335   0.07645717     1097.446    269.39464   -13.884534    8.6706755   -1076.3099   -1067.6392 
-   33400         3.34  0.076457107    1081.3925    264.90836   -13.877973    8.5262812   -1076.1655   -1067.6392 
-   33450        3.345  0.076457118    1078.1638    261.34438   -13.882973    8.4115716   -1076.0508   -1067.6392 
-   33500         3.35  0.076457263    1098.4302    259.43885   -13.901235    8.3502409   -1075.9895   -1067.6392 
-   33550        3.355    0.0764573     1113.653    258.79858   -13.925503    8.3296331   -1075.9689   -1067.6392 
-   33600         3.36  0.076457139    1102.1918    258.64576   -13.952352    8.3247147   -1075.9639   -1067.6392 
-   33650        3.365  0.076457044    1079.3943    258.32267   -13.984128    8.3143157   -1075.9535   -1067.6392 
-   33700         3.37  0.076457092    1080.4816     257.3355   -14.022263    8.2825429   -1075.9218   -1067.6392 
-   33750        3.375  0.076457159    1091.9482    255.16753   -14.058006    8.2127649    -1075.852   -1067.6392 
-   33800         3.38  0.076457132    1093.3842     251.7622   -14.081909    8.1031619   -1075.7424   -1067.6392 
-   33850        3.385  0.076457194    1089.6902     248.0965   -14.095869    7.9851785   -1075.6244   -1067.6392 
-   33900         3.39   0.07645727    1096.6474    246.01593   -14.105391    7.9182138   -1075.5574   -1067.6392 
-   33950        3.395  0.076457209     1126.664    247.11823   -14.104952    7.9536921   -1075.5929   -1067.6392 
-   34000          3.4  0.076457164    1147.9196    251.93896   -14.093155    8.1088509   -1075.7481   -1067.6392 
-   34050        3.405  0.076457179    1139.0305    259.69551   -14.085668    8.3585014   -1075.9977   -1067.6392 
-   34100         3.41  0.076457311    1111.5824    268.28371   -14.096523    8.6349193   -1076.2742   -1067.6392 
-   34150        3.415  0.076457318    1093.8889    274.76774   -14.115851    8.8436128   -1076.4828   -1067.6392 
-   34200         3.42  0.076457165     1080.138    277.06119   -14.126901    8.9174293   -1076.5567   -1067.6392 
-   34250        3.425  0.076457126    1068.8702    275.51584   -14.137497     8.867691   -1076.5069   -1067.6392 
-   34300         3.43  0.076457173    1079.0654    272.17988   -14.166544    8.7603208   -1076.3996   -1067.6392 
-   34350        3.435  0.076457237    1097.2929    268.53315   -14.204534    8.6429479   -1076.2822   -1067.6392 
-   34400         3.44  0.076457306    1090.4064    265.24166   -14.230854    8.5370086   -1076.1762   -1067.6392 
-   34450        3.445  0.076457334    1094.1532    263.10158    -14.24558    8.4681285   -1076.1074   -1067.6392 
-   34500         3.45  0.076457326    1091.6462    262.74486   -14.260327    8.4566473   -1076.0959   -1067.6392 
-   34550        3.455  0.076457285    1048.9417    263.68384   -14.279645     8.486869   -1076.1261   -1067.6392 
-   34600         3.46  0.076457322    1035.8659    264.38837   -14.298673     8.509545   -1076.1488   -1067.6392 
-   34650        3.465  0.076457348    1072.1468    263.89728   -14.317443    8.4937389    -1076.133   -1067.6392 
-   34700         3.47  0.076457257    1099.9068     262.7456   -14.336515    8.4566712   -1076.0959   -1067.6392 
-   34750        3.475   0.07645724    1086.8308    262.31079   -14.346872    8.4426763   -1076.0819   -1067.6392 
-   34800         3.48  0.076457278    1063.2908     263.8317   -14.348034     8.491628   -1076.1309   -1067.6392 
-   34850        3.485  0.076457253    1055.3547    267.54832   -14.355638    8.6112503   -1076.2505   -1067.6392 
-   34900         3.49  0.076457295    1035.2728    272.01532   -14.373099    8.7550243   -1076.3943   -1067.6392 
-   34950        3.495  0.076457375     1040.634    275.06802   -14.390413    8.8532777   -1076.4925   -1067.6392 
-   35000          3.5  0.076457344    1063.0087     275.5042   -14.407745    8.8673167   -1076.5065   -1067.6392 
-   35050        3.505  0.076457312    1058.6708    273.65876   -14.433515    8.8079196   -1076.4472   -1067.6392 
-   35100         3.51  0.076457257    1060.8523    271.14098   -14.474773    8.7268829   -1076.3661   -1067.6392 
-   35150        3.515  0.076457289    1067.0827    269.23085   -14.526301    8.6654039   -1076.3046   -1067.6392 
-   35200         3.52   0.07645742    1062.2236    268.14335   -14.573177    8.6304019   -1076.2696   -1067.6392 
-   35250        3.525  0.076457337    1070.5812    267.81607    -14.60424    8.6198681   -1076.2591   -1067.6392 
-   35300         3.53  0.076457217    1072.5143    267.83883   -14.617097    8.6206007   -1076.2598   -1067.6392 
-   35350        3.535  0.076457254    1028.3355    267.52283   -14.622569    8.6104298   -1076.2497   -1067.6392 
-   35400         3.54  0.076457305    1002.1085    266.59937   -14.633762    8.5807077   -1076.2199   -1067.6392 
-   35450        3.545  0.076457409     1029.413    265.25698   -14.649797    8.5375018   -1076.1767   -1067.6392 
-   35500         3.55  0.076457478    1063.6674    263.65567   -14.671113    8.4859625   -1076.1252   -1067.6392 
-   35550        3.555  0.076457385    1064.2389    261.55993   -14.712306    8.4185094   -1076.0577   -1067.6392 
-   35600         3.56  0.076457248     1043.973    258.13746   -14.765767    8.3083544   -1075.9476   -1067.6392 
-   35650        3.565  0.076457197    1018.5052    253.81996   -14.810087    8.1693925   -1075.8086   -1067.6392 
-   35700         3.57  0.076457358    1000.6206    251.22894   -14.843694    8.0859983   -1075.7252   -1067.6392 
-   35750        3.575  0.076457447    1017.4159    252.90054   -14.876657       8.1398    -1075.779   -1067.6392 
-   35800         3.58  0.076457294    1047.8317    258.96411   -14.909538    8.3349608   -1075.9742   -1067.6392 
-   35850        3.585  0.076457191    1082.9886    267.72357   -14.939208    8.6168909   -1076.2561   -1067.6392 
-   35900         3.59  0.076457278    1100.5702    277.23543   -14.962644    8.9230375   -1076.5623   -1067.6392 
-   35950        3.595  0.076457309     1086.933    285.96591   -14.977753    9.2040346   -1076.8433   -1067.6392 
-   36000          3.6  0.076457255    1074.2647     292.9362   -14.987968     9.428379   -1077.0676   -1067.6392 
-   36050        3.605   0.07645718    1055.2238    298.01121   -14.998446    9.5917221    -1077.231   -1067.6392 
-   36100         3.61  0.076457233    1047.2166    302.00821   -15.020568    9.7203687   -1077.3596   -1067.6392 
-   36150        3.615  0.076457349    1052.6407    305.28298   -15.059957    9.8257696    -1077.465   -1067.6392 
-   36200         3.62  0.076457311    1060.7211    306.93482    -15.10603    9.8789354   -1077.5182   -1067.6392 
-   36250        3.625  0.076457193    1068.8892    305.84803   -15.141949    9.8439561   -1077.4832   -1067.6392 
-   36300         3.63  0.076457194    1061.6868    301.87989    -15.16629    9.7162384   -1077.3555   -1067.6392 
-   36350        3.635  0.076457258    1057.9527     295.4431   -15.185933    9.5090656   -1077.1483   -1067.6392 
-   36400         3.64  0.076457264    1064.3799    287.24818   -15.203507    9.2453055   -1076.8845   -1067.6392 
-   36450        3.645  0.076457194    1063.7064    278.74515   -15.224498    8.9716288   -1076.6109   -1067.6392 
-   36500         3.65  0.076457136    1061.3588    271.32268     -15.2455     8.732731    -1076.372   -1067.6392 
-   36550        3.655  0.076457182    1067.1517    265.76761   -15.260325    8.5539369   -1076.1932   -1067.6392 
-   36600         3.66   0.07645727    1089.9772    261.85411   -15.267562    8.4279778   -1076.0672   -1067.6392 
-   36650        3.665  0.076457221     1104.789     258.4444   -15.265264    8.3182336   -1075.9575   -1067.6392 
-   36700         3.67   0.07645716    1092.8435    255.00082    -15.25529    8.2073992   -1075.8466   -1067.6392 
-   36750        3.675  0.076457168    1061.6595     252.8329   -15.247428    8.1376232   -1075.7769   -1067.6392 
-   36800         3.68  0.076457215    1035.3281    254.03876   -15.243457    8.1764346   -1075.8157   -1067.6392 
-   36850        3.685  0.076457264    1012.6747    259.66792   -15.232713    8.3576136   -1075.9968   -1067.6392 
-   36900         3.69   0.07645721    1000.1165    269.04132   -15.219475    8.6593036   -1076.2985   -1067.6392 
-   36950        3.695  0.076457158    1004.3738     279.5229   -15.222136    8.9966614   -1076.6359   -1067.6392 
-   37000          3.7  0.076457194    1015.0789    287.52665   -15.242557    9.2542684   -1076.8935   -1067.6392 
-   37050        3.705  0.076457209    1006.6001    291.33936   -15.269368    9.3769835   -1077.0162   -1067.6392 
-   37100         3.71  0.076457215    1009.5254    292.25598   -15.292099    9.4064856   -1077.0457   -1067.6392 
-   37150        3.715  0.076457221    1035.7983     292.7155   -15.306557    9.4212757   -1077.0605   -1067.6392 
-   37200         3.72  0.076457114    1030.9374    293.77202   -15.308274    9.4552805   -1077.0945   -1067.6392 
-   37250        3.725  0.076457028    982.50822     295.2423   -15.305932    9.5026027   -1077.1418   -1067.6392 
-   37300         3.73  0.076457035    948.55083    296.17303   -15.311999    9.5325589   -1077.1718   -1067.6392 
-   37350        3.735  0.076457098    937.47027    295.49824   -15.335364    9.5108401   -1077.1501   -1067.6392 
-   37400         3.74  0.076457181    936.77662    292.98591   -15.385092     9.429979   -1077.0692   -1067.6392 
-   37450        3.745  0.076457164    937.43311    288.88554    -15.44922    9.2980054   -1076.9372   -1067.6392 
-   37500         3.75  0.076457095    942.75677     284.1287   -15.497475    9.1449027   -1076.7841   -1067.6392 
-   37550        3.755  0.076457051    973.14442    280.71281   -15.516447    9.0349597   -1076.6742   -1067.6392 
-   37600         3.76  0.076457064    1023.9535    280.23051   -15.517936    9.0194364   -1076.6587   -1067.6392 
-   37650        3.765  0.076457028    1061.1038    282.66393   -15.519455    9.0977579    -1076.737   -1067.6392 
-   37700         3.77  0.076457072    1070.7829    287.04664   -15.525411    9.2388189   -1076.8781   -1067.6392 
-   37750        3.775  0.076457124    1066.3938    291.68394   -15.520525     9.388074   -1077.0273   -1067.6392 
-   37800         3.78  0.076457071    1048.9796    294.14399   -15.497921    9.4672528   -1077.1065   -1067.6392 
-   37850        3.785  0.076457038    1038.2533    292.47043   -15.480179    9.4133879   -1077.0526   -1067.6392 
-   37900         3.79  0.076457018     1045.648    286.41439   -15.491193    9.2184695   -1076.8577   -1067.6392 
-   37950        3.795  0.076457122    1065.9631    277.89366   -15.523881    8.9442232   -1076.5835   -1067.6392 
-   38000          3.8   0.07645714    1090.5261    270.72264   -15.554861    8.7134183   -1076.3526   -1067.6392 
-   38050        3.805  0.076457032    1113.2307    268.45698   -15.575531    8.6404964   -1076.2797   -1067.6392 
-   38100         3.81  0.076457024    1116.2952    271.45106   -15.582548    8.7368631   -1076.3761   -1067.6392 
-   38150        3.815   0.07645699    1093.8664    277.51108   -15.573712    8.9319094   -1076.5711   -1067.6392 
-   38200         3.82  0.076456911     1051.845    284.62475    -15.56289    9.1608685   -1076.8001   -1067.6392 
-   38250        3.825  0.076456883    1005.6732    291.31425   -15.566443    9.3761751   -1077.0154   -1067.6392 
-   38300         3.83  0.076456909    998.58464    295.80008   -15.577737    9.5205551   -1077.1598   -1067.6392 
-   38350        3.835  0.076456917    1023.8255    296.91935    -15.58617    9.5565797   -1077.1958   -1067.6392 
-   38400         3.84  0.076457007    1038.0022     294.9054   -15.596528    9.4917592    -1077.131   -1067.6392 
-   38450        3.845  0.076457031    1037.6121    290.96422   -15.616202    9.3649092   -1077.0041   -1067.6392 
-   38500         3.85  0.076456984    1040.5904    286.88024   -15.646786    9.2334631   -1076.8727   -1067.6392 
-   38550        3.855  0.076456918    1043.2321    284.56473   -15.689543    9.1589367   -1076.7982   -1067.6392 
-   38600         3.86  0.076456877    1038.0862    284.74376   -15.739663    9.1646989   -1076.8039   -1067.6392 
-   38650        3.865  0.076456988    1038.4376    285.95011   -15.776018    9.2035262   -1076.8428   -1067.6392 
-   38700         3.87  0.076457066    1046.7517    286.45113   -15.793545    9.2196518   -1076.8589   -1067.6392 
-   38750        3.875  0.076457085    1069.8363     286.1605   -15.809275    9.2102978   -1076.8495   -1067.6392 
-   38800         3.88  0.076457103    1099.7649    286.35508   -15.838882    9.2165605   -1076.8558   -1067.6392 
-   38850        3.885  0.076457029    1113.9425    288.09011   -15.885059    9.2724039   -1076.9116   -1067.6392 
-   38900         3.89  0.076457017    1105.7043    290.97132   -15.928294    9.3651376   -1077.0044   -1067.6392 
-   38950        3.895  0.076456995    1093.6515    294.07778   -15.945379    9.4651215   -1077.1044   -1067.6392 
-   39000          3.9   0.07645694    1103.4477     297.5125   -15.943567    9.5756706   -1077.2149   -1067.6392 
-   39050        3.905  0.076457006    1109.1277    301.82187   -15.951259    9.7143712   -1077.3536   -1067.6392 
-   39100         3.91  0.076456969    1114.3237    306.51524   -15.985628     9.865431   -1077.5047   -1067.6392 
-   39150        3.915  0.076456912    1114.4623    309.57518   -16.034747    9.9639174   -1077.6032   -1067.6392 
-   39200         3.92   0.07645697    1087.5299    308.28093   -16.061177    9.9222609   -1077.5615   -1067.6392 
-   39250        3.925  0.076457004    1085.9492    302.29555   -16.058242    9.7296168   -1077.3688   -1067.6392 
-   39300         3.93  0.076456952    1107.8421    294.53188   -16.053056    9.4797371    -1077.119   -1067.6392 
-   39350        3.935  0.076456973    1124.1513    288.15688   -16.067119    9.2745528   -1076.9138   -1067.6392 
-   39400         3.94  0.076457054    1137.2475    283.95115   -16.101525    9.1391882   -1076.7784   -1067.6392 
-   39450        3.945   0.07645698    1135.1662    281.54817   -16.141252    9.0618462   -1076.7011   -1067.6392 
-   39500         3.95  0.076456838    1099.0721    281.13694   -16.174509    9.0486105   -1076.6878   -1067.6392 
-   39550        3.955  0.076456882    1049.5257    282.67803   -16.205325    9.0982117   -1076.7374   -1067.6392 
-   39600         3.96  0.076457011    1027.3757    284.94192   -16.234406    9.1710768   -1076.8103   -1067.6392 
-   39650        3.965  0.076456971     1017.794    286.75472   -16.252188    9.2294233   -1076.8687   -1067.6392 
-   39700         3.97  0.076456888    1007.7805    288.56666    -16.25612    9.2877419    -1076.927   -1067.6392 
-   39750        3.975  0.076456865    1012.8541    292.07722   -16.261884    9.4007319     -1077.04   -1067.6392 
-   39800         3.98  0.076456816    1043.1577    297.78139   -16.277698     9.584325   -1077.2236   -1067.6392 
-   39850        3.985  0.076456836    1077.8248    304.26971   -16.297835    9.7931567   -1077.4324   -1067.6392 
-   39900         3.99   0.07645687    1094.0855    309.71669   -16.325371    9.9684719   -1077.6077   -1067.6392 
-   39950        3.995  0.076456883    1064.1015    312.41437   -16.358615    10.055299   -1077.6945   -1067.6392 
-   40000            4  0.076456877    1022.9431    310.99163   -16.375546    10.009507   -1077.6487   -1067.6392 
-   40050        4.005  0.076456756    1013.7056    306.64402   -16.373477    9.8695757   -1077.5088   -1067.6392 
-   40100         4.01  0.076456759    1007.6913    303.35311   -16.376022    9.7636554   -1077.4029   -1067.6392 
-   40150        4.015  0.076456864     1004.252    303.81576   -16.385329    9.7785462   -1077.4178   -1067.6392 
-   40200         4.02  0.076456912    1013.1412    307.22942   -16.384285    9.8884172   -1077.5276   -1067.6392 
-   40250        4.025  0.076456867    1030.3871    310.68562   -16.369477    9.9996578   -1077.6389   -1067.6392 
-   40300         4.03  0.076456789    1034.7373    311.09098   -16.352628    10.012705   -1077.6519   -1067.6392 
-   40350        4.035  0.076456729    1033.1387    307.52717   -16.345575    9.8980007   -1077.5372   -1067.6392 
-   40400         4.04   0.07645669    1062.9045    301.64635   -16.348471     9.708722    -1077.348   -1067.6392 
-   40450        4.045  0.076456729    1073.8352    295.54356   -16.354824    9.5122988   -1077.1515   -1067.6392 
-   40500         4.05  0.076456875    1045.0985    290.52511    -16.36464    9.3507761     -1076.99   -1067.6392 
-   40550        4.055  0.076456839    1027.9258    287.44019   -16.379541    9.2514857   -1076.8907   -1067.6392 
-   40600         4.06  0.076456646    1031.5216    286.57721   -16.388491      9.22371   -1076.8629   -1067.6392 
-   40650        4.065  0.076456606    1055.0251    287.81611   -16.386366    9.2635847   -1076.9028   -1067.6392 
-   40700         4.07  0.076456834    1081.6077    290.98909   -16.384202    9.3657097   -1077.0049   -1067.6392 
-   40750        4.075  0.076457031    1095.8624    295.35171   -16.381535    9.5061241   -1077.1454   -1067.6392 
-   40800         4.08  0.076456927    1091.1884    299.74612   -16.369379    9.6475614   -1077.2868   -1067.6392 
-   40850        4.085  0.076456677    1072.8108    303.12714   -16.353468    9.7563823   -1077.3956   -1067.6392 
-   40900         4.09  0.076456612    1071.4265    304.47082   -16.345218    9.7996295   -1077.4389   -1067.6392 
-   40950        4.095  0.076456759    1087.5691    303.62065   -16.343756    9.7722663   -1077.4115   -1067.6392 
-   41000          4.1   0.07645689    1093.1572    302.41466   -16.342931    9.7334506   -1077.3727   -1067.6392 
-   41050        4.105  0.076456787    1077.0283    303.03079   -16.350207    9.7532811   -1077.3925   -1067.6392 
-   41100         4.11    0.0764566    1063.8174    304.59541     -16.3659    9.8036396   -1077.4429   -1067.6392 
-   41150        4.115  0.076456666    1067.2044    305.05378   -16.383874    9.8183927   -1077.4576   -1067.6392 
-   41200         4.12  0.076456794    1067.5418    304.12177   -16.408325    9.7883952   -1077.4276   -1067.6392 
-   41250        4.125  0.076456816    1047.1076    301.87307   -16.437615     9.716019   -1077.3553   -1067.6392 
-   41300         4.13  0.076456766    1000.8676    298.01778   -16.464716    9.5919337   -1077.2312   -1067.6392 
-   41350        4.135  0.076456687    958.82868    293.49143   -16.485682    9.4462495   -1077.0855   -1067.6392 
-   41400         4.14  0.076456739    951.84883    290.80384   -16.499012    9.3597472    -1076.999   -1067.6392 
-   41450        4.145  0.076456812    963.65591    292.08601   -16.507392    9.4010149   -1077.0402   -1067.6392 
-   41500         4.15  0.076456843    975.72148    297.16323   -16.520849    9.5644292   -1077.2037   -1067.6392 
-   41550        4.155  0.076456845    984.53332    303.16542    -16.53794    9.7576142   -1077.3968   -1067.6392 
-   41600         4.16  0.076456751    985.80319    307.28815   -16.557303    9.8903077   -1077.5295   -1067.6392 
-   41650        4.165  0.076456683    1002.2286    308.88612   -16.587168    9.9417395    -1077.581   -1067.6392 
-   41700         4.17  0.076456643    1030.6323    308.39988   -16.625508    9.9260895   -1077.5653   -1067.6392 
-   41750        4.175   0.07645661    1034.2586    306.29955   -16.665355    9.8584887   -1077.4977   -1067.6392 
-   41800         4.18  0.076456559    1020.0175    303.06426   -16.703335    9.7543583   -1077.3936   -1067.6392 
-   41850        4.185  0.076456676    991.59829    299.14498   -16.725328    9.6282135   -1077.2674   -1067.6392 
-   41900         4.19  0.076456761    967.85853    296.19757   -16.730689    9.5333487   -1077.1726   -1067.6392 
-   41950        4.195  0.076456701    975.82892    296.71617   -16.740926    9.5500402   -1077.1893   -1067.6392 
-   42000          4.2  0.076456713    1002.2491    300.92024   -16.770609    9.6853516   -1077.3246   -1067.6392 
-   42050        4.205  0.076456664    1009.6687    305.97966   -16.813995    9.8481928   -1077.4874   -1067.6392 
-   42100         4.21  0.076456626    1003.7314    309.08496   -16.851376    9.9481394   -1077.5874   -1067.6392 
-   42150        4.215  0.076456675    1009.5258     310.0374   -16.864204    9.9787942    -1077.618   -1067.6392 
-   42200         4.22  0.076456733    1016.8827     310.8272    -16.85494    10.004215   -1077.6434   -1067.6392 
-   42250        4.225  0.076456828      1023.91    312.80966   -16.842511    10.068022   -1077.7073   -1067.6392 
-   42300         4.23  0.076456807    1019.5709    315.15173   -16.836523    10.143403   -1077.7826   -1067.6392 
-   42350        4.235  0.076456685    1017.6755    316.23931   -16.830978    10.178408   -1077.8176   -1067.6392 
-   42400         4.24  0.076456572    1035.9763    314.95382   -16.817532    10.137033   -1077.7763   -1067.6392 
-   42450        4.245  0.076456544     1057.572    310.93678   -16.799682    10.007741    -1077.647   -1067.6392 
-   42500         4.25  0.076456618    1077.1806    305.03796   -16.792574    9.8178834   -1077.4571   -1067.6392 
-   42550        4.255  0.076456744    1090.5444     299.3483   -16.809848    9.6347572    -1077.274   -1067.6392 
-   42600         4.26  0.076456726     1096.922    295.41747   -16.837401    9.5082406   -1077.1475   -1067.6392 
-   42650        4.265  0.076456617    1103.2531    293.46673   -16.859813    9.4454545   -1077.0847   -1067.6392 
-   42700         4.27  0.076456587    1104.4238    293.26317   -16.892288    9.4389029   -1077.0781   -1067.6392 
-   42750        4.275  0.076456665    1083.3823    294.65311   -16.933936    9.4836391   -1077.1229   -1067.6392 
-   42800         4.28  0.076456664    1042.3438    298.70068   -16.959665    9.6139133   -1077.2531   -1067.6392 
-   42850        4.285  0.076456687    1013.4416    306.95616   -16.966168    9.8796223   -1077.5189   -1067.6392 
-   42900         4.29  0.076456725    1011.1467    318.14544    -16.97008    10.239758    -1077.879   -1067.6392 
-   42950        4.295  0.076456665    1017.4449    328.03985   -16.982627    10.558217   -1078.1975   -1067.6392 
-   43000          4.3  0.076456617    1019.3575    333.03871   -17.008768    10.719109   -1078.3583   -1067.6392 
-   43050        4.305  0.076456693     999.2679    332.30906   -17.055549    10.695625   -1078.3349   -1067.6392 
-   43100         4.31  0.076456762     967.7236    326.28709   -17.109853    10.501803    -1078.141   -1067.6392 
-   43150        4.315  0.076456687    976.16726    316.29296   -17.144504    10.180134   -1077.8194   -1067.6392 
-   43200         4.32  0.076456692    1009.9146    306.30886   -17.155114    9.8587883    -1077.498   -1067.6392 
-   43250        4.325  0.076456822    1011.5832    301.46146   -17.160687    9.7027711    -1077.342   -1067.6392 
-   43300         4.33  0.076456891    993.25245    303.09136   -17.173125    9.7552307   -1077.3945   -1067.6392 
-   43350        4.335  0.076456691     978.1423    307.90834   -17.186565     9.910269   -1077.5495   -1067.6392 
-   43400         4.34   0.07645663     966.7299    311.62095   -17.191657    10.029762    -1077.669   -1067.6392 
-   43450        4.345  0.076456883    971.37208    311.68351   -17.189726    10.031776    -1077.671   -1067.6392 
-   43500         4.35  0.076456994    978.85437    307.94316   -17.193481    9.9113896   -1077.5506   -1067.6392 
-   43550        4.355  0.076456767    996.27549    302.13712   -17.211228    9.7245177   -1077.3637   -1067.6392 
-   43600         4.36  0.076456685    1016.7792     297.0799   -17.235609    9.5617472    -1077.201   -1067.6392 
-   43650        4.365  0.076456862    1020.5319    294.98379   -17.245695    9.4942822   -1077.1335   -1067.6392 
-   43700         4.37  0.076456832    1016.3483    296.10415   -17.238216     9.530342   -1077.1696   -1067.6392 
-   43750        4.375  0.076456643    1012.7306    299.25575   -17.241809    9.6317786    -1077.271   -1067.6392 
-   43800         4.38  0.076456789    1005.3285    303.54214   -17.262691    9.7697394    -1077.409   -1067.6392 
-   43850        4.385  0.076456982    1003.3326    310.06269   -17.281251    9.9796085   -1077.6188   -1067.6392 
-   43900         4.39  0.076456965    987.54044    320.52249   -17.299417    10.316265   -1077.9555   -1067.6392 
-   43950        4.395  0.076456761     963.2584    333.20523   -17.330466    10.724469   -1078.3637   -1067.6392 
-   44000          4.4  0.076456706    963.73639    342.88698   -17.367857    11.036084   -1078.6753   -1067.6392 
-   44050        4.405  0.076456821    986.80537    345.16932   -17.395458    11.109542   -1078.7488   -1067.6392 
-   44100         4.41  0.076456831    1009.8445    339.67355    -17.41311    10.932657   -1078.5719   -1067.6392 
-   44150        4.415  0.076456785    1014.6601    330.05625   -17.436389    10.623116   -1078.2623   -1067.6392 
-   44200         4.42  0.076456797    984.52199     321.8216    -17.48274    10.358078   -1077.9973   -1067.6392 
-   44250        4.425  0.076456753    957.80787    317.33913    -17.54731    10.213806    -1077.853   -1067.6392 
-   44300         4.43  0.076456643    940.00066    314.53772   -17.596853    10.123641   -1077.7629   -1067.6392 
-   44350        4.435  0.076456628     918.4875    312.37225   -17.612235    10.053943   -1077.6932   -1067.6392 
-   44400         4.44   0.07645672    913.57846     310.8786   -17.595301    10.005869   -1077.6451   -1067.6392 
-   44450        4.445  0.076456761     919.4865    309.82858   -17.561225    9.9720734   -1077.6113   -1067.6392 
-   44500         4.45   0.07645674     926.5393    309.78037   -17.534259    9.9705218   -1077.6097   -1067.6392 
-   44550        4.455  0.076456708    929.10063    311.77335   -17.538056    10.034667   -1077.6739   -1067.6392 
-   44600         4.46  0.076456694    933.10594    315.21765   -17.566473    10.145525   -1077.7848   -1067.6392 
-   44650        4.465  0.076456702    926.71966    318.06782   -17.591174     10.23726   -1077.8765   -1067.6392 
-   44700         4.47  0.076456707    911.59951    319.12218   -17.602472    10.271195   -1077.9104   -1067.6392 
-   44750        4.475  0.076456688    910.70606     318.9204   -17.609049    10.264701   -1077.9039   -1067.6392 
-   44800         4.48    0.0764567    905.05917    318.54255   -17.616129    10.252539   -1077.8918   -1067.6392 
-   44850        4.485  0.076456621    894.49408    318.42782   -17.623448    10.248847   -1077.8881   -1067.6392 
-   44900         4.49  0.076456517     906.7452    318.55777   -17.630547    10.253029   -1077.8923   -1067.6392 
-   44950        4.495  0.076456564     912.1438    318.94548   -17.639597    10.265508   -1077.9047   -1067.6392 
-   45000          4.5  0.076456621    904.16689     319.6676   -17.650569     10.28875    -1077.928   -1067.6392 
-   45050        4.505  0.076456591    906.29138    321.41748   -17.664978    10.345071   -1077.9843   -1067.6392 
-   45100         4.51  0.076456544    905.96789    325.06187   -17.678666    10.462369   -1078.1016   -1067.6392 
-   45150        4.515  0.076456576    898.50939    330.26103   -17.687185    10.629708   -1078.2689   -1067.6392 
-   45200         4.52  0.076456663    905.35412    334.94433   -17.701241    10.780443   -1078.4197   -1067.6392 
-   45250        4.525   0.07645673    930.80225    336.07069    -17.72859    10.816696   -1078.4559   -1067.6392 
-   45300         4.53  0.076456595     959.3922     331.6008   -17.765016    10.672829   -1078.3121   -1067.6392 
-   45350        4.535  0.076456568    984.36318    321.62814   -17.802524    10.351851   -1077.9911   -1067.6392 
-   45400         4.54   0.07645668    990.20053     308.8639   -17.836056    9.9410245   -1077.5803   -1067.6392 
-   45450        4.545  0.076456648    947.25396    298.78614   -17.865782    9.6166638   -1077.2559   -1067.6392 
-   45500         4.55  0.076456577    910.56022    297.55292   -17.905424    9.5769716   -1077.2162   -1067.6392 
-   45550        4.555  0.076456563    888.63811    306.74089   -17.960609    9.8726936   -1077.5119   -1067.6392 
-   45600         4.56  0.076456599    859.98987    321.07118   -18.005145    10.333925   -1077.9732   -1067.6392 
-   45650        4.565  0.076456612    856.19145    333.40125   -18.019594    10.730778     -1078.37   -1067.6392 
-   45700         4.57  0.076456557    878.62104    340.06144   -18.020894    10.945141   -1078.5844   -1067.6392 
-   45750        4.575  0.076456566    897.45139    340.97037   -18.029395    10.974396   -1078.6136   -1067.6392 
-   45800         4.58  0.076456592    900.06632    337.73275   -18.042178    10.870191   -1078.5094   -1067.6392 
-   45850        4.585  0.076456653    905.65224    333.13083   -18.060834    10.722074   -1078.3613   -1067.6392 
-   45900         4.59  0.076456731    911.50958    329.86483    -18.10231    10.616955   -1078.2562   -1067.6392 
-   45950        4.595  0.076456674    934.98117    327.78934   -18.158233    10.550154   -1078.1894   -1067.6392 
-   46000          4.6  0.076456573    960.91441    324.26975   -18.195778    10.436874   -1078.0761   -1067.6392 
-   46050        4.605  0.076456596    962.59058     317.8452   -18.203481    10.230095   -1077.8693   -1067.6392 
-   46100         4.61  0.076456671    960.19967    310.62901   -18.213042    9.9978359   -1077.6371   -1067.6392 
-   46150        4.615  0.076456686    958.71855    305.95972   -18.235837    9.8475511   -1077.4868   -1067.6392 
-   46200         4.62  0.076456612    966.32277     305.9278    -18.25351    9.8465235   -1077.4858   -1067.6392 
-   46250        4.625  0.076456484    976.33095    310.79103   -18.261143     10.00305   -1077.6423   -1067.6392 
-   46300         4.63  0.076456455     971.1525    319.21516   -18.262509    10.274188   -1077.9134   -1067.6392 
-   46350        4.635  0.076456555    942.98388      329.128   -18.258965     10.59324   -1078.2325   -1067.6392 
-   46400         4.64   0.07645659    931.95574    338.94782   -18.258301    10.909299   -1078.5485   -1067.6392 
-   46450        4.645  0.076456634    952.04764    347.69672   -18.270432    11.190889   -1078.8301   -1067.6392 
-   46500         4.65  0.076456695    954.27972    354.28335   -18.291901    11.402884   -1079.0421   -1067.6392 
-   46550        4.655  0.076456718    932.47699    357.80024   -18.314064    11.516078   -1079.1553   -1067.6392 
-   46600         4.66  0.076456571    917.15783      358.255    -18.33944    11.530715   -1079.1699   -1067.6392 
-   46650        4.665  0.076456487    914.53778    356.10608   -18.373204     11.46155   -1079.1008   -1067.6392 
-   46700         4.67   0.07645664    926.29271    351.32545   -18.410415    11.307682   -1078.9469   -1067.6392 
-   46750        4.675  0.076456722    955.90982    343.62423   -18.443075    11.059813    -1078.699   -1067.6392 
-   46800         4.68  0.076456662    968.52074    333.76849   -18.472665    10.742598   -1078.3818   -1067.6392 
-   46850        4.685  0.076456611    960.55547    323.74847   -18.502955    10.420096   -1078.0593   -1067.6392 
-   46900         4.69   0.07645658    969.48482    315.29249   -18.530555    10.147933   -1077.7872   -1067.6392 
-   46950        4.695  0.076456538    970.41435    309.50703   -18.552649    9.9617239    -1077.601   -1067.6392 
-   47000          4.7  0.076456607     973.5826    307.27705   -18.562429    9.8899503   -1077.5292   -1067.6392 
-   47050        4.705  0.076456741    971.31274    309.44374   -18.561975    9.9596868   -1077.5989   -1067.6392 
-   47100         4.71  0.076456567    974.56171    315.87966   -18.571858    10.166832   -1077.8061   -1067.6392 
-   47150        4.715  0.076456487      989.886     324.3948    -18.59552    10.440899   -1078.0801   -1067.6392 
-   47200         4.72  0.076456752    991.34022    333.02825   -18.624859    10.718773    -1078.358   -1067.6392 
-   47250        4.725  0.076456811    982.33055    341.27988   -18.652892    10.984358   -1078.6236   -1067.6392 
-   47300         4.73  0.076456654    969.07699    348.54206   -18.671538    11.218097   -1078.8573   -1067.6392 
-   47350        4.735  0.076456603    950.49208    353.80509   -18.681778    11.387491   -1079.0267   -1067.6392 
-   47400         4.74  0.076456655    932.53448    356.59027   -18.691148    11.477134   -1079.1164   -1067.6392 
-   47450        4.745   0.07645674    914.98082    356.88075   -18.707177    11.486484   -1079.1257   -1067.6392 
-   47500         4.75  0.076456846    910.29391    354.25323   -18.733572    11.401915   -1079.0411   -1067.6392 
-   47550        4.755  0.076456842    911.79249    348.56319   -18.768858    11.218777    -1078.858   -1067.6392 
-   47600         4.76  0.076456764    896.25715    341.13087   -18.817172    10.979562   -1078.6188   -1067.6392 
-   47650        4.765  0.076456752    893.56376    333.65355   -18.869281    10.738898   -1078.3781   -1067.6392 
-   47700         4.77  0.076456851    923.22366    328.05385   -18.908457    10.558668   -1078.1979   -1067.6392 
-   47750        4.775  0.076456872    942.84866    326.28411   -18.929889    10.501707   -1078.1409   -1067.6392 
-   47800         4.78  0.076456844    930.32583    328.44034   -18.932985    10.571107   -1078.2103   -1067.6392 
-   47850        4.785  0.076456902    912.36756    332.89004   -18.922464    10.714324   -1078.3536   -1067.6392 
-   47900         4.79  0.076456964    916.62133    338.11673   -18.919206    10.882549   -1078.5218   -1067.6392 
-   47950        4.795  0.076457014    930.75246    342.30195   -18.922007    11.017254   -1078.6565   -1067.6392 
-   48000          4.8  0.076457014    936.01421    343.78811   -18.908628    11.065087   -1078.7043   -1067.6392 
-   48050        4.805  0.076456953    944.54584    342.44511   -18.878537    11.021862   -1078.6611   -1067.6392 
-   48100         4.81  0.076456972    941.98405    339.08691   -18.851545    10.913775    -1078.553   -1067.6392 
-   48150        4.815  0.076456898    920.11331    334.61456   -18.839033    10.769829   -1078.4091   -1067.6392 
-   48200         4.82  0.076456871    907.83719    330.10701   -18.832157     10.62475    -1078.264   -1067.6392 
-   48250        4.825  0.076456918    912.20647    327.58291   -18.826744     10.54351   -1078.1827   -1067.6392 
-   48300         4.83   0.07645699    932.39917    329.24117   -18.830768    10.596882   -1078.2361   -1067.6392 
-   48350        4.835   0.07645701     945.1163     335.0398   -18.840255    10.783516   -1078.4227   -1067.6392 
-   48400         4.84  0.076456836    950.22061    342.35702   -18.841461    11.019026   -1078.6583   -1067.6392 
-   48450        4.845    0.0764567    952.16965    348.50659   -18.834984    11.216955   -1078.8562   -1067.6392 
-   48500         4.85  0.076456712    955.36854    352.21576   -18.825983    11.336338   -1078.9756   -1067.6392 
-   48550        4.855  0.076456801    959.48836    353.76389   -18.820533    11.386165   -1079.0254   -1067.6392 
-   48600         4.86  0.076456823    964.22846    354.04554   -18.822337    11.395231   -1079.0345   -1067.6392 
-   48650        4.865  0.076456815    974.22885    352.93972   -18.818132    11.359639   -1078.9989   -1067.6392 
-   48700         4.87  0.076456877    987.44079    349.70581   -18.807017    11.255553   -1078.8948   -1067.6392 
-   48750        4.875  0.076456856    980.80712    344.37973   -18.808379    11.084129   -1078.7234   -1067.6392 
-   48800         4.88  0.076456847    965.79638    337.63651    -18.81979    10.867093   -1078.5063   -1067.6392 
-   48850        4.885  0.076457001    966.05115     330.7499   -18.830692    10.645442   -1078.2847   -1067.6392 
-   48900         4.89  0.076457069    965.02834    325.77373   -18.849924     10.48528   -1078.1245   -1067.6392 
-   48950        4.895  0.076456805    951.50135    324.61657   -18.890071    10.448036   -1078.0873   -1067.6392 
-   49000          4.9  0.076456678    947.91103    327.27966   -18.934537     10.53375    -1078.173   -1067.6392 
-   49050        4.905  0.076456661    958.11234    332.39046   -18.962498    10.698245   -1078.3375   -1067.6392 
-   49100         4.91  0.076456829    970.05161    338.47836   -18.976168    10.894189   -1078.5334   -1067.6392 
-   49150        4.915   0.07645699    968.15446    343.93729    -18.98603    11.069889   -1078.7091   -1067.6392 
-   49200         4.92  0.076456985    960.59968    346.43043   -18.994109    11.150132   -1078.7894   -1067.6392 
-   49250        4.925  0.076456928    945.53084     343.0733   -18.986613    11.042081   -1078.6813   -1067.6392 
-   49300         4.93  0.076456888    920.51419    333.13647   -18.959986    10.722256   -1078.3615   -1067.6392 
-   49350        4.935  0.076456851    907.35436    320.38291   -18.938752    10.311773    -1077.951   -1067.6392 
-   49400         4.94   0.07645685    893.81547    310.99739   -18.938412    10.009692   -1077.6489   -1067.6392 
-   49450        4.945  0.076456896    870.23823    309.67527    -18.95594    9.9671388   -1077.6064   -1067.6392 
-   49500         4.95  0.076456955    872.77052    317.13999   -18.978605    10.207397   -1077.8466   -1067.6392 
-   49550        4.955  0.076456967    894.83445    330.73629    -18.98876    10.645004   -1078.2842   -1067.6392 
-   49600         4.96  0.076456979     912.1661    346.73247   -18.984428    11.159854   -1078.7991   -1067.6392 
-   49650        4.965  0.076456993    915.70238    361.26297   -18.978545    11.627529   -1079.2668   -1067.6392 
-   49700         4.97  0.076456983    924.58803    370.71298   -18.984487    11.931685   -1079.5709   -1067.6392 
-   49750        4.975  0.076456922    944.17323    372.65166   -18.998747    11.994083   -1079.6333   -1067.6392 
-   49800         4.98  0.076456923    948.92864    367.69228     -19.0113    11.834461   -1079.4737   -1067.6392 
-   49850        4.985  0.076456921    953.93531    359.51215   -19.018592    11.571177   -1079.2104   -1067.6392 
-   49900         4.99  0.076456974    963.60708    351.14054   -19.013112    11.301731    -1078.941   -1067.6392 
-   49950        4.995  0.076456997      970.081    343.67798   -19.003119    11.061543   -1078.7008   -1067.6392 
-   50000            5  0.076457012    1001.2522    337.57276   -19.005327    10.865041   -1078.5043   -1067.6392 
-Loop time of 149.65 on 1 procs for 50000 steps with 250 atoms
-
-Performance: 2.887 ns/day, 8.314 hours/ns, 334.113 timesteps/s
-98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 56.939     | 56.939     | 56.939     |   0.0 | 38.05
-Neigh   | 0.65017    | 0.65017    | 0.65017    |   0.0 |  0.43
-Comm    | 1.4958     | 1.4958     | 1.4958     |   0.0 |  1.00
-Output  | 37.503     | 37.503     | 37.503     |   0.0 | 25.06
-Modify  | 52.788     | 52.788     | 52.788     |   0.0 | 35.27
-Other   |            | 0.2742     |            |       |  0.18
-
-Nlocal:    250 ave 250 max 250 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1335 ave 1335 max 1335 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    7746 ave 7746 max 7746 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  15492 ave 15492 max 15492 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 15492
-Ave neighs/atom = 61.968
-Neighbor list builds = 608
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:02:29
diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4 b/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4
deleted file mode 100644
index 6fc3e307f0..0000000000
--- a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4
+++ /dev/null
@@ -1,1117 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# bcc iron in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	bcc 2.8665
-Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 250 atoms
-  create_atoms CPU = 0.00056982 secs
-
-# setting mass, mag. moments, and interactions for bcc iron
-
-mass		1 55.845
-
-set 		group all spin/random 31 2.2
-  250 settings made for spin/random
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
-pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
-pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		50000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.77337
-  ghost atom cutoff = 5.77337
-  binsize = 2.88668, bins = 5 5 5
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes
-Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng 
-       0            0  0.076456975    9109.0924    100.00358  -0.85791269    3.2186929   -1070.8579   -1067.6392 
-      50        0.005  0.076456995    9402.4007    96.298333  -0.85659448    3.0994366   -1070.7387   -1067.6392 
-     100         0.01  0.076457028    9589.1846    86.330828  -0.87003341    2.7786247   -1070.4179   -1067.6392 
-     150        0.015  0.076457074    9673.9268    71.603402  -0.89006992    2.3046111   -1069.9438   -1067.6392 
-     200         0.02  0.076457106    9509.1148    54.648817  -0.91124541    1.7589146   -1069.3981   -1067.6392 
-     250        0.025  0.076457128      9004.27    38.599515  -0.93187522    1.2423553   -1068.8816   -1067.6392 
-     300         0.03  0.076457157    8353.4371    26.383018  -0.95082226    0.8491579   -1068.4884   -1067.6392 
-     350        0.035  0.076457207    7911.1316     20.01039  -0.96826468   0.64404992   -1068.2833   -1067.6392 
-     400         0.04  0.076457243    7775.9492    20.097682  -0.98706373   0.64685949   -1068.2861   -1067.6392 
-     450        0.045  0.076457231    7737.1225    25.687511   -1.0095684   0.82677249    -1068.466   -1067.6392 
-     500         0.05  0.076457204    7676.9809    34.604697   -1.0349855     1.113779    -1068.753   -1067.6392 
-     550        0.055  0.076457196    7550.2809    44.251809   -1.0609123    1.4242788   -1069.0635   -1067.6392 
-     600         0.06  0.076457188    7209.7657    52.475202   -1.0880854    1.6889551   -1069.3282   -1067.6392 
-     650        0.065   0.07645718    6691.1787    57.926479   -1.1179657    1.8644087   -1069.5036   -1067.6392 
-     700         0.07  0.076457185    6276.4003    60.030548   -1.1469999    1.9321298   -1069.5714   -1067.6392 
-     750        0.075   0.07645719    6149.9253    59.122504   -1.1721939    1.9029037   -1069.5421   -1067.6392 
-     800         0.08  0.076457195    6207.0587    56.349146   -1.1949365     1.813641   -1069.4529   -1067.6392 
-     850        0.085  0.076457199    6328.4635    53.154464   -1.2164642    1.7108177     -1069.35   -1067.6392 
-     900         0.09  0.076457199    6456.2716    50.837416   -1.2366018    1.6362417   -1069.2755   -1067.6392 
-     950        0.095  0.076457222    6495.1064    50.234549   -1.2539657    1.6168379   -1069.2561   -1067.6392 
-    1000          0.1  0.076457266     6416.775    51.592727   -1.2671834    1.6605519   -1069.2998   -1067.6392 
-    1050        0.105  0.076457256    6305.9015    54.719414   -1.2794824    1.7611868   -1069.4004   -1067.6392 
-    1100         0.11  0.076457222     6165.987     59.01343   -1.2960617    1.8993931   -1069.5386   -1067.6392 
-    1150        0.115  0.076457194    5941.7807    63.475298    -1.317859    2.0430017   -1069.6822   -1067.6392 
-    1200         0.12  0.076457182    5692.0982    67.036713   -1.3432854    2.1576286   -1069.7969   -1067.6392 
-    1250        0.125  0.076457217    5543.1736    68.917405   -1.3719994    2.2181602   -1069.8574   -1067.6392 
-    1300         0.13  0.076457263    5507.9968    68.753418   -1.4042339    2.2128821   -1069.8521   -1067.6392 
-    1350        0.135  0.076457286    5500.7848    66.608286   -1.4385667    2.1438394   -1069.7831   -1067.6392 
-    1400         0.14  0.076457254     5523.456    62.967429   -1.4712143    2.0266556   -1069.6659   -1067.6392 
-    1450        0.145  0.076457188    5501.5777     58.75732   -1.4990458      1.89115   -1069.5304   -1067.6392 
-    1500         0.15  0.076457175    5324.4931    55.246308   -1.5236774    1.7781453   -1069.4174   -1067.6392 
-    1550        0.155  0.076457234    5025.5908    53.607297   -1.5492947    1.7253925   -1069.3646   -1067.6392 
-    1600         0.16  0.076457297    4742.9546    54.443418   -1.5785798    1.7523036   -1069.3915   -1067.6392 
-    1650        0.165  0.076457321     4558.083    57.572305   -1.6113848    1.8530093   -1069.4922   -1067.6392 
-    1700         0.17  0.076457304    4479.4352    62.073307   -1.6443595    1.9978776   -1069.6371   -1067.6392 
-    1750        0.175  0.076457272    4520.5577    66.677964   -1.6742729     2.146082   -1069.7853   -1067.6392 
-    1800         0.18  0.076457253    4659.9114    70.277293   -1.7021557    2.2619292   -1069.9012   -1067.6392 
-    1850        0.185  0.076457257    4734.1597    72.135028   -1.7307798    2.3217219    -1069.961   -1067.6392 
-    1900         0.19  0.076457279    4632.2637    71.873382   -1.7598165    2.3133006   -1069.9525   -1067.6392 
-    1950        0.195  0.076457276    4496.6621     69.52131   -1.7866398    2.2375973   -1069.8768   -1067.6392 
-    2000          0.2  0.076457276    4507.4594     65.61098   -1.8106776    2.1117403    -1069.751   -1067.6392 
-    2050        0.205  0.076457288    4652.9279    61.016261   -1.8317479    1.9638557   -1069.6031   -1067.6392 
-    2100         0.21  0.076457307    4738.4188    56.745795   -1.8489776    1.8264074   -1069.4656   -1067.6392 
-    2150        0.215  0.076457279     4643.423    53.837376   -1.8647516    1.7327977    -1069.372   -1067.6392 
-    2200         0.22  0.076457215    4517.9871    53.044053   -1.8828305     1.707264   -1069.3465   -1067.6392 
-    2250        0.225   0.07645717    4436.4399    54.521839   -1.9038753    1.7548277   -1069.3941   -1067.6392 
-    2300         0.23  0.076457132    4318.8261    57.895634   -1.9276454    1.8634159   -1069.5026   -1067.6392 
-    2350        0.235  0.076457114    4148.8616    62.484473   -1.9559372    2.0111113   -1069.6503   -1067.6392 
-    2400         0.24  0.076457144    4014.8498    67.404243   -1.9902034    2.1694579   -1069.8087   -1067.6392 
-    2450        0.245  0.076457189     4004.017    71.654167   -2.0278558     2.306245   -1069.9455   -1067.6392 
-    2500         0.25  0.076457202    4109.5497    74.379393   -2.0629968    2.3939585   -1070.0332   -1067.6392 
-    2550        0.255  0.076457205    4251.6933    75.255112   -2.0918484    2.4221442   -1070.0614   -1067.6392 
-    2600         0.26  0.076457208    4320.6876    74.700611   -2.1169691    2.4042972   -1070.0435   -1067.6392 
-    2650        0.265  0.076457197    4297.5527    73.627823       -2.143    2.3697686    -1070.009   -1067.6392 
-    2700         0.27  0.076457213    4198.4852    72.957211   -2.1702374    2.3481845   -1069.9874   -1067.6392 
-    2750        0.275  0.076457256    4019.2384    73.353574   -2.1967187    2.3609417   -1070.0002   -1067.6392 
-    2800         0.28  0.076457288    3867.2492    75.083781   -2.2227117    2.4166298   -1070.0559   -1067.6392 
-    2850        0.285  0.076457302    3879.8471     77.82546   -2.2488766    2.5048728   -1070.1441   -1067.6392 
-    2900         0.29  0.076457321    4003.8986    80.741745   -2.2742584    2.5987357    -1070.238   -1067.6392 
-    2950        0.295  0.076457347    4026.6754    82.934399   -2.3001834     2.669308   -1070.3085   -1067.6392 
-    3000          0.3  0.076457334    3857.2183    83.701738   -2.3291113    2.6940054   -1070.3332   -1067.6392 
-    3050        0.305  0.076457295    3640.7581    82.615991   -2.3614721    2.6590598   -1070.2983   -1067.6392 
-    3100         0.31   0.07645725     3489.102    79.573679   -2.3943974    2.5611406   -1070.2004   -1067.6392 
-    3150        0.315  0.076457232    3396.4301    74.896125   -2.4236621    2.4105899   -1070.0498   -1067.6392 
-    3200         0.32  0.076457259      3378.11    69.450128   -2.4483292    2.2353063   -1069.8745   -1067.6392 
-    3250        0.325  0.076457289    3463.7734    64.542714   -2.4729224    2.0773573   -1069.7166   -1067.6392 
-    3300         0.33  0.076457318    3637.4971    61.346221    -2.500303    1.9744757   -1069.6137   -1067.6392 
-    3350        0.335  0.076457361    3833.5389    60.346704   -2.5252732    1.9423055   -1069.5815   -1067.6392 
-    3400         0.34  0.076457387    3965.2081    61.464125   -2.5426842    1.9782706   -1069.6175   -1067.6392 
-    3450        0.345  0.076457375    3976.7956     64.41797   -2.5565409    2.0733424   -1069.7126   -1067.6392 
-    3500         0.35  0.076457371    3862.8334    68.714547   -2.5743062     2.211631   -1069.8509   -1067.6392 
-    3550        0.355  0.076457375     3697.284    73.534942   -2.5974674    2.3667792    -1070.006   -1067.6392 
-    3600         0.36  0.076457362    3575.9012    77.902682   -2.6209385    2.5073583   -1070.1466   -1067.6392 
-    3650        0.365  0.076457345    3550.0667    81.043684   -2.6394846    2.6084539   -1070.2477   -1067.6392 
-    3700         0.37  0.076457309    3535.0981    82.730976     -2.65464    2.6627607    -1070.302   -1067.6392 
-    3750        0.375  0.076457309    3444.1795    83.322515   -2.6736085    2.6817998    -1070.321   -1067.6392 
-    3800         0.38  0.076457348    3323.7191    83.436143   -2.7008525     2.685457   -1070.3247   -1067.6392 
-    3850        0.385  0.076457368    3252.5404     83.62535   -2.7353937    2.6915468   -1070.3308   -1067.6392 
-    3900         0.39  0.076457344    3219.5349    84.088597   -2.7722909    2.7064568   -1070.3457   -1067.6392 
-    3950        0.395  0.076457316    3210.4164    84.636475   -2.8060651    2.7240906   -1070.3633   -1067.6392 
-    4000          0.4  0.076457319    3223.9708    85.042888   -2.8352998    2.7371713   -1070.3764   -1067.6392 
-    4050        0.405  0.076457335    3232.7108    85.266853   -2.8607963    2.7443798   -1070.3836   -1067.6392 
-    4100         0.41  0.076457314    3206.1428    85.444074   -2.8837721    2.7500838   -1070.3893   -1067.6392 
-    4150        0.415  0.076457325    3146.4589    85.771643   -2.9074131    2.7606269   -1070.3999   -1067.6392 
-    4200         0.42  0.076457395    3092.6283     86.24875   -2.9341331     2.775983   -1070.4152   -1067.6392 
-    4250        0.425   0.07645742    3103.0319    86.563557   -2.9622203    2.7861153   -1070.4253   -1067.6392 
-    4300         0.43  0.076457425    3116.9053    86.320099   -2.9880208    2.7782794   -1070.4175   -1067.6392 
-    4350        0.435  0.076457427    3061.2259    85.306966   -3.0085539    2.7456709   -1070.3849   -1067.6392 
-    4400         0.44  0.076457432    3033.5229    83.703441   -3.0243431    2.6940602   -1070.3333   -1067.6392 
-    4450        0.445  0.076457411    3042.5167    82.058057   -3.0397518    2.6411023   -1070.2803   -1067.6392 
-    4500         0.45  0.076457387    2994.5161    81.002427   -3.0597817     2.607126   -1070.2464   -1067.6392 
-    4550        0.455  0.076457413     2868.381    80.936403    -3.086593     2.605001   -1070.2442   -1067.6392 
-    4600         0.46  0.076457454    2716.5128    81.904984   -3.1192161    2.6361755   -1070.2754   -1067.6392 
-    4650        0.465  0.076457402     2628.691    83.537981   -3.1529675    2.6887347    -1070.328   -1067.6392 
-    4700         0.47  0.076457327    2609.7253    85.196185   -3.1819342    2.7421053   -1070.3813   -1067.6392 
-    4750        0.475  0.076457328    2604.4797    86.479192   -3.2088497    2.7833999   -1070.4226   -1067.6392 
-    4800         0.48  0.076457385    2610.7583    87.294321    -3.242028    2.8096355   -1070.4489   -1067.6392 
-    4850        0.485  0.076457398    2649.7853    87.477655   -3.2810534    2.8155362   -1070.4548   -1067.6392 
-    4900         0.49  0.076457371    2678.8351    86.820207   -3.3154833    2.7943757   -1070.4336   -1067.6392 
-    4950        0.495  0.076457344     2687.924    85.543066   -3.3381845      2.75327   -1070.3925   -1067.6392 
-    5000          0.5  0.076457351    2720.6587    84.363474   -3.3508261    2.7153039   -1070.3545   -1067.6392 
-    5050        0.505  0.076457408    2755.8292    84.030245   -3.3582878    2.7045787   -1070.3438   -1067.6392 
-    5100         0.51  0.076457454    2753.2313    84.932962   -3.3648805    2.7336333   -1070.3729   -1067.6392 
-    5150        0.515  0.076457453    2706.7195    86.928397   -3.3711152    2.7978579   -1070.4371   -1067.6392 
-    5200         0.52  0.076457474     2678.177    89.583728   -3.3768576    2.8833218   -1070.5226   -1067.6392 
-    5250        0.525  0.076457519    2699.6154     92.51484   -3.3860255    2.9776619   -1070.6169   -1067.6392 
-    5300         0.53  0.076457531     2703.409    95.385751   -3.4040809    3.0700644   -1070.7093   -1067.6392 
-    5350        0.535  0.076457501    2642.6927    97.779641   -3.4335521    3.1471136   -1070.7863   -1067.6392 
-    5400         0.54  0.076457502    2536.3506     99.09318   -3.4686216    3.1893909   -1070.8286   -1067.6392 
-    5450        0.545  0.076457526     2496.939    98.768917   -3.4975315    3.1789543   -1070.8182   -1067.6392 
-    5500         0.55   0.07645752    2590.2956    96.816601   -3.5146308    3.1161175   -1070.7554   -1067.6392 
-    5550        0.555   0.07645751     2736.468    93.934193   -3.5252273    3.0233449   -1070.6626   -1067.6392 
-    5600         0.56  0.076457511    2852.5253    91.119522   -3.5395987    2.9327525    -1070.572   -1067.6392 
-    5650        0.565   0.07645752    2911.6956    89.034641   -3.5601373     2.865649   -1070.5049   -1067.6392 
-    5700         0.57  0.076457504    2872.1071    87.822315   -3.5786029    2.8266294   -1070.4659   -1067.6392 
-    5750        0.575  0.076457514    2742.4368    87.594068   -3.5903293    2.8192831   -1070.4585   -1067.6392 
-    5800         0.58  0.076457541    2620.8059     88.56771   -3.5997031    2.8506205   -1070.4899   -1067.6392 
-    5850        0.585  0.076457558    2577.6659    90.685494   -3.6121768     2.918783    -1070.558   -1067.6392 
-    5900         0.59  0.076457556    2603.2365    93.377823   -3.6265073    3.0054377   -1070.6447   -1067.6392 
-    5950        0.595  0.076457545    2622.1463    95.785547   -3.6355062    3.0829322   -1070.7222   -1067.6392 
-    6000          0.6  0.076457592    2584.5093    97.370119   -3.6379265    3.1339328   -1070.7732   -1067.6392 
-    6050        0.605  0.076457628    2511.2983    98.197844   -3.6436108    3.1605738   -1070.7998   -1067.6392 
-    6100         0.61  0.076457605    2460.1937    98.607325   -3.6641337    3.1737533    -1070.813   -1067.6392 
-    6150        0.615  0.076457552    2425.1581    98.777199   -3.7023507    3.1792208   -1070.8185   -1067.6392 
-    6200         0.62  0.076457529     2378.858    98.671036   -3.7529167    3.1758039    -1070.815   -1067.6392 
-    6250        0.625  0.076457536    2373.6174    98.176109   -3.8075652    3.1598743   -1070.7991   -1067.6392 
-    6300         0.63  0.076457584    2457.9895    97.287993   -3.8600038    3.1312896   -1070.7705   -1067.6392 
-    6350        0.635  0.076457603    2571.5862    96.270876   -3.9092349    3.0985529   -1070.7378   -1067.6392 
-    6400         0.64  0.076457558    2610.0136    95.435972   -3.9541069    3.0716808   -1070.7109   -1067.6392 
-    6450        0.645  0.076457543    2587.7608    94.898692   -3.9898247    3.0543881   -1070.6936   -1067.6392 
-    6500         0.65  0.076457571    2592.7016    94.731712   -4.0156706    3.0490137   -1070.6882   -1067.6392 
-    6550        0.655  0.076457601    2601.6484     95.02635   -4.0381241    3.0584968   -1070.6977   -1067.6392 
-    6600         0.66  0.076457634    2566.7083    95.637112   -4.0616073    3.0781547   -1070.7174   -1067.6392 
-    6650        0.665  0.076457648    2514.9403    96.272248   -4.0866876     3.098597   -1070.7378   -1067.6392 
-    6700         0.67  0.076457667    2469.8797    96.811623   -4.1148391    3.1159572   -1070.7552   -1067.6392 
-    6750        0.675  0.076457679    2455.7631    97.232703   -4.1435988      3.12951   -1070.7687   -1067.6392 
-    6800         0.68  0.076457673    2468.7416    97.598183   -4.1658052    3.1412733   -1070.7805   -1067.6392 
-    6850        0.685  0.076457641      2449.95    98.364331   -4.1815152    3.1659323   -1070.8052   -1067.6392 
-    6900         0.69  0.076457591    2353.8808    100.13602   -4.1974936    3.2229556   -1070.8622   -1067.6392 
-    6950        0.695  0.076457574     2209.815    103.01374   -4.2144943    3.3155771   -1070.9548   -1067.6392 
-    7000          0.7   0.07645757    2076.4955    106.68046   -4.2313525    3.4335935   -1071.0728   -1067.6392 
-    7050        0.705  0.076457532    2018.5608    110.71726   -4.2520006    3.5635208   -1071.2028   -1067.6392 
-    7100         0.71  0.076457492    2066.0289    114.55462   -4.2812097    3.6870294   -1071.3263   -1067.6392 
-    7150        0.715   0.07645748    2155.5953    117.31153   -4.3158511    3.7757627    -1071.415   -1067.6392 
-    7200         0.72  0.076457494     2209.404    118.11478   -4.3476294    3.8016159   -1071.4408   -1067.6392 
-    7250        0.725  0.076457549     2217.455    116.73546   -4.3751645    3.7572213   -1071.3965   -1067.6392 
-    7300         0.73  0.076457599    2194.7896    113.55484   -4.4007803    3.6548507   -1071.2941   -1067.6392 
-    7350        0.735   0.07645757    2162.9678    109.25541   -4.4240013    3.5164702   -1071.1557   -1067.6392 
-    7400         0.74  0.076457504    2179.1755     104.7762   -4.4454261    3.3723033   -1071.0115   -1067.6392 
-    7450        0.745  0.076457518    2259.3755    101.07852   -4.4663804    3.2532905   -1070.8925   -1067.6392 
-    7500         0.75  0.076457572    2343.5728    98.882923   -4.4874367    3.1826236   -1070.8219   -1067.6392 
-    7550        0.755  0.076457589    2398.3228    98.458717   -4.5060637    3.1689702   -1070.8082   -1067.6392 
-    7600         0.76  0.076457555    2420.6576    99.703599   -4.5200762    3.2090377   -1070.8483   -1067.6392 
-    7650        0.765  0.076457552    2412.3104    102.42619   -4.5351178    3.2966665   -1070.9359   -1067.6392 
-    7700         0.77  0.076457571     2388.742    106.24497   -4.5597331    3.4195769   -1071.0588   -1067.6392 
-    7750        0.775  0.076457574    2379.8392    110.33126   -4.5953993    3.5510971   -1071.1903   -1067.6392 
-    7800         0.78  0.076457547    2387.9692    113.47154   -4.6333122    3.6521696   -1071.2914   -1067.6392 
-    7850        0.785  0.076457584    2375.3173    114.64931   -4.6633154    3.6900771   -1071.3293   -1067.6392 
-    7900         0.79  0.076457607    2347.9452    113.52456   -4.6810365    3.6538759   -1071.2931   -1067.6392 
-    7950        0.795  0.076457576    2325.3437    110.51925   -4.6879165    3.5571478   -1071.1964   -1067.6392 
-    8000          0.8  0.076457576    2298.9574    106.80135   -4.6933853    3.4374844   -1071.0767   -1067.6392 
-    8050        0.805  0.076457591    2279.7296     103.7714   -4.7072185     3.339963   -1070.9792   -1067.6392 
-    8100         0.81  0.076457594    2277.4281    102.48909   -4.7324485     3.298691   -1070.9379   -1067.6392 
-    8150        0.815  0.076457634    2249.9673    103.46477   -4.7678493    3.3300941   -1070.9693   -1067.6392 
-    8200         0.82  0.076457642    2192.5499    106.44615   -4.8061066    3.4260518   -1071.0653   -1067.6392 
-    8250        0.825  0.076457605    2153.4317    110.64954   -4.8384076    3.5613412   -1071.2006   -1067.6392 
-    8300         0.83   0.07645754    2141.4131    115.25212   -4.8632501     3.709479   -1071.3487   -1067.6392 
-    8350        0.835  0.076457494    2140.5445    119.40588   -4.8830278    3.8431708   -1071.4824   -1067.6392 
-    8400         0.84  0.076457514     2137.788     122.1619   -4.8981204    3.9318754   -1071.5711   -1067.6392 
-    8450        0.845  0.076457574    2137.0667    122.97752   -4.9139635     3.958127   -1071.5974   -1067.6392 
-    8500         0.85  0.076457574    2145.0503    121.91147   -4.9379125    3.9238154    -1071.563   -1067.6392 
-    8550        0.855  0.076457593    2147.0889    119.37696   -4.9688875      3.84224   -1071.4815   -1067.6392 
-    8600         0.86   0.07645763    2081.6527    116.07646   -5.0006593     3.736011   -1071.3752   -1067.6392 
-    8650        0.865  0.076457595    1962.5911    112.96131   -5.0308687    3.6357476    -1071.275   -1067.6392 
-    8700         0.87  0.076457564    1869.6563    110.95387   -5.0615711    3.5711363   -1071.2104   -1067.6392 
-    8750        0.875  0.076457589    1834.0748    110.57729   -5.0928561    3.5590158   -1071.1982   -1067.6392 
-    8800         0.88  0.076457596      1854.43    111.81118   -5.1197787    3.5987297    -1071.238   -1067.6392 
-    8850        0.885  0.076457575    1865.6826    114.38971   -5.1401001    3.6817215    -1071.321   -1067.6392 
-    8900         0.89  0.076457601    1833.0206    117.96559   -5.1581048     3.796814    -1071.436   -1067.6392 
-    8950        0.895  0.076457671    1792.8832    121.88891   -5.1778019    3.9230893   -1071.5623   -1067.6392 
-    9000          0.9  0.076457726    1758.5023    125.25302   -5.2006688    4.0313657   -1071.6706   -1067.6392 
-    9050        0.905  0.076457731    1735.1309    127.17393   -5.2254334    4.0931918   -1071.7324   -1067.6392 
-    9100         0.91  0.076457741     1762.187    127.10436   -5.2491072    4.0909526   -1071.7302   -1067.6392 
-    9150        0.915  0.076457708    1843.8804    124.99484   -5.2685152    4.0230558   -1071.6623   -1067.6392 
-    9200         0.92  0.076457667    1957.8234    121.30407   -5.2827478    3.9042658   -1071.5435   -1067.6392 
-    9250        0.925  0.076457686    2062.5914    117.02709   -5.2984278    3.7666077   -1071.4058   -1067.6392 
-    9300         0.93  0.076457701    2105.5399    113.37476   -5.3254121    3.6490547   -1071.2883   -1067.6392 
-    9350        0.935  0.076457698    2097.1011    111.14541   -5.3634987    3.5773012   -1071.2165   -1067.6392 
-    9400         0.94  0.076457691    2074.0275    110.80542   -5.4086147    3.5663585   -1071.2056   -1067.6392 
-    9450        0.945  0.076457741    2084.2231    112.48714   -5.4565921    3.6204859   -1071.2597   -1067.6392 
-    9500         0.95  0.076457742    2098.9606    115.74433   -5.4989221     3.725321   -1071.3646   -1067.6392 
-    9550        0.955   0.07645769    2076.1518    119.81614   -5.5288469    3.8563755   -1071.4956   -1067.6392 
-    9600         0.96  0.076457671    2028.8268    123.94506   -5.5445735     3.989268   -1071.6285   -1067.6392 
-    9650        0.965    0.0764577    2001.4552     127.5336    -5.548578     4.104768    -1071.744   -1067.6392 
-    9700         0.97  0.076457704    1998.3789    130.13306   -5.5456805    4.1884336   -1071.8277   -1067.6392 
-    9750        0.975  0.076457717     1975.232     131.4781   -5.5424564    4.2317247    -1071.871   -1067.6392 
-    9800         0.98  0.076457754    1943.5946    131.52534    -5.543939    4.2332452   -1071.8725   -1067.6392 
-    9850        0.985  0.076457767    1925.7258    130.61182   -5.5541538    4.2038429   -1071.8431   -1067.6392 
-    9900         0.99  0.076457768    1912.4426    129.30485   -5.5732953    4.1617771    -1071.801   -1067.6392 
-    9950        0.995   0.07645781    1906.7982    128.04744   -5.5944645    4.1213064   -1071.7605   -1067.6392 
-   10000            1  0.076457853    1902.6667    127.24846   -5.6139316    4.0955905   -1071.7348   -1067.6392 
-   10050        1.005  0.076457894    1903.6495    127.22624   -5.6350055    4.0948754   -1071.7341   -1067.6392 
-   10100         1.01  0.076457899    1913.5279    127.69735   -5.6543581    4.1100384   -1071.7493   -1067.6392 
-   10150        1.015  0.076457799    1907.6348    128.06173   -5.6658197    4.1217662    -1071.761   -1067.6392 
-   10200         1.02  0.076457733    1899.2476    128.11218   -5.6733688      4.12339   -1071.7626   -1067.6392 
-   10250        1.025  0.076457747    1895.8986    127.94169   -5.6840919    4.1179026   -1071.7571   -1067.6392 
-   10300         1.03  0.076457816    1877.4598     127.6041   -5.7004798     4.107037   -1071.7463   -1067.6392 
-   10350        1.035  0.076457876    1829.2074    127.11751   -5.7241722    4.0913757   -1071.7306   -1067.6392 
-   10400         1.04  0.076457884    1806.0757    126.48167    -5.756364    4.0709108   -1071.7101   -1067.6392 
-   10450        1.045  0.076457869    1822.1953     125.5947   -5.7930905     4.042363   -1071.6816   -1067.6392 
-   10500         1.05  0.076457879    1827.9173    124.33858   -5.8252681    4.0019336   -1071.6412   -1067.6392 
-   10550        1.055  0.076457858    1812.1963    122.79649   -5.8435788    3.9523004   -1071.5915   -1067.6392 
-   10600         1.06  0.076457791    1797.2949    121.53225   -5.8488847    3.9116096   -1071.5508   -1067.6392 
-   10650        1.065  0.076457757      1775.25    121.32451   -5.8518555    3.9049236   -1071.5442   -1067.6392 
-   10700         1.07  0.076457792    1740.3273    122.44046   -5.8607258    3.9408413   -1071.5801   -1067.6392 
-   10750        1.075  0.076457855    1729.7945    124.41086   -5.8780857    4.0042601   -1071.6435   -1067.6392 
-   10800         1.08  0.076457901    1741.2893    126.28784   -5.9016509    4.0646721   -1071.7039   -1067.6392 
-   10850        1.085  0.076457859    1751.6811    127.09185   -5.9236888    4.0905498   -1071.7298   -1067.6392 
-   10900         1.09  0.076457795     1764.679    126.41883    -5.937278    4.0688881   -1071.7081   -1067.6392 
-   10950        1.095   0.07645779    1769.3986    124.77704   -5.9433211    4.0160458   -1071.6553   -1067.6392 
-   11000          1.1  0.076457827    1761.3552    123.29516   -5.9478426    3.9683506   -1071.6076   -1067.6392 
-   11050        1.105  0.076457857    1751.4218    123.17488   -5.9566275    3.9644792   -1071.6037   -1067.6392 
-   11100         1.11  0.076457863    1726.8666    125.22443   -5.9741936    4.0304456   -1071.6697   -1067.6392 
-   11150        1.115  0.076457878    1735.2828    129.42028   -6.0014992    4.1654923   -1071.8047   -1067.6392 
-   11200         1.12  0.076457903    1805.6904    134.81633   -6.0340926    4.3391683   -1071.9784   -1067.6392 
-   11250        1.125  0.076457923    1847.8249    139.98198   -6.0631111    4.5054288   -1072.1447   -1067.6392 
-   11300         1.13  0.076457865    1818.7912    143.90555   -6.0856034    4.6317119   -1072.2709   -1067.6392 
-   11350        1.135  0.076457825    1798.9525    146.44555   -6.1101917    4.7134638   -1072.3527   -1067.6392 
-   11400         1.14  0.076457815    1837.1775    147.67989   -6.1418356    4.7531917   -1072.3924   -1067.6392 
-   11450        1.145  0.076457893    1909.6101    147.41836   -6.1737085    4.7447744    -1072.384   -1067.6392 
-   11500         1.15  0.076457962    1946.7114    145.59364   -6.1998495    4.6860443   -1072.3253   -1067.6392 
-   11550        1.155  0.076457957     1967.998    142.69304   -6.2256371    4.5926863   -1072.2319   -1067.6392 
-   11600         1.16  0.076457903     2034.228    139.43936   -6.2585164    4.4879639   -1072.1272   -1067.6392 
-   11650        1.165  0.076457847    2063.6908     136.1161   -6.2925345    4.3810023   -1072.0202   -1067.6392 
-   11700         1.17  0.076457857    1990.1311    132.80435   -6.3184969    4.2744111   -1071.9136   -1067.6392 
-   11750        1.175  0.076457901      1933.95    129.89649   -6.3394362    4.1808193   -1071.8201   -1067.6392 
-   11800         1.18  0.076457953    1947.2099    127.68121   -6.3585167    4.1095189   -1071.7488   -1067.6392 
-   11850        1.185  0.076457986    1940.4995    126.35451   -6.3779087    4.0668179    -1071.706   -1067.6392 
-   11900         1.19  0.076457947    1896.3696    126.25109   -6.4040311    4.0634894   -1071.7027   -1067.6392 
-   11950        1.195  0.076457956    1843.5682     127.5666   -6.4410172    4.1058301   -1071.7451   -1067.6392 
-   12000          1.2  0.076457964    1811.4472    130.04643   -6.4846233    4.1856452   -1071.8249   -1067.6392 
-   12050        1.205  0.076457972    1814.5828    133.04634   -6.5254215    4.2821996   -1071.9214   -1067.6392 
-   12100         1.21  0.076457967    1813.6628    135.85077   -6.5555239    4.3724623   -1072.0117   -1067.6392 
-   12150        1.215  0.076457935    1806.3763    138.19822   -6.5770911     4.448017   -1072.0872   -1067.6392 
-   12200         1.22  0.076457946    1794.9644    140.31834   -6.5982636    4.5162546   -1072.1555   -1067.6392 
-   12250        1.225  0.076457982    1772.5404    142.42677   -6.6192794    4.5841162   -1072.2233   -1067.6392 
-   12300         1.23  0.076457963    1753.3843    144.61375   -6.6346864    4.6545058   -1072.2937   -1067.6392 
-   12350        1.235  0.076457949    1737.1545    146.94235   -6.6429412    4.7294536   -1072.3687   -1067.6392 
-   12400         1.24  0.076457977     1726.207    149.46271   -6.6518876    4.8105732   -1072.4498   -1067.6392 
-   12450        1.245  0.076457983    1731.0662    151.80715   -6.6670425    4.8860309   -1072.5253   -1067.6392 
-   12500         1.25  0.076457915    1760.4467    153.07641   -6.6813282    4.9268832   -1072.5661   -1067.6392 
-   12550        1.255  0.076457879    1799.0622    152.72464   -6.6918933    4.9155611   -1072.5548   -1067.6392 
-   12600         1.26  0.076457914    1822.2254    151.04918    -6.710248     4.861635   -1072.5009   -1067.6392 
-   12650        1.265   0.07645795    1816.7324    148.37072   -6.7389019    4.7754268   -1072.4147   -1067.6392 
-   12700         1.27  0.076457955    1812.8602    144.86733   -6.7666889    4.6626674   -1072.3019   -1067.6392 
-   12750        1.275  0.076457984    1810.7634    141.22215    -6.788381    4.5453446   -1072.1846   -1067.6392 
-   12800         1.28  0.076458017    1784.5198    138.39541   -6.8065328    4.4543636   -1072.0936   -1067.6392 
-   12850        1.285  0.076458007    1723.1734    136.86317   -6.8200203    4.4050473   -1072.0443   -1067.6392 
-   12900         1.29  0.076457981    1676.1889    136.77495   -6.8278227    4.4022078   -1072.0414   -1067.6392 
-   12950        1.295   0.07645799     1686.883    138.26769   -6.8341741    4.4502528   -1072.0895   -1067.6392 
-   13000          1.3     0.076458    1750.0412    141.08411    -6.841283    4.5409017   -1072.1801   -1067.6392 
-   13050        1.305  0.076457933     1814.788    144.61706   -6.8510949    4.6546122   -1072.2938   -1067.6392 
-   13100         1.31  0.076457918    1840.2708    148.22464   -6.8662706     4.770725     -1072.41   -1067.6392 
-   13150        1.315   0.07645799    1855.2415     151.3832   -6.8883549    4.8723856   -1072.5116   -1067.6392 
-   13200         1.32  0.076458049    1867.3248    153.53322   -6.9142169    4.9415857   -1072.5808   -1067.6392 
-   13250        1.325  0.076458096    1847.9049    154.02873   -6.9377296    4.9575343   -1072.5968   -1067.6392 
-   13300         1.33  0.076458112     1840.483    152.42018   -6.9562822    4.9057618    -1072.545   -1067.6392 
-   13350        1.335  0.076458098    1855.9464    148.69839    -6.970188    4.7859732   -1072.4252   -1067.6392 
-   13400         1.34   0.07645806    1820.6867     143.5401   -6.9830712    4.6199497   -1072.2592   -1067.6392 
-   13450        1.345  0.076457976    1745.2435    138.19145   -6.9989611    4.4477992    -1072.087   -1067.6392 
-   13500         1.35  0.076457963    1697.5473    133.92117   -7.0152512     4.310357   -1071.9496   -1067.6392 
-   13550        1.355  0.076458016    1684.8882    131.80734   -7.0311044    4.2423215   -1071.8816   -1067.6392 
-   13600         1.36  0.076458061    1708.2521     132.4772    -7.051885    4.2638815   -1071.9031   -1067.6392 
-   13650        1.365   0.07645807    1723.4416    135.53906   -7.0750853      4.36243   -1072.0017   -1067.6392 
-   13700         1.37   0.07645806     1706.999    139.94405   -7.0945976    4.5042079   -1072.1434   -1067.6392 
-   13750        1.375  0.076458036    1712.8033    144.85597   -7.1159258    4.6623018   -1072.3015   -1067.6392 
-   13800         1.38  0.076457971    1751.0123    149.63395   -7.1458169    4.8160849   -1072.4553   -1067.6392 
-   13850        1.385  0.076458021    1772.9962    153.59227   -7.1786728    4.9434865   -1072.5827   -1067.6392 
-   13900         1.39  0.076458106    1773.7385    156.28506   -7.2050465     5.030156   -1072.6694   -1067.6392 
-   13950        1.395  0.076458102    1748.7335    157.81358   -7.2259294    5.0793525   -1072.7186   -1067.6392 
-   14000          1.4  0.076458031    1718.5394    158.78508   -7.2557377     5.110621   -1072.7499   -1067.6392 
-   14050        1.405  0.076457985    1759.6811     159.6226   -7.3026227    5.1375772   -1072.7768   -1067.6392 
-   14100         1.41  0.076457949     1848.058    160.13835    -7.353886     5.154177   -1072.7934   -1067.6392 
-   14150        1.415   0.07645791    1902.6843    160.00219    -7.387799    5.1497946    -1072.789   -1067.6392 
-   14200         1.42  0.076457928    1921.0383    159.34446   -7.3946089    5.1286251   -1072.7679   -1067.6392 
-   14250        1.425  0.076458016    1906.9383    158.81344   -7.3863965     5.111534   -1072.7508   -1067.6392 
-   14300         1.43  0.076458065    1861.3283      158.866   -7.3810737    5.1132253   -1072.7525   -1067.6392 
-   14350        1.435  0.076458033    1831.4331    159.34444   -7.3867848    5.1286245   -1072.7679   -1067.6392 
-   14400         1.44  0.076457975    1816.0391     159.7047   -7.4029452    5.1402197   -1072.7795   -1067.6392 
-   14450        1.445  0.076457983    1762.1574    159.29777   -7.4235285    5.1271223   -1072.7664   -1067.6392 
-   14500         1.45  0.076458063    1709.2993    157.82112   -7.4454745    5.0795953   -1072.7188   -1067.6392 
-   14550        1.455  0.076458051    1677.4867    155.54554   -7.4726077    5.0063538   -1072.6456   -1067.6392 
-   14600         1.46  0.076457997    1654.1484    152.98432    -7.507262    4.9239192   -1072.5632   -1067.6392 
-   14650        1.465  0.076457952    1662.1842    150.42233   -7.5432446    4.8414594   -1072.4807   -1067.6392 
-   14700         1.47  0.076457903    1676.4959    147.93139   -7.5725021    4.7612867   -1072.4005   -1067.6392 
-   14750        1.475  0.076457859    1647.8468    145.84289   -7.5959112    4.6940666   -1072.3333   -1067.6392 
-   14800         1.48  0.076457877    1565.6357     144.8914   -7.6195017    4.6634423   -1072.3027   -1067.6392 
-   14850        1.485  0.076457947    1482.0818    145.74233   -7.6439027      4.69083   -1072.3301   -1067.6392 
-   14900         1.49  0.076457952    1458.8328    148.56937   -7.6680645    4.7818206   -1072.4211   -1067.6392 
-   14950        1.495  0.076457894    1499.3699    152.90243   -7.6925072    4.9212832   -1072.5605   -1067.6392 
-   15000          1.5  0.076457943    1551.7726    157.93125   -7.7198204    5.0831399   -1072.7224   -1067.6392 
-   15050        1.505  0.076457986    1571.2434     162.8654   -7.7546524    5.2419492   -1072.8812   -1067.6392 
-   15100         1.51  0.076457935    1575.6395    166.87268   -7.7966882    5.3709267   -1073.0102   -1067.6392 
-   15150        1.515  0.076457852    1577.2167    169.36633   -7.8445178    5.4511868   -1073.0904   -1067.6392 
-   15200         1.52  0.076457871    1551.3549    170.15934   -7.8947687    5.4767104   -1073.1159   -1067.6392 
-   15250        1.525  0.076457931    1540.7825    169.38479   -7.9379114    5.4517809    -1073.091   -1067.6392 
-   15300         1.53  0.076457872    1542.7519      167.721   -7.9689255    5.3982305   -1073.0375   -1067.6392 
-   15350        1.535  0.076457794    1515.2436    166.07279   -7.9891151    5.3451817   -1072.9844   -1067.6392 
-   15400         1.54  0.076457791    1471.3138    164.91456   -8.0001719    5.3079031   -1072.9471   -1067.6392 
-   15450        1.545  0.076457806    1446.0781    164.17878    -8.005266    5.2842213   -1072.9235   -1067.6392 
-   15500         1.55  0.076457866    1437.1273    163.51385    -8.007144    5.2628202   -1072.9021   -1067.6392 
-   15550        1.555  0.076457955    1429.6394     162.9507   -8.0109974    5.2446946   -1072.8839   -1067.6392 
-   15600         1.56  0.076457952    1428.0365    163.16031   -8.0290067    5.2514413   -1072.8907   -1067.6392 
-   15650        1.565  0.076457861    1443.4131    164.39868   -8.0647449     5.291299   -1072.9305   -1067.6392 
-   15700         1.57  0.076457793    1455.1522    165.85145    -8.105615    5.3380576   -1072.9773   -1067.6392 
-   15750        1.575  0.076457798    1463.0529    166.37099   -8.1380795    5.3547794    -1072.994   -1067.6392 
-   15800         1.58    0.0764579    1465.1315    165.43643   -8.1598171    5.3246998   -1072.9639   -1067.6392 
-   15850        1.585  0.076457964    1481.9518    163.30816   -8.1737913    5.2561998   -1072.8954   -1067.6392 
-   15900         1.59  0.076457915    1527.4564    160.78551   -8.1825869    5.1750065   -1072.8142   -1067.6392 
-   15950        1.595  0.076457836    1575.6511    158.77652   -8.1876334    5.1103456   -1072.7496   -1067.6392 
-   16000          1.6   0.07645778    1614.7527    157.95908   -8.1929355    5.0840356   -1072.7233   -1067.6392 
-   16050        1.605  0.076457779    1617.7108     158.3895   -8.1978312    5.0978888   -1072.7371   -1067.6392 
-   16100         1.61  0.076457748     1603.592     159.6981   -8.1974276    5.1400074   -1072.7792   -1067.6392 
-   16150        1.615  0.076457683    1621.7853    161.62591   -8.1934309    5.2020553   -1072.8413   -1067.6392 
-   16200         1.62  0.076457713    1666.2189    163.90851   -8.1904572    5.2755226   -1072.9148   -1067.6392 
-   16250        1.625  0.076457784    1699.4521    166.19825   -8.1928336    5.3492197   -1072.9885   -1067.6392 
-   16300         1.63  0.076457822    1732.0779     168.1831   -8.2032476    5.4131037   -1073.0523   -1067.6392 
-   16350        1.635  0.076457792    1749.3266    169.69701   -8.2214781    5.4618299   -1073.1011   -1067.6392 
-   16400         1.64  0.076457743    1727.9265    170.72169   -8.2470147    5.4948102    -1073.134   -1067.6392 
-   16450        1.645  0.076457802    1695.7397    171.03962   -8.2748768    5.5050428   -1073.1443   -1067.6392 
-   16500         1.65  0.076457865    1654.9001     170.1718   -8.2900487    5.4771114   -1073.1163   -1067.6392 
-   16550        1.655  0.076457864    1599.4818    168.42964   -8.2855859    5.4210388   -1073.0603   -1067.6392 
-   16600         1.66  0.076457829    1549.0403    167.32713   -8.2743004    5.3855536   -1073.0248   -1067.6392 
-   16650        1.665  0.076457816    1552.8738    168.16653   -8.2712688    5.4125703   -1073.0518   -1067.6392 
-   16700         1.67  0.076457855    1613.3994    170.72875    -8.278589    5.4950374   -1073.1343   -1067.6392 
-   16750        1.675  0.076457923    1657.1911    173.60042    -8.287191    5.5874642   -1073.2267   -1067.6392 
-   16800         1.68  0.076457913     1642.492    175.54043    -8.290541    5.6499049   -1073.2891   -1067.6392 
-   16850        1.685  0.076457804    1591.5457    176.27819   -8.2944475    5.6736502   -1073.3129   -1067.6392 
-   16900         1.69  0.076457721    1535.2384    176.07329   -8.3085794    5.6670554   -1073.3063   -1067.6392 
-   16950        1.695  0.076457718     1505.622    175.05532   -8.3334071    5.6342912   -1073.2735   -1067.6392 
-   17000          1.7  0.076457759    1497.9484    173.29107   -8.3636107    5.5775077   -1073.2167   -1067.6392 
-   17050        1.705  0.076457839    1497.0049    170.93476   -8.3927083    5.5016678   -1073.1409   -1067.6392 
-   17100         1.71  0.076457875    1511.4053    168.29935   -8.4139231    5.4168451   -1073.0561   -1067.6392 
-   17150        1.715  0.076457846    1513.6863    166.13296   -8.4263326    5.3471182   -1072.9863   -1067.6392 
-   17200         1.72  0.076457792    1500.5415    165.41134   -8.4331329    5.3238925   -1072.9631   -1067.6392 
-   17250        1.725  0.076457779    1516.4257    166.86136   -8.4395441    5.3705623   -1073.0098   -1067.6392 
-   17300         1.73  0.076457719    1560.1678    170.36031   -8.4473104    5.4831788   -1073.1224   -1067.6392 
-   17350        1.735  0.076457713    1589.7681    174.76749   -8.4563024    5.6250272   -1073.2643   -1067.6392 
-   17400         1.74  0.076457713    1591.6237    178.46853   -8.4713912    5.7441481   -1073.3834   -1067.6392 
-   17450        1.745  0.076457675    1596.2649    179.85013   -8.4922285    5.7886159   -1073.4279   -1067.6392 
-   17500         1.75  0.076457641    1584.0194    177.91175   -8.5124955    5.7262277   -1073.3655   -1067.6392 
-   17550        1.755  0.076457729    1561.3047     172.8566   -8.5331849    5.5635239   -1073.2028   -1067.6392 
-   17600         1.76  0.076457773    1572.5958    165.81832   -8.5554415    5.3369913   -1072.9762   -1067.6392 
-   17650        1.765  0.076457741    1605.3403    158.62222   -8.5744278    5.1053792   -1072.7446   -1067.6392 
-   17700         1.77  0.076457777    1625.9857    153.83663   -8.5928174    4.9513512   -1072.5906   -1067.6392 
-   17750        1.775  0.076457794    1624.2493    153.59935   -8.6164551    4.9437143   -1072.5829   -1067.6392 
-   17800         1.78  0.076457697    1600.4975    158.02997    -8.639484    5.0863173   -1072.7255   -1067.6392 
-   17850        1.785  0.076457635    1572.3161    165.46312   -8.6573098    5.3255589   -1072.9648   -1067.6392 
-   17900         1.79  0.076457609    1561.9769    173.49259   -8.6712589    5.5839937   -1073.2232   -1067.6392 
-   17950        1.795  0.076457688    1562.7517    180.08491   -8.6850112    5.7961727   -1073.4354   -1067.6392 
-   18000          1.8  0.076457774    1534.5231    184.30185   -8.7046968    5.9318979   -1073.5711   -1067.6392 
-   18050        1.805  0.076457734    1514.7751    185.91513   -8.7282196    5.9838228   -1073.6231   -1067.6392 
-   18100         1.81  0.076457673    1529.4218     185.3585   -8.7536862    5.9659073   -1073.6051   -1067.6392 
-   18150        1.815  0.076457707    1528.0858    183.58143   -8.7834393    5.9087109   -1073.5479   -1067.6392 
-   18200         1.82    0.0764577     1527.873    181.50762   -8.8147286    5.8419635   -1073.4812   -1067.6392 
-   18250        1.825  0.076457665    1548.9614    179.99555   -8.8428647    5.7932965   -1073.4325   -1067.6392 
-   18300         1.83  0.076457588    1549.3007    179.95539   -8.8681457    5.7920039   -1073.4312   -1067.6392 
-   18350        1.835  0.076457533     1526.091    181.95841   -8.8948825    5.8564725   -1073.4957   -1067.6392 
-   18400         1.84  0.076457629    1493.8372    185.43374   -8.9193239     5.968329   -1073.6076   -1067.6392 
-   18450        1.845  0.076457747    1466.0305    188.93806   -8.9346392    6.0811179   -1073.7204   -1067.6392 
-   18500         1.85  0.076457732    1463.6299    191.18823   -8.9432273    6.1535417   -1073.7928   -1067.6392 
-   18550        1.855  0.076457611    1470.3581    191.71361   -8.9569487    6.1704514   -1073.8097   -1067.6392 
-   18600         1.86  0.076457576    1465.3642    190.61383   -8.9856472     6.135054   -1073.7743   -1067.6392 
-   18650        1.865  0.076457589    1435.5034     187.7372   -9.0216033    6.0424676   -1073.6817   -1067.6392 
-   18700         1.87  0.076457602    1387.1168    182.94758   -9.0538168    5.8883099   -1073.5275   -1067.6392 
-   18750        1.875  0.076457646    1370.2898     176.6874   -9.0814451     5.686821   -1073.3261   -1067.6392 
-   18800         1.88  0.076457607    1396.5471    169.73777   -9.1008384    5.4631417   -1073.1024   -1067.6392 
-   18850        1.885  0.076457617    1424.9718     163.2588    -9.109503    5.2546111   -1072.8938   -1067.6392 
-   18900         1.89  0.076457679    1428.3173    158.69622   -9.1168953     5.107761    -1072.747   -1067.6392 
-   18950        1.895  0.076457649    1439.2765    156.82172   -9.1272053    5.0474288   -1072.6867   -1067.6392 
-   19000          1.9  0.076457629    1459.8802    157.73056   -9.1321959    5.0766804   -1072.7159   -1067.6392 
-   19050        1.905  0.076457635     1504.363    162.01011   -9.1350256    5.2144212   -1072.8536   -1067.6392 
-   19100         1.91   0.07645765    1534.7588    170.14098   -9.1510965    5.4761196   -1073.1153   -1067.6392 
-   19150        1.915  0.076457653    1508.0173    180.71726   -9.1848155    5.8165254   -1073.4558   -1067.6392 
-   19200         1.92  0.076457613     1467.829    190.69721   -9.2245704    6.1377378    -1073.777   -1067.6392 
-   19250        1.925  0.076457631    1432.4759    197.48699   -9.2604662    6.3562721   -1073.9955   -1067.6392 
-   19300         1.93   0.07645763    1411.3494    200.09216   -9.2919631    6.4401214   -1074.0794   -1067.6392 
-   19350        1.935  0.076457594    1414.8241    198.83025   -9.3208023     6.399506   -1074.0387   -1067.6392 
-   19400         1.94  0.076457607     1435.692    194.74665   -9.3453509    6.2680721   -1073.9073   -1067.6392 
-   19450        1.945  0.076457654    1457.6905     189.4249   -9.3649457    6.0967875    -1073.736   -1067.6392 
-   19500         1.95  0.076457645    1449.0474     184.9571   -9.3864711    5.9529879   -1073.5922   -1067.6392 
-   19550        1.955  0.076457606    1409.8482    183.36678   -9.4200425     5.901802    -1073.541   -1067.6392 
-   19600         1.96  0.076457637    1376.8581     185.3704   -9.4660084    5.9662902   -1073.6055   -1067.6392 
-   19650        1.965  0.076457676    1394.1961    189.79341    -9.512099    6.1086483   -1073.7479   -1067.6392 
-   19700         1.97  0.076457666    1444.3533    194.43969   -9.5410671    6.2581922   -1073.8974   -1067.6392 
-   19750        1.975  0.076457652    1456.9001    197.74076   -9.5468975    6.3644397   -1074.0037   -1067.6392 
-   19800         1.98  0.076457697    1416.4247    199.50327   -9.5434518    6.4211677   -1074.0604   -1067.6392 
-   19850        1.985   0.07645765    1363.4589    200.03465   -9.5469461    6.4382705   -1074.0775   -1067.6392 
-   19900         1.99  0.076457547    1331.9006    199.31164   -9.5615968    6.4149999   -1074.0542   -1067.6392 
-   19950        1.995  0.076457526    1324.5585    197.29584   -9.5885975    6.3501197   -1073.9894   -1067.6392 
-   20000            2  0.076457553     1337.069    194.04585   -9.6231448    6.2455162   -1073.8847   -1067.6392 
-   20050        2.005  0.076457648    1351.0753    189.93086   -9.6575947     6.113072   -1073.7523   -1067.6392 
-   20100         2.01  0.076457655    1339.7133     185.8145   -9.6913164     5.980584   -1073.6198   -1067.6392 
-   20150        2.015  0.076457614    1318.0742    182.57664   -9.7225895    5.8763709   -1073.5156   -1067.6392 
-   20200         2.02  0.076457601    1288.6368    180.87905   -9.7460096    5.8217325    -1073.461   -1067.6392 
-   20250        2.025  0.076457595    1270.6138    181.09203   -9.7599966    5.8285875   -1073.4678   -1067.6392 
-   20300         2.03   0.07645759    1297.0333    183.14558    -9.771863    5.8946825   -1073.5339   -1067.6392 
-   20350        2.035  0.076457544     1322.481    186.19746   -9.7878745    5.9929098   -1073.6321   -1067.6392 
-   20400         2.04  0.076457529    1321.8589    188.69758   -9.8051647    6.0733781   -1073.7126   -1067.6392 
-   20450        2.045  0.076457552    1334.9839    189.43488   -9.8222144    6.0971087   -1073.7363   -1067.6392 
-   20500         2.05  0.076457581    1383.7092    188.25801   -9.8390497      6.05923   -1073.6985   -1067.6392 
-   20550        2.055  0.076457593    1422.9993     186.0328   -9.8547027    5.9876099   -1073.6268   -1067.6392 
-   20600         2.06   0.07645748    1399.9508    184.16392   -9.8728024    5.9274586   -1073.5667   -1067.6392 
-   20650        2.065  0.076457422    1335.1662    183.59411   -9.8931369    5.9091189   -1073.5483   -1067.6392 
-   20700         2.07  0.076457465     1306.751    184.55079   -9.9118543    5.9399103   -1073.5791   -1067.6392 
-   20750        2.075  0.076457483    1305.5888    187.07424   -9.9311695    6.0211296   -1073.6604   -1067.6392 
-   20800         2.08  0.076457441    1294.1667    191.05858   -9.9508151    6.1493686   -1073.7886   -1067.6392 
-   20850        2.085  0.076457401    1282.0253    196.07833   -9.9647464    6.3109334   -1073.9502   -1067.6392 
-   20900         2.09  0.076457455    1292.0201    201.33144   -9.9711707    6.4800088   -1074.1192   -1067.6392 
-   20950        2.095  0.076457576    1320.8835     205.6673   -9.9717153    6.6195616   -1074.2588   -1067.6392 
-   21000          2.1  0.076457569    1327.4497    207.97171   -9.9627916    6.6937308    -1074.333   -1067.6392 
-   21050        2.105  0.076457524    1302.0315    208.01339   -9.9425688    6.6950725   -1074.3343   -1067.6392 
-   21100         2.11  0.076457555    1283.4817    206.79741   -9.9230585    6.6559351   -1074.2952   -1067.6392 
-   21150        2.115  0.076457542    1295.1909     205.4375    -9.914788    6.6121654   -1074.2514   -1067.6392 
-   21200         2.12  0.076457479    1321.5201     204.1527    -9.909418    6.5708132     -1074.21   -1067.6392 
-   21250        2.125  0.076457453    1325.0561    202.79152   -9.8961399    6.5270024   -1074.1662   -1067.6392 
-   21300         2.13  0.076457519    1301.9167    201.35361   -9.8787376    6.4807223     -1074.12   -1067.6392 
-   21350        2.135  0.076457579    1274.9532    199.72664    -9.868175     6.428357   -1074.0676   -1067.6392 
-   21400         2.14  0.076457544    1261.6495     197.3916   -9.8684802    6.3532018   -1073.9924   -1067.6392 
-   21450        2.145  0.076457471    1267.8867    193.48031   -9.8693012    6.2273138   -1073.8665   -1067.6392 
-   21500         2.15  0.076457431    1293.2863    187.70474   -9.8616374    6.0414226   -1073.6807   -1067.6392 
-   21550        2.155   0.07645745    1323.0989    181.26349   -9.8574218    5.8341061   -1073.4733   -1067.6392 
-   21600         2.16  0.076457464    1324.9095    175.93101   -9.8707078     5.662476   -1073.3017   -1067.6392 
-   21650        2.165  0.076457483    1337.2372    172.83131   -9.9003355      5.56271   -1073.2019   -1067.6392 
-   21700         2.17  0.076457536    1353.6476    172.28199   -9.9335024    5.5450296   -1073.1843   -1067.6392 
-   21750        2.175  0.076457522    1337.4658    174.63693   -9.9656126    5.6208252   -1073.2601   -1067.6392 
-   21800         2.18  0.076457492    1319.6144    180.27032   -10.002014    5.8021402   -1073.4414   -1067.6392 
-   21850        2.185  0.076457468    1325.9534     188.6868   -10.042097     6.073031   -1073.7123   -1067.6392 
-   21900         2.19    0.0764574     1351.519    198.20437   -10.076426    6.3793615   -1074.0186   -1067.6392 
-   21950        2.195  0.076457412    1373.8526    206.68615   -10.099592    6.6523543   -1074.2916   -1067.6392 
-   22000          2.2  0.076457518     1392.659    212.65494    -10.12001    6.8444642   -1074.4837   -1067.6392 
-   22050        2.205  0.076457606    1390.3967    215.42094   -10.145572      6.93349   -1074.5727   -1067.6392 
-   22100         2.21  0.076457602    1347.4452    214.94045   -10.173725    6.9180253   -1074.5573   -1067.6392 
-   22150        2.215  0.076457513    1283.3202    211.98537   -10.199933    6.8229137   -1074.4621   -1067.6392 
-   22200         2.22  0.076457494    1222.5665    207.95995   -10.224493    6.6933523   -1074.3326   -1067.6392 
-   22250        2.225  0.076457542    1202.5195    204.45409   -10.254994    6.5805135   -1074.2197   -1067.6392 
-   22300         2.23  0.076457582    1210.7113    202.41627   -10.292456    6.5149247   -1074.1542   -1067.6392 
-   22350        2.235  0.076457593    1220.7645    201.90137   -10.329195    6.4983524   -1074.1376   -1067.6392 
-   22400         2.24  0.076457607    1234.7446    202.62559    -10.36471     6.521662   -1074.1609   -1067.6392 
-   22450        2.245  0.076457614    1256.0665    204.20591   -10.403554    6.5725258   -1074.2118   -1067.6392 
-   22500         2.25  0.076457647    1289.6179    206.08787    -10.44356    6.6330979   -1074.2723   -1067.6392 
-   22550        2.255  0.076457648    1318.2401    207.71118   -10.483186    6.6853454   -1074.3246   -1067.6392 
-   22600         2.26  0.076457621    1319.5232    208.34289   -10.522979    6.7056776   -1074.3449   -1067.6392 
-   22650        2.265  0.076457589    1316.8506    207.24251   -10.561044     6.670261   -1074.3095   -1067.6392 
-   22700         2.27  0.076457617     1331.642    204.29832   -10.595084    6.5755001   -1074.2147   -1067.6392 
-   22750        2.275  0.076457638    1346.6949    200.13918   -10.622417    6.4416347   -1074.0809   -1067.6392 
-   22800         2.28  0.076457572     1347.787      196.067   -10.645862    6.3105686   -1073.9498   -1067.6392 
-   22850        2.285  0.076457478    1357.3814    193.71126   -10.672581    6.2347474    -1073.874   -1067.6392 
-   22900         2.29  0.076457506    1359.0604    194.23136   -10.704942    6.2514872   -1073.8907   -1067.6392 
-   22950        2.295   0.07645755    1347.1653    197.67464   -10.741957    6.3623116   -1074.0015   -1067.6392 
-   23000          2.3  0.076457564    1321.3672    202.79941   -10.780161    6.5272563   -1074.1665   -1067.6392 
-   23050        2.305  0.076457626    1300.8493     207.8112   -10.812965    6.6885649   -1074.3278   -1067.6392 
-   23100         2.31  0.076457662    1289.7113     211.5894   -10.839288    6.8101691   -1074.4494   -1067.6392 
-   23150        2.315  0.076457654    1266.9494    213.84528    -10.86234    6.8827763    -1074.522   -1067.6392 
-   23200         2.32  0.076457651    1237.4556    214.46793   -10.878861    6.9028167    -1074.542   -1067.6392 
-   23250        2.325  0.076457588    1216.4817    213.53906    -10.88737    6.8729203   -1074.5122   -1067.6392 
-   23300         2.33  0.076457561    1198.6768     211.4015   -10.892244    6.8041213   -1074.4434   -1067.6392 
-   23350        2.335  0.076457617      1218.46    208.62206   -10.896503     6.714663   -1074.3539   -1067.6392 
-   23400         2.34  0.076457697    1274.0141    206.18082   -10.898818    6.6360899   -1074.2753   -1067.6392 
-   23450        2.345  0.076457697    1310.0462    205.39475   -10.899188    6.6107893     -1074.25   -1067.6392 
-   23500         2.35  0.076457625    1309.8688    206.85671   -10.898274    6.6578437   -1074.2971   -1067.6392 
-   23550        2.355  0.076457607    1294.4375    210.05998   -10.904793    6.7609436   -1074.4002   -1067.6392 
-   23600         2.36  0.076457638    1272.3829    213.64213   -10.924411    6.8762376   -1074.5155   -1067.6392 
-   23650        2.365   0.07645764    1263.3834    215.89726   -10.943246    6.9488208   -1074.5881   -1067.6392 
-   23700         2.37    0.0764576    1265.3339    216.28708    -10.95133    6.9613674   -1074.6006   -1067.6392 
-   23750        2.375  0.076457533    1265.7883    215.64775   -10.954658    6.9407901     -1074.58   -1067.6392 
-   23800         2.38  0.076457509     1270.324    215.14847   -10.964811    6.9247203    -1074.564   -1067.6392 
-   23850        2.385  0.076457647    1295.1389    215.59482   -10.992719    6.9390865   -1074.5783   -1067.6392 
-   23900         2.39   0.07645774    1317.1304    216.50299   -11.032267    6.9683166   -1074.6075   -1067.6392 
-   23950        2.395  0.076457678    1323.3993    216.86149    -11.06922    6.9798554   -1074.6191   -1067.6392 
-   24000          2.4  0.076457616    1327.0079    216.51416   -11.098994    6.9686763   -1074.6079   -1067.6392 
-   24050        2.405  0.076457602    1347.1187    215.98329   -11.123989    6.9515898   -1074.5908   -1067.6392 
-   24100         2.41  0.076457633    1373.0058     215.6582   -11.147405    6.9411267   -1074.5804   -1067.6392 
-   24150        2.415  0.076457606    1357.3622    215.33306   -11.168833    6.9306616   -1074.5699   -1067.6392 
-   24200         2.42  0.076457558    1293.9783     214.6673   -11.190176    6.9092338   -1074.5485   -1067.6392 
-   24250        2.425  0.076457575    1262.6983    213.59841   -11.211793    6.8748305   -1074.5141   -1067.6392 
-   24300         2.43  0.076457586    1296.1082    212.60059   -11.234851    6.8427151   -1074.4819   -1067.6392 
-   24350        2.435   0.07645758    1338.5152    212.36533   -11.263922    6.8351428   -1074.4744   -1067.6392 
-   24400         2.44   0.07645762    1359.7328    212.76414   -11.288804     6.847979   -1074.4872   -1067.6392 
-   24450        2.445  0.076457613    1354.6032    213.05104   -11.296422    6.8572131   -1074.4964   -1067.6392 
-   24500         2.45   0.07645752    1340.1858    212.64499   -11.294481    6.8441441   -1074.4834   -1067.6392 
-   24550        2.455   0.07645749    1331.5151    211.50434   -11.306624    6.8074314   -1074.4467   -1067.6392 
-   24600         2.46  0.076457509    1316.1319    209.75998   -11.338874    6.7512878   -1074.3905   -1067.6392 
-   24650        2.465  0.076457501    1303.2352    208.01652   -11.382268    6.6951732   -1074.3344   -1067.6392 
-   24700         2.47  0.076457554    1316.5042    207.54508   -11.432653    6.6799995   -1074.3192   -1067.6392 
-   24750        2.475  0.076457644    1323.4729    209.08952   -11.480943    6.7297085   -1074.3689   -1067.6392 
-   24800         2.48  0.076457563    1316.2449    212.60405   -11.521223    6.8428264   -1074.4821   -1067.6392 
-   24850        2.485  0.076457464     1303.023    217.39017   -11.549403    6.9968714   -1074.6361   -1067.6392 
-   24900         2.49  0.076457476    1306.7431    222.37347   -11.558822    7.1572628   -1074.7965   -1067.6392 
-   24950        2.495   0.07645745    1300.9383    226.66891     -11.5504    7.2955148   -1074.9347   -1067.6392 
-   25000          2.5  0.076457461    1270.8966    229.83334   -11.536542    7.3973644   -1075.0366   -1067.6392 
-   25050        2.505  0.076457456    1266.2646    231.90105   -11.533642    7.4639151   -1075.1031   -1067.6392 
-   25100         2.51  0.076457446    1270.2017    233.06025   -11.547509     7.501225   -1075.1405   -1067.6392 
-   25150        2.515   0.07645757    1231.6171    233.15738    -11.56954    7.5043513   -1075.1436   -1067.6392 
-   25200         2.52  0.076457709    1191.0767    231.73714   -11.589225    7.4586397   -1075.0979   -1067.6392 
-   25250        2.525  0.076457772    1193.1019    228.87762   -11.611584     7.366604   -1075.0058   -1067.6392 
-   25300         2.53  0.076457705    1202.8442    225.48075   -11.647482     7.257273   -1074.8965   -1067.6392 
-   25350        2.535  0.076457601    1201.3602    222.49225   -11.687125    7.1610856   -1074.8003   -1067.6392 
-   25400         2.54  0.076457625    1191.7307    220.47028   -11.711225    7.0960072   -1074.7352   -1067.6392 
-   25450        2.545  0.076457676     1184.558     219.7896    -11.72244     7.074099   -1074.7133   -1067.6392 
-   25500         2.55   0.07645769    1209.0131    220.21101   -11.729634    7.0876623   -1074.7269   -1067.6392 
-   25550        2.555  0.076457694    1252.4527    221.39919   -11.740381    7.1259047   -1074.7651   -1067.6392 
-   25600         2.56  0.076457651    1266.8561    223.37443   -11.758317    7.1894793   -1074.8287   -1067.6392 
-   25650        2.565  0.076457702    1260.0162    226.18443   -11.779767    7.2799214   -1074.9192   -1067.6392 
-   25700         2.57  0.076457766    1258.0807    229.46946   -11.803244    7.3856527   -1075.0249   -1067.6392 
-   25750        2.575    0.0764577    1260.0577    231.96891   -11.827028    7.4660992   -1075.1053   -1067.6392 
-   25800         2.58   0.07645766    1263.5682    232.00397   -11.843175    7.4672278   -1075.1065   -1067.6392 
-   25850        2.585  0.076457679    1267.6331    229.22367   -11.852724    7.3777416    -1075.017   -1067.6392 
-   25900         2.59  0.076457667    1273.4873    224.95936   -11.864844    7.2404915   -1074.8797   -1067.6392 
-   25950        2.595  0.076457638    1259.3238    220.69283   -11.875369    7.1031702   -1074.7424   -1067.6392 
-   26000          2.6   0.07645756    1234.4517    217.53504    -11.87838    7.0015342   -1074.6408   -1067.6392 
-   26050        2.605  0.076457531    1223.5843    216.47883   -11.885283     6.967539   -1074.6068   -1067.6392 
-   26100         2.61  0.076457579    1239.4383     217.6799   -11.906525    7.0061965   -1074.6454   -1067.6392 
-   26150        2.615  0.076457676    1254.9755    220.14626     -11.9364    7.0855781   -1074.7248   -1067.6392 
-   26200         2.62  0.076457691    1263.4276    222.78599    -11.96794      7.17054   -1074.8098   -1067.6392 
-   26250        2.625  0.076457661    1290.9982    225.11879   -12.002676    7.2456229   -1074.8849   -1067.6392 
-   26300         2.63  0.076457625    1320.5003    226.53955   -12.032325    7.2913511   -1074.9306   -1067.6392 
-   26350        2.635  0.076457604    1325.6925    226.42099   -12.045972    7.2875353   -1074.9268   -1067.6392 
-   26400         2.64  0.076457635    1323.8314    225.04813   -12.050265    7.2433489   -1074.8826   -1067.6392 
-   26450        2.645  0.076457683    1337.7763    223.39584   -12.056562    7.1901684   -1074.8294   -1067.6392 
-   26500         2.65  0.076457646      1356.26    222.47285   -12.072437    7.1604612   -1074.7997   -1067.6392 
-   26550        2.655  0.076457593    1368.7452    222.81131   -12.102517    7.1713548   -1074.8106   -1067.6392 
-   26600         2.66  0.076457577    1372.4772     224.2612   -12.136283    7.2180208   -1074.8573   -1067.6392 
-   26650        2.665  0.076457669    1353.1116    226.93203    -12.15666    7.3039835   -1074.9432   -1067.6392 
-   26700         2.67   0.07645782    1296.4345    231.54488   -12.162395    7.4524517   -1075.0917   -1067.6392 
-   26750        2.675   0.07645786     1233.171    238.00107    -12.16795    7.6602491   -1075.2995   -1067.6392 
-   26800         2.68    0.0764578    1205.1226    244.60391    -12.18481    7.8727668    -1075.512   -1067.6392 
-   26850        2.685  0.076457751    1203.9449    249.24116   -12.214765    8.0220202   -1075.6613   -1067.6392 
-   26900         2.69  0.076457871     1220.793    250.32595   -12.247789    8.0569351   -1075.6962   -1067.6392 
-   26950        2.695   0.07645797     1250.922    247.65941   -12.281839    7.9711102   -1075.6103   -1067.6392 
-   27000          2.7  0.076457916    1272.2527    242.25891   -12.319204    7.7972911   -1075.4365   -1067.6392 
-   27050        2.705  0.076457909    1260.7801     235.6016    -12.35094    7.5830204   -1075.2223   -1067.6392 
-   27100         2.71  0.076457849    1229.7859    229.49227   -12.367756    7.3863867   -1075.0256   -1067.6392 
-   27150        2.715  0.076457776    1230.1984    225.87326    -12.37385    7.2699062   -1074.9091   -1067.6392 
-   27200         2.72  0.076457788    1256.5205    226.01981   -12.383103    7.2746231   -1074.9139   -1067.6392 
-   27250        2.725  0.076457742     1269.109    229.57592   -12.401772    7.3890791   -1075.0283   -1067.6392 
-   27300         2.73  0.076457757    1278.2216    234.37745    -12.41951    7.5436201   -1075.1829   -1067.6392 
-   27350        2.735  0.076457815    1281.9146    237.72622   -12.426299     7.651403   -1075.2906   -1067.6392 
-   27400         2.74  0.076457895    1266.5327    238.04161   -12.428658    7.6615539   -1075.3008   -1067.6392 
-   27450        2.745  0.076457976    1238.9201    235.37217   -12.441314    7.5756359   -1075.2149   -1067.6392 
-   27500         2.75  0.076457843    1230.4481    230.70667   -12.466737    7.4254733   -1075.0647   -1067.6392 
-   27550        2.755  0.076457656    1236.7255    225.51713   -12.497899    7.2584439   -1074.8977   -1067.6392 
-   27600         2.76   0.07645776      1238.11    221.28548    -12.52521    7.1222449   -1074.7615   -1067.6392 
-   27650        2.765  0.076457889    1218.4037    219.08795   -12.543581    7.0515156   -1074.6907   -1067.6392 
-   27700         2.77  0.076457882    1198.4777    219.33613   -12.554891    7.0595037   -1074.6987   -1067.6392 
-   27750        2.775  0.076457863     1183.089    221.96976   -12.561518     7.144269   -1074.7835   -1067.6392 
-   27800         2.78  0.076457885      1169.37    227.37353   -12.573341    7.3181935   -1074.9574   -1067.6392 
-   27850        2.785  0.076457897    1169.7411    235.91312   -12.602269    7.5930469   -1075.2323   -1067.6392 
-   27900         2.79  0.076457851    1151.3464    246.28711   -12.644365    7.9269419   -1075.5662   -1067.6392 
-   27950        2.795  0.076457843    1106.9771    255.46726   -12.682364    8.2224121   -1075.8616   -1067.6392 
-   28000          2.8  0.076457826    1068.9543    260.54346    -12.70329    8.3857935    -1076.025   -1067.6392 
-   28050        2.805  0.076457783    1046.8631    260.38287   -12.707616    8.3806246   -1076.0199   -1067.6392 
-   28100         2.81  0.076457851    1035.4028    255.75262   -12.701329    8.2315965   -1075.8708   -1067.6392 
-   28150        2.815  0.076457914    1039.8478    248.80323   -12.698053    8.0079252   -1075.6472   -1067.6392 
-   28200         2.82  0.076457945    1077.5288    241.99763   -12.714207    7.7888815   -1075.4281   -1067.6392 
-   28250        2.825  0.076457907    1106.7726     236.8129   -12.748192    7.6220071   -1075.2612   -1067.6392 
-   28300         2.83  0.076457858    1088.3383    233.07492   -12.770565     7.501697   -1075.1409   -1067.6392 
-   28350        2.835  0.076457962    1067.6408     230.2341   -12.762291    7.4102632   -1075.0495   -1067.6392 
-   28400         2.84  0.076458053    1085.7765    228.74782   -12.741859     7.362426   -1075.0017   -1067.6392 
-   28450        2.845  0.076458069    1116.0156    229.35012   -12.732966    7.3818115    -1075.021   -1067.6392 
-   28500         2.85   0.07645799    1140.0561    231.95241   -12.737452    7.4655684   -1075.1048   -1067.6392 
-   28550        2.855  0.076457881    1175.3679    235.63809   -12.744967    7.5841948   -1075.2234   -1067.6392 
-   28600         2.86  0.076457945    1191.5122    239.06582   -12.744692    7.6945191   -1075.3338   -1067.6392 
-   28650        2.865  0.076458033    1165.8181     241.0619   -12.730571    7.7587645    -1075.398   -1067.6392 
-   28700         2.87  0.076458003    1144.2872    241.42924   -12.708938    7.7705875   -1075.4098   -1067.6392 
-   28750        2.875  0.076457916    1156.9296    241.00794    -12.69273    7.7570275   -1075.3963   -1067.6392 
-   28800         2.88  0.076457978    1169.6062    241.01439   -12.691343    7.7572351   -1075.3965   -1067.6392 
-   28850        2.885  0.076458067    1153.2461    242.11608   -12.703125    7.7926941   -1075.4319   -1067.6392 
-   28900         2.89  0.076458128    1137.1648    244.24646   -12.730476    7.8612619   -1075.5005   -1067.6392 
-   28950        2.895  0.076458132    1144.0676    245.87591   -12.765806    7.9137071   -1075.5529   -1067.6392 
-   29000          2.9  0.076458055    1166.7003    244.81325   -12.786467    7.8795045   -1075.5187   -1067.6392 
-   29050        2.905  0.076458115     1201.626    240.80417   -12.786117    7.7504692   -1075.3897   -1067.6392 
-   29100         2.91  0.076458234    1227.2794    235.81398   -12.775018    7.5898561   -1075.2291   -1067.6392 
-   29150        2.915  0.076458217    1233.5955    232.10337   -12.761015     7.470427   -1075.1097   -1067.6392 
-   29200         2.92  0.076458111    1222.4273    231.10647   -12.757278    7.4383412   -1075.0776   -1067.6392 
-   29250        2.925  0.076458074    1212.9521    232.98759   -12.778062    7.4988864   -1075.1381   -1067.6392 
-   29300         2.93  0.076458082    1220.2844    236.56821   -12.814589    7.6141315   -1075.2534   -1067.6392 
-   29350        2.935  0.076458085    1197.6267    240.71244   -12.847172    7.7475166   -1075.3867   -1067.6392 
-   29400         2.94  0.076458174    1166.2296     245.3581   -12.871897    7.8970407   -1075.5363   -1067.6392 
-   29450        2.945    0.0764582    1162.6548    250.15917   -12.892997    8.0515671   -1075.6908   -1067.6392 
-   29500         2.95  0.076458192    1166.7685    253.39653   -12.905195    8.1557639    -1075.795   -1067.6392 
-   29550        2.955  0.076458187    1155.8258    253.69254   -12.906863    8.1652912   -1075.8045   -1067.6392 
-   29600         2.96  0.076458159    1155.2633    251.58259   -12.911192    8.0973809   -1075.7366   -1067.6392 
-   29650        2.965  0.076458142    1187.0841      248.958    -12.92707    8.0129065   -1075.6521   -1067.6392 
-   29700         2.97  0.076458107    1216.9951    247.40312   -12.945328    7.9628616   -1075.6021   -1067.6392 
-   29750        2.975  0.076458054    1194.8857    246.85295   -12.955382    7.9451538   -1075.5844   -1067.6392 
-   29800         2.98  0.076458024    1170.1087    246.10026   -12.960888    7.9209279   -1075.5602   -1067.6392 
-   29850        2.985  0.076458073    1169.1596    244.20885   -12.971119    7.8600515   -1075.4993   -1067.6392 
-   29900         2.99  0.076458181    1160.4286    240.86241   -12.984094    7.7523436   -1075.3916   -1067.6392 
-   29950        2.995  0.076458232    1131.8843    236.46352   -12.994209    7.6107619     -1075.25   -1067.6392 
-   30000            3  0.076458157    1094.5416    232.18947     -13.0017    7.4731984   -1075.1124   -1067.6392 
-   30050        3.005  0.076458011    1065.8494    229.55114   -13.006404    7.3882816   -1075.0275   -1067.6392 
-   30100         3.01  0.076458026    1061.4657    229.77899   -13.012924    7.3956153   -1075.0348   -1067.6392 
-   30150        3.015  0.076458159    1064.4309    232.81858   -13.028261    7.4934467   -1075.1327   -1067.6392 
-   30200         3.02  0.076458266    1064.5403    237.18963   -13.051358    7.6341323   -1075.2734   -1067.6392 
-   30250        3.025  0.076458254     1077.435     241.1768    -13.07564    7.7624624   -1075.4017   -1067.6392 
-   30300         3.03  0.076458129    1120.7955    244.00429   -13.099282    7.8534675   -1075.4927   -1067.6392 
-   30350        3.035  0.076458123    1166.6115    245.76237   -13.120127    7.9100525   -1075.5493   -1067.6392 
-   30400         3.04  0.076458222    1186.7887    246.73143    -13.12997    7.9412425   -1075.5805   -1067.6392 
-   30450        3.045  0.076458192    1210.3729     247.3058   -13.131142    7.9597292    -1075.599   -1067.6392 
-   30500         3.05  0.076458205    1226.7005    247.41892   -13.129466    7.9633701   -1075.6026   -1067.6392 
-   30550        3.055  0.076458239    1218.1054    246.53578   -13.123602    7.9349454   -1075.5742   -1067.6392 
-   30600         3.06  0.076458222    1213.5049    244.89144   -13.119076     7.882021   -1075.5213   -1067.6392 
-   30650        3.065  0.076458209     1197.742    243.51998   -13.124172    7.8378794   -1075.4771   -1067.6392 
-   30700         3.07  0.076458217    1173.0375    243.32265   -13.142559    7.8315283   -1075.4708   -1067.6392 
-   30750        3.075  0.076458232    1174.7744     244.4044   -13.175375    7.8663454   -1075.5056   -1067.6392 
-   30800         3.08  0.076458215    1182.8312    245.99614   -13.218442    7.9175767   -1075.5568   -1067.6392 
-   30850        3.085  0.076458183      1183.66    247.03526   -13.258527    7.9510216   -1075.5903   -1067.6392 
-   30900         3.09  0.076458319     1177.992     247.2078   -13.284596    7.9565748   -1075.5958   -1067.6392 
-   30950        3.095  0.076458373    1176.7211    247.34132   -13.301899    7.9608722   -1075.6001   -1067.6392 
-   31000          3.1  0.076458253    1164.7417    248.53603   -13.327025    7.9993251   -1075.6386   -1067.6392 
-   31050        3.105  0.076458217    1128.9001    250.94808   -13.365858    8.0769586   -1075.7162   -1067.6392 
-   31100         3.11  0.076458294    1092.9077    253.74162   -13.407353    8.1668708   -1075.8061   -1067.6392 
-   31150        3.115  0.076458358    1079.4871    256.46396   -13.445278    8.2544917   -1075.8937   -1067.6392 
-   31200         3.12  0.076458421    1088.7747    259.60213   -13.488098    8.3554961   -1075.9947   -1067.6392 
-   31250        3.125   0.07645843    1133.6001      263.188   -13.540135      8.47091   -1076.1101   -1067.6392 
-   31300         3.13  0.076458393    1192.6693    265.96082   -13.591815    8.5601553   -1076.1994   -1067.6392 
-   31350        3.135  0.076458398    1206.7015    266.41337   -13.631689    8.5747211    -1076.214   -1067.6392 
-   31400         3.14   0.07645845    1184.8303    264.21376   -13.660682    8.5039248   -1076.1432   -1067.6392 
-   31450        3.145   0.07645848    1183.6347    260.39213   -13.689676     8.380923   -1076.0202   -1067.6392 
-   31500         3.15  0.076458598    1199.1745    256.21199   -13.723387    8.2463816   -1075.8856   -1067.6392 
-   31550        3.155  0.076458602    1226.3861    252.38445   -13.753029    8.1231895   -1075.7624   -1067.6392 
-   31600         3.16  0.076458505    1232.7936    249.62393   -13.772372    8.0343401   -1075.6736   -1067.6392 
-   31650        3.165  0.076458472    1194.1646    248.63142    -13.78451    8.0023952   -1075.6416   -1067.6392 
-   31700         3.17  0.076458402    1135.0204    248.67712   -13.784757    8.0038662   -1075.6431   -1067.6392 
-   31750        3.175  0.076458444    1088.5207     248.0804   -13.772118    7.9846602   -1075.6239   -1067.6392 
-   31800         3.18  0.076458483    1079.5555    246.27927   -13.761932    7.9266895   -1075.5659   -1067.6392 
-   31850        3.185  0.076458412    1103.2185     244.3339   -13.766697    7.8640762   -1075.5033   -1067.6392 
-   31900         3.19   0.07645842    1120.0872     243.8787   -13.782801    7.8494252   -1075.4887   -1067.6392 
-   31950        3.195  0.076458479    1119.4512    245.95725   -13.799444    7.9163248   -1075.5556   -1067.6392 
-   32000          3.2   0.07645851    1092.4855    250.30658   -13.803665    8.0563117   -1075.6955   -1067.6392 
-   32050        3.205  0.076458415     1067.424    255.82203   -13.785579    8.2338307   -1075.8731   -1067.6392 
-   32100         3.21  0.076458345    1068.4429    261.44517   -13.748535    8.4148156    -1076.054   -1067.6392 
-   32150        3.215   0.07645841    1080.7046    266.36957   -13.713453    8.5733114   -1076.2125   -1067.6392 
-   32200         3.22  0.076458507    1092.5849    269.83978   -13.708135    8.6850028   -1076.3242   -1067.6392 
-   32250        3.225  0.076458535    1099.8414     270.7057    -13.73358    8.7128731   -1076.3521   -1067.6392 
-   32300         3.23  0.076458534    1114.7135    268.29144   -13.763677    8.6351683   -1076.2744   -1067.6392 
-   32350        3.235  0.076458458    1109.1702    263.87403   -13.783235    8.4929906   -1076.1322   -1067.6392 
-   32400         3.24   0.07645842    1084.0276    259.90176   -13.803644      8.36514   -1076.0044   -1067.6392 
-   32450        3.245  0.076458464    1083.1937    257.32785   -13.835634    8.2822966   -1075.9215   -1067.6392 
-   32500         3.25   0.07645845    1114.4646    255.14878   -13.870961    8.2121616   -1075.8514   -1067.6392 
-   32550        3.255  0.076458381    1152.8289     252.6422   -13.897547    8.1314852   -1075.7707   -1067.6392 
-   32600         3.26  0.076458468     1177.486    250.67802   -13.912211    8.0682668   -1075.7075   -1067.6392 
-   32650        3.265  0.076458565    1185.3078    250.60277   -13.918256    8.0658447   -1075.7051   -1067.6392 
-   32700         3.27  0.076458542    1191.2786     252.7908   -13.926328     8.136268   -1075.7755   -1067.6392 
-   32750        3.275  0.076458529    1180.3288     256.6616   -13.948559    8.2608527   -1075.9001   -1067.6392 
-   32800         3.28  0.076458451    1153.7783    261.08347   -13.985264    8.4031741   -1076.0424   -1067.6392 
-   32850        3.285  0.076458392    1133.2496    264.84942   -14.024763    8.5243841   -1076.1636   -1067.6392 
-   32900         3.29  0.076458438    1115.3658    267.38276   -14.053439    8.6059217   -1076.2452   -1067.6392 
-   32950        3.295  0.076458471     1127.683    269.00733   -14.070131    8.6582097   -1076.2974   -1067.6392 
-   33000          3.3  0.076458479    1149.7773    269.98003   -14.072925    8.6895169   -1076.3287   -1067.6392 
-   33050        3.305  0.076458432    1151.5261    270.25086   -14.062159    8.6982337   -1076.3375   -1067.6392 
-   33100         3.31  0.076458345     1155.116    269.80119   -14.049957    8.6837609    -1076.323   -1067.6392 
-   33150        3.315  0.076458436      1135.61    268.22847   -14.036071    8.6331415   -1076.2724   -1067.6392 
-   33200         3.32  0.076458577     1111.738    265.73519   -14.027508    8.5528932   -1076.1921   -1067.6392 
-   33250        3.325  0.076458535    1116.9245    263.26799   -14.038682    8.4734846   -1076.1127   -1067.6392 
-   33300         3.33  0.076458501    1131.8225    261.47169   -14.068281    8.4156693   -1076.0549   -1067.6392 
-   33350        3.335  0.076458475    1120.8199    260.14815   -14.108099    8.3730701   -1076.0123   -1067.6392 
-   33400         3.34  0.076458435    1094.4035    258.29932   -14.149771    8.3135641   -1075.9528   -1067.6392 
-   33450        3.345  0.076458459    1082.1878    255.19265   -14.184258    8.2135735   -1075.8528   -1067.6392 
-   33500         3.35  0.076458528    1083.2242    251.14433   -14.202792    8.0832751   -1075.7225   -1067.6392 
-   33550        3.355  0.076458529    1103.4532    247.60346   -14.210592    7.9693094   -1075.6085   -1067.6392 
-   33600         3.36  0.076458486    1137.7183    246.24059   -14.222506    7.9254445   -1075.5647   -1067.6392 
-   33650        3.365  0.076458516    1150.4421    247.37214   -14.233399    7.9618644   -1075.6011   -1067.6392 
-   33700         3.37  0.076458507    1143.7496    250.70305   -14.237383    8.0690723   -1075.7083   -1067.6392 
-   33750        3.375  0.076458425    1135.9529    256.43973    -14.24743    8.2537116   -1075.8929   -1067.6392 
-   33800         3.38  0.076458392    1126.2288    264.31662   -14.271937    8.5072354   -1076.1465   -1067.6392 
-   33850        3.385   0.07645848    1105.1309    272.68103   -14.305504    8.7764506   -1076.4157   -1067.6392 
-   33900         3.39  0.076458564    1085.1215     279.2817   -14.345574    8.9888984   -1076.6281   -1067.6392 
-   33950        3.395  0.076458555    1076.9206    282.71636   -14.394902    9.0994454   -1076.7387   -1067.6392 
-   34000          3.4  0.076458512    1086.4333    282.84295   -14.446959      9.10352   -1076.7428   -1067.6392 
-   34050        3.405   0.07645848    1099.4638    280.63434   -14.486843    9.0324339   -1076.6717   -1067.6392 
-   34100         3.41  0.076458382     1093.368    278.40903   -14.515246    8.9608108      -1076.6   -1067.6392 
-   34150        3.415  0.076458423    1088.8094    278.43798   -14.545814    8.9617425    -1076.601   -1067.6392 
-   34200         3.42  0.076458529    1070.3036    280.46333   -14.587151    9.0269298   -1076.6662   -1067.6392 
-   34250        3.425  0.076458454    1052.8089    281.70843   -14.639127    9.0670046   -1076.7062   -1067.6392 
-   34300         3.43  0.076458324    1067.0859    279.60749   -14.693017    8.9993839   -1076.6386   -1067.6392 
-   34350        3.435   0.07645844    1078.4994    274.06548   -14.735218    8.8210102   -1076.4602   -1067.6392 
-   34400         3.44  0.076458576     1065.194    267.45347     -14.7594    8.6081974   -1076.2474   -1067.6392 
-   34450        3.445  0.076458493    1044.6764     262.6287   -14.769981    8.4529085   -1076.0921   -1067.6392 
-   34500         3.45  0.076458493    1031.1327    261.22703   -14.778334    8.4077947    -1076.047   -1067.6392 
-   34550        3.455  0.076458662    1001.3241     263.2628   -14.787349    8.4733177   -1076.1125   -1067.6392 
-   34600         3.46  0.076458744    972.94591    267.72772   -14.797072    8.6170244   -1076.2563   -1067.6392 
-   34650        3.465  0.076458639    990.70544    272.38909   -14.802726    8.7670542   -1076.4063   -1067.6392 
-   34700         3.47    0.0764585    1025.1974    274.74718   -14.798109    8.8429511   -1076.4822   -1067.6392 
-   34750        3.475  0.076458513    1061.0651    274.45565   -14.798547    8.8335681   -1076.4728   -1067.6392 
-   34800         3.48  0.076458471     1123.989    273.19344   -14.824615    8.7929427   -1076.4322   -1067.6392 
-   34850        3.485   0.07645842    1192.2777    272.33238   -14.868829    8.7652289   -1076.4045   -1067.6392 
-   34900         3.49  0.076458595    1219.3889     271.4554    -14.89476    8.7370026   -1076.3762   -1067.6392 
-   34950        3.495  0.076458742    1206.5159    270.21752   -14.898336    8.6971606   -1076.3364   -1067.6392 
-   35000          3.5  0.076458628    1197.9968    269.40678   -14.907691    8.6710664   -1076.3103   -1067.6392 
-   35050        3.505  0.076458539    1199.2614    270.09068   -14.937895    8.6930781   -1076.3323   -1067.6392 
-   35100         3.51  0.076458542    1195.6006    272.66182   -14.979789    8.7758322   -1076.4151   -1067.6392 
-   35150        3.515  0.076458532    1184.1758    276.31503   -15.015192    8.8934136   -1076.5326   -1067.6392 
-   35200         3.52  0.076458506    1177.2232    279.44786    -15.03426    8.9942462   -1076.6335   -1067.6392 
-   35250        3.525  0.076458498     1165.906    281.04835   -15.043888    9.0457593    -1076.685   -1067.6392 
-   35300         3.53  0.076458547    1122.7378    281.23471    -15.05217    9.0517575    -1076.691   -1067.6392 
-   35350        3.535   0.07645859    1089.1258    281.40192   -15.068688    9.0571393   -1076.6964   -1067.6392 
-   35400         3.54  0.076458581    1071.6628    283.20912   -15.098467    9.1153054   -1076.7545   -1067.6392 
-   35450        3.545  0.076458561    1061.0287     286.5938   -15.126471     9.224244   -1076.8635   -1067.6392 
-   35500         3.55  0.076458577    1073.4644    290.07888   -15.144262     9.336414   -1076.9756   -1067.6392 
-   35550        3.555  0.076458498    1108.9235    291.84501   -15.154818    9.3932582   -1077.0325   -1067.6392 
-   35600         3.56  0.076458531    1144.2606    290.86582   -15.170369    9.3617421    -1077.001   -1067.6392 
-   35650        3.565  0.076458588    1167.6046    287.19918   -15.196185    9.2437284    -1076.883   -1067.6392 
-   35700         3.57   0.07645856    1179.6333    282.11602   -15.229568    9.0801229   -1076.7194   -1067.6392 
-   35750        3.575  0.076458589    1168.0753    277.29692   -15.269679    8.9250164   -1076.5642   -1067.6392 
-   35800         3.58  0.076458495    1150.8477    273.36789   -15.307138    8.7985576   -1076.4378   -1067.6392 
-   35850        3.585  0.076458358    1134.8391    270.61841   -15.336424    8.7100634   -1076.3493   -1067.6392 
-   35900         3.59  0.076458438    1131.4083    269.61936   -15.365921    8.6779085   -1076.3171   -1067.6392 
-   35950        3.595  0.076458656    1156.3165    270.44071   -15.401487     8.704344   -1076.3436   -1067.6392 
-   36000          3.6  0.076458662    1183.5929    272.83276   -15.446386    8.7813341   -1076.4206   -1067.6392 
-   36050        3.605  0.076458511    1175.8081    276.36312   -15.497044    8.8949617   -1076.5342   -1067.6392 
-   36100         3.61  0.076458487    1137.1434    280.08603   -15.537522    9.0147862    -1076.654   -1067.6392 
-   36150        3.615  0.076458492    1123.4073     282.9067   -15.557122    9.1055719   -1076.7448   -1067.6392 
-   36200         3.62  0.076458546    1127.9754    284.11149   -15.565186    9.1443489   -1076.7836   -1067.6392 
-   36250        3.625  0.076458599    1122.4255    283.84703   -15.578297    9.1358371   -1076.7751   -1067.6392 
-   36300         3.63   0.07645858     1122.041    283.02913   -15.596263    9.1095122   -1076.7487   -1067.6392 
-   36350        3.635  0.076458589    1127.0768     282.3869   -15.600033    9.0888416   -1076.7281   -1067.6392 
-   36400         3.64   0.07645861    1130.6907    282.23737   -15.584507    9.0840287   -1076.7233   -1067.6392 
-   36450        3.645  0.076458646    1150.3415    282.27709   -15.560741    9.0853074   -1076.7245   -1067.6392 
-   36500         3.65  0.076458621    1161.8202    282.18974   -15.546059    9.0824956   -1076.7217   -1067.6392 
-   36550        3.655  0.076458506     1140.503    282.57893     -15.5606    9.0950221   -1076.7343   -1067.6392 
-   36600         3.66   0.07645853    1126.9511    283.97898   -15.602756    9.1400839   -1076.7793   -1067.6392 
-   36650        3.665  0.076458682    1117.8456    286.05487   -15.646548    9.2068979   -1076.8461   -1067.6392 
-   36700         3.67  0.076458755    1118.3433    288.56573   -15.675811    9.2877121   -1076.9269   -1067.6392 
-   36750        3.675  0.076458745    1135.4181    291.29108   -15.685173    9.3754294   -1077.0147   -1067.6392 
-   36800         3.68  0.076458756    1121.3092     293.8519   -15.677476    9.4578516   -1077.0971   -1067.6392 
-   36850        3.685  0.076458796    1089.7128    296.34944   -15.680319    9.5382369   -1077.1775   -1067.6392 
-   36900         3.69  0.076458813    1078.8527    298.59269   -15.709588    9.6104374   -1077.2497   -1067.6392 
-   36950        3.695  0.076458823    1068.4725    300.08588   -15.752456    9.6584969   -1077.2977   -1067.6392 
-   37000          3.7   0.07645894    1065.6302    300.97074   -15.794642    9.6869768   -1077.3262   -1067.6392 
-   37050        3.705  0.076458928    1060.1083    301.92719   -15.834491    9.7177609    -1077.357   -1067.6392 
-   37100         3.71  0.076458812    1062.0442    303.02051   -15.872538    9.7529504   -1077.3922   -1067.6392 
-   37150        3.715  0.076458776    1077.0906    303.12539   -15.902945     9.756326   -1077.3956   -1067.6392 
-   37200         3.72  0.076458783    1094.3589    300.82035   -15.918455    9.6821365   -1077.3214   -1067.6392 
-   37250        3.725  0.076458796     1106.983    295.78025   -15.917907     9.519917   -1077.1592   -1067.6392 
-   37300         3.73    0.0764587    1117.8928    288.74175   -15.902363    9.2933774   -1076.9326   -1067.6392 
-   37350        3.735  0.076458595     1115.003    281.03285   -15.877976    9.0452603   -1076.6845   -1067.6392 
-   37400         3.74  0.076458589    1067.6392    274.76086   -15.863011    8.8433914   -1076.4826   -1067.6392 
-   37450        3.745  0.076458768    1025.0964    271.80953    -15.86958    8.7484006   -1076.3876   -1067.6392 
-   37500         3.75  0.076458888    1008.1779    272.35831   -15.896126    8.7660636   -1076.4053   -1067.6392 
-   37550        3.755  0.076458753    1006.7337    275.07578   -15.933997    8.8535276   -1076.4928   -1067.6392 
-   37600         3.76   0.07645857    1015.7845    279.29514   -15.983502    8.9893309   -1076.6286   -1067.6392 
-   37650        3.765  0.076458646    1037.2238    285.21821   -16.044625    9.1799695   -1076.8192   -1067.6392 
-   37700         3.77  0.076458804     1064.362    291.89353   -16.093253    9.3948198   -1077.0341   -1067.6392 
-   37750        3.775  0.076458938    1093.2339    297.54927   -16.113154    9.5768541   -1077.2161   -1067.6392 
-   37800         3.78  0.076459003    1111.3525    301.09404   -16.115824    9.6909453   -1077.3302   -1067.6392 
-   37850        3.785  0.076458993    1106.8732    302.49314   -16.121107    9.7359763   -1077.3752   -1067.6392 
-   37900         3.79  0.076458927    1063.9114    302.20192   -16.138918    9.7266034   -1077.3658   -1067.6392 
-   37950        3.795  0.076458914    1026.1339    300.74509   -16.166089     9.679714   -1077.3189   -1067.6392 
-   38000          3.8  0.076458899    1031.7602    298.64261    -16.19177    9.6120443   -1077.2513   -1067.6392 
-   38050        3.805  0.076458867    1069.7247    296.45336   -16.206246    9.5415814   -1077.1808   -1067.6392 
-   38100         3.81  0.076458911    1107.4666     295.0445   -16.217521    9.4962363   -1077.1355   -1067.6392 
-   38150        3.815  0.076458901    1131.7783    294.91865   -16.235949    9.4921858   -1077.1314   -1067.6392 
-   38200         3.82  0.076458864    1148.5656    295.74562   -16.253565    9.5188023    -1077.158   -1067.6392 
-   38250        3.825  0.076458822    1148.7391    297.07753   -16.259815    9.5616709   -1077.2009   -1067.6392 
-   38300         3.83  0.076458755    1156.7033    299.00407   -16.260728     9.623678   -1077.2629   -1067.6392 
-   38350        3.835  0.076458804    1159.1829    301.28024   -16.263754    9.6969383   -1077.3362   -1067.6392 
-   38400         3.84  0.076458983    1147.0294    302.84565   -16.273506    9.7473221   -1077.3866   -1067.6392 
-   38450        3.845  0.076458991    1136.4112    302.27164   -16.282019    9.7288474   -1077.3681   -1067.6392 
-   38500         3.85   0.07645888    1113.9868    298.97061   -16.274402    9.6226012   -1077.2618   -1067.6392 
-   38550        3.855  0.076458691     1101.738    294.06527   -16.251341     9.464719    -1077.104   -1067.6392 
-   38600         3.86  0.076458665    1085.4951    289.46444   -16.218831    9.3166378   -1076.9559   -1067.6392 
-   38650        3.865   0.07645876    1061.2109    287.27235   -16.190308    9.2460835   -1076.8853   -1067.6392 
-   38700         3.87  0.076458765     1055.773    288.81749   -16.176864    9.2958149    -1076.935   -1067.6392 
-   38750        3.875  0.076458766     1051.082    293.80099   -16.177139    9.4562127   -1077.0954   -1067.6392 
-   38800         3.88  0.076458791    1034.9231    300.50343   -16.186889    9.6719362   -1077.3112   -1067.6392 
-   38850        3.885  0.076458765    1027.5343    306.11666   -16.197928    9.8526023   -1077.4918   -1067.6392 
-   38900         3.89  0.076458838    1018.2888    308.22875   -16.207065    9.9205815   -1077.5598   -1067.6392 
-   38950        3.895  0.076458884    1014.4073    306.63445   -16.226798    9.8692679   -1077.5085   -1067.6392 
-   39000          3.9  0.076458788    1003.5264    302.69876   -16.256287    9.7425945   -1077.3818   -1067.6392 
-   39050        3.905  0.076458731    996.07885     298.3808   -16.280659    9.6036175   -1077.2428   -1067.6392 
-   39100         3.91  0.076458769    1027.0513    295.40443   -16.293344    9.5078209   -1077.1471   -1067.6392 
-   39150        3.915  0.076458854    1072.3569    294.24208   -16.298011    9.4704097   -1077.1096   -1067.6392 
-   39200         3.92   0.07645888    1080.7481    294.38216   -16.312666    9.4749184   -1077.1142   -1067.6392 
-   39250        3.925  0.076458798    1074.2137    294.25738    -16.34058    9.4709023   -1077.1101   -1067.6392 
-   39300         3.93  0.076458746    1072.9308    292.45791   -16.371754    9.4129849   -1077.0522   -1067.6392 
-   39350        3.935  0.076458686     1052.258    289.46155    -16.40727    9.3165447   -1076.9558   -1067.6392 
-   39400         3.94  0.076458677    1011.4712    286.99005   -16.441308    9.2369974   -1076.8762   -1067.6392 
-   39450        3.945  0.076458657    968.89107    287.00247    -16.46678    9.2373973   -1076.8766   -1067.6392 
-   39500         3.95  0.076458611    967.37752    290.38424    -16.48508     9.346242   -1076.9855   -1067.6392 
-   39550        3.955  0.076458569    982.34862    295.78407   -16.492955    9.5200397   -1077.1593   -1067.6392 
-   39600         3.96  0.076458595     978.6948    301.01012   -16.490336    9.6882442   -1077.3275   -1067.6392 
-   39650        3.965  0.076458753    981.93177    304.90328   -16.481839    9.8135487   -1077.4528   -1067.6392 
-   39700         3.97  0.076458768     1019.382    308.08081   -16.477585    9.9158201   -1077.5551   -1067.6392 
-   39750        3.975  0.076458612    1051.8152    311.88767   -16.490813    10.038347   -1077.6776   -1067.6392 
-   39800         3.98  0.076458521    1042.8378    316.19618   -16.511509    10.177019   -1077.8163   -1067.6392 
-   39850        3.985  0.076458483     1001.149    319.35878   -16.519321     10.27881    -1077.918   -1067.6392 
-   39900         3.99  0.076458542     973.4915     319.4656   -16.514459    10.282248   -1077.9215   -1067.6392 
-   39950        3.995  0.076458719    972.67572    315.26025    -16.50944    10.146896   -1077.7861   -1067.6392 
-   40000            4  0.076458687    994.49843    307.54177   -16.514066    9.8984707   -1077.5377   -1067.6392 
-   40050        4.005  0.076458609    1020.1483    299.32861   -16.525567    9.6341236   -1077.2734   -1067.6392 
-   40100         4.01  0.076458534    1028.6046    293.95707   -16.536961    9.4612366   -1077.1005   -1067.6392 
-   40150        4.015  0.076458539     1021.124    292.82994    -16.54357     9.424959   -1077.0642   -1067.6392 
-   40200         4.02  0.076458617    1003.8564    295.01881   -16.539479    9.4954094   -1077.1346   -1067.6392 
-   40250        4.025  0.076458708    1006.3834    298.32236   -16.525081    9.6017365    -1077.241   -1067.6392 
-   40300         4.03  0.076458753    1049.8514    300.72691   -16.515775    9.6791289   -1077.3184   -1067.6392 
-   40350        4.035  0.076458712    1095.1887    301.23959   -16.528202    9.6956299   -1077.3349   -1067.6392 
-   40400         4.04   0.07645859    1095.7277    299.27704   -16.553461    9.6324637   -1077.2717   -1067.6392 
-   40450        4.045  0.076458512    1074.8132     294.7824   -16.567973    9.4878003    -1077.127   -1067.6392 
-   40500         4.05  0.076458607    1054.9582    288.94001   -16.563212    9.2997586    -1076.939   -1067.6392 
-   40550        4.055  0.076458679    1033.1657    283.78395   -16.555924    9.1338066    -1076.773   -1067.6392 
-   40600         4.06   0.07645866    1029.0046    281.14635   -16.566778    9.0489136   -1076.6881   -1067.6392 
-   40650        4.065  0.076458604    1026.6036     282.2669   -16.593805    9.0849793   -1076.7242   -1067.6392 
-   40700         4.07  0.076458581    1024.2464    287.64133   -16.619273    9.2579595   -1076.8972   -1067.6392 
-   40750        4.075  0.076458663    1014.2573    296.48178   -16.635414    9.5424961   -1077.1817   -1067.6392 
-   40800         4.08  0.076458634    1003.9119    306.29768   -16.644226    9.8584286   -1077.4977   -1067.6392 
-   40850        4.085  0.076458596    997.14687     313.7758   -16.644922    10.099118   -1077.7384   -1067.6392 
-   40900         4.09  0.076458698    1003.6464    316.62645   -16.638874    10.190868   -1077.8301   -1067.6392 
-   40950        4.095  0.076458737    1009.5074    314.15339   -16.626746    10.111271   -1077.7505   -1067.6392 
-   41000          4.1  0.076458626    990.49508    306.88333   -16.607056     9.877278   -1077.5165   -1067.6392 
-   41050        4.105  0.076458539    1003.9156    296.82556   -16.581033    9.5535609   -1077.1928   -1067.6392 
-   41100         4.11  0.076458624    1025.7889    287.94279   -16.555411    9.2676623   -1076.9069   -1067.6392 
-   41150        4.115  0.076458727    1019.8472    284.75687   -16.545411    9.1651209   -1076.8043   -1067.6392 
-   41200         4.12  0.076458658    1009.1747     288.8934   -16.556045    9.2982584   -1076.9375   -1067.6392 
-   41250        4.125  0.076458476    986.14702    297.74613   -16.573101    9.5831902   -1077.2224   -1067.6392 
-   41300         4.13  0.076458533    970.56183    307.17123   -16.586828    9.8865443   -1077.5258   -1067.6392 
-   41350        4.135  0.076458666    982.32883    313.98696   -16.593184    10.105914   -1077.7451   -1067.6392 
-   41400         4.14  0.076458558    998.00634    316.68471   -16.585096    10.192743    -1077.832   -1067.6392 
-   41450        4.145  0.076458375    988.08432    315.93321   -16.578349    10.168555   -1077.8078   -1067.6392 
-   41500         4.15  0.076458387    968.13272    312.86745   -16.587207    10.069882   -1077.7091   -1067.6392 
-   41550        4.155   0.07645851    962.22331    308.01319    -16.60083    9.9136436   -1077.5529   -1067.6392 
-   41600         4.16  0.076458592    977.28521      302.567    -16.60995    9.7383536   -1077.3776   -1067.6392 
-   41650        4.165  0.076458508    989.72477    297.98726   -16.609001    9.5909514   -1077.2302   -1067.6392 
-   41700         4.17  0.076458343    1002.0807    295.07216   -16.600686    9.4971264   -1077.1364   -1067.6392 
-   41750        4.175  0.076458382    1016.3945    293.91041   -16.584772    9.4597347    -1077.099   -1067.6392 
-   41800         4.18  0.076458495    1009.6321    295.39416   -16.566658    9.5074902   -1077.1467   -1067.6392 
-   41850        4.185  0.076458517    981.99051    300.65179   -16.561637    9.6767113   -1077.3159   -1067.6392 
-   41900         4.19  0.076458508    963.70095    308.76413   -16.575186    9.9378133    -1077.577   -1067.6392 
-   41950        4.195   0.07645848    934.77452    316.95219   -16.596303    10.201352   -1077.8406   -1067.6392 
-   42000          4.2  0.076458508    904.42332    322.22055   -16.611182    10.370919   -1078.0102   -1067.6392 
-   42050        4.205   0.07645857    902.29913    322.33865   -16.615342     10.37472    -1078.014   -1067.6392 
-   42100         4.21  0.076458573    919.95355    316.51673   -16.615481    10.187337   -1077.8266   -1067.6392 
-   42150        4.215  0.076458639    929.08587    305.64828   -16.617453    9.8375273   -1077.4768   -1067.6392 
-   42200         4.22  0.076458638    921.14374    292.41301   -16.622157    9.4115396   -1077.0508   -1067.6392 
-   42250        4.225  0.076458624    918.70221     281.1294   -16.634159    9.0483679   -1076.6876   -1067.6392 
-   42300         4.23  0.076458699    936.43193    275.83201     -16.6517    8.8778674   -1076.5171   -1067.6392 
-   42350        4.235   0.07645883    969.33399    278.31739   -16.669195    8.9578611   -1076.5971   -1067.6392 
-   42400         4.24  0.076458843    1009.9309    287.35916   -16.679204    9.2488775   -1076.8881   -1067.6392 
-   42450        4.245   0.07645864    1036.0019    299.66752   -16.672063    9.6450318   -1077.2843   -1067.6392 
-   42500         4.25  0.076458571    1027.6855    312.04895   -16.657188    10.043538   -1077.6828   -1067.6392 
-   42550        4.255  0.076458623    1015.0072    322.01276   -16.654314    10.364231   -1078.0035   -1067.6392 
-   42600         4.26  0.076458688    1013.2933    327.27486   -16.660339    10.533595   -1078.1728   -1067.6392 
-   42650        4.265  0.076458817    1018.1646    326.73267   -16.660439    10.516145   -1078.1554   -1067.6392 
-   42700         4.27  0.076458894    1010.1919    321.82992    -16.65551    10.358346   -1077.9976   -1067.6392 
-   42750        4.275  0.076458864    1005.0687    315.35709   -16.653726    10.150013   -1077.7892   -1067.6392 
-   42800         4.28  0.076458884    1010.6833     308.9802   -16.655199    9.9447675    -1077.584   -1067.6392 
-   42850        4.285  0.076458814    1016.6151    303.05879   -16.657304    9.7541825   -1077.3934   -1067.6392 
-   42900         4.29  0.076458713    1017.0053    298.08717   -16.662548    9.5941669   -1077.2334   -1067.6392 
-   42950        4.295  0.076458716    1044.7957    294.65223   -16.669187    9.4836106   -1077.1228   -1067.6392 
-   43000          4.3  0.076458705    1100.4358    292.80033   -16.665407    9.4240058   -1077.0632   -1067.6392 
-   43050        4.305  0.076458683    1131.0739    293.34724   -16.656462    9.4416087   -1077.0808   -1067.6392 
-   43100         4.31  0.076458605    1142.3657    296.86691   -16.653769     9.554892   -1077.1941   -1067.6392 
-   43150        4.315  0.076458599    1142.8044    301.19681   -16.655832     9.694253   -1077.3335   -1067.6392 
-   43200         4.32  0.076458671    1131.7209    302.63924   -16.652234    9.7406789   -1077.3799   -1067.6392 
-   43250        4.325   0.07645862     1107.868    299.38237   -16.640553    9.6358538   -1077.2751   -1067.6392 
-   43300         4.33  0.076458564    1086.9877     293.0869   -16.632969    9.4332293   -1077.0725   -1067.6392 
-   43350        4.335  0.076458694    1085.9393    287.23945   -16.637169    9.2450247   -1076.8843   -1067.6392 
-   43400         4.34  0.076458728    1084.4536    284.62782   -16.651022    9.1609673   -1076.8002   -1067.6392 
-   43450        4.345  0.076458737    1071.0304    286.42024   -16.664054    9.2186576   -1076.8579   -1067.6392 
-   43500         4.35   0.07645867    1071.4218    292.14965   -16.663945    9.4030633   -1077.0423   -1067.6392 
-   43550        4.355  0.076458545    1058.5175     299.7894   -16.651551    9.6489546   -1077.2882   -1067.6392 
-   43600         4.36  0.076458522    1017.0691    307.34199   -16.653799    9.8920404   -1077.5313   -1067.6392 
-   43650        4.365   0.07645853    984.06733    313.34684   -16.684092    10.085311   -1077.7245   -1067.6392 
-   43700         4.37  0.076458526    972.47105    317.13488   -16.726591    10.207232   -1077.8465   -1067.6392 
-   43750        4.375  0.076458563    982.95807    319.12477   -16.764918    10.271278   -1077.9105   -1067.6392 
-   43800         4.38  0.076458569    1000.5706    319.98217   -16.791105    10.298874   -1077.9381   -1067.6392 
-   43850        4.385  0.076458604    1012.6091    319.95908   -16.796106    10.298131   -1077.9374   -1067.6392 
-   43900         4.39  0.076458647    1016.6021    319.07693   -16.782232    10.269739    -1077.909   -1067.6392 
-   43950        4.395  0.076458717    1039.7933    317.11992   -16.765953    10.206751    -1077.846   -1067.6392 
-   44000          4.4   0.07645855    1076.1914    313.94493    -16.75837    10.104561   -1077.7438   -1067.6392 
-   44050        4.405  0.076458354    1103.7125    309.85364   -16.755308    9.9728798   -1077.6121   -1067.6392 
-   44100         4.41  0.076458497    1123.4426    305.92806   -16.754699    9.8465319   -1077.4858   -1067.6392 
-   44150        4.415  0.076458707     1128.503    303.80427   -16.759223    9.7781762   -1077.4174   -1067.6392 
-   44200         4.42   0.07645872    1109.8757    305.14407   -16.773282    9.8212987   -1077.4605   -1067.6392 
-   44250        4.425  0.076458604    1077.7556    310.10841   -16.799981    9.9810798   -1077.6203   -1067.6392 
-   44300         4.43  0.076458461    1058.8761    316.28846   -16.829881     10.17999   -1077.8192   -1067.6392 
-   44350        4.435  0.076458508    1050.5707    320.51508   -16.852668    10.316027   -1077.9553   -1067.6392 
-   44400         4.44  0.076458673    1056.8449    320.97804   -16.866357    10.330927   -1077.9702   -1067.6392 
-   44450        4.445  0.076458651    1050.8827    318.14487   -16.875492    10.239739    -1077.879   -1067.6392 
-   44500         4.45  0.076458481     1013.764    314.16723   -16.897045    10.111716   -1077.7509   -1067.6392 
-   44550        4.455  0.076458392     980.5404    310.15036   -16.935928    9.9824299   -1077.6217   -1067.6392 
-   44600         4.46  0.076458504    982.46196    305.57929   -16.974614    9.8353065   -1077.4745   -1067.6392 
-   44650        4.465  0.076458584     999.3409    300.38563   -17.000466    9.6681446   -1077.3074   -1067.6392 
-   44700         4.47  0.076458532    1009.2469    295.28724      -17.008    9.5040491   -1077.1433   -1067.6392 
-   44750        4.475  0.076458496    1041.4242    291.50055   -17.008549    9.3821713   -1077.0214   -1067.6392 
-   44800         4.48  0.076458487     1086.602    289.52839   -17.016148    9.3186959   -1076.9579   -1067.6392 
-   44850        4.485  0.076458613    1103.5806    288.55396   -17.029368     9.287333   -1076.9266   -1067.6392 
-   44900         4.49   0.07645858    1102.8142    287.89912   -17.042093    9.2662566   -1076.9055   -1067.6392 
-   44950        4.495   0.07645852    1106.0548    288.11976   -17.050281     9.273358   -1076.9126   -1067.6392 
-   45000          4.5  0.076458412    1109.2471    290.73864   -17.064227    9.3576488   -1076.9969   -1067.6392 
-   45050        4.505  0.076458467    1081.3367    296.40828   -17.091233    9.5401305   -1077.1794   -1067.6392 
-   45100         4.51  0.076458612    1061.7915     304.1106   -17.120168    9.7880355   -1077.4273   -1067.6392 
-   45150        4.515  0.076458508    1075.8664    312.21278   -17.139278    10.048811    -1077.688   -1067.6392 
-   45200         4.52  0.076458381    1086.9758     319.4826   -17.149932    10.282795    -1077.922   -1067.6392 
-   45250        4.525  0.076458463    1081.4821    325.45586   -17.161699     10.47505   -1078.1143   -1067.6392 
-   45300         4.53  0.076458584     1102.657    330.33928   -17.184503    10.632226   -1078.2715   -1067.6392 
-   45350        4.535  0.076458507    1115.9422    333.72518   -17.208225    10.741204   -1078.3804   -1067.6392 
-   45400         4.54  0.076458398    1094.6076    334.77591   -17.228637    10.775023   -1078.4143   -1067.6392 
-   45450        4.545  0.076458455    1089.9234    332.91387   -17.252893    10.715091   -1078.3543   -1067.6392 
-   45500         4.55  0.076458651    1088.2901    328.25855   -17.279739    10.565256   -1078.2045   -1067.6392 
-   45550        4.555  0.076458679    1067.4543    322.55465   -17.319717    10.381672   -1078.0209   -1067.6392 
-   45600         4.56  0.076458491    1051.2478     317.7723   -17.374362    10.227748    -1077.867   -1067.6392 
-   45650        4.565  0.076458315    1034.4257    314.73532   -17.430482    10.130001   -1077.7692   -1067.6392 
-   45700         4.57  0.076458379     1013.128    312.65325   -17.476583    10.062987   -1077.7022   -1067.6392 
-   45750        4.575  0.076458582    1006.4499    309.50085   -17.496142    9.9615252   -1077.6008   -1067.6392 
-   45800         4.58   0.07645865    1024.4651    304.73909    -17.49261    9.8082641   -1077.4475   -1067.6392 
-   45850        4.585  0.076458631    1046.9622    300.08416   -17.492695    9.6584417   -1077.2977   -1067.6392 
-   45900         4.59  0.076458586    1042.5796    296.72782    -17.49113    9.5504152   -1077.1896   -1067.6392 
-   45950        4.595  0.076458607    1008.0854    295.42286    -17.47404     9.508414   -1077.1476   -1067.6392 
-   46000          4.6   0.07645866    1008.1817     297.6509   -17.457674    9.5801252   -1077.2194   -1067.6392 
-   46050        4.605  0.076458648    1055.0177    303.82712   -17.454258    9.7789116   -1077.4181   -1067.6392 
-   46100         4.61  0.076458681    1067.8096    312.06106   -17.459314    10.043927   -1077.6832   -1067.6392 
-   46150        4.615  0.076458697    1032.3327    319.35809   -17.472054    10.278788    -1077.918   -1067.6392 
-   46200         4.62  0.076458669    1011.4049    323.68987   -17.497176     10.41821   -1078.0574   -1067.6392 
-   46250        4.625  0.076458694    1013.1694    324.55935   -17.524643    10.446195   -1078.0854   -1067.6392 
-   46300         4.63  0.076458699    1019.9594    322.92316   -17.537516    10.393533   -1078.0328   -1067.6392 
-   46350        4.635  0.076458638     1019.574    321.37933    -17.53535    10.343843   -1077.9831   -1067.6392 
-   46400         4.64  0.076458549    1012.1208     322.2852   -17.529784    10.372999   -1078.0122   -1067.6392 
-   46450        4.645  0.076458548    1009.7285    324.98438    -17.51749    10.459874   -1078.0991   -1067.6392 
-   46500         4.65  0.076458739    1028.6359    327.73895   -17.495382    10.548533   -1078.1878   -1067.6392 
-   46550        4.655  0.076458848    1054.5382    329.99374   -17.486615    10.621105   -1078.2603   -1067.6392 
-   46600         4.66  0.076458871    1059.0432    330.41234   -17.496838    10.634578   -1078.2738   -1067.6392 
-   46650        4.665  0.076458903    1042.6963    327.41225   -17.503279    10.538018   -1078.1773   -1067.6392 
-   46700         4.67  0.076458964    1022.4908    322.64011    -17.50695    10.384422   -1078.0237   -1067.6392 
-   46750        4.675  0.076458954    994.76603    319.77739    -17.52877    10.292284   -1077.9315   -1067.6392 
-   46800         4.68  0.076458851    984.77354    320.04823   -17.564766    10.301001   -1077.9402   -1067.6392 
-   46850        4.685  0.076458817    982.80807    322.12061    -17.59199    10.367702   -1078.0069   -1067.6392 
-   46900         4.69  0.076458814    979.08705    324.60632   -17.607769    10.447706   -1078.0869   -1067.6392 
-   46950        4.695  0.076458855    991.35981    325.87675   -17.625638    10.488596   -1078.1278   -1067.6392 
-   47000          4.7  0.076459013    990.03823    324.25249   -17.644352    10.436318   -1078.0756   -1067.6392 
-   47050        4.705  0.076459109    971.57257    320.13246   -17.664176    10.303712   -1077.9429   -1067.6392 
-   47100         4.71  0.076459008    942.51677    315.82868   -17.695488    10.165191   -1077.8044   -1067.6392 
-   47150        4.715  0.076458834    914.38458    312.92259   -17.729828    10.071656   -1077.7109   -1067.6392 
-   47200         4.72  0.076458733    915.09427    311.73756   -17.757168    10.033515   -1077.6727   -1067.6392 
-   47250        4.725  0.076458745    929.51292    311.72739   -17.778102    10.033188   -1077.6724   -1067.6392 
-   47300         4.73  0.076458807    924.69906     311.5334   -17.787073    10.026944   -1077.6662   -1067.6392 
-   47350        4.735  0.076458753    911.78727    310.21898   -17.784392    9.9846387   -1077.6239   -1067.6392 
-   47400         4.74  0.076458811    927.84413    308.28881   -17.783399    9.9225147   -1077.5617   -1067.6392 
-   47450        4.745  0.076458948    980.47197    307.41202   -17.799967    9.8942944   -1077.5335   -1067.6392 
-   47500         4.75  0.076458921    1017.4095    308.92974   -17.837931    9.9431434   -1077.5824   -1067.6392 
-   47550        4.755  0.076458813    1013.2842    313.10487   -17.889197    10.077523   -1077.7168   -1067.6392 
-   47600         4.76  0.076458768    999.59926    319.59121    -17.94301    10.286291   -1077.9255   -1067.6392 
-   47650        4.765   0.07645894    987.28899    327.28821   -17.990152    10.534025   -1078.1733   -1067.6392 
-   47700         4.77  0.076459039     970.5822    333.98868   -18.025704    10.749685   -1078.3889   -1067.6392 
-   47750        4.775  0.076458976    960.77569     337.1295   -18.039516    10.850774     -1078.49   -1067.6392 
-   47800         4.78  0.076458945    970.90315    335.79522   -18.031317     10.80783   -1078.4471   -1067.6392 
-   47850        4.785   0.07645907    982.20263    331.08028   -18.021902    10.656076   -1078.2953   -1067.6392 
-   47900         4.79  0.076459119    990.67784    324.66683   -18.027289    10.449654   -1078.0889   -1067.6392 
-   47950        4.795  0.076459083    998.43821    318.73987    -18.04994     10.25889   -1077.8981   -1067.6392 
-   48000          4.8  0.076459069    1008.9151    315.53792   -18.077243    10.155833   -1077.7951   -1067.6392 
-   48050        4.805  0.076458972    1028.1309    316.51509   -18.096678    10.187284   -1077.8265   -1067.6392 
-   48100         4.81  0.076458972    1046.4248     321.4715    -18.10541     10.34681    -1077.986   -1067.6392 
-   48150        4.815  0.076458847    1072.5091     328.3071   -18.108273    10.566819   -1078.2061   -1067.6392 
-   48200         4.82  0.076458729    1115.3266    334.27433   -18.108253    10.758879   -1078.3981   -1067.6392 
-   48250        4.825  0.076458863    1132.7705     338.0335   -18.108395    10.879871   -1078.5191   -1067.6392 
-   48300         4.83  0.076458983    1104.4857    340.31669   -18.122648    10.953357   -1078.5926   -1067.6392 
-   48350        4.835  0.076458942    1068.6895    341.52058   -18.147861    10.992105   -1078.6313   -1067.6392 
-   48400         4.84  0.076458895    1050.2826    340.59905   -18.165876    10.962445   -1078.6017   -1067.6392 
-   48450        4.845  0.076458979     1048.172    336.60118   -18.175839     10.83377    -1078.473   -1067.6392 
-   48500         4.85  0.076458957    1026.5586    330.00847   -18.186406    10.621579   -1078.2608   -1067.6392 
-   48550        4.855  0.076458886    999.91162    322.83938   -18.201023    10.390836   -1078.0301   -1067.6392 
-   48600         4.86  0.076458961    989.90718    317.46387   -18.226455    10.217821   -1077.8571   -1067.6392 
-   48650        4.865  0.076459015    982.96635    315.18649   -18.260376    10.144522   -1077.7838   -1067.6392 
-   48700         4.87  0.076458922    987.30339    316.51586   -18.291398    10.187309   -1077.8265   -1067.6392 
-   48750        4.875  0.076458754    1001.7173    321.20925   -18.314994    10.338369   -1077.9776   -1067.6392 
-   48800         4.88   0.07645878    1018.8788    327.87563   -18.327226    10.552932   -1078.1922   -1067.6392 
-   48850        4.885  0.076458771    1034.4957    334.62729   -18.332453    10.770239   -1078.4095   -1067.6392 
-   48900         4.89  0.076458899    1028.6393    339.07218   -18.341739    10.913301   -1078.5525   -1067.6392 
-   48950        4.895  0.076459103    1007.6856    338.61189   -18.356096    10.898487   -1078.5377   -1067.6392 
-   49000          4.9  0.076459192    999.24745    332.23323   -18.365334    10.693184   -1078.3324   -1067.6392 
-   49050        4.905  0.076459086    996.76706    322.52584   -18.367263    10.380744     -1078.02   -1067.6392 
-   49100         4.91  0.076459029    995.85019    315.08451   -18.370824     10.14124   -1077.7805   -1067.6392 
-   49150        4.915  0.076459032    983.16555    314.29119   -18.382926    10.115706   -1077.7549   -1067.6392 
-   49200         4.92  0.076459075     965.8709    319.65382   -18.396231    10.288306   -1077.9275   -1067.6392 
-   49250        4.925  0.076459124    962.09918    328.07092   -18.405747    10.559217   -1078.1984   -1067.6392 
-   49300         4.93  0.076459019      986.327    337.01122   -18.409264    10.846968   -1078.4862   -1067.6392 
-   49350        4.935  0.076458927      1004.57    345.36436   -18.407413     11.11582   -1078.7551   -1067.6392 
-   49400         4.94  0.076458977    993.98483    352.63606    -18.40944    11.349865   -1078.9891   -1067.6392 
-   49450        4.945  0.076459082    991.26185    357.60801   -18.416364    11.509891   -1079.1491   -1067.6392 
-   49500         4.95  0.076459093    1024.0819    359.05103   -18.425791    11.556336   -1079.1956   -1067.6392 
-   49550        4.955  0.076458927    1033.8368    356.67554   -18.441932    11.479879   -1079.1191   -1067.6392 
-   49600         4.96  0.076458838    1019.5756    350.49667   -18.455292    11.281007   -1078.9202   -1067.6392 
-   49650        4.965  0.076458925    1015.2811     341.2581    -18.44834    10.983657   -1078.6229   -1067.6392 
-   49700         4.97  0.076458904    1000.5326    331.64361   -18.423481    10.674207   -1078.3134   -1067.6392 
-   49750        4.975  0.076458763    997.47426    325.30523   -18.400499    10.470201   -1078.1094   -1067.6392 
-   49800         4.98  0.076458774    1001.6165     323.8013   -18.387438    10.421796    -1078.061   -1067.6392 
-   49850        4.985  0.076458923    1003.6919    325.43465   -18.371483    10.474367   -1078.1136   -1067.6392 
-   49900         4.99  0.076458997    1014.0371    327.90126   -18.352198    10.553757    -1078.193   -1067.6392 
-   49950        4.995  0.076458983    1024.0345    329.92754   -18.340929    10.618974   -1078.2582   -1067.6392 
-   50000            5  0.076458894    1024.5951    330.62163   -18.327421    10.641314   -1078.2805   -1067.6392 
-Loop time of 104.807 on 4 procs for 50000 steps with 250 atoms
-
-Performance: 4.122 ns/day, 5.823 hours/ns, 477.068 timesteps/s
-98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 16.436     | 16.633     | 16.862     |   4.5 | 15.87
-Neigh   | 0.16699    | 0.17008    | 0.17166    |   0.4 |  0.16
-Comm    | 4.1416     | 4.3331     | 4.5047     |   7.9 |  4.13
-Output  | 10.767     | 11.845     | 12.706     |  20.7 | 11.30
-Modify  | 70.815     | 71.648     | 72.683     |   8.2 | 68.36
-Other   |            | 0.1775     |            |       |  0.17
-
-Nlocal:    62.5 ave 65 max 60 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Nghost:    757.75 ave 776 max 743 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-Neighs:    1932.75 ave 2015 max 1844 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-FullNghs:  3865.5 ave 4024 max 3710 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 15462
-Ave neighs/atom = 61.848
-Neighbor list builds = 612
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:01:45
diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel
index 7096fda960..1d62188d8f 100644
--- a/examples/SPIN/nickel/in.spin.nickel
+++ b/examples/SPIN/nickel/in.spin.nickel
@@ -1,58 +1,57 @@
 # fcc nickel in a 3d periodic box
 
 clear 
-units 		metal
-atom_style 	spin
+units           metal
+atom_style      spin
 
-dimension 	3
-boundary 	p p p
+dimension       3
+boundary        p p p
 
 # necessary for the serial algorithm (sametag)
-atom_modify 	map array 
+atom_modify     map array 
 
-lattice 	fcc 3.524
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-create_atoms 	1 box
+lattice         fcc 3.524
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+create_atoms    1 box
 
 # setting mass, mag. moments, and interactions for cobalt
 
-mass		1 58.69
+mass            1 58.69
 
-set 		group all spin/random 31 0.63
-#set 		group all spin 0.63 0.0 0.0 1.0 
-velocity 	all create 100 4928459 rot yes dist gaussian
+set             group all spin/random 31 0.63
+#set            group all spin 0.63 0.0 0.0 1.0 
+velocity        all create 100 4928459 rot yes dist gaussian
 
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
-pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Ni99.eam.alloy Ni
+pair_coeff      * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
 
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
 
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
+fix             3 all nve/spin lattice moving
+timestep        0.0001
 
 # compute and output options
 
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
 
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
 
 thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		2000
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
+run             1000
diff --git a/examples/SPIN/nickel/in.spin.nickel_cubic b/examples/SPIN/nickel/in.spin.nickel_cubic
index 76ea23689a..1ae069a64f 100644
--- a/examples/SPIN/nickel/in.spin.nickel_cubic
+++ b/examples/SPIN/nickel/in.spin.nickel_cubic
@@ -54,7 +54,7 @@ thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
-run 		2000
+run 		1000
 
diff --git a/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1 b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1
new file mode 100644
index 0000000000..b73f7daad7
--- /dev/null
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1
@@ -0,0 +1,136 @@
+LAMMPS (30 Oct 2019)
+# fcc nickel in a 3d periodic box
+
+clear
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+lattice         fcc 3.524
+Lattice spacing in x,y,z = 3.524 3.524 3.524
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  create_atoms CPU = 0.00070715 secs
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass            1 58.69
+
+set             group all spin/random 31 0.63
+  500 settings made for spin/random
+#set            group all spin 0.63 0.0 0.0 1.0
+velocity        all create 100 4928459 rot yes dist gaussian
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Ni99.eam.alloy Ni
+pair_coeff      * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# compute and output options
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
+thermo          50
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run             1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.90375
+  ghost atom cutoff = 5.90375
+  binsize = 2.95187, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.885 | 7.885 | 7.885 Mbytes
+Step Time v_magnorm v_emag Temp v_tmag TotEng 
+       0            0  0.028733803   0.40997576    100.03408   -4775.0671   -2218.1018 
+      50        0.005  0.028733807  0.070491717    101.47879   -28153.519   -2218.1018 
+     100         0.01  0.028733815  -0.70937134     101.7311    2925.8177   -2218.1018 
+     150        0.015  0.028733823    -1.853981     99.63039    1197.9339   -2218.1018 
+     200         0.02  0.028733828   -3.2679239    94.850105    741.17431   -2218.1018 
+     250        0.025  0.028733824    -4.863967    88.444584    550.36979   -2218.1018 
+     300         0.03  0.028733807   -6.5763457    82.689581    449.78321   -2218.1018 
+     350        0.035  0.028733783   -8.3489158    80.108798    384.32228   -2218.1018 
+     400         0.04  0.028733763   -10.120216    82.374947    335.01545   -2218.1018 
+     450        0.045  0.028733755   -11.828932    89.814597    296.88965   -2218.1018 
+     500         0.05  0.028733762   -13.423712    101.39613    267.51686   -2218.1018 
+     550        0.055  0.028733783   -14.866724    115.07399    244.96012   -2218.1018 
+     600         0.06  0.028733801   -16.135279    128.57849    229.33327   -2218.1018 
+     650        0.065  0.028733804   -17.222838    140.22402    220.05718   -2218.1018 
+     700         0.07  0.028733795   -18.154813    149.61295    212.95678   -2218.1018 
+     750        0.075  0.028733781   -18.996903     157.5814    206.41327   -2218.1018 
+     800         0.08  0.028733768   -19.804249    164.92075    203.88977   -2218.1018 
+     850        0.085  0.028733752   -20.579151    171.67278    203.42363   -2218.1018 
+     900         0.09  0.028733728   -21.294277    177.67238    199.84817   -2218.1018 
+     950        0.095  0.028733715   -21.943945     183.2621     194.9614   -2218.1018 
+    1000          0.1   0.02873374   -22.551277    188.99284    191.59796   -2218.1018 
+Loop time of 5.15676 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 1.675 ns/day, 14.324 hours/ns, 193.920 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.4083     | 2.4083     | 2.4083     |   0.0 | 46.70
+Neigh   | 0.016825   | 0.016825   | 0.016825   |   0.0 |  0.33
+Comm    | 0.039891   | 0.039891   | 0.039891   |   0.0 |  0.77
+Output  | 0.018168   | 0.018168   | 0.018168   |   0.0 |  0.35
+Modify  | 2.6657     | 2.6657     | 2.6657     |   0.0 | 51.69
+Other   |            | 0.007864   |            |       |  0.15
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    19504 ave 19504 max 19504 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  39008 ave 39008 max 39008 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 39008
+Ave neighs/atom = 78.016
+Neighbor list builds = 9
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:05
diff --git a/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4 b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4
new file mode 100644
index 0000000000..92bcc4f533
--- /dev/null
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4
@@ -0,0 +1,136 @@
+LAMMPS (30 Oct 2019)
+# fcc nickel in a 3d periodic box
+
+clear
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+lattice         fcc 3.524
+Lattice spacing in x,y,z = 3.524 3.524 3.524
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  create_atoms CPU = 0.00071907 secs
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass            1 58.69
+
+set             group all spin/random 31 0.63
+  500 settings made for spin/random
+#set            group all spin 0.63 0.0 0.0 1.0
+velocity        all create 100 4928459 rot yes dist gaussian
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Ni99.eam.alloy Ni
+pair_coeff      * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# compute and output options
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
+thermo          50
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run             1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.90375
+  ghost atom cutoff = 5.90375
+  binsize = 2.95187, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.799 | 7.799 | 7.799 Mbytes
+Step Time v_magnorm v_emag Temp v_tmag TotEng 
+       0            0  0.028733803   0.40997576    100.03408   -4775.0671   -2218.1018 
+      50        0.005  0.028733805   0.25324083    98.741633   -7863.8744   -2218.1018 
+     100         0.01  0.028733812  -0.37320751    97.073875    5622.1863   -2218.1018 
+     150        0.015  0.028733819   -1.3971549    94.073447    1625.0258   -2218.1018 
+     200         0.02  0.028733825   -2.7238372    89.419944    919.37601   -2218.1018 
+     250        0.025  0.028733829   -4.2684428     84.07494    652.18375   -2218.1018 
+     300         0.03  0.028733824   -5.9636712     80.06368    512.89077   -2218.1018 
+     350        0.035   0.02873381   -7.7386326    79.366702    422.24864   -2218.1018 
+     400         0.04  0.028733802   -9.5148059    83.052751    357.60379   -2218.1018 
+     450        0.045  0.028733806   -11.234935    91.282747    310.87776   -2218.1018 
+     500         0.05   0.02873381   -12.875184    103.49836     275.0224   -2218.1018 
+     550        0.055  0.028733808   -14.413473    118.16526    247.85208   -2218.1018 
+     600         0.06  0.028733803   -15.812466    132.83837    230.67903   -2218.1018 
+     650        0.065  0.028733808   -17.061311    145.41049    222.19476   -2218.1018 
+     700         0.07  0.028733818   -18.181903    154.83414    219.42933   -2218.1018 
+     750        0.075  0.028733823   -19.176259    160.58645    218.45231   -2218.1018 
+     800         0.08  0.028733825   -20.035157    163.02829    214.86596   -2218.1018 
+     850        0.085  0.028733825   -20.806548     164.4197    209.86881   -2218.1018 
+     900         0.09  0.028733829   -21.571419     167.8571    205.79849   -2218.1018 
+     950        0.095  0.028733825   -22.365879    175.00875    201.33088   -2218.1018 
+    1000          0.1  0.028733821   -23.133464    184.68305    195.52912   -2218.1018 
+Loop time of 3.95668 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 2.184 ns/day, 10.991 hours/ns, 252.737 timesteps/s
+97.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.89404    | 0.99018    | 1.0827     |   8.5 | 25.03
+Neigh   | 0.0050189  | 0.0053826  | 0.0057576  |   0.5 |  0.14
+Comm    | 0.23366    | 0.32767    | 0.42737    |  15.2 |  8.28
+Output  | 0.0078192  | 0.0078953  | 0.0080998  |   0.1 |  0.20
+Modify  | 2.6171     | 2.6192     | 2.6219     |   0.1 | 66.20
+Other   |            | 0.006363   |            |       |  0.16
+
+Nlocal:    125 ave 139 max 112 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:    1099 ave 1112 max 1085 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:    4876 ave 5386 max 4426 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs:  9752 ave 10845 max 8737 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 39008
+Ave neighs/atom = 78.016
+Neighbor list builds = 9
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1 b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
similarity index 54%
rename from examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1
rename to examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
index 425572dedf..2aa4a9a0d3 100644
--- a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
@@ -1,9 +1,7 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
+LAMMPS (30 Oct 2019)
 # fcc nickel in a 3d periodic box
 
 clear
-  using 1 OpenMP thread(s) per MPI task
 units 		metal
 atom_style 	spin
 
@@ -21,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.00068903 secs
+  create_atoms CPU = 0.000488997 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -43,7 +41,7 @@ fix 		1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -62,9 +60,9 @@ thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
-run 		2000
+run 		1000
 Neighbor list info ...
   update every 10 steps, delay 20 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -82,79 +80,59 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.885 | 7.885 | 7.885 Mbytes
 Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803     0.455085    100.03408    -8603.706   -2218.0905 
-      50        0.005  0.028732021   0.11535308    101.47887   -34407.888   -2218.0904 
-     100         0.01    0.0287304    -0.665283    101.73105    6238.4535     -2218.09 
-     150        0.015  0.028729403   -1.8105707    99.629794    2452.7607   -2218.0896 
-     200         0.02  0.028731067    -3.224763    94.849715    1501.8625   -2218.0895 
-     250        0.025  0.028732765   -4.8207784    88.447019    1110.3291   -2218.0895 
-     300         0.03  0.028728169   -6.5331538    82.697813     905.2202   -2218.0896 
-     350        0.035   0.02871707   -8.3059526    80.122838    772.40218   -2218.0896 
-     400         0.04  0.028706605   -10.077613    82.389555    672.72236   -2218.0895 
-     450        0.045  0.028701727    -11.78634    89.823176    595.82956   -2218.0894 
-     500         0.05  0.028706691   -13.380919    101.39804    536.65866   -2218.0894 
-     550        0.055  0.028714065   -14.824128    115.07511    491.25787   -2218.0893 
-     600         0.06  0.028713691   -16.093505    128.58093    459.82107    -2218.089 
-     650        0.065  0.028713232   -17.181217    140.22137    441.15183    -2218.089 
-     700         0.07   0.02871245   -18.113035    149.60156    426.80154   -2218.0889 
-     750        0.075  0.028712431   -18.954952    157.56849    413.61924   -2218.0891 
-     800         0.08   0.02872489   -19.762756    164.91833    408.49483   -2218.0892 
-     850        0.085  0.028733709   -20.538757    171.69348    407.47868   -2218.0894 
-     900         0.09  0.028737031   -21.256095    177.71981    400.24086   -2218.0894 
-     950        0.095  0.028743446   -21.908156    183.31613    390.46773    -2218.089 
-    1000          0.1  0.028751809   -22.516179    189.01672    383.80802   -2218.0888 
-    1050        0.105  0.028761625   -23.084057    194.48882    376.54433    -2218.089 
-    1100         0.11  0.028768138   -23.565036    198.12295    366.13309   -2218.0891 
-    1150        0.115  0.028770301   -23.937136    198.95102    354.82763    -2218.089 
-    1200         0.12  0.028771334   -24.273509    198.31348    347.20512   -2218.0891 
-    1250        0.125  0.028769662   -24.672789    198.26173    344.02095   -2218.0889 
-    1300         0.13  0.028774175    -25.13917    199.48259    337.81596   -2218.0889 
-    1350        0.135  0.028795936   -25.594094    201.33509      329.891   -2218.0889 
-    1400         0.14  0.028824328   -25.978285     203.4984    328.81092   -2218.0886 
-    1450        0.145  0.028846467   -26.299501    206.52931    328.61151   -2218.0886 
-    1500         0.15  0.028858261   -26.605847    211.09044    324.29045   -2218.0888 
-    1550        0.155  0.028852825    -26.92321    216.70656    317.24339   -2218.0888 
-    1600         0.16   0.02885238   -27.232535    221.73117    312.50182   -2218.0888 
-    1650        0.165  0.028857985   -27.513725    224.82466    312.32346   -2218.0887 
-    1700         0.17  0.028863985   -27.764471    225.85697    312.80779   -2218.0887 
-    1750        0.175  0.028868714   -27.983273    225.71411    315.37238   -2218.0888 
-    1800         0.18  0.028871144   -28.187572    225.78979    319.44034   -2218.0888 
-    1850        0.185  0.028865191   -28.395615     226.7477    321.25107   -2218.0889 
-    1900         0.19  0.028855316   -28.597095    227.90237    319.98739   -2218.0889 
-    1950        0.195  0.028853072    -28.79277    228.54008    313.04557   -2218.0886 
-    2000          0.2  0.028855814   -29.015073     228.8643    300.40018   -2218.0885 
-Loop time of 16.5858 on 1 procs for 2000 steps with 500 atoms
+       0            0  0.028733803     0.455085    100.03408    -4301.853   -2218.0905 
+      50        0.005  0.028732021   0.11535308    101.47887   -17203.944   -2218.0904 
+     100         0.01    0.0287304    -0.665283    101.73105    3119.2267     -2218.09 
+     150        0.015  0.028729403   -1.8105707    99.629794    1226.3803   -2218.0896 
+     200         0.02  0.028731067    -3.224763    94.849715    750.93124   -2218.0895 
+     250        0.025  0.028732765   -4.8207784    88.447019    555.16456   -2218.0895 
+     300         0.03  0.028728169   -6.5331538    82.697813     452.6101   -2218.0896 
+     350        0.035   0.02871707   -8.3059526    80.122838    386.20109   -2218.0896 
+     400         0.04  0.028706605   -10.077613    82.389555    336.36118   -2218.0895 
+     450        0.045  0.028701727    -11.78634    89.823176    297.91478   -2218.0894 
+     500         0.05  0.028706691   -13.380919    101.39804    268.32933   -2218.0894 
+     550        0.055  0.028714065   -14.824128    115.07511    245.62893   -2218.0893 
+     600         0.06  0.028713691   -16.093505    128.58093    229.91054    -2218.089 
+     650        0.065  0.028713232   -17.181217    140.22137    220.57591    -2218.089 
+     700         0.07   0.02871245   -18.113035    149.60156    213.40077   -2218.0889 
+     750        0.075  0.028712431   -18.954952    157.56849    206.80962   -2218.0891 
+     800         0.08   0.02872489   -19.762756    164.91833    204.24742   -2218.0892 
+     850        0.085  0.028733709   -20.538757    171.69348    203.73934   -2218.0894 
+     900         0.09  0.028737031   -21.256095    177.71981    200.12043   -2218.0894 
+     950        0.095  0.028743446   -21.908156    183.31613    195.23386    -2218.089 
+    1000          0.1  0.028751809   -22.516179    189.01672    191.90401   -2218.0888 
+Loop time of 5.71018 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 1.042 ns/day, 23.036 hours/ns, 120.585 timesteps/s
-99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 1.513 ns/day, 15.862 hours/ns, 175.126 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.8835     | 5.8835     | 5.8835     |   0.0 | 35.47
-Neigh   | 0.05244    | 0.05244    | 0.05244    |   0.0 |  0.32
-Comm    | 0.092997   | 0.092997   | 0.092997   |   0.0 |  0.56
-Output  | 5.213      | 5.213      | 5.213      |   0.0 | 31.43
-Modify  | 5.3275     | 5.3275     | 5.3275     |   0.0 | 32.12
-Other   |            | 0.01636    |            |       |  0.10
+Pair    | 2.7307     | 2.7307     | 2.7307     |   0.0 | 47.82
+Neigh   | 0.018982   | 0.018982   | 0.018982   |   0.0 |  0.33
+Comm    | 0.044032   | 0.044032   | 0.044032   |   0.0 |  0.77
+Output  | 0.036037   | 0.036037   | 0.036037   |   0.0 |  0.63
+Modify  | 2.8713     | 2.8713     | 2.8713     |   0.0 | 50.28
+Other   |            | 0.009135   |            |       |  0.16
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 Nghost:    1956 ave 1956 max 1956 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    19507 ave 19507 max 19507 min
+Neighs:    19504 ave 19504 max 19504 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  39014 ave 39014 max 39014 min
+FullNghs:  39008 ave 39008 max 39008 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 39014
-Ave neighs/atom = 78.028
-Neighbor list builds = 21
+Total # of neighbors = 39008
+Ave neighs/atom = 78.016
+Neighbor list builds = 9
 Dangerous builds = 0
 
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:16
+Total wall time: 0:00:05
diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4 b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
similarity index 52%
rename from examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4
rename to examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
index fd9ce80533..0657d43f8a 100644
--- a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
@@ -1,9 +1,7 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
+LAMMPS (30 Oct 2019)
 # fcc nickel in a 3d periodic box
 
 clear
-  using 1 OpenMP thread(s) per MPI task
 units 		metal
 atom_style 	spin
 
@@ -21,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.000639439 secs
+  create_atoms CPU = 0.000617027 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -43,7 +41,7 @@ fix 		1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -62,9 +60,9 @@ thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
-run 		2000
+run 		1000
 Neighbor list info ...
   update every 10 steps, delay 20 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -82,79 +80,59 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.799 | 7.799 | 7.799 Mbytes
 Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803     0.455085    100.03408    -8603.706   -2218.0905 
-      50        0.005  0.028732088    0.2980989     98.74184   -13360.862   -2218.0904 
-     100         0.01   0.02873076  -0.32911738    97.074246    12749.405     -2218.09 
-     150        0.015  0.028730298   -1.3537059    94.073558    3353.8731   -2218.0897 
-     200         0.02  0.028733079   -2.6807428    89.419616    1868.0661   -2218.0895 
-     250        0.025  0.028735725   -4.2256641    84.074249    1317.4563   -2218.0893 
-     300         0.03  0.028728939   -5.9209085    80.063263    1033.1632   -2218.0893 
-     350        0.035  0.028716731   -7.6957087     79.36782     849.1925   -2218.0893 
-     400         0.04   0.02871114   -9.4720832    83.055773    718.36408   -2218.0893 
-     450        0.045   0.02870879    -11.19254     91.28713    624.04151   -2218.0891 
-     500         0.05  0.028708873   -12.832707    103.50343    551.85983   -2218.0892 
-     550        0.055  0.028710315   -14.370603    118.16778    497.19527   -2218.0893 
-     600         0.06  0.028707016   -15.769641    132.83264    462.57721    -2218.089 
-     650        0.065  0.028706727   -17.018362    145.39247    445.40608   -2218.0888 
-     700         0.07  0.028710482   -18.137792    154.80131    439.71677   -2218.0889 
-     750        0.075  0.028705169   -19.130471    160.53663    437.67621   -2218.0892 
-     800         0.08  0.028695336   -19.988452    162.95918    430.42912    -2218.089 
-     850        0.085  0.028688393   -20.758389    164.33238    420.42991   -2218.0889 
-     900         0.09  0.028684101   -21.521505    167.76167    412.29955    -2218.089 
-     950        0.095  0.028684705   -22.314351      174.918    403.31757   -2218.0891 
-    1000          0.1  0.028691284   -23.080026    184.60192      391.677   -2218.0893 
-    1050        0.105  0.028687846   -23.714845    193.76312    379.81345   -2218.0893 
-    1100         0.11  0.028682371   -24.191738    200.43041    372.65414   -2218.0893 
-    1150        0.115  0.028684765   -24.569816    204.39323    368.53291   -2218.0891 
-    1200         0.12  0.028678139   -24.892093      205.879    364.46365   -2218.0892 
-    1250        0.125  0.028669738   -25.160227    205.09197    361.98015   -2218.0893 
-    1300         0.13  0.028666626   -25.367813    202.69136    360.10649   -2218.0891 
-    1350        0.135  0.028665511   -25.520784    199.79027    359.68033   -2218.0892 
-    1400         0.14   0.02866749   -25.655936    197.91217      361.218   -2218.0892 
-    1450        0.145  0.028666916    -25.80086     198.1933     361.5167   -2218.0889 
-    1500         0.15  0.028660248   -25.953194     200.8243     356.0167    -2218.089 
-    1550        0.155  0.028641778   -26.137444    205.80307    349.94961   -2218.0887 
-    1600         0.16  0.028626894   -26.393372     212.6879    347.30341   -2218.0888 
-    1650        0.165  0.028619835   -26.707923    219.63834    340.80511   -2218.0885 
-    1700         0.17  0.028615681   -27.023214    224.25635    329.60947   -2218.0882 
-    1750        0.175   0.02861597   -27.301445    225.47908    321.35253   -2218.0884 
-    1800         0.18  0.028614544    -27.53764    224.03527    320.92639   -2218.0884 
-    1850        0.185   0.02860894   -27.741581    221.74286    323.07034   -2218.0884 
-    1900         0.19  0.028604135   -27.943034      220.659    322.60989   -2218.0884 
-    1950        0.195  0.028602672   -28.160901    221.85908     318.8957   -2218.0885 
-    2000          0.2  0.028597155   -28.365986    224.55298    311.53587   -2218.0886 
-Loop time of 7.21663 on 4 procs for 2000 steps with 500 atoms
+       0            0  0.028733803     0.455085    100.03408    -4301.853   -2218.0905 
+      50        0.005  0.028732088    0.2980989     98.74184   -6680.4308   -2218.0904 
+     100         0.01   0.02873076  -0.32911738    97.074246    6374.7026     -2218.09 
+     150        0.015  0.028730298   -1.3537059    94.073558    1676.9365   -2218.0897 
+     200         0.02  0.028733079   -2.6807428    89.419616    934.03305   -2218.0895 
+     250        0.025  0.028735725   -4.2256641    84.074249    658.72816   -2218.0893 
+     300         0.03  0.028728939   -5.9209085    80.063263    516.58161   -2218.0893 
+     350        0.035  0.028716731   -7.6957087     79.36782    424.59625   -2218.0893 
+     400         0.04   0.02871114   -9.4720832    83.055773    359.18204   -2218.0893 
+     450        0.045   0.02870879    -11.19254     91.28713    312.02076   -2218.0891 
+     500         0.05  0.028708873   -12.832707    103.50343    275.92991   -2218.0892 
+     550        0.055  0.028710315   -14.370603    118.16778    248.59763   -2218.0893 
+     600         0.06  0.028707016   -15.769641    132.83264     231.2886    -2218.089 
+     650        0.065  0.028706727   -17.018362    145.39247    222.70304   -2218.0888 
+     700         0.07  0.028710482   -18.137792    154.80131    219.85838   -2218.0889 
+     750        0.075  0.028705169   -19.130471    160.53663    218.83811   -2218.0892 
+     800         0.08  0.028695336   -19.988452    162.95918    215.21456    -2218.089 
+     850        0.085  0.028688393   -20.758389    164.33238    210.21496   -2218.0889 
+     900         0.09  0.028684101   -21.521505    167.76167    206.14977    -2218.089 
+     950        0.095  0.028684705   -22.314351      174.918    201.65878   -2218.0891 
+    1000          0.1  0.028691284   -23.080026    184.60192     195.8385   -2218.0893 
+Loop time of 3.6142 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 2.394 ns/day, 10.023 hours/ns, 277.138 timesteps/s
-98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 2.391 ns/day, 10.039 hours/ns, 276.686 timesteps/s
+98.8% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.6337     | 1.6726     | 1.7259     |   2.7 | 23.18
-Neigh   | 0.013023   | 0.01361    | 0.014188   |   0.4 |  0.19
-Comm    | 0.19005    | 0.24933    | 0.2905     |   7.5 |  3.45
-Output  | 1.4595     | 1.5171     | 1.5725     |   3.4 | 21.02
-Modify  | 3.6943     | 3.7537     | 3.8093     |   2.3 | 52.01
-Other   |            | 0.01025    |            |       |  0.14
+Pair    | 0.75407    | 0.87833    | 0.96493    |   8.8 | 24.30
+Neigh   | 0.004509   | 0.0051936  | 0.0056126  |   0.6 |  0.14
+Comm    | 0.19147    | 0.28312    | 0.4105     |  16.0 |  7.83
+Output  | 0.013854   | 0.013948   | 0.014158   |   0.1 |  0.39
+Modify  | 2.4267     | 2.4282     | 2.4319     |   0.1 | 67.19
+Other   |            | 0.005371   |            |       |  0.15
 
-Nlocal:    125 ave 132 max 121 min
-Histogram: 2 0 0 0 1 0 0 0 0 1
-Nghost:    1099 ave 1103 max 1092 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Neighs:    4877 ave 5097 max 4747 min
-Histogram: 2 0 0 0 1 0 0 0 0 1
-FullNghs:  9754 ave 10298 max 9440 min
-Histogram: 2 0 0 0 1 0 0 0 0 1
+Nlocal:    125 ave 139 max 112 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:    1099 ave 1112 max 1085 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:    4876 ave 5385 max 4427 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs:  9752 ave 10845 max 8737 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
 
-Total # of neighbors = 39016
-Ave neighs/atom = 78.032
-Neighbor list builds = 21
+Total # of neighbors = 39008
+Ave neighs/atom = 78.016
+Neighbor list builds = 9
 Dangerous builds = 0
 
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:07
+Total wall time: 0:00:03
diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1 b/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1
deleted file mode 100644
index 8d7284f5e2..0000000000
--- a/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1
+++ /dev/null
@@ -1,159 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# fcc nickel in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	fcc 3.524
-Lattice spacing in x,y,z = 3.524 3.524 3.524
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  create_atoms CPU = 0.000835896 secs
-
-# setting mass, mag. moments, and interactions for cobalt
-
-mass		1 58.69
-
-set 		group all spin/random 31 0.63
-  500 settings made for spin/random
-#set 		group all spin 0.63 0.0 0.0 1.0
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
-pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.90375
-  ghost atom cutoff = 5.90375
-  binsize = 2.95187, bins = 6 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes
-Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803   0.40997576    100.03408   -9550.1342   -2218.1018 
-      50        0.005  0.028733807  0.070491717    101.47879   -56307.038   -2218.1018 
-     100         0.01  0.028733815  -0.70937134     101.7311    5851.6355   -2218.1018 
-     150        0.015  0.028733823    -1.853981     99.63039    2395.8677   -2218.1018 
-     200         0.02  0.028733828   -3.2679239    94.850105    1482.3486   -2218.1018 
-     250        0.025  0.028733824    -4.863967    88.444584    1100.7396   -2218.1018 
-     300         0.03  0.028733807   -6.5763457    82.689581    899.56642   -2218.1018 
-     350        0.035  0.028733783   -8.3489158    80.108798    768.64457   -2218.1018 
-     400         0.04  0.028733763   -10.120216    82.374947    670.03091   -2218.1018 
-     450        0.045  0.028733755   -11.828932    89.814597    593.77931   -2218.1018 
-     500         0.05  0.028733762   -13.423712    101.39613    535.03371   -2218.1018 
-     550        0.055  0.028733783   -14.866724    115.07399    489.92024   -2218.1018 
-     600         0.06  0.028733801   -16.135279    128.57849    458.66654   -2218.1018 
-     650        0.065  0.028733804   -17.222838    140.22402    440.11437   -2218.1018 
-     700         0.07  0.028733795   -18.154813    149.61295    425.91356   -2218.1018 
-     750        0.075  0.028733781   -18.996903     157.5814    412.82654   -2218.1018 
-     800         0.08  0.028733768   -19.804249    164.92075    407.77954   -2218.1018 
-     850        0.085  0.028733752   -20.579151    171.67278    406.84726   -2218.1018 
-     900         0.09  0.028733728   -21.294277    177.67238    399.69633   -2218.1018 
-     950        0.095  0.028733715   -21.943945     183.2621    389.92281   -2218.1018 
-    1000          0.1   0.02873374   -22.551277    188.99284    383.19592   -2218.1018 
-    1050        0.105  0.028733783   -23.120147    194.51391    375.87245   -2218.1018 
-    1100         0.11  0.028733792   -23.602325    198.18631    365.37753   -2218.1018 
-    1150        0.115  0.028733774   -23.976048    199.04022    354.04863   -2218.1018 
-    1200         0.12   0.02873376    -24.31575    198.41999    346.40397   -2218.1018 
-    1250        0.125  0.028733759   -24.718347     198.3669     343.1701   -2218.1018 
-    1300         0.13  0.028733765   -25.189073    199.57949    336.90052   -2218.1018 
-    1350        0.135  0.028733774   -25.650252    201.45897    329.07023   -2218.1018 
-    1400         0.14  0.028733785   -26.042702     203.6926    327.97373   -2218.1018 
-    1450        0.145  0.028733791   -26.373965    206.80469    327.38747   -2218.1018 
-    1500         0.15  0.028733791   -26.691802    211.43923    322.75885   -2218.1018 
-    1550        0.155  0.028733794   -27.021573    217.10969    315.55781   -2218.1018 
-    1600         0.16  0.028733792   -27.344066    222.16052     310.6743   -2218.1018 
-    1650        0.165  0.028733788   -27.640017    225.28449    310.49671   -2218.1018 
-    1700         0.17  0.028733803   -27.907241    226.37676     310.9389   -2218.1018 
-    1750        0.175  0.028733828   -28.143477    226.31095    313.28034   -2218.1018 
-    1800         0.18  0.028733833   -28.363397    226.43633    317.31668   -2218.1018 
-    1850        0.185  0.028733811    -28.58153    227.36287    318.98645   -2218.1018 
-    1900         0.19  0.028733796   -28.785208    228.39889     316.9972   -2218.1018 
-    1950        0.195  0.028733826     -28.9724    228.84666     309.8027   -2218.1018 
-    2000          0.2   0.02873386   -29.175039      228.918    297.88519   -2218.1018 
-Loop time of 15.9256 on 1 procs for 2000 steps with 500 atoms
-
-Performance: 1.085 ns/day, 22.119 hours/ns, 125.584 timesteps/s
-99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 5.8677     | 5.8677     | 5.8677     |   0.0 | 36.84
-Neigh   | 0.051965   | 0.051965   | 0.051965   |   0.0 |  0.33
-Comm    | 0.088829   | 0.088829   | 0.088829   |   0.0 |  0.56
-Output  | 4.7019     | 4.7019     | 4.7019     |   0.0 | 29.52
-Modify  | 5.199      | 5.199      | 5.199      |   0.0 | 32.65
-Other   |            | 0.01632    |            |       |  0.10
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1956 ave 1956 max 1956 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    19508 ave 19508 max 19508 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  39016 ave 39016 max 39016 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 39016
-Ave neighs/atom = 78.032
-Neighbor list builds = 21
-Dangerous builds = 0
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:16
diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4 b/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4
deleted file mode 100644
index a186253db3..0000000000
--- a/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4
+++ /dev/null
@@ -1,159 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# fcc nickel in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	fcc 3.524
-Lattice spacing in x,y,z = 3.524 3.524 3.524
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  create_atoms CPU = 0.000492096 secs
-
-# setting mass, mag. moments, and interactions for cobalt
-
-mass		1 58.69
-
-set 		group all spin/random 31 0.63
-  500 settings made for spin/random
-#set 		group all spin 0.63 0.0 0.0 1.0
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
-pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.90375
-  ghost atom cutoff = 5.90375
-  binsize = 2.95187, bins = 6 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes
-Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803   0.40997576    100.03408   -9550.1342   -2218.1018 
-      50        0.005  0.028733805   0.25324083    98.741633   -15727.749   -2218.1018 
-     100         0.01  0.028733812  -0.37320751    97.073875    11244.373   -2218.1018 
-     150        0.015  0.028733819   -1.3971549    94.073447    3250.0517   -2218.1018 
-     200         0.02  0.028733825   -2.7238372    89.419944     1838.752   -2218.1018 
-     250        0.025  0.028733829   -4.2684428     84.07494    1304.3675   -2218.1018 
-     300         0.03  0.028733824   -5.9636712     80.06368    1025.7815   -2218.1018 
-     350        0.035   0.02873381   -7.7386326    79.366702    844.49729   -2218.1018 
-     400         0.04  0.028733802   -9.5148059    83.052751    715.20758   -2218.1018 
-     450        0.045  0.028733806   -11.234935    91.282747    621.75552   -2218.1018 
-     500         0.05   0.02873381   -12.875184    103.49836    550.04479   -2218.1018 
-     550        0.055  0.028733808   -14.413473    118.16526    495.70417   -2218.1018 
-     600         0.06  0.028733803   -15.812466    132.83837    461.35805   -2218.1018 
-     650        0.065  0.028733808   -17.061311    145.41049    444.38951   -2218.1018 
-     700         0.07  0.028733818   -18.181903    154.83414    438.85866   -2218.1018 
-     750        0.075  0.028733823   -19.176259    160.58645    436.90462   -2218.1018 
-     800         0.08  0.028733825   -20.035157    163.02829    429.73193   -2218.1018 
-     850        0.085  0.028733825   -20.806548     164.4197    419.73763   -2218.1018 
-     900         0.09  0.028733829   -21.571419     167.8571    411.59699   -2218.1018 
-     950        0.095  0.028733825   -22.365879    175.00875    402.66175   -2218.1018 
-    1000          0.1  0.028733821   -23.133464    184.68305    391.05824   -2218.1018 
-    1050        0.105  0.028733833   -23.770507    193.83795    379.23354   -2218.1018 
-    1100         0.11   0.02873385   -24.249882     200.5039    372.08521   -2218.1018 
-    1150        0.115  0.028733864   -24.630489    204.46984    367.92135   -2218.1018 
-    1200         0.12  0.028733877   -24.956281    205.96624    363.72367   -2218.1018 
-    1250        0.125  0.028733884   -25.227332    205.18503    361.09236   -2218.1018 
-    1300         0.13  0.028733877    -25.43568    202.76969    359.10924   -2218.1018 
-    1350        0.135  0.028733868   -25.588748    199.85462    358.69556   -2218.1018 
-    1400         0.14  0.028733866   -25.723582    197.99165    360.27856   -2218.1018 
-    1450        0.145  0.028733851   -25.866283    198.30283    360.46623   -2218.1018 
-    1500         0.15  0.028733812   -26.014569    200.95517    354.66722   -2218.1018 
-    1550        0.155   0.02873379   -26.192673    205.95485    348.37935   -2218.1018 
-    1600         0.16  0.028733795   -26.444059    212.87557    345.53576   -2218.1018 
-    1650        0.165  0.028733838    -26.75551    219.86449     338.9224   -2218.1018 
-    1700         0.17  0.028733868   -27.068513    224.47868    327.81241   -2218.1018 
-    1750        0.175  0.028733862   -27.344118    225.62318    319.85486   -2218.1018 
-    1800         0.18  0.028733849    -27.57563    224.07463    320.07064   -2218.1018 
-    1850        0.185  0.028733852   -27.774274    221.70618    323.12599   -2218.1018 
-    1900         0.19  0.028733864   -27.967999    220.53947     322.9504   -2218.1018 
-    1950        0.195  0.028733863   -28.173041    221.61407    318.63401   -2218.1018 
-    2000          0.2  0.028733853   -28.362177    224.22281    310.55185   -2218.1018 
-Loop time of 7.69012 on 4 procs for 2000 steps with 500 atoms
-
-Performance: 2.247 ns/day, 10.681 hours/ns, 260.074 timesteps/s
-98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.5623     | 1.5999     | 1.6541     |   2.7 | 20.80
-Neigh   | 0.012559   | 0.013043   | 0.013682   |   0.4 |  0.17
-Comm    | 0.1843     | 0.24254    | 0.27935    |   7.2 |  3.15
-Output  | 1.4749     | 1.5228     | 1.5694     |   2.9 | 19.80
-Modify  | 4.2492     | 4.3019     | 4.3507     |   1.8 | 55.94
-Other   |            | 0.009925   |            |       |  0.13
-
-Nlocal:    125 ave 132 max 120 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-Nghost:    1099 ave 1104 max 1092 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Neighs:    4876.5 ave 5100 max 4721 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-FullNghs:  9753 ave 10296 max 9362 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-
-Total # of neighbors = 39012
-Ave neighs/atom = 78.024
-Neighbor list builds = 21
-Dangerous builds = 0
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:07
diff --git a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
deleted file mode 120000
index 6a47c9eebe..0000000000
--- a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
+++ /dev/null
@@ -1 +0,0 @@
-../cobalt_fcc/Co_PurjaPun_2012.eam.alloy
\ No newline at end of file
diff --git a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
new file mode 100644
index 0000000000..3af058baf7
--- /dev/null
+++ b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
@@ -0,0 +1,6006 @@
+Cobalt EAM potential: G. P. Purja Pun and Y. Mishin, Phys. Rev. B xx, 004100 (2012) (in press)
+Data below r = 1.5 A is extrapolated. F(Rho) data not extrapolated.
+Created on Wed Sep 26 17:29:54 2012
+1 Co
+10000 4.788742913000000e-04 10000 6.499539000000001e-04 6.499539000000000e+00
+27 5.893320000000000e+01 2.507000000000000e+00 hcp
+ -1.680303080000000e-02 -1.879913964471138e-02 -2.091739081044659e-02 -2.303564197615629e-02 -2.503175082079116e-02
+ -2.681996612041136e-02 -2.846010103933253e-02 -3.003179469400266e-02 -3.154842562124295e-02 -3.300931506782415e-02
+ -3.442381570000001e-02 -3.580233366714632e-02 -3.714945763166951e-02 -3.846832763111274e-02 -3.976210669053554e-02
+ -4.103374908125148e-02 -4.228535107207521e-02 -4.351872320172212e-02 -4.473539109100971e-02 -4.593674531110434e-02
+ -4.712392115246503e-02 -4.829795108118731e-02 -4.945971154662068e-02 -5.061001094949964e-02 -5.174954151284258e-02
+ -5.287894548568519e-02 -5.399878139884967e-02 -5.510957102742049e-02 -5.621177284174523e-02 -5.730581735016625e-02
+ -5.839208651773948e-02 -5.947094067448531e-02 -6.054270215356945e-02 -6.160767623453070e-02 -6.266613797925552e-02
+ -6.371834880435967e-02 -6.476454576302854e-02 -6.580495483863194e-02 -6.683978209870683e-02 -6.786922452279202e-02
+ -6.889346265426707e-02 -6.991266949659354e-02 -7.092700432972064e-02 -7.193662011890395e-02 -7.294165829413661e-02
+ -7.394225494811188e-02 -7.493853635958479e-02 -7.593062425993033e-02 -7.691863200494162e-02 -7.790266905197404e-02
+ -7.888283764021425e-02 -7.985923664258643e-02 -8.083195868513401e-02 -8.180109346997461e-02 -8.276672525040257e-02
+ -8.372893572415932e-02 -8.468780181559693e-02 -8.564339820511864e-02 -8.659579537072190e-02 -8.754506181558984e-02
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+ 1.489871974108943e-05 1.454437762041471e-05 1.419635018600421e-05 1.385456300630342e-05 1.351894241351905e-05
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+ 1.021343974753131e-05 9.946217419267380e-06 9.684240838620889e-06 9.427441790773100e-06 9.175752643853506e-06
+ 8.929106280098344e-06 8.687435997194528e-06 8.450675338936148e-06 8.218758257424963e-06 7.991619584870982e-06
+ 7.769194298227330e-06 7.551417507621627e-06 7.338224987041431e-06 7.129552955942858e-06 6.925337997222138e-06
+ 6.725516977155444e-06 6.530027335862672e-06 6.338807194551445e-06 6.151794769434223e-06 5.968928615355085e-06
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+ 2.479051643033932e-06 2.386523210361943e-06 2.296598552297165e-06 2.209228971591383e-06 2.124366069775506e-06
+ 2.041961906232304e-06 1.961969019732135e-06 1.884340423438541e-06 1.809029507182080e-06 1.735990071613592e-06
+ 1.665176534356502e-06 1.596543687803830e-06 1.530046658503296e-06 1.465641105678908e-06 1.403283128309336e-06
+ 1.342929271825179e-06 1.284536503035511e-06 1.228062233226246e-06 1.173464436795038e-06 1.120701460082181e-06
+ 1.069732028902882e-06 1.020515399241352e-06 9.730112822753146e-07 9.271798002921477e-07 8.829815278752155e-07
+ 8.403775374680640e-07 7.993293716485992e-07 7.597989809176624e-07 7.217487560416926e-07 6.851415619710593e-07
+ 6.499407524191172e-07 6.161100929136179e-07 5.836137918783888e-07 5.524166028233452e-07 5.224836968385216e-07
+ 4.937806609639881e-07 4.662735849361845e-07 4.399289991547822e-07 4.147139110260500e-07 3.905957813609555e-07
+ 3.675425084859321e-07 3.455225231396512e-07 3.245046871736890e-07 3.044582778536548e-07 2.853530928283095e-07
+ 2.671593859185241e-07 2.498478511400059e-07 2.333896726605378e-07 2.177564985206194e-07 2.029204500538344e-07
+ 1.888541210793108e-07 1.755305458522738e-07 1.629232393506973e-07 1.510062144201093e-07 1.397539174372155e-07
+ 1.291412703741045e-07 1.191437050672961e-07 1.097370923617762e-07 1.008977778162274e-07 9.260259669902208e-08
+ 8.482883141984319e-08 7.755426670738778e-08 7.075715683240311e-08 6.441620467100832e-08 5.851063608240125e-08
+ 5.302013495440350e-08 4.792483459927075e-08 4.320538955913144e-08 3.884291294265582e-08 3.481898425658018e-08
+ 3.111569527451850e-08 2.771559342817648e-08 2.460171067137196e-08 2.175758348333717e-08 1.916719757773861e-08
+ 1.681503457183268e-08 1.468607978947252e-08 1.276576812429566e-08 1.104003874048358e-08 9.495328649625366e-09
+ 8.118528715645258e-09 6.897042498203040e-09 5.818760232281117e-09 4.872032311209139e-09 4.045732447740840e-09
+ 3.329210679517489e-09 2.712284881132093e-09 2.185301687016959e-09 1.739076161987666e-09 1.364901589086205e-09
+ 1.054599065845252e-09 8.004535320102697e-10 5.952414597054672e-10 4.322622496028902e-10 3.052766304104823e-10
+ 2.085502003918036e-10 1.368642901349301e-10 8.546164059834664e-11 5.010215808832263e-11 2.705311520847365e-11
+ 1.304599438344934e-11 5.339090781311160e-12 1.692041320615927e-12 3.321208355096226e-13 6.781366937015517e-15
diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart
index ad6f337890..ccce25b254 100644
--- a/examples/SPIN/read_restart/in.spin.restart
+++ b/examples/SPIN/read_restart/in.spin.restart
@@ -44,6 +44,6 @@ thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
 thermo_modify   format float %20.15g
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
 run 		100
diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4
deleted file mode 100644
index 56fed35307..0000000000
--- a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4
+++ /dev/null
@@ -1,112 +0,0 @@
-LAMMPS (11 May 2018)
-units 		metal
-dimension 	3
-boundary 	p p p
-
-atom_style 	spin
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-read_data 	Norm_randXY_8x8x32.data
-  orthogonal box = (0 0 0) to (28.32 28.32 113.28)
-  1 by 1 by 4 MPI processor grid
-  reading atoms ...
-  8192 atoms
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# define outputs and computes
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          10
-thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 8 8 31
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.994 | 8.25 Mbytes
-Step Time v_magnorm v_emag v_tmag Temp TotEng 
-       0                    0    0.980832325249103     -2984.9466433509     51.7121203365411                    0    -38881.8459242507 
-      10                0.001    0.980832325329477    -2984.94800197307     52.2550778515409  0.00128259391683994    -38881.8459243698 
-      20                0.002    0.980832324654401    -2984.95196908569     53.4253110612179  0.00502068532291255    -38881.8459246487 
-      30                0.003     0.98083232312993    -2984.95826683995      55.148898005011   0.0109316232931419      -38881.84592505 
-      40                0.004    0.980832320808156     -2984.9664981035     57.3218040934977   0.0186091337978305    -38881.8459255198 
-      50                0.005    0.980832317596783    -2984.97619813016      59.827198436387   0.0275752665472358    -38881.8459260035 
-      60                0.006    0.980832313514709    -2984.98688847322     62.5519331668858    0.037334879488755      -38881.84592645 
-      70                0.007    0.980832309220414    -2984.99812399537     65.3979760533737   0.0474235360022736    -38881.8459268243 
-      80                0.008    0.980832304490479    -2985.00952678209     68.2863250613635   0.0574425728014485    -38881.8459271068 
-      90                0.009    0.980832299379824    -2985.02080456789     71.1540940309591   0.0670788096168283    -38881.8459272917 
-     100                 0.01    0.980832294622694    -2985.03175503971     73.9487734241296   0.0761100584457276    -38881.8459273851 
-Loop time of 3.6612 on 4 procs for 100 steps with 8192 atoms
-
-Performance: 0.236 ns/day, 101.700 hours/ns, 27.313 timesteps/s
-98.8% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0622     | 1.076      | 1.0936     |   1.1 | 29.39
-Neigh   | 0.77462    | 0.79542    | 0.81798    |   1.9 | 21.73
-Comm    | 0.024701   | 0.066122   | 0.10261    |  11.1 |  1.81
-Output  | 0.50304    | 0.51253    | 0.52111    |   0.9 | 14.00
-Modify  | 1.2006     | 1.2082     | 1.2205     |   0.7 | 33.00
-Other   |            | 0.002962   |            |       |  0.08
-
-Nlocal:    2048 ave 2095 max 1981 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Nghost:    5765 ave 5832 max 5718 min
-Histogram: 1 0 0 2 0 0 0 0 0 1
-Neighs:    143360 ave 146361 max 139058 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-FullNghs:  286720 ave 293300 max 277340 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-
-Total # of neighbors = 1146880
-Ave neighs/atom = 140
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4
deleted file mode 100644
index f93605a10a..0000000000
--- a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4
+++ /dev/null
@@ -1,118 +0,0 @@
-LAMMPS (11 May 2018)
-# start a spin-lattice simulation from a data file
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-read_restart	restart_hcp_cobalt.equil
-WARNING: Restart file used different # of processors (../read_restart.cpp:723)
-  restoring atom style spin from restart
-  orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 2 by 2 MPI processor grid
-  restoring pair style spin/exchange from restart
-  500 atoms
-
-# setting mass, mag. moments, and interactions
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# define outputs
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          10
-thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 4 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.203 | 6.203 | 6.203 Mbytes
-Step Time v_magnorm v_emag v_tmag Temp TotEng 
-    1000                    0    0.106120063678768    -11.8110267448939     5244.87332482316                    0    -2206.81097898003 
-    1010                0.001    0.106120030254187    -11.8198467883806     5263.87550015043    0.136650306637598    -2206.81097929055 
-    1020                0.002    0.106119996655714    -11.8460960476455       5267.299198699    0.542282344092749    -2206.81098022997 
-    1030                0.003    0.106119967407682    -11.8891433919665     5252.95473019843     1.20401809237154    -2206.81098172552 
-    1040                0.004    0.106119960016585    -11.9479778326021     5220.88686874944     2.10120827278397    -2206.81098371049 
-    1050                0.005    0.106119961252471    -12.0212426191481     5172.58712301374     3.20622343988728    -2206.81098610703 
-    1060                0.006    0.106119967598995    -12.1072712483404     5110.57504803718     4.48535830705751    -2206.81098879724 
-    1070                0.007    0.106119967669058    -12.2041566468564     5038.48927079832     5.90031039867811    -2206.81099161179 
-    1080                0.008    0.106119969263395    -12.3098693905406     4961.03212459716     7.41044810751949     -2206.8109943465 
-    1090                0.009    0.106119960964075    -12.4224156966204     4883.31968289062     8.97568865379831    -2206.81099680112 
-    1100                 0.01    0.106119945605273    -12.5400036591612     4809.87930844463     10.5594596175303    -2206.81099883101 
-Loop time of 0.304678 on 4 procs for 100 steps with 500 atoms
-
-Performance: 2.836 ns/day, 8.463 hours/ns, 328.215 timesteps/s
-98.0% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.071445   | 0.073018   | 0.074151   |   0.4 | 23.97
-Neigh   | 0.054448   | 0.055709   | 0.057528   |   0.5 | 18.28
-Comm    | 0.0061178  | 0.0074609  | 0.0090766  |   1.2 |  2.45
-Output  | 0.037489   | 0.038586   | 0.039952   |   0.5 | 12.66
-Modify  | 0.12826    | 0.12954    | 0.13065    |   0.3 | 42.52
-Other   |            | 0.0003686  |            |       |  0.12
-
-Nlocal:    125 ave 129 max 120 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-Nghost:    1387 ave 1392 max 1383 min
-Histogram: 1 0 1 0 0 1 0 0 0 1
-Neighs:    9125 ave 9428 max 8740 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-FullNghs:  18250 ave 18834 max 17520 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-
-Total # of neighbors = 73000
-Ave neighs/atom = 146
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:00
diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
similarity index 50%
rename from examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1
rename to examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
index 405be50bd9..cc1cb29a6e 100644
--- a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (11 May 2018)
+LAMMPS (30 Oct 2019)
 units 		metal
 dimension 	3
 boundary 	p p p
@@ -12,6 +12,7 @@ read_data 	Norm_randXY_8x8x32.data
   1 by 1 by 1 MPI processor grid
   reading atoms ...
   8192 atoms
+  read_data CPU = 0.0207078 secs
 
 mass		1 58.93
 
@@ -25,12 +26,12 @@ neigh_modify 	every 1 check no delay 0
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # define outputs and computes
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp
@@ -45,7 +46,7 @@ thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
 thermo_modify   format float %20.15g
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
 run 		100
 Neighbor list info ...
@@ -65,33 +66,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 19.68 | 19.68 | 19.68 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-       0                    0    0.980832325249102     -2984.9466433509     51.7121203365409                    0    -38881.8459242429 
-      10                0.001    0.980832325038224    -2984.94800197308     52.2550760237226  0.00128259392155095    -38881.8459243688 
-      20                0.002    0.980832322622779    -2984.95196908579     53.4253029071033   0.0050206854169363    -38881.8459246487 
-      30                0.003    0.980832317889283    -2984.95826684048     55.1488791221993   0.0109316238061975    -38881.8459250502 
-      40                0.004    0.980832310888481    -2984.96649810512     57.3217709603901   0.0186091353316915    -38881.8459255204 
-      50                0.005    0.980832301939686    -2984.97619813381     59.8271487572311   0.0275752699737783    -38881.8459260027 
-      60                0.006    0.980832291654664    -2984.98688847988     62.5518654049861   0.0373348857300743    -38881.8459264498 
-      70                0.007    0.980832280861627    -2984.99812400566     65.3978892661935   0.0474235455824994     -38881.845926824 
-      80                0.008    0.980832270462785    -2985.00952679611      68.286219599829   0.0574425858114516    -38881.8459271072 
-      90                0.009    0.980832261284587    -2985.02080458573     71.1539714621652   0.0670788260497413    -38881.8459272915 
-     100                 0.01    0.980832253960703    -2985.03175506188     73.9486358176052   0.0761100787140068    -38881.8459273845 
-Loop time of 12.4286 on 1 procs for 100 steps with 8192 atoms
+       0                    0   0.0177864461018737    -1323.65841279979       1274.398774669                    0    -37220.5576936917 
+      10                0.001   0.0177864363786085    -1323.66900862123     1270.76616762926   0.0100007025152235    -37220.5576943558 
+      20                0.002   0.0177864377251544    -1323.70032173151     1259.90270462032   0.0394803272360477    -37220.5576959255 
+      30                0.003   0.0177864511986563    -1323.75117991179     1243.50772254923   0.0871132837928349    -37220.5576982168 
+      40                0.004   0.0177864729727686    -1323.81992477224     1223.91535595806    0.150986538096776    -37220.5577010151 
+      50                0.005    0.017786495620418    -1323.90456907402     1203.45497846157     0.22877054554493    -37220.5577041158 
+      60                0.006   0.0177865119365897    -1324.00293472823     1183.95496070422    0.317876389336898    -37220.5577073311 
+      70                0.007   0.0177865186121948    -1324.11277680481     1166.52445270059    0.415601818818485    -37220.5577104779 
+      80                0.008   0.0177865171615599    -1324.23190710734     1151.59958937508    0.519276751090729    -37220.5577133816 
+      90                0.009   0.0177865117923882    -1324.35831839963     1139.14485136813    0.626407059487507    -37220.5577158996 
+     100                 0.01   0.0177865063215865    -1324.49029089774     1128.88117273962    0.734797362055872    -37220.5577179524 
+Loop time of 17.5042 on 1 procs for 100 steps with 8192 atoms
 
-Performance: 0.070 ns/day, 345.239 hours/ns, 8.046 timesteps/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.049 ns/day, 486.227 hours/ns, 5.713 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 4.0123     | 4.0123     | 4.0123     |   0.0 | 32.28
-Neigh   | 3.005      | 3.005      | 3.005      |   0.0 | 24.18
-Comm    | 0.041798   | 0.041798   | 0.041798   |   0.0 |  0.34
-Output  | 1.8465     | 1.8465     | 1.8465     |   0.0 | 14.86
-Modify  | 3.5157     | 3.5157     | 3.5157     |   0.0 | 28.29
-Other   |            | 0.007261   |            |       |  0.06
+Pair    | 5.4555     | 5.4555     | 5.4555     |   0.0 | 31.17
+Neigh   | 3.9944     | 3.9944     | 3.9944     |   0.0 | 22.82
+Comm    | 0.086468   | 0.086468   | 0.086468   |   0.0 |  0.49
+Output  | 2.7685     | 2.7685     | 2.7685     |   0.0 | 15.82
+Modify  | 5.1645     | 5.1645     | 5.1645     |   0.0 | 29.50
+Other   |            | 0.0349     |            |       |  0.20
 
 Nlocal:    8192 ave 8192 max 8192 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -109,4 +110,4 @@ Dangerous builds not checked
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:12
+Total wall time: 0:00:17
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4
new file mode 100644
index 0000000000..8c477e633f
--- /dev/null
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4
@@ -0,0 +1,113 @@
+LAMMPS (30 Oct 2019)
+units 		metal
+dimension 	3
+boundary 	p p p
+
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+read_data 	Norm_randXY_8x8x32.data
+  orthogonal box = (0 0 0) to (28.32 28.32 113.28)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  8192 atoms
+  read_data CPU = 0.023248 secs
+
+mass		1 58.93
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor 	1.0 bin
+neigh_modify 	every 1 check no delay 0
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# define outputs and computes
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          10
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.49954
+  ghost atom cutoff = 7.49954
+  binsize = 3.74977, bins = 8 8 31
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.422 | 8.508 | 8.751 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0177864461018739    -1323.65841279979       1274.398774669                    0    -37220.5576936996 
+      10                0.001   0.0177864050983603    -1323.66900862096     1270.76618998865   0.0100007022583634    -37220.5576943555 
+      20                0.002   0.0177863936833753    -1323.70032172864     1259.90276925185   0.0394803245313843    -37220.5576959254 
+      30                0.003   0.0177864120892274    -1323.75117990111     1243.50783331745    0.087113273744231    -37220.5576982173 
+      40                0.004   0.0177864533855652     -1323.8199247464     1223.91551103958    0.150986513868405     -37220.557701015 
+      50                0.005   0.0177865078997919    -1323.90456902433     1203.45516787752    0.228770499151177    -37220.5577041159 
+      60                0.006   0.0177865576955448     -1324.0029346455     1183.95517338662    0.317876312538184    -37220.5577073314 
+      70                0.007   0.0177865860816348    -1324.11277667948     1166.52467969539    0.415601703342581    -37220.5577104775 
+      80                0.008   0.0177865881669081    -1324.23190693081     1151.59982868413    0.519276589926842     -37220.557713381 
+      90                0.009   0.0177865780982769    -1324.35831816525     1139.14509878533    0.626406847905203     -37220.557715901 
+     100                 0.01    0.017786564605084    -1324.49029060173     1128.88143013641    0.734797098519806     -37220.557717952 
+Loop time of 7.30477 on 4 procs for 100 steps with 8192 atoms
+
+Performance: 0.118 ns/day, 202.910 hours/ns, 13.690 timesteps/s
+98.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.9727     | 2.0433     | 2.1095     |   3.9 | 27.97
+Neigh   | 1.1665     | 1.3031     | 1.4137     |   8.7 | 17.84
+Comm    | 0.15743    | 0.31703    | 0.53111    |  28.2 |  4.34
+Output  | 1.0547     | 1.0747     | 1.094      |   1.4 | 14.71
+Modify  | 2.5296     | 2.5551     | 2.5794     |   1.1 | 34.98
+Other   |            | 0.01167    |            |       |  0.16
+
+Nlocal:    2048 ave 2061 max 2035 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    5765 ave 5778 max 5752 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:    143360 ave 144262 max 142469 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+FullNghs:  286720 ave 288540 max 284900 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 1146880
+Ave neighs/atom = 140
+Neighbor list builds = 100
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:07
diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
similarity index 54%
rename from examples/SPIN/read_restart/log.11May18.spin.restart.g++.1
rename to examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
index 16eb7c3f5e..4ca29113d3 100644
--- a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (11 May 2018)
+LAMMPS (30 Oct 2019)
 # start a spin-lattice simulation from a data file
 units 		metal
 atom_style 	spin
@@ -10,11 +10,13 @@ boundary 	p p p
 atom_modify 	map array
 
 read_restart	restart_hcp_cobalt.equil
+WARNING: Restart file used different # of processors: 4 vs. 1 (../read_restart.cpp:742)
   restoring atom style spin from restart
   orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 1 by 1 MPI processor grid
   restoring pair style spin/exchange from restart
   500 atoms
+  read_restart CPU = 0.000402927 secs
 
 # setting mass, mag. moments, and interactions
 
@@ -30,12 +32,12 @@ neigh_modify 	every 1 check no delay 0
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # define outputs
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp
@@ -70,33 +72,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.315 | 6.315 | 6.315 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 6.816 | 6.816 | 6.816 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-    1000                    0    0.106120063678768    -11.8110267448938     5244.87332482316                    0    -2206.81097898043 
-    1010                0.001    0.106120047478105    -11.8198467887534     5263.87502105137    0.136650312456579    -2206.81097929055 
-    1020                0.002    0.106120026430373    -11.8460960518731     5267.29822866382    0.542282409605327    -2206.81098022997 
-    1030                0.003    0.106120005015917    -11.8891434078861     5252.95323564256       1.204018338139    -2206.81098172551 
-    1040                0.004    0.106119988532653    -11.9479778701641     5220.88508622311     2.10120884995911    -2206.81098371047 
-    1050                0.005     0.10611998133687     -12.021242685853     5172.58549378915     3.20622445795757    -2206.81098610701 
-    1060                0.006     0.10611998489458     -12.107271344148     5110.57395203849     4.48535975411235    -2206.81098879725 
-    1070                0.007    0.106119996964771     -12.204156761765     5038.48903231346      5.9003121044977    -2206.81099161183 
-    1080                0.008    0.106120013042521    -12.3098695046152      4961.0327167967      7.4104497466856    -2206.81099434653 
-    1090                0.009    0.106120029236234    -12.4224157835754      4883.3210922213     8.97568980540163    -2206.81099680117 
-    1100                 0.01    0.106120044071404    -12.5400036896932     4809.88136080052      10.559459821976    -2206.81099883104 
-Loop time of 0.833234 on 1 procs for 100 steps with 500 atoms
+    1000                    0    0.108317262557656    -10.7649197733649      2538.4247868621                    0     -2205.7648720089 
+    1010                0.001    0.108317281393701    -10.7743543303502     2527.22692799144    0.146167392153018    -2205.76487255098 
+    1020                0.002    0.108317318482233    -10.8022550516195     2509.47863584151    0.577304300153637    -2205.76487378396 
+    1030                0.003    0.108317366763426    -10.8476659807571      2487.5614649682     1.27529086243277    -2205.76487555634 
+    1040                0.004    0.108317415532953    -10.9092708333549     2463.97963921611     2.21443906326453    -2205.76487769286 
+    1050                0.005    0.108317453851058      -10.98553406179     2440.70473642157     3.36396898978859     -2205.7648800529 
+    1060                0.006    0.108317473584086    -11.0748008072977     2418.66477599297     4.68991434259399    -2205.76488256723 
+    1070                0.007    0.108317471632913     -11.175325501803     2397.59274785581     6.15596240129541    -2205.76488520043 
+    1080                0.008    0.108317450667394    -11.2852665400894     2376.32871275528      7.7237909750654    -2205.76488786887 
+    1090                0.009    0.108317417687893    -11.4027246787047     2353.52646917989     9.35409156720424    -2205.76489041327 
+    1100                 0.01    0.108317381194814      -11.52585602487     2328.41541723561     11.0087303030003    -2205.76489265824 
+Loop time of 1.05153 on 1 procs for 100 steps with 500 atoms
 
-Performance: 1.037 ns/day, 23.145 hours/ns, 120.014 timesteps/s
+Performance: 0.822 ns/day, 29.209 hours/ns, 95.100 timesteps/s
 99.7% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.26558    | 0.26558    | 0.26558    |   0.0 | 31.87
-Neigh   | 0.21352    | 0.21352    | 0.21352    |   0.0 | 25.62
-Comm    | 0.0057988  | 0.0057988  | 0.0057988  |   0.0 |  0.70
-Output  | 0.12463    | 0.12463    | 0.12463    |   0.0 | 14.96
-Modify  | 0.22275    | 0.22275    | 0.22275    |   0.0 | 26.73
-Other   |            | 0.0009537  |            |       |  0.11
+Pair    | 0.3348     | 0.3348     | 0.3348     |   0.0 | 31.84
+Neigh   | 0.26691    | 0.26691    | 0.26691    |   0.0 | 25.38
+Comm    | 0.007993   | 0.007993   | 0.007993   |   0.0 |  0.76
+Output  | 0.14892    | 0.14892    | 0.14892    |   0.0 | 14.16
+Modify  | 0.29137    | 0.29137    | 0.29137    |   0.0 | 27.71
+Other   |            | 0.001526   |            |       |  0.15
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -114,4 +116,4 @@ Dangerous builds not checked
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:00
+Total wall time: 0:00:01
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4
new file mode 100644
index 0000000000..5d40efc29b
--- /dev/null
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4
@@ -0,0 +1,118 @@
+LAMMPS (30 Oct 2019)
+# start a spin-lattice simulation from a data file
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+read_restart	restart_hcp_cobalt.equil
+  restoring atom style spin from restart
+  orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
+  1 by 2 by 2 MPI processor grid
+  restoring pair style spin/exchange from restart
+  500 atoms
+  read_restart CPU = 0.000858784 secs
+
+# setting mass, mag. moments, and interactions
+
+mass		1 58.93
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor 	1.0 bin
+neigh_modify 	every 1 check no delay 0
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# define outputs
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          10
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.49954
+  ghost atom cutoff = 7.49954
+  binsize = 3.74977, bins = 4 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.704 | 6.704 | 6.704 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+    1000                    0    0.108317262557656    -10.7649197733649      2538.4247868621                    0     -2205.7648720085 
+    1010                0.001    0.108317290362529    -10.7743543303489     2527.22680531097    0.146167392137698    -2205.76487255096 
+    1020                0.002    0.108317316207642    -10.8022550521284     2509.47840782645    0.577304308061779    -2205.76487378396 
+    1030                0.003    0.108317335980455    -10.8476659832667     2487.56119588937     1.27529090130452    -2205.76487555634 
+    1040                0.004    0.108317347902639    -10.9092708400684     2463.97936529674     2.21443916694928    -2205.76487769286 
+    1050                0.005    0.108317349786635    -10.9855340757384      2440.7044253165     3.36396920446814    -2205.76488005291 
+    1060                0.006    0.108317342445881    -11.0748008315013     2418.66438763214     4.68991471343994    -2205.76488256723 
+    1070                0.007     0.10831733355314    -11.1753255362286     2397.59228728929     6.15596292529133    -2205.76488520046 
+    1080                0.008    0.108317320750099    -11.2852665775656     2376.32820919279      7.7237915384778    -2205.76488786888 
+    1090                0.009    0.108317304079233     -11.402724701646     2353.52588586648     9.35409189724323     -2205.7648904133 
+    1100                 0.01    0.108317284409678    -11.5258560062539     2328.41472376239     11.0087299868288    -2205.76489265829 
+Loop time of 0.603216 on 4 procs for 100 steps with 500 atoms
+
+Performance: 1.432 ns/day, 16.756 hours/ns, 165.778 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.1203     | 0.12952    | 0.13546    |   1.6 | 21.47
+Neigh   | 0.064357   | 0.080477   | 0.093005   |   4.4 | 13.34
+Comm    | 0.016533   | 0.035739   | 0.06195    |   9.9 |  5.92
+Output  | 0.063324   | 0.065044   | 0.066794   |   0.5 | 10.78
+Modify  | 0.29023    | 0.29189    | 0.29336    |   0.3 | 48.39
+Other   |            | 0.0005503  |            |       |  0.09
+
+Nlocal:    125 ave 127 max 122 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost:    1387 ave 1390 max 1385 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs:    9125 ave 9272 max 8945 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+FullNghs:  18250 ave 18542 max 17812 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 73000
+Ave neighs/atom = 146
+Neighbor list builds = 100
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
similarity index 64%
rename from examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1
rename to examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
index c3be90cb50..986f93e3e1 100644
--- a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (11 May 2018)
+LAMMPS (30 Oct 2019)
 # fcc cobalt in a 3d periodic box
 
 units 		metal
@@ -18,7 +18,7 @@ Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  Time spent = 0.00027585 secs
+  create_atoms CPU = 0.001122 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -36,12 +36,12 @@ neigh_modify 	every 10 check yes delay 20
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 100.0 0.01 21
 
-fix 		3 all nve/spin lattice no
+fix 		3 all nve/spin lattice frozen
 timestep	0.0001
 
 # compute and output options
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp
@@ -70,33 +70,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.446 | 6.446 | 6.446 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 6.947 | 6.947 | 6.947 Mbytes
 Step Time v_magnorm v_emag Temp TotEng 
        0            0  0.076558814    1.7982359            0    1.7982359 
-     100         0.01  0.079107243   0.56368447            0   0.56368447 
-     200         0.02   0.08225862  -0.42421042            0  -0.42421042 
-     300         0.03   0.08397714   -1.4964948            0   -1.4964948 
-     400         0.04  0.084704989   -2.6740652            0   -2.6740652 
-     500         0.05  0.087486342   -4.2043382            0   -4.2043382 
-     600         0.06   0.09187261   -5.6687169            0   -5.6687169 
-     700         0.07  0.096925249    -6.937499            0    -6.937499 
-     800         0.08  0.098988236   -8.2456715            0   -8.2456715 
-     900         0.09   0.10434092   -10.111953            0   -10.111953 
-    1000          0.1   0.10612006   -11.811027            0   -11.811027 
-Loop time of 2.60215 on 1 procs for 1000 steps with 500 atoms
+     100         0.01  0.077628154   0.73387834            0   0.73387834 
+     200         0.02  0.076678996   -0.4048463            0   -0.4048463 
+     300         0.03  0.079174837   -1.3519103            0   -1.3519103 
+     400         0.04  0.085031632   -3.0345702            0   -3.0345702 
+     500         0.05   0.08702747   -4.0853256            0   -4.0853256 
+     600         0.06  0.087066482    -5.259549            0    -5.259549 
+     700         0.07  0.089788894    -6.629076            0    -6.629076 
+     800         0.08  0.091699611   -8.0574087            0   -8.0574087 
+     900         0.09  0.090038899   -9.2012019            0   -9.2012019 
+    1000          0.1  0.093257309   -10.470452            0   -10.470452 
+Loop time of 3.56687 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 3.320 ns/day, 7.228 hours/ns, 384.297 timesteps/s
-99.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 2.422 ns/day, 9.908 hours/ns, 280.358 timesteps/s
+99.3% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.35178    | 0.35178    | 0.35178    |   0.0 | 13.52
+Pair    | 0.46568    | 0.46568    | 0.46568    |   0.0 | 13.06
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.014421   | 0.014421   | 0.014421   |   0.0 |  0.55
-Output  | 1.2046     | 1.2046     | 1.2046     |   0.0 | 46.29
-Modify  | 1.0274     | 1.0274     | 1.0274     |   0.0 | 39.48
-Other   |            | 0.004006   |            |       |  0.15
+Comm    | 0.022188   | 0.022188   | 0.022188   |   0.0 |  0.62
+Output  | 1.4417     | 1.4417     | 1.4417     |   0.0 | 40.42
+Modify  | 1.6335     | 1.6335     | 1.6335     |   0.0 | 45.80
+Other   |            | 0.003845   |            |       |  0.11
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -116,4 +116,4 @@ write_restart 	restart_hcp_cobalt.equil
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:02
+Total wall time: 0:00:03
diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
similarity index 64%
rename from examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4
rename to examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
index e54299b9dd..05f6091f79 100644
--- a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (11 May 2018)
+LAMMPS (30 Oct 2019)
 # fcc cobalt in a 3d periodic box
 
 units 		metal
@@ -18,7 +18,7 @@ Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  Time spent = 0.000257969 secs
+  create_atoms CPU = 0.000901937 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -36,12 +36,12 @@ neigh_modify 	every 10 check yes delay 20
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 100.0 0.01 21
 
-fix 		3 all nve/spin lattice no
+fix 		3 all nve/spin lattice frozen
 timestep	0.0001
 
 # compute and output options
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp
@@ -70,33 +70,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.367 | 6.367 | 6.367 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 6.868 | 6.868 | 6.868 Mbytes
 Step Time v_magnorm v_emag Temp TotEng 
        0            0  0.076558814    1.7982359            0    1.7982359 
-     100         0.01  0.081414414   0.70545723            0   0.70545723 
-     200         0.02  0.084519539  -0.33171078            0  -0.33171078 
-     300         0.03  0.089334139   -1.3988283            0   -1.3988283 
-     400         0.04  0.092873722   -2.8519371            0   -2.8519371 
-     500         0.05    0.0970839   -4.1531164            0   -4.1531164 
-     600         0.06  0.099626132   -5.7993765            0   -5.7993765 
-     700         0.07   0.10467169   -7.3011333            0   -7.3011333 
-     800         0.08   0.10893493   -8.6918141            0   -8.6918141 
-     900         0.09   0.11389657   -10.236174            0   -10.236174 
-    1000          0.1    0.1180057   -11.896933            0   -11.896933 
-Loop time of 1.05012 on 4 procs for 1000 steps with 500 atoms
+     100         0.01  0.078299981   0.88259584            0   0.88259584 
+     200         0.02  0.081260508  -0.43484722            0  -0.43484722 
+     300         0.03  0.081195603   -1.7408209            0   -1.7408209 
+     400         0.04  0.087298495   -3.4139038            0   -3.4139038 
+     500         0.05  0.087663924   -4.3766089            0   -4.3766089 
+     600         0.06  0.091713683   -5.8534921            0   -5.8534921 
+     700         0.07  0.093779119    -6.706628            0    -6.706628 
+     800         0.08  0.097960611   -7.8688568            0   -7.8688568 
+     900         0.09   0.10193463   -9.5888008            0   -9.5888008 
+    1000          0.1   0.10831726    -10.76492            0    -10.76492 
+Loop time of 2.36594 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 8.228 ns/day, 2.917 hours/ns, 952.272 timesteps/s
-98.1% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 3.652 ns/day, 6.572 hours/ns, 422.665 timesteps/s
+98.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.08972    | 0.090456   | 0.091872   |   0.3 |  8.61
+Pair    | 0.13515    | 0.15276    | 0.16507    |   2.8 |  6.46
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.016958   | 0.018047   | 0.019791   |   0.8 |  1.72
-Output  | 0.36286    | 0.37483    | 0.38975    |   1.6 | 35.69
-Modify  | 0.55131    | 0.56541    | 0.57702    |   1.3 | 53.84
-Other   |            | 0.001374   |            |       |  0.13
+Comm    | 0.08478    | 0.10161    | 0.12408    |   4.5 |  4.29
+Output  | 0.50658    | 0.52938    | 0.55066    |   2.3 | 22.38
+Modify  | 1.5629     | 1.5794     | 1.6014     |   1.3 | 66.75
+Other   |            | 0.002834   |            |       |  0.12
 
 Nlocal:    125 ave 125 max 125 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -116,4 +116,4 @@ write_restart 	restart_hcp_cobalt.equil
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:01
+Total wall time: 0:00:02
diff --git a/examples/SPIN/run_spin_examples.sh b/examples/SPIN/run_spin_examples.sh
new file mode 100755
index 0000000000..a71da82a04
--- /dev/null
+++ b/examples/SPIN/run_spin_examples.sh
@@ -0,0 +1,120 @@
+#!/bin/bash
+
+DATE=19Nov19
+
+# bfo
+cd bfo/
+../../../src/lmp_serial -in in.spin.bfo
+cp log.lammps log.${DATE}.spin.bfo.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo
+cp log.lammps log.${DATE}.spin.bfo.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# fcc cobalt
+cd cobalt_fcc/
+../../../src/lmp_serial -in in.spin.cobalt_fcc
+cp log.lammps log.${DATE}.spin.cobalt_fcc.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.cobalt_fcc
+cp log.lammps log.${DATE}.spin.cobalt_fcc.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# hcp cobalt
+cd cobalt_hcp/
+../../../src/lmp_serial -in in.spin.cobalt_hcp
+cp log.lammps log.${DATE}.spin.cobalt_hcp.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.cobalt_hcp
+cp log.lammps log.${DATE}.spin.cobalt_hcp.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# dipole spin
+cd dipole_spin/
+../../../src/lmp_serial -in in.spin.iron_dipole_cut
+cp log.lammps log.${DATE}.spin.iron_dipole_cut.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_dipole_cut
+cp log.lammps log.${DATE}.spin.iron_dipole_cut.g++.4
+../../../src/lmp_serial -in in.spin.iron_dipole_ewald
+cp log.lammps log.${DATE}.spin.iron_dipole_ewald.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_dipole_ewald
+cp log.lammps log.${DATE}.spin.iron_dipole_ewald.g++.4
+../../../src/lmp_serial -in in.spin.iron_dipole_pppm
+cp log.lammps log.${DATE}.spin.iron_dipole_pppm.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_dipole_pppm
+cp log.lammps log.${DATE}.spin.iron_dipole_pppm.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# bcc iron
+cd iron/
+../../../src/lmp_serial -in in.spin.iron
+cp log.lammps log.${DATE}.spin.iron.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron
+cp log.lammps log.${DATE}.spin.iron.g++.4
+../../../src/lmp_serial -in in.spin.iron_cubic
+cp log.lammps log.${DATE}.spin.iron_cubic.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_cubic
+cp log.lammps log.${DATE}.spin.iron_cubic.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# fcc nickel
+cd nickel/
+../../../src/lmp_serial -in in.spin.nickel
+cp log.lammps log.${DATE}.spin.nickel.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.nickel
+cp log.lammps log.${DATE}.spin.nickel.g++.4
+../../../src/lmp_serial -in in.spin.nickel_cubic
+cp log.lammps log.${DATE}.spin.nickel_cubic.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.nickel_cubic
+cp log.lammps log.${DATE}.spin.nickel_cubic.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# read restart
+cd read_restart/
+../../../src/lmp_serial -in in.spin.write_restart
+cp log.lammps log.${DATE}.spin.write_restart.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.write_restart
+cp log.lammps log.${DATE}.spin.write_restart.g++.4
+../../../src/lmp_serial -in in.spin.restart
+cp log.lammps log.${DATE}.spin.restart.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.restart
+cp log.lammps log.${DATE}.spin.restart.g++.4
+../../../src/lmp_serial -in in.spin.read_data
+cp log.lammps log.${DATE}.spin.read_data.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.read_data
+cp log.lammps log.${DATE}.spin.read_data.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# setforce
+cd setforce_spin/
+../../../src/lmp_serial -in in.spin.setforce
+cp log.lammps log.${DATE}.spin.setforce.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.setforce
+cp log.lammps log.${DATE}.spin.setforce.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# spin minimizers
+cd spinmin/
+../../../src/lmp_serial -in in.spin.bfo_min
+cp log.lammps log.${DATE}.spin.bfo_min.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo_min
+cp log.lammps log.${DATE}.spin.bfo_min.g++.4
+../../../src/lmp_serial -in in.spin.bfo_min_cg
+cp log.lammps log.${DATE}.spin.bfo_min_cg.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo_min_cg
+cp log.lammps log.${DATE}.spin.bfo_min_cg.g++.4
+../../../src/lmp_serial -in in.spin.bfo_min_lbfgs
+cp log.lammps log.${DATE}.spin.bfo_min_lbfgs.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo_min_lbfgs
+cp log.lammps log.${DATE}.spin.bfo_min_lbfgs.g++.4
+../../../src/lmp_serial -in in.spin.iron_min
+cp log.lammps log.${DATE}.spin.iron_min.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_min
+cp log.lammps log.${DATE}.spin.iron_min.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
diff --git a/examples/SPIN/setforce_spin/in.spinmin.setforce b/examples/SPIN/setforce_spin/in.spin.setforce
similarity index 86%
rename from examples/SPIN/setforce_spin/in.spinmin.setforce
rename to examples/SPIN/setforce_spin/in.spin.setforce
index 822768e0ef..0d65955a29 100644
--- a/examples/SPIN/setforce_spin/in.spinmin.setforce
+++ b/examples/SPIN/setforce_spin/in.spin.setforce
@@ -8,7 +8,7 @@ atom_style 	spin
 atom_modify 	map array 
 
 lattice 	sc 3.0
-region 		box block 0.0 10.0 0.0 10.0 0.0 1.0
+region 		box block 0.0 10.0 0.0 10.0 0.0 4.0
 create_box 	2 box
 region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
 region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
@@ -47,13 +47,13 @@ variable 	magnorm   equal c_out_mag[4]
 variable 	emag      equal c_out_mag[5]
 variable 	tmag      equal c_out_mag[6]
 
-thermo          1000
+thermo          100
 thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
 thermo_modify   format float %20.15g
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 1000 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
 
 min_style	spin
 min_modify 	alpha_damp 1.0 discrete_factor 20.0
-minimize        1.0e-16 1.0e-16 50000 1000
+minimize        1.0e-16 1.0e-16 1000 100
diff --git a/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1 b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1
new file mode 100644
index 0000000000..da8e705204
--- /dev/null
+++ b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1
@@ -0,0 +1,141 @@
+LAMMPS (30 Oct 2019)
+
+units 		metal
+dimension 	3
+boundary 	f f f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.0
+Lattice spacing in x,y,z = 3 3 3
+region 		box block 0.0 10.0 0.0 10.0 0.0 4.0
+create_box 	2 box
+Created orthogonal box = (0 0 0) to (30 30 12)
+  1 by 1 by 1 MPI processor grid
+region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
+region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
+create_atoms 	1 region reg1
+Created 120 atoms
+  create_atoms CPU = 0.000591993 secs
+create_atoms 	2 region reg2
+Created 80 atoms
+  create_atoms CPU = 2.19345e-05 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+mass		2 55.845
+set 		region reg1 spin 2.2 0.0 0.0 1.0
+  120 settings made for spin
+set 		region reg2 spin/random 31 2.2
+  80 settings made for spin/random
+
+group 		fixed_spin region reg1
+120 atoms in group fixed_spin
+
+pair_style 	hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
+pair_coeff 	* * spin/exchange exchange 3.1 -0.01593 0.06626915552 1.211
+pair_coeff	* * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
+fix_modify	1 energy yes
+fix 		2 fixed_spin setforce/spin 0.0 0.0 0.0
+fix 		3 all langevin/spin 0.0 0.1 21
+fix		4 all nve/spin lattice frozen
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 20.0
+minimize        1.0e-16 1.0e-16 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.2
+  ghost atom cutoff = 3.2
+  binsize = 1.6, bins = 19 19 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.215 | 7.215 | 7.215 Mbytes
+Step Time v_magx v_magz v_magnorm v_tmag TotEng 
+       0                    0 0.000143282585570239    0.615515043943419    0.615726279597251      21.735436446264    0.251043691626527 
+     100                 0.01 -0.00116085697754605    0.590264559350799    0.590315072966953  0.00283413081085227   0.0846048989956838 
+     200                 0.02 -0.00014757052323624      0.5896197627388    0.589686497206689 0.000451051163122381   0.0839054390713707 
+     300                 0.03 2.64982966536903e-05    0.590029694756149    0.590102003120244 5.22539631503911e-05   0.0838351677819021 
+     400                 0.04 1.77805448780044e-05    0.590195117338991    0.590268726215095 4.46490059775722e-06   0.0838382933245033 
+     500                 0.05 6.71566571038784e-06    0.590243842081075    0.590317756995865 3.63227563542099e-07   0.0838411433938002 
+     600                 0.06 2.24103407431009e-06    0.590257551861528    0.590331542128336 2.99360370345602e-08   0.0838420708305254 
+     700                 0.07 7.12179152899672e-07      0.5902614042958    0.590335413637883 2.51559188415894e-09   0.0838423375091772 
+     800                 0.08 2.20574733078571e-07    0.590262494529884    0.590336508799302 2.14455748236281e-10   0.0838424126463501 
+     900                 0.09 6.72564339382342e-08    0.590262805532644    0.590336821097688 1.84495767133404e-11   0.0838424338620733 
+    1000                  0.1 2.03001940418668e-08    0.590262894882646    0.590336910794094  1.5958531383517e-12   0.0838424398944954 
+Loop time of 0.128906 on 1 procs for 1000 steps with 200 atoms
+
+98.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        0.251043691627    0.0838424398641    0.0838424398945
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.11267    | 0.11267    | 0.11267    |   0.0 | 87.41
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00012422 | 0.00012422 | 0.00012422 |   0.0 |  0.10
+Output  | 0.0062549  | 0.0062549  | 0.0062549  |   0.0 |  4.85
+Modify  | 0.0036588  | 0.0036588  | 0.0036588  |   0.0 |  2.84
+Other   |            | 0.006197   |            |       |  4.81
+
+Nlocal:    200 ave 200 max 200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  920 ave 920 max 920 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 920
+Ave neighs/atom = 4.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4 b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4
new file mode 100644
index 0000000000..4889232f9d
--- /dev/null
+++ b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4
@@ -0,0 +1,141 @@
+LAMMPS (30 Oct 2019)
+
+units 		metal
+dimension 	3
+boundary 	f f f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.0
+Lattice spacing in x,y,z = 3 3 3
+region 		box block 0.0 10.0 0.0 10.0 0.0 4.0
+create_box 	2 box
+Created orthogonal box = (0 0 0) to (30 30 12)
+  2 by 2 by 1 MPI processor grid
+region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
+region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
+create_atoms 	1 region reg1
+Created 120 atoms
+  create_atoms CPU = 0.000560045 secs
+create_atoms 	2 region reg2
+Created 80 atoms
+  create_atoms CPU = 0.000101089 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+mass		2 55.845
+set 		region reg1 spin 2.2 0.0 0.0 1.0
+  120 settings made for spin
+set 		region reg2 spin/random 31 2.2
+  80 settings made for spin/random
+
+group 		fixed_spin region reg1
+120 atoms in group fixed_spin
+
+pair_style 	hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
+pair_coeff 	* * spin/exchange exchange 3.1 -0.01593 0.06626915552 1.211
+pair_coeff	* * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
+fix_modify	1 energy yes
+fix 		2 fixed_spin setforce/spin 0.0 0.0 0.0
+fix 		3 all langevin/spin 0.0 0.1 21
+fix		4 all nve/spin lattice frozen
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 20.0
+minimize        1.0e-16 1.0e-16 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.2
+  ghost atom cutoff = 3.2
+  binsize = 1.6, bins = 19 19 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.2 | 7.2 | 7.2 Mbytes
+Step Time v_magx v_magz v_magnorm v_tmag TotEng 
+       0                    0 0.000143282585570239    0.615515043943419    0.615726279597251      21.735436446264    0.251043691626527 
+     100                 0.01 -0.00116085697754605    0.590264559350799    0.590315072966953  0.00283413081085227   0.0846048989956832 
+     200                 0.02 -0.000147570523236238      0.5896197627388    0.589686497206689 0.000451051163122381   0.0839054390713705 
+     300                 0.03 2.64982966536902e-05     0.59002969475615    0.590102003120244 5.22539631503911e-05   0.0838351677819014 
+     400                 0.04 1.77805448780033e-05    0.590195117338991    0.590268726215095 4.46490059775722e-06   0.0838382933245032 
+     500                 0.05 6.71566571038784e-06    0.590243842081075    0.590317756995865 3.63227563542099e-07   0.0838411433937997 
+     600                 0.06  2.2410340743112e-06    0.590257551861528    0.590331542128336 2.99360370345601e-08   0.0838420708305252 
+     700                 0.07 7.12179152897591e-07      0.5902614042958    0.590335413637884 2.51559188415894e-09   0.0838423375091767 
+     800                 0.08 2.20574733079126e-07    0.590262494529884    0.590336508799302 2.14455748236281e-10   0.0838424126463497 
+     900                 0.09 6.72564339365689e-08    0.590262805532644    0.590336821097688 1.84495767133404e-11   0.0838424338620728 
+    1000                  0.1 2.03001940390912e-08    0.590262894882646    0.590336910794094  1.5958531383517e-12   0.0838424398944951 
+Loop time of 0.0892034 on 4 procs for 1000 steps with 200 atoms
+
+91.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        0.251043691627    0.0838424398641    0.0838424398945
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.032445   | 0.038594   | 0.054315   |   4.6 | 43.27
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.020121   | 0.035668   | 0.042827   |   4.8 | 39.98
+Output  | 0.0024662  | 0.0025705  | 0.0028648  |   0.3 |  2.88
+Modify  | 0.00099444 | 0.0010954  | 0.0011995  |   0.2 |  1.23
+Other   |            | 0.01128    |            |       | 12.64
+
+Nlocal:    50 ave 50 max 50 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    34.5 ave 48 max 22 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  230 ave 230 max 230 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 920
+Ave neighs/atom = 4.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/spinmin/in.spinmin.bfo b/examples/SPIN/spinmin/in.spin.bfo_min
similarity index 97%
rename from examples/SPIN/spinmin/in.spinmin.bfo
rename to examples/SPIN/spinmin/in.spin.bfo_min
index 5ebc9e0afe..701e049de3 100644
--- a/examples/SPIN/spinmin/in.spinmin.bfo
+++ b/examples/SPIN/spinmin/in.spin.bfo_min
@@ -9,7 +9,7 @@ atom_style 	spin
 atom_modify 	map array 
 
 lattice 	sc 3.96
-region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
 create_box 	1 box
 create_atoms 	1 box
 
diff --git a/examples/SPIN/spinmin/in.spinmin_cg.bfo b/examples/SPIN/spinmin/in.spin.bfo_min_cg
similarity index 94%
rename from examples/SPIN/spinmin/in.spinmin_cg.bfo
rename to examples/SPIN/spinmin/in.spin.bfo_min_cg
index 9d57399a56..7ce29b35ab 100644
--- a/examples/SPIN/spinmin/in.spinmin_cg.bfo
+++ b/examples/SPIN/spinmin/in.spin.bfo_min_cg
@@ -9,7 +9,7 @@ atom_style 	spin
 atom_modify 	map array 
 
 lattice 	sc 3.96
-region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -51,4 +51,4 @@ dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3
 
 min_style	spin/cg
 # min_modify 	line spin_none discrete_factor 10.0
-minimize        1.0e-10 1.0e-10 10000 10000
+minimize        1.0e-10 1.0e-10 1000 100
diff --git a/examples/SPIN/spinmin/in.spinmin_lbfgs.bfo b/examples/SPIN/spinmin/in.spin.bfo_min_lbfgs
similarity index 97%
rename from examples/SPIN/spinmin/in.spinmin_lbfgs.bfo
rename to examples/SPIN/spinmin/in.spin.bfo_min_lbfgs
index 56cd6b8fae..055903ab04 100644
--- a/examples/SPIN/spinmin/in.spinmin_lbfgs.bfo
+++ b/examples/SPIN/spinmin/in.spin.bfo_min_lbfgs
@@ -52,4 +52,4 @@ dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3
 min_style	spin/lbfgs
 # min_modify 	line spin_cubic discrete_factor 10.0
 min_modify	norm max
-minimize        1.0e-15 1.0e-10 10000 1000
+minimize        1.0e-15 1.0e-10 1000 100
diff --git a/examples/SPIN/spinmin/in.spinmin.iron b/examples/SPIN/spinmin/in.spin.iron_min
similarity index 94%
rename from examples/SPIN/spinmin/in.spinmin.iron
rename to examples/SPIN/spinmin/in.spin.iron_min
index ebbd229b89..9ed07eccc7 100644
--- a/examples/SPIN/spinmin/in.spinmin.iron
+++ b/examples/SPIN/spinmin/in.spin.iron_min
@@ -9,7 +9,7 @@ atom_style 	spin
 atom_modify 	map array 
 
 lattice 	bcc 2.8665
-region 		box block 0.0 4.0 0.0 4.0 0.0 4.0
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -52,4 +52,4 @@ dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[
 
 min_style	spin
 min_modify 	alpha_damp 1.0 discrete_factor 10.0
-minimize        1.0e-10 1.0e-10 100000 1000
+minimize        1.0e-10 1.0e-10 1000 100
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1
new file mode 100644
index 0000000000..134ff82ea0
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1
@@ -0,0 +1,148 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00103712 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 0.0 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.331 | 8.331 | 8.331 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0100717228668283   -0.162177519662199     14970.7090923449                    0   -0.157514482753568 
+      50                0.005  0.00013406177065452    -128.226118665465    0.102634444037433                    0     -128.28618242467 
+     100                 0.01 7.67769618983783e-06    -131.374599259781   0.0222596977749883                    0    -131.428418504308 
+     150                0.015 6.02904602224617e-07    -132.224372015825  0.00974271828169067                    0    -132.273190134603 
+     200                 0.02 6.50197247050607e-07    -132.573383315469  0.00374227079785919                    0    -132.617565541035 
+     250                0.025 4.40534385751331e-07    -132.729743470508  0.00193340972825779                    0    -132.770567114743 
+     300                 0.03 2.78356316513452e-07    -132.819255077939  0.00124938353773497                    0    -132.857574876413 
+     350                0.035 1.79684785125462e-07    -132.882714312877 0.000973166792896161                    0    -132.919261229743 
+     400                 0.04 1.10949878458879e-07    -132.935357748213 0.000852955460997589                    0    -132.970786605995 
+     450                0.045 6.49064465617783e-08    -132.982991683198 0.000790741148426227                    0    -133.017887798926 
+     500                 0.05 3.70514666560433e-08    -133.027689959766 0.000747949132882749                    0    -133.062561991888 
+     550                0.055 2.12433814830335e-08    -133.070148920145 0.000712637321271171                    0    -133.105417593747 
+     600                 0.06 1.24676590173818e-08    -133.110772798502 0.000685051841817329                    0    -133.146767469277 
+     650                0.065 7.53611859123344e-09    -133.150126417754 0.000669443562813207                    0    -133.187094895709 
+     700                 0.07 4.63539338668379e-09    -133.189024073453 0.000669619853917951                    0    -133.227152349437 
+     750                0.075 2.82145833993213e-09     -133.22844627026  0.00068733803508696                    0    -133.267881315199 
+     800                 0.08 1.64378151551878e-09    -133.269413776733  0.00072219769217513                    0    -133.310284062462 
+     850                0.085 8.88331010921243e-10    -133.312863108453 0.000771645398804489                    0    -133.355293578462 
+     900                 0.09 4.33874801673642e-10    -133.359507749172 0.000830255722998153                    0    -133.403626236688 
+     950                0.095 1.88127849216404e-10    -133.409630495316 0.000888348219681115                    0    -133.455560507802 
+    1000                  0.1 7.17748877096286e-11    -133.462806227865 0.000931427722404679                    0    -133.510640942679 
+Loop time of 11.213 on 1 procs for 1000 steps with 5780 atoms
+
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.157514482754     -133.509516066     -133.510640943
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 10.611     | 10.611     | 10.611     |   0.0 | 94.63
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.048211   | 0.048211   | 0.048211   |   0.0 |  0.43
+Output  | 0.37333    | 0.37333    | 0.37333    |   0.0 |  3.33
+Modify  | 0.038759   | 0.038759   | 0.038759   |   0.0 |  0.35
+Other   |            | 0.1419     |            |       |  1.27
+
+Nlocal:    5780 ave 5780 max 5780 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1065 ave 1065 max 1065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  92480 ave 92480 max 92480 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:11
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4
new file mode 100644
index 0000000000..16e51bd17a
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4
@@ -0,0 +1,148 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00216103 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 0.0 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0100717228668283   -0.162177519662199      14970.709092345                    0   -0.157514482753586 
+      50                0.005 0.000134061770654521    -128.226118665465    0.102634444037434                    0    -128.286182424672 
+     100                 0.01 7.67769618983817e-06    -131.374599259781   0.0222596977749883                    0    -131.428418504308 
+     150                0.015 6.02904602224806e-07    -132.224372015825  0.00974271828169071                    0    -132.273190134602 
+     200                 0.02 6.50197247050491e-07    -132.573383315469  0.00374227079785921                    0    -132.617565541034 
+     250                0.025  4.4053438575152e-07    -132.729743470508   0.0019334097282578                    0    -132.770567114743 
+     300                 0.03 2.78356316513274e-07    -132.819255077939  0.00124938353773497                    0    -132.857574876413 
+     350                0.035 1.79684785125388e-07    -132.882714312877 0.000973166792896165                    0    -132.919261229742 
+     400                 0.04 1.10949878459078e-07    -132.935357748213 0.000852955460997588                    0    -132.970786605995 
+     450                0.045 6.49064465617817e-08    -132.982991683198 0.000790741148426224                    0    -133.017887798927 
+     500                 0.05 3.70514666559952e-08    -133.027689959766  0.00074794913288275                    0     -133.06256199189 
+     550                0.055 2.12433814830885e-08    -133.070148920145  0.00071263732127117                    0    -133.105417593745 
+     600                 0.06 1.24676590171361e-08    -133.110772798503 0.000685051841817325                    0     -133.14676746928 
+     650                0.065 7.53611859129351e-09    -133.150126417754 0.000669443562813208                    0    -133.187094895708 
+     700                 0.07 4.63539338651321e-09    -133.189024073453 0.000669619853917953                    0    -133.227152349439 
+     750                0.075 2.82145833974835e-09     -133.22844627026 0.000687338035086961                    0    -133.267881315198 
+     800                 0.08 1.64378151566173e-09    -133.269413776733 0.000722197692175127                    0    -133.310284062463 
+     850                0.085   8.883310104497e-10    -133.312863108454 0.000771645398804486                    0    -133.355293578462 
+     900                 0.09 4.33874801863461e-10    -133.359507749172 0.000830255722998156                    0    -133.403626236688 
+     950                0.095  1.8812784924272e-10    -133.409630495316 0.000888348219681112                    0    -133.455560507802 
+    1000                  0.1 7.17748875671948e-11    -133.462806227865 0.000931427722404681                    0    -133.510640942679 
+Loop time of 3.46778 on 4 procs for 1000 steps with 5780 atoms
+
+99.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.157514482754     -133.509516066     -133.510640943
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.4063     | 2.831      | 3.0798     |  15.5 | 81.64
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.21179    | 0.45698    | 0.87844    |  38.4 | 13.18
+Output  | 0.1139     | 0.11396    | 0.11409    |   0.0 |  3.29
+Modify  | 0.0079708  | 0.0099814  | 0.011315   |   1.2 |  0.29
+Other   |            | 0.05581    |            |       |  1.61
+
+Nlocal:    1445 ave 1445 max 1445 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    555 ave 555 max 555 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  23120 ave 23120 max 23120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1
new file mode 100644
index 0000000000..0687081521
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1
@@ -0,0 +1,141 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00103903 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+# pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/cg
+# min_modify 	line spin_none discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Line search incompatible gneb (../min_spin_cg.cpp:105)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.331 | 8.331 | 8.331 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0100717228668283   -0.162177519662199     14970.7090923449                    0   -0.157514482753568 
+     100                 0.01 8.97646420937928e-06    -132.756468673032  0.00226858475243124                    0    -132.798812395869 
+     200                 0.02 5.70496744394871e-06    -133.065966570145 0.000924384747875191                    0    -133.105411060402 
+     300                 0.03 7.08166486347207e-06    -133.359072681024  0.00128114254070689                    0    -133.406669528642 
+     400                 0.04  4.6022497035281e-06    -133.668643035704  0.00082233479844806                    0    -133.725353643023 
+     500                 0.05 3.13737045264263e-06    -133.819548711647  0.00036967841746145                    0    -133.878037514586 
+     600                 0.06 2.55239214470191e-06    -133.889302880669 0.000169614248283497                    0    -133.948327309748 
+     700                 0.07 1.92236411979773e-06    -133.920147501261 7.31985644003828e-05                    0    -133.979597440787 
+     800                 0.08 1.40879742056288e-06    -133.933445418833 3.19349095035102e-05                    0    -133.993344750158 
+     900                 0.09 1.02629246258505e-06    -133.939321574068 1.44399877051466e-05                    0    -133.999611147323 
+    1000                  0.1 7.52253147839439e-07    -133.942032102451 6.85789018963958e-06                    0    -134.002604512511 
+Loop time of 10.4788 on 1 procs for 1000 steps with 5780 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.157514482754      -134.00257032     -134.002604513
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 2.122e-314 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.7413     | 9.7413     | 9.7413     |   0.0 | 92.96
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.033583   | 0.033583   | 0.033583   |   0.0 |  0.32
+Output  | 0.33068    | 0.33068    | 0.33068    |   0.0 |  3.16
+Modify  | 0.033124   | 0.033124   | 0.033124   |   0.0 |  0.32
+Other   |            | 0.3401     |            |       |  3.25
+
+Nlocal:    5780 ave 5780 max 5780 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1065 ave 1065 max 1065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  92480 ave 92480 max 92480 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:10
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4
new file mode 100644
index 0000000000..b1dfabd35e
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4
@@ -0,0 +1,141 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.000909805 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+# pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/cg
+# min_modify 	line spin_none discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Line search incompatible gneb (../min_spin_cg.cpp:105)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0100717228668283   -0.162177519662199      14970.709092345                    0   -0.157514482753586 
+     100                 0.01 8.97646420936397e-06    -132.756468673032  0.00226858475243123                    0     -132.79881239587 
+     200                 0.02  5.7049674439631e-06    -133.065966570145 0.000924384747875186                    0    -133.105411060402 
+     300                 0.03 7.08166486348038e-06    -133.359072681024  0.00128114254070688                    0    -133.406669528642 
+     400                 0.04 4.60224970353229e-06    -133.668643035703 0.000822334798448062                    0    -133.725353643022 
+     500                 0.05 3.13737045264193e-06    -133.819548711647 0.000369678417461456                    0    -133.878037514585 
+     600                 0.06 2.55239214469856e-06    -133.889302880669   0.0001696142482835                    0    -133.948327309746 
+     700                 0.07 1.92236411979341e-06    -133.920147501261 7.31985644003847e-05                    0    -133.979597440788 
+     800                 0.08 1.40879742055238e-06    -133.933445418833 3.19349095035109e-05                    0    -133.993344750158 
+     900                 0.09 1.02629246257047e-06    -133.939321574068 1.44399877051467e-05                    0    -133.999611147322 
+    1000                  0.1 7.52253147824893e-07    -133.942032102451 6.85789018963965e-06                    0    -134.002604512509 
+Loop time of 4.52508 on 4 procs for 1000 steps with 5780 atoms
+
+97.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.157514482754      -134.00257032     -134.002604513
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.7814     | 3.2998     | 3.808      |  25.6 | 72.92
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.37682    | 0.87552    | 1.3847     |  48.7 | 19.35
+Output  | 0.1621     | 0.16349    | 0.16483    |   0.3 |  3.61
+Modify  | 0.0099754  | 0.012567   | 0.014974   |   2.1 |  0.28
+Other   |            | 0.1737     |            |       |  3.84
+
+Nlocal:    1445 ave 1445 max 1445 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    555 ave 555 max 555 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  23120 ave 23120 max 23120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1
new file mode 100644
index 0000000000..b13ce090e4
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1
@@ -0,0 +1,139 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 3.96)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 1156 atoms
+  create_atoms CPU = 0.000702858 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  1156 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/lbfgs
+# min_modify 	line spin_cubic discrete_factor 10.0
+min_modify	norm max
+minimize        1.0e-15 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Line search incompatible gneb (../min_spin_lbfgs.cpp:109)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 2
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.748 | 7.748 | 7.748 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0205636053306396   -0.217760509274283     1541.29975585881                    0    -0.21723077139301 
+      50                0.005 0.000966655616832908    -19.2878369426356    0.312860071233838                    0    -19.3229939390148 
+     100                 0.01  0.00154452800146007    -19.5948898197921    0.365367666925721                    0    -19.6389064900417 
+     150                0.015 4.90329738897855e-05    -19.6962578948663 0.000386378108166462                    0     -19.704713985757 
+     200                 0.02 1.39636819172648e-06    -19.6975289055185 6.05740522809686e-05                    0    -19.7059135025107 
+     250                0.025 7.30255912392386e-08    -19.6975359463778 7.86050372080572e-09                    0    -19.7059189975433 
+     300                 0.03  2.3618265959146e-09    -19.6975359475117 1.36402599486317e-13                    0      -19.70591910974 
+     347               0.0347 1.42160367645076e-11    -19.6975359475123 2.85504863224395e-16                    0    -19.7059191162178 
+Loop time of 0.427798 on 1 procs for 347 steps with 1156 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = force tolerance
+  Energy initial, next-to-last, final = 
+       -0.217230771393     -19.7059191162     -19.7059191162
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 347 347
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.36166    | 0.36166    | 0.36166    |   0.0 | 84.54
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0016549  | 0.0016549  | 0.0016549  |   0.0 |  0.39
+Output  | 0.02019    | 0.02019    | 0.02019    |   0.0 |  4.72
+Modify  | 0.0024493  | 0.0024493  | 0.0024493  |   0.0 |  0.57
+Other   |            | 0.04184    |            |       |  9.78
+
+Nlocal:    1156 ave 1156 max 1156 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    213 ave 213 max 213 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  9248 ave 9248 max 9248 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9248
+Ave neighs/atom = 8
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4
new file mode 100644
index 0000000000..2a5917663e
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4
@@ -0,0 +1,139 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 3.96)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 1156 atoms
+  create_atoms CPU = 0.000618935 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  1156 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/lbfgs
+# min_modify 	line spin_cubic discrete_factor 10.0
+min_modify	norm max
+minimize        1.0e-15 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Line search incompatible gneb (../min_spin_lbfgs.cpp:109)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 2
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.619 | 7.619 | 7.619 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0205636053306396   -0.217760509274282     1541.29975585882                    0   -0.217230771393012 
+      50                0.005 0.000966655616837406    -19.2878369426356    0.312860071233841                    0    -19.3229939390148 
+     100                 0.01  0.00154452800191107    -19.5948898197917    0.365367666925029                    0    -19.6389064900413 
+     150                0.015 4.89955946750017e-05    -19.6962580067431 0.000385536538802408                    0    -19.7047140195852 
+     200                 0.02 5.66300530875654e-05    -19.6975252647309  9.8679922880911e-05                    0    -19.7059140354146 
+     250                0.025 5.21141123128679e-08    -19.6975359469038 2.52554968535685e-09                    0    -19.7059189333986 
+     300                 0.03  2.9845103782958e-09    -19.6975359475094 2.31782597655471e-11                    0    -19.7059191124033 
+     342               0.0342  1.0526549233076e-10    -19.6975359475123 3.65641352240487e-16                    0    -19.7059191178145 
+Loop time of 0.234594 on 4 procs for 342 steps with 1156 atoms
+
+93.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = force tolerance
+  Energy initial, next-to-last, final = 
+       -0.217230771393     -19.7059191178     -19.7059191178
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 342 342
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.097515   | 0.12325    | 0.15193    |   7.4 | 52.54
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.038284   | 0.061142   | 0.081045   |   8.1 | 26.06
+Output  | 0.008667   | 0.0086921  | 0.0087271  |   0.0 |  3.71
+Modify  | 0.00063705 | 0.00084341 | 0.0010526  |   0.0 |  0.36
+Other   |            | 0.04067    |            |       | 17.34
+
+Nlocal:    289 ave 289 max 289 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    111 ave 111 max 111 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  2312 ave 2312 max 2312 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9248
+Ave neighs/atom = 8
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1
new file mode 100644
index 0000000000..637c624a7c
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1
@@ -0,0 +1,126 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.00061512 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin/random 31 2.2
+  250 settings made for spin/random
+#set 		group all spin 2.2 1.0 1.0 -1.0
+
+pair_style 	spin/exchange 3.5
+pair_coeff 	* * exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
+fix 		1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.6
+  ghost atom cutoff = 3.6
+  binsize = 1.8, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.848 | 6.848 | 6.848 Mbytes
+Step Time v_magx v_magz v_magnorm v_tmag TotEng 
+       0                    0  -0.0285071136621457 -0.00948990815281275   0.0764569750905723     5048.56076237679   -0.701465876910694 
+     100                 0.01   -0.584953861980204  -0.0517163256267969    0.999992350892306 6.25556948778472e-05     -50.578744362023 
+     200                 0.02   -0.584864756506845  -0.0547143484057153    0.999999990495506 3.49782260454062e-06    -50.5787971409244 
+     300                 0.03     -0.5847600493607  -0.0578846348986585    0.999999999988174 3.83095226805016e-06    -50.5788061208586 
+     400                 0.04   -0.584642875238893  -0.0612373075362701    0.999999999999986 4.28575832708226e-06    -50.5788161053511 
+     500                 0.05   -0.584511765589529  -0.0647826190376231                    1 4.79421486949086e-06    -50.5788272748485 
+     600                 0.06   -0.584365074206159  -0.0685313536438759                    1 5.36242072641834e-06    -50.5788397688161 
+     700                 0.07   -0.584200963215273   -0.072494846958872                    1 5.99725249459222e-06    -50.5788537427261 
+     800                 0.08   -0.584017381477007  -0.0766850043611195    0.999999999999999 6.70634191991825e-06    -50.5788693699026 
+     900                 0.09   -0.583812040722351  -0.0811143180675364    0.999999999999999 7.49814943594148e-06    -50.5788868434701 
+    1000                  0.1   -0.583582389243979  -0.0857958823565731    0.999999999999998 8.38204259112222e-06    -50.5789063784909 
+Loop time of 0.215249 on 1 procs for 1000 steps with 250 atoms
+
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.701465876911     -50.5789061722     -50.5789063785
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.19278    | 0.19278    | 0.19278    |   0.0 | 89.56
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0062225  | 0.0062225  | 0.0062225  |   0.0 |  2.89
+Output  | 0.0085046  | 0.0085046  | 0.0085046  |   0.0 |  3.95
+Modify  | 0.0017273  | 0.0017273  | 0.0017273  |   0.0 |  0.80
+Other   |            | 0.006012   |            |       |  2.79
+
+Nlocal:    250 ave 250 max 250 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    315 ave 315 max 315 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  3200 ave 3200 max 3200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3200
+Ave neighs/atom = 12.8
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4
new file mode 100644
index 0000000000..70f395ab08
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4
@@ -0,0 +1,126 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.000644922 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin/random 31 2.2
+  250 settings made for spin/random
+#set 		group all spin 2.2 1.0 1.0 -1.0
+
+pair_style 	spin/exchange 3.5
+pair_coeff 	* * exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
+fix 		1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.6
+  ghost atom cutoff = 3.6
+  binsize = 1.8, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.828 | 6.829 | 6.829 Mbytes
+Step Time v_magx v_magz v_magnorm v_tmag TotEng 
+       0                    0  -0.0285071136621457 -0.00948990815281275   0.0764569750905723      5048.5607623768   -0.701465876910695 
+     100                 0.01   -0.584953861980204  -0.0517163256267969    0.999992350892306 6.25556948778489e-05    -50.5787443620229 
+     200                 0.02   -0.584864756506845  -0.0547143484057154    0.999999990495506 3.49782260454051e-06    -50.5787971409246 
+     300                 0.03     -0.5847600493607  -0.0578846348986585    0.999999999988173 3.83095226804998e-06    -50.5788061208592 
+     400                 0.04   -0.584642875238891    -0.06123730753627    0.999999999999984 4.28575832708228e-06    -50.5788161053499 
+     500                 0.05   -0.584511765589526  -0.0647826190376232    0.999999999999999 4.79421486949061e-06    -50.5788272748473 
+     600                 0.06   -0.584365074206158  -0.0685313536438759    0.999999999999999 5.36242072641826e-06    -50.5788397688148 
+     700                 0.07   -0.584200963215272  -0.0724948469588718                    1 5.99725249459218e-06    -50.5788537427249 
+     800                 0.08   -0.584017381477007  -0.0766850043611196                    1  6.7063419199184e-06    -50.5788693699014 
+     900                 0.09   -0.583812040722352  -0.0811143180675365    0.999999999999998 7.49814943594153e-06    -50.5788868434688 
+    1000                  0.1   -0.583582389243979  -0.0857958823565732    0.999999999999999 8.38204259112203e-06    -50.5789063784897 
+Loop time of 0.229203 on 4 procs for 1000 steps with 250 atoms
+
+85.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.701465876911     -50.5789061722     -50.5789063785
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.06774    | 0.080677   | 0.097769   |   4.4 | 35.20
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.10574    | 0.11072    | 0.11498    |   1.0 | 48.31
+Output  | 0.0061452  | 0.0061803  | 0.0062776  |   0.1 |  2.70
+Modify  | 0.00074291 | 0.00096381 | 0.0014563  |   0.0 |  0.42
+Other   |            | 0.03066    |            |       | 13.38
+
+Nlocal:    62.5 ave 65 max 60 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    217.5 ave 240 max 195 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  800 ave 825 max 775 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3200
+Ave neighs/atom = 12.8
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

From 51743655703cbfa3e31c41894316df5f451343bb Mon Sep 17 00:00:00 2001
From: ares20105 <ares201005@gmail.com>
Date: Wed, 20 Nov 2019 13:21:41 -0700
Subject: [PATCH 059/199] add force modifications. Previous code does not call
 force modify, thus the dynamical matrix calculation does not work for other
 potentials defined via modify

---
 src/USER-PHONON/dynamical_matrix.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp
index 1495219124..6bb843c16e 100644
--- a/src/USER-PHONON/dynamical_matrix.cpp
+++ b/src/USER-PHONON/dynamical_matrix.cpp
@@ -19,6 +19,7 @@
 #include "improper.h"
 #include "kspace.h"
 #include "update.h"
+#include "modify.h"
 #include "neighbor.h"
 #include "pair.h"
 #include "timer.h"
@@ -385,6 +386,7 @@ void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude)
 void DynamicalMatrix::update_force()
 {
     force_clear();
+    int n_post_force = modify->n_post_force;
 
     if (pair_compute_flag) {
         force->pair->compute(eflag,vflag);
@@ -405,6 +407,11 @@ void DynamicalMatrix::update_force()
         comm->reverse_comm();
         timer->stamp(Timer::COMM);
     }
+
+    // force modifications, 
+    if (n_post_force) modify->post_force(vflag);
+    timer->stamp(Timer::MODIFY);
+
     ++ update->nsteps;
 }
 

From c14ac53306d9c880f0fbaf511135d2e3b60846e5 Mon Sep 17 00:00:00 2001
From: lucienPan <lucien.pan0927@gmail.com>
Date: Thu, 21 Nov 2019 12:28:18 -0500
Subject: [PATCH 060/199] Patch of class2 dihedral in OMP and Kokkos

---
 src/KOKKOS/dihedral_class2_kokkos.cpp | 5 +++++
 src/USER-OMP/dihedral_class2_omp.cpp  | 5 +++++
 2 files changed, 10 insertions(+)

diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index 4b8d171f61..5f304d2620 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -253,6 +253,11 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
   const F_FLOAT costh13 = c0;
   const F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
 
+  costh12 = MAX(MIN(costh12, 1.0), -1.0);
+  costh13 = MAX(MIN(costh13, 1.0), -1.0);
+  costh23 = MAX(MIN(costh23, 1.0), -1.0);
+  c0 = costh13;
+
   // cos and sin of 2 angles and final c
 
   F_FLOAT sin2 = MAX(1.0 - costh12*costh12,0.0);
diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp
index a54603cc39..215677612b 100644
--- a/src/USER-OMP/dihedral_class2_omp.cpp
+++ b/src/USER-OMP/dihedral_class2_omp.cpp
@@ -159,6 +159,11 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
     costh13 = c0;
     costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
 
+    costh12 = MAX(MIN(costh12, 1.0), -1.0);
+    costh13 = MAX(MIN(costh13, 1.0), -1.0);
+    costh23 = MAX(MIN(costh23, 1.0), -1.0);
+    c0 = costh13;
+
     // cos and sin of 2 angles and final c
 
     sin2 = MAX(1.0 - costh12*costh12,0.0);

From babab9b5f770397497adb6d4535e1a9df33a1307 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 21 Nov 2019 17:09:24 -0500
Subject: [PATCH 061/199] replace non-UTF-8 compliant character with ASCII

---
 src/USER-INTEL/intel_intrinsics.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/USER-INTEL/intel_intrinsics.h b/src/USER-INTEL/intel_intrinsics.h
index 069eb5bed5..ee20cd1119 100644
--- a/src/USER-INTEL/intel_intrinsics.h
+++ b/src/USER-INTEL/intel_intrinsics.h
@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing author: Markus Höhnerbach (RWTH)
+   Contributing author: Markus Hoehnerbach (RWTH)
 ------------------------------------------------------------------------- */
 
 // This file provides an intrinsics abstraction that allows access to the

From 0085aaabd292270f8f254f0a61c65728b5440cef Mon Sep 17 00:00:00 2001
From: lucienPan <lucien.pan0927@gmail.com>
Date: Thu, 21 Nov 2019 18:00:18 -0500
Subject: [PATCH 062/199] Patch of Dihedral class2 KOKKOS

Since the costh12 costh13 costh13 and costh0 are declared as const,
a hack using const_cast is used to work around this.
---
 src/KOKKOS/dihedral_class2_kokkos.cpp | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index 5f304d2620..39be838d7e 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -253,10 +253,16 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
   const F_FLOAT costh13 = c0;
   const F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
 
-  costh12 = MAX(MIN(costh12, 1.0), -1.0);
-  costh13 = MAX(MIN(costh13, 1.0), -1.0);
-  costh23 = MAX(MIN(costh23, 1.0), -1.0);
-  c0 = costh13;
+  {
+    F_FLOAT& ctmp12 = const_cast<F_FLOAT&>(costh12);
+    F_FLOAT& ctmp13 = const_cast<F_FLOAT&>(costh13);
+    F_FLOAT& ctmp23 = const_cast<F_FLOAT&>(costh23);
+    F_FLOAT& ctmp0  = const_cast<F_FLOAT&>(c0);
+    ctmp12 = MAX(MIN(costh12, 1.0), -1.0);
+    ctmp13 = MAX(MIN(costh13, 1.0), -1.0);
+    ctmp23 = MAX(MIN(costh23, 1.0), -1.0);
+    ctmp0  = costh13;
+  }
 
   // cos and sin of 2 angles and final c
 

From 54f998bde53e67a7ea263b04bae65275399b26b5 Mon Sep 17 00:00:00 2001
From: lucienPan <lucien.pan0927@gmail.com>
Date: Thu, 21 Nov 2019 18:00:18 -0500
Subject: [PATCH 063/199] Patch of Dihedral class2 KOKKOS

Since the costh12, costh13, costh23 and c0 are declared as const,
a hack using const_cast is used to work around this.
---
 src/KOKKOS/dihedral_class2_kokkos.cpp | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index 5f304d2620..39be838d7e 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -253,10 +253,16 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
   const F_FLOAT costh13 = c0;
   const F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
 
-  costh12 = MAX(MIN(costh12, 1.0), -1.0);
-  costh13 = MAX(MIN(costh13, 1.0), -1.0);
-  costh23 = MAX(MIN(costh23, 1.0), -1.0);
-  c0 = costh13;
+  {
+    F_FLOAT& ctmp12 = const_cast<F_FLOAT&>(costh12);
+    F_FLOAT& ctmp13 = const_cast<F_FLOAT&>(costh13);
+    F_FLOAT& ctmp23 = const_cast<F_FLOAT&>(costh23);
+    F_FLOAT& ctmp0  = const_cast<F_FLOAT&>(c0);
+    ctmp12 = MAX(MIN(costh12, 1.0), -1.0);
+    ctmp13 = MAX(MIN(costh13, 1.0), -1.0);
+    ctmp23 = MAX(MIN(costh23, 1.0), -1.0);
+    ctmp0  = costh13;
+  }
 
   // cos and sin of 2 angles and final c
 

From 89bb2ef83fd8e22fc534fe0a7b6e71dc2e4e0484 Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Fri, 22 Nov 2019 12:07:05 -0700
Subject: [PATCH 064/199] Commit JT 112219 - improved figure in precession/spin
 documentation - corrected other pair/spin interactions

---
 doc/src/JPG/zeeman_langevin.jpg   | Bin 46268 -> 174590 bytes
 src/SPIN/pair_spin_dipole_cut.cpp |   2 +-
 src/SPIN/pair_spin_dmi.cpp        |   7 +++----
 src/SPIN/pair_spin_exchange.cpp   |   3 ++-
 src/SPIN/pair_spin_magelec.cpp    |  26 +++++++++++++-------------
 src/SPIN/pair_spin_neel.cpp       |   2 +-
 6 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/doc/src/JPG/zeeman_langevin.jpg b/doc/src/JPG/zeeman_langevin.jpg
index c42c49b6c0a5c37387965c779ccbf1fa07d53959..53ce77d2a8d94d200577e8e1b0164ed238d2d483 100644
GIT binary patch
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diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp
index a393fe7021..a7372b480d 100644
--- a/src/SPIN/pair_spin_dipole_cut.cpp
+++ b/src/SPIN/pair_spin_dipole_cut.cpp
@@ -252,7 +252,7 @@ void PairSpinDipoleCut::compute(int eflag, int vflag)
       if (eflag) {
         if (rsq <= local_cut2) {
           evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-          evdwl *= hbar;
+          evdwl *= 0.5*hbar;
         }
       } else evdwl = 0.0;
 
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index af68c0d256..04c2dc408d 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -319,7 +319,6 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
   // if interaction applies to type ii,
   // locflag = 1 and compute pair interaction
 
-  //i = ilist[ii];
   if (locflag == 1) {
 
     xi[0] = x[ii][0];
@@ -373,9 +372,9 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double
   dmiy = eij[2]*v_dmx[itype][jtype] - eij[0]*v_dmz[itype][jtype];
   dmiz = eij[0]*v_dmy[itype][jtype] - eij[1]*v_dmx[itype][jtype];
 
-  fmi[0] -= 2.0*(dmiy*spj[2] - dmiz*spj[1]);
-  fmi[1] -= 2.0*(dmiz*spj[0] - dmix*spj[2]);
-  fmi[2] -= 2.0*(dmix*spj[1] - dmiy*spj[0]);
+  fmi[0] -= (dmiy*spj[2] - dmiz*spj[1]);
+  fmi[1] -= (dmiz*spj[0] - dmix*spj[2]);
+  fmi[2] -= (dmix*spj[1] - dmiy*spj[0]);
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index 2aa8b99f32..6eacb04ee3 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -242,7 +242,8 @@ void PairSpinExchange::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        evdwl *= hbar;
+        evdwl *= 0.5*hbar;
+        // evdwl *= hbar;
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
index 664f8df56c..fabad4ae4d 100644
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@@ -251,7 +251,7 @@ void PairSpinMagelec::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        evdwl *= hbar;
+        evdwl *= 0.5*hbar;
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
@@ -362,17 +362,17 @@ void PairSpinMagelec::compute_magelec(int i, int j, double eij[3], double fmi[3]
   vy = v_mey[itype][jtype];
   vz = v_mez[itype][jtype];
 
-  meix = vy*eij[2] - vz*eij[1];
-  meiy = vz*eij[0] - vx*eij[2];
-  meiz = vx*eij[1] - vy*eij[0];
+  meix = (vy*eij[2] - vz*eij[1]);
+  meiy = (vz*eij[0] - vx*eij[2]);
+  meiz = (vx*eij[1] - vy*eij[0]);
 
   meix *= ME[itype][jtype];
   meiy *= ME[itype][jtype];
   meiz *= ME[itype][jtype];
 
-  fmi[0] += spj[1]*meiz - spj[2]*meiy;
-  fmi[1] += spj[2]*meix - spj[0]*meiz;
-  fmi[2] += spj[0]*meiy - spj[1]*meix;
+  fmi[0] += (spj[1]*meiz - spj[2]*meiy);
+  fmi[1] += (spj[2]*meix - spj[0]*meiz);
+  fmi[2] += (spj[0]*meiy - spj[1]*meix);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -391,17 +391,17 @@ void PairSpinMagelec::compute_magelec_mech(int i, int j, double fi[3], double sp
   vy = v_mey[itype][jtype];
   vz = v_mez[itype][jtype];
 
-  meix = spi[1]*spi[2] - spi[2]*spj[1];
-  meiy = spi[2]*spi[0] - spi[0]*spj[2];
-  meiz = spi[0]*spi[1] - spi[1]*spj[0];
+  meix = (spi[1]*spi[2] - spi[2]*spj[1]);
+  meiy = (spi[2]*spi[0] - spi[0]*spj[2]);
+  meiz = (spi[0]*spi[1] - spi[1]*spj[0]);
 
   meix *= ME_mech[itype][jtype];
   meiy *= ME_mech[itype][jtype];
   meiz *= ME_mech[itype][jtype];
 
-  fi[0] += meiy*vz - meiz*vy;
-  fi[1] += meiz*vx - meix*vz;
-  fi[2] += meix*vy - meiy*vx;
+  fi[0] += (meiy*vz - meiz*vy);
+  fi[1] += (meiz*vx - meix*vz);
+  fi[2] += (meix*vy - meiy*vx);
 
 }
 
diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp
index a3114497a6..4a5d453de2 100644
--- a/src/SPIN/pair_spin_neel.cpp
+++ b/src/SPIN/pair_spin_neel.cpp
@@ -260,7 +260,7 @@ void PairSpinNeel::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl = (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        evdwl *= hbar;
+        evdwl *= 0.5*hbar;
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,

From 8bca0b13f182e1c440df5838bf83185a2862201c Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Fri, 22 Nov 2019 16:29:37 -0700
Subject: [PATCH 065/199] Commit2 JT 112219 - correcting issue in
 src/SPIN/atom_vec_spin.cpp (inconsistency packing/unpacking hybrid) -
 rerunning all examples with corrections of former commit

---
 doc/src/pair_spin_exchange.rst                |   4 +-
 doc/txt/pair_spin_exchange.txt                |   5 +-
 examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1  | 122 +++++-----
 examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4  |  20 +-
 .../log.19Nov19.spin.cobalt_fcc.g++.1         |  64 ++---
 .../log.19Nov19.spin.cobalt_fcc.g++.4         |  22 +-
 .../log.19Nov19.spin.cobalt_hcp.g++.1         | 220 +++++++++---------
 .../log.19Nov19.spin.cobalt_hcp.g++.4         |  22 +-
 .../log.19Nov19.spin.iron_dipole_cut.g++.1    |  24 +-
 .../log.19Nov19.spin.iron_dipole_cut.g++.4    |  20 +-
 .../log.19Nov19.spin.iron_dipole_ewald.g++.1  |  28 +--
 .../log.19Nov19.spin.iron_dipole_ewald.g++.4  |  22 +-
 .../log.19Nov19.spin.iron_dipole_pppm.g++.1   |  26 +--
 .../log.19Nov19.spin.iron_dipole_pppm.g++.4   |  22 +-
 .../SPIN/iron/log.19Nov19.spin.iron.g++.1     |  64 ++---
 .../SPIN/iron/log.19Nov19.spin.iron.g++.4     |  22 +-
 .../iron/log.19Nov19.spin.iron_cubic.g++.1    |  60 ++---
 .../iron/log.19Nov19.spin.iron_cubic.g++.4    |  22 +-
 .../SPIN/nickel/log.19Nov19.spin.nickel.g++.1 |  64 ++---
 .../SPIN/nickel/log.19Nov19.spin.nickel.g++.4 |  22 +-
 .../log.19Nov19.spin.nickel_cubic.g++.1       |  64 ++---
 .../log.19Nov19.spin.nickel_cubic.g++.4       |  22 +-
 .../log.19Nov19.spin.read_data.g++.1          |  44 ++--
 .../log.19Nov19.spin.read_data.g++.4          |  22 +-
 .../log.19Nov19.spin.restart.g++.1            |  42 ++--
 .../log.19Nov19.spin.restart.g++.4            |  20 +-
 .../log.19Nov19.spin.write_restart.g++.1      |  40 ++--
 .../log.19Nov19.spin.write_restart.g++.4      |  20 +-
 .../log.19Nov19.spin.setforce.g++.1           |  42 ++--
 .../log.19Nov19.spin.setforce.g++.4           |  18 +-
 .../spinmin/log.19Nov19.spin.bfo_min.g++.1    |  62 ++---
 .../spinmin/log.19Nov19.spin.bfo_min.g++.4    |  18 +-
 .../spinmin/log.19Nov19.spin.bfo_min_cg.g++.1 |  42 ++--
 .../spinmin/log.19Nov19.spin.bfo_min_cg.g++.4 |  18 +-
 .../log.19Nov19.spin.bfo_min_lbfgs.g++.1      |  38 +--
 .../log.19Nov19.spin.bfo_min_lbfgs.g++.4      |  16 +-
 .../spinmin/log.19Nov19.spin.iron_min.g++.1   |  38 +--
 .../spinmin/log.19Nov19.spin.iron_min.g++.4   |  16 +-
 .../llg_exchange.py                           |   4 +-
 .../plot_precession.py                        |   2 +-
 ...bench-exchange.sh => run-test-exchange.sh} |   0
 .../validation_damped_exchange/two_spins.data |  22 --
 .../{run-bench-prec.sh => run-test-prec.sh}   |   0
 .../{run-bench-prec.sh => run-test-prec.sh}   |   0
 src/SPIN/atom_vec_spin.cpp                    |   9 +-
 src/SPIN/pair_spin_dipole_long.cpp            |   2 +-
 46 files changed, 737 insertions(+), 759 deletions(-)
 rename examples/SPIN/test_problems/validation_damped_exchange/{run-bench-exchange.sh => run-test-exchange.sh} (100%)
 delete mode 100644 examples/SPIN/test_problems/validation_damped_exchange/two_spins.data
 rename examples/SPIN/test_problems/validation_damped_precession/{run-bench-prec.sh => run-test-prec.sh} (100%)
 rename examples/SPIN/test_problems/validation_langevin_precession/{run-bench-prec.sh => run-test-prec.sh} (100%)

diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst
index 5f7a630c60..add69f272c 100644
--- a/doc/src/pair_spin_exchange.rst
+++ b/doc/src/pair_spin_exchange.rst
@@ -35,7 +35,9 @@ pairs of magnetic spins:
 
 where si and sj are two neighboring magnetic spins of two particles,
 rij = \|ri - rj\| is the inter-atomic distance between the two particles,
-and J(rij) is a function defining the intensity and the sign of the exchange
+and
+
+J(rij) is a function defining the intensity and the sign of the exchange
 interaction for different neighboring shells. This function is defined as:
 
 .. image:: Eqs/pair_spin_exchange_function.jpg
diff --git a/doc/txt/pair_spin_exchange.txt b/doc/txt/pair_spin_exchange.txt
index 7bc6b5fef7..dea2d57f62 100644
--- a/doc/txt/pair_spin_exchange.txt
+++ b/doc/txt/pair_spin_exchange.txt
@@ -30,8 +30,9 @@ pairs of magnetic spins:
 :c,image(Eqs/pair_spin_exchange_interaction.jpg)
 
 where si and sj are two neighboring magnetic spins of two particles,
-rij = |ri - rj| is the inter-atomic distance between the two particles,
-and J(rij) is a function defining the intensity and the sign of the exchange
+rij = |ri - rj| is the inter-atomic distance between the two
+particles. The summation is over pairs of nearest neighbours. 
+J(rij) is a function defining the intensity and the sign of the exchange
 interaction for different neighboring shells. This function is defined as:
 
 :c,image(Eqs/pair_spin_exchange_function.jpg)
diff --git a/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1 b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1
index e7eb5cea59..b14210e9d0 100644
--- a/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1
+++ b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 5780 atoms
-  create_atoms CPU = 0.00234604 secs
+  create_atoms CPU = 0.00226784 secs
 
 # setting mass, mag. moments, and interactions for bfo
 
@@ -82,71 +82,71 @@ Neighbor list info ...
       bin: none
 Per MPI rank memory allocation (min/avg/max) = 8.154 | 8.154 | 8.154 Mbytes
 Step Time v_magnorm PotEng KinEng v_emag Temp TotEng 
-       0            0  0.010071723  -0.11868622            0  -0.12966919            0  -0.11868622 
-      10        0.002  0.010030399  -0.37068593            0  -0.38171598            0  -0.37068593 
-      20        0.004 0.0099889925   -0.6223216            0   -0.6334048            0   -0.6223216 
-      30        0.006 0.0099474775  -0.87359358            0  -0.88473539            0  -0.87359358 
-      40        0.008 0.0099058307   -1.1245034            0   -1.1357086            0   -1.1245034 
-      50         0.01 0.0098640297   -1.3750538            0   -1.3863265            0   -1.3750538 
-      60        0.012 0.0098220536   -1.6252482            0   -1.6365919            0   -1.6252482 
-      70        0.014 0.0097798824   -1.8750914            0   -1.8865086            0   -1.8750914 
-      80        0.016 0.0097374974   -2.1245886            0   -2.1360814            0   -2.1245886 
-      90        0.018 0.0096948809   -2.3737458            0   -2.3853154            0   -2.3737458 
-     100         0.02  0.009652016   -2.6225698            0   -2.6342168            0   -2.6225698 
-     110        0.022 0.0096088867   -2.8710677            0   -2.8827919            0   -2.8710677 
-     120        0.024 0.0095654777   -3.1192468            0   -3.1310475            0   -3.1192468 
-     130        0.026 0.0095217747    -3.367115            0   -3.3789906            0    -3.367115 
-     140        0.028 0.0094777639     -3.61468            0   -3.6266285            0     -3.61468 
-     150         0.03 0.0094334324   -3.8619496            0   -3.8739683            0   -3.8619496 
-     160        0.032 0.0093887681   -4.1089316            0   -4.1210173            0   -4.1089316 
-     170        0.034 0.0093437598   -4.3556334            0   -4.3677824            0   -4.3556334 
-     180        0.036 0.0092983974   -4.6020625            0   -4.6142704            0   -4.6020625 
-     190        0.038 0.0092526719   -4.8482255            0   -4.8604877            0   -4.8482255 
-     200         0.04 0.0092065757   -5.0941291            0   -5.1064403            0   -5.0941291 
-     210        0.042 0.0091601026   -5.3397792            0   -5.3521339            0   -5.3397792 
-     220        0.044 0.0091132479   -5.5851813            0   -5.5975736            0   -5.5851813 
-     230        0.046  0.009066009   -5.8303404            0    -5.842764            0   -5.8303404 
-     240        0.048 0.0090183848   -6.0752609            0   -6.0877092            0   -6.0752609 
-     250         0.05 0.0089703766   -6.3199467            0   -6.3324129            0   -6.3199467 
-     260        0.052 0.0089219875   -6.5644011            0   -6.5768782            0   -6.5644011 
-     270        0.054  0.008873223    -6.808627            0   -6.8211078            0    -6.808627 
-     280        0.056 0.0088240907   -7.0526266            0   -7.0651038            0   -7.0526266 
-     290        0.058 0.0087746007    -7.296402            0   -7.3088682            0    -7.296402 
-     300         0.06 0.0087247649   -7.5399545            0   -7.5524024            0   -7.5399545 
-     310        0.062 0.0086745977   -7.7832854            0   -7.7957077            0   -7.7832854 
-     320        0.064 0.0086241151   -8.0263956            0    -8.038785            0   -8.0263956 
-     330        0.066 0.0085733351   -8.2692858            0    -8.281635            0   -8.2692858 
-     340        0.068 0.0085222773   -8.5119564            0   -8.5242586            0   -8.5119564 
-     350         0.07 0.0084709628   -8.7544078            0   -8.7666562            0   -8.7544078 
-     360        0.072 0.0084194137   -8.9966403            0   -9.0088285            0   -8.9966403 
-     370        0.074 0.0083676531   -9.2386543            0   -9.2507761            0   -9.2386543 
-     380        0.076 0.0083157047   -9.4804501            0   -9.4924997            0   -9.4804501 
-     390        0.078 0.0082635926   -9.7220281            0   -9.7340001            0   -9.7220281 
-     400         0.08 0.0082113413   -9.9633888            0   -9.9752784            0   -9.9633888 
-     410        0.082 0.0081589748   -10.204533            0   -10.216336            0   -10.204533 
-     420        0.084 0.0081065174   -10.445462            0   -10.457173            0   -10.445462 
-     430        0.086 0.0080539926   -10.686176            0   -10.697793            0   -10.686176 
-     440        0.088 0.0080014236   -10.926676            0   -10.938197            0   -10.926676 
-     450         0.09  0.007948833   -11.166966            0   -11.178387            0   -11.166966 
-     460        0.092 0.0078962428   -11.407045            0   -11.418366            0   -11.407045 
-     470        0.094 0.0078436745   -11.646917            0   -11.658136            0   -11.646917 
-     480        0.096 0.0077911488   -11.886583            0     -11.8977            0   -11.886583 
-     490        0.098 0.0077386861   -12.126047            0   -12.137063            0   -12.126047 
-     500          0.1 0.0076863063   -12.365311            0   -12.376226            0   -12.365311 
-Loop time of 19.2298 on 1 procs for 500 steps with 5780 atoms
+       0            0  0.010071723 -0.059343109            0  -0.13132609            0 -0.059343109 
+      10        0.002   0.01003044  -0.18537022            0  -0.38338861            0  -0.18537022 
+      20        0.004 0.0099890716  -0.31121926            0  -0.63509581            0  -0.31121926 
+      30        0.006 0.0099475919  -0.43689013            0  -0.88644739            0  -0.43689013 
+      40        0.008 0.0099059782   -0.5623833            0   -1.1374442            0   -0.5623833 
+      50         0.01 0.0098642085  -0.68769978            0    -1.388088            0  -0.68769978 
+      60        0.012 0.0098222618  -0.81284106            0   -1.6383818            0  -0.81284106 
+      70        0.014 0.0097801186  -0.93780907            0   -1.8883294            0  -0.93780907 
+      80        0.016 0.0097377603   -1.0626062            0   -2.1379352            0   -1.0626062 
+      90        0.018 0.0096951693    -1.187235            0   -2.3872045            0    -1.187235 
+     100         0.02 0.0096523288   -1.3116986            0   -2.6361432            0   -1.3116986 
+     110        0.022 0.0096092227   -1.4360002            0   -2.8847577            0   -1.4360002 
+     120        0.024  0.009565836   -1.5601431            0   -3.1330547            0   -1.5601431 
+     130        0.026 0.0095221542   -1.6841309            0   -3.3810411            0   -1.6841309 
+     140        0.028 0.0094781635   -1.8079673            0   -3.6287241            0   -1.8079673 
+     150         0.03 0.0094338509   -1.9316557            0   -3.8761109            0   -1.9316557 
+     160        0.032 0.0093892044   -2.0551997            0   -4.1232085            0   -2.0551997 
+     170        0.034 0.0093442126    -2.178603            0    -4.370024            0    -2.178603 
+     180        0.036 0.0092988654   -2.3018687            0   -4.6165639            0   -2.3018687 
+     190        0.038 0.0092531537   -2.4250002            0   -4.8628348            0   -2.4250002 
+     200         0.04 0.0092070698   -2.5480003            0   -5.1088426            0   -2.5480003 
+     210        0.042 0.0091606073    -2.670872            0   -5.3545929            0    -2.670872 
+     220        0.044 0.0091137617   -2.7936178            0   -5.6000909            0   -2.7936178 
+     230        0.046 0.0090665298   -2.9162399            0   -5.8453412            0   -2.9162399 
+     240        0.048 0.0090189108   -3.0387405            0   -6.0903478            0   -3.0387405 
+     250         0.05 0.0089709056   -3.1611214            0   -6.3351146            0   -3.1611214 
+     260        0.052 0.0089225173   -3.2833841            0   -6.5796445            0   -3.2833841 
+     270        0.054 0.0088737511   -3.4055299            0   -6.8239403            0   -3.4055299 
+     280        0.056 0.0088246147     -3.52756            0   -7.0680043            0     -3.52756 
+     290        0.058 0.0087751176   -3.6494754            0   -7.3118383            0   -3.6494754 
+     300         0.06  0.008725272   -3.7712768            0   -7.5554438            0   -3.7712768 
+     310        0.062 0.0086750916   -3.8929648            0   -7.7988222            0   -3.8929648 
+     320        0.064 0.0086245927   -4.0145399            0   -8.0419744            0   -4.0145399 
+     330        0.066 0.0085737928   -4.1360026            0   -8.2849013            0   -4.1360026 
+     340        0.068 0.0085227116   -4.2573532            0   -8.5276035            0   -4.2573532 
+     350         0.07 0.0084713698    -4.378592            0   -8.7700818            0    -4.378592 
+     360        0.072 0.0084197895   -4.4997194            0   -9.0123367            0   -4.4997194 
+     370        0.074 0.0083679936   -4.6207358            0   -9.2543688            0   -4.6207358 
+     380        0.076 0.0083160058   -4.7416414            0    -9.496179            0   -4.7416414 
+     390        0.078 0.0082638503   -4.8624367            0   -9.7377681            0   -4.8624367 
+     400         0.08 0.0082115512   -4.9831222            0   -9.9791371            0   -4.9831222 
+     410        0.082 0.0081591329   -5.1036986            0   -10.220287            0   -5.1036986 
+     420        0.084 0.0081066195   -5.2241665            0    -10.46122            0   -5.2241665 
+     430        0.086 0.0080540347   -5.3445267            0   -10.701936            0   -5.3445267 
+     440        0.088  0.008001402   -5.4647802            0   -10.942439            0   -5.4647802 
+     450         0.09 0.0079487439   -5.5849281            0    -11.18273            0   -5.5849281 
+     460        0.092 0.0078960829   -5.7049716            0   -11.422811            0   -5.7049716 
+     470        0.094 0.0078434404    -5.824912            0   -11.662686            0    -5.824912 
+     480        0.096 0.0077908378   -5.9447508            0   -11.902357            0   -5.9447508 
+     490        0.098 0.0077382955   -6.0644896            0   -12.141828            0   -6.0644896 
+     500          0.1 0.0076858338   -6.1841301            0   -12.381101            0   -6.1841301 
+Loop time of 13.543 on 1 procs for 500 steps with 5780 atoms
 
-Performance: 0.449 ns/day, 53.416 hours/ns, 26.001 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.638 ns/day, 37.619 hours/ns, 36.919 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.2712     | 5.2712     | 5.2712     |   0.0 | 27.41
+Pair    | 3.8138     | 3.8138     | 3.8138     |   0.0 | 28.16
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.039467   | 0.039467   | 0.039467   |   0.0 |  0.21
-Output  | 0.060013   | 0.060013   | 0.060013   |   0.0 |  0.31
-Modify  | 13.82      | 13.82      | 13.82      |   0.0 | 71.87
-Other   |            | 0.03928    |            |       |  0.20
+Comm    | 0.011875   | 0.011875   | 0.011875   |   0.0 |  0.09
+Output  | 0.049726   | 0.049726   | 0.049726   |   0.0 |  0.37
+Modify  | 9.655      | 9.655      | 9.655      |   0.0 | 71.29
+Other   |            | 0.01262    |            |       |  0.09
 
 Nlocal:    5780 ave 5780 max 5780 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -164,4 +164,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:19
+Total wall time: 0:00:13
diff --git a/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4 b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4
index 8e3990787a..8c701c93c1 100644
--- a/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4
+++ b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
   2 by 2 by 1 MPI processor grid
 create_atoms 	1 box
 Created 5780 atoms
-  create_atoms CPU = 0.000843048 secs
+  create_atoms CPU = 0.00149798 secs
 
 # setting mass, mag. moments, and interactions for bfo
 
@@ -133,20 +133,20 @@ Step Time v_magnorm PotEng KinEng v_emag Temp TotEng
      480        0.096 0.0077911486   -11.886583            0     -11.8977            0   -11.886583 
      490        0.098  0.007738686   -12.126047            0   -12.137063            0   -12.126047 
      500          0.1 0.0076863062   -12.365311            0   -12.376226            0   -12.365311 
-Loop time of 5.69323 on 4 procs for 500 steps with 5780 atoms
+Loop time of 3.94852 on 4 procs for 500 steps with 5780 atoms
 
-Performance: 1.518 ns/day, 15.815 hours/ns, 87.824 timesteps/s
-99.5% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 2.188 ns/day, 10.968 hours/ns, 126.630 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.2634     | 1.2866     | 1.3017     |   1.3 | 22.60
+Pair    | 0.97416    | 0.98668    | 1.0022     |   1.0 | 24.99
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.17396    | 0.18913    | 0.21531    |   3.6 |  3.32
-Output  | 0.020815   | 0.021116   | 0.021569   |   0.2 |  0.37
-Modify  | 4.1846     | 4.1875     | 4.1896     |   0.1 | 73.55
-Other   |            | 0.008815   |            |       |  0.15
+Comm    | 0.032618   | 0.04948    | 0.062614   |   5.0 |  1.25
+Output  | 0.014166   | 0.014229   | 0.014374   |   0.1 |  0.36
+Modify  | 2.8947     | 2.8957     | 2.8965     |   0.0 | 73.34
+Other   |            | 0.002385   |            |       |  0.06
 
 Nlocal:    1445 ave 1445 max 1445 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -164,4 +164,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:05
+Total wall time: 0:00:03
diff --git a/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1 b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1
index fb95d9ab48..06774d0858 100644
--- a/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1
+++ b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.00110412 secs
+  create_atoms CPU = 0.000470161 secs
 
 # setting mass, mag. moments, and interactions for fcc cobalt
 
@@ -87,41 +87,41 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 5.718 | 5.718 | 5.718 Mbytes
 Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
-       0            0 -0.099570972            0            0            1   -188.09051    100.00543   -2372.6129 
-      50        0.005 -0.099570972            0            0            1   -188.09048    95.094679   -2372.6129 
-     100         0.01 -0.099570972            0            0            1   -188.09007    81.578321   -2372.6129 
-     150        0.015 -0.099570972            0            0            1   -188.08848    62.802727   -2372.6129 
-     200         0.02 -0.099570972            0            0            1   -188.08487     43.35108   -2372.6129 
-     250        0.025 -0.099570972            0            0            1   -188.07877    27.749821   -2372.6129 
-     300         0.03 -0.099570972            0            0            1   -188.07054    19.149389   -2372.6129 
-     350        0.035 -0.099570972            0            0            1   -188.06135    18.453387   -2372.6129 
-     400         0.04 -0.099570972            0            0            1     -188.053    24.249423   -2372.6129 
-     450        0.045 -0.099570972            0            0            1   -188.04742    33.548008   -2372.6129 
-     500         0.05 -0.099570972            0            0            1   -188.04604    42.973172   -2372.6129 
-     550        0.055 -0.099570972            0            0            1   -188.04935    49.902539   -2372.6129 
-     600         0.06 -0.099570972            0            0            1    -188.0567    53.166772   -2372.6129 
-     650        0.065 -0.099570972            0            0            1   -188.06642    53.153416   -2372.6129 
-     700         0.07 -0.099570972            0            0            1   -188.07628    51.377187   -2372.6129 
-     750        0.075 -0.099570972            0            0            1   -188.08415    49.725449   -2372.6129 
-     800         0.08 -0.099570972            0            0            1   -188.08857    49.663576   -2372.6129 
-     850        0.085 -0.099570972            0            0            1    -188.0891    51.681567   -2372.6129 
-     900         0.09 -0.099570972            0            0            1   -188.08636    55.166554   -2372.6129 
-     950        0.095 -0.099570972            0            0            1   -188.08174    58.718232   -2372.6129 
-    1000          0.1 -0.099570972            0            0            1    -188.0769     60.75567   -2372.6129 
-Loop time of 5.66302 on 1 procs for 1000 steps with 500 atoms
+       0            0 -0.099570972            0            0            1   -188.09051    100.00543   -2278.6175 
+      50        0.005 -0.099570972            0            0            1   -188.09048    95.094679   -2278.6175 
+     100         0.01 -0.099570972            0            0            1   -188.09007    81.578321   -2278.6177 
+     150        0.015 -0.099570972            0            0            1   -188.08848    62.802727   -2278.6185 
+     200         0.02 -0.099570972            0            0            1   -188.08487     43.35108   -2278.6203 
+     250        0.025 -0.099570972            0            0            1   -188.07877    27.749821   -2278.6233 
+     300         0.03 -0.099570972            0            0            1   -188.07054    19.149389   -2278.6274 
+     350        0.035 -0.099570972            0            0            1   -188.06135    18.453387    -2278.632 
+     400         0.04 -0.099570972            0            0            1     -188.053    24.249423   -2278.6362 
+     450        0.045 -0.099570972            0            0            1   -188.04742    33.548008    -2278.639 
+     500         0.05 -0.099570972            0            0            1   -188.04604    42.973172   -2278.6397 
+     550        0.055 -0.099570972            0            0            1   -188.04935    49.902539    -2278.638 
+     600         0.06 -0.099570972            0            0            1    -188.0567    53.166772   -2278.6344 
+     650        0.065 -0.099570972            0            0            1   -188.06642    53.153416   -2278.6295 
+     700         0.07 -0.099570972            0            0            1   -188.07628    51.377187   -2278.6246 
+     750        0.075 -0.099570972            0            0            1   -188.08415    49.725449   -2278.6206 
+     800         0.08 -0.099570972            0            0            1   -188.08857    49.663576   -2278.6184 
+     850        0.085 -0.099570972            0            0            1    -188.0891    51.681567   -2278.6182 
+     900         0.09 -0.099570972            0            0            1   -188.08636    55.166554   -2278.6195 
+     950        0.095 -0.099570972            0            0            1   -188.08174    58.718232   -2278.6218 
+    1000          0.1 -0.099570972            0            0            1    -188.0769     60.75567   -2278.6243 
+Loop time of 4.6196 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 1.526 ns/day, 15.731 hours/ns, 176.584 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.870 ns/day, 12.832 hours/ns, 216.469 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.8546     | 2.8546     | 2.8546     |   0.0 | 50.41
-Neigh   | 0.012496   | 0.012496   | 0.012496   |   0.0 |  0.22
-Comm    | 0.041981   | 0.041981   | 0.041981   |   0.0 |  0.74
-Output  | 0.0014014  | 0.0014014  | 0.0014014  |   0.0 |  0.02
-Modify  | 2.7441     | 2.7441     | 2.7441     |   0.0 | 48.46
-Other   |            | 0.008486   |            |       |  0.15
+Pair    | 2.3116     | 2.3116     | 2.3116     |   0.0 | 50.04
+Neigh   | 0.011227   | 0.011227   | 0.011227   |   0.0 |  0.24
+Comm    | 0.032837   | 0.032837   | 0.032837   |   0.0 |  0.71
+Output  | 0.00039411 | 0.00039411 | 0.00039411 |   0.0 |  0.01
+Modify  | 2.2584     | 2.2584     | 2.2584     |   0.0 | 48.89
+Other   |            | 0.005152   |            |       |  0.11
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -139,4 +139,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:05
+Total wall time: 0:00:04
diff --git a/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4 b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4
index 6d8e74f37f..331ed60315 100644
--- a/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4
+++ b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.00073719 secs
+  create_atoms CPU = 0.000808001 secs
 
 # setting mass, mag. moments, and interactions for fcc cobalt
 
@@ -108,20 +108,20 @@ Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng
      900         0.09 -0.099570972            0            0            1   -188.08348    55.551378   -2372.6129 
      950        0.095 -0.099570972            0            0            1   -188.07838    57.540047   -2372.6129 
     1000          0.1 -0.099570972            0            0            1   -188.07314    58.088674   -2372.6129 
-Loop time of 3.36398 on 4 procs for 1000 steps with 500 atoms
+Loop time of 2.54753 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 2.568 ns/day, 9.344 hours/ns, 297.267 timesteps/s
-99.1% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 3.392 ns/day, 7.076 hours/ns, 392.538 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.67186    | 0.78327    | 0.87877    |   8.5 | 23.28
-Neigh   | 0.0027554  | 0.0033352  | 0.0038562  |   0.7 |  0.10
-Comm    | 0.20661    | 0.30174    | 0.41594    |  14.1 |  8.97
-Output  | 0.0007627  | 0.00084305 | 0.0010374  |   0.0 |  0.03
-Modify  | 2.2674     | 2.2712     | 2.2779     |   0.3 | 67.52
-Other   |            | 0.003571   |            |       |  0.11
+Pair    | 0.62017    | 0.6485     | 0.66275    |   2.1 | 25.46
+Neigh   | 0.0027115  | 0.0029724  | 0.0030868  |   0.3 |  0.12
+Comm    | 0.095047   | 0.1102     | 0.13819    |   5.0 |  4.33
+Output  | 0.00039029 | 0.00042999 | 0.00049996 |   0.0 |  0.02
+Modify  | 1.7801     | 1.7834     | 1.7852     |   0.1 | 70.01
+Other   |            | 0.002028   |            |       |  0.08
 
 Nlocal:    125 ave 133 max 116 min
 Histogram: 1 0 0 0 0 2 0 0 0 1
@@ -139,4 +139,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:03
+Total wall time: 0:00:02
diff --git a/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1 b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1
index c534241f34..781e2264a7 100644
--- a/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1
+++ b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.000491858 secs
+  create_atoms CPU = 0.00105 secs
 
 # setting mass, mag. moments, and interactions for hcp cobalt
 
@@ -84,121 +84,121 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 7.902 | 7.902 | 7.902 Mbytes
 Step Time v_magnorm v_emag Temp Press TotEng 
-       0            0  0.076558814   -5.1073764    100.00543   -552.75983   -2190.3478 
-      10        0.001  0.074494403   -6.2746901    100.01038   -1571.7966   -2191.5266 
-      20        0.002  0.072366265   -7.4280779    99.885587   -2535.9845   -2192.6673 
-      30        0.003  0.070127018   -8.5667999    99.611653   -3445.9872   -2193.7707 
-      40        0.004  0.067755946   -9.6899272    99.164813   -4302.5715   -2194.8376 
-      50        0.005  0.065261592    -10.79648    98.520535   -5107.2841   -2195.8697 
-      60        0.006  0.062676613   -11.885341    97.657148   -5862.7198   -2196.8696 
-      70        0.007  0.060046709   -12.955115    96.558718   -6572.0571   -2197.8404 
-      80        0.008  0.057417313   -14.004096    95.216748   -7238.1396   -2198.7846 
-      90        0.009  0.054822275   -15.030416    93.630634   -7862.5226   -2199.7028 
-     100         0.01  0.052277835   -16.032345     91.80711   -8445.2646   -2200.5936 
-     110        0.011  0.049783153   -17.008652    89.759163   -8985.5937   -2201.4546 
-     120        0.012  0.047326373   -17.958895    87.504922   -9483.1141   -2202.2836 
-     130        0.013  0.044893289   -18.883574    85.066818   -9938.8838     -2203.08 
-     140        0.014  0.042474822   -19.784052    82.471014   -10355.911   -2203.8457 
-     150        0.015  0.040070404   -20.662271    79.746901   -10739.081   -2204.5843 
-     160        0.016  0.037686856   -21.520294    76.926428   -11094.793   -2205.3015 
-     170        0.017  0.035334961   -22.359822    74.043181   -11430.247   -2206.0035 
-     180        0.018  0.033026799   -23.181822    71.131269   -11752.268   -2206.6955 
-     190        0.019  0.030775544   -23.986406    68.224204   -12065.774   -2207.3807 
-     200         0.02  0.028597121   -24.773013    65.353995   -12372.712   -2208.0582 
-     210        0.021  0.026511775   -25.540835     62.55053   -12672.055   -2208.7235 
-     220        0.022   0.02454383   -26.289327    59.841288   -12961.112   -2209.3704 
-     230        0.023   0.02271918   -27.018625    57.251361   -13237.544   -2209.9931 
-     240        0.024  0.021061271   -27.729714     54.80373   -13501.028   -2210.5885 
-     250        0.025  0.019587072    -28.42449    52.519717   -13754.325   -2211.1572 
-     260        0.026  0.018304494   -29.105398    50.419388   -14002.718   -2211.7031 
-     270        0.027  0.017211977   -29.775134    48.521812   -14253.089   -2212.2321 
-     280        0.028  0.016300002   -30.436204    46.845075   -14512.437   -2212.7508 
-     290        0.029  0.015553519   -31.090499    45.405985    -14786.53   -2213.2644 
-     300         0.03  0.014954102   -31.739026    44.219544   -15079.165   -2213.7764 
-     310        0.031  0.014481189   -32.381585    43.298175   -15391.531   -2214.2875 
-     320        0.032  0.014112494   -33.016984    42.650874   -15722.828   -2214.7966 
-     330        0.033  0.013824206   -33.643289    42.282535   -16070.874   -2215.3011 
-     340        0.034  0.013591568   -34.258323     42.19365   -16433.065   -2215.7983 
-     350        0.035  0.013390035   -34.860184    42.380506   -16807.186    -2216.286 
-     360        0.036   0.01319679   -35.447655    42.835832   -17191.816    -2216.763 
-     370        0.037  0.012992271   -36.020512    43.549656   -17586.676   -2217.2292 
-     380        0.038  0.012761486   -36.579332    44.510078   -17991.857   -2217.6857 
-     390        0.039  0.012494918   -37.125414    45.703757   -18407.738   -2218.1336 
-     400         0.04    0.0121888   -37.660321    47.115967   -18834.276   -2218.5743 
-     410        0.041  0.011844474   -38.185489    48.730291   -19270.674   -2219.0083 
-     420        0.042  0.011466715    -38.70192    50.528119   -19715.276   -2219.4355 
-     430        0.043  0.011061388    -39.21005    52.488204    -20165.66   -2219.8551 
-     440        0.044  0.010633241   -39.709778    54.586528   -20618.997    -2220.266 
-     450        0.045  0.010184696   -40.200724     56.79654   -21072.538   -2220.6671 
-     460        0.046 0.0097161044   -40.682449    59.089699   -21523.873   -2221.0575 
-     470        0.047 0.0092271788   -41.154614    61.436133   -21970.922   -2221.4371 
-     480        0.048 0.0087187266   -41.617256    63.805414    -22412.32   -2221.8064 
-     490        0.049 0.0081937768   -42.070708    66.167399   -22847.061   -2222.1664 
-     500         0.05 0.0076576327    -42.51563    68.493235   -23274.619   -2222.5187 
-     510        0.051 0.0071170477   -42.952841    70.756444   -23694.559   -2222.8652 
-     520        0.052  0.006579078   -43.383338    72.933996   -24106.717   -2223.2075 
-     530        0.053  0.006050144   -43.807962    75.007131   -24510.338   -2223.5467 
-     540        0.054 0.0055354475   -44.227552    76.961803   -24904.495   -2223.8833 
-     550        0.055 0.0050386503    -44.64268    78.788647   -25287.341   -2224.2166 
-     560        0.056 0.0045617699   -45.053996      80.4825    -25657.11   -2224.5456 
-     570        0.057 0.0041054334   -45.461923    82.041527   -26011.443   -2224.8688 
-     580        0.058  0.003669689   -45.866895    83.466142   -26348.265   -2225.1846 
-     590        0.059 0.0032553824   -46.269219    84.757926   -26665.834    -2225.492 
-     600         0.06 0.0028655752   -46.669125    85.918711    -26963.24   -2225.7906 
-     610        0.061 0.0025060765   -47.066641        86.95   -27240.331   -2226.0806 
-     620        0.062 0.0021839971   -47.461566    87.852838   -27497.728   -2226.3626 
-     630        0.063 0.0019039581   -47.853462    88.628142   -27736.503   -2226.6376 
-     640        0.064 0.0016633855   -48.241747    89.277364    -27957.91   -2226.9064 
-     650        0.065 0.0014502904   -48.625803    89.803307    -28163.11   -2227.1692 
-     660        0.066 0.0012463786   -49.005026    90.210807   -28352.881   -2227.4258 
-     670        0.067 0.0010345087   -49.378935    90.507107   -28527.721   -2227.6754 
-     680        0.068 0.00080788134   -49.747325    90.701795   -28688.395   -2227.9175 
-     690        0.069  0.000586442   -50.110227     90.80636   -28836.094   -2228.1522 
-     700         0.07 0.00046855102   -50.467799    90.833539   -28972.361   -2228.3797 
-     710        0.071 0.00061091693    -50.82044    90.796649    -29099.44   -2228.6011 
-     720        0.072 0.00094960177   -51.168606    90.709122   -29219.676   -2228.8175 
-     730        0.073 0.0013742455   -51.512913    90.584346   -29335.643   -2229.0301 
-     740        0.074 0.0018397629   -51.853957    90.435783   -29449.521   -2229.2396 
-     750        0.075 0.0023216474   -52.192407    90.277231   -29563.316   -2229.4468 
-     760        0.076 0.0028000512   -52.528883    90.123061   -29678.726   -2229.6522 
-     770        0.077 0.0032569295   -52.863859     89.98824   -29797.079   -2229.8564 
-     780        0.078 0.0036765431   -53.197843    89.888047   -29919.964     -2230.06 
-     790        0.079 0.0040467094   -53.530921    89.837568   -30048.271   -2230.2638 
-     800         0.08 0.0043597837   -53.862938    89.850978   -30182.622   -2230.4682 
-     810        0.081 0.0046129296   -54.193489    89.940884   -30323.293   -2230.6737 
-     820        0.082 0.0048076151   -54.522077    90.117797   -30470.468   -2230.8804 
-     830        0.083  0.004948533    -54.84813    90.389814   -30624.056   -2231.0884 
-     840        0.084 0.0050423324   -55.171024    90.762454   -30783.658   -2231.2974 
-     850        0.085 0.0050965581   -55.490357    91.238681   -30949.141   -2231.5072 
-     860        0.086 0.0051190641   -55.805904    91.818973     -31120.5   -2231.7177 
-     870        0.087 0.0051180301   -56.117429    92.501449   -31297.412   -2231.9286 
-     880        0.088 0.0051024116   -56.424751    93.281992   -31479.436   -2232.1393 
-     890        0.089  0.005082454   -56.727832    94.154367   -31666.293   -2232.3495 
-     900         0.09 0.0050697645   -57.026442    95.110386   -31857.043   -2232.5582 
-     910        0.091 0.0050765431   -57.320291    96.140056   -32050.436   -2232.7645 
-     920        0.092 0.0051139309   -57.609075    97.231838   -32245.079   -2232.9672 
-     930        0.093 0.0051899535    -57.89236    98.372982   -32439.141   -2233.1648 
-     940        0.094 0.0053078572   -58.169742     99.54995   -32630.727   -2233.3559 
-     950        0.095 0.0054654923    -58.44083    100.74893   -32817.882   -2233.5392 
-     960        0.096 0.0056558757   -58.705483    101.95638   -32999.116   -2233.7136 
-     970        0.097 0.0058685513   -58.963698    103.15953   -33173.159   -2233.8785 
-     980        0.098 0.0060912487   -59.215624    104.34681   -33338.961   -2234.0336 
-     990        0.099 0.0063114886   -59.461806    105.50819   -33496.345   -2234.1794 
-    1000          0.1 0.0065179843   -59.702883    106.63524   -33645.259   -2234.3168 
-Loop time of 5.86376 on 1 procs for 1000 steps with 500 atoms
+       0            0  0.076558814   -5.1073764    100.00543   -552.75983   -2189.4486 
+      10        0.001  0.074494403   -6.2746901    100.01038   -1571.7966   -2190.0317 
+      20        0.002  0.072366265   -7.4280779    99.885587   -2535.9845   -2190.5874 
+      30        0.003  0.070127018   -8.5667999    99.611653   -3445.9872   -2191.1169 
+      40        0.004  0.067755946   -9.6899272    99.164813   -4302.5715   -2191.6215 
+      50        0.005  0.065261592    -10.79648    98.520535   -5107.2841    -2192.103 
+      60        0.006  0.062676613   -11.885341    97.657148   -5862.7198   -2192.5638 
+      70        0.007  0.060046709   -12.955115    96.558718   -6572.0571   -2193.0064 
+      80        0.008  0.057417313   -14.004096    95.216748   -7238.1396   -2193.4327 
+      90        0.009  0.054822275   -15.030416    93.630634   -7862.5226   -2193.8437 
+     100         0.01  0.052277835   -16.032345     91.80711   -8445.2646   -2194.2391 
+     110        0.011  0.049783153   -17.008652    89.759163   -8985.5937   -2194.6181 
+     120        0.012  0.047326373   -17.958895    87.504922   -9483.1141     -2194.98 
+     130        0.013  0.044893289   -18.883574    85.066818   -9938.8838   -2195.3247 
+     140        0.014  0.042474822   -19.784052    82.471014   -10355.911   -2195.6533 
+     150        0.015  0.040070404   -20.662271    79.746901   -10739.081   -2195.9677 
+     160        0.016  0.037686856   -21.520294    76.926428   -11094.793   -2196.2709 
+     170        0.017  0.035334961   -22.359822    74.043181   -11430.247   -2196.5659 
+     180        0.018  0.033026799   -23.181822    71.131269   -11752.268   -2196.8556 
+     190        0.019  0.030775544   -23.986406    68.224204   -12065.774   -2197.1412 
+     200         0.02  0.028597121   -24.773013    65.353995   -12372.712   -2197.4226 
+     210        0.021  0.026511775   -25.540835     62.55053   -12672.055   -2197.6975 
+     220        0.022   0.02454383   -26.289327    59.841288   -12961.112   -2197.9631 
+     230        0.023   0.02271918   -27.018625    57.251361   -13237.544   -2198.2165 
+     240        0.024  0.021061271   -27.729714     54.80373   -13501.028   -2198.4564 
+     250        0.025  0.019587072    -28.42449    52.519717   -13754.325   -2198.6833 
+     260        0.026  0.018304494   -29.105398    50.419388   -14002.718   -2198.8994 
+     270        0.027  0.017211977   -29.775134    48.521812   -14253.089   -2199.1079 
+     280        0.028  0.016300002   -30.436204    46.845075   -14512.437   -2199.3119 
+     290        0.029  0.015553519   -31.090499    45.405985    -14786.53   -2199.5143 
+     300         0.03  0.014954102   -31.739026    44.219544   -15079.165   -2199.7168 
+     310        0.031  0.014481189   -32.381585    43.298175   -15391.531   -2199.9198 
+     320        0.032  0.014112494   -33.016984    42.650874   -15722.828   -2200.1226 
+     330        0.033  0.013824206   -33.643289    42.282535   -16070.874    -2200.324 
+     340        0.034  0.013591568   -34.258323     42.19365   -16433.065   -2200.5226 
+     350        0.035  0.013390035   -34.860184    42.380506   -16807.186   -2200.7174 
+     360        0.036   0.01319679   -35.447655    42.835832   -17191.816   -2200.9077 
+     370        0.037  0.012992271   -36.020512    43.549656   -17586.676   -2201.0935 
+     380        0.038  0.012761486   -36.579332    44.510078   -17991.857   -2201.2754 
+     390        0.039  0.012494918   -37.125414    45.703757   -18407.738   -2201.4538 
+     400         0.04    0.0121888   -37.660321    47.115967   -18834.276   -2201.6292 
+     410        0.041  0.011844474   -38.185489    48.730291   -19270.674   -2201.8019 
+     420        0.042  0.011466715    -38.70192    50.528119   -19715.276   -2201.9716 
+     430        0.043  0.011061388    -39.21005    52.488204    -20165.66   -2202.1377 
+     440        0.044  0.010633241   -39.709778    54.586528   -20618.997   -2202.2998 
+     450        0.045  0.010184696   -40.200724     56.79654   -21072.538   -2202.4571 
+     460        0.046 0.0097161044   -40.682449    59.089699   -21523.873   -2202.6094 
+     470        0.047 0.0092271788   -41.154614    61.436133   -21970.922   -2202.7565 
+     480        0.048 0.0087187266   -41.617256    63.805414    -22412.32   -2202.8989 
+     490        0.049 0.0081937768   -42.070708    66.167399   -22847.061    -2203.037 
+     500         0.05 0.0076576327    -42.51563    68.493235   -23274.619    -2203.172 
+     510        0.051 0.0071170477   -42.952841    70.756444   -23694.559   -2203.3046 
+     520        0.052  0.006579078   -43.383338    72.933996   -24106.717   -2203.4358 
+     530        0.053  0.006050144   -43.807962    75.007131   -24510.338   -2203.5662 
+     540        0.054 0.0055354475   -44.227552    76.961803   -24904.495   -2203.6957 
+     550        0.055 0.0050386503    -44.64268    78.788647   -25287.341   -2203.8241 
+     560        0.056 0.0045617699   -45.053996      80.4825    -25657.11   -2203.9504 
+     570        0.057 0.0041054334   -45.461923    82.041527   -26011.443   -2204.0737 
+     580        0.058  0.003669689   -45.866895    83.466142   -26348.265   -2204.1931 
+     590        0.059 0.0032553824   -46.269219    84.757926   -26665.834   -2204.3077 
+     600         0.06 0.0028655752   -46.669125    85.918711    -26963.24   -2204.4173 
+     610        0.061 0.0025060765   -47.066641        86.95   -27240.331   -2204.5218 
+     620        0.062 0.0021839971   -47.461566    87.852838   -27497.728   -2204.6218 
+     630        0.063 0.0019039581   -47.853462    88.628142   -27736.503   -2204.7177 
+     640        0.064 0.0016633855   -48.241747    89.277364    -27957.91     -2204.81 
+     650        0.065 0.0014502904   -48.625803    89.803307    -28163.11    -2204.899 
+     660        0.066 0.0012463786   -49.005026    90.210807   -28352.881   -2204.9847 
+     670        0.067 0.0010345087   -49.378935    90.507107   -28527.721   -2205.0668 
+     680        0.068 0.00080788134   -49.747325    90.701795   -28688.395   -2205.1453 
+     690        0.069  0.000586442   -50.110227     90.80636   -28836.094     -2205.22 
+     700         0.07 0.00046855102   -50.467799    90.833539   -28972.361   -2205.2911 
+     710        0.071 0.00061091693    -50.82044    90.796649    -29099.44   -2205.3592 
+     720        0.072 0.00094960177   -51.168606    90.709122   -29219.676   -2205.4249 
+     730        0.073 0.0013742455   -51.512913    90.584346   -29335.643   -2205.4887 
+     740        0.074 0.0018397629   -51.853957    90.435783   -29449.521   -2205.5511 
+     750        0.075 0.0023216474   -52.192407    90.277231   -29563.316   -2205.6124 
+     760        0.076 0.0028000512   -52.528883    90.123061   -29678.726   -2205.6729 
+     770        0.077 0.0032569295   -52.863859     89.98824   -29797.079   -2205.7329 
+     780        0.078 0.0036765431   -53.197843    89.888047   -29919.964   -2205.7925 
+     790        0.079 0.0040467094   -53.530921    89.837568   -30048.271   -2205.8521 
+     800         0.08 0.0043597837   -53.862938    89.850978   -30182.622   -2205.9119 
+     810        0.081 0.0046129296   -54.193489    89.940884   -30323.293   -2205.9718 
+     820        0.082 0.0048076151   -54.522077    90.117797   -30470.468   -2206.0321 
+     830        0.083  0.004948533    -54.84813    90.389814   -30624.056   -2206.0926 
+     840        0.084 0.0050423324   -55.171024    90.762454   -30783.658   -2206.1532 
+     850        0.085 0.0050965581   -55.490357    91.238681   -30949.141   -2206.2139 
+     860        0.086 0.0051190641   -55.805904    91.818973     -31120.5   -2206.2745 
+     870        0.087 0.0051180301   -56.117429    92.501449   -31297.412   -2206.3349 
+     880        0.088 0.0051024116   -56.424751    93.281992   -31479.436   -2206.3949 
+     890        0.089  0.005082454   -56.727832    94.154367   -31666.293   -2206.4544 
+     900         0.09 0.0050697645   -57.026442    95.110386   -31857.043    -2206.513 
+     910        0.091 0.0050765431   -57.320291    96.140056   -32050.436   -2206.5703 
+     920        0.092 0.0051139309   -57.609075    97.231838   -32245.079   -2206.6257 
+     930        0.093 0.0051899535    -57.89236    98.372982   -32439.141   -2206.6788 
+     940        0.094 0.0053078572   -58.169742     99.54995   -32630.727   -2206.7288 
+     950        0.095 0.0054654923    -58.44083    100.74893   -32817.882   -2206.7752 
+     960        0.096 0.0056558757   -58.705483    101.95638   -32999.116   -2206.8176 
+     970        0.097 0.0058685513   -58.963698    103.15953   -33173.159   -2206.8557 
+     980        0.098 0.0060912487   -59.215624    104.34681   -33338.961   -2206.8893 
+     990        0.099 0.0063114886   -59.461806    105.50819   -33496.345   -2206.9188 
+    1000          0.1 0.0065179843   -59.702883    106.63524   -33645.259   -2206.9444 
+Loop time of 5.20295 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 1.473 ns/day, 16.288 hours/ns, 170.539 timesteps/s
+Performance: 1.661 ns/day, 14.453 hours/ns, 192.199 timesteps/s
 100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.9866     | 2.9866     | 2.9866     |   0.0 | 50.93
-Neigh   | 0.016013   | 0.016013   | 0.016013   |   0.0 |  0.27
-Comm    | 0.046018   | 0.046018   | 0.046018   |   0.0 |  0.78
-Output  | 0.011075   | 0.011075   | 0.011075   |   0.0 |  0.19
-Modify  | 2.7957     | 2.7957     | 2.7957     |   0.0 | 47.68
-Other   |            | 0.008332   |            |       |  0.14
+Pair    | 2.6241     | 2.6241     | 2.6241     |   0.0 | 50.43
+Neigh   | 0.01424    | 0.01424    | 0.01424    |   0.0 |  0.27
+Comm    | 0.041207   | 0.041207   | 0.041207   |   0.0 |  0.79
+Output  | 0.0090086  | 0.0090086  | 0.0090086  |   0.0 |  0.17
+Modify  | 2.5084     | 2.5084     | 2.5084     |   0.0 | 48.21
+Other   |            | 0.006008   |            |       |  0.12
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4 b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4
index 21adab3f19..de00d5be32 100644
--- a/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4
+++ b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.000671148 secs
+  create_atoms CPU = 0.00101995 secs
 
 # setting mass, mag. moments, and interactions for hcp cobalt
 
@@ -185,20 +185,20 @@ Step Time v_magnorm v_emag Temp Press TotEng
      980        0.098  0.010180127   -59.986126    110.79823   -33816.218   -2234.0455 
      990        0.099  0.010181304    -60.24929    112.17528   -34000.522   -2234.1984 
     1000          0.1   0.01012881   -60.508632    113.46137   -34179.052   -2234.3508 
-Loop time of 4.82687 on 4 procs for 1000 steps with 500 atoms
+Loop time of 2.93788 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 1.790 ns/day, 13.408 hours/ns, 207.173 timesteps/s
-97.6% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 2.941 ns/day, 8.161 hours/ns, 340.381 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.1741     | 1.3056     | 1.4605     |  11.5 | 27.05
-Neigh   | 0.0042465  | 0.0048378  | 0.0051758  |   0.5 |  0.10
-Comm    | 0.31356    | 0.406      | 0.47906    |  11.6 |  8.41
-Output  | 0.0090122  | 0.0094153  | 0.010493   |   0.6 |  0.20
-Modify  | 3.0298     | 3.0936     | 3.1534     |   3.4 | 64.09
-Other   |            | 0.007349   |            |       |  0.15
+Pair    | 0.72349    | 0.73783    | 0.7554     |   1.3 | 25.11
+Neigh   | 0.00353    | 0.0036981  | 0.0038559  |   0.2 |  0.13
+Comm    | 0.12285    | 0.14476    | 0.16041    |   3.6 |  4.93
+Output  | 0.0046515  | 0.0047909  | 0.0050418  |   0.2 |  0.16
+Modify  | 2.0407     | 2.0439     | 2.0482     |   0.2 | 69.57
+Other   |            | 0.00288    |            |       |  0.10
 
 Nlocal:    125 ave 136 max 119 min
 Histogram: 1 1 1 0 0 0 0 0 0 1
@@ -216,4 +216,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:04
+Total wall time: 0:00:02
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1
index 9c4b9e6877..c2af23d167 100644
--- a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 3456 atoms
-  create_atoms CPU = 0.00068903 secs
+  create_atoms CPU = 0.000741005 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -88,23 +88,23 @@ Neighbor list info ...
       bin: none
 Per MPI rank memory allocation (min/avg/max) = 13.4 | 13.4 | 13.4 Mbytes
 Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
-       0            0           -1            0            0            1 1.0737264e-35   -768.37511   -15560.055   -15515.394 
-      50        0.005           -1 -2.7722752e-10 -2.1828666e-10            1 6.8846921e-09   -768.35793   -15558.423   -15515.394 
-     100         0.01           -1 -2.0983066e-09 -1.7330951e-09            1 1.0038885e-08   -768.30868    -15553.81   -15515.394 
-Loop time of 9.81833 on 1 procs for 100 steps with 3456 atoms
+       0            0           -1            0            0            1 1.0737264e-35   -768.37511   -15175.868   -15131.207 
+      50        0.005           -1 -2.7722752e-10 -2.1828666e-10            1 6.8846921e-09   -768.35793   -15174.244   -15131.215 
+     100         0.01           -1 -2.0983066e-09 -1.7330951e-09            1 1.0038885e-08   -768.30868   -15169.656    -15131.24 
+Loop time of 7.86359 on 1 procs for 100 steps with 3456 atoms
 
-Performance: 0.088 ns/day, 272.731 hours/ns, 10.185 timesteps/s
+Performance: 0.110 ns/day, 218.433 hours/ns, 12.717 timesteps/s
 100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 4.5684     | 4.5684     | 4.5684     |   0.0 | 46.53
+Pair    | 3.6134     | 3.6134     | 3.6134     |   0.0 | 45.95
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.022333   | 0.022333   | 0.022333   |   0.0 |  0.23
-Output  | 0.0062339  | 0.0062339  | 0.0062339  |   0.0 |  0.06
-Modify  | 5.2097     | 5.2097     | 5.2097     |   0.0 | 53.06
-Other   |            | 0.01171    |            |       |  0.12
+Comm    | 0.014062   | 0.014062   | 0.014062   |   0.0 |  0.18
+Output  | 0.006057   | 0.006057   | 0.006057   |   0.0 |  0.08
+Modify  | 4.226      | 4.226      | 4.226      |   0.0 | 53.74
+Other   |            | 0.004064   |            |       |  0.05
 
 Nlocal:    3456 ave 3456 max 3456 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -122,4 +122,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:09
+Total wall time: 0:00:07
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4
index 6bd13bff4b..1f8157bb29 100644
--- a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 3456 atoms
-  create_atoms CPU = 0.00121498 secs
+  create_atoms CPU = 0.00090003 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -91,20 +91,20 @@ Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng
        0            0           -1            0            0            1 1.0737264e-35   -768.37511   -15560.055   -15515.394 
       50        0.005           -1 9.6204015e-11 -3.3767807e-10            1 6.6905249e-09   -768.35767   -15558.438   -15515.394 
      100         0.01           -1 7.8881609e-10 -2.7017321e-09            1 9.8111281e-09   -768.30769   -15553.868   -15515.394 
-Loop time of 4.21054 on 4 procs for 100 steps with 3456 atoms
+Loop time of 2.29116 on 4 procs for 100 steps with 3456 atoms
 
-Performance: 0.205 ns/day, 116.959 hours/ns, 23.750 timesteps/s
-97.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.377 ns/day, 63.643 hours/ns, 43.646 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.5515     | 1.5909     | 1.6287     |   2.8 | 37.78
+Pair    | 0.92259    | 0.92963    | 0.93393    |   0.4 | 40.57
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.1219     | 0.15371    | 0.18852    |   8.1 |  3.65
-Output  | 0.0032659  | 0.0032846  | 0.0033138  |   0.0 |  0.08
-Modify  | 2.4491     | 2.4549     | 2.4589     |   0.3 | 58.30
-Other   |            | 0.007701   |            |       |  0.18
+Comm    | 0.02284    | 0.027597   | 0.035185   |   2.8 |  1.20
+Output  | 0.0018489  | 0.0018544  | 0.0018642  |   0.0 |  0.08
+Modify  | 1.3296     | 1.3303     | 1.3308     |   0.0 | 58.06
+Other   |            | 0.001818   |            |       |  0.08
 
 Nlocal:    864 ave 864 max 864 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -122,4 +122,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:04
+Total wall time: 0:00:02
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1
index 9bd3b04a06..9a38445af5 100644
--- a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 3456 atoms
-  create_atoms CPU = 0.000730038 secs
+  create_atoms CPU = 0.00166988 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -97,24 +97,24 @@ Neighbor list info ...
       bin: none
 Per MPI rank memory allocation (min/avg/max) = 30.07 | 30.07 | 30.07 Mbytes
 Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
-       0            0           -1            0            0            1 2.5872886e-37   -767.88567   -15559.577   -15514.916 
-      50        0.005           -1 4.3660916e-09 -2.1918692e-09            1 5.3480999e-10   -767.86847   -15557.945   -15514.916 
-     100         0.01           -1 9.9854966e-09 -4.2823677e-09            1 2.3267629e-09   -767.81917   -15553.332   -15514.916 
-Loop time of 30.1001 on 1 procs for 100 steps with 3456 atoms
+       0            0           -1            0            0            1 2.5872886e-37   -767.88567    -15175.39   -15130.729 
+      50        0.005           -1 4.3660916e-09 -2.1918692e-09            1 5.3480999e-10   -767.86847   -15173.766   -15130.738 
+     100         0.01           -1 9.9854966e-09 -4.2823677e-09            1 2.3267629e-09   -767.81917   -15169.178   -15130.762 
+Loop time of 24.9345 on 1 procs for 100 steps with 3456 atoms
 
-Performance: 0.029 ns/day, 836.115 hours/ns, 3.322 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.035 ns/day, 692.624 hours/ns, 4.011 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.6659     | 5.6659     | 5.6659     |   0.0 | 18.82
-Kspace  | 12.686     | 12.686     | 12.686     |   0.0 | 42.14
+Pair    | 4.8022     | 4.8022     | 4.8022     |   0.0 | 19.26
+Kspace  | 10.337     | 10.337     | 10.337     |   0.0 | 41.46
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.022781   | 0.022781   | 0.022781   |   0.0 |  0.08
-Output  | 0.00965    | 0.00965    | 0.00965    |   0.0 |  0.03
-Modify  | 11.705     | 11.705     | 11.705     |   0.0 | 38.89
-Other   |            | 0.01108    |            |       |  0.04
+Comm    | 0.013856   | 0.013856   | 0.013856   |   0.0 |  0.06
+Output  | 0.007138   | 0.007138   | 0.007138   |   0.0 |  0.03
+Modify  | 9.7705     | 9.7705     | 9.7705     |   0.0 | 39.18
+Other   |            | 0.004077   |            |       |  0.02
 
 Nlocal:    3456 ave 3456 max 3456 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -132,4 +132,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:30
+Total wall time: 0:00:25
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4
index 4989210d1d..306799f576 100644
--- a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 3456 atoms
-  create_atoms CPU = 0.00238299 secs
+  create_atoms CPU = 0.00088191 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -100,21 +100,21 @@ Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng
        0            0           -1            0            0            1 3.5107565e-37   -767.88567   -15559.577   -15514.916 
       50        0.005           -1 4.3196063e-09 -2.1966927e-09            1 5.1719577e-10   -767.86822    -15557.96   -15514.916 
      100         0.01           -1 9.7636593e-09 -4.3236953e-09            1 2.2443181e-09   -767.81819    -15553.39   -15514.916 
-Loop time of 11.709 on 4 procs for 100 steps with 3456 atoms
+Loop time of 6.80139 on 4 procs for 100 steps with 3456 atoms
 
-Performance: 0.074 ns/day, 325.251 hours/ns, 8.540 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.127 ns/day, 188.927 hours/ns, 14.703 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.7524     | 1.9105     | 2.0593     |   9.8 | 16.32
-Kspace  | 4.1375     | 4.4309     | 4.7029     |  12.3 | 37.84
+Pair    | 1.248      | 1.2649     | 1.2816     |   1.1 | 18.60
+Kspace  | 2.523      | 2.5743     | 2.6505     |   3.0 | 37.85
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.063121   | 0.47268    | 0.94431    |  59.7 |  4.04
-Output  | 0.0032601  | 0.0033116  | 0.0033839  |   0.1 |  0.03
-Modify  | 4.8621     | 4.8828     | 4.9008     |   0.8 | 41.70
-Other   |            | 0.008918   |            |       |  0.08
+Comm    | 0.029461   | 0.087268   | 0.13754    |  13.0 |  1.28
+Output  | 0.0018618  | 0.001869   | 0.0018811  |   0.0 |  0.03
+Modify  | 2.8692     | 2.8709     | 2.8741     |   0.1 | 42.21
+Other   |            | 0.002119   |            |       |  0.03
 
 Nlocal:    864 ave 864 max 864 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -132,4 +132,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:11
+Total wall time: 0:00:06
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1
index 5984976c8d..b0e87d786d 100644
--- a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 3456 atoms
-  create_atoms CPU = 0.000930071 secs
+  create_atoms CPU = 0.00166583 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -99,24 +99,24 @@ Neighbor list info ...
       bin: none
 Per MPI rank memory allocation (min/avg/max) = 16.27 | 16.27 | 16.27 Mbytes
 Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
-       0            0           -1            0            0            1 3.7996771e-37   -767.89759    -15559.59   -15514.929 
-      50        0.005           -1 3.6585337e-09 -1.9445403e-09            1 5.1405121e-10   -767.88039   -15557.958   -15514.929 
-     100         0.01           -1 7.3585728e-09 -3.8640878e-09            1 2.0194927e-09   -767.83109   -15553.345   -15514.929 
-Loop time of 18.493 on 1 procs for 100 steps with 3456 atoms
+       0            0           -1            0            0            1 3.7996771e-37   -767.89759   -15175.402   -15130.741 
+      50        0.005           -1 3.6585337e-09 -1.9445403e-09            1 5.1405121e-10   -767.88039   -15173.779    -15130.75 
+     100         0.01           -1 7.3585728e-09 -3.8640878e-09            1 2.0194927e-09   -767.83109   -15169.191   -15130.774 
+Loop time of 15.3615 on 1 procs for 100 steps with 3456 atoms
 
-Performance: 0.047 ns/day, 513.694 hours/ns, 5.407 timesteps/s
+Performance: 0.056 ns/day, 426.709 hours/ns, 6.510 timesteps/s
 99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.7715     | 5.7715     | 5.7715     |   0.0 | 31.21
-Kspace  | 0.82553    | 0.82553    | 0.82553    |   0.0 |  4.46
+Pair    | 4.8418     | 4.8418     | 4.8418     |   0.0 | 31.52
+Kspace  | 0.66626    | 0.66626    | 0.66626    |   0.0 |  4.34
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.022319   | 0.022319   | 0.022319   |   0.0 |  0.12
-Output  | 0.0066397  | 0.0066397  | 0.0066397  |   0.0 |  0.04
-Modify  | 11.857     | 11.857     | 11.857     |   0.0 | 64.12
-Other   |            | 0.009629   |            |       |  0.05
+Comm    | 0.014248   | 0.014248   | 0.014248   |   0.0 |  0.09
+Output  | 0.0064788  | 0.0064788  | 0.0064788  |   0.0 |  0.04
+Modify  | 9.8279     | 9.8279     | 9.8279     |   0.0 | 63.98
+Other   |            | 0.00478    |            |       |  0.03
 
 Nlocal:    3456 ave 3456 max 3456 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -134,4 +134,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:19
+Total wall time: 0:00:16
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4
index 154e39958d..4fbd0eb52b 100644
--- a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 3456 atoms
-  create_atoms CPU = 0.00089097 secs
+  create_atoms CPU = 0.00123286 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -102,21 +102,21 @@ Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng
        0            0           -1            0            0            1 2.3173191e-37   -767.89759    -15559.59   -15514.929 
       50        0.005           -1 3.6593054e-09 -1.9379563e-09            1 4.9747018e-10   -767.88014   -15557.972   -15514.929 
      100         0.01           -1 7.3731919e-09 -3.8151563e-09            1 1.9544299e-09    -767.8301   -15553.402   -15514.929 
-Loop time of 6.23322 on 4 procs for 100 steps with 3456 atoms
+Loop time of 4.4084 on 4 procs for 100 steps with 3456 atoms
 
-Performance: 0.139 ns/day, 173.145 hours/ns, 16.043 timesteps/s
-99.5% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.196 ns/day, 122.455 hours/ns, 22.684 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.6633     | 1.6906     | 1.7152     |   1.4 | 27.12
-Kspace  | 0.38875    | 0.41372    | 0.44184    |   3.0 |  6.64
+Pair    | 1.2326     | 1.2513     | 1.2693     |   1.3 | 28.38
+Kspace  | 0.22823    | 0.24585    | 0.26385    |   2.8 |  5.58
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.05118    | 0.053267   | 0.054998   |   0.6 |  0.85
-Output  | 0.0070119  | 0.0070257  | 0.0070462  |   0.0 |  0.11
-Modify  | 4.0616     | 4.0629     | 4.0646     |   0.1 | 65.18
-Other   |            | 0.005713   |            |       |  0.09
+Comm    | 0.025352   | 0.028409   | 0.032299   |   1.6 |  0.64
+Output  | 0.001868   | 0.0018761  | 0.0018861  |   0.0 |  0.04
+Modify  | 2.8753     | 2.8788     | 2.8818     |   0.1 | 65.30
+Other   |            | 0.002175   |            |       |  0.05
 
 Nlocal:    864 ave 864 max 864 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -134,4 +134,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:06
+Total wall time: 0:00:04
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1 b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1
index cee42d433b..cbc749a1f7 100644
--- a/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.000509977 secs
+  create_atoms CPU = 0.000422955 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -81,41 +81,41 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 7.82 | 7.82 | 7.82 Mbytes
 Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng Press TotEng 
-       0            0  0.076456975    4554.5462    100.00358  -0.85791269    3.2186929   -1070.8579    394.43342   -1067.6392 
-      50        0.005  0.076456974     4658.383    96.663685  -0.86504718    3.1111957   -1070.7504    709.50826   -1067.6392 
-     100         0.01  0.076456983    4744.1872    86.965803  -0.88035771    2.7990619   -1070.4383    1466.6938   -1067.6392 
-     150        0.015  0.076456973    4794.5283    72.421197   -0.8996913    2.3309324   -1069.9702    2534.3867   -1067.6392 
-     200         0.02  0.076456944    4707.6548    55.633188    -0.921682    1.7905973   -1069.4298     3732.183   -1067.6392 
-     250        0.025  0.076456953    4439.4697    39.802206  -0.94649004    1.2810649   -1068.9203    4831.5559   -1067.6392 
-     300         0.03  0.076457027    4101.6694    27.882295  -0.97253854    0.8974133   -1068.5366    5612.0928   -1067.6392 
-     350        0.035  0.076457103    3860.1545    21.776538  -0.99708692   0.70089477   -1068.3401    5906.3057   -1067.6392 
-     400         0.04  0.076457117    3765.5341    21.857102   -1.0190244   0.70348778   -1068.3427    5682.0053   -1067.6392 
-     450        0.045  0.076457072    3739.9037    26.959407   -1.0389343   0.86770942   -1068.5069    5066.5077   -1067.6392 
-     500         0.05  0.076457001    3730.8342     34.92521   -1.0582008     1.124095   -1068.7633    4279.2424   -1067.6392 
-     550        0.055  0.076456962    3698.0556    43.405912   -1.0785156     1.397053   -1069.0363    3533.4153   -1067.6392 
-     600         0.06  0.076456997     3560.947    50.544844    -1.102048     1.626825   -1069.2661    2975.8479   -1067.6392 
-     650        0.065  0.076457079    3341.7402    55.261218   -1.1296588    1.7786252   -1069.4179    2683.3023   -1067.6392 
-     700         0.07  0.076457136    3156.8448     57.25083   -1.1595102    1.8426624   -1069.4819    2640.5967   -1067.6392 
-     750        0.075  0.076457132    3099.5181    56.934336   -1.1893875    1.8324758   -1069.4717    2778.3261   -1067.6392 
-     800         0.08  0.076457116    3132.9985    55.266343   -1.2181223    1.7787901    -1069.418    3020.1175   -1067.6392 
-     850        0.085  0.076457116    3163.2943    53.376453   -1.2443326    1.7179626   -1069.3572    3287.9042   -1067.6392 
-     900         0.09  0.076457121     3168.063    52.279557   -1.2676425    1.6826581   -1069.3219    3504.7334   -1067.6392 
-     950        0.095  0.076457122    3144.2102    52.667743   -1.2902335    1.6951522   -1069.3344    3622.1382   -1067.6392 
-    1000          0.1  0.076457135    3061.0811    54.684094    -1.314147      1.76005   -1069.3993    3625.2935   -1067.6392 
-Loop time of 2.06841 on 1 procs for 1000 steps with 250 atoms
+       0            0  0.076456975    4554.5462    100.00358  -0.85791269    3.2186929    -1070.429    394.43342   -1067.2103 
+      50        0.005  0.076456974     4658.383    96.663685  -0.86504718    3.1111957   -1070.3179    709.50826   -1067.2067 
+     100         0.01  0.076456983    4744.1872    86.965803  -0.88035771    2.7990619   -1069.9981    1466.6938   -1067.1991 
+     150        0.015  0.076456973    4794.5283    72.421197   -0.8996913    2.3309324   -1069.5203    2534.3867   -1067.1894 
+     200         0.02  0.076456944    4707.6548    55.633188    -0.921682    1.7905973    -1068.969     3732.183   -1067.1784 
+     250        0.025  0.076456953    4439.4697    39.802206  -0.94649004    1.2810649    -1068.447    4831.5559    -1067.166 
+     300         0.03  0.076457027    4101.6694    27.882295  -0.97253854    0.8974133   -1068.0504    5612.0928    -1067.153 
+     350        0.035  0.076457103    3860.1545    21.776538  -0.99708692   0.70089477   -1067.8416    5906.3057   -1067.1407 
+     400         0.04  0.076457117    3765.5341    21.857102   -1.0190244   0.70348778   -1067.8332    5682.0053   -1067.1297 
+     450        0.045  0.076457072    3739.9037    26.959407   -1.0389343   0.86770942   -1067.9875    5066.5077   -1067.1198 
+     500         0.05  0.076457001    3730.8342     34.92521   -1.0582008     1.124095   -1068.2342    4279.2424   -1067.1101 
+     550        0.055  0.076456962    3698.0556    43.405912   -1.0785156     1.397053    -1068.497    3533.4153      -1067.1 
+     600         0.06  0.076456997     3560.947    50.544844    -1.102048     1.626825    -1068.715    2975.8479   -1067.0882 
+     650        0.065  0.076457079    3341.7402    55.261218   -1.1296588    1.7786252    -1068.853    2683.3023   -1067.0744 
+     700         0.07  0.076457136    3156.8448     57.25083   -1.1595102    1.8426624   -1068.9021    2640.5967   -1067.0595 
+     750        0.075  0.076457132    3099.5181    56.934336   -1.1893875    1.8324758    -1068.877    2778.3261   -1067.0445 
+     800         0.08  0.076457116    3132.9985    55.266343   -1.2181223    1.7787901    -1068.809    3020.1175   -1067.0302 
+     850        0.085  0.076457116    3163.2943    53.376453   -1.2443326    1.7179626    -1068.735    3287.9042   -1067.0171 
+     900         0.09  0.076457121     3168.063    52.279557   -1.2676425    1.6826581   -1068.6881    3504.7334   -1067.0054 
+     950        0.095  0.076457122    3144.2102    52.667743   -1.2902335    1.6951522   -1068.6893    3622.1382   -1066.9941 
+    1000          0.1  0.076457135    3061.0811    54.684094    -1.314147      1.76005   -1068.7422    3625.2935   -1066.9822 
+Loop time of 1.6779 on 1 procs for 1000 steps with 250 atoms
 
-Performance: 4.177 ns/day, 5.746 hours/ns, 483.464 timesteps/s
-99.3% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 5.149 ns/day, 4.661 hours/ns, 595.982 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.96898    | 0.96898    | 0.96898    |   0.0 | 46.85
-Neigh   | 0.005435   | 0.005435   | 0.005435   |   0.0 |  0.26
-Comm    | 0.028027   | 0.028027   | 0.028027   |   0.0 |  1.36
-Output  | 0.0051067  | 0.0051067  | 0.0051067  |   0.0 |  0.25
-Modify  | 1.0569     | 1.0569     | 1.0569     |   0.0 | 51.10
-Other   |            | 0.003989   |            |       |  0.19
+Pair    | 0.78285    | 0.78285    | 0.78285    |   0.0 | 46.66
+Neigh   | 0.004487   | 0.004487   | 0.004487   |   0.0 |  0.27
+Comm    | 0.022926   | 0.022926   | 0.022926   |   0.0 |  1.37
+Output  | 0.003927   | 0.003927   | 0.003927   |   0.0 |  0.23
+Modify  | 0.86033    | 0.86033    | 0.86033    |   0.0 | 51.27
+Other   |            | 0.003381   |            |       |  0.20
 
 Nlocal:    250 ave 250 max 250 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -133,4 +133,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:02
+Total wall time: 0:00:01
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4 b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4
index 63ddc9d4fe..a5cc9d7f0b 100644
--- a/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.000626087 secs
+  create_atoms CPU = 0.000705957 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -102,20 +102,20 @@ Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng Press TotEng
      900         0.09  0.076457199    3228.1358    50.837416   -1.2366018    1.6362417   -1069.2755    3917.0758   -1067.6392 
      950        0.095  0.076457222    3247.5532    50.234549   -1.2539657    1.6168379   -1069.2561    4059.9275   -1067.6392 
     1000          0.1  0.076457266    3208.3875    51.592727   -1.2671834    1.6605519   -1069.2998    4001.4995   -1067.6392 
-Loop time of 2.27244 on 4 procs for 1000 steps with 250 atoms
+Loop time of 1.47769 on 4 procs for 1000 steps with 250 atoms
 
-Performance: 3.802 ns/day, 6.312 hours/ns, 440.055 timesteps/s
-97.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5.847 ns/day, 4.105 hours/ns, 676.731 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.33296    | 0.37066    | 0.40364    |   4.3 | 16.31
-Neigh   | 0.0013368  | 0.0025837  | 0.0056586  |   3.5 |  0.11
-Comm    | 0.12627    | 0.16094    | 0.20183    |   7.1 |  7.08
-Output  | 0.0033641  | 0.003438   | 0.0036473  |   0.2 |  0.15
-Modify  | 1.7249     | 1.7261     | 1.7272     |   0.1 | 75.96
-Other   |            | 0.008682   |            |       |  0.38
+Pair    | 0.21791    | 0.22724    | 0.23568    |   1.4 | 15.38
+Neigh   | 0.001137   | 0.0011771  | 0.0012221  |   0.1 |  0.08
+Comm    | 0.066727   | 0.074288   | 0.083826   |   2.3 |  5.03
+Output  | 0.0017431  | 0.0017657  | 0.0018256  |   0.1 |  0.12
+Modify  | 1.1707     | 1.1718     | 1.1725     |   0.1 | 79.30
+Other   |            | 0.001427   |            |       |  0.10
 
 Nlocal:    62.5 ave 66 max 60 min
 Histogram: 1 0 0 2 0 0 0 0 0 1
@@ -133,4 +133,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:02
+Total wall time: 0:00:01
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1 b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1
index 26fdfb0004..22957c8498 100644
--- a/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.000481129 secs
+  create_atoms CPU = 0.00101709 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -81,41 +81,41 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 7.82 | 7.82 | 7.82 Mbytes
 Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
-       0            0           -1            0            0            1            0    -55.58269   -1125.5827    -1122.364 
-      50        0.005           -1            0            0            1            0   -55.581417   -1125.4672    -1122.364 
-     100         0.01           -1            0            0            1            0   -55.577759   -1125.1389    -1122.364 
-     150        0.015           -1            0            0            1            0    -55.57219   -1124.6538    -1122.364 
-     200         0.02           -1            0            0            1            0   -55.565438    -1124.099    -1122.364 
-     250        0.025           -1            0            0            1            0   -55.558379   -1123.5779    -1122.364 
-     300         0.03           -1            0            0            1            0   -55.551886   -1123.1862    -1122.364 
-     350        0.035           -1            0            0            1            0   -55.546675   -1122.9858    -1122.364 
-     400         0.04           -1            0            0            1            0   -55.543187   -1122.9869    -1122.364 
-     450        0.045           -1            0            0            1            0    -55.54154   -1123.1498    -1122.364 
-     500         0.05           -1            0            0            1            0   -55.541574   -1123.4037    -1122.364 
-     550        0.055           -1            0            0            1            0   -55.542941    -1123.672    -1122.364 
-     600         0.06           -1            0            0            1            0   -55.545209   -1123.8931    -1122.364 
-     650        0.065           -1            0            0            1            0   -55.547951   -1124.0315    -1122.364 
-     700         0.07           -1            0            0            1            0   -55.550801   -1124.0798    -1122.364 
-     750        0.075           -1            0            0            1            0   -55.553483   -1124.0546    -1122.364 
-     800         0.08           -1            0            0            1            0   -55.555816   -1123.9877    -1122.364 
-     850        0.085           -1            0            0            1            0   -55.557706    -1123.916    -1122.364 
-     900         0.09           -1            0            0            1            0    -55.55913   -1123.8714    -1122.364 
-     950        0.095           -1            0            0            1            0   -55.560111   -1123.8726    -1122.364 
-    1000          0.1           -1            0            0            1            0   -55.560705   -1123.9215    -1122.364 
-Loop time of 1.95614 on 1 procs for 1000 steps with 250 atoms
+       0            0           -1            0            0            1            0    -55.58269   -1097.7914   -1094.5727 
+      50        0.005           -1            0            0            1            0   -55.581417   -1097.6764   -1094.5733 
+     100         0.01           -1            0            0            1            0   -55.577759     -1097.35   -1094.5751 
+     150        0.015           -1            0            0            1            0    -55.57219   -1096.8677   -1094.5779 
+     200         0.02           -1            0            0            1            0   -55.565438   -1096.3163   -1094.5813 
+     250        0.025           -1            0            0            1            0   -55.558379   -1095.7987   -1094.5848 
+     300         0.03           -1            0            0            1            0   -55.551886   -1095.4103   -1094.5881 
+     350        0.035           -1            0            0            1            0   -55.546675   -1095.2124   -1094.5907 
+     400         0.04           -1            0            0            1            0   -55.543187   -1095.2153   -1094.5924 
+     450        0.045           -1            0            0            1            0    -55.54154    -1095.379   -1094.5932 
+     500         0.05           -1            0            0            1            0   -55.541574    -1095.633   -1094.5932 
+     550        0.055           -1            0            0            1            0   -55.542941   -1095.9006   -1094.5925 
+     600         0.06           -1            0            0            1            0   -55.545209   -1096.1205   -1094.5914 
+     650        0.065           -1            0            0            1            0   -55.547951   -1096.2575     -1094.59 
+     700         0.07           -1            0            0            1            0   -55.550801   -1096.3044   -1094.5886 
+     750        0.075           -1            0            0            1            0   -55.553483   -1096.2778   -1094.5873 
+     800         0.08           -1            0            0            1            0   -55.555816   -1096.2098   -1094.5861 
+     850        0.085           -1            0            0            1            0   -55.557706   -1096.1372   -1094.5852 
+     900         0.09           -1            0            0            1            0    -55.55913   -1096.0919   -1094.5844 
+     950        0.095           -1            0            0            1            0   -55.560111   -1096.0925    -1094.584 
+    1000          0.1           -1            0            0            1            0   -55.560705   -1096.1411   -1094.5837 
+Loop time of 1.74825 on 1 procs for 1000 steps with 250 atoms
 
-Performance: 4.417 ns/day, 5.434 hours/ns, 511.211 timesteps/s
+Performance: 4.942 ns/day, 4.856 hours/ns, 571.999 timesteps/s
 100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.90008    | 0.90008    | 0.90008    |   0.0 | 46.01
-Neigh   | 0.005214   | 0.005214   | 0.005214   |   0.0 |  0.27
-Comm    | 0.026026   | 0.026026   | 0.026026   |   0.0 |  1.33
-Output  | 0.0045307  | 0.0045307  | 0.0045307  |   0.0 |  0.23
-Modify  | 1.0168     | 1.0168     | 1.0168     |   0.0 | 51.98
-Other   |            | 0.003449   |            |       |  0.18
+Pair    | 0.80384    | 0.80384    | 0.80384    |   0.0 | 45.98
+Neigh   | 0.004528   | 0.004528   | 0.004528   |   0.0 |  0.26
+Comm    | 0.022954   | 0.022954   | 0.022954   |   0.0 |  1.31
+Output  | 0.0034568  | 0.0034568  | 0.0034568  |   0.0 |  0.20
+Modify  | 0.91007    | 0.91007    | 0.91007    |   0.0 | 52.06
+Other   |            | 0.003404   |            |       |  0.19
 
 Nlocal:    250 ave 250 max 250 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4 b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
index 2c911cb9bb..60db1064e0 100644
--- a/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.000656843 secs
+  create_atoms CPU = 0.000651121 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -102,20 +102,20 @@ Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng
      900         0.09           -1            0            0            1            0   -55.560147   -1123.8404    -1122.364 
      950        0.095           -1            0            0            1            0   -55.560992   -1123.8312    -1122.364 
     1000          0.1           -1            0            0            1            0   -55.561635   -1123.8853    -1122.364 
-Loop time of 2.38457 on 4 procs for 1000 steps with 250 atoms
+Loop time of 1.5074 on 4 procs for 1000 steps with 250 atoms
 
-Performance: 3.623 ns/day, 6.624 hours/ns, 419.362 timesteps/s
-97.2% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5.732 ns/day, 4.187 hours/ns, 663.393 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.32773    | 0.36909    | 0.41504    |   6.0 | 15.48
-Neigh   | 0.0014782  | 0.0015869  | 0.001724   |   0.2 |  0.07
-Comm    | 0.14716    | 0.19316    | 0.23754    |   8.4 |  8.10
-Output  | 0.0030437  | 0.0032653  | 0.0035224  |   0.3 |  0.14
-Modify  | 1.8109     | 1.8139     | 1.8175     |   0.2 | 76.07
-Other   |            | 0.003611   |            |       |  0.15
+Pair    | 0.22156    | 0.23223    | 0.24219    |   1.5 | 15.41
+Neigh   | 0.0011292  | 0.0011852  | 0.0012362  |   0.1 |  0.08
+Comm    | 0.067507   | 0.076341   | 0.087237   |   2.6 |  5.06
+Output  | 0.0015073  | 0.0015442  | 0.0015914  |   0.1 |  0.10
+Modify  | 1.1934     | 1.1947     | 1.1955     |   0.1 | 79.25
+Other   |            | 0.001434   |            |       |  0.10
 
 Nlocal:    62.5 ave 66 max 60 min
 Histogram: 1 1 0 0 0 1 0 0 0 1
@@ -136,4 +136,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:02
+Total wall time: 0:00:01
diff --git a/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1 b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1
index b73f7daad7..7871d82ae9 100644
--- a/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
   1 by 1 by 1 MPI processor grid
 create_atoms    1 box
 Created 500 atoms
-  create_atoms CPU = 0.00070715 secs
+  create_atoms CPU = 0.000484943 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -81,41 +81,41 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 7.885 | 7.885 | 7.885 Mbytes
 Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803   0.40997576    100.03408   -4775.0671   -2218.1018 
-      50        0.005  0.028733807  0.070491717    101.47879   -28153.519   -2218.1018 
-     100         0.01  0.028733815  -0.70937134     101.7311    2925.8177   -2218.1018 
-     150        0.015  0.028733823    -1.853981     99.63039    1197.9339   -2218.1018 
-     200         0.02  0.028733828   -3.2679239    94.850105    741.17431   -2218.1018 
-     250        0.025  0.028733824    -4.863967    88.444584    550.36979   -2218.1018 
-     300         0.03  0.028733807   -6.5763457    82.689581    449.78321   -2218.1018 
-     350        0.035  0.028733783   -8.3489158    80.108798    384.32228   -2218.1018 
-     400         0.04  0.028733763   -10.120216    82.374947    335.01545   -2218.1018 
-     450        0.045  0.028733755   -11.828932    89.814597    296.88965   -2218.1018 
-     500         0.05  0.028733762   -13.423712    101.39613    267.51686   -2218.1018 
-     550        0.055  0.028733783   -14.866724    115.07399    244.96012   -2218.1018 
-     600         0.06  0.028733801   -16.135279    128.57849    229.33327   -2218.1018 
-     650        0.065  0.028733804   -17.222838    140.22402    220.05718   -2218.1018 
-     700         0.07  0.028733795   -18.154813    149.61295    212.95678   -2218.1018 
-     750        0.075  0.028733781   -18.996903     157.5814    206.41327   -2218.1018 
-     800         0.08  0.028733768   -19.804249    164.92075    203.88977   -2218.1018 
-     850        0.085  0.028733752   -20.579151    171.67278    203.42363   -2218.1018 
-     900         0.09  0.028733728   -21.294277    177.67238    199.84817   -2218.1018 
-     950        0.095  0.028733715   -21.943945     183.2621     194.9614   -2218.1018 
-    1000          0.1   0.02873374   -22.551277    188.99284    191.59796   -2218.1018 
-Loop time of 5.15676 on 1 procs for 1000 steps with 500 atoms
+       0            0  0.028733803   0.40997576    100.03408   -4775.0671   -2218.3068 
+      50        0.005  0.028733807  0.070491717    101.47879   -28153.519   -2218.1371 
+     100         0.01  0.028733815  -0.70937134     101.7311    2925.8177   -2217.7471 
+     150        0.015  0.028733823    -1.853981     99.63039    1197.9339   -2217.1748 
+     200         0.02  0.028733828   -3.2679239    94.850105    741.17431   -2216.4678 
+     250        0.025  0.028733824    -4.863967    88.444584    550.36979   -2215.6698 
+     300         0.03  0.028733807   -6.5763457    82.689581    449.78321   -2214.8136 
+     350        0.035  0.028733783   -8.3489158    80.108798    384.32228   -2213.9273 
+     400         0.04  0.028733763   -10.120216    82.374947    335.01545   -2213.0417 
+     450        0.045  0.028733755   -11.828932    89.814597    296.88965   -2212.1873 
+     500         0.05  0.028733762   -13.423712    101.39613    267.51686     -2211.39 
+     550        0.055  0.028733783   -14.866724    115.07399    244.96012   -2210.6684 
+     600         0.06  0.028733801   -16.135279    128.57849    229.33327   -2210.0342 
+     650        0.065  0.028733804   -17.222838    140.22402    220.05718   -2209.4904 
+     700         0.07  0.028733795   -18.154813    149.61295    212.95678   -2209.0244 
+     750        0.075  0.028733781   -18.996903     157.5814    206.41327   -2208.6034 
+     800         0.08  0.028733768   -19.804249    164.92075    203.88977   -2208.1997 
+     850        0.085  0.028733752   -20.579151    171.67278    203.42363   -2207.8122 
+     900         0.09  0.028733728   -21.294277    177.67238    199.84817   -2207.4547 
+     950        0.095  0.028733715   -21.943945     183.2621     194.9614   -2207.1298 
+    1000          0.1   0.02873374   -22.551277    188.99284    191.59796   -2206.8262 
+Loop time of 4.30614 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 1.675 ns/day, 14.324 hours/ns, 193.920 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 2.006 ns/day, 11.961 hours/ns, 232.227 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.4083     | 2.4083     | 2.4083     |   0.0 | 46.70
-Neigh   | 0.016825   | 0.016825   | 0.016825   |   0.0 |  0.33
-Comm    | 0.039891   | 0.039891   | 0.039891   |   0.0 |  0.77
-Output  | 0.018168   | 0.018168   | 0.018168   |   0.0 |  0.35
-Modify  | 2.6657     | 2.6657     | 2.6657     |   0.0 | 51.69
-Other   |            | 0.007864   |            |       |  0.15
+Pair    | 2.038      | 2.038      | 2.038      |   0.0 | 47.33
+Neigh   | 0.01566    | 0.01566    | 0.01566    |   0.0 |  0.36
+Comm    | 0.032802   | 0.032802   | 0.032802   |   0.0 |  0.76
+Output  | 0.014146   | 0.014146   | 0.014146   |   0.0 |  0.33
+Modify  | 2.2003     | 2.2003     | 2.2003     |   0.0 | 51.10
+Other   |            | 0.005288   |            |       |  0.12
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -133,4 +133,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:05
+Total wall time: 0:00:04
diff --git a/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4 b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4
index 92bcc4f533..638ab5e635 100644
--- a/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
   1 by 2 by 2 MPI processor grid
 create_atoms    1 box
 Created 500 atoms
-  create_atoms CPU = 0.00071907 secs
+  create_atoms CPU = 0.000733852 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -102,20 +102,20 @@ Step Time v_magnorm v_emag Temp v_tmag TotEng
      900         0.09  0.028733829   -21.571419     167.8571    205.79849   -2218.1018 
      950        0.095  0.028733825   -22.365879    175.00875    201.33088   -2218.1018 
     1000          0.1  0.028733821   -23.133464    184.68305    195.52912   -2218.1018 
-Loop time of 3.95668 on 4 procs for 1000 steps with 500 atoms
+Loop time of 2.47211 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 2.184 ns/day, 10.991 hours/ns, 252.737 timesteps/s
-97.8% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 3.495 ns/day, 6.867 hours/ns, 404.513 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.89404    | 0.99018    | 1.0827     |   8.5 | 25.03
-Neigh   | 0.0050189  | 0.0053826  | 0.0057576  |   0.5 |  0.14
-Comm    | 0.23366    | 0.32767    | 0.42737    |  15.2 |  8.28
-Output  | 0.0078192  | 0.0078953  | 0.0080998  |   0.1 |  0.20
-Modify  | 2.6171     | 2.6192     | 2.6219     |   0.1 | 66.20
-Other   |            | 0.006363   |            |       |  0.16
+Pair    | 0.5549     | 0.56708    | 0.58627    |   1.6 | 22.94
+Neigh   | 0.0039728  | 0.0041007  | 0.0042598  |   0.2 |  0.17
+Comm    | 0.087296   | 0.10802    | 0.11917    |   3.8 |  4.37
+Output  | 0.0046923  | 0.0047188  | 0.0047917  |   0.1 |  0.19
+Modify  | 1.7832     | 1.7862     | 1.7879     |   0.1 | 72.25
+Other   |            | 0.002016   |            |       |  0.08
 
 Nlocal:    125 ave 139 max 112 min
 Histogram: 1 0 1 0 0 0 1 0 0 1
@@ -133,4 +133,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:03
+Total wall time: 0:00:02
diff --git a/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1 b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
index 2aa4a9a0d3..4f3b94df53 100644
--- a/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.000488997 secs
+  create_atoms CPU = 0.00109196 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -82,41 +82,41 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 7.885 | 7.885 | 7.885 Mbytes
 Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803     0.455085    100.03408    -4301.853   -2218.0905 
-      50        0.005  0.028732021   0.11535308    101.47887   -17203.944   -2218.0904 
-     100         0.01    0.0287304    -0.665283    101.73105    3119.2267     -2218.09 
-     150        0.015  0.028729403   -1.8105707    99.629794    1226.3803   -2218.0896 
-     200         0.02  0.028731067    -3.224763    94.849715    750.93124   -2218.0895 
-     250        0.025  0.028732765   -4.8207784    88.447019    555.16456   -2218.0895 
-     300         0.03  0.028728169   -6.5331538    82.697813     452.6101   -2218.0896 
-     350        0.035   0.02871707   -8.3059526    80.122838    386.20109   -2218.0896 
-     400         0.04  0.028706605   -10.077613    82.389555    336.36118   -2218.0895 
-     450        0.045  0.028701727    -11.78634    89.823176    297.91478   -2218.0894 
-     500         0.05  0.028706691   -13.380919    101.39804    268.32933   -2218.0894 
-     550        0.055  0.028714065   -14.824128    115.07511    245.62893   -2218.0893 
-     600         0.06  0.028713691   -16.093505    128.58093    229.91054    -2218.089 
-     650        0.065  0.028713232   -17.181217    140.22137    220.57591    -2218.089 
-     700         0.07   0.02871245   -18.113035    149.60156    213.40077   -2218.0889 
-     750        0.075  0.028712431   -18.954952    157.56849    206.80962   -2218.0891 
-     800         0.08   0.02872489   -19.762756    164.91833    204.24742   -2218.0892 
-     850        0.085  0.028733709   -20.538757    171.69348    203.73934   -2218.0894 
-     900         0.09  0.028737031   -21.256095    177.71981    200.12043   -2218.0894 
-     950        0.095  0.028743446   -21.908156    183.31613    195.23386    -2218.089 
-    1000          0.1  0.028751809   -22.516179    189.01672    191.90401   -2218.0888 
-Loop time of 5.71018 on 1 procs for 1000 steps with 500 atoms
+       0            0  0.028733803     0.455085    100.03408    -4301.853   -2218.2955 
+      50        0.005  0.028732021   0.11535308    101.47887   -17203.944   -2218.1258 
+     100         0.01    0.0287304    -0.665283    101.73105    3119.2267   -2217.7358 
+     150        0.015  0.028729403   -1.8105707    99.629794    1226.3803   -2217.1636 
+     200         0.02  0.028731067    -3.224763    94.849715    750.93124   -2216.4566 
+     250        0.025  0.028732765   -4.8207784    88.447019    555.16456   -2215.6585 
+     300         0.03  0.028728169   -6.5331538    82.697813     452.6101   -2214.8022 
+     350        0.035   0.02871707   -8.3059526    80.122838    386.20109   -2213.9158 
+     400         0.04  0.028706605   -10.077613    82.389555    336.36118     -2213.03 
+     450        0.045  0.028701727    -11.78634    89.823176    297.91478   -2212.1758 
+     500         0.05  0.028706691   -13.380919    101.39804    268.32933   -2211.3785 
+     550        0.055  0.028714065   -14.824128    115.07511    245.62893   -2210.6569 
+     600         0.06  0.028713691   -16.093505    128.58093    229.91054   -2210.0225 
+     650        0.065  0.028713232   -17.181217    140.22137    220.57591   -2209.4787 
+     700         0.07   0.02871245   -18.113035    149.60156    213.40077   -2209.0127 
+     750        0.075  0.028712431   -18.954952    157.56849    206.80962   -2208.5916 
+     800         0.08   0.02872489   -19.762756    164.91833    204.24742   -2208.1876 
+     850        0.085  0.028733709   -20.538757    171.69348    203.73934   -2207.7993 
+     900         0.09  0.028737031   -21.256095    177.71981    200.12043   -2207.4406 
+     950        0.095  0.028743446   -21.908156    183.31613    195.23386   -2207.1149 
+    1000          0.1  0.028751809   -22.516179    189.01672    191.90401   -2206.8111 
+Loop time of 4.3661 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 1.513 ns/day, 15.862 hours/ns, 175.126 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.979 ns/day, 12.128 hours/ns, 229.037 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.7307     | 2.7307     | 2.7307     |   0.0 | 47.82
-Neigh   | 0.018982   | 0.018982   | 0.018982   |   0.0 |  0.33
-Comm    | 0.044032   | 0.044032   | 0.044032   |   0.0 |  0.77
-Output  | 0.036037   | 0.036037   | 0.036037   |   0.0 |  0.63
-Modify  | 2.8713     | 2.8713     | 2.8713     |   0.0 | 50.28
-Other   |            | 0.009135   |            |       |  0.16
+Pair    | 2.0467     | 2.0467     | 2.0467     |   0.0 | 46.88
+Neigh   | 0.015636   | 0.015636   | 0.015636   |   0.0 |  0.36
+Comm    | 0.032918   | 0.032918   | 0.032918   |   0.0 |  0.75
+Output  | 0.027737   | 0.027737   | 0.027737   |   0.0 |  0.64
+Modify  | 2.2379     | 2.2379     | 2.2379     |   0.0 | 51.26
+Other   |            | 0.005233   |            |       |  0.12
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -135,4 +135,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:05
+Total wall time: 0:00:04
diff --git a/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4 b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
index 0657d43f8a..1724ef9df8 100644
--- a/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.000617027 secs
+  create_atoms CPU = 0.000827074 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -103,20 +103,20 @@ Step Time v_magnorm v_emag Temp v_tmag TotEng
      900         0.09  0.028684101   -21.521505    167.76167    206.14977    -2218.089 
      950        0.095  0.028684705   -22.314351      174.918    201.65878   -2218.0891 
     1000          0.1  0.028691284   -23.080026    184.60192     195.8385   -2218.0893 
-Loop time of 3.6142 on 4 procs for 1000 steps with 500 atoms
+Loop time of 2.5947 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 2.391 ns/day, 10.039 hours/ns, 276.686 timesteps/s
-98.8% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 3.330 ns/day, 7.207 hours/ns, 385.402 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.75407    | 0.87833    | 0.96493    |   8.8 | 24.30
-Neigh   | 0.004509   | 0.0051936  | 0.0056126  |   0.6 |  0.14
-Comm    | 0.19147    | 0.28312    | 0.4105     |  16.0 |  7.83
-Output  | 0.013854   | 0.013948   | 0.014158   |   0.1 |  0.39
-Modify  | 2.4267     | 2.4282     | 2.4319     |   0.1 | 67.19
-Other   |            | 0.005371   |            |       |  0.15
+Pair    | 0.56409    | 0.58139    | 0.605      |   2.0 | 22.41
+Neigh   | 0.0039618  | 0.0041058  | 0.0042889  |   0.2 |  0.16
+Comm    | 0.095324   | 0.12147    | 0.13892    |   4.8 |  4.68
+Output  | 0.008945   | 0.0089793  | 0.0090477  |   0.0 |  0.35
+Modify  | 1.8745     | 1.8765     | 1.8795     |   0.1 | 72.32
+Other   |            | 0.002217   |            |       |  0.09
 
 Nlocal:    125 ave 139 max 112 min
 Histogram: 1 0 1 0 0 0 1 0 0 1
@@ -135,4 +135,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:03
+Total wall time: 0:00:02
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
index cc1cb29a6e..d5c38a9967 100644
--- a/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
@@ -12,7 +12,7 @@ read_data 	Norm_randXY_8x8x32.data
   1 by 1 by 1 MPI processor grid
   reading atoms ...
   8192 atoms
-  read_data CPU = 0.0207078 secs
+  read_data CPU = 0.0127251 secs
 
 mass		1 58.93
 
@@ -68,31 +68,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 19.68 | 19.68 | 19.68 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-       0                    0   0.0177864461018737    -1323.65841279979       1274.398774669                    0    -37220.5576936917 
-      10                0.001   0.0177864363786085    -1323.66900862123     1270.76616762926   0.0100007025152235    -37220.5576943558 
-      20                0.002   0.0177864377251544    -1323.70032173151     1259.90270462032   0.0394803272360477    -37220.5576959255 
-      30                0.003   0.0177864511986563    -1323.75117991179     1243.50772254923   0.0871132837928349    -37220.5576982168 
-      40                0.004   0.0177864729727686    -1323.81992477224     1223.91535595806    0.150986538096776    -37220.5577010151 
-      50                0.005    0.017786495620418    -1323.90456907402     1203.45497846157     0.22877054554493    -37220.5577041158 
-      60                0.006   0.0177865119365897    -1324.00293472823     1183.95496070422    0.317876389336898    -37220.5577073311 
-      70                0.007   0.0177865186121948    -1324.11277680481     1166.52445270059    0.415601818818485    -37220.5577104779 
-      80                0.008   0.0177865171615599    -1324.23190710734     1151.59958937508    0.519276751090729    -37220.5577133816 
-      90                0.009   0.0177865117923882    -1324.35831839963     1139.14485136813    0.626407059487507    -37220.5577158996 
-     100                 0.01   0.0177865063215865    -1324.49029089774     1128.88117273962    0.734797362055872    -37220.5577179524 
-Loop time of 17.5042 on 1 procs for 100 steps with 8192 atoms
+       0                    0   0.0177864461018737    -1323.65841279979       1274.398774669                    0    -36558.7284872918 
+      10                0.001   0.0177864363786085    -1323.66900862123     1270.76616762926   0.0100007025152235    -36558.7231900452 
+      20                0.002   0.0177864377251544    -1323.70032173151     1259.90270462032   0.0394803272360477    -36558.7075350597 
+      30                0.003   0.0177864511986563    -1323.75117991179     1243.50772254923   0.0871132837928349    -36558.6821082609 
+      40                0.004   0.0177864729727686    -1323.81992477224     1223.91535595806    0.150986538096776    -36558.6477386289 
+      50                0.005    0.017786495620418    -1323.90456907402     1203.45497846157     0.22877054554493    -36558.6054195788 
+      60                0.006   0.0177865119365897    -1324.00293472823     1183.95496070422    0.317876389336898     -36558.556239967 
+      70                0.007   0.0177865186121948    -1324.11277680481     1166.52445270059    0.415601818818485    -36558.5013220755 
+      80                0.008   0.0177865171615599    -1324.23190710734     1151.59958937508    0.519276751090729    -36558.4417598279 
+      90                0.009   0.0177865117923882    -1324.35831839963     1139.14485136813    0.626407059487507    -36558.3785566998 
+     100                 0.01   0.0177865063215865    -1324.49029089774     1128.88117273962    0.734797362055872    -36558.3125725035 
+Loop time of 14.8985 on 1 procs for 100 steps with 8192 atoms
 
-Performance: 0.049 ns/day, 486.227 hours/ns, 5.713 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.058 ns/day, 413.847 hours/ns, 6.712 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.4555     | 5.4555     | 5.4555     |   0.0 | 31.17
-Neigh   | 3.9944     | 3.9944     | 3.9944     |   0.0 | 22.82
-Comm    | 0.086468   | 0.086468   | 0.086468   |   0.0 |  0.49
-Output  | 2.7685     | 2.7685     | 2.7685     |   0.0 | 15.82
-Modify  | 5.1645     | 5.1645     | 5.1645     |   0.0 | 29.50
-Other   |            | 0.0349     |            |       |  0.20
+Pair    | 4.5996     | 4.5996     | 4.5996     |   0.0 | 30.87
+Neigh   | 3.6        | 3.6        | 3.6        |   0.0 | 24.16
+Comm    | 0.057512   | 0.057512   | 0.057512   |   0.0 |  0.39
+Output  | 2.4463     | 2.4463     | 2.4463     |   0.0 | 16.42
+Modify  | 4.1766     | 4.1766     | 4.1766     |   0.0 | 28.03
+Other   |            | 0.01854    |            |       |  0.12
 
 Nlocal:    8192 ave 8192 max 8192 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -110,4 +110,4 @@ Dangerous builds not checked
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:17
+Total wall time: 0:00:15
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4
index 8c477e633f..decd7f66de 100644
--- a/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4
@@ -12,7 +12,7 @@ read_data 	Norm_randXY_8x8x32.data
   1 by 1 by 4 MPI processor grid
   reading atoms ...
   8192 atoms
-  read_data CPU = 0.023248 secs
+  read_data CPU = 0.0103889 secs
 
 mass		1 58.93
 
@@ -79,20 +79,20 @@ Step Time v_magnorm v_emag v_tmag Temp TotEng
       80                0.008   0.0177865881669081    -1324.23190693081     1151.59982868413    0.519276589926842     -37220.557713381 
       90                0.009   0.0177865780982769    -1324.35831816525     1139.14509878533    0.626406847905203     -37220.557715901 
      100                 0.01    0.017786564605084    -1324.49029060173     1128.88143013641    0.734797098519806     -37220.557717952 
-Loop time of 7.30477 on 4 procs for 100 steps with 8192 atoms
+Loop time of 4.32342 on 4 procs for 100 steps with 8192 atoms
 
-Performance: 0.118 ns/day, 202.910 hours/ns, 13.690 timesteps/s
-98.0% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.200 ns/day, 120.095 hours/ns, 23.130 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.9727     | 2.0433     | 2.1095     |   3.9 | 27.97
-Neigh   | 1.1665     | 1.3031     | 1.4137     |   8.7 | 17.84
-Comm    | 0.15743    | 0.31703    | 0.53111    |  28.2 |  4.34
-Output  | 1.0547     | 1.0747     | 1.094      |   1.4 | 14.71
-Modify  | 2.5296     | 2.5551     | 2.5794     |   1.1 | 34.98
-Other   |            | 0.01167    |            |       |  0.16
+Pair    | 1.185      | 1.1925     | 1.1991     |   0.5 | 27.58
+Neigh   | 0.93459    | 0.93934    | 0.94983    |   0.6 | 21.73
+Comm    | 0.042462   | 0.059373   | 0.069249   |   4.1 |  1.37
+Output  | 0.61823    | 0.63273    | 0.64528    |   1.3 | 14.63
+Modify  | 1.4827     | 1.4955     | 1.5099     |   0.8 | 34.59
+Other   |            | 0.003968   |            |       |  0.09
 
 Nlocal:    2048 ave 2061 max 2035 min
 Histogram: 1 0 0 1 0 0 1 0 0 1
@@ -110,4 +110,4 @@ Dangerous builds not checked
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:07
+Total wall time: 0:00:04
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
index 4ca29113d3..c7544dedfa 100644
--- a/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
@@ -16,7 +16,7 @@ WARNING: Restart file used different # of processors: 4 vs. 1 (../read_restart.c
   1 by 1 by 1 MPI processor grid
   restoring pair style spin/exchange from restart
   500 atoms
-  read_restart CPU = 0.000402927 secs
+  read_restart CPU = 0.000396967 secs
 
 # setting mass, mag. moments, and interactions
 
@@ -74,31 +74,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 6.816 | 6.816 | 6.816 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-    1000                    0    0.108317262557656    -10.7649197733649      2538.4247868621                    0     -2205.7648720089 
-    1010                0.001    0.108317281393701    -10.7743543303502     2527.22692799144    0.146167392153018    -2205.76487255098 
-    1020                0.002    0.108317318482233    -10.8022550516195     2509.47863584151    0.577304300153637    -2205.76487378396 
-    1030                0.003    0.108317366763426    -10.8476659807571      2487.5614649682     1.27529086243277    -2205.76487555634 
-    1040                0.004    0.108317415532953    -10.9092708333549     2463.97963921611     2.21443906326453    -2205.76487769286 
-    1050                0.005    0.108317453851058      -10.98553406179     2440.70473642157     3.36396898978859     -2205.7648800529 
-    1060                0.006    0.108317473584086    -11.0748008072977     2418.66477599297     4.68991434259399    -2205.76488256723 
-    1070                0.007    0.108317471632913     -11.175325501803     2397.59274785581     6.15596240129541    -2205.76488520043 
-    1080                0.008    0.108317450667394    -11.2852665400894     2376.32871275528      7.7237909750654    -2205.76488786887 
-    1090                0.009    0.108317417687893    -11.4027246787047     2353.52646917989     9.35409156720424    -2205.76489041327 
-    1100                 0.01    0.108317381194814      -11.52585602487     2328.41541723561     11.0087303030003    -2205.76489265824 
-Loop time of 1.05153 on 1 procs for 100 steps with 500 atoms
+    1000                    0    0.108317262557656    -10.7649197733649      2538.4247868621                    0    -2200.38241212222 
+    1010                0.001    0.108317281393701    -10.7743543303502     2527.22692799144    0.146167392153018     -2200.3776953858 
+    1020                0.002    0.108317318482233    -10.8022550516195     2509.47863584151    0.577304300153637    -2200.36374625815 
+    1030                0.003    0.108317366763426    -10.8476659807571      2487.5614649682     1.27529086243277    -2200.34104256596 
+    1040                0.004    0.108317415532953    -10.9092708333549     2463.97963921611     2.21443906326453    -2200.31024227618 
+    1050                0.005    0.108317453851058      -10.98553406179     2440.70473642157     3.36396898978859    -2200.27211302201 
+    1060                0.006    0.108317473584086    -11.0748008072977     2418.66477599297     4.68991434259399    -2200.22748216359 
+    1070                0.007    0.108317471632913     -11.175325501803     2397.59274785581     6.15596240129541    -2200.17722244953 
+    1080                0.008    0.108317450667394    -11.2852665400894     2376.32871275528      7.7237909750654    -2200.12225459883 
+    1090                0.009    0.108317417687893    -11.4027246787047     2353.52646917989     9.35409156720424    -2200.06352807392 
+    1100                 0.01    0.108317381194814      -11.52585602487     2328.41541723561     11.0087303030003     -2200.0019646458 
+Loop time of 0.964681 on 1 procs for 100 steps with 500 atoms
 
-Performance: 0.822 ns/day, 29.209 hours/ns, 95.100 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.896 ns/day, 26.797 hours/ns, 103.661 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.3348     | 0.3348     | 0.3348     |   0.0 | 31.84
-Neigh   | 0.26691    | 0.26691    | 0.26691    |   0.0 | 25.38
-Comm    | 0.007993   | 0.007993   | 0.007993   |   0.0 |  0.76
-Output  | 0.14892    | 0.14892    | 0.14892    |   0.0 | 14.16
-Modify  | 0.29137    | 0.29137    | 0.29137    |   0.0 | 27.71
-Other   |            | 0.001526   |            |       |  0.15
+Pair    | 0.29842    | 0.29842    | 0.29842    |   0.0 | 30.93
+Neigh   | 0.25359    | 0.25359    | 0.25359    |   0.0 | 26.29
+Comm    | 0.0069926  | 0.0069926  | 0.0069926  |   0.0 |  0.72
+Output  | 0.14398    | 0.14398    | 0.14398    |   0.0 | 14.93
+Modify  | 0.26045    | 0.26045    | 0.26045    |   0.0 | 27.00
+Other   |            | 0.001249   |            |       |  0.13
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4
index 5d40efc29b..6443d341cd 100644
--- a/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4
@@ -15,7 +15,7 @@ read_restart	restart_hcp_cobalt.equil
   1 by 2 by 2 MPI processor grid
   restoring pair style spin/exchange from restart
   500 atoms
-  read_restart CPU = 0.000858784 secs
+  read_restart CPU = 0.000922918 secs
 
 # setting mass, mag. moments, and interactions
 
@@ -84,20 +84,20 @@ Step Time v_magnorm v_emag v_tmag Temp TotEng
     1080                0.008    0.108317320750099    -11.2852665775656     2376.32820919279      7.7237915384778    -2205.76488786888 
     1090                0.009    0.108317304079233     -11.402724701646     2353.52588586648     9.35409189724323     -2205.7648904133 
     1100                 0.01    0.108317284409678    -11.5258560062539     2328.41472376239     11.0087299868288    -2205.76489265829 
-Loop time of 0.603216 on 4 procs for 100 steps with 500 atoms
+Loop time of 0.410707 on 4 procs for 100 steps with 500 atoms
 
-Performance: 1.432 ns/day, 16.756 hours/ns, 165.778 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 2.104 ns/day, 11.409 hours/ns, 243.483 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.1203     | 0.12952    | 0.13546    |   1.6 | 21.47
-Neigh   | 0.064357   | 0.080477   | 0.093005   |   4.4 | 13.34
-Comm    | 0.016533   | 0.035739   | 0.06195    |   9.9 |  5.92
-Output  | 0.063324   | 0.065044   | 0.066794   |   0.5 | 10.78
-Modify  | 0.29023    | 0.29189    | 0.29336    |   0.3 | 48.39
-Other   |            | 0.0005503  |            |       |  0.09
+Pair    | 0.083043   | 0.083714   | 0.084202   |   0.1 | 20.38
+Neigh   | 0.063158   | 0.064429   | 0.065314   |   0.3 | 15.69
+Comm    | 0.012237   | 0.013588   | 0.014798   |   0.8 |  3.31
+Output  | 0.039088   | 0.040653   | 0.042176   |   0.6 |  9.90
+Modify  | 0.20645    | 0.20795    | 0.20945    |   0.2 | 50.63
+Other   |            | 0.0003724  |            |       |  0.09
 
 Nlocal:    125 ave 127 max 122 min
 Histogram: 1 0 0 0 1 0 0 0 0 2
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
index 986f93e3e1..9dbe1a3548 100644
--- a/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
@@ -18,7 +18,7 @@ Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.001122 secs
+  create_atoms CPU = 0.000552893 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -72,31 +72,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 6.947 | 6.947 | 6.947 Mbytes
 Step Time v_magnorm v_emag Temp TotEng 
-       0            0  0.076558814    1.7982359            0    1.7982359 
-     100         0.01  0.077628154   0.73387834            0   0.73387834 
-     200         0.02  0.076678996   -0.4048463            0   -0.4048463 
-     300         0.03  0.079174837   -1.3519103            0   -1.3519103 
-     400         0.04  0.085031632   -3.0345702            0   -3.0345702 
-     500         0.05   0.08702747   -4.0853256            0   -4.0853256 
-     600         0.06  0.087066482    -5.259549            0    -5.259549 
-     700         0.07  0.089788894    -6.629076            0    -6.629076 
-     800         0.08  0.091699611   -8.0574087            0   -8.0574087 
-     900         0.09  0.090038899   -9.2012019            0   -9.2012019 
-    1000          0.1  0.093257309   -10.470452            0   -10.470452 
-Loop time of 3.56687 on 1 procs for 1000 steps with 500 atoms
+       0            0  0.076558814    1.7982359            0   0.89911794 
+     100         0.01  0.077628154   0.73387834            0   0.36693917 
+     200         0.02  0.076678996   -0.4048463            0  -0.20242315 
+     300         0.03  0.079174837   -1.3519103            0  -0.67595514 
+     400         0.04  0.085031632   -3.0345702            0   -1.5172851 
+     500         0.05   0.08702747   -4.0853256            0   -2.0426628 
+     600         0.06  0.087066482    -5.259549            0   -2.6297745 
+     700         0.07  0.089788894    -6.629076            0    -3.314538 
+     800         0.08  0.091699611   -8.0574087            0   -4.0287043 
+     900         0.09  0.090038899   -9.2012019            0    -4.600601 
+    1000          0.1  0.093257309   -10.470452            0   -5.2352261 
+Loop time of 3.37852 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 2.422 ns/day, 9.908 hours/ns, 280.358 timesteps/s
-99.3% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 2.557 ns/day, 9.385 hours/ns, 295.987 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.46568    | 0.46568    | 0.46568    |   0.0 | 13.06
+Pair    | 0.45808    | 0.45808    | 0.45808    |   0.0 | 13.56
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.022188   | 0.022188   | 0.022188   |   0.0 |  0.62
-Output  | 1.4417     | 1.4417     | 1.4417     |   0.0 | 40.42
-Modify  | 1.6335     | 1.6335     | 1.6335     |   0.0 | 45.80
-Other   |            | 0.003845   |            |       |  0.11
+Comm    | 0.019707   | 0.019707   | 0.019707   |   0.0 |  0.58
+Output  | 1.3865     | 1.3865     | 1.3865     |   0.0 | 41.04
+Modify  | 1.5106     | 1.5106     | 1.5106     |   0.0 | 44.71
+Other   |            | 0.003624   |            |       |  0.11
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
index 05f6091f79..cb98274603 100644
--- a/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
@@ -18,7 +18,7 @@ Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.000901937 secs
+  create_atoms CPU = 0.000751972 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -83,20 +83,20 @@ Step Time v_magnorm v_emag Temp TotEng
      800         0.08  0.097960611   -7.8688568            0   -7.8688568 
      900         0.09   0.10193463   -9.5888008            0   -9.5888008 
     1000          0.1   0.10831726    -10.76492            0    -10.76492 
-Loop time of 2.36594 on 4 procs for 1000 steps with 500 atoms
+Loop time of 1.70473 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 3.652 ns/day, 6.572 hours/ns, 422.665 timesteps/s
-98.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5.068 ns/day, 4.735 hours/ns, 586.602 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.13515    | 0.15276    | 0.16507    |   2.8 |  6.46
+Pair    | 0.11636    | 0.11927    | 0.12069    |   0.5 |  7.00
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.08478    | 0.10161    | 0.12408    |   4.5 |  4.29
-Output  | 0.50658    | 0.52938    | 0.55066    |   2.3 | 22.38
-Modify  | 1.5629     | 1.5794     | 1.6014     |   1.3 | 66.75
-Other   |            | 0.002834   |            |       |  0.12
+Comm    | 0.049208   | 0.052445   | 0.057424   |   1.4 |  3.08
+Output  | 0.38579    | 0.40345    | 0.4199     |   2.0 | 23.67
+Modify  | 1.1138     | 1.1282     | 1.1436     |   1.1 | 66.18
+Other   |            | 0.001322   |            |       |  0.08
 
 Nlocal:    125 ave 125 max 125 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -116,4 +116,4 @@ write_restart 	restart_hcp_cobalt.equil
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:02
+Total wall time: 0:00:01
diff --git a/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1 b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1
index da8e705204..ed5c037feb 100644
--- a/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1
+++ b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1
@@ -18,10 +18,10 @@ region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
 region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
 create_atoms 	1 region reg1
 Created 120 atoms
-  create_atoms CPU = 0.000591993 secs
+  create_atoms CPU = 0.000998974 secs
 create_atoms 	2 region reg2
 Created 80 atoms
-  create_atoms CPU = 2.19345e-05 secs
+  create_atoms CPU = 4.1008e-05 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -88,25 +88,25 @@ Neighbor list info ...
       bin: none
 Per MPI rank memory allocation (min/avg/max) = 7.215 | 7.215 | 7.215 Mbytes
 Step Time v_magx v_magz v_magnorm v_tmag TotEng 
-       0                    0 0.000143282585570239    0.615515043943419    0.615726279597251      21.735436446264    0.251043691626527 
-     100                 0.01 -0.00116085697754605    0.590264559350799    0.590315072966953  0.00283413081085227   0.0846048989956838 
-     200                 0.02 -0.00014757052323624      0.5896197627388    0.589686497206689 0.000451051163122381   0.0839054390713707 
-     300                 0.03 2.64982966536903e-05    0.590029694756149    0.590102003120244 5.22539631503911e-05   0.0838351677819021 
-     400                 0.04 1.77805448780044e-05    0.590195117338991    0.590268726215095 4.46490059775722e-06   0.0838382933245033 
-     500                 0.05 6.71566571038784e-06    0.590243842081075    0.590317756995865 3.63227563542099e-07   0.0838411433938002 
-     600                 0.06 2.24103407431009e-06    0.590257551861528    0.590331542128336 2.99360370345602e-08   0.0838420708305254 
-     700                 0.07 7.12179152899672e-07      0.5902614042958    0.590335413637883 2.51559188415894e-09   0.0838423375091772 
-     800                 0.08 2.20574733078571e-07    0.590262494529884    0.590336508799302 2.14455748236281e-10   0.0838424126463501 
-     900                 0.09 6.72564339382342e-08    0.590262805532644    0.590336821097688 1.84495767133404e-11   0.0838424338620733 
-    1000                  0.1 2.03001940418668e-08    0.590262894882646    0.590336910794094  1.5958531383517e-12   0.0838424398944954 
-Loop time of 0.128906 on 1 procs for 1000 steps with 200 atoms
+       0                    0 0.000143282585570239    0.615515043943419    0.615726279597251     24.9364200982478    0.121881906963737 
+     100                 0.01 0.000616167502203097    0.594467364025194    0.594498630048783  0.00188964439583802   0.0371335982020527 
+     200                 0.02 0.000498981016106215    0.595175581059792    0.595218717456538 0.000158614984300385    0.036877233648055 
+     300                 0.03 0.000211899815837572    0.595357874794342    0.595402442288391 1.44454891242177e-05   0.0368548794182375 
+     400                 0.04 7.98967577397158e-05    0.595395828381057    0.595440657806237 1.50721782707597e-06   0.0368527556548781 
+     500                 0.05  2.9121648914103e-05    0.595403174462525    0.595448064489507 1.74330474543395e-07   0.0368525254239539 
+     600                 0.06 1.04772320898497e-05    0.595404457003426    0.595449362424563 2.12204214498221e-08   0.0368524982492743 
+     700                 0.07 3.74634771616422e-06    0.595404627382825    0.595449536940641 2.63852407890463e-09    0.036852494912626 
+     800                 0.08 1.33525617457914e-06    0.595404626884198    0.595449537611055 3.30772506699851e-10   0.0368524944963445 
+     900                 0.09 4.75054785504803e-07    0.595404613763238    0.595449524836571 4.15940445257144e-11   0.0368524944440918 
+    1000                  0.1 1.68843135202601e-07     0.59540460640039    0.595449517580793 5.23632581178917e-12    0.036852494437518 
+Loop time of 0.0966749 on 1 procs for 1000 steps with 200 atoms
 
-98.9% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
   Energy initial, next-to-last, final = 
-        0.251043691627    0.0838424398641    0.0838424398945
+        0.121881906964    0.0368524944375    0.0368524944375
   Force two-norm initial, final = 0 0
   Force max component initial, final = 0 0
   Final line search alpha, max atom move = 0 0
@@ -115,12 +115,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.11267    | 0.11267    | 0.11267    |   0.0 | 87.41
+Pair    | 0.08679    | 0.08679    | 0.08679    |   0.0 | 89.77
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00012422 | 0.00012422 | 0.00012422 |   0.0 |  0.10
-Output  | 0.0062549  | 0.0062549  | 0.0062549  |   0.0 |  4.85
-Modify  | 0.0036588  | 0.0036588  | 0.0036588  |   0.0 |  2.84
-Other   |            | 0.006197   |            |       |  4.81
+Comm    | 7.2956e-05 | 7.2956e-05 | 7.2956e-05 |   0.0 |  0.08
+Output  | 0.0033231  | 0.0033231  | 0.0033231  |   0.0 |  3.44
+Modify  | 0.0022919  | 0.0022919  | 0.0022919  |   0.0 |  2.37
+Other   |            | 0.004197   |            |       |  4.34
 
 Nlocal:    200 ave 200 max 200 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4 b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4
index 4889232f9d..4ce1497957 100644
--- a/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4
+++ b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4
@@ -18,10 +18,10 @@ region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
 region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
 create_atoms 	1 region reg1
 Created 120 atoms
-  create_atoms CPU = 0.000560045 secs
+  create_atoms CPU = 0.000770092 secs
 create_atoms 	2 region reg2
 Created 80 atoms
-  create_atoms CPU = 0.000101089 secs
+  create_atoms CPU = 7.9155e-05 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -99,9 +99,9 @@ Step Time v_magx v_magz v_magnorm v_tmag TotEng
      800                 0.08 2.20574733079126e-07    0.590262494529884    0.590336508799302 2.14455748236281e-10   0.0838424126463497 
      900                 0.09 6.72564339365689e-08    0.590262805532644    0.590336821097688 1.84495767133404e-11   0.0838424338620728 
     1000                  0.1 2.03001940390912e-08    0.590262894882646    0.590336910794094  1.5958531383517e-12   0.0838424398944951 
-Loop time of 0.0892034 on 4 procs for 1000 steps with 200 atoms
+Loop time of 0.0617704 on 4 procs for 1000 steps with 200 atoms
 
-91.7% CPU use with 4 MPI tasks x no OpenMP threads
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
@@ -115,12 +115,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.032445   | 0.038594   | 0.054315   |   4.6 | 43.27
+Pair    | 0.023753   | 0.029762   | 0.035936   |   3.3 | 48.18
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.020121   | 0.035668   | 0.042827   |   4.8 | 39.98
-Output  | 0.0024662  | 0.0025705  | 0.0028648  |   0.3 |  2.88
-Modify  | 0.00099444 | 0.0010954  | 0.0011995  |   0.2 |  1.23
-Other   |            | 0.01128    |            |       | 12.64
+Comm    | 0.011783   | 0.019131   | 0.025404   |   4.3 | 30.97
+Output  | 0.0019517  | 0.0019774  | 0.0020368  |   0.1 |  3.20
+Modify  | 0.0006361  | 0.00087249 | 0.0011525  |   0.0 |  1.41
+Other   |            | 0.01003    |            |       | 16.23
 
 Nlocal:    50 ave 50 max 50 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1
index 134ff82ea0..61b6ad8700 100644
--- a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 5780 atoms
-  create_atoms CPU = 0.00103712 secs
+  create_atoms CPU = 0.00107217 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -88,35 +88,35 @@ Neighbor list info ...
       bin: none
 Per MPI rank memory allocation (min/avg/max) = 8.331 | 8.331 | 8.331 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-       0                    0   0.0100717228668283   -0.162177519662199     14970.7090923449                    0   -0.157514482753568 
-      50                0.005  0.00013406177065452    -128.226118665465    0.102634444037433                    0     -128.28618242467 
-     100                 0.01 7.67769618983783e-06    -131.374599259781   0.0222596977749883                    0    -131.428418504308 
-     150                0.015 6.02904602224617e-07    -132.224372015825  0.00974271828169067                    0    -132.273190134603 
-     200                 0.02 6.50197247050607e-07    -132.573383315469  0.00374227079785919                    0    -132.617565541035 
-     250                0.025 4.40534385751331e-07    -132.729743470508  0.00193340972825779                    0    -132.770567114743 
-     300                 0.03 2.78356316513452e-07    -132.819255077939  0.00124938353773497                    0    -132.857574876413 
-     350                0.035 1.79684785125462e-07    -132.882714312877 0.000973166792896161                    0    -132.919261229743 
-     400                 0.04 1.10949878458879e-07    -132.935357748213 0.000852955460997589                    0    -132.970786605995 
-     450                0.045 6.49064465617783e-08    -132.982991683198 0.000790741148426227                    0    -133.017887798926 
-     500                 0.05 3.70514666560433e-08    -133.027689959766 0.000747949132882749                    0    -133.062561991888 
-     550                0.055 2.12433814830335e-08    -133.070148920145 0.000712637321271171                    0    -133.105417593747 
-     600                 0.06 1.24676590173818e-08    -133.110772798502 0.000685051841817329                    0    -133.146767469277 
-     650                0.065 7.53611859123344e-09    -133.150126417754 0.000669443562813207                    0    -133.187094895709 
-     700                 0.07 4.63539338668379e-09    -133.189024073453 0.000669619853917951                    0    -133.227152349437 
-     750                0.075 2.82145833993213e-09     -133.22844627026  0.00068733803508696                    0    -133.267881315199 
-     800                 0.08 1.64378151551878e-09    -133.269413776733  0.00072219769217513                    0    -133.310284062462 
-     850                0.085 8.88331010921243e-10    -133.312863108453 0.000771645398804489                    0    -133.355293578462 
-     900                 0.09 4.33874801673642e-10    -133.359507749172 0.000830255722998153                    0    -133.403626236688 
-     950                0.095 1.88127849216404e-10    -133.409630495316 0.000888348219681115                    0    -133.455560507802 
-    1000                  0.1 7.17748877096286e-11    -133.462806227865 0.000931427722404679                    0    -133.510640942679 
-Loop time of 11.213 on 1 procs for 1000 steps with 5780 atoms
+       0                    0   0.0100717228668283   -0.163834417271778     14831.3069413956                    0  -0.0819172086358848 
+      50                0.005 0.000106105812337003    -128.307447484203    0.104264818055985                    0    -64.1537237421011 
+     100                 0.01 7.95347901119144e-06    -131.449389798071   0.0221943604064967                    0    -65.7246948990356 
+     150                0.015 5.63006161138875e-07    -132.296453030419   0.0085472877724348                    0    -66.1482265152089 
+     200                 0.02 5.07390677383517e-07    -132.622857703805  0.00361380451198708                    0    -66.3114288519012 
+     250                0.025 3.28458336892231e-07    -132.774411992703  0.00187753161968493                    0    -66.3872059963511 
+     300                 0.03 1.93294839202864e-07    -132.861283726084  0.00121374398924599                    0    -66.4306418630428 
+     350                0.035 1.13872157437693e-07    -132.923137019136 0.000954736871701507                    0    -66.4615685095675 
+     400                 0.04 6.42075545620808e-08    -132.975239148591 0.000854064736183609                    0    -66.4876195742954 
+     450                0.045 3.44210513403008e-08    -133.023523287306 0.000812909459005007                    0    -66.5117616436536 
+     500                 0.05 1.80394981485933e-08    -133.070071976252 0.000789742875305133                    0    -66.5350359881254 
+     550                0.055 9.54697157105863e-09     -133.11541233939 0.000769860218895372                    0    -66.5577061696963 
+     600                 0.06 5.22455110720346e-09    -133.159676447906 0.000752941158466282                    0    -66.5798382239526 
+     650                0.065 2.95172977724016e-09    -133.203196195612 0.000745065216626277                    0    -66.6015980978057 
+     700                 0.07  1.6727567441294e-09    -133.246696814329 0.000752898926000619                    0    -66.6233484071653 
+     750                0.075 9.17127001723567e-10    -133.291227007554 0.000780491405791262                    0    -66.6456135037769 
+     800                 0.08 4.72669535949609e-10    -133.337962593396 0.000827942834401386                    0    -66.6689812966976 
+     850                0.085 2.25696738407094e-10    -133.387945245851 0.000890246383931885                    0    -66.6939726229243 
+     900                 0.09  1.0030717061716e-10    -133.441737087546 0.000955403731484674                    0     -66.720868543773 
+     950                0.095 4.19867626359036e-11    -133.498969798312  0.00100352240545389                    0    -66.7494848991554 
+    1000                  0.1 1.64283478182092e-11    -133.557979904763  0.00101162410316333                    0    -66.7789899523816 
+Loop time of 9.23057 on 1 procs for 1000 steps with 5780 atoms
 
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
   Energy initial, next-to-last, final = 
-       -0.157514482754     -133.509516066     -133.510640943
+      -0.0819172086359      -66.778399627     -66.7789899524
   Force two-norm initial, final = 0 0
   Force max component initial, final = 0 0
   Final line search alpha, max atom move = 0 0
@@ -125,12 +125,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 10.611     | 10.611     | 10.611     |   0.0 | 94.63
+Pair    | 8.7576     | 8.7576     | 8.7576     |   0.0 | 94.88
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.048211   | 0.048211   | 0.048211   |   0.0 |  0.43
-Output  | 0.37333    | 0.37333    | 0.37333    |   0.0 |  3.33
-Modify  | 0.038759   | 0.038759   | 0.038759   |   0.0 |  0.35
-Other   |            | 0.1419     |            |       |  1.27
+Comm    | 0.023815   | 0.023815   | 0.023815   |   0.0 |  0.26
+Output  | 0.31665    | 0.31665    | 0.31665    |   0.0 |  3.43
+Modify  | 0.029446   | 0.029446   | 0.029446   |   0.0 |  0.32
+Other   |            | 0.1031     |            |       |  1.12
 
 Nlocal:    5780 ave 5780 max 5780 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -145,4 +145,4 @@ Total # of neighbors = 92480
 Ave neighs/atom = 16
 Neighbor list builds = 0
 Dangerous builds = 0
-Total wall time: 0:00:11
+Total wall time: 0:00:09
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4
index 16e51bd17a..efc4628b9e 100644
--- a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
   2 by 2 by 1 MPI processor grid
 create_atoms 	1 box
 Created 5780 atoms
-  create_atoms CPU = 0.00216103 secs
+  create_atoms CPU = 0.00102711 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -109,9 +109,9 @@ Step Time v_magnorm v_emag v_tmag Temp TotEng
      900                 0.09 4.33874801863461e-10    -133.359507749172 0.000830255722998156                    0    -133.403626236688 
      950                0.095  1.8812784924272e-10    -133.409630495316 0.000888348219681112                    0    -133.455560507802 
     1000                  0.1 7.17748875671948e-11    -133.462806227865 0.000931427722404681                    0    -133.510640942679 
-Loop time of 3.46778 on 4 procs for 1000 steps with 5780 atoms
+Loop time of 2.53419 on 4 procs for 1000 steps with 5780 atoms
 
-99.2% CPU use with 4 MPI tasks x no OpenMP threads
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
@@ -125,12 +125,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.4063     | 2.831      | 3.0798     |  15.5 | 81.64
+Pair    | 2.2697     | 2.2995     | 2.3564     |   2.2 | 90.74
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.21179    | 0.45698    | 0.87844    |  38.4 | 13.18
-Output  | 0.1139     | 0.11396    | 0.11409    |   0.0 |  3.29
-Modify  | 0.0079708  | 0.0099814  | 0.011315   |   1.2 |  0.29
-Other   |            | 0.05581    |            |       |  1.61
+Comm    | 0.05711    | 0.11414    | 0.14368    |  10.1 |  4.50
+Output  | 0.084883   | 0.084915   | 0.084985   |   0.0 |  3.35
+Modify  | 0.0071826  | 0.0072024  | 0.0072234  |   0.0 |  0.28
+Other   |            | 0.02847    |            |       |  1.12
 
 Nlocal:    1445 ave 1445 max 1445 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -145,4 +145,4 @@ Total # of neighbors = 92480
 Ave neighs/atom = 16
 Neighbor list builds = 0
 Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:02
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1
index 0687081521..ffd244b146 100644
--- a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 5780 atoms
-  create_atoms CPU = 0.00103903 secs
+  create_atoms CPU = 0.00135589 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -88,25 +88,25 @@ Neighbor list info ...
       bin: none
 Per MPI rank memory allocation (min/avg/max) = 8.331 | 8.331 | 8.331 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-       0                    0   0.0100717228668283   -0.162177519662199     14970.7090923449                    0   -0.157514482753568 
-     100                 0.01 8.97646420937928e-06    -132.756468673032  0.00226858475243124                    0    -132.798812395869 
-     200                 0.02 5.70496744394871e-06    -133.065966570145 0.000924384747875191                    0    -133.105411060402 
-     300                 0.03 7.08166486347207e-06    -133.359072681024  0.00128114254070689                    0    -133.406669528642 
-     400                 0.04  4.6022497035281e-06    -133.668643035704  0.00082233479844806                    0    -133.725353643023 
-     500                 0.05 3.13737045264263e-06    -133.819548711647  0.00036967841746145                    0    -133.878037514586 
-     600                 0.06 2.55239214470191e-06    -133.889302880669 0.000169614248283497                    0    -133.948327309748 
-     700                 0.07 1.92236411979773e-06    -133.920147501261 7.31985644003828e-05                    0    -133.979597440787 
-     800                 0.08 1.40879742056288e-06    -133.933445418833 3.19349095035102e-05                    0    -133.993344750158 
-     900                 0.09 1.02629246258505e-06    -133.939321574068 1.44399877051466e-05                    0    -133.999611147323 
-    1000                  0.1 7.52253147839439e-07    -133.942032102451 6.85789018963958e-06                    0    -134.002604512511 
-Loop time of 10.4788 on 1 procs for 1000 steps with 5780 atoms
+       0                    0   0.0100717228668283   -0.163834417271778     14831.3069413956                    0  -0.0819172086358848 
+     100                 0.01 8.80197005314557e-06     -132.80634639767  0.00226660536216922                    0    -66.4031731988347 
+     200                 0.02 6.70903250218956e-06    -133.127078243354  0.00103783628361662                    0     -66.563539121677 
+     300                 0.03  4.5381603452565e-06    -133.471076972345  0.00144833375067451                    0    -66.7355384861738 
+     400                 0.04 9.04820921016732e-07    -133.767843456662 0.000682239601485924                    0    -66.8839217283314 
+     500                 0.05  1.6866160174916e-06    -133.893922160731  0.00032462625992713                    0     -66.946961080365 
+     600                 0.06 1.78038217785001e-06    -133.957222680701 0.000160730704849448                    0    -66.9786113403509 
+     700                 0.07 1.49199057723078e-06    -133.987255887786 7.39864656758093e-05                    0    -66.9936279438931 
+     800                 0.08 1.15173756711067e-06    -134.000921126053 3.33959465206462e-05                    0    -67.0004605630278 
+     900                 0.09 8.48526364752965e-07    -134.007049858868 1.49345737358251e-05                    0    -67.0035249294347 
+    1000                  0.1 6.10346492876059e-07    -134.009791515671 6.71648807105468e-06                    0    -67.0048957578347 
+Loop time of 9.4449 on 1 procs for 1000 steps with 5780 atoms
 
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
   Energy initial, next-to-last, final = 
-       -0.157514482754      -134.00257032     -134.002604513
+      -0.0819172086359     -67.0048809251     -67.0048957578
   Force two-norm initial, final = 0 0
   Force max component initial, final = 0 0
   Final line search alpha, max atom move = 2.122e-314 0
@@ -115,12 +115,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 9.7413     | 9.7413     | 9.7413     |   0.0 | 92.96
+Pair    | 8.7686     | 8.7686     | 8.7686     |   0.0 | 92.84
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.033583   | 0.033583   | 0.033583   |   0.0 |  0.32
-Output  | 0.33068    | 0.33068    | 0.33068    |   0.0 |  3.16
-Modify  | 0.033124   | 0.033124   | 0.033124   |   0.0 |  0.32
-Other   |            | 0.3401     |            |       |  3.25
+Comm    | 0.02386    | 0.02386    | 0.02386    |   0.0 |  0.25
+Output  | 0.31808    | 0.31808    | 0.31808    |   0.0 |  3.37
+Modify  | 0.029416   | 0.029416   | 0.029416   |   0.0 |  0.31
+Other   |            | 0.305      |            |       |  3.23
 
 Nlocal:    5780 ave 5780 max 5780 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -138,4 +138,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:10
+Total wall time: 0:00:09
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4
index b1dfabd35e..730bf477d4 100644
--- a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
   2 by 2 by 1 MPI processor grid
 create_atoms 	1 box
 Created 5780 atoms
-  create_atoms CPU = 0.000909805 secs
+  create_atoms CPU = 0.00138712 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -99,9 +99,9 @@ Step Time v_magnorm v_emag v_tmag Temp TotEng
      800                 0.08 1.40879742055238e-06    -133.933445418833 3.19349095035109e-05                    0    -133.993344750158 
      900                 0.09 1.02629246257047e-06    -133.939321574068 1.44399877051467e-05                    0    -133.999611147322 
     1000                  0.1 7.52253147824893e-07    -133.942032102451 6.85789018963965e-06                    0    -134.002604512509 
-Loop time of 4.52508 on 4 procs for 1000 steps with 5780 atoms
+Loop time of 2.49676 on 4 procs for 1000 steps with 5780 atoms
 
-97.3% CPU use with 4 MPI tasks x no OpenMP threads
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
@@ -115,12 +115,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.7814     | 3.2998     | 3.808      |  25.6 | 72.92
+Pair    | 2.2509     | 2.2589     | 2.2629     |   0.3 | 90.47
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.37682    | 0.87552    | 1.3847     |  48.7 | 19.35
-Output  | 0.1621     | 0.16349    | 0.16483    |   0.3 |  3.61
-Modify  | 0.0099754  | 0.012567   | 0.014974   |   2.1 |  0.28
-Other   |            | 0.1737     |            |       |  3.84
+Comm    | 0.06036    | 0.064254   | 0.072356   |   1.9 |  2.57
+Output  | 0.084002   | 0.085009   | 0.085985   |   0.3 |  3.40
+Modify  | 0.0072496  | 0.0072694  | 0.0073116  |   0.0 |  0.29
+Other   |            | 0.08134    |            |       |  3.26
 
 Nlocal:    1445 ave 1445 max 1445 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -138,4 +138,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:04
+Total wall time: 0:00:02
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1
index b13ce090e4..a8685eb2cf 100644
--- a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (134.64 134.64 3.96)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 1156 atoms
-  create_atoms CPU = 0.000702858 secs
+  create_atoms CPU = 0.00136805 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -89,36 +89,36 @@ Neighbor list info ...
       bin: none
 Per MPI rank memory allocation (min/avg/max) = 7.748 | 7.748 | 7.748 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-       0                    0   0.0205636053306396   -0.217760509274283     1541.29975585881                    0    -0.21723077139301 
-      50                0.005 0.000966655616832908    -19.2878369426356    0.312860071233838                    0    -19.3229939390148 
-     100                 0.01  0.00154452800146007    -19.5948898197921    0.365367666925721                    0    -19.6389064900417 
-     150                0.015 4.90329738897855e-05    -19.6962578948663 0.000386378108166462                    0     -19.704713985757 
-     200                 0.02 1.39636819172648e-06    -19.6975289055185 6.05740522809686e-05                    0    -19.7059135025107 
-     250                0.025 7.30255912392386e-08    -19.6975359463778 7.86050372080572e-09                    0    -19.7059189975433 
-     300                 0.03  2.3618265959146e-09    -19.6975359475117 1.36402599486317e-13                    0      -19.70591910974 
-     347               0.0347 1.42160367645076e-11    -19.6975359475123 2.85504863224395e-16                    0    -19.7059191162178 
-Loop time of 0.427798 on 1 procs for 347 steps with 1156 atoms
+       0                    0   0.0205636053306396   -0.218504643888467     1537.40479337332                    0   -0.109252321944233 
+      50                0.005 0.000800557938107919    -19.2937186217138    0.293526226015746                    0    -9.65918446070018 
+     100                 0.01 0.000434178067296136    -19.6225314972776    0.136842093090897                    0    -9.81803976806459 
+     150                0.015 9.48307628510239e-06    -19.7062424007137 0.000835148627123792                    0    -9.85315267460932 
+     200                 0.02 9.40072944704056e-06    -19.7072931204571 7.72334770010361e-06                    0    -9.85364693487844 
+     250                0.025 5.05117500164935e-07    -19.7072952885901 5.72437821949831e-08                    0    -9.85364764712939 
+     300                 0.03 2.15063977474981e-09     -19.707295295749 2.09970244523395e-12                    0     -9.8536476478746 
+     303               0.0303 1.43831710574092e-09    -19.7072952957498 1.70336397715489e-13                    0    -9.85364764787493 
+Loop time of 0.335897 on 1 procs for 303 steps with 1156 atoms
 
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 Minimization stats:
-  Stopping criterion = force tolerance
+  Stopping criterion = energy tolerance
   Energy initial, next-to-last, final = 
-       -0.217230771393     -19.7059191162     -19.7059191162
+       -0.109252321944     -9.85364764787     -9.85364764787
   Force two-norm initial, final = 0 0
   Force max component initial, final = 0 0
   Final line search alpha, max atom move = 0 0
-  Iterations, force evaluations = 347 347
+  Iterations, force evaluations = 303 303
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.36166    | 0.36166    | 0.36166    |   0.0 | 84.54
+Pair    | 0.28129    | 0.28129    | 0.28129    |   0.0 | 83.74
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.0016549  | 0.0016549  | 0.0016549  |   0.0 |  0.39
-Output  | 0.02019    | 0.02019    | 0.02019    |   0.0 |  4.72
-Modify  | 0.0024493  | 0.0024493  | 0.0024493  |   0.0 |  0.57
-Other   |            | 0.04184    |            |       |  9.78
+Comm    | 0.0010796  | 0.0010796  | 0.0010796  |   0.0 |  0.32
+Output  | 0.017942   | 0.017942   | 0.017942   |   0.0 |  5.34
+Modify  | 0.001771   | 0.001771   | 0.001771   |   0.0 |  0.53
+Other   |            | 0.03382    |            |       | 10.07
 
 Nlocal:    1156 ave 1156 max 1156 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4
index 2a5917663e..f2756d0f5e 100644
--- a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (134.64 134.64 3.96)
   2 by 2 by 1 MPI processor grid
 create_atoms 	1 box
 Created 1156 atoms
-  create_atoms CPU = 0.000618935 secs
+  create_atoms CPU = 0.000981808 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -97,9 +97,9 @@ Step Time v_magnorm v_emag v_tmag Temp TotEng
      250                0.025 5.21141123128679e-08    -19.6975359469038 2.52554968535685e-09                    0    -19.7059189333986 
      300                 0.03  2.9845103782958e-09    -19.6975359475094 2.31782597655471e-11                    0    -19.7059191124033 
      342               0.0342  1.0526549233076e-10    -19.6975359475123 3.65641352240487e-16                    0    -19.7059191178145 
-Loop time of 0.234594 on 4 procs for 342 steps with 1156 atoms
+Loop time of 0.117672 on 4 procs for 342 steps with 1156 atoms
 
-93.1% CPU use with 4 MPI tasks x no OpenMP threads
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = force tolerance
@@ -113,12 +113,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.097515   | 0.12325    | 0.15193    |   7.4 | 52.54
+Pair    | 0.084558   | 0.086668   | 0.091471   |   1.0 | 73.65
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.038284   | 0.061142   | 0.081045   |   8.1 | 26.06
-Output  | 0.008667   | 0.0086921  | 0.0087271  |   0.0 |  3.71
-Modify  | 0.00063705 | 0.00084341 | 0.0010526  |   0.0 |  0.36
-Other   |            | 0.04067    |            |       | 17.34
+Comm    | 0.0052197  | 0.010042   | 0.012191   |   2.8 |  8.53
+Output  | 0.0050647  | 0.0050726  | 0.0050921  |   0.0 |  4.31
+Modify  | 0.00052595 | 0.00053537 | 0.00055242 |   0.0 |  0.45
+Other   |            | 0.01535    |            |       | 13.05
 
 Nlocal:    289 ave 289 max 289 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1
index 637c624a7c..6df5959c0b 100644
--- a/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.00061512 secs
+  create_atoms CPU = 0.000965834 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -76,25 +76,25 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 6.848 | 6.848 | 6.848 Mbytes
 Step Time v_magx v_magz v_magnorm v_tmag TotEng 
-       0                    0  -0.0285071136621457 -0.00948990815281275   0.0764569750905723     5048.56076237679   -0.701465876910694 
-     100                 0.01   -0.584953861980204  -0.0517163256267969    0.999992350892306 6.25556948778472e-05     -50.578744362023 
-     200                 0.02   -0.584864756506845  -0.0547143484057153    0.999999990495506 3.49782260454062e-06    -50.5787971409244 
-     300                 0.03     -0.5847600493607  -0.0578846348986585    0.999999999988174 3.83095226805016e-06    -50.5788061208586 
-     400                 0.04   -0.584642875238893  -0.0612373075362701    0.999999999999986 4.28575832708226e-06    -50.5788161053511 
-     500                 0.05   -0.584511765589529  -0.0647826190376231                    1 4.79421486949086e-06    -50.5788272748485 
-     600                 0.06   -0.584365074206159  -0.0685313536438759                    1 5.36242072641834e-06    -50.5788397688161 
-     700                 0.07   -0.584200963215273   -0.072494846958872                    1 5.99725249459222e-06    -50.5788537427261 
-     800                 0.08   -0.584017381477007  -0.0766850043611195    0.999999999999999 6.70634191991825e-06    -50.5788693699026 
-     900                 0.09   -0.583812040722351  -0.0811143180675364    0.999999999999999 7.49814943594148e-06    -50.5788868434701 
-    1000                  0.1   -0.583582389243979  -0.0857958823565731    0.999999999999998 8.38204259112222e-06    -50.5789063784909 
-Loop time of 0.215249 on 1 procs for 1000 steps with 250 atoms
+       0                    0  -0.0285071136621457 -0.00948990815281275   0.0764569750905723     5048.56076237679   -0.354774619362398 
+     100                 0.01   -0.584953861980204  -0.0517163256267969    0.999992350892306 6.25556948778472e-05    -25.2894057771132 
+     200                 0.02   -0.584864756506845  -0.0547143484057153    0.999999990495506 3.49782260454062e-06     -25.289435991418 
+     300                 0.03     -0.5847600493607  -0.0578846348986585    0.999999999988174 3.83095226805016e-06    -25.2894449433165 
+     400                 0.04   -0.584642875238893  -0.0612373075362701    0.999999999999986 4.28575832708226e-06    -25.2894549277735 
+     500                 0.05   -0.584511765589529  -0.0647826190376231                    1 4.79421486949086e-06    -25.2894660972709 
+     600                 0.06   -0.584365074206159  -0.0685313536438759                    1 5.36242072641834e-06    -25.2894785912384 
+     700                 0.07   -0.584200963215273   -0.072494846958872                    1 5.99725249459222e-06    -25.2894925651485 
+     800                 0.08   -0.584017381477007  -0.0766850043611195    0.999999999999999 6.70634191991825e-06     -25.289508192325 
+     900                 0.09   -0.583812040722351  -0.0811143180675364    0.999999999999999 7.49814943594148e-06    -25.2895256658925 
+    1000                  0.1   -0.583582389243979  -0.0857958823565731    0.999999999999998 8.38204259112222e-06    -25.2895452009133 
+Loop time of 0.195254 on 1 procs for 1000 steps with 250 atoms
 
 100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
   Energy initial, next-to-last, final = 
-       -0.701465876911     -50.5789061722     -50.5789063785
+       -0.354774619362     -25.2895449946     -25.2895452009
   Force two-norm initial, final = 0 0
   Force max component initial, final = 0 0
   Final line search alpha, max atom move = 0 0
@@ -103,12 +103,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.19278    | 0.19278    | 0.19278    |   0.0 | 89.56
+Pair    | 0.17668    | 0.17668    | 0.17668    |   0.0 | 90.49
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.0062225  | 0.0062225  | 0.0062225  |   0.0 |  2.89
-Output  | 0.0085046  | 0.0085046  | 0.0085046  |   0.0 |  3.95
-Modify  | 0.0017273  | 0.0017273  | 0.0017273  |   0.0 |  0.80
-Other   |            | 0.006012   |            |       |  2.79
+Comm    | 0.0052176  | 0.0052176  | 0.0052176  |   0.0 |  2.67
+Output  | 0.0067751  | 0.0067751  | 0.0067751  |   0.0 |  3.47
+Modify  | 0.0013788  | 0.0013788  | 0.0013788  |   0.0 |  0.71
+Other   |            | 0.005203   |            |       |  2.66
 
 Nlocal:    250 ave 250 max 250 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4
index 70f395ab08..b0cdd4f94a 100644
--- a/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4
@@ -17,7 +17,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.000644922 secs
+  create_atoms CPU = 0.000759125 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -87,9 +87,9 @@ Step Time v_magx v_magz v_magnorm v_tmag TotEng
      800                 0.08   -0.584017381477007  -0.0766850043611196                    1  6.7063419199184e-06    -50.5788693699014 
      900                 0.09   -0.583812040722352  -0.0811143180675365    0.999999999999998 7.49814943594153e-06    -50.5788868434688 
     1000                  0.1   -0.583582389243979  -0.0857958823565732    0.999999999999999 8.38204259112203e-06    -50.5789063784897 
-Loop time of 0.229203 on 4 procs for 1000 steps with 250 atoms
+Loop time of 0.0845464 on 4 procs for 1000 steps with 250 atoms
 
-85.9% CPU use with 4 MPI tasks x no OpenMP threads
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
@@ -103,12 +103,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.06774    | 0.080677   | 0.097769   |   4.4 | 35.20
+Pair    | 0.043007   | 0.045307   | 0.04776    |   0.8 | 53.59
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.10574    | 0.11072    | 0.11498    |   1.0 | 48.31
-Output  | 0.0061452  | 0.0061803  | 0.0062776  |   0.1 |  2.70
-Modify  | 0.00074291 | 0.00096381 | 0.0014563  |   0.0 |  0.42
-Other   |            | 0.03066    |            |       | 13.38
+Comm    | 0.026827   | 0.029139   | 0.031438   |   1.0 | 34.47
+Output  | 0.0023198  | 0.0023302  | 0.0023572  |   0.0 |  2.76
+Modify  | 0.00041103 | 0.0004673  | 0.00054026 |   0.0 |  0.55
+Other   |            | 0.007303   |            |       |  8.64
 
 Nlocal:    62.5 ave 65 max 60 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
diff --git a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
index a8639925f6..dd1c543bb3 100755
--- a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
+++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
@@ -65,8 +65,6 @@ for t in range (0,N):
   # calc. average magnetization
   Sm = (S1+S2)*0.5
   # calc. energy
-  # en = -hbar*(np.dot(S1,wf1)+np.dot(S2,wf2))
-  en = -2.0*J0*(np.dot(S1,S2))
+  en = -J0*(np.dot(S1,S2))
   # print res. in ps for comparison with LAMMPS
   print(t*dt/1000.0,Sm[0],Sm[1],Sm[2],en)
-  # print(t*dt/1000.0,S1[0],S2[0],S1[1],S2[1],S1[2],S2[2],en)
diff --git a/examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py b/examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py
index 6c8afca569..bbc7c8f54e 100755
--- a/examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py
+++ b/examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py
@@ -15,7 +15,7 @@ if len(argv) != 3:
 lammps_file = sys.argv[1]
 llg_file = sys.argv[2]
 
-t_lmp,Sx_lmp,Sy_lmp,Sz_lmp,e_lmp = np.loadtxt(lammps_file,skiprows=0, usecols=(1,2,3,4,5),unpack=True)
+t_lmp,Sx_lmp,Sy_lmp,Sz_lmp,e_lmp = np.loadtxt(lammps_file,skiprows=0, usecols=(1,2,3,4,7),unpack=True)
 t_llg,Sx_llg,Sy_llg,Sz_llg,e_llg = np.loadtxt(llg_file,skiprows=0, usecols=(0,1,2,3,4),unpack=True)
 
 plt.figure()
diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-bench-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh
similarity index 100%
rename from examples/SPIN/test_problems/validation_damped_exchange/run-bench-exchange.sh
rename to examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh
diff --git a/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data b/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data
deleted file mode 100644
index 013f813751..0000000000
--- a/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data
+++ /dev/null
@@ -1,22 +0,0 @@
-LAMMPS data file via write_data, version 19 Sep 2019, timestep = 0
-
-2 atoms
-1 atom types
-
-0.0 6.0 xlo xhi
-0.0 3.0 ylo yhi
-0.0 3.0 zlo zhi
-
-Masses
-
-1 1
-
-Atoms # spin
-
-1 1 2.0 0.0 0.0 0.0 1.0 0.0 0.0 0 0 0
-2 1 2.0 3.0 0.0 0.0 0.0 1.0 0.0 0 0 0
-
-Velocities
-
-1 0.0 0.0 0.0
-2 0.0 0.0 0.0
diff --git a/examples/SPIN/test_problems/validation_damped_precession/run-bench-prec.sh b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh
similarity index 100%
rename from examples/SPIN/test_problems/validation_damped_precession/run-bench-prec.sh
rename to examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh
diff --git a/examples/SPIN/test_problems/validation_langevin_precession/run-bench-prec.sh b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh
similarity index 100%
rename from examples/SPIN/test_problems/validation_langevin_precession/run-bench-prec.sh
rename to examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh
diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp
index ad1384ffd2..28c52bb39d 100644
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@@ -848,17 +848,16 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values)
 
 int AtomVecSpin::data_atom_hybrid(int nlocal, char **values)
 {
-
-  sp[nlocal][0] = utils::numeric(FLERR,values[0],true,lmp);
-  sp[nlocal][1] = utils::numeric(FLERR,values[1],true,lmp);
-  sp[nlocal][2] = utils::numeric(FLERR,values[2],true,lmp);
+  sp[nlocal][3] = utils::numeric(FLERR,values[0],true,lmp);
+  sp[nlocal][0] = utils::numeric(FLERR,values[1],true,lmp);
+  sp[nlocal][1] = utils::numeric(FLERR,values[2],true,lmp);
+  sp[nlocal][2] = utils::numeric(FLERR,values[3],true,lmp);
   double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] +
                           sp[nlocal][1]*sp[nlocal][1] +
                           sp[nlocal][2]*sp[nlocal][2]);
   sp[nlocal][0] *= inorm;
   sp[nlocal][1] *= inorm;
   sp[nlocal][2] *= inorm;
-  sp[nlocal][3] = utils::numeric(FLERR,values[3],true,lmp);
 
   return 4;
 }
diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp
index 356f73a809..124522a9b9 100644
--- a/src/SPIN/pair_spin_dipole_long.cpp
+++ b/src/SPIN/pair_spin_dipole_long.cpp
@@ -296,7 +296,7 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
         if (rsq <= local_cut2) {
           evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] +
             spi[2]*fmi[2];
-          evdwl *= hbar;
+          evdwl *= 0.5*hbar;
         }
       } else evdwl = 0.0;
 

From 65381d7a690d5c82c72eb9de575afea252f2f189 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sun, 24 Nov 2019 18:11:35 -0700
Subject: [PATCH 066/199] Add new table_from_list extension

---
 doc/src/_ext/table_from_list.py | 56 +++++++++++++++++++++++++++++++++
 doc/utils/sphinx-config/conf.py |  5 ++-
 2 files changed, 60 insertions(+), 1 deletion(-)
 create mode 100644 doc/src/_ext/table_from_list.py

diff --git a/doc/src/_ext/table_from_list.py b/doc/src/_ext/table_from_list.py
new file mode 100644
index 0000000000..44c85fc378
--- /dev/null
+++ b/doc/src/_ext/table_from_list.py
@@ -0,0 +1,56 @@
+from docutils import nodes
+from sphinx.util.docutils import SphinxDirective
+from docutils.nodes import Element, Node
+from typing import Any, Dict, List
+from sphinx import addnodes
+from sphinx.util import logging
+
+class TableFromList(SphinxDirective):
+    has_content = True
+    required_arguments = 0
+    optional_arguments = 0
+    final_argument_whitespace = False
+    option_spec = {
+        'columns': int,
+    }
+
+    def run(self) -> List[Node]:
+        ncolumns = self.options.get('columns', 2)
+        node = addnodes.compact_paragraph()
+        node.document = self.state.document
+        self.state.nested_parse(self.content, self.content_offset, node)
+        if len(node.children) != 1 or not isinstance(node.children[0],
+                                                     nodes.bullet_list):
+            reporter = self.state.document.reporter
+            return [reporter.warning('.. table_from_list content is not a list', line=self.lineno)]
+        fulllist = node.children[0]
+        table = nodes.table()
+        tgroup = nodes.tgroup(cols=ncolumns)
+        table += tgroup
+
+        for i in range(ncolumns):
+            tgroup += nodes.colspec(colwidth=1)
+
+        tbody = nodes.tbody()
+        tgroup += tbody
+        current_row = nodes.row()
+
+        for idx, cell in enumerate(fulllist.children):
+            if len(current_row.children) == ncolumns:
+                tbody += current_row
+                current_row = nodes.row()
+            entry = nodes.entry()
+            current_row += entry
+            if len(cell.children) > 0:
+                entry += cell.children[0]
+
+        tbody += current_row
+        return [table]
+
+def setup(app):
+    app.add_directive("table_from_list", TableFromList)
+    return {
+        'version': '0.1',
+        'parallel_read_safe': True,
+        'parallel_write_safe': True,
+    }
diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py
index 70a96e1614..0b6dfcca2d 100644
--- a/doc/utils/sphinx-config/conf.py
+++ b/doc/utils/sphinx-config/conf.py
@@ -20,6 +20,7 @@ import os
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #sys.path.insert(0, os.path.abspath('.'))
+sys.path.append(os.path.join(os.path.dirname(__file__), '../../src/_ext'))
 
 # -- General configuration ------------------------------------------------
 
@@ -30,7 +31,9 @@ import os
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.mathjax', 'sphinx.ext.imgmath'
+    'sphinx.ext.mathjax',
+    'sphinx.ext.imgmath',
+    'table_from_list',
 ]
 # 2017-12-07: commented out, since this package is broken with Sphinx 16.x
 #             yet we can no longer use Sphinx 15.x, since that breaks with

From 2c33b5589df13ad6f6bf20413e009c72a197c97d Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sun, 24 Nov 2019 18:12:24 -0700
Subject: [PATCH 067/199] Remove txt/Commands*.txt

---
 doc/txt/Commands.txt           |  60 --------
 doc/txt/Commands_all.txt       | 139 ------------------
 doc/txt/Commands_bond.txt      | 148 -------------------
 doc/txt/Commands_category.txt  | 141 ------------------
 doc/txt/Commands_compute.txt   | 166 ---------------------
 doc/txt/Commands_fix.txt       | 240 -------------------------------
 doc/txt/Commands_kspace.txt    |  37 -----
 doc/txt/Commands_pair.txt      | 253 ---------------------------------
 doc/txt/Commands_removed.txt   |  66 ---------
 doc/txt/Commands_structure.txt |  95 -------------
 10 files changed, 1345 deletions(-)
 delete mode 100644 doc/txt/Commands.txt
 delete mode 100644 doc/txt/Commands_all.txt
 delete mode 100644 doc/txt/Commands_bond.txt
 delete mode 100644 doc/txt/Commands_category.txt
 delete mode 100644 doc/txt/Commands_compute.txt
 delete mode 100644 doc/txt/Commands_fix.txt
 delete mode 100644 doc/txt/Commands_kspace.txt
 delete mode 100644 doc/txt/Commands_pair.txt
 delete mode 100644 doc/txt/Commands_removed.txt
 delete mode 100644 doc/txt/Commands_structure.txt

diff --git a/doc/txt/Commands.txt b/doc/txt/Commands.txt
deleted file mode 100644
index bcbbe524a8..0000000000
--- a/doc/txt/Commands.txt
+++ /dev/null
@@ -1,60 +0,0 @@
-"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Packages.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html#comm)
-
-:line
-
-Commands :h2
-
-These pages describe how a LAMMPS input script is formatted and the
-commands in it are used to define a LAMMPS simulation.
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   Commands_input
-   Commands_parse
-   Commands_structure
-   Commands_category
-
-.. toctree::
-   :maxdepth: 1
-
-   Commands_all
-   Commands_fix
-   Commands_compute
-   Commands_pair
-   Commands_bond
-   Commands_kspace
-
-.. toctree::
-   :maxdepth: 1
-
-   Commands_removed
-
-END_RST -->
-
-<!-- HTML_ONLY -->
-
-"LAMMPS input scripts"_Commands_input.html
-"Parsing rules for input scripts"_Commands_parse.html
-"Input script structure"_Commands_structure.html
-"Commands by category"_Commands_category.html :all(b)
-
-"General commands"_Commands_all.html
-"Fix commands"_Commands_fix.html
-"Compute commands"_Commands_compute.html
-"Pair commands"_Commands_pair.html
-"Bond, angle, dihedral, improper commands"_Commands_bond.html
-"KSpace solvers"_Commands_kspace.html  :all(b)
-
-"Removed commands and packages"_Commands_removed.html  :all(b)
-
-<!-- END_HTML_ONLY -->
-
diff --git a/doc/txt/Commands_all.txt b/doc/txt/Commands_all.txt
deleted file mode 100644
index ecd21e42e7..0000000000
--- a/doc/txt/Commands_all.txt
+++ /dev/null
@@ -1,139 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-General commands :h3
-
-An alphabetic list of all general LAMMPS commands.
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"clear"_clear.html,
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"create_box"_create_box.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"dimension"_dimension.html,
-"displace_atoms"_displace_atoms.html,
-"dump"_dump.html,
-"dump adios"_dump_adios.html,
-"dump image"_dump_image.html,
-"dump movie"_dump_image.html,
-"dump netcdf"_dump_netcdf.html,
-"dump netcdf/mpiio"_dump_netcdf.html,
-"dump vtk"_dump_vtk.html,
-"dump_modify"_dump_modify.html,
-"dynamical_matrix"_dynamical_matrix.html,
-"echo"_echo.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"group"_group.html,
-"group2ndx"_group2ndx.html,
-"hyper"_hyper.html,
-"if"_if.html,
-"info"_info.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"include"_include.html,
-"jump"_jump.html,
-"kim_init"_kim_commands.html,
-"kim_interactions"_kim_commands.html,
-"kim_query"_kim_commands.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"label"_label.html,
-"lattice"_lattice.html,
-"log"_log.html,
-"mass"_mass.html,
-"message"_message.html,
-"minimize"_minimize.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"min_style spin"_min_spin.html,
-"molecule"_molecule.html,
-"ndx2group"_group2ndx.html,
-"neb"_neb.html,
-"neb/spin"_neb_spin.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"newton"_newton.html,
-"next"_next.html,
-"package"_package.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"partition"_partition.html,
-"prd"_prd.html,
-"print"_print.html,
-"processors"_processors.html,
-"python"_python.html,
-"quit"_quit.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"region"_region.html,
-"replicate"_replicate.html,
-"rerun"_rerun.html,
-"reset_ids"_reset_ids.html,
-"reset_timestep"_reset_timestep.html,
-"restart"_restart.html,
-"run"_run.html,
-"run_style"_run_style.html,
-"server"_server.html,
-"set"_set.html,
-"shell"_shell.html,
-"special_bonds"_special_bonds.html,
-"suffix"_suffix.html,
-"tad"_tad.html,
-"temper"_temper.html,
-"temper/grem"_temper_grem.html,
-"temper/npt"_temper_npt.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"third_order"_third_order.html,
-"timer"_timer.html,
-"timestep"_timestep.html,
-"uncompute"_uncompute.html,
-"undump"_undump.html,
-"unfix"_unfix.html,
-"units"_units.html,
-"variable"_variable.html,
-"velocity"_velocity.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :tb(c=6,ea=c)
diff --git a/doc/txt/Commands_bond.txt b/doc/txt/Commands_bond.txt
deleted file mode 100644
index aecbf4cca0..0000000000
--- a/doc/txt/Commands_bond.txt
+++ /dev/null
@@ -1,148 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html#bond,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-Bond, angle, dihedral, and improper commands :h3
-
-:line
-
-Bond_style potentials :h3,link(bond)
-
-All LAMMPS "bond_style"_bond_style.html commands.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_bond_none.html,
-"zero"_bond_zero.html,
-"hybrid"_bond_hybrid.html,
-,
-,
-,
-,
-,
-"class2 (ko)"_bond_class2.html,
-"fene (iko)"_bond_fene.html,
-"fene/expand (o)"_bond_fene_expand.html,
-"gromos (o)"_bond_gromos.html,
-"harmonic (iko)"_bond_harmonic.html,
-"harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"mm3"_bond_mm3.html,
-"morse (o)"_bond_morse.html,
-"nonlinear (o)"_bond_nonlinear.html,
-"oxdna/fene"_bond_oxdna.html,
-"oxdna2/fene"_bond_oxdna.html,
-"quartic (o)"_bond_quartic.html,
-"table (o)"_bond_table.html :tb(c=4,ea=c)
-
-:line
-
-Angle_style potentials :h3,link(angle)
-
-All LAMMPS "angle_style"_angle_style.html commands.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_angle_none.html,
-"zero"_angle_zero.html,
-"hybrid"_angle_hybrid.html,
-,
-,
-,
-,
-,
-"charmm (iko)"_angle_charmm.html,
-"class2 (ko)"_angle_class2.html,
-"class2/p6"_angle_class2.html,
-"cosine (ko)"_angle_cosine.html,
-"cosine/buck6d"_angle_cosine_buck6d.html,
-"cosine/delta (o)"_angle_cosine_delta.html,
-"cosine/periodic (o)"_angle_cosine_periodic.html,
-"cosine/shift (o)"_angle_cosine_shift.html,
-"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
-"cosine/squared (o)"_angle_cosine_squared.html,
-"cross"_angle_cross.html,
-"dipole (o)"_angle_dipole.html,
-"fourier (o)"_angle_fourier.html,
-"fourier/simple (o)"_angle_fourier_simple.html,
-"harmonic (iko)"_angle_harmonic.html,
-"mm3"_angle_mm3.html,
-"quartic (o)"_angle_quartic.html,
-"sdk (o)"_angle_sdk.html,
-"table (o)"_angle_table.html :tb(c=4,ea=c)
-
-:line
-
-Dihedral_style potentials :h3,link(dihedral)
-
-All LAMMPS "dihedral_style"_dihedral_style.html commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_dihedral_none.html,
-"zero"_dihedral_zero.html,
-"hybrid"_dihedral_hybrid.html,
-,
-,
-,
-,
-,
-"charmm (iko)"_dihedral_charmm.html,
-"charmmfsw"_dihedral_charmm.html,
-"class2 (ko)"_dihedral_class2.html,
-"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (io)"_dihedral_fourier.html,
-"harmonic (iko)"_dihedral_harmonic.html,
-"helix (o)"_dihedral_helix.html,
-"multi/harmonic (o)"_dihedral_multi_harmonic.html,
-"nharmonic (o)"_dihedral_nharmonic.html,
-"opls (iko)"_dihedral_opls.html,
-"quadratic (o)"_dihedral_quadratic.html,
-"spherical"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html,
-"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
-
-:line
-
-Improper_style potentials :h3,link(improper)
-
-All LAMMPS "improper_style"_improper_style.html commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_improper_none.html,
-"zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html,
-,
-,
-,
-,
-,
-"class2 (ko)"_improper_class2.html,
-"cossq (o)"_improper_cossq.html,
-"cvff (io)"_improper_cvff.html,
-"distance"_improper_distance.html,
-"distharm"_improper_distharm.html,
-"fourier (o)"_improper_fourier.html,
-"harmonic (iko)"_improper_harmonic.html,
-"inversion/harmonic"_improper_inversion_harmonic.html,
-"ring (o)"_improper_ring.html,
-"sqdistharm"_improper_sqdistharm.html,
-"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
diff --git a/doc/txt/Commands_category.txt b/doc/txt/Commands_category.txt
deleted file mode 100644
index 14a328b227..0000000000
--- a/doc/txt/Commands_category.txt
+++ /dev/null
@@ -1,141 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Commands by category :h3
-
-This page lists most of the LAMMPS commands, grouped by category.  The
-"General commands"_Commands_all.html doc page lists all general commands
-alphabetically.  Style options for entries like fix, compute, pair etc.
-have their own pages where they are listed alphabetically.
-
-Initialization:
-
-"newton"_newton.html,
-"package"_package.html,
-"processors"_processors.html,
-"suffix"_suffix.html,
-"units"_units.html :ul
-
-Setup simulation box:
-
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"create_box"_create_box.html,
-"dimension"_dimension.html,
-"lattice"_lattice.html,
-"region"_region.html :ul
-
-Setup atoms:
-
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html,
-"group"_group.html,
-"mass"_mass.html,
-"molecule"_molecule.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"replicate"_replicate.html,
-"set"_set.html,
-"velocity"_velocity.html :ul
-
-Force fields:
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"special_bonds"_special_bonds.html :ul
-
-Settings:
-
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"info"_info.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"partition"_partition.html,
-"reset_timestep"_reset_timestep.html,
-"run_style"_run_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html :ul
-
-Operations within timestepping (fixes) and diagnostics (computes):
-
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"uncompute"_uncompute.html,
-"unfix"_unfix.html :ul
-
-Output:
-
-"dump image"_dump_image.html,
-"dump movie"_dump_image.html,
-"dump"_dump.html,
-"dump_modify"_dump_modify.html,
-"restart"_restart.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"undump"_undump.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :ul
-
-Actions:
-
-"minimize"_minimize.html,
-"neb"_neb.html,
-"neb_spin"_neb_spin.html,
-"prd"_prd.html,
-"rerun"_rerun.html,
-"run"_run.html,
-"tad"_tad.html,
-"temper"_temper.html :ul
-
-Input script control:
-
-"clear"_clear.html,
-"echo"_echo.html,
-"if"_if.html,
-"include"_include.html,
-"jump"_jump.html,
-"label"_label.html,
-"log"_log.html,
-"next"_next.html,
-"print"_print.html,
-"python"_python.html,
-"quit"_quit.html,
-"shell"_shell.html,
-"variable"_variable.html :ul
-
diff --git a/doc/txt/Commands_compute.txt b/doc/txt/Commands_compute.txt
deleted file mode 100644
index caf627188b..0000000000
--- a/doc/txt/Commands_compute.txt
+++ /dev/null
@@ -1,166 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-Compute commands :h3
-
-An alphabetic list of all LAMMPS "compute"_compute.html commands.
-Some styles have accelerated versions.  This is indicated by
-additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"ackland/atom"_compute_ackland_atom.html,
-"adf"_compute_adf.html,
-"aggregate/atom"_compute_cluster_atom.html,
-"angle"_compute_angle.html,
-"angle/local"_compute_angle_local.html,
-"angmom/chunk"_compute_angmom_chunk.html,
-"basal/atom"_compute_basal_atom.html,
-"body/local"_compute_body_local.html,
-"bond"_compute_bond.html,
-"bond/local"_compute_bond_local.html,
-"centro/atom"_compute_centro_atom.html,
-"centroid/stress/atom"_compute_stress_atom.html,
-"chunk/atom"_compute_chunk_atom.html,
-"chunk/spread/atom"_compute_chunk_spread_atom.html,
-"cluster/atom"_compute_cluster_atom.html,
-"cna/atom"_compute_cna_atom.html,
-"cnp/atom"_compute_cnp_atom.html,
-"com"_compute_com.html,
-"com/chunk"_compute_com_chunk.html,
-"contact/atom"_compute_contact_atom.html,
-"coord/atom"_compute_coord_atom.html,
-"damage/atom"_compute_damage_atom.html,
-"dihedral"_compute_dihedral.html,
-"dihedral/local"_compute_dihedral_local.html,
-"dilatation/atom"_compute_dilatation_atom.html,
-"dipole/chunk"_compute_dipole_chunk.html,
-"displace/atom"_compute_displace_atom.html,
-"dpd"_compute_dpd.html,
-"dpd/atom"_compute_dpd_atom.html,
-"edpd/temp/atom"_compute_edpd_temp_atom.html,
-"entropy/atom"_compute_entropy_atom.html,
-"erotate/asphere"_compute_erotate_asphere.html,
-"erotate/rigid"_compute_erotate_rigid.html,
-"erotate/sphere"_compute_erotate_sphere.html,
-"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
-"event/displace"_compute_event_displace.html,
-"fep"_compute_fep.html,
-"force/tally"_compute_tally.html,
-"fragment/atom"_compute_cluster_atom.html,
-"global/atom"_compute_global_atom.html,
-"group/group"_compute_group_group.html,
-"gyration"_compute_gyration.html,
-"gyration/chunk"_compute_gyration_chunk.html,
-"gyration/shape"_compute_gyration_shape.html,
-"gyration/shape/chunk"_compute_gyration_shape_chunk.html,
-"heat/flux"_compute_heat_flux.html,
-"heat/flux/tally"_compute_tally.html,
-"hexorder/atom"_compute_hexorder_atom.html,
-"hma"_compute_hma.html,
-"improper"_compute_improper.html,
-"improper/local"_compute_improper_local.html,
-"inertia/chunk"_compute_inertia_chunk.html,
-"ke"_compute_ke.html,
-"ke/atom"_compute_ke_atom.html,
-"ke/atom/eff"_compute_ke_atom_eff.html,
-"ke/eff"_compute_ke_eff.html,
-"ke/rigid"_compute_ke_rigid.html,
-"meso/e/atom"_compute_meso_e_atom.html,
-"meso/rho/atom"_compute_meso_rho_atom.html,
-"meso/t/atom"_compute_meso_t_atom.html,
-"momentum"_compute_momentum.html,
-"msd"_compute_msd.html,
-"msd/chunk"_compute_msd_chunk.html,
-"msd/nongauss"_compute_msd_nongauss.html,
-"omega/chunk"_compute_omega_chunk.html,
-"orientorder/atom"_compute_orientorder_atom.html,
-"pair"_compute_pair.html,
-"pair/local"_compute_pair_local.html,
-"pe"_compute_pe.html,
-"pe/atom"_compute_pe_atom.html,
-"pe/mol/tally"_compute_tally.html,
-"pe/tally"_compute_tally.html,
-"plasticity/atom"_compute_plasticity_atom.html,
-"pressure"_compute_pressure.html,
-"pressure/cylinder"_compute_pressure_cylinder.html,
-"pressure/uef"_compute_pressure_uef.html,
-"property/atom"_compute_property_atom.html,
-"property/chunk"_compute_property_chunk.html,
-"property/local"_compute_property_local.html,
-"ptm/atom"_compute_ptm_atom.html,
-"rdf"_compute_rdf.html,
-"reduce"_compute_reduce.html,
-"reduce/chunk"_compute_reduce_chunk.html,
-"reduce/region"_compute_reduce.html,
-"rigid/local"_compute_rigid_local.html,
-"saed"_compute_saed.html,
-"slice"_compute_slice.html,
-"smd/contact/radius"_compute_smd_contact_radius.html,
-"smd/damage"_compute_smd_damage.html,
-"smd/hourglass/error"_compute_smd_hourglass_error.html,
-"smd/internal/energy"_compute_smd_internal_energy.html,
-"smd/plastic/strain"_compute_smd_plastic_strain.html,
-"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
-"smd/rho"_compute_smd_rho.html,
-"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
-"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
-"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
-"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
-"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
-"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
-"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
-"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
-"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
-"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
-"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
-"smd/vol"_compute_smd_vol.html,
-"sna/atom"_compute_sna_atom.html,
-"snad/atom"_compute_sna_atom.html,
-"snav/atom"_compute_sna_atom.html,
-"spin"_compute_spin.html,
-"stress/atom"_compute_stress_atom.html,
-"stress/mop"_compute_stress_mop.html,
-"stress/mop/profile"_compute_stress_mop.html,
-"stress/tally"_compute_tally.html,
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
-"temp (k)"_compute_temp.html,
-"temp/asphere"_compute_temp_asphere.html,
-"temp/body"_compute_temp_body.html,
-"temp/chunk"_compute_temp_chunk.html,
-"temp/com"_compute_temp_com.html,
-"temp/cs"_compute_temp_cs.html,
-"temp/deform"_compute_temp_deform.html,
-"temp/deform/eff"_compute_temp_deform_eff.html,
-"temp/drude"_compute_temp_drude.html,
-"temp/eff"_compute_temp_eff.html,
-"temp/partial"_compute_temp_partial.html,
-"temp/profile"_compute_temp_profile.html,
-"temp/ramp"_compute_temp_ramp.html,
-"temp/region"_compute_temp_region.html,
-"temp/region/eff"_compute_temp_region_eff.html,
-"temp/rotate"_compute_temp_rotate.html,
-"temp/sphere"_compute_temp_sphere.html,
-"temp/uef"_compute_temp_uef.html,
-"ti"_compute_ti.html,
-"torque/chunk"_compute_torque_chunk.html,
-"vacf"_compute_vacf.html,
-"vcm/chunk"_compute_vcm_chunk.html,
-"voronoi/atom"_compute_voronoi_atom.html,
-"xrd"_compute_xrd.html :tb(c=6,ea=c)
diff --git a/doc/txt/Commands_fix.txt b/doc/txt/Commands_fix.txt
deleted file mode 100644
index cfd2bcf2ef..0000000000
--- a/doc/txt/Commands_fix.txt
+++ /dev/null
@@ -1,240 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-Fix commands :h3
-
-An alphabetic list of all LAMMPS "fix"_fix.html commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"adapt"_fix_adapt.html,
-"adapt/fep"_fix_adapt_fep.html,
-"addforce"_fix_addforce.html,
-"addtorque"_fix_addtorque.html,
-"append/atoms"_fix_append_atoms.html,
-"atc"_fix_atc.html,
-"atom/swap"_fix_atom_swap.html,
-"ave/atom"_fix_ave_atom.html,
-"ave/chunk"_fix_ave_chunk.html,
-"ave/correlate"_fix_ave_correlate.html,
-"ave/correlate/long"_fix_ave_correlate_long.html,
-"ave/histo"_fix_ave_histo.html,
-"ave/histo/weight"_fix_ave_histo.html,
-"ave/time"_fix_ave_time.html,
-"aveforce"_fix_aveforce.html,
-"balance"_fix_balance.html,
-"bocs"_fix_bocs.html,
-"bond/break"_fix_bond_break.html,
-"bond/create"_fix_bond_create.html,
-"bond/react"_fix_bond_react.html,
-"bond/swap"_fix_bond_swap.html,
-"box/relax"_fix_box_relax.html,
-"client/md"_fix_client_md.html,
-"cmap"_fix_cmap.html,
-"colvars"_fix_colvars.html,
-"controller"_fix_controller.html,
-"deform (k)"_fix_deform.html,
-"deposit"_fix_deposit.html,
-"dpd/energy (k)"_fix_dpd_energy.html,
-"drag"_fix_drag.html,
-"drude"_fix_drude.html,
-"drude/transform/direct"_fix_drude_transform.html,
-"drude/transform/inverse"_fix_drude_transform.html,
-"dt/reset"_fix_dt_reset.html,
-"edpd/source"_fix_dpd_source.html,
-"efield"_fix_efield.html,
-"ehex"_fix_ehex.html,
-"electron/stopping"_fix_electron_stopping.html,
-"enforce2d (k)"_fix_enforce2d.html,
-"eos/cv"_fix_eos_cv.html,
-"eos/table"_fix_eos_table.html,
-"eos/table/rx (k)"_fix_eos_table_rx.html,
-"evaporate"_fix_evaporate.html,
-"external"_fix_external.html,
-"ffl"_fix_ffl.html,
-"filter/corotate"_fix_filter_corotate.html,
-"flow/gauss"_fix_flow_gauss.html,
-"freeze (k)"_fix_freeze.html,
-"gcmc"_fix_gcmc.html,
-"gld"_fix_gld.html,
-"gle"_fix_gle.html,
-"gravity (ko)"_fix_gravity.html,
-"grem"_fix_grem.html,
-"halt"_fix_halt.html,
-"heat"_fix_heat.html,
-"hyper/global"_fix_hyper_global.html,
-"hyper/local"_fix_hyper_local.html,
-"imd"_fix_imd.html,
-"indent"_fix_indent.html,
-"ipi"_fix_ipi.html,
-"langevin (k)"_fix_langevin.html,
-"langevin/drude"_fix_langevin_drude.html,
-"langevin/eff"_fix_langevin_eff.html,
-"langevin/spin"_fix_langevin_spin.html,
-"latte"_fix_latte.html,
-"lb/fluid"_fix_lb_fluid.html,
-"lb/momentum"_fix_lb_momentum.html,
-"lb/pc"_fix_lb_pc.html,
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
-"lb/viscous"_fix_lb_viscous.html,
-"lineforce"_fix_lineforce.html,
-"manifoldforce"_fix_manifoldforce.html,
-"meso"_fix_meso.html,
-"meso/move"_fix_meso_move.html,
-"meso/stationary"_fix_meso_stationary.html,
-"momentum (k)"_fix_momentum.html,
-"move"_fix_move.html,
-"mscg"_fix_mscg.html,
-"msst"_fix_msst.html,
-"mvv/dpd"_fix_mvv_dpd.html,
-"mvv/edpd"_fix_mvv_dpd.html,
-"mvv/tdpd"_fix_mvv_dpd.html,
-"neb"_fix_neb.html,
-"neb_spin"_fix_neb_spin.html,
-"nph (ko)"_fix_nh.html,
-"nph/asphere (o)"_fix_nph_asphere.html,
-"nph/body"_fix_nph_body.html,
-"nph/eff"_fix_nh_eff.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
-"nphug (o)"_fix_nphug.html,
-"npt (iko)"_fix_nh.html,
-"npt/asphere (o)"_fix_npt_asphere.html,
-"npt/body"_fix_npt_body.html,
-"npt/eff"_fix_nh_eff.html,
-"npt/sphere (o)"_fix_npt_sphere.html,
-"npt/uef"_fix_nh_uef.html,
-"nve (iko)"_fix_nve.html,
-"nve/asphere (i)"_fix_nve_asphere.html,
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
-"nve/awpmd"_fix_nve_awpmd.html,
-"nve/body"_fix_nve_body.html,
-"nve/dot"_fix_nve_dot.html,
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
-"nve/eff"_fix_nve_eff.html,
-"nve/limit"_fix_nve_limit.html,
-"nve/line"_fix_nve_line.html,
-"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
-"nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (ko)"_fix_nve_sphere.html,
-"nve/spin"_fix_nve_spin.html,
-"nve/tri"_fix_nve_tri.html,
-"nvk"_fix_nvk.html,
-"nvt (iko)"_fix_nh.html,
-"nvt/asphere (o)"_fix_nvt_asphere.html,
-"nvt/body"_fix_nvt_body.html,
-"nvt/eff"_fix_nh_eff.html,
-"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
-"nvt/sllod (io)"_fix_nvt_sllod.html,
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
-"nvt/sphere (o)"_fix_nvt_sphere.html,
-"nvt/uef"_fix_nh_uef.html,
-"oneway"_fix_oneway.html,
-"orient/bcc"_fix_orient.html,
-"orient/fcc"_fix_orient.html,
-"phonon"_fix_phonon.html,
-"pimd"_fix_pimd.html,
-"planeforce"_fix_planeforce.html,
-"plumed"_fix_plumed.html,
-"poems"_fix_poems.html,
-"pour"_fix_pour.html,
-"precession/spin"_fix_precession_spin.html,
-"press/berendsen"_fix_press_berendsen.html,
-"print"_fix_print.html,
-"property/atom (k)"_fix_property_atom.html,
-"python/invoke"_fix_python_invoke.html,
-"python/move"_fix_python_move.html,
-"qbmsst"_fix_qbmsst.html,
-"qeq/comb (o)"_fix_qeq_comb.html,
-"qeq/dynamic"_fix_qeq.html,
-"qeq/fire"_fix_qeq.html,
-"qeq/point"_fix_qeq.html,
-"qeq/reax (ko)"_fix_qeq_reax.html,
-"qeq/shielded"_fix_qeq.html,
-"qeq/slater"_fix_qeq.html,
-"qmmm"_fix_qmmm.html,
-"qtb"_fix_qtb.html,
-"rattle"_fix_shake.html,
-"reax/c/bonds (k)"_fix_reaxc_bonds.html,
-"reax/c/species (k)"_fix_reaxc_species.html,
-"recenter"_fix_recenter.html,
-"restrain"_fix_restrain.html,
-"rhok"_fix_rhok.html,
-"rigid (o)"_fix_rigid.html,
-"rigid/meso"_fix_rigid_meso.html,
-"rigid/nph (o)"_fix_rigid.html,
-"rigid/nph/small"_fix_rigid.html,
-"rigid/npt (o)"_fix_rigid.html,
-"rigid/npt/small"_fix_rigid.html,
-"rigid/nve (o)"_fix_rigid.html,
-"rigid/nve/small"_fix_rigid.html,
-"rigid/nvt (o)"_fix_rigid.html,
-"rigid/nvt/small"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
-"rx (k)"_fix_rx.html,
-"saed/vtk"_fix_saed_vtk.html,
-"setforce (k)"_fix_setforce.html,
-"shake"_fix_shake.html,
-"shardlow (k)"_fix_shardlow.html,
-"smd"_fix_smd.html,
-"smd/adjust_dt"_fix_smd_adjust_dt.html,
-"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
-"smd/setvel"_fix_smd_setvel.html,
-"smd/wall_surface"_fix_smd_wall_surface.html,
-"spring"_fix_spring.html,
-"spring/chunk"_fix_spring_chunk.html,
-"spring/rg"_fix_spring_rg.html,
-"spring/self"_fix_spring_self.html,
-"srd"_fix_srd.html,
-"store/force"_fix_store_force.html,
-"store/state"_fix_store_state.html,
-"tdpd/source"_fix_dpd_source.html,
-"temp/berendsen"_fix_temp_berendsen.html,
-"temp/csld"_fix_temp_csvr.html,
-"temp/csvr"_fix_temp_csvr.html,
-"temp/rescale"_fix_temp_rescale.html,
-"temp/rescale/eff"_fix_temp_rescale_eff.html,
-"tfmc"_fix_tfmc.html,
-"thermal/conductivity"_fix_thermal_conductivity.html,
-"ti/spring"_fix_ti_spring.html,
-"tmd"_fix_tmd.html,
-"ttm"_fix_ttm.html,
-"ttm/mod"_fix_ttm.html,
-"tune/kspace"_fix_tune_kspace.html,
-"vector"_fix_vector.html,
-"viscosity"_fix_viscosity.html,
-"viscous"_fix_viscous.html,
-"wall/body/polygon"_fix_wall_body_polygon.html,
-"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
-"wall/colloid"_fix_wall.html,
-"wall/ees"_fix_wall_ees.html,
-"wall/gran"_fix_wall_gran.html,
-"wall/gran/region"_fix_wall_gran_region.html,
-"wall/harmonic"_fix_wall.html,
-"wall/lj1043"_fix_wall.html,
-"wall/lj126"_fix_wall.html,
-"wall/lj93 (k)"_fix_wall.html,
-"wall/morse"_fix_wall.html,
-"wall/piston"_fix_wall_piston.html,
-"wall/reflect (k)"_fix_wall_reflect.html,
-"wall/region"_fix_wall_region.html,
-"wall/region/ees"_fix_wall_ees.html,
-"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)
diff --git a/doc/txt/Commands_kspace.txt b/doc/txt/Commands_kspace.txt
deleted file mode 100644
index 02b41b9d67..0000000000
--- a/doc/txt/Commands_kspace.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-KSpace solvers :h3
-
-All LAMMPS "kspace_style"_kspace_style.html solvers.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"ewald (o)"_kspace_style.html,
-"ewald/disp"_kspace_style.html,
-"msm (o)"_kspace_style.html,
-"msm/cg (o)"_kspace_style.html,
-"pppm (gok)"_kspace_style.html,
-"pppm/cg (o)"_kspace_style.html,
-"pppm/disp (i)"_kspace_style.html,
-"pppm/disp/tip4p"_kspace_style.html,
-"pppm/stagger"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html,
-"scafacos"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/txt/Commands_pair.txt b/doc/txt/Commands_pair.txt
deleted file mode 100644
index e6ebd21987..0000000000
--- a/doc/txt/Commands_pair.txt
+++ /dev/null
@@ -1,253 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-Pair_style potentials :h3
-
-All LAMMPS "pair_style"_pair_style.html commands.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_pair_none.html,
-"zero"_pair_zero.html,
-"hybrid (k)"_pair_hybrid.html,
-"hybrid/overlay (k)"_pair_hybrid.html,
-,
-,
-,
-,
-"adp (o)"_pair_adp.html,
-"agni (o)"_pair_agni.html,
-"airebo (io)"_pair_airebo.html,
-"airebo/morse (io)"_pair_airebo.html,
-"atm"_pair_atm.html,
-"awpmd/cut"_pair_awpmd.html,
-"beck (go)"_pair_beck.html,
-"body/nparticle"_pair_body_nparticle.html,
-"body/rounded/polygon"_pair_body_rounded_polygon.html,
-"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html,
-"bop"_pair_bop.html,
-"born (go)"_pair_born.html,
-"born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_cs.html,
-"born/coul/long (go)"_pair_born.html,
-"born/coul/long/cs (g)"_pair_cs.html,
-"born/coul/msm (o)"_pair_born.html,
-"born/coul/wolf (go)"_pair_born.html,
-"born/coul/wolf/cs (g)"_pair_cs.html,
-"brownian (o)"_pair_brownian.html,
-"brownian/poly (o)"_pair_brownian.html,
-"buck (giko)"_pair_buck.html,
-"buck/coul/cut (giko)"_pair_buck.html,
-"buck/coul/long (giko)"_pair_buck.html,
-"buck/coul/long/cs"_pair_cs.html,
-"buck/coul/msm (o)"_pair_buck.html,
-"buck/long/coul/long (o)"_pair_buck_long.html,
-"buck/mdf"_pair_mdf.html,
-"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
-"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
-"colloid (go)"_pair_colloid.html,
-"comb (o)"_pair_comb.html,
-"comb3"_pair_comb.html,
-"cosine/squared"_pair_cosine_squared.html,
-"coul/cut (gko)"_pair_coul.html,
-"coul/cut/soft (o)"_pair_fep_soft.html,
-"coul/debye (gko)"_pair_coul.html,
-"coul/diel (o)"_pair_coul_diel.html,
-"coul/dsf (gko)"_pair_coul.html,
-"coul/long (gko)"_pair_coul.html,
-"coul/long/cs (g)"_pair_cs.html,
-"coul/long/soft (o)"_pair_fep_soft.html,
-"coul/msm (o)"_pair_coul.html,
-"coul/shield"_pair_coul_shield.html,
-"coul/streitz"_pair_coul.html,
-"coul/wolf (ko)"_pair_coul.html,
-"coul/wolf/cs"_pair_cs.html,
-"dpd (gio)"_pair_dpd.html,
-"dpd/fdt"_pair_dpd_fdt.html,
-"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
-"dpd/tstat (go)"_pair_dpd.html,
-"dsmc"_pair_dsmc.html,
-"e3b"_pair_e3b.html,
-"drip"_pair_drip.html,
-"eam (gikot)"_pair_eam.html,
-"eam/alloy (gikot)"_pair_eam.html,
-"eam/cd (o)"_pair_eam.html,
-"eam/cd/old (o)"_pair_eam.html,
-"eam/fs (gikot)"_pair_eam.html,
-"edip (o)"_pair_edip.html,
-"edip/multi"_pair_edip.html,
-"edpd"_pair_meso.html,
-"eff/cut"_pair_eff.html,
-"eim (o)"_pair_eim.html,
-"exp6/rx (k)"_pair_exp6_rx.html,
-"extep"_pair_extep.html,
-"gauss (go)"_pair_gauss.html,
-"gauss/cut (o)"_pair_gauss.html,
-"gayberne (gio)"_pair_gayberne.html,
-"gran/hertz/history (o)"_pair_gran.html,
-"gran/hooke (o)"_pair_gran.html,
-"gran/hooke/history (ko)"_pair_gran.html,
-"granular"_pair_granular.html,
-"gw"_pair_gw.html,
-"gw/zbl"_pair_gw.html,
-"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
-"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
-"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
-"kim"_pair_kim.html,
-"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
-"lcbop"_pair_lcbop.html,
-"lebedeva/z"_pair_lebedeva_z.html,
-"lennard/mdf"_pair_mdf.html,
-"line/lj"_pair_line_lj.html,
-"list"_pair_list.html,
-"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
-"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (gikot)"_pair_charmm.html,
-"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
-"lj/charmm/coul/msm (o)"_pair_charmm.html,
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
-"lj/charmmfsw/coul/long"_pair_charmm.html,
-"lj/class2 (gko)"_pair_class2.html,
-"lj/class2/coul/cut (ko)"_pair_class2.html,
-"lj/class2/coul/cut/soft"_pair_fep_soft.html,
-"lj/class2/coul/long (gko)"_pair_class2.html,
-"lj/class2/coul/long/soft"_pair_fep_soft.html,
-"lj/class2/soft"_pair_fep_soft.html,
-"lj/cubic (go)"_pair_lj_cubic.html,
-"lj/cut (gikot)"_pair_lj.html,
-"lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
-"lj/cut/coul/debye (gko)"_pair_lj.html,
-"lj/cut/coul/dsf (gko)"_pair_lj.html,
-"lj/cut/coul/long (gikot)"_pair_lj.html,
-"lj/cut/coul/long/cs"_pair_cs.html,
-"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
-"lj/cut/coul/msm (go)"_pair_lj.html,
-"lj/cut/coul/wolf (o)"_pair_lj.html,
-"lj/cut/dipole/cut (go)"_pair_dipole.html,
-"lj/cut/dipole/long (g)"_pair_dipole.html,
-"lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_fep_soft.html,
-"lj/cut/thole/long (o)"_pair_thole.html,
-"lj/cut/tip4p/cut (o)"_pair_lj.html,
-"lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
-"lj/expand (gko)"_pair_lj_expand.html,
-"lj/expand/coul/long (g)"_pair_lj_expand.html,
-"lj/gromacs (gko)"_pair_gromacs.html,
-"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (iot)"_pair_lj_long.html,
-"lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long (o)"_pair_lj_long.html,
-"lj/mdf"_pair_mdf.html,
-"lj/sdk (gko)"_pair_sdk.html,
-"lj/sdk/coul/long (go)"_pair_sdk.html,
-"lj/sdk/coul/msm (o)"_pair_sdk.html,
-"lj/sf/dipole/sf (go)"_pair_dipole.html,
-"lj/smooth (o)"_pair_lj_smooth.html,
-"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
-"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
-"lj96/cut (go)"_pair_lj96.html,
-"local/density"_pair_local_density.html,
-"lubricate (o)"_pair_lubricate.html,
-"lubricate/poly (o)"_pair_lubricate.html,
-"lubricateU"_pair_lubricateU.html,
-"lubricateU/poly"_pair_lubricateU.html,
-"mdpd"_pair_meso.html,
-"mdpd/rhosum"_pair_meso.html,
-"meam/c"_pair_meamc.html,
-"meam/spline (o)"_pair_meam_spline.html,
-"meam/sw/spline"_pair_meam_sw_spline.html,
-"mgpt"_pair_mgpt.html,
-"mie/cut (g)"_pair_mie.html,
-"momb"_pair_momb.html,
-"morse (gkot)"_pair_morse.html,
-"morse/smooth/linear (o)"_pair_morse.html,
-"morse/soft"_pair_fep_soft.html,
-"multi/lucy"_pair_multi_lucy.html,
-"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"nb3b/harmonic"_pair_nb3b_harmonic.html,
-"nm/cut (o)"_pair_nm.html,
-"nm/cut/coul/cut (o)"_pair_nm.html,
-"nm/cut/coul/long (o)"_pair_nm.html,
-"oxdna/coaxstk"_pair_oxdna.html,
-"oxdna/excv"_pair_oxdna.html,
-"oxdna/hbond"_pair_oxdna.html,
-"oxdna/stk"_pair_oxdna.html,
-"oxdna/xstk"_pair_oxdna.html,
-"oxdna2/coaxstk"_pair_oxdna2.html,
-"oxdna2/dh"_pair_oxdna2.html,
-"oxdna2/excv"_pair_oxdna2.html,
-"oxdna2/hbond"_pair_oxdna2.html,
-"oxdna2/stk"_pair_oxdna2.html,
-"oxdna2/xstk"_pair_oxdna2.html,
-"peri/eps"_pair_peri.html,
-"peri/lps (o)"_pair_peri.html,
-"peri/pmb (o)"_pair_peri.html,
-"peri/ves"_pair_peri.html,
-"polymorphic"_pair_polymorphic.html,
-"python"_pair_python.html,
-"quip"_pair_quip.html,
-"reax/c (ko)"_pair_reaxc.html,
-"rebo (io)"_pair_airebo.html,
-"resquared (go)"_pair_resquared.html,
-"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
-"smd/hertz"_pair_smd_hertz.html,
-"smd/tlsph"_pair_smd_tlsph.html,
-"smd/tri_surface"_pair_smd_triangulated_surface.html,
-"smd/ulsph"_pair_smd_ulsph.html,
-"smtbq"_pair_smtbq.html,
-"snap (k)"_pair_snap.html,
-"snap (k)"_pair_snap.html,
-"soft (go)"_pair_soft.html,
-"sph/heatconduction"_pair_sph_heatconduction.html,
-"sph/idealgas"_pair_sph_idealgas.html,
-"sph/lj"_pair_sph_lj.html,
-"sph/rhosum"_pair_sph_rhosum.html,
-"sph/taitwater"_pair_sph_taitwater.html,
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
-"spin/dipole/cut"_pair_spin_dipole.html,
-"spin/dipole/long"_pair_spin_dipole.html,
-"spin/dmi"_pair_spin_dmi.html,
-"spin/exchange"_pair_spin_exchange.html,
-"spin/magelec"_pair_spin_magelec.html,
-"spin/neel"_pair_spin_neel.html,
-"srp"_pair_srp.html,
-"sw (giko)"_pair_sw.html,
-"table (gko)"_pair_table.html,
-"table/rx (k)"_pair_table_rx.html,
-"tdpd"_pair_meso.html,
-"tersoff (giko)"_pair_tersoff.html,
-"tersoff/mod (gko)"_pair_tersoff_mod.html,
-"tersoff/mod/c (o)"_pair_tersoff_mod.html,
-"tersoff/table (o)"_pair_tersoff.html,
-"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
-"thole"_pair_thole.html,
-"tip4p/cut (o)"_pair_coul.html,
-"tip4p/long (o)"_pair_coul.html,
-"tip4p/long/soft (o)"_pair_fep_soft.html,
-"tri/lj"_pair_tri_lj.html,
-"ufm (got)"_pair_ufm.html,
-"vashishta (gko)"_pair_vashishta.html,
-"vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gko)"_pair_yukawa.html,
-"yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)
diff --git a/doc/txt/Commands_removed.txt b/doc/txt/Commands_removed.txt
deleted file mode 100644
index 1eee6e45e0..0000000000
--- a/doc/txt/Commands_removed.txt
+++ /dev/null
@@ -1,66 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands.html)
-
-:line
-
-Removed commands and packages :h3
-
-This page lists LAMMPS commands and packages that have been removed from
-the distribution and provides suggestions for alternatives or replacements.
-LAMMPS has special dummy styles implemented, that will stop LAMMPS and
-print a suitable error message in most cases, when a style/command is used
-that has been removed.
-
-Fix ave/spatial and fix ave/spatial/sphere :h4
-
-The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
-since they were superseded by the more general and extensible "chunk
-infrastructure".  Here the system is partitioned in one of many possible
-ways through the "compute chunk/atom"_compute_chunk_atom.html command
-and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
-Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
-
-MEAM package :h4
-
-The MEAM package has been removed since it was superseded by the
-"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
-the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
-which removes several restrictions (e.g. there can be multiple instances
-in hybrid pair styles) and allows for some optimizations leading
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-the exact same syntax as the old "meam" pair style and thus pair style
-"meam"_pair_meamc.html is an alias to the new style and backward
-compatibility of old inputs is preserved.
-
-REAX package :h4
-
-The REAX package has been removed since it was superseded by the
-"USER-REAXC package"_Package_details.html#PKG-USER-REAXC.  The USER-REAXC
-package has been tested to yield equivalent results to the REAX package,
-offers better performance, supports OpenMP multi-threading via USER-OMP,
-and GPU and threading parallelization through KOKKOS.  The new pair styles
-are not syntax compatible with the removed reax pair style, so input
-files will have to be adapted.
-
-USER-CUDA package :h4
-
-The USER-CUDA package had been removed, since it had been unmaintained
-for a long time and had known bugs and problems.  Significant parts of
-the design were transferred to the
-"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
-performance characteristics on Nvidia GPUs. Both, the KOKKOS
-and the "GPU package"_Package_details.html#PKG-GPU are maintained
-and allow running LAMMPS with GPU acceleration.
-
-restart2data tool :h4
-
-The functionality of the restart2data tool has been folded into the
-LAMMPS executable directly instead of having a separate tool.  A
-combination of the commands "read_restart"_read_restart.html and
-"write_data"_write_data.html can be used to the same effect.  For added
-convenience this conversion can also be triggered by "command line
-flags"_Run_options.html
diff --git a/doc/txt/Commands_structure.txt b/doc/txt/Commands_structure.txt
deleted file mode 100644
index b5d2c7b07b..0000000000
--- a/doc/txt/Commands_structure.txt
+++ /dev/null
@@ -1,95 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Input script structure :h3
-
-This page describes the structure of a typical LAMMPS input script.
-The examples directory in the LAMMPS distribution contains many sample
-input scripts; it is discussed on the "Examples"_Examples.html doc
-page.
-
-A LAMMPS input script typically has 4 parts:
-
-Initialization
-Atom definition
-Settings
-Run a simulation :ol
-
-The last 2 parts can be repeated as many times as desired.  I.e. run a
-simulation, change some settings, run some more, etc.  Each of the 4
-parts is now described in more detail.  Remember that almost all
-commands need only be used if a non-default value is desired.
-
-(1) Initialization
-
-Set parameters that need to be defined before atoms are created or
-read-in from a file.
-
-The relevant commands are "units"_units.html,
-"dimension"_dimension.html, "newton"_newton.html,
-"processors"_processors.html, "boundary"_boundary.html,
-"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
-
-If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-"pair_style"_pair_style.html, "bond_style"_bond_style.html,
-"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
-"improper_style"_improper_style.html.
-
-(2) Atom definition
-
-There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the "read_data"_read_data.html or
-"read_restart"_read_restart.html commands.  These files can contain
-molecular topology information.  Or create atoms on a lattice (with no
-molecular topology), using these commands: "lattice"_lattice.html,
-"region"_region.html, "create_box"_create_box.html,
-"create_atoms"_create_atoms.html.  The entire set of atoms can be
-duplicated to make a larger simulation using the
-"replicate"_replicate.html command.
-
-(3) Settings
-
-Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-
-Force field coefficients are set by these commands (they can also be
-set in the read-in files): "pair_coeff"_pair_coeff.html,
-"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"improper_coeff"_improper_coeff.html,
-"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
-"special_bonds"_special_bonds.html.
-
-Various simulation parameters are set by these commands:
-"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
-"group"_group.html, "timestep"_timestep.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"min_style"_min_style.html, "min_modify"_min_modify.html.
-
-Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options.  The "fix"_fix.html command comes in many flavors.
-
-Various computations can be specified for execution during a
-simulation using the "compute"_compute.html,
-"compute_modify"_compute_modify.html, and "variable"_variable.html
-commands.
-
-Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
-and "restart"_restart.html commands.
-
-(4) Run a simulation
-
-A molecular dynamics simulation is run using the "run"_run.html
-command.  Energy minimization (molecular statics) is performed using
-the "minimize"_minimize.html command.  A parallel tempering
-(replica-exchange) simulation can be run using the
-"temper"_temper.html command.
-

From 7d289063b414e11a7c1b50de77d41351d95c0b8e Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sun, 24 Nov 2019 19:23:16 -0700
Subject: [PATCH 068/199] Update src/Command*.rst files

---
 doc/src/Commands.rst           |   8 +-
 doc/src/Commands_all.rst       | 180 +++++++++++-----
 doc/src/Commands_angle.rst     |  55 +++++
 doc/src/Commands_bond.rst      | 140 ++++---------
 doc/src/Commands_category.rst  |   5 -
 doc/src/Commands_compute.rst   | 218 +++++++++++++------
 doc/src/Commands_dihedral.rst  |  51 +++++
 doc/src/Commands_fix.rst       | 314 ++++++++++++++++++++--------
 doc/src/Commands_improper.rst  |  46 +++++
 doc/src/Commands_input.rst     |   5 -
 doc/src/Commands_kspace.rst    |  44 ++--
 doc/src/Commands_pair.rst      | 368 ++++++++++++++++++++++-----------
 doc/src/Commands_parse.rst     |   5 -
 doc/src/Commands_structure.rst |   5 -
 14 files changed, 978 insertions(+), 466 deletions(-)
 create mode 100644 doc/src/Commands_angle.rst
 create mode 100644 doc/src/Commands_dihedral.rst
 create mode 100644 doc/src/Commands_improper.rst

diff --git a/doc/src/Commands.rst b/doc/src/Commands.rst
index e845faa903..79fa30003d 100644
--- a/doc/src/Commands.rst
+++ b/doc/src/Commands.rst
@@ -21,14 +21,12 @@ commands in it are used to define a LAMMPS simulation.
    Commands_compute
    Commands_pair
    Commands_bond
+   Commands_angle
+   Commands_dihedral
+   Commands_improper
    Commands_kspace
 
 .. toctree::
    :maxdepth: 1
 
    Commands_removed
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst
index 583e9e3c3a..b9f5578137 100644
--- a/doc/src/Commands_all.rst
+++ b/doc/src/Commands_all.rst
@@ -1,59 +1,135 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 General commands
 ================
 
 An alphabetic list of all general LAMMPS commands.
 
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`angle\_coeff <angle_coeff>`       | :doc:`angle\_style <angle_style>`       | :doc:`atom\_modify <atom_modify>`       | :doc:`atom\_style <atom_style>`         | :doc:`balance <balance>`                    | :doc:`bond\_coeff <bond_coeff>`         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`bond\_style <bond_style>`         | :doc:`bond\_write <bond_write>`         | :doc:`boundary <boundary>`              | :doc:`box <box>`                        | :doc:`change\_box <change_box>`             | :doc:`clear <clear>`                    |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`comm\_modify <comm_modify>`       | :doc:`comm\_style <comm_style>`         | :doc:`compute <compute>`                | :doc:`compute\_modify <compute_modify>` | :doc:`create\_atoms <create_atoms>`         | :doc:`create\_bonds <create_bonds>`     |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`create\_box <create_box>`         | :doc:`delete\_atoms <delete_atoms>`     | :doc:`delete\_bonds <delete_bonds>`     | :doc:`dielectric <dielectric>`          | :doc:`dihedral\_coeff <dihedral_coeff>`     | :doc:`dihedral\_style <dihedral_style>` |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`dimension <dimension>`            | :doc:`displace\_atoms <displace_atoms>` | :doc:`dump <dump>`                      | :doc:`dump adios <dump_adios>`          | :doc:`dump image <dump_image>`              | :doc:`dump movie <dump_image>`          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`dump netcdf <dump_netcdf>`        | :doc:`dump netcdf/mpiio <dump_netcdf>`  | :doc:`dump vtk <dump_vtk>`              | :doc:`dump\_modify <dump_modify>`       | :doc:`dynamical\_matrix <dynamical_matrix>` | :doc:`echo <echo>`                      |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`fix <fix>`                        | :doc:`fix\_modify <fix_modify>`         | :doc:`group <group>`                    | :doc:`group2ndx <group2ndx>`            | :doc:`hyper <hyper>`                        | :doc:`if <if>`                          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`info <info>`                      | :doc:`improper\_coeff <improper_coeff>` | :doc:`improper\_style <improper_style>` | :doc:`include <include>`                | :doc:`jump <jump>`                          | :doc:`kim\_init <kim_commands>`         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`kim\_interactions <kim_commands>` | :doc:`kim\_query <kim_commands>`        | :doc:`kspace\_modify <kspace_modify>`   | :doc:`kspace\_style <kspace_style>`     | :doc:`label <label>`                        | :doc:`lattice <lattice>`                |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`log <log>`                        | :doc:`mass <mass>`                      | :doc:`message <message>`                | :doc:`minimize <minimize>`              | :doc:`min\_modify <min_modify>`             | :doc:`min\_style <min_style>`           |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`min\_style spin <min_spin>`       | :doc:`molecule <molecule>`              | :doc:`ndx2group <group2ndx>`            | :doc:`neb <neb>`                        | :doc:`neb/spin <neb_spin>`                  | :doc:`neigh\_modify <neigh_modify>`     |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`neighbor <neighbor>`              | :doc:`newton <newton>`                  | :doc:`next <next>`                      | :doc:`package <package>`                | :doc:`pair\_coeff <pair_coeff>`             | :doc:`pair\_modify <pair_modify>`       |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`pair\_style <pair_style>`         | :doc:`pair\_write <pair_write>`         | :doc:`partition <partition>`            | :doc:`prd <prd>`                        | :doc:`print <print>`                        | :doc:`processors <processors>`          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`python <python>`                  | :doc:`quit <quit>`                      | :doc:`read\_data <read_data>`           | :doc:`read\_dump <read_dump>`           | :doc:`read\_restart <read_restart>`         | :doc:`region <region>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`replicate <replicate>`            | :doc:`rerun <rerun>`                    | :doc:`reset\_ids <reset_ids>`           | :doc:`reset\_timestep <reset_timestep>` | :doc:`restart <restart>`                    | :doc:`run <run>`                        |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`run\_style <run_style>`           | :doc:`server <server>`                  | :doc:`set <set>`                        | :doc:`shell <shell>`                    | :doc:`special\_bonds <special_bonds>`       | :doc:`suffix <suffix>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`tad <tad>`                        | :doc:`temper <temper>`                  | :doc:`temper/grem <temper_grem>`        | :doc:`temper/npt <temper_npt>`          | :doc:`thermo <thermo>`                      | :doc:`thermo\_modify <thermo_modify>`   |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`thermo\_style <thermo_style>`     | :doc:`third\_order <third_order>`       | :doc:`timer <timer>`                    | :doc:`timestep <timestep>`              | :doc:`uncompute <uncompute>`                | :doc:`undump <undump>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`unfix <unfix>`                    | :doc:`units <units>`                    | :doc:`variable <variable>`              | :doc:`velocity <velocity>`              | :doc:`write\_coeff <write_coeff>`           | :doc:`write\_data <write_data>`         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`write\_dump <write_dump>`         | :doc:`write\_restart <write_restart>`   |                                         |                                         |                                             |                                         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+.. table_from_list::
+   :columns: 6
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`angle_coeff <angle_coeff>`
+   * :doc:`angle_style <angle_style>`
+   * :doc:`atom_modify <atom_modify>`
+   * :doc:`atom_style <atom_style>`
+   * :doc:`balance <balance>`
+   * :doc:`bond_coeff <bond_coeff>`
+   * :doc:`bond\_style <bond_style>`
+   * :doc:`bond\_write <bond_write>`
+   * :doc:`boundary <boundary>`
+   * :doc:`box <box>`
+   * :doc:`change\_box <change_box>`
+   * :doc:`clear <clear>`
+   * :doc:`comm\_modify <comm_modify>`
+   * :doc:`comm\_style <comm_style>`
+   * :doc:`compute <compute>`
+   * :doc:`compute\_modify <compute_modify>`
+   * :doc:`create\_atoms <create_atoms>`
+   * :doc:`create\_bonds <create_bonds>`
+   * :doc:`create\_box <create_box>`
+   * :doc:`delete\_atoms <delete_atoms>`
+   * :doc:`delete\_bonds <delete_bonds>`
+   * :doc:`dielectric <dielectric>`
+   * :doc:`dihedral\_coeff <dihedral_coeff>`
+   * :doc:`dihedral\_style <dihedral_style>`
+   * :doc:`dimension <dimension>`
+   * :doc:`displace\_atoms <displace_atoms>`
+   * :doc:`dump <dump>`
+   * :doc:`dump adios <dump_adios>`
+   * :doc:`dump image <dump_image>`
+   * :doc:`dump movie <dump_image>`
+   * :doc:`dump netcdf <dump_netcdf>`
+   * :doc:`dump netcdf/mpiio <dump_netcdf>`
+   * :doc:`dump vtk <dump_vtk>`
+   * :doc:`dump\_modify <dump_modify>`
+   * :doc:`dynamical\_matrix <dynamical_matrix>`
+   * :doc:`echo <echo>`
+   * :doc:`fix <fix>`
+   * :doc:`fix\_modify <fix_modify>`
+   * :doc:`group <group>`
+   * :doc:`group2ndx <group2ndx>`
+   * :doc:`hyper <hyper>`
+   * :doc:`if <if>`
+   * :doc:`improper\_coeff <improper_coeff>`
+   * :doc:`improper\_style <improper_style>`
+   * :doc:`include <include>`
+   * :doc:`jump <jump>`
+   * :doc:`kim\_init <kim_commands>`
+   * :doc:`kim\_interactions <kim_commands>`
+   * :doc:`kim\_query <kim_commands>`
+   * :doc:`kspace\_modify <kspace_modify>`
+   * :doc:`kspace\_style <kspace_style>`
+   * :doc:`label <label>`
+   * :doc:`lattice <lattice>`
+   * :doc:`log <log>`
+   * :doc:`mass <mass>`
+   * :doc:`message <message>`
+   * :doc:`minimize <minimize>`
+   * :doc:`min\_modify <min_modify>`
+   * :doc:`min\_style <min_style>`
+   * :doc:`min\_style spin <min_spin>`
+   * :doc:`molecule <molecule>`
+   * :doc:`ndx2group <group2ndx>`
+   * :doc:`neb <neb>`
+   * :doc:`neb/spin <neb_spin>`
+   * :doc:`neigh\_modify <neigh_modify>`
+   * :doc:`neighbor <neighbor>`
+   * :doc:`newton <newton>`
+   * :doc:`next <next>`
+   * :doc:`package <package>`
+   * :doc:`pair\_coeff <pair_coeff>`
+   * :doc:`pair\_modify <pair_modify>`
+   * :doc:`pair\_write <pair_write>`
+   * :doc:`partition <partition>`
+   * :doc:`prd <prd>`
+   * :doc:`print <print>`
+   * :doc:`processors <processors>`
+   * :doc:`python <python>`
+   * :doc:`quit <quit>`
+   * :doc:`read\_data <read_data>`
+   * :doc:`read\_dump <read_dump>`
+   * :doc:`read\_restart <read_restart>`
+   * :doc:`region <region>`
+   * :doc:`replicate <replicate>`
+   * :doc:`rerun <rerun>`
+   * :doc:`reset\_ids <reset_ids>`
+   * :doc:`reset\_timestep <reset_timestep>`
+   * :doc:`restart <restart>`
+   * :doc:`run <run>`
+   * :doc:`run\_style <run_style>`
+   * :doc:`server <server>`
+   * :doc:`set <set>`
+   * :doc:`shell <shell>`
+   * :doc:`special\_bonds <special_bonds>`
+   * :doc:`suffix <suffix>`
+   * :doc:`tad <tad>`
+   * :doc:`temper <temper>`
+   * :doc:`temper/grem <temper_grem>`
+   * :doc:`temper/npt <temper_npt>`
+   * :doc:`thermo <thermo>`
+   * :doc:`thermo\_modify <thermo_modify>`
+   * :doc:`thermo\_style <thermo_style>`
+   * :doc:`third\_order <third_order>`
+   * :doc:`timer <timer>`
+   * :doc:`timestep <timestep>`
+   * :doc:`uncompute <uncompute>`
+   * :doc:`undump <undump>`
+   * :doc:`unfix <unfix>`
+   * :doc:`units <units>`
+   * :doc:`variable <variable>`
+   * :doc:`velocity <velocity>`
+   * :doc:`write\_coeff <write_coeff>`
+   * :doc:`write\_data <write_data>`
+   * :doc:`write\_dump <write_dump>`
+   * :doc:`write\_restart <write_restart>`
diff --git a/doc/src/Commands_angle.rst b/doc/src/Commands_angle.rst
new file mode 100644
index 0000000000..ca5e96d57e
--- /dev/null
+++ b/doc/src/Commands_angle.rst
@@ -0,0 +1,55 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+
+.. _angle:
+
+Angle\_style potentials
+=======================
+
+All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <angle_none>`
+   * :doc:`zero <angle_zero>`
+   * :doc:`hybrid <angle_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <angle_charmm>`
+   * :doc:`class2 (ko) <angle_class2>`
+   * :doc:`class2/p6 <angle_class2>`
+   * :doc:`cosine (ko) <angle_cosine>`
+   * :doc:`cosine/buck6d <angle_cosine_buck6d>`
+   * :doc:`cosine/delta (o) <angle_cosine_delta>`
+   * :doc:`cosine/periodic (o) <angle_cosine_periodic>`
+   * :doc:`cosine/shift (o) <angle_cosine_shift>`
+   * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
+   * :doc:`cosine/squared (o) <angle_cosine_squared>`
+   * :doc:`cross <angle_cross>`
+   * :doc:`dipole (o) <angle_dipole>`
+   * :doc:`fourier (o) <angle_fourier>`
+   * :doc:`fourier/simple (o) <angle_fourier_simple>`
+   * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`mm3 <angle_mm3>`
+   * :doc:`quartic (o) <angle_quartic>`
+   * :doc:`sdk (o) <angle_sdk>`
+   * :doc:`table (o) <angle_table>`
+   *
diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
index 2eb6c1f8c7..a7e22274e9 100644
--- a/doc/src/Commands_bond.rst
+++ b/doc/src/Commands_bond.rst
@@ -1,3 +1,16 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
 .. _bond:
 
 Bond\_style potentials
@@ -8,105 +21,30 @@ accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`none <bond_none>`               | :doc:`zero <bond_zero>`                         | :doc:`hybrid <bond_hybrid>`                             |                                 |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-|                                       |                                                 |                                                         |                                 |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`class2 (ko) <bond_class2>`      | :doc:`fene (iko) <bond_fene>`                   | :doc:`fene/expand (o) <bond_fene_expand>`               | :doc:`gromos (o) <bond_gromos>` |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`harmonic (iko) <bond_harmonic>` | :doc:`harmonic/shift (o) <bond_harmonic_shift>` | :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>` | :doc:`mm3 <bond_mm3>`           |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`morse (o) <bond_morse>`         | :doc:`nonlinear (o) <bond_nonlinear>`           | :doc:`oxdna/fene <bond_oxdna>`                          | :doc:`oxdna2/fene <bond_oxdna>` |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`quartic (o) <bond_quartic>`     | :doc:`table (o) <bond_table>`                   |                                                         |                                 |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
+.. table_from_list::
+   :columns: 4
 
-
-----------
-
-
-.. _angle:
-
-Angle\_style potentials
-===================================
-
-All LAMMPS :doc:`angle\_style <angle_style>` commands.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`none <angle_none>`                             | :doc:`zero <angle_zero>`                         | :doc:`hybrid <angle_hybrid>`                       |                                              |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-|                                                      |                                                  |                                                    |                                              |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`charmm (iko) <angle_charmm>`                   | :doc:`class2 (ko) <angle_class2>`                | :doc:`class2/p6 <angle_class2>`                    | :doc:`cosine (ko) <angle_cosine>`            |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`cosine/buck6d <angle_cosine_buck6d>`           | :doc:`cosine/delta (o) <angle_cosine_delta>`     | :doc:`cosine/periodic (o) <angle_cosine_periodic>` | :doc:`cosine/shift (o) <angle_cosine_shift>` |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>` | :doc:`cosine/squared (o) <angle_cosine_squared>` | :doc:`cross <angle_cross>`                         | :doc:`dipole (o) <angle_dipole>`             |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`fourier (o) <angle_fourier>`                   | :doc:`fourier/simple (o) <angle_fourier_simple>` | :doc:`harmonic (iko) <angle_harmonic>`             | :doc:`mm3 <angle_mm3>`                       |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`quartic (o) <angle_quartic>`                   | :doc:`sdk (o) <angle_sdk>`                       | :doc:`table (o) <angle_table>`                     |                                              |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-
-
-----------
-
-
-.. _dihedral:
-
-Dihedral\_style potentials
-=========================================
-
-All LAMMPS :doc:`dihedral\_style <dihedral_style>` commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`none <dihedral_none>`               | :doc:`zero <dihedral_zero>`               | :doc:`hybrid <dihedral_hybrid>`           |                                                         |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-|                                           |                                           |                                           |                                                         |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`charmm (iko) <dihedral_charmm>`     | :doc:`charmmfsw <dihedral_charmm>`        | :doc:`class2 (ko) <dihedral_class2>`      | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`fourier (io) <dihedral_fourier>`    | :doc:`harmonic (iko) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>`         | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`     |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`opls (iko) <dihedral_opls>`         | :doc:`quadratic (o) <dihedral_quadratic>` | :doc:`spherical <dihedral_spherical>`                   |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`table (o) <dihedral_table>`         | :doc:`table/cut <dihedral_table_cut>`     |                                           |                                                         |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-
-
-----------
-
-
-.. _improper:
-
-Improper\_style potentials
-=========================================
-
-All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`none <improper_none>`          | :doc:`zero <improper_zero>`             | :doc:`hybrid <improper_hybrid>`           |                                                         |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-|                                      |                                         |                                           |                                                         |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`class2 (ko) <improper_class2>` | :doc:`cossq (o) <improper_cossq>`       | :doc:`cvff (io) <improper_cvff>`          | :doc:`distance <improper_distance>`                     |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`distharm <improper_distharm>`  | :doc:`fourier (o) <improper_fourier>`   | :doc:`harmonic (iko) <improper_harmonic>` | :doc:`inversion/harmonic <improper_inversion_harmonic>` |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`ring (o) <improper_ring>`      | :doc:`sqdistharm <improper_sqdistharm>` | :doc:`umbrella (o) <improper_umbrella>`   |                                                         |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`none <bond_none>`
+   * :doc:`zero <bond_zero>`
+   * :doc:`hybrid <bond_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <bond_class2>`
+   * :doc:`fene (iko) <bond_fene>`
+   * :doc:`fene/expand (o) <bond_fene_expand>`
+   * :doc:`gromos (o) <bond_gromos>`
+   * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
+   * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`mm3 <bond_mm3>`
+   * :doc:`morse (o) <bond_morse>`
+   * :doc:`nonlinear (o) <bond_nonlinear>`
+   * :doc:`oxdna/fene <bond_oxdna>`
+   * :doc:`oxdna2/fene <bond_oxdna>`
+   * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`table (o) <bond_table>`
+   *
+   *
diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst
index 14a354ad13..b1b0e0cadc 100644
--- a/doc/src/Commands_category.rst
+++ b/doc/src/Commands_category.rst
@@ -130,8 +130,3 @@ Input script control:
 * :doc:`quit <quit>`,
 * :doc:`shell <shell>`,
 * :doc:`variable <variable>`
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index ab30339035..1b3465eb53 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -1,10 +1,15 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 Compute commands
 ================
@@ -14,57 +19,150 @@ Some styles have accelerated versions.  This is indicated by
 additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`ackland/atom <compute_ackland_atom>`                 | :doc:`adf <compute_adf>`                               | :doc:`aggregate/atom <compute_cluster_atom>`                     | :doc:`angle <compute_angle>`                                 | :doc:`angle/local <compute_angle_local>`                 | :doc:`angmom/chunk <compute_angmom_chunk>`                   |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`basal/atom <compute_basal_atom>`                     | :doc:`body/local <compute_body_local>`                 | :doc:`bond <compute_bond>`                                       | :doc:`bond/local <compute_bond_local>`                       | :doc:`centro/atom <compute_centro_atom>`                 | :doc:`centroid/stress/atom <compute_stress_atom>`            |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`chunk/atom <compute_chunk_atom>`                     | :doc:`chunk/spread/atom <compute_chunk_spread_atom>`   | :doc:`cluster/atom <compute_cluster_atom>`                       | :doc:`cna/atom <compute_cna_atom>`                           | :doc:`cnp/atom <compute_cnp_atom>`                       | :doc:`com <compute_com>`                                     |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`com/chunk <compute_com_chunk>`                       | :doc:`contact/atom <compute_contact_atom>`             | :doc:`coord/atom <compute_coord_atom>`                           | :doc:`damage/atom <compute_damage_atom>`                     | :doc:`dihedral <compute_dihedral>`                       | :doc:`dihedral/local <compute_dihedral_local>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`dilatation/atom <compute_dilatation_atom>`           | :doc:`dipole/chunk <compute_dipole_chunk>`             | :doc:`displace/atom <compute_displace_atom>`                     | :doc:`dpd <compute_dpd>`                                     | :doc:`dpd/atom <compute_dpd_atom>`                       | :doc:`edpd/temp/atom <compute_edpd_temp_atom>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`entropy/atom <compute_entropy_atom>`                 | :doc:`erotate/asphere <compute_erotate_asphere>`       | :doc:`erotate/rigid <compute_erotate_rigid>`                     | :doc:`erotate/sphere <compute_erotate_sphere>`               | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`fep <compute_fep>`                                   | :doc:`force/tally <compute_tally>`                     | :doc:`fragment/atom <compute_cluster_atom>`                      | :doc:`global/atom <compute_global_atom>`                     | :doc:`group/group <compute_group_group>`                 | :doc:`gyration <compute_gyration>`                           |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`gyration/chunk <compute_gyration_chunk>`             | :doc:`gyration/shape <compute_gyration_shape>`         | :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`       | :doc:`heat/flux <compute_heat_flux>`                         | :doc:`heat/flux/tally <compute_tally>`                   | :doc:`hexorder/atom <compute_hexorder_atom>`                 |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`hma <compute_hma>`                                   | :doc:`improper <compute_improper>`                     | :doc:`improper/local <compute_improper_local>`                   | :doc:`inertia/chunk <compute_inertia_chunk>`                 | :doc:`ke <compute_ke>`                                   | :doc:`ke/atom <compute_ke_atom>`                             |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`ke/atom/eff <compute_ke_atom_eff>`                   | :doc:`ke/eff <compute_ke_eff>`                         | :doc:`ke/rigid <compute_ke_rigid>`                               | :doc:`meso/e/atom <compute_meso_e_atom>`                     | :doc:`meso/rho/atom <compute_meso_rho_atom>`             | :doc:`meso/t/atom <compute_meso_t_atom>`                     |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`momentum <compute_momentum>`                         | :doc:`msd <compute_msd>`                               | :doc:`msd/chunk <compute_msd_chunk>`                             | :doc:`msd/nongauss <compute_msd_nongauss>`                   | :doc:`omega/chunk <compute_omega_chunk>`                 | :doc:`orientorder/atom <compute_orientorder_atom>`           |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`pair <compute_pair>`                                 | :doc:`pair/local <compute_pair_local>`                 | :doc:`pe <compute_pe>`                                           | :doc:`pe/atom <compute_pe_atom>`                             | :doc:`pe/mol/tally <compute_tally>`                      | :doc:`pe/tally <compute_tally>`                              |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`plasticity/atom <compute_plasticity_atom>`           | :doc:`pressure <compute_pressure>`                     | :doc:`pressure/cylinder <compute_pressure_cylinder>`             | :doc:`pressure/uef <compute_pressure_uef>`                   | :doc:`property/atom <compute_property_atom>`             | :doc:`property/chunk <compute_property_chunk>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`property/local <compute_property_local>`             | :doc:`ptm/atom <compute_ptm_atom>`                     | :doc:`rdf <compute_rdf>`                                         | :doc:`reduce <compute_reduce>`                               | :doc:`reduce/chunk <compute_reduce_chunk>`               | :doc:`reduce/region <compute_reduce>`                        |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`rigid/local <compute_rigid_local>`                   | :doc:`saed <compute_saed>`                             | :doc:`slice <compute_slice>`                                     | :doc:`smd/contact/radius <compute_smd_contact_radius>`       | :doc:`smd/damage <compute_smd_damage>`                   | :doc:`smd/hourglass/error <compute_smd_hourglass_error>`     |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`smd/internal/energy <compute_smd_internal_energy>`   | :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>`                             | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`     | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`                   |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`       | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`               | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`       | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                         | :doc:`sna/atom <compute_sna_atom>`                           |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`snad/atom <compute_sna_atom>`                        | :doc:`snav/atom <compute_sna_atom>`                    | :doc:`spin <compute_spin>`                                       | :doc:`stress/atom <compute_stress_atom>`                     | :doc:`stress/mop <compute_stress_mop>`                   | :doc:`stress/mop/profile <compute_stress_mop>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`stress/tally <compute_tally>`                        | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`             | :doc:`temp (k) <compute_temp>`                                   | :doc:`temp/asphere <compute_temp_asphere>`                   | :doc:`temp/body <compute_temp_body>`                     | :doc:`temp/chunk <compute_temp_chunk>`                       |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`temp/com <compute_temp_com>`                         | :doc:`temp/cs <compute_temp_cs>`                       | :doc:`temp/deform <compute_temp_deform>`                         | :doc:`temp/deform/eff <compute_temp_deform_eff>`             | :doc:`temp/drude <compute_temp_drude>`                   | :doc:`temp/eff <compute_temp_eff>`                           |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`temp/partial <compute_temp_partial>`                 | :doc:`temp/profile <compute_temp_profile>`             | :doc:`temp/ramp <compute_temp_ramp>`                             | :doc:`temp/region <compute_temp_region>`                     | :doc:`temp/region/eff <compute_temp_region_eff>`         | :doc:`temp/rotate <compute_temp_rotate>`                     |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`temp/sphere <compute_temp_sphere>`                   | :doc:`temp/uef <compute_temp_uef>`                     | :doc:`ti <compute_ti>`                                           | :doc:`torque/chunk <compute_torque_chunk>`                   | :doc:`vacf <compute_vacf>`                               | :doc:`vcm/chunk <compute_vcm_chunk>`                         |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`voronoi/atom <compute_voronoi_atom>`                 | :doc:`xrd <compute_xrd>`                               |                                                                  |                                                              |                                                          |                                                              |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+.. table_from_list::
+   :columns: 6
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`ackland/atom <compute_ackland_atom>`
+   * :doc:`adf <compute_adf>`
+   * :doc:`aggregate/atom <compute_cluster_atom>`
+   * :doc:`angle <compute_angle>`
+   * :doc:`angle/local <compute_angle_local>`
+   * :doc:`angmom/chunk <compute_angmom_chunk>`
+   * :doc:`basal/atom <compute_basal_atom>`
+   * :doc:`body/local <compute_body_local>`
+   * :doc:`bond <compute_bond>`
+   * :doc:`bond/local <compute_bond_local>`
+   * :doc:`centro/atom <compute_centro_atom>`
+   * :doc:`centroid/stress/atom <compute_stress_atom>`
+   * :doc:`chunk/atom <compute_chunk_atom>`
+   * :doc:`chunk/spread/atom <compute_chunk_spread_atom>`
+   * :doc:`cluster/atom <compute_cluster_atom>`
+   * :doc:`cna/atom <compute_cna_atom>`
+   * :doc:`cnp/atom <compute_cnp_atom>`
+   * :doc:`com <compute_com>`
+   * :doc:`com/chunk <compute_com_chunk>`
+   * :doc:`contact/atom <compute_contact_atom>`
+   * :doc:`coord/atom <compute_coord_atom>`
+   * :doc:`damage/atom <compute_damage_atom>`
+   * :doc:`dihedral <compute_dihedral>`
+   * :doc:`dihedral/local <compute_dihedral_local>`
+   * :doc:`dilatation/atom <compute_dilatation_atom>`
+   * :doc:`dipole/chunk <compute_dipole_chunk>`
+   * :doc:`displace/atom <compute_displace_atom>`
+   * :doc:`dpd <compute_dpd>`
+   * :doc:`dpd/atom <compute_dpd_atom>`
+   * :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
+   * :doc:`entropy/atom <compute_entropy_atom>`
+   * :doc:`erotate/asphere <compute_erotate_asphere>`
+   * :doc:`erotate/rigid <compute_erotate_rigid>`
+   * :doc:`erotate/sphere <compute_erotate_sphere>`
+   * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
+   * :doc:`event/displace <compute_event_displace>`
+   * :doc:`fep <compute_fep>`
+   * :doc:`force/tally <compute_tally>`
+   * :doc:`fragment/atom <compute_cluster_atom>`
+   * :doc:`global/atom <compute_global_atom>`
+   * :doc:`group/group <compute_group_group>`
+   * :doc:`gyration <compute_gyration>`
+   * :doc:`gyration/chunk <compute_gyration_chunk>`
+   * :doc:`gyration/shape <compute_gyration_shape>`
+   * :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
+   * :doc:`heat/flux <compute_heat_flux>`
+   * :doc:`heat/flux/tally <compute_tally>`
+   * :doc:`hexorder/atom <compute_hexorder_atom>`
+   * :doc:`hma <compute_hma>`
+   * :doc:`improper <compute_improper>`
+   * :doc:`improper/local <compute_improper_local>`
+   * :doc:`inertia/chunk <compute_inertia_chunk>`
+   * :doc:`ke <compute_ke>`
+   * :doc:`ke/atom <compute_ke_atom>`
+   * :doc:`ke/atom/eff <compute_ke_atom_eff>`
+   * :doc:`ke/eff <compute_ke_eff>`
+   * :doc:`ke/rigid <compute_ke_rigid>`
+   * :doc:`meso/e/atom <compute_meso_e_atom>`
+   * :doc:`meso/rho/atom <compute_meso_rho_atom>`
+   * :doc:`meso/t/atom <compute_meso_t_atom>`
+   * :doc:`momentum <compute_momentum>`
+   * :doc:`msd <compute_msd>`
+   * :doc:`msd/chunk <compute_msd_chunk>`
+   * :doc:`msd/nongauss <compute_msd_nongauss>`
+   * :doc:`omega/chunk <compute_omega_chunk>`
+   * :doc:`orientorder/atom <compute_orientorder_atom>`
+   * :doc:`pair <compute_pair>`
+   * :doc:`pair/local <compute_pair_local>`
+   * :doc:`pe <compute_pe>`
+   * :doc:`pe/atom <compute_pe_atom>`
+   * :doc:`pe/mol/tally <compute_tally>`
+   * :doc:`pe/tally <compute_tally>`
+   * :doc:`plasticity/atom <compute_plasticity_atom>`
+   * :doc:`pressure <compute_pressure>`
+   * :doc:`pressure/cylinder <compute_pressure_cylinder>`
+   * :doc:`pressure/uef <compute_pressure_uef>`
+   * :doc:`property/atom <compute_property_atom>`
+   * :doc:`property/chunk <compute_property_chunk>`
+   * :doc:`property/local <compute_property_local>`
+   * :doc:`ptm/atom <compute_ptm_atom>`
+   * :doc:`rdf <compute_rdf>`
+   * :doc:`reduce <compute_reduce>`
+   * :doc:`reduce/chunk <compute_reduce_chunk>`
+   * :doc:`reduce/region <compute_reduce>`
+   * :doc:`rigid/local <compute_rigid_local>`
+   * :doc:`saed <compute_saed>`
+   * :doc:`slice <compute_slice>`
+   * :doc:`smd/contact/radius <compute_smd_contact_radius>`
+   * :doc:`smd/damage <compute_smd_damage>`
+   * :doc:`smd/hourglass/error <compute_smd_hourglass_error>`
+   * :doc:`smd/internal/energy <compute_smd_internal_energy>`
+   * :doc:`smd/plastic/strain <compute_smd_plastic_strain>`
+   * :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>`
+   * :doc:`smd/rho <compute_smd_rho>`
+   * :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`
+   * :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`
+   * :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>`
+   * :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`
+   * :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`
+   * :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
+   * :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
+   * :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
+   * :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
+   * :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
+   * :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
+   * :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`
+   * :doc:`smd/vol <compute_smd_vol>`
+   * :doc:`sna/atom <compute_sna_atom>`
+   * :doc:`snad/atom <compute_sna_atom>`
+   * :doc:`snav/atom <compute_sna_atom>`
+   * :doc:`spin <compute_spin>`
+   * :doc:`stress/atom <compute_stress_atom>`
+   * :doc:`stress/mop <compute_stress_mop>`
+   * :doc:`stress/mop/profile <compute_stress_mop>`
+   * :doc:`stress/tally <compute_tally>`
+   * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
+   * :doc:`temp (k) <compute_temp>`
+   * :doc:`temp/asphere <compute_temp_asphere>`
+   * :doc:`temp/body <compute_temp_body>`
+   * :doc:`temp/chunk <compute_temp_chunk>`
+   * :doc:`temp/com <compute_temp_com>`
+   * :doc:`temp/cs <compute_temp_cs>`
+   * :doc:`temp/deform <compute_temp_deform>`
+   * :doc:`temp/deform/eff <compute_temp_deform_eff>`
+   * :doc:`temp/drude <compute_temp_drude>`
+   * :doc:`temp/eff <compute_temp_eff>`
+   * :doc:`temp/partial <compute_temp_partial>`
+   * :doc:`temp/profile <compute_temp_profile>`
+   * :doc:`temp/ramp <compute_temp_ramp>`
+   * :doc:`temp/region <compute_temp_region>`
+   * :doc:`temp/region/eff <compute_temp_region_eff>`
+   * :doc:`temp/rotate <compute_temp_rotate>`
+   * :doc:`temp/sphere <compute_temp_sphere>`
+   * :doc:`temp/uef <compute_temp_uef>`
+   * :doc:`ti <compute_ti>`
+   * :doc:`torque/chunk <compute_torque_chunk>`
+   * :doc:`vacf <compute_vacf>`
+   * :doc:`vcm/chunk <compute_vcm_chunk>`
+   * :doc:`voronoi/atom <compute_voronoi_atom>`
+   * :doc:`xrd <compute_xrd>`
+   *
+   *
+   *
+   *
diff --git a/doc/src/Commands_dihedral.rst b/doc/src/Commands_dihedral.rst
new file mode 100644
index 0000000000..84ddb3d004
--- /dev/null
+++ b/doc/src/Commands_dihedral.rst
@@ -0,0 +1,51 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+.. _dihedral:
+
+Dihedral\_style potentials
+==========================
+
+All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <dihedral_none>`
+   * :doc:`zero <dihedral_zero>`
+   * :doc:`hybrid <dihedral_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <dihedral_charmm>`
+   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`class2 (ko) <dihedral_class2>`
+   * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
+   * :doc:`fourier (io) <dihedral_fourier>`
+   * :doc:`harmonic (iko) <dihedral_harmonic>`
+   * :doc:`helix (o) <dihedral_helix>`
+   * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
+   * :doc:`nharmonic (o) <dihedral_nharmonic>`
+   * :doc:`opls (iko) <dihedral_opls>`
+   * :doc:`quadratic (o) <dihedral_quadratic>`
+   * :doc:`spherical <dihedral_spherical>`
+   * :doc:`table (o) <dihedral_table>`
+   * :doc:`table/cut <dihedral_table_cut>`
+   *
+   *
diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index cb9afd3497..11ae9a4a38 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -1,10 +1,15 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 Fix commands
 ============
@@ -14,81 +19,222 @@ have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`adapt <fix_adapt>`                         | :doc:`adapt/fep <fix_adapt_fep>`                       | :doc:`addforce <fix_addforce>`                        | :doc:`addtorque <fix_addtorque>`                       | :doc:`append/atoms <fix_append_atoms>`                         | :doc:`atc <fix_atc>`                           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`atom/swap <fix_atom_swap>`                 | :doc:`ave/atom <fix_ave_atom>`                         | :doc:`ave/chunk <fix_ave_chunk>`                      | :doc:`ave/correlate <fix_ave_correlate>`               | :doc:`ave/correlate/long <fix_ave_correlate_long>`             | :doc:`ave/histo <fix_ave_histo>`               |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`ave/histo/weight <fix_ave_histo>`          | :doc:`ave/time <fix_ave_time>`                         | :doc:`aveforce <fix_aveforce>`                        | :doc:`balance <fix_balance>`                           | :doc:`bocs <fix_bocs>`                                         | :doc:`bond/break <fix_bond_break>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`bond/create <fix_bond_create>`             | :doc:`bond/react <fix_bond_react>`                     | :doc:`bond/swap <fix_bond_swap>`                      | :doc:`box/relax <fix_box_relax>`                       | :doc:`client/md <fix_client_md>`                               | :doc:`cmap <fix_cmap>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`colvars <fix_colvars>`                     | :doc:`controller <fix_controller>`                     | :doc:`deform (k) <fix_deform>`                        | :doc:`deposit <fix_deposit>`                           | :doc:`dpd/energy (k) <fix_dpd_energy>`                         | :doc:`drag <fix_drag>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`drude <fix_drude>`                         | :doc:`drude/transform/direct <fix_drude_transform>`    | :doc:`drude/transform/inverse <fix_drude_transform>`  | :doc:`dt/reset <fix_dt_reset>`                         | :doc:`edpd/source <fix_dpd_source>`                            | :doc:`efield <fix_efield>`                     |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`ehex <fix_ehex>`                           | :doc:`electron/stopping <fix_electron_stopping>`       | :doc:`enforce2d (k) <fix_enforce2d>`                  | :doc:`eos/cv <fix_eos_cv>`                             | :doc:`eos/table <fix_eos_table>`                               | :doc:`eos/table/rx (k) <fix_eos_table_rx>`     |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`evaporate <fix_evaporate>`                 | :doc:`external <fix_external>`                         | :doc:`ffl <fix_ffl>`                                  | :doc:`filter/corotate <fix_filter_corotate>`           | :doc:`flow/gauss <fix_flow_gauss>`                             | :doc:`freeze (k) <fix_freeze>`                 |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`gcmc <fix_gcmc>`                           | :doc:`gld <fix_gld>`                                   | :doc:`gle <fix_gle>`                                  | :doc:`gravity (ko) <fix_gravity>`                      | :doc:`grem <fix_grem>`                                         | :doc:`halt <fix_halt>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`heat <fix_heat>`                           | :doc:`hyper/global <fix_hyper_global>`                 | :doc:`hyper/local <fix_hyper_local>`                  | :doc:`imd <fix_imd>`                                   | :doc:`indent <fix_indent>`                                     | :doc:`ipi <fix_ipi>`                           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`langevin (k) <fix_langevin>`               | :doc:`langevin/drude <fix_langevin_drude>`             | :doc:`langevin/eff <fix_langevin_eff>`                | :doc:`langevin/spin <fix_langevin_spin>`               | :doc:`latte <fix_latte>`                                       | :doc:`lb/fluid <fix_lb_fluid>`                 |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`lb/momentum <fix_lb_momentum>`             | :doc:`lb/pc <fix_lb_pc>`                               | :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`    | :doc:`lb/viscous <fix_lb_viscous>`                     | :doc:`lineforce <fix_lineforce>`                               | :doc:`manifoldforce <fix_manifoldforce>`       |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`meso <fix_meso>`                           | :doc:`meso/move <fix_meso_move>`                       | :doc:`meso/stationary <fix_meso_stationary>`          | :doc:`momentum (k) <fix_momentum>`                     | :doc:`move <fix_move>`                                         | :doc:`mscg <fix_mscg>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`msst <fix_msst>`                           | :doc:`mvv/dpd <fix_mvv_dpd>`                           | :doc:`mvv/edpd <fix_mvv_dpd>`                         | :doc:`mvv/tdpd <fix_mvv_dpd>`                          | :doc:`neb <fix_neb>`                                           | :doc:`neb\_spin <fix_neb_spin>`                |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nph (ko) <fix_nh>`                         | :doc:`nph/asphere (o) <fix_nph_asphere>`               | :doc:`nph/body <fix_nph_body>`                        | :doc:`nph/eff <fix_nh_eff>`                            | :doc:`nph/sphere (o) <fix_nph_sphere>`                         | :doc:`nphug (o) <fix_nphug>`                   |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`npt (iko) <fix_nh>`                        | :doc:`npt/asphere (o) <fix_npt_asphere>`               | :doc:`npt/body <fix_npt_body>`                        | :doc:`npt/eff <fix_nh_eff>`                            | :doc:`npt/sphere (o) <fix_npt_sphere>`                         | :doc:`npt/uef <fix_nh_uef>`                    |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nve (iko) <fix_nve>`                       | :doc:`nve/asphere (i) <fix_nve_asphere>`               | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`  | :doc:`nve/awpmd <fix_nve_awpmd>`                       | :doc:`nve/body <fix_nve_body>`                                 | :doc:`nve/dot <fix_nve_dot>`                   |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>` | :doc:`nve/eff <fix_nve_eff>`                           | :doc:`nve/limit <fix_nve_limit>`                      | :doc:`nve/line <fix_nve_line>`                         | :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`           | :doc:`nve/noforce <fix_nve_noforce>`           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nve/sphere (ko) <fix_nve_sphere>`          | :doc:`nve/spin <fix_nve_spin>`                         | :doc:`nve/tri <fix_nve_tri>`                          | :doc:`nvk <fix_nvk>`                                   | :doc:`nvt (iko) <fix_nh>`                                      | :doc:`nvt/asphere (o) <fix_nvt_asphere>`       |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nvt/body <fix_nvt_body>`                   | :doc:`nvt/eff <fix_nh_eff>`                            | :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`  | :doc:`nvt/sllod (io) <fix_nvt_sllod>`                  | :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`                       | :doc:`nvt/sphere (o) <fix_nvt_sphere>`         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nvt/uef <fix_nh_uef>`                      | :doc:`oneway <fix_oneway>`                             | :doc:`orient/bcc <fix_orient>`                        | :doc:`orient/fcc <fix_orient>`                         | :doc:`phonon <fix_phonon>`                                     | :doc:`pimd <fix_pimd>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`planeforce <fix_planeforce>`               | :doc:`plumed <fix_plumed>`                             | :doc:`poems <fix_poems>`                              | :doc:`pour <fix_pour>`                                 | :doc:`precession/spin <fix_precession_spin>`                   | :doc:`press/berendsen <fix_press_berendsen>`   |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`print <fix_print>`                         | :doc:`property/atom (k) <fix_property_atom>`           | :doc:`python/invoke <fix_python_invoke>`              | :doc:`python/move <fix_python_move>`                   | :doc:`qbmsst <fix_qbmsst>`                                     | :doc:`qeq/comb (o) <fix_qeq_comb>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`qeq/dynamic <fix_qeq>`                     | :doc:`qeq/fire <fix_qeq>`                              | :doc:`qeq/point <fix_qeq>`                            | :doc:`qeq/reax (ko) <fix_qeq_reax>`                    | :doc:`qeq/shielded <fix_qeq>`                                  | :doc:`qeq/slater <fix_qeq>`                    |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`qmmm <fix_qmmm>`                           | :doc:`qtb <fix_qtb>`                                   | :doc:`rattle <fix_shake>`                             | :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`              | :doc:`reax/c/species (k) <fix_reaxc_species>`                  | :doc:`recenter <fix_recenter>`                 |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`restrain <fix_restrain>`                   | :doc:`rhok <fix_rhok>`                                 | :doc:`rigid (o) <fix_rigid>`                          | :doc:`rigid/meso <fix_rigid_meso>`                     | :doc:`rigid/nph (o) <fix_rigid>`                               | :doc:`rigid/nph/small <fix_rigid>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`rigid/npt (o) <fix_rigid>`                 | :doc:`rigid/npt/small <fix_rigid>`                     | :doc:`rigid/nve (o) <fix_rigid>`                      | :doc:`rigid/nve/small <fix_rigid>`                     | :doc:`rigid/nvt (o) <fix_rigid>`                               | :doc:`rigid/nvt/small <fix_rigid>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`rigid/small (o) <fix_rigid>`               | :doc:`rx (k) <fix_rx>`                                 | :doc:`saed/vtk <fix_saed_vtk>`                        | :doc:`setforce (k) <fix_setforce>`                     | :doc:`shake <fix_shake>`                                       | :doc:`shardlow (k) <fix_shardlow>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`smd <fix_smd>`                             | :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`              | :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`  | :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`smd/wall\_surface <fix_smd_wall_surface>`  | :doc:`spring <fix_spring>`                             | :doc:`spring/chunk <fix_spring_chunk>`                | :doc:`spring/rg <fix_spring_rg>`                       | :doc:`spring/self <fix_spring_self>`                           | :doc:`srd <fix_srd>`                           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`store/force <fix_store_force>`             | :doc:`store/state <fix_store_state>`                   | :doc:`tdpd/source <fix_dpd_source>`                   | :doc:`temp/berendsen <fix_temp_berendsen>`             | :doc:`temp/csld <fix_temp_csvr>`                               | :doc:`temp/csvr <fix_temp_csvr>`               |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`temp/rescale <fix_temp_rescale>`           | :doc:`temp/rescale/eff <fix_temp_rescale_eff>`         | :doc:`tfmc <fix_tfmc>`                                | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`ti/spring <fix_ti_spring>`                               | :doc:`tmd <fix_tmd>`                           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`ttm <fix_ttm>`                             | :doc:`ttm/mod <fix_ttm>`                               | :doc:`tune/kspace <fix_tune_kspace>`                  | :doc:`vector <fix_vector>`                             | :doc:`viscosity <fix_viscosity>`                               | :doc:`viscous <fix_viscous>`                   |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`wall/body/polygon <fix_wall_body_polygon>` | :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` | :doc:`wall/colloid <fix_wall>`                        | :doc:`wall/ees <fix_wall_ees>`                         | :doc:`wall/gran <fix_wall_gran>`                               | :doc:`wall/gran/region <fix_wall_gran_region>` |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`wall/harmonic <fix_wall>`                  | :doc:`wall/lj1043 <fix_wall>`                          | :doc:`wall/lj126 <fix_wall>`                          | :doc:`wall/lj93 (k) <fix_wall>`                        | :doc:`wall/morse <fix_wall>`                                   | :doc:`wall/piston <fix_wall_piston>`           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`wall/reflect (k) <fix_wall_reflect>`       | :doc:`wall/region <fix_wall_region>`                   | :doc:`wall/region/ees <fix_wall_ees>`                 | :doc:`wall/srd <fix_wall_srd>`                         |                                                                |                                                |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+.. table_from_list::
+   :columns: 6
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`adapt <fix_adapt>`
+   * :doc:`adapt/fep <fix_adapt_fep>`
+   * :doc:`addforce <fix_addforce>`
+   * :doc:`addtorque <fix_addtorque>`
+   * :doc:`append/atoms <fix_append_atoms>`
+   * :doc:`atc <fix_atc>`
+   * :doc:`atom/swap <fix_atom_swap>`
+   * :doc:`ave/atom <fix_ave_atom>`
+   * :doc:`ave/chunk <fix_ave_chunk>`
+   * :doc:`ave/correlate <fix_ave_correlate>`
+   * :doc:`ave/correlate/long <fix_ave_correlate_long>`
+   * :doc:`ave/histo <fix_ave_histo>`
+   * :doc:`ave/histo/weight <fix_ave_histo>`
+   * :doc:`ave/time <fix_ave_time>`
+   * :doc:`aveforce <fix_aveforce>`
+   * :doc:`balance <fix_balance>`
+   * :doc:`bocs <fix_bocs>`
+   * :doc:`bond/break <fix_bond_break>`
+   * :doc:`bond/create <fix_bond_create>`
+   * :doc:`bond/react <fix_bond_react>`
+   * :doc:`bond/swap <fix_bond_swap>`
+   * :doc:`box/relax <fix_box_relax>`
+   * :doc:`client/md <fix_client_md>`
+   * :doc:`cmap <fix_cmap>`
+   * :doc:`colvars <fix_colvars>`
+   * :doc:`controller <fix_controller>`
+   * :doc:`deform (k) <fix_deform>`
+   * :doc:`deposit <fix_deposit>`
+   * :doc:`dpd/energy (k) <fix_dpd_energy>`
+   * :doc:`drag <fix_drag>`
+   * :doc:`drude <fix_drude>`
+   * :doc:`drude/transform/direct <fix_drude_transform>`
+   * :doc:`drude/transform/inverse <fix_drude_transform>`
+   * :doc:`dt/reset <fix_dt_reset>`
+   * :doc:`edpd/source <fix_dpd_source>`
+   * :doc:`efield <fix_efield>`
+   * :doc:`ehex <fix_ehex>`
+   * :doc:`electron/stopping <fix_electron_stopping>`
+   * :doc:`enforce2d (k) <fix_enforce2d>`
+   * :doc:`eos/cv <fix_eos_cv>`
+   * :doc:`eos/table <fix_eos_table>`
+   * :doc:`eos/table/rx (k) <fix_eos_table_rx>`
+   * :doc:`evaporate <fix_evaporate>`
+   * :doc:`external <fix_external>`
+   * :doc:`ffl <fix_ffl>`
+   * :doc:`filter/corotate <fix_filter_corotate>`
+   * :doc:`flow/gauss <fix_flow_gauss>`
+   * :doc:`freeze (k) <fix_freeze>`
+   * :doc:`gcmc <fix_gcmc>`
+   * :doc:`gld <fix_gld>`
+   * :doc:`gle <fix_gle>`
+   * :doc:`gravity (ko) <fix_gravity>`
+   * :doc:`grem <fix_grem>`
+   * :doc:`halt <fix_halt>`
+   * :doc:`heat <fix_heat>`
+   * :doc:`hyper/global <fix_hyper_global>`
+   * :doc:`hyper/local <fix_hyper_local>`
+   * :doc:`imd <fix_imd>`
+   * :doc:`indent <fix_indent>`
+   * :doc:`ipi <fix_ipi>`
+   * :doc:`langevin (k) <fix_langevin>`
+   * :doc:`langevin/drude <fix_langevin_drude>`
+   * :doc:`langevin/eff <fix_langevin_eff>`
+   * :doc:`langevin/spin <fix_langevin_spin>`
+   * :doc:`latte <fix_latte>`
+   * :doc:`lb/fluid <fix_lb_fluid>`
+   * :doc:`lb/momentum <fix_lb_momentum>`
+   * :doc:`lb/pc <fix_lb_pc>`
+   * :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
+   * :doc:`lb/viscous <fix_lb_viscous>`
+   * :doc:`lineforce <fix_lineforce>`
+   * :doc:`manifoldforce <fix_manifoldforce>`
+   * :doc:`meso <fix_meso>`
+   * :doc:`meso/move <fix_meso_move>`
+   * :doc:`meso/stationary <fix_meso_stationary>`
+   * :doc:`momentum (k) <fix_momentum>`
+   * :doc:`move <fix_move>`
+   * :doc:`mscg <fix_mscg>`
+   * :doc:`msst <fix_msst>`
+   * :doc:`mvv/dpd <fix_mvv_dpd>`
+   * :doc:`mvv/edpd <fix_mvv_dpd>`
+   * :doc:`mvv/tdpd <fix_mvv_dpd>`
+   * :doc:`neb <fix_neb>`
+   * :doc:`neb\_spin <fix_neb_spin>`
+   * :doc:`nph (ko) <fix_nh>`
+   * :doc:`nph/asphere (o) <fix_nph_asphere>`
+   * :doc:`nph/body <fix_nph_body>`
+   * :doc:`nph/eff <fix_nh_eff>`
+   * :doc:`nph/sphere (o) <fix_nph_sphere>`
+   * :doc:`nphug (o) <fix_nphug>`
+   * :doc:`npt (iko) <fix_nh>`
+   * :doc:`npt/asphere (o) <fix_npt_asphere>`
+   * :doc:`npt/body <fix_npt_body>`
+   * :doc:`npt/eff <fix_nh_eff>`
+   * :doc:`npt/sphere (o) <fix_npt_sphere>`
+   * :doc:`npt/uef <fix_nh_uef>`
+   * :doc:`nve (iko) <fix_nve>`
+   * :doc:`nve/asphere (i) <fix_nve_asphere>`
+   * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
+   * :doc:`nve/awpmd <fix_nve_awpmd>`
+   * :doc:`nve/body <fix_nve_body>`
+   * :doc:`nve/dot <fix_nve_dot>`
+   * :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
+   * :doc:`nve/eff <fix_nve_eff>`
+   * :doc:`nve/limit <fix_nve_limit>`
+   * :doc:`nve/line <fix_nve_line>`
+   * :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
+   * :doc:`nve/noforce <fix_nve_noforce>`
+   * :doc:`nve/sphere (ko) <fix_nve_sphere>`
+   * :doc:`nve/spin <fix_nve_spin>`
+   * :doc:`nve/tri <fix_nve_tri>`
+   * :doc:`nvk <fix_nvk>`
+   * :doc:`nvt (iko) <fix_nh>`
+   * :doc:`nvt/asphere (o) <fix_nvt_asphere>`
+   * :doc:`nvt/body <fix_nvt_body>`
+   * :doc:`nvt/eff <fix_nh_eff>`
+   * :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
+   * :doc:`nvt/sllod (io) <fix_nvt_sllod>`
+   * :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
+   * :doc:`nvt/sphere (o) <fix_nvt_sphere>`
+   * :doc:`nvt/uef <fix_nh_uef>`
+   * :doc:`oneway <fix_oneway>`
+   * :doc:`orient/bcc <fix_orient>`
+   * :doc:`orient/fcc <fix_orient>`
+   * :doc:`phonon <fix_phonon>`
+   * :doc:`pimd <fix_pimd>`
+   * :doc:`planeforce <fix_planeforce>`
+   * :doc:`plumed <fix_plumed>`
+   * :doc:`poems <fix_poems>`
+   * :doc:`pour <fix_pour>`
+   * :doc:`precession/spin <fix_precession_spin>`
+   * :doc:`press/berendsen <fix_press_berendsen>`
+   * :doc:`print <fix_print>`
+   * :doc:`property/atom (k) <fix_property_atom>`
+   * :doc:`python/invoke <fix_python_invoke>`
+   * :doc:`python/move <fix_python_move>`
+   * :doc:`qbmsst <fix_qbmsst>`
+   * :doc:`qeq/comb (o) <fix_qeq_comb>`
+   * :doc:`qeq/dynamic <fix_qeq>`
+   * :doc:`qeq/fire <fix_qeq>`
+   * :doc:`qeq/point <fix_qeq>`
+   * :doc:`qeq/reax (ko) <fix_qeq_reax>`
+   * :doc:`qeq/shielded <fix_qeq>`
+   * :doc:`qeq/slater <fix_qeq>`
+   * :doc:`qmmm <fix_qmmm>`
+   * :doc:`qtb <fix_qtb>`
+   * :doc:`rattle <fix_shake>`
+   * :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
+   * :doc:`reax/c/species (k) <fix_reaxc_species>`
+   * :doc:`recenter <fix_recenter>`
+   * :doc:`restrain <fix_restrain>`
+   * :doc:`rhok <fix_rhok>`
+   * :doc:`rigid (o) <fix_rigid>`
+   * :doc:`rigid/meso <fix_rigid_meso>`
+   * :doc:`rigid/nph (o) <fix_rigid>`
+   * :doc:`rigid/nph/small <fix_rigid>`
+   * :doc:`rigid/npt (o) <fix_rigid>`
+   * :doc:`rigid/npt/small <fix_rigid>`
+   * :doc:`rigid/nve (o) <fix_rigid>`
+   * :doc:`rigid/nve/small <fix_rigid>`
+   * :doc:`rigid/nvt (o) <fix_rigid>`
+   * :doc:`rigid/nvt/small <fix_rigid>`
+   * :doc:`rigid/small (o) <fix_rigid>`
+   * :doc:`rx (k) <fix_rx>`
+   * :doc:`saed/vtk <fix_saed_vtk>`
+   * :doc:`setforce (k) <fix_setforce>`
+   * :doc:`shake <fix_shake>`
+   * :doc:`shardlow (k) <fix_shardlow>`
+   * :doc:`smd <fix_smd>`
+   * :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`
+   * :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>`
+   * :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`
+   * :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>`
+   * :doc:`smd/setvel <fix_smd_setvel>`
+   * :doc:`smd/wall\_surface <fix_smd_wall_surface>`
+   * :doc:`spring <fix_spring>`
+   * :doc:`spring/chunk <fix_spring_chunk>`
+   * :doc:`spring/rg <fix_spring_rg>`
+   * :doc:`spring/self <fix_spring_self>`
+   * :doc:`srd <fix_srd>`
+   * :doc:`store/force <fix_store_force>`
+   * :doc:`store/state <fix_store_state>`
+   * :doc:`tdpd/source <fix_dpd_source>`
+   * :doc:`temp/berendsen <fix_temp_berendsen>`
+   * :doc:`temp/csld <fix_temp_csvr>`
+   * :doc:`temp/csvr <fix_temp_csvr>`
+   * :doc:`temp/rescale <fix_temp_rescale>`
+   * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
+   * :doc:`tfmc <fix_tfmc>`
+   * :doc:`thermal/conductivity <fix_thermal_conductivity>`
+   * :doc:`ti/spring <fix_ti_spring>`
+   * :doc:`tmd <fix_tmd>`
+   * :doc:`ttm <fix_ttm>`
+   * :doc:`ttm/mod <fix_ttm>`
+   * :doc:`tune/kspace <fix_tune_kspace>`
+   * :doc:`vector <fix_vector>`
+   * :doc:`viscosity <fix_viscosity>`
+   * :doc:`viscous <fix_viscous>`
+   * :doc:`wall/body/polygon <fix_wall_body_polygon>`
+   * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
+   * :doc:`wall/colloid <fix_wall>`
+   * :doc:`wall/ees <fix_wall_ees>`
+   * :doc:`wall/gran <fix_wall_gran>`
+   * :doc:`wall/gran/region <fix_wall_gran_region>`
+   * :doc:`wall/harmonic <fix_wall>`
+   * :doc:`wall/lj1043 <fix_wall>`
+   * :doc:`wall/lj126 <fix_wall>`
+   * :doc:`wall/lj93 (k) <fix_wall>`
+   * :doc:`wall/morse <fix_wall>`
+   * :doc:`wall/piston <fix_wall_piston>`
+   * :doc:`wall/reflect (k) <fix_wall_reflect>`
+   * :doc:`wall/region <fix_wall_region>`
+   * :doc:`wall/region/ees <fix_wall_ees>`
+   * :doc:`wall/srd <fix_wall_srd>`
+   *
+   *
diff --git a/doc/src/Commands_improper.rst b/doc/src/Commands_improper.rst
new file mode 100644
index 0000000000..7bbfa5b01b
--- /dev/null
+++ b/doc/src/Commands_improper.rst
@@ -0,0 +1,46 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+.. _improper:
+
+Improper\_style potentials
+=========================================
+
+All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <improper_none>`
+   * :doc:`zero <improper_zero>`
+   * :doc:`hybrid <improper_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <improper_class2>`
+   * :doc:`cossq (o) <improper_cossq>`
+   * :doc:`cvff (io) <improper_cvff>`
+   * :doc:`distance <improper_distance>`
+   * :doc:`distharm <improper_distharm>`
+   * :doc:`fourier (o) <improper_fourier>`
+   * :doc:`harmonic (iko) <improper_harmonic>`
+   * :doc:`inversion/harmonic <improper_inversion_harmonic>`
+   * :doc:`ring (o) <improper_ring>`
+   * :doc:`sqdistharm <improper_sqdistharm>`
+   * :doc:`umbrella (o) <improper_umbrella>`
+   *
diff --git a/doc/src/Commands_input.rst b/doc/src/Commands_input.rst
index ce93f65d81..c66b530dd0 100644
--- a/doc/src/Commands_input.rst
+++ b/doc/src/Commands_input.rst
@@ -55,8 +55,3 @@ Many input script errors are detected by LAMMPS and an ERROR or
 WARNING message is printed.  The :doc:`Errors <Errors>` doc page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst
index 9281c54ddd..62e97f1a6a 100644
--- a/doc/src/Commands_kspace.rst
+++ b/doc/src/Commands_kspace.rst
@@ -1,10 +1,15 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 KSpace solvers
 ==============
@@ -14,15 +19,18 @@ accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
-| :doc:`ewald (o) <kspace_style>`    | :doc:`ewald/disp <kspace_style>`     | :doc:`msm (o) <kspace_style>`       | :doc:`msm/cg (o) <kspace_style>`      |
-+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
-| :doc:`pppm (gok) <kspace_style>`   | :doc:`pppm/cg (o) <kspace_style>`    | :doc:`pppm/disp (i) <kspace_style>` | :doc:`pppm/disp/tip4p <kspace_style>` |
-+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
-| :doc:`pppm/stagger <kspace_style>` | :doc:`pppm/tip4p (o) <kspace_style>` | :doc:`scafacos <kspace_style>`      |                                       |
-+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
+.. table_from_list::
+   :columns: 4
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`ewald (o) <kspace_style>`
+   * :doc:`ewald/disp <kspace_style>`
+   * :doc:`msm (o) <kspace_style>`
+   * :doc:`msm/cg (o) <kspace_style>`
+   * :doc:`pppm (gok) <kspace_style>`
+   * :doc:`pppm/cg (o) <kspace_style>`
+   * :doc:`pppm/disp (i) <kspace_style>`
+   * :doc:`pppm/disp/tip4p <kspace_style>`
+   * :doc:`pppm/stagger <kspace_style>`
+   * :doc:`pppm/tip4p (o) <kspace_style>`
+   * :doc:`scafacos <kspace_style>`
+   *
diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index d5ed86886a..c65164c02d 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -1,10 +1,15 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :doc:`Bond styles <Commands_bond>`
+   * :doc:`Angle styles <Commands_angle>`
+   * :doc:`Dihedral styles <Commands_dihedral>`
+   * :doc:`Improper styles <Commands_improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 Pair\_style potentials
 ======================
@@ -14,123 +19,234 @@ accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`none <pair_none>`                                      | :doc:`zero <pair_zero>`                                           | :doc:`hybrid (k) <pair_hybrid>`                     | :doc:`hybrid/overlay (k) <pair_hybrid>`                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-|                                                              |                                                                   |                                                     |                                                             |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`adp (o) <pair_adp>`                                    | :doc:`agni (o) <pair_agni>`                                       | :doc:`airebo (io) <pair_airebo>`                    | :doc:`airebo/morse (io) <pair_airebo>`                      |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`atm <pair_atm>`                                        | :doc:`awpmd/cut <pair_awpmd>`                                     | :doc:`beck (go) <pair_beck>`                        | :doc:`body/nparticle <pair_body_nparticle>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`body/rounded/polygon <pair_body_rounded_polygon>`      | :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`     | :doc:`bop <pair_bop>`                               | :doc:`born (go) <pair_born>`                                |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`born/coul/dsf <pair_born>`                             | :doc:`born/coul/dsf/cs <pair_cs>`                                 | :doc:`born/coul/long (go) <pair_born>`              | :doc:`born/coul/long/cs (g) <pair_cs>`                      |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`born/coul/msm (o) <pair_born>`                         | :doc:`born/coul/wolf (go) <pair_born>`                            | :doc:`born/coul/wolf/cs (g) <pair_cs>`              | :doc:`brownian (o) <pair_brownian>`                         |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`brownian/poly (o) <pair_brownian>`                     | :doc:`buck (giko) <pair_buck>`                                    | :doc:`buck/coul/cut (giko) <pair_buck>`             | :doc:`buck/coul/long (giko) <pair_buck>`                    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`buck/coul/long/cs <pair_cs>`                           | :doc:`buck/coul/msm (o) <pair_buck>`                              | :doc:`buck/long/coul/long (o) <pair_buck_long>`     | :doc:`buck/mdf <pair_mdf>`                                  |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`        | :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`            | :doc:`colloid (go) <pair_colloid>`                  | :doc:`comb (o) <pair_comb>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`comb3 <pair_comb>`                                     | :doc:`cosine/squared <pair_cosine_squared>`                       | :doc:`coul/cut (gko) <pair_coul>`                   | :doc:`coul/cut/soft (o) <pair_fep_soft>`                    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`coul/debye (gko) <pair_coul>`                          | :doc:`coul/diel (o) <pair_coul_diel>`                             | :doc:`coul/dsf (gko) <pair_coul>`                   | :doc:`coul/long (gko) <pair_coul>`                          |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`coul/long/cs (g) <pair_cs>`                            | :doc:`coul/long/soft (o) <pair_fep_soft>`                         | :doc:`coul/msm (o) <pair_coul>`                     | :doc:`coul/shield <pair_coul_shield>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`coul/streitz <pair_coul>`                              | :doc:`coul/wolf (ko) <pair_coul>`                                 | :doc:`coul/wolf/cs <pair_cs>`                       | :doc:`dpd (gio) <pair_dpd>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`dpd/fdt <pair_dpd_fdt>`                                | :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`                          | :doc:`dpd/tstat (go) <pair_dpd>`                    | :doc:`dsmc <pair_dsmc>`                                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`e3b <pair_e3b>`                                        | :doc:`drip <pair_drip>`                                           | :doc:`eam (gikot) <pair_eam>`                       | :doc:`eam/alloy (gikot) <pair_eam>`                         |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`eam/cd (o) <pair_eam>`                                 | :doc:`eam/cd/old (o) <pair_eam>`                                  | :doc:`eam/fs (gikot) <pair_eam>`                    | :doc:`edip (o) <pair_edip>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`edip/multi <pair_edip>`                                | :doc:`edpd <pair_meso>`                                           | :doc:`eff/cut <pair_eff>`                           | :doc:`eim (o) <pair_eim>`                                   |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`exp6/rx (k) <pair_exp6_rx>`                            | :doc:`extep <pair_extep>`                                         | :doc:`gauss (go) <pair_gauss>`                      | :doc:`gauss/cut (o) <pair_gauss>`                           |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`gayberne (gio) <pair_gayberne>`                        | :doc:`gran/hertz/history (o) <pair_gran>`                         | :doc:`gran/hooke (o) <pair_gran>`                   | :doc:`gran/hooke/history (ko) <pair_gran>`                  |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`granular <pair_granular>`                              | :doc:`gw <pair_gw>`                                               | :doc:`gw/zbl <pair_gw>`                             | :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`          |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`        | :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`                   | :doc:`kim <pair_kim>`                               | :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`        | :doc:`lcbop <pair_lcbop>`                                         | :doc:`lebedeva/z <pair_lebedeva_z>`                 | :doc:`lennard/mdf <pair_mdf>`                               |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`line/lj <pair_line_lj>`                                | :doc:`list <pair_list>`                                           | :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`    | :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`             | :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`               | :doc:`lj/charmm/coul/msm (o) <pair_charmm>`         | :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`            |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/charmmfsw/coul/long <pair_charmm>`                  | :doc:`lj/class2 (gko) <pair_class2>`                              | :doc:`lj/class2/coul/cut (ko) <pair_class2>`        | :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`              |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/class2/coul/long (gko) <pair_class2>`               | :doc:`lj/class2/coul/long/soft <pair_fep_soft>`                   | :doc:`lj/class2/soft <pair_fep_soft>`               | :doc:`lj/cubic (go) <pair_lj_cubic>`                        |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut (gikot) <pair_lj>`                              | :doc:`lj/cut/coul/cut (gko) <pair_lj>`                            | :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`     | :doc:`lj/cut/coul/debye (gko) <pair_lj>`                    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut/coul/dsf (gko) <pair_lj>`                       | :doc:`lj/cut/coul/long (gikot) <pair_lj>`                         | :doc:`lj/cut/coul/long/cs <pair_cs>`                | :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`            |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut/coul/msm (go) <pair_lj>`                        | :doc:`lj/cut/coul/wolf (o) <pair_lj>`                             | :doc:`lj/cut/dipole/cut (go) <pair_dipole>`         | :doc:`lj/cut/dipole/long (g) <pair_dipole>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut/dipole/sf (go) <pair_dipole>`                   | :doc:`lj/cut/soft (o) <pair_fep_soft>`                            | :doc:`lj/cut/thole/long (o) <pair_thole>`           | :doc:`lj/cut/tip4p/cut (o) <pair_lj>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut/tip4p/long (ot) <pair_lj>`                      | :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`                 | :doc:`lj/expand (gko) <pair_lj_expand>`             | :doc:`lj/expand/coul/long (g) <pair_lj_expand>`             |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/gromacs (gko) <pair_gromacs>`                       | :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`                | :doc:`lj/long/coul/long (iot) <pair_lj_long>`       | :doc:`lj/long/dipole/long <pair_dipole>`                    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/long/tip4p/long (o) <pair_lj_long>`                 | :doc:`lj/mdf <pair_mdf>`                                          | :doc:`lj/sdk (gko) <pair_sdk>`                      | :doc:`lj/sdk/coul/long (go) <pair_sdk>`                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/sdk/coul/msm (o) <pair_sdk>`                        | :doc:`lj/sf/dipole/sf (go) <pair_dipole>`                         | :doc:`lj/smooth (o) <pair_lj_smooth>`               | :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`         |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>` | :doc:`lj96/cut (go) <pair_lj96>`                                  | :doc:`local/density <pair_local_density>`           | :doc:`lubricate (o) <pair_lubricate>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lubricate/poly (o) <pair_lubricate>`                   | :doc:`lubricateU <pair_lubricateU>`                               | :doc:`lubricateU/poly <pair_lubricateU>`            | :doc:`mdpd <pair_meso>`                                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`mdpd/rhosum <pair_meso>`                               | :doc:`meam/c <pair_meamc>`                                        | :doc:`meam/spline (o) <pair_meam_spline>`           | :doc:`meam/sw/spline <pair_meam_sw_spline>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`mgpt <pair_mgpt>`                                      | :doc:`mie/cut (g) <pair_mie>`                                     | :doc:`momb <pair_momb>`                             | :doc:`morse (gkot) <pair_morse>`                            |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`morse/smooth/linear (o) <pair_morse>`                  | :doc:`morse/soft <pair_fep_soft>`                                 | :doc:`multi/lucy <pair_multi_lucy>`                 | :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`               |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`nb3b/harmonic <pair_nb3b_harmonic>`                    | :doc:`nm/cut (o) <pair_nm>`                                       | :doc:`nm/cut/coul/cut (o) <pair_nm>`                | :doc:`nm/cut/coul/long (o) <pair_nm>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`oxdna/coaxstk <pair_oxdna>`                            | :doc:`oxdna/excv <pair_oxdna>`                                    | :doc:`oxdna/hbond <pair_oxdna>`                     | :doc:`oxdna/stk <pair_oxdna>`                               |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`oxdna/xstk <pair_oxdna>`                               | :doc:`oxdna2/coaxstk <pair_oxdna2>`                               | :doc:`oxdna2/dh <pair_oxdna2>`                      | :doc:`oxdna2/excv <pair_oxdna2>`                            |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`oxdna2/hbond <pair_oxdna2>`                            | :doc:`oxdna2/stk <pair_oxdna2>`                                   | :doc:`oxdna2/xstk <pair_oxdna2>`                    | :doc:`peri/eps <pair_peri>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`peri/lps (o) <pair_peri>`                              | :doc:`peri/pmb (o) <pair_peri>`                                   | :doc:`peri/ves <pair_peri>`                         | :doc:`polymorphic <pair_polymorphic>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`python <pair_python>`                                  | :doc:`quip <pair_quip>`                                           | :doc:`reax/c (ko) <pair_reaxc>`                     | :doc:`rebo (io) <pair_airebo>`                              |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`resquared (go) <pair_resquared>`                       | :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | :doc:`smd/hertz <pair_smd_hertz>`                   | :doc:`smd/tlsph <pair_smd_tlsph>`                           |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`      | :doc:`smd/ulsph <pair_smd_ulsph>`                                 | :doc:`smtbq <pair_smtbq>`                           | :doc:`snap (k) <pair_snap>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`snap (k) <pair_snap>`                                  | :doc:`soft (go) <pair_soft>`                                      | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>`                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`sph/lj <pair_sph_lj>`                                  | :doc:`sph/rhosum <pair_sph_rhosum>`                               | :doc:`sph/taitwater <pair_sph_taitwater>`           | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`spin/dipole/cut <pair_spin_dipole>`                    | :doc:`spin/dipole/long <pair_spin_dipole>`                        | :doc:`spin/dmi <pair_spin_dmi>`                     | :doc:`spin/exchange <pair_spin_exchange>`                   |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`spin/magelec <pair_spin_magelec>`                      | :doc:`spin/neel <pair_spin_neel>`                                 | :doc:`srp <pair_srp>`                               | :doc:`sw (giko) <pair_sw>`                                  |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`table (gko) <pair_table>`                              | :doc:`table/rx (k) <pair_table_rx>`                               | :doc:`tdpd <pair_meso>`                             | :doc:`tersoff (giko) <pair_tersoff>`                        |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`tersoff/mod (gko) <pair_tersoff_mod>`                  | :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`                       | :doc:`tersoff/table (o) <pair_tersoff>`             | :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`thole <pair_thole>`                                    | :doc:`tip4p/cut (o) <pair_coul>`                                  | :doc:`tip4p/long (o) <pair_coul>`                   | :doc:`tip4p/long/soft (o) <pair_fep_soft>`                  |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`tri/lj <pair_tri_lj>`                                  | :doc:`ufm (got) <pair_ufm>`                                       | :doc:`vashishta (gko) <pair_vashishta>`             | :doc:`vashishta/table (o) <pair_vashishta>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`yukawa (gko) <pair_yukawa>`                            | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`                  | :doc:`zbl (gko) <pair_zbl>`                         |                                                             |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+.. table_from_list::
+   :columns: 4
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`none <pair_none>`
+   * :doc:`zero <pair_zero>`
+   * :doc:`hybrid (k) <pair_hybrid>`
+   * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   *
+   *
+   *
+   *
+   * :doc:`adp (o) <pair_adp>`
+   * :doc:`agni (o) <pair_agni>`
+   * :doc:`airebo (io) <pair_airebo>`
+   * :doc:`airebo/morse (io) <pair_airebo>`
+   * :doc:`atm <pair_atm>`
+   * :doc:`awpmd/cut <pair_awpmd>`
+   * :doc:`beck (go) <pair_beck>`
+   * :doc:`body/nparticle <pair_body_nparticle>`
+   * :doc:`body/rounded/polygon <pair_body_rounded_polygon>`
+   * :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`
+   * :doc:`bop <pair_bop>`
+   * :doc:`born (go) <pair_born>`
+   * :doc:`born/coul/dsf <pair_born>`
+   * :doc:`born/coul/dsf/cs <pair_cs>`
+   * :doc:`born/coul/long (go) <pair_born>`
+   * :doc:`born/coul/long/cs (g) <pair_cs>`
+   * :doc:`born/coul/msm (o) <pair_born>`
+   * :doc:`born/coul/wolf (go) <pair_born>`
+   * :doc:`born/coul/wolf/cs (g) <pair_cs>`
+   * :doc:`brownian (o) <pair_brownian>`
+   * :doc:`brownian/poly (o) <pair_brownian>`
+   * :doc:`buck (giko) <pair_buck>`
+   * :doc:`buck/coul/cut (giko) <pair_buck>`
+   * :doc:`buck/coul/long (giko) <pair_buck>`
+   * :doc:`buck/coul/long/cs <pair_cs>`
+   * :doc:`buck/coul/msm (o) <pair_buck>`
+   * :doc:`buck/long/coul/long (o) <pair_buck_long>`
+   * :doc:`buck/mdf <pair_mdf>`
+   * :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`
+   * :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`
+   * :doc:`colloid (go) <pair_colloid>`
+   * :doc:`comb (o) <pair_comb>`
+   * :doc:`comb3 <pair_comb>`
+   * :doc:`cosine/squared <pair_cosine_squared>`
+   * :doc:`coul/cut (gko) <pair_coul>`
+   * :doc:`coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`coul/debye (gko) <pair_coul>`
+   * :doc:`coul/diel (o) <pair_coul_diel>`
+   * :doc:`coul/dsf (gko) <pair_coul>`
+   * :doc:`coul/long (gko) <pair_coul>`
+   * :doc:`coul/long/cs (g) <pair_cs>`
+   * :doc:`coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`coul/msm (o) <pair_coul>`
+   * :doc:`coul/shield <pair_coul_shield>`
+   * :doc:`coul/streitz <pair_coul>`
+   * :doc:`coul/wolf (ko) <pair_coul>`
+   * :doc:`coul/wolf/cs <pair_cs>`
+   * :doc:`dpd (gio) <pair_dpd>`
+   * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
+   * :doc:`dpd/tstat (go) <pair_dpd>`
+   * :doc:`dsmc <pair_dsmc>`
+   * :doc:`e3b <pair_e3b>`
+   * :doc:`drip <pair_drip>`
+   * :doc:`eam (gikot) <pair_eam>`
+   * :doc:`eam/alloy (gikot) <pair_eam>`
+   * :doc:`eam/cd (o) <pair_eam>`
+   * :doc:`eam/cd/old (o) <pair_eam>`
+   * :doc:`eam/fs (gikot) <pair_eam>`
+   * :doc:`edip (o) <pair_edip>`
+   * :doc:`edip/multi <pair_edip>`
+   * :doc:`edpd <pair_meso>`
+   * :doc:`eff/cut <pair_eff>`
+   * :doc:`eim (o) <pair_eim>`
+   * :doc:`exp6/rx (k) <pair_exp6_rx>`
+   * :doc:`extep <pair_extep>`
+   * :doc:`gauss (go) <pair_gauss>`
+   * :doc:`gauss/cut (o) <pair_gauss>`
+   * :doc:`gayberne (gio) <pair_gayberne>`
+   * :doc:`gran/hertz/history (o) <pair_gran>`
+   * :doc:`gran/hooke (o) <pair_gran>`
+   * :doc:`gran/hooke/history (ko) <pair_gran>`
+   * :doc:`granular <pair_granular>`
+   * :doc:`gw <pair_gw>`
+   * :doc:`gw/zbl <pair_gw>`
+   * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
+   * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
+   * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
+   * :doc:`kim <pair_kim>`
+   * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
+   * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
+   * :doc:`lcbop <pair_lcbop>`
+   * :doc:`lebedeva/z <pair_lebedeva_z>`
+   * :doc:`lennard/mdf <pair_mdf>`
+   * :doc:`line/lj <pair_line_lj>`
+   * :doc:`list <pair_list>`
+   * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
+   * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/long <pair_charmm>`
+   * :doc:`lj/class2 (gko) <pair_class2>`
+   * :doc:`lj/class2/coul/cut (ko) <pair_class2>`
+   * :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
+   * :doc:`lj/class2/coul/long (gko) <pair_class2>`
+   * :doc:`lj/class2/coul/long/soft <pair_fep_soft>`
+   * :doc:`lj/class2/soft <pair_fep_soft>`
+   * :doc:`lj/cubic (go) <pair_lj_cubic>`
+   * :doc:`lj/cut (gikot) <pair_lj>`
+   * :doc:`lj/cut/coul/cut (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/debye (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/long (gikot) <pair_lj>`
+   * :doc:`lj/cut/coul/long/cs <pair_cs>`
+   * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/msm (go) <pair_lj>`
+   * :doc:`lj/cut/coul/wolf (o) <pair_lj>`
+   * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
+   * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
+   * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
+   * :doc:`lj/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/thole/long (o) <pair_thole>`
+   * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long (ot) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/expand (gko) <pair_lj_expand>`
+   * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
+   * :doc:`lj/gromacs (gko) <pair_gromacs>`
+   * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
+   * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
+   * :doc:`lj/long/dipole/long <pair_dipole>`
+   * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
+   * :doc:`lj/mdf <pair_mdf>`
+   * :doc:`lj/sdk (gko) <pair_sdk>`
+   * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
+   * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
+   * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
+   * :doc:`lj/smooth (o) <pair_lj_smooth>`
+   * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
+   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
+   * :doc:`lj96/cut (go) <pair_lj96>`
+   * :doc:`local/density <pair_local_density>`
+   * :doc:`lubricate (o) <pair_lubricate>`
+   * :doc:`lubricate/poly (o) <pair_lubricate>`
+   * :doc:`lubricateU <pair_lubricateU>`
+   * :doc:`lubricateU/poly <pair_lubricateU>`
+   * :doc:`mdpd <pair_meso>`
+   * :doc:`mdpd/rhosum <pair_meso>`
+   * :doc:`meam/c <pair_meamc>`
+   * :doc:`meam/spline (o) <pair_meam_spline>`
+   * :doc:`meam/sw/spline <pair_meam_sw_spline>`
+   * :doc:`mgpt <pair_mgpt>`
+   * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`momb <pair_momb>`
+   * :doc:`morse (gkot) <pair_morse>`
+   * :doc:`morse/smooth/linear (o) <pair_morse>`
+   * :doc:`morse/soft <pair_fep_soft>`
+   * :doc:`multi/lucy <pair_multi_lucy>`
+   * :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
+   * :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
+   * :doc:`nm/cut (o) <pair_nm>`
+   * :doc:`nm/cut/coul/cut (o) <pair_nm>`
+   * :doc:`nm/cut/coul/long (o) <pair_nm>`
+   * :doc:`oxdna/coaxstk <pair_oxdna>`
+   * :doc:`oxdna/excv <pair_oxdna>`
+   * :doc:`oxdna/hbond <pair_oxdna>`
+   * :doc:`oxdna/stk <pair_oxdna>`
+   * :doc:`oxdna/xstk <pair_oxdna>`
+   * :doc:`oxdna2/coaxstk <pair_oxdna2>`
+   * :doc:`oxdna2/dh <pair_oxdna2>`
+   * :doc:`oxdna2/excv <pair_oxdna2>`
+   * :doc:`oxdna2/hbond <pair_oxdna2>`
+   * :doc:`oxdna2/stk <pair_oxdna2>`
+   * :doc:`oxdna2/xstk <pair_oxdna2>`
+   * :doc:`peri/eps <pair_peri>`
+   * :doc:`peri/lps (o) <pair_peri>`
+   * :doc:`peri/pmb (o) <pair_peri>`
+   * :doc:`peri/ves <pair_peri>`
+   * :doc:`python <pair_python>`
+   * :doc:`quip <pair_quip>`
+   * :doc:`reax/c (ko) <pair_reaxc>`
+   * :doc:`rebo (io) <pair_airebo>`
+   * :doc:`resquared (go) <pair_resquared>`
+   * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
+   * :doc:`smd/hertz <pair_smd_hertz>`
+   * :doc:`smd/tlsph <pair_smd_tlsph>`
+   * :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`
+   * :doc:`smd/ulsph <pair_smd_ulsph>`
+   * :doc:`smtbq <pair_smtbq>`
+   * :doc:`snap (k) <pair_snap>`
+   * :doc:`snap (k) <pair_snap>`
+   * :doc:`soft (go) <pair_soft>`
+   * :doc:`sph/heatconduction <pair_sph_heatconduction>`
+   * :doc:`sph/idealgas <pair_sph_idealgas>`
+   * :doc:`sph/lj <pair_sph_lj>`
+   * :doc:`sph/rhosum <pair_sph_rhosum>`
+   * :doc:`sph/taitwater <pair_sph_taitwater>`
+   * :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
+   * :doc:`spin/dipole/cut <pair_spin_dipole>`
+   * :doc:`spin/dipole/long <pair_spin_dipole>`
+   * :doc:`spin/dmi <pair_spin_dmi>`
+   * :doc:`spin/exchange <pair_spin_exchange>`
+   * :doc:`spin/magelec <pair_spin_magelec>`
+   * :doc:`spin/neel <pair_spin_neel>`
+   * :doc:`srp <pair_srp>`
+   * :doc:`sw (giko) <pair_sw>`
+   * :doc:`table (gko) <pair_table>`
+   * :doc:`table/rx (k) <pair_table_rx>`
+   * :doc:`tdpd <pair_meso>`
+   * :doc:`tersoff (giko) <pair_tersoff>`
+   * :doc:`tersoff/mod (gko) <pair_tersoff_mod>`
+   * :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`
+   * :doc:`tersoff/table (o) <pair_tersoff>`
+   * :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
+   * :doc:`thole <pair_thole>`
+   * :doc:`tip4p/cut (o) <pair_coul>`
+   * :doc:`tip4p/long (o) <pair_coul>`
+   * :doc:`tip4p/long/soft (o) <pair_fep_soft>`
+   * :doc:`tri/lj <pair_tri_lj>`
+   * :doc:`ufm (got) <pair_ufm>`
+   * :doc:`vashishta (gko) <pair_vashishta>`
+   * :doc:`vashishta/table (o) <pair_vashishta>`
+   * :doc:`yukawa (gko) <pair_yukawa>`
+   * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
+   * :doc:`zbl (gko) <pair_zbl>`
+   *
+   *
diff --git a/doc/src/Commands_parse.rst b/doc/src/Commands_parse.rst
index 91a11089a8..ec1c8c1e46 100644
--- a/doc/src/Commands_parse.rst
+++ b/doc/src/Commands_parse.rst
@@ -146,8 +146,3 @@ comment indicator in (2) or substituted for as a variable in (3).
    triple quotes can be nested in the usual manner.  See the doc pages
    for those commands for examples.  Only one of level of nesting is
    allowed, but that should be sufficient for most use cases.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/src/Commands_structure.rst b/doc/src/Commands_structure.rst
index d04d2cd98e..b419074212 100644
--- a/doc/src/Commands_structure.rst
+++ b/doc/src/Commands_structure.rst
@@ -84,8 +84,3 @@ command.  Energy minimization (molecular statics) is performed using
 the :doc:`minimize <minimize>` command.  A parallel tempering
 (replica-exchange) simulation can be run using the
 :doc:`temper <temper>` command.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

From 4c13001a6f48f9d5acf76757dbe0fe942d0b9652 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sun, 24 Nov 2019 19:49:59 -0700
Subject: [PATCH 069/199] Add extension errors that stop the build

---
 doc/src/_ext/table_from_list.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/doc/src/_ext/table_from_list.py b/doc/src/_ext/table_from_list.py
index 44c85fc378..715a3c2488 100644
--- a/doc/src/_ext/table_from_list.py
+++ b/doc/src/_ext/table_from_list.py
@@ -4,6 +4,7 @@ from docutils.nodes import Element, Node
 from typing import Any, Dict, List
 from sphinx import addnodes
 from sphinx.util import logging
+from sphinx.errors import SphinxError
 
 class TableFromList(SphinxDirective):
     has_content = True
@@ -22,8 +23,12 @@ class TableFromList(SphinxDirective):
         if len(node.children) != 1 or not isinstance(node.children[0],
                                                      nodes.bullet_list):
             reporter = self.state.document.reporter
-            return [reporter.warning('.. table_from_list content is not a list', line=self.lineno)]
+            raise SphinxError('table_from_list content is not a list')
         fulllist = node.children[0]
+
+        if (len(fulllist) % ncolumns) != 0:
+            raise SphinxError('number of list elements not a multiple of column number')
+
         table = nodes.table()
         tgroup = nodes.tgroup(cols=ncolumns)
         table += tgroup

From 2e4f514d40c59ec141404521bfc36b2d7c05014b Mon Sep 17 00:00:00 2001
From: "Aidan P. Thompson" <athomps@sandia.gov>
Date: Mon, 25 Nov 2019 14:32:37 -0700
Subject: [PATCH 070/199] Fixed some minor errors and omissions

---
 doc/src/Commands_compute.rst | 14 +++++++-------
 doc/src/compute.rst          |  7 ++++---
 doc/src/compute_sna_atom.rst |  2 +-
 doc/txt/Commands_compute.txt |  1 +
 doc/txt/compute.txt          |  7 ++++---
 doc/txt/compute_sna_atom.txt |  2 +-
 6 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index 351eca3709..7165e42110 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -49,19 +49,19 @@ KOKKOS, o = USER-OMP, t = OPT.
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
 | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`       | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`               | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`       | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` | :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` |
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                         | :doc:`sna/atom <compute_sna_atom>`                           | :doc:`snad/atom <compute_sna_atom>`                        |
+| :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                         | :doc:`snap <compute_sna_atom>`                               | :doc:`sna/atom <compute_sna_atom>`                         |
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`snav/atom <compute_sna_atom>`                    | :doc:`spin <compute_spin>`                                       | :doc:`stress/atom <compute_stress_atom>`                     | :doc:`stress/mop <compute_stress_mop>`                   | :doc:`stress/mop/profile <compute_stress_mop>`               | :doc:`stress/tally <compute_tally>`                        |
+| :doc:`snad/atom <compute_sna_atom>`                    | :doc:`snav/atom <compute_sna_atom>`                              | :doc:`spin <compute_spin>`                                   | :doc:`stress/atom <compute_stress_atom>`                 | :doc:`stress/mop <compute_stress_mop>`                       | :doc:`stress/mop/profile <compute_stress_mop>`             |
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`             | :doc:`temp (k) <compute_temp>`                                   | :doc:`temp/asphere <compute_temp_asphere>`                   | :doc:`temp/body <compute_temp_body>`                     | :doc:`temp/chunk <compute_temp_chunk>`                       | :doc:`temp/com <compute_temp_com>`                         |
+| :doc:`stress/tally <compute_tally>`                    | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`                       | :doc:`temp (k) <compute_temp>`                               | :doc:`temp/asphere <compute_temp_asphere>`               | :doc:`temp/body <compute_temp_body>`                         | :doc:`temp/chunk <compute_temp_chunk>`                     |
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`temp/cs <compute_temp_cs>`                       | :doc:`temp/deform <compute_temp_deform>`                         | :doc:`temp/deform/eff <compute_temp_deform_eff>`             | :doc:`temp/drude <compute_temp_drude>`                   | :doc:`temp/eff <compute_temp_eff>`                           | :doc:`temp/partial <compute_temp_partial>`                 |
+| :doc:`temp/com <compute_temp_com>`                     | :doc:`temp/cs <compute_temp_cs>`                                 | :doc:`temp/deform <compute_temp_deform>`                     | :doc:`temp/deform/eff <compute_temp_deform_eff>`         | :doc:`temp/drude <compute_temp_drude>`                       | :doc:`temp/eff <compute_temp_eff>`                         |
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`temp/profile <compute_temp_profile>`             | :doc:`temp/ramp <compute_temp_ramp>`                             | :doc:`temp/region <compute_temp_region>`                     | :doc:`temp/region/eff <compute_temp_region_eff>`         | :doc:`temp/rotate <compute_temp_rotate>`                     | :doc:`temp/sphere <compute_temp_sphere>`                   |
+| :doc:`temp/partial <compute_temp_partial>`             | :doc:`temp/profile <compute_temp_profile>`                       | :doc:`temp/ramp <compute_temp_ramp>`                         | :doc:`temp/region <compute_temp_region>`                 | :doc:`temp/region/eff <compute_temp_region_eff>`             | :doc:`temp/rotate <compute_temp_rotate>`                   |
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`temp/uef <compute_temp_uef>`                     | :doc:`ti <compute_ti>`                                           | :doc:`torque/chunk <compute_torque_chunk>`                   | :doc:`vacf <compute_vacf>`                               | :doc:`vcm/chunk <compute_vcm_chunk>`                         | :doc:`voronoi/atom <compute_voronoi_atom>`                 |
+| :doc:`temp/sphere <compute_temp_sphere>`               | :doc:`temp/uef <compute_temp_uef>`                               | :doc:`ti <compute_ti>`                                       | :doc:`torque/chunk <compute_torque_chunk>`               | :doc:`vacf <compute_vacf>`                                   | :doc:`vcm/chunk <compute_vcm_chunk>`                       |
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`xrd <compute_xrd>`                               |                                                                  |                                                              |                                                          |                                                              |                                                            |
+| :doc:`voronoi/atom <compute_voronoi_atom>`             | :doc:`xrd <compute_xrd>`                                         |                                                              |                                                          |                                                              |                                                            |
 +--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
 
 
diff --git a/doc/src/compute.rst b/doc/src/compute.rst
index 419352a9ac..0e774a78ca 100644
--- a/doc/src/compute.rst
+++ b/doc/src/compute.rst
@@ -286,9 +286,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
 * :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` -
 * :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
 * :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
-* :doc:`sna/atom <compute_sna_atom>` - calculate bispectrum coefficients for each atom
-* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum coefficients for each atom
-* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum coefficients for each atom
+* :doc:`snap <compute_sna_atom>` - bispectrum components and related quantities for a group of atoms
+* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
+* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
+* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
 * :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
 * :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
 * :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst
index 1119c21996..8556b3971b 100644
--- a/doc/src/compute_sna_atom.rst
+++ b/doc/src/compute_sna_atom.rst
@@ -166,7 +166,7 @@ out by type. In between these are 3\*\ *N* rows containing the same values
 computed by *snad/atom* (these are already summed over all atoms and
 broken out by type). The element in the last column of each row contains
 the potential energy, force, or stress, according to the row.
-These quantities correspond to the user-specified refence potential
+These quantities correspond to the user-specified reference potential
 that must be subtracted from the target data when fitting SNAP.
 The potential energy calculation uses the built in compute *thermo\_pe*.
 The stress calculation uses a compute called *snap\_press* that is
diff --git a/doc/txt/Commands_compute.txt b/doc/txt/Commands_compute.txt
index 1bff982586..aa9b0be324 100644
--- a/doc/txt/Commands_compute.txt
+++ b/doc/txt/Commands_compute.txt
@@ -130,6 +130,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
 "smd/ulsph/stress"_compute_smd_ulsph_stress.html,
 "smd/vol"_compute_smd_vol.html,
+"snap"_compute_sna_atom.html,
 "sna/atom"_compute_sna_atom.html,
 "snad/atom"_compute_sna_atom.html,
 "snav/atom"_compute_sna_atom.html,
diff --git a/doc/txt/compute.txt b/doc/txt/compute.txt
index 2d6d26ff16..659965dbcf 100644
--- a/doc/txt/compute.txt
+++ b/doc/txt/compute.txt
@@ -277,9 +277,10 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
 "smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
 "smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
-"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
-"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
-"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
+"snap"_compute_sna_atom.html - bispectrum components and related quantities for a group of atoms
+"sna/atom"_compute_sna_atom.html - bispectrum components for each atom
+"snad/atom"_compute_sna_atom.html - derivative of bispectrum components for each atom
+"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum components for each atom
 "spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
 "stress/atom"_compute_stress_atom.html - stress tensor for each atom
 "stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
diff --git a/doc/txt/compute_sna_atom.txt b/doc/txt/compute_sna_atom.txt
index 05a0bee923..0bf63019f9 100644
--- a/doc/txt/compute_sna_atom.txt
+++ b/doc/txt/compute_sna_atom.txt
@@ -146,7 +146,7 @@ out by type. In between these are 3*{N} rows containing the same values
 computed by {snad/atom} (these are already summed over all atoms and
 broken out by type). The element in the last column of each row contains
 the potential energy, force, or stress, according to the row.
-These quantities correspond to the user-specified refence potential
+These quantities correspond to the user-specified reference potential
 that must be subtracted from the target data when fitting SNAP.
 The potential energy calculation uses the built in compute {thermo_pe}.
 The stress calculation uses a compute called {snap_press} that is

From 3b6a42dc79b7a189559ca65f7e9bbdb082217e79 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 26 Nov 2019 14:46:32 -0500
Subject: [PATCH 071/199] clarify the impact of the lack of potential energy in
 pair style agni

---
 doc/src/pair_agni.rst       | 7 +++++--
 doc/txt/pair_agni.txt       | 7 +++++--
 src/USER-MISC/pair_agni.cpp | 2 +-
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst
index 5194d670b4..96bcf5eccd 100644
--- a/doc/src/pair_agni.rst
+++ b/doc/src/pair_agni.rst
@@ -105,8 +105,11 @@ Restrictions
 
 
 Currently, only elemental systems are implemented. Also, the method
-only provides access to the forces and not energies or
-stresses. However, one can access the energy via thermodynamic
+only provides access to the forces and not energies or stresses.
+The lack of potential energy data makes this pair style incompatible with
+several of the :doc:`minimizer algorthms <min_style>` like *cg* or *sd*\ .
+It should work with damped dynamics based minimizers like *fire* or
+*quickmin*\ .  However, one can access the energy via thermodynamic
 integration of the forces as discussed in
 :ref:`(Botu3) <Botu2016construct>`.  This pair style is part of the
 USER-MISC package. It is only enabled if LAMMPS was built with that
diff --git a/doc/txt/pair_agni.txt b/doc/txt/pair_agni.txt
index 8cb1bf34e4..aae9c161ca 100644
--- a/doc/txt/pair_agni.txt
+++ b/doc/txt/pair_agni.txt
@@ -97,8 +97,11 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]
 
 Currently, only elemental systems are implemented. Also, the method
-only provides access to the forces and not energies or
-stresses. However, one can access the energy via thermodynamic
+only provides access to the forces and not energies or stresses.
+The lack of potential energy data makes this pair style incompatible with
+several of the "minimizer algorthms"_min_style.html like {cg} or {sd}.
+It should work with damped dynamics based minimizers like {fire} or
+{quickmin}.  However, one can access the energy via thermodynamic
 integration of the forces as discussed in
 "(Botu3)"_#Botu2016construct.  This pair style is part of the
 USER-MISC package. It is only enabled if LAMMPS was built with that
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index b3abc647ef..a03e24ed35 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -243,7 +243,7 @@ void PairAGNI::allocate()
    global settings
 ------------------------------------------------------------------------- */
 
-void PairAGNI::settings(int narg, char **/*arg*/)
+void PairAGNI::settings(int narg, char ** /* arg */)
 {
   if (narg != 0) error->all(FLERR,"Illegal pair_style command");
 }

From 3bd3c7a19641e7c729914734a4dffd26f5275aec Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 26 Nov 2019 14:48:08 -0500
Subject: [PATCH 072/199] remove compute head/flux txt style docs as it is out
 of sync with the rst version

---
 doc/txt/compute_heat_flux.txt | 192 ----------------------------------
 1 file changed, 192 deletions(-)
 delete mode 100644 doc/txt/compute_heat_flux.txt

diff --git a/doc/txt/compute_heat_flux.txt b/doc/txt/compute_heat_flux.txt
deleted file mode 100644
index edd46f7587..0000000000
--- a/doc/txt/compute_heat_flux.txt
+++ /dev/null
@@ -1,192 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-compute heat/flux command :h3
-
-[Syntax:]
-
-compute ID group-ID heat/flux ke-ID pe-ID stress-ID :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-heat/flux = style name of this compute command
-ke-ID = ID of a compute that calculates per-atom kinetic energy
-pe-ID = ID of a compute that calculates per-atom potential energy
-stress-ID = ID of a compute that calculates per-atom stress :ul
-
-[Examples:]
-
-compute myFlux all heat/flux myKE myPE myStress :pre
-
-[Description:]
-
-Define a computation that calculates the heat flux vector based on
-contributions from atoms in the specified group.  This can be used by
-itself to measure the heat flux through a set of atoms (e.g. a region
-between two thermostatted reservoirs held at different temperatures),
-or to calculate a thermal conductivity using the equilibrium
-Green-Kubo formalism.
-
-For other non-equilibrium ways to compute a thermal conductivity, see
-the "Howto kappa"_Howto_kappa.html doc page..  These include use of
-the "fix thermal/conductivity"_fix_thermal_conductivity.html command
-for the Muller-Plathe method.  Or the "fix heat"_fix_heat.html command
-which can add or subtract heat from groups of atoms.
-
-The compute takes three arguments which are IDs of other
-"computes"_compute.html.  One calculates per-atom kinetic energy
-({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
-third calculates per-atom stress ({stress-ID}).
-
-NOTE: These other computes should provide values for all the atoms in
-the group this compute specifies.  That means the other computes could
-use the same group as this compute, or they can just use group "all"
-(or any group whose atoms are superset of the atoms in this compute's
-group).  LAMMPS does not check for this.
-
-The Green-Kubo formulas relate the ensemble average of the
-auto-correlation of the heat flux J to the thermal conductivity kappa:
-
-:c,image(Eqs/heat_flux_J.jpg)
-
-:c,image(Eqs/heat_flux_k.jpg)
-
-Ei in the first term of the equation for J is the per-atom energy
-(potential and kinetic).  This is calculated by the computes {ke-ID}
-and {pe-ID}.  Si in the second term of the equation for J is the
-per-atom stress tensor calculated by the compute {stress-ID}.  The
-tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a
-vector.  Note that as discussed below, the 1/V scaling factor in the
-equation for J is NOT included in the calculation performed by this
-compute; you need to add it for a volume appropriate to the atoms
-included in the calculation.
-
-NOTE: The "compute pe/atom"_compute_pe_atom.html and "compute
-stress/atom"_compute_stress_atom.html commands have options for which
-terms to include in their calculation (pair, bond, etc).  The heat
-flux calculation will thus include exactly the same terms.  Normally
-you should use "compute stress/atom virial"_compute_stress_atom.html
-so as not to include a kinetic energy term in the heat flux.
-
-This compute calculates 6 quantities and stores them in a 6-component
-vector.  The first 3 components are the x, y, z components of the full
-heat flux vector, i.e. (Jx, Jy, Jz).  The next 3 components are the x,
-y, z components of just the convective portion of the flux, i.e. the
-first term in the equation for J above.
-
-:line
-
-The heat flux can be output every so many timesteps (e.g. via the
-"thermo_style custom"_thermo_style.html command).  Then as a
-post-processing operation, an auto-correlation can be performed, its
-integral estimated, and the Green-Kubo formula above evaluated.
-
-The "fix ave/correlate"_fix_ave_correlate.html command can calculate
-the auto-correlation.  The trap() function in the
-"variable"_variable.html command can calculate the integral.
-
-An example LAMMPS input script for solid Ar is appended below.  The
-result should be: average conductivity ~0.29 in W/mK.
-
-:line
-
-[Output info:]
-
-This compute calculates a global vector of length 6 (total heat flux
-vector, followed by convective heat flux vector), which can be
-accessed by indices 1-6.  These values can be used by any command that
-uses global vector values from a compute as input.  See the "Howto
-output"_Howto_output.html doc page for an overview of LAMMPS output
-options.
-
-The vector values calculated by this compute are "extensive", meaning
-they scale with the number of atoms in the simulation.  They can be
-divided by the appropriate volume to get a flux, which would then be
-an "intensive" value, meaning independent of the number of atoms in
-the simulation.  Note that if the compute is "all", then the
-appropriate volume to divide by is the simulation box volume.
-However, if a sub-group is used, it should be the volume containing
-those atoms.
-
-The vector values will be in energy*velocity "units"_units.html.  Once
-divided by a volume the units will be that of flux, namely
-energy/area/time "units"_units.html
-
-[Restrictions:] none
-
-[Related commands:]
-
-"fix thermal/conductivity"_fix_thermal_conductivity.html,
-"fix ave/correlate"_fix_ave_correlate.html,
-"variable"_variable.html
-
-[Default:] none
-
-:line
-
-# Sample LAMMPS input script for thermal conductivity of solid Ar :pre
-
-units       real
-variable    T equal 70
-variable    V equal vol
-variable    dt equal 4.0
-variable    p equal 200     # correlation length
-variable    s equal 10      # sample interval
-variable    d equal $p*$s   # dump interval :pre
-
-# convert from LAMMPS real units to SI :pre
-
-variable    kB equal 1.3806504e-23    # \[J/K\] Boltzmann
-variable    kCal2J equal 4186.0/6.02214e23
-variable    A2m equal 1.0e-10
-variable    fs2s equal 1.0e-15
-variable    convert equal $\{kCal2J\}*$\{kCal2J\}/$\{fs2s\}/$\{A2m\} :pre
-
-# setup problem :pre
-
-dimension    3
-boundary     p p p
-lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
-region       box block 0 4 0 4 0 4
-create_box   1 box
-create_atoms 1 box
-mass         1 39.948
-pair_style   lj/cut 13.0
-pair_coeff   * * 0.2381 3.405
-timestep     $\{dt\}
-thermo       $d :pre
-
-# equilibration and thermalization :pre
-
-velocity     all create $T 102486 mom yes rot yes dist gaussian
-fix          NVT all nvt temp $T $T 10 drag 0.2
-run          8000 :pre
-
-# thermal conductivity calculation, switch to NVE if desired :pre
-
-#unfix       NVT
-#fix         NVE all nve :pre
-
-reset_timestep 0
-compute      myKE all ke/atom
-compute      myPE all pe/atom
-compute      myStress all stress/atom NULL virial
-compute      flux all heat/flux myKE myPE myStress
-variable     Jx equal c_flux\[1\]/vol
-variable     Jy equal c_flux\[2\]/vol
-variable     Jz equal c_flux\[3\]/vol
-fix          JJ all ave/correlate $s $p $d &
-             c_flux\[1\] c_flux\[2\] c_flux\[3\] type auto file J0Jt.dat ave running
-variable     scale equal $\{convert\}/$\{kB\}/$T/$T/$V*$s*$\{dt\}
-variable     k11 equal trap(f_JJ\[3\])*$\{scale\}
-variable     k22 equal trap(f_JJ\[4\])*$\{scale\}
-variable     k33 equal trap(f_JJ\[5\])*$\{scale\}
-thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
-run          100000
-variable     k equal (v_k11+v_k22+v_k33)/3.0
-variable     ndens equal count(all)/vol
-print        "average conductivity: $k\[W/mK\] @ $T K, $\{ndens\} /A^3" :pre

From 3aed4eb74c1b17bfae7595c22e37e4067db878d1 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Tue, 26 Nov 2019 21:52:31 +0100
Subject: [PATCH 073/199] Update Howto_pylammps.rst

---
 doc/src/Howto_pylammps.rst | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst
index 64f1cc6036..2711e26914 100644
--- a/doc/src/Howto_pylammps.rst
+++ b/doc/src/Howto_pylammps.rst
@@ -362,18 +362,17 @@ accessible through its thermo name:
 
 .. code-block:: Python
 
-   L.runs[0].step # list of time steps in first run
-   L.runs[0].ke   # list of kinetic energy values in first run
+   L.runs[0].thermo.Step # list of time steps in first run
+   L.runs[0].thermo.Ke   # list of kinetic energy values in first run
 
 Together with matplotlib plotting data out of LAMMPS becomes simple:
 
-import matplotlib.plot as plt
-
 
 .. code-block:: Python
 
-   steps = L.runs[0].step
-   ke    = L.runs[0].ke
+   import matplotlib.plot as plt
+   steps = L.runs[0].thermo.Step
+   ke    = L.runs[0].thermo.Ke
    plt.plot(steps, ke)
 
 Error handling with PyLammps

From 87a04db02c2ef792f4fc10547f959b4a72acbea6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 26 Nov 2019 16:24:03 -0500
Subject: [PATCH 074/199] add prototype of style checking script (incomplete)

so far, this code can compile a list of styles with flags
indicating support for accelerated styles
---
 doc/utils/check-styles.py | 125 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 125 insertions(+)
 create mode 100755 doc/utils/check-styles.py

diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
new file mode 100755
index 0000000000..3acd2aa0a9
--- /dev/null
+++ b/doc/utils/check-styles.py
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+from glob import glob
+import os, re
+
+headers = glob(os.path.join('..', '..', 'src', '*', '*.h'))
+headers += glob(os.path.join('..', '..', 'src', '*.h'))
+
+angle = {}
+atom = {}
+body = {}
+bond = {}
+command = {}
+compute = {}
+dihedral = {}
+dump = {}
+fix = {}
+improper = {}
+integrate = {}
+kspace = {}
+minimize = {}
+pair = {}
+reader = {}
+region = {}
+
+upper = re.compile("[A-Z]+")
+gpu = re.compile("(.+)/gpu$")
+intel = re.compile("(.+)/intel$")
+kokkos = re.compile("(.+)/kk$")
+kokkos_skip = re.compile("(.+)/kk/(host|device)$")
+omp = re.compile("(.+)/omp$")
+opt = re.compile("(.+)/opt$")
+removed = re.compile("(.+)Deprecated$")
+
+def register_style(list,style,info):
+    if style in list.keys():
+        list[style]['gpu'] += info['gpu']
+        list[style]['intel'] += info['intel']
+        list[style]['kokkos'] += info['kokkos']
+        list[style]['omp'] += info['omp']
+        list[style]['opt'] += info['opt']
+        list[style]['removed'] += info['removed']
+    else:
+        list[style] = info
+
+for h in headers:
+    # print("Checking ", h)
+    fp = open(h)
+    text = fp.read()
+    matches = re.findall("(.+)Style\((.+),(.+)\)",text,re.MULTILINE)
+    for m in matches:
+
+        # skip over internal styles w/o explicit documentation
+        style = m[1]
+        if upper.match(style):
+            continue
+
+        # detect, process, and flag suffix styles:
+        info = { 'kokkos':  0, 'gpu':     0, 'intel':   0, \
+                 'omp':     0, 'opt':     0, 'removed': 0 }
+        suffix = kokkos_skip.match(style)
+        if suffix:
+            continue
+        suffix = gpu.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['gpu'] = 1
+        suffix = intel.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['intel'] = 1
+        suffix = kokkos.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['kokkos'] = 1
+        suffix = omp.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['omp'] = 1
+        suffix = opt.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['opt'] = 1
+        deprecated = removed.match(m[2])
+        if deprecated:
+            info['removed'] = 1
+
+        # register style and suffix flags
+        if m[0] == 'Angle':
+            register_style(angle,style,info)
+        elif m[0] == 'Atom':
+            register_style(atom,style,info)
+        elif m[0] == 'Body':
+            register_style(body,style,info)
+        elif m[0] == 'Bond':
+            register_style(bond,style,info)
+        elif m[0] == 'Command':
+            register_style(command,style,info)
+        elif m[0] == 'Compute':
+            register_style(compute,style,info)
+        elif m[0] == 'Dihedral':
+            register_style(dihedral,style,info)
+        elif m[0] == 'Dump':
+            register_style(dump,style,info)
+        elif m[0] == 'Fix':
+            register_style(fix,style,info)
+        elif m[0] == 'Improper':
+            register_style(improper,style,info)
+        elif m[0] == 'Integrate':
+            register_style(integrate,style,info)
+        elif m[0] == 'KSpace':
+            register_style(kspace,style,info)
+        elif m[0] == 'Minimize':
+            register_style(minimize,style,info)
+        elif m[0] == 'Pair':
+            register_style(pair,style,info)
+        elif m[0] == 'Reader':
+            register_style(reader,style,info)
+        elif m[0] == 'Region':
+            register_style(region,style,info)
+        else:
+            print("Skipping over: ",m)
+fp.close()
+

From d806ee5d7ea9a4e6ff9f1ddeb262b5a0c7e03aad Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 26 Nov 2019 17:25:51 -0500
Subject: [PATCH 075/199] Fixes misleading indentation

---
 src/pair_hybrid.cpp | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index b6324f0d03..eb9423aa57 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -173,11 +173,14 @@ void PairHybrid::compute(int eflag, int vflag)
             cvatom[i][j] += cvatom_substyle[i][j];
       } else {
         double **vatom_substyle = styles[m]->vatom;
-        for (i = 0; i < n; i++)
-          for (j = 0; j < 6; j++)
+        for (i = 0; i < n; i++) {
+          for (j = 0; j < 6; j++) {
             cvatom[i][j] += vatom_substyle[i][j];
-          for (j = 6; j < 9; j++)
+          }
+          for (j = 6; j < 9; j++) {
             cvatom[i][j] += vatom_substyle[i][j-3];
+          }
+        }
       }
     }
 

From 60d5244526d31896a80c6444c437eac9cb2f3a9d Mon Sep 17 00:00:00 2001
From: lucienPan <lucien.pan0927@gmail.com>
Date: Tue, 26 Nov 2019 18:05:06 -0500
Subject: [PATCH 076/199] Remove the const of costh12, costh13 costh23 in
 KOKKOS class dihedral

---
 src/KOKKOS/dihedral_class2_kokkos.cpp | 22 ++++++++--------------
 1 file changed, 8 insertions(+), 14 deletions(-)

diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index 39be838d7e..0310053b5e 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -243,26 +243,20 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
   const F_FLOAT sb3 = 1.0/r3mag2;
   const F_FLOAT rb3 = 1.0/r3;
 
-  const F_FLOAT c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
+  F_FLOAT c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
 
   // 1st and 2nd angle
 
   const F_FLOAT r12c1 = rb1*rb2;
   const F_FLOAT r12c2 = rb2*rb3;
-  const F_FLOAT costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
-  const F_FLOAT costh13 = c0;
-  const F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
+  F_FLOAT costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
+  F_FLOAT costh13 = c0;
+  F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
 
-  {
-    F_FLOAT& ctmp12 = const_cast<F_FLOAT&>(costh12);
-    F_FLOAT& ctmp13 = const_cast<F_FLOAT&>(costh13);
-    F_FLOAT& ctmp23 = const_cast<F_FLOAT&>(costh23);
-    F_FLOAT& ctmp0  = const_cast<F_FLOAT&>(c0);
-    ctmp12 = MAX(MIN(costh12, 1.0), -1.0);
-    ctmp13 = MAX(MIN(costh13, 1.0), -1.0);
-    ctmp23 = MAX(MIN(costh23, 1.0), -1.0);
-    ctmp0  = costh13;
-  }
+  costh12 = MAX(MIN(costh12, 1.0), -1.0);
+  costh13 = MAX(MIN(costh13, 1.0), -1.0);
+  costh23 = MAX(MIN(costh23, 1.0), -1.0);
+  c0 = costh13;
 
   // cos and sin of 2 angles and final c
 

From 1f83c7d03743afeee105725eca96173f482c4b0d Mon Sep 17 00:00:00 2001
From: julient31 <julien.tranchida1@gmail.com>
Date: Wed, 27 Nov 2019 06:26:34 -0700
Subject: [PATCH 077/199] Commit JT 112719 - correcting 'neighbours' in doc -
 modifying README is src/SPIN

---
 doc/txt/pair_spin_exchange.txt | 2 +-
 src/SPIN/README                | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/doc/txt/pair_spin_exchange.txt b/doc/txt/pair_spin_exchange.txt
index dea2d57f62..d8e22539de 100644
--- a/doc/txt/pair_spin_exchange.txt
+++ b/doc/txt/pair_spin_exchange.txt
@@ -31,7 +31,7 @@ pairs of magnetic spins:
 
 where si and sj are two neighboring magnetic spins of two particles,
 rij = |ri - rj| is the inter-atomic distance between the two
-particles. The summation is over pairs of nearest neighbours. 
+particles. The summation is over pairs of nearest neighbors. 
 J(rij) is a function defining the intensity and the sign of the exchange
 interaction for different neighboring shells. This function is defined as:
 
diff --git a/src/SPIN/README b/src/SPIN/README
index a4eb4ff22b..ad296c69b7 100644
--- a/src/SPIN/README
+++ b/src/SPIN/README
@@ -8,7 +8,6 @@ atom in the system
 * integrating the equations of motion for the coupled spin-lattice system
 * implementing magnetic pair interactions and magnetic forces
 * thermostating and applying a transverse damping to the magnetic spins
-* minimizing spin configurations with an adaptive timestep scheme
 * performing geodesic NEB calculations
 * computing and outputing magnetic quantities
 * minimizing the energy or total torque of a magnetic system

From b49957c1919c2ec9da061c5f237800f323080bbb Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 22 Aug 2019 10:41:35 -0600
Subject: [PATCH 078/199] Fix memory leak

---
 python/lammps.py | 60 +++++++++++++++++++++++-------------------------
 1 file changed, 29 insertions(+), 31 deletions(-)

diff --git a/python/lammps.py b/python/lammps.py
index 9a73688f65..d4f68ba138 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -221,8 +221,8 @@ class lammps(object):
 
     # add way to insert Python callback for fix external
     self.callback = {}
-    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, c_void_p, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
-    self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, c_void_p]
+    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
+    self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, py_object]
     self.lib.lammps_set_fix_external_callback.restype = None
 
   # shut-down LAMMPS instance
@@ -357,26 +357,38 @@ class lammps(object):
           else:
             c_int_type = c_int
 
+          if dim == 1:
+            raw_ptr = self.lmp.extract_atom(name, 0)
+          else:
+            raw_ptr = self.lmp.extract_atom(name, 1)
+
+          return self.iarray(c_int_type, raw_ptr, nelem, dim)
+
+        def extract_atom_darray(self, name, nelem, dim=1):
+          if dim == 1:
+            raw_ptr = self.lmp.extract_atom(name, 2)
+          else:
+            raw_ptr = self.lmp.extract_atom(name, 3)
+
+          return self.darray(raw_ptr, nelem, dim)
+
+        def iarray(self, c_int_type, raw_ptr, nelem, dim=1):
           np_int_type = self._ctype_to_numpy_int(c_int_type)
 
           if dim == 1:
-            tmp = self.lmp.extract_atom(name, 0)
-            ptr = cast(tmp, POINTER(c_int_type * nelem))
+            ptr = cast(raw_ptr, POINTER(c_int_type * nelem))
           else:
-            tmp = self.lmp.extract_atom(name, 1)
-            ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
+            ptr = cast(raw_ptr[0], POINTER(c_int_type * nelem * dim))
 
           a = np.frombuffer(ptr.contents, dtype=np_int_type)
           a.shape = (nelem, dim)
           return a
 
-        def extract_atom_darray(self, name, nelem, dim=1):
+        def darray(self, raw_ptr, nelem, dim=1):
           if dim == 1:
-            tmp = self.lmp.extract_atom(name, 2)
-            ptr = cast(tmp, POINTER(c_double * nelem))
+            ptr = cast(raw_ptr, POINTER(c_double * nelem))
           else:
-            tmp = self.lmp.extract_atom(name, 3)
-            ptr = cast(tmp[0], POINTER(c_double * nelem * dim))
+            ptr = cast(raw_ptr[0], POINTER(c_double * nelem * dim))
 
           a = np.frombuffer(ptr.contents)
           a.shape = (nelem, dim)
@@ -617,28 +629,14 @@ class lammps(object):
             return np.int64
           return np.intc
 
-    def callback_wrapper(caller_ptr, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
-      if cast(caller_ptr,POINTER(py_object)).contents:
-        pyCallerObj = cast(caller_ptr,POINTER(py_object)).contents.value
-      else:
-        pyCallerObj = None
-
-      tptr = cast(tag_ptr, POINTER(self.c_tagint * nlocal))
-      tag = np.frombuffer(tptr.contents, dtype=_ctype_to_numpy_int(self.c_tagint))
-      tag.shape = (nlocal)
-
-      xptr = cast(x_ptr[0], POINTER(c_double * nlocal * 3))
-      x = np.frombuffer(xptr.contents)
-      x.shape = (nlocal, 3)
-
-      fptr = cast(fext_ptr[0], POINTER(c_double * nlocal * 3))
-      f = np.frombuffer(fptr.contents)
-      f.shape = (nlocal, 3)
-
-      callback(pyCallerObj, ntimestep, nlocal, tag, x, f)
+    def callback_wrapper(caller, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
+      tag = self.numpy.iarray(self.c_tagint, tag_ptr, nlocal, 1)
+      x   = self.numpy.darray(x_ptr, nlocal, 3)
+      f   = self.numpy.darray(fext_ptr, nlocal, 3)
+      callback(caller, ntimestep, nlocal, tag, x, f)
 
     cFunc   = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper)
-    cCaller = cast(pointer(py_object(caller)), c_void_p)
+    cCaller = caller
 
     self.callback[fix_name] = { 'function': cFunc, 'caller': caller }
 

From e3da3cadad32cb0b562a90286ad4eb1632a62e18 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 22 Aug 2019 10:45:24 -0600
Subject: [PATCH 079/199] Remove magic numbers and additional data types in
 extract_global

---
 python/lammps.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/python/lammps.py b/python/lammps.py
index d4f68ba138..6c84e8c9b4 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -32,6 +32,11 @@ import select
 import re
 import sys
 
+LAMMPS_INT    = 0
+LAMMPS_DOUBLE = 1
+LAMMPS_BIGINT = 2
+LAMMPS_TAGINT = 3
+
 def get_ctypes_int(size):
   if size == 4:
     return c_int32
@@ -283,10 +288,14 @@ class lammps(object):
 
   def extract_global(self,name,type):
     if name: name = name.encode()
-    if type == 0:
+    if type == LAMMPS_INT:
       self.lib.lammps_extract_global.restype = POINTER(c_int)
-    elif type == 1:
+    elif type == LAMMPS_DOUBLE:
       self.lib.lammps_extract_global.restype = POINTER(c_double)
+    elif type == LAMMPS_BIGINT:
+      self.lib.lammps_extract_global.restype = POINTER(self.c_bigint)
+    elif type == LAMMPS_TAGINT:
+      self.lib.lammps_extract_global.restype = POINTER(self.c_tagint)
     else: return None
     ptr = self.lib.lammps_extract_global(self.lmp,name)
     return ptr[0]

From 66a076b819c0f6a60cb999a43ec2b7ac0d132ff4 Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Wed, 27 Nov 2019 19:49:12 +0300
Subject: [PATCH 080/199] Delete "float.h" from TIP4P GPU kernel for better
 OpenCL compatibility

According to Khronos OpenCL docs, "The C99 standard headers <...>, float.h, <...> are not available and cannot be included by a program"
---
 lib/gpu/lal_lj_tip4p_long.cu | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
index 2301cb39a7..65f3cf9f67 100644
--- a/lib/gpu/lal_lj_tip4p_long.cu
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -29,8 +29,6 @@ texture<int2> q_tex;
 #define q_tex q_
 #endif
 
-#include <float.h>
-
 ucl_inline int atom_mapping(const __global int *map, int glob){
 	return map[glob];
 }
@@ -184,6 +182,8 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
   int tid, ii, offset;
   atom_info(t_per_atom,ii,tid,offset);
 
+  const numtyp eq_zero = 1e-6;
+
   acctyp energy = (acctyp)0;
   acctyp e_coul = (acctyp)0;
   acctyp4 f, fO;
@@ -230,7 +230,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
         iH1 = hneigh[i*4  ];
         iH2 = hneigh[i*4+1];
       }
-      if(fabs(m[iO].w) <= FLT_EPSILON) {
+      if(fabs(m[iO].w) <= eq_zero) {
         compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
         m[iO].w = qtmp;
       }
@@ -270,7 +270,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
       }
       if (iO >= inum) {
         non_local_oxy = 1;
-        if(fabs(m[iO].w) <= FLT_EPSILON) {
+        if(fabs(m[iO].w) <= eq_zero) {
           compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
           numtyp qO; fetch(qO,iO,q_tex);
           m[iO].w = qO;
@@ -346,7 +346,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
               jH1 = hneigh[j*4  ];
               jH2 = hneigh[j*4+1];
             }
-            if (fabs(m[j].w) <= FLT_EPSILON) {
+            if (fabs(m[j].w) <= eq_zero) {
               compute_newsite(j, jH1, jH2, &m[j], alpha, x_);
               m[j].w = qj;
             }

From 5c93b6ad6f808996794d286562ff48feb7f2af0a Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 27 Nov 2019 15:17:11 -0500
Subject: [PATCH 081/199] Update docs: compute_spin, fix_precession_spin,
 pair_spin_exchange, pair_spin_neel

---
 doc/src/Eqs/fix_spin_cubic.jpg                | Bin 25265 -> 0 bytes
 doc/src/Eqs/fix_spin_cubic.tex                |  21 ---
 doc/src/Eqs/fix_spin_zeeman.jpg               | Bin 5896 -> 0 bytes
 doc/src/Eqs/fix_spin_zeeman.tex               |  12 --
 doc/src/Eqs/force_spin_aniso.jpg              | Bin 6089 -> 0 bytes
 doc/src/Eqs/force_spin_aniso.tex              |  11 --
 doc/src/Eqs/pair_spin_exchange_forces.jpg     | Bin 13255 -> 0 bytes
 doc/src/Eqs/pair_spin_exchange_forces.tex     |  16 --
 doc/src/Eqs/pair_spin_exchange_function.jpg   | Bin 10597 -> 0 bytes
 doc/src/Eqs/pair_spin_exchange_function.tex   |  13 --
 .../Eqs/pair_spin_exchange_interaction.jpg    | Bin 5554 -> 0 bytes
 .../Eqs/pair_spin_exchange_interaction.tex    |  15 --
 doc/src/Eqs/pair_spin_neel_functions.jpg      | Bin 5936 -> 0 bytes
 doc/src/Eqs/pair_spin_neel_functions.tex      |  13 --
 doc/src/Eqs/pair_spin_neel_interaction.jpg    | Bin 11029 -> 0 bytes
 doc/src/Eqs/pair_spin_neel_interaction.tex    |  16 --
 doc/src/compute_spin.rst                      |  19 ++-
 doc/src/fix_precession_spin.rst               |  84 +++++-----
 doc/src/pair_spin_exchange.rst                |  72 ++++-----
 doc/src/pair_spin_neel.rst                    |  61 ++++----
 doc/txt/compute_spin.txt                      |  75 ---------
 doc/txt/fix_precession_spin.txt               | 143 ------------------
 doc/txt/pair_spin_exchange.txt                | 100 ------------
 doc/txt/pair_spin_neel.txt                    |  83 ----------
 24 files changed, 127 insertions(+), 627 deletions(-)
 delete mode 100644 doc/src/Eqs/fix_spin_cubic.jpg
 delete mode 100644 doc/src/Eqs/fix_spin_cubic.tex
 delete mode 100644 doc/src/Eqs/fix_spin_zeeman.jpg
 delete mode 100644 doc/src/Eqs/fix_spin_zeeman.tex
 delete mode 100644 doc/src/Eqs/force_spin_aniso.jpg
 delete mode 100644 doc/src/Eqs/force_spin_aniso.tex
 delete mode 100644 doc/src/Eqs/pair_spin_exchange_forces.jpg
 delete mode 100644 doc/src/Eqs/pair_spin_exchange_forces.tex
 delete mode 100644 doc/src/Eqs/pair_spin_exchange_function.jpg
 delete mode 100644 doc/src/Eqs/pair_spin_exchange_function.tex
 delete mode 100644 doc/src/Eqs/pair_spin_exchange_interaction.jpg
 delete mode 100644 doc/src/Eqs/pair_spin_exchange_interaction.tex
 delete mode 100644 doc/src/Eqs/pair_spin_neel_functions.jpg
 delete mode 100644 doc/src/Eqs/pair_spin_neel_functions.tex
 delete mode 100644 doc/src/Eqs/pair_spin_neel_interaction.jpg
 delete mode 100644 doc/src/Eqs/pair_spin_neel_interaction.tex
 delete mode 100644 doc/txt/compute_spin.txt
 delete mode 100644 doc/txt/fix_precession_spin.txt
 delete mode 100644 doc/txt/pair_spin_exchange.txt
 delete mode 100644 doc/txt/pair_spin_neel.txt

diff --git a/doc/src/Eqs/fix_spin_cubic.jpg b/doc/src/Eqs/fix_spin_cubic.jpg
deleted file mode 100644
index 871641111c9e43edfd878c4fa138da7231b5bbd9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/doc/src/Eqs/fix_spin_cubic.tex b/doc/src/Eqs/fix_spin_cubic.tex
deleted file mode 100644
index 9c402294d7..0000000000
--- a/doc/src/Eqs/fix_spin_cubic.tex
+++ /dev/null
@@ -1,21 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \bm{H}_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
-    \Big[
-    \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2 +
-    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 +
-    \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \Big]
-    +K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
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diff --git a/doc/src/Eqs/fix_spin_zeeman.tex b/doc/src/Eqs/fix_spin_zeeman.tex
deleted file mode 100644
index 79dd49526a..0000000000
--- a/doc/src/Eqs/fix_spin_zeeman.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \bm{H}_{Zeeman} = -g \sum_{i=0}^{N}\mu_{i}\, 
-    \vec{s}_{i} \cdot\vec{B}_{ext} \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
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diff --git a/doc/src/Eqs/force_spin_aniso.tex b/doc/src/Eqs/force_spin_aniso.tex
deleted file mode 100644
index d6abfd580d..0000000000
--- a/doc/src/Eqs/force_spin_aniso.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \bm{H}_{aniso}  = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/pair_spin_exchange_forces.jpg b/doc/src/Eqs/pair_spin_exchange_forces.jpg
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diff --git a/doc/src/Eqs/pair_spin_exchange_forces.tex b/doc/src/Eqs/pair_spin_exchange_forces.tex
deleted file mode 100644
index ac5ef682f3..0000000000
--- a/doc/src/Eqs/pair_spin_exchange_forces.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} 
-    \left(r_{ij} \right)\,\vec{s}_{j} 
-    ~~{\rm and}~~ 
-    \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
-    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}  
-    \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/pair_spin_exchange_function.jpg b/doc/src/Eqs/pair_spin_exchange_function.jpg
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diff --git a/doc/src/Eqs/pair_spin_exchange_function.tex b/doc/src/Eqs/pair_spin_exchange_function.tex
deleted file mode 100644
index 054c6992f0..0000000000
--- a/doc/src/Eqs/pair_spin_exchange_function.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d}  
-    \right)^2 }\Theta (R_c - r_{ij}) \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.jpg b/doc/src/Eqs/pair_spin_exchange_interaction.jpg
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diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.tex b/doc/src/Eqs/pair_spin_exchange_interaction.tex
deleted file mode 100644
index 8bb58e0885..0000000000
--- a/doc/src/Eqs/pair_spin_exchange_interaction.tex
+++ /dev/null
@@ -1,15 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    H_{ex} = 
-    -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j 
-    %&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F  
-  , \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/pair_spin_neel_functions.jpg b/doc/src/Eqs/pair_spin_neel_functions.jpg
deleted file mode 100644
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diff --git a/doc/src/Eqs/pair_spin_neel_functions.tex b/doc/src/Eqs/pair_spin_neel_functions.tex
deleted file mode 100644
index ead5a2b87a..0000000000
--- a/doc/src/Eqs/pair_spin_neel_functions.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{eqnarray}
-    g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\
-    q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\
-    q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber
-  \end{eqnarray}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/pair_spin_neel_interaction.jpg b/doc/src/Eqs/pair_spin_neel_interaction.jpg
deleted file mode 100644
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diff --git a/doc/src/Eqs/pair_spin_neel_interaction.tex b/doc/src/Eqs/pair_spin_neel_interaction.tex
deleted file mode 100644
index 8b4ac33e73..0000000000
--- a/doc/src/Eqs/pair_spin_neel_interaction.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij}
-    \cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
-    +q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right)
-    \left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
-    + q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot
-    {\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/compute_spin.rst b/doc/src/compute_spin.rst
index 7538746911..034d2ab685 100644
--- a/doc/src/compute_spin.rst
+++ b/doc/src/compute_spin.rst
@@ -7,7 +7,7 @@ Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID spin
 
@@ -18,7 +18,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute out_mag all spin
 
@@ -43,7 +43,7 @@ is to define some of the quantities as variables, and to use the thermo and
 thermo\_style commands, for example:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute out_mag         all spin
 
@@ -72,9 +72,13 @@ The *spin* compute is part of the SPIN package.  This compute is only
 enabled if LAMMPS was built with this package.  See the :doc:`Build package <Build_package>` doc page for more info.  The atom\_style
 has to be "spin" for this compute to be valid.
 
-**Related commands:** none
+**Related commands:**
 
-**Default:** none
+none
+
+**Default:**
+
+none
 
 
 ----------
@@ -85,8 +89,3 @@ has to be "spin" for this compute to be valid.
 
 
 **(Nurdin)** Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst
index e47b9bd855..2c84eaa304 100644
--- a/doc/src/fix_precession_spin.rst
+++ b/doc/src/fix_precession_spin.rst
@@ -7,7 +7,7 @@ Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group precession/spin style args
 
@@ -37,7 +37,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
    fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
@@ -53,25 +53,26 @@ Style *zeeman* is used for the simulation of the interaction
 between the magnetic spins in the defined group and an external
 magnetic field:
 
-.. image:: Eqs/fix_spin_zeeman.jpg
-   :align: center
+.. math::
+
+   H_{Zeeman} = -g \sum_{i=0}^{N}\mu_{i}\, \vec{s}_{i} \cdot\vec{B}_{ext}
 
 with:
 
-* Bext the external magnetic field (in T)
-* g the Lande factor (hard-coded as g=2.0)
-* si the unitary vector describing the orientation of spin i
-* mui the atomic moment of spin i given as a multiple of the
-  Bohr magneton muB (for example, mui ~ 2.2 in bulk iron).
+* :math:`\vec{B}_{ext}` the external magnetic field (in T)
+* :math:`g` the Lande factor (hard-coded as :math:`g=2.0`)
+* :math:`\vec{s}_i` the unitary vector describing the orientation of spin :math:`i`
+* :math:`\mu_i` the atomic moment of spin :math:`i` given as a multiple of the
+  Bohr magneton :math:`\mu_B` (for example, :math:`\mu_i \approx 2.2` in bulk iron).
 
 
 The field value in Tesla is multiplied by the gyromagnetic
-ratio, g\*muB/hbar, converting it into a precession frequency in
-rad.THz (in metal units and with muB = 5.788 eV/T).
+ratio, :math:`g \cdot \mu_B/\hbar`, converting it into a precession frequency in
+rad.THz (in metal units and with :math:`\mu_B = 5.788 eV/T`).
 
 As a comparison, the figure below displays the simulation of a
-single spin (of norm mui = 1.0) submitted to an external
-magnetic field of \|Bext\| = 10.0 Tesla (and oriented along the z
+single spin (of norm :math:`\mu_i = 1.0`) submitted to an external
+magnetic field of :math:`\vert B_{ext}\vert = 10.0\; \mathrm{Tesla}` (and oriented along the z
 axis). 
 The upper plot shows the average magnetization along the
 external magnetic field axis and the lower plot the Zeeman
@@ -83,40 +84,52 @@ function for the same parameters.
    :align: center
 
 The temperature effects are accounted for by connecting the spin
-i to a thermal bath using a Langevin thermostat (see 
+:math:`i` to a thermal bath using a Langevin thermostat (see
 :doc:`fix\_langevin\_spin <fix_langevin_spin>` for the definition of 
 this thermostat).
 
 Style *anisotropy* is used to simulate an easy axis or an easy plane
 for the magnetic spins in the defined group:
 
-.. image:: Eqs/force_spin_aniso.jpg
-   :align: center
+.. math::
 
-with n defining the direction of the anisotropy, and K (in eV) its intensity.
-If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
+   H_{aniso}  = -\sum_{{ i}=1}^{N} K_{an}(\mathbf{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2
+
+with :math:`n` defining the direction of the anisotropy, and :math:`K` (in eV) its intensity.
+If :math:`K > 0`, an easy axis is defined, and if :math:`K < 0`, an easy plane is defined.
 
 Style *cubic* is used to simulate a cubic anisotropy, with three
 possible easy axis for the magnetic spins in the defined group:
 
-.. image:: Eqs/fix_spin_cubic.jpg
-   :align: center
+.. math::
 
-with K1 and K2c (in eV) the intensity coefficients and
-n1, n2 and n3 defining the three anisotropic directions
-defined by the command (from n1x to n3z).
-For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
-iron type anisotropy (easy axis along the (001)-type cube
-edges), and K1 > 0 defines a nickel type anisotropy (easy axis
-along the (111)-type cube diagonals).
-K2\^c > 0 also defines easy axis along the (111)-type cube
+   H_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
+   \Big[
+   \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2 +
+   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2 +
+   \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2 \Big]
+   +K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2
+
+with :math:`K_1` and :math:`K_{2c}` (in eV) the intensity coefficients and
+:math:`\vec{n}_1`, :math:`\vec{n}_2` and :math:`\vec{n}_3` defining the three anisotropic directions
+defined by the command (from *n1x* to *n3z*).
+For :math:`\vec{n}_1 = (1 0 0)`, :math:`\vec{n}_2 = (0 1 0)`, and :math:`\vec{n}_3 = (0 0 1)`, :math:`K_1 < 0` defines an
+iron type anisotropy (easy axis along the :math:`(0 0 1)`-type cube
+edges), and :math:`K_1 > 0` defines a nickel type anisotropy (easy axis
+along the :math:`(1 1 1)`-type cube diagonals).
+:math:`K_2^c > 0` also defines easy axis along the :math:`(1 1 1)`-type cube
 diagonals.
 See chapter 2 of :ref:`(Skomski) <Skomski1>` for more details on cubic
 anisotropies.
 
-In all cases, the choice of (x y z) only imposes the vector
+In all cases, the choice of :math:`(x y z)` only imposes the vector
 directions for the forces. Only the direction of the vector is
-important; it's length is ignored (the entered vectors are
+important; its length is ignored (the entered vectors are
 normalized).
 
 Those styles can be combined within one single command line.
@@ -133,7 +146,7 @@ The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this fix
 to add this magnetic potential energy to the potential energy of the system,
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix             1 all precession/spin zeeman 1.0 0.0 0.0 1.0
    fix_modify      1 energy yes
@@ -156,7 +169,9 @@ Related commands
 
 :doc:`atom\_style spin <atom_style>`
 
-**Default:** none
+**Default:**
+
+none
 
 
 ----------
@@ -168,8 +183,3 @@ Related commands
 
 **(Skomski)** Skomski, R. (2008). Simple models of magnetism.
 Oxford University Press.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst
index add69f272c..3bbbed421b 100644
--- a/doc/src/pair_spin_exchange.rst
+++ b/doc/src/pair_spin_exchange.rst
@@ -7,7 +7,7 @@ Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style spin/exchange cutoff
 
@@ -18,10 +18,10 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style spin/exchange 4.0
-   pair_coeff \* \* exchange 4.0 0.0446928 0.003496 1.4885
+   pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
    pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965
 
 Description
@@ -30,38 +30,43 @@ Description
 Style *spin/exchange* computes the exchange interaction between
 pairs of magnetic spins:
 
-.. image:: Eqs/pair_spin_exchange_interaction.jpg
-   :align: center
+.. math::
 
-where si and sj are two neighboring magnetic spins of two particles,
-rij = \|ri - rj\| is the inter-atomic distance between the two particles,
-and
+   H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j 
 
-J(rij) is a function defining the intensity and the sign of the exchange
+where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two neighboring magnetic spins of two particles,
+:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance between the two
+particles. The summation is over pairs of nearest neighbors. 
+:math:`J(r_{ij})` is a function defining the intensity and the sign of the exchange
 interaction for different neighboring shells. This function is defined as:
 
-.. image:: Eqs/pair_spin_exchange_function.jpg
-   :align: center
+.. math::
 
-where a, b and d are the three constant coefficients defined in the associated
-"pair\_coeff" command, and Rc is the radius cutoff associated to
+    {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
+
+where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the associated
+"pair\_coeff" command, and :math:`R_c` is the radius cutoff associated to
 the pair interaction (see below for more explanations).
 
-The coefficients a, b, and d need to be fitted so that the function above matches with
-the value of the exchange interaction for the N neighbor shells taken into account.
+The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function above matches with
+the value of the exchange interaction for the :math:`N` neighbor shells taken into account.
 Examples and more explanations about this function and its parameterization are reported
 in :ref:`(Tranchida) <Tranchida3>`.
 
-From this exchange interaction, each spin i will be submitted
-to a magnetic torque omega, and its associated atom can be submitted to a
-force F for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
+From this exchange interaction, each spin :math:`i` will be submitted
+to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
+force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
 such as:
 
-.. image:: Eqs/pair_spin_exchange_forces.jpg
-   :align: center
+.. math::
 
-with h the Planck constant (in metal units), and eij = (ri - rj)/\|ri-rj\| the unit
-vector between sites i and j.
+   \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} 
+   \left(r_{ij} \right)\,\vec{s}_{j} 
+   ~~{\rm and}~~ 
+   \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}  
+
+with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij} = \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
+vector between sites :math:`i` and :math:`j`.
 
 More details about the derivation of these torques/forces are reported in
 :ref:`(Tranchida) <Tranchida3>`.
@@ -72,14 +77,14 @@ the examples above, or in the data file or restart files read by the
 :doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` commands, and
 set in the following order:
 
-* rc (distance units)
-* a  (energy units)
-* b  (adim parameter)
-* d  (distance units)
+* :math:`R_c` (distance units)
+* :math:`a`  (energy units)
+* :math:`b`  (adim parameter)
+* :math:`d`  (distance units)
 
-Note that rc is the radius cutoff of the considered exchange interaction,
-and a, b and d are the three coefficients performing the parameterization
-of the function J(rij) defined above.
+Note that :math:`R_c` is the radius cutoff of the considered exchange interaction,
+and :math:`a`, :math:`b` and :math:`d` are the three coefficients performing the parameterization
+of the function :math:`J(r_{ij})` defined above.
 
 None of those coefficients is optional. If not specified, the
 *spin/exchange* pair style cannot be used.
@@ -102,7 +107,9 @@ Related commands
 :doc:`atom\_style spin <atom_style>`, :doc:`pair\_coeff <pair_coeff>`,
 :doc:`pair\_eam <pair_eam>`,
 
-**Default:** none
+**Default:**
+
+none
 
 
 ----------
@@ -114,8 +121,3 @@ Related commands
 
 **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
 Journal of Computational Physics, 372, 406-425, (2018).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/src/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst
index caaf4f2326..ecdb8f30f6 100644
--- a/doc/src/pair_spin_neel.rst
+++ b/doc/src/pair_spin_neel.rst
@@ -1,13 +1,13 @@
-.. index:: pair\_style spin/neel
+.. index:: pair_style spin/neel
 
-pair\_style spin/neel command
-=============================
+pair_style spin/neel command
+============================
 
 Syntax
 """"""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style spin/neel cutoff
 
@@ -18,10 +18,10 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    pair_style spin/neel 4.0
-   pair_coeff \* \* neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+   pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
    pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0
 
 Description
@@ -30,28 +30,38 @@ Description
 Style *spin/neel* computes the Neel pair anisotropy model
 between pairs of magnetic spins:
 
-.. image:: Eqs/pair_spin_neel_interaction.jpg
-   :align: center
+.. math::
 
-where si and sj are two neighboring magnetic spins of two particles,
-rij = ri - rj is the inter-atomic distance between the two particles,
-eij = (ri - rj)/\|ri-rj\| is their normalized separation vector and g1,
-q1 and q2 are three functions defining the intensity of the dipolar
+   \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})({\mathbf{e}}_{ij}
+   \cdot {\mathbf{s}}_{j})-\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3} \right)
+   +q_1(r_{ij})\left( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^2 -\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3}\right)
+   \left( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^2 -\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3} \right)
+   + q_2(r_{ij}) \Big( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i}) ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{j})^3 + ({\mathbf{e}}_{ij}\cdot
+   {\mathbf{s}}_{j}) ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^3\Big)
+
+where :math:`\mathbf{s}_i` and :math:`\mathbf{s}_j` are two neighboring magnetic spins of two particles,
+:math:`r_{ij} = \vert \mathbf{r}_i - \mathbf{r}_j \vert` is the inter-atomic distance between the two particles,
+:math:`\mathbf{e}_{ij} = \frac{\mathbf{r}_i - \mathbf{r}_j}{\vert \mathbf{r}_i - \mathbf{r}_j\vert}` is their normalized separation vector and :math:`g_1`,
+:math:`q_1` and :math:`q_2` are three functions defining the intensity of the dipolar
 and quadrupolar contributions, with:
 
-.. image:: Eqs/pair_spin_neel_functions.jpg
-   :align: center
+.. math::
 
-With the functions g(rij) and q(rij) defined and fitted according to
+   g_1(r_{ij}) &= g(r_{ij}) + \frac{12}{35} q(r_{ij}) \\
+   q_1(r_{ij}) &= \frac{9}{5} q(r_{ij}) \\
+   q_2(r_{ij}) &= - \frac{2}{5} q(r_{ij})
+
+With the functions :math:`g(r_{ij})` and :math:`q(r_{ij})` defined and fitted according to
 the same Bethe-Slater function used to fit the exchange interaction:
 
-.. image:: Eqs/pair_spin_exchange_function.jpg
-   :align: center
+.. math::
 
-where a, b and d are the three constant coefficients defined in the
+   {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
+
+where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the
 associated "pair\_coeff" command.
 
-The coefficients a, b, and d need to be fitted so that the function
+The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function
 above matches with the values of the magneto-elastic constant of the
 materials at stake.
 
@@ -59,8 +69,8 @@ Examples and more explanations about this function and its
 parameterization are reported in :ref:`(Tranchida) <Tranchida6>`. More
 examples of parameterization will be provided in future work.
 
-From this DM interaction, each spin i will be submitted to a magnetic
-torque omega and its associated atom to a force F (for spin-lattice
+From this DM interaction, each spin :math:`i` will be submitted to a magnetic
+torque :math:`\mathbf{\omega}` and its associated atom to a force :math:`\mathbf{F}` (for spin-lattice
 calculations only).
 
 More details about the derivation of these torques/forces are reported
@@ -84,7 +94,9 @@ Related commands
 :doc:`atom\_style spin <atom_style>`, :doc:`pair\_coeff <pair_coeff>`,
 :doc:`pair\_eam <pair_eam>`,
 
-**Default:** none
+**Default:**
+
+none
 
 
 ----------
@@ -96,8 +108,3 @@ Related commands
 
 **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
 Journal of Computational Physics, 372, 406-425, (2018).
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
diff --git a/doc/txt/compute_spin.txt b/doc/txt/compute_spin.txt
deleted file mode 100644
index dddbc856c4..0000000000
--- a/doc/txt/compute_spin.txt
+++ /dev/null
@@ -1,75 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-compute spin command :h3
-
-[Syntax:]
-
-compute ID group-ID spin :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-spin = style name of this compute command :ul
-
-[Examples:]
-
-compute out_mag all spin :pre
-
-[Description:]
-
-Define a computation that calculates magnetic quantities for a system
-of atoms having spins.
-
-This compute calculates the following 6 magnetic quantities:
-
-the three first quantities are the x,y and z coordinates of the total
-magnetization, :ulb,l
-the fourth quantity is the norm of the total magnetization, :l
-The fifth quantity is the magnetic energy (in eV), :l
-The sixth one is referred to as the spin temperature, according
-to the work of "(Nurdin)"_#Nurdin1. :l
-:ule
-
-The simplest way to output the results of the compute spin calculation
-is to define some of the quantities as variables, and to use the thermo and
-thermo_style commands, for example:
-
-compute out_mag         all spin :pre
-
-variable mag_z          equal c_out_mag\[3\]
-variable mag_norm       equal c_out_mag\[4\]
-variable temp_mag       equal c_out_mag\[6\] :pre
-
-thermo                  10
-thermo_style            custom step v_mag_z v_mag_norm v_temp_mag :pre
-
-This series of commands evaluates the total magnetization along z, the norm of
-the total magnetization, and the magnetic temperature. Three variables are
-assigned to those quantities. The thermo and thermo_style commands print them
-every 10 timesteps.
-
-[Output info:]
-
-The array values are "intensive".  The array values will be in
-metal units ("units"_units.html).
-
-[Restrictions:]
-
-The {spin} compute is part of the SPIN package.  This compute is only
-enabled if LAMMPS was built with this package.  See the "Build
-package"_Build_package.html doc page for more info.  The atom_style
-has to be "spin" for this compute to be valid.
-
-[Related commands:] none
-
-[Default:] none
-
-:line
-
-:link(Nurdin1)
-[(Nurdin)] Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
-
diff --git a/doc/txt/fix_precession_spin.txt b/doc/txt/fix_precession_spin.txt
deleted file mode 100644
index 152f717155..0000000000
--- a/doc/txt/fix_precession_spin.txt
+++ /dev/null
@@ -1,143 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix precession/spin command :h3
-
-[Syntax:]
-
-fix ID group precession/spin style args :pre
-
-ID, group are documented in "fix"_fix.html command :ulb,l
-precession/spin = style name of this fix command :l
-style = {zeeman} or {anisotropy} or {cubic} :l
-  {zeeman} args = H x y z
-    H = intensity of the magnetic field (in Tesla)
-    x y z = vector direction of the field
-  {anisotropy} args = K x y z
-    K = intensity of the magnetic anisotropy (in eV)
-    x y z = vector direction of the anisotropy :pre
-  {cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z
-    K1 and K2c = intensity of the magnetic anisotropy (in eV)
-    n1x to n3z = three direction vectors of the cubic anisotropy :pre
-:ule
-
-[Examples:]
-
-fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
-fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
-fix 1 iron precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
-fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre
-
-[Description:]
-
-This fix applies a precession torque to each magnetic spin in the group.
-
-Style {zeeman} is used for the simulation of the interaction
-between the magnetic spins in the defined group and an external
-magnetic field:
-
-:c,image(Eqs/fix_spin_zeeman.jpg)
-
-with:
-
-Bext the external magnetic field (in T) :ulb,l
-g the Lande factor (hard-coded as g=2.0) :l
-si the unitary vector describing the orientation of spin i :l
-mui the atomic moment of spin i given as a multiple of the
-Bohr magneton muB (for example, mui ~ 2.2 in bulk iron).  :l
-:ule
-
-The field value in Tesla is multiplied by the gyromagnetic
-ratio, g*muB/hbar, converting it into a precession frequency in
-rad.THz (in metal units and with muB = 5.788 eV/T).
-
-As a comparison, the figure below displays the simulation of a
-single spin (of norm mui = 1.0) submitted to an external
-magnetic field of |Bext| = 10.0 Tesla (and oriented along the z
-axis). 
-The upper plot shows the average magnetization along the
-external magnetic field axis and the lower plot the Zeeman
-energy, both as a function of temperature.
-The reference result is provided by the plot of the Langevin 
-function for the same parameters.
-
-:c,image(JPG/zeeman_langevin.jpg)
-
-The temperature effects are accounted for by connecting the spin
-i to a thermal bath using a Langevin thermostat (see 
-"fix_langevin_spin"_fix_langevin_spin.html for the definition of 
-this thermostat).
-
-Style {anisotropy} is used to simulate an easy axis or an easy plane
-for the magnetic spins in the defined group:
-
-:c,image(Eqs/force_spin_aniso.jpg)
-
-with n defining the direction of the anisotropy, and K (in eV) its intensity.
-If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
-
-Style {cubic} is used to simulate a cubic anisotropy, with three
-possible easy axis for the magnetic spins in the defined group:
-
-:c,image(Eqs/fix_spin_cubic.jpg)
-
-with K1 and K2c (in eV) the intensity coefficients and
-n1, n2 and n3 defining the three anisotropic directions
-defined by the command (from n1x to n3z).
-For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
-iron type anisotropy (easy axis along the (001)-type cube
-edges), and K1 > 0 defines a nickel type anisotropy (easy axis
-along the (111)-type cube diagonals).
-K2^c > 0 also defines easy axis along the (111)-type cube
-diagonals.
-See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic
-anisotropies.
-
-In all cases, the choice of (x y z) only imposes the vector
-directions for the forces. Only the direction of the vector is
-important; it's length is ignored (the entered vectors are
-normalized).
-
-Those styles can be combined within one single command line.
-
-:line
-
-[Restart, fix_modify, output, run start/stop, minimize info:]
-
-By default, the energy associated to this fix is not added to the potential
-energy of the system.
-The "fix_modify"_fix_modify.html {energy} option is supported by this fix
-to add this magnetic potential energy to the potential energy of the system,
-
-fix             1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix_modify      1 energy yes :pre
-
-This fix computes a global scalar which can be accessed by various
-"output commands"_Howto_output.html.
-
-No information about this fix is written to "binary restart
-files"_restart.html.
-
-[Restrictions:]
-
-The {precession/spin} style is part of the SPIN package.  This style
-is only enabled if LAMMPS was built with this package, and if the
-atom_style "spin" was declared.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"atom_style spin"_atom_style.html
-
-[Default:] none
-
-:line
-
-:link(Skomski1)
-[(Skomski)] Skomski, R. (2008). Simple models of magnetism.
-Oxford University Press.
diff --git a/doc/txt/pair_spin_exchange.txt b/doc/txt/pair_spin_exchange.txt
deleted file mode 100644
index d8e22539de..0000000000
--- a/doc/txt/pair_spin_exchange.txt
+++ /dev/null
@@ -1,100 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style spin/exchange command :h3
-
-[Syntax:]
-
-pair_style spin/exchange cutoff :pre
-
-cutoff = global cutoff pair (distance in metal units) :ulb,l
-
-:ule
-
-[Examples:]
-
-pair_style spin/exchange 4.0
-pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
-pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre
-
-[Description:]
-
-Style {spin/exchange} computes the exchange interaction between
-pairs of magnetic spins:
-
-:c,image(Eqs/pair_spin_exchange_interaction.jpg)
-
-where si and sj are two neighboring magnetic spins of two particles,
-rij = |ri - rj| is the inter-atomic distance between the two
-particles. The summation is over pairs of nearest neighbors. 
-J(rij) is a function defining the intensity and the sign of the exchange
-interaction for different neighboring shells. This function is defined as:
-
-:c,image(Eqs/pair_spin_exchange_function.jpg)
-
-where a, b and d are the three constant coefficients defined in the associated
-"pair_coeff" command, and Rc is the radius cutoff associated to
-the pair interaction (see below for more explanations).
-
-The coefficients a, b, and d need to be fitted so that the function above matches with
-the value of the exchange interaction for the N neighbor shells taken into account.
-Examples and more explanations about this function and its parameterization are reported
-in "(Tranchida)"_#Tranchida3.
-
-From this exchange interaction, each spin i will be submitted
-to a magnetic torque omega, and its associated atom can be submitted to a
-force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html),
-such as:
-
-:c,image(Eqs/pair_spin_exchange_forces.jpg)
-
-with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit
-vector between sites i and j.
-
-More details about the derivation of these torques/forces are reported in
-"(Tranchida)"_#Tranchida3.
-
-For the {spin/exchange} pair style, the following coefficients must be defined
-for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
-the examples above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html commands, and
-set in the following order:
-
-rc (distance units)
-a  (energy units)
-b  (adim parameter)
-d  (distance units) :ul
-
-Note that rc is the radius cutoff of the considered exchange interaction,
-and a, b and d are the three coefficients performing the parameterization
-of the function J(rij) defined above.
-
-None of those coefficients is optional. If not specified, the
-{spin/exchange} pair style cannot be used.
-
-:line
-
-[Restrictions:]
-
-All the {pair/spin} styles are part of the SPIN package.  These styles
-are only enabled if LAMMPS was built with this package, and if the
-atom_style "spin" was declared.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
-"pair_eam"_pair_eam.html,
-
-[Default:] none
-
-:line
-
-:link(Tranchida3)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, 372, 406-425, (2018).
diff --git a/doc/txt/pair_spin_neel.txt b/doc/txt/pair_spin_neel.txt
deleted file mode 100644
index b255f23a09..0000000000
--- a/doc/txt/pair_spin_neel.txt
+++ /dev/null
@@ -1,83 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style spin/neel command :h3
-
-[Syntax:]
-
-pair_style spin/neel cutoff :pre
-
-cutoff = global cutoff pair (distance in metal units) :ulb,l
-
-:ule
-
-[Examples:]
-
-pair_style spin/neel 4.0
-pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
-pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre
-
-[Description:]
-
-Style {spin/neel} computes the Neel pair anisotropy model
-between pairs of magnetic spins:
-
-:c,image(Eqs/pair_spin_neel_interaction.jpg)
-
-where si and sj are two neighboring magnetic spins of two particles,
-rij = ri - rj is the inter-atomic distance between the two particles,
-eij = (ri - rj)/|ri-rj| is their normalized separation vector and g1,
-q1 and q2 are three functions defining the intensity of the dipolar
-and quadrupolar contributions, with:
-
-:c,image(Eqs/pair_spin_neel_functions.jpg)
-
-With the functions g(rij) and q(rij) defined and fitted according to
-the same Bethe-Slater function used to fit the exchange interaction:
-
-:c,image(Eqs/pair_spin_exchange_function.jpg)
-
-where a, b and d are the three constant coefficients defined in the
-associated "pair_coeff" command.
-
-The coefficients a, b, and d need to be fitted so that the function
-above matches with the values of the magneto-elastic constant of the
-materials at stake.
-
-Examples and more explanations about this function and its
-parameterization are reported in "(Tranchida)"_#Tranchida6. More
-examples of parameterization will be provided in future work.
-
-From this DM interaction, each spin i will be submitted to a magnetic
-torque omega and its associated atom to a force F (for spin-lattice
-calculations only).
-
-More details about the derivation of these torques/forces are reported
-in "(Tranchida)"_#Tranchida6.
-
-:line
-
-[Restrictions:]
-
-All the {pair/spin} styles are part of the SPIN package.  These styles
-are only enabled if LAMMPS was built with this package, and if the
-atom_style "spin" was declared.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
-"pair_eam"_pair_eam.html,
-
-[Default:] none
-
-:line
-
-:link(Tranchida6)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, 372, 406-425, (2018).

From 0c29c2827a062fe9d3bc6dacdfe5e783149c5057 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 29 Nov 2019 10:16:22 -0500
Subject: [PATCH 082/199] check if one of the required defines is set and
 correct dependent API check

---
 src/library.h | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/library.h b/src/library.h
index 5ff10faf6f..bda55e9068 100644
--- a/src/library.h
+++ b/src/library.h
@@ -16,6 +16,10 @@
    new LAMMPS-specific functions can be added
 */
 
+#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)
+#error Must define LAMMPS_BIGBIG, LAMMPS_SMALLBIG, or LAMMPS_SMALLSMALL
+#endif
+
 #include <mpi.h>
 #if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
 #include <inttypes.h>  /* for int64_t */
@@ -58,10 +62,10 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
 void lammps_scatter_atoms(void *, char *, int, int, void *);
 void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
 
-#ifdef LAMMPS_BIGBIG
+#if defined(LAMMPS_BIGBIG)
 typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
 void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
-#elif LAMMPS_SMALLBIG
+#elif defined(LAMMPS_SMALLBIG)
 typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
 void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
 #else

From 914070070154a6c80bec9d2b69fc22fb08924846 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 29 Nov 2019 10:37:30 -0500
Subject: [PATCH 083/199] rather than abort with an error, assume
 -DLAMMPS_SMALLBIG if no define is set

---
 src/library.h | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/library.h b/src/library.h
index bda55e9068..53ce45d46c 100644
--- a/src/library.h
+++ b/src/library.h
@@ -16,8 +16,12 @@
    new LAMMPS-specific functions can be added
 */
 
+/*
+ * Follow the behavior of regular LAMMPS compilation and assume
+ * -DLAMMPS_SMALLBIG when no define is set.
+ */
 #if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)
-#error Must define LAMMPS_BIGBIG, LAMMPS_SMALLBIG, or LAMMPS_SMALLSMALL
+#define LAMMPS_SMALLBIG
 #endif
 
 #include <mpi.h>

From acf02bb1a35608080bcb3072d6cb3d0f7cbe2370 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sun, 1 Dec 2019 14:50:29 -0500
Subject: [PATCH 084/199] Revert split of Commands_bond.rst as requested by
 @sjplimp

---
 doc/src/Commands.rst          |   3 -
 doc/src/Commands_all.rst      |   8 +-
 doc/src/Commands_angle.rst    |  55 --------------
 doc/src/Commands_bond.rst     | 133 ++++++++++++++++++++++++++++++++--
 doc/src/Commands_compute.rst  |   8 +-
 doc/src/Commands_dihedral.rst |  51 -------------
 doc/src/Commands_fix.rst      |   8 +-
 doc/src/Commands_improper.rst |  46 ------------
 doc/src/Commands_kspace.rst   |   8 +-
 doc/src/Commands_pair.rst     |   8 +-
 10 files changed, 146 insertions(+), 182 deletions(-)
 delete mode 100644 doc/src/Commands_angle.rst
 delete mode 100644 doc/src/Commands_dihedral.rst
 delete mode 100644 doc/src/Commands_improper.rst

diff --git a/doc/src/Commands.rst b/doc/src/Commands.rst
index 79fa30003d..f192d6a59d 100644
--- a/doc/src/Commands.rst
+++ b/doc/src/Commands.rst
@@ -21,9 +21,6 @@ commands in it are used to define a LAMMPS simulation.
    Commands_compute
    Commands_pair
    Commands_bond
-   Commands_angle
-   Commands_dihedral
-   Commands_improper
    Commands_kspace
 
 .. toctree::
diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst
index b9f5578137..d47c3299d0 100644
--- a/doc/src/Commands_all.rst
+++ b/doc/src/Commands_all.rst
@@ -5,10 +5,10 @@
    * :doc:`Fix styles <Commands_fix>`
    * :doc:`Compute styles <Commands_compute>`
    * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
 General commands
diff --git a/doc/src/Commands_angle.rst b/doc/src/Commands_angle.rst
deleted file mode 100644
index ca5e96d57e..0000000000
--- a/doc/src/Commands_angle.rst
+++ /dev/null
@@ -1,55 +0,0 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-
-
-.. _angle:
-
-Angle\_style potentials
-=======================
-
-All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-.. table_from_list::
-   :columns: 4
-
-   * :doc:`none <angle_none>`
-   * :doc:`zero <angle_zero>`
-   * :doc:`hybrid <angle_hybrid>`
-   *
-   *
-   *
-   *
-   *
-   * :doc:`charmm (iko) <angle_charmm>`
-   * :doc:`class2 (ko) <angle_class2>`
-   * :doc:`class2/p6 <angle_class2>`
-   * :doc:`cosine (ko) <angle_cosine>`
-   * :doc:`cosine/buck6d <angle_cosine_buck6d>`
-   * :doc:`cosine/delta (o) <angle_cosine_delta>`
-   * :doc:`cosine/periodic (o) <angle_cosine_periodic>`
-   * :doc:`cosine/shift (o) <angle_cosine_shift>`
-   * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
-   * :doc:`cosine/squared (o) <angle_cosine_squared>`
-   * :doc:`cross <angle_cross>`
-   * :doc:`dipole (o) <angle_dipole>`
-   * :doc:`fourier (o) <angle_fourier>`
-   * :doc:`fourier/simple (o) <angle_fourier_simple>`
-   * :doc:`harmonic (iko) <angle_harmonic>`
-   * :doc:`mm3 <angle_mm3>`
-   * :doc:`quartic (o) <angle_quartic>`
-   * :doc:`sdk (o) <angle_sdk>`
-   * :doc:`table (o) <angle_table>`
-   *
diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
index a7e22274e9..dbf7344394 100644
--- a/doc/src/Commands_bond.rst
+++ b/doc/src/Commands_bond.rst
@@ -5,18 +5,18 @@
    * :doc:`Fix styles <Commands_fix>`
    * :doc:`Compute styles <Commands_compute>`
    * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
 .. _bond:
 
-Bond\_style potentials
-=================================
+bond_style potentials
+=====================
 
-All LAMMPS :doc:`bond\_style <bond_style>` commands.  Some styles have
+All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
@@ -48,3 +48,122 @@ OPT.
    * :doc:`table (o) <bond_table>`
    *
    *
+
+---
+
+.. _angle:
+
+angle_style potentials
+======================
+
+All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <angle_none>`
+   * :doc:`zero <angle_zero>`
+   * :doc:`hybrid <angle_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <angle_charmm>`
+   * :doc:`class2 (ko) <angle_class2>`
+   * :doc:`class2/p6 <angle_class2>`
+   * :doc:`cosine (ko) <angle_cosine>`
+   * :doc:`cosine/buck6d <angle_cosine_buck6d>`
+   * :doc:`cosine/delta (o) <angle_cosine_delta>`
+   * :doc:`cosine/periodic (o) <angle_cosine_periodic>`
+   * :doc:`cosine/shift (o) <angle_cosine_shift>`
+   * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
+   * :doc:`cosine/squared (o) <angle_cosine_squared>`
+   * :doc:`cross <angle_cross>`
+   * :doc:`dipole (o) <angle_dipole>`
+   * :doc:`fourier (o) <angle_fourier>`
+   * :doc:`fourier/simple (o) <angle_fourier_simple>`
+   * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`mm3 <angle_mm3>`
+   * :doc:`quartic (o) <angle_quartic>`
+   * :doc:`sdk (o) <angle_sdk>`
+   * :doc:`table (o) <angle_table>`
+   *
+
+---
+
+.. _dihedral:
+
+dihedral_style potentials
+=========================
+
+All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <dihedral_none>`
+   * :doc:`zero <dihedral_zero>`
+   * :doc:`hybrid <dihedral_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <dihedral_charmm>`
+   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`class2 (ko) <dihedral_class2>`
+   * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
+   * :doc:`fourier (io) <dihedral_fourier>`
+   * :doc:`harmonic (iko) <dihedral_harmonic>`
+   * :doc:`helix (o) <dihedral_helix>`
+   * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
+   * :doc:`nharmonic (o) <dihedral_nharmonic>`
+   * :doc:`opls (iko) <dihedral_opls>`
+   * :doc:`quadratic (o) <dihedral_quadratic>`
+   * :doc:`spherical <dihedral_spherical>`
+   * :doc:`table (o) <dihedral_table>`
+   * :doc:`table/cut <dihedral_table_cut>`
+   *
+   *
+
+.. _improper:
+
+improper_style potentials
+=========================
+
+All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <improper_none>`
+   * :doc:`zero <improper_zero>`
+   * :doc:`hybrid <improper_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <improper_class2>`
+   * :doc:`cossq (o) <improper_cossq>`
+   * :doc:`cvff (io) <improper_cvff>`
+   * :doc:`distance <improper_distance>`
+   * :doc:`distharm <improper_distharm>`
+   * :doc:`fourier (o) <improper_fourier>`
+   * :doc:`harmonic (iko) <improper_harmonic>`
+   * :doc:`inversion/harmonic <improper_inversion_harmonic>`
+   * :doc:`ring (o) <improper_ring>`
+   * :doc:`sqdistharm <improper_sqdistharm>`
+   * :doc:`umbrella (o) <improper_umbrella>`
+   *
diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index 1b3465eb53..a5093f1985 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -5,10 +5,10 @@
    * :doc:`Fix styles <Commands_fix>`
    * :doc:`Compute styles <Commands_compute>`
    * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
 Compute commands
diff --git a/doc/src/Commands_dihedral.rst b/doc/src/Commands_dihedral.rst
deleted file mode 100644
index 84ddb3d004..0000000000
--- a/doc/src/Commands_dihedral.rst
+++ /dev/null
@@ -1,51 +0,0 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-
-.. _dihedral:
-
-Dihedral\_style potentials
-==========================
-
-All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-
-.. table_from_list::
-   :columns: 4
-
-   * :doc:`none <dihedral_none>`
-   * :doc:`zero <dihedral_zero>`
-   * :doc:`hybrid <dihedral_hybrid>`
-   *
-   *
-   *
-   *
-   *
-   * :doc:`charmm (iko) <dihedral_charmm>`
-   * :doc:`charmmfsw <dihedral_charmm>`
-   * :doc:`class2 (ko) <dihedral_class2>`
-   * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
-   * :doc:`fourier (io) <dihedral_fourier>`
-   * :doc:`harmonic (iko) <dihedral_harmonic>`
-   * :doc:`helix (o) <dihedral_helix>`
-   * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
-   * :doc:`nharmonic (o) <dihedral_nharmonic>`
-   * :doc:`opls (iko) <dihedral_opls>`
-   * :doc:`quadratic (o) <dihedral_quadratic>`
-   * :doc:`spherical <dihedral_spherical>`
-   * :doc:`table (o) <dihedral_table>`
-   * :doc:`table/cut <dihedral_table_cut>`
-   *
-   *
diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index 11ae9a4a38..4cd9a4487c 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -5,10 +5,10 @@
    * :doc:`Fix styles <Commands_fix>`
    * :doc:`Compute styles <Commands_compute>`
    * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
 Fix commands
diff --git a/doc/src/Commands_improper.rst b/doc/src/Commands_improper.rst
deleted file mode 100644
index 7bbfa5b01b..0000000000
--- a/doc/src/Commands_improper.rst
+++ /dev/null
@@ -1,46 +0,0 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-
-.. _improper:
-
-Improper\_style potentials
-=========================================
-
-All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-.. table_from_list::
-   :columns: 4
-
-   * :doc:`none <improper_none>`
-   * :doc:`zero <improper_zero>`
-   * :doc:`hybrid <improper_hybrid>`
-   *
-   *
-   *
-   *
-   *
-   * :doc:`class2 (ko) <improper_class2>`
-   * :doc:`cossq (o) <improper_cossq>`
-   * :doc:`cvff (io) <improper_cvff>`
-   * :doc:`distance <improper_distance>`
-   * :doc:`distharm <improper_distharm>`
-   * :doc:`fourier (o) <improper_fourier>`
-   * :doc:`harmonic (iko) <improper_harmonic>`
-   * :doc:`inversion/harmonic <improper_inversion_harmonic>`
-   * :doc:`ring (o) <improper_ring>`
-   * :doc:`sqdistharm <improper_sqdistharm>`
-   * :doc:`umbrella (o) <improper_umbrella>`
-   *
diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst
index 62e97f1a6a..fc2418ecf7 100644
--- a/doc/src/Commands_kspace.rst
+++ b/doc/src/Commands_kspace.rst
@@ -5,10 +5,10 @@
    * :doc:`Fix styles <Commands_fix>`
    * :doc:`Compute styles <Commands_compute>`
    * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
 KSpace solvers
diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index c65164c02d..b4371420a7 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -5,10 +5,10 @@
    * :doc:`Fix styles <Commands_fix>`
    * :doc:`Compute styles <Commands_compute>`
    * :doc:`Pair styles <Commands_pair>`
-   * :doc:`Bond styles <Commands_bond>`
-   * :doc:`Angle styles <Commands_angle>`
-   * :doc:`Dihedral styles <Commands_dihedral>`
-   * :doc:`Improper styles <Commands_improper>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
 Pair\_style potentials

From dfcb4edca7dec9d71ab6fd71851c0ba64fc7518d Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Sun, 1 Dec 2019 15:26:16 -0500
Subject: [PATCH 085/199] Fix trailing whitespace

---
 src/SNAP/compute_snap.cpp | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 1a34c8cbc5..11e8bd0d12 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -19,8 +19,8 @@
 -DONE: size_array_rows = 1 + total number of atoms + 6
 -DONE: size_peratom = (3+6)*nperdim*ntypes
 INCOMPLETE: Mappy from local to global
-INCOMPLETE: modify->find_compute() 
-DONE: eliminate local peratom array for viral, replace with fdotr 
+INCOMPLETE: modify->find_compute()
+DONE: eliminate local peratom array for viral, replace with fdotr
 
  */
 #include "compute_snap.h"
@@ -191,7 +191,7 @@ void ComputeSnap::init()
                  "snap:snapall");
   array = snapall;
 
-  // INCOMPLETE: modify->find_compute() 
+  // INCOMPLETE: modify->find_compute()
   // was called 223960 times by snappy Ta example
   // that is over 600 times per config?
   // how is this possible???
@@ -397,7 +397,7 @@ void ComputeSnap::compute_array()
       }
 
       // Accumulate Bi
-      
+
       // linear contributions
 
       for (int icoeff = 0; icoeff < ncoeff; icoeff++)
@@ -458,24 +458,24 @@ void ComputeSnap::compute_array()
 
   int irow = 0;
   double reference_energy = c_pe->compute_scalar();
-  snapall[irow++][lastcol] = reference_energy; 
+  snapall[irow++][lastcol] = reference_energy;
 
   // assign virial stress to last column
   // switch to Voigt notation
 
   c_virial->compute_vector();
   irow += 3*natoms;
-  snapall[irow++][lastcol] = c_virial->vector[0]; 
-  snapall[irow++][lastcol] = c_virial->vector[1]; 
-  snapall[irow++][lastcol] = c_virial->vector[2]; 
-  snapall[irow++][lastcol] = c_virial->vector[5]; 
-  snapall[irow++][lastcol] = c_virial->vector[4]; 
-  snapall[irow++][lastcol] = c_virial->vector[3]; 
+  snapall[irow++][lastcol] = c_virial->vector[0];
+  snapall[irow++][lastcol] = c_virial->vector[1];
+  snapall[irow++][lastcol] = c_virial->vector[2];
+  snapall[irow++][lastcol] = c_virial->vector[5];
+  snapall[irow++][lastcol] = c_virial->vector[4];
+  snapall[irow++][lastcol] = c_virial->vector[3];
 
 }
 
 /* ----------------------------------------------------------------------
-   compute global virial contributions via summing r_i.dB^j/dr_i over 
+   compute global virial contributions via summing r_i.dB^j/dr_i over
    own & ghost atoms
 ------------------------------------------------------------------------- */
 
@@ -515,9 +515,9 @@ void ComputeSnap::dbdotr_compute()
 double ComputeSnap::memory_usage()
 {
 
-  double bytes = size_array_rows*size_array_cols * 
+  double bytes = size_array_rows*size_array_cols *
     sizeof(double);                                     // snap
-  bytes += size_array_rows*size_array_cols * 
+  bytes += size_array_rows*size_array_cols *
     sizeof(double);                                     // snapall
   bytes += nmax*size_peratom * sizeof(double);          // snap_peratom
   bytes += snaptr->memory_usage();                      // SNA object

From 36e102516fcc36b7cd6741dd8987263260087e9f Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Mon, 2 Dec 2019 10:34:03 -0500
Subject: [PATCH 086/199] angle constraint bugfix

ghost atom fix
---
 src/USER-MISC/fix_bond_react.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 33aab5b4ad..3b5719156a 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1675,6 +1675,7 @@ int FixBondReact::check_constraints()
         delx1 = x[atom1][0] - x[atom2][0];
         dely1 = x[atom1][1] - x[atom2][1];
         delz1 = x[atom1][2] - x[atom2][2];
+        domain->minimum_image(delx1,dely1,delz1); // ghost location fix
         rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
         r1 = sqrt(rsq1);
 
@@ -1682,6 +1683,7 @@ int FixBondReact::check_constraints()
         delx2 = x[atom3][0] - x[atom2][0];
         dely2 = x[atom3][1] - x[atom2][1];
         delz2 = x[atom3][2] - x[atom2][2];
+        domain->minimum_image(delx2,dely2,delz2); // ghost location fix
         rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
         r2 = sqrt(rsq2);
 

From 819fe9ec5668319fb17c465e8998c3cf21f9379c Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Mon, 2 Dec 2019 12:27:57 -0500
Subject: [PATCH 087/199] add option to enforce atom chirality

---
 src/USER-MISC/fix_bond_react.cpp | 94 +++++++++++++++++++++++++++++++-
 src/USER-MISC/fix_bond_react.h   | 17 +++++-
 2 files changed, 109 insertions(+), 2 deletions(-)

diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 3b5719156a..dbdb8ef0a7 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -36,6 +36,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
 #include "group.h"
 #include "citeme.h"
 #include "math_const.h"
+#include "math_extra.h"
 #include "memory.h"
 #include "error.h"
 
@@ -297,6 +298,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
   memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges");
   memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
+  memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms");
 
   for (int j = 0; j < nreacts; j++)
     for (int i = 0; i < max_natoms; i++) {
@@ -304,6 +306,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
       if (update_edges_flag[j] == 1) custom_edges[i][j] = 1;
       else custom_edges[i][j] = 0;
       delete_atoms[i][j] = 0;
+      for (int k = 0; k < 6; k++) {
+        chiral_atoms[i][k][j] = 0;
+      }
     }
 
   // read all map files afterward
@@ -430,6 +435,7 @@ FixBondReact::~FixBondReact()
   memory->destroy(landlocked_atoms);
   memory->destroy(custom_edges);
   memory->destroy(delete_atoms);
+  memory->destroy(chiral_atoms);
 
   memory->destroy(nevery);
   memory->destroy(cutsq);
@@ -1649,10 +1655,11 @@ evaluate constraints: return 0 if any aren't satisfied
 int FixBondReact::check_constraints()
 {
   tagint atom1,atom2,atom3;
-  double delx,dely,delz,rsq;
+  double unwrap[3],delx,dely,delz,rsq;
   double delx1,dely1,delz1,delx2,dely2,delz2;
   double rsq1,rsq2,r1,r2,c,t,prrhob;
 
+  imageint *image = atom->image;
   double **x = atom->x;
 
   for (int i = 0; i < nconstraints; i++) {
@@ -1701,6 +1708,30 @@ int FixBondReact::check_constraints()
       }
     }
   }
+
+  // let's also check chirality within 'check_constraint'
+  for (int i = 0; i < onemol->natoms; i++) {
+    if (chiral_atoms[i][0][rxnID] == 1) {
+      double my4coords[12];
+      // already ensured, by transitive property, that chiral simulation atom has four neighs
+      for (int j = 0; j < 4; j++) {
+        atom1 = atom->map(glove[i][1]);
+        // loop over known types involved in chiral center
+        for (int jj = 0; jj < 4; jj++) {
+          if (atom->type[atom->map(xspecial[atom1][j])] == chiral_atoms[i][jj+2][rxnID]) {
+            atom2 = atom->map(xspecial[atom1][j]);
+            domain->unmap(x[atom2],image[atom2],unwrap);
+            for (int k = 0; k < 3; k++) {
+              my4coords[3*jj+k] = unwrap[k];
+            }
+            break;
+          }
+        }
+      }
+      if (get_chirality(my4coords) != chiral_atoms[i][1][rxnID]) return 0;
+    }
+  }
+
   return 1;
 }
 
@@ -1741,6 +1772,33 @@ double FixBondReact::get_temperature()
   return t;
 }
 
+/* ----------------------------------------------------------------------
+return handedness (1 or -1) of a chiral center, given ordered set of coordinates
+------------------------------------------------------------------------- */
+
+int FixBondReact::get_chirality(double four_coords[12])
+{
+  // define oriented plane with first three coordinates
+  double vec1[3],vec2[3],vec3[3],vec4[3],mean3[3],dot;
+
+  for (int i = 0; i < 3; i++) {
+    vec1[i] = four_coords[i]-four_coords[i+3];
+    vec2[i] = four_coords[i+3]-four_coords[i+6];
+  }
+
+  MathExtra::cross3(vec1,vec2,vec3);
+
+  for (int i = 0; i < 3; i++) {
+    mean3[i] = (four_coords[i] + four_coords[i+3] +
+                                 four_coords[i+6])/3;
+    vec4[i] = four_coords[i+9] - mean3[i];
+  }
+
+  dot = MathExtra::dot3(vec3,vec4);
+  dot = dot/fabs(dot);
+  return (int) dot;
+}
+
 /* ----------------------------------------------------------------------
   Get xspecials for current molecule templates
 ------------------------------------------------------------------------- */
@@ -2869,6 +2927,7 @@ void FixBondReact::read(int myrxn)
     }
     else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
     else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
+    else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral);
     else if (strstr(line,"constraints")) {
       sscanf(line,"%d",&nconstr);
       memory->grow(constraints,nconstraints+nconstr,MAXCONARGS,"bond/react:constraints");
@@ -2900,6 +2959,8 @@ void FixBondReact::read(int myrxn)
       CustomEdges(line, myrxn);
     } else if (strcmp(keyword,"DeleteIDs") == 0) {
       DeleteAtoms(line, myrxn);
+    } else if (strcmp(keyword,"ChiralIDs") == 0) {
+      ChiralCenters(line, myrxn);
     } else if (strcmp(keyword,"Constraints") == 0) {
       Constraints(line, myrxn);
     } else error->one(FLERR,"Bond/react: Unknown section in map file");
@@ -2977,6 +3038,37 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn)
   }
 }
 
+void FixBondReact::ChiralCenters(char *line, int myrxn)
+{
+  int tmp;
+  for (int i = 0; i < nchiral; i++) {
+    readline(line);
+    sscanf(line,"%d",&tmp);
+    chiral_atoms[tmp-1][0][myrxn] = 1;
+    if (onemol->xflag == 0)
+      error->one(FLERR,"Bond/react: Molecule template 'Coords' section required for chiralIDs keyword");
+    if ((int) onemol_nxspecial[tmp-1][0] != 4)
+      error->one(FLERR,"Bond/react: Chiral atoms must have exactly four first neighbors");
+    for (int j = 0; j < 4; j++) {
+      for (int k = j+1; k < 4; k++) {
+        if (onemol->type[onemol_xspecial[tmp-1][j]-1] ==
+            onemol->type[onemol_xspecial[tmp-1][k]-1])
+          error->one(FLERR,"Bond/react: First neighbors of chiral atoms must be of mutually different types");
+      }
+    }
+    // record order of atom types, and coords
+    double my4coords[12];
+    for (int j = 0; j < 4; j++) {
+      chiral_atoms[tmp-1][j+2][myrxn] = onemol->type[onemol_xspecial[tmp-1][j]-1];
+      for (int k = 0; k < 3; k++) {
+        my4coords[3*j+k] = onemol->x[onemol_xspecial[tmp-1][j]-1][k];
+      }
+    }
+    // get orientation
+    chiral_atoms[tmp-1][1][myrxn] = get_chirality(my4coords);
+  }
+}
+
 void FixBondReact::Constraints(char *line, int myrxn)
 {
   double tmp[MAXCONARGS];
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
index f59e051ed1..a5bf2bc587 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-MISC/fix_bond_react.h
@@ -110,7 +110,7 @@ class FixBondReact : public Fix {
 
   int *ibonding,*jbonding;
   int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
-  int nedge,nequivalent,ncustom,ndelete,nconstr; // # edge, equivalent, custom atoms in mapping file
+  int nedge,nequivalent,ncustom,ndelete,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file
   int attempted_rxn; // there was an attempt!
   int *local_rxn_count;
   int *ghostly_rxn_count;
@@ -126,6 +126,7 @@ class FixBondReact : public Fix {
   int **landlocked_atoms; // all atoms at least three bonds away from edge atoms
   int **custom_edges; // atoms in molecule templates with incorrect valences
   int **delete_atoms; // atoms in pre-reacted templates to delete
+  int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types
 
   int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors
   tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list
@@ -149,6 +150,7 @@ class FixBondReact : public Fix {
   void Equivalences(char *,int);
   void CustomEdges(char *,int);
   void DeleteAtoms(char *,int);
+  void ChiralCenters(char *,int);
   void Constraints(char *,int);
 
   void make_a_guess ();
@@ -159,6 +161,7 @@ class FixBondReact : public Fix {
   void ring_check();
   int check_constraints();
   double get_temperature();
+  int get_chirality(double[12]); // get handedness given an ordered set of coordinates
 
   void open(char *);
   void readline(char *);
@@ -249,6 +252,18 @@ E: Bond/react: A deleted atom cannot remain bonded to an atom that is not delete
 
 Self-explanatory.
 
+E: Bond/react: First neighbors of chiral atoms must be of mutually different types
+
+Self-explanatory.
+
+E: Bond/react: Chiral atoms must have exactly four first neighbors
+
+Self-explanatory.
+
+E: Bond/react: Molecule template 'Coords' section required for chiralIDs keyword
+
+The coordinates of atoms in the pre-reacted template are used to determine chirality.
+
 E: Bond/react special bond generation overflow
 
 The number of special bonds per-atom created by a reaction exceeds the

From 4cb797e63dc3dd1bdab4ec3faf7002206ed8d241 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Mon, 2 Dec 2019 14:25:58 -0500
Subject: [PATCH 088/199] correct image atom mistake

---
 src/USER-MISC/fix_bond_react.cpp | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index dbdb8ef0a7..2995a596a5 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1655,11 +1655,10 @@ evaluate constraints: return 0 if any aren't satisfied
 int FixBondReact::check_constraints()
 {
   tagint atom1,atom2,atom3;
-  double unwrap[3],delx,dely,delz,rsq;
+  double delx,dely,delz,rsq;
   double delx1,dely1,delz1,delx2,dely2,delz2;
   double rsq1,rsq2,r1,r2,c,t,prrhob;
 
-  imageint *image = atom->image;
   double **x = atom->x;
 
   for (int i = 0; i < nconstraints; i++) {
@@ -1720,9 +1719,9 @@ int FixBondReact::check_constraints()
         for (int jj = 0; jj < 4; jj++) {
           if (atom->type[atom->map(xspecial[atom1][j])] == chiral_atoms[i][jj+2][rxnID]) {
             atom2 = atom->map(xspecial[atom1][j]);
-            domain->unmap(x[atom2],image[atom2],unwrap);
+            atom2 = domain->closest_image(atom1,atom2);
             for (int k = 0; k < 3; k++) {
-              my4coords[3*jj+k] = unwrap[k];
+              my4coords[3*jj+k] = x[atom2][k];
             }
             break;
           }

From 28fda045260a885f1c2bc9a2a4bcf4d552c9832c Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Mon, 2 Dec 2019 15:11:59 -0500
Subject: [PATCH 089/199] chiral centers docs

---
 doc/src/fix_bond_react.rst | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst
index ab63aa232c..7f72d1f428 100644
--- a/doc/src/fix_bond_react.rst
+++ b/doc/src/fix_bond_react.rst
@@ -20,9 +20,9 @@ Syntax
 * the common keyword/values may be appended directly after 'bond/react'
 * this applies to all reaction specifications (below)
 * common\_keyword = *stabilization*
-  
+
   .. parsed-literal::
-  
+
        *stabilization* values = *no* or *yes* *group-ID* *xmax*
          *no* = no reaction site stabilization
          *yes* = perform reaction site stabilization
@@ -40,9 +40,9 @@ Syntax
 * map\_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
 * zero or more individual keyword/value pairs may be appended to each react argument
 * individual\_keyword = *prob* or *max\_rxn* or *stabilize\_steps* or *update\_edges*
-  
+
   .. parsed-literal::
-  
+
          *prob* values = fraction seed
            fraction = initiate reaction with this probability if otherwise eligible
            seed = random number seed (positive integer)
@@ -269,10 +269,11 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'customIDs' and
 
    N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
    N *deleteIDs* = # of atoms N that are specified for deletion
+   N *chiralIDs* = # of specified chiral centers N
    N *customIDs* = # of atoms N that are specified for a custom update
    N *constraints* = # of specified reaction constraints N
 
-The body of the map file contains two mandatory sections and four
+The body of the map file contains two mandatory sections and five
 optional sections. The first mandatory section begins with the keyword
 'BondingIDs' and lists the atom IDs of the bonding atom pair in the
 pre-reacted molecule template. The second mandatory section begins
@@ -284,12 +285,14 @@ molecule template. The first optional section begins with the keyword
 'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
 molecule template. The second optional section begins with the keyword
 'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
-delete. The third optional section begins with the keyword 'Custom
+delete. The third optional section begins with the keyword 'ChiralIDs'
+lists the atom IDs of chiral atoms whose handedness should be
+enforced. The fourth optional section begins with the keyword 'Custom
 Edges' and allows for forcing the update of a specific atom's atomic
 charge. The first column is the ID of an atom near the edge of the
 pre-reacted molecule template, and the value of the second column is
 either 'none' or 'charges.' Further details are provided in the
-discussion of the 'update\_edges' keyword. The fourth optional section
+discussion of the 'update\_edges' keyword. The fifth optional section
 begins with the keyword 'Constraints' and lists additional criteria
 that must be satisfied in order for the reaction to occur. Currently,
 there are three types of constraints available, as discussed below.
@@ -332,6 +335,15 @@ A sample map file is given below:
 ----------
 
 
+The handedness of atoms that are chiral centers can be enforced by
+listing their IDs in the ChiralIDs section. A chiral atom must be
+bonded to four atoms with mutually different atom types. This feature
+uses the coordinates and types of the involved atoms in the
+pre-reaction template to determine handedness. Three atoms bonded to
+the chiral center are arbitrarily chosen, to define an oriented plane,
+and the relative position of the fourth bonded atom determines the
+chiral center's handedness.
+
 Any number of additional constraints may be specified in the
 Constraints section of the map file. The constraint of type 'distance'
 has syntax as follows:

From e69e96ffbe900d48e6b7d7e592af004903d86016 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Mon, 2 Dec 2019 15:20:01 -0500
Subject: [PATCH 090/199] Update Errors_messages.rst

---
 doc/src/Errors_messages.rst | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst
index 71de83afa9..a1795a6776 100644
--- a/doc/src/Errors_messages.rst
+++ b/doc/src/Errors_messages.rst
@@ -518,6 +518,16 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
    Self-explanatory.
 
+*Bond/react: First neighbors of chiral atoms must be of mutually different types*
+   Self-explanatory.
+
+*Bond/react: Chiral atoms must have exactly four first neighbors*
+   Self-explanatory.
+
+*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
+   The coordinates of atoms in the pre-reacted template are used to determine
+   chirality.
+
 *Bond/react special bond generation overflow*
    The number of special bonds per-atom created by a reaction exceeds the
    system setting. See the read\_data or create\_box command for how to

From 7233c3fedfb1374575e3ec84961d82fb14ef5ea8 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Mon, 2 Dec 2019 18:30:38 -0700
Subject: [PATCH 091/199] Fixed error in compute snap for quadratic and add log
 files for regression testing

---
 examples/snap/in.snap.compute                 |  18 +-
 examples/snap/in.snap.compute.quadratic       | 100 +++++++++
 examples/snap/log.27Nov18.snap.compute.g++.1  | 198 +++++++++++++++++
 examples/snap/log.27Nov18.snap.compute.g++.4  | 199 ++++++++++++++++++
 .../log.27Nov18.snap.compute.quadratic.g++.1  | 198 +++++++++++++++++
 .../log.27Nov18.snap.compute.quadratic.g++.4  | 199 ++++++++++++++++++
 src/SNAP/compute_snap.cpp                     |  19 +-
 7 files changed, 910 insertions(+), 21 deletions(-)
 create mode 100644 examples/snap/in.snap.compute.quadratic
 create mode 100644 examples/snap/log.27Nov18.snap.compute.g++.1
 create mode 100644 examples/snap/log.27Nov18.snap.compute.g++.4
 create mode 100644 examples/snap/log.27Nov18.snap.compute.quadratic.g++.1
 create mode 100644 examples/snap/log.27Nov18.snap.compute.quadratic.g++.4

diff --git a/examples/snap/in.snap.compute b/examples/snap/in.snap.compute
index 8955500e0e..e698a134a6 100644
--- a/examples/snap/in.snap.compute
+++ b/examples/snap/in.snap.compute
@@ -4,7 +4,6 @@
 
 variable 	nsteps index 0
 variable 	nrep equal 1
-#variable 	a equal 3.316
 variable 	a equal 2.0
 units		metal
 
@@ -16,6 +15,7 @@ variable 	nz equal ${nrep}
 
 boundary	p p p
 
+atom_modify	map hash
 lattice         bcc $a
 region		box block 0 ${nx} 0 ${ny} 0 ${nz}
 create_box	2 box
@@ -35,8 +35,11 @@ variable 	radelem1 equal 2.3
 variable 	radelem2 equal 2.0
 variable	wj1 equal 1.0
 variable	wj2 equal 0.96
+variable	quadratic equal 0
+variable	bzero equal 0
+variable	switch equal 0
 variable 	snap_options string &
-"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0"
+"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
 
 # set up dummy potential to satisfy cutoff
 
@@ -67,6 +70,7 @@ compute         bsum2 snapgroup2 reduce sum c_b[*]
 # fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
 compute		vbsum all reduce sum c_vb[*]
 # fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_30 equal c_db[2][30]
 
 # set up compute snap generating global array
 
@@ -78,12 +82,14 @@ thermo 		100
 # test output:   1: total potential energy
 #                2: xy component of stress tensor
 #                3: Sum(B_{000}^i, all i of type 2) 
-#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dr_j), all i of type 2), all j) 
-#                followed by counterparts from compute snap
+#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
 
 thermo_style	custom &
-		pe            pxy            c_bsum2[1]   c_vbsum[60] &
-       		c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] 
+		pe            pxy            c_bsum2[1]   c_vbsum[60]    v_db_2_30 &
+		c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10] 
 thermo_modify 	norm no
 
 # dump 		mydump_db all custom 1000 dump_db id c_db[*]
diff --git a/examples/snap/in.snap.compute.quadratic b/examples/snap/in.snap.compute.quadratic
new file mode 100644
index 0000000000..00e46bd3a8
--- /dev/null
+++ b/examples/snap/in.snap.compute.quadratic
@@ -0,0 +1,100 @@
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	ny equal ${nrep}
+variable 	nz equal ${nrep}
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	2 box
+create_atoms	2 box
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 1
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string &
+"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_coeff 	* * ${zblz} ${zblz}
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	vb all snav/atom ${snap_options}
+compute 	db all snad/atom ${snap_options}
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+group 		snapgroup2 type 2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_120 equal c_db[2][120]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2) 
+#                4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j) 
+#                5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom &
+		pe            pxy            c_bsum2[20]   c_vbsum[240]   v_db_2_120 & 
+		c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
diff --git a/examples/snap/log.27Nov18.snap.compute.g++.1 b/examples/snap/log.27Nov18.snap.compute.g++.1
new file mode 100644
index 0000000000..b189c552da
--- /dev/null
+++ b/examples/snap/log.27Nov18.snap.compute.g++.1
@@ -0,0 +1,198 @@
+LAMMPS (20 Nov 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	nx equal 1
+variable 	ny equal ${nrep}
+variable 	ny equal 1
+variable 	nz equal ${nrep}
+variable 	nz equal 1
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+lattice         bcc 2
+Lattice spacing in x,y,z = 2 2 2
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 1 0 ${ny} 0 ${nz}
+region		box block 0 1 0 1 0 ${nz}
+region		box block 0 1 0 1 0 1
+create_box	2 box
+Created orthogonal box = (0 0 0) to (2 2 2)
+  1 by 1 by 1 MPI processor grid
+create_atoms	2 box
+Created 2 atoms
+  create_atoms CPU = 0.000478029 secs
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 0
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_style 	zero 1
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_style 	zbl 4 ${zblcutouter}
+pair_style 	zbl 4 4.8
+pair_coeff 	* * ${zblz} ${zblz}
+pair_coeff 	* * 73 ${zblz}
+pair_coeff 	* * 73 73
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${snap_options}
+compute 	vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${snap_options}
+compute 	db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+0 atoms in group snapgroup1
+group 		snapgroup2 type 2
+2 atoms in group snapgroup2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_30 equal c_db[2][30]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+compute 	snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(B_{000}^i, all i of type 2)
+#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom 		pe            pxy            c_bsum2[1]   c_vbsum[60]    v_db_2_30 		c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
+run             0
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 1 1 1
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair zbl, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute sna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute snav/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute snad/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute snap, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.06 | 10.06 Mbytes
+PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10] 
+   322.86952    1505558.1    364182.88    381.32218   -855.04473    322.86952    1505558.1    364182.88    381.32218   -855.04473 
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 2 atoms
+
+104.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 9.537e-07  |            |       |100.00
+
+Nlocal:    2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    853 ave 853 max 853 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    330 ave 330 max 330 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  660 ave 660 max 660 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 660
+Ave neighs/atom = 330
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/snap/log.27Nov18.snap.compute.g++.4 b/examples/snap/log.27Nov18.snap.compute.g++.4
new file mode 100644
index 0000000000..f979123b2a
--- /dev/null
+++ b/examples/snap/log.27Nov18.snap.compute.g++.4
@@ -0,0 +1,199 @@
+LAMMPS (20 Nov 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	nx equal 1
+variable 	ny equal ${nrep}
+variable 	ny equal 1
+variable 	nz equal ${nrep}
+variable 	nz equal 1
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+lattice         bcc 2
+Lattice spacing in x,y,z = 2 2 2
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 1 0 ${ny} 0 ${nz}
+region		box block 0 1 0 1 0 ${nz}
+region		box block 0 1 0 1 0 1
+create_box	2 box
+Created orthogonal box = (0 0 0) to (2 2 2)
+  1 by 2 by 2 MPI processor grid
+create_atoms	2 box
+Created 2 atoms
+  create_atoms CPU = 0.000610113 secs
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 0
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_style 	zero 1
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_style 	zbl 4 ${zblcutouter}
+pair_style 	zbl 4 4.8
+pair_coeff 	* * ${zblz} ${zblz}
+pair_coeff 	* * 73 ${zblz}
+pair_coeff 	* * 73 73
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${snap_options}
+compute 	vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${snap_options}
+compute 	db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+0 atoms in group snapgroup1
+group 		snapgroup2 type 2
+2 atoms in group snapgroup2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_30 equal c_db[2][30]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+compute 	snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(B_{000}^i, all i of type 2)
+#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom 		pe            pxy            c_bsum2[1]   c_vbsum[60]    v_db_2_30 		c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
+run             0
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 1 1 1
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair zbl, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute sna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute snav/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute snad/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute snap, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:936)
+Per MPI rank memory allocation (min/avg/max) = 8.211 | 8.254 | 8.295 Mbytes
+PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10] 
+   322.86952    1505558.1    364182.88    381.32218   -855.04473    322.86952    1505558.1    364182.88    381.32218   -855.04473 
+Loop time of 2.38419e-06 on 4 procs for 0 steps with 2 atoms
+
+104.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 2.384e-06  |            |       |100.00
+
+Nlocal:    0.5 ave 1 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    734.5 ave 735 max 734 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    82.5 ave 177 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+FullNghs:  165 ave 330 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 660
+Ave neighs/atom = 330
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/snap/log.27Nov18.snap.compute.quadratic.g++.1 b/examples/snap/log.27Nov18.snap.compute.quadratic.g++.1
new file mode 100644
index 0000000000..c2054023ed
--- /dev/null
+++ b/examples/snap/log.27Nov18.snap.compute.quadratic.g++.1
@@ -0,0 +1,198 @@
+LAMMPS (20 Nov 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	nx equal 1
+variable 	ny equal ${nrep}
+variable 	ny equal 1
+variable 	nz equal ${nrep}
+variable 	nz equal 1
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+lattice         bcc 2
+Lattice spacing in x,y,z = 2 2 2
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 1 0 ${ny} 0 ${nz}
+region		box block 0 1 0 1 0 ${nz}
+region		box block 0 1 0 1 0 1
+create_box	2 box
+Created orthogonal box = (0 0 0) to (2 2 2)
+  1 by 1 by 1 MPI processor grid
+create_atoms	2 box
+Created 2 atoms
+  create_atoms CPU = 0.000473976 secs
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 1
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_style 	zero 1
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_style 	zbl 4 ${zblcutouter}
+pair_style 	zbl 4 4.8
+pair_coeff 	* * ${zblz} ${zblz}
+pair_coeff 	* * 73 ${zblz}
+pair_coeff 	* * 73 73
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${snap_options}
+compute 	vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${snap_options}
+compute 	db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+0 atoms in group snapgroup1
+group 		snapgroup2 type 2
+2 atoms in group snapgroup2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_120 equal c_db[2][120]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+compute 	snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
+#                4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom 		pe            pxy            c_bsum2[20]   c_vbsum[240]   v_db_2_120 		c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
+run             0
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 1 1 1
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair zbl, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute sna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute snav/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute snad/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute snap, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 21.78 | 21.78 | 21.78 Mbytes
+PotEng Pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40] 
+   322.86952    1505558.1 4.2492771e+08    7860489.6    -17625699    322.86952    1505558.1 4.2492771e+08    7860489.6    -17625699 
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 2 atoms
+
+93.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 2.146e-06  |            |       |100.00
+
+Nlocal:    2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    853 ave 853 max 853 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    330 ave 330 max 330 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  660 ave 660 max 660 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 660
+Ave neighs/atom = 330
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/snap/log.27Nov18.snap.compute.quadratic.g++.4 b/examples/snap/log.27Nov18.snap.compute.quadratic.g++.4
new file mode 100644
index 0000000000..819397f745
--- /dev/null
+++ b/examples/snap/log.27Nov18.snap.compute.quadratic.g++.4
@@ -0,0 +1,199 @@
+LAMMPS (20 Nov 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	nx equal 1
+variable 	ny equal ${nrep}
+variable 	ny equal 1
+variable 	nz equal ${nrep}
+variable 	nz equal 1
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+lattice         bcc 2
+Lattice spacing in x,y,z = 2 2 2
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 1 0 ${ny} 0 ${nz}
+region		box block 0 1 0 1 0 ${nz}
+region		box block 0 1 0 1 0 1
+create_box	2 box
+Created orthogonal box = (0 0 0) to (2 2 2)
+  1 by 2 by 2 MPI processor grid
+create_atoms	2 box
+Created 2 atoms
+  create_atoms CPU = 0.000118971 secs
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 1
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_style 	zero 1
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_style 	zbl 4 ${zblcutouter}
+pair_style 	zbl 4 4.8
+pair_coeff 	* * ${zblz} ${zblz}
+pair_coeff 	* * 73 ${zblz}
+pair_coeff 	* * 73 73
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${snap_options}
+compute 	vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${snap_options}
+compute 	db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+0 atoms in group snapgroup1
+group 		snapgroup2 type 2
+2 atoms in group snapgroup2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_120 equal c_db[2][120]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+compute 	snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
+#                4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom 		pe            pxy            c_bsum2[20]   c_vbsum[240]   v_db_2_120 		c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
+run             0
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 1 1 1
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair zbl, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute sna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute snav/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute snad/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute snap, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:936)
+Per MPI rank memory allocation (min/avg/max) = 19.7 | 19.74 | 19.78 Mbytes
+PotEng Pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40] 
+   322.86952    1505558.1 4.2492771e+08    7860489.6    -17625699    322.86952    1505558.1 4.2492771e+08    7860489.6    -17625699 
+Loop time of 2.80142e-06 on 4 procs for 0 steps with 2 atoms
+
+107.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 2.801e-06  |            |       |100.00
+
+Nlocal:    0.5 ave 1 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    734.5 ave 735 max 734 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    82.5 ave 177 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+FullNghs:  165 ave 330 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 660
+Ave neighs/atom = 330
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
index 11e8bd0d12..43b6a419da 100644
--- a/src/SNAP/compute_snap.cpp
+++ b/src/SNAP/compute_snap.cpp
@@ -10,19 +10,7 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
-/* IDEAS
 
--DONE: Need to define a local peratom array for snad and snad on local and ghost atoms
--DONE: Reverse communicate local peratom array
--DONE: Copy peratom array into output array
--DONE: size_array_cols = nperdim (ncoeff [+quadratic])
--DONE: size_array_rows = 1 + total number of atoms + 6
--DONE: size_peratom = (3+6)*nperdim*ntypes
-INCOMPLETE: Mappy from local to global
-INCOMPLETE: modify->find_compute()
-DONE: eliminate local peratom array for viral, replace with fdotr
-
- */
 #include "compute_snap.h"
 #include <cstring>
 #include <cstdlib>
@@ -400,18 +388,19 @@ void ComputeSnap::compute_array()
 
       // linear contributions
 
+      int k = typeoffset_global;
       for (int icoeff = 0; icoeff < ncoeff; icoeff++)
-        snap[0][icoeff+typeoffset_global] += snaptr->blist[icoeff];
+        snap[0][k++] += snaptr->blist[icoeff];
 
       // quadratic contributions
 
       if (quadraticflag) {
         for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
           double bveci = snaptr->blist[icoeff];
-          snap[0][icoeff+typeoffset_global] += 0.5*bveci*bveci;
+          snap[0][k++] += 0.5*bveci*bveci;
           for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
             double bvecj = snaptr->blist[jcoeff];
-            snap[0][icoeff+typeoffset_global] += bveci*bvecj;
+            snap[0][k++] += bveci*bvecj;
           }
         }
       }

From cd6d2c55d171e619b163f0d77fe3e919842daf52 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Thu, 22 Aug 2019 16:52:43 +0200
Subject: [PATCH 092/199] MEAM/C: helper function for x=1

---
 src/USER-MEAMC/meam.h             | 4 ++++
 src/USER-MEAMC/meam_dens_init.cpp | 2 +-
 src/USER-MEAMC/meam_force.cpp     | 4 ++--
 src/USER-MEAMC/pair_meamc.cpp     | 2 +-
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 4e5b298ffb..9be4628022 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -234,6 +234,10 @@ static inline bool iszero(const double f) {
   return fabs(f) < 1e-20;
 }
 
+static inline bool isone(const double f) {
+  return fabs(f-1.0) < 1e-20;
+}
+
 // Helper functions
 
 static inline double fdiv_zero(const double n, const double d) {
diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp
index 155941422c..39e3ff9467 100644
--- a/src/USER-MEAMC/meam_dens_init.cpp
+++ b/src/USER-MEAMC/meam_dens_init.cpp
@@ -197,7 +197,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
     //     Now compute derivatives
     dscrfcn[jn] = 0.0;
     sfcij = sij * fcij;
-    if (!iszero(sfcij) && !iszero(sfcij - 1.0)) {
+    if (!iszero(sfcij) && !isone(sfcij)) {
       for (kn = 0; kn < numneigh_full; kn++) {
         k = firstneigh_full[kn];
         if (k == j) continue;
diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp
index 09aad90111..8c50296358 100644
--- a/src/USER-MEAMC/meam_force.cpp
+++ b/src/USER-MEAMC/meam_force.cpp
@@ -410,7 +410,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
 
         //     Now compute forces on other atoms k due to change in sij
 
-        if (iszero(sij) || iszero(sij - 1.0)) continue; //: cont jn loop
+        if (iszero(sij) || isone(sij)) continue; //: cont jn loop
 
         double dxik(0), dyik(0), dzik(0);
         double dxjk(0), dyjk(0), dzjk(0);
@@ -429,7 +429,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
 
             dsij1 = 0.0;
             dsij2 = 0.0;
-            if (!iszero(sij) && !iszero(sij - 1.0)) {
+            if (!iszero(sij) && !isone(sij)) {
               const double rbound = rij2 * this->ebound_meam[elti][eltj];
               delc = Cmax - Cmin;
               dxjk = x[k][0] - x[j][0];
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index a9034a1af3..dc2e194dea 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -458,7 +458,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
     rozero[i] = atof(words[17]);
     ibar[i] = atoi(words[18]);
 
-    if (!iszero(t0[i]-1.0))
+    if (!isone(t0[i]))
       error->all(FLERR,"Unsupported parameter in MEAM potential file");
 
     nset++;

From 204529bcafcf76326edd2e25196b2cdfa9673ff4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Wed, 21 Aug 2019 18:38:45 +0200
Subject: [PATCH 093/199] MEAM/C: remove unused vars, refactoring for
 extensibility

---
 src/USER-MEAMC/meam.h                |  29 ++++-
 src/USER-MEAMC/meam_impl.cpp         |   2 +-
 src/USER-MEAMC/meam_setup_done.cpp   | 184 ++++++++++++++-------------
 src/USER-MEAMC/meam_setup_global.cpp |  28 ++--
 src/USER-MEAMC/pair_meamc.cpp        |  24 +---
 5 files changed, 151 insertions(+), 116 deletions(-)

diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 9be4628022..698f620694 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -2,6 +2,7 @@
 #define LMP_MEAM_H
 
 #include <cmath>
+#include <cstring>
 
 #define maxelt 5
 
@@ -26,7 +27,6 @@ private:
 
   // Ec_meam = cohesive energy
   // re_meam = nearest-neighbor distance
-  // Omega_meam = atomic volume
   // B_meam = bulk modulus
   // Z_meam = number of first neighbors for reference structure
   // ielt_meam = atomic number of element
@@ -65,7 +65,7 @@ private:
   // nrar,rdrar = spline coeff array parameters
 
   double Ec_meam[maxelt][maxelt], re_meam[maxelt][maxelt];
-  double Omega_meam[maxelt], Z_meam[maxelt];
+  double Z_meam[maxelt];
   double A_meam[maxelt], alpha_meam[maxelt][maxelt], rho0_meam[maxelt];
   double delta_meam[maxelt][maxelt];
   double beta0_meam[maxelt], beta1_meam[maxelt];
@@ -212,6 +212,31 @@ protected:
   void interpolate_meam(int);
 
 public:
+  //-----------------------------------------------------------------------------
+  // convert lattice spec to lattice_t
+  // only use single-element lattices if single=true
+  // return false on failure
+  // return true and set lat on success
+  static bool str_to_lat(const char* str, bool single, lattice_t& lat)
+  {
+    if (strcmp(str,"fcc") == 0) lat = FCC;
+    else if (strcmp(str,"bcc") == 0) lat = BCC;
+    else if (strcmp(str,"hcp") == 0) lat = HCP;
+    else if (strcmp(str,"dim") == 0) lat = DIM;
+    else if (strcmp(str,"dia") == 0) lat = DIA;
+    else {
+      if (single)
+        return false;
+      
+      if (strcmp(str,"b1")  == 0) lat = B1;
+      else if (strcmp(str,"c11") == 0) lat = C11;
+      else if (strcmp(str,"l12") == 0) lat = L12;
+      else if (strcmp(str,"b2")  == 0) lat = B2;
+      else return false;
+    }
+    return true;
+  }
+  
   void meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt, double* alpha,
                          double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
                          double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp
index 74e8af1cde..96ef364fa3 100644
--- a/src/USER-MEAMC/meam_impl.cpp
+++ b/src/USER-MEAMC/meam_impl.cpp
@@ -38,7 +38,7 @@ MEAM::MEAM(Memory* mem)
 
   neltypes = 0;
   for (int i = 0; i < maxelt; i++) {
-    Omega_meam[i] = Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] =
+    Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] =
       beta1_meam[i]= beta2_meam[i] = beta3_meam[i] =
       t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] =
       rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0;
diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp
index 37bfce5873..1c0fc3a53c 100644
--- a/src/USER-MEAMC/meam_setup_done.cpp
+++ b/src/USER-MEAMC/meam_setup_done.cpp
@@ -161,10 +161,10 @@ void
 MEAM::compute_pair_meam(void)
 {
 
-  double r /*ununsed:, temp*/;
+  double r;
   int j, a, b, nv2;
   double astar, frac, phizbl;
-  int n, nmax, Z1, Z2;
+  int n, Z1, Z2;
   double arat, rarat, scrn, scrn2;
   double phiaa, phibb /*unused:,phitmp*/;
   double C, s111, s112, s221, S11, S22;
@@ -230,9 +230,8 @@ MEAM::compute_pair_meam(void)
             Z1 = get_Zij(this->lattce_meam[a][a]);
             Z2 = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
                      this->Cmax_meam[a][a][a], arat, scrn);
-            nmax = 10;
             if (scrn > 0.0) {
-              for (n = 1; n <= nmax; n++) {
+              for (n = 1; n <= 10; n++) {
                 phiaa = phiaa + pow((-Z2 * scrn / Z1), n) * phi_meam(rarat * pow(arat, n), a, a);
               }
             }
@@ -242,9 +241,8 @@ MEAM::compute_pair_meam(void)
             Z1 = get_Zij(this->lattce_meam[b][b]);
             Z2 = get_Zij2(this->lattce_meam[b][b], this->Cmin_meam[b][b][b],
                      this->Cmax_meam[b][b][b], arat, scrn);
-            nmax = 10;
             if (scrn > 0.0) {
-              for (n = 1; n <= nmax; n++) {
+              for (n = 1; n <= 10; n++) {
                 phibb = phibb + pow((-Z2 * scrn / Z1), n) * phi_meam(rarat * pow(arat, n), b, b);
               }
             }
@@ -279,8 +277,7 @@ MEAM::compute_pair_meam(void)
             }
 
           } else {
-            nmax = 10;
-            for (n = 1; n <= nmax; n++) {
+            for (n = 1; n <= 10; n++) {
               this->phir[nv2][j] =
                 this->phir[nv2][j] + pow((-Z2 * scrn / Z1), n) * phi_meam(r * pow(arat, n), a, b);
             }
@@ -330,7 +327,7 @@ MEAM::phi_meam(double r, int a, int b)
   double Eu;
   double arat, scrn /*unused:,scrn2*/;
   int Z12, errorflag;
-  int n, nmax, Z1nn, Z2nn;
+  int n, Z1nn, Z2nn;
   lattice_t latta /*unused:,lattb*/;
   double rho_bkgd1, rho_bkgd2;
 
@@ -476,9 +473,8 @@ MEAM::phi_meam(double r, int a, int b)
     Z1nn = get_Zij(this->lattce_meam[a][a]);
     Z2nn = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
              this->Cmax_meam[a][a][a], arat, scrn);
-    nmax = 10;
     if (scrn > 0.0) {
-      for (n = 1; n <= nmax; n++) {
+      for (n = 1; n <= 10; n++) {
         phiaa = phiaa + pow((-Z2nn * scrn / Z1nn), n) * phi_meam(r * pow(arat, n), a, a);
       }
     }
@@ -555,30 +551,38 @@ MEAM::get_tavref(double* t11av, double* t21av, double* t31av, double* t12av, dou
     *t12av = t12;
     *t22av = t22;
     *t32av = t32;
-  } else if (latt == FCC || latt == BCC || latt == DIA || latt == HCP || latt == B1 || latt == DIM || latt == B2) {
-    //     all neighbors are of the opposite type
-    *t11av = t12;
-    *t21av = t22;
-    *t31av = t32;
-    *t12av = t11;
-    *t22av = t21;
-    *t32av = t31;
-  } else {
-    a1 = r / this->re_meam[a][a] - 1.0;
-    a2 = r / this->re_meam[b][b] - 1.0;
-    rhoa01 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * a1);
-    rhoa02 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
-    if (latt == L12) {
-      rho01 = 8 * rhoa01 + 4 * rhoa02;
-      *t11av = (8 * t11 * rhoa01 + 4 * t12 * rhoa02) / rho01;
+  } else switch (latt)  {
+    case FCC:
+    case BCC:
+    case DIA:
+    case HCP:
+    case B1:
+    case DIM:
+    case B2:
+      //     all neighbors are of the opposite type
+      *t11av = t12;
+      *t21av = t22;
+      *t31av = t32;
       *t12av = t11;
-      *t21av = (8 * t21 * rhoa01 + 4 * t22 * rhoa02) / rho01;
       *t22av = t21;
-      *t31av = (8 * t31 * rhoa01 + 4 * t32 * rhoa02) / rho01;
       *t32av = t31;
-    } else {
-      //      call error('Lattice not defined in get_tavref.')
-    }
+      break;
+    default:
+      a1 = r / this->re_meam[a][a] - 1.0;
+      a2 = r / this->re_meam[b][b] - 1.0;
+      rhoa01 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * a1);
+      rhoa02 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
+      if (latt == L12) {
+        rho01 = 8 * rhoa01 + 4 * rhoa02;
+        *t11av = (8 * t11 * rhoa01 + 4 * t12 * rhoa02) / rho01;
+        *t12av = t11;
+        *t21av = (8 * t21 * rhoa01 + 4 * t22 * rhoa02) / rho01;
+        *t22av = t21;
+        *t31av = (8 * t31 * rhoa01 + 4 * t32 * rhoa02) / rho01;
+        *t32av = t31;
+      } else {
+        //      call error('Lattice not defined in get_tavref.')
+      }
   }
 }
 
@@ -627,59 +631,69 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
   *rho12 = 0.0;
   *rho22 = 0.0;
   *rho32 = 0.0;
-
-  if (lat == FCC) {
-    *rho01 = 12.0 * rhoa02;
-    *rho02 = 12.0 * rhoa01;
-  } else if (lat == BCC) {
-    *rho01 = 8.0 * rhoa02;
-    *rho02 = 8.0 * rhoa01;
-  } else if (lat == B1) {
-    *rho01 = 6.0 * rhoa02;
-    *rho02 = 6.0 * rhoa01;
-  } else if (lat == DIA) {
-    *rho01 = 4.0 * rhoa02;
-    *rho02 = 4.0 * rhoa01;
-    *rho31 = 32.0 / 9.0 * rhoa32 * rhoa32;
-    *rho32 = 32.0 / 9.0 * rhoa31 * rhoa31;
-  } else if (lat == HCP) {
-    *rho01 = 12 * rhoa02;
-    *rho02 = 12 * rhoa01;
-    *rho31 = 1.0 / 3.0 * rhoa32 * rhoa32;
-    *rho32 = 1.0 / 3.0 * rhoa31 * rhoa31;
-  } else if (lat == DIM) {
-    get_shpfcn(DIM, s);
-    *rho01 = rhoa02;
-    *rho02 = rhoa01;
-    *rho11 = s[0] * rhoa12 * rhoa12;
-    *rho12 = s[0] * rhoa11 * rhoa11;
-    *rho21 = s[1] * rhoa22 * rhoa22;
-    *rho22 = s[1] * rhoa21 * rhoa21;
-    *rho31 = s[2] * rhoa32 * rhoa32;
-    *rho32 = s[2] * rhoa31 * rhoa31;
-  } else if (lat == C11) {
-    *rho01 = rhoa01;
-    *rho02 = rhoa02;
-    *rho11 = rhoa11;
-    *rho12 = rhoa12;
-    *rho21 = rhoa21;
-    *rho22 = rhoa22;
-    *rho31 = rhoa31;
-    *rho32 = rhoa32;
-  } else if (lat == L12) {
-    *rho01 = 8 * rhoa01 + 4 * rhoa02;
-    *rho02 = 12 * rhoa01;
-    if (this->ialloy == 1) {
-      *rho21 = 8. / 3. * MathSpecial::square(rhoa21 * this->t2_meam[a] - rhoa22 * this->t2_meam[b]);
-      denom = 8 * rhoa01 * MathSpecial::square(this->t2_meam[a]) + 4 * rhoa02 * MathSpecial::square(this->t2_meam[b]);
-      if (denom > 0.)
-        *rho21 = *rho21 / denom * *rho01;
-    } else
-      *rho21 = 8. / 3. * (rhoa21 - rhoa22) * (rhoa21 - rhoa22);
-  } else if (lat == B2) {
-    *rho01 = 8.0 * rhoa02;
-    *rho02 = 8.0 * rhoa01;
-  } else {
+  
+  switch (lat) {
+    case FCC:
+      *rho01 = 12.0 * rhoa02;
+      *rho02 = 12.0 * rhoa01;
+      break;
+    case BCC:
+      *rho01 = 8.0 * rhoa02;
+      *rho02 = 8.0 * rhoa01;
+      break;
+    case B1:
+      *rho01 = 6.0 * rhoa02;
+      *rho02 = 6.0 * rhoa01;
+      break;
+    case DIA:
+      *rho01 = 4.0 * rhoa02;
+      *rho02 = 4.0 * rhoa01;
+      *rho31 = 32.0 / 9.0 * rhoa32 * rhoa32;
+      *rho32 = 32.0 / 9.0 * rhoa31 * rhoa31;
+      break;
+    case HCP:
+      *rho01 = 12 * rhoa02;
+      *rho02 = 12 * rhoa01;
+      *rho31 = 1.0 / 3.0 * rhoa32 * rhoa32;
+      *rho32 = 1.0 / 3.0 * rhoa31 * rhoa31;
+      break;
+    case DIM:
+      get_shpfcn(DIM, s);
+      *rho01 = rhoa02;
+      *rho02 = rhoa01;
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+      break;
+    case C11:
+      *rho01 = rhoa01;
+      *rho02 = rhoa02;
+      *rho11 = rhoa11;
+      *rho12 = rhoa12;
+      *rho21 = rhoa21;
+      *rho22 = rhoa22;
+      *rho31 = rhoa31;
+      *rho32 = rhoa32;
+      break;
+    case L12:
+      *rho01 = 8 * rhoa01 + 4 * rhoa02;
+      *rho02 = 12 * rhoa01;
+      if (this->ialloy == 1) {
+        *rho21 = 8. / 3. * MathSpecial::square(rhoa21 * this->t2_meam[a] - rhoa22 * this->t2_meam[b]);
+        denom = 8 * rhoa01 * MathSpecial::square(this->t2_meam[a]) + 4 * rhoa02 * MathSpecial::square(this->t2_meam[b]);
+        if (denom > 0.)
+          *rho21 = *rho21 / denom * *rho01;
+      } else
+        *rho21 = 8. / 3. * (rhoa21 - rhoa22) * (rhoa21 - rhoa22);
+      break;
+    case B2:
+      *rho01 = 8.0 * rhoa02;
+      *rho02 = 8.0 * rhoa01;
+      break;
+    // default:
     //        call error('Lattice not defined in get_densref.')
   }
 
diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp
index b66aafa06c..2306ac53c6 100644
--- a/src/USER-MEAMC/meam_setup_global.cpp
+++ b/src/USER-MEAMC/meam_setup_global.cpp
@@ -49,17 +49,23 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, doub
     this->rho0_meam[i] = rozero[i];
     this->ibar_meam[i] = ibar[i];
 
-    if (this->lattce_meam[i][i] == FCC)
-      this->re_meam[i][i] = tmplat[i] / sqrt(2.0);
-    else if (this->lattce_meam[i][i] == BCC)
-      this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 2.0;
-    else if (this->lattce_meam[i][i] == HCP)
-      this->re_meam[i][i] = tmplat[i];
-    else if (this->lattce_meam[i][i] == DIM)
-      this->re_meam[i][i] = tmplat[i];
-    else if (this->lattce_meam[i][i] == DIA)
-      this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 4.0;
-    else {
+    switch(this->lattce_meam[i][i]) {
+      case FCC:
+        this->re_meam[i][i] = tmplat[i] / sqrt(2.0);
+        break;
+      case BCC:
+        this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 2.0;
+        break;
+      case HCP:
+        this->re_meam[i][i] = tmplat[i];
+        break;
+      case DIM:
+        this->re_meam[i][i] = tmplat[i];
+        break;
+      case DIA:
+        this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 4.0;
+        break;
+      //default:
       //           error
     }
   }
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index dc2e194dea..bc366854b6 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -430,13 +430,9 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
     found[i] = true;
 
     // map lat string to an integer
-
-    if (strcmp(words[1],"fcc") == 0) lat[i] = FCC;
-    else if (strcmp(words[1],"bcc") == 0) lat[i] = BCC;
-    else if (strcmp(words[1],"hcp") == 0) lat[i] = HCP;
-    else if (strcmp(words[1],"dim") == 0) lat[i] = DIM;
-    else if (strcmp(words[1],"dia") == 0) lat[i] = DIA;
-    else error->all(FLERR,"Unrecognized lattice type in MEAM file 1");
+    
+    if (!MEAM::str_to_lat(words[1], true, lat[i]))
+      error->all(FLERR,"Unrecognized lattice type in MEAM file 1");
 
     // store parameters
 
@@ -523,6 +519,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
 
   int which;
   double value;
+  lattice_t latt;
   int nindex,index[3];
   int maxparams = 6;
   char **params = new char*[maxparams];
@@ -571,16 +568,9 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
     // map lattce_meam value to an integer
 
     if (which == 4) {
-      if (strcmp(params[nparams-1],"fcc") == 0) value = FCC;
-      else if (strcmp(params[nparams-1],"bcc") == 0) value = BCC;
-      else if (strcmp(params[nparams-1],"hcp") == 0) value = HCP;
-      else if (strcmp(params[nparams-1],"dim") == 0) value = DIM;
-      else if (strcmp(params[nparams-1],"dia") == 0) value = DIA;
-      else if (strcmp(params[nparams-1],"b1")  == 0) value = B1;
-      else if (strcmp(params[nparams-1],"c11") == 0) value = C11;
-      else if (strcmp(params[nparams-1],"l12") == 0) value = L12;
-      else if (strcmp(params[nparams-1],"b2")  == 0) value = B2;
-      else error->all(FLERR,"Unrecognized lattice type in MEAM file 2");
+      if (!MEAM::str_to_lat(params[nparams-1], false, latt))
+        error->all(FLERR,"Unrecognized lattice type in MEAM file 2");
+      value = latt;
     }
     else value = atof(params[nparams-1]);
 

From 2c65659421f935b4cceb874cc938241d87822b50 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Sat, 6 Jul 2019 18:23:53 +0200
Subject: [PATCH 094/199] MEAM/C: implement scaling factor for reversible
 scaling calculations

---
 src/USER-MEAMC/meam.h              |  4 ++--
 src/USER-MEAMC/meam_dens_final.cpp |  5 ++++-
 src/USER-MEAMC/meam_force.cpp      | 18 ++++++++++++++----
 src/USER-MEAMC/pair_meamc.cpp      | 27 ++++++++++++++++++++++-----
 src/USER-MEAMC/pair_meamc.h        |  2 ++
 5 files changed, 44 insertions(+), 12 deletions(-)

diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 698f620694..6e7dedfe2d 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -247,9 +247,9 @@ public:
   void meam_dens_init(int i, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
                       int numneigh_full, int* firstneigh_full, int fnoffset);
   void meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl,
-                       double* eatom, int ntype, int* type, int* fmap, int& errorflag);
+                       double* eatom, int ntype, int* type, int* fmap, double** scale, int& errorflag);
   void meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl,
-                  double* eatom, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
+                  double* eatom, int ntype, int* type, int* fmap, double** scale, double** x, int numneigh, int* firstneigh,
                   int numneigh_full, int* firstneigh_full, int fnoffset, double** f, double** vatom);
 };
 
diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp
index 867106df88..f59ad1b08a 100644
--- a/src/USER-MEAMC/meam_dens_final.cpp
+++ b/src/USER-MEAMC/meam_dens_final.cpp
@@ -4,18 +4,20 @@ using namespace LAMMPS_NS;
 
 void
 MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl,
-                      double* eatom, int /*ntype*/, int* type, int* fmap, int& errorflag)
+                      double* eatom, int /*ntype*/, int* type, int* fmap, double** scale, int& errorflag)
 {
   int i, elti;
   int m;
   double rhob, G, dG, Gbar, dGbar, gam, shp[3], Z;
   double denom, rho_bkgd, Fl;
+  double scaleii;
 
   //     Complete the calculation of density
 
   for (i = 0; i < nlocal; i++) {
     elti = fmap[type[i]];
     if (elti >= 0) {
+      scaleii = scale[type[i]][type[i]];
       rho1[i] = 0.0;
       rho2[i] = -1.0 / 3.0 * arho2b[i] * arho2b[i];
       rho3[i] = 0.0;
@@ -113,6 +115,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
       Fl = embedding(this->A_meam[elti], this->Ec_meam[elti][elti], rhob, frhop[i]);
 
       if (eflag_either != 0) {
+        Fl *= scaleii;
         if (eflag_global != 0) {
           *eng_vdwl = *eng_vdwl + Fl;
         }
diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp
index 8c50296358..924d88f6ff 100644
--- a/src/USER-MEAMC/meam_force.cpp
+++ b/src/USER-MEAMC/meam_force.cpp
@@ -8,7 +8,7 @@ using namespace LAMMPS_NS;
 
 void
 MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl,
-                 double* eatom, int /*ntype*/, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
+                 double* eatom, int /*ntype*/, int* type, int* fmap, double** scale, double** x, int numneigh, int* firstneigh,
                  int numneigh_full, int* firstneigh_full, int fnoffset, double** f, double** vatom)
 {
   int j, jn, k, kn, kk, m, n, p, q;
@@ -42,6 +42,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
   double arg1i1, arg1j1, arg1i2, arg1j2, arg1i3, arg1j3, arg3i3, arg3j3;
   double dsij1, dsij2, force1, force2;
   double t1i, t2i, t3i, t1j, t2j, t3j;
+  double scaleij;
 
   third = 1.0 / 3.0;
   sixth = 1.0 / 6.0;
@@ -59,6 +60,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
   for (jn = 0; jn < numneigh; jn++) {
     j = firstneigh[jn];
     eltj = fmap[type[j]];
+    scaleij = scale[type[i]][type[j]];
 
     if (!iszero(scrfcn[fnoffset + jn]) && eltj >= 0) {
 
@@ -84,11 +86,12 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
         recip = 1.0 / r;
 
         if (eflag_either != 0) {
+          double phi_sc = phi * scaleij;
           if (eflag_global != 0)
-            *eng_vdwl = *eng_vdwl + phi * sij;
+            *eng_vdwl = *eng_vdwl + phi_sc * sij;
           if (eflag_atom != 0) {
-            eatom[i] = eatom[i] + 0.5 * phi * sij;
-            eatom[j] = eatom[j] + 0.5 * phi * sij;
+            eatom[i] = eatom[i] + 0.5 * phi_sc * sij;
+            eatom[j] = eatom[j] + 0.5 * phi_sc * sij;
           }
         }
 
@@ -379,6 +382,13 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
         for (m = 0; m < 3; m++) {
           dUdrijm[m] = frhop[i] * drhodrm1[m] + frhop[j] * drhodrm2[m];
         }
+        if (!isone(scaleij)) {
+          dUdrij *= scaleij;
+          dUdsij *= scaleij;
+          dUdrijm[0] *= scaleij;
+          dUdrijm[1] *= scaleij;
+          dUdrijm[2] *= scaleij;
+        }
 
         //     Add the part of the force due to dUdrij and dUdsij
 
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index bc366854b6..2a2a168fd4 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -56,6 +56,7 @@ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp)
   elements = NULL;
   mass = NULL;
   meam_inst = new MEAM(memory);
+  scale = NULL;
 
   // set comm size needed by this Pair
 
@@ -79,6 +80,7 @@ PairMEAMC::~PairMEAMC()
   if (allocated) {
     memory->destroy(setflag);
     memory->destroy(cutsq);
+    memory->destroy(scale);
     delete [] map;
   }
 }
@@ -143,7 +145,7 @@ void PairMEAMC::compute(int eflag, int vflag)
   comm->reverse_comm_pair(this);
 
   meam_inst->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom,
-                   &eng_vdwl,eatom,ntype,type,map,errorflag);
+                   &eng_vdwl,eatom,ntype,type,map,scale,errorflag);
   if (errorflag) {
     char str[128];
     sprintf(str,"MEAM library error %d",errorflag);
@@ -164,7 +166,7 @@ void PairMEAMC::compute(int eflag, int vflag)
   for (ii = 0; ii < inum_half; ii++) {
     i = ilist_half[ii];
     meam_inst->meam_force(i,eflag_either,eflag_global,eflag_atom,
-                vflag_atom,&eng_vdwl,eatom,ntype,type,map,x,
+                vflag_atom,&eng_vdwl,eatom,ntype,type,map,scale,x,
                 numneigh_half[i],firstneigh_half[i],
                 numneigh_full[i],firstneigh_full[i],
                 offset,f,vptr);
@@ -183,6 +185,7 @@ void PairMEAMC::allocate()
 
   memory->create(setflag,n+1,n+1,"pair:setflag");
   memory->create(cutsq,n+1,n+1,"pair:cutsq");
+  memory->create(scale,n+1,n+1,"pair:scale");
 
   map = new int[n+1];
 }
@@ -267,13 +270,16 @@ void PairMEAMC::coeff(int narg, char **arg)
   // set mass for i,i in atom class
 
   int count = 0;
-  for (int i = 1; i <= n; i++)
-    for (int j = i; j <= n; j++)
+  for (int i = 1; i <= n; i++) {
+    for (int j = i; j <= n; j++) {
       if (map[i] >= 0 && map[j] >= 0) {
         setflag[i][j] = 1;
         if (i == j) atom->set_mass(FLERR,i,mass[map[i]]);
         count++;
       }
+      scale[i][j] = 1.0;
+    }
+  }
 
   if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
 }
@@ -312,8 +318,10 @@ void PairMEAMC::init_list(int id, NeighList *ptr)
    init for one type pair i,j and corresponding j,i
 ------------------------------------------------------------------------- */
 
-double PairMEAMC::init_one(int /*i*/, int /*j*/)
+double PairMEAMC::init_one(int i, int j)
 {
+  if (setflag[i][j] == 0) scale[i][j] = 1.0;
+  scale[j][i] = scale[i][j];
   return cutmax;
 }
 
@@ -773,3 +781,12 @@ void PairMEAMC::neigh_strip(int inum, int *ilist,
     for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK;
   }
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *PairMEAMC::extract(const char *str, int &dim)
+{
+  dim = 2;
+  if (strcmp(str,"scale") == 0) return (void *) scale;
+  return NULL;
+}
diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h
index 31dd8ba022..102985f0ca 100644
--- a/src/USER-MEAMC/pair_meamc.h
+++ b/src/USER-MEAMC/pair_meamc.h
@@ -35,6 +35,7 @@ class PairMEAMC : public Pair {
   void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
+  virtual void *extract(const char *, int &);
 
   int pack_forward_comm(int, int *, double *, int, int *);
   void unpack_forward_comm(int, int, double *);
@@ -50,6 +51,7 @@ class PairMEAMC : public Pair {
   double *mass;                 // mass of each element
 
   int *map;                     // mapping from atom types (1-indexed) to elements (1-indexed)
+  double **scale;               // scaling factor for adapt
 
   void allocate();
   void read_files(char *, char *);

From 7e14dda789c071b27a26546beff3fb0bfc313cd5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Thu, 22 Aug 2019 11:36:25 +0200
Subject: [PATCH 095/199] MEAM/C: warn if z given and expected by lattice do
 not agree

---
 src/USER-MEAMC/meam.h         | 2 +-
 src/USER-MEAMC/pair_meamc.cpp | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 6e7dedfe2d..d19a653ee2 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -192,7 +192,6 @@ protected:
   static double erose(const double r, const double re, const double alpha, const double Ec, const double repuls, const double attrac, const int form);
 
   static void get_shpfcn(const lattice_t latt, double (&s)[3]);
-  static int get_Zij(const lattice_t latt);
   static int get_Zij2(const lattice_t latt, const double cmin, const double cmax, double &a, double &S);
 protected:
   void meam_checkindex(int, int, int, int*, int*);
@@ -237,6 +236,7 @@ public:
     return true;
   }
   
+  static int get_Zij(const lattice_t latt);
   void meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt, double* alpha,
                          double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
                          double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 2a2a168fd4..37e3fdd8c8 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -463,7 +463,10 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
     ibar[i] = atoi(words[18]);
 
     if (!isone(t0[i]))
-      error->all(FLERR,"Unsupported parameter in MEAM potential file");
+      error->all(FLERR,"Unsupported parameter in MEAM potential file: t0!=1");
+    
+    if (z[i] != MEAM::get_Zij(lat[i]))
+      error->warning(FLERR,"Unsupported parameter in MEAM potential file: z!=lat", true);
 
     nset++;
   }

From ce05ed4cca9f02250ea75c36f1c3465a9c612566 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Thu, 22 Aug 2019 13:21:56 +0200
Subject: [PATCH 096/199] MEAM/C: infer z parameter from lattice structure,
 eliminates possible user mistakes

---
 doc/txt/pair_meamc.txt               |  2 ++
 src/USER-MEAMC/meam.h                |  4 +---
 src/USER-MEAMC/meam_dens_final.cpp   |  2 +-
 src/USER-MEAMC/meam_funcs.cpp        |  6 +++---
 src/USER-MEAMC/meam_impl.cpp         |  2 +-
 src/USER-MEAMC/meam_setup_done.cpp   | 17 ++++++++---------
 src/USER-MEAMC/meam_setup_global.cpp |  3 +--
 src/USER-MEAMC/pair_meamc.cpp        |  5 +++--
 8 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/doc/txt/pair_meamc.txt b/doc/txt/pair_meamc.txt
index 7c42e9d2f2..2831600e08 100644
--- a/doc/txt/pair_meamc.txt
+++ b/doc/txt/pair_meamc.txt
@@ -139,6 +139,8 @@ potential parameters:
 
 lat      = lattice structure of reference configuration
 z        = number of nearest neighbors in the reference structure
+             This field is only read for compatibility, the correct
+             value is inferred from the lattice structure
 ielement = atomic number
 atwt     = atomic weight
 alat     = lattice constant of reference structure
diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index d19a653ee2..6bf3b93652 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -28,7 +28,6 @@ private:
   // Ec_meam = cohesive energy
   // re_meam = nearest-neighbor distance
   // B_meam = bulk modulus
-  // Z_meam = number of first neighbors for reference structure
   // ielt_meam = atomic number of element
   // A_meam = adjustable parameter
   // alpha_meam = sqrt(9*Omega*B/Ec)
@@ -65,7 +64,6 @@ private:
   // nrar,rdrar = spline coeff array parameters
 
   double Ec_meam[maxelt][maxelt], re_meam[maxelt][maxelt];
-  double Z_meam[maxelt];
   double A_meam[maxelt], alpha_meam[maxelt][maxelt], rho0_meam[maxelt];
   double delta_meam[maxelt][maxelt];
   double beta0_meam[maxelt], beta1_meam[maxelt];
@@ -237,7 +235,7 @@ public:
   }
   
   static int get_Zij(const lattice_t latt);
-  void meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt, double* alpha,
+  void meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* atwt, double* alpha,
                          double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
                          double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
                          int* ibar);
diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp
index f59ad1b08a..eac8af44dc 100644
--- a/src/USER-MEAMC/meam_dens_final.cpp
+++ b/src/USER-MEAMC/meam_dens_final.cpp
@@ -54,7 +54,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
         gamma[i] = gamma[i] / (rho0[i] * rho0[i]);
       }
 
-      Z = this->Z_meam[elti];
+      Z = get_Zij(this->lattce_meam[elti][elti]);
 
       G = G_gam(gamma[i], this->ibar_meam[elti], errorflag);
       if (errorflag != 0)
diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp
index 312caff686..15e06ce78f 100644
--- a/src/USER-MEAMC/meam_funcs.cpp
+++ b/src/USER-MEAMC/meam_funcs.cpp
@@ -232,7 +232,7 @@ MEAM::get_shpfcn(const lattice_t latt, double (&s)[3])
 }
 
 //-----------------------------------------------------------------------------
-// Number of neighbors for the reference structure
+// Number of first neighbors for reference structure
 //
 int
 MEAM::get_Zij(const lattice_t latt)
@@ -244,12 +244,12 @@ MEAM::get_Zij(const lattice_t latt)
       return 8;
     case HCP:
       return 12;
-    case B1:
-      return 6;
     case DIA:
       return 4;
     case DIM:
       return 1;
+    case B1:
+      return 6;
     case C11:
       return 10;
     case L12:
diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp
index 96ef364fa3..0a0b95e14a 100644
--- a/src/USER-MEAMC/meam_impl.cpp
+++ b/src/USER-MEAMC/meam_impl.cpp
@@ -38,7 +38,7 @@ MEAM::MEAM(Memory* mem)
 
   neltypes = 0;
   for (int i = 0; i < maxelt; i++) {
-    Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] =
+    A_meam[i] = rho0_meam[i] = beta0_meam[i] =
       beta1_meam[i]= beta2_meam[i] = beta3_meam[i] =
       t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] =
       rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0;
diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp
index 1c0fc3a53c..8232c2aed5 100644
--- a/src/USER-MEAMC/meam_setup_done.cpp
+++ b/src/USER-MEAMC/meam_setup_done.cpp
@@ -327,7 +327,7 @@ MEAM::phi_meam(double r, int a, int b)
   double Eu;
   double arat, scrn /*unused:,scrn2*/;
   int Z12, errorflag;
-  int n, Z1nn, Z2nn;
+  int n, Z1nn;
   lattice_t latta /*unused:,lattb*/;
   double rho_bkgd1, rho_bkgd2;
 
@@ -338,6 +338,8 @@ MEAM::phi_meam(double r, int a, int b)
 
   // get number of neighbors in the reference structure
   //   Nref[i][j] = # of i's neighbors of type j
+  Z1 = get_Zij(this->lattce_meam[a][a]);
+  Z2 = get_Zij(this->lattce_meam[b][b]);
   Z12 = get_Zij(this->lattce_meam[a][b]);
 
   get_densref(r, a, b, &rho01, &rho11, &rho21, &rho31, &rho02, &rho12, &rho22, &rho32);
@@ -398,8 +400,6 @@ MEAM::phi_meam(double r, int a, int b)
     //     If using mixing rule for t, apply to reference structure; else
     //     use precomputed values
     if (this->mix_ref_t == 1) {
-      Z1 = this->Z_meam[a];
-      Z2 = this->Z_meam[b];
       if (this->ibar_meam[a] <= 0)
         G1 = 1.0;
       else {
@@ -436,8 +436,8 @@ MEAM::phi_meam(double r, int a, int b)
       rho_bkgd2 = rho0_2;
     } else {
       if (this->bkgd_dyn == 1) {
-        rho_bkgd1 = this->rho0_meam[a] * this->Z_meam[a];
-        rho_bkgd2 = this->rho0_meam[b] * this->Z_meam[b];
+        rho_bkgd1 = this->rho0_meam[a] * Z1;
+        rho_bkgd2 = this->rho0_meam[b] * Z2;
       } else {
         rho_bkgd1 = this->rho_ref_meam[a];
         rho_bkgd2 = this->rho_ref_meam[b];
@@ -470,12 +470,11 @@ MEAM::phi_meam(double r, int a, int b)
   } else if (this->lattce_meam[a][b] == L12) {
     phiaa = phi_meam(r, a, a);
     //       account for second neighbor a-a potential here...
-    Z1nn = get_Zij(this->lattce_meam[a][a]);
-    Z2nn = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
+    Z1nn = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
              this->Cmax_meam[a][a][a], arat, scrn);
     if (scrn > 0.0) {
       for (n = 1; n <= 10; n++) {
-        phiaa = phiaa + pow((-Z2nn * scrn / Z1nn), n) * phi_meam(r * pow(arat, n), a, a);
+        phiaa = phiaa + pow((-Z1nn * scrn / Z1), n) * phi_meam(r * pow(arat, n), a, a);
       }
     }
     phi_m = Eu / 3.0 - F1 / 4.0 - F2 / 12.0 - phiaa;
@@ -506,7 +505,7 @@ MEAM::compute_reference_density(void)
 
   // loop over element types
   for (a = 0; a < this->neltypes; a++) {
-    Z = (int)this->Z_meam[a];
+    Z = get_Zij(this->lattce_meam[a][a]);
     if (this->ibar_meam[a] <= 0)
       Gbar = 1.0;
     else {
diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp
index 2306ac53c6..56bac1d5af 100644
--- a/src/USER-MEAMC/meam_setup_global.cpp
+++ b/src/USER-MEAMC/meam_setup_global.cpp
@@ -18,7 +18,7 @@ static inline void setall3d(TYPE (&arr)[maxi][maxj][maxk], const TYPE v) {
 }
 
 void
-MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* /*atwt*/, double* alpha,
+MEAM::meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* /*atwt*/, double* alpha,
                         double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
                         double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
                         int* ibar)
@@ -32,7 +32,6 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, doub
   for (i = 0; i < nelt; i++) {
     this->lattce_meam[i][i] = lat[i];
 
-    this->Z_meam[i] = z[i];
     this->ielt_meam[i] = ielement[i];
     this->alpha_meam[i][i] = alpha[i];
     this->beta0_meam[i] = b0[i];
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 37e3fdd8c8..77a5e9a461 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -465,8 +465,9 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
     if (!isone(t0[i]))
       error->all(FLERR,"Unsupported parameter in MEAM potential file: t0!=1");
     
+    // z given is ignored: if this is mismatched, we definitely won't do what the user said -> fatal error
     if (z[i] != MEAM::get_Zij(lat[i]))
-      error->warning(FLERR,"Unsupported parameter in MEAM potential file: z!=lat", true);
+      error->all(FLERR,"Mismatched parameter in MEAM potential file: z!=lat");
 
     nset++;
   }
@@ -478,7 +479,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
 
   // pass element parameters to MEAM package
 
-  meam_inst->meam_setup_global(nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3,
+  meam_inst->meam_setup_global(nelements,lat,ielement,atwt,alpha,b0,b1,b2,b3,
                        alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
 
   // set element masses

From 81fb0d613f97084f4d60751795204fe266c516d7 Mon Sep 17 00:00:00 2001
From: Sungkwang Mun <munsungkwang@gmail.com>
Date: Fri, 30 Aug 2019 17:54:43 +0200
Subject: [PATCH 097/199] * This commit includes the addition of new reference
 structures such as ch4: methane-like structure only for binary system. dia3:
 diamond structure with primary 1NN and secondary 3NN inteation tri: H2O-like
 structure that has an angle zig: zigzag structure with a uniform angle lin:
 linear structure (180 degree angle)

** tri, zig, and lin reference structures require angle information (in degree)
such as the following.
   theta = 109.5
---
 src/USER-MEAMC/meam.h                |  32 ++++-
 src/USER-MEAMC/meam_dens_final.cpp   |   4 +-
 src/USER-MEAMC/meam_force.cpp        |   5 +-
 src/USER-MEAMC/meam_funcs.cpp        |  90 +++++++++++--
 src/USER-MEAMC/meam_setup_done.cpp   | 192 +++++++++++++++++++++------
 src/USER-MEAMC/meam_setup_global.cpp |  10 +-
 src/USER-MEAMC/meam_setup_param.cpp  |  17 +++
 src/USER-MEAMC/pair_meamc.cpp        |   4 +-
 8 files changed, 294 insertions(+), 60 deletions(-)

diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 6bf3b93652..719e1af6f0 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -3,13 +3,14 @@
 
 #include <cmath>
 #include <cstring>
+#include "math_const.h"
 
 #define maxelt 5
 
 namespace LAMMPS_NS {
 class Memory;
 
-typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t;
+typedef enum { FCC, BCC, HCP, DIM, DIA, DIA3, B1, C11, L12, B2, CH4, LIN, ZIG, TRI } lattice_t;
 
 class MEAM
 {
@@ -63,6 +64,10 @@ private:
   // nr,dr = pair function discretization parameters
   // nrar,rdrar = spline coeff array parameters
 
+  // theta = angle between three atoms in line, zigzag, and trimer reference structures
+  // stheta_meam = sin(theta/2) in radian used in line, zigzag, and trimer reference structures
+  // ctheta_meam = cos(theta/2) in radian used in line, zigzag, and trimer reference structures
+
   double Ec_meam[maxelt][maxelt], re_meam[maxelt][maxelt];
   double A_meam[maxelt], alpha_meam[maxelt][maxelt], rho0_meam[maxelt];
   double delta_meam[maxelt][maxelt];
@@ -106,6 +111,10 @@ public:
   int maxneigh;
   double *scrfcn, *dscrfcn, *fcpair;
 
+  //angle for trimer, zigzag, line reference structures
+  double stheta_meam[maxelt][maxelt];
+  double ctheta_meam[maxelt][maxelt];
+
 protected:
   // meam_funcs.cpp
 
@@ -189,8 +198,12 @@ protected:
   double embedding(const double A, const double Ec, const double rhobar, double& dF) const;
   static double erose(const double r, const double re, const double alpha, const double Ec, const double repuls, const double attrac, const int form);
 
-  static void get_shpfcn(const lattice_t latt, double (&s)[3]);
-  static int get_Zij2(const lattice_t latt, const double cmin, const double cmax, double &a, double &S);
+  static void get_shpfcn(const lattice_t latt, const double sthe, const double cthe, double (&s)[3]);
+
+  static int get_Zij2(const lattice_t latt, const double cmin, const double cmax,
+                      const double sthe, double &a, double &S);
+  static int get_Zij2_b2nn(const lattice_t latt, const double cmin, const double cmax, double &S);
+
 protected:
   void meam_checkindex(int, int, int, int*, int*);
   void getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** x, int numneigh,
@@ -201,6 +214,7 @@ protected:
   void alloyparams();
   void compute_pair_meam();
   double phi_meam(double, int, int);
+  const double phi_meam_series(const double scrn, const int Z1, const int Z2, const int a, const int b, const double r, const double arat);
   void compute_reference_density();
   void get_tavref(double*, double*, double*, double*, double*, double*, double, double, double, double,
                   double, double, double, int, int, lattice_t);
@@ -221,19 +235,27 @@ public:
     else if (strcmp(str,"hcp") == 0) lat = HCP;
     else if (strcmp(str,"dim") == 0) lat = DIM;
     else if (strcmp(str,"dia") == 0) lat = DIA;
+    else if (strcmp(str,"dia3") == 0) lat = DIA3;
+    else if (strcmp(str,"lin") == 0) lat = LIN;
+    else if (strcmp(str,"zig") == 0) lat = ZIG;
+    else if (strcmp(str,"tri") == 0) lat = TRI;
     else {
       if (single)
         return false;
-      
+
       if (strcmp(str,"b1")  == 0) lat = B1;
       else if (strcmp(str,"c11") == 0) lat = C11;
       else if (strcmp(str,"l12") == 0) lat = L12;
       else if (strcmp(str,"b2")  == 0) lat = B2;
+      else if (strcmp(str,"ch4")  == 0) lat = CH4;
+      else if (strcmp(str,"lin")  == 0) lat =LIN;
+      else if (strcmp(str,"zig")  == 0) lat = ZIG;
+      else if (strcmp(str,"tri")  == 0) lat = TRI;
       else return false;
     }
     return true;
   }
-  
+
   static int get_Zij(const lattice_t latt);
   void meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* atwt, double* alpha,
                          double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp
index eac8af44dc..fe9e74ca7c 100644
--- a/src/USER-MEAMC/meam_dens_final.cpp
+++ b/src/USER-MEAMC/meam_dens_final.cpp
@@ -59,7 +59,9 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
       G = G_gam(gamma[i], this->ibar_meam[elti], errorflag);
       if (errorflag != 0)
         return;
-      get_shpfcn(this->lattce_meam[elti][elti], shp);
+
+      get_shpfcn(this->lattce_meam[elti][elti], this->stheta_meam[elti][elti], this->ctheta_meam[elti][elti], shp);
+
       if (this->ibar_meam[elti] <= 0) {
         Gbar = 1.0;
         dGbar = 0.0;
diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp
index 924d88f6ff..5a2f544d8b 100644
--- a/src/USER-MEAMC/meam_force.cpp
+++ b/src/USER-MEAMC/meam_force.cpp
@@ -290,8 +290,9 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
         }
 
         //     Compute derivatives of total density wrt rij, sij and rij(3)
-        get_shpfcn(this->lattce_meam[elti][elti], shpi);
-        get_shpfcn(this->lattce_meam[eltj][eltj], shpj);
+        get_shpfcn(this->lattce_meam[elti][elti], this->stheta_meam[elti][elti], this->ctheta_meam[elti][elti], shpi);
+        get_shpfcn(this->lattce_meam[eltj][eltj], this->stheta_meam[elti][elti], this->ctheta_meam[elti][elti], shpj);
+
         drhodr1 = dgamma1[i] * drho0dr1 +
           dgamma2[i] * (dt1dr1 * rho1[i] + t1i * drho1dr1 + dt2dr1 * rho2[i] + t2i * drho2dr1 +
                         dt3dr1 * rho3[i] + t3i * drho3dr1) -
diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp
index 15e06ce78f..da984cfeb7 100644
--- a/src/USER-MEAMC/meam_funcs.cpp
+++ b/src/USER-MEAMC/meam_funcs.cpp
@@ -198,7 +198,7 @@ MEAM::erose(const double r, const double re, const double alpha, const double Ec
 // Shape factors for various configurations
 //
 void
-MEAM::get_shpfcn(const lattice_t latt, double (&s)[3])
+MEAM::get_shpfcn(const lattice_t latt, const double sthe, const double cthe, double (&s)[3])
 {
   switch (latt) {
     case FCC:
@@ -214,7 +214,9 @@ MEAM::get_shpfcn(const lattice_t latt, double (&s)[3])
       s[1] = 0.0;
       s[2] = 1.0 / 3.0;
       break;
+    case CH4: // CH4 actually needs shape factor for diamond for C, dimer for H
     case DIA:
+    case DIA3:
       s[0] = 0.0;
       s[1] = 0.0;
       s[2] = 32.0 / 9.0;
@@ -222,8 +224,20 @@ MEAM::get_shpfcn(const lattice_t latt, double (&s)[3])
     case DIM:
       s[0] = 1.0;
       s[1] = 2.0 / 3.0;
-      //        s(3) = 1.d0
-      s[2] = 0.40;
+      //        s(3) = 1.d0 // this should be 0.4 unless (1-legendre) is multiplied in the density calc.
+      s[2] = 0.40; // this is (1-legendre) where legendre = 0.6 in dynamo is accounted.
+      break;
+    case LIN: //linear, theta being 180
+      s[0] = 0.0;
+      s[1] = 8.0 / 3.0; // 4*(co**4 + si**4 - 1.0/3.0) in zig become 4*(1-1/3)
+      s[2] = 0.0;
+      break;
+    case ZIG: //zig-zag
+    case TRI: //trimer e.g. H2O
+      s[0] = 4.0*pow(cthe,2);
+      s[1] = 4.0*(pow(cthe,4) + pow(sthe,4) - 1.0/3.0);
+      s[2] = 4.0*(pow(cthe,2) * (3*pow(sthe,4) + pow(cthe,4)));
+      s[2] = s[2] - 0.6*s[0]; //legend in dyn, 0.6 is default value.
       break;
     default:
       s[0] = 0.0;
@@ -245,6 +259,7 @@ MEAM::get_Zij(const lattice_t latt)
     case HCP:
       return 12;
     case DIA:
+    case DIA3:
       return 4;
     case DIM:
       return 1;
@@ -256,6 +271,12 @@ MEAM::get_Zij(const lattice_t latt)
       return 12;
     case B2:
       return 8;
+    case CH4: // DYNAMO currenly implemented this way while it needs two Z values, 4 and 1
+      return 4;
+    case LIN:
+    case ZIG:
+    case TRI:
+      return 2;
       //        call error('Lattice not defined in get_Zij.')
   }
   return 0;
@@ -263,11 +284,13 @@ MEAM::get_Zij(const lattice_t latt)
 
 //-----------------------------------------------------------------------------
 // Number of second neighbors for the reference structure
-//   a = distance ratio R1/R2
-//   S = second neighbor screening function
+//   a = distance ratio R1/R2 (a2nn in dynamo)
+//   numscr = number of atoms that screen the 2NN bond
+//   S = second neighbor screening function (xfac, a part of b2nn in dynamo)
 //
 int
-MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, double& a, double& S)
+MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax,
+                const double stheta, double& a, double& S)
 {
 
   double C, x, sijk;
@@ -299,7 +322,7 @@ MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, doubl
     numscr = 2;
     break;
 
-  case DIA:
+  case DIA: // 2NN
     Zij2 = 12;
     a = sqrt(8.0 / 3.0);
     numscr = 1;
@@ -308,12 +331,35 @@ MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, doubl
     }
     break;
 
+  case DIA3: // 3NN
+    Zij2 = 12;
+    a = sqrt(11.0 / 3.0);
+    numscr = 4;
+    if (cmin < 0.500001) {
+        //          call error('can not do 2NN MEAM for dia')
+    }
+    break;
+
+  case CH4: //does not have 2nn structure so it returns 0
+  case LIN: //line
   case DIM:
     //        this really shouldn't be allowed; make sure screening is zero
     a = 1.0;
     S = 0.0;
     return 0;
 
+  case TRI: //TRI
+    Zij2 = 1;
+    a = 2.0*stheta;
+    numscr=2;
+    break;
+
+  case ZIG: //zig-zag
+    Zij2 = 2;
+    a = 2.0*stheta;
+    numscr=1;
+    break;
+
   case L12:
     Zij2 = 6;
     a = sqrt(2.0);
@@ -335,10 +381,38 @@ MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, doubl
   }
 
   // Compute screening for each first neighbor
-  C = 4.0 / (a * a) - 1.0;
+  if (latt==DIA3){ // special case for 3NN diamond structure
+	C = 1.0;
+  } else {
+	C = 4.0 / (a * a) - 1.0;
+  }
   x = (C - cmin) / (cmax - cmin);
   sijk = fcut(x);
   // There are numscr first neighbors screening the second neighbors
   S = MathSpecial::powint(sijk, numscr);
   return Zij2;
 }
+
+int
+MEAM::get_Zij2_b2nn(const lattice_t latt, const double cmin, const double cmax, double &S)
+{
+
+  double x, sijk, C;
+  int numscr = 0, Zij2 = 0;
+  switch (latt) {
+  case ZIG: //zig-zag for b11s and b22s term
+  case TRI: //trimer for b11s
+    Zij2 = 2;
+    numscr=1;
+    break;
+  default:
+    // unknown lattic flag in get Zij
+    //        call error('Lattice not defined in get_Zij.')
+    break;
+  }
+  C = 1.0;
+  x = (C - cmin) / (cmax - cmin);
+  sijk = fcut(x);
+  S = MathSpecial::powint(sijk, numscr);
+  return Zij2;
+}
\ No newline at end of file
diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp
index 8232c2aed5..99b330a83a 100644
--- a/src/USER-MEAMC/meam_setup_done.cpp
+++ b/src/USER-MEAMC/meam_setup_done.cpp
@@ -103,6 +103,9 @@ MEAM::alloyparams(void)
         this->alpha_meam[i][j] = this->alpha_meam[j][i];
         this->lattce_meam[i][j] = this->lattce_meam[j][i];
         this->nn2_meam[i][j] = this->nn2_meam[j][i];
+	    // theta for lin,tri,zig references
+        this->stheta_meam[i][j] = this->stheta_meam[j][i];
+        this->ctheta_meam[i][j] = this->ctheta_meam[j][i];
         // If i<j and term is unset, use default values (e.g. mean of i-i and
         // j-j)
       } else if (j > i) {
@@ -161,7 +164,7 @@ void
 MEAM::compute_pair_meam(void)
 {
 
-  double r;
+  double r, b2nn, phi_val;
   int j, a, b, nv2;
   double astar, frac, phizbl;
   int n, Z1, Z2;
@@ -215,7 +218,7 @@ MEAM::compute_pair_meam(void)
         if (this->nn2_meam[a][b] == 1) {
           Z1 = get_Zij(this->lattce_meam[a][b]);
           Z2 = get_Zij2(this->lattce_meam[a][b], this->Cmin_meam[a][a][b],
-                   this->Cmax_meam[a][a][b], arat, scrn);
+                     this->Cmax_meam[a][a][b], this->stheta_meam[a][b], arat, scrn);
 
           //     The B1, B2,  and L12 cases with NN2 have a trick to them; we need to
           //     compute the contributions from second nearest neighbors, like a-a
@@ -229,33 +232,26 @@ MEAM::compute_pair_meam(void)
             phiaa = phi_meam(rarat, a, a);
             Z1 = get_Zij(this->lattce_meam[a][a]);
             Z2 = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
-                     this->Cmax_meam[a][a][a], arat, scrn);
-            if (scrn > 0.0) {
-              for (n = 1; n <= 10; n++) {
-                phiaa = phiaa + pow((-Z2 * scrn / Z1), n) * phi_meam(rarat * pow(arat, n), a, a);
-              }
-            }
+                     this->Cmax_meam[a][a][a], this->stheta_meam[a][a], arat, scrn);
+            phiaa+= phi_meam_series(scrn, Z1, Z2, a, a, rarat, arat);
 
             //               phi_bb
             phibb = phi_meam(rarat, b, b);
             Z1 = get_Zij(this->lattce_meam[b][b]);
             Z2 = get_Zij2(this->lattce_meam[b][b], this->Cmin_meam[b][b][b],
-                     this->Cmax_meam[b][b][b], arat, scrn);
-            if (scrn > 0.0) {
-              for (n = 1; n <= 10; n++) {
-                phibb = phibb + pow((-Z2 * scrn / Z1), n) * phi_meam(rarat * pow(arat, n), b, b);
-              }
-            }
+                     this->Cmax_meam[b][b][b], this->stheta_meam[b][b], arat, scrn);
+            phibb+= phi_meam_series(scrn, Z1, Z2, b, b, rarat, arat);
 
             if (this->lattce_meam[a][b] == B1 || this->lattce_meam[a][b] == B2 ||
                 this->lattce_meam[a][b] == DIA) {
               //     Add contributions to the B1 or B2 potential
               Z1 = get_Zij(this->lattce_meam[a][b]);
               Z2 = get_Zij2(this->lattce_meam[a][b], this->Cmin_meam[a][a][b],
-                       this->Cmax_meam[a][a][b], arat, scrn);
+                       this->Cmax_meam[a][a][b], this->stheta_meam[a][b],  arat, scrn);
               this->phir[nv2][j] = this->phir[nv2][j] - Z2 * scrn / (2 * Z1) * phiaa;
               Z2 = get_Zij2(this->lattce_meam[a][b], this->Cmin_meam[b][b][a],
-                       this->Cmax_meam[b][b][a], arat, scrn2);
+                       this->Cmax_meam[b][b][a], this->stheta_meam[a][b], arat, scrn2);
+
               this->phir[nv2][j] = this->phir[nv2][j] - Z2 * scrn2 / (2 * Z1) * phibb;
 
             } else if (this->lattce_meam[a][b] == L12) {
@@ -277,10 +273,7 @@ MEAM::compute_pair_meam(void)
             }
 
           } else {
-            for (n = 1; n <= 10; n++) {
-              this->phir[nv2][j] =
-                this->phir[nv2][j] + pow((-Z2 * scrn / Z1), n) * phi_meam(r * pow(arat, n), a, b);
-            }
+            this->phir[nv2][j]+= phi_meam_series(scrn, Z1, Z2, a, b, r, arat);
           }
         }
 
@@ -325,11 +318,12 @@ MEAM::phi_meam(double r, int a, int b)
   double rho02, rho12, rho22, rho32;
   double scalfac, phiaa, phibb;
   double Eu;
-  double arat, scrn /*unused:,scrn2*/;
+  double arat, scrn, scrn2;
   int Z12, errorflag;
-  int n, Z1nn;
+  int n, Z1nn, Z2nn;
   lattice_t latta /*unused:,lattb*/;
   double rho_bkgd1, rho_bkgd2;
+  double b11s, b22s;
 
   double phi_m = 0.0;
 
@@ -403,14 +397,14 @@ MEAM::phi_meam(double r, int a, int b)
       if (this->ibar_meam[a] <= 0)
         G1 = 1.0;
       else {
-        get_shpfcn(this->lattce_meam[a][a], s1);
+        get_shpfcn(this->lattce_meam[a][a], this->stheta_meam[a][a], this->ctheta_meam[a][a], s1);
         Gam1 = (s1[0] * t11av + s1[1] * t21av + s1[2] * t31av) / (Z1 * Z1);
         G1 = G_gam(Gam1, this->ibar_meam[a], errorflag);
       }
       if (this->ibar_meam[b] <= 0)
         G2 = 1.0;
       else {
-        get_shpfcn(this->lattce_meam[b][b], s2);
+        get_shpfcn(this->lattce_meam[b][b], this->stheta_meam[b][b], this->ctheta_meam[b][b],  s2);
         Gam2 = (s2[0] * t12av + s2[1] * t22av + s2[2] * t32av) / (Z2 * Z2);
         G2 = G_gam(Gam2, this->ibar_meam[b], errorflag);
       }
@@ -470,20 +464,46 @@ MEAM::phi_meam(double r, int a, int b)
   } else if (this->lattce_meam[a][b] == L12) {
     phiaa = phi_meam(r, a, a);
     //       account for second neighbor a-a potential here...
-    Z1nn = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
-             this->Cmax_meam[a][a][a], arat, scrn);
-    if (scrn > 0.0) {
-      for (n = 1; n <= 10; n++) {
-        phiaa = phiaa + pow((-Z1nn * scrn / Z1), n) * phi_meam(r * pow(arat, n), a, a);
-      }
-    }
+    Z1nn = get_Zij(this->lattce_meam[a][a]);
+    Z2nn = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
+             this->Cmax_meam[a][a][a], this->stheta_meam[a][b], arat, scrn);
+
+
+    phiaa += phi_meam_series(scrn, Z1nn, Z2nn, a, a, r, arat);
     phi_m = Eu / 3.0 - F1 / 4.0 - F2 / 12.0 - phiaa;
 
+  } else if (this->lattce_meam[a][b] == CH4) {
+    phi_m = (5 * Eu - F1 - 4*F2)/4;
+
+  } else if (this->lattce_meam[a][b] == ZIG){
+      if (a==b){
+        phi_m = (2 * Eu - F1 - F2) / Z12;
+      } else{
+        Z1 = get_Zij(this->lattce_meam[a][b]);
+        Z2 = get_Zij2_b2nn(this->lattce_meam[a][b], this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b], scrn);
+        b11s = -Z2/Z1*scrn;
+        Z2 = get_Zij2_b2nn(this->lattce_meam[a][b], this->Cmin_meam[b][b][a], this->Cmax_meam[b][b][a], scrn2);
+        b22s = -Z2/Z1*scrn2;
+
+        phiaa = phi_meam(2.0*this->stheta_meam[a][b]*r, a, a);
+        phibb = phi_meam(2.0*this->stheta_meam[a][b]*r, b, b);
+        phi_m = (2.0*Eu - F1 - F2 + phiaa*b11s + phibb*b22s) / Z12;
+      }
+
+  } else if (this->lattce_meam[a][b] == TRI) {
+      if (a==b){
+        phi_m = (3.0*Eu - 2.0*F1 - F2) / Z12;
+     } else {
+        Z1 = get_Zij(this->lattce_meam[a][b]);
+        Z2 = get_Zij2_b2nn(this->lattce_meam[a][b], this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b], scrn);
+        b11s = -Z2/Z1*scrn;
+        phiaa = phi_meam(2.0*this->stheta_meam[a][b]*r, a, a);
+        phi_m = (3.0*Eu - 2.0*F1 - F2 + phiaa*b11s) / Z12;
+      }
+
   } else {
-    //
     // potential is computed from Rose function and embedding energy
     phi_m = (2 * Eu - F1 - F2) / Z12;
-    //
   }
 
   // if r = 0, just return 0
@@ -494,6 +514,31 @@ MEAM::phi_meam(double r, int a, int b)
   return phi_m;
 }
 
+//----------------------------------------------------------------------c
+// Compute 2NN series terms for phi
+//   To avoid nan values of phir due to rapid decrease of b2nn^n or/and
+//   argument of phi_meam, i.e. r*arat^n, in some cases (3NN dia with low Cmin value)
+//
+const double
+MEAM::phi_meam_series(const double scrn, const int Z1, const int Z2, const int a, const int b, const double r, const double arat)
+{
+  double phi_sum = 0.0;
+  double b2nn, phi_val;
+  if (scrn > 0.0) {
+    b2nn = -Z2*scrn/Z1;
+    for (int n = 1; n <= 10; n++) {
+      phi_val = MathSpecial::powint(b2nn,n) * phi_meam(r * MathSpecial::powint(arat, n), a, b);
+      if (iszero(phi_val)) {
+        // once either term becomes zero at some point, all folliwng will also be zero
+        // necessary to avoid numerical error (nan or infty) due to exponential decay in phi_meam
+        break;
+      }
+      phi_sum += phi_val;
+    }
+  }
+  return phi_sum;
+}
+
 //----------------------------------------------------------------------c
 // Compute background density for reference structure of each element
 void
@@ -509,7 +554,7 @@ MEAM::compute_reference_density(void)
     if (this->ibar_meam[a] <= 0)
       Gbar = 1.0;
     else {
-      get_shpfcn(this->lattce_meam[a][a], shp);
+      get_shpfcn(this->lattce_meam[a][a], this->stheta_meam[a][a], this->ctheta_meam[a][a], shp);
       gam = (this->t1_meam[a] * shp[0] + this->t2_meam[a] * shp[1] + this->t3_meam[a] * shp[2]) / (Z * Z);
       Gbar = G_gam(gam, this->ibar_meam[a], errorflag);
     }
@@ -524,7 +569,7 @@ MEAM::compute_reference_density(void)
     //     screening)
     if (this->nn2_meam[a][a] == 1) {
       Z2 = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
-               this->Cmax_meam[a][a][a], arat, scrn);
+               this->Cmax_meam[a][a][a], this->stheta_meam[a][a], arat, scrn);
       rho0_2nn = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * (arat - 1));
       rho0 = rho0 + Z2 * rho0_2nn * scrn;
     }
@@ -554,10 +599,15 @@ MEAM::get_tavref(double* t11av, double* t21av, double* t31av, double* t12av, dou
     case FCC:
     case BCC:
     case DIA:
+    case DIA3:
     case HCP:
     case B1:
     case DIM:
     case B2:
+    case CH4:
+    case LIN:
+    case ZIG:
+    case TRI:
       //     all neighbors are of the opposite type
       *t11av = t12;
       *t21av = t22;
@@ -603,7 +653,7 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
   double a1, a2;
   double s[3];
   lattice_t lat;
-  int Zij2nn;
+  int Zij,Zij2nn;
   double rhoa01nn, rhoa02nn;
   double rhoa01, rhoa11, rhoa21, rhoa31;
   double rhoa02, rhoa12, rhoa22, rhoa32;
@@ -624,13 +674,15 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
 
   lat = this->lattce_meam[a][b];
 
+  Zij = get_Zij(lat);
+
   *rho11 = 0.0;
   *rho21 = 0.0;
   *rho31 = 0.0;
   *rho12 = 0.0;
   *rho22 = 0.0;
   *rho32 = 0.0;
-  
+
   switch (lat) {
     case FCC:
       *rho01 = 12.0 * rhoa02;
@@ -645,6 +697,7 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
       *rho02 = 6.0 * rhoa01;
       break;
     case DIA:
+    case DIA3:
       *rho01 = 4.0 * rhoa02;
       *rho02 = 4.0 * rhoa01;
       *rho31 = 32.0 / 9.0 * rhoa32 * rhoa32;
@@ -657,7 +710,7 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
       *rho32 = 1.0 / 3.0 * rhoa31 * rhoa31;
       break;
     case DIM:
-      get_shpfcn(DIM, s);
+      get_shpfcn(DIM, 0, 0, s);
       *rho01 = rhoa02;
       *rho02 = rhoa01;
       *rho11 = s[0] * rhoa12 * rhoa12;
@@ -692,13 +745,71 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
       *rho01 = 8.0 * rhoa02;
       *rho02 = 8.0 * rhoa01;
       break;
+    case CH4:
+      *rho01 = 4.0 * rhoa02; //in assumption that 'a' represent carbon
+      *rho02 = rhoa01;	//in assumption that 'b' represent hydrogen
+
+      get_shpfcn(DIM, 0, 0, s);	//H
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+
+      get_shpfcn(CH4, 0, 0, s); //C
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      break;
+    case LIN:
+      *rho01 = rhoa02*Zij;
+      *rho02 = rhoa01*Zij;
+
+      get_shpfcn(LIN, this->stheta_meam[a][b], this->ctheta_meam[a][b], s);
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      break;
+    case ZIG:
+      *rho01 = rhoa02*Zij;
+      *rho02 = rhoa01*Zij;
+
+      get_shpfcn(ZIG, this->stheta_meam[a][b], this->ctheta_meam[a][b], s);
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      break;
+    case TRI:
+      *rho01 = rhoa02;
+      *rho02 = rhoa01*Zij;
+
+      get_shpfcn(TRI, this->stheta_meam[a][b], this->ctheta_meam[a][b], s);
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+      s[0] = 1.0;
+      s[1] = 2.0/3.0;
+      s[2] = 1.0 - 0.6*s[0];
+
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      break;
+
+
     // default:
     //        call error('Lattice not defined in get_densref.')
   }
 
   if (this->nn2_meam[a][b] == 1) {
 
-    Zij2nn = get_Zij2(lat, this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b], arat, scrn);
+
+    Zij2nn = get_Zij2(lat, this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b],
+                      this->stheta_meam[a][b], arat, scrn);
 
     a1 = arat * r / this->re_meam[a][a] - 1.0;
     a2 = arat * r / this->re_meam[b][b] - 1.0;
@@ -725,7 +836,8 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
       *rho01 = *rho01 + Zij2nn * scrn * rhoa01nn;
 
       //     Assume Zij2nn and arat don't depend on order, but scrn might
-      Zij2nn = get_Zij2(lat, this->Cmin_meam[b][b][a], this->Cmax_meam[b][b][a], arat, scrn);
+      Zij2nn = get_Zij2(lat, this->Cmin_meam[b][b][a], this->Cmax_meam[b][b][a],
+                        this->stheta_meam[a][b], arat, scrn);
       *rho02 = *rho02 + Zij2nn * scrn * rhoa02nn;
     }
   }
diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp
index 56bac1d5af..ac5718914c 100644
--- a/src/USER-MEAMC/meam_setup_global.cpp
+++ b/src/USER-MEAMC/meam_setup_global.cpp
@@ -56,12 +56,15 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* /*atwt*
         this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 2.0;
         break;
       case HCP:
-        this->re_meam[i][i] = tmplat[i];
-        break;
       case DIM:
+      case CH4:
+      case LIN:
+      case ZIG:
+      case TRI:
         this->re_meam[i][i] = tmplat[i];
         break;
       case DIA:
+      case DIA3:
         this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 4.0;
         break;
       //default:
@@ -87,4 +90,7 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* /*atwt*
   this->emb_lin_neg = 0;
   this->bkgd_dyn = 0;
   this->erose_form = 0;
+  // for trimer, zigzag, line refernece structure, sungkwang
+  setall2d(this->stheta_meam, 1.0); // stheta = sin(theta/2*pi/180) where theta is 180, so 1.0
+  setall2d(this->ctheta_meam, 0.0); // stheta = cos(theta/2*pi/180) where theta is 180, so 0
 }
diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/USER-MEAMC/meam_setup_param.cpp
index 585b5b5712..70d8b63598 100644
--- a/src/USER-MEAMC/meam_setup_param.cpp
+++ b/src/USER-MEAMC/meam_setup_param.cpp
@@ -1,6 +1,7 @@
 #include "meam.h"
 #include <algorithm>
 using namespace LAMMPS_NS;
+using namespace MathConst;
 
 //
 //     do a sanity check on index parameters
@@ -46,6 +47,8 @@ MEAM::meam_checkindex(int num, int lim, int nidx, int* idx /*idx(3)*/, int* ierr
 //     18 = zbl_meam
 //     19 = emb_lin_neg
 //     20 = bkgd_dyn
+//     21 = theta
+
 
 void
 MEAM::meam_setup_param(int which, double value, int nindex, int* index /*index(3)*/, int* errorflag)
@@ -203,6 +206,20 @@ MEAM::meam_setup_param(int which, double value, int nindex, int* index /*index(3
       this->bkgd_dyn = (int)value;
       break;
 
+    //     21 = theta
+    // see alloyparams(void) in meam_setup_done.cpp
+    case 21:
+      // const double PI = 3.141592653589793238463;
+      meam_checkindex(2, neltypes, nindex, index, errorflag);
+      if (*errorflag != 0)
+        return;
+      i1 = std::min(index[0], index[1]);
+      i2 = std::max(index[0], index[1]);
+      // we don't use theta, instead stheta and ctheta
+      this->stheta_meam[i1][i2] = sin(value/2*MY_PI/180.0);
+      this->ctheta_meam[i1][i2] = cos(value/2*MY_PI/180.0);
+      break;
+
     default:
       *errorflag = 1;
   }
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 77a5e9a461..9733ee2dad 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -33,13 +33,13 @@ using namespace LAMMPS_NS;
 
 #define MAXLINE 1024
 
-static const int nkeywords = 21;
+static const int nkeywords = 22;
 static const char *keywords[] = {
   "Ec","alpha","rho0","delta","lattce",
   "attrac","repuls","nn2","Cmin","Cmax","rc","delr",
   "augt1","gsmooth_factor","re","ialloy",
   "mixture_ref_t","erose_form","zbl",
-  "emb_lin_neg","bkgd_dyn"};
+  "emb_lin_neg","bkgd_dyn", "theta"};
 
 /* ---------------------------------------------------------------------- */
 

From f6bdf5662ec9af4f0eefcfc31fe4c61ba1d1bd10 Mon Sep 17 00:00:00 2001
From: "Jibril B. Coulibaly"
 <43829860+jibril-b-coulibaly@users.noreply.github.com>
Date: Fri, 6 Dec 2019 10:40:04 -0600
Subject: [PATCH 098/199] Update pair_granular.rst

Correct formula for tangent stiffness, consistent with `PairGranular::mix_stiffnessG()`
---
 doc/src/pair_granular.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst
index d5f522462d..294bec9b8c 100644
--- a/doc/src/pair_granular.rst
+++ b/doc/src/pair_granular.rst
@@ -432,7 +432,7 @@ option by an additional factor of *a*\ , the radius of the contact region. The t
 Here, *a* is the radius of the contact region, given by :math:`a =\sqrt{R\delta}`
 for all normal contact models, except for *jkr*\ , where it is given
 implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see
-discussion above. To match the Mindlin solution, one should set :math:`k_t = 8G`, where :math:`G` is the shear modulus, related to Young's modulus
+discussion above. To match the Mindlin solution, one should set :math:`k_t = 4G/(2-\nu)`, where :math:`G` is the shear modulus, related to Young's modulus
 :math:`E` by :math:`G = E/(2(1+\nu))`, where :math:`\nu` is Poisson's ratio. This
 can also be achieved by specifying *NULL* for :math:`k_t`, in which case a
 normal contact model that specifies material parameters :math:`E` and

From 38e82cbbcc9c599c67a1ab5273e220feea357469 Mon Sep 17 00:00:00 2001
From: Tongtong Shen <shen276@halstead-fe02.rcac.purdue.edu>
Date: Fri, 6 Dec 2019 12:02:42 -0500
Subject: [PATCH 099/199] This fix_deposit document added the description of
 the new rotation flag and its use.

---
 doc/src/fix_deposit.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index fb597b6374..45ef7d655e 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -19,7 +19,7 @@ type = atom type to assign to inserted atoms (offset for molecule insertion) :l
 M = insert a single atom or molecule every M steps :l
 seed = random # seed (positive integer) :l
 one or more keyword/value pairs may be appended to args :l
-keyword = {region} or {id} or {global} or {local} or {near} or {gaussian} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} :l
+keyword = {region} or {id} or {global} or {local} or {near} or {gaussian} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} or {orientation} :l
   {region} value = region-ID
     region-ID = ID of region to use as insertion volume
   {id} value = {max} or {next}
@@ -248,6 +248,8 @@ command must have been previously used to define the lattice spacing.
 Note that the units choice affects all the keyword values that have
 units of distance or velocity.
 
+The {orientation} keyword determines the fixed rotation axis r = (rx,ry,rz) for randomly rotated of any inserted molecules. Note that the for a 2d simulation, (rx,ry,rz) should equal to (0,0,1).
+
 NOTE: If you are monitoring the temperature of a system where the atom
 count is changing due to adding particles, you typically should use
 the "compute_modify dynamic yes"_compute_modify.html command for the

From 5859b18d2f7b1d63b45a9e541a6908f598b0a16b Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 6 Dec 2019 11:04:50 -0700
Subject: [PATCH 100/199] enable fix rigid commands to add gravity to COM of
 rigid bodies

---
 src/RIGID/fix_rigid.cpp       | 62 +++++++++++++++++++++++++++++------
 src/RIGID/fix_rigid.h         |  6 +++-
 src/RIGID/fix_rigid_small.cpp | 40 ++++++++++++++++++++--
 src/RIGID/fix_rigid_small.h   |  3 ++
 src/fix_gravity.cpp           | 52 +++++++++++++++++++++++++----
 src/fix_gravity.h             |  5 ++-
 6 files changed, 146 insertions(+), 22 deletions(-)

diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 3e6130ac7c..5e994810ac 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -52,8 +52,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),
   tflag(NULL), langextra(NULL), sum(NULL), all(NULL),
   remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),
-  dorient(NULL), id_dilate(NULL), random(NULL), avec_ellipsoid(NULL),
-  avec_line(NULL), avec_tri(NULL)
+  dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL), 
+  avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL)
 {
   int i,ibody;
 
@@ -124,14 +124,17 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
     if (custom_flag) {
       if (narg < 5) error->all(FLERR,"Illegal fix rigid command");
 
-      // determine whether atom-style variable or atom property is used.
+      // determine whether atom-style variable or atom property is used
+
       if (strstr(arg[4],"i_") == arg[4]) {
         int is_double=0;
         int custom_index = atom->find_custom(arg[4]+2,is_double);
         if (custom_index == -1)
-          error->all(FLERR,"Fix rigid custom requires previously defined property/atom");
+          error->all(FLERR,"Fix rigid custom requires "
+                     "previously defined property/atom");
         else if (is_double)
-          error->all(FLERR,"Fix rigid custom requires integer-valued property/atom");
+          error->all(FLERR,"Fix rigid custom requires "
+                     "integer-valued property/atom");
         int minval = INT_MAX;
         int *value = atom->ivector[custom_index];
         for (i = 0; i < nlocal; i++)
@@ -163,12 +166,15 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
           if (mask[i] & groupbit)
             molecule[i] = (tagint)((tagint)value[i] - minval + 1);
         delete[] value;
+
       } else error->all(FLERR,"Unsupported fix rigid custom property");
+
     } else {
       if (atom->molecule_flag == 0)
         error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");
       molecule = atom->molecule;
     }
+
     iarg = 4 + custom_flag;
 
     tagint maxmol_tag = -1;
@@ -297,6 +303,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   }
 
   // number of linear rigid bodies is counted later
+
   nlinear = 0;
 
   // parse optional args
@@ -308,12 +315,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   tstat_flag = 0;
   pstat_flag = 0;
   allremap = 1;
-  id_dilate = NULL;
   t_chain = 10;
   t_iter = 1;
   t_order = 3;
   p_chain = 10;
+
   inpfile = NULL;
+  id_gravity = NULL;
+  id_dilate = NULL;
 
   pcouple = NONE;
   pstyle = ANISO;
@@ -543,12 +552,20 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
 
     } else if (strcmp(arg[iarg],"reinit") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
       if (strcmp("yes",arg[iarg+1]) == 0) reinitflag = 1;
       else if  (strcmp("no",arg[iarg+1]) == 0) reinitflag = 0;
       else error->all(FLERR,"Illegal fix rigid command");
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"gravity") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
+      delete [] id_gravity;
+      int n = strlen(arg[iarg+1]) + 1;
+      id_gravity = new char[n];
+      strcpy(id_gravity,arg[iarg+1]);
+      iarg += 2;
+
     } else error->all(FLERR,"Illegal fix rigid command");
   }
 
@@ -621,6 +638,9 @@ FixRigid::~FixRigid()
 
   delete random;
   delete [] inpfile;
+  delete [] id_dilate;
+  delete [] id_gravity;
+
   memory->destroy(mol2body);
   memory->destroy(body2mol);
 
@@ -687,7 +707,7 @@ void FixRigid::init()
   avec_tri = (AtomVecTri *) atom->style_match("tri");
 
   // warn if more than one rigid fix
-  // if earlyflag, warn if any post-force fixes come after POEMS fix
+  // if earlyflag, warn if any post-force fixes come after a rigid fix
 
   int count = 0;
   for (i = 0; i < modify->nfix; i++)
@@ -701,7 +721,8 @@ void FixRigid::init()
       if (rflag && (modify->fmask[i] & POST_FORCE) &&
           !modify->fix[i]->rigid_flag) {
         char str[128];
-        snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
+        snprintf(str,128,"Fix %s alters forces after fix rigid",
+                 modify->fix[i]->id);
         error->warning(FLERR,str);
       }
     }
@@ -713,12 +734,24 @@ void FixRigid::init()
     if (strcmp(modify->fix[i]->style,"npt") == 0) break;
     if (strcmp(modify->fix[i]->style,"nph") == 0) break;
   }
+
   if (i < modify->nfix) {
     for (int j = i; j < modify->nfix; j++)
       if (strcmp(modify->fix[j]->style,"rigid") == 0)
         error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
   }
 
+  // add gravity forces based on gravity vector from fix
+
+  if (id_gravity) {
+    int ifix = modify->find_fix(id_gravity);
+    if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 
+      error->all(FLERR,"Fix rigid gravity fix is invalid");
+    int tmp;
+    gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
+  }
+
   // timestep info
 
   dtv = update->dt;
@@ -1061,8 +1094,17 @@ void FixRigid::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
-}
 
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+    for (ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
+}
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h
index 8c4ab9ed49..c261d89cce 100644
--- a/src/RIGID/fix_rigid.h
+++ b/src/RIGID/fix_rigid.h
@@ -66,7 +66,8 @@ class FixRigid : public Fix {
   double *step_respa;
   int triclinic;
 
-  char *inpfile;             // file to read rigid body attributes from
+  char *inpfile;            // file to read rigid body attributes from
+
   int rstyle;               // SINGLE,MOLECULE,GROUP
   int setupflag;            // 1 if body properties are setup, else 0
   int earlyflag;            // 1 if forces/torques computed at post_force()
@@ -131,6 +132,9 @@ class FixRigid : public Fix {
   int dilate_group_bit;      // mask for dilation group
   char *id_dilate;           // group name to dilate
 
+  char *id_gravity;         // ID of fix gravity command to add gravity forces
+  double *gvec;             // ptr to gravity vector inside the fix
+
   class RanMars *random;
   class AtomVecEllipsoid *avec_ellipsoid;
   class AtomVecLine *avec_line;
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index ba570d5840..4d2776b9ff 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -57,7 +57,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
   xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
   avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
   itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL),
-  id_dilate(NULL), onemols(NULL)
+  id_dilate(NULL), id_gravity(NULL), onemols(NULL)
 {
   int i;
 
@@ -107,7 +107,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       bodyID = new tagint[nlocal];
       customflag = 1;
 
-      // determine whether atom-style variable or atom property is used.
+      // determine whether atom-style variable or atom property is used
+
       if (strstr(arg[4],"i_") == arg[4]) {
         int is_double=0;
         int custom_index = atom->find_custom(arg[4]+2,is_double);
@@ -356,6 +357,13 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       p_chain = force->numeric(FLERR,arg[iarg+1]);
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"gravity") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
+      delete [] id_gravity;
+      int n = strlen(arg[iarg+1]) + 1;
+      id_gravity = new char[n];
+      strcpy(id_gravity,arg[iarg+1]);
+      iarg += 2;
 
     } else error->all(FLERR,"Illegal fix rigid/small command");
   }
@@ -515,6 +523,8 @@ FixRigidSmall::~FixRigidSmall()
 
   delete random;
   delete [] inpfile;
+  delete [] id_dilate;
+  delete [] id_gravity;
 
   memory->destroy(langextra);
   memory->destroy(mass_body);
@@ -543,6 +553,7 @@ void FixRigidSmall::init()
   triclinic = domain->triclinic;
 
   // warn if more than one rigid fix
+  // if earlyflag, warn if any post-force fixes come after a rigid fix
 
   int count = 0;
   for (i = 0; i < modify->nfix; i++)
@@ -575,6 +586,17 @@ void FixRigidSmall::init()
         error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
   }
 
+  // add gravity forces based on gravity vector from fix
+
+  if (id_gravity) {
+    int ifix = modify->find_fix(id_gravity);
+    if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 
+      error->all(FLERR,"Fix rigid/small gravity fix is invalid");
+    int tmp;
+    gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
+  }
+
   // timestep info
 
   dtv = update->dt;
@@ -954,8 +976,20 @@ void FixRigidSmall::compute_forces_and_torques()
       tcm[2] += langextra[ibody][5];
     }
   }
-}
 
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+    double mass;
+    for (ibody = 0; ibody < nlocal_body; ibody++) {
+      mass = body[ibody].mass;
+      fcm = body[ibody].fcm;
+      fcm[0] += gvec[0]*mass;
+      fcm[1] += gvec[1]*mass;
+      fcm[2] += gvec[2]*mass;
+    }
+  }
+}
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index 0d1cdb5963..974f5711e2 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -164,6 +164,9 @@ class FixRigidSmall : public Fix {
   int dilate_group_bit;      // mask for dilation group
   char *id_dilate;           // group name to dilate
 
+  char *id_gravity;         // ID of fix gravity command to add gravity forces
+  double *gvec;             // ptr to gravity vector inside the fix
+
   double p_current[3],p_target[3];
 
   // molecules added on-the-fly as rigid bodies
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 14ba913c01..c36d2230c5 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -37,7 +37,8 @@ enum{CONSTANT,EQUAL};
 
 FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), xstr(NULL), ystr(NULL), zstr(NULL)
+  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), 
+  xstr(NULL), ystr(NULL), zstr(NULL)
 {
   if (narg < 5) error->all(FLERR,"Illegal fix gravity command");
 
@@ -61,8 +62,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
     mstyle = CONSTANT;
   }
 
+  int iarg;
+
   if (strcmp(arg[4],"chute") == 0) {
-    if (narg != 6) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 6) error->all(FLERR,"Illegal fix gravity command");
     style = CHUTE;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -73,9 +76,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       vert = force->numeric(FLERR,arg[5]);
       vstyle = CONSTANT;
     }
+    iarg = 6;
 
   } else if (strcmp(arg[4],"spherical") == 0) {
-    if (narg != 7) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 7) error->all(FLERR,"Illegal fix gravity command");
     style = SPHERICAL;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -95,9 +99,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       theta = force->numeric(FLERR,arg[6]);
       tstyle = CONSTANT;
     }
+    iarg = 7;
 
   } else if (strcmp(arg[4],"vector") == 0) {
-    if (narg != 8) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 8) error->all(FLERR,"Illegal fix gravity command");
     style = VECTOR;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -126,9 +131,23 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       zdir = force->numeric(FLERR,arg[7]);
       zstyle = CONSTANT;
     }
+    iarg = 8;
 
   } else error->all(FLERR,"Illegal fix gravity command");
 
+  // optional keywords
+
+  disable = 0;
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"disable") == 0) {
+      disable = 1;
+      iarg++;
+    } else error->all(FLERR,"Illegal fix gravity command");
+  }
+
+  // initializations
+
   degree2rad = MY_PI/180.0;
   time_origin = update->ntimestep;
 
@@ -266,6 +285,12 @@ void FixGravity::post_force(int /*vflag*/)
     set_acceleration();
   }
 
+  // just exit if application of force is disabled
+
+  if (disable) return;
+
+  // apply gravity force to each particle
+
   double **x = atom->x;
   double **f = atom->f;
   double *rmass = atom->rmass;
@@ -338,9 +363,9 @@ void FixGravity::set_acceleration()
     }
   }
 
-  xacc = magnitude*xgrav;
-  yacc = magnitude*ygrav;
-  zacc = magnitude*zgrav;
+  gvec[0] = xacc = magnitude*xgrav;
+  gvec[1] = yacc = magnitude*ygrav;
+  gvec[2] = zacc = magnitude*zgrav;
 }
 
 /* ----------------------------------------------------------------------
@@ -357,3 +382,16 @@ double FixGravity::compute_scalar()
   }
   return egrav_all;
 }
+
+/* ----------------------------------------------------------------------
+   extract current gravity direction vector
+------------------------------------------------------------------------- */
+
+void *FixGravity::extract(const char *name, int &dim)
+{
+  if (strcmp(name,"gvec") == 0) {
+    dim = 1;
+    return (void *) gvec;
+  }
+  return NULL;
+}
diff --git a/src/fix_gravity.h b/src/fix_gravity.h
index 1f18ee274b..ba6a61ee0d 100644
--- a/src/fix_gravity.h
+++ b/src/fix_gravity.h
@@ -36,9 +36,10 @@ class FixGravity : public Fix {
   virtual void post_force(int);
   virtual void post_force_respa(int, int, int);
   double compute_scalar();
+  void *extract(const char *, int &);
 
  protected:
-  int style;
+  int style,disable;
   double magnitude;
   double vert,phi,theta;
   double xdir,ydir,zdir;
@@ -46,6 +47,8 @@ class FixGravity : public Fix {
   double degree2rad;
   int ilevel_respa;
   int time_origin;
+  double gvec[3];
+
   int eflag;
   double egrav,egrav_all;
 

From a2f9fa8e78dbea0c599395e9c266d5aa4f5f3cbc Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Fri, 6 Dec 2019 21:41:02 +0300
Subject: [PATCH 101/199] Separate the computation of hneigh into another
 kernel

Simplify the main GPU kernel and add another kernel 'k_pair_reneigh'. It works good on GTX1070 (Pascal), but still there is a problem with non-deterministic results on Volta.

I reimplement BaseCharge::compute methods in the child class LJ_TIP4PLong to correctly embed a new kernel in the code.

Also commit includes some codestyle fixes.
---
 lib/gpu/lal_lj_tip4p_long.cpp          | 160 ++++++++++++++++++++++---
 lib/gpu/lal_lj_tip4p_long.cu           | 139 ++++++++++-----------
 lib/gpu/lal_lj_tip4p_long.h            |  27 ++++-
 lib/gpu/lal_lj_tip4p_long_ext.cpp      |  12 +-
 src/GPU/pair_lj_cut_tip4p_long_gpu.cpp |  19 +--
 5 files changed, 252 insertions(+), 105 deletions(-)

diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
index 9b20aea638..890bbab3bd 100644
--- a/lib/gpu/lal_lj_tip4p_long.cpp
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -24,26 +24,26 @@ const char *lj_tip4p=0;
 #include "lal_lj_tip4p_long.h"
 #include <cassert>
 using namespace LAMMPS_AL;
-#define LJ_TIP4PLong_T LJ_TIP4PLong<numtyp, acctyp>
+#define LJTIP4PLongT LJ_TIP4PLong<numtyp, acctyp>
 
 extern Device<PRECISION,ACC_PRECISION> device;
 
 template <class numtyp, class acctyp>
-LJ_TIP4PLong<numtyp, acctyp>::LJ_TIP4PLong(): BaseCharge<numtyp,acctyp>(), _allocated(false) {
+LJTIP4PLongT::LJ_TIP4PLong(): BaseCharge<numtyp,acctyp>(), _allocated(false) {
 }
 
 template <class numtyp, class acctyp>
-LJ_TIP4PLong<numtyp, acctyp>::~LJ_TIP4PLong() {
+LJTIP4PLongT::~LJ_TIP4PLong() {
   clear();
 }
 
 template <class numtyp, class acctyp>
-int LJ_TIP4PLong<numtyp, acctyp>::bytes_per_atom(const int max_nbors) const {
+int LJTIP4PLongT::bytes_per_atom(const int max_nbors) const {
   return this->bytes_per_atom_atomic(max_nbors);
 }
 
 template <class numtyp, class acctyp>
-int LJ_TIP4PLong<numtyp, acctyp>::init(const int ntypes,
+int LJTIP4PLongT::init(const int ntypes,
     double **host_cutsq, double **host_lj1,
     double **host_lj2, double **host_lj3,
     double **host_lj4, double **host_offset,
@@ -65,6 +65,7 @@ int LJ_TIP4PLong<numtyp, acctyp>::init(const int ntypes,
   if (success!=0)
     return success;
   k_pair_distrib.set_function(*this->pair_program,"k_lj_tip4p_long_distrib");
+  k_pair_reneigh.set_function(*this->pair_program,"k_lj_tip4p_reneigh");
 
   TypeH = tH;
   TypeO = tO;
@@ -143,7 +144,7 @@ int LJ_TIP4PLong<numtyp, acctyp>::init(const int ntypes,
 
 
 template <class numtyp, class acctyp>
-void LJ_TIP4PLong<numtyp, acctyp>::clear() {
+void LJTIP4PLongT::clear() {
   if (!_allocated)
     return;
   _allocated=false;
@@ -161,12 +162,13 @@ void LJ_TIP4PLong<numtyp, acctyp>::clear() {
   //force_comp.clear();
 
   k_pair_distrib.clear();
+  k_pair_reneigh.clear();
 
   this->clear_atomic();
 }
 
 template <class numtyp, class acctyp>
-double LJ_TIP4PLong<numtyp, acctyp>::host_memory_usage() const {
+double LJTIP4PLongT::host_memory_usage() const {
   return this->host_memory_usage_atomic()+sizeof(LJ_TIP4PLong<numtyp,acctyp>);
 }
 
@@ -174,7 +176,7 @@ double LJ_TIP4PLong<numtyp, acctyp>::host_memory_usage() const {
 // Calculate energies, forces, and torques
 // ---------------------------------------------------------------------------
 template <class numtyp, class acctyp>
-void LJ_TIP4PLong<numtyp, acctyp>::loop(const bool _eflag, const bool _vflag) {
+void LJTIP4PLongT::loop(const bool _eflag, const bool _vflag) {
   // Compute the block size and grid size to keep all cores busy
   const int BX=this->block_size();
   int eflag, vflag;
@@ -188,13 +190,24 @@ void LJ_TIP4PLong<numtyp, acctyp>::loop(const bool _eflag, const bool _vflag) {
   else
     vflag=0;
 
-  int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
-                               (BX/this->_threads_per_atom)));
-
   int ainum=this->ans->inum();
+  const int nall = this->atom->nall();
   int nbor_pitch=this->nbor->nbor_pitch();
   this->time_pair.start();
+  int GX;
 
+  if (t_ago == 0) {
+    GX=static_cast<int>(ceil(static_cast<double>(nall)/BX));
+    this->k_pair_reneigh.set_size(GX,BX);
+    this->k_pair_reneigh.run(&this->atom->x,
+        &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+        &nall, &ainum,&nbor_pitch, &this->_threads_per_atom,
+        &hneight, &m, &TypeO, &TypeH,
+        &tag, &map_array, &atom_sametag);
+  }
+
+  GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
+                               (BX/this->_threads_per_atom)));
   this->k_pair.set_size(GX,BX);
   if (vflag){
 	  this->ansO.resize_ib(ainum*3);
@@ -213,17 +226,16 @@ void LJ_TIP4PLong<numtyp, acctyp>::loop(const bool _eflag, const bool _vflag) {
           &atom_sametag, &this->ansO);
   GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
   this->k_pair_distrib.set_size(GX,BX);
-  this->k_pair_distrib.run(&this->atom->x, &this->ans->force, &this->ans->engv, &eflag, &vflag,
-      &ainum, &nbor_pitch, &this->_threads_per_atom,
-      &hneight, &m, &TypeO, &TypeH, &alpha,
-      &this->atom->q,  &this->ansO);
+  this->k_pair_distrib.run(&this->atom->x, &this->ans->force, &this->ans->engv,
+      &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom,
+      &hneight, &m, &TypeO, &TypeH, &alpha,&this->atom->q,  &this->ansO);
   this->time_pair.stop();
 }
 
 
 template <class numtyp, class acctyp>
-void LJ_TIP4PLong<numtyp, acctyp>::copy_relations_data(int **hn, double **newsite, int n,
-    int* tag, int *map_array, int map_size, int *sametag, int max_same, int ago){
+void LJTIP4PLongT::copy_relations_data(int n, int* tag, int *map_array,
+                      int map_size, int *sametag, int max_same, int ago){
   int nall = n;
   const int hn_sz = n*4; // matrix size = col size * col number
   hneight.resize_ib(hn_sz);
@@ -250,4 +262,118 @@ void LJ_TIP4PLong<numtyp, acctyp>::copy_relations_data(int **hn, double **newsit
   host_tag_write.clear();
 }
 
+
+
+
+// ---------------------------------------------------------------------------
+// Copy nbor list from host if necessary and then calculate forces, virials,..
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+void LJTIP4PLongT::compute(const int f_ago, const int inum_full,
+                               const int nall, double **host_x, int *host_type,
+                               int *ilist, int *numj, int **firstneigh,
+                               const bool eflag, const bool vflag,
+                               const bool eatom, const bool vatom,
+                               int &host_start, const double cpu_time,
+                               bool &success, double *host_q,
+                               const int nlocal, double *boxlo, double *prd) {
+  this->acc_timers();
+  if (inum_full==0) {
+    host_start=0;
+    // Make sure textures are correct if realloc by a different hybrid style
+    this->resize_atom(0,nall,success);
+    this->zero_timers();
+    return;
+  }
+
+  int ago=this->hd_balancer.ago_first(f_ago);
+  int inum=this->hd_balancer.balance(ago,inum_full,cpu_time);
+  this->ans->inum(inum);
+  host_start=inum;
+
+  if (ago==0) {
+    this->reset_nbors(nall, inum, ilist, numj, firstneigh, success);
+    if (!success)
+      return;
+  }
+
+  this->atom->cast_x_data(host_x,host_type);
+  this->atom->cast_q_data(host_q);
+  this->hd_balancer.start_timer();
+  this->atom->add_x_data(host_x,host_type);
+  this->atom->add_q_data();
+
+  this->device->precompute(f_ago,nlocal,nall,host_x,host_type,success,host_q,
+                     boxlo, prd);
+
+  t_ago = ago;
+  loop(eflag,vflag);
+  this->ans->copy_answers(eflag,vflag,eatom,vatom,ilist);
+  this->device->add_ans_object(this->ans);
+  this->hd_balancer.stop_timer();
+}
+
+// ---------------------------------------------------------------------------
+// Reneighbor on GPU if necessary and then compute forces, virials, energies
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+int** LJTIP4PLongT::compute(const int ago, const int inum_full,
+                                const int nall, double **host_x, int *host_type,
+                                double *sublo, double *subhi, tagint *tag,
+                                int *map_array, int map_size, int *sametag, int max_same,
+                                int **nspecial, tagint **special, const bool eflag,
+                                const bool vflag, const bool eatom,
+                                const bool vatom, int &host_start,
+                                int **ilist, int **jnum,
+                                const double cpu_time, bool &success,
+                                double *host_q, double *boxlo, double *prd) {
+  this->acc_timers();
+  if (inum_full==0) {
+    host_start=0;
+    // Make sure textures are correct if realloc by a different hybrid style
+    this->resize_atom(0,nall,success);
+    this->zero_timers();
+    return NULL;
+  }
+
+  this->hd_balancer.balance(cpu_time);
+  int inum=this->hd_balancer.get_gpu_count(ago,inum_full);
+  this->ans->inum(inum);
+  host_start=inum;
+
+  // Build neighbor list on GPU if necessary
+  if (ago==0) {
+    this->build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
+                    sublo, subhi, tag, nspecial, special, success);
+    if (!success)
+      return NULL;
+    this->atom->cast_q_data(host_q);
+    this->hd_balancer.start_timer();
+  } else {
+    this->atom->cast_x_data(host_x,host_type);
+    this->atom->cast_q_data(host_q);
+    this->hd_balancer.start_timer();
+    this->atom->add_x_data(host_x,host_type);
+  }
+  this->atom->add_q_data();
+  *ilist=this->nbor->host_ilist.begin();
+  *jnum=this->nbor->host_acc.begin();
+
+  copy_relations_data(nall, tag, map_array, map_size, sametag, max_same, ago);
+
+  this->device->precompute(ago,inum_full,nall,host_x,host_type,success,host_q,
+                     boxlo, prd);
+
+  t_ago = ago;
+  loop(eflag,vflag);
+  this->ans->copy_answers(eflag,vflag,eatom,vatom);
+  this->device->add_ans_object(this->ans);
+  this->hd_balancer.stop_timer();
+
+  return this->nbor->host_jlist.begin()-host_start;
+}
+
+
+
+
 template class LJ_TIP4PLong<PRECISION,ACC_PRECISION>;
diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
index 65f3cf9f67..2b98586eaf 100644
--- a/lib/gpu/lal_lj_tip4p_long.cu
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -158,6 +158,62 @@ __kernel void k_lj_tip4p_long_distrib(const __global numtyp4 *restrict x_,
   } // if ii
 }
 
+__kernel void k_lj_tip4p_reneigh(const __global numtyp4 *restrict x_,
+    const __global int * dev_nbor,
+    const __global int * dev_packed,
+    const int nall, const int inum,
+    const int nbor_pitch, const int t_per_atom,
+    __global int *restrict hneigh,
+    __global numtyp4 *restrict m,
+    const int typeO, const int typeH,
+    const __global int *restrict tag, const __global int *restrict map,
+    const __global int *restrict sametag) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+  int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
+
+  if (i<nall) {
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+
+    int iH1, iH2, iO;
+    int itype = ix.w;
+    if(itype == typeO) {
+      iO  = i;
+      if (hneigh[i*4+2] != -1) {
+        iH1 = atom_mapping(map, tag[i] + 1);
+        iH2 = atom_mapping(map, tag[i] + 2);
+        // set iH1,iH2 to closest image to O
+        iH1 = closest_image(i, iH1, sametag, x_);
+        iH2 = closest_image(i, iH2, sametag, x_);
+        hneigh[i*4  ] = iH1;
+        hneigh[i*4+1] = iH2;
+        hneigh[i*4+2] = -1;
+      }
+    } else {
+      if (hneigh[i*4+2] != -1) {
+        int iI, iH;
+        iI = atom_mapping(map,tag[i] - 1);
+        numtyp4 iIx; fetch4(iIx,iI,pos_tex); //x_[iI];
+        if ((int)iIx.w == typeH) {
+          iO = atom_mapping(map,tag[i] - 2);
+          iO  = closest_image(i, iO, sametag, x_);
+          iH1 = closest_image(i, iI, sametag, x_);
+          iH2 = i;
+        } else { //if ((int)iIx.w == typeO)
+          iH = atom_mapping(map, tag[i] + 1);
+          iO  = closest_image(i,iI,sametag, x_);
+          iH1 = i;
+          iH2 = closest_image(i,iH,sametag, x_);
+        }
+        hneigh[i*4+0] = iO;
+        hneigh[i*4+1] += -1;
+        hneigh[i*4+2] = -1;
+      }
+    }
+  }
+}
+
+
 __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
     const __global numtyp4 *restrict lj1,
     const __global numtyp4 *restrict lj3,
@@ -211,63 +267,17 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
 
     if(itype == typeO) {
       iO  = i;
-      if (hneigh[i*4+2] != -1) {
-        iH1 = atom_mapping(map, tag[i] + 1);
-        iH2 = atom_mapping(map, tag[i] + 2);
-        // set iH1,iH2 to closest image to O
-        iH1 = closest_image(i, iH1, sametag, x_);
-        iH2 = closest_image(i, iH2, sametag, x_);
-        hneigh[  i*4  ] = iH1;
-        hneigh[  i*4+1] = iH2;
-        hneigh[  i*4+2] = -1;
-        hneigh[iH1*4  ] = i;
-        hneigh[iH1*4+1] += -1;
-        hneigh[iH1*4+2] = -1;
-        hneigh[iH2*4  ] = i;
-        hneigh[iH2*4+1] += -1;
-        hneigh[iH2*4+2] = -1;
-      } else {
-        iH1 = hneigh[i*4  ];
-        iH2 = hneigh[i*4+1];
-      }
+      iH1 = hneigh[i*4  ];
+      iH2 = hneigh[i*4+1];
       if(fabs(m[iO].w) <= eq_zero) {
         compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
         m[iO].w = qtmp;
       }
       x1 = m[iO];
     } else {
-      if (hneigh[i*4+2] != -1) {
-        int iI, iH;
-        iI = atom_mapping(map,tag[i] - 1);
-        numtyp4 iIx; fetch4(iIx,iI,pos_tex); //x_[iI];
-        if ((int)iIx.w == typeH) {
-          iO = atom_mapping(map,tag[i] - 2);
-          iO  = closest_image(i, iO, sametag, x_);
-          iH1 = closest_image(i, iI, sametag, x_);
-          iH2 = i;
-        } else { //if ((int)iIx.w == typeO)
-          iH = atom_mapping(map, tag[i] + 1);
-          iO  = closest_image(i,iI,sametag, x_);
-          iH1 = i;
-          iH2 = closest_image(i,iH,sametag, x_);
-        }
-
-        hneigh[iH1*4+0] = iO;
-        hneigh[iH1*4+1] += -1;
-        hneigh[iH1*4+2] = -1;
-
-        hneigh[iH2*4+0] = iO;
-        hneigh[iH2*4+1] += -1;
-        hneigh[iH2*4+2] = -1;
-
-        hneigh[iO*4+0] = iH1;
-        hneigh[iO*4+1] = iH2;
-        hneigh[iO*4+2] = -1;
-      } else {
-        iO  = hneigh[i *4  ];
-        iH1 = hneigh[iO*4  ];
-        iH2 = hneigh[iO*4+1];
-      }
+      iO  = hneigh[i *4  ];
+      iH1 = hneigh[iO*4  ];
+      iH2 = hneigh[iO*4+1];
       if (iO >= inum) {
         non_local_oxy = 1;
         if(fabs(m[iO].w) <= eq_zero) {
@@ -327,25 +337,8 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
         if(itype == typeO || jtype == typeO) {
           if (jtype == typeO) {
             jO = j;
-            if (hneigh[j*4+2] != -1) {
-              jH1 = atom_mapping(map,tag[j] + 1);
-              jH2 = atom_mapping(map,tag[j] + 2);
-              // set iH1,iH2 to closest image to O
-              jH1 = closest_image(j, jH1, sametag, x_);
-              jH2 = closest_image(j, jH2, sametag, x_);
-              hneigh[j*4  ] = jH1;
-              hneigh[j*4+1] = jH2;
-              hneigh[j*4+2] = -1;
-              hneigh[jH1*4  ] = j;
-              hneigh[jH1*4+1] += -1;
-              hneigh[jH1*4+2] = -1;
-              hneigh[jH2*4  ] = j;
-              hneigh[jH2*4+1] += -1;
-              hneigh[jH2*4+2] = -1;
-            } else {
-              jH1 = hneigh[j*4  ];
-              jH2 = hneigh[j*4+1];
-            }
+            jH1 = hneigh[j*4  ];
+            jH2 = hneigh[j*4+1];
             if (fabs(m[j].w) <= eq_zero) {
               compute_newsite(j, jH1, jH2, &m[j], alpha, x_);
               m[j].w = qj;
@@ -405,7 +398,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
                 vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
                 vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
                 vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
-                vdj.w = vdj.w;
+                //vdj.w = vdj.w;
                 virial[0] += (ix.x - vdj.x)*fd.x;
                 virial[1] += (ix.y - vdj.y)*fd.y;
                 virial[2] += (ix.z - vdj.z)*fd.z;
@@ -422,7 +415,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
               vdi.x = xO.x*cO + xH1.x*cH + xH2.x*cH;
               vdi.y = xO.y*cO + xH1.y*cH + xH2.y*cH;
               vdi.z = xO.z*cO + xH1.z*cH + xH2.z*cH;
-              vdi.w = vdi.w;
+              //vdi.w = vdi.w;
               if (jtype != typeH){
                 numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
                 numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
@@ -430,7 +423,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
                 vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
                 vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
                 vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
-                vdj.w = vdj.w;
+                //vdj.w = vdj.w;
               } else vdj = jx;
               vO[0] += 0.5*(vdi.x - vdj.x)*fd.x;
               vO[1] += 0.5*(vdi.y - vdj.y)*fd.y;
diff --git a/lib/gpu/lal_lj_tip4p_long.h b/lib/gpu/lal_lj_tip4p_long.h
index 57df235467..67c43def9b 100644
--- a/lib/gpu/lal_lj_tip4p_long.h
+++ b/lib/gpu/lal_lj_tip4p_long.h
@@ -62,10 +62,29 @@ public:
   /// Total host memory used by library for pair style
   double host_memory_usage() const;
 
-  /// Copy data which is easier to compute in LAMMPS_NS
-  void copy_relations_data(int **hn, double **m, int n,int* tag, int *map_array, int map_size,
+  /// Copy data from LAMMPS_NS
+  void copy_relations_data(int n,int* tag, int *map_array, int map_size,
       int *sametag, int max_same, int ago);
 
+  /// Reimplement BaseCharge pair loop with host neighboring
+  void compute(const int f_ago, const int inum_full, const int nall,
+               double **host_x, int *host_type, int *ilist, int *numj,
+               int **firstneigh, const bool eflag, const bool vflag,
+               const bool eatom, const bool vatom, int &host_start,
+               const double cpu_time, bool &success, double *charge,
+               const int nlocal, double *boxlo, double *prd);
+
+  /// Reimplement BaseCharge pair loop with device neighboring
+  int** compute(const int ago, const int inum_full, const int nall,
+                double **host_x, int *host_type, double *sublo,
+                double *subhi, tagint *tag,int *map_array, int map_size, int *sametag, int max_same,
+                int **nspecial,
+                tagint **special, const bool eflag, const bool vflag,
+                const bool eatom, const bool vatom, int &host_start,
+                int **ilist, int **numj, const double cpu_time, bool &success,
+                double *charge, double *boxlo, double *prd);
+
+
   // --------------------------- TYPE DATA --------------------------
 
   /// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq_vdw
@@ -77,7 +96,6 @@ public:
   /// Special LJ values [0-3] and Special Coul values [4-7]
   UCL_D_Vec<numtyp> sp_lj;
 
-  /// If atom type constants fit in shared memory, use fast kernels
   bool shared_types;
 
   /// Number of atom types
@@ -98,10 +116,11 @@ public:
   UCL_D_Vec<int> map_array;
   UCL_D_Vec<int> atom_sametag;
 
-  UCL_Kernel k_pair_distrib;
+  UCL_Kernel k_pair_distrib, k_pair_reneigh;
 
  private:
   bool _allocated;
+  int t_ago;
   void loop(const bool _eflag, const bool _vflag);
 };
 
diff --git a/lib/gpu/lal_lj_tip4p_long_ext.cpp b/lib/gpu/lal_lj_tip4p_long_ext.cpp
index 7ddd8f03b6..dc0623bf82 100644
--- a/lib/gpu/lal_lj_tip4p_long_ext.cpp
+++ b/lib/gpu/lal_lj_tip4p_long_ext.cpp
@@ -112,14 +112,18 @@ void ljtip4p_long_gpu_clear() {
 
 int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum_full,
                         const int nall, double **host_x, int *host_type,
-                        double *sublo, double *subhi, tagint *tag, int **nspecial,
+                        double *sublo, double *subhi,
+                        tagint *tag, int *map_array, int map_size,
+                        int *sametag, int max_same,
+                        int **nspecial,
                         tagint **special, const bool eflag, const bool vflag,
                         const bool eatom, const bool vatom, int &host_start,
                         int **ilist, int **jnum, const double cpu_time,
                         bool &success, double *host_q, double *boxlo,
                         double *prd) {
   return LJTIP4PLMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
-                       subhi, tag, nspecial, special, eflag, vflag, eatom,
+                       subhi, tag, map_array, map_size, sametag, max_same,
+                       nspecial, special, eflag, vflag, eatom,
                        vatom, host_start, ilist, jnum, cpu_time, success,
                        host_q,boxlo, prd);
 }
@@ -139,10 +143,10 @@ double ljtip4p_long_gpu_bytes() {
   return LJTIP4PLMF.host_memory_usage();
 }
 
-void ljtip4p_long_copy_molecule_data(int **hn, double **m, int n, int* tag,
+void ljtip4p_long_copy_molecule_data(int n, int* tag,
     int *map_array, int map_size,
     int *sametag, int max_same, int ago){
-  LJTIP4PLMF.copy_relations_data(hn, m, n, tag,map_array,map_size,sametag, max_same, ago);
+  LJTIP4PLMF.copy_relations_data(n, tag, map_array, map_size, sametag, max_same, ago);
 }
 
 
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
index 244da6a146..3e20a28b75 100644
--- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -64,7 +64,10 @@ int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
 void ljtip4p_long_gpu_clear();
 int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum,
     const int nall, double **host_x, int *host_type,
-    double *sublo, double *subhi, tagint *tag, int **nspecial,
+    double *sublo, double *subhi,
+    tagint *tag, int *map_array, int map_size,
+    int *sametag, int max_same,
+    int **nspecial,
     tagint **special, const bool eflag, const bool vflag,
     const bool eatom, const bool vatom, int &host_start,
     int **ilist, int **jnum,
@@ -78,7 +81,7 @@ void ljtip4p_long_gpu_compute(const int ago, const int inum, const int nall,
     bool &success, double *host_q, const int nlocal,
     double *boxlo, double *prd);
 double ljtip4p_long_gpu_bytes();
-void ljtip4p_long_copy_molecule_data(int **, double **, int, int* , int *,
+void ljtip4p_long_copy_molecule_data(int, int* , int *,
 		int, int *, int , int);
 
 /* ---------------------------------------------------------------------- */
@@ -112,17 +115,16 @@ void PairLJCutTIP4PLongGPU::compute(int eflag, int vflag)
   int nall = atom->nlocal + atom->nghost;
   int inum, host_start;
 
-  ljtip4p_long_copy_molecule_data(hneigh, newsite, nall, atom->tag,
-      atom->get_map_array(), atom->get_map_size(),
-      atom->sametag, atom->get_max_same(), neighbor->ago);
-
   bool success = true;
   int *ilist, *numneigh, **firstneigh;
   if (gpu_mode != GPU_FORCE) {
     inum = atom->nlocal;
     firstneigh = ljtip4p_long_gpu_compute_n(neighbor->ago, inum, nall,
         atom->x, atom->type, domain->sublo,
-        domain->subhi, atom->tag, atom->nspecial,
+        domain->subhi,
+        atom->tag, atom->get_map_array(), atom->get_map_size(),
+        atom->sametag, atom->get_max_same(),
+        atom->nspecial,
         atom->special, eflag, vflag, eflag_atom,
         vflag_atom, host_start, &ilist, &numneigh,
         cpu_time, success, atom->q, domain->boxlo,
@@ -132,6 +134,9 @@ void PairLJCutTIP4PLongGPU::compute(int eflag, int vflag)
     ilist = list->ilist;
     numneigh = list->numneigh;
     firstneigh = list->firstneigh;
+    ljtip4p_long_copy_molecule_data(nall, atom->tag,
+        atom->get_map_array(), atom->get_map_size(),
+        atom->sametag, atom->get_max_same(), neighbor->ago);
     ljtip4p_long_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
         ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
         vflag_atom, host_start, cpu_time, success, atom->q,

From 2d4d07521dd61650e97d809fcf3d869ff5c11535 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Fri, 6 Dec 2019 14:43:19 -0500
Subject: [PATCH 102/199] Add false positives to spell check

---
 doc/utils/sphinx-config/false_positives.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index e0a97f8ecd..3182c8605e 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -2079,7 +2079,9 @@ Ouyang
 overlayed
 Ovito
 oxdna
+oxrna
 oxDNA
+oxRNA
 padua
 Padua
 palegoldenrod

From 00547d906b35e5fa7e70015715fec68fa8ebfae9 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Fri, 6 Dec 2019 14:43:45 -0500
Subject: [PATCH 103/199] Fix whitespace

---
 src/USER-CGDNA/pair_oxdna2_dh.h      |  2 +-
 src/USER-CGDNA/pair_oxrna2_dh.cpp    |  2 +-
 src/USER-CGDNA/pair_oxrna2_hbond.cpp |  2 +-
 src/USER-CGDNA/pair_oxrna2_stk.cpp   | 16 ++++++++--------
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/USER-CGDNA/pair_oxdna2_dh.h
index 2a41524126..da72060927 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.h
+++ b/src/USER-CGDNA/pair_oxdna2_dh.h
@@ -28,7 +28,7 @@ class PairOxdna2Dh : public Pair {
  public:
   PairOxdna2Dh(class LAMMPS *);
   virtual ~PairOxdna2Dh();
-  virtual void compute_interaction_sites(double *, double *, double *, 
+  virtual void compute_interaction_sites(double *, double *, double *,
     double *);
   virtual void compute(int, int);
   void settings(int, char **);
diff --git a/src/USER-CGDNA/pair_oxrna2_dh.cpp b/src/USER-CGDNA/pair_oxrna2_dh.cpp
index 045a6aa6bc..7cc785ad39 100644
--- a/src/USER-CGDNA/pair_oxrna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxrna2_dh.cpp
@@ -35,7 +35,7 @@ PairOxrna2Dh::~PairOxrna2Dh()
 /* ----------------------------------------------------------------------
     compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
 ------------------------------------------------------------------------- */
-void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], 
+void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3],
   double e3[3], double r[3])
 {
   double d_cs_x=-0.4, d_cs_z=+0.2;
diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.cpp b/src/USER-CGDNA/pair_oxrna2_hbond.cpp
index 65f266ba36..08e1b1d737 100644
--- a/src/USER-CGDNA/pair_oxrna2_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxrna2_hbond.cpp
@@ -27,7 +27,7 @@ PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp)
 
   // sequence-specific base-pairing strength
   // A:0 C:1 G:2 U:3, 5'- [i][j] -3'
-   
+
   alpha_hb[0][0] = 1.00000;
   alpha_hb[0][1] = 1.00000;
   alpha_hb[0][2] = 1.00000;
diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp
index 5fd32099f3..de2cd63799 100644
--- a/src/USER-CGDNA/pair_oxrna2_stk.cpp
+++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp
@@ -49,7 +49,7 @@ PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp)
   // sequence-specific stacking strength
   // A:0 C:1 G:2 U:3, 5'- [i][j] -3'
 
-  eta_st[0][0] = 0.93851; 
+  eta_st[0][0] = 0.93851;
   eta_st[0][1] = 1.12901;
   eta_st[0][2] = 1.15626;
   eta_st[0][3] = 0.88850;
@@ -133,7 +133,7 @@ PairOxrna2Stk::~PairOxrna2Stk()
    tally energy and virial into global and per-atom accumulators
 
    NOTE: Although this is a pair style interaction, the algorithm below
-   follows the virial incrementation of the bond style. This is because 
+   follows the virial incrementation of the bond style. This is because
    the bond topology is used in the main compute loop.
 ------------------------------------------------------------------------- */
 
@@ -391,13 +391,13 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
     if (cost6p < -1.0) cost6p = -1.0;
     theta6p = acos(cost6p);
 
-    aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0]; 
-    aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1]; 
-    aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2]; 
+    aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0];
+    aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1];
+    aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2];
 
-    aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0]; 
-    aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1]; 
-    aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2]; 
+    aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0];
+    aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1];
+    aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2];
 
     cost9 = MathExtra::dot3(delr_ss_norm,aux3p);
     if (cost9 >  1.0) cost9 =  1.0;

From 4a51e1660f1104d7bc31caffe1404df3fa16c040 Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Sat, 7 Dec 2019 01:16:39 +0300
Subject: [PATCH 104/199] Add thread fence in kernel to fix Volta indeterminacy

---
 lib/gpu/lal_lj_tip4p_long.cu | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
index 2b98586eaf..5bb99d0426 100644
--- a/lib/gpu/lal_lj_tip4p_long.cu
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -271,6 +271,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
       iH2 = hneigh[i*4+1];
       if(fabs(m[iO].w) <= eq_zero) {
         compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
+        __threadfence();
         m[iO].w = qtmp;
       }
       x1 = m[iO];
@@ -283,6 +284,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
         if(fabs(m[iO].w) <= eq_zero) {
           compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
           numtyp qO; fetch(qO,iO,q_tex);
+          __threadfence();
           m[iO].w = qO;
         }
       }
@@ -341,6 +343,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
             jH2 = hneigh[j*4+1];
             if (fabs(m[j].w) <= eq_zero) {
               compute_newsite(j, jH1, jH2, &m[j], alpha, x_);
+              __threadfence();
               m[j].w = qj;
             }
             x2 = m[j];

From a3fca53e97846850d14614cb7cfd49829d8d3048 Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Sat, 7 Dec 2019 15:54:20 +0300
Subject: [PATCH 105/199] Separate the computation of newsite into another
 kernel

This eliminates the need for thread fence and makes the calculation stable on GTX1070 (CUDA and OpenCL) and TitanV
---
 lib/gpu/lal_lj_tip4p_long.cpp | 13 ++++++--
 lib/gpu/lal_lj_tip4p_long.cu  | 59 +++++++++++++++++++++++------------
 lib/gpu/lal_lj_tip4p_long.h   |  2 +-
 3 files changed, 51 insertions(+), 23 deletions(-)

diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
index 890bbab3bd..200f185e63 100644
--- a/lib/gpu/lal_lj_tip4p_long.cpp
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -66,6 +66,7 @@ int LJTIP4PLongT::init(const int ntypes,
     return success;
   k_pair_distrib.set_function(*this->pair_program,"k_lj_tip4p_long_distrib");
   k_pair_reneigh.set_function(*this->pair_program,"k_lj_tip4p_reneigh");
+  k_pair_newsite.set_function(*this->pair_program,"k_lj_tip4p_newsite");
 
   TypeH = tH;
   TypeO = tO;
@@ -163,6 +164,7 @@ void LJTIP4PLongT::clear() {
 
   k_pair_distrib.clear();
   k_pair_reneigh.clear();
+  k_pair_newsite.clear();
 
   this->clear_atomic();
 }
@@ -195,9 +197,8 @@ void LJTIP4PLongT::loop(const bool _eflag, const bool _vflag) {
   int nbor_pitch=this->nbor->nbor_pitch();
   this->time_pair.start();
   int GX;
-
+  GX=static_cast<int>(ceil(static_cast<double>(nall)/BX));
   if (t_ago == 0) {
-    GX=static_cast<int>(ceil(static_cast<double>(nall)/BX));
     this->k_pair_reneigh.set_size(GX,BX);
     this->k_pair_reneigh.run(&this->atom->x,
         &this->nbor->dev_nbor, &this->_nbor_data->begin(),
@@ -205,6 +206,14 @@ void LJTIP4PLongT::loop(const bool _eflag, const bool _vflag) {
         &hneight, &m, &TypeO, &TypeH,
         &tag, &map_array, &atom_sametag);
   }
+  this->k_pair_newsite.set_size(GX,BX);
+  this->k_pair_newsite.run(&this->atom->x,
+          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+          &nall, &ainum,
+          &nbor_pitch, &this->_threads_per_atom,
+          &hneight, &m, &TypeO, &TypeH, &alpha,
+          &this->atom->q, &tag, &map_array,
+          &atom_sametag);
 
   GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
                                (BX/this->_threads_per_atom)));
diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
index 5bb99d0426..fae5744224 100644
--- a/lib/gpu/lal_lj_tip4p_long.cu
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -65,11 +65,12 @@ ucl_inline int closest_image(int i, int j, const __global int* sametag,
 }
 
 ucl_inline void compute_newsite(int iO, int  iH1, int  iH2,
-    __global numtyp4 *xM,
+    __global numtyp4 *xM, numtyp q,
     numtyp alpha, const __global numtyp4 *restrict x_){
   numtyp4 xO;  fetch4(xO,iO,pos_tex);
   numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
   numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+  numtyp4 M;
 
   numtyp delx1 = xH1.x - xO.x;
   numtyp dely1 = xH1.y - xO.y;
@@ -81,9 +82,12 @@ ucl_inline void compute_newsite(int iO, int  iH1, int  iH2,
 
   numtyp ap = alpha * (numtyp)0.5;
 
-  (*xM).x = xO.x + ap * (delx1 + delx2);
-  (*xM).y = xO.y + ap * (dely1 + dely2);
-  (*xM).z = xO.z + ap * (delz1 + delz2);
+  M.x = xO.x + ap * (delx1 + delx2);
+  M.y = xO.y + ap * (dely1 + dely2);
+  M.z = xO.z + ap * (delz1 + delz2);
+  M.w = q;
+
+  *xM = M;
 }
 
 __kernel void k_lj_tip4p_long_distrib(const __global numtyp4 *restrict x_,
@@ -214,6 +218,37 @@ __kernel void k_lj_tip4p_reneigh(const __global numtyp4 *restrict x_,
 }
 
 
+__kernel void k_lj_tip4p_newsite(const __global numtyp4 *restrict x_,
+    const __global int * dev_nbor,
+    const __global int * dev_packed,
+    const int nall, const int inum,
+    const int nbor_pitch, const int t_per_atom,
+    __global int *restrict hneigh,
+    __global numtyp4 *restrict m,
+    const int typeO, const int typeH,
+    const numtyp alpha, const __global numtyp *restrict q_,
+    const __global int *restrict tag, const __global int *restrict map,
+    const __global int *restrict sametag) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+  int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
+
+  if (i<nall) {
+    int iO, iH1, iH2;
+    iO  = i;
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype = ix.w;
+    if (itype == typeO){
+      int iH1, iH2, iO;
+      iH1 = hneigh[i*4  ];
+      iH2 = hneigh[i*4+1];
+      iO  = i;
+      numtyp qO; fetch(qO,iO,q_tex);
+      compute_newsite(iO,iH1,iH2, &m[iO], qO, alpha, x_);
+    }
+  }
+}
+
 __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
     const __global numtyp4 *restrict lj1,
     const __global numtyp4 *restrict lj3,
@@ -269,11 +304,6 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
       iO  = i;
       iH1 = hneigh[i*4  ];
       iH2 = hneigh[i*4+1];
-      if(fabs(m[iO].w) <= eq_zero) {
-        compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
-        __threadfence();
-        m[iO].w = qtmp;
-      }
       x1 = m[iO];
     } else {
       iO  = hneigh[i *4  ];
@@ -281,12 +311,6 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
       iH2 = hneigh[iO*4+1];
       if (iO >= inum) {
         non_local_oxy = 1;
-        if(fabs(m[iO].w) <= eq_zero) {
-          compute_newsite(iO,iH1,iH2, &m[iO], alpha, x_);
-          numtyp qO; fetch(qO,iO,q_tex);
-          __threadfence();
-          m[iO].w = qO;
-        }
       }
     }
 
@@ -341,11 +365,6 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
             jO = j;
             jH1 = hneigh[j*4  ];
             jH2 = hneigh[j*4+1];
-            if (fabs(m[j].w) <= eq_zero) {
-              compute_newsite(j, jH1, jH2, &m[j], alpha, x_);
-              __threadfence();
-              m[j].w = qj;
-            }
             x2 = m[j];
           }
           delx = x1.x-x2.x;
diff --git a/lib/gpu/lal_lj_tip4p_long.h b/lib/gpu/lal_lj_tip4p_long.h
index 67c43def9b..ccf507caa0 100644
--- a/lib/gpu/lal_lj_tip4p_long.h
+++ b/lib/gpu/lal_lj_tip4p_long.h
@@ -116,7 +116,7 @@ public:
   UCL_D_Vec<int> map_array;
   UCL_D_Vec<int> atom_sametag;
 
-  UCL_Kernel k_pair_distrib, k_pair_reneigh;
+  UCL_Kernel k_pair_distrib, k_pair_reneigh, k_pair_newsite;
 
  private:
   bool _allocated;

From 1b9214c3e996551b3cb8a62d39ee65f0cc8ba60f Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Mon, 9 Dec 2019 15:21:47 -0700
Subject: [PATCH 106/199] Fix issues with CUDA-aware MPI

---
 src/KOKKOS/kokkos.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index 720dd3b3b2..60a3cfd2d1 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -220,7 +220,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
 
   int nmpi = 0;
   MPI_Comm_size(world,&nmpi);
-  if (nmpi > 0) {
+  if (nmpi > 1) {
 
 #if defined(MPI_VERSION) && (MPI_VERSION > 2)
     // Check for IBM Spectrum MPI
@@ -397,6 +397,8 @@ void KokkosLMP::accelerator(int narg, char **arg)
     } else error->all(FLERR,"Illegal package kokkos command");
   }
 
+#ifdef KOKKOS_ENABLE_CUDA
+
   // if "cuda/aware off" and "comm device", change to "comm host"
 
   if (!cuda_aware_flag) {
@@ -431,6 +433,8 @@ void KokkosLMP::accelerator(int narg, char **arg)
     }
   }
 
+#endif
+
   // set newton flags
   // set neighbor binsize, same as neigh_modify command
 

From bf1ee204033cd3e0dd4636aed438c4b52dc967d5 Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Tue, 10 Dec 2019 14:46:24 +0000
Subject: [PATCH 107/199] Added oxRNA2 files to Install.sh script

---
 src/USER-CGDNA/Install.sh | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/USER-CGDNA/Install.sh b/src/USER-CGDNA/Install.sh
index fa62b0daf2..9ef10d3f62 100755
--- a/src/USER-CGDNA/Install.sh
+++ b/src/USER-CGDNA/Install.sh
@@ -30,8 +30,10 @@ action () {
 
 action  bond_oxdna_fene.cpp bond_fene.h
 action  bond_oxdna2_fene.cpp bond_fene.h
+action  bond_oxrna2_fene.cpp bond_fene.h
 action  bond_oxdna_fene.h bond_fene.h
 action  bond_oxdna2_fene.h bond_fene.h
+action  bond_oxrna2_fene.h bond_fene.h
 action  fix_nve_dotc_langevin.cpp atom_vec_ellipsoid.h
 action  fix_nve_dotc_langevin.h atom_vec_ellipsoid.h
 action  fix_nve_dot.cpp atom_vec_ellipsoid.h
@@ -43,13 +45,23 @@ action  pair_oxdna_coaxstk.h atom_vec_ellipsoid.h
 action  pair_oxdna2_coaxstk.h atom_vec_ellipsoid.h
 action  pair_oxdna_excv.cpp atom_vec_ellipsoid.h
 action  pair_oxdna2_excv.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_excv.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_excv.h atom_vec_ellipsoid.h
 action  pair_oxdna2_excv.h atom_vec_ellipsoid.h
+action  pair_oxrna2_excv.h atom_vec_ellipsoid.h
 action  pair_oxdna_hbond.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_hbond.h atom_vec_ellipsoid.h
+action  pair_oxrna2_hbond.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_hbond.h atom_vec_ellipsoid.h
 action  pair_oxdna_stk.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_stk.h atom_vec_ellipsoid.h
+action  pair_oxrna2_stk.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_stk.h atom_vec_ellipsoid.h
 action  pair_oxdna_xstk.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_xstk.h atom_vec_ellipsoid.h
+action  pair_oxrna2_xstk.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_xstk.h atom_vec_ellipsoid.h
 action  pair_oxdna2_dh.cpp atom_vec_ellipsoid.h
 action  pair_oxdna2_dh.h atom_vec_ellipsoid.h
+action  pair_oxrna2_dh.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_dh.h atom_vec_ellipsoid.h

From fba97b94cbc961dc01b98fefd45b6dca77e60654 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Tue, 10 Dec 2019 10:10:12 -0700
Subject: [PATCH 108/199] Don't change comm flags when there is only 1 MPI rank

---
 doc/src/package.rst   | 8 ++++----
 src/KOKKOS/kokkos.cpp | 5 ++++-
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/doc/src/package.rst b/doc/src/package.rst
index 804b2e126e..06cebea6c4 100644
--- a/doc/src/package.rst
+++ b/doc/src/package.rst
@@ -547,10 +547,10 @@ the *cuda/aware* keyword is automatically set to *off* by default. When
 the *cuda/aware* keyword is set to *off* while any of the *comm*
 keywords are set to *device*\ , the value for these *comm* keywords will
 be automatically changed to *host*\ . This setting has no effect if not
-running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later
-versions), Mvapich2 1.9 (or later) when the "MV2\_USE\_CUDA" environment
-variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu"
-flag is used.
+running on GPUs or if using only one MPI rank. CUDA-aware MPI is available
+for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the
+"MV2\_USE\_CUDA" environment variable is set to "1", CrayMPI, and IBM
+Spectrum MPI when the "-gpu" flag is used.
 
 
 ----------
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index 60a3cfd2d1..8f60f3526d 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -399,9 +399,12 @@ void KokkosLMP::accelerator(int narg, char **arg)
 
 #ifdef KOKKOS_ENABLE_CUDA
 
+  int nmpi = 0;
+  MPI_Comm_size(world,&nmpi);
+
   // if "cuda/aware off" and "comm device", change to "comm host"
 
-  if (!cuda_aware_flag) {
+  if (!cuda_aware_flag && nmpi > 1) {
     if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) {
       exchange_comm_on_host = 1;
       exchange_comm_changed = 1;

From e0a771d5cb5bf3f1cb3abb96c16ed0ae19ee6231 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 10 Dec 2019 13:46:30 -0500
Subject: [PATCH 109/199] Remove outdated package.txt

---
 doc/txt/package.txt | 660 --------------------------------------------
 1 file changed, 660 deletions(-)
 delete mode 100644 doc/txt/package.txt

diff --git a/doc/txt/package.txt b/doc/txt/package.txt
deleted file mode 100644
index 4ecb5d96d0..0000000000
--- a/doc/txt/package.txt
+++ /dev/null
@@ -1,660 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-package command :h3
-
-[Syntax:]
-
-package style args :pre
-
-style = {gpu} or {intel} or {kokkos} or {omp} :ulb,l
-args = arguments specific to the style :l
-  {gpu} args = Ngpu keyword value ...
-    Ngpu = # of GPUs per node
-    zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {newton} or {binsize} or {split} or {gpuID} or {tpa} or {device} or {blocksize}
-      {neigh} value = {yes} or {no}
-        yes = neighbor list build on GPU (default)
-        no = neighbor list build on CPU
-      {newton} = {off} or {on}
-        off = set Newton pairwise flag off (default and required)
-        on = set Newton pairwise flag on (currently not allowed)
-      {binsize} value = size
-        size = bin size for neighbor list construction (distance units)
-      {split} = fraction
-        fraction = fraction of atoms assigned to GPU (default = 1.0)
-      {gpuID} values = first last
-        first = ID of first GPU to be used on each node
-        last = ID of last GPU to be used on each node
-      {tpa} value = Nthreads
-        Nthreads = # of GPU threads used per atom
-      {device} value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13
-        platform_id = numerical OpenCL platform id (default: -1)
-        device_type = {kepler} or {fermi} or {cypress} or {intel} or {phi} or {generic} or {custom}
-        val1,val2,... = custom OpenCL tune parameters (see below for details)
-      {blocksize} value = size
-        size = thread block size for pair force computation
-  {intel} args = NPhi keyword value ...
-    Nphi = # of co-processors per node
-    zero or more keyword/value pairs may be appended
-    keywords = {mode} or {omp} or {lrt} or {balance} or {ghost} or {tpc} or {tptask} or {no_affinity}
-      {mode} value = {single} or {mixed} or {double}
-        single = perform force calculations in single precision
-        mixed = perform force calculations in mixed precision
-        double = perform force calculations in double precision
-      {omp} value = Nthreads
-        Nthreads = number of OpenMP threads to use on CPU (default = 0)
-      {lrt} value = {yes} or {no}
-        yes = use additional thread dedicated for some PPPM calculations
-        no = do not dedicate an extra thread for some PPPM calculations
-      {balance} value = split
-        split = fraction of work to offload to co-processor, -1 for dynamic
-      {ghost} value = {yes} or {no}
-        yes = include ghost atoms for offload
-        no = do not include ghost atoms for offload
-      {tpc} value = Ntpc
-        Ntpc = max number of co-processor threads per co-processor core (default = 4)
-      {tptask} value = Ntptask
-        Ntptask = max number of co-processor threads per MPI task (default = 240)
-      {no_affinity} values = none
-  {kokkos} args = keyword value ...
-    zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {cuda/aware}
-      {neigh} value = {full} or {half}
-        full = full neighbor list
-        half = half neighbor list built in thread-safe manner
-      {neigh/qeq} value = {full} or {half}
-        full = full neighbor list
-        half = half neighbor list built in thread-safe manner
-      {neigh/thread} value = {off} or {on}
-        off = thread only over atoms
-        on = thread over both atoms and neighbors
-      {newton} = {off} or {on}
-        off = set Newton pairwise and bonded flags off
-        on = set Newton pairwise and bonded flags on
-      {binsize} value = size
-        size = bin size for neighbor list construction (distance units)
-      {comm} value = {no} or {host} or {device}
-        use value for comm/exchange and comm/forward and comm/reverse
-      {comm/exchange} value = {no} or {host} or {device}
-      {comm/forward} value = {no} or {host} or {device}
-      {comm/reverse} value = {no} or {host} or {device}
-        no = perform communication pack/unpack in non-KOKKOS mode
-        host = perform pack/unpack on host (e.g. with OpenMP threading)
-        device = perform pack/unpack on device (e.g. on GPU)
-      {cuda/aware} = {off} or {on}
-        off = do not use CUDA-aware MPI
-        on = use CUDA-aware MPI (default)
-  {omp} args = Nthreads keyword value ...
-    Nthread = # of OpenMP threads to associate with each MPI process
-    zero or more keyword/value pairs may be appended
-    keywords = {neigh}
-      {neigh} value = {yes} or {no}
-        yes = threaded neighbor list build (default)
-        no = non-threaded neighbor list build :pre
-:ule
-
-[Examples:]
-
-package gpu 1
-package gpu 1 split 0.75
-package gpu 2 split -1.0
-package gpu 1 device kepler
-package gpu 1 device 2:generic
-package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128
-package kokkos neigh half comm device
-package omp 0 neigh no
-package omp 4
-package intel 1
-package intel 2 omp 4 mode mixed balance 0.5 :pre
-
-[Description:]
-
-This command invokes package-specific settings for the various
-accelerator packages available in LAMMPS.  Currently the following
-packages use settings from this command: GPU, USER-INTEL, KOKKOS, and
-USER-OMP.
-
-If this command is specified in an input script, it must be near the
-top of the script, before the simulation box has been defined.  This
-is because it specifies settings that the accelerator packages use in
-their initialization, before a simulation is defined.
-
-This command can also be specified from the command-line when
-launching LAMMPS, using the "-pk" "command-line
-switch"_Run_options.html.  The syntax is exactly the same as when used
-in an input script.
-
-Note that all of the accelerator packages require the package command
-to be specified (except the OPT package), if the package is to be used
-in a simulation (LAMMPS can be built with an accelerator package
-without using it in a particular simulation).  However, in all cases,
-a default version of the command is typically invoked by other
-accelerator settings.
-
-The KOKKOS package requires a "-k on" "command-line
-switch"_Run_options.html respectively, which invokes a "package
-kokkos" command with default settings.
-
-For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
-intel" or "-sf omp" "command-line switch"_Run_options.html is used to
-auto-append accelerator suffixes to various styles in the input
-script, then those switches also invoke a "package gpu", "package
-intel", or "package omp" command with default settings.
-
-NOTE: A package command for a particular style can be invoked multiple
-times when a simulation is setup, e.g. by the "-c on, -k on, -sf, and
--pk command-line switches"_Run_options.html, and by using this command
-in an input script.  Each time it is used all of the style options are
-set, either to default values or to specified settings.  I.e. settings
-from previous invocations do not persist across multiple invocations.
-
-See the "Speed packages"_Speed_packages.html doc page for more details
-about using the various accelerator packages for speeding up LAMMPS
-simulations.
-
-:line
-
-The {gpu} style invokes settings associated with the use of the GPU
-package.
-
-The {Ngpu} argument sets the number of GPUs per node.  There must be
-at least as many MPI tasks per node as GPUs, as set by the mpirun or
-mpiexec command.  If there are more MPI tasks (per node)
-than GPUs, multiple MPI tasks will share each GPU.
-
-Optional keyword/value pairs can also be specified.  Each has a
-default value as listed below.
-
-The {neigh} keyword specifies where neighbor lists for pair style
-computation will be built.  If {neigh} is {yes}, which is the default,
-neighbor list building is performed on the GPU.  If {neigh} is {no},
-neighbor list building is performed on the CPU.  GPU neighbor list
-building currently cannot be used with a triclinic box.  GPU neighbor
-lists are not compatible with commands that are not GPU-enabled.  When
-a non-GPU enabled command requires a neighbor list, it will also be
-built on the CPU.  In these cases, it will typically be more efficient
-to only use CPU neighbor list builds.
-
-The {newton} keyword sets the Newton flags for pairwise (not bonded)
-interactions to {off} or {on}, the same as the "newton"_newton.html
-command allows.  Currently, only an {off} value is allowed, since all
-the GPU package pair styles require this setting.  This means more
-computation is done, but less communication.  In the future a value of
-{on} may be allowed, so the {newton} keyword is included as an option
-for compatibility with the package command for other accelerator
-styles.  Note that the newton setting for bonded interactions is not
-affected by this keyword.
-
-The {binsize} keyword sets the size of bins used to bin atoms in
-neighbor list builds performed on the GPU, if {neigh} = {yes} is set.
-If {binsize} is set to 0.0 (the default), then bins = the size of the
-pairwise cutoff + neighbor skin distance.  This is 2x larger than the
-LAMMPS default used for neighbor list building on the CPU.  This will
-be close to optimal for the GPU, so you do not normally need to use
-this keyword.  Note that if you use a longer-than-usual pairwise
-cutoff, e.g. to allow for a smaller fraction of KSpace work with a
-"long-range Coulombic solver"_kspace_style.html because the GPU is
-faster at performing pairwise interactions, then it may be optimal to
-make the {binsize} smaller than the default.  For example, with a
-cutoff of 20*sigma in LJ "units"_units.html and a neighbor skin
-distance of sigma, a {binsize} = 5.25*sigma can be more efficient than
-the default.
-
-The {split} keyword can be used for load balancing force calculations
-between CPU and GPU cores in GPU-enabled pair styles. If 0 < {split} <
-1.0, a fixed fraction of particles is offloaded to the GPU while force
-calculation for the other particles occurs simultaneously on the CPU.
-If {split} < 0.0, the optimal fraction (based on CPU and GPU timings)
-is calculated every 25 timesteps, i.e. dynamic load-balancing across
-the CPU and GPU is performed.  If {split} = 1.0, all force
-calculations for GPU accelerated pair styles are performed on the GPU.
-In this case, other "hybrid"_pair_hybrid.html pair interactions,
-"bond"_bond_style.html, "angle"_angle_style.html,
-"dihedral"_dihedral_style.html, "improper"_improper_style.html, and
-"long-range"_kspace_style.html calculations can be performed on the
-CPU while the GPU is performing force calculations for the GPU-enabled
-pair style.  If all CPU force computations complete before the GPU
-completes, LAMMPS will block until the GPU has finished before
-continuing the timestep.
-
-As an example, if you have two GPUs per node and 8 CPU cores per node,
-and would like to run on 4 nodes (32 cores) with dynamic balancing of
-force calculation across CPU and GPU cores, you could specify
-
-mpirun -np 32 -sf gpu -in in.script    # launch command
-package gpu 2 split -1                 # input script command :pre
-
-In this case, all CPU cores and GPU devices on the nodes would be
-utilized.  Each GPU device would be shared by 4 CPU cores. The CPU
-cores would perform force calculations for some fraction of the
-particles at the same time the GPUs performed force calculation for
-the other particles.
-
-The {gpuID} keyword allows selection of which GPUs on each node will
-be used for a simulation.  The {first} and {last} values specify the
-GPU IDs to use (from 0 to Ngpu-1).  By default, first = 0 and last =
-Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number
-of physical GPUs.  If you only wish to use a subset, set Ngpu to a
-smaller number and first/last to a sub-range of the available GPUs.
-
-The {tpa} keyword sets the number of GPU thread per atom used to
-perform force calculations.  With a default value of 1, the number of
-threads will be chosen based on the pair style, however, the value can
-be set explicitly with this keyword to fine-tune performance.  For
-large cutoffs or with a small number of particles per GPU, increasing
-the value can improve performance. The number of threads per atom must
-be a power of 2 and currently cannot be greater than 32.
-
-The {device} keyword can be used to tune parameters optimized for a
-specific accelerator and platform when using OpenCL. OpenCL supports
-the concept of a [platform], which represents one or more devices that
-share the same driver (e.g. there would be a different platform for
-GPUs from different vendors or for CPU based accelerator support).
-In LAMMPS only one platform can be active at a time and by default
-the first platform with an accelerator is selected. This is equivalent
-to using a platform ID of -1. The platform ID is a number corresponding
-to the output of the ocl_get_devices tool. The platform ID is passed
-to the GPU library, by prefixing the {device} keyword with that number
-separated by a colon. For CUDA, the {device} keyword is ignored.
-Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA
-Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device.
-More devices may be added later.  The default device type can be
-specified when building LAMMPS with the GPU library, via setting a
-variable in the lib/gpu/Makefile that is used.
-
-In addition, a device type {custom} is available, which is followed by
-13 comma separated numbers, which allows to set those tweakable parameters
-from the package command. It can be combined with the (colon separated)
-platform id. The individual settings are:
-
-MEM_THREADS
-THREADS_PER_ATOM
-THREADS_PER_CHARGE
-BLOCK_PAIR
-MAX_SHARED_TYPES
-BLOCK_NBOR_BUILD
-BLOCK_BIO_PAIR
-BLOCK_ELLIPSE
-WARP_SIZE
-PPPM_BLOCK_1D
-BLOCK_CELL_2D
-BLOCK_CELL_ID
-MAX_BIO_SHARED_TYPES :ul
-
-The {blocksize} keyword allows you to tweak the number of threads used
-per thread block. This number should be a multiple of 32 (for GPUs)
-and its maximum depends on the specific GPU hardware. Typical choices
-are 64, 128, or 256. A larger block size increases occupancy of
-individual GPU cores, but reduces the total number of thread blocks,
-thus may lead to load imbalance.
-
-:line
-
-The {intel} style invokes settings associated with the use of the
-USER-INTEL package.  All of its settings, except the {omp} and {mode}
-keywords, are ignored if LAMMPS was not built with Xeon Phi
-co-processor support.  All of its settings, including the {omp} and
-{mode} keyword are applicable if LAMMPS was built with co-processor
-support.
-
-The {Nphi} argument sets the number of co-processors per node.
-This can be set to any value, including 0, if LAMMPS was not
-built with co-processor support.
-
-Optional keyword/value pairs can also be specified.  Each has a
-default value as listed below.
-
-The {omp} keyword determines the number of OpenMP threads allocated
-for each MPI task when any portion of the interactions computed by a
-USER-INTEL pair style are run on the CPU.  This can be the case even
-if LAMMPS was built with co-processor support; see the {balance}
-keyword discussion below.  If you are running with less MPI tasks/node
-than there are CPUs, it can be advantageous to use OpenMP threading on
-the CPUs.
-
-NOTE: The {omp} keyword has nothing to do with co-processor threads on
-the Xeon Phi; see the {tpc} and {tptask} keywords below for a
-discussion of co-processor threads.
-
-The {Nthread} value for the {omp} keyword sets the number of OpenMP
-threads allocated for each MPI task.  Setting {Nthread} = 0 (the
-default) instructs LAMMPS to use whatever value is the default for the
-given OpenMP environment. This is usually determined via the
-{OMP_NUM_THREADS} environment variable or the compiler runtime, which
-is usually a value of 1.
-
-For more details, including examples of how to set the OMP_NUM_THREADS
-environment variable, see the discussion of the {Nthreads} setting on
-this doc page for the "package omp" command.  Nthreads is a required
-argument for the USER-OMP package.  Its meaning is exactly the same
-for the USER-INTEL package.
-
-NOTE: If you build LAMMPS with both the USER-INTEL and USER-OMP
-packages, be aware that both packages allow setting of the {Nthreads}
-value via their package commands, but there is only a single global
-{Nthreads} value used by OpenMP.  Thus if both package commands are
-invoked, you should insure the two values are consistent.  If they are
-not, the last one invoked will take precedence, for both packages.
-Also note that if the "-sf hybrid intel omp command-line
-switch"_Run_options.html is used, it invokes a "package intel"
-command, followed by a "package omp" command, both with a setting of
-{Nthreads} = 0.
-
-The {mode} keyword determines the precision mode to use for
-computing pair style forces, either on the CPU or on the co-processor,
-when using a USER-INTEL supported "pair style"_pair_style.html.  It
-can take a value of {single}, {mixed} which is the default, or
-{double}.  {Single} means single precision is used for the entire
-force calculation.  {Mixed} means forces between a pair of atoms are
-computed in single precision, but accumulated and stored in double
-precision, including storage of forces, torques, energies, and virial
-quantities.  {Double} means double precision is used for the entire
-force calculation.
-
-The {lrt} keyword can be used to enable "Long Range Thread (LRT)"
-mode. It can take a value of {yes} to enable and {no} to disable.
-LRT mode generates an extra thread (in addition to any OpenMP threads
-specified with the OMP_NUM_THREADS environment variable or the {omp}
-keyword). The extra thread is dedicated for performing part of the
-"PPPM solver"_kspace_style.html computations and communications. This
-can improve parallel performance on processors supporting
-Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel
-processors. In this mode, one additional thread is generated per MPI
-process. LAMMPS will generate a warning in the case that more threads
-are used than available in SMT hardware on a node. If the PPPM solver
-from the USER-INTEL package is not used, then the LRT setting is
-ignored and no extra threads are generated. Enabling LRT will replace
-the "run_style"_run_style.html with the {verlet/lrt/intel} style that
-is identical to the default {verlet} style aside from supporting the
-LRT feature. This feature requires setting the pre-processor flag
--DLMP_INTEL_USELRT in the makefile when compiling LAMMPS.
-
-The {balance} keyword sets the fraction of "pair
-style"_pair_style.html work offloaded to the co-processor for split
-values between 0.0 and 1.0 inclusive.  While this fraction of work is
-running on the co-processor, other calculations will run on the host,
-including neighbor and pair calculations that are not offloaded, as
-well as angle, bond, dihedral, kspace, and some MPI communications.
-If {split} is set to -1, the fraction of work is dynamically adjusted
-automatically throughout the run.  This typically give performance
-within 5 to 10 percent of the optimal fixed fraction.
-
-The {ghost} keyword determines whether or not ghost atoms, i.e. atoms
-at the boundaries of processor sub-domains, are offloaded for neighbor
-and force calculations.  When the value = "no", ghost atoms are not
-offloaded.  This option can reduce the amount of data transfer with
-the co-processor and can also overlap MPI communication of forces with
-computation on the co-processor when the "newton pair"_newton.html
-setting is "on".  When the value = "yes", ghost atoms are offloaded.
-In some cases this can provide better performance, especially if the
-{balance} fraction is high.
-
-The {tpc} keyword sets the max # of co-processor threads {Ntpc} that
-will run on each core of the co-processor.  The default value = 4,
-which is the number of hardware threads per core supported by the
-current generation Xeon Phi chips.
-
-The {tptask} keyword sets the max # of co-processor threads (Ntptask}
-assigned to each MPI task.  The default value = 240, which is the
-total # of threads an entire current generation Xeon Phi chip can run
-(240 = 60 cores * 4 threads/core).  This means each MPI task assigned
-to the Phi will enough threads for the chip to run the max allowed,
-even if only 1 MPI task is assigned.  If 8 MPI tasks are assigned to
-the Phi, each will run with 30 threads.  If you wish to limit the
-number of threads per MPI task, set {tptask} to a smaller value.
-E.g. for {tptask} = 16, if 8 MPI tasks are assigned, each will run
-with 16 threads, for a total of 128.
-
-Note that the default settings for {tpc} and {tptask} are fine for
-most problems, regardless of how many MPI tasks you assign to a Phi.
-
-The {no_affinity} keyword will turn off automatic setting of core
-affinity for MPI tasks and OpenMP threads on the host when using
-offload to a co-processor. Affinity settings are used when possible
-to prevent MPI tasks and OpenMP threads from being on separate NUMA
-domains and to prevent offload threads from interfering with other
-processes/threads used for LAMMPS.
-
-:line
-
-The {kokkos} style invokes settings associated with the use of the
-KOKKOS package.
-
-All of the settings are optional keyword/value pairs. Each has a default
-value as listed below.
-
-The {neigh} keyword determines how neighbor lists are built. A value of
-{half} uses a thread-safe variant of half-neighbor lists, the same as
-used by most pair styles in LAMMPS, which is the default when running on
-CPUs (i.e. the Kokkos CUDA back end is not enabled).
-
-A value of {full} uses a full neighbor lists and is the default when
-running on GPUs. This performs twice as much computation as the {half}
-option, however that is often a win because it is thread-safe and
-doesn't require atomic operations in the calculation of pair forces. For
-that reason, {full} is the default setting for GPUs. However, when
-running on CPUs, a {half} neighbor list is the default because it are
-often faster, just as it is for non-accelerated pair styles. Similarly,
-the {neigh/qeq} keyword determines how neighbor lists are built for "fix
-qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of
-{neigh/qeq} will match {neigh}.
-
-If the {neigh/thread} keyword is set to {off}, then the KOKKOS package
-threads only over atoms. However, for small systems, this may not expose
-enough parallelism to keep a GPU busy. When this keyword is set to {on},
-the KOKKOS package threads over both atoms and neighbors of atoms. When
-using {neigh/thread} {on}, a full neighbor list must also be used. Using
-{neigh/thread} {on} may be slower for large systems, so this this option
-is turned on by default only when there are 16K atoms or less owned by
-an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
-potentials support this keyword yet, and only thread over atoms. Many
-simple pair-wise potentials such as Lennard-Jones do support threading
-over both atoms and neighbors.
-
-The {newton} keyword sets the Newton flags for pairwise and bonded
-interactions to {off} or {on}, the same as the "newton"_newton.html
-command allows. The default for GPUs is {off} because this will almost
-always give better performance for the KOKKOS package. This means more
-computation is done, but less communication. However, when running on
-CPUs a value of {on} is the default since it can often be faster, just
-as it is for non-accelerated pair styles
-
-The {binsize} keyword sets the size of bins used to bin atoms in
-neighbor list builds. The same value can be set by the "neigh_modify
-binsize"_neigh_modify.html command. Making it an option in the package
-kokkos command allows it to be set from the command line. The default
-value for CPUs is 0.0, which means the LAMMPS default will be used,
-which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
-distance. This is fine when neighbor lists are built on the CPU. For GPU
-builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin
-is often faster, which is the default. Note that if you use a
-longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction
-of KSpace work with a "long-range Coulombic solver"_kspace_style.html
-because the GPU is faster at performing pairwise interactions, then this
-rule of thumb may give too large a binsize and the default should be
-overridden with a smaller value.
-
-The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse}
-keywords determine whether the host or device performs the packing and
-unpacking of data when communicating per-atom data between processors.
-"Exchange" communication happens only on timesteps that neighbor lists
-are rebuilt. The data is only for atoms that migrate to new processors.
-"Forward" communication happens every timestep. "Reverse" communication
-happens every timestep if the {newton} option is on. The data is for
-atom coordinates and any other atom properties that needs to be updated
-for ghost atoms owned by each processor.
-
-The {comm} keyword is simply a short-cut to set the same value for both
-the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
-
-The value options for all 3 keywords are {no} or {host} or {device}. A
-value of {no} means to use the standard non-KOKKOS method of
-packing/unpacking data for the communication. A value of {host} means to
-use the host, typically a multi-core CPU, and perform the
-packing/unpacking in parallel with threads. A value of {device} means to
-use the device, typically a GPU, to perform the packing/unpacking
-operation.
-
-The optimal choice for these keywords depends on the input script and
-the hardware used. The {no} value is useful for verifying that the
-Kokkos-based {host} and {device} values are working correctly. It is the
-default when running on CPUs since it is usually the fastest.
-
-When running on CPUs or Xeon Phi, the {host} and {device} values work
-identically. When using GPUs, the {device} value is the default since it
-will typically be optimal if all of your styles used in your input
-script are supported by the KOKKOS package. In this case data can stay
-on the GPU for many timesteps without being moved between the host and
-GPU, if you use the {device} value. If your script uses styles (e.g.
-fixes) which are not yet supported by the KOKKOS package, then data has
-to be move between the host and device anyway, so it is typically faster
-to let the host handle communication, by using the {host} value. Using
-{host} instead of {no} will enable use of multiple threads to
-pack/unpack communicated data. When running small systems on a GPU,
-performing the exchange pack/unpack on the host CPU can give speedup
-since it reduces the number of CUDA kernel launches.
-
-The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When
-this keyword is set to {on}, buffers in GPU memory are passed directly
-through MPI send/receive calls. This reduces overhead of first copying
-the data to the host CPU. However CUDA-aware MPI is not supported on all
-systems, which can lead to segmentation faults and would require using a
-value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not
-available (currently only possible with OpenMPI v2.0.0 or later), then
-the {cuda/aware} keyword is automatically set to {off} by default. When
-the {cuda/aware} keyword is set to {off} while any of the {comm}
-keywords are set to {device}, the value for these {comm} keywords will
-be automatically changed to {host}. This setting has no effect if not
-running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later
-versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment
-variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu"
-flag is used.
-
-:line
-
-The {omp} style invokes settings associated with the use of the
-USER-OMP package.
-
-The {Nthread} argument sets the number of OpenMP threads allocated for
-each MPI task.  For example, if your system has nodes with dual
-quad-core processors, it has a total of 8 cores per node.  You could
-use two MPI tasks per node (e.g. using the -ppn option of the mpirun
-command in MPICH or -npernode in OpenMPI), and set {Nthreads} = 4.
-This would use all 8 cores on each node.  Note that the product of MPI
-tasks * threads/task should not exceed the physical number of cores
-(on a node), otherwise performance will suffer.
-
-Setting {Nthread} = 0 instructs LAMMPS to use whatever value is the
-default for the given OpenMP environment. This is usually determined
-via the {OMP_NUM_THREADS} environment variable or the compiler
-runtime.  Note that in most cases the default for OpenMP capable
-compilers is to use one thread for each available CPU core when
-{OMP_NUM_THREADS} is not explicitly set, which can lead to poor
-performance.
-
-Here are examples of how to set the environment variable when
-launching LAMMPS:
-
-env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
-env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
-mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script :pre
-
-or you can set it permanently in your shell's start-up script.
-All three of these examples use a total of 4 CPU cores.
-
-Note that different MPI implementations have different ways of passing
-the OMP_NUM_THREADS environment variable to all MPI processes.  The
-2nd example line above is for MPICH; the 3rd example line with -x is
-for OpenMPI.  Check your MPI documentation for additional details.
-
-What combination of threads and MPI tasks gives the best performance
-is difficult to predict and can depend on many components of your
-input.  Not all features of LAMMPS support OpenMP threading via the
-USER-OMP package and the parallel efficiency can be very different,
-too.
-
-Optional keyword/value pairs can also be specified.  Each has a
-default value as listed below.
-
-The {neigh} keyword specifies whether neighbor list building will be
-multi-threaded in addition to force calculations.  If {neigh} is set
-to {no} then neighbor list calculation is performed only by MPI tasks
-with no OpenMP threading.  If {mode} is {yes} (the default), a
-multi-threaded neighbor list build is used.  Using {neigh} = {yes} is
-almost always faster and should produce identical neighbor lists at the
-expense of using more memory.  Specifically, neighbor list pages are
-allocated for all threads at the same time and each thread works
-within its own pages.
-
-:line
-
-[Restrictions:]
-
-This command cannot be used after the simulation box is defined by a
-"read_data"_read_data.html or "create_box"_create_box.html command.
-
-The gpu style of this command can only be invoked if LAMMPS was built
-with the GPU package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-The intel style of this command can only be invoked if LAMMPS was
-built with the USER-INTEL package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-The kk style of this command can only be invoked if LAMMPS was built
-with the KOKKOS package.  See the "Build package"_Build_package.html
-doc page for more info.
-
-The omp style of this command can only be invoked if LAMMPS was built
-with the USER-OMP package.  See the "Build package"_Build_package.html
-doc page for more info.
-
-[Related commands:]
-
-"suffix"_suffix.html, "-pk command-line switch"_Run_options.html
-
-[Default:]
-
-For the GPU package, the default is Ngpu = 1 and the option defaults
-are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
-to Ngpu-1, tpa = 1, and device = not used.  These settings are made
-automatically if the "-sf gpu" "command-line switch"_Run_options.html
-is used.  If it is not used, you must invoke the package gpu command
-in your input script or via the "-pk gpu" "command-line
-switch"_Run_options.html.
-
-For the USER-INTEL package, the default is Nphi = 1 and the option
-defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
-tptask = 240.  The default ghost option is determined by the pair
-style being used.  This value is output to the screen in the offload
-report at the end of each run.  Note that all of these settings,
-except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
-Phi co-processor support.  These settings are made automatically if the
-"-sf intel" "command-line switch"_Run_options.html is used.  If it is
-not used, you must invoke the package intel command in your input
-script or via the "-pk intel" "command-line
-switch"_Run_options.html.
-
-For the KOKKOS package, the option defaults for GPUs are neigh = full,
-neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
-value, comm = device, cuda/aware = on. When LAMMPS can safely detect
-that CUDA-aware MPI is not available, the default value of cuda/aware
-becomes "off". For CPUs or Xeon Phis, the option defaults are neigh =
-half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The
-option neigh/thread = on when there are 16K atoms or less on an MPI
-rank, otherwise it is "off". These settings are made automatically by
-the required "-k on" "command-line switch"_Run_options.html. You can
-change them by using the package kokkos command in your input script or
-via the "-pk kokkos command-line switch"_Run_options.html.
-
-For the OMP package, the default is Nthreads = 0 and the option
-defaults are neigh = yes.  These settings are made automatically if
-the "-sf omp" "command-line switch"_Run_options.html is used.  If it
-is not used, you must invoke the package omp command in your input
-script or via the "-pk omp" "command-line switch"_Run_options.html.

From 876032b76243b69c28c7c607589298d82558174c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 11 Dec 2019 05:33:16 -0500
Subject: [PATCH 110/199] refactor MPI library info query so it can be added to
 -help flag output

---
 src/info.cpp   | 33 ++++++++++++++++++++-------------
 src/info.h     |  1 +
 src/lammps.cpp |  8 ++++++--
 3 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index 4b4c9a6a75..1e66c6644b 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -355,19 +355,7 @@ void Info::command(int narg, char **arg)
 
   if (flags & COMM) {
     int major,minor,len;
-#if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS)
-    char version[MPI_MAX_LIBRARY_VERSION_STRING];
-    MPI_Get_library_version(version,&len);
-#else
-    char version[] = "Undetected MPI implementation";
-    len = strlen(version);
-#endif
-
-    MPI_Get_version(&major,&minor);
-    if (len > 80) {
-      char *ptr = strchr(version+80,'\n');
-      if (ptr) *ptr = '\0';
-    }
+    const char *version = get_mpi_info(major,minor);
 
     fprintf(out,"\nCommunication information:\n");
     fprintf(out,"MPI library level: MPI v%d.%d\n",major,minor);
@@ -1209,6 +1197,25 @@ const char *Info::get_openmp_info()
 #endif
 }
 
+const char *Info::get_mpi_info(int &major, int &minor)
+{
+  int len;
+  #if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS)
+  static char version[MPI_MAX_LIBRARY_VERSION_STRING];
+  MPI_Get_library_version(version,&len);
+#else
+  static char version[] = "Undetected MPI implementation";
+  len = strlen(version);
+#endif
+
+  MPI_Get_version(&major,&minor);
+  if (len > 80) {
+    char *ptr = strchr(version+80,'\n');
+    if (ptr) *ptr = '\0';
+  }
+  return version;
+}
+
 const char *Info::get_cxx_info()
 {
 #if __cplusplus > 201703L
diff --git a/src/info.h b/src/info.h
index 8ac931aa68..01d6105ff2 100644
--- a/src/info.h
+++ b/src/info.h
@@ -43,6 +43,7 @@ class Info : protected Pointers {
   static char *get_os_info();
   static char *get_compiler_info();
   static const char *get_openmp_info();
+  static const char *get_mpi_info(int &, int &);
   static const char *get_cxx_info();
 
   char **get_variable_names(int &num);
diff --git a/src/lammps.cpp b/src/lammps.cpp
index a2d405855d..4b09429b52 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -1271,14 +1271,18 @@ void LAMMPS::print_config(FILE *fp)
   const char *pkg;
   int ncword, ncline = 0;
 
-  char *infobuf = Info::get_os_info();
+  const char *infobuf = Info::get_os_info();
   fprintf(fp,"OS: %s\n\n",infobuf);
   delete[] infobuf;
 
   infobuf = Info::get_compiler_info();
   fprintf(fp,"Compiler: %s with %s\n",infobuf,Info::get_openmp_info());
   delete[] infobuf;
-  fprintf(fp,"C++ standard: %s\n\n",Info::get_cxx_info());
+  fprintf(fp,"C++ standard: %s\n",Info::get_cxx_info());
+
+  int major,minor;
+  infobuf = Info::get_mpi_info(major,minor);
+  fprintf(fp,"MPI v%d.%d: %s\n\n",major,minor,infobuf);
 
   fputs("Active compile time flags:\n\n",fp);
   if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp);

From 5e983b899a6649ad84dfec33dc3bc8175d22f833 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 11 Dec 2019 08:34:56 -0500
Subject: [PATCH 111/199] remove unused variable

---
 src/info.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/info.cpp b/src/info.cpp
index 1e66c6644b..ca90a6cc2f 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -354,7 +354,7 @@ void Info::command(int narg, char **arg)
   }
 
   if (flags & COMM) {
-    int major,minor,len;
+    int major,minor;
     const char *version = get_mpi_info(major,minor);
 
     fprintf(out,"\nCommunication information:\n");

From 99ba15bf6afb3dc6843e2bf18cb939ce3ade276e Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Wed, 11 Dec 2019 16:29:42 -0600
Subject: [PATCH 112/199] Updated README and added -L$(CUDA_HOME)/lib64/stubs
 to the Makefile's

---
 lib/gpu/Makefile.fermi           | 2 +-
 lib/gpu/Makefile.lammps.standard | 2 +-
 lib/gpu/Makefile.linux           | 2 +-
 lib/gpu/Makefile.linux.double    | 2 +-
 lib/gpu/Makefile.linux.mixed     | 2 +-
 lib/gpu/Makefile.linux.single    | 2 +-
 lib/gpu/Makefile.linux_multi     | 2 +-
 lib/gpu/Makefile.mac             | 2 +-
 lib/gpu/Makefile.serial          | 2 +-
 lib/gpu/Makefile.shannon         | 2 +-
 lib/gpu/Makefile.xk7             | 2 +-
 lib/gpu/README                   | 5 +++--
 12 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/lib/gpu/Makefile.fermi b/lib/gpu/Makefile.fermi
index ce5ccaaf78..81ab0bcde5 100644
--- a/lib/gpu/Makefile.fermi
+++ b/lib/gpu/Makefile.fermi
@@ -4,7 +4,7 @@ EXTRAMAKE = Makefile.lammps.standard
 CUDA_ARCH = -arch=sm_35
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64 -lcudart
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64/stubs -lcudart
 CUDA_OPTS = -DUNIX -O3 --use_fast_math --ftz=true
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include
diff --git a/lib/gpu/Makefile.lammps.standard b/lib/gpu/Makefile.lammps.standard
index 1ceb93b342..9526e8e373 100644
--- a/lib/gpu/Makefile.lammps.standard
+++ b/lib/gpu/Makefile.lammps.standard
@@ -7,5 +7,5 @@ endif
 
 gpu_SYSINC =
 gpu_SYSLIB =  -lcudart -lcuda
-gpu_SYSPATH = -L$(CUDA_HOME)/lib64
+gpu_SYSPATH = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 
diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux
index 7001c6d8b9..a26fbe114c 100644
--- a/lib/gpu/Makefile.linux
+++ b/lib/gpu/Makefile.linux
@@ -54,7 +54,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
 
 CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
diff --git a/lib/gpu/Makefile.linux.double b/lib/gpu/Makefile.linux.double
index e65647f160..05f083697d 100644
--- a/lib/gpu/Makefile.linux.double
+++ b/lib/gpu/Makefile.linux.double
@@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_DOUBLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Makefile.linux.mixed b/lib/gpu/Makefile.linux.mixed
index a036b84ee3..ca414f1fc1 100644
--- a/lib/gpu/Makefile.linux.mixed
+++ b/lib/gpu/Makefile.linux.mixed
@@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Makefile.linux.single b/lib/gpu/Makefile.linux.single
index 808647cea7..1b349faac2 100644
--- a/lib/gpu/Makefile.linux.single
+++ b/lib/gpu/Makefile.linux.single
@@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_SINGLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Makefile.linux_multi b/lib/gpu/Makefile.linux_multi
index 2f75ca0e2b..ba50170f39 100644
--- a/lib/gpu/Makefile.linux_multi
+++ b/lib/gpu/Makefile.linux_multi
@@ -40,7 +40,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98"
 
 CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
diff --git a/lib/gpu/Makefile.mac b/lib/gpu/Makefile.mac
index f9f8d5179a..b571e8d85a 100644
--- a/lib/gpu/Makefile.mac
+++ b/lib/gpu/Makefile.mac
@@ -14,7 +14,7 @@ NVCC = nvcc -m64
 CUDA_ARCH = -arch=sm_11
 CUDA_PRECISION = -D_SINGLE_SINGLE
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib
+CUDA_LIB = -L$(CUDA_HOME)/lib -L$(CUDA_HOME)/lib/stubs
 CUDA_OPTS = -DUNIX -DUCL_NO_EXIT -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -m64
diff --git a/lib/gpu/Makefile.serial b/lib/gpu/Makefile.serial
index 99153fc471..b0cfb3c86b 100644
--- a/lib/gpu/Makefile.serial
+++ b/lib/gpu/Makefile.serial
@@ -34,7 +34,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64 -L../../src/STUBS -lmpi_stubs
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs -L../../src/STUBS -lmpi_stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC)
 
 CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -fPIC -I../../src/STUBS
diff --git a/lib/gpu/Makefile.shannon b/lib/gpu/Makefile.shannon
index 22c2dc89d7..b14bd01ec2 100644
--- a/lib/gpu/Makefile.shannon
+++ b/lib/gpu/Makefile.shannon
@@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_DOUBLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Makefile.xk7 b/lib/gpu/Makefile.xk7
index 0b9f029399..f3050575e1 100644
--- a/lib/gpu/Makefile.xk7
+++ b/lib/gpu/Makefile.xk7
@@ -14,7 +14,7 @@ CUDA_ARCH = -arch=sm_35
 
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = CC -DCUDA_PROXY -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/README b/lib/gpu/README
index 6cc386270d..92be2d408c 100644
--- a/lib/gpu/README
+++ b/lib/gpu/README
@@ -3,7 +3,7 @@
                   --------------------------------
                      
                        W. Michael Brown (ORNL)
-                        Trung Dac Nguyen (ORNL)
+                        Trung Dac Nguyen (ORNL/Northwestern)
                           Peng Wang (NVIDIA)
                        Axel Kohlmeyer (Temple)
                          Steve Plimpton (SNL)
@@ -129,7 +129,8 @@ that ships with the CUDA toolkit, but also with the CUDA driver library
 on the head node of a GPU cluster, this library may not be installed,
 so you may need to copy it over from one of the compute nodes (best into
 this directory). Recent CUDA toolkits starting from CUDA 9 provide a dummy
-libcuda.so library, that can be used for linking (but not for running).
+libcuda.so library (typically under $(CUDA_HOME)/lib64/stubs), that can be used for
+linking (but not for running).
 
 The gpu library supports 3 precision modes as determined by 
 the CUDA_PRECISION variable:

From bde8b57f0bae7fb8876fbf63a030e7e1c8347372 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Wed, 11 Dec 2019 23:10:11 -0700
Subject: [PATCH 113/199] Update fix_bond_react.rst

---
 doc/src/fix_bond_react.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst
index 7f72d1f428..b2866eb9c7 100644
--- a/doc/src/fix_bond_react.rst
+++ b/doc/src/fix_bond_react.rst
@@ -253,7 +253,7 @@ A discussion of correctly handling this is also provided on the
 The map file is a text document with the following format:
 
 A map file has a header and a body. The header of map file the
-contains one mandatory keyword and four optional keywords. The
+contains one mandatory keyword and five optional keywords. The
 mandatory keyword is 'equivalences':
 
 

From 7e8a04d9857c9ed3685d7d933bf2f5a6981b3bb5 Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Thu, 12 Dec 2019 09:57:49 -0600
Subject: [PATCH 114/199] More minor update to README

---
 lib/gpu/README | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/gpu/README b/lib/gpu/README
index 92be2d408c..2d98749a40 100644
--- a/lib/gpu/README
+++ b/lib/gpu/README
@@ -130,7 +130,7 @@ on the head node of a GPU cluster, this library may not be installed,
 so you may need to copy it over from one of the compute nodes (best into
 this directory). Recent CUDA toolkits starting from CUDA 9 provide a dummy
 libcuda.so library (typically under $(CUDA_HOME)/lib64/stubs), that can be used for
-linking (but not for running).
+linking.
 
 The gpu library supports 3 precision modes as determined by 
 the CUDA_PRECISION variable:

From b0d0037f50d58e467d6e5b81c2872b7f1bb43851 Mon Sep 17 00:00:00 2001
From: Yaser Afshar <ya.afshar@gmail.com>
Date: Thu, 12 Dec 2019 12:57:34 -0600
Subject: [PATCH 115/199] Certificate Verification

if SSL report an error ("certificate verify failed") during the
handshake and thus refuses further communication with that server,
you can specify your own CA cert path by setting the environment
variable CURL_CA_BUNDLE to the path of your choice.
---
 cmake/Modules/Packages/KIM.cmake |  8 ++++++++
 doc/src/Build_extras.rst         | 20 ++++++++++++++++++++
 doc/txt/Build_extras.txt         | 23 ++++++++++++++++++++++-
 src/KIM/kim_query.cpp            | 19 +++++++++++++++++--
 4 files changed, 67 insertions(+), 3 deletions(-)

diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake
index 8d17225760..eda8ffe82e 100644
--- a/cmake/Modules/Packages/KIM.cmake
+++ b/cmake/Modules/Packages/KIM.cmake
@@ -5,6 +5,14 @@ if(PKG_KIM)
     include_directories(${CURL_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
     add_definitions(-DLMP_KIM_CURL)
+    set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
+    if(LMP_DEBUG_CURL)
+      add_definitions(-DLMP_DEBUG_CURL)
+    endif()
+    set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
+    if(LMP_NO_SSL_CHECK)
+      add_definitions(-DLMP_NO_SSL_CHECK)
+    endif()
   endif()
   find_package(KIM-API QUIET)
   if(KIM-API_FOUND)
diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst
index 6162940015..c02b24641e 100644
--- a/doc/src/Build_extras.rst
+++ b/doc/src/Build_extras.rst
@@ -195,12 +195,32 @@ minutes to hours) to build.  Of course you only need to do that once.)
 .. parsed-literal::
 
    -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes
+   -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on
+   -D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes
 
 If DOWNLOAD\_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
 environment variable so that libkim-api can be found.
 
+For using KIM web queries.
+
+If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
+libcurl calls within the KIM web query display a lot of information about
+libcurl operations. You hardly ever want this set in production use, you will
+almost always want this when you debug/report problems.
+
+The libcurl performs peer SSL certificate verification by default. This
+verification is done using a CA certificate store that the SSL library can
+use to make sure the peer's server certificate is valid. If SSL reports an
+error ("certificate verify failed") during the handshake and thus refuses
+further communication with that server, you can set LMP\_NO\_SSL\_CHECK.
+If LMP\_NO\_SSL\_CHECK is set, libcurl does not verify the peer and connection
+succeeds regardless of the names in the certificate. This option is insecure.
+As an alternative, you can specify your own CA cert path by setting the
+environment variable CURL\_CA\_BUNDLE to the path of your choice. A call to the
+KIM web query would get this value from the environmental variable.
+
 **Traditional make**\ :
 
 You can download and build the KIM library manually if you prefer;
diff --git a/doc/txt/Build_extras.txt b/doc/txt/Build_extras.txt
index 114aeda7af..4cf40bbee4 100644
--- a/doc/txt/Build_extras.txt
+++ b/doc/txt/Build_extras.txt
@@ -186,13 +186,34 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
 [CMake build]:
 
--D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes :pre
+-D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes
+-D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on
+-D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes
+:pre
 
 If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
 environment variable so that libkim-api can be found.
 
+For using OpenKIM web queries in LAMMPS.
+
+If LMP_DEBUG_CURL is set, the libcurl verbose mode will be on, and any
+libcurl calls within the KIM web query display a lot of information about
+libcurl operations. You hardly ever want this set in production use, you will
+almost always want this when you debug/report problems.
+
+The libcurl performs peer SSL certificate verification by default. This
+verification is done using a CA certificate store that the SSL library can
+use to make sure the peer's server certificate is valid. If SSL reports an
+error ("certificate verify failed") during the handshake and thus refuses
+further communication with that server, you can set LMP_NO_SSL_CHECK.
+If LMP_NO_SSL_CHECK is set, libcurl does not verify the peer and connection
+succeeds regardless of the names in the certificate. This option is insecure.
+As an alternative, you can specify your own CA cert path by setting the
+environment variable CURL_CA_BUNDLE to the path of your choice. A call to the
+KIM web query would get this value from the environmental variable.
+
 [Traditional make]:
 
 You can download and build the KIM library manually if you prefer;
diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp
index 38ae57c25a..12c93c80c2 100644
--- a/src/KIM/kim_query.cpp
+++ b/src/KIM/kim_query.cpp
@@ -72,6 +72,7 @@
 #if defined(LMP_KIM_CURL)
 #include <sys/types.h>
 #include <curl/curl.h>
+#include <cstdlib>
 #endif
 
 using namespace LAMMPS_NS;
@@ -257,11 +258,25 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
       curl_easy_setopt(handle, CURLOPT_VERBOSE, 1L);
 #endif
 
-#if defined(LMP_NO_SSL_CHECK)
-      // disable verifying SSL certificate and host name
+#if LMP_NO_SSL_CHECK
+      // Certificate Verification
+      // by telling libcurl to not verify the peer.
+      // Disable verifying SSL certificate and host name. Insecure.
       curl_easy_setopt(handle, CURLOPT_SSL_VERIFYPEER, 0L);
       curl_easy_setopt(handle, CURLOPT_SSL_VERIFYHOST, 0L);
 #endif
+
+      {
+        char *env_c = std::getenv("CURL_CA_BUNDLE");
+        if (env_c)
+        {
+          // Certificate Verification
+          // by specifying your own CA cert path. Set the environment variable
+          // CURL_CA_BUNDLE to the path of your choice.
+          curl_easy_setopt(handle, CURLOPT_CAINFO, env_c);
+        }
+      }
+
       std::string user_agent = std::string("kim_query--LAMMPS/")
                                + LAMMPS_VERSION
                                + " (" + Info::get_os_info() + ")";

From 1f9f85e7982e85a2124f23fc50500dc772762fe6 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 12 Dec 2019 14:17:32 -0500
Subject: [PATCH 116/199] Mark LMP_NO_SSL_CHECK and LMP_DEBUG_CURL as advanced
 options

---
 cmake/Modules/Packages/KIM.cmake | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake
index eda8ffe82e..a75e248097 100644
--- a/cmake/Modules/Packages/KIM.cmake
+++ b/cmake/Modules/Packages/KIM.cmake
@@ -6,10 +6,12 @@ if(PKG_KIM)
     list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
     add_definitions(-DLMP_KIM_CURL)
     set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
+    mark_as_advanced(LMP_DEBUG_CURL)
     if(LMP_DEBUG_CURL)
       add_definitions(-DLMP_DEBUG_CURL)
     endif()
     set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
+    mark_as_advanced(LMP_NO_SSL_CHECK)
     if(LMP_NO_SSL_CHECK)
       add_definitions(-DLMP_NO_SSL_CHECK)
     endif()

From 55fde76d597fbda9f105f165a8cbb637eb07ca77 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 16 Dec 2019 07:22:41 -0500
Subject: [PATCH 117/199] may only close files on MPI ranks that have a file
 reader instance

---
 src/read_dump.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index dd9395c092..c61c467a59 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -434,8 +434,9 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip)
   // all filereader procs close all their files and return
 
   if (ntimestep < 0) {
-    for (int i = 0; i < nreader; i++)
-      readers[i]->close_file();
+    if (filereader)
+      for (int i = 0; i < nreader; i++)
+        readers[i]->close_file();
     return ntimestep;
   }
 

From 4c3ec145f3c1f2f456e4be1ed90fc36394da2114 Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Tue, 17 Dec 2019 14:05:39 -0600
Subject: [PATCH 118/199] Corrected the wrong use of the stubs path in -rpath

---
 lib/gpu/Makefile.fermi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/gpu/Makefile.fermi b/lib/gpu/Makefile.fermi
index 81ab0bcde5..ce5ccaaf78 100644
--- a/lib/gpu/Makefile.fermi
+++ b/lib/gpu/Makefile.fermi
@@ -4,7 +4,7 @@ EXTRAMAKE = Makefile.lammps.standard
 CUDA_ARCH = -arch=sm_35
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64/stubs -lcudart
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64 -lcudart
 CUDA_OPTS = -DUNIX -O3 --use_fast_math --ftz=true
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include

From 1be9364a895ceb67cbc352ad114fc4924d02c563 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Tue, 3 Dec 2019 19:47:23 +0100
Subject: [PATCH 119/199] MEAM/C: document new reference structures

---
 doc/src/pair_meamc.rst | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst
index daa10906c7..ac858ce24b 100644
--- a/doc/src/pair_meamc.rst
+++ b/doc/src/pair_meamc.rst
@@ -233,15 +233,20 @@ where
    Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
                  by K (I<=J); default = 2.0
    lattce(I,J) = lattice structure of I-J reference structure:
-                   dia = diamond (interlaced fcc for alloy)
                    fcc = face centered cubic
                    bcc = body centered cubic
-                   dim = dimer
-                   b1  = rock salt (NaCl structure)
                    hcp = hexagonal close-packed
+                   dim = dimer
+                   dia = diamond (interlaced fcc for alloy)
+                   dia3= diamond structure with primary 1NN and secondary 3NN interation
+                   b1  = rock salt (NaCl structure)
                    c11 = MoSi2 structure
                    l12 = Cu3Au structure (lower case L, followed by 12)
                    b2  = CsCl structure (interpenetrating simple cubic)
+                   ch4 = methane-like structure, only for binary system
+                   lin = linear structure (180 degree angle)
+                   zig = zigzag structure with a uniform angle
+                   tri = H2O-like structure that has an angle
    nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for
                  I-J pair (see for example :ref:`(Lee) <Lee>`).
                    0 = second-nearest neighbor formulation off
@@ -254,6 +259,8 @@ where
    zbl(I,J)    = blend the MEAM I-J pair potential with the ZBL potential for small
                  atom separations :ref:`(ZBL) <ZBL>`
                    default = 1
+   theta(I,J)  = angle between three atoms in line, zigzag, and trimer reference structures in degrees
+                   default = 180
    gsmooth_factor  = factor determining the length of the G-function smoothing
                      region; only significant for ibar=0 or ibar=4.
                          99.0 = short smoothing region, sharp step

From a231197c10a246448720f7e99cca61256a6c1e73 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Tue, 17 Dec 2019 21:47:15 +0100
Subject: [PATCH 120/199] MEAM/C: remove unused variable alias

---
 src/USER-MEAMC/meam_force.cpp | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp
index 5a2f544d8b..2b6832e155 100644
--- a/src/USER-MEAMC/meam_force.cpp
+++ b/src/USER-MEAMC/meam_force.cpp
@@ -17,7 +17,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
   double v[6], fi[3], fj[3];
   double third, sixth;
   double pp, dUdrij, dUdsij, dUdrijm[3], force, forcem;
-  double r, recip, phi, phip;
+  double recip, phi, phip;
   double sij;
   double a1, a1i, a1j, a2, a2i, a2j;
   double a3i, a3j;
@@ -71,7 +71,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
       rij2 = delij[0] * delij[0] + delij[1] * delij[1] + delij[2] * delij[2];
       if (rij2 < this->cutforcesq) {
         rij = sqrt(rij2);
-        r = rij;
+        recip = 1.0 / rij;
 
         //     Compute phi and phip
         ind = this->eltind[elti][eltj];
@@ -80,10 +80,8 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
         kk = std::min(kk, this->nrar - 2);
         pp = pp - kk;
         pp = std::min(pp, 1.0);
-        phi = ((this->phirar3[ind][kk] * pp + this->phirar2[ind][kk]) * pp + this->phirar1[ind][kk]) * pp +
-          this->phirar[ind][kk];
+        phi = ((this->phirar3[ind][kk] * pp + this->phirar2[ind][kk]) * pp + this->phirar1[ind][kk]) * pp + this->phirar[ind][kk];
         phip = (this->phirar6[ind][kk] * pp + this->phirar5[ind][kk]) * pp + this->phirar4[ind][kk];
-        recip = 1.0 / r;
 
         if (eflag_either != 0) {
           double phi_sc = phi * scaleij;

From cb20cb9f25c9f18cf9891dcfef8795a2a68b6006 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Tue, 17 Dec 2019 22:23:19 +0100
Subject: [PATCH 121/199] Add range checks for MathSpecial::fm_exp

---
 src/math_special.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/math_special.cpp b/src/math_special.cpp
index bf11a1ad45..d4abc36f25 100644
--- a/src/math_special.cpp
+++ b/src/math_special.cpp
@@ -538,6 +538,8 @@ double MathSpecial::exp2_x86(double x)
 double MathSpecial::fm_exp(double x)
 {
 #if defined(__BYTE_ORDER__) && (__BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__)
+    if (x < -1022.0/FM_DOUBLE_LOG2OFE) return 0;
+    if (x > 1023.0/FM_DOUBLE_LOG2OFE) return INFINITY;
     return exp2_x86(FM_DOUBLE_LOG2OFE * x);
 #else
     return ::exp(x);

From 3be04e4671734ce6dab12bda8d5af5351431e3ac Mon Sep 17 00:00:00 2001
From: Michael Brown <michael.w.brown@intel.com>
Date: Wed, 18 Dec 2019 01:27:39 -0800
Subject: [PATCH 122/199] Bug fix for USER-INTEL package with triclinic
 neighbor builds.

---
 src/USER-INTEL/npair_intel.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
index a82d3f29e5..4256e03b3c 100644
--- a/src/USER-INTEL/npair_intel.cpp
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -360,7 +360,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
             if (THREE) ttag[u] = tag[j];
           }
 
-          if (FULL == 0 || TRI == 1) {
+          if (FULL == 0 && TRI != 1) {
             icount = 0;
             istart = ncount;
             IP_PRE_edge_align(istart, sizeof(int));
@@ -392,7 +392,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
         // ---------------------- Loop over i bin
 
         int n = 0;
-        if (FULL == 0 || TRI == 1) {
+        if (FULL == 0 && TRI != 1) {
           #if defined(LMP_SIMD_COMPILER)
           #pragma vector aligned
           #pragma ivdep

From d05f32d15228c76a216d2097cb68e2bc14d069f2 Mon Sep 17 00:00:00 2001
From: Oliver Henrich <ohenrich@users.noreply.github.com>
Date: Wed, 18 Dec 2019 11:31:02 +0000
Subject: [PATCH 123/199] Added oxRNA2 files to .gitignore

---
 src/.gitignore | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/.gitignore b/src/.gitignore
index 5848874d94..1b7dc7e6b2 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -280,6 +280,8 @@
 /bond_oxdna_fene.h
 /bond_oxdna2_fene.cpp
 /bond_oxdna2_fene.h
+/bond_oxrna2_fene.cpp
+/bond_oxrna2_fene.h
 /bond_quartic.cpp
 /bond_quartic.h
 /bond_table.cpp
@@ -982,6 +984,8 @@
 /pair_oxdna_*.h
 /pair_oxdna2_*.cpp
 /pair_oxdna2_*.h
+/pair_oxrna2_*.cpp
+/pair_oxrna2_*.h
 /mf_oxdna.h
 /pair_peri_eps.cpp
 /pair_peri_eps.h

From 081839b44956a292ce5e96150cf1a6a1d7e35302 Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Thu, 19 Dec 2019 16:44:32 +0300
Subject: [PATCH 124/199] Fix the example according to the convention

---
 examples/TIP4P/gpu_dump/data.spce             |    1 +
 .../dump.force_cpu.19Dec19.tip4p.g++.1        | 9018 ++++++++++++++++
 ...p.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp | 9018 ++++++++++++++++
 examples/TIP4P/gpu_dump/in.tip4p              |   49 +
 .../TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1    |  127 +
 .../log.19Dec19.tip4p.g++.1.gtx1070.dp        |  120 +
 examples/water/data.spce                      | 9029 -----------------
 examples/water/data_file                      |   19 -
 examples/water/in_massive                     |   80 -
 9 files changed, 18333 insertions(+), 9128 deletions(-)
 create mode 120000 examples/TIP4P/gpu_dump/data.spce
 create mode 100644 examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1
 create mode 100644 examples/TIP4P/gpu_dump/dump.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp
 create mode 100644 examples/TIP4P/gpu_dump/in.tip4p
 create mode 100644 examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1
 create mode 100644 examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp
 delete mode 100644 examples/water/data.spce
 delete mode 100644 examples/water/data_file
 delete mode 100644 examples/water/in_massive

diff --git a/examples/TIP4P/gpu_dump/data.spce b/examples/TIP4P/gpu_dump/data.spce
new file mode 120000
index 0000000000..4c8051fdff
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/data.spce
@@ -0,0 +1 @@
+../../rdf-adf/data.spce
\ No newline at end of file
diff --git a/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1 b/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1
new file mode 100644
index 0000000000..faa6d3c117
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1
@@ -0,0 +1,9018 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+4500
+ITEM: BOX BOUNDS pp pp pp
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6409999999999999e-02 3.5473599999999998e+01
+ITEM: ATOMS id type x y z fx fy fz 
+1 1 12.1247 28.092 22.2745 44.3296 17.0725 48.5356 
+2 2 12.4974 28.7565 22.854 -24.598 -41.7029 -32.885 
+3 2 11.5314 28.5784 21.7021 -26.0334 10.24 -23.1056 
+4 1 1.17081 29.3781 23.7307 -74.0189 -7.00332 56.5394 
+5 2 1.86259 29.4619 23.0745 28.6874 -4.77355 -53.1747 
+6 2 0.455888 28.9379 23.2709 28.8474 14.4006 -7.70694 
+7 1 29.6824 14.7369 21.6275 -6.84135 -10.4682 -14.9806 
+8 2 30.5192 14.9459 21.2125 -6.0991 2.52794 20.3786 
+9 2 29.7669 15.072 22.5202 13.979 5.65532 2.32707 
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+ITEM: TIMESTEP
+1
+ITEM: NUMBER OF ATOMS
+4500
+ITEM: BOX BOUNDS pp pp pp
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6409999999999999e-02 3.5473599999999998e+01
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diff --git a/examples/TIP4P/gpu_dump/dump.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp b/examples/TIP4P/gpu_dump/dump.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp
new file mode 100644
index 0000000000..faa6d3c117
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/dump.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp
@@ -0,0 +1,9018 @@
+ITEM: TIMESTEP
+0
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+ITEM: TIMESTEP
+1
+ITEM: NUMBER OF ATOMS
+4500
+ITEM: BOX BOUNDS pp pp pp
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6409999999999999e-02 3.5473599999999998e+01
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+4357 1 28.0502 19.8274 0.200166 -14.718 -13.8365 8.14135 
+4358 2 27.3541 20.1731 0.758914 0.586214 2.00411 -2.90586 
+4359 2 27.6786 19.0326 35.2649 -1.29562 -1.13825 1.86866 
+4360 1 13.8259 16.066 19.2377 3.42806 -1.9108 -8.46231 
+4361 2 14.739 15.8494 19.4262 -0.173301 -1.04149 -2.1628 
+4362 2 13.3196 15.4176 19.727 -1.00489 5.59839 2.6295 
+4363 1 14.0833 21.9737 33.177 1.55338 -10.2777 0.601086 
+4364 2 14.8552 22.1139 33.7254 -0.592833 3.48917 -2.04988 
+4365 2 14.3993 22.0966 32.2819 -4.6893 3.47479 -0.636361 
+4366 1 16.3426 25.3935 3.01903 8.64182 -10.3293 -7.26207 
+4367 2 16.7982 26.2352 3.03233 1.45724 -1.73979 2.17777 
+4368 2 16.9769 24.7832 2.64282 0.517788 -0.592036 1.01179 
+4369 1 34.4109 25.5041 0.147232 -4.97865 0.544753 -0.984839 
+4370 2 34.8322 26.3303 0.384396 -0.932015 -0.895181 -0.271714 
+4371 2 33.5198 25.5827 0.487847 1.51715 -0.291147 -0.624421 
+4372 1 27.8648 21.35 28.119 -0.690813 2.64901 0.101312 
+4373 2 28.7387 21.0626 27.8543 -1.28703 -2.80379 3.83509 
+4374 2 27.2858 21.0223 27.4309 2.06622 3.35093 -2.82638 
+4375 1 0.240252 27.2384 27.9971 -0.91815 -14.2657 -2.87632 
+4376 2 0.781723 26.637 28.5084 1.49113 0.267903 -1.08884 
+4377 2 34.9499 26.7426 27.8083 0.127613 -0.916031 2.36942 
+4378 1 21.6858 25.3229 17.7964 -5.16014 -6.43428 -1.59847 
+4379 2 21.9921 26.2272 17.7279 -0.0319833 -0.570092 0.694787 
+4380 2 21.3181 25.1281 16.9343 1.91105 0.442844 0.0444748 
+4381 1 30.9762 0.893719 8.90624 6.84658 4.89315 4.34164 
+4382 2 31.2866 0.970928 8.00407 -1.30872 -1.28953 0.0387564 
+4383 2 30.0457 1.11331 8.85952 1.85147 1.23716 1.21913 
+4384 1 25.4566 22.8733 21.0012 8.46941 -6.2365 -4.41175 
+4385 2 26.2934 22.4661 21.2251 -0.0869085 0.997113 -0.522472 
+4386 2 25.6712 23.793 20.8454 -2.04348 -0.380031 3.58637 
+4387 1 24.8743 30.4839 12.6069 5.18592 -5.90954 -3.66721 
+4388 2 25.6363 30.6355 12.0478 -2.47753 -1.31299 -1.73489 
+4389 2 25.0041 29.602 12.9557 1.098 0.771613 1.03075 
+4390 1 13.8113 7.99004 5.29125 -6.25539 2.54191 5.22156 
+4391 2 13.7892 8.73645 4.69241 1.40451 -0.877124 -0.322734 
+4392 2 14.7345 7.89861 5.52688 -0.824712 -3.60413 -2.23204 
+4393 1 33.9717 12.8445 16.8206 -5.08834 3.24579 2.32558 
+4394 2 34.7638 12.3611 17.0557 -0.912544 -1.123 -1.64622 
+4395 2 33.6042 13.1252 17.6586 -0.0818337 -2.83827 1.19082 
+4396 1 26.5929 21.8369 5.4998 15.2188 -12.8758 -3.5611 
+4397 2 27.193 22.4961 5.15108 1.54123 -0.472239 4.36294 
+4398 2 27.1503 21.0829 5.69232 0.775207 0.532331 0.731822 
+4399 1 5.16966 25.9262 12.3542 3.63388 -10.9707 -4.2268 
+4400 2 4.39065 25.3778 12.4469 0.868663 0.512582 0.49162 
+4401 2 5.73068 25.672 13.0869 1.15015 -1.40555 -2.02342 
+4402 1 26.7931 35.4254 5.15069 -2.58439 4.8653 0.22666 
+4403 2 26.5925 34.8211 5.86542 2.47532 -0.574882 -0.655596 
+4404 2 27.2131 0.665389 5.57819 2.08955 -0.944702 -1.56575 
+4405 1 1.20884 3.82973 0.244724 1.66138 -1.50883 -2.97877 
+4406 2 2.01641 3.42102 0.556221 -0.565104 -0.453085 -0.98583 
+4407 2 0.510904 3.36319 0.704569 -0.652139 1.89174 -3.14661 
+4408 1 26.4335 3.26352 13.8621 2.94116 4.56618 2.38726 
+4409 2 26.7833 4.04332 14.2931 1.33818 -0.0840263 -3.07679 
+4410 2 25.7332 3.59406 13.2994 -3.10068 -2.3533 4.10846 
+4411 1 33.2055 12.6395 8.23391 5.45516 1.9919 5.8193 
+4412 2 32.6787 12.8131 9.01402 -0.345731 -1.59928 -1.24485 
+4413 2 34.1053 12.8183 8.50726 -0.805487 1.53365 1.78742 
+4414 1 29.9023 24.5626 20.7116 3.42295 -6.98403 -0.952027 
+4415 2 29.4679 25.4132 20.6473 -0.48284 -2.69496 0.222901 
+4416 2 30.2739 24.4166 19.8417 -0.244826 -2.35878 0.7128 
+4417 1 15.2998 4.02453 16.4417 -2.15742 4.79241 6.05563 
+4418 2 15.7057 4.6226 17.0692 0.191126 1.42105 -2.21766 
+4419 2 14.9946 3.28953 16.9736 -0.120429 1.69431 2.26192 
+4420 1 31.2753 25.1783 0.424078 -3.05861 -1.08728 17.9787 
+4421 2 31.0586 24.4517 35.287 4.05906 -1.40755 1.82856 
+4422 2 30.7422 25.0259 1.20438 -1.38424 0.164027 -0.204301 
+4423 1 12.1221 3.02324 0.180171 5.54245 -1.23026 6.11818 
+4424 2 11.8464 2.17458 35.281 1.14317 0.150516 -0.180026 
+4425 2 11.3607 3.34415 0.66332 2.03454 -2.74467 1.9593 
+4426 1 32.8431 11.557 14.38 0.147749 2.67556 -1.98289 
+4427 2 31.9068 11.5678 14.1811 0.291943 -1.00905 2.75821 
+4428 2 32.9664 12.2812 14.9936 1.19966 -2.12497 2.082 
+4429 1 20.5645 17.4424 12.4515 6.55406 0.156517 0.559841 
+4430 2 19.8459 16.8903 12.1433 -1.42603 2.83887 0.952488 
+4431 2 20.6495 17.2292 13.3808 1.56555 -1.24922 -0.696423 
+4432 1 15.2816 11.6269 18.8168 5.55975 3.4447 3.66971 
+4433 2 14.386 11.8473 19.0727 -0.646747 -2.40537 -4.21442 
+4434 2 15.3862 10.7109 19.0741 1.74861 1.0941 -0.195148 
+4435 1 29.7377 20.372 3.36652 0.797329 -7.98301 -8.63454 
+4436 2 30.4736 19.7997 3.5836 -1.83703 -0.890419 1.54523 
+4437 2 29.86 20.5792 2.44008 0.781849 -1.5009 -0.273719 
+4438 1 10.4638 28.1009 15.3794 8.14468 4.22684 -0.814723 
+4439 2 9.53379 28.2306 15.5652 0.0260372 -2.67835 -1.69305 
+4440 2 10.6322 28.642 14.608 -0.570693 -1.3859 -1.11001 
+4441 1 16.7704 6.13101 17.944 -0.211983 -1.47772 3.31 
+4442 2 17.2683 6.32159 18.7389 1.86764 1.15901 -3.46209 
+4443 2 16.6681 6.98075 17.5153 -2.39931 -1.61441 -0.74807 
+4444 1 21.5135 0.327334 25.1409 8.66564 11.1895 -11.7105 
+4445 2 22.2279 0.15114 25.7531 -4.2921 0.404201 4.61487 
+4446 2 21.4118 35.0184 24.6498 0.519456 -0.928846 2.19863 
+4447 1 8.71062 23.6629 10.1362 3.05079 1.60887 0.77512 
+4448 2 9.03714 24.1011 10.9221 0.259856 1.17771 -1.23482 
+4449 2 9.41576 23.0672 9.88307 -1.85123 -1.62472 0.915088 
+4450 1 20.2468 3.67222 10.3704 0.4777 5.10365 7.10224 
+4451 2 20.359 3.07898 11.1132 -0.765711 0.100413 -2.14552 
+4452 2 19.4836 3.33128 9.90403 2.85534 1.08452 -0.754728 
+4453 1 5.99164 17.0864 14.8678 -5.37574 3.84131 -0.459775 
+4454 2 6.63127 17.7689 14.6646 3.22934 -2.98012 2.44679 
+4455 2 5.554 17.396 15.6608 -0.457156 0.512177 -0.289605 
+4456 1 9.83882 21.0265 7.18035 5.95081 -1.40299 -8.14061 
+4457 2 9.12061 21.5838 6.88056 -2.6067 -3.24929 2.7288 
+4458 2 9.85976 21.1517 8.1291 3.24078 0.788148 -1.58199 
+4459 1 14.2806 22.3479 30.4744 -5.28704 8.01428 14.3895 
+4460 2 13.8253 23.128 30.1575 2.20354 -0.167513 -4.00018 
+4461 2 14.4934 21.8556 29.6816 1.73645 -3.40489 3.93134 
+4462 1 9.99574 22.3649 18.625 -1.24662 -2.70761 -10.6994 
+4463 2 10.4595 21.9481 17.8987 0.183494 1.6516 0.642745 
+4464 2 10.6595 22.4657 19.3072 -3.1201 -0.222712 1.57266 
+4465 1 13.5444 23.3091 25.3305 6.03923 1.55312 0.42896 
+4466 2 13.2633 22.9728 26.1815 -0.932337 -1.00851 -1.27722 
+4467 2 14.4265 22.9566 25.2126 -1.02044 -2.61951 -0.48294 
+4468 1 20.38 18.6937 28.3968 7.14119 -6.8925 -2.09374 
+4469 2 20.0167 18.9886 27.5617 0.316244 -5.43562 -1.75257 
+4470 2 21.3206 18.6184 28.2361 0.666353 0.344779 0.815735 
+4471 1 31.9689 7.20731 11.1996 7.34708 3.16447 9.75319 
+4472 2 31.6099 7.15114 12.0852 0.998483 0.911771 -1.0382 
+4473 2 32.8409 6.81882 11.269 -0.906482 -0.425175 -2.58612 
+4474 1 3.59826 34.1759 15.1126 -11.7123 -5.68349 5.97393 
+4475 2 3.21043 33.454 14.6179 1.39026 0.0576551 1.52481 
+4476 2 3.54331 33.8972 16.0267 0.654449 -1.39662 -0.127074 
+4477 1 16.7556 18.4081 28.9987 8.31009 -1.52636 -3.73736 
+4478 2 17.6307 18.6606 29.2931 -1.43242 0.172472 0.00350369 
+4479 2 16.5433 17.6311 29.5158 -4.3853 4.025 1.85791 
+4480 1 4.3102 29.9995 27.41 12.3163 -5.69934 9.04024 
+4481 2 5.14895 30.4141 27.2079 -1.45489 3.42303 0.773461 
+4482 2 3.71946 30.3049 26.7216 -0.489848 -3.13791 0.780952 
+4483 1 6.15571 15.7166 24.0745 -10.4675 14.0348 8.09529 
+4484 2 5.31022 15.8535 24.5019 -1.15491 -4.01696 -1.7966 
+4485 2 6.50126 14.9194 24.4761 0.366863 0.626035 -2.42182 
+4486 1 1.16849 28.775 19.8427 0.210476 14.8941 -2.95759 
+4487 2 0.55835 28.0645 19.6452 -0.37833 1.16517 1.01041 
+4488 2 2.02094 28.3459 19.9163 -1.22217 1.3797 3.29741 
+4489 1 23.2346 29.7445 8.55319 -3.19073 0.0591217 -1.71373 
+4490 2 24.177 29.8703 8.66448 -1.37464 0.315561 0.0894517 
+4491 2 22.981 30.3965 7.89984 0.244518 -1.23007 0.476314 
+4492 1 19.4825 19.1594 6.42054 2.91673 9.05689 -8.3853 
+4493 2 19.0036 18.5381 5.87205 1.04646 3.76482 -1.27192 
+4494 2 18.8796 19.8942 6.5334 2.07477 2.20963 -2.23813 
+4495 1 33.0425 24.822 13.641 6.63183 6.2187 -2.78039 
+4496 2 33.7809 24.3577 13.2468 -0.641414 -1.92179 0.68381 
+4497 2 32.2751 24.3054 13.3949 -0.245517 -1.04267 4.99319 
+4498 1 26.0476 6.03912 17.2588 1.74441 -5.97008 8.24573 
+4499 2 26.4147 5.4419 17.9106 -0.885223 -2.61028 -1.33276 
+4500 2 26.4184 5.74408 16.4271 1.8916 3.73175 0.920143 
diff --git a/examples/TIP4P/gpu_dump/in.tip4p b/examples/TIP4P/gpu_dump/in.tip4p
new file mode 100644
index 0000000000..b31960d203
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/in.tip4p
@@ -0,0 +1,49 @@
+# sample script to compare and debug GPU accelerated tip4p water
+# use '-sf gpu' to enables the GPU accelerated pair style
+# without it the original lj/cut/tip4p/long from module KSPACE will be used
+
+units         real
+boundary      p p p
+
+atom_style    full
+bond_style    harmonic
+angle_style   harmonic
+atom_modify   map array
+
+pair_style    lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
+pair_modify   table 0
+
+#long-range solver for TIP4P from module KSPACE works on CPU
+suffix off
+newton on
+kspace_style  pppm/tip4p 1.0e-5
+suffix on
+
+read_data     data.spce
+
+pair_coeff    * * 0.0 0.0
+pair_coeff    1 1 0.1852 3.1589
+
+bond_coeff    1 0.0 0.9572
+angle_coeff   1 0.0 104.52
+
+group water type 1 2
+
+#maintain the water molecule rigid
+fix           1 water shake 1.0e-4 200 0 b 1 a 1
+fix           2 water nve
+
+thermo        100
+thermo_style  custom step etotal ke pe temp  evdwl ecoul elong press
+thermo_modify format float "%.15g"
+
+velocity      water create 300 123
+
+if $(is_active(package,gpu)) &
+ then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz"&
+ else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+dump_modify 11 sort id
+
+timestep      1
+
+run           1
diff --git a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1 b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1
new file mode 100644
index 0000000000..57b0db597c
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1
@@ -0,0 +1,127 @@
+LAMMPS (30 Oct 2019)
+#
+
+units         real
+boundary      p p p
+
+atom_style    full
+bond_style    harmonic
+angle_style   harmonic
+atom_modify   map array
+
+pair_style    lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
+pair_modify   table 0
+
+#long-range solver for TIP4P from module KSPACE works on CPU
+suffix off
+newton on
+kspace_style  pppm/tip4p 1.0e-5
+suffix on
+
+read_data     data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.00143709 secs
+  read_data CPU = 0.0185545 secs
+
+pair_coeff    * * 0.0 0.0
+pair_coeff    1 1 0.1852 3.1589
+
+bond_coeff    1 0.0 0.9572
+angle_coeff   1 0.0 104.52
+
+group water type 1 2
+4500 atoms in group water
+
+#maintain the water molecule rigid
+fix           1 water shake 1.0e-4 200 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  1500 = # of frozen angles
+fix           2 water nve
+
+thermo        100
+thermo_style  custom step etotal ke pe temp  evdwl ecoul elong press
+thermo_modify format float "%.15g"
+
+velocity      water create 300 123
+
+if $(is_active(package,gpu))  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+if 0  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz
+dump_modify 11 sort id
+
+timestep      1
+
+run           1
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using polynomial approximation for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.342797
+  grid = 36 36 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00261362
+  estimated relative force accuracy = 7.87083e-06
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 79507 46656
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.3092
+  ghost atom cutoff = 11.3092
+  binsize = 5.6546, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/tip4p/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 30.18 | 30.18 | 30.18 Mbytes
+Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press 
+       0 -6581.1098053463 2681.834801985 -9262.9446073313 300 3652.16918734499 90723.8782743546 -103638.992069031 20828.2770003273 
+       1 -6293.09711304554 1787.55263217222 -8080.64974521776 199.96227554909 3652.66537554581 91910.2042281151 -103643.519348879 20986.2037813061 
+Loop time of 0.0943946 on 1 procs for 1 steps with 4500 atoms
+
+Performance: 0.915 ns/day, 26.221 hours/ns, 10.594 timesteps/s
+101.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.071838   | 0.071838   | 0.071838   |   0.0 | 76.10
+Bond    | 1.974e-06  | 1.974e-06  | 1.974e-06  |   0.0 |  0.00
+Kspace  | 0.012686   | 0.012686   | 0.012686   |   0.0 | 13.44
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00012462 | 0.00012462 | 0.00012462 |   0.0 |  0.13
+Output  | 0.0093175  | 0.0093175  | 0.0093175  |   0.0 |  9.87
+Modify  | 0.00038138 | 0.00038138 | 0.00038138 |   0.0 |  0.40
+Other   |            | 4.484e-05  |            |       |  0.05
+
+Nlocal:    4500 ave 4500 max 4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    15219 ave 15219 max 15219 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.37151e+06 ave 1.37151e+06 max 1.37151e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1371514
+Ave neighs/atom = 304.781
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp
new file mode 100644
index 0000000000..4441a448da
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp
@@ -0,0 +1,120 @@
+LAMMPS (30 Oct 2019)
+package gpu 1
+#
+
+units         real
+boundary      p p p
+
+atom_style    full
+bond_style    harmonic
+angle_style   harmonic
+atom_modify   map array
+
+pair_style    lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
+pair_modify   table 0
+
+#long-range solver for TIP4P from module KSPACE works on CPU
+suffix off
+newton on
+kspace_style  pppm/tip4p 1.0e-5
+suffix on
+
+read_data     data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.000921346 secs
+  read_data CPU = 0.0115216 secs
+
+pair_coeff    * * 0.0 0.0
+pair_coeff    1 1 0.1852 3.1589
+
+bond_coeff    1 0.0 0.9572
+angle_coeff   1 0.0 104.52
+
+group water type 1 2
+4500 atoms in group water
+
+#maintain the water molecule rigid
+fix           1 water shake 1.0e-4 200 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  1500 = # of frozen angles
+fix           2 water nve
+
+thermo        100
+thermo_style  custom step etotal ke pe temp  evdwl ecoul elong press
+thermo_modify format float "%.15g"
+
+velocity      water create 300 123
+
+if $(is_active(package,gpu))  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+if 1  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz
+dump_modify 11 sort id
+
+timestep      1
+
+run           1
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using polynomial approximation for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.342797
+  grid = 36 36 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00261362
+  estimated relative force accuracy = 7.87083e-06
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 79507 46656
+WARNING: Increasing communication cutoff for TIP4P GPU style (../pair_lj_cut_tip4p_long_gpu.cpp:220)
+Per MPI rank memory allocation (min/avg/max) = 25.12 | 25.12 | 25.12 Mbytes
+Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press 
+       0 -6581.10980534572 2681.834801985 -9262.94460733072 300 3652.169187345 90723.8782743551 -103638.992069031 20828.2770003278 
+       1 -6293.09711304691 1787.55263217221 -8080.64974521913 199.96227554909 3652.6653755458 91910.2042281137 -103643.519348879 20986.203781307 
+Loop time of 0.0230916 on 1 procs for 1 steps with 4500 atoms
+
+Performance: 3.742 ns/day, 6.414 hours/ns, 43.306 timesteps/s
+103.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.000606   | 0.000606   | 0.000606   |   0.0 |  2.62
+Bond    | 1.682e-06  | 1.682e-06  | 1.682e-06  |   0.0 |  0.01
+Kspace  | 0.012588   | 0.012588   | 0.012588   |   0.0 | 54.51
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00015025 | 0.00015025 | 0.00015025 |   0.0 |  0.65
+Output  | 0.0093124  | 0.0093124  | 0.0093124  |   0.0 | 40.33
+Modify  | 0.00039674 | 0.00039674 | 0.00039674 |   0.0 |  1.72
+Other   |            | 3.623e-05  |            |       |  0.16
+
+Nlocal:    4500 ave 4500 max 4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    16834 ave 16834 max 16834 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/water/data.spce b/examples/water/data.spce
deleted file mode 100644
index 1e8a4a0913..0000000000
--- a/examples/water/data.spce
+++ /dev/null
@@ -1,9029 +0,0 @@
-LAMMPS Atom File
-
-         4500 atoms
-         3000 bonds
-         1500 angles
-            0 dihedrals
-            0 impropers
-
-        2 atom types
-        1 bond types
-        1 angle types
-
-     0.02645   35.53280  xlo xhi
-     0.02645   35.53280  ylo yhi
-     0.02641   35.47360  zlo zhi
-
-Masses
-
-	1	15.9994
-	2	1.00794
-
-Atoms
-
-      1    1  1 -0.8472   12.12456   28.09298   22.27452  0  1  0
-      2    1  2  0.4236   12.53683   28.75606   22.89928  0  1  0
-      3    1  2  0.4236   11.49482   28.56390   21.65678  0  1  0
-      4    2  1 -0.8472    1.17079   29.37777   23.72984  1 -1  0
-      5    2  2  0.4236    1.91804   29.48483   23.07399  1 -1  0
-      6    2  2  0.4236    0.40074   28.91964   23.28586  1 -1  0
-      7    3  1 -0.8472   29.68313   14.73733   21.62793 -1  0  0
-      8    3  2  0.4236   30.54284   14.93741   21.15800 -1  0  0
-      9    3  2  0.4236   29.73135   15.07344   22.56848 -1  0  0
-     10    4  1 -0.8472   10.87272    7.00153   35.10920  0  1  0
-     11    4  2  0.4236   11.11057    6.21663   34.53712  0  1  0
-     12    4  2  0.4236    9.95658    7.32301   34.86983  0  1  0
-     13    5  1 -0.8472    9.46588    6.43648   19.79899  0  1  0
-     14    5  2  0.4236    9.04840    6.32936   18.89668  0  1  0
-     15    5  2  0.4236   10.31722    5.91326   19.83657  0  1  0
-     16    6  1 -0.8472    3.17905   29.69801   22.11922  0  0  0
-     17    6  2  0.4236    3.19240   30.63289   21.76465  0  0  0
-     18    6  2  0.4236    3.38651   29.05797   21.37944  0  0  0
-     19    7  1 -0.8472   23.38618   11.29979   30.78238  0  0  0
-     20    7  2  0.4236   23.69882   10.46688   31.23897  0  0  0
-     21    7  2  0.4236   24.17354   11.79208   30.41132  0  0  0
-     22    8  1 -0.8472   11.03761   10.46106   30.14741  0  1  0
-     23    8  2  0.4236   10.94682   11.45112   30.25464  0  1  0
-     24    8  2  0.4236   11.60678   10.09680   30.88450  0  1  0
-     25    9  1 -0.8472   26.24001   25.40937   21.06754  0  0  0
-     26    9  2  0.4236   25.67045   26.09258   21.52442  0  0  0
-     27    9  2  0.4236   26.22311   25.56759   20.08030  0  0  0
-     28   10  1 -0.8472   10.84087   35.33915   19.78347  0 -1  0
-     29   10  2  0.4236   10.20697    0.54421   19.48018  0  0  0
-     30   10  2  0.4236   11.06253   34.74012   19.01405  0 -1  0
-     31   11  1 -0.8472   20.07383    4.95885   33.62365  0  1  0
-     32   11  2  0.4236   19.77359    5.87080   33.90322  0  1  0
-     33   11  2  0.4236   20.68149    4.57954   34.32139  0  1  0
-     34   12  1 -0.8472   12.43897   28.56656   17.39837  0  0  0
-     35   12  2  0.4236   12.80348   27.99505   18.13354  0  0  0
-     36   12  2  0.4236   11.63887   28.12177   16.99597  0  0  0
-     37   13  1 -0.8472   14.80338    7.14199    1.42116  0  0  0
-     38   13  2  0.4236   14.86001    6.68442    0.53382  0  0  0
-     39   13  2  0.4236   14.13589    6.67036    1.99737  0  0  0
-     40   14  1 -0.8472   15.87968   22.18330   24.13468  1 -1  0
-     41   14  2  0.4236   15.97100   22.71526   23.29285  1 -1  0
-     42   14  2  0.4236   16.69618   22.30846   24.69826  1 -1  0
-     43   15  1 -0.8472   13.29194   18.30473   12.37157  1  0  0
-     44   15  2  0.4236   12.55838   18.63231   12.96701  1  0  0
-     45   15  2  0.4236   13.24823   18.78335   11.49467  1  0  0
-     46   16  1 -0.8472   20.27409   23.94157   15.50212  0  0  0
-     47   16  2  0.4236   20.17851   24.67734   14.83167  0  0  0
-     48   16  2  0.4236   20.62006   23.12024   15.04857  0  0  0
-     49   17  1 -0.8472   30.10203   10.78182   14.24321  1  0  0
-     50   17  2  0.4236   29.40171   11.00523   13.56532  1  0  0
-     51   17  2  0.4236   29.70120   10.21329   14.96159  1  0  0
-     52   18  1 -0.8472   19.71525   12.98975   25.40578  0  0  0
-     53   18  2  0.4236   20.21522   13.35852   26.18938  0  0  0
-     54   18  2  0.4236   18.75253   12.87297   25.64962  0  0  0
-     55   19  1 -0.8472    4.22362   18.99305   32.62946  1  0  0
-     56   19  2  0.4236    4.05067   18.17865   32.07556  1  0  0
-     57   19  2  0.4236    3.38513   19.53353   32.69833  1  0  0
-     58   20  1 -0.8472   17.67279   30.86798   34.86933  1 -1  0
-     59   20  2  0.4236   17.18866   31.74218   34.90528  1 -1  0
-     60   20  2  0.4236   18.18607   30.80612   34.01339  1 -1  0
-     61   21  1 -0.8472    7.49194   27.84024   34.65598  0  0  0
-     62   21  2  0.4236    7.36412   27.37987   33.77752  0  0  0
-     63   21  2  0.4236    7.83650   27.18529   35.32848  0  0  0
-     64   22  1 -0.8472    9.58199    8.75878   28.38767  0  0  0
-     65   22  2  0.4236    8.89931    8.96106   27.68557  0  0  0
-     66   22  2  0.4236    9.61451    9.50981   29.04713  0  0  0
-     67   23  1 -0.8472   18.15447    7.97877    4.02967  1  0  0
-     68   23  2  0.4236   17.65379    8.02465    3.16529  1  0  0
-     69   23  2  0.4236   17.56073    7.59903    4.73904  1  0  0
-     70   24  1 -0.8472   13.45467   10.30195   21.94603  0  0  0
-     71   24  2  0.4236   14.12655   11.01716   21.75366  0  0  0
-     72   24  2  0.4236   13.15542   10.37304   22.89754  0  0  0
-     73   25  1 -0.8472   28.77370    1.83495    6.23711  0  0  0
-     74   25  2  0.4236   29.55410    1.23316    6.06742  0  0  0
-     75   25  2  0.4236   28.43863    1.69170    7.16831  0  0  0
-     76   26  1 -0.8472   21.17410    3.00906    4.56251  0  1  0
-     77   26  2  0.4236   21.00772    2.96011    5.54734  0  1  0
-     78   26  2  0.4236   21.17488    3.96581    4.27178  0  1  0
-     79   27  1 -0.8472   15.86257   20.77629   10.34675  1 -1  0
-     80   27  2  0.4236   15.84751   19.99231   10.96732  1 -1  0
-     81   27  2  0.4236   15.76759   20.45695    9.40393  1 -1  0
-     82   28  1 -0.8472   19.37283    6.41248   28.33230  0  0  0
-     83   28  2  0.4236   19.86925    6.14505   27.50645  0  0  0
-     84   28  2  0.4236   19.23659    7.40311   28.33322  0  0  0
-     85   29  1 -0.8472   19.69874   26.80111   22.56675 -1 -1  0
-     86   29  2  0.4236   20.51873   26.54536   22.05471 -1 -1  0
-     87   29  2  0.4236   19.52519   26.12131   23.27927 -1 -1  0
-     88   30  1 -0.8472   10.44934    1.95847    4.23874  1  1  0
-     89   30  2  0.4236   10.99436    1.49085    4.93460  1  1  0
-     90   30  2  0.4236   10.84502    2.85816    4.05448  1  1  0
-     91   31  1 -0.8472    6.35411   29.19722   23.17920  0  0  0
-     92   31  2  0.4236    5.50252   29.65394   23.43641  0  0  0
-     93   31  2  0.4236    7.01350   29.87731   22.85887  0  0  0
-     94   32  1 -0.8472   27.70305   33.63868    1.45545  0  0  0
-     95   32  2  0.4236   27.45511   34.56848    1.72731  0  0  0
-     96   32  2  0.4236   28.23820   33.21008    2.18338  0  0  0
-     97   33  1 -0.8472   34.54150   25.90721   10.97268  0  0  0
-     98   33  2  0.4236   34.26945   25.07242   10.49403  0  0  0
-     99   33  2  0.4236   34.74630   26.62266   10.30478  0  0  0
-    100   34  1 -0.8472   35.13701   10.35159   32.75388 -1  0  0
-    101   34  2  0.4236   35.31674    9.89658   31.88174 -1  0  0
-    102   34  2  0.4236   35.40693    9.74994   33.50557 -1  0  0
-    103   35  1 -0.8472   19.45549   25.22953   13.06888  1  0  0
-    104   35  2  0.4236   18.63554   25.79082   12.95680  1  0  0
-    105   35  2  0.4236   19.57263   24.64638   12.26505  1  0  0
-    106   36  1 -0.8472    8.76637   34.60601   24.20146  0  0  0
-    107   36  2  0.4236    9.50956   34.70873   24.86259  0  0  0
-    108   36  2  0.4236    9.11640   34.17220   23.37125  0  0  0
-    109   37  1 -0.8472   18.52185   34.00287   24.76220  0  0  0
-    110   37  2  0.4236   19.50193   33.87409   24.61123  0  0  0
-    111   37  2  0.4236   18.00811   33.44318   24.11196  0  0  0
-    112   38  1 -0.8472    5.46879   16.75651   12.09359  0 -1  0
-    113   38  2  0.4236    5.19937   17.67659   11.80934  0 -1  0
-    114   38  2  0.4236    5.65240   16.75172   13.07654  0 -1  0
-115  39  1  -0.8472  26.78187  26.54273  35.17124  1  0  0
-116  39  2  0.4236  27.38399  26.93341  0.42029  1  0  1
-117  39  2  0.4236  27.18089  25.69431  34.82353  1  0  0
-    118   40  1 -0.8472   14.04248   15.27305   12.41517  0  0  0
-    119   40  2  0.4236   14.36157   15.76500   13.22517  0  0  0
-    120   40  2  0.4236   14.30963   15.77579   11.59307  0  0  0
-    121   41  1 -0.8472    6.75576    6.34672    6.04938  1  1  0
-    122   41  2  0.4236    7.58170    5.78427    6.08735  1  1  0
-    123   41  2  0.4236    5.98388    5.83092    6.42094  1  1  0
-    124   42  1 -0.8472   10.86576   34.93065   25.98166  0  0  0
-    125   42  2  0.4236   10.69405   35.32452   26.88460  0  0  0
-    126   42  2  0.4236   11.59169   35.44574   25.52591  0  0  0
-    127   43  1 -0.8472   18.34531   30.51202   26.27445  0  0  0
-    128   43  2  0.4236   18.04166   30.29551   25.34662  0  0  0
-    129   43  2  0.4236   19.17552   31.06784   26.23227  0  0  0
-    130   44  1 -0.8472   13.18486    0.77946   20.62491 -1  1  0
-    131   44  2  0.4236   13.44906    0.56426   21.56501 -1  1  0
-    132   44  2  0.4236   12.29152    0.37510   20.42885 -1  1  0
-    133   45  1 -0.8472   24.47790   24.05885   28.20937 -1  0  0
-    134   45  2  0.4236   24.15706   23.14172   27.97301 -1  0  0
-    135   45  2  0.4236   23.74391   24.71952   28.05213 -1  0  0
-136  46  1  -0.8472  30.79103  15.33785  34.86738  0  0  0
-137  46  2  0.4236  31.17614  15.32312  0.34290  0  0  1
-138  46  2  0.4236  29.97833  14.75605  34.83605  0  0  0
-    139   47  1 -0.8472   18.30892   19.76908   34.23734  0  0  0
-    140   47  2  0.4236   17.75981   20.19846   33.52035  0  0  0
-    141   47  2  0.4236   19.04827   19.24096   33.81970  0  0  0
-    142   48  1 -0.8472   24.18923   16.21113   25.53917  0  0  0
-    143   48  2  0.4236   24.35093   17.17602   25.33219  0  0  0
-    144   48  2  0.4236   24.25573   16.06630   26.52637  0  0  0
-    145   49  1 -0.8472    9.29176    8.02479   32.23837 -1 -1  0
-    146   49  2  0.4236   10.25650    7.88688   32.46243 -1 -1  0
-    147   49  2  0.4236    8.95956    7.24816   31.70319 -1 -1  0
-    148   50  1 -0.8472    5.32982    1.15354   27.64551  0  0  0
-    149   50  2  0.4236    4.51900    0.59091   27.48437  0  0  0
-    150   50  2  0.4236    5.05010    2.09452   27.83594  0  0  0
-    151   51  1 -0.8472   22.89850   21.33836   11.63894  1  0  0
-    152   51  2  0.4236   23.24391   20.51986   12.09802  1  0  0
-    153   51  2  0.4236   22.43572   21.07543   10.79239  1  0  0
-    154   52  1 -0.8472   16.88462   32.60779   23.16332 -1  0  0
-    155   52  2  0.4236   15.90624   32.80151   23.09101 -1  0  0
-    156   52  2  0.4236   17.01667   31.65114   23.42276 -1  0  0
-    157   53  1 -0.8472   29.24409    7.09722   23.70701 -1  0  0
-    158   53  2  0.4236   28.47748    7.53121   24.18023 -1  0  0
-    159   53  2  0.4236   29.54220    7.68009   22.95113 -1  0  0
-    160   54  1 -0.8472   34.29952    6.85677    2.08156 -1  0  0
-    161   54  2  0.4236   34.97347    6.89704    1.34390 -1  0  0
-    162   54  2  0.4236   33.70962    7.66305    2.03849 -1  0  0
-    163   55  1 -0.8472   32.95408   29.26891   19.25970 -1 -1  0
-    164   55  2  0.4236   32.57416   28.37248   19.48784 -1 -1  0
-    165   55  2  0.4236   33.66659   29.16225   18.56621 -1 -1  0
-    166   56  1 -0.8472    9.78186   33.73160   21.96701  0 -1  0
-    167   56  2  0.4236    9.24351   33.11436   21.39330  0 -1  0
-    168   56  2  0.4236   10.15276   34.47066   21.40475  0 -1  0
-    169   57  1 -0.8472    7.86139    6.97451    8.72713  0  0  0
-    170   57  2  0.4236    8.16632    6.08021    9.05452  0  0  0
-    171   57  2  0.4236    7.15204    6.85123    8.03315  0  0  0
-    172   58  1 -0.8472   34.25223   27.81706   31.79312 -1 -1  0
-    173   58  2  0.4236   34.70046   28.60821   31.37704 -1 -1  0
-    174   58  2  0.4236   33.75216   28.10807   32.60872 -1 -1  0
-    175   59  1 -0.8472   34.94048   26.84844   19.52041 -1 -1  0
-    176   59  2  0.4236   35.40459   26.00577   19.79339 -1 -1  0
-    177   59  2  0.4236   34.15050   26.62404   18.94986 -1 -1  0
-    178   60  1 -0.8472   21.76411   32.20568   20.89158  0  0  0
-    179   60  2  0.4236   22.66239   31.82480   21.11072  0  0  0
-    180   60  2  0.4236   21.76667   33.18956   21.07031  0  0  0
-    181   61  1 -0.8472   34.30787    3.43694   14.24158 -1  0  0
-    182   61  2  0.4236   34.88829    2.82261   13.70711 -1  0  0
-    183   61  2  0.4236   34.87977    4.10183   14.72200 -1  0  0
-    184   62  1 -0.8472   17.88110   18.91029   14.42187  0  1  0
-    185   62  2  0.4236   17.92538   18.97676   15.41864  0  1  0
-    186   62  2  0.4236   18.59574   19.48109   14.01766  0  1  0
-    187   63  1 -0.8472   19.08402   14.22906   20.78379  0  0  0
-    188   63  2  0.4236   19.62169   13.82628   21.52446  0  0  0
-    189   63  2  0.4236   18.62450   13.50292   20.27246  0  0  0
-    190   64  1 -0.8472    7.85997   17.97828    9.48138  1  0  0
-    191   64  2  0.4236    7.51843   18.85870    9.15243  1  0  0
-    192   64  2  0.4236    8.12328   17.41050    8.70147  1  0  0
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-   1344  448  2  0.4236    9.39604   18.33981   10.45869  1  1  0
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-   1353  451  2  0.4236   21.33321   31.35654    6.45064  0 -1  0
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-   1389  463  2  0.4236   25.62255    1.43400   29.64665 -1  1  0
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-   1401  467  2  0.4236   17.38714   10.74099    9.84429  0 -1  0
-   1402  468  1 -0.8472   22.32508    9.87101    1.19557 -2  1  0
-   1403  468  2  0.4236   21.56595   10.42438    0.85287 -2  1  0
-   1404  468  2  0.4236   21.96657    9.12144    1.75194 -2  1  0
-   1405  469  1 -0.8472   10.90773   22.43777   26.25786  0 -1  0
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-   1407  469  2  0.4236   11.59943   21.72491   26.37335  0 -1  0
-   1408  470  1 -0.8472    1.31955   18.38600    3.47899  1  0  0
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-   1410  470  2  0.4236    1.03894   19.34578    3.47019  1  0  0
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-   1413  471  2  0.4236    6.98271    9.37573   21.15747  0  0  0
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-   1417  473  1 -0.8472   21.99977   23.12994   31.80630  0  0  0
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-   1440  480  2  0.4236   32.39596    9.44025   18.11653  0  0  0
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-   1448  483  2  0.4236   17.82202   25.24420   24.08463  1 -1  0
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-   1454  485  2  0.4236   21.73532    6.12073   27.28041  0  0  0
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-   1458  486  2  0.4236   20.30686   25.59152    2.23185  0  0  0
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-   1467  489  2  0.4236    1.21014   19.78158   32.97220  1 -1  0
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-   1475  492  2  0.4236   19.48670   25.39677    6.86130  0 -1  0
-   1476  492  2  0.4236   19.88068   26.69918    7.76403  0 -1  0
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-   1482  494  2  0.4236   32.90409   10.06601   29.41082 -1  1  0
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-   1485  495  2  0.4236   13.69810   20.81986   27.84554  0 -1  0
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-   1487  496  2  0.4236   30.81962   23.35913    7.99394 -1  0  0
-   1488  496  2  0.4236   30.83904   22.68007    6.50902 -1  0  0
-   1489  497  1 -0.8472   22.37756   28.64677   11.27235  0  0  0
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-   1496  499  2  0.4236   19.60036   19.35866   29.67089  1 -1  0
-   1497  499  2  0.4236   19.30682   19.39935   31.27672  1 -1  0
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-   1499  500  2  0.4236   35.11968   30.98319   31.35042 -1  0  0
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-   1502  501  2  0.4236    2.76383   19.17197   28.51776  1 -1  0
-   1503  501  2  0.4236    4.10894   20.08431   28.36038  1 -1  0
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-   1506  502  2  0.4236    8.43680   18.25484   16.02450  1  0  0
-   1507  503  1 -0.8472   15.08821   12.02710   30.35400  0  0  0
-   1508  503  2  0.4236   14.28360   12.09424   30.94394  0  0  0
-   1509  503  2  0.4236   15.19533   11.08291   30.04259  0  0  0
-   1510  504  1 -0.8472   34.24491   30.19634   12.70342 -1  0  0
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-   1514  505  2  0.4236   15.95641   12.21333   34.05231 -1  0  0
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-   1517  506  2  0.4236   11.71571   19.77015   33.07439  0 -1  0
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-   1520  507  2  0.4236   16.72807    2.34873   13.76804  0  0  0
-   1521  507  2  0.4236   15.44831    1.50881   13.19951  0  0  0
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-   1527  509  2  0.4236    2.80596   25.55275   16.19905  1 -1  0
-   1528  510  1 -0.8472   12.49813    4.72433    6.90178  1  1  0
-   1529  510  2  0.4236   12.68152    4.46705    5.95300  1  1  0
-   1530  510  2  0.4236   11.92587    5.54417    6.92011  1  1  0
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-   1536  512  2  0.4236   17.51187   16.36413   12.89214  0 -1  0
-   1537  513  1 -0.8472   26.90199   18.56808    6.14062 -1  0  0
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-   1539  513  2  0.4236   26.92006   18.28708    5.18110 -1  0  0
-   1540  514  1 -0.8472   33.44158    4.98761   23.03192  0  0  0
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-   1542  514  2  0.4236   33.92571    4.11266   23.03447  0  0  0
-   1543  515  1 -0.8472   26.44129    7.53555   13.32226  1  0  0
-   1544  515  2  0.4236   26.54376    8.50657   13.53799  1  0  0
-   1545  515  2  0.4236   25.48592    7.34289   13.09834  1  0  0
-   1546  516  1 -0.8472    3.43874   25.26348   19.52892  1  0  0
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-   1548  516  2  0.4236    3.04847   24.83353   20.34304  1  0  0
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-   1551  517  2  0.4236   31.70046   26.70873   17.87892  0  0  0
-   1552  518  1 -0.8472   27.98216    0.07525   33.15709 -1  1  0
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-   1560  520  2  0.4236   35.06089    8.04691   30.09137 -1  0  0
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-   1596  532  2  0.4236   26.31855    7.85233   32.10215  0  0  0
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-   1599  533  2  0.4236    1.96186   31.75034   13.77598  0  0  0
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-   1605  535  2  0.4236    3.86213    2.75509   32.26949  0  0  0
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-   1635  545  2  0.4236   33.49807   25.96909   15.16346  0  0  0
-   1636  546  1 -0.8472   10.26907    4.84569   26.02852  1 -1  0
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-   1638  546  2  0.4236    9.95023    4.88603   25.08162  1 -1  0
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-   1641  547  2  0.4236   22.18941   12.60184   30.56679  0  0  0
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-   1644  548  2  0.4236   15.95691    9.19731   23.20178  0  1  0
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-   1647  549  2  0.4236    6.60968   35.32665   28.45087  0  0  0
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-   1659  553  2  0.4236   25.45123    1.52498   19.54094  0  0  0
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-   1704  568  2  0.4236   27.04703    9.88443   17.45157 -1  1  0
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-   1777  593  1 -0.8472   10.69717   24.26781   31.92530  0  0  0
-   1778  593  2  0.4236   10.60386   23.69449   32.73927  0  0  0
-   1779  593  2  0.4236   11.64253   24.58417   31.84703  0  0  0
-   1780  594  1 -0.8472   15.95641   28.97606   35.05433  0  0  0
-   1781  594  2  0.4236   15.96032   28.35359   34.27173  0  0  0
-   1782  594  2  0.4236   16.63849   29.69350   34.91293  0  0  0
-   1783  595  1 -0.8472    1.56519    0.69624   33.04969  1  0  0
-   1784  595  2  0.4236    2.41404    1.17829   33.26655  1  0  0
-   1785  595  2  0.4236    1.02145    0.58791   33.88191  1  0  0
-   1786  596  1 -0.8472   26.14808    0.15636   10.03297 -1  0  0
-   1787  596  2  0.4236   25.35902    0.37673    9.45958 -1  0  0
-   1788  596  2  0.4236   26.26507   34.67035   10.07186 -1 -1  0
-   1789  597  1 -0.8472    9.77710   17.72509    3.30862  0  0  0
-   1790  597  2  0.4236    9.87566   17.93734    4.28081  0  0  0
-   1791  597  2  0.4236    9.23151   16.89378    3.20261  0  0  0
-   1792  598  1 -0.8472    8.75437    5.30451    3.09848  0  0  0
-   1793  598  2  0.4236    8.58717    5.03388    4.04651  0  0  0
-   1794  598  2  0.4236    9.12882    6.23147    3.07757  0  0  0
-   1795  599  1 -0.8472   20.48155   15.91696    9.33594  0  1  0
-   1796  599  2  0.4236   20.56631   15.50253    8.42984  0  1  0
-   1797  599  2  0.4236   20.25513   15.21003   10.00593  0  1  0
-   1798  600  1 -0.8472   16.82592   18.58235   26.17211  0  0  0
-   1799  600  2  0.4236   16.58729   18.45481   27.13479  0  0  0
-   1800  600  2  0.4236   17.21880   17.73656   25.81123  0  0  0
-   1801  601  1 -0.8472   13.75988   16.98609   22.32067  0  0  0
-   1802  601  2  0.4236   13.58551   17.90045   21.95528  0  0  0
-   1803  601  2  0.4236   13.59282   16.98375   23.30660  0  0  0
-   1804  602  1 -0.8472   32.62092   30.40547    6.88962 -1 -1  0
-   1805  602  2  0.4236   33.54931   30.43647    6.51938 -1 -1  0
-   1806  602  2  0.4236   32.51760   29.59252    7.46270 -1 -1  0
-   1807  603  1 -0.8472   17.63259   14.60870   27.18186  0  0  0
-   1808  603  2  0.4236   17.90163   15.20858   27.93536  0  0  0
-   1809  603  2  0.4236   17.69519   15.10944   26.31855  0  0  0
-   1810  604  1 -0.8472   11.62304   21.25939   16.47149  0 -1  0
-   1811  604  2  0.4236   11.45555   21.34865   15.48971  0 -1  0
-   1812  604  2  0.4236   12.53275   21.61367   16.68797  0 -1  0
-   1813  605  1 -0.8472    1.37600   22.27800   20.75203  1 -1  0
-   1814  605  2  0.4236    2.16943   21.85760   20.31195  1 -1  0
-   1815  605  2  0.4236    0.71462   21.56840   20.99487  1 -1  0
-   1816  606  1 -0.8472    7.18336    3.26655   24.36441  0  0  0
-   1817  606  2  0.4236    7.73090    3.12923   23.53899  0  0  0
-   1818  606  2  0.4236    6.93062    2.37846   24.74831  0  0  0
-   1819  607  1 -0.8472   17.64928   11.95310    5.42292  0  1  0
-   1820  607  2  0.4236   17.65692   12.93297    5.62238  0  1  0
-   1821  607  2  0.4236   17.41402   11.81051    4.46152  0  1  0
-   1822  608  1 -0.8472   12.84893   11.66550   32.14876  0  0  0
-   1823  608  2  0.4236   12.95939   10.67321   32.09304  0  0  0
-   1824  608  2  0.4236   12.82748   11.94512   33.10860  0  0  0
-   1825  609  1 -0.8472   28.12575   28.57384    6.21194  0  0  0
-   1826  609  2  0.4236   28.72740   27.81667    6.46617  0  0  0
-   1827  609  2  0.4236   28.67723   29.34738    5.89972  0  0  0
-   1828  610  1 -0.8472    9.60709   10.13056    3.09602  1 -1  0
-   1829  610  2  0.4236    9.17047   10.54496    3.89451  1 -1  0
-   1830  610  2  0.4236    8.91309    9.92399    2.40636  1 -1  0
-   1831  611  1 -0.8472   14.42399    9.53487   14.30475  0  1  0
-   1832  611  2  0.4236   13.60791    9.60745   14.87804  0  1  0
-   1833  611  2  0.4236   14.17935    9.71599   13.35221  0  1  0
-   1834  612  1 -0.8472    6.04272   31.14841   20.46104  0  0  0
-   1835  612  2  0.4236    6.17572   30.16410   20.34531  0  0  0
-   1836  612  2  0.4236    5.07705   31.33535   20.64129  0  0  0
-   1837  613  1 -0.8472    8.78576   13.58167   21.88541  0  1  0
-   1838  613  2  0.4236    8.51872   14.54379   21.93947  0  1  0
-   1839  613  2  0.4236    8.23602   13.12187   21.18806  0  1  0
-   1840  614  1 -0.8472   23.47264   35.27453    4.51530  0 -1  0
-   1841  614  2  0.4236   22.72332   35.48142    5.14431  0 -1  0
-   1842  614  2  0.4236   24.07799   34.59518    4.92999  0 -1  0
-   1843  615  1 -0.8472   22.09421   26.54415   21.45579  0 -1  0
-   1844  615  2  0.4236   22.63260   26.42361   22.28983  0 -1  0
-   1845  615  2  0.4236   22.48660   27.28439   20.90987  0 -1  0
-   1846  616  1 -0.8472    1.89433   19.06162   16.66270  0  0  0
-   1847  616  2  0.4236    1.86443   20.00623   16.33594  0  0  0
-   1848  616  2  0.4236    2.02229   19.05590   17.65444  0  0  0
-   1849  617  1 -0.8472   23.96341   29.62000    2.08747  0 -1  0
-   1850  617  2  0.4236   23.99764   29.18700    1.18675  0 -1  0
-   1851  617  2  0.4236   23.53567   30.52040    2.00840  0 -1  0
-   1852  618  1 -0.8472    1.04699   21.68909   30.59706  1  0  0
-   1853  618  2  0.4236    0.06322   21.75332   30.42968  1  0  0
-   1854  618  2  0.4236    1.52221   21.52537   29.73261  1  0  0
-   1855  619  1 -0.8472   13.73343   18.77132   16.05091  0  0  0
-   1856  619  2  0.4236   14.06321   19.15745   16.91235  0  0  0
-   1857  619  2  0.4236   13.14349   17.98673   16.24155  0  0  0
-   1858  620  1 -0.8472   15.02561    6.07506   33.93037 -1  0  0
-   1859  620  2  0.4236   14.69203    5.58795   33.12331 -1  0  0
-   1860  620  2  0.4236   16.00179    5.89373   34.04930 -1  0  0
-   1861  621  1 -0.8472   31.82004    4.72525   13.93145 -1  0  0
-   1862  621  2  0.4236   32.80133    4.70708   14.12290 -1  0  0
-   1863  621  2  0.4236   31.64404    4.28540   13.05084 -1  0  0
-   1864  622  1 -0.8472   24.24718   18.83076    7.32403  0 -1  0
-   1865  622  2  0.4236   24.38484   18.48542    8.25232  0 -1  0
-   1866  622  2  0.4236   25.05566   18.63064    6.77066  0 -1  0
-   1867  623  1 -0.8472   30.09284    6.70704    9.34689  0  1  0
-   1868  623  2  0.4236   30.69726    6.91436   10.11606  0  1  0
-   1869  623  2  0.4236   30.28333    5.78402    9.01266  0  1  0
-   1870  624  1 -0.8472    6.44543   22.20950   16.52672  1  0  0
-   1871  624  2  0.4236    6.63187   21.34098   16.98587  1  0  0
-   1872  624  2  0.4236    6.77340   22.16484   15.58312  1  0  0
-   1873  625  1 -0.8472   26.53478    4.89718   31.49008  0  1  0
-   1874  625  2  0.4236   26.41051    4.03196   31.00435  0  1  0
-   1875  625  2  0.4236   26.22715    5.65186   30.91066  0  1  0
-   1876  626  1 -0.8472   16.62247   30.95933   12.57652  1  0  0
-   1877  626  2  0.4236   17.56488   31.25972   12.42949  1  0  0
-   1878  626  2  0.4236   16.48769   30.74633   13.54423  1  0  0
-   1879  627  1 -0.8472    4.87356   34.61588   34.44684  1  0  0
-   1880  627  2  0.4236    5.82893   34.71196   34.72609  1  0  0
-   1881  627  2  0.4236    4.56619   35.46296   34.01332  1  0  0
-   1882  628  1 -0.8472    2.50288   12.28157   26.08722  0  0  0
-   1883  628  2  0.4236    3.13155   12.43414   25.32471  0  0  0
-   1884  628  2  0.4236    2.99882   11.86718   26.85029  0  0  0
-   1885  629  1 -0.8472   11.00864   34.29008    8.17472  1  0  0
-   1886  629  2  0.4236   10.75288   34.35239    9.13942  1  0  0
-   1887  629  2  0.4236   11.92072   33.88754    8.09702  1  0  0
-   1888  630  1 -0.8472   10.46049   16.76421   26.41355  1  0  0
-   1889  630  2  0.4236   10.39178   17.07209   27.36247  1  0  0
-   1890  630  2  0.4236   11.33817   17.05388   26.03185  1  0  0
-   1891  631  1 -0.8472   17.21021    4.69788   34.67997  0  0  0
-   1892  631  2  0.4236   18.05686    4.48907   34.19055  0  0  0
-   1893  631  2  0.4236   16.82710    3.85507   35.05788  0  0  0
-   1894  632  1 -0.8472    6.97884   35.13516   32.26371  1  0  0
-   1895  632  2  0.4236    7.59758   34.77477   32.96174  1  0  0
-   1896  632  2  0.4236    6.61568    0.51094   32.56360  1  1  0
-   1897  633  1 -0.8472   30.26859    4.69039   18.04698 -1  1  0
-   1898  633  2  0.4236   29.55779    4.00235   17.90097 -1  1  0
-   1899  633  2  0.4236   30.81486    4.44085   18.84653 -1  1  0
-   1900  634  1 -0.8472   14.15940   29.63583   31.68196  0  0  0
-   1901  634  2  0.4236   14.48471   30.44261   31.18878  0  0  0
-   1902  634  2  0.4236   13.52149   29.12674   31.10417  0  0  0
-   1903  635  1 -0.8472   22.40695    9.51538    9.73709  0 -1  0
-   1904  635  2  0.4236   22.71650    9.39313   10.68006  0 -1  0
-   1905  635  2  0.4236   23.02803    9.03544    9.11755  0 -1  0
-1906  636  1  -0.8472  22.24110  0.13405  35.41380  0  1  0
-1907  636  2  0.4236  23.18710  0.36198  0.19705  0  1  1
-1908  636  2  0.4236  21.82447  35.13999  0.72551  0  0  1
-   1909  637  1 -0.8472   30.80385   21.12738   11.62863 -1  0  0
-   1910  637  2  0.4236   31.14074   21.74078   10.91430 -1  0  0
-   1911  637  2  0.4236   31.43501   20.35877   11.73284 -1  0  0
-   1912  638  1 -0.8472   27.44982    5.23264   21.39756 -1  1  0
-   1913  638  2  0.4236   27.87749    4.69834   22.12667 -1  1  0
-   1914  638  2  0.4236   26.53230    5.51030   21.68213 -1  1  0
-   1915  639  1 -0.8472   34.24917   16.52998   18.53573  0  0  0
-   1916  639  2  0.4236   34.91854   15.83455   18.79704  0  0  0
-   1917  639  2  0.4236   33.88140   16.31527   17.63097  0  0  0
-   1918  640  1 -0.8472   32.11496   35.09444   16.48223 -1 -1  0
-   1919  640  2  0.4236   32.98099   34.62132   16.64370 -1 -1  0
-   1920  640  2  0.4236   32.28074    0.41008   15.93745 -1  0  0
-   1921  641  1 -0.8472    5.27734   31.52491   24.59110  0  0  0
-   1922  641  2  0.4236    5.60492   31.56543   25.53502  0  0  0
-   1923  641  2  0.4236    5.51573   32.37348   24.11884  0  0  0
-   1924  642  1 -0.8472   25.79032   25.41548   18.29376 -1 -1  0
-   1925  642  2  0.4236   25.40295   24.65387   17.77428 -1 -1  0
-   1926  642  2  0.4236   25.77416   26.24352   17.73341 -1 -1  0
-   1927  643  1 -0.8472    4.93641   22.51784   12.73054  0  0  0
-   1928  643  2  0.4236    4.69948   21.69044   13.23963  0  0  0
-   1929  643  2  0.4236    4.10361   23.03009   12.52080  0  0  0
-   1930  644  1 -0.8472   12.37112    3.40763   24.86826  0  1  0
-   1931  644  2  0.4236   11.49379    3.77028   25.18239  0  1  0
-   1932  644  2  0.4236   12.78779    4.05198   24.22706  0  1  0
-   1933  645  1 -0.8472   17.22029   21.06776   32.22767  0 -1  0
-   1934  645  2  0.4236   16.31836   21.34141   31.89361  0 -1  0
-   1935  645  2  0.4236   17.79546   20.80136   31.45424  0 -1  0
-   1936  646  1 -0.8472   25.41708   13.65890   27.43081 -1  1  0
-   1937  646  2  0.4236   25.98599   14.41622   27.11030 -1  1  0
-   1938  646  2  0.4236   25.01532   13.18819   26.64533 -1  1  0
-   1939  647  1 -0.8472   31.34632    0.92208    6.09316  0  0  0
-   1940  647  2  0.4236   31.49282    0.15259    5.47156  0  0  0
-   1941  647  2  0.4236   31.97499    1.66376    5.85935  0  0  0
-   1942  648  1 -0.8472   14.52004   27.14727    0.85218 -1  0  0
-   1943  648  2  0.4236   15.06648   27.88580    0.45734 -1  0  0
-   1944  648  2  0.4236   14.58562   27.18061    1.84945 -1  0  0
-   1945  649  1 -0.8472   28.87721   13.80291   31.40189 -1  0  0
-   1946  649  2  0.4236   29.22211   14.24724   32.22866 -1  0  0
-   1947  649  2  0.4236   28.79132   14.47981   30.67082 -1  0  0
-   1948  650  1 -0.8472   32.29796    1.69820   30.01991  0 -1  0
-   1949  650  2  0.4236   33.00137    1.81610   29.31905  0 -1  0
-   1950  650  2  0.4236   31.71924    2.51309   30.05174  0 -1  0
-   1951  651  1 -0.8472   12.62275    8.26297   20.33641  0  0  0
-   1952  651  2  0.4236   12.83214    8.94927   21.03291  0  0  0
-   1953  651  2  0.4236   12.11033    8.68982   19.59131  0  0  0
-   1954  652  1 -0.8472   12.52870   25.44736    7.87215  0 -1  0
-   1955  652  2  0.4236   13.00949   24.63086    8.19160  0 -1  0
-   1956  652  2  0.4236   11.64782   25.18323    7.47946  0 -1  0
-   1957  653  1 -0.8472    1.10135   20.97932    6.76187  1  1  0
-   1958  653  2  0.4236    0.77452   21.00470    5.81713  1  1  0
-   1959  653  2  0.4236    1.95251   21.49916    6.83418  1  1  0
-   1960  654  1 -0.8472    4.82318    0.41033   13.47479  0  0  0
-   1961  654  2  0.4236    4.34431    1.17994   13.05247  0  0  0
-   1962  654  2  0.4236    4.19429   35.42103   14.07377  0 -1  0
-   1963  655  1 -0.8472    7.97884   14.32280   18.39989  0  0  0
-   1964  655  2  0.4236    7.48239   15.14935   18.66497  0  0  0
-   1965  655  2  0.4236    7.76346   13.58505   19.03968  0  0  0
-   1966  656  1 -0.8472    6.57446   10.83838    7.69395  0  0  0
-   1967  656  2  0.4236    6.93009   11.43436    6.97402  0  0  0
-   1968  656  2  0.4236    5.66493   11.15166    7.96697  0  0  0
-   1969  657  1 -0.8472   10.13095   13.45872    3.45462  0  1  0
-   1970  657  2  0.4236    9.41951   14.02714    3.04153  0  1  0
-   1971  657  2  0.4236   11.02593   13.74220    3.11019  0  1  0
-   1972  658  1 -0.8472    2.78532   23.98202   22.68429  0  0  0
-   1973  658  2  0.4236    2.24782   23.30083   22.18728  0  0  0
-   1974  658  2  0.4236    2.17788   24.69474   23.03500  0  0  0
-   1975  659  1 -0.8472   29.67656   34.06660    9.42289 -1  0  0
-   1976  659  2  0.4236   29.37866   33.82615   10.34668 -1  0  0
-   1977  659  2  0.4236   30.23579   34.89486    9.45798 -1  0  0
-   1978  660  1 -0.8472   17.39594   25.01387    9.24906  0  0  0
-   1979  660  2  0.4236   18.05931   25.56908    8.74748  0  0  0
-   1980  660  2  0.4236   17.77142   24.09901    9.39751  0  0  0
-   1981  661  1 -0.8472   11.13962   14.07290   32.95291  1  1  0
-   1982  661  2  0.4236   12.10521   14.31041   33.05855  1  1  0
-   1983  661  2  0.4236   10.89910   13.35632   33.60762  1  1  0
-   1984  662  1 -0.8472    1.12560   32.01749   27.53520  1 -1  0
-   1985  662  2  0.4236    0.50802   31.29622   27.84873  1 -1  0
-   1986  662  2  0.4236    1.59583   31.71636   26.70563  1 -1  0
-   1987  663  1 -0.8472   16.74625   10.36654   22.14588  0  0  0
-   1988  663  2  0.4236   17.64843   10.13447   22.50939  0  0  0
-   1989  663  2  0.4236   16.51070   11.30163   22.41056  0  0  0
-   1990  664  1 -0.8472    3.76112   22.81755   16.72253  1  0  0
-   1991  664  2  0.4236    3.76488   23.70592   16.26345  1  0  0
-   1992  664  2  0.4236    4.62662   22.34826   16.54749  1  0  0
-   1993  665  1 -0.8472    1.85948    2.74210   27.37838  0  0  0
-   1994  665  2  0.4236    2.54531    2.13125   27.77390  0  0  0
-   1995  665  2  0.4236    2.26198    3.24393   26.61279  0  0  0
-   1996  666  1 -0.8472   20.97424   33.57107   23.88091  0 -1  0
-   1997  666  2  0.4236   21.63334   32.88392   24.18640  0 -1  0
-   1998  666  2  0.4236   21.20496   33.86510   22.95340  0 -1  0
-   1999  667  1 -0.8472   14.93408    6.66163   21.35215  0  0  0
-   2000  667  2  0.4236   14.05135    6.86086   20.92664  0  0  0
-   2001  667  2  0.4236   15.24543    5.75568   21.06534  0  0  0
-   2002  668  1 -0.8472   22.24661    5.18993   17.87120 -1  0  0
-   2003  668  2  0.4236   21.88334    5.84047   17.20429 -1  0  0
-   2004  668  2  0.4236   23.18057    5.45019   18.11607 -1  0  0
-   2005  669  1 -0.8472   31.73682   29.92390   26.37363  0  0  0
-   2006  669  2  0.4236   32.14422   30.71878   26.82324  0  0  0
-   2007  669  2  0.4236   32.44996   29.40671   25.90048  0  0  0
-   2008  670  1 -0.8472   24.55434   23.28950    6.20609  0  0  0
-   2009  670  2  0.4236   25.36818   22.74753    5.99656  0  0  0
-   2010  670  2  0.4236   24.07519   22.88402    6.98448  0  0  0
-   2011  671  1 -0.8472   25.88342   13.36903   31.69745 -1  0  0
-   2012  671  2  0.4236   26.03190   12.91533   30.81878 -1  0  0
-   2013  671  2  0.4236   26.76589   13.60848   32.10225 -1  0  0
-   2014  672  1 -0.8472   31.90813   10.22292   30.85168  0  0  0
-   2015  672  2  0.4236   32.27321   10.76208   31.61060  0  0  0
-   2016  672  2  0.4236   31.57679    9.34449   31.19597  0  0  0
-   2017  673  1 -0.8472    0.84917    3.66386   11.68793  1  0  0
-   2018  673  2  0.4236    0.87147    4.59942   12.04035  1  0  0
-   2019  673  2  0.4236    0.11734    3.57978   11.01167  1  0  0
-   2020  674  1 -0.8472   12.64903    6.40652   27.25223  0  0  0
-   2021  674  2  0.4236   11.96507    5.83731   26.79599  0  0  0
-   2022  674  2  0.4236   12.95893    7.12172   26.62584  0  0  0
-   2023  675  1 -0.8472   15.96014    7.99372   15.88506  0  0  0
-   2024  675  2  0.4236   16.82916    7.82162   15.42119  0  0  0
-   2025  675  2  0.4236   15.41302    8.63081   15.34222  0  0  0
-   2026  676  1 -0.8472   20.03414   20.13508   12.66468  0  0  0
-   2027  676  2  0.4236   19.40056   20.36704   11.92663  0  0  0
-   2028  676  2  0.4236   20.38174   19.20773   12.52643  0  0  0
-   2029  677  1 -0.8472   21.35607    6.30596   10.13191 -1 -1  0
-   2030  677  2  0.4236   20.87120    5.49454   10.45802 -1 -1  0
-   2031  677  2  0.4236   21.92900    6.66958   10.86641 -1 -1  0
-   2032  678  1 -0.8472   35.15594   30.93388    9.83376  0 -1  0
-   2033  678  2  0.4236    0.35036   31.64684    9.85606  1 -1  0
-   2034  678  2  0.4236   34.54498   31.04238   10.61796  0 -1  0
-   2035  679  1 -0.8472    4.27599   27.25591   26.29171  1  0  0
-   2036  679  2  0.4236    3.35993   27.34560   25.90091  1  0  0
-   2037  679  2  0.4236    4.46769   28.04433   26.87613  1  0  0
-   2038  680  1 -0.8472   26.85910   19.33388   13.68598  0  0  0
-   2039  680  2  0.4236   25.94374   19.21433   14.07041  0  0  0
-   2040  680  2  0.4236   27.54078   19.00690   14.34044  0  0  0
-   2041  681  1 -0.8472    7.83799   28.18316   15.83373  0 -1  0
-   2042  681  2  0.4236    7.63358   27.28088   16.21326  0 -1  0
-   2043  681  2  0.4236    7.00487   28.73603   15.82129  0 -1  0
-   2044  682  1 -0.8472   32.63008   18.22477   29.78603  0  1  0
-   2045  682  2  0.4236   32.15689   17.45297   29.36130  0  1  0
-   2046  682  2  0.4236   31.95728   18.87141   30.14536  0  1  0
-   2047  683  1 -0.8472    3.25697   33.47986    7.39333 -1 -1  0
-   2048  683  2  0.4236    4.14306   33.83996    7.68509 -1 -1  0
-   2049  683  2  0.4236    3.20470   33.49200    6.39478 -1 -1  0
-   2050  684  1 -0.8472    0.84315    3.50002    3.05779  0  0  0
-   2051  684  2  0.4236    1.36600    4.15296    3.60572  0  0  0
-   2052  684  2  0.4236    1.42306    2.71869    2.82722  0  0  0
-   2053  685  1 -0.8472   25.12323   15.97604   21.47090  0  0  0
-   2054  685  2  0.4236   25.42059   15.67903   22.37827  0  0  0
-   2055  685  2  0.4236   25.51738   16.87233   21.26778  0  0  0
-   2056  686  1 -0.8472    7.27468   22.21053   14.03439  0  0  0
-   2057  686  2  0.4236    7.89057   21.43472   13.89746  0  0  0
-   2058  686  2  0.4236    6.46872   22.10302   13.45235  0  0  0
-   2059  687  1 -0.8472   14.24074    9.72792   11.56220  0  1  0
-   2060  687  2  0.4236   13.63511    9.58057   10.78023  0  1  0
-   2061  687  2  0.4236   15.02007   10.28708   11.27947  0  1  0
-   2062  688  1 -0.8472   24.56624   34.10605   22.50422  0 -1  0
-   2063  688  2  0.4236   24.42631   33.16115   22.20827  0 -1  0
-   2064  688  2  0.4236   24.89936   34.11414   23.44704  0 -1  0
-   2065  689  1 -0.8472   28.18228   24.21568   14.50155  0  0  0
-   2066  689  2  0.4236   28.15529   24.11183   15.49574  0  0  0
-   2067  689  2  0.4236   27.53670   23.57749   14.08211  0  0  0
-   2068  690  1 -0.8472   35.20714    9.78963    0.99118  0  1  0
-   2069  690  2  0.4236    0.60853   10.16753    0.80907  1  1  0
-   2070  690  2  0.4236   34.53749   10.53157    1.02295  0  1  0
-   2071  691  1 -0.8472    0.69131   26.23859   12.99395  0  0  0
-   2072  691  2  0.4236    0.05017   25.81851   12.35175  0  0  0
-   2073  691  2  0.4236    0.86619   27.18423   12.71973  0  0  0
-   2074  692  1 -0.8472   22.19338   29.11773    4.33016  0 -1  0
-   2075  692  2  0.4236   21.46426   28.43597    4.38932  0 -1  0
-   2076  692  2  0.4236   22.95489   28.74612    3.79919  0 -1  0
-   2077  693  1 -0.8472   17.91530   28.67983   14.99455  0  0  0
-   2078  693  2  0.4236   18.48897   28.40781   15.76712  0  0  0
-   2079  693  2  0.4236   17.45208   27.87490   14.62374  0  0  0
-   2080  694  1 -0.8472   12.79492   25.77029   32.65179  0 -1  0
-   2081  694  2  0.4236   13.77749   25.61527   32.75437  0 -1  0
-   2082  694  2  0.4236   12.43237   26.17705   33.49026  0 -1  0
-   2083  695  1 -0.8472   30.87195   23.17070   13.46252  0  0  0
-   2084  695  2  0.4236   30.40061   23.03858   14.33449  0  0  0
-   2085  695  2  0.4236   30.94240   22.29458   12.98565  0  0  0
-   2086  696  1 -0.8472    9.82436   23.58229    1.74889  0  0  0
-   2087  696  2  0.4236    9.70115   23.45578    0.76463  0  0  0
-   2088  696  2  0.4236   10.38990   22.84180    2.11190  0  0  0
-   2089  697  1 -0.8472    6.89586   12.57425    5.59544  1  0  0
-   2090  697  2  0.4236    7.86359   12.41511    5.40009  1  0  0
-   2091  697  2  0.4236    6.36472   12.47100    4.75450  1  0  0
-   2092  698  1 -0.8472   11.02525   29.55403   32.81425  0 -1  0
-   2093  698  2  0.4236   11.59857   29.39549   33.61808  0 -1  0
-   2094  698  2  0.4236   11.36970   29.01280   32.04720  0 -1  0
-   2095  699  1 -0.8472    5.68577   15.11644   32.97163  1  0  0
-   2096  699  2  0.4236    6.45292   15.18049   32.33340  1  0  0
-   2097  699  2  0.4236    5.80866   15.78136   33.70833  1  0  0
-   2098  700  1 -0.8472   21.25974   27.21306   29.97592  0  0  0
-   2099  700  2  0.4236   21.13419   27.98997   30.59288  0  0  0
-   2100  700  2  0.4236   20.57820   27.25410   29.24532  0  0  0
-   2101  701  1 -0.8472    6.19813    8.13823   30.34241  0  0  0
-   2102  701  2  0.4236    7.03828    7.67736   30.05652  0  0  0
-   2103  701  2  0.4236    5.46127    7.46723   30.42450  0  0  0
-   2104  702  1 -0.8472   32.41076   28.40941    3.86814  0  0  0
-   2105  702  2  0.4236   32.55062   27.42269    3.95038  0  0  0
-   2106  702  2  0.4236   31.47031   28.63505    4.12222  0  0  0
-   2107  703  1 -0.8472   23.98855   26.62099   31.21987  0  0  0
-   2108  703  2  0.4236   23.15933   26.86421   30.71666  0  0  0
-   2109  703  2  0.4236   24.52935   27.44488   31.38923  0  0  0
-   2110  704  1 -0.8472   28.50283   29.57437   20.87556 -1 -1  0
-   2111  704  2  0.4236   29.24214   30.01036   20.36250 -1 -1  0
-   2112  704  2  0.4236   28.88225   29.10445   21.67252 -1 -1  0
-   2113  705  1 -0.8472   27.75031   21.27721   18.51655  0  0  0
-   2114  705  2  0.4236   27.38498   20.41242   18.17211  0  0  0
-   2115  705  2  0.4236   28.28475   21.10710   19.34442  0  0  0
-   2116  706  1 -0.8472   25.25588   27.43813   16.54983  0  0  0
-   2117  706  2  0.4236   25.68771   28.33889   16.59591  0  0  0
-   2118  706  2  0.4236   24.90231   27.28485   15.62711  0  0  0
-   2119  707  1 -0.8472    5.61274    2.12353   21.50202  0  1  0
-   2120  707  2  0.4236    4.74517    2.16269   21.99775  0  1  0
-   2121  707  2  0.4236    5.95246    1.18305   21.49858  0  1  0
-   2122  708  1 -0.8472   14.20520   17.29851    2.13547 -1  0  0
-   2123  708  2  0.4236   13.44849   17.62485    1.56903 -1  0  0
-   2124  708  2  0.4236   13.92488   17.29329    3.09534 -1  0  0
-2125  709  1  -0.8472  33.77325  2.92399  0.15598  -1  1  0
-2126  709  2  0.4236  33.43998  3.50499  34.86065  -1  1  -1
-2127  709  2  0.4236  33.65455  3.39756  1.02868  -1  1  0
-   2128  710  1 -0.8472    0.22885   13.68528    9.35288  0  0  0
-   2129  710  2  0.4236    0.61334   13.37045   10.22063  0  0  0
-   2130  710  2  0.4236    0.84262   13.43233    8.60505  0  0  0
-   2131  711  1 -0.8472   27.57011   24.36623   33.91899  0  0  0
-   2132  711  2  0.4236   26.97918   24.28932   33.11594  0  0  0
-   2133  711  2  0.4236   28.12870   23.54099   34.00201  0  0  0
-   2134  712  1 -0.8472   18.75243   23.43472   22.11490  0  1  0
-   2135  712  2  0.4236   17.78133   23.32273   21.90431  0  1  0
-   2136  712  2  0.4236   19.23205   23.77381   21.30561  0  1  0
-   2137  713  1 -0.8472    2.29530   10.87158    1.51153  0  1  0
-   2138  713  2  0.4236    2.47430   11.79162    1.86004  0  1  0
-   2139  713  2  0.4236    2.87595   10.21436    1.99197  0  1  0
-   2140  714  1 -0.8472   25.61886   25.89666   25.24432  0 -1  0
-   2141  714  2  0.4236   25.42787   26.64268   25.88223  0 -1  0
-   2142  714  2  0.4236   26.42453   25.39162   25.55370  0 -1  0
-   2143  715  1 -0.8472   16.92797   16.32560    9.80037  0  0  0
-   2144  715  2  0.4236   17.19604   17.12020    9.25562  0  0  0
-   2145  715  2  0.4236   17.34592   16.38653   10.70675  0  0  0
-   2146  716  1 -0.8472   10.47600   17.21124   29.11058  1  0  0
-   2147  716  2  0.4236   10.94213   18.08313   29.26056  1  0  0
-   2148  716  2  0.4236   10.16834   16.84254   29.98769  1  0  0
-   2149  717  1 -0.8472   16.06644   22.36974    1.69499  0  0  0
-   2150  717  2  0.4236   15.33260   23.01429    1.48056  0  0  0
-   2151  717  2  0.4236   16.89555   22.63246    1.20148  0  0  0
-   2152  718  1 -0.8472   16.33203   27.58130   32.80553  0  0  0
-   2153  718  2  0.4236   15.97264   26.66864   32.61096  0  0  0
-   2154  718  2  0.4236   15.82791   28.25908   32.27034  0  0  0
-   2155  719  1 -0.8472   20.49220   11.62449   35.26514  1  0  0
-   2156  719  2  0.4236   21.01717   12.11061   34.56651  1  0  0
-   2157  719  2  0.4236   19.68795   11.20396   34.84526  1  0  0
-   2158  720  1 -0.8472   30.40952   26.57771    6.51282  0  0  0
-   2159  720  2  0.4236   30.16665   26.78894    5.56606  0  0  0
-   2160  720  2  0.4236   30.45919   25.58598    6.63086  0  0  0
-   2161  721  1 -0.8472   12.37322   16.37428    4.55968  0  0  0
-   2162  721  2  0.4236   12.38784   15.52288    4.03541  0  0  0
-   2163  721  2  0.4236   11.65794   16.97416    4.20127  0  0  0
-   2164  722  1 -0.8472   33.56731   11.90620   21.46299  0  0  0
-   2165  722  2  0.4236   33.23117   12.42030   20.67390  0  0  0
-   2166  722  2  0.4236   32.79888   11.66522   22.05577  0  0  0
-   2167  723  1 -0.8472   31.32107   31.23181    1.41386 -1  0  0
-   2168  723  2  0.4236   31.49725   32.04700    0.86213 -1  0  0
-   2169  723  2  0.4236   31.18817   30.44435    0.81204 -1  0  0
-   2170  724  1 -0.8472   28.87096   19.63852   21.22815 -1 -1  0
-   2171  724  2  0.4236   29.73458   19.39950   20.78432 -1 -1  0
-   2172  724  2  0.4236   28.83879   20.62564   21.38486 -1 -1  0
-   2173  725  1 -0.8472    4.42927   23.17098   25.42492 -1 -1  0
-   2174  725  2  0.4236    3.94617   23.57806   24.64980 -1 -1  0
-   2175  725  2  0.4236    4.55071   22.19140   25.26477 -1 -1  0
-   2176  726  1 -0.8472   24.00712   31.99530   18.18540 -1  0  0
-   2177  726  2  0.4236   23.23226   32.61152   18.04443 -1  0  0
-   2178  726  2  0.4236   23.69523   31.04742   18.12064 -1  0  0
-   2179  727  1 -0.8472   12.59691   11.80803   19.01561 -1  0  0
-   2180  727  2  0.4236   12.20861   11.09527   18.43151 -1  0  0
-   2181  727  2  0.4236   12.30089   12.70527   18.68815 -1  0  0
-   2182  728  1 -0.8472   22.60920   27.90494   24.82016  0  0  0
-   2183  728  2  0.4236   23.54351   28.24544   24.92530  0  0  0
-   2184  728  2  0.4236   22.02693   28.30545   25.52765  0  0  0
-   2185  729  1 -0.8472   10.89154   10.44597   15.79910  0  1  0
-   2186  729  2  0.4236   10.71507    9.97810   14.93312  0  1  0
-   2187  729  2  0.4236   10.96922   11.42960   15.63671  0  1  0
-   2188  730  1 -0.8472    0.08050    9.79588    3.64393  1  0  0
-   2189  730  2  0.4236   35.44276    8.87250    3.99968  0  0  0
-   2190  730  2  0.4236    0.10043    9.76868    2.64453  1  0  0
-   2191  731  1 -0.8472   30.40682   21.08786    5.84641 -1 -1  0
-   2192  731  2  0.4236   30.08055   20.97761    4.90763 -1 -1  0
-   2193  731  2  0.4236   30.13488   20.29333    6.38928 -1 -1  0
-   2194  732  1 -0.8472   24.67265   21.92020    3.54047  0  0  0
-   2195  732  2  0.4236   24.31684   22.84343    3.39577  0  0  0
-   2196  732  2  0.4236   25.25080   21.90987    4.35632  0  0  0
-   2197  733  1 -0.8472   28.95227   32.91147   27.71368 -1  0  0
-   2198  733  2  0.4236   28.22236   33.56969   27.89800 -1  0  0
-   2199  733  2  0.4236   29.69126   33.36429   27.21490 -1  0  0
-   2200  734  1 -0.8472   30.03521   19.21092    7.99937  0  0  0
-   2201  734  2  0.4236   30.75755   18.74029    8.50601  0  0  0
-   2202  734  2  0.4236   29.43004   19.68149    8.64149  0  0  0
-   2203  735  1 -0.8472   24.49927   23.34755   12.15367  0 -1  0
-   2204  735  2  0.4236   25.45013   23.07497   12.30028  0 -1  0
-   2205  735  2  0.4236   23.95535   22.54362   11.91337  0 -1  0
-   2206  736  1 -0.8472   31.77314   12.63461    3.01134 -1  0  0
-   2207  736  2  0.4236   30.89137   12.32301    3.36544 -1  0  0
-   2208  736  2  0.4236   32.34380   12.95066    3.76924 -1  0  0
-   2209  737  1 -0.8472   14.30093   32.51323   11.88551  1 -1  0
-   2210  737  2  0.4236   15.16348   32.00737   11.89441  1 -1  0
-   2211  737  2  0.4236   14.04074   32.74491   12.82281  1 -1  0
-   2212  738  1 -0.8472   29.43476   16.82816    3.26399  1  0  0
-   2213  738  2  0.4236   29.24168   16.37876    4.13619  1  0  0
-   2214  738  2  0.4236   30.06337   17.59119    3.41419  1  0  0
-   2215  739  1 -0.8472   16.93347    0.29074   22.92551  0  1  0
-   2216  739  2  0.4236   17.69583   35.41574   23.44835  0  0  0
-   2217  739  2  0.4236   16.96046   35.44329   21.99062  0  0  0
-   2218  740  1 -0.8472    6.39175   32.07466   27.11458  1 -1  0
-   2219  740  2  0.4236    7.22451   31.66481   27.48671  1 -1  0
-   2220  740  2  0.4236    6.37538   33.05084   27.33071  1 -1  0
-   2221  741  1 -0.8472   11.38564    0.73620   34.44418  0  0  0
-   2222  741  2  0.4236   11.86164    0.78090   33.56590  0  0  0
-   2223  741  2  0.4236   11.33377   35.29097   34.74711  0 -1  0
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-   2490  830  2  0.4236   23.75542    0.35991   12.11613  0  0  0
-   2491  831  1 -0.8472   30.84135   19.97655   31.52762  0  0  0
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-   2493  831  2  0.4236   30.39532   20.75442   31.08499  0  0  0
-   2494  832  1 -0.8472   30.16396   12.12918   29.67611 -1  0  0
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-   2496  832  2  0.4236   30.99193   11.65024   29.96762 -1  0  0
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-   2499  833  2  0.4236    7.88880   25.70294   31.00970  0  0  0
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-   2502  834  2  0.4236    6.03640    8.13191    5.91504  0  0  0
-   2503  835  1 -0.8472   11.25292   34.76600   31.52106  1  0  0
-   2504  835  2  0.4236   12.23126   34.77144   31.31419  1  0  0
-   2505  835  2  0.4236   10.93027    0.19972   31.63102  1  1  0
-   2506  836  1 -0.8472    5.35443   22.01777   22.23507  1 -1  0
-   2507  836  2  0.4236    5.97242   21.37209   22.68358  1 -1  0
-   2508  836  2  0.4236    5.66259   22.95233   22.41273  1 -1  0
-   2509  837  1 -0.8472   33.55893   31.09610    3.22281 -1  0  0
-   2510  837  2  0.4236   32.83407   31.61340    2.76793 -1  0  0
-   2511  837  2  0.4236   33.28962   30.13559    3.29237 -1  0  0
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-   2513  838  2  0.4236   26.80640   29.16573    6.92195  0 -1  0
-   2514  838  2  0.4236   25.58609   30.19055    6.56546  0 -1  0
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-   2517  839  2  0.4236   33.75503    5.17533    2.33928  0  1  0
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-   2520  840  2  0.4236   14.72533   25.52182    3.29245  1  0  0
-   2521  841  1 -0.8472   30.88527    4.38191    2.92050  0  0  0
-   2522  841  2  0.4236   31.38047    3.51892    2.82042  0  0  0
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-   2526  842  2  0.4236   12.88025    4.95661   33.27201  1  0  0
-   2527  843  1 -0.8472    7.37641   22.99672   25.99460  1 -1  0
-   2528  843  2  0.4236    7.72980   23.93199   26.01296  1 -1  0
-   2529  843  2  0.4236    6.39689   23.01440   25.79418  1 -1  0
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-   2532  844  2  0.4236    6.57485   13.74763    7.05594  0  1  0
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-   2535  845  2  0.4236    2.94499   17.17090   24.79634  0  0  0
-   2536  846  1 -0.8472   11.89267   13.73016   11.88059  0  0  0
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-   2538  846  2  0.4236   12.59005   14.42090   12.07165  0  0  0
-   2539  847  1 -0.8472   27.08577    4.13603   19.06782  0  1  0
-   2540  847  2  0.4236   27.68203    3.34019   18.96269  0  1  0
-   2541  847  2  0.4236   27.28308    4.58777   19.93784  0  1  0
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-   2547  849  2  0.4236    9.43475   11.28818   16.91944  0  0  0
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-   2550  850  2  0.4236   13.65180   17.94136   25.09526  0  1  0
-   2551  851  1 -0.8472   25.29362   29.77548   23.45629  0 -1  0
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-   2565  855  2  0.4236   33.73202   20.88576    1.45652  0  0  0
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-   2892  964  2  0.4236   18.57188   23.63143   13.99125  0 -1  0
-   2893  965  1 -0.8472    7.47643    4.12395   28.94377  1  1  0
-   2894  965  2  0.4236    6.53643    4.10965   28.60301  1  1  0
-   2895  965  2  0.4236    8.06807    3.62466   28.31082  1  1  0
-   2896  966  1 -0.8472   24.00375   12.48900   25.21944  0  1  0
-   2897  966  2  0.4236   24.26664   12.12701   24.32514  0  1  0
-   2898  966  2  0.4236   23.24029   11.95566   25.58362  0  1  0
-   2899  967  1 -0.8472   29.91768    1.50145   13.03496 -1  1  0
-   2900  967  2  0.4236   29.05335    1.37915   12.54717 -1  1  0
-   2901  967  2  0.4236   30.45234    0.65805   12.98236 -1  1  0
-   2902  968  1 -0.8472   10.68432   11.21692   11.70509  1  0  0
-   2903  968  2  0.4236   10.03839   11.20065   10.94187  1  0  0
-   2904  968  2  0.4236   10.94732   12.16199   11.89905  1  0  0
-   2905  969  1 -0.8472   26.83864    6.78430   27.89995  0  1  0
-   2906  969  2  0.4236   27.65156    6.22192   28.05128  0  1  0
-   2907  969  2  0.4236   26.70471    6.91923   26.91824  0  1  0
-   2908  970  1 -0.8472   19.45471   27.26305   28.04780  0 -1  0
-   2909  970  2  0.4236   19.04134   26.44985   27.63821  0 -1  0
-   2910  970  2  0.4236   18.84070   27.63413   28.74441  0 -1  0
-   2911  971  1 -0.8472    9.18329   17.54386   23.21323  0  0  0
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-   2913  971  2  0.4236    9.51723   17.13593   24.06294  0  0  0
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-   2915  972  2  0.4236   17.34524   34.34596   20.33775  1 -1  0
-   2916  972  2  0.4236   18.85770   34.74797   19.87159  1 -1  0
-   2917  973  1 -0.8472   32.52843   32.10108   29.97826  1 -1  0
-   2918  973  2  0.4236   33.25404   32.71935   30.28020  1 -1  0
-   2919  973  2  0.4236   31.64947   32.57665   30.01282  1 -1  0
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-   2922  974  2  0.4236    3.77571   11.27632    9.12598  0  0  0
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-   2925  975  2  0.4236   18.78222   31.79206   31.88727  0 -1  0
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-   2928  976  2  0.4236   12.65347   27.92404   10.10514  0 -1  0
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-   2931  977  2  0.4236    9.83717   12.48936    4.67747  0  1  0
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-   2934  978  2  0.4236    7.51467    1.45316    3.02810  0  1  0
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-   2937  979  2  0.4236   29.64333   11.21599   10.12102 -1  0  0
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-   2940  980  2  0.4236    3.13862   15.22111    0.53729  0  0  0
-   2941  981  1 -0.8472   28.30108    1.63976    9.02932 -1  0  0
-   2942  981  2  0.4236   28.30413    2.50150    9.53661 -1  0  0
-   2943  981  2  0.4236   27.77598    0.95633    9.53643 -1  0  0
-   2944  982  1 -0.8472    8.86171   20.46625   30.05231  1  0  0
-   2945  982  2  0.4236    8.40488   20.55409   29.16712  1  0  0
-   2946  982  2  0.4236    8.28711   19.93206   30.67235  1  0  0
-   2947  983  1 -0.8472   18.15383   12.23297   19.15095  0  0  0
-   2948  983  2  0.4236   18.65379   11.76439   18.42265  0  0  0
-   2949  983  2  0.4236   17.17857   12.02685   19.07172  0  0  0
-   2950  984  1 -0.8472   30.27019   30.12955   18.83444  1 -1  0
-   2951  984  2  0.4236   31.18072   29.72570   18.74618  1 -1  0
-   2952  984  2  0.4236   29.82132   30.13800   17.94092  1 -1  0
-   2953  985  1 -0.8472   28.72211   14.94210    4.97487  0  1  0
-   2954  985  2  0.4236   29.12355   14.04801    5.17337  0  1  0
-   2955  985  2  0.4236   27.75045   14.83217    4.76577  0  1  0
-   2956  986  1 -0.8472   30.79139   17.34339   25.87787 -1  1  0
-   2957  986  2  0.4236   31.64276   17.65688   25.45739 -1  1  0
-   2958  986  2  0.4236   30.40203   16.60291   25.33010 -1  1  0
-   2959  987  1 -0.8472   20.85050   21.78155   22.79995  0  0  0
-   2960  987  2  0.4236   19.95588   22.19630   22.63385  0  0  0
-   2961  987  2  0.4236   21.56993   22.42549   22.53966  0  0  0
-   2962  988  1 -0.8472    3.21863   15.29262   10.93758  0  0  0
-   2963  988  2  0.4236    3.54765   14.72274   11.69052  0  0  0
-   2964  988  2  0.4236    3.77983   16.11786   10.87424  0  0  0
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-   2966  989  2  0.4236   34.05946    8.56683    7.05938  0  0  0
-   2967  989  2  0.4236   34.43072    7.64604    5.76290  0  0  0
-   2968  990  1 -0.8472   33.09880    6.74056   25.13263  0  0  0
-   2969  990  2  0.4236   33.49921    6.29904   24.32971  0  0  0
-   2970  990  2  0.4236   32.69648    7.61622   24.86557  0  0  0
-   2971  991  1 -0.8472   29.48955   24.63672   11.59942  0  0  0
-   2972  991  2  0.4236   29.87987   24.05306   12.31141  0  0  0
-   2973  991  2  0.4236   28.56720   24.32043   11.37763  0  0  0
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-   2976  992  2  0.4236    2.62003    2.56305   20.63002  1  0  0
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-2979  993  2  0.4236  11.86807  30.86173  0.13383  0  1  0
-   2980  994  1 -0.8472   34.93665    6.07698   11.10142  0  0  0
-   2981  994  2  0.4236    0.18436    6.56576   10.66276  1  0  0
-   2982  994  2  0.4236   34.63985    5.32489   10.51300  0  0  0
-   2983  995  1 -0.8472   20.00992   11.13905   17.51811  0  0  0
-   2984  995  2  0.4236   20.59134   10.54105   16.96644  0  0  0
-   2985  995  2  0.4236   20.46099   11.33089   18.38972  0  0  0
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-   3012 1004  2  0.4236   16.83643   26.75059   22.68468  0 -1  0
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-   3030 1010  2  0.4236    7.65350   19.10536   18.06190  0  0  0
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-   3036 1012  2  0.4236    6.84495   35.03042   11.23290  0  0  0
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-   3038 1013  2  0.4236   21.37983    3.73264   27.66317  0 -1  0
-   3039 1013  2  0.4236   20.77001    2.84809   28.89286  0 -1  0
-   3040 1014  1 -0.8472   24.81563    5.45260   22.57323 -1  0  0
-   3041 1014  2  0.4236   24.32945    4.64426   22.24134 -1  0  0
-   3042 1014  2  0.4236   24.64602    6.22053   21.95564 -1  0  0
-   3043 1015  1 -0.8472   34.44382    0.14050    3.28625 -1  1  0
-   3044 1015  2  0.4236   34.61155   35.38786    2.33507 -1  0  0
-   3045 1015  2  0.4236   35.31692    0.29608    3.74826 -1  1  0
-   3046 1016  1 -0.8472    4.27791    2.41161    7.98065  1  1  0
-   3047 1016  2  0.4236    4.66546    1.93228    7.19326  1  1  0
-   3048 1016  2  0.4236    3.77390    3.21600    7.66616  1  1  0
-   3049 1017  1 -0.8472   24.52356   31.65334   21.53988  0 -1  0
-   3050 1017  2  0.4236   24.66693   30.96367   22.24963  0 -1  0
-   3051 1017  2  0.4236   25.23898   31.57129   20.84603  0 -1  0
-   3052 1018  1 -0.8472   34.42078   34.68317   25.27342  0 -1  0
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-   3054 1018  2  0.4236   33.89777   34.10967   25.90389  0 -1  0
-   3055 1019  1 -0.8472   11.26425    8.85731   13.25615  0  0  0
-   3056 1019  2  0.4236   11.21883    9.47948   12.47465  0  0  0
-   3057 1019  2  0.4236   10.33767    8.63461   13.55915  0  0  0
-3058  1020  1  -0.8472  17.04930  2.12995  0.32083  0  0  0
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-   3061 1021  1 -0.8472   24.82320   22.07636   14.94227  0  0  0
-   3062 1021  2  0.4236   25.10356   22.41409   15.84075  0  0  0
-   3063 1021  2  0.4236   24.74082   22.84510   14.30805  0  0  0
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-   3065 1022  2  0.4236   17.50573   29.18071    8.74291  0  0  0
-   3066 1022  2  0.4236   17.68695   28.30413    7.37716  0  0  0
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-   3068 1023  2  0.4236   14.75054   24.05867   11.90618  0 -1  0
-   3069 1023  2  0.4236   13.88820   25.16342   12.74426  0 -1  0
-   3070 1024  1 -0.8472   24.42854   23.40458   24.83813 -1  0  0
-   3071 1024  2  0.4236   24.80885   24.10174   25.44580 -1  0  0
-   3072 1024  2  0.4236   23.67780   23.79831   24.30777 -1  0  0
-3073  1025  1  -0.8472  11.88653  15.08214  0.29503  1  0  0
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-3075  1025  2  0.4236  11.40432  15.95808  0.28467  1  0  0
-   3076 1026  1 -0.8472   11.00548   18.76354   17.70020  1  0  0
-   3077 1026  2  0.4236   11.20683   19.08015   18.62714  1  0  0
-   3078 1026  2  0.4236   11.36832   19.41906   17.03794  1  0  0
-   3079 1027  1 -0.8472    0.21383   34.43335   28.44343  0 -1  0
-   3080 1027  2  0.4236   35.41456   34.46051   29.39515 -1 -1  0
-   3081 1027  2  0.4236    0.52632   33.51015   28.21990  0 -1  0
-   3082 1028  1 -0.8472   27.69776    7.75551    5.28429  0  0  0
-   3083 1028  2  0.4236   28.61915    7.37076    5.22974  0  0  0
-   3084 1028  2  0.4236   27.22506    7.37690    6.08001  0  0  0
-   3085 1029  1 -0.8472   18.57223    5.67473   20.22081  0  0  0
-   3086 1029  2  0.4236   19.11772    6.30191   20.77677  0  0  0
-   3087 1029  2  0.4236   19.17712    5.02379   19.76220  0  0  0
-   3088 1030  1 -0.8472    2.33426   13.17303   32.36357  1  1  0
-   3089 1030  2  0.4236    1.55811   13.79024   32.49242  1  1  0
-   3090 1030  2  0.4236    2.00010   12.26705   32.10388  1  1  0
-   3091 1031  1 -0.8472   35.01515   31.73394    0.97577  0  0  0
-   3092 1031  2  0.4236   34.61233   31.43018    1.83914  0  0  0
-   3093 1031  2  0.4236   34.51750   31.32192    0.21256  0  0  0
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-   3095 1032  2  0.4236   16.50516    3.96386   15.25821  0  1  0
-   3096 1032  2  0.4236   17.89736    3.21428   14.85032  0  1  0
-   3097 1033  1 -0.8472   23.73791    2.45782    3.91262 -1  1  0
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-   3099 1033  2  0.4236   22.76894    2.70462    3.92407 -1  1  0
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-   3101 1034  2  0.4236   22.76962   29.36450   21.85291 -1  1  0
-   3102 1034  2  0.4236   22.69303   28.69928   23.34222 -1  1  0
-   3103 1035  1 -0.8472    8.33742    6.62626   29.93646  0  0  0
-   3104 1035  2  0.4236    8.89033    7.18506   29.31844  0  0  0
-   3105 1035  2  0.4236    8.14846    5.74280   29.50784  0  0  0
-   3106 1036  1 -0.8472   35.17706   29.80069   28.03160  0  0  0
-   3107 1036  2  0.4236   35.01927   29.87252   29.01643  0  0  0
-   3108 1036  2  0.4236   35.31696   28.84163   27.78553  0  0  0
-   3109 1037  1 -0.8472   30.28414    0.50891   35.01782  0  2  0
-   3110 1037  2  0.4236   29.35072    0.49034   34.65963  0  2  0
-   3111 1037  2  0.4236   30.92912    0.62031   34.26180  0  2  0
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-   3113 1038  2  0.4236   10.01843   33.94915   34.37094  0 -1  0
-   3114 1038  2  0.4236    8.90680   33.28308   33.37739  0 -1  0
-   3115 1039  1 -0.8472    8.19458    7.90346   34.62935  0  1  0
-   3116 1039  2  0.4236    8.09541    8.76794   35.12211  0  1  0
-   3117 1039  2  0.4236    8.56665    8.08000   33.71811  0  1  0
-   3118 1040  1 -0.8472   16.36566   30.72861   16.14680  0  1  0
-   3119 1040  2  0.4236   15.39278   30.64034   16.36047  0  1  0
-   3120 1040  2  0.4236   16.69757   29.87490   15.74557  0  1  0
-   3121 1041  1 -0.8472    1.38336   21.51866   15.82979  1 -1  0
-   3122 1041  2  0.4236    2.18483   22.02775   16.14354  1 -1  0
-   3123 1041  2  0.4236    1.45028   21.36630   14.84376  1 -1  0
-   3124 1042  1 -0.8472   24.49576   16.91647   14.41347 -1  0  0
-   3125 1042  2  0.4236   24.46970   15.94853   14.16378 -1  0  0
-   3126 1042  2  0.4236   23.81844   17.41789   13.87513 -1  0  0
-   3127 1043  1 -0.8472    6.59665   30.08094   32.96472  1 -1  0
-   3128 1043  2  0.4236    6.38187   29.47645   33.73180  1 -1  0
-   3129 1043  2  0.4236    5.91582   30.81166   32.91541  1 -1  0
-   3130 1044  1 -0.8472   13.78850    1.75258   32.98996  0  1  0
-   3131 1044  2  0.4236   13.86420    0.79825   32.70103  0  1  0
-   3132 1044  2  0.4236   13.84481    1.80443   33.98698  0  1  0
-   3133 1045  1 -0.8472    4.51044   20.46650   25.38327  0 -1  0
-   3134 1045  2  0.4236    4.07148   20.23567   26.25162  0 -1  0
-   3135 1045  2  0.4236    5.12949   19.72804   25.11607  0 -1  0
-   3136 1046  1 -0.8472    8.55000    4.97817   10.53916 -1  0  0
-   3137 1046  2  0.4236    9.43556    4.58181   10.29702 -1  0  0
-   3138 1046  2  0.4236    7.81839    4.44049   10.12007 -1  0  0
-   3139 1047  1 -0.8472    6.56871   13.42917   12.46635  1  0  0
-   3140 1047  2  0.4236    6.84090   14.14672   11.82525  1  0  0
-   3141 1047  2  0.4236    6.79037   13.71379   13.39897  1  0  0
-   3142 1048  1 -0.8472   17.30718   29.56617   18.82292  0  0  0
-   3143 1048  2  0.4236   16.96795   30.09198   18.04294  0  0  0
-   3144 1048  2  0.4236   17.82287   30.16861   19.43211  0  0  0
-   3145 1049  1 -0.8472    7.07716   33.67983   15.88066  1  0  0
-   3146 1049  2  0.4236    8.00388   33.31507   15.97055  1  0  0
-   3147 1049  2  0.4236    7.04393   34.60331   16.26278  1  0  0
-   3148 1050  1 -0.8472    4.32190   32.08805    0.42408  0  0  0
-   3149 1050  2  0.4236    5.29471   32.01881    0.20306  0  0  0
-   3150 1050  2  0.4236    3.99734   33.01036    0.21455  0  0  0
-   3151 1051  1 -0.8472   12.50008   15.43329    7.00231  0  1  0
-   3152 1051  2  0.4236   12.41639   16.01705    7.80983  0  1  0
-   3153 1051  2  0.4236   12.42069   15.99245    6.17710  0  1  0
-   3154 1052  1 -0.8472   20.22282   27.44026    4.69087 -1  0  0
-   3155 1052  2  0.4236   20.73730   27.36336    5.54490 -1  0  0
-   3156 1052  2  0.4236   20.53211   26.73685    4.05097 -1  0  0
-   3157 1053  1 -0.8472   30.00375   27.99420   32.63038  1  1  0
-   3158 1053  2  0.4236   30.47584   28.62820   32.01789  1  1  0
-   3159 1053  2  0.4236   30.56692   27.17887   32.76465  1  1  0
-   3160 1054  1 -0.8472   14.63493    3.86305    1.20786  0  0  0
-   3161 1054  2  0.4236   15.22310    3.05436    1.20241  0  0  0
-   3162 1054  2  0.4236   13.73513    3.62321    0.84348  0  0  0
-   3163 1055  1 -0.8472    4.28675    7.12818    1.70239  1  1  0
-   3164 1055  2  0.4236    4.90666    6.75032    1.01472  1  1  0
-   3165 1055  2  0.4236    4.14189    6.45424    2.42680  1  1  0
-   3166 1056  1 -0.8472   29.16030   26.19530   28.88081  0 -1  0
-   3167 1056  2  0.4236   29.28848   26.91125   28.19459  0 -1  0
-   3168 1056  2  0.4236   28.24711   26.27605   29.28020  0 -1  0
-   3169 1057  1 -0.8472    3.63095   32.78344   28.91318  0  0  0
-   3170 1057  2  0.4236    3.02331   32.00049   28.78007  0  0  0
-   3171 1057  2  0.4236    4.53711   32.45965   29.18516  0  0  0
-   3172 1058  1 -0.8472   23.76056   25.84720    5.67648  0  0  0
-   3173 1058  2  0.4236   23.89776   24.87390    5.86034  0  0  0
-   3174 1058  2  0.4236   24.62472   26.25609    5.38322  0  0  0
-   3175 1059  1 -0.8472   25.38019   33.27871    0.14931 -1  0  0
-   3176 1059  2  0.4236   26.31880   33.35051    0.48664 -1  0  0
-   3177 1059  2  0.4236   24.90181   34.14226    0.30861 -1  0  0
-   3178 1060  1 -0.8472    0.68491    1.52207   17.07190  0  1  0
-   3179 1060  2  0.4236    0.51175    2.44926   17.40397  0  1  0
-   3180 1060  2  0.4236    1.30523    1.55905   16.28844  0  1  0
-   3181 1061  1 -0.8472   23.65181    8.67747   18.77421  0  0  0
-   3182 1061  2  0.4236   22.68856    8.74187   18.51354  0  0  0
-   3183 1061  2  0.4236   24.14900    9.46503   18.41024  0  0  0
-   3184 1062  1 -0.8472   33.05211   15.62986   13.34261  0  0  0
-   3185 1062  2  0.4236   34.00020   15.64431   13.02507  0  0  0
-   3186 1062  2  0.4236   32.54828   14.91657   12.85545  0  0  0
-   3187 1063  1 -0.8472   18.32997   24.65156   30.13550  0  0  0
-   3188 1063  2  0.4236   18.99945   24.85640   30.84948  0  0  0
-   3189 1063  2  0.4236   18.12862   25.48369   29.61879  0  0  0
-   3190 1064  1 -0.8472    5.36408   26.76539    9.70657  1  0  0
-   3191 1064  2  0.4236    4.61487   26.83602    9.04804  1  0  0
-   3192 1064  2  0.4236    5.01332   26.41228   10.57390  1  0  0
-   3193 1065  1 -0.8472   10.10567   10.08061   21.54331  0  0  0
-   3194 1065  2  0.4236   10.54602   10.94036   21.28469  0  0  0
-   3195 1065  2  0.4236    9.48169    9.79389   20.81643  0  0  0
-   3196 1066  1 -0.8472   19.00683   35.07186   29.84480  0  0  0
-   3197 1066  2  0.4236   19.04738    0.45529   29.39029  0  1  0
-   3198 1066  2  0.4236   19.86037   34.57629   29.68408  0  0  0
-   3199 1067  1 -0.8472   29.99711   14.98272   24.72885 -1  0  0
-   3200 1067  2  0.4236   29.69719   14.56470   25.58631 -1  0  0
-   3201 1067  2  0.4236   30.81369   14.51127   24.39589 -1  0  0
-   3202 1068  1 -0.8472    6.63614   29.00766   30.49536  1  0  0
-   3203 1068  2  0.4236    7.11384   29.32519   29.67625  1  0  0
-   3204 1068  2  0.4236    6.90641   29.56908   31.27747  1  0  0
-   3205 1069  1 -0.8472   10.11551   30.29423   18.30231  0  0  0
-   3206 1069  2  0.4236   10.98545   30.70152   18.58028  0  0  0
-   3207 1069  2  0.4236   10.19849   29.93235   17.37380  0  0  0
-   3208 1070  1 -0.8472   32.38903   34.15199    4.78994  0  0  0
-   3209 1070  2  0.4236   33.33485   34.20962    4.47042  0  0  0
-   3210 1070  2  0.4236   32.32473   33.47169    5.51998  0  0  0
-   3211 1071  1 -0.8472    8.26907   25.90440   25.87939  0  0  0
-   3212 1071  2  0.4236    7.44369   26.19768   25.39703  0  0  0
-   3213 1071  2  0.4236    8.21908   26.19751   26.83413  0  0  0
-   3214 1072  1 -0.8472   34.39606   28.76401   22.33914 -1  0  0
-   3215 1072  2  0.4236   34.78287   28.19023   21.61726 -1  0  0
-   3216 1072  2  0.4236   33.95646   29.56347   21.92983 -1  0  0
-   3217 1073  1 -0.8472   26.17808    0.33318   20.75823  0  0  0
-   3218 1073  2  0.4236   27.03602    0.13193   21.23088  0  0  0
-   3219 1073  2  0.4236   25.41800   35.41922   21.25378  0 -1  0
-   3220 1074  1 -0.8472   10.61100   26.37578   18.41595  0 -1  0
-   3221 1074  2  0.4236   10.08330   25.72318   17.87230  0 -1  0
-   3222 1074  2  0.4236   10.12037   26.57693   19.26374  0 -1  0
-   3223 1075  1 -0.8472    8.64359    7.64068   22.40826  1  1  0
-   3224 1075  2  0.4236    9.38042    7.39398   21.77883  1  1  0
-   3225 1075  2  0.4236    9.00778    7.70978   23.33701  1  1  0
-   3226 1076  1 -0.8472   34.94158    6.28899   29.47998 -1  1  0
-   3227 1076  2  0.4236   34.74992    5.34456   29.21292 -1  1  0
-   3228 1076  2  0.4236   35.35594    6.30049   30.38998 -1  1  0
-   3229 1077  1 -0.8472   22.96785    8.26787   24.97489  0  0  0
-   3230 1077  2  0.4236   23.63128    8.57475   24.29249  0  0  0
-   3231 1077  2  0.4236   22.64048    9.05422   25.49872  0  0  0
-   3232 1078  1 -0.8472   11.45410   14.58764   29.16903 -1 -1  0
-   3233 1078  2  0.4236   11.28686   15.56996   29.25265 -1 -1  0
-   3234 1078  2  0.4236   10.98431   14.10543   29.90843 -1 -1  0
-   3235 1079  1 -0.8472   30.98568   28.19268   16.35175 -1 -1  0
-   3236 1079  2  0.4236   30.86407   29.08556   15.91827 -1 -1  0
-   3237 1079  2  0.4236   31.87810   27.81855   16.09965 -1 -1  0
-   3238 1080  1 -0.8472   19.60511   34.63779    0.73034  0 -1  0
-   3239 1080  2  0.4236   20.07181   34.47947    1.60044  0 -1  0
-   3240 1080  2  0.4236   19.65749    0.10212    0.49583  0  0  0
-   3241 1081  1 -0.8472    6.52788   20.20134    8.34657 -1  0  0
-   3242 1081  2  0.4236    6.44859   20.82437    9.12471 -1  0  0
-   3243 1081  2  0.4236    6.75885   20.72214    7.52476 -1  0  0
-   3244 1082  1 -0.8472    2.22359    5.95019   13.03372  1  0  0
-   3245 1082  2  0.4236    3.20048    5.73680   13.04474  1  0  0
-   3246 1082  2  0.4236    1.93257    6.22714   13.94943  1  0  0
-   3247 1083  1 -0.8472   33.54633    3.02522   18.32549 -1  0  0
-   3248 1083  2  0.4236   33.26547    2.84323   19.26782 -1  0  0
-   3249 1083  2  0.4236   32.87661    2.63119   17.69609 -1  0  0
-   3250 1084  1 -0.8472   27.71341    5.53405   14.97739  0  0  0
-   3251 1084  2  0.4236   28.61577    5.86831   15.24942  0  0  0
-   3252 1084  2  0.4236   27.30630    6.16972   14.32155  0  0  0
-   3253 1085  1 -0.8472   15.94416   23.73383   21.56160  0  1  0
-   3254 1085  2  0.4236   15.98176   24.62802   22.00764  0  1  0
-   3255 1085  2  0.4236   15.63717   23.84542   20.61651  0  1  0
-   3256 1086  1 -0.8472    6.69227   14.39868   15.10160  0  0  0
-   3257 1086  2  0.4236    7.68503   14.51748   15.11791  0  0  0
-   3258 1086  2  0.4236    6.25284   15.28527   14.95723  0  0  0
-   3259 1087  1 -0.8472    5.95374   12.14523    3.05261  0  0  0
-   3260 1087  2  0.4236    6.30415   12.22359    2.11933  0  0  0
-   3261 1087  2  0.4236    5.21340   11.47341    3.07535  0  0  0
-   3262 1088  1 -0.8472   12.10252   30.80971   11.22350  1  1  0
-   3263 1088  2  0.4236   12.52277   29.92727   11.01224  1  1  0
-   3264 1088  2  0.4236   12.81790   31.48717   11.39446  1  1  0
-   3265 1089  1 -0.8472   18.93365    2.00832   15.99019  0 -1  0
-   3266 1089  2  0.4236   19.47296    1.23800   15.65004  0 -1  0
-   3267 1089  2  0.4236   18.54763    1.77650   16.88304  0 -1  0
-   3268 1090  1 -0.8472   23.96448   13.72856   20.70151 -1  1  0
-   3269 1090  2  0.4236   24.48869   14.52327   21.00735 -1  1  0
-   3270 1090  2  0.4236   23.44154   13.96884   19.88371 -1  1  0
-   3271 1091  1 -0.8472    8.25157    5.78700   16.02100  0  1  0
-   3272 1091  2  0.4236    8.74962    5.11181   16.56511  0  1  0
-   3273 1091  2  0.4236    8.66944    5.85908   15.11539  0  1  0
-   3274 1092  1 -0.8472   28.35054   22.25648   21.49869 -1 -1  0
-   3275 1092  2  0.4236   29.09362   22.80409   21.11415 -1 -1  0
-   3276 1092  2  0.4236   28.28496   22.42712   22.48181 -1 -1  0
-   3277 1093  1 -0.8472    1.81162    0.06670    2.46594  0  1  0
-   3278 1093  2  0.4236    1.21799   34.98582    1.91575  0  0  0
-   3279 1093  2  0.4236    1.94043   35.16403    3.36929  0  0  0
-   3280 1094  1 -0.8472   35.53166   20.98042    3.82252 -1  0  0
-   3281 1094  2  0.4236   34.63470   21.34595    3.57389 -1  0  0
-   3282 1094  2  0.4236    0.74022   21.58995    3.47998  0  0  0
-   3283 1095  1 -0.8472   11.17694    3.63400   11.43282  0  0  0
-   3284 1095  2  0.4236   10.46131    2.93763   11.37926  0  0  0
-   3285 1095  2  0.4236   11.26616    3.94827   12.37791  0  0  0
-   3286 1096  1 -0.8472    9.92654   28.89578   20.68262  0  0  0
-   3287 1096  2  0.4236    9.98108   29.33694   19.78687  0  0  0
-   3288 1096  2  0.4236    9.37314   28.06585   20.61226  0  0  0
-   3289 1097  1 -0.8472    8.08827    0.98702    4.46142  1  1  0
-   3290 1097  2  0.4236    8.92399    1.53197    4.39386  1  1  0
-   3291 1097  2  0.4236    8.30273   35.53173    4.29053  1  0  0
-   3292 1098  1 -0.8472    2.10866   25.58374   29.35790  0 -1  0
-   3293 1098  2  0.4236    2.19232   25.06311   30.20753  0 -1  0
-   3294 1098  2  0.4236    3.01122   25.90930   29.07623  0 -1  0
-   3295 1099  1 -0.8472    0.21720   17.12702    5.62458  1  0  0
-   3296 1099  2  0.4236    0.72164   16.95368    6.47042  1  0  0
-   3297 1099  2  0.4236   34.80790   17.46284    5.84542  0  0  0
-   3298 1100  1 -0.8472   29.35960   32.88200    7.15034  0  0  0
-   3299 1100  2  0.4236   28.43114   33.02456    6.80738  0  0  0
-   3300 1100  2  0.4236   29.47698   33.37806    8.01064  0  0  0
-   3301 1101  1 -0.8472   33.46143   17.44437   24.98963  1  0  0
-   3302 1101  2  0.4236   33.72538   16.51329   25.24138  1  0  0
-   3303 1101  2  0.4236   33.83439   18.08860   25.65735  1  0  0
-   3304 1102  1 -0.8472   14.63472   31.97268   20.11819  1 -1  0
-   3305 1102  2  0.4236   14.36253   32.40462   20.97800  1 -1  0
-   3306 1102  2  0.4236   15.60752   31.74378   20.15354  1 -1  0
-   3307 1103  1 -0.8472   17.90095   30.19602   29.07393  0  0  0
-   3308 1103  2  0.4236   17.96731   30.36446   28.09048  0  0  0
-   3309 1103  2  0.4236   18.56336   30.76959   29.55576  0  0  0
-   3310 1104  1 -0.8472   29.81731   30.58982    9.54416 -1 -1  0
-   3311 1104  2  0.4236   29.63821   31.39695    8.98161 -1 -1  0
-   3312 1104  2  0.4236   30.53858   30.79746   10.20493 -1 -1  0
-   3313 1105  1 -0.8472   21.82976    0.18004    6.59623  0  1  0
-   3314 1105  2  0.4236   21.32664   34.98930    7.10702  0  0  0
-   3315 1105  2  0.4236   21.47662    1.08550    6.83159  0  1  0
-   3316 1106  1 -0.8472   29.69215   11.04418   25.02770  0  0  0
-   3317 1106  2  0.4236   28.84149   10.53054   24.91587  0  0  0
-   3318 1106  2  0.4236   29.59049   11.69820   25.77727  0  0  0
-   3319 1107  1 -0.8472    7.91759   12.41881   27.49079  1  0  0
-   3320 1107  2  0.4236    7.27216   12.31040   28.24684  1  0  0
-   3321 1107  2  0.4236    8.07535   13.39211   27.32415  1  0  0
-   3322 1108  1 -0.8472    1.58250   18.15258   25.23805  0  0  0
-   3323 1108  2  0.4236    0.92416   18.82419   25.57788  0  0  0
-   3324 1108  2  0.4236    1.37849   17.93983   24.28250  0  0  0
-   3325 1109  1 -0.8472    6.93347   23.53201    2.35517  1 -1  0
-   3326 1109  2  0.4236    6.65652   22.58772    2.17757  1 -1  0
-   3327 1109  2  0.4236    7.76609   23.73748    1.84092  1 -1  0
-   3328 1110  1 -0.8472    4.74464    5.25742    7.60193  0  1  0
-   3329 1110  2  0.4236    5.42640    4.59168    7.90511  0  1  0
-   3330 1110  2  0.4236    4.27163    5.63599    8.39747  0  1  0
-   3331 1111  1 -0.8472    8.12552    1.12029    8.50091  1  0  0
-   3332 1111  2  0.4236    7.73332    0.58543    9.24927  1  0  0
-   3333 1111  2  0.4236    8.35748    0.51169    7.74213  1  0  0
-   3334 1112  1 -0.8472   19.74359   22.07163    2.67622  0  0  0
-   3335 1112  2  0.4236   20.34968   22.23695    3.45421  0  0  0
-   3336 1112  2  0.4236   19.04678   21.40195    2.93298  0  0  0
-3337  1113  1  -0.8472  26.99679  3.40644  0.23973  0  1  0
-3338  1113  2  0.4236  27.37894  4.26925  35.35606  0  1  -1
-3339  1113  2  0.4236  27.54590  3.07037  1.00492  0  1  0
-   3340 1114  1 -0.8472    2.76236   30.72744   25.44148  1  0  0
-   3341 1114  2  0.4236    2.26842   30.38711   24.64140  1  0  0
-   3342 1114  2  0.4236    3.56792   31.23927   25.14305  1  0  0
-   3343 1115  1 -0.8472   32.12430   13.85696   23.83760 -1  0  0
-   3344 1115  2  0.4236   32.83244   14.29542   24.39093 -1  0  0
-   3345 1115  2  0.4236   32.25120   12.86530   23.85869 -1  0  0
-   3346 1116  1 -0.8472   10.21628   20.26624   34.40125  1  0  0
-   3347 1116  2  0.4236   10.71138   21.11413   34.59057  1  0  0
-   3348 1116  2  0.4236    9.23602   20.45695   34.35014  1  0  0
-   3349 1117  1 -0.8472   23.09081   20.87638   25.30398 -1 -1  0
-   3350 1117  2  0.4236   22.37116   20.90702   25.99764 -1 -1  0
-   3351 1117  2  0.4236   23.32969   21.80796   25.03015 -1 -1  0
-   3352 1118  1 -0.8472   29.45887   17.10774   18.22032  0  0  0
-   3353 1118  2  0.4236   30.22190   17.47370   18.75302  0  0  0
-   3354 1118  2  0.4236   28.68228   17.73528   18.27593  0  0  0
-   3355 1119  1 -0.8472   20.05651   13.40407   10.45749  1  1  0
-   3356 1119  2  0.4236   19.47165   13.23293   11.25034  1  1  0
-   3357 1119  2  0.4236   19.78197   12.80508    9.70530  1  1  0
-   3358 1120  1 -0.8472   20.70762   15.06236    6.66545 -1  0  0
-   3359 1120  2  0.4236   21.25889   14.32457    6.27596 -1  0  0
-   3360 1120  2  0.4236   21.16718   15.93745    6.51395 -1  0  0
-   3361 1121  1 -0.8472   18.89325   16.33477   29.01551  0  0  0
-   3362 1121  2  0.4236   19.58381   17.05767   29.03667  0  0  0
-   3363 1121  2  0.4236   18.82390   15.91345   29.91973  0  0  0
-   3364 1122  1 -0.8472   32.53070   22.11236   16.33258  0  0  0
-   3365 1122  2  0.4236   31.61485   21.71487   16.27572  0  0  0
-   3366 1122  2  0.4236   32.95674   22.09858   15.42800  0  0  0
-   3367 1123  1 -0.8472   25.66860   12.05813   29.52616  0  0  0
-   3368 1123  2  0.4236   25.53751   12.57429   28.67979  0  0  0
-   3369 1123  2  0.4236   26.45841   11.45268   29.42833  0  0  0
-   3370 1124  1 -0.8472   17.50953   29.89865   23.74962  0  0  0
-   3371 1124  2  0.4236   18.29724   29.81518   23.13925  0  0  0
-   3372 1124  2  0.4236   16.70119   29.51259   23.30525  0  0  0
-   3373 1125  1 -0.8472   20.42758    5.60773    4.90458  0  0  0
-   3374 1125  2  0.4236   20.79830    5.93925    5.77208  0  0  0
-   3375 1125  2  0.4236   19.45567    5.40009    5.01507  0  0  0
-   3376 1126  1 -0.8472   21.22300    7.21858   16.33609  0  0  0
-   3377 1126  2  0.4236   21.71859    8.08305   16.25232  0  0  0
-   3378 1126  2  0.4236   20.23901    7.39452   16.30900  0  0  0
-   3379 1127  1 -0.8472    8.72497   17.28708   17.55696 -1 -1  0
-   3380 1127  2  0.4236    9.58423   17.79092   17.64519 -1 -1  0
-   3381 1127  2  0.4236    8.91490   16.35639   17.24449 -1 -1  0
-   3382 1128  1 -0.8472    8.76414   18.06755   33.54747  0  1  0
-   3383 1128  2  0.4236    9.30454   18.84130   33.87802  0  1  0
-   3384 1128  2  0.4236    7.81310   18.35231   33.42741  0  1  0
-   3385 1129  1 -0.8472   32.82700   35.52108   32.09864  0  0  0
-   3386 1129  2  0.4236   32.18718   34.75823   32.19162  0  0  0
-   3387 1129  2  0.4236   32.43608    0.70537   31.49022  0  1  0
-   3388 1130  1 -0.8472    9.68869   32.41541   15.80987  0 -2  0
-   3389 1130  2  0.4236   10.32198   32.88836   15.19734  0 -2  0
-   3390 1130  2  0.4236    9.49060   31.50514   15.44640  0 -2  0
-   3391 1131  1 -0.8472    3.13703    9.32361    6.33009  0  0  0
-   3392 1131  2  0.4236    2.73001   10.14381    5.92815  0  0  0
-   3393 1131  2  0.4236    3.81597    8.94572    5.70069  0  0  0
-   3394 1132  1 -0.8472    8.17658   30.34937   28.56505  0  0  0
-   3395 1132  2  0.4236    8.28700   29.89563   27.68082  0  0  0
-   3396 1132  2  0.4236    8.88873   31.04267   28.67515  0  0  0
-   3397 1133  1 -0.8472    5.53061    5.11969   25.83483  1  1  0
-   3398 1133  2  0.4236    6.24983    4.47405   25.57827  1  1  0
-   3399 1133  2  0.4236    5.62889    5.95828   25.29905  1  1  0
-   3400 1134  1 -0.8472   27.96519   26.59699   23.46335  0  0  0
-   3401 1134  2  0.4236   27.46175   26.09209   22.76224  0  0  0
-   3402 1134  2  0.4236   27.32121   27.10484   24.03546  0  0  0
-   3403 1135  1 -0.8472    8.76854   34.46179   30.13004  0  0  0
-   3404 1135  2  0.4236    7.98772   34.69897   30.70797  0  0  0
-   3405 1135  2  0.4236    9.57720   34.32484   30.70212  0  0  0
-   3406 1136  1 -0.8472    6.61675   26.68586   32.41993  0  1  0
-   3407 1136  2  0.4236    6.44110   27.45464   31.80503  0  1  0
-   3408 1136  2  0.4236    5.81960   26.08236   32.43514  0  1  0
-   3409 1137  1 -0.8472   20.61037    1.66831   21.21259  0  1  0
-   3410 1137  2  0.4236   20.46142    2.52558   20.71980  0  1  0
-   3411 1137  2  0.4236   19.80342    1.08529   21.11862  0  1  0
-   3412 1138  1 -0.8472   17.10976   11.94341   25.70251  0  1  0
-   3413 1138  2  0.4236   16.57575   12.22093   24.90392  0  1  0
-   3414 1138  2  0.4236   17.05537   12.65457   26.40341  0  1  0
-   3415 1139  1 -0.8472   35.29388   32.21867   32.51401 -1 -1  0
-   3416 1139  2  0.4236    0.72519   31.87316   32.55062  0 -1  0
-   3417 1139  2  0.4236   35.30112   33.17035   32.20707 -1 -1  0
-   3418 1140  1 -0.8472   18.63749   20.06698   10.24470 -1  0  0
-   3419 1140  2  0.4236   18.71657   19.22662    9.70852 -1  0  0
-   3420 1140  2  0.4236   17.74969   20.08665   10.70452 -1  0  0
-   3421 1141  1 -0.8472   15.67168   16.70914   30.84639 -1 -1  0
-   3422 1141  2  0.4236   15.18511   17.13458   31.60940 -1 -1  0
-   3423 1141  2  0.4236   15.07898   16.03321   30.40844 -1 -1  0
-   3424 1142  1 -0.8472   25.32085   32.99754   32.93324  0  0  0
-   3425 1142  2  0.4236   25.32696   32.97137   33.93285  0  0  0
-   3426 1142  2  0.4236   26.15749   32.57590   32.58366  0  0  0
-   3427 1143  1 -0.8472   21.95911   34.91495   21.68096  0 -1  0
-   3428 1143  2  0.4236   22.86918   35.09934   22.05209  0 -1  0
-   3429 1143  2  0.4236   21.54269    0.26581   21.37813  0  0  0
-   3430 1144  1 -0.8472    9.90943   22.86932   28.54732  0 -1  0
-   3431 1144  2  0.4236    9.65403   22.01433   28.99867  0 -1  0
-   3432 1144  2  0.4236    9.79947   23.62979   29.18729  0 -1  0
-   3433 1145  1 -0.8472   18.92073    1.83062   28.54452  0  0  0
-   3434 1145  2  0.4236   18.77899    1.62596   27.57604  0  0  0
-   3435 1145  2  0.4236   18.45840    2.68673   28.77539  0  0  0
-   3436 1146  1 -0.8472   16.83842   26.30374   13.63728  1  0  0
-   3437 1146  2  0.4236   16.31083   25.83360   14.34480  1  0  0
-   3438 1146  2  0.4236   16.31854   27.08861   13.30007  1  0  0
-   3439 1147  1 -0.8472   23.03513   33.97776   14.66518 -1  0  0
-   3440 1147  2  0.4236   22.86690   33.83634   15.64068 -1  0  0
-   3441 1147  2  0.4236   23.46646   34.86929   14.52711 -1  0  0
-3442  1148  1  -0.8472  26.37468  30.43214  35.25468  0  0  0
-3443  1148  2  0.4236  25.71419  30.35818  34.50752  0  0  0
-3444  1148  2  0.4236  26.42258  31.38172  0.11725  0  0  1
-   3445 1149  1 -0.8472   32.63917   13.78229   28.38877 -1  0  0
-   3446 1149  2  0.4236   32.58013   13.67594   29.38133 -1  0  0
-   3447 1149  2  0.4236   33.03290   12.95516   27.98776 -1  0  0
-   3448 1150  1 -0.8472    1.19545   11.88827    7.42402  0  0  0
-   3449 1150  2  0.4236    1.37418   11.89679    6.44019  0  0  0
-   3450 1150  2  0.4236    0.43544   11.26847    7.61937  0  0  0
-   3451 1151  1 -0.8472   35.00393   34.58219   14.67872 -1  0  0
-   3452 1151  2  0.4236   35.36912   34.75521   13.76404 -1  0  0
-   3453 1151  2  0.4236   35.20028   35.36471   15.26952 -1  0  0
-   3454 1152  1 -0.8472    9.91103   32.33524   28.62464  1  0  0
-   3455 1152  2  0.4236   10.87005   32.22620   28.36321  1  0  0
-   3456 1152  2  0.4236    9.82922   33.07729   29.28991  1  0  0
-   3457 1153  1 -0.8472    6.36330   25.82391   16.66394  1 -1  0
-   3458 1153  2  0.4236    6.42232   25.33261   15.79498  1 -1  0
-   3459 1153  2  0.4236    5.42022   25.80214   16.99576  1 -1  0
-   3460 1154  1 -0.8472   32.81749   28.00308    1.05981  0  0  0
-   3461 1154  2  0.4236   32.64819   27.98472    2.04517  0  0  0
-   3462 1154  2  0.4236   33.80293   27.98990    0.89062  0  0  0
-   3463 1155  1 -0.8472    2.09892   25.00453    9.72837  1 -1  0
-   3464 1155  2  0.4236    1.31233   25.44939    9.30021  1 -1  0
-   3465 1155  2  0.4236    2.79673   24.82249    9.03567  1 -1  0
-   3466 1156  1 -0.8472    3.70573    6.67896   30.88514  1  0  0
-   3467 1156  2  0.4236    3.24241    7.52493   30.62130  1  0  0
-   3468 1156  2  0.4236    3.21166    5.89633   30.50649  1  0  0
-   3469 1157  1 -0.8472   22.91846   23.35707   22.00831 -1 -1  0
-   3470 1157  2  0.4236   23.89673   23.33055   21.80272 -1 -1  0
-   3471 1157  2  0.4236   22.69047   24.23401   22.43137 -1 -1  0
-   3472 1158  1 -0.8472    4.20157    8.41273   26.79776  0  1  0
-   3473 1158  2  0.4236    4.90641    7.70392   26.82417  0  1  0
-   3474 1158  2  0.4236    3.43075    8.09587   26.24514  0  1  0
-   3475 1159  1 -0.8472   27.83257   24.37855    5.10280  0 -1  0
-   3476 1159  2  0.4236   28.60423   24.78261    4.61164  0 -1  0
-   3477 1159  2  0.4236   27.02864   24.96430    5.00022  0 -1  0
-   3478 1160  1 -0.8472   28.25521   34.70625   30.38048  0  0  0
-   3479 1160  2  0.4236   28.81969   33.89251   30.51886  0  0  0
-   3480 1160  2  0.4236   28.61204   35.23210   29.60840  0  0  0
-   3481 1161  1 -0.8472   30.16072   30.72861   15.64472  0 -1  0
-   3482 1161  2  0.4236   29.37415   31.30921   15.85493  0 -1  0
-   3483 1161  2  0.4236   30.99754   31.17198   15.96580  0 -1  0
-   3484 1162  1 -0.8472   14.30036   15.88614    9.70147  1 -1  0
-   3485 1162  2  0.4236   14.12425   15.15890    9.03808  1 -1  0
-   3486 1162  2  0.4236   15.27146   16.12414    9.68516  1 -1  0
-   3487 1163  1 -0.8472   32.30744   26.75439   30.27938 -2 -1  0
-   3488 1163  2  0.4236   31.79334   27.51898   29.89077 -2 -1  0
-   3489 1163  2  0.4236   33.17053   27.09038   30.65636 -2 -1  0
-   3490 1164  1 -0.8472   26.38370   26.69069    5.02854  0  0  0
-   3491 1164  2  0.4236   26.06841   26.98085    4.12499  0  0  0
-   3492 1164  2  0.4236   26.97407   27.39737    5.41835  0  0  0
-   3493 1165  1 -0.8472   20.86392   29.03407   31.88890  0  0  0
-   3494 1165  2  0.4236   21.65113   29.58265   32.17038  0  0  0
-   3495 1165  2  0.4236   20.02838   29.43015   32.26960  0  0  0
-   3496 1166  1 -0.8472   25.81223   29.44957   19.78123 -1 -1  0
-   3497 1166  2  0.4236   26.68614   29.32640   20.25133 -1 -1  0
-   3498 1166  2  0.4236   25.97911   29.70752   18.82962 -1 -1  0
-   3499 1167  1 -0.8472    9.81268    4.84917   23.38536  1  0  0
-   3500 1167  2  0.4236   10.63486    5.32563   23.07407  1  0  0
-   3501 1167  2  0.4236    9.19011    4.71979   22.61361  1  0  0
-   3502 1168  1 -0.8472   27.09504   22.27136   13.03967  1 -1  0
-   3503 1168  2  0.4236   27.07533   21.30935   13.31187  1 -1  0
-   3504 1168  2  0.4236   27.49938   22.35174   12.12861  1 -1  0
-   3505 1169  1 -0.8472   29.74324    0.48259   28.65165  0  1  0
-   3506 1169  2  0.4236   30.70461    0.21026   28.61248  0  1  0
-   3507 1169  2  0.4236   29.63711    1.23896   29.29707  0  1  0
-   3508 1170  1 -0.8472   23.29461    4.02585   30.19760  0  1  0
-   3509 1170  2  0.4236   23.97815    4.36071   29.54906  0  1  0
-   3510 1170  2  0.4236   22.50367    3.67469   29.69656  0  1  0
-   3511 1171  1 -0.8472   10.11973    1.62285   31.79003  0  0  0
-   3512 1171  2  0.4236   10.13259    2.60573   31.97369  0  0  0
-   3513 1171  2  0.4236    9.27443    1.38412   31.31210  0  0  0
-   3514 1172  1 -0.8472   23.98447   35.12348    7.95924 -1 -1  0
-   3515 1172  2  0.4236   23.32600   35.43441    7.27390 -1 -1  0
-   3516 1172  2  0.4236   24.62710   34.48366    7.53784 -1 -1  0
-   3517 1173  1 -0.8472   18.95755   12.21646   15.09912  0  1  0
-   3518 1173  2  0.4236   19.29259   11.86381   15.97282  0  1  0
-   3519 1173  2  0.4236   18.12141   11.73165   14.84259  0  1  0
-   3520 1174  1 -0.8472   20.64435   34.05811   11.96399  0 -1  0
-   3521 1174  2  0.4236   20.04418   34.42348   11.25246  0 -1  0
-   3522 1174  2  0.4236   21.38622   33.53873   11.53994  0 -1  0
-   3523 1175  1 -0.8472    1.02047   25.62099   23.79503  1  0  0
-   3524 1175  2  0.4236    1.42266   26.30733   24.40092  1  0  0
-   3525 1175  2  0.4236    0.53030   24.94115   24.34042  1  0  0
-   3526 1176  1 -0.8472   10.99120   19.54610   23.24843  1  0  0
-   3527 1176  2  0.4236   10.59016   20.42272   23.51428  1  0  0
-   3528 1176  2  0.4236   11.87233   19.70414   22.80279  1  0  0
-   3529 1177  1 -0.8472   27.88427   14.09439    8.71746  0  0  0
-   3530 1177  2  0.4236   28.03205   13.69075    9.62033  0  0  0
-   3531 1177  2  0.4236   28.05850   13.40695    8.01245  0  0  0
-   3532 1178  1 -0.8472   24.85221   12.37059   16.45030  0  0  0
-   3533 1178  2  0.4236   24.81993   11.76201   17.24311  0  0  0
-   3534 1178  2  0.4236   25.21529   13.26013   16.72749  0  0  0
-3535  1179  1  -0.8472  3.37410  29.51426  35.24851  1  0  0
-3536  1179  2  0.4236  3.67043  30.43590  0.05182  1  0  1
-3537  1179  2  0.4236  3.66223  28.86794  0.50788  1  0  1
-   3538 1180  1 -0.8472    0.35240   31.88385   22.28260  0  0  0
-   3539 1180  2  0.4236    0.75035   32.67685   22.74384  0  0  0
-   3540 1180  2  0.4236    0.12386   31.18441   22.95971  0  0  0
-   3541 1181  1 -0.8472   22.09365   22.96551   19.30426 -1  1  0
-   3542 1181  2  0.4236   22.15372   23.84283   18.82824 -1  1  0
-   3543 1181  2  0.4236   22.25424   23.10473   20.28136 -1  1  0
-   3544 1182  1 -0.8472   21.04348   34.07945   16.88194  0 -1  0
-   3545 1182  2  0.4236   20.64076   33.23881   17.24399  0 -1  0
-   3546 1182  2  0.4236   20.84507   34.83819   17.50233  0 -1  0
-   3547 1183  1 -0.8472   33.55073   31.23980   34.07326 -1 -1  0
-   3548 1183  2  0.4236   33.07430   31.97063   34.56197 -1 -1  0
-   3549 1183  2  0.4236   34.22507   31.63882   33.45194 -1 -1  0
-   3550 1184  1 -0.8472   18.03786   31.41193   20.73579 -1  0  0
-   3551 1184  2  0.4236   18.60060   30.70706   21.16754 -1  0  0
-   3552 1184  2  0.4236   17.84513   32.13633   21.39763 -1  0  0
-   3553 1185  1 -0.8472   21.11935   11.51623   20.22975  1  0  0
-   3554 1185  2  0.4236   21.20219   11.22096   21.18154  1  0  0
-   3555 1185  2  0.4236   21.20649   12.51119   20.18069  1  0  0
-   3556 1186  1 -0.8472    2.50377   22.45553   28.26102  0  0  0
-   3557 1186  2  0.4236    2.69363   23.41750   28.06489  0  0  0
-   3558 1186  2  0.4236    3.26130   22.06638   28.78510  0  0  0
-   3559 1187  1 -0.8472    1.89482   15.34996    4.09798  1  0  0
-   3560 1187  2  0.4236    1.58103   16.17698    4.56436  1  0  0
-   3561 1187  2  0.4236    1.10474   14.83228    3.76974  1  0  0
-   3562 1188  1 -0.8472   11.31662   29.94794   26.07063  1  0  0
-   3563 1188  2  0.4236   10.36281   30.18370   25.88446  1  0  0
-   3564 1188  2  0.4236   11.60685   30.38189   26.92349  1  0  0
-   3565 1189  1 -0.8472   10.46187    0.48151   28.47016  0  0  0
-   3566 1189  2  0.4236   11.30710    0.79408   28.90357  0  0  0
-   3567 1189  2  0.4236    9.81615    0.18539   29.17392  0  0  0
-   3568 1190  1 -0.8472   20.01390   21.11502   19.40053  0  0  0
-   3569 1190  2  0.4236   19.92265   20.43003   20.12333  0  0  0
-   3570 1190  2  0.4236   20.72410   21.77249   19.65214  0  0  0
-   3571 1191  1 -0.8472   17.49785   14.90201   31.45641  0  1  0
-   3572 1191  2  0.4236   17.50843   14.17303   30.77203  0  1  0
-   3573 1191  2  0.4236   16.85603   15.61498   31.17410  0  1  0
-   3574 1192  1 -0.8472   23.93241   26.17915    0.41284 -1 -1  0
-   3575 1192  2  0.4236   23.77665   25.45312    1.08259 -1 -1  0
-   3576 1192  2  0.4236   24.91551   26.30253    0.27758 -1 -1  0
-   3577 1193  1 -0.8472   15.48155   12.36384    9.66953  0  0  0
-   3578 1193  2  0.4236   14.53261   12.38191    9.35473  0  0  0
-   3579 1193  2  0.4236   16.05799   12.85827    9.01897  0  0  0
-   3580 1194  1 -0.8472   24.94921    4.70274   28.23684 -1  0  0
-   3581 1194  2  0.4236   25.43668    5.57148   28.32404 -1  0  0
-   3582 1194  2  0.4236   25.25172    4.23253   27.40777 -1  0  0
-   3583 1195  1 -0.8472    7.23520   24.31872    5.42817  0  0  0
-   3584 1195  2  0.4236    7.41578   24.72360    6.32449  0  0  0
-   3585 1195  2  0.4236    8.06583   24.35494    4.87261  0  0  0
-   3586 1196  1 -0.8472   28.58261   14.10891   13.19958  0  1  0
-   3587 1196  2  0.4236   27.78762   14.51354   12.74766  0  1  0
-   3588 1196  2  0.4236   28.68835   13.16021   12.90164  0  1  0
-   3589 1197  1 -0.8472   34.03337   15.87375    9.37663 -1  0  0
-   3590 1197  2  0.4236   34.58744   16.59549    9.79136 -1  0  0
-   3591 1197  2  0.4236   34.53727   15.01038    9.40222 -1  0  0
-   3592 1198  1 -0.8472   31.82828   18.36860    3.71224 -1 -1  0
-   3593 1198  2  0.4236   32.31781   17.82539    4.39432 -1 -1  0
-   3594 1198  2  0.4236   32.15945   18.13334    2.79850 -1 -1  0
-   3595 1199  1 -0.8472   23.59606   11.47870   18.85195 -1  0  0
-   3596 1199  2  0.4236   23.08158   11.20644   19.66507 -1  0  0
-   3597 1199  2  0.4236   23.26663   12.36661   18.53091 -1  0  0
-   3598 1200  1 -0.8472   15.34275   31.40288   27.99920  0  0  0
-   3599 1200  2  0.4236   16.12521   31.94953   27.70102  0  0  0
-   3600 1200  2  0.4236   15.34691   30.52552   27.51943  0  0  0
-   3601 1201  1 -0.8472   13.77256    0.54624    8.10259  0  1  0
-   3602 1201  2  0.4236   13.86377   35.20962    8.63274  0  0  0
-   3603 1201  2  0.4236   13.42179    1.27416    8.69169  0  1  0
-   3604 1202  1 -0.8472   29.74122   21.73816   15.80987  0  0  0
-   3605 1202  2  0.4236   28.91356   22.21483   16.10610  0  0  0
-   3606 1202  2  0.4236   29.58403   20.75090   15.83419  0  0  0
-   3607 1203  1 -0.8472    9.34349    5.53388   13.38007  1  0  0
-   3608 1203  2  0.4236    8.89988    5.78430   12.51959  1  0  0
-   3609 1203  2  0.4236   10.20861    6.02809   13.46529  1  0  0
-   3610 1204  1 -0.8472   33.68754   33.26661   18.34318  0 -1  0
-   3611 1204  2  0.4236   34.19102   32.52776   18.79102  0 -1  0
-   3612 1204  2  0.4236   33.14660   33.76135   19.02330  0 -1  0
-   3613 1205  1 -0.8472    8.49063   30.24622    2.44138  1  1  0
-   3614 1205  2  0.4236    8.21723   31.11119    2.02057  1  1  0
-   3615 1205  2  0.4236    7.88983   30.04774    3.21571  1  1  0
-   3616 1206  1 -0.8472   25.31936    5.99106   34.51443  1  0  0
-   3617 1206  2  0.4236   25.28141    5.19128   33.91538  1  0  0
-   3618 1206  2  0.4236   25.62081    5.71091   35.42578  1  0  0
-   3619 1207  1 -0.8472   26.73560   34.72965   14.29355  0 -1  0
-   3620 1207  2  0.4236   26.80598   35.39294   15.03854  0 -1  0
-   3621 1207  2  0.4236   25.87589   34.86993   13.80250  0 -1  0
-   3622 1208  1 -0.8472   21.83502    2.05714   14.53069  0  0  0
-   3623 1208  2  0.4236   21.33580    1.21622   14.73940  0  0  0
-   3624 1208  2  0.4236   21.32241    2.84341   14.87559  0  0  0
-   3625 1209  1 -0.8472   35.01867    0.23622   21.00335  0  0  0
-   3626 1209  2  0.4236   35.14727    0.04188   20.03089  0  0  0
-   3627 1209  2  0.4236    0.26234   35.33762   21.52623  1 -1  0
-   3628 1210  1 -0.8472   22.35916    9.63134   16.26225  0  0  0
-   3629 1210  2  0.4236   23.23198    9.14331   16.26402  0  0  0
-   3630 1210  2  0.4236   22.39939   10.38390   15.60499  0  0  0
-   3631 1211  1 -0.8472   11.20172   33.59575   17.81686  1  0  0
-   3632 1211  2  0.4236   10.69181   33.24651   17.03074  1  0  0
-   3633 1211  2  0.4236   11.65801   32.83712   18.28189  1  0  0
-   3634 1212  1 -0.8472   31.82608   18.51865   34.56225  0 -1  0
-   3635 1212  2  0.4236   31.28986   19.16910   35.10013  0 -1  0
-   3636 1212  2  0.4236   31.53461   18.55633   33.60645  0 -1  0
-   3637 1213  1 -0.8472   30.88253   31.96225   12.90618  0 -1  0
-   3638 1213  2  0.4236   31.38406   31.32256   12.32378  0 -1  0
-   3639 1213  2  0.4236   30.61549   31.50276   13.75323  0 -1  0
-   3640 1214  1 -0.8472   13.98169   21.39098   19.92118  0  0  0
-   3641 1214  2  0.4236   13.95328   20.40141   19.78017  0  0  0
-   3642 1214  2  0.4236   14.32905   21.83552   19.09554  0  0  0
-   3643 1215  1 -0.8472    4.16081   28.17702    1.92690  1  0  0
-   3644 1215  2  0.4236    5.01126   27.72808    2.20102  1  0  0
-   3645 1215  2  0.4236    3.39356   27.76728    2.42026  1  0  0
-   3646 1216  1 -0.8472    2.61206   16.00836   16.04875  1  0  0
-   3647 1216  2  0.4236    1.74345   15.51304   16.05970  1  0  0
-   3648 1216  2  0.4236    2.43904   16.98712   16.15867  1  0  0
-   3649 1217  1 -0.8472   13.59737   19.95485   22.53633  1  0  0
-   3650 1217  2  0.4236   14.21305   20.60053   22.08473  1  0  0
-   3651 1217  2  0.4236   13.73769   19.99671   23.52552  1  0  0
-   3652 1218  1 -0.8472    7.18982   10.71677   12.05084  1  0  0
-   3653 1218  2  0.4236    6.43794   10.12559   11.75911  1  0  0
-   3654 1218  2  0.4236    6.83195   11.62130   12.28263  1  0  0
-   3655 1219  1 -0.8472   15.07429   14.72118    6.25090  1  0  0
-   3656 1219  2  0.4236   14.14374   14.54507    6.57184  1  0  0
-   3657 1219  2  0.4236   15.07706   14.77984    5.25263  1  0  0
-   3658 1220  1 -0.8472   17.76755   16.08175   24.87563  0  0  0
-   3659 1220  2  0.4236   17.58977   15.62862   24.00214  0  0  0
-   3660 1220  2  0.4236   18.65997   16.53165   24.84217  0  0  0
-   3661 1221  1 -0.8472   17.65901    7.92406    7.74964  1  0  0
-   3662 1221  2  0.4236   18.59311    8.23144    7.93120  1  0  0
-   3663 1221  2  0.4236   17.05661    8.71812    7.66886  1  0  0
-   3664 1222  1 -0.8472    3.05199   13.20694    2.89879  0  0  0
-   3665 1222  2  0.4236    3.57780   13.70311    2.20789  0  0  0
-   3666 1222  2  0.4236    2.63537   13.85891    3.53230  0  0  0
-   3667 1223  1 -0.8472    5.26002    2.13592   16.40436  0 -1  0
-   3668 1223  2  0.4236    6.09694    1.78456   15.98477  0 -1  0
-   3669 1223  2  0.4236    4.80845    2.76476   15.77141  0 -1  0
-   3670 1224  1 -0.8472   12.61256   32.52531    4.71798  0  0  0
-   3671 1224  2  0.4236   11.90890   33.23199    4.79132  0  0  0
-   3672 1224  2  0.4236   12.25715   31.75468    4.18908  0  0  0
-   3673 1225  1 -0.8472   33.05943   19.81815   12.71554  0  1  0
-   3674 1225  2  0.4236   32.86723   19.31471   13.55788  0  1  0
-   3675 1225  2  0.4236   33.70078   19.29557   12.15385  0  1  0
-   3676 1226  1 -0.8472    8.67356   22.94470   34.61606  0  0  0
-   3677 1226  2  0.4236    8.08575   22.17542   34.86632  0  0  0
-   3678 1226  2  0.4236    8.33529   23.36200   33.77263  0  0  0
-   3679 1227  1 -0.8472    0.86965   12.09925   11.68222  1  0  0
-   3680 1227  2  0.4236    0.73608   12.60411   12.53501  1  0  0
-   3681 1227  2  0.4236    0.57426   11.15194   11.80597  1  0  0
-   3682 1228  1 -0.8472   27.29430   18.02558   25.87602  0  0  0
-   3683 1228  2  0.4236   26.33030   18.09609   25.61981  0  0  0
-   3684 1228  2  0.4236   27.85129   18.53772   25.22227  0  0  0
-   3685 1229  1 -0.8472   20.96856    4.94099   22.32248  0  0  0
-   3686 1229  2  0.4236   21.44516    4.83664   23.19537  0  0  0
-   3687 1229  2  0.4236   20.65070    5.88429   22.22695  0  0  0
-   3688 1230  1 -0.8472   22.27256   31.32924   24.77039  0  0  0
-   3689 1230  2  0.4236   22.20439   30.66428   24.02667  0  0  0
-   3690 1230  2  0.4236   23.23365   31.45980   25.01366  0  0  0
-   3691 1231  1 -0.8472   22.66253   15.15411   23.54686  0  0  0
-   3692 1231  2  0.4236   23.07572   15.58551   22.74490  0  0  0
-   3693 1231  2  0.4236   23.21000   15.36328   24.35708  0  0  0
-   3694 1232  1 -0.8472   11.19746    9.41692   24.15577  0  1  0
-   3695 1232  2  0.4236   10.84190    9.88305   23.34570  0  1  0
-   3696 1232  2  0.4236   11.55668   10.09332   24.79875  0  1  0
-   3697 1233  1 -0.8472   11.99905   23.28826   34.33738  0  0  0
-   3698 1233  2  0.4236   12.52234   23.62944   35.11821  0  0  0
-   3699 1233  2  0.4236   12.62467   22.89914   33.66126  0  0  0
-   3700 1234  1 -0.8472   23.22442   18.59940   28.07421  0  0  0
-   3701 1234  2  0.4236   23.49579   19.56080   28.11912  0  0  0
-   3702 1234  2  0.4236   24.00062   18.02181   28.32688  0  0  0
-   3703 1235  1 -0.8472   30.92539    3.09568   32.51957  0  1  0
-   3704 1235  2  0.4236   31.84312    3.44347   32.71134  0  1  0
-   3705 1235  2  0.4236   30.25006    3.80152   32.73328  0  1  0
-   3706 1236  1 -0.8472    1.33811   18.35817   13.38681  1 -1  0
-   3707 1236  2  0.4236    1.22509   18.30768   14.37908  1 -1  0
-   3708 1236  2  0.4236    0.99542   17.51674   12.96910  1 -1  0
-   3709 1237  1 -0.8472    9.40393   27.68480    1.86054  0  0  0
-   3710 1237  2  0.4236    9.19178   28.63569    2.08582  0  0  0
-   3711 1237  2  0.4236    8.65357   27.09582    2.16051  0  0  0
-   3712 1238  1 -0.8472   22.59500   25.15458   24.16226  0  0  0
-   3713 1238  2  0.4236   22.11992   24.61236   24.85525  0  0  0
-   3714 1238  2  0.4236   22.72289   26.08747   24.49890  0  0  0
-   3715 1239  1 -0.8472   34.94268   12.24206   24.23039  0  1  0
-   3716 1239  2  0.4236   34.99080   11.48130   24.87762  0  1  0
-   3717 1239  2  0.4236   34.50585   11.93365   23.38540  0  1  0
-   3718 1240  1 -0.8472   13.66060   32.55204   14.55827  0  0  0
-   3719 1240  2  0.4236   13.52586   31.65916   14.98789  0  0  0
-   3720 1240  2  0.4236   14.30011   33.09209   15.10536  0  0  0
-   3721 1241  1 -0.8472   25.84720    7.64647   30.19310  0  0  0
-   3722 1241  2  0.4236   26.49207    7.44799   29.45506  0  0  0
-   3723 1241  2  0.4236   24.99842    8.00675   29.80616  0  0  0
-   3724 1242  1 -0.8472   31.34937    3.95974    8.27135 -1  0  0
-   3725 1242  2  0.4236   31.73419    4.48651    7.51346 -1  0  0
-   3726 1242  2  0.4236   30.58520    3.40699    7.93900 -1  0  0
-   3727 1243  1 -0.8472   32.08346    7.74273   18.98396  0  1  0
-   3728 1243  2  0.4236   31.48557    6.94437   18.91249  0  1  0
-   3729 1243  2  0.4236   32.68945    7.63585   19.77216  0  1  0
-   3730 1244  1 -0.8472   33.86230   32.04057   14.82923 -1 -1  0
-   3731 1244  2  0.4236   34.19829   32.96445   14.64614 -1 -1  0
-   3732 1244  2  0.4236   33.23522   32.06216   15.60786 -1 -1  0
-   3733 1245  1 -0.8472   15.80498    9.53892   29.22621  0  0  0
-   3734 1245  2  0.4236   16.28878    9.52316   28.35120  0  0  0
-   3735 1245  2  0.4236   14.88959    9.15417   29.10789  0  0  0
-   3736 1246  1 -0.8472   14.75644   31.78471   33.95051  1 -1  0
-   3737 1246  2  0.4236   14.87879   31.63463   32.96947  1 -1  0
-   3738 1246  2  0.4236   14.49184   30.92567   34.38867  1 -1  0
-   3739 1247  1 -0.8472   19.54738   27.88289   17.04095  0 -1  0
-   3740 1247  2  0.4236   19.89389   28.26231   17.89881  0 -1  0
-   3741 1247  2  0.4236   20.31297   27.55072   16.49007  0 -1  0
-   3742 1248  1 -0.8472   29.41360    2.42179   30.27314  0  0  0
-   3743 1248  2  0.4236   29.56706    3.38868   30.06936  0  0  0
-   3744 1248  2  0.4236   29.72219    2.22420   31.20356  0  0  0
-   3745 1249  1 -0.8472   25.21448   16.45875   28.33471  0  1  0
-   3746 1249  2  0.4236   26.21071   16.47683   28.25035  0  1  0
-   3747 1249  2  0.4236   24.95734   15.91164   29.13128  0  1  0
-   3748 1250  1 -0.8472    4.35720   14.20875   17.03220  1  0  0
-   3749 1250  2  0.4236    5.27798   14.24944   16.64433  1  0  0
-   3750 1250  2  0.4236    3.76871   14.86764   16.56366  1  0  0
-   3751 1251  1 -0.8472   29.13693    0.84916   24.77184 -1  1  0
-   3752 1251  2  0.4236   29.74416    1.35202   25.38696 -1  1  0
-   3753 1251  2  0.4236   29.68242    0.27811   24.15840 -1  1  0
-   3754 1252  1 -0.8472   27.62042   10.22750   23.30181 -1  0  0
-   3755 1252  2  0.4236   28.40039    9.89629   22.77089 -1  0  0
-   3756 1252  2  0.4236   27.57125   11.22405   23.23563 -1  0  0
-   3757 1253  1 -0.8472   13.10422   23.78581   22.52010  0  0  0
-   3758 1253  2  0.4236   13.33878   23.51699   23.45427  0  0  0
-   3759 1253  2  0.4236   13.86548   23.56773   21.90941  0  0  0
-   3760 1254  1 -0.8472   33.19233    2.34733    4.32601  0  1  0
-   3761 1254  2  0.4236   33.68352    3.06983    3.83950  0  1  0
-   3762 1254  2  0.4236   33.54114    1.45534    4.03853  0  1  0
-   3763 1255  1 -0.8472   25.94719   28.29984    2.89677  0  1  0
-   3764 1255  2  0.4236   25.07124   28.70411    2.63365  0  1  0
-   3765 1255  2  0.4236   26.66612   28.63786    2.28947  0  1  0
-   3766 1256  1 -0.8472    9.90709    2.77986    7.29641 -1  0  0
-   3767 1256  2  0.4236    9.28065    2.13448    7.73344 -1  0  0
-   3768 1256  2  0.4236   10.84882    2.54552    7.53760 -1  0  0
-   3769 1257  1 -0.8472   16.30796   34.86244   16.12167  1  0  0
-   3770 1257  2  0.4236   16.62176   35.28557   15.27171  1  0  0
-   3771 1257  2  0.4236   15.30895   34.81894   16.12330  1  0  0
-   3772 1258  1 -0.8472    7.61771    9.73779   26.78220  1  1  0
-   3773 1258  2  0.4236    7.47927   10.72185   26.89368  1  1  0
-   3774 1258  2  0.4236    8.00824    9.55632   25.87971  1  1  0
-   3775 1259  1 -0.8472    3.53455   14.19611    8.20227  0  1  0
-   3776 1259  2  0.4236    3.27523   14.50182    9.11836  0  1  0
-   3777 1259  2  0.4236    3.41713   13.20527    8.13587  0  1  0
-   3778 1260  1 -0.8472   17.36729   21.51876   20.34297  0  0  0
-   3779 1260  2  0.4236   18.19977   21.66761   19.80934  0  0  0
-   3780 1260  2  0.4236   16.76176   22.30825   20.24311  0  0  0
-   3781 1261  1 -0.8472   24.85956   10.53353    5.64142 -1  1  0
-   3782 1261  2  0.4236   24.62252    9.97391    6.43551 -1  1  0
-   3783 1261  2  0.4236   24.04025   10.69600    5.09160 -1  1  0
-   3784 1262  1 -0.8472   17.54124   19.88458   23.16534  0 -1  0
-   3785 1262  2  0.4236   18.30863   20.31961   23.63629  0 -1  0
-   3786 1262  2  0.4236   16.71124   20.42236   23.31326  0 -1  0
-   3787 1263  1 -0.8472    9.13809    2.62440   27.30937  0  1  0
-   3788 1263  2  0.4236    9.78967    1.98344   27.71510  0  1  0
-   3789 1263  2  0.4236    8.56054    2.14095   26.65161  0  1  0
-   3790 1264  1 -0.8472   14.26627   24.14780    0.96270  0  0  0
-   3791 1264  2  0.4236   13.73311   24.38448    1.77489  0  0  0
-   3792 1264  2  0.4236   14.80771   24.93859    0.67731  0  0  0
-   3793 1265  1 -0.8472   34.12753    0.60519   34.36017  0  0  0
-   3794 1265  2  0.4236   33.98288    1.43738   34.89542  0  0  0
-   3795 1265  2  0.4236   33.66886    0.69362   33.47601  0  0  0
-   3796 1266  1 -0.8472   12.28580   18.19129    0.67816  0  0  0
-   3797 1266  2  0.4236   12.91440   18.64946    0.04978  0  0  0
-   3798 1266  2  0.4236   11.43961   18.71959    0.74726  0  0  0
-   3799 1267  1 -0.8472   12.16281    6.42562   30.34156  0  0  0
-   3800 1267  2  0.4236   12.59339    5.68077   30.85118  0  0  0
-   3801 1267  2  0.4236   12.60106    6.51449   29.44712  0  0  0
-   3802 1268  1 -0.8472   22.54245   21.32955   17.15786  0  0  0
-   3803 1268  2  0.4236   22.26706   21.46728   16.20646  0  0  0
-   3804 1268  2  0.4236   22.14968   22.05228   17.72650  0  0  0
-   3805 1269  1 -0.8472   16.46941   17.24841   22.22819  0 -1  0
-   3806 1269  2  0.4236   16.69927   18.02693   22.81218  0 -1  0
-   3807 1269  2  0.4236   15.47597   17.13973   22.19338  0 -1  0
-   3808 1270  1 -0.8472   15.89729    2.63284   27.11334  0  1  0
-   3809 1270  2  0.4236   15.95407    1.69174   26.78010  0  1  0
-   3810 1270  2  0.4236   16.01219    3.26519   26.34726  0  1  0
-   3811 1271  1 -0.8472   17.56428   29.20553   10.53540  0 -1  0
-   3812 1271  2  0.4236   16.89516   29.75865   11.03170  0 -1  0
-   3813 1271  2  0.4236   18.48421   29.42333   10.86137  0 -1  0
-   3814 1272  1 -0.8472   14.13472    0.57957   23.40535  0  0  0
-   3815 1272  2  0.4236   15.12428    0.71936   23.37111  0  0  0
-   3816 1272  2  0.4236   13.74827    1.11485   24.15637  0  0  0
-   3817 1273  1 -0.8472   14.94299   16.74046   14.49758  0  0  0
-   3818 1273  2  0.4236   14.51357   17.57578   14.84078  0  0  0
-   3819 1273  2  0.4236   15.77043   16.54983   15.02574  0  0  0
-   3820 1274  1 -0.8472   18.60554   10.10070   33.85186  0  0  0
-   3821 1274  2  0.4236   18.03410    9.28115   33.89305  0  0  0
-   3822 1274  2  0.4236   19.47154    9.88099   33.40267  0  0  0
-   3823 1275  1 -0.8472   21.91949   17.78066    6.96782 -1  0  0
-   3824 1275  2  0.4236   22.76969   18.25566    7.19482 -1  0  0
-   3825 1275  2  0.4236   21.34876   18.37255    6.39871 -1  0  0
-   3826 1276  1 -0.8472    9.21876   31.25393    9.94935  0  0  0
-   3827 1276  2  0.4236    9.97547   30.68146   10.26497  0  0  0
-   3828 1276  2  0.4236    9.23222   31.30335    8.95070  0  0  0
-   3829 1277  1 -0.8472   13.41060    7.95548   25.27966  1  1  0
-   3830 1277  2  0.4236   12.62868    8.49127   24.96117  1  1  0
-   3831 1277  2  0.4236   14.22917    8.22717   24.77362  1  1  0
-   3832 1278  1 -0.8472   12.07574   15.03988   21.04418  0  0  0
-   3833 1278  2  0.4236   11.95903   14.17033   21.52403  0  0  0
-   3834 1278  2  0.4236   12.31435   15.75417   21.70205  0  0  0
-   3835 1279  1 -0.8472    9.88529   18.41150    5.93407  0  0  0
-   3836 1279  2  0.4236    9.71670   19.36165    6.19620  0  0  0
-   3837 1279  2  0.4236    9.38429   17.80224    6.54865  0  0  0
-   3838 1280  1 -0.8472   17.69317    1.78597   18.64760  0  0  0
-   3839 1280  2  0.4236   17.13270    0.95939   18.69861  0  0  0
-   3840 1280  2  0.4236   17.23908    2.52755   19.14138  0  0  0
-   3841 1281  1 -0.8472   31.78581   31.55779   20.70371  0 -1  0
-   3842 1281  2  0.4236   30.92713   31.48884   20.19593  0 -1  0
-   3843 1281  2  0.4236   32.50326   31.06227   20.21415  0 -1  0
-   3844 1282  1 -0.8472    3.88805   14.07173   13.16821  0  0  0
-   3845 1282  2  0.4236    4.86565   13.88586   13.06952  0  0  0
-   3846 1282  2  0.4236    3.59566   13.83494   14.09469  0  0  0
-   3847 1283  1 -0.8472   17.40159    4.33028    2.50015 -1  0  0
-   3848 1283  2  0.4236   16.66174    4.99386    2.38964 -1  0  0
-   3849 1283  2  0.4236   17.65489    4.27123    3.46570 -1  0  0
-   3850 1284  1 -0.8472   32.95401   16.04344   16.03578  0  0  0
-   3851 1284  2  0.4236   32.18345   15.56378   16.45540  0  0  0
-   3852 1284  2  0.4236   33.06983   15.72825   15.09387  0  0  0
-   3853 1285  1 -0.8472   26.81393   18.75179    3.07330 -1 -1  0
-   3854 1285  2  0.4236   26.78553   17.98088    2.43704 -1 -1  0
-   3855 1285  2  0.4236   27.76469   19.01741    3.23286 -1 -1  0
-   3856 1286  1 -0.8472   31.29948   29.38498   30.48980 -1 -1  0
-   3857 1286  2  0.4236   30.36542   29.67830   30.28626 -1 -1  0
-   3858 1286  2  0.4236   31.94439   30.07640   30.16425 -1 -1  0
-   3859 1287  1 -0.8472    7.70452   13.58317   24.43091  0  1  0
-   3860 1287  2  0.4236    8.11380   13.58285   23.51854  0  1  0
-   3861 1287  2  0.4236    8.38876   13.86587   25.10306  0  1  0
-   3862 1288  1 -0.8472    6.40123   28.60910   19.73785  0  0  0
-   3863 1288  2  0.4236    6.93446   28.83300   18.92206  0  0  0
-   3864 1288  2  0.4236    6.51282   27.63896   19.95312  0  0  0
-   3865 1289  1 -0.8472    3.04379   10.50807   22.19377  0  1  0
-   3866 1289  2  0.4236    2.93294    9.89004   21.41549  0  1  0
-   3867 1289  2  0.4236    2.80507   11.43883   21.91689  0  1  0
-   3868 1290  1 -0.8472   14.37599   26.93440   28.59915  0  0  0
-   3869 1290  2  0.4236   13.74025   27.42354   28.00208  0  0  0
-   3870 1290  2  0.4236   15.27401   27.37252   28.56009  0  0  0
-   3871 1291  1 -0.8472   34.12274   21.85242   14.14839  0 -1  0
-   3872 1291  2  0.4236   33.61787   21.07635   13.77045  0 -1  0
-   3873 1291  2  0.4236   35.09050   21.76777   13.91132  0 -1  0
-   3874 1292  1 -0.8472   32.64567    5.25739    5.99940 -1  1  0
-   3875 1292  2  0.4236   33.11844    4.88493    5.20085 -1  1  0
-   3876 1292  2  0.4236   33.08134    6.11426    6.27500 -1  1  0
-   3877 1293  1 -0.8472   23.64858    3.21683   21.36377  0  0  0
-   3878 1293  2  0.4236   22.71597    3.53283   21.18962  0  0  0
-   3879 1293  2  0.4236   23.97889    2.70125   20.57320  0  0  0
-   3880 1294  1 -0.8472   32.64212   16.11772   31.97213 -1  0  0
-   3881 1294  2  0.4236   31.81837   16.41178   32.45680 -1  0  0
-   3882 1294  2  0.4236   33.26061   16.89594   31.86352 -1  0  0
-   3883 1295  1 -0.8472    6.29229   17.36253    3.95587  0  0  0
-   3884 1295  2  0.4236    6.77184   17.44356    4.82957  0  0  0
-   3885 1295  2  0.4236    6.12602   16.39715    3.75517  0  0  0
-   3886 1296  1 -0.8472   31.92486   23.30850   22.00260  0  0  0
-   3887 1296  2  0.4236   31.25077   23.84248   21.49234  0  0  0
-   3888 1296  2  0.4236   32.82945   23.72002   21.89141  0  0  0
-   3889 1297  1 -0.8472   27.33250   28.07000   32.92133  0  0  0
-   3890 1297  2  0.4236   27.07320   27.40863   33.62506  0  0  0
-   3891 1297  2  0.4236   28.29881   27.95187   32.69273  0  0  0
-   3892 1298  1 -0.8472    2.64561   33.53042   18.92001  1  0  0
-   3893 1298  2  0.4236    1.69345   33.79700   18.77078  1  0  0
-   3894 1298  2  0.4236    3.23109   34.33901   18.86227  1  0  0
-   3895 1299  1 -0.8472   20.25726   25.40408   31.93927 -1  0  0
-   3896 1299  2  0.4236   19.93756   25.82497   32.78816 -1  0  0
-   3897 1299  2  0.4236   20.87305   26.03411   31.46615 -1  0  0
-   3898 1300  1 -0.8472    3.04174   13.82425   29.63913  1  0  0
-   3899 1300  2  0.4236    2.19951   13.71557   29.11115  1  0  0
-   3900 1300  2  0.4236    2.90738   13.45836   30.56002  1  0  0
-   3901 1301  1 -0.8472   27.74001   30.99889   32.58650  0  0  0
-   3902 1301  2  0.4236   28.31372   31.33194   33.33475  0  0  0
-   3903 1301  2  0.4236   27.55154   30.02577   32.71868  0  0  0
-   3904 1302  1 -0.8472   31.54537    3.17343   11.48007 -1  0  0
-   3905 1302  2  0.4236   31.00105    2.58309   12.07601 -1  0  0
-   3906 1302  2  0.4236   31.24008    3.06453   10.53409 -1  0  0
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-3909  1303  2  0.4236  13.10919  29.56198  0.72764  0  -1  1
-3910  1304  1  -0.8472  23.77746  14.97626  35.08085  0  0  0
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-3912  1304  2  0.4236  23.98557  14.02508  34.85299  0  0  0
-   3913 1305  1 -0.8472    9.02720   31.44392    7.07983  1  0  0
-   3914 1305  2  0.4236    8.96368   32.37089    6.71012  1  0  0
-   3915 1305  2  0.4236    8.13255   31.00077    7.02393  1  0  0
-   3916 1306  1 -0.8472   31.36549   11.59481   10.42094  0  0  0
-   3917 1306  2  0.4236   31.65377   12.22675   11.14031  0  0  0
-   3918 1306  2  0.4236   32.09618   10.93542   10.24406  0  0  0
-   3919 1307  1 -0.8472   29.50183   27.32803    3.75836  0 -1  0
-   3920 1307  2  0.4236   29.53439   26.49065    3.21279  0 -1  0
-   3921 1307  2  0.4236   29.08094   28.05932    3.22170  0 -1  0
-   3922 1308  1 -0.8472   33.81990   14.88458   25.76164  0  0  0
-   3923 1308  2  0.4236   34.72524   14.95250   25.34251  0  0  0
-   3924 1308  2  0.4236   33.89155   14.39907   26.63289  0  0  0
-   3925 1309  1 -0.8472    7.98850   21.50658   20.41280  0  0  0
-   3926 1309  2  0.4236    8.56246   21.56801   19.59624  0  0  0
-   3927 1309  2  0.4236    8.56179   21.31560   21.20954  0  0  0
-   3928 1310  1 -0.8472   32.46665   14.83711    6.59392  0  0  0
-   3929 1310  2  0.4236   32.73572   14.17385    7.29220  0  0  0
-   3930 1310  2  0.4236   31.57544   15.22519    6.82865  0  0  0
-   3931 1311  1 -0.8472   19.27221   16.62720   16.91022  0 -1  0
-   3932 1311  2  0.4236   18.39566   16.51808   16.44147  0 -1  0
-   3933 1311  2  0.4236   19.11058   16.84716   17.87223  0 -1  0
-   3934 1312  1 -0.8472   10.75317   25.30896   14.90281  1 -1  0
-   3935 1312  2  0.4236   10.02110   24.75819   15.30365  1 -1  0
-   3936 1312  2  0.4236   10.68350   26.24920   15.23605  1 -1  0
-   3937 1313  1 -0.8472   10.59250    3.58120   20.02809  0  0  0
-   3938 1313  2  0.4236   10.10365    3.59853   20.90027  0  0  0
-   3939 1313  2  0.4236   11.56509    3.41878   20.19430  0  0  0
-   3940 1314  1 -0.8472   23.15667   28.53308   20.17853  0 -1  0
-   3941 1314  2  0.4236   23.99072   29.08474   20.18023  0 -1  0
-   3942 1314  2  0.4236   23.01997   28.13839   19.26998  0 -1  0
-   3943 1315  1 -0.8472    6.61160   15.88142   29.17336  1  0  0
-   3944 1315  2  0.4236    5.96957   16.51911   28.74778  1  0  0
-   3945 1315  2  0.4236    6.23172   14.95687   29.14422  1  0  0
-   3946 1316  1 -0.8472   33.84117   10.87684    5.32296 -1  0  0
-   3947 1316  2  0.4236   34.05499   11.83082    5.11283 -1  0  0
-   3948 1316  2  0.4236   34.38758   10.27642    4.73908 -1  0  0
-   3949 1317  1 -0.8472    5.10908    7.98804   15.75723  0  1  0
-   3950 1317  2  0.4236    5.83685    8.64150   15.96527  0  1  0
-   3951 1317  2  0.4236    4.52699    8.35699   15.03262  0  1  0
-   3952 1318  1 -0.8472   21.73216    9.98499   28.65661  0  0  0
-   3953 1318  2  0.4236   22.11985    9.08867   28.44162  0  0  0
-   3954 1318  2  0.4236   22.22861   10.38703   29.42592  0  0  0
-   3955 1319  1 -0.8472   15.11924   17.54695    6.96555  1  0  0
-   3956 1319  2  0.4236   15.24394   16.65784    6.52526  1  0  0
-   3957 1319  2  0.4236   14.14970   17.79152    6.95414  1  0  0
-   3958 1320  1 -0.8472    9.36217   21.72925   23.47370  0  0  0
-   3959 1320  2  0.4236    9.44785   22.47012   22.80757  0  0  0
-   3960 1320  2  0.4236    9.25579   22.11545   24.38994  0  0  0
-   3961 1321  1 -0.8472    9.43645   15.00189   14.94078  1  0  0
-   3962 1321  2  0.4236   10.25430   14.52785   15.26696  1  0  0
-   3963 1321  2  0.4236    9.65662   15.51329   14.11018  1  0  0
-   3964 1322  1 -0.8472    8.59033   10.76868    9.86814  0  0  0
-   3965 1322  2  0.4236    7.82215   10.93745    9.25058  0  0  0
-   3966 1322  2  0.4236    8.25906   10.73652   10.81111  0  0  0
-   3967 1323  1 -0.8472   11.61768   13.08370   14.89370  0  0  0
-   3968 1323  2  0.4236   11.67363   13.04553   13.89601  0  0  0
-   3969 1323  2  0.4236   12.47416   13.44533   15.26196  0  0  0
-   3970 1324  1 -0.8472   16.11690   13.08391   16.65249  0  0  0
-   3971 1324  2  0.4236   16.28495   12.57915   15.80576  0  0  0
-   3972 1324  2  0.4236   15.93060   12.43894   17.39362  0  0  0
-   3973 1325  1 -0.8472   15.86534   31.96218    1.66332  0  0  0
-   3974 1325  2  0.4236   15.01496   31.44332    1.57625  0  0  0
-   3975 1325  2  0.4236   15.96614   32.57132    0.87672  0  0  0
-   3976 1326  1 -0.8472   24.92119   12.54887   34.11767  0  0  0
-   3977 1326  2  0.4236   25.52292   11.78246   34.34234  0  0  0
-   3978 1326  2  0.4236   25.18156   12.92786   33.22969  0  0  0
-   3979 1327  1 -0.8472   11.53054   35.48053    2.50601  0 -1  0
-   3980 1327  2  0.4236   11.26027    0.86465    2.87208  0  0  0
-   3981 1327  2  0.4236   11.70360    0.05592    1.52453  0  0  0
-   3982 1328  1 -0.8472   30.37646   11.06481   19.98364 -1  1  0
-   3983 1328  2  0.4236   31.07807   10.97906   19.27629 -1  1  0
-   3984 1328  2  0.4236   29.60175   11.58441   19.62339 -1  1  0
-   3985 1329  1 -0.8472    5.33838   10.35688   23.82633  0  1  0
-   3986 1329  2  0.4236    4.49407   10.43102   23.29565  0  1  0
-   3987 1329  2  0.4236    5.42533   11.15151   24.42705  0  1  0
-   3988 1330  1 -0.8472   17.21081    5.64167    9.21177 -1  1  0
-   3989 1330  2  0.4236   17.44537    5.70658   10.18167 -1  1  0
-   3990 1330  2  0.4236   17.43319    6.50384    8.75666 -1  1  0
-   3991 1331  1 -0.8472    8.48413   30.64049   22.56444  0 -1  0
-   3992 1331  2  0.4236    9.06406   29.97286   22.09767  0 -1  0
-   3993 1331  2  0.4236    8.37563   31.44943   21.98669  0 -1  0
-   3994 1332  1 -0.8472    1.13258   13.38927   14.12372  1  1  0
-   3995 1332  2  0.4236    1.00638   14.05274   14.86113  1  1  0
-   3996 1332  2  0.4236    1.57468   12.56864   14.48574  1  1  0
-   3997 1333  1 -0.8472    3.61348   27.78485   20.21784  1 -1  0
-   3998 1333  2  0.4236    3.54423   26.84230   19.89108  1 -1  0
-   3999 1333  2  0.4236    4.49674   28.16750   19.94691  1 -1  0
-   4000 1334  1 -0.8472   34.87963   19.16306   19.16038 -1  1  0
-   4001 1334  2  0.4236   34.72652   18.19533   18.96042 -1  1  0
-   4002 1334  2  0.4236   34.73462   19.70187   18.33056 -1  1  0
-   4003 1335  1 -0.8472   33.17028   25.43707    7.09681 -1  0  0
-   4004 1335  2  0.4236   32.75169   26.26784    6.73000 -1  0  0
-   4005 1335  2  0.4236   32.53585   24.67095    6.99433 -1  0  0
-   4006 1336  1 -0.8472   10.03853    8.39253    8.37546  0  1  0
-   4007 1336  2  0.4236    9.83643    9.29993    8.74386  0  1  0
-   4008 1336  2  0.4236    9.26076    7.78562    8.53887  0  1  0
-   4009 1337  1 -0.8472    8.03214   12.07162   19.93674  1  0  0
-   4010 1337  2  0.4236    7.62829   11.35734   20.50829  1  0  0
-   4011 1337  2  0.4236    8.51882   11.65059   19.17133  1  0  0
-   4012 1338  1 -0.8472    1.41857   21.54262   10.36366  0  0  0
-   4013 1338  2  0.4236    2.20565   20.94132   10.22637  0  0  0
-   4014 1338  2  0.4236    1.66063   22.47502   10.09525  0  0  0
-   4015 1339  1 -0.8472   34.50038   20.54422   16.81189 -1  0  0
-   4016 1339  2  0.4236   35.23362   20.99512   16.30298 -1  0  0
-   4017 1339  2  0.4236   33.70511   21.14879   16.85659 -1  0  0
-   4018 1340  1 -0.8472    9.44547   24.80491    4.00309  1  0  0
-   4019 1340  2  0.4236   10.06637   25.56510    3.81178  1  0  0
-   4020 1340  2  0.4236    9.34559   24.24167    3.18290  1  0  0
-   4021 1341  1 -0.8472    4.73779   28.13530    4.76587  1  0  0
-   4022 1341  2  0.4236    4.64675   27.24203    5.20595  1  0  0
-   4023 1341  2  0.4236    5.38013   28.06692    4.00255  1  0  0
-   4024 1342  1 -0.8472   28.79309   11.26361   32.56261 -1  0  0
-   4025 1342  2  0.4236   28.66814   12.07106   31.98609 -1  0  0
-   4026 1342  2  0.4236   28.00130   11.15780   33.16414 -1  0  0
-   4027 1343  1 -0.8472   29.00688    2.02184   18.32003  0  1  0
-   4028 1343  2  0.4236   29.92131    1.72090   18.59060  0  1  0
-   4029 1343  2  0.4236   28.91878    1.96743   17.32545  0  1  0
-   4030 1344  1 -0.8472   31.38630   11.70534    6.36117  0  1  0
-   4031 1344  2  0.4236   31.72496   12.31115    7.08107  0  1  0
-   4032 1344  2  0.4236   32.14258   11.15776    6.00323  0  1  0
-   4033 1345  1 -0.8472   14.04432   34.74239   31.23302 -1 -1  0
-   4034 1345  2  0.4236   14.42009   35.30378   30.49572 -1 -1  0
-   4035 1345  2  0.4236   14.59804   33.91641   31.33837 -1 -1  0
-   4036 1346  1 -0.8472   11.74166   19.24522   20.21415  0  0  0
-   4037 1346  2  0.4236   12.20073   18.37581   20.39670  0  0  0
-   4038 1346  2  0.4236   11.64250   19.75559   21.06832  0  0  0
-   4039 1347  1 -0.8472   35.52179    6.24067   32.03171  0  0  0
-   4040 1347  2  0.4236    0.50438    6.83174   32.67320  1  0  0
-   4041 1347  2  0.4236    0.29816    5.29165   32.17109  1  0  0
-   4042 1348  1 -0.8472   15.57283    9.26811   33.08255  0  0  0
-   4043 1348  2  0.4236   15.53601   10.10503   33.62861  0  0  0
-   4044 1348  2  0.4236   15.19689    8.50778   33.61220  0  0  0
-   4045 1349  1 -0.8472   17.80359   31.80829    5.14239  1 -1  0
-   4046 1349  2  0.4236   16.85934   32.13019    5.07387  1 -1  0
-   4047 1349  2  0.4236   17.97257   31.11858    4.43838  1 -1  0
-   4048 1350  1 -0.8472   30.38406   19.12162   16.07527  0  0  0
-   4049 1350  2  0.4236   31.29341   19.04947   15.66557  0  0  0
-   4050 1350  2  0.4236   30.08197   18.21753   16.37749  0  0  0
-   4051 1351  1 -0.8472   11.10369    6.99773    6.45008  0  1  0
-   4052 1351  2  0.4236   12.01908    7.37712    6.31577  0  1  0
-   4053 1351  2  0.4236   10.59371    7.57531    7.08745  0  1  0
-   4054 1352  1 -0.8472   12.27206   16.59023   16.74848  1 -1  0
-   4055 1352  2  0.4236   11.81988   17.30736   17.27877  1 -1  0
-   4056 1352  2  0.4236   12.89672   16.08136   17.34073  1 -1  0
-   4057 1353  1 -0.8472   20.33587   18.83981   32.69894  0  1  0
-   4058 1353  2  0.4236   20.70478   19.62858   33.19059  0  1  0
-   4059 1353  2  0.4236   20.73393   18.00044   33.06900  0  1  0
-   4060 1354  1 -0.8472    2.03095   27.60334    3.55915  1  0  0
-   4061 1354  2  0.4236    1.49012   28.34142    3.15579  1  0  0
-   4062 1354  2  0.4236    2.33241   27.87255    4.47382  1  0  0
-   4063 1355  1 -0.8472   18.88135   18.11410    0.87201  0  1  0
-   4064 1355  2  0.4236   19.39275   17.48421    0.28749  0  1  0
-   4065 1355  2  0.4236   18.56634   18.89200    0.32833  0  1  0
-   4066 1356  1 -0.8472   16.25484    6.69873    5.58205 -1  1  0
-   4067 1356  2  0.4236   16.87855    7.00828    6.29978 -1  1  0
-   4068 1356  2  0.4236   16.02398    5.73754    5.73284 -1  1  0
-   4069 1357  1 -0.8472    4.91653   23.82036    8.55004  0  0  0
-   4070 1357  2  0.4236    5.34761   23.21217    9.21648  0  0  0
-   4071 1357  2  0.4236    5.41269   24.68806    8.52083  0  0  0
-   4072 1358  1 -0.8472   33.30943   33.20561   10.09238 -1  0  0
-   4073 1358  2  0.4236   33.26590   34.05918   10.61147 -1  0  0
-   4074 1358  2  0.4236   32.96598   33.36084    9.16618 -1  0  0
-   4075 1359  1 -0.8472   16.61015    7.10659   25.54548  0  0  0
-   4076 1359  2  0.4236   17.06577    7.76016   26.14985  0  0  0
-   4077 1359  2  0.4236   16.33132    7.56921   24.70396  0  0  0
-   4078 1360  1 -0.8472   21.90262    1.55066   18.37026  0  1  0
-   4079 1360  2  0.4236   22.89510    1.63523   18.45827  0  1  0
-   4080 1360  2  0.4236   21.50605    2.45082   18.19019  0  1  0
-   4081 1361  1 -0.8472    3.86501    3.59828   14.83734  0  0  0
-   4082 1361  2  0.4236    4.42352    4.42579   14.89434  0  0  0
-   4083 1361  2  0.4236    3.15744    3.62445   15.54349  0  0  0
-   4084 1362  1 -0.8472   21.92304    8.04648    5.73415  0  0  0
-   4085 1362  2  0.4236   21.15202    8.10038    6.36865  0  0  0
-   4086 1362  2  0.4236   21.92013    8.84868    5.13715  0  0  0
-   4087 1363  1 -0.8472    3.88461   21.70830   19.87333  0  0  0
-   4088 1363  2  0.4236    3.77326   22.48610   19.25477  0  0  0
-   4089 1363  2  0.4236    4.65296   21.88004   20.48982  0  0  0
-   4090 1364  1 -0.8472   12.50665   27.83119   26.83785  0  0  0
-   4091 1364  2  0.4236   11.81736   27.12241   26.68791  0  0  0
-   4092 1364  2  0.4236   12.13096   28.72130   26.57993  0  0  0
-   4093 1365  1 -0.8472   32.46832   31.16200   16.94950  0  0  0
-   4094 1365  2  0.4236   33.05634   30.35349   16.92696  0  0  0
-   4095 1365  2  0.4236   32.80140   31.79707   17.64643  0  0  0
-   4096 1366  1 -0.8472    4.04609   20.23787   14.72111  0  1  0
-   4097 1366  2  0.4236    4.07606   19.71469   15.57277  0  1  0
-   4098 1366  2  0.4236    3.88322   19.61722   13.95421  0  1  0
-   4099 1367  1 -0.8472   13.76311   15.06580   33.41259  0  0  0
-   4100 1367  2  0.4236   14.68056   14.84069   33.74052  0  0  0
-   4101 1367  2  0.4236   13.74788   16.01155   33.08807  0  0  0
-   4102 1368  1 -0.8472    7.97774    4.02759   21.41028  1  1  0
-   4103 1368  2  0.4236    7.63454    3.91294   20.47809  1  1  0
-   4104 1368  2  0.4236    7.20683    4.12630   22.03950  1  1  0
-   4105 1369  1 -0.8472   20.29710    6.13425   12.62094  1  1  0
-   4106 1369  2  0.4236   19.31701    6.01240   12.46433  1  1  0
-   4107 1369  2  0.4236   20.56868    7.05305   12.33463  1  1  0
-   4108 1370  1 -0.8472    5.16656    5.52045    3.92872  1  1  0
-   4109 1370  2  0.4236    5.60269    5.98846    4.69728  1  1  0
-   4110 1370  2  0.4236    5.86909    5.12236    3.33884  1  1  0
-   4111 1371  1 -0.8472   17.27686   18.91878   19.63934  0  0  0
-   4112 1371  2  0.4236   18.05111   18.28992   19.71027  0  0  0
-   4113 1371  2  0.4236   17.49359   19.76961   20.11795  0  0  0
-   4114 1372  1 -0.8472   14.92005    7.12502   11.97112  0  0  0
-   4115 1372  2  0.4236   14.48733    6.58039   11.25271  0  0  0
-   4116 1372  2  0.4236   14.49309    8.02852   12.00724  0  0  0
-   4117 1373  1 -0.8472    1.10019    6.63116    0.49417  0  0  0
-   4118 1373  2  0.4236    1.99111    6.89491    0.86381  0  0  0
-   4119 1373  2  0.4236    1.03948    5.63397    0.45037  0  0  0
-   4120 1374  1 -0.8472   22.59485    0.72080   27.60450  1  1  0
-   4121 1374  2  0.4236   22.17357    1.60200   27.81888  1  1  0
-   4122 1374  2  0.4236   23.51241    0.68494   28.00041  1  1  0
-   4123 1375  1 -0.8472   15.78119   12.79592   23.35569  0  0  0
-   4124 1375  2  0.4236   16.02480   13.73623   23.11820  0  0  0
-   4125 1375  2  0.4236   14.85064   12.77490   23.72119  0  0  0
-   4126 1376  1 -0.8472   33.58141    6.89870   20.97751 -1  1  0
-   4127 1376  2  0.4236   34.40863    7.44824   21.09409 -1  1  0
-   4128 1376  2  0.4236   33.57629    6.15751   21.64870 -1  1  0
-   4129 1377  1 -0.8472    1.92074   17.89289   29.55807  1  0  0
-   4130 1377  2  0.4236    1.00224   17.93553   29.95110  1  0  0
-   4131 1377  2  0.4236    2.57668   17.64257   30.27013  1  0  0
-   4132 1378  1 -0.8472   11.63025   22.33197   20.78411  0  0  0
-   4133 1378  2  0.4236   11.83395   22.71874   21.68347  0  0  0
-   4134 1378  2  0.4236   12.46780   21.96046   20.38359  0  0  0
-   4135 1379  1 -0.8472   18.99923   25.73489    1.07719  0  0  0
-   4136 1379  2  0.4236   19.23105   26.05481    0.15857  0  0  0
-   4137 1379  2  0.4236   18.34556   26.36595    1.49482  0  0  0
-   4138 1380  1 -0.8472   26.73163    0.58642    2.49028 -1  1  0
-   4139 1380  2  0.4236   27.25801    1.43411    2.55567 -1  1  0
-   4140 1380  2  0.4236   26.60863    0.19913    3.40397 -1  1  0
-   4141 1381  1 -0.8472   10.39938   13.91835   25.30518  0  1  0
-   4142 1381  2  0.4236   10.62229   13.45115   26.16077  0  1  0
-   4143 1381  2  0.4236   10.41238   14.90734   25.45229  0  1  0
-   4144 1382  1 -0.8472   21.36317   34.04409   28.83108  0 -1  0
-   4145 1382  2  0.4236   21.78783   34.69929   28.20632  0 -1  0
-   4146 1382  2  0.4236   22.07522   33.53628   29.31593  0 -1  0
-   4147 1383  1 -0.8472    6.60638   30.22876    4.76665  0 -1  0
-   4148 1383  2  0.4236    6.87058   30.19293    5.73043  0 -1  0
-   4149 1383  2  0.4236    5.62090   30.38335    4.69672  0 -1  0
-   4150 1384  1 -0.8472    6.99525    5.86455   18.49351  1  0  0
-   4151 1384  2  0.4236    6.79939    4.89785   18.65820  1  0  0
-   4152 1384  2  0.4236    7.16656    6.00860   17.51892  1  0  0
-   4153 1385  1 -0.8472   27.85100   24.40461   26.76259 -1  0  0
-   4154 1385  2  0.4236   28.16466   23.49121   27.02200 -1  0  0
-   4155 1385  2  0.4236   27.50868   24.88178   27.57192 -1  0  0
-   4156 1386  1 -0.8472   26.18497    0.14061   24.90006  0  0  0
-   4157 1386  2  0.4236   27.13608    0.23417   24.60577  0  0  0
-   4158 1386  2  0.4236   25.60583    0.74498   24.35296  0  0  0
-   4159 1387  1 -0.8472   28.23866   32.55211   16.47504  0 -1  0
-   4160 1387  2  0.4236   27.78773   32.40987   17.35615  0 -1  0
-   4161 1387  2  0.4236   27.95660   33.43281   16.09458  0 -1  0
-   4162 1388  1 -0.8472    3.71190   17.69512   22.13922  0  0  0
-   4163 1388  2  0.4236    4.11270   18.60508   22.24549  0  0  0
-   4164 1388  2  0.4236    3.85950   17.16622   22.97496  0  0  0
-   4165 1389  1 -0.8472   21.99849   17.97835   20.53867  0 -1  0
-   4166 1389  2  0.4236   22.74324   18.54152   20.18072  0 -1  0
-   4167 1389  2  0.4236   21.44970   18.51802   21.17704  0 -1  0
-   4168 1390  1 -0.8472   10.41557   21.36907    9.81845  0 -1  0
-   4169 1390  2  0.4236   10.99340   21.92631   10.41470  0 -1  0
-   4170 1390  2  0.4236   10.29063   20.46447   10.22595  0 -1  0
-   4171 1391  1 -0.8472   26.10008   27.35743    8.93223 -2  0  0
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-   4173 1391  2  0.4236   25.82174   28.05715    8.27430 -2  0  0
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-4177  1393  1  -0.8472  16.76823  15.96965  35.38491  0  0  0
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-4179  1393  2  0.4236  17.75158  16.03673  35.21615  0  0  0
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-   4182 1394  2  0.4236    5.12424   20.42993    2.20919  0  0  0
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-   4185 1395  2  0.4236   14.11509    4.10815   22.55919  1  0  0
-   4186 1396  1 -0.8472   25.20454    3.81448   25.19998  0  1  0
-   4187 1396  2  0.4236   25.43529    4.37239   24.40284  0  1  0
-   4188 1396  2  0.4236   24.75751    2.97209   24.89910  0  1  0
-   4189 1397  1 -0.8472   34.55435   24.91541   25.79393  0  0  0
-   4190 1397  2  0.4236   35.08581   24.14893   26.15450  0  0  0
-   4191 1397  2  0.4236   33.85857   25.18160   26.46101  0  0  0
-   4192 1398  1 -0.8472   26.21632   33.11524   29.54084  0  0  0
-   4193 1398  2  0.4236   26.88558   33.61308   30.09236  0  0  0
-   4194 1398  2  0.4236   26.05296   33.61059   28.68766  0  0  0
-   4195 1399  1 -0.8472   12.75839   12.33150    9.28135  0  0  0
-   4196 1399  2  0.4236   12.49269   12.46848   10.23559  0  0  0
-   4197 1399  2  0.4236   12.18297   12.89711    8.69066  0  0  0
-   4198 1400  1 -0.8472   30.89915   15.99270   28.39554 -1  0  0
-   4199 1400  2  0.4236   31.44059   15.15457   28.46154 -1  0  0
-   4200 1400  2  0.4236   30.93487   16.33963   27.45835 -1  0  0
-   4201 1401  1 -0.8472    0.81922   11.50629   17.18912  0  0  0
-   4202 1401  2  0.4236    0.61583   10.52916   17.25048  0  0  0
-   4203 1401  2  0.4236    1.64440   11.64122   16.64065  0  0  0
-   4204 1402  1 -0.8472    6.31281   10.44238   16.76762  0  0  0
-   4205 1402  2  0.4236    7.01406   11.14835   16.66862  0  0  0
-   4206 1402  2  0.4236    5.76953   10.62481   17.58709  0  0  0
-   4207 1403  1 -0.8472    0.54456    9.54460   23.55923  0  0  0
-   4208 1403  2  0.4236    0.32188    9.63088   24.53027  0  0  0
-   4209 1403  2  0.4236    1.35608   10.09147   23.35353  0  0  0
-   4210 1404  1 -0.8472    1.24532   29.21899   12.99820  0 -1  0
-   4211 1404  2  0.4236    2.10877   28.72424   12.90008  0 -1  0
-   4212 1404  2  0.4236    1.18386   29.60264   13.91958  0 -1  0
-   4213 1405  1 -0.8472    9.87755    0.56243   14.38546  1  1  0
-   4214 1405  2  0.4236   10.32219   35.29136   13.94064  1  0  0
-   4215 1405  2  0.4236   10.56154    1.10058   14.87789  1  1  0
-   4216 1406  1 -0.8472   20.62159    2.62651    7.23282  1  1  0
-   4217 1406  2  0.4236   21.26312    3.32400    7.55202  1  1  0
-   4218 1406  2  0.4236   19.72502    2.78378    7.64684  1  1  0
-   4219 1407  1 -0.8472   26.24895    1.51497   16.19898  0  0  0
-   4220 1407  2  0.4236   25.40298    1.65532   16.71335  0  0  0
-   4221 1407  2  0.4236   26.29696    2.17550   15.44973  0  0  0
-   4222 1408  1 -0.8472   21.52089   15.53065    3.18350  0 -1  0
-   4223 1408  2  0.4236   21.15454   15.06314    2.37904  0 -1  0
-   4224 1408  2  0.4236   20.93898   16.31204    3.40870  0 -1  0
-   4225 1409  1 -0.8472    9.60116   12.81307   30.75366  0  0  0
-   4226 1409  2  0.4236   10.22636   13.08164   31.48643  0  0  0
-   4227 1409  2  0.4236    9.05604   12.02934   31.05121  0  0  0
-   4228 1410  1 -0.8472    5.23729    9.36348    2.76133  0  1  0
-   4229 1410  2  0.4236    5.49223    9.14952    3.70430  0  1  0
-   4230 1410  2  0.4236    4.82716    8.55685    2.33574  0  1  0
-   4231 1411  1 -0.8472   30.15622   30.86325    5.78803 -1  0  0
-   4232 1411  2  0.4236   31.03997   30.61950    6.18741 -1  0  0
-   4233 1411  2  0.4236   29.77296   31.64556    6.27901 -1  0  0
-   4234 1412  1 -0.8472    3.00118    7.40350   17.66433  1  1  0
-   4235 1412  2  0.4236    3.31933    7.97153   18.42332  1  1  0
-   4236 1412  2  0.4236    3.68758    7.40392   16.93713  1  1  0
-   4237 1413  1 -0.8472    1.27143    7.78395   33.63201  1  0  0
-   4238 1413  2  0.4236    1.04920    7.43066   34.54070  1  0  0
-   4239 1413  2  0.4236    1.85411    8.59165   33.72173  1  0  0
-   4240 1414  1 -0.8472   10.36647   16.58874   31.95040  1  0  0
-   4241 1414  2  0.4236    9.90077   17.17268   32.61532  1  0  0
-   4242 1414  2  0.4236   10.58267   15.70882   32.37335  1  0  0
-   4243 1415  1 -0.8472    2.92649   20.78950   22.99831  0  0  0
-   4244 1415  2  0.4236    3.38630   20.43813   23.81381  0  0  0
-   4245 1415  2  0.4236    3.60510   21.17464   22.37292  0  0  0
-   4246 1416  1 -0.8472   31.24310   32.56486   23.40585 -1  0  0
-   4247 1416  2  0.4236   30.76987   31.83084   23.89290 -1  0  0
-   4248 1416  2  0.4236   31.66708   32.19655   22.57848 -1  0  0
-   4249 1417  1 -0.8472   20.50168   18.67424    3.60469  0  1  0
-   4250 1417  2  0.4236   20.50225   18.74384    2.60714  0  1  0
-   4251 1417  2  0.4236   21.11534   19.36488    3.98731  0  1  0
-   4252 1418  1 -0.8472   29.26181   22.02665   30.81917  0  0  0
-   4253 1418  2  0.4236   29.77498   22.84230   31.08623  0  0  0
-   4254 1418  2  0.4236   28.58254   22.27185   30.12749  0  0  0
-   4255 1419  1 -0.8472    1.85161   27.62341   34.11640 -1  0  0
-   4256 1419  2  0.4236    2.16253   28.55236   34.31717 -1  0  0
-   4257 1419  2  0.4236    1.65257   27.54234   33.13979 -1  0  0
-   4258 1420  1 -0.8472    7.53004    9.50217    1.47002  0  1  0
-   4259 1420  2  0.4236    6.61551    9.21649    1.75623  0  1  0
-   4260 1420  2  0.4236    7.45608   10.27834    0.84390  0  1  0
-   4261 1421  1 -0.8472   16.58285   11.39480   14.39794  0  0  0
-   4262 1421  2  0.4236   16.18969   11.93603   13.65465  0  0  0
-   4263 1421  2  0.4236   16.00811   10.59421   14.56741  0  0  0
-   4264 1422  1 -0.8472    2.10592    5.43627    4.72316  0  1  0
-   4265 1422  2  0.4236    3.08841    5.34757    4.55950  0  1  0
-   4266 1422  2  0.4236    1.92931    5.42178    5.70732  0  1  0
-   4267 1423  1 -0.8472    3.71506    8.98264   20.01685 -1  0  0
-   4268 1423  2  0.4236    3.94387    9.91834   19.74841 -1  0  0
-   4269 1423  2  0.4236    4.50529    8.56072   20.46122 -1  0  0
-   4270 1424  1 -0.8472    1.86906   28.23419   30.94543  0  0  0
-   4271 1424  2  0.4236    2.78640   28.42230   30.59465  0  0  0
-   4272 1424  2  0.4236    1.58999   27.31365   30.67214  0  0  0
-   4273 1425  1 -0.8472   25.91892    1.73795   33.90733  1  1  0
-   4274 1425  2  0.4236   26.38470    2.45005   34.43262  1  1  0
-   4275 1425  2  0.4236   25.22904    2.15669   33.31689  1  1  0
-   4276 1426  1 -0.8472    4.30326   25.01135   31.69404  1  0  0
-   4277 1426  2  0.4236    4.77681   24.60093   30.91477  1  0  0
-   4278 1426  2  0.4236    3.42338   24.55523   31.82725  1  0  0
-   4279 1427  1 -0.8472   19.66466   33.96005    4.92748  0 -1  0
-   4280 1427  2  0.4236   19.99973   33.92475    5.86895  0 -1  0
-   4281 1427  2  0.4236   19.05768   33.18317    4.76034  0 -1  0
-   4282 1428  1 -0.8472   21.52853   24.53570   28.70701  0 -1  0
-   4283 1428  2  0.4236   21.55814   23.79625   29.37955  0 -1  0
-   4284 1428  2  0.4236   21.25506   25.38540   29.15776  0 -1  0
-   4285 1429  1 -0.8472   26.10586   14.96142   24.05624  0  0  0
-   4286 1429  2  0.4236   26.93664   15.23325   24.54190  0  0  0
-   4287 1429  2  0.4236   25.31446   15.40773   24.47395  0  0  0
-   4288 1430  1 -0.8472    8.93989    1.91730   34.66523  0  1  0
-   4289 1430  2  0.4236    9.71720    1.70768   34.07209  0  1  0
-   4290 1430  2  0.4236    9.19437    2.64332   35.30406  0  1  0
-   4291 1431  1 -0.8472    5.49155   24.85029   22.62250  1  0  0
-   4292 1431  2  0.4236    4.52301   24.64929   22.47596  1  0  0
-   4293 1431  2  0.4236    5.58611   25.50776   23.37001  1  0  0
-   4294 1432  1 -0.8472   30.35913   16.66043   13.69265  0  0  0
-   4295 1432  2  0.4236   31.35846   16.64719   13.65890  0  0  0
-   4296 1432  2  0.4236   30.01994   15.73968   13.88523  0  0  0
-   4297 1433  1 -0.8472   23.73905   30.09756   28.00530  0 -1  0
-   4298 1433  2  0.4236   22.88636   29.76565   27.60195  0 -1  0
-   4299 1433  2  0.4236   23.54863   30.89468   28.57831  0 -1  0
-   4300 1434  1 -0.8472    6.27457   22.28510   10.31293  0  0  0
-   4301 1434  2  0.4236    7.20338   22.65451   10.28568  0  0  0
-   4302 1434  2  0.4236    5.87861   22.44520   11.21712  0  0  0
-   4303 1435  1 -0.8472   34.26671   24.67070   21.96499 -1  0  0
-   4304 1435  2  0.4236   34.87274   24.93575   21.21504 -1  0  0
-   4305 1435  2  0.4236   34.76260   24.73063   22.83129 -1  0  0
-   4306 1436  1 -0.8472   18.92162    1.08281    4.46925 -1 -1  0
-   4307 1436  2  0.4236   19.78754    1.54407    4.27592 -1 -1  0
-   4308 1436  2  0.4236   19.09471    0.11779    4.66605 -1 -1  0
-   4309 1437  1 -0.8472   12.57287   31.40153   18.46855  1  0  0
-   4310 1437  2  0.4236   12.50938   30.52513   17.99122  1  0  0
-   4311 1437  2  0.4236   13.40979   31.42337   19.01540  1  0  0
-   4312 1438  1 -0.8472   18.33881   32.50240   15.43232  0  0  0
-   4313 1438  2  0.4236   17.94420   33.42056   15.39759  0  0  0
-   4314 1438  2  0.4236   17.69459   31.87927   15.87577  0  0  0
-   4315 1439  1 -0.8472    7.67654   27.84873    9.04314  0  0  0
-   4316 1439  2  0.4236    8.43198   27.95713    9.68931  0  0  0
-   4317 1439  2  0.4236    6.89338   27.43980    9.51151  0  0  0
-   4318 1440  1 -0.8472   21.65035   35.23355   32.90414 -1  0  0
-   4319 1440  2  0.4236   21.89201   35.27549   33.87358 -1  0  0
-   4320 1440  2  0.4236   21.11552    0.53569   32.65870 -1  1  0
-   4321 1441  1 -0.8472   26.98866   12.66178    1.39463  0  0  0
-   4322 1441  2  0.4236   27.22858   13.05128    0.50543  0  0  0
-   4323 1441  2  0.4236   26.30814   11.93983    1.26961  0  0  0
-   4324 1442  1 -0.8472   33.90498    1.20205   27.79719 -1  0  0
-   4325 1442  2  0.4236   33.57512    1.17136   26.85369 -1  0  0
-   4326 1442  2  0.4236   34.38097    0.34922   28.01175 -1  0  0
-   4327 1443  1 -0.8472   16.09059   23.00449   11.90689  0 -1  0
-   4328 1443  2  0.4236   15.59851   22.16519   11.67591  0 -1  0
-   4329 1443  2  0.4236   16.68248   23.26450   11.14399  0 -1  0
-   4330 1444  1 -0.8472   21.66203   22.49671    5.11467  0 -1  0
-   4331 1444  2  0.4236   21.48400   22.99703    5.96197  0 -1  0
-   4332 1444  2  0.4236   22.09350   21.62052    5.32931  0 -1  0
-   4333 1445  1 -0.8472   28.27062   28.47059   10.54210  0 -1  0
-   4334 1445  2  0.4236   28.73699   29.21139   10.05878  0 -1  0
-   4335 1445  2  0.4236   28.92304   27.99473   11.13191  0 -1  0
-   4336 1446  1 -0.8472   11.81133    6.08344   22.22918  2  0  0
-   4337 1446  2  0.4236   11.98293    6.96727   21.79400  2  0  0
-   4338 1446  2  0.4236   12.67690    5.59722   22.34885  2  0  0
-   4339 1447  1 -0.8472   11.54720   20.00403   29.64998  0  0  0
-   4340 1447  2  0.4236   12.20847   19.94668   30.39788  0  0  0
-   4341 1447  2  0.4236   10.65105   20.25502   30.01590  0  0  0
-   4342 1448  1 -0.8472   23.63295   15.75324    6.26015 -1  0  0
-   4343 1448  2  0.4236   24.01845   15.46731    7.13740 -1  0  0
-   4344 1448  2  0.4236   23.17822   16.63724    6.36819 -1  0  0
-   4345 1449  1 -0.8472   18.59627   17.84478    8.51395  0  0  0
-   4346 1449  2  0.4236   19.30661   17.22786    8.85265  0  0  0
-   4347 1449  2  0.4236   18.88270   18.23432    7.63866  0  0  0
-   4348 1450  1 -0.8472   24.95837   31.64730   25.42719  0  0  0
-   4349 1450  2  0.4236   25.82533   31.64851   24.92884  0  0  0
-   4350 1450  2  0.4236   25.13906   31.67401   26.41036  0  0  0
-   4351 1451  1 -0.8472   16.66874   15.84535   16.59843  0  0  0
-   4352 1451  2  0.4236   16.30160   16.17484   17.46823  0  0  0
-   4353 1451  2  0.4236   16.72463   14.84712   16.61697  0  0  0
-   4354 1452  1 -0.8472   33.01487    0.03301   11.50236  0  1  0
-   4355 1452  2  0.4236   32.49598    0.68423   10.94864  0  1  0
-   4356 1452  2  0.4236   32.63147   35.50688   12.42537  0  0  0
-4357  1453  1  -0.8472  28.05328  19.82767  0.19572  0  0  0
-4358  1453  2  0.4236  27.36733  20.21266  0.81312  0  0  0
-4359  1453  2  0.4236  27.69662  18.99018  35.22901  0  0  -1
-   4360 1454  1 -0.8472   13.82727   16.06989   19.24354  0  0  0
-   4361 1454  2  0.4236   14.79294   15.86683   19.40546  0  0  0
-   4362 1454  2  0.4236   13.26084   15.39722   19.71956  0  0  0
-   4363 1455  1 -0.8472   14.08001   21.97765   33.17988  1  0  0
-   4364 1455  2  0.4236   14.86867   22.09727   33.78291  1  0  0
-   4365 1455  2  0.4236   14.36835   22.08619   32.22855  1  0  0
-   4366 1456  1 -0.8472   16.33725   25.39311    3.01993  0 -1  0
-   4367 1456  2  0.4236   16.78886   26.28499    3.04273  0 -1  0
-   4368 1456  2  0.4236   16.96355   24.71199    2.64072  0 -1  0
-   4369 1457  1 -0.8472   34.41055   25.51007    0.15059  0  0  0
-   4370 1457  2  0.4236   34.86965   26.36478    0.39277  0  0  0
-   4371 1457  2  0.4236   33.46228   25.53993    0.46653  0  0  0
-   4372 1458  1 -0.8472   27.86190   21.35174   28.12153 -1  0  0
-   4373 1458  2  0.4236   28.79121   21.05583   27.90073 -1  0  0
-   4374 1458  2  0.4236   27.23273   21.03009   27.41397 -1  0  0
-   4375 1459  1 -0.8472    0.23515   27.24082   28.00084  1 -1  0
-   4376 1459  2  0.4236    0.82580   26.63370   28.53233  1 -1  0
-   4377 1459  2  0.4236   34.89553   26.76177   27.76667  0 -1  0
-   4378 1460  1 -0.8472   21.68728   25.32330   17.79708  0  0  0
-   4379 1460  2  0.4236   22.01241   26.26845   17.76638  0  0  0
-   4380 1460  2  0.4236   21.31354   25.07022   16.90477  0  0  0
-   4381 1461  1 -0.8472   30.97176    0.89911    8.90394 -1  2  0
-   4382 1461  2  0.4236   31.32718    0.98094    7.97285 -1  2  0
-   4383 1461  2  0.4236   29.99239    1.10098    8.90582 -1  2  0
-   4384 1462  1 -0.8472   25.45716   22.87578   20.99721  0  0  0
-   4385 1462  2  0.4236   26.30239   22.39353   21.22734  0  0  0
-   4386 1462  2  0.4236   25.66033   23.83885   20.82076  0  0  0
-   4387 1463  1 -0.8472   24.87472   30.47978   12.60569  0  0  0
-   4388 1463  2  0.4236   25.65927   30.69811   12.02542  0  0  0
-   4389 1463  2  0.4236   24.98656   29.56166   12.98590  0  0  0
-   4390 1464  1 -0.8472   13.80973    7.99429    5.29049  0  1  0
-   4391 1464  2  0.4236   13.73023    8.76929    4.66357  0  1  0
-   4392 1464  2  0.4236   14.76858    7.86828    5.54475  0  1  0
-   4393 1465  1 -0.8472   33.97510   12.84300   16.82412 -1  0  0
-   4394 1465  2  0.4236   34.81504   12.34044   17.02876 -1  0  0
-   4395 1465  2  0.4236   33.55414   13.15013   17.67758 -1  0  0
-   4396 1466  1 -0.8472   26.59067   21.83864    5.49548  0  0  0
-   4397 1466  2  0.4236   27.17656   22.56826    5.14296  0  0  0
-   4398 1466  2  0.4236   27.14602   21.03034    5.69097  0  0  0
-   4399 1467  1 -0.8472    5.16628   25.92485   12.35774  0  0  0
-   4400 1467  2  0.4236    4.34860   25.35313   12.42442  0  0  0
-   4401 1467  2  0.4236    5.79329   25.69800   13.10298  0  0  0
-   4402 1468  1 -0.8472   26.79149   35.42791    5.15590 -1  0  0
-   4403 1468  2  0.4236   26.57100   34.75869    5.86548 -1  0  0
-   4404 1468  2  0.4236   27.24633    0.70960    5.57074 -1  1  0
-   4405 1469  1 -0.8472    1.20630    3.82773    0.24514  0  0  0
-   4406 1469  2  0.4236    2.07387    3.42063    0.53070  0  0  0
-   4407 1469  2  0.4236    0.45018    3.34497    0.68691  0  0  0
-   4408 1470  1 -0.8472   26.43671    3.26559   13.86247 -1  0  0
-   4409 1470  2  0.4236   26.83179    4.06661   14.31219 -1  0  0
-   4410 1470  2  0.4236   25.70088    3.55590   13.25073 -1  0  0
-   4411 1471  1 -0.8472   33.20618   12.63476    8.22853  0  0  0
-   4412 1471  2  0.4236   32.62856   12.82716    9.02181  0  0  0
-   4413 1471  2  0.4236   34.16325   12.80270    8.46454  0  0  0
-   4414 1472  1 -0.8472   29.90540   24.56808   20.70513 -1  0  0
-   4415 1472  2  0.4236   29.45905   25.46288   20.69386 -1  0  0
-   4416 1472  2  0.4236   30.31745   24.38988   19.81161 -1  0  0
-   4417 1473  1 -0.8472   15.29819    4.02922   16.44477  0  1  0
-   4418 1473  2  0.4236   15.74731    4.67008   17.06729  0  1  0
-   4419 1473  2  0.4236   14.96500    3.24064   16.96159  0  1  0
-4420  1474  1  -0.8472  31.27200  25.18131  0.42504  0  0  0
-4421  1474  2  0.4236  31.06216  24.44154  35.23295  0  0  -1
-4422  1474  2  0.4236  30.72503  25.06997  1.25474  0  0  0
-4423  1475  1  -0.8472  12.12236  3.02649  0.17854  1  1  0
-4424  1475  2  0.4236  11.88057  2.13716  35.23770  1  1  -1
-4425  1475  2  0.4236  11.35234  3.37843  0.71066  1  1  0
-   4426 1476  1 -0.8472   32.84202   11.55156   14.38224 -1  1  0
-   4427 1476  2  0.4236   31.87238   11.54439   14.13797 -1  1  0
-   4428 1476  2  0.4236   33.01945   12.30064   15.02046 -1  1  0
-   4429 1477  1 -0.8472   20.56141   17.44100   12.45462  0  0  0
-   4430 1477  2  0.4236   19.82341   16.87961   12.08022  0  0  0
-   4431 1477  2  0.4236   20.67251   17.23961   13.42779  0  0  0
-   4432 1478  1 -0.8472   15.28058   11.62137   18.81314  0  0  0
-   4433 1478  2  0.4236   14.35106   11.87755   19.07832  0  0  0
-   4434 1478  2  0.4236   15.44910   10.66895   19.06701  0  0  0
-   4435 1479  1 -0.8472   29.74122   20.36633    3.36258  1  0  0
-   4436 1479  2  0.4236   30.50489   19.77988    3.63245  1  0  0
-   4437 1479  2  0.4236   29.83808   20.61761    2.39955  1  0  0
-   4438 1480  1 -0.8472   10.45942   28.09788   15.37735  0  0  0
-   4439 1480  2  0.4236    9.49177   28.21579   15.60027  0  0  0
-   4440 1480  2  0.4236   10.68404   28.64230   14.56918  0  0  0
-   4441 1481  1 -0.8472   16.77284    6.13546   17.93915 -1  1  0
-   4442 1481  2  0.4236   17.27231    6.27930   18.79343 -1  1  0
-   4443 1481  2  0.4236   16.65241    7.01137   17.47196 -1  1  0
-   4444 1482  1 -0.8472   21.51809    0.32169   25.14138  1  0  0
-   4445 1482  2  0.4236   22.25467    0.17201   25.80091  1  0  0
-   4446 1482  2  0.4236   21.38164   34.99836   24.60010  1 -1  0
-   4447 1483  1 -0.8472    8.70687   23.66278   10.13832  1  0  0
-   4448 1483  2  0.4236    9.01094   24.13022   10.96842  1  0  0
-   4449 1483  2  0.4236    9.40929   23.01447    9.84461  1  0  0
-   4450 1484  1 -0.8472   20.24838    3.67061   10.36639  0  1  0
-   4451 1484  2  0.4236   20.42013    3.09249   11.16402  0  1  0
-   4452 1484  2  0.4236   19.45158    3.32583    9.87020  0  1  0
-   4453 1485  1 -0.8472    5.99031   17.08661   14.86595  0 -1  0
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-
-Bonds
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-    533   1   1598   1597   1599
-    534   1   1601   1600   1602
-    535   1   1604   1603   1605
-    536   1   1607   1606   1608
-    537   1   1610   1609   1611
-    538   1   1613   1612   1614
-    539   1   1616   1615   1617
-    540   1   1619   1618   1620
-    541   1   1622   1621   1623
-    542   1   1625   1624   1626
-    543   1   1628   1627   1629
-    544   1   1631   1630   1632
-    545   1   1634   1633   1635
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-    547   1   1640   1639   1641
-    548   1   1643   1642   1644
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-    554   1   1661   1660   1662
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-    566   1   1697   1696   1698
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-    568   1   1703   1702   1704
-    569   1   1706   1705   1707
-    570   1   1709   1708   1710
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-    572   1   1715   1714   1716
-    573   1   1718   1717   1719
-    574   1   1721   1720   1722
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-    578   1   1733   1732   1734
-    579   1   1736   1735   1737
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-    611   1   1832   1831   1833
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-    618   1   1853   1852   1854
-    619   1   1856   1855   1857
-    620   1   1859   1858   1860
-    621   1   1862   1861   1863
-    622   1   1865   1864   1866
-    623   1   1868   1867   1869
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-    629   1   1886   1885   1887
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-    631   1   1892   1891   1893
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-    634   1   1901   1900   1902
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-    636   1   1907   1906   1908
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-    638   1   1913   1912   1914
-    639   1   1916   1915   1917
-    640   1   1919   1918   1920
-    641   1   1922   1921   1923
-    642   1   1925   1924   1926
-    643   1   1928   1927   1929
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-    645   1   1934   1933   1935
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-    648   1   1943   1942   1944
-    649   1   1946   1945   1947
-    650   1   1949   1948   1950
-    651   1   1952   1951   1953
-    652   1   1955   1954   1956
-    653   1   1958   1957   1959
-    654   1   1961   1960   1962
-    655   1   1964   1963   1965
-    656   1   1967   1966   1968
-    657   1   1970   1969   1971
-    658   1   1973   1972   1974
-    659   1   1976   1975   1977
-    660   1   1979   1978   1980
-    661   1   1982   1981   1983
-    662   1   1985   1984   1986
-    663   1   1988   1987   1989
-    664   1   1991   1990   1992
-    665   1   1994   1993   1995
-    666   1   1997   1996   1998
-    667   1   2000   1999   2001
-    668   1   2003   2002   2004
-    669   1   2006   2005   2007
-    670   1   2009   2008   2010
-    671   1   2012   2011   2013
-    672   1   2015   2014   2016
-    673   1   2018   2017   2019
-    674   1   2021   2020   2022
-    675   1   2024   2023   2025
-    676   1   2027   2026   2028
-    677   1   2030   2029   2031
-    678   1   2033   2032   2034
-    679   1   2036   2035   2037
-    680   1   2039   2038   2040
-    681   1   2042   2041   2043
-    682   1   2045   2044   2046
-    683   1   2048   2047   2049
-    684   1   2051   2050   2052
-    685   1   2054   2053   2055
-    686   1   2057   2056   2058
-    687   1   2060   2059   2061
-    688   1   2063   2062   2064
-    689   1   2066   2065   2067
-    690   1   2069   2068   2070
-    691   1   2072   2071   2073
-    692   1   2075   2074   2076
-    693   1   2078   2077   2079
-    694   1   2081   2080   2082
-    695   1   2084   2083   2085
-    696   1   2087   2086   2088
-    697   1   2090   2089   2091
-    698   1   2093   2092   2094
-    699   1   2096   2095   2097
-    700   1   2099   2098   2100
-    701   1   2102   2101   2103
-    702   1   2105   2104   2106
-    703   1   2108   2107   2109
-    704   1   2111   2110   2112
-    705   1   2114   2113   2115
-    706   1   2117   2116   2118
-    707   1   2120   2119   2121
-    708   1   2123   2122   2124
-    709   1   2126   2125   2127
-    710   1   2129   2128   2130
-    711   1   2132   2131   2133
-    712   1   2135   2134   2136
-    713   1   2138   2137   2139
-    714   1   2141   2140   2142
-    715   1   2144   2143   2145
-    716   1   2147   2146   2148
-    717   1   2150   2149   2151
-    718   1   2153   2152   2154
-    719   1   2156   2155   2157
-    720   1   2159   2158   2160
-    721   1   2162   2161   2163
-    722   1   2165   2164   2166
-    723   1   2168   2167   2169
-    724   1   2171   2170   2172
-    725   1   2174   2173   2175
-    726   1   2177   2176   2178
-    727   1   2180   2179   2181
-    728   1   2183   2182   2184
-    729   1   2186   2185   2187
-    730   1   2189   2188   2190
-    731   1   2192   2191   2193
-    732   1   2195   2194   2196
-    733   1   2198   2197   2199
-    734   1   2201   2200   2202
-    735   1   2204   2203   2205
-    736   1   2207   2206   2208
-    737   1   2210   2209   2211
-    738   1   2213   2212   2214
-    739   1   2216   2215   2217
-    740   1   2219   2218   2220
-    741   1   2222   2221   2223
-    742   1   2225   2224   2226
-    743   1   2228   2227   2229
-    744   1   2231   2230   2232
-    745   1   2234   2233   2235
-    746   1   2237   2236   2238
-    747   1   2240   2239   2241
-    748   1   2243   2242   2244
-    749   1   2246   2245   2247
-    750   1   2249   2248   2250
-    751   1   2252   2251   2253
-    752   1   2255   2254   2256
-    753   1   2258   2257   2259
-    754   1   2261   2260   2262
-    755   1   2264   2263   2265
-    756   1   2267   2266   2268
-    757   1   2270   2269   2271
-    758   1   2273   2272   2274
-    759   1   2276   2275   2277
-    760   1   2279   2278   2280
-    761   1   2282   2281   2283
-    762   1   2285   2284   2286
-    763   1   2288   2287   2289
-    764   1   2291   2290   2292
-    765   1   2294   2293   2295
-    766   1   2297   2296   2298
-    767   1   2300   2299   2301
-    768   1   2303   2302   2304
-    769   1   2306   2305   2307
-    770   1   2309   2308   2310
-    771   1   2312   2311   2313
-    772   1   2315   2314   2316
-    773   1   2318   2317   2319
-    774   1   2321   2320   2322
-    775   1   2324   2323   2325
-    776   1   2327   2326   2328
-    777   1   2330   2329   2331
-    778   1   2333   2332   2334
-    779   1   2336   2335   2337
-    780   1   2339   2338   2340
-    781   1   2342   2341   2343
-    782   1   2345   2344   2346
-    783   1   2348   2347   2349
-    784   1   2351   2350   2352
-    785   1   2354   2353   2355
-    786   1   2357   2356   2358
-    787   1   2360   2359   2361
-    788   1   2363   2362   2364
-    789   1   2366   2365   2367
-    790   1   2369   2368   2370
-    791   1   2372   2371   2373
-    792   1   2375   2374   2376
-    793   1   2378   2377   2379
-    794   1   2381   2380   2382
-    795   1   2384   2383   2385
-    796   1   2387   2386   2388
-    797   1   2390   2389   2391
-    798   1   2393   2392   2394
-    799   1   2396   2395   2397
-    800   1   2399   2398   2400
-    801   1   2402   2401   2403
-    802   1   2405   2404   2406
-    803   1   2408   2407   2409
-    804   1   2411   2410   2412
-    805   1   2414   2413   2415
-    806   1   2417   2416   2418
-    807   1   2420   2419   2421
-    808   1   2423   2422   2424
-    809   1   2426   2425   2427
-    810   1   2429   2428   2430
-    811   1   2432   2431   2433
-    812   1   2435   2434   2436
-    813   1   2438   2437   2439
-    814   1   2441   2440   2442
-    815   1   2444   2443   2445
-    816   1   2447   2446   2448
-    817   1   2450   2449   2451
-    818   1   2453   2452   2454
-    819   1   2456   2455   2457
-    820   1   2459   2458   2460
-    821   1   2462   2461   2463
-    822   1   2465   2464   2466
-    823   1   2468   2467   2469
-    824   1   2471   2470   2472
-    825   1   2474   2473   2475
-    826   1   2477   2476   2478
-    827   1   2480   2479   2481
-    828   1   2483   2482   2484
-    829   1   2486   2485   2487
-    830   1   2489   2488   2490
-    831   1   2492   2491   2493
-    832   1   2495   2494   2496
-    833   1   2498   2497   2499
-    834   1   2501   2500   2502
-    835   1   2504   2503   2505
-    836   1   2507   2506   2508
-    837   1   2510   2509   2511
-    838   1   2513   2512   2514
-    839   1   2516   2515   2517
-    840   1   2519   2518   2520
-    841   1   2522   2521   2523
-    842   1   2525   2524   2526
-    843   1   2528   2527   2529
-    844   1   2531   2530   2532
-    845   1   2534   2533   2535
-    846   1   2537   2536   2538
-    847   1   2540   2539   2541
-    848   1   2543   2542   2544
-    849   1   2546   2545   2547
-    850   1   2549   2548   2550
-    851   1   2552   2551   2553
-    852   1   2555   2554   2556
-    853   1   2558   2557   2559
-    854   1   2561   2560   2562
-    855   1   2564   2563   2565
-    856   1   2567   2566   2568
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-    859   1   2576   2575   2577
-    860   1   2579   2578   2580
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-    863   1   2588   2587   2589
-    864   1   2591   2590   2592
-    865   1   2594   2593   2595
-    866   1   2597   2596   2598
-    867   1   2600   2599   2601
-    868   1   2603   2602   2604
-    869   1   2606   2605   2607
-    870   1   2609   2608   2610
-    871   1   2612   2611   2613
-    872   1   2615   2614   2616
-    873   1   2618   2617   2619
-    874   1   2621   2620   2622
-    875   1   2624   2623   2625
-    876   1   2627   2626   2628
-    877   1   2630   2629   2631
-    878   1   2633   2632   2634
-    879   1   2636   2635   2637
-    880   1   2639   2638   2640
-    881   1   2642   2641   2643
-    882   1   2645   2644   2646
-    883   1   2648   2647   2649
-    884   1   2651   2650   2652
-    885   1   2654   2653   2655
-    886   1   2657   2656   2658
-    887   1   2660   2659   2661
-    888   1   2663   2662   2664
-    889   1   2666   2665   2667
-    890   1   2669   2668   2670
-    891   1   2672   2671   2673
-    892   1   2675   2674   2676
-    893   1   2678   2677   2679
-    894   1   2681   2680   2682
-    895   1   2684   2683   2685
-    896   1   2687   2686   2688
-    897   1   2690   2689   2691
-    898   1   2693   2692   2694
-    899   1   2696   2695   2697
-    900   1   2699   2698   2700
-    901   1   2702   2701   2703
-    902   1   2705   2704   2706
-    903   1   2708   2707   2709
-    904   1   2711   2710   2712
-    905   1   2714   2713   2715
-    906   1   2717   2716   2718
-    907   1   2720   2719   2721
-    908   1   2723   2722   2724
-    909   1   2726   2725   2727
-    910   1   2729   2728   2730
-    911   1   2732   2731   2733
-    912   1   2735   2734   2736
-    913   1   2738   2737   2739
-    914   1   2741   2740   2742
-    915   1   2744   2743   2745
-    916   1   2747   2746   2748
-    917   1   2750   2749   2751
-    918   1   2753   2752   2754
-    919   1   2756   2755   2757
-    920   1   2759   2758   2760
-    921   1   2762   2761   2763
-    922   1   2765   2764   2766
-    923   1   2768   2767   2769
-    924   1   2771   2770   2772
-    925   1   2774   2773   2775
-    926   1   2777   2776   2778
-    927   1   2780   2779   2781
-    928   1   2783   2782   2784
-    929   1   2786   2785   2787
-    930   1   2789   2788   2790
-    931   1   2792   2791   2793
-    932   1   2795   2794   2796
-    933   1   2798   2797   2799
-    934   1   2801   2800   2802
-    935   1   2804   2803   2805
-    936   1   2807   2806   2808
-    937   1   2810   2809   2811
-    938   1   2813   2812   2814
-    939   1   2816   2815   2817
-    940   1   2819   2818   2820
-    941   1   2822   2821   2823
-    942   1   2825   2824   2826
-    943   1   2828   2827   2829
-    944   1   2831   2830   2832
-    945   1   2834   2833   2835
-    946   1   2837   2836   2838
-    947   1   2840   2839   2841
-    948   1   2843   2842   2844
-    949   1   2846   2845   2847
-    950   1   2849   2848   2850
-    951   1   2852   2851   2853
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-    953   1   2858   2857   2859
-    954   1   2861   2860   2862
-    955   1   2864   2863   2865
-    956   1   2867   2866   2868
-    957   1   2870   2869   2871
-    958   1   2873   2872   2874
-    959   1   2876   2875   2877
-    960   1   2879   2878   2880
-    961   1   2882   2881   2883
-    962   1   2885   2884   2886
-    963   1   2888   2887   2889
-    964   1   2891   2890   2892
-    965   1   2894   2893   2895
-    966   1   2897   2896   2898
-    967   1   2900   2899   2901
-    968   1   2903   2902   2904
-    969   1   2906   2905   2907
-    970   1   2909   2908   2910
-    971   1   2912   2911   2913
-    972   1   2915   2914   2916
-    973   1   2918   2917   2919
-    974   1   2921   2920   2922
-    975   1   2924   2923   2925
-    976   1   2927   2926   2928
-    977   1   2930   2929   2931
-    978   1   2933   2932   2934
-    979   1   2936   2935   2937
-    980   1   2939   2938   2940
-    981   1   2942   2941   2943
-    982   1   2945   2944   2946
-    983   1   2948   2947   2949
-    984   1   2951   2950   2952
-    985   1   2954   2953   2955
-    986   1   2957   2956   2958
-    987   1   2960   2959   2961
-    988   1   2963   2962   2964
-    989   1   2966   2965   2967
-    990   1   2969   2968   2970
-    991   1   2972   2971   2973
-    992   1   2975   2974   2976
-    993   1   2978   2977   2979
-    994   1   2981   2980   2982
-    995   1   2984   2983   2985
-    996   1   2987   2986   2988
-    997   1   2990   2989   2991
-    998   1   2993   2992   2994
-    999   1   2996   2995   2997
-   1000   1   2999   2998   3000
-   1001   1   3002   3001   3003
-   1002   1   3005   3004   3006
-   1003   1   3008   3007   3009
-   1004   1   3011   3010   3012
-   1005   1   3014   3013   3015
-   1006   1   3017   3016   3018
-   1007   1   3020   3019   3021
-   1008   1   3023   3022   3024
-   1009   1   3026   3025   3027
-   1010   1   3029   3028   3030
-   1011   1   3032   3031   3033
-   1012   1   3035   3034   3036
-   1013   1   3038   3037   3039
-   1014   1   3041   3040   3042
-   1015   1   3044   3043   3045
-   1016   1   3047   3046   3048
-   1017   1   3050   3049   3051
-   1018   1   3053   3052   3054
-   1019   1   3056   3055   3057
-   1020   1   3059   3058   3060
-   1021   1   3062   3061   3063
-   1022   1   3065   3064   3066
-   1023   1   3068   3067   3069
-   1024   1   3071   3070   3072
-   1025   1   3074   3073   3075
-   1026   1   3077   3076   3078
-   1027   1   3080   3079   3081
-   1028   1   3083   3082   3084
-   1029   1   3086   3085   3087
-   1030   1   3089   3088   3090
-   1031   1   3092   3091   3093
-   1032   1   3095   3094   3096
-   1033   1   3098   3097   3099
-   1034   1   3101   3100   3102
-   1035   1   3104   3103   3105
-   1036   1   3107   3106   3108
-   1037   1   3110   3109   3111
-   1038   1   3113   3112   3114
-   1039   1   3116   3115   3117
-   1040   1   3119   3118   3120
-   1041   1   3122   3121   3123
-   1042   1   3125   3124   3126
-   1043   1   3128   3127   3129
-   1044   1   3131   3130   3132
-   1045   1   3134   3133   3135
-   1046   1   3137   3136   3138
-   1047   1   3140   3139   3141
-   1048   1   3143   3142   3144
-   1049   1   3146   3145   3147
-   1050   1   3149   3148   3150
-   1051   1   3152   3151   3153
-   1052   1   3155   3154   3156
-   1053   1   3158   3157   3159
-   1054   1   3161   3160   3162
-   1055   1   3164   3163   3165
-   1056   1   3167   3166   3168
-   1057   1   3170   3169   3171
-   1058   1   3173   3172   3174
-   1059   1   3176   3175   3177
-   1060   1   3179   3178   3180
-   1061   1   3182   3181   3183
-   1062   1   3185   3184   3186
-   1063   1   3188   3187   3189
-   1064   1   3191   3190   3192
-   1065   1   3194   3193   3195
-   1066   1   3197   3196   3198
-   1067   1   3200   3199   3201
-   1068   1   3203   3202   3204
-   1069   1   3206   3205   3207
-   1070   1   3209   3208   3210
-   1071   1   3212   3211   3213
-   1072   1   3215   3214   3216
-   1073   1   3218   3217   3219
-   1074   1   3221   3220   3222
-   1075   1   3224   3223   3225
-   1076   1   3227   3226   3228
-   1077   1   3230   3229   3231
-   1078   1   3233   3232   3234
-   1079   1   3236   3235   3237
-   1080   1   3239   3238   3240
-   1081   1   3242   3241   3243
-   1082   1   3245   3244   3246
-   1083   1   3248   3247   3249
-   1084   1   3251   3250   3252
-   1085   1   3254   3253   3255
-   1086   1   3257   3256   3258
-   1087   1   3260   3259   3261
-   1088   1   3263   3262   3264
-   1089   1   3266   3265   3267
-   1090   1   3269   3268   3270
-   1091   1   3272   3271   3273
-   1092   1   3275   3274   3276
-   1093   1   3278   3277   3279
-   1094   1   3281   3280   3282
-   1095   1   3284   3283   3285
-   1096   1   3287   3286   3288
-   1097   1   3290   3289   3291
-   1098   1   3293   3292   3294
-   1099   1   3296   3295   3297
-   1100   1   3299   3298   3300
-   1101   1   3302   3301   3303
-   1102   1   3305   3304   3306
-   1103   1   3308   3307   3309
-   1104   1   3311   3310   3312
-   1105   1   3314   3313   3315
-   1106   1   3317   3316   3318
-   1107   1   3320   3319   3321
-   1108   1   3323   3322   3324
-   1109   1   3326   3325   3327
-   1110   1   3329   3328   3330
-   1111   1   3332   3331   3333
-   1112   1   3335   3334   3336
-   1113   1   3338   3337   3339
-   1114   1   3341   3340   3342
-   1115   1   3344   3343   3345
-   1116   1   3347   3346   3348
-   1117   1   3350   3349   3351
-   1118   1   3353   3352   3354
-   1119   1   3356   3355   3357
-   1120   1   3359   3358   3360
-   1121   1   3362   3361   3363
-   1122   1   3365   3364   3366
-   1123   1   3368   3367   3369
-   1124   1   3371   3370   3372
-   1125   1   3374   3373   3375
-   1126   1   3377   3376   3378
-   1127   1   3380   3379   3381
-   1128   1   3383   3382   3384
-   1129   1   3386   3385   3387
-   1130   1   3389   3388   3390
-   1131   1   3392   3391   3393
-   1132   1   3395   3394   3396
-   1133   1   3398   3397   3399
-   1134   1   3401   3400   3402
-   1135   1   3404   3403   3405
-   1136   1   3407   3406   3408
-   1137   1   3410   3409   3411
-   1138   1   3413   3412   3414
-   1139   1   3416   3415   3417
-   1140   1   3419   3418   3420
-   1141   1   3422   3421   3423
-   1142   1   3425   3424   3426
-   1143   1   3428   3427   3429
-   1144   1   3431   3430   3432
-   1145   1   3434   3433   3435
-   1146   1   3437   3436   3438
-   1147   1   3440   3439   3441
-   1148   1   3443   3442   3444
-   1149   1   3446   3445   3447
-   1150   1   3449   3448   3450
-   1151   1   3452   3451   3453
-   1152   1   3455   3454   3456
-   1153   1   3458   3457   3459
-   1154   1   3461   3460   3462
-   1155   1   3464   3463   3465
-   1156   1   3467   3466   3468
-   1157   1   3470   3469   3471
-   1158   1   3473   3472   3474
-   1159   1   3476   3475   3477
-   1160   1   3479   3478   3480
-   1161   1   3482   3481   3483
-   1162   1   3485   3484   3486
-   1163   1   3488   3487   3489
-   1164   1   3491   3490   3492
-   1165   1   3494   3493   3495
-   1166   1   3497   3496   3498
-   1167   1   3500   3499   3501
-   1168   1   3503   3502   3504
-   1169   1   3506   3505   3507
-   1170   1   3509   3508   3510
-   1171   1   3512   3511   3513
-   1172   1   3515   3514   3516
-   1173   1   3518   3517   3519
-   1174   1   3521   3520   3522
-   1175   1   3524   3523   3525
-   1176   1   3527   3526   3528
-   1177   1   3530   3529   3531
-   1178   1   3533   3532   3534
-   1179   1   3536   3535   3537
-   1180   1   3539   3538   3540
-   1181   1   3542   3541   3543
-   1182   1   3545   3544   3546
-   1183   1   3548   3547   3549
-   1184   1   3551   3550   3552
-   1185   1   3554   3553   3555
-   1186   1   3557   3556   3558
-   1187   1   3560   3559   3561
-   1188   1   3563   3562   3564
-   1189   1   3566   3565   3567
-   1190   1   3569   3568   3570
-   1191   1   3572   3571   3573
-   1192   1   3575   3574   3576
-   1193   1   3578   3577   3579
-   1194   1   3581   3580   3582
-   1195   1   3584   3583   3585
-   1196   1   3587   3586   3588
-   1197   1   3590   3589   3591
-   1198   1   3593   3592   3594
-   1199   1   3596   3595   3597
-   1200   1   3599   3598   3600
-   1201   1   3602   3601   3603
-   1202   1   3605   3604   3606
-   1203   1   3608   3607   3609
-   1204   1   3611   3610   3612
-   1205   1   3614   3613   3615
-   1206   1   3617   3616   3618
-   1207   1   3620   3619   3621
-   1208   1   3623   3622   3624
-   1209   1   3626   3625   3627
-   1210   1   3629   3628   3630
-   1211   1   3632   3631   3633
-   1212   1   3635   3634   3636
-   1213   1   3638   3637   3639
-   1214   1   3641   3640   3642
-   1215   1   3644   3643   3645
-   1216   1   3647   3646   3648
-   1217   1   3650   3649   3651
-   1218   1   3653   3652   3654
-   1219   1   3656   3655   3657
-   1220   1   3659   3658   3660
-   1221   1   3662   3661   3663
-   1222   1   3665   3664   3666
-   1223   1   3668   3667   3669
-   1224   1   3671   3670   3672
-   1225   1   3674   3673   3675
-   1226   1   3677   3676   3678
-   1227   1   3680   3679   3681
-   1228   1   3683   3682   3684
-   1229   1   3686   3685   3687
-   1230   1   3689   3688   3690
-   1231   1   3692   3691   3693
-   1232   1   3695   3694   3696
-   1233   1   3698   3697   3699
-   1234   1   3701   3700   3702
-   1235   1   3704   3703   3705
-   1236   1   3707   3706   3708
-   1237   1   3710   3709   3711
-   1238   1   3713   3712   3714
-   1239   1   3716   3715   3717
-   1240   1   3719   3718   3720
-   1241   1   3722   3721   3723
-   1242   1   3725   3724   3726
-   1243   1   3728   3727   3729
-   1244   1   3731   3730   3732
-   1245   1   3734   3733   3735
-   1246   1   3737   3736   3738
-   1247   1   3740   3739   3741
-   1248   1   3743   3742   3744
-   1249   1   3746   3745   3747
-   1250   1   3749   3748   3750
-   1251   1   3752   3751   3753
-   1252   1   3755   3754   3756
-   1253   1   3758   3757   3759
-   1254   1   3761   3760   3762
-   1255   1   3764   3763   3765
-   1256   1   3767   3766   3768
-   1257   1   3770   3769   3771
-   1258   1   3773   3772   3774
-   1259   1   3776   3775   3777
-   1260   1   3779   3778   3780
-   1261   1   3782   3781   3783
-   1262   1   3785   3784   3786
-   1263   1   3788   3787   3789
-   1264   1   3791   3790   3792
-   1265   1   3794   3793   3795
-   1266   1   3797   3796   3798
-   1267   1   3800   3799   3801
-   1268   1   3803   3802   3804
-   1269   1   3806   3805   3807
-   1270   1   3809   3808   3810
-   1271   1   3812   3811   3813
-   1272   1   3815   3814   3816
-   1273   1   3818   3817   3819
-   1274   1   3821   3820   3822
-   1275   1   3824   3823   3825
-   1276   1   3827   3826   3828
-   1277   1   3830   3829   3831
-   1278   1   3833   3832   3834
-   1279   1   3836   3835   3837
-   1280   1   3839   3838   3840
-   1281   1   3842   3841   3843
-   1282   1   3845   3844   3846
-   1283   1   3848   3847   3849
-   1284   1   3851   3850   3852
-   1285   1   3854   3853   3855
-   1286   1   3857   3856   3858
-   1287   1   3860   3859   3861
-   1288   1   3863   3862   3864
-   1289   1   3866   3865   3867
-   1290   1   3869   3868   3870
-   1291   1   3872   3871   3873
-   1292   1   3875   3874   3876
-   1293   1   3878   3877   3879
-   1294   1   3881   3880   3882
-   1295   1   3884   3883   3885
-   1296   1   3887   3886   3888
-   1297   1   3890   3889   3891
-   1298   1   3893   3892   3894
-   1299   1   3896   3895   3897
-   1300   1   3899   3898   3900
-   1301   1   3902   3901   3903
-   1302   1   3905   3904   3906
-   1303   1   3908   3907   3909
-   1304   1   3911   3910   3912
-   1305   1   3914   3913   3915
-   1306   1   3917   3916   3918
-   1307   1   3920   3919   3921
-   1308   1   3923   3922   3924
-   1309   1   3926   3925   3927
-   1310   1   3929   3928   3930
-   1311   1   3932   3931   3933
-   1312   1   3935   3934   3936
-   1313   1   3938   3937   3939
-   1314   1   3941   3940   3942
-   1315   1   3944   3943   3945
-   1316   1   3947   3946   3948
-   1317   1   3950   3949   3951
-   1318   1   3953   3952   3954
-   1319   1   3956   3955   3957
-   1320   1   3959   3958   3960
-   1321   1   3962   3961   3963
-   1322   1   3965   3964   3966
-   1323   1   3968   3967   3969
-   1324   1   3971   3970   3972
-   1325   1   3974   3973   3975
-   1326   1   3977   3976   3978
-   1327   1   3980   3979   3981
-   1328   1   3983   3982   3984
-   1329   1   3986   3985   3987
-   1330   1   3989   3988   3990
-   1331   1   3992   3991   3993
-   1332   1   3995   3994   3996
-   1333   1   3998   3997   3999
-   1334   1   4001   4000   4002
-   1335   1   4004   4003   4005
-   1336   1   4007   4006   4008
-   1337   1   4010   4009   4011
-   1338   1   4013   4012   4014
-   1339   1   4016   4015   4017
-   1340   1   4019   4018   4020
-   1341   1   4022   4021   4023
-   1342   1   4025   4024   4026
-   1343   1   4028   4027   4029
-   1344   1   4031   4030   4032
-   1345   1   4034   4033   4035
-   1346   1   4037   4036   4038
-   1347   1   4040   4039   4041
-   1348   1   4043   4042   4044
-   1349   1   4046   4045   4047
-   1350   1   4049   4048   4050
-   1351   1   4052   4051   4053
-   1352   1   4055   4054   4056
-   1353   1   4058   4057   4059
-   1354   1   4061   4060   4062
-   1355   1   4064   4063   4065
-   1356   1   4067   4066   4068
-   1357   1   4070   4069   4071
-   1358   1   4073   4072   4074
-   1359   1   4076   4075   4077
-   1360   1   4079   4078   4080
-   1361   1   4082   4081   4083
-   1362   1   4085   4084   4086
-   1363   1   4088   4087   4089
-   1364   1   4091   4090   4092
-   1365   1   4094   4093   4095
-   1366   1   4097   4096   4098
-   1367   1   4100   4099   4101
-   1368   1   4103   4102   4104
-   1369   1   4106   4105   4107
-   1370   1   4109   4108   4110
-   1371   1   4112   4111   4113
-   1372   1   4115   4114   4116
-   1373   1   4118   4117   4119
-   1374   1   4121   4120   4122
-   1375   1   4124   4123   4125
-   1376   1   4127   4126   4128
-   1377   1   4130   4129   4131
-   1378   1   4133   4132   4134
-   1379   1   4136   4135   4137
-   1380   1   4139   4138   4140
-   1381   1   4142   4141   4143
-   1382   1   4145   4144   4146
-   1383   1   4148   4147   4149
-   1384   1   4151   4150   4152
-   1385   1   4154   4153   4155
-   1386   1   4157   4156   4158
-   1387   1   4160   4159   4161
-   1388   1   4163   4162   4164
-   1389   1   4166   4165   4167
-   1390   1   4169   4168   4170
-   1391   1   4172   4171   4173
-   1392   1   4175   4174   4176
-   1393   1   4178   4177   4179
-   1394   1   4181   4180   4182
-   1395   1   4184   4183   4185
-   1396   1   4187   4186   4188
-   1397   1   4190   4189   4191
-   1398   1   4193   4192   4194
-   1399   1   4196   4195   4197
-   1400   1   4199   4198   4200
-   1401   1   4202   4201   4203
-   1402   1   4205   4204   4206
-   1403   1   4208   4207   4209
-   1404   1   4211   4210   4212
-   1405   1   4214   4213   4215
-   1406   1   4217   4216   4218
-   1407   1   4220   4219   4221
-   1408   1   4223   4222   4224
-   1409   1   4226   4225   4227
-   1410   1   4229   4228   4230
-   1411   1   4232   4231   4233
-   1412   1   4235   4234   4236
-   1413   1   4238   4237   4239
-   1414   1   4241   4240   4242
-   1415   1   4244   4243   4245
-   1416   1   4247   4246   4248
-   1417   1   4250   4249   4251
-   1418   1   4253   4252   4254
-   1419   1   4256   4255   4257
-   1420   1   4259   4258   4260
-   1421   1   4262   4261   4263
-   1422   1   4265   4264   4266
-   1423   1   4268   4267   4269
-   1424   1   4271   4270   4272
-   1425   1   4274   4273   4275
-   1426   1   4277   4276   4278
-   1427   1   4280   4279   4281
-   1428   1   4283   4282   4284
-   1429   1   4286   4285   4287
-   1430   1   4289   4288   4290
-   1431   1   4292   4291   4293
-   1432   1   4295   4294   4296
-   1433   1   4298   4297   4299
-   1434   1   4301   4300   4302
-   1435   1   4304   4303   4305
-   1436   1   4307   4306   4308
-   1437   1   4310   4309   4311
-   1438   1   4313   4312   4314
-   1439   1   4316   4315   4317
-   1440   1   4319   4318   4320
-   1441   1   4322   4321   4323
-   1442   1   4325   4324   4326
-   1443   1   4328   4327   4329
-   1444   1   4331   4330   4332
-   1445   1   4334   4333   4335
-   1446   1   4337   4336   4338
-   1447   1   4340   4339   4341
-   1448   1   4343   4342   4344
-   1449   1   4346   4345   4347
-   1450   1   4349   4348   4350
-   1451   1   4352   4351   4353
-   1452   1   4355   4354   4356
-   1453   1   4358   4357   4359
-   1454   1   4361   4360   4362
-   1455   1   4364   4363   4365
-   1456   1   4367   4366   4368
-   1457   1   4370   4369   4371
-   1458   1   4373   4372   4374
-   1459   1   4376   4375   4377
-   1460   1   4379   4378   4380
-   1461   1   4382   4381   4383
-   1462   1   4385   4384   4386
-   1463   1   4388   4387   4389
-   1464   1   4391   4390   4392
-   1465   1   4394   4393   4395
-   1466   1   4397   4396   4398
-   1467   1   4400   4399   4401
-   1468   1   4403   4402   4404
-   1469   1   4406   4405   4407
-   1470   1   4409   4408   4410
-   1471   1   4412   4411   4413
-   1472   1   4415   4414   4416
-   1473   1   4418   4417   4419
-   1474   1   4421   4420   4422
-   1475   1   4424   4423   4425
-   1476   1   4427   4426   4428
-   1477   1   4430   4429   4431
-   1478   1   4433   4432   4434
-   1479   1   4436   4435   4437
-   1480   1   4439   4438   4440
-   1481   1   4442   4441   4443
-   1482   1   4445   4444   4446
-   1483   1   4448   4447   4449
-   1484   1   4451   4450   4452
-   1485   1   4454   4453   4455
-   1486   1   4457   4456   4458
-   1487   1   4460   4459   4461
-   1488   1   4463   4462   4464
-   1489   1   4466   4465   4467
-   1490   1   4469   4468   4470
-   1491   1   4472   4471   4473
-   1492   1   4475   4474   4476
-   1493   1   4478   4477   4479
-   1494   1   4481   4480   4482
-   1495   1   4484   4483   4485
-   1496   1   4487   4486   4488
-   1497   1   4490   4489   4491
-   1498   1   4493   4492   4494
-   1499   1   4496   4495   4497
-   1500   1   4499   4498   4500
diff --git a/examples/water/data_file b/examples/water/data_file
deleted file mode 100644
index 2f9d10f9d9..0000000000
--- a/examples/water/data_file
+++ /dev/null
@@ -1,19 +0,0 @@
-#  data
-
-3 atoms
-
-1 atom types
-
--10 10 xlo xhi
--10 10 ylo yhi
--10 10 zlo zhi
-
-Masses
-
-1 1.00794
-
-Atoms
-
-1 1 0 0 0
-2 1 1.5 0 0
-3 1 0 1.5 0
diff --git a/examples/water/in_massive b/examples/water/in_massive
deleted file mode 100644
index 22d4e0c661..0000000000
--- a/examples/water/in_massive
+++ /dev/null
@@ -1,80 +0,0 @@
-#LAMMPS input file
-#All informations can be find on http://lammps.sandia.gov/
-
-#choose the system of unit (real, metal, SI...)
-units           real
-
-#define the boundary conditions, periodic here
-boundary        p p p
-
-#define the atom style, bond style and angle style
-atom_style      full
-bond_style      harmonic
-angle_style     harmonic
-atom_modify	map array
-
-#comm_modify cutoff 15
-#atom_modify first water
-#neigh_modify cluster yes
-
-#choose the interaction between water molecules:
-pair_style		lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 
-pair_modify		table 0
-#water model is TIP4P/2005
-#water molecules less than 1nm from each other interact via a cut lennard jones potential 
-#water molecules interact via coulomb interactions calculated in real or conjugate space depending on the distance separating molecules
-
-#define the long-range solver (here for long range coulombic interaction)
-suffix off
-newton on
-kspace_style	pppm/tip4p 1.0e-5
-suffix on
-
-#neighbor 5.0 bin
-#neigh_modify	every 1 check yes
-
-#import the initial position of atoms, the coordinates of the box, etc
-read_data	data.spce
-replicate 2 2 2
-
-#define the pair coeff for LJ interaction
-pair_coeff      * * 0.0 0.0
-pair_coeff      1 1 0.1852 3.1589
-
-#define the coef for water molecule (distances between O-H and angle between H-O-H atoms)
-bond_coeff      1 0.0 0.9572
-angle_coeff     1 0.0 104.52
-
-#define groups
-group		water type 1 2
-
-#maintain the water molecule rigid
-fix             1 water shake 1.0e-4 200 0 b 1 a 1
-
-#udate position and velocity each timesteps using constant NVE integration
-fix		2 water nve
-
-#apply Langevin thermostat on water molecules
-#fix             3 water langevin 300.0 300.0 100.0 123
-
-#choose how often you want thermodynamic info to be print during the computation
-thermo          1000
-thermo_modify   flush yes
-thermo_style custom step etotal ke pe temp  evdwl ecoul elong press
-#thermo_modify  format float "%.15g"
-#give an initial random velocity to water molecule (corresponding to a temperature equal to 300K)
-velocity		water create 300 123
-
-#print the position of atoms to visualise it with VMD for example
-#dump			4 all atom 1 dump.lammpstrj
-#dump_modify		4 flush yes
-
-#if $(is_active(package,gpu)) &
-# then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz"&
-# else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
-
-#choose the timestep, 2fs is a common choice
-timestep		1
-
-#run during 50000 timestep (0.1 ns)
-run		50000

From 7d16783366c33dc19e8cf1afb67d005dfa5f567f Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Thu, 19 Dec 2019 09:31:30 -0700
Subject: [PATCH 125/199] Fix issue in Kokkos minimize

---
 src/min.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/min.h b/src/min.h
index fe7f0be8c6..ba47f95410 100644
--- a/src/min.h
+++ b/src/min.h
@@ -39,9 +39,9 @@ class Min : protected Pointers {
   virtual bigint memory_usage() {return 0;}
   void modify_params(int, char **);
   virtual int modify_param(int, char **) {return 0;}
-  double fnorm_sqr();
-  double fnorm_inf();
-  double fnorm_max();
+  virtual double fnorm_sqr();
+  virtual double fnorm_inf();
+  virtual double fnorm_max();
 
   enum{TWO,MAX,INF};
 

From 92b2e4256b474f1e564a2918faad92c06a14beab Mon Sep 17 00:00:00 2001
From: Jianhua Pan <lucien.pan0927@gmail.com>
Date: Mon, 2 Dec 2019 23:07:58 -0500
Subject: [PATCH 126/199] Bug fix for lj/class2/coul/long/gpu

---
 src/CLASS2/pair_lj_class2_coul_long.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp
index 1544232e49..0bb802579c 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_long.cpp
@@ -48,6 +48,7 @@ PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp)
   respa_enable = 1;
   writedata = 1;
   ftable = NULL;
+  cut_respa = NULL;
 }
 
 /* ---------------------------------------------------------------------- */

From a11b886b5c39e42c51686e31945b1fdf5394f85f Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Thu, 19 Dec 2019 16:17:14 -0700
Subject: [PATCH 127/199] add warning if gravity is used incorrectly with
 overlapped rigid bodies

---
 src/RIGID/fix_rigid.cpp       | 17 +++++++++++++++++
 src/RIGID/fix_rigid_small.cpp | 17 +++++++++++++++++
 2 files changed, 34 insertions(+)

diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 5e994810ac..d852a47381 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -728,6 +728,23 @@ void FixRigid::init()
     }
   }
 
+  // warn if body properties are read from inpfile
+  //   and the gravity keyword is not set and a gravity fix exists
+  // this could mean body particles are overlapped
+  //   and gravity is not applied correctly
+
+  if (inpfile && !id_gravity) {
+    for (i = 0; i < modify->nfix; i++) {
+      if (strcmp(modify->fix[i]->style,"gravity") == 0) {
+        if (comm->me == 0) 
+          error->warning(FLERR,"Gravity may not be correctly applied "
+                         "to rigid bodies if they consist of "
+                         "overlapped particles");
+        break;
+      }
+    }
+  }
+
   // error if npt,nph fix comes before rigid fix
 
   for (i = 0; i < modify->nfix; i++) {
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 4d2776b9ff..cbdc877d09 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -574,6 +574,23 @@ void FixRigidSmall::init()
     }
   }
 
+  // warn if body properties are read from inpfile or a mol template file
+  //   and the gravity keyword is not set and a gravity fix exists
+  // this could mean body particles are overlapped
+  //   and gravity is not applied correctly
+
+  if ((inpfile || onemols) && !id_gravity) {
+    for (i = 0; i < modify->nfix; i++) {
+      if (strcmp(modify->fix[i]->style,"gravity") == 0) {
+        if (comm->me == 0) 
+          error->warning(FLERR,"Gravity may not be correctly applied "
+                         "to rigid bodies if they consist of "
+                         "overlapped particles");
+        break;
+      }
+    }
+  }
+
   // error if npt,nph fix comes before rigid fix
 
   for (i = 0; i < modify->nfix; i++) {

From 21f454c040d11fec1d8f27cbda10efc763a4db2d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 20 Dec 2019 03:48:08 -0500
Subject: [PATCH 128/199] correct truncated AlCu.bop.table potential file from
 Xiaoweng Zhou

---
 potentials/AlCu.bop.table | 361 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 358 insertions(+), 3 deletions(-)

diff --git a/potentials/AlCu.bop.table b/potentials/AlCu.bop.table
index cc74dbb62a..8e19658c62 100644
--- a/potentials/AlCu.bop.table
+++ b/potentials/AlCu.bop.table
@@ -1,4 +1,4 @@
-# DATE: 2015-07-06 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, Don Ward, donward@sandia.gov, CITATION: Zhou, Ward, and Foster, Phys. Chem. Chem. Phys., under consideration
+# DATE: 2015-07-06 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, Don Ward, donward@sandia.gov, CITATION: Zhou, Ward, and Foster, J. Alloys Compd., 680, 752 (2016).
     2
    13  2.69800000e+01 Al
    29  6.35500000e+01 Cu
@@ -4835,7 +4835,7 @@
   0.00000000e+00
   0.00000000e+00
   0.00000000e+00
-  4.90000000e+00
+  0.00000000e+00
   0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
@@ -5681,4 +5681,359 @@
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
-  0.00000000e+00  0.00000000e+00  
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
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+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
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+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00

From c8a53d560a55748744d6f7c5f468976843663232 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20H=C3=B6rmann?=
 <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 18 Dec 2019 12:09:21 +0100
Subject: [PATCH 129/199] Find parallel NetCDF with cmake for USER-NETCDF

Conflicts:
	cmake/presets/forhlr2-gnu.cmake
---
 cmake/Modules/FindNetCDF.cmake           |  6 ++-
 cmake/Modules/FindPNetCDF.cmake          | 55 ++++++++++++++++++++++++
 cmake/Modules/Packages/USER-NETCDF.cmake | 26 +++++++++--
 3 files changed, 82 insertions(+), 5 deletions(-)
 create mode 100644 cmake/Modules/FindPNetCDF.cmake

diff --git a/cmake/Modules/FindNetCDF.cmake b/cmake/Modules/FindNetCDF.cmake
index a28c959acf..3d4aed947d 100644
--- a/cmake/Modules/FindNetCDF.cmake
+++ b/cmake/Modules/FindNetCDF.cmake
@@ -46,10 +46,14 @@ endif()
 find_path (NETCDF_INCLUDE_DIR netcdf.h
   HINTS "${NETCDF_DIR}/include")
 mark_as_advanced (NETCDF_INCLUDE_DIR)
+
 set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 
+string(REGEX REPLACE "/include/?$" "/lib"
+  NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
+
 find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib")
+  HINTS "${NETCDF_DIR}/lib" "${NETCDF_LIB_HINT}")
 mark_as_advanced (NETCDF_LIBRARY)
 
 set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
new file mode 100644
index 0000000000..0cc2c1faa8
--- /dev/null
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -0,0 +1,55 @@
+# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake
+# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)
+#
+# - Find PNetCDF
+# Find the native PNetCDF includes and library
+#
+#  PNETCDF_INCLUDES    - where to find netcdf.h, etc
+#  PNETCDF_LIBRARIES   - Link these libraries when using NetCDF
+#  PNETCDF_FOUND       - True if PNetCDF was found
+#
+# Normal usage would be:
+#  find_package (PNetCDF REQUIRED)
+#  target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})
+
+if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+  # Already in cache, be silent
+  set (PNETCDF_FIND_QUIETLY TRUE)
+endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+
+find_path (PNETCDF_INCLUDES pnetcdf.h
+  HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
+
+string(REGEX REPLACE "/include/?$" "/lib"
+  PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
+
+find_library (PNETCDF_LIBRARIES
+  NAMES pnetcdf
+  HINTS ${PNETCDF_LIB_HINT})
+
+if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
+  message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")
+
+  file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)
+
+  find_library(PNETCDF_LIBRARIES
+    NAMES pnetcdf
+    HINTS ${LD_LIBRARY_PATH})
+
+  if (PNETCDF_LIBRARIES)
+    get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
+    string(REGEX REPLACE "/lib/?$" "/include"
+      PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
+
+    find_path (PNETCDF_INCLUDES pnetcdf.h
+      HINTS ${PNETCDF_H_HINT}
+      DOC "Path to pnetcdf.h")
+  endif()
+endif()
+
+# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
+
+mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)
diff --git a/cmake/Modules/Packages/USER-NETCDF.cmake b/cmake/Modules/Packages/USER-NETCDF.cmake
index a90725bbbc..f60c046ab9 100644
--- a/cmake/Modules/Packages/USER-NETCDF.cmake
+++ b/cmake/Modules/Packages/USER-NETCDF.cmake
@@ -1,6 +1,24 @@
 if(PKG_USER-NETCDF)
-  find_package(NetCDF REQUIRED)
-  include_directories(${NETCDF_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
-  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+  # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
+  # NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
+  find_package(NetCDF)
+  if(NETCDF_FOUND)
+    find_package(PNetCDF)
+  else(NETCDF_FOUND)
+    find_package(PNetCDF REQUIRED)
+  endif(NETCDF_FOUND)
+
+  if(NETCDF_FOUND)
+    include_directories(${NETCDF_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_NETCDF)
+  endif(NETCDF_FOUND)
+
+  if(PNETCDF_FOUND)
+    include_directories(${PNETCDF_INCLUDES})
+    list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_PNETCDF)
+  endif(PNETCDF_FOUND)
+
+  add_definitions(-DNC_64BIT_DATA=0x0020)
 endif()

From 3b76ab56f05c705fc71952a1709e97a1898b4ddc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 20 Dec 2019 12:09:50 -0500
Subject: [PATCH 130/199] port gravity changes to rigid fixes to USER-OMP
 package versions

---
 src/USER-OMP/fix_rigid_nh_omp.cpp    | 13 +++++++++++++
 src/USER-OMP/fix_rigid_omp.cpp       | 13 +++++++++++++
 src/USER-OMP/fix_rigid_small_omp.cpp | 15 +++++++++++++++
 3 files changed, 41 insertions(+)

diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp
index d92a82a6bf..da512cb428 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nh_omp.cpp
@@ -383,6 +383,19 @@ void FixRigidNHOMP::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+    for (ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 20d3009d40..1cdf1018b2 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -256,6 +256,19 @@ void FixRigidOMP::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+    for (int ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index 705f0e6bd0..bdd10b0ca7 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -196,6 +196,21 @@ void FixRigidSmallOMP::compute_forces_and_torques()
       tcm[2] += langextra[ibody][5];
     }
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+    for (int ibody = 0; ibody < nbody; ibody++) {
+      double * _noalias const fcm = body[ibody].fcm;
+      const double mass = body[ibody].mass;
+      fcm[0] += gvec[0]*mass;
+      fcm[1] += gvec[1]*mass;
+      fcm[2] += gvec[2]*mass;
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */

From a88a00dbbb86fdcc2b4ed7bde34f50180bbaa89d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 20 Dec 2019 15:08:51 -0500
Subject: [PATCH 131/199] remove trailing whitespace

---
 src/RIGID/fix_rigid.cpp       | 6 +++---
 src/RIGID/fix_rigid_small.cpp | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index d852a47381..101b94c2a4 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -52,7 +52,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),
   tflag(NULL), langextra(NULL), sum(NULL), all(NULL),
   remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),
-  dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL), 
+  dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL),
   avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL)
 {
   int i,ibody;
@@ -736,7 +736,7 @@ void FixRigid::init()
   if (inpfile && !id_gravity) {
     for (i = 0; i < modify->nfix; i++) {
       if (strcmp(modify->fix[i]->style,"gravity") == 0) {
-        if (comm->me == 0) 
+        if (comm->me == 0)
           error->warning(FLERR,"Gravity may not be correctly applied "
                          "to rigid bodies if they consist of "
                          "overlapped particles");
@@ -763,7 +763,7 @@ void FixRigid::init()
   if (id_gravity) {
     int ifix = modify->find_fix(id_gravity);
     if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");
-    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
       error->all(FLERR,"Fix rigid gravity fix is invalid");
     int tmp;
     gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index cbdc877d09..33105418ff 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -582,7 +582,7 @@ void FixRigidSmall::init()
   if ((inpfile || onemols) && !id_gravity) {
     for (i = 0; i < modify->nfix; i++) {
       if (strcmp(modify->fix[i]->style,"gravity") == 0) {
-        if (comm->me == 0) 
+        if (comm->me == 0)
           error->warning(FLERR,"Gravity may not be correctly applied "
                          "to rigid bodies if they consist of "
                          "overlapped particles");
@@ -608,7 +608,7 @@ void FixRigidSmall::init()
   if (id_gravity) {
     int ifix = modify->find_fix(id_gravity);
     if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");
-    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
       error->all(FLERR,"Fix rigid/small gravity fix is invalid");
     int tmp;
     gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);

From a72f53e367eaa42e25f11ff835eb72c863e1fc0e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 21 Dec 2019 16:18:26 -0500
Subject: [PATCH 132/199] add stan/steve as code owners for minimizer changes

---
 .github/CODEOWNERS | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 7d1f1a417b..a4fc5b7b4f 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -111,6 +111,7 @@ src/exceptions.h          @rbberger
 src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
+src/min*                  @sjplimp @stanmoore1
 
 # tools
 tools/msi2lmp/*       @akohlmey

From 4e7bcee8e386dd6c467aa8cd9ef04214a227be22 Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Sun, 22 Dec 2019 13:24:34 +0100
Subject: [PATCH 133/199] Update cmake/Modules/FindNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindNetCDF.cmake b/cmake/Modules/FindNetCDF.cmake
index 3d4aed947d..4181e3f027 100644
--- a/cmake/Modules/FindNetCDF.cmake
+++ b/cmake/Modules/FindNetCDF.cmake
@@ -53,7 +53,7 @@ string(REGEX REPLACE "/include/?$" "/lib"
   NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
 
 find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib" "${NETCDF_LIB_HINT}")
+  HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)
 mark_as_advanced (NETCDF_LIBRARY)
 
 set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})

From 0c7d6a01e8f93669f94170acbc335c128058f7fe Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Sun, 22 Dec 2019 13:25:08 +0100
Subject: [PATCH 134/199] Update cmake/Modules/FindNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindNetCDF.cmake b/cmake/Modules/FindNetCDF.cmake
index 4181e3f027..2a992b6b3b 100644
--- a/cmake/Modules/FindNetCDF.cmake
+++ b/cmake/Modules/FindNetCDF.cmake
@@ -49,7 +49,7 @@ mark_as_advanced (NETCDF_INCLUDE_DIR)
 
 set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 
-string(REGEX REPLACE "/include/?$" "/lib"
+string(REGEX REPLACE "/include/?$" ""
   NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
 
 find_library (NETCDF_LIBRARY NAMES netcdf

From 3f24144abd499042720c8d1f200a10e843f5b69a Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Sun, 22 Dec 2019 13:25:24 +0100
Subject: [PATCH 135/199] Update cmake/Modules/FindPNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindPNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
index 0cc2c1faa8..e95ed4e559 100644
--- a/cmake/Modules/FindPNetCDF.cmake
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -38,7 +38,7 @@ if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
 
   if (PNETCDF_LIBRARIES)
     get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
-    string(REGEX REPLACE "/lib/?$" "/include"
+    string(REGEX REPLACE "/(lib|lib64)/?$" "/include"
       PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
 
     find_path (PNETCDF_INCLUDES pnetcdf.h

From 337b0fd6495b30272b61af8eff27567d7daa8428 Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Sun, 22 Dec 2019 20:20:12 +0300
Subject: [PATCH 136/199] Fix 'sametag' transfer

---
 lib/gpu/lal_lj_tip4p_long.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
index 200f185e63..874cda718c 100644
--- a/lib/gpu/lal_lj_tip4p_long.cpp
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -259,9 +259,9 @@ void LJTIP4PLongT::copy_relations_data(int n, int* tag, int *map_array,
   ucl_copy(this->tag, host_tag_write, nall, false);
 
   host_tag_write.resize_ib(max_same);
-  this->atom_sametag.resize_ib(nall);
-  for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
-  ucl_copy(this->atom_sametag, host_tag_write, nall, false);
+  this->atom_sametag.resize_ib(max_same);
+  for(int i=0; i<max_same; ++i) host_tag_write[i] = sametag[i];
+  ucl_copy(this->atom_sametag, host_tag_write, max_same, false);
 
   host_tag_write.resize_ib(map_size);
   this->map_array.resize_ib(map_size);

From e11374d433895faee5b34c56e106d36f487e7075 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 3 Jan 2020 01:37:12 -0500
Subject: [PATCH 137/199] print intel package status message only once per run

---
 src/USER-INTEL/fix_intel.cpp | 5 ++++-
 src/USER-INTEL/fix_intel.h   | 4 +++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 83a22f0562..507ffa6d6f 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -63,6 +63,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) :  Fix(lmp, narg, arg)
   _three_body_neighbor = 0;
   _pair_intel_count = 0;
   _hybrid_nonpair = 0;
+  _print_pkg_info = 1;
 
   _precision_mode = PREC_MODE_MIXED;
   _offload_balance = -1.0;
@@ -290,6 +291,7 @@ int FixIntel::setmask()
   mask |= POST_FORCE;
   mask |= MIN_POST_FORCE;
   #endif
+  mask |= POST_RUN;
   return mask;
 }
 
@@ -475,7 +477,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
   set_offload_affinity();
   #endif
 
-  if (comm->me == 0) {
+  if (_print_pkg_info && comm->me == 0) {
     if (screen) {
       fprintf(screen,
               "----------------------------------------------------------\n");
@@ -498,6 +500,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
               "----------------------------------------------------------\n");
     }
   }
+  _print_pkg_info = 0;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index f23e305ca7..7c176fb069 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -54,6 +54,8 @@ class FixIntel : public Fix {
   inline void min_pre_reverse(int eflag = 0, int vflag = 0)
     { pre_reverse(eflag, vflag); }
 
+  void post_run() { _print_pkg_info = 1; }
+
   // Get all forces, calculation results from coprocesser
   void sync_coprocessor();
 
@@ -101,7 +103,7 @@ class FixIntel : public Fix {
   IntelBuffers<double,double> *_double_buffers;
 
   int _precision_mode, _nthreads, _nbor_pack_width, _three_body_neighbor;
-  int _pair_intel_count, _pair_hybrid_flag;
+  int _pair_intel_count, _pair_hybrid_flag, _print_pkg_info;
   // These should be removed in subsequent update w/ simpler hybrid arch
   int _pair_hybrid_zero, _hybrid_nonpair, _zero_master;
 

From 2f6018b099ddb58ca95d005e970fb360bc423e0a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 3 Jan 2020 01:39:35 -0500
Subject: [PATCH 138/199] use regex pattern matching to make style lookup more
 specific with less code

---
 src/USER-INTEL/fix_intel.cpp | 21 +++++----------------
 src/USER-INTEL/fix_intel.h   |  5 ++---
 2 files changed, 7 insertions(+), 19 deletions(-)

diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 507ffa6d6f..be9d0c49b0 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -312,12 +312,7 @@ void FixIntel::init()
   #endif
 
   const int nstyles = _pair_intel_count;
-  if (force->pair_match("hybrid", 1) != NULL) {
-    _pair_hybrid_flag = 1;
-    if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute)
-      error->all(FLERR,
-                 "Intel package requires fdotr virial with newton on.");
-  } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
+  if (force->pair_match("^hybrid", 0) != NULL) {
     _pair_hybrid_flag = 1;
     if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute)
       error->all(FLERR,
@@ -513,12 +508,9 @@ void FixIntel::bond_init_check()
       "USER-INTEL package requires same setting for newton bond and non-bond.");
 
   int intel_pair = 0;
-  if (force->pair_match("/intel", 0) != NULL)
+  if (force->pair_match("/intel$", 0) != NULL)
     intel_pair = 1;
-  else if (force->pair_match("hybrid", 1) != NULL) {
-    _hybrid_nonpair = 1;
-    if (_pair_intel_count) intel_pair = 1;
-  } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
+  else if (force->pair_match("^hybrid", 1) != NULL) {
     _hybrid_nonpair = 1;
     if (_pair_intel_count) intel_pair = 1;
   }
@@ -533,12 +525,9 @@ void FixIntel::bond_init_check()
 void FixIntel::kspace_init_check()
 {
   int intel_pair = 0;
-  if (force->pair_match("/intel", 0) != NULL)
+  if (force->pair_match("/intel$", 0) != NULL)
     intel_pair = 1;
-  else if (force->pair_match("hybrid", 1) != NULL) {
-    _hybrid_nonpair = 1;
-    if (_pair_intel_count) intel_pair = 1;
-  } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
+  else if (force->pair_match("^hybrid", 0) != NULL) {
     _hybrid_nonpair = 1;
     if (_pair_intel_count) intel_pair = 1;
   }
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index 7c176fb069..a699a6d2b9 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -85,13 +85,12 @@ class FixIntel : public Fix {
   }
   inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; }
   inline int lrt() {
-    if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1)
+    if (force->kspace_match("^pppm/.*intel$", 0) && update->whichflag == 1)
       return _lrt;
     else return 0;
   }
   inline int pppm_table() {
-    if (force->kspace_match("pppm/intel", 0) ||
-        force->kspace_match("pppm/disp/intel",0))
+    if (force->kspace_match("^pppm/.*intel$", 0))
       return INTEL_P3M_TABLE;
     else return 0;
   }

From a63792a07abe6a3482d1face4c315620315f7b21 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 3 Jan 2020 01:40:20 -0500
Subject: [PATCH 139/199] need to explicitly run pair_init_check() inside
 kspace_init_check() for hybrid styles

---
 src/USER-INTEL/fix_intel.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index be9d0c49b0..3d59a49acd 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -529,6 +529,7 @@ void FixIntel::kspace_init_check()
     intel_pair = 1;
   else if (force->pair_match("^hybrid", 0) != NULL) {
     _hybrid_nonpair = 1;
+    pair_init_check();     // need to run this here explicitly, since pair->init() was not run yet.
     if (_pair_intel_count) intel_pair = 1;
   }
 

From 394e5459b63f99602f0fb94b54691e23bf6eafeb Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 6 Jan 2020 15:16:08 -0500
Subject: [PATCH 140/199] correct whitespace issues in pair_meamc.cpp

---
 src/USER-MEAMC/pair_meamc.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 9733ee2dad..3d7d0b2a17 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -438,7 +438,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
     found[i] = true;
 
     // map lat string to an integer
-    
+
     if (!MEAM::str_to_lat(words[1], true, lat[i]))
       error->all(FLERR,"Unrecognized lattice type in MEAM file 1");
 
@@ -464,7 +464,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
 
     if (!isone(t0[i]))
       error->all(FLERR,"Unsupported parameter in MEAM potential file: t0!=1");
-    
+
     // z given is ignored: if this is mismatched, we definitely won't do what the user said -> fatal error
     if (z[i] != MEAM::get_Zij(lat[i]))
       error->all(FLERR,"Mismatched parameter in MEAM potential file: z!=lat");

From 5500198b4eb712c78665c17065a6cb2a6fa2163f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 6 Jan 2020 15:21:18 -0500
Subject: [PATCH 141/199] correct whitespace issue in dynamical_matrix.cpp

---
 src/USER-PHONON/dynamical_matrix.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp
index 6bb843c16e..d03a8d3ab0 100644
--- a/src/USER-PHONON/dynamical_matrix.cpp
+++ b/src/USER-PHONON/dynamical_matrix.cpp
@@ -408,7 +408,8 @@ void DynamicalMatrix::update_force()
         timer->stamp(Timer::COMM);
     }
 
-    // force modifications, 
+    // force modifications
+
     if (n_post_force) modify->post_force(vflag);
     timer->stamp(Timer::MODIFY);
 

From 8ac2da792c26b4e4fdf03895d84ad6e00226e622 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 6 Jan 2020 16:18:23 -0500
Subject: [PATCH 142/199] fix typo in fix ave/atom docs

---
 doc/src/fix_ave_atom.rst | 2 +-
 doc/txt/fix_ave_atom.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst
index 2886eb8f4e..3a066ab55b 100644
--- a/doc/src/fix_ave_atom.rst
+++ b/doc/src/fix_ave_atom.rst
@@ -88,7 +88,7 @@ command creates a per-atom array with 6 columns:
 
    compute my_stress all stress/atom NULL
    fix 1 all ave/atom 10 20 1000 c_my_stress[\*]
-   fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
+   fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[2] &
                                  c_my_stress[3] c_my_stress[4] &
                                  c_my_stress[5] c_my_stress[6]
 
diff --git a/doc/txt/fix_ave_atom.txt b/doc/txt/fix_ave_atom.txt
index 10deaf64cd..596f9ee46c 100644
--- a/doc/txt/fix_ave_atom.txt
+++ b/doc/txt/fix_ave_atom.txt
@@ -80,7 +80,7 @@ command creates a per-atom array with 6 columns:
 
 compute my_stress all stress/atom NULL
 fix 1 all ave/atom 10 20 1000 c_my_stress\[*\]
-fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[1\] &
+fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[2\] &
                               c_my_stress\[3\] c_my_stress\[4\] &
                               c_my_stress\[5\] c_my_stress\[6\] :pre
 

From 66a473455e3c6fa206c0efacccb61a8f9785e279 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 6 Jan 2020 17:34:26 -0500
Subject: [PATCH 143/199] silence warnings from generic OpenCL header files (as
 seen on Fedora 31)

---
 lib/gpu/geryon/ocl_device.h | 8 ++++++++
 lib/gpu/geryon/ocl_macros.h | 8 ++++++++
 2 files changed, 16 insertions(+)

diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h
index 14455e38a5..e414e7b69c 100644
--- a/lib/gpu/geryon/ocl_device.h
+++ b/lib/gpu/geryon/ocl_device.h
@@ -28,6 +28,14 @@
 #include <vector>
 #include <iostream>
 
+/* We default to OpenCL 1.2 as target version for now as
+ * there are known issues with OpenCL 2.0 and later.
+ * This is also to silence warnings from generic OpenCL headers */
+
+#if !defined(CL_TARGET_OPENCL_VERSION)
+#define CL_TARGET_OPENCL_VERSION 120
+#endif
+
 #ifdef __APPLE__
 #include <OpenCL/cl.h>
 #include <OpenCL/cl_platform.h>
diff --git a/lib/gpu/geryon/ocl_macros.h b/lib/gpu/geryon/ocl_macros.h
index 5fb7665817..aeff689859 100644
--- a/lib/gpu/geryon/ocl_macros.h
+++ b/lib/gpu/geryon/ocl_macros.h
@@ -4,6 +4,14 @@
 #include <cstdio>
 #include <cassert>
 
+/* We default to OpenCL 1.2 as target version for now as
+ * there are known issues with OpenCL 2.0 and later.
+ * This is also to silence warnings from generic OpenCL headers */
+
+#if !defined(CL_TARGET_OPENCL_VERSION)
+#define CL_TARGET_OPENCL_VERSION 120
+#endif
+
 #ifdef __APPLE__
 #include <OpenCL/cl.h>
 #else

From 6aa4f4caf644398b17722f546be19dd91030b0f3 Mon Sep 17 00:00:00 2001
From: "Dan S. Bolintineanu" <dsbolin@sandia.gov>
Date: Mon, 6 Jan 2020 21:18:00 -0700
Subject: [PATCH 144/199] Added example script and input data file showing
 benefits of new fix gravity and fix rigid options

---
 examples/rigid/in.rigid.gravity | 62 +++++++++++++++++++++++++++++++++
 examples/rigid/molecule.data    | 41 ++++++++++++++++++++++
 2 files changed, 103 insertions(+)
 create mode 100644 examples/rigid/in.rigid.gravity
 create mode 100644 examples/rigid/molecule.data

diff --git a/examples/rigid/in.rigid.gravity b/examples/rigid/in.rigid.gravity
new file mode 100644
index 0000000000..22abb0740e
--- /dev/null
+++ b/examples/rigid/in.rigid.gravity
@@ -0,0 +1,62 @@
+#Pour composite granular particles on flat wall
+
+newton		on
+atom_style	sphere
+atom_modify	map array sort 0 0
+
+thermo_modify	flush yes
+units 		si  
+
+variable	minrad equal 0.5
+variable	maxrad equal 1.4
+
+variable 	skin equal 0.3*${maxrad}
+
+boundary	p p f
+region		reg block 0 20 0 20 0 200 units box
+create_box	1 reg
+
+fix             prop all property/atom mol ghost yes
+
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+pair_style	gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0
+pair_coeff	* *
+
+timestep 	0.0001
+
+group		particles type 1
+atom_modify     first particles
+
+neighbor        ${skin} bin
+group		rigid type 1
+neigh_modify	every 1 delay 0 check yes exclude molecule/intra all 
+
+thermo 		${logfreq}
+thermo_style	custom step cpu atoms ke
+thermo_modify	flush yes lost warn
+
+comm_modify	vel yes cutoff 3
+
+molecule	mymol molecule.data
+region		pourreg block 5 15 5 15 80 100 side in units box
+
+#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity
+# and the 'gravity' keyword to fix rigid/small were not available.
+# These settings produce undesirable behavior, where gravity can induce
+# torque on rigid bodies.
+#fix		gravfix all gravity 9.8 vector 0 0 -1 #disable
+#fix		rigidfix all rigid/small molecule mol mymol #gravity gravfix
+
+#The correct behavior is recovered with the following settings:
+fix		gravfix all gravity 9.8 vector 0 0 -1 disable
+fix		rigidfix all rigid/small molecule mol mymol gravity gravfix
+fix		pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix
+
+fix		zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL
+
+dump		1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
+
+run		100000
+
diff --git a/examples/rigid/molecule.data b/examples/rigid/molecule.data
new file mode 100644
index 0000000000..e0677b0f63
--- /dev/null
+++ b/examples/rigid/molecule.data
@@ -0,0 +1,41 @@
+LAMMPS data file created for rigid body molecule template
+
+5 atoms
+
+2.3388800000000005 mass
+
+6.002239704473936 4.99 4.989999999999999 com
+
+116.79265620480001 144.26721336320003 144.26721336320006 -70.05220681600004 -70.05220681600002 -58.238345888000005 inertia
+
+Coords
+
+1 5 5 5
+2 5.1 5.0 5.0
+3 5.2 5.0 5.0
+4 6.2 5.0 5.0
+5 7.2 5.0 5.0
+
+Types
+
+1 1
+2 1
+3 1
+4 1
+5 1
+
+Diameters
+
+1 1.0
+2 0.9
+3 1.2
+4 1.2
+5 1.0
+
+Masses
+
+1 0.5235987755982988
+2 0.3817035074111599
+3 0.9047786842338602
+4 0.9047786842338602
+5 0.5235987755982988

From 7bc8c8e9d8e200a5303377836a94b1106dac096f Mon Sep 17 00:00:00 2001
From: "Dan S. Bolintineanu" <dsbolin@sandia.gov>
Date: Mon, 6 Jan 2020 21:26:34 -0700
Subject: [PATCH 145/199] Minor tweaks to in.rigid.gravity example

---
 examples/rigid/in.rigid.gravity | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/examples/rigid/in.rigid.gravity b/examples/rigid/in.rigid.gravity
index 22abb0740e..1094681f18 100644
--- a/examples/rigid/in.rigid.gravity
+++ b/examples/rigid/in.rigid.gravity
@@ -52,11 +52,12 @@ region		pourreg block 5 15 5 15 80 100 side in units box
 #The correct behavior is recovered with the following settings:
 fix		gravfix all gravity 9.8 vector 0 0 -1 disable
 fix		rigidfix all rigid/small molecule mol mymol gravity gravfix
+
 fix		pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix
 
 fix		zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL
 
-dump		1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
+#dump		1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
 
 run		100000
 

From 24ef36dd4dc5671546dc74335ef54644c51c88df Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Tue, 7 Jan 2020 13:25:54 +0100
Subject: [PATCH 146/199] Update cmake/Modules/FindPNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindPNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
index e95ed4e559..8778335f62 100644
--- a/cmake/Modules/FindPNetCDF.cmake
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -20,7 +20,7 @@ endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
 find_path (PNETCDF_INCLUDES pnetcdf.h
   HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
 
-string(REGEX REPLACE "/include/?$" "/lib"
+string(REGEX REPLACE "/include/?$" ""
   PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
 
 find_library (PNETCDF_LIBRARIES

From 46584d45201f43d42e9fc396db6f47d38907881b Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Tue, 7 Jan 2020 13:26:01 +0100
Subject: [PATCH 147/199] Update cmake/Modules/FindPNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindPNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
index 8778335f62..bc3a5f9538 100644
--- a/cmake/Modules/FindPNetCDF.cmake
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -25,7 +25,7 @@ string(REGEX REPLACE "/include/?$" ""
 
 find_library (PNETCDF_LIBRARIES
   NAMES pnetcdf
-  HINTS ${PNETCDF_LIB_HINT})
+  HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)
 
 if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
   message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")

From 7470a120bb1ba629d288bf7825282f715cadbca4 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Jan 2020 11:13:43 -0500
Subject: [PATCH 148/199] fix small memory leak in USER-INTEL binning style

---
 src/USER-INTEL/nbin_intel.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp
index 8359587eb2..78c6246389 100644
--- a/src/USER-INTEL/nbin_intel.cpp
+++ b/src/USER-INTEL/nbin_intel.cpp
@@ -56,6 +56,8 @@ NBinIntel::~NBinIntel() {
       nocopy(binhead,bins,_atombin,_binpacked:alloc_if(0) free_if(1))
   }
   #endif
+  memory->destroy(_atombin);
+  memory->destroy(_binpacked);
 }
 
 /* ----------------------------------------------------------------------

From 4c974c6d5e93d3c55805f9a526781a7d5b93508a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Jan 2020 11:14:22 -0500
Subject: [PATCH 149/199] avoid uninitialized memory access when used with
 hybrid styles

---
 src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
index 929ac2123f..243c7f577d 100644
--- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
@@ -525,8 +525,10 @@ void PairLJCutCoulLongIntel::pack_force_const(ForceConst<flt_t> &fc,
       double cut;
       if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0))
         cut = init_one(i, j);
-      else
+      else { // need to set cutsq and cut_ljsq for hybrid pair_style
         cut = 0.0;
+        cut_ljsq[i][j] = cut_ljsq[j][i] = 0.0;
+      }
       cutsq[i][j] = cutsq[j][i] = cut*cut;
     }
   }

From f8ad7cc90f393782bebaa28c640bc443a31186a8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Jan 2020 15:09:50 -0500
Subject: [PATCH 150/199] refactor fix for detecting intel pair styles in
 hybrid pair styles

---
 src/USER-INTEL/fix_intel.cpp | 24 +++++++++++++++++++-----
 src/USER-INTEL/fix_intel.h   |  1 +
 src/pair.h                   |  1 +
 3 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 3d59a49acd..5ecae79b30 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -16,6 +16,7 @@
                         Anupama Kurpad (Intel) - Host Affinitization
 ------------------------------------------------------------------------- */
 
+#include "fix_intel.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -27,7 +28,7 @@
 #include "timer.h"
 #include "universe.h"
 #include "update.h"
-#include "fix_intel.h"
+#include "utils.h"
 
 #include <cstring>
 #include <cstdlib>
@@ -391,6 +392,20 @@ void FixIntel::setup_pre_reverse(int eflag, int vflag)
 
 /* ---------------------------------------------------------------------- */
 
+bool FixIntel::pair_hybrid_check()
+{
+  PairHybrid *ph = (PairHybrid *)force->pair;
+  bool has_intel = false;
+  int nstyles = ph->nstyles;
+
+  for (int i = 0; i < nstyles; ++i)
+    if (ph->styles[i]->suffix_flag & Suffix::INTEL) has_intel = true;
+
+  return has_intel;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void FixIntel::pair_init_check(const bool cdmessage)
 {
   #ifdef INTEL_VMASK
@@ -510,9 +525,9 @@ void FixIntel::bond_init_check()
   int intel_pair = 0;
   if (force->pair_match("/intel$", 0) != NULL)
     intel_pair = 1;
-  else if (force->pair_match("^hybrid", 1) != NULL) {
+  else if (force->pair_match("^hybrid", 0) != NULL) {
     _hybrid_nonpair = 1;
-    if (_pair_intel_count) intel_pair = 1;
+    if (pair_hybrid_check()) intel_pair = 1;
   }
 
   if (intel_pair == 0)
@@ -529,8 +544,7 @@ void FixIntel::kspace_init_check()
     intel_pair = 1;
   else if (force->pair_match("^hybrid", 0) != NULL) {
     _hybrid_nonpair = 1;
-    pair_init_check();     // need to run this here explicitly, since pair->init() was not run yet.
-    if (_pair_intel_count) intel_pair = 1;
+    if (pair_hybrid_check()) intel_pair = 1;
   }
 
   if (intel_pair == 0)
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index a699a6d2b9..4c50164d31 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -46,6 +46,7 @@ class FixIntel : public Fix {
   inline void min_setup(int in) { setup(in); }
   void setup_pre_reverse(int eflag = 0, int vflag = 0);
 
+  bool pair_hybrid_check();
   void pair_init_check(const bool cdmessage=false);
   void bond_init_check();
   void kspace_init_check();
diff --git a/src/pair.h b/src/pair.h
index 0aa48761ee..d578908b20 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -26,6 +26,7 @@ class Pair : protected Pointers {
   friend class DihedralCharmm;
   friend class DihedralCharmmOMP;
   friend class FixGPU;
+  friend class FixIntel;
   friend class FixOMP;
   friend class ThrOMP;
   friend class Info;

From 23b73a0ebcba58a6c640daa471133daf401834c7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Jan 2020 15:32:44 -0500
Subject: [PATCH 151/199] plug small memory leak

---
 src/USER-INTEL/pair_lj_cut_intel.cpp | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp
index f6f83b752a..b484cb68d9 100644
--- a/src/USER-INTEL/pair_lj_cut_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_intel.cpp
@@ -459,11 +459,8 @@ void PairLJCutIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
                                                    const int cop) {
   if (ntypes != _ntypes) {
     if (_ntypes > 0) {
-      fc_packed1 *oljc12o = ljc12o[0];
-      fc_packed2 *olj34 = lj34[0];
-
-      _memory->destroy(oljc12o);
-      _memory->destroy(olj34);
+      _memory->destroy(ljc12o);
+      _memory->destroy(lj34);
     }
     if (ntypes > 0) {
       _cop = cop;

From e8a941a0b91d5511931b01e65141352dbd1a2e03 Mon Sep 17 00:00:00 2001
From: Vsevak <thevsevak@gmail.com>
Date: Wed, 8 Jan 2020 01:48:47 +0300
Subject: [PATCH 152/199] Remove unnecessary data transfer from tip4p/gpu
 pairstyle init

Such data transfer is performed at each timestep, so it does not belong to the initialization
---
 lib/gpu/lal_lj_tip4p_long.cpp          | 20 ++------------------
 lib/gpu/lal_lj_tip4p_long.h            |  4 +---
 lib/gpu/lal_lj_tip4p_long_ext.cpp      | 13 ++++---------
 src/GPU/pair_lj_cut_tip4p_long_gpu.cpp | 10 ++++------
 4 files changed, 11 insertions(+), 36 deletions(-)

diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
index 874cda718c..0fbd9cc9be 100644
--- a/lib/gpu/lal_lj_tip4p_long.cpp
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -56,9 +56,7 @@ int LJTIP4PLongT::init(const int ntypes,
     double **host_cut_ljsq,
     const double host_cut_coulsq, const double host_cut_coulsqplus,
     double *host_special_coul, const double qqrd2e,
-    const double g_ewald, int* tag,
-    int *map_array, int map_size,
-    int *sametag, int max_same) {
+    const double g_ewald, int map_size, int max_same) {
   int success;
   success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
                             _screen,lj_tip4p_long,"k_lj_tip4p_long");
@@ -119,21 +117,9 @@ int LJTIP4PLongT::init(const int ntypes,
   m.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
   ansO.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
 
-  // Allocate a host write buffer for data initialization
-  UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_READ_WRITE);
   this->tag.alloc(nall,*(this->ucl_device), UCL_READ_ONLY);
-  for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
-  ucl_copy(this->tag, host_tag_write, nall, false);
-
-  //if(max_same>host_tag_write.cols()) host_tag_write.resize(max_same);
-  this->atom_sametag.alloc(nall, *(this->ucl_device), UCL_READ_ONLY);
-  for(int i=0; i<nall; ++i) host_tag_write[i] = sametag[i];
-  ucl_copy(this->atom_sametag, host_tag_write, nall, false);
-
-  host_tag_write.resize_ib(map_size);
+  this->atom_sametag.alloc(max_same, *(this->ucl_device), UCL_READ_ONLY);
   this->map_array.alloc(map_size,*(this->ucl_device), UCL_READ_ONLY);
-  for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
-  ucl_copy(this->map_array, host_tag_write, map_size, false);
 
   _allocated=true;
   this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+cutsq.row_bytes()+
@@ -267,8 +253,6 @@ void LJTIP4PLongT::copy_relations_data(int n, int* tag, int *map_array,
   this->map_array.resize_ib(map_size);
   for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
   ucl_copy(this->map_array, host_tag_write, map_size, false);
-
-  host_tag_write.clear();
 }
 
 
diff --git a/lib/gpu/lal_lj_tip4p_long.h b/lib/gpu/lal_lj_tip4p_long.h
index ccf507caa0..66d45f6b7a 100644
--- a/lib/gpu/lal_lj_tip4p_long.h
+++ b/lib/gpu/lal_lj_tip4p_long.h
@@ -48,9 +48,7 @@ public:
            double **host_cut_ljsq,
            const double host_cut_coulsq, const double host_cut_coulsqplus,
            double *host_special_coul, const double qqrd2e,
-           const double g_ewald, int* tag,
-           int *map_array, int map_size,
-           int *sametag, int max_same);
+           const double g_ewald, int map_size,int max_same);
 
   /// Clear all host and device data
   /** \note This is called at the beginning of the init() routine **/
diff --git a/lib/gpu/lal_lj_tip4p_long_ext.cpp b/lib/gpu/lal_lj_tip4p_long_ext.cpp
index dc0623bf82..944a2f09af 100644
--- a/lib/gpu/lal_lj_tip4p_long_ext.cpp
+++ b/lib/gpu/lal_lj_tip4p_long_ext.cpp
@@ -37,9 +37,7 @@ int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
     double **host_cut_ljsq,
     const double host_cut_coulsq, const double host_cut_coulsqplus,
     double *host_special_coul, const double qqrd2e,
-    const double g_ewald, int* tag,
-    int *map_array, int map_size,
-    int *sametag, int max_same) {
+    const double g_ewald, int map_size,int max_same) {
   LJTIP4PLMF.clear();
   gpu_mode=LJTIP4PLMF.device->gpu_mode();
   double gpu_split=LJTIP4PLMF.device->particle_split();
@@ -67,9 +65,7 @@ int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
         tH, tO, alpha, qdist, nall, 300,
         maxspecial, cell_size, gpu_split, screen,
         host_cut_ljsq, host_cut_coulsq, host_cut_coulsqplus,
-        host_special_coul, qqrd2e, g_ewald, tag,
-        map_array, map_size,
-        sametag, max_same);
+        host_special_coul, qqrd2e, g_ewald, map_size, max_same);
 
   LJTIP4PLMF.device->world_barrier();
   if (message)
@@ -90,9 +86,8 @@ int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
           tH, tO, alpha, qdist, nall, 300, maxspecial,
           cell_size, gpu_split, screen, host_cut_ljsq,
           host_cut_coulsq, host_cut_coulsqplus,
-          host_special_coul, qqrd2e, g_ewald,tag,
-          map_array, map_size,
-          sametag, max_same);
+          host_special_coul, qqrd2e,
+          g_ewald, map_size, max_same);
 
     LJTIP4PLMF.device->gpu_barrier();
     if (message)
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
index 3e20a28b75..266b64cb04 100644
--- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -58,9 +58,8 @@ int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
     const double cell_size, int &gpu_mode, FILE *screen,
     double **host_cut_ljsq, const double host_cut_coulsq,
     const double host_cut_coulsqplus, double *host_special_coul,
-    const double qqrd2e, const double g_ewald, int* tag,
-    int *map_array, int map_size,
-    int *sametag, int max_same);
+    const double qqrd2e, const double g_ewald,
+    int map_size, int max_same);
 void ljtip4p_long_gpu_clear();
 int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum,
     const int nall, double **host_x, int *host_type,
@@ -227,9 +226,8 @@ void PairLJCutTIP4PLongGPU::init_style()
                              cell_size, gpu_mode, screen, cut_ljsq,
                              cut_coulsq, cut_coulsqplus,
                              force->special_coul, force->qqrd2e,
-                             g_ewald,
-                             atom->tag, atom->get_map_array(), atom->get_map_size(),
-                             atom->sametag, atom->get_max_same());
+                             g_ewald, atom->get_map_size(),
+                             atom->get_max_same());
   GPU_EXTRA::check_flag(success,error,world);
   if (gpu_mode == GPU_FORCE) {
     int irequest = neighbor->request(this,instance_me);

From f1a23b1ea24187b3ab22f52d8a41d70a57cf1e9f Mon Sep 17 00:00:00 2001
From: tabedzki2 <59632999+tabedzki2@users.noreply.github.com>
Date: Tue, 7 Jan 2020 21:47:43 -0500
Subject: [PATCH 153/199] Updated Makefile.stampede: replacement options icc

The default options for Makefile.stampede did not compile. They had to be updated to include the `q` replacement options.
---
 src/MAKE/MACHINES/Makefile.stampede | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/MAKE/MACHINES/Makefile.stampede b/src/MAKE/MACHINES/Makefile.stampede
index 69da22c9c9..ecd0810d1d 100644
--- a/src/MAKE/MACHINES/Makefile.stampede
+++ b/src/MAKE/MACHINES/Makefile.stampede
@@ -6,13 +6,13 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		mpicc -openmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64
-MIC_OPT =       -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
-CCFLAGS =	-O3 -xhost -fp-model precise -restrict -override-limits $(MIC_OPT)
+CC =		mpicc -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64
+MIC_OPT =       -qoffload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
+CCFLAGS =	-O3 -xhost -fp-model precise -restrict -qoverride-limits $(MIC_OPT)
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpicc -openmp
+LINK =		mpicc -qopenmp
 LINKFLAGS =	-O3 -xhost
 LIB =           -ltbbmalloc
 SIZE =		size

From e243ca92b065fa198ebd27df383690673d68fef3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 8 Jan 2020 14:31:08 -0500
Subject: [PATCH 154/199] step version string for next patch release

---
 doc/lammps.1  | 2 +-
 src/version.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/lammps.1 b/doc/lammps.1
index a5045be5c4..4355e64961 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -1,4 +1,4 @@
-.TH LAMMPS "20 November 2019" "2019-11-20"
+.TH LAMMPS "9 January 2020" "2020-01-09"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
diff --git a/src/version.h b/src/version.h
index 38ec3883bf..1c5c4c6206 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "20 Nov 2019"
+#define LAMMPS_VERSION "09 Jan 2020"

From 9e3364ed39aec3078e3e3e10a75dd76c3c80bd8e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 8 Jan 2020 15:13:34 -0500
Subject: [PATCH 155/199] no need to flag ibody as private

---
 src/USER-OMP/fix_rigid_omp.cpp       | 2 +-
 src/USER-OMP/fix_rigid_small_omp.cpp | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 1cdf1018b2..770361d557 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -261,7 +261,7 @@ void FixRigidOMP::compute_forces_and_torques()
 
   if (id_gravity) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
     for (int ibody = 0; ibody < nbody; ibody++) {
       fcm[ibody][0] += gvec[0]*masstotal[ibody];
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index bdd10b0ca7..fc6b6fa57a 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -201,7 +201,7 @@ void FixRigidSmallOMP::compute_forces_and_torques()
 
   if (id_gravity) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
     for (int ibody = 0; ibody < nbody; ibody++) {
       double * _noalias const fcm = body[ibody].fcm;

From 2d71d9d47bf51d0975ca9681d2ddb9a9d407abd2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 8 Jan 2020 16:15:18 -0500
Subject: [PATCH 156/199] add citation for GPU accelerated TIP4P style

---
 src/GPU/fix_gpu.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp
index d4397503dc..cb2930a3ea 100644
--- a/src/GPU/fix_gpu.cpp
+++ b/src/GPU/fix_gpu.cpp
@@ -88,6 +88,12 @@ static const char cite_gpu_package[] =
   " year =    2017,\n"
   " volume =  212,\n"
   " pages =   {113--122}\n"
+  "}\n\n"
+  "@Article{Nikolskiy19,\n"
+  " author = {V. Nikolskiy, V. Stegailov},\n"
+  " title = {GPU acceleration of four-site water models in LAMMPS},\n"
+  " journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},\n"
+  " year =    2019\n"
   "}\n\n";
 
 /* ---------------------------------------------------------------------- */

From c482a04f80d6a20913cc8a1568a38a6b525175a9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 8 Jan 2020 17:21:35 -0500
Subject: [PATCH 157/199] fix whitespace issue

---
 src/fix_gravity.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index c36d2230c5..d130717470 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -37,7 +37,7 @@ enum{CONSTANT,EQUAL};
 
 FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), 
+  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL),
   xstr(NULL), ystr(NULL), zstr(NULL)
 {
   if (narg < 5) error->all(FLERR,"Illegal fix gravity command");

From 514271c984f3ccf0e4b0c7fb8532ff946eac0ed0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 8 Jan 2020 17:57:54 -0500
Subject: [PATCH 158/199] recover compilation with -DLAMMPS_BIGBIG and fix
 whitespace and formatting issues

---
 lib/gpu/lal_lj_tip4p_long.cpp          | 10 +++++-----
 lib/gpu/lal_lj_tip4p_long.cu           | 18 +++++++++---------
 lib/gpu/lal_lj_tip4p_long.h            |  4 ++--
 lib/gpu/lal_lj_tip4p_long_ext.cpp      |  6 +++---
 src/GPU/pair_lj_cut_tip4p_long_gpu.cpp |  4 ++--
 5 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
index 0fbd9cc9be..208d0ecbb0 100644
--- a/lib/gpu/lal_lj_tip4p_long.cpp
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -204,10 +204,10 @@ void LJTIP4PLongT::loop(const bool _eflag, const bool _vflag) {
   GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
                                (BX/this->_threads_per_atom)));
   this->k_pair.set_size(GX,BX);
-  if (vflag){
-	  this->ansO.resize_ib(ainum*3);
+  if (vflag) {
+          this->ansO.resize_ib(ainum*3);
   } else {
-	  this->ansO.resize_ib(ainum);
+          this->ansO.resize_ib(ainum);
   }
   this->ansO.zero();
   this->device->gpu->sync();
@@ -229,8 +229,8 @@ void LJTIP4PLongT::loop(const bool _eflag, const bool _vflag) {
 
 
 template <class numtyp, class acctyp>
-void LJTIP4PLongT::copy_relations_data(int n, int* tag, int *map_array,
-                      int map_size, int *sametag, int max_same, int ago){
+void LJTIP4PLongT::copy_relations_data(int n, tagint *tag, int *map_array,
+                      int map_size, int *sametag, int max_same, int ago) {
   int nall = n;
   const int hn_sz = n*4; // matrix size = col size * col number
   hneight.resize_ib(hn_sz);
diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
index fae5744224..10ac5b8454 100644
--- a/lib/gpu/lal_lj_tip4p_long.cu
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : thevsevak@gmail.com
-// ***************************************************************************/
+// ***************************************************************************
 
 #ifdef NV_KERNEL
 
@@ -29,12 +29,12 @@ texture<int2> q_tex;
 #define q_tex q_
 #endif
 
-ucl_inline int atom_mapping(const __global int *map, int glob){
-	return map[glob];
+ucl_inline int atom_mapping(const __global int *map, int glob) {
+  return map[glob];
 }
 
 ucl_inline int closest_image(int i, int j, const __global int* sametag,
-		const __global numtyp4 *restrict x_)
+                             const __global numtyp4 *restrict x_)
 {
   if (j < 0) return j;
 
@@ -66,7 +66,7 @@ ucl_inline int closest_image(int i, int j, const __global int* sametag,
 
 ucl_inline void compute_newsite(int iO, int  iH1, int  iH2,
     __global numtyp4 *xM, numtyp q,
-    numtyp alpha, const __global numtyp4 *restrict x_){
+    numtyp alpha, const __global numtyp4 *restrict x_) {
   numtyp4 xO;  fetch4(xO,iO,pos_tex);
   numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
   numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
@@ -238,7 +238,7 @@ __kernel void k_lj_tip4p_newsite(const __global numtyp4 *restrict x_,
     iO  = i;
     numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
     int itype = ix.w;
-    if (itype == typeO){
+    if (itype == typeO) {
       int iH1, iH2, iO;
       iH1 = hneigh[i*4  ];
       iH2 = hneigh[i*4+1];
@@ -404,7 +404,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
             fd.y = dely*force_coul;
             fd.z = delz*force_coul;
             if (itype == typeH) {
-              if (jtype == typeH){
+              if (jtype == typeH) {
                 virial[0] += delx*fd.x;
                 virial[1] += dely*fd.y;
                 virial[2] += delz*fd.z;
@@ -438,7 +438,7 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
               vdi.y = xO.y*cO + xH1.y*cH + xH2.y*cH;
               vdi.z = xO.z*cO + xH1.z*cH + xH2.z*cH;
               //vdi.w = vdi.w;
-              if (jtype != typeH){
+              if (jtype != typeH) {
                 numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
                 numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
                 numtyp4 xjO; fetch4(xjO,jO,pos_tex);
@@ -565,4 +565,4 @@ __kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
   } // if ii
 }
 
-__kernel void k_lj_tip4p_long_fast(){}
+__kernel void k_lj_tip4p_long_fast() {}
diff --git a/lib/gpu/lal_lj_tip4p_long.h b/lib/gpu/lal_lj_tip4p_long.h
index 66d45f6b7a..584a53e22b 100644
--- a/lib/gpu/lal_lj_tip4p_long.h
+++ b/lib/gpu/lal_lj_tip4p_long.h
@@ -61,8 +61,8 @@ public:
   double host_memory_usage() const;
 
   /// Copy data from LAMMPS_NS
-  void copy_relations_data(int n,int* tag, int *map_array, int map_size,
-      int *sametag, int max_same, int ago);
+  void copy_relations_data(int n, tagint* tag, int *map_array, int map_size,
+                           int *sametag, int max_same, int ago);
 
   /// Reimplement BaseCharge pair loop with host neighboring
   void compute(const int f_ago, const int inum_full, const int nall,
diff --git a/lib/gpu/lal_lj_tip4p_long_ext.cpp b/lib/gpu/lal_lj_tip4p_long_ext.cpp
index 944a2f09af..d0d6c7a3d2 100644
--- a/lib/gpu/lal_lj_tip4p_long_ext.cpp
+++ b/lib/gpu/lal_lj_tip4p_long_ext.cpp
@@ -138,9 +138,9 @@ double ljtip4p_long_gpu_bytes() {
   return LJTIP4PLMF.host_memory_usage();
 }
 
-void ljtip4p_long_copy_molecule_data(int n, int* tag,
-    int *map_array, int map_size,
-    int *sametag, int max_same, int ago){
+void ljtip4p_long_copy_molecule_data(int n, tagint* tag,
+                                     int *map_array, int map_size,
+                                     int *sametag, int max_same, int ago) {
   LJTIP4PLMF.copy_relations_data(n, tag, map_array, map_size, sametag, max_same, ago);
 }
 
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
index 266b64cb04..99668d26b8 100644
--- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -80,8 +80,8 @@ void ljtip4p_long_gpu_compute(const int ago, const int inum, const int nall,
     bool &success, double *host_q, const int nlocal,
     double *boxlo, double *prd);
 double ljtip4p_long_gpu_bytes();
-void ljtip4p_long_copy_molecule_data(int, int* , int *,
-		int, int *, int , int);
+void ljtip4p_long_copy_molecule_data(int, tagint *, int *,
+                                     int, int *, int, int);
 
 /* ---------------------------------------------------------------------- */
 

From d1222bd3c051730f0f7a7d9293d35b453b3f1f4c Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Thu, 9 Jan 2020 17:38:50 -0700
Subject: [PATCH 159/199] minor omissions in recent patch release

---
 doc/src/Commands_pair.rst | 2 +-
 doc/src/pair_lj.rst       | 3 +++
 examples/README           | 3 +++
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index b4371420a7..0844e0a2fe 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -146,7 +146,7 @@ OPT.
    * :doc:`lj/cut/soft (o) <pair_fep_soft>`
    * :doc:`lj/cut/thole/long (o) <pair_thole>`
    * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
-   * :doc:`lj/cut/tip4p/long (ot) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`
    * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/expand (gko) <pair_lj_expand>`
    * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst
index 54140a9faf..2b75c96a89 100644
--- a/doc/src/pair_lj.rst
+++ b/doc/src/pair_lj.rst
@@ -90,6 +90,9 @@ pair\_style lj/cut/coul/wolf/omp command
 pair\_style lj/cut/tip4p/cut command
 ====================================
 
+pair\_style lj/cut/tip4p/cut/gpu command
+====================================
+
 pair\_style lj/cut/tip4p/cut/omp command
 ========================================
 
diff --git a/examples/README b/examples/README
index 47463a85d8..fd57d5316d 100644
--- a/examples/README
+++ b/examples/README
@@ -164,6 +164,9 @@ The MC directory has an example script for using LAMMPS as an
 energy-evaluation engine in a iterative Monte Carlo energy-relaxation
 loop.
 
+The TIP4P directory has an example for comparing testing forces
+computed on a GPU.
+
 The UNITS directory contains examples of input scripts modeling the
 same Lennard-Jones liquid model, written in 3 different unit systems:
 lj, real, and metal.  So that you can see how to scale/unscale input

From 664227ff11c5dedbadbb64eeae79ed0f5b242295 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Thu, 9 Jan 2020 17:41:02 -0700
Subject: [PATCH 160/199] one more tweak

---
 examples/README | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/README b/examples/README
index fd57d5316d..8412f7b3ee 100644
--- a/examples/README
+++ b/examples/README
@@ -164,8 +164,8 @@ The MC directory has an example script for using LAMMPS as an
 energy-evaluation engine in a iterative Monte Carlo energy-relaxation
 loop.
 
-The TIP4P directory has an example for comparing testing forces
-computed on a GPU.
+The TIP4P directory has an example for testing forces computed on a
+GPU.
 
 The UNITS directory contains examples of input scripts modeling the
 same Lennard-Jones liquid model, written in 3 different unit systems:

From f073a64549431579119071e22f5c1de411d2bfaa Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 10 Jan 2020 15:29:53 -0500
Subject: [PATCH 161/199] add suffix_flag settings to GPU package styles

---
 src/GPU/pair_beck_gpu.cpp                | 2 ++
 src/GPU/pair_born_coul_long_cs_gpu.cpp   | 2 ++
 src/GPU/pair_born_coul_long_gpu.cpp      | 2 ++
 src/GPU/pair_born_coul_wolf_cs_gpu.cpp   | 2 ++
 src/GPU/pair_born_coul_wolf_gpu.cpp      | 2 ++
 src/GPU/pair_born_gpu.cpp                | 2 ++
 src/GPU/pair_buck_coul_cut_gpu.cpp       | 2 ++
 src/GPU/pair_buck_coul_long_gpu.cpp      | 2 ++
 src/GPU/pair_buck_gpu.cpp                | 2 ++
 src/GPU/pair_colloid_gpu.cpp             | 2 ++
 src/GPU/pair_coul_cut_gpu.cpp            | 2 ++
 src/GPU/pair_coul_debye_gpu.cpp          | 2 ++
 src/GPU/pair_coul_dsf_gpu.cpp            | 2 ++
 src/GPU/pair_coul_long_cs_gpu.cpp        | 2 ++
 src/GPU/pair_coul_long_gpu.cpp           | 2 ++
 src/GPU/pair_dpd_gpu.cpp                 | 2 ++
 src/GPU/pair_dpd_tstat_gpu.cpp           | 2 ++
 src/GPU/pair_eam_alloy_gpu.cpp           | 3 ++-
 src/GPU/pair_eam_fs_gpu.cpp              | 2 ++
 src/GPU/pair_eam_gpu.cpp                 | 2 ++
 src/GPU/pair_gauss_gpu.cpp               | 2 ++
 src/GPU/pair_gayberne_gpu.cpp            | 2 ++
 src/GPU/pair_lj96_cut_gpu.cpp            | 2 ++
 src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 2 ++
 src/GPU/pair_lj_class2_coul_long_gpu.cpp | 2 ++
 src/GPU/pair_lj_class2_gpu.cpp           | 2 ++
 src/GPU/pair_lj_cubic_gpu.cpp            | 2 ++
 src/GPU/pair_lj_cut_coul_cut_gpu.cpp     | 2 ++
 src/GPU/pair_lj_cut_coul_debye_gpu.cpp   | 2 ++
 src/GPU/pair_lj_cut_coul_dsf_gpu.cpp     | 2 ++
 src/GPU/pair_lj_cut_coul_long_gpu.cpp    | 2 ++
 src/GPU/pair_lj_cut_coul_msm_gpu.cpp     | 2 ++
 src/GPU/pair_lj_cut_dipole_cut_gpu.cpp   | 2 ++
 src/GPU/pair_lj_cut_dipole_long_gpu.cpp  | 2 ++
 src/GPU/pair_lj_cut_gpu.cpp              | 2 ++
 src/GPU/pair_lj_cut_tip4p_long_gpu.cpp   | 2 ++
 src/GPU/pair_lj_expand_coul_long_gpu.cpp | 2 ++
 src/GPU/pair_lj_expand_gpu.cpp           | 2 ++
 src/GPU/pair_lj_gromacs_gpu.cpp          | 2 ++
 src/GPU/pair_lj_sdk_coul_long_gpu.cpp    | 2 ++
 src/GPU/pair_lj_sdk_gpu.cpp              | 2 ++
 src/GPU/pair_lj_sf_dipole_sf_gpu.cpp     | 2 ++
 src/GPU/pair_mie_cut_gpu.cpp             | 2 ++
 src/GPU/pair_morse_gpu.cpp               | 2 ++
 src/GPU/pair_resquared_gpu.cpp           | 2 ++
 src/GPU/pair_soft_gpu.cpp                | 2 ++
 src/GPU/pair_sw_gpu.cpp                  | 2 ++
 src/GPU/pair_table_gpu.cpp               | 2 ++
 src/GPU/pair_tersoff_gpu.cpp             | 2 ++
 src/GPU/pair_tersoff_mod_gpu.cpp         | 2 ++
 src/GPU/pair_tersoff_zbl_gpu.cpp         | 2 ++
 src/GPU/pair_ufm_gpu.cpp                 | 2 ++
 src/GPU/pair_vashishta_gpu.cpp           | 2 ++
 src/GPU/pair_yukawa_colloid_gpu.cpp      | 2 ++
 src/GPU/pair_yukawa_gpu.cpp              | 2 ++
 src/GPU/pair_zbl_gpu.cpp                 | 2 ++
 56 files changed, 112 insertions(+), 1 deletion(-)

diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp
index d4d36a5837..f4b73ba5a6 100644
--- a/src/GPU/pair_beck_gpu.cpp
+++ b/src/GPU/pair_beck_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "gpu_extra.h"
 #include "math_special.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;
@@ -68,6 +69,7 @@ PairBeckGPU::PairBeckGPU(LAMMPS *lmp) : PairBeck(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp
index 7314024d71..bab66e0351 100644
--- a/src/GPU/pair_born_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -90,6 +91,7 @@ PairBornCoulLongCSGPU::PairBornCoulLongCSGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp
index 79c0d5f147..39d34420a8 100644
--- a/src/GPU/pair_born_coul_long_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -85,6 +86,7 @@ PairBornCoulLongGPU::PairBornCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
index 5f74d3fc7c..b00b5a0b56 100644
--- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -78,6 +79,7 @@ PairBornCoulWolfCSGPU::PairBornCoulWolfCSGPU(LAMMPS *lmp) : PairBornCoulWolfCS(l
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp
index 693c2abffb..c5243dc443 100644
--- a/src/GPU/pair_born_coul_wolf_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -76,6 +77,7 @@ PairBornCoulWolfGPU::PairBornCoulWolfGPU(LAMMPS *lmp) : PairBornCoulWolf(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp
index e9edc4f1c2..b71a296d66 100644
--- a/src/GPU/pair_born_gpu.cpp
+++ b/src/GPU/pair_born_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairBornGPU::PairBornGPU(LAMMPS *lmp) : PairBorn(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp
index 182673fb0d..5d27ee8c51 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.cpp
+++ b/src/GPU/pair_buck_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index 75e784fafa..e30230d5a0 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -81,6 +82,7 @@ PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp
index 1559c45b88..b4d5677d53 100644
--- a/src/GPU/pair_buck_gpu.cpp
+++ b/src/GPU/pair_buck_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairBuckGPU::PairBuckGPU(LAMMPS *lmp) : PairBuck(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp
index 4db18dbc52..230adb3db0 100644
--- a/src/GPU/pair_colloid_gpu.cpp
+++ b/src/GPU/pair_colloid_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairColloidGPU::PairColloidGPU(LAMMPS *lmp) : PairColloid(lmp), gpu_mode(GPU_FOR
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp
index 8a3eb12f8d..0242c98343 100644
--- a/src/GPU/pair_coul_cut_gpu.cpp
+++ b/src/GPU/pair_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairCoulCutGPU::PairCoulCutGPU(LAMMPS *lmp) : PairCoulCut(lmp), gpu_mode(GPU_FOR
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp
index 1fc07f8dac..198f7f5f67 100644
--- a/src/GPU/pair_coul_debye_gpu.cpp
+++ b/src/GPU/pair_coul_debye_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairCoulDebyeGPU::PairCoulDebyeGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp
index 408be036dd..67d025ff70 100644
--- a/src/GPU/pair_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_coul_dsf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
@@ -81,6 +82,7 @@ PairCoulDSFGPU::PairCoulDSFGPU(LAMMPS *lmp) : PairCoulDSF(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp
index c70424e472..afd0d6cf56 100644
--- a/src/GPU/pair_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_coul_long_cs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -83,6 +84,7 @@ PairCoulLongCSGPU::PairCoulLongCSGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index 9623c25f2f..485e45ddc6 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -78,6 +79,7 @@ PairCoulLongGPU::PairCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp
index 5fcad6a350..9e14164c57 100644
--- a/src/GPU/pair_dpd_gpu.cpp
+++ b/src/GPU/pair_dpd_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -209,6 +210,7 @@ PairDPDGPU::PairDPDGPU(LAMMPS *lmp) : PairDPD(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp
index 2d6798a12d..920eb8dd8a 100644
--- a/src/GPU/pair_dpd_tstat_gpu.cpp
+++ b/src/GPU/pair_dpd_tstat_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -212,6 +213,7 @@ PairDPDTstatGPU::PairDPDTstatGPU(LAMMPS *lmp) : PairDPDTstat(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index bc55c66676..e7503839f6 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -30,7 +30,7 @@
 #include "gpu_extra.h"
 #include "domain.h"
 #include "utils.h"
-
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +72,7 @@ PairEAMAlloyGPU::PairEAMAlloyGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index ac379a9ce6..6edfa69359 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -29,6 +29,7 @@
 #include "neigh_request.h"
 #include "gpu_extra.h"
 #include "domain.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairEAMFSGPU::PairEAMFSGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index 57106f48a4..fb851770f9 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -30,6 +30,7 @@
 #include "error.h"
 #include "neigh_request.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MAXLINE 1024
 
@@ -71,6 +72,7 @@ PairEAMGPU::PairEAMGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp
index 842b84acf2..17125f9875 100644
--- a/src/GPU/pair_gauss_gpu.cpp
+++ b/src/GPU/pair_gauss_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -66,6 +67,7 @@ PairGaussGPU::PairGaussGPU(LAMMPS *lmp) : PairGauss(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index f00accda15..445c74487f 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "update.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -74,6 +75,7 @@ PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
   quat_nmax = 0;
   reinitflag = 0;
   quat = NULL;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index 16b6b835c0..f6f9bd379b 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -66,6 +67,7 @@ PairLJ96CutGPU::PairLJ96CutGPU(LAMMPS *lmp) : PairLJ96Cut(lmp), gpu_mode(GPU_FOR
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index bacbb400b1..6eda677928 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index e34dbb0f99..4ee776b4ff 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -80,6 +81,7 @@ PairLJClass2CoulLongGPU::PairLJClass2CoulLongGPU(LAMMPS *lmp) :
 {
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp
index 68f27598f3..643e3ff090 100644
--- a/src/GPU/pair_lj_class2_gpu.cpp
+++ b/src/GPU/pair_lj_class2_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -65,6 +66,7 @@ PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_
 {
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp
index 542de37840..64fd6119c3 100644
--- a/src/GPU/pair_lj_cubic_gpu.cpp
+++ b/src/GPU/pair_lj_cubic_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace PairLJCubicConstants;
@@ -70,6 +71,7 @@ PairLJCubicGPU::PairLJCubicGPU(LAMMPS *lmp) : PairLJCubic(lmp),
   respa_enable = 0;
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index cf3dd711dc..e52a971786 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJCutCoulCutGPU::PairLJCutCoulCutGPU(LAMMPS *lmp) : PairLJCutCoulCut(lmp), g
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
index 20354e732c..4c8920450f 100644
--- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairLJCutCoulDebyeGPU::PairLJCutCoulDebyeGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
index ccaf86efa6..acfbcd847e 100644
--- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
@@ -82,6 +83,7 @@ PairLJCutCoulDSFGPU::PairLJCutCoulDSFGPU(LAMMPS *lmp) : PairLJCutCoulDSF(lmp), g
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index 36c72f1143..24ce118c6d 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJCutCoulLongGPU::PairLJCutCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
index 79ca90698a..0e700f6fb2 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairLJCutCoulMSMGPU::PairLJCutCoulMSMGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
index e2c8b8d686..6c53b02227 100644
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairLJCutDipoleCutGPU::PairLJCutDipoleCutGPU(LAMMPS *lmp) : PairLJCutDipoleCut(l
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
index fb76376d34..0535735820 100644
--- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
@@ -36,6 +36,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -84,6 +85,7 @@ PairLJCutDipoleLongGPU::PairLJCutDipoleLongGPU(LAMMPS *lmp) : PairLJCutDipoleLon
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index 809e5cf05e..c6f61a7e96 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairLJCutGPU::PairLJCutGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
index 99668d26b8..a7875f15c4 100644
--- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -37,6 +37,7 @@
 #include "angle.h"
 #include "bond.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -91,6 +92,7 @@ PairLJCutTIP4PLongGPU::PairLJCutTIP4PLongGPU(LAMMPS *lmp)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
index a530f7ff9a..a906f57707 100644
--- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJExpandCoulLongGPU::PairLJExpandCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp
index 86f8a76b52..db88e8dae8 100644
--- a/src/GPU/pair_lj_expand_gpu.cpp
+++ b/src/GPU/pair_lj_expand_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairLJExpandGPU::PairLJExpandGPU(LAMMPS *lmp) : PairLJExpand(lmp), gpu_mode(GPU_
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp
index 78f8b8b461..6989d73d50 100644
--- a/src/GPU/pair_lj_gromacs_gpu.cpp
+++ b/src/GPU/pair_lj_gromacs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJGromacsGPU::PairLJGromacsGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
index 24ff8a4f28..3bcaa78d46 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -86,6 +87,7 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp
index 2621f49aeb..c0a3e8ec39 100644
--- a/src/GPU/pair_lj_sdk_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
index cf26cdf3b4..d001c282e2 100644
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairLJSFDipoleSFGPU::PairLJSFDipoleSFGPU(LAMMPS *lmp) : PairLJSFDipoleSF(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp
index f3a384113f..84cc903dee 100644
--- a/src/GPU/pair_mie_cut_gpu.cpp
+++ b/src/GPU/pair_mie_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -67,6 +68,7 @@ PairMIECutGPU::PairMIECutGPU(LAMMPS *lmp) : PairMIECut(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index dcad227045..5bcda54d85 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -65,6 +66,7 @@ PairMorseGPU::PairMorseGPU(LAMMPS *lmp) : PairMorse(lmp), gpu_mode(GPU_FORCE)
 {
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index b12a790c81..b03834d5d1 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "update.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -76,6 +77,7 @@ PairRESquaredGPU::PairRESquaredGPU(LAMMPS *lmp) : PairRESquared(lmp),
     error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
   quat_nmax = 0;
   quat = NULL;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp
index 0efcb20c8d..04efb1e96a 100644
--- a/src/GPU/pair_soft_gpu.cpp
+++ b/src/GPU/pair_soft_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "gpu_extra.h"
 #include "math_const.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairSoftGPU::PairSoftGPU(LAMMPS *lmp) : PairSoft(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp
index 906f8a7e83..8e75aff545 100644
--- a/src/GPU/pair_sw_gpu.cpp
+++ b/src/GPU/pair_sw_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairSWGPU::PairSWGPU(LAMMPS *lmp) : PairSW(lmp), gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index 4432265874..563b070bda 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define LOOKUP 0
 #define LINEAR 1
@@ -73,6 +74,7 @@ PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp
index 15fc5c95da..33bac49e5e 100644
--- a/src/GPU/pair_tersoff_gpu.cpp
+++ b/src/GPU/pair_tersoff_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -76,6 +77,7 @@ extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
 PairTersoffGPU::PairTersoffGPU(LAMMPS *lmp) : PairTersoff(lmp), gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp
index 2ff09c3248..ebcdf0f7dd 100644
--- a/src/GPU/pair_tersoff_mod_gpu.cpp
+++ b/src/GPU/pair_tersoff_mod_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairTersoffMODGPU::PairTersoffMODGPU(LAMMPS *lmp) : PairTersoffMOD(lmp),
   gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp
index b8d02f09ab..09b5a7f838 100644
--- a/src/GPU/pair_tersoff_zbl_gpu.cpp
+++ b/src/GPU/pair_tersoff_zbl_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -77,6 +78,7 @@ PairTersoffZBLGPU::PairTersoffZBLGPU(LAMMPS *lmp) : PairTersoffZBL(lmp),
   gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index 97c2eebf24..49ed6289e1 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -36,6 +36,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairUFMGPU::PairUFMGPU(LAMMPS *lmp) : PairUFM(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp
index 56199f7e54..6f0d938440 100644
--- a/src/GPU/pair_vashishta_gpu.cpp
+++ b/src/GPU/pair_vashishta_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairVashishtaGPU::PairVashishtaGPU(LAMMPS *lmp) : PairVashishta(lmp), gpu_mode(G
   cpu_time = 0.0;
   reinitflag = 0;
   gpu_allocated = false;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp
index 51c7e683db..7bbed7d89b 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.cpp
+++ b/src/GPU/pair_yukawa_colloid_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -68,6 +69,7 @@ PairYukawaColloidGPU::PairYukawaColloidGPU(LAMMPS *lmp) : PairYukawaColloid(lmp)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index 5dc13c7750..9d702daf20 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -67,6 +68,7 @@ PairYukawaGPU::PairYukawaGPU(LAMMPS *lmp) : PairYukawa(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp
index 5e24281145..23c3c077fa 100644
--- a/src/GPU/pair_zbl_gpu.cpp
+++ b/src/GPU/pair_zbl_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairZBLGPU::PairZBLGPU(LAMMPS *lmp) : PairZBL(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 

From 4989c3a878a27f3fcea4457a547cc72c90a3a6f2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 10 Jan 2020 15:30:26 -0500
Subject: [PATCH 162/199] convert static const ints to an enumerator

---
 src/suffix.h | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/suffix.h b/src/suffix.h
index 817600dfd5..88629aa796 100644
--- a/src/suffix.h
+++ b/src/suffix.h
@@ -16,13 +16,14 @@
 
 namespace LAMMPS_NS {
 
-namespace Suffix {
-  static const int NONE = 0;
-  static const int OPT  = 1<<0;
-  static const int GPU  = 1<<1;
-  static const int OMP  = 1<<2;
-  static const int INTEL  = 1<<3;
-}
+enum Suffix {
+  NONE   = 0,
+  OPT    = 1<<0,
+  GPU    = 1<<1,
+  OMP    = 1<<2,
+  INTEL  = 1<<3,
+  KOKKOS = 1<<4
+};
 
 }
 

From 6e3559a6e710989b7bd73ef4c3c91639c2f40094 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 10 Jan 2020 14:09:38 -0700
Subject: [PATCH 163/199] added rerun example dir

---
 examples/README                            |   1 +
 examples/rerun/in.first                    |  33 ++++++
 examples/rerun/in.read_dump                |  37 +++++++
 examples/rerun/in.rerun                    |  29 +++++
 examples/rerun/log.20Jan20.first.g++.4     |  97 +++++++++++++++++
 examples/rerun/log.20Jan20.read_dump.g++.4 | 118 +++++++++++++++++++++
 examples/rerun/log.20Jan20.rerun.g++.4     |  86 +++++++++++++++
 7 files changed, 401 insertions(+)
 create mode 100644 examples/rerun/in.first
 create mode 100644 examples/rerun/in.read_dump
 create mode 100644 examples/rerun/in.rerun
 create mode 100644 examples/rerun/log.20Jan20.first.g++.4
 create mode 100644 examples/rerun/log.20Jan20.read_dump.g++.4
 create mode 100644 examples/rerun/log.20Jan20.rerun.g++.4

diff --git a/examples/README b/examples/README
index 47463a85d8..0589055e4a 100644
--- a/examples/README
+++ b/examples/README
@@ -101,6 +101,7 @@ prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   use of PYTHON package to invoke Python code from input script
 qeq:      use of QEQ package for charge equilibration
 reax:     RDX and TATB and several other models using ReaxFF
+rerun:    use of rerun and read_dump commands
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
 snap:     examples for using several bundled SNAP potentials
diff --git a/examples/rerun/in.first b/examples/rerun/in.first
new file mode 100644
index 0000000000..2aa4c1974c
--- /dev/null
+++ b/examples/rerun/in.first
@@ -0,0 +1,33 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z vx vy vz
+
+thermo          100
+run		1000
diff --git a/examples/rerun/in.read_dump b/examples/rerun/in.read_dump
new file mode 100644
index 0000000000..3c1310b305
--- /dev/null
+++ b/examples/rerun/in.read_dump
@@ -0,0 +1,37 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+read_dump       lj.dump 200 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 800 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 600 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 400 x y z vx vy vz
+run             0 post no
diff --git a/examples/rerun/in.rerun b/examples/rerun/in.rerun
new file mode 100644
index 0000000000..a695006f26
--- /dev/null
+++ b/examples/rerun/in.rerun
@@ -0,0 +1,29 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+rerun           lj.dump first 200 last 800 every 200 &
+                dump x y z vx vy vz
+
diff --git a/examples/rerun/log.20Jan20.first.g++.4 b/examples/rerun/log.20Jan20.first.g++.4
new file mode 100644
index 0000000000..cabc17c851
--- /dev/null
+++ b/examples/rerun/log.20Jan20.first.g++.4
@@ -0,0 +1,97 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00173283 secs
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z vx vy vz
+
+thermo          100
+run		1000
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.869 | 7.869 | 7.869 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+     200   0.75953175   -5.7618892            0   -4.6226272   0.20910575 
+     300   0.74624286    -5.741962            0   -4.6226327   0.32016436 
+     400   0.74155675   -5.7343359            0   -4.6220356    0.3777989 
+     500   0.73249345   -5.7206946            0   -4.6219887   0.44253023 
+     600   0.72087255   -5.7029314            0   -4.6216563   0.55730354 
+     700   0.71489947    -5.693532            0   -4.6212164   0.61322381 
+     800   0.70876958   -5.6840594            0   -4.6209382   0.66822293 
+     900   0.70799522   -5.6828388            0   -4.6208791   0.66961272 
+    1000   0.70325878   -5.6750833            0   -4.6202281    0.7112575 
+Loop time of 6.3349 on 4 procs for 1000 steps with 32000 atoms
+
+Performance: 68193.673 tau/day, 157.856 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.3538     | 4.6712     | 5.0021     |  12.8 | 73.74
+Neigh   | 0.59378    | 0.65229    | 0.75202    |   8.0 | 10.30
+Comm    | 0.28101    | 0.69839    | 1.0586     |  38.5 | 11.02
+Output  | 0.21601    | 0.21682    | 0.21718    |   0.1 |  3.42
+Modify  | 0.074002   | 0.074803   | 0.075779   |   0.2 |  1.18
+Other   |            | 0.0214     |            |       |  0.34
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    8632.5 ave 8685 max 8591 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs:    299934 ave 303105 max 295137 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 1199738
+Ave neighs/atom = 37.4918
+Neighbor list builds = 50
+Dangerous builds not checked
+Total wall time: 0:00:06
diff --git a/examples/rerun/log.20Jan20.read_dump.g++.4 b/examples/rerun/log.20Jan20.read_dump.g++.4
new file mode 100644
index 0000000000..874309aaa3
--- /dev/null
+++ b/examples/rerun/log.20Jan20.read_dump.g++.4
@@ -0,0 +1,118 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.001724 secs
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+read_dump       lj.dump 200 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     200   0.75953173   -5.7618854            0   -4.6226234   0.20912952 
+Loop time of 2.26498e-06 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 800 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     800   0.70876957   -5.6840545            0   -4.6209334   0.66823926 
+Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 600 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     600   0.72087256   -5.7029306            0   -4.6216556   0.55729873 
+Loop time of 7.7486e-07 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 400 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     400   0.74155677   -5.7343336            0   -4.6220332   0.37780193 
+Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
+
+Total wall time: 0:00:00
diff --git a/examples/rerun/log.20Jan20.rerun.g++.4 b/examples/rerun/log.20Jan20.rerun.g++.4
new file mode 100644
index 0000000000..f654e2c777
--- /dev/null
+++ b/examples/rerun/log.20Jan20.rerun.g++.4
@@ -0,0 +1,86 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00100017 secs
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+rerun           lj.dump first 200 last 800 every 200                 dump x y z vx vy vz
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.716 | 6.718 | 6.721 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     200   0.75953173   -5.7618854            0   -4.6226234   0.20912952 
+     400   0.74155677   -5.7343336            0   -4.6220332   0.37780193 
+     600   0.72087256   -5.7029306            0   -4.6216556   0.55729873 
+     800   0.70876957   -5.6840545            0   -4.6209334   0.66823926 
+Loop time of 0.375898 on 4 procs for 4 steps with 32000 atoms
+
+Performance: 4596.990 tau/day, 10.641 timesteps/s
+98.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.3759     |            |       |100.00
+
+Nlocal:    8000 ave 8073 max 7933 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:    8693.25 ave 8731 max 8658 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    299786 ave 302947 max 293888 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 1199142
+Ave neighs/atom = 37.4732
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00

From d5192c10438964e2593c9ed92273d2e10e30fae1 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 10 Jan 2020 14:37:45 -0700
Subject: [PATCH 164/199] added an example for recalculating the RDF at a
 longer cutoff via rerun

---
 examples/rerun/README                      |  17 ++++
 examples/rerun/in.rdf.first                |  36 +++++++
 examples/rerun/in.rdf.rerun                |  31 ++++++
 examples/rerun/log.20Jan20.rdf.first.g++.4 | 105 +++++++++++++++++++++
 examples/rerun/log.20Jan20.rdf.rerun.g++.4 | 100 ++++++++++++++++++++
 examples/rerun/rdf.20Jan20.first.g++.4     |  54 +++++++++++
 examples/rerun/rdf.20Jan20.rerun.g++.4     | 104 ++++++++++++++++++++
 7 files changed, 447 insertions(+)
 create mode 100644 examples/rerun/README
 create mode 100644 examples/rerun/in.rdf.first
 create mode 100644 examples/rerun/in.rdf.rerun
 create mode 100644 examples/rerun/log.20Jan20.rdf.first.g++.4
 create mode 100644 examples/rerun/log.20Jan20.rdf.rerun.g++.4
 create mode 100644 examples/rerun/rdf.20Jan20.first.g++.4
 create mode 100644 examples/rerun/rdf.20Jan20.rerun.g++.4

diff --git a/examples/rerun/README b/examples/rerun/README
new file mode 100644
index 0000000000..66db685d92
--- /dev/null
+++ b/examples/rerun/README
@@ -0,0 +1,17 @@
+Examples of how to use the rerun and read_dump commands
+
+in.first - run on any number of procs for any size problem
+in.rerun - run on same or different proc count for same size problem
+in.read_dump - ditto to in.rerun
+
+The thermo output on the same timesteps should be identical
+to within round-off errors.
+
+in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma
+in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma
+
+In both bases the time averaged RDF is computed 10x times, every 100
+steps for 1000 total.  In the rerun, the pair style cutoff is changed
+so the RDF can be computed to a longer distance without re-running the
+simulation.  The RDF values in the 2 files should be the same (within
+round-off) for the first 50 bins.
diff --git a/examples/rerun/in.rdf.first b/examples/rerun/in.rdf.first
new file mode 100644
index 0000000000..f9d1ecf55e
--- /dev/null
+++ b/examples/rerun/in.rdf.first
@@ -0,0 +1,36 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z
+
+compute         myRDF all rdf 50 cutoff 2.5
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
+
+thermo          100
+run		1000
diff --git a/examples/rerun/in.rdf.rerun b/examples/rerun/in.rdf.rerun
new file mode 100644
index 0000000000..5562cac74d
--- /dev/null
+++ b/examples/rerun/in.rdf.rerun
@@ -0,0 +1,31 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 5.0
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+
+compute         myRDF all rdf 100 cutoff 5.0
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
+
+thermo          100
+
+rerun           lj.dump dump x y z
+
diff --git a/examples/rerun/log.20Jan20.rdf.first.g++.4 b/examples/rerun/log.20Jan20.rdf.first.g++.4
new file mode 100644
index 0000000000..7d029f23d4
--- /dev/null
+++ b/examples/rerun/log.20Jan20.rdf.first.g++.4
@@ -0,0 +1,105 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00100017 secs
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z
+
+compute         myRDF all rdf 50 cutoff 2.5
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
+
+thermo          100
+run		1000
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute rdf, occasional
+      attributes: half, newton on, cut 2.8
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.487 | 8.487 | 8.487 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+     200   0.75953175   -5.7618892            0   -4.6226272   0.20910575 
+     300   0.74624286    -5.741962            0   -4.6226327   0.32016436 
+     400   0.74155675   -5.7343359            0   -4.6220356    0.3777989 
+     500   0.73249345   -5.7206946            0   -4.6219887   0.44253023 
+     600   0.72087255   -5.7029314            0   -4.6216563   0.55730354 
+     700   0.71489947    -5.693532            0   -4.6212164   0.61322381 
+     800   0.70876958   -5.6840594            0   -4.6209382   0.66822293 
+     900   0.70799522   -5.6828388            0   -4.6208791   0.66961272 
+    1000   0.70325878   -5.6750833            0   -4.6202281    0.7112575 
+Loop time of 7.44016 on 4 procs for 1000 steps with 32000 atoms
+
+Performance: 58063.267 tau/day, 134.406 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.3881     | 5.5809     | 5.7111     |   5.4 | 75.01
+Neigh   | 0.80101    | 0.82776    | 0.85702    |   2.2 | 11.13
+Comm    | 0.31801    | 0.48426    | 0.72201    |  22.5 |  6.51
+Output  | 0.17801    | 0.17801    | 0.17801    |   0.0 |  2.39
+Modify  | 0.31201    | 0.33076    | 0.33701    |   1.9 |  4.45
+Other   |            | 0.0385     |            |       |  0.52
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    8632.5 ave 8685 max 8591 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs:    299934 ave 303105 max 295137 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 1199738
+Ave neighs/atom = 37.4918
+Neighbor list builds = 50
+Dangerous builds not checked
+Total wall time: 0:00:07
diff --git a/examples/rerun/log.20Jan20.rdf.rerun.g++.4 b/examples/rerun/log.20Jan20.rdf.rerun.g++.4
new file mode 100644
index 0000000000..7c5137bb08
--- /dev/null
+++ b/examples/rerun/log.20Jan20.rdf.rerun.g++.4
@@ -0,0 +1,100 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00183487 secs
+mass		1 1.0
+
+pair_style	lj/cut 5.0
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+
+compute         myRDF all rdf 100 cutoff 5.0
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
+
+thermo          100
+
+rerun           lj.dump dump x y z
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.3
+  ghost atom cutoff = 5.3
+  binsize = 2.65, bins = 13 13 13
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute rdf, occasional
+      attributes: half, newton on, cut 5.3
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -7.1616928            0   -7.1616928   -6.8899898 
+     100            0   -6.1442754            0   -6.1442754   -1.0825318 
+     200            0   -6.1472483            0   -6.1472483   -1.0817213 
+     300            0   -6.1274033            0   -6.1274033  -0.95961014 
+     400            0   -6.1202956            0   -6.1202956   -0.8988851 
+     500            0   -6.1067136            0   -6.1067136  -0.82660368 
+     600            0   -6.0893179            0   -6.0893179  -0.70264528 
+     700            0   -6.0803044            0   -6.0803044  -0.64232743 
+     800            0   -6.0710303            0   -6.0710303   -0.5824798 
+     900            0   -6.0698963            0   -6.0698963  -0.58057929 
+    1000            0   -6.0627642            0   -6.0627642  -0.53599799 
+Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms
+
+Performance: 1544.558 tau/day, 3.575 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 3.077      |            |       |100.00
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    20028 ave 20060 max 19988 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:    2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 8416685
+Ave neighs/atom = 263.021
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03
diff --git a/examples/rerun/rdf.20Jan20.first.g++.4 b/examples/rerun/rdf.20Jan20.first.g++.4
new file mode 100644
index 0000000000..d78e0ce2c1
--- /dev/null
+++ b/examples/rerun/rdf.20Jan20.first.g++.4
@@ -0,0 +1,54 @@
+# Time-averaged data for fix 2
+# TimeStep Number-of-rows
+# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
+1000 50
+1 0.025 0 0
+2 0.075 0 0
+3 0.125 0 0
+4 0.175 0 0
+5 0.225 0 0
+6 0.275 0 0
+7 0.325 0 0
+8 0.375 0 0
+9 0.425 0 0
+10 0.475 0 0
+11 0.525 0 0
+12 0.575 0 0
+13 0.625 0 0
+14 0.675 0 0
+15 0.725 0 0
+16 0.775 0 0
+17 0.825 0 0
+18 0.875 1.53863e-05 6.25e-06
+19 0.925 0.0217263 0.00986875
+20 0.975 0.506735 0.265431
+21 1.025 1.92083 1.33605
+22 1.075 2.8749 3.09855
+23 1.125 2.7805 4.96541
+24 1.175 2.21879 6.59047
+25 1.225 1.67622 7.92484
+26 1.275 1.25407 9.00629
+27 1.325 0.963413 9.90353
+28 1.375 0.774441 10.6802
+29 1.425 0.656196 11.3871
+30 1.475 0.589364 12.0672
+31 1.525 0.560681 12.7589
+32 1.575 0.560195 13.4961
+33 1.625 0.587995 14.3197
+34 1.675 0.632155 15.2605
+35 1.725 0.706585 16.3758
+36 1.775 0.805303 17.7216
+37 1.825 0.925415 19.3565
+38 1.875 1.05672 21.3271
+39 1.925 1.17634 23.6394
+40 1.975 1.2557 26.2375
+41 2.025 1.30009 29.0653
+42 2.075 1.30889 32.0546
+43 2.125 1.27704 35.1135
+44 2.175 1.21808 38.17
+45 2.225 1.13622 41.1536
+46 2.275 1.05072 44.0382
+47 2.325 0.973786 46.8303
+48 2.375 0.910095 49.5533
+49 2.425 0.866474 52.256
+50 2.475 0.841724 54.991
diff --git a/examples/rerun/rdf.20Jan20.rerun.g++.4 b/examples/rerun/rdf.20Jan20.rerun.g++.4
new file mode 100644
index 0000000000..3fa6acc461
--- /dev/null
+++ b/examples/rerun/rdf.20Jan20.rerun.g++.4
@@ -0,0 +1,104 @@
+# Time-averaged data for fix 2
+# TimeStep Number-of-rows
+# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
+1000 100
+1 0.025 0 0
+2 0.075 0 0
+3 0.125 0 0
+4 0.175 0 0
+5 0.225 0 0
+6 0.275 0 0
+7 0.325 0 0
+8 0.375 0 0
+9 0.425 0 0
+10 0.475 0 0
+11 0.525 0 0
+12 0.575 0 0
+13 0.625 0 0
+14 0.675 0 0
+15 0.725 0 0
+16 0.775 0 0
+17 0.825 0 0
+18 0.875 1.53863e-05 6.25e-06
+19 0.925 0.021685 0.00985
+20 0.975 0.506834 0.265463
+21 1.025 1.92047 1.33588
+22 1.075 2.87514 3.09853
+23 1.125 2.78062 4.96547
+24 1.175 2.21869 6.59046
+25 1.225 1.67626 7.92486
+26 1.275 1.25409 9.00633
+27 1.325 0.963245 9.90341
+28 1.375 0.774535 10.6802
+29 1.425 0.65626 11.3871
+30 1.475 0.58925 12.0672
+31 1.525 0.560782 12.759
+32 1.575 0.560133 13.496
+33 1.625 0.588008 14.3197
+34 1.675 0.632185 15.2605
+35 1.725 0.706541 16.3757
+36 1.775 0.805341 17.7216
+37 1.825 0.925351 19.3565
+38 1.875 1.05677 21.3271
+39 1.925 1.17639 23.6395
+40 1.975 1.25571 26.2376
+41 2.025 1.30011 29.0655
+42 2.075 1.30883 32.0547
+43 2.125 1.27702 35.1134
+44 2.175 1.21813 38.17
+45 2.225 1.13617 41.1536
+46 2.275 1.05073 44.0382
+47 2.325 0.97376 46.8302
+48 2.375 0.91012 49.5533
+49 2.425 0.866556 52.2563
+50 2.475 0.841651 54.991
+51 2.525 0.839516 57.8301
+52 2.575 0.848795 60.8153
+53 2.625 0.868861 63.991
+54 2.675 0.896335 67.393
+55 2.725 0.925794 71.0395
+56 2.775 0.961909 74.9685
+57 2.825 0.999727 79.2005
+58 2.875 1.03745 83.749
+59 2.925 1.07355 88.6208
+60 2.975 1.10406 93.8039
+61 3.025 1.11993 99.2397
+62 3.075 1.12062 104.86
+63 3.125 1.10531 110.586
+64 3.175 1.07711 116.345
+65 3.225 1.04268 122.097
+66 3.275 1.00838 127.834
+67 3.325 0.974855 133.55
+68 3.375 0.949817 139.289
+69 3.425 0.936519 145.116
+70 3.475 0.92942 151.069
+71 3.525 0.930926 157.205
+72 3.575 0.940561 163.581
+73 3.625 0.94956 170.199
+74 3.675 0.964202 177.107
+75 3.725 0.97905 184.312
+76 3.775 0.991906 191.81
+77 3.825 1.00093 199.577
+78 3.875 1.01248 207.641
+79 3.925 1.02301 216.001
+80 3.975 1.03474 224.673
+81 4.025 1.04171 233.624
+82 4.075 1.04725 242.849
+83 4.125 1.04997 252.325
+84 4.175 1.04758 262.01
+85 4.225 1.03985 271.856
+86 4.275 1.02755 281.817
+87 4.325 1.00883 291.826
+88 4.375 0.99045 301.882
+89 4.425 0.97287 311.986
+90 4.475 0.958469 322.166
+91 4.525 0.952552 332.512
+92 4.575 0.948064 343.037
+93 4.625 0.952592 353.845
+94 4.675 0.958837 364.96
+95 4.725 0.970831 376.457
+96 4.775 0.985248 388.372
+97 4.825 0.998873 400.707
+98 4.875 1.0119 413.462
+99 4.925 1.02446 426.643
+100 4.975 1.03613 440.245

From d0eb41b61eed5c50cfa177fcdb9c189866da120b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 10 Jan 2020 16:58:39 -0500
Subject: [PATCH 165/199] disallow per substyle special bond factors with
 certain suffix styles

---
 src/pair_hybrid.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index eb9423aa57..b88fa49a85 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -27,6 +27,7 @@
 #include "error.h"
 #include "respa.h"
 #include "utils.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -919,6 +920,12 @@ void PairHybrid::modify_special(int m, int /*narg*/, char **arg)
   special[2] = force->numeric(FLERR,arg[2]);
   special[3] = force->numeric(FLERR,arg[3]);
 
+  // have to cast to PairHybrid to work around C++ access restriction
+
+  if (((PairHybrid *)styles[m])->suffix_flag & (Suffix::INTEL|Suffix::GPU))
+    error->all(FLERR,"Pair_modify special is not compatible with "
+                     "suffix version of hybrid substyle");
+
   if (strcmp(arg[0],"lj/coul") == 0) {
     if (!special_lj[m]) special_lj[m] = new double[4];
     if (!special_coul[m]) special_coul[m] = new double[4];

From 8fa0700df10c79183778a171236d8fcd46a0cb4f Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 10 Jan 2020 16:49:09 -0700
Subject: [PATCH 166/199] add warning to fix bond/create

---
 src/MC/fix_bond_break.cpp  |  3 ++-
 src/MC/fix_bond_create.cpp | 14 ++++++++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 2ff0e4126f..520abb9d32 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -33,7 +33,8 @@ using namespace FixConst;
 
 FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL), broken(NULL), copy(NULL), random(NULL)
+  partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL), 
+  broken(NULL), copy(NULL), random(NULL)
 {
   if (narg < 6) error->all(FLERR,"Illegal fix bond/break command");
 
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 3f63a22d60..a7f955ad0b 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -18,6 +18,7 @@
 #include "respa.h"
 #include "atom.h"
 #include "force.h"
+#include "modify.h"
 #include "pair.h"
 #include "comm.h"
 #include "neighbor.h"
@@ -216,6 +217,19 @@ void FixBondCreate::init()
   if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
     error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
 
+  // warn if more than one fix bond/create or also a fix bond/break
+  // because this fix stores per-atom state in bondcount
+  //   if other fixes create/break bonds, this fix will not know about it
+
+  int count = 0;
+  for (int i = 0; i < modify->nfix; i++) {
+    if (strcmp(modify->fix[i]->style,"bond/create") == 0) count++;
+    if (strcmp(modify->fix[i]->style,"bond/break") == 0) count++;
+  }
+  if (count > 1 && me == 0) 
+    error->warning(FLERR,"Fix bond/create is used multiple times "
+                   " or with fix bond/break - may not work as expected");
+
   // enable angle/dihedral/improper creation if atype/dtype/itype
   //   option was used and a force field has been specified
 

From cb8313d947a367c50279d9c48a260e4b4b69fed5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 16:08:37 -0500
Subject: [PATCH 167/199] document added warning for fix bond/create

---
 doc/src/Errors_warnings.rst | 6 ++++++
 doc/txt/Errors_warnings.txt | 7 +++++++
 src/MC/fix_bond_create.h    | 7 +++++++
 3 files changed, 20 insertions(+)

diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst
index ad5323c6ad..4a944eeb18 100644
--- a/doc/src/Errors_warnings.rst
+++ b/doc/src/Errors_warnings.rst
@@ -195,6 +195,12 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Fix SRD walls overlap but fix srd overlap not set*
    You likely want to set this in your input script.
 
+* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
+   When using fix bond/create multiple times or in combination with
+   fix bond/break, the individual fix instances do not share information
+   about changes they made at the same time step and thus it may result
+   in unexpected behavior.
+
 *Fix bond/swap will ignore defined angles*
    See the doc page for fix bond/swap for more info on this
    restriction.
diff --git a/doc/txt/Errors_warnings.txt b/doc/txt/Errors_warnings.txt
index 06474e1bb3..cb22b7ad0c 100644
--- a/doc/txt/Errors_warnings.txt
+++ b/doc/txt/Errors_warnings.txt
@@ -239,6 +239,13 @@ will be truncated to attempt to prevent the bond from blowing up. :dd
 
 You likely want to set this in your input script. :dd
 
+{ Fix bond/create is used multiple times or with fix bond/break - may not work as expected} :dt
+
+When using fix bond/create multiple times or in combination with
+fix bond/break, the individual fix instances do not share information
+about changes they made at the same time step and thus it may result
+in unexpected behavior. :dd
+
 {Fix bond/swap will ignore defined angles} :dt
 
 See the doc page for fix bond/swap for more info on this
diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h
index 403b1ae340..1e4b9a11c1 100644
--- a/src/MC/fix_bond_create.h
+++ b/src/MC/fix_bond_create.h
@@ -170,4 +170,11 @@ See the read_data command for info on setting the "extra special per
 atom" header value to allow for additional special values to be
 stored.
 
+W: Fix bond/create is used multiple times or with fix bond/break - may not work as expected
+
+When using fix bond/create multiple times or in combination with
+fix bond/break, the individual fix instances do not share information
+about changes they made at the same time step and thus it may result
+in unexpected behavior.
+
 */

From 67b9fd10cc2ee43e6e0f162c061d26b60207d721 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 16:12:58 -0500
Subject: [PATCH 168/199] rename output files to correctly match the used
 version

---
 .../rerun/{log.20Jan20.first.g++.4 => log.09Jan20.first.g++.4}    | 0
 .../{log.20Jan20.rdf.first.g++.4 => log.09Jan20.rdf.first.g++.4}  | 0
 .../{log.20Jan20.rdf.rerun.g++.4 => log.09Jan20.rdf.rerun.g++.4}  | 0
 .../{log.20Jan20.read_dump.g++.4 => log.09Jan20.read_dump.g++.4}  | 0
 .../rerun/{log.20Jan20.rerun.g++.4 => log.09Jan20.rerun.g++.4}    | 0
 .../rerun/{rdf.20Jan20.first.g++.4 => rdf.09Jan20.first.g++.4}    | 0
 .../rerun/{rdf.20Jan20.rerun.g++.4 => rdf.09Jan20.rerun.g++.4}    | 0
 7 files changed, 0 insertions(+), 0 deletions(-)
 rename examples/rerun/{log.20Jan20.first.g++.4 => log.09Jan20.first.g++.4} (100%)
 rename examples/rerun/{log.20Jan20.rdf.first.g++.4 => log.09Jan20.rdf.first.g++.4} (100%)
 rename examples/rerun/{log.20Jan20.rdf.rerun.g++.4 => log.09Jan20.rdf.rerun.g++.4} (100%)
 rename examples/rerun/{log.20Jan20.read_dump.g++.4 => log.09Jan20.read_dump.g++.4} (100%)
 rename examples/rerun/{log.20Jan20.rerun.g++.4 => log.09Jan20.rerun.g++.4} (100%)
 rename examples/rerun/{rdf.20Jan20.first.g++.4 => rdf.09Jan20.first.g++.4} (100%)
 rename examples/rerun/{rdf.20Jan20.rerun.g++.4 => rdf.09Jan20.rerun.g++.4} (100%)

diff --git a/examples/rerun/log.20Jan20.first.g++.4 b/examples/rerun/log.09Jan20.first.g++.4
similarity index 100%
rename from examples/rerun/log.20Jan20.first.g++.4
rename to examples/rerun/log.09Jan20.first.g++.4
diff --git a/examples/rerun/log.20Jan20.rdf.first.g++.4 b/examples/rerun/log.09Jan20.rdf.first.g++.4
similarity index 100%
rename from examples/rerun/log.20Jan20.rdf.first.g++.4
rename to examples/rerun/log.09Jan20.rdf.first.g++.4
diff --git a/examples/rerun/log.20Jan20.rdf.rerun.g++.4 b/examples/rerun/log.09Jan20.rdf.rerun.g++.4
similarity index 100%
rename from examples/rerun/log.20Jan20.rdf.rerun.g++.4
rename to examples/rerun/log.09Jan20.rdf.rerun.g++.4
diff --git a/examples/rerun/log.20Jan20.read_dump.g++.4 b/examples/rerun/log.09Jan20.read_dump.g++.4
similarity index 100%
rename from examples/rerun/log.20Jan20.read_dump.g++.4
rename to examples/rerun/log.09Jan20.read_dump.g++.4
diff --git a/examples/rerun/log.20Jan20.rerun.g++.4 b/examples/rerun/log.09Jan20.rerun.g++.4
similarity index 100%
rename from examples/rerun/log.20Jan20.rerun.g++.4
rename to examples/rerun/log.09Jan20.rerun.g++.4
diff --git a/examples/rerun/rdf.20Jan20.first.g++.4 b/examples/rerun/rdf.09Jan20.first.g++.4
similarity index 100%
rename from examples/rerun/rdf.20Jan20.first.g++.4
rename to examples/rerun/rdf.09Jan20.first.g++.4
diff --git a/examples/rerun/rdf.20Jan20.rerun.g++.4 b/examples/rerun/rdf.09Jan20.rerun.g++.4
similarity index 100%
rename from examples/rerun/rdf.20Jan20.rerun.g++.4
rename to examples/rerun/rdf.09Jan20.rerun.g++.4

From 4f35682828e533489ce567d8c9714aab1ba0c901 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 16:15:49 -0500
Subject: [PATCH 169/199] list added example folder in manual

---
 doc/src/Examples.rst | 2 ++
 doc/txt/Examples.txt | 1 +
 2 files changed, 3 insertions(+)

diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst
index a223939d5a..993090baf1 100644
--- a/doc/src/Examples.rst
+++ b/doc/src/Examples.rst
@@ -133,6 +133,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | reax        | RDX and TATB models using the ReaxFF                             |
 +-------------+------------------------------------------------------------------+
+| rerun       | use of rerun and read\_dump commands                             |
++-------------+------------------------------------------------------------------+
 | rigid       | rigid bodies modeled as independent or coupled                   |
 +-------------+------------------------------------------------------------------+
 | shear       | sideways shear applied to 2d solid, with and without a void      |
diff --git a/doc/txt/Examples.txt b/doc/txt/Examples.txt
index 86617e13df..04c211cb1d 100644
--- a/doc/txt/Examples.txt
+++ b/doc/txt/Examples.txt
@@ -94,6 +94,7 @@ python:   using embedded Python in a LAMMPS input script
 qeq:      use of the QEQ package for charge equilibration
 rdf-adf:  computing radial and angle distribution functions for water
 reax:     RDX and TATB models using the ReaxFF
+rerun:    use of rerun and read_dump commands
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
 snap:     NVE dynamics for BCC tantalum crystal using SNAP potential

From 9c207bb751d3de378ae2d40e66b856ea4b26ba02 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 16:20:13 -0500
Subject: [PATCH 170/199] remove outdated .txt file for pair style meam/c

---
 doc/txt/pair_meamc.txt | 402 -----------------------------------------
 1 file changed, 402 deletions(-)
 delete mode 100644 doc/txt/pair_meamc.txt

diff --git a/doc/txt/pair_meamc.txt b/doc/txt/pair_meamc.txt
deleted file mode 100644
index 2831600e08..0000000000
--- a/doc/txt/pair_meamc.txt
+++ /dev/null
@@ -1,402 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style meam/c command :h3
-
-[Syntax:]
-
-pair_style style :pre
-
-style = {meam/c}
-
-[Examples:]
-
-pair_style meam/c
-pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
-pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
-
-[Description:]
-
-NOTE: The behavior of the MEAM potential for alloy systems has changed
-as of November 2010; see description below of the mixture_ref_t
-parameter
-
-Style {meam/c} computes pairwise interactions for a variety of materials
-using modified embedded-atom method (MEAM) potentials
-"(Baskes)"_#Baskes.  Conceptually, it is an extension to the original
-"EAM potentials"_pair_eam.html which adds angular forces.  It is
-thus suitable for modeling metals and alloys with fcc, bcc, hcp and
-diamond cubic structures, as well as covalently bonded materials like
-silicon and carbon. Style {meam/c} is a translation of the (now obsolete)
-{meam} code from Fortran to C++. It is functionally equivalent to {meam}
-but more efficient, and thus {meam} has been removed from LAMMPS after
-the 12 December 2018 release.
-
-In the MEAM formulation, the total energy E of a system of atoms is
-given by:
-
-:c,image(Eqs/pair_meam.jpg)
-
-where F is the embedding energy which is a function of the atomic
-electron density rho, and phi is a pair potential interaction.  The
-pair interaction is summed over all neighbors J of atom I within the
-cutoff distance.  As with EAM, the multi-body nature of the MEAM
-potential is a result of the embedding energy term.  Details of the
-computation of the embedding and pair energies, as implemented in
-LAMMPS, are given in "(Gullet)"_#Gullet and references therein.
-
-The various parameters in the MEAM formulas are listed in two files
-which are specified by the "pair_coeff"_pair_coeff.html command.
-These are ASCII text files in a format consistent with other MD codes
-that implement MEAM potentials, such as the serial DYNAMO code and
-Warp.  Several MEAM potential files with parameters for different
-materials are included in the "potentials" directory of the LAMMPS
-distribution with a ".meam" suffix.  All of these are parameterized in
-terms of LAMMPS "metal units"_units.html.
-
-Note that unlike for other potentials, cutoffs for MEAM potentials are
-not set in the pair_style or pair_coeff command; they are specified in
-the MEAM potential files themselves.
-
-Only a single pair_coeff command is used with the {meam} style which
-specifies two MEAM files and the element(s) to extract information
-for.  The MEAM elements are mapped to LAMMPS atom types by specifying
-N additional arguments after the 2nd filename in the pair_coeff
-command, where N is the number of LAMMPS atom types:
-
-MEAM library file
-Elem1, Elem2, ...
-MEAM parameter file
-N element names = mapping of MEAM elements to atom types :ul
-
-See the "pair_coeff"_pair_coeff.html doc page for alternate ways
-to specify the path for the potential files.
-
-As an example, the potentials/library.meam file has generic MEAM
-settings for a variety of elements.  The potentials/SiC.meam file has
-specific parameter settings for a Si and C alloy system.  If your
-LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
-and the 4th to be C, you would use the following pair_coeff command:
-
-pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre
-
-The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
-The two filenames are for the library and parameter file respectively.
-The Si and C arguments (between the file names) are the two elements
-for which info will be extracted from the library file.  The first
-three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si
-element.  The final C argument maps LAMMPS atom type 4 to the MEAM C
-element.
-
-If the 2nd filename is specified as NULL, no parameter file is read,
-which simply means the generic parameters in the library file are
-used.  Use of the NULL specification for the parameter file is
-discouraged for systems with more than a single element type
-(e.g. alloys), since the parameter file is expected to set element
-interaction terms that are not captured by the information in the
-library file.
-
-If a mapping value is specified as NULL, the mapping is not performed.
-This can be used when a {meam} potential is used as part of the
-{hybrid} pair style.  The NULL values are placeholders for atom types
-that will be used with other potentials.
-
-NOTE: If the 2nd filename is NULL, the element names between the two
-filenames can appear in any order, e.g. "Si C" or "C Si" in the
-example above.  However, if the 2nd filename is not NULL (as in the
-example above), it contains settings that are Fortran-indexed for the
-elements that preceed it.  Thus you need to insure you list the
-elements between the filenames in an order consistent with how the
-values in the 2nd filename are indexed.  See details below on the
-syntax for settings in the 2nd file.
-
-The MEAM library file provided with LAMMPS has the name
-potentials/library.meam.  It is the "meamf" file used by other MD
-codes.  Aside from blank and comment lines (start with #) which can
-appear anywhere, it is formatted as a series of entries, each of which
-has 19 parameters and can span multiple lines:
-
-elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub,
-t0, t1, t2, t3, rozero, ibar
-
-The "elt" and "lat" parameters are text strings, such as elt = Si or
-Cu and lat = dia or fcc.  Because the library file is used by Fortran
-MD codes, these strings may be enclosed in single quotes, but this is
-not required.  The other numeric parameters match values in the
-formulas above.  The value of the "elt" string is what is used in the
-pair_coeff command to identify which settings from the library file
-you wish to read in.  There can be multiple entries in the library
-file with the same "elt" value; LAMMPS reads the 1st matching entry it
-finds and ignores the rest.
-
-Other parameters in the MEAM library file correspond to single-element
-potential parameters:
-
-lat      = lattice structure of reference configuration
-z        = number of nearest neighbors in the reference structure
-             This field is only read for compatibility, the correct
-             value is inferred from the lattice structure
-ielement = atomic number
-atwt     = atomic weight
-alat     = lattice constant of reference structure
-esub     = energy per atom (eV) in the reference structure at equilibrium
-asub     = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre
-
-The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
-standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b
-parameters are the standard beta parameters). Note that only parameters
-normalized to t0 = 1.0 are supported.  The rozero parameter is
-an element-dependent density scaling that weights the reference
-background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and
-is typically 1.0 for single-element systems.  The ibar parameter
-selects the form of the function G(Gamma) used to compute the electron
-density; options are
-
-   0 => G = sqrt(1+Gamma)
-   1 => G = exp(Gamma/2)
-   2 => not implemented
-   3 => G = 2/(1+exp(-Gamma))
-   4 => G = sqrt(1+Gamma)
-  -5 => G = +-sqrt(abs(1+Gamma)) :pre
-
-If used, the MEAM parameter file contains settings that override or
-complement the library file settings.  Examples of such parameter
-files are in the potentials directory with a ".meam" suffix.  Their
-format is the same as is read by other Fortran MD codes.  Aside from
-blank and comment lines (start with #) which can appear anywhere, each
-line has one of the following forms.  Each line can also have a
-trailing comment (starting with #) which is ignored.
-
-keyword = value
-keyword(I) = value
-keyword(I,J) = value
-keyword(I,J,K) = value :pre
-
-The indices I, J, K correspond to the elements selected from the
-MEAM library file numbered in the order of how those elements were
-selected starting from 1. Thus for the example given below
-
-pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre
-
-an index of 1 would refer to Si and an index of 2 to C.
-
-The recognized keywords for the parameter file are as follows:
-
-Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,
-augt1, gsmooth_factor, re
-
-where
-
-rc          = cutoff radius for cutoff function; default = 4.0
-delr        = length of smoothing distance for cutoff function; default = 0.1
-rho0(I)     = relative density for element I (overwrites value
-              read from meamf file)
-Ec(I,J)     = cohesive energy of reference structure for I-J mixture
-delta(I,J)  = heat of formation for I-J alloy; if Ec_IJ is input as
-              zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
-alpha(I,J)  = alpha parameter for pair potential between I and J (can
-              be computed from bulk modulus of reference structure
-re(I,J)     = equilibrium distance between I and J in the reference
-              structure
-Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened
-              by K (I<=J); default = 2.8
-Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
-              by K (I<=J); default = 2.0
-lattce(I,J) = lattice structure of I-J reference structure:
-                dia = diamond (interlaced fcc for alloy)
-                fcc = face centered cubic
-                bcc = body centered cubic
-                dim = dimer
-                b1  = rock salt (NaCl structure)
-                hcp = hexagonal close-packed
-                c11 = MoSi2 structure
-                l12 = Cu3Au structure (lower case L, followed by 12)
-                b2  = CsCl structure (interpenetrating simple cubic)
-nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for
-              I-J pair (see for example "(Lee)"_#Lee).
-                0 = second-nearest neighbor formulation off
-                1 = second-nearest neighbor formulation on
-                default = 0
-attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
-                default = 0
-repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
-                default = 0
-zbl(I,J)    = blend the MEAM I-J pair potential with the ZBL potential for small
-              atom separations "(ZBL)"_#ZBL
-                default = 1
-gsmooth_factor  = factor determining the length of the G-function smoothing
-                  region; only significant for ibar=0 or ibar=4.
-                      99.0 = short smoothing region, sharp step
-                      0.5  = long smoothing region, smooth step
-                      default = 99.0
-augt1           = integer flag for whether to augment t1 parameter by
-                  3/5*t3 to account for old vs. new meam formulations;
-                    0 = don't augment t1
-                    1 = augment t1
-                    default = 1
-ialloy          = integer flag to use alternative averaging rule for t parameters,
-                  for comparison with the DYNAMO MEAM code
-                    0 = standard averaging (matches ialloy=0 in DYNAMO)
-                    1 = alternative averaging (matches ialloy=1 in DYNAMO)
-                    2 = no averaging of t (use single-element values)
-                    default = 0
-mixture_ref_t   = integer flag to use mixture average of t to compute the background
-                  reference density for alloys, instead of the single-element values
-                  (see description and warning elsewhere in this doc page)
-                    0 = do not use mixture averaging for t in the reference density
-                    1 = use mixture averaging for t in the reference density
-                    default = 0
-erose_form      = integer value to select the form of the Rose energy function
-                  (see description below).
-                    default = 0
-emb_lin_neg     = integer value to select embedding function for negative densities
-                    0 = F(rho)=0
-                    1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO)
-                    default = 0
-bkgd_dyn        = integer value to select background density formula
-                    0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
-                    1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO)
-                    default = 0 :pre
-
-Rc, delr, re are in distance units (Angstroms in the case of metal
-units).  Ec and delta are in energy units (eV in the case of metal
-units).
-
-Each keyword represents a quantity which is either a scalar, vector,
-2d array, or 3d array and must be specified with the correct
-corresponding array syntax.  The indices I,J,K each run from 1 to N
-where N is the number of MEAM elements being used.
-
-Thus these lines
-
-rho0(2) = 2.25
-alpha(1,2) = 4.37 :pre
-
-set rho0 for the 2nd element to the value 2.25 and set alpha for the
-alloy interaction between elements 1 and 2 to 4.37.
-
-The augt1 parameter is related to modifications in the MEAM
-formulation of the partial electron density function.  In recent
-literature, an extra term is included in the expression for the
-third-order density in order to make the densities orthogonal (see for
-example "(Wang)"_#Wang2, equation 3d); this term is included in the
-MEAM implementation in lammps.  However, in earlier published work
-this term was not included when deriving parameters, including most of
-those provided in the library.meam file included with lammps, and to
-account for this difference the parameter t1 must be augmented by
-3/5*t3.  If augt1=1, the default, this augmentation is done
-automatically.  When parameter values are fit using the modified
-density function, as in more recent literature, augt1 should be set to
-0.
-
-The mixture_ref_t parameter is available to match results with those
-of previous versions of lammps (before January 2011).  Newer versions
-of lammps, by default, use the single-element values of the t
-parameters to compute the background reference density.  This is the
-proper way to compute these parameters.  Earlier versions of lammps
-used an alloy mixture averaged value of t to compute the background
-reference density.  Setting mixture_ref_t=1 gives the old behavior.
-WARNING: using mixture_ref_t=1 will give results that are demonstrably
-incorrect for second-neighbor MEAM, and non-standard for
-first-neighbor MEAM; this option is included only for matching with
-previous versions of lammps and should be avoided if possible.
-
-The parameters attrac and repuls, along with the integer selection
-parameter erose_form, can be used to modify the Rose energy function
-used to compute the pair potential.  This function gives the energy of
-the reference state as a function of interatomic spacing.  The form of
-this function is:
-
-astar = alpha * (r/re - 1.d0)
-if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
-if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
-if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
-a3 = repuls, astar < 0
-a3 = attrac, astar >= 0 :pre
-
-Most published MEAM parameter sets use the default values attrac=repulse=0.
-Setting repuls=attrac=delta corresponds to the form used in several
-recent published MEAM parameter sets, such as "(Valone)"_#Valone
-
-NOTE: The default form of the erose expression in LAMMPS was corrected
-in March 2009.  The current version is correct, but may show different
-behavior compared with earlier versions of lammps with the attrac
-and/or repuls parameters are non-zero.  To obtain the previous default
-form, use erose_form = 1 (this form does not seem to appear in the
-literature).  An alternative form (see e.g. "(Lee2)"_#Lee2) is
-available using erose_form = 2.
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-For atom type pairs I,J and I != J, where types I and J correspond to
-two different element types, mixing is performed by LAMMPS with
-user-specifiable parameters as described above.  You never need to
-specify a pair_coeff command with I != J arguments for this style.
-
-This pair style does not support the "pair_modify"_pair_modify.html
-shift, table, and tail options.
-
-This pair style does not write its information to "binary restart
-files"_restart.html, since it is stored in potential files.  Thus, you
-need to re-specify the pair_style and pair_coeff commands in an input
-script that reads a restart file.
-
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
-
-:line
-
-[Restrictions:]
-
-The {meam/c} style is provided in the USER-MEAMC package. It is
-only enabled if LAMMPS was built with that package.
-See the "Build package"_Build_package.html doc page for more info.
-
-The maximum number of elements, that can be read from the MEAM
-library file, is determined at compile time. The default is 5.
-If you need support for more elements, you have to change the
-define for the constant 'maxelt' at the beginning of the file
-src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no
-limit on the number of atoms types.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html,
-"pair_style meam/spline"_pair_meam_spline.html
-
-[Default:] none
-
-:line
-
-:link(Baskes)
-[(Baskes)] Baskes, Phys Rev B, 46, 2727-2742 (1992).
-
-:link(Gullet)
-[(Gullet)] Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
-This report may be accessed on-line via "this link"_sandreport.
-
-:link(sandreport,http://infoserve.sandia.gov/sand_doc/2003/038782.pdf)
-
-:link(Lee)
-[(Lee)] Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
-
-:link(Lee2)
-[(Lee2)] Lee, Baskes, Kim, Cho.  Phys. Rev. B, 64, 184102 (2001).
-
-:link(Valone)
-[(Valone)] Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
-
-:link(Wang2)
-[(Wang)] Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).
-
-:link(ZBL)
-[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges
-of Ions in Matter", Vol 1, 1985, Pergamon Press.

From e1849232b85122eb702f79cc42d6fa6d237b0426 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 16:21:42 -0500
Subject: [PATCH 171/199] remove redundant lj/cut/tip4p/long/gpu entry and
 correct underline length

---
 doc/src/Build_extras.rst | 2 +-
 doc/src/pair_lj.rst      | 5 +----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst
index c02b24641e..2cba59bde0 100644
--- a/doc/src/Build_extras.rst
+++ b/doc/src/Build_extras.rst
@@ -203,7 +203,7 @@ inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
 environment variable so that libkim-api can be found.
 
-For using KIM web queries.
+For using OpenKIM web queries in LAMMPS.
 
 If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
 libcurl calls within the KIM web query display a lot of information about
diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst
index 2b75c96a89..7a46f0a0db 100644
--- a/doc/src/pair_lj.rst
+++ b/doc/src/pair_lj.rst
@@ -91,7 +91,7 @@ pair\_style lj/cut/tip4p/cut command
 ====================================
 
 pair\_style lj/cut/tip4p/cut/gpu command
-====================================
+========================================
 
 pair\_style lj/cut/tip4p/cut/omp command
 ========================================
@@ -105,9 +105,6 @@ pair\_style lj/cut/tip4p/long/omp command
 pair\_style lj/cut/tip4p/long/opt command
 =========================================
 
-pair\_style lj/cut/tip4p/long/gpu command
-=====================================
-
 Syntax
 """"""
 

From d7d1d571705e6a4451bdb7b79494b3b0ba653f9f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 16:35:27 -0500
Subject: [PATCH 172/199] remove outdated txt files

---
 doc/txt/fix_nve_dot.txt           |  63 -------------
 doc/txt/fix_nve_dotc_langevin.txt | 143 ------------------------------
 doc/txt/pair_oxdna.txt            | 112 -----------------------
 doc/txt/pair_oxdna2.txt           | 121 -------------------------
 4 files changed, 439 deletions(-)
 delete mode 100644 doc/txt/fix_nve_dot.txt
 delete mode 100644 doc/txt/fix_nve_dotc_langevin.txt
 delete mode 100644 doc/txt/pair_oxdna.txt
 delete mode 100644 doc/txt/pair_oxdna2.txt

diff --git a/doc/txt/fix_nve_dot.txt b/doc/txt/fix_nve_dot.txt
deleted file mode 100644
index fcd8926c13..0000000000
--- a/doc/txt/fix_nve_dot.txt
+++ /dev/null
@@ -1,63 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix nve/dot command :h3
-
-[Syntax:]
-
-fix ID group-ID nve/dot :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-nve/dot = style name of this fix command :l
-:ule
-
-[Examples:]
-
-fix 1 all nve/dot :pre
-
-[Description:]
-
-Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
-to a group of atoms, but without Langevin dynamics.
-This command performs Molecular dynamics (MD)
-via a velocity-Verlet algorithm and an evolution operator that rotates
-the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
-
-This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-without damping and noise and can be used to determine the stability range
-in a NVE ensemble prior to using the Langevin-type DOTC-integrator
-(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
-The command is equivalent to the "fix nve"_fix_nve.html.
-The particles are always considered to have a finite size.
-
-An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
-Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html
-
-[Default:] none
-
-:line
-
-:link(Davidchack1)
-[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller1)
-[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
-:link(Henrich3)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
diff --git a/doc/txt/fix_nve_dotc_langevin.txt b/doc/txt/fix_nve_dotc_langevin.txt
deleted file mode 100644
index 898ca5132b..0000000000
--- a/doc/txt/fix_nve_dotc_langevin.txt
+++ /dev/null
@@ -1,143 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix nve/dotc/langevin command :h3
-
-[Syntax:]
-
-fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-nve/dotc/langevin = style name of this fix command :l
-Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
-damp = damping parameter (time units) :l
-seed = random number seed to use for white noise (positive integer) :l
-keyword = {angmom} :l
-  {angmom} value = factor
-    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
-:ule
-
-[Examples:]
-
-fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
-fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
-
-[Description:]
-
-Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
-as described in "(Davidchack)"_#Davidchack2
-to a group of atoms, which models an interaction with an implicit background
-solvent.  This command performs Brownian dynamics (BD)
-via a technique that splits the integration into a deterministic Hamiltonian
-part and the Ornstein-Uhlenbeck process for noise and damping.
-The quaternion degrees of freedom are updated though an evolution
-operator which performs a rotation in quaternion space, preserves
-the quaternion norm and is akin to "(Miller)"_#Miller2.
-
-In terms of syntax this command has been closely modelled on the
-"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
-the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
-one single command. The main feature is improved stability
-over the standard integrator, permitting slightly larger timestep sizes.
-
-NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
-also time integration of the translational and quaternion degrees of freedom.
-
-The total force on each atom will have the form:
-
-F = Fc + Ff + Fr
-Ff = - (m / damp) v
-Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
-
-Fc is the conservative force computed via the usual inter-particle
-interactions ("pair_style"_pair_style.html,
-"bond_style"_bond_style.html, etc).
-
-The Ff and Fr terms are implicitly taken into account by this fix
-on a per-particle basis.
-
-Ff is a frictional drag or viscous damping term proportional to the
-particle's velocity.  The proportionality constant for each atom is
-computed as m/damp, where m is the mass of the particle and damp is
-the damping factor specified by the user.
-
-Fr is a force due to solvent atoms at a temperature T randomly bumping
-into the particle.  As derived from the fluctuation/dissipation
-theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
-dt damp), where Kb is the Boltzmann constant, T is the desired
-temperature, m is the mass of the particle, dt is the timestep size,
-and damp is the damping factor.  Random numbers are used to randomize
-the direction and magnitude of this force as described in
-"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of
-a Gaussian random number) for speed.
-
-:line
-
-{Tstart} and {Tstop} have to be constant values, i.e. they cannot
-be variables. If used together with the oxDNA force field for
-coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
-corresponds to T = 300 K.
-
-The {damp} parameter is specified in time units and determines how
-rapidly the temperature is relaxed.  For example, a value of 0.03
-means to relax the temperature in a timespan of (roughly) 0.03 time
-units tau (see the "units"_units.html command).
-The damp factor can be thought of as inversely related to the
-viscosity of the solvent, i.e. a small relaxation time implies a
-hi-viscosity solvent and vice versa.  See the discussion about gamma
-and viscosity in the documentation for the "fix
-viscous"_fix_viscous.html command for more details.
-Note that the value 78.9375 in the second example above corresponds
-to a diffusion constant, which is about an order of magnitude larger
-than realistic ones. This has been used to sample configurations faster
-in Brownian dynamics simulations.
-
-The random # {seed} must be a positive integer. A Marsaglia random
-number generator is used.  Each processor uses the input seed to
-generate its own unique seed and its own stream of random numbers.
-Thus the dynamics of the system will not be identical on two runs on
-different numbers of processors.
-
-The keyword/value option has to be used in the following way:
-
-This fix has to be used together with the {angmom} keyword. The
-particles are always considered to have a finite size.
-The keyword {angmom} enables thermostatting of the rotational degrees of
-freedom in addition to the usual translational degrees of freedom.
-
-The scale factor after the {angmom} keyword gives the ratio of the rotational to
-the translational friction coefficient.
-
-An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
-
-[Default:] none
-
-:line
-
-:link(Davidchack2)
-[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller2)
-[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
-:link(Dunweg3)
-[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
-:link(Henrich4)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
diff --git a/doc/txt/pair_oxdna.txt b/doc/txt/pair_oxdna.txt
deleted file mode 100644
index 8f3f9933e6..0000000000
--- a/doc/txt/pair_oxdna.txt
+++ /dev/null
@@ -1,112 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style oxdna/excv command :h3
-pair_style oxdna/stk command :h3
-pair_style oxdna/hbond command :h3
-pair_style oxdna/xstk command :h3
-pair_style oxdna/coaxstk command :h3
-
-[Syntax:]
-
-pair_style style1 :pre
-
-pair_coeff * * style2 args :pre
-
-style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
-
-style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
-args = list of arguments for these particular styles :ul
-
-  {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    xi = temperature-independent coefficient in stacking strength
-    kappa = coefficient of linear temperature dependence in stacking strength
-  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
-    eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
-
-[Examples:]
-
-pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
-pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
-
-[Description:]
-
-The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
-excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
-and coaxial stacking interaction {oxdna/coaxstk} as well
-as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
-opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported "(Sulc)"_#Sulc1. Quasi-unique base-pairing between nucleotides can be achieved by using 
-more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
-This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
-up and down along the backbone.
-
-The exact functional form of the pair styles is rather complex.
-The individual potentials consist of products of modulation factors,
-which themselves are constructed from a number of more basic potentials
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
-for a detailed description of the oxDNA force field.
-
-NOTE: These pair styles have to be used together with the related oxDNA bond style
-{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
-in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
-Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
-and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
-When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
-or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-the temperature coefficients have to be matched to the one used in the fix.
-
-Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
-A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-
-Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
-"Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
-"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
-
-[Default:] none
-
-:line
-
-:link(Henrich1)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
-
-:link(Sulc1)
-[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
-:link(Ouldridge-DPhil1)
-[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
-
-:link(Ouldridge1)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
diff --git a/doc/txt/pair_oxdna2.txt b/doc/txt/pair_oxdna2.txt
deleted file mode 100644
index 64a686d5d9..0000000000
--- a/doc/txt/pair_oxdna2.txt
+++ /dev/null
@@ -1,121 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style oxdna2/excv command :h3
-pair_style oxdna2/stk command :h3
-pair_style oxdna2/hbond command :h3
-pair_style oxdna2/xstk command :h3
-pair_style oxdna2/coaxstk command :h3
-pair_style oxdna2/dh command :h3
-
-[Syntax:]
-
-pair_style style1 :pre
-
-pair_coeff * * style2 args :pre
-
-style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
-
-style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
-args = list of arguments for these particular styles :ul
-
-  {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    xi = temperature-independent coefficient in stacking strength
-    kappa = coefficient of linear temperature dependence in stacking strength
-  {oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
-    eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
-  {oxdna2/dh} args = T rhos qeff
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    rhos = salt concentration (mole per litre)
-    qeff = effective charge (elementary charges) :pre
-
-[Examples:]
-
-pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
-pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
-pair_coeff * * oxdna2/dh      0.1 1.0 0.815 :pre
-
-[Description:]
-
-The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
-excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
-and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
-as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
-opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported "(Sulc)"_#Sulc2. Quasi-unique base-pairing between nucleotides can be achieved by using 
-more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
-This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
-up and down along the backbone.
-
-The exact functional form of the pair styles is rather complex.
-The individual potentials consist of products of modulation factors,
-which themselves are constructed from a number of more basic potentials
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
-and  "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
-
-NOTE: These pair styles have to be used together with the related oxDNA2 bond style
-{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
-in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
-Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
-the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients
-after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
-e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-the temperature coefficients have to be matched to the one used in the fix.
-
-Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
-A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-
-Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
-"Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
-"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
-
-[Default:] none
-
-:line
-
-:link(Henrich)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
-
-:link(Sulc2)
-[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
-:link(Snodin)
-[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
-
-:link(Ouldridge-DPhil2)
-[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
-
-:link(Ouldridge2)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

From a38cf075db29b32807880847a13565e6bde6ec10 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 18:53:09 -0500
Subject: [PATCH 173/199] add checks for global commands, pair and bonded
 styles

---
 doc/utils/check-styles.py | 130 ++++++++++++++++++++++++++++++++++++--
 1 file changed, 125 insertions(+), 5 deletions(-)

diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
index 3acd2aa0a9..ffa827e10c 100755
--- a/doc/utils/check-styles.py
+++ b/doc/utils/check-styles.py
@@ -2,10 +2,39 @@
 
 from __future__ import print_function
 from glob import glob
-import os, re
+from argparse import ArgumentParser
+import os, re, sys
 
-headers = glob(os.path.join('..', '..', 'src', '*', '*.h'))
-headers += glob(os.path.join('..', '..', 'src', '*.h'))
+parser = ArgumentParser(prog='check-styles.py',
+                        description="Check style table completeness")
+
+parser.add_argument("-v", "--verbose",
+                    action='store_const',
+                    const=True, default=False,
+                    help="Enable verbose output")
+
+parser.add_argument("-d", "--doc",
+                    help="Path to LAMMPS documentation sources")
+parser.add_argument("-s", "--src",
+                    help="Path to LAMMPS sources")
+
+args = parser.parse_args()
+verbose = args.verbose
+src = args.src
+doc = args.doc
+
+if not args.src or not args.doc:
+  parser.print_help()
+  sys.exit(1)
+
+if not os.path.isdir(src):
+    sys.exit("LAMMPS source path %s does not exist" % src)
+
+if not os.path.isdir(doc):
+    sys.exit("LAMMPS documentation source path %s does not exist" % doc)
+
+headers = glob(os.path.join(src, '*', '*.h'))
+headers += glob(os.path.join(src, '*.h'))
 
 angle = {}
 atom = {}
@@ -44,10 +73,28 @@ def register_style(list,style,info):
     else:
         list[style] = info
 
+def add_suffix(list,style):
+    suffix = ""
+    if list[style]['gpu']:
+        suffix += 'g'
+    if list[style]['intel']:
+        suffix += 'i'
+    if list[style]['kokkos']:
+        suffix += 'k'
+    if list[style]['omp']:
+        suffix += 'o'
+    if list[style]['opt']:
+        suffix += 't'
+    if suffix:
+        return style + ' (' + suffix + ')'
+    else:
+        return style
+        
 for h in headers:
-    # print("Checking ", h)
+    if verbose: print("Checking ", h)
     fp = open(h)
     text = fp.read()
+    fp.close()
     matches = re.findall("(.+)Style\((.+),(.+)\)",text,re.MULTILINE)
     for m in matches:
 
@@ -121,5 +168,78 @@ for h in headers:
             register_style(region,style,info)
         else:
             print("Skipping over: ",m)
-fp.close()
+
+
+if verbose:
+    print("""
+Parsed styles from %s:
+  Angle styles:     %3d
+  Atom styles:      %3d
+  Body styles:      %3d
+  Bond styles:      %3d
+  Command styles:   %3d
+  Compute styles:   %3d
+  Dihedral styles:  %3d
+  Dump styles:      %3d
+  Fix styles:       %3d
+  Improper styles:  %3d
+  Integrate styles: %3d
+  Kspace styles:    %3d
+  Minimize styles:  %3d
+  Pair styles:      %3d
+  Reader styles:    %3d
+  Region styles:    %3d
+""" % (src, len(angle), len(atom), len(body), len(bond),     \
+       len(command), len(compute), len(dihedral), len(dump), \
+       len(fix), len(improper), len(integrate), len(kspace), \
+       len(minimize), len(pair), len(reader), len(region)))
+
+
+# check main commands lists
+f = os.path.join(doc, 'Commands_all.rst')
+fp = open(f)
+text = fp.read()
+fp.close()
+matches = re.findall(":doc:`(.+) <.+>`",text,re.MULTILINE)
+for c in command.keys():
+    if not c in matches:
+        print("Command %s is missing in Commands_all.rst" % c)
+
+
+f = os.path.join(doc, 'Commands_pair.rst')
+fp = open(f)
+text = fp.read()
+fp.close()
+matches = re.findall(":doc:`(.+) <pair.+>`",text,re.MULTILINE)
+for c in pair.keys():
+    # known undocumented aliases we need to skip
+    if c in ('meam','lj/sf'): continue
+    if not add_suffix(pair,c) in matches:
+        if not pair[c]['removed']:
+            print("Pair style entry %s is missing or" % c,
+                  "incomplete in Commands_pair.rst")
+
+f = os.path.join(doc, 'Commands_bond.rst')
+fp = open(f)
+text = fp.read()
+fp.close()
+matches = re.findall(":doc:`(.+) <bond.+>`",text,re.MULTILINE)
+for c in bond.keys():
+    if not add_suffix(bond,c) in matches:
+        print("Bond style entry %s is missing or incomplete in Commands_bond.rst" % c)
+
+matches = re.findall(":doc:`(.+) <angle.+>`",text,re.MULTILINE)
+for c in angle.keys():
+    if not add_suffix(angle,c) in matches:
+        print("Angle style entry %s is missing or incomplete in Commands_bond.rst" % c)
+
+matches = re.findall(":doc:`(.+) <dihedral.+>`",text,re.MULTILINE)
+for c in dihedral.keys():
+    if not add_suffix(dihedral,c) in matches:
+        print("Dihedral style entry %s is missing or incomplete in Commands_bond.rst" % c)
+
+matches = re.findall(":doc:`(.+) <improper.+>`",text,re.MULTILINE)
+for c in improper.keys():
+    if not add_suffix(improper,c) in matches:
+        print("Improper style entry %s is missing or incomplete in Commands_bond.rst" % c)
 

From 297d31ab8f44166a0f07723a3ca52fd985b61ba0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:02:49 -0500
Subject: [PATCH 174/199] clean up and update general command overview

---
 doc/src/Commands_all.rst | 96 +++++++++++++++++++++-------------------
 1 file changed, 51 insertions(+), 45 deletions(-)

diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst
index d47c3299d0..5ad8fff44c 100644
--- a/doc/src/Commands_all.rst
+++ b/doc/src/Commands_all.rst
@@ -25,26 +25,26 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`atom_style <atom_style>`
    * :doc:`balance <balance>`
    * :doc:`bond_coeff <bond_coeff>`
-   * :doc:`bond\_style <bond_style>`
-   * :doc:`bond\_write <bond_write>`
+   * :doc:`bond_style <bond_style>`
+   * :doc:`bond_write <bond_write>`
    * :doc:`boundary <boundary>`
    * :doc:`box <box>`
-   * :doc:`change\_box <change_box>`
+   * :doc:`change_box <change_box>`
    * :doc:`clear <clear>`
-   * :doc:`comm\_modify <comm_modify>`
-   * :doc:`comm\_style <comm_style>`
+   * :doc:`comm_modify <comm_modify>`
+   * :doc:`comm_style <comm_style>`
    * :doc:`compute <compute>`
-   * :doc:`compute\_modify <compute_modify>`
-   * :doc:`create\_atoms <create_atoms>`
-   * :doc:`create\_bonds <create_bonds>`
-   * :doc:`create\_box <create_box>`
-   * :doc:`delete\_atoms <delete_atoms>`
-   * :doc:`delete\_bonds <delete_bonds>`
+   * :doc:`compute_modify <compute_modify>`
+   * :doc:`create_atoms <create_atoms>`
+   * :doc:`create_bonds <create_bonds>`
+   * :doc:`create_box <create_box>`
+   * :doc:`delete_atoms <delete_atoms>`
+   * :doc:`delete_bonds <delete_bonds>`
    * :doc:`dielectric <dielectric>`
-   * :doc:`dihedral\_coeff <dihedral_coeff>`
-   * :doc:`dihedral\_style <dihedral_style>`
+   * :doc:`dihedral_coeff <dihedral_coeff>`
+   * :doc:`dihedral_style <dihedral_style>`
    * :doc:`dimension <dimension>`
-   * :doc:`displace\_atoms <displace_atoms>`
+   * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
    * :doc:`dump adios <dump_adios>`
    * :doc:`dump image <dump_image>`
@@ -52,75 +52,77 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`dump netcdf <dump_netcdf>`
    * :doc:`dump netcdf/mpiio <dump_netcdf>`
    * :doc:`dump vtk <dump_vtk>`
-   * :doc:`dump\_modify <dump_modify>`
-   * :doc:`dynamical\_matrix <dynamical_matrix>`
+   * :doc:`dump_modify <dump_modify>`
+   * :doc:`dynamical_matrix <dynamical_matrix>`
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
-   * :doc:`fix\_modify <fix_modify>`
+   * :doc:`fix_modify <fix_modify>`
    * :doc:`group <group>`
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`if <if>`
-   * :doc:`improper\_coeff <improper_coeff>`
-   * :doc:`improper\_style <improper_style>`
+   * :doc:`improper_coeff <improper_coeff>`
+   * :doc:`improper_style <improper_style>`
    * :doc:`include <include>`
+   * :doc:`info <info>`
    * :doc:`jump <jump>`
-   * :doc:`kim\_init <kim_commands>`
-   * :doc:`kim\_interactions <kim_commands>`
-   * :doc:`kim\_query <kim_commands>`
-   * :doc:`kspace\_modify <kspace_modify>`
-   * :doc:`kspace\_style <kspace_style>`
+   * :doc:`kim_init <kim_commands>`
+   * :doc:`kim_interactions <kim_commands>`
+   * :doc:`kim_param <kim_commands>`
+   * :doc:`kim_query <kim_commands>`
+   * :doc:`kspace_modify <kspace_modify>`
+   * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`
    * :doc:`message <message>`
    * :doc:`minimize <minimize>`
-   * :doc:`min\_modify <min_modify>`
-   * :doc:`min\_style <min_style>`
-   * :doc:`min\_style spin <min_spin>`
+   * :doc:`min_modify <min_modify>`
+   * :doc:`min_style <min_style>`
+   * :doc:`min_style spin <min_spin>`
    * :doc:`molecule <molecule>`
    * :doc:`ndx2group <group2ndx>`
    * :doc:`neb <neb>`
    * :doc:`neb/spin <neb_spin>`
-   * :doc:`neigh\_modify <neigh_modify>`
+   * :doc:`neigh_modify <neigh_modify>`
    * :doc:`neighbor <neighbor>`
    * :doc:`newton <newton>`
    * :doc:`next <next>`
    * :doc:`package <package>`
-   * :doc:`pair\_coeff <pair_coeff>`
-   * :doc:`pair\_modify <pair_modify>`
-   * :doc:`pair\_write <pair_write>`
+   * :doc:`pair_coeff <pair_coeff>`
+   * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
    * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`
    * :doc:`python <python>`
    * :doc:`quit <quit>`
-   * :doc:`read\_data <read_data>`
-   * :doc:`read\_dump <read_dump>`
-   * :doc:`read\_restart <read_restart>`
+   * :doc:`read_data <read_data>`
+   * :doc:`read_dump <read_dump>`
+   * :doc:`read_restart <read_restart>`
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset\_ids <reset_ids>`
-   * :doc:`reset\_timestep <reset_timestep>`
+   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`
-   * :doc:`run\_style <run_style>`
+   * :doc:`run_style <run_style>`
    * :doc:`server <server>`
    * :doc:`set <set>`
    * :doc:`shell <shell>`
-   * :doc:`special\_bonds <special_bonds>`
+   * :doc:`special_bonds <special_bonds>`
    * :doc:`suffix <suffix>`
    * :doc:`tad <tad>`
    * :doc:`temper <temper>`
    * :doc:`temper/grem <temper_grem>`
    * :doc:`temper/npt <temper_npt>`
    * :doc:`thermo <thermo>`
-   * :doc:`thermo\_modify <thermo_modify>`
-   * :doc:`thermo\_style <thermo_style>`
-   * :doc:`third\_order <third_order>`
+   * :doc:`thermo_modify <thermo_modify>`
+   * :doc:`thermo_style <thermo_style>`
+   * :doc:`third_order <third_order>`
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
    * :doc:`uncompute <uncompute>`
@@ -129,7 +131,11 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`units <units>`
    * :doc:`variable <variable>`
    * :doc:`velocity <velocity>`
-   * :doc:`write\_coeff <write_coeff>`
-   * :doc:`write\_data <write_data>`
-   * :doc:`write\_dump <write_dump>`
-   * :doc:`write\_restart <write_restart>`
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`
+   *
+   *
+   *
+   *

From f713e9acc3a4dfa3b48236a66eab72b6fd1a892e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:03:20 -0500
Subject: [PATCH 175/199] add missing bond style

---
 doc/src/Commands_bond.rst | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
index dbf7344394..8e43605c80 100644
--- a/doc/src/Commands_bond.rst
+++ b/doc/src/Commands_bond.rst
@@ -44,12 +44,10 @@ OPT.
    * :doc:`nonlinear (o) <bond_nonlinear>`
    * :doc:`oxdna/fene <bond_oxdna>`
    * :doc:`oxdna2/fene <bond_oxdna>`
+   * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
    * :doc:`table (o) <bond_table>`
    *
-   *
-
----
 
 .. _angle:
 
@@ -93,8 +91,6 @@ OPT.
    * :doc:`table (o) <angle_table>`
    *
 
----
-
 .. _dihedral:
 
 dihedral_style potentials

From 84a975439a6f491d557d16caba686982b56bface Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:04:02 -0500
Subject: [PATCH 176/199] clean up pair style command overview some

---
 doc/src/Commands_pair.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index 0844e0a2fe..757a676c16 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -11,10 +11,10 @@
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
-Pair\_style potentials
+Pair_style potentials
 ======================
 
-All LAMMPS :doc:`pair\_style <pair_style>` commands.  Some styles have
+All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
@@ -209,7 +209,7 @@ OPT.
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
    * :doc:`smd/hertz <pair_smd_hertz>`
    * :doc:`smd/tlsph <pair_smd_tlsph>`
-   * :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`
+   * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (k) <pair_snap>`

From 66296616ae92d8457a62059984551ade0bbe4a44 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:10:21 -0500
Subject: [PATCH 177/199] handle removed styles on bonded command table

---
 doc/utils/check-styles.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
index ffa827e10c..133184ff63 100755
--- a/doc/utils/check-styles.py
+++ b/doc/utils/check-styles.py
@@ -226,20 +226,28 @@ fp.close()
 matches = re.findall(":doc:`(.+) <bond.+>`",text,re.MULTILINE)
 for c in bond.keys():
     if not add_suffix(bond,c) in matches:
-        print("Bond style entry %s is missing or incomplete in Commands_bond.rst" % c)
+        if not bond[c]['removed']:
+            print("Bond style entry %s is missing or" % c,
+                  "incomplete in Commands_bond.rst")
 
 matches = re.findall(":doc:`(.+) <angle.+>`",text,re.MULTILINE)
 for c in angle.keys():
     if not add_suffix(angle,c) in matches:
-        print("Angle style entry %s is missing or incomplete in Commands_bond.rst" % c)
+        if not angle[c]['removed']:
+            print("Angle style entry %s is missing or" % c,
+                  "incomplete in Commands_bond.rst")
 
 matches = re.findall(":doc:`(.+) <dihedral.+>`",text,re.MULTILINE)
 for c in dihedral.keys():
     if not add_suffix(dihedral,c) in matches:
-        print("Dihedral style entry %s is missing or incomplete in Commands_bond.rst" % c)
+        if not dihedral[c]['removed']:
+            print("Dihedral style entry %s is missing or" % c,
+                  "incomplete in Commands_bond.rst")
 
 matches = re.findall(":doc:`(.+) <improper.+>`",text,re.MULTILINE)
 for c in improper.keys():
     if not add_suffix(improper,c) in matches:
-        print("Improper style entry %s is missing or incomplete in Commands_bond.rst" % c)
+        if not improper[c]['removed']:
+            print("Improper style entry %s is missing or" % c,
+                  "incomplete in Commands_bond.rst")
 

From ff7110028b14758e8042ccd46ca5d89173ea00a7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:16:34 -0500
Subject: [PATCH 178/199] make doc of pair style mm3/switch3/coulgauss/long
 consistent and complete

---
 doc/src/Commands_pair.rst                     |  2 +-
 ...st => pair_mm3_switch3_coulgauss_long.rst} |  2 +-
 doc/src/pair_style.rst                        |  2 +-
 doc/txt/pair_mm3_switch3_coulgauss.txt        | 88 -------------------
 4 files changed, 3 insertions(+), 91 deletions(-)
 rename doc/src/{pair_mm3_switch3_coulgauss.rst => pair_mm3_switch3_coulgauss_long.rst} (98%)
 delete mode 100644 doc/txt/pair_mm3_switch3_coulgauss.txt

diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index 757a676c16..eaf0e680a0 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -176,6 +176,7 @@ OPT.
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
    * :doc:`morse/smooth/linear (o) <pair_morse>`
@@ -249,4 +250,3 @@ OPT.
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`
    *
-   *
diff --git a/doc/src/pair_mm3_switch3_coulgauss.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst
similarity index 98%
rename from doc/src/pair_mm3_switch3_coulgauss.rst
rename to doc/src/pair_mm3_switch3_coulgauss_long.rst
index c124b9b9b8..3f3a7cbc72 100644
--- a/doc/src/pair_mm3_switch3_coulgauss.rst
+++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst
@@ -37,7 +37,7 @@ Examples
 Description
 """""""""""
 
-The *mm3/switch3/coulgauss* style evaluates the MM3
+The *mm3/switch3/coulgauss/long* style evaluates the MM3
 vdW potential :ref:`(Allinger) <mm3-allinger1989>`
 
 .. image:: Eqs/pair_mm3_switch3.jpg
diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst
index f6f686fc12..db3056ed64 100644
--- a/doc/src/pair_style.rst
+++ b/doc/src/pair_style.rst
@@ -245,7 +245,7 @@ accelerated styles exist.
 * :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
 * :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
 * :doc:`mie/cut <pair_mie>` - Mie potential
-* `mm3/switch3/coulgauss <pair_mm3_switch3_coulgauss>`_ - smoothed MM3 vdW potential with Gaussian electrostatics
+* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`_ - smoothed MM3 vdW potential with Gaussian electrostatics
 * :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
 * :doc:`morse <pair_morse>` - Morse potential
 * :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential
diff --git a/doc/txt/pair_mm3_switch3_coulgauss.txt b/doc/txt/pair_mm3_switch3_coulgauss.txt
deleted file mode 100644
index 86e6a0d1d9..0000000000
--- a/doc/txt/pair_mm3_switch3_coulgauss.txt
+++ /dev/null
@@ -1,88 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style mm3/switch3/coulgauss/long command :h3
-
-[Syntax:]
-
-pair_style style args :pre
-
-style = {mm3/switch3/coulgauss/long}
-args = list of arguments for a particular style :ul
-  {mm3/switch3/coulgauss/long} args = cutoff (cutoff2) width
-    cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-    width  = width parameter of the smoothing function (distance units) :pre
-
-[Examples:]
-
-pair_style mm3/switch3/coulgauss/long    12.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-[Description:]
-
-The {mm3/switch3/coulgauss} style evaluates the MM3
-vdW potential "(Allinger)"_#mm3-allinger1989
-
-:c,image(Eqs/pair_mm3_switch3.jpg)
-
-, which goes smoothly to zero at the cutoff r_c as defined
-by the switching function
-
-:c,image(Eqs/pair_switch3.jpg)
-
-where w is the width defined in the arguments. This potential
-is combined with Coulomb interaction between Gaussian charge densities:
-
-:c,image(Eqs/pair_coulgauss.jpg)
-
-where qi and qj are the
-charges on the 2 atoms, epsilon is the dielectric constant which
-can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
-are the widths of the Gaussian charge distribution and erf() is the error-function.
-This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
-
-If one cutoff is specified it is used for both the vdW and Coulomb
-terms.  If two cutoffs are specified, the first is used as the cutoff
-for the vdW terms, and the second is the cutoff for the Coulombic term.
-
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-epsilon (energy)
-r_v (distance)
-gamma (distance) :ul
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-Mixing rules are fixed for this style as defined above.
-
-Shifting the potential energy is not necessary because the switching
-function ensures that the potential is zero at the cut-off.
-
-
-[Restrictions:]
-
-These styles are part of the USER-YAFF package.  They are only
-enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html
-
-[Default:] none
-

From 1d838dad19f8db330a88d70a8c754b61f6acfd6b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:41:59 -0500
Subject: [PATCH 179/199] add checking of kspace styles

---
 doc/utils/check-styles.py | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
index 133184ff63..23d7e9ab05 100755
--- a/doc/utils/check-styles.py
+++ b/doc/utils/check-styles.py
@@ -203,8 +203,8 @@ fp.close()
 matches = re.findall(":doc:`(.+) <.+>`",text,re.MULTILINE)
 for c in command.keys():
     if not c in matches:
-        print("Command %s is missing in Commands_all.rst" % c)
-
+        if not command[c]['removed']:
+            print("Command %s is missing in Commands_all.rst" % c)
 
 f = os.path.join(doc, 'Commands_pair.rst')
 fp = open(f)
@@ -251,3 +251,14 @@ for c in improper.keys():
             print("Improper style entry %s is missing or" % c,
                   "incomplete in Commands_bond.rst")
 
+f = os.path.join(doc, 'Commands_kspace.rst')
+fp = open(f)
+text = fp.read()
+fp.close()
+matches = re.findall(":doc:`(.+) <kspace_style>`",text,re.MULTILINE)
+for c in kspace.keys():
+    if not add_suffix(kspace,c) in matches:
+        if not kspace[c]['removed']:
+            print("KSpace style entry %s is missing or" % c,
+                  "incomplete in Commands_kspace.rst")
+            print(kspace[c])

From 7ea366b3ced9b66d08ece6cb86c7ec6cb64b33fc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:42:40 -0500
Subject: [PATCH 180/199] fix formatting issue

---
 doc/src/Commands_bond.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
index 8e43605c80..27ff2d19da 100644
--- a/doc/src/Commands_bond.rst
+++ b/doc/src/Commands_bond.rst
@@ -13,7 +13,7 @@
 
 .. _bond:
 
-bond_style potentials
+Bond_style potentials
 =====================
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
@@ -51,7 +51,7 @@ OPT.
 
 .. _angle:
 
-angle_style potentials
+Angle_style potentials
 ======================
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
@@ -93,7 +93,7 @@ OPT.
 
 .. _dihedral:
 
-dihedral_style potentials
+Dihedral_style potentials
 =========================
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
@@ -132,7 +132,7 @@ OPT.
 
 .. _improper:
 
-improper_style potentials
+Improper_style potentials
 =========================
 
 All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles

From 019c70140fd735b8f9fcc406abeb9af98dfe2ac1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:43:00 -0500
Subject: [PATCH 181/199] add and correct kspace style entries

---
 doc/src/Commands_kspace.rst | 10 +++++++---
 doc/src/kspace_style.rst    | 27 ++++++++++++++++-----------
 2 files changed, 23 insertions(+), 14 deletions(-)

diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst
index fc2418ecf7..3a23520171 100644
--- a/doc/src/Commands_kspace.rst
+++ b/doc/src/Commands_kspace.rst
@@ -24,12 +24,16 @@ OPT.
 
    * :doc:`ewald (o) <kspace_style>`
    * :doc:`ewald/disp <kspace_style>`
+   * :doc:`ewald/dipole <kspace_style>`
+   * :doc:`ewald/dipole/spin <kspace_style>`
    * :doc:`msm (o) <kspace_style>`
    * :doc:`msm/cg (o) <kspace_style>`
-   * :doc:`pppm (gok) <kspace_style>`
+   * :doc:`pppm (giko) <kspace_style>`
    * :doc:`pppm/cg (o) <kspace_style>`
-   * :doc:`pppm/disp (i) <kspace_style>`
-   * :doc:`pppm/disp/tip4p <kspace_style>`
+   * :doc:`pppm/dipole <kspace_style>`
+   * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/disp (io) <kspace_style>`
+   * :doc:`pppm/disp/tip4p (o) <kspace_style>`
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
    * :doc:`scafacos <kspace_style>`
diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst
index b5c649a885..c35e38d1db 100644
--- a/doc/src/kspace_style.rst
+++ b/doc/src/kspace_style.rst
@@ -11,26 +11,30 @@ Syntax
 
    kspace_style style value
 
-* style = *none* or *ewald* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
+* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
   
   .. parsed-literal::
   
        *none* value = none
        *ewald* value = accuracy
          accuracy = desired relative error in forces
-       *ewald/disp* value = accuracy
-         accuracy = desired relative error in forces
-       *ewald/omp* value = accuracy
-         accuracy = desired relative error in forces
        *ewald/dipole* value = accuracy
          accuracy = desired relative error in forces
        *ewald/dipole/spin* value = accuracy
          accuracy = desired relative error in forces
+       *ewald/disp* value = accuracy
+         accuracy = desired relative error in forces
+       *ewald/omp* value = accuracy
+         accuracy = desired relative error in forces
        *pppm* value = accuracy
          accuracy = desired relative error in forces
        *pppm/cg* values = accuracy (smallq)
          accuracy = desired relative error in forces
          smallq = cutoff for charges to be considered (optional) (charge units)
+       *pppm/dipole* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/dipole/spin* value = accuracy
+         accuracy = desired relative error in forces
        *pppm/disp* value = accuracy
          accuracy = desired relative error in forces
        *pppm/tip4p* value = accuracy
@@ -41,22 +45,23 @@ Syntax
          accuracy = desired relative error in forces
        *pppm/intel* value = accuracy
          accuracy = desired relative error in forces
+       *pppm/disp/intel* value = accuracy
+         accuracy = desired relative error in forces
        *pppm/kk* value = accuracy
          accuracy = desired relative error in forces
        *pppm/omp* value = accuracy
          accuracy = desired relative error in forces
-       *pppm/cg/omp* value = accuracy
+       *pppm/cg/omp* values = accuracy (smallq)
          accuracy = desired relative error in forces
-       *pppm/disp/intel* value = accuracy
+         smallq = cutoff for charges to be considered (optional) (charge units)
+       *pppm/disp/omp* value = accuracy
          accuracy = desired relative error in forces
        *pppm/tip4p/omp* value = accuracy
          accuracy = desired relative error in forces
+       *pppm/disp/tip4p/omp* value = accuracy
+         accuracy = desired relative error in forces
        *pppm/stagger* value = accuracy
          accuracy = desired relative error in forces
-       *pppm/dipole* value = accuracy
-         accuracy = desired relative error in forces
-       *pppm/dipole/spin* value = accuracy
-         accuracy = desired relative error in forces
        *msm* value = accuracy
          accuracy = desired relative error in forces
        *msm/cg* value = accuracy (smallq)

From 05b68d9e0d6ab24b6915d8af3806543bd580cb0f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:43:29 -0500
Subject: [PATCH 182/199] add missing pair style entries

---
 doc/src/Commands_pair.rst | 8 ++++++++
 doc/src/pair_style.rst    | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index eaf0e680a0..23765c84f6 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -198,10 +198,17 @@ OPT.
    * :doc:`oxdna2/hbond <pair_oxdna2>`
    * :doc:`oxdna2/stk <pair_oxdna2>`
    * :doc:`oxdna2/xstk <pair_oxdna2>`
+   * :doc:`oxrna2/excv <pair_oxrna2>`
+   * :doc:`oxrna2/hbond <pair_oxrna2>`
+   * :doc:`oxrna2/dh <pair_oxrna2>`
+   * :doc:`oxrna2/stk <pair_oxrna2>`
+   * :doc:`oxrna2/xstk <pair_oxrna2>`
+   * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
    * :doc:`peri/ves <pair_peri>`
+   * :doc:`polymorphic <pair_polymorphic>`
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
    * :doc:`reax/c (ko) <pair_reaxc>`
@@ -250,3 +257,4 @@ OPT.
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`
    *
+   *
diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst
index db3056ed64..84548720c0 100644
--- a/doc/src/pair_style.rst
+++ b/doc/src/pair_style.rst
@@ -245,7 +245,7 @@ accelerated styles exist.
 * :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
 * :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
 * :doc:`mie/cut <pair_mie>` - Mie potential
-* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`_ - smoothed MM3 vdW potential with Gaussian electrostatics
+* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
 * :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
 * :doc:`morse <pair_morse>` - Morse potential
 * :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential

From bc9436a04f149fc0cece2daaf933d01bcc586690 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 19:58:31 -0500
Subject: [PATCH 183/199] add support for computes and fixes

---
 doc/utils/check-styles.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
index 23d7e9ab05..1bd1c10981 100755
--- a/doc/utils/check-styles.py
+++ b/doc/utils/check-styles.py
@@ -206,6 +206,30 @@ for c in command.keys():
         if not command[c]['removed']:
             print("Command %s is missing in Commands_all.rst" % c)
 
+f = os.path.join(doc, 'Commands_compute.rst')
+fp = open(f)
+text = fp.read()
+fp.close()
+matches = re.findall(":doc:`(.+) <compute.+>`",text,re.MULTILINE)
+for c in compute.keys():
+    if not add_suffix(compute,c) in matches:
+        if not compute[c]['removed']:
+            print("Compute style entry %s is missing or" % c,
+                  "incomplete in Commands_compute.rst")
+
+f = os.path.join(doc, 'Commands_fix.rst')
+fp = open(f)
+text = fp.read()
+fp.close()
+matches = re.findall(":doc:`(.+) <fix.+>`",text,re.MULTILINE)
+for c in fix.keys():
+    # known undocumented aliases we need to skip
+    if c in ('python'): continue
+    if not add_suffix(fix,c) in matches:
+        if not fix[c]['removed']:
+            print("Fix style entry %s is missing or" % c,
+                  "incomplete in Commands_fix.rst")
+
 f = os.path.join(doc, 'Commands_pair.rst')
 fp = open(f)
 text = fp.read()

From b4a87d79a0f5c505621b9713c8d9c6fca9d63a7e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 20:02:04 -0500
Subject: [PATCH 184/199] make anchors and file names for
 lj/switch3/coulgauss/long consistent

---
 doc/src/Commands_pair.rst                                     | 2 +-
 doc/src/Packages_details.rst                                  | 4 ++--
 ...itch3_coulgauss.rst => pair_lj_switch3_coulgauss_long.rst} | 0
 doc/src/pair_style.rst                                        | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)
 rename doc/src/{pair_lj_switch3_coulgauss.rst => pair_lj_switch3_coulgauss_long.rst} (100%)

diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index 23765c84f6..06eda554a3 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -162,7 +162,7 @@ OPT.
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/smooth (o) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
-   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
+   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`lj96/cut (go) <pair_lj96>`
    * :doc:`local/density <pair_local_density>`
    * :doc:`lubricate (o) <pair_lubricate>`
diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst
index a8274d5403..62615a8fb7 100644
--- a/doc/src/Packages_details.rst
+++ b/doc/src/Packages_details.rst
@@ -2438,8 +2438,8 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 * :doc:`bond\_style mm3 <bond_mm3>`
 * :doc:`improper\_style distharm <improper_distharm>`
 * :doc:`improper\_style sqdistharm <improper_sqdistharm>`
-* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss>`
-* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
+* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * examples/USER/yaff
 
 
diff --git a/doc/src/pair_lj_switch3_coulgauss.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst
similarity index 100%
rename from doc/src/pair_lj_switch3_coulgauss.rst
rename to doc/src/pair_lj_switch3_coulgauss_long.rst
diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst
index 84548720c0..d8fe77d1dc 100644
--- a/doc/src/pair_style.rst
+++ b/doc/src/pair_style.rst
@@ -231,7 +231,7 @@ accelerated styles exist.
 * :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
 * :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
 * :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
-* `lj/switch3/coulgauss <pair_lj_switch3_coulgauss>`_ - smoothed LJ vdW potential with Gaussian electrostatics
+* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed LJ vdW potential with Gaussian electrostatics
 * :doc:`lj96/cut <pair_lj96>` - Lennard-Jones 9/6 potential
 * :doc:`local/density <pair_local_density>` - generalized basic local density potential
 * :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces

From b2c438566199613db0e516afaf89315d7b618056 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 20:02:23 -0500
Subject: [PATCH 185/199] clean up and correct fix style command overview

---
 doc/src/Commands_fix.rst | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index 4cd9a4487c..9584cbf64f 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -105,13 +105,13 @@ OPT.
    * :doc:`mvv/edpd <fix_mvv_dpd>`
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
-   * :doc:`neb\_spin <fix_neb_spin>`
+   * :doc:`neb/spin <fix_neb_spin>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
    * :doc:`nph/body <fix_nph_body>`
    * :doc:`nph/eff <fix_nh_eff>`
    * :doc:`nph/sphere (o) <fix_nph_sphere>`
-   * :doc:`nphug (o) <fix_nphug>`
+   * :doc:`nphug <fix_nphug>`
    * :doc:`npt (iko) <fix_nh>`
    * :doc:`npt/asphere (o) <fix_npt_asphere>`
    * :doc:`npt/body <fix_npt_body>`
@@ -188,15 +188,16 @@ OPT.
    * :doc:`rx (k) <fix_rx>`
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
+   * :doc:`setforce/spin <fix_setforce>`
    * :doc:`shake <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`
-   * :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`
-   * :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>`
-   * :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`
-   * :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>`
+   * :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
+   * :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`
+   * :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`
+   * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
    * :doc:`smd/setvel <fix_smd_setvel>`
-   * :doc:`smd/wall\_surface <fix_smd_wall_surface>`
+   * :doc:`smd/wall_surface <fix_smd_wall_surface>`
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`
@@ -237,4 +238,3 @@ OPT.
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
    *
-   *

From 26830d09f88ad626815973c0c9fb6b7803b93abd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 20:39:58 -0500
Subject: [PATCH 186/199] hook style check into makefile

---
 doc/Makefile | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/doc/Makefile b/doc/Makefile
index eceae88da6..c82b414fff 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
 OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check
 
 # ------------------------------------------
 
@@ -46,6 +46,7 @@ help:
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  anchor_check  scan for duplicate anchor labels"
+	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  spelling   spell-check the manual"
 
 # ------------------------------------------
@@ -69,6 +70,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -126,6 +128,8 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
                 sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
                 echo "############################################" ;\
                 rst_anchor_check src/*.rst ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
                 echo "############################################" ;\
                 deactivate ;\
 	)
@@ -166,6 +170,13 @@ anchor_check : $(ANCHORCHECK)
 		deactivate ;\
 	)
 
+style_check :
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		deactivate ;\
+	)
+
 # ------------------------------------------
 
 $(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)

From d7242eaa6afe069edd17a90e8b58e98e9a76aeb8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 20:41:14 -0500
Subject: [PATCH 187/199] print total styles and count/report the number of
 issues

---
 doc/utils/check-styles.py                     | 46 ++++++++++---------
 .../converters/lammpsdoc/rst_anchor_check.py  |  2 +-
 2 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
index 1bd1c10981..b725efeef9 100755
--- a/doc/utils/check-styles.py
+++ b/doc/utils/check-styles.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 from __future__ import print_function
 from glob import glob
@@ -170,31 +170,22 @@ for h in headers:
             print("Skipping over: ",m)
 
 
-if verbose:
-    print("""
-Parsed styles from %s:
-  Angle styles:     %3d
-  Atom styles:      %3d
-  Body styles:      %3d
-  Bond styles:      %3d
-  Command styles:   %3d
-  Compute styles:   %3d
-  Dihedral styles:  %3d
-  Dump styles:      %3d
-  Fix styles:       %3d
-  Improper styles:  %3d
-  Integrate styles: %3d
-  Kspace styles:    %3d
-  Minimize styles:  %3d
-  Pair styles:      %3d
-  Reader styles:    %3d
-  Region styles:    %3d
-""" % (src, len(angle), len(atom), len(body), len(bond),     \
+print("""Parsed styles from C++ tree in %s:
+   Angle styles:     %3d    Atom styles:      %3d
+   Body styles:      %3d    Bond styles:      %3d
+   Command styles:   %3d    Compute styles:   %3d
+   Dihedral styles:  %3d    Dump styles:      %3d
+   Fix styles:       %3d    Improper styles:  %3d
+   Integrate styles: %3d    Kspace styles:    %3d
+   Minimize styles:  %3d    Pair styles:      %3d
+   Reader styles:    %3d    Region styles:    %3d""" \
+      % (src, len(angle), len(atom), len(body), len(bond),   \
        len(command), len(compute), len(dihedral), len(dump), \
        len(fix), len(improper), len(integrate), len(kspace), \
        len(minimize), len(pair), len(reader), len(region)))
 
 
+counter = 0
 # check main commands lists
 f = os.path.join(doc, 'Commands_all.rst')
 fp = open(f)
@@ -205,6 +196,7 @@ for c in command.keys():
     if not c in matches:
         if not command[c]['removed']:
             print("Command %s is missing in Commands_all.rst" % c)
+            counter += 1
 
 f = os.path.join(doc, 'Commands_compute.rst')
 fp = open(f)
@@ -216,6 +208,7 @@ for c in compute.keys():
         if not compute[c]['removed']:
             print("Compute style entry %s is missing or" % c,
                   "incomplete in Commands_compute.rst")
+            counter += 1
 
 f = os.path.join(doc, 'Commands_fix.rst')
 fp = open(f)
@@ -229,6 +222,7 @@ for c in fix.keys():
         if not fix[c]['removed']:
             print("Fix style entry %s is missing or" % c,
                   "incomplete in Commands_fix.rst")
+            counter += 1
 
 f = os.path.join(doc, 'Commands_pair.rst')
 fp = open(f)
@@ -242,6 +236,7 @@ for c in pair.keys():
         if not pair[c]['removed']:
             print("Pair style entry %s is missing or" % c,
                   "incomplete in Commands_pair.rst")
+            counter += 1
 
 f = os.path.join(doc, 'Commands_bond.rst')
 fp = open(f)
@@ -253,6 +248,7 @@ for c in bond.keys():
         if not bond[c]['removed']:
             print("Bond style entry %s is missing or" % c,
                   "incomplete in Commands_bond.rst")
+            counter += 1
 
 matches = re.findall(":doc:`(.+) <angle.+>`",text,re.MULTILINE)
 for c in angle.keys():
@@ -260,6 +256,7 @@ for c in angle.keys():
         if not angle[c]['removed']:
             print("Angle style entry %s is missing or" % c,
                   "incomplete in Commands_bond.rst")
+            counter += 1
 
 matches = re.findall(":doc:`(.+) <dihedral.+>`",text,re.MULTILINE)
 for c in dihedral.keys():
@@ -267,6 +264,7 @@ for c in dihedral.keys():
         if not dihedral[c]['removed']:
             print("Dihedral style entry %s is missing or" % c,
                   "incomplete in Commands_bond.rst")
+            counter += 1
 
 matches = re.findall(":doc:`(.+) <improper.+>`",text,re.MULTILINE)
 for c in improper.keys():
@@ -274,6 +272,7 @@ for c in improper.keys():
         if not improper[c]['removed']:
             print("Improper style entry %s is missing or" % c,
                   "incomplete in Commands_bond.rst")
+            counter += 1
 
 f = os.path.join(doc, 'Commands_kspace.rst')
 fp = open(f)
@@ -286,3 +285,8 @@ for c in kspace.keys():
             print("KSpace style entry %s is missing or" % c,
                   "incomplete in Commands_kspace.rst")
             print(kspace[c])
+            counter += 1
+
+if counter:
+    print("Found %d issue(s) with style lists" % counter)
+
diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py
index 9c097e7d0e..64a1308601 100644
--- a/doc/utils/converters/lammpsdoc/rst_anchor_check.py
+++ b/doc/utils/converters/lammpsdoc/rst_anchor_check.py
@@ -42,7 +42,7 @@ def main():
                     else:
                         anchors[label] = [(filename, line_number+1)]
 
-    print("found %d anchor labels" % len(anchors))
+    print("Found %d anchor labels" % len(anchors))
 
     count = 0
 

From 3b3214133092465d99d204f5045fa8a42ba3b77b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 20:47:10 -0500
Subject: [PATCH 188/199] update documentation for style check

---
 doc/src/Manual_build.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/src/Manual_build.rst b/doc/src/Manual_build.rst
index a8bc093812..c1cd1aabb9 100644
--- a/doc/src/Manual_build.rst
+++ b/doc/src/Manual_build.rst
@@ -55,9 +55,9 @@ the doc dir.
    make mobi         # generate LAMMPS.mobi in MOBI format using ebook-convert
    make clean        # remove intermediate RST files created by HTML build
    make clean-all    # remove entire build folder and any cached data
-
-make anchor\_check # check for duplicate anchor labels
-make spelling     # spell-check the manual
+   make anchor_check # check for duplicate anchor labels
+   style_check       # check for complete and consistent style lists
+   make spelling     # spell-check the manual
 
 
 ----------

From a957d1c4c20bb7e929fa7a3dafc37da3b27ab650 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 11 Jan 2020 21:05:08 -0500
Subject: [PATCH 189/199] fix whitespace issue

---
 src/MC/fix_bond_break.cpp  | 2 +-
 src/MC/fix_bond_create.cpp | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 520abb9d32..2e8200f751 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -33,7 +33,7 @@ using namespace FixConst;
 
 FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL), 
+  partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL),
   broken(NULL), copy(NULL), random(NULL)
 {
   if (narg < 6) error->all(FLERR,"Illegal fix bond/break command");
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index a7f955ad0b..629e6defff 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -226,7 +226,7 @@ void FixBondCreate::init()
     if (strcmp(modify->fix[i]->style,"bond/create") == 0) count++;
     if (strcmp(modify->fix[i]->style,"bond/break") == 0) count++;
   }
-  if (count > 1 && me == 0) 
+  if (count > 1 && me == 0)
     error->warning(FLERR,"Fix bond/create is used multiple times "
                    " or with fix bond/break - may not work as expected");
 

From a0ecf539f6c31609287fe21560c04d7ba03b3f03 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 12 Jan 2020 10:08:14 -0500
Subject: [PATCH 190/199] clean up and correct some documentation link issues

---
 doc/src/bond_style.rst |   1 +
 doc/src/fix.rst        |  22 +--
 doc/src/pair_style.rst |  33 ++--
 doc/txt/pair_style.txt | 338 -----------------------------------------
 4 files changed, 33 insertions(+), 361 deletions(-)
 delete mode 100644 doc/txt/pair_style.txt

diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst
index 3c5c97b96b..dd3acb6833 100644
--- a/doc/src/bond_style.rst
+++ b/doc/src/bond_style.rst
@@ -100,6 +100,7 @@ accelerated styles exist.
 * :doc:`nonlinear <bond_nonlinear>` - nonlinear bond
 * :doc:`oxdna/fene <bond_oxdna>` - modified FENE bond suitable for DNA modeling
 * :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
+* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
 * :doc:`quartic <bond_quartic>` - breakable quartic bond
 * :doc:`table <bond_table>` - tabulated by bond length
 
diff --git a/doc/src/fix.rst b/doc/src/fix.rst
index a9ec639b33..cc99940f81 100644
--- a/doc/src/fix.rst
+++ b/doc/src/fix.rst
@@ -64,16 +64,16 @@ with new settings).  This is the same as if an "unfix" command were
 first performed on the old fix, except that the new fix is kept in the
 same order relative to the existing fixes as the old one originally
 was.  Note that this operation also wipes out any additional changes
-made to the old fix via the :doc:`fix\_modify <fix_modify>` command.
+made to the old fix via the :doc:`fix_modify <fix_modify>` command.
 
 The :doc:`fix modify <fix_modify>` command allows settings for some
 fixes to be reset.  See the doc page for individual fixes for details.
 
 Some fixes store an internal "state" which is written to binary
 restart files via the :doc:`restart <restart>` or
-:doc:`write\_restart <write_restart>` commands.  This allows the fix to
+:doc:`write_restart <write_restart>` commands.  This allows the fix to
 continue on with its calculations in a restarted simulation.  See the
-:doc:`read\_restart <read_restart>` command for info on how to re-specify
+:doc:`read_restart <read_restart>` command for info on how to re-specify
 a fix in an input script that reads a restart file.  See the doc pages
 for individual fixes for info on which ones can be restarted.
 
@@ -133,7 +133,7 @@ various commands explain the details.
 
 In LAMMPS, the values generated by a fix can be used in several ways:
 
-* Global values can be output via the :doc:`thermo\_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
+* Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
   Or the values can be referenced in a :doc:`variable equal <variable>` or
   :doc:`variable atom <variable>` command.
 * Per-atom values can be output via the :doc:`dump custom <dump>` command.
@@ -257,6 +257,7 @@ accelerated styles exist.
 * :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm
 * :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
 * :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
+* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
 * :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
 * :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
 * :doc:`nph/body <fix_nph_body>` - NPH for body particles
@@ -339,15 +340,16 @@ accelerated styles exist.
 * :doc:`rx <fix_rx>` -
 * :doc:`saed/vtk <fix_saed_vtk>` -
 * :doc:`setforce <fix_setforce>` - set the force on each atom
+* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
 * :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
 * :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
 * :doc:`smd <fix_smd>` - applied a steered MD force to a group
-* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` -
-* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` -
-* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` -
-* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` -
+* :doc:`smd/adjust_dt <fix_smd_adjust_dt>` -
+* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>` -
+* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>` -
+* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
 * :doc:`smd/setvel <fix_smd_setvel>` -
-* :doc:`smd/wall\_surface <fix_smd_wall_surface>` -
+* :doc:`smd/wall_surface <fix_smd_wall_surface>` -
 * :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
 * :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
 * :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
@@ -399,7 +401,7 @@ individual fixes tell if it is part of a package.
 Related commands
 """"""""""""""""
 
-:doc:`unfix <unfix>`, :doc:`fix\_modify <fix_modify>`
+:doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`
 
 **Default:** none
 
diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst
index d8fe77d1dc..9b23266ca8 100644
--- a/doc/src/pair_style.rst
+++ b/doc/src/pair_style.rst
@@ -32,7 +32,7 @@ Description
 Set the formula(s) LAMMPS uses to compute pairwise interactions.  In
 LAMMPS, pair potentials are defined between pairs of atoms that are
 within a cutoff distance and the set of active interactions typically
-changes over time.  See the :doc:`bond\_style <bond_style>` command to
+changes over time.  See the :doc:`bond_style <bond_style>` command to
 define potentials between pairs of bonded atoms, which typically
 remain in place for the duration of a simulation.
 
@@ -48,11 +48,11 @@ different pair potentials can be setup using the *hybrid* pair style.
 
 The coefficients associated with a pair style are typically set for
 each pair of atom types, and are specified by the
-:doc:`pair\_coeff <pair_coeff>` command or read from a file by the
-:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+:doc:`pair_coeff <pair_coeff>` command or read from a file by the
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands.
 
-The :doc:`pair\_modify <pair_modify>` command sets options for mixing of
+The :doc:`pair_modify <pair_modify>` command sets options for mixing of
 type I-J interaction coefficients and adding energy offsets or tail
 corrections to Lennard-Jones potentials.  Details on these options as
 they pertain to individual potentials are described on the doc page
@@ -70,11 +70,11 @@ cutoffs for all pairs of atom types.  The distance(s) can be smaller
 or larger than the dimensions of the simulation box.
 
 Typically, the global cutoff value can be overridden for a specific
-pair of atom types by the :doc:`pair\_coeff <pair_coeff>` command.  The
+pair of atom types by the :doc:`pair_coeff <pair_coeff>` command.  The
 pair style settings (including global cutoffs) can be changed by a
 subsequent pair\_style command using the same style.  This will reset
 the cutoffs for all atom type pairs, including those previously set
-explicitly by a :doc:`pair\_coeff <pair_coeff>` command.  The exceptions
+explicitly by a :doc:`pair_coeff <pair_coeff>` command.  The exceptions
 to this are that pair\_style *table* and *hybrid* settings cannot be
 reset.  A new pair\_style command for these styles will wipe out all
 previously specified pair\_coeff values.
@@ -88,7 +88,7 @@ also listed in more compact form on the :doc:`Commands pair <Commands_pair>` doc
 
 Click on the style to display the formula it computes, any additional
 arguments specified in the pair\_style command, and coefficients
-specified by the associated :doc:`pair\_coeff <pair_coeff>` command.
+specified by the associated :doc:`pair_coeff <pair_coeff>` command.
 
 There are also additional accelerated pair styles included in the
 LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
@@ -170,6 +170,7 @@ accelerated styles exist.
 * :doc:`gauss <pair_gauss>` - Gaussian potential
 * :doc:`gauss/cut <pair_gauss>` - generalized Gaussian potential
 * :doc:`gayberne <pair_gayberne>` - Gay-Berne ellipsoidal potential
+* :doc:`granular <pair_granular>` - Generalized granular potential
 * :doc:`gran/hertz/history <pair_gran>` - granular potential with Hertzian interactions
 * :doc:`gran/hooke <pair_gran>` - granular potential with history effects
 * :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects
@@ -267,6 +268,12 @@ accelerated styles exist.
 * :doc:`oxdna2/hbond <pair_oxdna2>` -
 * :doc:`oxdna2/stk <pair_oxdna2>` -
 * :doc:`oxdna2/xstk <pair_oxdna2>` -
+* :doc:`oxrna2/coaxstk <pair_oxrna2>` -
+* :doc:`oxrna2/dh <pair_oxrna2>` -
+* :doc:`oxrna2/excv <pair_oxrna2>` -
+* :doc:`oxrna2/hbond <pair_oxrna2>` -
+* :doc:`oxrna2/stk <pair_oxrna2>` -
+* :doc:`oxrna2/xstk <pair_oxrna2>` -
 * :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
 * :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
 * :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
@@ -280,7 +287,7 @@ accelerated styles exist.
 * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
 * :doc:`smd/hertz <pair_smd_hertz>` -
 * :doc:`smd/tlsph <pair_smd_tlsph>` -
-* :doc:`smd/tri\_surface <pair_smd_triangulated_surface>` -
+* :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
 * :doc:`smd/ulsph <pair_smd_ulsph>` -
 * :doc:`smtbq <pair_smtbq>` -
 * :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
@@ -328,8 +335,8 @@ Restrictions
 
 
 This command must be used before any coefficients are set by the
-:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`, or
-:doc:`read\_restart <read_restart>` commands.
+:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`, or
+:doc:`read_restart <read_restart>` commands.
 
 Some pair styles are part of specific packages.  They are only enabled
 if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  The doc pages for
@@ -338,9 +345,9 @@ individual pair potentials tell if it is part of a package.
 Related commands
 """"""""""""""""
 
-:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`,
-:doc:`pair\_modify <pair_modify>`, :doc:`kspace\_style <kspace_style>`,
-:doc:`dielectric <dielectric>`, :doc:`pair\_write <pair_write>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`,
+:doc:`pair_modify <pair_modify>`, :doc:`kspace_style <kspace_style>`,
+:doc:`dielectric <dielectric>`, :doc:`pair_write <pair_write>`
 
 Default
 """""""
diff --git a/doc/txt/pair_style.txt b/doc/txt/pair_style.txt
deleted file mode 100644
index 7ba982cd2d..0000000000
--- a/doc/txt/pair_style.txt
+++ /dev/null
@@ -1,338 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style command :h3
-
-[Syntax:]
-
-pair_style style args :pre
-
-style = one of the styles from the list below
-args = arguments used by a particular style :ul
-
-[Examples:]
-
-pair_style lj/cut 2.5
-pair_style eam/alloy
-pair_style hybrid lj/charmm/coul/long 10.0 eam
-pair_style table linear 1000
-pair_style none :pre
-
-[Description:]
-
-Set the formula(s) LAMMPS uses to compute pairwise interactions.  In
-LAMMPS, pair potentials are defined between pairs of atoms that are
-within a cutoff distance and the set of active interactions typically
-changes over time.  See the "bond_style"_bond_style.html command to
-define potentials between pairs of bonded atoms, which typically
-remain in place for the duration of a simulation.
-
-In LAMMPS, pairwise force fields encompass a variety of interactions,
-some of which include many-body effects, e.g. EAM, Stillinger-Weber,
-Tersoff, REBO potentials.  They are still classified as "pairwise"
-potentials because the set of interacting atoms changes with time
-(unlike molecular bonds) and thus a neighbor list is used to find
-nearby interacting atoms.
-
-Hybrid models where specified pairs of atom types interact via
-different pair potentials can be setup using the {hybrid} pair style.
-
-The coefficients associated with a pair style are typically set for
-each pair of atom types, and are specified by the
-"pair_coeff"_pair_coeff.html command or read from a file by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands.
-
-The "pair_modify"_pair_modify.html command sets options for mixing of
-type I-J interaction coefficients and adding energy offsets or tail
-corrections to Lennard-Jones potentials.  Details on these options as
-they pertain to individual potentials are described on the doc page
-for the potential.  Likewise, info on whether the potential
-information is stored in a "restart file"_write_restart.html is listed
-on the potential doc page.
-
-In the formulas listed for each pair style, {E} is the energy of a
-pairwise interaction between two atoms separated by a distance {r}.
-The force between the atoms is the negative derivative of this
-expression.
-
-If the pair_style command has a cutoff argument, it sets global
-cutoffs for all pairs of atom types.  The distance(s) can be smaller
-or larger than the dimensions of the simulation box.
-
-Typically, the global cutoff value can be overridden for a specific
-pair of atom types by the "pair_coeff"_pair_coeff.html command.  The
-pair style settings (including global cutoffs) can be changed by a
-subsequent pair_style command using the same style.  This will reset
-the cutoffs for all atom type pairs, including those previously set
-explicitly by a "pair_coeff"_pair_coeff.html command.  The exceptions
-to this are that pair_style {table} and {hybrid} settings cannot be
-reset.  A new pair_style command for these styles will wipe out all
-previously specified pair_coeff values.
-
-:line
-
-Here is an alphabetic list of pair styles defined in LAMMPS.  They are
-also listed in more compact form on the "Commands
-pair"_Commands_pair.html doc page.
-
-Click on the style to display the formula it computes, any additional
-arguments specified in the pair_style command, and coefficients
-specified by the associated "pair_coeff"_pair_coeff.html command.
-
-There are also additional accelerated pair styles included in the
-LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
-The individual style names on the "Commands pair"_Commands_pair.html
-doc page are followed by one or more of (g,i,k,o,t) to indicate which
-accelerated styles exist.
-
-"none"_pair_none.html - turn off pairwise interactions
-"hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
-"hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions
-"zero"_pair_zero.html - neighbor list but no interactions :ul
-
-"adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
-"agni"_pair_agni.html - machine learned potential mapping atomic environment to forces
-"airebo"_pair_airebo.html - AIREBO potential of Stuart
-"airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
-"atm"_pair_atm.html - Axilrod-Teller-Muto potential
-"awpmd/cut"_pair_awpmd.html - Antisymmetrized Wave Packet MD potential for atoms and electrons
-"beck"_pair_beck.html - Beck potential
-"body/nparticle"_pair_body_nparticle.html - interactions between body particles
-"body/rounded/polygon"_pair_body_rounded_polygon.html - granular-style 2d polygon potential
-"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - granular-style 3d polyhedron potential
-"bop"_pair_bop.html - BOP potential of Pettifor
-"born"_pair_born.html - Born-Mayer-Huggins potential
-"born/coul/dsf"_pair_born.html - Born with damped-shifted-force model
-"born/coul/dsf/cs"_pair_cs.html - Born with damped-shifted-force and core/shell model
-"born/coul/long"_pair_born.html - Born with long-range Coulombics
-"born/coul/long/cs"_pair_cs.html - Born with long-range Coulombics and core/shell
-"born/coul/msm"_pair_born.html - Born with long-range MSM Coulombics
-"born/coul/wolf"_pair_born.html - Born with Wolf potential for Coulombics
-"born/coul/wolf/cs"_pair_cs.html - Born with Wolf potential for Coulombics and core/shell model
-"brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
-"brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
-"buck"_pair_buck.html - Buckingham potential
-"buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
-"buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics
-"buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell
-"buck/coul/msm"_pair_buck.html - Buckingham with long-range MSM Coulombics
-"buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics
-"buck/mdf"_pair_mdf.html - Buckingham with a taper function
-"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with damped-shift-force model
-"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with long-range Coulombics
-"colloid"_pair_colloid.html - integrated colloidal potential
-"comb"_pair_comb.html - charge-optimized many-body (COMB) potential
-"comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
-"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential
-"coul/cut"_pair_coul.html - cutoff Coulombic potential
-"coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
-"coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
-"coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity
-"coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model
-"coul/long"_pair_coul.html - long-range Coulombic potential
-"coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell
-"coul/long/soft"_pair_fep_soft.html - long-range Coulombic potential with a soft core
-"coul/msm"_pair_coul.html - long-range MSM Coulombics
-"coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential
-"coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals
-"coul/wolf"_pair_coul.html - Coulombics via Wolf potential
-"coul/wolf/cs"_pair_cs.html - ditto with core/shell adjustments
-"dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
-"dpd/fdt"_pair_dpd_fdt.html - DPD for constant temperature and pressure
-"dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy
-"dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting
-"dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
-"e3b"_pair_e3b.html - Explicit-three body (E3B) water model
-"drip"_pair_drip.html - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
-"eam"_pair_eam.html - embedded atom method (EAM)
-"eam/alloy"_pair_eam.html - alloy EAM
-"eam/cd"_pair_eam.html - concentration-dependent EAM
-"eam/cd/old"_pair_eam.html - older two-site model for concentration-dependent EAM
-"eam/fs"_pair_eam.html - Finnis-Sinclair EAM
-"edip"_pair_edip.html - three-body EDIP potential
-"edip/multi"_pair_edip.html - multi-element EDIP potential
-"edpd"_pair_meso.html - eDPD particle interactions
-"eff/cut"_pair_eff.html - electron force field with a cutoff
-"eim"_pair_eim.html - embedded ion method (EIM)
-"exp6/rx"_pair_exp6_rx.html - reactive DPD potential
-"extep"_pair_extep.html - extended Tersoff potential
-"gauss"_pair_gauss.html - Gaussian potential
-"gauss/cut"_pair_gauss.html - generalized Gaussian potential
-"gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
-"gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
-"gran/hooke"_pair_gran.html - granular potential with history effects
-"gran/hooke/history"_pair_gran.html - granular potential without history effects
-"gw"_pair_gw.html - Gao-Weber potential
-"gw/zbl"_pair_gw.html - Gao-Weber potential with a repulsive ZBL core
-"hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
-"hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
-"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - registry-dependent interlayer potential (ILP)
-"kim"_pair_kim.html - interface to potentials provided by KIM project
-"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
-"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
-"lebedeva/z"_pair_lebedeva_z.html - Lebedeva interlayer potential for graphene with normals along z-axis
-"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
-"line/lj"_pair_line_lj.html - LJ potential between line segments
-"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file
-"lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
-"lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
-"lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
-"lj/charmm/coul/long/soft"_pair_fep_soft.html - CHARMM with long-range Coulomb and a soft core
-"lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - CHARMM with force switching and shifting
-"lj/charmmfsw/coul/long"_pair_charmm.html - CHARMM with force switching and long-rnage Coulombics
-"lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
-"lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
-"lj/class2/coul/cut/soft"_pair_fep_soft.html - COMPASS with cutoff Coulomb with a soft core
-"lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
-"lj/class2/coul/long/soft"_pair_fep_soft.html - COMPASS with long-range Coulomb with a soft core
-"lj/class2/soft"_pair_fep_soft.html - COMPASS (class 2) force field with no Coulomb with a soft core
-"lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point
-"lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
-"lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
-"lj/cut/coul/cut/soft"_pair_fep_soft.html - LJ with cutoff Coulomb with a soft core
-"lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
-"lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
-"lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
-"lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments
-"lj/cut/coul/long/soft"_pair_fep_soft.html - LJ with long-range Coulombics with a soft core
-"lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
-"lj/cut/coul/wolf"_pair_lj.html - LJ with Coulombics via Wolf potential
-"lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff
-"lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald
-"lj/cut/soft"_pair_fep_soft.html - LJ with a soft core
-"lj/cut/thole/long"_pair_thole.html - LJ with Coulombics with thole damping
-"lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
-"lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
-"lj/cut/tip4p/long/soft"_pair_fep_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core
-"lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
-"lj/expand/coul/long"_pair_lj_expand.html - Lennard-Jones for variable size particles with long-range Coulombics
-"lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
-"lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
-"lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics
-"lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles
-"lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulombics for TIP4P water
-"lj/mdf"_pair_mdf.html - LJ potential with a taper function
-"lj/sdk"_pair_sdk.html - LJ for SDK coarse-graining
-"lj/sdk/coul/long"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics
-"lj/sdk/coul/msm"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics via MSM
-"lj/sf/dipole/sf"_pair_dipole.html - LJ with dipole interaction with shifted forces
-"lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
-"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential
-"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
-"lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
-"local/density"_pair_local_density.html - generalized basic local density potential
-"lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
-"lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
-"lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics
-"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
-"mdpd"_pair_meso.html - mDPD particle interactions
-"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
-"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
-"meam/spline"_pair_meam_spline.html - splined version of MEAM
-"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
-"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
-"mie/cut"_pair_mie.html - Mie potential
-"mm3/switch3/coulgauss"_pair_mm3_switch3_coulgauss - smoothed MM3 vdW potential with Gaussian electrostatics
-"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field
-"morse"_pair_morse.html - Morse potential
-"morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential
-"morse/soft"_pair_morse.html - Morse potential with a soft core
-"multi/lucy"_pair_multi_lucy.html - DPD potential with density-dependent force
-"multi/lucy/rx"_pair_multi_lucy_rx.html - reactive DPD potential with density-dependent force
-"nb3b/harmonic"_pair_nb3b_harmonic.html - non-bonded 3-body harmonic potential
-"nm/cut"_pair_nm.html - N-M potential
-"nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb
-"nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics
-"oxdna/coaxstk"_pair_oxdna.html -
-"oxdna/excv"_pair_oxdna.html -
-"oxdna/hbond"_pair_oxdna.html -
-"oxdna/stk"_pair_oxdna.html -
-"oxdna/xstk"_pair_oxdna.html -
-"oxdna2/coaxstk"_pair_oxdna2.html -
-"oxdna2/dh"_pair_oxdna2.html -
-"oxdna2/excv"_pair_oxdna2.html -
-"oxdna2/hbond"_pair_oxdna2.html -
-"oxdna2/stk"_pair_oxdna2.html -
-"oxdna2/xstk"_pair_oxdna2.html -
-"peri/eps"_pair_peri.html - peridynamic EPS potential
-"peri/lps"_pair_peri.html - peridynamic LPS potential
-"peri/pmb"_pair_peri.html - peridynamic PMB potential
-"peri/ves"_pair_peri.html - peridynamic VES potential
-"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
-"python"_pair_python.html -
-"quip"_pair_quip.html -
-"reax/c"_pair_reaxc.html - ReaxFF potential in C
-"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
-"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
-"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions
-"smd/hertz"_pair_smd_hertz.html -
-"smd/tlsph"_pair_smd_tlsph.html -
-"smd/tri_surface"_pair_smd_triangulated_surface.html -
-"smd/ulsph"_pair_smd_ulsph.html -
-"smtbq"_pair_smtbq.html -
-"snap"_pair_snap.html - SNAP quantum-accurate potential
-"soft"_pair_soft.html - Soft (cosine) potential
-"sph/heatconduction"_pair_sph_heatconduction.html -
-"sph/idealgas"_pair_sph_idealgas.html -
-"sph/lj"_pair_sph_lj.html -
-"sph/rhosum"_pair_sph_rhosum.html -
-"sph/taitwater"_pair_sph_taitwater.html -
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html -
-"spin/dipole/cut"_pair_spin_dipole.html -
-"spin/dipole/long"_pair_spin_dipole.html -
-"spin/dmi"_pair_spin_dmi.html -
-"spin/exchange"_pair_spin_exchange.html -
-"spin/magelec"_pair_spin_magelec.html -
-"spin/neel"_pair_spin_neel.html -
-"srp"_pair_srp.html -
-"sw"_pair_sw.html - Stillinger-Weber 3-body potential
-"table"_pair_table.html - tabulated pair potential
-"table/rx"_pair_table_rx.html -
-"tdpd"_pair_meso.html - tDPD particle interactions
-"tersoff"_pair_tersoff.html - Tersoff 3-body potential
-"tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential
-"tersoff/mod/c"_pair_tersoff_mod.html -
-"tersoff/table"_pair_tersoff.html -
-"tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential
-"thole"_pair_thole.html - Coulomb interactions with thole damping
-"tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
-"tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
-"tip4p/long/soft"_pair_fep_soft.html -
-"tri/lj"_pair_tri_lj.html - LJ potential between triangles
-"ufm"_pair_ufm.html -
-"vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential
-"vashishta/table"_pair_vashishta.html -
-"yukawa"_pair_yukawa.html - Yukawa potential
-"yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles
-"zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul
-
-:line
-
-[Restrictions:]
-
-This command must be used before any coefficients are set by the
-"pair_coeff"_pair_coeff.html, "read_data"_read_data.html, or
-"read_restart"_read_restart.html commands.
-
-Some pair styles are part of specific packages.  They are only enabled
-if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  The doc pages for
-individual pair potentials tell if it is part of a package.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html, "read_data"_read_data.html,
-"pair_modify"_pair_modify.html, "kspace_style"_kspace_style.html,
-"dielectric"_dielectric.html, "pair_write"_pair_write.html
-
-[Default:]
-
-pair_style none :pre

From 7b9abda6c4c46b31a61b74ee830bddd7a6cfbc9b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 12 Jan 2020 10:17:14 -0500
Subject: [PATCH 191/199] refactor to use a function to process files with
 lists of styles

---
 doc/utils/check-styles.py | 154 +++++++++++++-------------------------
 1 file changed, 53 insertions(+), 101 deletions(-)

diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
index b725efeef9..a5bf31801c 100755
--- a/doc/utils/check-styles.py
+++ b/doc/utils/check-styles.py
@@ -89,7 +89,26 @@ def add_suffix(list,style):
         return style + ' (' + suffix + ')'
     else:
         return style
-        
+
+def check_style(file,dir,pattern,list,name,suffix=False,skip=()):
+    f = os.path.join(dir, file)
+    fp = open(f)
+    text = fp.read()
+    fp.close()
+    matches = re.findall(pattern,text,re.MULTILINE)
+    counter = 0
+    for c in list.keys():
+        # known undocumented aliases we need to skip
+        if c in skip: continue
+        s = c
+        if suffix: s = add_suffix(list,c)
+        if not s in matches:
+            if not list[c]['removed']:
+                print("%s style entry %s" % (name,s),
+                      "is missing or incomplete in %s" % file)
+                counter += 1
+    return counter
+
 for h in headers:
     if verbose: print("Checking ", h)
     fp = open(h)
@@ -170,7 +189,7 @@ for h in headers:
             print("Skipping over: ",m)
 
 
-print("""Parsed styles from C++ tree in %s:
+print("""Parsed style names w/o suffixes from C++ tree in %s:
    Angle styles:     %3d    Atom styles:      %3d
    Body styles:      %3d    Bond styles:      %3d
    Command styles:   %3d    Compute styles:   %3d
@@ -186,106 +205,39 @@ print("""Parsed styles from C++ tree in %s:
 
 
 counter = 0
-# check main commands lists
-f = os.path.join(doc, 'Commands_all.rst')
-fp = open(f)
-text = fp.read()
-fp.close()
-matches = re.findall(":doc:`(.+) <.+>`",text,re.MULTILINE)
-for c in command.keys():
-    if not c in matches:
-        if not command[c]['removed']:
-            print("Command %s is missing in Commands_all.rst" % c)
-            counter += 1
 
-f = os.path.join(doc, 'Commands_compute.rst')
-fp = open(f)
-text = fp.read()
-fp.close()
-matches = re.findall(":doc:`(.+) <compute.+>`",text,re.MULTILINE)
-for c in compute.keys():
-    if not add_suffix(compute,c) in matches:
-        if not compute[c]['removed']:
-            print("Compute style entry %s is missing or" % c,
-                  "incomplete in Commands_compute.rst")
-            counter += 1
-
-f = os.path.join(doc, 'Commands_fix.rst')
-fp = open(f)
-text = fp.read()
-fp.close()
-matches = re.findall(":doc:`(.+) <fix.+>`",text,re.MULTILINE)
-for c in fix.keys():
-    # known undocumented aliases we need to skip
-    if c in ('python'): continue
-    if not add_suffix(fix,c) in matches:
-        if not fix[c]['removed']:
-            print("Fix style entry %s is missing or" % c,
-                  "incomplete in Commands_fix.rst")
-            counter += 1
-
-f = os.path.join(doc, 'Commands_pair.rst')
-fp = open(f)
-text = fp.read()
-fp.close()
-matches = re.findall(":doc:`(.+) <pair.+>`",text,re.MULTILINE)
-for c in pair.keys():
-    # known undocumented aliases we need to skip
-    if c in ('meam','lj/sf'): continue
-    if not add_suffix(pair,c) in matches:
-        if not pair[c]['removed']:
-            print("Pair style entry %s is missing or" % c,
-                  "incomplete in Commands_pair.rst")
-            counter += 1
-
-f = os.path.join(doc, 'Commands_bond.rst')
-fp = open(f)
-text = fp.read()
-fp.close()
-matches = re.findall(":doc:`(.+) <bond.+>`",text,re.MULTILINE)
-for c in bond.keys():
-    if not add_suffix(bond,c) in matches:
-        if not bond[c]['removed']:
-            print("Bond style entry %s is missing or" % c,
-                  "incomplete in Commands_bond.rst")
-            counter += 1
-
-matches = re.findall(":doc:`(.+) <angle.+>`",text,re.MULTILINE)
-for c in angle.keys():
-    if not add_suffix(angle,c) in matches:
-        if not angle[c]['removed']:
-            print("Angle style entry %s is missing or" % c,
-                  "incomplete in Commands_bond.rst")
-            counter += 1
-
-matches = re.findall(":doc:`(.+) <dihedral.+>`",text,re.MULTILINE)
-for c in dihedral.keys():
-    if not add_suffix(dihedral,c) in matches:
-        if not dihedral[c]['removed']:
-            print("Dihedral style entry %s is missing or" % c,
-                  "incomplete in Commands_bond.rst")
-            counter += 1
-
-matches = re.findall(":doc:`(.+) <improper.+>`",text,re.MULTILINE)
-for c in improper.keys():
-    if not add_suffix(improper,c) in matches:
-        if not improper[c]['removed']:
-            print("Improper style entry %s is missing or" % c,
-                  "incomplete in Commands_bond.rst")
-            counter += 1
-
-f = os.path.join(doc, 'Commands_kspace.rst')
-fp = open(f)
-text = fp.read()
-fp.close()
-matches = re.findall(":doc:`(.+) <kspace_style>`",text,re.MULTILINE)
-for c in kspace.keys():
-    if not add_suffix(kspace,c) in matches:
-        if not kspace[c]['removed']:
-            print("KSpace style entry %s is missing or" % c,
-                  "incomplete in Commands_kspace.rst")
-            print(kspace[c])
-            counter += 1
+counter += check_style('Commands_all.rst',doc,":doc:`(.+) <.+>`",
+                       command,'Command',suffix=False)
+counter += check_style('Commands_compute.rst',doc,":doc:`(.+) <compute.+>`",
+                       compute,'Compute',suffix=True)
+counter += check_style('compute.rst',doc,":doc:`(.+) <compute.+>` -",
+                       compute,'Compute',suffix=False)
+counter += check_style('Commands_fix.rst',doc,":doc:`(.+) <fix.+>`",
+                       fix,'Fix',skip=('python'),suffix=True)
+counter += check_style('fix.rst',doc,":doc:`(.+) <fix.+>` -",
+                       fix,'Fix',skip=('python'),suffix=False)
+counter += check_style('Commands_pair.rst',doc,":doc:`(.+) <pair.+>`",
+                       pair,'Pair',skip=('meam','lj/sf'),suffix=True)
+counter += check_style('pair_style.rst',doc,":doc:`(.+) <pair.+>` -",
+                       pair,'Pair',skip=('meam','lj/sf'),suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <bond.+>`",
+                       bond,'Bond',suffix=True)
+counter += check_style('bond_style.rst',doc,":doc:`(.+) <bond.+>` -",
+                       bond,'Bond',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <angle.+>`",
+                       angle,'Angle',suffix=True)
+counter += check_style('angle_style.rst',doc,":doc:`(.+) <angle.+>` -",
+                       angle,'Angle',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <dihedral.+>`",
+                       dihedral,'Dihedral',suffix=True)
+counter += check_style('dihedral_style.rst',doc,":doc:`(.+) <dihedral.+>` -",
+                       dihedral,'Dihedral',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <improper.+>`",
+                       improper,'Improper',suffix=True)
+counter += check_style('improper_style.rst',doc,":doc:`(.+) <improper.+>` -",
+                       improper,'Improper',suffix=False)
+counter += check_style('Commands_kspace.rst',doc,":doc:`(.+) <kspace_style>`",
+                       kspace,'KSpace',suffix=True)
 
 if counter:
     print("Found %d issue(s) with style lists" % counter)

From 81c9b0b12e33a86920a877b1756908c5a3617f06 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 12 Jan 2020 10:17:56 -0500
Subject: [PATCH 192/199] small update to kspace overview

---
 doc/src/kspace_style.rst |   4 +-
 doc/txt/kspace_style.txt | 495 ---------------------------------------
 2 files changed, 2 insertions(+), 497 deletions(-)
 delete mode 100644 doc/txt/kspace_style.txt

diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst
index c35e38d1db..32179f8be0 100644
--- a/doc/src/kspace_style.rst
+++ b/doc/src/kspace_style.rst
@@ -12,9 +12,9 @@ Syntax
    kspace_style style value
 
 * style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
-  
+
   .. parsed-literal::
-  
+
        *none* value = none
        *ewald* value = accuracy
          accuracy = desired relative error in forces
diff --git a/doc/txt/kspace_style.txt b/doc/txt/kspace_style.txt
deleted file mode 100644
index 04b845acaa..0000000000
--- a/doc/txt/kspace_style.txt
+++ /dev/null
@@ -1,495 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-kspace_style command :h3
-
-[Syntax:]
-
-kspace_style style value :pre
-
-style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l
-  {none} value = none
-  {ewald} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/disp} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/dipole} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/dipole/spin} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/cg} values = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {pppm/disp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/tip4p} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/disp/tip4p} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/gpu} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/intel} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/kk} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/cg/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/disp/intel} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/tip4p/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/stagger} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/dipole} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/dipole/spin} value = accuracy
-    accuracy = desired relative error in forces
-  {msm} value = accuracy
-    accuracy = desired relative error in forces
-  {msm/cg} value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {msm/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {msm/cg/omp} value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {scafacos} values = method accuracy
-    method = fmm or p2nfft or p3m or ewald or direct
-    accuracy = desired relative error in forces :pre
-:ule
-
-[Examples:]
-
-kspace_style pppm 1.0e-4
-kspace_style pppm/cg 1.0e-5 1.0e-6
-kspace style msm 1.0e-4
-kspace style scafacos fmm 1.0e-4
-kspace_style none :pre
-
-[Description:]
-
-Define a long-range solver for LAMMPS to use each timestep to compute
-long-range Coulombic interactions or long-range 1/r^6 interactions.
-Most of the long-range solvers perform their computation in K-space,
-hence the name of this command.
-
-When such a solver is used in conjunction with an appropriate pair
-style, the cutoff for Coulombic or 1/r^N interactions is effectively
-infinite.  If the Coulombic case, this means each charge in the system
-interacts with charges in an infinite array of periodic images of the
-simulation domain.
-
-Note that using a long-range solver requires use of a matching "pair
-style"_pair_style.html to perform consistent short-range pairwise
-calculations.  This means that the name of the pair style contains a
-matching keyword to the name of the KSpace style, as in this table:
-
-Pair style : KSpace style
-coul/long : ewald or pppm
-coul/msm : msm
-lj/long or buck/long : disp (for dispersion)
-tip4p/long : tip4p :tb(s=:,ea=c)
-
-:line
-
-The {ewald} style performs a standard Ewald summation as described in
-any solid-state physics text.
-
-The {ewald/disp} style adds a long-range dispersion sum option for
-1/r^6 potentials and is useful for simulation of interfaces
-"(Veld)"_#Veld.  It also performs standard Coulombic Ewald summations,
-but in a more efficient manner than the {ewald} style.  The 1/r^6
-capability means that Lennard-Jones or Buckingham potentials can be
-used without a cutoff, i.e. they become full long-range potentials.
-The {ewald/disp} style can also be used with point-dipoles, see
-"(Toukmaji)"_#Toukmaji.
-
-The {ewald/dipole} style adds long-range standard Ewald summations
-for dipole-dipole interactions, see "(Toukmaji)"_#Toukmaji.
-
-The {ewald/dipole/spin} style adds long-range standard Ewald
-summations for magnetic dipole-dipole interactions between
-magnetic spins.
-
-:line
-
-The {pppm} style invokes a particle-particle particle-mesh solver
-"(Hockney)"_#Hockney which maps atom charge to a 3d mesh, uses 3d FFTs
-to solve Poisson's equation on the mesh, then interpolates electric
-fields on the mesh points back to the atoms.  It is closely related to
-the particle-mesh Ewald technique (PME) "(Darden)"_#Darden used in
-AMBER and CHARMM.  The cost of traditional Ewald summation scales as
-N^(3/2) where N is the number of atoms in the system.  The PPPM solver
-scales as Nlog(N) due to the FFTs, so it is almost always a faster
-choice "(Pollock)"_#Pollock.
-
-The {pppm/cg} style is identical to the {pppm} style except that it
-has an optimization for systems where most particles are uncharged.
-Similarly the {msm/cg} style implements the same optimization for {msm}.
-The optional {smallq} argument defines the cutoff for the absolute
-charge value which determines whether a particle is considered charged
-or not.  Its default value is 1.0e-5.
-
-The {pppm/dipole} style invokes a particle-particle particle-mesh solver
-for dipole-dipole interactions, following the method of "(Cerda)"_#Cerda2008.
-
-The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver
-for magnetic dipole-dipole interactions between magnetic spins.
-
-The {pppm/tip4p} style is identical to the {pppm} style except that it
-adds a charge at the massless 4th site in each TIP4P water molecule.
-It should be used with "pair styles"_pair_style.html with a
-{tip4p/long} in their style name.
-
-The {pppm/stagger} style performs calculations using two different
-meshes, one shifted slightly with respect to the other.  This can
-reduce force aliasing errors and increase the accuracy of the method
-for a given mesh size.  Or a coarser mesh can be used for the same
-target accuracy, which saves CPU time.  However, there is a trade-off
-since FFTs on two meshes are now performed which increases the
-computation required.  See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov,
-and "(Hockney)"_#Hockney for details of the method.
-
-For high relative accuracy, using staggered PPPM allows the mesh size
-to be reduced by a factor of 2 in each dimension as compared to
-regular PPPM (for the same target accuracy).  This can give up to a 4x
-speedup in the KSpace time (8x less mesh points, 2x more expensive).
-However, for low relative accuracy, the staggered PPPM mesh size may
-be essentially the same as for regular PPPM, which means the method
-will be up to 2x slower in the KSpace time (simply 2x more expensive).
-For more details and timings, see the "Speed tips"_Speed_tips.html doc
-page.
-
-NOTE: Using {pppm/stagger} may not give the same increase in the
-accuracy of energy and pressure as it does in forces, so some caution
-must be used if energy and/or pressure are quantities of interest,
-such as when using a barostat.
-
-:line
-
-The {pppm/disp} and {pppm/disp/tip4p} styles add a mesh-based long-range
-dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder2012,
-similar to the {ewald/disp} style. The 1/r^6 capability means
-that Lennard-Jones or Buckingham potentials can be used without a cutoff,
-i.e. they become full long-range potentials.
-
-For these styles, you will possibly want to adjust the default choice
-of parameters by using the "kspace_modify"_kspace_modify.html command.
-This can be done by either choosing the Ewald and grid parameters, or
-by specifying separate accuracies for the real and kspace
-calculations. When not making any settings, the simulation will stop
-with an error message. Further information on the influence of the
-parameters and how to choose them is described in
-"(Isele-Holder)"_#Isele-Holder2012,
-"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto
-dispersion"_Howto_dispersion.html doc page.
-
-:line
-
-NOTE: All of the PPPM styles can be used with single-precision FFTs by
-using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
-lo-level Makefile.  This setting also changes some of the PPPM
-operations (e.g. mapping charge to mesh and interpolating electric
-fields to particles) to be performed in single precision.  This option
-can speed-up long-range calculations, particularly in parallel or on
-GPUs.  The use of the -DFFT_SINGLE flag is discussed on the "Build
-settings"_Build_settings.html doc page. MSM does not currently support
-the -DFFT_SINGLE compiler switch.
-
-:line
-
-The {msm} style invokes a multi-level summation method MSM solver,
-"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge
-to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
-meshes on which direct Coulomb solvers are done.  This method does not
-use FFTs and scales as N. It may therefore be faster than the other
-K-space solvers for relatively large problems when running on large
-core counts. MSM can also be used for non-periodic boundary conditions
-and for mixed periodic and non-periodic boundaries.
-
-MSM is most competitive versus Ewald and PPPM when only relatively
-low accuracy forces, about 1e-4 relative error or less accurate,
-are needed. Note that use of a larger Coulombic cutoff (i.e. 15
-angstroms instead of 10 angstroms) provides better MSM accuracy for
-both the real space and grid computed forces.
-
-Currently calculation of the full pressure tensor in MSM is expensive.
-Using the "kspace_modify"_kspace_modify.html {pressure/scalar yes}
-command provides a less expensive way to compute the scalar pressure
-(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
-to run an isotropic barostat. If the full pressure tensor is needed,
-then calculating the pressure at every timestep or using a fixed
-pressure simulation with MSM will cause the code to run slower.
-
-:line
-
-The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver
-library"_http://www.scafacos.de which provides a variety of solver
-methods which can be used with LAMMPS.  The paper by "(Who)"_#Who2012
-gives an overview of ScaFaCoS.
-
-ScaFaCoS was developed by a consortium of German research facilities
-with a BMBF (German Ministry of Science and Education) funded project
-in 2009-2012. Participants of the consortium were the Universities of
-Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
-Forschungszentrum Juelich.
-
-The library is available for download at "http://scafacos.de" or can
-be cloned from the git-repository
-"git://github.com/scafacos/scafacos.git".
-
-In order to use this KSpace style, you must download and build the
-ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package
-installed package which links LAMMPS to the ScaFaCoS library.
-See details on "this page"_Section_packages.html#USER-SCAFACOS.
-
-NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
-Coulombic interactions, both short- and long-range.  Thus you should
-NOT use a Coulombic pair style when using kspace_style scafacos.  This
-also means the total Coulombic energy (short- and long-range) will be
-tallied for "thermodynamic output"_thermo_style.html command as part
-of the {elong} keyword; the {ecoul} keyword will be zero.
-
-NOTE: See the current restriction below about use of ScaFaCoS in
-LAMMPS with molecular charged systems or the TIP4P water model.
-
-The specified {method} determines which ScaFaCoS algorithm is used.
-These are the ScaFaCoS methods currently available from LAMMPS:
-
-{fmm} = Fast Multi-Pole method
-{p2nfft} = FFT-based Coulomb solver
-{ewald} = Ewald summation
-{direct} = direct O(N^2) summation
-{p3m} = PPPM :ul
-
-We plan to support additional ScaFaCoS solvers from LAMMPS in the
-future.  For an overview of the included solvers, refer to
-"(Sutmann)"_#Sutmann2013
-
-The specified {accuracy} is similar to the accuracy setting for other
-LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
-it in different ways for different methods it supports.  Within the
-ScaFaCoS library the {accuracy} is treated as a tolerance level
-(either absolute or relative) for the chosen quantity, where the
-quantity can be either the Columic field values, the per-atom Columic
-energy or the total Columic energy.  To select from these options, see
-the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
-
-The "kspace_modify scafacos"_kspace_modify.html command also explains
-other ScaFaCoS options currently exposed to LAMMPS.
-
-:line
-
-The specified {accuracy} determines the relative RMS error in per-atom
-forces calculated by the long-range solver.  It is set as a
-dimensionless number, relative to the force that two unit point
-charges (e.g. 2 monovalent ions) exert on each other at a distance of
-1 Angstrom.  This reference value was chosen as representative of the
-magnitude of electrostatic forces in atomic systems.  Thus an accuracy
-value of 1.0e-4 means that the RMS error will be a factor of 10000
-smaller than the reference force.
-
-The accuracy setting is used in conjunction with the pairwise cutoff
-to determine the number of K-space vectors for style {ewald} or the
-grid size for style {pppm} or {msm}.
-
-Note that style {pppm} only computes the grid size at the beginning of
-a simulation, so if the length or triclinic tilt of the simulation
-cell increases dramatically during the course of the simulation, the
-accuracy of the simulation may degrade.  Likewise, if the
-"kspace_modify slab"_kspace_modify.html option is used with
-shrink-wrap boundaries in the z-dimension, and the box size changes
-dramatically in z.  For example, for a triclinic system with all three
-tilt factors set to the maximum limit, the PPPM grid should be
-increased roughly by a factor of 1.5 in the y direction and 2.0 in the
-z direction as compared to the same system using a cubic orthogonal
-simulation cell.  One way to handle this issue if you have a long
-simulation where the box size changes dramatically, is to break it
-into shorter simulations (multiple "run"_run.html commands).  This
-works because the grid size is re-computed at the beginning of each
-run.  Another way to ensure the described accuracy requirement is met
-is to run a short simulation at the maximum expected tilt or length,
-note the required grid size, and then use the
-"kspace_modify"_kspace_modify.html {mesh} command to manually set the
-PPPM grid size to this value for the long run.  The simulation then
-will be "too accurate" for some portion of the run.
-
-RMS force errors in real space for {ewald} and {pppm} are estimated
-using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
-equation 9 of "(Petersen)"_#Petersen. RMS force errors in K-space for
-{ewald} are estimated using equation 11 of "(Petersen)"_#Petersen,
-which is similar to equation 32 of "(Kolafa)"_#Kolafa. RMS force
-errors in K-space for {pppm} are estimated using equation 38 of
-"(Deserno)"_#Deserno. RMS force errors for {msm} are estimated
-using ideas from chapter 3 of "(Hardy)"_#Hardy2006, with equation 3.197
-of particular note. When using {msm} with non-periodic boundary
-conditions, it is expected that the error estimation will be too
-pessimistic. RMS force errors for dipoles when using {ewald/disp}
-or {ewald/dipole} are estimated using equations 33 and 46 of
-"(Wang)"_#Wang. The RMS force errors for {pppm/dipole} are estimated
-using the equations in "(Cerda)"_#Cerda2008.
-
-
-See the "kspace_modify"_kspace_modify.html command for additional
-options of the K-space solvers that can be set, including a {force}
-option for setting an absolute RMS error in forces, as opposed to a
-relative RMS error.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-More specifically, the {pppm/gpu} style performs charge assignment and
-force interpolation calculations on the GPU.  These processes are
-performed either in single or double precision, depending on whether
-the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
-discussed above.  The FFTs themselves are still calculated on the CPU.
-If {pppm/gpu} is used with a GPU-enabled pair style, part of the PPPM
-calculation can be performed concurrently on the GPU while other
-calculations for non-bonded and bonded force calculation are performed
-on the CPU.
-
-The {pppm/kk} style also performs charge assignment and force
-interpolation calculations on the GPU while the FFTs themselves are
-calculated on the CPU in non-threaded mode.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP, and OPT packages respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-Note that the long-range electrostatic solvers in LAMMPS assume conducting
-metal (tinfoil) boundary conditions for both charge and dipole
-interactions. Vacuum boundary conditions are not currently supported.
-
-The {ewald/disp}, {ewald}, {pppm}, and {msm} styles support
-non-orthogonal (triclinic symmetry) simulation boxes. However,
-triclinic simulation cells may not yet be supported by suffix versions
-of these styles.
-
-All of the kspace styles are part of the KSPACE package.  They are
-only enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-For MSM, a simulation must be 3d and one can use any combination of
-periodic, non-periodic, or shrink-wrapped boundaries (specified using
-the "boundary"_boundary.html command).
-
-For Ewald and PPPM, a simulation must be 3d and periodic in all
-dimensions.  The only exception is if the slab option is set with
-"kspace_modify"_kspace_modify.html, in which case the xy dimensions
-must be periodic and the z dimension must be non-periodic.
-
-The scafacos KSpace style will only be enabled if LAMMPS is built with
-the USER-SCAFACOS package.  See the "Build package"_Build_package.html
-doc page for more info.
-
-The use of ScaFaCos in LAMMPS does not yet support molecular charged
-systems where the short-range Coulombic interactions between atoms in
-the same bond/angle/dihedral are weighted by the
-"special_bonds"_special_bonds.html command.  Likewise it does not
-support the "TIP4P water style" where a fictitious charge site is
-introduced in each water molecule.
-Finally, the methods {p3m} and {ewald} do not support computing the
-virial, so this contribution is not included.
-
-[Related commands:]
-
-"kspace_modify"_kspace_modify.html, "pair_style
-lj/cut/coul/long"_pair_lj.html, "pair_style
-lj/charmm/coul/long"_pair_charmm.html, "pair_style
-lj/long/coul/long"_pair_lj_long.html, "pair_style
-buck/coul/long"_pair_buck.html
-
-[Default:]
-
-kspace_style none :pre
-
-:line
-
-:link(Darden)
-[(Darden)] Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
-
-:link(Deserno)
-[(Deserno)] Deserno and Holm, J Chem Phys, 109, 7694 (1998).
-
-:link(Hockney)
-[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
-Adam Hilger, NY (1989).
-
-:link(Kolafa)
-[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
-
-:link(Petersen)
-[(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995).
-
-:link(Wang)
-[(Wang)] Wang and Holm, J Chem Phys, 115, 6277 (2001).
-
-:link(Pollock)
-[(Pollock)] Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
-
-:link(Cerutti)
-[(Cerutti)] Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
-and Computation 5, 2322 (2009)
-
-:link(Neelov)
-[(Neelov)] Neelov, Holm, J Chem Phys 132, 234103 (2010)
-
-:link(Veld)
-[(Veld)] In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
-
-:link(Toukmaji)
-[(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
-10913 (2000).
-
-:link(Isele-Holder2012)
-[(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
-174107 (2012).
-
-:link(Isele-Holder2013)
-[(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
-J Chem Theory Comput 9, 5412 (2013).
-
-:link(Hardy2006)
-[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
-Evaluation of Forces for the Simulation of Biomolecules, University of
-Illinois at Urbana-Champaign, (2006).
-
-:link(Hardy2009)
-[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
-(2009).
-
-:link(Sutmann2013)
-[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
-
-:link(Cerda2008)
-[(Cerda)] Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
-
-:link(Who2012)
-[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
-(2012).

From 64e72b1cd5944b0545d4eb3bfbcc4829637a0996 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 12 Jan 2020 12:34:54 -0500
Subject: [PATCH 193/199] indent consistently with tabs only

---
 doc/Makefile | 33 +++++++++++++++++----------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/doc/Makefile b/doc/Makefile
index c82b414fff..a3c4906cec 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -124,26 +124,27 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 		cd ../../; \
 	)
 	@(\
-                . $(VENV)/bin/activate ;\
-                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-                echo "############################################" ;\
-                rst_anchor_check src/*.rst ;\
+		. $(VENV)/bin/activate ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		echo "############################################" ;\
+		rst_anchor_check src/*.rst ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		python utils/check-styles.py -s ../src -d src ;\
-                echo "############################################" ;\
-                deactivate ;\
+		echo "############################################" ;\
+		deactivate ;\
 	)
 	@cd latex && \
-          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
-	  mv temp Makefile && \
-	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  make && \
-	  make && \
-	  mv LAMMPS.pdf ../Manual.pdf && \
-	  cd ../;
+		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+		mv temp Makefile && \
+		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		make && \
+		make && \
+		make && \
+		mv LAMMPS.pdf ../Manual.pdf && \
+		cd ../;
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER

From bfaea66e66d5051fed19a4ce36cf855997fc56f1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 12 Jan 2020 23:03:45 -0500
Subject: [PATCH 194/199] update documentation

---
 doc/src/pair_modify.rst |   7 +-
 doc/txt/pair_modify.txt | 281 ----------------------------------------
 2 files changed, 5 insertions(+), 283 deletions(-)
 delete mode 100644 doc/txt/pair_modify.txt

diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst
index 664937ef61..b45a50573a 100644
--- a/doc/src/pair_modify.rst
+++ b/doc/src/pair_modify.rst
@@ -247,7 +247,9 @@ or *lj/coul* to change both to the same set of 3 values.  The wt1,wt2,wt3
 values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
 1-3, and 1-4 bond topology neighbors, respectively. The *special*
 keyword can only be used in conjunction with the *pair* keyword
-and has to directly follow it.
+and has to directly follow it.  This option is not compatible with
+pair styles from the GPU or the USER-INTEL package and attempting
+it will cause an error.
 
 .. note::
 
@@ -278,10 +280,11 @@ and allows to selectively disable or enable processing of the various
 
 Restrictions
 """"""""""""
- none
 
 You cannot use *shift* yes with *tail* yes, since those are
 conflicting options.  You cannot use *tail* yes with 2d simulations.
+You cannot use *special* with pair styles from the GPU or
+USER-INTEL package.
 
 Related commands
 """"""""""""""""
diff --git a/doc/txt/pair_modify.txt b/doc/txt/pair_modify.txt
deleted file mode 100644
index c446aa29d0..0000000000
--- a/doc/txt/pair_modify.txt
+++ /dev/null
@@ -1,281 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_modify command :h3
-
-[Syntax:]
-
-pair_modify keyword values ... :pre
-
-one or more keyword/value pairs may be listed :ulb,l
-keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner}
-or {tabinner/disp} or {tail} or {compute} or {nofdotr} :l
-  {pair} values = sub-style N {special} which wt1 wt2 wt3
-               or sub-style N {compute/tally} flag
-    sub-style = sub-style of "pair hybrid"_pair_hybrid.html
-    N = which instance of sub-style (only if sub-style is used multiple times)
-      {special} which wt1 wt2 wt3 = override {special_bonds} settings (optional)
-        which = {lj/coul} or {lj} or {coul}
-        w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
-      {compute/tally} flag = {yes} or {no}
-  {mix} value = {geometric} or {arithmetic} or {sixthpower}
-  {shift} value = {yes} or {no}
-  {table} value = N
-    2^N = # of values in table
-  {table/disp} value = N
-    2^N = # of values in table
-  {tabinner} value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  {tabinner/disp} value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  {tail} value = {yes} or {no}
-  {compute} value = {yes} or {no}
-  {nofdotr} :pre
-:ule
-
-[Examples:]
-
-pair_modify shift yes mix geometric
-pair_modify tail yes
-pair_modify table 12
-pair_modify pair lj/cut compute no
-pair_modify pair tersoff compute/tally no
-pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0 :pre
-
-[Description:]
-
-Modify the parameters of the currently defined pair style.  Not all
-parameters are relevant to all pair styles.
-
-If used, the {pair} keyword must appear first in the list of keywords.
-It can only be used with the "hybrid and
-hybrid/overlay"_pair_hybrid.html pair styles.  It means that all the
-following parameters will only be modified for the specified
-sub-style.  If the sub-style is defined multiple times, then an
-additional numeric argument {N} must also be specified, which is a
-number from 1 to M where M is the number of times the sub-style was
-listed in the "pair_style hybrid"_pair_hybrid.html command.  The extra
-number indicates which instance of the sub-style the remaining
-keywords will be applied to.  Note that if the {pair} keyword is not
-used, and the pair style is {hybrid} or {hybrid/overlay}, then all the
-specified keywords will be applied to all sub-styles.
-
-The {special} and {compute/tally} keywords can [only] be used in
-conjunction with the {pair} keyword and must directly follow it.
-{special} allows to override the
-"special_bonds"_special_bonds.html settings for the specified sub-style.
-{compute/tally} allows to disable or enable registering
-"compute */tally"_compute_tally.html computes for a given sub-style.
-More details are given below.
-
-The {mix} keyword affects pair coefficients for interactions between
-atoms of type I and J, when I != J and the coefficients are not
-explicitly set in the input script.  Note that coefficients for I = J
-must be set explicitly, either in the input script via the
-"pair_coeff" command or in the "Pair Coeffs" section of the "data
-file"_read_data.html.  For some pair styles it is not necessary to
-specify coefficients when I != J, since a "mixing" rule will create
-them from the I,I and J,J settings.  The pair_modify {mix} value
-determines what formulas are used to compute the mixed coefficients.
-In each case, the cutoff distance is mixed the same way as sigma.
-
-Note that not all pair styles support mixing.  Also, some mix options
-are not available for certain pair styles.  See the doc page for
-individual pair styles for those restrictions.  Note also that the
-"pair_coeff"_pair_coeff.html command also can be to directly set
-coefficients for a specific I != J pairing, in which case no mixing is
-performed.
-
-mix {geometric}
-
-epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = sqrt(sigma_i * sigma_j) :pre
-
-mix {arithmetic}
-
-epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = (sigma_i + sigma_j) / 2 :pre
-
-mix {sixthpower}
-
-epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
-             (sigma_i^6 + sigma_j^6)
-sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
-
-The {shift} keyword determines whether a Lennard-Jones potential is
-shifted at its cutoff to 0.0.  If so, this adds an energy term to each
-pairwise interaction which will be included in the thermodynamic
-output, but does not affect pair forces or atom trajectories.  See the
-doc page for individual pair styles to see which ones support this
-option.
-
-The {table} and {table/disp} keywords apply to pair styles with a
-long-range Coulombic term or long-range dispersion term respectively;
-see the doc page for individual styles to see which potentials support
-these options.  If N is non-zero, a table of length 2^N is
-pre-computed for forces and energies, which can shrink their
-computational cost by up to a factor of 2.  The table is indexed via a
-bit-mapping technique "(Wolff)"_#Wolff1 and a linear interpolation is
-performed between adjacent table values.  In our experiments with
-different table styles (lookup, linear, spline), this method typically
-gave the best performance in terms of speed and accuracy.
-
-The choice of table length is a tradeoff in accuracy versus speed.  A
-larger N yields more accurate force computations, but requires more
-memory which can slow down the computation due to cache misses.  A
-reasonable value of N is between 8 and 16.  The default value of 12
-(table of length 4096) gives approximately the same accuracy as the
-no-table (N = 0) option.  For N = 0, forces and energies are computed
-directly, using a polynomial fit for the needed erfc() function
-evaluation, which is what earlier versions of LAMMPS did.  Values
-greater than 16 typically slow down the simulation and will not
-improve accuracy; values from 1 to 8 give unreliable results.
-
-The {tabinner} and {tabinner/disp} keywords set an inner cutoff above
-which the pairwise computation is done by table lookup (if tables are
-invoked), for the corresponding Coulombic and dispersion tables
-discussed with the {table} and {table/disp} keywords.  The smaller the
-cutoff is set, the less accurate the table becomes (for a given number
-of table values), which can require use of larger tables.  The default
-cutoff value is sqrt(2.0) distance units which means nearly all
-pairwise interactions are computed via table lookup for simulations
-with "real" units, but some close pairs may be computed directly
-(non-table) for simulations with "lj" units.
-
-When the {tail} keyword is set to {yes}, certain pair styles will add
-a long-range VanderWaals tail "correction" to the energy and pressure.
-These corrections are bookkeeping terms which do not affect dynamics,
-unless a constant-pressure simulation is being performed.  See the doc
-page for individual styles to see which support this option.  These
-corrections are included in the calculation and printing of
-thermodynamic quantities (see the "thermo_style"_thermo_style.html
-command).  Their effect will also be included in constant NPT or NPH
-simulations where the pressure influences the simulation box
-dimensions (e.g. the "fix npt"_fix_nh.html and "fix nph"_fix_nh.html
-commands).  The formulas used for the long-range corrections come from
-equation 5 of "(Sun)"_#Sun.
-
-NOTE: The tail correction terms are computed at the beginning of each
-run, using the current atom counts of each atom type.  If atoms are
-deleted (or lost) or created during a simulation, e.g. via the "fix
-gcmc"_fix_gcmc.html command, the correction factors are not
-re-computed.  If you expect the counts to change dramatically, you can
-break a run into a series of shorter runs so that the correction
-factors are re-computed more frequently.
-
-Several additional assumptions are inherent in using tail corrections,
-including the following:
-
-The simulated system is a 3d bulk homogeneous liquid. This option
-should not be used for systems that are non-liquid, 2d, have a slab
-geometry (only 2d periodic), or inhomogeneous. :ulb,l
-
-G(r), the radial distribution function (rdf), is unity beyond the
-cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
-LJ fluid), and it is probably a good idea to verify this assumption by
-checking the rdf.  The rdf is not exactly unity beyond the cutoff for
-each pair of interaction types, so the tail correction is necessarily
-an approximation. :l
-
-The tail corrections are computed at the beginning of each simulation
-run.  If the number of atoms changes during the run, e.g. due to atoms
-leaving the simulation domain, or use of the "fix gcmc"_fix_gcmc.html
-command, then the corrections are not updated to reflect the changed
-atom count.  If this is a large effect in your simulation, you should
-break the long run into several short runs, so that the correction
-factors are re-computed multiple times.
-
-Thermophysical properties obtained from calculations with this option
-enabled will not be thermodynamically consistent with the truncated
-force-field that was used.  In other words, atoms do not feel any LJ
-pair interactions beyond the cutoff, but the energy and pressure
-reported by the simulation include an estimated contribution from
-those interactions. :l
-:ule
-
-The {compute} keyword allows pairwise computations to be turned off,
-even though a "pair_style"_pair_style.html is defined.  This is not
-useful for running a real simulation, but can be useful for debugging
-purposes or for performing a "rerun"_rerun.html simulation, when you
-only wish to compute partial forces that do not include the pairwise
-contribution.
-
-Two examples are as follows.  First, this option allows you to perform
-a simulation with "pair_style hybrid"_pair_hybrid.html with only a
-subset of the hybrid sub-styles enabled.  Second, this option allows
-you to perform a simulation with only long-range interactions but no
-short-range pairwise interactions.  Doing this by simply not defining
-a pair style will not work, because the
-"kspace_style"_kspace_style.html command requires a Kspace-compatible
-pair style be defined.
-
-The {nofdotr} keyword allows to disable an optimization that computes
-the global stress tensor from the total forces and atom positions rather
-than from summing forces between individual pairs of atoms.
-
-:line
-
-The {special} keyword allows to override the 1-2, 1-3, and 1-4
-exclusion settings for individual sub-styles of a
-"hybrid pair style"_pair_hybrid.html. It requires 4 arguments similar
-to the "special_bonds"_special_bonds.html command, {which} and
-wt1,wt2,wt3.  The {which} argument can be {lj} to change the
-Lennard-Jones settings, {coul} to change the Coulombic settings,
-or {lj/coul} to change both to the same set of 3 values.  The wt1,wt2,wt3
-values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
-1-3, and 1-4 bond topology neighbors, respectively. The {special}
-keyword can only be used in conjunction with the {pair} keyword
-and has to directly follow it.
-
-NOTE: The global settings specified by the
-"special_bonds"_special_bonds.html command affect the construction of
-neighbor lists.  Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
-exclude those pairs from the neighbor list entirely.  Weights of 1.0
-store the neighbor with no weighting applied. Thus only global values
-different from exactly 0.0 or 1.0 can be overridden and an error is
-generated if the requested setting is not compatible with the global
-setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
-usually a sufficient workaround in this case without causing a
-significant error.
-
-The {compute/tally} keyword takes exactly 1 argument ({no} or {yes}),
-and allows to selectively disable or enable processing of the various
-"compute */tally"_compute_tally.html styles for a given
-"pair hybrid or hybrid/overlay"_pair_hybrid.html sub-style.
-
-NOTE: Any "pair_modify pair compute/tally" command must be issued
-[before] the corresponding compute style is defined.
-
-:line
-
-[Restrictions:] none
-
-You cannot use {shift} yes with {tail} yes, since those are
-conflicting options.  You cannot use {tail} yes with 2d simulations.
-
-[Related commands:]
-
-"pair_style"_pair_style.html, "pair_style hybrid"_pair_hybrid.html,
-pair_coeff"_pair_coeff.html, "thermo_style"_thermo_style.html,
-"compute */tally"_compute_tally.html
-
-[Default:]
-
-The option defaults are mix = geometric, shift = no, table = 12,
-tabinner = sqrt(2.0), tail = no, and compute = yes.
-
-Note that some pair styles perform mixing, but only a certain style of
-mixing.  See the doc pages for individual pair styles for details.
-
-:line
-
-:link(Wolff1)
-[(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
-
-:link(Sun)
-[(Sun)] Sun, J Phys Chem B, 102, 7338-7364 (1998).

From e8d11931ecb003a2473bb555aa07fff83f85dfd2 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Mon, 13 Jan 2020 10:34:31 -0700
Subject: [PATCH 195/199] merged in current master

---
 .github/CODEOWNERS                            |    1 +
 .github/CONTRIBUTING.md                       |    3 +-
 cmake/CMakeLists.txt                          |   28 +-
 cmake/Modules/Documentation.cmake             |   23 +-
 cmake/Modules/FindNetCDF.cmake                |    6 +-
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 cmake/Modules/Packages/KIM.cmake              |   10 +
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 cmake/Modules/Packages/MESSAGE.cmake          |    3 +
 cmake/Modules/Packages/USER-COLVARS.cmake     |   42 +
 cmake/Modules/Packages/USER-MOLFILE.cmake     |    4 +
 cmake/Modules/Packages/USER-NETCDF.cmake      |   26 +-
 cmake/Modules/Packages/USER-PLUMED.cmake      |    4 +-
 cmake/README.md                               |   26 +
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 doc/.gitignore                                |    2 +
 doc/Makefile                                  |  105 +-
 doc/README                                    |   43 +-
 doc/lammps.1                                  |    2 +-
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 doc/src/Build_extras.rst                      | 1419 +++
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 ...{Commands_parse.txt => Commands_parse.rst} |   94 +-
 ...mands_removed.txt => Commands_removed.rst} |   57 +-
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 .../{force_spin_aniso.tex => norm_two.tex}    |    8 +-
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 ...omos.tex => pair_local_density_energy.tex} |    5 +-
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 doc/src/Errors.rst                            |   22 +
 doc/src/Errors_bugs.rst                       |   32 +
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 doc/src/Errors_messages.rst                   | 8418 +++++++++++++++
 doc/src/Errors_warnings.rst                   |  802 ++
 doc/src/Examples.rst                          |  237 +
 doc/src/Howto.rst                             |  106 +
 doc/src/Howto_2d.rst                          |   48 +
 doc/src/Howto_barostat.rst                    |   68 +
 doc/src/Howto_bash.rst                        |  291 +
 doc/src/Howto_bioFF.rst                       |  151 +
 doc/src/Howto_body.rst                        |  519 +
 doc/src/Howto_chunk.rst                       |  219 +
 doc/src/Howto_client_server.rst               |  135 +
 doc/src/Howto_coreshell.rst                   |  271 +
 doc/src/Howto_couple.rst                      |  125 +
 doc/src/Howto_diffusion.rst                   |   32 +
 doc/src/Howto_dispersion.rst                  |  105 +
 doc/src/Howto_drude.rst                       |   72 +
 doc/src/Howto_drude2.rst                      |  542 +
 doc/src/Howto_elastic.rst                     |   49 +
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 doc/src/Howto_multiple.rst                    |  103 +
 doc/src/Howto_nemd.rst                        |   60 +
 doc/src/Howto_output.rst                      |  349 +
 doc/src/Howto_polarizable.rst                 |   78 +
 doc/src/Howto_pylammps.rst                    |  584 ++
 doc/src/Howto_pylammps.txt                    |  481 -
 doc/src/Howto_replica.rst                     |   60 +
 doc/src/Howto_restart.rst                     |  105 +
 doc/src/Howto_spc.rst                         |   57 +
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 doc/src/PDF/pair_gayberne_extra.tex           |   10 +-
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 doc/src/Packages_details.rst                  | 2448 +++++
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 doc/src/Packages_user.rst                     |  126 +
 doc/src/Python_call.rst                       |   84 +
 doc/src/Python_examples.rst                   |  116 +
 doc/src/Python_head.rst                       |   49 +
 doc/src/Python_install.rst                    |   70 +
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 doc/src/Python_library.txt                    |  256 -
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 doc/src/Python_overview.rst                   |   30 +
 doc/src/Python_pylammps.rst                   |   10 +
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 doc/src/Python_test.rst                       |  170 +
 doc/src/Run_basics.rst                        |   96 +
 doc/src/Run_head.rst                          |   21 +
 doc/src/Run_options.rst                       |  646 ++
 doc/src/Run_output.rst                        |  197 +
 doc/src/Run_windows.rst                       |   81 +
 doc/src/Speed.rst                             |   35 +
 doc/src/Speed_bench.rst                       |   82 +
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 doc/src/Speed_gpu.rst                         |  185 +
 doc/src/Speed_intel.rst                       |  553 +
 doc/src/Speed_kokkos.rst                      |  451 +
 doc/src/Speed_measure.rst                     |   51 +
 doc/src/Speed_omp.rst                         |  167 +
 doc/src/Speed_opt.rst                         |   58 +
 doc/src/Speed_packages.rst                    |  195 +
 doc/src/Speed_tips.rst                        |   61 +
 doc/src/Tools.rst                             |  748 ++
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 doc/src/angle_class2.rst                      |  169 +
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 doc/src/{angle_coeff.txt => angle_coeff.rst}  |   85 +-
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 doc/src/angle_cosine_buck6d.rst               |   76 +
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 doc/src/angle_cosine_squared.rst              |   89 +
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 doc/src/angle_dipole.rst                      |  159 +
 doc/src/angle_dipole.txt                      |  126 -
 doc/src/angle_fourier.rst                     |   84 +
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 doc/src/angle_mm3.rst                         |   62 +
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 doc/src/angle_sdk.rst                         |   97 +
 doc/src/angle_sdk.txt                         |   83 -
 doc/src/angle_style.rst                       |  126 +
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 doc/src/{angle_table.txt => angle_table.rst}  |  135 +-
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 doc/src/angles.rst                            |    9 +
 doc/src/angles.txt                            |   30 -
 doc/src/{atom_modify.txt => atom_modify.rst}  |  175 +-
 doc/src/atom_style.rst                        |  373 +
 doc/src/atom_style.txt                        |  338 -
 doc/src/balance.rst                           |  574 ++
 doc/src/bond_class2.rst                       |  102 +
 doc/src/bond_class2.txt                       |   81 -
 doc/src/{bond_coeff.txt => bond_coeff.rst}    |   85 +-
 doc/src/bond_fene.rst                         |  111 +
 doc/src/bond_fene.txt                         |   88 -
 doc/src/bond_fene_expand.rst                  |  109 +
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 doc/src/bond_hybrid.rst                       |   85 +
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 doc/src/bond_mm3.rst                          |   73 +
 doc/src/bond_mm3.txt                          |   58 -
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 doc/src/bond_none.rst                         |   40 +
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 doc/src/bond_quartic.txt                      |  112 -
 doc/src/bond_style.rst                        |  132 +
 doc/src/bond_style.txt                        |  115 -
 doc/src/{bond_table.txt => bond_table.rst}    |  138 +-
 doc/src/{bond_write.txt => bond_write.rst}    |   58 +-
 doc/src/bond_zero.rst                         |   55 +
 doc/src/bond_zero.txt                         |   48 -
 doc/src/bonds.rst                             |    9 +
 doc/src/bonds.txt                             |   25 -
 doc/src/boundary.rst                          |  126 +
 doc/src/box.rst                               |   76 +
 doc/src/change_box.rst                        |  387 +
 doc/src/clear.rst                             |   49 +
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 doc/src/comm_style.rst                        |   78 +
 doc/src/commands_list.rst                     |  124 +
 doc/src/compute.rst                           |  339 +
 doc/src/compute_ackland_atom.rst              |  104 +
 doc/src/compute_adf.rst                       |  234 +
 doc/src/compute_angle.rst                     |   62 +
 doc/src/compute_angle_local.rst               |  158 +
 doc/src/compute_angmom_chunk.rst              |  100 +
 doc/src/compute_basal_atom.rst                |   90 +
 doc/src/compute_body_local.rst                |  110 +
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 doc/src/compute_bond_local.rst                |  214 +
 doc/src/compute_centro_atom.rst               |  180 +
 doc/src/compute_chunk_atom.rst                |  707 ++
 doc/src/compute_chunk_spread_atom.rst         |  237 +
 doc/src/compute_cluster_atom.rst              |  117 +
 doc/src/compute_cna_atom.rst                  |  119 +
 doc/src/compute_cnp_atom.rst                  |  133 +
 doc/src/compute_com.rst                       |   69 +
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 doc/src/compute_contact_atom.rst              |   66 +
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 doc/src/compute_damage_atom.rst               |   72 +
 doc/src/compute_dihedral.rst                  |   61 +
 doc/src/compute_dihedral_local.rst            |  151 +
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 doc/src/compute_edpd_temp_atom.rst            |   80 +
 doc/src/compute_entropy_atom.rst              |  164 +
 doc/src/compute_erotate_asphere.rst           |   82 +
 doc/src/compute_erotate_rigid.rst             |   70 +
 doc/src/compute_erotate_sphere.rst            |   71 +
 doc/src/compute_erotate_sphere_atom.rst       |   67 +
 doc/src/compute_event_displace.rst            |   76 +
 doc/src/compute_fep.rst                       |  349 +
 doc/src/compute_global_atom.rst               |  250 +
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 .../log.19Nov19.spin.restart.g++.4            |  118 +
 ...1 => log.19Nov19.spin.write_restart.g++.1} |   50 +-
 ...4 => log.19Nov19.spin.write_restart.g++.4} |   46 +-
 examples/SPIN/run_spin_examples.sh            |  120 +
 .../{in.spinmin.setforce => in.spin.setforce} |   10 +-
 .../log.19Nov19.spin.setforce.g++.1           |  141 +
 .../log.19Nov19.spin.setforce.g++.4           |  141 +
 .../{in.spinmin.bfo => in.spin.bfo_min}       |    2 +-
 examples/SPIN/spinmin/in.spin.bfo_min_cg      |   54 +
 examples/SPIN/spinmin/in.spin.bfo_min_lbfgs   |   55 +
 .../{in.spinmin.iron => in.spin.iron_min}     |    4 +-
 .../spinmin/log.19Nov19.spin.bfo_min.g++.1    |  148 +
 .../spinmin/log.19Nov19.spin.bfo_min.g++.4    |  148 +
 .../spinmin/log.19Nov19.spin.bfo_min_cg.g++.1 |  141 +
 .../spinmin/log.19Nov19.spin.bfo_min_cg.g++.4 |  141 +
 .../log.19Nov19.spin.bfo_min_lbfgs.g++.1      |  139 +
 .../log.19Nov19.spin.bfo_min_lbfgs.g++.4      |  139 +
 .../spinmin/log.19Nov19.spin.iron_min.g++.1   |  126 +
 .../spinmin/log.19Nov19.spin.iron_min.g++.4   |  126 +
 examples/SPIN/test_problems/README            |   47 +
 .../bench-spin-precession.in                  |   39 +
 .../llg_exchange.py                           |   70 +
 .../plot_precession.py                        |   44 +
 .../run-test-exchange.sh                      |   19 +
 .../bench-spin-precession.in                  |   47 +
 .../llg_precession.py                         |   52 +
 .../plot_precession.py                        |   45 +
 .../run-test-prec.sh                          |   19 +
 .../bench-prec-spin.template                  |   46 +
 .../langevin.py                               |   27 +
 .../plot_precession.py                        |   37 +
 .../run-test-prec.sh                          |   27 +
 examples/TIP4P/gpu_dump/data.spce             |    1 +
 .../dump.force_cpu.19Dec19.tip4p.g++.1        | 9018 +++++++++++++++++
 ...p.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp | 9018 +++++++++++++++++
 examples/TIP4P/gpu_dump/in.tip4p              |   49 +
 .../TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1    |  127 +
 .../log.19Dec19.tip4p.g++.1.gtx1070.dp        |  120 +
 examples/UNITS/README                         |   54 +
 examples/UNITS/in.ar.lj                       |   43 +
 examples/UNITS/in.ar.metal                    |   98 +
 examples/UNITS/in.ar.real                     |   98 +
 examples/UNITS/log.ar.lj.8Oct19.g++.1         |  109 +
 examples/UNITS/log.ar.lj.8Oct19.g++.4         |  109 +
 examples/UNITS/log.ar.metal.8Oct19.g++.1      |  197 +
 examples/UNITS/log.ar.metal.8Oct19.g++.4      |  197 +
 examples/UNITS/log.ar.real.8Oct19.g++.1       |  197 +
 examples/UNITS/log.ar.real.8Oct19.g++.4       |  197 +
 examples/USER/cgdna/README                    |   73 +-
 .../cgdna/examples/oxDNA/duplex1/in.duplex1   |    2 +-
 .../oxDNA/duplex1/log.07Aug19.duplex1.g++.1   | 1166 +++
 .../oxDNA/duplex1/log.07Aug19.duplex1.g++.4   | 1166 +++
 .../oxDNA/duplex1/log.18Jun19.duplex1.g++.1   | 1165 ---
 .../oxDNA/duplex1/log.18Jun19.duplex1.g++.4   | 1165 ---
 .../cgdna/examples/oxDNA/duplex2/in.duplex2   |    2 +-
 .../oxDNA/duplex2/log.07Aug19.duplex2.g++.1   | 1168 +++
 .../oxDNA/duplex2/log.07Aug19.duplex2.g++.4   | 1168 +++
 .../oxDNA/duplex2/log.18Jun19.duplex2.g++.1   | 1167 ---
 .../oxDNA/duplex2/log.18Jun19.duplex2.g++.4   | 1167 ---
 .../cgdna/examples/oxDNA2/duplex1/in.duplex1  |    6 +-
 ...uplex1.g++.1 => log.07Aug19.duplex1.g++.1} |   34 +-
 ...uplex1.g++.4 => log.07Aug19.duplex1.g++.4} |   36 +-
 .../cgdna/examples/oxDNA2/duplex2/in.duplex2  |    7 +-
 ...uplex2.g++.1 => log.07Aug19.duplex2.g++.1} |   37 +-
 ...uplex2.g++.4 => log.07Aug19.duplex2.g++.4} |   37 +-
 .../cgdna/examples/oxDNA2/duplex3/in.duplex3  |    8 +-
 ...uplex3.g++.1 => log.07Aug19.duplex3.g++.1} |   38 +-
 ...uplex3.g++.4 => log.07Aug19.duplex3.g++.4} |   38 +-
 .../oxDNA2/unique_bp/data.duplex4.4type       |  130 +
 .../oxDNA2/unique_bp/data.duplex4.8type       |  130 +
 .../oxDNA2/unique_bp/generate_unique.py       |  828 ++
 .../oxDNA2/unique_bp/in.duplex4.4type         |   94 +
 .../oxDNA2/unique_bp/in.duplex4.8type         |   94 +
 .../unique_bp/log.07Aug19.duplex4.4type.g++1  |  232 +
 .../unique_bp/log.07Aug19.duplex4.4type.g++4  |  232 +
 .../unique_bp/log.07Aug19.duplex4.8type.g++1  |  274 +
 .../unique_bp/log.07Aug19.duplex4.8type.g++4  |  274 +
 .../examples/oxRNA2/duplex4/data.duplex4      |   96 +
 .../cgdna/examples/oxRNA2/duplex4/in.duplex4  |   80 +
 .../oxRNA2/duplex4/log.30Oct19.duplex4.g++.1  | 1174 +++
 .../oxRNA2/duplex4/log.30Oct19.duplex4.g++.4  | 1174 +++
 examples/USER/drude/toluene/data.toluene      |    8 +-
 examples/USER/drude/toluene/in.toluene.lang   |    4 +-
 examples/USER/drude/toluene/in.toluene.nh     |    4 +-
 .../toluene/log.27Nov18.toluene.lang.g++.1    |   14 -
 .../toluene/log.27Nov18.toluene.lang.g++.4    |   14 -
 .../toluene/log.27Nov18.toluene.nh.g++.1      |   14 -
 .../toluene/log.27Nov18.toluene.nh.g++.4      |   14 -
 .../toluene/log.7Aug19.toluene.lang.g++.1     |  254 +
 .../toluene/log.7Aug19.toluene.lang.g++.4     |  254 +
 .../drude/toluene/log.7Aug19.toluene.nh.g++.1 |  262 +
 .../drude/toluene/log.7Aug19.toluene.nh.g++.4 |  262 +
 .../benzene_water/benzene_water.data          | 1406 +++
 .../benzene_water/benzene_water.in            |   62 +
 .../benzene_water.localdensity.table          | 2024 ++++
 .../benzene_water/benzene_water.pair.table    | 2024 ++++
 .../benzene_water/log.04Sep19.g++.1           |  267 +
 .../methanol_implicit_water/log.04Sep19.g++.1 |  226 +
 .../methanol_implicit_water.data              | 2525 +++++
 .../methanol_implicit_water.in                |   68 +
 ...methanol_implicit_water.localdensity.table |  509 +
 .../methanol_implicit_water.pair.table        | 1012 ++
 .../dynamical_matrix_command/python/README.md |   12 +
 .../dynamical_matrix_command/python/dynmat.py |   42 +
 examples/gcmc/CO2.txt                         |   14 +-
 examples/gcmc/H2O.txt                         |   14 +-
 examples/gjf/README.md                        |   13 +
 examples/gjf/argon.lmp                        |  886 ++
 examples/gjf/ff-argon.lmp                     |   20 +
 examples/gjf/in.gjf.vfull                     |   23 +
 examples/gjf/in.gjf.vhalf                     |   23 +
 examples/gjf/log.15Oct19.gjf.vfull.g++.1      |  125 +
 examples/gjf/log.15Oct19.gjf.vfull.g++.4      |  125 +
 examples/gjf/log.15Oct19.gjf.vhalf.g++.1      |  125 +
 examples/gjf/log.15Oct19.gjf.vhalf.g++.4      |  125 +
 .../python/in.fix_python_invoke_neighlist     |   72 +
 examples/rerun/README                         |   17 +
 examples/rerun/in.first                       |   33 +
 examples/rerun/in.rdf.first                   |   36 +
 examples/rerun/in.rdf.rerun                   |   31 +
 examples/rerun/in.read_dump                   |   37 +
 examples/rerun/in.rerun                       |   29 +
 examples/rerun/log.09Jan20.first.g++.4        |   97 +
 examples/rerun/log.09Jan20.rdf.first.g++.4    |  105 +
 examples/rerun/log.09Jan20.rdf.rerun.g++.4    |  100 +
 examples/rerun/log.09Jan20.read_dump.g++.4    |  118 +
 examples/rerun/log.09Jan20.rerun.g++.4        |   86 +
 examples/rerun/rdf.09Jan20.first.g++.4        |   54 +
 examples/rerun/rdf.09Jan20.rerun.g++.4        |  104 +
 examples/rigid/in.rigid.gravity               |   63 +
 examples/rigid/molecule.data                  |   41 +
 examples/snap/WBe_Wood_PRB2019.snap           |    1 +
 examples/snap/WBe_Wood_PRB2019.snapcoeff      |    1 +
 examples/snap/WBe_Wood_PRB2019.snapparam      |    1 +
 examples/snap/in.snap.Mo_Chen                 |   14 +-
 examples/snap/in.snap.Ta06A                   |   12 +-
 examples/snap/in.snap.W.2940                  |   14 +-
 examples/snap/in.snap.WBe.PRB2019             |   48 +
 examples/snap/in.snap.compute                 |  100 +
 examples/snap/in.snap.compute.quadratic       |  100 +
 examples/snap/in.snap.hybrid.WSNAP.HePair     |   20 +-
 examples/snap/log.18Sep19.snap.WBeSNAP.g++.1  |  154 +
 examples/snap/log.18Sep19.snap.WBeSNAP.g++.4  |  154 +
 examples/snap/log.27Nov18.snap.compute.g++.1  |  198 +
 examples/snap/log.27Nov18.snap.compute.g++.4  |  199 +
 .../log.27Nov18.snap.compute.quadratic.g++.1  |  198 +
 .../log.27Nov18.snap.compute.quadratic.g++.4  |  199 +
 lib/atc/ATC_Coupling.cpp                      |    2 +-
 lib/atc/ATC_Coupling.h                        |    2 +-
 lib/atc/ATC_CouplingMomentumEnergy.cpp        |    2 +-
 lib/atc/ATC_Method.h                          |    8 +-
 lib/atc/ATC_Transfer.cpp                      |    2 +-
 lib/atc/ATC_TransferPartitionOfUnity.cpp      |    2 +-
 lib/atc/AtomicRegulator.cpp                   |    2 +-
 lib/atc/AtomicRegulator.h                     |   35 +-
 lib/atc/BodyForce.h                           |    6 +-
 lib/atc/CbPotential.h                         |    8 +-
 lib/atc/ChargeRegulator.cpp                   |   10 +-
 lib/atc/ChargeRegulator.h                     |    6 +-
 lib/atc/CloneVector.h                         |    6 +-
 lib/atc/ConcentrationRegulator.cpp            |    8 +-
 lib/atc/ConcentrationRegulator.h              |   20 +-
 lib/atc/DenseVector.h                         |    8 +-
 lib/atc/DiagonalMatrix.h                      |   13 +-
 lib/atc/ElasticTimeIntegrator.cpp             |    6 +-
 lib/atc/ElectronChargeDensity.cpp             |    2 +-
 lib/atc/ElectronChargeDensity.h               |   22 +-
 lib/atc/ElectronDragPower.cpp                 |    2 +-
 lib/atc/ElectronDragPower.h                   |    6 +-
 lib/atc/ElectronFlux.cpp                      |    2 +-
 lib/atc/ElectronFlux.h                        |    4 +-
 lib/atc/ElectronHeatCapacity.h                |    4 +-
 lib/atc/ElectronHeatFlux.h                    |    4 +-
 lib/atc/ElectronPhononExchange.h              |    4 +-
 lib/atc/ExtrinsicModel.cpp                    |    4 +-
 lib/atc/ExtrinsicModel.h                      |   10 +-
 lib/atc/ExtrinsicModelElectrostatic.cpp       |    2 +-
 lib/atc/FE_Engine.cpp                         |    6 +-
 lib/atc/FE_Engine.h                           |    5 +-
 lib/atc/FE_Mesh.cpp                           |    9 +-
 lib/atc/FE_Mesh.h                             |    2 +-
 lib/atc/FieldEulerIntegrator.cpp              |   10 +-
 lib/atc/FieldEulerIntegrator.h                |    4 +-
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 lib/atc/Function.h                            |   38 +-
 lib/atc/FundamentalAtomicQuantity.h           |   38 +-
 lib/atc/KernelFunction.cpp                    |   18 +-
 lib/atc/KernelFunction.h                      |    4 +-
 lib/atc/KinetoThermostat.cpp                  |   10 +-
 lib/atc/KinetoThermostat.h                    |   33 +-
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 lib/atc/LammpsInterface.cpp                   |    4 +-
 lib/atc/Material.cpp                          |    8 +-
 lib/atc/Matrix.h                              |    2 +-
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 lib/atc/MoleculeSet.cpp                       |    2 +-
 lib/atc/NonLinearSolver.h                     |    2 +-
 lib/atc/OutputManager.cpp                     |    6 +-
 lib/atc/POEMSChain.h                          |   73 -
 lib/atc/PerAtomQuantity-inl.h                 |   12 +-
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 lib/atc/PerAtomQuantityLibrary.h              |   14 +-
 lib/atc/PerPairQuantity.cpp                   |    2 -
 lib/atc/PhysicsModel.h                        |    2 +-
 lib/atc/PoissonSolver.cpp                     |    2 +-
 lib/atc/PolynomialSolver.cpp                  |    2 +-
 lib/atc/SchrodingerSolver.cpp                 |   10 +-
 lib/atc/SchrodingerSolver.h                   |    4 +-
 lib/atc/SparseMatrix-inl.h                    |    4 +-
 lib/atc/SparseVector-inl.h                    |   14 +-
 lib/atc/SpeciesTimeIntegrator.cpp             |    6 +-
 lib/atc/Stress.cpp                            |    8 +-
 lib/atc/Stress.h                              |    6 +-
 lib/atc/SystemProcessor.h                     |  283 -
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 lib/awpmd/ivutils/include/pairhash.h          |    2 +-
 lib/awpmd/ivutils/include/wavepacket.h        |    4 +-
 lib/awpmd/systems/interact/TCP/wpmd.h         |    2 +-
 lib/awpmd/systems/interact/TCP/wpmd_split.cpp |   11 +-
 lib/colvars/Install.py                        |   22 +-
 lib/colvars/Makefile.common                   |   20 +-
 lib/colvars/Makefile.g++                      |    2 +-
 lib/colvars/Makefile.g++-debug                |    2 +-
 lib/colvars/Makefile.g++-no-lepton            |    5 +
 lib/colvars/README                            |  112 +-
 .../include/lepton/CompiledExpression.h       |   11 +-
 .../lepton/include/lepton/CustomFunction.h    |   32 +
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 lib/colvars/lepton/include/lepton/Operation.h |   34 +-
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 lib/colvars/lepton/src/MSVC_erfc.h            |    6 +-
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 lib/colvars/lepton/src/ParsedExpression.cpp   |   10 +
 lib/colvars/lepton/src/Parser.cpp             |    7 +-
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 lib/gpu/Makefile.shannon                      |    2 +-
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 lib/gpu/lal_gayberne.cu                       |    7 +-
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 lib/gpu/lal_lj_tip4p_long.cu                  |  568 ++
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 lib/gpu/lal_lj_tip4p_long_ext.cpp             |  147 +
 lib/gpu/lal_pppm.cpp                          |   15 +-
 lib/message/cslib/src/cslib.cpp               |    1 +
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 create mode 100644 lib/gpu/lal_lj_tip4p_long_ext.cpp
 create mode 100644 potentials/WBe_Wood_PRB2019.snap
 create mode 100644 potentials/WBe_Wood_PRB2019.snapcoeff
 create mode 100644 potentials/WBe_Wood_PRB2019.snapparam
 create mode 100644 src/COMPRESS/dump_local_gz.cpp
 create mode 100644 src/COMPRESS/dump_local_gz.h
 create mode 100644 src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
 create mode 100644 src/GPU/pair_lj_cut_tip4p_long_gpu.h
 create mode 100644 src/KIM/kim_param.cpp
 create mode 100644 src/KIM/kim_param.h
 create mode 100644 src/SNAP/compute_snap.cpp
 create mode 100644 src/SNAP/compute_snap.h
 create mode 100644 src/SPIN/min_spin_cg.cpp
 create mode 100644 src/SPIN/min_spin_cg.h
 create mode 100644 src/SPIN/min_spin_lbfgs.cpp
 create mode 100644 src/SPIN/min_spin_lbfgs.h
 delete mode 100644 src/USER-CGDNA/README
 create mode 100644 src/USER-CGDNA/README.md
 create mode 100644 src/USER-CGDNA/bond_oxrna2_fene.cpp
 create mode 100644 src/USER-CGDNA/bond_oxrna2_fene.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_dh.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_dh.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_excv.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_excv.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_hbond.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_hbond.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_stk.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_stk.h
 create mode 100644 src/USER-CGDNA/pair_oxrna2_xstk.cpp
 create mode 100644 src/USER-CGDNA/pair_oxrna2_xstk.h
 create mode 100644 src/USER-MISC/compute_gyration_shape_chunk.cpp
 create mode 100644 src/USER-MISC/compute_gyration_shape_chunk.h
 create mode 100644 src/USER-MISC/pair_local_density.cpp
 create mode 100644 src/USER-MISC/pair_local_density.h
 create mode 100644 src/USER-PHONON/third_order.cpp
 create mode 100644 src/USER-PHONON/third_order.h
 create mode 100644 src/compute_centroid_stress_atom.cpp
 create mode 100644 src/compute_centroid_stress_atom.h
 create mode 100644 tools/singularity/README.md
 create mode 100644 tools/singularity/centos7.def
 create mode 100644 tools/singularity/centos8.def
 create mode 100644 tools/singularity/ubuntu16.04.def
 create mode 100644 tools/singularity/ubuntu18.04.def

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 7d1f1a417b..a4fc5b7b4f 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -111,6 +111,7 @@ src/exceptions.h          @rbberger
 src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
+src/min*                  @sjplimp @stanmoore1
 
 # tools
 tools/msi2lmp/*       @akohlmey
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 5a67c547df..3ff672a05d 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -68,7 +68,8 @@ How quickly your contribution will be integrated depends largely on how much eff
 Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
 
 * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
-* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers outside of <cstdio>, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.txt'.
 * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
 * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 91fb930be2..ddad6c2626 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -52,8 +52,15 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckCCompilerFlag)
 include(CheckIncludeFileCXX)
 
-if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
-  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11")
+endif()
+
+option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
+if(DISABLE_CXX11_REQUIREMENT)
+  add_definitions(-DLAMMPS_CXX98)
+# else()
+#  set(CMAKE_CXX_STANDARD 11)
 endif()
 
 # GNU compiler features
@@ -241,6 +248,7 @@ if(BUILD_OMP)
 endif()
 
 if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+  enable_language(C)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -315,13 +323,14 @@ endif()
 include(Packages/KSPACE)
 include(Packages/PYTHON)
 include(Packages/VORONOI)
-include(Packages/USER-SCAFACOS)
-include(Packages/USER-PLUMED)
+include(Packages/USER-COLVARS)
 include(Packages/USER-MOLFILE)
 include(Packages/USER-NETCDF)
-include(Packages/USER-SMD)
-include(Packages/USER-QUIP)
+include(Packages/USER-PLUMED)
 include(Packages/USER-QMMM)
+include(Packages/USER-QUIP)
+include(Packages/USER-SCAFACOS)
+include(Packages/USER-SMD)
 include(Packages/USER-VTK)
 include(Packages/KIM)
 include(Packages/LATTE)
@@ -411,8 +420,7 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
-  USER-QMMM)
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
@@ -426,10 +434,6 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
       target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
     elseif(PKG_LIB STREQUAL h5md)
       target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
-    elseif(PKG_LIB STREQUAL colvars)
-      target_compile_options(colvars PRIVATE -DLEPTON)
-      target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
-      target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
     else()
       target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
     endif()
diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake
index 99f570820a..feff66a9b2 100644
--- a/cmake/Modules/Documentation.cmake
+++ b/cmake/Modules/Documentation.cmake
@@ -9,9 +9,7 @@ if(BUILD_DOC)
 
   set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
 
-  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
-  file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
-  list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
   add_custom_command(
     OUTPUT docenv
@@ -28,25 +26,10 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
   )
 
-  set(RST_FILES "")
-  set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
-  file(MAKE_DIRECTORY ${RST_DIR})
-  foreach(TXT_FILE ${DOC_SOURCES})
-    get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
-    set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
-    list(APPEND RST_FILES ${RST_FILE})
-    add_custom_command(
-      OUTPUT ${RST_FILE}
-      DEPENDS requirements.txt docenv ${TXT_FILE}
-      COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
-    )
-  endforeach()
-
   add_custom_command(
     OUTPUT html
-    DEPENDS ${RST_FILES}
-    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
-    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
+    DEPENDS ${DOC_SOURCES} docenv requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
   )
 
   add_custom_target(
diff --git a/cmake/Modules/FindNetCDF.cmake b/cmake/Modules/FindNetCDF.cmake
index a28c959acf..2a992b6b3b 100644
--- a/cmake/Modules/FindNetCDF.cmake
+++ b/cmake/Modules/FindNetCDF.cmake
@@ -46,10 +46,14 @@ endif()
 find_path (NETCDF_INCLUDE_DIR netcdf.h
   HINTS "${NETCDF_DIR}/include")
 mark_as_advanced (NETCDF_INCLUDE_DIR)
+
 set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 
+string(REGEX REPLACE "/include/?$" ""
+  NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
+
 find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib")
+  HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)
 mark_as_advanced (NETCDF_LIBRARY)
 
 set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
new file mode 100644
index 0000000000..bc3a5f9538
--- /dev/null
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -0,0 +1,55 @@
+# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake
+# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)
+#
+# - Find PNetCDF
+# Find the native PNetCDF includes and library
+#
+#  PNETCDF_INCLUDES    - where to find netcdf.h, etc
+#  PNETCDF_LIBRARIES   - Link these libraries when using NetCDF
+#  PNETCDF_FOUND       - True if PNetCDF was found
+#
+# Normal usage would be:
+#  find_package (PNetCDF REQUIRED)
+#  target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})
+
+if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+  # Already in cache, be silent
+  set (PNETCDF_FIND_QUIETLY TRUE)
+endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+
+find_path (PNETCDF_INCLUDES pnetcdf.h
+  HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
+
+string(REGEX REPLACE "/include/?$" ""
+  PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
+
+find_library (PNETCDF_LIBRARIES
+  NAMES pnetcdf
+  HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)
+
+if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
+  message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")
+
+  file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)
+
+  find_library(PNETCDF_LIBRARIES
+    NAMES pnetcdf
+    HINTS ${LD_LIBRARY_PATH})
+
+  if (PNETCDF_LIBRARIES)
+    get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
+    string(REGEX REPLACE "/(lib|lib64)/?$" "/include"
+      PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
+
+    find_path (PNETCDF_INCLUDES pnetcdf.h
+      HINTS ${PNETCDF_H_HINT}
+      DOC "Path to pnetcdf.h")
+  endif()
+endif()
+
+# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
+
+mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)
diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake
index 8d17225760..a75e248097 100644
--- a/cmake/Modules/Packages/KIM.cmake
+++ b/cmake/Modules/Packages/KIM.cmake
@@ -5,6 +5,16 @@ if(PKG_KIM)
     include_directories(${CURL_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
     add_definitions(-DLMP_KIM_CURL)
+    set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
+    mark_as_advanced(LMP_DEBUG_CURL)
+    if(LMP_DEBUG_CURL)
+      add_definitions(-DLMP_DEBUG_CURL)
+    endif()
+    set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
+    mark_as_advanced(LMP_NO_SSL_CHECK)
+    if(LMP_NO_SSL_CHECK)
+      add_definitions(-DLMP_NO_SSL_CHECK)
+    endif()
   endif()
   find_package(KIM-API QUIET)
   if(KIM-API_FOUND)
diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake
index cc1e051629..428588ec9d 100644
--- a/cmake/Modules/Packages/KOKKOS.cmake
+++ b/cmake/Modules/Packages/KOKKOS.cmake
@@ -1,15 +1,24 @@
 if(PKG_KOKKOS)
-  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
-  set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
+  # TODO: this option needs to be documented when this works with a
+  # regular release version of KOKKOS, and a version compatibility check
+  # of external KOKKOS lib versus what the KOKKOS package needs is required.
+  option(EXTERNAL_KOKKOS "Build against external kokkos library")
+  if(EXTERNAL_KOKKOS)
+    find_package(Kokkos REQUIRED)
+    list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
+  else()
+    set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
+    set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
+    add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  
+    set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
+                            ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
+                            ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
+                            ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+    include_directories(${Kokkos_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS kokkos)
+  endif()
   add_definitions(-DLMP_KOKKOS)
-  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-
-  set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
-                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
-                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
-                          ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-  include_directories(${Kokkos_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS kokkos)
 
   set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
   set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
diff --git a/cmake/Modules/Packages/MESSAGE.cmake b/cmake/Modules/Packages/MESSAGE.cmake
index 3c1bdde855..aff9c2964a 100644
--- a/cmake/Modules/Packages/MESSAGE.cmake
+++ b/cmake/Modules/Packages/MESSAGE.cmake
@@ -1,4 +1,7 @@
 if(PKG_MESSAGE)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
+    message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
   option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
   file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
       ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
diff --git a/cmake/Modules/Packages/USER-COLVARS.cmake b/cmake/Modules/Packages/USER-COLVARS.cmake
new file mode 100644
index 0000000000..b7fb91917c
--- /dev/null
+++ b/cmake/Modules/Packages/USER-COLVARS.cmake
@@ -0,0 +1,42 @@
+if(PKG_USER-COLVARS)
+
+  set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+
+  file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+
+  # Build Lepton by default
+  set(COLVARS_LEPTON_DEFAULT ON)
+  # but not if C++11 is disabled per user request
+  if(DEFINED DISABLE_CXX11_REQUIREMENT)
+    if(DISABLE_CXX11_REQUIREMENT)
+      set(COLVARS_LEPTON_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})
+
+  # Verify that the user's choice is consistent
+  if(DEFINED DISABLE_CXX11_REQUIREMENT)
+    if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
+      message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
+    endif()
+  endif()
+
+  if(COLVARS_LEPTON)
+    set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
+    file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
+    add_library(lepton STATIC ${LEPTON_SOURCES})
+    target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
+  endif()
+
+  add_library(colvars STATIC ${COLVARS_SOURCES})
+  target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+  list(APPEND LAMMPS_LINK_LIBS colvars)
+
+  if(COLVARS_LEPTON)
+    list(APPEND LAMMPS_LINK_LIBS lepton)
+    target_compile_options(colvars PRIVATE -DLEPTON)
+    target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
+  endif()
+
+endif()
diff --git a/cmake/Modules/Packages/USER-MOLFILE.cmake b/cmake/Modules/Packages/USER-MOLFILE.cmake
index 16ffc34994..b8c4234d26 100644
--- a/cmake/Modules/Packages/USER-MOLFILE.cmake
+++ b/cmake/Modules/Packages/USER-MOLFILE.cmake
@@ -1,4 +1,8 @@
 if(PKG_USER-MOLFILE)
+  if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library
+    message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later")
+  endif()
+
   set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
diff --git a/cmake/Modules/Packages/USER-NETCDF.cmake b/cmake/Modules/Packages/USER-NETCDF.cmake
index a90725bbbc..f60c046ab9 100644
--- a/cmake/Modules/Packages/USER-NETCDF.cmake
+++ b/cmake/Modules/Packages/USER-NETCDF.cmake
@@ -1,6 +1,24 @@
 if(PKG_USER-NETCDF)
-  find_package(NetCDF REQUIRED)
-  include_directories(${NETCDF_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
-  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+  # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
+  # NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
+  find_package(NetCDF)
+  if(NETCDF_FOUND)
+    find_package(PNetCDF)
+  else(NETCDF_FOUND)
+    find_package(PNetCDF REQUIRED)
+  endif(NETCDF_FOUND)
+
+  if(NETCDF_FOUND)
+    include_directories(${NETCDF_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_NETCDF)
+  endif(NETCDF_FOUND)
+
+  if(PNETCDF_FOUND)
+    include_directories(${PNETCDF_INCLUDES})
+    list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_PNETCDF)
+  endif(PNETCDF_FOUND)
+
+  add_definitions(-DNC_64BIT_DATA=0x0020)
 endif()
diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake
index 5c35e13bda..bf5c502d84 100644
--- a/cmake/Modules/Packages/USER-PLUMED.cmake
+++ b/cmake/Modules/Packages/USER-PLUMED.cmake
@@ -49,8 +49,8 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz
-      URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a
+      URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
+      URL_MD5 de30d6e7c2dcc0973298e24a6da24286
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}
diff --git a/cmake/README.md b/cmake/README.md
index 01b6f6a60e..6255307ef3 100644
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -1798,6 +1798,32 @@ Requires installation of the Voro++ library
 </tbody>
 </table>
 
+### USER-COLVARS Package
+
+Requires a C++11 compiler to compile with the Lepton library included.
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>COLVARS_LEPTON</code></td>
+  <td>Enable the use of the Lepton library inside the Colvars library.
+  <td>
+  <dl>
+    <dt><code>on</code> (default)</dt>
+    <dt><code>off</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
 ### USER-LATTE Package
 
 Requires installation of the LATTE library
diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake
index 35ad7ba55c..eed560b995 100644
--- a/cmake/presets/most.cmake
+++ b/cmake/presets/most.cmake
@@ -4,10 +4,10 @@
 
 set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
         GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
-        PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI
+        PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI
         USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
         USER-DRUDE USER-FEP USER-MEAMC USER-MESO
-        USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
+        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
         USER-SPH USER-SMD USER-UEF USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
diff --git a/doc/.gitignore b/doc/.gitignore
index 88679898a8..ca450f00f9 100644
--- a/doc/.gitignore
+++ b/doc/.gitignore
@@ -6,3 +6,5 @@
 /LAMMPS.mobi
 /Manual.pdf
 /Developer.pdf
+/doctrees
+/docenv
diff --git a/doc/Makefile b/doc/Makefile
index 5c679440b8..a3c4906cec 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -1,12 +1,12 @@
 # Makefile for LAMMPS documentation
 
 SHELL         = /bin/bash
-SHA1          = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
-BUILDDIR      = /tmp/lammps-docs-$(SHA1)
-RSTDIR        = $(BUILDDIR)/rst
+BUILDDIR      = ${CURDIR}
+RSTDIR        = $(BUILDDIR)/src
+TXTDIR        = $(BUILDDIR)/txt
 VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
-ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
+ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
 
 PYTHON        = $(shell which python3)
 VIRTUALENV     = virtualenv
@@ -28,10 +28,10 @@ HAS_VIRTUALENV = YES
 endif
 
 SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
-SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
-OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
+SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
+OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check
 
 # ------------------------------------------
 
@@ -39,36 +39,38 @@ help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       create HTML doc pages in html dir"
 	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"
-	@echo "  old        create old-style HTML doc pages and Manual.pdf in old dir"
 	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
 	@echo "  epub       create ePUB format manual for e-book readers"
 	@echo "  mobi       convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
 	@echo "                      (requires ebook-convert tool from calibre)"
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
-	@echo "  txt2html   build txt2html tool"
 	@echo "  anchor_check  scan for duplicate anchor labels"
+	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  spelling   spell-check the manual"
 
 # ------------------------------------------
 
 clean-all: clean
-	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
+	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees
 
 clean:
-	rm -rf $(RSTDIR) html old epub latex
+	rm -rf html epub latex
 	rm -rf spelling
 
 clean-spelling:
 	rm -rf spelling
 
+rst: clean $(OBJECTS) $(ANCHORCHECK)
+
 html: $(OBJECTS) $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
-		doc_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -88,8 +90,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
 	@(\
 		. $(VENV)/bin/activate ;\
 		pip install sphinxcontrib-spelling ;\
-		cp -r src/* $(RSTDIR)/ ;\
-        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
+		cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
 		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
 		deactivate ;\
 	)
@@ -102,7 +103,6 @@ epub: $(OBJECTS)
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
-		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		deactivate ;\
 	)
@@ -124,25 +124,27 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 		cd ../../; \
 	)
 	@(\
-                . $(VENV)/bin/activate ;\
-                cp -r src/* $(RSTDIR)/ ;\
-                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-                echo "############################################" ;\
-                doc_anchor_check src/*.txt ;\
-                echo "############################################" ;\
-                deactivate ;\
+		. $(VENV)/bin/activate ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		echo "############################################" ;\
+		rst_anchor_check src/*.rst ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		echo "############################################" ;\
+		deactivate ;\
 	)
 	@cd latex && \
-          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
-	  mv temp Makefile && \
-	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  make && \
-	  make && \
-	  mv LAMMPS.pdf ../Manual.pdf && \
-	  cd ../;
+		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+		mv temp Makefile && \
+		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		make && \
+		make && \
+		make && \
+		mv LAMMPS.pdf ../Manual.pdf && \
+		cd ../;
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER
@@ -154,27 +156,6 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 	@rm -rf latex/USER/*/*.[sg]*
 	@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
 
-old: utils/txt2html/txt2html.exe
-	@rm -rf old
-	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
-	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
-	  mv *.html ../old; \
-	  cp Eqs/*.jpg ../old/Eqs; \
-	  cp JPG/* ../old/JPG; \
-	  cp PDF/* ../old/PDF;
-	@(      set -e;\
-		cd src/Developer; \
-		pdflatex developer; \
-		pdflatex developer; \
-		mv developer.pdf ../../old/Developer.pdf; \
-		cd ../../old; \
-	        for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q ^$$s ../src/lammps.book || \
-			echo WARNING: doc file $$s missing in src/lammps.book; done; \
-		htmldoc --batch ../src/lammps.book;          \
-	)
-
-
 fetch:
 	@rm -rf html_www Manual_www.pdf Developer_www.pdf
 	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@@ -183,21 +164,23 @@ fetch:
 	@tar xzf lammps-doc.tar.gz
 	@rm -f lammps-doc.tar.gz
 
-txt2html: utils/txt2html/txt2html.exe
-
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		doc_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.txt ;\
+		deactivate ;\
+	)
+
+style_check :
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 # ------------------------------------------
 
-utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
-	g++ -O -Wall -o $@ $<
-
-$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
+$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
 	@(\
 		mkdir -p $(RSTDIR) ; \
 		. $(VENV)/bin/activate ;\
diff --git a/doc/README b/doc/README
index 6db4ba3ca7..1416584eed 100644
--- a/doc/README
+++ b/doc/README
@@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file:
 
 src             content files for LAMMPS documentation
 html            HTML version of the LAMMPS manual (see html/Manual.html)
-tools           tools and settings for building the documentation
+utils           utilities and settings for building the documentation
 Manual.pdf      large PDF version of entire manual
 Developer.pdf   small PDF with info about how LAMMPS is structured
 LAMMPS.epub     Manual in ePUB format
@@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source
 code will not, unless you update your local repository).
 
 (b) You can build the HTML and PDF files yourself, by typing "make
-html" followed by "make pdf".  Note that the PDF make requires the
-HTML files already exist.  This requires various tools including
-Sphinx, which the build process will attempt to download and install
-on your system, if not already available.  See more details below.
-
-(c) You can genererate an older, simpler, less-fancy style of HTML
-documentation by typing "make old".  This will create an "old"
-directory.  This can be useful if (b) does not work on your box for
-some reason, or you want to quickly view the HTML version of a doc
-page you have created or edited yourself within the src directory.
-E.g. if you are planning to submit a new feature to LAMMPS.
+html" or by "make pdf", respectively.  This requires various tools
+including the Python documentation processing tool Sphinx, which the
+build process will attempt to download and install on your system into
+a python virtual environment, if not already available.  The PDF file
+will require a working LaTeX installation with several add-on packages
+in addition to the Python/Sphinx setup.  See more details below.
 
 ----------------
 
@@ -46,11 +41,10 @@ Options:
 
 make html         # generate HTML in html dir using Sphinx
 make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
-                  #   in this dir via htmldoc and pdflatex
-make old          # generate old-style HTML pages in old dir via txt2html
+                  #   in this dir via Sphinx and PDFLaTeX
 make fetch        # fetch HTML doc pages and 2 PDF files from web site
                   #   as a tarball and unpack into html dir and 2 PDFs
-make epub         # generate LAMMPS.epub in ePUB format using Sphinx 
+make epub         # generate LAMMPS.epub in ePUB format using Sphinx
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data
 
@@ -94,8 +88,17 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
-
+Same as for HTML plus a compatible LaTeX installation with
+support for PDFLaTeX. Also the following LaTeX packages need
+to be installed (e.g. from texlive):
+- amsmath
+- babel
+- cmap
+- fncychap
+- geometry
+- hyperref
+- hypcap
+- times
 ----------------
 
 Installing prerequisites for epub build
@@ -103,7 +106,11 @@ Installing prerequisites for epub build
 ## ePUB
 
 Same as for HTML. This uses the same tools and configuration
-files as the HTML tree.
+files as the HTML tree. The ePUB format conversion currently
+does not support processing mathematical expressions via MathJAX,
+so there will be limitations on some pages. For the time being
+until this is resolved, building and using the PDF format file
+is recommended instead.
 
 For converting the generated ePUB file to a mobi format file
 (for e-book readers like Kindle, that cannot read ePUB), you
diff --git a/doc/lammps.1 b/doc/lammps.1
index ac19749dd6..4355e64961 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -1,4 +1,4 @@
-.TH LAMMPS "7 August 2019" "2019-08-07"
+.TH LAMMPS "9 January 2020" "2020-01-09"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
diff --git a/doc/src/.gitignore b/doc/src/.gitignore
new file mode 100644
index 0000000000..e0b9693457
--- /dev/null
+++ b/doc/src/.gitignore
@@ -0,0 +1,3 @@
+/Eqs
+/JPG
+/false_positives.txt
diff --git a/doc/src/Build.rst b/doc/src/Build.rst
new file mode 100644
index 0000000000..2eba3ddd48
--- /dev/null
+++ b/doc/src/Build.rst
@@ -0,0 +1,28 @@
+Build LAMMPS
+************
+
+LAMMPS can be built as an executable or library from source code via
+either traditional makefiles (which may require manual editing)
+for use with GNU make or gmake, or a build environment generated by CMake
+(Unix Makefiles, Xcode, Visual Studio, KDevelop or more).  As an
+alternative you can download a package with pre-built executables
+as described on the :doc:`Install <Install>` doc page.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Build_cmake
+   Build_make
+   Build_link
+   Build_basics
+   Build_settings
+   Build_package
+   Build_extras
+   Build_windows
+   Build_development
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst
new file mode 100644
index 0000000000..cf77c81e69
--- /dev/null
+++ b/doc/src/Build_basics.rst
@@ -0,0 +1,437 @@
+Basic build options
+===================
+
+The following topics are covered on this page, for building both with
+CMake and make:
+
+* :ref:`Serial vs parallel build <serial>`
+* :ref:`Choice of compiler and compile/link options <compile>`
+* :ref:`Build LAMMPS as an executable or a library <exe>`
+* :ref:`Build the LAMMPS documentation <doc>`
+* :ref:`Install LAMMPS after a build <install>`
+
+
+----------
+
+
+.. _serial:
+
+Serial vs parallel build
+-------------------------------------
+
+LAMMPS can be built to run in parallel using the ubiquitous `MPI (message-passing interface) <https://en.wikipedia.org/wiki/Message_Passing_Interface>`_
+library.  Or it can built to run on a single processor (serial)
+without MPI.  It can also be built with support for OpenMP threading
+(see more discussion below).
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
+   -D BUILD_OMP=value        # yes or no (default)
+   -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
+                             # no default value
+
+The executable created by CMake (after running make) is lmp\_name.  If
+the LAMMPS\_MACHINE variable is not specified, the executable is just
+lmp.  Using BUILD\_MPI=no will produce a serial executable.
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/src
+   make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
+   make serial             # serial build, produces lmp_serial using Makefile/serial
+   make mybox          # uses Makefile.mybox to produce lmp_mybox
+
+Serial build (see src/MAKE/Makefile.serial):
+
+
+.. parsed-literal::
+
+   MPI_INC =       -I../STUBS
+   MPI_PATH =      -L../STUBS
+   MPI_LIB =       -lmpi_stubs
+
+For a parallel build, if MPI is installed on your system in the usual
+place (e.g. under /usr/local), you do not need to specify the 3
+variables MPI\_INC, MPI\_PATH, MPI\_LIB.  The MPI wrapper on the compiler
+(e.g. mpicxx, mpiCC) knows where to find the needed include and
+library files.  Failing this, these 3 variables can be used to specify
+where the mpi.h file (MPI\_INC), and the MPI library files (MPI\_PATH)
+are found, and the name of the library files (MPI\_LIB).
+
+For a serial build, you need to specify the 3 variables, as shown
+above.
+
+For a serial LAMMPS build, use the dummy MPI library provided in
+src/STUBS.  You also need to build the STUBS library for your platform
+before making LAMMPS itself.  A "make serial" build does this for.
+Otherwise, type "make mpi-stubs" from the src directory, or "make"
+from the src/STUBS dir.  If the build fails, you will need to edit the
+STUBS/Makefile for your platform.
+
+The file STUBS/mpi.c provides a CPU timer function called MPI\_Wtime()
+that calls gettimeofday() .  If your system doesn't support
+gettimeofday() , you'll need to insert code to call another timer.
+Note that the ANSI-standard function clock() rolls over after an hour
+or so, and is therefore insufficient for timing long LAMMPS
+simulations.
+
+**CMake and make info**\ :
+
+If you are installing MPI yourself, we recommend MPICH2 from Argonne
+National Laboratory or OpenMPI.  MPICH can be downloaded from the
+`Argonne MPI site <http://www.mcs.anl.gov/research/projects/mpich2/>`_.
+OpenMPI can be downloaded from the `OpenMPI site <http://www.open-mpi.org>`_.  Other MPI packages should also work.
+If you are running on a large parallel machine, your system admins or
+the vendor should have already installed a version of MPI, which is
+likely to be faster than a self-installed MPICH or OpenMPI, so find
+out how to build and link with it.
+
+The majority of OpenMP (threading) support in LAMMPS is provided by
+the USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
+details. The USER-INTEL package also provides OpenMP support (it is
+compatible with USER-OMP) and adds vectorization support when compiled
+with the Intel compilers on top of that. Also, the KOKKOS package can
+be compiled for using OpenMP threading.
+
+However, there are a few commands in LAMMPS that have native OpenMP
+support.  These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
+USER-DPD packages.  In addition some packages support OpenMP threading
+indirectly through the libraries they interface to: e.g. LATTE and
+USER-COLVARS.  See the :doc:`Packages details <Packages_details>` doc
+page for more info on these packages and the doc pages for their
+respective commands for OpenMP threading info.
+
+For CMake, if you use BUILD\_OMP=yes, you can use these packages and
+turn on their native OpenMP support and turn on their native OpenMP
+support at run time, by setting the OMP\_NUM\_THREADS environment
+variable before you launch LAMMPS.
+
+For building via conventional make, the CCFLAGS and LINKFLAGS
+variables in Makefile.machine need to include the compiler flag that
+enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel
+compilers it is -qopenmp.  If you are using a different compiler,
+please refer to its documentation.
+
+.. _default-none-issues:
+
+**OpenMP Compiler compatibility info**\ : 
+
+Some compilers do not fully support the 'default(none)' directive
+and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
+semantics, which are incompatible with the OpenMP 3.1 directives used
+in LAMMPS (for maximal compatibility with compiler versions in use).
+In those case, all 'default(none)' directives (which aid in detecting
+incorrect and unwanted sharing) can be replaced with 'default(shared)'
+while dropping all 'shared()' directives. The script
+'src/USER-OMP/hack\_openmp\_for\_pgi\_gcc9.sh' can be used to automate
+this conversion.
+
+
+----------
+
+
+.. _compile:
+
+Choice of compiler and compile/link options
+---------------------------------------------------------
+
+The choice of compiler and compiler flags can be important for
+performance.  Vendor compilers can produce faster code than
+open-source compilers like GNU.  On boxes with Intel CPUs, we suggest
+trying the `Intel C++ compiler <intel_>`_.
+
+.. _intel: https://software.intel.com/en-us/intel-compilers
+
+
+
+On parallel clusters or supercomputers which use "modules" for their
+compile/link environments, you can often access different compilers by
+simply loading the appropriate module before building LAMMPS.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D CMAKE_CXX_COMPILER=name            # name of C++ compiler
+   -D CMAKE_C_COMPILER=name              # name of C compiler
+   -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler
+
+   -D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
+   -D CMAKE_C_FLAGS=string               # flags to use with C compiler
+   -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
+
+By default CMake will use a compiler it finds and it will add
+optimization flags appropriate to that compiler and any :doc:`accelerator packages <Speed_packages>` you have included in the build.
+
+You can tell CMake to look for a specific compiler with these variable
+settings.  Likewise you can specify the FLAGS variables if you want to
+experiment with alternate optimization flags.  You should specify all
+3 compilers, so that the small number of LAMMPS source files written
+in C or Fortran are built with a compiler consistent with the one used
+for all the C++ files:
+
+
+.. parsed-literal::
+
+   Building with GNU Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+   Building with Intel Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+   Building with LLVM/Clang Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+
+.. note::
+
+   When the cmake command completes, it prints info to the screen
+   as to which compilers it is using, and what flags will be used in the
+   compilation.  Note that if the top-level compiler is mpicxx, it is
+   simply a wrapper on a real compiler.  The underlying compiler info is
+   what will be listed in the CMake output.  You should check to insure
+   you are using the compiler and optimization flags are the ones you
+   want.
+
+**Makefile.machine settings**\ :
+
+Parallel build (see src/MAKE/Makefile.mpi):
+
+
+.. parsed-literal::
+
+   CC =            mpicxx
+   CCFLAGS =       -g -O3
+   LINK =          mpicxx
+   LINKFLAGS =     -g -O
+
+Serial build (see src/MAKE/Makefile.serial):
+
+
+.. parsed-literal::
+
+   CC =            g++
+   CCFLAGS =       -g -O3
+   LINK =          g++
+   LINKFLAGS =     -g -O
+
+The "compiler/linker settings" section of a Makefile.machine lists
+compiler and linker settings for your C++ compiler, including
+optimization flags.  You should always use mpicxx or mpiCC for
+a parallel build, since these compiler wrappers will include
+a variety of settings appropriate for your MPI installation.
+
+.. note::
+
+   If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>` included, they have specific
+   optimization flags that are either required or recommended for optimal
+   performance.  You need to include these in the CCFLAGS and LINKFLAGS
+   settings above.  For details, see the individual package doc pages
+   listed on the :doc:`Speed packages <Speed_packages>` doc page.  Or
+   examine these files in the src/MAKE/OPTIONS directory.  They
+   correspond to each of the 5 accelerator packages and their hardware
+   variants:
+
+
+.. parsed-literal::
+
+   Makefile.opt                   # OPT package
+   Makefile.omp                   # USER-OMP package
+   Makefile.intel_cpu             # USER-INTEL package for CPUs
+   Makefile.intel_coprocessor     # USER-INTEL package for KNLs
+   Makefile.gpu                   # GPU package
+   Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
+   Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
+   Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP)
+
+
+----------
+
+
+.. _exe:
+
+Build LAMMPS as an executable or a library
+----------------------------------------------------
+
+LAMMPS can be built as either an executable or as a static or shared
+library.  The LAMMPS library can be called from another application or
+a scripting language.  See the :doc:`Howto couple <Howto_couple>` doc
+page for more info on coupling LAMMPS to other codes.  See the
+:doc:`Python <Python_head>` doc page for more info on wrapping and
+running LAMMPS from Python via its library interface.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D BUILD_EXE=value           # yes (default) or no
+   -D BUILD_LIB=value           # yes or no (default)
+   -D BUILD_SHARED_LIBS=value   # yes or no (default)
+   -D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+                                # no default value
+
+Setting BUILD\_EXE=no will not produce an executable.  Setting
+BUILD\_LIB=yes will produce a static library named liblammps.a.
+Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a
+shared library named liblammps.so. If LAMMPS\_LIB\_SUFFIX is set the generated
+libraries will be named liblammps\_name.a or liblammps\_name.so instead.
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/src
+   make machine               # build LAMMPS executable lmp_machine
+   make mode=lib machine      # build LAMMPS static lib liblammps_machine.a
+   make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so
+
+The two library builds also create generic soft links, named
+liblammps.a and liblammps.so, which point to the liblammps\_machine
+files.
+
+**CMake and make info**\ :
+
+Note that for a shared library to be usable by a calling program, all
+the auxiliary libraries it depends on must also exist as shared
+libraries.  This will be the case for libraries included with LAMMPS,
+such as the dummy MPI library in src/STUBS or any package libraries in
+the lib/packages directory, since they are always built as shared
+libraries using the -fPIC switch.  However, if a library like MPI or
+FFTW does not exist as a shared library, the shared library build will
+generate an error.  This means you will need to install a shared
+library version of the auxiliary library.  The build instructions for
+the library should tell you how to do this.
+
+As an example, here is how to build and install the `MPICH library <mpich_>`_, a popular open-source version of MPI, distributed by
+Argonne National Lab, as a shared library in the default
+/usr/local/lib location:
+
+.. _mpich: http://www-unix.mcs.anl.gov/mpi
+
+
+
+
+.. parsed-literal::
+
+   ./configure --enable-shared
+   make
+   make install
+
+You may need to use "sudo make install" in place of the last line if
+you do not have write privileges for /usr/local/lib.  The end result
+should be the file /usr/local/lib/libmpich.so.
+
+
+----------
+
+
+.. _doc:
+
+Build the LAMMPS documentation
+----------------------------------------
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D BUILD_DOC=value       # yes or no (default)
+
+This will create the HTML doc pages within the CMake build directory.
+The reason to do this is if you want to "install" LAMMPS on a system
+after the CMake build via "make install", and include the doc pages in
+the install.
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/doc
+   make html       # html doc pages
+   make pdf        # single Manual.pdf file
+
+This will create a lammps/doc/html dir with the HTML doc pages so that
+you can browse them locally on your system.  Type "make" from the
+lammps/doc dir to see other options.
+
+.. note::
+
+   You can also download a tarball of the documentation for the
+   current LAMMPS version (HTML and PDF files), from the website
+   `download page <http://lammps.sandia.gov/download.html>`_.
+
+
+----------
+
+
+.. _tools:
+
+Build LAMMPS tools
+------------------------------
+
+Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
+using CMake or Make.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D BUILD_TOOLS=value       # yes or no (default)
+
+The generated binaries will also become part of the LAMMPS installation (see below)
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/tools
+   make all              # build all binaries of tools
+   make binary2txt       # build only binary2txt tool
+   make chain            # build only chain tool
+   make micelle2d        # build only micelle2d tool
+   make thermo_extract   # build only thermo_extract tool
+
+
+----------
+
+
+.. _install:
+
+Install LAMMPS after a build
+------------------------------------------
+
+After building LAMMPS, you may wish to copy the LAMMPS executable of
+library, along with other LAMMPS files (library header, doc files) to
+a globally visible place on your system, for others to access.  Note
+that you may need super-user privileges (e.g. sudo) if the directory
+you want to copy files to is protected.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
+   make                        # perform make after CMake command
+   make install                # perform the installation into prefix
+
+**Traditional make**\ :
+
+There is no "install" option in the src/Makefile for LAMMPS.  If you
+wish to do this you will need to first build LAMMPS, then manually
+copy the desired LAMMPS files to the appropriate system directories.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst
new file mode 100644
index 0000000000..78459bb990
--- /dev/null
+++ b/doc/src/Build_cmake.rst
@@ -0,0 +1,245 @@
+Build LAMMPS with CMake
+=======================
+
+This page is a short summary of how to use CMake to build LAMMPS.
+Details on CMake variables that enable specific LAMMPS build options
+are given on the pages linked to from the :doc:`Build <Build>` doc page.
+
+Richard Berger (Temple U) has also written a `more comprehensive guide <https://github.com/lammps/lammps/blob/master/cmake/README.md>`_
+for how to use CMake to build LAMMPS.  If you are new to CMake it is a
+good place to start.
+
+
+----------
+
+
+Building LAMMPS with CMake is a two-step process.  First you use CMake
+to create a build environment in a new directory.  On Linux systems,
+this will be based on makefiles for use with make.  Then you use the
+make command to build LAMMPS, which uses the created
+Makefile(s). Example:
+
+
+.. parsed-literal::
+
+   cd lammps                        # change to the LAMMPS distribution directory
+   mkdir build; cd build            # create a new directory (folder) for build
+   cmake [options ...] ../cmake     # configuration with (command-line) cmake
+   make                             # compilation
+
+The cmake command will detect available features, enable selected
+packages and options, and will generate the build environment.  By default
+this build environment will be created for "Unix Makefiles" on most
+platforms and particularly on Linux.  However, alternate build tools
+(e.g. Ninja) and support files for Integrated Development Environments
+(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
+selected via the "-G" command line flag. For the rest of the documentation
+we will assume that the build environment is generated for makefiles
+and thus the make command will be used to compile and link LAMMPS as
+indicated above, producing (by default) an executable called "lmp" and
+a library called "liblammps.a" in the "build" folder.  When generating
+a build environment for the "Ninja" build tool, the build command would
+be "ninja" instead of "make".
+
+If your machine has multiple CPU cores (most do these days), using a
+command like "make -jN" (with N being the number of available local
+CPU cores) can be much faster.  If you plan to do development on
+LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
+ccache (= Compiler Cache) software may speed up repeated compilation
+even more.
+
+After compilation, you may optionally install the LAMMPS executable into
+your system with:
+
+
+.. parsed-literal::
+
+   make install    # optional, copy LAMMPS executable & library elsewhere
+
+This will install the lammps executable and library (if requested), some
+tools (if configured) and additional files like library API headers,
+manpages, potential and force field files. The location of the installation
+tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults
+to ${HOME}/.local
+
+
+----------
+
+
+There are 3 variants of CMake: a command-line version (cmake), a text mode
+UI version (ccmake), and a graphical GUI version (cmake-GUI).  You can use
+any of them interchangeably to configure and create the LAMMPS build
+environment.  On Linux all the versions produce a Makefile as their
+output.  See more details on each below.
+
+You can specify a variety of options with any of the 3 versions, which
+affect how the build is performed and what is included in the LAMMPS
+executable.  Links to pages explaining all the options are listed on
+the :doc:`Build <Build>` doc page.
+
+You must perform the CMake build system generation and compilation in
+a new directory you create.  It can be anywhere on your local machine.
+In these Build pages we assume that you are building in a directory
+called "lammps/build".  You can perform separate builds independently
+with different options, so long as you perform each of them in a
+separate directory you create.  All the auxiliary files created by one
+build process (executable, object files, log files, etc) are stored in
+this directory or sub-directories within it that CMake creates.
+
+.. note::
+
+   To perform a CMake build, no packages can be installed or a
+   build been previously attempted in the LAMMPS src directory by using
+   "make" commands to :doc:`perform a conventional LAMMPS build <Build_make>`.  CMake detects if this is the case and
+   generates an error, telling you to type "make no-all purge" in the src
+   directory to un-install all packages.  The purge removes all the \*.h
+   files auto-generated by make.
+
+You must have CMake version 2.8 or later on your system to build
+LAMMPS.  A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
+later version.  CMake will print a message telling you if a later
+version is required.  Installation instructions for CMake are below.
+
+After the initial build, if you edit LAMMPS source files, or add your
+own new files to the source directory, you can just re-type make from
+your build directory and it will re-compile only the files that have
+changed.  If you want to change CMake options you can run cmake (or
+ccmake or cmake-gui) again from the same build directory and alter
+various options; see details below.  Or you can remove the entire build
+folder, recreate the directory and start over.
+
+
+----------
+
+
+**Command-line version of CMake**\ :
+
+
+.. parsed-literal::
+
+   cmake [options ...] /path/to/lammps/cmake  # build from any dir
+   cmake [options ...] ../cmake               # build from lammps/build
+
+The cmake command takes one required argument, which is the LAMMPS
+cmake directory which contains the CMakeLists.txt file.
+
+The argument can be preceeded or followed by various CMake
+command-line options.  Several useful ones are:
+
+
+.. parsed-literal::
+
+   -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
+   -D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
+   -G output                     # style of output CMake generates
+   -DVARIABLE=value              # setting for a LAMMPS feature to enable
+   -D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir
+   -C path/to/preset/file        # load some CMake settings before configuring
+
+All the LAMMPS-specific -D variables that a LAMMPS build supports are
+described on the pages linked to from the :doc:`Build <Build>` doc page.
+All of these variable names are upper-case and their values are
+lower-case, e.g. -D LAMMPS\_SIZES=smallbig.  For boolean values, any of
+these forms can be used: yes/no, on/off, 1/0.
+
+On Unix/Linux machines, CMake generates a Makefile by default to
+perform the LAMMPS build.  Alternate forms of build info can be
+generated via the -G switch, e.g. Visual Studio on a Windows machine,
+Xcode on MacOS, or KDevelop on Linux.  Type "cmake --help" to see the
+"Generator" styles of output your system supports.
+
+.. note::
+
+   When CMake runs, it prints configuration info to the screen.
+   You should review this to verify all the features you requested were
+   enabled, including packages.  You can also see what compilers and
+   compile options will be used for the build.  Any errors in CMake
+   variable syntax will also be flagged, e.g. mis-typed variable names or
+   variable values.
+
+CMake creates a CMakeCache.txt file when it runs.  This stores all the
+settings, so that when running CMake again you can use the current
+folder '.' instead of the path to the LAMMPS cmake folder as the
+required argument to the CMake command. Either way the existing
+settings will be inherited unless the CMakeCache.txt file is removed.
+
+If you later want to change a setting you can rerun cmake in the build
+directory with different setting. Please note that some automatically
+detected variables will not change their value when you rerun cmake.
+In these cases it is usually better to first remove all the
+files/directories in the build directory, or start with a fresh build
+directory.
+
+
+----------
+
+
+**Curses version (terminal-style menu) of CMake**\ :
+
+
+.. parsed-literal::
+
+   ccmake ../cmake
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to type **c**\ , for the second you
+have to type **g**\ . You may need to type **c** multiple times, and may be
+required to edit some of the entries of CMake configuration variables
+in between.  Please see the `ccmake manual <https://cmake.org/cmake/help/latest/manual/ccmake.1.html>`_ for
+more information.
+
+
+----------
+
+
+**GUI version of CMake**\ :
+
+
+.. parsed-literal::
+
+   cmake-gui ../cmake
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to click on the **Configure** button,
+for the second you have to click on the **Generate** button.  You may
+need to click on **Configure** multiple times, and may be required to
+edit some of the entries of CMake configuration variables in between.
+Please see the `cmake-gui manual <https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html>`_
+for more information.
+
+
+----------
+
+
+**Installing CMake**
+
+Check if your machine already has CMake installed:
+
+
+.. parsed-literal::
+
+   which cmake             # do you have it?
+   which cmake3            # version 3 may have this name
+   cmake --version         # what specific version you have
+
+On clusters or supercomputers which use environment modules to manage
+software packages, do this:
+
+
+.. parsed-literal::
+
+   module list            # is a cmake module already loaded?
+   module avail           # is a cmake module available?
+   module load cmake3     # load cmake module with appropriate name
+
+Most Linux distributions offer pre-compiled cmake packages through
+their package management system. If you do not have CMake or a new
+enough version, you can download the latest version at
+`https://cmake.org/download/ <https://cmake.org/download/>`_.
+Instructions on how to install it on various platforms can be found
+`on this page <https://cmake.org/install/>`_.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst
new file mode 100644
index 0000000000..7286caf7b3
--- /dev/null
+++ b/doc/src/Build_development.rst
@@ -0,0 +1,120 @@
+Development build options (CMake only)
+======================================
+
+The CMake build of LAMMPS has a few extra options which are useful during
+development,  testing or debugging.
+
+
+----------
+
+
+.. _compilation:
+
+Verify compilation flags
+------------------------------------------
+
+Sometimes it is necessary to verify the complete sequence of compilation flags
+generated by the CMake build. To enable a more verbose output during
+compilation you can use the following option.
+
+
+.. parsed-literal::
+
+   -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes
+
+Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+
+
+.. parsed-literal::
+
+   make VERBOSE=1
+
+
+----------
+
+
+.. _sanitizer:
+
+Address, Undefined Behavior, and Thread Sanitizer Support
+-------------------------------------------------------------------------
+
+Compilers such as GCC and Clang support generating binaries which use different
+sanitizers to detect problems in code during run-time. They can detect `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_,
+code that runs into `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_ of the
+language and `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_ in threaded code.
+
+The following settings allow you enable these features if your compiler supports
+it. Please note that they come with a performance hit. However, they are
+usually faster than using tools like Valgrind.
+
+
+.. parsed-literal::
+
+   -D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
+   -D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+   -D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
+
+
+----------
+
+
+.. _testing:
+
+Code Coverage and Testing
+---------------------------------------
+
+We do extensive regression testing of the LAMMPS code base on a continuous
+basis. Some of the logic to do this has been added to the CMake build so
+developers can run the tests directly on their workstation.
+
+.. note::
+
+   this is incomplete and only represents a small subset of tests that we run
+
+
+.. parsed-literal::
+
+   -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+   -D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
+   -D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+
+If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+
+
+.. parsed-literal::
+
+   make test
+
+The test cases used come from the lammps-testing repository. They are
+derivatives of the examples folder with some modifications to make the run
+faster.
+
+You can also collect code coverage metrics while running the tests by enabling
+coverage support during building.
+
+
+.. parsed-literal::
+
+   -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes
+
+This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+
+
+.. parsed-literal::
+
+   make test               # run tests first!
+   make gen_coverage_html  # generate coverage report in HTML format
+   make gen_coverage_xml   # generate coverage report in XML format
+
+These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+
+
+.. parsed-literal::
+
+   pip install git+https://github.com/gcovr/gcovr.git
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst
new file mode 100644
index 0000000000..2cba59bde0
--- /dev/null
+++ b/doc/src/Build_extras.rst
@@ -0,0 +1,1419 @@
+Packages with extra build options
+=================================
+
+When building with some packages, additional steps may be required,
+in addition to:
+
+
+.. parsed-literal::
+
+   -D PKG_NAME=yes    # CMake
+   make yes-name      # make
+
+as described on the :doc:`Build\_package <Build_package>` doc page.
+
+For a CMake build there may be additional optional or required
+variables to set.  For a build with make, a provided library under the
+lammps/lib directory may need to be built first.  Or an external
+library may need to exist on your system or be downloaded and built.
+You may need to tell LAMMPS where it is found on your system.
+
+This is the list of packages that may require additional steps.
+
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`COMPRESS <compress>`       | :ref:`GPU <gpu>`                 | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`MSCG <mscg>`               | :ref:`OPT <opt>`                 | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-ATC <user-atc>`       | :ref:`USER-AWPMD <user-awpmd>`   | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+
+
+----------
+
+
+.. _compress:
+
+COMPRESS package
+-------------------------------
+
+To build with this package you must have the zlib compression library
+available on your system.
+
+**CMake build**\ :
+
+If CMake cannot find the library, you can set these variables:
+
+
+.. parsed-literal::
+
+   -D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
+   -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
+
+**Traditional make**\ :
+
+If make cannot find the library, you can edit the
+lib/compress/Makefile.lammps file to specify the paths and library
+name.
+
+
+----------
+
+
+.. _gpu:
+
+GPU package
+---------------------
+
+To build with this package, you must choose options for precision and
+which GPU hardware to build for.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D GPU_API=value          # value = opencl (default) or cuda
+   -D GPU_PREC=value         # precision setting
+                             # value = double or mixed (default) or single
+   -D OCL_TUNE=value         # hardware choice for GPU_API=opencl
+                             # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
+   -D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
+                             # value = sm_XX, see below
+                             # default is sm_30
+   -D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
+                             # enables CUDA Performance Primitives Optimizations
+                             # value = yes (default) or no
+   -D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
+                             # value = yes or no (default)
+
+GPU\_ARCH settings for different GPU hardware is as follows:
+
+* sm\_12 or sm\_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
+* sm\_20 or sm\_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
+* sm\_30 or sm\_35 or sm\_37 for Kepler (supported since CUDA 5)
+* sm\_50 or sm\_52 for Maxwell (supported since CUDA 6)
+* sm\_60 or sm\_61 for Pascal (supported since CUDA 8)
+* sm\_70 for Volta (supported since CUDA 9)
+* sm\_75 for Turing (supported since CUDA 10)
+
+A more detailed list can be found, for example,
+at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
+
+CMake can detect which version of the CUDA toolkit is used and thus can
+include support for **all** major GPU architectures supported by this toolkit.
+Thus the GPU\_ARCH setting is merely an optimization, to have code for
+the preferred GPU architecture directly included rather than having to wait
+for the JIT compiler of the CUDA driver to translate it.
+
+**Traditional make**\ :
+
+Before building LAMMPS, you must build the GPU library in lib/gpu.
+You can do this manually if you prefer; follow the instructions in
+lib/gpu/README.  Note that the GPU library uses MPI calls, so you must
+use the same MPI library (or the STUBS library) settings as the main
+LAMMPS code.  This also applies to the -DLAMMPS\_BIGBIG,
+-DLAMMPS\_SMALLBIG, or -DLAMMPS\_SMALLSMALL settings in whichever
+Makefile you use.
+
+You can also build the library in one step from the lammps/src dir,
+using a command like these, which simply invoke the lib/gpu/Install.py
+script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-gpu               # print help message
+   make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+   make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+   make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
+
+Note that this procedure starts with a Makefile.machine in lib/gpu, as
+specified by the "-m" switch.  For your convenience, machine makefiles
+for "mpi" and "serial" are provided, which have the same settings as
+the corresponding machine makefiles in the main LAMMPS source
+folder. In addition you can alter 4 important settings in the
+Makefile.machine you start from via the corresponding -c, -a, -p, -e
+switches (as in the examples above), and also save a copy of the new
+Makefile if desired:
+
+* CUDA\_HOME = where NVIDIA CUDA software is installed on your system
+* CUDA\_ARCH = sm\_XX, what GPU hardware you have, same as CMake GPU\_ARCH above
+* CUDA\_PRECISION = precision (double, mixed, single)
+* EXTRAMAKE = which Makefile.lammps.\* file to copy to Makefile.lammps
+
+The file Makefile.linux\_multi is set up to include support for multiple
+GPU architectures as supported by the CUDA toolkit in use. This is done
+through using the "--gencode " flag, which can be used multiple times and
+thus support all GPU architectures supported by your CUDA compiler.
+
+If the library build is successful, 3 files should be created:
+lib/gpu/libgpu.a, lib/gpu/nvc\_get\_devices, and
+lib/gpu/Makefile.lammps.  The latter has settings that enable LAMMPS
+to link with CUDA libraries.  If the settings in Makefile.lammps for
+your machine are not correct, the LAMMPS build will fail, and
+lib/gpu/Makefile.lammps may need to be edited.
+
+.. note::
+
+   If you re-build the GPU library in lib/gpu, you should always
+   un-install the GPU package in lammps/src, then re-install it and
+   re-build LAMMPS.  This is because the compilation of files in the GPU
+   package uses the library settings from the lib/gpu/Makefile.machine
+   used to build the GPU library.
+
+
+----------
+
+
+.. _kim:
+
+KIM package
+---------------------
+
+To build with this package, the KIM library with API v2 must be downloaded
+and built on your system.  It must include the KIM models that you want to
+use with LAMMPS. If you want to use the :doc:`kim\_query <kim_commands>`
+command, you also need to have libcurl installed with the matching
+development headers and the curl-config tool.
+
+See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+See the list of all KIM models here: https://openkim.org/browse/models
+
+(Also note that when downloading and installing from source
+the KIM API library with all its models, may take a long time (tens of
+minutes to hours) to build.  Of course you only need to do that once.)
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes
+   -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on
+   -D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes
+
+If DOWNLOAD\_KIM is set, the KIM library will be downloaded and built
+inside the CMake build directory.  If the KIM library is already on
+your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
+environment variable so that libkim-api can be found.
+
+For using OpenKIM web queries in LAMMPS.
+
+If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
+libcurl calls within the KIM web query display a lot of information about
+libcurl operations. You hardly ever want this set in production use, you will
+almost always want this when you debug/report problems.
+
+The libcurl performs peer SSL certificate verification by default. This
+verification is done using a CA certificate store that the SSL library can
+use to make sure the peer's server certificate is valid. If SSL reports an
+error ("certificate verify failed") during the handshake and thus refuses
+further communication with that server, you can set LMP\_NO\_SSL\_CHECK.
+If LMP\_NO\_SSL\_CHECK is set, libcurl does not verify the peer and connection
+succeeds regardless of the names in the certificate. This option is insecure.
+As an alternative, you can specify your own CA cert path by setting the
+environment variable CURL\_CA\_BUNDLE to the path of your choice. A call to the
+KIM web query would get this value from the environmental variable.
+
+**Traditional make**\ :
+
+You can download and build the KIM library manually if you prefer;
+follow the instructions in lib/kim/README.  You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/kim/Install.py script with the specified args.
+
+
+.. parsed-literal::
+
+   make lib-kim              # print help message
+   make lib-kim args="-b "   # (re-)install KIM API lib with only example models
+   make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+   make lib-kim args="-b -a everything"     # install KIM API lib with all models
+   make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
+   make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+   make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
+
+
+----------
+
+
+.. _kokkos:
+
+KOKKOS package
+---------------------------
+
+To build with this package, you must choose which hardware you want to
+build for, either CPUs (multi-threading via OpenMP) or KNLs (OpenMP)
+or GPUs (NVIDIA Cuda).
+
+For a CMake or make build, these are the possible choices for the
+KOKKOS\_ARCH settings described below.  Note that for CMake, these are
+really Kokkos variables, not LAMMPS variables.  Hence you must use
+case-sensitive values, e.g. BDW, not bdw.
+
+* ARMv80 = ARMv8.0 Compatible CPU
+* ARMv81 = ARMv8.1 Compatible CPU
+* ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
+* BGQ = IBM Blue Gene/Q CPUs
+* Power8 = IBM POWER8 CPUs
+* Power9 = IBM POWER9 CPUs
+* SNB = Intel Sandy/Ivy Bridge CPUs
+* HSW = Intel Haswell CPUs
+* BDW = Intel Broadwell Xeon E-class CPUs
+* SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
+* KNC = Intel Knights Corner Xeon Phi
+* KNL = Intel Knights Landing Xeon Phi
+* Kepler30 = NVIDIA Kepler generation CC 3.0
+* Kepler32 = NVIDIA Kepler generation CC 3.2
+* Kepler35 = NVIDIA Kepler generation CC 3.5
+* Kepler37 = NVIDIA Kepler generation CC 3.7
+* Maxwell50 = NVIDIA Maxwell generation CC 5.0
+* Maxwell52 = NVIDIA Maxwell generation CC 5.2
+* Maxwell53 = NVIDIA Maxwell generation CC 5.3
+* Pascal60 = NVIDIA Pascal generation CC 6.0
+* Pascal61 = NVIDIA Pascal generation CC 6.1
+* Volta70 = NVIDIA Volta generation CC 7.0
+* Volta72 = NVIDIA Volta generation CC 7.2
+* Turing75 = NVIDIA Turing generation CC 7.5
+
+**CMake build**\ :
+
+For multicore CPUs using OpenMP, set these 2 variables.
+
+
+.. parsed-literal::
+
+   -D KOKKOS_ARCH=archCPU         # archCPU = CPU from list above
+   -D KOKKOS_ENABLE_OPENMP=yes
+
+For Intel KNLs using OpenMP, set these 2 variables:
+
+
+.. parsed-literal::
+
+   -D KOKKOS_ARCH=KNL
+   -D KOKKOS_ENABLE_OPENMP=yes
+
+For NVIDIA GPUs using CUDA, set these 4 variables:
+
+
+.. parsed-literal::
+
+   -D KOKKOS_ARCH="archCPU;archGPU"   # archCPU = CPU from list above that is hosting the GPU
+                                      # archGPU = GPU from list above
+   -D KOKKOS_ENABLE_CUDA=yes
+   -D KOKKOS_ENABLE_OPENMP=yes
+   -D CMAKE_CXX_COMPILER=wrapper      # wrapper = full path to Cuda nvcc wrapper
+
+The wrapper value is the Cuda nvcc compiler wrapper provided in the
+Kokkos library: lib/kokkos/bin/nvcc\_wrapper.  The setting should
+include the full path name to the wrapper, e.g.
+
+
+.. parsed-literal::
+
+   -D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper
+
+**Traditional make**\ :
+
+Choose which hardware to support in Makefile.machine via
+KOKKOS\_DEVICES and KOKKOS\_ARCH settings.  See the
+src/MAKE/OPTIONS/Makefile.kokkos\* files for examples.
+
+For multicore CPUs using OpenMP:
+
+
+.. parsed-literal::
+
+   KOKKOS_DEVICES = OpenMP
+   KOKKOS_ARCH = archCPU      # archCPU = CPU from list above
+
+For Intel KNLs using OpenMP:
+
+
+.. parsed-literal::
+
+   KOKKOS_DEVICES = OpenMP
+   KOKKOS_ARCH = KNL
+
+For NVIDIA GPUs using CUDA:
+
+
+.. parsed-literal::
+
+   KOKKOS_DEVICES = Cuda
+   KOKKOS_ARCH = archCPU,archGPU    # archCPU = CPU from list above that is hosting the GPU
+                                    # archGPU = GPU from list above
+
+For GPUs, you also need these 2 lines in your Makefile.machine before
+the CC line is defined, in this case for use with OpenMPI mpicxx.  The
+2 lines define a nvcc wrapper compiler, which will use nvcc for
+compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA
+files.
+
+
+.. parsed-literal::
+
+   KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
+   export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
+   CC =            mpicxx
+
+
+----------
+
+
+.. _latte:
+
+LATTE package
+-------------------------
+
+To build with this package, you must download and build the LATTE
+library.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D DOWNLOAD_LATTE=value    # download LATTE for build, value = no (default) or yes
+   -D LATTE_LIBRARY=path      # LATTE library file (only needed if a custom location)
+
+If DOWNLOAD\_LATTE is set, the LATTE library will be downloaded and
+built inside the CMake build directory.  If the LATTE library is
+already on your system (in a location CMake cannot find it),
+LATTE\_LIBRARY is the filename (plus path) of the LATTE library file,
+not the directory the library file is in.
+
+**Traditional make**\ :
+
+You can download and build the LATTE library manually if you prefer;
+follow the instructions in lib/latte/README.  You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invokes the lib/latte/Install.py script with the specified
+args:
+
+
+.. parsed-literal::
+
+   make lib-latte                          # print help message
+   make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
+   make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
+   make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
+                                           #   copy Makefile.lammps.gfortran to Makefile.lammps
+
+Note that 3 symbolic (soft) links, "includelink" and "liblink" and
+"filelink.o", are created in lib/latte to point into the LATTE home
+dir.  When LAMMPS itself is built it will use these links.  You should
+also check that the Makefile.lammps file you create is appropriate for
+the compiler you use on your system to build LATTE.
+
+
+----------
+
+
+.. _message:
+
+MESSAGE package
+-----------------------------
+
+This package can optionally include support for messaging via sockets,
+using the open-source `ZeroMQ library <http://zeromq.org>`_, which must
+be installed on your system.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes
+   -D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)
+   -D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
+
+**Traditional make**\ :
+
+Before building LAMMPS, you must build the CSlib library in
+lib/message.  You can build the CSlib library manually if you prefer;
+follow the instructions in lib/message/README.  You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/message/Install.py script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-message               # print help message
+   make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
+   make lib-message args="-s"     # build as serial lib with no ZMQ support
+
+The build should produce two files: lib/message/cslib/src/libmessage.a
+and lib/message/Makefile.lammps.  The latter is copied from an
+existing Makefile.lammps.\* and has settings to link with the ZeroMQ
+library if requested in the build.
+
+
+----------
+
+
+.. _mscg:
+
+MSCG package
+-----------------------
+
+To build with this package, you must download and build the MS-CG
+library.  Building the MS-CG library and using it from LAMMPS requires
+a C++11 compatible compiler and that the GSL (GNU Scientific Library)
+headers and libraries are installed on your machine.  See the
+lib/mscg/README and MSCG/Install files for more details.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D DOWNLOAD_MSCG=value    # download MSCG for build, value = no (default) or yes
+   -D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location)
+   -D MSCG_INCLUDE_DIR=path  # MSCG include directory (only needed if a custom location)
+
+If DOWNLOAD\_MSCG is set, the MSCG library will be downloaded and built
+inside the CMake build directory.  If the MSCG library is already on
+your system (in a location CMake cannot find it), MSCG\_LIBRARY is the
+filename (plus path) of the MSCG library file, not the directory the
+library file is in.  MSCG\_INCLUDE\_DIR is the directory the MSCG
+include file is in.
+
+**Traditional make**\ :
+
+You can download and build the MS-CG library manually if you prefer;
+follow the instructions in lib/mscg/README.  You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/mscg/Install.py script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-mscg             # print help message
+   make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+                                       # with the settings compatible with "make serial"
+   make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+                                       # with the settings compatible with "make mpi"
+   make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", will
+be created in lib/mscg to point to the MS-CG src/installation dir.
+When LAMMPS is built in src it will use these links.  You should not
+need to edit the lib/mscg/Makefile.lammps file.
+
+
+----------
+
+
+.. _opt:
+
+OPT package
+---------------------
+
+**CMake build**\ :
+
+No additional settings are needed besides "-D PKG\_OPT=yes".
+
+**Traditional make**\ :
+
+The compile flag "-restrict" must be used to build LAMMPS with the OPT
+package when using Intel compilers.  It should be added to the CCFLAGS
+line of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.opt for
+an example.
+
+
+----------
+
+
+.. _poems:
+
+POEMS package
+-------------------------
+
+**CMake build**\ :
+
+No additional settings are needed besides "-D PKG\_OPT=yes".
+
+**Traditional make**\ :
+
+Before building LAMMPS, you must build the POEMS library in lib/poems.
+You can do this manually if you prefer; follow the instructions in
+lib/poems/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/poems/Install.py script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-poems                   # print help message
+   make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+   make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+   make lib-poems args="-m icc"     # build with Intel icc compiler
+
+The build should produce two files: lib/poems/libpoems.a and
+lib/poems/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.\* and has settings needed to build LAMMPS with the
+POEMS library (though typically the settings are just blank).  If
+necessary, you can edit/create a new lib/poems/Makefile.machine file
+for your system, which should define an EXTRAMAKE variable to specify
+a corresponding Makefile.lammps.machine file.
+
+
+----------
+
+
+.. _python:
+
+PYTHON package
+---------------------------
+
+Building with the PYTHON package requires you have a Python shared
+library available on your system, which needs to be a Python 2
+version, 2.6 or later.  Python 3 is not yet supported.  See
+lib/python/README for more details.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D PYTHON_EXECUTABLE=path   # path to Python executable to use
+
+Without this setting, CMake will guess the default Python on your
+system.  To use a different Python version, you can either create a
+virtualenv, activate it and then run cmake.  Or you can set the
+PYTHON\_EXECUTABLE variable to specify which Python interpreter should
+be used.  Note note that you will also need to have the development
+headers installed for this version, e.g. python2-devel.
+
+**Traditional make**\ :
+
+The build uses the lib/python/Makefile.lammps file in the compile/link
+process to find Python.  You should only need to create a new
+Makefile.lammps.\* file (and copy it to Makefile.lammps) if the LAMMPS
+build fails.
+
+
+----------
+
+
+.. _voronoi:
+
+VORONOI package
+-----------------------------
+
+To build with this package, you must download and build the `Voro++ library <voro-home_>`_.
+
+.. _voro-home: http://math.lbl.gov/voro++
+
+
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D DOWNLOAD_VORO=value    # download Voro++ for build, value = no (default) or yes
+   -D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location)
+   -D VORO_INCLUDE_DIR=path  # Voro++ include directory (only needed if at custom location)
+
+If DOWNLOAD\_VORO is set, the Voro++ library will be downloaded and
+built inside the CMake build directory.  If the Voro++ library is
+already on your system (in a location CMake cannot find it),
+VORO\_LIBRARY is the filename (plus path) of the Voro++ library file,
+not the directory the library file is in.  VORO\_INCLUDE\_DIR is the
+directory the Voro++ include file is in.
+
+**Traditional make**\ :
+
+You can download and build the Voro++ library manually if you prefer;
+follow the instructions in lib/voronoi/README.  You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/voronoi/Install.py script with the specified
+args:
+
+
+.. parsed-literal::
+
+   make lib-voronoi                          # print help message
+   make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+   make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+   make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/voronoi to point to the Voro++ src dir.  When LAMMPS
+builds in src it will use these links.  You should not need to edit
+the lib/voronoi/Makefile.lammps file.
+
+
+----------
+
+
+.. _user-adios:
+
+USER-ADIOS package
+-----------------------------------
+
+The USER-ADIOS package requires the `ADIOS I/O library <https://github.com/ornladios/ADIOS2>`_,
+version 2.3.1 or newer. Make sure that you have ADIOS built either with or
+without MPI to match if you build LAMMPS with or without MPI.
+ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
+and LD\_LIBRARY\_PATH environment variables have been updated for the local ADIOS
+installation and the instructions below are followed for the respective build systems.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
+   -D PKG_USER-ADIOS=yes
+
+**Traditional make**\ :
+
+Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
+
+
+.. parsed-literal::
+
+   make yes-user-adios
+
+otherwise, set ADIOS2\_DIR environment variable when turning on the package:
+
+
+.. parsed-literal::
+
+   ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed
+
+
+----------
+
+
+.. _user-atc:
+
+USER-ATC package
+-------------------------------
+
+The USER-ATC package requires the MANYBODY package also be installed.
+
+**CMake build**\ :
+
+No additional settings are needed besides "-D PKG\_USER-ATC=yes"
+and "-D PKG\_MANYBODY=yes".
+
+**Traditional make**\ :
+
+Before building LAMMPS, you must build the ATC library in lib/atc.
+You can do this manually if you prefer; follow the instructions in
+lib/atc/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/atc/Install.py script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-atc                      # print help message
+   make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+   make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+   make lib-atc args="-m icc"        # build with Intel icc compiler
+
+The build should produce two files: lib/atc/libatc.a and
+lib/atc/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.\* and has settings needed to build LAMMPS with the ATC
+library.  If necessary, you can edit/create a new
+lib/atc/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
+
+Note that the Makefile.lammps file has settings for the BLAS and
+LAPACK linear algebra libraries.  As explained in lib/atc/README these
+can either exist on your system, or you can use the files provided in
+lib/linalg.  In the latter case you also need to build the library in
+lib/linalg with a command like these:
+
+
+.. parsed-literal::
+
+   make lib-linalg                     # print help message
+   make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+   make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+   make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+
+
+----------
+
+
+.. _user-awpmd:
+
+USER-AWPMD package
+-----------------------------------
+
+**CMake build**\ :
+
+No additional settings are needed besides "-D PKG\_USER-AQPMD=yes".
+
+**Traditional make**\ :
+
+Before building LAMMPS, you must build the AWPMD library in lib/awpmd.
+You can do this manually if you prefer; follow the instructions in
+lib/awpmd/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/awpmd/Install.py script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-awpmd                   # print help message
+   make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+   make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+   make lib-awpmd args="-m icc"     # build with Intel icc compiler
+
+The build should produce two files: lib/awpmd/libawpmd.a and
+lib/awpmd/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.\* and has settings needed to build LAMMPS with the
+AWPMD library.  If necessary, you can edit/create a new
+lib/awpmd/Makefile.machine file for your system, which should define
+an EXTRAMAKE variable to specify a corresponding
+Makefile.lammps.machine file.
+
+Note that the Makefile.lammps file has settings for the BLAS and
+LAPACK linear algebra libraries.  As explained in lib/awpmd/README
+these can either exist on your system, or you can use the files
+provided in lib/linalg.  In the latter case you also need to build the
+library in lib/linalg with a command like these:
+
+
+.. parsed-literal::
+
+   make lib-linalg                     # print help message
+   make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+   make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+   make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+
+
+----------
+
+
+.. _user-colvars:
+
+USER-COLVARS package
+---------------------------------------
+
+This package includes into the LAMMPS distribution the Colvars library, which
+can be built for the most part with all major versions of the C++ language.
+
+A few of the most recent features require C++11 support.  In particular, the
+library is optionally built together with the
+`Lepton <https://simtk.org/projects/lepton>`_ library, a copy of which is also
+included in the LAMMPS distribution.  Lepton implements the
+`customFunction <http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction>`_
+feature, and requires C++11 support.
+
+See `here <https://colvars.github.io/README-c++11.html>`_ for a detailed list of
+C++11-only features.
+
+**CMake build**\ :
+
+This is the recommended build recipe: no additional settings are normally
+needed besides "-D PKG\_USER-COLVARS=yes".
+
+Building and linking of Lepton (or other C++11-only features) is enabled
+automatically when compilation is carried out with C++11 support, and disabled
+otherwise.  Optionally, Lepton build may be manually controlled with the flag
+"-D COLVARS\_LEPTON=yes\|no".
+
+**Traditional make**\ :
+
+Before building LAMMPS, one must build the Colvars library in lib/colvars.
+
+This can be done manually in the same folder by using or adapting one of the
+provided Makefiles: for example, Makefile.g++ for the GNU compiler.
+
+In general, it is safer to use build setting consistent with the rest of
+LAMMPS.  This is best carried out from the LAMMPS src directory using a
+command like these, which simply invoke the lib/colvars/Install.py script with
+the specified args:
+
+
+.. parsed-literal::
+
+   make lib-colvars                      # print help message
+   make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+   make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+   make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
+
+The "machine" argument of the "-m" flag is used to find a Makefile.machine to
+use as build recipe.  If it does not already exist in lib/colvars, it will be
+auto-generated by using compiler flags consistent with those parsed from the
+core LAMMPS makefiles.
+
+Optional flags may be specified as environment variables:
+
+COLVARS\_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+COLVARS\_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+
+The build should produce two files: the library lib/colvars/libcolvars.a
+(which also includes Lepton objects if enabled) and the specification file
+lib/colvars/Makefile.lammps.  The latter is auto-generated, and normally does
+not need to be edited.
+
+
+----------
+
+
+.. _user-plumed:
+
+USER-PLUMED package
+-------------------------------------
+
+.. _plumedinstall: http://plumed.github.io/doc-master/user-doc/html/\_installation.html
+
+Before building LAMMPS with this package, you must first build PLUMED.
+PLUMED can be built as part of the LAMMPS build or installed separately
+from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.
+
+
+PLUMED can be linked into MD codes in three different modes: static,
+shared, and runtime.  With the "static" mode, all the code that PLUMED
+requires is linked statically into LAMMPS. LAMMPS is then fully
+independent from the PLUMED installation, but you have to rebuild/relink
+it in order to update the PLUMED code inside it.  With the "shared"
+linkage mode, LAMMPS is linked to a shared library that contains the
+PLUMED code.  This library should preferably be installed in a globally
+accessible location. When PLUMED is linked in this way the same library
+can be used by multiple MD packages.  Furthermore, the PLUMED library
+LAMMPS uses can be updated without the need for a recompile of LAMMPS
+for as long as the shared PLUMED library is ABI-compatible.
+
+The third linkage mode is "runtime" which allows the user to specify
+which PLUMED kernel should be used at runtime by using the PLUMED\_KERNEL
+environment variable. This variable should point to the location of the
+libplumedKernel.so dynamical shared object, which is then loaded at
+runtime. This mode of linking is particularly convenient for doing
+PLUMED development and comparing multiple PLUMED versions as these sorts
+of comparisons can be done without recompiling the hosting MD code. All
+three linkage modes are supported by LAMMPS on selected operating
+systems (e.g. Linux) and using either CMake or traditional make
+build. The "static" mode should be the most portable, while the
+"runtime" mode support in LAMMPS makes the most assumptions about
+operating system and compiler environment. If one mode does not work,
+try a different one, switch to a different build system, consider a
+global PLUMED installation or consider downloading PLUMED during the
+LAMMPS build.
+
+**CMake build**\ :
+
+When the "-D PKG\_USER-PLUMED" flag is included in the cmake command you
+must ensure that GSL is installed in locations that are specified in
+your environment.  There are then two additional commands that control
+the manner in which PLUMED is obtained and linked into LAMMPS.
+
+
+.. parsed-literal::
+
+   -D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
+   -D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime
+
+If DOWNLOAD\_PLUMED is set to "yes", the PLUMED library will be
+downloaded (the version of PLUMED that will be downloaded is hard-coded
+to a vetted version of PLUMED, usually a recent stable release version)
+and built inside the CMake build directory.  If DOWNLOAD\_PLUMED is set
+to "no" (the default), CMake will try to detect and link to an installed
+version of PLUMED.  For this to work, the PLUMED library has to be
+installed into a location where the pkg-config tool can find it or the
+PKG\_CONFIG\_PATH environment variable has to be set up accordingly.
+PLUMED should be installed in such a location if you compile it using
+the default make; make install commands.
+
+The PLUMED\_MODE setting determines the linkage mode for the PLUMED
+library.  The allowed values for this flag are "static" (default),
+"shared", or "runtime".  For a discussion of PLUMED linkage modes,
+please see above.  When DOWNLOAD\_PLUMED is enabled the static linkage
+mode is recommended.
+
+**Traditional make**\ :
+
+PLUMED needs to be installed before the USER-PLUMED package is installed
+so that LAMMPS can find the right settings when compiling and linking
+the LAMMPS executable.  You can either download and build PLUMED inside
+the LAMMPS plumed library folder or use a previously installed PLUMED
+library and point LAMMPS to its location. You also have to choose the
+linkage mode: "static" (default), "shared" or "runtime".  For a
+discussion of PLUMED linkage modes, please see above.
+
+Download/compilation/configuration of the plumed library can be done
+from the src folder through the following make args:
+
+
+.. parsed-literal::
+
+   make lib-plumed                         # print help message
+   make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+   make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+   make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+                                                   # /usr/local and use shared linkage mode
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink" are
+created in lib/plumed that point to the location of the PLUMED build to
+use. A new file lib/plumed/Makefile.lammps is also created with settings
+suitable for LAMMPS to compile and link PLUMED using the desired linkage
+mode. After this step is completed, you can install the USER-PLUMED
+package and compile LAMMPS in the usual manner:
+
+
+.. parsed-literal::
+
+   make yes-user-plumed
+   make machine
+
+Once this compilation completes you should be able to run LAMMPS in the
+usual way.  For shared linkage mode, libplumed.so must be found by the
+LAMMPS executable, which on many operating systems means, you have to
+set the LD\_LIBRARY\_PATH environment variable accordingly.
+
+Support for the different linkage modes in LAMMPS varies for different
+operating systems, using the static linkage is expected to be the most
+portable, and thus set to be the default.
+
+If you want to change the linkage mode, you have to re-run "make
+lib-plumed" with the desired settings **and** do a re-install if the
+USER-PLUMED package with "make yes-user-plumed" to update the required
+makefile settings with the changes in the lib/plumed folder.
+
+
+----------
+
+
+.. _user-h5md:
+
+USER-H5MD package
+---------------------------------
+
+To build with this package you must have the HDF5 software package
+installed on your system, which should include the h5cc compiler and
+the HDF5 library.
+
+**CMake build**\ :
+
+No additional settings are needed besides "-D PKG\_USER-H5MD=yes".
+
+This should auto-detect the H5MD library on your system.  Several
+advanced CMake H5MD options exist if you need to specify where it is
+installed.  Use the ccmake (terminal window) or cmake-gui (graphical)
+tools to see these options and set them interactively from their user
+interfaces.
+
+**Traditional make**\ :
+
+Before building LAMMPS, you must build the CH5MD library in lib/h5md.
+You can do this manually if you prefer; follow the instructions in
+lib/h5md/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/h5md/Install.py script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-h5md                     # print help message
+   make lib-h5md args="-m h5cc"      # build with h5cc compiler
+
+The build should produce two files: lib/h5md/libch5md.a and
+lib/h5md/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.\* and has settings needed to build LAMMPS with the
+system HDF5 library.  If necessary, you can edit/create a new
+lib/h5md/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
+
+
+----------
+
+
+.. _user-intel:
+
+USER-INTEL package
+-----------------------------------
+
+To build with this package, you must choose which hardware you want to
+build for, either x86 CPUs or Intel KNLs in offload mode.  You should
+also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
+used in tandem with the USER-INTEL package to good effect, as explained
+on the :doc:`Speed intel <Speed_intel>` doc page.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D INTEL_ARCH=value     # value = cpu (default) or knl
+   -D INTEL_LRT_MODE=value # value = threads, none, or c++11
+
+In Long-range thread mode (LRT) a modified verlet style is used, that
+operates the Kspace calculation in a separate thread concurrently to
+other calculations. This has to be enabled in the :doc:`package intel <package>`
+command at runtime. With the setting "threads" it used the pthreads
+library, while c++11 will use the built-in thread support of C++11
+compilers. The option "none" skips compilation of this feature. The
+default is to use "threads" if pthreads is available and otherwise "none".
+
+Best performance is achieved with Intel hardware, Intel compilers, as well as
+the Intel TBB and MKL libraries. However, the code also compiles, links, and
+runs with other compilers and without TBB and MKL.
+
+**Traditional make**\ :
+
+Choose which hardware to compile for in Makefile.machine via the
+following settings.  See src/MAKE/OPTIONS/Makefile.intel\_cpu\* and
+Makefile.knl files for examples. and src/USER-INTEL/README for
+additional information.
+
+For CPUs:
+
+
+.. parsed-literal::
+
+   OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
+   CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+   LINKFLAGS =     -g -qopenmp $(OPTFLAGS)
+   LIB =           -ltbbmalloc
+
+For KNLs:
+
+
+.. parsed-literal::
+
+   OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
+   CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+   LINKFLAGS =     -g -qopenmp $(OPTFLAGS)
+   LIB =           -ltbbmalloc
+
+
+----------
+
+
+.. _user-molfile:
+
+USER-MOLFILE package
+---------------------------------------
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed
+   -D PKG_USER-MOLFILE=yes
+
+Using "-D PKG\_USER-MOLFILE=yes" enables the package, and setting
+"-D MOLFILE\_INCLUDE DIRS" allows to provide a custom location for
+the molfile plugin header files. These should match the ABI of the
+plugin files used, and thus one typically sets them to include
+folder of the local VMD installation in use. LAMMPS ships with a
+couple of default header files that correspond to a popular VMD
+version, usually the latest release.
+
+**Traditional make**\ :
+
+The lib/molfile/Makefile.lammps file has a setting for a dynamic
+loading library libdl.a that is typically present on all systems.  It
+is required for LAMMPS to link with this package.  If the setting is
+not valid for your system, you will need to edit the Makefile.lammps
+file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
+details. It is also possible to configure a different folder with
+the VMD molfile plugin header files. LAMMPS ships with a couple of
+default headers, but these are not compatible with all VMD versions,
+so it is often best to change this setting to the location of the
+same include files of the local VMD installation in use.
+
+
+----------
+
+
+.. _user-netcdf:
+
+USER-NETCDF package
+-------------------------------------
+
+To build with this package you must have the NetCDF library installed
+on your system.
+
+**CMake build**\ :
+
+No additional settings are needed besides "-D PKG\_USER-NETCDF=yes".
+
+This should auto-detect the NETCDF library if it is installed on your
+system at standard locations.  Several advanced CMake NETCDF options
+exist if you need to specify where it was installed.  Use the ccmake
+(terminal window) or cmake-gui (graphical) tools to see these options
+and set them interactively from their user interfaces.
+
+**Traditional make**\ :
+
+The lib/netcdf/Makefile.lammps file has settings for NetCDF include
+and library files which LAMMPS needs to build with this package.  If
+the settings are not valid for your system, you will need to edit the
+Makefile.lammps file.  See lib/netcdf/README for details.
+
+
+----------
+
+
+.. _user-omp:
+
+USER-OMP package
+-------------------------------
+
+**CMake build**\ :
+
+No additional settings are required besides "-D PKG\_USER-OMP=yes".  If
+CMake detects OpenMP support, the USER-OMP code will be compiled with
+multi-threading support enabled, otherwise as optimized serial code.
+
+**Traditional make**\ :
+
+To enable multi-threading support in the USER-OMP package (and other
+styles supporting OpenMP) the following compile and link flags must
+be added to your Makefile.machine file.
+See src/MAKE/OPTIONS/Makefile.omp for an example.
+
+
+.. parsed-literal::
+
+   CCFLAGS: -fopenmp               # for GNU Compilers
+   CCFLAGS: -qopenmp -restrict     # for Intel compilers on Linux
+   LINKFLAGS: -fopenmp             # for GNU Compilers
+   LINKFLAGS: -qopenmp             # for Intel compilers on Linux
+
+For other platforms and compilers, please consult the documentation
+about OpenMP support for your compiler. Please see the note about
+how to address compatibility :ref:`issues with the 'default(none)' directive <default-none-issues>` of some compilers.
+
+
+----------
+
+
+.. _user-qmmm:
+
+USER-QMMM package
+---------------------------------
+
+.. note::
+
+   The LAMMPS executable these steps produce is not yet functional
+   for a QM/MM simulation.  You must also build Quantum ESPRESSO and
+   create a new executable (pwqmmm.x) which links LAMMPS and Quantum
+   ESPRESSO together.  These are steps 3 and 4 described in the
+   lib/qmmm/README file.  Unfortunately, the Quantum ESPRESSO developers
+   have been breaking the interface that the QM/MM code in LAMMPS is using,
+   so that currently (Summer 2018) using this feature requires either
+   correcting the library interface feature in recent Quantum ESPRESSO
+   releases, or using an outdated version of QE. The last version of
+   Quantum ESPRESSO known to work with this QM/MM interface was version
+   5.4.1 from 2016.
+
+**CMake build**\ :
+
+The CMake build system currently does not support building the full
+QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
+You must use the traditional make build for this package.
+
+**Traditional make**\ :
+
+Before building LAMMPS, you must build the QMMM library in lib/qmmm.
+You can do this manually if you prefer; follow the first two steps
+explained in lib/qmmm/README.  You can also do it in one step from the
+lammps/src dir, using a command like these, which simply invoke the
+lib/qmmm/Install.py script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-qmmm                      # print help message
+   make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+   make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
+   make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
+
+The build should produce two files: lib/qmmm/libqmmm.a and
+lib/qmmm/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.\* and has settings needed to build LAMMPS with the
+QMMM library (though typically the settings are just blank).  If
+necessary, you can edit/create a new lib/qmmm/Makefile.machine file
+for your system, which should define an EXTRAMAKE variable to specify
+a corresponding Makefile.lammps.machine file.
+
+You can then install QMMM package and build LAMMPS in the usual
+manner.  After completing the LAMMPS build and compiling Quantum
+ESPRESSO with external library support, go back to the lib/qmmm folder
+and follow the instructions on the README file to build the combined
+LAMMPS/QE QM/MM executable (pwqmmm.x) in the lib/qmmm folder.
+
+
+----------
+
+
+.. _user-quip:
+
+USER-QUIP package
+---------------------------------
+
+To build with this package, you must download and build the QUIP
+library.  It can be obtained from GitHub.  For support of GAP
+potentials, additional files with specific licensing conditions need
+to be downloaded and configured.  See step 1 and step 1.1 in the
+lib/quip/README file for details on how to do this.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
+
+CMake will not download and build the QUIP library.  But once you have
+done that, a CMake build of LAMMPS with "-D PKG\_USER-QUIP=yes" should
+work.  Set QUIP\_LIBRARY if CMake cannot find the QUIP library.
+
+**Traditional make**\ :
+
+The download/build procedure for the QUIP library, described in
+lib/quip/README file requires setting two environment variables,
+QUIP\_ROOT and QUIP\_ARCH.  These are accessed by the
+lib/quip/Makefile.lammps file which is used when you compile and link
+LAMMPS with this package.  You should only need to edit
+Makefile.lammps if the LAMMPS build can not use its settings to
+successfully build on your system.
+
+
+----------
+
+
+.. _user-scafacos:
+
+USER-SCAFACOS package
+-----------------------------------------
+
+To build with this package, you must download and build the `ScaFaCoS Coulomb solver library <scafacos-home_>`_
+
+.. _scafacos-home: http://www.scafacos.de
+
+
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D DOWNLOAD_SCAFACOS=value    # download ScaFaCoS for build, value = no (default) or yes
+   -D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location)
+   -D SCAFACOS_INCLUDE_DIR=path  # ScaFaCoS include directory (only needed if at custom location)
+
+If DOWNLOAD\_SCAFACOS is set, the ScaFaCoS library will be downloaded
+and built inside the CMake build directory.  If the ScaFaCoS library
+is already on your system (in a location CMake cannot find it),
+SCAFACOS\_LIBRARY is the filename (plus path) of the ScaFaCoS library
+file, not the directory the library file is in.  SCAFACOS\_INCLUDE\_DIR
+is the directory the ScaFaCoS include file is in.
+
+**Traditional make**\ :
+
+You can download and build the ScaFaCoS library manually if you
+prefer; follow the instructions in lib/scafacos/README.  You can also
+do it in one step from the lammps/src dir, using a command like these,
+which simply invoke the lib/scafacos/Install.py script with the
+specified args:
+
+make lib-scafacos                         # print help message
+make lib-scafacos args="-b"               # download and build in lib/scafacos/scafacos-<version>
+make lib-scafacos args="-p $HOME/scafacos  # use existing ScaFaCoS installation in $HOME/scafacos
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/scafacos to point to the ScaFaCoS src dir.  When LAMMPS
+builds in src it will use these links.  You should not need to edit
+the lib/scafacos/Makefile.lammps file.
+
+
+----------
+
+
+.. _user-smd:
+
+USER-SMD package
+-------------------------------
+
+To build with this package, you must download the Eigen3 library.
+Eigen3 is a template library, so you do not need to build it.
+
+**CMake build**\ :
+
+
+.. parsed-literal::
+
+   -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
+   -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
+
+If DOWNLOAD\_EIGEN3 is set, the Eigen3 library will be downloaded and
+inside the CMake build directory.  If the Eigen3 library is already on
+your system (in a location CMake cannot find it), EIGEN3\_INCLUDE\_DIR
+is the directory the Eigen3++ include file is in.
+
+**Traditional make**\ :
+
+You can download the Eigen3 library manually if you prefer; follow the
+instructions in lib/smd/README.  You can also do it in one step from
+the lammps/src dir, using a command like these, which simply invoke
+the lib/smd/Install.py script with the specified args:
+
+
+.. parsed-literal::
+
+   make lib-smd                         # print help message
+   make lib-smd args="-b"               # download to lib/smd/eigen3
+   make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+
+Note that a symbolic (soft) link named "includelink" is created in
+lib/smd to point to the Eigen dir.  When LAMMPS builds it will use
+this link.  You should not need to edit the lib/smd/Makefile.lammps
+file.
+
+
+----------
+
+
+.. _user-vtk:
+
+USER-VTK package
+-------------------------------
+
+To build with this package you must have the VTK library installed on
+your system.
+
+**CMake build**\ :
+
+No additional settings are needed besides "-D PKG\_USER-VTK=yes".
+
+This should auto-detect the VTK library if it is installed on your
+system at standard locations.  Several advanced VTK options exist if
+you need to specify where it was installed.  Use the ccmake (terminal
+window) or cmake-gui (graphical) tools to see these options and set
+them interactively from their user interfaces.
+
+**Traditional make**\ :
+
+The lib/vtk/Makefile.lammps file has settings for accessing VTK files
+and its library, which LAMMPS needs to build with this package.  If
+the settings are not valid for your system, check if one of the other
+lib/vtk/Makefile.lammps.\* files is compatible and copy it to
+Makefile.lammps.  If none of the provided files work, you will need to
+edit the Makefile.lammps file.  See lib/vtk/README for details.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_link.rst b/doc/src/Build_link.rst
new file mode 100644
index 0000000000..8306fcb86f
--- /dev/null
+++ b/doc/src/Build_link.rst
@@ -0,0 +1,91 @@
+Link LAMMPS as a library to another code
+========================================
+
+LAMMPS can be used as a library by another application, including
+Python scripts.  The files src/library.cpp and library.h define the
+C-style API for using LAMMPS as a library.  See the :doc:`Howto library <Howto_library>` doc page for a description of the
+interface and how to extend it for your needs.
+
+The :doc:`Build basics <Build_basics>` doc page explains how to build
+LAMMPS as either a shared or static library.  This results in one of
+these 2 files:
+
+liblammps.so      # shared library
+liblammps.a       # static library
+
+
+----------
+
+
+**Link with LAMMPS as a static library**\ :
+
+The calling application can link to LAMMPS as a static library with a
+link command like this:
+
+g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
+
+The -L argument is the path to where the liblammps.a file is.  The
+-llammps argument is shorthand for the file liblammps.a.
+
+
+----------
+
+
+**Link with LAMMPS as a shared library**\ :
+
+If you wish to link to liblammps.so, the operating system finds shared
+libraries to load at run-time using the environment variable
+LD\_LIBRARY\_PATH.  To enable this you can do one of two things:
+
+(1) Copy the liblammps.so file to a location the system can find it,
+such as /usr/local/lib.  I.e. a directory already listed in your
+LD\_LIBRARY\_PATH variable.  You can type
+
+
+.. parsed-literal::
+
+   printenv LD_LIBRARY_PATH
+
+to see what directories are in that list.
+
+(2) Add the LAMMPS src directory (or the directory you perform CMake
+build in) to your LD\_LIBRARY\_PATH, so that the current version of the
+shared library is always available to programs that use it.
+
+For the csh or tcsh shells, you would add something like this to your
+~/.cshrc file:
+
+
+.. parsed-literal::
+
+   setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
+
+
+----------
+
+
+**Calling the LAMMPS library**\ :
+
+Either flavor of library (static or shared) allows one or more LAMMPS
+objects to be instantiated from the calling program.
+
+When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS\_NS
+namespace; you can safely use any of its classes and methods from
+within the calling code, as needed.
+
+When used from a C or Fortran program, the library has a simple
+C-style interface, provided in src/library.cpp and src/library.h.
+
+See the :doc:`Python library <Python_library>` doc page for a
+description of the Python interface to LAMMPS, which wraps the C-style
+interface.
+
+See the sample codes in examples/COUPLE/simple for examples of C++ and
+C and Fortran codes that invoke LAMMPS through its library interface.
+Other examples in the COUPLE directory use coupling ideas discussed on
+the :doc:`Howto couple <Howto_couple>` doc page.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst
new file mode 100644
index 0000000000..8f1966f101
--- /dev/null
+++ b/doc/src/Build_make.rst
@@ -0,0 +1,94 @@
+Build LAMMPS with make
+======================
+
+Building LAMMPS with traditional makefiles requires that you have a
+Makefile."machine" file appropriate for your system in the src/MAKE,
+src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
+below).  It can include various options for customizing your LAMMPS
+build with a number of global compilation options and features.
+
+To include LAMMPS packages (i.e. optional commands and styles) you
+must install them first, as discussed on the :doc:`Build package <Build_package>` doc page.  If the packages require
+provided or external libraries, you must build those libraries before
+building LAMMPS.  Building :doc:`LAMMPS with CMake <Build_cmake>` can
+automate all of this for many types of machines, especially
+workstations, desktops and laptops, so we suggest you try it first.
+
+These commands perform a default LAMMPS build, producing the LAMMPS
+executable lmp\_serial or lmp\_mpi in lammps/src:
+
+
+.. parsed-literal::
+
+   cd lammps/src
+   make serial     # build a serial LAMMPS executable
+   make mpi        # build a parallel LAMMPS executable with MPI
+   make            # see a variety of make options
+
+This initial compilation can take a long time, since LAMMPS is a large
+project with many features. If your machine has multiple CPU cores
+(most do these days), using a command like "make -jN mpi" (with N =
+the number of available CPU cores) can be much faster.  If you plan to
+do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
+installation of the ccache (= Compiler Cache) software may speed up
+compilation even more.
+
+After the initial build, whenever you edit LAMMPS source files, or add
+or remove new files to the source directory (e.g. by installing or
+uninstalling packages), you must re-compile and relink the LAMMPS
+executable with the same "make" command.  This makefiles dependencies
+should insure that only the subset of files that need to be are
+re-compiled.
+
+.. note::
+
+   When you build LAMMPS for the first time, a long list of \*.d
+   files will be printed out rapidly.  This is not an error; it is the
+   Makefile doing its normal creation of dependencies.
+
+
+----------
+
+
+The lammps/src/MAKE tree contains all the Makefile.machine files
+included in the LAMMPS distribution.  Typing "make machine" uses
+Makefile.machine.  Thus the "make serial" or "make mpi" lines above
+use Makefile.serial and Makefile.mpi.  Others are in these dirs:
+
+
+.. parsed-literal::
+
+   OPTIONS      # Makefiles which enable specific options
+   MACHINES     # Makefiles for specific machines
+   MINE         # customized Makefiles you create (you may need to create this folder)
+
+Typing "make" lists all the available Makefile.machine files.  A file
+with the same name can appear in multiple folders (not a good idea).
+The order the dirs are searched is as follows: src/MAKE/MINE,
+src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.  This gives preference
+to a customized file you put in src/MAKE/MINE.
+
+Makefiles you may wish to try include these (some require a package
+first be installed).  Many of these include specific compiler flags
+for optimized performance.  Please note, however, that some of these
+customized machine Makefile are contributed by users.  Since both
+compilers, OS configurations, and LAMMPS itself keep changing, their
+settings may become outdated:
+
+
+.. parsed-literal::
+
+   make mac             # build serial LAMMPS on a Mac
+   make mac_mpi         # build parallel LAMMPS on a Mac
+   make intel_cpu       # build with the USER-INTEL package optimized for CPUs
+   make knl             # build with the USER-INTEL package optimized for KNLs
+   make opt             # build with the OPT package optimized for CPUs
+   make omp             # build with the USER-OMP package optimized for OpenMP
+   make kokkos_omp      # build with the KOKKOS package for OpenMP
+   make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
+   make kokkos_phi      # build with the KOKKOS package for KNLs
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst
new file mode 100644
index 0000000000..9f56f3f329
--- /dev/null
+++ b/doc/src/Build_package.rst
@@ -0,0 +1,265 @@
+Include packages in build
+=========================
+
+In LAMMPS, a package is a group of files that enable a specific set of
+features.  For example, force fields for molecular systems or
+rigid-body constraints are in packages.  In the src directory, each
+package is a sub-directory with the package name in capital letters.
+
+An overview of packages is given on the :doc:`Packages <Packages>` doc
+page.  Brief overviews of each package are on the :doc:`Packages details <Packages_details>` doc page.
+
+When building LAMMPS, you can choose to include or exclude each
+package.  In general there is no need to include a package if you
+never plan to use its features.
+
+If you get a run-time error that a LAMMPS command or style is
+"Unknown", it is often because the command is contained in a package,
+and your build did not include that package.  Running LAMMPS with the
+:doc:`-h command-line switch <Run_options>` will print all the included
+packages and commands for that executable.
+
+For the majority of packages, if you follow the single step below to
+include it, you can then build LAMMPS exactly the same as you would
+without any packages installed.  A few packages may require additional
+steps, as explained on the :doc:`Build extras <Build_extras>` doc page.
+
+These links take you to the extra instructions for those select
+packages:
+
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`COMPRESS <compress>`       | :ref:`GPU <gpu>`                 | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`MSCG <mscg>`               | :ref:`OPT <opt>`                 | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-ATC <user-atc>`       | :ref:`USER-AWPMD <user-awpmd>`   | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+
+The mechanism for including packages is simple but different for CMake
+versus make.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D PKG_NAME=value          # yes or no (default)
+
+Examples:
+
+
+.. parsed-literal::
+
+   -D PKG_MANYBODY=yes
+   -D PKG_USER-INTEL=yes
+
+All standard and user packages are included the same way.  Note that
+USER packages have a hyphen between USER and the rest of the package
+name, not an underscore.
+
+See the shortcut section below for how to install many packages at
+once with CMake.
+
+.. note::
+
+   If you toggle back and forth between building with CMake vs
+   make, no packages in the src directory can be installed when you
+   invoke cmake.  CMake will give an error if that is not the case,
+   indicating how you can un-install all packages in the src dir.
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/src
+   make ps                    # check which packages are currently installed
+   make yes-name              # install a package with name
+   make no-name               # un-install a package with name
+   make mpi                   # build LAMMPS with whatever packages are now installed
+
+Examples:
+
+
+.. parsed-literal::
+
+   make no-rigid
+   make yes-user-intel
+
+All standard and user packages are included the same way.
+
+See the shortcut section below for how to install many packages at
+once with make.
+
+.. note::
+
+   You must always re-build LAMMPS (via make) after installing or
+   un-installing a package, for the action to take effect.
+
+.. note::
+
+   You cannot install or un-install packages and build LAMMPS in a
+   single make command with multiple targets, e.g. make yes-colloid mpi.
+   This is because the make procedure creates a list of source files that
+   will be out-of-date for the build if the package configuration changes
+   within the same command.  You can include or exclude multiple packages
+   in a single make command, e.g. make yes-colloid no-manybody.
+
+**CMake and make info**\ :
+
+Any package can be included or excluded in a LAMMPS build, independent
+of all other packages.  However, some packages include files derived
+from files in other packages.  LAMMPS checks for this and does the
+right thing.  Individual files are only included if their dependencies
+are already included.  Likewise, if a package is excluded, other files
+dependent on that package are also excluded.
+
+When you download a LAMMPS tarball or download LAMMPS source files
+from the Git or SVN repositories, no packages are pre-installed in the
+src directory.
+
+.. note::
+
+   Prior to Aug 2018, if you downloaded a tarball, 3 packages
+   (KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory.
+   That is no longer the case, so that CMake will build as-is without the
+   need to un-install those packages.
+
+
+----------
+
+
+**CMake shortcuts for installing many packages**\ :
+
+Instead of specifying all the CMake options via the command-line,
+CMake allows initializing the variable cache using script files. These
+are regular CMake files which can manipulate and set variables, and
+can also contain control flow constructs.
+
+LAMMPS includes several of these files to define configuration
+"presets", similar to the options that exist for the Make based
+system. Using these files you can enable/disable portions of the
+available packages in LAMMPS. If you need a custom preset you can take
+one of them as a starting point and customize it to your needs.
+
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/all\_on.cmake  [OPTIONS] ../cmake | enable all packages                                       |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/all\_off.cmake [OPTIONS] ../cmake | disable all packages                                      |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  | enable just a few core packages                           |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  | enable most common packages                               |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  | disable packages that do require extra libraries or tools |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  | change settings to use the Clang compilers by default     |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/mingw.cmake [OPTIONS] ../cmake    | enable all packages compatible with MinGW compilers       |
++-------------------------------------------------------------+-----------------------------------------------------------+
+
+.. note::
+
+   Running cmake this way manipulates the variable cache in your
+   current build directory. You can combine multiple presets and options
+   in a single cmake run, or change settings incrementally by running
+   cmake with new flags.
+
+**Example:**
+
+
+.. parsed-literal::
+
+   # build LAMMPS with most commonly used packages, but then remove
+   # those requiring additional library or tools, but still enable
+   # GPU package and configure it for using CUDA. You can run.
+   mkdir build
+   cd build
+   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
+
+   # to add another package, say BODY to the previous configuration you can run:
+   cmake -D PKG_BODY=on .
+
+   # to reset the package selection from above to the default of no packages
+   # but leaving all other settings untouched. You can run:
+   cmake -C ../cmake/presets/no_all.cmake .
+
+
+----------
+
+
+**Make shortcuts for installing many packages**\ :
+
+The following commands are useful for managing package source files
+and their installation when building LAMMPS via traditional make.
+Just type "make" in lammps/src to see a one-line summary.
+
+These commands install/un-install sets of packages:
+
++-----------------------------------+-----------------------------------------------------+
+| make yes-all                      | install all packages                                |
++-----------------------------------+-----------------------------------------------------+
+| make no-all                       | un-install all packages                             |
++-----------------------------------+-----------------------------------------------------+
+| make yes-standard or make yes-std | install standard packages                           |
++-----------------------------------+-----------------------------------------------------+
+| make no-standard or make no-std   | un-install standard packages                        |
++-----------------------------------+-----------------------------------------------------+
+| make yes-user                     | install user packages                               |
++-----------------------------------+-----------------------------------------------------+
+| make no-user                      | un-install user packages                            |
++-----------------------------------+-----------------------------------------------------+
+| make yes-lib                      | install packages that require extra libraries       |
++-----------------------------------+-----------------------------------------------------+
+| make no-lib                       | un-install packages that require extra libraries    |
++-----------------------------------+-----------------------------------------------------+
+| make yes-ext                      | install packages that require external libraries    |
++-----------------------------------+-----------------------------------------------------+
+| make no-ext                       | un-install packages that require external libraries |
++-----------------------------------+-----------------------------------------------------+
+
+which install/un-install various sets of packages.  Typing "make
+package" will list all the these commands.
+
+.. note::
+
+   Installing or un-installing a package works by simply copying
+   files back and forth between the main src directory and
+   sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+   so that the files are included or excluded when LAMMPS is built.
+
+The following make commands help manage files that exist in both the
+src directory and in package sub-directories.  You do not normally
+need to use these commands unless you are editing LAMMPS files or are
+:doc:`installing a patch <Install_patch>` downloaded from the LAMMPS web
+site.
+
+Type "make package-status" or "make ps" to show which packages are
+currently installed.  For those that are installed, it will list any
+files that are different in the src directory and package
+sub-directory.
+
+Type "make package-installed" or "make pi" to show which packages are
+currently installed, without listing the status of packages that are
+not installed.
+
+Type "make package-update" or "make pu" to overwrite src files with
+files from the package sub-directories if the package is installed.
+It should be used after a :doc:`patch has been applied <Install_patch>`,
+since patches only update the files in the package sub-directory, but
+not the src files.
+
+Type "make package-overwrite" to overwrite files in the package
+sub-directories with src files.
+
+Type "make package-diff" to list all differences between pairs of
+files in both the src dir and a package dir.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst
new file mode 100644
index 0000000000..07d427db49
--- /dev/null
+++ b/doc/src/Build_settings.rst
@@ -0,0 +1,479 @@
+Optional build settings
+=======================
+
+LAMMPS can be built with several optional settings.  Each sub-section
+explain how to do this for building both with CMake and make.
+
+| :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS
+| :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command
+| :ref:`Size of LAMMPS data types <size>`
+| :ref:`Read or write compressed files <gzip>`
+| :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
+| :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command
+| :ref:`Memory allocation alignment <align>`
+| :ref:`Workaround for long long integers <longlong>`
+| :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library 
+| 
+
+
+----------
+
+
+.. _cxx11:
+
+C++11 standard compliance test
+------------------------------------------
+
+The LAMMPS developers plan to transition to make the C++11 standard the
+minimum requirement for compiling LAMMPS.  Currently this only applies to
+some packages like KOKKOS while the rest aims to be compatible with the C++98
+standard.  Most currently used compilers are compatible with C++11; some need
+to set extra flags to switch.  To determine the impact of requiring C++11,
+we have added a simple compliance test to the source code, that will cause
+the compilation to abort, if C++11 compliance is not available or enabled.
+To bypass this check, you need to change a setting in the makefile or
+when calling CMake.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D DISABLE_CXX11_REQUIREMENT=yes
+
+You can set additional C++ compiler flags (beyond those selected by CMake)
+through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
+
+
+.. parsed-literal::
+
+   -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_CXX98
+
+
+----------
+
+
+.. _fft:
+
+FFT library
+---------------------
+
+When the KSPACE package is included in a LAMMPS build, the
+:doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which
+require use of an FFT library to compute 1d FFTs.  The KISS FFT
+library is included with LAMMPS but other libraries can be faster.
+LAMMPS can use them if they are available on your system.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+   -D FFT_SINGLE=value       # yes or no (default), no = double precision
+   -D FFT_PACK=value         # array (default) or pointer or memcpy
+
+.. note::
+
+   The values for the FFT variable must be in upper-case.  This is
+   an exception to the rule that all CMake variables can be specified
+   with lower-case values.
+
+Usually these settings are all that is needed.  If CMake cannot find
+the FFT library, you can set these variables:
+
+
+.. parsed-literal::
+
+   -D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
+   -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+   -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+   -D MKL_LIBRARIES=path
+
+**Makefile.machine settings**\ :
+
+
+.. parsed-literal::
+
+   FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
+                                 # default is KISS if not specified
+   FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+   FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
+
+# default is FFT\_PACK\_ARRAY if not specified
+
+
+.. parsed-literal::
+
+   FFT_INC =       -I/usr/local/include
+   FFT_PATH =      -L/usr/local/lib
+   FFT_LIB =       -lfftw3             # FFTW3 double precision
+   FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier
+
+As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
+make can find the FFT header and library files.  You must specify
+FFT\_LIB with the appropriate FFT libraries to include in the link.
+
+**CMake and make info**\ :
+
+The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
+distribution.  It is portable across all platforms.  Depending on the
+size of the FFTs and the number of processors used, the other
+libraries listed here can be faster.
+
+However, note that long-range Coulombics are only a portion of the
+per-timestep CPU cost, FFTs are only a portion of long-range
+Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+communication can be costly).  A breakdown of these timings is printed
+to the screen at the end of a run using the :doc:`kspace\_style pppm <kspace_style>` command.  The :doc:`Run output <Run_output>`
+doc page gives more details.
+
+FFTW is a fast, portable FFT library that should also work on any
+platform and can be faster than the KISS FFT library.  You can
+download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
+version 3.X; the legacy version 2.1.X is no longer supported.
+
+Building FFTW for your box should be as simple as ./configure; make;
+make install.  The install command typically requires root privileges
+(e.g. invoke it via sudo), unless you specify a local directory with
+the "--prefix" option of configure.  Type "./configure --help" to see
+various options.
+
+The Intel MKL math library is part of the Intel compiler suite.  It
+can be used with the Intel or GNU compiler (see FFT\_LIB setting above).
+
+Performing 3d FFTs in parallel can be time consuming due to data
+access and required communication.  This cost can be reduced by
+performing single-precision FFTs instead of double precision.  Single
+precision means the real and imaginary parts of a complex datum are
+4-byte floats.  Double precision means they are 8-byte doubles.  Note
+that Fourier transform and related PPPM operations are somewhat less
+sensitive to floating point truncation errors and thus the resulting
+error is less than the difference in precision. Using the -DFFT\_SINGLE
+setting trades off a little accuracy for reduced memory use and
+parallel communication costs for transposing 3d FFT data.
+
+When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW
+library a second time with support for single-precision.
+
+For FFTW3, do the following, which should produce the additional
+library libfftw3f.a
+
+
+.. parsed-literal::
+
+   make clean
+   ./configure --enable-single; make; make install
+
+Performing 3d FFTs requires communication to transpose the 3d FFT
+grid.  The data packing/unpacking for this can be done in one of 3
+modes (ARRAY, POINTER, MEMCPY) as set by the FFT\_PACK syntax above.
+Depending on the machine, the size of the FFT grid, the number of
+processors used, one option may be slightly faster.  The default is
+ARRAY mode.
+
+
+----------
+
+
+.. _size:
+
+Size of LAMMPS data types
+------------------------------------
+
+LAMMPS has a few integer data types which can be defined as 4-byte or
+8-byte integers.  The default setting of "smallbig" is almost always
+adequate.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
+
+# default is LAMMPS\_SMALLBIG if not specified
+**CMake and make info**\ :
+
+The default "smallbig" setting allows for simulations with:
+
+* total atom count = 2\^63 atoms (about 9e18)
+* total timesteps = 2\^63 (about 9e18)
+* atom IDs = 2\^31 (about 2 billion)
+* image flags = roll over at 512
+
+The "bigbig" setting increases the latter two limits.  It allows for:
+
+* total atom count = 2\^63 atoms (about 9e18)
+* total timesteps = 2\^63 (about 9e18)
+* atom IDs = 2\^63 (about 9e18)
+* image flags = roll over at about 1 million (2\^20)
+
+The "smallsmall" setting is only needed if your machine does not
+support 8-byte integers.  It allows for:
+
+* total atom count = 2\^31 atoms (about 2 billion)
+* total timesteps = 2\^31 (about 2 billion)
+* atom IDs = 2\^31 (about 2 billion)
+* image flags = roll over at 512 (2\^9)
+
+Atom IDs are not required for atomic systems which do not store bond
+topology information, though IDs are enabled by default.  The
+:doc:`atom\_modify id no <atom_modify>` command will turn them off.  Atom
+IDs are required for molecular systems with bond topology (bonds,
+angles, dihedrals, etc).  Thus if you model a molecular system with
+more than 2 billion atoms, you need the "bigbig" setting.
+
+Image flags store 3 values per atom which count the number of times an
+atom has moved through the periodic box in each dimension.  See the
+:doc:`dump <dump>` doc page for a discussion.  If an atom moves through
+the periodic box more than this limit, the value will "roll over",
+e.g. from 511 to -512, which can cause diagnostics like the
+mean-squared displacement, as calculated by the :doc:`compute msd <compute_msd>` command, to be faulty.
+
+Note that the USER-ATC package and the USER-INTEL package are currently
+not compatible with the "bigbig" setting. Also, there are limitations
+when using the library interface. Some functions with known issues
+have been replaced by dummy calls printing a corresponding error rather
+than crashing randomly or corrupting data.
+
+Also note that the GPU package requires its lib/gpu library to be
+compiled with the same size setting, or the link will fail.  A CMake
+build does this automatically.  When building with make, the setting
+in whichever lib/gpu/Makefile is used must be the same as above.
+
+
+----------
+
+
+.. _graphics:
+
+Output of JPG, PNG, and movie files
+--------------------------------------------------
+
+The :doc:`dump image <dump_image>` command has options to output JPEG or
+PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
+outputs movie files in MPEG format.  Using these options requires the
+following settings:
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D WITH_JPEG=value      # yes or no
+                             # default = yes if CMake finds JPEG files, else no
+   -D WITH_PNG=value       # yes or no
+                             # default = yes if CMake finds PNG and ZLIB files, else no
+   -D WITH_FFMPEG=value    # yes or no
+                             # default = yes if CMake can find ffmpeg, else no
+
+Usually these settings are all that is needed.  If CMake cannot find
+the graphics header, library, executable files, you can set these
+variables:
+
+
+.. parsed-literal::
+
+   -D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
+   -D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file
+   -D PNG_INCLUDE_DIR=path     # path to png.h header file
+   -D PNG_LIBRARIES=path       # path to libpng.a (.so) file
+   -D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
+   -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
+   -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable
+
+**Makefile.machine settings**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_JPEG
+   LMP_INC = -DLAMMPS_PNG
+   LMP_INC = -DLAMMPS_FFMPEG
+
+   JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
+   JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
+   JPG_LIB = -ljpeg -lpng -lz       # library names
+
+As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
+find the graphics header and library files.  You must specify JPG\_LIB
+with a list of graphics libraries to include in the link.  You must
+insure ffmpeg is in a directory where LAMMPS can find it at runtime,
+i.e. a dir in your PATH environment variable.
+
+**CMake and make info**\ :
+
+Using ffmpeg to output movie files requires that your machine
+supports the "popen" function in the standard runtime library.
+
+.. note::
+
+   On some clusters with high-speed networks, using the fork()
+   library calls (required by popen()) can interfere with the fast
+   communication library and lead to simulations using ffmpeg to hang or
+   crash.
+
+
+----------
+
+
+.. _gzip:
+
+Read or write compressed files
+-----------------------------------------
+
+If this option is enabled, large files can be read or written with
+gzip compression by several LAMMPS commands, including
+:doc:`read\_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D WITH_GZIP=value       # yes or no
+                            # default is yes if CMake can find gzip, else no
+   -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_GZIP
+
+**CMake and make info**\ :
+
+This option requires that your machine supports the "popen()" function
+in the standard runtime library and that a gzip executable can be
+found by LAMMPS during a run.
+
+.. note::
+
+   On some clusters with high-speed networks, using the fork()
+   library calls (required by popen()) can interfere with the fast
+   communication library and lead to simulations using compressed output
+   or input to hang or crash. For selected operations, compressed file
+   I/O is also available using a compression library instead, which is
+   what the :ref:`COMPRESS package <PKG-COMPRESS>` enables.
+
+
+----------
+
+
+.. _align:
+
+Memory allocation alignment
+---------------------------------------
+
+This setting enables the use of the posix\_memalign() call instead of
+malloc() when LAMMPS allocates large chunks or memory.  This can make
+vector instructions on CPUs more efficient, if dynamically allocated
+memory is aligned on larger-than-default byte boundaries.
+On most current systems, the malloc() implementation returns
+pointers that are aligned to 16-byte boundaries. Using SSE vector
+instructions efficiently, however, requires memory blocks being
+aligned on 64-byte boundaries.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
+
+Use a LAMMPS\_MEMALIGN value of 0 to disable using posix\_memalign()
+and revert to using the malloc() C-library function instead.  When
+compiling LAMMPS for Windows systems, malloc() will always be used
+and this setting ignored.
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
+
+Do not set -DLAMMPS\_MEMALIGN, if you want to have memory allocated
+with the malloc() function call instead. -DLAMMPS\_MEMALIGN **cannot**
+be used on Windows, as it does use different function calls for
+allocating aligned memory, that are not compatible with how LAMMPS
+manages its dynamical memory.
+
+
+----------
+
+
+.. _longlong:
+
+Workaround for long long integers
+------------------------------------------------
+
+If your system or MPI version does not recognize "long long" data
+types, the following setting will be needed.  It converts "long long"
+to a "long" data type, which should be the desired 8-byte integer on
+those systems:
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
+
+
+----------
+
+
+.. _exceptions:
+
+Exception handling when using LAMMPS as a library
+------------------------------------------------------------------
+
+This setting is useful when external codes drive LAMMPS as a library.
+With this option enabled LAMMPS errors do not kill the caller.
+Instead, the call stack is unwound and control returns to the caller,
+e.g. to Python.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_EXCEPTIONS
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build_windows.rst b/doc/src/Build_windows.rst
new file mode 100644
index 0000000000..fd96b37983
--- /dev/null
+++ b/doc/src/Build_windows.rst
@@ -0,0 +1,111 @@
+Notes for building LAMMPS on Windows
+====================================
+
+* :ref:`General remarks <generic>`
+* :ref:`Running Linux on Windows <linux>`
+* :ref:`Using GNU GCC ported to Windows <gnu>`
+* :ref:`Using a cross-compiler <cross>`
+
+
+----------
+
+
+.. _generic:
+
+General remarks
+-----------------------------
+
+LAMMPS is developed and tested primarily on Linux machines.  The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+.. _linux:
+
+Running Linux on Windows
+------------------------------------
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers).  If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see :doc:`this tutorial <Howto_bash>`
+
+.. _gnu:
+
+Using GNU GCC ported to Windows
+-----------------------------------------
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. Using CMake for this mode of compilation
+is untested and not likely to work.
+
+When compiling for Windows do **not** set the -DLAMMPS\_MEMALIGN define
+in the LMP\_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested.
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin.  If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS GitHub project.
+
+.. _cross:
+
+Using a cross-compiler
+----------------------------------
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows.  There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+with the cross-compiler environment on Fedora machines. A CMake preset
+selecting all packages compatible with this cross-compilation build
+is provided. You likely need to disable the GPU package unless you
+download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
+into your MinGW64 cross-compiler environment. The cross-compilation
+currently will only produce non-MPI serial binaries.
+
+Please keep in mind, though, that this only applies to compiling LAMMPS.
+Whether the resulting binaries do work correctly is no tested by the
+LAMMPS developers.  We instead rely on the feedback of the users
+of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
+issues to the best of our abilities if we become aware of them. However
+this is subject to time constraints and focus on HPC platforms.
+
+.. _native:
+
+Native Visual C++ support
+--------------------------------------
+
+Support for the Visual C++ compilers is currently not available. The
+CMake build system is capable of creating suitable a Visual Studio
+style build environment, but the LAMMPS code itself is not fully ported
+to support Visual C++. Volunteers to take on this task are welcome.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Commands.rst b/doc/src/Commands.rst
new file mode 100644
index 0000000000..f192d6a59d
--- /dev/null
+++ b/doc/src/Commands.rst
@@ -0,0 +1,29 @@
+Commands
+********
+
+These pages describe how a LAMMPS input script is formatted and the
+commands in it are used to define a LAMMPS simulation.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_input
+   Commands_parse
+   Commands_structure
+   Commands_category
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_all
+   Commands_fix
+   Commands_compute
+   Commands_pair
+   Commands_bond
+   Commands_kspace
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_removed
diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt
deleted file mode 100644
index bcbbe524a8..0000000000
--- a/doc/src/Commands.txt
+++ /dev/null
@@ -1,60 +0,0 @@
-"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Packages.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html#comm)
-
-:line
-
-Commands :h2
-
-These pages describe how a LAMMPS input script is formatted and the
-commands in it are used to define a LAMMPS simulation.
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   Commands_input
-   Commands_parse
-   Commands_structure
-   Commands_category
-
-.. toctree::
-   :maxdepth: 1
-
-   Commands_all
-   Commands_fix
-   Commands_compute
-   Commands_pair
-   Commands_bond
-   Commands_kspace
-
-.. toctree::
-   :maxdepth: 1
-
-   Commands_removed
-
-END_RST -->
-
-<!-- HTML_ONLY -->
-
-"LAMMPS input scripts"_Commands_input.html
-"Parsing rules for input scripts"_Commands_parse.html
-"Input script structure"_Commands_structure.html
-"Commands by category"_Commands_category.html :all(b)
-
-"General commands"_Commands_all.html
-"Fix commands"_Commands_fix.html
-"Compute commands"_Commands_compute.html
-"Pair commands"_Commands_pair.html
-"Bond, angle, dihedral, improper commands"_Commands_bond.html
-"KSpace solvers"_Commands_kspace.html  :all(b)
-
-"Removed commands and packages"_Commands_removed.html  :all(b)
-
-<!-- END_HTML_ONLY -->
-
diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst
new file mode 100644
index 0000000000..5ad8fff44c
--- /dev/null
+++ b/doc/src/Commands_all.rst
@@ -0,0 +1,141 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+General commands
+================
+
+An alphabetic list of all general LAMMPS commands.
+
+.. table_from_list::
+   :columns: 6
+
+   * :doc:`angle_coeff <angle_coeff>`
+   * :doc:`angle_style <angle_style>`
+   * :doc:`atom_modify <atom_modify>`
+   * :doc:`atom_style <atom_style>`
+   * :doc:`balance <balance>`
+   * :doc:`bond_coeff <bond_coeff>`
+   * :doc:`bond_style <bond_style>`
+   * :doc:`bond_write <bond_write>`
+   * :doc:`boundary <boundary>`
+   * :doc:`box <box>`
+   * :doc:`change_box <change_box>`
+   * :doc:`clear <clear>`
+   * :doc:`comm_modify <comm_modify>`
+   * :doc:`comm_style <comm_style>`
+   * :doc:`compute <compute>`
+   * :doc:`compute_modify <compute_modify>`
+   * :doc:`create_atoms <create_atoms>`
+   * :doc:`create_bonds <create_bonds>`
+   * :doc:`create_box <create_box>`
+   * :doc:`delete_atoms <delete_atoms>`
+   * :doc:`delete_bonds <delete_bonds>`
+   * :doc:`dielectric <dielectric>`
+   * :doc:`dihedral_coeff <dihedral_coeff>`
+   * :doc:`dihedral_style <dihedral_style>`
+   * :doc:`dimension <dimension>`
+   * :doc:`displace_atoms <displace_atoms>`
+   * :doc:`dump <dump>`
+   * :doc:`dump adios <dump_adios>`
+   * :doc:`dump image <dump_image>`
+   * :doc:`dump movie <dump_image>`
+   * :doc:`dump netcdf <dump_netcdf>`
+   * :doc:`dump netcdf/mpiio <dump_netcdf>`
+   * :doc:`dump vtk <dump_vtk>`
+   * :doc:`dump_modify <dump_modify>`
+   * :doc:`dynamical_matrix <dynamical_matrix>`
+   * :doc:`echo <echo>`
+   * :doc:`fix <fix>`
+   * :doc:`fix_modify <fix_modify>`
+   * :doc:`group <group>`
+   * :doc:`group2ndx <group2ndx>`
+   * :doc:`hyper <hyper>`
+   * :doc:`if <if>`
+   * :doc:`improper_coeff <improper_coeff>`
+   * :doc:`improper_style <improper_style>`
+   * :doc:`include <include>`
+   * :doc:`info <info>`
+   * :doc:`jump <jump>`
+   * :doc:`kim_init <kim_commands>`
+   * :doc:`kim_interactions <kim_commands>`
+   * :doc:`kim_param <kim_commands>`
+   * :doc:`kim_query <kim_commands>`
+   * :doc:`kspace_modify <kspace_modify>`
+   * :doc:`kspace_style <kspace_style>`
+   * :doc:`label <label>`
+   * :doc:`lattice <lattice>`
+   * :doc:`log <log>`
+   * :doc:`mass <mass>`
+   * :doc:`message <message>`
+   * :doc:`minimize <minimize>`
+   * :doc:`min_modify <min_modify>`
+   * :doc:`min_style <min_style>`
+   * :doc:`min_style spin <min_spin>`
+   * :doc:`molecule <molecule>`
+   * :doc:`ndx2group <group2ndx>`
+   * :doc:`neb <neb>`
+   * :doc:`neb/spin <neb_spin>`
+   * :doc:`neigh_modify <neigh_modify>`
+   * :doc:`neighbor <neighbor>`
+   * :doc:`newton <newton>`
+   * :doc:`next <next>`
+   * :doc:`package <package>`
+   * :doc:`pair_coeff <pair_coeff>`
+   * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_write <pair_write>`
+   * :doc:`partition <partition>`
+   * :doc:`prd <prd>`
+   * :doc:`print <print>`
+   * :doc:`processors <processors>`
+   * :doc:`python <python>`
+   * :doc:`quit <quit>`
+   * :doc:`read_data <read_data>`
+   * :doc:`read_dump <read_dump>`
+   * :doc:`read_restart <read_restart>`
+   * :doc:`region <region>`
+   * :doc:`replicate <replicate>`
+   * :doc:`rerun <rerun>`
+   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_timestep <reset_timestep>`
+   * :doc:`restart <restart>`
+   * :doc:`run <run>`
+   * :doc:`run_style <run_style>`
+   * :doc:`server <server>`
+   * :doc:`set <set>`
+   * :doc:`shell <shell>`
+   * :doc:`special_bonds <special_bonds>`
+   * :doc:`suffix <suffix>`
+   * :doc:`tad <tad>`
+   * :doc:`temper <temper>`
+   * :doc:`temper/grem <temper_grem>`
+   * :doc:`temper/npt <temper_npt>`
+   * :doc:`thermo <thermo>`
+   * :doc:`thermo_modify <thermo_modify>`
+   * :doc:`thermo_style <thermo_style>`
+   * :doc:`third_order <third_order>`
+   * :doc:`timer <timer>`
+   * :doc:`timestep <timestep>`
+   * :doc:`uncompute <uncompute>`
+   * :doc:`undump <undump>`
+   * :doc:`unfix <unfix>`
+   * :doc:`units <units>`
+   * :doc:`variable <variable>`
+   * :doc:`velocity <velocity>`
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`
+   *
+   *
+   *
+   *
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
deleted file mode 100644
index d0d7657c07..0000000000
--- a/doc/src/Commands_all.txt
+++ /dev/null
@@ -1,138 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-General commands :h3
-
-An alphabetic list of all general LAMMPS commands.
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"clear"_clear.html,
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"create_box"_create_box.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"dimension"_dimension.html,
-"displace_atoms"_displace_atoms.html,
-"dump"_dump.html,
-"dump adios"_dump_adios.html,
-"dump image"_dump_image.html,
-"dump movie"_dump_image.html,
-"dump netcdf"_dump_netcdf.html,
-"dump netcdf/mpiio"_dump_netcdf.html,
-"dump vtk"_dump_vtk.html,
-"dump_modify"_dump_modify.html,
-"dynamical_matrix"_dynamical_matrix.html,
-"echo"_echo.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"group"_group.html,
-"group2ndx"_group2ndx.html,
-"hyper"_hyper.html,
-"if"_if.html,
-"info"_info.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"include"_include.html,
-"jump"_jump.html,
-"kim_init"_kim_commands.html,
-"kim_interactions"_kim_commands.html,
-"kim_query"_kim_commands.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"label"_label.html,
-"lattice"_lattice.html,
-"log"_log.html,
-"mass"_mass.html,
-"message"_message.html,
-"minimize"_minimize.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"min_style spin"_min_spin.html,
-"molecule"_molecule.html,
-"ndx2group"_group2ndx.html,
-"neb"_neb.html,
-"neb/spin"_neb_spin.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"newton"_newton.html,
-"next"_next.html,
-"package"_package.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"partition"_partition.html,
-"prd"_prd.html,
-"print"_print.html,
-"processors"_processors.html,
-"python"_python.html,
-"quit"_quit.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"region"_region.html,
-"replicate"_replicate.html,
-"rerun"_rerun.html,
-"reset_ids"_reset_ids.html,
-"reset_timestep"_reset_timestep.html,
-"restart"_restart.html,
-"run"_run.html,
-"run_style"_run_style.html,
-"server"_server.html,
-"set"_set.html,
-"shell"_shell.html,
-"special_bonds"_special_bonds.html,
-"suffix"_suffix.html,
-"tad"_tad.html,
-"temper"_temper.html,
-"temper/grem"_temper_grem.html,
-"temper/npt"_temper_npt.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html,
-"uncompute"_uncompute.html,
-"undump"_undump.html,
-"unfix"_unfix.html,
-"units"_units.html,
-"variable"_variable.html,
-"velocity"_velocity.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
new file mode 100644
index 0000000000..27ff2d19da
--- /dev/null
+++ b/doc/src/Commands_bond.rst
@@ -0,0 +1,165 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+.. _bond:
+
+Bond_style potentials
+=====================
+
+All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <bond_none>`
+   * :doc:`zero <bond_zero>`
+   * :doc:`hybrid <bond_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <bond_class2>`
+   * :doc:`fene (iko) <bond_fene>`
+   * :doc:`fene/expand (o) <bond_fene_expand>`
+   * :doc:`gromos (o) <bond_gromos>`
+   * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
+   * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`mm3 <bond_mm3>`
+   * :doc:`morse (o) <bond_morse>`
+   * :doc:`nonlinear (o) <bond_nonlinear>`
+   * :doc:`oxdna/fene <bond_oxdna>`
+   * :doc:`oxdna2/fene <bond_oxdna>`
+   * :doc:`oxrna2/fene <bond_oxdna>`
+   * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`table (o) <bond_table>`
+   *
+
+.. _angle:
+
+Angle_style potentials
+======================
+
+All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <angle_none>`
+   * :doc:`zero <angle_zero>`
+   * :doc:`hybrid <angle_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <angle_charmm>`
+   * :doc:`class2 (ko) <angle_class2>`
+   * :doc:`class2/p6 <angle_class2>`
+   * :doc:`cosine (ko) <angle_cosine>`
+   * :doc:`cosine/buck6d <angle_cosine_buck6d>`
+   * :doc:`cosine/delta (o) <angle_cosine_delta>`
+   * :doc:`cosine/periodic (o) <angle_cosine_periodic>`
+   * :doc:`cosine/shift (o) <angle_cosine_shift>`
+   * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
+   * :doc:`cosine/squared (o) <angle_cosine_squared>`
+   * :doc:`cross <angle_cross>`
+   * :doc:`dipole (o) <angle_dipole>`
+   * :doc:`fourier (o) <angle_fourier>`
+   * :doc:`fourier/simple (o) <angle_fourier_simple>`
+   * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`mm3 <angle_mm3>`
+   * :doc:`quartic (o) <angle_quartic>`
+   * :doc:`sdk (o) <angle_sdk>`
+   * :doc:`table (o) <angle_table>`
+   *
+
+.. _dihedral:
+
+Dihedral_style potentials
+=========================
+
+All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <dihedral_none>`
+   * :doc:`zero <dihedral_zero>`
+   * :doc:`hybrid <dihedral_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <dihedral_charmm>`
+   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`class2 (ko) <dihedral_class2>`
+   * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
+   * :doc:`fourier (io) <dihedral_fourier>`
+   * :doc:`harmonic (iko) <dihedral_harmonic>`
+   * :doc:`helix (o) <dihedral_helix>`
+   * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
+   * :doc:`nharmonic (o) <dihedral_nharmonic>`
+   * :doc:`opls (iko) <dihedral_opls>`
+   * :doc:`quadratic (o) <dihedral_quadratic>`
+   * :doc:`spherical <dihedral_spherical>`
+   * :doc:`table (o) <dihedral_table>`
+   * :doc:`table/cut <dihedral_table_cut>`
+   *
+   *
+
+.. _improper:
+
+Improper_style potentials
+=========================
+
+All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <improper_none>`
+   * :doc:`zero <improper_zero>`
+   * :doc:`hybrid <improper_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <improper_class2>`
+   * :doc:`cossq (o) <improper_cossq>`
+   * :doc:`cvff (io) <improper_cvff>`
+   * :doc:`distance <improper_distance>`
+   * :doc:`distharm <improper_distharm>`
+   * :doc:`fourier (o) <improper_fourier>`
+   * :doc:`harmonic (iko) <improper_harmonic>`
+   * :doc:`inversion/harmonic <improper_inversion_harmonic>`
+   * :doc:`ring (o) <improper_ring>`
+   * :doc:`sqdistharm <improper_sqdistharm>`
+   * :doc:`umbrella (o) <improper_umbrella>`
+   *
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
deleted file mode 100644
index aecbf4cca0..0000000000
--- a/doc/src/Commands_bond.txt
+++ /dev/null
@@ -1,148 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html#bond,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-Bond, angle, dihedral, and improper commands :h3
-
-:line
-
-Bond_style potentials :h3,link(bond)
-
-All LAMMPS "bond_style"_bond_style.html commands.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_bond_none.html,
-"zero"_bond_zero.html,
-"hybrid"_bond_hybrid.html,
-,
-,
-,
-,
-,
-"class2 (ko)"_bond_class2.html,
-"fene (iko)"_bond_fene.html,
-"fene/expand (o)"_bond_fene_expand.html,
-"gromos (o)"_bond_gromos.html,
-"harmonic (iko)"_bond_harmonic.html,
-"harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"mm3"_bond_mm3.html,
-"morse (o)"_bond_morse.html,
-"nonlinear (o)"_bond_nonlinear.html,
-"oxdna/fene"_bond_oxdna.html,
-"oxdna2/fene"_bond_oxdna.html,
-"quartic (o)"_bond_quartic.html,
-"table (o)"_bond_table.html :tb(c=4,ea=c)
-
-:line
-
-Angle_style potentials :h3,link(angle)
-
-All LAMMPS "angle_style"_angle_style.html commands.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_angle_none.html,
-"zero"_angle_zero.html,
-"hybrid"_angle_hybrid.html,
-,
-,
-,
-,
-,
-"charmm (iko)"_angle_charmm.html,
-"class2 (ko)"_angle_class2.html,
-"class2/p6"_angle_class2.html,
-"cosine (ko)"_angle_cosine.html,
-"cosine/buck6d"_angle_cosine_buck6d.html,
-"cosine/delta (o)"_angle_cosine_delta.html,
-"cosine/periodic (o)"_angle_cosine_periodic.html,
-"cosine/shift (o)"_angle_cosine_shift.html,
-"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
-"cosine/squared (o)"_angle_cosine_squared.html,
-"cross"_angle_cross.html,
-"dipole (o)"_angle_dipole.html,
-"fourier (o)"_angle_fourier.html,
-"fourier/simple (o)"_angle_fourier_simple.html,
-"harmonic (iko)"_angle_harmonic.html,
-"mm3"_angle_mm3.html,
-"quartic (o)"_angle_quartic.html,
-"sdk (o)"_angle_sdk.html,
-"table (o)"_angle_table.html :tb(c=4,ea=c)
-
-:line
-
-Dihedral_style potentials :h3,link(dihedral)
-
-All LAMMPS "dihedral_style"_dihedral_style.html commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_dihedral_none.html,
-"zero"_dihedral_zero.html,
-"hybrid"_dihedral_hybrid.html,
-,
-,
-,
-,
-,
-"charmm (iko)"_dihedral_charmm.html,
-"charmmfsw"_dihedral_charmm.html,
-"class2 (ko)"_dihedral_class2.html,
-"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (io)"_dihedral_fourier.html,
-"harmonic (iko)"_dihedral_harmonic.html,
-"helix (o)"_dihedral_helix.html,
-"multi/harmonic (o)"_dihedral_multi_harmonic.html,
-"nharmonic (o)"_dihedral_nharmonic.html,
-"opls (iko)"_dihedral_opls.html,
-"quadratic (o)"_dihedral_quadratic.html,
-"spherical"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html,
-"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
-
-:line
-
-Improper_style potentials :h3,link(improper)
-
-All LAMMPS "improper_style"_improper_style.html commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_improper_none.html,
-"zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html,
-,
-,
-,
-,
-,
-"class2 (ko)"_improper_class2.html,
-"cossq (o)"_improper_cossq.html,
-"cvff (io)"_improper_cvff.html,
-"distance"_improper_distance.html,
-"distharm"_improper_distharm.html,
-"fourier (o)"_improper_fourier.html,
-"harmonic (iko)"_improper_harmonic.html,
-"inversion/harmonic"_improper_inversion_harmonic.html,
-"ring (o)"_improper_ring.html,
-"sqdistharm"_improper_sqdistharm.html,
-"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst
new file mode 100644
index 0000000000..b1b0e0cadc
--- /dev/null
+++ b/doc/src/Commands_category.rst
@@ -0,0 +1,132 @@
+Commands by category
+====================
+
+This page lists most of the LAMMPS commands, grouped by category.  The
+:doc:`General commands <Commands_all>` doc page lists all general commands
+alphabetically.  Style options for entries like fix, compute, pair etc.
+have their own pages where they are listed alphabetically.
+
+Initialization:
+
+* :doc:`newton <newton>`,
+* :doc:`package <package>`,
+* :doc:`processors <processors>`,
+* :doc:`suffix <suffix>`,
+* :doc:`units <units>`
+
+Setup simulation box:
+
+* :doc:`boundary <boundary>`,
+* :doc:`box <box>`,
+* :doc:`change\_box <change_box>`,
+* :doc:`create\_box <create_box>`,
+* :doc:`dimension <dimension>`,
+* :doc:`lattice <lattice>`,
+* :doc:`region <region>`
+
+Setup atoms:
+
+* :doc:`atom\_modify <atom_modify>`,
+* :doc:`atom\_style <atom_style>`,
+* :doc:`balance <balance>`,
+* :doc:`create\_atoms <create_atoms>`,
+* :doc:`create\_bonds <create_bonds>`,
+* :doc:`delete\_atoms <delete_atoms>`,
+* :doc:`delete\_bonds <delete_bonds>`,
+* :doc:`displace\_atoms <displace_atoms>`,
+* :doc:`group <group>`,
+* :doc:`mass <mass>`,
+* :doc:`molecule <molecule>`,
+* :doc:`read\_data <read_data>`,
+* :doc:`read\_dump <read_dump>`,
+* :doc:`read\_restart <read_restart>`,
+* :doc:`replicate <replicate>`,
+* :doc:`set <set>`,
+* :doc:`velocity <velocity>`
+
+Force fields:
+
+* :doc:`angle\_coeff <angle_coeff>`,
+* :doc:`angle\_style <angle_style>`,
+* :doc:`bond\_coeff <bond_coeff>`,
+* :doc:`bond\_style <bond_style>`,
+* :doc:`bond\_write <bond_write>`,
+* :doc:`dielectric <dielectric>`,
+* :doc:`dihedral\_coeff <dihedral_coeff>`,
+* :doc:`dihedral\_style <dihedral_style>`,
+* :doc:`improper\_coeff <improper_coeff>`,
+* :doc:`improper\_style <improper_style>`,
+* :doc:`kspace\_modify <kspace_modify>`,
+* :doc:`kspace\_style <kspace_style>`,
+* :doc:`pair\_coeff <pair_coeff>`,
+* :doc:`pair\_modify <pair_modify>`,
+* :doc:`pair\_style <pair_style>`,
+* :doc:`pair\_write <pair_write>`,
+* :doc:`special\_bonds <special_bonds>`
+
+Settings:
+
+* :doc:`comm\_modify <comm_modify>`,
+* :doc:`comm\_style <comm_style>`,
+* :doc:`info <info>`,
+* :doc:`min\_modify <min_modify>`,
+* :doc:`min\_style <min_style>`,
+* :doc:`neigh\_modify <neigh_modify>`,
+* :doc:`neighbor <neighbor>`,
+* :doc:`partition <partition>`,
+* :doc:`reset\_timestep <reset_timestep>`,
+* :doc:`run\_style <run_style>`,
+* :doc:`timer <timer>`,
+* :doc:`timestep <timestep>`
+
+Operations within timestepping (fixes) and diagnostics (computes):
+
+* :doc:`compute <compute>`,
+* :doc:`compute\_modify <compute_modify>`,
+* :doc:`fix <fix>`,
+* :doc:`fix\_modify <fix_modify>`,
+* :doc:`uncompute <uncompute>`,
+* :doc:`unfix <unfix>`
+
+Output:
+
+* :doc:`dump image <dump_image>`,
+* :doc:`dump movie <dump_image>`,
+* :doc:`dump <dump>`,
+* :doc:`dump\_modify <dump_modify>`,
+* :doc:`restart <restart>`,
+* :doc:`thermo <thermo>`,
+* :doc:`thermo\_modify <thermo_modify>`,
+* :doc:`thermo\_style <thermo_style>`,
+* :doc:`undump <undump>`,
+* :doc:`write\_coeff <write_coeff>`,
+* :doc:`write\_data <write_data>`,
+* :doc:`write\_dump <write_dump>`,
+* :doc:`write\_restart <write_restart>`
+
+Actions:
+
+* :doc:`minimize <minimize>`,
+* :doc:`neb <neb>`,
+* :doc:`neb\_spin <neb_spin>`,
+* :doc:`prd <prd>`,
+* :doc:`rerun <rerun>`,
+* :doc:`run <run>`,
+* :doc:`tad <tad>`,
+* :doc:`temper <temper>`
+
+Input script control:
+
+* :doc:`clear <clear>`,
+* :doc:`echo <echo>`,
+* :doc:`if <if>`,
+* :doc:`include <include>`,
+* :doc:`jump <jump>`,
+* :doc:`label <label>`,
+* :doc:`log <log>`,
+* :doc:`next <next>`,
+* :doc:`print <print>`,
+* :doc:`python <python>`,
+* :doc:`quit <quit>`,
+* :doc:`shell <shell>`,
+* :doc:`variable <variable>`
diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt
deleted file mode 100644
index 14a328b227..0000000000
--- a/doc/src/Commands_category.txt
+++ /dev/null
@@ -1,141 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Commands by category :h3
-
-This page lists most of the LAMMPS commands, grouped by category.  The
-"General commands"_Commands_all.html doc page lists all general commands
-alphabetically.  Style options for entries like fix, compute, pair etc.
-have their own pages where they are listed alphabetically.
-
-Initialization:
-
-"newton"_newton.html,
-"package"_package.html,
-"processors"_processors.html,
-"suffix"_suffix.html,
-"units"_units.html :ul
-
-Setup simulation box:
-
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"create_box"_create_box.html,
-"dimension"_dimension.html,
-"lattice"_lattice.html,
-"region"_region.html :ul
-
-Setup atoms:
-
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html,
-"group"_group.html,
-"mass"_mass.html,
-"molecule"_molecule.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"replicate"_replicate.html,
-"set"_set.html,
-"velocity"_velocity.html :ul
-
-Force fields:
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"special_bonds"_special_bonds.html :ul
-
-Settings:
-
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"info"_info.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"partition"_partition.html,
-"reset_timestep"_reset_timestep.html,
-"run_style"_run_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html :ul
-
-Operations within timestepping (fixes) and diagnostics (computes):
-
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"uncompute"_uncompute.html,
-"unfix"_unfix.html :ul
-
-Output:
-
-"dump image"_dump_image.html,
-"dump movie"_dump_image.html,
-"dump"_dump.html,
-"dump_modify"_dump_modify.html,
-"restart"_restart.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"undump"_undump.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :ul
-
-Actions:
-
-"minimize"_minimize.html,
-"neb"_neb.html,
-"neb_spin"_neb_spin.html,
-"prd"_prd.html,
-"rerun"_rerun.html,
-"run"_run.html,
-"tad"_tad.html,
-"temper"_temper.html :ul
-
-Input script control:
-
-"clear"_clear.html,
-"echo"_echo.html,
-"if"_if.html,
-"include"_include.html,
-"jump"_jump.html,
-"label"_label.html,
-"log"_log.html,
-"next"_next.html,
-"print"_print.html,
-"python"_python.html,
-"quit"_quit.html,
-"shell"_shell.html,
-"variable"_variable.html :ul
-
diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
new file mode 100644
index 0000000000..01943ac803
--- /dev/null
+++ b/doc/src/Commands_compute.rst
@@ -0,0 +1,168 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+Compute commands
+================
+
+An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
+Some styles have accelerated versions.  This is indicated by
+additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+
+.. table_from_list::
+   :columns: 6
+
+   * :doc:`ackland/atom <compute_ackland_atom>`
+   * :doc:`adf <compute_adf>`
+   * :doc:`aggregate/atom <compute_cluster_atom>`
+   * :doc:`angle <compute_angle>`
+   * :doc:`angle/local <compute_angle_local>`
+   * :doc:`angmom/chunk <compute_angmom_chunk>`
+   * :doc:`basal/atom <compute_basal_atom>`
+   * :doc:`body/local <compute_body_local>`
+   * :doc:`bond <compute_bond>`
+   * :doc:`bond/local <compute_bond_local>`
+   * :doc:`centro/atom <compute_centro_atom>`
+   * :doc:`centroid/stress/atom <compute_stress_atom>`
+   * :doc:`chunk/atom <compute_chunk_atom>`
+   * :doc:`chunk/spread/atom <compute_chunk_spread_atom>`
+   * :doc:`cluster/atom <compute_cluster_atom>`
+   * :doc:`cna/atom <compute_cna_atom>`
+   * :doc:`cnp/atom <compute_cnp_atom>`
+   * :doc:`com <compute_com>`
+   * :doc:`com/chunk <compute_com_chunk>`
+   * :doc:`contact/atom <compute_contact_atom>`
+   * :doc:`coord/atom <compute_coord_atom>`
+   * :doc:`damage/atom <compute_damage_atom>`
+   * :doc:`dihedral <compute_dihedral>`
+   * :doc:`dihedral/local <compute_dihedral_local>`
+   * :doc:`dilatation/atom <compute_dilatation_atom>`
+   * :doc:`dipole/chunk <compute_dipole_chunk>`
+   * :doc:`displace/atom <compute_displace_atom>`
+   * :doc:`dpd <compute_dpd>`
+   * :doc:`dpd/atom <compute_dpd_atom>`
+   * :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
+   * :doc:`entropy/atom <compute_entropy_atom>`
+   * :doc:`erotate/asphere <compute_erotate_asphere>`
+   * :doc:`erotate/rigid <compute_erotate_rigid>`
+   * :doc:`erotate/sphere <compute_erotate_sphere>`
+   * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
+   * :doc:`event/displace <compute_event_displace>`
+   * :doc:`fep <compute_fep>`
+   * :doc:`force/tally <compute_tally>`
+   * :doc:`fragment/atom <compute_cluster_atom>`
+   * :doc:`global/atom <compute_global_atom>`
+   * :doc:`group/group <compute_group_group>`
+   * :doc:`gyration <compute_gyration>`
+   * :doc:`gyration/chunk <compute_gyration_chunk>`
+   * :doc:`gyration/shape <compute_gyration_shape>`
+   * :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
+   * :doc:`heat/flux <compute_heat_flux>`
+   * :doc:`heat/flux/tally <compute_tally>`
+   * :doc:`hexorder/atom <compute_hexorder_atom>`
+   * :doc:`hma <compute_hma>`
+   * :doc:`improper <compute_improper>`
+   * :doc:`improper/local <compute_improper_local>`
+   * :doc:`inertia/chunk <compute_inertia_chunk>`
+   * :doc:`ke <compute_ke>`
+   * :doc:`ke/atom <compute_ke_atom>`
+   * :doc:`ke/atom/eff <compute_ke_atom_eff>`
+   * :doc:`ke/eff <compute_ke_eff>`
+   * :doc:`ke/rigid <compute_ke_rigid>`
+   * :doc:`meso/e/atom <compute_meso_e_atom>`
+   * :doc:`meso/rho/atom <compute_meso_rho_atom>`
+   * :doc:`meso/t/atom <compute_meso_t_atom>`
+   * :doc:`momentum <compute_momentum>`
+   * :doc:`msd <compute_msd>`
+   * :doc:`msd/chunk <compute_msd_chunk>`
+   * :doc:`msd/nongauss <compute_msd_nongauss>`
+   * :doc:`omega/chunk <compute_omega_chunk>`
+   * :doc:`orientorder/atom <compute_orientorder_atom>`
+   * :doc:`pair <compute_pair>`
+   * :doc:`pair/local <compute_pair_local>`
+   * :doc:`pe <compute_pe>`
+   * :doc:`pe/atom <compute_pe_atom>`
+   * :doc:`pe/mol/tally <compute_tally>`
+   * :doc:`pe/tally <compute_tally>`
+   * :doc:`plasticity/atom <compute_plasticity_atom>`
+   * :doc:`pressure <compute_pressure>`
+   * :doc:`pressure/cylinder <compute_pressure_cylinder>`
+   * :doc:`pressure/uef <compute_pressure_uef>`
+   * :doc:`property/atom <compute_property_atom>`
+   * :doc:`property/chunk <compute_property_chunk>`
+   * :doc:`property/local <compute_property_local>`
+   * :doc:`ptm/atom <compute_ptm_atom>`
+   * :doc:`rdf <compute_rdf>`
+   * :doc:`reduce <compute_reduce>`
+   * :doc:`reduce/chunk <compute_reduce_chunk>`
+   * :doc:`reduce/region <compute_reduce>`
+   * :doc:`rigid/local <compute_rigid_local>`
+   * :doc:`saed <compute_saed>`
+   * :doc:`slice <compute_slice>`
+   * :doc:`smd/contact/radius <compute_smd_contact_radius>`
+   * :doc:`smd/damage <compute_smd_damage>`
+   * :doc:`smd/hourglass/error <compute_smd_hourglass_error>`
+   * :doc:`smd/internal/energy <compute_smd_internal_energy>`
+   * :doc:`smd/plastic/strain <compute_smd_plastic_strain>`
+   * :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>`
+   * :doc:`smd/rho <compute_smd_rho>`
+   * :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`
+   * :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`
+   * :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>`
+   * :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`
+   * :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`
+   * :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
+   * :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
+   * :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
+   * :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
+   * :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
+   * :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
+   * :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`
+   * :doc:`smd/vol <compute_smd_vol>`
+   * :doc:`snap <compute_sna_atom>`
+   * :doc:`sna/atom <compute_sna_atom>`
+   * :doc:`snad/atom <compute_sna_atom>`
+   * :doc:`snav/atom <compute_sna_atom>`
+   * :doc:`spin <compute_spin>`
+   * :doc:`stress/atom <compute_stress_atom>`
+   * :doc:`stress/mop <compute_stress_mop>`
+   * :doc:`stress/mop/profile <compute_stress_mop>`
+   * :doc:`stress/tally <compute_tally>`
+   * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
+   * :doc:`temp (k) <compute_temp>`
+   * :doc:`temp/asphere <compute_temp_asphere>`
+   * :doc:`temp/body <compute_temp_body>`
+   * :doc:`temp/chunk <compute_temp_chunk>`
+   * :doc:`temp/com <compute_temp_com>`
+   * :doc:`temp/cs <compute_temp_cs>`
+   * :doc:`temp/deform <compute_temp_deform>`
+   * :doc:`temp/deform/eff <compute_temp_deform_eff>`
+   * :doc:`temp/drude <compute_temp_drude>`
+   * :doc:`temp/eff <compute_temp_eff>`
+   * :doc:`temp/partial <compute_temp_partial>`
+   * :doc:`temp/profile <compute_temp_profile>`
+   * :doc:`temp/ramp <compute_temp_ramp>`
+   * :doc:`temp/region <compute_temp_region>`
+   * :doc:`temp/region/eff <compute_temp_region_eff>`
+   * :doc:`temp/rotate <compute_temp_rotate>`
+   * :doc:`temp/sphere <compute_temp_sphere>`
+   * :doc:`temp/uef <compute_temp_uef>`
+   * :doc:`ti <compute_ti>`
+   * :doc:`torque/chunk <compute_torque_chunk>`
+   * :doc:`vacf <compute_vacf>`
+   * :doc:`vcm/chunk <compute_vcm_chunk>`
+   * :doc:`voronoi/atom <compute_voronoi_atom>`
+   * :doc:`xrd <compute_xrd>`
+   *
+   *
+   *
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
deleted file mode 100644
index e035eb8431..0000000000
--- a/doc/src/Commands_compute.txt
+++ /dev/null
@@ -1,163 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-Compute commands :h3
-
-An alphabetic list of all LAMMPS "compute"_compute.html commands.
-Some styles have accelerated versions.  This is indicated by
-additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"ackland/atom"_compute_ackland_atom.html,
-"adf"_compute_adf.html,
-"aggregate/atom"_compute_cluster_atom.html,
-"angle"_compute_angle.html,
-"angle/local"_compute_angle_local.html,
-"angmom/chunk"_compute_angmom_chunk.html,
-"basal/atom"_compute_basal_atom.html,
-"body/local"_compute_body_local.html,
-"bond"_compute_bond.html,
-"bond/local"_compute_bond_local.html,
-"centro/atom"_compute_centro_atom.html,
-"chunk/atom"_compute_chunk_atom.html,
-"chunk/spread/atom"_compute_chunk_spread_atom.html,
-"cluster/atom"_compute_cluster_atom.html,
-"cna/atom"_compute_cna_atom.html,
-"cnp/atom"_compute_cnp_atom.html,
-"com"_compute_com.html,
-"com/chunk"_compute_com_chunk.html,
-"contact/atom"_compute_contact_atom.html,
-"coord/atom"_compute_coord_atom.html,
-"damage/atom"_compute_damage_atom.html,
-"dihedral"_compute_dihedral.html,
-"dihedral/local"_compute_dihedral_local.html,
-"dilatation/atom"_compute_dilatation_atom.html,
-"dipole/chunk"_compute_dipole_chunk.html,
-"displace/atom"_compute_displace_atom.html,
-"dpd"_compute_dpd.html,
-"dpd/atom"_compute_dpd_atom.html,
-"edpd/temp/atom"_compute_edpd_temp_atom.html,
-"entropy/atom"_compute_entropy_atom.html,
-"erotate/asphere"_compute_erotate_asphere.html,
-"erotate/rigid"_compute_erotate_rigid.html,
-"erotate/sphere"_compute_erotate_sphere.html,
-"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
-"event/displace"_compute_event_displace.html,
-"fep"_compute_fep.html,
-"force/tally"_compute_tally.html,
-"fragment/atom"_compute_cluster_atom.html,
-"global/atom"_compute_global_atom.html,
-"group/group"_compute_group_group.html,
-"gyration"_compute_gyration.html,
-"gyration/chunk"_compute_gyration_chunk.html,
-"gyration/shape"_compute_gyration_shape.html,
-"heat/flux"_compute_heat_flux.html,
-"heat/flux/tally"_compute_tally.html,
-"hexorder/atom"_compute_hexorder_atom.html,
-"improper"_compute_improper.html,
-"improper/local"_compute_improper_local.html,
-"inertia/chunk"_compute_inertia_chunk.html,
-"ke"_compute_ke.html,
-"ke/atom"_compute_ke_atom.html,
-"ke/atom/eff"_compute_ke_atom_eff.html,
-"ke/eff"_compute_ke_eff.html,
-"ke/rigid"_compute_ke_rigid.html,
-"meso/e/atom"_compute_meso_e_atom.html,
-"meso/rho/atom"_compute_meso_rho_atom.html,
-"meso/t/atom"_compute_meso_t_atom.html,
-"momentum"_compute_momentum.html,
-"msd"_compute_msd.html,
-"msd/chunk"_compute_msd_chunk.html,
-"msd/nongauss"_compute_msd_nongauss.html,
-"omega/chunk"_compute_omega_chunk.html,
-"orientorder/atom"_compute_orientorder_atom.html,
-"pair"_compute_pair.html,
-"pair/local"_compute_pair_local.html,
-"pe"_compute_pe.html,
-"pe/atom"_compute_pe_atom.html,
-"pe/mol/tally"_compute_tally.html,
-"pe/tally"_compute_tally.html,
-"plasticity/atom"_compute_plasticity_atom.html,
-"pressure"_compute_pressure.html,
-"pressure/cylinder"_compute_pressure_cylinder.html,
-"pressure/uef"_compute_pressure_uef.html,
-"property/atom"_compute_property_atom.html,
-"property/chunk"_compute_property_chunk.html,
-"property/local"_compute_property_local.html,
-"ptm/atom"_compute_ptm_atom.html,
-"rdf"_compute_rdf.html,
-"reduce"_compute_reduce.html,
-"reduce/chunk"_compute_reduce_chunk.html,
-"reduce/region"_compute_reduce.html,
-"rigid/local"_compute_rigid_local.html,
-"saed"_compute_saed.html,
-"slice"_compute_slice.html,
-"smd/contact/radius"_compute_smd_contact_radius.html,
-"smd/damage"_compute_smd_damage.html,
-"smd/hourglass/error"_compute_smd_hourglass_error.html,
-"smd/internal/energy"_compute_smd_internal_energy.html,
-"smd/plastic/strain"_compute_smd_plastic_strain.html,
-"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
-"smd/rho"_compute_smd_rho.html,
-"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
-"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
-"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
-"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
-"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
-"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
-"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
-"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
-"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
-"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
-"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
-"smd/vol"_compute_smd_vol.html,
-"sna/atom"_compute_sna_atom.html,
-"snad/atom"_compute_sna_atom.html,
-"snav/atom"_compute_sna_atom.html,
-"spin"_compute_spin.html,
-"stress/atom"_compute_stress_atom.html,
-"stress/mop"_compute_stress_mop.html,
-"stress/mop/profile"_compute_stress_mop.html,
-"stress/tally"_compute_tally.html,
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
-"temp (k)"_compute_temp.html,
-"temp/asphere"_compute_temp_asphere.html,
-"temp/body"_compute_temp_body.html,
-"temp/chunk"_compute_temp_chunk.html,
-"temp/com"_compute_temp_com.html,
-"temp/cs"_compute_temp_cs.html,
-"temp/deform"_compute_temp_deform.html,
-"temp/deform/eff"_compute_temp_deform_eff.html,
-"temp/drude"_compute_temp_drude.html,
-"temp/eff"_compute_temp_eff.html,
-"temp/partial"_compute_temp_partial.html,
-"temp/profile"_compute_temp_profile.html,
-"temp/ramp"_compute_temp_ramp.html,
-"temp/region"_compute_temp_region.html,
-"temp/region/eff"_compute_temp_region_eff.html,
-"temp/rotate"_compute_temp_rotate.html,
-"temp/sphere"_compute_temp_sphere.html,
-"temp/uef"_compute_temp_uef.html,
-"ti"_compute_ti.html,
-"torque/chunk"_compute_torque_chunk.html,
-"vacf"_compute_vacf.html,
-"vcm/chunk"_compute_vcm_chunk.html,
-"voronoi/atom"_compute_voronoi_atom.html,
-"xrd"_compute_xrd.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
new file mode 100644
index 0000000000..9584cbf64f
--- /dev/null
+++ b/doc/src/Commands_fix.rst
@@ -0,0 +1,240 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+Fix commands
+============
+
+An alphabetic list of all LAMMPS :doc:`fix <fix>` commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 6
+
+   * :doc:`adapt <fix_adapt>`
+   * :doc:`adapt/fep <fix_adapt_fep>`
+   * :doc:`addforce <fix_addforce>`
+   * :doc:`addtorque <fix_addtorque>`
+   * :doc:`append/atoms <fix_append_atoms>`
+   * :doc:`atc <fix_atc>`
+   * :doc:`atom/swap <fix_atom_swap>`
+   * :doc:`ave/atom <fix_ave_atom>`
+   * :doc:`ave/chunk <fix_ave_chunk>`
+   * :doc:`ave/correlate <fix_ave_correlate>`
+   * :doc:`ave/correlate/long <fix_ave_correlate_long>`
+   * :doc:`ave/histo <fix_ave_histo>`
+   * :doc:`ave/histo/weight <fix_ave_histo>`
+   * :doc:`ave/time <fix_ave_time>`
+   * :doc:`aveforce <fix_aveforce>`
+   * :doc:`balance <fix_balance>`
+   * :doc:`bocs <fix_bocs>`
+   * :doc:`bond/break <fix_bond_break>`
+   * :doc:`bond/create <fix_bond_create>`
+   * :doc:`bond/react <fix_bond_react>`
+   * :doc:`bond/swap <fix_bond_swap>`
+   * :doc:`box/relax <fix_box_relax>`
+   * :doc:`client/md <fix_client_md>`
+   * :doc:`cmap <fix_cmap>`
+   * :doc:`colvars <fix_colvars>`
+   * :doc:`controller <fix_controller>`
+   * :doc:`deform (k) <fix_deform>`
+   * :doc:`deposit <fix_deposit>`
+   * :doc:`dpd/energy (k) <fix_dpd_energy>`
+   * :doc:`drag <fix_drag>`
+   * :doc:`drude <fix_drude>`
+   * :doc:`drude/transform/direct <fix_drude_transform>`
+   * :doc:`drude/transform/inverse <fix_drude_transform>`
+   * :doc:`dt/reset <fix_dt_reset>`
+   * :doc:`edpd/source <fix_dpd_source>`
+   * :doc:`efield <fix_efield>`
+   * :doc:`ehex <fix_ehex>`
+   * :doc:`electron/stopping <fix_electron_stopping>`
+   * :doc:`enforce2d (k) <fix_enforce2d>`
+   * :doc:`eos/cv <fix_eos_cv>`
+   * :doc:`eos/table <fix_eos_table>`
+   * :doc:`eos/table/rx (k) <fix_eos_table_rx>`
+   * :doc:`evaporate <fix_evaporate>`
+   * :doc:`external <fix_external>`
+   * :doc:`ffl <fix_ffl>`
+   * :doc:`filter/corotate <fix_filter_corotate>`
+   * :doc:`flow/gauss <fix_flow_gauss>`
+   * :doc:`freeze (k) <fix_freeze>`
+   * :doc:`gcmc <fix_gcmc>`
+   * :doc:`gld <fix_gld>`
+   * :doc:`gle <fix_gle>`
+   * :doc:`gravity (ko) <fix_gravity>`
+   * :doc:`grem <fix_grem>`
+   * :doc:`halt <fix_halt>`
+   * :doc:`heat <fix_heat>`
+   * :doc:`hyper/global <fix_hyper_global>`
+   * :doc:`hyper/local <fix_hyper_local>`
+   * :doc:`imd <fix_imd>`
+   * :doc:`indent <fix_indent>`
+   * :doc:`ipi <fix_ipi>`
+   * :doc:`langevin (k) <fix_langevin>`
+   * :doc:`langevin/drude <fix_langevin_drude>`
+   * :doc:`langevin/eff <fix_langevin_eff>`
+   * :doc:`langevin/spin <fix_langevin_spin>`
+   * :doc:`latte <fix_latte>`
+   * :doc:`lb/fluid <fix_lb_fluid>`
+   * :doc:`lb/momentum <fix_lb_momentum>`
+   * :doc:`lb/pc <fix_lb_pc>`
+   * :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
+   * :doc:`lb/viscous <fix_lb_viscous>`
+   * :doc:`lineforce <fix_lineforce>`
+   * :doc:`manifoldforce <fix_manifoldforce>`
+   * :doc:`meso <fix_meso>`
+   * :doc:`meso/move <fix_meso_move>`
+   * :doc:`meso/stationary <fix_meso_stationary>`
+   * :doc:`momentum (k) <fix_momentum>`
+   * :doc:`move <fix_move>`
+   * :doc:`mscg <fix_mscg>`
+   * :doc:`msst <fix_msst>`
+   * :doc:`mvv/dpd <fix_mvv_dpd>`
+   * :doc:`mvv/edpd <fix_mvv_dpd>`
+   * :doc:`mvv/tdpd <fix_mvv_dpd>`
+   * :doc:`neb <fix_neb>`
+   * :doc:`neb/spin <fix_neb_spin>`
+   * :doc:`nph (ko) <fix_nh>`
+   * :doc:`nph/asphere (o) <fix_nph_asphere>`
+   * :doc:`nph/body <fix_nph_body>`
+   * :doc:`nph/eff <fix_nh_eff>`
+   * :doc:`nph/sphere (o) <fix_nph_sphere>`
+   * :doc:`nphug <fix_nphug>`
+   * :doc:`npt (iko) <fix_nh>`
+   * :doc:`npt/asphere (o) <fix_npt_asphere>`
+   * :doc:`npt/body <fix_npt_body>`
+   * :doc:`npt/eff <fix_nh_eff>`
+   * :doc:`npt/sphere (o) <fix_npt_sphere>`
+   * :doc:`npt/uef <fix_nh_uef>`
+   * :doc:`nve (iko) <fix_nve>`
+   * :doc:`nve/asphere (i) <fix_nve_asphere>`
+   * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
+   * :doc:`nve/awpmd <fix_nve_awpmd>`
+   * :doc:`nve/body <fix_nve_body>`
+   * :doc:`nve/dot <fix_nve_dot>`
+   * :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
+   * :doc:`nve/eff <fix_nve_eff>`
+   * :doc:`nve/limit <fix_nve_limit>`
+   * :doc:`nve/line <fix_nve_line>`
+   * :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
+   * :doc:`nve/noforce <fix_nve_noforce>`
+   * :doc:`nve/sphere (ko) <fix_nve_sphere>`
+   * :doc:`nve/spin <fix_nve_spin>`
+   * :doc:`nve/tri <fix_nve_tri>`
+   * :doc:`nvk <fix_nvk>`
+   * :doc:`nvt (iko) <fix_nh>`
+   * :doc:`nvt/asphere (o) <fix_nvt_asphere>`
+   * :doc:`nvt/body <fix_nvt_body>`
+   * :doc:`nvt/eff <fix_nh_eff>`
+   * :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
+   * :doc:`nvt/sllod (io) <fix_nvt_sllod>`
+   * :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
+   * :doc:`nvt/sphere (o) <fix_nvt_sphere>`
+   * :doc:`nvt/uef <fix_nh_uef>`
+   * :doc:`oneway <fix_oneway>`
+   * :doc:`orient/bcc <fix_orient>`
+   * :doc:`orient/fcc <fix_orient>`
+   * :doc:`phonon <fix_phonon>`
+   * :doc:`pimd <fix_pimd>`
+   * :doc:`planeforce <fix_planeforce>`
+   * :doc:`plumed <fix_plumed>`
+   * :doc:`poems <fix_poems>`
+   * :doc:`pour <fix_pour>`
+   * :doc:`precession/spin <fix_precession_spin>`
+   * :doc:`press/berendsen <fix_press_berendsen>`
+   * :doc:`print <fix_print>`
+   * :doc:`property/atom (k) <fix_property_atom>`
+   * :doc:`python/invoke <fix_python_invoke>`
+   * :doc:`python/move <fix_python_move>`
+   * :doc:`qbmsst <fix_qbmsst>`
+   * :doc:`qeq/comb (o) <fix_qeq_comb>`
+   * :doc:`qeq/dynamic <fix_qeq>`
+   * :doc:`qeq/fire <fix_qeq>`
+   * :doc:`qeq/point <fix_qeq>`
+   * :doc:`qeq/reax (ko) <fix_qeq_reax>`
+   * :doc:`qeq/shielded <fix_qeq>`
+   * :doc:`qeq/slater <fix_qeq>`
+   * :doc:`qmmm <fix_qmmm>`
+   * :doc:`qtb <fix_qtb>`
+   * :doc:`rattle <fix_shake>`
+   * :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
+   * :doc:`reax/c/species (k) <fix_reaxc_species>`
+   * :doc:`recenter <fix_recenter>`
+   * :doc:`restrain <fix_restrain>`
+   * :doc:`rhok <fix_rhok>`
+   * :doc:`rigid (o) <fix_rigid>`
+   * :doc:`rigid/meso <fix_rigid_meso>`
+   * :doc:`rigid/nph (o) <fix_rigid>`
+   * :doc:`rigid/nph/small <fix_rigid>`
+   * :doc:`rigid/npt (o) <fix_rigid>`
+   * :doc:`rigid/npt/small <fix_rigid>`
+   * :doc:`rigid/nve (o) <fix_rigid>`
+   * :doc:`rigid/nve/small <fix_rigid>`
+   * :doc:`rigid/nvt (o) <fix_rigid>`
+   * :doc:`rigid/nvt/small <fix_rigid>`
+   * :doc:`rigid/small (o) <fix_rigid>`
+   * :doc:`rx (k) <fix_rx>`
+   * :doc:`saed/vtk <fix_saed_vtk>`
+   * :doc:`setforce (k) <fix_setforce>`
+   * :doc:`setforce/spin <fix_setforce>`
+   * :doc:`shake <fix_shake>`
+   * :doc:`shardlow (k) <fix_shardlow>`
+   * :doc:`smd <fix_smd>`
+   * :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
+   * :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`
+   * :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`
+   * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
+   * :doc:`smd/setvel <fix_smd_setvel>`
+   * :doc:`smd/wall_surface <fix_smd_wall_surface>`
+   * :doc:`spring <fix_spring>`
+   * :doc:`spring/chunk <fix_spring_chunk>`
+   * :doc:`spring/rg <fix_spring_rg>`
+   * :doc:`spring/self <fix_spring_self>`
+   * :doc:`srd <fix_srd>`
+   * :doc:`store/force <fix_store_force>`
+   * :doc:`store/state <fix_store_state>`
+   * :doc:`tdpd/source <fix_dpd_source>`
+   * :doc:`temp/berendsen <fix_temp_berendsen>`
+   * :doc:`temp/csld <fix_temp_csvr>`
+   * :doc:`temp/csvr <fix_temp_csvr>`
+   * :doc:`temp/rescale <fix_temp_rescale>`
+   * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
+   * :doc:`tfmc <fix_tfmc>`
+   * :doc:`thermal/conductivity <fix_thermal_conductivity>`
+   * :doc:`ti/spring <fix_ti_spring>`
+   * :doc:`tmd <fix_tmd>`
+   * :doc:`ttm <fix_ttm>`
+   * :doc:`ttm/mod <fix_ttm>`
+   * :doc:`tune/kspace <fix_tune_kspace>`
+   * :doc:`vector <fix_vector>`
+   * :doc:`viscosity <fix_viscosity>`
+   * :doc:`viscous <fix_viscous>`
+   * :doc:`wall/body/polygon <fix_wall_body_polygon>`
+   * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
+   * :doc:`wall/colloid <fix_wall>`
+   * :doc:`wall/ees <fix_wall_ees>`
+   * :doc:`wall/gran <fix_wall_gran>`
+   * :doc:`wall/gran/region <fix_wall_gran_region>`
+   * :doc:`wall/harmonic <fix_wall>`
+   * :doc:`wall/lj1043 <fix_wall>`
+   * :doc:`wall/lj126 <fix_wall>`
+   * :doc:`wall/lj93 (k) <fix_wall>`
+   * :doc:`wall/morse <fix_wall>`
+   * :doc:`wall/piston <fix_wall_piston>`
+   * :doc:`wall/reflect (k) <fix_wall_reflect>`
+   * :doc:`wall/region <fix_wall_region>`
+   * :doc:`wall/region/ees <fix_wall_ees>`
+   * :doc:`wall/srd <fix_wall_srd>`
+   *
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
deleted file mode 100644
index cfd2bcf2ef..0000000000
--- a/doc/src/Commands_fix.txt
+++ /dev/null
@@ -1,240 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-Fix commands :h3
-
-An alphabetic list of all LAMMPS "fix"_fix.html commands.  Some styles
-have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"adapt"_fix_adapt.html,
-"adapt/fep"_fix_adapt_fep.html,
-"addforce"_fix_addforce.html,
-"addtorque"_fix_addtorque.html,
-"append/atoms"_fix_append_atoms.html,
-"atc"_fix_atc.html,
-"atom/swap"_fix_atom_swap.html,
-"ave/atom"_fix_ave_atom.html,
-"ave/chunk"_fix_ave_chunk.html,
-"ave/correlate"_fix_ave_correlate.html,
-"ave/correlate/long"_fix_ave_correlate_long.html,
-"ave/histo"_fix_ave_histo.html,
-"ave/histo/weight"_fix_ave_histo.html,
-"ave/time"_fix_ave_time.html,
-"aveforce"_fix_aveforce.html,
-"balance"_fix_balance.html,
-"bocs"_fix_bocs.html,
-"bond/break"_fix_bond_break.html,
-"bond/create"_fix_bond_create.html,
-"bond/react"_fix_bond_react.html,
-"bond/swap"_fix_bond_swap.html,
-"box/relax"_fix_box_relax.html,
-"client/md"_fix_client_md.html,
-"cmap"_fix_cmap.html,
-"colvars"_fix_colvars.html,
-"controller"_fix_controller.html,
-"deform (k)"_fix_deform.html,
-"deposit"_fix_deposit.html,
-"dpd/energy (k)"_fix_dpd_energy.html,
-"drag"_fix_drag.html,
-"drude"_fix_drude.html,
-"drude/transform/direct"_fix_drude_transform.html,
-"drude/transform/inverse"_fix_drude_transform.html,
-"dt/reset"_fix_dt_reset.html,
-"edpd/source"_fix_dpd_source.html,
-"efield"_fix_efield.html,
-"ehex"_fix_ehex.html,
-"electron/stopping"_fix_electron_stopping.html,
-"enforce2d (k)"_fix_enforce2d.html,
-"eos/cv"_fix_eos_cv.html,
-"eos/table"_fix_eos_table.html,
-"eos/table/rx (k)"_fix_eos_table_rx.html,
-"evaporate"_fix_evaporate.html,
-"external"_fix_external.html,
-"ffl"_fix_ffl.html,
-"filter/corotate"_fix_filter_corotate.html,
-"flow/gauss"_fix_flow_gauss.html,
-"freeze (k)"_fix_freeze.html,
-"gcmc"_fix_gcmc.html,
-"gld"_fix_gld.html,
-"gle"_fix_gle.html,
-"gravity (ko)"_fix_gravity.html,
-"grem"_fix_grem.html,
-"halt"_fix_halt.html,
-"heat"_fix_heat.html,
-"hyper/global"_fix_hyper_global.html,
-"hyper/local"_fix_hyper_local.html,
-"imd"_fix_imd.html,
-"indent"_fix_indent.html,
-"ipi"_fix_ipi.html,
-"langevin (k)"_fix_langevin.html,
-"langevin/drude"_fix_langevin_drude.html,
-"langevin/eff"_fix_langevin_eff.html,
-"langevin/spin"_fix_langevin_spin.html,
-"latte"_fix_latte.html,
-"lb/fluid"_fix_lb_fluid.html,
-"lb/momentum"_fix_lb_momentum.html,
-"lb/pc"_fix_lb_pc.html,
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
-"lb/viscous"_fix_lb_viscous.html,
-"lineforce"_fix_lineforce.html,
-"manifoldforce"_fix_manifoldforce.html,
-"meso"_fix_meso.html,
-"meso/move"_fix_meso_move.html,
-"meso/stationary"_fix_meso_stationary.html,
-"momentum (k)"_fix_momentum.html,
-"move"_fix_move.html,
-"mscg"_fix_mscg.html,
-"msst"_fix_msst.html,
-"mvv/dpd"_fix_mvv_dpd.html,
-"mvv/edpd"_fix_mvv_dpd.html,
-"mvv/tdpd"_fix_mvv_dpd.html,
-"neb"_fix_neb.html,
-"neb_spin"_fix_neb_spin.html,
-"nph (ko)"_fix_nh.html,
-"nph/asphere (o)"_fix_nph_asphere.html,
-"nph/body"_fix_nph_body.html,
-"nph/eff"_fix_nh_eff.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
-"nphug (o)"_fix_nphug.html,
-"npt (iko)"_fix_nh.html,
-"npt/asphere (o)"_fix_npt_asphere.html,
-"npt/body"_fix_npt_body.html,
-"npt/eff"_fix_nh_eff.html,
-"npt/sphere (o)"_fix_npt_sphere.html,
-"npt/uef"_fix_nh_uef.html,
-"nve (iko)"_fix_nve.html,
-"nve/asphere (i)"_fix_nve_asphere.html,
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
-"nve/awpmd"_fix_nve_awpmd.html,
-"nve/body"_fix_nve_body.html,
-"nve/dot"_fix_nve_dot.html,
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
-"nve/eff"_fix_nve_eff.html,
-"nve/limit"_fix_nve_limit.html,
-"nve/line"_fix_nve_line.html,
-"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
-"nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (ko)"_fix_nve_sphere.html,
-"nve/spin"_fix_nve_spin.html,
-"nve/tri"_fix_nve_tri.html,
-"nvk"_fix_nvk.html,
-"nvt (iko)"_fix_nh.html,
-"nvt/asphere (o)"_fix_nvt_asphere.html,
-"nvt/body"_fix_nvt_body.html,
-"nvt/eff"_fix_nh_eff.html,
-"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
-"nvt/sllod (io)"_fix_nvt_sllod.html,
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
-"nvt/sphere (o)"_fix_nvt_sphere.html,
-"nvt/uef"_fix_nh_uef.html,
-"oneway"_fix_oneway.html,
-"orient/bcc"_fix_orient.html,
-"orient/fcc"_fix_orient.html,
-"phonon"_fix_phonon.html,
-"pimd"_fix_pimd.html,
-"planeforce"_fix_planeforce.html,
-"plumed"_fix_plumed.html,
-"poems"_fix_poems.html,
-"pour"_fix_pour.html,
-"precession/spin"_fix_precession_spin.html,
-"press/berendsen"_fix_press_berendsen.html,
-"print"_fix_print.html,
-"property/atom (k)"_fix_property_atom.html,
-"python/invoke"_fix_python_invoke.html,
-"python/move"_fix_python_move.html,
-"qbmsst"_fix_qbmsst.html,
-"qeq/comb (o)"_fix_qeq_comb.html,
-"qeq/dynamic"_fix_qeq.html,
-"qeq/fire"_fix_qeq.html,
-"qeq/point"_fix_qeq.html,
-"qeq/reax (ko)"_fix_qeq_reax.html,
-"qeq/shielded"_fix_qeq.html,
-"qeq/slater"_fix_qeq.html,
-"qmmm"_fix_qmmm.html,
-"qtb"_fix_qtb.html,
-"rattle"_fix_shake.html,
-"reax/c/bonds (k)"_fix_reaxc_bonds.html,
-"reax/c/species (k)"_fix_reaxc_species.html,
-"recenter"_fix_recenter.html,
-"restrain"_fix_restrain.html,
-"rhok"_fix_rhok.html,
-"rigid (o)"_fix_rigid.html,
-"rigid/meso"_fix_rigid_meso.html,
-"rigid/nph (o)"_fix_rigid.html,
-"rigid/nph/small"_fix_rigid.html,
-"rigid/npt (o)"_fix_rigid.html,
-"rigid/npt/small"_fix_rigid.html,
-"rigid/nve (o)"_fix_rigid.html,
-"rigid/nve/small"_fix_rigid.html,
-"rigid/nvt (o)"_fix_rigid.html,
-"rigid/nvt/small"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
-"rx (k)"_fix_rx.html,
-"saed/vtk"_fix_saed_vtk.html,
-"setforce (k)"_fix_setforce.html,
-"shake"_fix_shake.html,
-"shardlow (k)"_fix_shardlow.html,
-"smd"_fix_smd.html,
-"smd/adjust_dt"_fix_smd_adjust_dt.html,
-"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
-"smd/setvel"_fix_smd_setvel.html,
-"smd/wall_surface"_fix_smd_wall_surface.html,
-"spring"_fix_spring.html,
-"spring/chunk"_fix_spring_chunk.html,
-"spring/rg"_fix_spring_rg.html,
-"spring/self"_fix_spring_self.html,
-"srd"_fix_srd.html,
-"store/force"_fix_store_force.html,
-"store/state"_fix_store_state.html,
-"tdpd/source"_fix_dpd_source.html,
-"temp/berendsen"_fix_temp_berendsen.html,
-"temp/csld"_fix_temp_csvr.html,
-"temp/csvr"_fix_temp_csvr.html,
-"temp/rescale"_fix_temp_rescale.html,
-"temp/rescale/eff"_fix_temp_rescale_eff.html,
-"tfmc"_fix_tfmc.html,
-"thermal/conductivity"_fix_thermal_conductivity.html,
-"ti/spring"_fix_ti_spring.html,
-"tmd"_fix_tmd.html,
-"ttm"_fix_ttm.html,
-"ttm/mod"_fix_ttm.html,
-"tune/kspace"_fix_tune_kspace.html,
-"vector"_fix_vector.html,
-"viscosity"_fix_viscosity.html,
-"viscous"_fix_viscous.html,
-"wall/body/polygon"_fix_wall_body_polygon.html,
-"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
-"wall/colloid"_fix_wall.html,
-"wall/ees"_fix_wall_ees.html,
-"wall/gran"_fix_wall_gran.html,
-"wall/gran/region"_fix_wall_gran_region.html,
-"wall/harmonic"_fix_wall.html,
-"wall/lj1043"_fix_wall.html,
-"wall/lj126"_fix_wall.html,
-"wall/lj93 (k)"_fix_wall.html,
-"wall/morse"_fix_wall.html,
-"wall/piston"_fix_wall_piston.html,
-"wall/reflect (k)"_fix_wall_reflect.html,
-"wall/region"_fix_wall_region.html,
-"wall/region/ees"_fix_wall_ees.html,
-"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_input.txt b/doc/src/Commands_input.rst
similarity index 74%
rename from doc/src/Commands_input.txt
rename to doc/src/Commands_input.rst
index 8b3dda741b..c66b530dd0 100644
--- a/doc/src/Commands_input.txt
+++ b/doc/src/Commands_input.rst
@@ -1,13 +1,5 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-LAMMPS input scripts :h3
+LAMMPS input scripts
+====================
 
 LAMMPS executes by reading commands from a input script (text file),
 one line at a time.  When the input script ends, LAMMPS exits.  Each
@@ -24,15 +16,21 @@ simulation with all the settings.  Rather, the input script is read
 one line at a time and each command takes effect when it is read.
 Thus this sequence of commands:
 
-timestep 0.5
-run      100
-run      100 :pre
+
+.. code-block:: LAMMPS
+
+   timestep 0.5
+   run      100
+   run      100
 
 does something different than this sequence:
 
-run      100
-timestep 0.5
-run      100 :pre
+
+.. code-block:: LAMMPS
+
+   run      100
+   timestep 0.5
+   run      100
 
 In the first case, the specified timestep (0.5 fs) is used for two
 simulations of 100 timesteps each.  In the 2nd case, the default
@@ -47,14 +45,13 @@ belong to the group.
 (3) Sometimes command B will use values that can be set by command A.
 This means command A must precede command B in the input script if it
 is to have the desired effect.  For example, the
-"read_data"_read_data.html command initializes the system by setting
+:doc:`read\_data <read_data>` command initializes the system by setting
 up the simulation box and assigning atoms to processors.  If default
-values are not desired, the "processors"_processors.html and
-"boundary"_boundary.html commands need to be used before read_data to
+values are not desired, the :doc:`processors <processors>` and
+:doc:`boundary <boundary>` commands need to be used before read\_data to
 tell LAMMPS how to map processors to the simulation box.
 
 Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  The "Errors"_Errors.html doc page gives
+WARNING message is printed.  The :doc:`Errors <Errors>` doc page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.
-
diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst
new file mode 100644
index 0000000000..3a23520171
--- /dev/null
+++ b/doc/src/Commands_kspace.rst
@@ -0,0 +1,40 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+KSpace solvers
+==============
+
+All LAMMPS :doc:`kspace\_style <kspace_style>` solvers.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`ewald (o) <kspace_style>`
+   * :doc:`ewald/disp <kspace_style>`
+   * :doc:`ewald/dipole <kspace_style>`
+   * :doc:`ewald/dipole/spin <kspace_style>`
+   * :doc:`msm (o) <kspace_style>`
+   * :doc:`msm/cg (o) <kspace_style>`
+   * :doc:`pppm (giko) <kspace_style>`
+   * :doc:`pppm/cg (o) <kspace_style>`
+   * :doc:`pppm/dipole <kspace_style>`
+   * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/disp (io) <kspace_style>`
+   * :doc:`pppm/disp/tip4p (o) <kspace_style>`
+   * :doc:`pppm/stagger <kspace_style>`
+   * :doc:`pppm/tip4p (o) <kspace_style>`
+   * :doc:`scafacos <kspace_style>`
+   *
diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt
deleted file mode 100644
index 02b41b9d67..0000000000
--- a/doc/src/Commands_kspace.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-KSpace solvers :h3
-
-All LAMMPS "kspace_style"_kspace_style.html solvers.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"ewald (o)"_kspace_style.html,
-"ewald/disp"_kspace_style.html,
-"msm (o)"_kspace_style.html,
-"msm/cg (o)"_kspace_style.html,
-"pppm (gok)"_kspace_style.html,
-"pppm/cg (o)"_kspace_style.html,
-"pppm/disp (i)"_kspace_style.html,
-"pppm/disp/tip4p"_kspace_style.html,
-"pppm/stagger"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html,
-"scafacos"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
new file mode 100644
index 0000000000..06eda554a3
--- /dev/null
+++ b/doc/src/Commands_pair.rst
@@ -0,0 +1,260 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+Pair_style potentials
+======================
+
+All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`none <pair_none>`
+   * :doc:`zero <pair_zero>`
+   * :doc:`hybrid (k) <pair_hybrid>`
+   * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   *
+   *
+   *
+   *
+   * :doc:`adp (o) <pair_adp>`
+   * :doc:`agni (o) <pair_agni>`
+   * :doc:`airebo (io) <pair_airebo>`
+   * :doc:`airebo/morse (io) <pair_airebo>`
+   * :doc:`atm <pair_atm>`
+   * :doc:`awpmd/cut <pair_awpmd>`
+   * :doc:`beck (go) <pair_beck>`
+   * :doc:`body/nparticle <pair_body_nparticle>`
+   * :doc:`body/rounded/polygon <pair_body_rounded_polygon>`
+   * :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`
+   * :doc:`bop <pair_bop>`
+   * :doc:`born (go) <pair_born>`
+   * :doc:`born/coul/dsf <pair_born>`
+   * :doc:`born/coul/dsf/cs <pair_cs>`
+   * :doc:`born/coul/long (go) <pair_born>`
+   * :doc:`born/coul/long/cs (g) <pair_cs>`
+   * :doc:`born/coul/msm (o) <pair_born>`
+   * :doc:`born/coul/wolf (go) <pair_born>`
+   * :doc:`born/coul/wolf/cs (g) <pair_cs>`
+   * :doc:`brownian (o) <pair_brownian>`
+   * :doc:`brownian/poly (o) <pair_brownian>`
+   * :doc:`buck (giko) <pair_buck>`
+   * :doc:`buck/coul/cut (giko) <pair_buck>`
+   * :doc:`buck/coul/long (giko) <pair_buck>`
+   * :doc:`buck/coul/long/cs <pair_cs>`
+   * :doc:`buck/coul/msm (o) <pair_buck>`
+   * :doc:`buck/long/coul/long (o) <pair_buck_long>`
+   * :doc:`buck/mdf <pair_mdf>`
+   * :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`
+   * :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`
+   * :doc:`colloid (go) <pair_colloid>`
+   * :doc:`comb (o) <pair_comb>`
+   * :doc:`comb3 <pair_comb>`
+   * :doc:`cosine/squared <pair_cosine_squared>`
+   * :doc:`coul/cut (gko) <pair_coul>`
+   * :doc:`coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`coul/debye (gko) <pair_coul>`
+   * :doc:`coul/diel (o) <pair_coul_diel>`
+   * :doc:`coul/dsf (gko) <pair_coul>`
+   * :doc:`coul/long (gko) <pair_coul>`
+   * :doc:`coul/long/cs (g) <pair_cs>`
+   * :doc:`coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`coul/msm (o) <pair_coul>`
+   * :doc:`coul/shield <pair_coul_shield>`
+   * :doc:`coul/streitz <pair_coul>`
+   * :doc:`coul/wolf (ko) <pair_coul>`
+   * :doc:`coul/wolf/cs <pair_cs>`
+   * :doc:`dpd (gio) <pair_dpd>`
+   * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
+   * :doc:`dpd/tstat (go) <pair_dpd>`
+   * :doc:`dsmc <pair_dsmc>`
+   * :doc:`e3b <pair_e3b>`
+   * :doc:`drip <pair_drip>`
+   * :doc:`eam (gikot) <pair_eam>`
+   * :doc:`eam/alloy (gikot) <pair_eam>`
+   * :doc:`eam/cd (o) <pair_eam>`
+   * :doc:`eam/cd/old (o) <pair_eam>`
+   * :doc:`eam/fs (gikot) <pair_eam>`
+   * :doc:`edip (o) <pair_edip>`
+   * :doc:`edip/multi <pair_edip>`
+   * :doc:`edpd <pair_meso>`
+   * :doc:`eff/cut <pair_eff>`
+   * :doc:`eim (o) <pair_eim>`
+   * :doc:`exp6/rx (k) <pair_exp6_rx>`
+   * :doc:`extep <pair_extep>`
+   * :doc:`gauss (go) <pair_gauss>`
+   * :doc:`gauss/cut (o) <pair_gauss>`
+   * :doc:`gayberne (gio) <pair_gayberne>`
+   * :doc:`gran/hertz/history (o) <pair_gran>`
+   * :doc:`gran/hooke (o) <pair_gran>`
+   * :doc:`gran/hooke/history (ko) <pair_gran>`
+   * :doc:`granular <pair_granular>`
+   * :doc:`gw <pair_gw>`
+   * :doc:`gw/zbl <pair_gw>`
+   * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
+   * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
+   * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
+   * :doc:`kim <pair_kim>`
+   * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
+   * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
+   * :doc:`lcbop <pair_lcbop>`
+   * :doc:`lebedeva/z <pair_lebedeva_z>`
+   * :doc:`lennard/mdf <pair_mdf>`
+   * :doc:`line/lj <pair_line_lj>`
+   * :doc:`list <pair_list>`
+   * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
+   * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/long <pair_charmm>`
+   * :doc:`lj/class2 (gko) <pair_class2>`
+   * :doc:`lj/class2/coul/cut (ko) <pair_class2>`
+   * :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
+   * :doc:`lj/class2/coul/long (gko) <pair_class2>`
+   * :doc:`lj/class2/coul/long/soft <pair_fep_soft>`
+   * :doc:`lj/class2/soft <pair_fep_soft>`
+   * :doc:`lj/cubic (go) <pair_lj_cubic>`
+   * :doc:`lj/cut (gikot) <pair_lj>`
+   * :doc:`lj/cut/coul/cut (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/debye (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/long (gikot) <pair_lj>`
+   * :doc:`lj/cut/coul/long/cs <pair_cs>`
+   * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/msm (go) <pair_lj>`
+   * :doc:`lj/cut/coul/wolf (o) <pair_lj>`
+   * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
+   * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
+   * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
+   * :doc:`lj/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/thole/long (o) <pair_thole>`
+   * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/expand (gko) <pair_lj_expand>`
+   * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
+   * :doc:`lj/gromacs (gko) <pair_gromacs>`
+   * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
+   * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
+   * :doc:`lj/long/dipole/long <pair_dipole>`
+   * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
+   * :doc:`lj/mdf <pair_mdf>`
+   * :doc:`lj/sdk (gko) <pair_sdk>`
+   * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
+   * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
+   * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
+   * :doc:`lj/smooth (o) <pair_lj_smooth>`
+   * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
+   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
+   * :doc:`lj96/cut (go) <pair_lj96>`
+   * :doc:`local/density <pair_local_density>`
+   * :doc:`lubricate (o) <pair_lubricate>`
+   * :doc:`lubricate/poly (o) <pair_lubricate>`
+   * :doc:`lubricateU <pair_lubricateU>`
+   * :doc:`lubricateU/poly <pair_lubricateU>`
+   * :doc:`mdpd <pair_meso>`
+   * :doc:`mdpd/rhosum <pair_meso>`
+   * :doc:`meam/c <pair_meamc>`
+   * :doc:`meam/spline (o) <pair_meam_spline>`
+   * :doc:`meam/sw/spline <pair_meam_sw_spline>`
+   * :doc:`mgpt <pair_mgpt>`
+   * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+   * :doc:`momb <pair_momb>`
+   * :doc:`morse (gkot) <pair_morse>`
+   * :doc:`morse/smooth/linear (o) <pair_morse>`
+   * :doc:`morse/soft <pair_fep_soft>`
+   * :doc:`multi/lucy <pair_multi_lucy>`
+   * :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
+   * :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
+   * :doc:`nm/cut (o) <pair_nm>`
+   * :doc:`nm/cut/coul/cut (o) <pair_nm>`
+   * :doc:`nm/cut/coul/long (o) <pair_nm>`
+   * :doc:`oxdna/coaxstk <pair_oxdna>`
+   * :doc:`oxdna/excv <pair_oxdna>`
+   * :doc:`oxdna/hbond <pair_oxdna>`
+   * :doc:`oxdna/stk <pair_oxdna>`
+   * :doc:`oxdna/xstk <pair_oxdna>`
+   * :doc:`oxdna2/coaxstk <pair_oxdna2>`
+   * :doc:`oxdna2/dh <pair_oxdna2>`
+   * :doc:`oxdna2/excv <pair_oxdna2>`
+   * :doc:`oxdna2/hbond <pair_oxdna2>`
+   * :doc:`oxdna2/stk <pair_oxdna2>`
+   * :doc:`oxdna2/xstk <pair_oxdna2>`
+   * :doc:`oxrna2/excv <pair_oxrna2>`
+   * :doc:`oxrna2/hbond <pair_oxrna2>`
+   * :doc:`oxrna2/dh <pair_oxrna2>`
+   * :doc:`oxrna2/stk <pair_oxrna2>`
+   * :doc:`oxrna2/xstk <pair_oxrna2>`
+   * :doc:`oxrna2/coaxstk <pair_oxrna2>`
+   * :doc:`peri/eps <pair_peri>`
+   * :doc:`peri/lps (o) <pair_peri>`
+   * :doc:`peri/pmb (o) <pair_peri>`
+   * :doc:`peri/ves <pair_peri>`
+   * :doc:`polymorphic <pair_polymorphic>`
+   * :doc:`python <pair_python>`
+   * :doc:`quip <pair_quip>`
+   * :doc:`reax/c (ko) <pair_reaxc>`
+   * :doc:`rebo (io) <pair_airebo>`
+   * :doc:`resquared (go) <pair_resquared>`
+   * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
+   * :doc:`smd/hertz <pair_smd_hertz>`
+   * :doc:`smd/tlsph <pair_smd_tlsph>`
+   * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
+   * :doc:`smd/ulsph <pair_smd_ulsph>`
+   * :doc:`smtbq <pair_smtbq>`
+   * :doc:`snap (k) <pair_snap>`
+   * :doc:`snap (k) <pair_snap>`
+   * :doc:`soft (go) <pair_soft>`
+   * :doc:`sph/heatconduction <pair_sph_heatconduction>`
+   * :doc:`sph/idealgas <pair_sph_idealgas>`
+   * :doc:`sph/lj <pair_sph_lj>`
+   * :doc:`sph/rhosum <pair_sph_rhosum>`
+   * :doc:`sph/taitwater <pair_sph_taitwater>`
+   * :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
+   * :doc:`spin/dipole/cut <pair_spin_dipole>`
+   * :doc:`spin/dipole/long <pair_spin_dipole>`
+   * :doc:`spin/dmi <pair_spin_dmi>`
+   * :doc:`spin/exchange <pair_spin_exchange>`
+   * :doc:`spin/magelec <pair_spin_magelec>`
+   * :doc:`spin/neel <pair_spin_neel>`
+   * :doc:`srp <pair_srp>`
+   * :doc:`sw (giko) <pair_sw>`
+   * :doc:`table (gko) <pair_table>`
+   * :doc:`table/rx (k) <pair_table_rx>`
+   * :doc:`tdpd <pair_meso>`
+   * :doc:`tersoff (giko) <pair_tersoff>`
+   * :doc:`tersoff/mod (gko) <pair_tersoff_mod>`
+   * :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`
+   * :doc:`tersoff/table (o) <pair_tersoff>`
+   * :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
+   * :doc:`thole <pair_thole>`
+   * :doc:`tip4p/cut (o) <pair_coul>`
+   * :doc:`tip4p/long (o) <pair_coul>`
+   * :doc:`tip4p/long/soft (o) <pair_fep_soft>`
+   * :doc:`tri/lj <pair_tri_lj>`
+   * :doc:`ufm (got) <pair_ufm>`
+   * :doc:`vashishta (gko) <pair_vashishta>`
+   * :doc:`vashishta/table (o) <pair_vashishta>`
+   * :doc:`yukawa (gko) <pair_yukawa>`
+   * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
+   * :doc:`zbl (gko) <pair_zbl>`
+   *
+   *
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
deleted file mode 100644
index 47d4c40d8e..0000000000
--- a/doc/src/Commands_pair.txt
+++ /dev/null
@@ -1,252 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-"General commands"_Commands_all.html,
-"Fix styles"_Commands_fix.html,
-"Compute styles"_Commands_compute.html,
-"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
-"Angle styles"_Commands_bond.html#angle,
-"Dihedral styles"_Commands_bond.html#dihedral,
-"Improper styles"_Commands_bond.html#improper,
-"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
-
-Pair_style potentials :h3
-
-All LAMMPS "pair_style"_pair_style.html commands.  Some styles have
-accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_pair_none.html,
-"zero"_pair_zero.html,
-"hybrid (k)"_pair_hybrid.html,
-"hybrid/overlay (k)"_pair_hybrid.html,
-,
-,
-,
-,
-"adp (o)"_pair_adp.html,
-"agni (o)"_pair_agni.html,
-"airebo (io)"_pair_airebo.html,
-"airebo/morse (io)"_pair_airebo.html,
-"atm"_pair_atm.html,
-"awpmd/cut"_pair_awpmd.html,
-"beck (go)"_pair_beck.html,
-"body/nparticle"_pair_body_nparticle.html,
-"body/rounded/polygon"_pair_body_rounded_polygon.html,
-"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html,
-"bop"_pair_bop.html,
-"born (go)"_pair_born.html,
-"born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_cs.html,
-"born/coul/long (go)"_pair_born.html,
-"born/coul/long/cs (g)"_pair_cs.html,
-"born/coul/msm (o)"_pair_born.html,
-"born/coul/wolf (go)"_pair_born.html,
-"born/coul/wolf/cs (g)"_pair_cs.html,
-"brownian (o)"_pair_brownian.html,
-"brownian/poly (o)"_pair_brownian.html,
-"buck (giko)"_pair_buck.html,
-"buck/coul/cut (giko)"_pair_buck.html,
-"buck/coul/long (giko)"_pair_buck.html,
-"buck/coul/long/cs"_pair_cs.html,
-"buck/coul/msm (o)"_pair_buck.html,
-"buck/long/coul/long (o)"_pair_buck_long.html,
-"buck/mdf"_pair_mdf.html,
-"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
-"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
-"colloid (go)"_pair_colloid.html,
-"comb (o)"_pair_comb.html,
-"comb3"_pair_comb.html,
-"cosine/squared"_pair_cosine_squared.html,
-"coul/cut (gko)"_pair_coul.html,
-"coul/cut/soft (o)"_pair_fep_soft.html,
-"coul/debye (gko)"_pair_coul.html,
-"coul/diel (o)"_pair_coul_diel.html,
-"coul/dsf (gko)"_pair_coul.html,
-"coul/long (gko)"_pair_coul.html,
-"coul/long/cs (g)"_pair_cs.html,
-"coul/long/soft (o)"_pair_fep_soft.html,
-"coul/msm (o)"_pair_coul.html,
-"coul/shield"_pair_coul_shield.html,
-"coul/streitz"_pair_coul.html,
-"coul/wolf (ko)"_pair_coul.html,
-"coul/wolf/cs"_pair_cs.html,
-"dpd (gio)"_pair_dpd.html,
-"dpd/fdt"_pair_dpd_fdt.html,
-"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
-"dpd/tstat (go)"_pair_dpd.html,
-"dsmc"_pair_dsmc.html,
-"e3b"_pair_e3b.html,
-"drip"_pair_drip.html,
-"eam (gikot)"_pair_eam.html,
-"eam/alloy (gikot)"_pair_eam.html,
-"eam/cd (o)"_pair_eam.html,
-"eam/cd/old (o)"_pair_eam.html,
-"eam/fs (gikot)"_pair_eam.html,
-"edip (o)"_pair_edip.html,
-"edip/multi"_pair_edip.html,
-"edpd"_pair_meso.html,
-"eff/cut"_pair_eff.html,
-"eim (o)"_pair_eim.html,
-"exp6/rx (k)"_pair_exp6_rx.html,
-"extep"_pair_extep.html,
-"gauss (go)"_pair_gauss.html,
-"gauss/cut (o)"_pair_gauss.html,
-"gayberne (gio)"_pair_gayberne.html,
-"gran/hertz/history (o)"_pair_gran.html,
-"gran/hooke (o)"_pair_gran.html,
-"gran/hooke/history (ko)"_pair_gran.html,
-"granular"_pair_granular.html,
-"gw"_pair_gw.html,
-"gw/zbl"_pair_gw.html,
-"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
-"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
-"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
-"kim"_pair_kim.html,
-"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
-"lcbop"_pair_lcbop.html,
-"lebedeva/z"_pair_lebedeva_z.html,
-"lennard/mdf"_pair_mdf.html,
-"line/lj"_pair_line_lj.html,
-"list"_pair_list.html,
-"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
-"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (gikot)"_pair_charmm.html,
-"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
-"lj/charmm/coul/msm (o)"_pair_charmm.html,
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
-"lj/charmmfsw/coul/long"_pair_charmm.html,
-"lj/class2 (gko)"_pair_class2.html,
-"lj/class2/coul/cut (ko)"_pair_class2.html,
-"lj/class2/coul/cut/soft"_pair_fep_soft.html,
-"lj/class2/coul/long (gko)"_pair_class2.html,
-"lj/class2/coul/long/soft"_pair_fep_soft.html,
-"lj/class2/soft"_pair_fep_soft.html,
-"lj/cubic (go)"_pair_lj_cubic.html,
-"lj/cut (gikot)"_pair_lj.html,
-"lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
-"lj/cut/coul/debye (gko)"_pair_lj.html,
-"lj/cut/coul/dsf (gko)"_pair_lj.html,
-"lj/cut/coul/long (gikot)"_pair_lj.html,
-"lj/cut/coul/long/cs"_pair_cs.html,
-"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
-"lj/cut/coul/msm (go)"_pair_lj.html,
-"lj/cut/coul/wolf (o)"_pair_lj.html,
-"lj/cut/dipole/cut (go)"_pair_dipole.html,
-"lj/cut/dipole/long (g)"_pair_dipole.html,
-"lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_fep_soft.html,
-"lj/cut/thole/long (o)"_pair_thole.html,
-"lj/cut/tip4p/cut (o)"_pair_lj.html,
-"lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
-"lj/expand (gko)"_pair_lj_expand.html,
-"lj/expand/coul/long (g)"_pair_lj_expand.html,
-"lj/gromacs (gko)"_pair_gromacs.html,
-"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (iot)"_pair_lj_long.html,
-"lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long (o)"_pair_lj_long.html,
-"lj/mdf"_pair_mdf.html,
-"lj/sdk (gko)"_pair_sdk.html,
-"lj/sdk/coul/long (go)"_pair_sdk.html,
-"lj/sdk/coul/msm (o)"_pair_sdk.html,
-"lj/sf/dipole/sf (go)"_pair_dipole.html,
-"lj/smooth (o)"_pair_lj_smooth.html,
-"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
-"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
-"lj96/cut (go)"_pair_lj96.html,
-"lubricate (o)"_pair_lubricate.html,
-"lubricate/poly (o)"_pair_lubricate.html,
-"lubricateU"_pair_lubricateU.html,
-"lubricateU/poly"_pair_lubricateU.html,
-"mdpd"_pair_meso.html,
-"mdpd/rhosum"_pair_meso.html,
-"meam/c"_pair_meamc.html,
-"meam/spline (o)"_pair_meam_spline.html,
-"meam/sw/spline"_pair_meam_sw_spline.html,
-"mgpt"_pair_mgpt.html,
-"mie/cut (g)"_pair_mie.html,
-"momb"_pair_momb.html,
-"morse (gkot)"_pair_morse.html,
-"morse/smooth/linear (o)"_pair_morse.html,
-"morse/soft"_pair_fep_soft.html,
-"multi/lucy"_pair_multi_lucy.html,
-"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"nb3b/harmonic"_pair_nb3b_harmonic.html,
-"nm/cut (o)"_pair_nm.html,
-"nm/cut/coul/cut (o)"_pair_nm.html,
-"nm/cut/coul/long (o)"_pair_nm.html,
-"oxdna/coaxstk"_pair_oxdna.html,
-"oxdna/excv"_pair_oxdna.html,
-"oxdna/hbond"_pair_oxdna.html,
-"oxdna/stk"_pair_oxdna.html,
-"oxdna/xstk"_pair_oxdna.html,
-"oxdna2/coaxstk"_pair_oxdna2.html,
-"oxdna2/dh"_pair_oxdna2.html,
-"oxdna2/excv"_pair_oxdna2.html,
-"oxdna2/hbond"_pair_oxdna2.html,
-"oxdna2/stk"_pair_oxdna2.html,
-"oxdna2/xstk"_pair_oxdna2.html,
-"peri/eps"_pair_peri.html,
-"peri/lps (o)"_pair_peri.html,
-"peri/pmb (o)"_pair_peri.html,
-"peri/ves"_pair_peri.html,
-"polymorphic"_pair_polymorphic.html,
-"python"_pair_python.html,
-"quip"_pair_quip.html,
-"reax/c (ko)"_pair_reaxc.html,
-"rebo (io)"_pair_airebo.html,
-"resquared (go)"_pair_resquared.html,
-"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
-"smd/hertz"_pair_smd_hertz.html,
-"smd/tlsph"_pair_smd_tlsph.html,
-"smd/tri_surface"_pair_smd_triangulated_surface.html,
-"smd/ulsph"_pair_smd_ulsph.html,
-"smtbq"_pair_smtbq.html,
-"snap (k)"_pair_snap.html,
-"snap (k)"_pair_snap.html,
-"soft (go)"_pair_soft.html,
-"sph/heatconduction"_pair_sph_heatconduction.html,
-"sph/idealgas"_pair_sph_idealgas.html,
-"sph/lj"_pair_sph_lj.html,
-"sph/rhosum"_pair_sph_rhosum.html,
-"sph/taitwater"_pair_sph_taitwater.html,
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
-"spin/dipole/cut"_pair_spin_dipole.html,
-"spin/dipole/long"_pair_spin_dipole.html,
-"spin/dmi"_pair_spin_dmi.html,
-"spin/exchange"_pair_spin_exchange.html,
-"spin/magelec"_pair_spin_magelec.html,
-"spin/neel"_pair_spin_neel.html,
-"srp"_pair_srp.html,
-"sw (giko)"_pair_sw.html,
-"table (gko)"_pair_table.html,
-"table/rx (k)"_pair_table_rx.html,
-"tdpd"_pair_meso.html,
-"tersoff (giko)"_pair_tersoff.html,
-"tersoff/mod (gko)"_pair_tersoff_mod.html,
-"tersoff/mod/c (o)"_pair_tersoff_mod.html,
-"tersoff/table (o)"_pair_tersoff.html,
-"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
-"thole"_pair_thole.html,
-"tip4p/cut (o)"_pair_coul.html,
-"tip4p/long (o)"_pair_coul.html,
-"tip4p/long/soft (o)"_pair_fep_soft.html,
-"tri/lj"_pair_tri_lj.html,
-"ufm (got)"_pair_ufm.html,
-"vashishta (gko)"_pair_vashishta.html,
-"vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gko)"_pair_yukawa.html,
-"yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.rst
similarity index 70%
rename from doc/src/Commands_parse.txt
rename to doc/src/Commands_parse.rst
index 13a4c2699d..ec1c8c1e46 100644
--- a/doc/src/Commands_parse.txt
+++ b/doc/src/Commands_parse.rst
@@ -1,13 +1,5 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Parsing rules for input scripts :h3
+Parsing rules for input scripts
+===============================
 
 Each non-blank line in the input script is treated as a command.
 LAMMPS commands are case sensitive.  Command names are lower-case, as
@@ -30,6 +22,10 @@ comment after a trailing "&" character will prevent the command from
 continuing on the next line.  Also note that for multi-line commands a
 single leading "#" will comment out the entire command.
 
+.. code-block:: LAMMPS
+
+   # this is a comment
+
 (3) The line is searched repeatedly for $ characters, which indicate
 variables that are replaced with a text string.  See an exception in
 (6).
@@ -37,11 +33,11 @@ variables that are replaced with a text string.  See an exception in
 If the $ is followed by curly brackets, then the variable name is the
 text inside the curly brackets.  If no curly brackets follow the $,
 then the variable name is the single character immediately following
-the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
+the $.  Thus ${myTemp} and $x refer to variable names "myTemp" and
 "x".
 
 How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable.html doc page for details.
+of variable it is; see the :doc:`variable <variable>` doc page for details.
 It can be a variable that stores multiple text strings, and return one
 of them.  The returned text string can be multiple "words" (space
 separated) which will then be interpreted as multiple arguments in the
@@ -50,17 +46,23 @@ will be evaluated and its numeric result returned as a string.
 
 As a special case, if the $ is followed by parenthesis, then the text
 inside the parenthesis is treated as an "immediate" variable and
-evaluated as an "equal-style variable"_variable.html.  This is a way
+evaluated as an :doc:`equal-style variable <variable>`.  This is a way
 to use numeric formulas in an input script without having to assign
 them to variable names.  For example, these 3 input script lines:
 
-variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete :pre
+
+.. code-block:: LAMMPS
+
+   variable X equal (xlo+xhi)/2+sqrt(v_area)
+   region 1 block $X 2 INF INF EDGE EDGE
+   variable X delete
 
 can be replaced by
 
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
+
+.. code-block:: LAMMPS
+
+   region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
 
 so that you do not have to define (or discard) a temporary variable X.
 
@@ -73,21 +75,27 @@ specified a high-precision "%.20g" is used as the default.
 
 This can be useful for formatting print output to a desired precision:
 
-print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
+.. code-block:: LAMMPS
+
+   print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
 
 Note that neither the curly-bracket or immediate form of variables can
 contain nested $ characters for other variables to substitute for.
 Thus you cannot do this:
 
-variable        a equal 2
-variable        b2 equal 4
-print           "B2 = $\{b$a\}" :pre
+
+.. code-block:: LAMMPS
+
+   variable        a equal 2
+   variable        b2 equal 4
+   print           "B2 = ${b$a}"
 
 Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-"equal-style variable"_variable.html.
+you could use $(v\_x-1.0), since the latter is valid syntax for an
+:doc:`equal-style variable <variable>`.
 
-See the "variable"_variable.html command for more details of how
+See the :doc:`variable <variable>` command for more details of how
 strings are assigned to variables and evaluated, and how they can be
 used in input script commands.
 
@@ -108,29 +116,33 @@ multiple lines of an argument to retain their line breaks, the text
 can be enclosed in triple quotes, in which case "&" characters are not
 needed.  For example:
 
-print "Volume = $v"
-print 'Volume = $v'
-if "$\{steps\} > 1000" then quit
-variable a string "red green blue &
-                   purple orange cyan"
-print """
-System volume = $v
-System temperature = $t
-""" :pre
+
+.. code-block:: LAMMPS
+
+   print "Volume = $v"
+   print 'Volume = $v'
+   if "${steps} > 1000" then quit
+   variable a string "red green blue &
+                      purple orange cyan"
+   print """
+   System volume = $v
+   System temperature = $t
+   """
 
 In each case, the single, double, or triple quotes are removed when
 the single argument they enclose is stored internally.
 
-See the "dump modify format"_dump_modify.html, "print"_print.html,
-"if"_if.html, and "python"_python.html commands for examples.
+See the :doc:`dump modify format <dump_modify>`, :doc:`print <print>`,
+:doc:`if <if>`, and :doc:`python <python>` commands for examples.
 
 A "#" or "$" character that is between quotes will not be treated as a
 comment indicator in (2) or substituted for as a variable in (3).
 
-NOTE: If the argument is itself a command that requires a quoted
-argument (e.g. using a "print"_print.html command as part of an
-"if"_if.html or "run every"_run.html command), then single, double, or
-triple quotes can be nested in the usual manner.  See the doc pages
-for those commands for examples.  Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
+.. note::
 
+   If the argument is itself a command that requires a quoted
+   argument (e.g. using a :doc:`print <print>` command as part of an
+   :doc:`if <if>` or :doc:`run every <run>` command), then single, double, or
+   triple quotes can be nested in the usual manner.  See the doc pages
+   for those commands for examples.  Only one of level of nesting is
+   allowed, but that should be sufficient for most use cases.
diff --git a/doc/src/Commands_removed.txt b/doc/src/Commands_removed.rst
similarity index 58%
rename from doc/src/Commands_removed.txt
rename to doc/src/Commands_removed.rst
index 1eee6e45e0..ee87296863 100644
--- a/doc/src/Commands_removed.txt
+++ b/doc/src/Commands_removed.rst
@@ -1,13 +1,5 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands.html)
-
-:line
-
-Removed commands and packages :h3
+Removed commands and packages
+=============================
 
 This page lists LAMMPS commands and packages that have been removed from
 the distribution and provides suggestions for alternatives or replacements.
@@ -15,52 +7,61 @@ LAMMPS has special dummy styles implemented, that will stop LAMMPS and
 print a suitable error message in most cases, when a style/command is used
 that has been removed.
 
-Fix ave/spatial and fix ave/spatial/sphere :h4
+Fix ave/spatial and fix ave/spatial/sphere
+------------------------------------------
 
 The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
 since they were superseded by the more general and extensible "chunk
 infrastructure".  Here the system is partitioned in one of many possible
-ways through the "compute chunk/atom"_compute_chunk_atom.html command
-and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
-Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
+ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
+and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
+Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
 
-MEAM package :h4
+MEAM package
+------------
 
 The MEAM package has been removed since it was superseded by the
-"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
+:ref:`USER-MEAMC package <PKG-USER-MEAMC>`. The code in
 the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
 which removes several restrictions (e.g. there can be multiple instances
 in hybrid pair styles) and allows for some optimizations leading
-to better performance.  The new pair style "meam/c"_pair_meamc.html has
+to better performance.  The new pair style :doc:`meam/c <pair_meamc>` has
 the exact same syntax as the old "meam" pair style and thus pair style
-"meam"_pair_meamc.html is an alias to the new style and backward
+:doc:`meam <pair_meamc>` is an alias to the new style and backward
 compatibility of old inputs is preserved.
 
-REAX package :h4
+REAX package
+------------
 
 The REAX package has been removed since it was superseded by the
-"USER-REAXC package"_Package_details.html#PKG-USER-REAXC.  The USER-REAXC
+:ref:`USER-REAXC package <PKG-USER-REAXC>`.  The USER-REAXC
 package has been tested to yield equivalent results to the REAX package,
 offers better performance, supports OpenMP multi-threading via USER-OMP,
 and GPU and threading parallelization through KOKKOS.  The new pair styles
 are not syntax compatible with the removed reax pair style, so input
 files will have to be adapted.
 
-USER-CUDA package :h4
+USER-CUDA package
+-----------------
 
 The USER-CUDA package had been removed, since it had been unmaintained
 for a long time and had known bugs and problems.  Significant parts of
 the design were transferred to the
-"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
+:ref:`KOKKOS package <PKG-KOKKOS>`, which has similar
 performance characteristics on Nvidia GPUs. Both, the KOKKOS
-and the "GPU package"_Package_details.html#PKG-GPU are maintained
+and the :ref:`GPU package <PKG-GPU>` are maintained
 and allow running LAMMPS with GPU acceleration.
 
-restart2data tool :h4
+restart2data tool
+-----------------
 
 The functionality of the restart2data tool has been folded into the
 LAMMPS executable directly instead of having a separate tool.  A
-combination of the commands "read_restart"_read_restart.html and
-"write_data"_write_data.html can be used to the same effect.  For added
-convenience this conversion can also be triggered by "command line
-flags"_Run_options.html
+combination of the commands :doc:`read\_restart <read_restart>` and
+:doc:`write\_data <write_data>` can be used to the same effect.  For added
+convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Commands_structure.rst b/doc/src/Commands_structure.rst
new file mode 100644
index 0000000000..b419074212
--- /dev/null
+++ b/doc/src/Commands_structure.rst
@@ -0,0 +1,86 @@
+Input script structure
+======================
+
+This page describes the structure of a typical LAMMPS input script.
+The examples directory in the LAMMPS distribution contains many sample
+input scripts; it is discussed on the :doc:`Examples <Examples>` doc
+page.
+
+A LAMMPS input script typically has 4 parts:
+
+1. Initialization
+2. Atom definition
+3. Settings
+4. Run a simulation
+
+The last 2 parts can be repeated as many times as desired.  I.e. run a
+simulation, change some settings, run some more, etc.  Each of the 4
+parts is now described in more detail.  Remember that almost all
+commands need only be used if a non-default value is desired.
+
+(1) Initialization
+
+Set parameters that need to be defined before atoms are created or
+read-in from a file.
+
+The relevant commands are :doc:`units <units>`,
+:doc:`dimension <dimension>`, :doc:`newton <newton>`,
+:doc:`processors <processors>`, :doc:`boundary <boundary>`,
+:doc:`atom\_style <atom_style>`, :doc:`atom\_modify <atom_modify>`.
+
+If force-field parameters appear in the files that will be read, these
+commands tell LAMMPS what kinds of force fields are being used:
+:doc:`pair\_style <pair_style>`, :doc:`bond\_style <bond_style>`,
+:doc:`angle\_style <angle_style>`, :doc:`dihedral\_style <dihedral_style>`,
+:doc:`improper\_style <improper_style>`.
+
+(2) Atom definition
+
+There are 3 ways to define atoms in LAMMPS.  Read them in from a data
+or restart file via the :doc:`read\_data <read_data>` or
+:doc:`read\_restart <read_restart>` commands.  These files can contain
+molecular topology information.  Or create atoms on a lattice (with no
+molecular topology), using these commands: :doc:`lattice <lattice>`,
+:doc:`region <region>`, :doc:`create\_box <create_box>`,
+:doc:`create\_atoms <create_atoms>`.  The entire set of atoms can be
+duplicated to make a larger simulation using the
+:doc:`replicate <replicate>` command.
+
+(3) Settings
+
+Once atoms and molecular topology are defined, a variety of settings
+can be specified: force field coefficients, simulation parameters,
+output options, etc.
+
+Force field coefficients are set by these commands (they can also be
+set in the read-in files): :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_coeff <bond_coeff>`, :doc:`angle\_coeff <angle_coeff>`,
+:doc:`dihedral\_coeff <dihedral_coeff>`,
+:doc:`improper\_coeff <improper_coeff>`,
+:doc:`kspace\_style <kspace_style>`, :doc:`dielectric <dielectric>`,
+:doc:`special\_bonds <special_bonds>`.
+
+Various simulation parameters are set by these commands:
+:doc:`neighbor <neighbor>`, :doc:`neigh\_modify <neigh_modify>`,
+:doc:`group <group>`, :doc:`timestep <timestep>`,
+:doc:`reset\_timestep <reset_timestep>`, :doc:`run\_style <run_style>`,
+:doc:`min\_style <min_style>`, :doc:`min\_modify <min_modify>`.
+
+Fixes impose a variety of boundary conditions, time integration, and
+diagnostic options.  The :doc:`fix <fix>` command comes in many flavors.
+
+Various computations can be specified for execution during a
+simulation using the :doc:`compute <compute>`,
+:doc:`compute\_modify <compute_modify>`, and :doc:`variable <variable>`
+commands.
+
+Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,
+and :doc:`restart <restart>` commands.
+
+(4) Run a simulation
+
+A molecular dynamics simulation is run using the :doc:`run <run>`
+command.  Energy minimization (molecular statics) is performed using
+the :doc:`minimize <minimize>` command.  A parallel tempering
+(replica-exchange) simulation can be run using the
+:doc:`temper <temper>` command.
diff --git a/doc/src/Commands_structure.txt b/doc/src/Commands_structure.txt
deleted file mode 100644
index b5d2c7b07b..0000000000
--- a/doc/src/Commands_structure.txt
+++ /dev/null
@@ -1,95 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Input script structure :h3
-
-This page describes the structure of a typical LAMMPS input script.
-The examples directory in the LAMMPS distribution contains many sample
-input scripts; it is discussed on the "Examples"_Examples.html doc
-page.
-
-A LAMMPS input script typically has 4 parts:
-
-Initialization
-Atom definition
-Settings
-Run a simulation :ol
-
-The last 2 parts can be repeated as many times as desired.  I.e. run a
-simulation, change some settings, run some more, etc.  Each of the 4
-parts is now described in more detail.  Remember that almost all
-commands need only be used if a non-default value is desired.
-
-(1) Initialization
-
-Set parameters that need to be defined before atoms are created or
-read-in from a file.
-
-The relevant commands are "units"_units.html,
-"dimension"_dimension.html, "newton"_newton.html,
-"processors"_processors.html, "boundary"_boundary.html,
-"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
-
-If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-"pair_style"_pair_style.html, "bond_style"_bond_style.html,
-"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
-"improper_style"_improper_style.html.
-
-(2) Atom definition
-
-There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the "read_data"_read_data.html or
-"read_restart"_read_restart.html commands.  These files can contain
-molecular topology information.  Or create atoms on a lattice (with no
-molecular topology), using these commands: "lattice"_lattice.html,
-"region"_region.html, "create_box"_create_box.html,
-"create_atoms"_create_atoms.html.  The entire set of atoms can be
-duplicated to make a larger simulation using the
-"replicate"_replicate.html command.
-
-(3) Settings
-
-Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-
-Force field coefficients are set by these commands (they can also be
-set in the read-in files): "pair_coeff"_pair_coeff.html,
-"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"improper_coeff"_improper_coeff.html,
-"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
-"special_bonds"_special_bonds.html.
-
-Various simulation parameters are set by these commands:
-"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
-"group"_group.html, "timestep"_timestep.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"min_style"_min_style.html, "min_modify"_min_modify.html.
-
-Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options.  The "fix"_fix.html command comes in many flavors.
-
-Various computations can be specified for execution during a
-simulation using the "compute"_compute.html,
-"compute_modify"_compute_modify.html, and "variable"_variable.html
-commands.
-
-Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
-and "restart"_restart.html commands.
-
-(4) Run a simulation
-
-A molecular dynamics simulation is run using the "run"_run.html
-command.  Energy minimization (molecular statics) is performed using
-the "minimize"_minimize.html command.  A parallel tempering
-(replica-exchange) simulation can be run using the
-"temper"_temper.html command.
-
diff --git a/doc/src/Eqs/angle_charmm.jpg b/doc/src/Eqs/angle_charmm.jpg
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diff --git a/doc/src/Eqs/angle_charmm.tex b/doc/src/Eqs/angle_charmm.tex
deleted file mode 100644
index 00b37ba335..0000000000
--- a/doc/src/Eqs/angle_charmm.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2 
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/angle_class2.jpg b/doc/src/Eqs/angle_class2.jpg
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diff --git a/doc/src/Eqs/angle_class2.tex b/doc/src/Eqs/angle_class2.tex
deleted file mode 100644
index e5a542e87a..0000000000
--- a/doc/src/Eqs/angle_class2.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  E & = & E_a + E_{bb} + E_{ba} \\
-  E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\
-  E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\
-  E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0)
-\end{eqnarray*}
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/angle_cosine.jpg b/doc/src/Eqs/angle_cosine.jpg
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diff --git a/doc/src/Eqs/angle_cosine.tex b/doc/src/Eqs/angle_cosine.tex
deleted file mode 100644
index e766676099..0000000000
--- a/doc/src/Eqs/angle_cosine.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [1 + \cos(\theta)] 
-$$
-
-\end{document}
\ No newline at end of file
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diff --git a/doc/src/Eqs/angle_cosine_buck6d.tex b/doc/src/Eqs/angle_cosine_buck6d.tex
deleted file mode 100644
index 49be2fc8c2..0000000000
--- a/doc/src/Eqs/angle_cosine_buck6d.tex
+++ /dev/null
@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-$$
-  E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
-$$
-
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:
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diff --git a/doc/src/Eqs/angle_cosine_shift.tex b/doc/src/Eqs/angle_cosine_shift.tex
deleted file mode 100644
index e795d6beff..0000000000
--- a/doc/src/Eqs/angle_cosine_shift.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
-$$
-
-\end{document}
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diff --git a/doc/src/Eqs/angle_cosine_shift_exp.tex b/doc/src/Eqs/angle_cosine_shift_exp.tex
deleted file mode 100644
index 4afa01356c..0000000000
--- a/doc/src/Eqs/angle_cosine_shift_exp.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-U_{min} 
-\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
-\quad\mbox{with}\quad
-U(\theta,\theta_0)
-=-0.5 \left(1+\cos(\theta-\theta_0) \right)
-$$
-
-\end{document}
diff --git a/doc/src/Eqs/angle_cosine_squared.jpg b/doc/src/Eqs/angle_cosine_squared.jpg
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diff --git a/doc/src/Eqs/angle_cosine_squared.tex b/doc/src/Eqs/angle_cosine_squared.tex
deleted file mode 100644
index 57ae47ae45..0000000000
--- a/doc/src/Eqs/angle_cosine_squared.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [\cos(\theta) - \cos(\theta_0)]^2 
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/angle_cross.jpg b/doc/src/Eqs/angle_cross.jpg
deleted file mode 100644
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diff --git a/doc/src/Eqs/angle_cross.tex b/doc/src/Eqs/angle_cross.tex
deleted file mode 100644
index 9d1fdcb7f8..0000000000
--- a/doc/src/Eqs/angle_cross.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
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-$$
-
-\end{document}
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diff --git a/doc/src/Eqs/angle_dipole_couple.tex b/doc/src/Eqs/angle_dipole_couple.tex
deleted file mode 100644
index a857d83d7a..0000000000
--- a/doc/src/Eqs/angle_dipole_couple.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
--\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\
-\vec{F_j} & = & -\vec{F_i} \\
-\end{eqnarray*}                           
-
-\end{document}
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diff --git a/doc/src/Eqs/angle_dipole_gamma.tex b/doc/src/Eqs/angle_dipole_gamma.tex
deleted file mode 100644
index 965b74ad96..0000000000
--- a/doc/src/Eqs/angle_dipole_gamma.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   \cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/angle_dipole_potential.jpg b/doc/src/Eqs/angle_dipole_potential.jpg
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diff --git a/doc/src/Eqs/angle_dipole_potential.tex b/doc/src/Eqs/angle_dipole_potential.tex
deleted file mode 100644
index 8949835eb7..0000000000
--- a/doc/src/Eqs/angle_dipole_potential.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K (\cos\gamma - \cos\gamma_0)^2 
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/angle_dipole_torque.jpg b/doc/src/Eqs/angle_dipole_torque.jpg
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diff --git a/doc/src/Eqs/angle_dipole_torque.tex b/doc/src/Eqs/angle_dipole_torque.tex
deleted file mode 100644
index 9527459fdc..0000000000
--- a/doc/src/Eqs/angle_dipole_torque.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
-           \vec{r_{ij}} \times \vec{\mu_j}
-$$
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/angle_fourier.jpg b/doc/src/Eqs/angle_fourier.jpg
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diff --git a/doc/src/Eqs/angle_harmonic.tex b/doc/src/Eqs/angle_harmonic.tex
deleted file mode 100644
index c566376b5b..0000000000
--- a/doc/src/Eqs/angle_harmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K (\theta - \theta_0)^2 
-$$
-
-\end{document}
\ No newline at end of file
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diff --git a/doc/src/Eqs/angle_mm3.tex b/doc/src/Eqs/angle_mm3.tex
deleted file mode 100644
index e2d96f2d69..0000000000
--- a/doc/src/Eqs/angle_mm3.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
-$$
-
-\end{document}
diff --git a/doc/src/Eqs/angle_quartic.jpg b/doc/src/Eqs/angle_quartic.jpg
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diff --git a/doc/src/Eqs/angle_quartic.tex b/doc/src/Eqs/angle_quartic.tex
deleted file mode 100644
index ff9ff9a7dc..0000000000
--- a/doc/src/Eqs/angle_quartic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
-$$
-
-\end{document}
diff --git a/doc/src/Eqs/bond_class2.jpg b/doc/src/Eqs/bond_class2.jpg
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diff --git a/doc/src/Eqs/bond_class2.tex b/doc/src/Eqs/bond_class2.tex
deleted file mode 100644
index 0735b61025..0000000000
--- a/doc/src/Eqs/bond_class2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4 
-$$
-
-\end{document}
\ No newline at end of file
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diff --git a/doc/src/Eqs/bond_fene.tex b/doc/src/Eqs/bond_fene.tex
deleted file mode 100644
index ec4dd8efa2..0000000000
--- a/doc/src/Eqs/bond_fene.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = -0.5 K R_0^2  \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
-  4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
-    \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/bond_fene_expand.jpg b/doc/src/Eqs/bond_fene_expand.jpg
deleted file mode 100644
index 1d04acec326963cf9dd8b1fed6dbce12efa487d8..0000000000000000000000000000000000000000
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diff --git a/doc/src/Eqs/bond_fene_expand.tex b/doc/src/Eqs/bond_fene_expand.tex
deleted file mode 100644
index 5fd96e7ad5..0000000000
--- a/doc/src/Eqs/bond_fene_expand.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = -0.5 K R_0^2
-  \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 
-  4 \epsilon \left[ \left(\frac{\sigma}{\left(r - 
-      \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - 
-      \Delta\right)}\right)^6 \right] + \epsilon
-$$
-
-\end{document}
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diff --git a/doc/src/Eqs/bond_harmonic.tex b/doc/src/Eqs/bond_harmonic.tex
deleted file mode 100644
index 2461086898..0000000000
--- a/doc/src/Eqs/bond_harmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K (r - r_0)^2 
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/bond_harmonic_shift.jpg b/doc/src/Eqs/bond_harmonic_shift.jpg
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diff --git a/doc/src/Eqs/bond_harmonic_shift.tex b/doc/src/Eqs/bond_harmonic_shift.tex
deleted file mode 100644
index 3daa16724f..0000000000
--- a/doc/src/Eqs/bond_harmonic_shift.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
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-
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\ No newline at end of file
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diff --git a/doc/src/Eqs/bond_harmonic_shift_cut.tex b/doc/src/Eqs/bond_harmonic_shift_cut.tex
deleted file mode 100644
index 3daa16724f..0000000000
--- a/doc/src/Eqs/bond_harmonic_shift_cut.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] 
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/bond_mm3.jpg b/doc/src/Eqs/bond_mm3.jpg
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diff --git a/doc/src/Eqs/bond_mm3.tex b/doc/src/Eqs/bond_mm3.tex
deleted file mode 100644
index 549500ebac..0000000000
--- a/doc/src/Eqs/bond_mm3.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
-$$
-
-\end{document}
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diff --git a/doc/src/Eqs/bond_morse.tex b/doc/src/Eqs/bond_morse.tex
deleted file mode 100644
index a0d7a89961..0000000000
--- a/doc/src/Eqs/bond_morse.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-%   E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2 
-   E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 
-$$
-
-\end{document}
\ No newline at end of file
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diff --git a/doc/src/Eqs/bond_nonlinear.tex b/doc/src/Eqs/bond_nonlinear.tex
deleted file mode 100644
index b8cdc96169..0000000000
--- a/doc/src/Eqs/bond_nonlinear.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
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-$$
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-\end{document}
\ No newline at end of file
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diff --git a/doc/src/Eqs/bond_oxdna_fene.tex b/doc/src/Eqs/bond_oxdna_fene.tex
deleted file mode 100644
index ba7248e20b..0000000000
--- a/doc/src/Eqs/bond_oxdna_fene.tex
+++ /dev/null
@@ -1,10 +0,0 @@
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-\begin{document}
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diff --git a/doc/src/Eqs/bond_quartic.tex b/doc/src/Eqs/bond_quartic.tex
deleted file mode 100644
index 0d0cceb353..0000000000
--- a/doc/src/Eqs/bond_quartic.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
-  4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
-    \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/src/Eqs/fix_bond_react.jpg b/doc/src/Eqs/fix_bond_react.jpg
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diff --git a/doc/src/Eqs/fix_bond_react.tex b/doc/src/Eqs/fix_bond_react.tex
new file mode 100644
index 0000000000..9400656038
--- /dev/null
+++ b/doc/src/Eqs/fix_bond_react.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+   k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
+\end{eqnarray*}                           
+
+\end{document}
diff --git a/doc/src/Eqs/fix_spin_cubic.jpg b/doc/src/Eqs/fix_spin_cubic.jpg
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diff --git a/doc/src/Eqs/fix_spin_cubic.tex b/doc/src/Eqs/fix_spin_cubic.tex
deleted file mode 100644
index 9c402294d7..0000000000
--- a/doc/src/Eqs/fix_spin_cubic.tex
+++ /dev/null
@@ -1,21 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \bm{H}_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
-    \Big[
-    \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2 +
-    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 +
-    \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \Big]
-    +K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2
-    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/force_spin_aniso.jpg b/doc/src/Eqs/force_spin_aniso.jpg
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diff --git a/doc/src/Eqs/force_spin_zeeman.tex b/doc/src/Eqs/force_spin_zeeman.tex
deleted file mode 100644
index d623ef85ae..0000000000
--- a/doc/src/Eqs/force_spin_zeeman.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber 
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/norm_inf.jpg b/doc/src/Eqs/norm_inf.jpg
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diff --git a/doc/src/Eqs/pair_spin_exchange_function.tex b/doc/src/Eqs/norm_inf.tex
similarity index 54%
rename from doc/src/Eqs/pair_spin_exchange_function.tex
rename to doc/src/Eqs/norm_inf.tex
index 054c6992f0..b97a9f88f7 100644
--- a/doc/src/Eqs/pair_spin_exchange_function.tex
+++ b/doc/src/Eqs/norm_inf.tex
@@ -6,8 +6,10 @@
 \begin{document}
 \begin{varwidth}{50in}
   \begin{equation}
-    {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d}  
-    \right)^2 }\Theta (R_c - r_{ij}) \nonumber
+    || \vec{F} ||_{inf} 
+    = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, 
+    |F_N^1|, |F_N^2|, |F_N^3|\right)
+    \nonumber
   \end{equation}
 \end{varwidth}
 \end{document}
diff --git a/doc/src/Eqs/norm_max.jpg b/doc/src/Eqs/norm_max.jpg
new file mode 100644
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diff --git a/doc/src/Eqs/norm_max.tex b/doc/src/Eqs/norm_max.tex
new file mode 100644
index 0000000000..3b2198bdf0
--- /dev/null
+++ b/doc/src/Eqs/norm_max.tex
@@ -0,0 +1,15 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    % \left| \left| \vec{F} \right| \right|_2 
+    || \vec{F} ||_{max} 
+    = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}
diff --git a/doc/src/Eqs/norm_two.jpg b/doc/src/Eqs/norm_two.jpg
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diff --git a/doc/src/Eqs/force_spin_aniso.tex b/doc/src/Eqs/norm_two.tex
similarity index 52%
rename from doc/src/Eqs/force_spin_aniso.tex
rename to doc/src/Eqs/norm_two.tex
index d6abfd580d..d428081a49 100644
--- a/doc/src/Eqs/force_spin_aniso.tex
+++ b/doc/src/Eqs/norm_two.tex
@@ -1,11 +1,15 @@
 \documentclass[preview]{standalone}
 \usepackage{varwidth}
 \usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
 \begin{document}
 \begin{varwidth}{50in}
   \begin{equation}
-    \bm{H}_{aniso}  = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber
+    % \left| \left| \vec{F} \right| \right|_2 
+    || \vec{F} ||_{2} 
+    = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N}
+    \nonumber
   \end{equation}
 \end{varwidth}
 \end{document}
diff --git a/doc/src/Eqs/pair_local_density_energy.jpg b/doc/src/Eqs/pair_local_density_energy.jpg
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diff --git a/doc/src/Eqs/bond_gromos.tex b/doc/src/Eqs/pair_local_density_energy.tex
similarity index 59%
rename from doc/src/Eqs/bond_gromos.tex
rename to doc/src/Eqs/pair_local_density_energy.tex
index 2cd8c39535..a77b513051 100644
--- a/doc/src/Eqs/bond_gromos.tex
+++ b/doc/src/Eqs/pair_local_density_energy.tex
@@ -1,10 +1,11 @@
 \documentclass[12pt]{article}
-\pagestyle{empty}
 
 \begin{document}
 
 $$
-   E = K (r^2 - r_0^2)^2
+ U_{LD} = \sum_i F(\rho_i)
 $$
 
+
 \end{document}
+~                  
diff --git a/doc/src/Eqs/pair_local_density_energy_implement.jpg b/doc/src/Eqs/pair_local_density_energy_implement.jpg
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diff --git a/doc/src/Eqs/pair_local_density_energy_implement.tex b/doc/src/Eqs/pair_local_density_energy_implement.tex
new file mode 100644
index 0000000000..4b1f1c3df2
--- /dev/null
+++ b/doc/src/Eqs/pair_local_density_energy_implement.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right] 
+$$
+
+\end{document}
diff --git a/doc/src/Eqs/pair_local_density_energy_multi.jpg b/doc/src/Eqs/pair_local_density_energy_multi.jpg
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diff --git a/doc/src/Eqs/angle_cosine_delta.tex b/doc/src/Eqs/pair_local_density_energy_multi.tex
similarity index 65%
rename from doc/src/Eqs/angle_cosine_delta.tex
rename to doc/src/Eqs/pair_local_density_energy_multi.tex
index 918e9e5046..4ca0b7e8b9 100644
--- a/doc/src/Eqs/angle_cosine_delta.tex
+++ b/doc/src/Eqs/pair_local_density_energy_multi.tex
@@ -3,7 +3,7 @@
 \begin{document}
 
 $$
-  E = K [1 - \cos(\theta - \theta_0)]
+U_{LD} = \sum_i a_\alpha F(\rho_i)
 $$
 
 \end{document}
diff --git a/doc/src/Eqs/pair_local_density_indicator_func.jpg b/doc/src/Eqs/pair_local_density_indicator_func.jpg
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diff --git a/doc/src/Eqs/pair_local_density_indicator_func.tex b/doc/src/Eqs/pair_local_density_indicator_func.tex
new file mode 100644
index 0000000000..aa595c96dc
--- /dev/null
+++ b/doc/src/Eqs/pair_local_density_indicator_func.tex
@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+\usepackage[utf8]{inputenc}
+\usepackage{amsmath}
+\usepackage{amsfonts}
+
+\begin{document}
+\[
+  \varphi(r) = 
+    \begin{cases}
+       1 & r \le R_1 \\
+       c_0 + c_2r^2 + c_4r^4 + c_6r^6  & r \in (R_1, R_2) \\
+       0 & r \ge R_2
+  \end{cases}
+\]
+
+\end{document}
diff --git a/doc/src/Eqs/pair_local_density_ld.jpg b/doc/src/Eqs/pair_local_density_ld.jpg
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diff --git a/doc/src/Eqs/angle_fourier_simple.tex b/doc/src/Eqs/pair_local_density_ld.tex
similarity index 62%
rename from doc/src/Eqs/angle_fourier_simple.tex
rename to doc/src/Eqs/pair_local_density_ld.tex
index 3228315a13..1affa67cd3 100644
--- a/doc/src/Eqs/angle_fourier_simple.tex
+++ b/doc/src/Eqs/pair_local_density_ld.tex
@@ -2,8 +2,9 @@
 
 \begin{document}
 
+
 $$
-   E = K [ 1.0 + c \cos ( n \theta) ] 
+\rho_i = \sum_{j \neq i} \varphi(r_{ij})
 $$
 
 \end{document}
diff --git a/doc/src/Eqs/pair_local_density_ld_implement.jpg b/doc/src/Eqs/pair_local_density_ld_implement.jpg
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diff --git a/doc/src/Eqs/angle_cosine_periodic.tex b/doc/src/Eqs/pair_local_density_ld_implement.tex
similarity index 54%
rename from doc/src/Eqs/angle_cosine_periodic.tex
rename to doc/src/Eqs/pair_local_density_ld_implement.tex
index 69aa1bba6a..85ee8bad21 100644
--- a/doc/src/Eqs/angle_cosine_periodic.tex
+++ b/doc/src/Eqs/pair_local_density_ld_implement.tex
@@ -2,8 +2,9 @@
 
 \begin{document}
 
+
 $$
-E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]  
+\rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij})
 $$
 
 \end{document}
diff --git a/doc/src/Eqs/pair_local_density_ld_multi.jpg b/doc/src/Eqs/pair_local_density_ld_multi.jpg
new file mode 100644
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diff --git a/doc/src/Eqs/angle_fourier.tex b/doc/src/Eqs/pair_local_density_ld_multi.tex
similarity index 54%
rename from doc/src/Eqs/angle_fourier.tex
rename to doc/src/Eqs/pair_local_density_ld_multi.tex
index f7f76462e3..c441288c5d 100644
--- a/doc/src/Eqs/angle_fourier.tex
+++ b/doc/src/Eqs/pair_local_density_ld_multi.tex
@@ -2,8 +2,9 @@
 
 \begin{document}
 
+
 $$
-   E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ] 
+\rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij})
 $$
 
 \end{document}
diff --git a/doc/src/Eqs/pair_spin_exchange_forces.jpg b/doc/src/Eqs/pair_spin_exchange_forces.jpg
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diff --git a/doc/src/Eqs/pair_spin_exchange_forces.tex b/doc/src/Eqs/pair_spin_exchange_forces.tex
deleted file mode 100644
index ac5ef682f3..0000000000
--- a/doc/src/Eqs/pair_spin_exchange_forces.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} 
-    \left(r_{ij} \right)\,\vec{s}_{j} 
-    ~~{\rm and}~~ 
-    \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
-    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}  
-    \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/pair_spin_exchange_function.jpg b/doc/src/Eqs/pair_spin_exchange_function.jpg
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diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.tex b/doc/src/Eqs/pair_spin_exchange_interaction.tex
deleted file mode 100644
index f20b3e5740..0000000000
--- a/doc/src/Eqs/pair_spin_exchange_interaction.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/pair_spin_neel_functions.jpg b/doc/src/Eqs/pair_spin_neel_functions.jpg
deleted file mode 100644
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diff --git a/doc/src/Eqs/pair_spin_neel_functions.tex b/doc/src/Eqs/pair_spin_neel_functions.tex
deleted file mode 100644
index ead5a2b87a..0000000000
--- a/doc/src/Eqs/pair_spin_neel_functions.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{eqnarray}
-    g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\
-    q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\
-    q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber
-  \end{eqnarray}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Eqs/pair_spin_neel_interaction.jpg b/doc/src/Eqs/pair_spin_neel_interaction.jpg
deleted file mode 100644
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diff --git a/doc/src/Eqs/pair_spin_neel_interaction.tex b/doc/src/Eqs/pair_spin_neel_interaction.tex
deleted file mode 100644
index 8b4ac33e73..0000000000
--- a/doc/src/Eqs/pair_spin_neel_interaction.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm}
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij}
-    \cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
-    +q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right)
-    \left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
-    + q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot
-    {\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}
diff --git a/doc/src/Errors.rst b/doc/src/Errors.rst
new file mode 100644
index 0000000000..eccb94b7b0
--- /dev/null
+++ b/doc/src/Errors.rst
@@ -0,0 +1,22 @@
+Errors
+******
+
+These doc pages describe the errors you can encounter when using
+LAMMPS.  The common problems include conceptual issues.  The messages
+and warnings doc pages give complete lists of all the messages the
+code may generate (except those generated by USER packages), with
+additional details for many of them.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Errors_common
+   Errors_bugs
+   Errors_messages
+   Errors_warnings
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Errors_bugs.rst b/doc/src/Errors_bugs.rst
new file mode 100644
index 0000000000..5c297a3a1a
--- /dev/null
+++ b/doc/src/Errors_bugs.rst
@@ -0,0 +1,32 @@
+Reporting bugs
+==============
+
+If you are confident that you have found a bug in LAMMPS, follow these
+steps.
+
+Check the `New features and bug fixes <http://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site <lws_>`_ to see if the bug has already been reported or fixed or the
+`Unfixed bug <http://lammps.sandia.gov/unbug.html>`_ to see if a fix is
+pending.
+
+Check the `mailing list <http://lammps.sandia.gov/mail.html>`_ to see if
+it has been discussed before.
+
+If not, send an email to the mailing list describing the problem with
+any ideas you have as to what is causing it or where in the code the
+problem might be.  The developers will ask for more info if needed,
+such as an input script or data files.
+
+The most useful thing you can do to help us fix the bug is to isolate
+the problem.  Run it on the smallest number of atoms and fewest number
+of processors and with the simplest input script that reproduces the
+bug and try to identify what command or combination of commands is
+causing the problem.
+
+.. note::
+
+   this page needs to have GitHub issues info added
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst
new file mode 100644
index 0000000000..8137c64e96
--- /dev/null
+++ b/doc/src/Errors_common.rst
@@ -0,0 +1,128 @@
+Common problems
+===============
+
+If two LAMMPS runs do not produce the exact same answer on different
+machines or different numbers of processors, this is typically not a
+bug.  In theory you should get identical answers on any number of
+processors and on any machine.  In practice, numerical round-off can
+cause slight differences and eventual divergence of molecular dynamics
+phase space trajectories within a few 100s or few 1000s of timesteps.
+However, the statistical properties of the two runs (e.g. average
+energy or temperature) should still be the same.
+
+If the :doc:`velocity <velocity>` command is used to set initial atom
+velocities, a particular atom can be assigned a different velocity
+when the problem is run on a different number of processors or on
+different machines.  If this happens, the phase space trajectories of
+the two simulations will rapidly diverge.  See the discussion of the
+*loop* option in the :doc:`velocity <velocity>` command for details and
+options that avoid this issue.
+
+Similarly, the :doc:`create\_atoms <create_atoms>` command generates a
+lattice of atoms.  For the same physical system, the ordering and
+numbering of atoms by atom ID may be different depending on the number
+of processors.
+
+Some commands use random number generators which may be setup to
+produce different random number streams on each processor and hence
+will produce different effects when run on different numbers of
+processors.  A commonly-used example is the :doc:`fix langevin <fix_langevin>` command for thermostatting.
+
+A LAMMPS simulation typically has two stages, setup and run.  Most
+LAMMPS errors are detected at setup time; others like a bond
+stretching too far may not occur until the middle of a run.
+
+LAMMPS tries to flag errors and print informative error messages so
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other!  If you run into errors that LAMMPS
+doesn't catch that you think it should flag, please send an email to
+the `developers <http://lammps.sandia.gov/authors.html>`_.
+
+If you get an error message about an invalid command in your input
+script, you can determine what command is causing the problem by
+looking in the log.lammps file or using the :doc:`echo command <echo>`
+to see it on the screen.  If you get an error like "Invalid ...
+style", with ... being fix, compute, pair, etc, it means that you
+mistyped the style name or that the command is part of an optional
+package which was not compiled into your executable.  The list of
+available styles in your executable can be listed by using :doc:`the -h command-line swith <Run_options>`.  The installation and
+compilation of optional packages is explained on the :doc:`Build packages <Build_package>` doc page.
+
+For a given command, LAMMPS expects certain arguments in a specified
+order.  If you mess this up, LAMMPS will often flag the error, but it
+may also simply read a bogus argument and assign a value that is
+valid, but not what you wanted.  E.g. trying to read the string "abc"
+as an integer value of 0.  Careful reading of the associated doc page
+for the command should allow you to fix these problems. In most cases,
+where LAMMPS expects to read a number, either integer or floating point,
+it performs a stringent test on whether the provided input actually
+is an integer or floating-point number, respectively, and reject the
+input with an error message (for instance, when an integer is required,
+but a floating-point number 1.0 is provided):
+
+
+.. parsed-literal::
+
+   ERROR: Expected integer parameter instead of '1.0' in input script or data file
+
+Some commands allow for using variable references in place of numeric
+constants so that the value can be evaluated and may change over the
+course of a run.  This is typically done with the syntax *v\_name* for a
+parameter, where name is the name of the variable. On the other hand,
+immediate variable expansion with the syntax $\ *name* is performed while
+reading the input and before parsing commands,
+
+.. note::
+
+   Using a variable reference (i.e. *v\_name*) is only allowed if
+   the documentation of the corresponding command explicitly says it is.
+   Otherwise, you will receive an error message of this kind:
+
+
+.. parsed-literal::
+
+   ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
+
+Generally, LAMMPS will print a message to the screen and logfile and
+exit gracefully when it encounters a fatal error.  Sometimes it will
+print a WARNING to the screen and logfile and continue on; you can
+decide if the WARNING is important or not.  A WARNING message that is
+generated in the middle of a run is only printed to the screen, not to
+the logfile, to avoid cluttering up thermodynamic output.  If LAMMPS
+crashes or hangs without spitting out an error message first then it
+could be a bug (see :doc:`this section <Errors_bugs>`) or one of the following
+cases:
+
+LAMMPS runs in the available memory a processor allows to be
+allocated.  Most reasonable MD runs are compute limited, not memory
+limited, so this shouldn't be a bottleneck on most platforms.  Almost
+all large memory allocations in the code are done via C-style malloc's
+which will generate an error message if you run out of memory.
+Smaller chunks of memory are allocated via C++ "new" statements.  If
+you are unlucky you could run out of memory just when one of these
+small requests is made, in which case the code will crash or hang (in
+parallel), since LAMMPS doesn't trap on those errors.
+
+Illegal arithmetic can cause LAMMPS to run slow or crash.  This is
+typically due to invalid physics and numerics that your simulation is
+computing.  If you see wild thermodynamic values or NaN values in your
+LAMMPS output, something is wrong with your simulation.  If you
+suspect this is happening, it is a good idea to print out
+thermodynamic info frequently (e.g. every timestep) via the
+:doc:`thermo <thermo>` so you can monitor what is happening.
+Visualizing the atom movement is also a good idea to insure your model
+is behaving as you expect.
+
+In parallel, one way LAMMPS can hang is due to how different MPI
+implementations handle buffering of messages.  If the code hangs
+without an error message, it may be that you need to specify an MPI
+setting or two (usually via an environment variable) to enable
+buffering or boost the sizes of messages that can be buffered.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst
new file mode 100644
index 0000000000..a1795a6776
--- /dev/null
+++ b/doc/src/Errors_messages.rst
@@ -0,0 +1,8418 @@
+Error messages
+==============
+
+This is an alphabetic list of the ERROR messages LAMMPS prints out and
+the reason why.  If the explanation here is not sufficient, the
+documentation for the offending command may help.  Error messages also
+list the source file and line number where the error was generated.
+For example, a message like this:
+
+
+.. parsed-literal::
+
+   ERROR: Illegal velocity command (velocity.cpp:78)
+
+means that line #78 in the file src/velocity.cpp generated the error.
+Looking in the source code may help you figure out what went wrong.
+
+Note that error messages from :doc:`user-contributed packages <Packages_user>` are not listed here.  If such an error
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
+
+Doc page with :doc:`WARNING messages <Errors_warnings>`
+
+
+----------
+
+
+
+
+*1-3 bond count is inconsistent*
+   An inconsistency was detected when computing the number of 1-3
+   neighbors for each atom.  This likely means something is wrong with
+   the bond topologies you have defined.
+
+*1-4 bond count is inconsistent*
+   An inconsistency was detected when computing the number of 1-4
+   neighbors for each atom.  This likely means something is wrong with
+   the bond topologies you have defined.
+
+*Accelerator sharing is not currently supported on system*
+   Multiple MPI processes cannot share the accelerator on your
+   system. For NVIDIA GPUs, see the nvidia-smi command to change this
+   setting.
+
+*All angle coeffs are not set*
+   All angle coefficients must be set in the data file or by the
+   angle\_coeff command before running a simulation.
+
+*All atom IDs = 0 but atom\_modify id = yes*
+   Self-explanatory.
+
+*All atoms of a swapped type must have same charge.*
+   Self-explanatory.
+
+*All atoms of a swapped type must have the same charge.*
+   Self-explanatory.
+
+*All bond coeffs are not set*
+   All bond coefficients must be set in the data file or by the
+   bond\_coeff command before running a simulation.
+
+*All dihedral coeffs are not set*
+   All dihedral coefficients must be set in the data file or by the
+   dihedral\_coeff command before running a simulation.
+
+*All improper coeffs are not set*
+   All improper coefficients must be set in the data file or by the
+   improper\_coeff command before running a simulation.
+
+*All masses are not set*
+   For atom styles that define masses for each atom type, all masses must
+   be set in the data file or by the mass command before running a
+   simulation.  They must also be set before using the velocity
+   command.
+
+*All mol IDs should be set for fix gcmc group atoms*
+   The molecule flag is on, yet not all molecule ids in the fix group
+   have been set to non-zero positive values by the user. This is an
+   error since all atoms in the fix gcmc group are eligible for deletion,
+   rotation, and translation and therefore must have valid molecule ids.
+
+*All pair coeffs are not set*
+   All pair coefficients must be set in the data file or by the
+   pair\_coeff command before running a simulation.
+
+*All read\_dump x,y,z fields must be specified for scaled, triclinic coords*
+   For triclinic boxes and scaled coordinates you must specify all 3 of
+   the x,y,z fields, else LAMMPS cannot reconstruct the unscaled
+   coordinates.
+
+*All universe/uloop variables must have same # of values*
+   Self-explanatory.
+
+*All variables in next command must be same style*
+   Self-explanatory.
+
+*Angle atom missing in delete\_bonds*
+   The delete\_bonds command cannot find one or more atoms in a particular
+   angle on a particular processor.  The pairwise cutoff is too short or
+   the atoms are too far apart to make a valid angle.
+
+*Angle atom missing in set command*
+   The set command cannot find one or more atoms in a particular angle on
+   a particular processor.  The pairwise cutoff is too short or the atoms
+   are too far apart to make a valid angle.
+
+*Angle atoms %d %d %d missing on proc %d at step %ld*
+   One or more of 3 atoms needed to compute a particular angle are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the angle has blown apart and an atom is
+   too far away.
+
+*Angle atoms missing on proc %d at step %ld*
+   One or more of 3 atoms needed to compute a particular angle are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the angle has blown apart and an atom is
+   too far away.
+
+*Angle coeff for hybrid has invalid style*
+   Angle style hybrid uses another angle style as one of its
+   coefficients.  The angle style used in the angle\_coeff command or read
+   from a restart file is not recognized.
+
+*Angle coeffs are not set*
+   No angle coefficients have been assigned in the data file or via the
+   angle\_coeff command.
+
+*Angle extent > half of periodic box length*
+   This error was detected by the neigh\_modify check yes setting.  It is
+   an error because the angle atoms are so far apart it is ambiguous how
+   it should be defined.
+
+*Angle potential must be defined for SHAKE*
+   When shaking angles, an angle\_style potential must be used.
+
+*Angle style hybrid cannot have hybrid as an argument*
+   Self-explanatory.
+
+*Angle style hybrid cannot have none as an argument*
+   Self-explanatory.
+
+*Angle style hybrid cannot use same angle style twice*
+   Self-explanatory.
+
+*Angle table must range from 0 to 180 degrees*
+   Self-explanatory.
+
+*Angle table parameters did not set N*
+   List of angle table parameters must include N setting.
+
+*Angle\_coeff command before angle\_style is defined*
+   Coefficients cannot be set in the data file or via the angle\_coeff
+   command until an angle\_style has been assigned.
+
+*Angle\_coeff command before simulation box is defined*
+   The angle\_coeff command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Angle\_coeff command when no angles allowed*
+   The chosen atom style does not allow for angles to be defined.
+
+*Angle\_style command when no angles allowed*
+   The chosen atom style does not allow for angles to be defined.
+
+*Angles assigned incorrectly*
+   Angles read in from the data file were not assigned correctly to
+   atoms.  This means there is something invalid about the topology
+   definitions.
+
+*Angles defined but no angle types*
+   The data file header lists angles but no angle types.
+
+*Append boundary must be shrink/minimum*
+   The boundary style of the face where atoms are added
+   must be of type m (shrink/minimum).
+
+*Arccos of invalid value in variable formula*
+   Argument of arccos() must be between -1 and 1.
+
+*Arcsin of invalid value in variable formula*
+   Argument of arcsin() must be between -1 and 1.
+
+*Assigning body parameters to non-body atom*
+   Self-explanatory.
+
+*Assigning ellipsoid parameters to non-ellipsoid atom*
+   Self-explanatory.
+
+*Assigning line parameters to non-line atom*
+   Self-explanatory.
+
+*Assigning quat to non-body atom*
+   Self-explanatory.
+
+*Assigning tri parameters to non-tri atom*
+   Self-explanatory.
+
+*At least one atom of each swapped type must be present to define charges.*
+   Self-explanatory.
+
+*Atom IDs must be consecutive for velocity create loop all*
+   Self-explanatory.
+
+*Atom IDs must be used for molecular systems*
+   Atom IDs are used to identify and find partner atoms in bonds.
+
+*Atom count changed in fix neb*
+   This is not allowed in a NEB calculation.
+
+*Atom count is inconsistent, cannot write data file*
+   The sum of atoms across processors does not equal the global number
+   of atoms.  Probably some atoms have been lost.
+
+*Atom count is inconsistent, cannot write restart file*
+   Sum of atoms across processors does not equal initial total count.
+   This is probably because you have lost some atoms.
+
+*Atom in too many rigid bodies - boost MAXBODY*
+   Fix poems has a parameter MAXBODY (in fix\_poems.cpp) which determines
+   the maximum number of rigid bodies a single atom can belong to (i.e. a
+   multibody joint).  The bodies you have defined exceed this limit.
+
+*Atom sort did not operate correctly*
+   This is an internal LAMMPS error.  Please report it to the
+   developers.
+
+*Atom style hybrid cannot have hybrid as an argument*
+   Self-explanatory.
+
+*Atom style hybrid cannot use same atom style twice*
+   Self-explanatory.
+
+*Atom style template molecule must have atom types*
+   The defined molecule(s) does not specify atom types.
+
+*Atom style was redefined after using fix property/atom*
+   This is not allowed.
+
+*Atom type must be zero in fix gcmc mol command*
+   Self-explanatory.
+
+*Atom vector in equal-style variable formula*
+   Atom vectors generate one value per atom which is not allowed
+   in an equal-style variable.
+
+*Atom-style variable in equal-style variable formula*
+   Atom-style variables generate one value per atom which is not allowed
+   in an equal-style variable.
+
+*Atom\_modify id command after simulation box is defined*
+   The atom\_modify id command cannot be used after a read\_data,
+   read\_restart, or create\_box command.
+
+*Atom\_modify map command after simulation box is defined*
+   The atom\_modify map command cannot be used after a read\_data,
+   read\_restart, or create\_box command.
+
+*Atom\_modify sort and first options cannot be used together*
+   Self-explanatory.
+
+*Atom\_style command after simulation box is defined*
+   The atom\_style command cannot be used after a read\_data,
+   read\_restart, or create\_box command.
+
+*Atom\_style line can only be used in 2d simulations*
+   Self-explanatory.
+
+*Atom\_style tri can only be used in 3d simulations*
+   Self-explanatory.
+
+*Atomfile variable could not read values*
+   Check the file assigned to the variable.
+
+*Atomfile variable in equal-style variable formula*
+   Self-explanatory.
+
+*Atomfile-style variable in equal-style variable formula*
+   Self-explanatory.
+
+*Attempt to pop empty stack in fix box/relax*
+   Internal LAMMPS error.  Please report it to the developers.
+
+*Attempt to push beyond stack limit in fix box/relax*
+   Internal LAMMPS error.  Please report it to the developers.
+
+*Attempting to rescale a 0.0 temperature*
+   Cannot rescale a temperature that is already 0.0.
+
+*Bad FENE bond*
+   Two atoms in a FENE bond have become so far apart that the bond cannot
+   be computed.
+
+*Bad TIP4P angle type for PPPM/TIP4P*
+   Specified angle type is not valid.
+
+*Bad TIP4P angle type for PPPMDisp/TIP4P*
+   Specified angle type is not valid.
+
+*Bad TIP4P bond type for PPPM/TIP4P*
+   Specified bond type is not valid.
+
+*Bad TIP4P bond type for PPPMDisp/TIP4P*
+   Specified bond type is not valid.
+
+*Bad fix ID in fix append/atoms command*
+   The value of the fix\_id for keyword spatial must start with 'f\_'.
+
+*Bad grid of processors*
+   The 3d grid of processors defined by the processors command does not
+   match the number of processors LAMMPS is being run on.
+
+*Bad kspace\_modify kmax/ewald parameter*
+   Kspace\_modify values for the kmax/ewald keyword must be integers > 0
+
+*Bad kspace\_modify slab parameter*
+   Kspace\_modify value for the slab/volume keyword must be >= 2.0.
+
+*Bad matrix inversion in mldivide3*
+   This error should not occur unless the matrix is badly formed.
+
+*Bad principal moments*
+   Fix rigid did not compute the principal moments of inertia of a rigid
+   group of atoms correctly.
+
+*Bad quadratic solve for particle/line collision*
+   This is an internal error.  It should normally not occur.
+
+*Bad quadratic solve for particle/tri collision*
+   This is an internal error.  It should normally not occur.
+
+*Bad real space Coulombic cutoff in fix tune/kspace*
+   Fix tune/kspace tried to find the optimal real space Coulombic cutoff using
+   the Newton-Rhaphson method, but found a non-positive or NaN cutoff
+
+*Balance command before simulation box is defined*
+   The balance command cannot be used before a read\_data, read\_restart,
+   or create\_box command.
+
+*Balance produced bad splits*
+   This should not occur.  It means two or more cutting plane locations
+   are on top of each other or out of order.  Report the problem to the
+   developers.
+
+*Balance rcb cannot be used with comm\_style brick*
+   Comm\_style tiled must be used instead.
+
+*Balance shift string is invalid*
+   The string can only contain the characters "x", "y", or "z".
+
+*Bias compute does not calculate a velocity bias*
+   The specified compute must compute a bias for temperature.
+
+*Bias compute does not calculate temperature*
+   The specified compute must compute temperature.
+
+*Bias compute group does not match compute group*
+   The specified compute must operate on the same group as the parent
+   compute.
+
+*Big particle in fix srd cannot be point particle*
+   Big particles must be extended spheroids or ellipsoids.
+
+*Bigint setting in lmptype.h is invalid*
+   Size of bigint is less than size of tagint.
+
+*Bigint setting in lmptype.h is not compatible*
+   Format of bigint stored in restart file is not consistent with LAMMPS
+   version you are running.  See the settings in src/lmptype.h
+
+*Bitmapped lookup tables require int/float be same size*
+   Cannot use pair tables on this machine, because of word sizes.  Use
+   the pair\_modify command with table 0 instead.
+
+*Bitmapped table in file does not match requested table*
+   Setting for bitmapped table in pair\_coeff command must match table
+   in file exactly.
+
+*Bitmapped table is incorrect length in table file*
+   Number of table entries is not a correct power of 2.
+
+*Bond and angle potentials must be defined for TIP4P*
+   Cannot use TIP4P pair potential unless bond and angle potentials
+   are defined.
+
+*Bond atom missing in box size check*
+   The 2nd atoms needed to compute a particular bond is missing on this
+   processor.  Typically this is because the pairwise cutoff is set too
+   short or the bond has blown apart and an atom is too far away.
+
+*Bond atom missing in delete\_bonds*
+   The delete\_bonds command cannot find one or more atoms in a particular
+   bond on a particular processor.  The pairwise cutoff is too short or
+   the atoms are too far apart to make a valid bond.
+
+*Bond atom missing in image check*
+   The 2nd atom in a particular bond is missing on this processor.
+   Typically this is because the pairwise cutoff is set too short or the
+   bond has blown apart and an atom is too far away.
+
+*Bond atom missing in set command*
+   The set command cannot find one or more atoms in a particular bond on
+   a particular processor.  The pairwise cutoff is too short or the atoms
+   are too far apart to make a valid bond.
+
+*Bond atoms %d %d missing on proc %d at step %ld*
+   The 2nd atom needed to compute a particular bond is missing on this
+   processor.  Typically this is because the pairwise cutoff is set too
+   short or the bond has blown apart and an atom is too far away.
+
+*Bond atoms missing on proc %d at step %ld*
+   The 2nd atom needed to compute a particular bond is missing on this
+   processor.  Typically this is because the pairwise cutoff is set too
+   short or the bond has blown apart and an atom is too far away.
+
+*Bond coeff for hybrid has invalid style*
+   Bond style hybrid uses another bond style as one of its coefficients.
+   The bond style used in the bond\_coeff command or read from a restart
+   file is not recognized.
+
+*Bond coeffs are not set*
+   No bond coefficients have been assigned in the data file or via the
+   bond\_coeff command.
+
+*Bond extent > half of periodic box length*
+   This error was detected by the neigh\_modify check yes setting.  It is
+   an error because the bond atoms are so far apart it is ambiguous how
+   it should be defined.
+
+*Bond potential must be defined for SHAKE*
+   Cannot use fix shake unless bond potential is defined.
+
+*Bond style hybrid cannot have hybrid as an argument*
+   Self-explanatory.
+
+*Bond style hybrid cannot have none as an argument*
+   Self-explanatory.
+
+*Bond style hybrid cannot use same bond style twice*
+   Self-explanatory.
+
+*Bond style quartic cannot be used with 3,4-body interactions*
+   No angle, dihedral, or improper styles can be defined when using
+   bond style quartic.
+
+*Bond style quartic cannot be used with atom style template*
+   This bond style can change the bond topology which is not
+   allowed with this atom style.
+
+*Bond style quartic requires special\_bonds = 1,1,1*
+   This is a restriction of the current bond quartic implementation.
+
+*Bond table parameters did not set N*
+   List of bond table parameters must include N setting.
+
+*Bond table values are not increasing*
+   The values in the tabulated file must be monotonically increasing.
+
+*BondAngle coeff for hybrid angle has invalid format*
+   No "ba" field should appear in data file entry.
+
+*BondBond coeff for hybrid angle has invalid format*
+   No "bb" field should appear in data file entry.
+
+*Bond\_coeff command before bond\_style is defined*
+   Coefficients cannot be set in the data file or via the bond\_coeff
+   command until an bond\_style has been assigned.
+
+*Bond\_coeff command before simulation box is defined*
+   The bond\_coeff command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Bond\_coeff command when no bonds allowed*
+   The chosen atom style does not allow for bonds to be defined.
+
+*Bond\_style command when no bonds allowed*
+   The chosen atom style does not allow for bonds to be defined.
+
+*Bonds assigned incorrectly*
+   Bonds read in from the data file were not assigned correctly to atoms.
+   This means there is something invalid about the topology definitions.
+
+*Bonds defined but no bond types*
+   The data file header lists bonds but no bond types.
+
+*Bond/react: Cannot use fix bond/react with non-molecular systems*
+   Only systems with bonds that can be changed can be used. Atom\_style
+   template does not qualify.
+
+*Bond/react: Rmax cutoff is longer than pairwise cutoff*
+   This is not allowed because bond creation is done using the pairwise
+   neighbor list.
+
+*Bond/react: Molecule template ID for fix bond/react does not exist*
+   A valid molecule template must have been created with the molecule
+   command.
+
+*Bond/react: Reaction templates must contain the same number of atoms*
+   There should be a one-to-one correspondence between atoms in the
+   pre-reacted and post-reacted templates, as specified by the map file.
+
+*Bond/react: Unknown section in map file*
+   Please ensure reaction map files are properly formatted.
+
+*Bond/react: Atom affected by reaction too close to template edge*
+   This means an atom which changes type or connectivity during the
+   reaction is too close to an 'edge' atom defined in the superimpose
+   file. This could cause incorrect assignment of bonds, angle, etc.
+   Generally, this means you must include more atoms in your templates,
+   such that there are at least two atoms between each atom involved in
+   the reaction and an edge atom.
+
+*Bond/react: Fix bond/react needs ghost atoms from farther away*
+   This is because a processor needs to superimpose the entire unreacted
+   molecule template onto simulation atoms it knows about. The
+   comm\_modify cutoff command can be used to extend the communication
+   range.
+
+*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
+   Self-explanatory.
+
+*Bond/react: First neighbors of chiral atoms must be of mutually different types*
+   Self-explanatory.
+
+*Bond/react: Chiral atoms must have exactly four first neighbors*
+   Self-explanatory.
+
+*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
+   The coordinates of atoms in the pre-reacted template are used to determine
+   chirality.
+
+*Bond/react special bond generation overflow*
+   The number of special bonds per-atom created by a reaction exceeds the
+   system setting. See the read\_data or create\_box command for how to
+   specify this value.
+
+*Bond/react topology/atom exceed system topology/atom*
+   The number of bonds, angles etc per-atom created by a reaction exceeds
+   the system setting. See the read\_data or create\_box command for how to
+   specify this value.
+
+*Both restart files must use % or neither*
+   Self-explanatory.
+
+*Both restart files must use MPI-IO or neither*
+   Self-explanatory.
+
+*Both sides of boundary must be periodic*
+   Cannot specify a boundary as periodic only on the lo or hi side.  Must
+   be periodic on both sides.
+
+*Boundary command after simulation box is defined*
+   The boundary command cannot be used after a read\_data, read\_restart,
+   or create\_box command.
+
+*Box bounds are invalid*
+   The box boundaries specified in the read\_data file are invalid.  The
+   lo value must be less than the hi value for all 3 dimensions.
+
+*Box command after simulation box is defined*
+   The box command cannot be used after a read\_data, read\_restart, or
+   create\_box command.
+
+*CPU neighbor lists must be used for ellipsoid/sphere mix.*
+   When using Gay-Berne or RE-squared pair styles with both ellipsoidal and
+   spherical particles, the neighbor list must be built on the CPU
+
+*Can not specify Pxy/Pxz/Pyz in fix box/relax with non-triclinic box*
+   Only triclinic boxes can be used with off-diagonal pressure components.
+   See the region prism command for details.
+
+*Can not specify Pxy/Pxz/Pyz in fix nvt/npt/nph with non-triclinic box*
+   Only triclinic boxes can be used with off-diagonal pressure components.
+   See the region prism command for details.
+
+*Can only use -plog with multiple partitions*
+   Self-explanatory.  See doc page discussion of command-line switches.
+
+*Can only use -pscreen with multiple partitions*
+   Self-explanatory.  See doc page discussion of command-line switches.
+
+*Can only use Kokkos supported regions with Kokkos package*
+   Self-explanatory.
+
+*Can only use NEB with 1-processor replicas*
+   This is current restriction for NEB as implemented in LAMMPS.
+
+*Can only use TAD with 1-processor replicas for NEB*
+   This is current restriction for NEB as implemented in LAMMPS.
+
+*Cannot (yet) do analytic differentiation with pppm/gpu*
+   This is a current restriction of this command.
+
+*Cannot (yet) request ghost atoms with Kokkos half neighbor list*
+   This feature is not yet supported.
+
+*Cannot (yet) use 'electron' units with dipoles*
+   This feature is not yet supported.
+
+*Cannot (yet) use Ewald with triclinic box and slab correction*
+   This feature is not yet supported.
+
+*Cannot (yet) use K-space slab correction with compute group/group for triclinic systems*
+   This option is not yet supported.
+
+*Cannot (yet) use MSM with 2d simulation*
+   This feature is not yet supported.
+
+*Cannot (yet) use PPPM with triclinic box and TIP4P*
+   This feature is not yet supported.
+
+*Cannot (yet) use PPPM with triclinic box and kspace\_modify diff ad*
+   This feature is not yet supported.
+
+*Cannot (yet) use PPPM with triclinic box and slab correction*
+   This feature is not yet supported.
+
+*Cannot (yet) use kspace slab correction with long-range dipoles and non-neutral systems or per-atom energy*
+   This feature is not yet supported.
+
+*Cannot (yet) use kspace\_modify diff ad with compute group/group*
+   This option is not yet supported.
+
+*Cannot (yet) use kspace\_style pppm/stagger with triclinic systems*
+   This feature is not yet supported.
+
+*Cannot (yet) use molecular templates with Kokkos*
+   Self-explanatory.
+
+*Cannot (yet) use respa with Kokkos*
+   Self-explanatory.
+
+*Cannot (yet) use rigid bodies with fix deform and Kokkos*
+   Self-explanatory.
+
+*Cannot (yet) use rigid bodies with fix nh and Kokkos*
+   Self-explanatory.
+
+*Cannot (yet) use single precision with MSM (remove -DFFT\_SINGLE from Makefile and re-compile)*
+   Single precision cannot be used with MSM.
+
+*Cannot add atoms to fix move variable*
+   Atoms can not be added afterwards to this fix option.
+
+*Cannot append atoms to a triclinic box*
+   The simulation box must be defined with edges aligned with the
+   Cartesian axes.
+
+*Cannot balance in z dimension for 2d simulation*
+   Self-explanatory.
+
+*Cannot change box ortho/triclinic with certain fixes defined*
+   This is because those fixes store the shape of the box.  You need to
+   use unfix to discard the fix, change the box, then redefine a new
+   fix.
+
+*Cannot change box ortho/triclinic with dumps defined*
+   This is because some dumps store the shape of the box.  You need to
+   use undump to discard the dump, change the box, then redefine a new
+   dump.
+
+*Cannot change box tilt factors for orthogonal box*
+   Cannot use tilt factors unless the simulation box is non-orthogonal.
+
+*Cannot change box to orthogonal when tilt is non-zero*
+   Self-explanatory.
+
+*Cannot change box z boundary to non-periodic for a 2d simulation*
+   Self-explanatory.
+
+*Cannot change dump\_modify every for dump dcd*
+   The frequency of writing dump dcd snapshots cannot be changed.
+
+*Cannot change dump\_modify every for dump xtc*
+   The frequency of writing dump xtc snapshots cannot be changed.
+
+*Cannot change timestep once fix srd is setup*
+   This is because various SRD properties depend on the timestep
+   size.
+
+*Cannot change timestep with fix pour*
+   This is because fix pour pre-computes the time delay for particles to
+   fall out of the insertion volume due to gravity.
+
+*Cannot change to comm\_style brick from tiled layout*
+   Self-explanatory.
+
+*Cannot change\_box after reading restart file with per-atom info*
+   This is because the restart file info cannot be migrated with the
+   atoms.  You can get around this by performing a 0-timestep run which
+   will assign the restart file info to actual atoms.
+
+*Cannot change\_box in xz or yz for 2d simulation*
+   Self-explanatory.
+
+*Cannot change\_box in z dimension for 2d simulation*
+   Self-explanatory.
+
+*Cannot clear group all*
+   This operation is not allowed.
+
+*Cannot close restart file - MPI error: %s*
+   This error was generated by MPI when reading/writing an MPI-IO restart
+   file.
+
+*Cannot compute initial g\_ewald\_disp*
+   LAMMPS failed to compute an initial guess for the PPPM\_disp g\_ewald\_6
+   factor that partitions the computation between real space and k-space
+   for Dispersion interactions.
+
+*Cannot create an atom map unless atoms have IDs*
+   The simulation requires a mapping from global atom IDs to local atoms,
+   but the atoms that have been defined have no IDs.
+
+*Cannot create atoms with undefined lattice*
+   Must use the lattice command before using the create\_atoms
+   command.
+
+*Cannot create/grow a vector/array of pointers for %s*
+   LAMMPS code is making an illegal call to the templated memory
+   allocaters, to create a vector or array of pointers.
+
+*Cannot create\_atoms after reading restart file with per-atom info*
+   The per-atom info was stored to be used when by a fix that you may
+   re-define.  If you add atoms before re-defining the fix, then there
+   will not be a correct amount of per-atom info.
+
+*Cannot create\_box after simulation box is defined*
+   A simulation box can only be defined once.
+
+*Cannot currently use pair reax with pair hybrid*
+   This is not yet supported.
+
+*Cannot currently use pppm/gpu with fix balance.*
+   Self-explanatory.
+
+*Cannot delete group all*
+   Self-explanatory.
+
+*Cannot delete group currently used by a compute*
+   Self-explanatory.
+
+*Cannot delete group currently used by a dump*
+   Self-explanatory.
+
+*Cannot delete group currently used by a fix*
+   Self-explanatory.
+
+*Cannot delete group currently used by atom\_modify first*
+   Self-explanatory.
+
+*Cannot delete\_atoms bond yes for non-molecular systems*
+   Self-explanatory.
+
+*Cannot displace\_atoms after reading restart file with per-atom info*
+   This is because the restart file info cannot be migrated with the
+   atoms.  You can get around this by performing a 0-timestep run which
+   will assign the restart file info to actual atoms.
+
+*Cannot do GCMC on atoms in atom\_modify first group*
+   This is a restriction due to the way atoms are organized in a list to
+   enable the atom\_modify first command.
+
+*Cannot do atom/swap on atoms in atom\_modify first group*
+   This is a restriction due to the way atoms are organized in a list to
+   enable the atom\_modify first command.
+
+*Cannot dump sort on atom IDs with no atom IDs defined*
+   Self-explanatory.
+
+*Cannot dump sort when multiple dump files are written*
+   In this mode, each processor dumps its atoms to a file, so
+   no sorting is allowed.
+
+*Cannot embed Python when also extending Python with LAMMPS*
+   When running LAMMPS via Python through the LAMMPS library interface
+   you cannot also user the input script python command.
+
+*Cannot evaporate atoms in atom\_modify first group*
+   This is a restriction due to the way atoms are organized in
+   a list to enable the atom\_modify first command.
+
+*Cannot find create\_bonds group ID*
+   Self-explanatory.
+
+*Cannot find delete\_bonds group ID*
+   Group ID used in the delete\_bonds command does not exist.
+
+*Cannot find specified group ID for core particles*
+   Self-explanatory.
+
+*Cannot find specified group ID for shell particles*
+   Self-explanatory.
+
+*Cannot have both pair\_modify shift and tail set to yes*
+   These 2 options are contradictory.
+
+*Cannot intersect groups using a dynamic group*
+   This operation is not allowed.
+
+*Cannot mix molecular and molecule template atom styles*
+   Self-explanatory.
+
+*Cannot open -reorder file*
+   Self-explanatory.
+
+*Cannot open ADP potential file %s*
+   The specified ADP potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open AIREBO potential file %s*
+   The specified AIREBO potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open BOP potential file %s*
+   The specified BOP potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open COMB potential file %s*
+   The specified COMB potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open COMB3 lib.comb3 file*
+   The COMB3 library file cannot be opened.  Check that the path and name
+   are correct.
+
+*Cannot open COMB3 potential file %s*
+   The specified COMB3 potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open EAM potential file %s*
+   The specified EAM potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open EIM potential file %s*
+   The specified EIM potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open LCBOP potential file %s*
+   The specified LCBOP potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open MEAM potential file %s*
+   The specified MEAM potential file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open SNAP coefficient file %s*
+   The specified SNAP coefficient file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open SNAP parameter file %s*
+   The specified SNAP parameter file cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open Stillinger-Weber potential file %s*
+   The specified SW potential file cannot be opened.  Check that the path
+   and name are correct.
+
+*Cannot open Tersoff potential file %s*
+   The specified potential file cannot be opened.  Check that the path
+   and name are correct.
+
+*Cannot open Vashishta potential file %s*
+   The specified Vashishta potential file cannot be opened.  Check that the path
+   and name are correct.
+
+*Cannot open balance output file*
+   Self-explanatory.
+
+*Cannot open coul/streitz potential file %s*
+   The specified coul/streitz potential file cannot be opened.  Check
+   that the path and name are correct.
+
+*Cannot open custom file*
+   Self-explanatory.
+
+*Cannot open data file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open dir to search for restart file*
+   Using a "\*" in the name of the restart file will open the current
+   directory to search for matching file names.
+
+*Cannot open dump file*
+   Self-explanatory.
+
+*Cannot open dump file %s*
+   The output file for the dump command cannot be opened.  Check that the
+   path and name are correct.
+
+*Cannot open file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct. If the file is a compressed file, also check that the gzip
+   executable can be found and run.
+
+*Cannot open file variable file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix ave/chunk file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix ave/correlate file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix ave/histo file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix ave/time file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix balance output file*
+   Self-explanatory.
+
+*Cannot open fix poems file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix print file %s*
+   The output file generated by the fix print command cannot be opened
+
+*Cannot open fix qeq parameter file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix qeq/comb file %s*
+   The output file for the fix qeq/combs command cannot be opened.
+   Check that the path and name are correct.
+
+*Cannot open fix reax/bonds file %s*
+   The output file for the fix reax/bonds command cannot be opened.
+   Check that the path and name are correct.
+
+*Cannot open fix rigid infile %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix rigid restart file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix rigid/small infile %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open fix tmd file %s*
+   The output file for the fix tmd command cannot be opened.  Check that
+   the path and name are correct.
+
+*Cannot open fix ttm file %s*
+   The output file for the fix ttm command cannot be opened.  Check that
+   the path and name are correct.
+
+*Cannot open gzipped file*
+   LAMMPS was compiled without support for reading and writing gzipped
+   files through a pipeline to the gzip program with -DLAMMPS\_GZIP.
+
+*Cannot open input script %s*
+   Self-explanatory.
+
+*Cannot open log.cite file*
+   This file is created when you use some LAMMPS features, to indicate
+   what paper you should cite on behalf of those who implemented
+   the feature.  Check that you have write privileges into the directory
+   you are running in.
+
+*Cannot open log.lammps for writing*
+   The default LAMMPS log file cannot be opened.  Check that the
+   directory you are running in allows for files to be created.
+
+*Cannot open logfile*
+   The LAMMPS log file named in a command-line argument cannot be opened.
+   Check that the path and name are correct.
+
+*Cannot open logfile %s*
+   The LAMMPS log file specified in the input script cannot be opened.
+   Check that the path and name are correct.
+
+*Cannot open molecule file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct.
+
+*Cannot open nb3b/harmonic potential file %s*
+   The specified potential file cannot be opened.  Check that the path
+   and name are correct.
+
+*Cannot open pair\_write file*
+   The specified output file for pair energies and forces cannot be
+   opened.  Check that the path and name are correct.
+
+*Cannot open polymorphic potential file %s*
+   The specified polymorphic potential file cannot be opened.  Check that
+   the path and name are correct.
+
+*Cannot open print file %s*
+   Self-explanatory.
+
+*Cannot open processors output file*
+   Self-explanatory.
+
+*Cannot open restart file %s*
+   Self-explanatory.
+
+*Cannot open restart file for reading - MPI error: %s*
+   This error was generated by MPI when reading/writing an MPI-IO restart
+   file.
+
+*Cannot open restart file for writing - MPI error: %s*
+   This error was generated by MPI when reading/writing an MPI-IO restart
+   file.
+
+*Cannot open screen file*
+   The screen file specified as a command-line argument cannot be
+   opened.  Check that the directory you are running in allows for files
+   to be created.
+
+*Cannot open temporary file for world counter.*
+   Self-explanatory.
+
+*Cannot open universe log file*
+   For a multi-partition run, the master log file cannot be opened.
+   Check that the directory you are running in allows for files to be
+   created.
+
+*Cannot open universe screen file*
+   For a multi-partition run, the master screen file cannot be opened.
+   Check that the directory you are running in allows for files to be
+   created.
+
+*Cannot read from restart file - MPI error: %s*
+   This error was generated by MPI when reading/writing an MPI-IO restart
+   file.
+
+*Cannot read\_data without add keyword after simulation box is defined*
+   Self-explanatory.
+
+*Cannot read\_restart after simulation box is defined*
+   The read\_restart command cannot be used after a read\_data,
+   read\_restart, or create\_box command.
+
+*Cannot redefine variable as a different style*
+   An equal-style variable can be re-defined but only if it was
+   originally an equal-style variable.
+
+*Cannot replicate 2d simulation in z dimension*
+   The replicate command cannot replicate a 2d simulation in the z
+   dimension.
+
+*Cannot replicate with fixes that store atom quantities*
+   Either fixes are defined that create and store atom-based vectors or a
+   restart file was read which included atom-based vectors for fixes.
+   The replicate command cannot duplicate that information for new atoms.
+   You should use the replicate command before fixes are applied to the
+   system.
+
+*Cannot reset timestep with a dynamic region defined*
+   Dynamic regions (see the region command) have a time dependence.
+   Thus you cannot change the timestep when one or more of these
+   are defined.
+
+*Cannot reset timestep with a time-dependent fix defined*
+   You cannot reset the timestep when a fix that keeps track of elapsed
+   time is in place.
+
+*Cannot run 2d simulation with non-periodic Z dimension*
+   Use the boundary command to make the z dimension periodic in order to
+   run a 2d simulation.
+
+*Cannot set bond topology types for atom style template*
+   The bond, angle, etc types cannot be changed for this atom style since
+   they are static settings in the molecule template files.
+
+*Cannot set both respa pair and inner/middle/outer*
+   In the rRESPA integrator, you must compute pairwise potentials either
+   all together (pair), or in pieces (inner/middle/outer).  You can't do
+   both.
+
+*Cannot set cutoff/multi before simulation box is defined*
+   Self-explanatory.
+
+*Cannot set dpd/theta for this atom style*
+   Self-explanatory.
+
+*Cannot set dump\_modify flush for dump xtc*
+   Self-explanatory.
+
+*Cannot set mass for this atom style*
+   This atom style does not support mass settings for each atom type.
+   Instead they are defined on a per-atom basis in the data file.
+
+*Cannot set meso/cv for this atom style*
+   Self-explanatory.
+
+*Cannot set meso/e for this atom style*
+   Self-explanatory.
+
+*Cannot set meso/rho for this atom style*
+   Self-explanatory.
+
+*Cannot set non-zero image flag for non-periodic dimension*
+   Self-explanatory.
+
+*Cannot set non-zero z velocity for 2d simulation*
+   Self-explanatory.
+
+*Cannot set quaternion for atom that has none*
+   Self-explanatory.
+
+*Cannot set quaternion with xy components for 2d system*
+   Self-explanatory.
+
+*Cannot set respa hybrid and any of pair/inner/middle/outer*
+   In the rRESPA integrator, you must compute pairwise potentials either
+   all together (pair), with different cutoff regions (inner/middle/outer),
+   or per hybrid sub-style (hybrid).  You cannot mix those.
+
+*Cannot set respa middle without inner/outer*
+   In the rRESPA integrator, you must define both a inner and outer
+   setting in order to use a middle setting.
+
+*Cannot set restart file size - MPI error: %s*
+   This error was generated by MPI when reading/writing an MPI-IO restart
+   file.
+
+*Cannot set smd/contact/radius for this atom style*
+   Self-explanatory.
+
+*Cannot set smd/mass/density for this atom style*
+   Self-explanatory.
+
+*Cannot set temperature for fix rigid/nph*
+   The temp keyword cannot be specified.
+
+*Cannot set theta for atom that is not a line*
+   Self-explanatory.
+
+*Cannot set this attribute for this atom style*
+   The attribute being set does not exist for the defined atom style.
+
+*Cannot set variable z velocity for 2d simulation*
+   Self-explanatory.
+
+*Cannot skew triclinic box in z for 2d simulation*
+   Self-explanatory.
+
+*Cannot subtract groups using a dynamic group*
+   This operation is not allowed.
+
+*Cannot union groups using a dynamic group*
+   This operation is not allowed.
+
+*Cannot use -kokkos on without KOKKOS installed*
+   Self-explanatory.
+
+*Cannot use -reorder after -partition*
+   Self-explanatory.  See doc page discussion of command-line switches.
+
+*Cannot use Ewald with 2d simulation*
+   The kspace style ewald cannot be used in 2d simulations.  You can use
+   2d Ewald in a 3d simulation; see the kspace\_modify command.
+
+*Cannot use Ewald/disp solver on system with no charge, dipole, or LJ particles*
+   No atoms in system have a non-zero charge or dipole, or are LJ
+   particles.  Change charges/dipoles or change options of the kspace
+   solver/pair style.
+
+*Cannot use EwaldDisp with 2d simulation*
+   This is a current restriction of this command.
+
+*Cannot use Kokkos pair style with rRESPA inner/middle*
+   Self-explanatory.
+
+*Cannot use NEB unless atom map exists*
+   Use the atom\_modify command to create an atom map.
+
+*Cannot use NEB with a single replica*
+   Self-explanatory.
+
+*Cannot use NEB with atom\_modify sort enabled*
+   This is current restriction for NEB implemented in LAMMPS.
+
+*Cannot use PPPM with 2d simulation*
+   The kspace style pppm cannot be used in 2d simulations.  You can use
+   2d PPPM in a 3d simulation; see the kspace\_modify command.
+
+*Cannot use PPPMDisp with 2d simulation*
+   The kspace style pppm/disp cannot be used in 2d simulations.  You can
+   use 2d pppm/disp in a 3d simulation; see the kspace\_modify command.
+
+*Cannot use PRD with a changing box*
+   The current box dimensions are not copied between replicas
+
+*Cannot use PRD with a time-dependent fix defined*
+   PRD alters the timestep in ways that will mess up these fixes.
+
+*Cannot use PRD with a time-dependent region defined*
+   PRD alters the timestep in ways that will mess up these regions.
+
+*Cannot use PRD with atom\_modify sort enabled*
+   This is a current restriction of PRD.  You must turn off sorting,
+   which is enabled by default, via the atom\_modify command.
+
+*Cannot use PRD with multi-processor replicas unless atom map exists*
+   Use the atom\_modify command to create an atom map.
+
+*Cannot use TAD unless atom map exists for NEB*
+   See atom\_modify map command to set this.
+
+*Cannot use TAD with a single replica for NEB*
+   NEB requires multiple replicas.
+
+*Cannot use TAD with atom\_modify sort enabled for NEB*
+   This is a current restriction of NEB.
+
+*Cannot use a damped dynamics min style with fix box/relax*
+   This is a current restriction in LAMMPS.  Use another minimizer
+   style.
+
+*Cannot use a damped dynamics min style with per-atom DOF*
+   This is a current restriction in LAMMPS.  Use another minimizer
+   style.
+
+*Cannot use append/atoms in periodic dimension*
+   The boundary style of the face where atoms are added can not be of
+   type p (periodic).
+
+*Cannot use atomfile-style variable unless atom map exists*
+   Self-explanatory.  See the atom\_modify command to create a map.
+
+*Cannot use both com and bias with compute temp/chunk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with buck/coul/cut/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with buck/coul/long/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with buck/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with coul/cut/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with coul/debye/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with coul/dsf/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with coul/wolf/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with lj/charmm/coul/charmm/implicit/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/charmm/coul/charmm/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/charmm/coul/long/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/class2/coul/cut/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/class2/coul/long/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/class2/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/cut/coul/cut/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with lj/cut/coul/debye/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/cut/coul/long/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with lj/cut/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with lj/expand/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/gromacs/coul/gromacs/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/gromacs/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/sdk/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with pair eam/kk*
+   That style is not supported by Kokkos.
+
+*Cannot use chosen neighbor list style with pair eam/kk/alloy*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with pair eam/kk/fs*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with pair sw/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with tersoff/kk*
+   Self-explanatory.
+
+*Cannot use chosen neighbor list style with tersoff/zbl/kk*
+   Self-explanatory.
+
+*Cannot use compute chunk/atom bin z for 2d model*
+   Self-explanatory.
+
+*Cannot use compute cluster/atom unless atoms have IDs*
+   Atom IDs are used to identify clusters.
+
+*Cannot use create\_atoms rotate unless single style*
+   Self-explanatory.
+
+*Cannot use create\_bonds unless atoms have IDs*
+   This command requires a mapping from global atom IDs to local atoms,
+   but the atoms that have been defined have no IDs.
+
+*Cannot use create\_bonds with non-molecular system*
+   Self-explanatory.
+
+*Cannot use cwiggle in variable formula between runs*
+   This is a function of elapsed time.
+
+*Cannot use delete\_atoms bond yes with atom\_style template*
+   This is because the bonds for that atom style are hardwired in the
+   molecule template.
+
+*Cannot use delete\_atoms unless atoms have IDs*
+   Your atoms do not have IDs, so the delete\_atoms command cannot be
+   used.
+
+*Cannot use delete\_bonds with non-molecular system*
+   Your choice of atom style does not have bonds.
+
+*Cannot use dump\_modify fileper without % in dump file name*
+   Self-explanatory.
+
+*Cannot use dump\_modify nfile without % in dump file name*
+   Self-explanatory.
+
+*Cannot use dynamic group with fix adapt atom*
+   This is not yet supported.
+
+*Cannot use fix TMD unless atom map exists*
+   Using this fix requires the ability to lookup an atom index, which is
+   provided by an atom map.  An atom map does not exist (by default) for
+   non-molecular problems.  Using the atom\_modify map command will force
+   an atom map to be created.
+
+*Cannot use fix bond/break with non-molecular systems*
+   Only systems with bonds that can be changed can be used.  Atom\_style
+   template does not qualify.
+
+*Cannot use fix bond/create with non-molecular systems*
+   Only systems with bonds that can be changed can be used.  Atom\_style
+   template does not qualify.
+
+*Cannot use fix bond/swap with non-molecular systems*
+   Only systems with bonds that can be changed can be used.  Atom\_style
+   template does not qualify.
+
+*Cannot use fix box/relax on a 2nd non-periodic dimension*
+   When specifying an off-diagonal pressure component, the 2nd of the two
+   dimensions must be periodic.  E.g. if the xy component is specified,
+   then the y dimension must be periodic.
+
+*Cannot use fix box/relax on a non-periodic dimension*
+   When specifying a diagonal pressure component, the dimension must be
+   periodic.
+
+*Cannot use fix box/relax with both relaxation and scaling on a tilt factor*
+   When specifying scaling on a tilt factor component, that component can not
+   also be controlled by the barostat. E.g. if scalexy yes is specified and
+   also keyword tri or xy, this is wrong.
+
+*Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension*
+   When specifying scaling on a tilt factor component, the 2nd of the two
+   dimensions must be periodic.  E.g. if the xy component is specified,
+   then the y dimension must be periodic.
+
+*Cannot use fix deform on a shrink-wrapped boundary*
+   The x, y, z options cannot be applied to shrink-wrapped
+   dimensions.
+
+*Cannot use fix deform tilt on a shrink-wrapped 2nd dim*
+   This is because the shrink-wrapping will change the value
+   of the strain implied by the tilt factor.
+
+*Cannot use fix deform trate on a box with zero tilt*
+   The trate style alters the current strain.
+
+*Cannot use fix deposit rigid and not molecule*
+   Self-explanatory.
+
+*Cannot use fix deposit rigid and shake*
+   These two attributes are conflicting.
+
+*Cannot use fix deposit shake and not molecule*
+   Self-explanatory.
+
+*Cannot use fix enforce2d with 3d simulation*
+   Self-explanatory.
+
+*Cannot use fix gcmc in a 2d simulation*
+   Fix gcmc is set up to run in 3d only. No 2d simulations with fix gcmc
+   are allowed.
+
+*Cannot use fix gcmc shake and not molecule*
+   Self-explanatory.
+
+*Cannot use fix msst without per-type mass defined*
+   Self-explanatory.
+
+*Cannot use fix npt and fix deform on same component of stress tensor*
+   This would be changing the same box dimension twice.
+
+*Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension*
+   When specifying an off-diagonal pressure component, the 2nd of the two
+   dimensions must be periodic.  E.g. if the xy component is specified,
+   then the y dimension must be periodic.
+
+*Cannot use fix nvt/npt/nph on a non-periodic dimension*
+   When specifying a diagonal pressure component, the dimension must be
+   periodic.
+
+*Cannot use fix nvt/npt/nph with both xy dynamics and xy scaling*
+   Self-explanatory.
+
+*Cannot use fix nvt/npt/nph with both xz dynamics and xz scaling*
+   Self-explanatory.
+
+*Cannot use fix nvt/npt/nph with both yz dynamics and yz scaling*
+   Self-explanatory.
+
+*Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension*
+   The 2nd dimension in the barostatted tilt factor must be periodic.
+
+*Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension*
+   The 2nd dimension in the barostatted tilt factor must be periodic.
+
+*Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension*
+   The 2nd dimension in the barostatted tilt factor must be periodic.
+
+*Cannot use fix pour rigid and not molecule*
+   Self-explanatory.
+
+*Cannot use fix pour rigid and shake*
+   These two attributes are conflicting.
+
+*Cannot use fix pour shake and not molecule*
+   Self-explanatory.
+
+*Cannot use fix pour with triclinic box*
+   This option is not yet supported.
+
+*Cannot use fix press/berendsen and fix deform on same component of stress tensor*
+   These commands both change the box size/shape, so you cannot use both
+   together.
+
+*Cannot use fix press/berendsen on a non-periodic dimension*
+   Self-explanatory.
+
+*Cannot use fix press/berendsen with triclinic box*
+   Self-explanatory.
+
+*Cannot use fix reax/bonds without pair\_style reax*
+   Self-explanatory.
+
+*Cannot use fix rigid npt/nph and fix deform on same component of stress tensor*
+   This would be changing the same box dimension twice.
+
+*Cannot use fix rigid npt/nph on a non-periodic dimension*
+   When specifying a diagonal pressure component, the dimension must be
+   periodic.
+
+*Cannot use fix rigid/small npt/nph on a non-periodic dimension*
+   When specifying a diagonal pressure component, the dimension must be
+   periodic.
+
+*Cannot use fix shake with non-molecular system*
+   Your choice of atom style does not have bonds.
+
+*Cannot use fix ttm with 2d simulation*
+   This is a current restriction of this fix due to the grid it creates.
+
+*Cannot use fix ttm with triclinic box*
+   This is a current restriction of this fix due to the grid it creates.
+
+*Cannot use fix tune/kspace without a kspace style*
+   Self-explanatory.
+
+*Cannot use fix tune/kspace without a pair style*
+   This fix (tune/kspace) can only be used when a pair style has been specified.
+
+*Cannot use fix wall in periodic dimension*
+   Self-explanatory.
+
+*Cannot use fix wall zlo/zhi for a 2d simulation*
+   Self-explanatory.
+
+*Cannot use fix wall/reflect in periodic dimension*
+   Self-explanatory.
+
+*Cannot use fix wall/reflect zlo/zhi for a 2d simulation*
+   Self-explanatory.
+
+*Cannot use fix wall/srd in periodic dimension*
+   Self-explanatory.
+
+*Cannot use fix wall/srd more than once*
+   Nor is their a need to since multiple walls can be specified
+   in one command.
+
+*Cannot use fix wall/srd without fix srd*
+   Self-explanatory.
+
+*Cannot use fix wall/srd zlo/zhi for a 2d simulation*
+   Self-explanatory.
+
+*Cannot use fix\_deposit unless atoms have IDs*
+   Self-explanatory.
+
+*Cannot use fix\_pour unless atoms have IDs*
+   Self-explanatory.
+
+*Cannot use include command within an if command*
+   Self-explanatory.
+
+*Cannot use lines with fix srd unless overlap is set*
+   This is because line segments are connected to each other.
+
+*Cannot use multiple fix wall commands with pair brownian*
+   Self-explanatory.
+
+*Cannot use multiple fix wall commands with pair lubricate*
+   Self-explanatory.
+
+*Cannot use multiple fix wall commands with pair lubricate/poly*
+   Self-explanatory.
+
+*Cannot use multiple fix wall commands with pair lubricateU*
+   Self-explanatory.
+
+*Cannot use neigh\_modify exclude with GPU neighbor builds*
+   This is a current limitation of the GPU implementation
+   in LAMMPS.
+
+*Cannot use neighbor bins - box size << cutoff*
+   Too many neighbor bins will be created.  This typically happens when
+   the simulation box is very small in some dimension, compared to the
+   neighbor cutoff.  Use the "nsq" style instead of "bin" style.
+
+*Cannot use newton pair with beck/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with born/coul/long/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with born/coul/wolf/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with born/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with buck/coul/cut/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with buck/coul/long/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with buck/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with colloid/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with coul/cut/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with coul/debye/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with coul/dsf/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with coul/long/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with dipole/cut/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with dipole/sf/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with dpd/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with dpd/tstat/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with eam/alloy/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with eam/fs/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with eam/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with gauss/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with gayberne/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/charmm/coul/long/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/class2/coul/long/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/class2/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/cubic/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/cut/coul/cut/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/cut/coul/debye/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/cut/coul/dsf/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/cut/coul/long/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/cut/coul/msm/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/cut/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/expand/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/gromacs/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj/sdk/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with lj96/cut/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with mie/cut/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with morse/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with resquared/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with soft/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with table/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with yukawa/colloid/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with yukawa/gpu pair style*
+   Self-explanatory.
+
+*Cannot use newton pair with zbl/gpu pair style*
+   Self-explanatory.
+
+*Cannot use non-zero forces in an energy minimization*
+   Fix setforce cannot be used in this manner.  Use fix addforce
+   instead.
+
+*Cannot use non-periodic boundares with fix ttm*
+   This fix requires a fully periodic simulation box.
+
+*Cannot use non-periodic boundaries with Ewald*
+   For kspace style ewald, all 3 dimensions must have periodic boundaries
+   unless you use the kspace\_modify command to define a 2d slab with a
+   non-periodic z dimension.
+
+*Cannot use non-periodic boundaries with EwaldDisp*
+   For kspace style ewald/disp, all 3 dimensions must have periodic
+   boundaries unless you use the kspace\_modify command to define a 2d
+   slab with a non-periodic z dimension.
+
+*Cannot use non-periodic boundaries with PPPM*
+   For kspace style pppm, all 3 dimensions must have periodic boundaries
+   unless you use the kspace\_modify command to define a 2d slab with a
+   non-periodic z dimension.
+
+*Cannot use non-periodic boundaries with PPPMDisp*
+   For kspace style pppm/disp, all 3 dimensions must have periodic
+   boundaries unless you use the kspace\_modify command to define a 2d
+   slab with a non-periodic z dimension.
+
+*Cannot use order greater than 8 with pppm/gpu.*
+   Self-explanatory.
+
+*Cannot use package gpu neigh yes with triclinic box*
+   This is a current restriction in LAMMPS.
+
+*Cannot use pair tail corrections with 2d simulations*
+   The correction factors are only currently defined for 3d systems.
+
+*Cannot use processors part command without using partitions*
+   See the command-line -partition switch.
+
+*Cannot use ramp in variable formula between runs*
+   This is because the ramp() function is time dependent.
+
+*Cannot use read\_data add before simulation box is defined*
+   Self-explanatory.
+
+*Cannot use read\_data extra with add flag*
+   Self-explanatory.
+
+*Cannot use read\_data offset without add flag*
+   Self-explanatory.
+
+*Cannot use read\_data shift without add flag*
+   Self-explanatory.
+
+*Cannot use region INF or EDGE when box does not exist*
+   Regions that extend to the box boundaries can only be used after the
+   create\_box command has been used.
+
+*Cannot use set atom with no atom IDs defined*
+   Atom IDs are not defined, so they cannot be used to identify an atom.
+
+*Cannot use set mol with no molecule IDs defined*
+   Self-explanatory.
+
+*Cannot use swiggle in variable formula between runs*
+   This is a function of elapsed time.
+
+*Cannot use tris with fix srd unless overlap is set*
+   This is because triangles are connected to each other.
+
+*Cannot use variable energy with constant efield in fix efield*
+   LAMMPS computes the energy itself when the E-field is constant.
+
+*Cannot use variable energy with constant force in fix addforce*
+   This is because for constant force, LAMMPS can compute the change
+   in energy directly.
+
+*Cannot use variable every setting for dump dcd*
+   The format of DCD dump files requires snapshots be output
+   at a constant frequency.
+
+*Cannot use variable every setting for dump xtc*
+   The format of this file requires snapshots at regular intervals.
+
+*Cannot use vdisplace in variable formula between runs*
+   This is a function of elapsed time.
+
+*Cannot use velocity bias command without temp keyword*
+   Self-explanatory.
+
+*Cannot use velocity create loop all unless atoms have IDs*
+   Atoms in the simulation to do not have IDs, so this style
+   of velocity creation cannot be performed.
+
+*Cannot use wall in periodic dimension*
+   Self-explanatory.
+
+*Cannot use write\_restart fileper without % in restart file name*
+   Self-explanatory.
+
+*Cannot use write\_restart nfile without % in restart file name*
+   Self-explanatory.
+
+*Cannot wiggle and shear fix wall/gran*
+   Cannot specify both options at the same time.
+
+*Cannot write to restart file - MPI error: %s*
+   This error was generated by MPI when reading/writing an MPI-IO restart
+   file.
+
+*Cannot yet use KSpace solver with grid with comm style tiled*
+   This is current restriction in LAMMPS.
+
+*Cannot yet use comm\_style tiled with multi-mode comm*
+   Self-explanatory.
+
+*Cannot yet use comm\_style tiled with triclinic box*
+   Self-explanatory.
+
+*Cannot yet use compute tally with Kokkos*
+   This feature is not yet supported.
+
+*Cannot yet use fix bond/break with this improper style*
+   This is a current restriction in LAMMPS.
+
+*Cannot yet use fix bond/create with this improper style*
+   This is a current restriction in LAMMPS.
+
+*Cannot yet use minimize with Kokkos*
+   This feature is not yet supported.
+
+*Cannot yet use pair hybrid with Kokkos*
+   This feature is not yet supported.
+
+*Cannot zero Langevin force of 0 atoms*
+   The group has zero atoms, so you cannot request its force
+   be zeroed.
+
+*Cannot zero gld force for zero atoms*
+   There are no atoms currently in the group.
+
+*Cannot zero momentum of no atoms*
+   Self-explanatory.
+
+*Change\_box command before simulation box is defined*
+   Self-explanatory.
+
+*Change\_box volume used incorrectly*
+   The "dim volume" option must be used immediately following one or two
+   settings for "dim1 ..." (and optionally "dim2 ...") and must be for a
+   different dimension, i.e. dim != dim1 and dim != dim2.
+
+*Chunk/atom compute does not exist for compute angmom/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute com/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute gyration/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute inertia/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute msd/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute omega/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute property/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute temp/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute torque/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for compute vcm/chunk*
+   Self-explanatory.
+
+*Chunk/atom compute does not exist for fix ave/chunk*
+   Self-explanatory.
+
+*Comm tiled invalid index in box drop brick*
+   Internal error check in comm\_style tiled which should not occur.
+   Contact the developers.
+
+*Comm tiled mis-match in box drop brick*
+   Internal error check in comm\_style tiled which should not occur.
+   Contact the developers.
+
+*Comm\_modify group != atom\_modify first group*
+   Self-explanatory.
+
+*Communication cutoff for comm\_style tiled cannot exceed periodic box length*
+   Self-explanatory.
+
+*Communication cutoff too small for SNAP micro load balancing*
+   This can happen if you change the neighbor skin after your pair\_style
+   command or if your box dimensions grow during a run. You can set the
+   cutoff explicitly via the comm\_modify cutoff command.
+
+*Compute %s does not allow use of dynamic group*
+   Dynamic groups have not yet been enabled for this compute.
+
+*Compute ID for compute chunk /atom does not exist*
+   Self-explanatory.
+
+*Compute ID for compute chunk/atom does not exist*
+   Self-explanatory.
+
+*Compute gyration ID does not exist for compute gyration/shape*
+   Self-explanatory. Provide a valid compute ID.
+
+*Compute gyration/shape compute ID does not point to a gyration compute*
+   Self-explanatory. Provide and ID of a compute gyration command.
+
+*Compute ID for compute reduce does not exist*
+   Self-explanatory.
+
+*Compute ID for compute slice does not exist*
+   Self-explanatory.
+
+*Compute ID for fix ave/atom does not exist*
+   Self-explanatory.
+
+*Compute ID for fix ave/chunk does not exist*
+   Self-explanatory.
+
+*Compute ID for fix ave/correlate does not exist*
+   Self-explanatory.
+
+*Compute ID for fix ave/histo does not exist*
+   Self-explanatory.
+
+*Compute ID for fix ave/time does not exist*
+   Self-explanatory.
+
+*Compute ID for fix store/state does not exist*
+   Self-explanatory.
+
+*Compute ID for fix vector does not exist*
+   Self-explanatory.
+
+*Compute ID must be alphanumeric or underscore characters*
+   Self-explanatory.
+
+*Compute angle/local used when angles are not allowed*
+   The atom style does not support angles.
+
+*Compute angmom/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute body/local requires atom style body*
+   Self-explanatory.
+
+*Compute bond/local used when bonds are not allowed*
+   The atom style does not support bonds.
+
+*Compute centro/atom requires a pair style be defined*
+   This is because the computation of the centro-symmetry values
+   uses a pairwise neighbor list.
+
+*Compute chunk/atom bin/cylinder radius is too large for periodic box*
+   Radius cannot be bigger than 1/2 of a non-axis  periodic dimension.
+
+*Compute chunk/atom bin/sphere radius is too large for periodic box*
+   Radius cannot be bigger than 1/2 of any periodic dimension.
+
+*Compute chunk/atom compute array is accessed out-of-range*
+   The index for the array is out of bounds.
+
+*Compute chunk/atom compute does not calculate a per-atom array*
+   Self-explanatory.
+
+*Compute chunk/atom compute does not calculate a per-atom vector*
+   Self-explanatory.
+
+*Compute chunk/atom compute does not calculate per-atom values*
+   Self-explanatory.
+
+*Compute chunk/atom cylinder axis must be z for 2d*
+   Self-explanatory.
+
+*Compute chunk/atom fix array is accessed out-of-range*
+   the index for the array is out of bounds.
+
+*Compute chunk/atom fix does not calculate a per-atom array*
+   Self-explanatory.
+
+*Compute chunk/atom fix does not calculate a per-atom vector*
+   Self-explanatory.
+
+*Compute chunk/atom fix does not calculate per-atom values*
+   Self-explanatory.
+
+*Compute chunk/atom for triclinic boxes requires units reduced*
+   Self-explanatory.
+
+*Compute chunk/atom ids once but nchunk is not once*
+   You cannot assign chunks IDs to atom permanently if the number of
+   chunks may change.
+
+*Compute chunk/atom molecule for non-molecular system*
+   Self-explanatory.
+
+*Compute chunk/atom sphere z origin must be 0.0 for 2d*
+   Self-explanatory.
+
+*Compute chunk/atom stores no IDs for compute property/chunk*
+   It will only store IDs if its compress option is enabled.
+
+*Compute chunk/atom stores no coord1 for compute property/chunk*
+   Only certain binning options for compute chunk/atom store coordinates.
+
+*Compute chunk/atom stores no coord2 for compute property/chunk*
+   Only certain binning options for compute chunk/atom store coordinates.
+
+*Compute chunk/atom stores no coord3 for compute property/chunk*
+   Only certain binning options for compute chunk/atom store coordinates.
+
+*Compute chunk/atom variable is not atom-style variable*
+   Self-explanatory.
+
+*Compute chunk/atom without bins cannot use discard mixed*
+   That discard option only applies to the binning styles.
+
+*Compute cluster/atom cutoff is longer than pairwise cutoff*
+   Cannot identify clusters beyond cutoff.
+
+*Compute cluster/atom requires a pair style be defined*
+   This is so that the pair style defines a cutoff distance which
+   is used to find clusters.
+
+*Compute cna/atom cutoff is longer than pairwise cutoff*
+   Self-explanatory.
+
+*Compute cna/atom requires a pair style be defined*
+   Self-explanatory.
+
+*Compute com/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute contact/atom requires a pair style be defined*
+   Self-explanatory.
+
+*Compute contact/atom requires atom style sphere*
+   Self-explanatory.
+
+*Compute coord/atom cutoff is longer than pairwise cutoff*
+   Cannot compute coordination at distances longer than the pair cutoff,
+   since those atoms are not in the neighbor list.
+
+*Compute coord/atom requires a pair style be defined*
+   Self-explanatory.
+
+*Compute damage/atom requires peridynamic potential*
+   Damage is a Peridynamic-specific metric.  It requires you
+   to be running a Peridynamics simulation.
+
+*Compute dihedral/local used when dihedrals are not allowed*
+   The atom style does not support dihedrals.
+
+*Compute dilatation/atom cannot be used with this pair style*
+   Self-explanatory.
+
+*Compute dilatation/atom requires Peridynamic pair style*
+   Self-explanatory.
+
+*Compute does not allow an extra compute or fix to be reset*
+   This is an internal LAMMPS error.  Please report it to the
+   developers.
+
+*Compute erotate/asphere requires atom style ellipsoid or line or tri*
+   Self-explanatory.
+
+*Compute erotate/asphere requires extended particles*
+   This compute cannot be used with point particles.
+
+*Compute erotate/rigid with non-rigid fix-ID*
+   Self-explanatory.
+
+*Compute erotate/sphere requires atom style sphere*
+   Self-explanatory.
+
+*Compute erotate/sphere/atom requires atom style sphere*
+   Self-explanatory.
+
+*Compute event/displace has invalid fix event assigned*
+   This is an internal LAMMPS error.  Please report it to the
+   developers.
+
+*Compute group/group group ID does not exist*
+   Self-explanatory.
+
+*Compute gyration/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute heat/flux compute ID does not compute ke/atom*
+   Self-explanatory.
+
+*Compute heat/flux compute ID does not compute pe/atom*
+   Self-explanatory.
+
+*Compute heat/flux compute ID does not compute stress/atom*
+   Self-explanatory.
+
+*Compute hexorder/atom cutoff is longer than pairwise cutoff*
+   Cannot compute order parameter beyond cutoff.
+
+*Compute hexorder/atom requires a pair style be defined*
+   Self-explanatory.
+
+*Compute improper/local used when impropers are not allowed*
+   The atom style does not support impropers.
+
+*Compute inertia/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute ke/rigid with non-rigid fix-ID*
+   Self-explanatory.
+
+*Compute msd/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute msd/chunk nchunk is not static*
+   This is required because the MSD cannot be computed consistently if
+   the number of chunks is changing.  Compute chunk/atom allows setting
+   nchunk to be static.
+
+*Compute nve/asphere requires atom style ellipsoid*
+   Self-explanatory.
+
+*Compute nvt/nph/npt asphere requires atom style ellipsoid*
+   Self-explanatory.
+
+*Compute nvt/nph/npt body requires atom style body*
+   Self-explanatory.
+
+*Compute omega/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute orientorder/atom cutoff is longer than pairwise cutoff*
+   Cannot compute order parameter beyond cutoff.
+
+*Compute orientorder/atom requires a pair style be defined*
+   Self-explanatory.
+
+*Compute pair must use group all*
+   Pair styles accumulate energy on all atoms.
+
+*Compute pe must use group all*
+   Energies computed by potentials (pair, bond, etc) are computed on all
+   atoms.
+
+*Compute plasticity/atom cannot be used with this pair style*
+   Self-explanatory.
+
+*Compute plasticity/atom requires Peridynamic pair style*
+   Self-explanatory.
+
+*Compute pressure must use group all*
+   Virial contributions computed by potentials (pair, bond, etc) are
+   computed on all atoms.
+
+*Compute pressure requires temperature ID to include kinetic energy*
+   The keflag cannot be used unless a temperature compute is provided.
+
+*Compute pressure temperature ID does not compute temperature*
+   The compute ID assigned to a pressure computation must compute
+   temperature.
+
+*Compute property/atom floating point vector does not exist*
+   The command is accessing a vector added by the fix property/atom
+   command, that does not exist.
+
+*Compute property/atom for atom property that isn't allocated*
+   Self-explanatory.
+
+*Compute property/atom integer vector does not exist*
+   The command is accessing a vector added by the fix property/atom
+   command, that does not exist.
+
+*Compute property/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute property/local cannot use these inputs together*
+   Only inputs that generate the same number of datums can be used
+   together.  E.g. bond and angle quantities cannot be mixed.
+
+*Compute property/local does not (yet) work with atom\_style template*
+   Self-explanatory.
+
+*Compute property/local for property that isn't allocated*
+   Self-explanatory.
+
+*Compute rdf requires a pair style be defined*
+   Self-explanatory.
+
+*Compute reduce compute array is accessed out-of-range*
+   An index for the array is out of bounds.
+
+*Compute reduce compute calculates global values*
+   A compute that calculates peratom or local values is required.
+
+*Compute reduce compute does not calculate a local array*
+   Self-explanatory.
+
+*Compute reduce compute does not calculate a local vector*
+   Self-explanatory.
+
+*Compute reduce compute does not calculate a per-atom array*
+   Self-explanatory.
+
+*Compute reduce compute does not calculate a per-atom vector*
+   Self-explanatory.
+
+*Compute reduce fix array is accessed out-of-range*
+   An index for the array is out of bounds.
+
+*Compute reduce fix calculates global values*
+   A fix that calculates peratom or local values is required.
+
+*Compute reduce fix does not calculate a local array*
+   Self-explanatory.
+
+*Compute reduce fix does not calculate a local vector*
+   Self-explanatory.
+
+*Compute reduce fix does not calculate a per-atom array*
+   Self-explanatory.
+
+*Compute reduce fix does not calculate a per-atom vector*
+   Self-explanatory.
+
+*Compute reduce replace requires min or max mode*
+   Self-explanatory.
+
+*Compute reduce variable is not atom-style variable*
+   Self-explanatory.
+
+*Compute slice compute array is accessed out-of-range*
+   An index for the array is out of bounds.
+
+*Compute slice compute does not calculate a global array*
+   Self-explanatory.
+
+*Compute slice compute does not calculate a global vector*
+   Self-explanatory.
+
+*Compute slice compute does not calculate global vector or array*
+   Self-explanatory.
+
+*Compute slice compute vector is accessed out-of-range*
+   The index for the vector is out of bounds.
+
+*Compute slice fix array is accessed out-of-range*
+   An index for the array is out of bounds.
+
+*Compute slice fix does not calculate a global array*
+   Self-explanatory.
+
+*Compute slice fix does not calculate a global vector*
+   Self-explanatory.
+
+*Compute slice fix does not calculate global vector or array*
+   Self-explanatory.
+
+*Compute slice fix vector is accessed out-of-range*
+   The index for the vector is out of bounds.
+
+*Compute sna/atom cutoff is longer than pairwise cutoff*
+   Self-explanatory.
+
+*Compute sna/atom requires a pair style be defined*
+   Self-explanatory.
+
+*Compute snad/atom cutoff is longer than pairwise cutoff*
+   Self-explanatory.
+
+*Compute snad/atom requires a pair style be defined*
+   Self-explanatory.
+
+*Compute snav/atom cutoff is longer than pairwise cutoff*
+   Self-explanatory.
+
+*Compute snav/atom requires a pair style be defined*
+   Self-explanatory.
+
+*Compute stress/atom temperature ID does not compute temperature*
+   The specified compute must compute temperature.
+
+*Compute temp/asphere requires atom style ellipsoid*
+   Self-explanatory.
+
+*Compute temp/asphere requires extended particles*
+   This compute cannot be used with point particles.
+
+*Compute temp/body requires atom style body*
+   Self-explanatory.
+
+*Compute temp/body requires bodies*
+   This compute can only be applied to body particles.
+
+*Compute temp/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute temp/cs requires ghost atoms store velocity*
+   Use the comm\_modify vel yes command to enable this.
+
+*Compute temp/cs used when bonds are not allowed*
+   This compute only works on pairs of bonded particles.
+
+*Compute temp/partial cannot use vz for 2d systemx*
+   Self-explanatory.
+
+*Compute temp/profile cannot bin z for 2d systems*
+   Self-explanatory.
+
+*Compute temp/profile cannot use vz for 2d systemx*
+   Self-explanatory.
+
+*Compute temp/sphere requires atom style sphere*
+   Self-explanatory.
+
+*Compute ti kspace style does not exist*
+   Self-explanatory.
+
+*Compute ti pair style does not exist*
+   Self-explanatory.
+
+*Compute ti tail when pair style does not compute tail corrections*
+   Self-explanatory.
+
+*Compute torque/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Compute used in dump between runs is not current*
+   The compute was not invoked on the current timestep, therefore it
+   cannot be used in a dump between runs.
+
+*Compute used in variable between runs is not current*
+   Computes cannot be invoked by a variable in between runs.  Thus they
+   must have been evaluated on the last timestep of the previous run in
+   order for their value(s) to be accessed.  See the doc page for the
+   variable command for more info.
+
+*Compute used in variable thermo keyword between runs is not current*
+   Some thermo keywords rely on a compute to calculate their value(s).
+   Computes cannot be invoked by a variable in between runs.  Thus they
+   must have been evaluated on the last timestep of the previous run in
+   order for their value(s) to be accessed.  See the doc page for the
+   variable command for more info.
+
+*Compute vcm/chunk does not use chunk/atom compute*
+   The style of the specified compute is not chunk/atom.
+
+*Computed temperature for fix temp/berendsen cannot be 0.0*
+   Self-explanatory.
+
+*Computed temperature for fix temp/rescale cannot be 0.0*
+   Cannot rescale the temperature to a new value if the current
+   temperature is 0.0.
+
+*Core/shell partner atom not found*
+   Could not find one of the atoms in the bond pair.
+
+*Core/shell partners were not all found*
+   Could not find or more atoms in the bond pairs.
+
+*Could not adjust g\_ewald\_6*
+   The Newton-Raphson solver failed to converge to a good value for
+   g\_ewald.  This error should not occur for typical problems.  Please
+   send an email to the developers.
+
+*Could not compute g\_ewald*
+   The Newton-Raphson solver failed to converge to a good value for
+   g\_ewald.  This error should not occur for typical problems.  Please
+   send an email to the developers.
+
+*Could not compute grid size*
+   The code is unable to compute a grid size consistent with the desired
+   accuracy.  This error should not occur for typical problems.  Please
+   send an email to the developers.
+
+*Could not compute grid size for Coulomb interaction*
+   The code is unable to compute a grid size consistent with the desired
+   accuracy.  This error should not occur for typical problems.  Please
+   send an email to the developers.
+
+*Could not compute grid size for Dispersion*
+   The code is unable to compute a grid size consistent with the desired
+   accuracy.  This error should not occur for typical problems.  Please
+   send an email to the developers.
+
+*Could not create 3d FFT plan*
+   The FFT setup for the PPPM solver failed, typically due
+   to lack of memory.  This is an unusual error.  Check the
+   size of the FFT grid you are requesting.
+
+*Could not create 3d grid of processors*
+   The specified constraints did not allow a Px by Py by Pz grid to be
+   created where Px \* Py \* Pz = P = total number of processors.
+
+*Could not create 3d remap plan*
+   The FFT setup in pppm failed.
+
+*Could not create Python function arguments*
+   This is an internal Python error, possibly because the number
+   of inputs to the function is too large.
+
+*Could not create numa grid of processors*
+   The specified constraints did not allow this style of grid to be
+   created.  Usually this is because the total processor count is not a
+   multiple of the cores/node or the user specified processor count is >
+   1 in one of the dimensions.
+
+*Could not create twolevel 3d grid of processors*
+   The specified constraints did not allow this style of grid to be
+   created.
+
+*Could not evaluate Python function input variable*
+   Self-explanatory.
+
+*Could not find Python function*
+   The provided Python code was run successfully, but it not
+   define a callable function with the required name.
+
+*Could not find atom\_modify first group ID*
+   Self-explanatory.
+
+*Could not find change\_box group ID*
+   Group ID used in the change\_box command does not exist.
+
+*Could not find compute ID for PRD*
+   Self-explanatory.
+
+*Could not find compute ID for TAD*
+   Self-explanatory.
+
+*Could not find compute ID for temperature bias*
+   Self-explanatory.
+
+*Could not find compute ID to delete*
+   Self-explanatory.
+
+*Could not find compute displace/atom fix ID*
+   Self-explanatory.
+
+*Could not find compute event/displace fix ID*
+   Self-explanatory.
+
+*Could not find compute group ID*
+   Self-explanatory.
+
+*Could not find compute heat/flux compute ID*
+   Self-explanatory.
+
+*Could not find compute msd fix ID*
+   Self-explanatory.
+
+*Could not find compute msd/chunk fix ID*
+   The compute creates an internal fix, which has been deleted.
+
+*Could not find compute pressure temperature ID*
+   The compute ID for calculating temperature does not exist.
+
+*Could not find compute stress/atom temperature ID*
+   Self-explanatory.
+
+*Could not find compute vacf fix ID*
+   Self-explanatory.
+
+*Could not find compute/voronoi surface group ID*
+   Self-explanatory.
+
+*Could not find compute\_modify ID*
+   Self-explanatory.
+
+*Could not find custom per-atom property ID*
+   Self-explanatory.
+
+*Could not find delete\_atoms group ID*
+   Group ID used in the delete\_atoms command does not exist.
+
+*Could not find delete\_atoms region ID*
+   Region ID used in the delete\_atoms command does not exist.
+
+*Could not find displace\_atoms group ID*
+   Group ID used in the displace\_atoms command does not exist.
+
+*Could not find dump custom compute ID*
+   Self-explanatory.
+
+*Could not find dump custom fix ID*
+   Self-explanatory.
+
+*Could not find dump custom variable name*
+   Self-explanatory.
+
+*Could not find dump group ID*
+   A group ID used in the dump command does not exist.
+
+*Could not find dump local compute ID*
+   Self-explanatory.
+
+*Could not find dump local fix ID*
+   Self-explanatory.
+
+*Could not find dump modify compute ID*
+   Self-explanatory.
+
+*Could not find dump modify custom atom floating point property ID*
+   Self-explanatory.
+
+*Could not find dump modify custom atom integer property ID*
+   Self-explanatory.
+
+*Could not find dump modify fix ID*
+   Self-explanatory.
+
+*Could not find dump modify variable name*
+   Self-explanatory.
+
+*Could not find fix ID to delete*
+   Self-explanatory.
+
+*Could not find fix adapt storage fix ID*
+   This should not happen unless you explicitly deleted
+   a secondary fix that fix adapt created internally.
+
+*Could not find fix gcmc exclusion group ID*
+   Self-explanatory.
+
+*Could not find fix gcmc rotation group ID*
+   Self-explanatory.
+
+*Could not find fix group ID*
+   A group ID used in the fix command does not exist.
+
+*Could not find fix msst compute ID*
+   Self-explanatory.
+
+*Could not find fix poems group ID*
+   A group ID used in the fix poems command does not exist.
+
+*Could not find fix recenter group ID*
+   A group ID used in the fix recenter command does not exist.
+
+*Could not find fix rigid group ID*
+   A group ID used in the fix rigid command does not exist.
+
+*Could not find fix srd group ID*
+   Self-explanatory.
+
+*Could not find fix\_modify ID*
+   A fix ID used in the fix\_modify command does not exist.
+
+*Could not find fix\_modify pressure ID*
+   The compute ID for computing pressure does not exist.
+
+*Could not find fix\_modify temperature ID*
+   The compute ID for computing temperature does not exist.
+
+*Could not find group clear group ID*
+   Self-explanatory.
+
+*Could not find group delete group ID*
+   Self-explanatory.
+
+*Could not find pair fix ID*
+   A fix is created internally by the pair style to store shear
+   history information.  You cannot delete it.
+
+*Could not find set group ID*
+   Group ID specified in set command does not exist.
+
+*Could not find specified fix gcmc group ID*
+   Self-explanatory.
+
+*Could not find thermo compute ID*
+   Compute ID specified in thermo\_style command does not exist.
+
+*Could not find thermo custom compute ID*
+   The compute ID needed by thermo style custom to compute a requested
+   quantity does not exist.
+
+*Could not find thermo custom fix ID*
+   The fix ID needed by thermo style custom to compute a requested
+   quantity does not exist.
+
+*Could not find thermo custom variable name*
+   Self-explanatory.
+
+*Could not find thermo fix ID*
+   Fix ID specified in thermo\_style command does not exist.
+
+*Could not find thermo variable name*
+   Self-explanatory.
+
+*Could not find thermo\_modify pressure ID*
+   The compute ID needed by thermo style custom to compute pressure does
+   not exist.
+
+*Could not find thermo\_modify temperature ID*
+   The compute ID needed by thermo style custom to compute temperature does
+   not exist.
+
+*Could not find undump ID*
+   A dump ID used in the undump command does not exist.
+
+*Could not find velocity group ID*
+   A group ID used in the velocity command does not exist.
+
+*Could not find velocity temperature ID*
+   The compute ID needed by the velocity command to compute temperature
+   does not exist.
+
+*Could not find/initialize a specified accelerator device*
+   Could not initialize at least one of the devices specified for the gpu
+   package
+
+*Could not grab element entry from EIM potential file*
+   Self-explanatory
+
+*Could not grab global entry from EIM potential file*
+   Self-explanatory.
+
+*Could not grab pair entry from EIM potential file*
+   Self-explanatory.
+
+*Could not initialize embedded Python*
+   The main module in Python was not accessible.
+
+*Could not open Python file*
+   The specified file of Python code cannot be opened.  Check that the
+   path and name are correct.
+
+*Could not process Python file*
+   The Python code in the specified file was not run successfully by
+   Python, probably due to errors in the Python code.
+
+*Could not process Python string*
+   The Python code in the here string was not run successfully by Python,
+   probably due to errors in the Python code.
+
+*Coulomb PPPMDisp order has been reduced below minorder*
+   The default minimum order is 2.  This can be reset by the
+   kspace\_modify minorder command.
+
+*Coulombic cutoff not supported in pair\_style buck/long/coul/coul*
+   Must use long-range Coulombic interactions.
+
+*Coulombic cutoff not supported in pair\_style lj/long/coul/long*
+   Must use long-range Coulombic interactions.
+
+*Coulombic cutoff not supported in pair\_style lj/long/tip4p/long*
+   Must use long-range Coulombic interactions.
+
+*Coulombic cutoffs of pair hybrid sub-styles do not match*
+   If using a Kspace solver, all Coulombic cutoffs of long pair styles must
+   be the same.
+
+*Coulombic cut not supported in pair\_style lj/long/dipole/long*
+   Must use long-range Coulombic interactions.
+
+*Cound not find dump\_modify ID*
+   Self-explanatory.
+
+*Create\_atoms command before simulation box is defined*
+   The create\_atoms command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Create\_atoms molecule has atom IDs, but system does not*
+   The atom\_style id command can be used to force atom IDs to be stored.
+
+*Create\_atoms molecule must have atom types*
+   The defined molecule does not specify atom types.
+
+*Create\_atoms molecule must have coordinates*
+   The defined molecule does not specify coordinates.
+
+*Create\_atoms region ID does not exist*
+   A region ID used in the create\_atoms command does not exist.
+
+*Create\_bonds command before simulation box is defined*
+   Self-explanatory.
+
+*Create\_bonds command requires no kspace\_style be defined*
+   This is so that atom pairs that are already bonded to not appear
+   in the neighbor list.
+
+*Create\_bonds command requires special\_bonds 1-2 weights be 0.0*
+   This is so that atom pairs that are already bonded to not appear in
+   the neighbor list.
+
+*Create\_bonds max distance > neighbor cutoff*
+   Can only create bonds for atom pairs that will be in neighbor list.
+
+*Create\_bonds requires a pair style be defined*
+   Self-explanatory.
+
+*Create\_box region ID does not exist*
+   Self-explanatory.
+
+*Create\_box region does not support a bounding box*
+   Not all regions represent bounded volumes.  You cannot use
+   such a region with the create\_box command.
+
+*Custom floating point vector for fix store/state does not exist*
+   The command is accessing a vector added by the fix property/atom
+   command, that does not exist.
+
+*Custom integer vector for fix store/state does not exist*
+   The command is accessing a vector added by the fix property/atom
+   command, that does not exist.
+
+*Custom per-atom property ID is not floating point*
+   Self-explanatory.
+
+*Custom per-atom property ID is not integer*
+   Self-explanatory.
+
+*Cut-offs missing in pair\_style lj/long/dipole/long*
+   Self-explanatory.
+
+*Cutoffs missing in pair\_style buck/long/coul/long*
+   Self-explanatory.
+
+*Cutoffs missing in pair\_style lj/long/coul/long*
+   Self-explanatory.
+
+*Cyclic loop in joint connections*
+   Fix poems cannot (yet) work with coupled bodies whose joints connect
+   the bodies in a ring (or cycle).
+
+*Degenerate lattice primitive vectors*
+   Invalid set of 3 lattice vectors for lattice command.
+
+*Delete region ID does not exist*
+   Self-explanatory.
+
+*Delete\_atoms command before simulation box is defined*
+   The delete\_atoms command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Delete\_atoms cutoff > max neighbor cutoff*
+   Can only delete atoms in atom pairs that will be in neighbor list.
+
+*Delete\_atoms mol yes requires atom attribute molecule*
+   Cannot use this option with a non-molecular system.
+
+*Delete\_atoms requires a pair style be defined*
+   This is because atom deletion within a cutoff uses a pairwise
+   neighbor list.
+
+*Delete\_bonds command before simulation box is defined*
+   The delete\_bonds command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Delete\_bonds command with no atoms existing*
+   No atoms are yet defined so the delete\_bonds command cannot be used.
+
+*Deposition region extends outside simulation box*
+   Self-explanatory.
+
+*Did not assign all atoms correctly*
+   Atoms read in from a data file were not assigned correctly to
+   processors.  This is likely due to some atom coordinates being
+   outside a non-periodic simulation box.
+
+*Did not assign all restart atoms correctly*
+   Atoms read in from the restart file were not assigned correctly to
+   processors.  This is likely due to some atom coordinates being outside
+   a non-periodic simulation box.  Normally this should not happen.  You
+   may wish to use the "remap" option on the read\_restart command to see
+   if this helps.
+
+*Did not find all elements in MEAM library file*
+   The requested elements were not found in the MEAM file.
+
+*Did not find fix shake partner info*
+   Could not find bond partners implied by fix shake command.  This error
+   can be triggered if the delete\_bonds command was used before fix
+   shake, and it removed bonds without resetting the 1-2, 1-3, 1-4
+   weighting list via the special keyword.
+
+*Did not find keyword in table file*
+   Keyword used in pair\_coeff command was not found in table file.
+
+*Did not set pressure for fix rigid/nph*
+   The press keyword must be specified.
+
+*Did not set temp for fix rigid/nvt/small*
+   Self-explanatory.
+
+*Did not set temp or press for fix rigid/npt/small*
+   Self-explanatory.
+
+*Did not set temperature for fix rigid/nvt*
+   The temp keyword must be specified.
+
+*Did not set temperature or pressure for fix rigid/npt*
+   The temp and press keywords must be specified.
+
+*Dihedral atom missing in delete\_bonds*
+   The delete\_bonds command cannot find one or more atoms in a particular
+   dihedral on a particular processor.  The pairwise cutoff is too short
+   or the atoms are too far apart to make a valid dihedral.
+
+*Dihedral atom missing in set command*
+   The set command cannot find one or more atoms in a particular dihedral
+   on a particular processor.  The pairwise cutoff is too short or the
+   atoms are too far apart to make a valid dihedral.
+
+*Dihedral atoms %d %d %d %d missing on proc %d at step %ld*
+   One or more of 4 atoms needed to compute a particular dihedral are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the dihedral has blown apart and an atom is
+   too far away.
+
+*Dihedral atoms missing on proc %d at step %ld*
+   One or more of 4 atoms needed to compute a particular dihedral are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the dihedral has blown apart and an atom is
+   too far away.
+
+*Dihedral charmm is incompatible with Pair style*
+   Dihedral style charmm must be used with a pair style charmm
+   in order for the 1-4 epsilon/sigma parameters to be defined.
+
+*Dihedral coeff for hybrid has invalid style*
+   Dihedral style hybrid uses another dihedral style as one of its
+   coefficients.  The dihedral style used in the dihedral\_coeff command
+   or read from a restart file is not recognized.
+
+*Dihedral coeffs are not set*
+   No dihedral coefficients have been assigned in the data file or via
+   the dihedral\_coeff command.
+
+*Dihedral style hybrid cannot have hybrid as an argument*
+   Self-explanatory.
+
+*Dihedral style hybrid cannot have none as an argument*
+   Self-explanatory.
+
+*Dihedral style hybrid cannot use same dihedral style twice*
+   Self-explanatory.
+
+*Dihedral/improper extent > half of periodic box length*
+   This error was detected by the neigh\_modify check yes setting.  It is
+   an error because the dihedral atoms are so far apart it is ambiguous
+   how it should be defined.
+
+*Dihedral\_coeff command before dihedral\_style is defined*
+   Coefficients cannot be set in the data file or via the dihedral\_coeff
+   command until an dihedral\_style has been assigned.
+
+*Dihedral\_coeff command before simulation box is defined*
+   The dihedral\_coeff command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Dihedral\_coeff command when no dihedrals allowed*
+   The chosen atom style does not allow for dihedrals to be defined.
+
+*Dihedral\_style command when no dihedrals allowed*
+   The chosen atom style does not allow for dihedrals to be defined.
+
+*Dihedrals assigned incorrectly*
+   Dihedrals read in from the data file were not assigned correctly to
+   atoms.  This means there is something invalid about the topology
+   definitions.
+
+*Dihedrals defined but no dihedral types*
+   The data file header lists dihedrals but no dihedral types.
+
+*Dimension command after simulation box is defined*
+   The dimension command cannot be used after a read\_data,
+   read\_restart, or create\_box command.
+
+*Dispersion PPPMDisp order has been reduced below minorder*
+   The default minimum order is 2.  This can be reset by the
+   kspace\_modify minorder command.
+
+*Displace\_atoms command before simulation box is defined*
+   The displace\_atoms command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Distance must be > 0 for compute event/displace*
+   Self-explanatory.
+
+*Divide by 0 in influence function*
+   This should not normally occur.  It is likely a problem with your
+   model.
+
+*Divide by 0 in influence function of pair peri/lps*
+   This should not normally occur.  It is likely a problem with your
+   model.
+
+*Divide by 0 in variable formula*
+   Self-explanatory.
+
+*Domain too large for neighbor bins*
+   The domain has become extremely large so that neighbor bins cannot be
+   used.  Most likely, one or more atoms have been blown out of the
+   simulation box to a great distance.
+
+*Double precision is not supported on this accelerator*
+   Self-explanatory
+
+*Dump atom/gz only writes compressed files*
+   The dump atom/gz output file name must have a .gz suffix.
+
+*Dump cfg arguments can not mix xs\|ys\|zs with xsu\|ysu\|zsu*
+   Self-explanatory.
+
+*Dump cfg arguments must start with 'mass type xs ys zs' or 'mass type xsu ysu zsu'*
+   This is a requirement of the CFG output format.  See the dump cfg doc
+   page for more details.
+
+*Dump cfg requires one snapshot per file*
+   Use the wildcard "\*" character in the filename.
+
+*Dump cfg/gz only writes compressed files*
+   The dump cfg/gz output file name must have a .gz suffix.
+
+*Dump custom and fix not computed at compatible times*
+   The fix must produce per-atom quantities on timesteps that dump custom
+   needs them.
+
+*Dump custom compute does not calculate per-atom array*
+   Self-explanatory.
+
+*Dump custom compute does not calculate per-atom vector*
+   Self-explanatory.
+
+*Dump custom compute does not compute per-atom info*
+   Self-explanatory.
+
+*Dump custom compute vector is accessed out-of-range*
+   Self-explanatory.
+
+*Dump custom fix does not compute per-atom array*
+   Self-explanatory.
+
+*Dump custom fix does not compute per-atom info*
+   Self-explanatory.
+
+*Dump custom fix does not compute per-atom vector*
+   Self-explanatory.
+
+*Dump custom fix vector is accessed out-of-range*
+   Self-explanatory.
+
+*Dump custom variable is not atom-style variable*
+   Only atom-style variables generate per-atom quantities, needed for
+   dump output.
+
+*Dump custom/gz only writes compressed files*
+   The dump custom/gz output file name must have a .gz suffix.
+
+*Dump dcd of non-matching # of atoms*
+   Every snapshot written by dump dcd must contain the same # of atoms.
+
+*Dump dcd requires sorting by atom ID*
+   Use the dump\_modify sort command to enable this.
+
+*Dump every variable returned a bad timestep*
+   The variable must return a timestep greater than the current timestep.
+
+*Dump file MPI-IO output not allowed with % in filename*
+   This is because a % signifies one file per processor and MPI-IO
+   creates one large file for all processors.
+
+*Dump file does not contain requested snapshot*
+   Self-explanatory.
+
+*Dump file is incorrectly formatted*
+   Self-explanatory.
+
+*Dump image body yes requires atom style body*
+   Self-explanatory.
+
+*Dump image bond not allowed with no bond types*
+   Self-explanatory.
+
+*Dump image cannot perform sorting*
+   Self-explanatory.
+
+*Dump image line requires atom style line*
+   Self-explanatory.
+
+*Dump image persp option is not yet supported*
+   Self-explanatory.
+
+*Dump image requires one snapshot per file*
+   Use a "\*" in the filename.
+
+*Dump image tri requires atom style tri*
+   Self-explanatory.
+
+*Dump local and fix not computed at compatible times*
+   The fix must produce per-atom quantities on timesteps that dump local
+   needs them.
+
+*Dump local attributes contain no compute or fix*
+   Self-explanatory.
+
+*Dump local cannot sort by atom ID*
+   This is because dump local does not really dump per-atom info.
+
+*Dump local compute does not calculate local array*
+   Self-explanatory.
+
+*Dump local compute does not calculate local vector*
+   Self-explanatory.
+
+*Dump local compute does not compute local info*
+   Self-explanatory.
+
+*Dump local compute vector is accessed out-of-range*
+   Self-explanatory.
+
+*Dump local count is not consistent across input fields*
+   Every column of output must be the same length.
+
+*Dump local fix does not compute local array*
+   Self-explanatory.
+
+*Dump local fix does not compute local info*
+   Self-explanatory.
+
+*Dump local fix does not compute local vector*
+   Self-explanatory.
+
+*Dump local fix vector is accessed out-of-range*
+   Self-explanatory.
+
+*Dump modify bcolor not allowed with no bond types*
+   Self-explanatory.
+
+*Dump modify bdiam not allowed with no bond types*
+   Self-explanatory.
+
+*Dump modify compute ID does not compute per-atom array*
+   Self-explanatory.
+
+*Dump modify compute ID does not compute per-atom info*
+   Self-explanatory.
+
+*Dump modify compute ID does not compute per-atom vector*
+   Self-explanatory.
+
+*Dump modify compute ID vector is not large enough*
+   Self-explanatory.
+
+*Dump modify element names do not match atom types*
+   Number of element names must equal number of atom types.
+
+*Dump modify fix ID does not compute per-atom array*
+   Self-explanatory.
+
+*Dump modify fix ID does not compute per-atom info*
+   Self-explanatory.
+
+*Dump modify fix ID does not compute per-atom vector*
+   Self-explanatory.
+
+*Dump modify fix ID vector is not large enough*
+   Self-explanatory.
+
+*Dump modify variable is not atom-style variable*
+   Self-explanatory.
+
+*Dump sort column is invalid*
+   Self-explanatory.
+
+*Dump xtc requires sorting by atom ID*
+   Use the dump\_modify sort command to enable this.
+
+*Dump xyz/gz only writes compressed files*
+   The dump xyz/gz output file name must have a .gz suffix.
+
+*Dump\_modify buffer yes not allowed for this style*
+   Self-explanatory.
+
+*Dump\_modify format string is too short*
+   There are more fields to be dumped in a line of output than your
+   format string specifies.
+
+*Dump\_modify region ID does not exist*
+   Self-explanatory.
+
+*Dumping an atom property that isn't allocated*
+   The chosen atom style does not define the per-atom quantity being
+   dumped.
+
+*Duplicate atom IDs exist*
+   Self-explanatory.
+
+*Duplicate fields in read\_dump command*
+   Self-explanatory.
+
+*Duplicate particle in PeriDynamic bond - simulation box is too small*
+   This is likely because your box length is shorter than 2 times
+   the bond length.
+
+*Electronic temperature dropped below zero*
+   Something has gone wrong with the fix ttm electron temperature model.
+
+*Element not defined in potential file*
+   The specified element is not in the potential file.
+
+*Empty brackets in variable*
+   There is no variable syntax that uses empty brackets.  Check
+   the variable doc page.
+
+*Energy was not tallied on needed timestep*
+   You are using a thermo keyword that requires potentials to
+   have tallied energy, but they didn't on this timestep.  See the
+   variable doc page for ideas on how to make this work.
+
+*Epsilon or sigma reference not set by pair style in PPPMDisp*
+   Self-explanatory.
+
+*Epsilon or sigma reference not set by pair style in ewald/n*
+   The pair style is not providing the needed epsilon or sigma values.
+
+*Error in vdw spline: inner radius > outer radius*
+   A pre-tabulated spline is invalid.  Likely a problem with the
+   potential parameters.
+
+*Error writing averaged chunk data*
+   Something in the output to the file triggered an error.
+
+*Error writing file header*
+   Something in the output to the file triggered an error.
+
+*Error writing out correlation data*
+   Something in the output to the file triggered an error.
+
+*Error writing out histogram data*
+   Something in the output to the file triggered an error.
+
+*Error writing out time averaged data*
+   Something in the output to the file triggered an error.
+
+*Failed to allocate %ld bytes for array %s*
+   Your LAMMPS simulation has run out of memory.  You need to run a
+   smaller simulation or on more processors.
+
+*Failed to open FFmpeg pipeline to file %s*
+   The specified file cannot be opened.  Check that the path and name are
+   correct and writable and that the FFmpeg executable can be found and run.
+
+*Failed to reallocate %ld bytes for array %s*
+   Your LAMMPS simulation has run out of memory.  You need to run a
+   smaller simulation or on more processors.
+
+*Fewer SRD bins than processors in some dimension*
+   This is not allowed.  Make your SRD bin size smaller.
+
+*File variable could not read value*
+   Check the file assigned to the variable.
+
+*Final box dimension due to fix deform is < 0.0*
+   Self-explanatory.
+
+*Fix %s does not allow use of dynamic group*
+   Dynamic groups have not yet been enabled for this fix.
+
+*Fix ID for compute chunk/atom does not exist*
+   Self-explanatory.
+
+*Fix ID for compute erotate/rigid does not exist*
+   Self-explanatory.
+
+*Fix ID for compute ke/rigid does not exist*
+   Self-explanatory.
+
+*Fix ID for compute reduce does not exist*
+   Self-explanatory.
+
+*Fix ID for compute slice does not exist*
+   Self-explanatory.
+
+*Fix ID for fix ave/atom does not exist*
+   Self-explanatory.
+
+*Fix ID for fix ave/chunk does not exist*
+   Self-explanatory.
+
+*Fix ID for fix ave/correlate does not exist*
+   Self-explanatory.
+
+*Fix ID for fix ave/histo does not exist*
+   Self-explanatory.
+
+*Fix ID for fix ave/time does not exist*
+   Self-explanatory.
+
+*Fix ID for fix store/state does not exist*
+   Self-explanatory
+
+*Fix ID for fix vector does not exist*
+   Self-explanatory.
+
+*Fix ID for read\_data does not exist*
+   Self-explanatory.
+
+*Fix ID for velocity does not exist*
+   Self-explanatory.
+
+*Fix ID must be alphanumeric or underscore characters*
+   Self-explanatory.
+
+*Fix SRD: bad bin assignment for SRD advection*
+   Something has gone wrong in your SRD model; try using more
+   conservative settings.
+
+*Fix SRD: bad search bin assignment*
+   Something has gone wrong in your SRD model; try using more
+   conservative settings.
+
+*Fix SRD: bad stencil bin for big particle*
+   Something has gone wrong in your SRD model; try using more
+   conservative settings.
+
+*Fix SRD: too many big particles in bin*
+   Reset the ATOMPERBIN parameter at the top of fix\_srd.cpp
+   to a larger value, and re-compile the code.
+
+*Fix SRD: too many walls in bin*
+   This should not happen unless your system has been setup incorrectly.
+
+*Fix adapt interface to this pair style not supported*
+   New coding for the pair style would need to be done.
+
+*Fix adapt kspace style does not exist*
+   Self-explanatory.
+
+*Fix adapt pair style does not exist*
+   Self-explanatory
+
+*Fix adapt pair style param not supported*
+   The pair style does not know about the parameter you specified.
+
+*Fix adapt requires atom attribute charge*
+   The atom style being used does not specify an atom charge.
+
+*Fix adapt requires atom attribute diameter*
+   The atom style being used does not specify an atom diameter.
+
+*Fix adapt type pair range is not valid for pair hybrid sub-style*
+   Self-explanatory.
+
+*Fix append/atoms requires a lattice be defined*
+   Use the lattice command for this purpose.
+
+*Fix ave/atom compute array is accessed out-of-range*
+   Self-explanatory.
+
+*Fix ave/atom compute does not calculate a per-atom array*
+   Self-explanatory.
+
+*Fix ave/atom compute does not calculate a per-atom vector*
+   A compute used by fix ave/atom must generate per-atom values.
+
+*Fix ave/atom compute does not calculate per-atom values*
+   A compute used by fix ave/atom must generate per-atom values.
+
+*Fix ave/atom fix array is accessed out-of-range*
+   Self-explanatory.
+
+*Fix ave/atom fix does not calculate a per-atom array*
+   Self-explanatory.
+
+*Fix ave/atom fix does not calculate a per-atom vector*
+   A fix used by fix ave/atom must generate per-atom values.
+
+*Fix ave/atom fix does not calculate per-atom values*
+   A fix used by fix ave/atom must generate per-atom values.
+
+*Fix ave/atom variable is not atom-style variable*
+   A variable used by fix ave/atom must generate per-atom values.
+
+*Fix ave/chunk compute does not calculate a per-atom array*
+   Self-explanatory.
+
+*Fix ave/chunk compute does not calculate a per-atom vector*
+   Self-explanatory.
+
+*Fix ave/chunk compute does not calculate per-atom values*
+   Self-explanatory.
+
+*Fix ave/chunk compute vector is accessed out-of-range*
+   Self-explanatory.
+
+*Fix ave/chunk does not use chunk/atom compute*
+   The specified compute is not for a compute chunk/atom command.
+
+*Fix ave/chunk fix does not calculate a per-atom array*
+   Self-explanatory.
+
+*Fix ave/chunk fix does not calculate a per-atom vector*
+   Self-explanatory.
+
+*Fix ave/chunk fix does not calculate per-atom values*
+   Self-explanatory.
+
+*Fix ave/chunk fix vector is accessed out-of-range*
+   Self-explanatory.
+
+*Fix ave/chunk variable is not atom-style variable*
+   Self-explanatory.
+
+*Fix ave/correlate compute does not calculate a scalar*
+   Self-explanatory.
+
+*Fix ave/correlate compute does not calculate a vector*
+   Self-explanatory.
+
+*Fix ave/correlate compute vector is accessed out-of-range*
+   The index for the vector is out of bounds.
+
+*Fix ave/correlate fix does not calculate a scalar*
+   Self-explanatory.
+
+*Fix ave/correlate fix does not calculate a vector*
+   Self-explanatory.
+
+*Fix ave/correlate fix vector is accessed out-of-range*
+   The index for the vector is out of bounds.
+
+*Fix ave/correlate variable is not equal-style variable*
+   Self-explanatory.
+
+*Fix ave/histo cannot input local values in scalar mode*
+   Self-explanatory.
+
+*Fix ave/histo cannot input per-atom values in scalar mode*
+   Self-explanatory.
+
+*Fix ave/histo compute array is accessed out-of-range*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate a global array*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate a global scalar*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate a global vector*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate a local array*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate a local vector*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate a per-atom array*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate a per-atom vector*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate local values*
+   Self-explanatory.
+
+*Fix ave/histo compute does not calculate per-atom values*
+   Self-explanatory.
+
+*Fix ave/histo compute vector is accessed out-of-range*
+   Self-explanatory.
+
+*Fix ave/histo fix array is accessed out-of-range*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate a global array*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate a global scalar*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate a global vector*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate a local array*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate a local vector*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate a per-atom array*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate a per-atom vector*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate local values*
+   Self-explanatory.
+
+*Fix ave/histo fix does not calculate per-atom values*
+   Self-explanatory.
+
+*Fix ave/histo fix vector is accessed out-of-range*
+   Self-explanatory.
+
+*Fix ave/histo input is invalid compute*
+   Self-explanatory.
+
+*Fix ave/histo input is invalid fix*
+   Self-explanatory.
+
+*Fix ave/histo input is invalid variable*
+   Self-explanatory.
+
+*Fix ave/histo inputs are not all global, peratom, or local*
+   All inputs in a single fix ave/histo command must be of the
+   same style.
+
+*Fix ave/histo/weight value and weight vector lengths do not match*
+   Self-explanatory.
+
+*Fix ave/time cannot set output array intensive/extensive from these inputs*
+   One of more of the vector inputs has individual elements which are
+   flagged as intensive or extensive.  Such an input cannot be flagged as
+   all intensive/extensive when turned into an array by fix ave/time.
+
+*Fix ave/time cannot use variable with vector mode*
+   Variables produce scalar values.
+
+*Fix ave/time columns are inconsistent lengths*
+   Self-explanatory.
+
+*Fix ave/time compute array is accessed out-of-range*
+   An index for the array is out of bounds.
+
+*Fix ave/time compute does not calculate a scalar*
+   Self-explanatory.
+
+*Fix ave/time compute does not calculate a vector*
+   Self-explanatory.
+
+*Fix ave/time compute does not calculate an array*
+   Self-explanatory.
+
+*Fix ave/time compute vector is accessed out-of-range*
+   The index for the vector is out of bounds.
+
+*Fix ave/time fix array cannot be variable length*
+   Self-explanatory.
+
+*Fix ave/time fix array is accessed out-of-range*
+   An index for the array is out of bounds.
+
+*Fix ave/time fix does not calculate a scalar*
+   Self-explanatory.
+
+*Fix ave/time fix does not calculate a vector*
+   Self-explanatory.
+
+*Fix ave/time fix does not calculate an array*
+   Self-explanatory.
+
+*Fix ave/time fix vector cannot be variable length*
+   Self-explanatory.
+
+*Fix ave/time fix vector is accessed out-of-range*
+   The index for the vector is out of bounds.
+
+*Fix ave/time variable is not equal-style variable*
+   Self-explanatory.
+
+*Fix balance rcb cannot be used with comm\_style brick*
+   Comm\_style tiled must be used instead.
+
+*Fix balance shift string is invalid*
+   The string can only contain the characters "x", "y", or "z".
+
+*Fix bond/break needs ghost atoms from further away*
+   This is because the fix needs to walk bonds to a certain distance to
+   acquire needed info, The comm\_modify cutoff command can be used to
+   extend the communication range.
+
+*Fix bond/create angle type is invalid*
+   Self-explanatory.
+
+*Fix bond/create cutoff is longer than pairwise cutoff*
+   This is not allowed because bond creation is done using the
+   pairwise neighbor list.
+
+*Fix bond/create dihedral type is invalid*
+   Self-explanatory.
+
+*Fix bond/create improper type is invalid*
+   Self-explanatory.
+
+*Fix bond/create induced too many angles/dihedrals/impropers per atom*
+   See the read\_data command for info on using the "extra/angle/per/atom",
+   (or dihedral, improper) keywords to allow for additional
+   angles, dihedrals, and impropers to be formed.
+
+*Fix bond/create needs ghost atoms from further away*
+   This is because the fix needs to walk bonds to a certain distance to
+   acquire needed info, The comm\_modify cutoff command can be used to
+   extend the communication range.
+
+*Fix bond/swap cannot use dihedral or improper styles*
+   These styles cannot be defined when using this fix.
+
+*Fix bond/swap requires pair and bond styles*
+   Self-explanatory.
+
+*Fix bond/swap requires special\_bonds = 0,1,1*
+   Self-explanatory.
+
+*Fix box/relax generated negative box length*
+   The pressure being applied is likely too large.  Try applying
+   it incrementally, to build to the high pressure.
+
+*Fix command before simulation box is defined*
+   The fix command cannot be used before a read\_data, read\_restart, or
+   create\_box command.
+
+*Fix deform cannot use yz variable with xy*
+   The yz setting cannot be a variable if xy deformation is also
+   specified.  This is because LAMMPS cannot determine if the yz setting
+   will induce a box flip which would be invalid if xy is also changing.
+
+*Fix deform is changing yz too much with xy*
+   When both yz and xy are changing, it induces changes in xz if the
+   box must flip from one tilt extreme to another.  Thus it is not
+   allowed for yz to grow so much that a flip is induced.
+
+*Fix deform tilt factors require triclinic box*
+   Cannot deform the tilt factors of a simulation box unless it
+   is a triclinic (non-orthogonal) box.
+
+*Fix deform volume setting is invalid*
+   Cannot use volume style unless other dimensions are being controlled.
+
+*Fix deposit and fix rigid/small not using same molecule template ID*
+   Self-explanatory.
+
+*Fix deposit and fix shake not using same molecule template ID*
+   Self-explanatory.
+
+*Fix deposit molecule must have atom types*
+   The defined molecule does not specify atom types.
+
+*Fix deposit molecule must have coordinates*
+   The defined molecule does not specify coordinates.
+
+*Fix deposit molecule template ID must be same as atom\_style template ID*
+   When using atom\_style template, you cannot deposit molecules that are
+   not in that template.
+
+*Fix deposit region cannot be dynamic*
+   Only static regions can be used with fix deposit.
+
+*Fix deposit region does not support a bounding box*
+   Not all regions represent bounded volumes.  You cannot use
+   such a region with the fix deposit command.
+
+*Fix deposit shake fix does not exist*
+   Self-explanatory.
+
+*Fix efield requires atom attribute q or mu*
+   The atom style defined does not have this attribute.
+
+*Fix efield with dipoles cannot use atom-style variables*
+   This option is not supported.
+
+*Fix evaporate molecule requires atom attribute molecule*
+   The atom style being used does not define a molecule ID.
+
+*Fix external callback function not set*
+   This must be done by an external program in order to use this fix.
+
+*Fix for fix ave/atom not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Fix ave/atom is
+   requesting a value on a non-allowed timestep.
+
+*Fix for fix ave/chunk not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Fix ave/chunk is
+   requesting a value on a non-allowed timestep.
+
+*Fix for fix ave/correlate not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Fix ave/correlate
+   is requesting a value on a non-allowed timestep.
+
+*Fix for fix ave/histo not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Fix ave/histo is
+   requesting a value on a non-allowed timestep.
+
+*Fix for fix ave/spatial not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Fix ave/spatial is
+   requesting a value on a non-allowed timestep.
+
+*Fix for fix ave/time not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Fix ave/time
+   is requesting a value on a non-allowed timestep.
+
+*Fix for fix store/state not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Fix store/state
+   is requesting a value on a non-allowed timestep.
+
+*Fix for fix vector not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Fix vector is
+   requesting a value on a non-allowed timestep.
+
+*Fix freeze requires atom attribute torque*
+   The atom style defined does not have this attribute.
+
+*Fix gcmc and fix shake not using same molecule template ID*
+   Self-explanatory.
+
+*Fix gcmc atom has charge, but atom style does not*
+   Self-explanatory.
+
+*Fix gcmc cannot exchange individual atoms belonging to a molecule*
+   This is an error since you should not delete only one atom of a
+   molecule.  The user has specified atomic (non-molecular) gas
+   exchanges, but an atom belonging to a molecule could be deleted.
+
+*Fix gcmc does not (yet) work with atom\_style template*
+   Self-explanatory.
+
+*Fix gcmc molecule command requires that atoms have molecule attributes*
+   Should not choose the gcmc molecule feature if no molecules are being
+   simulated. The general molecule flag is off, but gcmc's molecule flag
+   is on.
+
+*Fix gcmc molecule has charges, but atom style does not*
+   Self-explanatory.
+
+*Fix gcmc molecule must have atom types*
+   The defined molecule does not specify atom types.
+
+*Fix gcmc molecule must have coordinates*
+   The defined molecule does not specify coordinates.
+
+*Fix gcmc molecule template ID must be same as atom\_style template ID*
+   When using atom\_style template, you cannot insert molecules that are
+   not in that template.
+
+*Fix gcmc put atom outside box*
+   This should not normally happen.  Contact the developers.
+
+*Fix gcmc ran out of available atom IDs*
+   See the setting for tagint in the src/lmptype.h file.
+
+*Fix gcmc ran out of available molecule IDs*
+   See the setting for tagint in the src/lmptype.h file.
+
+*Fix gcmc region cannot be dynamic*
+   Only static regions can be used with fix gcmc.
+
+*Fix gcmc region does not support a bounding box*
+   Not all regions represent bounded volumes.  You cannot use
+   such a region with the fix gcmc command.
+
+*Fix gcmc region extends outside simulation box*
+   Self-explanatory.
+
+*Fix gcmc shake fix does not exist*
+   Self-explanatory.
+
+*Fix gld c coefficients must be >= 0*
+   Self-explanatory.
+
+*Fix gld needs more prony series coefficients*
+   Self-explanatory.
+
+*Fix gld prony terms must be > 0*
+   Self-explanatory.
+
+*Fix gld series type must be pprony for now*
+   Self-explanatory.
+
+*Fix gld start temperature must be >= 0*
+   Self-explanatory.
+
+*Fix gld stop temperature must be >= 0*
+   Self-explanatory.
+
+*Fix gld tau coefficients must be > 0*
+   Self-explanatory.
+
+*Fix heat group has no atoms*
+   Self-explanatory.
+
+*Fix heat kinetic energy of an atom went negative*
+   This will cause the velocity rescaling about to be performed by fix
+   heat to be invalid.
+
+*Fix heat kinetic energy went negative*
+   This will cause the velocity rescaling about to be performed by fix
+   heat to be invalid.
+
+*Fix in variable not computed at compatible time*
+   Fixes generate their values on specific timesteps.  The variable is
+   requesting the values on a non-allowed timestep.
+
+*Fix langevin angmom is not yet implemented with kokkos*
+   This option is not yet available.
+
+*Fix langevin angmom requires atom style ellipsoid*
+   Self-explanatory.
+
+*Fix langevin angmom requires extended particles*
+   This fix option cannot be used with point particles.
+
+*Fix langevin gjf and respa are not compatible*
+   Self-explanatory.
+
+*Fix langevin gjf cannot have period equal to dt/2*
+   If the period is equal to dt/2 then division by zero will happen.
+
+*Fix langevin gjf should come before fix nve*
+   Self-explanatory.
+
+*Fix langevin gjf with tbias is not yet implemented with kokkos*
+   This option is not yet available.
+
+*Fix langevin omega is not yet implemented with kokkos*
+   This option is not yet available.
+
+*Fix langevin omega requires atom style sphere*
+   Self-explanatory.
+
+*Fix langevin omega requires extended particles*
+   One of the particles has radius 0.0.
+
+*Fix langevin period must be > 0.0*
+   The time window for temperature relaxation must be > 0
+
+*Fix langevin variable returned negative temperature*
+   Self-explanatory.
+
+*Fix momentum group has no atoms*
+   Self-explanatory.
+
+*Fix move cannot define z or vz variable for 2d problem*
+   Self-explanatory.
+
+*Fix move cannot rotate aroung non z-axis for 2d problem*
+   Self-explanatory.
+
+*Fix move cannot set linear z motion for 2d problem*
+   Self-explanatory.
+
+*Fix move cannot set wiggle z motion for 2d problem*
+   Self-explanatory.
+
+*Fix msst compute ID does not compute potential energy*
+   Self-explanatory.
+
+*Fix msst compute ID does not compute pressure*
+   Self-explanatory.
+
+*Fix msst compute ID does not compute temperature*
+   Self-explanatory.
+
+*Fix msst requires a periodic box*
+   Self-explanatory.
+
+*Fix msst tscale must satisfy 0 <= tscale < 1*
+   Self-explanatory.
+
+*Fix npt/nph has tilted box too far in one step - periodic cell is too far from equilibrium state*
+   Self-explanatory.  The change in the box tilt is too extreme
+   on a short timescale.
+
+*Fix nve/asphere requires extended particles*
+   This fix can only be used for particles with a shape setting.
+
+*Fix nve/asphere/noforce requires atom style ellipsoid*
+   Self-explanatory.
+
+*Fix nve/asphere/noforce requires extended particles*
+   One of the particles is not an ellipsoid.
+
+*Fix nve/body requires atom style body*
+   Self-explanatory.
+
+*Fix nve/body requires bodies*
+   This fix can only be used for particles that are bodies.
+
+*Fix nve/line can only be used for 2d simulations*
+   Self-explanatory.
+
+*Fix nve/line requires atom style line*
+   Self-explanatory.
+
+*Fix nve/line requires line particles*
+   Self-explanatory.
+
+*Fix nve/sphere dipole requires atom attribute mu*
+   An atom style with this attribute is needed.
+
+*Fix nve/sphere requires atom style sphere*
+   Self-explanatory.
+
+*Fix nve/sphere requires extended particles*
+   This fix can only be used for particles of a finite size.
+
+*Fix nve/tri can only be used for 3d simulations*
+   Self-explanatory.
+
+*Fix nve/tri requires atom style tri*
+   Self-explanatory.
+
+*Fix nve/tri requires tri particles*
+   Self-explanatory.
+
+*Fix nvt/nph/npt asphere requires extended particles*
+   The shape setting for a particle in the fix group has shape = 0.0,
+   which means it is a point particle.
+
+*Fix nvt/nph/npt body requires bodies*
+   Self-explanatory.
+
+*Fix nvt/nph/npt sphere requires atom style sphere*
+   Self-explanatory.
+
+*Fix nvt/npt/nph damping parameters must be > 0.0*
+   Self-explanatory.
+
+*Fix nvt/npt/nph dilate group ID does not exist*
+   Self-explanatory.
+
+*Fix nvt/sphere requires extended particles*
+   This fix can only be used for particles of a finite size.
+
+*Fix orient/fcc file open failed*
+   The fix orient/fcc command could not open a specified file.
+
+*Fix orient/fcc file read failed*
+   The fix orient/fcc command could not read the needed parameters from a
+   specified file.
+
+*Fix orient/fcc found self twice*
+   The neighbor lists used by fix orient/fcc are messed up.  If this
+   error occurs, it is likely a bug, so send an email to the
+   `developers <http://lammps.sandia.gov/authors.html>`_.
+
+*Fix peri neigh does not exist*
+   Somehow a fix that the pair style defines has been deleted.
+
+*Fix pour and fix rigid/small not using same molecule template ID*
+   Self-explanatory.
+
+*Fix pour and fix shake not using same molecule template ID*
+   Self-explanatory.
+
+*Fix pour insertion count per timestep is 0*
+   Self-explanatory.
+
+*Fix pour molecule must have atom types*
+   The defined molecule does not specify atom types.
+
+*Fix pour molecule must have coordinates*
+   The defined molecule does not specify coordinates.
+
+*Fix pour molecule template ID must be same as atom style template ID*
+   When using atom\_style template, you cannot pour molecules that are
+   not in that template.
+
+*Fix pour polydisperse fractions do not sum to 1.0*
+   Self-explanatory.
+
+*Fix pour region ID does not exist*
+   Self-explanatory.
+
+*Fix pour region cannot be dynamic*
+   Only static regions can be used with fix pour.
+
+*Fix pour region does not support a bounding box*
+   Not all regions represent bounded volumes.  You cannot use
+   such a region with the fix pour command.
+
+*Fix pour requires atom attributes radius, rmass*
+   The atom style defined does not have these attributes.
+
+*Fix pour rigid fix does not exist*
+   Self-explanatory.
+
+*Fix pour shake fix does not exist*
+   Self-explanatory.
+
+*Fix press/berendsen damping parameters must be > 0.0*
+   Self-explanatory.
+
+*Fix property/atom cannot specify mol twice*
+   Self-explanatory.
+
+*Fix property/atom cannot specify q twice*
+   Self-explanatory.
+
+*Fix property/atom mol when atom\_style already has molecule attribute*
+   Self-explanatory.
+
+*Fix property/atom q when atom\_style already has charge attribute*
+   Self-explanatory.
+
+*Fix property/atom vector name already exists*
+   The name for an integer or floating-point vector must be unique.
+
+*Fix qeq has negative upper Taper radius cutoff*
+   Self-explanatory.
+
+*Fix qeq/comb group has no atoms*
+   Self-explanatory.
+
+*Fix qeq/comb requires atom attribute q*
+   An atom style with charge must be used to perform charge equilibration.
+
+*Fix qeq/dynamic group has no atoms*
+   Self-explanatory.
+
+*Fix qeq/dynamic requires atom attribute q*
+   Self-explanatory.
+
+*Fix qeq/fire group has no atoms*
+   Self-explanatory.
+
+*Fix qeq/fire requires atom attribute q*
+   Self-explanatory.
+
+*Fix qeq/point group has no atoms*
+   Self-explanatory.
+
+*Fix qeq/point has insufficient QEq matrix size*
+   Occurs when number of neighbor atoms for an atom increased too much
+   during a run.  Increase SAFE\_ZONE and MIN\_CAP in fix\_qeq.h and
+   re-compile.
+
+*Fix qeq/point requires atom attribute q*
+   Self-explanatory.
+
+*Fix qeq/shielded group has no atoms*
+   Self-explanatory.
+
+*Fix qeq/shielded has insufficient QEq matrix size*
+   Occurs when number of neighbor atoms for an atom increased too much
+   during a run.  Increase SAFE\_ZONE and MIN\_CAP in fix\_qeq.h and
+   re-compile.
+
+*Fix qeq/shielded requires atom attribute q*
+   Self-explanatory.
+
+*Fix qeq/slater could not extract params from pair coul/streitz*
+   This should not happen unless pair coul/streitz has been altered.
+
+*Fix qeq/slater group has no atoms*
+   Self-explanatory.
+
+*Fix qeq/slater has insufficient QEq matrix size*
+   Occurs when number of neighbor atoms for an atom increased too much
+   during a run.  Increase SAFE\_ZONE and MIN\_CAP in fix\_qeq.h and
+   re-compile.
+
+*Fix qeq/slater requires atom attribute q*
+   Self-explanatory.
+
+*Fix reax/bonds numbonds > nsbmax\_most*
+   The limit of the number of bonds expected by the ReaxFF force field
+   was exceeded.
+
+*Fix recenter group has no atoms*
+   Self-explanatory.
+
+*Fix restrain requires an atom map, see atom\_modify*
+   Self-explanatory.
+
+*Fix rigid atom has non-zero image flag in a non-periodic dimension*
+   Image flags for non-periodic dimensions should not be set.
+
+*Fix rigid file has no lines*
+   Self-explanatory.
+
+*Fix rigid langevin period must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid molecule requires atom attribute molecule*
+   Self-explanatory.
+
+*Fix rigid npt/nph dilate group ID does not exist*
+   Self-explanatory.
+
+*Fix rigid npt/nph does not yet allow triclinic box*
+   This is a current restriction in LAMMPS.
+
+*Fix rigid npt/nph period must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid npt/small t\_chain should not be less than 1*
+   Self-explanatory.
+
+*Fix rigid npt/small t\_order must be 3 or 5*
+   Self-explanatory.
+
+*Fix rigid nvt/npt/nph damping parameters must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid nvt/small t\_chain should not be less than 1*
+   Self-explanatory.
+
+*Fix rigid nvt/small t\_iter should not be less than 1*
+   Self-explanatory.
+
+*Fix rigid nvt/small t\_order must be 3 or 5*
+   Self-explanatory.
+
+*Fix rigid xy torque cannot be on for 2d simulation*
+   Self-explanatory.
+
+*Fix rigid z force cannot be on for 2d simulation*
+   Self-explanatory.
+
+*Fix rigid/npt period must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid/npt temperature order must be 3 or 5*
+   Self-explanatory.
+
+*Fix rigid/npt/small period must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid/nvt period must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid/nvt temperature order must be 3 or 5*
+   Self-explanatory.
+
+*Fix rigid/nvt/small period must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid/small atom has non-zero image flag in a non-periodic dimension*
+   Image flags for non-periodic dimensions should not be set.
+
+*Fix rigid/small langevin period must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid/small molecule must have atom types*
+   The defined molecule does not specify atom types.
+
+*Fix rigid/small molecule must have coordinates*
+   The defined molecule does not specify coordinates.
+
+*Fix rigid/small npt/nph period must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid/small nvt/npt/nph damping parameters must be > 0.0*
+   Self-explanatory.
+
+*Fix rigid/small nvt/npt/nph dilate group ID does not exist*
+   Self-explanatory.
+
+*Fix rigid/small requires an atom map, see atom\_modify*
+   Self-explanatory.
+
+*Fix rigid/small requires atom attribute molecule*
+   Self-explanatory.
+
+*Fix rigid: Bad principal moments*
+   The principal moments of inertia computed for a rigid body
+   are not within the required tolerances.
+
+*Fix shake cannot be used with minimization*
+   Cannot use fix shake while doing an energy minimization since
+   it turns off bonds that should contribute to the energy.
+
+*Fix shake molecule template must have shake info*
+   The defined molecule does not specify SHAKE information.
+
+*Fix spring couple group ID does not exist*
+   Self-explanatory.
+
+*Fix srd can only currently be used with comm\_style brick*
+   This is a current restriction in LAMMPS.
+
+*Fix srd lamda must be >= 0.6 of SRD grid size*
+   This is a requirement for accuracy reasons.
+
+*Fix srd no-slip requires atom attribute torque*
+   This is because the SRD collisions will impart torque to the solute
+   particles.
+
+*Fix srd requires SRD particles all have same mass*
+   Self-explanatory.
+
+*Fix srd requires ghost atoms store velocity*
+   Use the comm\_modify vel yes command to enable this.
+
+*Fix srd requires newton pair on*
+   Self-explanatory.
+
+*Fix store/state compute array is accessed out-of-range*
+   Self-explanatory.
+
+*Fix store/state compute does not calculate a per-atom array*
+   The compute calculates a per-atom vector.
+
+*Fix store/state compute does not calculate a per-atom vector*
+   The compute calculates a per-atom vector.
+
+*Fix store/state compute does not calculate per-atom values*
+   Computes that calculate global or local quantities cannot be used
+   with fix store/state.
+
+*Fix store/state fix array is accessed out-of-range*
+   Self-explanatory.
+
+*Fix store/state fix does not calculate a per-atom array*
+   The fix calculates a per-atom vector.
+
+*Fix store/state fix does not calculate a per-atom vector*
+   The fix calculates a per-atom array.
+
+*Fix store/state fix does not calculate per-atom values*
+   Fixes that calculate global or local quantities cannot be used with
+   fix store/state.
+
+*Fix store/state for atom property that isn't allocated*
+   Self-explanatory.
+
+*Fix store/state variable is not atom-style variable*
+   Only atom-style variables calculate per-atom quantities.
+
+*Fix temp/berendsen period must be > 0.0*
+   Self-explanatory.
+
+*Fix temp/berendsen variable returned negative temperature*
+   Self-explanatory.
+
+*Fix temp/csld is not compatible with fix rattle or fix shake*
+   These two commands cannot currently be used together with fix temp/csld.
+
+*Fix temp/csld variable returned negative temperature*
+   Self-explanatory.
+
+*Fix temp/csvr variable returned negative temperature*
+   Self-explanatory.
+
+*Fix temp/rescale variable returned negative temperature*
+   Self-explanatory.
+
+*Fix tfmc displacement length must be > 0*
+   Self-explanatory.
+
+*Fix tfmc is not compatible with fix shake*
+   These two commands cannot currently be used together.
+
+*Fix tfmc temperature must be > 0*
+   Self-explanatory.
+
+*Fix thermal/conductivity swap value must be positive*
+   Self-explanatory.
+
+*Fix tmd must come after integration fixes*
+   Any fix tmd command must appear in the input script after all time
+   integration fixes (nve, nvt, npt).  See the fix tmd documentation for
+   details.
+
+*Fix ttm electron temperatures must be > 0.0*
+   Self-explanatory.
+
+*Fix ttm electronic\_density must be > 0.0*
+   Self-explanatory.
+
+*Fix ttm electronic\_specific\_heat must be > 0.0*
+   Self-explanatory.
+
+*Fix ttm electronic\_thermal\_conductivity must be >= 0.0*
+   Self-explanatory.
+
+*Fix ttm gamma\_p must be > 0.0*
+   Self-explanatory.
+
+*Fix ttm gamma\_s must be >= 0.0*
+   Self-explanatory.
+
+*Fix ttm number of nodes must be > 0*
+   Self-explanatory.
+
+*Fix ttm v\_0 must be >= 0.0*
+   Self-explanatory.
+
+*Fix used in compute chunk/atom not computed at compatible time*
+   The chunk/atom compute cannot query the output of the fix on a timestep
+   it is needed.
+
+*Fix used in compute reduce not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Compute reduce is
+   requesting a value on a non-allowed timestep.
+
+*Fix used in compute slice not computed at compatible time*
+   Fixes generate their values on specific timesteps.  Compute slice is
+   requesting a value on a non-allowed timestep.
+
+*Fix vector cannot set output array intensive/extensive from these inputs*
+   The inputs to the command have conflicting intensive/extensive attributes.
+   You need to use more than one fix vector command.
+
+*Fix vector compute does not calculate a scalar*
+   Self-explanatory.
+
+*Fix vector compute does not calculate a vector*
+   Self-explanatory.
+
+*Fix vector compute vector is accessed out-of-range*
+   Self-explanatory.
+
+*Fix vector fix does not calculate a scalar*
+   Self-explanatory.
+
+*Fix vector fix does not calculate a vector*
+   Self-explanatory.
+
+*Fix vector fix vector is accessed out-of-range*
+   Self-explanatory.
+
+*Fix vector variable is not equal-style variable*
+   Self-explanatory.
+
+*Fix viscosity swap value must be positive*
+   Self-explanatory.
+
+*Fix viscosity vtarget value must be positive*
+   Self-explanatory.
+
+*Fix wall cutoff <= 0.0*
+   Self-explanatory.
+
+*Fix wall/colloid requires atom style sphere*
+   Self-explanatory.
+
+*Fix wall/colloid requires extended particles*
+   One of the particles has radius 0.0.
+
+*Fix wall/gran is incompatible with Pair style*
+   Must use a granular pair style to define the parameters needed for
+   this fix.
+
+*Fix wall/gran requires atom style sphere*
+   Self-explanatory.
+
+*Fix wall/piston command only available at zlo*
+   The face keyword must be zlo.
+
+*Fix wall/region colloid requires atom style sphere*
+   Self-explanatory.
+
+*Fix wall/region colloid requires extended particles*
+   One of the particles has radius 0.0.
+
+*Fix wall/region cutoff <= 0.0*
+   Self-explanatory.
+
+*Fix\_modify pressure ID does not compute pressure*
+   The compute ID assigned to the fix must compute pressure.
+
+*Fix\_modify temperature ID does not compute temperature*
+   The compute ID assigned to the fix must compute temperature.
+
+*For triclinic deformation, specified target stress must be hydrostatic*
+   Triclinic pressure control is allowed using the tri keyword, but
+   non-hydrostatic pressure control can not be used in this case.
+
+*Found no restart file matching pattern*
+   When using a "\*" in the restart file name, no matching file was found.
+
+*GPU library not compiled for this accelerator*
+   Self-explanatory.
+
+*GPU package does not (yet) work with atom\_style template*
+   Self-explanatory.
+
+*GPU particle split must be set to 1 for this pair style.*
+   For this pair style, you cannot run part of the force calculation on
+   the host.  See the package command.
+
+*GPUs are requested but Kokkos has not been compiled for CUDA*
+   Re-compile Kokkos with CUDA support to use GPUs.
+
+*Ghost velocity forward comm not yet implemented with Kokkos*
+   This is a current restriction.
+
+*Gmask function in equal-style variable formula*
+   Gmask is per-atom operation.
+
+*Gravity changed since fix pour was created*
+   The gravity vector defined by fix gravity must be static.
+
+*Gravity must point in -y to use with fix pour in 2d*
+   Self-explanatory.
+
+*Gravity must point in -z to use with fix pour in 3d*
+   Self-explanatory.
+
+*Grmask function in equal-style variable formula*
+   Grmask is per-atom operation.
+
+*Group ID does not exist*
+   A group ID used in the group command does not exist.
+
+*Group ID in variable formula does not exist*
+   Self-explanatory.
+
+*Group all cannot be made dynamic*
+   This operation is not allowed.
+
+*Group command before simulation box is defined*
+   The group command cannot be used before a read\_data, read\_restart, or
+   create\_box command.
+
+*Group dynamic cannot reference itself*
+   Self-explanatory.
+
+*Group dynamic parent group cannot be dynamic*
+   Self-explanatory.
+
+*Group dynamic parent group does not exist*
+   Self-explanatory.
+
+*Group region ID does not exist*
+   A region ID used in the group command does not exist.
+
+*If read\_dump purges it cannot replace or trim*
+   These operations are not compatible.  See the read\_dump doc
+   page for details.
+
+*Illegal ... command*
+   Self-explanatory.  Check the input script syntax and compare to the
+   documentation for the command.  You can use -echo screen as a
+   command-line option when running LAMMPS to see the offending line.
+
+*Illegal COMB parameter*
+   One or more of the coefficients defined in the potential file is
+   invalid.
+
+*Illegal COMB3 parameter*
+   One or more of the coefficients defined in the potential file is
+   invalid.
+
+*Illegal Stillinger-Weber parameter*
+   One or more of the coefficients defined in the potential file is
+   invalid.
+
+*Illegal Tersoff parameter*
+   One or more of the coefficients defined in the potential file is
+   invalid.
+
+*Illegal Vashishta parameter*
+   One or more of the coefficients defined in the potential file is
+   invalid.
+
+*Illegal compute voronoi/atom command (occupation and (surface or edges))*
+   Self-explanatory.
+
+*Illegal coul/streitz parameter*
+   One or more of the coefficients defined in the potential file is
+   invalid.
+
+*Illegal dump\_modify sfactor value (must be > 0.0)*
+   Self-explanatory.
+
+*Illegal dump\_modify tfactor value (must be > 0.0)*
+   Self-explanatory.
+
+*Illegal fix gcmc gas mass <= 0*
+   The computed mass of the designated gas molecule or atom type was less
+   than or equal to zero.
+
+*Illegal fix tfmc random seed*
+   Seeds can only be nonzero positive integers.
+
+*Illegal fix wall/piston velocity*
+   The piston velocity must be positive.
+
+*Illegal integrate style*
+   Self-explanatory.
+
+*Illegal nb3b/harmonic parameter*
+   One or more of the coefficients defined in the potential file is
+   invalid.
+
+*Illegal number of angle table entries*
+   There must be at least 2 table entries.
+
+*Illegal number of bond table entries*
+   There must be at least 2 table entries.
+
+*Illegal number of pair table entries*
+   There must be at least 2 table entries.
+
+*Illegal or unset periodicity in restart*
+   This error should not normally occur unless the restart file is invalid.
+
+*Illegal range increment value*
+   The increment must be >= 1.
+
+*Illegal simulation box*
+   The lower bound of the simulation box is greater than the upper bound.
+
+*Illegal size double vector read requested*
+   This error should not normally occur unless the restart file is invalid.
+
+*Illegal size integer vector read requested*
+   This error should not normally occur unless the restart file is invalid.
+
+*Illegal size string or corrupt restart*
+   This error should not normally occur unless the restart file is invalid.
+
+*Imageint setting in lmptype.h is invalid*
+   Imageint must be as large or larger than smallint.
+
+*Imageint setting in lmptype.h is not compatible*
+   Format of imageint stored in restart file is not consistent with
+   LAMMPS version you are running.  See the settings in src/lmptype.h
+
+*Improper atom missing in delete\_bonds*
+   The delete\_bonds command cannot find one or more atoms in a particular
+   improper on a particular processor.  The pairwise cutoff is too short
+   or the atoms are too far apart to make a valid improper.
+
+*Improper atom missing in set command*
+   The set command cannot find one or more atoms in a particular improper
+   on a particular processor.  The pairwise cutoff is too short or the
+   atoms are too far apart to make a valid improper.
+
+*Improper atoms %d %d %d %d missing on proc %d at step %ld*
+   One or more of 4 atoms needed to compute a particular improper are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the improper has blown apart and an atom is
+   too far away.
+
+*Improper atoms missing on proc %d at step %ld*
+   One or more of 4 atoms needed to compute a particular improper are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the improper has blown apart and an atom is
+   too far away.
+
+*Improper coeff for hybrid has invalid style*
+   Improper style hybrid uses another improper style as one of its
+   coefficients.  The improper style used in the improper\_coeff command
+   or read from a restart file is not recognized.
+
+*Improper coeffs are not set*
+   No improper coefficients have been assigned in the data file or via
+   the improper\_coeff command.
+
+*Improper style hybrid cannot have hybrid as an argument*
+   Self-explanatory.
+
+*Improper style hybrid cannot have none as an argument*
+   Self-explanatory.
+
+*Improper style hybrid cannot use same improper style twice*
+   Self-explanatory.
+
+*Improper\_coeff command before improper\_style is defined*
+   Coefficients cannot be set in the data file or via the improper\_coeff
+   command until an improper\_style has been assigned.
+
+*Improper\_coeff command before simulation box is defined*
+   The improper\_coeff command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Improper\_coeff command when no impropers allowed*
+   The chosen atom style does not allow for impropers to be defined.
+
+*Improper\_style command when no impropers allowed*
+   The chosen atom style does not allow for impropers to be defined.
+
+*Impropers assigned incorrectly*
+   Impropers read in from the data file were not assigned correctly to
+   atoms.  This means there is something invalid about the topology
+   definitions.
+
+*Impropers defined but no improper types*
+   The data file header lists improper but no improper types.
+
+*Incompatible KIM Simulator Model*
+   The requested KIM Simulator Model was defined for a different MD code
+   and thus is not compatible with LAMMPS.
+
+*Incompatible units for KIM Simulator Model*
+   The selected unit style is not compatible with the requested KIM
+   Simulator Model.
+
+*Incomplete use of variables in create\_atoms command*
+   The var and set options must be used together.
+
+*Inconsistent iparam/jparam values in fix bond/create command*
+   If itype and jtype are the same, then their maxbond and newtype
+   settings must also be the same.
+
+*Inconsistent line segment in data file*
+   The end points of the line segment are not equal distances from the
+   center point which is the atom coordinate.
+
+*Inconsistent triangle in data file*
+   The centroid of the triangle as defined by the corner points is not
+   the atom coordinate.
+
+*Inconsistent use of finite-size particles by molecule template molecules*
+   Not all of the molecules define a radius for their constituent
+   particles.
+
+*Incorrect # of floating-point values in Bodies section of data file*
+   See doc page for body style.
+
+*Incorrect # of integer values in Bodies section of data file*
+   See doc page for body style.
+
+*Incorrect %s format in data file*
+   A section of the data file being read by fix property/atom does
+   not have the correct number of values per line.
+
+*Incorrect SNAP parameter file*
+   The file cannot be parsed correctly, check its internal syntax.
+
+*Incorrect args for angle coefficients*
+   Self-explanatory.  Check the input script or data file.
+
+*Incorrect args for bond coefficients*
+   Self-explanatory.  Check the input script or data file.
+
+*Incorrect args for dihedral coefficients*
+   Self-explanatory.  Check the input script or data file.
+
+*Incorrect args for improper coefficients*
+   Self-explanatory.  Check the input script or data file.
+
+*Incorrect args for pair coefficients*
+   Self-explanatory.  Check the input script or data file.
+
+*Incorrect args in pair\_style command*
+   Self-explanatory.
+
+*Incorrect atom format in data file*
+   Number of values per atom line in the data file is not consistent with
+   the atom style.
+
+*Incorrect atom format in neb file*
+   The number of fields per line is not what expected.
+
+*Incorrect bonus data format in data file*
+   See the read\_data doc page for a description of how various kinds of
+   bonus data must be formatted for certain atom styles.
+
+*Incorrect boundaries with slab Ewald*
+   Must have periodic x,y dimensions and non-periodic z dimension to use
+   2d slab option with Ewald.
+
+*Incorrect boundaries with slab EwaldDisp*
+   Must have periodic x,y dimensions and non-periodic z dimension to use
+   2d slab option with Ewald.
+
+*Incorrect boundaries with slab PPPM*
+   Must have periodic x,y dimensions and non-periodic z dimension to use
+   2d slab option with PPPM.
+
+*Incorrect boundaries with slab PPPMDisp*
+   Must have periodic x,y dimensions and non-periodic z dimension to use
+   2d slab option with pppm/disp.
+
+*Incorrect conversion in format string*
+   A format style variable was not using either a %f, a %g, or a %e conversion.
+   Or an immediate variable with format suffix was not using either
+   a %f, a %g or a %e conversion in the format suffix.
+
+*Incorrect element names in ADP potential file*
+   The element names in the ADP file do not match those requested.
+
+*Incorrect element names in EAM potential file*
+   The element names in the EAM file do not match those requested.
+
+*Incorrect format of ... section in data file*
+   Number or type of values per line in the given section of the data file
+   is not consistent with the requirements for this section.
+
+*Incorrect format in COMB potential file*
+   Incorrect number of words per line in the potential file.
+
+*Incorrect format in COMB3 potential file*
+   Incorrect number of words per line in the potential file.
+
+*Incorrect format in MEAM potential file*
+   Incorrect number of words per line in the potential file.
+
+*Incorrect format in SNAP coefficient file*
+   Incorrect number of words per line in the coefficient file.
+
+*Incorrect format in SNAP parameter file*
+   Incorrect number of words per line in the parameter file.
+
+*Incorrect format in Stillinger-Weber potential file*
+   Incorrect number of words per line in the potential file.
+
+*Incorrect format in TMD target file*
+   Format of file read by fix tmd command is incorrect.
+
+*Incorrect format in Tersoff potential file*
+   Incorrect number of words per line in the potential file.
+
+*Incorrect format in Vashishta potential file*
+   Incorrect number of words per line in the potential file.
+
+*Incorrect format in coul/streitz potential file*
+   Incorrect number of words per line in the potential file.
+
+*Incorrect format in nb3b/harmonic potential file*
+   Incorrect number of words per line in the potential file.
+
+*Incorrect integer value in Bodies section of data file*
+   See doc page for body style.
+
+*Incorrect multiplicity arg for dihedral coefficients*
+   Self-explanatory.  Check the input script or data file.
+
+*Incorrect number of elements in potential file*
+   Self-explanatory.
+
+*Incorrect rigid body format in fix rigid file*
+   The number of fields per line is not what expected.
+
+*Incorrect rigid body format in fix rigid/small file*
+   The number of fields per line is not what expected.
+
+*Incorrect sign arg for dihedral coefficients*
+   Self-explanatory.  Check the input script or data file.
+
+*Incorrect table format check for element types*
+   Self-explanatory.
+
+*Incorrect velocity format in data file*
+   Each atom style defines a format for the Velocity section
+   of the data file.  The read-in lines do not match.
+
+*Incorrect weight arg for dihedral coefficients*
+   Self-explanatory.  Check the input script or data file.
+
+*Index between variable brackets must be positive*
+   Self-explanatory.
+
+*Indexed per-atom vector in variable formula without atom map*
+   Accessing a value from an atom vector requires the ability to lookup
+   an atom index, which is provided by an atom map.  An atom map does not
+   exist (by default) for non-molecular problems.  Using the atom\_modify
+   map command will force an atom map to be created.
+
+*Initial temperatures not all set in fix ttm*
+   Self-explanatory.
+
+*Input line quote not followed by white-space*
+   An end quote must be followed by white-space.
+
+*Insertion region extends outside simulation box*
+   Self-explanatory.
+
+*Insufficient Jacobi rotations for POEMS body*
+   Eigensolve for rigid body was not sufficiently accurate.
+
+*Insufficient Jacobi rotations for body nparticle*
+   Eigensolve for rigid body was not sufficiently accurate.
+
+*Insufficient Jacobi rotations for rigid body*
+   Eigensolve for rigid body was not sufficiently accurate.
+
+*Insufficient Jacobi rotations for rigid molecule*
+   Eigensolve for rigid body was not sufficiently accurate.
+
+*Insufficient Jacobi rotations for triangle*
+   The calculation of the inertia tensor of the triangle failed.  This
+   should not happen if it is a reasonably shaped triangle.
+
+*Insufficient memory on accelerator*
+   There is insufficient memory on one of the devices specified for the gpu
+   package
+
+*Internal error in atom\_style body*
+   This error should not occur.  Contact the developers.
+
+*Invalid -reorder N value*
+   Self-explanatory.
+
+*Invalid Angles section in molecule file*
+   Self-explanatory.
+
+*Invalid Bonds section in molecule file*
+   Self-explanatory.
+
+*Invalid Boolean syntax in if command*
+   Self-explanatory.
+
+*Invalid Charges section in molecule file*
+   Self-explanatory.
+
+*Invalid Coords section in molecule file*
+   Self-explanatory.
+
+*Invalid Diameters section in molecule file*
+   Self-explanatory.
+
+*Invalid Dihedrals section in molecule file*
+   Self-explanatory.
+
+*Invalid Impropers section in molecule file*
+   Self-explanatory.
+
+*Invalid Kokkos command-line args*
+   Self-explanatory.  See Section 2.7 of the manual for details.
+
+*Invalid LAMMPS restart file*
+   The file does not appear to be a LAMMPS restart file since
+   it doesn't contain the correct magic string at the beginning.
+
+*Invalid Masses section in molecule file*
+   Self-explanatory.
+
+*Invalid REAX atom type*
+   There is a mis-match between LAMMPS atom types and the elements
+   listed in the ReaxFF force field file.
+
+*Invalid Special Bond Counts section in molecule file*
+   Self-explanatory.
+
+*Invalid Types section in molecule file*
+   Self-explanatory.
+
+*Invalid angle count in molecule file*
+   Self-explanatory.
+
+*Invalid angle table length*
+   Length must be 2 or greater.
+
+*Invalid angle type in Angles section of data file*
+   Angle type must be positive integer and within range of specified angle
+   types.
+
+*Invalid angle type in Angles section of molecule file*
+   Self-explanatory.
+
+*Invalid angle type index for fix shake*
+   Self-explanatory.
+
+*Invalid args for non-hybrid pair coefficients*
+   "NULL" is only supported in pair\_coeff calls when using pair hybrid
+
+*Invalid argument to factorial %d*
+   N must be >= 0 and <= 167, otherwise the factorial result is too
+   large.
+
+*Invalid atom ID in %s section of data file*
+   An atom in a section of the data file being read by fix property/atom
+   has an invalid atom ID that is <= 0 or > the maximum existing atom ID.
+
+*Invalid atom ID in Angles section of data file*
+   Atom IDs must be positive integers and within range of defined
+   atoms.
+
+*Invalid atom ID in Angles section of molecule file*
+   Self-explanatory.
+
+*Invalid atom ID in Atoms section of data file*
+   Atom IDs must be positive integers.
+
+*Invalid atom ID in Bodies section of data file*
+   Atom IDs must be positive integers and within range of defined
+   atoms.
+
+*Invalid atom ID in Bonds section of data file*
+   Atom IDs must be positive integers and within range of defined
+   atoms.
+
+*Invalid atom ID in Bonds section of molecule file*
+   Self-explanatory.
+
+*Invalid atom ID in Bonus section of data file*
+   Atom IDs must be positive integers and within range of defined
+   atoms.
+
+*Invalid atom ID in Dihedrals section of data file*
+   Atom IDs must be positive integers and within range of defined
+   atoms.
+
+*Invalid atom ID in Impropers section of data file*
+   Atom IDs must be positive integers and within range of defined
+   atoms.
+
+*Invalid atom ID in Velocities section of data file*
+   Atom IDs must be positive integers and within range of defined
+   atoms.
+
+*Invalid atom ID in dihedrals section of molecule file*
+   Self-explanatory.
+
+*Invalid atom ID in impropers section of molecule file*
+   Self-explanatory.
+
+*Invalid atom ID in variable file*
+   Self-explanatory.
+
+*Invalid atom IDs in neb file*
+   An ID in the file was not found in the system.
+
+*Invalid atom diameter in molecule file*
+   Diameters must be >= 0.0.
+
+*Invalid atom mass for fix shake*
+   Mass specified in fix shake command must be > 0.0.
+
+*Invalid atom mass in molecule file*
+   Masses must be > 0.0.
+
+*Invalid atom type in Atoms section of data file*
+   Atom types must range from 1 to specified # of types.
+
+*Invalid atom type in create\_atoms command*
+   The create\_box command specified the range of valid atom types.
+   An invalid type is being requested.
+
+*Invalid atom type in create\_atoms mol command*
+   The atom types in the defined molecule are added to the value
+   specified in the create\_atoms command, as an offset.  The final value
+   for each atom must be between 1 to N, where N is the number of atom
+   types.
+
+*Invalid atom type in fix atom/swap command*
+   The atom type specified in the atom/swap command does not exist.
+
+*Invalid atom type in fix bond/create command*
+   Self-explanatory.
+
+*Invalid atom type in fix deposit command*
+   Self-explanatory.
+
+*Invalid atom type in fix deposit mol command*
+   The atom types in the defined molecule are added to the value
+   specified in the create\_atoms command, as an offset.  The final value
+   for each atom must be between 1 to N, where N is the number of atom
+   types.
+
+*Invalid atom type in fix gcmc command*
+   The atom type specified in the gcmc command does not exist.
+
+*Invalid atom type in fix pour command*
+   Self-explanatory.
+
+*Invalid atom type in fix pour mol command*
+   The atom types in the defined molecule are added to the value
+   specified in the create\_atoms command, as an offset.  The final value
+   for each atom must be between 1 to N, where N is the number of atom
+   types.
+
+*Invalid atom type in molecule file*
+   Atom types must range from 1 to specified # of types.
+
+*Invalid atom type in neighbor exclusion list*
+   Atom types must range from 1 to Ntypes inclusive.
+
+*Invalid atom type index for fix shake*
+   Atom types must range from 1 to Ntypes inclusive.
+
+*Invalid atom types in pair\_write command*
+   Atom types must range from 1 to Ntypes inclusive.
+
+*Invalid atom vector in variable formula*
+   The atom vector is not recognized.
+
+*Invalid atom\_style body command*
+   No body style argument was provided.
+
+*Invalid atom\_style command*
+   Self-explanatory.
+
+*Invalid attribute in dump custom command*
+   Self-explanatory.
+
+*Invalid attribute in dump local command*
+   Self-explanatory.
+
+*Invalid attribute in dump modify command*
+   Self-explanatory.
+
+*Invalid basis setting in create\_atoms command*
+   The basis index must be between 1 to N where N is the number of basis
+   atoms in the lattice.  The type index must be between 1 to N where N
+   is the number of atom types.
+
+*Invalid basis setting in fix append/atoms command*
+   The basis index must be between 1 to N where N is the number of basis
+   atoms in the lattice.  The type index must be between 1 to N where N
+   is the number of atom types.
+
+*Invalid bin bounds in compute chunk/atom*
+   The lo/hi values are inconsistent.
+
+*Invalid bin bounds in fix ave/spatial*
+   The lo/hi values are inconsistent.
+
+*Invalid body nparticle command*
+   Arguments in atom-style command are not correct.
+
+*Invalid bond count in molecule file*
+   Self-explanatory.
+
+*Invalid bond table length*
+   Length must be 2 or greater.
+
+*Invalid bond type in Bonds section of data file*
+   Bond type must be positive integer and within range of specified bond
+   types.
+
+*Invalid bond type in Bonds section of molecule file*
+   Self-explanatory.
+
+*Invalid bond type in create\_bonds command*
+   Self-explanatory.
+
+*Invalid bond type in fix bond/break command*
+   Self-explanatory.
+
+*Invalid bond type in fix bond/create command*
+   Self-explanatory.
+
+*Invalid bond type index for fix shake*
+   Self-explanatory.  Check the fix shake command in the input script.
+
+*Invalid coeffs for this dihedral style*
+   Cannot set class 2 coeffs in data file for this dihedral style.
+
+*Invalid color in dump\_modify command*
+   The specified color name was not in the list of recognized colors.
+   See the dump\_modify doc page.
+
+*Invalid color map min/max values*
+   The min/max values are not consistent with either each other or
+   with values in the color map.
+
+*Invalid command-line argument*
+   One or more command-line arguments is invalid.  Check the syntax of
+   the command you are using to launch LAMMPS.
+
+*Invalid compute ID in variable formula*
+   The compute is not recognized.
+
+*Invalid create\_atoms rotation vector for 2d model*
+   The rotation vector can only have a z component.
+
+*Invalid custom OpenCL parameter string.*
+   There are not enough or too many parameters in the custom string for package
+   GPU.
+
+*Invalid cutoff in comm\_modify command*
+   Specified cutoff must be >= 0.0.
+
+*Invalid cutoffs in pair\_write command*
+   Inner cutoff must be larger than 0.0 and less than outer cutoff.
+
+*Invalid d1 or d2 value for pair colloid coeff*
+   Neither d1 or d2 can be < 0.
+
+*Invalid data file section: Angle Coeffs*
+   Atom style does not allow angles.
+
+*Invalid data file section: AngleAngle Coeffs*
+   Atom style does not allow impropers.
+
+*Invalid data file section: AngleAngleTorsion Coeffs*
+   Atom style does not allow dihedrals.
+
+*Invalid data file section: AngleTorsion Coeffs*
+   Atom style does not allow dihedrals.
+
+*Invalid data file section: Angles*
+   Atom style does not allow angles.
+
+*Invalid data file section: Bodies*
+   Atom style does not allow bodies.
+
+*Invalid data file section: Bond Coeffs*
+   Atom style does not allow bonds.
+
+*Invalid data file section: BondAngle Coeffs*
+   Atom style does not allow angles.
+
+*Invalid data file section: BondBond Coeffs*
+   Atom style does not allow angles.
+
+*Invalid data file section: BondBond13 Coeffs*
+   Atom style does not allow dihedrals.
+
+*Invalid data file section: Bonds*
+   Atom style does not allow bonds.
+
+*Invalid data file section: Dihedral Coeffs*
+   Atom style does not allow dihedrals.
+
+*Invalid data file section: Dihedrals*
+   Atom style does not allow dihedrals.
+
+*Invalid data file section: Ellipsoids*
+   Atom style does not allow ellipsoids.
+
+*Invalid data file section: EndBondTorsion Coeffs*
+   Atom style does not allow dihedrals.
+
+*Invalid data file section: Improper Coeffs*
+   Atom style does not allow impropers.
+
+*Invalid data file section: Impropers*
+   Atom style does not allow impropers.
+
+*Invalid data file section: Lines*
+   Atom style does not allow lines.
+
+*Invalid data file section: MiddleBondTorsion Coeffs*
+   Atom style does not allow dihedrals.
+
+*Invalid data file section: Triangles*
+   Atom style does not allow triangles.
+
+*Invalid delta\_conf in tad command*
+   The value must be between 0 and 1 inclusive.
+
+*Invalid density in Atoms section of data file*
+   Density value cannot be <= 0.0.
+
+*Invalid density in set command*
+   Density must be > 0.0.
+
+*Invalid diameter in set command*
+   Self-explanatory.
+
+*Invalid dihedral count in molecule file*
+   Self-explanatory.
+
+*Invalid dihedral type in Dihedrals section of data file*
+   Dihedral type must be positive integer and within range of specified
+   dihedral types.
+
+*Invalid dihedral type in dihedrals section of molecule file*
+   Self-explanatory.
+
+*Invalid dipole length in set command*
+   Self-explanatory.
+
+*Invalid displace\_atoms rotate axis for 2d*
+   Axis must be in z direction.
+
+*Invalid dump dcd filename*
+   Filenames used with the dump dcd style cannot be binary or compressed
+   or cause multiple files to be written.
+
+*Invalid dump frequency*
+   Dump frequency must be 1 or greater.
+
+*Invalid dump image element name*
+   The specified element name was not in the standard list of elements.
+   See the dump\_modify doc page.
+
+*Invalid dump image filename*
+   The file produced by dump image cannot be binary and must
+   be for a single processor.
+
+*Invalid dump image persp value*
+   Persp value must be >= 0.0.
+
+*Invalid dump image theta value*
+   Theta must be between 0.0 and 180.0 inclusive.
+
+*Invalid dump image zoom value*
+   Zoom value must be > 0.0.
+
+*Invalid dump movie filename*
+   The file produced by dump movie cannot be binary or compressed
+   and must be a single file for a single processor.
+
+*Invalid dump xtc filename*
+   Filenames used with the dump xtc style cannot be binary or compressed
+   or cause multiple files to be written.
+
+*Invalid dump xyz filename*
+   Filenames used with the dump xyz style cannot be binary or cause files
+   to be written by each processor.
+
+*Invalid dump\_modify threshold operator*
+   Operator keyword used for threshold specification in not recognized.
+
+*Invalid entry in -reorder file*
+   Self-explanatory.
+
+*Invalid fix ID in variable formula*
+   The fix is not recognized.
+
+*Invalid fix ave/time off column*
+   Self-explanatory.
+
+*Invalid fix box/relax command for a 2d simulation*
+   Fix box/relax styles involving the z dimension cannot be used in
+   a 2d simulation.
+
+*Invalid fix box/relax command pressure settings*
+   If multiple dimensions are coupled, those dimensions must be specified.
+
+*Invalid fix box/relax pressure settings*
+   Settings for coupled dimensions must be the same.
+
+*Invalid fix nvt/npt/nph command for a 2d simulation*
+   Cannot control z dimension in a 2d model.
+
+*Invalid fix nvt/npt/nph command pressure settings*
+   If multiple dimensions are coupled, those dimensions must be
+   specified.
+
+*Invalid fix nvt/npt/nph pressure settings*
+   Settings for coupled dimensions must be the same.
+
+*Invalid fix press/berendsen for a 2d simulation*
+   The z component of pressure cannot be controlled for a 2d model.
+
+*Invalid fix press/berendsen pressure settings*
+   Settings for coupled dimensions must be the same.
+
+*Invalid fix qeq parameter file*
+   Element index > number of atom types.
+
+*Invalid fix rigid npt/nph command for a 2d simulation*
+   Cannot control z dimension in a 2d model.
+
+*Invalid fix rigid npt/nph command pressure settings*
+   If multiple dimensions are coupled, those dimensions must be
+   specified.
+
+*Invalid fix rigid/small npt/nph command for a 2d simulation*
+   Cannot control z dimension in a 2d model.
+
+*Invalid fix rigid/small npt/nph command pressure settings*
+   If multiple dimensions are coupled, those dimensions must be
+   specified.
+
+*Invalid flag in force field section of restart file*
+   Unrecognized entry in restart file.
+
+*Invalid flag in header section of restart file*
+   Unrecognized entry in restart file.
+
+*Invalid flag in peratom section of restart file*
+   The format of this section of the file is not correct.
+
+*Invalid flag in type arrays section of restart file*
+   Unrecognized entry in restart file.
+
+*Invalid frequency in temper command*
+   Nevery must be > 0.
+
+*Invalid group ID in neigh\_modify command*
+   A group ID used in the neigh\_modify command does not exist.
+
+*Invalid group function in variable formula*
+   Group function is not recognized.
+
+*Invalid group in comm\_modify command*
+   Self-explanatory.
+
+*Invalid image up vector*
+   Up vector cannot be (0,0,0).
+
+*Invalid immediate variable*
+   Syntax of immediate value is incorrect.
+
+*Invalid improper count in molecule file*
+   Self-explanatory.
+
+*Invalid improper type in Impropers section of data file*
+   Improper type must be positive integer and within range of specified
+   improper types.
+
+*Invalid improper type in impropers section of molecule file*
+   Self-explanatory.
+
+*Invalid index for non-body particles in compute body/local command*
+   Only indices 1,2,3 can be used for non-body particles.
+
+*Invalid index in compute body/local command*
+   Self-explanatory.
+
+*Invalid is\_active() function in variable formula*
+   Self-explanatory.
+
+*Invalid is\_available() function in variable formula*
+   Self-explanatory.
+
+*Invalid is\_defined() function in variable formula*
+   Self-explanatory.
+
+*Invalid keyword in angle table parameters*
+   Self-explanatory.
+
+*Invalid keyword in bond table parameters*
+   Self-explanatory.
+
+*Invalid keyword in compute angle/local command*
+   Self-explanatory.
+
+*Invalid keyword in compute bond/local command*
+   Self-explanatory.
+
+*Invalid keyword in compute dihedral/local command*
+   Self-explanatory.
+
+*Invalid keyword in compute improper/local command*
+   Self-explanatory.
+
+*Invalid keyword in compute pair/local command*
+   Self-explanatory.
+
+*Invalid keyword in compute property/atom command*
+   Self-explanatory.
+
+*Invalid keyword in compute property/chunk command*
+   Self-explanatory.
+
+*Invalid keyword in compute property/local command*
+   Self-explanatory.
+
+*Invalid keyword in dump cfg command*
+   Self-explanatory.
+
+*Invalid keyword in pair table parameters*
+   Keyword used in list of table parameters is not recognized.
+
+*Invalid length in set command*
+   Self-explanatory.
+
+*Invalid mass in set command*
+   Self-explanatory.
+
+*Invalid mass line in data file*
+   Self-explanatory.
+
+*Invalid mass value*
+   Self-explanatory.
+
+*Invalid math function in variable formula*
+   Self-explanatory.
+
+*Invalid math/group/special function in variable formula*
+   Self-explanatory.
+
+*Invalid option in lattice command for non-custom style*
+   Certain lattice keywords are not supported unless the
+   lattice style is "custom".
+
+*Invalid order of forces within respa levels*
+   For respa, ordering of force computations within respa levels must
+   obey certain rules.  E.g. bonds cannot be compute less frequently than
+   angles, pairwise forces cannot be computed less frequently than
+   kspace, etc.
+
+*Invalid pair table cutoff*
+   Cutoffs in pair\_coeff command are not valid with read-in pair table.
+
+*Invalid pair table length*
+   Length of read-in pair table is invalid
+
+*Invalid param file for fix qeq/shielded*
+   Invalid value of gamma.
+
+*Invalid param file for fix qeq/slater*
+   Zeta value is 0.0.
+
+*Invalid partitions in processors part command*
+   Valid partitions are numbered 1 to N and the sender and receiver
+   cannot be the same partition.
+
+*Invalid python command*
+   Self-explanatory.  Check the input script syntax and compare to the
+   documentation for the command.  You can use -echo screen as a
+   command-line option when running LAMMPS to see the offending line.
+
+*Invalid radius in Atoms section of data file*
+   Radius must be >= 0.0.
+
+*Invalid random number seed in fix ttm command*
+   Random number seed must be > 0.
+
+*Invalid random number seed in set command*
+   Random number seed must be > 0.
+
+*Invalid replace values in compute reduce*
+   Self-explanatory.
+
+*Invalid rigid body ID in fix rigid file*
+   The ID does not match the number of an existing ID of rigid bodies
+   that are defined by the fix rigid command.
+
+*Invalid rigid body ID in fix rigid/small file*
+   The ID does not match the number of an existing ID of rigid bodies
+   that are defined by the fix rigid/small command.
+
+*Invalid run command N value*
+   The number of timesteps must fit in a 32-bit integer.  If you want to
+   run for more steps than this, perform multiple shorter runs.
+
+*Invalid run command start/stop value*
+   Self-explanatory.
+
+*Invalid run command upto value*
+   Self-explanatory.
+
+*Invalid seed for Marsaglia random # generator*
+   The initial seed for this random number generator must be a positive
+   integer less than or equal to 900 million.
+
+*Invalid seed for Park random # generator*
+   The initial seed for this random number generator must be a positive
+   integer.
+
+*Invalid shake angle type in molecule file*
+   Self-explanatory.
+
+*Invalid shake atom in molecule file*
+   Self-explanatory.
+
+*Invalid shake bond type in molecule file*
+   Self-explanatory.
+
+*Invalid shake flag in molecule file*
+   Self-explanatory.
+
+*Invalid shape in Ellipsoids section of data file*
+   Self-explanatory.
+
+*Invalid shape in Triangles section of data file*
+   Two or more of the triangle corners are duplicate points.
+
+*Invalid shape in set command*
+   Self-explanatory.
+
+*Invalid shear direction for fix wall/gran*
+   Self-explanatory.
+
+*Invalid special atom index in molecule file*
+   Self-explanatory.
+
+*Invalid special function in variable formula*
+   Self-explanatory.
+
+*Invalid style in pair\_write command*
+   Self-explanatory.  Check the input script.
+
+*Invalid syntax in variable formula*
+   Self-explanatory.
+
+*Invalid t\_event in prd command*
+   Self-explanatory.
+
+*Invalid t\_event in tad command*
+   The value must be greater than 0.
+
+*Invalid template atom in Atoms section of data file*
+   The atom indices must be between 1 to N, where N is the number of
+   atoms in the template molecule the atom belongs to.
+
+*Invalid template index in Atoms section of data file*
+   The template indices must be between 1 to N, where N is the number of
+   molecules in the template.
+
+*Invalid thermo keyword in variable formula*
+   The keyword is not recognized.
+
+*Invalid threads\_per\_atom specified.*
+   For 3-body potentials on the GPU, the threads\_per\_atom setting cannot be
+   greater than 4 for NVIDIA GPUs.
+
+*Invalid timestep reset for fix ave/atom*
+   Resetting the timestep has invalidated the sequence of timesteps this
+   fix needs to process.
+
+*Invalid timestep reset for fix ave/chunk*
+   Resetting the timestep has invalidated the sequence of timesteps this
+   fix needs to process.
+
+*Invalid timestep reset for fix ave/correlate*
+   Resetting the timestep has invalidated the sequence of timesteps this
+   fix needs to process.
+
+*Invalid timestep reset for fix ave/histo*
+   Resetting the timestep has invalidated the sequence of timesteps this
+   fix needs to process.
+
+*Invalid timestep reset for fix ave/spatial*
+   Resetting the timestep has invalidated the sequence of timesteps this
+   fix needs to process.
+
+*Invalid timestep reset for fix ave/time*
+   Resetting the timestep has invalidated the sequence of timesteps this
+   fix needs to process.
+
+*Invalid tmax in tad command*
+   The value must be greater than 0.0.
+
+*Invalid type for mass set*
+   Mass command must set a type from 1-N where N is the number of atom
+   types.
+
+*Invalid use of library file() function*
+   This function is called through the library interface.  This
+   error should not occur.  Contact the developers if it does.
+
+*Invalid value in set command*
+   The value specified for the setting is invalid, likely because it is
+   too small or too large.
+
+*Invalid variable evaluation in variable formula*
+   A variable used in a formula could not be evaluated.
+
+*Invalid variable in next command*
+   Self-explanatory.
+
+*Invalid variable name*
+   Variable name used in an input script line is invalid.
+
+*Invalid variable name in variable formula*
+   Variable name is not recognized.
+
+*Invalid variable style in special function next*
+   Only file-style or atomfile-style variables can be used with next().
+
+*Invalid variable style with next command*
+   Variable styles *equal* and *world* cannot be used in a next
+   command.
+
+*Invalid volume in set command*
+   Volume must be > 0.0.
+
+*Invalid wiggle direction for fix wall/gran*
+   Self-explanatory.
+
+*Invoked angle equil angle on angle style none*
+   Self-explanatory.
+
+*Invoked angle single on angle style none*
+   Self-explanatory.
+
+*Invoked bond equil distance on bond style none*
+   Self-explanatory.
+
+*Invoked bond single on bond style none*
+   Self-explanatory.
+
+*Invoked pair single on pair style none*
+   A command (e.g. a dump) attempted to invoke the single() function on a
+   pair style none, which is illegal.  You are probably attempting to
+   compute per-atom quantities with an undefined pair style.
+
+*Invoking coulombic in pair style lj/coul requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Invoking coulombic in pair style lj/long/dipole/long requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*KIM Simulator Model has no Model definition*
+   There is no model definition (key: model-defn) in the KIM Simulator
+   Model.  Please contact the OpenKIM database maintainers to verify
+   and potentially correct this.
+
+*KOKKOS package does not yet support comm\_style tiled*
+   Self-explanatory.
+
+*KOKKOS package requires a kokkos enabled atom\_style*
+   Self-explanatory.
+
+*KSpace accuracy must be > 0*
+   The kspace accuracy designated in the input must be greater than zero.
+
+*KSpace accuracy too large to estimate G vector*
+   Reduce the accuracy request or specify gewald explicitly
+   via the kspace\_modify command.
+
+*KSpace accuracy too low*
+   Requested accuracy must be less than 1.0.
+
+*KSpace solver requires a pair style*
+   No pair style is defined.
+
+*KSpace style does not yet support triclinic geometries*
+   The specified kspace style does not allow for non-orthogonal
+   simulation boxes.
+
+*KSpace style has not yet been set*
+   Cannot use kspace\_modify command until a kspace style is set.
+
+*KSpace style is incompatible with Pair style*
+   Setting a kspace style requires that a pair style with matching
+   long-range Coulombic or dispersion components be used.
+
+*Keyword %s in MEAM parameter file not recognized*
+   Self-explanatory.
+
+*Kokkos has been compiled for CUDA but no GPUs are requested*
+   One or more GPUs must be used when Kokkos is compiled for CUDA.
+
+*Kspace\_modify mesh parameter must be all zero or all positive*
+   Valid kspace mesh parameters are >0. The code will try to auto-detect
+   suitable values when all three mesh sizes are set to zero (the default).
+
+*Kspace\_modify mesh/disp parameter must be all zero or all positive*
+   Valid kspace mesh/disp parameters are >0. The code will try to auto-detect
+   suitable values when all three mesh sizes are set to zero **and**
+   the required accuracy via *force/disp/real* as well as
+   *force/disp/kspace* is set.
+
+*Kspace style does not support compute group/group*
+   Self-explanatory.
+
+*Kspace style pppm/disp/tip4p requires newton on*
+   Self-explanatory.
+
+*Kspace style pppm/tip4p requires newton on*
+   Self-explanatory.
+
+*Kspace style requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Kspace\_modify eigtol must be smaller than one*
+   Self-explanatory.
+
+*LAMMPS is not built with Python embedded*
+   This is done by including the PYTHON package before LAMMPS is built.
+   This is required to use python-style variables.
+
+*LAMMPS unit\_style lj not supported by KIM models*
+   Self-explanatory. Check the input script or data file.
+
+*LJ6 off not supported in pair\_style buck/long/coul/long*
+   Self-explanatory.
+
+*Label wasn't found in input script*
+   Self-explanatory.
+
+*Lattice orient vectors are not orthogonal*
+   The three specified lattice orientation vectors must be mutually
+   orthogonal.
+
+*Lattice orient vectors are not right-handed*
+   The three specified lattice orientation vectors must create a
+   right-handed coordinate system such that a1 cross a2 = a3.
+
+*Lattice primitive vectors are collinear*
+   The specified lattice primitive vectors do not for a unit cell with
+   non-zero volume.
+
+*Lattice settings are not compatible with 2d simulation*
+   One or more of the specified lattice vectors has a non-zero z
+   component.
+
+*Lattice spacings are invalid*
+   Each x,y,z spacing must be > 0.
+
+*Lattice style incompatible with simulation dimension*
+   2d simulation can use sq, sq2, or hex lattice.  3d simulation can use
+   sc, bcc, or fcc lattice.
+
+*Log of zero/negative value in variable formula*
+   Self-explanatory.
+
+*Lost atoms via balance: original %ld current %ld*
+   This should not occur.  Report the problem to the developers.
+
+*Lost atoms: original %ld current %ld*
+   Lost atoms are checked for each time thermo output is done.  See the
+   thermo\_modify lost command for options.  Lost atoms usually indicate
+   bad dynamics, e.g. atoms have been blown far out of the simulation
+   box, or moved further than one processor's sub-domain away before
+   reneighboring.
+
+*MEAM library error %d*
+   A call to the MEAM Fortran library returned an error.
+
+*MPI\_LMP\_BIGINT and bigint in lmptype.h are not compatible*
+   The size of the MPI datatype does not match the size of a bigint.
+
+*MPI\_LMP\_TAGINT and tagint in lmptype.h are not compatible*
+   The size of the MPI datatype does not match the size of a tagint.
+
+*MSM can only currently be used with comm\_style brick*
+   This is a current restriction in LAMMPS.
+
+*MSM grid is too large*
+   The global MSM grid is larger than OFFSET in one or more dimensions.
+   OFFSET is currently set to 16384.  You likely need to decrease the
+   requested accuracy.
+
+*MSM order must be 4, 6, 8, or 10*
+   This is a limitation of the MSM implementation in LAMMPS:
+   the MSM order can only be 4, 6, 8, or 10.
+
+*Mass command before simulation box is defined*
+   The mass command cannot be used before a read\_data, read\_restart, or
+   create\_box command.
+
+*Matrix factorization to split dispersion coefficients failed*
+   This should not normally happen.  Contact the developers.
+
+*Min\_style command before simulation box is defined*
+   The min\_style command cannot be used before a read\_data, read\_restart,
+   or create\_box command.
+
+*Minimization could not find thermo\_pe compute*
+   This compute is created by the thermo command.  It must have been
+   explicitly deleted by a uncompute command.
+
+*Minimize command before simulation box is defined*
+   The minimize command cannot be used before a read\_data, read\_restart,
+   or create\_box command.
+
+*Mismatched brackets in variable*
+   Self-explanatory.
+
+*Mismatched compute in variable formula*
+   A compute is referenced incorrectly or a compute that produces per-atom
+   values is used in an equal-style variable formula.
+
+*Mismatched fix in variable formula*
+   A fix is referenced incorrectly or a fix that produces per-atom
+   values is used in an equal-style variable formula.
+
+*Mismatched variable in variable formula*
+   A variable is referenced incorrectly or an atom-style variable that
+   produces per-atom values is used in an equal-style variable
+   formula.
+
+*Modulo 0 in variable formula*
+   Self-explanatory.
+
+*Molecule IDs too large for compute chunk/atom*
+   The IDs must not be larger than can be stored in a 32-bit integer
+   since chunk IDs are 32-bit integers.
+
+*Molecule auto special bond generation overflow*
+   Counts exceed maxspecial setting for other atoms in system.
+
+*Molecule file has angles but no nangles setting*
+   Self-explanatory.
+
+*Molecule file has body params but no setting for them*
+   Self-explanatory.
+
+*Molecule file has bonds but no nbonds setting*
+   Self-explanatory.
+
+*Molecule file has dihedrals but no ndihedrals setting*
+   Self-explanatory.
+
+*Molecule file has impropers but no nimpropers setting*
+   Self-explanatory.
+
+*Molecule file has no Body Doubles section*
+   Self-explanatory.
+
+*Molecule file has no Body Integers section*
+   Self-explanatory.
+
+*Molecule file has special flags but no bonds*
+   Self-explanatory.
+
+*Molecule file needs both Special Bond sections*
+   Self-explanatory.
+
+*Molecule file requires atom style body*
+   Self-explanatory.
+
+*Molecule file shake flags not before shake atoms*
+   The order of the two sections is important.
+
+*Molecule file shake flags not before shake bonds*
+   The order of the two sections is important.
+
+*Molecule file shake info is incomplete*
+   All 3 SHAKE sections are needed.
+
+*Molecule file special list does not match special count*
+   The number of values in an atom's special list does not match count.
+
+*Molecule file z center-of-mass must be 0.0 for 2d*
+   Self-explanatory.
+
+*Molecule file z coord must be 0.0 for 2d*
+   Self-explanatory.
+
+*Molecule natoms must be 1 for body particle*
+   Self-explanatory.
+
+*Molecule sizescale must be 1.0 for body particle*
+   Self-explanatory.
+
+*Molecule template ID for atom\_style template does not exist*
+   Self-explanatory.
+
+*Molecule template ID for create\_atoms does not exist*
+   Self-explanatory.
+
+*Molecule template ID for fix deposit does not exist*
+   Self-explanatory.
+
+*Molecule template ID for fix gcmc does not exist*
+   Self-explanatory.
+
+*Molecule template ID for fix pour does not exist*
+   Self-explanatory.
+
+*Molecule template ID for fix rigid/small does not exist*
+   Self-explanatory.
+
+*Molecule template ID for fix shake does not exist*
+   Self-explanatory.
+
+*Molecule template ID must be alphanumeric or underscore characters*
+   Self-explanatory.
+
+*Molecule topology/atom exceeds system topology/atom*
+   The number of bonds, angles, etc per-atom in the molecule exceeds the
+   system setting.  See the create\_box command for how to specify these
+   values.
+
+*Molecule topology type exceeds system topology type*
+   The number of bond, angle, etc types in the molecule exceeds the
+   system setting.  See the create\_box command for how to specify these
+   values.
+
+*More than one fix deform*
+   Only one fix deform can be defined at a time.
+
+*More than one fix freeze*
+   Only one of these fixes can be defined, since the granular pair
+   potentials access it.
+
+*More than one fix shake*
+   Only one fix shake can be defined.
+
+*Mu not allowed when not using semi-grand in fix atom/swap command*
+   Self-explanatory.
+
+*Must define angle\_style before Angle Coeffs*
+   Must use an angle\_style command before reading a data file that
+   defines Angle Coeffs.
+
+*Must define angle\_style before BondAngle Coeffs*
+   Must use an angle\_style command before reading a data file that
+   defines Angle Coeffs.
+
+*Must define angle\_style before BondBond Coeffs*
+   Must use an angle\_style command before reading a data file that
+   defines Angle Coeffs.
+
+*Must define bond\_style before Bond Coeffs*
+   Must use a bond\_style command before reading a data file that
+   defines Bond Coeffs.
+
+*Must define dihedral\_style before AngleAngleTorsion Coeffs*
+   Must use a dihedral\_style command before reading a data file that
+   defines AngleAngleTorsion Coeffs.
+
+*Must define dihedral\_style before AngleTorsion Coeffs*
+   Must use a dihedral\_style command before reading a data file that
+   defines AngleTorsion Coeffs.
+
+*Must define dihedral\_style before BondBond13 Coeffs*
+   Must use a dihedral\_style command before reading a data file that
+   defines BondBond13 Coeffs.
+
+*Must define dihedral\_style before Dihedral Coeffs*
+   Must use a dihedral\_style command before reading a data file that
+   defines Dihedral Coeffs.
+
+*Must define dihedral\_style before EndBondTorsion Coeffs*
+   Must use a dihedral\_style command before reading a data file that
+   defines EndBondTorsion Coeffs.
+
+*Must define dihedral\_style before MiddleBondTorsion Coeffs*
+   Must use a dihedral\_style command before reading a data file that
+   defines MiddleBondTorsion Coeffs.
+
+*Must define improper\_style before AngleAngle Coeffs*
+   Must use an improper\_style command before reading a data file that
+   defines AngleAngle Coeffs.
+
+*Must define improper\_style before Improper Coeffs*
+   Must use an improper\_style command before reading a data file that
+   defines Improper Coeffs.
+
+*Must define pair\_style before Pair Coeffs*
+   Must use a pair\_style command before reading a data file that defines
+   Pair Coeffs.
+
+*Must define pair\_style before PairIJ Coeffs*
+   Must use a pair\_style command before reading a data file that defines
+   PairIJ Coeffs.
+
+*Must have more than one processor partition to temper*
+   Cannot use the temper command with only one processor partition.  Use
+   the -partition command-line option.
+
+*Must read Atoms before Angles*
+   The Atoms section of a data file must come before an Angles section.
+
+*Must read Atoms before Bodies*
+   The Atoms section of a data file must come before a Bodies section.
+
+*Must read Atoms before Bonds*
+   The Atoms section of a data file must come before a Bonds section.
+
+*Must read Atoms before Dihedrals*
+   The Atoms section of a data file must come before a Dihedrals section.
+
+*Must read Atoms before Ellipsoids*
+   The Atoms section of a data file must come before a Ellipsoids
+   section.
+
+*Must read Atoms before Impropers*
+   The Atoms section of a data file must come before an Impropers
+   section.
+
+*Must read Atoms before Lines*
+   The Atoms section of a data file must come before a Lines section.
+
+*Must read Atoms before Triangles*
+   The Atoms section of a data file must come before a Triangles section.
+
+*Must read Atoms before Velocities*
+   The Atoms section of a data file must come before a Velocities
+   section.
+
+*Must re-specify non-restarted pair style (xxx) after read\_restart*
+   For pair styles, that do not store their settings in a restart file,
+   it must be defined with a new 'pair\_style' command after read\_restart.
+
+*Must set both respa inner and outer*
+   Cannot use just the inner or outer option with respa without using the
+   other.
+
+*Must set number of threads via package omp command*
+   Because you are using the USER-OMP package, set the number of threads
+   via its settings, not by the pair\_style snap nthreads setting.
+
+*Must shrink-wrap piston boundary*
+   The boundary style of the face where the piston is applied must be of
+   type s (shrink-wrapped).
+
+*Must specify a region in fix deposit*
+   The region keyword must be specified with this fix.
+
+*Must specify a region in fix pour*
+   Self-explanatory.
+
+*Must specify at least 2 types in fix atom/swap command*
+   Self-explanatory.
+
+*Must use 'kim\_style init' command before simulation box is defined*
+   Self-explanatory.
+
+*Must use 'kim\_style define' command after simulation box is defined*
+   Self-explanatory.
+
+*Must use 'kim\_style init' command before 'kim\_style define'*
+   Self-explanatory.
+
+*Must use 'kspace\_modify pressure/scalar no' for rRESPA with kspace\_style MSM*
+   The kspace scalar pressure option cannot (yet) be used with rRESPA.
+
+*Must use 'kspace\_modify pressure/scalar no' for tensor components with kspace\_style msm*
+   Otherwise MSM will compute only a scalar pressure.  See the kspace\_modify
+   command for details on this setting.
+
+*Must use 'kspace\_modify pressure/scalar no' to obtain per-atom virial with kspace\_style MSM*
+   The kspace scalar pressure option cannot be used to obtain per-atom virial.
+
+*Must use 'kspace\_modify pressure/scalar no' with GPU MSM Pair styles*
+   The kspace scalar pressure option is not (yet) compatible with GPU MSM Pair styles.
+
+*Must use 'kspace\_modify pressure/scalar no' with kspace\_style msm/cg*
+   The kspace scalar pressure option is not compatible with kspace\_style msm/cg.
+
+*Must use -in switch with multiple partitions*
+   A multi-partition simulation cannot read the input script from stdin.
+   The -in command-line option must be used to specify a file.
+
+*Must use Kokkos half/thread or full neighbor list with threads or GPUs*
+   Using Kokkos half-neighbor lists with threading is not allowed.
+
+*Must use a block or cylinder region with fix pour*
+   Self-explanatory.
+
+*Must use a block region with fix pour for 2d simulations*
+   Self-explanatory.
+
+*Must use a bond style with TIP4P potential*
+   TIP4P potentials assume bond lengths in water are constrained
+   by a fix shake command.
+
+*Must use a molecular atom style with fix poems molecule*
+   Self-explanatory.
+
+*Must use a z-axis cylinder region with fix pour*
+   Self-explanatory.
+
+*Must use an angle style with TIP4P potential*
+   TIP4P potentials assume angles in water are constrained by a fix shake
+   command.
+
+*Must use atom map style array with Kokkos*
+   See the atom\_modify map command.
+
+*Must use atom style with molecule IDs with fix bond/swap*
+   Self-explanatory.
+
+*Must use pair\_style comb or comb3 with fix qeq/comb*
+   Self-explanatory.
+
+*Must use variable energy with fix addforce*
+   Must define an energy variable when applying a dynamic
+   force during minimization.
+
+*Must use variable energy with fix efield*
+   You must define an energy when performing a minimization with a
+   variable E-field.
+
+*NEB command before simulation box is defined*
+   Self-explanatory.
+
+*NEB requires damped dynamics minimizer*
+   Use a different minimization style.
+
+*NEB requires use of fix neb*
+   Self-explanatory.
+
+*NL ramp in wall/piston only implemented in zlo for now*
+   The ramp keyword can only be used for piston applied to face zlo.
+
+*Need nswaptypes mu values in fix atom/swap command*
+   Self-explanatory.
+
+*Needed bonus data not in data file*
+   Some atom styles require bonus data.  See the read\_data doc page for
+   details.
+
+*Needed molecular topology not in data file*
+   The header of the data file indicated bonds, angles, etc would be
+   included, but they are not present.
+
+*Neigh\_modify exclude molecule requires atom attribute molecule*
+   Self-explanatory.
+
+*Neigh\_modify include group != atom\_modify first group*
+   Self-explanatory.
+
+*Neighbor delay must be 0 or multiple of every setting*
+   The delay and every parameters set via the neigh\_modify command are
+   inconsistent.  If the delay setting is non-zero, then it must be a
+   multiple of the every setting.
+
+*Neighbor include group not allowed with ghost neighbors*
+   This is a current restriction within LAMMPS.
+
+*Neighbor list overflow, boost neigh\_modify one*
+   There are too many neighbors of a single atom.  Use the neigh\_modify
+   command to increase the max number of neighbors allowed for one atom.
+   You may also want to boost the page size.
+
+*Neighbor multi not yet enabled for ghost neighbors*
+   This is a current restriction within LAMMPS.
+
+*Neighbor multi not yet enabled for granular*
+   Self-explanatory.
+
+*Neighbor multi not yet enabled for rRESPA*
+   Self-explanatory.
+
+*Neighbor page size must be >= 10x the one atom setting*
+   This is required to prevent wasting too much memory.
+
+*New atom IDs exceed maximum allowed ID*
+   See the setting for tagint in the src/lmptype.h file.
+
+*New bond exceeded bonds per atom in create\_bonds*
+See the read\_data command for info on using the "extra/bond/per/atom"
+keyword to allow for additional bonds to be formed
+
+*New bond exceeded bonds per atom in fix bond/create*
+   See the read\_data command for info on using the "extra/bond/per/atom"
+   keyword to allow for additional bonds to be formed
+
+*New bond exceeded special list size in fix bond/create*
+   See the "read\_data extra/special/per/atom" command
+   (or the "create\_box extra/special/per/atom" command)
+   for info on how to leave space in the special bonds
+   list to allow for additional bonds to be formed.
+
+*Newton bond change after simulation box is defined*
+   The newton command cannot be used to change the newton bond value
+   after a read\_data, read\_restart, or create\_box command.
+
+*Next command must list all universe and uloop variables*
+   This is to insure they stay in sync.
+
+*No Kspace style defined for compute group/group*
+   Self-explanatory.
+
+*No OpenMP support compiled in*
+   An OpenMP flag is set, but LAMMPS was not built with
+   OpenMP support.
+
+*No angle style is defined for compute angle/local*
+   Self-explanatory.
+
+*No angles allowed with this atom style*
+   Self-explanatory.
+
+*No atoms in data file*
+   The header of the data file indicated that atoms would be included,
+   but they are not present.
+
+*No basis atoms in lattice*
+   Basis atoms must be defined for lattice style user.
+
+*No bodies allowed with this atom style*
+   Self-explanatory.  Check data file.
+
+*No bond style is defined for compute bond/local*
+   Self-explanatory.
+
+*No bonds allowed with this atom style*
+   Self-explanatory.
+
+*No box information in dump. You have to use 'box no'*
+   Self-explanatory.
+
+*No count or invalid atom count in molecule file*
+   The number of atoms must be specified.
+
+*No dihedral style is defined for compute dihedral/local*
+   Self-explanatory.
+
+*No dihedrals allowed with this atom style*
+   Self-explanatory.
+
+*No dump custom arguments specified*
+   The dump custom command requires that atom quantities be specified to
+   output to dump file.
+
+*No dump local arguments specified*
+   Self-explanatory.
+
+*No ellipsoids allowed with this atom style*
+   Self-explanatory.  Check data file.
+
+*No fix gravity defined for fix pour*
+   Gravity is required to use fix pour.
+
+*No improper style is defined for compute improper/local*
+   Self-explanatory.
+
+*No impropers allowed with this atom style*
+   Self-explanatory.
+
+*No input values for fix ave/spatial*
+   Self-explanatory.
+
+*No lines allowed with this atom style*
+   Self-explanatory.  Check data file.
+
+*No matching element in ADP potential file*
+   The ADP potential file does not contain elements that match the
+   requested elements.
+
+*No matching element in EAM potential file*
+   The EAM potential file does not contain elements that match the
+   requested elements.
+
+*No molecule topology allowed with atom style template*
+   The data file cannot specify the number of bonds, angles, etc,
+   because this info if inferred from the molecule templates.
+
+*No overlap of box and region for create\_atoms*
+   Self-explanatory.
+
+*No pair coul/streitz for fix qeq/slater*
+   These commands must be used together.
+
+*No pair hbond/dreiding coefficients set*
+   Self-explanatory.
+
+*No pair style defined for compute group/group*
+   Cannot calculate group interactions without a pair style defined.
+
+*No pair style is defined for compute pair/local*
+   Self-explanatory.
+
+*No pair style is defined for compute property/local*
+   Self-explanatory.
+
+*No rigid bodies defined*
+   The fix specification did not end up defining any rigid bodies.
+
+*No triangles allowed with this atom style*
+   Self-explanatory.  Check data file.
+
+*No values in fix ave/chunk command*
+   Self-explanatory.
+
+*No values in fix ave/time command*
+   Self-explanatory.
+
+*Non digit character between brackets in variable*
+   Self-explanatory.
+
+*Non integer # of swaps in temper command*
+   Swap frequency in temper command must evenly divide the total # of
+   timesteps.
+
+*Non-numeric box dimensions - simulation unstable*
+   The box size has apparently blown up.
+
+*Non-zero atom IDs with atom\_modify id = no*
+   Self-explanatory.
+
+*Non-zero read\_data shift z value for 2d simulation*
+   Self-explanatory.
+
+*Nprocs not a multiple of N for -reorder*
+   Self-explanatory.
+
+*Number of core atoms != number of shell atoms*
+   There must be a one-to-one pairing of core and shell atoms.
+
+*Numeric index is out of bounds*
+   A command with an argument that specifies an integer or range of
+   integers is using a value that is less than 1 or greater than the
+   maximum allowed limit.
+
+*One or more Atom IDs is negative*
+   Atom IDs must be positive integers.
+
+*One or more atom IDs is too big*
+   The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
+   setting in your LAMMPS build.  See the :doc:`Build settings <Build_settings>` doc page for more info.
+
+*One or more atom IDs is zero*
+   Either all atoms IDs must be zero or none of them.
+
+*One or more atoms belong to multiple rigid bodies*
+   Two or more rigid bodies defined by the fix rigid command cannot
+   contain the same atom.
+
+*One or more rigid bodies are a single particle*
+   Self-explanatory.
+
+*One or zero atoms in rigid body*
+   Any rigid body defined by the fix rigid command must contain 2 or more
+   atoms.
+
+*Only 2 types allowed when not using semi-grand in fix atom/swap command*
+   Self-explanatory.
+
+*Only one cut-off allowed when requesting all long*
+   Self-explanatory.
+
+*Only one cutoff allowed when requesting all long*
+   Self-explanatory.
+
+*Only zhi currently implemented for fix append/atoms*
+   Self-explanatory.
+
+*Out of range atoms - cannot compute MSM*
+   One or more atoms are attempting to map their charge to a MSM grid point
+   that is not owned by a processor.  This is likely for one of two
+   reasons, both of them bad.  First, it may mean that an atom near the
+   boundary of a processor's sub-domain has moved more than 1/2 the
+   :doc:`neighbor skin distance <neighbor>` without neighbor lists being
+   rebuilt and atoms being migrated to new processors.  This also means
+   you may be missing pairwise interactions that need to be computed.
+   The solution is to change the re-neighboring criteria via the
+   :doc:`neigh\_modify <neigh_modify>` command.  The safest settings are
+   "delay 0 every 1 check yes".  Second, it may mean that an atom has
+   moved far outside a processor's sub-domain or even the entire
+   simulation box. This indicates bad physics, e.g. due to highly
+   overlapping atoms, too large a timestep, etc.
+
+*Out of range atoms - cannot compute PPPM*
+   One or more atoms are attempting to map their charge to a PPPM grid
+   point that is not owned by a processor.  This is likely for one of two
+   reasons, both of them bad.  First, it may mean that an atom near the
+   boundary of a processor's sub-domain has moved more than 1/2 the
+   :doc:`neighbor skin distance <neighbor>` without neighbor lists being
+   rebuilt and atoms being migrated to new processors.  This also means
+   you may be missing pairwise interactions that need to be computed.
+   The solution is to change the re-neighboring criteria via the
+   :doc:`neigh\_modify <neigh_modify>` command.  The safest settings are
+   "delay 0 every 1 check yes".  Second, it may mean that an atom has
+   moved far outside a processor's sub-domain or even the entire
+   simulation box. This indicates bad physics, e.g. due to highly
+   overlapping atoms, too large a timestep, etc.
+
+*Out of range atoms - cannot compute PPPMDisp*
+   One or more atoms are attempting to map their charge to a PPPM grid
+   point that is not owned by a processor.  This is likely for one of two
+   reasons, both of them bad.  First, it may mean that an atom near the
+   boundary of a processor's sub-domain has moved more than 1/2 the
+   :doc:`neighbor skin distance <neighbor>` without neighbor lists being
+   rebuilt and atoms being migrated to new processors.  This also means
+   you may be missing pairwise interactions that need to be computed.
+   The solution is to change the re-neighboring criteria via the
+   :doc:`neigh\_modify <neigh_modify>` command.  The safest settings are
+   "delay 0 every 1 check yes".  Second, it may mean that an atom has
+   moved far outside a processor's sub-domain or even the entire
+   simulation box. This indicates bad physics, e.g. due to highly
+   overlapping atoms, too large a timestep, etc.
+
+*Overflow of allocated fix vector storage*
+   This should not normally happen if the fix correctly calculated
+   how long the vector will grow to.  Contact the developers.
+
+*Overlapping large/large in pair colloid*
+   This potential is infinite when there is an overlap.
+
+*Overlapping small/large in pair colloid*
+   This potential is infinite when there is an overlap.
+
+*POEMS fix must come before NPT/NPH fix*
+   NPT/NPH fix must be defined in input script after all poems fixes,
+   else the fix contribution to the pressure virial is incorrect.
+
+*PPPM can only currently be used with comm\_style brick*
+   This is a current restriction in LAMMPS.
+
+*PPPM grid is too large*
+   The global PPPM grid is larger than OFFSET in one or more dimensions.
+   OFFSET is currently set to 4096.  You likely need to decrease the
+   requested accuracy.
+
+*PPPM grid stencil extends beyond nearest neighbor processor*
+   This is not allowed if the kspace\_modify overlap setting is no.
+
+*PPPM order < minimum allowed order*
+   The default minimum order is 2.  This can be reset by the
+   kspace\_modify minorder command.
+
+*PPPM order cannot be < 2 or > than %d*
+   This is a limitation of the PPPM implementation in LAMMPS.
+
+*PPPMDisp Coulomb grid is too large*
+   The global PPPM grid is larger than OFFSET in one or more dimensions.
+   OFFSET is currently set to 4096.  You likely need to decrease the
+   requested accuracy.
+
+*PPPMDisp Dispersion grid is too large*
+   The global PPPM grid is larger than OFFSET in one or more dimensions.
+   OFFSET is currently set to 4096.  You likely need to decrease the
+   requested accuracy.
+
+*PPPMDisp can only currently be used with comm\_style brick*
+   This is a current restriction in LAMMPS.
+
+*PPPMDisp coulomb order cannot be greater than %d*
+   This is a limitation of the PPPM implementation in LAMMPS.
+
+*PPPMDisp used but no parameters set, for further information please see the pppm/disp documentation*
+   An efficient and accurate usage of the pppm/disp requires settings via the kspace\_modify command. Please see the pppm/disp documentation for further instructions.
+
+*PRD command before simulation box is defined*
+   The prd command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*PRD nsteps must be multiple of t\_event*
+   Self-explanatory.
+
+*PRD t\_corr must be multiple of t\_event*
+   Self-explanatory.
+
+*Package command after simulation box is defined*
+   The package command cannot be used after a read\_data, read\_restart, or
+   create\_box command.
+
+*Package gpu command without GPU package installed*
+   The GPU package must be installed via "make yes-gpu" before LAMMPS is
+   built.
+
+*Package intel command without USER-INTEL package installed*
+   The USER-INTEL package must be installed via "make yes-user-intel"
+   before LAMMPS is built.
+
+*Package kokkos command without KOKKOS package enabled*
+   The KOKKOS package must be installed via "make yes-kokkos" before
+   LAMMPS is built, and the "-k on" must be used to enable the package.
+
+*Package omp command without USER-OMP package installed*
+   The USER-OMP package must be installed via "make yes-user-omp" before
+   LAMMPS is built.
+
+*Pair body requires atom style body*
+   Self-explanatory.
+
+*Pair body requires body style nparticle*
+   This pair style is specific to the nparticle body style.
+
+*Pair brownian requires atom style sphere*
+   Self-explanatory.
+
+*Pair brownian requires extended particles*
+   One of the particles has radius 0.0.
+
+*Pair brownian requires monodisperse particles*
+   All particles must be the same finite size.
+
+*Pair brownian/poly requires atom style sphere*
+   Self-explanatory.
+
+*Pair brownian/poly requires extended particles*
+   One of the particles has radius 0.0.
+
+*Pair brownian/poly requires newton pair off*
+   Self-explanatory.
+
+*Pair coeff for hybrid has invalid style*
+   Style in pair coeff must have been listed in pair\_style command.
+
+*Pair coul/wolf requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair cutoff < Respa interior cutoff*
+   One or more pairwise cutoffs are too short to use with the specified
+   rRESPA cutoffs.
+
+*Pair dipole/cut requires atom attributes q, mu, torque*
+   The atom style defined does not have these attributes.
+
+*Pair dipole/cut/gpu requires atom attributes q, mu, torque*
+   The atom style defined does not have this attribute.
+
+*Pair dipole/long requires atom attributes q, mu, torque*
+   The atom style defined does not have these attributes.
+
+*Pair dipole/sf/gpu requires atom attributes q, mu, torque*
+   The atom style defined does not one or more of these attributes.
+
+*Pair distance < table inner cutoff*
+   Two atoms are closer together than the pairwise table allows.
+
+*Pair distance > table outer cutoff*
+   Two atoms are further apart than the pairwise table allows.
+
+*Pair dpd requires ghost atoms store velocity*
+   Use the comm\_modify vel yes command to enable this.
+
+*Pair gayberne epsilon a,b,c coeffs are not all set*
+   Each atom type involved in pair\_style gayberne must
+   have these 3 coefficients set at least once.
+
+*Pair gayberne requires atom style ellipsoid*
+   Self-explanatory.
+
+*Pair gayberne requires atoms with same type have same shape*
+   Self-explanatory.
+
+*Pair gayberne/gpu requires atom style ellipsoid*
+   Self-explanatory.
+
+*Pair gayberne/gpu requires atoms with same type have same shape*
+   Self-explanatory.
+
+*Pair granular requires atom attributes radius, rmass*
+   The atom style defined does not have these attributes.
+
+*Pair granular requires ghost atoms store velocity*
+   Use the comm\_modify vel yes command to enable this.
+
+*Pair granular with shear history requires newton pair off*
+   This is a current restriction of the implementation of pair
+   granular styles with history.
+
+*Pair hybrid single calls do not support per sub-style special bond values*
+   Self-explanatory.
+
+*Pair hybrid sub-style does not support single call*
+   You are attempting to invoke a single() call on a pair style
+   that doesn't support it.
+
+*Pair hybrid sub-style is not used*
+   No pair\_coeff command used a sub-style specified in the pair\_style
+   command.
+
+*Pair inner cutoff < Respa interior cutoff*
+   One or more pairwise cutoffs are too short to use with the specified
+   rRESPA cutoffs.
+
+*Pair inner cutoff >= Pair outer cutoff*
+   The specified cutoffs for the pair style are inconsistent.
+
+*Pair line/lj requires atom style line*
+   Self-explanatory.
+
+*Pair lj/long/dipole/long requires atom attributes mu, torque*
+   The atom style defined does not have these attributes.
+
+*Pair lubricate requires atom style sphere*
+   Self-explanatory.
+
+*Pair lubricate requires ghost atoms store velocity*
+   Use the comm\_modify vel yes command to enable this.
+
+*Pair lubricate requires monodisperse particles*
+   All particles must be the same finite size.
+
+*Pair lubricate/poly requires atom style sphere*
+   Self-explanatory.
+
+*Pair lubricate/poly requires extended particles*
+   One of the particles has radius 0.0.
+
+*Pair lubricate/poly requires ghost atoms store velocity*
+   Use the comm\_modify vel yes command to enable this.
+
+*Pair lubricate/poly requires newton pair off*
+   Self-explanatory.
+
+*Pair lubricateU requires atom style sphere*
+   Self-explanatory.
+
+*Pair lubricateU requires ghost atoms store velocity*
+   Use the comm\_modify vel yes command to enable this.
+
+*Pair lubricateU requires monodisperse particles*
+   All particles must be the same finite size.
+
+*Pair lubricateU/poly requires ghost atoms store velocity*
+   Use the comm\_modify vel yes command to enable this.
+
+*Pair lubricateU/poly requires newton pair off*
+   Self-explanatory.
+
+*Pair peri lattice is not identical in x, y, and z*
+   The lattice defined by the lattice command must be cubic.
+
+*Pair peri requires a lattice be defined*
+   Use the lattice command for this purpose.
+
+*Pair peri requires an atom map, see atom\_modify*
+   Even for atomic systems, an atom map is required to find Peridynamic
+   bonds.  Use the atom\_modify command to define one.
+
+*Pair resquared epsilon a,b,c coeffs are not all set*
+   Self-explanatory.
+
+*Pair resquared epsilon and sigma coeffs are not all set*
+   Self-explanatory.
+
+*Pair resquared requires atom style ellipsoid*
+   Self-explanatory.
+
+*Pair resquared requires atoms with same type have same shape*
+   Self-explanatory.
+
+*Pair resquared/gpu requires atom style ellipsoid*
+   Self-explanatory.
+
+*Pair resquared/gpu requires atoms with same type have same shape*
+   Self-explanatory.
+
+*Pair style AIREBO requires atom IDs*
+   This is a requirement to use the AIREBO potential.
+
+*Pair style AIREBO requires newton pair on*
+   See the newton command.  This is a restriction to use the AIREBO
+   potential.
+
+*Pair style BOP requires atom IDs*
+   This is a requirement to use the BOP potential.
+
+*Pair style BOP requires newton pair on*
+   See the newton command.  This is a restriction to use the BOP
+   potential.
+
+*Pair style COMB requires atom IDs*
+   This is a requirement to use the AIREBO potential.
+
+*Pair style COMB requires atom attribute q*
+   Self-explanatory.
+
+*Pair style COMB requires newton pair on*
+   See the newton command.  This is a restriction to use the COMB
+   potential.
+
+*Pair style COMB3 requires atom IDs*
+   This is a requirement to use the COMB3 potential.
+
+*Pair style COMB3 requires atom attribute q*
+   Self-explanatory.
+
+*Pair style COMB3 requires newton pair on*
+   See the newton command.  This is a restriction to use the COMB3
+   potential.
+
+*Pair style LCBOP requires atom IDs*
+   This is a requirement to use the LCBOP potential.
+
+*Pair style LCBOP requires newton pair on*
+   See the newton command.  This is a restriction to use the Tersoff
+   potential.
+
+*Pair style MEAM requires newton pair on*
+   See the newton command.  This is a restriction to use the MEAM
+   potential.
+
+*Pair style SNAP requires newton pair on*
+   See the newton command.  This is a restriction to use the SNAP
+   potential.
+
+*Pair style Stillinger-Weber requires atom IDs*
+   This is a requirement to use the SW potential.
+
+*Pair style Stillinger-Weber requires newton pair on*
+   See the newton command.  This is a restriction to use the SW
+   potential.
+
+*Pair style Tersoff requires atom IDs*
+   This is a requirement to use the Tersoff potential.
+
+*Pair style Tersoff requires newton pair on*
+   See the newton command.  This is a restriction to use the Tersoff
+   potential.
+
+*Pair style Vashishta requires atom IDs*
+   This is a requirement to use the Vashishta potential.
+
+*Pair style Vashishta requires newton pair on*
+   See the newton command.  This is a restriction to use the Vashishta
+   potential.
+
+*Pair style bop requires comm ghost cutoff at least 3x larger than %g*
+   Use the communicate ghost command to set this.  See the pair bop
+   doc page for more details.
+
+*Pair style born/coul/long requires atom attribute q*
+   An atom style that defines this attribute must be used.
+
+*Pair style born/coul/long/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style born/coul/wolf requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style buck/coul/cut requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style buck/coul/long requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style buck/coul/long/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style buck/long/coul/long requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style coul/cut requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style coul/cut/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style coul/debye/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style coul/dsf requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style coul/dsf/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style coul/long/gpu requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style coul/streitz requires atom attribute q*
+   Self-explanatory.
+
+*Pair style does not have extra field requested by compute pair/local*
+   The pair style does not support the pN value requested by the compute
+   pair/local command.
+
+*Pair style does not support bond\_style quartic*
+   The pair style does not have a single() function, so it can
+   not be invoked by bond\_style quartic.
+
+*Pair style does not support compute group/group*
+   The pair\_style does not have a single() function, so it cannot be
+   invoked by the compute group/group command.
+
+*Pair style does not support compute pair/local*
+   The pair style does not have a single() function, so it can
+   not be invoked by compute pair/local.
+
+*Pair style does not support compute property/local*
+   The pair style does not have a single() function, so it can
+   not be invoked by fix bond/swap.
+
+*Pair style does not support fix bond/swap*
+   The pair style does not have a single() function, so it can
+   not be invoked by fix bond/swap.
+
+*Pair style does not support pair\_write*
+   The pair style does not have a single() function, so it can
+   not be invoked by pair write.
+
+*Pair style does not support rRESPA inner/middle/outer*
+   You are attempting to use rRESPA options with a pair style that
+   does not support them.
+
+*Pair style granular with history requires atoms have IDs*
+   Atoms in the simulation do not have IDs, so history effects
+   cannot be tracked by the granular pair potential.
+
+*Pair style hbond/dreiding requires an atom map, see atom\_modify*
+   Self-explanatory.
+
+*Pair style hbond/dreiding requires atom IDs*
+   Self-explanatory.
+
+*Pair style hbond/dreiding requires molecular system*
+   Self-explanatory.
+
+*Pair style hbond/dreiding requires newton pair on*
+   See the newton command for details.
+
+*Pair style hybrid cannot have hybrid as an argument*
+   Self-explanatory.
+
+*Pair style hybrid cannot have none as an argument*
+   Self-explanatory.
+
+*Pair style is incompatible with KSpace style*
+   If a pair style with a long-range Coulombic component is selected,
+   then a kspace style must also be used.
+
+*Pair style is incompatible with TIP4P KSpace style*
+   The pair style does not have the requires TIP4P settings.
+
+*Pair style lj/charmm/coul/charmm requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style lj/charmm/coul/long requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style lj/charmm/coul/long/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/class2/coul/cut requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/class2/coul/long requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/class2/coul/long/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/cut/coul/cut requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/cut/coul/cut/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/cut/coul/debye/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/cut/coul/dsf requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style lj/cut/coul/dsf/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/cut/coul/long requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/cut/coul/long/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/cut/tip4p/cut requires atom IDs*
+   This is a requirement to use this potential.
+
+*Pair style lj/cut/tip4p/cut requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style lj/cut/tip4p/cut requires newton pair on*
+   See the newton command.  This is a restriction to use this
+   potential.
+
+*Pair style lj/cut/tip4p/long requires atom IDs*
+   There are no atom IDs defined in the system and the TIP4P potential
+   requires them to find O,H atoms with a water molecule.
+
+*Pair style lj/cut/tip4p/long requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style lj/cut/tip4p/long requires newton pair on*
+   This is because the computation of constraint forces within a water
+   molecule adds forces to atoms owned by other processors.
+
+*Pair style lj/gromacs/coul/gromacs requires atom attribute q*
+   An atom\_style with this attribute is needed.
+
+*Pair style lj/long/dipole/long does not currently support respa*
+   This feature is not yet supported.
+
+*Pair style lj/long/tip4p/long requires atom IDs*
+   There are no atom IDs defined in the system and the TIP4P potential
+   requires them to find O,H atoms with a water molecule.
+
+*Pair style lj/long/tip4p/long requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style lj/long/tip4p/long requires newton pair on*
+   This is because the computation of constraint forces within a water
+   molecule adds forces to atoms owned by other processors.
+
+*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style nb3b/harmonic requires atom IDs*
+   This is a requirement to use this potential.
+
+*Pair style nb3b/harmonic requires newton pair on*
+   See the newton command.  This is a restriction to use this potential.
+
+*Pair style nm/cut/coul/cut requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style nm/cut/coul/long requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style peri requires atom style peri*
+   Self-explanatory.
+
+*Pair style polymorphic requires atom IDs*
+   This is a requirement to use the polymorphic potential.
+
+*Pair style polymorphic requires newton pair on*
+   See the newton command.  This is a restriction to use the polymorphic
+   potential.
+
+*Pair style reax requires atom IDs*
+   This is a requirement to use the ReaxFF potential.
+
+*Pair style reax requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style reax requires newton pair on*
+   This is a requirement to use the ReaxFF potential.
+
+*Pair style requires a KSpace style*
+   No kspace style is defined.
+
+*Pair style requires use of kspace\_style ewald/disp*
+   Self-explanatory.
+
+*Pair style sw/gpu requires atom IDs*
+   This is a requirement to use this potential.
+
+*Pair style sw/gpu requires newton pair off*
+   See the newton command.  This is a restriction to use this potential.
+
+*Pair style vashishta/gpu requires atom IDs*
+   This is a requirement to use this potential.
+
+*Pair style vashishta/gpu requires newton pair off*
+   See the newton command.  This is a restriction to use this potential.
+
+*Pair style tersoff/gpu requires atom IDs*
+   This is a requirement to use the tersoff/gpu potential.
+
+*Pair style tersoff/gpu requires newton pair off*
+   See the newton command.  This is a restriction to use this pair style.
+
+*Pair style tip4p/cut requires atom IDs*
+   This is a requirement to use this potential.
+
+*Pair style tip4p/cut requires atom attribute q*
+   The atom style defined does not have this attribute.
+
+*Pair style tip4p/cut requires newton pair on*
+   See the newton command.  This is a restriction to use this potential.
+
+*Pair style tip4p/long requires atom IDs*
+   There are no atom IDs defined in the system and the TIP4P potential
+   requires them to find O,H atoms with a water molecule.
+
+*Pair style tip4p/long requires atom attribute q*
+   The atom style defined does not have these attributes.
+
+*Pair style tip4p/long requires newton pair on*
+   This is because the computation of constraint forces within a water
+   molecule adds forces to atoms owned by other processors.
+
+*Pair table cutoffs must all be equal to use with KSpace*
+   When using pair style table with a long-range KSpace solver, the
+   cutoffs for all atom type pairs must all be the same, since the
+   long-range solver starts at that cutoff.
+
+*Pair table parameters did not set N*
+   List of pair table parameters must include N setting.
+
+*Pair tersoff/zbl requires metal or real units*
+   This is a current restriction of this pair potential.
+
+*Pair tersoff/zbl/kk requires metal or real units*
+   This is a current restriction of this pair potential.
+
+*Pair tri/lj requires atom style tri*
+   Self-explanatory.
+
+*Pair yukawa/colloid requires atom style sphere*
+   Self-explanatory.
+
+*Pair yukawa/colloid requires atoms with same type have same radius*
+   Self-explanatory.
+
+*Pair yukawa/colloid/gpu requires atom style sphere*
+   Self-explanatory.
+
+*PairKIM only works with 3D problems*
+   This is a current limitation.
+
+*Pair\_coeff command before pair\_style is defined*
+   Self-explanatory.
+
+*Pair\_coeff command before simulation box is defined*
+   The pair\_coeff command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Pair\_modify command before pair\_style is defined*
+   Self-explanatory.
+
+*Pair\_modify special setting for pair hybrid incompatible with global special\_bonds setting*
+   Cannot override a setting of 0.0 or 1.0 or change a setting between
+   0.0 and 1.0.
+
+*Pair\_write command before pair\_style is defined*
+   Self-explanatory.
+
+*Particle on or inside fix wall surface*
+   Particles must be "exterior" to the wall in order for energy/force to
+   be calculated.
+
+*Particle outside surface of region used in fix wall/region*
+   Particles must be inside the region for energy/force to be calculated.
+   A particle outside the region generates an error.
+
+*Per-atom compute in equal-style variable formula*
+   Equal-style variables cannot use per-atom quantities.
+
+*Per-atom energy was not tallied on needed timestep*
+   You are using a thermo keyword that requires potentials to
+   have tallied energy, but they didn't on this timestep.  See the
+   variable doc page for ideas on how to make this work.
+
+*Per-atom fix in equal-style variable formula*
+   Equal-style variables cannot use per-atom quantities.
+
+*Per-atom virial was not tallied on needed timestep*
+   You are using a thermo keyword that requires potentials to have
+   tallied the virial, but they didn't on this timestep.  See the
+   variable doc page for ideas on how to make this work.
+
+*Per-processor system is too big*
+   The number of owned atoms plus ghost atoms on a single
+   processor must fit in 32-bit integer.
+
+*Potential energy ID for fix neb does not exist*
+   Self-explanatory.
+
+*Potential energy ID for fix nvt/nph/npt does not exist*
+   A compute for potential energy must be defined.
+
+*Potential file has duplicate entry*
+   The potential file has more than one entry for the same element.
+
+*Potential file is missing an entry*
+   The potential file does not have a needed entry.
+
+*Power by 0 in variable formula*
+   Self-explanatory.
+
+*Pressure ID for fix box/relax does not exist*
+   The compute ID needed to compute pressure for the fix does not
+   exist.
+
+*Pressure ID for fix modify does not exist*
+   Self-explanatory.
+
+*Pressure ID for fix npt/nph does not exist*
+   Self-explanatory.
+
+*Pressure ID for fix press/berendsen does not exist*
+   The compute ID needed to compute pressure for the fix does not
+   exist.
+
+*Pressure ID for fix rigid npt/nph does not exist*
+   Self-explanatory.
+
+*Pressure ID for thermo does not exist*
+   The compute ID needed to compute pressure for thermodynamics does not
+   exist.
+
+*Pressure control can not be used with fix nvt*
+   Self-explanatory.
+
+*Pressure control can not be used with fix nvt/asphere*
+   Self-explanatory.
+
+*Pressure control can not be used with fix nvt/body*
+   Self-explanatory.
+
+*Pressure control can not be used with fix nvt/sllod*
+   Self-explanatory.
+
+*Pressure control can not be used with fix nvt/sphere*
+   Self-explanatory.
+
+*Pressure control must be used with fix nph*
+   Self-explanatory.
+
+*Pressure control must be used with fix nph/asphere*
+   Self-explanatory.
+
+*Pressure control must be used with fix nph/body*
+   Self-explanatory.
+
+*Pressure control must be used with fix nph/small*
+   Self-explanatory.
+
+*Pressure control must be used with fix nph/sphere*
+   Self-explanatory.
+
+*Pressure control must be used with fix nphug*
+   A pressure control keyword (iso, aniso, tri, x, y, or z) must be
+   provided.
+
+*Pressure control must be used with fix npt*
+   Self-explanatory.
+
+*Pressure control must be used with fix npt/asphere*
+   Self-explanatory.
+
+*Pressure control must be used with fix npt/body*
+   Self-explanatory.
+
+*Pressure control must be used with fix npt/sphere*
+   Self-explanatory.
+
+*Processor count in z must be 1 for 2d simulation*
+   Self-explanatory.
+
+*Processor partitions do not match number of allocated processors*
+   The total number of processors in all partitions must match the number
+   of processors LAMMPS is running on.
+
+*Processors command after simulation box is defined*
+   The processors command cannot be used after a read\_data, read\_restart,
+   or create\_box command.
+
+*Processors custom grid file is inconsistent*
+   The vales in the custom file are not consistent with the number of
+   processors you are running on or the Px,Py,Pz settings of the
+   processors command.  Or there was not a setting for every processor.
+
+*Processors grid numa and map style are incompatible*
+   Using numa for gstyle in the processors command requires using
+   cart for the map option.
+
+*Processors part option and grid style are incompatible*
+   Cannot use gstyle numa or custom with the part option.
+
+*Processors twogrid requires proc count be a multiple of core count*
+   Self-explanatory.
+
+*Pstart and Pstop must have the same value*
+   Self-explanatory.
+
+*Python function evaluation failed*
+   The Python function did not run successfully and/or did not return a
+   value (if it is supposed to return a value).  This is probably due to
+   some error condition in the function.
+
+*Python function is not callable*
+   The provided Python code was run successfully, but it not
+   define a callable function with the required name.
+
+*Python invoke of undefined function*
+   Cannot invoke a function that has not been previously defined.
+
+*Python variable does not match Python function*
+   This matching is defined by the python-style variable and the python
+   command.
+
+*Python variable has no function*
+   No python command was used to define the function associated with the
+   python-style variable.
+
+*QEQ with 'newton pair off' not supported*
+   See the newton command.  This is a restriction to use the QEQ fixes.
+
+*R0 < 0 for fix spring command*
+   Equilibrium spring length is invalid.
+
+*RATTLE coordinate constraints are not satisfied up to desired tolerance*
+   Self-explanatory.
+
+*RATTLE determinant = 0.0*
+   The determinant of the matrix being solved for a single cluster
+   specified by the fix rattle command is numerically invalid.
+
+*RATTLE failed*
+   Certain constraints were not satisfied.
+
+*RATTLE velocity constraints are not satisfied up to desired tolerance*
+   Self-explanatory.
+
+*Read data add offset is too big*
+   It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit
+   integer.
+
+*Read dump of atom property that isn't allocated*
+   Self-explanatory.
+
+*Read rerun dump file timestep > specified stop*
+   Self-explanatory.
+
+*Read restart MPI-IO input not allowed with % in filename*
+   This is because a % signifies one file per processor and MPI-IO
+   creates one large file for all processors.
+
+*Read\_data shrink wrap did not assign all atoms correctly*
+   This is typically because the box-size specified in the data file is
+   large compared to the actual extent of atoms in a shrink-wrapped
+   dimension.  When LAMMPS shrink-wraps the box atoms will be lost if the
+   processor they are re-assigned to is too far away.  Choose a box
+   size closer to the actual extent of the atoms.
+
+*Read\_dump command before simulation box is defined*
+   The read\_dump command cannot be used before a read\_data, read\_restart,
+   or create\_box command.
+
+*Read\_dump field not found in dump file*
+   Self-explanatory.
+
+*Read\_dump triclinic status does not match simulation*
+   Both the dump snapshot and the current LAMMPS simulation must
+   be using either an orthogonal or triclinic box.
+
+*Read\_dump xyz fields do not have consistent scaling/wrapping*
+   Self-explanatory.
+
+*Reading from MPI-IO filename when MPIIO package is not installed*
+   Self-explanatory.
+
+*Reax\_defs.h setting for NATDEF is too small*
+   Edit the setting in the ReaxFF library and re-compile the
+   library and re-build LAMMPS.
+
+*Reax\_defs.h setting for NNEIGHMAXDEF is too small*
+   Edit the setting in the ReaxFF library and re-compile the
+   library and re-build LAMMPS.
+
+*Receiving partition in processors part command is already a receiver*
+   Cannot specify a partition to be a receiver twice.
+
+*Region ID for compute chunk/atom does not exist*
+   Self-explanatory.
+
+*Region ID for compute reduce/region does not exist*
+   Self-explanatory.
+
+*Region ID for compute temp/region does not exist*
+   Self-explanatory.
+
+*Region ID for dump custom does not exist*
+   Self-explanatory.
+
+*Region ID for fix addforce does not exist*
+   Self-explanatory.
+
+*Region ID for fix atom/swap does not exist*
+   Self-explanatory.
+
+*Region ID for fix ave/spatial does not exist*
+   Self-explanatory.
+
+*Region ID for fix aveforce does not exist*
+   Self-explanatory.
+
+*Region ID for fix deposit does not exist*
+   Self-explanatory.
+
+*Region ID for fix efield does not exist*
+   Self-explanatory.
+
+*Region ID for fix evaporate does not exist*
+   Self-explanatory.
+
+*Region ID for fix gcmc does not exist*
+   Self-explanatory.
+
+*Region ID for fix heat does not exist*
+   Self-explanatory.
+
+*Region ID for fix setforce does not exist*
+   Self-explanatory.
+
+*Region ID for fix wall/region does not exist*
+   Self-explanatory.
+
+*Region ID for group dynamic does not exist*
+   Self-explanatory.
+
+*Region ID in variable formula does not exist*
+   Self-explanatory.
+
+*Region cannot have 0 length rotation vector*
+   Self-explanatory.
+
+*Region for fix oneway does not exist*
+   Self-explanatory.
+
+*Region intersect region ID does not exist*
+   Self-explanatory.
+
+*Region union or intersect cannot be dynamic*
+   The sub-regions can be dynamic, but not the combined region.
+
+*Region union region ID does not exist*
+   One or more of the region IDs specified by the region union command
+   does not exist.
+
+*Replacing a fix, but new style != old style*
+   A fix ID can be used a 2nd time, but only if the style matches the
+   previous fix.  In this case it is assumed you with to reset a fix's
+   parameters.  This error may mean you are mistakenly re-using a fix ID
+   when you do not intend to.
+
+*Replicate command before simulation box is defined*
+   The replicate command cannot be used before a read\_data, read\_restart,
+   or create\_box command.
+
+*Replicate did not assign all atoms correctly*
+   Atoms replicated by the replicate command were not assigned correctly
+   to processors.  This is likely due to some atom coordinates being
+   outside a non-periodic simulation box.
+
+*Replicated system atom IDs are too big*
+   See the setting for tagint in the src/lmptype.h file.
+
+*Replicated system is too big*
+   See the setting for bigint in the src/lmptype.h file.
+
+*Required border comm not yet implemented with Kokkos*
+   There are various limitations in the communication options supported
+   by Kokkos.
+
+*Rerun command before simulation box is defined*
+   The rerun command cannot be used before a read\_data, read\_restart, or
+   create\_box command.
+
+*Rerun dump file does not contain requested snapshot*
+   Self-explanatory.
+
+*Resetting timestep size is not allowed with fix move*
+   This is because fix move is moving atoms based on elapsed time.
+
+*Respa inner cutoffs are invalid*
+   The first cutoff must be <= the second cutoff.
+
+*Respa levels must be >= 1*
+   Self-explanatory.
+
+*Respa middle cutoffs are invalid*
+   The first cutoff must be <= the second cutoff.
+
+*Restart file MPI-IO output not allowed with % in filename*
+   This is because a % signifies one file per processor and MPI-IO
+   creates one large file for all processors.
+
+*Restart file byte ordering is not recognized*
+   The file does not appear to be a LAMMPS restart file since it doesn't
+   contain a recognized byte-ordering flag at the beginning.
+
+*Restart file byte ordering is swapped*
+   The file was written on a machine with different byte-ordering than
+   the machine you are reading it on.  Convert it to a text data file
+   instead, on the machine you wrote it on.
+
+*Restart file incompatible with current version*
+   This is probably because you are trying to read a file created with a
+   version of LAMMPS that is too old compared to the current version.
+   Use your older version of LAMMPS and convert the restart file
+   to a data file.
+
+*Restart file is a MPI-IO file*
+   The file is inconsistent with the filename you specified for it.
+
+*Restart file is a multi-proc file*
+   The file is inconsistent with the filename you specified for it.
+
+*Restart file is not a MPI-IO file*
+   The file is inconsistent with the filename you specified for it.
+
+*Restart file is not a multi-proc file*
+   The file is inconsistent with the filename you specified for it.
+
+*Restart variable returned a bad timestep*
+   The variable must return a timestep greater than the current timestep.
+
+*Restrain atoms %d %d %d %d missing on proc %d at step %ld*
+   The 4 atoms in a restrain dihedral specified by the fix restrain
+   command are not all accessible to a processor.  This probably means an
+   atom has moved too far.
+
+*Restrain atoms %d %d %d missing on proc %d at step %ld*
+   The 3 atoms in a restrain angle specified by the fix restrain
+   command are not all accessible to a processor.  This probably means an
+   atom has moved too far.
+
+*Restrain atoms %d %d missing on proc %d at step %ld*
+   The 2 atoms in a restrain bond specified by the fix restrain
+   command are not all accessible to a processor.  This probably means an
+   atom has moved too far.
+
+*Reuse of compute ID*
+   A compute ID cannot be used twice.
+
+*Reuse of dump ID*
+   A dump ID cannot be used twice.
+
+*Reuse of molecule template ID*
+   The template IDs must be unique.
+
+*Reuse of region ID*
+   A region ID cannot be used twice.
+
+*Rigid body atoms %d %d missing on proc %d at step %ld*
+   This means that an atom cannot find the atom that owns the rigid body
+   it is part of, or vice versa.  The solution is to use the communicate
+   cutoff command to insure ghost atoms are acquired from far enough away
+   to encompass the max distance printed when the fix rigid/small command
+   was invoked.
+
+*Rigid body has degenerate moment of inertia*
+   Fix poems will only work with bodies (collections of atoms) that have
+   non-zero principal moments of inertia.  This means they must be 3 or
+   more non-collinear atoms, even with joint atoms removed.
+
+*Rigid fix must come before NPT/NPH fix*
+   NPT/NPH fix must be defined in input script after all rigid fixes,
+   else the rigid fix contribution to the pressure virial is
+   incorrect.
+
+*Rmask function in equal-style variable formula*
+   Rmask is per-atom operation.
+
+*Run command before simulation box is defined*
+   The run command cannot be used before a read\_data, read\_restart, or
+   create\_box command.
+
+*Run command start value is after start of run*
+   Self-explanatory.
+
+*Run command stop value is before end of run*
+   Self-explanatory.
+
+*Run\_style command before simulation box is defined*
+   The run\_style command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*SRD bin size for fix srd differs from user request*
+   Fix SRD had to adjust the bin size to fit the simulation box.  See the
+   cubic keyword if you want this message to be an error vs warning.
+
+*SRD bins for fix srd are not cubic enough*
+   The bin shape is not within tolerance of cubic.  See the cubic
+   keyword if you want this message to be an error vs warning.
+
+*SRD particle %d started inside big particle %d on step %ld bounce %d*
+   See the inside keyword if you want this message to be an error vs
+   warning.
+
+*SRD particle %d started inside wall %d on step %ld bounce %d*
+   See the inside keyword if you want this message to be an error vs
+   warning.
+
+*Same dimension twice in fix ave/spatial*
+   Self-explanatory.
+
+*Sending partition in processors part command is already a sender*
+   Cannot specify a partition to be a sender twice.
+
+*Set command before simulation box is defined*
+   The set command cannot be used before a read\_data, read\_restart,
+   or create\_box command.
+
+*Set command floating point vector does not exist*
+   Self-explanatory.
+
+*Set command integer vector does not exist*
+   Self-explanatory.
+
+*Set command with no atoms existing*
+   No atoms are yet defined so the set command cannot be used.
+
+*Set region ID does not exist*
+   Region ID specified in set command does not exist.
+
+*Shake angles have different bond types*
+   All 3-atom angle-constrained SHAKE clusters specified by the fix shake
+   command that are the same angle type, must also have the same bond
+   types for the 2 bonds in the angle.
+
+*Shake atoms %d %d %d %d missing on proc %d at step %ld*
+   The 4 atoms in a single shake cluster specified by the fix shake
+   command are not all accessible to a processor.  This probably means
+   an atom has moved too far.
+
+*Shake atoms %d %d %d missing on proc %d at step %ld*
+   The 3 atoms in a single shake cluster specified by the fix shake
+   command are not all accessible to a processor.  This probably means
+   an atom has moved too far.
+
+*Shake atoms %d %d missing on proc %d at step %ld*
+   The 2 atoms in a single shake cluster specified by the fix shake
+   command are not all accessible to a processor.  This probably means
+   an atom has moved too far.
+
+*Shake cluster of more than 4 atoms*
+   A single cluster specified by the fix shake command can have no more
+   than 4 atoms.
+
+*Shake clusters are connected*
+   A single cluster specified by the fix shake command must have a single
+   central atom with up to 3 other atoms bonded to it.
+
+*Shake determinant = 0.0*
+   The determinant of the matrix being solved for a single cluster
+   specified by the fix shake command is numerically invalid.
+
+*Shake fix must come before NPT/NPH fix*
+   NPT fix must be defined in input script after SHAKE fix, else the
+   SHAKE fix contribution to the pressure virial is incorrect.
+
+*Shear history overflow, boost neigh\_modify one*
+   There are too many neighbors of a single atom.  Use the neigh\_modify
+   command to increase the max number of neighbors allowed for one atom.
+   You may also want to boost the page size.
+
+*Small to big integers are not sized correctly*
+   This error occurs when the sizes of smallint, imageint, tagint, bigint,
+   as defined in src/lmptype.h are not what is expected.  Contact
+   the developers if this occurs.
+
+*Smallint setting in lmptype.h is invalid*
+   It has to be the size of an integer.
+
+*Smallint setting in lmptype.h is not compatible*
+   Smallint stored in restart file is not consistent with LAMMPS version
+   you are running.
+
+*Special list size exceeded in fix bond/create*
+   See the "read\_data extra/special/per/atom" command
+   (or the "create\_box extra/special/per/atom" command)
+   for info on how to leave space in the special bonds
+   list to allow for additional bonds to be formed.
+
+*Species XXX is not supported by this KIM Simulator Model*
+   The kim\_style define command was referencing a species that is not
+   present in the requested KIM Simulator Model.
+
+*Specified processors != physical processors*
+   The 3d grid of processors defined by the processors command does not
+   match the number of processors LAMMPS is being run on.
+
+*Specified target stress must be uniaxial or hydrostatic*
+   Self-explanatory.
+
+*Sqrt of negative value in variable formula*
+   Self-explanatory.
+
+*Subsequent read data induced too many angles per atom*
+   See the extra/angle/per/atom keyword for the create\_box
+   or the read\_data command to set this limit larger
+
+*Subsequent read data induced too many bonds per atom*
+   See the extra/bond/per/atom keyword for the create\_box
+   or the read\_data command to set this limit larger
+
+*Subsequent read data induced too many dihedrals per atom*
+   See the extra/dihedral/per/atom keyword for the create\_box
+   or the read\_data command to set this limit larger
+
+*Subsequent read data induced too many impropers per atom*
+   See the extra/improper/per/atom keyword for the create\_box
+   or the read\_data command to set this limit larger
+
+*Substitution for illegal variable*
+   Input script line contained a variable that could not be substituted
+   for.
+
+*Support for writing images in JPEG format not included*
+   LAMMPS was not built with the -DLAMMPS\_JPEG switch in the Makefile.
+
+*Support for writing images in PNG format not included*
+   LAMMPS was not built with the -DLAMMPS\_PNG switch in the Makefile.
+
+*Support for writing movies not included*
+   LAMMPS was not built with the -DLAMMPS\_FFMPEG switch in the Makefile
+
+*System in data file is too big*
+   See the setting for bigint in the src/lmptype.h file.
+
+*System is not charge neutral, net charge = %g*
+   The total charge on all atoms on the system is not 0.0.
+   For some KSpace solvers this is an error.
+
+*TAD nsteps must be multiple of t\_event*
+   Self-explanatory.
+
+*TIP4P hydrogen has incorrect atom type*
+   The TIP4P pairwise computation found an H atom whose type does not
+   agree with the specified H type.
+
+*TIP4P hydrogen is missing*
+   The TIP4P pairwise computation failed to find the correct H atom
+   within a water molecule.
+
+*TMD target file did not list all group atoms*
+   The target file for the fix tmd command did not list all atoms in the
+   fix group.
+
+*Tad command before simulation box is defined*
+   Self-explanatory.
+
+*Tagint setting in lmptype.h is invalid*
+   Tagint must be as large or larger than smallint.
+
+*Tagint setting in lmptype.h is not compatible*
+   Format of tagint stored in restart file is not consistent with LAMMPS
+   version you are running.  See the settings in src/lmptype.h
+
+*Target pressure for fix rigid/nph cannot be < 0.0*
+   Self-explanatory.
+
+*Target pressure for fix rigid/npt/small cannot be < 0.0*
+   Self-explanatory.
+
+*Target temperature for fix nvt/npt/nph cannot be 0.0*
+   Self-explanatory.
+
+*Target temperature for fix rigid/npt cannot be 0.0*
+   Self-explanatory.
+
+*Target temperature for fix rigid/npt/small cannot be 0.0*
+   Self-explanatory.
+
+*Target temperature for fix rigid/nvt cannot be 0.0*
+   Self-explanatory.
+
+*Target temperature for fix rigid/nvt/small cannot be 0.0*
+   Self-explanatory.
+
+*Temper command before simulation box is defined*
+   The temper command cannot be used before a read\_data, read\_restart, or
+   create\_box command.
+
+*Temperature ID for fix bond/swap does not exist*
+   Self-explanatory.
+
+*Temperature ID for fix box/relax does not exist*
+   Self-explanatory.
+
+*Temperature ID for fix nvt/npt does not exist*
+   Self-explanatory.
+
+*Temperature ID for fix press/berendsen does not exist*
+   Self-explanatory.
+
+*Temperature ID for fix rigid nvt/npt/nph does not exist*
+   Self-explanatory.
+
+*Temperature ID for fix temp/berendsen does not exist*
+   Self-explanatory.
+
+*Temperature ID for fix temp/csld does not exist*
+   Self-explanatory.
+
+*Temperature ID for fix temp/csvr does not exist*
+   Self-explanatory.
+
+*Temperature ID for fix temp/rescale does not exist*
+   Self-explanatory.
+
+*Temperature compute degrees of freedom < 0*
+   This should not happen if you are calculating the temperature
+   on a valid set of atoms.
+
+*Temperature control can not be used with fix nph*
+   Self-explanatory.
+
+*Temperature control can not be used with fix nph/asphere*
+   Self-explanatory.
+
+*Temperature control can not be used with fix nph/body*
+   Self-explanatory.
+
+*Temperature control can not be used with fix nph/sphere*
+   Self-explanatory.
+
+*Temperature control must be used with fix nphug*
+   The temp keyword must be provided.
+
+*Temperature control must be used with fix npt*
+   Self-explanatory.
+
+*Temperature control must be used with fix npt/asphere*
+   Self-explanatory.
+
+*Temperature control must be used with fix npt/body*
+   Self-explanatory.
+
+*Temperature control must be used with fix npt/sphere*
+   Self-explanatory.
+
+*Temperature control must be used with fix nvt*
+   Self-explanatory.
+
+*Temperature control must be used with fix nvt/asphere*
+   Self-explanatory.
+
+*Temperature control must be used with fix nvt/body*
+   Self-explanatory.
+
+*Temperature control must be used with fix nvt/sllod*
+   Self-explanatory.
+
+*Temperature control must be used with fix nvt/sphere*
+   Self-explanatory.
+
+*Temperature control must not be used with fix nph/small*
+   Self-explanatory.
+
+*Temperature for fix nvt/sllod does not have a bias*
+   The specified compute must compute temperature with a bias.
+
+*Tempering could not find thermo\_pe compute*
+   This compute is created by the thermo command.  It must have been
+   explicitly deleted by a uncompute command.
+
+*Tempering fix ID is not defined*
+   The fix ID specified by the temper command does not exist.
+
+*Tempering temperature fix is not valid*
+   The fix specified by the temper command is not one that controls
+   temperature (nvt or langevin).
+
+*Test\_descriptor\_string already allocated*
+   This is an internal error.  Contact the developers.
+
+*The package gpu command is required for gpu styles*
+   Self-explanatory.
+
+*Thermo and fix not computed at compatible times*
+   Fixes generate values on specific timesteps.  The thermo output
+   does not match these timesteps.
+
+*Thermo compute array is accessed out-of-range*
+   Self-explanatory.
+
+*Thermo compute does not compute array*
+   Self-explanatory.
+
+*Thermo compute does not compute scalar*
+   Self-explanatory.
+
+*Thermo compute does not compute vector*
+   Self-explanatory.
+
+*Thermo compute vector is accessed out-of-range*
+   Self-explanatory.
+
+*Thermo custom variable cannot be indexed*
+   Self-explanatory.
+
+*Thermo custom variable is not equal-style variable*
+   Only equal-style variables can be output with thermodynamics, not
+   atom-style variables.
+
+*Thermo every variable returned a bad timestep*
+   The variable must return a timestep greater than the current timestep.
+
+*Thermo fix array is accessed out-of-range*
+   Self-explanatory.
+
+*Thermo fix does not compute array*
+   Self-explanatory.
+
+*Thermo fix does not compute scalar*
+   Self-explanatory.
+
+*Thermo fix does not compute vector*
+   Self-explanatory.
+
+*Thermo fix vector is accessed out-of-range*
+   Self-explanatory.
+
+*Thermo keyword in variable requires thermo to use/init pe*
+   You are using a thermo keyword in a variable that requires
+   potential energy to be calculated, but your thermo output
+   does not use it.  Add it to your thermo output.
+
+*Thermo keyword in variable requires thermo to use/init press*
+   You are using a thermo keyword in a variable that requires pressure to
+   be calculated, but your thermo output does not use it.  Add it to your
+   thermo output.
+
+*Thermo keyword in variable requires thermo to use/init temp*
+   You are using a thermo keyword in a variable that requires temperature
+   to be calculated, but your thermo output does not use it.  Add it to
+   your thermo output.
+
+*Thermo style does not use press*
+   Cannot use thermo\_modify to set this parameter since the thermo\_style
+   is not computing this quantity.
+
+*Thermo style does not use temp*
+   Cannot use thermo\_modify to set this parameter since the thermo\_style
+   is not computing this quantity.
+
+*Thermo\_modify every variable returned a bad timestep*
+   The returned timestep is less than or equal to the current timestep.
+
+*Thermo\_modify int format does not contain d character*
+   Self-explanatory.
+
+*Thermo\_modify pressure ID does not compute pressure*
+   The specified compute ID does not compute pressure.
+
+*Thermo\_modify temperature ID does not compute temperature*
+   The specified compute ID does not compute temperature.
+
+*Thermo\_style command before simulation box is defined*
+   The thermo\_style command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*This variable thermo keyword cannot be used between runs*
+   Keywords that refer to time (such as cpu, elapsed) do not
+   make sense in between runs.
+
+*Threshhold for an atom property that isn't allocated*
+   A dump threshold has been requested on a quantity that is
+   not defined by the atom style used in this simulation.
+
+*Timestep must be >= 0*
+   Specified timestep is invalid.
+
+*Too big a problem to use velocity create loop all*
+   The system size must fit in a 32-bit integer to use this option.
+
+*Too big a timestep for dump dcd*
+   The timestep must fit in a 32-bit integer to use this dump style.
+
+*Too big a timestep for dump xtc*
+   The timestep must fit in a 32-bit integer to use this dump style.
+
+*Too few bits for lookup table*
+   Table size specified via pair\_modify command does not work with your
+   machine's floating point representation.
+
+*Too few lines in %s section of data file*
+   Self-explanatory.
+
+*Too few values in body lines in data file*
+   Self-explanatory.
+
+*Too few values in body section of molecule file*
+   Self-explanatory.
+
+*Too many -pk arguments in command line*
+   The string formed by concatenating the arguments is too long.  Use a
+   package command in the input script instead.
+
+*Too many MSM grid levels*
+   The max number of MSM grid levels is hardwired to 10.
+
+*Too many args in variable function*
+   More args are used than any variable function allows.
+
+*Too many atom pairs for pair bop*
+   The number of atomic pairs exceeds the expected number.  Check your
+   atomic structure to ensure that it is realistic.
+
+*Too many atom sorting bins*
+   This is likely due to an immense simulation box that has blown up
+   to a large size.
+
+*Too many atom triplets for pair bop*
+   The number of three atom groups for angle determinations exceeds the
+   expected number.  Check your atomic structure to ensure that it is
+   realistic.
+
+*Too many atoms for dump dcd*
+   The system size must fit in a 32-bit integer to use this dump
+   style.
+
+*Too many atoms for dump xtc*
+   The system size must fit in a 32-bit integer to use this dump
+   style.
+
+*Too many atoms to dump sort*
+   Cannot sort when running with more than 2\^31 atoms.
+
+*Too many exponent bits for lookup table*
+   Table size specified via pair\_modify command does not work with your
+   machine's floating point representation.
+
+*Too many groups*
+   The maximum number of atom groups (including the "all" group) is
+   given by MAX\_GROUP in group.cpp and is 32.
+
+*Too many iterations*
+   You must use a number of iterations that fit in a 32-bit integer
+   for minimization.
+
+*Too many lines in one body in data file - boost MAXBODY*
+   MAXBODY is a setting at the top of the src/read\_data.cpp file.
+   Set it larger and re-compile the code.
+
+*Too many local+ghost atoms for neighbor list*
+   The number of nlocal + nghost atoms on a processor
+   is limited by the size of a 32-bit integer with 2 bits
+   removed for masking 1-2, 1-3, 1-4 neighbors.
+
+*Too many mantissa bits for lookup table*
+   Table size specified via pair\_modify command does not work with your
+   machine's floating point representation.
+
+*Too many masses for fix shake*
+   The fix shake command cannot list more masses than there are atom
+   types.
+
+*Too many molecules for fix poems*
+   The limit is 2\^31 = ~2 billion molecules.
+
+*Too many molecules for fix rigid*
+   The limit is 2\^31 = ~2 billion molecules.
+
+*Too many neighbor bins*
+   This is likely due to an immense simulation box that has blown up
+   to a large size.
+
+*Too many timesteps*
+   The cumulative timesteps must fit in a 64-bit integer.
+
+*Too many timesteps for NEB*
+   You must use a number of timesteps that fit in a 32-bit integer
+   for NEB.
+
+*Too many total atoms*
+   See the setting for bigint in the src/lmptype.h file.
+
+*Too many total bits for bitmapped lookup table*
+   Table size specified via pair\_modify command is too large.  Note that
+   a value of N generates a 2\^N size table.
+
+*Too many values in body lines in data file*
+   Self-explanatory.
+
+*Too many values in body section of molecule file*
+   Self-explanatory.
+
+*Too much buffered per-proc info for dump*
+   The size of the buffered string must fit in a 32-bit integer for a
+   dump.
+
+*Too much per-proc info for dump*
+   Number of local atoms times number of columns must fit in a 32-bit
+   integer for dump.
+
+*Tree structure in joint connections*
+   Fix poems cannot (yet) work with coupled bodies whose joints connect
+   the bodies in a tree structure.
+
+*Triclinic box skew is too large*
+   The displacement in a skewed direction must be less than half the box
+   length in that dimension.  E.g. the xy tilt must be between -half and
+   +half of the x box length.  This constraint can be relaxed by using
+   the box tilt command.
+
+*Tried to convert a double to int, but input\_double > INT\_MAX*
+   Self-explanatory.
+
+*Trying to build an occasional neighbor list before initialization completed*
+   This is not allowed.  Source code caller needs to be modified.
+
+*Two fix ave commands using same compute chunk/atom command in incompatible ways*
+   They are both attempting to "lock" the chunk/atom command so that the
+   chunk assignments persist for some number of timesteps, but are doing
+   it in different ways.
+
+*Two groups cannot be the same in fix spring couple*
+   Self-explanatory.
+
+*Unable to initialize accelerator for use*
+   There was a problem initializing an accelerator for the gpu package
+
+*Unbalanced quotes in input line*
+   No matching end double quote was found following a leading double
+   quote.
+
+*Unexpected end of -reorder file*
+   Self-explanatory.
+
+*Unexpected empty line in AngleCoeffs section*
+   Read a blank line where there should be coefficient data.
+
+*Unexpected empty line in BondCoeffs section*
+   Read a blank line where there should be coefficient data.
+
+*Unexpected empty line in DihedralCoeffs section*
+   Read a blank line where there should be coefficient data.
+
+*Unexpected empty line in ImproperCoeffs section*
+   Read a blank line where there should be coefficient data.
+
+*Unexpected empty line in PairCoeffs section*
+   Read a blank line where there should be coefficient data.
+
+*Unexpected end of custom file*
+   Self-explanatory.
+
+*Unexpected end of data file*
+   LAMMPS hit the end of the data file while attempting to read a
+   section.  Something is wrong with the format of the data file.
+
+*Unexpected end of dump file*
+   A read operation from the file failed.
+
+*Unexpected end of fix rigid file*
+   A read operation from the file failed.
+
+*Unexpected end of fix rigid/small file*
+   A read operation from the file failed.
+
+*Unexpected end of molecule file*
+   Self-explanatory.
+
+*Unexpected end of neb file*
+   A read operation from the file failed.
+
+*Units command after simulation box is defined*
+   The units command cannot be used after a read\_data, read\_restart, or
+   create\_box command.
+
+*Universe/uloop variable count < # of partitions*
+   A universe or uloop style variable must specify a number of values >= to the
+   number of processor partitions.
+
+*Unrecognized angle style*
+   The choice of angle style is unknown.
+
+*Unrecognized atom style*
+   The choice of atom style is unknown.
+
+*Unrecognized body style*
+   The choice of body style is unknown.
+
+*Unrecognized bond style*
+   The choice of bond style is unknown.
+
+*Unknown category for info is\_active()*
+   Self-explanatory.
+
+*Unknown category for info is\_available()*
+   Self-explanatory.
+
+*Unknown category for info is\_defined()*
+   Self-explanatory.
+
+*Unrecognized command: %s*
+   The command is not known to LAMMPS.  Check the input script.
+
+*Unrecognized compute style*
+   The choice of compute style is unknown.
+
+*Unrecognized dihedral style*
+   The choice of dihedral style is unknown.
+
+*Unrecognized dump reader style*
+   The choice of dump reader style via the format keyword is unknown.
+
+*Unrecognized dump style*
+   The choice of dump style is unknown.
+
+*Unknown error in GPU library*
+   Self-explanatory.
+
+*Unrecognized fix style*
+   The choice of fix style is unknown.
+
+*Unknown identifier in data file: %s*
+   A section of the data file cannot be read by LAMMPS.
+
+*Unrecognized improper style*
+   The choice of improper style is unknown.
+
+*Unknown keyword in thermo\_style custom command*
+   One or more specified keywords are not recognized.
+
+*Unrecognized kspace style*
+   The choice of kspace style is unknown.
+
+*Unknown name for info newton category*
+   Self-explanatory.
+
+*Unknown name for info package category*
+   Self-explanatory.
+
+*Unknown name for info pair category*
+   Self-explanatory.
+
+*Unrecognized pair style*
+   The choice of pair style is unknown.
+
+*Unknown pair\_modify hybrid sub-style*
+   The choice of sub-style is unknown.
+
+*Unrecognized region style*
+   The choice of region style is unknown.
+
+*Unknown section in molecule file*
+   Self-explanatory.
+
+*Unknown table style in angle style table*
+   Self-explanatory.
+
+*Unknown table style in bond style table*
+   Self-explanatory.
+
+*Unknown table style in pair\_style command*
+   Style of table is invalid for use with pair\_style table command.
+
+*Unknown unit\_style*
+   Self-explanatory. Check the input script or data file.
+
+*Unrecognized lattice type in MEAM file 1*
+   The lattice type in an entry of the MEAM library file is not
+   valid.
+
+*Unrecognized lattice type in MEAM file 2*
+   The lattice type in an entry of the MEAM parameter file is not
+   valid.
+
+*Unrecognized pair style in compute pair command*
+   Self-explanatory.
+
+*Unsupported mixing rule in kspace\_style ewald/disp*
+   Only geometric mixing is supported.
+
+*Unsupported order in kspace\_style ewald/disp*
+   Only 1/r\^6 dispersion or dipole terms are supported.
+
+*Unsupported order in kspace\_style pppm/disp, pair\_style %s*
+   Only pair styles with 1/r and 1/r\^6 dependence are currently supported.
+
+*Use cutoff keyword to set cutoff in single mode*
+   Mode is single so cutoff/multi keyword cannot be used.
+
+*Use cutoff/multi keyword to set cutoff in multi mode*
+   Mode is multi so cutoff keyword cannot be used.
+
+*Using fix nvt/sllod with inconsistent fix deform remap option*
+   Fix nvt/sllod requires that deforming atoms have a velocity profile
+   provided by "remap v" as a fix deform option.
+
+*Using fix nvt/sllod with no fix deform defined*
+   Self-explanatory.
+
+*Using fix srd with inconsistent fix deform remap option*
+   When shearing the box in an SRD simulation, the remap v option for fix
+   deform needs to be used.
+
+*Using pair lubricate with inconsistent fix deform remap option*
+   Must use remap v option with fix deform with this pair style.
+
+*Using pair lubricate/poly with inconsistent fix deform remap option*
+   If fix deform is used, the remap v option is required.
+
+*Using suffix gpu without GPU package installed*
+   Self-explanatory.
+
+*Using suffix intel without USER-INTEL package installed*
+   Self-explanatory.
+
+*Using suffix kk without KOKKOS package enabled*
+   Self-explanatory.
+
+*Using suffix omp without USER-OMP package installed*
+   Self-explanatory.
+
+*Using update dipole flag requires atom attribute mu*
+   Self-explanatory.
+
+*Using update dipole flag requires atom style sphere*
+   Self-explanatory.
+
+*Variable ID in variable formula does not exist*
+   Self-explanatory.
+
+*Variable atom ID is too large*
+   Specified ID is larger than the maximum allowed atom ID.
+
+*Variable evaluation before simulation box is defined*
+   Cannot evaluate a compute or fix or atom-based value in a variable
+   before the simulation has been setup.
+
+*Variable evaluation in fix wall gave bad value*
+   The returned value for epsilon or sigma < 0.0.
+
+*Variable evaluation in region gave bad value*
+   Variable returned a radius < 0.0.
+
+*Variable for compute ti is invalid style*
+   Self-explanatory.
+
+*Variable for create\_atoms is invalid style*
+   The variables must be equal-style variables.
+
+*Variable for displace\_atoms is invalid style*
+   It must be an equal-style or atom-style variable.
+
+*Variable for dump every is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for dump image center is invalid style*
+   Must be an equal-style variable.
+
+*Variable for dump image persp is invalid style*
+   Must be an equal-style variable.
+
+*Variable for dump image phi is invalid style*
+   Must be an equal-style variable.
+
+*Variable for dump image theta is invalid style*
+   Must be an equal-style variable.
+
+*Variable for dump image zoom is invalid style*
+   Must be an equal-style variable.
+
+*Variable for fix adapt is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix addforce is invalid style*
+   Self-explanatory.
+
+*Variable for fix aveforce is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix deform is invalid style*
+   The variable must be an equal-style variable.
+
+*Variable for fix efield is invalid style*
+   The variable must be an equal- or atom-style variable.
+
+*Variable for fix gravity is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix heat is invalid style*
+   Only equal-style or atom-style variables can be used.
+
+*Variable for fix indent is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix indent is not equal style*
+   Only equal-style variables can be used.
+
+*Variable for fix langevin is invalid style*
+   It must be an equal-style variable.
+
+*Variable for fix move is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix setforce is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix temp/berendsen is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix temp/csld is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix temp/csvr is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix temp/rescale is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix wall is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix wall/reflect is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for fix wall/srd is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for group dynamic is invalid style*
+   The variable must be an atom-style variable.
+
+*Variable for group is invalid style*
+   Only atom-style variables can be used.
+
+*Variable for region cylinder is invalid style*
+   Only equal-style variables are allowed.
+
+*Variable for region is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for region is not equal style*
+   Self-explanatory.
+
+*Variable for region sphere is invalid style*
+   Only equal-style variables are allowed.
+
+*Variable for restart is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for set command is invalid style*
+   Only atom-style variables can be used.
+
+*Variable for thermo every is invalid style*
+   Only equal-style variables can be used.
+
+*Variable for velocity set is invalid style*
+   Only atom-style variables can be used.
+
+*Variable for voronoi radius is not atom style*
+   Self-explanatory.
+
+*Variable formula compute array is accessed out-of-range*
+   Self-explanatory.
+
+*Variable formula compute vector is accessed out-of-range*
+   Self-explanatory.
+
+*Variable formula fix array is accessed out-of-range*
+   Self-explanatory.
+
+*Variable formula fix vector is accessed out-of-range*
+   Self-explanatory.
+
+*Variable has circular dependency*
+   A circular dependency is when variable "a" in used by variable "b" and
+   variable "b" is also used by variable "a".  Circular dependencies with
+   longer chains of dependence are also not allowed.
+
+*Variable name between brackets must be alphanumeric or underscore characters*
+   Self-explanatory.
+
+*Variable name for compute chunk/atom does not exist*
+   Self-explanatory.
+
+*Variable name for compute reduce does not exist*
+   Self-explanatory.
+
+*Variable name for compute ti does not exist*
+   Self-explanatory.
+
+*Variable name for create\_atoms does not exist*
+   Self-explanatory.
+
+*Variable name for displace\_atoms does not exist*
+   Self-explanatory.
+
+*Variable name for dump every does not exist*
+   Self-explanatory.
+
+*Variable name for dump image center does not exist*
+   Self-explanatory.
+
+*Variable name for dump image persp does not exist*
+   Self-explanatory.
+
+*Variable name for dump image phi does not exist*
+   Self-explanatory.
+
+*Variable name for dump image theta does not exist*
+   Self-explanatory.
+
+*Variable name for dump image zoom does not exist*
+   Self-explanatory.
+
+*Variable name for fix adapt does not exist*
+   Self-explanatory.
+
+*Variable name for fix addforce does not exist*
+   Self-explanatory.
+
+*Variable name for fix ave/atom does not exist*
+   Self-explanatory.
+
+*Variable name for fix ave/chunk does not exist*
+   Self-explanatory.
+
+*Variable name for fix ave/correlate does not exist*
+   Self-explanatory.
+
+*Variable name for fix ave/histo does not exist*
+   Self-explanatory.
+
+*Variable name for fix ave/spatial does not exist*
+   Self-explanatory.
+
+*Variable name for fix ave/time does not exist*
+   Self-explanatory.
+
+*Variable name for fix aveforce does not exist*
+   Self-explanatory.
+
+*Variable name for fix deform does not exist*
+   Self-explanatory.
+
+*Variable name for fix efield does not exist*
+   Self-explanatory.
+
+*Variable name for fix gravity does not exist*
+   Self-explanatory.
+
+*Variable name for fix heat does not exist*
+   Self-explanatory.
+
+*Variable name for fix indent does not exist*
+   Self-explanatory.
+
+*Variable name for fix langevin does not exist*
+   Self-explanatory.
+
+*Variable name for fix move does not exist*
+   Self-explanatory.
+
+*Variable name for fix setforce does not exist*
+   Self-explanatory.
+
+*Variable name for fix store/state does not exist*
+   Self-explanatory.
+
+*Variable name for fix temp/berendsen does not exist*
+   Self-explanatory.
+
+*Variable name for fix temp/csld does not exist*
+   Self-explanatory.
+
+*Variable name for fix temp/csvr does not exist*
+   Self-explanatory.
+
+*Variable name for fix temp/rescale does not exist*
+   Self-explanatory.
+
+*Variable name for fix vector does not exist*
+   Self-explanatory.
+
+*Variable name for fix wall does not exist*
+   Self-explanatory.
+
+*Variable name for fix wall/reflect does not exist*
+   Self-explanatory.
+
+*Variable name for fix wall/srd does not exist*
+   Self-explanatory.
+
+*Variable name for group does not exist*
+   Self-explanatory.
+
+*Variable name for group dynamic does not exist*
+   Self-explanatory.
+
+*Variable name for region cylinder does not exist*
+   Self-explanatory.
+
+*Variable name for region does not exist*
+   Self-explanatory.
+
+*Variable name for region sphere does not exist*
+   Self-explanatory.
+
+*Variable name for restart does not exist*
+   Self-explanatory.
+
+*Variable name for set command does not exist*
+   Self-explanatory.
+
+*Variable name for thermo every does not exist*
+   Self-explanatory.
+
+*Variable name for velocity set does not exist*
+   Self-explanatory.
+
+*Variable name for voronoi radius does not exist*
+   Self-explanatory.
+
+*Variable name must be alphanumeric or underscore characters*
+   Self-explanatory.
+
+*Variable uses atom property that isn't allocated*
+   Self-explanatory.
+
+*Velocity command before simulation box is defined*
+   The velocity command cannot be used before a read\_data, read\_restart,
+   or create\_box command.
+
+*Velocity command with no atoms existing*
+   A velocity command has been used, but no atoms yet exist.
+
+*Velocity ramp in z for a 2d problem*
+   Self-explanatory.
+
+*Velocity rigid used with non-rigid fix-ID*
+   Self-explanatory.
+
+*Velocity temperature ID does calculate a velocity bias*
+   The specified compute must compute a bias for temperature.
+
+*Velocity temperature ID does not compute temperature*
+   The compute ID given to the velocity command must compute
+   temperature.
+
+*Verlet/split can only currently be used with comm\_style brick*
+   This is a current restriction in LAMMPS.
+
+*Verlet/split does not yet support TIP4P*
+   This is a current limitation.
+
+*Verlet/split requires 2 partitions*
+   See the -partition command-line switch.
+
+*Verlet/split requires Rspace partition layout be multiple of Kspace partition layout in each dim*
+   This is controlled by the processors command.
+
+*Verlet/split requires Rspace partition size be multiple of Kspace partition size*
+   This is so there is an equal number of Rspace processors for every
+   Kspace processor.
+
+*Virial was not tallied on needed timestep*
+   You are using a thermo keyword that requires potentials to
+   have tallied the virial, but they didn't on this timestep.  See the
+   variable doc page for ideas on how to make this work.
+
+*Voro++ error: narea and neigh have a different size*
+   This error is returned by the Voro++ library.
+
+*Wall defined twice in fix wall command*
+   Self-explanatory.
+
+*Wall defined twice in fix wall/reflect command*
+   Self-explanatory.
+
+*Wall defined twice in fix wall/srd command*
+   Self-explanatory.
+
+*Water H epsilon must be 0.0 for pair style lj/cut/tip4p/cut*
+   This is because LAMMPS does not compute the Lennard-Jones interactions
+   with these particles for efficiency reasons.
+
+*Water H epsilon must be 0.0 for pair style lj/cut/tip4p/long*
+   This is because LAMMPS does not compute the Lennard-Jones interactions
+   with these particles for efficiency reasons.
+
+*Water H epsilon must be 0.0 for pair style lj/long/tip4p/long*
+   This is because LAMMPS does not compute the Lennard-Jones interactions
+   with these particles for efficiency reasons.
+
+*World variable count doesn't match # of partitions*
+   A world-style variable must specify a number of values equal to the
+   number of processor partitions.
+
+*Write\_data command before simulation box is defined*
+   Self-explanatory.
+
+*Write\_restart command before simulation box is defined*
+   The write\_restart command cannot be used before a read\_data,
+   read\_restart, or create\_box command.
+
+*Writing to MPI-IO filename when MPIIO package is not installed*
+   Self-explanatory.
+
+*Zero length rotation vector with displace\_atoms*
+   Self-explanatory.
+
+*Zero length rotation vector with fix move*
+   Self-explanatory.
+
+*Zero-length lattice orient vector*
+   Self-explanatory.
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst
new file mode 100644
index 0000000000..4a944eeb18
--- /dev/null
+++ b/doc/src/Errors_warnings.rst
@@ -0,0 +1,802 @@
+Warning messages
+================
+
+This is an alphabetic list of the WARNING messages LAMMPS prints out
+and the reason why.  If the explanation here is not sufficient, the
+documentation for the offending command may help.  Warning messages
+also list the source file and line number where the warning was
+generated.  For example, a message like this:
+
+
+.. parsed-literal::
+
+   WARNING: Bond atom missing in box size check (domain.cpp:187)
+
+means that line #187 in the file src/domain.cpp generated the error.
+Looking in the source code may help you figure out what went wrong.
+
+Note that warning messages from :doc:`user-contributed packages <Packages_user>` are not listed here.  If such a warning
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
+
+Doc page with :doc:`ERROR messages <Errors_messages>`
+
+
+----------
+
+
+
+
+*Adjusting Coulombic cutoff for MSM, new cutoff = %g*
+   The adjust/cutoff command is turned on and the Coulombic cutoff has been
+   adjusted to match the user-specified accuracy.
+
+*Angle atoms missing at step %ld*
+   One or more of 3 atoms needed to compute a particular angle are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the angle has blown apart and an atom is
+   too far away.
+
+*Angle style in data file differs from currently defined angle style*
+   Self-explanatory.
+
+*Angles are defined but no angle style is set*
+   The topology contains angles, but there are no angle forces computed
+   since there was no angle\_style command.
+
+*Atom style in data file differs from currently defined atom style*
+   Self-explanatory.
+
+*Bond atom missing in box size check*
+   The 2nd atoms needed to compute a particular bond is missing on this
+   processor.  Typically this is because the pairwise cutoff is set too
+   short or the bond has blown apart and an atom is too far away.
+
+*Bond atom missing in image check*
+   The 2nd atom in a particular bond is missing on this processor.
+   Typically this is because the pairwise cutoff is set too short or the
+   bond has blown apart and an atom is too far away.
+
+*Bond atoms missing at step %ld*
+   The 2nd atom needed to compute a particular bond is missing on this
+   processor.  Typically this is because the pairwise cutoff is set too
+   short or the bond has blown apart and an atom is too far away.
+
+*Bond style in data file differs from currently defined bond style*
+   Self-explanatory.
+
+*Bonds are defined but no bond style is set*
+   The topology contains bonds, but there are no bond forces computed
+   since there was no bond\_style command.
+
+*Bond/angle/dihedral extent > half of periodic box length*
+   This is a restriction because LAMMPS can be confused about which image
+   of an atom in the bonded interaction is the correct one to use.
+   "Extent" in this context means the maximum end-to-end length of the
+   bond/angle/dihedral.  LAMMPS computes this by taking the maximum bond
+   length, multiplying by the number of bonds in the interaction (e.g. 3
+   for a dihedral) and adding a small amount of stretch.
+
+*Bond/react: Atom affected by reaction too close to template edge*
+   This means an atom which changes type or connectivity during the
+   reaction is too close to an 'edge' atom defined in the superimpose
+   file. This could cause incorrect assignment of bonds, angle, etc.
+   Generally, this means you must include more atoms in your templates,
+   such that there are at least two atoms between each atom involved in
+   the reaction and an edge atom.
+
+*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
+   Self-explanatory.
+
+*Calling write\_dump before a full system init.*
+   The write\_dump command is used before the system has been fully
+   initialized as part of a 'run' or 'minimize' command. Not all dump
+   styles and features are fully supported at this point and thus the
+   command may fail or produce incomplete or incorrect output. Insert
+   a "run 0" command, if a full system init is required.
+
+*Cannot count rigid body degrees-of-freedom before bodies are fully initialized*
+   This means the temperature associated with the rigid bodies may be
+   incorrect on this timestep.
+
+*Cannot count rigid body degrees-of-freedom before bodies are initialized*
+   This means the temperature associated with the rigid bodies may be
+   incorrect on this timestep.
+
+*Cannot include log terms without 1/r terms; setting flagHI to 1*
+   Self-explanatory.
+
+*Cannot include log terms without 1/r terms; setting flagHI to 1.*
+   Self-explanatory.
+
+*Charges are set, but coulombic solver is not used*
+   Self-explanatory.
+
+*Charges did not converge at step %ld: %lg*
+   Self-explanatory.
+
+*Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost*
+   The communication cutoff defaults to the maximum of what is inferred from
+   pair and bond styles (will be zero, if none are defined) and what is specified
+   via :doc:`comm\_modify cutoff <comm_modify>` (defaults to 0.0).  If this results
+   to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use
+   incorrect periodic images of atoms in interaction lists.  To avoid, either use
+   :doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm\_modify cutoff <comm_modify>`.
+
+*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
+   Self-explanatory.
+
+*Compute cna/atom cutoff may be too large to find ghost atom neighbors*
+   The neighbor cutoff used may not encompass enough ghost atoms
+   to perform this operation correctly.
+
+*Computing temperature of portions of rigid bodies*
+   The group defined by the temperature compute does not encompass all
+   the atoms in one or more rigid bodies, so the change in
+   degrees-of-freedom for the atoms in those partial rigid bodies will
+   not be accounted for.
+
+*Create\_bonds max distance > minimum neighbor cutoff*
+   This means atom pairs for some atom types may not be in the neighbor
+   list and thus no bond can be created between them.
+
+*Delete\_atoms cutoff > minimum neighbor cutoff*
+   This means atom pairs for some atom types may not be in the neighbor
+   list and thus an atom in that pair cannot be deleted.
+
+*Dihedral atoms missing at step %ld*
+   One or more of 4 atoms needed to compute a particular dihedral are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the dihedral has blown apart and an atom is
+   too far away.
+
+*Dihedral problem*
+   Conformation of the 4 listed dihedral atoms is extreme; you may want
+   to check your simulation geometry.
+
+*Dihedral problem: %d %ld %d %d %d %d*
+   Conformation of the 4 listed dihedral atoms is extreme; you may want
+   to check your simulation geometry.
+
+*Dihedral style in data file differs from currently defined dihedral style*
+   Self-explanatory.
+
+*Dihedrals are defined but no dihedral style is set*
+   The topology contains dihedrals, but there are no dihedral forces computed
+   since there was no dihedral\_style command.
+
+*Dump dcd/xtc timestamp may be wrong with fix dt/reset*
+   If the fix changes the timestep, the dump dcd file will not
+   reflect the change.
+
+*Energy due to X extra global DOFs will be included in minimizer energies*
+   When using fixes like box/relax, the potential energy used by the minimizer
+   is augmented by an additional energy provided by the fix. Thus the printed
+   converged energy may be different from the total potential energy.
+
+*Estimated error in splitting of dispersion coeffs is %g*
+   Error is greater than 0.0001 percent.
+
+*Ewald/disp Newton solver failed, using old method to estimate g\_ewald*
+   Self-explanatory. Choosing a different cutoff value may help.
+
+*FENE bond too long*
+   A FENE bond has stretched dangerously far.  It's interaction strength
+   will be truncated to attempt to prevent the bond from blowing up.
+
+*FENE bond too long: %ld %d %d %g*
+   A FENE bond has stretched dangerously far.  It's interaction strength
+   will be truncated to attempt to prevent the bond from blowing up.
+
+*FENE bond too long: %ld %g*
+   A FENE bond has stretched dangerously far.  It's interaction strength
+   will be truncated to attempt to prevent the bond from blowing up.
+
+*Fix SRD walls overlap but fix srd overlap not set*
+   You likely want to set this in your input script.
+
+* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
+   When using fix bond/create multiple times or in combination with
+   fix bond/break, the individual fix instances do not share information
+   about changes they made at the same time step and thus it may result
+   in unexpected behavior.
+
+*Fix bond/swap will ignore defined angles*
+   See the doc page for fix bond/swap for more info on this
+   restriction.
+
+*Fix deposit near setting < possible overlap separation %g*
+   This test is performed for finite size particles with a diameter, not
+   for point particles.  The near setting is smaller than the particle
+   diameter which can lead to overlaps.
+
+*Fix evaporate may delete atom with non-zero molecule ID*
+   This is probably an error, since you should not delete only one atom
+   of a molecule.
+
+*Fix gcmc using full\_energy option*
+   Fix gcmc has automatically turned on the full\_energy option since it
+   is required for systems like the one specified by the user. User input
+   included one or more of the following: kspace, triclinic, a hybrid
+   pair style, an eam pair style, or no "single" function for the pair
+   style.
+
+*Fix langevin gjf using random gaussians is not implemented with kokkos*
+This will most likely cause errors in kinetic fluctuations.
+
+*Fix property/atom mol or charge w/out ghost communication*
+   A model typically needs these properties defined for ghost atoms.
+
+*Fix qeq CG convergence failed (%g) after %d iterations at %ld step*
+   Self-explanatory.
+
+*Fix qeq has non-zero lower Taper radius cutoff*
+   Absolute value must be <= 0.01.
+
+*Fix qeq has very low Taper radius cutoff*
+   Value should typically be >= 5.0.
+
+*Fix qeq/dynamic tolerance may be too small for damped dynamics*
+   Self-explanatory.
+
+*Fix qeq/fire tolerance may be too small for damped fires*
+   Self-explanatory.
+
+*Fix rattle should come after all other integration fixes*
+   This fix is designed to work after all other integration fixes change
+   atom positions.  Thus it should be the last integration fix specified.
+   If not, it will not satisfy the desired constraints as well as it
+   otherwise would.
+
+*Fix recenter should come after all other integration fixes*
+   Other fixes may change the position of the center-of-mass, so
+   fix recenter should come last.
+
+*Fix srd SRD moves may trigger frequent reneighboring*
+   This is because the SRD particles may move long distances.
+
+*Fix srd grid size > 1/4 of big particle diameter*
+   This may cause accuracy problems.
+
+*Fix srd particle moved outside valid domain*
+   This may indicate a problem with your simulation parameters.
+
+*Fix srd particles may move > big particle diameter*
+   This may cause accuracy problems.
+
+*Fix srd viscosity < 0.0 due to low SRD density*
+   This may cause accuracy problems.
+
+*Fixes cannot send data in Kokkos communication, switching to classic communication*
+   This is current restriction with Kokkos.
+
+*For better accuracy use 'pair\_modify table 0'*
+   The user-specified force accuracy cannot be achieved unless the table
+   feature is disabled by using 'pair\_modify table 0'.
+
+*Geometric mixing assumed for 1/r\^6 coefficients*
+   Self-explanatory.
+
+*Group for fix\_modify temp != fix group*
+   The fix\_modify command is specifying a temperature computation that
+   computes a temperature on a different group of atoms than the fix
+   itself operates on.  This is probably not what you want to do.
+
+*H matrix size has been exceeded: m\_fill=%d H.m=%d\n*
+   This is the size of the matrix.
+
+*Ignoring unknown or incorrect info command flag*
+   Self-explanatory.  An unknown argument was given to the info command.
+   Compare your input with the documentation.
+
+*Improper atoms missing at step %ld*
+   One or more of 4 atoms needed to compute a particular improper are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the improper has blown apart and an atom is
+   too far away.
+
+*Improper problem: %d %ld %d %d %d %d*
+   Conformation of the 4 listed improper atoms is extreme; you may want
+   to check your simulation geometry.
+
+*Improper style in data file differs from currently defined improper style*
+   Self-explanatory.
+
+*Impropers are defined but no improper style is set*
+   The topology contains impropers, but there are no improper forces computed
+   since there was no improper\_style command.
+
+*Inconsistent image flags*
+   The image flags for a pair on bonded atoms appear to be inconsistent.
+   Inconsistent means that when the coordinates of the two atoms are
+   unwrapped using the image flags, the two atoms are far apart.
+   Specifically they are further apart than half a periodic box length.
+   Or they are more than a box length apart in a non-periodic dimension.
+   This is usually due to the initial data file not having correct image
+   flags for the 2 atoms in a bond that straddles a periodic boundary.
+   They should be different by 1 in that case.  This is a warning because
+   inconsistent image flags will not cause problems for dynamics or most
+   LAMMPS simulations.  However they can cause problems when such atoms
+   are used with the fix rigid or replicate commands.  Note that if you
+   have an infinite periodic crystal with bonds then it is impossible to
+   have fully consistent image flags, since some bonds will cross
+   periodic boundaries and connect two atoms with the same image
+   flag.
+
+*Increasing communication cutoff for GPU style*
+   The pair style has increased the communication cutoff to be consistent with
+   the communication cutoff requirements for this pair style when run on the GPU.
+
+*KIM Model does not provide 'energy'; Potential energy will be zero*
+   Self-explanatory.
+
+*KIM Model does not provide 'forces'; Forces will be zero*
+   Self-explanatory.
+
+*KIM Model does not provide 'particleEnergy'; energy per atom will be zero*
+   Self-explanatory.
+
+*KIM Model does not provide 'particleVirial'; virial per atom will be zero*
+   Self-explanatory.
+
+*Kspace\_modify slab param < 2.0 may cause unphysical behavior*
+   The kspace\_modify slab parameter should be larger to insure periodic
+   grids padded with empty space do not overlap.
+
+*Less insertions than requested*
+   The fix pour command was unsuccessful at finding open space
+   for as many particles as it tried to insert.
+
+*Library error in lammps\_gather\_atoms*
+   This library function cannot be used if atom IDs are not defined
+   or are not consecutively numbered.
+
+*Library error in lammps\_scatter\_atoms*
+   This library function cannot be used if atom IDs are not defined or
+   are not consecutively numbered, or if no atom map is defined.  See the
+   atom\_modify command for details about atom maps.
+
+*Likewise 1-2 special neighbor interactions != 1.0*
+   The topology contains bonds, but there is no bond style defined
+   and a 1-2 special neighbor scaling factor was not 1.0. This
+   means that pair style interactions may have scaled or missing
+   pairs in the neighbor list in expectation of interactions for
+   those pairs being computed from the bond style.
+
+*Likewise 1-3 special neighbor interactions != 1.0*
+   The topology contains angles, but there is no angle style defined
+   and a 1-3 special neighbor scaling factor was not 1.0. This
+   means that pair style interactions may have scaled or missing
+   pairs in the neighbor list in expectation of interactions for
+   those pairs being computed from the angle style.
+
+*Likewise 1-4 special neighbor interactions != 1.0*
+   The topology contains dihedrals, but there is no dihedral style defined
+   and a 1-4 special neighbor scaling factor was not 1.0. This
+   means that pair style interactions may have scaled or missing
+   pairs in the neighbor list in expectation of interactions for
+   those pairs being computed from the dihedral style.
+
+*Lost atoms via change\_box: original %ld current %ld*
+   The command options you have used caused atoms to be lost.
+
+*Lost atoms via displace\_atoms: original %ld current %ld*
+   The command options you have used caused atoms to be lost.
+
+*Lost atoms: original %ld current %ld*
+   Lost atoms are checked for each time thermo output is done.  See the
+   thermo\_modify lost command for options.  Lost atoms usually indicate
+   bad dynamics, e.g. atoms have been blown far out of the simulation
+   box, or moved further than one processor's sub-domain away before
+   reneighboring.
+
+*MSM mesh too small, increasing to 2 points in each direction*
+   Self-explanatory.
+
+*Mismatch between velocity and compute groups*
+   The temperature computation used by the velocity command will not be
+   on the same group of atoms that velocities are being set for.
+
+*Mixing forced for lj coefficients*
+   Self-explanatory.
+
+*Molecule attributes do not match system attributes*
+   An attribute is specified (e.g. diameter, charge) that is
+   not defined for the specified atom style.
+
+*Molecule has bond topology but no special bond settings*
+   This means the bonded atoms will not be excluded in pair-wise
+   interactions.
+
+*Molecule template for create\_atoms has multiple molecules*
+   The create\_atoms command will only create molecules of a single type,
+   i.e. the first molecule in the template.
+
+*Molecule template for fix gcmc has multiple molecules*
+   The fix gcmc command will only create molecules of a single type,
+   i.e. the first molecule in the template.
+
+*Molecule template for fix shake has multiple molecules*
+   The fix shake command will only recognize molecules of a single
+   type, i.e. the first molecule in the template.
+
+*More than one compute centro/atom*
+   It is not efficient to use compute centro/atom more than once.
+
+*More than one compute cluster/atom*
+   It is not efficient to use compute cluster/atom  more than once.
+
+*More than one compute cna/atom defined*
+   It is not efficient to use compute cna/atom  more than once.
+
+*More than one compute contact/atom*
+   It is not efficient to use compute contact/atom more than once.
+
+*More than one compute coord/atom*
+   It is not efficient to use compute coord/atom more than once.
+
+*More than one compute damage/atom*
+   It is not efficient to use compute ke/atom more than once.
+
+*More than one compute dilatation/atom*
+   Self-explanatory.
+
+*More than one compute erotate/sphere/atom*
+   It is not efficient to use compute erorate/sphere/atom more than once.
+
+*More than one compute hexorder/atom*
+   It is not efficient to use compute hexorder/atom more than once.
+
+*More than one compute ke/atom*
+   It is not efficient to use compute ke/atom more than once.
+
+*More than one compute orientorder/atom*
+   It is not efficient to use compute orientorder/atom more than once.
+
+*More than one compute plasticity/atom*
+   Self-explanatory.
+
+*More than one compute sna/atom*
+   Self-explanatory.
+
+*More than one compute snad/atom*
+   Self-explanatory.
+
+*More than one compute snav/atom*
+   Self-explanatory.
+
+*More than one fix poems*
+   It is not efficient to use fix poems more than once.
+
+*More than one fix rigid*
+   It is not efficient to use fix rigid more than once.
+
+*Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
+   This is because excluding specific pair interactions also excludes
+   them from long-range interactions which may not be the desired effect.
+   The special\_bonds command handles this consistently by insuring
+   excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
+   consistently by both the short-range pair style and the long-range
+   solver.  This is not done for exclusions of charged atom pairs via the
+   neigh\_modify exclude command.
+
+*New thermo\_style command, previous thermo\_modify settings will be lost*
+   If a thermo\_style command is used after a thermo\_modify command, the
+   settings changed by the thermo\_modify command will be reset to their
+   default values.  This is because the thermo\_modify command acts on
+   the currently defined thermo style, and a thermo\_style command creates
+   a new style.
+
+*No Kspace calculation with verlet/split*
+   The 2nd partition performs a kspace calculation so the kspace\_style
+   command must be used.
+
+*No automatic unit conversion to XTC file format conventions possible for units lj*
+   This means no scaling will be performed.
+
+*No fixes defined, atoms won't move*
+   If you are not using a fix like nve, nvt, npt then atom velocities and
+   coordinates will not be updated during timestepping.
+
+*No joints between rigid bodies, use fix rigid instead*
+   The bodies defined by fix poems are not connected by joints.  POEMS
+   will integrate the body motion, but it would be more efficient to use
+   fix rigid.
+
+*Not using real units with pair reax*
+   This is most likely an error, unless you have created your own ReaxFF
+   parameter file in a different set of units.
+
+*Number of MSM mesh points changed to be a multiple of 2*
+   MSM requires that the number of grid points in each direction be a multiple
+   of two and the number of grid points in one or more directions have been
+   adjusted to meet this requirement.
+
+*OMP\_NUM\_THREADS environment is not set.*
+   This environment variable must be set appropriately to use the
+   USER-OMP package.
+
+*One or more atoms are time integrated more than once*
+   This is probably an error since you typically do not want to
+   advance the positions or velocities of an atom more than once
+   per timestep.
+
+*One or more chunks do not contain all atoms in molecule*
+   This may not be what you intended.
+
+*One or more dynamic groups may not be updated at correct point in timestep*
+   If there are other fixes that act immediately after the initial stage
+   of time integration within a timestep (i.e. after atoms move), then
+   the command that sets up the dynamic group should appear after those
+   fixes.  This will insure that dynamic group assignments are made
+   after all atoms have moved.
+
+*One or more respa levels compute no forces*
+   This is computationally inefficient.
+
+*Pair COMB charge %.10f with force %.10f hit max barrier*
+   Something is possibly wrong with your model.
+
+*Pair COMB charge %.10f with force %.10f hit min barrier*
+   Something is possibly wrong with your model.
+
+*Pair brownian needs newton pair on for momentum conservation*
+   Self-explanatory.
+
+*Pair dpd needs newton pair on for momentum conservation*
+   Self-explanatory.
+
+*Pair dsmc: num\_of\_collisions > number\_of\_A*
+   Collision model in DSMC is breaking down.
+
+*Pair dsmc: num\_of\_collisions > number\_of\_B*
+   Collision model in DSMC is breaking down.
+
+*Pair style in data file differs from currently defined pair style*
+   Self-explanatory.
+
+*Pair style restartinfo set but has no restart support*
+   This pair style has a bug, where it does not support reading and
+   writing information to a restart file, but does not set the member
+   variable "restartinfo" to 0 as required in that case.
+
+*Particle deposition was unsuccessful*
+   The fix deposit command was not able to insert as many atoms as
+   needed.  The requested volume fraction may be too high, or other atoms
+   may be in the insertion region.
+
+*Proc sub-domain size < neighbor skin, could lead to lost atoms*
+   The decomposition of the physical domain (likely due to load
+   balancing) has led to a processor's sub-domain being smaller than the
+   neighbor skin in one or more dimensions.  Since reneighboring is
+   triggered by atoms moving the skin distance, this may lead to lost
+   atoms, if an atom moves all the way across a neighboring processor's
+   sub-domain before reneighboring is triggered.
+
+*Reducing PPPM order b/c stencil extends beyond nearest neighbor processor*
+   This may lead to a larger grid than desired.  See the kspace\_modify overlap
+   command to prevent changing of the PPPM order.
+
+*Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor*
+   This may lead to a larger grid than desired.  See the kspace\_modify overlap
+   command to prevent changing of the PPPM order.
+
+*Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor*
+   This may lead to a larger grid than desired.  See the kspace\_modify overlap
+   command to prevent changing of the PPPM order.
+
+*Replacing a fix, but new group != old group*
+   The ID and style of a fix match for a fix you are changing with a fix
+   command, but the new group you are specifying does not match the old
+   group.
+
+*Replicating in a non-periodic dimension*
+   The parameters for a replicate command will cause a non-periodic
+   dimension to be replicated; this may cause unwanted behavior.
+
+*Resetting reneighboring criteria during PRD*
+   A PRD simulation requires that neigh\_modify settings be delay = 0,
+   every = 1, check = yes.  Since these settings were not in place,
+   LAMMPS changed them and will restore them to their original values
+   after the PRD simulation.
+
+*Resetting reneighboring criteria during TAD*
+   A TAD simulation requires that neigh\_modify settings be delay = 0,
+   every = 1, check = yes.  Since these settings were not in place,
+   LAMMPS changed them and will restore them to their original values
+   after the PRD simulation.
+
+*Resetting reneighboring criteria during minimization*
+   Minimization requires that neigh\_modify settings be delay = 0, every =
+   1, check = yes.  Since these settings were not in place, LAMMPS
+   changed them and will restore them to their original values after the
+   minimization.
+
+*Restart file used different # of processors*
+   The restart file was written out by a LAMMPS simulation running on a
+   different number of processors.  Due to round-off, the trajectories of
+   your restarted simulation may diverge a little more quickly than if
+   you ran on the same # of processors.
+
+*Restart file used different 3d processor grid*
+   The restart file was written out by a LAMMPS simulation running on a
+   different 3d grid of processors.  Due to round-off, the trajectories
+   of your restarted simulation may diverge a little more quickly than if
+   you ran on the same # of processors.
+
+*Restart file used different boundary settings, using restart file values*
+   Your input script cannot change these restart file settings.
+
+*Restart file used different newton bond setting, using restart file value*
+   The restart file value will override the setting in the input script.
+
+*Restart file used different newton pair setting, using input script value*
+   The input script value will override the setting in the restart file.
+
+*Restrain problem: %d %ld %d %d %d %d*
+   Conformation of the 4 listed dihedral atoms is extreme; you may want
+   to check your simulation geometry.
+
+*Running PRD with only one replica*
+   This is allowed, but you will get no parallel speed-up.
+
+*SRD bin shifting turned on due to small lamda*
+   This is done to try to preserve accuracy.
+
+*SRD bin size for fix srd differs from user request*
+   Fix SRD had to adjust the bin size to fit the simulation box.  See the
+   cubic keyword if you want this message to be an error vs warning.
+
+*SRD bins for fix srd are not cubic enough*
+   The bin shape is not within tolerance of cubic.  See the cubic
+   keyword if you want this message to be an error vs warning.
+
+*SRD particle %d started inside big particle %d on step %ld bounce %d*
+   See the inside keyword if you want this message to be an error vs
+   warning.
+
+*SRD particle %d started inside wall %d on step %ld bounce %d*
+   See the inside keyword if you want this message to be an error vs
+   warning.
+
+*Shake determinant < 0.0*
+   The determinant of the quadratic equation being solved for a single
+   cluster specified by the fix shake command is numerically suspect.  LAMMPS
+   will set it to 0.0 and continue.
+
+*Shell command '%s' failed with error '%s'*
+   Self-explanatory.
+
+*Shell command returned with non-zero status*
+   This may indicate the shell command did not operate as expected.
+
+*Should not allow rigid bodies to bounce off reflecting walls*
+   LAMMPS allows this, but their dynamics are not computed correctly.
+
+*Should not use fix nve/limit with fix shake or fix rattle*
+   This will lead to invalid constraint forces in the SHAKE/RATTLE
+   computation.
+
+*Simulations might be very slow because of large number of structure factors*
+   Self-explanatory.
+
+*Slab correction not needed for MSM*
+   Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM.
+
+*System is not charge neutral, net charge = %g*
+   The total charge on all atoms on the system is not 0.0.
+   For some KSpace solvers this is only a warning.
+
+*Table inner cutoff >= outer cutoff*
+   You specified an inner cutoff for a Coulombic table that is longer
+   than the global cutoff.  Probably not what you wanted.
+
+*Temperature for MSST is not for group all*
+   User-assigned temperature to MSST fix does not compute temperature for
+   all atoms.  Since MSST computes a global pressure, the kinetic energy
+   contribution from the temperature is assumed to also be for all atoms.
+   Thus the pressure used by MSST could be inaccurate.
+
+*Temperature for NPT is not for group all*
+   User-assigned temperature to NPT fix does not compute temperature for
+   all atoms.  Since NPT computes a global pressure, the kinetic energy
+   contribution from the temperature is assumed to also be for all atoms.
+   Thus the pressure used by NPT could be inaccurate.
+
+*Temperature for fix modify is not for group all*
+   The temperature compute is being used with a pressure calculation
+   which does operate on group all, so this may be inconsistent.
+
+*Temperature for thermo pressure is not for group all*
+   User-assigned temperature to thermo via the thermo\_modify command does
+   not compute temperature for all atoms.  Since thermo computes a global
+   pressure, the kinetic energy contribution from the temperature is
+   assumed to also be for all atoms.  Thus the pressure printed by thermo
+   could be inaccurate.
+
+*The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015*
+   Self-explanatory.
+
+*The minimizer does not re-orient dipoles when using fix efield*
+   This means that only the atom coordinates will be minimized,
+   not the orientation of the dipoles.
+
+*Too many common neighbors in CNA %d times*
+   More than the maximum # of neighbors was found multiple times.  This
+   was unexpected.
+
+*Too many inner timesteps in fix ttm*
+   Self-explanatory.
+
+*Too many neighbors in CNA for %d atoms*
+   More than the maximum # of neighbors was found multiple times.  This
+   was unexpected.
+
+*Triclinic box skew is large*
+   The displacement in a skewed direction is normally required to be less
+   than half the box length in that dimension.  E.g. the xy tilt must be
+   between -half and +half of the x box length.  You have relaxed the
+   constraint using the box tilt command, but the warning means that a
+   LAMMPS simulation may be inefficient as a result.
+
+*Use special bonds = 0,1,1 with bond style fene*
+   Most FENE models need this setting for the special\_bonds command.
+
+*Use special bonds = 0,1,1 with bond style fene/expand*
+   Most FENE models need this setting for the special\_bonds command.
+
+*Using a many-body potential with bonds/angles/dihedrals and special\_bond exclusions*
+   This is likely not what you want to do.  The exclusion settings will
+   eliminate neighbors in the neighbor list, which the many-body potential
+   needs to calculated its terms correctly.
+
+*Using compute temp/deform with inconsistent fix deform remap option*
+   Fix nvt/sllod assumes deforming atoms have a velocity profile provided
+   by "remap v" or "remap none" as a fix deform option.
+
+*Using compute temp/deform with no fix deform defined*
+   This is probably an error, since it makes little sense to use
+   compute temp/deform in this case.
+
+*Using fix srd with box deformation but no SRD thermostat*
+   The deformation will heat the SRD particles so this can
+   be dangerous.
+
+*Using kspace solver on system with no charge*
+   Self-explanatory.
+
+*Using largest cut-off for lj/long/dipole/long long long*
+   Self-explanatory.
+
+*Using largest cutoff for buck/long/coul/long*
+   Self-explanatory.
+
+*Using largest cutoff for lj/long/coul/long*
+   Self-explanatory.
+
+*Using largest cutoff for pair\_style lj/long/tip4p/long*
+   Self-explanatory.
+
+*Using package gpu without any pair style defined*
+   Self-explanatory.
+
+*Using pair potential shift with pair\_modify compute no*
+   The shift effects will thus not be computed.
+
+*Using pair tail corrections with nonperiodic system*
+   This is probably a bogus thing to do, since tail corrections are
+   computed by integrating the density of a periodic system out to
+   infinity.
+
+*Using pair tail corrections with pair\_modify compute no*
+   The tail corrections will thus not be computed.
+
+*pair style reax is now deprecated and will soon be retired. Users should switch to pair\_style reax/c*
+   Self-explanatory.
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst
new file mode 100644
index 0000000000..993090baf1
--- /dev/null
+++ b/doc/src/Examples.rst
@@ -0,0 +1,237 @@
+Example scripts
+===============
+
+The LAMMPS distribution includes an examples sub-directory with many
+sample problems.  Many are 2d models that run quickly and are
+straightforward to visualize, requiring at most a couple of minutes to
+run on a desktop machine.  Each problem has an input script (in.\*) and
+produces a log file (log.\*) when it runs.  Some use a data file
+(data.\*) of initial coordinates as additional input.  A few sample log
+file run on different machines and different numbers of processors are
+included in the directories to compare your answers to.  E.g. a log
+file like log.date.crack.foo.P means the "crack" example was run on P
+processors of machine "foo" on that date (i.e. with that version of
+LAMMPS).
+
+Many of the input files have commented-out lines for creating dump
+files and image files.
+
+If you uncomment the :doc:`dump <dump>` command in the input script, a
+text dump file will be produced, which can be animated by various
+`visualization programs <http://lammps.sandia.gov/viz.html>`_.
+
+If you uncomment the :doc:`dump image <dump>` command in the input
+script, and assuming you have built LAMMPS with a JPG library, JPG
+snapshot images will be produced when the simulation runs.  They can
+be quickly post-processed into a movie using commands described on the
+:doc:`dump image <dump_image>` doc page.
+
+Animations of many of the examples can be viewed on the Movies section
+of the `LAMMPS web site <lws_>`_.
+
+There are two kinds of sub-directories in the examples dir.  Lowercase
+dirs contain one or a few simple, quick-to-run problems.  Uppercase
+dirs contain up to several complex scripts that illustrate a
+particular kind of simulation method or model.  Some of these run for
+longer times, e.g. to measure a particular quantity.
+
+Lists of both kinds of directories are given below.
+
+
+----------
+
+
+Lowercase directories
+---------------------
+
++-------------+------------------------------------------------------------------+
+| accelerate  | run with various acceleration options (OpenMP, GPU, Phi)         |
++-------------+------------------------------------------------------------------+
+| airebo      | polyethylene with AIREBO potential                               |
++-------------+------------------------------------------------------------------+
+| atm         | Axilrod-Teller-Muto potential example                            |
++-------------+------------------------------------------------------------------+
+| balance     | dynamic load balancing, 2d system                                |
++-------------+------------------------------------------------------------------+
+| body        | body particles, 2d system                                        |
++-------------+------------------------------------------------------------------+
+| cmap        | CMAP 5-body contributions to CHARMM force field                  |
++-------------+------------------------------------------------------------------+
+| colloid     | big colloid particles in a small particle solvent, 2d system     |
++-------------+------------------------------------------------------------------+
+| comb        | models using the COMB potential                                  |
++-------------+------------------------------------------------------------------+
+| controller  | use of fix controller as a thermostat                            |
++-------------+------------------------------------------------------------------+
+| coreshell   | core/shell model using CORESHELL package                         |
++-------------+------------------------------------------------------------------+
+| crack       | crack propagation in a 2d solid                                  |
++-------------+------------------------------------------------------------------+
+| deposit     | deposit atoms and molecules on a surface                         |
++-------------+------------------------------------------------------------------+
+| dipole      | point dipolar particles, 2d system                               |
++-------------+------------------------------------------------------------------+
+| dreiding    | methanol via Dreiding FF                                         |
++-------------+------------------------------------------------------------------+
+| eim         | NaCl using the EIM potential                                     |
++-------------+------------------------------------------------------------------+
+| ellipse     | ellipsoidal particles in spherical solvent, 2d system            |
++-------------+------------------------------------------------------------------+
+| flow        | Couette and Poiseuille flow in a 2d channel                      |
++-------------+------------------------------------------------------------------+
+| friction    | frictional contact of spherical asperities between 2d surfaces   |
++-------------+------------------------------------------------------------------+
+| gcmc        | Grand Canonical Monte Carlo (GCMC) via the fix gcmc command      |
++-------------+------------------------------------------------------------------+
+| granregion  | use of fix wall/region/gran as boundary on granular particles    |
++-------------+------------------------------------------------------------------+
+| hugoniostat | Hugoniostat shock dynamics                                       |
++-------------+------------------------------------------------------------------+
+| hyper       | global and local hyperdynamics of diffusion on Pt surface        |
++-------------+------------------------------------------------------------------+
+| indent      | spherical indenter into a 2d solid                               |
++-------------+------------------------------------------------------------------+
+| kim         | use of potentials from the `OpenKIM Repository <openkim_>`_      |
++-------------+------------------------------------------------------------------+
+| latte       | examples for using fix latte for DFTB via the LATTE library      |
++-------------+------------------------------------------------------------------+
+| meam        | MEAM test for SiC and shear (same as shear examples)             |
++-------------+------------------------------------------------------------------+
+| melt        | rapid melt of 3d LJ system                                       |
++-------------+------------------------------------------------------------------+
+| message     | demos for LAMMPS client/server coupling with the MESSAGE package |
++-------------+------------------------------------------------------------------+
+| micelle     | self-assembly of small lipid-like molecules into 2d bilayers     |
++-------------+------------------------------------------------------------------+
+| min         | energy minimization of 2d LJ melt                                |
++-------------+------------------------------------------------------------------+
+| mscg        | parameterize a multi-scale coarse-graining (MSCG) model          |
++-------------+------------------------------------------------------------------+
+| msst        | MSST shock dynamics                                              |
++-------------+------------------------------------------------------------------+
+| nb3b        | use of non-bonded 3-body harmonic pair style                     |
++-------------+------------------------------------------------------------------+
+| neb         | nudged elastic band (NEB) calculation for barrier finding        |
++-------------+------------------------------------------------------------------+
+| nemd        | non-equilibrium MD of 2d sheared system                          |
++-------------+------------------------------------------------------------------+
+| obstacle    | flow around two voids in a 2d channel                            |
++-------------+------------------------------------------------------------------+
+| peptide     | dynamics of a small solvated peptide chain (5-mer)               |
++-------------+------------------------------------------------------------------+
+| peri        | Peridynamic model of cylinder impacted by indenter               |
++-------------+------------------------------------------------------------------+
+| pour        | pouring of granular particles into a 3d box, then chute flow     |
++-------------+------------------------------------------------------------------+
+| prd         | parallel replica dynamics of vacancy diffusion in bulk Si        |
++-------------+------------------------------------------------------------------+
+| python      | using embedded Python in a LAMMPS input script                   |
++-------------+------------------------------------------------------------------+
+| qeq         | use of the QEQ package for charge equilibration                  |
++-------------+------------------------------------------------------------------+
+| rdf-adf     | computing radial and angle distribution functions for water      |
++-------------+------------------------------------------------------------------+
+| reax        | RDX and TATB models using the ReaxFF                             |
++-------------+------------------------------------------------------------------+
+| rerun       | use of rerun and read\_dump commands                             |
++-------------+------------------------------------------------------------------+
+| rigid       | rigid bodies modeled as independent or coupled                   |
++-------------+------------------------------------------------------------------+
+| shear       | sideways shear applied to 2d solid, with and without a void      |
++-------------+------------------------------------------------------------------+
+| snap        | NVE dynamics for BCC tantalum crystal using SNAP potential       |
++-------------+------------------------------------------------------------------+
+| srd         | stochastic rotation dynamics (SRD) particles as solvent          |
++-------------+------------------------------------------------------------------+
+| streitz     | use of Streitz/Mintmire potential with charge equilibration      |
++-------------+------------------------------------------------------------------+
+| tad         | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
++-------------+------------------------------------------------------------------+
+| threebody   | regression test input for a variety of manybody potentials       |
++-------------+------------------------------------------------------------------+
+| vashishta   | use of the Vashishta potential                                   |
++-------------+------------------------------------------------------------------+
+| voronoi     | Voronoi tesselation via compute voronoi/atom command             |
++-------------+------------------------------------------------------------------+
+
+Here is how you can run and visualize one of the sample problems:
+
+
+.. parsed-literal::
+
+   cd indent
+   cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
+   lmp_linux -in in.indent            # run the problem
+
+Running the simulation produces the files *dump.indent* and
+*log.lammps*\ .  You can visualize the dump file of snapshots with a
+variety of 3rd-party tools highlighted on the
+`Visualization <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
+web site.
+
+If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
+script a series of JPG images will be produced by the run (assuming
+you built LAMMPS with JPG support; see the
+:doc:`Build\_settings <Build_settings>` doc page for details).  These can
+be viewed individually or turned into a movie or animated by tools
+like ImageMagick or QuickTime or various Windows-based tools.  See the
+:doc:`dump image <dump_image>` doc page for more details.  E.g. this
+Imagemagick command would create a GIF file suitable for viewing in a
+browser.
+
+
+.. parsed-literal::
+
+   % convert -loop 1 \*.jpg foo.gif
+
+
+----------
+
+
+Uppercase directories
+---------------------
+
++------------+--------------------------------------------------------------------------------------------------+
+| ASPHERE    | various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc |
++------------+--------------------------------------------------------------------------------------------------+
+| COUPLE     | examples of how to use LAMMPS as a library                                                       |
++------------+--------------------------------------------------------------------------------------------------+
+| DIFFUSE    | compute diffusion coefficients via several methods                                               |
++------------+--------------------------------------------------------------------------------------------------+
+| ELASTIC    | compute elastic constants at zero temperature                                                    |
++------------+--------------------------------------------------------------------------------------------------+
+| ELASTIC\_T | compute elastic constants at finite temperature                                                  |
++------------+--------------------------------------------------------------------------------------------------+
+| HEAT       | compute thermal conductivity for LJ and water via fix ehex                                       |
++------------+--------------------------------------------------------------------------------------------------+
+| KAPPA      | compute thermal conductivity via several methods                                                 |
++------------+--------------------------------------------------------------------------------------------------+
+| MC         | using LAMMPS in a Monte Carlo mode to relax the energy of a system                               |
++------------+--------------------------------------------------------------------------------------------------+
+| SPIN       | examples for features of the SPIN package                                                        |
++------------+--------------------------------------------------------------------------------------------------+
+| UNITS      | examples that run the same simulation in lj, real, metal units                                   |
++------------+--------------------------------------------------------------------------------------------------+
+| USER       | examples for USER packages and USER-contributed commands                                         |
++------------+--------------------------------------------------------------------------------------------------+
+| VISCOSITY  | compute viscosity via several methods                                                            |
++------------+--------------------------------------------------------------------------------------------------+
+
+Nearly all of these directories have README files which give more
+details on how to understand and use their contents.
+
+The USER directory has a large number of sub-directories which
+correspond by name to a USER package.  They contain scripts that
+illustrate how to use the command(s) provided in that package.  Many
+of the sub-directories have their own README files which give further
+instructions.  See the :doc:`Packages\_details <Packages_details>` doc
+page for more info on specific USER packages.
+
+.. _openkim: https://openkim.org
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst
new file mode 100644
index 0000000000..9f310a4645
--- /dev/null
+++ b/doc/src/Howto.rst
@@ -0,0 +1,106 @@
+Howto discussions
+*****************
+
+These doc pages describe how to perform various tasks with LAMMPS,
+both for users and developers.  The
+`glossary <http://lammps.sandia.gov>`_ website page also lists MD
+terminology with links to corresponding LAMMPS manual pages.  The
+example input scripts included in the examples dir of the LAMMPS
+distribution and highlighted on the :doc:`Examples <Examples>` doc page
+also show how to setup and run various kinds of simulations.
+
+Tutorials howto
+===============
+
+
+.. toctree::
+   :name: tutorials
+   :maxdepth: 1
+
+   Howto_github
+   Howto_pylammps
+   Howto_bash
+
+General howto
+=============
+
+
+.. toctree::
+   :name: general_howto
+   :maxdepth: 1
+
+   Howto_restart
+   Howto_viz
+   Howto_multiple
+   Howto_replica
+   Howto_library
+   Howto_couple
+   Howto_client_server
+
+Settings howto
+==============
+
+
+.. toctree::
+   :name: settings
+   :maxdepth: 1
+
+   Howto_2d
+   Howto_triclinic
+   Howto_thermostat
+   Howto_barostat
+   Howto_walls
+   Howto_nemd
+   Howto_dispersion
+
+Analysis howto
+==============
+
+
+.. toctree::
+   :name: analysis
+   :maxdepth: 1
+
+   Howto_output
+   Howto_chunk
+   Howto_temperature
+   Howto_elastic
+   Howto_kappa
+   Howto_viscosity
+   Howto_diffusion
+
+Force fields howto
+==================
+
+
+.. toctree::
+   :name: force
+   :maxdepth: 1
+
+   Howto_bioFF
+   Howto_tip3p
+   Howto_tip4p
+   Howto_spc
+
+Packages howto
+==============
+
+
+.. toctree::
+   :name: packages
+   :maxdepth: 1
+
+   Howto_spherical
+   Howto_granular
+   Howto_body
+   Howto_polarizable
+   Howto_coreshell
+   Howto_drude
+   Howto_drude2
+   Howto_manifold
+   Howto_spins
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst
new file mode 100644
index 0000000000..ee978f3521
--- /dev/null
+++ b/doc/src/Howto_2d.rst
@@ -0,0 +1,48 @@
+2d simulations
+==============
+
+Use the :doc:`dimension <dimension>` command to specify a 2d simulation.
+
+Make the simulation box periodic in z via the :doc:`boundary <boundary>`
+command.  This is the default.
+
+If using the :doc:`create box <create_box>` command to define a
+simulation box, set the z dimensions narrow, but finite, so that the
+create\_atoms command will tile the 3d simulation box with a single z
+plane of atoms - e.g.
+
+
+.. parsed-literal::
+
+   :doc:`create box <create_box>` 1 -10 10 -10 10 -0.25 0.25
+
+If using the :doc:`read data <read_data>` command to read in a file of
+atom coordinates, set the "zlo zhi" values to be finite but narrow,
+similar to the create\_box command settings just described.  For each
+atom in the file, assign a z coordinate so it falls inside the
+z-boundaries of the box - e.g. 0.0.
+
+Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
+defined fix to insure that the z-components of velocities and forces
+are zeroed out every timestep.  The reason to make it the last fix is
+so that any forces induced by other fixes will be zeroed out.
+
+Many of the example input scripts included in the LAMMPS distribution
+are for 2d models.
+
+.. note::
+
+   Some models in LAMMPS treat particles as finite-size spheres, as
+   opposed to point particles.  See the :doc:`atom\_style sphere <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>`
+   commands for details.  By default, for 2d simulations, such particles
+   will still be modeled as 3d spheres, not 2d discs (circles), meaning
+   their moment of inertia will be that of a sphere.  If you wish to
+   model them as 2d discs, see the :doc:`set density/disc <set>` command
+   and the *disc* option for the :doc:`fix nve/sphere <fix_nve_sphere>`,
+   :doc:`fix nvt/sphere <fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>`
+   commands.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_barostat.rst b/doc/src/Howto_barostat.rst
new file mode 100644
index 0000000000..0c46c696c7
--- /dev/null
+++ b/doc/src/Howto_barostat.rst
@@ -0,0 +1,68 @@
+Barostats
+=========
+
+Barostatting means controlling the pressure in an MD simulation.
+:doc:`Thermostatting <Howto_thermostat>` means controlling the
+temperature of the particles.  Since the pressure includes a kinetic
+component due to particle velocities, both these operations require
+calculation of the temperature.  Typically a target temperature (T)
+and/or pressure (P) is specified by the user, and the thermostat or
+barostat attempts to equilibrate the system to the requested T and/or
+P.
+
+Barostatting in LAMMPS is performed by :doc:`fixes <fix>`.  Two
+barostatting methods are currently available: Nose-Hoover (npt and
+nph) and Berendsen:
+
+* :doc:`fix npt <fix_nh>`
+* :doc:`fix npt/sphere <fix_npt_sphere>`
+* :doc:`fix npt/asphere <fix_npt_asphere>`
+* :doc:`fix nph <fix_nh>`
+* :doc:`fix press/berendsen <fix_press_berendsen>`
+
+The :doc:`fix npt <fix_nh>` commands include a Nose-Hoover thermostat
+and barostat.  :doc:`Fix nph <fix_nh>` is just a Nose/Hoover barostat;
+it does no thermostatting.  Both :doc:`fix nph <fix_nh>` and :doc:`fix press/berendsen <fix_press_berendsen>` can be used in conjunction
+with any of the thermostatting fixes.
+
+As with the :doc:`thermostats <Howto_thermostat>`, :doc:`fix npt <fix_nh>`
+and :doc:`fix nph <fix_nh>` only use translational motion of the
+particles in computing T and P and performing thermo/barostatting.
+:doc:`Fix npt/sphere <fix_npt_sphere>` and :doc:`fix npt/asphere <fix_npt_asphere>` thermo/barostat using not only
+translation velocities but also rotational velocities for spherical
+and aspherical particles.
+
+All of the barostatting fixes use the :doc:`compute pressure <compute_pressure>` compute to calculate a current
+pressure.  By default, this compute is created with a simple :doc:`compute temp <compute_temp>` (see the last argument of the :doc:`compute pressure <compute_pressure>` command), which is used to calculated
+the kinetic component of the pressure.  The barostatting fixes can
+also use temperature computes that remove bias for the purpose of
+computing the kinetic component which contributes to the current
+pressure.  See the doc pages for the individual fixes and for the
+:doc:`fix\_modify <fix_modify>` command for instructions on how to assign
+a temperature or pressure compute to a barostatting fix.
+
+.. note::
+
+   As with the thermostats, the Nose/Hoover methods (:doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`) perform time integration.
+   :doc:`Fix press/berendsen <fix_press_berendsen>` does NOT, so it should
+   be used with one of the constant NVE fixes or with one of the NVT
+   fixes.
+
+Thermodynamic output, which can be setup via the
+:doc:`thermo\_style <thermo_style>` command, often includes pressure
+values.  As explained on the doc page for the
+:doc:`thermo\_style <thermo_style>` command, the default pressure is
+setup by the thermo command itself.  It is NOT the pressure associated
+with any barostatting fix you have defined or with any compute you
+have defined that calculates a pressure.  The doc pages for the
+barostatting fixes explain the ID of the pressure compute they create.
+Thus if you want to view these pressures, you need to specify them
+explicitly via the :doc:`thermo\_style custom <thermo_style>` command.
+Or you can use the :doc:`thermo\_modify <thermo_modify>` command to
+re-define what pressure compute is used for default thermodynamic
+output.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_bash.rst b/doc/src/Howto_bash.rst
new file mode 100644
index 0000000000..be636c9e9d
--- /dev/null
+++ b/doc/src/Howto_bash.rst
@@ -0,0 +1,291 @@
+Using LAMMPS with Bash on Windows
+=================================
+
+**written by Richard Berger**
+
+
+----------
+
+
+Starting with Windows 10 you can install Linux tools directly in Windows. This
+allows you to compile LAMMPS following the same procedure as on a real Ubuntu
+Linux installation. Software can be easily installed using the package manager
+via apt-get and all files are accessible in both the Windows Explorer and your
+Linux shell (bash). This avoids switching to a different operating system or
+installing a virtual machine. Everything runs on Windows.
+
+Installing Bash on Windows
+--------------------------
+
+Prerequisites
+^^^^^^^^^^^^^
+
+* Windows 10 (64bit only)
+* Latest updates installed
+
+Enable developer mode
+^^^^^^^^^^^^^^^^^^^^^
+
+You enable this feature by first opening Windows Settings and enabling
+Developer mode. Go to the Windows settings and search for "developer". This
+will allow you to install software which comes from outside of the Windows
+Store.  You might be prompted to reboot your compute. Please do so.
+
+.. image:: JPG/bow_tutorial_01_small.png
+   :target: JPG/bow_tutorial_01.png
+
+.. image:: JPG/bow_tutorial_02_small.png
+   :target: JPG/bow_tutorial_02.png
+
+.. image:: JPG/bow_tutorial_03_small.png
+   :target: JPG/bow_tutorial_03.png
+
+Install Windows Subsystem for Linux
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Next you must ensure that the Window Subsystem for Linux is installed. Again,
+search for "enable windows features" in the Settings dialog. This opens a
+dialog with a list of features you can install. Add a checkmark to Windows
+Subsystem for Linux (Beta) and press OK.
+
+.. image:: JPG/bow_tutorial_04_small.png
+   :target: JPG/bow_tutorial_04.png
+
+.. image:: JPG/bow_tutorial_05.png
+   :target: JPG/bow_tutorial_05.png
+
+Install Bash for Windows
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+After installation completes, type "bash" in the Windows Start menu search.
+Select the first found option. This will launch a command-line window which
+will prompt you about installing Ubuntu on Windows. Confirm with "y" and press
+enter. This will then download Ubuntu for Windows.
+
+.. image:: JPG/bow_tutorial_06.png
+
+.. image:: JPG/bow_tutorial_07.png
+
+During installation, you will be asked for a new password. This will be used
+for installing new software and running commands with sudo.
+
+.. image:: JPG/bow_tutorial_08.png
+
+Type exit to close the command-line window.
+
+Go to the Start menu and type "bash" again. This time you will see a "Bash on
+Ubuntu on Windows" Icon. Start this program.
+
+.. image:: JPG/bow_tutorial_09.png
+
+Congratulations, you have installed **Bash on Ubuntu on Windows**\ .
+
+.. image:: JPG/bow_tutorial_10.png
+
+
+----------
+
+
+Compiling LAMMPS in Bash on Windows
+-----------------------------------
+
+The installation of LAMMPS in this environment is identical to working inside
+of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.
+
+Installing prerequisite packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+First upgrade all existing packages using
+
+
+.. parsed-literal::
+
+   sudo apt update
+   sudo apt upgrade -y
+
+Next install the following packages, which include compilers and libraries
+needed for various LAMMPS features:
+
+
+.. parsed-literal::
+
+   sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
+
+Files in Ubuntu on Windows
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
+user home directory /home/\ **username**\ . You can access your Windows user directory
+using the /mnt/c/Users/\ **username** folder.
+
+Download LAMMPS
+^^^^^^^^^^^^^^^
+
+Obtain a copy of the LAMMPS code and go into it using "cd"
+
+Option 1: Downloading LAMMPS tarball using wget
+"""""""""""""""""""""""""""""""""""""""""""""""
+
+
+.. parsed-literal::
+
+   wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
+   tar xvzf lammps-stable.tar.gz
+   cd lammps-31Mar17
+
+Option 2: Obtaining LAMMPS code from GitHub
+"""""""""""""""""""""""""""""""""""""""""""
+
+
+.. parsed-literal::
+
+   git clone https://github.com/lammps/lammps.git
+   cd lammps
+
+Compiling LAMMPS
+^^^^^^^^^^^^^^^^
+
+At this point you can compile LAMMPS like on Ubuntu Linux.
+
+Compiling serial version
+""""""""""""""""""""""""
+
+
+.. parsed-literal::
+
+   cd src/
+   make -j 4 serial
+
+This will create an executable called lmp\_serial in the src/ directory
+
+Compiling MPI version
+"""""""""""""""""""""
+
+
+.. parsed-literal::
+
+   cd src/
+   make -j 4 mpi
+
+This will create an executable called lmp\_mpi in the src/ directory
+
+
+----------
+
+
+Finally, please note the absolute path of your src folder. You can get this using
+
+
+.. parsed-literal::
+
+   pwd
+
+or
+
+
+.. parsed-literal::
+
+   echo $PWD
+
+To run any examples you need the location of the executable. For now, let us
+save this location in a temporary variable
+
+
+.. parsed-literal::
+
+   LAMMPS_DIR=$PWD
+
+
+----------
+
+
+Running an example script
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Once compiled you can execute some of the LAMMPS examples. Switch into the
+examples/melt folder
+
+
+.. parsed-literal::
+
+   cd ../examples/melt
+
+The full path of the serial executable is $LAMMPS\_DIR/lmp\_serial, while the mpi
+version is $LAMMPS\_DIR/lmp\_mpi. You can run the melt example with either
+version as follows:
+
+
+.. parsed-literal::
+
+   $LAMMPS_DIR/lmp_serial -in in.melt
+
+or
+
+
+.. parsed-literal::
+
+   mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt
+
+Note the use of our variable $LAMMPS\_DIR, which expands into the full path of
+the LAMMPS src folder we saved earlier.
+
+Adding your executable directory to your PATH
+"""""""""""""""""""""""""""""""""""""""""""""
+
+You can avoid having to type the full path of your LAMMPS binary by adding its
+parent folder to the PATH environment variable as follows:
+
+
+.. parsed-literal::
+
+   export PATH=$LAMMPS_DIR:$PATH
+
+Input scripts can then be run like this:
+
+
+.. parsed-literal::
+
+   lmp_serial -in in.melt
+
+or
+
+
+.. parsed-literal::
+
+   mpirun -np 4 lmp_mpi -in in.melt
+
+However, this PATH variable will not persist if you close your bash window.
+To persist this setting edit the $HOME/.bashrc file using your favorite editor
+and add this line
+
+
+.. parsed-literal::
+
+   export PATH=/full/path/to/your/lammps/src:$PATH
+
+**Example:**
+
+For an executable lmp\_serial with a full path
+
+
+.. parsed-literal::
+
+   /home/richard/lammps/src/lmp_serial
+
+the PATH variable should be
+
+
+.. parsed-literal::
+
+   export PATH=/home/richard/lammps/src:$PATH
+
+.. note::
+
+   This should give you a jump start when trying to run LAMMPS on Windows.
+   To become effective in this environment I encourage you to look into Linux
+   tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst
new file mode 100644
index 0000000000..0ec0c16be8
--- /dev/null
+++ b/doc/src/Howto_bioFF.rst
@@ -0,0 +1,151 @@
+CHARMM, AMBER, COMPASS, and DREIDING force fields
+=================================================
+
+A force field has 2 parts: the formulas that define it and the
+coefficients used for a particular system.  Here we only discuss
+formulas implemented in LAMMPS that correspond to formulas commonly
+used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+coefficients is done either from special sections in an input data file
+via the :doc:`read\_data <read_data>` command or in the input script with
+commands like :doc:`pair\_coeff <pair_coeff>` or
+:doc:`bond\_coeff <bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc
+page for additional tools that can use CHARMM, AMBER, or Materials
+Studio generated files to assign force field coefficients and convert
+their output into LAMMPS input.
+
+See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
+field.  See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
+force field.  See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
+force field.
+
+.. _charmm: http://www.scripps.edu/brooks
+
+
+
+.. _amber: http://amber.scripps.edu
+
+
+
+The interaction styles listed below compute force field formulas that
+are consistent with common options in CHARMM or AMBER.  See each
+command's documentation for the formula it computes.
+
+* :doc:`bond\_style <bond_harmonic>` harmonic
+* :doc:`angle\_style <angle_charmm>` charmm
+* :doc:`dihedral\_style <dihedral_charmm>` charmmfsh
+* :doc:`dihedral\_style <dihedral_charmm>` charmm
+* :doc:`pair\_style <pair_charmm>` lj/charmmfsw/coul/charmmfsh
+* :doc:`pair\_style <pair_charmm>` lj/charmmfsw/coul/long
+* :doc:`pair\_style <pair_charmm>` lj/charmm/coul/charmm
+* :doc:`pair\_style <pair_charmm>` lj/charmm/coul/charmm/implicit
+* :doc:`pair\_style <pair_charmm>` lj/charmm/coul/long
+
+* :doc:`special\_bonds <special_bonds>` charmm
+* :doc:`special\_bonds <special_bonds>` amber
+
+.. note::
+
+   For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released
+   in March 2017.  We recommend they be used instead of the older *charmm*
+   styles.  See discussion of the differences on the :doc:`pair charmm <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
+   pages.
+
+COMPASS is a general force field for atomistic simulation of common
+organic molecules, inorganic small molecules, and polymers which was
+developed using ab initio and empirical parameterization techniques.
+See the :doc:`Tools <Tools>` doc page for the msi2lmp tool for creating
+LAMMPS template input and data files from BIOVIA's Materials Studio
+files.  Please note that the msi2lmp tool is very old and largely
+unmaintained, so it does not support all features of Materials Studio
+provided force field files, especially additions during the last decade.
+You should watch the output carefully and compare results, where
+possible.  See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS force
+field.
+
+These interaction styles listed below compute force field formulas that
+are consistent with the COMPASS force field.  See each command's
+documentation for the formula it computes.
+
+* :doc:`bond\_style <bond_class2>` class2
+* :doc:`angle\_style <angle_class2>` class2
+* :doc:`dihedral\_style <dihedral_class2>` class2
+* :doc:`improper\_style <improper_class2>` class2
+
+* :doc:`pair\_style <pair_class2>` lj/class2
+* :doc:`pair\_style <pair_class2>` lj/class2/coul/cut
+* :doc:`pair\_style <pair_class2>` lj/class2/coul/long
+
+* :doc:`special\_bonds <special_bonds>` lj/coul 0 0 1
+
+DREIDING is a generic force field developed by the `Goddard group <http://www.wag.caltech.edu>`_ at Caltech and is useful for
+predicting structures and dynamics of organic, biological and main-group
+inorganic molecules. The philosophy in DREIDING is to use general force
+constants and geometry parameters based on simple hybridization
+considerations, rather than individual force constants and geometric
+parameters that depend on the particular combinations of atoms involved
+in the bond, angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond term <pair_hbond_dreiding>` to describe interactions involving a
+hydrogen atom on very electronegative atoms (N, O, F).
+
+See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
+
+The interaction styles listed below compute force field formulas that
+are consistent with the DREIDING force field.  See each command's
+documentation for the formula it computes.
+
+* :doc:`bond\_style <bond_harmonic>` harmonic
+* :doc:`bond\_style <bond_morse>` morse
+
+* :doc:`angle\_style <angle_harmonic>` harmonic
+* :doc:`angle\_style <angle_cosine>` cosine
+* :doc:`angle\_style <angle_cosine_periodic>` cosine/periodic
+
+* :doc:`dihedral\_style <dihedral_charmm>` charmm
+* :doc:`improper\_style <improper_umbrella>` umbrella
+
+* :doc:`pair\_style <pair_buck>` buck
+* :doc:`pair\_style <pair_buck>` buck/coul/cut
+* :doc:`pair\_style <pair_buck>` buck/coul/long
+* :doc:`pair\_style <pair_lj>` lj/cut
+* :doc:`pair\_style <pair_lj>` lj/cut/coul/cut
+* :doc:`pair\_style <pair_lj>` lj/cut/coul/long
+
+* :doc:`pair\_style <pair_hbond_dreiding>` hbond/dreiding/lj
+* :doc:`pair\_style <pair_hbond_dreiding>` hbond/dreiding/morse
+
+* :doc:`special\_bonds <special_bonds>` dreiding
+
+
+----------
+
+
+.. _howto-MacKerell:
+
+
+
+**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
+.. _howto-Cornell:
+
+
+
+**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+
+.. _howto-Sun:
+
+
+
+**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
+
+.. _howto-Mayo:
+
+
+
+**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst
new file mode 100644
index 0000000000..4819ea97df
--- /dev/null
+++ b/doc/src/Howto_body.rst
@@ -0,0 +1,519 @@
+Body particles
+==============
+
+**Overview:**
+
+In LAMMPS, body particles are generalized finite-size particles.
+Individual body particles can represent complex entities, such as
+surface meshes of discrete points, collections of sub-particles,
+deformable objects, etc.  Note that other kinds of finite-size
+spherical and aspherical particles are also supported by LAMMPS, such
+as spheres, ellipsoids, line segments, and triangles, but they are
+simpler entities that body particles.  See the :doc:`Howto spherical <Howto_spherical>` doc page for a general overview of all
+these particle types.
+
+Body particles are used via the :doc:`atom\_style body <atom_style>`
+command.  It takes a body style as an argument.  The current body
+styles supported by LAMMPS are as follows.  The name in the first
+column is used as the *bstyle* argument for the :doc:`atom\_style body <atom_style>` command.
+
++----------------------+---------------------------------------------------+
+| *nparticle*          | rigid body with N sub-particles                   |
++----------------------+---------------------------------------------------+
+| *rounded/polygon*    | 2d polygons with N vertices                       |
++----------------------+---------------------------------------------------+
+| *rounded/polyhedron* | 3d polyhedra with N vertices, E edges and F faces |
++----------------------+---------------------------------------------------+
+
+The body style determines what attributes are stored for each body and
+thus how they can be used to compute pairwise body/body or
+bond/non-body (point particle) interactions.  More details of each
+style are described below.
+
+More styles may be added in the future.  See the :doc:`Modify body <Modify_body>` doc page for details on how to add a new body
+style to the code.
+
+
+----------
+
+
+**When to use body particles:**
+
+You should not use body particles to model a rigid body made of
+simpler particles (e.g. point, sphere, ellipsoid, line segment,
+triangular particles), if the interaction between pairs of rigid
+bodies is just the summation of pairwise interactions between the
+simpler particles.  LAMMPS already supports this kind of model via the
+:doc:`fix rigid <fix_rigid>` command.  Any of the numerous pair styles
+that compute interactions between simpler particles can be used.  The
+:doc:`fix rigid <fix_rigid>` command time integrates the motion of the
+rigid bodies.  All of the standard LAMMPS commands for thermostatting,
+adding constraints, performing output, etc will operate as expected on
+the simple particles.
+
+By contrast, when body particles are used, LAMMPS treats an entire
+body as a single particle for purposes of computing pairwise
+interactions, building neighbor lists, migrating particles between
+processors, output of particles to a dump file, etc.  This means that
+interactions between pairs of bodies or between a body and non-body
+(point) particle need to be encoded in an appropriate pair style.  If
+such a pair style were to mimic the :doc:`fix rigid <fix_rigid>` model,
+it would need to loop over the entire collection of interactions
+between pairs of simple particles within the two bodies, each time a
+single body/body interaction was computed.
+
+Thus it only makes sense to use body particles and develop such a pair
+style, when particle/particle interactions are more complex than what
+the :doc:`fix rigid <fix_rigid>` command can already calculate.  For
+example, consider particles with one or more of the following
+attributes:
+
+* represented by a surface mesh
+* represented by a collection of geometric entities (e.g. planes + spheres)
+* deformable
+* internal stress that induces fragmentation
+
+For these models, the interaction between pairs of particles is likely
+to be more complex than the summation of simple pairwise interactions.
+An example is contact or frictional forces between particles with
+planar surfaces that inter-penetrate.  Likewise, the body particle may
+store internal state, such as a stress tensor used to compute a
+fracture criterion.
+
+These are additional LAMMPS commands that can be used with body
+particles of different styles
+
++------------------------------------------------+-----------------------------------------------------+
+| :doc:`fix nve/body <fix_nve_body>`             | integrate motion of a body particle in NVE ensemble |
++------------------------------------------------+-----------------------------------------------------+
+| :doc:`fix nvt/body <fix_nvt_body>`             | ditto for NVT ensemble                              |
++------------------------------------------------+-----------------------------------------------------+
+| :doc:`fix npt/body <fix_npt_body>`             | ditto for NPT ensemble                              |
++------------------------------------------------+-----------------------------------------------------+
+| :doc:`fix nph/body <fix_nph_body>`             | ditto for NPH ensemble                              |
++------------------------------------------------+-----------------------------------------------------+
+| :doc:`compute body/local <compute_body_local>` | store sub-particle attributes of a body particle    |
++------------------------------------------------+-----------------------------------------------------+
+| :doc:`compute temp/body <compute_temp_body>`   | compute temperature of body particles               |
++------------------------------------------------+-----------------------------------------------------+
+| :doc:`dump local <dump>`                       | output sub-particle attributes of a body particle   |
++------------------------------------------------+-----------------------------------------------------+
+| :doc:`dump image <dump_image>`                 | output body particle attributes as an image         |
++------------------------------------------------+-----------------------------------------------------+
+
+The pair styles defined for use with specific body styles are listed
+in the sections below.
+
+
+----------
+
+
+**Specifics of body style nparticle:**
+
+The *nparticle* body style represents body particles as a rigid body
+with a variable number N of sub-particles.  It is provided as a
+vanilla, prototypical example of a body particle, although as
+mentioned above, the :doc:`fix rigid <fix_rigid>` command already
+duplicates its functionality.
+
+The atom\_style body command for this body style takes two additional
+arguments:
+
+
+.. parsed-literal::
+
+   atom_style body nparticle Nmin Nmax
+   Nmin = minimum # of sub-particles in any body in the system
+   Nmax = maximum # of sub-particles in any body in the system
+
+The Nmin and Nmax arguments are used to bound the size of data
+structures used internally by each particle.
+
+When the :doc:`read\_data <read_data>` command reads a data file for this
+body style, the following information must be provided for each entry
+in the *Bodies* section of the data file:
+
+
+.. parsed-literal::
+
+   atom-ID 1 M
+   N
+   ixx iyy izz ixy ixz iyz
+   x1 y1 z1
+   ...
+   xN yN zN
+
+where M = 6 + 3\*N, and N is the number of sub-particles in the body
+particle.
+
+The integer line has a single value N.  The floating point line(s)
+list 6 moments of inertia followed by the coordinates of the N
+sub-particles (x1 to zN) as 3N values.  These values can be listed on
+as many lines as you wish; see the :doc:`read\_data <read_data>` command
+for more details.
+
+The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
+values consistent with the current orientation of the rigid body
+around its center of mass.  The values are with respect to the
+simulation box XYZ axes, not with respect to the principal axes of the
+rigid body itself.  LAMMPS performs the latter calculation internally.
+The coordinates of each sub-particle are specified as its x,y,z
+displacement from the center-of-mass of the body particle.  The
+center-of-mass position of the particle is specified by the x,y,z
+values in the *Atoms* section of the data file, as is the total mass
+of the body particle.
+
+The :doc:`pair\_style body/nparticle <pair_body_nparticle>` command can be used
+with this body style to compute body/body and body/non-body interactions.
+
+For output purposes via the :doc:`compute body/local <compute_body_local>` and :doc:`dump local <dump>`
+commands, this body style produces one datum for each of the N
+sub-particles in a body particle.  The datum has 3 values:
+
+
+.. parsed-literal::
+
+   1 = x position of sub-particle
+   2 = y position of sub-particle
+   3 = z position of sub-particle
+
+These values are the current position of the sub-particle within the
+simulation domain, not a displacement from the center-of-mass (COM) of
+the body particle itself.  These values are calculated using the
+current COM and orientation of the body particle.
+
+For images created by the :doc:`dump image <dump_image>` command, if the
+*body* keyword is set, then each body particle is drawn as a
+collection of spheres, one for each sub-particle.  The size of each
+sphere is determined by the *bflag1* parameter for the *body* keyword.
+The *bflag2* argument is ignored.
+
+
+----------
+
+
+**Specifics of body style rounded/polygon:**
+
+The *rounded/polygon* body style represents body particles as a 2d
+polygon with a variable number of N vertices.  This style can only be
+used for 2d models; see the :doc:`boundary <boundary>` command.  See the
+"pair\_style body/rounded/polygon" doc page for a diagram of two
+squares with rounded circles at the vertices.  Special cases for N = 1
+(circle) and N = 2 (rod with rounded ends) can also be specified.
+
+One use of this body style is for 2d discrete element models, as
+described in :ref:`Fraige <body-Fraige>`.
+
+Similar to body style *nparticle*\ , the atom\_style body command for
+this body style takes two additional arguments:
+
+
+.. parsed-literal::
+
+   atom_style body rounded/polygon Nmin Nmax
+   Nmin = minimum # of vertices in any body in the system
+   Nmax = maximum # of vertices in any body in the system
+
+The Nmin and Nmax arguments are used to bound the size of data
+structures used internally by each particle.
+
+When the :doc:`read\_data <read_data>` command reads a data file for this
+body style, the following information must be provided for each entry
+in the *Bodies* section of the data file:
+
+
+.. parsed-literal::
+
+   atom-ID 1 M
+   N
+   ixx iyy izz ixy ixz iyz
+   x1 y1 z1
+   ...
+   xN yN zN
+   i j j k k ...
+   diameter
+
+where M = 6 + 3\*N + 2\*N + 1, and N is the number of vertices in the
+body particle.
+
+The integer line has a single value N.  The floating point line(s)
+list 6 moments of inertia followed by the coordinates of the N
+vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by
+2N vertex indices corresponding to the end points of the N edges,
+followed by a single diameter value = the rounded diameter of the
+circle that surrounds each vertex. The diameter value can be different
+for each body particle. These floating-point values can be listed on
+as many lines as you wish; see the :doc:`read\_data <read_data>` command
+for more details.
+
+The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
+values consistent with the current orientation of the rigid body
+around its center of mass.  The values are with respect to the
+simulation box XYZ axes, not with respect to the principal axes of the
+rigid body itself.  LAMMPS performs the latter calculation internally.
+The coordinates of each vertex are specified as its x,y,z displacement
+from the center-of-mass of the body particle.  The center-of-mass
+position of the particle is specified by the x,y,z values in the
+*Atoms* section of the data file.
+
+For example, the following information would specify a square particle
+whose edge length is sqrt(2) and rounded diameter is 1.0.  The
+orientation of the square is aligned with the xy coordinate axes which
+is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
+1 1 4 0 0 0. Note that only Izz matters in 2D simulations.
+
+
+.. parsed-literal::
+
+   3 1 27
+   4
+   1 1 4 0 0 0
+   -0.7071 -0.7071 0
+   -0.7071 0.7071 0
+   0.7071 0.7071 0
+   0.7071 -0.7071 0
+   0 1
+   1 2
+   2 3
+   3 0
+   1.0
+
+A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends
+by circles of diameter 0.5, is specified as follows:
+
+
+.. parsed-literal::
+
+   1 1 13
+   2
+   1 1 1.33333 0 0 0
+   -2 0 0
+   2 0 0
+   0.5
+
+A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
+
+
+.. parsed-literal::
+
+   1 1 10
+   1
+   1 1 4.5 0 0 0
+   0 0 0
+   3.0
+
+The :doc:`pair\_style body/rounded/polygon <pair_body_rounded_polygon>`
+command can be used with this body style to compute body/body
+interactions.  The :doc:`fix wall/body/polygon <fix_wall_body_polygon>`
+command can be used with this body style to compute the interaction of
+body particles with a wall.
+
+
+----------
+
+
+**Specifics of body style rounded/polyhedron:**
+
+The *rounded/polyhedron* body style represents body particles as a 3d
+polyhedron with a variable number of N vertices, E edges and F faces.
+This style can only be used for 3d models; see the
+:doc:`boundary <boundary>` command.  See the "pair\_style
+body/rounded/polygon" doc page for a diagram of a two 2d squares with
+rounded circles at the vertices.  A 3d cube with rounded spheres at
+the 8 vertices and 12 rounded edges would be similar.  Special cases
+for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be
+specified.
+
+This body style is for 3d discrete element models, as described in
+:ref:`Wang <body-Wang>`.
+
+Similar to body style *rounded/polygon*\ , the atom\_style body command
+for this body style takes two additional arguments:
+
+
+.. parsed-literal::
+
+   atom_style body rounded/polyhedron Nmin Nmax
+   Nmin = minimum # of vertices in any body in the system
+   Nmax = maximum # of vertices in any body in the system
+
+The Nmin and Nmax arguments are used to bound the size of data
+structures used internally by each particle.
+
+When the :doc:`read\_data <read_data>` command reads a data file for this
+body style, the following information must be provided for each entry
+in the *Bodies* section of the data file:
+
+
+.. parsed-literal::
+
+   atom-ID 3 M
+   N E F
+   ixx iyy izz ixy ixz iyz
+   x1 y1 z1
+   ...
+   xN yN zN
+   0 1
+   1 2
+   2 3
+   ...
+   0 1 2 -1
+   0 2 3 -1
+   ...
+   1 2 3 4
+   diameter
+
+where M = 6 + 3\*N + 2\*E + 4\*F + 1, and N is the number of vertices in
+the body particle, E = number of edges, F = number of faces.
+
+The integer line has three values: number of vertices (N), number of
+edges (E) and number of faces (F). The floating point line(s) list 6
+moments of inertia followed by the coordinates of the N vertices (x1
+to zN) as 3N values, followed by 2N vertex indices corresponding to
+the end points of the E edges, then 4\*F vertex indices defining F
+faces.  The last value is the diameter value = the rounded diameter of
+the sphere that surrounds each vertex. The diameter value can be
+different for each body particle. These floating-point values can be
+listed on as many lines as you wish; see the
+:doc:`read\_data <read_data>` command for more details.  Because the
+maximum number of vertices per face is hard-coded to be 4
+(i.e. quadrilaterals), faces with more than 4 vertices need to be
+split into triangles or quadrilaterals.  For triangular faces, the
+last vertex index should be set to -1.
+
+The ordering of the 4 vertices within a face should follow
+the right-hand rule so that the normal vector of the face points
+outwards from the center of mass.
+
+The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
+values consistent with the current orientation of the rigid body
+around its center of mass.  The values are with respect to the
+simulation box XYZ axes, not with respect to the principal axes of the
+rigid body itself.  LAMMPS performs the latter calculation internally.
+The coordinates of each vertex are specified as its x,y,z displacement
+from the center-of-mass of the body particle.  The center-of-mass
+position of the particle is specified by the x,y,z values in the
+*Atoms* section of the data file.
+
+For example, the following information would specify a cubic particle
+whose edge length is 2.0 and rounded diameter is 0.5.
+The orientation of the cube is aligned with the xyz coordinate axes
+which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz
+iyz = 0.667 0.667 0.667 0 0 0.
+
+
+.. parsed-literal::
+
+   1 3 79
+   8 12 6
+   0.667 0.667 0.667 0 0 0
+   1 1 1
+   1 -1 1
+   -1 -1 1
+   -1 1 1
+   1 1 -1
+   1 -1 -1
+   -1 -1 -1
+   -1 1 -1
+   0 1
+   1 2
+   2 3
+   3 0
+   4 5
+   5 6
+   6 7
+   7 4
+   0 4
+   1 5
+   2 6
+   3 7
+   0 1 2 3
+   4 5 6 7
+   0 1 5 4
+   1 2 6 5
+   2 3 7 6
+   3 0 4 7
+   0.5
+
+A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends
+by circles of diameter 0.5, is specified as follows:
+
+
+.. parsed-literal::
+
+   1 1 13
+   2
+   0 1.33333 1.33333 0 0 0
+   -2 0 0
+   2 0 0
+   0.5
+
+A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
+
+
+.. parsed-literal::
+
+   1 1 10
+   1
+   0.9 0.9 0.9 0 0 0
+   0 0 0
+   3.0
+
+The :doc:`pair\_style body/rounded/polhedron <pair_body_rounded_polyhedron>` command can
+be used with this body style to compute body/body interactions.  The
+:doc:`fix wall/body/polyhedron <fix_wall_body_polygon>` command can be
+used with this body style to compute the interaction of body particles
+with a wall.
+
+
+----------
+
+
+For output purposes via the :doc:`compute body/local <compute_body_local>` and :doc:`dump local <dump>`
+commands, this body style produces one datum for each of the N
+sub-particles in a body particle.  The datum has 3 values:
+
+
+.. parsed-literal::
+
+   1 = x position of vertex
+   2 = y position of vertex
+   3 = z position of vertex
+
+These values are the current position of the vertex within the
+simulation domain, not a displacement from the center-of-mass (COM) of
+the body particle itself.  These values are calculated using the
+current COM and orientation of the body particle.
+
+For images created by the :doc:`dump image <dump_image>` command, if the
+*body* keyword is set, then each body particle is drawn as a polygon
+consisting of N line segments.  Note that the line segments are drawn
+between the N vertices, which does not correspond exactly to the
+physical extent of the body (because the :doc:`pair\_style rounded/polygon <pair_body_rounded_polygon>` defines finite-size
+spheres at those point and the line segments between the spheres are
+tangent to the spheres).  The drawn diameter of each line segment is
+determined by the *bflag1* parameter for the *body* keyword.  The
+*bflag2* argument is ignored.
+
+
+----------
+
+
+.. _body-Fraige:
+
+
+
+**(Fraige)** F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
+Particuology, 6, 455 (2008).
+
+.. _body-Wang:
+
+
+
+**(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
+Matter, 13, 1 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_chunk.rst b/doc/src/Howto_chunk.rst
new file mode 100644
index 0000000000..337a24c9b7
--- /dev/null
+++ b/doc/src/Howto_chunk.rst
@@ -0,0 +1,219 @@
+Use chunks to calculate system properties
+=========================================
+
+In LAMMS, "chunks" are collections of atoms, as defined by the
+:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns
+each atom to a chunk ID (or to no chunk at all).  The number of chunks
+and the assignment of chunk IDs to atoms can be static or change over
+time.  Examples of "chunks" are molecules or spatial bins or atoms
+with similar values (e.g. coordination number or potential energy).
+
+The per-atom chunk IDs can be used as input to two other kinds of
+commands, to calculate various properties of a system:
+
+* :doc:`fix ave/chunk <fix_ave_chunk>`
+* any of the :doc:`compute \*/chunk <compute>` commands
+
+Here a brief overview for each of the 4 kinds of chunk-related commands
+is provided.  Then some examples are given of how to compute different
+properties with chunk commands.
+
+Compute chunk/atom command:
+---------------------------
+
+This compute can assign atoms to chunks of various styles.  Only atoms
+in the specified group and optional specified region are assigned to a
+chunk.  Here are some possible chunk definitions:
+
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+| atoms in same molecule                                  | chunk ID = molecule ID                                                                                                          |
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+| atoms of same atom type                                 | chunk ID = atom type                                                                                                            |
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+| all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom                                                                                      |
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+| atoms in same cluster                                   | chunk ID = output of :doc:`compute cluster/atom <compute_cluster_atom>` command                                                 |
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+| atoms in same spatial bin                               | chunk ID = bin ID                                                                                                               |
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+| atoms in same rigid body                                | chunk ID = molecule ID used to define rigid bodies                                                                              |
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+| atoms with similar potential energy                     | chunk ID = output of :doc:`compute pe/atom <compute_pe_atom>`                                                                   |
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+| atoms with same local defect structure                  | chunk ID = output of :doc:`compute centro/atom <compute_centro_atom>` or :doc:`compute coord/atom <compute_coord_atom>` command |
++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+
+
+Note that chunk IDs are integer values, so for atom properties or
+computes that produce a floating point value, they will be truncated
+to an integer.  You could also use the compute in a variable that
+scales the floating point value to spread it across multiple integers.
+
+Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
+pencils, 3d bins = boxes, spherical bins, cylindrical bins.
+
+This compute also calculates the number of chunks *Nchunk*\ , which is
+used by other commands to tally per-chunk data.  *Nchunk* can be a
+static value or change over time (e.g. the number of clusters).  The
+chunk ID for an individual atom can also be static (e.g. a molecule
+ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
+
+Note that this compute allows the per-atom output of other
+:doc:`computes <compute>`, :doc:`fixes <fix>`, and
+:doc:`variables <variable>` to be used to define chunk IDs for each
+atom.  This means you can write your own compute or fix to output a
+per-atom quantity to use as chunk ID.  See the :doc:`Modify <Modify>`
+doc pages for info on how to do this.  You can also define a :doc:`per-atom variable <variable>` in the input script that uses a formula to
+generate a chunk ID for each atom.
+
+Fix ave/chunk command:
+----------------------
+
+This fix takes the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input.  For each chunk,
+it then sums one or more specified per-atom values over the atoms in
+each chunk.  The per-atom values can be any atom property, such as
+velocity, force, charge, potential energy, kinetic energy, stress,
+etc.  Additional keywords are defined for per-chunk properties like
+density and temperature.  More generally any per-atom value generated
+by other :doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom variables <variable>`, can be summed over atoms in each chunk.
+
+Similar to other averaging fixes, this fix allows the summed per-chunk
+values to be time-averaged in various ways, and output to a file.  The
+fix produces a global array as output with one row of values per
+chunk.
+
+Compute \*/chunk commands:
+--------------------------
+
+The following computes operate on chunks of atoms to produce per-chunk
+values.  Any compute whose style name ends in "/chunk" is in this
+category:
+
+* :doc:`compute com/chunk <compute_com_chunk>`
+* :doc:`compute gyration/chunk <compute_gyration_chunk>`
+* :doc:`compute inertia/chunk <compute_inertia_chunk>`
+* :doc:`compute msd/chunk <compute_msd_chunk>`
+* :doc:`compute property/chunk <compute_property_chunk>`
+* :doc:`compute temp/chunk <compute_temp_chunk>`
+* :doc:`compute torque/chunk <compute_vcm_chunk>`
+* :doc:`compute vcm/chunk <compute_vcm_chunk>`
+
+They each take the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input.  As their names
+indicate, they calculate the center-of-mass, radius of gyration,
+moments of inertia, mean-squared displacement, temperature, torque,
+and velocity of center-of-mass for each chunk of atoms.  The :doc:`compute property/chunk <compute_property_chunk>` command can tally the
+count of atoms in each chunk and extract other per-chunk properties.
+
+The reason these various calculations are not part of the :doc:`fix ave/chunk command <fix_ave_chunk>`, is that each requires a more
+complicated operation than simply summing and averaging over per-atom
+values in each chunk.  For example, many of them require calculation
+of a center of mass, which requires summing mass\*position over the
+atoms and then dividing by summed mass.
+
+All of these computes produce a global vector or global array as
+output, wih one or more values per chunk.  The output can be used in
+various ways:
+
+* As input to the :doc:`fix ave/time <fix_ave_time>` command, which can
+  write the values to a file and optionally time average them.
+* As input to the :doc:`fix ave/histo <fix_ave_histo>` command to
+  histogram values across chunks.  E.g. a histogram of cluster sizes or
+  molecule diffusion rates.
+* As input to special functions of :doc:`equal-style variables <variable>`, like sum() and max() and ave().  E.g. to
+  find the largest cluster or fastest diffusing molecule or average
+  radius-of-gyration of a set of molecules (chunks).
+
+Other chunk commands:
+---------------------
+
+* :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
+* :doc:`compute reduce/chunk <compute_reduce_chunk>`
+
+The :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command
+spreads per-chunk values to each atom in the chunk, producing per-atom
+values as its output.  This can be useful for outputting per-chunk
+values to a per-atom :doc:`dump file <dump>`.  Or for using an atom's
+associated chunk value in an :doc:`atom-style variable <variable>`.  Or
+as input to the :doc:`fix ave/chunk <fix_ave_chunk>` command to
+spatially average per-chunk values calculated by a per-chunk compute.
+
+The :doc:`compute reduce/chunk <compute_reduce_chunk>` command reduces a
+peratom value across the atoms in each chunk to produce a value per
+chunk.  When used with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can
+create peratom values that induce a new set of chunks with a second
+:doc:`compute chunk/atom <compute_chunk_atom>` command.
+
+Example calculations with chunks
+--------------------------------
+
+Here are examples using chunk commands to calculate various
+properties:
+
+(1) Average velocity in each of 1000 2d spatial bins:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
+   fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
+
+(2) Temperature in each spatial bin, after subtracting a flow
+velocity:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
+   compute vbias all temp/profile 1 0 0 y 10
+   fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
+
+(3) Center of mass of each molecule:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all com/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+(4) Total force on each molecule and ave/max across all molecules:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
+   variable xave equal ave(f_1[2])
+   variable xmax equal max(f_1[2])
+   thermo 1000
+   thermo_style custom step temp v_xave v_xmax
+
+(5) Histogram of cluster sizes:
+
+
+.. parsed-literal::
+
+   compute cluster all cluster/atom 1.0
+   compute cc1 all chunk/atom c_cluster compress yes
+   compute size all property/chunk cc1 count
+   fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
+
+(6) An example for using a per-chunk value to apply per-atom forces to
+compress individual polymer chains (molecules) in a mixture, is
+explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
+
+(7) An example for using one set of per-chunk values for molecule
+chunks, to create a 2nd set of micelle-scale chunks (clustered
+molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page.
+
+(8) An example for using one set of per-chunk values (dipole moment
+vectors) for molecule chunks, spreading the values to each atom in
+each chunk, then defining a second set of chunks as spatial bins, and
+using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an
+average dipole moment vector for each bin.  This example is explained
+on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
+command doc page.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_client_server.rst b/doc/src/Howto_client_server.rst
new file mode 100644
index 0000000000..6e36369667
--- /dev/null
+++ b/doc/src/Howto_client_server.rst
@@ -0,0 +1,135 @@
+Using LAMMPS in client/server mode
+==================================
+
+Client/server coupling of two codes is where one code is the "client"
+and sends request messages to a "server" code.  The server responds to
+each request with a reply message.  This enables the two codes to work
+in tandem to perform a simulation.  LAMMPS can act as either a client
+or server code.
+
+Some advantages of client/server coupling are that the two codes run
+as stand-alone executables; they are not linked together.  Thus
+neither code needs to have a library interface.  This often makes it
+easier to run the two codes on different numbers of processors.  If a
+message protocol (format and content) is defined for a particular kind
+of simulation, then in principle any code that implements the
+client-side protocol can be used in tandem with any code that
+implements the server-side protocol, without the two codes needing to
+know anything more specific about each other.
+
+A simple example of client/server coupling is where LAMMPS is the
+client code performing MD timestepping.  Each timestep it sends a
+message to a server quantum code containing current coords of all the
+atoms.  The quantum code computes energy and forces based on the
+coords.  It returns them as a message to LAMMPS, which completes the
+timestep.
+
+Alternate methods for code coupling with LAMMPS are described on
+the :doc:`Howto couple <Howto_couple>` doc page.
+
+LAMMPS support for client/server coupling is in its :ref:`MESSAGE package <PKG-MESSAGE>` which implements several
+commands that enable LAMMPS to act as a client or server, as discussed
+below.  The MESSAGE package also wraps a client/server library called
+CSlib which enables two codes to exchange messages in different ways,
+either via files, sockets, or MPI.  The CSlib is provided with LAMMPS
+in the lib/message dir.  The CSlib has its own
+`website <http://cslib.sandia.gov>`_ with documentation and test
+programs.
+
+.. note::
+
+   For client/server coupling to work between LAMMPS and another
+   code, the other code also has to use the CSlib.  This can sometimes be
+   done without any modifications to the other code by simply wrapping it
+   with a Python script that exchanges CSlib messages with LAMMPS and
+   prepares input for or processes output from the other code.  The other
+   code also has to implement a matching protocol for the format and
+   content of messages that LAMMPS exchanges with it.
+
+These are the commands currently in the MESSAGE package for two
+protocols, MD and MC (Monte Carlo).  New protocols can easily be
+defined and added to this directory, where LAMMPS acts as either the
+client or server.
+
+* :doc:`message <message>`
+* :doc:`fix client md <fix_client_md>` = LAMMPS is a client for running MD
+* :doc:`server md <server_md>` = LAMMPS is a server for computing MD forces
+* :doc:`server mc <server_mc>` = LAMMPS is a server for computing a Monte Carlo energy
+
+The server doc files give details of the message protocols
+for data that is exchanged between the client and server.
+
+These example directories illustrate how to use LAMMPS as either a
+client or server code:
+
+* examples/message
+* examples/COUPLE/README
+* examples/COUPLE/lammps\_mc
+* examples/COUPLE/lammps\_vasp
+
+The examples/message dir couples a client instance of LAMMPS to a
+server instance of LAMMPS.
+
+The lammps\_mc dir shows how to couple LAMMPS as a server to a simple
+Monte Carlo client code as the driver.
+
+The lammps\_vasp dir shows how to couple LAMMPS as a client code
+running MD timestepping to VASP acting as a server providing quantum
+DFT forces, through a Python wrapper script on VASP.
+
+Here is how to launch a client and server code together for any of the
+4 modes of message exchange that the :doc:`message <message>` command
+and the CSlib support.  Here LAMMPS is used as both the client and
+server code.  Another code could be substituted for either.
+
+The examples below show launching both codes from the same window (or
+batch script), using the "&" character to launch the first code in the
+background.  For all modes except *mpi/one*\ , you could also launch the
+codes in separate windows on your desktop machine.  It does not
+matter whether you launch the client or server first.
+
+In these examples either code can be run on one or more processors.
+If running in a non-MPI mode (file or zmq) you can launch a code on a
+single processor without using mpirun.
+
+IMPORTANT: If you run in mpi/two mode, you must launch both codes via
+mpirun, even if one or both of them runs on a single processor.  This
+is so that MPI can figure out how to connect both MPI processes
+together to exchange MPI messages between them.
+
+For message exchange in *file*\ , *zmq*\ , or *mpi/two* modes:
+
+
+.. parsed-literal::
+
+   % mpirun -np 1 lmp_mpi -log log.client < in.client &
+   % mpirun -np 2 lmp_mpi -log log.server < in.server
+
+   % mpirun -np 4 lmp_mpi -log log.client < in.client &
+   % mpirun -np 1 lmp_mpi -log log.server < in.server
+
+   % mpirun -np 2 lmp_mpi -log log.client < in.client &
+   % mpirun -np 4 lmp_mpi -log log.server < in.server
+
+For message exchange in *mpi/one* mode:
+
+Launch both codes in a single mpirun command:
+
+
+.. parsed-literal::
+
+   mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server
+
+The two -np values determine how many procs the client and the server
+run on.
+
+A LAMMPS executable run in this manner must use the -mpicolor color
+command-line option as their its option, where color is an integer
+label that will be used to distinguish one executable from another in
+the multiple executables that the mpirun command launches.  In this
+example the client was colored with a 0, and the server with a 1.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_coreshell.rst b/doc/src/Howto_coreshell.rst
new file mode 100644
index 0000000000..c39f87fac2
--- /dev/null
+++ b/doc/src/Howto_coreshell.rst
@@ -0,0 +1,271 @@
+Adiabatic core/shell model
+==========================
+
+The adiabatic core-shell model by :ref:`Mitchell and Fincham <MitchellFincham>` is a simple method for adding polarizability
+to a system.  In order to mimic the electron shell of an ion, a
+satellite particle is attached to it. This way the ions are split into
+a core and a shell where the latter is meant to react to the
+electrostatic environment inducing polarizability.  See the :doc:`Howto polarizable <Howto_polarizable>` doc page for a discussion of all
+the polarizable models available in LAMMPS.
+
+Technically, shells are attached to the cores by a spring force f =
+k\*r where k is a parameterized spring constant and r is the distance
+between the core and the shell. The charges of the core and the shell
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This
+setup introduces the ion polarizability (alpha) given by
+alpha = q(shell)\^2 / k. In a
+similar fashion the mass of the ion is distributed on the core and the
+shell with the core having the larger mass.
+
+To run this model in LAMMPS, :doc:`atom\_style <atom_style>` *full* can
+be used since atom charge and bonds are needed.  Each kind of
+core/shell pair requires two atom types and a bond type.  The core and
+shell of a core/shell pair should be bonded to each other with a
+harmonic bond that provides the spring force. For example, a data file
+for NaCl, as found in examples/coreshell, has this format:
+
+
+.. parsed-literal::
+
+   432   atoms  # core and shell atoms
+   216   bonds  # number of core/shell springs
+
+   4     atom types  # 2 cores and 2 shells for Na and Cl
+   2     bond types
+
+   0.0 24.09597 xlo xhi
+   0.0 24.09597 ylo yhi
+   0.0 24.09597 zlo zhi
+
+   Masses       # core/shell mass ratio = 0.1
+
+   1 20.690784  # Na core
+   2 31.90500   # Cl core
+   3 2.298976   # Na shell
+   4 3.54500    # Cl shell
+
+   Atoms
+
+   1    1    2   1.5005    0.00000000   0.00000000   0.00000000 # core of core/shell pair 1
+   2    1    4  -2.5005    0.00000000   0.00000000   0.00000000 # shell of core/shell pair 1
+   3    2    1   1.5056    4.01599500   4.01599500   4.01599500 # core of core/shell pair 2
+   4    2    3  -0.5056    4.01599500   4.01599500   4.01599500 # shell of core/shell pair 2
+   (...)
+
+   Bonds   # Bond topology for spring forces
+
+   1     2     1     2   # spring for core/shell pair 1
+   2     2     3     4   # spring for core/shell pair 2
+   (...)
+
+Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
+defined between the shells.  Coulombic interactions are defined
+between all cores and shells.  If desired, additional bonds can be
+specified between cores.
+
+The :doc:`special\_bonds <special_bonds>` command should be used to
+turn-off the Coulombic interaction within core/shell pairs, since that
+interaction is set by the bond spring.  This is done using the
+:doc:`special\_bonds <special_bonds>` command with a 1-2 weight = 0.0,
+which is the default value.  It needs to be considered whether one has
+to adjust the :doc:`special\_bonds <special_bonds>` weighting according
+to the molecular topology since the interactions of the shells are
+bypassed over an extra bond.
+
+Note that this core/shell implementation does not require all ions to
+be polarized.  One can mix core/shell pairs and ions without a
+satellite particle if desired.
+
+Since the core/shell model permits distances of r = 0.0 between the
+core and shell, a pair style with a "cs" suffix needs to be used to
+implement a valid long-range Coulombic correction.  Several such pair
+styles are provided in the CORESHELL package.  See :doc:`this doc page <pair_cs>` for details.  All of the core/shell enabled pair
+styles require the use of a long-range Coulombic solver, as specified
+by the :doc:`kspace\_style <kspace_style>` command.  Either the PPPM or
+Ewald solvers can be used.
+
+For the NaCL example problem, these pair style and bond style settings
+are used:
+
+
+.. parsed-literal::
+
+   pair_style      born/coul/long/cs 20.0 20.0
+   pair_coeff      \* \*      0.0 1.000   0.00  0.00   0.00
+   pair_coeff      3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+   pair_coeff      3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+   pair_coeff      4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
+   bond_style      harmonic
+   bond_coeff      1 63.014 0.0
+   bond_coeff      2 25.724 0.0
+
+When running dynamics with the adiabatic core/shell model, the
+following issues should be considered.  The relative motion of
+the core and shell particles corresponds to the polarization,
+hereby an instantaneous relaxation of the shells is approximated
+and a fast core/shell spring frequency ensures a nearly constant
+internal kinetic energy during the simulation.
+Thermostats can alter this polarization behavior, by scaling the
+internal kinetic energy, meaning the shell will not react freely to
+its electrostatic environment.
+Therefore it is typically desirable to decouple the relative motion of
+the core/shell pair, which is an imaginary degree of freedom, from the
+real physical system.  To do that, the :doc:`compute temp/cs <compute_temp_cs>` command can be used, in conjunction with
+any of the thermostat fixes, such as :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>`.  This compute uses the center-of-mass velocity
+of the core/shell pairs to calculate a temperature, and insures that
+velocity is what is rescaled for thermostatting purposes.  This
+compute also works for a system with both core/shell pairs and
+non-polarized ions (ions without an attached satellite particle).  The
+:doc:`compute temp/cs <compute_temp_cs>` command requires input of two
+groups, one for the core atoms, another for the shell atoms.
+Non-polarized ions which might also be included in the treated system
+should not be included into either of these groups, they are taken
+into account by the *group-ID* (2nd argument) of the compute.  The
+groups can be defined using the :doc:`group *type*\ <group>` command.
+Note that to perform thermostatting using this definition of
+temperature, the :doc:`fix modify temp <fix_modify>` command should be
+used to assign the compute to the thermostat fix.  Likewise the
+:doc:`thermo\_modify temp <thermo_modify>` command can be used to make
+this temperature be output for the overall system.
+
+For the NaCl example, this can be done as follows:
+
+
+.. parsed-literal::
+
+   group cores type 1 2
+   group shells type 3 4
+   compute CSequ all temp/cs cores shells
+   fix thermoberendsen all temp/berendsen 1427 1427 0.4    # thermostat for the true physical system
+   fix thermostatequ all nve                               # integrator as needed for the berendsen thermostat
+   fix_modify thermoberendsen temp CSequ
+   thermo_modify temp CSequ                                # output of center-of-mass derived temperature
+
+The pressure for the core/shell system is computed via the regular
+LAMMPS convention by :ref:`treating the cores and shells as individual particles <MitchellFincham2>`. For the thermo output of the pressure
+as well as for the application of a barostat, it is necessary to
+use an additional :doc:`pressure <compute_pressure>` compute based on
+the default :doc:`temperature <compute_temp>` and specifying it as a
+second argument in :doc:`fix modify <fix_modify>` and
+:doc:`thermo\_modify <thermo_modify>` resulting in:
+
+
+.. parsed-literal::
+
+   (...)
+   compute CSequ all temp/cs cores shells
+   compute thermo_press_lmp all pressure thermo_temp       # pressure for individual particles
+   thermo_modify temp CSequ press thermo_press_lmp         # modify thermo to regular pressure
+   fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
+   fix_modify press_bar temp CSequ press thermo_press_lmp  # pressure modification for correct kinetic scalar
+
+If :doc:`compute temp/cs <compute_temp_cs>` is used, the decoupled
+relative motion of the core and the shell should in theory be
+stable.  However numerical fluctuation can introduce a small
+momentum to the system, which is noticeable over long trajectories.
+Therefore it is recommendable to use the :doc:`fix momentum <fix_momentum>` command in combination with :doc:`compute temp/cs <compute_temp_cs>` when equilibrating the system to
+prevent any drift.
+
+When initializing the velocities of a system with core/shell pairs, it
+is also desirable to not introduce energy into the relative motion of
+the core/shell particles, but only assign a center-of-mass velocity to
+the pairs.  This can be done by using the *bias* keyword of the
+:doc:`velocity create <velocity>` command and assigning the :doc:`compute temp/cs <compute_temp_cs>` command to the *temp* keyword of the
+:doc:`velocity <velocity>` command, e.g.
+
+
+.. parsed-literal::
+
+   velocity all create 1427 134 bias yes temp CSequ
+   velocity all scale 1427 temp CSequ
+
+To maintain the correct polarizability of the core/shell pairs, the
+kinetic energy of the internal motion shall remain nearly constant.
+Therefore the choice of spring force and mass ratio need to ensure
+much faster relative motion of the 2 atoms within the core/shell pair
+than their center-of-mass velocity. This allows the shells to
+effectively react instantaneously to the electrostatic environment and
+limits energy transfer to or from the core/shell oscillators.
+This fast movement also dictates the timestep that can be used.
+
+The primary literature of the adiabatic core/shell model suggests that
+the fast relative motion of the core/shell pairs only allows negligible
+energy transfer to the environment.
+The mentioned energy transfer will typically lead to a small drift
+in total energy over time.  This internal energy can be monitored
+using the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`compute temp/chunk <compute_temp_chunk>` commands.  The internal kinetic
+energies of each core/shell pair can then be summed using the sum()
+special function of the :doc:`variable <variable>` command.  Or they can
+be time/averaged and output using the :doc:`fix ave/time <fix_ave_time>`
+command.  To use these commands, each core/shell pair must be defined
+as a "chunk".  If each core/shell pair is defined as its own molecule,
+the molecule ID can be used to define the chunks.  If cores are bonded
+to each other to form larger molecules, the chunks can be identified
+by the :doc:`fix property/atom <fix_property_atom>` via assigning a
+core/shell ID to each atom using a special field in the data file read
+by the :doc:`read\_data <read_data>` command.  This field can then be
+accessed by the :doc:`compute property/atom <compute_property_atom>`
+command, to use as input to the :doc:`compute chunk/atom <compute_chunk_atom>` command to define the core/shell
+pairs as chunks.
+
+For example if core/shell pairs are the only molecules:
+
+
+.. parsed-literal::
+
+   read_data NaCl_CS_x0.1_prop.data
+   compute prop all property/atom molecule
+   compute cs_chunk all chunk/atom c_prop
+   compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
+   fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
+
+For example if core/shell pairs and other molecules are present:
+
+
+.. parsed-literal::
+
+   fix csinfo all property/atom i_CSID                       # property/atom command
+   read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
+   compute prop all property/atom i_CSID
+   (...)
+
+The additional section in the date file would be formatted like this:
+
+
+.. parsed-literal::
+
+   CS-Info         # header of additional section
+
+   1   1           # column 1 = atom ID, column 2 = core/shell ID
+   2   1
+   3   2
+   4   2
+   5   3
+   6   3
+   7   4
+   8   4
+   (...)
+
+
+----------
+
+
+.. _MitchellFincham:
+
+
+
+**(Mitchell and Fincham)** Mitchell, Fincham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+
+.. _MitchellFincham2:
+
+
+
+**(Fincham)** Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
+6, 393-404 (1994).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_couple.rst b/doc/src/Howto_couple.rst
new file mode 100644
index 0000000000..e92e985ab4
--- /dev/null
+++ b/doc/src/Howto_couple.rst
@@ -0,0 +1,125 @@
+Coupling LAMMPS to other codes
+==============================
+
+LAMMPS is designed to allow it to be coupled to other codes.  For
+example, a quantum mechanics code might compute forces on a subset of
+atoms and pass those forces to LAMMPS.  Or a continuum finite element
+(FE) simulation might use atom positions as boundary conditions on FE
+nodal points, compute a FE solution, and return interpolated forces on
+MD atoms.
+
+LAMMPS can be coupled to other codes in at least 4 ways.  Each has
+advantages and disadvantages, which you'll have to think about in the
+context of your application.
+
+
+----------
+
+
+(1) Define a new :doc:`fix <fix>` command that calls the other code.  In
+this scenario, LAMMPS is the driver code.  During its timestepping,
+the fix is invoked, and can make library calls to the other code,
+which has been linked to LAMMPS as a library.  This is the way the
+`POEMS <poems_>`_ package that performs constrained rigid-body motion on
+groups of atoms is hooked to LAMMPS.  See the :doc:`fix poems <fix_poems>` command for more details.  See the
+:doc:`Modify <Modify>` doc pages for info on how to add a new fix to
+LAMMPS.
+
+.. _poems: http://www.rpi.edu/~anderk5/lab
+
+
+
+
+----------
+
+
+(2) Define a new LAMMPS command that calls the other code.  This is
+conceptually similar to method (1), but in this case LAMMPS and the
+other code are on a more equal footing.  Note that now the other code
+is not called during the timestepping of a LAMMPS run, but between
+runs.  The LAMMPS input script can be used to alternate LAMMPS runs
+with calls to the other code, invoked via the new command.  The
+:doc:`run <run>` command facilitates this with its *every* option, which
+makes it easy to run a few steps, invoke the command, run a few steps,
+invoke the command, etc.
+
+In this scenario, the other code can be called as a library, as in
+(1), or it could be a stand-alone code, invoked by a system() call
+made by the command (assuming your parallel machine allows one or more
+processors to start up another program).  In the latter case the
+stand-alone code could communicate with LAMMPS through files that the
+command writes and reads.
+
+See the :doc:`Modify command <Modify_command>` doc page for info on how
+to add a new command to LAMMPS.
+
+
+----------
+
+
+(3) Use LAMMPS as a library called by another code.  In this case the
+other code is the driver and calls LAMMPS as needed.  Or a wrapper
+code could link and call both LAMMPS and another code as libraries.
+Again, the :doc:`run <run>` command has options that allow it to be
+invoked with minimal overhead (no setup or clean-up) if you wish to do
+multiple short runs, driven by another program.
+
+Examples of driver codes that call LAMMPS as a library are included in
+the examples/COUPLE directory of the LAMMPS distribution; see
+examples/COUPLE/README for more details:
+
+* simple: simple driver programs in C++ and C which invoke LAMMPS as a
+  library
+* lammps\_quest: coupling of LAMMPS and `Quest <quest_>`_, to run classical
+  MD with quantum forces calculated by a density functional code
+* lammps\_spparks: coupling of LAMMPS and `SPPARKS <spparks_>`_, to couple
+  a kinetic Monte Carlo model for grain growth using MD to calculate
+  strain induced across grain boundaries
+
+
+.. _quest: http://dft.sandia.gov/Quest
+
+
+
+.. _spparks: http://www.sandia.gov/~sjplimp/spparks.html
+
+
+
+The :doc:`Build basics <Build_basics>` doc page describes how to build
+LAMMPS as a library.  Once this is done, you can interface with LAMMPS
+either via C++, C, Fortran, or Python (or any other language that
+supports a vanilla C-like interface).  For example, from C++ you could
+create one (or more) "instances" of LAMMPS, pass it an input script to
+process, or execute individual commands, all by invoking the correct
+class methods in LAMMPS.  From C or Fortran you can make function
+calls to do the same things.  See the :doc:`Python <Python_head>` doc
+pages for a description of the Python wrapper provided with LAMMPS
+that operates through the LAMMPS library interface.
+
+The files src/library.cpp and library.h contain the C-style interface
+to LAMMPS.  See the :doc:`Howto library <Howto_library>` doc page for a
+description of the interface and how to extend it for your needs.
+
+Note that the lammps\_open() function that creates an instance of
+LAMMPS takes an MPI communicator as an argument.  This means that
+instance of LAMMPS will run on the set of processors in the
+communicator.  Thus the calling code can run LAMMPS on all or a subset
+of processors.  For example, a wrapper script might decide to
+alternate between LAMMPS and another code, allowing them both to run
+on all the processors.  Or it might allocate half the processors to
+LAMMPS and half to the other code and run both codes simultaneously
+before syncing them up periodically.  Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.
+
+
+----------
+
+
+(4) Couple LAMMPS with another code in a client/server mode.  This is
+described on the :doc:`Howto client/server <Howto_client_server>` doc
+page.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_diffusion.rst b/doc/src/Howto_diffusion.rst
new file mode 100644
index 0000000000..8c5dbd7a8f
--- /dev/null
+++ b/doc/src/Howto_diffusion.rst
@@ -0,0 +1,32 @@
+Calculate diffusion coefficients
+================================
+
+The diffusion coefficient D of a material can be measured in at least
+2 ways using various options in LAMMPS.  See the examples/DIFFUSE
+directory for scripts that implement the 2 methods discussed here for
+a simple Lennard-Jones fluid model.
+
+The first method is to measure the mean-squared displacement (MSD) of
+the system, via the :doc:`compute msd <compute_msd>` command.  The slope
+of the MSD versus time is proportional to the diffusion coefficient.
+The instantaneous MSD values can be accumulated in a vector via the
+:doc:`fix vector <fix_vector>` command, and a line fit to the vector to
+compute its slope via the :doc:`variable slope <variable>` function, and
+thus extract D.
+
+The second method is to measure the velocity auto-correlation function
+(VACF) of the system, via the :doc:`compute vacf <compute_vacf>`
+command.  The time-integral of the VACF is proportional to the
+diffusion coefficient.  The instantaneous VACF values can be
+accumulated in a vector via the :doc:`fix vector <fix_vector>` command,
+and time integrated via the :doc:`variable trap <variable>` function,
+and thus extract D.
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_dispersion.rst b/doc/src/Howto_dispersion.rst
new file mode 100644
index 0000000000..c6a0813516
--- /dev/null
+++ b/doc/src/Howto_dispersion.rst
@@ -0,0 +1,105 @@
+Long-range dispersion settings
+==============================
+
+The PPPM method computes interactions by splitting the pair potential
+into two parts, one of which is computed in a normal pairwise fashion,
+the so-called real-space part, and one of which is computed using the
+Fourier transform, the so called reciprocal-space or kspace part.  For
+both parts, the potential is not computed exactly but is approximated.
+Thus, there is an error in both parts of the computation, the
+real-space and the kspace error. The just mentioned facts are true
+both for the PPPM for Coulomb as well as dispersion interactions. The
+deciding difference - and also the reason why the parameters for
+pppm/disp have to be selected with more care - is the impact of the
+errors on the results: The kspace error of the PPPM for Coulomb and
+dispersion interaction and the real-space error of the PPPM for
+Coulomb interaction have the character of noise. In contrast, the
+real-space error of the PPPM for dispersion has a clear physical
+interpretation: the underprediction of cohesion. As a consequence, the
+real-space error has a much stronger effect than the kspace error on
+simulation results for pppm/disp.  Parameters must thus be chosen in a
+way that this error is much smaller than the kspace error.
+
+When using pppm/disp and not making any specifications on the PPPM
+parameters via the kspace modify command, parameters will be tuned
+such that the real-space error and the kspace error are equal.  This
+will result in simulations that are either inaccurate or slow, both of
+which is not desirable. For selecting parameters for the pppm/disp
+that provide fast and accurate simulations, there are two approaches,
+which both have their up- and downsides.
+
+The first approach is to set desired real-space an kspace accuracies
+via the *kspace\_modify force/disp/real* and *kspace\_modify
+force/disp/kspace* commands. Note that the accuracies have to be
+specified in force units and are thus dependent on the chosen unit
+settings. For real units, 0.0001 and 0.002 seem to provide reasonable
+accurate and efficient computations for the real-space and kspace
+accuracies.  0.002 and 0.05 work well for most systems using lj
+units. PPPM parameters will be generated based on the desired
+accuracies. The upside of this approach is that it usually provides a
+good set of parameters and will work for both the *kspace\_modify diff
+ad* and *kspace\_modify diff ik* options.  The downside of the method
+is that setting the PPPM parameters will take some time during the
+initialization of the simulation.
+
+The second approach is to set the parameters for the pppm/disp
+explicitly using the *kspace\_modify mesh/disp*, *kspace\_modify
+order/disp*, and *kspace\_modify gewald/disp* commands. This approach
+requires a more experienced user who understands well the impact of
+the choice of parameters on the simulation accuracy and
+performance. This approach provides a fast initialization of the
+simulation. However, it is sensitive to errors: A combination of
+parameters that will perform well for one system might result in
+far-from-optimal conditions for other simulations. For example,
+parameters that provide accurate and fast computations for
+all-atomistic force fields can provide insufficient accuracy or
+united-atomistic force fields (which is related to that the latter
+typically have larger dispersion coefficients).
+
+To avoid inaccurate or inefficient simulations, the pppm/disp stops
+simulations with an error message if no action is taken to control the
+PPPM parameters. If the automatic parameter generation is desired and
+real-space and kspace accuracies are desired to be equal, this error
+message can be suppressed using the *kspace\_modify disp/auto yes*
+command.
+
+A reasonable approach that combines the upsides of both methods is to
+make the first run using the *kspace\_modify force/disp/real* and
+*kspace\_modify force/disp/kspace* commands, write down the PPPM
+parameters from the output, and specify these parameters using the
+second approach in subsequent runs (which have the same composition,
+force field, and approximately the same volume).
+
+Concerning the performance of the pppm/disp there are two more things
+to consider. The first is that when using the pppm/disp, the cutoff
+parameter does no longer affect the accuracy of the simulation
+(subject to that gewald/disp is adjusted when changing the cutoff).
+The performance can thus be increased by examining different values
+for the cutoff parameter. A lower bound for the cutoff is only set by
+the truncation error of the repulsive term of pair potentials.
+
+The second is that the mixing rule of the pair style has an impact on
+the computation time when using the pppm/disp. Fastest computations
+are achieved when using the geometric mixing rule. Using the
+arithmetic mixing rule substantially increases the computational cost.
+The computational overhead can be reduced using the *kspace\_modify
+mix/disp geom* and *kspace\_modify splittol* commands. The first
+command simply enforces geometric mixing of the dispersion
+coefficients in kspace computations.  This introduces some error in
+the computations but will also significantly speed-up the
+simulations. The second keyword sets the accuracy with which the
+dispersion coefficients are approximated using a matrix factorization
+approach.  This may result in better accuracy then using the first
+command, but will usually also not provide an equally good increase of
+efficiency.
+
+Finally, pppm/disp can also be used when no mixing rules apply.
+This can be achieved using the *kspace\_modify mix/disp none* command.
+Note that the code does not check automatically whether any mixing
+rule is fulfilled. If mixing rules do not apply, the user will have
+to specify this command explicitly.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_drude.rst b/doc/src/Howto_drude.rst
new file mode 100644
index 0000000000..d786c66ef8
--- /dev/null
+++ b/doc/src/Howto_drude.rst
@@ -0,0 +1,72 @@
+Drude induced dipoles
+=====================
+
+The thermalized Drude model represents induced dipoles by a pair of
+charges (the core atom and the Drude particle) connected by a harmonic
+spring.  See the :doc:`Howto polarizable <Howto_polarizable>` doc page
+for a discussion of all the polarizable models available in LAMMPS.
+
+The Drude model has a number of features aimed at its use in
+molecular systems (:ref:`Lamoureux and Roux <howto-Lamoureux>`):
+
+* Thermostatting of the additional degrees of freedom associated with the
+  induced dipoles at very low temperature, in terms of the reduced
+  coordinates of the Drude particles with respect to their cores. This
+  makes the trajectory close to that of relaxed induced dipoles.
+* Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
+  pair represents a single (polarizable) atom, so the special screening
+  factors in a covalent structure should be the same for the core and
+  the Drude particle.  Drude particles have to inherit the 1-2, 1-3, 1-4
+  special neighbor relations from their respective cores.
+* Stabilization of the interactions between induced dipoles. Drude
+  dipoles on covalently bonded atoms interact too strongly due to the
+  short distances, so an atom may capture the Drude particle of a
+  neighbor, or the induced dipoles within the same molecule may align
+  too much. To avoid this, damping at short range can be done by Thole
+  functions (for which there are physical grounds). This Thole damping
+  is applied to the point charges composing the induced dipole (the
+  charge of the Drude particle and the opposite charge on the core, not
+  to the total charge of the core atom).
+
+A detailed tutorial covering the usage of Drude induced dipoles in
+LAMMPS is on the :doc:`Howto drude2e <Howto_drude2>` doc page.
+
+As with the core-shell model, the cores and Drude particles should
+appear in the data file as standard atoms. The same holds for the
+springs between them, which are described by standard harmonic bonds.
+The nature of the atoms (core, Drude particle or non-polarizable) is
+specified via the :doc:`fix drude <fix_drude>` command.  The special
+list of neighbors is automatically refactored to account for the
+equivalence of core and Drude particles as regards special 1-2 to 1-4
+screening. It may be necessary to use the *extra/special/per/atom*
+keyword of the :doc:`read\_data <read_data>` command. If using :doc:`fix shake <fix_shake>`, make sure no Drude particle is in this fix
+group.
+
+There are two ways to thermostat the Drude particles at a low
+temperature: use either :doc:`fix langevin/drude <fix_langevin_drude>`
+for a Langevin thermostat, or :doc:`fix drude/transform/\* <fix_drude_transform>` for a Nose-Hoover
+thermostat. The former requires use of the command :doc:`comm\_modify vel yes <comm_modify>`. The latter requires two separate integration
+fixes like *nvt* or *npt*\ . The correct temperatures of the reduced
+degrees of freedom can be calculated using the :doc:`compute temp/drude <compute_temp_drude>`. This requires also to use the
+command *comm\_modify vel yes*.
+
+Short-range damping of the induced dipole interactions can be achieved
+using Thole functions through the :doc:`pair style thole <pair_thole>` in :doc:`pair\_style hybrid/overlay <pair_hybrid>`
+with a Coulomb pair style. It may be useful to use *coul/long/cs* or
+similar from the CORESHELL package if the core and Drude particle come
+too close, which can cause numerical issues.
+
+
+----------
+
+
+.. _howto-Lamoureux:
+
+
+
+**(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst
new file mode 100644
index 0000000000..baf9a38f08
--- /dev/null
+++ b/doc/src/Howto_drude2.rst
@@ -0,0 +1,542 @@
+Tutorial for Thermalized Drude oscillators in LAMMPS
+====================================================
+
+This tutorial explains how to use Drude oscillators in LAMMPS to
+simulate polarizable systems using the USER-DRUDE package. As an
+illustration, the input files for a simulation of 250 phenol molecules
+are documented. First of all, LAMMPS has to be compiled with the
+USER-DRUDE package activated. Then, the data file and input scripts
+have to be modified to include the Drude dipoles and how to handle
+them.
+
+
+----------
+
+
+**Overview of Drude induced dipoles**
+
+Polarizable atoms acquire an induced electric dipole moment under the
+action of an external electric field, for example the electric field
+created by the surrounding particles.  Drude oscillators represent
+these dipoles by two fixed charges: the core (DC) and the Drude
+particle (DP) bound by a harmonic potential. The Drude particle can be
+thought of as the electron cloud whose center can be displaced from
+the position of the corresponding nucleus.
+
+The sum of the masses of a core-Drude pair should be the mass of the
+initial (unsplit) atom, :math:`m_C + m_D = m`.  The sum of their charges
+should be the charge of the initial (unsplit) atom, :math:`q_C + q_D = q`.
+A harmonic potential between the core and Drude partners should be
+present, with force constant :math:`k_D` and an equilibrium distance of
+zero. The (half-)stiffness of the :doc:`harmonic bond <bond_harmonic>`
+:math:`K_D = k_D/2` and the Drude charge :math:`q_D` are related to the atom
+polarizability :math:`\alpha` by
+
+
+.. math::
+
+   \begin{equation} K_D = \frac 1 2\, \frac {q_D^2} \alpha\end{equation}
+
+Ideally, the mass of the Drude particle should be small, and the
+stiffness of the harmonic bond should be large, so that the Drude
+particle remains close ot the core. The values of Drude mass, Drude
+charge, and force constant can be chosen following different
+strategies, as in the following examples of polarizable force
+fields:
+
+* :ref:`Lamoureux and Roux <Lamoureux2>` suggest adopting a global half-stiffness, :math:`K_D` = 500 kcal/(mol Ang :math:`{}^2`) - which corresponds to a force constant :math:`k_D` = 4184 kJ/(mol Ang :math:`{}^2`) - for all types of core-Drude bond, a global mass :math:`m_D` = 0.4 g/mol (or u) for all types of Drude particles, and to calculate the Drude charges for individual atom types from the atom polarizabilities using equation (1). This choice is followed in the polarizable CHARMM force field.
+* Alternately :ref:`Schroeder and Steinhauser <Schroeder>` suggest adopting a global charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K.
+* In both these force fields hydrogen atoms are treated as non-polarizable.
+
+
+The motion of of the Drude particles can be calculated by minimizing
+the energy of the induced dipoles at each timestep, by an iterative,
+self-consistent procedure. The Drude particles can be massless and
+therefore do not contribute to the kinetic energy. However, the
+relaxed method is computational slow. An extended-lagrangian method
+can be used to calculate the positions of the Drude particles, but
+this requires them to have mass. It is important in this case to
+decouple the degrees of freedom associated with the Drude oscillators
+from those of the normal atoms. Thermalizing the Drude dipoles at
+temperatures comparable to the rest of the simulation leads to several
+problems (kinetic energy transfer, very short timestep, etc.), which
+can be remedied by the "cold Drude" technique (:ref:`Lamoureux and Roux <Lamoureux2>`).
+
+Two closely related models are used to represent polarization through
+"charges on a spring": the core-shell model and the Drude
+model. Although the basic idea is the same, the core-shell model is
+normally used for ionic/crystalline materials, whereas the Drude model
+is normally used for molecular systems and fluid states. In ionic
+crystals the symmetry around each ion and the distance between them
+are such that the core-shell model is sufficiently stable. But to be
+applicable to molecular/covalent systems the Drude model includes two
+important features:
+
+#. The possibility to thermostat the additional degrees of freedom associated with the induced dipoles at very low temperature, in terms of the reduced coordinates of the Drude particles with respect to their cores. This makes the trajectory close to that of relaxed induced dipoles.
+#. The Drude dipoles on covalently bonded atoms interact too strongly due to the short distances, so an atom may capture the Drude particle (shell) of a neighbor, or the induced dipoles within the same molecule may align too much.  To avoid this, damping at short of the interactions between the point charges composing the induced dipole can be done by :ref:`Thole <Thole2>` functions.
+
+
+
+----------
+
+
+**Preparation of the data file**
+
+The data file is similar to a standard LAMMPS data file for
+*atom\_style full*.  The DPs and the *harmonic bonds* connecting them
+to their DC should appear in the data file as normal atoms and bonds.
+
+You can use the *polarizer* tool (Python script distributed with the
+USER-DRUDE package) to convert a non-polarizable data file (here
+*data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ )
+
+
+.. parsed-literal::
+
+   polarizer -q -f phenol.dff data.102494.lmp data-p.lmp
+
+This will automatically insert the new atoms and bonds.
+The masses and charges of DCs and DPs are computed
+from *phenol.dff*\ , as well as the DC-DP bond constants.  The file
+*phenol.dff* contains the polarizabilities of the atom types
+and the mass of the Drude particles, for instance:
+
+
+.. parsed-literal::
+
+   # units: kJ/mol, A, deg
+   # kforce is in the form k/2 r_D\^2
+   # type  m_D/u   q_D/e    k_D   alpha/A3  thole
+   OH      0.4    -1.0    4184.0   0.63     0.67
+   CA      0.4    -1.0    4184.0   1.36     2.51
+   CAI     0.4    -1.0    4184.0   1.09     2.51
+
+The hydrogen atoms are absent from this file, so they will be treated
+as non-polarizable atoms.  In the non-polarizable data file
+*data.102494.lmp*\ , atom names corresponding to the atom type numbers
+have to be specified as comments at the end of lines of the *Masses*
+section.  You probably need to edit it to add these names. It should
+look like
+
+
+.. parsed-literal::
+
+   Masses
+
+   1 12.011 # CAI
+   2 12.011 # CA
+   3 15.999 # OH
+   4 1.008  # HA
+   5 1.008  # HO
+
+
+----------
+
+
+**Basic input file**
+
+The atom style should be set to (or derive from) *full*\ , so that you
+can define atomic charges and molecular bonds, angles, dihedrals...
+
+The *polarizer* tool also outputs certain lines related to the input
+script (the use of these lines will be explained below).  In order for
+LAMMPS to recognize that you are using Drude oscillators, you should
+use the fix *drude*\ . The command is
+
+
+.. parsed-literal::
+
+   fix DRUDE all drude C C C N N D D D
+
+The N, C, D following the *drude* keyword have the following meaning:
+There is one tag for each atom type. This tag is C for DCs, D for DPs
+and N for non-polarizable atoms.  Here the atom types 1 to 3 (C and O
+atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and
+the atom types 6 to 8 are the newly created DPs.
+
+By recognizing the fix *drude*\ , LAMMPS will find and store matching
+DC-DP pairs and will treat DP as equivalent to their DC in the
+*special bonds* relations.  It may be necessary to extend the space
+for storing such special relations.  In this case extra space should
+be reserved by using the *extra/special/per/atom* keyword of either
+the :doc:`read\_data <read_data>` or :doc:`create\_box <create_box>`
+command.  With our phenol, there is 1 more special neighbor for which
+space is required.  Otherwise LAMMPS crashes and gives the required
+value.
+
+
+.. parsed-literal::
+
+   read_data data-p.lmp extra/special/per/atom 1
+
+Let us assume we want to run a simple NVT simulation at 300 K.  Note
+that Drude oscillators need to be thermalized at a low temperature in
+order to approximate a self-consistent field (SCF), therefore it is not
+possible to simulate an NVE ensemble with this package.  Since dipoles
+are approximated by a charged DC-DP pair, the *pair\_style* must
+include Coulomb interactions, for instance *lj/cut/coul/long* with
+*kspace\_style pppm*. For example, with a cutoff of 10. and a precision
+1.e-4:
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/coul/long 10.0
+   kspace_style pppm 1.0e-4
+
+As compared to the non-polarizable input file, *pair\_coeff* lines need
+to be added for the DPs.  Since the DPs have no Lennard-Jones
+interactions, their *epsilon* is 0. so the only *pair\_coeff* line
+that needs to be added is
+
+
+.. parsed-literal::
+
+   pair_coeff \* 6\* 0.0 0.0 # All-DPs
+
+Now for the thermalization, the simplest choice is to use the :doc:`fix langevin/drude <fix_langevin_drude>`.
+
+
+.. parsed-literal::
+
+   fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+
+This applies a Langevin thermostat at temperature 300. to the centers
+of mass of the DC-DP pairs, with relaxation time 100 and with random
+seed 12345.  This fix applies also a Langevin thermostat at temperature
+1. to the relative motion of the DPs around their DCs, with relaxation
+time 20 and random seed 13977.  Only the DCs and non-polarizable
+atoms need to be in this fix's group.  LAMMPS will thermostat the DPs
+together with their DC.  For this, ghost atoms need to know their
+velocities. Thus you need to add the following command:
+
+
+.. parsed-literal::
+
+   comm_modify vel yes
+
+In order to avoid that the center of mass of the whole system
+drifts due to the random forces of the Langevin thermostat on DCs, you
+can add the *zero yes* option at the end of the fix line.
+
+If the fix *shake* is used to constrain the C-H bonds, it should be
+invoked after the fix *langevin/drude* for more accuracy.
+
+
+.. parsed-literal::
+
+   fix SHAKE ATOMS shake 0.0001 20 0 t 4 5
+
+.. note::
+
+   The group of the fix *shake* must not include the DPs.  If the
+   group *ATOMS* is defined by non-DPs atom types, you could use
+
+Since the fix *langevin/drude* does not perform time integration (just
+modification of forces but no position/velocity updates), the fix
+*nve* should be used in conjunction.
+
+
+.. parsed-literal::
+
+   fix NVE all nve
+
+Finally, do not forget to update the atom type elements if you use
+them in a *dump\_modify ... element ...* command, by adding the element
+type of the DPs. Here for instance
+
+
+.. parsed-literal::
+
+   dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz
+   dump_modify DUMP element C C O H H D D D
+
+The input file should now be ready for use!
+
+You will notice that the global temperature *thermo\_temp* computed by
+LAMMPS is not 300. K as wanted.  This is because LAMMPS treats DPs as
+standard atoms in his default compute.  If you want to output the
+temperatures of the DC-DP pair centers of mass and of the DPs relative
+to their DCs, you should use the :doc:`compute temp\_drude <compute_temp_drude>`
+
+
+.. parsed-literal::
+
+   compute TDRUDE all temp/drude
+
+And then output the correct temperatures of the Drude oscillators
+using *thermo\_style custom* with respectively *c\_TDRUDE[1]* and
+*c\_TDRUDE[2]*. These should be close to 300.0 and 1.0 on average.
+
+
+.. parsed-literal::
+
+   thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2]
+
+
+----------
+
+
+**Thole screening**
+
+Dipolar interactions represented by point charges on springs may not
+be stable, for example if the atomic polarizability is too high for
+instance, a DP can escape from its DC and be captured by another DC,
+which makes the force and energy diverge and the simulation
+crash. Even without reaching this extreme case, the correlation
+between nearby dipoles on the same molecule may be exaggerated.  Often,
+special bond relations prevent bonded neighboring atoms to see the
+charge of each other's DP, so that the problem does not always appear.
+It is possible to use screened dipole-dipole interactions by using the
+:doc:`*pair\_style thole* <pair_thole>`.  This is implemented as a
+correction to the Coulomb pair\_styles, which dampens at short distance
+the interactions between the charges representing the induced dipoles.
+It is to be used as *hybrid/overlay* with any standard *coul* pair
+style.  In our example, we would use
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0
+
+This tells LAMMPS that we are using two pair\_styles.  The first one is
+as above (\ *lj/cut/coul/long 10.0*\ ).  The second one is a *thole*
+pair\_style with default screening factor 2.6 (:ref:`Noskov <Noskov2>`) and
+cutoff 10.0.
+
+Since *hybrid/overlay* does not support mixing rules, the interaction
+coefficients of all the pairs of atom types with i < j should be
+explicitly defined.  The output of the *polarizer* script can be used
+to complete the *pair\_coeff* section of the input file.  In our
+example, this will look like:
+
+
+.. parsed-literal::
+
+   pair_coeff    1    1 lj/cut/coul/long    0.0700   3.550
+   pair_coeff    1    2 lj/cut/coul/long    0.0700   3.550
+   pair_coeff    1    3 lj/cut/coul/long    0.1091   3.310
+   pair_coeff    1    4 lj/cut/coul/long    0.0458   2.985
+   pair_coeff    2    2 lj/cut/coul/long    0.0700   3.550
+   pair_coeff    2    3 lj/cut/coul/long    0.1091   3.310
+   pair_coeff    2    4 lj/cut/coul/long    0.0458   2.985
+   pair_coeff    3    3 lj/cut/coul/long    0.1700   3.070
+   pair_coeff    3    4 lj/cut/coul/long    0.0714   2.745
+   pair_coeff    4    4 lj/cut/coul/long    0.0300   2.420
+   pair_coeff    \*    5 lj/cut/coul/long    0.0000   0.000
+   pair_coeff    \*   6\* lj/cut/coul/long    0.0000   0.000
+   pair_coeff    1    1 thole   1.090   2.510
+   pair_coeff    1    2 thole   1.218   2.510
+   pair_coeff    1    3 thole   0.829   1.590
+   pair_coeff    1    6 thole   1.090   2.510
+   pair_coeff    1    7 thole   1.218   2.510
+   pair_coeff    1    8 thole   0.829   1.590
+   pair_coeff    2    2 thole   1.360   2.510
+   pair_coeff    2    3 thole   0.926   1.590
+   pair_coeff    2    6 thole   1.218   2.510
+   pair_coeff    2    7 thole   1.360   2.510
+   pair_coeff    2    8 thole   0.926   1.590
+   pair_coeff    3    3 thole   0.630   0.670
+   pair_coeff    3    6 thole   0.829   1.590
+   pair_coeff    3    7 thole   0.926   1.590
+   pair_coeff    3    8 thole   0.630   0.670
+   pair_coeff    6    6 thole   1.090   2.510
+   pair_coeff    6    7 thole   1.218   2.510
+   pair_coeff    6    8 thole   0.829   1.590
+   pair_coeff    7    7 thole   1.360   2.510
+   pair_coeff    7    8 thole   0.926   1.590
+   pair_coeff    8    8 thole   0.630   0.670
+
+For the *thole* pair style the coefficients are
+
+#. the atom polarizability in units of cubic length
+#. the screening factor of the Thole function (optional, default value
+   specified by the pair\_style command)
+#. the cutoff (optional, default value defined by the pair\_style command)
+
+
+The special neighbors have charge-charge and charge-dipole
+interactions screened by the *coul* factors of the *special\_bonds*
+command (0.0, 0.0, and 0.5 in the example above).  Without using the
+pair\_style *thole*\ , dipole-dipole interactions are screened by the
+same factor.  By using the pair\_style *thole*\ , dipole-dipole
+interactions are screened by Thole's function, whatever their special
+relationship (except within each DC-DP pair of course).  Consider for
+example 1-2 neighbors: using the pair\_style *thole*\ , their dipoles
+will see each other (despite the *coul* factor being 0.) and the
+interactions between these dipoles will be damped by Thole's function.
+
+
+----------
+
+
+**Thermostats and barostats**
+
+Using a Nose-Hoover barostat with the *langevin/drude* thermostat is
+straightforward using fix *nph* instead of *nve*\ .  For example:
+
+
+.. parsed-literal::
+
+   fix NPH all nph iso 1. 1. 500
+
+It is also possible to use a Nose-Hoover instead of a Langevin
+thermostat.  This requires to use :doc:`\ *fix drude/transform*\ <fix_drude_transform>` just before and after the
+time integration fixes.  The *fix drude/transform/direct* converts the
+atomic masses, positions, velocities and forces into a reduced
+representation, where the DCs transform into the centers of mass of
+the DC-DP pairs and the DPs transform into their relative position
+with respect to their DC. The *fix drude/transform/inverse* performs
+the reverse transformation.  For a NVT simulation, with the DCs and
+atoms at 300 K and the DPs at 1 K relative to their DC one would use
+
+
+.. parsed-literal::
+
+   fix DIRECT all drude/transform/direct
+   fix NVT1 ATOMS nvt temp 300. 300. 100
+   fix NVT2 DRUDES nvt temp 1. 1. 20
+   fix INVERSE all drude/transform/inverse
+
+For our phenol example, the groups would be defined as
+
+
+.. parsed-literal::
+
+   group ATOMS  type 1 2 3 4 5 # DCs and non-polarizable atoms
+   group CORES  type 1 2 3     # DCs
+   group DRUDES type 6 7 8     # DPs
+
+Note that with the fixes *drude/transform*\ , it is not required to
+specify *comm\_modify vel yes* because the fixes do it anyway (several
+times and for the forces also).  To avoid the flying ice cube artifact
+:ref:`(Lamoureux) <Lamoureux2>`, where the atoms progressively freeze and the
+center of mass of the whole system drifts faster and faster, the *fix
+momentum* can be used. For instance:
+
+
+.. parsed-literal::
+
+   fix MOMENTUM all momentum 100 linear 1 1 1
+
+It is a bit more tricky to run a NPT simulation with Nose-Hoover
+barostat and thermostat.  First, the volume should be integrated only
+once. So the fix for DCs and atoms should be *npt* while the fix for
+DPs should be *nvt* (or vice versa).  Second, the *fix npt* computes a
+global pressure and thus a global temperature whatever the fix group.
+We do want the pressure to correspond to the whole system, but we want
+the temperature to correspond to the fix group only.  We must then use
+the *fix\_modify* command for this.  In the end, the block of
+instructions for thermostatting and barostatting will look like
+
+
+.. parsed-literal::
+
+   compute TATOMS ATOMS temp
+   fix DIRECT all drude/transform/direct
+   fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500
+   fix_modify NPT temp TATOMS press thermo_press
+   fix NVT DRUDES nvt temp 1. 1. 20
+   fix INVERSE all drude/transform/inverse
+
+
+----------
+
+
+**Rigid bodies**
+
+You may want to simulate molecules as rigid bodies (but polarizable).
+Common cases are water models such as :ref:`SWM4-NDP <SWM4-NDP>`, which is a
+kind of polarizable TIP4P water.  The rigid bodies and the DPs should
+be integrated separately, even with the Langevin thermostat.  Let us
+review the different thermostats and ensemble combinations.
+
+NVT ensemble using Langevin thermostat:
+
+
+.. parsed-literal::
+
+   comm_modify vel yes
+   fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+   fix RIGID ATOMS rigid/nve/small molecule
+   fix NVE DRUDES nve
+
+NVT ensemble using Nose-Hoover thermostat:
+
+
+.. parsed-literal::
+
+   fix DIRECT all drude/transform/direct
+   fix RIGID ATOMS rigid/nvt/small molecule temp 300. 300. 100
+   fix NVT DRUDES nvt temp 1. 1. 20
+   fix INVERSE all drude/transform/inverse
+
+NPT ensemble with Langevin thermostat:
+
+
+.. parsed-literal::
+
+   comm_modify vel yes
+   fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+   fix RIGID ATOMS rigid/nph/small molecule iso 1. 1. 500
+   fix NVE DRUDES nve
+
+NPT ensemble using Nose-Hoover thermostat:
+
+
+.. parsed-literal::
+
+   compute TATOM ATOMS temp
+   fix DIRECT all drude/transform/direct
+   fix RIGID ATOMS rigid/npt/small molecule temp 300. 300. 100 iso 1. 1. 500
+   fix_modify RIGID temp TATOM press thermo_press
+   fix NVT DRUDES nvt temp 1. 1. 20
+   fix INVERSE all drude/transform/inverse
+
+
+----------
+
+
+.. _Lamoureux2:
+
+
+
+**(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)
+
+.. _Schroeder:
+
+
+
+**(Schroeder)**  Schroeder and Steinhauser, J Chem Phys, 133,
+154511 (2010).
+
+.. _Jiang2:
+
+
+
+**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
+ J Phys Chem Lett, 2, 87-92 (2011).
+
+.. _Thole2:
+
+
+
+**(Thole)** Chem Phys, 59, 341 (1981).
+
+.. _Noskov2:
+
+
+
+**(Noskov)** Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).
+
+.. _SWM4-NDP:
+
+
+
+**(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
+Let, 418, 245-249 (2006)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_elastic.rst b/doc/src/Howto_elastic.rst
new file mode 100644
index 0000000000..f249ea2df7
--- /dev/null
+++ b/doc/src/Howto_elastic.rst
@@ -0,0 +1,49 @@
+Calculate elastic constants
+===========================
+
+Elastic constants characterize the stiffness of a material. The formal
+definition is provided by the linear relation that holds between the
+stress and strain tensors in the limit of infinitesimal deformation.
+In tensor notation, this is expressed as s\_ij = C\_ijkl \* e\_kl, where
+the repeated indices imply summation. s\_ij are the elements of the
+symmetric stress tensor. e\_kl are the elements of the symmetric strain
+tensor. C\_ijkl are the elements of the fourth rank tensor of elastic
+constants. In three dimensions, this tensor has 3\^4=81 elements. Using
+Voigt notation, the tensor can be written as a 6x6 matrix, where C\_ij
+is now the derivative of s\_i w.r.t. e\_j. Because s\_i is itself a
+derivative w.r.t. e\_i, it follows that C\_ij is also symmetric, with at
+most 7\*6/2 = 21 distinct elements.
+
+At zero temperature, it is easy to estimate these derivatives by
+deforming the simulation box in one of the six directions using the
+:doc:`change\_box <change_box>` command and measuring the change in the
+stress tensor. A general-purpose script that does this is given in the
+examples/elastic directory described on the :doc:`Examples <Examples>`
+doc page.
+
+Calculating elastic constants at finite temperature is more
+challenging, because it is necessary to run a simulation that performs
+time averages of differential properties. One way to do this is to
+measure the change in average stress tensor in an NVT simulations when
+the cell volume undergoes a finite deformation. In order to balance
+the systematic and statistical errors in this method, the magnitude of
+the deformation must be chosen judiciously, and care must be taken to
+fully equilibrate the deformed cell before sampling the stress
+tensor. Another approach is to sample the triclinic cell fluctuations
+that occur in an NPT simulation. This method can also be slow to
+converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`
+
+
+----------
+
+
+.. _Shinoda1:
+
+
+
+**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst
new file mode 100644
index 0000000000..d4925a8324
--- /dev/null
+++ b/doc/src/Howto_github.rst
@@ -0,0 +1,499 @@
+LAMMPS GitHub tutorial
+======================
+
+**written by Stefan Paquay**
+
+
+----------
+
+
+This document describes the process of how to use GitHub to integrate
+changes or additions you have made to LAMMPS into the official LAMMPS
+distribution.  It uses the process of updating this very tutorial as
+an example to describe the individual steps and options.  You need to
+be familiar with git and you may want to have a look at the
+`Git book <http://git-scm.com/book/>`_ to reacquaint yourself with some
+of the more advanced git features used below.
+
+As of fall 2016, submitting contributions to LAMMPS via pull requests
+on GitHub is the preferred option for integrating contributed features
+or improvements to LAMMPS, as it significantly reduces the amount of
+work required by the LAMMPS developers. Consequently, creating a pull
+request will increase your chances to have your contribution included
+and will reduce the time until the integration is complete. For more
+information on the requirements to have your code included into LAMMPS
+please see the :doc:`Modify contribute <Modify_contribute>` doc page.
+
+
+----------
+
+
+**Making an account**
+
+First of all, you need a GitHub account. This is fairly simple, just
+go to `GitHub <https://github.com>`_ and create an account by clicking
+the "Sign up for GitHub" button. Once your account is created, you
+can sign in by clicking the button in the top left and filling in your
+username or e-mail address and password.
+
+
+----------
+
+
+**Forking the repository**
+
+To get changes into LAMMPS, you need to first fork the `lammps/lammps`
+repository on GitHub. At the time of writing, *master* is the preferred
+target branch. Thus go to `LAMMPS on GitHub <https://github.com/lammps/lammps>`_
+and make sure branch is set to "master", as shown in the figure below.
+
+.. image:: JPG/tutorial_branch.png
+   :align: center
+
+If it is not, use the button to change it to *master*\ . Once it is, use the
+fork button to create a fork.
+
+.. image:: JPG/tutorial_fork.png
+   :align: center
+
+This will create a fork (which is essentially a copy, but uses less
+resources) of the LAMMPS repository under your own GitHub account. You
+can make changes in this fork and later file *pull requests* to allow
+the upstream repository to merge changes from your own fork into the one
+we just forked from (or others that were forked from the same repository).
+At the same time, you can set things up, so you can include changes from
+upstream into your repository and thus keep it in sync with the ongoing
+LAMMPS development.
+
+
+----------
+
+
+**Adding changes to your own fork**
+
+Additions to the upstream version of LAMMPS are handled using *feature
+branches*\ .  For every new feature, a so-called feature branch is
+created, which contains only those modification relevant to one specific
+feature. For example, adding a single fix would consist of creating a
+branch with only the fix header and source file and nothing else.  It is
+explained in more detail here: `feature branch workflow <https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow>`_.
+
+**Feature branches**
+
+First of all, create a clone of your version on github on your local
+machine via HTTPS:
+
+
+.. parsed-literal::
+
+     $ git clone https://github.com/<your user name>/lammps.git <some name>
+
+or, if you have set up your GitHub account for using SSH keys, via SSH:
+
+
+.. parsed-literal::
+
+     $ git clone git@github.com:<your user name>/lammps.git
+
+You can find the proper URL by clicking the "Clone or download"-button:
+
+.. image:: JPG/tutorial_https_block.png
+   :align: center
+
+The above command copies ("clones") the git repository to your local
+machine to a directory with the name you chose. If none is given, it will
+default to "lammps". Typical names are "mylammps" or something similar.
+
+You can use this local clone to make changes and
+test them without interfering with the repository on GitHub.
+
+To pull changes from upstream into this copy, you can go to the directory
+and use git pull:
+
+
+.. parsed-literal::
+
+     $ cd mylammps
+     $ git checkout master
+     $ git pull https://github.com/lammps/lammps
+
+You can also add this URL as a remote:
+
+
+.. parsed-literal::
+
+     $ git remote add lammps_upstream https://www.github.com/lammps/lammps
+
+At this point, you typically make a feature branch from the updated master
+branch for the feature you want to work on. This tutorial contains the
+workflow that updated this tutorial, and hence we will call the branch
+"github-tutorial-update":
+
+
+.. parsed-literal::
+
+    $ git checkout -b github-tutorial-update master
+
+Now that we have changed branches, we can make our changes to our local
+repository. Just remember that if you want to start working on another,
+unrelated feature, you should switch branches!
+
+**After changes are made**
+
+After everything is done, add the files to the branch and commit them:
+
+
+.. parsed-literal::
+
+    $ git add doc/src/Howto_github.txt
+    $ git add doc/src/JPG/tutorial\*.png
+
+.. warning::
+
+   Do not use *git commit -a* (or *git add -A*\ ).  The -a
+   flag (or -A flag) will automatically include \_all\\_ modified or new files
+   and that is rarely the behavior you want.  It can easily lead to
+   accidentally adding unrelated and unwanted changes into the repository.
+   Instead it is preferable to explicitly use *git add*\ , *git rm*\ , *git mv*
+   for adding, removing, renaming individual files, respectively, and then
+   *git commit* to finalize the commit.  Carefully check all pending
+   changes with *git status* before committing them.  If you find doing
+   this on the command line too tedious, consider using a GUI, for example
+   the one included in git distributions written in Tk, i.e. use *git gui*
+   (on some Linux distributions it may be required to install an additional
+   package to use it).
+
+After adding all files, the change set can be committed with some
+useful message that explains the change.
+
+
+.. parsed-literal::
+
+     $ git commit -m 'Finally updated the github tutorial'
+
+After the commit, the changes can be pushed to the same branch on GitHub:
+
+
+.. parsed-literal::
+
+   $ git push
+
+Git will ask you for your user name and password on GitHub if you have
+not configured anything. If your local branch is not present on GitHub yet,
+it will ask you to add it by running
+
+
+.. parsed-literal::
+
+     $ git push --set-upstream origin github-tutorial-update
+
+If you correctly type your user name and
+password, the feature branch should be added to your fork on GitHub.
+
+If you want to make really sure you push to the right repository
+(which is good practice), you can provide it explicitly:
+
+
+.. parsed-literal::
+
+   $ git push origin
+
+or using an explicit URL:
+
+
+.. parsed-literal::
+
+   $ git push git@github.com:Pakketeretet2/lammps.git
+
+
+----------
+
+
+**Filing a pull request**
+
+Up to this point in the tutorial, all changes were to *your* clones of
+LAMMPS.  Eventually, however, you want this feature to be included into
+the official LAMMPS version.  To do this, you will want to file a pull
+request by clicking on the "New pull request" button:
+
+.. image:: JPG/tutorial_new_pull_request.png
+   :align: center
+
+Make sure that the current branch is set to the correct one, which, in
+this case, is "github-tutorial-update". If done correctly, the only
+changes you will see are those that were made on this branch.
+
+This will open up a new window that lists changes made to the
+repository. If you are just adding new files, there is not much to do,
+but I suppose merge conflicts are to be resolved here if there are
+changes in existing files. If all changes can automatically be merged,
+green text at the top will say so and you can click the "Create pull
+request" button, see image.
+
+.. image:: JPG/tutorial_create_new_pull_request1.png
+   :align: center
+
+Before creating the pull request, make sure the short title is accurate
+and add a comment with details about your pull request.  Here you write
+what your modifications do and why they should be incorporated upstream.
+
+Note the checkbox that says "Allow edits from maintainers".
+This is checked by default checkbox (although in my version of Firefox, only the checkmark is visible):
+
+.. image:: JPG/tutorial_edits_maintainers.png
+   :align: center
+
+If it is checked, maintainers can immediately add their own edits to the
+pull request.  This helps the inclusion of your branch significantly, as
+simple/trivial changes can be added directly to your pull request branch
+by the LAMMPS maintainers.  The alternative would be that they make
+changes on their own version of the branch and file a reverse pull
+request to you.  Just leave this box checked unless you have a very good
+reason not to.
+
+Now just write some nice comments and click on "Create pull request".
+
+.. image:: JPG/tutorial_create_new_pull_request2.png
+   :align: center
+
+
+----------
+
+
+**After filing a pull request**
+
+.. note::
+
+   When you submit a pull request (or ask for a pull request) for the
+   first time, you will receive an invitation to become a LAMMPS project
+   collaborator. Please accept this invite as being a collaborator will
+   simplify certain administrative tasks and will probably speed up the
+   merging of your feature, too.
+
+You will notice that after filing the pull request, some checks are
+performed automatically:
+
+.. image:: JPG/tutorial_automated_checks.png
+   :align: center
+
+If all is fine, you will see this:
+
+.. image:: JPG/tutorial_automated_checks_passed.png
+   :align: center
+
+If any of the checks are failing, your pull request will not be
+processed, as your changes may break compilation for certain
+configurations or may not merge cleanly. It is your responsibility
+to remove the reason(s) for the failed test(s). If you need help
+with this, please contact the LAMMPS developers by adding a comment
+explaining your problems with resolving the failed tests.
+
+A few further interesting things (can) happen to pull requests before
+they are included.
+
+**Additional changes**
+
+First of all, any additional changes you push into your branch in your
+repository will automatically become part of the pull request:
+
+.. image:: JPG/tutorial_additional_changes.png
+   :align: center
+
+This means you can add changes that should be part of the feature after
+filing the pull request, which is useful in case you have forgotten
+them, or if a developer has requested that something needs to be changed
+before the feature can be accepted into the official LAMMPS version.
+After each push, the automated checks are run again.
+
+**Labels**
+
+LAMMPS developers may add labels to your pull request to assign it to
+categories (mostly for bookkeeping purposes), but a few of them are
+important: needs\_work, work\_in\_progress, test-for-regression, and
+full-regression-test. The first two indicate, that your pull request
+is not considered to be complete. With "needs\_work" the burden is on
+exclusively on you; while "work\_in\_progress" can also mean, that a
+LAMMPS developer may want to add changes. Please watch the comments
+to the pull requests. The two "test" labels are used to trigger
+extended tests before the code is merged. This is sometimes done by
+LAMMPS developers, if they suspect that there may be some subtle
+side effects from your changes. It is not done by default, because
+those tests are very time consuming.
+
+**Reviews**
+
+As of Summer 2018, a pull request needs at least 1 approving review
+from a LAMMPS developer with write access to the repository.
+In case your changes touch code that certain developers are associated
+with, they are auto-requested by the GitHub software.  Those associations
+are set in the file
+`.github/CODEOWNERS <https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS>`_
+Thus if you want to be automatically notified to review when anybody
+changes files or packages, that you have contributed to LAMMPS, you can
+add suitable patterns to that file, or a LAMMPS developer may add you.
+
+Otherwise, you can also manually request reviews from specific developers,
+or LAMMPS developers - in their assessment of your pull request - may
+determine who else should be reviewing your contribution and add that person.
+Through reviews, LAMMPS developers also may request specific changes from you.
+If those are not addressed, your pull requests cannot be merged.
+
+**Assignees**
+
+There is an assignee property for pull requests. If the request has not
+been reviewed by any developer yet, it is not assigned to anyone. After
+revision, a developer can choose to assign it to either a) you, b) a
+LAMMPS developer (including him/herself) or c) Axel Kohlmeyer (akohlmey).
+
+* Case a) happens if changes are required on your part
+* Case b) means that at the moment, it is being tested and reviewed by a
+  LAMMPS developer with the expectation that some changes would be required.
+  After the review, the developer can choose to implement changes directly
+  or suggest them to you.
+* Case c) means that the pull request has been assigned to the developer
+  overseeing the merging of pull requests into the master branch.
+
+In this case, Axel assigned the tutorial to Steve:
+
+.. image:: JPG/tutorial_steve_assignee.png
+   :align: center
+
+**Edits from LAMMPS maintainers**
+
+If you allowed edits from maintainers (the default), any LAMMPS
+maintainer can add changes to your pull request.  In this case, both
+Axel and Richard made changes to the tutorial:
+
+.. image:: JPG/tutorial_changes_others.png
+   :align: center
+
+**Reverse pull requests**
+
+Sometimes, however, you might not feel comfortable having other people
+push changes into your own branch, or maybe the maintainers are not sure
+their idea was the right one.  In such a case, they can make changes,
+reassign you as the assignee, and file a "reverse pull request", i.e.
+file a pull request in your GitHub repository to include changes in the
+branch, that you have submitted as a pull request yourself.  In that
+case, you can choose to merge their changes back into your branch,
+possibly make additional changes or corrections and proceed from there.
+It looks something like this:
+
+.. image:: JPG/tutorial_reverse_pull_request.png
+   :align: center
+
+For some reason, the highlighted button didn't work in my case, but I
+can go to my own repository and merge the pull request from there:
+
+.. image:: JPG/tutorial_reverse_pull_request2.png
+   :align: center
+
+Be sure to check the changes to see if you agree with them by clicking
+on the tab button:
+
+.. image:: JPG/tutorial_reverse_pull_request3.png
+   :align: center
+
+In this case, most of it is changes in the markup and a short rewrite of
+Axel's explanation of the "git gui" and "git add" commands.
+
+.. image:: JPG/tutorial_reverse_pull_request4.png
+   :align: center
+
+Because the changes are OK with us, we are going to merge by clicking on
+"Merge pull request".  After a merge it looks like this:
+
+.. image:: JPG/tutorial_reverse_pull_request5.png
+   :align: center
+
+Now, since in the meantime our local text for the tutorial also changed,
+we need to pull Axel's change back into our branch, and merge them:
+
+
+.. parsed-literal::
+
+    $ git add Howto_github.txt
+    $ git add JPG/tutorial_reverse_pull_request\*.png
+    $ git commit -m "Updated text and images on reverse pull requests"
+    $ git pull
+
+In this case, the merge was painless because git could auto-merge:
+
+.. image:: JPG/tutorial_reverse_pull_request6.png
+   :align: center
+
+With Axel's changes merged in and some final text updates, our feature
+branch is now perfect as far as we are concerned, so we are going to
+commit and push again:
+
+
+.. parsed-literal::
+
+    $ git add Howto_github.txt
+    $ git add JPG/tutorial_reverse_pull_request6.png
+    $ git commit -m "Merged Axel's suggestions and updated text"
+    $ git push git@github.com:Pakketeretet2/lammps
+
+This merge also shows up on the lammps GitHub page:
+
+.. image:: JPG/tutorial_reverse_pull_request7.png
+   :align: center
+
+
+----------
+
+
+**After a merge**
+
+When everything is fine, the feature branch is merged into the master branch:
+
+.. image:: JPG/tutorial_merged.png
+   :align: center
+
+Now one question remains: What to do with the feature branch that got
+merged into upstream?
+
+It is in principle safe to delete them from your own fork. This helps
+keep it a bit more tidy. Note that you first have to switch to another
+branch!
+
+
+.. parsed-literal::
+
+   $ git checkout master
+   $ git pull master
+   $ git branch -d github-tutorial-update
+
+If you do not pull first, it is not really a problem but git will warn
+you at the next statement that you are deleting a local branch that
+was not yet fully merged into HEAD. This is because git does not yet
+know your branch just got merged into LAMMPS upstream. If you
+first delete and then pull, everything should still be fine.
+
+Finally, if you delete the branch locally, you might want to push this
+to your remote(s) as well:
+
+
+.. parsed-literal::
+
+   $ git push origin :github-tutorial-update
+
+**Recent changes in the workflow**
+
+Some changes to the workflow are not captured in this tutorial.  For
+example, in addition to the master branch, to which all new features
+should be submitted, there is now also an "unstable" and a "stable"
+branch; these have the same content as "master", but are only updated
+after a patch release or stable release was made.
+Furthermore, the naming of the patches now follow the pattern
+"patch\_<Day><Month><Year>" to simplify comparisons between releases.
+Finally, all patches and submissions are subject to automatic testing
+and code checks to make sure they at the very least compile.
+
+A discussion of the LAMMPS developer GitHub workflow can be found in the file
+`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md>`_
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_granular.rst b/doc/src/Howto_granular.rst
new file mode 100644
index 0000000000..d6c983efe1
--- /dev/null
+++ b/doc/src/Howto_granular.rst
@@ -0,0 +1,55 @@
+Granular models
+===============
+
+Granular system are composed of spherical particles with a diameter,
+as opposed to point particles.  This means they have an angular
+velocity and torque can be imparted to them to cause them to rotate.
+
+To run a simulation of a granular model, you will want to use
+the following commands:
+
+* :doc:`atom\_style sphere <atom_style>`
+* :doc:`fix nve/sphere <fix_nve_sphere>`
+* :doc:`fix gravity <fix_gravity>`
+
+This compute
+
+* :doc:`compute erotate/sphere <compute_erotate_sphere>`
+
+calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
+
+Use one of these 3 pair potentials, which compute forces and torques
+between interacting pairs of particles:
+
+* :doc:`pair\_style <pair_style>` gran/history
+* :doc:`pair\_style <pair_style>` gran/no\_history
+* :doc:`pair\_style <pair_style>` gran/hertzian
+
+These commands implement fix options specific to granular systems:
+
+* :doc:`fix freeze <fix_freeze>`
+* :doc:`fix pour <fix_pour>`
+* :doc:`fix viscous <fix_viscous>`
+* :doc:`fix wall/gran <fix_wall_gran>`
+
+The fix style *freeze* zeroes both the force and torque of frozen
+atoms, and should be used for granular system instead of the fix style
+*setforce*\ .
+
+For computational efficiency, you can eliminate needless pairwise
+computations between frozen atoms by using this command:
+
+* :doc:`neigh\_modify <neigh_modify>` exclude
+
+.. note::
+
+   By default, for 2d systems, granular particles are still modeled
+   as 3d spheres, not 2d discs (circles), meaning their moment of inertia
+   will be the same as in 3d.  If you wish to model granular particles in
+   2d as 2d discs, see the note on this topic on the :doc:`Howto 2d <Howto_2d>`
+   doc page, where 2d simulations are discussed.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_kappa.rst b/doc/src/Howto_kappa.rst
new file mode 100644
index 0000000000..d7fb3b3ee2
--- /dev/null
+++ b/doc/src/Howto_kappa.rst
@@ -0,0 +1,86 @@
+Calculate thermal conductivity
+==============================
+
+The thermal conductivity kappa of a material can be measured in at
+least 4 ways using various options in LAMMPS.  See the examples/KAPPA
+directory for scripts that implement the 4 methods discussed here for
+a simple Lennard-Jones fluid model.  Also, see the :doc:`Howto viscosity <Howto_viscosity>` doc page for an analogous discussion
+for viscosity.
+
+The thermal conductivity tensor kappa is a measure of the propensity
+of a material to transmit heat energy in a diffusive manner as given
+by Fourier's law
+
+J = -kappa grad(T)
+
+where J is the heat flux in units of energy per area per time and
+grad(T) is the spatial gradient of temperature.  The thermal
+conductivity thus has units of energy per distance per time per degree
+K and is often approximated as an isotropic quantity, i.e. as a
+scalar.
+
+The first method is to setup two thermostatted regions at opposite
+ends of a simulation box, or one in the middle and one at the end of a
+periodic box.  By holding the two regions at different temperatures
+with a :doc:`thermostatting fix <Howto_thermostat>`, the energy added to
+the hot region should equal the energy subtracted from the cold region
+and be proportional to the heat flux moving between the regions.  See
+the papers by :ref:`Ikeshoji and Hafskjold <howto-Ikeshoji>` and
+:ref:`Wirnsberger et al <howto-Wirnsberger>` for details of this idea.  Note
+that thermostatting fixes such as :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, and :doc:`fix temp/rescale <fix_temp_rescale>` store the cumulative energy they
+add/subtract.
+
+Alternatively, as a second method, the :doc:`fix heat <fix_heat>` or
+:doc:`fix ehex <fix_ehex>` commands can be used in place of thermostats
+on each of two regions to add/subtract specified amounts of energy to
+both regions.  In both cases, the resulting temperatures of the two
+regions can be monitored with the "compute temp/region" command and
+the temperature profile of the intermediate region can be monitored
+with the :doc:`fix ave/chunk <fix_ave_chunk>` and :doc:`compute ke/atom <compute_ke_atom>` commands.
+
+The third method is to perform a reverse non-equilibrium MD simulation
+using the :doc:`fix thermal/conductivity <fix_thermal_conductivity>`
+command which implements the rNEMD algorithm of Muller-Plathe.
+Kinetic energy is swapped between atoms in two different layers of the
+simulation box.  This induces a temperature gradient between the two
+layers which can be monitored with the :doc:`fix ave/chunk <fix_ave_chunk>` and :doc:`compute ke/atom <compute_ke_atom>` commands.  The fix tallies the
+cumulative energy transfer that it performs.  See the :doc:`fix thermal/conductivity <fix_thermal_conductivity>` command for
+details.
+
+The fourth method is based on the Green-Kubo (GK) formula which
+relates the ensemble average of the auto-correlation of the heat flux
+to kappa.  The heat flux can be calculated from the fluctuations of
+per-atom potential and kinetic energies and per-atom stress tensor in
+a steady-state equilibrated simulation.  This is in contrast to the
+two preceding non-equilibrium methods, where energy flows continuously
+between hot and cold regions of the simulation box.
+
+The :doc:`compute heat/flux <compute_heat_flux>` command can calculate
+the needed heat flux and describes how to implement the Green\_Kubo
+formalism using additional LAMMPS commands, such as the :doc:`fix ave/correlate <fix_ave_correlate>` command to calculate the needed
+auto-correlation.  See the doc page for the :doc:`compute heat/flux <compute_heat_flux>` command for an example input script
+that calculates the thermal conductivity of solid Ar via the GK
+formalism.
+
+
+----------
+
+
+.. _howto-Ikeshoji:
+
+
+
+**(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
+(1994).
+
+.. _howto-Wirnsberger:
+
+
+
+**(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
+(2015).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_library.rst b/doc/src/Howto_library.rst
new file mode 100644
index 0000000000..c60a9ef788
--- /dev/null
+++ b/doc/src/Howto_library.rst
@@ -0,0 +1,227 @@
+Library interface to LAMMPS
+===========================
+
+As described on the :doc:`Build basics <Build_basics>` doc page, LAMMPS
+can be built as a library, so that it can be called by another code,
+used in a :doc:`coupled manner <Howto_couple>` with other codes, or
+driven through a :doc:`Python interface <Python_head>`.
+
+All of these methodologies use a C-style interface to LAMMPS that is
+provided in the files src/library.cpp and src/library.h.  The
+functions therein have a C-style argument list, but contain C++ code
+you could write yourself in a C++ application that was invoking LAMMPS
+directly.  The C++ code in the functions illustrates how to invoke
+internal LAMMPS operations.  Note that LAMMPS classes are defined
+within a LAMMPS namespace (LAMMPS\_NS) if you use them from another C++
+application.
+
+The examples/COUPLE and python/examples directories have example C++
+and C and Python codes which show how a driver code can link to LAMMPS
+as a library, run LAMMPS on a subset of processors, grab data from
+LAMMPS, change it, and put it back into LAMMPS.
+
+The file src/library.cpp contains the following functions for creating
+and destroying an instance of LAMMPS and sending it commands to
+execute.  See the documentation in the src/library.cpp file for
+details.
+
+.. note::
+
+   You can write code for additional functions as needed to define
+   how your code talks to LAMMPS and add them to src/library.cpp and
+   src/library.h, as well as to the :doc:`Python interface <Python_head>`.
+   The added functions can access or change any internal LAMMPS data you
+   wish.
+
+
+.. parsed-literal::
+
+   void lammps_open(int, char \*\*, MPI_Comm, void \*\*)
+   void lammps_open_no_mpi(int, char \*\*, void \*\*)
+   void lammps_close(void \*)
+   int lammps_version(void \*)
+   void lammps_file(void \*, char \*)
+   char \*lammps_command(void \*, char \*)
+   void lammps_commands_list(void \*, int, char \*\*)
+   void lammps_commands_string(void \*, char \*)
+   void lammps_free(void \*)
+
+The lammps\_open() function is used to initialize LAMMPS, passing in a
+list of strings as if they were :doc:`command-line arguments <Run_options>` when LAMMPS is run in stand-alone mode
+from the command line, and a MPI communicator for LAMMPS to run under.
+It returns a ptr to the LAMMPS object that is created, and which is
+used in subsequent library calls.  The lammps\_open() function can be
+called multiple times, to create multiple instances of LAMMPS.
+
+LAMMPS will run on the set of processors in the communicator.  This
+means the calling code can run LAMMPS on all or a subset of
+processors.  For example, a wrapper script might decide to alternate
+between LAMMPS and another code, allowing them both to run on all the
+processors.  Or it might allocate half the processors to LAMMPS and
+half to the other code and run both codes simultaneously before
+syncing them up periodically.  Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.
+
+The lammps\_open\_no\_mpi() function is similar except that no MPI
+communicator is passed from the caller.  Instead, MPI\_COMM\_WORLD is
+used to instantiate LAMMPS, and MPI is initialized if necessary.
+
+The lammps\_close() function is used to shut down an instance of LAMMPS
+and free all its memory.
+
+The lammps\_version() function can be used to determined the specific
+version of the underlying LAMMPS code. This is particularly useful
+when loading LAMMPS as a shared library via dlopen(). The code using
+the library interface can than use this information to adapt to
+changes to the LAMMPS command syntax between versions. The returned
+LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
+20150902) that grows with every new LAMMPS version.
+
+The lammps\_file(), lammps\_command(), lammps\_commands\_list(), and
+lammps\_commands\_string() functions are used to pass one or more
+commands to LAMMPS to execute, the same as if they were coming from an
+input script.
+
+Via these functions, the calling code can read or generate a series of
+LAMMPS commands one or multiple at a time and pass it through the library
+interface to setup a problem and then run it in stages.  The caller
+can interleave the command function calls with operations it performs,
+calls to extract information from or set information within LAMMPS, or
+calls to another code's library.
+
+The lammps\_file() function passes the filename of an input script.
+The lammps\_command() function passes a single command as a string.
+The lammps\_commands\_list() function passes multiple commands in a
+char\*\* list.  In both lammps\_command() and lammps\_commands\_list(),
+individual commands may or may not have a trailing newline.  The
+lammps\_commands\_string() function passes multiple commands
+concatenated into one long string, separated by newline characters.
+In both lammps\_commands\_list() and lammps\_commands\_string(), a single
+command can be spread across multiple lines, if the last printable
+character of all but the last line is "&", the same as if the lines
+appeared in an input script.
+
+The lammps\_free() function is a clean-up function to free memory that
+the library allocated previously via other function calls.  See
+comments in src/library.cpp file for which other functions need this
+clean-up.
+
+The file src/library.cpp also contains these functions for extracting
+information from LAMMPS and setting value within LAMMPS.  Again, see
+the documentation in the src/library.cpp file for details, including
+which quantities can be queried by name:
+
+
+.. parsed-literal::
+
+   int lammps_extract_setting(void \*, char \*)
+   void \*lammps_extract_global(void \*, char \*)
+   void lammps_extract_box(void \*, double \*, double \*,
+                           double \*, double \*, double \*, int \*, int \*)
+   void \*lammps_extract_atom(void \*, char \*)
+   void \*lammps_extract_compute(void \*, char \*, int, int)
+   void \*lammps_extract_fix(void \*, char \*, int, int, int, int)
+   void \*lammps_extract_variable(void \*, char \*, char \*)
+
+The extract\_setting() function returns info on the size
+of data types (e.g. 32-bit or 64-bit atom IDs) used
+by the LAMMPS executable (a compile-time choice).
+
+The other extract functions return a pointer to various global or
+per-atom quantities stored in LAMMPS or to values calculated by a
+compute, fix, or variable.  The pointer returned by the
+extract\_global() function can be used as a permanent reference to a
+value which may change.  For the extract\_atom() method, see the
+extract() method in the src/atom.cpp file for a list of valid per-atom
+properties.  New names could easily be added if the property you want
+is not listed.  For the other extract functions, the underlying
+storage may be reallocated as LAMMPS runs, so you need to re-call the
+function to assure a current pointer or returned value(s).
+
+
+.. parsed-literal::
+
+   double lammps_get_thermo(void \*, char \*)
+   int lammps_get_natoms(void \*)
+
+   int lammps_set_variable(void \*, char \*, char \*)
+   void lammps_reset_box(void \*, double \*, double \*, double, double, double)
+
+The lammps\_get\_thermo() function returns the current value of a thermo
+keyword as a double precision value.
+
+The lammps\_get\_natoms() function returns the total number of atoms in
+the system and can be used by the caller to allocate memory for the
+lammps\_gather\_atoms() and lammps\_scatter\_atoms() functions.
+
+The lammps\_set\_variable() function can set an existing string-style
+variable to a new string value, so that subsequent LAMMPS commands can
+access the variable.
+
+The lammps\_reset\_box() function resets the size and shape of the
+simulation box, e.g. as part of restoring a previously extracted and
+saved state of a simulation.
+
+
+.. parsed-literal::
+
+   void lammps_gather_atoms(void \*, char \*, int, int, void \*)
+   void lammps_gather_atoms_concat(void \*, char \*, int, int, void \*)
+   void lammps_gather_atoms_subset(void \*, char \*, int, int, int, int \*, void \*)
+   void lammps_scatter_atoms(void \*, char \*, int, int, void \*)
+   void lammps_scatter_atoms_subset(void \*, char \*, int, int, int, int \*, void \*)
+
+The gather functions collect peratom info of the requested type (atom
+coords, atom types, forces, etc) from all processors, and returns the
+same vector of values to each calling processor.  The scatter
+functions do the inverse.  They distribute a vector of peratom values,
+passed by all calling processors, to individual atoms, which may be
+owned by different processors.
+
+.. warning::
+
+   These functions are not compatible with the
+   -DLAMMPS\_BIGBIG setting when compiling LAMMPS.  Dummy functions
+   that result in an error message and abort will be substituted
+   instead of resulting in random crashes and memory corruption.
+
+The lammps\_gather\_atoms() function does this for all N atoms in the
+system, ordered by atom ID, from 1 to N.  The
+lammps\_gather\_atoms\_concat() function does it for all N atoms, but
+simply concatenates the subset of atoms owned by each processor.  The
+resulting vector is not ordered by atom ID.  Atom IDs can be requested
+by the same function if the caller needs to know the ordering.  The
+lammps\_gather\_subset() function allows the caller to request values
+for only a subset of atoms (identified by ID).
+For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
+If the count is specified as 1, they are returned
+in a packed format with all three image flags stored in a single integer.
+If the count is specified as 3, the values are unpacked into xyz flags
+by the library before returning them.
+
+The lammps\_scatter\_atoms() function takes a list of values for all N
+atoms in the system, ordered by atom ID, from 1 to N, and assigns
+those values to each atom in the system.  The
+lammps\_scatter\_atoms\_subset() function takes a subset of IDs as an
+argument and only scatters those values to the owning atoms.
+
+
+.. parsed-literal::
+
+   void lammps_create_atoms(void \*, int, tagint \*, int \*, double \*, double \*,
+                            imageint \*, int)
+
+The lammps\_create\_atoms() function takes a list of N atoms as input
+with atom types and coords (required), an optionally atom IDs and
+velocities and image flags.  It uses the coords of each atom to assign
+it as a new atom to the processor that owns it.  This function is
+useful to add atoms to a simulation or (in tandem with
+lammps\_reset\_box()) to restore a previously extracted and saved state
+of a simulation.  Additional properties for the new atoms can then be
+assigned via the lammps\_scatter\_atoms() or lammps\_extract\_atom()
+functions.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_manifold.rst b/doc/src/Howto_manifold.rst
new file mode 100644
index 0000000000..4e3893993f
--- /dev/null
+++ b/doc/src/Howto_manifold.rst
@@ -0,0 +1,57 @@
+Manifolds (surfaces)
+====================
+
+**Overview:**
+
+This doc page is not about a LAMMPS input script command, but about
+manifolds, which are generalized surfaces, as defined and used by the
+USER-MANIFOLD package, to track particle motion on the manifolds.  See
+the src/USER-MANIFOLD/README file for more details about the package
+and its commands.
+
+Below is a list of currently supported manifolds by the USER-MANIFOLD
+package, their parameters and a short description of them.  The
+parameters listed here are in the same order as they should be passed
+to the relevant fixes.
+
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| *manifold*     | *parameters*   | *equation*                                                                                                                             | *description*                                                                                                                      |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| cylinder       | R              | x\^2 + y\^2 - R\^2 = 0                                                                                                                 | Cylinder along z-axis, axis going through (0,0,0)                                                                                  |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| cylinder\_dent | R l a          | x\^2 + y\^2 - r(z)\^2 = 0, r(x) = R if \| z \| > l, r(z) = R - a\*(1 + cos(z/l))/2 otherwise                                           | A cylinder with a dent around z = 0                                                                                                |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| dumbbell       | a A B c        | -( x\^2 + y\^2 ) + (a\^2 - z\^2/c\^2) \* ( 1 + (A\*sin(B\*z\^2))\^4) = 0                                                               | A dumbbell                                                                                                                         |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| ellipsoid      | a  b c         | (x/a)\^2 + (y/b)\^2 + (z/c)\^2 = 0                                                                                                     | An ellipsoid                                                                                                                       |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| gaussian\_bump | A l rc1 rc2    | if( x < rc1) -z + A \* exp( -x\^2 / (2 l\^2) ); else if( x < rc2 ) -z + a + b\*x + c\*x\^2 + d\*x\^3; else z                           | A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0.                                                              |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| plane          | a b c x0 y0 z0 | a\*(x-x0) + b\*(y-y0) + c\*(z-z0) = 0                                                                                                  | A plane with normal (a,b,c) going through point (x0,y0,z0)                                                                         |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| plane\_wiggle  | a w            | z - a\*sin(w\*x) = 0                                                                                                                   | A plane with a sinusoidal modulation on z along x.                                                                                 |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| sphere         | R              | x\^2 + y\^2 + z\^2 - R\^2 = 0                                                                                                          | A sphere of radius R                                                                                                               |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| supersphere    | R q            | \| x \|\^q + \| y \|\^q + \| z \|\^q - R\^q = 0                                                                                        | A supersphere of hyperradius R                                                                                                     |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| spine          | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | An approximation to a dendritic spine                                                                                              |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| spine\_two     | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendritic spine                                                                                         |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| thylakoid      | wB LB lB       | Various, see :ref:`(Paquay) <Paquay1>`                                                                                                 | A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+| torus          | R r            | (R - sqrt( x\^2 + y\^2 ) )\^2 + z\^2 - r\^2                                                                                            | A torus with large radius R and small radius r, centered on (0,0,0)                                                                |
++----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
+
+.. _Paquay1:
+
+
+
+**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
+preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_multiple.rst b/doc/src/Howto_multiple.rst
new file mode 100644
index 0000000000..5f36863fa4
--- /dev/null
+++ b/doc/src/Howto_multiple.rst
@@ -0,0 +1,103 @@
+Run multiple simulations from one input script
+==============================================
+
+This can be done in several ways.  See the documentation for
+individual commands for more details on how these examples work.
+
+If "multiple simulations" means continue a previous simulation for
+more timesteps, then you simply use the :doc:`run <run>` command
+multiple times.  For example, this script
+
+
+.. parsed-literal::
+
+   units lj
+   atom_style atomic
+   read_data data.lj
+   run 10000
+   run 10000
+   run 10000
+   run 10000
+   run 10000
+
+would run 5 successive simulations of the same system for a total of
+50,000 timesteps.
+
+If you wish to run totally different simulations, one after the other,
+the :doc:`clear <clear>` command can be used in between them to
+re-initialize LAMMPS.  For example, this script
+
+
+.. parsed-literal::
+
+   units lj
+   atom_style atomic
+   read_data data.lj
+   run 10000
+   clear
+   units lj
+   atom_style atomic
+   read_data data.lj.new
+   run 10000
+
+would run 2 independent simulations, one after the other.
+
+For large numbers of independent simulations, you can use
+:doc:`variables <variable>` and the :doc:`next <next>` and
+:doc:`jump <jump>` commands to loop over the same input script
+multiple times with different settings.  For example, this
+script, named in.polymer
+
+
+.. parsed-literal::
+
+   variable d index run1 run2 run3 run4 run5 run6 run7 run8
+   shell cd $d
+   read_data data.polymer
+   run 10000
+   shell cd ..
+   clear
+   next d
+   jump in.polymer
+
+would run 8 simulations in different directories, using a data.polymer
+file in each directory.  The same concept could be used to run the
+same system at 8 different temperatures, using a temperature variable
+and storing the output in different log and dump files, for example
+
+
+.. parsed-literal::
+
+   variable a loop 8
+   variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
+   log log.$a
+   read data.polymer
+   velocity all create $t 352839
+   fix 1 all nvt $t $t 100.0
+   dump 1 all atom 1000 dump.$a
+   run 100000
+   clear
+   next t
+   next a
+   jump in.polymer
+
+All of the above examples work whether you are running on 1 or
+multiple processors, but assumed you are running LAMMPS on a single
+partition of processors.  LAMMPS can be run on multiple partitions via
+the :doc:`-partition command-line switch <Run_options>`.
+
+In the last 2 examples, if LAMMPS were run on 3 partitions, the same
+scripts could be used if the "index" and "loop" variables were
+replaced with *universe*\ -style variables, as described in the
+:doc:`variable <variable>` command.  Also, the "next t" and "next a"
+commands would need to be replaced with a single "next a t" command.
+With these modifications, the 8 simulations of each script would run
+on the 3 partitions one after the other until all were finished.
+Initially, 3 simulations would be started simultaneously, one on each
+partition.  When one finished, that partition would then start
+the 4th simulation, and so forth, until all 8 were completed.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_nemd.rst b/doc/src/Howto_nemd.rst
new file mode 100644
index 0000000000..c29065e672
--- /dev/null
+++ b/doc/src/Howto_nemd.rst
@@ -0,0 +1,60 @@
+NEMD simulations
+================
+
+Non-equilibrium molecular dynamics or NEMD simulations are typically
+used to measure a fluid's rheological properties such as viscosity.
+In LAMMPS, such simulations can be performed by first setting up a
+non-orthogonal simulation box (see the preceding Howto section).
+
+A shear strain can be applied to the simulation box at a desired
+strain rate by using the :doc:`fix deform <fix_deform>` command.  The
+:doc:`fix nvt/sllod <fix_nvt_sllod>` command can be used to thermostat
+the sheared fluid and integrate the SLLOD equations of motion for the
+system.  Fix nvt/sllod uses :doc:`compute temp/deform <compute_temp_deform>` to compute a thermal temperature
+by subtracting out the streaming velocity of the shearing atoms.  The
+velocity profile or other properties of the fluid can be monitored via
+the :doc:`fix ave/chunk <fix_ave_chunk>` command.
+
+.. note::
+
+   A recent (2017) book by :ref:`(Daivis and Todd) <Daivis-nemd>`
+   discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+   thermostatting generally, for both simple and complex fluids,
+   e.g. molecular systems.  The latter can be tricky to do correctly.
+
+As discussed in the previous section on non-orthogonal simulation
+boxes, the amount of tilt or skew that can be applied is limited by
+LAMMPS for computational efficiency to be 1/2 of the parallel box
+length.  However, :doc:`fix deform <fix_deform>` can continuously strain
+a box by an arbitrary amount.  As discussed in the :doc:`fix deform <fix_deform>` command, when the tilt value reaches a limit,
+the box is flipped to the opposite limit which is an equivalent tiling
+of periodic space.  The strain rate can then continue to change as
+before.  In a long NEMD simulation these box re-shaping events may
+occur many times.
+
+In a NEMD simulation, the "remap" option of :doc:`fix deform <fix_deform>` should be set to "remap v", since that is what
+:doc:`fix nvt/sllod <fix_nvt_sllod>` assumes to generate a velocity
+profile consistent with the applied shear strain rate.
+
+An alternative method for calculating viscosities is provided via the
+:doc:`fix viscosity <fix_viscosity>` command.
+
+NEMD simulations can also be used to measure transport properties of a fluid
+through a pore or channel. Simulations of steady-state flow can be performed
+using the :doc:`fix flow/gauss <fix_flow_gauss>` command.
+
+
+----------
+
+
+.. _Daivis-nemd:
+
+
+
+**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst
new file mode 100644
index 0000000000..6a5788cab3
--- /dev/null
+++ b/doc/src/Howto_output.rst
@@ -0,0 +1,349 @@
+Output from LAMMPS (thermo, dumps, computes, fixes, variables)
+==============================================================
+
+There are four basic kinds of LAMMPS output:
+
+* :doc:`Thermodynamic output <thermo_style>`, which is a list
+  of quantities printed every few timesteps to the screen and logfile.
+* :doc:`Dump files <dump>`, which contain snapshots of atoms and various
+  per-atom values and are written at a specified frequency.
+* Certain fixes can output user-specified quantities to files: :doc:`fix ave/time <fix_ave_time>` for time averaging, :doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and :doc:`fix print <fix_print>` for single-line output of
+  :doc:`variables <variable>`.  Fix print can also output to the
+  screen.
+* :doc:`Restart files <restart>`.
+
+
+A simulation prints one set of thermodynamic output and (optionally)
+restart files.  It can generate any number of dump files and fix
+output files, depending on what :doc:`dump <dump>` and :doc:`fix <fix>`
+commands you specify.
+
+As discussed below, LAMMPS gives you a variety of ways to determine
+what quantities are computed and printed when the thermodynamics,
+dump, or fix commands listed above perform output.  Throughout this
+discussion, note that users can also :doc:`add their own computes and fixes to LAMMPS <Modify>` which can then generate values that can then be
+output with these commands.
+
+The following sub-sections discuss different LAMMPS command related
+to output and the kind of data they operate on and produce:
+
+* :ref:`Global/per-atom/local data <global>`
+* :ref:`Scalar/vector/array data <scalar>`
+* :ref:`Thermodynamic output <thermo>`
+* :ref:`Dump file output <dump>`
+* :ref:`Fixes that write output files <fixoutput>`
+* :ref:`Computes that process output quantities <computeoutput>`
+* :ref:`Fixes that process output quantities <fixprocoutput>`
+* :ref:`Computes that generate values to output <compute>`
+* :ref:`Fixes that generate values to output <fix>`
+* :ref:`Variables that generate values to output <variable>`
+* :ref:`Summary table of output options and data flow between commands <table>`
+
+.. _global:
+
+Global/per-atom/local data
+---------------------------------------
+
+Various output-related commands work with three different styles of
+data: global, per-atom, or local.  A global datum is one or more
+system-wide values, e.g. the temperature of the system.  A per-atom
+datum is one or more values per atom, e.g. the kinetic energy of each
+atom.  Local datums are calculated by each processor based on the
+atoms it owns, but there may be zero or more per atom, e.g. a list of
+bond distances.
+
+.. _scalar:
+
+Scalar/vector/array data
+-------------------------------------
+
+Global, per-atom, and local datums can each come in three kinds: a
+single scalar value, a vector of values, or a 2d array of values.  The
+doc page for a "compute" or "fix" or "variable" that generates data
+will specify both the style and kind of data it produces, e.g. a
+per-atom vector.
+
+When a quantity is accessed, as in many of the output commands
+discussed below, it can be referenced via the following bracket
+notation, where ID in this case is the ID of a compute.  The leading
+"c\_" would be replaced by "f\_" for a fix, or "v\_" for a variable:
+
++-------------+--------------------------------------------+
+| c\_ID       | entire scalar, vector, or array            |
++-------------+--------------------------------------------+
+| c\_ID[I]    | one element of vector, one column of array |
++-------------+--------------------------------------------+
+| c\_ID[I][J] | one element of array                       |
++-------------+--------------------------------------------+
+
+In other words, using one bracket reduces the dimension of the data
+once (vector -> scalar, array -> vector).  Using two brackets reduces
+the dimension twice (array -> scalar).  Thus a command that uses
+scalar values as input can typically also process elements of a vector
+or array.
+
+.. _thermo:
+
+Thermodynamic output
+---------------------------------
+
+The frequency and format of thermodynamic output is set by the
+:doc:`thermo <thermo>`, :doc:`thermo\_style <thermo_style>`, and
+:doc:`thermo\_modify <thermo_modify>` commands.  The
+:doc:`thermo\_style <thermo_style>` command also specifies what values
+are calculated and written out.  Pre-defined keywords can be specified
+(e.g. press, etotal, etc).  Three additional kinds of keywords can
+also be specified (c\_ID, f\_ID, v\_name), where a :doc:`compute <compute>`
+or :doc:`fix <fix>` or :doc:`variable <variable>` provides the value to be
+output.  In each case, the compute, fix, or variable must generate
+global values for input to the :doc:`thermo\_style custom <dump>`
+command.
+
+Note that thermodynamic output values can be "extensive" or
+"intensive".  The former scale with the number of atoms in the system
+(e.g. total energy), the latter do not (e.g. temperature).  The
+setting for :doc:`thermo\_modify norm <thermo_modify>` determines whether
+extensive quantities are normalized or not.  Computes and fixes
+produce either extensive or intensive values; see their individual doc
+pages for details.  :doc:`Equal-style variables <variable>` produce only
+intensive values; you can include a division by "natoms" in the
+formula if desired, to make an extensive calculation produce an
+intensive result.
+
+.. _dump:
+
+Dump file output
+---------------------------
+
+Dump file output is specified by the :doc:`dump <dump>` and
+:doc:`dump\_modify <dump_modify>` commands.  There are several
+pre-defined formats (dump atom, dump xtc, etc).
+
+There is also a :doc:`dump custom <dump>` format where the user
+specifies what values are output with each atom.  Pre-defined atom
+attributes can be specified (id, x, fx, etc).  Three additional kinds
+of keywords can also be specified (c\_ID, f\_ID, v\_name), where a
+:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable <variable>`
+provides the values to be output.  In each case, the compute, fix, or
+variable must generate per-atom values for input to the :doc:`dump custom <dump>` command.
+
+There is also a :doc:`dump local <dump>` format where the user specifies
+what local values to output.  A pre-defined index keyword can be
+specified to enumerate the local values.  Two additional kinds of
+keywords can also be specified (c\_ID, f\_ID), where a
+:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable <variable>`
+provides the values to be output.  In each case, the compute or fix
+must generate local values for input to the :doc:`dump local <dump>`
+command.
+
+.. _fixoutput:
+
+Fixes that write output files
+---------------------------------------------
+
+Several fixes take various quantities as input and can write output
+files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`fix ave/correlate <fix_ave_correlate>`, and :doc:`fix print <fix_print>`.
+
+The :doc:`fix ave/time <fix_ave_time>` command enables direct output to
+a file and/or time-averaging of global scalars or vectors.  The user
+specifies one or more quantities as input.  These can be global
+:doc:`compute <compute>` values, global :doc:`fix <fix>` values, or
+:doc:`variables <variable>` of any style except the atom style which
+produces per-atom values.  Since a variable can refer to keywords used
+by the :doc:`thermo\_style custom <thermo_style>` command (like temp or
+press) and individual per-atom values, a wide variety of quantities
+can be time averaged and/or output in this way.  If the inputs are one
+or more scalar values, then the fix generate a global scalar or vector
+of output.  If the inputs are one or more vector values, then the fix
+generates a global vector or array of output.  The time-averaged
+output of this fix can also be used as input to other output commands.
+
+The :doc:`fix ave/chunk <fix_ave_chunk>` command enables direct output
+to a file of chunk-averaged per-atom quantities like those output in
+dump files.  Chunks can represent spatial bins or other collections of
+atoms, e.g. individual molecules.  The per-atom quantities can be atom
+density (mass or number) or atom attributes such as position,
+velocity, force.  They can also be per-atom quantities calculated by a
+:doc:`compute <compute>`, by a :doc:`fix <fix>`, or by an atom-style
+:doc:`variable <variable>`.  The chunk-averaged output of this fix can
+also be used as input to other output commands.
+
+The :doc:`fix ave/histo <fix_ave_histo>` command enables direct output
+to a file of histogrammed quantities, which can be global or per-atom
+or local quantities.  The histogram output of this fix can also be
+used as input to other output commands.
+
+The :doc:`fix ave/correlate <fix_ave_correlate>` command enables direct
+output to a file of time-correlated quantities, which can be global
+values.  The correlation matrix output of this fix can also be used as
+input to other output commands.
+
+The :doc:`fix print <fix_print>` command can generate a line of output
+written to the screen and log file or to a separate file, periodically
+during a running simulation.  The line can contain one or more
+:doc:`variable <variable>` values for any style variable except the
+vector or atom styles).  As explained above, variables themselves can
+contain references to global values generated by :doc:`thermodynamic keywords <thermo_style>`, :doc:`computes <compute>`,
+:doc:`fixes <fix>`, or other :doc:`variables <variable>`, or to per-atom
+values for a specific atom.  Thus the :doc:`fix print <fix_print>`
+command is a means to output a wide variety of quantities separate
+from normal thermodynamic or dump file output.
+
+.. _computeoutput:
+
+Computes that process output quantities
+-----------------------------------------------------------
+
+The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom
+or local vector quantities as inputs and "reduce" them (sum, min, max,
+ave) to scalar quantities.  These are produced as output values which
+can be used as input to other output commands.
+
+The :doc:`compute slice <compute_slice>` command take one or more global
+vector or array quantities as inputs and extracts a subset of their
+values to create a new vector or array.  These are produced as output
+values which can be used as input to other output commands.
+
+The :doc:`compute property/atom <compute_property_atom>` command takes a
+list of one or more pre-defined atom attributes (id, x, fx, etc) and
+stores the values in a per-atom vector or array.  These are produced
+as output values which can be used as input to other output commands.
+The list of atom attributes is the same as for the :doc:`dump custom <dump>` command.
+
+The :doc:`compute property/local <compute_property_local>` command takes
+a list of one or more pre-defined local attributes (bond info, angle
+info, etc) and stores the values in a local vector or array.  These
+are produced as output values which can be used as input to other
+output commands.
+
+.. _fixprocoutput:
+
+Fixes that process output quantities
+--------------------------------------------------------
+
+The :doc:`fix vector <fix_vector>` command can create global vectors as
+output from global scalars as input, accumulating them one element at
+a time.
+
+The :doc:`fix ave/atom <fix_ave_atom>` command performs time-averaging
+of per-atom vectors.  The per-atom quantities can be atom attributes
+such as position, velocity, force.  They can also be per-atom
+quantities calculated by a :doc:`compute <compute>`, by a
+:doc:`fix <fix>`, or by an atom-style :doc:`variable <variable>`.  The
+time-averaged per-atom output of this fix can be used as input to
+other output commands.
+
+The :doc:`fix store/state <fix_store_state>` command can archive one or
+more per-atom attributes at a particular time, so that the old values
+can be used in a future calculation or output.  The list of atom
+attributes is the same as for the :doc:`dump custom <dump>` command,
+including per-atom quantities calculated by a :doc:`compute <compute>`,
+by a :doc:`fix <fix>`, or by an atom-style :doc:`variable <variable>`.
+The output of this fix can be used as input to other output commands.
+
+.. _compute:
+
+Computes that generate values to output
+-----------------------------------------------------
+
+Every :doc:`compute <compute>` in LAMMPS produces either global or
+per-atom or local values.  The values can be scalars or vectors or
+arrays of data.  These values can be output using the other commands
+described in this section.  The doc page for each compute command
+describes what it produces.  Computes that produce per-atom or local
+values have the word "atom" or "local" in their style name.  Computes
+without the word "atom" or "local" produce global values.
+
+.. _fix:
+
+Fixes that generate values to output
+----------------------------------------------
+
+Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
+local values which can be accessed by other commands.  The values can
+be scalars or vectors or arrays of data.  These values can be output
+using the other commands described in this section.  The doc page for
+each fix command tells whether it produces any output quantities and
+describes them.
+
+.. _variable:
+
+Variables that generate values to output
+-------------------------------------------------------
+
+:doc:`Variables <variable>` defined in an input script can store one or
+more strings.  But equal-style, vector-style, and atom-style or
+atomfile-style variables generate a global scalar value, global vector
+or values, or a per-atom vector, respectively, when accessed.  The
+formulas used to define these variables can contain references to the
+thermodynamic keywords and to global and per-atom data generated by
+computes, fixes, and other variables.  The values generated by
+variables can be used as input to and thus output by the other
+commands described in this section.
+
+.. _table:
+
+Summary table of output options and data flow between commands
+--------------------------------------------------------------------------
+
+This table summarizes the various commands that can be used for
+generating output from LAMMPS.  Each command produces output data of
+some kind and/or writes data to a file.  Most of the commands can take
+data from other commands as input.  Thus you can link many of these
+commands together in pipeline form, where data produced by one command
+is used as input to another command and eventually written to the
+screen or to a file.  Note that to hook two commands together the
+output and input data types must match, e.g. global/per-atom/local
+data and scalar/vector/array data.
+
+Also note that, as described above, when a command takes a scalar as
+input, that could be an element of a vector or array.  Likewise a
+vector input could be a column of an array.
+
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| Command                                                | Input                                        | Output                                    |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`thermo\_style custom <thermo_style>`             | global scalars                               | screen, log file                          |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`dump custom <dump>`                              | per-atom vectors                             | dump file                                 |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`dump local <dump>`                               | local vectors                                | dump file                                 |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fix print <fix_print>`                           | global scalar from variable                  | screen, file                              |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`print <print>`                                   | global scalar from variable                  | screen                                    |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`computes <compute>`                              | N/A                                          | global/per-atom/local scalar/vector/array |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fixes <fix>`                                     | N/A                                          | global/per-atom/local scalar/vector/array |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`variables <variable>`                            | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`compute reduce <compute_reduce>`                 | per-atom/local vectors                       | global scalar/vector                      |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`compute slice <compute_slice>`                   | global vectors/arrays                        | global vector/array                       |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`compute property/atom <compute_property_atom>`   | per-atom vectors                             | per-atom vector/array                     |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`compute property/local <compute_property_local>` | local vectors                                | local vector/array                        |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fix vector <fix_vector>`                         | global scalars                               | global vector                             |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fix ave/atom <fix_ave_atom>`                     | per-atom vectors                             | per-atom vector/array                     |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fix ave/time <fix_ave_time>`                     | global scalars/vectors                       | global scalar/vector/array, file          |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fix ave/chunk <fix_ave_chunk>`                   | per-atom vectors                             | global array, file                        |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fix ave/histo <fix_ave_histo>`                   | global/per-atom/local scalars and vectors    | global array, file                        |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fix ave/correlate <fix_ave_correlate>`           | global scalars                               | global array, file                        |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+| :doc:`fix store/state <fix_store_state>`               | per-atom vectors                             | per-atom vector/array                     |
++--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_polarizable.rst b/doc/src/Howto_polarizable.rst
new file mode 100644
index 0000000000..e9bca43128
--- /dev/null
+++ b/doc/src/Howto_polarizable.rst
@@ -0,0 +1,78 @@
+Polarizable models
+==================
+
+In polarizable force fields the charge distributions in molecules and
+materials respond to their electrostatic environments. Polarizable
+systems can be simulated in LAMMPS using three methods:
+
+* the fluctuating charge method, implemented in the :doc:`QEQ <fix_qeq>`
+  package,
+* the adiabatic core-shell method, implemented in the
+  :doc:`CORESHELL <Howto_coreshell>` package,
+* the thermalized Drude dipole method, implemented in the
+  :doc:`USER-DRUDE <Howto_drude>` package.
+
+The fluctuating charge method calculates instantaneous charges on
+interacting atoms based on the electronegativity equalization
+principle. It is implemented in the :doc:`fix qeq <fix_qeq>` which is
+available in several variants. It is a relatively efficient technique
+since no additional particles are introduced. This method allows for
+charge transfer between molecules or atom groups. However, because the
+charges are located at the interaction sites, off-plane components of
+polarization cannot be represented in planar molecules or atom groups.
+
+The two other methods share the same basic idea: polarizable atoms are
+split into one core atom and one satellite particle (called shell or
+Drude particle) attached to it by a harmonic spring.  Both atoms bear
+a charge and they represent collectively an induced electric dipole.
+These techniques are computationally more expensive than the QEq
+method because of additional particles and bonds. These two
+charge-on-spring methods differ in certain features, with the
+core-shell model being normally used for ionic/crystalline materials,
+whereas the so-called Drude model is normally used for molecular
+systems and fluid states.
+
+The core-shell model is applicable to crystalline materials where the
+high symmetry around each site leads to stable trajectories of the
+core-shell pairs. However, bonded atoms in molecules can be so close
+that a core would interact too strongly or even capture the Drude
+particle of a neighbor. The Drude dipole model is relatively more
+complex in order to remedy this and other issues. Specifically, the
+Drude model includes specific thermostatting of the core-Drude pairs
+and short-range damping of the induced dipoles.
+
+The three polarization methods can be implemented through a
+self-consistent calculation of charges or induced dipoles at each
+timestep. In the fluctuating charge scheme this is done by the matrix
+inversion method in :doc:`fix qeq/point <fix_qeq>`, but for core-shell
+or Drude-dipoles the relaxed-dipoles technique would require an slow
+iterative procedure. These self-consistent solutions yield accurate
+trajectories since the additional degrees of freedom representing
+polarization are massless.  An alternative is to attribute a mass to
+the additional degrees of freedom and perform time integration using
+an extended Lagrangian technique. For the fluctuating charge scheme
+this is done by :doc:`fix qeq/dynamic <fix_qeq>`, and for the
+charge-on-spring models by the methods outlined in the next two
+sections. The assignment of masses to the additional degrees of
+freedom can lead to unphysical trajectories if care is not exerted in
+choosing the parameters of the polarizable models and the simulation
+conditions.
+
+In the core-shell model the vibration of the shells is kept faster
+than the ionic vibrations to mimic the fast response of the
+polarizable electrons.  But in molecular systems thermalizing the
+core-Drude pairs at temperatures comparable to the rest of the
+simulation leads to several problems (kinetic energy transfer, too
+short a timestep, etc.) In order to avoid these problems the relative
+motion of the Drude particles with respect to their cores is kept
+"cold" so the vibration of the core-Drude pairs is very slow,
+approaching the self-consistent regime.  In both models the
+temperature is regulated using the velocities of the center of mass of
+core+shell (or Drude) pairs, but in the Drude model the actual
+relative core-Drude particle motion is thermostatted separately as
+well.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst
new file mode 100644
index 0000000000..2711e26914
--- /dev/null
+++ b/doc/src/Howto_pylammps.rst
@@ -0,0 +1,584 @@
+PyLammps Tutorial
+=================
+
+.. contents::
+
+Overview
+--------
+
+PyLammps is a Python wrapper class which can be created on its own or
+use an existing lammps Python object.  It creates a simpler,
+Python-like interface to common LAMMPS functionality, in contrast to
+the lammps.py wrapper on the C-style LAMMPS library interface which is
+written using Python ctypes.  The lammps.py wrapper is discussed on
+the :doc:`Python library <Python_library>` doc page.
+
+Unlike the flat ctypes interface, PyLammps exposes a discoverable API.
+It no longer requires knowledge of the underlying C++ code
+implementation.  Finally, the IPyLammps wrapper builds on top of
+PyLammps and adds some additional features for IPython integration
+into IPython notebooks, e.g. for embedded visualization output from
+dump/image.
+
+Comparison of lammps and PyLammps interfaces
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+lammps.lammps
+"""""""""""""
+
+* uses C-Types
+* direct memory access to native C++ data
+* provides functions to send and receive data to LAMMPS
+* requires knowledge of how LAMMPS internally works (C pointers, etc)
+
+lammps.PyLammps
+"""""""""""""""
+
+* higher-level abstraction built on top of original C-Types interface
+* manipulation of Python objects
+* communication with LAMMPS is hidden from API user
+* shorter, more concise Python
+* better IPython integration, designed for quick prototyping
+
+Quick Start
+-----------
+
+System-wide Installation
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+Step 1: Building LAMMPS as a shared library
+"""""""""""""""""""""""""""""""""""""""""""
+
+To use LAMMPS inside of Python it has to be compiled as shared library. This
+library is then loaded by the Python interface. In this example we enable the
+MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
+output support enabled.
+
+Step 1a: For the CMake based build system, the steps are:
+
+
+.. code-block:: bash
+
+   mkdir $LAMMPS_DIR/build-shared
+   cd  $LAMMPS_DIR/build-shared
+
+   # MPI, PNG, Jpeg, FFMPEG are auto-detected
+   cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
+   make
+
+Step 1b: For the legacy, make based build system, the steps are:
+
+
+.. code-block:: bash
+
+   cd $LAMMPS_DIR/src
+
+   # add packages if necessary
+   make yes-MOLECULE
+
+   # compile shared library using Makefile
+   make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg"
+
+Step 2: Installing the LAMMPS Python package
+""""""""""""""""""""""""""""""""""""""""""""
+
+PyLammps is part of the lammps Python package. To install it simply install
+that package into your current Python installation with:
+
+
+.. code-block:: bash
+
+   make install-python
+
+.. note::
+
+   Recompiling the shared library requires re-installing the Python package
+
+Installation inside of a virtualenv
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can use virtualenv to create a custom Python environment specifically tuned
+for your workflow.
+
+Benefits of using a virtualenv
+""""""""""""""""""""""""""""""
+
+* isolation of your system Python installation from your development installation
+* installation can happen in your user directory without root access (useful for HPC clusters)
+* installing packages through pip allows you to get newer versions of packages than e.g., through apt-get or yum package managers (and without root access)
+* you can even install specific old versions of a package if necessary
+
+**Prerequisite (e.g. on Ubuntu)**
+
+
+.. code-block:: bash
+
+   apt-get install python-virtualenv
+
+Creating a virtualenv with lammps installed
+"""""""""""""""""""""""""""""""""""""""""""
+
+
+.. code-block:: bash
+
+   # create virtualenv named 'testing'
+   virtualenv $HOME/python/testing
+
+   # activate 'testing' environment
+   source $HOME/python/testing/bin/activate
+
+Now configure and compile the LAMMPS shared library as outlined above.
+When using CMake and the shared library has already been build, you
+need to re-run CMake to update the location of the python executable
+to the location in the virtual environment with:
+
+
+.. code-block:: bash
+
+   cmake . -DPYTHON_EXECUTABLE=$(which python)
+
+   # install LAMMPS package in virtualenv
+   (testing) make install-python
+
+   # install other useful packages
+   (testing) pip install matplotlib jupyter mpi4py
+
+   ...
+
+   # return to original shell
+   (testing) deactivate
+
+Creating a new instance of PyLammps
+-----------------------------------
+
+To create a PyLammps object you need to first import the class from the lammps
+module. By using the default constructor, a new *lammps* instance is created.
+
+
+.. code-block:: Python
+
+   from lammps import PyLammps
+   L = PyLammps()
+
+You can also initialize PyLammps on top of this existing *lammps* object:
+
+
+.. code-block:: Python
+
+   from lammps import lammps, PyLammps
+   lmp = lammps()
+   L = PyLammps(ptr=lmp)
+
+Commands
+--------
+
+Sending a LAMMPS command with the existing library interfaces is done using
+the command method of the lammps object instance.
+
+For instance, let's take the following LAMMPS command:
+
+
+.. code-block:: LAMMPS
+
+   region box block 0 10 0 5 -0.5 0.5
+
+In the original interface this command can be executed with the following
+Python code if *L* was a lammps instance:
+
+
+.. code-block:: Python
+
+   L.command("region box block 0 10 0 5 -0.5 0.5")
+
+With the PyLammps interface, any command can be split up into arbitrary parts
+separated by white-space, passed as individual arguments to a region method.
+
+
+.. code-block:: Python
+
+   L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
+
+Note that each parameter is set as Python literal floating-point number. In the
+PyLammps interface, each command takes an arbitrary parameter list and transparently
+merges it to a single command string, separating individual parameters by white-space.
+
+The benefit of this approach is avoiding redundant command calls and easier
+parameterization. In the original interface parameterization needed to be done
+manually by creating formatted strings.
+
+
+.. code-block:: Python
+
+   L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
+
+In contrast, methods of PyLammps accept parameters directly and will convert
+them automatically to a final command string.
+
+
+.. code-block:: Python
+
+   L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
+
+System state
+------------
+
+In addition to dispatching commands directly through the PyLammps object, it
+also provides several properties which allow you to query the system state.
+
+
+
+L.system
+   Is a dictionary describing the system such as the bounding box or number of atoms
+
+L.system.xlo, L.system.xhi
+   bounding box limits along x-axis
+
+L.system.ylo, L.system.yhi
+   bounding box limits along y-axis
+
+L.system.zlo, L.system.zhi
+   bounding box limits along z-axis
+
+L.communication
+   configuration of communication subsystem, such as the number of threads or processors
+
+L.communication.nthreads
+   number of threads used by each LAMMPS process
+
+L.communication.nprocs
+   number of MPI processes used by LAMMPS
+
+L.fixes
+   List of fixes in the current system
+
+L.computes
+   List of active computes in the current system
+
+L.dump
+   List of active dumps in the current system
+
+L.groups
+   List of groups present in the current system
+
+
+
+Working with LAMMPS variables
+-----------------------------
+
+LAMMPS variables can be both defined and accessed via the PyLammps interface.
+
+To define a variable you can use the :doc:`variable <variable>` command:
+
+
+.. code-block:: Python
+
+   L.variable("a index 2")
+
+A dictionary of all variables is returned by L.variables
+
+you can access an individual variable by retrieving a variable object from the
+L.variables dictionary by name
+
+
+.. code-block:: Python
+
+   a = L.variables['a']
+
+The variable value can then be easily read and written by accessing the value
+property of this object.
+
+
+.. code-block:: Python
+
+   print(a.value)
+   a.value = 4
+
+Retrieving the value of an arbitrary LAMMPS expressions
+-------------------------------------------------------
+
+LAMMPS expressions can be immediately evaluated by using the eval method. The
+passed string parameter can be any expression containing global thermo values,
+variables, compute or fix data.
+
+
+.. code-block:: Python
+
+   result = L.eval("ke") # kinetic energy
+   result = L.eval("pe") # potential energy
+
+   result = L.eval("v_t/2.0")
+
+Accessing atom data
+-------------------
+
+All atoms in the current simulation can be accessed by using the L.atoms list.
+Each element of this list is an object which exposes its properties (id, type,
+position, velocity, force, etc.).
+
+
+.. code-block:: Python
+
+   # access first atom
+   L.atoms[0].id
+   L.atoms[0].type
+
+   # access second atom
+   L.atoms[1].position
+   L.atoms[1].velocity
+   L.atoms[1].force
+
+Some properties can also be used to set:
+
+
+.. code-block:: Python
+
+   # set position in 2D simulation
+   L.atoms[0].position = (1.0, 0.0)
+
+   # set position in 3D simulation
+   L.atoms[0].position = (1.0, 0.0, 1.)
+
+Evaluating thermo data
+----------------------
+
+Each simulation run usually produces thermo output based on system state,
+computes, fixes or variables. The trajectories of these values can be queried
+after a run via the L.runs list. This list contains a growing list of run data.
+The first element is the output of the first run, the second element that of
+the second run.
+
+
+.. code-block:: Python
+
+   L.run(1000)
+   L.runs[0] # data of first 1000 time steps
+
+   L.run(1000)
+   L.runs[1] # data of second 1000 time steps
+
+Each run contains a dictionary of all trajectories. Each trajectory is
+accessible through its thermo name:
+
+
+.. code-block:: Python
+
+   L.runs[0].thermo.Step # list of time steps in first run
+   L.runs[0].thermo.Ke   # list of kinetic energy values in first run
+
+Together with matplotlib plotting data out of LAMMPS becomes simple:
+
+
+.. code-block:: Python
+
+   import matplotlib.plot as plt
+   steps = L.runs[0].thermo.Step
+   ke    = L.runs[0].thermo.Ke
+   plt.plot(steps, ke)
+
+Error handling with PyLammps
+----------------------------
+
+Compiling the shared library with C++ exception support provides a better error
+handling experience.  Without exceptions the LAMMPS code will terminate the
+current Python process with an error message.  C++ exceptions allow capturing
+them on the C++ side and rethrowing them on the Python side. This way you
+can handle LAMMPS errors through the Python exception handling mechanism.
+
+.. warning::
+
+   Capturing a LAMMPS exception in Python can still mean that the
+   current LAMMPS process is in an illegal state and must be terminated. It is
+   advised to save your data and terminate the Python instance as quickly as
+   possible.
+
+Using PyLammps in IPython notebooks and Jupyter
+-----------------------------------------------
+
+If the LAMMPS Python package is installed for the same Python interpreter as
+IPython, you can use PyLammps directly inside of an IPython notebook inside of
+Jupyter. Jupyter is a powerful integrated development environment (IDE) for
+many dynamic languages like Python, Julia and others, which operates inside of
+any web browser. Besides auto-completion and syntax highlighting it allows you
+to create formatted documents using Markup, mathematical formulas, graphics and
+animations intermixed with executable Python code. It is a great format for
+tutorials and showcasing your latest research.
+
+To launch an instance of Jupyter simply run the following command inside your
+Python environment (this assumes you followed the Quick Start instructions):
+
+
+.. code-block:: bash
+
+   jupyter notebook
+
+IPyLammps Examples
+------------------
+
+Examples of IPython notebooks can be found in the python/examples/pylammps
+sub-directory. To open these notebooks launch *jupyter notebook* inside this
+directory and navigate to one of them. If you compiled and installed
+a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
+you should be able to rerun all of these notebooks.
+
+Validating a dihedral potential
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example showcases how an IPython Notebook can be used to compare a simple
+LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
+Four atoms are placed in the simulation and the dihedral potential is applied on
+them using a datafile. Then one of the atoms is rotated along the central axis by
+setting its position from Python, which changes the dihedral angle.
+
+
+.. code-block:: Python
+
+   phi = [d \* math.pi / 180 for d in range(360)]
+
+   pos = [(1.0, math.cos(p), math.sin(p)) for p in phi]
+
+   pe = []
+   for p in pos:
+       L.atoms[3].position = p
+       L.run(0)
+       pe.append(L.eval("pe"))
+
+By evaluating the potential energy for each position we can verify that
+trajectory with the analytical formula.  To compare both solutions, we plot
+both trajectories over each other using matplotlib, which embeds the generated
+plot inside the IPython notebook.
+
+.. image:: JPG/pylammps_dihedral.jpg
+   :align: center
+
+Running a Monte Carlo relaxation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation
+simulation, computing and plotting energy terms and even embedding video output.
+
+Initially, a 2D system is created in a state with minimal energy.
+
+.. image:: JPG/pylammps_mc_minimum.jpg
+   :align: center
+
+It is then disordered by moving each atom by a random delta.
+
+
+.. code-block:: Python
+
+   random.seed(27848)
+   deltaperturb = 0.2
+
+   for i in range(L.system.natoms):
+       x, y = L.atoms[i].position
+       dx = deltaperturb \* random.uniform(-1, 1)
+       dy = deltaperturb \* random.uniform(-1, 1)
+       L.atoms[i].position  = (x+dx, y+dy)
+
+   L.run(0)
+
+.. image:: JPG/pylammps_mc_disordered.jpg
+   :align: center
+
+Finally, the Monte Carlo algorithm is implemented in Python. It continuously
+moves random atoms by a random delta and only accepts certain moves.
+
+
+.. code-block:: Python
+
+   estart = L.eval("pe")
+   elast = estart
+
+   naccept = 0
+   energies = [estart]
+
+   niterations = 3000
+   deltamove = 0.1
+   kT = 0.05
+
+   natoms = L.system.natoms
+
+   for i in range(niterations):
+       iatom = random.randrange(0, natoms)
+       current_atom = L.atoms[iatom]
+
+       x0, y0 = current_atom.position
+
+       dx = deltamove \* random.uniform(-1, 1)
+       dy = deltamove \* random.uniform(-1, 1)
+
+       current_atom.position = (x0+dx, y0+dy)
+
+       L.run(1, "pre no post no")
+
+       e = L.eval("pe")
+       energies.append(e)
+
+       if e <= elast:
+           naccept += 1
+           elast = e
+       elif random.random() <= math.exp(natoms\*(elast-e)/kT):
+           naccept += 1
+           elast = e
+       else:
+           current_atom.position = (x0, y0)
+
+The energies of each iteration are collected in a Python list and finally plotted using matplotlib.
+
+.. image:: JPG/pylammps_mc_energies_plot.jpg
+   :align: center
+
+The IPython notebook also shows how to use dump commands and embed video files
+inside of the IPython notebook.
+
+Using PyLammps and mpi4py (Experimental)
+----------------------------------------
+
+PyLammps can be run in parallel using mpi4py. This python package can be installed using
+
+
+.. code-block:: bash
+
+   pip install mpi4py
+
+The following is a short example which reads in an existing LAMMPS input file and
+executes it in parallel.  You can find in.melt in the examples/melt folder.
+
+
+.. code-block:: Python
+
+   from mpi4py import MPI
+   from lammps import PyLammps
+
+   L = PyLammps()
+   L.file("in.melt")
+
+   if MPI.COMM_WORLD.rank == 0:
+       print("Potential energy: ", L.eval("pe"))
+
+   MPI.Finalize()
+
+To run this script (melt.py) in parallel using 4 MPI processes we invoke the
+following mpirun command:
+
+
+.. code-block:: bash
+
+   mpirun -np 4 python melt.py
+
+.. warning::
+
+   Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0.
+
+Feedback and Contributing
+-------------------------
+
+If you find this Python interface useful, please feel free to provide feedback
+and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
+want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
+and maybe their latest research results.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_pylammps.txt b/doc/src/Howto_pylammps.txt
deleted file mode 100644
index 54f17d912a..0000000000
--- a/doc/src/Howto_pylammps.txt
+++ /dev/null
@@ -1,481 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-PyLammps Tutorial :h3
-
-<!-- RST
-.. contents::
-
-END_RST -->
-
-Overview :h4
-
-PyLammps is a Python wrapper class which can be created on its own or
-use an existing lammps Python object.  It creates a simpler,
-Python-like interface to common LAMMPS functionality, in contrast to
-the lammps.py wrapper on the C-style LAMMPS library interface which is
-written using Python ctypes.  The lammps.py wrapper is discussed on
-the "Python library"_Python_library.html doc page.
-
-Unlike the flat ctypes interface, PyLammps exposes a discoverable API.
-It no longer requires knowledge of the underlying C++ code
-implementation.  Finally, the IPyLammps wrapper builds on top of
-PyLammps and adds some additional features for IPython integration
-into IPython notebooks, e.g. for embedded visualization output from
-dump/image.
-
-Comparison of lammps and PyLammps interfaces :h5
-
-lammps.lammps :h6
-
-uses C-Types
-direct memory access to native C++ data
-provides functions to send and receive data to LAMMPS
-requires knowledge of how LAMMPS internally works (C pointers, etc) :ul
-
-lammps.PyLammps :h6
-
-higher-level abstraction built on top of original C-Types interface
-manipulation of Python objects
-communication with LAMMPS is hidden from API user
-shorter, more concise Python
-better IPython integration, designed for quick prototyping :ul
-
-Quick Start :h4
-
-System-wide Installation :h5
-
-Step 1: Building LAMMPS as a shared library :h6
-
-To use LAMMPS inside of Python it has to be compiled as shared library. This
-library is then loaded by the Python interface. In this example we enable the
-MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
-output support enabled.
-
-Step 1a: For the CMake based build system, the steps are:
-
-mkdir $LAMMPS_DIR/build-shared
-cd  $LAMMPS_DIR/build-shared :pre
-
-# MPI, PNG, Jpeg, FFMPEG are auto-detected
-cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
-make :pre
-
-Step 1b: For the legacy, make based build system, the steps are:
-
-cd $LAMMPS_DIR/src :pre
-
-# add packages if necessary
-make yes-MOLECULE :pre
-
-# compile shared library using Makefile
-make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg" :pre
-
-Step 2: Installing the LAMMPS Python package :h6
-
-PyLammps is part of the lammps Python package. To install it simply install
-that package into your current Python installation with:
-
-make install-python :pre
-
-NOTE: Recompiling the shared library requires re-installing the Python package
-
-
-Installation inside of a virtualenv :h5
-
-You can use virtualenv to create a custom Python environment specifically tuned
-for your workflow.
-
-Benefits of using a virtualenv :h6
-
-isolation of your system Python installation from your development installation
-installation can happen in your user directory without root access (useful for HPC clusters)
-installing packages through pip allows you to get newer versions of packages than e.g., through apt-get or yum package managers (and without root access)
-you can even install specific old versions of a package if necessary :ul
-
-[Prerequisite (e.g. on Ubuntu)]
-
-apt-get install python-virtualenv :pre
-
-Creating a virtualenv with lammps installed :h6
-
-# create virtualenv named 'testing'
-virtualenv $HOME/python/testing :pre
-
-# activate 'testing' environment
-source $HOME/python/testing/bin/activate :pre
-
-Now configure and compile the LAMMPS shared library as outlined above.
-When using CMake and the shared library has already been build, you
-need to re-run CMake to update the location of the python executable
-to the location in the virtual environment with:
-
-cmake . -DPYTHON_EXECUTABLE=$(which python) :pre
-
-# install LAMMPS package in virtualenv
-(testing) make install-python :pre
-
-# install other useful packages
-(testing) pip install matplotlib jupyter mpi4py :pre
-
-... :pre
-
-# return to original shell
-(testing) deactivate :pre
-
-
-Creating a new instance of PyLammps :h4
-
-To create a PyLammps object you need to first import the class from the lammps
-module. By using the default constructor, a new {lammps} instance is created.
-
-from lammps import PyLammps
-L = PyLammps() :pre
-
-You can also initialize PyLammps on top of this existing {lammps} object:
-
-from lammps import lammps, PyLammps
-lmp = lammps()
-L = PyLammps(ptr=lmp) :pre
-
-Commands :h4
-
-Sending a LAMMPS command with the existing library interfaces is done using
-the command method of the lammps object instance.
-
-For instance, let's take the following LAMMPS command:
-
-region box block 0 10 0 5 -0.5 0.5 :pre
-
-In the original interface this command can be executed with the following
-Python code if {L} was a lammps instance:
-
-L.command("region box block 0 10 0 5 -0.5 0.5") :pre
-
-With the PyLammps interface, any command can be split up into arbitrary parts
-separated by white-space, passed as individual arguments to a region method.
-
-L.region("box block", 0, 10, 0, 5, -0.5, 0.5) :pre
-
-Note that each parameter is set as Python literal floating-point number. In the
-PyLammps interface, each command takes an arbitrary parameter list and transparently
-merges it to a single command string, separating individual parameters by white-space.
-
-The benefit of this approach is avoiding redundant command calls and easier
-parameterization. In the original interface parameterization needed to be done
-manually by creating formatted strings.
-
-L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) :pre
-
-In contrast, methods of PyLammps accept parameters directly and will convert
-them automatically to a final command string.
-
-L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) :pre
-
-System state :h4
-
-In addition to dispatching commands directly through the PyLammps object, it
-also provides several properties which allow you to query the system state.
-
-:dlb
-
-L.system :dt
-
-Is a dictionary describing the system such as the bounding box or number of atoms :dd
-
-L.system.xlo, L.system.xhi :dt
-
-bounding box limits along x-axis :dd
-
-L.system.ylo, L.system.yhi :dt
-
-bounding box limits along y-axis :dd
-
-L.system.zlo, L.system.zhi :dt
-
-bounding box limits along z-axis :dd
-
-L.communication :dt
-
-configuration of communication subsystem, such as the number of threads or processors :dd
-
-L.communication.nthreads :dt
-
-number of threads used by each LAMMPS process :dd
-
-L.communication.nprocs :dt
-
-number of MPI processes used by LAMMPS :dd
-
-L.fixes :dt
-
-List of fixes in the current system :dd
-
-L.computes :dt
-
-List of active computes in the current system :dd
-
-L.dump :dt
-
-List of active dumps in the current system :dd
-
-L.groups :dt
-
-List of groups present in the current system :dd
-
-:dle
-
-Working with LAMMPS variables :h4
-
-LAMMPS variables can be both defined and accessed via the PyLammps interface.
-
-To define a variable you can use the "variable"_variable.html command:
-
-L.variable("a index 2") :pre
-
-A dictionary of all variables is returned by L.variables
-
-you can access an individual variable by retrieving a variable object from the
-L.variables dictionary by name
-
-a = L.variables\['a'\] :pre
-
-The variable value can then be easily read and written by accessing the value
-property of this object.
-
-print(a.value)
-a.value = 4 :pre
-
-Retrieving the value of an arbitrary LAMMPS expressions :h4
-
-LAMMPS expressions can be immediately evaluated by using the eval method. The
-passed string parameter can be any expression containing global thermo values,
-variables, compute or fix data.
-
-result = L.eval("ke") # kinetic energy
-result = L.eval("pe") # potential energy :pre
-
-result = L.eval("v_t/2.0") :pre
-
-Accessing atom data :h4
-
-All atoms in the current simulation can be accessed by using the L.atoms list.
-Each element of this list is an object which exposes its properties (id, type,
-position, velocity, force, etc.).
-
-# access first atom
-L.atoms\[0\].id
-L.atoms\[0\].type :pre
-
-# access second atom
-L.atoms\[1\].position
-L.atoms\[1\].velocity
-L.atoms\[1\].force :pre
-
-Some properties can also be used to set:
-
-# set position in 2D simulation
-L.atoms\[0\].position = (1.0, 0.0) :pre
-
-# set position in 3D simulation
-L.atoms\[0\].position = (1.0, 0.0, 1.) :pre
-
-Evaluating thermo data :h4
-
-Each simulation run usually produces thermo output based on system state,
-computes, fixes or variables. The trajectories of these values can be queried
-after a run via the L.runs list. This list contains a growing list of run data.
-The first element is the output of the first run, the second element that of
-the second run.
-
-L.run(1000)
-L.runs\[0\] # data of first 1000 time steps :pre
-
-L.run(1000)
-L.runs\[1\] # data of second 1000 time steps :pre
-
-Each run contains a dictionary of all trajectories. Each trajectory is
-accessible through its thermo name:
-
-L.runs\[0\].step # list of time steps in first run
-L.runs\[0\].ke   # list of kinetic energy values in first run :pre
-
-Together with matplotlib plotting data out of LAMMPS becomes simple:
-
-import matplotlib.plot as plt
-
-steps = L.runs\[0\].step
-ke    = L.runs\[0\].ke
-plt.plot(steps, ke) :pre
-
-Error handling with PyLammps :h4
-
-Compiling the shared library with C++ exception support provides a better error
-handling experience.  Without exceptions the LAMMPS code will terminate the
-current Python process with an error message.  C++ exceptions allow capturing
-them on the C++ side and rethrowing them on the Python side. This way you
-can handle LAMMPS errors through the Python exception handling mechanism.
-
-IMPORTANT NOTE: Capturing a LAMMPS exception in Python can still mean that the
-current LAMMPS process is in an illegal state and must be terminated. It is
-advised to save your data and terminate the Python instance as quickly as
-possible.
-
-Using PyLammps in IPython notebooks and Jupyter :h4
-
-If the LAMMPS Python package is installed for the same Python interpreter as
-IPython, you can use PyLammps directly inside of an IPython notebook inside of
-Jupyter. Jupyter is a powerful integrated development environment (IDE) for
-many dynamic languages like Python, Julia and others, which operates inside of
-any web browser. Besides auto-completion and syntax highlighting it allows you
-to create formatted documents using Markup, mathematical formulas, graphics and
-animations intermixed with executable Python code. It is a great format for
-tutorials and showcasing your latest research.
-
-To launch an instance of Jupyter simply run the following command inside your
-Python environment (this assumes you followed the Quick Start instructions):
-
-jupyter notebook :pre
-
-IPyLammps Examples :h4
-
-Examples of IPython notebooks can be found in the python/examples/pylammps
-sub-directory. To open these notebooks launch {jupyter notebook} inside this
-directory and navigate to one of them. If you compiled and installed
-a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
-you should be able to rerun all of these notebooks.
-
-Validating a dihedral potential :h5
-
-This example showcases how an IPython Notebook can be used to compare a simple
-LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
-Four atoms are placed in the simulation and the dihedral potential is applied on
-them using a datafile. Then one of the atoms is rotated along the central axis by
-setting its position from Python, which changes the dihedral angle.
-
-phi = \[d * math.pi / 180 for d in range(360)\] :pre
-
-pos = \[(1.0, math.cos(p), math.sin(p)) for p in phi\] :pre
-
-pe = \[\]
-for p in pos:
-    L.atoms\[3\].position = p
-    L.run(0)
-    pe.append(L.eval("pe")) :pre
-
-By evaluating the potential energy for each position we can verify that
-trajectory with the analytical formula.  To compare both solutions, we plot
-both trajectories over each other using matplotlib, which embeds the generated
-plot inside the IPython notebook.
-
-:c,image(JPG/pylammps_dihedral.jpg)
-
-Running a Monte Carlo relaxation :h5
-
-This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation
-simulation, computing and plotting energy terms and even embedding video output.
-
-Initially, a 2D system is created in a state with minimal energy.
-
-:c,image(JPG/pylammps_mc_minimum.jpg)
-
-It is then disordered by moving each atom by a random delta.
-
-random.seed(27848)
-deltaperturb = 0.2 :pre
-
-for i in range(L.system.natoms):
-    x, y = L.atoms\[i\].position
-    dx = deltaperturb * random.uniform(-1, 1)
-    dy = deltaperturb * random.uniform(-1, 1)
-    L.atoms\[i\].position  = (x+dx, y+dy) :pre
-
-L.run(0) :pre
-
-:c,image(JPG/pylammps_mc_disordered.jpg)
-
-Finally, the Monte Carlo algorithm is implemented in Python. It continuously
-moves random atoms by a random delta and only accepts certain moves.
-
-estart = L.eval("pe")
-elast = estart :pre
-
-naccept = 0
-energies = \[estart\] :pre
-
-niterations = 3000
-deltamove = 0.1
-kT = 0.05 :pre
-
-natoms = L.system.natoms :pre
-
-for i in range(niterations):
-    iatom = random.randrange(0, natoms)
-    current_atom = L.atoms\[iatom\] :pre
-
-    x0, y0 = current_atom.position :pre
-
-    dx = deltamove * random.uniform(-1, 1)
-    dy = deltamove * random.uniform(-1, 1) :pre
-
-    current_atom.position = (x0+dx, y0+dy) :pre
-
-    L.run(1, "pre no post no") :pre
-
-    e = L.eval("pe")
-    energies.append(e) :pre
-
-    if e <= elast:
-        naccept += 1
-        elast = e
-    elif random.random() <= math.exp(natoms*(elast-e)/kT):
-        naccept += 1
-        elast = e
-    else:
-        current_atom.position = (x0, y0) :pre
-
-The energies of each iteration are collected in a Python list and finally plotted using matplotlib.
-
-:c,image(JPG/pylammps_mc_energies_plot.jpg)
-
-The IPython notebook also shows how to use dump commands and embed video files
-inside of the IPython notebook.
-
-Using PyLammps and mpi4py (Experimental) :h4
-
-PyLammps can be run in parallel using mpi4py. This python package can be installed using
-
-pip install mpi4py :pre
-
-The following is a short example which reads in an existing LAMMPS input file and
-executes it in parallel.  You can find in.melt in the examples/melt folder.
-
-from mpi4py import MPI
-from lammps import PyLammps :pre
-
-L = PyLammps()
-L.file("in.melt") :pre
-
-if MPI.COMM_WORLD.rank == 0:
-    print("Potential energy: ", L.eval("pe")) :pre
-
-MPI.Finalize() :pre
-
-To run this script (melt.py) in parallel using 4 MPI processes we invoke the
-following mpirun command:
-
-mpirun -np 4 python melt.py :pre
-
-IMPORTANT NOTE: Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0.
-
-Feedback and Contributing :h4
-
-If you find this Python interface useful, please feel free to provide feedback
-and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
-want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
-and maybe their latest research results.
diff --git a/doc/src/Howto_replica.rst b/doc/src/Howto_replica.rst
new file mode 100644
index 0000000000..49150ae985
--- /dev/null
+++ b/doc/src/Howto_replica.rst
@@ -0,0 +1,60 @@
+Multi-replica simulations
+=========================
+
+Several commands in LAMMPS run multi-replica simulations, meaning
+that multiple instances (replicas) of your simulation are run
+simultaneously, with small amounts of data exchanged between replicas
+periodically.
+
+These are the relevant commands:
+
+* :doc:`neb <neb>` for nudged elastic band calculations
+* :doc:`neb\_spin <neb_spin>` for magnetic nudged elastic band calculations
+* :doc:`prd <prd>` for parallel replica dynamics
+* :doc:`tad <tad>` for temperature accelerated dynamics
+* :doc:`temper <temper>` for parallel tempering
+* :doc:`fix pimd <fix_pimd>` for path-integral molecular dynamics (PIMD)
+
+NEB is a method for finding transition states and barrier energies.
+PRD and TAD are methods for performing accelerated dynamics to find
+and perform infrequent events.  Parallel tempering or replica exchange
+runs different replicas at a series of temperature to facilitate
+rare-event sampling.
+
+These commands can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+PIMD runs different replicas whose individual particles are coupled
+together by springs to model a system or ring-polymers.
+
+This commands can only be used if LAMMPS was built with the USER-MISC
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+In all these cases, you must run with one or more processors per
+replica.  The processors assigned to each replica are determined at
+run-time by using the :doc:`-partition command-line switch <Run_options>` to launch LAMMPS on multiple partitions,
+which in this context are the same as replicas.  E.g.  these commands:
+
+
+.. parsed-literal::
+
+   mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
+   mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
+
+would each run 8 replicas, on either 16 or 8 processors.  Note the use
+of the :doc:`-in command-line switch <Run_options>` to specify the input
+script which is required when running in multi-replica mode.
+
+Also note that with MPI installed on a machine (e.g. your desktop),
+you can run on more (virtual) processors than you have physical
+processors.  Thus the above commands could be run on a
+single-processor (or few-processor) desktop so that you can run
+a multi-replica simulation on more replicas than you have
+physical processors.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_restart.rst b/doc/src/Howto_restart.rst
new file mode 100644
index 0000000000..608246ccbc
--- /dev/null
+++ b/doc/src/Howto_restart.rst
@@ -0,0 +1,105 @@
+Restart a simulation
+====================
+
+There are 3 ways to continue a long LAMMPS simulation.  Multiple
+:doc:`run <run>` commands can be used in the same input script.  Each
+run will continue from where the previous run left off.  Or binary
+restart files can be saved to disk using the :doc:`restart <restart>`
+command.  At a later time, these binary files can be read via a
+:doc:`read\_restart <read_restart>` command in a new script.  Or they can
+be converted to text data files using the :doc:`-r command-line switch <Run_options>` and read by a :doc:`read\_data <read_data>`
+command in a new script.
+
+Here we give examples of 2 scripts that read either a binary restart
+file or a converted data file and then issue a new run command to
+continue where the previous run left off.  They illustrate what
+settings must be made in the new script.  Details are discussed in the
+documentation for the :doc:`read\_restart <read_restart>` and
+:doc:`read\_data <read_data>` commands.
+
+Look at the *in.chain* input script provided in the *bench* directory
+of the LAMMPS distribution to see the original script that these 2
+scripts are based on.  If that script had the line
+
+
+.. parsed-literal::
+
+   restart         50 tmp.restart
+
+added to it, it would produce 2 binary restart files (tmp.restart.50
+and tmp.restart.100) as it ran.
+
+This script could be used to read the 1st restart file and re-run the
+last 50 timesteps:
+
+
+.. parsed-literal::
+
+   read_restart    tmp.restart.50
+
+   neighbor        0.4 bin
+   neigh_modify    every 1 delay 1
+
+   fix             1 all nve
+   fix             2 all langevin 1.0 1.0 10.0 904297
+
+   timestep        0.012
+
+   run             50
+
+Note that the following commands do not need to be repeated because
+their settings are included in the restart file: *units, atom\_style,
+special\_bonds, pair\_style, bond\_style*.  However these commands do
+need to be used, since their settings are not in the restart file:
+*neighbor, fix, timestep*\ .
+
+If you actually use this script to perform a restarted run, you will
+notice that the thermodynamic data match at step 50 (if you also put a
+"thermo 50" command in the original script), but do not match at step
+100.  This is because the :doc:`fix langevin <fix_langevin>` command
+uses random numbers in a way that does not allow for perfect restarts.
+
+As an alternate approach, the restart file could be converted to a data
+file as follows:
+
+
+.. parsed-literal::
+
+   lmp_g++ -r tmp.restart.50 tmp.restart.data
+
+Then, this script could be used to re-run the last 50 steps:
+
+
+.. parsed-literal::
+
+   units           lj
+   atom_style      bond
+   pair_style      lj/cut 1.12
+   pair_modify     shift yes
+   bond_style      fene
+   special_bonds   0.0 1.0 1.0
+
+   read_data       tmp.restart.data
+
+   neighbor        0.4 bin
+   neigh_modify    every 1 delay 1
+
+   fix             1 all nve
+   fix             2 all langevin 1.0 1.0 10.0 904297
+
+   timestep        0.012
+
+   reset_timestep  50
+   run             50
+
+Note that nearly all the settings specified in the original *in.chain*
+script must be repeated, except the *pair\_coeff* and *bond\_coeff*
+commands since the new data file lists the force field coefficients.
+Also, the :doc:`reset\_timestep <reset_timestep>` command is used to tell
+LAMMPS the current timestep.  This value is stored in restart files,
+but not in data files.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst
new file mode 100644
index 0000000000..353f32c193
--- /dev/null
+++ b/doc/src/Howto_spc.rst
@@ -0,0 +1,57 @@
+SPC water model
+===============
+
+The SPC water model specifies a 3-site rigid water molecule with
+charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
+the two O-H bonds and the H-O-H angle rigid.  A bond style of
+*harmonic* and an angle style of *harmonic* or *charmm* should also be
+used.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid SPC model.
+
+| O mass = 15.9994
+| H mass = 1.008
+| O charge = -0.820
+| H charge = 0.410
+| LJ epsilon of OO = 0.1553
+| LJ sigma of OO = 3.166
+| LJ epsilon, sigma of OH, HH = 0.0
+| r0 of OH bond = 1.0
+| theta of HOH angle = 109.47
+| 
+
+Note that as originally proposed, the SPC model was run with a 9
+Angstrom cutoff for both LJ and Coulombic terms.  It can also be used
+with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
+any of the parameters above, though it becomes a different model in
+that mode of usage.
+
+The SPC/E (extended) water model is the same, except
+the partial charge assignments change:
+
+| O charge = -0.8476
+| H charge = 0.4238
+| 
+
+See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
+the SPC and SPC/E models.
+
+Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+
+
+----------
+
+
+.. _howto-Berendsen:
+
+
+
+**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91,
+6269-6271 (1987).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_spherical.rst b/doc/src/Howto_spherical.rst
new file mode 100644
index 0000000000..23ea6435f8
--- /dev/null
+++ b/doc/src/Howto_spherical.rst
@@ -0,0 +1,243 @@
+Finite-size spherical and aspherical particles
+==============================================
+
+Typical MD models treat atoms or particles as point masses.  Sometimes
+it is desirable to have a model with finite-size particles such as
+spheroids or ellipsoids or generalized aspherical bodies.  The
+difference is that such particles have a moment of inertia, rotational
+energy, and angular momentum.  Rotation is induced by torque coming
+from interactions with other particles.
+
+LAMMPS has several options for running simulations with these kinds of
+particles.  The following aspects are discussed in turn:
+
+* atom styles
+* pair potentials
+* time integration
+* computes, thermodynamics, and dump output
+* rigid bodies composed of finite-size particles
+
+Example input scripts for these kinds of models are in the body,
+colloid, dipole, ellipse, line, peri, pour, and tri directories of the
+:doc:`examples directory <Examples>` in the LAMMPS distribution.
+
+Atom styles
+-----------
+
+There are several :doc:`atom styles <atom_style>` that allow for
+definition of finite-size particles: sphere, dipole, ellipsoid, line,
+tri, peri, and body.
+
+The sphere style defines particles that are spheroids and each
+particle can have a unique diameter and mass (or density).  These
+particles store an angular velocity (omega) and can be acted upon by
+torque.  The "set" command can be used to modify the diameter and mass
+of individual particles, after then are created.
+
+The dipole style does not actually define finite-size particles, but
+is often used in conjunction with spherical particles, via a command
+like
+
+
+.. parsed-literal::
+
+   atom_style hybrid sphere dipole
+
+This is because when dipoles interact with each other, they induce
+torques, and a particle must be finite-size (i.e. have a moment of
+inertia) in order to respond and rotate.  See the :doc:`atom\_style dipole <atom_style>` command for details.  The "set" command can be
+used to modify the orientation and length of the dipole moment of
+individual particles, after then are created.
+
+The ellipsoid style defines particles that are ellipsoids and thus can
+be aspherical.  Each particle has a shape, specified by 3 diameters,
+and mass (or density).  These particles store an angular momentum and
+their orientation (quaternion), and can be acted upon by torque.  They
+do not store an angular velocity (omega), which can be in a different
+direction than angular momentum, rather they compute it as needed.
+The "set" command can be used to modify the diameter, orientation, and
+mass of individual particles, after then are created.  It also has a
+brief explanation of what quaternions are.
+
+The line style defines line segment particles with two end points and
+a mass (or density).  They can be used in 2d simulations, and they can
+be joined together to form rigid bodies which represent arbitrary
+polygons.
+
+The tri style defines triangular particles with three corner points
+and a mass (or density).  They can be used in 3d simulations, and they
+can be joined together to form rigid bodies which represent arbitrary
+particles with a triangulated surface.
+
+The peri style is used with :doc:`Peridynamic models <pair_peri>` and
+defines particles as having a volume, that is used internally in the
+:doc:`pair\_style peri <pair_peri>` potentials.
+
+The body style allows for definition of particles which can represent
+complex entities, such as surface meshes of discrete points,
+collections of sub-particles, deformable objects, etc.  The body style
+is discussed in more detail on the :doc:`Howto body <Howto_body>` doc
+page.
+
+Note that if one of these atom styles is used (or multiple styles via
+the :doc:`atom\_style hybrid <atom_style>` command), not all particles in
+the system are required to be finite-size or aspherical.
+
+For example, in the ellipsoid style, if the 3 shape parameters are set
+to the same value, the particle will be a sphere rather than an
+ellipsoid.  If the 3 shape parameters are all set to 0.0 or if the
+diameter is set to 0.0, it will be a point particle.  In the line or
+tri style, if the lineflag or triflag is specified as 0, then it
+will be a point particle.
+
+Some of the pair styles used to compute pairwise interactions between
+finite-size particles also compute the correct interaction with point
+particles as well, e.g. the interaction between a point particle and a
+finite-size particle or between two point particles.  If necessary,
+:doc:`pair\_style hybrid <pair_hybrid>` can be used to insure the correct
+interactions are computed for the appropriate style of interactions.
+Likewise, using groups to partition particles (ellipsoids versus
+spheres versus point particles) will allow you to use the appropriate
+time integrators and temperature computations for each class of
+particles.  See the doc pages for various commands for details.
+
+Also note that for :doc:`2d simulations <dimension>`, atom styles sphere
+and ellipsoid still use 3d particles, rather than as circular disks or
+ellipses.  This means they have the same moment of inertia as the 3d
+object.  When temperature is computed, the correct degrees of freedom
+are used for rotation in a 2d versus 3d system.
+
+Pair potentials
+---------------
+
+When a system with finite-size particles is defined, the particles
+will only rotate and experience torque if the force field computes
+such interactions.  These are the various :doc:`pair styles <pair_style>` that generate torque:
+
+* :doc:`pair\_style gran/history <pair_gran>`
+* :doc:`pair\_style gran/hertzian <pair_gran>`
+* :doc:`pair\_style gran/no\_history <pair_gran>`
+* :doc:`pair\_style dipole/cut <pair_dipole>`
+* :doc:`pair\_style gayberne <pair_gayberne>`
+* :doc:`pair\_style resquared <pair_resquared>`
+* :doc:`pair\_style brownian <pair_brownian>`
+* :doc:`pair\_style lubricate <pair_lubricate>`
+* :doc:`pair\_style line/lj <pair_line_lj>`
+* :doc:`pair\_style tri/lj <pair_tri_lj>`
+* :doc:`pair\_style body/nparticle <pair_body_nparticle>`
+
+The granular pair styles are used with spherical particles.  The
+dipole pair style is used with the dipole atom style, which could be
+applied to spherical or ellipsoidal particles.  The GayBerne and
+REsquared potentials require ellipsoidal particles, though they will
+also work if the 3 shape parameters are the same (a sphere).  The
+Brownian and lubrication potentials are used with spherical particles.
+The line, tri, and body potentials are used with line segment,
+triangular, and body particles respectively.
+
+Time integration
+----------------
+
+There are several fixes that perform time integration on finite-size
+spherical particles, meaning the integrators update the rotational
+orientation and angular velocity or angular momentum of the particles:
+
+* :doc:`fix nve/sphere <fix_nve_sphere>`
+* :doc:`fix nvt/sphere <fix_nvt_sphere>`
+* :doc:`fix npt/sphere <fix_npt_sphere>`
+
+Likewise, there are 3 fixes that perform time integration on
+ellipsoidal particles:
+
+* :doc:`fix nve/asphere <fix_nve_asphere>`
+* :doc:`fix nvt/asphere <fix_nvt_asphere>`
+* :doc:`fix npt/asphere <fix_npt_asphere>`
+
+The advantage of these fixes is that those which thermostat the
+particles include the rotational degrees of freedom in the temperature
+calculation and thermostatting.  The :doc:`fix langevin <fix_langevin>`
+command can also be used with its *omgea* or *angmom* options to
+thermostat the rotational degrees of freedom for spherical or
+ellipsoidal particles.  Other thermostatting fixes only operate on the
+translational kinetic energy of finite-size particles.
+
+These fixes perform constant NVE time integration on line segment,
+triangular, and body particles:
+
+* :doc:`fix nve/line <fix_nve_line>`
+* :doc:`fix nve/tri <fix_nve_tri>`
+* :doc:`fix nve/body <fix_nve_body>`
+
+Note that for mixtures of point and finite-size particles, these
+integration fixes can only be used with :doc:`groups <group>` which
+contain finite-size particles.
+
+Computes, thermodynamics, and dump output
+-----------------------------------------
+
+There are several computes that calculate the temperature or
+rotational energy of spherical or ellipsoidal particles:
+
+* :doc:`compute temp/sphere <compute_temp_sphere>`
+* :doc:`compute temp/asphere <compute_temp_asphere>`
+* :doc:`compute erotate/sphere <compute_erotate_sphere>`
+* :doc:`compute erotate/asphere <compute_erotate_asphere>`
+
+These include rotational degrees of freedom in their computation.  If
+you wish the thermodynamic output of temperature or pressure to use
+one of these computes (e.g. for a system entirely composed of
+finite-size particles), then the compute can be defined and the
+:doc:`thermo\_modify <thermo_modify>` command used.  Note that by default
+thermodynamic quantities will be calculated with a temperature that
+only includes translational degrees of freedom.  See the
+:doc:`thermo\_style <thermo_style>` command for details.
+
+These commands can be used to output various attributes of finite-size
+particles:
+
+* :doc:`dump custom <dump>`
+* :doc:`compute property/atom <compute_property_atom>`
+* :doc:`dump local <dump>`
+* :doc:`compute body/local <compute_body_local>`
+
+Attributes include the dipole moment, the angular velocity, the
+angular momentum, the quaternion, the torque, the end-point and
+corner-point coordinates (for line and tri particles), and
+sub-particle attributes of body particles.
+
+Rigid bodies composed of finite-size particles
+----------------------------------------------
+
+The :doc:`fix rigid <fix_rigid>` command treats a collection of
+particles as a rigid body, computes its inertia tensor, sums the total
+force and torque on the rigid body each timestep due to forces on its
+constituent particles, and integrates the motion of the rigid body.
+
+If any of the constituent particles of a rigid body are finite-size
+particles (spheres or ellipsoids or line segments or triangles), then
+their contribution to the inertia tensor of the body is different than
+if they were point particles.  This means the rotational dynamics of
+the rigid body will be different.  Thus a model of a dimer is
+different if the dimer consists of two point masses versus two
+spheroids, even if the two particles have the same mass.  Finite-size
+particles that experience torque due to their interaction with other
+particles will also impart that torque to a rigid body they are part
+of.
+
+See the "fix rigid" command for example of complex rigid-body models
+it is possible to define in LAMMPS.
+
+Note that the :doc:`fix shake <fix_shake>` command can also be used to
+treat 2, 3, or 4 particles as a rigid body, but it always assumes the
+particles are point masses.
+
+Also note that body particles cannot be modeled with the :doc:`fix rigid <fix_rigid>` command.  Body particles are treated by LAMMPS
+as single particles, though they can store internal state, such as a
+list of sub-particles.  Individual body particles are typically treated
+as rigid bodies, and their motion integrated with a command like :doc:`fix nve/body <fix_nve_body>`.  Interactions between pairs of body
+particles are computed via a command like :doc:`pair\_style body/nparticle <pair_body_nparticle>`.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_spins.rst b/doc/src/Howto_spins.rst
new file mode 100644
index 0000000000..eb1cf1e956
--- /dev/null
+++ b/doc/src/Howto_spins.rst
@@ -0,0 +1,73 @@
+Magnetic spins
+==============
+
+The magnetic spin simulations are enabled by the SPIN package, whose
+implementation is detailed in :ref:`Tranchida <Tranchida>`.
+
+The model represents the simulation of atomic magnetic spins coupled
+to lattice vibrations. The dynamics of those magnetic spins can be used
+to simulate a broad range a phenomena related to magneto-elasticity, or
+or to study the influence of defects on the magnetic properties of
+materials.
+
+The magnetic spins are interacting with each others and with the
+lattice via pair interactions. Typically, the magnetic exchange
+interaction can be defined using the
+:doc:`pair/spin/exchange <pair_spin_exchange>` command. This exchange
+applies a magnetic torque to a given spin, considering the orientation
+of its neighboring spins and their relative distances.
+It also applies a force on the atoms as a function of the spin
+orientations and their associated inter-atomic distances.
+
+The command :doc:`fix precession/spin <fix_precession_spin>` allows to
+apply a constant magnetic torque on all the spins in the system. This
+torque can be an external magnetic field (Zeeman interaction), or an
+uniaxial magnetic anisotropy.
+
+A Langevin thermostat can be applied to those magnetic spins using
+:doc:`fix langevin/spin <fix_langevin_spin>`. Typically, this thermostat
+can be coupled to another Langevin thermostat applied to the atoms
+using :doc:`fix langevin <fix_langevin>` in order to simulate
+thermostatted spin-lattice systems.
+
+The magnetic Gilbert damping can also be applied using :doc:`fix langevin/spin <fix_langevin_spin>`. It allows to either dissipate
+the thermal energy of the Langevin thermostat, or to perform a
+relaxation of the magnetic configuration toward an equilibrium state.
+
+The command :doc:`fix setforce/spin <fix_setforce>` allows to set the
+components of the magnetic precession vectors (while erasing and
+replacing the previously computed magnetic precession vectors on
+the atom).
+This command can be used to freeze the magnetic moment of certain
+atoms in the simulation by zeroing their precession vector.
+
+The command :doc:`fix nve/spin <fix_nve_spin>` can be used to
+perform a symplectic integration of the combined dynamics of spins
+and atomic motions.
+
+The minimization style :doc:`min/spin <min_spin>` can be applied
+to the spins to perform a minimization of the spin configuration.
+
+All the computed magnetic properties can be output by two main
+commands. The first one is :doc:`compute spin <compute_spin>`, that
+enables to evaluate magnetic averaged quantities, such as the total
+magnetization of the system along x, y, or z, the spin temperature, or
+the magnetic energy. The second command is :doc:`compute property/atom <compute_property_atom>`. It enables to output all the
+per atom magnetic quantities. Typically, the orientation of a given
+magnetic spin, or the magnetic force acting on this spin.
+
+
+----------
+
+
+.. _Tranchida:
+
+
+
+**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, 372, 406-425, (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_temperature.rst b/doc/src/Howto_temperature.rst
new file mode 100644
index 0000000000..ec9cdae2e6
--- /dev/null
+++ b/doc/src/Howto_temperature.rst
@@ -0,0 +1,38 @@
+Calculate temperature
+=====================
+
+Temperature is computed as kinetic energy divided by some number of
+degrees of freedom (and the Boltzmann constant).  Since kinetic energy
+is a function of particle velocity, there is often a need to
+distinguish between a particle's advection velocity (due to some
+aggregate motion of particles) and its thermal velocity.  The sum of
+the two is the particle's total velocity, but the latter is often what
+is wanted to compute a temperature.
+
+LAMMPS has several options for computing temperatures, any of which
+can be used in :doc:`thermostatting <Howto_thermostat>` and
+:doc:`barostatting <Howto_barostat>`.  These :doc:`compute commands <compute>` calculate temperature:
+
+* :doc:`compute temp <compute_temp>`
+* :doc:`compute temp/sphere <compute_temp_sphere>`
+* :doc:`compute temp/asphere <compute_temp_asphere>`
+* :doc:`compute temp/com <compute_temp_com>`
+* :doc:`compute temp/deform <compute_temp_deform>`
+* :doc:`compute temp/partial <compute_temp_partial>`
+* :doc:`compute temp/profile <compute_temp_profile>`
+* :doc:`compute temp/ramp <compute_temp_ramp>`
+* :doc:`compute temp/region <compute_temp_region>`
+
+All but the first 3 calculate velocity biases directly (e.g. advection
+velocities) that are removed when computing the thermal temperature.
+:doc:`Compute temp/sphere <compute_temp_sphere>` and :doc:`compute temp/asphere <compute_temp_asphere>` compute kinetic energy for
+finite-size particles that includes rotational degrees of freedom.
+They both allow for velocity biases indirectly, via an optional extra
+argument which is another temperature compute that subtracts a
+velocity bias.  This allows the translational velocity of spherical or
+aspherical particles to be adjusted in prescribed ways.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst
new file mode 100644
index 0000000000..89d0c7b693
--- /dev/null
+++ b/doc/src/Howto_thermostat.rst
@@ -0,0 +1,99 @@
+Thermostats
+===========
+
+Thermostatting means controlling the temperature of particles in an MD
+simulation.  :doc:`Barostatting <Howto_barostat>` means controlling the
+pressure.  Since the pressure includes a kinetic component due to
+particle velocities, both these operations require calculation of the
+temperature.  Typically a target temperature (T) and/or pressure (P)
+is specified by the user, and the thermostat or barostat attempts to
+equilibrate the system to the requested T and/or P.
+
+Thermostatting in LAMMPS is performed by :doc:`fixes <fix>`, or in one
+case by a pair style.  Several thermostatting fixes are available:
+Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
+(temp/rescale).  Dissipative particle dynamics (DPD) thermostatting
+can be invoked via the *dpd/tstat* pair style:
+
+* :doc:`fix nvt <fix_nh>`
+* :doc:`fix nvt/sphere <fix_nvt_sphere>`
+* :doc:`fix nvt/asphere <fix_nvt_asphere>`
+* :doc:`fix nvt/sllod <fix_nvt_sllod>`
+* :doc:`fix temp/berendsen <fix_temp_berendsen>`
+* :doc:`fix temp/csvr <fix_temp_csvr>`
+* :doc:`fix langevin <fix_langevin>`
+* :doc:`fix temp/rescale <fix_temp_rescale>`
+* :doc:`pair\_style dpd/tstat <pair_dpd>`
+
+:doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
+particles.  :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except
+that it subtracts out a velocity bias due to a deforming box and
+integrates the SLLOD equations of motion.  See the :doc:`Howto nemd <Howto_nemd>` doc page for further details.  :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
+velocities but also rotational velocities for spherical and aspherical
+particles.
+
+.. note::
+
+   A recent (2017) book by :ref:`(Daivis and Todd) <Daivis-thermostat>`
+   discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+   thermostatting generally, for both simple and complex fluids,
+   e.g. molecular systems.  The latter can be tricky to do correctly.
+
+DPD thermostatting alters pairwise interactions in a manner analogous
+to the per-particle thermostatting of :doc:`fix langevin <fix_langevin>`.
+
+Any of the thermostatting fixes can use :doc:`temperature computes <Howto_thermostat>` that remove bias which has two
+effects.  First, the current calculated temperature, which is compared
+to the requested target temperature, is calculated with the velocity
+bias removed.  Second, the thermostat adjusts only the thermal
+temperature component of the particle's velocities, which are the
+velocities with the bias removed.  The removed bias is then added back
+to the adjusted velocities.  See the doc pages for the individual
+fixes and for the :doc:`fix\_modify <fix_modify>` command for
+instructions on how to assign a temperature compute to a
+thermostatting fix.  For example, you can apply a thermostat to only
+the x and z components of velocity by using it in conjunction with
+:doc:`compute temp/partial <compute_temp_partial>`.  Of you could
+thermostat only the thermal temperature of a streaming flow of
+particles without affecting the streaming velocity, by using :doc:`compute temp/profile <compute_temp_profile>`.
+
+.. note::
+
+   Only the nvt fixes perform time integration, meaning they update
+   the velocities and positions of particles due to forces and velocities
+   respectively.  The other thermostat fixes only adjust velocities; they
+   do NOT perform time integration updates.  Thus they should be used in
+   conjunction with a constant NVE integration fix such as these:
+
+* :doc:`fix nve <fix_nve>`
+* :doc:`fix nve/sphere <fix_nve_sphere>`
+* :doc:`fix nve/asphere <fix_nve_asphere>`
+
+Thermodynamic output, which can be setup via the
+:doc:`thermo\_style <thermo_style>` command, often includes temperature
+values.  As explained on the doc page for the
+:doc:`thermo\_style <thermo_style>` command, the default temperature is
+setup by the thermo command itself.  It is NOT the temperature
+associated with any thermostatting fix you have defined or with any
+compute you have defined that calculates a temperature.  The doc pages
+for the thermostatting fixes explain the ID of the temperature compute
+they create.  Thus if you want to view these temperatures, you need to
+specify them explicitly via the :doc:`thermo\_style custom <thermo_style>` command.  Or you can use the
+:doc:`thermo\_modify <thermo_modify>` command to re-define what
+temperature compute is used for default thermodynamic output.
+
+
+----------
+
+
+.. _Daivis-thermostat:
+
+
+
+**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst
new file mode 100644
index 0000000000..a83fa0dd0d
--- /dev/null
+++ b/doc/src/Howto_tip3p.rst
@@ -0,0 +1,81 @@
+TIP3P water model
+=================
+
+The TIP3P water model as implemented in CHARMM
+:ref:`(MacKerell) <howto-tip3p>` specifies a 3-site rigid water molecule with
+charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
+the two O-H bonds and the H-O-H angle rigid.  A bond style of
+*harmonic* and an angle style of *harmonic* or *charmm* should also be
+used.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
+cutoff.  The K values can be used if a flexible TIP3P model (without
+fix shake) is desired.  If the LJ epsilon and sigma for HH and OH are
+set to 0.0, it corresponds to the original 1983 TIP3P model
+:ref:`(Jorgensen) <Jorgensen1>`.
+
+| O mass = 15.9994
+| H mass = 1.008
+| O charge = -0.834
+| H charge = 0.417
+| LJ epsilon of OO = 0.1521
+| LJ sigma of OO = 3.1507
+| LJ epsilon of HH = 0.0460
+| LJ sigma of HH = 0.4000
+| LJ epsilon of OH = 0.0836
+| LJ sigma of OH = 1.7753
+| K of OH bond = 450
+| r0 of OH bond = 0.9572
+| K of HOH angle = 55
+| theta of HOH angle = 104.52
+| 
+
+These are the parameters to use for TIP3P with a long-range Coulombic
+solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) <Price1>` for
+details:
+
+| O mass = 15.9994
+| H mass = 1.008
+| O charge = -0.830
+| H charge = 0.415
+| LJ epsilon of OO = 0.102
+| LJ sigma of OO = 3.188
+| LJ epsilon, sigma of OH, HH = 0.0
+| K of OH bond = 450
+| r0 of OH bond = 0.9572
+| K of HOH angle = 55
+| theta of HOH angle = 104.52
+| 
+
+Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+
+
+----------
+
+
+.. _howto-tip3p:
+
+
+
+**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
+.. _Jorgensen1:
+
+
+
+**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+
+.. _Price1:
+
+
+
+**(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst
new file mode 100644
index 0000000000..449aa8e9f7
--- /dev/null
+++ b/doc/src/Howto_tip4p.rst
@@ -0,0 +1,116 @@
+TIP4P water model
+=================
+
+The four-point TIP4P rigid water model extends the traditional
+three-point TIP3P model by adding an additional site, usually
+massless, where the charge associated with the oxygen atom is placed.
+This site M is located at a fixed distance away from the oxygen along
+the bisector of the HOH bond angle.  A bond style of *harmonic* and an
+angle style of *harmonic* or *charmm* should also be used.
+
+A TIP4P model is run with LAMMPS using either this command
+for a cutoff model:
+
+:doc:`pair\_style lj/cut/tip4p/cut <pair_lj>`
+
+or these two commands for a long-range model:
+
+* :doc:`pair\_style lj/cut/tip4p/long <pair_lj>`
+* :doc:`kspace\_style pppm/tip4p <kspace_style>`
+
+For both models, the bond lengths and bond angles should be held fixed
+using the :doc:`fix shake <fix_shake>` command.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid TIP4P model with a cutoff
+:ref:`(Jorgensen) <Jorgensen5>`.  Note that the OM distance is specified in
+the :doc:`pair\_style <pair_style>` command, not as part of the pair
+coefficients.
+
+| O mass = 15.9994
+| H mass = 1.008
+| O charge = -1.040
+| H charge = 0.520
+| r0 of OH bond = 0.9572
+| theta of HOH angle = 104.52
+| OM distance = 0.15
+| LJ epsilon of O-O = 0.1550
+| LJ sigma of O-O = 3.1536
+| LJ epsilon, sigma of OH, HH = 0.0
+| Coulombic cutoff = 8.5
+| 
+
+For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
+http://dx.doi.org/10.1063/1.1931662) these values can be used:
+
+| O mass = 15.9994
+| H mass =  1.008
+| O charge = -1.1794
+| H charge =  0.5897
+| r0 of OH bond = 0.9572
+| theta of HOH angle = 104.52
+| OM distance = 0.1577
+| LJ epsilon of O-O = 0.21084
+| LJ sigma of O-O = 3.1668
+| LJ epsilon, sigma of OH, HH = 0.0
+| Coulombic cutoff = 8.5
+| 
+
+For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
+http://dx.doi.org/10.1063/1.2121687), these values can be used:
+
+| O mass = 15.9994
+| H mass =  1.008
+| O charge = -1.1128
+| H charge = 0.5564
+| r0 of OH bond = 0.9572
+| theta of HOH angle = 104.52
+| OM distance = 0.1546
+| LJ epsilon of O-O = 0.1852
+| LJ sigma of O-O = 3.1589
+| LJ epsilon, sigma of OH, HH = 0.0
+| Coulombic cutoff = 8.5
+| 
+
+These are the parameters to use for TIP4P with a long-range Coulombic
+solver (e.g. Ewald or PPPM in LAMMPS):
+
+| O mass = 15.9994
+| H mass = 1.008
+| O charge = -1.0484
+| H charge = 0.5242
+| r0 of OH bond = 0.9572
+| theta of HOH angle = 104.52
+| OM distance = 0.1250
+| LJ epsilon of O-O = 0.16275
+| LJ sigma of O-O = 3.16435
+| LJ epsilon, sigma of OH, HH = 0.0
+| 
+
+Note that the when using the TIP4P pair style, the neighbor list
+cutoff for Coulomb interactions is effectively extended by a distance
+2 \* (OM distance), to account for the offset distance of the
+fictitious charges on O atoms in water molecules.  Thus it is
+typically best in an efficiency sense to use a LJ cutoff >= Coulomb
+cutoff + 2\*(OM distance), to shrink the size of the neighbor list.
+This leads to slightly larger cost for the long-range calculation, so
+you can test the trade-off for your model.  The OM distance and the LJ
+and Coulombic cutoffs are set in the :doc:`pair\_style lj/cut/tip4p/long <pair_lj>` command.
+
+Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+
+
+----------
+
+
+.. _Jorgensen5:
+
+
+
+**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst
new file mode 100644
index 0000000000..6e341907a8
--- /dev/null
+++ b/doc/src/Howto_triclinic.rst
@@ -0,0 +1,228 @@
+:doc:`Higher level section <Howto>` - `LAMMPS WWW Site <lws_>`_ - `LAMMPS Documentation <ld_>`_ - `LAMMPS Commands <lc_>`_ 
+
+.. _lws: http://lammps.sandia.gov
+
+
+
+.. _ld: Manual.html
+
+
+
+.. _lc: Commands\_all.html
+
+
+
+Triclinic (non-orthogonal) simulation boxes
+===========================================
+
+By default, LAMMPS uses an orthogonal simulation box to encompass the
+particles.  The :doc:`boundary <boundary>` command sets the boundary
+conditions of the box (periodic, non-periodic, etc).  The orthogonal
+box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
+starting from the origin given by **a** = (xhi-xlo,0,0); **b** =
+(0,yhi-ylo,0); **c** = (0,0,zhi-zlo).  The 6 parameters
+(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
+is created, e.g. by the :doc:`create\_box <create_box>` or
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands.  Additionally, LAMMPS defines box size parameters lx,ly,lz
+where lx = xhi-xlo, and similarly in the y and z dimensions.  The 6
+parameters, as well as lx,ly,lz, can be output via the :doc:`thermo\_style custom <thermo_style>` command.
+
+LAMMPS also allows simulations to be performed in triclinic
+(non-orthogonal) simulation boxes shaped as a parallelepiped with
+triclinic symmetry.  The parallelepiped has its "origin" at
+(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
+origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** =
+(xz,yz,zhi-zlo).  *xy,xz,yz* can be 0.0 or positive or negative values
+and are called "tilt factors" because they are the amount of
+displacement applied to faces of an originally orthogonal box to
+transform it into the parallelepiped.  In LAMMPS the triclinic
+simulation box edge vectors **a**\ , **b**\ , and **c** cannot be arbitrary
+vectors.  As indicated, **a** must lie on the positive x axis.  **b** must
+lie in the xy plane, with strictly positive y component. **c** may have
+any orientation with strictly positive z component.  The requirement
+that **a**\ , **b**\ , and **c** have strictly positive x, y, and z components,
+respectively, ensures that **a**\ , **b**\ , and **c** form a complete
+right-handed basis.  These restrictions impose no loss of generality,
+since it is possible to rotate/invert any set of 3 crystal basis
+vectors so that they conform to the restrictions.
+
+For example, assume that the 3 vectors **A**\ ,\ **B**\ ,\ **C** are the edge
+vectors of a general parallelepiped, where there is no restriction on
+**A**\ ,\ **B**\ ,\ **C** other than they form a complete right-handed basis i.e.
+**A** x **B** . **C** > 0.  The equivalent LAMMPS **a**\ ,\ **b**\ ,\ **c** are a linear
+rotation of **A**\ , **B**\ , and **C** and can be computed as follows:
+
+.. image:: Eqs/transform.jpg
+   :align: center
+
+where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^)
+indicates the corresponding unit vector. *beta* and *gamma* are angles
+between the vectors described below. Note that by construction,
+**a**\ , **b**\ , and **c** have strictly positive x, y, and z components, respectively.
+If it should happen that
+**A**\ , **B**\ , and **C** form a left-handed basis, then the above equations
+are not valid for **c**\ . In this case, it is necessary
+to first apply an inversion. This can be achieved
+by interchanging two basis vectors or by changing the sign of one of them.
+
+For consistency, the same rotation/inversion applied to the basis vectors
+must also be applied to atom positions, velocities,
+and any other vector quantities.
+This can be conveniently achieved by first converting to
+fractional coordinates in the
+old basis and then converting to distance coordinates in the new basis.
+The transformation is given by the following equation:
+
+.. image:: Eqs/rotate.jpg
+   :align: center
+
+where *V* is the volume of the box, **X** is the original vector quantity and
+**x** is the vector in the LAMMPS basis.
+
+There is no requirement that a triclinic box be periodic in any
+dimension, though it typically should be in at least the 2nd dimension
+of the tilt (y in xy) if you want to enforce a shift in periodic
+boundary conditions across that boundary.  Some commands that work
+with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
+boundary conditions in specific dimensions.  See the command doc pages
+for details.
+
+The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
+time the simulation box is created.  This happens in one of 3 ways.
+If the :doc:`create\_box <create_box>` command is used with a region of
+style *prism*\ , then a triclinic box is setup.  See the
+:doc:`region <region>` command for details.  If the
+:doc:`read\_data <read_data>` command is used to define the simulation
+box, and the header of the data file contains a line with the "xy xz
+yz" keyword, then a triclinic box is setup.  See the
+:doc:`read\_data <read_data>` command for details.  Finally, if the
+:doc:`read\_restart <read_restart>` command reads a restart file which
+was written from a simulation using a triclinic box, then a triclinic
+box will be setup for the restarted simulation.
+
+Note that you can define a triclinic box with all 3 tilt factors =
+0.0, so that it is initially orthogonal.  This is necessary if the box
+will become non-orthogonal, e.g. due to the :doc:`fix npt <fix_nh>` or
+:doc:`fix deform <fix_deform>` commands.  Alternatively, you can use the
+:doc:`change\_box <change_box>` command to convert a simulation box from
+orthogonal to triclinic and vice versa.
+
+As with orthogonal boxes, LAMMPS defines triclinic box size parameters
+lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
+The 9 parameters, as well as lx,ly,lz, can be output via the
+:doc:`thermo\_style custom <thermo_style>` command.
+
+To avoid extremely tilted boxes (which would be computationally
+inefficient), LAMMPS normally requires that no tilt factor can skew
+the box more than half the distance of the parallel box length, which
+is the 1st dimension in the tilt factor (x for xz).  This is required
+both when the simulation box is created, e.g. via the
+:doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` commands,
+as well as when the box shape changes dynamically during a simulation,
+e.g. via the :doc:`fix deform <fix_deform>` or :doc:`fix npt <fix_nh>`
+commands.
+
+For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
+the xy tilt factor must be between -5 and 5.  Similarly, both xz and
+yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is
+not a limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are geometrically all equivalent.  If the box tilt exceeds this
+limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
+command), then the box is "flipped" to an equivalent shape with a tilt
+factor within the bounds, so the run can continue.  See the :doc:`fix deform <fix_deform>` doc page for further details.
+
+One exception to this rule is if the 1st dimension in the tilt
+factor (x for xy) is non-periodic.  In that case, the limits on the
+tilt factor are not enforced, since flipping the box in that dimension
+does not change the atom positions due to non-periodicity.  In this
+mode, if you tilt the system to extreme angles, the simulation will
+simply become inefficient, due to the highly skewed simulation box.
+
+The limitation on not creating a simulation box with a tilt factor
+skewing the box more than half the distance of the parallel box length
+can be overridden via the :doc:`box <box>` command.  Setting the *tilt*
+keyword to *large* allows any tilt factors to be specified.
+
+Box flips that may occur using the :doc:`fix deform <fix_deform>` or
+:doc:`fix npt <fix_nh>` commands can be turned off using the *flip no*
+option with either of the commands.
+
+Note that if a simulation box has a large tilt factor, LAMMPS will run
+less efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped sub-domain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+
+Triclinic crystal structures are often defined using three lattice
+constants *a*\ , *b*\ , and *c*\ , and three angles *alpha*\ , *beta* and
+*gamma*\ . Note that in this nomenclature, the a, b, and c lattice
+constants are the scalar lengths of the edge vectors **a**\ , **b**\ , and **c**
+defined above.  The relationship between these 6 quantities
+(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
+(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
+
+.. image:: Eqs/box.jpg
+   :align: center
+
+The inverse relationship can be written as follows:
+
+.. image:: Eqs/box_inverse.jpg
+   :align: center
+
+The values of *a*\ , *b*\ , *c* , *alpha*\ , *beta* , and *gamma* can be printed
+out or accessed by computes using the
+:doc:`thermo\_style custom <thermo_style>` keywords
+*cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ , *cellgamma*\ ,
+respectively.
+
+As discussed on the :doc:`dump <dump>` command doc page, when the BOX
+BOUNDS for a snapshot is written to a dump file for a triclinic box,
+an orthogonal bounding box which encloses the triclinic simulation box
+is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
+box, formatted as follows:
+
+
+.. parsed-literal::
+
+   ITEM: BOX BOUNDS xy xz yz
+   xlo_bound xhi_bound xy
+   ylo_bound yhi_bound xz
+   zlo_bound zhi_bound yz
+
+This bounding box is convenient for many visualization programs and is
+calculated from the 9 triclinic box parameters
+(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
+
+
+.. parsed-literal::
+
+   xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
+   xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
+   ylo_bound = ylo + MIN(0.0,yz)
+   yhi_bound = yhi + MAX(0.0,yz)
+   zlo_bound = zlo
+   zhi_bound = zhi
+
+These formulas can be inverted if you need to convert the bounding box
+back into the triclinic box parameters, e.g. xlo = xlo\_bound -
+MIN(0.0,xy,xz,xy+xz).
+
+One use of triclinic simulation boxes is to model solid-state crystals
+with triclinic symmetry.  The :doc:`lattice <lattice>` command can be
+used with non-orthogonal basis vectors to define a lattice that will
+tile a triclinic simulation box via the
+:doc:`create\_atoms <create_atoms>` command.
+
+A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt <fix_nh>` command, which will adjust the xy, xz, yz tilt
+factors to compensate for off-diagonal components of the pressure
+tensor.  The analog for an :doc:`energy minimization <minimize>` is
+the :doc:`fix box/relax <fix_box_relax>` command.
+
+A third use is to shear a bulk solid to study the response of the
+material.  The :doc:`fix deform <fix_deform>` command can be used for
+this purpose.  It allows dynamic control of the xy, xz, yz tilt
+factors as a simulation runs.  This is discussed in the next section
+on non-equilibrium MD (NEMD) simulations.
+
diff --git a/doc/src/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst
new file mode 100644
index 0000000000..0b74784534
--- /dev/null
+++ b/doc/src/Howto_viscosity.rst
@@ -0,0 +1,148 @@
+Calculate viscosity
+===================
+
+The shear viscosity eta of a fluid can be measured in at least 5 ways
+using various options in LAMMPS.  See the examples/VISCOSITY directory
+for scripts that implement the 5 methods discussed here for a simple
+Lennard-Jones fluid model.  Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
+thermal conductivity.
+
+Eta is a measure of the propensity of a fluid to transmit momentum in
+a direction perpendicular to the direction of velocity or momentum
+flow.  Alternatively it is the resistance the fluid has to being
+sheared.  It is given by
+
+J = -eta grad(Vstream)
+
+where J is the momentum flux in units of momentum per area per time.
+and grad(Vstream) is the spatial gradient of the velocity of the fluid
+moving in another direction, normal to the area through which the
+momentum flows.  Viscosity thus has units of pressure-time.
+
+The first method is to perform a non-equilibrium MD (NEMD) simulation
+by shearing the simulation box via the :doc:`fix deform <fix_deform>`
+command, and using the :doc:`fix nvt/sllod <fix_nvt_sllod>` command to
+thermostat the fluid via the SLLOD equations of motion.
+Alternatively, as a second method, one or more moving walls can be
+used to shear the fluid in between them, again with some kind of
+thermostat that modifies only the thermal (non-shearing) components of
+velocity to prevent the fluid from heating up.
+
+.. note::
+
+   A recent (2017) book by :ref:`(Daivis and Todd) <Daivis-viscosity>`
+   discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+   thermostatting generally, for both simple and complex fluids,
+   e.g. molecular systems.  The latter can be tricky to do correctly.
+
+In both cases, the velocity profile setup in the fluid by this
+procedure can be monitored by the :doc:`fix ave/chunk <fix_ave_chunk>`
+command, which determines grad(Vstream) in the equation above.
+E.g. the derivative in the y-direction of the Vx component of fluid
+motion or grad(Vstream) = dVx/dy.  The Pxy off-diagonal component of
+the pressure or stress tensor, as calculated by the :doc:`compute pressure <compute_pressure>` command, can also be monitored, which
+is the J term in the equation above.  See the :doc:`Howto nemd <Howto_nemd>` doc page for details on NEMD simulations.
+
+The third method is to perform a reverse non-equilibrium MD simulation
+using the :doc:`fix viscosity <fix_viscosity>` command which implements
+the rNEMD algorithm of Muller-Plathe.  Momentum in one dimension is
+swapped between atoms in two different layers of the simulation box in
+a different dimension.  This induces a velocity gradient which can be
+monitored with the :doc:`fix ave/chunk <fix_ave_chunk>` command.
+The fix tallies the cumulative momentum transfer that it performs.
+See the :doc:`fix viscosity <fix_viscosity>` command for details.
+
+The fourth method is based on the Green-Kubo (GK) formula which
+relates the ensemble average of the auto-correlation of the
+stress/pressure tensor to eta.  This can be done in a fully
+equilibrated simulation which is in contrast to the two preceding
+non-equilibrium methods, where momentum flows continuously through the
+simulation box.
+
+Here is an example input script that calculates the viscosity of
+liquid Ar via the GK formalism:
+
+
+.. parsed-literal::
+
+   # Sample LAMMPS input script for viscosity of liquid Ar
+
+   units       real
+   variable    T equal 86.4956
+   variable    V equal vol
+   variable    dt equal 4.0
+   variable    p equal 400     # correlation length
+   variable    s equal 5       # sample interval
+   variable    d equal $p\*$s   # dump interval
+
+   # convert from LAMMPS real units to SI
+
+   variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
+   variable    atm2Pa equal 101325.0
+   variable    A2m equal 1.0e-10
+   variable    fs2s equal 1.0e-15
+   variable    convert equal ${atm2Pa}\*${atm2Pa}\*${fs2s}\*${A2m}\*${A2m}\*${A2m}
+
+   # setup problem
+
+   dimension    3
+   boundary     p p p
+   lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+   region       box block 0 4 0 4 0 4
+   create_box   1 box
+   create_atoms 1 box
+   mass         1 39.948
+   pair_style   lj/cut 13.0
+   pair_coeff   \* \* 0.2381 3.405
+   timestep     ${dt}
+   thermo       $d
+
+   # equilibration and thermalization
+
+   velocity     all create $T 102486 mom yes rot yes dist gaussian
+   fix          NVT all nvt temp $T $T 10 drag 0.2
+   run          8000
+
+   # viscosity calculation, switch to NVE if desired
+
+   #unfix       NVT
+   #fix         NVE all nve
+
+   reset_timestep 0
+   variable     pxy equal pxy
+   variable     pxz equal pxz
+   variable     pyz equal pyz
+   fix          SS all ave/correlate $s $p $d &
+                v_pxy v_pxz v_pyz type auto file S0St.dat ave running
+   variable     scale equal ${convert}/(${kB}\*$T)\*$V\*$s\*${dt}
+   variable     v11 equal trap(f_SS[3])\*${scale}
+   variable     v22 equal trap(f_SS[4])\*${scale}
+   variable     v33 equal trap(f_SS[5])\*${scale}
+   thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
+   run          100000
+   variable     v equal (v_v11+v_v22+v_v33)/3.0
+   variable     ndens equal count(all)/vol
+   print        "average viscosity: $v [Pa.s] @ $T K, ${ndens} /A\^3"
+
+The fifth method is related to the above Green-Kubo method,
+but uses the Einstein formulation, analogous to the Einstein
+mean-square-displacement formulation for self-diffusivity. The
+time-integrated momentum fluxes play the role of Cartesian
+coordinates, whose mean-square displacement increases linearly
+with time at sufficiently long times.
+
+
+----------
+
+
+.. _Daivis-viscosity:
+
+
+
+**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_viz.rst b/doc/src/Howto_viz.rst
new file mode 100644
index 0000000000..c2cdc56b48
--- /dev/null
+++ b/doc/src/Howto_viz.rst
@@ -0,0 +1,43 @@
+Visualize LAMMPS snapshots
+==========================
+
+LAMMPS itself does not do visualization, but snapshots from LAMMPS
+simulations can be visualized (and analyzed) in a variety of ways.
+
+Mention dump image and dump movie.
+
+LAMMPS snapshots are created by the :doc:`dump <dump>` command which can
+create files in several formats. The native LAMMPS dump format is a
+text file (see "dump atom" or "dump custom") which can be visualized
+by several popular visualization tools. The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>` styles can
+output internally rendered images and convert a sequence of them to a
+movie during the MD run.  Several programs included with LAMMPS as
+auxiliary tools can convert between LAMMPS format files and other
+formats.  See the :doc:`Tools <Tools>` doc page for details.
+
+A Python-based toolkit distributed by our group can read native LAMMPS
+dump files, including custom dump files with additional columns of
+user-specified atom information, and convert them to various formats
+or pipe them into visualization software directly.  See the `Pizza.py WWW site <pizza_>`_ for details.  Specifically, Pizza.py can convert
+LAMMPS dump files into PDB, XYZ, `Ensight <ensight_>`_, and VTK formats.
+Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
+RasMol visualization programs.  Pizza.py has tools that do interactive
+3d OpenGL visualization and one that creates SVG images of dump file
+snapshots.
+
+.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
+
+
+
+.. _ensight: http://www.ensight.com
+
+
+
+.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Howto_walls.rst b/doc/src/Howto_walls.rst
new file mode 100644
index 0000000000..f04b7f1057
--- /dev/null
+++ b/doc/src/Howto_walls.rst
@@ -0,0 +1,76 @@
+Walls
+=====
+
+Walls in an MD simulation are typically used to bound particle motion,
+i.e. to serve as a boundary condition.
+
+Walls in LAMMPS can be of rough (made of particles) or idealized
+surfaces.  Ideal walls can be smooth, generating forces only in the
+normal direction, or frictional, generating forces also in the
+tangential direction.
+
+Rough walls, built of particles, can be created in various ways.  The
+particles themselves can be generated like any other particle, via the
+:doc:`lattice <lattice>` and :doc:`create\_atoms <create_atoms>` commands,
+or read in via the :doc:`read\_data <read_data>` command.
+
+Their motion can be constrained by many different commands, so that
+they do not move at all, move together as a group at constant velocity
+or in response to a net force acting on them, move in a prescribed
+fashion (e.g. rotate around a point), etc.  Note that if a time
+integration fix like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>`
+is not used with the group that contains wall particles, their
+positions and velocities will not be updated.
+
+* :doc:`fix aveforce <fix_aveforce>` - set force on particles to average value, so they move together
+* :doc:`fix setforce <fix_setforce>` - set force on particles to a value, e.g. 0.0
+* :doc:`fix freeze <fix_freeze>` - freeze particles for use as granular walls
+* :doc:`fix nve/noforce <fix_nve_noforce>` - advect particles by their velocity, but without force
+* :doc:`fix move <fix_move>` - prescribe motion of particles by a linear velocity, oscillation, rotation, variable
+
+The :doc:`fix move <fix_move>` command offers the most generality, since
+the motion of individual particles can be specified with
+:doc:`variable <variable>` formula which depends on time and/or the
+particle position.
+
+For rough walls, it may be useful to turn off pairwise interactions
+between wall particles via the :doc:`neigh\_modify exclude <neigh_modify>` command.
+
+Rough walls can also be created by specifying frozen particles that do
+not move and do not interact with mobile particles, and then tethering
+other particles to the fixed particles, via a :doc:`bond <bond_style>`.
+The bonded particles do interact with other mobile particles.
+
+Idealized walls can be specified via several fix commands.  :doc:`Fix wall/gran <fix_wall_gran>` creates frictional walls for use with
+granular particles; all the other commands create smooth walls.
+
+* :doc:`fix wall/reflect <fix_wall_reflect>` - reflective flat walls
+* :doc:`fix wall/lj93 <fix_wall>` - flat walls, with Lennard-Jones 9/3 potential
+* :doc:`fix wall/lj126 <fix_wall>` - flat walls, with Lennard-Jones 12/6 potential
+* :doc:`fix wall/colloid <fix_wall>` - flat walls, with :doc:`pair\_style colloid <pair_colloid>` potential
+* :doc:`fix wall/harmonic <fix_wall>` - flat walls, with repulsive harmonic spring potential
+* :doc:`fix wall/morse <fix_wall>` - flat walls, with Morse potential
+* :doc:`fix wall/region <fix_wall_region>` - use region surface as wall
+* :doc:`fix wall/gran <fix_wall_gran>` - flat or curved walls with :doc:`pair\_style granular <pair_gran>` potential
+
+The *lj93*\ , *lj126*\ , *colloid*\ , *harmonic*\ , and *morse* styles all
+allow the flat walls to move with a constant velocity, or oscillate in
+time.  The :doc:`fix wall/region <fix_wall_region>` command offers the
+most generality, since the region surface is treated as a wall, and
+the geometry of the region can be a simple primitive volume (e.g. a
+sphere, or cube, or plane), or a complex volume made from the union
+and intersection of primitive volumes.  :doc:`Regions <region>` can also
+specify a volume "interior" or "exterior" to the specified primitive
+shape or *union* or *intersection*\ .  :doc:`Regions <region>` can also be
+"dynamic" meaning they move with constant velocity, oscillate, or
+rotate.
+
+The only frictional idealized walls currently in LAMMPS are flat or
+curved surfaces specified by the :doc:`fix wall/gran <fix_wall_gran>`
+command.  At some point we plan to allow regoin surfaces to be used as
+frictional walls, as well as triangulated surfaces.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install.rst b/doc/src/Install.rst
new file mode 100644
index 0000000000..4a403a336d
--- /dev/null
+++ b/doc/src/Install.rst
@@ -0,0 +1,58 @@
+Install LAMMPS
+**************
+
+You can download LAMMPS as an executable or as source code.
+
+With source code, you also have to :doc:`build LAMMPS <Build>`.  But you
+have more flexibility as to what features to include or exclude in the
+build.  If you plan to :doc:`modify or extend LAMMPS <Modify>`, then you
+need the source code.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Install_linux
+   Install_mac
+   Install_windows
+   Install_conda
+
+   Install_tarball
+   Install_git
+   Install_svn
+   Install_patch
+
+These are the files and sub-directories in the LAMMPS distribution:
+
++------------+-------------------------------------------+
+| README     | text file                                 |
++------------+-------------------------------------------+
+| LICENSE    | GNU General Public License (GPL)          |
++------------+-------------------------------------------+
+| bench      | benchmark problems                        |
++------------+-------------------------------------------+
+| cmake      | CMake build files                         |
++------------+-------------------------------------------+
+| doc        | documentation                             |
++------------+-------------------------------------------+
+| examples   | simple test problems                      |
++------------+-------------------------------------------+
+| lib        | additional provided or external libraries |
++------------+-------------------------------------------+
+| potentials | interatomic potential files               |
++------------+-------------------------------------------+
+| python     | Python wrapper on LAMMPS                  |
++------------+-------------------------------------------+
+| src        | source files                              |
++------------+-------------------------------------------+
+| tools      | pre- and post-processing tools            |
++------------+-------------------------------------------+
+
+You will have all of these if you download source.  You will only have
+some of them if you download executables, as explained on the pages
+listed above.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install.txt b/doc/src/Install.txt
deleted file mode 100644
index 0a2e870a5d..0000000000
--- a/doc/src/Install.txt
+++ /dev/null
@@ -1,65 +0,0 @@
-"Previous Section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Build.html
-:c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Install LAMMPS :h2
-
-You can download LAMMPS as an executable or as source code.
-
-With source code, you also have to "build LAMMPS"_Build.html.  But you
-have more flexibility as to what features to include or exclude in the
-build.  If you plan to "modify or extend LAMMPS"_Modify.html, then you
-need the source code.
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   Install_linux
-   Install_mac
-   Install_windows
-
-   Install_tarball
-   Install_git
-   Install_svn
-   Install_patch
-
-END_RST -->
-
-<!-- HTML_ONLY -->
-
-"Download an executable for Linux"_Install_linux.html
-"Download an executable for Mac"_Install_mac.html
-"Download an executable for Windows"_Install_windows.html :all(b)
-
-"Download source as a tarball"_Install_tarball.html
-"Donwload source via Git"_Install_git.html
-"Donwload source via SVN"_Install_svn.html
-"Install patch files"_Install_patch.html :all(b)
-
-<!-- END_HTML_ONLY -->
-
-These are the files and sub-directories in the LAMMPS distribution:
-
-README: text file
-LICENSE: GNU General Public License (GPL)
-bench: benchmark problems
-cmake: CMake build files
-doc: documentation
-examples: simple test problems
-lib: additional provided or external libraries
-potentials: interatomic potential files
-python: Python wrapper on LAMMPS
-src: source files
-tools: pre- and post-processing tools :tb(s=:,a=l)
-
-You will have all of these if you download source.  You will only have
-some of them if you download executables, as explained on the pages
-listed above.
diff --git a/doc/src/Install_conda.rst b/doc/src/Install_conda.rst
new file mode 100644
index 0000000000..33188e2540
--- /dev/null
+++ b/doc/src/Install_conda.rst
@@ -0,0 +1,48 @@
+Download an executable for Linux or Mac via Conda
+=================================================
+
+Binaries are available for macOS or Linux via `Conda <conda_>`_.
+
+First, one must setup the Conda package manager on your system.  Follow the
+instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
+environment (named `my-lammps-env` or whatever you prefer) for your lammps
+install:
+
+.. parsed-literal::
+
+   % conda config --add channels conda-forge
+   % conda create -n my-lammps-env
+
+Then, you can install lammps on your system with the following command:
+
+.. parsed-literal::
+
+   % conda activate my-lammps-env
+   % conda install lammps
+
+The LAMMPS binary is built with the :ref:`KIM package <kim>` which
+results in Conda also installing the `kim-api` binaries when LAMMPS is
+installed.  In order to use potentials from `openkim.org <openkim_>`_, you can
+install the `openkim-models` package
+
+
+.. parsed-literal::
+
+   % conda install openkim-models
+
+If you have problems with the installation you can post issues to
+`this link <conda_forge_lammps_>`_.
+Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting
+up the Conda capability.
+
+.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
+
+.. _openkim: https://openkim.org
+
+.. _conda: https://docs.conda.io/en/latest/index.html
+
+.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst
new file mode 100644
index 0000000000..9d9d36f8f6
--- /dev/null
+++ b/doc/src/Install_git.rst
@@ -0,0 +1,128 @@
+Download source via Git
+=======================
+
+All LAMMPS development is coordinated through the "LAMMPS GitHub
+site".  If you clone the LAMMPS repository onto your local machine, it
+has several advantages:
+
+* You can stay current with changes to LAMMPS with a single git
+  command.
+* You can create your own development branches to add code to LAMMPS.
+* You can submit your new features back to GitHub for inclusion in
+  LAMMPS.
+
+You must have `Git <git_>`_ installed on your system to communicate with
+the public Git server for LAMMPS.
+
+.. warning::
+
+   As of Oct 2016, the official home of public LAMMPS
+   development is on GitHub.  The previously advertised LAMMPS git
+   repositories on git.lammps.org and bitbucket.org are now deprecated,
+   may not be up-to-date, and may go away at any time.
+
+.. _git: http://git-scm.com
+
+
+
+You can follow LAMMPS development on 3 different Git branches:
+
+* **stable**   :  this branch is updated with every stable release
+* **unstable** :  this branch is updated with every patch release
+* **master**   :  this branch continuously follows ongoing development
+
+To access the Git repositories on your box, use the clone command to
+create a local copy of the LAMMPS repository with a command like:
+
+
+.. parsed-literal::
+
+   git clone -b unstable https://github.com/lammps/lammps.git mylammps
+
+where "mylammps" is the name of the directory you wish to create on
+your machine and "unstable" is one of the 3 branches listed above.
+(Note that you actually download all 3 branches; you can switch
+between them at any time using "git checkout <branch name>".)
+
+Once the command completes, your directory will contain the same files
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included.  They can be fetched
+from the LAMMPS website by typing "make fetch" in the doc directory.
+Or they can be generated from the content provided in doc/src by
+typing "make html" from the doc directory.
+
+After initial cloning, as bug fixes and new features are added to
+LAMMPS, as listed on :doc:`this page <Errors_bugs>`, you can stay
+up-to-date by typing the following Git commands from within the
+"mylammps" directory:
+
+
+.. parsed-literal::
+
+   git checkout unstable      # not needed if you always stay in this branch
+   git checkout stable        # use one of the 3 checkout commands
+   git checkout master
+   git pull
+
+Doing a "pull" will not change any files you have added to the LAMMPS
+directory structure.  It will also not change any existing LAMMPS
+files you have edited, unless those files have changed in the
+repository.  In that case, Git will attempt to merge the new
+repository file with your version of the file and tell you if there
+are any conflicts.  See the Git documentation for details.
+
+If you want to access a particular previous release version of LAMMPS,
+you can instead "checkout" any version with a published tag. See the
+output of "git tag -l" for the list of tags.  The Git command to do
+this is as follows.
+
+
+.. parsed-literal::
+
+   git checkout tagID
+
+Stable versions and what tagID to use for a particular stable version
+are discussed on :doc:`this page <Errors_bugs>`.  Note that this command
+will print some warnings, because in order to get back to the latest
+revision and to be able to update with "git pull" again, you first
+will need to first type "git checkout unstable" (or check out any
+other desired branch).
+
+Once you have updated your local files with a "git pull" (or "git
+checkout"), you still need to re-build LAMMPS if any source files have
+changed.  To do this, you should cd to the src directory and type:
+
+
+.. parsed-literal::
+
+   make purge             # remove any deprecated src files
+   make package-update    # sync package files with src files
+   make foo               # re-build for your machine (mpi, serial, etc)
+
+just as described on the :doc:`Install patch <Install_patch>` doc page,
+after a patch has been installed.
+
+.. warning::
+
+   If you wish to edit/change a src file that is from a
+   package, you should edit the version of the file inside the package
+   sub-directory with src, then re-install the package.  The version in
+   the src dir is merely a copy and will be wiped out if you type "make
+   package-update".
+
+.. warning::
+
+   The GitHub servers support both the "git://" and
+   "https://" access protocols for anonymous read-only access.  If you
+   have a correspondingly configured GitHub account, you may also use SSH
+   with "git@github.com:/lammps/lammps.git".
+
+The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
+junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
+gmail.com) and Richard Berger (Temple U, richard.berger at
+temple.edu).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install_linux.rst b/doc/src/Install_linux.rst
new file mode 100644
index 0000000000..e690afdd58
--- /dev/null
+++ b/doc/src/Install_linux.rst
@@ -0,0 +1,269 @@
+Download an executable for Linux
+================================
+
+Binaries are available for different versions of Linux:
+
+| :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
+| :ref:`Pre-built Fedora Linux executables <fedora>`
+| :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
+| :ref:`Pre-built OpenSuse Linux executables <opensuse>`
+| :ref:`Gentoo Linux executable <gentoo>`
+| :ref:`Arch Linux build-script <arch>` 
+| 
+
+
+----------
+
+
+.. _ubuntu:
+
+Pre-built Ubuntu Linux executables
+-----------------------------------------------
+
+A pre-built LAMMPS executable suitable for running on the latest
+Ubuntu Linux versions, can be downloaded as a Debian package.  This
+allows you to install LAMMPS with a single command, and stay
+up-to-date with the current version of LAMMPS by simply updating your
+operating system.
+
+To install the appropriate personal-package archive (PPA), do the
+following once:
+
+
+.. parsed-literal::
+
+   sudo add-apt-repository ppa:gladky-anton/lammps
+   sudo apt-get update
+
+To install LAMMPS do the following once:
+
+
+.. parsed-literal::
+
+   sudo apt-get install lammps-daily
+
+This downloads an executable named "lmp\_daily" to your box, which
+can then be used in the usual way to run input scripts:
+
+
+.. parsed-literal::
+
+   lmp_daily -in in.lj
+
+To update LAMMPS to the most current version, do the following:
+
+
+.. parsed-literal::
+
+   sudo apt-get update
+
+which will also update other packages on your system.
+
+To get a copy of the current documentation and examples:
+
+
+.. parsed-literal::
+
+   sudo apt-get install lammps-daily-doc
+
+which will download the doc files in
+/usr/share/doc/lammps-daily-doc/doc and example problems in
+/usr/share/doc/lammps-doc/examples.
+
+Note that you may still wish to download the tarball to get potential
+files and auxiliary tools.
+
+To un-install LAMMPS, do the following:
+
+
+.. parsed-literal::
+
+   sudo apt-get remove lammps-daily
+
+Note that the lammps-daily executable is built with the following
+sequence of make commands, as if you had done the same with the
+unpacked tarball files in the src directory:
+
+make yes-all; make no-lib; make openmpi
+
+Thus it builds with FFTW3 and OpenMPI.
+
+Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
+Ubuntu package capability.
+
+
+----------
+
+
+.. _fedora:
+
+Pre-built Fedora Linux executables
+-----------------------------------------------
+
+Pre-built LAMMPS packages for stable releases are available
+in the Fedora Linux distribution as of version 28. The packages
+can be installed via the dnf package manager. There are 3 basic
+varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
+lammps-openmpi = OpenMPI MPI library) and for each support for
+linking to the C library interface (lammps-devel, lammps-mpich-devel,
+lammps-openmpi-devel), the header for compiling programs using
+the C library interface (lammps-headers), and the LAMMPS python
+module for Python 3. All packages can be installed at the same
+time and the name of the LAMMPS executable is *lmp* and *lmp\_openmpi*
+or *lmp\_mpich* respectively.  By default, *lmp* will refer to the
+serial executable, unless one of the MPI environment modules is loaded
+("module load mpi/mpich-x86\_64" or "module load mpi/openmpi-x86\_64").
+Then the corresponding parallel LAMMPS executable can be used.
+The same mechanism applies when loading the LAMMPS python module.
+
+To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
+
+
+.. parsed-literal::
+
+   dnf install lammps-openmpi
+   module load mpi/openmpi-x86_64
+   mpirun -np 2 lmp -in in.lj
+
+The "dnf install" command is needed only once. In case of a new LAMMPS
+stable release, "dnf update" will automatically update to the newer
+version as soon at the RPM files are built and uploaded to the download
+mirrors. The "module load" command is needed once per (shell) session
+or shell terminal instance, unless it is automatically loaded from the
+shell profile.
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
+
+
+----------
+
+
+.. _epel:
+
+Pre-built EPEL Linux executable
+------------------------------------------
+
+Pre-built LAMMPS packages for stable releases are available
+in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedoraproject.org/wiki/EPEL>`_
+for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
+and compatible Linux distributions. Names of packages, executable,
+and content are the same as described above for Fedora Linux.
+But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
+in Fedora 28.
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
+
+
+----------
+
+
+.. _opensuse:
+
+Pre-built OpenSuse Linux executable
+--------------------------------------------------
+
+A pre-built LAMMPS package for stable releases is available
+in OpenSuse as of Leap 15.0. You can install the package with:
+
+
+.. parsed-literal::
+
+   zypper install lammps
+
+This includes support for OpenMPI. The name of the LAMMPS executable
+is *lmp*\ . Thus to run an input in parallel on 2 CPUs you would do:
+
+
+.. parsed-literal::
+
+   mpirun -np 2 lmp -in in.lj
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
+
+
+----------
+
+
+.. _gentoo:
+
+Gentoo Linux executable
+------------------------------------
+
+LAMMPS is part of Gentoo's main package tree and can be installed by
+typing:
+
+
+.. parsed-literal::
+
+   % emerge --ask lammps
+
+Note that in Gentoo the LAMMPS source is downloaded and the package is
+built on the your machine.
+
+Certain LAMMPS packages can be enable via USE flags, type
+
+
+.. parsed-literal::
+
+   % equery uses lammps
+
+for details.
+
+Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up
+this Gentoo capability.
+
+
+----------
+
+
+.. _arch:
+
+Archlinux build-script
+---------------------------------
+
+LAMMPS is available via Arch's unofficial Arch User repository (AUR).
+
+There are three scripts available, named lammps, lammps-beta and lammps-git.
+They respectively package the stable, patch and git releases.
+
+To install, you will need to have the git package installed. You may use
+any of the above names in-place of lammps.
+
+
+.. parsed-literal::
+
+   $ git clone https://aur.archlinux.org/lammps.git
+
+   $ cd lammps
+
+   $ makepkg -s
+
+   # makepkg -i
+
+To update, you may repeat the above, or change into the cloned directory,
+and execute the following, after which, if there are any changes, you may
+use makepkg as above.
+
+
+.. parsed-literal::
+
+   $ git pull
+
+Alternatively, you may use an AUR helper to install these packages.
+
+Note that the AUR provides build-scripts that download the source and
+the build the package on your machine.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install_mac.rst b/doc/src/Install_mac.rst
new file mode 100644
index 0000000000..cc8bbc9a92
--- /dev/null
+++ b/doc/src/Install_mac.rst
@@ -0,0 +1,54 @@
+Download an executable for Mac
+==============================
+
+LAMMPS can be downloaded, built, and configured for OS X on a Mac with
+`Homebrew <homebrew_>`_.  (Alternatively, see the install instructions for
+:doc:`Download an executable via Conda <Install_conda>`.)  The following LAMMPS
+packages are unavailable at this time because of additional needs not yet met:
+GPU, KOKKOS, LATTE, MSCG, MESSAGE, MPIIO POEMS VORONOI.
+
+After installing Homebrew, you can install LAMMPS on your system with
+the following commands:
+
+
+.. parsed-literal::
+
+   % brew install lammps
+
+This will install the executables "lammps\_serial" and "lammps\_mpi", as well as
+the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
+
+Once LAMMPS is installed, you can test the installation with the
+Lennard-Jones benchmark file:
+
+
+.. parsed-literal::
+
+   % brew test lammps -v
+
+The LAMMPS binary is built with the :ref:`KIM package <kim>` which
+results in Homebrew also installing the `kim-api` binaries when LAMMPS is
+installed.  In order to use potentials from `openkim.org <openkim_>`_, you can
+install the `openkim-models` package
+
+
+.. parsed-literal::
+
+   % brew install openkim-models
+
+If you have problems with the installation you can post issues to
+`this link <homebrew_>`_.
+
+.. _homebrew: https://github.com/Homebrew/homebrew-core/issues
+
+Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
+up the Homebrew capability.
+
+
+.. _openkim: https://openkim.org
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install_mac.txt b/doc/src/Install_mac.txt
deleted file mode 100644
index 773c9ec93a..0000000000
--- a/doc/src/Install_mac.txt
+++ /dev/null
@@ -1,43 +0,0 @@
-"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Download an executable for Mac :h3
-
-LAMMPS can be downloaded, built, and configured for OS X on a Mac with
-"Homebrew"_homebrew.  The following LAMMPS packages are unavailable at this
-time because of additional needs not yet met: GPU, KOKKOS, LATTE, MSCG,
-MESSAGE, MPIIO POEMS VORONOI.
-
-After installing Homebrew, you can install LAMMPS on your system with
-the following commands:
-
-% brew install lammps :pre
-
-This will install the executables "lammps_serial" and "lammps_mpi", as well as
-the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
-
-Once LAMMPS is installed, you can test the installation with the
-Lennard-Jones benchmark file:
-
-% brew test lammps -v :pre
-
-The LAMMPS binary is built with the "KIM package"_Build_extras#kim which
-results in Homebrew also installing the `kim-api` binaries when LAMMPS is
-installed.  In order to use potentials from "openkim.org"_openkim, you can
-install the `openkim-models` package
-
-% brew install openkim-models :pre
-
-If you have problems with the installation you can post issues to
-"this link"_homebrew.
-
-Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
-up the Homebrew capability.
-:link(homebrew,https://github.com/Homebrew/homebrew-core/issues)
-:link(openkim,https://openkim.org)
diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst
new file mode 100644
index 0000000000..537d8ae4b9
--- /dev/null
+++ b/doc/src/Install_patch.rst
@@ -0,0 +1,68 @@
+Applying patches
+================
+
+It is easy to stay current with the most recent LAMMPS patch releases
+if you use Git or SVN to track LAMMPS development.  Instructions for
+how to stay current are on the :doc:`Install git <Install_git>` and
+:doc:`Install svn <Install_svn>` doc pages.
+
+If you prefer to download a tarball, as described on the :doc:`Install git <Install_tarball>` doc page, you can stay current by
+downloading "patch files" when new patch releases are made.  A link to
+a patch file is posted on the `bug and feature page <http://lammps.sandia.gov/bug.html>`_ of the LAMMPS website, along
+with a list of changed files and details about what is in the new patch
+release.  This page explains how to apply the patch file to your local
+LAMMPS directory.
+
+.. note::
+
+   You should not apply patch files to a local Git or SVN repo of
+   LAMMPS, only to an unpacked tarball.  Use Git and SVN commands to
+   update repo versions of LAMMPS.
+
+Here are the steps to apply a patch file.  Note that if your version
+of LAMMPS is several patch releases behind, you need to apply all the
+intervening patch files in succession to bring your version of LAMMPS
+up to date.
+
+* Download the patch file.  You may have to shift-click in your browser
+  to download the file instead of display it.  Patch files have names
+  like patch.12Dec16.
+* Put the patch file in your top-level LAMMPS directory, where the
+  LICENSE and README files are.
+* Apply the patch by typing the following command from your top-level
+  LAMMPS directory, where the redirected file is the name of the patch
+  file.
+  
+  .. parsed-literal::
+  
+     patch -bp1 < patch.12Dec16
+
+* A list of updated files print out to the screen.  The -b switch
+  creates backup files of your originals (e.g. src/force.cpp.orig), so
+  you can manually undo the patch if something goes wrong.
+* Type the following from the src directory, to enforce consistency
+  between the src and package directories.  This is OK to do even if you
+  don't use one or more packages.  If you are applying several patches
+  successively, you only need to type this once at the end. The purge
+  command removes deprecated src files if any were removed by the patch
+  from package sub-directories.
+  
+  .. parsed-literal::
+  
+     make purge
+     make package-update
+
+* Re-build LAMMPS via the "make" command.
+
+.. warning::
+
+   If you wish to edit/change a src file that is from a
+   package, you should edit the version of the file inside the package
+   sub-dir of src, then re-install the package.  The version in the src
+   dir is merely a copy and will be wiped out if you type "make
+   package-update".
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install_svn.rst b/doc/src/Install_svn.rst
new file mode 100644
index 0000000000..097caf5cce
--- /dev/null
+++ b/doc/src/Install_svn.rst
@@ -0,0 +1,102 @@
+Download source via SVN
+=======================
+
+.. warning::
+
+   As of Oct 2016, SVN support is now implemented via a
+   git-to-subversion interface service on GitHub and no longer through a
+   mirror of the internal SVN repository at Sandia.
+
+You must have the `Subversion (SVN) client software <svn_>`_ installed on
+your system to communicate with the Git server in this mode.
+
+.. _svn: http://subversion.apache.org
+
+
+
+You can follow LAMMPS development on 3 different SVN branches:
+
+* **stable**   :  this branch is updated with every stable release
+* **unstable** :  this branch is updated with every patch release
+* **master**   :  this branch continuously follows ongoing development
+
+The corresponding command lines to do an initial checkout are as
+follows.  (Note that unlike Git, you must perform a separate checkout
+into a unique directory for each of the 3 branches.)
+
+
+.. parsed-literal::
+
+   svn checkout https://github.com/lammps/lammps.git/branches/unstable mylammps
+   svn checkout https://github.com/lammps/lammps.git/branches/stable mylammps
+   svn checkout https://github.com/lammps/lammps.git/trunk mylammps
+
+where "mylammps" is the name of the directory you wish to create on
+your machine.
+
+Once the command completes, your directory will contain the same files
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included.  They can be fetched
+from the LAMMPS website by typing "make fetch" in the doc directory.
+Or they can be generated from the content provided in doc/src by
+typing "make html" from the doc directory.
+
+After initial checkout, as bug fixes and new features are added to
+LAMMPS, as listed on :doc:`this page <Errors_bugs>`, you can stay
+up-to-date by typing the following SVN commands from within the
+"mylammps" directory:
+
+
+.. parsed-literal::
+
+   svn update
+
+You can also check if there are any updates by typing:
+
+
+.. parsed-literal::
+
+   svn -qu status
+
+Doing an "update" will not change any files you have added to the
+LAMMPS directory structure.  It will also not change any existing
+LAMMPS files you have edited, unless those files have changed in the
+repository.  In that case, SVN will attempt to merge the new
+repository file with your version of the file and tell you if there
+are any conflicts.  See the SVN documentation for details.
+
+Please refer to the `subversion client support help pages on GitHub <https://help.github.com/articles/support-for-subversion-clients>`_
+if you want to use advanced features like accessing particular
+previous release versions via tags.
+
+Once you have updated your local files with an "svn update" (or "svn
+co"), you still need to re-build LAMMPS if any source files have
+changed.  To do this, you should cd to the src directory and type:
+
+
+.. parsed-literal::
+
+   make purge             # remove any deprecated src files
+   make package-update    # sync package files with src files
+   make foo               # re-build for your machine (mpi, serial, etc)
+
+just as described on the :doc:`Install patch <Install_patch>` doc page,
+after a patch has been installed.
+
+.. warning::
+
+   If you wish to edit/change a src file that is from a
+   package, you should edit the version of the file inside the package
+   sub-directory with src, then re-install the package.  The version in
+   the src dir is merely a copy and will be wiped out if you type "make
+   package-update".
+
+The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
+junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
+gmail.com) and Richard Berger (Temple U, richard.berger at
+temple.edu).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst
new file mode 100644
index 0000000000..37db83157a
--- /dev/null
+++ b/doc/src/Install_tarball.rst
@@ -0,0 +1,84 @@
+Download source and documentation as a tarball
+==============================================
+
+You can download a current LAMMPS tarball from the `download page <download_>`_
+of the `LAMMPS website <lws_>`_.
+
+.. _download: http://lammps.sandia.gov/download.html
+
+
+
+.. _bug: http://lammps.sandia.gov/bug.html
+
+
+
+.. _older: http://lammps.sandia.gov/tars
+
+
+
+You have two choices of tarballs, either the most recent stable
+release or the most current patch release.  Stable releases occur a
+few times per year, and undergo more testing before release.  Patch
+releases occur a couple times per month.  The new contents in all
+releases are listed on the `bug and feature page <bug_>`_ of the website.
+
+Both tarballs include LAMMPS documentation (HTML and PDF files)
+corresponding to that version.  The download page also has an option
+to download the current-version LAMMPS documentation by itself.
+
+Older versions of LAMMPS can also be downloaded from `this page <older_>`_.
+
+Once you have a tarball, unzip and untar it with the following
+command:
+
+
+.. parsed-literal::
+
+   tar -xzvf lammps\*.tar.gz
+
+This will create a LAMMPS directory with the version date
+in its name, e.g. lammps-23Jun18.
+
+
+----------
+
+
+You can also download a zip file via the "Clone or download" button on
+the `LAMMPS GitHub site <git_>`_.  The file name will be lammps-master.zip
+which can be unzipped with the following command, to create
+a lammps-master dir:
+
+
+.. parsed-literal::
+
+   unzip lammps\*.zip
+
+This version is the most up-to-date LAMMPS development version.  It
+will have the date of the most recent patch release (see the file
+src/version.h).  But it will also include any new bug-fixes or
+features added since the last patch release.  They will be included in
+the next patch release tarball.
+
+.. _git: https://github.com/lammps/lammps
+
+
+
+
+----------
+
+
+If you download a current LAMMPS tarball, one way to stay current as
+new patch tarballs are released, is to download a patch file which you
+can apply to your local directory to update it for each new patch
+release.  (Or of course you could just download the newest tarball
+periodically.)
+
+The patch files are posted on the `bug and feature page <bug_>`_ of the
+website, along with a list of changed files and details about what is
+in the new patch release.  Instructions for applying a patch file are
+on the :doc:`Install patch <Install_patch>` doc page.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst
new file mode 100644
index 0000000000..aed6d935c2
--- /dev/null
+++ b/doc/src/Install_windows.rst
@@ -0,0 +1,49 @@
+Download an executable for Windows
+==================================
+
+Pre-compiled Windows installers which install LAMMPS executables on a
+Windows system can be downloaded from this site:
+
+`http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_
+
+Note that each installer package has a date in its name, which
+corresponds to the LAMMPS version of the same date.  Installers for
+current and older versions of LAMMPS are available.  32-bit and 64-bit
+installers are available, and each installer contains both a serial
+and parallel executable.  The installer site also explains how to
+install the Windows MPI package (MPICH2 from Argonne National Labs),
+needed to run in parallel.
+
+The LAMMPS binaries contain all optional packages included in the
+source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
+The serial version also does not include the MPIIO and
+USER-LB packages.  GPU support is provided for OpenCL.
+
+The installer site also has instructions on how to run LAMMPS under
+Windows, once it is installed, in both serial and parallel.
+
+When you download the installer package, you run it on your Windows
+machine.  It will then prompt you with a dialog, where you can choose
+the installation directory, unpack and copy several executables,
+potential files, documentation pdfs, selected example files, etc.  It
+will then update a few system settings (e.g. PATH, LAMMPS\_POTENTIALS)
+and add an entry into the Start Menu (with references to the
+documentation, LAMMPS homepage and more).  From that menu, there is
+also a link to an uninstaller that removes the files and undoes the
+environment manipulations.
+
+Note that to update to a newer version of LAMMPS, you should typically
+uninstall the version you currently have, download a new installer,
+and go through the install procedure described above.  I.e. the same
+procedure for installing/updating most Windows programs.  You can
+install multiple versions of LAMMPS (in different directories), but
+only the executable for the last-installed package will be found
+automatically, so this should only be done for debugging purposes.
+
+Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
+up this Windows capability.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Intro.rst b/doc/src/Intro.rst
new file mode 100644
index 0000000000..218dd4653a
--- /dev/null
+++ b/doc/src/Intro.rst
@@ -0,0 +1,21 @@
+Introduction
+************
+
+These pages provide a brief introduction to LAMMPS.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Intro_overview
+   Manual_version
+   Intro_features
+   Intro_nonfeatures
+   Intro_opensource
+   Intro_authors
+   Intro_website
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst
new file mode 100644
index 0000000000..26a6f6846e
--- /dev/null
+++ b/doc/src/Intro_authors.rst
@@ -0,0 +1,69 @@
+Authors of LAMMPS
+=================
+
+The primary LAMMPS developers are at Sandia National Labs and Temple
+University:
+
+* `Steve Plimpton <sjp_>`_, sjplimp at sandia.gov
+* Aidan Thompson, athomps at sandia.gov
+* Stan Moore, stamoor at sandia.gov
+* Axel Kohlmeyer, akohlmey at gmail.com
+* Richard Berger, richard.berger at temple.edu
+
+.. _sjp: http://www.cs.sandia.gov/~sjplimp
+
+
+
+Past developers include Paul Crozier and Mark Stevens, both at Sandia,
+and Ray Shan, now at Materials Design.
+
+
+----------
+
+
+The `Authors page <http://lammps.sandia.gov/authors.html>`_ of the
+`LAMMPS website <lws_>`_ has a comprehensive list of all the individuals
+who have contributed code for a new feature or command or tool to
+LAMMPS.
+
+
+----------
+
+
+The following folks deserve special recognition.  Many of the packages
+they have written are unique for an MD code and LAMMPS would not be as
+general-purpose as it is without their expertise and efforts.
+
+* Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF
+* Mike Brown (Intel), GPU and USER-INTEL packages
+* Colin Denniston (U Western Ontario), USER-LB package
+* Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages
+* Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field
+* Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling
+* Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS
+* Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion
+* Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
+* Mike Parks (Sandia), PERI package for Peridynamics
+* Roy Pollock (LLNL), Ewald and PPPM solvers
+* Christian Trott (Sandia), USER-CUDA and KOKKOS packages
+* Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD
+* Greg Wagner (Northwestern U), MEAM package for MEAM potential
+
+
+----------
+
+
+As discussed on the `History page <http://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
+originated as a cooperative project between DOE labs and industrial
+partners.  Folks involved in the design and testing of the original
+version of LAMMPS were the following:
+
+* John Carpenter (Mayo Clinic, formerly at Cray Research)
+* Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
+* Steve Lustig (Dupont)
+* Jim Belak and Roy Pollock (LLNL)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst
new file mode 100644
index 0000000000..67d37b917a
--- /dev/null
+++ b/doc/src/Intro_features.rst
@@ -0,0 +1,231 @@
+LAMMPS features
+===============
+
+LAMMPS is a classical molecular dynamics (MD) code with these general
+classes of functionality:
+
+* :ref:`General features <general>`
+* :ref:`Particle and model types <particle>`
+* :ref:`Interatomic potentials (force fields) <ff>`
+* :ref:`Atom creation <create>`
+* :ref:`Ensembles, constraints, and boundary conditions <ensemble>`
+* :ref:`Integrators <integrate>`
+* :ref:`Diagnostics <diag>`
+* :ref:`Output <output>`
+* :ref:`Multi-replica models <replica1>`
+* :ref:`Pre- and post-processing <prepost>`
+* :ref:`Specialized features (beyond MD itself) <special>`
+
+
+----------
+
+
+.. _general:
+
+General features
+------------------------------
+
+* runs on a single processor or in parallel
+* distributed-memory message-passing parallelism (MPI)
+* spatial-decomposition of simulation domain for parallelism
+* open-source distribution
+* highly portable C++
+* optional libraries used: MPI and single-processor FFT
+* GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
+* easy to extend with new features and functionality
+* runs from an input script
+* syntax for defining and using variables and formulas
+* syntax for looping over runs and breaking out of loops
+* run one or multiple simulations simultaneously (in parallel) from one script
+* build as library, invoke LAMMPS through library interface or provided Python wrapper
+* couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both
+
+.. _particle:
+
+Particle and model types
+---------------------------------------
+
+(:doc:`atom style <atom_style>` command)
+
+* atoms
+* coarse-grained particles (e.g. bead-spring polymers)
+* united-atom polymers or organic molecules
+* all-atom polymers, organic molecules, proteins, DNA
+* metals
+* granular materials
+* coarse-grained mesoscale models
+* finite-size spherical and ellipsoidal particles
+* finite-size  line segment (2d) and triangle (3d) particles
+* point dipole particles
+* rigid collections of particles
+* hybrid combinations of these
+
+.. _ff:
+
+Interatomic potentials (force fields)
+----------------------------------------------
+
+(:doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`,
+:doc:`angle style <angle_style>`, :doc:`dihedral style <dihedral_style>`,
+:doc:`improper style <improper_style>`, :doc:`kspace style <kspace_style>`
+commands)
+
+* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins,     Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
+* charged pairwise potentials: Coulombic, point-dipole
+* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM),     embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff,     REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
+* long-range interactions for charge, point-dipoles, and LJ dispersion:     Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
+* polarization models: :doc:`QEq <fix_qeq>`,     :doc:`core/shell model <Howto_coreshell>`,     :doc:`Drude dipole model <Howto_drude>`
+* charge equilibration (QEq via dynamic, point, shielded, Slater methods)
+* coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
+* mesoscopic potentials: granular, Peridynamics, SPH
+* electron force field (eFF, AWPMD)
+* bond potentials: harmonic, FENE, Morse, nonlinear, class 2,     quartic (breakable)
+* angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic,     class 2 (COMPASS)
+* dihedral potentials: harmonic, CHARMM, multi-harmonic, helix,     class 2 (COMPASS), OPLS
+* improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
+* polymer potentials: all-atom, united-atom, bead-spring, breakable
+* water potentials: TIP3P, TIP4P, SPC
+* implicit solvent potentials: hydrodynamic lubrication, Debye
+* force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options
+* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim\_init, kim\_interactions, and kim\_query <kim_commands>` commands
+* hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation
+* overlaid potentials: superposition of multiple pair potentials
+
+.. _create:
+
+Atom creation
+--------------------------
+
+(:doc:`read\_data <read_data>`, :doc:`lattice <lattice>`,
+:doc:`create\_atoms <create_atoms>`, :doc:`delete\_atoms <delete_atoms>`,
+:doc:`displace\_atoms <displace_atoms>`, :doc:`replicate <replicate>` commands)
+
+* read in atom coords from files
+* create atoms on one or more lattices (e.g. grain boundaries)
+* delete geometric or logical groups of atoms (e.g. voids)
+* replicate existing atoms multiple times
+* displace atoms
+
+.. _ensemble:
+
+Ensembles, constraints, and boundary conditions
+--------------------------------------------------------------
+
+(:doc:`fix <fix>` command)
+
+* 2d or 3d systems
+* orthogonal or non-orthogonal (triclinic symmetry) simulation domains
+* constant NVE, NVT, NPT, NPH, Parrinello/Rahman integrators
+* thermostatting options for groups and geometric regions of atoms
+* pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
+* simulation box deformation (tensile and shear)
+* harmonic (umbrella) constraint forces
+* rigid body constraints
+* SHAKE bond and angle constraints
+* Monte Carlo bond breaking, formation, swapping
+* atom/molecule insertion and deletion
+* walls of various kinds
+* non-equilibrium molecular dynamics (NEMD)
+* variety of additional boundary conditions and constraints
+
+.. _integrate:
+
+Integrators
+---------------------------
+
+(:doc:`run <run>`, :doc:`run\_style <run_style>`, :doc:`minimize <minimize>` commands)
+
+* velocity-Verlet integrator
+* Brownian dynamics
+* rigid body integration
+* energy minimization via conjugate gradient or steepest descent relaxation
+* rRESPA hierarchical timestepping
+* rerun command for post-processing of dump files
+
+.. _diag:
+
+Diagnostics
+----------------------
+
+* see various flavors of the :doc:`fix <fix>` and :doc:`compute <compute>` commands
+
+.. _output:
+
+Output
+-------------------
+
+(:doc:`dump <dump>`, :doc:`restart <restart>` commands)
+
+* log file of thermodynamic info
+* text dump files of atom coords, velocities, other per-atom quantities
+* binary restart files
+* parallel I/O of dump and restart files
+* per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
+* user-defined system-wide (log file) or per-atom (dump file) calculations
+* spatial and time averaging of per-atom quantities
+* time averaging of system-wide quantities
+* atom snapshots in native, XYZ, XTC, DCD, CFG formats
+
+.. _replica1:
+
+Multi-replica models
+-----------------------------------
+
+* :doc:`nudged elastic band <neb>`
+* :doc:`parallel replica dynamics <prd>`
+* :doc:`temperature accelerated dynamics <tad>`
+* :doc:`parallel tempering <temper>`
+
+.. _prepost:
+
+Pre- and post-processing
+--------------------------------------
+
+* A handful of pre- and post-processing tools are packaged with LAMMPS,
+  some of which can convert input and output files to/from formats used
+  by other codes; see the :doc:`Toos <Tools>` doc page.
+* Our group has also written and released a separate toolkit called
+  `Pizza.py <pizza_>`_ which provides tools for doing setup, analysis,
+  plotting, and visualization for LAMMPS simulations.  Pizza.py is
+  written in `Python <python_>`_ and is available for download from `the Pizza.py WWW site <pizza_>`_.
+
+.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
+
+
+
+.. _python: http://www.python.org
+
+
+
+.. _special:
+
+Specialized features
+----------------------------------
+
+LAMMPS can be built with optional packages which implement a variety
+of additional capabilities.  See the :doc:`Packages <Packages>` doc
+page for details.
+
+These are LAMMPS capabilities which you may not think of as typical
+classical MD options:
+
+* :doc:`static <balance>` and :doc:`dynamic load-balancing <fix_balance>`
+* :doc:`generalized aspherical particles <Howto_body>`
+* :doc:`stochastic rotation dynamics (SRD) <fix_srd>`
+* :doc:`real-time visualization and interactive MD <fix_imd>`
+* calculate :doc:`virtual diffraction patterns <compute_xrd>`
+* :doc:`atom-to-continuum coupling <fix_atc>` with finite elements
+* coupled rigid body integration via the :doc:`POEMS <fix_poems>` library
+* :doc:`QM/MM coupling <fix_qmmm>`
+* Monte Carlo via :doc:`GCMC <fix_gcmc>` and :doc:`tfMC <fix_tfmc>` and :doc:`atom swapping <fix_atom_swap>`
+* :doc:`path-integral molecular dynamics (PIMD) <fix_ipi>` and :doc:`this as well <fix_pimd>`
+* :doc:`Direct Simulation Monte Carlo <pair_dsmc>` for low-density fluids
+* :doc:`Peridynamics mesoscale modeling <pair_peri>`
+* :doc:`Lattice Boltzmann fluid <fix_lb_fluid>`
+* :doc:`targeted <fix_tmd>` and :doc:`steered <fix_smd>` molecular dynamics
+* :doc:`two-temperature electron model <fix_ttm>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst
new file mode 100644
index 0000000000..9c09eb0466
--- /dev/null
+++ b/doc/src/Intro_nonfeatures.rst
@@ -0,0 +1,87 @@
+LAMMPS non-features
+===================
+
+LAMMPS is designed to be a fast, parallel engine for molecular
+dynamics (MD) simulations.  It provides only a modest amount of
+functionality for setting up simulations and analyzing their output.
+
+Specifically, LAMMPS was not conceived and designed for:
+
+* being run through a GUI
+* building molecular systems, or building molecular topologies
+* assign force-field coefficients automagically
+* perform sophisticated analysis of your MD simulation
+* visualize your MD simulation interactively
+* plot your output data
+
+Although over the years these limitations have been somewhat
+reduced through features added to LAMMPS or external tools
+that either closely interface with LAMMPS or extend LAMMPS.
+
+Here are suggestions on how to perform these tasks:
+
+* **GUI:** LAMMPS can be built as a library and a Python wrapper that wraps
+  the library interface is provided.  Thus, GUI interfaces can be
+  written in Python (or C or C++ if desired) that run LAMMPS and
+  visualize or plot its output.  Examples of this are provided in the
+  python directory and described on the :doc:`Python <Python_head>` doc
+  page.  Also, there are several external wrappers or GUI front ends.
+* **Builder:** Several pre-processing tools are packaged with LAMMPS.  Some
+  of them convert input files in formats produced by other MD codes such
+  as CHARMM, AMBER, or Insight into LAMMPS input formats.  Some of them
+  are simple programs that will build simple molecular systems, such as
+  linear bead-spring polymer chains.  The moltemplate program is a true
+  molecular builder that will generate complex molecular models.  See
+  the :doc:`Tools <Tools>` doc page for details on tools packaged with
+  LAMMPS.  The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
+  describes a variety of 3rd party tools for this task.  Furthermore,
+  some LAMMPS internal commands allow to reconstruct, or selectively add
+  topology information, as well as provide the option to insert molecule
+  templates instead of atoms for building bulk molecular systems.
+* **Force-field assignment:** The conversion tools described in the previous
+  bullet for CHARMM, AMBER, and Insight will also assign force field
+  coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
+  or BIOVIA (formerly Accelrys) force field files. The tools
+  `ParmEd <https://parmed.github.io/ParmEd/html/index.html>`_ and
+  `InterMol <https://github.com/shirtsgroup/InterMol>`_ are particularly
+  powerful and flexible in converting force field and topology data
+  between various MD simulation programs.
+* **Simulation analysis:** If you want to perform analysis on-the-fly as
+  your simulation runs, see the :doc:`compute <compute>` and
+  :doc:`fix <fix>` doc pages, which list commands that can be used in a
+  LAMMPS input script.  Also see the :doc:`Modify <Modify>` doc page for
+  info on how to add your own analysis code or algorithms to LAMMPS.
+  For post-processing, LAMMPS output such as :doc:`dump file snapshots <dump>` can be converted into formats used by other MD or
+  post-processing codes.  To some degree, that conversion can be done
+  directly inside of LAMMPS by interfacing to the VMD molfile plugins.
+  The :doc:`rerun <rerun>` command also allows to do some post-processing
+  of existing trajectories, and through being able to read a variety
+  of file formats, this can also be used for analyzing trajectories
+  from other MD codes.  Some post-processing tools packaged with
+  LAMMPS will do these conversions.  Scripts provided in the
+  tools/python directory can extract and massage data in dump files to
+  make it easier to import into other programs.  See the
+  :doc:`Tools <Tools>` doc page for details on these various options.
+* **Visualization:** LAMMPS can produce NETPBM, JPG or PNG snapshot images
+  on-the-fly via its :doc:`dump image <dump_image>` command and pass
+  them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
+  movies from them.  For high-quality, interactive visualization there are
+  many excellent and free tools available.  See the `Other Codes page <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS website for
+  visualization packages that can use LAMMPS output data.
+* **Plotting:** See the next bullet about Pizza.py as well as the
+  :doc:`Python <Python_head>` doc page for examples of plotting LAMMPS
+  output.  Scripts provided with the *python* tool in the tools
+  directory will extract and massage data in log and dump files to make
+  it easier to analyze and plot.  See the :doc:`Tools <Tools>` doc page
+  for more discussion of the various tools.
+* **Pizza.py:** Our group has also written a separate toolkit called
+  `Pizza.py <http://pizza.sandia.gov>`_ which can do certain kinds of
+  setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
+  simulations.  It thus provides some functionality for several of the
+  above bullets.  Pizza.py is written in `Python <http://www.python.org>`_
+  and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Intro_opensource.rst b/doc/src/Intro_opensource.rst
new file mode 100644
index 0000000000..211e812eaa
--- /dev/null
+++ b/doc/src/Intro_opensource.rst
@@ -0,0 +1,49 @@
+LAMMPS open-source license
+==========================
+
+LAMMPS is a freely-available open-source code, distributed under the
+terms of the `GNU Public License <gnu_>`_, which means you can use or
+modify the code however you wish.
+
+LAMMPS comes with no warranty of any kind.  As each source file states
+in its header, it is a copyrighted code that is distributed free-of-
+charge, under the terms of the `GNU Public License <gnu_>`_ (GPL).  This
+is often referred to as open-source distribution - see
+`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_.  The legal
+text of the GPL is in the LICENSE file included in the LAMMPS
+distribution.
+
+.. _gnu: http://www.gnu.org/copyleft/gpl.html
+
+
+
+.. _gnuorg: http://www.gnu.org
+
+
+
+.. _opensource: http://www.opensource.org
+
+
+
+Here is a summary of what the GPL means for LAMMPS users:
+
+(1) Anyone is free to use, modify, or extend LAMMPS in any way they
+choose, including for commercial purposes.
+
+(2) If you distribute a modified version of LAMMPS, it must remain
+open-source, meaning you distribute it under the terms of the GPL.
+You should clearly annotate such a code as a derivative version of
+LAMMPS.
+
+(3) If you release any code that includes LAMMPS source code, then it
+must also be open-sourced, meaning you distribute it under the terms
+of the GPL.
+
+(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
+source file headers (including the copyright and GPL notices) should
+remain part of the code.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst
new file mode 100644
index 0000000000..a97adc8235
--- /dev/null
+++ b/doc/src/Intro_overview.rst
@@ -0,0 +1,54 @@
+Overview of LAMMPS
+==================
+
+LAMMPS is a classical molecular dynamics (MD) code that models
+ensembles of particles in a liquid, solid, or gaseous state.  It can
+model atomic, polymeric, biological, solid-state (metals, ceramics,
+oxides), granular, coarse-grained, or macroscopic systems using a
+variety of interatomic potentials (force fields) and boundary
+conditions.  It can model 2d or 3d systems with only a few particles
+up to millions or billions.
+
+LAMMPS can be built and run on a laptop or desktop machine, but is
+designed for parallel computers.  It will run on any parallel machine
+that supports the `MPI <mpi_>`_ message-passing library.  This includes
+shared-memory boxes and distributed-memory clusters and
+supercomputers.
+
+.. _mpi: http://www-unix.mcs.anl.gov/mpi
+
+
+
+LAMMPS is written in C++.  Earlier versions were written in F77 and
+F90.  See the `History page <http://lammps.sandia.gov/history.html>`_ of
+the website for details.  All versions can be downloaded from the
+`LAMMPS website <lws_>`_.
+
+LAMMPS is designed to be easy to modify or extend with new
+capabilities, such as new force fields, atom types, boundary
+conditions, or diagnostics.  See the :doc:`Modify <Modify>` doc page for
+more details.
+
+In the most general sense, LAMMPS integrates Newton's equations of
+motion for a collection of interacting particles.  A single particle
+can be an atom or molecule or electron, a coarse-grained cluster of
+atoms, or a mesoscopic or macroscopic clump of material.  The
+interaction models that LAMMPS includes are mostly short-range in
+nature; some long-range models are included as well.
+
+LAMMPS uses neighbor lists to keep track of nearby particles.  The
+lists are optimized for systems with particles that are repulsive at
+short distances, so that the local density of particles never becomes
+too large.  This is in contrast to methods used for modeling plasma
+or gravitational bodies (e.g. galaxy formation).
+
+On parallel machines, LAMMPS uses spatial-decomposition techniques to
+partition the simulation domain into small sub-domains of equal
+computational cost, one of which is assigned to each processor.
+Processors communicate and store "ghost" atom information for atoms
+that border their sub-domain.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Intro_website.rst b/doc/src/Intro_website.rst
new file mode 100644
index 0000000000..6adbd05e8c
--- /dev/null
+++ b/doc/src/Intro_website.rst
@@ -0,0 +1,39 @@
+Additional website links
+========================
+
+The `LAMMPS website <lws_>`_ has a variety of additional info about
+LAMMPS, beyond what is in this manual.  Some of the other pages in
+this Intr are included in this list.
+
+* `Brief intro and recently added significant features <lws_>`_
+* `List of features <http://lammps.sandia.gov/features.html>`_
+* `List of non-features <http://lammps.sandia.gov/non_features.html>`_
+* `Recent bug fixes and new features <http://lammps.sandia.gov/bug.html>`_
+
+* `Download info <http://lammps.sandia.gov/download.html>`_
+* `GitHub site <https://github.com/lammps/lammps>`_
+* `SourceForge site <https://sourceforge.net/projects/lammps>`_
+* `LAMMPS open-source license <http://lammps.sandia.gov/open_source.html>`_
+
+* `Glossary of MD terms relevant to LAMMPS <http://lammps.sandia.gov/glossary.html>`_
+* `LAMMPS highlights with images <http://lammps.sandia.gov/pictures.html>`_
+* `LAMMPS highlights with movies <http://lammps.sandia.gov/movies.html>`_
+* `Mail list <http://lammps.sandia.gov/mail.html>`_
+* `Workshops <http://lammps.sandia.gov/workshops.html>`_
+* `Tutorials <http://lammps.sandia.gov/tutorials.html>`_
+* `Developer guide <http://lammps.sandia.gov/Developer.pdf>`_
+
+* `Pre- and post-processing tools for LAMMPS <http://lammps.sandia.gov/prepost.html>`_
+* `Other software usable with LAMMPS <http://lammps.sandia.gov/offsite.html>`_
+* `Viz tools usable with LAMMPS <http://lammps.sandia.gov/viz.html>`_
+
+* `Benchmark performance <http://lammps.sandia.gov/bench.html>`_
+* `Publications that have cited LAMMPS <http://lammps.sandia.gov/papers.html>`_
+* `Authors of LAMMPS <http://lammps.sandia.gov/authors.html>`_
+* `History of LAMMPS development <http://lammps.sandia.gov/history.html>`_
+* `Funding for LAMMPS <http://lammps.sandia.gov/funding.html>`_
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/JPG/dynamical_matrix_dynmat.jpg b/doc/src/JPG/dynamical_matrix_dynmat.jpg
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diff --git a/doc/src/JPG/third_order_force_constant.png b/doc/src/JPG/third_order_force_constant.png
new file mode 100644
index 0000000000000000000000000000000000000000..f6171ccf097e9df5fee54241d1bc2f142de2d398
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diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst
new file mode 100644
index 0000000000..dd67a13427
--- /dev/null
+++ b/doc/src/Manual.rst
@@ -0,0 +1,92 @@
+LAMMPS Documentation
+####################
+
+|version| version
+*****************
+
+:doc:`What is a LAMMPS version? <Manual_version>`
+
+LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
+Simulator.
+
+LAMMPS is a classical molecular dynamics simulation code with a focus
+on materials modeling.  It was designed to run efficiently on parallel
+computers.  It was developed originally at Sandia National
+Laboratories, a US Department of Energy facility.  The majority of
+funding for LAMMPS has come from the US Department of Energy (DOE).
+LAMMPS is an open-source code, distributed freely under the terms of
+the GNU Public License (GPL).
+
+The `LAMMPS website <lws_>`_ has a variety of information about the code.
+It includes links to an on-line version of this manual, a `mailing list <http://lammps.sandia.gov/mail.html>`_ where users can post
+questions, and a `GitHub site <https://github.com/lammps/lammps>`_ where
+all LAMMPS development is coordinated.
+
+
+----------
+
+
+The content for this manual is part of the LAMMPS distribution.  You
+can build a local copy of the Manual as HTML pages or a PDF file, by
+following the steps on the :doc:`Manual build <Manual_build>` doc page.
+There is also a `Developer.pdf <Developer.pdf>`_ document which gives
+a brief description of the basic code structure of LAMMPS.
+
+
+----------
+
+
+Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for
+every LAMMPS command.
+
+
+.. toctree::
+   :maxdepth: 2
+   :numbered: 3
+   :caption: User Documentation
+   :name: userdoc
+   :includehidden:
+
+   Intro
+   Install
+   Build
+   Run_head
+   Commands
+   Packages
+   Speed
+   Howto
+   Examples
+   Tools
+   Modify
+   Python_head
+   Errors
+   Manual_build
+
+.. toctree::
+   :caption: Index
+   :name: index
+   :hidden:
+
+   commands_list
+   fixes
+   computes
+   pairs
+   bonds
+   angles
+   dihedrals
+   impropers
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`
+
+.. raw:: html
+
+   </BODY>
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
deleted file mode 100644
index c63137ef6f..0000000000
--- a/doc/src/Manual.txt
+++ /dev/null
@@ -1,124 +0,0 @@
-<!-- HTML_ONLY -->
-<HEAD>
-<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="7 Aug 2019 version">
-<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
-<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
-</HEAD>
-
-<BODY>
-
-<H1></H1>
-
-<!-- END_HTML_ONLY -->
-
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html#comm)
-
-:line
-
-LAMMPS Documentation :c,h1
-7 Aug 2019 version :c,h2
-
-"What is a LAMMPS version?"_Manual_version.html
-
-LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
-Simulator.
-
-LAMMPS is a classical molecular dynamics simulation code with a focus
-on materials modeling.  It was designed to run efficiently on parallel
-computers.  It was developed originally at Sandia National
-Laboratories, a US Department of Energy facility.  The majority of
-funding for LAMMPS has come from the US Department of Energy (DOE).
-LAMMPS is an open-source code, distributed freely under the terms of
-the GNU Public License (GPL).
-
-The "LAMMPS website"_lws has a variety of information about the code.
-It includes links to an on-line version of this manual, a "mailing
-list"_http://lammps.sandia.gov/mail.html where users can post
-questions, and a "GitHub site"_https://github.com/lammps/lammps where
-all LAMMPS development is coordinated.
-
-:line
-
-The content for this manual is part of the LAMMPS distribution.  You
-can build a local copy of the Manual as HTML pages or a PDF file, by
-following the steps on the "Manual build"_Manual_build.html doc page.
-There is also a "Developer.pdf"_Developer.pdf document which gives
-a brief description of the basic code structure of LAMMPS.
-
-:line
-
-Once you are familiar with LAMMPS, you may want to bookmark "this
-page"_Commands.html since it gives quick access to a doc page for
-every LAMMPS command.
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 2
-   :numbered: 3
-   :caption: User Documentation
-   :name: userdoc
-   :includehidden:
-
-   Intro
-   Install
-   Build
-   Run_head
-   Commands
-   Packages
-   Speed
-   Howto
-   Examples
-   Tools
-   Modify
-   Python_head
-   Errors
-   Manual_build
-
-.. toctree::
-   :caption: Index
-   :name: index
-   :hidden:
-
-   commands_list
-   fixes
-   computes
-   pairs
-   bonds
-   angles
-   dihedrals
-   impropers
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`search`
-
-END_RST -->
-
-<!-- HTML_ONLY -->
-"Introduction"_Intro.html :olb,l
-"Install LAMMPS"_Install.html :l
-"Build LAMMPS"_Build.html :l
-"Run LAMMPS"_Run_head.html :l
-"Commands"_Commands.html :l
-"Optional packages"_Packages.html :l
-"Accelerate performance"_Speed.html :l
-"How-to discussions"_Howto.html :l
-"Example scripts"_Examples.html :l
-"Auxiliary tools"_Tools.html :l
-"Modify & extend LAMMPS"_Modify.html :l
-"Use Python with LAMMPS"_Python_head.html :l
-"Errors"_Errors.html :l
-"Building the LAMMPS manual"_Manual_build.html :l
-:ole
-
-<!-- END_HTML_ONLY -->
-
-</BODY>
diff --git a/doc/src/Manual_build.rst b/doc/src/Manual_build.rst
new file mode 100644
index 0000000000..c1cd1aabb9
--- /dev/null
+++ b/doc/src/Manual_build.rst
@@ -0,0 +1,141 @@
+Building the LAMMPS manual
+**************************
+
+Depending on how you obtained LAMMPS, the doc directory has 2 or 3
+sub-directories and optionally 2 PDF files and 2 e-book format files:
+
+
+.. parsed-literal::
+
+   src             # content files for LAMMPS documentation
+   html            # HTML version of the LAMMPS manual (see html/Manual.html)
+   tools           # tools and settings for building the documentation
+   Manual.pdf      # large PDF version of entire manual
+   Developer.pdf   # small PDF with info about how LAMMPS is structured
+   LAMMPS.epub     # Manual in ePUB e-book format
+   LAMMPS.mobi     # Manual in MOBI e-book format
+
+If you downloaded LAMMPS as a tarball from the web site, all these
+directories and files should be included.
+
+If you downloaded LAMMPS from the public SVN or Git repositories, then
+the HTML and PDF files are not included.  Instead you need to create
+them, in one of two ways:
+
+a. You can "fetch" the current HTML and PDF files from the LAMMPS web site.
+   Just type "make fetch".  This should create a html\_www dir and
+   Manual\_www.pdf/Developer\_www.pdf files.  Note that if new LAMMPS features
+   have been added more recently than the date of your version, the fetched
+   documentation will include those changes (but your source code will not, unless
+   you update your local repository).
+
+b. You can build the HTML and PDF files yourself, by typing "make
+   html" followed by "make pdf".  Note that the PDF make requires the
+   HTML files already exist.  This requires various tools including
+   Sphinx, which the build process will attempt to download and install
+   on your system, if not already available.  See more details below.
+
+----------
+
+
+The generation of all documentation is managed by the Makefile in
+the doc dir.
+
+
+.. code-block:: bash
+
+   Documentation Build Options:
+
+   make html         # generate HTML in html dir using Sphinx
+   make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
+                     #   in doc dir via htmldoc and pdflatex
+   make fetch        # fetch HTML doc pages and 2 PDF files from web site
+                     #   as a tarball and unpack into html dir and 2 PDFs
+   make epub         # generate LAMMPS.epub in ePUB format using Sphinx
+   make mobi         # generate LAMMPS.mobi in MOBI format using ebook-convert
+   make clean        # remove intermediate RST files created by HTML build
+   make clean-all    # remove entire build folder and any cached data
+   make anchor_check # check for duplicate anchor labels
+   style_check       # check for complete and consistent style lists
+   make spelling     # spell-check the manual
+
+
+----------
+
+
+Installing prerequisites for HTML build
+=======================================
+
+To run the HTML documentation build toolchain, Python 3 and virtualenv
+have to be installed.  Here are instructions for common setups:
+
+Ubuntu
+------
+
+
+.. code-block:: bash
+
+   sudo apt-get install python-virtualenv
+
+Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
+------------------------------------------------------------------------------------
+
+
+.. code-block:: bash
+
+   sudo yum install python3-virtualenv
+
+Fedora (since version 22)
+-------------------------
+
+
+.. code-block:: bash
+
+   sudo dnf install python3-virtualenv
+
+MacOS X
+-------
+
+Python 3
+^^^^^^^^
+
+Download the latest Python 3 MacOS X package from
+`https://www.python.org <https://www.python.org>`_
+and install it.  This will install both Python 3
+and pip3.
+
+virtualenv
+^^^^^^^^^^
+
+Once Python 3 is installed, open a Terminal and type
+
+
+.. code-block:: bash
+
+   pip3 install virtualenv
+
+This will install virtualenv from the Python Package Index.
+
+
+----------
+
+
+Installing prerequisites for epub build
+=======================================
+
+ePUB
+----
+
+Same as for HTML. This uses the same tools and configuration
+files as the HTML tree.
+
+For converting the generated ePUB file to a MOBI format file
+(for e-book readers like Kindle, that cannot read ePUB), you
+also need to have the 'ebook-convert' tool from the "calibre"
+software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
+You first create the ePUB file and then convert it with 'make mobi'
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt
deleted file mode 100644
index e9df0d2cfc..0000000000
--- a/doc/src/Manual_build.txt
+++ /dev/null
@@ -1,133 +0,0 @@
-"Previous Section"_Errors.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Manual.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Building the LAMMPS manual :h2
-
-Depending on how you obtained LAMMPS, the doc directory has 2 or 3
-sub-directories and optionally 2 PDF files and 2 e-book format files:
-
-src             # content files for LAMMPS documentation
-html            # HTML version of the LAMMPS manual (see html/Manual.html)
-tools           # tools and settings for building the documentation
-Manual.pdf      # large PDF version of entire manual
-Developer.pdf   # small PDF with info about how LAMMPS is structured
-LAMMPS.epub     # Manual in ePUB e-book format
-LAMMPS.mobi     # Manual in MOBI e-book format :pre
-
-If you downloaded LAMMPS as a tarball from the web site, all these
-directories and files should be included.
-
-If you downloaded LAMMPS from the public SVN or Git repositories, then
-the HTML and PDF files are not included.  Instead you need to create
-them, in one of three ways:
-
-(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
-site.  Just type "make fetch".  This should create a html_www dir and
-Manual_www.pdf/Developer_www.pdf files.  Note that if new LAMMPS
-features have been added more recently than the date of your version,
-the fetched documentation will include those changes (but your source
-code will not, unless you update your local repository).
-
-(b) You can build the HTML and PDF files yourself, by typing "make
-html" followed by "make pdf".  Note that the PDF make requires the
-HTML files already exist.  This requires various tools including
-Sphinx, which the build process will attempt to download and install
-on your system, if not already available.  See more details below.
-
-(c) You can generate an older, simpler, less-fancy style of HTML
-documentation by typing "make old".  This will create an "old"
-directory.  This can be useful if (b) does not work on your box for
-some reason, or you want to quickly view the HTML version of a doc
-page you have created or edited yourself within the src directory.
-E.g. if you are planning to submit a new feature to LAMMPS.
-
-:line
-
-The generation of all documentation is managed by the Makefile in
-the doc dir.
-
-Documentation Build Options: :pre
-
-make html         # generate HTML in html dir using Sphinx
-make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
-                  #   in doc dir via htmldoc and pdflatex
-make old          # generate old-style HTML pages in old dir via txt2html
-make fetch        # fetch HTML doc pages and 2 PDF files from web site
-                  #   as a tarball and unpack into html dir and 2 PDFs
-make epub         # generate LAMMPS.epub in ePUB format using Sphinx
-make mobi         # generate LAMMPS.mobi in MOBI format using ebook-convert
-make clean        # remove intermediate RST files created by HTML build
-make clean-all    # remove entire build folder and any cached data :pre
-make anchor_check # check for duplicate anchor labels
-make spelling     # spell-check the manual
-
-:line
-
-Installing prerequisites for HTML build :h3
-
-To run the HTML documentation build toolchain, Python 3 and virtualenv
-have to be installed.  Here are instructions for common setups:
-
-Ubuntu :h4
-
-sudo apt-get install python-virtualenv :pre
-
-Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x) :h4
-
-sudo yum install python3-virtualenv :pre
-
-Fedora (since version 22) :h4
-
-sudo dnf install python3-virtualenv :pre
-
-MacOS X :h4
-
-Python 3 :h5
-
-Download the latest Python 3 MacOS X package from
-"https://www.python.org"_https://www.python.org
-and install it.  This will install both Python 3
-and pip3.
-
-virtualenv :h5
-
-Once Python 3 is installed, open a Terminal and type
-
-pip3 install virtualenv :pre
-
-This will install virtualenv from the Python Package Index.
-
-:line
-
-Installing prerequisites for PDF build
-
-Building the PDF manual requires a working C++ compiler (to
-compile the txt2html tool and a working installation of
-"HTMLDOC"_https://www.msweet.org/htmldoc/
-HTMLDOC has its own list of prerequisites, but in most cases
-you can install a binary package of it either through your
-Linux package manager or MacOS (dmg) and Windows installer
-(msi) packages from its
-"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases
-
-:line
-
-Installing prerequisites for epub build :h3
-
-ePUB :h4
-
-Same as for HTML. This uses the same tools and configuration
-files as the HTML tree.
-
-For converting the generated ePUB file to a MOBI format file
-(for e-book readers like Kindle, that cannot read ePUB), you
-also need to have the 'ebook-convert' tool from the "calibre"
-software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/
-You first create the ePUB file and then convert it with 'make mobi'
diff --git a/doc/src/Manual_version.rst b/doc/src/Manual_version.rst
new file mode 100644
index 0000000000..ca3819aed8
--- /dev/null
+++ b/doc/src/Manual_version.rst
@@ -0,0 +1,28 @@
+What does a LAMMPS version mean
+===============================
+
+The LAMMPS "version" is the date when it was released, such as 1 May
+2014. LAMMPS is updated continuously.  Whenever we fix a bug or add a
+feature, we release it in the next *patch* release, which are
+typically made every couple of weeks.  Info on patch releases are on
+`this website page <http://lammps.sandia.gov/bug.html>`_. Every few
+months, the latest patch release is subjected to more thorough testing
+and labeled as a *stable* version.
+
+Each version of LAMMPS contains all the features and bug-fixes up to
+and including its version date.
+
+The version date is printed to the screen and logfile every time you
+run LAMMPS. It is also in the file src/version.h and in the LAMMPS
+directory name created when you unpack a tarball.  And it is on the
+first page of the :doc:`manual <Manual>`.
+
+* If you browse the HTML doc pages on the LAMMPS WWW site, they always
+  describe the most current patch release of LAMMPS.
+* If you browse the HTML doc pages included in your tarball, they
+  describe the version you have, which may be older.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify.rst b/doc/src/Modify.rst
new file mode 100644
index 0000000000..f875084d50
--- /dev/null
+++ b/doc/src/Modify.rst
@@ -0,0 +1,40 @@
+Modify & extend LAMMPS
+**********************
+
+LAMMPS is designed in a modular fashion so as to be easy to modify and
+extend with new functionality.  In fact, about 95% of its source code
+is add-on files.  These doc pages give basic instructions on how to do
+this.
+
+If you add a new feature to LAMMPS and think it will be of interest to
+general users, we encourage you to submit it for inclusion in LAMMPS
+as a pull request on our `GitHub site <https://github.com/lammps/lammps>`_, after reading the :doc:`Modify contribute <Modify_contribute>` doc page.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Modify_overview
+   Modify_contribute
+
+.. toctree::
+   :maxdepth: 1
+
+   Modify_atom
+   Modify_pair
+   Modify_bond
+   Modify_compute
+   Modify_fix
+   Modify_command
+   Modify_dump
+   Modify_kspace
+   Modify_min
+   Modify_region
+   Modify_body
+   Modify_thermo
+   Modify_variable
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_atom.rst b/doc/src/Modify_atom.rst
new file mode 100644
index 0000000000..d44a805161
--- /dev/null
+++ b/doc/src/Modify_atom.rst
@@ -0,0 +1,124 @@
+Atom styles
+===========
+
+Classes that define an :doc:`atom style <atom_style>` are derived from
+the AtomVec class and managed by the Atom class.  The atom style
+determines what attributes are associated with an atom.  A new atom
+style can be created if one of the existing atom styles does not
+define all the attributes you need to store and communicate with
+atoms.
+
+Atom\_vec\_atomic.cpp is a simple example of an atom style.
+
+Here is a brief description of methods you define in your new derived
+class.  See atom\_vec.h for details.
+
++-------------------------+--------------------------------------------------------------------------------+
+| init                    | one time setup (optional)                                                      |
++-------------------------+--------------------------------------------------------------------------------+
+| grow                    | re-allocate atom arrays to longer lengths (required)                           |
++-------------------------+--------------------------------------------------------------------------------+
+| grow\_reset             | make array pointers in Atom and AtomVec classes consistent (required)          |
++-------------------------+--------------------------------------------------------------------------------+
+| copy                    | copy info for one atom to another atom's array locations (required)            |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_comm              | store an atom's info in a buffer communicated every timestep (required)        |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_comm\_vel         | add velocity info to communication buffer (required)                           |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_comm\_hybrid      | store extra info unique to this atom style (optional)                          |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_comm            | retrieve an atom's info from the buffer (required)                             |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_comm\_vel       | also retrieve velocity info (required)                                         |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_comm\_hybrid    | retrieve extra info unique to this atom style (optional)                       |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_reverse           | store an atom's info in a buffer communicating partial forces  (required)      |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_reverse\_hybrid   | store extra info unique to this atom style (optional)                          |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_reverse         | retrieve an atom's info from the buffer (required)                             |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_reverse\_hybrid | retrieve extra info unique to this atom style (optional)                       |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_border            | store an atom's info in a buffer communicated on neighbor re-builds (required) |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_border\_vel       | add velocity info to buffer (required)                                         |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_border\_hybrid    | store extra info unique to this atom style (optional)                          |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_border          | retrieve an atom's info from the buffer (required)                             |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_border\_vel     | also retrieve velocity info (required)                                         |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_border\_hybrid  | retrieve extra info unique to this atom style (optional)                       |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_exchange          | store all an atom's info to migrate to another processor (required)            |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_exchange        | retrieve an atom's info from the buffer (required)                             |
++-------------------------+--------------------------------------------------------------------------------+
+| size\_restart           | number of restart quantities associated with proc's atoms (required)           |
++-------------------------+--------------------------------------------------------------------------------+
+| pack\_restart           | pack atom quantities into a buffer (required)                                  |
++-------------------------+--------------------------------------------------------------------------------+
+| unpack\_restart         | unpack atom quantities from a buffer (required)                                |
++-------------------------+--------------------------------------------------------------------------------+
+| create\_atom            | create an individual atom of this style (required)                             |
++-------------------------+--------------------------------------------------------------------------------+
+| data\_atom              | parse an atom line from the data file (required)                               |
++-------------------------+--------------------------------------------------------------------------------+
+| data\_atom\_hybrid      | parse additional atom info unique to this atom style (optional)                |
++-------------------------+--------------------------------------------------------------------------------+
+| data\_vel               | parse one line of velocity information from data file (optional)               |
++-------------------------+--------------------------------------------------------------------------------+
+| data\_vel\_hybrid       | parse additional velocity data unique to this atom style (optional)            |
++-------------------------+--------------------------------------------------------------------------------+
+| memory\_usage           | tally memory allocated by atom arrays (required)                               |
++-------------------------+--------------------------------------------------------------------------------+
+
+The constructor of the derived class sets values for several variables
+that you must set when defining a new atom style, which are documented
+in atom\_vec.h.  New atom arrays are defined in atom.cpp.  Search for
+the word "customize" and you will find locations you will need to
+modify.
+
+.. note::
+
+   It is possible to add some attributes, such as a molecule ID, to
+   atom styles that do not have them via the :doc:`fix property/atom <fix_property_atom>` command.  This command also
+   allows new custom attributes consisting of extra integer or
+   floating-point values to be added to atoms.  See the :doc:`fix property/atom <fix_property_atom>` doc page for examples of cases
+   where this is useful and details on how to initialize, access, and
+   output the custom values.
+
+New :doc:`pair styles <pair_style>`, :doc:`fixes <fix>`, or
+:doc:`computes <compute>` can be added to LAMMPS, as discussed below.
+The code for these classes can use the per-atom properties defined by
+fix property/atom.  The Atom class has a find\_custom() method that is
+useful in this context:
+
+
+.. parsed-literal::
+
+   int index = atom->find_custom(char \*name, int &flag);
+
+The "name" of a custom attribute, as specified in the :doc:`fix property/atom <fix_property_atom>` command, is checked to verify
+that it exists and its index is returned.  The method also sets flag =
+0/1 depending on whether it is an integer or floating-point attribute.
+The vector of values associated with the attribute can then be
+accessed using the returned index as
+
+
+.. parsed-literal::
+
+   int \*ivector = atom->ivector[index];
+   double \*dvector = atom->dvector[index];
+
+Ivector or dvector are vectors of length Nlocal = # of owned atoms,
+which store the attributes of individual atoms.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_body.rst b/doc/src/Modify_body.rst
new file mode 100644
index 0000000000..5e40e237fc
--- /dev/null
+++ b/doc/src/Modify_body.rst
@@ -0,0 +1,40 @@
+Body styles
+===========
+
+Classes that define body particles are derived from the Body class.
+Body particles can represent complex entities, such as surface meshes
+of discrete points, collections of sub-particles, deformable objects,
+etc.
+
+See the :doc:`Howto body <Howto_body>` doc page for an overview of using
+body particles and the various body styles LAMMPS supports.  New
+styles can be created to add new kinds of body particles to LAMMPS.
+
+Body\_nparticle.cpp is an example of a body particle that is treated as
+a rigid body containing N sub-particles.
+
+Here is a brief description of methods you define in your new derived
+class.  See body.h for details.
+
++----------------------+-----------------------------------------------------------+
+| data\_body           | process a line from the Bodies section of a data file     |
++----------------------+-----------------------------------------------------------+
+| noutrow              | number of sub-particles output is generated for           |
++----------------------+-----------------------------------------------------------+
+| noutcol              | number of values per-sub-particle output is generated for |
++----------------------+-----------------------------------------------------------+
+| output               | output values for the Mth sub-particle                    |
++----------------------+-----------------------------------------------------------+
+| pack\_comm\_body     | body attributes to communicate every timestep             |
++----------------------+-----------------------------------------------------------+
+| unpack\_comm\_body   | unpacking of those attributes                             |
++----------------------+-----------------------------------------------------------+
+| pack\_border\_body   | body attributes to communicate when reneighboring is done |
++----------------------+-----------------------------------------------------------+
+| unpack\_border\_body | unpacking of those attributes                             |
++----------------------+-----------------------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_bond.rst b/doc/src/Modify_bond.rst
new file mode 100644
index 0000000000..f1fd0894a0
--- /dev/null
+++ b/doc/src/Modify_bond.rst
@@ -0,0 +1,41 @@
+Bond, angle, dihedral, improper styles
+======================================
+
+Classes that compute molecular interactions are derived from the Bond,
+Angle, Dihedral, and Improper classes.  New styles can be created to
+add new potentials to LAMMPS.
+
+Bond\_harmonic.cpp is the simplest example of a bond style.  Ditto for
+the harmonic forms of the angle, dihedral, and improper style
+commands.
+
+Here is a brief description of common methods you define in your
+new derived class.  See bond.h, angle.h, dihedral.h, and improper.h
+for details and specific additional methods.
+
++-----------------------+---------------------------------------------------------------------------+
+| init                  | check if all coefficients are set, calls *init\_style* (optional)         |
++-----------------------+---------------------------------------------------------------------------+
+| init\_style           | check if style specific conditions are met (optional)                     |
++-----------------------+---------------------------------------------------------------------------+
+| compute               | compute the molecular interactions (required)                             |
++-----------------------+---------------------------------------------------------------------------+
+| settings              | apply global settings for all types (optional)                            |
++-----------------------+---------------------------------------------------------------------------+
+| coeff                 | set coefficients for one type (required)                                  |
++-----------------------+---------------------------------------------------------------------------+
+| equilibrium\_distance | length of bond, used by SHAKE (required, bond only)                       |
++-----------------------+---------------------------------------------------------------------------+
+| equilibrium\_angle    | opening of angle, used by SHAKE (required, angle only)                    |
++-----------------------+---------------------------------------------------------------------------+
+| write & read\_restart | writes/reads coeffs to restart files (required)                           |
++-----------------------+---------------------------------------------------------------------------+
+| single                | force and energy of a single bond or angle (required, bond or angle only) |
++-----------------------+---------------------------------------------------------------------------+
+| memory\_usage         | tally memory allocated by the style (optional)                            |
++-----------------------+---------------------------------------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_command.rst b/doc/src/Modify_command.rst
new file mode 100644
index 0000000000..9487f4c35b
--- /dev/null
+++ b/doc/src/Modify_command.rst
@@ -0,0 +1,25 @@
+Input script command style
+==========================
+
+New commands can be added to LAMMPS input scripts by adding new
+classes that have a "command" method.  For example, the create\_atoms,
+read\_data, velocity, and run commands are all implemented in this
+fashion.  When such a command is encountered in the LAMMPS input
+script, LAMMPS simply creates a class with the corresponding name,
+invokes the "command" method of the class, and passes it the arguments
+from the input script.  The command method can perform whatever
+operations it wishes on LAMMPS data structures.
+
+The single method your new class must define is as follows:
+
++---------+-----------------------------------------+
+| command | operations performed by the new command |
++---------+-----------------------------------------+
+
+Of course, the new class can define other methods and variables as
+needed.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_compute.rst b/doc/src/Modify_compute.rst
new file mode 100644
index 0000000000..81c55b5ed2
--- /dev/null
+++ b/doc/src/Modify_compute.rst
@@ -0,0 +1,62 @@
+Compute styles
+==============
+
+Classes that compute scalar and vector quantities like temperature
+and the pressure tensor, as well as classes that compute per-atom
+quantities like kinetic energy and the centro-symmetry parameter
+are derived from the Compute class.  New styles can be created
+to add new calculations to LAMMPS.
+
+Compute\_temp.cpp is a simple example of computing a scalar
+temperature.  Compute\_ke\_atom.cpp is a simple example of computing
+per-atom kinetic energy.
+
+Here is a brief description of methods you define in your new derived
+class.  See compute.h for details.
+
++-----------------------+------------------------------------------------------------------+
+| init                  | perform one time setup (required)                                |
++-----------------------+------------------------------------------------------------------+
+| init\_list            | neighbor list setup, if needed (optional)                        |
++-----------------------+------------------------------------------------------------------+
+| compute\_scalar       | compute a scalar quantity (optional)                             |
++-----------------------+------------------------------------------------------------------+
+| compute\_vector       | compute a vector of quantities (optional)                        |
++-----------------------+------------------------------------------------------------------+
+| compute\_peratom      | compute one or more quantities per atom (optional)               |
++-----------------------+------------------------------------------------------------------+
+| compute\_local        | compute one or more quantities per processor (optional)          |
++-----------------------+------------------------------------------------------------------+
+| pack\_comm            | pack a buffer with items to communicate (optional)               |
++-----------------------+------------------------------------------------------------------+
+| unpack\_comm          | unpack the buffer (optional)                                     |
++-----------------------+------------------------------------------------------------------+
+| pack\_reverse         | pack a buffer with items to reverse communicate (optional)       |
++-----------------------+------------------------------------------------------------------+
+| unpack\_reverse       | unpack the buffer (optional)                                     |
++-----------------------+------------------------------------------------------------------+
+| remove\_bias          | remove velocity bias from one atom (optional)                    |
++-----------------------+------------------------------------------------------------------+
+| remove\_bias\_all     | remove velocity bias from all atoms in group (optional)          |
++-----------------------+------------------------------------------------------------------+
+| restore\_bias         | restore velocity bias for one atom after remove\_bias (optional) |
++-----------------------+------------------------------------------------------------------+
+| restore\_bias\_all    | same as before, but for all atoms in group (optional)            |
++-----------------------+------------------------------------------------------------------+
+| pair\_tally\_callback | callback function for *tally*\ -style computes (optional).       |
++-----------------------+------------------------------------------------------------------+
+| memory\_usage         | tally memory usage (optional)                                    |
++-----------------------+------------------------------------------------------------------+
+
+Tally-style computes are a special case, as their computation is done
+in two stages: the callback function is registered with the pair style
+and then called from the Pair::ev\_tally() function, which is called for
+each pair after force and energy has been computed for this pair. Then
+the tallied values are retrieved with the standard compute\_scalar or
+compute\_vector or compute\_peratom methods. The USER-TALLY package
+provides *examples*\ \_compute\_tally.html for utilizing this mechanism.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst
new file mode 100644
index 0000000000..740ddb555d
--- /dev/null
+++ b/doc/src/Modify_contribute.rst
@@ -0,0 +1,203 @@
+Submitting new features for inclusion in LAMMPS
+===============================================
+
+We encourage users to submit new features or modifications for LAMMPS
+to `the core developers <http://lammps.sandia.gov/authors.html>`_ so they
+can be added to the LAMMPS distribution. The preferred way to manage
+and coordinate this is as of Fall 2016 via the LAMMPS project on
+`GitHub <https://github.com/lammps/lammps>`_. An alternative is to
+contact the LAMMPS developers or the indicated developer of a package
+or feature directly and send in your contribution via e-mail.
+
+For any larger modifications or programming project, you are
+encouraged to contact the LAMMPS developers ahead of time, in order to
+discuss implementation strategies and coding guidelines, that will
+make it easier to integrate your contribution and result in less work
+for everybody involved. You are also encouraged to search through the
+list of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_ and submit a new issue
+for a planned feature, so you would not duplicate the work of others
+(and possibly get scooped by them) or have your work duplicated by
+others.
+
+How quickly your contribution will be integrated depends largely on
+how much effort it will cause to integrate and test it, how much it
+requires changes to the core codebase, and of how much interest it is
+to the larger LAMMPS community.  Please see below for a checklist of
+typical requirements. Once you have prepared everything, see the
+:doc:`Using GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on how to
+submit your changes or new files through a GitHub pull request. If you
+prefer to submit patches or full files, you should first make certain,
+that your code works correctly with the latest patch-level version of
+LAMMPS and contains all bug fixes from it. Then create a gzipped tar
+file of all changed or added files or a corresponding patch file using
+'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
+compression, as this works well on all platforms.
+
+If the new features/files are broadly useful we may add them as core
+files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`.  Else we will add them as a
+user-contributed file or :doc:`user package <Packages_user>`.  Examples
+of user packages are in src sub-directories that start with USER.  The
+USER-MISC package is simply a collection of (mostly) unrelated single
+files, which is the simplest way to have your contribution quickly
+added to the LAMMPS distribution.  All the standard and user packages
+are listed and described on the :doc:`Packages details <Packages_details>` doc page.
+
+Note that by providing us files to release, you are agreeing to make
+them open-source, i.e. we can release them under the terms of the GPL,
+used as a license for the rest of LAMMPS.  See the `Open source <http://lammps.sandia.gov/open_source.html>`_ page on the LAMMPS
+website for details.
+
+With user packages and files, all we are really providing (aside from
+the fame and fortune that accompanies having your name in the source
+code and on the `Authors page <http://lammps.sandia.gov/authors.html>`_
+of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
+work to the LAMMPS user community, and a mechanism for others to
+easily try out your new feature.  This may help you find bugs or make
+contact with new collaborators.  Note that you're also implicitly
+agreeing to support your code which means answer questions, fix bugs,
+and maintain it if LAMMPS changes in some way that breaks it (an
+unusual event).
+
+.. note::
+
+   If you prefer to actively develop and support your add-on
+   feature yourself, then you may wish to make it available for download
+   from your own website, as a user package that LAMMPS users can add to
+   their copy of LAMMPS.  See the `Offsite LAMMPS packages and tools <http://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
+   site for examples of groups that do this.  We are happy to advertise
+   your package and web site from that page.  Simply email the
+   `developers <http://lammps.sandia.gov/authors.html>`_ with info about
+   your package and we will post it there.
+
+The previous sections of this doc page describe how to add new "style"
+files of various kinds to LAMMPS.  Packages are simply collections of
+one or more new class files which are invoked as a new style within a
+LAMMPS input script.  If designed correctly, these additions typically
+do not require changes to the main core of LAMMPS; they are simply
+add-on files.  If you think your new feature requires non-trivial
+changes in core LAMMPS files, you'll need to `communicate with the developers <http://lammps.sandia.gov/authors.html>`_, since we may or may
+not want to make those changes.  An example of a trivial change is
+making a parent-class method "virtual" when you derive a new child
+class from it.
+
+Here is a checklist of steps you need to follow to submit a single file
+or user package for our consideration.  Following these steps will save
+both you and us time. See existing files in packages in the src dir for
+examples. If you are uncertain, please ask.
+
+* All source files you provide must compile with the most current
+  version of LAMMPS with multiple configurations. In particular you
+  need to test compiling LAMMPS from scratch with -DLAMMPS\_BIGBIG
+  set in addition to the default -DLAMMPS\_SMALLBIG setting. Your code
+  will need to work correctly in serial and in parallel using MPI.
+* For consistency with the rest of LAMMPS and especially, if you want
+  your contribution(s) to be added to main LAMMPS code or one of its
+  standard packages, it needs to be written in a style compatible with
+  other LAMMPS source files. This means: 2-character indentation per
+  level, **no tabs**\ , no lines over 80 characters. I/O is done via
+  the C-style stdio library (mixing of stdio and iostreams is generally
+  discouraged), class header files should not import any system headers
+  outside of <cstdio>, STL containers should be avoided in headers,
+  system header from the C library should use the C++-style names
+  (<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
+  <stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
+  used where possible or needed to avoid including headers.
+  All added code should be placed into the LAMMPS\_NS namespace or a
+  sub-namespace; global or static variables should be avoided, as they
+  conflict with the modular nature of LAMMPS and the C++ class structure.
+  Header files must **not** import namespaces with *using*\ .
+  This all is so the developers can more easily understand, integrate,
+  and maintain your contribution and reduce conflicts with other parts
+  of LAMMPS.  This basically means that the code accesses data
+  structures, performs its operations, and is formatted similar to other
+  LAMMPS source files, including the use of the error class for error
+  and warning messages.
+* If you want your contribution to be added as a user-contributed
+  feature, and it's a single file (actually a \*.cpp and \*.h file) it can
+  rapidly be added to the USER-MISC directory.  Send us the one-line
+  entry to add to the USER-MISC/README file in that dir, along with the
+  2 source files.  You can do this multiple times if you wish to
+  contribute several individual features.
+* If you want your contribution to be added as a user-contribution and
+  it is several related features, it is probably best to make it a user
+  package directory with a name like USER-FOO.  In addition to your new
+  files, the directory should contain a README text file.  The README
+  should contain your name and contact information and a brief
+  description of what your new package does.  If your files depend on
+  other LAMMPS style files also being installed (e.g. because your file
+  is a derived class from the other LAMMPS class), then an Install.sh
+  file is also needed to check for those dependencies.  See other README
+  and Install.sh files in other USER directories as examples.  Send us a
+  tarball of this USER-FOO directory.
+
+  Your new source files need to have the LAMMPS copyright, GPL notice,
+  and your name and email address at the top, like other
+  user-contributed LAMMPS source files.  They need to create a class
+  that is inside the LAMMPS namespace.  If the file is for one of the
+
+* USER packages, including USER-MISC, then we are not as picky about the
+  coding style (see above).  I.e. the files do not need to be in the
+  same stylistic format and syntax as other LAMMPS files, though that
+  would be nice for developers as well as users who try to read your
+  code.
+* You **must** also create a **documentation** file for each new command or
+  style you are adding to LAMMPS. For simplicity and convenience, the
+  documentation of groups of closely related commands or styles may be
+  combined into a single file.  This will be one file for a single-file
+  feature.  For a package, it might be several files.  These are simple
+  text files with a specific markup language, that are then auto-converted
+  to HTML and PDF. The tools for this conversion are included in the
+  source distribution, and the translation can be as simple as doing
+  "make html pdf" in the doc folder.
+  Thus the documentation source files must be in the same format and
+  style as other \*.txt files in the lammps/doc/src directory for similar
+  commands and styles; use one or more of them as a starting point.
+  A description of the markup can also be found in
+  lammps/doc/utils/txt2html/README.html
+  As appropriate, the text files can include links to equations
+  (see doc/Eqs/\*.tex for examples, we auto-create the associated JPG
+  files), or figures (see doc/JPG for examples), or even additional PDF
+  files with further details (see doc/PDF for examples).  The doc page
+  should also include literature citations as appropriate; see the
+  bottom of doc/fix\_nh.txt for examples and the earlier part of the same
+  file for how to format the cite itself.  The "Restrictions" section of
+  the doc page should indicate that your command is only available if
+  LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
+  See other user package doc files for examples of how to do this. The
+  prerequisite for building the HTML format files are Python 3.x and
+  virtualenv, the requirement for generating the PDF format manual
+  is the `htmldoc <http://www.htmldoc.org/>`_ software. Please run at least
+  "make html" and carefully inspect and proofread the resulting HTML format
+  doc page before submitting your code.
+* For a new package (or even a single command) you should include one or
+  more example scripts demonstrating its use.  These should run in no
+  more than a couple minutes, even on a single processor, and not require
+  large data files as input.  See directories under examples/USER for
+  examples of input scripts other users provided for their packages.
+  These example inputs are also required for validating memory accesses
+  and testing for memory leaks with valgrind
+* If there is a paper of yours describing your feature (either the
+  algorithm/science behind the feature itself, or its initial usage, or
+  its implementation in LAMMPS), you can add the citation to the \*.cpp
+  source file.  See src/USER-EFF/atom\_vec\_electron.cpp for an example.
+  A LaTeX citation is stored in a variable at the top of the file and a
+  single line of code that references the variable is added to the
+  constructor of the class.  Whenever a user invokes your feature from
+  their input script, this will cause LAMMPS to output the citation to a
+  log.cite file and prompt the user to examine the file.  Note that you
+  should only use this for a paper you or your group authored.
+  E.g. adding a cite in the code for a paper by Nose and Hoover if you
+  write a fix that implements their integrator is not the intended
+  usage.  That kind of citation should just be in the doc page you
+  provide.
+
+
+Finally, as a general rule-of-thumb, the more clear and
+self-explanatory you make your documentation and README files, and the
+easier you make it for people to get started, e.g. by providing example
+scripts, the more likely it is that users will try out your new feature.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_dump.rst b/doc/src/Modify_dump.rst
new file mode 100644
index 0000000000..c44aa0a96a
--- /dev/null
+++ b/doc/src/Modify_dump.rst
@@ -0,0 +1,37 @@
+Dump styles
+===========
+
+Classes that dump per-atom info to files are derived from the Dump
+class.  To dump new quantities or in a new format, a new derived dump
+class can be added, but it is typically simpler to modify the
+DumpCustom class contained in the dump\_custom.cpp file.
+
+Dump\_atom.cpp is a simple example of a derived dump class.
+
+Here is a brief description of methods you define in your new derived
+class.  See dump.h for details.
+
++---------------+---------------------------------------------------+
+| write\_header | write the header section of a snapshot of atoms   |
++---------------+---------------------------------------------------+
+| count         | count the number of lines a processor will output |
++---------------+---------------------------------------------------+
+| pack          | pack a proc's output data into a buffer           |
++---------------+---------------------------------------------------+
+| write\_data   | write a proc's data to a file                     |
++---------------+---------------------------------------------------+
+
+See the :doc:`dump <dump>` command and its *custom* style for a list of
+keywords for atom information that can already be dumped by
+DumpCustom.  It includes options to dump per-atom info from Compute
+classes, so adding a new derived Compute class is one way to calculate
+new quantities to dump.
+
+Note that new keywords for atom properties are not typically
+added to the :doc:`dump custom <dump>` command.  Instead they are added
+to the :doc:`compute property/atom <compute_property_atom>` command.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_fix.rst b/doc/src/Modify_fix.rst
new file mode 100644
index 0000000000..cafde08af6
--- /dev/null
+++ b/doc/src/Modify_fix.rst
@@ -0,0 +1,158 @@
+Fix styles
+==========
+
+In LAMMPS, a "fix" is any operation that is computed during
+timestepping that alters some property of the system.  Essentially
+everything that happens during a simulation besides force computation,
+neighbor list construction, and output, is a "fix".  This includes
+time integration (update of coordinates and velocities), force
+constraints or boundary conditions (SHAKE or walls), and diagnostics
+(compute a diffusion coefficient).  New styles can be created to add
+new options to LAMMPS.
+
+Fix\_setforce.cpp is a simple example of setting forces on atoms to
+prescribed values.  There are dozens of fix options already in LAMMPS;
+choose one as a template that is similar to what you want to
+implement.
+
+Here is a brief description of methods you can define in your new
+derived class.  See fix.h for details.
+
++---------------------------+--------------------------------------------------------------------------------------------+
+| setmask                   | determines when the fix is called during the timestep (required)                           |
++---------------------------+--------------------------------------------------------------------------------------------+
+| init                      | initialization before a run (optional)                                                     |
++---------------------------+--------------------------------------------------------------------------------------------+
+| setup\_pre\_exchange      | called before atom exchange in setup (optional)                                            |
++---------------------------+--------------------------------------------------------------------------------------------+
+| setup\_pre\_force         | called before force computation in setup (optional)                                        |
++---------------------------+--------------------------------------------------------------------------------------------+
+| setup                     | called immediately before the 1st timestep and after forces are computed (optional)        |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_setup\_pre\_force    | like setup\_pre\_force, but for minimizations instead of MD runs (optional)                |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_setup                | like setup, but for minimizations instead of MD runs (optional)                            |
++---------------------------+--------------------------------------------------------------------------------------------+
+| initial\_integrate        | called at very beginning of each timestep (optional)                                       |
++---------------------------+--------------------------------------------------------------------------------------------+
+| pre\_exchange             | called before atom exchange on re-neighboring steps (optional)                             |
++---------------------------+--------------------------------------------------------------------------------------------+
+| pre\_neighbor             | called before neighbor list build (optional)                                               |
++---------------------------+--------------------------------------------------------------------------------------------+
+| pre\_force                | called before pair & molecular forces are computed (optional)                              |
++---------------------------+--------------------------------------------------------------------------------------------+
+| post\_force               | called after pair & molecular forces are computed and communicated (optional)              |
++---------------------------+--------------------------------------------------------------------------------------------+
+| final\_integrate          | called at end of each timestep (optional)                                                  |
++---------------------------+--------------------------------------------------------------------------------------------+
+| end\_of\_step             | called at very end of timestep (optional)                                                  |
++---------------------------+--------------------------------------------------------------------------------------------+
+| write\_restart            | dumps fix info to restart file (optional)                                                  |
++---------------------------+--------------------------------------------------------------------------------------------+
+| restart                   | uses info from restart file to re-initialize the fix (optional)                            |
++---------------------------+--------------------------------------------------------------------------------------------+
+| grow\_arrays              | allocate memory for atom-based arrays used by fix (optional)                               |
++---------------------------+--------------------------------------------------------------------------------------------+
+| copy\_arrays              | copy atom info when an atom migrates to a new processor (optional)                         |
++---------------------------+--------------------------------------------------------------------------------------------+
+| pack\_exchange            | store atom's data in a buffer (optional)                                                   |
++---------------------------+--------------------------------------------------------------------------------------------+
+| unpack\_exchange          | retrieve atom's data from a buffer (optional)                                              |
++---------------------------+--------------------------------------------------------------------------------------------+
+| pack\_restart             | store atom's data for writing to restart file (optional)                                   |
++---------------------------+--------------------------------------------------------------------------------------------+
+| unpack\_restart           | retrieve atom's data from a restart file buffer (optional)                                 |
++---------------------------+--------------------------------------------------------------------------------------------+
+| size\_restart             | size of atom's data (optional)                                                             |
++---------------------------+--------------------------------------------------------------------------------------------+
+| maxsize\_restart          | max size of atom's data (optional)                                                         |
++---------------------------+--------------------------------------------------------------------------------------------+
+| setup\_pre\_force\_respa  | same as setup\_pre\_force, but for rRESPA (optional)                                       |
++---------------------------+--------------------------------------------------------------------------------------------+
+| initial\_integrate\_respa | same as initial\_integrate, but for rRESPA (optional)                                      |
++---------------------------+--------------------------------------------------------------------------------------------+
+| post\_integrate\_respa    | called after the first half integration step is done in rRESPA (optional)                  |
++---------------------------+--------------------------------------------------------------------------------------------+
+| pre\_force\_respa         | same as pre\_force, but for rRESPA (optional)                                              |
++---------------------------+--------------------------------------------------------------------------------------------+
+| post\_force\_respa        | same as post\_force, but for rRESPA (optional)                                             |
++---------------------------+--------------------------------------------------------------------------------------------+
+| final\_integrate\_respa   | same as final\_integrate, but for rRESPA (optional)                                        |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_pre\_force           | called after pair & molecular forces are computed in minimizer (optional)                  |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_post\_force          | called after pair & molecular forces are computed and communicated in minimizer (optional) |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_store                | store extra data for linesearch based minimization on a LIFO stack (optional)              |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_pushstore            | push the minimization LIFO stack one element down (optional)                               |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_popstore             | pop the minimization LIFO stack one element up (optional)                                  |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_clearstore           | clear minimization LIFO stack (optional)                                                   |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_step                 | reset or move forward on line search minimization (optional)                               |
++---------------------------+--------------------------------------------------------------------------------------------+
+| min\_dof                  | report number of degrees of freedom *added* by this fix in minimization (optional)         |
++---------------------------+--------------------------------------------------------------------------------------------+
+| max\_alpha                | report maximum allowed step size during linesearch minimization (optional)                 |
++---------------------------+--------------------------------------------------------------------------------------------+
+| pack\_comm                | pack a buffer to communicate a per-atom quantity (optional)                                |
++---------------------------+--------------------------------------------------------------------------------------------+
+| unpack\_comm              | unpack a buffer to communicate a per-atom quantity (optional)                              |
++---------------------------+--------------------------------------------------------------------------------------------+
+| pack\_reverse\_comm       | pack a buffer to reverse communicate a per-atom quantity (optional)                        |
++---------------------------+--------------------------------------------------------------------------------------------+
+| unpack\_reverse\_comm     | unpack a buffer to reverse communicate a per-atom quantity (optional)                      |
++---------------------------+--------------------------------------------------------------------------------------------+
+| dof                       | report number of degrees of freedom *removed* by this fix during MD (optional)             |
++---------------------------+--------------------------------------------------------------------------------------------+
+| compute\_scalar           | return a global scalar property that the fix computes (optional)                           |
++---------------------------+--------------------------------------------------------------------------------------------+
+| compute\_vector           | return a component of a vector property that the fix computes (optional)                   |
++---------------------------+--------------------------------------------------------------------------------------------+
+| compute\_array            | return a component of an array property that the fix computes (optional)                   |
++---------------------------+--------------------------------------------------------------------------------------------+
+| deform                    | called when the box size is changed (optional)                                             |
++---------------------------+--------------------------------------------------------------------------------------------+
+| reset\_target             | called when a change of the target temperature is requested during a run (optional)        |
++---------------------------+--------------------------------------------------------------------------------------------+
+| reset\_dt                 | is called when a change of the time step is requested during a run (optional)              |
++---------------------------+--------------------------------------------------------------------------------------------+
+| modify\_param             | called when a fix\_modify request is executed (optional)                                   |
++---------------------------+--------------------------------------------------------------------------------------------+
+| memory\_usage             | report memory used by fix (optional)                                                       |
++---------------------------+--------------------------------------------------------------------------------------------+
+| thermo                    | compute quantities for thermodynamic output (optional)                                     |
++---------------------------+--------------------------------------------------------------------------------------------+
+
+Typically, only a small fraction of these methods are defined for a
+particular fix.  Setmask is mandatory, as it determines when the fix
+will be invoked during the timestep.  Fixes that perform time
+integration (\ *nve*\ , *nvt*\ , *npt*\ ) implement initial\_integrate() and
+final\_integrate() to perform velocity Verlet updates.  Fixes that
+constrain forces implement post\_force().
+
+Fixes that perform diagnostics typically implement end\_of\_step().  For
+an end\_of\_step fix, one of your fix arguments must be the variable
+"nevery" which is used to determine when to call the fix and you must
+set this variable in the constructor of your fix.  By convention, this
+is the first argument the fix defines (after the ID, group-ID, style).
+
+If the fix needs to store information for each atom that persists from
+timestep to timestep, it can manage that memory and migrate the info
+with the atoms as they move from processors to processor by
+implementing the grow\_arrays, copy\_arrays, pack\_exchange, and
+unpack\_exchange methods.  Similarly, the pack\_restart and
+unpack\_restart methods can be implemented to store information about
+the fix in restart files.  If you wish an integrator or force
+constraint fix to work with rRESPA (see the :doc:`run\_style <run_style>`
+command), the initial\_integrate, post\_force\_integrate, and
+final\_integrate\_respa methods can be implemented.  The thermo method
+enables a fix to contribute values to thermodynamic output, as printed
+quantities and/or to be summed to the potential energy of the system.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_kspace.rst b/doc/src/Modify_kspace.rst
new file mode 100644
index 0000000000..41ad5a3602
--- /dev/null
+++ b/doc/src/Modify_kspace.rst
@@ -0,0 +1,26 @@
+Kspace styles
+=============
+
+Classes that compute long-range Coulombic interactions via K-space
+representations (Ewald, PPPM) are derived from the KSpace class.  New
+styles can be created to add new K-space options to LAMMPS.
+
+Ewald.cpp is an example of computing K-space interactions.
+
+Here is a brief description of methods you define in your new derived
+class.  See kspace.h for details.
+
++---------------+----------------------------------------------+
+| init          | initialize the calculation before a run      |
++---------------+----------------------------------------------+
+| setup         | computation before the 1st timestep of a run |
++---------------+----------------------------------------------+
+| compute       | every-timestep computation                   |
++---------------+----------------------------------------------+
+| memory\_usage | tally of memory usage                        |
++---------------+----------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_min.rst b/doc/src/Modify_min.rst
new file mode 100644
index 0000000000..2cdd620f0e
--- /dev/null
+++ b/doc/src/Modify_min.rst
@@ -0,0 +1,24 @@
+Minimization styles
+===================
+
+Classes that perform energy minimization derived from the Min class.
+New styles can be created to add new minimization algorithms to
+LAMMPS.
+
+Min\_cg.cpp is an example of conjugate gradient minimization.
+
+Here is a brief description of methods you define in your new derived
+class.  See min.h for details.
+
++---------------+------------------------------------------+
+| init          | initialize the minimization before a run |
++---------------+------------------------------------------+
+| run           | perform the minimization                 |
++---------------+------------------------------------------+
+| memory\_usage | tally of memory usage                    |
++---------------+------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_overview.rst b/doc/src/Modify_overview.rst
new file mode 100644
index 0000000000..85a0677513
--- /dev/null
+++ b/doc/src/Modify_overview.rst
@@ -0,0 +1,107 @@
+Overview
+========
+
+The best way to add a new feature to LAMMPS is to find a similar
+feature and look at the corresponding source and header files to figure
+out what it does.  You will need some knowledge of C++ to be able to
+understand the hi-level structure of LAMMPS and its class
+organization, but functions (class methods) that do actual
+computations are written in vanilla C-style code and operate on simple
+C-style data structures (vectors and arrays).
+
+Most of the new features described on the :doc:`Modify <Modify>` doc
+page require you to write a new C++ derived class (except for
+exceptions described below, where you can make small edits to existing
+files).  Creating a new class requires 2 files, a source code file
+(\*.cpp) and a header file (\*.h).  The derived class must provide
+certain methods to work as a new option.  Depending on how different
+your new feature is compared to existing features, you can either
+derive from the base class itself, or from a derived class that
+already exists.  Enabling LAMMPS to invoke the new class is as simple
+as putting the two source files in the src dir and re-building LAMMPS.
+
+The advantage of C++ and its object-orientation is that all the code
+and variables needed to define the new feature are in the 2 files you
+write, and thus shouldn't make the rest of LAMMPS more complex or
+cause side-effect bugs.
+
+Here is a concrete example.  Suppose you write 2 files pair\_foo.cpp
+and pair\_foo.h that define a new class PairFoo that computes pairwise
+potentials described in the classic 1997 :ref:`paper <Foo>` by Foo, et al.
+If you wish to invoke those potentials in a LAMMPS input script with a
+command like
+
+
+.. parsed-literal::
+
+   pair_style foo 0.1 3.5
+
+then your pair\_foo.h file should be structured as follows:
+
+
+.. parsed-literal::
+
+   #ifdef PAIR_CLASS
+   PairStyle(foo,PairFoo)
+   #else
+   ...
+   (class definition for PairFoo)
+   ...
+   #endif
+
+where "foo" is the style keyword in the pair\_style command, and
+PairFoo is the class name defined in your pair\_foo.cpp and pair\_foo.h
+files.
+
+When you re-build LAMMPS, your new pairwise potential becomes part of
+the executable and can be invoked with a pair\_style command like the
+example above.  Arguments like 0.1 and 3.5 can be defined and
+processed by your new class.
+
+As illustrated by this pairwise example, many kinds of options are
+referred to in the LAMMPS documentation as the "style" of a particular
+command.
+
+The :doc:`Modify page <Modify>` lists all the common styles in LAMMPS,
+and discusses the header file for the base class that these styles are
+derived from.  Public variables in that file are ones used and set by
+the derived classes which are also used by the base class.  Sometimes
+they are also used by the rest of LAMMPS.  Virtual functions in the
+base class header file which are set = 0 are ones you must define in
+your new derived class to give it the functionality LAMMPS expects.
+Virtual functions that are not set to 0 are functions you can
+optionally define.
+
+Additionally, new output options can be added directly to the
+thermo.cpp, dump\_custom.cpp, and variable.cpp files.  These are also
+listed on the :doc:`Modify page <Modify>`.
+
+Here are additional guidelines for modifying LAMMPS and adding new
+functionality:
+
+* Think about whether what you want to do would be better as a pre- or
+  post-processing step.  Many computations are more easily and more
+  quickly done that way.
+* Don't do anything within the timestepping of a run that isn't
+  parallel.  E.g. don't accumulate a bunch of data on a single processor
+  and analyze it.  You run the risk of seriously degrading the parallel
+  efficiency.
+* If your new feature reads arguments or writes output, make sure you
+  follow the unit conventions discussed by the :doc:`units <units>`
+  command.
+
+
+
+----------
+
+
+.. _Foo:
+
+
+
+**(Foo)** Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_pair.rst b/doc/src/Modify_pair.rst
new file mode 100644
index 0000000000..84292bd10f
--- /dev/null
+++ b/doc/src/Modify_pair.rst
@@ -0,0 +1,40 @@
+Pair styles
+===========
+
+Classes that compute pairwise interactions are derived from the Pair
+class.  In LAMMPS, pairwise calculation include many-body potentials
+such as EAM or Tersoff where particles interact without a static bond
+topology.  New styles can be created to add new pair potentials to
+LAMMPS.
+
+Pair\_lj\_cut.cpp is a simple example of a Pair class, though it
+includes some optional methods to enable its use with rRESPA.
+
+Here is a brief description of the class methods in pair.h:
+
++---------------------------------+-------------------------------------------------------------------+
+| compute                         | workhorse routine that computes pairwise interactions             |
++---------------------------------+-------------------------------------------------------------------+
+| settings                        | reads the input script line with arguments you define             |
++---------------------------------+-------------------------------------------------------------------+
+| coeff                           | set coefficients for one i,j type pair                            |
++---------------------------------+-------------------------------------------------------------------+
+| init\_one                       | perform initialization for one i,j type pair                      |
++---------------------------------+-------------------------------------------------------------------+
+| init\_style                     | initialization specific to this pair style                        |
++---------------------------------+-------------------------------------------------------------------+
+| write & read\_restart           | write/read i,j pair coeffs to restart files                       |
++---------------------------------+-------------------------------------------------------------------+
+| write & read\_restart\_settings | write/read global settings to restart files                       |
++---------------------------------+-------------------------------------------------------------------+
+| single                          | force and energy of a single pairwise interaction between 2 atoms |
++---------------------------------+-------------------------------------------------------------------+
+| compute\_inner/middle/outer     | versions of compute used by rRESPA                                |
++---------------------------------+-------------------------------------------------------------------+
+
+The inner/middle/outer routines are optional.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_region.rst b/doc/src/Modify_region.rst
new file mode 100644
index 0000000000..196f97c4ea
--- /dev/null
+++ b/doc/src/Modify_region.rst
@@ -0,0 +1,27 @@
+Region styles
+=============
+
+Classes that define geometric regions are derived from the Region
+class.  Regions are used elsewhere in LAMMPS to group atoms, delete
+atoms to create a void, insert atoms in a specified region, etc.  New
+styles can be created to add new region shapes to LAMMPS.
+
+Region\_sphere.cpp is an example of a spherical region.
+
+Here is a brief description of methods you define in your new derived
+class.  See region.h for details.
+
++-------------------+---------------------------------------------------------------------+
+| inside            | determine whether a point is in the region                          |
++-------------------+---------------------------------------------------------------------+
+| surface\_interior | determine if a point is within a cutoff distance inside of surface  |
++-------------------+---------------------------------------------------------------------+
+| surface\_exterior | determine if a point is within a cutoff distance outside of surface |
++-------------------+---------------------------------------------------------------------+
+| shape\_update     | change region shape if set by time-dependent variable               |
++-------------------+---------------------------------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_thermo.rst b/doc/src/Modify_thermo.rst
new file mode 100644
index 0000000000..f3a3f00e2f
--- /dev/null
+++ b/doc/src/Modify_thermo.rst
@@ -0,0 +1,32 @@
+Thermodynamic output options
+============================
+
+There is one class that computes and prints thermodynamic information
+to the screen and log file; see the file thermo.cpp.
+
+There are two styles defined in thermo.cpp: "one" and "multi".  There
+is also a flexible "custom" style which allows the user to explicitly
+list keywords for quantities to print when thermodynamic info is
+output.  See the :doc:`thermo\_style <thermo_style>` command for a list
+of defined quantities.
+
+The thermo styles (one, multi, etc) are simply lists of keywords.
+Adding a new style thus only requires defining a new list of keywords.
+Search for the word "customize" with references to "thermo style" in
+thermo.cpp to see the two locations where code will need to be added.
+
+New keywords can also be added to thermo.cpp to compute new quantities
+for output.  Search for the word "customize" with references to
+"keyword" in thermo.cpp to see the several locations where code will
+need to be added.
+
+Note that the :doc:`thermo\_style custom <thermo>` command already allows
+for thermo output of quantities calculated by :doc:`fixes <fix>`,
+:doc:`computes <compute>`, and :doc:`variables <variable>`.  Thus, it may
+be simpler to compute what you wish via one of those constructs, than
+by adding a new keyword to the thermo command.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Modify_variable.rst b/doc/src/Modify_variable.rst
new file mode 100644
index 0000000000..bd3f70588b
--- /dev/null
+++ b/doc/src/Modify_variable.rst
@@ -0,0 +1,45 @@
+Variable options
+================
+
+There is one class that computes and stores :doc:`variable <variable>`
+information in LAMMPS; see the file variable.cpp.  The value
+associated with a variable can be periodically printed to the screen
+via the :doc:`print <print>`, :doc:`fix print <fix_print>`, or
+:doc:`thermo\_style custom <thermo_style>` commands.  Variables of style
+"equal" can compute complex equations that involve the following types
+of arguments:
+
+
+.. parsed-literal::
+
+   thermo keywords = ke, vol, atoms, ...
+   other variables = v_a, v_myvar, ...
+   math functions = div(x,y), mult(x,y), add(x,y), ...
+   group functions = mass(group), xcm(group,x), ...
+   atom values = x[123], y[3], vx[34], ...
+   compute values = c_mytemp[0], c_thermo_press[3], ...
+
+Adding keywords for the :doc:`thermo\_style custom <thermo_style>`
+command (which can then be accessed by variables) is discussed on the
+:doc:`Modify thermo <Modify_thermo>` doc page.
+
+Adding a new math function of one or two arguments can be done by
+editing one section of the Variable::evaluate() method.  Search for
+the word "customize" to find the appropriate location.
+
+Adding a new group function can be done by editing one section of the
+Variable::evaluate() method.  Search for the word "customize" to find
+the appropriate location.  You may need to add a new method to the
+Group class as well (see the group.cpp file).
+
+Accessing a new atom-based vector can be done by editing one section
+of the Variable::evaluate() method.  Search for the word "customize"
+to find the appropriate location.
+
+Adding new :doc:`compute styles <compute>` (whose calculated values can
+then be accessed by variables) is discussed on the :doc:`Modify compute <Modify_compute>` doc page.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/PDF/pair_gayberne_extra.pdf b/doc/src/PDF/pair_gayberne_extra.pdf
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diff --git a/doc/src/PDF/pair_gayberne_extra.tex b/doc/src/PDF/pair_gayberne_extra.tex
index 5f0d97d7ab..0568b54dcf 100644
--- a/doc/src/PDF/pair_gayberne_extra.tex
+++ b/doc/src/PDF/pair_gayberne_extra.tex
@@ -48,8 +48,8 @@ $$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
 \mathbf{G}_2. $$
 
 Let the relative energy matrices $\mathbf{E}_i = \mbox{diag}
-(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by 
-the relative well depths (dimensionless energy scales 
+(\epsilon_{ia}^{-1/\mu}, \epsilon_{ib}^{-1/\mu}, \epsilon_{ic}^{-1/\mu})$
+be given by the relative well depths (dimensionless energy scales 
 inversely proportional to the well-depths of the respective 
 orthogonal configurations of the interacting molecules). The 
 $\chi$ orientation-dependent energy based on the user-specified 
@@ -62,8 +62,8 @@ $$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$
 
 and
 
-$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 +
-\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 +
+$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 = \mathbf{B}_1 +
 \mathbf{B}_2. $$
 
 Here, we use the distance of closest approach approximation given by the
@@ -131,7 +131,7 @@ and
 
 $$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot
 r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i
-\times \mathbf{\iota} ). $$
+\times \mathbf{\iota} ) \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu}. $$
 
 For the derivative of the $\eta$ term, we were unable to find a matrix
 expression due to the determinant. Let $a_{mi}$ be the mth row of the
diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst
new file mode 100644
index 0000000000..ded2ae27e0
--- /dev/null
+++ b/doc/src/Packages.rst
@@ -0,0 +1,25 @@
+Optional packages
+*****************
+
+This section gives an overview of the optional packages that extend
+LAMMPS functionality.  Packages are groups of files that enable a
+specific set of features.  For example, force fields for molecular
+systems or rigid-body constraints are in packages.  You can see the
+list of all packages and "make" commands to manage them by typing
+"make package" from within the src directory of the LAMMPS
+distribution.  The :doc:`Build package <Build_package>` doc page gives
+general info on how to install and un-install packages as part of the
+LAMMPS build process.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Packages_standard
+   Packages_user
+   Packages_details
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst
new file mode 100644
index 0000000000..62615a8fb7
--- /dev/null
+++ b/doc/src/Packages_details.rst
@@ -0,0 +1,2448 @@
+Package details
+===============
+
+Here is a brief description of all the standard and user packages in
+LAMMPS.  It lists authors (if applicable) and summarizes the package
+contents.  It has specific instructions on how to install the package,
+including, if necessary, info on how to download or build any extra
+library it requires.  It also gives links to documentation, example
+scripts, and pictures/movies (if available) that illustrate use of the
+package.
+
+The majority of packages can be included in a LAMMPS build with a
+single setting (-D PGK\_NAME for CMake) or command ("make yes-name" for
+make).  See the :doc:`Build package <Build_package>` doc page for more
+info.  A few packages may require additional steps; this is indicated
+in the descriptions below.  The :doc:`Build extras <Build_extras>` doc
+page gives those details.
+
+.. note::
+
+   To see the complete list of commands a package adds to LAMMPS,
+   you can examine the files in its src directory, e.g. "ls
+   src/GRANULAR".  Files with names that start with fix, compute, atom,
+   pair, bond, angle, etc correspond to commands with the same style name
+   as contained in the file name.
+
++------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
+| :ref:`ASPHERE <PKG-ASPHERE>` | :ref:`BODY <PKG-BODY>`         | :ref:`CLASS2 <PKG-CLASS2>`     | :ref:`COLLOID <PKG-COLLOID>` | :ref:`COMPRESS <PKG-COMPRESS>` | :ref:`CORESHELL <PKG-CORESHELL>` |
++------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
+| :ref:`DIPOLE <PKG-DIPOLE>`   | :ref:`GPU <PKG-GPU>`           | :ref:`GRANULAR <PKG-GRANULAR>` | :ref:`KIM <PKG-KIM>`         | :ref:`KOKKOS <PKG-KOKKOS>`     | :ref:`KSPACE <PKG-KSPACE>`       |
++------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
+| :ref:`LATTE <PKG-LATTE>`     | :ref:`MANYBODY <PKG-MANYBODY>` | :ref:`MC <PKG-MC>`             | :ref:`MESSAGE <PKG-MESSAGE>` | :ref:`MISC <PKG-MISC>`         | :ref:`MOLECULE <PKG-MOLECULE>`   |
++------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
+| :ref:`MPIIO <PKG-MPIIO>`     | :ref:`MSCG <PKG-MSCG>`         | :ref:`OPT <PKG-OPT>`           | :ref:`PERI <PKG-PERI>`       | :ref:`POEMS <PKG-POEMS>`       | :ref:`PYTHON <PKG-PYTHON>`       |
++------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
+| :ref:`QEQ <PKG-QEQ>`         | :ref:`REPLICA <PKG-REPLICA2>`  | :ref:`RIGID <PKG-RIGID>`       | :ref:`SHOCK <PKG-SHOCK>`     | :ref:`SNAP <PKG-SNAP>`         | :ref:`SPIN <PKG-SPIN>`           |
++------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
+| :ref:`SRD <PKG-SRD>`         | :ref:`VORONOI <PKG-VORONOI>`   |                                |                              |                                |                                  |
++------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
+
++----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+
+| :ref:`USER-ADIOS <PKG-USER-ADIOS>`     | :ref:`USER-ATC <PKG-USER-ATC>`                 | :ref:`USER-AWPMD <PKG-USER-AWPMD>` | :ref:`USER-BOCS <PKG-USER-BOCS>`         | :ref:`USER-CGDNA <PKG-USER-CGDNA>`   | :ref:`USER-CGSDK <PKG-USER-CGSDK>` |
++----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+
+| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | :ref:`USER-DPD <PKG-USER-DPD>`     | :ref:`USER-DRUDE <PKG-USER-DRUDE>`       | :ref:`USER-EFF <PKG-USER-EFF>`       | :ref:`USER-FEP <PKG-USER-FEP>`     |
++----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+
+| :ref:`USER-H5MD <PKG-USER-H5MD>`       | :ref:`USER-INTEL <PKG-USER-INTEL>`             | :ref:`USER-LB <PKG-USER-LB>`       | :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | :ref:`USER-MEAMC <PKG-USER-MEAMC>`   | :ref:`USER-MESO <PKG-USER-MESO>`   |
++----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+
+| :ref:`USER-MGPT <PKG-USER-MGPT>`       | :ref:`USER-MISC <PKG-USER-MISC>`               | :ref:`USER-MOFFF <PKG-USER-MOFFF>` | :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`   | :ref:`USER-NETCDF <PKG-USER-NETCDF>` | :ref:`USER-OMP <PKG-USER-OMP>`     |
++----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+
+| :ref:`USER-PHONON <PKG-USER-PHONON>`   | :ref:`USER-PLUMED <PKG-USER-PLUMED>`           | :ref:`USER-PTM <PKG-USER-PTM>`     | :ref:`USER-QMMM <PKG-USER-QMMM>`         | :ref:`USER-QTB <PKG-USER-QTB>`       | :ref:`USER-QUIP <PKG-USER-QUIP>`   |
++----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+
+| :ref:`USER-REAXC <PKG-USER-REAXC>`     | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`       | :ref:`USER-SDPD <PKG-USER-SDPD>`   | :ref:`USER-SMD <PKG-USER-SMD>`           | :ref:`USER-SMTBQ <PKG-USER-SMTBQ>`   | :ref:`USER-SPH <PKG-USER-SPH>`     |
++----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+
+| :ref:`USER-TALLY <PKG-USER-TALLY>`     | :ref:`USER-UEF <PKG-USER-UEF>`                 | :ref:`USER-VTK <PKG-USER-VTK>`     | :ref:`USER-YAFF <PKG-USER-YAFF>`         |                                      |                                    |
++----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+
+
+
+----------
+
+
+.. _PKG-ASPHERE:
+
+ASPHERE package
+---------------
+
+**Contents:**
+
+Computes, time-integration fixes, and pair styles for aspherical
+particle models including ellipsoids, 2d lines, and 3d triangles.
+
+**Supporting info:**
+
+* src/ASPHERE: filenames -> commands
+* :doc:`Howto spherical <Howto_spherical>`
+* :doc:`pair\_style gayberne <pair_gayberne>`
+* :doc:`pair\_style resquared <pair_resquared>`
+* `doc/PDF/pair\_gayberne\_extra.pdf <PDF/pair_gayberne_extra.pdf>`_
+* `doc/PDF/pair\_resquared\_extra.pdf <PDF/pair_resquared_extra.pdf>`_
+* examples/ASPHERE
+* examples/ellipse
+* http://lammps.sandia.gov/movies.html#line
+* http://lammps.sandia.gov/movies.html#tri
+
+
+----------
+
+
+.. _PKG-BODY:
+
+BODY package
+------------
+
+**Contents:**
+
+Body-style particles with internal structure.  Computes,
+time-integration fixes, pair styles, as well as the body styles
+themselves.  See the :doc:`Howto body <Howto_body>` doc page for an
+overview.
+
+**Supporting info:**
+
+* src/BODY filenames -> commands
+* :doc:`Howto\_body <Howto_body>`
+* :doc:`atom\_style body <atom_style>`
+* :doc:`fix nve/body <fix_nve_body>`
+* :doc:`pair\_style body/nparticle <pair_body_nparticle>`
+* examples/body
+
+
+----------
+
+
+.. _PKG-CLASS2:
+
+CLASS2 package
+--------------
+
+**Contents:**
+
+Bond, angle, dihedral, improper, and pair styles for the COMPASS
+CLASS2 molecular force field.
+
+**Supporting info:**
+
+* src/CLASS2: filenames -> commands
+* :doc:`bond\_style class2 <bond_class2>`
+* :doc:`angle\_style class2 <angle_class2>`
+* :doc:`dihedral\_style class2 <dihedral_class2>`
+* :doc:`improper\_style class2 <improper_class2>`
+* :doc:`pair\_style lj/class2 <pair_class2>`
+
+
+----------
+
+
+.. _PKG-COLLOID:
+
+COLLOID package
+---------------
+
+**Contents:**
+
+Coarse-grained finite-size colloidal particles.  Pair styles and fix
+wall styles for colloidal interactions.  Includes the Fast Lubrication
+Dynamics (FLD) method for hydrodynamic interactions, which is a
+simplified approximation to Stokesian dynamics.
+
+**Authors:** This package includes Fast Lubrication Dynamics pair styles
+which were created by Amit Kumar and Michael Bybee from Jonathan
+Higdon's group at UIUC.
+
+**Supporting info:**
+
+* src/COLLOID: filenames -> commands
+* :doc:`fix wall/colloid <fix_wall>`
+* :doc:`pair\_style colloid <pair_colloid>`
+* :doc:`pair\_style yukawa/colloid <pair_yukawa_colloid>`
+* :doc:`pair\_style brownian <pair_brownian>`
+* :doc:`pair\_style lubricate <pair_lubricate>`
+* :doc:`pair\_style lubricateU <pair_lubricateU>`
+* examples/colloid
+* examples/srd
+
+
+----------
+
+
+.. _PKG-COMPRESS:
+
+COMPRESS package
+----------------
+
+**Contents:**
+
+Compressed output of dump files via the zlib compression library,
+using dump styles with a "gz" in their style name.
+
+To use this package you must have the zlib compression library
+available on your system.
+
+**Author:** Axel Kohlmeyer (Temple U).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <compress>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/COMPRESS: filenames -> commands
+* src/COMPRESS/README
+* lib/compress/README
+* :doc:`dump atom/gz <dump>`
+* :doc:`dump cfg/gz <dump>`
+* :doc:`dump custom/gz <dump>`
+* :doc:`dump xyz/gz <dump>`
+
+
+----------
+
+
+.. _PKG-CORESHELL:
+
+CORESHELL package
+-----------------
+
+**Contents:**
+
+Compute and pair styles that implement the adiabatic core/shell model
+for polarizability.  The pair styles augment Born, Buckingham, and
+Lennard-Jones styles with core/shell capabilities.  The :doc:`compute temp/cs <compute_temp_cs>` command calculates the temperature of a
+system with core/shell particles.  See the :doc:`Howto coreshell <Howto_coreshell>` doc page for an overview of how to use
+this package.
+
+**Author:** Hendrik Heenen (Technical U of Munich).
+
+**Supporting info:**
+
+* src/CORESHELL: filenames -> commands
+* :doc:`Howto coreshell <Howto_coreshell>`
+* :doc:`Howto polarizable <Howto_polarizable>`
+* :doc:`compute temp/cs <compute_temp_cs>`
+* :doc:`pair\_style born/coul/long/cs <pair_cs>`
+* :doc:`pair\_style buck/coul/long/cs <pair_cs>`
+* :doc:`pair\_style lj/cut/coul/long/cs <pair_lj>`
+* examples/coreshell
+
+
+----------
+
+
+.. _PKG-DIPOLE:
+
+DIPOLE package
+--------------
+
+**Contents:**
+
+An atom style and several pair styles for point dipole models with
+short-range or long-range interactions.
+
+**Supporting info:**
+
+* src/DIPOLE: filenames -> commands
+* :doc:`atom\_style dipole <atom_style>`
+* :doc:`pair\_style lj/cut/dipole/cut <pair_dipole>`
+* :doc:`pair\_style lj/cut/dipole/long <pair_dipole>`
+* :doc:`pair\_style lj/long/dipole/long <pair_dipole>`
+* examples/dipole
+
+
+----------
+
+
+.. _PKG-GPU:
+
+GPU package
+-----------
+
+**Contents:**
+
+Dozens of pair styles and a version of the PPPM long-range Coulombic
+solver optimized for GPUs.  All such styles have a "gpu" as a suffix
+in their style name. The GPU code can be compiled with either CUDA or
+OpenCL, however the OpenCL variants are no longer actively maintained
+and only the CUDA versions are regularly tested.  The :doc:`Speed gpu <Speed_gpu>` doc page gives details of what hardware and GPU
+software is required on your system, and details on how to build and
+use this package.  Its styles can be invoked at run time via the "-sf
+gpu" or "-suffix gpu" :doc:`command-line switches <Run_options>`.  See
+also the :ref:`KOKKOS <PKG-KOKKOS>` package, which has GPU-enabled styles.
+
+**Authors:** Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
+(Northwestern U) while at ORNL.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <gpu>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/GPU: filenames -> commands
+* src/GPU/README
+* lib/gpu/README
+* :doc:`Speed packages <Speed_packages>`
+* :doc:`Speed gpu <Speed_gpu>`
+* :doc:`Section 2.6 -sf gpu <Run_options>`
+* :doc:`Section 2.6 -pk gpu <Run_options>`
+* :doc:`package gpu <package>`
+* `Commands all <lc_>`_ pages (pair,kspace) for styles followed by (g)
+* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
+
+
+----------
+
+
+.. _PKG-GRANULAR:
+
+GRANULAR package
+----------------
+
+**Contents:**
+
+Pair styles and fixes for finite-size granular particles, which
+interact with each other and boundaries via frictional and dissipative
+potentials.
+
+**Supporting info:**
+
+* src/GRANULAR: filenames -> commands
+* :doc:`Howto granular <Howto_granular>`
+* :doc:`fix pour <fix_pour>`
+* :doc:`fix wall/gran <fix_wall_gran>`
+* :doc:`pair\_style gran/hooke <pair_gran>`
+* :doc:`pair\_style gran/hertz/history <pair_gran>`
+* examples/granregion
+* examples/pour
+* bench/in.chute
+* http://lammps.sandia.gov/pictures.html#jamming
+* http://lammps.sandia.gov/movies.html#hopper
+* http://lammps.sandia.gov/movies.html#dem
+* http://lammps.sandia.gov/movies.html#brazil
+* http://lammps.sandia.gov/movies.html#granregion
+
+
+----------
+
+
+.. _PKG-KIM:
+
+KIM package
+-----------
+
+**Contents:**
+
+This package contains a set of commands that serve as a wrapper on the
+`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
+repository of interatomic models (IMs)
+enabling compatible ones to be used in LAMMPS simulations.
+This includes :doc:`kim\_init and kim\_interactions <kim_commands>`
+commands to select, initialize and instantiate the IM, and a
+:doc:`kim\_query <kim_commands>` command to perform web queries
+for material property predictions of OpenKIM IMs.
+Support for KIM IMs that conform to the
+`KIM Application Programming Interface (API) <https://openkim.org/kim-api/>`_
+is provided by the :doc:`pair\_style kim <pair_kim>` command.
+
+.. note::
+
+   The command *pair\_style kim* is called by *kim\_interactions* and
+   is not recommended to be directly used in input scripts.
+
+To use this package you must have the KIM API library available on your
+system. The KIM API is available for download on the
+`OpenKIM website <https://openkim.org/kim-api/>`_.
+When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed.
+
+Information about the KIM project can be found at its website:
+`https://openkim.org <https://openkim.org>`_.
+The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota)
+and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
+
+**Authors:** Ryan Elliott (U Minnesota) is the main developer for the KIM
+API and the *pair\_style kim* command. Axel Kohlmeyer (Temple U) and
+Ellad Tadmor (U Minnesota) contributed to the :doc:`kim\_commands <kim_commands>`
+interface in close collaboration with Ryan Elliott.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <kim>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* :doc:`kim\_commands <kim_commands>`
+* :doc:`pair\_style kim <pair_kim>`
+* src/KIM: filenames -> commands
+* src/KIM/README
+* lib/kim/README
+* examples/kim
+
+
+----------
+
+
+.. _PKG-KOKKOS:
+
+KOKKOS package
+--------------
+
+**Contents:**
+
+Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
+styles adapted to compile using the Kokkos library which can convert
+them to OpenMP or CUDA code so that they run efficiently on multicore
+CPUs, KNLs, or GPUs.  All the styles have a "kk" as a suffix in their
+style name.  The :doc:`Speed kokkos <Speed_kokkos>` doc page gives
+details of what hardware and software is required on your system, and
+how to build and use this package.  Its styles can be invoked at run
+time via the "-sf kk" or "-suffix kk" :doc:`command-line switches <Run_options>`.  Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`,
+:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
+have styles optimized for CPUs, KNLs, and GPUs.
+
+You must have a C++11 compatible compiler to use this package.
+KOKKOS makes extensive use of advanced C++ features, which can
+expose compiler bugs, especially when compiling for maximum
+performance at high optimization levels. Please see the file
+lib/kokkos/README for a list of compilers and their respective
+platforms, that are known to work.
+
+**Authors:** The KOKKOS package was created primarily by Christian Trott
+and Stan Moore (Sandia), with contributions from other folks as well.
+It uses the open-source `Kokkos library <https://github.com/kokkos>`_
+which was developed by Carter Edwards, Christian Trott, and others at
+Sandia, and which is included in the LAMMPS distribution in
+lib/kokkos.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <kokkos>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/KOKKOS: filenames -> commands
+* src/KOKKOS/README
+* lib/kokkos/README
+* :doc:`Speed packages <Speed_packages>`
+* :doc:`Speed kokkos <Speed_kokkos>`
+* :doc:`Section 2.6 -k on ... <Run_options>`
+* :doc:`Section 2.6 -sf kk <Run_options>`
+* :doc:`Section 2.6 -pk kokkos <Run_options>`
+* :doc:`package kokkos <package>`
+* `Commands all <lc_>`_ pages (fix,compute,pair,etc) for styles followed by (k)
+* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
+
+
+----------
+
+
+.. _PKG-KSPACE:
+
+KSPACE package
+--------------
+
+**Contents:**
+
+A variety of long-range Coulombic solvers, as well as pair styles
+which compute the corresponding short-range pairwise Coulombic
+interactions.  These include Ewald, particle-particle particle-mesh
+(PPPM), and multilevel summation method (MSM) solvers.
+
+**Install:**
+
+Building with this package requires a 1d FFT library be present on
+your system for use by the PPPM solvers.  This can be the KISS FFT
+library provided with LAMMPS, 3rd party libraries like FFTW, or a
+vendor-supplied FFT library.  See the :doc:`Build settings <Build_settings>` doc page for details on how to select
+different FFT options for your LAMPMS build.
+
+**Supporting info:**
+
+* src/KSPACE: filenames -> commands
+* :doc:`kspace\_style <kspace_style>`
+* `doc/PDF/kspace.pdf <PDF/kspace.pdf>`_
+* :doc:`Howto tip3p <Howto_tip3p>`
+* :doc:`Howto tip4p <Howto_tip4p>`
+* :doc:`Howto spc <Howto_spc>`
+* :doc:`pair\_style coul <pair_coul>`
+* :doc:`Commands pair <Commands_pair>` page for styles with "long" or "msm" in name
+* examples/peptide
+* bench/in.rhodo
+
+
+----------
+
+
+.. _PKG-LATTE:
+
+LATTE package
+-------------
+
+**Contents:**
+
+A fix command which wraps the LATTE DFTB code, so that molecular
+dynamics can be run with LAMMPS using density-functional tight-binding
+quantum forces calculated by LATTE.
+
+More information on LATTE can be found at this web site:
+`https://github.com/lanl/LATTE <latte-home_>`_.  A brief technical
+description is given with the :doc:`fix latte <fix_latte>` command.
+
+.. _latte-home: https://github.com/lanl/LATTE
+
+
+
+**Authors:** Christian Negre (LANL) and Steve Plimpton (Sandia).  LATTE
+itself is developed at Los Alamos National Laboratory by Marc
+Cawkwell, Anders Niklasson, and Christian Negre.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <latte>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/LATTE: filenames -> commands
+* src/LATTE/README
+* lib/latte/README
+* :doc:`fix latte <fix_latte>`
+* examples/latte
+* `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_
+
+
+----------
+
+
+.. _PKG-MANYBODY:
+
+MANYBODY package
+----------------
+
+**Contents:**
+
+A variety of many-body and bond-order potentials.  These include
+(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
+
+**Supporting info:**
+
+* src/MANYBODY: filenames -> commands
+* :doc:`Commands pair <Commands_pair>` page
+* examples/comb
+* examples/eim
+* examples/nb3d
+* examples/shear
+* examples/streitz
+* examples/vashishta
+* bench/in.eam
+
+
+----------
+
+
+.. _PKG-MC:
+
+MC package
+----------
+
+**Contents:**
+
+Several fixes and a pair style that have Monte Carlo (MC) or MC-like
+attributes.  These include fixes for creating, breaking, and swapping
+bonds, for performing atomic swaps, and performing grand-canonical MC
+(GCMC) in conjunction with dynamics.
+
+**Supporting info:**
+
+* src/MC: filenames -> commands
+* :doc:`fix atom/swap <fix_atom_swap>`
+* :doc:`fix bond/break <fix_bond_break>`
+* :doc:`fix bond/create <fix_bond_create>`
+* :doc:`fix bond/swap <fix_bond_swap>`
+* :doc:`fix gcmc <fix_gcmc>`
+* :doc:`pair\_style dsmc <pair_dsmc>`
+* http://lammps.sandia.gov/movies.html#gcmc
+
+
+----------
+
+
+.. _PKG-MESSAGE:
+
+MESSAGE package
+---------------
+
+**Contents:**
+
+Commands to use LAMMPS as either a client or server and couple it to
+another application.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <message>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/MESSAGE: filenames -> commands
+* lib/message/README
+* :doc:`message <message>`
+* :doc:`fix client/md <fix_client_md>`
+* :doc:`server md <server_md>`
+* :doc:`server mc <server_mc>`
+* examples/message
+
+
+----------
+
+
+.. _PKG-MISC:
+
+MISC package
+------------
+
+**Contents:**
+
+A variety of compute, fix, pair, dump styles with specialized
+capabilities that don't align with other packages.  Do a directory
+listing, "ls src/MISC", to see the list of commands.
+
+.. note::
+
+   the MISC package contains styles that require using the
+   -restrict flag, when compiling with Intel compilers.
+
+**Supporting info:**
+
+* src/MISC: filenames -> commands
+* :doc:`compute ti <compute_ti>`
+* :doc:`fix evaporate <fix_evaporate>`
+* :doc:`fix orient/fcc <fix_orient>`
+* :doc:`fix ttm <fix_ttm>`
+* :doc:`fix thermal/conductivity <fix_thermal_conductivity>`
+* :doc:`fix viscosity <fix_viscosity>`
+* examples/KAPPA
+* examples/VISCOSITY
+* http://lammps.sandia.gov/pictures.html#ttm
+* http://lammps.sandia.gov/movies.html#evaporation
+
+
+----------
+
+
+.. _PKG-MOLECULE:
+
+MOLECULE package
+----------------
+
+**Contents:**
+
+A large number of atom, pair, bond, angle, dihedral, improper styles
+that are used to model molecular systems with fixed covalent bonds.
+The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
+force fields, and a TIP4P water model.
+
+**Supporting info:**
+
+* src/MOLECULE: filenames -> commands
+* :doc:`atom\_style <atom_style>`
+* :doc:`bond\_style <bond_style>`
+* :doc:`angle\_style <angle_style>`
+* :doc:`dihedral\_style <dihedral_style>`
+* :doc:`improper\_style <improper_style>`
+* :doc:`pair\_style hbond/dreiding/lj <pair_hbond_dreiding>`
+* :doc:`pair\_style lj/charmm/coul/charmm <pair_charmm>`
+* :doc:`Howto bioFF <Howto_bioFF>`
+* examples/cmap
+* examples/dreiding
+* examples/micelle,
+* examples/peptide
+* bench/in.chain
+* bench/in.rhodo
+
+
+----------
+
+
+.. _PKG-MPIIO:
+
+MPIIO package
+-------------
+
+**Contents:**
+
+Support for parallel output/input of dump and restart files via the
+MPIIO library.  It adds :doc:`dump styles <dump>` with a "mpiio" in
+their style name.  Restart files with an ".mpiio" suffix are also
+written and read in parallel.
+
+**Supporting info:**
+
+* src/MPIIO: filenames -> commands
+* :doc:`dump <dump>`
+* :doc:`restart <restart>`
+* :doc:`write\_restart <write_restart>`
+* :doc:`read\_restart <read_restart>`
+
+
+----------
+
+
+.. _PKG-mscg:
+
+MSCG package
+------------
+
+**Contents:**
+
+A :doc:`fix mscg <fix_mscg>` command which can parameterize a
+Multi-Scale Coarse-Graining (MSCG) model using the open-source `MS-CG library <mscg-home_>`_.
+
+.. _mscg-home: https://github.com/uchicago-voth/MSCG-release
+
+
+
+To use this package you must have the MS-CG library available on your
+system.
+
+**Authors:** The fix was written by Lauren Abbott (Sandia).  The MS-CG
+library was developed by Jacob Wagner in Greg Voth's group at the
+University of Chicago.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <mscg>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/MSCG: filenames -> commands
+* src/MSCG/README
+* lib/mscg/README
+* examples/mscg
+
+
+----------
+
+
+.. _PKG-OPT:
+
+OPT package
+-----------
+
+**Contents:**
+
+A handful of pair styles which are optimized for improved CPU
+performance on single or multiple cores.  These include EAM, LJ,
+CHARMM, and Morse potentials.  The styles have an "opt" suffix in
+their style name.  The :doc:`Speed opt <Speed_opt>` doc page gives
+details of how to build and use this package.  Its styles can be
+invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switches <Run_options>`.  See also the :ref:`KOKKOS <PKG-KOKKOS>`,
+:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
+have styles optimized for CPU performance.
+
+**Authors:** James Fischer (High Performance Technologies), David Richie,
+and Vincent Natoli (Stone Ridge Technolgy).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <opt>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/OPT: filenames -> commands
+* :doc:`Speed packages <Speed_packages>`
+* :doc:`Speed opt <Speed_opt>`
+* :doc:`Section 2.6 -sf opt <Run_options>`
+* :doc:`Commands pair <Commands_pair>` for styles followed by (t)
+* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
+
+
+----------
+
+
+.. _PKG-PERI:
+
+PERI package
+------------
+
+**Contents:**
+
+An atom style, several pair styles which implement different
+Peridynamics materials models, and several computes which calculate
+diagnostics.  Peridynamics is a particle-based meshless continuum
+model.
+
+**Authors:** The original package was created by Mike Parks (Sandia).
+Additional Peridynamics models were added by Rezwanur Rahman and John
+Foster (UTSA).
+
+**Supporting info:**
+
+* src/PERI: filenames -> commands
+* `doc/PDF/PDLammps\_overview.pdf <PDF/PDLammps_overview.pdf>`_
+* `doc/PDF/PDLammps\_EPS.pdf <PDF/PDLammps_EPS.pdf>`_
+* `doc/PDF/PDLammps\_VES.pdf <PDF/PDLammps_VES.pdf>`_
+* :doc:`atom\_style peri <atom_style>`
+* :doc:`pair\_style peri/\* <pair_peri>`
+* :doc:`compute damage/atom <compute_damage_atom>`
+* :doc:`compute plasticity/atom <compute_plasticity_atom>`
+* examples/peri
+* http://lammps.sandia.gov/movies.html#peri
+
+
+----------
+
+
+.. _PKG-POEMS:
+
+POEMS package
+-------------
+
+**Contents:**
+
+A fix that wraps the Parallelizable Open source Efficient Multibody
+Software (POEMS) library, which is able to simulate the dynamics of
+articulated body systems.  These are systems with multiple rigid
+bodies (collections of particles) whose motion is coupled by
+connections at hinge points.
+
+**Author:** Rudra Mukherjee (JPL) while at RPI.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <poems>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/POEMS: filenames -> commands
+* src/POEMS/README
+* lib/poems/README
+* :doc:`fix poems <fix_poems>`
+* examples/rigid
+
+
+----------
+
+
+.. _PKG-PYTHON:
+
+PYTHON package
+--------------
+
+**Contents:**
+
+A :doc:`python <python>` command which allow you to execute Python code
+from a LAMMPS input script.  The code can be in a separate file or
+embedded in the input script itself.  See the :doc:`Python call <Python_call>` doc page for an overview of using Python from
+LAMMPS in this manner and all the :doc:`Python <Python_head>` doc pages
+for other ways to use LAMMPS and Python together.
+
+.. note::
+
+   Building with the PYTHON package assumes you have a Python
+   shared library available on your system, which needs to be a Python 2
+   version, 2.6 or later.  Python 3 is not yet supported.  See the
+   lib/python/README for more details.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <python>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/PYTHON: filenames -> commands
+* :doc:`Python call <Python_head>`
+* lib/python/README
+* examples/python
+
+
+----------
+
+
+.. _PKG-QEQ:
+
+QEQ package
+-----------
+
+**Contents:**
+
+Several fixes for performing charge equilibration (QEq) via different
+algorithms.  These can be used with pair styles that perform QEq as
+part of their formulation.
+
+**Supporting info:**
+
+* src/QEQ: filenames -> commands
+* :doc:`fix qeq/\* <fix_qeq>`
+* examples/qeq
+* examples/streitz
+
+
+----------
+
+
+.. _PKG-REPLICA2:
+
+REPLICA package
+---------------
+
+**Contents:**
+
+A collection of multi-replica methods which can be used when running
+multiple LAMMPS simulations (replicas).  See the :doc:`Howto replica <Howto_replica>` doc page for an overview of how to run
+multi-replica simulations in LAMMPS.  Methods in the package include
+nudged elastic band (NEB), parallel replica dynamics (PRD),
+temperature accelerated dynamics (TAD), parallel tempering, and a
+verlet/split algorithm for performing long-range Coulombics on one set
+of processors, and the remainder of the force field calculation on
+another set.
+
+**Supporting info:**
+
+* src/REPLICA: filenames -> commands
+* :doc:`Howto replica <Howto_replica>`
+* :doc:`neb <neb>`
+* :doc:`prd <prd>`
+* :doc:`tad <tad>`
+* :doc:`temper <temper>`,
+* :doc:`run\_style verlet/split <run_style>`
+* examples/neb
+* examples/prd
+* examples/tad
+
+
+----------
+
+
+.. _PKG-RIGID:
+
+RIGID package
+-------------
+
+**Contents:**
+
+Fixes which enforce rigid constraints on collections of atoms or
+particles.  This includes SHAKE and RATTLE, as well as various
+rigid-body integrators for a few large bodies or many small bodies.
+Also several computes which calculate properties of rigid bodies.
+
+**Supporting info:**
+
+* src/RIGID: filenames -> commands
+* :doc:`compute erotate/rigid <compute_erotate_rigid>`
+* fix shake"_fix\_shake.html
+* :doc:`fix rattle <fix_shake>`
+* :doc:`fix rigid/\* <fix_rigid>`
+* examples/ASPHERE
+* examples/rigid
+* bench/in.rhodo
+* http://lammps.sandia.gov/movies.html#box
+* http://lammps.sandia.gov/movies.html#star
+
+
+----------
+
+
+.. _PKG-SHOCK:
+
+SHOCK package
+-------------
+
+**Contents:**
+
+Fixes for running impact simulations where a shock-wave passes through
+a material.
+
+**Supporting info:**
+
+* src/SHOCK: filenames -> commands
+* :doc:`fix append/atoms <fix_append_atoms>`
+* :doc:`fix msst <fix_msst>`
+* :doc:`fix nphug <fix_nphug>`
+* :doc:`fix wall/piston <fix_wall_piston>`
+* examples/hugoniostat
+* examples/msst
+
+
+----------
+
+
+.. _PKG-SNAP:
+
+SNAP package
+------------
+
+**Contents:**
+
+A pair style for the spectral neighbor analysis potential (SNAP).
+SNAP is methodology for deriving a highly accurate classical potential
+fit to a large archive of quantum mechanical (DFT) data. Also several
+computes which analyze attributes of the potential.
+
+**Author:** Aidan Thompson (Sandia).
+
+**Supporting info:**
+
+* src/SNAP: filenames -> commands
+* :doc:`pair\_style snap <pair_snap>`
+* :doc:`compute sna/atom <compute_sna_atom>`
+* :doc:`compute snad/atom <compute_sna_atom>`
+* :doc:`compute snav/atom <compute_sna_atom>`
+* examples/snap
+
+
+----------
+
+
+.. _PKG-SPIN:
+
+SPIN package
+------------
+
+**Contents:**
+
+Model atomic magnetic spins classically, coupled to atoms moving in
+the usual manner via MD.  Various pair, fix, and compute styles.
+
+**Author:** Julien Tranchida (Sandia).
+
+**Supporting info:**
+
+* src/SPIN: filenames -> commands
+* :doc:`Howto spins <Howto_spins>`
+* :doc:`pair\_style spin/dipole/cut <pair_spin_dipole>`
+* :doc:`pair\_style spin/dipole/long <pair_spin_dipole>`
+* :doc:`pair\_style spin/dmi <pair_spin_dmi>`
+* :doc:`pair\_style spin/exchange <pair_spin_exchange>`
+* :doc:`pair\_style spin/magelec <pair_spin_magelec>`
+* :doc:`pair\_style spin/neel <pair_spin_neel>`
+* :doc:`fix nve/spin <fix_nve_spin>`
+* :doc:`fix precession/spin <fix_precession_spin>`
+* :doc:`compute spin <compute_spin>`
+* :doc:`neb/spin <neb_spin>`
+* examples/SPIN
+
+
+----------
+
+
+.. _PKG-SRD:
+
+SRD package
+-----------
+
+**Contents:**
+
+A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
+method for coarse-graining of a solvent, typically around large
+colloidal particles.
+
+**Supporting info:**
+
+* src/SRD: filenames -> commands
+* :doc:`fix srd <fix_srd>`
+* :doc:`fix wall/srd <fix_wall_srd>`
+* examples/srd
+* examples/ASPHERE
+* http://lammps.sandia.gov/movies.html#tri
+* http://lammps.sandia.gov/movies.html#line
+* http://lammps.sandia.gov/movies.html#poly
+
+
+----------
+
+
+.. _PKG-VORONOI:
+
+VORONOI package
+---------------
+
+**Contents:**
+
+A compute command which calculates the Voronoi tesselation of a
+collection of atoms by wrapping the `Voro++ library <voro-home_>`_.  This
+can be used to calculate the local volume or each atoms or its near
+neighbors.
+
+.. _voro-home: http://math.lbl.gov/voro++
+
+
+
+To use this package you must have the Voro++ library available on your
+system.
+
+**Author:** Daniel Schwen (INL) while at LANL.  The open-source Voro++
+library was written by Chris Rycroft (Harvard U) while at UC Berkeley
+and LBNL.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <voronoi>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/VORONOI: filenames -> commands
+* src/VORONOI/README
+* lib/voronoi/README
+* :doc:`compute voronoi/atom <compute_voronoi_atom>`
+* examples/voronoi
+
+
+----------
+
+
+.. _PKG-USER-ADIOS:
+
+USER-ADIOS package
+------------------
+
+**Contents:**
+
+ADIOS is a high-performance I/O library. This package implements the
+dump "atom/adios" and dump "custom/adios" commands to write data using
+the ADIOS library.
+
+**Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-adios>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-ADIOS: filenames -> commands
+* src/USER-ADIOS/README
+* examples/USER/adios
+* https://github.com/ornladios/ADIOS2
+
+
+----------
+
+
+.. _PKG-USER-ATC:
+
+USER-ATC package
+----------------
+
+**Contents:**
+
+ATC stands for atoms-to-continuum.  This package implements a :doc:`fix atc <fix_atc>` command to either couple molecular dynamics with
+continuum finite element equations or perform on-the-fly conversion of
+atomic information to continuum fields.
+
+**Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-atc>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-ATC: filenames -> commands
+* src/USER-ATC/README
+* :doc:`fix atc <fix_atc>`
+* examples/USER/atc
+* http://lammps.sandia.gov/pictures.html#atc
+
+
+----------
+
+
+.. _PKG-USER-AWPMD:
+
+USER-AWPMD package
+------------------
+
+**Contents:**
+
+AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics.  This
+package implements an atom, pair, and fix style which allows electrons
+to be treated as explicit particles in a classical molecular dynamics
+model.
+
+**Author:** Ilya Valuev (JIHT, Russia).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-awpmd>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-AWPMD: filenames -> commands
+* src/USER-AWPMD/README
+* :doc:`pair\_style awpmd/cut <pair_awpmd>`
+* examples/USER/awpmd
+
+
+----------
+
+
+.. _PKG-USER-BOCS:
+
+USER-BOCS package
+-----------------
+
+**Contents:**
+
+This package provides :doc:`fix bocs <fix_bocs>`, a modified version
+of :doc:`fix npt <fix_nh>` which includes the pressure correction to
+the barostat as outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
+Pennsylvania State University)
+
+**Supporting info:**
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+`https://github.com/noid-group/BOCS <https://github.com/noid-group/BOCS>`_
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
+
+
+----------
+
+
+.. _PKG-USER-CGDNA:
+
+USER-CGDNA package
+------------------
+
+**Contents:**
+
+Several pair styles, a bond style, and integration fixes for
+coarse-grained models of single- and double-stranded DNA based on the
+oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
+This includes Langevin-type rigid-body integrators with improved
+stability.
+
+**Author:** Oliver Henrich (University of Strathclyde, Glasgow).
+
+**Supporting info:**
+
+* src/USER-CGDNA: filenames -> commands
+* /src/USER-CGDNA/README
+* :doc:`pair\_style oxdna/\* <pair_oxdna>`
+* :doc:`pair\_style oxdna2/\* <pair_oxdna2>`
+* :doc:`bond\_style oxdna/\* <bond_oxdna>`
+* :doc:`bond\_style oxdna2/\* <bond_oxdna>`
+* :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+
+
+----------
+
+
+.. _PKG-USER-CGSDK:
+
+USER-CGSDK package
+------------------
+
+**Contents:**
+
+Several pair styles and an angle style which implement the
+coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
+simulation of ionic liquids, electrolytes, lipids and charged amino
+acids.
+
+**Author:** Axel Kohlmeyer (Temple U).
+
+**Supporting info:**
+
+* src/USER-CGSDK: filenames -> commands
+* src/USER-CGSDK/README
+* :doc:`pair\_style lj/sdk/\* <pair_sdk>`
+* :doc:`angle\_style sdk <angle_sdk>`
+* examples/USER/cgsdk
+* http://lammps.sandia.gov/pictures.html#cg
+
+
+----------
+
+
+.. _PKG-USER-COLVARS:
+
+USER-COLVARS package
+--------------------
+
+**Contents:**
+
+COLVARS stands for collective variables, which can be used to
+implement various enhanced sampling methods, including Adaptive
+Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and
+Restraints.  A :doc:`fix colvars <fix_colvars>` command is implemented
+which wraps a COLVARS library, which implements these methods.
+simulations.
+
+**Authors:** The COLVARS library is written and maintained by
+Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
+and Jerome Henin (LISM, CNRS, Marseille, France), originally for
+the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
+(Temple U) provided the interface to LAMMPS.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-colvars>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-COLVARS: filenames -> commands
+* `doc/PDF/colvars-refman-lammps.pdf <PDF/colvars-refman-lammps.pdf>`_
+* src/USER-COLVARS/README
+* lib/colvars/README
+* :doc:`fix colvars <fix_colvars>`
+* examples/USER/colvars
+
+
+----------
+
+
+.. _PKG-USER-PLUMED:
+
+USER-PLUMED package
+-------------------
+
+**Contents:**
+
+The fix plumed command allows you to use the PLUMED free energy plugin
+for molecular dynamics to analyze and bias your LAMMPS trajectory on
+the fly.  The PLUMED library is called from within the LAMMPS input
+script by using the :doc:`fix plumed <fix_plumed>` command.
+
+**Authors:** The :ref:`PLUMED library <PLUMED>` is written and maintained by
+Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth
+Tribello.
+
+.. _PLUMED: http://www.plumed.org
+
+
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-plumed>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-PLUMED/README
+* lib/plumed/README
+* :doc:`fix plumed <fix_plumed>`
+* examples/USER/plumed
+
+
+----------
+
+
+.. _PKG-USER-DIFFRACTION:
+
+USER-DIFFRACTION package
+------------------------
+
+**Contents:**
+
+Two computes and a fix for calculating x-ray and electron diffraction
+intensities based on kinematic diffraction theory.
+
+**Author:** Shawn Coleman while at the U Arkansas.
+
+**Supporting info:**
+
+* src/USER-DIFFRACTION: filenames -> commands
+* :doc:`compute saed <compute_saed>`
+* :doc:`compute xrd <compute_xrd>`
+* :doc:`fix saed/vtk <fix_saed_vtk>`
+* examples/USER/diffraction
+
+
+----------
+
+
+.. _PKG-USER-DPD:
+
+USER-DPD package
+----------------
+
+**Contents:**
+
+DPD stands for dissipative particle dynamics.  This package implements
+coarse-grained DPD-based models for energetic, reactive molecular
+crystalline materials.  It includes many pair styles specific to these
+systems, including for reactive DPD, where each particle has internal
+state for multiple species and a coupled set of chemical reaction ODEs
+are integrated each timestep.  Highly accurate time integrators for
+isothermal, isoenergetic, isobaric and isenthalpic conditions are
+included.  These enable long timesteps via the Shardlow splitting
+algorithm.
+
+**Authors:** Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John
+Brennan (ARL).
+
+**Supporting info:**
+
+* src/USER-DPD: filenames -> commands
+* /src/USER-DPD/README
+* :doc:`compute dpd <compute_dpd>`
+* :doc:`compute dpd/atom <compute_dpd_atom>`
+* :doc:`fix eos/cv <fix_eos_table>`
+* :doc:`fix eos/table <fix_eos_table>`
+* :doc:`fix eos/table/rx <fix_eos_table_rx>`
+* :doc:`fix shardlow <fix_shardlow>`
+* :doc:`fix rx <fix_rx>`
+* :doc:`pair\_style table/rx <pair_table_rx>`
+* :doc:`pair\_style dpd/fdt <pair_dpd_fdt>`
+* :doc:`pair\_style dpd/fdt/energy <pair_dpd_fdt>`
+* :doc:`pair\_style exp6/rx <pair_exp6_rx>`
+* :doc:`pair\_style multi/lucy <pair_multi_lucy>`
+* :doc:`pair\_style multi/lucy/rx <pair_multi_lucy_rx>`
+* examples/USER/dpd
+
+
+----------
+
+
+.. _PKG-USER-DRUDE:
+
+USER-DRUDE package
+------------------
+
+**Contents:**
+
+Fixes, pair styles, and a compute to simulate thermalized Drude
+oscillators as a model of polarization.  See the :doc:`Howto drude <Howto_drude>` and :doc:`Howto drude2 <Howto_drude2>` doc pages
+for an overview of how to use the package.  There are auxiliary tools
+for using this package in tools/drude.
+
+**Authors:** Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
+Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
+
+**Supporting info:**
+
+* src/USER-DRUDE: filenames -> commands
+* :doc:`Howto drude <Howto_drude>`
+* :doc:`Howto drude2 <Howto_drude2>`
+* :doc:`Howto polarizable <Howto_polarizable>`
+* src/USER-DRUDE/README
+* :doc:`fix drude <fix_drude>`
+* :doc:`fix drude/transform/\* <fix_drude_transform>`
+* :doc:`compute temp/drude <compute_temp_drude>`
+* :doc:`pair\_style thole <pair_thole>`
+* :doc:`pair\_style lj/cut/thole/long <pair_thole>`
+* examples/USER/drude
+* tools/drude
+
+
+----------
+
+
+.. _PKG-USER-EFF:
+
+USER-EFF package
+----------------
+
+**Contents:**
+
+EFF stands for electron force field which allows a classical MD code
+to model electrons as particles of variable radius.  This package
+contains atom, pair, fix and compute styles which implement the eFF as
+described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
+JCC, 2010.  The eFF potential was first introduced by Su and Goddard,
+in 2007.  There are auxiliary tools for using this package in
+tools/eff; see its README file.
+
+**Author:** Andres Jaramillo-Botero (CalTech).
+
+**Supporting info:**
+
+* src/USER-EFF: filenames -> commands
+* src/USER-EFF/README
+* :doc:`atom\_style electron <atom_style>`
+* :doc:`fix nve/eff <fix_nve_eff>`
+* :doc:`fix nvt/eff <fix_nh_eff>`
+* :doc:`fix npt/eff <fix_nh_eff>`
+* :doc:`fix langevin/eff <fix_langevin_eff>`
+* :doc:`compute temp/eff <compute_temp_eff>`
+* :doc:`pair\_style eff/cut <pair_eff>`
+* :doc:`pair\_style eff/inline <pair_eff>`
+* examples/USER/eff
+* tools/eff/README
+* tools/eff
+* http://lammps.sandia.gov/movies.html#eff
+
+
+----------
+
+
+.. _PKG-USER-FEP:
+
+USER-FEP package
+----------------
+
+**Contents:**
+
+FEP stands for free energy perturbation.  This package provides
+methods for performing FEP simulations by using a :doc:`fix adapt/fep <fix_adapt_fep>` command with soft-core pair potentials,
+which have a "soft" in their style name.  There are auxiliary tools
+for using this package in tools/fep; see its README file.
+
+**Author:** Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
+
+**Supporting info:**
+
+* src/USER-FEP: filenames -> commands
+* src/USER-FEP/README
+* :doc:`fix adapt/fep <fix_adapt_fep>`
+* :doc:`compute fep <compute_fep>`
+* :doc:`pair\_style \*/soft <pair_fep_soft>`
+* examples/USER/fep
+* tools/fep/README
+* tools/fep
+
+
+----------
+
+
+.. _PKG-USER-H5MD:
+
+USER-H5MD package
+-----------------
+
+**Contents:**
+
+H5MD stands for HDF5 for MD.  `HDF5 <HDF5_>`_ is a portable, binary,
+self-describing file format, used by many scientific simulations.
+H5MD is a format for molecular simulations, built on top of HDF5.
+This package implements a :doc:`dump h5md <dump_h5md>` command to output
+LAMMPS snapshots in this format.
+
+.. _HDF5: http://www.hdfgroup.org/HDF5
+
+
+
+To use this package you must have the HDF5 library available on your
+system.
+
+**Author:** Pierre de Buyl (KU Leuven) created both the package and the
+H5MD format.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-h5md>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-H5MD: filenames -> commands
+* src/USER-H5MD/README
+* lib/h5md/README
+* :doc:`dump h5md <dump_h5md>`
+
+
+----------
+
+
+.. _PKG-USER-INTEL:
+
+USER-INTEL package
+------------------
+
+**Contents:**
+
+Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
+styles which are optimized for Intel CPUs and KNLs (Knights Landing).
+All of them have an "intel" in their style name.  The :doc:`Speed intel <Speed_intel>` doc page gives details of what hardware and
+compilers are required on your system, and how to build and use this
+package.  Its styles can be invoked at run time via the "-sf intel" or
+"-suffix intel" :doc:`command-line switches <Run_options>`.  Also see
+the :ref:`KOKKOS <PKG-KOKKOS>`, :ref:`OPT <PKG-OPT>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages,
+which have styles optimized for CPUs and KNLs.
+
+You need to have an Intel compiler, version 14 or higher to take full
+advantage of this package. While compilation with GNU compilers is
+supported, performance will be sub-optimal.
+
+.. note::
+
+   the USER-INTEL package contains styles that require using the
+   -restrict flag, when compiling with Intel compilers.
+
+**Author:** Mike Brown (Intel).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-intel>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-INTEL: filenames -> commands
+* src/USER-INTEL/README
+* :doc:`Speed packages <Speed_packages>`
+* :doc:`Speed intel <Speed_intel>`
+* :doc:`Section 2.6 -sf intel <Run_options>`
+* :doc:`Section 2.6 -pk intel <Run_options>`
+* :doc:`package intel <package>`
+* `Commands all <lc_>`_ pages (fix,compute,pair,etc) for styles followed by (i)
+* src/USER-INTEL/TEST
+* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
+
+
+----------
+
+
+.. _PKG-USER-LB:
+
+USER-LB package
+---------------
+
+**Contents:**
+
+Fixes which implement a background Lattice-Boltzmann (LB) fluid, which
+can be used to model MD particles influenced by hydrodynamic forces.
+
+**Authors:** Frances Mackay and Colin Denniston (University of Western
+Ontario).
+
+**Supporting info:**
+
+* src/USER-LB: filenames -> commands
+* src/USER-LB/README
+* :doc:`fix lb/fluid <fix_lb_fluid>`
+* :doc:`fix lb/momentum <fix_lb_momentum>`
+* :doc:`fix lb/viscous <fix_lb_viscous>`
+* examples/USER/lb
+
+
+----------
+
+
+.. _PKG-USER-MGPT:
+
+USER-MGPT package
+-----------------
+
+**Contents:**
+
+A pair style which provides a fast implementation of the quantum-based
+MGPT multi-ion potentials.  The MGPT or model GPT method derives from
+first-principles DFT-based generalized pseudopotential theory (GPT)
+through a series of systematic approximations valid for mid-period
+transition metals with nearly half-filled d bands.  The MGPT method
+was originally developed by John Moriarty at LLNL.  The pair style in
+this package calculates forces and energies using an optimized
+matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
+
+**Authors:** Tomas Oppelstrup and John Moriarty (LLNL).
+
+**Supporting info:**
+
+* src/USER-MGPT: filenames -> commands
+* src/USER-MGPT/README
+* :doc:`pair\_style mgpt <pair_mgpt>`
+* examples/USER/mgpt
+
+
+----------
+
+
+.. _PKG-USER-MISC:
+
+USER-MISC package
+-----------------
+
+**Contents:**
+
+A potpourri of (mostly) unrelated features contributed to LAMMPS by
+users.  Each feature is a single fix, compute, pair, bond, angle,
+dihedral, improper, or command style.
+
+**Authors:** The author for each style in the package is listed in the
+src/USER-MISC/README file.
+
+**Supporting info:**
+
+* src/USER-MISC: filenames -> commands
+* src/USER-MISC/README
+* one doc page per individual command listed in src/USER-MISC/README
+* examples/USER/misc
+
+
+----------
+
+
+.. _PKG-USER-MANIFOLD:
+
+USER-MANIFOLD package
+---------------------
+
+**Contents:**
+
+Several fixes and a "manifold" class which enable simulations of
+particles constrained to a manifold (a 2D surface within the 3D
+simulation box).  This is done by applying the RATTLE constraint
+algorithm to formulate single-particle constraint functions
+g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
+n = grad(g).
+
+**Author:** Stefan Paquay (until 2017: Eindhoven University of
+Technology (TU/e), The Netherlands; since 2017: Brandeis University,
+Waltham, MA, USA)
+
+**Supporting info:**
+
+* src/USER-MANIFOLD: filenames -> commands
+* src/USER-MANIFOLD/README
+* :doc:`Howto manifold <Howto_manifold>`
+* :doc:`fix manifoldforce <fix_manifoldforce>`
+* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
+* :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
+* examples/USER/manifold
+* http://lammps.sandia.gov/movies.html#manifold
+
+
+----------
+
+
+.. _PKG-USER-MEAMC:
+
+USER-MEAMC package
+------------------
+
+**Contents:**
+
+A pair style for the modified embedded atom (MEAM) potential
+translated from the Fortran version in the (obsolete) "MEAM" package
+to plain C++. The USER-MEAMC fully replaces the MEAM package, which
+has been removed from LAMMPS after the 12 December 2018 version.
+
+**Author:** Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
+based on the Fortran version of Greg Wagner (Northwestern U) while at
+Sandia.
+
+**Supporting info:**
+
+* src/USER-MEAMC: filenames -> commands
+* src/USER-MEAMC/README
+* :doc:`pair\_style meam/c <pair_meamc>`
+* examples/meamc
+
+
+----------
+
+
+.. _PKG-USER-MESO:
+
+USER-MESO package
+-----------------
+
+**Contents:**
+
+Several extensions of the dissipative particle dynamics (DPD)
+method.  Specifically, energy-conserving DPD (eDPD) that can model
+non-isothermal processes, many-body DPD (mDPD) for simulating
+vapor-liquid coexistence, and transport DPD (tDPD) for modeling
+advection-diffusion-reaction systems. The equations of motion of these
+DPD extensions are integrated through a modified velocity-Verlet (MVV)
+algorithm.
+
+**Author:** Zhen Li (Division of Applied Mathematics, Brown University)
+
+**Supporting info:**
+
+* src/USER-MESO: filenames -> commands
+* src/USER-MESO/README
+* :doc:`atom\_style edpd <atom_style>`
+* :doc:`pair\_style edpd <pair_meso>`
+* :doc:`pair\_style mdpd <pair_meso>`
+* :doc:`pair\_style tdpd <pair_meso>`
+* :doc:`fix mvv/dpd <fix_mvv_dpd>`
+* examples/USER/meso
+* http://lammps.sandia.gov/movies.html#mesodpd
+
+
+----------
+
+
+.. _PKG-USER-MOFFF:
+
+USER-MOFFF package
+------------------
+
+**Contents:**
+
+Pair, angle and improper styles needed to employ the MOF-FF
+force field by Schmid and coworkers with LAMMPS.
+MOF-FF is a first principles derived force field with the primary aim
+to simulate MOFs and related porous framework materials, using spherical
+Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
+2013, 250, 1128-1141.
+For the usage of MOF-FF see the example in the example directory as
+well as the `MOF+ <MOFplus_>`_ website.
+
+.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
+
+
+
+**Author:** Hendrik Heenen (Technical U of Munich),
+Rochus Schmid (Ruhr-University Bochum).
+
+**Supporting info:**
+
+* src/USER-MOFFF: filenames -> commands
+* src/USER-MOFFF/README
+* :doc:`pair\_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`
+* :doc:`angle\_style class2 <angle_class2>`
+* :doc:`angle\_style cosine/buck6d <angle_cosine_buck6d>`
+* :doc:`improper\_style inversion/harmonic <improper_inversion_harmonic>`
+* examples/USER/mofff
+
+
+----------
+
+
+.. _PKG-USER-MOLFILE:
+
+USER-MOLFILE package
+--------------------
+
+**Contents:**
+
+A :doc:`dump molfile <dump_molfile>` command which uses molfile plugins
+that are bundled with the `VMD <vmd-home_>`_
+molecular visualization and analysis program, to enable LAMMPS to dump
+snapshots in formats compatible with various molecular simulation
+tools.
+
+To use this package you must have the desired VMD plugins available on
+your system.
+
+Note that this package only provides the interface code, not the
+plugins themselves, which will be accessed when requesting a specific
+plugin via the :doc:`dump molfile <dump_molfile>` command.  Plugins can
+be obtained from a VMD installation which has to match the platform
+that you are using to compile LAMMPS for. By adding plugins to VMD,
+support for new file formats can be added to LAMMPS (or VMD or other
+programs that use them) without having to re-compile the application
+itself.  More information about the VMD molfile plugins can be found
+at
+`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile <http://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
+
+**Author:** Axel Kohlmeyer (Temple U).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-molfile>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-MOLFILE: filenames -> commands
+* src/USER-MOLFILE/README
+* lib/molfile/README
+* :doc:`dump molfile <dump_molfile>`
+
+
+----------
+
+
+.. _PKG-USER-NETCDF:
+
+USER-NETCDF package
+-------------------
+
+**Contents:**
+
+Dump styles for writing NetCDF formatted dump files.  NetCDF is a
+portable, binary, self-describing file format developed on top of
+HDF5. The file contents follow the AMBER NetCDF trajectory conventions
+(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
+
+To use this package you must have the NetCDF library available on your
+system.
+
+Note that NetCDF files can be directly visualized with the following
+tools:
+
+* `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)
+* `VMD <vmd-home_>`_
+* `AtomEye <atomeye_>`_ (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution)
+
+.. _ovito: http://www.ovito.org
+
+
+
+.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
+
+
+
+.. _atomeye: http://www.libatoms.org
+
+
+
+**Author:** Lars Pastewka (Karlsruhe Institute of Technology).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-netcdf>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-NETCDF: filenames -> commands
+* src/USER-NETCDF/README
+* lib/netcdf/README
+* :doc:`dump netcdf <dump_netcdf>`
+
+
+----------
+
+
+.. _PKG-USER-OMP:
+
+USER-OMP package
+----------------
+
+**Contents:**
+
+Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
+kspace styles which are altered to enable threading on many-core CPUs
+via OpenMP directives.  All of them have an "omp" in their style name.
+The :doc:`Speed omp <Speed_omp>` doc page gives details of what hardware
+and compilers are required on your system, and how to build and use
+this package.  Its styles can be invoked at run time via the "-sf omp"
+or "-suffix omp" :doc:`command-line switches <Run_options>`.  Also see
+the :ref:`KOKKOS <PKG-KOKKOS>`, :ref:`OPT <PKG-OPT>`, and :ref:`USER-INTEL <PKG-USER-INTEL>`
+packages, which have styles optimized for CPUs.
+
+**Author:** Axel Kohlmeyer (Temple U).
+
+.. note::
+
+   To enable multi-threading support the compile flag "-fopenmp"
+   and the link flag "-fopenmp" (for GNU compilers, you have to look up
+   the equivalent flags for other compilers) must be used to build LAMMPS.
+   When using Intel compilers, also the "-restrict" flag is required.
+   The USER-OMP package can be compiled without enabling OpenMP; then
+   all code will be compiled as serial and the only improvement over the
+   regular styles are some data access optimization. These flags should
+   be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
+   See src/MAKE/OPTIONS/Makefile.omp for an example.
+
+Once you have an appropriate Makefile.machine, you can
+install/un-install the package and build LAMMPS in the usual manner:
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-omp>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-OMP: filenames -> commands
+* src/USER-OMP/README
+* :doc:`Speed packages <Speed_packages>`
+* :doc:`Speed omp <Speed_omp>`
+* :doc:`Section 2.6 -sf omp <Run_options>`
+* :doc:`Section 2.6 -pk omp <Run_options>`
+* :doc:`package omp <package>`
+* `Commands all <lc_>`_ pages (fix,compute,pair,etc) for styles followed by (o)
+* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
+
+
+----------
+
+
+.. _PKG-USER-PHONON:
+
+USER-PHONON package
+-------------------
+
+**Contents:**
+
+A :doc:`fix phonon <fix_phonon>` command that calculates dynamical
+matrices, which can then be used to compute phonon dispersion
+relations, directly from molecular dynamics simulations.
+And a :doc:`dynamical\_matrix <dynamical_matrix>` as well as a
+:doc:`third\_order <third_order>` command to compute the dynamical matrix
+and third order tensor from finite differences.
+
+**Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
+and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order"
+
+**Supporting info:**
+
+* src/USER-PHONON: filenames -> commands
+* src/USER-PHONON/README
+* :doc:`fix phonon <fix_phonon>`
+* :doc:`dynamical\_matrix <dynamical_matrix>`
+* :doc:`third\_order <third_order>`
+* examples/USER/phonon
+
+
+----------
+
+
+.. _PKG-USER-PTM:
+
+USER-PTM package
+----------------
+
+**Contents:**
+
+A :doc:`compute ptm/atom <compute_ptm_atom>` command that calculates
+local structure characterization using the Polyhedral Template
+Matching methodology.
+
+**Author:** Peter Mahler Larsen (MIT).
+
+**Supporting info:**
+
+* src/USER-PTM: filenames not starting with ptm\\_ -> commands
+* src/USER-PTM: filenames starting with ptm\\_ -> supporting code
+* src/USER-PTM/LICENSE
+* :doc:`compute ptm/atom <compute_ptm_atom>`
+
+
+----------
+
+
+.. _PKG-USER-QMMM:
+
+USER-QMMM package
+-----------------
+
+**Contents:**
+
+A :doc:`fix qmmm <fix_qmmm>` command which allows LAMMPS to be used in a
+QM/MM simulation, currently only in combination with the `Quantum ESPRESSO <espresso_>`_ package.
+
+.. _espresso: http://www.quantum-espresso.org
+
+
+
+To use this package you must have Quantum ESPRESSO available on your
+system.
+
+The current implementation only supports an ONIOM style mechanical
+coupling to the Quantum ESPRESSO plane wave DFT package.
+Electrostatic coupling is in preparation and the interface has been
+written in a manner that coupling to other QM codes should be possible
+without changes to LAMMPS itself.
+
+**Author:** Axel Kohlmeyer (Temple U).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-qmmm>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-QMMM: filenames -> commands
+* src/USER-QMMM/README
+* lib/qmmm/README
+* :doc:`fix phonon <fix_phonon>`
+* lib/qmmm/example-ec/README
+* lib/qmmm/example-mc/README
+
+
+----------
+
+
+.. _PKG-USER-QTB:
+
+USER-QTB package
+----------------
+
+**Contents:**
+
+Two fixes which provide a self-consistent quantum treatment of
+vibrational modes in a classical molecular dynamics simulation.  By
+coupling the MD simulation to a colored thermostat, it introduces zero
+point energy into the system, altering the energy power spectrum and
+the heat capacity to account for their quantum nature. This is useful
+when modeling systems at temperatures lower than their classical
+limits or when temperatures ramp across the classical limits in a
+simulation.
+
+**Author:** Yuan Shen (Stanford U).
+
+**Supporting info:**
+
+* src/USER-QTB: filenames -> commands
+* src/USER-QTB/README
+* :doc:`fix qtb <fix_qtb>`
+* :doc:`fix qbmsst <fix_qbmsst>`
+* examples/USER/qtb
+
+
+----------
+
+
+.. _PKG-USER-QUIP:
+
+USER-QUIP package
+-----------------
+
+**Contents:**
+
+A :doc:`pair\_style quip <pair_quip>` command which wraps the `QUIP libAtoms library <quip_>`_, which includes a variety of interatomic
+potentials, including Gaussian Approximation Potential (GAP) models
+developed by the Cambridge University group.
+
+.. _quip: https://github.com/libAtoms/QUIP
+
+
+
+To use this package you must have the QUIP libAtoms library available
+on your system.
+
+**Author:** Albert Bartok (Cambridge University)
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-quip>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-QUIP: filenames -> commands
+* src/USER-QUIP/README
+* :doc:`pair\_style quip <pair_quip>`
+* examples/USER/quip
+
+
+----------
+
+
+.. _PKG-USER-REAXC:
+
+USER-REAXC package
+------------------
+
+**Contents:**
+
+A pair style which implements the ReaxFF potential in C/C++.  ReaxFF
+is a universal reactive force field.  See the src/USER-REAXC/README file
+for more info on differences between the two packages.  Also two fixes
+for monitoring molecules as bonds are created and destroyed.
+
+**Author:** Hasan Metin Aktulga (MSU) while at Purdue University.
+
+**Supporting info:**
+
+* src/USER-REAXC: filenames -> commands
+* src/USER-REAXC/README
+* :doc:`pair\_style reax/c <pair_reaxc>`
+* :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
+* :doc:`fix reax/c/species <fix_reaxc_species>`
+* examples/reax
+
+
+----------
+
+
+.. _PKG-USER-SCAFACOS:
+
+USER-SCAFACOS package
+---------------------
+
+**Contents:**
+
+A KSpace style which wraps the `ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_ to compute long-range Coulombic
+interactions.
+
+To use this package you must have the ScaFaCoS library available on
+your system.
+
+**Author:** Rene Halver (JSC) wrote the scafacos LAMMPS command.
+
+ScaFaCoS itself was developed by a consortium of German research
+facilities with a BMBF (German Ministry of Science and Education)
+funded project in 2009-2012. Participants of the consortium were the
+Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
+the Forschungszentrum Juelich.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-scafacos>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-SCAFACOS: filenames -> commands
+* src/USER-SCAFACOS/README
+* :doc:`kspace\_style scafacos <kspace_style>`
+* :doc:`kspace\_modify <kspace_modify>`
+* examples/USER/scafacos
+
+
+----------
+
+
+.. _PKG-USER-SDPD:
+
+USER-SDPD package
+-----------------
+
+**Contents:**
+
+A pair style for smoothed dissipative particle dynamics (SDPD), which
+is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
+where thermal fluctuations are important (see the
+:ref:`USER-SPH package <PKG-USER-SPH>`).
+Also two fixes for moving and rigid body integration of SPH/SDPD particles
+(particles of atom\_style meso).
+
+**Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic
+Sciences, Iran).
+
+**Supporting info:**
+
+* src/USER-SDPD: filenames -> commands
+* src/USER-SDPD/README
+* :doc:`pair\_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
+* :doc:`fix meso/move <fix_meso_move>`
+* :doc:`fix rigid/meso <fix_rigid_meso>`
+* examples/USER/sdpd
+
+
+----------
+
+
+.. _PKG-USER-SMD:
+
+USER-SMD package
+----------------
+
+**Contents:**
+
+An atom style, fixes, computes, and several pair styles which
+implements smoothed Mach dynamics (SMD) for solids, which is a model
+related to smoothed particle hydrodynamics (SPH) for liquids (see the
+:ref:`USER-SPH package <PKG-USER-SPH>`).
+
+This package solves solids mechanics problems via a state of the art
+stabilized meshless method with hourglass control.  It can specify
+hydrostatic interactions independently from material strength models,
+i.e. pressure and deviatoric stresses are separated.  It provides many
+material models (Johnson-Cook, plasticity with hardening,
+Mie-Grueneisen, Polynomial EOS) and allows new material models to be
+added.  It implements rigid boundary conditions (walls) which can be
+specified as surface geometries from \*.STL files.
+
+**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
+Dynamics, Ernst Mach Institute, Germany).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-smd>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-SMD: filenames -> commands
+* src/USER-SMD/README
+* doc/PDF/SMD\_LAMMPS\_userguide.pdf
+* examples/USER/smd
+* http://lammps.sandia.gov/movies.html#smd
+
+
+----------
+
+
+.. _PKG-USER-SMTBQ:
+
+USER-SMTBQ package
+------------------
+
+**Contents:**
+
+A pair style which implements a Second Moment Tight Binding model with
+QEq charge equilibration (SMTBQ) potential for the description of
+ionocovalent bonds in oxides.
+
+**Authors:** Nicolas Salles, Emile Maras, Olivier Politano, and Robert
+Tetot (LAAS-CNRS, France).
+
+**Supporting info:**
+
+* src/USER-SMTBQ: filenames -> commands
+* src/USER-SMTBQ/README
+* :doc:`pair\_style smtbq <pair_smtbq>`
+* examples/USER/smtbq
+
+
+----------
+
+
+.. _PKG-USER-SPH:
+
+USER-SPH package
+----------------
+
+**Contents:**
+
+An atom style, fixes, computes, and several pair styles which
+implements smoothed particle hydrodynamics (SPH) for liquids.  See the
+related :ref:`USER-SMD package <PKG-USER-SMD>` package for smooth Mach dynamics
+(SMD) for solids.
+
+This package contains ideal gas, Lennard-Jones equation of states,
+Tait, and full support for complete (i.e. internal-energy dependent)
+equations of state.  It allows for plain or Monaghans XSPH integration
+of the equations of motion.  It has options for density continuity or
+density summation to propagate the density field.  It has
+:doc:`set <set>` command options to set the internal energy and density
+of particles from the input script and allows the same quantities to
+be output with thermodynamic output or to dump files via the :doc:`compute property/atom <compute_property_atom>` command.
+
+**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
+Dynamics, Ernst Mach Institute, Germany).
+
+**Supporting info:**
+
+* src/USER-SPH: filenames -> commands
+* src/USER-SPH/README
+* doc/PDF/SPH\_LAMMPS\_userguide.pdf
+* examples/USER/sph
+* http://lammps.sandia.gov/movies.html#sph
+
+
+----------
+
+
+.. _PKG-USER-TALLY:
+
+USER-TALLY package
+------------------
+
+**Contents:**
+
+Several compute styles that can be called when pairwise interactions
+are calculated to tally information (forces, heat flux, energy,
+stress, etc) about individual interactions.
+
+**Author:** Axel Kohlmeyer (Temple U).
+
+**Supporting info:**
+
+* src/USER-TALLY: filenames -> commands
+* src/USER-TALLY/README
+* :doc:`compute \*/tally <compute_tally>`
+* examples/USER/tally
+
+
+----------
+
+
+.. _PKG-USER-UEF:
+
+USER-UEF package
+----------------
+
+**Contents:**
+
+A fix style for the integration of the equations of motion under
+extensional flow with proper boundary conditions, as well as several
+supporting compute styles and an output option.
+
+**Author:** David Nicholson (MIT).
+
+**Supporting info:**
+
+* src/USER-UEF: filenames -> commands
+* src/USER-UEF/README
+* :doc:`fix nvt/uef <fix_nh_uef>`
+* :doc:`fix npt/uef <fix_nh_uef>`
+* :doc:`compute pressure/uef <compute_pressure_uef>`
+* :doc:`compute temp/uef <compute_temp_uef>`
+* :doc:`dump cfg/uef <dump_cfg_uef>`
+* examples/uef
+
+
+----------
+
+
+.. _PKG-USER-VTK:
+
+USER-VTK package
+----------------
+
+**Contents:**
+
+A :doc:`dump vtk <dump_vtk>` command which outputs snapshot info in the
+`VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or
+other visualization packages.
+
+.. _vtk: http://www.vtk.org
+
+
+
+.. _paraview: http://www.paraview.org
+
+
+
+To use this package you must have VTK library available on your
+system.
+
+**Authors:** Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-vtk>` on the :doc:`Build extras <Build_extras>` doc page.
+
+**Supporting info:**
+
+* src/USER-VTK: filenames -> commands
+* src/USER-VTK/README
+* lib/vtk/README
+* :doc:`dump vtk <dump_vtk>`
+
+
+----------
+
+
+.. _PKG-USER-YAFF:
+
+USER-YAFF package
+-----------------
+
+**Contents:**
+
+Some potentials that are also implemented in the Yet Another Force Field (`YAFF <yaff_>`_) code.
+The expressions and their use are discussed in the following papers
+
+* Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) `link <vanduyfhuys2015_>`_
+* Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) `link <vanduyfhuys2018_>`_
+
+which discuss the `QuickFF <quickff_>`_ methodology.
+
+.. _vanduyfhuys2015: http://dx.doi.org/10.1002/jcc.23877
+
+
+
+.. _vanduyfhuys2018: http://dx.doi.org/10.1002/jcc.25173
+
+
+
+.. _quickff: http://molmod.github.io/QuickFF
+
+
+
+.. _yaff: https://github.com/molmod/yaff
+
+
+
+**Author:** Steven Vandenbrande.
+
+**Supporting info:**
+
+* src/USER-YAFF/README
+* :doc:`angle\_style cross <angle_cross>`
+* :doc:`angle\_style mm3 <angle_mm3>`
+* :doc:`bond\_style mm3 <bond_mm3>`
+* :doc:`improper\_style distharm <improper_distharm>`
+* :doc:`improper\_style sqdistharm <improper_sqdistharm>`
+* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
+* examples/USER/yaff
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst
new file mode 100644
index 0000000000..c234f8198d
--- /dev/null
+++ b/doc/src/Packages_standard.rst
@@ -0,0 +1,96 @@
+Standard packages
+=================
+
+This is the list of standard packages in LAMMPS.  The link for each
+package name gives more details.
+
+Standard packages are supported by the LAMMPS developers and are
+written in a syntax and style consistent with the rest of LAMMPS.
+This means the developers will answer questions about them, debug and
+fix them if necessary, and keep them compatible with future changes to
+LAMMPS.
+
+The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory; USER/atc
+refers to the examples/USER/atc directory.  The "Library" column
+indicates whether an extra library is needed to build and use the
+package:
+
+* no  = no library
+* sys = system library: you likely have it on your machine
+* int = internal library: provided with LAMMPS, but you may need to build it
+* ext = external library: you will need to download and install it on your machine
+
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| Package                          | Description                          | Doc page                                           | Example                                             | Library |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`ASPHERE <PKG-ASPHERE>`     | aspherical particle models           | :doc:`Howto spherical <Howto_spherical>`           | ellipse                                             | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`BODY <PKG-BODY>`           | body-style particles                 | :doc:`Howto body <Howto_body>`                     | body                                                | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`CLASS2 <PKG-CLASS2>`       | class 2 force fields                 | :doc:`pair\_style lj/class2 <pair_class2>`         | n/a                                                 | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`COLLOID <PKG-COLLOID>`     | colloidal particles                  | :doc:`atom\_style colloid <atom_style>`            | colloid                                             | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`COMPRESS <PKG-COMPRESS>`   | I/O compression                      | :doc:`dump \*/gz <dump>`                           | n/a                                                 | sys     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`CORESHELL <PKG-CORESHELL>` | adiabatic core/shell model           | :doc:`Howto coreshell <Howto_coreshell>`           | coreshell                                           | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`DIPOLE <PKG-DIPOLE>`       | point dipole particles               | :doc:`pair\_style dipole/cut <pair_dipole>`        | dipole                                              | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`GPU <PKG-GPU>`             | GPU-enabled styles                   | :doc:`Section gpu <Speed_gpu>`                     | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | int     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`GRANULAR <PKG-GRANULAR>`   | granular systems                     | :doc:`Howto granular <Howto_granular>`             | pour                                                | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`KIM <PKG-KIM>`             | OpenKIM wrapper                      | :doc:`pair\_style kim <pair_kim>`                  | kim                                                 | ext     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`KOKKOS <PKG-KOKKOS>`       | Kokkos-enabled styles                | :doc:`Speed kokkos <Speed_kokkos>`                 | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`KSPACE <PKG-KSPACE>`       | long-range Coulombic solvers         | :doc:`kspace\_style <kspace_style>`                | peptide                                             | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`LATTE <PKG-LATTE>`         | quantum DFTB forces via LATTE        | :doc:`fix latte <fix_latte>`                       | latte                                               | ext     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`MANYBODY <PKG-MANYBODY>`   | many-body potentials                 | :doc:`pair\_style tersoff <pair_tersoff>`          | shear                                               | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`MC <PKG-MC>`               | Monte Carlo options                  | :doc:`fix gcmc <fix_gcmc>`                         | n/a                                                 | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`MESSAGE <PKG-MESSAGE>`     | client/server messaging              | :doc:`message <message>`                           | message                                             | int     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`MISC <PKG-MISC>`           | miscellaneous single-file commands   | n/a                                                | no                                                  | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`MOLECULE <PKG-MOLECULE>`   | molecular system force fields        | :doc:`Howto bioFF <Howto_bioFF>`                   | peptide                                             | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`MPIIO <PKG-MPIIO>`         | MPI parallel I/O dump and restart    | :doc:`dump <dump>`                                 | n/a                                                 | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`MSCG <PKG-MSCG>`           | multi-scale coarse-graining wrapper  | :doc:`fix mscg <fix_mscg>`                         | mscg                                                | ext     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`OPT <PKG-OPT>`             | optimized pair styles                | :doc:`Speed opt <Speed_opt>`                       | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`PERI <PKG-PERI>`           | Peridynamics models                  | :doc:`pair\_style peri <pair_peri>`                | peri                                                | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`POEMS <PKG-POEMS>`         | coupled rigid body motion            | :doc:`fix poems <fix_poems>`                       | rigid                                               | int     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`PYTHON <PKG-PYTHON>`       | embed Python code in an input script | :doc:`python <python>`                             | python                                              | sys     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`QEQ <PKG-QEQ>`             | QEq charge equilibration             | :doc:`fix qeq <fix_qeq>`                           | qeq                                                 | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`REPLICA <PKG-REPLICA2>`    | multi-replica methods                | :doc:`Howto replica <Howto_replica>`               | tad                                                 | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`RIGID <PKG-RIGID>`         | rigid bodies and constraints         | :doc:`fix rigid <fix_rigid>`                       | rigid                                               | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`SHOCK <PKG-SHOCK>`         | shock loading methods                | :doc:`fix msst <fix_msst>`                         | n/a                                                 | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`SNAP <PKG-SNAP>`           | quantum-fitted potential             | :doc:`pair\_style snap <pair_snap>`                | snap                                                | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`SPIN <PKG-SPIN>`           | magnetic atomic spin dynamics        | :doc:`Howto spins <Howto_spins>`                   | SPIN                                                | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`SRD <PKG-SRD>`             | stochastic rotation dynamics         | :doc:`fix srd <fix_srd>`                           | srd                                                 | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`VORONOI <PKG-VORONOI>`     | Voronoi tesselation                  | :doc:`compute voronoi/atom <compute_voronoi_atom>` | n/a                                                 | ext     |
++----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst
new file mode 100644
index 0000000000..702d014c57
--- /dev/null
+++ b/doc/src/Packages_user.rst
@@ -0,0 +1,126 @@
+User packages
+=============
+
+This is a list of user packages in LAMMPS.  The link for each package
+name gives more details.
+
+User packages have been contributed by users, and begin with the
+"user" prefix.  If a contribution is a single command (single file),
+it is typically in the user-misc package.  User packages don't
+necessarily meet the requirements of the :doc:`standard packages <Packages_standard>`. This means the developers will try
+to keep things working and usually can answer technical questions
+about compiling the package. If you have problems using a specific
+feature provided in a user package, you may need to contact the
+contributor directly to get help.  Information on how to submit
+additions you make to LAMMPS as single files or as a standard or user
+package is explained on the :doc:`Modify contribute <Modify_contribute>`
+doc page.
+
+The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory; USER/atc
+refers to the examples/USER/atc directory.  The "Library" column
+indicates whether an extra library is needed to build and use the
+package:
+
+* no  = no library
+* sys = system library: you likely have it on your machine
+* int = internal library: provided with LAMMPS, but you may need to build it
+* ext = external library: you will need to download and install it on your machine
+
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| Package                                        | Description                                                     | Doc page                                                                      | Example                                             | Library |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-ADIOS <PKG-USER-ADIOS>`             | dump output via ADIOS                                           | :doc:`dump adios <dump_adios>`                                                | USER/adios                                          | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-ATC <PKG-USER-ATC>`                 | Atom-to-Continuum coupling                                      | :doc:`fix atc <fix_atc>`                                                      | USER/atc                                            | int     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-AWPMD <PKG-USER-AWPMD>`             | wave packet MD                                                  | :doc:`pair\_style awpmd/cut <pair_awpmd>`                                     | USER/awpmd                                          | int     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-BOCS <PKG-USER-BOCS>`               | BOCS bottom up coarse graining                                  | :doc:`fix bocs <fix_bocs>`                                                    | USER/bocs                                           | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-CGDNA <PKG-USER-CGDNA>`             | coarse-grained DNA force fields                                 | src/USER-CGDNA/README                                                         | USER/cgdna                                          | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-CGSDK <PKG-USER-CGSDK>`             | SDK coarse-graining model                                       | :doc:`pair\_style lj/sdk <pair_sdk>`                                          | USER/cgsdk                                          | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-COLVARS <PKG-USER-COLVARS>`         | collective variables library                                    | :doc:`fix colvars <fix_colvars>`                                              | USER/colvars                                        | int     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | virtual x-ray and electron diffraction                          | :doc:`compute xrd <compute_xrd>`                                              | USER/diffraction                                    | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-DPD <PKG-USER-DPD>`                 | reactive dissipative particle dynamics                          | src/USER-DPD/README                                                           | USER/dpd                                            | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-DRUDE <PKG-USER-DRUDE>`             | Drude oscillators                                               | :doc:`Howto drude <Howto_drude>`                                              | USER/drude                                          | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-EFF <PKG-USER-EFF>`                 | electron force field                                            | :doc:`pair\_style eff/cut <pair_eff>`                                         | USER/eff                                            | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-FEP <PKG-USER-FEP>`                 | free energy perturbation                                        | :doc:`compute fep <compute_fep>`                                              | USER/fep                                            | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-H5MD <PKG-USER-H5MD>`               | dump output via HDF5                                            | :doc:`dump h5md <dump_h5md>`                                                  | n/a                                                 | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-INTEL <PKG-USER-INTEL>`             | optimized Intel CPU and KNL styles                              | :doc:`Speed intel <Speed_intel>`                                              | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-LB <PKG-USER-LB>`                   | Lattice Boltzmann fluid                                         | :doc:`fix lb/fluid <fix_lb_fluid>`                                            | USER/lb                                             | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`       | motion on 2d surfaces                                           | :doc:`fix manifoldforce <fix_manifoldforce>`                                  | USER/manifold                                       | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-MEAMC <PKG-USER-MEAMC>`             | modified EAM potential (C++)                                    | :doc:`pair\_style meam/c <pair_meamc>`                                        | meamc                                               | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-MESO <PKG-USER-MESO>`               | mesoscale DPD models                                            | :doc:`pair\_style edpd <pair_meso>`                                           | USER/meso                                           | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-MGPT <PKG-USER-MGPT>`               | fast MGPT multi-ion potentials                                  | :doc:`pair\_style mgpt <pair_mgpt>`                                           | USER/mgpt                                           | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-MISC <PKG-USER-MISC>`               | single-file contributions                                       | USER-MISC/README                                                              | USER/misc                                           | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-MOFFF <PKG-USER-MOFFF>`             | styles for `MOF-FF <MOFplus_>`_ force field                     | :doc:`pair\_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`                 | USER/mofff                                          | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`         | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>`                                            | n/a                                                 | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-NETCDF <PKG-USER-NETCDF>`           | dump output via NetCDF                                          | :doc:`dump netcdf <dump_netcdf>`                                              | n/a                                                 | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-OMP <PKG-USER-OMP>`                 | OpenMP-enabled styles                                           | :doc:`Speed omp <Speed_omp>`                                                  | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-PHONON <PKG-USER-PHONON>`           | phonon dynamical matrix                                         | :doc:`fix phonon <fix_phonon>`                                                | USER/phonon                                         | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-PLUMED <PKG-USER-PLUMED>`           | :ref:`PLUMED <PLUMED>` free energy library                      | :doc:`fix plumed <fix_plumed>`                                                | USER/plumed                                         | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-PTM <PKG-USER-PTM>`                 | Polyhedral Template Matching                                    | :doc:`compute ptm/atom <compute_ptm_atom>`                                    | n/a                                                 | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-QMMM <PKG-USER-QMMM>`               | QM/MM coupling                                                  | :doc:`fix qmmm <fix_qmmm>`                                                    | USER/qmmm                                           | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-QTB <PKG-USER-QTB>`                 | quantum nuclear effects                                         | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>`                       | qtb                                                 | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-QUIP <PKG-USER-QUIP>`               | QUIP/libatoms interface                                         | :doc:`pair\_style quip <pair_quip>`                                           | USER/quip                                           | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-REAXC <PKG-USER-REAXC>`             | ReaxFF potential (C/C++)                                        | :doc:`pair\_style reaxc <pair_reaxc>`                                         | reax                                                | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`       | wrapper on ScaFaCoS solver                                      | :doc:`kspace\_style scafacos <kspace_style>`                                  | USER/scafacos                                       | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-SDPD <PKG-USER-SDPD>`               | smoothed dissipative particle dynamics                          | :doc:`pair\_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd                                           | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-SMD <PKG-USER-SMD>`                 | smoothed Mach dynamics                                          | `SMD User Guide <PDF/SMD_LAMMPS_userguide.pdf>`_                              | USER/smd                                            | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>`             | second moment tight binding QEq potential                       | :doc:`pair\_style smtbq <pair_smtbq>`                                         | USER/smtbq                                          | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-SPH <PKG-USER-SPH>`                 | smoothed particle hydrodynamics                                 | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_                              | USER/sph                                            | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-TALLY <PKG-USER-TALLY>`             | pairwise tally computes                                         | :doc:`compute XXX/tally <compute_tally>`                                      | USER/tally                                          | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-UEF <PKG-USER-UEF>`                 | extensional flow                                                | :doc:`fix nvt/uef <fix_nh_uef>`                                               | USER/uef                                            | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-VTK <PKG-USER-VTK>`                 | dump output via VTK                                             | :doc:`compute vtk <dump_vtk>`                                                 | n/a                                                 | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-YAFF <PKG-USER-YAFF>`               | additional styles implemented in YAFF                           | :doc:`angle\_style cross <angle_cross>`                                       | USER/yaff                                           | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+
+.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
+
+
+
+.. _PLUMED: http://www.plumed.org
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_call.rst b/doc/src/Python_call.rst
new file mode 100644
index 0000000000..6b53b263c3
--- /dev/null
+++ b/doc/src/Python_call.rst
@@ -0,0 +1,84 @@
+Call Python from a LAMMPS input script
+======================================
+
+LAMMPS has several commands which can be used to invoke Python
+code directly from an input script:
+
+* :doc:`python <python>`
+* :doc:`variable python <variable>`
+* :doc:`fix python/invoke <fix_python_invoke>`
+* :doc:`pair\_style python <pair_python>`
+
+The :doc:`python <python>` command which can be used to define and
+execute a Python function that you write the code for.  The Python
+function can also be assigned to a LAMMPS python-style variable via
+the :doc:`variable <variable>` command.  Each time the variable is
+evaluated, either in the LAMMPS input script itself, or by another
+LAMMPS command that uses the variable, this will trigger the Python
+function to be invoked.
+
+The Python code for the function can be included directly in the input
+script or in an auxiliary file.  The function can have arguments which
+are mapped to LAMMPS variables (also defined in the input script) and
+it can return a value to a LAMMPS variable.  This is thus a mechanism
+for your input script to pass information to a piece of Python code,
+ask Python to execute the code, and return information to your input
+script.
+
+Note that a Python function can be arbitrarily complex.  It can import
+other Python modules, instantiate Python classes, call other Python
+functions, etc.  The Python code that you provide can contain more
+code than the single function.  It can contain other functions or
+Python classes, as well as global variables or other mechanisms for
+storing state between calls from LAMMPS to the function.
+
+The Python function you provide can consist of "pure" Python code that
+only performs operations provided by standard Python.  However, the
+Python function can also "call back" to LAMMPS through its
+Python-wrapped library interface, in the manner described in the
+:doc:`Python run <Python_run>` doc page.  This means it can issue LAMMPS
+input script commands or query and set internal LAMMPS state.  As an
+example, this can be useful in an input script to create a more
+complex loop with branching logic, than can be created using the
+simple looping and branching logic enabled by the :doc:`next <next>` and
+:doc:`if <if>` commands.
+
+See the :doc:`python <python>` doc page and the :doc:`variable <variable>`
+doc page for its python-style variables for more info, including
+examples of Python code you can write for both pure Python operations
+and callbacks to LAMMPS.
+
+The :doc:`fix python/invoke <fix_python_invoke>` command can execute
+Python code at selected timesteps during a simulation run.
+
+The :doc:`pair\_style python <pair_python>` command allows you to define
+pairwise potentials as python code which encodes a single pairwise
+interaction.  This is useful for rapid development and debugging of a
+new potential.
+
+To use any of these commands, you only need to build LAMMPS with the
+PYTHON package installed:
+
+
+.. parsed-literal::
+
+   make yes-python
+   make machine
+
+Note that this will link LAMMPS with the Python library on your
+system, which typically requires several auxiliary system libraries to
+also be linked.  The list of these libraries and the paths to find
+them are specified in the lib/python/Makefile.lammps file.  You need
+to insure that file contains the correct information for your version
+of Python and your machine to successfully build LAMMPS.  See the
+lib/python/README file for more info.
+
+If you want to write Python code with callbacks to LAMMPS, then you
+must also follow the steps summarized in the :doc:`Python run <Python_run>` doc page.  I.e. you must build LAMMPS as a shared
+library and insure that Python can find the python/lammps.py file and
+the shared library.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst
new file mode 100644
index 0000000000..f3d9e4983e
--- /dev/null
+++ b/doc/src/Python_examples.rst
@@ -0,0 +1,116 @@
+Example Python scripts that use LAMMPS
+======================================
+
+These are the Python scripts included as demos in the python/examples
+directory of the LAMMPS distribution, to illustrate the kinds of
+things that are possible when Python wraps LAMMPS.  If you create your
+own scripts, send them to us and we can include them in the LAMMPS
+distribution.
+
++----------------------------------------------------------------+--------------------------------------------------+
+| trivial.py                                                     | read/run a LAMMPS input script through Python    |
++----------------------------------------------------------------+--------------------------------------------------+
+| demo.py                                                        | invoke various LAMMPS library interface routines |
++----------------------------------------------------------------+--------------------------------------------------+
+| simple.py                                                      | run in parallel                                  |
++----------------------------------------------------------------+--------------------------------------------------+
+| similar to examples/COUPLE/simple/simple.cpp                   | split.py                                         |
++----------------------------------------------------------------+--------------------------------------------------+
+| same as simple.py but running in parallel on a subset of procs | gui.py                                           |
++----------------------------------------------------------------+--------------------------------------------------+
+| GUI go/stop/temperature-slider to control LAMMPS               | plot.py                                          |
++----------------------------------------------------------------+--------------------------------------------------+
+| real-time temperature plot with GnuPlot via Pizza.py           | viz\_tool.py                                     |
++----------------------------------------------------------------+--------------------------------------------------+
+| real-time viz via some viz package                             | vizplotgui\_tool.py                              |
++----------------------------------------------------------------+--------------------------------------------------+
+| combination of viz\_tool.py and plot.py and gui.py             |                                                  |
++----------------------------------------------------------------+--------------------------------------------------+
+
+
+----------
+
+
+For the viz\_tool.py and vizplotgui\_tool.py commands, replace "tool"
+with "gl" or "atomeye" or "pymol" or "vmd", depending on what
+visualization package you have installed.
+
+Note that for GL, you need to be able to run the Pizza.py GL tool,
+which is included in the pizza sub-directory.  See the `Pizza.py doc pages <pizza_>`_ for more info:
+
+.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
+
+
+
+Note that for AtomEye, you need version 3, and there is a line in the
+scripts that specifies the path and name of the executable.  See the
+AtomEye WWW pages `here <atomeye_>`_ or `here <atomeye3_>`_ for more details:
+
+
+.. parsed-literal::
+
+   http://mt.seas.upenn.edu/Archive/Graphics/A
+   http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
+
+.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
+
+
+
+.. _atomeye3: http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
+
+
+
+The latter link is to AtomEye 3 which has the scripting
+capability needed by these Python scripts.
+
+Note that for PyMol, you need to have built and installed the
+open-source version of PyMol in your Python, so that you can import it
+from a Python script.  See the PyMol WWW pages `here <pymolhome_>`_ or
+`here <pymolopen_>`_ for more details:
+
+
+.. parsed-literal::
+
+   http://www.pymol.org
+   http://sourceforge.net/scm/?type=svn&group_id=4546
+
+.. _pymolhome: http://www.pymol.org
+
+
+
+.. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546
+
+
+
+The latter link is to the open-source version.
+
+Note that for VMD, you need a fairly current version (1.8.7 works for
+me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
+variables that have to match the VMD installation on your system.
+
+
+----------
+
+
+See the python/README file for instructions on how to run them and the
+source code for individual scripts for comments about what they do.
+
+Here are screenshots of the vizplotgui\_tool.py script in action for
+different visualization package options.  Click to see larger images:
+
+.. image:: JPG/screenshot_gl_small.jpg
+   :target: JPG/screenshot_gl.jpg
+
+.. image:: JPG/screenshot_atomeye_small.jpg
+   :target: JPG/screenshot_atomeye.jpg
+
+.. image:: JPG/screenshot_pymol_small.jpg
+   :target: JPG/screenshot_pymol.jpg
+
+.. image:: JPG/screenshot_vmd_small.jpg
+   :target: JPG/screenshot_vmd.jpg
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_head.rst b/doc/src/Python_head.rst
new file mode 100644
index 0000000000..a9b79b5305
--- /dev/null
+++ b/doc/src/Python_head.rst
@@ -0,0 +1,49 @@
+Use Python with LAMMPS
+**********************
+
+These doc pages describe various ways that LAMMPS and Python can be
+used together.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Python_overview
+   Python_run
+   Python_shlib
+   Python_install
+   Python_mpi
+   Python_test
+   Python_library
+   Python_pylammps
+   Python_examples
+   Python_call
+
+If you're not familiar with `Python <http://www.python.org>`_, it's a
+powerful scripting and programming language which can do most
+everything that lower-level languages like C or C++ can do in fewer
+lines of code.  The only drawback is slower execution speed.  Python
+is also easy to use as a "glue" language to drive a program through
+its library interface, or to hook multiple pieces of software
+together, such as a simulation code plus a visualization tool, or to
+run a coupled multiscale or multiphysics model.
+
+See the :doc:`Howto\_couple <Howto_couple>` doc page for more ideas about
+coupling LAMMPS to other codes.  See the :doc:`Howto library <Howto_library>` doc page for a description of the LAMMPS
+library interface provided in src/library.h and src/library.h.  That
+interface is exposed to Python either when calling LAMMPS from Python
+or when calling Python from a LAMMPS input script and then calling
+back to LAMMPS from Python code.  The library interface is designed to
+be easy to add functionality to.  Thus the Python interface to LAMMPS
+is also easy to extend as well.
+
+If you create interesting Python scripts that run LAMMPS or
+interesting Python functions that can be called from a LAMMPS input
+script, that you think would be generally useful, please post them as
+a pull request to our `GitHub site <https://github.com/lammps/lammps>`_,
+and they can be added to the LAMMPS distribution or webpage.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst
new file mode 100644
index 0000000000..29d9964c64
--- /dev/null
+++ b/doc/src/Python_install.rst
@@ -0,0 +1,70 @@
+Installing LAMMPS in Python
+===========================
+
+For Python to invoke LAMMPS, there are 2 files it needs to know about:
+
+* python/lammps.py
+* liblammps.so or liblammps.dylib
+
+The python source code in lammps.py is the Python wrapper on the
+LAMMPS library interface. The liblammps.so or liblammps.dylib file
+is the shared LAMMPS library that Python loads dynamically.
+
+You can achieve that Python can find these files in one of two ways:
+
+* set two environment variables pointing to the location in the source tree
+* run "make install-python" or run the python/install.py script explicitly
+
+When calling "make install-python" LAMMPS will try to install the
+python module and the shared library into the python site-packages folders;
+either the system-wide ones, or the local users ones (in case of insufficient
+permissions for the global install). Python will then find the module
+and shared library file automatically. The exact location of these folders
+depends on your python version and your operating system.
+
+If you set the paths to these files as environment variables, you only
+have to do it once.  For the csh or tcsh shells, add something like
+this to your ~/.cshrc file, one line for each of the two files:
+
+
+.. parsed-literal::
+
+   setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
+   setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
+
+On MacOSX you may also need to set DYLD\_LIBRARY\_PATH accordingly.
+For Bourne/Korn shells accordingly into the corresponding files using
+the "export" shell builtin.
+
+If you use "make install-python" or the python/install.py script, you need
+to invoke it every time you rebuild LAMMPS (as a shared library) or
+make changes to the python/lammps.py file, so that the site-packages
+files are updated with the new version.
+
+If the default settings of "make install-python" are not what you want,
+you can invoke install.py from the python directory manually as
+
+
+.. parsed-literal::
+
+   % python install.py -m \<python module\> -l <shared library> -v <version.h file> [-d \<pydir\>]
+
+* The -m flag points to the lammps.py python module file to be installed,
+* the -l flag points to the LAMMPS shared library file to be installed,
+* the -v flag points to the version.h file in the LAMMPS source
+* and the optional -d flag to a custom (legacy) installation folder
+
+If you use a legacy installation folder, you will need to set your
+PYTHONPATH and LD\_LIBRARY\_PATH (and/or DYLD\_LIBRARY\_PATH) environment
+variables accordingly, as described above.
+
+Note that if you want Python to be able to load different versions of
+the LAMMPS shared library (see :doc:`this section <Python_shlib>`), you will
+need to manually copy files like liblammps\_g++.so into the appropriate
+system directory.  This is not needed if you set the LD\_LIBRARY\_PATH
+environment variable as described above.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_library.rst b/doc/src/Python_library.rst
new file mode 100644
index 0000000000..e079df1a04
--- /dev/null
+++ b/doc/src/Python_library.rst
@@ -0,0 +1,280 @@
+Python library interface
+========================
+
+As described previously, the Python interface to LAMMPS consists of a
+Python "lammps" module, the source code for which is in
+python/lammps.py, which creates a "lammps" object, with a set of
+methods that can be invoked on that object.  The sample Python code
+below assumes you have first imported the "lammps" module in your
+Python script, as follows:
+
+
+.. code-block:: Python
+
+   from lammps import lammps
+
+These are the methods defined by the lammps module.  If you look at
+the files src/library.cpp and src/library.h you will see they
+correspond one-to-one with calls you can make to the LAMMPS library
+from a C++ or C or Fortran program, and which are described on the
+:doc:`Howto library <Howto_library>` doc page.
+
+The python/examples directory has Python scripts which show how Python
+can run LAMMPS, grab data, change it, and put it back into LAMMPS.
+
+
+.. code-block:: Python
+
+   lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
+                            # 4 optional args are allowed: name, cmdargs, ptr, comm
+   lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
+   lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
+   lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
+   lmp = lammps(name="g++",cmdargs=list)    # add LAMMPS command-line args, e.g. list = ["-echo","screen"]
+
+   lmp.close()              # destroy a LAMMPS object
+
+   version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
+
+   lmp.file(file)           # run an entire input script, file = "in.lj"
+   lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100"
+   lmp.commands_list(cmdlist)     # invoke commands in cmdlist = **"run 10", "run 20"**
+   lmp.commands_string(multicmd)  # invoke commands in multicmd = "run 10\nrun 20"
+
+   size = lmp.extract_setting(name)     # return data type info
+
+   xlo = lmp.extract_global(name,type)  # extract a global quantity
+                                        # name = "boxxlo", "nlocal", etc
+                                        # type = 0 = int
+                                        #        1 = double
+
+   boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box()  # extract box info
+
+   coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
+                                             # name = "x", "type", etc
+                                             # type = 0 = vector of ints
+                                             #        1 = array of ints
+                                             #        2 = vector of doubles
+                                             #        3 = array of doubles
+
+   eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
+   v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
+                                             # id = ID of compute or fix
+                                             # style = 0 = global data
+                                             #         1 = per-atom data
+                                             #         2 = local data
+                                             # type = 0 = scalar
+                                             #        1 = vector
+                                             #        2 = array
+                                             # i,j = indices of value in global vector or array
+
+   var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
+                                                # name = name of variable
+                                                # group = group ID (ignored for equal-style variables)
+                                                # flag = 0 = equal-style variable
+                                                #        1 = atom-style variable
+
+   value = lmp.get_thermo(name)              # return current value of a thermo keyword
+   natoms = lmp.get_natoms()                 # total # of atoms as int
+
+   flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
+   lmp.reset_box(boxlo,boxhi,xy,yz,xz)       # reset the simulation box size
+
+   data = lmp.gather_atoms(name,type,count)  # return per-atom property of all atoms gathered into data, ordered by atom ID
+                                             # name = "x", "charge", "type", etc
+   data = lmp.gather_atoms_concat(name,type,count)  # ditto, but concatenated atom values from each proc (unordered)
+   data = lmp.gather_atoms_subset(name,type,count,ndata,ids)  # ditto, but for subset of Ndata atoms with IDs
+
+   lmp.scatter_atoms(name,type,count,data)   # scatter per-atom property to all atoms from data, ordered by atom ID
+                                             # name = "x", "charge", "type", etc
+                                             # count = # of per-atom values, 1 or 3, etc
+
+   lmp.scatter_atoms_subset(name,type,count,ndata,ids,data)  # ditto, but for subset of Ndata atoms with IDs
+
+   lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed)   # create N atoms with IDs, types, x, v, and image flags
+
+
+----------
+
+
+The lines
+
+
+.. code-block:: Python
+
+   from lammps import lammps
+   lmp = lammps()
+
+create an instance of LAMMPS, wrapped in a Python class by the lammps
+Python module, and return an instance of the Python class as lmp.  It
+is used to make all subsequent calls to the LAMMPS library.
+
+Additional arguments to lammps() can be used to tell Python the name
+of the shared library to load or to pass arguments to the LAMMPS
+instance, the same as if LAMMPS were launched from a command-line
+prompt.
+
+If the ptr argument is set like this:
+
+
+.. code-block:: Python
+
+   lmp = lammps(ptr=lmpptr)
+
+then lmpptr must be an argument passed to Python via the LAMMPS
+:doc:`python <python>` command, when it is used to define a Python
+function that is invoked by the LAMMPS input script.  This mode of
+calling Python from LAMMPS is described in the :doc:`Python call <Python_call>` doc page.  The variable lmpptr refers to the
+instance of LAMMPS that called the embedded Python interpreter.  Using
+it as an argument to lammps() allows the returned Python class
+instance "lmp" to make calls to that instance of LAMMPS.  See the
+:doc:`python <python>` command doc page for examples using this syntax.
+
+Note that you can create multiple LAMMPS objects in your Python
+script, and coordinate and run multiple simulations, e.g.
+
+
+.. code-block:: Python
+
+   from lammps import lammps
+   lmp1 = lammps()
+   lmp2 = lammps()
+   lmp1.file("in.file1")
+   lmp2.file("in.file2")
+
+The file(), command(), commands\_list(), commands\_string() methods
+allow an input script, a single command, or multiple commands to be
+invoked.
+
+The extract\_setting(), extract\_global(), extract\_box(),
+extract\_atom(), extract\_compute(), extract\_fix(), and
+extract\_variable() methods return values or pointers to data
+structures internal to LAMMPS.
+
+For extract\_global() see the src/library.cpp file for the list of
+valid names.  New names could easily be added.  A double or integer is
+returned.  You need to specify the appropriate data type via the type
+argument.
+
+For extract\_atom(), a pointer to internal LAMMPS atom-based data is
+returned, which you can use via normal Python subscripting.  See the
+extract() method in the src/atom.cpp file for a list of valid names.
+Again, new names could easily be added if the property you want is not
+listed.  A pointer to a vector of doubles or integers, or a pointer to
+an array of doubles (double \*\*) or integers (int \*\*) is returned.  You
+need to specify the appropriate data type via the type argument.
+
+For extract\_compute() and extract\_fix(), the global, per-atom, or
+local data calculated by the compute or fix can be accessed.  What is
+returned depends on whether the compute or fix calculates a scalar or
+vector or array.  For a scalar, a single double value is returned.  If
+the compute or fix calculates a vector or array, a pointer to the
+internal LAMMPS data is returned, which you can use via normal Python
+subscripting.  The one exception is that for a fix that calculates a
+global vector or array, a single double value from the vector or array
+is returned, indexed by I (vector) or I and J (array).  I,J are
+zero-based indices.  The I,J arguments can be left out if not needed.
+See the :doc:`Howto output <Howto_output>` doc page for a discussion of
+global, per-atom, and local data, and of scalar, vector, and array
+data types.  See the doc pages for individual :doc:`computes <compute>`
+and :doc:`fixes <fix>` for a description of what they calculate and
+store.
+
+For extract\_variable(), an :doc:`equal-style or atom-style variable <variable>` is evaluated and its result returned.
+
+For equal-style variables a single double value is returned and the
+group argument is ignored.  For atom-style variables, a vector of
+doubles is returned, one value per atom, which you can use via normal
+Python subscripting. The values will be zero for atoms not in the
+specified group.
+
+The get\_thermo() method returns the current value of a thermo
+keyword as a float.
+
+The get\_natoms() method returns the total number of atoms in the
+simulation, as an int.
+
+The set\_variable() method sets an existing string-style variable to a
+new string value, so that subsequent LAMMPS commands can access the
+variable.
+
+The reset\_box() method resets the size and shape of the simulation
+box, e.g. as part of restoring a previously extracted and saved state
+of a simulation.
+
+The gather methods collect peratom info of the requested type (atom
+coords, atom types, forces, etc) from all processors, and returns the
+same vector of values to each calling processor.  The scatter
+functions do the inverse.  They distribute a vector of peratom values,
+passed by all calling processors, to individual atoms, which may be
+owned by different processors.
+
+Note that the data returned by the gather methods,
+e.g. gather\_atoms("x"), is different from the data structure returned
+by extract\_atom("x") in four ways.  (1) Gather\_atoms() returns a
+vector which you index as x[i]; extract\_atom() returns an array
+which you index as x[i][j].  (2) Gather\_atoms() orders the atoms
+by atom ID while extract\_atom() does not.  (3) Gather\_atoms() returns
+a list of all atoms in the simulation; extract\_atoms() returns just
+the atoms local to each processor.  (4) Finally, the gather\_atoms()
+data structure is a copy of the atom coords stored internally in
+LAMMPS, whereas extract\_atom() returns an array that effectively
+points directly to the internal data.  This means you can change
+values inside LAMMPS from Python by assigning a new values to the
+extract\_atom() array.  To do this with the gather\_atoms() vector, you
+need to change values in the vector, then invoke the scatter\_atoms()
+method.
+
+For the scatter methods, the array of coordinates passed to must be a
+ctypes vector of ints or doubles, allocated and initialized something
+like this:
+
+
+.. code-block:: Python
+
+   from ctypes import \*
+   natoms = lmp.get_natoms()
+   n3 = 3\*natoms
+   x = (n3\*c_double)()
+   x[0] = x coord of atom with ID 1
+   x[1] = y coord of atom with ID 1
+   x[2] = z coord of atom with ID 1
+   x[3] = x coord of atom with ID 2
+   ...
+   x[n3-1] = z coord of atom with ID natoms
+   lmp.scatter_atoms("x",1,3,x)
+
+Alternatively, you can just change values in the vector returned by
+the gather methods, since they are also ctypes vectors.
+
+
+----------
+
+
+As noted above, these Python class methods correspond one-to-one with
+the functions in the LAMMPS library interface in src/library.cpp and
+library.h.  This means you can extend the Python wrapper via the
+following steps:
+
+* Add a new interface function to src/library.cpp and
+  src/library.h.
+* Rebuild LAMMPS as a shared library.
+* Add a wrapper method to python/lammps.py for this interface
+  function.
+* You should now be able to invoke the new interface function from a
+  Python script.
+
+
+----------
+
+.. autoclass:: lammps.lammps
+   :members:
+   :no-undoc-members:
+
+.. autoclass:: lammps.NeighList
+   :members:
+   :no-undoc-members:
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt
deleted file mode 100644
index d9ddbe0cbb..0000000000
--- a/doc/src/Python_library.txt
+++ /dev/null
@@ -1,256 +0,0 @@
-"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Python library interface :h3
-
-As described previously, the Python interface to LAMMPS consists of a
-Python "lammps" module, the source code for which is in
-python/lammps.py, which creates a "lammps" object, with a set of
-methods that can be invoked on that object.  The sample Python code
-below assumes you have first imported the "lammps" module in your
-Python script, as follows:
-
-from lammps import lammps :pre
-
-These are the methods defined by the lammps module.  If you look at
-the files src/library.cpp and src/library.h you will see they
-correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program, and which are described on the
-"Howto library"_Howto_library.html doc page.
-
-The python/examples directory has Python scripts which show how Python
-can run LAMMPS, grab data, change it, and put it back into LAMMPS.
-
-lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-                         # 4 optional args are allowed: name, cmdargs, ptr, comm
-lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
-lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
-lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
-lmp = lammps(name="g++",cmdargs=list)    # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre
-
-lmp.close()              # destroy a LAMMPS object :pre
-
-version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre
-
-lmp.file(file)           # run an entire input script, file = "in.lj"
-lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100"
-lmp.commands_list(cmdlist)     # invoke commands in cmdlist = ["run 10", "run 20"]
-lmp.commands_string(multicmd)  # invoke commands in multicmd = "run 10\nrun 20" :pre
-
-size = lmp.extract_setting(name)     # return data type info :pre
-
-xlo = lmp.extract_global(name,type)  # extract a global quantity
-                                     # name = "boxxlo", "nlocal", etc
-                                     # type = 0 = int
-                                     #        1 = double :pre
-
-boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box()  # extract box info :pre
-
-coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
-                                          # name = "x", "type", etc
-                                          # type = 0 = vector of ints
-                                          #        1 = array of ints
-                                          #        2 = vector of doubles
-                                          #        3 = array of doubles :pre
-
-eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
-v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
-                                          # id = ID of compute or fix
-                                          # style = 0 = global data
-                                          #         1 = per-atom data
-                                          #         2 = local data
-                                          # type = 0 = scalar
-                                          #        1 = vector
-                                          #        2 = array
-                                          # i,j = indices of value in global vector or array :pre
-
-var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
-                                             # name = name of variable
-                                             # group = group ID (ignored for equal-style variables)
-                                             # flag = 0 = equal-style variable
-                                             #        1 = atom-style variable :pre
-
-value = lmp.get_thermo(name)              # return current value of a thermo keyword
-natoms = lmp.get_natoms()                 # total # of atoms as int :pre
-
-flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
-lmp.reset_box(boxlo,boxhi,xy,yz,xz)       # reset the simulation box size :pre
-
-data = lmp.gather_atoms(name,type,count)  # return per-atom property of all atoms gathered into data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-data = lmp.gather_atoms_concat(name,type,count)  # ditto, but concatenated atom values from each proc (unordered)
-data = lmp.gather_atoms_subset(name,type,count,ndata,ids)  # ditto, but for subset of Ndata atoms with IDs :pre
-
-lmp.scatter_atoms(name,type,count,data)   # scatter per-atom property to all atoms from data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-                                          # count = # of per-atom values, 1 or 3, etc :pre
-lmp.scatter_atoms_subset(name,type,count,ndata,ids,data)  # ditto, but for subset of Ndata atoms with IDs :pre
-
-lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed)   # create N atoms with IDs, types, x, v, and image flags :pre
-
-:line
-
-The lines
-
-from lammps import lammps
-lmp = lammps() :pre
-
-create an instance of LAMMPS, wrapped in a Python class by the lammps
-Python module, and return an instance of the Python class as lmp.  It
-is used to make all subsequent calls to the LAMMPS library.
-
-Additional arguments to lammps() can be used to tell Python the name
-of the shared library to load or to pass arguments to the LAMMPS
-instance, the same as if LAMMPS were launched from a command-line
-prompt.
-
-If the ptr argument is set like this:
-
-lmp = lammps(ptr=lmpptr) :pre
-
-then lmpptr must be an argument passed to Python via the LAMMPS
-"python"_python.html command, when it is used to define a Python
-function that is invoked by the LAMMPS input script.  This mode of
-calling Python from LAMMPS is described in the "Python
-call"_Python_call.html doc page.  The variable lmpptr refers to the
-instance of LAMMPS that called the embedded Python interpreter.  Using
-it as an argument to lammps() allows the returned Python class
-instance "lmp" to make calls to that instance of LAMMPS.  See the
-"python"_python.html command doc page for examples using this syntax.
-
-Note that you can create multiple LAMMPS objects in your Python
-script, and coordinate and run multiple simulations, e.g.
-
-from lammps import lammps
-lmp1 = lammps()
-lmp2 = lammps()
-lmp1.file("in.file1")
-lmp2.file("in.file2") :pre
-
-The file(), command(), commands_list(), commands_string() methods
-allow an input script, a single command, or multiple commands to be
-invoked.
-
-The extract_setting(), extract_global(), extract_box(),
-extract_atom(), extract_compute(), extract_fix(), and
-extract_variable() methods return values or pointers to data
-structures internal to LAMMPS.
-
-For extract_global() see the src/library.cpp file for the list of
-valid names.  New names could easily be added.  A double or integer is
-returned.  You need to specify the appropriate data type via the type
-argument.
-
-For extract_atom(), a pointer to internal LAMMPS atom-based data is
-returned, which you can use via normal Python subscripting.  See the
-extract() method in the src/atom.cpp file for a list of valid names.
-Again, new names could easily be added if the property you want is not
-listed.  A pointer to a vector of doubles or integers, or a pointer to
-an array of doubles (double **) or integers (int **) is returned.  You
-need to specify the appropriate data type via the type argument.
-
-For extract_compute() and extract_fix(), the global, per-atom, or
-local data calculated by the compute or fix can be accessed.  What is
-returned depends on whether the compute or fix calculates a scalar or
-vector or array.  For a scalar, a single double value is returned.  If
-the compute or fix calculates a vector or array, a pointer to the
-internal LAMMPS data is returned, which you can use via normal Python
-subscripting.  The one exception is that for a fix that calculates a
-global vector or array, a single double value from the vector or array
-is returned, indexed by I (vector) or I and J (array).  I,J are
-zero-based indices.  The I,J arguments can be left out if not needed.
-See the "Howto output"_Howto_output.html doc page for a discussion of
-global, per-atom, and local data, and of scalar, vector, and array
-data types.  See the doc pages for individual "computes"_compute.html
-and "fixes"_fix.html for a description of what they calculate and
-store.
-
-For extract_variable(), an "equal-style or atom-style
-variable"_variable.html is evaluated and its result returned.
-
-For equal-style variables a single double value is returned and the
-group argument is ignored.  For atom-style variables, a vector of
-doubles is returned, one value per atom, which you can use via normal
-Python subscripting. The values will be zero for atoms not in the
-specified group.
-
-The get_thermo() method returns the current value of a thermo
-keyword as a float.
-
-The get_natoms() method returns the total number of atoms in the
-simulation, as an int.
-
-The set_variable() method sets an existing string-style variable to a
-new string value, so that subsequent LAMMPS commands can access the
-variable.
-
-The reset_box() method resets the size and shape of the simulation
-box, e.g. as part of restoring a previously extracted and saved state
-of a simulation.
-
-The gather methods collect peratom info of the requested type (atom
-coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each calling processor.  The scatter
-functions do the inverse.  They distribute a vector of peratom values,
-passed by all calling processors, to individual atoms, which may be
-owned by different processors.
-
-Note that the data returned by the gather methods,
-e.g. gather_atoms("x"), is different from the data structure returned
-by extract_atom("x") in four ways.  (1) Gather_atoms() returns a
-vector which you index as x\[i\]; extract_atom() returns an array
-which you index as x\[i\]\[j\].  (2) Gather_atoms() orders the atoms
-by atom ID while extract_atom() does not.  (3) Gather_atoms() returns
-a list of all atoms in the simulation; extract_atoms() returns just
-the atoms local to each processor.  (4) Finally, the gather_atoms()
-data structure is a copy of the atom coords stored internally in
-LAMMPS, whereas extract_atom() returns an array that effectively
-points directly to the internal data.  This means you can change
-values inside LAMMPS from Python by assigning a new values to the
-extract_atom() array.  To do this with the gather_atoms() vector, you
-need to change values in the vector, then invoke the scatter_atoms()
-method.
-
-For the scatter methods, the array of coordinates passed to must be a
-ctypes vector of ints or doubles, allocated and initialized something
-like this:
-
-from ctypes import *
-natoms = lmp.get_natoms()
-n3 = 3*natoms
-x = (n3*c_double)()
-x\[0\] = x coord of atom with ID 1
-x\[1\] = y coord of atom with ID 1
-x\[2\] = z coord of atom with ID 1
-x\[3\] = x coord of atom with ID 2
-...
-x\[n3-1\] = z coord of atom with ID natoms
-lmp.scatter_atoms("x",1,3,x) :pre
-
-Alternatively, you can just change values in the vector returned by
-the gather methods, since they are also ctypes vectors.
-
-:line
-
-As noted above, these Python class methods correspond one-to-one with
-the functions in the LAMMPS library interface in src/library.cpp and
-library.h.  This means you can extend the Python wrapper via the
-following steps:
-
-Add a new interface function to src/library.cpp and
-src/library.h. :ulb,l
-
-Rebuild LAMMPS as a shared library. :l
-
-Add a wrapper method to python/lammps.py for this interface
-function. :l
-
-You should now be able to invoke the new interface function from a
-Python script. :l
-:ule
diff --git a/doc/src/Python_mpi.rst b/doc/src/Python_mpi.rst
new file mode 100644
index 0000000000..ec5ec35ceb
--- /dev/null
+++ b/doc/src/Python_mpi.rst
@@ -0,0 +1,79 @@
+Extending Python to run in parallel
+===================================
+
+If you wish to run LAMMPS in parallel from Python, you need to extend
+your Python with an interface to MPI.  This also allows you to
+make MPI calls directly from Python in your script, if you desire.
+
+We recommend use of mpi4py:
+
+* `PyPar <https://github.com/daleroberts/pypar>`_
+
+As of version 2.0.0 it allows passing a custom MPI communicator to
+the LAMMPS constructor, which means one can easily run one or more
+LAMMPS instances on subsets of the total MPI ranks.
+
+To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it
+and from its main directory, type
+
+
+.. parsed-literal::
+
+   python setup.py build
+   sudo python setup.py install
+
+Again, the "sudo" is only needed if required to copy mpi4py files into
+your Python distribution's site-packages directory. To install with
+user privilege into the user local directory type
+
+
+.. parsed-literal::
+
+   python setup.py install --user
+
+If you have successfully installed mpi4py, you should be able to run
+Python and type
+
+
+.. parsed-literal::
+
+   from mpi4py import MPI
+
+without error.  You should also be able to run python in parallel
+on a simple test script
+
+
+.. parsed-literal::
+
+   % mpirun -np 4 python test.py
+
+where test.py contains the lines
+
+
+.. parsed-literal::
+
+   from mpi4py import MPI
+   comm = MPI.COMM_WORLD
+   print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size())
+
+and see one line of output for each processor you run on.
+
+.. note::
+
+   To use mpi4py and LAMMPS in parallel from Python, you must
+   insure both are using the same version of MPI.  If you only have one
+   MPI installed on your system, this is not an issue, but it can be if
+   you have multiple MPIs.  Your LAMMPS build is explicit about which MPI
+   it is using, since you specify the details in your lo-level
+   src/MAKE/Makefile.foo file.  Mpi4py uses the "mpicc" command to find
+   information about the MPI it uses to build against.  And it tries to
+   load "libmpi.so" from the LD\_LIBRARY\_PATH.  This may or may not find
+   the MPI library that LAMMPS is using.  If you have problems running
+   both mpi4py and LAMMPS together, this is an issue you may need to
+   address, e.g. by moving other MPI installations so that mpi4py finds
+   the right one.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_overview.rst b/doc/src/Python_overview.rst
new file mode 100644
index 0000000000..173ab06ade
--- /dev/null
+++ b/doc/src/Python_overview.rst
@@ -0,0 +1,30 @@
+Overview of Python and LAMMPS
+=============================
+
+LAMMPS can work together with Python in three ways.  First, Python can
+wrap LAMMPS through the its :doc:`library interface <Howto_library>`, so
+that a Python script can create one or more instances of LAMMPS and
+launch one or more simulations.  In Python lingo, this is called
+"extending" Python with a LAMMPS module.
+
+Second, a lower-level Python interface can be used indirectly through
+the provided PyLammps and IPyLammps wrapper classes, written in Python.
+These wrappers try to simplify the usage of LAMMPS in Python by
+providing an object-based interface to common LAMMPS functionality.
+They also reduces the amount of code necessary to parameterize LAMMPS
+scripts through Python and make variables and computes directly
+accessible.
+
+Third, LAMMPS can use the Python interpreter, so that a LAMMPS
+input script or styles can invoke Python code directly, and pass
+information back-and-forth between the input script and Python
+functions you write.  This Python code can also callback to LAMMPS
+to query or change its attributes through the LAMMPS Python module
+mentioned above.  In Python lingo, this is "embedding" Python in
+LAMMPS.  When used in this mode, Python can perform script operations
+that the simple LAMMPS input script syntax can not.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_pylammps.rst b/doc/src/Python_pylammps.rst
new file mode 100644
index 0000000000..f8f653afae
--- /dev/null
+++ b/doc/src/Python_pylammps.rst
@@ -0,0 +1,10 @@
+PyLammps interface
+==================
+
+PyLammps is a Python wrapper class which can be created on its own or
+use an existing lammps Python object.  It has its own :doc:`Howto pylammps <Howto_pylammps>` doc page.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_run.rst b/doc/src/Python_run.rst
new file mode 100644
index 0000000000..31ce016612
--- /dev/null
+++ b/doc/src/Python_run.rst
@@ -0,0 +1,37 @@
+Run LAMMPS from Python
+======================
+
+The LAMMPS distribution includes a python directory with all you need
+to run LAMMPS from Python.  The python/lammps.py file wraps the LAMMPS
+library interface, with one wrapper function per LAMMPS library
+function.  This file makes it is possible to do the following either
+from a Python script, or interactively from a Python prompt: create
+one or more instances of LAMMPS, invoke LAMMPS commands or give it an
+input script, run LAMMPS incrementally, extract LAMMPS results, an
+modify internal LAMMPS variables.  From a Python script you can do
+this in serial or parallel.  Running Python interactively in parallel
+does not generally work, unless you have a version of Python that
+extends Python to enable multiple instances of Python to read what you
+type.
+
+To do all of this, you must first build LAMMPS as a shared library,
+then insure that your Python can find the python/lammps.py file and
+the shared library.
+
+Two advantages of using Python to run LAMMPS are how concise the
+language is, and that it can be run interactively, enabling rapid
+development and debugging.  If you use it to mostly invoke costly
+operations within LAMMPS, such as running a simulation for a
+reasonable number of timesteps, then the overhead cost of invoking
+LAMMPS through Python will be negligible.
+
+The Python wrapper for LAMMPS uses the "ctypes" package in Python,
+which auto-generates the interface code needed between Python and a
+set of C-style library functions.  Ctypes is part of standard Python
+for versions 2.5 and later.  You can check which version of Python you
+have by simply typing "python" at a shell prompt.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_shlib.rst b/doc/src/Python_shlib.rst
new file mode 100644
index 0000000000..9dd1fbde6d
--- /dev/null
+++ b/doc/src/Python_shlib.rst
@@ -0,0 +1,86 @@
+Build LAMMPS as a shared library
+================================
+
+Build LAMMPS as a shared library using make
+-------------------------------------------
+
+Instructions on how to build LAMMPS as a shared library are given on
+the :doc:`Build\_basics <Build_basics>` doc page.  A shared library is
+one that is dynamically loadable, which is what Python requires to
+wrap LAMMPS.  On Linux this is a library file that ends in ".so", not
+".a".
+
+From the src directory, type
+
+
+.. parsed-literal::
+
+   make foo mode=shlib
+
+where foo is the machine target name, such as mpi or serial.
+This should create the file liblammps\_foo.so in the src directory, as
+well as a soft link liblammps.so, which is what the Python wrapper will
+load by default.  Note that if you are building multiple machine
+versions of the shared library, the soft link is always set to the
+most recently built version.
+
+.. note::
+
+   If you are building LAMMPS with an MPI or FFT library or other
+   auxiliary libraries (used by various packages), then all of these
+   extra libraries must also be shared libraries.  If the LAMMPS
+   shared-library build fails with an error complaining about this, see
+   the :doc:`Build\_basics <Build_basics>` doc page.
+
+Build LAMMPS as a shared library using CMake
+--------------------------------------------
+
+When using CMake the following two options are necessary to generate the LAMMPS
+shared library:
+
+
+.. parsed-literal::
+
+   -D BUILD_LIB=on            # enable building LAMMPS as a library
+   -D BUILD_SHARED_LIBS=on    # enable building of LAMMPS shared library (both options are needed!)
+
+What this does is create a liblammps.so which contains the majority of LAMMPS
+code. The generated lmp binary also dynamically links to this library. This
+means that either this liblammps.so file has to be in the same directory, a system
+library path (e.g. /usr/lib64/) or in the LD\_LIBRARY\_PATH.
+
+If you want to use the shared library with Python the recommended way is to create a virtualenv and use it as
+CMAKE\_INSTALL\_PREFIX.
+
+
+.. parsed-literal::
+
+   # create virtualenv
+   virtualenv --python=$(which python3) myenv3
+   source myenv3/bin/activate
+
+   # build library
+   mkdir build
+   cd build
+   cmake -D PKG_PYTHON=on -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on -D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV ../cmake
+   make -j 4
+
+   # install into prefix
+   make install
+
+This will also install the Python module into your virtualenv. Since virtualenv
+doesn't change your LD\_LIBRARY\_PATH, you still need to add its lib64 folder to
+it, which contains the installed liblammps.so.
+
+
+.. parsed-literal::
+
+   export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib64:$LD_LIBRARY_PATH
+
+Starting Python outside (!) of your build directory, but with the virtualenv
+enabled and with the LD\_LIBRARY\_PATH set gives you access to LAMMPS via Python.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Python_test.rst b/doc/src/Python_test.rst
new file mode 100644
index 0000000000..562ab88986
--- /dev/null
+++ b/doc/src/Python_test.rst
@@ -0,0 +1,170 @@
+Test the Python/LAMMPS interface
+================================
+
+To test if LAMMPS is callable from Python, launch Python interactively
+and type:
+
+
+.. parsed-literal::
+
+   >>> from lammps import lammps
+   >>> lmp = lammps()
+
+If you get no errors, you're ready to use LAMMPS from Python.  If the
+2nd command fails, the most common error to see is
+
+
+.. parsed-literal::
+
+   OSError: Could not load LAMMPS dynamic library
+
+which means Python was unable to load the LAMMPS shared library.  This
+typically occurs if the system can't find the LAMMPS shared library or
+one of the auxiliary shared libraries it depends on, or if something
+about the library is incompatible with your Python.  The error message
+should give you an indication of what went wrong.
+
+You can also test the load directly in Python as follows, without
+first importing from the lammps.py file:
+
+
+.. parsed-literal::
+
+   >>> from ctypes import CDLL
+   >>> CDLL("liblammps.so")
+
+If an error occurs, carefully go through the steps on the
+:doc:`Build\_basics <Build_basics>` doc page about building a shared
+library and the :doc:`Python\_install <Python_install>` doc page about
+insuring Python can find the necessary two files it needs.
+
+**Test LAMMPS and Python in serial:**
+-------------------------------------
+
+To run a LAMMPS test in serial, type these lines into Python
+interactively from the bench directory:
+
+
+.. parsed-literal::
+
+   >>> from lammps import lammps
+   >>> lmp = lammps()
+   >>> lmp.file("in.lj")
+
+Or put the same lines in the file test.py and run it as
+
+
+.. parsed-literal::
+
+   % python test.py
+
+Either way, you should see the results of running the in.lj benchmark
+on a single processor appear on the screen, the same as if you had
+typed something like:
+
+
+.. parsed-literal::
+
+   lmp_g++ -in in.lj
+
+**Test LAMMPS and Python in parallel:**
+---------------------------------------
+
+To run LAMMPS in parallel, assuming you have installed the
+`PyPar <https://github.com/daleroberts/pypar>`_ package as discussed
+above, create a test.py file containing these lines:
+
+
+.. parsed-literal::
+
+   import pypar
+   from lammps import lammps
+   lmp = lammps()
+   lmp.file("in.lj")
+   print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
+   pypar.finalize()
+
+To run LAMMPS in parallel, assuming you have installed the
+`mpi4py <https://bitbucket.org/mpi4py/mpi4py>`_ package as discussed
+above, create a test.py file containing these lines:
+
+
+.. parsed-literal::
+
+   from mpi4py import MPI
+   from lammps import lammps
+   lmp = lammps()
+   lmp.file("in.lj")
+   me = MPI.COMM_WORLD.Get_rank()
+   nprocs = MPI.COMM_WORLD.Get_size()
+   print "Proc %d out of %d procs has" % (me,nprocs),lmp
+   MPI.Finalize()
+
+You can either script in parallel as:
+
+
+.. parsed-literal::
+
+   % mpirun -np 4 python test.py
+
+and you should see the same output as if you had typed
+
+
+.. parsed-literal::
+
+   % mpirun -np 4 lmp_g++ -in in.lj
+
+Note that if you leave out the 3 lines from test.py that specify PyPar
+commands you will instantiate and run LAMMPS independently on each of
+the P processors specified in the mpirun command.  In this case you
+should get 4 sets of output, each showing that a LAMMPS run was made
+on a single processor, instead of one set of output showing that
+LAMMPS ran on 4 processors.  If the 1-processor outputs occur, it
+means that PyPar is not working correctly.
+
+Also note that once you import the PyPar module, PyPar initializes MPI
+for you, and you can use MPI calls directly in your Python script, as
+described in the PyPar documentation.  The last line of your Python
+script should be pypar.finalize(), to insure MPI is shut down
+correctly.
+
+**Running Python scripts:**
+---------------------------
+
+Note that any Python script (not just for LAMMPS) can be invoked in
+one of several ways:
+
+
+.. parsed-literal::
+
+   % python foo.script
+   % python -i foo.script
+   % foo.script
+
+The last command requires that the first line of the script be
+something like this:
+
+
+.. parsed-literal::
+
+   #!/usr/local/bin/python
+   #!/usr/local/bin/python -i
+
+where the path points to where you have Python installed, and that you
+have made the script file executable:
+
+
+.. parsed-literal::
+
+   % chmod +x foo.script
+
+Without the "-i" flag, Python will exit when the script finishes.
+With the "-i" flag, you will be left in the Python interpreter when
+the script finishes, so you can type subsequent commands.  As
+mentioned above, you can only run Python interactively when running
+Python on a single processor, not in parallel.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst
new file mode 100644
index 0000000000..fb5ca1736f
--- /dev/null
+++ b/doc/src/Run_basics.rst
@@ -0,0 +1,96 @@
+Basics of running LAMMPS
+========================
+
+LAMMPS is run from the command line, reading commands from a
+file via the -in command line flag, or from standard input.
+Using the "-in in.file" variant is recommended:
+
+
+.. parsed-literal::
+
+   lmp_serial < in.file
+   lmp_serial -in in.file
+   /path/to/lammps/src/lmp_serial < in.file
+   mpirun -np 4 lmp_mpi -in in.file
+   mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file
+   mpirun -np 6 /usr/local/bin/lmp -in in.file
+
+You normally run the LAMMPS command in the directory where your
+input script is located.  That is also where output files are
+produced by default, unless you provide specific other paths in
+your input script or on the command line.  As in some of the
+examples above, the LAMMPS executable itself can be placed elsewhere.
+
+.. note::
+
+   The redirection operator "<" will not always work when running
+   in parallel with mpirun; for those systems the -in form is required.
+
+As LAMMPS runs it prints info to the screen and a logfile named
+log.lammps.  More info about output is given on the :doc:`Run output <Run_output>` doc page.
+
+If LAMMPS encounters errors in the input script or while running a
+simulation it will print an ERROR message and stop or a WARNING
+message and continue.  See the :doc:`Errors <Errors>` doc page for a
+discussion of the various kinds of errors LAMMPS can or can't detect,
+a list of all ERROR and WARNING messages, and what to do about them.
+
+
+----------
+
+
+LAMMPS can run the same problem on any number of processors, including
+a single processor.  In theory you should get identical answers on any
+number of processors and on any machine.  In practice, numerical
+round-off can cause slight differences and eventual divergence of
+molecular dynamics phase space trajectories.  See the :doc:`Errors common <Errors_common>` doc page for discussion of this.
+
+LAMMPS can run as large a problem as will fit in the physical memory
+of one or more processors.  If you run out of memory, you must run on
+more processors or define a smaller problem.
+
+If you run LAMMPS in parallel via mpirun, you should be aware of the
+:doc:`processors <processors>` command which controls how MPI tasks are
+mapped to the simulation box, as well as mpirun options that control
+how MPI tasks are assigned to physical cores of the node(s) of the
+machine you are running on.  These settings can improve performance,
+though the defaults are often adequate.
+
+For example, it is often important to bind MPI tasks (processes) to
+physical cores (processor affinity), so that the operating system does
+not migrate them during a simulation.  If this is not the default
+behavior on your machine, the mpirun option "--bind-to core" (OpenMPI)
+or "-bind-to core" (MPICH) can be used.
+
+If the LAMMPS command(s) you are using support multi-threading, you
+can set the number of threads per MPI task via the environment
+variable OMP\_NUM\_THREADS, before you launch LAMMPS:
+
+
+.. parsed-literal::
+
+   export OMP_NUM_THREADS=2     # bash
+   setenv OMP_NUM_THREADS 2     # csh or tcsh
+
+This can also be done via the :doc:`package <package>` command or via
+the :doc:`-pk command-line switch <Run_options>` which invokes the
+package command.  See the :doc:`package <package>` command or
+:doc:`Speed <Speed>` doc pages for more details about which accelerator
+packages and which commands support multi-threading.
+
+
+----------
+
+
+You can experiment with running LAMMPS using any of the input scripts
+provided in the examples or bench directory.  Input scripts are named
+in.\* and sample outputs are named log.\*.P where P is the number of
+processors it was run on.
+
+Some of the examples or benchmarks require LAMMPS to be built with
+optional packages.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Run_head.rst b/doc/src/Run_head.rst
new file mode 100644
index 0000000000..02db16bf25
--- /dev/null
+++ b/doc/src/Run_head.rst
@@ -0,0 +1,21 @@
+Run LAMMPS
+**********
+
+These pages explain how to run LAMMPS once you have :doc:`installed an executable <Install>` or :doc:`downloaded the source code <Install>`
+and :doc:`built an executable <Build>`.  The :doc:`Commands <Commands>`
+doc page describes how input scripts are structured and the commands
+they can contain.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Run_basics
+   Run_options
+   Run_output
+   Run_windows
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst
new file mode 100644
index 0000000000..1e0091f057
--- /dev/null
+++ b/doc/src/Run_options.rst
@@ -0,0 +1,646 @@
+Command-line options
+====================
+
+At run time, LAMMPS recognizes several optional command-line switches
+which may be used in any order.  Either the full word or a one-or-two
+letter abbreviation can be used:
+
+* :ref:`-e or -echo <echo>`
+* :ref:`-h or -help <help>`
+* :ref:`-i or -in <file>`
+* :ref:`-k or -kokkos <run-kokkos>`
+* :ref:`-l or -log <log>`
+* :ref:`-m or -mpicolor <mpicolor>`
+* :ref:`-nc or -nocite <nocite>`
+* :ref:`-pk or -package <package>`
+* :ref:`-p or -partition <partition>`
+* :ref:`-pl or -plog <plog>`
+* :ref:`-ps or -pscreen <pscreen>`
+* :ref:`-ro or -reorder <reorder>`
+* :ref:`-r2data or -restart2data <restart2data>`
+* :ref:`-r2dump or -restart2dump <restart2dump>`
+* :ref:`-sc or -screen <screen>`
+* :ref:`-sf or -suffix <suffix>`
+* :ref:`-v or -var <var>`
+
+For example, the lmp\_mpi executable might be launched as follows:
+
+
+.. parsed-literal::
+
+   mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
+   mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy
+
+
+----------
+
+
+.. _echo:
+
+**-echo style** 
+
+Set the style of command echoing.  The style can be *none* or *screen*
+or *log* or *both*\ .  Depending on the style, each command read from
+the input script will be echoed to the screen and/or logfile.  This
+can be useful to figure out which line of your script is causing an
+input error.  The default value is *log*\ .  The echo style can also be
+set by using the :doc:`echo <echo>` command in the input script itself.
+
+
+----------
+
+
+.. _help:
+
+**-help** 
+
+Print a brief help summary and a list of options compiled into this
+executable for each LAMMPS style (atom\_style, fix, compute,
+pair\_style, bond\_style, etc).  This can tell you if the command you
+want to use was included via the appropriate package at compile time.
+LAMMPS will print the info and immediately exit if this switch is
+used.
+
+
+----------
+
+
+.. _file:
+
+**-in file** 
+
+Specify a file to use as an input script.  This is an optional switch
+when running LAMMPS in one-partition mode.  If it is not specified,
+LAMMPS reads its script from standard input, typically from a script
+via I/O redirection; e.g. lmp\_linux < in.run.  I/O redirection should
+also work in parallel, but if it does not (in the unlikely case that
+an MPI implementation does not support it), then use the -in flag.
+Note that this is a required switch when running LAMMPS in
+multi-partition mode, since multiple processors cannot all read from
+stdin.
+
+
+----------
+
+
+.. _run-kokkos:
+
+**-kokkos on/off keyword/value ...** 
+
+Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
+package.  Even if LAMMPS is built with this package, as described
+in :doc:`Speed kokkos <Speed_kokkos>`, this switch must be set to enable
+running with KOKKOS-enabled styles the package provides.  If the
+switch is not set (the default), LAMMPS will operate as if the KOKKOS
+package were not installed; i.e. you can run standard LAMMPS or with
+the GPU or USER-OMP packages, for testing or benchmarking purposes.
+
+Additional optional keyword/value pairs can be specified which
+determine how Kokkos will use the underlying hardware on your
+platform.  These settings apply to each MPI task you launch via the
+"mpirun" or "mpiexec" command.  You may choose to run one or more MPI
+tasks per physical node.  Note that if you are running on a desktop
+machine, you typically have one physical node.  On a cluster or
+supercomputer there may be dozens or 1000s of physical nodes.
+
+Either the full word or an abbreviation can be used for the keywords.
+Note that the keywords do not use a leading minus sign.  I.e. the
+keyword is "t", not "-t".  Also note that each of the keywords has a
+default setting.  Examples of when to use these options and what
+settings to use on different platforms is given on the :doc:`Speed kokkos <Speed_kokkos>` doc page.
+
+* d or device
+* g or gpus
+* t or threads
+* n or numa
+
+
+.. parsed-literal::
+
+   device Nd
+
+This option is only relevant if you built LAMMPS with CUDA=yes, you
+have more than one GPU per node, and if you are running with only one
+MPI task per node.  The Nd setting is the ID of the GPU on the node to
+run on.  By default Nd = 0.  If you have multiple GPUs per node, they
+have consecutive IDs numbered as 0,1,2,etc.  This setting allows you
+to launch multiple independent jobs on the node, each with a single
+MPI task per node, and assign each job to run on a different GPU.
+
+
+.. parsed-literal::
+
+   gpus Ng Ns
+
+This option is only relevant if you built LAMMPS with CUDA=yes, you
+have more than one GPU per node, and you are running with multiple MPI
+tasks per node (up to one per GPU).  The Ng setting is how many GPUs
+you will use.  The Ns setting is optional.  If set, it is the ID of a
+GPU to skip when assigning MPI tasks to GPUs.  This may be useful if
+your desktop system reserves one GPU to drive the screen and the rest
+are intended for computational work like running LAMMPS.  By default
+Ng = 1 and Ns is not set.
+
+Depending on which flavor of MPI you are running, LAMMPS will look for
+one of these 4 environment variables
+
+
+.. parsed-literal::
+
+   SLURM_LOCALID (various MPI variants compiled with SLURM support)
+   MPT_LRANK (HPE MPI)
+   MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
+   OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
+
+which are initialized by the "srun", "mpirun" or "mpiexec" commands.
+The environment variable setting for each MPI rank is used to assign a
+unique GPU ID to the MPI task.
+
+
+.. parsed-literal::
+
+   threads Nt
+
+This option assigns Nt number of threads to each MPI task for
+performing work when Kokkos is executing in OpenMP or pthreads mode.
+The default is Nt = 1, which essentially runs in MPI-only mode.  If
+there are Np MPI tasks per physical node, you generally want Np\*Nt =
+the number of physical cores per node, to use your available hardware
+optimally.  This also sets the number of threads used by the host when
+LAMMPS is compiled with CUDA=yes.
+
+
+.. parsed-literal::
+
+   numa Nm
+
+This option is only relevant when using pthreads with hwloc support.
+In this case Nm defines the number of NUMA regions (typically sockets)
+on a node which will be utilized by a single MPI rank.  By default Nm
+= 1.  If this option is used the total number of worker-threads per
+MPI rank is threads\*numa.  Currently it is always almost better to
+assign at least one MPI rank per NUMA region, and leave numa set to
+its default value of 1. This is because letting a single process span
+multiple NUMA regions induces a significant amount of cross NUMA data
+traffic which is slow.
+
+
+----------
+
+
+.. _log:
+
+**-log file** 
+
+Specify a log file for LAMMPS to write status information to.  In
+one-partition mode, if the switch is not used, LAMMPS writes to the
+file log.lammps.  If this switch is used, LAMMPS writes to the
+specified file.  In multi-partition mode, if the switch is not used, a
+log.lammps file is created with hi-level status information.  Each
+partition also writes to a log.lammps.N file where N is the partition
+ID.  If the switch is specified in multi-partition mode, the hi-level
+logfile is named "file" and each partition also logs information to a
+file.N.  For both one-partition and multi-partition mode, if the
+specified file is "none", then no log files are created.  Using a
+:doc:`log <log>` command in the input script will override this setting.
+Option -plog will override the name of the partition log files file.N.
+
+
+----------
+
+
+.. _mpicolor:
+
+**-mpicolor** color 
+
+If used, this must be the first command-line argument after the LAMMPS
+executable name.  It is only used when LAMMPS is launched by an mpirun
+command which also launches another executable(s) at the same time.
+(The other executable could be LAMMPS as well.)  The color is an
+integer value which should be different for each executable (another
+application may set this value in a different way).  LAMMPS and the
+other executable(s) perform an MPI\_Comm\_split() with their own colors
+to shrink the MPI\_COMM\_WORLD communication to be the subset of
+processors they are actually running on.
+
+Currently, this is only used in LAMMPS to perform client/server
+messaging with another application.  LAMMPS can act as either a client
+or server (or both).  More details are given on the :doc:`Howto client/server <Howto_client_server>` doc page.
+
+Specifically, this refers to the "mpi/one" mode of messaging provided
+by the :doc:`message <message>` command and the CSlib library LAMMPS
+links with from the lib/message directory.  See the
+:doc:`message <message>` command for more details.
+
+
+----------
+
+
+.. _nocite:
+
+**-nocite** 
+
+Disable writing the log.cite file which is normally written to list
+references for specific cite-able features used during a LAMMPS run.
+See the `citation page <http://lammps.sandia.gov/cite.html>`_ for more
+details.
+
+
+----------
+
+
+.. _package:
+
+**-package style args ....** 
+
+Invoke the :doc:`package <package>` command with style and args.  The
+syntax is the same as if the command appeared at the top of the input
+script.  For example "-package gpu 2" or "-pk gpu 2" is the same as
+:doc:`package gpu 2 <package>` in the input script.  The possible styles
+and args are documented on the :doc:`package <package>` doc page.  This
+switch can be used multiple times, e.g. to set options for the
+USER-INTEL and USER-OMP packages which can be used together.
+
+Along with the "-suffix" command-line switch, this is a convenient
+mechanism for invoking accelerator packages and their options without
+having to edit an input script.
+
+
+----------
+
+
+.. _partition:
+
+**-partition 8x2 4 5 ...** 
+
+Invoke LAMMPS in multi-partition mode.  When LAMMPS is run on P
+processors and this switch is not used, LAMMPS runs in one partition,
+i.e. all P processors run a single simulation.  If this switch is
+used, the P processors are split into separate partitions and each
+partition runs its own simulation.  The arguments to the switch
+specify the number of processors in each partition.  Arguments of the
+form MxN mean M partitions, each with N processors.  Arguments of the
+form N mean a single partition with N processors.  The sum of
+processors in all partitions must equal P.  Thus the command
+"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
+processors.
+
+Running with multiple partitions can be useful for running
+:doc:`multi-replica simulations <Howto_replica>`, where each replica
+runs on one or a few processors.  Note that with MPI installed on a
+machine (e.g. your desktop), you can run on more (virtual) processors
+than you have physical processors.
+
+To run multiple independent simulations from one input script, using
+multiple partitions, see the :doc:`Howto multiple <Howto_multiple>` doc
+page.  World- and universe-style :doc:`variables <variable>` are useful
+in this context.
+
+
+----------
+
+
+.. _plog:
+
+**-plog file** 
+
+Specify the base name for the partition log files, so partition N
+writes log information to file.N. If file is none, then no partition
+log files are created.  This overrides the filename specified in the
+-log command-line option.  This option is useful when working with
+large numbers of partitions, allowing the partition log files to be
+suppressed (-plog none) or placed in a sub-directory (-plog
+replica\_files/log.lammps) If this option is not used the log file for
+partition N is log.lammps.N or whatever is specified by the -log
+command-line option.
+
+
+----------
+
+
+.. _pscreen:
+
+**-pscreen file** 
+
+Specify the base name for the partition screen file, so partition N
+writes screen information to file.N. If file is none, then no
+partition screen files are created.  This overrides the filename
+specified in the -screen command-line option.  This option is useful
+when working with large numbers of partitions, allowing the partition
+screen files to be suppressed (-pscreen none) or placed in a
+sub-directory (-pscreen replica\_files/screen).  If this option is not
+used the screen file for partition N is screen.N or whatever is
+specified by the -screen command-line option.
+
+
+----------
+
+
+.. _reorder:
+
+**-reorder** 
+
+This option has 2 forms:
+
+
+.. parsed-literal::
+
+   -reorder nth N
+   -reorder custom filename
+
+Reorder the processors in the MPI communicator used to instantiate
+LAMMPS, in one of several ways.  The original MPI communicator ranks
+all P processors from 0 to P-1.  The mapping of these ranks to
+physical processors is done by MPI before LAMMPS begins.  It may be
+useful in some cases to alter the rank order.  E.g. to insure that
+cores within each node are ranked in a desired order.  Or when using
+the :doc:`run\_style verlet/split <run_style>` command with 2 partitions
+to insure that a specific Kspace processor (in the 2nd partition) is
+matched up with a specific set of processors in the 1st partition.
+See the :doc:`Speed tips <Speed_tips>` doc page for more details.
+
+If the keyword *nth* is used with a setting *N*\ , then it means every
+Nth processor will be moved to the end of the ranking.  This is useful
+when using the :doc:`run\_style verlet/split <run_style>` command with 2
+partitions via the -partition command-line switch.  The first set of
+processors will be in the first partition, the 2nd set in the 2nd
+partition.  The -reorder command-line switch can alter this so that
+the 1st N procs in the 1st partition and one proc in the 2nd partition
+will be ordered consecutively, e.g. as the cores on one physical node.
+This can boost performance.  For example, if you use "-reorder nth 4"
+and "-partition 9 3" and you are running on 12 processors, the
+processors will be reordered from
+
+
+.. parsed-literal::
+
+   0 1 2 3 4 5 6 7 8 9 10 11
+
+to
+
+
+.. parsed-literal::
+
+   0 1 2 4 5 6 8 9 10 3 7 11
+
+so that the processors in each partition will be
+
+
+.. parsed-literal::
+
+   0 1 2 4 5 6 8 9 10
+   3 7 11
+
+See the "processors" command for how to insure processors from each
+partition could then be grouped optimally for quad-core nodes.
+
+If the keyword is *custom*\ , then a file that specifies a permutation
+of the processor ranks is also specified.  The format of the reorder
+file is as follows.  Any number of initial blank or comment lines
+(starting with a "#" character) can be present.  These should be
+followed by P lines of the form:
+
+
+.. parsed-literal::
+
+   I J
+
+where P is the number of processors LAMMPS was launched with.  Note
+that if running in multi-partition mode (see the -partition switch
+above) P is the total number of processors in all partitions.  The I
+and J values describe a permutation of the P processors.  Every I and
+J should be values from 0 to P-1 inclusive.  In the set of P I values,
+every proc ID should appear exactly once.  Ditto for the set of P J
+values.  A single I,J pairing means that the physical processor with
+rank I in the original MPI communicator will have rank J in the
+reordered communicator.
+
+Note that rank ordering can also be specified by many MPI
+implementations, either by environment variables that specify how to
+order physical processors, or by config files that specify what
+physical processors to assign to each MPI rank.  The -reorder switch
+simply gives you a portable way to do this without relying on MPI
+itself.  See the :doc:`processors out <processors>` command for how
+to output info on the final assignment of physical processors to
+the LAMMPS simulation domain.
+
+
+----------
+
+
+.. _restart2data:
+
+**-restart2data restartfile [remap] datafile keyword value ...**
+
+
+Convert the restart file into a data file and immediately exit.  This
+is the same operation as if the following 2-line input script were
+run:
+
+
+.. parsed-literal::
+
+   read_restart restartfile [remap]
+   write_data datafile keyword value ...
+
+The specified restartfile and/or datafile name may contain the wild-card
+character "\*".  The restartfile name may also contain the wild-card
+character "%".  The meaning of these characters is explained on the
+:doc:`read\_restart <read_restart>` and :doc:`write\_data <write_data>` doc
+pages.  The use of "%" means that a parallel restart file can be read.
+Note that a filename such as file.\* may need to be enclosed in quotes or
+the "\*" character prefixed with a backslash ("\") to avoid shell
+expansion of the "\*" character.
+
+Following restartfile argument, the optional word "remap" may be used.
+This has the same effect like adding it to a
+:doc:`read\_restart <read_restart>` command, and operates as explained on
+its doc page.  This is useful if reading the restart file triggers an
+error that atoms have been lost.  In that case, use of the remap flag
+should allow the data file to still be produced.
+
+The syntax following restartfile (or remap), namely
+
+
+.. parsed-literal::
+
+   datafile keyword value ...
+
+is identical to the arguments of the :doc:`write\_data <write_data>`
+command.  See its doc page for details.  This includes its
+optional keyword/value settings.
+
+
+----------
+
+
+.. _restart2dump:
+
+**-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...** 
+
+Convert the restart file into a dump file and immediately exit.  This
+is the same operation as if the following 2-line input script were
+run:
+
+
+.. parsed-literal::
+
+   read_restart restartfile [remap]
+   write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
+
+Note that the specified restartfile and dumpfile names may contain
+wild-card characters ("\*","%") as explained on the
+:doc:`read\_restart <read_restart>` and :doc:`write\_dump <write_dump>` doc
+pages.  The use of "%" means that a parallel restart file and/or
+parallel dump file can be read and/or written.  Note that a filename
+such as file.\* may need to be enclosed in quotes or the "\*" character
+prefixed with a backslash ("\") to avoid shell expansion of the "\*"
+character.
+
+Note that following the restartfile argument, the optional word "remap"
+can be used.  This has the effect as adding it to the
+:doc:`read\_restart <read_restart>` command, as explained on its doc page.
+This is useful if reading the restart file triggers an error that atoms
+have been lost.  In that case, use of the remap flag should allow the
+dump file to still be produced.
+
+The syntax following restartfile (or remap), namely
+
+
+.. parsed-literal::
+
+   group-ID dumpstyle dumpfile arg1 arg2 ...
+
+is identical to the arguments of the :doc:`write\_dump <write_dump>`
+command.  See its doc page for details.  This includes what per-atom
+fields are written to the dump file and optional dump\_modify settings,
+including ones that affect how parallel dump files are written, e.g.
+the *nfile* and *fileper* keywords.  See the
+:doc:`dump\_modify <dump_modify>` doc page for details.
+
+
+----------
+
+
+.. _screen:
+
+**-screen file** 
+
+Specify a file for LAMMPS to write its screen information to.  In
+one-partition mode, if the switch is not used, LAMMPS writes to the
+screen.  If this switch is used, LAMMPS writes to the specified file
+instead and you will see no screen output.  In multi-partition mode,
+if the switch is not used, hi-level status information is written to
+the screen.  Each partition also writes to a screen.N file where N is
+the partition ID.  If the switch is specified in multi-partition mode,
+the hi-level screen dump is named "file" and each partition also
+writes screen information to a file.N.  For both one-partition and
+multi-partition mode, if the specified file is "none", then no screen
+output is performed. Option -pscreen will override the name of the
+partition screen files file.N.
+
+
+----------
+
+
+.. _suffix:
+
+**-suffix style args** 
+
+Use variants of various styles if they exist.  The specified style can
+be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt*\ , or *hybrid*\ .  These
+refer to optional packages that LAMMPS can be built with, as described
+in :doc:`Accelerate performance <Speed>`.  The "gpu" style corresponds to the
+GPU package, the "intel" style to the USER-INTEL package, the "kk"
+style to the KOKKOS package, the "opt" style to the OPT package, and
+the "omp" style to the USER-OMP package. The hybrid style is the only
+style that accepts arguments. It allows for two packages to be
+specified. The first package specified is the default and will be used
+if it is available. If no style is available for the first package,
+the style for the second package will be used if available. For
+example, "-suffix hybrid intel omp" will use styles from the
+USER-INTEL package if they are installed and available, but styles for
+the USER-OMP package otherwise.
+
+Along with the "-package" command-line switch, this is a convenient
+mechanism for invoking accelerator packages and their options without
+having to edit an input script.
+
+As an example, all of the packages provide a :doc:`pair\_style lj/cut <pair_lj>` variant, with style names lj/cut/gpu,
+lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt.  A variant style
+can be specified explicitly in your input script, e.g. pair\_style
+lj/cut/gpu.  If the -suffix switch is used the specified suffix
+(gpu,intel,kk,omp,opt) is automatically appended whenever your input
+script command creates a new :doc:`atom <atom_style>`,
+:doc:`pair <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, or
+:doc:`run <run_style>` style.  If the variant version does not exist,
+the standard version is created.
+
+For the GPU package, using this command-line switch also invokes the
+default GPU settings, as if the command "package gpu 1" were used at
+the top of your input script.  These settings can be changed by using
+the "-package gpu" command-line switch or the :doc:`package gpu <package>` command in your script.
+
+For the USER-INTEL package, using this command-line switch also
+invokes the default USER-INTEL settings, as if the command "package
+intel 1" were used at the top of your input script.  These settings
+can be changed by using the "-package intel" command-line switch or
+the :doc:`package intel <package>` command in your script. If the
+USER-OMP package is also installed, the hybrid style with "intel omp"
+arguments can be used to make the omp suffix a second choice, if a
+requested style is not available in the USER-INTEL package.  It will
+also invoke the default USER-OMP settings, as if the command "package
+omp 0" were used at the top of your input script.  These settings can
+be changed by using the "-package omp" command-line switch or the
+:doc:`package omp <package>` command in your script.
+
+For the KOKKOS package, using this command-line switch also invokes
+the default KOKKOS settings, as if the command "package kokkos" were
+used at the top of your input script.  These settings can be changed
+by using the "-package kokkos" command-line switch or the :doc:`package kokkos <package>` command in your script.
+
+For the OMP package, using this command-line switch also invokes the
+default OMP settings, as if the command "package omp 0" were used at
+the top of your input script.  These settings can be changed by using
+the "-package omp" command-line switch or the :doc:`package omp <package>` command in your script.
+
+The :doc:`suffix <suffix>` command can also be used within an input
+script to set a suffix, or to turn off or back on any suffix setting
+made via the command line.
+
+
+----------
+
+
+.. _var:
+
+**-var name value1 value2 ...** 
+
+Specify a variable that will be defined for substitution purposes when
+the input script is read.  This switch can be used multiple times to
+define multiple variables.  "Name" is the variable name which can be a
+single character (referenced as $x in the input script) or a full
+string (referenced as ${abc}).  An :doc:`index-style variable <variable>` will be created and populated with the
+subsequent values, e.g. a set of filenames.  Using this command-line
+option is equivalent to putting the line "variable name index value1
+value2 ..."  at the beginning of the input script.  Defining an index
+variable as a command-line argument overrides any setting for the same
+index variable in the input script, since index variables cannot be
+re-defined.
+
+See the :doc:`variable <variable>` command for more info on defining
+index and other kinds of variables and the :doc:`Commands parse <Commands_parse>` page for more info on using variables in
+input scripts.
+
+.. note::
+
+   Currently, the command-line parser looks for arguments that
+   start with "-" to indicate new switches.  Thus you cannot specify
+   multiple variable values if any of them start with a "-", e.g. a
+   negative numeric value.  It is OK if the first value1 starts with a
+   "-", since it is automatically skipped.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst
new file mode 100644
index 0000000000..41a6dcd4f3
--- /dev/null
+++ b/doc/src/Run_output.rst
@@ -0,0 +1,197 @@
+Screen and logfile output
+=========================
+
+As LAMMPS reads an input script, it prints information to both the
+screen and a log file about significant actions it takes to setup a
+simulation.  When the simulation is ready to begin, LAMMPS performs
+various initializations, and prints info about the run it is about to
+perform, including the amount of memory (in MBytes per processor) that
+the simulation requires.  It also prints details of the initial
+thermodynamic state of the system.  During the run itself,
+thermodynamic information is printed periodically, every few
+timesteps.  When the run concludes, LAMMPS prints the final
+thermodynamic state and a total run time for the simulation.  It also
+appends statistics about the CPU time and storage requirements for the
+simulation.  An example set of statistics is shown here:
+
+
+.. parsed-literal::
+
+   Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+
+   Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
+   97.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+   MPI task timings breakdown:
+   Section \|  min time  \|  avg time  \|  max time  \|%varavg\| %total
+   ---------------------------------------------------------------
+   Pair    \| 1.9808     \| 2.0134     \| 2.0318     \|   1.4 \| 71.60
+   Bond    \| 0.0021894  \| 0.0060319  \| 0.010058   \|   4.7 \|  0.21
+   Kspace  \| 0.3207     \| 0.3366     \| 0.36616    \|   3.1 \| 11.97
+   Neigh   \| 0.28411    \| 0.28464    \| 0.28516    \|   0.1 \| 10.12
+   Comm    \| 0.075732   \| 0.077018   \| 0.07883    \|   0.4 \|  2.74
+   Output  \| 0.00030518 \| 0.00042665 \| 0.00078821 \|   1.0 \|  0.02
+   Modify  \| 0.086606   \| 0.086631   \| 0.086668   \|   0.0 \|  3.08
+   Other   \|            \| 0.007178   \|            \|       \|  0.26
+
+   Nlocal:    501 ave 508 max 490 min
+   Histogram: 1 0 0 0 0 0 1 1 0 1
+   Nghost:    6586.25 ave 6628 max 6548 min
+   Histogram: 1 0 1 0 0 0 1 0 0 1
+   Neighs:    177007 ave 180562 max 170212 min
+   Histogram: 1 0 0 0 0 0 0 1 1 1
+
+   Total # of neighbors = 708028
+   Ave neighs/atom = 353.307
+   Ave special neighs/atom = 2.34032
+   Neighbor list builds = 26
+   Dangerous builds = 0
+
+
+----------
+
+
+The first section provides a global loop timing summary. The *loop
+time* is the total wall-clock time for the simulation to run.  The
+*Performance* line is provided for convenience to help predict how
+long it will take to run a desired physical simulation.  The *CPU use*
+line provides the CPU utilization per MPI task; it should be close to
+100% times the number of OpenMP threads (or 1 of not using OpenMP).
+Lower numbers correspond to delays due to file I/O or insufficient
+thread utilization.
+
+
+----------
+
+
+The *MPI task* section gives the breakdown of the CPU run time (in
+seconds) into major categories:
+
+* *Pair* = non-bonded force computations
+* *Bond* = bonded interactions: bonds, angles, dihedrals, impropers
+* *Kspace* = long-range interactions: Ewald, PPPM, MSM
+* *Neigh* = neighbor list construction
+* *Comm* = inter-processor communication of atoms and their properties
+* *Output* = output of thermodynamic info and dump files
+* *Modify* = fixes and computes invoked by fixes
+* *Other* = all the remaining time
+
+For each category, there is a breakdown of the least, average and most
+amount of wall time any processor spent on this category of
+computation.  The "%varavg" is the percentage by which the max or min
+varies from the average.  This is an indication of load imbalance.  A
+percentage close to 0 is perfect load balance.  A large percentage is
+imbalance.  The final "%total" column is the percentage of the total
+loop time is spent in this category.
+
+When using the :doc:`timer full <timer>` setting, an additional column
+is added that also prints the CPU utilization in percent. In addition,
+when using *timer full* and the :doc:`package omp <package>` command are
+active, a similar timing summary of time spent in threaded regions to
+monitor thread utilization and load balance is provided. A new *Thread
+timings* section is also added, which lists the time spent in reducing
+the per-thread data elements to the storage for non-threaded
+computation. These thread timings are measured for the first MPI rank
+only and thus, because the breakdown for MPI tasks can change from
+MPI rank to MPI rank, this breakdown can be very different for
+individual ranks. Here is an example output for this section:
+
+
+.. parsed-literal::
+
+   Thread timings breakdown (MPI rank 0):
+   Total threaded time 0.6846 / 90.6%
+   Section \|  min time  \|  avg time  \|  max time  \|%varavg\| %total
+   ---------------------------------------------------------------
+   Pair    \| 0.5127     \| 0.5147     \| 0.5167     \|   0.3 \| 75.18
+   Bond    \| 0.0043139  \| 0.0046779  \| 0.0050418  \|   0.5 \|  0.68
+   Kspace  \| 0.070572   \| 0.074541   \| 0.07851    \|   1.5 \| 10.89
+   Neigh   \| 0.084778   \| 0.086969   \| 0.089161   \|   0.7 \| 12.70
+   Reduce  \| 0.0036485  \| 0.003737   \| 0.0038254  \|   0.1 \|  0.55
+
+
+----------
+
+
+The third section above lists the number of owned atoms (Nlocal),
+ghost atoms (Nghost), and pair-wise neighbors stored per processor.
+The max and min values give the spread of these values across
+processors with a 10-bin histogram showing the distribution. The total
+number of histogram counts is equal to the number of processors.
+
+
+----------
+
+
+The last section gives aggregate statistics (across all processors)
+for pair-wise neighbors and special neighbors that LAMMPS keeps track
+of (see the :doc:`special\_bonds <special_bonds>` command).  The number
+of times neighbor lists were rebuilt is tallied, as is the number of
+potentially *dangerous* rebuilds.  If atom movement triggered neighbor
+list rebuilding (see the :doc:`neigh\_modify <neigh_modify>` command),
+then dangerous reneighborings are those that were triggered on the
+first timestep atom movement was checked for.  If this count is
+non-zero you may wish to reduce the delay factor to insure no force
+interactions are missed by atoms moving beyond the neighbor skin
+distance before a rebuild takes place.
+
+
+----------
+
+
+If an energy minimization was performed via the
+:doc:`minimize <minimize>` command, additional information is printed,
+e.g.
+
+
+.. parsed-literal::
+
+   Minimization stats:
+     Stopping criterion = linesearch alpha is zero
+     Energy initial, next-to-last, final =
+            -6372.3765206     -8328.46998942     -8328.46998942
+     Force two-norm initial, final = 1059.36 5.36874
+     Force max component initial, final = 58.6026 1.46872
+     Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
+     Iterations, force evaluations = 701 1516
+
+The first line prints the criterion that determined minimization was
+converged. The next line lists the initial and final energy, as well
+as the energy on the next-to-last iteration.  The next 2 lines give a
+measure of the gradient of the energy (force on all atoms).  The
+2-norm is the "length" of this 3N-component force vector; the largest
+component (x, y, or z) of force (infinity-norm) is also given.  Then
+information is provided about the line search and statistics on how
+many iterations and force-evaluations the minimizer required.
+Multiple force evaluations are typically done at each iteration to
+perform a 1d line minimization in the search direction.  See the
+:doc:`minimize <minimize>` doc page for more details.
+
+
+----------
+
+
+If a :doc:`kspace\_style <kspace_style>` long-range Coulombics solver
+that performs FFTs was used during the run (PPPM, Ewald), then
+additional information is printed, e.g.
+
+
+.. parsed-literal::
+
+   FFT time (% of Kspce) = 0.200313 (8.34477)
+   FFT Gflps 3d 1d-only = 2.31074 9.19989
+
+The first line is the time spent doing 3d FFTs (several per timestep)
+and the fraction it represents of the total KSpace time (listed
+above).  Each 3d FFT requires computation (3 sets of 1d FFTs) and
+communication (transposes).  The total flops performed is 5Nlog\_2(N),
+where N is the number of points in the 3d grid.  The FFTs are timed
+with and without the communication and a Gflop rate is computed.  The
+3d rate is with communication; the 1d rate is without (just the 1d
+FFTs).  Thus you can estimate what fraction of your FFT time was spent
+in communication, roughly 75% in the example above.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst
new file mode 100644
index 0000000000..7892079029
--- /dev/null
+++ b/doc/src/Run_windows.rst
@@ -0,0 +1,81 @@
+Running LAMMPS on Windows
+=========================
+
+To run a serial (non-MPI) executable, follow these steps:
+
+* Get a command prompt by going to Start->Run... ,
+  then typing "cmd".
+* Move to the directory where you have your input script,
+  (e.g. by typing: cd "Documents").
+* At the command prompt, type "lmp\_serial -in in.file", where
+  in.file is the name of your LAMMPS input script.
+
+Note that the serial executable includes support for multi-threading
+parallelization from the styles in the USER-OMP packages.  To run with
+4 threads, you can type this:
+
+
+.. parsed-literal::
+
+   lmp_serial -in in.lj -pk omp 4 -sf omp
+
+
+----------
+
+
+For the MPI executable, which allows you to run LAMMPS under Windows
+in parallel, follow these steps.
+
+Download and install a compatible MPI library binary package:
+
+* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
+* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
+
+The LAMMPS Windows installer packages will automatically adjust your
+path for the default location of this MPI package. After the
+installation of the MPICH2 software, it needs to be integrated into
+the system.  For this you need to start a Command Prompt in
+*Administrator Mode* (right click on the icon and select it). Change
+into the MPICH2 installation directory, then into the sub-directory
+**bin** and execute **smpd.exe -install**\ . Exit the command window.
+
+* Get a new, regular command prompt by going to Start->Run... ,
+  then typing "cmd".
+* Move to the directory where you have your input file
+  (e.g. by typing: cd "Documents").
+
+Then type something like this:
+
+
+.. parsed-literal::
+
+   mpiexec -localonly 4 lmp_mpi -in in.file
+   mpiexec -np 4 lmp_mpi -in in.file
+
+where in.file is the name of your LAMMPS input script. For the latter
+case, you may be prompted to enter your password.
+
+In this mode, output may not immediately show up on the screen, so if
+your input script takes a long time to execute, you may need to be
+patient before the output shows up.
+
+The parallel executable can also run on a single processor by typing
+something like this:
+
+
+.. parsed-literal::
+
+   lmp_mpi -in in.lj
+
+Note that the parallel executable also includes OpenMP
+multi-threading, which can be combined with MPI using something like:
+
+
+.. parsed-literal::
+
+   mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed.rst b/doc/src/Speed.rst
new file mode 100644
index 0000000000..4953a9fdda
--- /dev/null
+++ b/doc/src/Speed.rst
@@ -0,0 +1,35 @@
+Accelerate performance
+**********************
+
+This section describes various methods for improving LAMMPS
+performance for different classes of problems running on different
+kinds of machines.
+
+There are two thrusts to the discussion that follows.  The first is
+using code options that implement alternate algorithms that can
+speed-up a simulation.  The second is to use one of the several
+accelerator packages provided with LAMMPS that contain code optimized
+for certain kinds of hardware, including multi-core CPUs, GPUs, and
+Intel Xeon Phi co-processors.
+
+The `Benchmark page <http://lammps.sandia.gov/bench.html>`_ of the LAMMPS
+web site gives performance results for the various accelerator
+packages discussed on the :doc:`Speed packages <Speed_packages>` doc
+page, for several of the standard LAMMPS benchmark problems, as a
+function of problem size and number of compute nodes, on different
+hardware platforms.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Speed_bench
+   Speed_measure
+   Speed_tips
+   Speed_packages
+   Speed_compare
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_bench.rst b/doc/src/Speed_bench.rst
new file mode 100644
index 0000000000..8de5ee5d07
--- /dev/null
+++ b/doc/src/Speed_bench.rst
@@ -0,0 +1,82 @@
+Benchmarks
+==========
+
+Current LAMMPS performance is discussed on the `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of the `LAMMPS website <lws_>`_
+where timings and parallel efficiency are listed.  The page has
+several sections, which are briefly described below:
+
+* CPU performance on 5 standard problems, strong and weak scaling
+* GPU and Xeon Phi performance on same and related problems
+* Comparison of cost of interatomic potentials
+* Performance of huge, billion-atom problems
+
+The 5 standard problems are as follow:
+
+#. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
+   neighbors per atom), NVE integration
+#. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
+   pairwise interactions with a 2\^(1/6) sigma cutoff (5 neighbors per
+   atom), NVE integration
+#. EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
+   neighbors per atom), NVE integration
+#. Chute = granular chute flow, frictional history potential with 1.1
+   sigma cutoff (7 neighbors per atom), NVE integration
+#. Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
+   field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
+   particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
+   integration
+
+
+Input files for these 5 problems are provided in the bench directory
+of the LAMMPS distribution.  Each has 32,000 atoms and runs for 100
+timesteps.  The size of the problem (number of atoms) can be varied
+using command-line switches as described in the bench/README file.
+This is an easy way to test performance and either strong or weak
+scalability on your machine.
+
+The bench directory includes a few log.\* files that show performance
+of these 5 problems on 1 or 4 cores of Linux desktop.  The bench/FERMI
+and bench/KEPLER dirs have input files and scripts and instructions
+for running the same (or similar) problems using OpenMP or GPU or Xeon
+Phi acceleration options.  See the README files in those dirs and the
+:doc:`Speed packages <Speed_packages>` doc pages for instructions on how
+to build LAMMPS and run on that kind of hardware.
+
+The bench/POTENTIALS directory has input files which correspond to the
+table of results on the
+`Potentials <http://lammps.sandia.gov/bench.html#potentials>`_ section of
+the Benchmarks web page.  So you can also run those test problems on
+your machine.
+
+The `billion-atom <http://lammps.sandia.gov/bench.html#billion>`_ section
+of the Benchmarks web page has performance data for very large
+benchmark runs of simple Lennard-Jones (LJ) models, which use the
+bench/in.lj input script.
+
+
+----------
+
+
+For all the benchmarks, a useful metric is the CPU cost per atom per
+timestep.  Since performance scales roughly linearly with problem size
+and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained
+potentials), the run time of any problem using the same model (atom
+style, force field, cutoff, etc) can then be estimated.
+
+Performance on a parallel machine can also be predicted from one-core
+or one-node timings if the parallel efficiency can be estimated.  The
+communication bandwidth and latency of a particular parallel machine
+affects the efficiency.  On most machines LAMMPS will give a parallel
+efficiency on these benchmarks above 50% so long as the number of
+atoms/core is a few 100 or greater, and closer to 100% for large
+numbers of atoms/core.  This is for all-MPI mode with one MPI task per
+core.  For nodes with accelerator options or hardware (OpenMP, GPU,
+Phi), you should first measure single node performance.  Then you can
+estimate parallel performance for multi-node runs using the same logic
+as for all-MPI mode, except that now you will typically need many more
+atoms/node to achieve good scalability.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst
new file mode 100644
index 0000000000..4e97ecd264
--- /dev/null
+++ b/doc/src/Speed_compare.rst
@@ -0,0 +1,101 @@
+Comparison of various accelerator packages
+==========================================
+
+The next section compares and contrasts the various accelerator
+options, since there are multiple ways to perform OpenMP threading,
+run on GPUs, optimize for vector units on CPUs and run on Intel
+Xeon Phi (co-)processors.
+
+All of these packages can accelerate a LAMMPS calculation taking
+advantage of hardware features, but they do it in different ways
+and acceleration is not always guaranteed.
+
+As a consequence, for a particular simulation on specific hardware,
+one package may be faster than the other.  We give some guidelines
+below, but the best way to determine which package is faster for your
+input script is to try multiple of them on your machine and experiment
+with available performance tuning settings.  See the benchmarking
+section below for examples where this has been done.
+
+**Guidelines for using each package optimally:**
+
+* Both, the GPU and the KOKKOS package allows you to assign multiple
+  MPI ranks (= CPU cores) to the same GPU. For the GPU package, this
+  can lead to a speedup through better utilization of the GPU (by
+  overlapping computation and data transfer) and more efficient
+  computation of the non-GPU accelerated parts of LAMMPS through MPI
+  parallelization, as all system data is maintained and updated on
+  the host. For KOKKOS, there is less to no benefit from this, due
+  to its different memory management model, which tries to retain
+  data on the GPU.
+* The GPU package moves per-atom data (coordinates, forces, and
+  (optionally) neighbor list data, if not computed on the GPU) between
+  the CPU and GPU at every timestep.  The KOKKOS/CUDA package only does
+  this on timesteps when a CPU calculation is required (e.g. to invoke
+  a fix or compute that is non-GPU-ized). Hence, if you can formulate
+  your input script to only use GPU-ized fixes and computes, and avoid
+  doing I/O too often (thermo output, dump file snapshots, restart files),
+  then the data transfer cost of the KOKKOS/CUDA package can be very low,
+  causing it to run faster than the GPU package.
+* The GPU package is often faster than the KOKKOS/CUDA package, when the
+  number of atoms per GPU is on the smaller side.  The crossover point,
+  in terms of atoms/GPU at which the KOKKOS/CUDA package becomes faster
+  depends strongly on the pair style.  For example, for a simple Lennard Jones
+  system the crossover (in single precision) is often about 50K-100K
+  atoms per GPU.  When performing double precision calculations the
+  crossover point can be significantly smaller.
+* Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
+  etc) on the CPU.  If the GPU package is running with several MPI processes
+  assigned to one GPU, the cost of computing the bonded interactions is
+  spread across more CPUs and hence the GPU package can run faster in these
+  cases.
+* When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
+  performance depends to some extent on the available bandwidth between
+  the CPUs and the GPU. This can differ significantly based on the
+  available bus technology, capability of the host CPU and mainboard,
+  the wiring of the buses and whether switches are used to increase the
+  number of available bus slots, or if GPUs are housed in an external
+  enclosure.  This can become quite complex.
+* To achieve significant acceleration through GPUs, both KOKKOS and GPU
+  package require capable GPUs with fast on-device memory and efficient
+  data transfer rates. This requests capable upper mid-level to high-end
+  (desktop) GPUs. Using lower performance GPUs (e.g. on laptops) may
+  result in a slowdown instead.
+* For the GPU package, specifically when running in parallel with MPI,
+  if it often more efficient to exclude the PPPM kspace style from GPU
+  acceleration and instead run it - concurrently with a GPU accelerated
+  pair style - on the CPU. This can often be easily achieved with placing
+  a *suffix off* command before and a *suffix on* command after the
+  *kspace\_style pppm* command.
+* The KOKKOS/OpenMP and USER-OMP package have different thread management
+  strategies, which should result in USER-OMP being more efficient for a
+  small number of threads with increasing overhead as the number of threads
+  per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that
+  case, but have lower performance with few threads.
+* The USER-INTEL package contains many options and settings for achieving
+  additional performance on Intel hardware (CPU and accelerator cards), but
+  to unlock this potential, an Intel compiler is required. The package code
+  will compile with GNU gcc, but it will not be as efficient.
+
+
+**Differences between the GPU and KOKKOS packages:**
+
+* The GPU package accelerates only pair force, neighbor list, and (parts
+  of) PPPM calculations. The KOKKOS package attempts to run most of the
+  calculation on the GPU, but can transparently support non-accelerated
+  code (with a performance penalty due to having data transfers between
+  host and GPU).
+* The GPU package requires neighbor lists to be built on the CPU when using
+  exclusion lists, or a triclinic simulation box.
+* The GPU package can be compiled for CUDA or OpenCL and thus supports
+  both, Nvidia and AMD GPUs well. On Nvidia hardware, using CUDA is typically
+  resulting in equal or better performance over OpenCL.
+* OpenCL in the GPU package does theoretically also support Intel CPUs or
+  Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL)
+  is superior.
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst
new file mode 100644
index 0000000000..dca32f1bb1
--- /dev/null
+++ b/doc/src/Speed_gpu.rst
@@ -0,0 +1,185 @@
+GPU package
+===========
+
+The GPU package was developed by Mike Brown while at SNL and ORNL
+and his collaborators, particularly Trung Nguyen (now at Northwestern).
+It provides GPU versions of many pair styles and for parts of the
+:doc:`kspace\_style pppm <kspace_style>` for long-range Coulombics.
+It has the following general features:
+
+* It is designed to exploit common GPU hardware configurations where one
+  or more GPUs are coupled to many cores of one or more multi-core CPUs,
+  e.g. within a node of a parallel machine.
+* Atom-based data (e.g. coordinates, forces) are moved back-and-forth
+  between the CPU(s) and GPU every timestep.
+* Neighbor lists can be built on the CPU or on the GPU
+* The charge assignment and force interpolation portions of PPPM can be
+  run on the GPU.  The FFT portion, which requires MPI communication
+  between processors, runs on the CPU.
+* Force computations of different style (pair vs. bond/angle/dihedral/improper)
+  can be performed concurrently on the GPU and CPU(s), respectively.
+* It allows for GPU computations to be performed in single or double
+  precision, or in mixed-mode precision, where pairwise forces are
+  computed in single precision, but accumulated into double-precision
+  force vectors.
+* LAMMPS-specific code is in the GPU package.  It makes calls to a
+  generic GPU library in the lib/gpu directory.  This library provides
+  NVIDIA support as well as more general OpenCL support, so that the
+  same functionality is supported on a variety of hardware.
+
+
+**Required hardware/software:**
+
+To compile and use this package in CUDA mode, you currently need
+to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
+toolkit software on your system (this is primarily tested on Linux
+and completely unsupported on Windows):
+
+* Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information
+* Go to http://www.nvidia.com/object/cuda\_get.html
+* Install a driver and toolkit appropriate for your system (SDK is not necessary)
+* Run lammps/lib/gpu/nvc\_get\_devices (after building the GPU library, see below) to
+  list supported devices and properties
+
+To compile and use this package in OpenCL mode, you currently need
+to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
+In OpenCL mode, the acceleration depends on having an `OpenCL Installable Client Driver (ICD) <https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader>`_
+installed. There can be multiple of them for the same or different hardware
+(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
+as 'platforms'.  The GPU library will select the **first** suitable platform,
+but this can be overridden using the device option of the :doc:`package <package>`
+command. run lammps/lib/gpu/ocl\_get\_devices to get a list of available
+platforms and devices with a suitable ICD available.
+
+**Building LAMMPS with the GPU package:**
+
+See the :ref:`Build extras <gpu>` doc page for
+instructions.
+
+**Run with the GPU package from the command line:**
+
+The mpirun or mpiexec command sets the total number of MPI tasks used
+by LAMMPS (one or multiple per compute node) and the number of MPI
+tasks used per node.  E.g. the mpirun command in MPICH does this via
+its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
+
+When using the GPU package, you cannot assign more than one GPU to a
+single MPI task.  However multiple MPI tasks can share the same GPU,
+and in many cases it will be more efficient to run this way.  Likewise
+it may be more efficient to use less MPI tasks/node than the available
+# of CPU cores.  Assignment of multiple MPI tasks to a GPU will happen
+automatically if you create more MPI tasks/node than there are
+GPUs/mode.  E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
+shared by 4 MPI tasks.
+
+Use the "-sf gpu" :doc:`command-line switch <Run_options>`, which will
+automatically append "gpu" to styles that support it.  Use the "-pk
+gpu Ng" :doc:`command-line switch <Run_options>` to set Ng = # of
+GPUs/node to use.
+
+
+.. parsed-literal::
+
+   lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
+   mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script           # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
+   mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script   # ditto on 4 16-core nodes
+
+Note that if the "-sf gpu" switch is used, it also issues a default
+:doc:`package gpu 1 <package>` command, which sets the number of
+GPUs/node to 1.
+
+Using the "-pk" switch explicitly allows for setting of the number of
+GPUs/node to use and additional options.  Its syntax is the same as
+same as the "package gpu" command.  See the :doc:`package <package>`
+command doc page for details, including the default values used for
+all its options if it is not specified.
+
+Note that the default for the :doc:`package gpu <package>` command is to
+set the Newton flag to "off" pairwise interactions.  It does not
+affect the setting for bonded interactions (LAMMPS default is "on").
+The "off" setting for pairwise interaction is currently required for
+GPU package pair styles.
+
+**Or run with the GPU package by editing an input script:**
+
+The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+and use of multiple MPI tasks/GPU is the same.
+
+Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
+"gpu" suffix to individual styles in your input script, e.g.
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/gpu 2.5
+
+You must also use the :doc:`package gpu <package>` command to enable the
+GPU package, unless the "-sf gpu" or "-pk gpu" :doc:`command-line switches <Run_options>` were used.  It specifies the number of
+GPUs/node to use, as well as other options.
+
+**Speed-ups to expect:**
+
+The performance of a GPU versus a multi-core CPU is a function of your
+hardware, which pair style is used, the number of atoms/GPU, and the
+precision used on the GPU (double, single, mixed). Using the GPU package
+in OpenCL mode on CPUs (which uses vectorization and multithreading) is
+usually resulting in inferior performance compared to using LAMMPS' native
+threading and vectorization support in the USER-OMP and USER-INTEL packages.
+
+See the `Benchmark page <http://lammps.sandia.gov/bench.html>`_ of the
+LAMMPS web site for performance of the GPU package on various
+hardware, including the Titan HPC platform at ORNL.
+
+You should also experiment with how many MPI tasks per GPU to use to
+give the best performance for your problem and machine.  This is also
+a function of the problem size and the pair style being using.
+Likewise, you should experiment with the precision setting for the GPU
+library to see if single or mixed precision will give accurate
+results, since they will typically be faster.
+
+**Guidelines for best performance:**
+
+* Using multiple MPI tasks per GPU will often give the best performance,
+  as allowed my most multi-core CPU/GPU configurations.
+* If the number of particles per MPI task is small (e.g. 100s of
+  particles), it can be more efficient to run with fewer MPI tasks per
+  GPU, even if you do not use all the cores on the compute node.
+* The :doc:`package gpu <package>` command has several options for tuning
+  performance.  Neighbor lists can be built on the GPU or CPU.  Force
+  calculations can be dynamically balanced across the CPU cores and
+  GPUs.  GPU-specific settings can be made which can be optimized
+  for different hardware.  See the :doc:`package <package>` command
+  doc page for details.
+* As described by the :doc:`package gpu <package>` command, GPU
+  accelerated pair styles can perform computations asynchronously with
+  CPU computations. The "Pair" time reported by LAMMPS will be the
+  maximum of the time required to complete the CPU pair style
+  computations and the time required to complete the GPU pair style
+  computations. Any time spent for GPU-enabled pair styles for
+  computations that run simultaneously with :doc:`bond <bond_style>`,
+  :doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`,
+  :doc:`improper <improper_style>`, and :doc:`long-range <kspace_style>`
+  calculations will not be included in the "Pair" time.
+* When the *mode* setting for the package gpu command is force/neigh,
+  the time for neighbor list calculations on the GPU will be added into
+  the "Pair" time, not the "Neigh" time.  An additional breakdown of the
+  times required for various tasks on the GPU (data copy, neighbor
+  calculations, force computations, etc) are output only with the LAMMPS
+  screen output (not in the log file) at the end of each run.  These
+  timings represent total time spent on the GPU for each routine,
+  regardless of asynchronous CPU calculations.
+* The output section "GPU Time Info (average)" reports "Max Mem / Proc".
+  This is the maximum memory used at one time on the GPU for data
+  storage by a single MPI process.
+
+
+Restrictions
+""""""""""""
+
+
+None.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst
new file mode 100644
index 0000000000..f70852701b
--- /dev/null
+++ b/doc/src/Speed_intel.rst
@@ -0,0 +1,553 @@
+USER-INTEL package
+==================
+
+The USER-INTEL package is maintained by Mike Brown at Intel
+Corporation.  It provides two methods for accelerating simulations,
+depending on the hardware you have.  The first is acceleration on
+Intel CPUs by running in single, mixed, or double precision with
+vectorization.  The second is acceleration on Intel Xeon Phi
+co-processors via offloading neighbor list and non-bonded force
+calculations to the Phi.  The same C++ code is used in both cases.
+When offloading to a co-processor from a CPU, the same routine is run
+twice, once on the CPU and once with an offload flag. This allows
+LAMMPS to run on the CPU cores and co-processor cores simultaneously.
+
+**Currently Available USER-INTEL Styles:**
+
+* Angle Styles: charmm, harmonic
+* Bond Styles: fene, fourier, harmonic
+* Dihedral Styles: charmm, fourier, harmonic, opls
+* Fixes: nve, npt, nvt, nvt/sllod, nve/asphere
+* Improper Styles: cvff, harmonic
+* Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
+  buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
+  lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long,
+  rebo, sw, tersoff
+* K-Space Styles: pppm, pppm/disp
+
+
+.. warning::
+
+   None of the styles in the USER-INTEL package currently
+   support computing per-atom stress.  If any compute or fix in your
+   input requires it, LAMMPS will abort with an error message.
+
+**Speed-ups to expect:**
+
+The speedups will depend on your simulation, the hardware, which
+styles are used, the number of atoms, and the floating-point
+precision mode. Performance improvements are shown compared to
+LAMMPS *without using other acceleration packages* as these are
+under active development (and subject to performance changes). The
+measurements were performed using the input files available in
+the src/USER-INTEL/TEST directory with the provided run script.
+These are scalable in size; the results given are with 512K
+particles (524K for Liquid Crystal). Most of the simulations are
+standard LAMMPS benchmarks (indicated by the filename extension in
+parenthesis) with modifications to the run length and to add a
+warm-up run (for use with offload benchmarks).
+
+.. image:: JPG/user_intel.png
+   :align: center
+
+Results are speedups obtained on Intel Xeon E5-2697v4 processors
+(code-named Broadwell), Intel Xeon Phi 7250 processors (code-named
+Knights Landing), and Intel Xeon Gold 6148 processors (code-named
+Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
+2017 update 2. Results are with 1 MPI task per physical core. See
+*src/USER-INTEL/TEST/README* for the raw simulation rates and
+instructions to reproduce.
+
+
+----------
+
+
+**Accuracy and order of operations:**
+
+In most molecular dynamics software, parallelization parameters
+(# of MPI, OpenMP, and vectorization) can change the results due
+to changing the order of operations with finite-precision
+calculations. The USER-INTEL package is deterministic. This means
+that the results should be reproducible from run to run with the
+*same* parallel configurations and when using deterministic
+libraries or library settings (MPI, OpenMP, FFT). However, there
+are differences in the USER-INTEL package that can change the
+order of operations compared to LAMMPS without acceleration:
+
+* Neighbor lists can be created in a different order
+* Bins used for sorting atoms can be oriented differently
+* The default stencil order for PPPM is 7. By default, LAMMPS will
+  calculate other PPPM parameters to fit the desired accuracy with
+  this order
+* The *newton* setting applies to all atoms, not just atoms shared
+  between MPI tasks
+* Vectorization can change the order for adding pairwise forces
+* When using the -DLMP\_USE\_MKL\_RNG define (all included intel optimized
+  makefiles do) at build time, the random number generator for
+  dissipative particle dynamics (pair style dpd/intel) uses the Mersenne
+  Twister generator included in the Intel MKL library (that should be
+  more robust than the default Masaglia random number generator)
+
+
+The precision mode (described below) used with the USER-INTEL
+package can change the *accuracy* of the calculations. For the
+default *mixed* precision option, calculations between pairs or
+triplets of atoms are performed in single precision, intended to
+be within the inherent error of MD simulations. All accumulation
+is performed in double precision to prevent the error from growing
+with the number of atoms in the simulation. *Single* precision
+mode should not be used without appropriate validation.
+
+
+----------
+
+
+**Quick Start for Experienced Users:**
+
+LAMMPS should be built with the USER-INTEL package installed.
+Simulations should be run with 1 MPI task per physical *core*\ ,
+not *hardware thread*\ .
+
+* Edit src/MAKE/OPTIONS/Makefile.intel\_cpu\_intelmpi as necessary.
+* Set the environment variable KMP\_BLOCKTIME=0
+* "-pk intel 0 omp $t -sf intel" added to LAMMPS command-line
+* $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi
+* For some of the simple 2-body potentials without long-range
+  electrostatics, performance and scalability can be better with
+  the "newton off" setting added to the input script
+* For simulations on higher node counts, add "processors \* \* \* grid
+  numa" to the beginning of the input script for better scalability
+* If using *kspace\_style pppm* in the input script, add
+  "kspace\_modify diff ad" for better performance
+
+
+For Intel Xeon Phi CPUs:
+
+* Runs should be performed using MCDRAM.
+
+
+For simulations using *kspace\_style pppm* on Intel CPUs supporting
+AVX-512:
+
+* Add "kspace\_modify diff ad" to the input script
+* The command-line option should be changed to
+  "-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
+  threads minus 1.
+* Do not use thread affinity (set KMP\_AFFINITY=none)
+* The "newton off" setting may provide better scalability
+
+
+For Intel Xeon Phi co-processors (Offload):
+
+* Edit src/MAKE/OPTIONS/Makefile.intel\_co-processor as necessary
+* "-pk intel N omp 1" added to command-line where N is the number of
+  co-processors per node.
+
+
+
+----------
+
+
+**Required hardware/software:**
+
+In order to use offload to co-processors, an Intel Xeon Phi
+co-processor and an Intel compiler are required. For this, the
+recommended version of the Intel compiler is 14.0.1.106 or
+versions 15.0.2.044 and higher.
+
+Although any compiler can be used with the USER-INTEL package,
+currently, vectorization directives are disabled by default when
+not using Intel compilers due to lack of standard support and
+observations of decreased performance. The OpenMP standard now
+supports directives for vectorization and we plan to transition the
+code to this standard once it is available in most compilers. We
+expect this to allow improved performance and support with other
+compilers.
+
+For Intel Xeon Phi x200 series processors (code-named Knights
+Landing), there are multiple configuration options for the hardware.
+For best performance, we recommend that the MCDRAM is configured in
+"Flat" mode and with the cluster mode set to "Quadrant" or "SNC4".
+"Cache" mode can also be used, although the performance might be
+slightly lower.
+
+**Notes about Simultaneous Multithreading:**
+
+Modern CPUs often support Simultaneous Multithreading (SMT). On
+Intel processors, this is called Hyper-Threading (HT) technology.
+SMT is hardware support for running multiple threads efficiently on
+a single core. *Hardware threads* or *logical cores* are often used
+to refer to the number of threads that are supported in hardware.
+For example, the Intel Xeon E5-2697v4 processor is described
+as having 36 cores and 72 threads. This means that 36 MPI processes
+or OpenMP threads can run simultaneously on separate cores, but that
+up to 72 MPI processes or OpenMP threads can be running on the CPU
+without costly operating system context switches.
+
+Molecular dynamics simulations will often run faster when making use
+of SMT. If a thread becomes stalled, for example because it is
+waiting on data that has not yet arrived from memory, another thread
+can start running so that the CPU pipeline is still being used
+efficiently. Although benefits can be seen by launching a MPI task
+for every hardware thread, for multinode simulations, we recommend
+that OpenMP threads are used for SMT instead, either with the
+USER-INTEL package, :doc:`USER-OMP package <Speed_omp>`, or
+:doc:`KOKKOS package <Speed_kokkos>`. In the example above, up
+to 36X speedups can be observed by using all 36 physical cores with
+LAMMPS. By using all 72 hardware threads, an additional 10-30%
+performance gain can be achieved.
+
+The BIOS on many platforms allows SMT to be disabled, however, we do
+not recommend this on modern processors as there is little to no
+benefit for any software package in most cases. The operating system
+will report every hardware thread as a separate core allowing one to
+determine the number of hardware threads available. On Linux systems,
+this information can normally be obtained with:
+
+
+.. parsed-literal::
+
+   cat /proc/cpuinfo
+
+**Building LAMMPS with the USER-INTEL package:**
+
+See the :ref:`Build extras <user-intel>` doc page for
+instructions.  Some additional details are covered here.
+
+For building with make, several example Makefiles for building with
+the Intel compiler are included with LAMMPS in the src/MAKE/OPTIONS/
+directory:
+
+
+.. parsed-literal::
+
+   Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
+   Makefile.knl                # Intel Compiler, Intel MPI, No Offload
+   Makefile.intel_cpu_mpich    # Intel Compiler, MPICH, No Offload
+   Makefile.intel_cpu_openpmi  # Intel Compiler, OpenMPI, No Offload
+   Makefile.intel_co-processor  # Intel Compiler, Intel MPI, Offload
+
+Makefile.knl is identical to Makefile.intel\_cpu\_intelmpi except that
+it explicitly specifies that vectorization should be for Intel Xeon
+Phi x200 processors making it easier to cross-compile. For users with
+recent installations of Intel Parallel Studio, the process can be as
+simple as:
+
+
+.. parsed-literal::
+
+   make yes-user-intel
+   source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
+   # or psxevars.csh for C-shell
+   make intel_cpu_intelmpi
+
+Note that if you build with support for a Phi co-processor, the same
+binary can be used on nodes with or without co-processors installed.
+However, if you do not have co-processors on your system, building
+without offload support will produce a smaller binary.
+
+The general requirements for Makefiles with the USER-INTEL package
+are as follows. When using Intel compilers, "-restrict" is required
+and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS.
+CCFLAGS should include "-DLMP\_INTEL\_USELRT" (unless POSIX Threads
+are not supported in the build environment) and "-DLMP\_USE\_MKL\_RNG"
+(unless Intel Math Kernel Library (MKL) is not available in the build
+environment). For Intel compilers, LIB should include "-ltbbmalloc"
+or if the library is not available, "-DLMP\_INTEL\_NO\_TBB" can be added
+to CCFLAGS. For builds supporting offload, "-DLMP\_INTEL\_OFFLOAD" is
+required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
+recommended CCFLAG options for best performance are "-O2 -fno-alias
+-ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div".
+
+.. note::
+
+   See the src/USER-INTEL/README file for additional flags that
+   might be needed for best performance on Intel server processors
+   code-named "Skylake".
+
+.. note::
+
+   The vectorization and math capabilities can differ depending on
+   the CPU. For Intel compilers, the "-x" flag specifies the type of
+   processor for which to optimize. "-xHost" specifies that the compiler
+   should build for the processor used for compiling. For Intel Xeon Phi
+   x200 series processors, this option is "-xMIC-AVX512". For fourth
+   generation Intel Xeon (v4/Broadwell) processors, "-xCORE-AVX2" should
+   be used. For older Intel Xeon processors, "-xAVX" will perform best
+   in general for the different simulations in LAMMPS. The default
+   in most of the example Makefiles is to use "-xHost", however this
+   should not be used when cross-compiling.
+
+**Running LAMMPS with the USER-INTEL package:**
+
+Running LAMMPS with the USER-INTEL package is similar to normal use
+with the exceptions that one should 1) specify that LAMMPS should use
+the USER-INTEL package, 2) specify the number of OpenMP threads, and
+3) optionally specify the specific LAMMPS styles that should use the
+USER-INTEL package. 1) and 2) can be performed from the command-line
+or by editing the input script. 3) requires editing the input script.
+Advanced performance tuning options are also described below to get
+the best performance.
+
+When running on a single node (including runs using offload to a
+co-processor), best performance is normally obtained by using 1 MPI
+task per physical core and additional OpenMP threads with SMT. For
+Intel Xeon processors, 2 OpenMP threads should be used for SMT.
+For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used
+(best choice depends on the simulation). In cases where the user
+specifies that LRT mode is used (described below), 1 or 3 OpenMP
+threads should be used. For multi-node runs, using 1 MPI task per
+physical core will often perform best, however, depending on the
+machine and scale, users might get better performance by decreasing
+the number of MPI tasks and using more OpenMP threads. For
+performance, the product of the number of MPI tasks and OpenMP
+threads should not exceed the number of available hardware threads in
+almost all cases.
+
+.. note::
+
+   Setting core affinity is often used to pin MPI tasks and OpenMP
+   threads to a core or group of cores so that memory access can be
+   uniform. Unless disabled at build time, affinity for MPI tasks and
+   OpenMP threads on the host (CPU) will be set by default on the host
+   *when using offload to a co-processor*\ . In this case, it is unnecessary
+   to use other methods to control affinity (e.g. taskset, numactl,
+   I\_MPI\_PIN\_DOMAIN, etc.). This can be disabled with the *no\_affinity*
+   option to the :doc:`package intel <package>` command or by disabling the
+   option at build time (by adding -DINTEL\_OFFLOAD\_NOAFFINITY to the
+   CCFLAGS line of your Makefile). Disabling this option is not
+   recommended, especially when running on a machine with Intel
+   Hyper-Threading technology disabled.
+
+**Run with the USER-INTEL package from the command line:**
+
+To enable USER-INTEL optimizations for all available styles used in
+the input script, the "-sf intel" :doc:`command-line switch <Run_options>` can be used without any requirement for
+editing the input script. This switch will automatically append
+"intel" to styles that support it. It also invokes a default command:
+:doc:`package intel 1 <package>`. This package command is used to set
+options for the USER-INTEL package.  The default package command will
+specify that USER-INTEL calculations are performed in mixed precision,
+that the number of OpenMP threads is specified by the OMP\_NUM\_THREADS
+environment variable, and that if co-processors are present and the
+binary was built with offload support, that 1 co-processor per node
+will be used with automatic balancing of work between the CPU and the
+co-processor.
+
+You can specify different options for the USER-INTEL package by using
+the "-pk intel Nphi" :doc:`command-line switch <Run_options>` with
+keyword/value pairs as specified in the documentation. Here, Nphi = #
+of Xeon Phi co-processors/node (ignored without offload
+support). Common options to the USER-INTEL package include *omp* to
+override any OMP\_NUM\_THREADS setting and specify the number of OpenMP
+threads, *mode* to set the floating-point precision mode, and *lrt* to
+enable Long-Range Thread mode as described below. See the :doc:`package intel <package>` command for details, including the default values
+used for all its options if not specified, and how to set the number
+of OpenMP threads via the OMP\_NUM\_THREADS environment variable if
+desired.
+
+Examples (see documentation for your MPI/Machine for differences in
+launching MPI applications):
+
+
+.. parsed-literal::
+
+   mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script                                 # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
+   mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision
+
+**Or run with the USER-INTEL package by editing an input script:**
+
+As an alternative to adding command-line arguments, the input script
+can be edited to enable the USER-INTEL package. This requires adding
+the :doc:`package intel <package>` command to the top of the input
+script. For the second example above, this would be:
+
+
+.. parsed-literal::
+
+   package intel 0 omp 2 mode double
+
+To enable the USER-INTEL package only for individual styles, you can
+add an "intel" suffix to the individual style, e.g.:
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/intel 2.5
+
+Alternatively, the :doc:`suffix intel <suffix>` command can be added to
+the input script to enable USER-INTEL styles for the commands that
+follow in the input script.
+
+**Tuning for Performance:**
+
+.. note::
+
+   The USER-INTEL package will perform better with modifications
+   to the input script when :doc:`PPPM <kspace_style>` is used:
+   :doc:`kspace\_modify diff ad <kspace_modify>` should be added to the
+   input script.
+
+Long-Range Thread (LRT) mode is an option to the :doc:`package intel <package>` command that can improve performance when using
+:doc:`PPPM <kspace_style>` for long-range electrostatics on processors
+with SMT. It generates an extra pthread for each MPI task. The thread
+is dedicated to performing some of the PPPM calculations and MPI
+communications. This feature requires setting the pre-processor flag
+-DLMP\_INTEL\_USELRT in the makefile when compiling LAMMPS. It is unset
+in the default makefiles (\ *Makefile.mpi* and *Makefile.serial*\ ) but
+it is set in all makefiles tuned for the USER-INTEL package.  On Intel
+Xeon Phi x200 series CPUs, the LRT feature will likely improve
+performance, even on a single node. On Intel Xeon processors, using
+this mode might result in better performance when using multiple nodes,
+depending on the specific machine configuration. To enable LRT mode,
+specify that the number of OpenMP threads is one less than would
+normally be used for the run and add the "lrt yes" option to the "-pk"
+command-line suffix or "package intel" command. For example, if a run
+would normally perform best with "-pk intel 0 omp 4", instead use
+"-pk intel 0 omp 3 lrt yes". When using LRT, you should set the
+environment variable "KMP\_AFFINITY=none". LRT mode is not supported
+when using offload.
+
+.. note::
+
+   Changing the :doc:`newton <newton>` setting to off can improve
+   performance and/or scalability for simple 2-body potentials such as
+   lj/cut or when using LRT mode on processors supporting AVX-512.
+
+Not all styles are supported in the USER-INTEL package. You can mix
+the USER-INTEL package with styles from the :doc:`OPT <Speed_opt>`
+package or the :doc:`USER-OMP package <Speed_omp>`. Of course, this
+requires that these packages were installed at build time. This can
+performed automatically by using "-sf hybrid intel opt" or "-sf hybrid
+intel omp" command-line options. Alternatively, the "opt" and "omp"
+suffixes can be appended manually in the input script. For the latter,
+the :doc:`package omp <package>` command must be in the input script or
+the "-pk omp Nt" :doc:`command-line switch <Run_options>` must be used
+where Nt is the number of OpenMP threads. The number of OpenMP threads
+should not be set differently for the different packages. Note that
+the :doc:`suffix hybrid intel omp <suffix>` command can also be used
+within the input script to automatically append the "omp" suffix to
+styles when USER-INTEL styles are not available.
+
+.. note::
+
+   For simulations on higher node counts, add :doc:`processors \* \* \* grid numa <processors>` to the beginning of the input script for
+   better scalability.
+
+When running on many nodes, performance might be better when using
+fewer OpenMP threads and more MPI tasks. This will depend on the
+simulation and the machine. Using the :doc:`verlet/split <run_style>`
+run style might also give better performance for simulations with
+:doc:`PPPM <kspace_style>` electrostatics. Note that this is an
+alternative to LRT mode and the two cannot be used together.
+
+Currently, when using Intel MPI with Intel Xeon Phi x200 series
+CPUs, better performance might be obtained by setting the
+environment variable "I\_MPI\_SHM\_LMT=shm" for Linux kernels that do
+not yet have full support for AVX-512. Runs on Intel Xeon Phi x200
+series processors will always perform better using MCDRAM. Please
+consult your system documentation for the best approach to specify
+that MPI runs are performed in MCDRAM.
+
+**Tuning for Offload Performance:**
+
+The default settings for offload should give good performance.
+
+When using LAMMPS with offload to Intel co-processors, best performance
+will typically be achieved with concurrent calculations performed on
+both the CPU and the co-processor. This is achieved by offloading only
+a fraction of the neighbor and pair computations to the co-processor or
+using :doc:`hybrid <pair_hybrid>` pair styles where only one style uses
+the "intel" suffix. For simulations with long-range electrostatics or
+bond, angle, dihedral, improper calculations, computation and data
+transfer to the co-processor will run concurrently with computations
+and MPI communications for these calculations on the host CPU. This
+is illustrated in the figure below for the rhodopsin protein benchmark
+running on E5-2697v2 processors with a Intel Xeon Phi 7120p
+co-processor. In this plot, the vertical access is time and routines
+running at the same time are running concurrently on both the host and
+the co-processor.
+
+.. image:: JPG/offload_knc.png
+   :align: center
+
+The fraction of the offloaded work is controlled by the *balance*
+keyword in the :doc:`package intel <package>` command. A balance of 0
+runs all calculations on the CPU.  A balance of 1 runs all
+supported calculations on the co-processor.  A balance of 0.5 runs half
+of the calculations on the co-processor.  Setting the balance to -1
+(the default) will enable dynamic load balancing that continuously
+adjusts the fraction of offloaded work throughout the simulation.
+Because data transfer cannot be timed, this option typically produces
+results within 5 to 10 percent of the optimal fixed balance.
+
+If running short benchmark runs with dynamic load balancing, adding a
+short warm-up run (10-20 steps) will allow the load-balancer to find a
+near-optimal setting that will carry over to additional runs.
+
+The default for the :doc:`package intel <package>` command is to have
+all the MPI tasks on a given compute node use a single Xeon Phi
+co-processor.  In general, running with a large number of MPI tasks on
+each node will perform best with offload.  Each MPI task will
+automatically get affinity to a subset of the hardware threads
+available on the co-processor.  For example, if your card has 61 cores,
+with 60 cores available for offload and 4 hardware threads per core
+(240 total threads), running with 24 MPI tasks per node will cause
+each MPI task to use a subset of 10 threads on the co-processor.  Fine
+tuning of the number of threads to use per MPI task or the number of
+threads to use per core can be accomplished with keyword settings of
+the :doc:`package intel <package>` command.
+
+The USER-INTEL package has two modes for deciding which atoms will be
+handled by the co-processor.  This choice is controlled with the *ghost*
+keyword of the :doc:`package intel <package>` command.  When set to 0,
+ghost atoms (atoms at the borders between MPI tasks) are not offloaded
+to the card.  This allows for overlap of MPI communication of forces
+with computation on the co-processor when the :doc:`newton <newton>`
+setting is "on".  The default is dependent on the style being used,
+however, better performance may be achieved by setting this option
+explicitly.
+
+When using offload with CPU Hyper-Threading disabled, it may help
+performance to use fewer MPI tasks and OpenMP threads than available
+cores.  This is due to the fact that additional threads are generated
+internally to handle the asynchronous offload tasks.
+
+If pair computations are being offloaded to an Intel Xeon Phi
+co-processor, a diagnostic line is printed to the screen (not to the
+log file), during the setup phase of a run, indicating that offload
+mode is being used and indicating the number of co-processor threads
+per MPI task.  Additionally, an offload timing summary is printed at
+the end of each run.  When offloading, the frequency for :doc:`atom sorting <atom_modify>` is changed to 1 so that the per-atom data is
+effectively sorted at every rebuild of the neighbor lists. All the
+available co-processor threads on each Phi will be divided among MPI
+tasks, unless the *tptask* option of the "-pk intel" :doc:`command-line switch <Run_options>` is used to limit the co-processor threads per
+MPI task.
+
+Restrictions
+""""""""""""
+
+
+When offloading to a co-processor, :doc:`hybrid <pair_hybrid>` styles
+that require skip lists for neighbor builds cannot be offloaded.
+Using :doc:`hybrid/overlay <pair_hybrid>` is allowed.  Only one intel
+accelerated style may be used with hybrid styles when offloading.
+:doc:`Special\_bonds <special_bonds>` exclusion lists are not currently
+supported with offload, however, the same effect can often be
+accomplished by setting cutoffs for excluded atom types to 0.  None of
+the pair styles in the USER-INTEL package currently support the
+"inner", "middle", "outer" options for rRESPA integration via the
+:doc:`run\_style respa <run_style>` command; only the "pair" option is
+supported.
+
+**References:**
+
+* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
+* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
+* Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst
new file mode 100644
index 0000000000..6d3828ee68
--- /dev/null
+++ b/doc/src/Speed_kokkos.rst
@@ -0,0 +1,451 @@
+KOKKOS package
+==============
+
+Kokkos is a templated C++ library that provides abstractions to allow
+a single implementation of an application kernel (e.g. a pair style)
+to run efficiently on different kinds of hardware, such as GPUs, Intel
+Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
+different back end languages such as CUDA, OpenMP, or Pthreads.  The
+Kokkos library also provides data abstractions to adjust (at compile
+time) the memory layout of data structures like 2d and 3d arrays to
+optimize performance on different hardware. For more information on
+Kokkos, see `GitHub <https://github.com/kokkos/kokkos>`_. Kokkos is part
+of `Trilinos <http://trilinos.sandia.gov/packages/kokkos>`_. The Kokkos
+library was written primarily by Carter Edwards, Christian Trott, and
+Dan Sunderland (all Sandia).
+
+The LAMMPS KOKKOS package contains versions of pair, fix, and atom
+styles that use data structures and macros provided by the Kokkos
+library, which is included with LAMMPS in /lib/kokkos. The KOKKOS
+package was developed primarily by Christian Trott (Sandia) and Stan
+Moore (Sandia) with contributions of various styles by others,
+including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
+(Sandia). For more information on developing using Kokkos abstractions
+see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos\_PG.pdf.
+
+Kokkos currently provides support for 3 modes of execution (per MPI
+task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
+(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
+GPUs). You choose the mode at build time to produce an executable
+compatible with specific hardware.
+
+.. note::
+
+   Kokkos support within LAMMPS must be built with a C++11 compatible
+   compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
+   Clang 3.5.2 or later is required.
+
+.. note::
+
+   To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA
+   software version 7.5 or later must be installed on your system. See
+   the discussion for the :doc:`GPU package <Speed_gpu>` for details of how
+   to check and do this.
+
+.. note::
+
+   Kokkos with CUDA currently implicitly assumes that the MPI library
+   is CUDA-aware. This is not always the case, especially when using
+   pre-compiled MPI libraries provided by a Linux distribution. This is not
+   a problem when using only a single GPU with a single MPI rank. When
+   running with multiple MPI ranks, you may see segmentation faults without
+   CUDA-aware MPI support. These can be avoided by adding the flags :doc:`-pk kokkos cuda/aware off <Run_options>` to the LAMMPS command line or by
+   using the command :doc:`package kokkos cuda/aware off <package>` in the
+   input file.
+
+**Building LAMMPS with the KOKKOS package:**
+
+See the :ref:`Build extras <kokkos>` doc page for instructions.
+
+**Running LAMMPS with the KOKKOS package:**
+
+All Kokkos operations occur within the context of an individual MPI
+task running on a single node of the machine. The total number of MPI
+tasks used by LAMMPS (one or multiple per compute node) is set in the
+usual manner via the mpirun or mpiexec commands, and is independent of
+Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
+-npernode switches. Ditto for MPICH via -np and -ppn.
+
+**Running on a multi-core CPU:**
+
+Here is a quick overview of how to use the KOKKOS package
+for CPU acceleration, assuming one or more 16-core nodes.
+
+
+.. parsed-literal::
+
+   mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj        # 1 node, 16 MPI tasks/node, no multi-threading
+   mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj  # 2 nodes, 1 MPI task/node, 16 threads/task
+   mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj          # 1 node,  2 MPI tasks/node, 8 threads/task
+   mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj  # 8 nodes, 4 MPI tasks/node, 4 threads/task
+
+To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
+kokkos" :doc:`command-line switches <Run_options>` in your mpirun
+command.  You must use the "-k on" :doc:`command-line switch <Run_options>` to enable the KOKKOS package. It takes
+additional arguments for hardware settings appropriate to your system.
+For OpenMP use:
+
+
+.. parsed-literal::
+
+   -k on t Nt
+
+The "t Nt" option specifies how many OpenMP threads per MPI task to
+use with a node. The default is Nt = 1, which is MPI-only mode.  Note
+that the product of MPI tasks \* OpenMP threads/task should not exceed
+the physical number of cores (on a node), otherwise performance will
+suffer. If Hyper-Threading (HT) is enabled, then the product of MPI
+tasks \* OpenMP threads/task should not exceed the physical number of
+cores \* hardware threads.  The "-k on" switch also issues a
+"package kokkos" command (with no additional arguments) which sets
+various KOKKOS options to default values, as discussed on the
+:doc:`package <package>` command doc page.
+
+The "-sf kk" :doc:`command-line switch <Run_options>` will automatically
+append the "/kk" suffix to styles that support it.  In this manner no
+modification to the input script is needed. Alternatively, one can run
+with the KOKKOS package by editing the input script as described
+below.
+
+.. note::
+
+   When using a single OpenMP thread, the Kokkos Serial back end (i.e.
+   Makefile.kokkos\_mpi\_only) will give better performance than the OpenMP
+   back end (i.e. Makefile.kokkos\_omp) because some of the overhead to make
+   the code thread-safe is removed.
+
+.. note::
+
+   Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to
+   change the default :doc:`package kokkos <package>` options. See its doc
+   page for details and default settings. Experimenting with its options
+   can provide a speed-up for specific calculations. For example:
+
+
+.. parsed-literal::
+
+   mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm
+
+If the :doc:`newton <newton>` command is used in the input
+script, it can also override the Newton flag defaults.
+
+For half neighbor lists and OpenMP, the KOKKOS package uses data
+duplication (i.e. thread-private arrays) by default to avoid
+thread-level write conflicts in the force arrays (and other data
+structures as necessary). Data duplication is typically fastest for
+small numbers of threads (i.e. 8 or less) but does increase memory
+footprint and is not scalable to large numbers of threads. An
+alternative to data duplication is to use thread-level atomic operations
+which do not require data duplication. The use of atomic operations can
+be enforced by compiling LAMMPS with the "-DLMP\_KOKKOS\_USE\_ATOMICS"
+pre-processor flag. Most but not all Kokkos-enabled pair\_styles support
+data duplication. Alternatively, full neighbor lists avoid the need for
+duplication or atomic operations but require more compute operations per
+atom.  When using the Kokkos Serial back end or the OpenMP back end with
+a single thread, no duplication or atomic operations are used. For CUDA
+and half neighbor lists, the KOKKOS package always uses atomic operations.
+
+**Core and Thread Affinity:**
+
+When using multi-threading, it is important for performance to bind
+both MPI tasks to physical cores, and threads to physical cores, so
+they do not migrate during a simulation.
+
+If you are not certain MPI tasks are being bound (check the defaults
+for your MPI installation), binding can be forced with these flags:
+
+
+.. parsed-literal::
+
+   OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
+   Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...
+
+For binding threads with KOKKOS OpenMP, use thread affinity
+environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
+later, intel 12 or later) setting the environment variable
+OMP\_PROC\_BIND=true should be sufficient. In general, for best
+performance with OpenMP 4.0 or better set OMP\_PROC\_BIND=spread and
+OMP\_PLACES=threads.  For binding threads with the KOKKOS pthreads
+option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.
+
+**Running on Knight's Landing (KNL) Intel Xeon Phi:**
+
+Here is a quick overview of how to use the KOKKOS package for the
+Intel Knight's Landing (KNL) Xeon Phi:
+
+KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
+reserved for the OS, and only 64 or 66 cores are used. Each core has 4
+Hyper-Threads,so there are effectively N = 256 (4\*64) or N = 264 (4\*66)
+cores to run on. The product of MPI tasks \* OpenMP threads/task should
+not exceed this limit, otherwise performance will suffer. Note that
+with the KOKKOS package you do not need to specify how many KNLs there
+are per node; each KNL is simply treated as running some number of MPI
+tasks.
+
+Examples of mpirun commands that follow these rules are shown below.
+
+
+.. parsed-literal::
+
+   Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
+   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 64 MPI tasks/node, 4 threads/task
+   mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 66 MPI tasks/node, 4 threads/task
+   mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj      # 1 node, 32 MPI tasks/node, 8 threads/task
+   mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj  # 8 nodes, 64 MPI tasks/node, 4 threads/task
+
+The -np setting of the mpirun command sets the number of MPI
+tasks/node. The "-k on t Nt" command-line switch sets the number of
+threads/task as Nt. The product of these two values should be N, i.e.
+256 or 264.
+
+.. note::
+
+   The default for the :doc:`package kokkos <package>` command when
+   running on KNL is to use "half" neighbor lists and set the Newton flag
+   to "on" for both pairwise and bonded interactions. This will typically
+   be best for many-body potentials. For simpler pair-wise potentials, it
+   may be faster to use a "full" neighbor list with Newton flag to "off".
+   Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
+   the default :doc:`package kokkos <package>` options. See its doc page for
+   details and default settings. Experimenting with its options can provide
+   a speed-up for specific calculations. For example:
+
+
+.. parsed-literal::
+
+   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax      #  Newton on, half neighbor list, threaded comm
+   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm
+
+.. note::
+
+   MPI tasks and threads should be bound to cores as described
+   above for CPUs.
+
+.. note::
+
+   To build with Kokkos support for Intel Xeon Phi co-processors
+   such as Knight's Corner (KNC), your system must be configured to use
+   them in "native" mode, not "offload" mode like the USER-INTEL package
+   supports.
+
+**Running on GPUs:**
+
+Use the "-k" :doc:`command-line switch <Run_options>` to specify the
+number of GPUs per node. Typically the -np setting of the mpirun command
+should set the number of MPI tasks/node to be equal to the number of
+physical GPUs on the node. You can assign multiple MPI tasks to the same
+GPU with the KOKKOS package, but this is usually only faster if some
+portions of the input script have not been ported to use Kokkos. In this
+case, also packing/unpacking communication buffers on the host may give
+speedup (see the KOKKOS :doc:`package <package>` command). Using CUDA MPS
+is recommended in this scenario.
+
+Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
+avoided by using :doc:`-pk kokkos cuda/aware no <package>`. As above for
+multi-core CPUs (and no GPU), if N is the number of physical cores/node,
+then the number of MPI tasks/node should not exceed N.
+
+
+.. parsed-literal::
+
+   -k on g Ng
+
+Here are examples of how to use the KOKKOS package for GPUs, assuming
+one or more nodes, each with two GPUs:
+
+
+.. parsed-literal::
+
+   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
+   mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total)
+
+.. note::
+
+   The default for the :doc:`package kokkos <package>` command when
+   running on GPUs is to use "full" neighbor lists and set the Newton flag
+   to "off" for both pairwise and bonded interactions, along with threaded
+   communication. When running on Maxwell or Kepler GPUs, this will
+   typically be best. For Pascal GPUs, using "half" neighbor lists and
+   setting the Newton flag to "on" may be faster. For many pair styles,
+   setting the neighbor binsize equal to twice the CPU default value will
+   give speedup, which is the default when running on GPUs. Use the "-pk
+   kokkos" :doc:`command-line switch <Run_options>` to change the default
+   :doc:`package kokkos <package>` options. See its doc page for details and
+   default settings. Experimenting with its options can provide a speed-up
+   for specific calculations. For example:
+
+
+.. parsed-literal::
+
+   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
+
+.. note::
+
+   For good performance of the KOKKOS package on GPUs, you must
+   have Kepler generation GPUs (or later). The Kokkos library exploits
+   texture cache options not supported by Telsa generation GPUs (or
+   older).
+
+.. note::
+
+   When using a GPU, you will achieve the best performance if your
+   input script does not use fix or compute styles which are not yet
+   Kokkos-enabled. This allows data to stay on the GPU for multiple
+   timesteps, without being copied back to the host CPU. Invoking a
+   non-Kokkos fix or compute, or performing I/O for
+   :doc:`thermo <thermo_style>` or :doc:`dump <dump>` output will cause data
+   to be copied back to the CPU incurring a performance penalty.
+
+.. note::
+
+   To get an accurate timing breakdown between time spend in pair,
+   kspace, etc., you must set the environment variable CUDA\_LAUNCH\_BLOCKING=1.
+   However, this will reduce performance and is not recommended for production runs.
+
+**Run with the KOKKOS package by editing an input script:**
+
+Alternatively the effect of the "-sf" or "-pk" switches can be
+duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.
+
+The discussion above for building LAMMPS with the KOKKOS package, the
+mpirun/mpiexec command, and setting appropriate thread are the same.
+
+You must still use the "-k on" :doc:`command-line switch <Run_options>`
+to enable the KOKKOS package, and specify its additional arguments for
+hardware options appropriate to your system, as documented above.
+
+You can use the :doc:`suffix kk <suffix>` command, or you can explicitly add a
+"kk" suffix to individual styles in your input script, e.g.
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/kk 2.5
+
+You only need to use the :doc:`package kokkos <package>` command if you
+wish to change any of its option defaults, as set by the "-k on"
+:doc:`command-line switch <Run_options>`.
+
+**Using OpenMP threading and CUDA together (experimental):**
+
+With the KOKKOS package, both OpenMP multi-threading and GPUs can be
+used together in a few special cases. In the Makefile, the
+KOKKOS\_DEVICES variable must include both "Cuda" and "OpenMP", as is
+the case for /src/MAKE/OPTIONS/Makefile.kokkos\_cuda\_mpi
+
+
+.. parsed-literal::
+
+   KOKKOS_DEVICES=Cuda,OpenMP
+
+The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
+using the "-sf kk" in the command line gives the default CUDA version
+everywhere.  However, if the "/kk/host" suffix is added to a specific
+style in the input script, the Kokkos OpenMP (CPU) version of that
+specific style will be used instead.  Set the number of OpenMP threads
+as "t Nt" and the number of GPUs as "g Ng"
+
+
+.. parsed-literal::
+
+   -k on t Nt g Ng
+
+For example, the command to run with 1 GPU and 8 OpenMP threads is then:
+
+
+.. parsed-literal::
+
+   mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk
+
+Conversely, if the "-sf kk/host" is used in the command line and then
+the "/kk" or "/kk/device" suffix is added to a specific style in your
+input script, then only that specific style will run on the GPU while
+everything else will run on the CPU in OpenMP mode. Note that the
+execution of the CPU and GPU styles will NOT overlap, except for a
+special case:
+
+A kspace style and/or molecular topology (bonds, angles, etc.) running
+on the host CPU can overlap with a pair style running on the
+GPU. First compile with "--default-stream per-thread" added to CCFLAGS
+in the Kokkos CUDA Makefile.  Then explicitly use the "/kk/host"
+suffix for kspace and bonds, angles, etc.  in the input file and the
+"kk" suffix (equal to "kk/device") on the command line.  Also make
+sure the environment variable CUDA\_LAUNCH\_BLOCKING is not set to "1"
+so CPU/GPU overlap can occur.
+
+**Speed-ups to expect:**
+
+The performance of KOKKOS running in different modes is a function of
+your hardware, which KOKKOS-enable styles are used, and the problem
+size.
+
+Generally speaking, the following rules of thumb apply:
+
+* When running on CPUs only, with a single thread per MPI task,
+  performance of a KOKKOS style is somewhere between the standard
+  (un-accelerated) styles (MPI-only mode), and those provided by the
+  USER-OMP package. However the difference between all 3 is small (less
+  than 20%).
+* When running on CPUs only, with multiple threads per MPI task,
+  performance of a KOKKOS style is a bit slower than the USER-OMP
+  package.
+* When running large number of atoms per GPU, KOKKOS is typically faster
+  than the GPU package.
+* When running on Intel hardware, KOKKOS is not as fast as
+  the USER-INTEL package, which is optimized for that hardware.
+
+
+See the `Benchmark page <http://lammps.sandia.gov/bench.html>`_ of the
+LAMMPS web site for performance of the KOKKOS package on different
+hardware.
+
+**Advanced Kokkos options:**
+
+There are other allowed options when building with the KOKKOS package.
+As explained on the :ref:`Build extras <kokkos>` doc page,
+they can be set either as variables on the make command line or in
+Makefile.machine, or they can be specified as CMake variables.  Each
+takes a value shown below.  The default value is listed, which is set
+in the lib/kokkos/Makefile.kokkos file.
+
+* KOKKOS\_DEBUG, values = *yes*\ , *no*\ , default = *no*
+* KOKKOS\_USE\_TPLS, values = *hwloc*\ , *librt*\ , *experimental\_memkind*, default = *none*
+* KOKKOS\_CXX\_STANDARD, values = *c++11*\ , *c++1z*\ , default = *c++11*
+* KOKKOS\_OPTIONS, values = *aggressive\_vectorization*, *disable\_profiling*, default = *none*
+* KOKKOS\_CUDA\_OPTIONS, values = *force\_uvm*, *use\_ldg*, *rdc*\ , *enable\_lambda*, default = *enable\_lambda*
+
+KOKKOS\_USE\_TPLS=hwloc binds threads to hardware cores, so they do not
+migrate during a simulation. KOKKOS\_USE\_TPLS=hwloc should always be
+used if running with KOKKOS\_DEVICES=Pthreads for pthreads. It is not
+necessary for KOKKOS\_DEVICES=OpenMP for OpenMP, because OpenMP
+provides alternative methods via environment variables for binding
+threads to hardware cores.  More info on binding threads to cores is
+given on the :doc:`Speed omp <Speed_omp>` doc page.
+
+KOKKOS\_USE\_TPLS=librt enables use of a more accurate timer mechanism
+on most Unix platforms. This library is not available on all
+platforms.
+
+KOKKOS\_DEBUG is only useful when developing a Kokkos-enabled style
+within LAMMPS. KOKKOS\_DEBUG=yes enables printing of run-time
+debugging information that can be useful. It also enables runtime
+bounds checking on Kokkos data structures.
+
+KOKKOS\_CXX\_STANDARD and KOKKOS\_OPTIONS are typically not changed when
+building LAMMPS.
+
+KOKKOS\_CUDA\_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
+package must be compiled with the *enable\_lambda* option when using
+GPUs.
+
+Restrictions
+""""""""""""
+
+
+Currently, there are no precision options with the KOKKOS package. All
+compilation and computation is performed in double precision.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_measure.rst b/doc/src/Speed_measure.rst
new file mode 100644
index 0000000000..9d538616eb
--- /dev/null
+++ b/doc/src/Speed_measure.rst
@@ -0,0 +1,51 @@
+Measuring performance
+=====================
+
+Before trying to make your simulation run faster, you should
+understand how it currently performs and where the bottlenecks are.
+
+The best way to do this is run the your system (actual number of
+atoms) for a modest number of timesteps (say 100 steps) on several
+different processor counts, including a single processor if possible.
+Do this for an equilibrium version of your system, so that the
+100-step timings are representative of a much longer run.  There is
+typically no need to run for 1000s of timesteps to get accurate
+timings; you can simply extrapolate from short runs.
+
+For the set of runs, look at the timing data printed to the screen and
+log file at the end of each LAMMPS run.  The
+:doc:`Run\_output <Run_output>` doc page gives an overview.
+
+Running on one (or a few processors) should give a good estimate of
+the serial performance and what portions of the timestep are taking
+the most time.  Running the same problem on a few different processor
+counts should give an estimate of parallel scalability.  I.e. if the
+simulation runs 16x faster on 16 processors, its 100% parallel
+efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
+
+The most important data to look at in the timing info is the timing
+breakdown and relative percentages.  For example, trying different
+options for speeding up the long-range solvers will have little impact
+if they only consume 10% of the run time.  If the pairwise time is
+dominating, you may want to look at GPU or OMP versions of the pair
+style, as discussed below.  Comparing how the percentages change as
+you increase the processor count gives you a sense of how different
+operations within the timestep are scaling.  Note that if you are
+running with a Kspace solver, there is additional output on the
+breakdown of the Kspace time.  For PPPM, this includes the fraction
+spent on FFTs, which can be communication intensive.
+
+Another important detail in the timing info are the histograms of
+atoms counts and neighbor counts.  If these vary widely across
+processors, you have a load-imbalance issue.  This often results in
+inaccurate relative timing data, because processors have to wait when
+communication occurs for other processors to catch up.  Thus the
+reported times for "Communication" or "Other" may be higher than they
+really are, due to load-imbalance.  If this is an issue, you can
+uncomment the MPI\_Barrier() lines in src/timer.cpp, and re-compile
+LAMMPS, to obtain synchronized timings.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst
new file mode 100644
index 0000000000..fab7f671d7
--- /dev/null
+++ b/doc/src/Speed_omp.rst
@@ -0,0 +1,167 @@
+USER-OMP package
+================
+
+The USER-OMP package was developed by Axel Kohlmeyer at Temple
+University.  It provides optimized and multi-threaded versions
+of many pair styles, nearly all bonded styles (bond, angle, dihedral,
+improper), several Kspace styles, and a few fix styles.  It uses
+the OpenMP interface for multi-threading, but can also be compiled
+without OpenMP support, providing optimized serial styles in that case.
+
+**Required hardware/software:**
+
+To enable multi-threading, your compiler must support the OpenMP interface.
+You should have one or more multi-core CPUs, as multiple threads can only be
+launched by each MPI task on the local node (using shared memory).
+
+**Building LAMMPS with the USER-OMP package:**
+
+See the :ref:`Build extras <user-omp>` doc page for
+instructions.
+
+**Run with the USER-OMP package from the command line:**
+
+These examples assume one or more 16-core nodes.
+
+
+.. parsed-literal::
+
+   env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script           # 1 MPI task, 16 threads according to OMP_NUM_THREADS
+   lmp_mpi -sf omp -in in.script                                  # 1 MPI task, no threads, optimized kernels
+   mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
+   mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task
+
+The mpirun or mpiexec command sets the total number of MPI tasks used
+by LAMMPS (one or multiple per compute node) and the number of MPI
+tasks used per node.  E.g. the mpirun command in MPICH does this via
+its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
+
+You need to choose how many OpenMP threads per MPI task will be used
+by the USER-OMP package.  Note that the product of MPI tasks \*
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.
+
+As in the lines above, use the "-sf omp" :doc:`command-line switch <Run_options>`, which will automatically append "omp" to
+styles that support it.  The "-sf omp" switch also issues a default
+:doc:`package omp 0 <package>` command, which will set the number of
+threads per MPI task via the OMP\_NUM\_THREADS environment variable.
+
+You can also use the "-pk omp Nt" :doc:`command-line switch <Run_options>`, to explicitly set Nt = # of OpenMP threads
+per MPI task to use, as well as additional options.  Its syntax is the
+same as the :doc:`package omp <package>` command whose doc page gives
+details, including the default values used if it is not specified.  It
+also gives more details on how to set the number of threads via the
+OMP\_NUM\_THREADS environment variable.
+
+**Or run with the USER-OMP package by editing an input script:**
+
+The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+and threads/MPI task is the same.
+
+Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
+"omp" suffix to individual styles in your input script, e.g.
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/omp 2.5
+
+You must also use the :doc:`package omp <package>` command to enable the
+USER-OMP package.  When you do this you also specify how many threads
+per MPI task to use.  The command doc page explains other options and
+how to set the number of threads via the OMP\_NUM\_THREADS environment
+variable.
+
+**Speed-ups to expect:**
+
+Depending on which styles are accelerated, you should look for a
+reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
+time" values printed at the end of a run.
+
+You may see a small performance advantage (5 to 20%) when running a
+USER-OMP style (in serial or parallel) with a single thread per MPI
+task, versus running standard LAMMPS with its standard un-accelerated
+styles (in serial or all-MPI parallelization with 1 task/core).  This
+is because many of the USER-OMP styles contain similar optimizations
+to those used in the OPT package, described in :doc:`Section 5.3.5 <Speed_opt>`.
+
+With multiple threads/task, the optimal choice of number of MPI
+tasks/node and OpenMP threads/task can vary a lot and should always be
+tested via benchmark runs for a specific simulation running on a
+specific machine, paying attention to guidelines discussed in the next
+sub-section.
+
+A description of the multi-threading strategy used in the USER-OMP
+package and some performance examples are `presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_
+
+**Guidelines for best performance:**
+
+For many problems on current generation CPUs, running the USER-OMP
+package with a single thread/task is faster than running with multiple
+threads/task.  This is because the MPI parallelization in LAMMPS is
+often more efficient than multi-threading as implemented in the
+USER-OMP package.  The parallel efficiency (in a threaded sense) also
+varies for different USER-OMP styles.
+
+Using multiple threads/task can be more effective under the following
+circumstances:
+
+* Individual compute nodes have a significant number of CPU cores but
+  the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx
+  (Clovertown) and 54xx (Harpertown) quad-core processors.  Running one
+  MPI task per CPU core will result in significant performance
+  degradation, so that running with 4 or even only 2 MPI tasks per node
+  is faster.  Running in hybrid MPI+OpenMP mode will reduce the
+  inter-node communication bandwidth contention in the same way, but
+  offers an additional speedup by utilizing the otherwise idle CPU
+  cores.
+* The interconnect used for MPI communication does not provide
+  sufficient bandwidth for a large number of MPI tasks per node.  For
+  example, this applies to running over gigabit ethernet or on Cray XT4
+  or XT5 series supercomputers.  As in the aforementioned case, this
+  effect worsens when using an increasing number of nodes.
+* The system has a spatially inhomogeneous particle density which does
+  not map well to the :doc:`domain decomposition scheme <processors>` or
+  :doc:`load-balancing <balance>` options that LAMMPS provides.  This is
+  because multi-threading achieves parallelism over the number of
+  particles, not via their distribution in space.
+* A machine is being used in "capability mode", i.e. near the point
+  where MPI parallelism is maxed out.  For example, this can happen when
+  using the :doc:`PPPM solver <kspace_style>` for long-range
+  electrostatics on large numbers of nodes.  The scaling of the KSpace
+  calculation (see the :doc:`kspace\_style <kspace_style>` command) becomes
+  the performance-limiting factor.  Using multi-threading allows less
+  MPI tasks to be invoked and can speed-up the long-range solver, while
+  increasing overall performance by parallelizing the pairwise and
+  bonded calculations via OpenMP.  Likewise additional speedup can be
+  sometimes be achieved by increasing the length of the Coulombic cutoff
+  and thus reducing the work done by the long-range solver.  Using the
+  :doc:`run\_style verlet/split <run_style>` command, which is compatible
+  with the USER-OMP package, is an alternative way to reduce the number
+  of MPI tasks assigned to the KSpace calculation.
+
+
+Additional performance tips are as follows:
+
+* The best parallel efficiency from *omp* styles is typically achieved
+  when there is at least one MPI task per physical CPU chip, i.e. socket
+  or die.
+* It is usually most efficient to restrict threading to a single
+  socket, i.e. use one or more MPI task per socket.
+* NOTE: By default, several current MPI implementations use a processor
+  affinity setting that restricts each MPI task to a single CPU core.
+  Using multi-threading in this mode will force all threads to share the
+  one core and thus is likely to be counterproductive.  Instead, binding
+  MPI tasks to a (multi-core) socket, should solve this issue.
+
+
+Restrictions
+""""""""""""
+
+
+None.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_opt.rst b/doc/src/Speed_opt.rst
new file mode 100644
index 0000000000..8e7b3e7ffd
--- /dev/null
+++ b/doc/src/Speed_opt.rst
@@ -0,0 +1,58 @@
+OPT package
+===========
+
+The OPT package was developed by James Fischer (High Performance
+Technologies), David Richie, and Vincent Natoli (Stone Ridge
+Technologies).  It contains a handful of pair styles whose compute()
+methods were rewritten in C++ templated form to reduce the overhead
+due to if tests and other conditional code.
+
+**Required hardware/software:**
+
+None.
+
+**Building LAMMPS with the OPT package:**
+
+See the :ref:`Build extras <opt>` doc page for instructions.
+
+**Run with the OPT package from the command line:**
+
+
+.. parsed-literal::
+
+   lmp_mpi -sf opt -in in.script                # run in serial
+   mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel
+
+Use the "-sf opt" :doc:`command-line switch <Run_options>`, which will
+automatically append "opt" to styles that support it.
+
+**Or run with the OPT package by editing an input script:**
+
+Use the :doc:`suffix opt <suffix>` command, or you can explicitly add an
+"opt" suffix to individual styles in your input script, e.g.
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/opt 2.5
+
+**Speed-ups to expect:**
+
+You should see a reduction in the "Pair time" value printed at the end
+of a run.  On most machines for reasonable problem sizes, it will be a
+5 to 20% savings.
+
+**Guidelines for best performance:**
+
+Just try out an OPT pair style to see how it performs.
+
+Restrictions
+""""""""""""
+
+
+None.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst
new file mode 100644
index 0000000000..3ec76d4de2
--- /dev/null
+++ b/doc/src/Speed_packages.rst
@@ -0,0 +1,195 @@
+Accelerator packages
+====================
+
+Accelerated versions of various :doc:`pair\_style <pair_style>`,
+:doc:`fixes <fix>`, :doc:`computes <compute>`, and other commands have
+been added to LAMMPS, which will typically run faster than the
+standard non-accelerated versions.  Some require appropriate hardware
+to be present on your system, e.g. GPUs or Intel Xeon Phi
+co-processors.
+
+All of these commands are in packages provided with LAMMPS.  An
+overview of packages is give on the :doc:`Packages <Packages>` doc
+pages.
+
+These are the accelerator packages currently in LAMMPS, either as
+standard or user packages:
+
++-----------------------------------------+-------------------------------------------------------+
+| :doc:`GPU Package <Speed_gpu>`          | for NVIDIA GPUs as well as OpenCL support             |
++-----------------------------------------+-------------------------------------------------------+
+| :doc:`USER-INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi                     |
++-----------------------------------------+-------------------------------------------------------+
+| :doc:`KOKKOS Package <Speed_kokkos>`    | for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading |
++-----------------------------------------+-------------------------------------------------------+
+| :doc:`USER-OMP Package <Speed_omp>`     | for OpenMP threading and generic CPU optimizations    |
++-----------------------------------------+-------------------------------------------------------+
+| :doc:`OPT Package <Speed_opt>`          | generic CPU optimizations                             |
++-----------------------------------------+-------------------------------------------------------+
+
+
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+
+   Speed_gpu
+   Speed_intel
+   Speed_kokkos
+   Speed_omp
+   Speed_opt
+
+Inverting this list, LAMMPS currently has acceleration support for
+three kinds of hardware, via the listed packages:
+
++----------------+-----------------------------------------------------------------------------------------------------------------------------+
+| Many-core CPUs | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`USER-OMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
++----------------+-----------------------------------------------------------------------------------------------------------------------------+
+| NVIDIA GPUs    | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages                                                               |
++----------------+-----------------------------------------------------------------------------------------------------------------------------+
+| Intel Phi      | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages                                                      |
++----------------+-----------------------------------------------------------------------------------------------------------------------------+
+
+Which package is fastest for your hardware may depend on the size
+problem you are running and what commands (accelerated and
+non-accelerated) are invoked by your input script.  While these doc
+pages include performance guidelines, there is no substitute for
+trying out the different packages appropriate to your hardware.
+
+Any accelerated style has the same name as the corresponding standard
+style, except that a suffix is appended.  Otherwise, the syntax for
+the command that uses the style is identical, their functionality is
+the same, and the numerical results it produces should also be the
+same, except for precision and round-off effects.
+
+For example, all of these styles are accelerated variants of the
+Lennard-Jones :doc:`pair\_style lj/cut <pair_lj>`:
+
+* :doc:`pair\_style lj/cut/gpu <pair_lj>`
+* :doc:`pair\_style lj/cut/intel <pair_lj>`
+* :doc:`pair\_style lj/cut/kk <pair_lj>`
+* :doc:`pair\_style lj/cut/omp <pair_lj>`
+* :doc:`pair\_style lj/cut/opt <pair_lj>`
+
+To see what accelerate styles are currently available for a particular
+style, find the style name in the `Commands\_all <lc_>`_
+style pages (fix,compute,pair,etc) and see what suffixes are listed
+(g,i,k,o,t) with it.  The doc pages for individual commands
+(e.g. :doc:`pair lj/cut <pair_lj>` or :doc:`fix nve <fix_nve>`) also list
+any accelerated variants available for that style.
+
+To use an accelerator package in LAMMPS, and one or more of the styles
+it provides, follow these general steps.  Details vary from package to
+package and are explained in the individual accelerator doc pages,
+listed above:
+
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+| build the accelerator library                                                                                                  | only for GPU package                                                 |
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+| install the accelerator package                                                                                                | make yes-opt, make yes-user-intel, etc                               |
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+| add compile/link flags to Makefile.machine in src/MAKE                                                                         | only for USER-INTEL, KOKKOS, USER-OMP, OPT packages                  |
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+| re-build LAMMPS                                                                                                                | make machine                                                         |
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+| prepare and test a regular LAMMPS simulation                                                                                   | lmp\_machine -in in.script; mpirun -np 32 lmp\_machine -in in.script |
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+| enable specific accelerator support via '-k on' :doc:`command-line switch <Run_options>`,                                      | only needed for KOKKOS package                                       |
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+| set any needed options for the package via "-pk" :doc:`command-line switch <Run_options>` or :doc:`package <package>` command, | only if defaults need to be changed                                  |
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+| use accelerated styles in your input via "-sf" :doc:`command-line switch <Run_options>` or :doc:`suffix <suffix>` command      | lmp\_machine -in in.script -sf gpu                                   |
++--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
+
+Note that the first 4 steps can be done as a single command with
+suitable make command invocations. This is discussed on the
+:doc:`Packages <Packages>` doc pages, and its use is illustrated in the
+individual accelerator sections.  Typically these steps only need to
+be done once, to create an executable that uses one or more
+accelerator packages.
+
+The last 4 steps can all be done from the command-line when LAMMPS is
+launched, without changing your input script, as illustrated in the
+individual accelerator sections.  Or you can add
+:doc:`package <package>` and :doc:`suffix <suffix>` commands to your input
+script.
+
+.. note::
+
+   With a few exceptions, you can build a single LAMMPS executable
+   with all its accelerator packages installed.  Note however that the
+   USER-INTEL and KOKKOS packages require you to choose one of their
+   hardware options when building for a specific platform.  I.e. CPU or
+   Phi option for the USER-INTEL package.  Or the OpenMP, Cuda, or Phi
+   option for the KOKKOS package.
+
+These are the exceptions.  You cannot build a single executable with:
+
+* both the USER-INTEL Phi and KOKKOS Phi options
+* the USER-INTEL Phi or Kokkos Phi option, and the GPU package
+
+See the examples/accelerate/README and make.list files for sample
+Make.py commands that build LAMMPS with any or all of the accelerator
+packages.  As an example, here is a command that builds with all the
+GPU related packages installed (GPU, KOKKOS with Cuda), including
+settings to build the needed auxiliary GPU libraries for Kepler GPUs:
+
+
+.. parsed-literal::
+
+   Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi   -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
+
+The examples/accelerate directory also has input scripts that can be
+used with all of the accelerator packages.  See its README file for
+details.
+
+Likewise, the bench directory has FERMI and KEPLER and PHI
+sub-directories with Make.py commands and input scripts for using all
+the accelerator packages on various machines.  See the README files in
+those dirs.
+
+As mentioned above, the `Benchmark page <http://lammps.sandia.gov/bench.html>`_ of the LAMMPS web site gives
+performance results for the various accelerator packages for several
+of the standard LAMMPS benchmark problems, as a function of problem
+size and number of compute nodes, on different hardware platforms.
+
+Here is a brief summary of what the various packages provide.  Details
+are in the individual accelerator sections.
+
+* Styles with a "gpu" suffix are part of the GPU package, and can be run
+  on NVIDIA GPUs.  The speed-up on a GPU depends on a variety of
+  factors, discussed in the accelerator sections.
+* Styles with an "intel" suffix are part of the USER-INTEL
+  package. These styles support vectorized single and mixed precision
+  calculations, in addition to full double precision.  In extreme cases,
+  this can provide speedups over 3.5x on CPUs.  The package also
+  supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
+  co-processors.  This can result in additional speedup over 2x depending
+  on the hardware configuration.
+* Styles with a "kk" suffix are part of the KOKKOS package, and can be
+  run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
+  Xeon Phi in "native" mode.  The speed-up depends on a variety of
+  factors, as discussed on the KOKKOS accelerator page.
+* Styles with an "omp" suffix are part of the USER-OMP package and allow
+  a pair-style to be run in multi-threaded mode using OpenMP.  This can
+  be useful on nodes with high-core counts when using less MPI processes
+  than cores is advantageous, e.g. when running with PPPM so that FFTs
+  are run on fewer MPI processors or when the many MPI tasks would
+  overload the available bandwidth for communication.
+* Styles with an "opt" suffix are part of the OPT package and typically
+  speed-up the pairwise calculations of your simulation by 5-25% on a
+  CPU.
+
+
+The individual accelerator package doc pages explain:
+
+* what hardware and software the accelerated package requires
+* how to build LAMMPS with the accelerated package
+* how to run with the accelerated package either via command-line switches or modifying the input script
+* speed-ups to expect
+* guidelines for best performance
+* restrictions
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Speed_tips.rst b/doc/src/Speed_tips.rst
new file mode 100644
index 0000000000..ed7eef5b28
--- /dev/null
+++ b/doc/src/Speed_tips.rst
@@ -0,0 +1,61 @@
+General tips
+============
+
+.. note::
+
+   this page is still a work in progress
+
+Here is a list of general ideas for improving simulation performance.
+Most of them are only applicable to certain models and certain
+bottlenecks in the current performance, so let the timing data you
+generate be your guide.  It is hard, if not impossible, to predict how
+much difference these options will make, since it is a function of
+problem size, number of processors used, and your machine.  There is
+no substitute for identifying performance bottlenecks, and trying out
+various options.
+
+* rRESPA
+* Two-FFT PPPM
+* Staggered PPPM
+* single vs double PPPM
+* partial charge PPPM
+* verlet/split run style
+* processor command for proc layout and numa layout
+* load-balancing: balance and fix balance
+
+Two-FFT PPPM, also called *analytic differentiation* or *ad* PPPM,
+uses 2 FFTs instead of the 4 FFTs used by the default *ik
+differentiation* PPPM. However, 2-FFT PPPM also requires a slightly
+larger mesh size to achieve the same accuracy as 4-FFT PPPM. For
+problems where the FFT cost is the performance bottleneck (typically
+large problems running on many processors), 2-FFT PPPM may be faster
+than 4-FFT PPPM.
+
+Staggered PPPM performs calculations using two different meshes, one
+shifted slightly with respect to the other.  This can reduce force
+aliasing errors and increase the accuracy of the method, but also
+doubles the amount of work required. For high relative accuracy, using
+staggered PPPM allows one to half the mesh size in each dimension as
+compared to regular PPPM, which can give around a 4x speedup in the
+kspace time. However, for low relative accuracy, using staggered PPPM
+gives little benefit and can be up to 2x slower in the kspace
+time. For example, the rhodopsin benchmark was run on a single
+processor, and results for kspace time vs. relative accuracy for the
+different methods are shown in the figure below.  For this system,
+staggered PPPM (using ik differentiation) becomes useful when using a
+relative accuracy of slightly greater than 1e-5 and above.
+
+.. image:: JPG/rhodo_staggered.jpg
+   :align: center
+
+.. note::
+
+   Using staggered PPPM may not give the same increase in accuracy
+   of energy and pressure as it does in forces, so some caution must be
+   used if energy and/or pressure are quantities of interest, such as
+   when using a barostat.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst
new file mode 100644
index 0000000000..baee955201
--- /dev/null
+++ b/doc/src/Tools.rst
@@ -0,0 +1,748 @@
+Auxiliary tools
+***************
+
+LAMMPS is designed to be a computational kernel for performing
+molecular dynamics computations.  Additional pre- and post-processing
+steps are often necessary to setup and analyze a simulation.  A list
+of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
+
+* `Pre/Post processing <http://lammps.sandia.gov/prepost.html>`_
+* `Offsite LAMMPS packages & tools <http://lammps.sandia.gov/offsite.html>`_
+* `Pizza.py toolkit <pizza_>`_
+
+The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at
+Sandia which provides tools for doing setup, analysis, plotting, and
+visualization for LAMMPS simulations.
+
+.. _pizza: http://pizza.sandia.gov
+
+
+
+.. _python: http://www.python.org
+
+
+
+Additional tools included in the LAMMPS distribution are described on
+this page.
+
+Note that many users write their own setup or analysis tools or use
+other existing codes and convert their output to a LAMMPS input format
+or vice versa.  The tools listed here are included in the LAMMPS
+distribution as examples of auxiliary tools.  Some of them are not
+actively supported by the LAMMPS developers, as they were contributed
+by LAMMPS users.  If you have problems using them, we can direct you
+to the authors.
+
+The source code for each of these codes is in the tools sub-directory
+of the LAMMPS distribution.  There is a Makefile (which you may need
+to edit for your platform) which will build several of the tools which
+reside in that directory.  Most of them are larger packages in their
+own sub-directories with their own Makefiles and/or README files.
+
+
+----------
+
+
+Pre-processing tools
+====================
+
++-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+
+| :ref:`amber2lmp <amber>`    | :ref:`ch2lmp <charmm>` | :ref:`chain <chain>` | :ref:`createatoms <createatoms>` | :ref:`drude <drude>`             | :ref:`eam database <eamdb>` |
++-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+
+| :ref:`eam generate <eamgn>` | :ref:`eff <eff>`       | :ref:`ipp <ipp>`     | :ref:`micelle2d <micelle>`       | :ref:`moltemplate <moltemplate>` | :ref:`msi2lmp <msi>`        |
++-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+
+| :ref:`polybond <polybond>`  |                        |                      |                                  |                                  |                             |
++-----------------------------+------------------------+----------------------+----------------------------------+----------------------------------+-----------------------------+
+
+Post-processing tools
+=====================
+
++--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
+| :ref:`amber2lmp <amber>` | :ref:`binary2txt <binary>` | :ref:`ch2lmp <charmm>` | :ref:`colvars <colvars>` | :ref:`eff <eff>`              | :ref:`fep <fep>`            |
++--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
+| :ref:`lmp2arc <arc>`     | :ref:`lmp2cfg <cfg>`       | :ref:`matlab <matlab>` | :ref:`phonon <phonon>`   | :ref:`pymol\_asphere <pymol>` | :ref:`python <pythontools>` |
++--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
+| :ref:`reax <reax_tool>`  | :ref:`replica <replica>`   | :ref:`smd <smd>`       | :ref:`spin <spin>`       | :ref:`xmgrace <xmgrace>`      |                             |
++--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
+
+Miscellaneous tools
+===================
+
++--------------------------+----------------------+-------------------+--------------------+---------------------------------------+
+| :ref:`doxygen <doxygen>` | :ref:`emacs <emacs>` | :ref:`i-pi <ipi>` | :ref:`kate <kate>` | :ref:`singularity <singularity_tool>` |
++--------------------------+----------------------+-------------------+--------------------+---------------------------------------+
+| :ref:`vim <vim>`         |                      |                   |                    |                                       |
++--------------------------+----------------------+-------------------+--------------------+---------------------------------------+
+
+
+----------
+
+
+Tool descriptions
+=================
+
+.. _amber:
+
+amber2lmp tool
+--------------------------
+
+The amber2lmp sub-directory contains two Python scripts for converting
+files back-and-forth between the AMBER MD code and LAMMPS.  See the
+README file in amber2lmp for more information.
+
+These tools were written by Keir Novik while he was at Queen Mary
+University of London.  Keir is no longer there and cannot support
+these tools which are out-of-date with respect to the current LAMMPS
+version (and maybe with respect to AMBER as well).  Since we don't use
+these tools at Sandia, you'll need to experiment with them and make
+necessary modifications yourself.
+
+
+----------
+
+
+.. _binary:
+
+binary2txt tool
+----------------------------
+
+The file binary2txt.cpp converts one or more binary LAMMPS dump file
+into ASCII text files.  The syntax for running the tool is
+
+
+.. parsed-literal::
+
+   binary2txt file1 file2 ...
+
+which creates file1.txt, file2.txt, etc.  This tool must be compiled
+on a platform that can read the binary file created by a LAMMPS run,
+since binary files are not compatible across all platforms.
+
+
+----------
+
+
+.. _charmm:
+
+ch2lmp tool
+------------------------
+
+The ch2lmp sub-directory contains tools for converting files
+back-and-forth between the CHARMM MD code and LAMMPS.
+
+They are intended to make it easy to use CHARMM as a builder and as a
+post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
+PDB file with associated CHARMM info, including CHARMM force field
+data, into its LAMMPS equivalent. Support for the CMAP correction of
+CHARMM22 and later is available as an option. This tool can also add
+solvent water molecules and Na+ or Cl- ions to the system.
+Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files.
+
+See the README file in the ch2lmp sub-directory for more information.
+
+These tools were created by Pieter in't Veld (pjintve at sandia.gov)
+and Paul Crozier (pscrozi at sandia.gov) at Sandia.
+
+CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and
+Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and
+Tigran Abramyan, (Clemson University) and
+Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
+
+
+----------
+
+
+.. _chain:
+
+chain tool
+----------------------
+
+The file chain.f creates a LAMMPS data file containing bead-spring
+polymer chains and/or monomer solvent atoms.  It uses a text file
+containing chain definition parameters as an input.  The created
+chains and solvent atoms can strongly overlap, so LAMMPS needs to run
+the system initially with a "soft" pair potential to un-overlap it.
+The syntax for running the tool is
+
+
+.. parsed-literal::
+
+   chain < def.chain > data.file
+
+See the def.chain or def.chain.ab files in the tools directory for
+examples of definition files.  This tool was used to create the system
+for the :doc:`chain benchmark <Speed_bench>`.
+
+
+----------
+
+
+.. _colvars:
+
+colvars tools
+---------------------------
+
+The colvars directory contains a collection of tools for post-processing
+data produced by the colvars collective variable library.
+To compile the tools, edit the makefile for your system and run "make".
+
+Please report problems and issues the colvars library and its tools
+at: https://github.com/colvars/colvars/issues
+
+abf\_integrate:
+
+MC-based integration of multidimensional free energy gradient
+Version 20110511
+
+
+.. parsed-literal::
+
+   Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0\|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
+
+The LAMMPS interface to the colvars collective variable library, as
+well as these tools, were created by Axel Kohlmeyer (akohlmey at
+gmail.com) at ICTP, Italy.
+
+
+----------
+
+
+.. _createatoms:
+
+createatoms tool
+----------------------------------
+
+The tools/createatoms directory contains a Fortran program called
+createAtoms.f which can generate a variety of interesting crystal
+structures and geometries and output the resulting list of atom
+coordinates in LAMMPS or other formats.
+
+See the included Manual.pdf for details.
+
+The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
+
+
+----------
+
+
+.. _doxygen:
+
+doxygen tool
+--------------------------
+
+The tools/doxygen directory contains a shell script called
+doxygen.sh which can generate a call graph and API lists using
+the `Doxygen software <http://doxygen.org>`_.
+
+See the included README file for details.
+
+The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
+
+
+----------
+
+
+.. _drude:
+
+drude tool
+----------------------
+
+The tools/drude directory contains a Python script called
+polarizer.py which can add Drude oscillators to a LAMMPS
+data file in the required format.
+
+See the header of the polarizer.py file for details.
+
+The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
+at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
+
+
+----------
+
+
+.. _eamdb:
+
+eam database tool
+-----------------------------
+
+The tools/eam\_database directory contains a Fortran program that will
+generate EAM alloy setfl potential files for any combination of 16
+elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
+Zr.  The files can then be used with the :doc:`pair\_style eam/alloy <pair_eam>` command.
+
+The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
+and is based on his paper:
+
+X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
+144113 (2004).
+
+
+----------
+
+
+.. _eamgn:
+
+eam generate tool
+-----------------------------
+
+The tools/eam\_generate directory contains several one-file C programs
+that convert an analytic formula into a tabulated :doc:`embedded atom method (EAM) <pair_eam>` setfl potential file.  The potentials they
+produce are in the potentials directory, and can be used with the
+:doc:`pair\_style eam/alloy <pair_eam>` command.
+
+The source files and potentials were provided by Gerolf Ziegenhain
+(gerolf at ziegenhain.com).
+
+
+----------
+
+
+.. _eff:
+
+eff tool
+------------------
+
+The tools/eff directory contains various scripts for generating
+structures and post-processing output for simulations using the
+electron force field (eFF).
+
+These tools were provided by Andres Jaramillo-Botero at CalTech
+(ajaramil at wag.caltech.edu).
+
+
+----------
+
+
+.. _emacs:
+
+emacs tool
+----------------------
+
+The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
+that enables a lammps-mode for editing input scripts when using GNU Emacs,
+with various highlighting options set up.
+
+These tools were provided by Aidan Thompson at Sandia
+(athomps at sandia.gov).
+
+
+----------
+
+
+.. _fep:
+
+fep tool
+------------------
+
+The tools/fep directory contains Python scripts useful for
+post-processing results from performing free-energy perturbation
+simulations using the USER-FEP package.
+
+The scripts were contributed by Agilio Padua (Universite Blaise
+Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
+
+See README file in the tools/fep directory.
+
+
+----------
+
+
+.. _ipi:
+
+i-pi tool
+-------------------
+
+The tools/i-pi directory contains a version of the i-PI package, with
+all the LAMMPS-unrelated files removed.  It is provided so that it can
+be used with the :doc:`fix ipi <fix_ipi>` command to perform
+path-integral molecular dynamics (PIMD).
+
+The i-PI package was created and is maintained by Michele Ceriotti,
+michele.ceriotti at gmail.com, to interface to a variety of molecular
+dynamics codes.
+
+See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
+:doc:`fix ipi <fix_ipi>` doc page for further details on running PIMD
+calculations with LAMMPS.
+
+
+----------
+
+
+.. _ipp:
+
+ipp tool
+------------------
+
+The tools/ipp directory contains a Perl script ipp which can be used
+to facilitate the creation of a complicated file (say, a lammps input
+script or tools/createatoms input file) using a template file.
+
+ipp was created and is maintained by Reese Jones (Sandia), rjones at
+sandia.gov.
+
+See two examples in the tools/ipp directory.  One of them is for the
+tools/createatoms tool's input file.
+
+
+----------
+
+
+.. _kate:
+
+kate tool
+--------------------
+
+The file in the tools/kate directory is an add-on to the Kate editor
+in the KDE suite that allow syntax highlighting of LAMMPS input
+scripts.  See the README.txt file for details.
+
+The file was provided by Alessandro Luigi Sellerio
+(alessandro.sellerio at ieni.cnr.it).
+
+
+----------
+
+
+.. _arc:
+
+lmp2arc tool
+----------------------
+
+The lmp2arc sub-directory contains a tool for converting LAMMPS output
+files to the format for Accelrys' Insight MD code (formerly
+MSI/Biosym and its Discover MD code).  See the README file for more
+information.
+
+This tool was written by John Carpenter (Cray), Michael Peachey
+(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
+(jec at mayo.edu), but still fields questions about the tool.
+
+This tool was updated for the current LAMMPS C++ version by Jeff
+Greathouse at Sandia (jagreat at sandia.gov).
+
+
+----------
+
+
+.. _cfg:
+
+lmp2cfg tool
+----------------------
+
+The lmp2cfg sub-directory contains a tool for converting LAMMPS output
+files into a series of \*.cfg files which can be read into the
+`AtomEye <http://mt.seas.upenn.edu/Archive/Graphics/A>`_ visualizer.  See
+the README file for more information.
+
+This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
+
+
+----------
+
+
+.. _matlab:
+
+matlab tool
+------------------------
+
+The matlab sub-directory contains several `MATLAB <matlabhome_>`_ scripts for
+post-processing LAMMPS output.  The scripts include readers for log
+and dump files, a reader for EAM potential files, and a converter that
+reads LAMMPS dump files and produces CFG files that can be visualized
+with the `AtomEye <http://mt.seas.upenn.edu/Archive/Graphics/A>`_
+visualizer.
+
+See the README.pdf file for more information.
+
+These scripts were written by Arun Subramaniyan at Purdue Univ
+(asubrama at purdue.edu).
+
+.. _matlabhome: http://www.mathworks.com
+
+
+
+
+----------
+
+
+.. _micelle:
+
+micelle2d tool
+----------------------------
+
+The file micelle2d.f creates a LAMMPS data file containing short lipid
+chains in a monomer solution.  It uses a text file containing lipid
+definition parameters as an input.  The created molecules and solvent
+atoms can strongly overlap, so LAMMPS needs to run the system
+initially with a "soft" pair potential to un-overlap it.  The syntax
+for running the tool is
+
+
+.. parsed-literal::
+
+   micelle2d < def.micelle2d > data.file
+
+See the def.micelle2d file in the tools directory for an example of a
+definition file.  This tool was used to create the system for the
+:doc:`micelle example <Examples>`.
+
+
+----------
+
+
+.. _moltemplate:
+
+moltemplate tool
+----------------------------------
+
+The moltemplate sub-directory contains instructions for installing
+moltemplate, a Python-based tool for building molecular systems based
+on a text-file description, and creating LAMMPS data files that encode
+their molecular topology as lists of bonds, angles, dihedrals, etc.
+See the README.txt file for more information.
+
+This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
+supports it.  It has its own WWW page at
+`http://moltemplate.org <http://moltemplate.org>`_.
+The latest sources can be found `on its GitHub page <https://github.com/jewettaij/moltemplate/releases>`_
+
+
+----------
+
+
+.. _msi:
+
+msi2lmp tool
+----------------------
+
+The msi2lmp sub-directory contains a tool for creating LAMMPS template
+input and data files from BIOVIA's Materias Studio files (formerly
+Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code).
+
+This tool was written by John Carpenter (Cray), Michael Peachey
+(Cray), and Steve Lustig (Dupont). Several people contributed changes
+to remove bugs and adapt its output to changes in LAMMPS.
+
+This tool has several known limitations and is no longer under active
+development, so there are no changes except for the occasional bug fix.
+
+See the README file in the tools/msi2lmp folder for more information.
+
+
+----------
+
+
+.. _phonon:
+
+phonon tool
+------------------------
+
+The phonon sub-directory contains a post-processing tool useful for
+analyzing the output of the :doc:`fix phonon <fix_phonon>` command in
+the USER-PHONON package.
+
+See the README file for instruction on building the tool and what
+library it needs.  And see the examples/USER/phonon directory
+for example problems that can be post-processed with this tool.
+
+This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
+University.
+
+
+----------
+
+
+.. _polybond:
+
+polybond tool
+----------------------------
+
+The polybond sub-directory contains a Python-based tool useful for
+performing "programmable polymer bonding".  The Python file
+lmpsdata.py provides a "Lmpsdata" class with various methods which can
+be invoked by a user-written Python script to create data files with
+complex bonding topologies.
+
+See the Manual.pdf for details and example scripts.
+
+This tool was written by Zachary Kraus at Georgia Tech.
+
+
+----------
+
+
+.. _pymol:
+
+pymol\_asphere tool
+-------------------------------
+
+The pymol\_asphere sub-directory contains a tool for converting a
+LAMMPS dump file that contains orientation info for ellipsoidal
+particles into an input file for the `PyMol visualization package <pymolhome_>`_ or its `open source variant <pymolopen_>`_.
+
+.. _pymolhome: http://www.pymol.org
+
+
+
+.. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546
+
+
+
+Specifically, the tool triangulates the ellipsoids so they can be
+viewed as true ellipsoidal particles within PyMol.  See the README and
+examples directory within pymol\_asphere for more information.
+
+This tool was written by Mike Brown at Sandia.
+
+
+----------
+
+
+.. _pythontools:
+
+python tool
+-----------------------------
+
+The python sub-directory contains several Python scripts
+that perform common LAMMPS post-processing tasks, such as:
+
+* extract thermodynamic info from a log file as columns of numbers
+* plot two columns of thermodynamic info from a log file using GnuPlot
+* sort the snapshots in a dump file by atom ID
+* convert multiple :doc:`NEB <neb>` dump files into one dump file for viz
+* convert dump files into XYZ, CFG, or PDB format for viz by other packages
+
+These are simple scripts built on `Pizza.py <pizza_>`_ modules.  See the
+README for more info on Pizza.py and how to use these scripts.
+
+
+----------
+
+
+.. _replica:
+
+replica tool
+--------------------------
+
+The tools/replica directory contains the reorder\_remd\_traj python script which
+can be used to reorder the replica trajectories (resulting from the use of the 
+temper command) according to temperature. This will produce discontinuous
+trajectories with all frames at the same temperature in each trajectory.
+Additional options can be used to calculate the canonical configurational
+log-weight for each frame at each temperature using the pymbar package. See
+the README.md file for further details. Try out the peptide example provided.
+
+This tool was written by (and is maintained by) Tanmoy Sanyal, 
+while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
+
+
+----------
+
+
+.. _reax\_tool:
+
+reax tool
+--------------------------
+
+The reax sub-directory contains stand-alone codes that can
+post-process the output of the :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
+command from a LAMMPS simulation using :doc:`ReaxFF <pair_reaxc>`.  See
+the README.txt file for more info.
+
+These tools were written by Aidan Thompson at Sandia.
+
+
+----------
+
+
+.. _smd:
+
+smd tool
+------------------
+
+The smd sub-directory contains a C++ file dump2vtk\_tris.cpp and
+Makefile which can be compiled and used to convert triangle output
+files created by the Smooth-Mach Dynamics (USER-SMD) package into a
+VTK-compatible unstructured grid file.  It could then be read in and
+visualized by VTK.
+
+See the header of dump2vtk.cpp for more details.
+
+This tool was written by the USER-SMD package author, Georg
+Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics,
+Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
+
+
+----------
+
+
+.. _spin:
+
+spin tool
+--------------------
+
+The spin sub-directory contains a C file interpolate.c which can
+be compiled and used to perform a cubic polynomial interpolation of
+the MEP following a GNEB calculation.
+
+See the README file in tools/spin/interpolate\_gneb for more details.
+
+This tool was written by the SPIN package author, Julien
+Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
+Ivanov, at University of Iceland (ali5 at hi.is).
+
+
+----------
+
+
+.. _singularity\_tool:
+
+singularity tool
+----------------------------------------
+
+The singularity sub-directory contains container definitions files
+that can be used to build container images for building and testing
+LAMMPS on specific OS variants using the `Singularity <https://sylabs.io>`_
+container software. Contributions for additional variants are welcome.
+
+
+----------
+
+
+.. _vim:
+
+vim tool
+------------------
+
+The files in the tools/vim directory are add-ons to the VIM editor
+that allow easier editing of LAMMPS input scripts.  See the README.txt
+file for details.
+
+These files were provided by Gerolf Ziegenhain (gerolf at
+ziegenhain.com)
+
+
+----------
+
+
+.. _xmgrace:
+
+xmgrace tool
+--------------------------
+
+The files in the tools/xmgrace directory can be used to plot the
+thermodynamic data in LAMMPS log files via the xmgrace plotting
+package.  There are several tools in the directory that can be used in
+post-processing mode.  The lammpsplot.cpp file can be compiled and
+used to create plots from the current state of a running LAMMPS
+simulation.
+
+See the README file for details.
+
+These files were provided by Vikas Varshney (vv0210 at gmail.com)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/_ext/table_from_list.py b/doc/src/_ext/table_from_list.py
new file mode 100644
index 0000000000..715a3c2488
--- /dev/null
+++ b/doc/src/_ext/table_from_list.py
@@ -0,0 +1,61 @@
+from docutils import nodes
+from sphinx.util.docutils import SphinxDirective
+from docutils.nodes import Element, Node
+from typing import Any, Dict, List
+from sphinx import addnodes
+from sphinx.util import logging
+from sphinx.errors import SphinxError
+
+class TableFromList(SphinxDirective):
+    has_content = True
+    required_arguments = 0
+    optional_arguments = 0
+    final_argument_whitespace = False
+    option_spec = {
+        'columns': int,
+    }
+
+    def run(self) -> List[Node]:
+        ncolumns = self.options.get('columns', 2)
+        node = addnodes.compact_paragraph()
+        node.document = self.state.document
+        self.state.nested_parse(self.content, self.content_offset, node)
+        if len(node.children) != 1 or not isinstance(node.children[0],
+                                                     nodes.bullet_list):
+            reporter = self.state.document.reporter
+            raise SphinxError('table_from_list content is not a list')
+        fulllist = node.children[0]
+
+        if (len(fulllist) % ncolumns) != 0:
+            raise SphinxError('number of list elements not a multiple of column number')
+
+        table = nodes.table()
+        tgroup = nodes.tgroup(cols=ncolumns)
+        table += tgroup
+
+        for i in range(ncolumns):
+            tgroup += nodes.colspec(colwidth=1)
+
+        tbody = nodes.tbody()
+        tgroup += tbody
+        current_row = nodes.row()
+
+        for idx, cell in enumerate(fulllist.children):
+            if len(current_row.children) == ncolumns:
+                tbody += current_row
+                current_row = nodes.row()
+            entry = nodes.entry()
+            current_row += entry
+            if len(cell.children) > 0:
+                entry += cell.children[0]
+
+        tbody += current_row
+        return [table]
+
+def setup(app):
+    app.add_directive("table_from_list", TableFromList)
+    return {
+        'version': '0.1',
+        'parallel_read_safe': True,
+        'parallel_write_safe': True,
+    }
diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst
new file mode 100644
index 0000000000..92ab8b5ea3
--- /dev/null
+++ b/doc/src/angle_charmm.rst
@@ -0,0 +1,113 @@
+.. index:: angle_style charmm
+
+angle_style charmm command
+==========================
+
+angle_style charmm/intel command
+================================
+
+angle_style charmm/kk command
+=============================
+
+angle_style charmm/omp command
+==============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style charmm
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style charmm
+   angle_coeff 1 300.0 107.0 50.0 3.0
+
+Description
+"""""""""""
+
+The *charmm* angle style uses the potential
+
+.. math::
+
+   E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
+
+
+with an additional Urey\_Bradley term based on the distance :math:`r` between
+the 1st and 3rd atoms in the angle.  :math:`K`, :math:`\theta_0`,
+:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
+type.
+
+See :ref:`(MacKerell) <angle-MacKerell>` for a description of the CHARMM force
+field.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/radian\^2)
+* :math:`\theta_0` (degrees)
+* :math:`K_{ub}` (energy/distance\^2)
+* :math:`r_{ub}` (distance)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of :math:`K` are in energy/radian\^2.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _angle-MacKerell:
+
+
+
+**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
deleted file mode 100644
index 8b0e298a43..0000000000
--- a/doc/src/angle_charmm.txt
+++ /dev/null
@@ -1,89 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style charmm command :h3
-angle_style charmm/intel command :h3
-angle_style charmm/kk command :h3
-angle_style charmm/omp command :h3
-
-[Syntax:]
-
-angle_style charmm :pre
-
-[Examples:]
-
-angle_style charmm
-angle_coeff 1 300.0 107.0 50.0 3.0 :pre
-
-[Description:]
-
-The {charmm} angle style uses the potential
-
-:c,image(Eqs/angle_charmm.jpg)
-
-with an additional Urey_Bradley term based on the distance {r} between
-the 1st and 3rd atoms in the angle.  K, theta0, Kub, and Rub are
-coefficients defined for each angle type.
-
-See "(MacKerell)"_#angle-MacKerell for a description of the CHARMM force
-field.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/radian^2)
-theta0 (degrees)
-K_ub (energy/distance^2)
-r_ub (distance) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian^2.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Build package"_Build_package.html doc page
-for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
-
-:line
-
-:link(angle-MacKerell)
-[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
-Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst
new file mode 100644
index 0000000000..9d1ff8e8e7
--- /dev/null
+++ b/doc/src/angle_class2.rst
@@ -0,0 +1,169 @@
+.. index:: angle_style class2
+
+angle_style class2 command
+==========================
+
+angle_style class2/kk command
+=============================
+
+angle_style class2/omp command
+==============================
+
+angle_style class2/p6 command
+=============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style class2
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style class2
+   angle_coeff * 75.0
+   angle_coeff 1 bb 10.5872 1.0119 1.5228
+   angle_coeff * ba 3.6551 24.895 1.0119 1.5228
+
+Description
+"""""""""""
+
+The *class2* angle style uses the potential
+
+.. math::
+
+   E & = E_a + E_{bb} + E_{ba} \\
+   E_a & = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4(\theta - \theta_0)^4 \\
+   E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
+   E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
+
+
+where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
+bond-angle term.  :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
+the equilibrium bond lengths.
+
+See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
+
+Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for
+each angle type via the :doc:`angle\_coeff <angle_coeff>` command as in
+the example above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands.
+
+These are the 4 coefficients for the :math:`E_a` formula:
+
+* :math:`\theta_0` (degrees)
+* :math:`K_2` (energy/radian\^2)
+* :math:`K_3` (energy/radian\^3)
+* :math:`K_4` (energy/radian\^4)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of the various :math:`K` are in per-radian.
+
+For the :math:`E_{bb}` formula, each line in a :doc:`angle\_coeff <angle_coeff>`
+command in the input script lists 4 coefficients, the first of which
+is "bb" to indicate they are BondBond coefficients.  In a data file,
+these coefficients should be listed under a "BondBond Coeffs" heading
+and you must leave out the "bb", i.e. only list 3 coefficients after
+the angle type.
+
+* bb
+* :math:`M` (energy/distance\^2)
+* :math:`r_1` (distance)
+* :math:`r_2` (distance)
+
+For the :math:`E_{ba}` formula, each line in a :doc:`angle\_coeff <angle_coeff>`
+command in the input script lists 5 coefficients, the first of which
+is "ba" to indicate they are BondAngle coefficients.  In a data file,
+these coefficients should be listed under a "BondAngle Coeffs" heading
+and you must leave out the "ba", i.e. only list 4 coefficients after
+the angle type.
+
+* ba
+* :math:`N_1` (energy/distance\^2)
+* :math:`N_2` (energy/distance\^2)
+* :math:`r_1` (distance)
+* :math:`r_2` (distance)
+
+The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
+since it is the same value from the :math:`E_a` formula.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
+
+.. math::
+
+   E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
+
+
+In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
+
+* :math:`\theta_0` (degrees)
+* :math:`K_2` (energy/radian\^2)
+* :math:`K_3` (energy/radian\^3)
+* :math:`K_4` (energy/radian\^4)
+* :math:`K_5` (energy/radian\^5)
+* :math:`K_6` (energy/radian\^6)
+
+The bond-bond and bond-angle terms remain unchanged.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the CLASS2
+package.  For the *class2/p6* style LAMMPS needs to be built with the
+USER-MOFFF package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _angle-Sun:
+
+
+
+**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
deleted file mode 100644
index 5a772f8fa9..0000000000
--- a/doc/src/angle_class2.txt
+++ /dev/null
@@ -1,138 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style class2 command :h3
-angle_style class2/kk command :h3
-angle_style class2/omp command :h3
-angle_style class2/p6 command :h3
-
-[Syntax:]
-
-angle_style class2 :pre
-
-[Examples:]
-
-angle_style class2
-angle_coeff * 75.0
-angle_coeff 1 bb 10.5872 1.0119 1.5228
-angle_coeff * ba 3.6551 24.895 1.0119 1.5228 :pre
-
-[Description:]
-
-The {class2} angle style uses the potential
-
-:c,image(Eqs/angle_class2.jpg)
-
-where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
-bond-angle term.  Theta0 is the equilibrium angle and r1 and r2 are
-the equilibrium bond lengths.
-
-See "(Sun)"_#angle-Sun for a description of the COMPASS class2 force field.
-
-Coefficients for the Ea, Ebb, and Eba formulas must be defined for
-each angle type via the "angle_coeff"_angle_coeff.html command as in
-the example above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands.
-
-These are the 4 coefficients for the Ea formula:
-
-theta0 (degrees)
-K2 (energy/radian^2)
-K3 (energy/radian^3)
-K4 (energy/radian^4) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of the various K are in per-radian.
-
-For the Ebb formula, each line in a "angle_coeff"_angle_coeff.html
-command in the input script lists 4 coefficients, the first of which
-is "bb" to indicate they are BondBond coefficients.  In a data file,
-these coefficients should be listed under a "BondBond Coeffs" heading
-and you must leave out the "bb", i.e. only list 3 coefficients after
-the angle type.
-
-bb
-M (energy/distance^2)
-r1 (distance)
-r2 (distance) :ul
-
-For the Eba formula, each line in a "angle_coeff"_angle_coeff.html
-command in the input script lists 5 coefficients, the first of which
-is "ba" to indicate they are BondAngle coefficients.  In a data file,
-these coefficients should be listed under a "BondAngle Coeffs" heading
-and you must leave out the "ba", i.e. only list 4 coefficients after
-the angle type.
-
-ba
-N1 (energy/distance^2)
-N2 (energy/distance^2)
-r1 (distance)
-r2 (distance) :ul
-
-The theta0 value in the Eba formula is not specified, since it is the
-same value from the Ea formula.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-The {class2/p6} angle style uses the {class2} potential expanded to sixth order:
-
-:c,image(Eqs/angle_class2_p6.jpg)
-
-In this expanded term 6 coefficients for the Ea formula need to be set:
-
-theta0 (degrees)
-K2 (energy/radian^2)
-K3 (energy/radian^3)
-K4 (energy/radian^4)
-K5 (energy/radian^5)
-K6 (energy/radian^6) :ul
-
-The bond-bond and bond-angle terms remain unchanged.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the CLASS2
-package.  For the {class2/p6} style LAMMPS needs to be built with the
-USER-MOFFF package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
-
-:line
-
-:link(angle-Sun)
-[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/src/angle_coeff.txt b/doc/src/angle_coeff.rst
similarity index 56%
rename from doc/src/angle_coeff.txt
rename to doc/src/angle_coeff.rst
index 5dc9c13381..5f9a71371a 100644
--- a/doc/src/angle_coeff.txt
+++ b/doc/src/angle_coeff.rst
@@ -1,87 +1,104 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+.. index:: angle_coeff
 
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
+angle_coeff command
+===================
 
-:line
+Syntax
+""""""
 
-angle_coeff command :h3
 
-[Syntax:]
+.. code-block:: LAMMPS
 
-angle_coeff N args :pre
+   angle_coeff N args
 
-N = angle type (see asterisk form below)
-args = coefficients for one or more angle types :ul
+* N = angle type (see asterisk form below)
+* args = coefficients for one or more angle types
 
-[Examples:]
+Examples
+""""""""
 
-angle_coeff 1 300.0 107.0
-angle_coeff * 5.0
-angle_coeff 2*10 5.0 :pre
 
-[Description:]
+.. code-block:: LAMMPS
+
+   angle_coeff 1 300.0 107.0
+   angle_coeff * 5.0
+   angle_coeff 2*10 5.0
+
+Description
+"""""""""""
 
 Specify the angle force field coefficients for one or more angle types.
 The number and meaning of the coefficients depends on the angle style.
 Angle coefficients can also be set in the data file read by the
-"read_data"_read_data.html command or in a restart file.
+:doc:`read_data <read_data>` command or in a restart file.
 
 N can be specified in one of two ways.  An explicit numeric value can
 be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple angle types.  This takes the
-form "*" or "*n" or "n*" or "m*n".  If N = the number of angle types,
+form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of angle types,
 then an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk
 means all types from m to n (inclusive).
 
-Note that using an angle_coeff command can override a previous setting
+Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
 for the same angle type.  For example, these commands set the coeffs
 for all angle types, then overwrite the coeffs for just angle type 2:
 
-angle_coeff * 200.0 107.0 1.2
-angle_coeff 2 50.0 107.0 :pre
+
+.. code-block:: LAMMPS
+
+   angle_coeff * 200.0 107.0 1.2
+   angle_coeff 2 50.0 107.0
 
 A line in a data file that specifies angle coefficients uses the exact
-same format as the arguments of the angle_coeff command in an input
+same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input
 script, except that wild-card asterisks should not be used since
 coefficients for all N types must be listed in the file.  For example,
 under the "Angle Coeffs" section of a data file, the line that
 corresponds to the 1st example above would be listed as
 
-1 300.0 107.0 :pre
 
-The "angle_style class2"_angle_class2.html is an exception to this
+.. parsed-literal::
+
+   1 300.0 107.0
+
+The :doc:`angle_style class2 <angle_class2>` is an exception to this
 rule, in that an additional argument is used in the input script to
 allow specification of the cross-term coefficients.   See its
 doc page for details.
 
-:line
+
+----------
+
 
 The list of all angle styles defined in LAMMPS is given on the
-"angle_style"_angle_style.html doc page.  They are also listed in more
-compact form on the "Commands angle"_Commands_bond.html#angle doc
+:doc:`angle_style <angle_style>` doc page.  They are also listed in more
+compact form on the :ref:`Commands angle <angle>` doc
 page.
 
 On either of those pages, click on the style to display the formula it
 computes and its coefficients as specified by the associated
-angle_coeff command.
+:doc:`angle_coeff <angle_coeff>` command.
 
-:line
 
-[Restrictions:]
+----------
+
+
+Restrictions
+""""""""""""
+
 
 This command must come after the simulation box is defined by a
-"read_data"_read_data.html, "read_restart"_read_restart.html, or
-"create_box"_create_box.html command.
+:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
+:doc:`create_box <create_box>` command.
 
 An angle style must be defined before any angle coefficients are
 set, either in the input script or in a data file.
 
-[Related commands:]
+Related commands
+""""""""""""""""
 
-"angle_style"_angle_style.html
+:doc:`angle_style <angle_style>`
 
-[Default:] none
+**Default:** none
diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst
new file mode 100644
index 0000000000..68bfdbb82b
--- /dev/null
+++ b/doc/src/angle_cosine.rst
@@ -0,0 +1,87 @@
+.. index:: angle_style cosine
+
+angle_style cosine command
+==========================
+
+angle_style cosine/omp command
+==============================
+
+angle_style cosine/kk command
+=============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine
+   angle_coeff * 75.0
+
+Description
+"""""""""""
+
+The *cosine* angle style uses the potential
+
+.. math::
+
+   E = K [1 + \cos(\theta)]
+
+
+where :math:`K` is defined for each angle type.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
deleted file mode 100644
index 93fed32c38..0000000000
--- a/doc/src/angle_cosine.txt
+++ /dev/null
@@ -1,71 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style cosine command :h3
-angle_style cosine/omp command :h3
-angle_style cosine/kk command :h3
-
-[Syntax:]
-
-angle_style cosine :pre
-
-[Examples:]
-
-angle_style cosine
-angle_coeff * 75.0 :pre
-
-[Description:]
-
-The {cosine} angle style uses the potential
-
-:c,image(Eqs/angle_cosine.jpg)
-
-where K is defined for each angle type.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Build package"_Build_package.html doc page
-for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
diff --git a/doc/src/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst
new file mode 100644
index 0000000000..2d00863b02
--- /dev/null
+++ b/doc/src/angle_cosine_buck6d.rst
@@ -0,0 +1,76 @@
+.. index:: angle_style cosine/buck6d
+
+angle_style cosine/buck6d command
+=================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/buck6d
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/buck6d
+   angle_coeff 1  cosine/buck6d  1.978350  4  180.000000
+
+Description
+"""""""""""
+
+The *cosine/buck6d* angle style uses the potential
+
+.. math::
+
+   E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
+
+where :math:`K` is the energy constant, :math:`n` is the periodic multiplicity and
+:math:`\theta_0` is the equilibrium angle.
+
+The coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands in the following order:
+
+* :math:`K` (energy)
+* :math:`n`
+* :math:`\theta_0` (degrees)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally.
+
+Additional to the cosine term the *cosine/buck6d* angle style computes
+the short range (vdW) interaction belonging to the
+:doc:`pair\_buck6d <pair_buck6d_coul_gauss>` between the end atoms of the
+angle.  For this reason this angle style only works in combination
+with the :doc:`pair\_buck6d <pair_buck6d_coul_gauss>` styles and needs
+the :doc:`special\_bonds <special_bonds>` 1-3 interactions to be weighted
+0.0 to prevent double counting.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+*cosine/buck6d* can only be used in combination with the
+:doc:`pair\_buck6d <pair_buck6d_coul_gauss>` style and with a
+:doc:`special\_bonds <special_bonds>` 0.0 weighting of 1-3 interactions.
+
+This angle style can only be used if LAMMPS was built with the
+USER-MOFFF package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt
deleted file mode 100644
index 1ce3556ea6..0000000000
--- a/doc/src/angle_cosine_buck6d.txt
+++ /dev/null
@@ -1,65 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style cosine/buck6d command :h3
-
-[Syntax:]
-
-angle_style cosine/buck6d :pre
-
-[Examples:]
-
-angle_style cosine/buck6d
-angle_coeff 1  cosine/buck6d  1.978350  4  180.000000 :pre
-
-[Description:]
-
-The {cosine/buck6d} angle style uses the potential
-
-:c,image(Eqs/angle_cosine_buck6d.jpg)
-
-where K is the energy constant, n is the periodic multiplicity and
-Theta0 is the equilibrium angle.
-
-The coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands in the following order:
-
-K (energy)
-n
-Theta0 (degrees) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally.
-
-Additional to the cosine term the {cosine/buck6d} angle style computes
-the short range (vdW) interaction belonging to the
-"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the
-angle.  For this reason this angle style only works in combination
-with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs
-the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
-0.0 to prevent double counting.
-
-:line
-
-[Restrictions:]
-
-{cosine/buck6d} can only be used in combination with the
-"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a
-"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
-
-This angle style can only be used if LAMMPS was built with the
-USER-MOFFF package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst
new file mode 100644
index 0000000000..9af93cb06a
--- /dev/null
+++ b/doc/src/angle_cosine_delta.rst
@@ -0,0 +1,89 @@
+.. index:: angle_style cosine/delta
+
+angle_style cosine/delta command
+================================
+
+angle_style cosine/delta/omp command
+====================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/delta
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/delta
+   angle_coeff 2*4 75.0 100.0
+
+Description
+"""""""""""
+
+The *cosine/delta* angle style uses the potential
+
+.. math::
+
+   E = K [1 - \cos(\theta - \theta_0)]
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy)
+* :math:`\theta_0` (degrees)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`, :doc:`angle\_style cosine/squared <angle_cosine_squared>`
+
+**Default:** none
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
deleted file mode 100644
index 1532e39b31..0000000000
--- a/doc/src/angle_cosine_delta.txt
+++ /dev/null
@@ -1,76 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style cosine/delta command :h3
-angle_style cosine/delta/omp command :h3
-
-[Syntax:]
-
-angle_style cosine/delta :pre
-
-[Examples:]
-
-angle_style cosine/delta
-angle_coeff 2*4 75.0 100.0 :pre
-
-[Description:]
-
-The {cosine/delta} angle style uses the potential
-
-:c,image(Eqs/angle_cosine_delta.jpg)
-
-where theta0 is the equilibrium value of the angle, and K is a
-prefactor.  Note that the usual 1/2 factor is included in K.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy)
-theta0 (degrees) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Build package"_Build_package.html doc page
-for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html, "angle_style
-cosine/squared"_angle_cosine_squared.html
-
-[Default:] none
diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst
new file mode 100644
index 0000000000..caaf15007a
--- /dev/null
+++ b/doc/src/angle_cosine_periodic.rst
@@ -0,0 +1,108 @@
+.. index:: angle_style cosine/periodic
+
+angle_style cosine/periodic command
+===================================
+
+angle_style cosine/periodic/omp command
+=======================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/periodic
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/periodic
+   angle_coeff * 75.0 1 6
+
+Description
+"""""""""""
+
+The *cosine/periodic* angle style uses the following potential, which
+is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
+particularly for organometallic systems where :math:`n` = 4 might be used
+for an octahedral complex and :math:`n` = 3 might be used for a trigonal
+center:
+
+.. math::
+
+   E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
+
+
+where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
+
+See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`C` (energy)
+* :math:`B` = 1 or -1
+* :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity
+
+Note that the prefactor :math:`C` is specified and not the overall force
+constant :math:`K = \frac{C}{n^2}`.  When :math:`B = 1`, it leads to a minimum for the
+linear geometry.  When :math:`B = -1`, it leads to a maximum for the linear
+geometry.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _cosine-Mayo:
+
+
+
+**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
deleted file mode 100644
index 039144797f..0000000000
--- a/doc/src/angle_cosine_periodic.txt
+++ /dev/null
@@ -1,89 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style cosine/periodic command :h3
-angle_style cosine/periodic/omp command :h3
-
-[Syntax:]
-
-angle_style cosine/periodic :pre
-
-[Examples:]
-
-angle_style cosine/periodic
-angle_coeff * 75.0 1 6 :pre
-
-[Description:]
-
-The {cosine/periodic} angle style uses the following potential, which
-is commonly used in the "DREIDING"_Howto_bioFF.html force field,
-particularly for organometallic systems where {n} = 4 might be used
-for an octahedral complex and {n} = 3 might be used for a trigonal
-center:
-
-:c,image(Eqs/angle_cosine_periodic.jpg)
-
-where C, B and n are coefficients defined for each angle type.
-
-See "(Mayo)"_#cosine-Mayo for a description of the DREIDING force field
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-C (energy)
-B = 1 or -1
-n = 1, 2, 3, 4, 5 or 6 for periodicity :ul
-
-Note that the prefactor C is specified and not the overall force
-constant K = C / n^2.  When B = 1, it leads to a minimum for the
-linear geometry.  When B = -1, it leads to a maximum for the linear
-geometry.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Build package"_Build_package.html doc page
-for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
-
-:line
-
-:link(cosine-Mayo)
-[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
-(1990).
diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst
new file mode 100644
index 0000000000..bd7b6416c7
--- /dev/null
+++ b/doc/src/angle_cosine_shift.rst
@@ -0,0 +1,88 @@
+.. index:: angle_style cosine/shift
+
+angle_style cosine/shift command
+=================================
+
+angle_style cosine/shift/omp command
+====================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/shift
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/shift
+   angle_coeff * 10.0 45.0
+
+Description
+"""""""""""
+
+The *cosine/shift* angle style uses the potential
+
+.. math::
+
+   E = -\frac{U_{\text{min}}}{2} \left[ 1 + \cos(\theta-\theta_0) \right]
+
+
+where :math:`\theta_0` is the equilibrium angle. The potential is bounded
+between :math:`-U_{\text{min}}` and zero. In the neighborhood of the minimum
+:math:`E = - U_{\text{min}} + U_{\text{min}}/4(\theta - \theta_0)^2` hence
+the spring constant is :math:`\frac{U_{\text{min}}}{2}`.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`U_{\text{min}}` (energy)
+* :math:`\theta` (angle)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER-MISC package.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`,
+:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
+
+**Default:** none
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
deleted file mode 100644
index 65dc0924e5..0000000000
--- a/doc/src/angle_cosine_shift.txt
+++ /dev/null
@@ -1,73 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style cosine/shift command :h3
-angle_style cosine/shift/omp command :h3
-
-[Syntax:]
-
-angle_style cosine/shift :pre
-
-[Examples:]
-
-angle_style cosine/shift
-angle_coeff * 10.0 45.0 :pre
-
-[Description:]
-
-The {cosine/shift} angle style uses the potential
-
-:c,image(Eqs/angle_cosine_shift.jpg)
-
-where theta0 is the equilibrium angle. The potential is bounded
-between -Umin and zero. In the neighborhood of the minimum E=- Umin +
-Umin/4(theta-theta0)^2 hence the spring constant is umin/2.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-umin (energy)
-theta (angle) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER-MISC package.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html,
-"angle_cosine_shift_exp"_angle_cosine_shift_exp.html
-
-[Default:] none
diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst
new file mode 100644
index 0000000000..331ccb9da7
--- /dev/null
+++ b/doc/src/angle_cosine_shift_exp.rst
@@ -0,0 +1,100 @@
+.. index:: angle_style cosine/shift/exp
+
+angle_style cosine/shift/exp command
+====================================
+
+angle_style cosine/shift/exp/omp command
+========================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/shift/exp
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/shift/exp
+   angle_coeff * 10.0 45.0 2.0
+
+Description
+"""""""""""
+
+The *cosine/shift/exp* angle style uses the potential
+
+.. math::
+
+   E = -U_{\text{min}} \frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad \text{with} \quad U(\theta,\theta_0) = -0.5 \left(1+\cos(\theta-\theta_0) \right)
+
+where :math:`U_{\text{min}}`, :math:`\theta`, and :math:`a` are defined for each angle type.
+
+The potential is bounded between :math:`[-U_{\text{min}}, 0]` and the minimum is
+located at the angle :math:`\theta_0`. The a parameter can be both positive or
+negative and is used to control the spring constant at the
+equilibrium.
+
+The spring constant is given by :math:`k = A \exp(A) U_{\text{min}} / [2 (\exp(a)-1)]`.
+For :math:`a > 3`, :math:`\frac{k}{U_{\text{min}}} = \frac{a}{2}` to better than 5% relative error. For negative
+values of the :math:`a` parameter, the spring constant is essentially zero,
+and anharmonic terms takes over. The potential is furthermore well
+behaved in the limit :math:`a \rightarrow 0`, where it has been implemented to linear
+order in :math:`a` for :math:`a < 0.001`. In this limit the potential reduces to the
+cosineshifted potential.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`U_min` (energy)
+* :math:`\theta` (angle)
+* :math:`A` (real number)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`,
+:doc:`angle\_cosine\_shift <angle_cosine_shift>`,
+:doc:`dihedral\_cosine\_shift\_exp <dihedral_cosine_shift_exp>`
+
+**Default:** none
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
deleted file mode 100644
index 3091e83885..0000000000
--- a/doc/src/angle_cosine_shift_exp.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style cosine/shift/exp command :h3
-angle_style cosine/shift/exp/omp command :h3
-
-[Syntax:]
-
-angle_style cosine/shift/exp :pre
-
-[Examples:]
-
-angle_style cosine/shift/exp
-angle_coeff * 10.0 45.0 2.0 :pre
-
-[Description:]
-
-The {cosine/shift/exp} angle style uses the potential
-
-:c,image(Eqs/angle_cosine_shift_exp.jpg)
-
-where Umin, theta, and a are defined for each angle type.
-
-The potential is bounded between \[-Umin:0\] and the minimum is
-located at the angle theta0. The a parameter can be both positive or
-negative and is used to control the spring constant at the
-equilibrium.
-
-The spring constant is given by k = A exp(A) Umin / \[2 (Exp(a)-1)\].
-For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
-values of the a parameter, the spring constant is essentially zero,
-and anharmonic terms takes over. The potential is furthermore well
-behaved in the limit a -> 0, where it has been implemented to linear
-order in a for a < 0.001. In this limit the potential reduces to the
-cosineshifted potential.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-umin (energy)
-theta (angle)
-A (real number) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER-MISC package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html,
-"angle_cosine_shift"_angle_cosine_shift.html,
-"dihedral_cosine_shift_exp"_dihedral_cosine_shift_exp.html
-
-[Default:] none
diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst
new file mode 100644
index 0000000000..b1a516880d
--- /dev/null
+++ b/doc/src/angle_cosine_squared.rst
@@ -0,0 +1,89 @@
+.. index:: angle_style cosine/squared
+
+angle_style cosine/squared command
+==================================
+
+angle_style cosine/squared/omp command
+======================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/squared
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/squared
+   angle_coeff 2*4 75.0 100.0
+
+Description
+"""""""""""
+
+The *cosine/squared* angle style uses the potential
+
+.. math::
+
+   E = K [\cos(\theta) - \cos(\theta_0)]^2
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy)
+* :math:`\theta_0` (degrees)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
deleted file mode 100644
index 07fcb1ceb4..0000000000
--- a/doc/src/angle_cosine_squared.txt
+++ /dev/null
@@ -1,75 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style cosine/squared command :h3
-angle_style cosine/squared/omp command :h3
-
-[Syntax:]
-
-angle_style cosine/squared :pre
-
-[Examples:]
-
-angle_style cosine/squared
-angle_coeff 2*4 75.0 100.0 :pre
-
-[Description:]
-
-The {cosine/squared} angle style uses the potential
-
-:c,image(Eqs/angle_cosine_squared.jpg)
-
-where theta0 is the equilibrium value of the angle, and K is a
-prefactor.  Note that the usual 1/2 factor is included in K.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy)
-theta0 (degrees) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Build package"_Build_package.html doc page
-for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst
new file mode 100644
index 0000000000..7dcff0264f
--- /dev/null
+++ b/doc/src/angle_cross.rst
@@ -0,0 +1,67 @@
+.. index:: angle_style cross
+
+angle_style cross command
+==========================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cross
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style cross
+   angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0
+
+Description
+"""""""""""
+
+The *cross* angle style uses a potential that couples the bond stretches of
+a bend with the angle stretch of that bend:
+
+.. math::
+
+   E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
+
+where :math:`r_{12,0}` is the rest value of the bond length between atom 1 and 2,
+:math:`r_{32,0}` is the rest value of the bond length between atom 3 and 2,
+and :math:`\theta_0` is the rest value of the angle. :math:`K_{SS}` is the force constant of
+the bond stretch-bond stretch term and :math:`K_{BS0}` and :math:`K_{BS1}` are the force constants
+of the bond stretch-angle stretch terms.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K_{SS}` (energy/distance\^2)
+* :math:`K_{BS0}` (energy/distance/rad)
+* :math:`K_{BS1}` (energy/distance/rad)
+* :math:`r_{12,0}` (distance)
+* :math:`r_{32,0}` (distance)
+* :math:`\theta_0` (degrees)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian.
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_YAFF package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_cross.txt b/doc/src/angle_cross.txt
deleted file mode 100644
index d9d83ed4b6..0000000000
--- a/doc/src/angle_cross.txt
+++ /dev/null
@@ -1,62 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style cross command :h3
-
-[Syntax:]
-
-angle_style cross :pre
-
-[Examples:]
-
-angle_style cross
-angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre
-
-[Description:]
-
-The {cross} angle style uses a potential that couples the bond stretches of
-a bend with the angle stretch of that bend:
-
-:c,image(Eqs/angle_cross.jpg)
-
-where r12,0 is the rest value of the bond length between atom 1 and 2,
-r32,0 is the rest value of the bond length between atom 2 and 2,
-and theta0 is the rest value of the angle. KSS is the force constant of
-the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
-of the bond stretch-angle stretch terms.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-KSS (energy/distance^2)
-KBS0 (energy/distance/rad)
-KBS1 (energy/distance/rad)
-r12,0 (distance)
-r32,0 (distance)
-theta0 (degrees) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER_YAFF package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
-
-:line
-
-
diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst
new file mode 100644
index 0000000000..351572cc22
--- /dev/null
+++ b/doc/src/angle_dipole.rst
@@ -0,0 +1,159 @@
+.. index:: angle_style dipole
+
+angle_style dipole command
+==========================
+
+angle_style dipole/omp command
+==============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style dipole
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style dipole
+   angle_coeff 6 2.1 180.0
+
+Description
+"""""""""""
+
+The *dipole* angle style is used to control the orientation of a dipolar
+atom within a molecule :ref:`(Orsi) <Orsi>`. Specifically, the *dipole* angle
+style restrains the orientation of a point dipole :math:`\mu_j` (embedded in atom
+:math:`j`) with respect to a reference (bond) vector
+:math:`\vec{r_{ij}} = \vec{r_i} - \vec{r_j}`, where :math:`i` is another atom of
+the same molecule (typically, :math:`i` and :math:`j` are also covalently bonded).
+
+It is convenient to define an angle gamma between the 'free' vector :math:`\vec{\mu_j}`
+and the reference (bond) vector :math:`\vec{r_{ij}}`:
+
+.. math::
+
+   \cos\gamma = \frac{\vec{\mu_j}\cdot\vec{r_{ij}}}{\mu_j\,r_{ij}}
+
+
+The *dipole* angle style uses the potential:
+
+.. math::
+
+   E = K (\cos\gamma - \cos\gamma_0)^2
+
+
+where :math:`K` is a rigidity constant and gamma0 is an equilibrium (reference)
+angle.
+
+The torque on the dipole can be obtained by differentiating the
+potential using the 'chain rule' as in appendix C.3 of
+:ref:`(Allen) <Allen1>`:
+
+.. math::
+
+   \vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, \vec{r_{ij}} \times \vec{\mu_j}
+
+
+Example: if :math:`\gamma_0` is set to 0 degrees, the torque generated by
+the potential will tend to align the dipole along the reference
+direction defined by the (bond) vector :math:`\vec{r_{ij}}` (in other words, :math:`\vec{\mu_j}` is
+restrained to point towards atom :math:`i`).
+
+The dipolar torque :math:`\vec{T_j}` must be counterbalanced in order to conserve
+the local angular momentum. This is achieved via an additional force
+couple generating a torque equivalent to the opposite of :math:`\vec{T_j}`:
+
+.. math::
+
+   -\vec{T_j} & = \vec{r_{ij}} \times \vec{F_i} \\
+   \vec{F_j}  & = -\vec{F_i}
+
+
+where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i`
+and :math:`j`, respectively.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy)
+* :math:`\gamma_0` (degrees)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+.. note::
+
+   In the "Angles" section of the data file, the atom ID :math:`j`
+   defining the direction of the dipole vector to restrain must come
+   before the atom ID of the reference atom :math:`i`. A third atom ID :math:`k` must
+   also be provided to comply with the requirement of a valid angle
+   definition. This atom ID :math:`k` should be chosen to be that of an atom
+   bonded to atom :math:`i` to avoid errors with "lost angle atoms" when running
+   in parallel. Since the LAMMPS code checks for valid angle definitions,
+   cannot use the same atom ID of either :math:`i` or :math:`j` (this was allowed
+   and recommended with older LAMMPS versions).
+
+The :doc:`newton <newton>` command for intramolecular interactions must be "on"
+(which is the default except when using some accelerator packages).
+
+This angle style should not be used with SHAKE.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`, :doc:`angle\_hybrid <angle_hybrid>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Orsi:
+
+
+
+**(Orsi)** Orsi & Essex, The ELBA force field for coarse-grain modeling of
+lipid membranes, PloS ONE 6(12): e28637, 2011.
+
+.. _Allen1:
+
+
+
+**(Allen)** Allen & Tildesley, Computer Simulation of Liquids,
+Clarendon Press, Oxford, 1987.
diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
deleted file mode 100644
index cdb11972ec..0000000000
--- a/doc/src/angle_dipole.txt
+++ /dev/null
@@ -1,126 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style dipole command :h3
-angle_style dipole/omp command :h3
-
-[Syntax:]
-
-angle_style dipole :pre
-
-[Examples:]
-
-angle_style dipole
-angle_coeff 6 2.1 180.0 :pre
-
-[Description:]
-
-The {dipole} angle style is used to control the orientation of a dipolar
-atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle
-style restrains the orientation of a point dipole mu_j (embedded in atom
-'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
-is another atom of the same molecule (typically, 'i' and 'j' are also
-covalently bonded).
-
-It is convenient to define an angle gamma between the 'free' vector mu_j
-and the reference (bond) vector r_ij:
-
-:c,image(Eqs/angle_dipole_gamma.jpg)
-
-The {dipole} angle style uses the potential:
-
-:c,image(Eqs/angle_dipole_potential.jpg)
-
-where K is a rigidity constant and gamma0 is an equilibrium (reference)
-angle.
-
-The torque on the dipole can be obtained by differentiating the
-potential using the 'chain rule' as in appendix C.3 of
-"(Allen)"_#Allen1:
-
-:c,image(Eqs/angle_dipole_torque.jpg)
-
-Example: if gamma0 is set to 0 degrees, the torque generated by
-the potential will tend to align the dipole along the reference
-direction defined by the (bond) vector r_ij (in other words, mu_j is
-restrained to point towards atom 'i').
-
-The dipolar torque T_j must be counterbalanced in order to conserve
-the local angular momentum. This is achieved via an additional force
-couple generating a torque equivalent to the opposite of T_j:
-
-:c,image(Eqs/angle_dipole_couple.jpg)
-
-where F_i and F_j are applied on atoms i and j, respectively.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy)
-gamma0 (degrees) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER-MISC package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-NOTE: In the "Angles" section of the data file, the atom ID 'j'
-defining the direction of the dipole vector to restrain must come
-before the atom ID of the reference atom 'i'. A third atom ID 'k' must
-also be provided to comply with the requirement of a valid angle
-definition. This atom ID k should be chosen to be that of an atom
-bonded to atom 'i' to avoid errors with "lost angle atoms" when running
-in parallel. Since the LAMMPS code checks for valid angle definitions,
-cannot use the same atom ID of either 'i' or 'j' (this was allowed
-and recommended with older LAMMPS versions).
-
-The "newton" command for intramolecular interactions must be "on"
-(which is the default except when using some accelerator packages).
-
-This angle style should not be used with SHAKE.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html, "angle_hybrid"_angle_hybrid.html
-
-[Default:] none
-
-:line
-
-:link(Orsi)
-[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
-lipid membranes, PloS ONE 6(12): e28637, 2011.
-
-:link(Allen1)
-[(Allen)] Allen & Tildesley, Computer Simulation of Liquids,
-Clarendon Press, Oxford, 1987.
diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst
new file mode 100644
index 0000000000..c814b7224e
--- /dev/null
+++ b/doc/src/angle_fourier.rst
@@ -0,0 +1,84 @@
+.. index:: angle_style fourier
+
+angle_style fourier command
+===========================
+
+angle_style fourier/omp command
+===============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style fourier
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style fourier
+   angle_coeff 75.0 1.0 1.0 1.0
+
+Description
+"""""""""""
+
+The *fourier* angle style uses the potential
+
+.. math::
+
+   E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
+
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy)
+* :math:`C_0` (real)
+* :math:`C_1` (real)
+* :math:`C_2` (real)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
deleted file mode 100644
index 7dc9975793..0000000000
--- a/doc/src/angle_fourier.txt
+++ /dev/null
@@ -1,71 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style fourier command :h3
-angle_style fourier/omp command :h3
-
-[Syntax:]
-
-angle_style fourier :pre
-
-[Examples:]
-
-angle_style fourier
-angle_coeff 75.0 1.0 1.0 1.0
-
-[Description:]
-
-The {fourier} angle style uses the potential
-
-:c,image(Eqs/angle_fourier.jpg)
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy)
-C0 (real)
-C1 (real)
-C2 (real) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER_MISC package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst
new file mode 100644
index 0000000000..5ad8b386d0
--- /dev/null
+++ b/doc/src/angle_fourier_simple.rst
@@ -0,0 +1,83 @@
+.. index:: angle_style fourier/simple
+
+angle_style fourier/simple command
+==================================
+
+angle_style fourier/simple/omp command
+======================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style fourier/simple
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style fourier/simple
+   angle_coeff 100.0 -1.0 1.0
+
+Description
+"""""""""""
+
+The *fourier/simple* angle style uses the potential
+
+.. math::
+
+   E = K [ 1.0 + c \cos ( n \theta) ]
+
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy)
+* :math:`c` (real)
+* :math:`n` (real)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
deleted file mode 100644
index ae5d308353..0000000000
--- a/doc/src/angle_fourier_simple.txt
+++ /dev/null
@@ -1,70 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style fourier/simple command :h3
-angle_style fourier/simple/omp command :h3
-
-[Syntax:]
-
-angle_style fourier/simple :pre
-
-[Examples:]
-
-angle_style fourier/simple
-angle_coeff 100.0 -1.0 1.0
-
-[Description:]
-
-The {fourier/simple} angle style uses the potential
-
-:c,image(Eqs/angle_fourier_simple.jpg)
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy)
-c (real)
-n (real) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER_MISC package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst
new file mode 100644
index 0000000000..1066621729
--- /dev/null
+++ b/doc/src/angle_harmonic.rst
@@ -0,0 +1,95 @@
+.. index:: angle_style harmonic
+
+angle_style harmonic command
+============================
+
+angle_style harmonic/intel command
+==================================
+
+angle_style harmonic/kk command
+===============================
+
+angle_style harmonic/omp command
+================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style harmonic
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style harmonic
+   angle_coeff 1 300.0 107.0
+
+Description
+"""""""""""
+
+The *harmonic* angle style uses the potential
+
+.. math::
+
+   E = K (\theta - \theta_0)^2
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/radian\^2)
+* :math:`\theta_0` (degrees)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of :math:`K` are in energy/radian\^2.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
deleted file mode 100644
index b632f68478..0000000000
--- a/doc/src/angle_harmonic.txt
+++ /dev/null
@@ -1,77 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style harmonic command :h3
-angle_style harmonic/intel command :h3
-angle_style harmonic/kk command :h3
-angle_style harmonic/omp command :h3
-
-[Syntax:]
-
-angle_style harmonic :pre
-
-[Examples:]
-
-angle_style harmonic
-angle_coeff 1 300.0 107.0 :pre
-
-[Description:]
-
-The {harmonic} angle style uses the potential
-
-:c,image(Eqs/angle_harmonic.jpg)
-
-where theta0 is the equilibrium value of the angle, and K is a
-prefactor.  Note that the usual 1/2 factor is included in K.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/radian^2)
-theta0 (degrees) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian^2.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
diff --git a/doc/src/angle_hybrid.rst b/doc/src/angle_hybrid.rst
new file mode 100644
index 0000000000..f685beacc8
--- /dev/null
+++ b/doc/src/angle_hybrid.rst
@@ -0,0 +1,105 @@
+.. index:: angle_style hybrid
+
+angle_style hybrid command
+==========================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style hybrid style1 style2 ...
+
+* style1,style2 = list of one or more angle styles
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style hybrid harmonic cosine
+   angle_coeff 1 harmonic 80.0 30.0
+   angle_coeff 2* cosine 50.0
+
+Description
+"""""""""""
+
+The *hybrid* style enables the use of multiple angle styles in one
+simulation.  An angle style is assigned to each angle type.  For
+example, angles in a polymer flow (of angle type 1) could be computed
+with a *harmonic* potential and angles in the wall boundary (of angle
+type 2) could be computed with a *cosine* potential.  The assignment
+of angle type to style is made via the :doc:`angle_coeff <angle_coeff>`
+command or in the data file.
+
+In the :doc:`angle_coeff <angle_coeff>` commands, the name of an angle style must be added
+after the angle type, with the remaining coefficients being those
+appropriate to that style.  In the example above, the 2 angle\_coeff
+commands set angles of angle type 1 to be computed with a *harmonic*
+potential with coefficients 80.0, 30.0 for :math:`K`, :math:`\theta_0`.  All other angle
+types :math:`(2 - N)` are computed with a *cosine* potential with coefficient
+50.0 for :math:`K`.
+
+If angle coefficients are specified in the data file read via the
+:doc:`read_data <read_data>` command, then the same rule applies.
+E.g. "harmonic" or "cosine", must be added after the angle type, for each
+line in the "Angle Coeffs" section, e.g.
+
+
+.. parsed-literal::
+
+   Angle Coeffs
+
+   1 harmonic 80.0 30.0
+   2 cosine 50.0
+   ...
+
+If *class2* is one of the angle hybrid styles, the same rule holds for
+specifying additional BondBond (and BondAngle) coefficients either via
+the input script or in the data file.  I.e. *class2* must be added to
+each line after the angle type.  For lines in the BondBond (or
+BondAngle) section of the data file for angle types that are not
+*class2*\ , you must use an angle style of *skip* as a placeholder, e.g.
+
+
+.. parsed-literal::
+
+   BondBond Coeffs
+
+   1 skip
+   2 class2 3.6512 1.0119 1.0119
+   ...
+
+Note that it is not necessary to use the angle style *skip* in the
+input script, since BondBond (or BondAngle) coefficients need not be
+specified at all for angle types that are not *class2*\ .
+
+An angle style of *none* with no additional coefficients can be used
+in place of an angle style, either in a input script :doc:`angle_coeff <angle_coeff>`
+command or in the data file, if you desire to turn off interactions
+for specific angle types.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Unlike other angle styles, the hybrid angle style does not store angle
+coefficient info for individual sub-styles in a :doc:`binary restart files <restart>`.  Thus when restarting a simulation from a restart
+file, you need to re-specify :doc:`angle_coeff <angle_coeff>` commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt
deleted file mode 100644
index 0046c161be..0000000000
--- a/doc/src/angle_hybrid.txt
+++ /dev/null
@@ -1,91 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style hybrid command :h3
-
-[Syntax:]
-
-angle_style hybrid style1 style2 ... :pre
-
-style1,style2 = list of one or more angle styles :ul
-
-[Examples:]
-
-angle_style hybrid harmonic cosine
-angle_coeff 1 harmonic 80.0 30.0
-angle_coeff 2* cosine 50.0  :pre
-
-[Description:]
-
-The {hybrid} style enables the use of multiple angle styles in one
-simulation.  An angle style is assigned to each angle type.  For
-example, angles in a polymer flow (of angle type 1) could be computed
-with a {harmonic} potential and angles in the wall boundary (of angle
-type 2) could be computed with a {cosine} potential.  The assignment
-of angle type to style is made via the "angle_coeff"_angle_coeff.html
-command or in the data file.
-
-In the angle_coeff commands, the name of an angle style must be added
-after the angle type, with the remaining coefficients being those
-appropriate to that style.  In the example above, the 2 angle_coeff
-commands set angles of angle type 1 to be computed with a {harmonic}
-potential with coefficients 80.0, 30.0 for K, theta0.  All other angle
-types (2-N) are computed with a {cosine} potential with coefficient
-50.0 for K.
-
-If angle coefficients are specified in the data file read via the
-"read_data"_read_data.html command, then the same rule applies.
-E.g. "harmonic" or "cosine", must be added after the angle type, for each
-line in the "Angle Coeffs" section, e.g.
-
-Angle Coeffs :pre
-
-1 harmonic 80.0 30.0
-2 cosine 50.0
-... :pre
-
-If {class2} is one of the angle hybrid styles, the same rule holds for
-specifying additional BondBond (and BondAngle) coefficients either via
-the input script or in the data file.  I.e. {class2} must be added to
-each line after the angle type.  For lines in the BondBond (or
-BondAngle) section of the data file for angle types that are not
-{class2}, you must use an angle style of {skip} as a placeholder, e.g.
-
-BondBond Coeffs :pre
-
-1 skip
-2 class2 3.6512 1.0119 1.0119
-... :pre
-
-Note that it is not necessary to use the angle style {skip} in the
-input script, since BondBond (or BondAngle) coefficients need not be
-specified at all for angle types that are not {class2}.
-
-An angle style of {none} with no additional coefficients can be used
-in place of an angle style, either in a input script angle_coeff
-command or in the data file, if you desire to turn off interactions
-for specific angle types.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Build package"_Build_package.html doc page
-for more info.
-
-Unlike other angle styles, the hybrid angle style does not store angle
-coefficient info for individual sub-styles in a "binary restart
-files"_restart.html.  Thus when restarting a simulation from a restart
-file, you need to re-specify angle_coeff commands.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
diff --git a/doc/src/angle_mm3.rst b/doc/src/angle_mm3.rst
new file mode 100644
index 0000000000..7cf7f9e720
--- /dev/null
+++ b/doc/src/angle_mm3.rst
@@ -0,0 +1,62 @@
+.. index:: angle_style mm3
+
+angle_style mm3 command
+=======================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style mm3
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style mm3
+   angle_coeff 1 100.0 107.0
+
+Description
+"""""""""""
+
+The *mm3* angle style uses the potential that is anharmonic in the angle
+as defined in :ref:`(Allinger) <mm3-allinger1989>`
+
+.. math::
+
+   E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example
+:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ...
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/radian\^2)
+* :math:`\theta_0` (degrees)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of :math:`K` are in energy/radian\^2.
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_YAFF package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_mm3.txt b/doc/src/angle_mm3.txt
deleted file mode 100644
index 9ae032c4ff..0000000000
--- a/doc/src/angle_mm3.txt
+++ /dev/null
@@ -1,55 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style mm3 command :h3
-
-[Syntax:]
-
-angle_style mm3 :pre
-
-[Examples:]
-
-angle_style mm3
-angle_coeff 1 100.0 107.0 :pre
-
-[Description:]
-
-The {mm3} angle style uses the potential that is anharmonic in the angle
-as defined in "(Allinger)"_#mm3-allinger1989
-
-:c,image(Eqs/angle_mm3.jpg)
-
-where theta0 is the equilibrium value of the angle, and K is a
-prefactor. The anharmonic prefactors have units deg^(-n), for example
--0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ...
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/radian^2)
-theta0 (degrees) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian^2.
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER_YAFF package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
-
-:line
-
diff --git a/doc/src/angle_none.rst b/doc/src/angle_none.rst
new file mode 100644
index 0000000000..e848391932
--- /dev/null
+++ b/doc/src/angle_none.rst
@@ -0,0 +1,42 @@
+.. index:: angle_style none
+
+angle_style none command
+========================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style none
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style none
+
+Description
+"""""""""""
+
+Using an angle style of none means angle forces and energies are not
+computed, even if triplets of angle atoms were listed in the data file
+read by the :doc:`read_data <read_data>` command.
+
+See the :doc:`angle_style zero <angle_zero>` command for a way to
+calculate angle statistics, but compute no angle interactions.
+
+Restrictions
+""""""""""""
+
+none
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_style zero <angle_zero>`
+
+**Default:** none
diff --git a/doc/src/angle_none.txt b/doc/src/angle_none.txt
deleted file mode 100644
index 1eca5cbbec..0000000000
--- a/doc/src/angle_none.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style none command :h3
-
-[Syntax:]
-
-angle_style none :pre
-
-[Examples:]
-
-angle_style none :pre
-
-[Description:]
-
-Using an angle style of none means angle forces and energies are not
-computed, even if triplets of angle atoms were listed in the data file
-read by the "read_data"_read_data.html command.
-
-See the "angle_style zero"_angle_zero.html command for a way to
-calculate angle statistics, but compute no angle interactions.
-
-[Restrictions:] none
-
-[Related commands:]
-
-"angle_style zero"_angle_zero.html
-
-[Default:] none
diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst
new file mode 100644
index 0000000000..104c0be802
--- /dev/null
+++ b/doc/src/angle_quartic.rst
@@ -0,0 +1,91 @@
+.. index:: angle_style quartic
+
+angle_style quartic command
+===========================
+
+angle_style quartic/omp command
+===============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style quartic
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style quartic
+   angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
+
+Description
+"""""""""""
+
+The *quartic* angle style uses the potential
+
+.. math::
+
+   E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
+
+
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`\theta_0` (degrees)
+* :math:`K_2` (energy/radian\^2)
+* :math:`K_3` (energy/radian\^3)
+* :math:`K_4` (energy/radian\^4)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of :math:`K` are in energy/radian\^2.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`
+
+**Default:** none
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
deleted file mode 100644
index b20a06eb8d..0000000000
--- a/doc/src/angle_quartic.txt
+++ /dev/null
@@ -1,77 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style quartic command :h3
-angle_style quartic/omp command :h3
-
-[Syntax:]
-
-angle_style quartic :pre
-
-[Examples:]
-
-angle_style quartic
-angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 :pre
-
-[Description:]
-
-The {quartic} angle style uses the potential
-
-:c,image(Eqs/angle_quartic.jpg)
-
-where theta0 is the equilibrium value of the angle, and K is a
-prefactor.  Note that the usual 1/2 factor is included in K.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-theta0 (degrees)
-K2 (energy/radian^2)
-K3 (energy/radian^3)
-K4 (energy/radian^4) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian^2.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER_MISC package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:] none
diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst
new file mode 100644
index 0000000000..0af22a5372
--- /dev/null
+++ b/doc/src/angle_sdk.rst
@@ -0,0 +1,97 @@
+.. index:: angle_style sdk
+
+angle_style sdk command
+=======================
+
+angle_style sdk/omp command
+===========================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style sdk
+
+   angle_style sdk/omp
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style sdk
+   angle_coeff 1 300.0 107.0
+
+Description
+"""""""""""
+
+The *sdk* angle style is a combination of the harmonic angle potential,
+
+.. math::
+
+   E = K (\theta - \theta_0)^2 
+
+
+where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor,
+with the *repulsive* part of the non-bonded *lj/sdk* pair style
+between the atoms 1 and 3.  This angle potential is intended for
+coarse grained MD simulations with the CMM parameterization using the
+:doc:`pair\_style lj/sdk <pair_sdk>`.  Relative to the pair\_style
+*lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden
+jumps.  Note that the usual 1/2 factor is included in :math:`K`.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle\_coeff <angle_coeff>` command as in the example above:
+
+* :math:`K` (energy/radian\^2)
+* :math:`\theta_0` (degrees)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of :math:`K` are in energy/radian\^2.
+The also required *lj/sdk* parameters will be extracted automatically
+from the pair\_style.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER-CGSDK package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle\_coeff <angle_coeff>`, :doc:`angle\_style harmonic <angle_harmonic>`, :doc:`pair\_style lj/sdk <pair_sdk>`,
+:doc:`pair\_style lj/sdk/coul/long <pair_sdk>`
+
+**Default:** none
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
deleted file mode 100644
index 9382d560d3..0000000000
--- a/doc/src/angle_sdk.txt
+++ /dev/null
@@ -1,83 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style sdk command :h3
-angle_style sdk/omp command :h3
-
-[Syntax:]
-
-angle_style sdk :pre
-angle_style sdk/omp :pre
-
-[Examples:]
-
-angle_style sdk
-angle_coeff 1 300.0 107.0 :pre
-
-[Description:]
-
-The {sdk} angle style is a combination of the harmonic angle potential,
-
-:c,image(Eqs/angle_harmonic.jpg)
-
-where theta0 is the equilibrium value of the angle and K a prefactor,
-with the {repulsive} part of the non-bonded {lj/sdk} pair style
-between the atoms 1 and 3.  This angle potential is intended for
-coarse grained MD simulations with the CMM parameterization using the
-"pair_style lj/sdk"_pair_sdk.html.  Relative to the pair_style
-{lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden
-jumps.  Note that the usual 1/2 factor is included in K.
-
-The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above:
-
-K (energy/radian^2)
-theta0 (degrees) :ul
-
-Theta0 is specified in degrees, but LAMMPS converts it to radians
-internally; hence the units of K are in energy/radian^2.
-The also required {lj/sdk} parameters will be extracted automatically
-from the pair_style.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This angle style can only be used if LAMMPS was built with the
-USER-CGSDK package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html, "angle_style
-harmonic"_angle_harmonic.html, "pair_style lj/sdk"_pair_sdk.html,
-"pair_style lj/sdk/coul/long"_pair_sdk.html
-
-[Default:] none
diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst
new file mode 100644
index 0000000000..3e22113d85
--- /dev/null
+++ b/doc/src/angle_style.rst
@@ -0,0 +1,126 @@
+.. index:: angle_style
+
+angle_style command
+===================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style style
+
+* style = *none* or *hybrid* or *charmm* or *class2* or *cosine* or         *cosine/squared* or *harmonic*
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style harmonic
+   angle_style charmm
+   angle_style hybrid harmonic cosine
+
+Description
+"""""""""""
+
+Set the formula(s) LAMMPS uses to compute angle interactions between
+triplets of atoms, which remain in force for the duration of the
+simulation.  The list of angle triplets is read in by a
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` command
+from a data or restart file.
+
+Hybrid models where angles are computed using different angle
+potentials can be setup using the *hybrid* angle style.
+
+The coefficients associated with a angle style can be specified in a
+data or restart file or via the :doc:`angle_coeff <angle_coeff>` command.
+
+All angle potentials store their coefficient data in binary restart
+files which means angle_style and :doc:`angle_coeff <angle_coeff>`
+commands do not need to be re-specified in an input script that
+restarts a simulation.  See the :doc:`read_restart <read_restart>`
+command for details on how to do this.  The one exception is that
+angle\_style *hybrid* only stores the list of sub-styles in the restart
+file; angle coefficients need to be re-specified.
+
+.. note::
+
+   When both an angle and pair style is defined, the
+   :doc:`special_bonds <special_bonds>` command often needs to be used to
+   turn off (or weight) the pairwise interaction that would otherwise
+   exist between 3 bonded atoms.
+
+In the formulas listed for each angle style, *theta* is the angle
+between the 3 atoms in the angle.
+
+
+----------
+
+
+Here is an alphabetic list of angle styles defined in LAMMPS.  Click on
+the style to display the formula it computes and coefficients
+specified by the associated :doc:`angle_coeff <angle_coeff>` command.
+
+Click on the style to display the formula it computes, any additional
+arguments specified in the angle\_style command, and coefficients
+specified by the associated :doc:`angle_coeff <angle_coeff>` command.
+
+There are also additional accelerated pair styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the :ref:`Commands angle <angle>` doc page are followed by one or more
+of (g,i,k,o,t) to indicate which accelerated styles exist.
+
+* :doc:`none <angle_none>` - turn off angle interactions
+* :doc:`zero <angle_zero>` - topology but no interactions
+* :doc:`hybrid <angle_hybrid>` - define multiple styles of angle interactions
+
+* :doc:`charmm <angle_charmm>` - CHARMM angle
+* :doc:`class2 <angle_class2>` - COMPASS (class 2) angle
+* :doc:`class2/p6 <angle_class2>` - COMPASS (class 2) angle expanded to 6th order
+* :doc:`cosine <angle_cosine>` - angle with cosine term
+* :doc:`cosine/buck6d <angle_cosine_buck6d>` - same as cosine with Buckingham term between 1-3 atoms
+* :doc:`cosine/delta <angle_cosine_delta>` - angle with difference of cosines
+* :doc:`cosine/periodic <angle_cosine_periodic>` - DREIDING angle
+* :doc:`cosine/shift <angle_cosine_shift>` - angle cosine with a shift
+* :doc:`cosine/shift/exp <angle_cosine_shift_exp>` - cosine with shift and exponential term in spring constant
+* :doc:`cosine/squared <angle_cosine_squared>` - angle with cosine squared term
+* :doc:`cross <angle_cross>` - cross term coupling angle and bond lengths
+* :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
+* :doc:`fourier <angle_fourier>` - angle with multiple cosine terms
+* :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
+* :doc:`harmonic <angle_harmonic>` - harmonic angle
+* :doc:`mm3 <angle_mm3>` - anharmonic angle
+* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
+* :doc:`sdk <angle_sdk>` - harmonic angle with repulsive SDK pair style between 1-3 atoms
+* :doc:`table <angle_table>` - tabulated by angle
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Angle styles can only be set for atom\_styles that allow angles to be
+defined.
+
+Most angle styles are part of the MOLECULE package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  The doc pages for
+individual bond potentials tell if it is part of a package.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_coeff <angle_coeff>`
+
+Default
+"""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style none
diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt
deleted file mode 100644
index 2f2da678d8..0000000000
--- a/doc/src/angle_style.txt
+++ /dev/null
@@ -1,112 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style command :h3
-
-[Syntax:]
-
-angle_style style :pre
-
-style = {none} or {hybrid} or {charmm} or {class2} or {cosine} or \
-        {cosine/squared} or {harmonic} :ul
-
-[Examples:]
-
-angle_style harmonic
-angle_style charmm
-angle_style hybrid harmonic cosine :pre
-
-[Description:]
-
-Set the formula(s) LAMMPS uses to compute angle interactions between
-triplets of atoms, which remain in force for the duration of the
-simulation.  The list of angle triplets is read in by a
-"read_data"_read_data.html or "read_restart"_read_restart.html command
-from a data or restart file.
-
-Hybrid models where angles are computed using different angle
-potentials can be setup using the {hybrid} angle style.
-
-The coefficients associated with a angle style can be specified in a
-data or restart file or via the "angle_coeff"_angle_coeff.html command.
-
-All angle potentials store their coefficient data in binary restart
-files which means angle_style and "angle_coeff"_angle_coeff.html
-commands do not need to be re-specified in an input script that
-restarts a simulation.  See the "read_restart"_read_restart.html
-command for details on how to do this.  The one exception is that
-angle_style {hybrid} only stores the list of sub-styles in the restart
-file; angle coefficients need to be re-specified.
-
-NOTE: When both an angle and pair style is defined, the
-"special_bonds"_special_bonds.html command often needs to be used to
-turn off (or weight) the pairwise interaction that would otherwise
-exist between 3 bonded atoms.
-
-In the formulas listed for each angle style, {theta} is the angle
-between the 3 atoms in the angle.
-
-:line
-
-Here is an alphabetic list of angle styles defined in LAMMPS.  Click on
-the style to display the formula it computes and coefficients
-specified by the associated "angle_coeff"_angle_coeff.html command.
-
-Click on the style to display the formula it computes, any additional
-arguments specified in the angle_style command, and coefficients
-specified by the associated "angle_coeff"_angle_coeff.html command.
-
-There are also additional accelerated pair styles included in the
-LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
-The individual style names on the "Commands
-angle"_Commands_bond.html#angle doc page are followed by one or more
-of (g,i,k,o,t) to indicate which accelerated styles exist.
-
-"none"_angle_none.html - turn off angle interactions
-"zero"_angle_zero.html - topology but no interactions
-"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
-
-"charmm"_angle_charmm.html - CHARMM angle
-"class2"_angle_class2.html - COMPASS (class 2) angle
-"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order
-"cosine"_angle_cosine.html - angle with cosine term
-"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms
-"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines
-"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
-"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
-"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
-"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
-"cross"_angle_cross.html - cross term coupling angle and bond lengths
-"dipole"_angle_dipole.html - angle that controls orientation of a point dipole
-"fourier"_angle_fourier.html - angle with multiple cosine terms
-"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
-"harmonic"_angle_harmonic.html - harmonic angle
-"mm3"_angle_mm3.html - anharmonic angle
-"quartic"_angle_quartic.html - angle with cubic and quartic terms
-"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
-"table"_angle_table.html - tabulated by angle :ul
-
-:line
-
-[Restrictions:]
-
-Angle styles can only be set for atom_styles that allow angles to be
-defined.
-
-Most angle styles are part of the MOLECULE package.  They are only
-enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  The doc pages for
-individual bond potentials tell if it is part of a package.
-
-[Related commands:]
-
-"angle_coeff"_angle_coeff.html
-
-[Default:]
-
-angle_style none :pre
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.rst
similarity index 59%
rename from doc/src/angle_table.txt
rename to doc/src/angle_table.rst
index 61c987f587..f63cf167d9 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.rst
@@ -1,87 +1,98 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+.. index:: angle_style table
 
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
+angle_style table command
+=========================
 
-:line
+angle_style table/omp command
+=============================
 
-angle_style table command :h3
-angle_style table/omp command :h3
+Syntax
+""""""
 
-[Syntax:]
 
-angle_style table style N :pre
+.. code-block:: LAMMPS
 
-style = {linear} or {spline} = method of interpolation
-N = use N values in table :ul
+   angle_style table style N
 
-[Examples:]
+* style = *linear* or *spline* = method of interpolation
+* N = use N values in table
 
-angle_style table linear 1000
-angle_coeff 3 file.table ENTRY1 :pre
+Examples
+""""""""
 
-[Description:]
 
-Style {table} creates interpolation tables of length {N} from angle
+.. code-block:: LAMMPS
+
+   angle_style table linear 1000
+   angle_coeff 3 file.table ENTRY1
+
+Description
+"""""""""""
+
+Style *table* creates interpolation tables of length *N* from angle
 potential and derivative values listed in a file(s) as a function of
-angle The files are read by the "angle_coeff"_angle_coeff.html
+angle The files are read by the :doc:`angle_coeff <angle_coeff>`
 command.
 
 The interpolation tables are created by fitting cubic splines to the
 file values and interpolating energy and derivative values at each of
-{N} angles.  During a simulation, these tables are used to interpolate
+*N* angles.  During a simulation, these tables are used to interpolate
 energy and force values on individual atoms as needed.  The
-interpolation is done in one of 2 styles: {linear} or {spline}.
+interpolation is done in one of 2 styles: *linear* or *spline*\ .
 
-For the {linear} style, the angle is used to find 2 surrounding table
+For the *linear* style, the angle is used to find 2 surrounding table
 values from which an energy or its derivative is computed by linear
 interpolation.
 
-For the {spline} style, a cubic spline coefficients are computed and
-stored at each of the {N} values in the table.  The angle is used to
+For the *spline* style, a cubic spline coefficients are computed and
+stored at each of the *N* values in the table.  The angle is used to
 find the appropriate set of coefficients which are used to evaluate a
 cubic polynomial which computes the energy or derivative.
 
 The following coefficients must be defined for each angle type via the
-"angle_coeff"_angle_coeff.html command as in the example above.
+:doc:`angle_coeff <angle_coeff>` command as in the example above.
 
-filename
-keyword :ul
+* filename
+* keyword
 
 The filename specifies a file containing tabulated energy and
 derivative values.  The keyword specifies a section of the file.  The
 format of this file is described below.
 
-:line
+
+----------
+
 
 The format of a tabulated file is as follows (without the
 parenthesized comments):
 
-# Angle potential for harmonic (one or more comment or blank lines) :pre
 
-HAM                           (keyword is the first text on line)
-N 181 FP 0 0 EQ 90.0          (N, FP, EQ parameters)
-                              (blank line)
-N 181 FP 0 0                  (N, FP parameters)
-1 0.0 200.5 2.5               (index, angle, energy, derivative)
-2 1.0 198.0 2.5
-...
-181 180.0 0.0 0.0 :pre
+.. parsed-literal::
+
+   # Angle potential for harmonic (one or more comment or blank lines)
+
+   HAM                           (keyword is the first text on line)
+   N 181 FP 0 0 EQ 90.0          (N, FP, EQ parameters)
+                                 (blank line)
+   N 181 FP 0 0                  (N, FP parameters)
+   1 0.0 200.5 2.5               (index, angle, energy, derivative)
+   2 1.0 198.0 2.5
+   ...
+   181 180.0 0.0 0.0
 
 A section begins with a non-blank line whose 1st character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.  The first line begins with a keyword which
 identifies the section.  The line can contain additional text, but the
 initial text must match the argument specified in the
-"angle_coeff"_angle_coeff.html command.  The next line lists (in any
+:doc:`angle_coeff <angle_coeff>` command.  The next line lists (in any
 order) one or more parameters for the table.  Each parameter is a
 keyword followed by one or more numeric values.
 
 The parameter "N" is required and its value is the number of table
-entries that follow.  Note that this may be different than the {N}
-specified in the "angle_style table"_angle_style.html command.  Let
-Ntable = {N} in the angle_style command, and Nfile = "N" in the
+entries that follow.  Note that this may be different than the *N*
+specified in the :doc:`angle_style table <angle_style>` command.  Let
+Ntable = *N* in the angle\_style command, and Nfile = "N" in the
 tabulated file.  What LAMMPS does is a preliminary interpolation by
 creating splines using the Nfile tabulated values as nodal points.  It
 uses these to interpolate as needed to generate energy and derivative
@@ -100,8 +111,7 @@ are estimated (less accurately) by the first two and last two
 derivative values in the table.
 
 The "EQ" parameter is also optional.  If used, it is followed by a the
-equilibrium angle value, which is used, for example, by the "fix
-shake"_fix_shake.html command.  If not used, the equilibrium angle is
+equilibrium angle value, which is used, for example, by the :doc:`fix shake <fix_shake>` command.  If not used, the equilibrium angle is
 set to 180.0.
 
 Following a blank line, the next N lines list the tabulated values.
@@ -119,48 +129,53 @@ Note that one file can contain many sections, each with a tabulated
 potential.  LAMMPS reads the file section by section until it finds
 one that matches the specified keyword.
 
-:line
 
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
 
 You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
 
-See the "Speed packages"_Speed_packages.html doc page for more
+See the :doc:`Speed packages <Speed_packages>` doc page for more
 instructions on how to use the accelerated styles effectively.
 
-:line
 
-[Restart info:]
+----------
 
-This angle style writes the settings for the "angle_style table"
-command to "binary restart files"_restart.html, so a angle_style
+
+**Restart info:**
+
+This angle style writes the settings for the "angle\_style table"
+command to :doc:`binary restart files <restart>`, so a angle\_style
 command does not need to specified in an input script that reads a
 restart file.  However, the coefficient information is not stored in
 the restart file, since it is tabulated in the potential files.  Thus,
-angle_coeff commands do need to be specified in the restart input
+angle\_coeff commands do need to be specified in the restart input
 script.
 
-[Restrictions:]
+Restrictions
+""""""""""""
+
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Build package"_Build_package.html doc page
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
 for more info.
 
-[Related commands:]
+Related commands
+""""""""""""""""
 
-"angle_coeff"_angle_coeff.html
+:doc:`angle_coeff <angle_coeff>`
 
-[Default:] none
+**Default:** none
diff --git a/doc/src/angle_zero.rst b/doc/src/angle_zero.rst
new file mode 100644
index 0000000000..e5dab4e3a0
--- /dev/null
+++ b/doc/src/angle_zero.rst
@@ -0,0 +1,56 @@
+.. index:: angle_style zero
+
+angle_style zero command
+========================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style zero *nocoeff*
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   angle_style zero
+   angle_style zero nocoeff
+   angle_coeff *
+   angle_coeff * 120.0
+
+Description
+"""""""""""
+
+Using an angle style of zero means angle forces and energies are not
+computed, but the geometry of angle triplets is still accessible to
+other commands.
+
+As an example, the :doc:`compute angle/local <compute_angle_local>`
+command can be used to compute the theta values for the list of
+triplets of angle atoms listed in the data file read by the
+:doc:`read_data <read_data>` command.  If no angle style is defined,
+this command cannot be used.
+
+The optional *nocoeff* flag allows to read data files with AngleCoeff
+section for any angle style. Similarly, any :doc:`angle_coeff <angle_coeff>` commands
+will only be checked for the angle type number and the rest ignored.
+
+Note that the :doc:`angle_coeff <angle_coeff>` command must be used for
+all angle types. If specified, there can be only one value, which is
+going to be used to assign an equilibrium angle, e.g. for use with
+:doc:`fix shake <fix_shake>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_style none <angle_none>`
+
+**Default:** none
diff --git a/doc/src/angle_zero.txt b/doc/src/angle_zero.txt
deleted file mode 100644
index c6c1958ec8..0000000000
--- a/doc/src/angle_zero.txt
+++ /dev/null
@@ -1,49 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-angle_style zero command :h3
-
-[Syntax:]
-
-angle_style zero {nocoeff} :pre
-
-[Examples:]
-
-angle_style zero
-angle_style zero nocoeff
-angle_coeff *
-angle_coeff * 120.0 :pre
-
-[Description:]
-
-Using an angle style of zero means angle forces and energies are not
-computed, but the geometry of angle triplets is still accessible to
-other commands.
-
-As an example, the "compute angle/local"_compute_angle_local.html
-command can be used to compute the theta values for the list of
-triplets of angle atoms listed in the data file read by the
-"read_data"_read_data.html command.  If no angle style is defined,
-this command cannot be used.
-
-The optional {nocoeff} flag allows to read data files with AngleCoeff
-section for any angle style. Similarly, any angle_coeff commands
-will only be checked for the angle type number and the rest ignored.
-
-Note that the "angle_coeff"_angle_coeff.html command must be used for
-all angle types. If specified, there can be only one value, which is
-going to be used to assign an equilibrium angle, e.g. for use with
-"fix shake"_fix_shake.html.
-
-[Restrictions:] none
-
-[Related commands:]
-
-"angle_style none"_angle_none.html
-
-[Default:] none
diff --git a/doc/src/angles.rst b/doc/src/angles.rst
new file mode 100644
index 0000000000..79c52a5525
--- /dev/null
+++ b/doc/src/angles.rst
@@ -0,0 +1,9 @@
+Angle Styles
+############
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   angle_*
diff --git a/doc/src/angles.txt b/doc/src/angles.txt
deleted file mode 100644
index 3d8a47b2eb..0000000000
--- a/doc/src/angles.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-Angle Styles :h1
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   angle_charmm
-   angle_class2
-   angle_cosine
-   angle_cosine_buck6d
-   angle_cosine_delta
-   angle_cosine_periodic
-   angle_cosine_shift
-   angle_cosine_shift_exp
-   angle_cosine_squared
-   angle_cross
-   angle_dipole
-   angle_fourier
-   angle_fourier_simple
-   angle_harmonic
-   angle_hybrid
-   angle_mm3
-   angle_none
-   angle_quartic
-   angle_sdk
-   angle_table
-   angle_zero
-
-END_RST -->
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.rst
similarity index 50%
rename from doc/src/atom_modify.txt
rename to doc/src/atom_modify.rst
index d598b4697c..ac2720d4f2 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.rst
@@ -1,52 +1,59 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS
-Commands"_lc :c
+.. index:: atom_modify
 
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
+atom_modify command
+===================
 
-:line
+Syntax
+""""""
 
-atom_modify command :h3
 
-[Syntax:]
+.. code-block:: LAMMPS
 
-atom_modify keyword values ... :pre
+   atom_modify keyword values ...
 
-one or more keyword/value pairs may be appended :ulb,l
-keyword = {id} or {map} or {first} or {sort} :l
-   {id} value = {yes} or {no}
-   {map} value = {yes} or {array} or {hash}
-   {first} value = group-ID = group whose atoms will appear first in internal atom lists
-   {sort} values = Nfreq binsize
-     Nfreq = sort atoms spatially every this many time steps
-     binsize = bin size for spatial sorting (distance units) :pre
-:ule
+* one or more keyword/value pairs may be appended
+* keyword = *id* or *map* or *first* or *sort*
+  
+  .. parsed-literal::
+  
+        *id* value = *yes* or *no*
+        *map* value = *yes* or *array* or *hash*
+        *first* value = group-ID = group whose atoms will appear first in internal atom lists
+        *sort* values = Nfreq binsize
+          Nfreq = sort atoms spatially every this many time steps
+          binsize = bin size for spatial sorting (distance units)
 
-[Examples:]
 
-atom_modify map yes
-atom_modify map hash sort 10000 2.0
-atom_modify first colloid :pre
 
-[Description:]
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   atom_modify map yes
+   atom_modify map hash sort 10000 2.0
+   atom_modify first colloid
+
+Description
+"""""""""""
 
 Modify certain attributes of atoms defined and stored within LAMMPS,
-in addition to what is specified by the "atom_style"_atom_style.html
-command.  The {id} and {map} keywords must be specified before a
+in addition to what is specified by the :doc:`atom\_style <atom_style>`
+command.  The *id* and *map* keywords must be specified before a
 simulation box is defined; other keywords can be specified any time.
 
-The {id} keyword determines whether non-zero atom IDs can be assigned
-to each atom.  If the value is {yes}, which is the default, IDs are
-assigned, whether you use the "create atoms"_create_atoms.html or
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands to initialize atoms.  If the value is {no} the IDs for all
+The *id* keyword determines whether non-zero atom IDs can be assigned
+to each atom.  If the value is *yes*\ , which is the default, IDs are
+assigned, whether you use the :doc:`create atoms <create_atoms>` or
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands to initialize atoms.  If the value is *no* the IDs for all
 atoms are assumed to be 0.
 
 If atom IDs are used, they must all be positive integers.  They should
 also be unique, though LAMMPS does not check for this.  Typically they
 should also be consecutively numbered (from 1 to Natoms), though this
-is not required.  Molecular "atom styles"_atom_style.html are those
+is not required.  Molecular :doc:`atom styles <atom_style>` are those
 that store bond topology information (styles bond, angle, molecular,
 full).  These styles require atom IDs since the IDs are used to encode
 the topology.  Some other LAMMPS commands also require the use of atom
@@ -55,77 +62,76 @@ computation of the I-J interaction between two atoms.
 
 The only reason not to use atom IDs is if you are running an atomic
 simulation so large that IDs cannot be uniquely assigned.  For a
-default LAMMPS build this limit is 2^31 or about 2 billion atoms.
-However, even in this case, you can use 64-bit atom IDs, allowing 2^63
-or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
-switch.  This is described on the "Build_settings"_Build_settings.html
+default LAMMPS build this limit is 2\^31 or about 2 billion atoms.
+However, even in this case, you can use 64-bit atom IDs, allowing 2\^63
+or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS\_BIGBIG
+switch.  This is described on the :doc:`Build\_settings <Build_settings>`
 doc page.  If atom IDs are not used, they must be specified as 0 for
 all atoms, e.g. in a data or restart file.
 
-The {map} keyword determines how atoms with specific IDs are found
+The *map* keyword determines how atoms with specific IDs are found
 when required.  An example are the bond (angle, etc) methods which
 need to find the local index of an atom with a specific global ID
 which is a bond (angle, etc) partner.  LAMMPS performs this operation
-efficiently by creating a "map", which is either an {array} or {hash}
+efficiently by creating a "map", which is either an *array* or *hash*
 table, as described below.
 
-When the {map} keyword is not specified in your input script, LAMMPS
-only creates a map for "atom_styles"_atom_style.html for molecular
+When the *map* keyword is not specified in your input script, LAMMPS
+only creates a map for :doc:`atom\_styles <atom_style>` for molecular
 systems which have permanent bonds (angles, etc).  No map is created
 for atomic systems, since it is normally not needed.  However some
 LAMMPS commands require a map, even for atomic systems, and will
-generate an error if one does not exist.  The {map} keyword thus
-allows you to force the creation of a map.  The {yes} value will
-create either an {array} or {hash} style map, as explained in the next
-paragraph.  The {array} and {hash} values create an atom-style or
+generate an error if one does not exist.  The *map* keyword thus
+allows you to force the creation of a map.  The *yes* value will
+create either an *array* or *hash* style map, as explained in the next
+paragraph.  The *array* and *hash* values create an atom-style or
 hash-style map respectively.
 
-For an {array}-style map, each processor stores a lookup table of
+For an *array*\ -style map, each processor stores a lookup table of
 length N, where N is the largest atom ID in the system.  This is a
 fast, simple method for many simulations, but requires too much memory
-for large simulations.  For a {hash}-style map, a hash table is
+for large simulations.  For a *hash*\ -style map, a hash table is
 created on each processor, which finds an atom ID in constant time
 (independent of the global number of atom IDs).  It can be slightly
-slower than the {array} map, but its memory cost is proportional to
+slower than the *array* map, but its memory cost is proportional to
 the number of atoms owned by a processor, i.e. N/P when N is the total
 number of atoms in the system and P is the number of processors.
 
-The {first} keyword allows a "group"_group.html to be specified whose
+The *first* keyword allows a :doc:`group <group>` to be specified whose
 atoms will be maintained as the first atoms in each processor's list
 of owned atoms.  This in only useful when the specified group is a
 small fraction of all the atoms, and there are other operations LAMMPS
 is performing that will be sped-up significantly by being able to loop
 over the smaller set of atoms.  Otherwise the reordering required by
-this option will be a net slow-down.  The "neigh_modify
-include"_neigh_modify.html and "comm_modify group"_comm_modify.html
+this option will be a net slow-down.  The :doc:`neigh\_modify include <neigh_modify>` and :doc:`comm\_modify group <comm_modify>`
 commands are two examples of commands that require this setting to
-work efficiently.  Several "fixes"_fix.html, most notably time
-integration fixes like "fix nve"_fix_nve.html, also take advantage of
+work efficiently.  Several :doc:`fixes <fix>`, most notably time
+integration fixes like :doc:`fix nve <fix_nve>`, also take advantage of
 this setting if the group they operate on is the group specified by
 this command.  Note that specifying "all" as the group-ID effectively
-turns off the {first} option.
+turns off the *first* option.
 
-It is OK to use the {first} keyword with a group that has not yet been
-defined, e.g. to use the atom_modify first command at the beginning of
+It is OK to use the *first* keyword with a group that has not yet been
+defined, e.g. to use the atom\_modify first command at the beginning of
 your input script.  LAMMPS does not use the group until a simulation
 is run.
 
-The {sort} keyword turns on a spatial sorting or reordering of atoms
-within each processor's sub-domain every {Nfreq} timesteps.  If
-{Nfreq} is set to 0, then sorting is turned off.  Sorting can improve
+The *sort* keyword turns on a spatial sorting or reordering of atoms
+within each processor's sub-domain every *Nfreq* timesteps.  If
+*Nfreq* is set to 0, then sorting is turned off.  Sorting can improve
 cache performance and thus speed-up a LAMMPS simulation, as discussed
-in a paper by "(Meloni)"_#Meloni.  Its efficacy depends on the problem
+in a paper by :ref:`(Meloni) <Meloni>`.  Its efficacy depends on the problem
 size (atoms/processor), how quickly the system becomes disordered, and
 various other factors.  As a general rule, sorting is typically more
 effective at speeding up simulations of liquids as opposed to solids.
 In tests we have done, the speed-up can range from zero to 3-4x.
 
-Reordering is performed every {Nfreq} timesteps during a dynamics run
+Reordering is performed every *Nfreq* timesteps during a dynamics run
 or iterations during a minimization.  More precisely, reordering
 occurs at the first reneighboring that occurs after the target
 timestep.  The reordering is performed locally by each processor,
-using bins of the specified {binsize}.  If {binsize} is set to 0.0,
-then a binsize equal to half the "neighbor"_neighbor.html cutoff
+using bins of the specified *binsize*\ .  If *binsize* is set to 0.0,
+then a binsize equal to half the :doc:`neighbor <neighbor>` cutoff
 distance (force cutoff plus skin distance) is used, which is a
 reasonable value.  After the atoms have been binned, they are
 reordered so that atoms in the same bin are adjacent to each other in
@@ -139,28 +145,32 @@ bins are too small, there will be few atoms/bin.  Likewise if bins are
 too large, there will be many atoms/bin.  In both cases, the goal of
 cache locality will be undermined.
 
-NOTE: Running a simulation with sorting on versus off should not
-change the simulation results in a statistical sense.  However, a
-different ordering will induce round-off differences, which will lead
-to diverging trajectories over time when comparing two simulations.
-Various commands, particularly those which use random numbers
-(e.g. "velocity create"_velocity.html, and "fix
-langevin"_fix_langevin.html), may generate (statistically identical)
-results which depend on the order in which atoms are processed.  The
-order of atoms in a "dump"_dump.html file will also typically change
-if sorting is enabled.
+.. note::
 
-[Restrictions:]
+   Running a simulation with sorting on versus off should not
+   change the simulation results in a statistical sense.  However, a
+   different ordering will induce round-off differences, which will lead
+   to diverging trajectories over time when comparing two simulations.
+   Various commands, particularly those which use random numbers
+   (e.g. :doc:`velocity create <velocity>`, and :doc:`fix langevin <fix_langevin>`), may generate (statistically identical)
+   results which depend on the order in which atoms are processed.  The
+   order of atoms in a :doc:`dump <dump>` file will also typically change
+   if sorting is enabled.
 
-The {first} and {sort} options cannot be used together.  Since sorting
-is on by default, it will be turned off if the {first} keyword is
+Restrictions
+""""""""""""
+
+
+The *first* and *sort* options cannot be used together.  Since sorting
+is on by default, it will be turned off if the *first* keyword is
 used with a group-ID that is not "all".
 
-[Related commands:] none
+**Related commands:** none
 
-[Default:]
+Default
+"""""""
 
-By default, {id} is yes.  By default, atomic systems (no bond topology
+By default, *id* is yes.  By default, atomic systems (no bond topology
 info) do not use a map.  For molecular systems (with bond topology
 info), a map is used.  The default map style is array if no atom ID is
 larger than 1 million, otherwise the default is hash.  By default, a
@@ -169,7 +179,12 @@ frequency of 1000 and a binsize of 0.0, which means the neighbor
 cutoff will be used to set the bin size. If no neighbor cutoff is
 defined, sorting will be turned off.
 
-:line
 
-:link(Meloni)
-[(Meloni)] Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
+----------
+
+
+.. _Meloni:
+
+
+
+**(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst
new file mode 100644
index 0000000000..d2ebc220d6
--- /dev/null
+++ b/doc/src/atom_style.rst
@@ -0,0 +1,373 @@
+.. index:: atom_style
+
+atom_style command
+==================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   atom_style style args
+
+* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or         *dpd* or *edpd* or *mdpd* or *tdpd* or *electron* or *ellipsoid* or         *full* or *line* or *meso* or *molecular* or *peri* or *smd* or         *sphere* or *spin* or *tri* or *template* or *hybrid*
+  
+  .. parsed-literal::
+  
+       args = none for any style except the following
+         *body* args = bstyle bstyle-args
+           bstyle = style of body particles
+           bstyle-args = additional arguments specific to the bstyle
+                         see the :doc:`Howto body <Howto_body>` doc page for details
+         *tdpd* arg = Nspecies
+           Nspecies = # of chemical species
+         *template* arg = template-ID
+           template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
+         *hybrid* args = list of one or more sub-styles, each with their args
+
+* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk*
+
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   atom_style atomic
+   atom_style bond
+   atom_style full
+   atom_style body nparticle 2 10
+   atom_style hybrid charge bond
+   atom_style hybrid charge body nparticle 2 5
+   atom_style spin
+   atom_style template myMols
+   atom_style tdpd 2
+
+Description
+"""""""""""
+
+Define what style of atoms to use in a simulation.  This determines
+what attributes are associated with the atoms.  This command must be
+used before a simulation is setup via a :doc:`read\_data <read_data>`,
+:doc:`read\_restart <read_restart>`, or :doc:`create\_box <create_box>`
+command.
+
+.. note::
+
+   Many of the atom styles discussed here are only enabled if
+   LAMMPS was built with a specific package, as listed below in the
+   Restrictions section.
+
+Once a style is assigned, it cannot be changed, so use a style general
+enough to encompass all attributes.  E.g. with style *bond*\ , angular
+terms cannot be used or added later to the model.  It is OK to use a
+style more general than needed, though it may be slightly inefficient.
+
+The choice of style affects what quantities are stored by each atom,
+what quantities are communicated between processors to enable forces
+to be computed, and what quantities are listed in the data file read
+by the :doc:`read\_data <read_data>` command.
+
+These are the additional attributes of each style and the typical
+kinds of physical systems they are used to model.  All styles store
+coordinates, velocities, atom IDs and types.  See the
+:doc:`read\_data <read_data>`, :doc:`create\_atoms <create_atoms>`, and
+:doc:`set <set>` commands for info on how to set these various
+quantities.
+
++--------------+-----------------------------------------------------+--------------------------------------+
+| *angle*      | bonds and angles                                    | bead-spring polymers with stiffness  |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *atomic*     | only the default values                             | coarse-grain liquids, solids, metals |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *body*       | mass, inertia moments, quaternion, angular momentum | arbitrary bodies                     |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *bond*       | bonds                                               | bead-spring polymers                 |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *charge*     | charge                                              | atomic system with charges           |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *dipole*     | charge and dipole moment                            | system with dipolar particles        |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *dpd*        | internal temperature and internal energies          | DPD particles                        |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *edpd*       | temperature and heat capacity                       | eDPD particles                       |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *mdpd*       | density                                             | mDPD particles                       |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *tdpd*       | chemical concentration                              | tDPD particles                       |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *electron*   | charge and spin and eradius                         | electronic force field               |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *ellipsoid*  | shape, quaternion, angular momentum                 | aspherical particles                 |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *full*       | molecular + charge                                  | bio-molecules                        |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *line*       | end points, angular velocity                        | rigid bodies                         |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *meso*       | rho, e, cv                                          | SPH particles                        |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *molecular*  | bonds, angles, dihedrals, impropers                 | uncharged molecules                  |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *peri*       | mass, volume                                        | mesoscopic Peridynamic models        |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *smd*        | volume, kernel diameter, contact radius, mass       | solid and fluid SPH particles        |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *sphere*     | diameter, mass, angular velocity                    | granular models                      |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *spin*       | magnetic moment                                     | system with magnetic particles       |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *template*   | template index, template atom                       | small molecules with fixed topology  |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *tri*        | corner points, angular momentum                     | rigid bodies                         |
++--------------+-----------------------------------------------------+--------------------------------------+
+| *wavepacket* | charge, spin, eradius, etag, cs\_re, cs\_im         | AWPMD                                |
++--------------+-----------------------------------------------------+--------------------------------------+
+
+.. note::
+
+   It is possible to add some attributes, such as a molecule ID, to
+   atom styles that do not have them via the :doc:`fix property/atom <fix_property_atom>` command.  This command also
+   allows new custom attributes consisting of extra integer or
+   floating-point values to be added to atoms.  See the :doc:`fix property/atom <fix_property_atom>` doc page for examples of cases
+   where this is useful and details on how to initialize, access, and
+   output the custom values.
+
+All of the above styles define point particles, except the *sphere*\ ,
+*ellipsoid*\ , *electron*\ , *peri*\ , *wavepacket*\ , *line*\ , *tri*\ , and
+*body* styles, which define finite-size particles.  See the :doc:`Howto spherical <Howto_spherical>` doc page for an overview of using
+finite-size particle models with LAMMPS.
+
+All of the point-particle styles assign mass to particles on a
+per-type basis, using the :doc:`mass <mass>` command, The finite-size
+particle styles assign mass to individual particles on a per-particle
+basis.
+
+For the *sphere* style, the particles are spheres and each stores a
+per-particle diameter and mass.  If the diameter > 0.0, the particle
+is a finite-size sphere.  If the diameter = 0.0, it is a point
+particle.  Note that by use of the *disc* keyword with the :doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
+:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>` commands, spheres can be effectively
+treated as 2d discs for a 2d simulation if desired.  See also the :doc:`set density/disc <set>` command.
+
+For the *ellipsoid* style, the particles are ellipsoids and each
+stores a flag which indicates whether it is a finite-size ellipsoid or
+a point particle.  If it is an ellipsoid, it also stores a shape
+vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
+with its orientation.
+
+For the *dipole* style, a point dipole is defined for each point
+particle.  Note that if you wish the particles to be finite-size
+spheres as in a Stockmayer potential for a dipolar fluid, so that the
+particles can rotate due to dipole-dipole interactions, then you need
+to use atom\_style hybrid sphere dipole, which will assign both a
+diameter and dipole moment to each particle.
+
+For the *electron* style, the particles representing electrons are 3d
+Gaussians with a specified position and bandwidth or uncertainty in
+position, which is represented by the eradius = electron size.
+
+For the *peri* style, the particles are spherical and each stores a
+per-particle mass and volume.
+
+The *dpd* style is for dissipative particle dynamics (DPD) particles.
+Note that it is part of the USER-DPD package, and is not for use with
+the :doc:`pair\_style dpd or dpd/stat <pair_dpd>` commands, which can
+simply use atom\_style atomic.  Atom\_style dpd extends DPD particle
+properties with internal temperature (dpdTheta), internal conductive
+energy (uCond), internal mechanical energy (uMech), and internal
+chemical energy (uChem).
+
+The *edpd* style is for energy-conserving dissipative particle
+dynamics (eDPD) particles which store a temperature (edpd\_temp), and
+heat capacity(edpd\_cv).
+
+The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
+particles which store a density (rho) for considering
+density-dependent many-body interactions.
+
+The *tdpd* style is for transport dissipative particle dynamics (tDPD)
+particles which store a set of chemical concentration. An integer
+"cc\_species" is required to specify the number of chemical species
+involved in a tDPD system.
+
+The *meso* style is for smoothed particle hydrodynamics (SPH)
+particles which store a density (rho), energy (e), and heat capacity
+(cv).
+
+The *smd* style is for a general formulation of Smooth Particle
+Hydrodynamics.  Both fluids and solids can be modeled.  Particles
+store the mass and volume of an integration point, a kernel diameter
+used for calculating the field variables (e.g. stress and deformation)
+and a contact radius for calculating repulsive forces which prevent
+individual physical bodies from penetrating each other.
+
+For the *spin* style, a magnetic spin is associated to each atom.
+Those spins have a norm (their magnetic moment) and a direction.
+
+The *wavepacket* style is similar to *electron*\ , but the electrons may
+consist of several Gaussian wave packets, summed up with coefficients
+cs= (cs\_re,cs\_im).  Each of the wave packets is treated as a separate
+particle in LAMMPS, wave packets belonging to the same electron must
+have identical *etag* values.
+
+For the *line* style, the particles are idealized line segments and
+each stores a per-particle mass and length and orientation (i.e. the
+end points of the line segment).
+
+For the *tri* style, the particles are planar triangles and each
+stores a per-particle mass and size and orientation (i.e. the corner
+points of the triangle).
+
+The *template* style allows molecular topology (bonds,angles,etc) to be
+defined via a molecule template using the :doc:`molecule <molecule>`
+command.  The template stores one or more molecules with a single copy
+of the topology info (bonds,angles,etc) of each.  Individual atoms
+only store a template index and template atom to identify which
+molecule and which atom-within-the-molecule they represent.  Using the
+*template* style instead of the *bond*\ , *angle*\ , *molecular* styles
+can save memory for systems comprised of a large number of small
+molecules, all of a single type (or small number of types).  See the
+paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
+can be advantageous for large-scale coarse-grained systems.
+
+.. note::
+
+   When using the *template* style with a :doc:`molecule template <molecule>` that contains multiple molecules, you should
+   insure the atom types, bond types, angle\_types, etc in all the
+   molecules are consistent.  E.g. if one molecule represents H2O and
+   another CO2, then you probably do not want each molecule file to
+   define 2 atom types and a single bond type, because they will conflict
+   with each other when a mixture system of H2O and CO2 molecules is
+   defined, e.g. by the :doc:`read\_data <read_data>` command.  Rather the
+   H2O molecule should define atom types 1 and 2, and bond type 1.  And
+   the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
+   2 if a single oxygen type is desired), and bond type 2.
+
+For the *body* style, the particles are arbitrary bodies with internal
+attributes defined by the "style" of the bodies, which is specified by
+the *bstyle* argument.  Body particles can represent complex entities,
+such as surface meshes of discrete points, collections of
+sub-particles, deformable objects, etc.
+
+The :doc:`Howto body <Howto_body>` doc page describes the body styles
+LAMMPS currently supports, and provides more details as to the kind of
+body particles they represent.  For all styles, each body particle
+stores moments of inertia and a quaternion 4-vector, so that its
+orientation and position can be time integrated due to forces and
+torques.
+
+Note that there may be additional arguments required along with the
+*bstyle* specification, in the atom\_style body command.  These
+arguments are described on the :doc:`Howto body <Howto_body>` doc page.
+
+
+----------
+
+
+Typically, simulations require only a single (non-hybrid) atom style.
+If some atoms in the simulation do not have all the properties defined
+by a particular style, use the simplest style that defines all the
+needed properties by any atom.  For example, if some atoms in a
+simulation are charged, but others are not, use the *charge* style.
+If some atoms have bonds, but others do not, use the *bond* style.
+
+The only scenario where the *hybrid* style is needed is if there is no
+single style which defines all needed properties of all atoms.  For
+example, as mentioned above, if you want dipolar particles which will
+rotate due to torque, you need to use "atom\_style hybrid sphere
+dipole".  When a hybrid style is used, atoms store and communicate the
+union of all quantities implied by the individual styles.
+
+When using the *hybrid* style, you cannot combine the *template* style
+with another molecular style that stores bond,angle,etc info on a
+per-atom basis.
+
+LAMMPS can be extended with new atom styles as well as new body
+styles; see the :doc:`Modify <Modify>` doc page.
+
+
+----------
+
+
+Styles with a *kk* suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in on
+the :doc:`Speed packages <Speed_packages>` doc page.  The accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
+
+Note that other acceleration packages in LAMMPS, specifically the GPU,
+USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
+styles.
+
+The accelerated styles are part of the KOKKOS package.  They are only
+enabled if LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+Restrictions
+""""""""""""
+
+
+This command cannot be used after the simulation box is defined by a
+:doc:`read\_data <read_data>` or :doc:`create\_box <create_box>` command.
+
+Many of the styles listed above are only enabled if LAMMPS was built
+with a specific package, as listed below.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The *angle*\ , *bond*\ , *full*\ , *molecular*\ , and *template* styles are
+part of the MOLECULE package.
+
+The *line* and *tri* styles are part of the ASPHERE package.
+
+The *body* style is part of the BODY package.
+
+The *dipole* style is part of the DIPOLE package.
+
+The *peri* style is part of the PERI package for Peridynamics.
+
+The *electron* style is part of the USER-EFF package for :doc:`electronic force fields <pair_eff>`.
+
+The *dpd* style is part of the USER-DPD package for dissipative
+particle dynamics (DPD).
+
+The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESO package
+for energy-conserving dissipative particle dynamics (eDPD), many-body
+dissipative particle dynamics (mDPD), and transport dissipative particle
+dynamics (tDPD), respectively.
+
+The *meso* style is part of the USER-SPH package for smoothed particle
+hydrodynamics (SPH).  See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
+
+The *spin* style is part of the SPIN package.
+
+The *wavepacket* style is part of the USER-AWPMD package for the
+:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`read\_data <read_data>`, :doc:`pair\_style <pair_style>`
+
+Default
+"""""""
+
+atom\_style atomic
+
+
+----------
+
+
+.. _Grime:
+
+
+
+**(Grime)** Grime and Voth, to appear in J Chem Theory & Computation
+(2014).
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
deleted file mode 100644
index ff96fedab9..0000000000
--- a/doc/src/atom_style.txt
+++ /dev/null
@@ -1,338 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-atom_style command :h3
-
-[Syntax:]
-
-atom_style style args :pre
-
-style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
-        {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
-        {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
-        {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l
-  args = none for any style except the following
-    {body} args = bstyle bstyle-args
-      bstyle = style of body particles
-      bstyle-args = additional arguments specific to the bstyle
-                    see the "Howto body"_Howto_body.html doc page for details
-    {tdpd} arg = Nspecies
-      Nspecies = # of chemical species
-    {template} arg = template-ID
-      template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
-    {hybrid} args = list of one or more sub-styles, each with their args :pre
-
-accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l
-:ule
-
-[Examples:]
-
-atom_style atomic
-atom_style bond
-atom_style full
-atom_style body nparticle 2 10
-atom_style hybrid charge bond
-atom_style hybrid charge body nparticle 2 5
-atom_style spin
-atom_style template myMols
-atom_style tdpd 2 :pre
-
-[Description:]
-
-Define what style of atoms to use in a simulation.  This determines
-what attributes are associated with the atoms.  This command must be
-used before a simulation is setup via a "read_data"_read_data.html,
-"read_restart"_read_restart.html, or "create_box"_create_box.html
-command.
-
-NOTE: Many of the atom styles discussed here are only enabled if
-LAMMPS was built with a specific package, as listed below in the
-Restrictions section.
-
-Once a style is assigned, it cannot be changed, so use a style general
-enough to encompass all attributes.  E.g. with style {bond}, angular
-terms cannot be used or added later to the model.  It is OK to use a
-style more general than needed, though it may be slightly inefficient.
-
-The choice of style affects what quantities are stored by each atom,
-what quantities are communicated between processors to enable forces
-to be computed, and what quantities are listed in the data file read
-by the "read_data"_read_data.html command.
-
-These are the additional attributes of each style and the typical
-kinds of physical systems they are used to model.  All styles store
-coordinates, velocities, atom IDs and types.  See the
-"read_data"_read_data.html, "create_atoms"_create_atoms.html, and
-"set"_set.html commands for info on how to set these various
-quantities.
-
-{angle} | bonds and angles | bead-spring polymers with stiffness |
-{atomic} | only the default values | coarse-grain liquids, solids, metals |
-{body} | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
-{bond} | bonds | bead-spring polymers |
-{charge} | charge | atomic system with charges |
-{dipole} | charge and dipole moment | system with dipolar particles |
-{dpd} | internal temperature and internal energies | DPD particles |
-{edpd} | temperature and heat capacity | eDPD particles |
-{mdpd} | density | mDPD particles |
-{tdpd} | chemical concentration | tDPD particles |
-{electron} | charge and spin and eradius | electronic force field |
-{ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
-{full} | molecular + charge | bio-molecules |
-{line} | end points, angular velocity | rigid bodies |
-{meso} | rho, e, cv | SPH particles |
-{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
-{peri} | mass, volume | mesoscopic Peridynamic models |
-{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
-{sphere} | diameter, mass, angular velocity | granular models |
-{spin} | magnetic moment | system with magnetic particles |
-{template} | template index, template atom | small molecules with fixed topology |
-{tri} | corner points, angular momentum | rigid bodies |
-{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
-
-NOTE: It is possible to add some attributes, such as a molecule ID, to
-atom styles that do not have them via the "fix
-property/atom"_fix_property_atom.html command.  This command also
-allows new custom attributes consisting of extra integer or
-floating-point values to be added to atoms.  See the "fix
-property/atom"_fix_property_atom.html doc page for examples of cases
-where this is useful and details on how to initialize, access, and
-output the custom values.
-
-All of the above styles define point particles, except the {sphere},
-{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
-{body} styles, which define finite-size particles.  See the "Howto
-spherical"_Howto_spherical.html doc page for an overview of using
-finite-size particle models with LAMMPS.
-
-All of the point-particle styles assign mass to particles on a
-per-type basis, using the "mass"_mass.html command, The finite-size
-particle styles assign mass to individual particles on a per-particle
-basis.
-
-For the {sphere} style, the particles are spheres and each stores a
-per-particle diameter and mass.  If the diameter > 0.0, the particle
-is a finite-size sphere.  If the diameter = 0.0, it is a point
-particle.  Note that by use of the {disc} keyword with the "fix
-nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html,
-"fix nph/sphere"_fix_nph_sphere.html, "fix
-npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively
-treated as 2d discs for a 2d simulation if desired.  See also the "set
-density/disc"_set.html command.
-
-For the {ellipsoid} style, the particles are ellipsoids and each
-stores a flag which indicates whether it is a finite-size ellipsoid or
-a point particle.  If it is an ellipsoid, it also stores a shape
-vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
-with its orientation.
-
-For the {dipole} style, a point dipole is defined for each point
-particle.  Note that if you wish the particles to be finite-size
-spheres as in a Stockmayer potential for a dipolar fluid, so that the
-particles can rotate due to dipole-dipole interactions, then you need
-to use atom_style hybrid sphere dipole, which will assign both a
-diameter and dipole moment to each particle.
-
-For the {electron} style, the particles representing electrons are 3d
-Gaussians with a specified position and bandwidth or uncertainty in
-position, which is represented by the eradius = electron size.
-
-For the {peri} style, the particles are spherical and each stores a
-per-particle mass and volume.
-
-The {dpd} style is for dissipative particle dynamics (DPD) particles.
-Note that it is part of the USER-DPD package, and is not for use with
-the "pair_style dpd or dpd/stat"_pair_dpd.html commands, which can
-simply use atom_style atomic.  Atom_style dpd extends DPD particle
-properties with internal temperature (dpdTheta), internal conductive
-energy (uCond), internal mechanical energy (uMech), and internal
-chemical energy (uChem).
-
-The {edpd} style is for energy-conserving dissipative particle
-dynamics (eDPD) particles which store a temperature (edpd_temp), and
-heat capacity(edpd_cv).
-
-The {mdpd} style is for many-body dissipative particle dynamics (mDPD)
-particles which store a density (rho) for considering
-density-dependent many-body interactions.
-
-The {tdpd} style is for transport dissipative particle dynamics (tDPD)
-particles which store a set of chemical concentration. An integer
-"cc_species" is required to specify the number of chemical species
-involved in a tDPD system.
-
-The {meso} style is for smoothed particle hydrodynamics (SPH)
-particles which store a density (rho), energy (e), and heat capacity
-(cv).
-
-The {smd} style is for a general formulation of Smooth Particle
-Hydrodynamics.  Both fluids and solids can be modeled.  Particles
-store the mass and volume of an integration point, a kernel diameter
-used for calculating the field variables (e.g. stress and deformation)
-and a contact radius for calculating repulsive forces which prevent
-individual physical bodies from penetrating each other.
-
-For the {spin} style, a magnetic spin is associated to each atom.
-Those spins have a norm (their magnetic moment) and a direction.
-
-The {wavepacket} style is similar to {electron}, but the electrons may
-consist of several Gaussian wave packets, summed up with coefficients
-cs= (cs_re,cs_im).  Each of the wave packets is treated as a separate
-particle in LAMMPS, wave packets belonging to the same electron must
-have identical {etag} values.
-
-For the {line} style, the particles are idealized line segments and
-each stores a per-particle mass and length and orientation (i.e. the
-end points of the line segment).
-
-For the {tri} style, the particles are planar triangles and each
-stores a per-particle mass and size and orientation (i.e. the corner
-points of the triangle).
-
-The {template} style allows molecular topology (bonds,angles,etc) to be
-defined via a molecule template using the "molecule"_molecule.html
-command.  The template stores one or more molecules with a single copy
-of the topology info (bonds,angles,etc) of each.  Individual atoms
-only store a template index and template atom to identify which
-molecule and which atom-within-the-molecule they represent.  Using the
-{template} style instead of the {bond}, {angle}, {molecular} styles
-can save memory for systems comprised of a large number of small
-molecules, all of a single type (or small number of types).  See the
-paper by Grime and Voth, in "(Grime)"_#Grime, for examples of how this
-can be advantageous for large-scale coarse-grained systems.
-
-NOTE: When using the {template} style with a "molecule
-template"_molecule.html that contains multiple molecules, you should
-insure the atom types, bond types, angle_types, etc in all the
-molecules are consistent.  E.g. if one molecule represents H2O and
-another CO2, then you probably do not want each molecule file to
-define 2 atom types and a single bond type, because they will conflict
-with each other when a mixture system of H2O and CO2 molecules is
-defined, e.g. by the "read_data"_read_data.html command.  Rather the
-H2O molecule should define atom types 1 and 2, and bond type 1.  And
-the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
-2 if a single oxygen type is desired), and bond type 2.
-
-For the {body} style, the particles are arbitrary bodies with internal
-attributes defined by the "style" of the bodies, which is specified by
-the {bstyle} argument.  Body particles can represent complex entities,
-such as surface meshes of discrete points, collections of
-sub-particles, deformable objects, etc.
-
-The "Howto body"_Howto_body.html doc page describes the body styles
-LAMMPS currently supports, and provides more details as to the kind of
-body particles they represent.  For all styles, each body particle
-stores moments of inertia and a quaternion 4-vector, so that its
-orientation and position can be time integrated due to forces and
-torques.
-
-Note that there may be additional arguments required along with the
-{bstyle} specification, in the atom_style body command.  These
-arguments are described on the "Howto body"_Howto_body.html doc page.
-
-:line
-
-Typically, simulations require only a single (non-hybrid) atom style.
-If some atoms in the simulation do not have all the properties defined
-by a particular style, use the simplest style that defines all the
-needed properties by any atom.  For example, if some atoms in a
-simulation are charged, but others are not, use the {charge} style.
-If some atoms have bonds, but others do not, use the {bond} style.
-
-The only scenario where the {hybrid} style is needed is if there is no
-single style which defines all needed properties of all atoms.  For
-example, as mentioned above, if you want dipolar particles which will
-rotate due to torque, you need to use "atom_style hybrid sphere
-dipole".  When a hybrid style is used, atoms store and communicate the
-union of all quantities implied by the individual styles.
-
-When using the {hybrid} style, you cannot combine the {template} style
-with another molecular style that stores bond,angle,etc info on a
-per-atom basis.
-
-LAMMPS can be extended with new atom styles as well as new body
-styles; see the "Modify"_Modify.html doc page.
-
-:line
-
-Styles with a {kk} suffix are functionally the same as the
-corresponding style without the suffix.  They have been optimized to
-run faster, depending on your available hardware, as discussed in on
-the "Speed packages"_Speed_packages.html doc page.  The accelerated
-styles take the same arguments and should produce the same results,
-except for round-off and precision issues.
-
-Note that other acceleration packages in LAMMPS, specifically the GPU,
-USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
-styles.
-
-The accelerated styles are part of the KOKKOS package.  They are only
-enabled if LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-[Restrictions:]
-
-This command cannot be used after the simulation box is defined by a
-"read_data"_read_data.html or "create_box"_create_box.html command.
-
-Many of the styles listed above are only enabled if LAMMPS was built
-with a specific package, as listed below.  See the "Build
-package"_Build_package.html doc page for more info.
-
-The {angle}, {bond}, {full}, {molecular}, and {template} styles are
-part of the MOLECULE package.
-
-The {line} and {tri} styles are part of the ASPHERE package.
-
-The {body} style is part of the BODY package.
-
-The {dipole} style is part of the DIPOLE package.
-
-The {peri} style is part of the PERI package for Peridynamics.
-
-The {electron} style is part of the USER-EFF package for "electronic
-force fields"_pair_eff.html.
-
-The {dpd} style is part of the USER-DPD package for dissipative
-particle dynamics (DPD).
-
-The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
-for energy-conserving dissipative particle dynamics (eDPD), many-body
-dissipative particle dynamics (mDPD), and transport dissipative particle
-dynamics (tDPD), respectively.
-
-The {meso} style is part of the USER-SPH package for smoothed particle
-hydrodynamics (SPH).  See "this PDF
-guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
-
-The {spin} style is part of the SPIN package.
-
-The {wavepacket} style is part of the USER-AWPMD package for the
-"antisymmetrized wave packet MD method"_pair_awpmd.html.
-
-[Related commands:]
-
-"read_data"_read_data.html, "pair_style"_pair_style.html
-
-[Default:]
-
-atom_style atomic
-
-:line
-
-:link(Grime)
-[(Grime)] Grime and Voth, to appear in J Chem Theory & Computation
-(2014).
diff --git a/doc/src/balance.rst b/doc/src/balance.rst
new file mode 100644
index 0000000000..67146b2ba9
--- /dev/null
+++ b/doc/src/balance.rst
@@ -0,0 +1,574 @@
+.. index:: balance
+
+balance command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   balance thresh style args ... keyword args ...
+
+* thresh = imbalance threshold that must be exceeded to perform a re-balance
+* one style/arg pair can be used (or multiple for *x*\ ,\ *y*\ ,\ *z*\ )
+* style = *x* or *y* or *z* or *shift* or *rcb*
+  
+  .. parsed-literal::
+  
+       *x* args = *uniform* or Px-1 numbers between 0 and 1
+         *uniform* = evenly spaced cuts between processors in x dimension
+         numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
+         *x* can be specified together with *y* or *z*
+       *y* args = *uniform* or Py-1 numbers between 0 and 1
+         *uniform* = evenly spaced cuts between processors in y dimension
+         numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
+         *y* can be specified together with *x* or *z*
+       *z* args = *uniform* or Pz-1 numbers between 0 and 1
+         *uniform* = evenly spaced cuts between processors in z dimension
+         numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
+         *z* can be specified together with *x* or *y*
+       *shift* args = dimstr Niter stopthresh
+         dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
+         Niter = # of times to iterate within each dimension of dimstr sequence
+         stopthresh = stop balancing when this imbalance threshold is reached
+       *rcb* args = none
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *weight* or *out*
+  
+  .. parsed-literal::
+  
+       *weight* style args = use weighted particle counts for the balancing
+         *style* = *group* or *neigh* or *time* or *var* or *store*
+           *group* args = Ngroup group1 weight1 group2 weight2 ...
+             Ngroup = number of groups with assigned weights
+             group1, group2, ... = group IDs
+             weight1, weight2, ...   = corresponding weight factors
+           *neigh* factor = compute weight based on number of neighbors
+             factor = scaling factor (> 0)
+           *time* factor = compute weight based on time spend computing
+             factor = scaling factor (> 0)
+           *var* name = take weight from atom-style variable
+             name = name of the atom-style variable
+           *store* name = store weight in custom atom property defined by :doc:`fix property/atom <fix_property_atom>` command
+             name = atom property name (without d\_ prefix)
+       *out* arg = filename
+         filename = write each processor's sub-domain to a file
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   balance 0.9 x uniform y 0.4 0.5 0.6
+   balance 1.2 shift xz 5 1.1
+   balance 1.0 shift xz 5 1.1
+   balance 1.1 rcb
+   balance 1.0 shift x 10 1.1 weight group 2 fast 0.5 slow 2.0
+   balance 1.0 shift x 10 1.1 weight time 0.8 weight neigh 0.5 weight store balance
+   balance 1.0 shift x 20 1.0 out tmp.balance
+
+Description
+"""""""""""
+
+This command adjusts the size and shape of processor sub-domains
+within the simulation box, to attempt to balance the number of atoms
+or particles and thus indirectly the computational cost (load) more
+evenly across processors.  The load balancing is "static" in the sense
+that this command performs the balancing once, before or between
+simulations.  The processor sub-domains will then remain static during
+the subsequent run.  To perform "dynamic" balancing, see the :doc:`fix balance <fix_balance>` command, which can adjust processor
+sub-domain sizes and shapes on-the-fly during a :doc:`run <run>`.
+
+Load-balancing is typically most useful if the particles in the
+simulation box have a spatially-varying density distribution or when
+the computational cost varies significantly between different
+particles.  E.g. a model of a vapor/liquid interface, or a solid with
+an irregular-shaped geometry containing void regions, or :doc:`hybrid pair style simulations <pair_hybrid>` which combine pair styles with
+different computational cost.  In these cases, the LAMMPS default of
+dividing the simulation box volume into a regular-spaced grid of 3d
+bricks, with one equal-volume sub-domain per processor, may assign
+numbers of particles per processor in a way that the computational
+effort varies significantly.  This can lead to poor performance when
+the simulation is run in parallel.
+
+The balancing can be performed with or without per-particle weighting.
+With no weighting, the balancing attempts to assign an equal number of
+particles to each processor.  With weighting, the balancing attempts
+to assign an equal aggregate computational weight to each processor,
+which typically induces a different number of atoms assigned to each
+processor.  Details on the various weighting options and examples for
+how they can be used are :ref:`given below <weighted_balance>`.
+
+Note that the :doc:`processors <processors>` command allows some control
+over how the box volume is split across processors.  Specifically, for
+a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
+Pz, subject to the constraint that Px \* Py \* Pz = P, the total number
+of processors.  This is sufficient to achieve good load-balance for
+some problems on some processor counts.  However, all the processor
+sub-domains will still have the same shape and same volume.
+
+The requested load-balancing operation is only performed if the
+current "imbalance factor" in particles owned by each processor
+exceeds the specified *thresh* parameter.  The imbalance factor is
+defined as the maximum number of particles (or weight) owned by any
+processor, divided by the average number of particles (or weight) per
+processor.  Thus an imbalance factor of 1.0 is perfect balance.
+
+As an example, for 10000 particles running on 10 processors, if the
+most heavily loaded processor has 1200 particles, then the factor is
+1.2, meaning there is a 20% imbalance.  Note that a re-balance can be
+forced even if the current balance is perfect (1.0) be specifying a
+*thresh* < 1.0.
+
+.. note::
+
+   Balancing is performed even if the imbalance factor does not
+   exceed the *thresh* parameter if a "grid" style is specified when the
+   current partitioning is "tiled".  The meaning of "grid" vs "tiled" is
+   explained below.  This is to allow forcing of the partitioning to
+   "grid" so that the :doc:`comm\_style brick <comm_style>` command can then
+   be used to replace a current :doc:`comm\_style tiled <comm_style>`
+   setting.
+
+When the balance command completes, it prints statistics about the
+result, including the change in the imbalance factor and the change in
+the maximum number of particles on any processor.  For "grid" methods
+(defined below) that create a logical 3d grid of processors, the
+positions of all cutting planes in each of the 3 dimensions (as
+fractions of the box length) are also printed.
+
+.. note::
+
+   This command attempts to minimize the imbalance factor, as
+   defined above.  But depending on the method a perfect balance (1.0)
+   may not be achieved.  For example, "grid" methods (defined below) that
+   create a logical 3d grid cannot achieve perfect balance for many
+   irregular distributions of particles.  Likewise, if a portion of the
+   system is a perfect lattice, e.g. the initial system is generated by
+   the :doc:`create\_atoms <create_atoms>` command, then "grid" methods may
+   be unable to achieve exact balance.  This is because entire lattice
+   planes will be owned or not owned by a single processor.
+
+.. note::
+
+   The imbalance factor is also an estimate of the maximum speed-up
+   you can hope to achieve by running a perfectly balanced simulation
+   versus an imbalanced one.  In the example above, the 10000 particle
+   simulation could run up to 20% faster if it were perfectly balanced,
+   versus when imbalanced.  However, computational cost is not strictly
+   proportional to particle count, and changing the relative size and
+   shape of processor sub-domains may lead to additional computational
+   and communication overheads, e.g. in the PPPM solver used via the
+   :doc:`kspace\_style <kspace_style>` command.  Thus you should benchmark
+   the run times of a simulation before and after balancing.
+
+
+----------
+
+
+The method used to perform a load balance is specified by one of the
+listed styles (or more in the case of *x*\ ,\ *y*\ ,\ *z*\ ), which are
+described in detail below.  There are 2 kinds of styles.
+
+The *x*\ , *y*\ , *z*\ , and *shift* styles are "grid" methods which produce
+a logical 3d grid of processors.  They operate by changing the cutting
+planes (or lines) between processors in 3d (or 2d), to adjust the
+volume (area in 2d) assigned to each processor, as in the following 2d
+diagram where processor sub-domains are shown and particles are
+colored by the processor that owns them.  The leftmost diagram is the
+default partitioning of the simulation box across processors (one
+sub-box for each of 16 processors); the middle diagram is after a
+"grid" method has been applied.
+
+.. image:: JPG/balance_uniform_small.jpg
+   :target: JPG/balance_uniform.jpg
+.. image:: JPG/balance_nonuniform_small.jpg
+   :target: JPG/balance_nonuniform.jpg
+.. image:: JPG/balance_rcb_small.jpg
+   :target: JPG/balance_rcb.jpg
+
+
+The *rcb* style is a "tiling" method which does not produce a logical
+3d grid of processors.  Rather it tiles the simulation domain with
+rectangular sub-boxes of varying size and shape in an irregular
+fashion so as to have equal numbers of particles (or weight) in each
+sub-box, as in the rightmost diagram above.
+
+The "grid" methods can be used with either of the
+:doc:`comm\_style <comm_style>` command options, *brick* or *tiled*\ .  The
+"tiling" methods can only be used with :doc:`comm\_style tiled <comm_style>`.  Note that it can be useful to use a "grid"
+method with :doc:`comm\_style tiled <comm_style>` to return the domain
+partitioning to a logical 3d grid of processors so that "comm\_style
+brick" can afterwords be specified for subsequent :doc:`run <run>`
+commands.
+
+When a "grid" method is specified, the current domain partitioning can
+be either a logical 3d grid or a tiled partitioning.  In the former
+case, the current logical 3d grid is used as a starting point and
+changes are made to improve the imbalance factor.  In the latter case,
+the tiled partitioning is discarded and a logical 3d grid is created
+with uniform spacing in all dimensions.  This becomes the starting
+point for the balancing operation.
+
+When a "tiling" method is specified, the current domain partitioning
+("grid" or "tiled") is ignored, and a new partitioning is computed
+from scratch.
+
+
+----------
+
+
+The *x*\ , *y*\ , and *z* styles invoke a "grid" method for balancing, as
+described above.  Note that any or all of these 3 styles can be
+specified together, one after the other, but they cannot be used with
+any other style.  This style adjusts the position of cutting planes
+between processor sub-domains in specific dimensions.  Only the
+specified dimensions are altered.
+
+The *uniform* argument spaces the planes evenly, as in the left
+diagrams above.  The *numeric* argument requires listing Ps-1 numbers
+that specify the position of the cutting planes.  This requires
+knowing Ps = Px or Py or Pz = the number of processors assigned by
+LAMMPS to the relevant dimension.  This assignment is made (and the
+Px, Py, Pz values printed out) when the simulation box is created by
+the "create\_box" or "read\_data" or "read\_restart" command and is
+influenced by the settings of the :doc:`processors <processors>`
+command.
+
+Each of the numeric values must be between 0 and 1, and they must be
+listed in ascending order.  They represent the fractional position of
+the cutting place.  The left (or lower) edge of the box is 0.0, and
+the right (or upper) edge is 1.0.  Neither of these values is
+specified.  Only the interior Ps-1 positions are specified.  Thus is
+there are 2 processors in the x dimension, you specify a single value
+such as 0.75, which would make the left processor's sub-domain 3x
+larger than the right processor's sub-domain.
+
+
+----------
+
+
+The *shift* style invokes a "grid" method for balancing, as
+described above.  It changes the positions of cutting planes between
+processors in an iterative fashion, seeking to reduce the imbalance
+factor, similar to how the :doc:`fix balance shift <fix_balance>`
+command operates.
+
+The *dimstr* argument is a string of characters, each of which must be
+an "x" or "y" or "z".  Eacn character can appear zero or one time,
+since there is no advantage to balancing on a dimension more than
+once.  You should normally only list dimensions where you expect there
+to be a density variation in the particles.
+
+Balancing proceeds by adjusting the cutting planes in each of the
+dimensions listed in *dimstr*\ , one dimension at a time.  For a single
+dimension, the balancing operation (described below) is iterated on up
+to *Niter* times.  After each dimension finishes, the imbalance factor
+is re-computed, and the balancing operation halts if the *stopthresh*
+criterion is met.
+
+A re-balance operation in a single dimension is performed using a
+recursive multisectioning algorithm, where the position of each
+cutting plane (line in 2d) in the dimension is adjusted independently.
+This is similar to a recursive bisectioning for a single value, except
+that the bounds used for each bisectioning take advantage of
+information from neighboring cuts if possible.  At each iteration, the
+count of particles on either side of each plane is tallied.  If the
+counts do not match the target value for the plane, the position of
+the cut is adjusted to be halfway between a low and high bound.  The
+low and high bounds are adjusted on each iteration, using new count
+information, so that they become closer together over time.  Thus as
+the recursion progresses, the count of particles on either side of the
+plane gets closer to the target value.
+
+Once the re-balancing is complete and final processor sub-domains
+assigned, particles are migrated to their new owning processor, and
+the balance procedure ends.
+
+.. note::
+
+   At each re-balance operation, the bisectioning for each cutting
+   plane (line in 2d) typically starts with low and high bounds separated
+   by the extent of a processor's sub-domain in one dimension.  The size
+   of this bracketing region shrinks by 1/2 every iteration.  Thus if
+   *Niter* is specified as 10, the cutting plane will typically be
+   positioned to 1 part in 1000 accuracy (relative to the perfect target
+   position).  For *Niter* = 20, it will be accurate to 1 part in a
+   million.  Thus there is no need ot set *Niter* to a large value.
+   LAMMPS will check if the threshold accuracy is reached (in a
+   dimension) is less iterations than *Niter* and exit early.  However,
+   *Niter* should also not be set too small, since it will take roughly
+   the same number of iterations to converge even if the cutting plane is
+   initially close to the target value.
+
+
+----------
+
+
+The *rcb* style invokes a "tiled" method for balancing, as described
+above.  It performs a recursive coordinate bisectioning (RCB) of the
+simulation domain. The basic idea is as follows.
+
+The simulation domain is cut into 2 boxes by an axis-aligned cut in
+one of the dimensions, leaving one new sub-box on either side of the
+cut.  Which dimension is chosen for the cut depends on the particle
+(weight) distribution within the parent box.  Normally the longest
+dimension of the box is cut, but if all (or most) of the particles are
+at one end of the box, a cut may be performed in another dimension to
+induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in
+shape.
+
+After the cut is made, all the processors are also partitioned into 2
+groups, half assigned to the box on the lower side of the cut, and
+half to the box on the upper side.  (If the processor count is odd,
+one side gets an extra processor.)  The cut is positioned so that the
+number of (weighted) particles in the lower box is exactly the number
+that the processors assigned to that box should own for load balance
+to be perfect.  This also makes load balance for the upper box
+perfect.  The positioning of the cut is done iteratively, by a
+bisectioning method (median search).  Note that counting particles on
+either side of the cut requires communication between all processors
+at each iteration.
+
+That is the procedure for the first cut.  Subsequent cuts are made
+recursively, in exactly the same manner.  The subset of processors
+assigned to each box make a new cut in one dimension of that box,
+splitting the box, the subset of processors, and the particles in the
+box in two.  The recursion continues until every processor is assigned
+a sub-box of the entire simulation domain, and owns the (weighted)
+particles in that sub-box.
+
+
+----------
+
+
+.. _weighted\_balance:
+
+This sub-section describes how to perform weighted load balancing
+using the *weight* keyword. 
+
+By default, all particles have a weight of 1.0, which means each
+particle is assumed to require the same amount of computation during a
+timestep.  There are, however, scenarios where this is not a good
+assumption.  Measuring the computational cost for each particle
+accurately would be impractical and slow down the computation.
+Instead the *weight* keyword implements several ways to influence the
+per-particle weights empirically by properties readily available or
+using the user's knowledge of the system.  Note that the absolute
+value of the weights are not important; only their relative ratios
+affect which particle is assigned to which processor.  A particle with
+a weight of 2.5 is assumed to require 5x more computational than a
+particle with a weight of 0.5.  For all the options below the weight
+assigned to a particle must be a positive value; an error will be be
+generated if a weight is <= 0.0.
+
+Below is a list of possible weight options with a short description of
+their usage and some example scenarios where they might be applicable.
+It is possible to apply multiple weight flags and the weightings they
+induce will be combined through multiplication.  Most of the time,
+however, it is sufficient to use just one method.
+
+The *group* weight style assigns weight factors to specified
+:doc:`groups <group>` of particles.  The *group* style keyword is
+followed by the number of groups, then pairs of group IDs and the
+corresponding weight factor.  If a particle belongs to none of the
+specified groups, its weight is not changed.  If it belongs to
+multiple groups, its weight is the product of the weight factors.
+
+This weight style is useful in combination with pair style
+:doc:`hybrid <pair_hybrid>`, e.g. when combining a more costly many-body
+potential with a fast pair-wise potential.  It is also useful when
+using :doc:`run\_style respa <run_style>` where some portions of the
+system have many bonded interactions and others none.  It assumes that
+the computational cost for each group remains constant over time.
+This is a purely empirical weighting, so a series test runs to tune
+the assigned weight factors for optimal performance is recommended.
+
+The *neigh* weight style assigns the same weight to each particle
+owned by a processor based on the total count of neighbors in the
+neighbor list owned by that processor.  The motivation is that more
+neighbors means a higher computational cost.  The style does not use
+neighbors per atom to assign a unique weight to each atom, because
+that value can vary depending on how the neighbor list is built.
+
+The *factor* setting is applied as an overall scale factor to the
+*neigh* weights which allows adjustment of their impact on the
+balancing operation.  The specified *factor* value must be positive.
+A value > 1.0 will increase the weights so that the ratio of max
+weight to min weight increases by *factor*\ .  A value < 1.0 will
+decrease the weights so that the ratio of max weight to min weight
+decreases by *factor*\ .  In both cases the intermediate weight values
+increase/decrease proportionally as well.  A value = 1.0 has no effect
+on the *neigh* weights.  As a rule of thumb, we have found a *factor*
+of about 0.8 often results in the best performance, since the number
+of neighbors is likely to overestimate the ideal weight.
+
+This weight style is useful for systems where there are different
+cutoffs used for different pairs of interactions, or the density
+fluctuates, or a large number of particles are in the vicinity of a
+wall, or a combination of these effects.  If a simulation uses
+multiple neighbor lists, this weight style will use the first suitable
+neighbor list it finds.  It will not request or compute a new list.  A
+warning will be issued if there is no suitable neighbor list available
+or if it is not current, e.g. if the balance command is used before a
+:doc:`run <run>` or :doc:`minimize <minimize>` command is used, in which
+case the neighbor list may not yet have been built.  In this case no
+weights are computed.  Inserting a :doc:`run 0 post no <run>` command
+before issuing the *balance* command, may be a workaround for this
+case, as it will induce the neighbor list to be built.
+
+The *time* weight style uses :doc:`timer data <timer>` to estimate
+weights.  It assigns the same weight to each particle owned by a
+processor based on the total computational time spent by that
+processor.  See details below on what time window is used.  It uses
+the same timing information as is used for the :doc:`MPI task timing breakdown <Run_output>`, namely, for sections *Pair*\ , *Bond*\ ,
+*Kspace*\ , and *Neigh*\ .  The time spent in those portions of the
+timestep are measured for each MPI rank, summed, then divided by the
+number of particles owned by that processor.  I.e. the weight is an
+effective CPU time/particle averaged over the particles on that
+processor.
+
+The *factor* setting is applied as an overall scale factor to the
+*time* weights which allows adjustment of their impact on the
+balancing operation.  The specified *factor* value must be positive.
+A value > 1.0 will increase the weights so that the ratio of max
+weight to min weight increases by *factor*\ .  A value < 1.0 will
+decrease the weights so that the ratio of max weight to min weight
+decreases by *factor*\ .  In both cases the intermediate weight values
+increase/decrease proportionally as well.  A value = 1.0 has no effect
+on the *time* weights.  As a rule of thumb, effective values to use
+are typically between 0.5 and 1.2.  Note that the timer quantities
+mentioned above can be affected by communication which occurs in the
+middle of the operations, e.g. pair styles with intermediate exchange
+of data witin the force computation, and likewise for KSpace solves.
+
+When using the *time* weight style with the *balance* command, the
+timing data is taken from the preceding run command, i.e. the timings
+are for the entire previous run.  For the *fix balance* command the
+timing data is for only the timesteps since the last balancing
+operation was performed.  If timing information for the required
+sections is not available, e.g. at the beginning of a run, or when the
+:doc:`timer <timer>` command is set to either *loop* or *off*\ , a warning
+is issued.  In this case no weights are computed.
+
+.. note::
+
+   The *time* weight style is the most generic option, and should
+   be tried first, unless the *group* style is easily applicable.
+   However, since the computed cost function is averaged over all
+   particles on a processor, the weights may not be highly accurate.
+   This style can also be effective as a secondary weight in combination
+   with either *group* or *neigh* to offset some of inaccuracies in
+   either of those heuristics.
+
+The *var* weight style assigns per-particle weights by evaluating an
+:doc:`atom-style variable <variable>` specified by *name*\ .  This is
+provided as a more flexible alternative to the *group* weight style,
+allowing definition of a more complex heuristics based on information
+(global and per atom) available inside of LAMMPS.  For example,
+atom-style variables can reference the position of a particle, its
+velocity, the volume of its Voronoi cell, etc.
+
+The *store* weight style does not compute a weight factor.  Instead it
+stores the current accumulated weights in a custom per-atom property
+specified by *name*\ .  This must be a property defined as *d\_name* via
+the :doc:`fix property/atom <fix_property_atom>` command.  Note that
+these custom per-atom properties can be output in a :doc:`dump <dump>`
+file, so this is a way to examine, debug, or visualize the
+per-particle weights computed during the load-balancing operation.
+
+
+----------
+
+
+The *out* keyword writes a text file to the specified *filename* with
+the results of the balancing operation.  The file contains the bounds
+of the sub-domain for each processor after the balancing operation
+completes.  The format of the file is compatible with the
+`Pizza.py <pizza_>`_ *mdump* tool which has support for manipulating and
+visualizing mesh files.  An example is shown here for a balancing by 4
+processors for a 2d problem:
+
+
+.. parsed-literal::
+
+   ITEM: TIMESTEP
+   0
+   ITEM: NUMBER OF NODES
+   16
+   ITEM: BOX BOUNDS
+   0 10
+   0 10
+   0 10
+   ITEM: NODES
+   1 1 0 0 0
+   2 1 5 0 0
+   3 1 5 5 0
+   4 1 0 5 0
+   5 1 5 0 0
+   6 1 10 0 0
+   7 1 10 5 0
+   8 1 5 5 0
+   9 1 0 5 0
+   10 1 5 5 0
+   11 1 5 10 0
+   12 1 10 5 0
+   13 1 5 5 0
+   14 1 10 5 0
+   15 1 10 10 0
+   16 1 5 10 0
+   ITEM: TIMESTEP
+   0
+   ITEM: NUMBER OF SQUARES
+   4
+   ITEM: SQUARES
+   1 1 1 2 3 4
+   2 1 5 6 7 8
+   3 1 9 10 11 12
+   4 1 13 14 15 16
+
+The coordinates of all the vertices are listed in the NODES section, 5
+per processor.  Note that the 4 sub-domains share vertices, so there
+will be duplicate nodes in the list.
+
+The "SQUARES" section lists the node IDs of the 4 vertices in a
+rectangle for each processor (1 to 4).
+
+For a 3d problem, the syntax is similar with 8 vertices listed for
+each processor, instead of 4, and "SQUARES" replaced by "CUBES".
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+For 2d simulations, the *z* style cannot be used.  Nor can a "z"
+appear in *dimstr* for the *shift* style.
+
+Balancing through recursive bisectioning (\ *rcb* style) requires
+:doc:`comm\_style tiled <comm_style>`
+
+Related commands
+""""""""""""""""
+
+:doc:`group <group>`, :doc:`processors <processors>`,
+:doc:`fix balance <fix_balance>`, :doc:`comm\_style <comm_style>`
+
+.. _pizza: http://pizza.sandia.gov
+
+**Default:** none
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst
new file mode 100644
index 0000000000..e3098ef6dc
--- /dev/null
+++ b/doc/src/bond_class2.rst
@@ -0,0 +1,102 @@
+.. index:: bond_style class2
+
+bond_style class2 command
+=========================
+
+bond_style class2/omp command
+=============================
+
+bond_style class2/kk command
+============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style class2
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style class2
+   bond_coeff 1 1.0 100.0 80.0 80.0
+
+Description
+"""""""""""
+
+The *class2* bond style uses the potential
+
+.. math::
+
+   E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
+
+
+where :math:`r_0` is the equilibrium bond distance.
+
+See :ref:`(Sun) <bond-Sun>` for a description of the COMPASS class2 force field.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`r_0` (distance)
+* :math:`K_2` (energy/distance\^2)
+* :math:`K_3` (energy/distance\^3)
+* :math:`K_4` (energy/distance\^4)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the CLASS2
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+**Default:** none
+
+
+----------
+
+
+.. _bond-Sun:
+
+
+
+**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
deleted file mode 100644
index 4390e3613c..0000000000
--- a/doc/src/bond_class2.txt
+++ /dev/null
@@ -1,81 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style class2 command :h3
-bond_style class2/omp command :h3
-bond_style class2/kk command :h3
-
-[Syntax:]
-
-bond_style class2 :pre
-
-[Examples:]
-
-bond_style class2
-bond_coeff 1 1.0 100.0 80.0 80.0 :pre
-
-[Description:]
-
-The {class2} bond style uses the potential
-
-:c,image(Eqs/bond_class2.jpg)
-
-where r0 is the equilibrium bond distance.
-
-See "(Sun)"_#bond-Sun for a description of the COMPASS class2 force field.
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-R0 (distance)
-K2 (energy/distance^2)
-K3 (energy/distance^3)
-K4 (energy/distance^4) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the CLASS2
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
-
-:line
-
-:link(bond-Sun)
-[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/src/bond_coeff.txt b/doc/src/bond_coeff.rst
similarity index 56%
rename from doc/src/bond_coeff.txt
rename to doc/src/bond_coeff.rst
index 1280ae3fb0..281dfc7095 100644
--- a/doc/src/bond_coeff.txt
+++ b/doc/src/bond_coeff.rst
@@ -1,82 +1,99 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+.. index:: bond_coeff
 
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
+bond_coeff command
+==================
 
-:line
+Syntax
+""""""
 
-bond_coeff command :h3
 
-[Syntax:]
+.. code-block:: LAMMPS
 
-bond_coeff N args :pre
+   bond_coeff N args
 
-N = bond type (see asterisk form below)
-args = coefficients for one or more bond types :ul
+* N = bond type (see asterisk form below)
+* args = coefficients for one or more bond types
 
-[Examples:]
+Examples
+""""""""
 
-bond_coeff 5 80.0 1.2
-bond_coeff * 30.0 1.5 1.0 1.0
-bond_coeff 1*4 30.0 1.5 1.0 1.0
-bond_coeff 1 harmonic 200.0 1.0 :pre
 
-[Description:]
+.. code-block:: LAMMPS
+
+   bond_coeff 5 80.0 1.2
+   bond_coeff * 30.0 1.5 1.0 1.0
+   bond_coeff 1*4 30.0 1.5 1.0 1.0
+   bond_coeff 1 harmonic 200.0 1.0
+
+Description
+"""""""""""
 
 Specify the bond force field coefficients for one or more bond types.
 The number and meaning of the coefficients depends on the bond style.
 Bond coefficients can also be set in the data file read by the
-"read_data"_read_data.html command or in a restart file.
+:doc:`read\_data <read_data>` command or in a restart file.
 
 N can be specified in one of two ways.  An explicit numeric value can
 be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple bond types.  This takes the
-form "*" or "*n" or "n*" or "m*n".  If N = the number of bond types,
+form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of bond types,
 then an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk
 means all types from m to n (inclusive).
 
-Note that using a bond_coeff command can override a previous setting
+Note that using a bond\_coeff command can override a previous setting
 for the same bond type.  For example, these commands set the coeffs
 for all bond types, then overwrite the coeffs for just bond type 2:
 
-bond_coeff * 100.0 1.2
-bond_coeff 2 200.0 1.2 :pre
+
+.. code-block:: LAMMPS
+
+   bond_coeff * 100.0 1.2
+   bond_coeff 2 200.0 1.2
 
 A line in a data file that specifies bond coefficients uses the exact
-same format as the arguments of the bond_coeff command in an input
+same format as the arguments of the bond\_coeff command in an input
 script, except that wild-card asterisks should not be used since
 coefficients for all N types must be listed in the file.  For example,
 under the "Bond Coeffs" section of a data file, the line that
 corresponds to the 1st example above would be listed as
 
-5 80.0 1.2 :pre
 
-:line
+.. parsed-literal::
+
+   5 80.0 1.2
+
+
+----------
+
 
 The list of all bond styles defined in LAMMPS is given on the
-"bond_style"_bond_style.html doc page.  They are also listed in more
-compact form on the "Commands bond"_Commands_bond.html doc page.
+:doc:`bond\_style <bond_style>` doc page.  They are also listed in more
+compact form on the :doc:`Commands bond <Commands_bond>` doc page.
 
 On either of those pages, click on the style to display the formula it
 computes and its coefficients as specified by the associated
-bond_coeff command.
+bond\_coeff command.
 
-:line
 
-[Restrictions:]
+----------
+
+
+Restrictions
+""""""""""""
+
 
 This command must come after the simulation box is defined by a
-"read_data"_read_data.html, "read_restart"_read_restart.html, or
-"create_box"_create_box.html command.
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
+:doc:`create\_box <create_box>` command.
 
 A bond style must be defined before any bond coefficients are set,
 either in the input script or in a data file.
 
-[Related commands:]
+Related commands
+""""""""""""""""
 
-"bond_style"_bond_style.html
+:doc:`bond\_style <bond_style>`
 
-[Default:] none
+**Default:** none
diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst
new file mode 100644
index 0000000000..d952321c20
--- /dev/null
+++ b/doc/src/bond_fene.rst
@@ -0,0 +1,111 @@
+.. index:: bond_style fene
+
+bond_style fene command
+=======================
+
+bond_style fene/intel command
+=============================
+
+bond_style fene/kk command
+==========================
+
+bond_style fene/omp command
+===========================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style fene
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style fene
+   bond_coeff 1 30.0 1.5 1.0 1.0
+
+Description
+"""""""""""
+
+The *fene* bond style uses the potential
+
+.. math::
+
+   E = -0.5 K R_0^2  \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
+
+
+to define a finite extensible nonlinear elastic (FENE) potential
+:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models.  The first
+term is attractive, the 2nd Lennard-Jones term is repulsive.  The
+first term extends to :math:`R_0`, the maximum extent of the bond.  The 2nd
+term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/distance\^2)
+* :math:`R_0` (distance)
+* :math:`\epsilon` (energy)
+* :math:`\sigma` (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+You typically should specify :doc:`special\_bonds fene <special_bonds>`
+or :doc:`special\_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
+style.  LAMMPS will issue a warning it that's not the case.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+**Default:** none
+
+
+----------
+
+
+.. _fene-Kremer:
+
+
+
+**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
deleted file mode 100644
index 9ec4017d00..0000000000
--- a/doc/src/bond_fene.txt
+++ /dev/null
@@ -1,88 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style fene command :h3
-bond_style fene/intel command :h3
-bond_style fene/kk command :h3
-bond_style fene/omp command :h3
-
-[Syntax:]
-
-bond_style fene :pre
-
-[Examples:]
-
-bond_style fene
-bond_coeff 1 30.0 1.5 1.0 1.0 :pre
-
-[Description:]
-
-The {fene} bond style uses the potential
-
-:c,image(Eqs/bond_fene.jpg)
-
-to define a finite extensible nonlinear elastic (FENE) potential
-"(Kremer)"_#fene-Kremer, used for bead-spring polymer models.  The first
-term is attractive, the 2nd Lennard-Jones term is repulsive.  The
-first term extends to R0, the maximum extent of the bond.  The 2nd
-term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/distance^2)
-R0 (distance)
-epsilon (energy)
-sigma (distance) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-You typically should specify "special_bonds fene"_special_bonds.html
-or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
-style.  LAMMPS will issue a warning it that's not the case.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
-
-:line
-
-:link(fene-Kremer)
-[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst
new file mode 100644
index 0000000000..5b5b858330
--- /dev/null
+++ b/doc/src/bond_fene_expand.rst
@@ -0,0 +1,109 @@
+.. index:: bond_style fene/expand
+
+bond_style fene/expand command
+==============================
+
+bond_style fene/expand/omp command
+==================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style fene/expand
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style fene/expand
+   bond_coeff 1 30.0 1.5 1.0 1.0 0.5
+
+Description
+"""""""""""
+
+The *fene/expand* bond style uses the potential
+
+.. math::
+
+   E = -0.5 K R_0^2 \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 4 \epsilon \left[ \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^6 \right] + \epsilon
+
+
+to define a finite extensible nonlinear elastic (FENE) potential
+:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models.  The first
+term is attractive, the 2nd Lennard-Jones term is repulsive.
+
+The *fene/expand* bond style is similar to *fene* except that an extra
+shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
+effectively change the bead size of the bonded atoms.  The first term
+now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/distance\^2)
+* :math:`R_0` (distance)
+* :math:`\epsilon` (energy)
+* :math:`\sigma` (distance)
+* :math:`\Delta` (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+You typically should specify :doc:`special\_bonds fene <special_bonds>`
+or :doc:`special\_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
+style.  LAMMPS will issue a warning it that's not the case.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+**Default:** none
+
+
+----------
+
+
+.. _feneexpand-Kremer:
+
+
+
+**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
deleted file mode 100644
index 4d7d2d5438..0000000000
--- a/doc/src/bond_fene_expand.txt
+++ /dev/null
@@ -1,91 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style fene/expand command :h3
-bond_style fene/expand/omp command :h3
-
-[Syntax:]
-
-bond_style fene/expand :pre
-
-[Examples:]
-
-bond_style fene/expand
-bond_coeff 1 30.0 1.5 1.0 1.0 0.5 :pre
-
-[Description:]
-
-The {fene/expand} bond style uses the potential
-
-:c,image(Eqs/bond_fene_expand.jpg)
-
-to define a finite extensible nonlinear elastic (FENE) potential
-"(Kremer)"_#feneexpand-Kremer, used for bead-spring polymer models.  The first
-term is attractive, the 2nd Lennard-Jones term is repulsive.
-
-The {fene/expand} bond style is similar to {fene} except that an extra
-shift factor of delta (positive or negative) is added to {r} to
-effectively change the bead size of the bonded atoms.  The first term
-now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
-+ delta.
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/distance^2)
-R0 (distance)
-epsilon (energy)
-sigma (distance)
-delta (distance) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-You typically should specify "special_bonds fene"_special_bonds.html
-or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
-style.  LAMMPS will issue a warning it that's not the case.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
-
-:line
-
-:link(feneexpand-Kremer)
-[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst
new file mode 100644
index 0000000000..5d0a4ab1c6
--- /dev/null
+++ b/doc/src/bond_gromos.rst
@@ -0,0 +1,86 @@
+.. index:: bond_style gromos
+
+bond_style gromos command
+=========================
+
+bond_style gromos/omp command
+=============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style gromos
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style gromos
+   bond_coeff 5 80.0 1.2
+
+Description
+"""""""""""
+
+The *gromos* bond style uses the potential
+
+.. math::
+
+   E = K (r^2 - r_0^2)^2
+
+
+where :math:`r_0` is the equilibrium bond distance.  Note that the usual 1/4
+factor is included in :math:`K`.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/distance\^4)
+* :math:`r_0` (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+**Default:** none
diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt
deleted file mode 100644
index e039e6c411..0000000000
--- a/doc/src/bond_gromos.txt
+++ /dev/null
@@ -1,72 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style gromos command :h3
-bond_style gromos/omp command :h3
-
-[Syntax:]
-
-bond_style gromos :pre
-
-[Examples:]
-
-bond_style gromos
-bond_coeff 5 80.0 1.2 :pre
-
-[Description:]
-
-The {gromos} bond style uses the potential
-
-:c,image(Eqs/bond_gromos.jpg)
-
-where r0 is the equilibrium bond distance.  Note that the usual 1/4
-factor is included in K.
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/distance^4)
-r0 (distance) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst
new file mode 100644
index 0000000000..d65f0337f0
--- /dev/null
+++ b/doc/src/bond_harmonic.rst
@@ -0,0 +1,92 @@
+.. index:: bond_style harmonic
+
+bond_style harmonic command
+===========================
+
+bond_style harmonic/intel command
+=================================
+
+bond_style harmonic/kk command
+==============================
+
+bond_style harmonic/omp command
+===============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic
+   bond_coeff 5 80.0 1.2
+
+Description
+"""""""""""
+
+The *harmonic* bond style uses the potential
+
+.. math::
+
+   E = K (r - r_0)^2
+
+
+where :math:`r_0` is the equilibrium bond distance.  Note that the usual 1/2
+factor is included in :math:`K`.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/distance\^2)
+* :math:`r_0` (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+**Default:** none
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
deleted file mode 100644
index 3afdf4ceba..0000000000
--- a/doc/src/bond_harmonic.txt
+++ /dev/null
@@ -1,74 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style harmonic command :h3
-bond_style harmonic/intel command :h3
-bond_style harmonic/kk command :h3
-bond_style harmonic/omp command :h3
-
-[Syntax:]
-
-bond_style harmonic :pre
-
-[Examples:]
-
-bond_style harmonic
-bond_coeff 5 80.0 1.2 :pre
-
-[Description:]
-
-The {harmonic} bond style uses the potential
-
-:c,image(Eqs/bond_harmonic.jpg)
-
-where r0 is the equilibrium bond distance.  Note that the usual 1/2
-factor is included in K.
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/distance^2)
-r0 (distance) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst
new file mode 100644
index 0000000000..cc39bda7a7
--- /dev/null
+++ b/doc/src/bond_harmonic_shift.rst
@@ -0,0 +1,92 @@
+.. index:: bond_style harmonic/shift
+
+bond_style harmonic/shift command
+=================================
+
+bond_style harmonic/shift/omp command
+=====================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic/shift
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic/shift
+   bond_coeff 5 10.0 0.5 1.0
+
+Description
+"""""""""""
+
+The *harmonic/shift* bond style is a shifted harmonic bond that uses
+the potential
+
+.. math::
+
+   E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
+
+
+where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance.
+The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is
+:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`U_{\text{min}}` (energy)
+
+* :math:`r_0` (distance)
+
+* :math:`r_c` (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`,
+:doc:`bond\_harmonic <bond_harmonic>`
+
+**Default:** none
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
deleted file mode 100644
index 23d3dcb5d5..0000000000
--- a/doc/src/bond_harmonic_shift.txt
+++ /dev/null
@@ -1,76 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style harmonic/shift command :h3
-bond_style harmonic/shift/omp command :h3
-
-[Syntax:]
-
-bond_style harmonic/shift :pre
-
-[Examples:]
-
-bond_style harmonic/shift
-bond_coeff 5 10.0 0.5 1.0 :pre
-
-[Description:]
-
-The {harmonic/shift} bond style is a shifted harmonic bond that uses
-the potential
-
-:c,image(Eqs/bond_harmonic_shift.jpg)
-
-where r0 is the equilibrium bond distance, and rc the critical distance.
-The potential is -Umin at r0 and zero at rc. The spring constant is
-k = Umin / \[ 2 (r0-rc)^2\].
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-Umin (energy) :ul
-r0 (distance) :ul
-rc (distance) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the
-USER-MISC package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
-"bond_harmonic"_bond_harmonic.html
-
-[Default:] none
diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst
new file mode 100644
index 0000000000..459acfdbfb
--- /dev/null
+++ b/doc/src/bond_harmonic_shift_cut.rst
@@ -0,0 +1,91 @@
+.. index:: bond_style harmonic/shift/cut
+
+bond_style harmonic/shift/cut command
+=====================================
+
+bond_style harmonic/shift/cut/omp command
+=========================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic/shift/cut
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic/shift/cut
+   bond_coeff 5 10.0 0.5 1.0
+
+Description
+"""""""""""
+
+The *harmonic/shift/cut* bond style is a shifted harmonic bond that
+uses the potential
+
+.. math::
+
+   E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
+
+
+where :math:`r_0` is the equilibrium bond distance, and rc the critical distance.
+The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}`
+at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`U_{\text{min}}` (energy)
+* :math:`r_0` (distance)
+* :math:`r_c` (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`,
+:doc:`bond\_harmonic <bond_harmonic>`,
+:doc:`bond\_harmonic\_shift <bond_harmonic_shift>`
+
+**Default:** none
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
deleted file mode 100644
index 13ccb5843b..0000000000
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ /dev/null
@@ -1,77 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style harmonic/shift/cut command :h3
-bond_style harmonic/shift/cut/omp command :h3
-
-[Syntax:]
-
-bond_style harmonic/shift/cut :pre
-
-[Examples:]
-
-bond_style harmonic/shift/cut
-bond_coeff 5 10.0 0.5 1.0 :pre
-
-[Description:]
-
-The {harmonic/shift/cut} bond style is a shifted harmonic bond that
-uses the potential
-
-:c,image(Eqs/bond_harmonic_shift_cut.jpg)
-
-where r0 is the equilibrium bond distance, and rc the critical distance.
-The bond potential is zero for distances r > rc. The potential is -Umin
-at r0 and zero at rc. The spring constant is k = Umin / \[ 2 (r0-rc)^2\].
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-Umin (energy)
-r0 (distance)
-rc (distance) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the
-USER-MISC package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
-"bond_harmonic"_bond_harmonic.html,
-"bond_harmonic_shift"_bond_harmonic_shift.html
-
-[Default:] none
diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst
new file mode 100644
index 0000000000..6b8175858f
--- /dev/null
+++ b/doc/src/bond_hybrid.rst
@@ -0,0 +1,85 @@
+.. index:: bond_style hybrid
+
+bond_style hybrid command
+=========================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style hybrid style1 style2 ...
+
+* style1,style2 = list of one or more bond styles
+
+Examples
+""""""""
+
+
+.. code-block: LAMMPS
+
+   bond_style hybrid harmonic fene
+   bond_coeff 1 harmonic 80.0 1.2
+   bond_coeff 2* fene 30.0 1.5 1.0 1.0
+
+Description
+"""""""""""
+
+The *hybrid* style enables the use of multiple bond styles in one
+simulation.  A bond style is assigned to each bond type.  For example,
+bonds in a polymer flow (of bond type 1) could be computed with a
+*fene* potential and bonds in the wall boundary (of bond type 2) could
+be computed with a *harmonic* potential.  The assignment of bond type
+to style is made via the :doc:`bond_coeff <bond_coeff>` command or in
+the data file.
+
+In the bond\_coeff commands, the name of a bond style must be added
+after the bond type, with the remaining coefficients being those
+appropriate to that style.  In the example above, the 2 bond\_coeff
+commands set bonds of bond type 1 to be computed with a *harmonic*
+potential with coefficients 80.0, 1.2 for :math:`K`, :math:`r_0`.  All other bond types
+(2-N) are computed with a *fene* potential with coefficients 30.0,
+1.5, 1.0, 1.0 for :math:`K`, :math:`R_0`, :math:`\epsilon`, :math:`\sigma`.
+
+If bond coefficients are specified in the data file read via the
+:doc:`read_data <read_data>` command, then the same rule applies.
+E.g. "harmonic" or "fene" must be added after the bond type, for each
+line in the "Bond Coeffs" section, e.g.
+
+
+.. parsed-literal::
+
+   Bond Coeffs
+
+   1 harmonic 80.0 1.2
+   2 fene 30.0 1.5 1.0 1.0
+   ...
+
+A bond style of *none* with no additional coefficients can be used in
+place of a bond style, either in a input script bond\_coeff command or
+in the data file, if you desire to turn off interactions for specific
+bond types.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Unlike other bond styles, the hybrid bond style does not store bond
+coefficient info for individual sub-styles in a :doc:`binary restart files <restart>`.  Thus when restarting a simulation from a restart
+file, you need to re-specify bond\_coeff commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
+
+**Default:** none
diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt
deleted file mode 100644
index 0996f72ce3..0000000000
--- a/doc/src/bond_hybrid.txt
+++ /dev/null
@@ -1,74 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style hybrid command :h3
-
-[Syntax:]
-
-bond_style hybrid style1 style2 ... :pre
-
-style1,style2 = list of one or more bond styles :ul
-
-[Examples:]
-
-bond_style hybrid harmonic fene
-bond_coeff 1 harmonic 80.0 1.2
-bond_coeff 2* fene 30.0 1.5 1.0 1.0 :pre
-
-[Description:]
-
-The {hybrid} style enables the use of multiple bond styles in one
-simulation.  A bond style is assigned to each bond type.  For example,
-bonds in a polymer flow (of bond type 1) could be computed with a
-{fene} potential and bonds in the wall boundary (of bond type 2) could
-be computed with a {harmonic} potential.  The assignment of bond type
-to style is made via the "bond_coeff"_bond_coeff.html command or in
-the data file.
-
-In the bond_coeff commands, the name of a bond style must be added
-after the bond type, with the remaining coefficients being those
-appropriate to that style.  In the example above, the 2 bond_coeff
-commands set bonds of bond type 1 to be computed with a {harmonic}
-potential with coefficients 80.0, 1.2 for K, r0.  All other bond types
-(2-N) are computed with a {fene} potential with coefficients 30.0,
-1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
-
-If bond coefficients are specified in the data file read via the
-"read_data"_read_data.html command, then the same rule applies.
-E.g. "harmonic" or "fene" must be added after the bond type, for each
-line in the "Bond Coeffs" section, e.g.
-
-Bond Coeffs :pre
-
-1 harmonic 80.0 1.2
-2 fene 30.0 1.5 1.0 1.0
-... :pre
-
-A bond style of {none} with no additional coefficients can be used in
-place of a bond style, either in a input script bond_coeff command or
-in the data file, if you desire to turn off interactions for specific
-bond types.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-Unlike other bond styles, the hybrid bond style does not store bond
-coefficient info for individual sub-styles in a "binary restart
-files"_restart.html.  Thus when restarting a simulation from a restart
-file, you need to re-specify bond_coeff commands.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst
new file mode 100644
index 0000000000..5794592ce4
--- /dev/null
+++ b/doc/src/bond_mm3.rst
@@ -0,0 +1,73 @@
+.. index:: bond_style mm3
+
+bond_style mm3 command
+======================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style mm3
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style mm3
+   bond_coeff 1 100.0 107.0
+
+Description
+"""""""""""
+
+The *mm3* bond style uses the potential that is anharmonic in the bond
+as defined in :ref:`(Allinger) <mm3-allinger1989>`
+
+.. math::
+
+   E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
+
+
+where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a
+prefactor. The anharmonic prefactors have units angstrom\^(-n):
+-2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes
+care of the necessary unit conversion for these factors internally.
+Note that the MM3 papers contains an error in Eq (1):
+(7/12)2.55 should be replaced with (7/12)2.55\^2
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/distance\^2)
+* :math:`r_0` (distance)
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the
+USER\_YAFF package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _mm3-allinger1989:
+
+
+
+**(Allinger)** Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
+(1989),
diff --git a/doc/src/bond_mm3.txt b/doc/src/bond_mm3.txt
deleted file mode 100644
index c3d0e39f52..0000000000
--- a/doc/src/bond_mm3.txt
+++ /dev/null
@@ -1,58 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style mm3 command :h3
-
-[Syntax:]
-
-bond_style mm3 :pre
-
-[Examples:]
-
-bond_style mm3
-bond_coeff 1 100.0 107.0 :pre
-
-[Description:]
-
-The {mm3} bond style uses the potential that is anharmonic in the bond
-as defined in "(Allinger)"_#mm3-allinger1989
-
-:c,image(Eqs/bond_mm3.jpg)
-
-where r0 is the equilibrium value of the bond, and K is a
-prefactor. The anharmonic prefactors have units angstrom^(-n):
--2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
-care of the necessary unit conversion for these factors internally.
-Note that the MM3 papers contains an error in Eq (1):
-(7/12)2.55 should be replaced with (7/12)2.55^2
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/distance^2)
-r0 (distance) :ul
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the
-USER_YAFF package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html
-
-[Default:] none
-
-:line
-
-:link(mm3-allinger1989)
-[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
-(1989),
diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst
new file mode 100644
index 0000000000..26471424c5
--- /dev/null
+++ b/doc/src/bond_morse.rst
@@ -0,0 +1,87 @@
+.. index:: bond_style morse
+
+bond_style morse command
+========================
+
+bond_style morse/omp command
+============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style morse
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style morse
+   bond_coeff 5 1.0 2.0 1.2
+
+Description
+"""""""""""
+
+The *morse* bond style uses the potential
+
+.. math::
+
+   E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
+
+
+where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffness
+parameter, and :math:`D` determines the depth of the potential well.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`D` (energy)
+* :math:`\alpha` (inverse distance)
+* :math:`r_0` (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+**Default:** none
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
deleted file mode 100644
index 60fd16e17a..0000000000
--- a/doc/src/bond_morse.txt
+++ /dev/null
@@ -1,73 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style morse command :h3
-bond_style morse/omp command :h3
-
-[Syntax:]
-
-bond_style morse :pre
-
-[Examples:]
-
-bond_style morse
-bond_coeff 5 1.0 2.0 1.2 :pre
-
-[Description:]
-
-The {morse} bond style uses the potential
-
-:c,image(Eqs/bond_morse.jpg)
-
-where r0 is the equilibrium bond distance, alpha is a stiffness
-parameter, and D determines the depth of the potential well.
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-D (energy)
-alpha (inverse distance)
-r0 (distance) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
diff --git a/doc/src/bond_none.rst b/doc/src/bond_none.rst
new file mode 100644
index 0000000000..ac838581be
--- /dev/null
+++ b/doc/src/bond_none.rst
@@ -0,0 +1,40 @@
+.. index:: bond_style none
+
+bond_style none command
+=======================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style none
+
+Examples
+""""""""
+
+
+.. code-blocK:: LAMMPS
+
+   bond_style none
+
+Description
+"""""""""""
+
+Using a bond style of none means bond forces and energies are not
+computed, even if pairs of bonded atoms were listed in the data file
+read by the :doc:`read_data <read_data>` command.
+
+See the :doc:`bond_style zero <bond_zero>` command for a way to
+calculate bond statistics, but compute no bond interactions.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+:doc:`bond_style zero <bond_zero>`
+
+**Default:** none
diff --git a/doc/src/bond_none.txt b/doc/src/bond_none.txt
deleted file mode 100644
index cace1919e1..0000000000
--- a/doc/src/bond_none.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style none command :h3
-
-[Syntax:]
-
-bond_style none :pre
-
-[Examples:]
-
-bond_style none :pre
-
-[Description:]
-
-Using a bond style of none means bond forces and energies are not
-computed, even if pairs of bonded atoms were listed in the data file
-read by the "read_data"_read_data.html command.
-
-See the "bond_style zero"_bond_zero.html command for a way to
-calculate bond statistics, but compute no bond interactions.
-
-[Restrictions:] none
-
-[Related commands:] none
-
-"bond_style zero"_bond_zero.html
-
-[Default:] none
diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst
new file mode 100644
index 0000000000..0003257e0b
--- /dev/null
+++ b/doc/src/bond_nonlinear.rst
@@ -0,0 +1,97 @@
+.. index:: bond_style nonlinear
+
+bond_style nonlinear command
+============================
+
+bond_style nonlinear/omp command
+================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style nonlinear
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style nonlinear
+   bond_coeff 2 100.0 1.1 1.4
+
+Description
+"""""""""""
+
+The *nonlinear* bond style uses the potential
+
+.. math::
+
+   E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
+
+
+to define an anharmonic spring :ref:`(Rector) <Rector>` of equilibrium
+length :math:`r_0` and maximum extension lamda.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`\epsilon` (energy)
+* :math:`r_0` (distance)
+* :math:`\lambda` (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Rector:
+
+
+
+**(Rector)** Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
deleted file mode 100644
index af51383213..0000000000
--- a/doc/src/bond_nonlinear.txt
+++ /dev/null
@@ -1,78 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style nonlinear command :h3
-bond_style nonlinear/omp command :h3
-
-[Syntax:]
-
-bond_style nonlinear :pre
-
-[Examples:]
-
-bond_style nonlinear
-bond_coeff 2 100.0 1.1 1.4 :pre
-
-[Description:]
-
-The {nonlinear} bond style uses the potential
-
-:c,image(Eqs/bond_nonlinear.jpg)
-
-to define an anharmonic spring "(Rector)"_#Rector of equilibrium
-length r0 and maximum extension lamda.
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-epsilon (energy)
-r0 (distance)
-lamda (distance) :ul
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
-
-:line
-
-:link(Rector)
-[(Rector)] Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst
new file mode 100644
index 0000000000..03863eb5cf
--- /dev/null
+++ b/doc/src/bond_oxdna.rst
@@ -0,0 +1,146 @@
+.. index:: bond_style oxdna/fene
+
+bond_style oxdna/fene command
+=============================
+
+bond_style oxdna2/fene command
+==============================
+
+bond_style oxrna2/fene command
+==============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style oxdna/fene
+
+   bond_style oxdna2/fene
+
+   bond_style oxrna2/fene
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style oxdna/fene
+   bond_coeff * 2.0 0.25 0.7525
+
+   bond_style oxdna2/fene
+   bond_coeff * 2.0 0.25 0.7564
+
+   bond_style oxrna2/fene
+   bond_coeff \* 2.0 0.25 0.76107
+
+Description
+"""""""""""
+
+The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential
+
+.. math::
+
+   E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]
+
+
+to define a modified finite extensible nonlinear elastic (FENE)
+potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
+phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
+modelling of DNA/RNA.
+
+The following coefficients must be defined for the bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as given in the above example, or
+in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* :math:`\epsilon` (energy)
+* :math:`\Delta` (distance)
+* :math:`r_0` (distance)
+
+.. note::
+
+   The oxDNA bond style has to be used together with the
+   corresponding oxDNA pair styles for excluded volume interaction
+   *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
+   coaxial stacking interaction *oxdna/coaxstk* as well as
+   hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
+   :doc:`pair\_style oxdna/excv <pair_oxdna>`). For the oxDNA2
+   :ref:`(Snodin) <Snodin0>` bond style the analogous pair styles 
+   *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
+   *oxdna2/hbond* and an additional Debye-Hueckel pair style 
+   *oxdna2/dh* have to be defined. The same applies to the oxRNA2
+   :ref:`(Sulc1) <Sulc01>` styles. 
+   The coefficients in the above example have to be kept fixed and cannot
+   be changed without reparameterizing the entire model.
+
+Example input and data files for DNA and RNA duplexes can be found in
+examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/.  A simple python
+setup tool which creates single straight or helical DNA strands, DNA/RNA
+duplexes or arrays of DNA/RNA duplexes can be found in
+examples/USER/cgdna/util/.
+
+Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses 
+this implementation.  The article contains general information 
+on the model, its implementation and performance as well as the structure of 
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA/oxRNA publications. These are 
+:ref:`(Ouldridge) <Ouldridge0>` and 
+:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA, 
+:ref:`(Snodin) <Snodin0>` for oxDNA2, 
+:ref:`(Sulc1) <Sulc01>` for oxRNA2 
+and for sequence-specific hydrogen-bonding and stacking interactions 
+:ref:`(Sulc2) <Sulc02>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+:doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`, 
+:doc:`bond\_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+
+**Default:**
+
+none
+
+
+----------
+
+.. _Henrich0:
+
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
+.. _Ouldridge-DPhil0:
+
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+.. _Ouldridge0:
+
+**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+
+.. _Snodin0:
+
+**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
+
+.. _Sulc01:
+
+**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
+
+.. _Sulc02:
+
+**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
deleted file mode 100644
index 88afe435e6..0000000000
--- a/doc/src/bond_oxdna.txt
+++ /dev/null
@@ -1,99 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style oxdna/fene command :h3
-bond_style oxdna2/fene command :h3
-
-[Syntax:]
-
-bond_style oxdna/fene :pre
-bond_style oxdna2/fene :pre
-
-[Examples:]
-
-bond_style oxdna/fene
-bond_coeff * 2.0 0.25 0.7525 :pre
-
-bond_style oxdna2/fene
-bond_coeff * 2.0 0.25 0.7564 :pre
-
-[Description:]
-
-The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
-
-:c,image(Eqs/bond_oxdna_fene.jpg)
-
-to define a modified finite extensible nonlinear elastic (FENE)
-potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the
-phosphate backbone in the oxDNA force field for coarse-grained
-modelling of DNA.
-
-The following coefficients must be defined for the bond type via the
-"bond_coeff"_bond_coeff.html command as given in the above example, or
-in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-epsilon (energy)
-Delta (distance)
-r0 (distance) :ul
-
-NOTE: The oxDNA bond style has to be used together with the
-corresponding oxDNA pair styles for excluded volume interaction
-{oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and
-coaxial stacking interaction {oxdna/coaxstk} as well as
-hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
-"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2
-"(Snodin)"_#oxdna2 bond style the analogous pair styles and an
-additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
-The coefficients in the above example have to be kept fixed and cannot
-be changed without reparameterizing the entire model.
-
-Example input and data files for DNA duplexes can be found in
-examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.  A simple python
-setup tool which creates single straight or helical DNA strands, DNA
-duplexes or arrays of DNA duplexes can be found in
-examples/USER/cgdna/util/.
-
-Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in
-any publication that uses this implementation.  The article contains
-more information on the model, the structure of the input file, the
-setup tool and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found
-"here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
-"Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_style oxdna/excv"_pair_oxdna.html, "pair_style
-oxdna2/excv"_pair_oxdna2.html, "fix
-nve/dotc/langevin"_fix_nve_dotc_langevin.html,
-"bond_coeff"_bond_coeff.html
-
-[Default:] none
-
-:line
-
-:link(Henrich2)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
-T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
-
-:link(oxdna_fene)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
-J. Chem. Phys. 134, 085101 (2011).
-
-:link(oxdna2)
-[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
-J. Chem. Phys. 142, 234901 (2015).
diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst
new file mode 100644
index 0000000000..898aa9315a
--- /dev/null
+++ b/doc/src/bond_quartic.rst
@@ -0,0 +1,135 @@
+.. index:: bond_style quartic
+
+bond_style quartic command
+==========================
+
+bond_style quartic/omp command
+==============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style quartic
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style quartic
+   bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
+
+Description
+"""""""""""
+
+The *quartic* bond style uses the potential
+
+.. math::
+
+   E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
+
+to define a bond that can be broken as the simulation proceeds (e.g.
+due to a polymer being stretched).  The :math:`\sigma` and :math:`\epsilon` used in the
+LJ portion of the formula are both set equal to 1.0 by LAMMPS.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* :math:`K` (energy/distance\^4)
+* :math:`B_1` (distance)
+* :math:`B_2` (distance)
+* :math:`R_c` (distance)
+* :math:`U_0` (energy)
+
+This potential was constructed to mimic the FENE bond potential for
+coarse-grained polymer chains.  When monomers with :math:`\sigma = \epsilon = 1.0`
+are used, the following choice of parameters gives a quartic potential that
+looks nearly like the FENE potential: 
+
+.. math::
+
+   K &= 1200 \\
+   B_1 &= -0.55 \\
+   B_2 &= 0.25 \\
+   R_c &= 1.3 \\
+   U_0 &= 34.6878
+   
+Different parameters can be specified using the :doc:`bond_coeff <bond_coeff>`
+command, but you will need to choose them carefully so they form a suitable
+bond potential.
+
+:math:`R_c` is the cutoff length at which the bond potential goes smoothly to a
+local maximum.  If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks"
+the bond, which means two things.  First, the bond potential is turned
+off by setting its type to 0, and is no longer computed.  Second, a
+pairwise interaction between the two atoms is turned on, since they
+are no longer bonded.
+
+LAMMPS does the second task via a computational sleight-of-hand.  It
+subtracts the pairwise interaction as part of the bond computation.
+When the bond breaks, the subtraction stops.  For this to work, the
+pairwise interaction must always be computed by the
+:doc:`pair\_style <pair_style>` command, whether the bond is broken or
+not.  This means that :doc:`special\_bonds <special_bonds>` must be set
+to 1,1,1, as indicated as a restriction below.
+
+Note that when bonds are dumped to a file via the :doc:`dump local <dump>` command, bonds with type 0 are not included.  The
+:doc:`delete\_bonds <delete_bonds>` command can also be used to query the
+status of broken bonds or permanently delete them, e.g.:
+
+
+.. code-block:: LAMMPS
+
+   delete_bonds all stats
+   delete_bonds all bond 0 remove
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+The *quartic* style requires that :doc:`special\_bonds <special_bonds>`
+parameters be set to 1,1,1.  Three- and four-body interactions (angle,
+dihedral, etc) cannot be used with *quartic* bonds.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+**Default:** none
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
deleted file mode 100644
index b7b1ee4ce6..0000000000
--- a/doc/src/bond_quartic.txt
+++ /dev/null
@@ -1,112 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style quartic command :h3
-bond_style quartic/omp command :h3
-
-[Syntax:]
-
-bond_style quartic :pre
-
-[Examples:]
-
-bond_style quartic
-bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre
-
-[Description:]
-
-The {quartic} bond style uses the potential
-
-:c,image(Eqs/bond_quartic.jpg)
-
-to define a bond that can be broken as the simulation proceeds (e.g.
-due to a polymer being stretched).  The sigma and epsilon used in the
-LJ portion of the formula are both set equal to 1.0 by LAMMPS.
-
-The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-K (energy/distance^4)
-B1 (distance)
-B2 (distance)
-Rc (distance)
-U0 (energy) :ul
-
-This potential was constructed to mimic the FENE bond potential for
-coarse-grained polymer chains.  When monomers with sigma = epsilon =
-1.0 are used, the following choice of parameters gives a quartic
-potential that looks nearly like the FENE potential: K = 1200, B1 =
--0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878.  Different parameters
-can be specified using the "bond_coeff"_bond_coeff.html command, but
-you will need to choose them carefully so they form a suitable bond
-potential.
-
-Rc is the cutoff length at which the bond potential goes smoothly to a
-local maximum.  If a bond length ever becomes > Rc, LAMMPS "breaks"
-the bond, which means two things.  First, the bond potential is turned
-off by setting its type to 0, and is no longer computed.  Second, a
-pairwise interaction between the two atoms is turned on, since they
-are no longer bonded.
-
-LAMMPS does the second task via a computational sleight-of-hand.  It
-subtracts the pairwise interaction as part of the bond computation.
-When the bond breaks, the subtraction stops.  For this to work, the
-pairwise interaction must always be computed by the
-"pair_style"_pair_style.html command, whether the bond is broken or
-not.  This means that "special_bonds"_special_bonds.html must be set
-to 1,1,1, as indicated as a restriction below.
-
-Note that when bonds are dumped to a file via the "dump
-local"_dump.html command, bonds with type 0 are not included.  The
-"delete_bonds"_delete_bonds.html command can also be used to query the
-status of broken bonds or permanently delete them, e.g.:
-
-delete_bonds all stats
-delete_bonds all bond 0 remove :pre
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
-info.
-
-The {quartic} style requires that "special_bonds"_special_bonds.html
-parameters be set to 1,1,1.  Three- and four-body interactions (angle,
-dihedral, etc) cannot be used with {quartic} bonds.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:] none
diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst
new file mode 100644
index 0000000000..dd3acb6833
--- /dev/null
+++ b/doc/src/bond_style.rst
@@ -0,0 +1,132 @@
+.. index:: bond_style
+
+bond_style command
+==================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style style args
+
+* style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or         *harmonic* or *morse* or *nonlinear* or *quartic*
+
+* args = none for any style except *hybrid*
+
+  * *hybrid* args = list of one or more styles
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic
+   bond_style fene
+   bond_style hybrid harmonic fene
+
+Description
+"""""""""""
+
+Set the formula(s) LAMMPS uses to compute bond interactions between
+pairs of atoms.  In LAMMPS, a bond differs from a pairwise
+interaction, which are set via the :doc:`pair\_style <pair_style>`
+command.  Bonds are defined between specified pairs of atoms and
+remain in force for the duration of the simulation (unless the bond
+breaks which is possible in some bond potentials).  The list of bonded
+atoms is read in by a :doc:`read\_data <read_data>` or
+:doc:`read\_restart <read_restart>` command from a data or restart file.
+By contrast, pair potentials are typically defined between all pairs
+of atoms within a cutoff distance and the set of active interactions
+changes over time.
+
+Hybrid models where bonds are computed using different bond potentials
+can be setup using the *hybrid* bond style.
+
+The coefficients associated with a bond style can be specified in a
+data or restart file or via the :doc:`bond\_coeff <bond_coeff>` command.
+
+All bond potentials store their coefficient data in binary restart
+files which means bond\_style and :doc:`bond\_coeff <bond_coeff>` commands
+do not need to be re-specified in an input script that restarts a
+simulation.  See the :doc:`read\_restart <read_restart>` command for
+details on how to do this.  The one exception is that bond\_style
+*hybrid* only stores the list of sub-styles in the restart file; bond
+coefficients need to be re-specified.
+
+.. note::
+
+   When both a bond and pair style is defined, the
+   :doc:`special\_bonds <special_bonds>` command often needs to be used to
+   turn off (or weight) the pairwise interaction that would otherwise
+   exist between 2 bonded atoms.
+
+In the formulas listed for each bond style, *r* is the distance
+between the 2 atoms in the bond.
+
+
+----------
+
+
+Here is an alphabetic list of bond styles defined in LAMMPS.  Click on
+the style to display the formula it computes and coefficients
+specified by the associated :doc:`bond_coeff <bond_coeff>` command.
+
+Click on the style to display the formula it computes, any additional
+arguments specified in the bond\_style command, and coefficients
+specified by the associated :doc:`bond_coeff <bond_coeff>` command.
+
+There are also additional accelerated pair styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the :doc:`Commands bond <Commands_bond>`
+doc page are followed by one or more of (g,i,k,o,t) to indicate which
+accelerated styles exist.
+
+* :doc:`none <bond_none>` - turn off bonded interactions
+* :doc:`zero <bond_zero>` - topology but no interactions
+* :doc:`hybrid <bond_hybrid>` - define multiple styles of bond interactions
+
+* :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
+* :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
+* :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles
+* :doc:`gromos <bond_gromos>` - GROMOS force field bond
+* :doc:`harmonic <bond_harmonic>` - harmonic bond
+* :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
+* :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
+* :doc:`mm3 <bond_mm3>` - MM3 anharmonic bond
+* :doc:`morse <bond_morse>` - Morse bond
+* :doc:`nonlinear <bond_nonlinear>` - nonlinear bond
+* :doc:`oxdna/fene <bond_oxdna>` - modified FENE bond suitable for DNA modeling
+* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
+* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
+* :doc:`quartic <bond_quartic>` - breakable quartic bond
+* :doc:`table <bond_table>` - tabulated by bond length
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Bond styles can only be set for atom styles that allow bonds to be
+defined.
+
+Most bond styles are part of the MOLECULE package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  The doc pages for
+individual bond potentials tell if it is part of a package.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
+
+Default
+"""""""
+
+.. code-block:: LAMMPS
+
+   bond_style none
diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt
deleted file mode 100644
index aba6d3a778..0000000000
--- a/doc/src/bond_style.txt
+++ /dev/null
@@ -1,115 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style command :h3
-
-[Syntax:]
-
-bond_style style args :pre
-
-style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \
-        {harmonic} or {morse} or {nonlinear} or {quartic} :ul
-  args = none for any style except {hybrid}
-  {hybrid} args = list of one or more styles :pre
-
-[Examples:]
-
-bond_style harmonic
-bond_style fene
-bond_style hybrid harmonic fene :pre
-
-[Description:]
-
-Set the formula(s) LAMMPS uses to compute bond interactions between
-pairs of atoms.  In LAMMPS, a bond differs from a pairwise
-interaction, which are set via the "pair_style"_pair_style.html
-command.  Bonds are defined between specified pairs of atoms and
-remain in force for the duration of the simulation (unless the bond
-breaks which is possible in some bond potentials).  The list of bonded
-atoms is read in by a "read_data"_read_data.html or
-"read_restart"_read_restart.html command from a data or restart file.
-By contrast, pair potentials are typically defined between all pairs
-of atoms within a cutoff distance and the set of active interactions
-changes over time.
-
-Hybrid models where bonds are computed using different bond potentials
-can be setup using the {hybrid} bond style.
-
-The coefficients associated with a bond style can be specified in a
-data or restart file or via the "bond_coeff"_bond_coeff.html command.
-
-All bond potentials store their coefficient data in binary restart
-files which means bond_style and "bond_coeff"_bond_coeff.html commands
-do not need to be re-specified in an input script that restarts a
-simulation.  See the "read_restart"_read_restart.html command for
-details on how to do this.  The one exception is that bond_style
-{hybrid} only stores the list of sub-styles in the restart file; bond
-coefficients need to be re-specified.
-
-NOTE: When both a bond and pair style is defined, the
-"special_bonds"_special_bonds.html command often needs to be used to
-turn off (or weight) the pairwise interaction that would otherwise
-exist between 2 bonded atoms.
-
-In the formulas listed for each bond style, {r} is the distance
-between the 2 atoms in the bond.
-
-:line
-
-Here is an alphabetic list of bond styles defined in LAMMPS.  Click on
-the style to display the formula it computes and coefficients
-specified by the associated "bond_coeff"_bond_coeff.html command.
-
-Click on the style to display the formula it computes, any additional
-arguments specified in the bond_style command, and coefficients
-specified by the associated "bond_coeff"_bond_coeff.html command.
-
-There are also additional accelerated pair styles included in the
-LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
-The individual style names on the "Commands bond"_Commands_bond.html
-doc page are followed by one or more of (g,i,k,o,t) to indicate which
-accelerated styles exist.
-
-"none"_bond_none.html - turn off bonded interactions
-"zero"_bond_zero.html - topology but no interactions
-"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
-
-"class2"_bond_class2.html - COMPASS (class 2) bond
-"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
-"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
-"gromos"_bond_gromos.html - GROMOS force field bond
-"harmonic"_bond_harmonic.html - harmonic bond
-"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
-"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
-"mm3"_bond_mm3.html - MM3 anharmonic bond
-"morse"_bond_morse.html - Morse bond
-"nonlinear"_bond_nonlinear.html - nonlinear bond
-"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
-"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
-"quartic"_bond_quartic.html - breakable quartic bond
-"table"_bond_table.html - tabulated by bond length :ul
-
-:line
-
-[Restrictions:]
-
-Bond styles can only be set for atom styles that allow bonds to be
-defined.
-
-Most bond styles are part of the MOLECULE package.  They are only
-enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  The doc pages for
-individual bond potentials tell if it is part of a package.
-
-[Related commands:]
-
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
-
-[Default:]
-
-bond_style none
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.rst
similarity index 58%
rename from doc/src/bond_table.txt
rename to doc/src/bond_table.rst
index 7235214af0..5378df3cff 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.rst
@@ -1,86 +1,97 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+.. index:: bond_style table
 
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
+bond_style table command
+========================
 
-:line
+bond_style table/omp command
+============================
 
-bond_style table command :h3
-bond_style table/omp command :h3
+Syntax
+""""""
 
-[Syntax:]
 
-bond_style table style N :pre
+.. code-block:: LAMMPS
 
-style = {linear} or {spline} = method of interpolation
-N = use N values in table :ul
+   bond_style table style N
 
-[Examples:]
+* style = *linear* or *spline* = method of interpolation
+* N = use N values in table
 
-bond_style table linear 1000
-bond_coeff 1 file.table ENTRY1 :pre
+Examples
+""""""""
 
-[Description:]
 
-Style {table} creates interpolation tables of length {N} from bond
+.. code-block:: LAMMPS
+
+   bond_style table linear 1000
+   bond_coeff 1 file.table ENTRY1
+
+Description
+"""""""""""
+
+Style *table* creates interpolation tables of length *N* from bond
 potential and force values listed in a file(s) as a function of bond
-length.  The files are read by the "bond_coeff"_bond_coeff.html
+length.  The files are read by the :doc:`bond_coeff <bond_coeff>`
 command.
 
 The interpolation tables are created by fitting cubic splines to the
-file values and interpolating energy and force values at each of {N}
+file values and interpolating energy and force values at each of *N*
 distances.  During a simulation, these tables are used to interpolate
 energy and force values as needed.  The interpolation is done in one
-of 2 styles: {linear} or {spline}.
+of 2 styles: *linear* or *spline*.
 
-For the {linear} style, the bond length is used to find 2 surrounding
+For the *linear* style, the bond length is used to find 2 surrounding
 table values from which an energy or force is computed by linear
 interpolation.
 
-For the {spline} style, a cubic spline coefficients are computed and
-stored at each of the {N} values in the table.  The bond length is
+For the *spline* style, a cubic spline coefficients are computed and
+stored at each of the *N* values in the table.  The bond length is
 used to find the appropriate set of coefficients which are used to
 evaluate a cubic polynomial which computes the energy or force.
 
 The following coefficients must be defined for each bond type via the
-"bond_coeff"_bond_coeff.html command as in the example above.
+:doc:`bond_coeff <bond_coeff>` command as in the example above.
 
-filename
-keyword :ul
+* filename
+* keyword
 
 The filename specifies a file containing tabulated energy and force
 values.  The keyword specifies a section of the file.  The format of
 this file is described below.
 
-:line
+
+----------
+
 
 The format of a tabulated file is as follows (without the
 parenthesized comments):
 
-# Bond potential for harmonic (one or more comment or blank lines) :pre
 
-HAM                           (keyword is the first text on line)
-N 101 FP 0 0 EQ 0.5           (N, FP, EQ  parameters)
-                              (blank line)
-1 0.00 338.0000 1352.0000     (index, bond-length, energy, force)
-2 0.01 324.6152 1324.9600
-...
-101 1.00 338.0000 -1352.0000 :pre
+.. parsed-literal::
+
+   # Bond potential for harmonic (one or more comment or blank lines)
+
+   HAM                           (keyword is the first text on line)
+   N 101 FP 0 0 EQ 0.5           (N, FP, EQ  parameters)
+                                 (blank line)
+   1 0.00 338.0000 1352.0000     (index, bond-length, energy, force)
+   2 0.01 324.6152 1324.9600
+   ...
+   101 1.00 338.0000 -1352.0000
 
 A section begins with a non-blank line whose 1st character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.  The first line begins with a keyword which
 identifies the section.  The line can contain additional text, but the
 initial text must match the argument specified in the
-"bond_coeff"_bond_coeff.html command.  The next line lists (in any
+:doc:`bond_coeff <bond_coeff>` command.  The next line lists (in any
 order) one or more parameters for the table.  Each parameter is a
 keyword followed by one or more numeric values.
 
 The parameter "N" is required and its value is the number of table
-entries that follow.  Note that this may be different than the {N}
-specified in the "bond_style table"_bond_style.html command.  Let
-Ntable = {N} in the bond_style command, and Nfile = "N" in the
+entries that follow.  Note that this may be different than the *N*
+specified in the :doc:`bond\_style table <bond_style>` command.  Let
+Ntable = *N* in the bond_style command, and Nfile = "N" in the
 tabulated file.  What LAMMPS does is a preliminary interpolation by
 creating splines using the Nfile tabulated values as nodal points.  It
 uses these to interpolate as needed to generate energy and force
@@ -99,8 +110,7 @@ are estimated (less accurately) by the first two and last two force
 values in the table.
 
 The "EQ" parameter is also optional.  If used, it is followed by a the
-equilibrium bond length, which is used, for example, by the "fix
-shake"_fix_shake.html command.  If not used, the equilibrium bond
+equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix_shake>` command.  If not used, the equilibrium bond
 length is to the distance in the table with the lowest potential energy.
 
 Following a blank line, the next N lines list the tabulated values.
@@ -109,55 +119,61 @@ the bond length r (in distance units), the 3rd value is the energy (in
 energy units), and the 4th is the force (in force units).  The bond
 lengths must range from a LO value to a HI value, and increase from
 one line to the next.  If the actual bond length is ever smaller than
-the LO value or larger than the HI value, then the bond energy and
-force is evaluated as if the bond were the LO or HI length.
+the LO value or larger than the HI value, then the calculation is
+aborted with an error, so it is advisable to cover the whole range
+of possible bond lengths.
 
 Note that one file can contain many sections, each with a tabulated
 potential.  LAMMPS reads the file section by section until it finds
 one that matches the specified keyword.
 
-:line
 
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
 
 You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
 
-See the "Speed packages"_Speed_packages.html doc page for more
+See the :doc:`Speed packages <Speed_packages>` doc page for more
 instructions on how to use the accelerated styles effectively.
 
-:line
 
-[Restart info:]
+----------
 
-This bond style writes the settings for the "bond_style table"
-command to "binary restart files"_restart.html, so a bond_style
+
+**Restart info:**
+
+This bond style writes the settings for the "bond\_style table"
+command to :doc:`binary restart files <restart>`, so a bond\_style
 command does not need to specified in an input script that reads a
 restart file.  However, the coefficient information is not stored in
 the restart file, since it is tabulated in the potential files.  Thus,
-bond_coeff commands do need to be specified in the restart input
+bond\_coeff commands do need to be specified in the restart input
 script.
 
-[Restrictions:]
+Restrictions
+""""""""""""
+
 
 This bond style can only be used if LAMMPS was built with the MOLECULE
-package.  See the "Build package"_Build_package.html doc page for more
+package.  See the :doc:`Build package <Build_package>` doc page for more
 info.
 
-[Related commands:]
+Related commands
+""""""""""""""""
 
-"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
+:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-[Default:] none
+**Default:** none
diff --git a/doc/src/bond_write.txt b/doc/src/bond_write.rst
similarity index 55%
rename from doc/src/bond_write.txt
rename to doc/src/bond_write.rst
index 711bd2c296..f7055d42aa 100644
--- a/doc/src/bond_write.txt
+++ b/doc/src/bond_write.rst
@@ -1,31 +1,34 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+.. index:: bond_write
 
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
+bond_write command
+==================
 
-:line
+Syntax
+""""""
 
-bond_write command :h3
 
-[Syntax:]
+.. code-block:: LAMMPS
 
-bond_write btype N inner outer file keyword itype jtype :pre
+   bond_write btype N inner outer file keyword itype jtype
 
-btype = bond types
-N = # of values
-inner,outer = inner and outer bond length (distance units)
-file = name of file to write values to
-keyword = section name in file for this set of tabulated values
-itype,jtype = 2 atom types (optional)
-:ul
+* btype = bond types
+* N = # of values
+* inner,outer = inner and outer bond length (distance units)
+* file = name of file to write values to
+* keyword = section name in file for this set of tabulated values
+* itype,jtype = 2 atom types (optional)
 
-[Examples:]
+Examples
+""""""""
 
-bond_write 1 500 0.5 3.5 table.txt Harmonic_1
-bond_write 3 1000 0.1 6.0 table.txt Morse :pre
 
-[Description:]
+.. code-block:: LAMMPS
+
+   bond_write 1 500 0.5 3.5 table.txt Harmonic_1
+   bond_write 3 1000 0.1 6.0 table.txt Morse
+
+Description
+"""""""""""
 
 Write energy and force values to a file as a function of distance for
 the currently defined bond potential.  This is useful for plotting the
@@ -36,19 +39,21 @@ file.
 
 The energy and force values are computed at distances from inner to
 outer for 2 interacting atoms forming a bond of type btype, using the
-appropriate "bond_coeff"_bond_coeff.html coefficients. N evenly spaced
+appropriate :doc:`bond_coeff <bond_coeff>` coefficients. N evenly spaced
 distances are used.
 
 For example, for N = 7, inner = 1.0, and outer = 4.0,
 values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
 
 The file is written in the format used as input for the
-"bond_style"_bond_style.html {table} option with {keyword} as the
+:doc:`bond_style <bond_style>` *table* option with *keyword* as the
 section name.  Each line written to the file lists an index number
 (1-N), a distance (in distance units), an energy (in energy units),
 and a force (in force units).
 
-[Restrictions:]
+Restrictions
+""""""""""""
+
 
 All force field coefficients for bond and other kinds of interactions
 must be set before this command can be invoked.
@@ -56,9 +61,10 @@ must be set before this command can be invoked.
 Due to how the bond force is computed, an inner value > 0.0 must
 be specified even if the potential has a finite value at r = 0.0.
 
-[Related commands:]
+Related commands
+""""""""""""""""
 
-"bond_style table"_bond_table.html,
-"bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html
+:doc:`bond_style table <bond_table>`,
+:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
 
-[Default:] none
+**Default:** none
diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst
new file mode 100644
index 0000000000..43a0af33e2
--- /dev/null
+++ b/doc/src/bond_zero.rst
@@ -0,0 +1,55 @@
+.. index:: bond_style zero
+
+bond_style zero command
+=======================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style zero [nocoeff]
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style zero
+   bond_style zero nocoeff
+   bond_coeff *
+   bond_coeff * 2.14
+
+Description
+"""""""""""
+
+Using an bond style of zero means bond forces and energies are not
+computed, but the geometry of bond pairs is still accessible to other
+commands.
+
+As an example, the :doc:`compute bond/local <compute_bond_local>`
+command can be used to compute distances for the list of pairs of bond
+atoms listed in the data file read by the :doc:`read\_data <read_data>`
+command.  If no bond style is defined, this command cannot be used.
+
+The optional *nocoeff* flag allows to read data files with a BondCoeff
+section for any bond style. Similarly, any bond\_coeff commands
+will only be checked for the bond type number and the rest ignored.
+
+Note that the :doc:`bond\_coeff <bond_coeff>` command must be used for
+all bond types. If specified, there can be only one value, which is
+going to be used to assign an equilibrium distance, e.g. for use with
+:doc:`fix shake <fix_shake>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_style none <bond_none>`
+
+**Default:** none
diff --git a/doc/src/bond_zero.txt b/doc/src/bond_zero.txt
deleted file mode 100644
index 554f26e7f0..0000000000
--- a/doc/src/bond_zero.txt
+++ /dev/null
@@ -1,48 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-bond_style zero command :h3
-
-[Syntax:]
-
-bond_style zero {nocoeff} :pre
-
-[Examples:]
-
-bond_style zero
-bond_style zero nocoeff
-bond_coeff *
-bond_coeff * 2.14 :pre
-
-[Description:]
-
-Using an bond style of zero means bond forces and energies are not
-computed, but the geometry of bond pairs is still accessible to other
-commands.
-
-As an example, the "compute bond/local"_compute_bond_local.html
-command can be used to compute distances for the list of pairs of bond
-atoms listed in the data file read by the "read_data"_read_data.html
-command.  If no bond style is defined, this command cannot be used.
-
-The optional {nocoeff} flag allows to read data files with a BondCoeff
-section for any bond style. Similarly, any bond_coeff commands
-will only be checked for the bond type number and the rest ignored.
-
-Note that the "bond_coeff"_bond_coeff.html command must be used for
-all bond types. If specified, there can be only one value, which is
-going to be used to assign an equilibrium distance, e.g. for use with
-"fix shake"_fix_shake.html.
-
-[Restrictions:] none
-
-[Related commands:]
-
-"bond_style none"_bond_none.html
-
-[Default:] none
diff --git a/doc/src/bonds.rst b/doc/src/bonds.rst
new file mode 100644
index 0000000000..3019e0c177
--- /dev/null
+++ b/doc/src/bonds.rst
@@ -0,0 +1,9 @@
+Bond Styles
+###########
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   bond_*
diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt
deleted file mode 100644
index 48896e711c..0000000000
--- a/doc/src/bonds.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-Bond Styles :h1
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   bond_class2
-   bond_fene
-   bond_fene_expand
-   bond_gromos
-   bond_harmonic
-   bond_harmonic_shift
-   bond_harmonic_shift_cut
-   bond_hybrid
-   bond_mm3
-   bond_morse
-   bond_none
-   bond_nonlinear
-   bond_oxdna
-   bond_quartic
-   bond_table
-   bond_zero
-
-END_RST -->
diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst
new file mode 100644
index 0000000000..909ee3b446
--- /dev/null
+++ b/doc/src/boundary.rst
@@ -0,0 +1,126 @@
+.. index:: boundary
+
+boundary command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   boundary x y z
+
+* x,y,z = *p* or *s* or *f* or *m*\ , one or two letters
+  
+  .. parsed-literal::
+  
+       *p* is periodic
+       *f* is non-periodic and fixed
+       *s* is non-periodic and shrink-wrapped
+       *m* is non-periodic and shrink-wrapped with a minimum value
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   boundary p p f
+   boundary p fs p
+   boundary s f fm
+
+Description
+"""""""""""
+
+Set the style of boundaries for the global simulation box in each
+dimension.  A single letter assigns the same style to both the lower
+and upper face of the box.  Two letters assigns the first style to the
+lower face and the second style to the upper face.  The initial size
+of the simulation box is set by the :doc:`read\_data <read_data>`,
+:doc:`read\_restart <read_restart>`, or :doc:`create\_box <create_box>`
+commands.
+
+The style *p* means the box is periodic, so that particles interact
+across the boundary, and they can exit one end of the box and re-enter
+the other end.  A periodic dimension can change in size due to
+constant pressure boundary conditions or box deformation (see the :doc:`fix npt <fix_nh>` and :doc:`fix deform <fix_deform>` commands).  The *p*
+style must be applied to both faces of a dimension.
+
+The styles *f*\ , *s*\ , and *m* mean the box is non-periodic, so that
+particles do not interact across the boundary and do not move from one
+side of the box to the other.
+
+For style *f*\ , the position of the face is fixed.  If an atom moves
+outside the face it will be deleted on the next timestep that
+reneighboring occurs.  This will typically generate an error unless
+you have set the :doc:`thermo\_modify lost <thermo_modify>` option to
+allow for lost atoms.
+
+For style *s*\ , the position of the face is set so as to encompass the
+atoms in that dimension (shrink-wrapping), no matter how far they
+move. Note that when the difference between the current box dimensions
+and the shrink-wrap box dimensions is large, this can lead to lost
+atoms at the beginning of a run when running in parallel. This is due
+to the large change in the (global) box dimensions also causing
+significant changes in the individual sub-domain sizes. If these
+changes are farther than the communication cutoff, atoms will be lost.
+This is best addressed by setting initial box dimensions to match the
+shrink-wrapped dimensions more closely, by using *m* style boundaries
+(see below).
+
+For style *m*\ , shrink-wrapping occurs, but is bounded by the value
+specified in the data or restart file or set by the
+:doc:`create\_box <create_box>` command.  For example, if the upper z
+face has a value of 50.0 in the data file, the face will always be
+positioned at 50.0 or above, even if the maximum z-extent of all the
+atoms becomes less than 50.0.  This can be useful if you start a
+simulation with an empty box or if you wish to leave room on one side
+of the box, e.g. for atoms to evaporate from a surface.
+
+For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
+of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
+enforced with the tilt factor offset.  If the 1st dimension is
+shrink-wrapped, then the shrink wrapping is applied to the tilted box
+face, to encompass the atoms.  E.g. for a positive xy tilt, the xlo
+and xhi faces of the box are planes tilting in the +y direction as y
+increases.  These tilted planes are shrink-wrapped around the atoms to
+determine the x extent of the box.
+
+See the :doc:`Howto triclinic <Howto_triclinic>` doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
+triclinic representations.
+
+Restrictions
+""""""""""""
+
+
+This command cannot be used after the simulation box is defined by a
+:doc:`read\_data <read_data>` or :doc:`create\_box <create_box>` command or
+:doc:`read\_restart <read_restart>` command.  See the
+:doc:`change\_box <change_box>` command for how to change the simulation
+box boundaries after it has been defined.
+
+For 2d simulations, the z dimension must be periodic.
+
+Related commands
+""""""""""""""""
+
+See the :doc:`thermo\_modify <thermo_modify>` command for a discussion
+of lost atoms.
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   boundary p p p
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/box.rst b/doc/src/box.rst
new file mode 100644
index 0000000000..3338e138fb
--- /dev/null
+++ b/doc/src/box.rst
@@ -0,0 +1,76 @@
+.. index:: box
+
+box command
+===========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   box keyword value ...
+
+* one or more keyword/value pairs may be appended
+* keyword = *tilt*
+  
+  .. parsed-literal::
+  
+       *tilt* value = *small* or *large*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   box tilt large
+   box tilt small
+
+Description
+"""""""""""
+
+Set attributes of the simulation box.
+
+For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword
+allows simulation domains to be created with arbitrary tilt factors,
+e.g. via the :doc:`create\_box <create_box>` or
+:doc:`read\_data <read_data>` commands.  Tilt factors determine how
+skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` doc page for a discussion of triclinic
+boxes in LAMMPS.
+
+LAMMPS normally requires that no tilt factor can skew the box more
+than half the distance of the parallel box length, which is the 1st
+dimension in the tilt factor (x for xz).  If *tilt* is set to
+*small*\ , which is the default, then an error will be
+generated if a box is created which exceeds this limit.  If *tilt*
+is set to *large*\ , then no limit is enforced.  You can create
+a box with any tilt factors you wish.
+
+Note that if a simulation box has a large tilt factor, LAMMPS will run
+less efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped sub-domain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+
+Restrictions
+""""""""""""
+
+
+This command cannot be used after the simulation box is defined by a
+:doc:`read\_data <read_data>` or :doc:`create\_box <create_box>` command or
+:doc:`read\_restart <read_restart>` command.
+
+**Related commands:** none
+
+Default
+"""""""
+
+The default value is tilt = small.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst
new file mode 100644
index 0000000000..bc34db9262
--- /dev/null
+++ b/doc/src/change_box.rst
@@ -0,0 +1,387 @@
+.. index:: change\_box
+
+change\_box command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   change_box group-ID parameter args ... keyword args ...
+
+* group-ID = ID of group of atoms to (optionally) displace
+* one or more parameter/arg pairs may be appended
+  
+  .. parsed-literal::
+  
+     parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *boundary* or *ortho* or *triclinic* or *set* or *remap*
+       *x*\ , *y*\ , *z* args = style value(s)
+         style = *final* or *delta* or *scale* or *volume*
+           *final* values = lo hi
+             lo hi = box boundaries after displacement (distance units)
+           *delta* values = dlo dhi
+             dlo dhi = change in box boundaries after displacement (distance units)
+           *scale* values = factor
+             factor = multiplicative factor for change in box length after displacement
+           *volume* value = none = adjust this dim to preserve volume of system
+       *xy*\ , *xz*\ , *yz* args = style value
+         style = *final* or *delta*
+           *final* value = tilt
+             tilt = tilt factor after displacement (distance units)
+           *delta* value = dtilt
+             dtilt = change in tilt factor after displacement (distance units)
+       *boundary* args = x y z
+         x,y,z = *p* or *s* or *f* or *m*\ , one or two letters
+         *p* is periodic
+         *f* is non-periodic and fixed
+         *s* is non-periodic and shrink-wrapped
+         *m* is non-periodic and shrink-wrapped with a minimum value
+       *ortho* args = none = change box to orthogonal
+       *triclinic* args = none = change box to triclinic
+       *set* args = none = store state of current box
+       *remap* args = none = remap atom coords from last saved state to current box
+
+* zero or more keyword/value pairs may be appended
+* keyword = *units*
+  
+  .. parsed-literal::
+  
+       *units* value = *lattice* or *box*
+         lattice = distances are defined in lattice units
+         box = distances are defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
+   change_box all x scale 1.1 y volume z volume remap
+
+Description
+"""""""""""
+
+Change the volume and/or shape and/or boundary conditions for the
+simulation box.  Orthogonal simulation boxes have 3 adjustable size
+parameters (x,y,z).  Triclinic (non-orthogonal) simulation boxes have
+6 adjustable size/shape parameters (x,y,z,xy,xz,yz).  Any or all of
+them can be adjusted independently by this command.  Thus it can be
+used to expand or contract a box, or to apply a shear strain to a
+non-orthogonal box.  It can also be used to change the boundary
+conditions for the simulation box, similar to the
+:doc:`boundary <boundary>` command.
+
+The size and shape of the initial simulation box are specified by the
+:doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` or
+:doc:`read\_restart <read_restart>` command used to setup the simulation.
+The size and shape may be altered by subsequent runs, e.g. by use of
+the :doc:`fix npt <fix_nh>` or :doc:`fix deform <fix_deform>` commands.
+The :doc:`create\_box <create_box>`, :doc:`read data <read_data>`, and
+:doc:`read\_restart <read_restart>` commands also determine whether the
+simulation box is orthogonal or triclinic and their doc pages explain
+the meaning of the xy,xz,yz tilt factors.
+
+See the :doc:`Howto triclinic <Howto_triclinic>` doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
+triclinic representations.
+
+The keywords used in this command are applied sequentially to the
+simulation box and the atoms in it, in the order specified.
+
+Before the sequence of keywords are invoked, the current box
+size/shape is stored, in case a *remap* keyword is used to map the
+atom coordinates from a previously stored box size/shape to the
+current one.
+
+After all the keywords have been processed, any shrink-wrap boundary
+conditions are invoked (see the :doc:`boundary <boundary>` command)
+which may change simulation box boundaries, and atoms are migrated to
+new owning processors.
+
+.. note::
+
+   This means that you cannot use the change\_box command to enlarge
+   a shrink-wrapped box, e.g. to make room to insert more atoms via the
+   :doc:`create\_atoms <create_atoms>` command, because the simulation box
+   will be re-shrink-wrapped before the change\_box command completes.
+   Instead you could do something like this, assuming the simulation box
+   is non-periodic and atoms extend from 0 to 20 in all dimensions:
+
+
+.. parsed-literal::
+
+   change_box all x final -10 20
+   create_atoms 1 single -5 5 5       # this will fail to insert an atom
+
+   change_box all x final -10 20 boundary f s s
+   create_atoms 1 single -5 5 5
+   change_box all boundary s s s      # this will work
+
+.. note::
+
+   Unlike the earlier "displace\_box" version of this command, atom
+   remapping is NOT performed by default.  This command allows remapping
+   to be done in a more general way, exactly when you specify it (zero or
+   more times) in the sequence of transformations.  Thus if you do not
+   use the *remap* keyword, atom coordinates will not be changed even if
+   the box size/shape changes.  If a uniformly strained state is desired,
+   the *remap* keyword should be specified.
+
+.. note::
+
+   It is possible to lose atoms with this command.  E.g. by
+   changing the box without remapping the atoms, and having atoms end up
+   outside of non-periodic boundaries.  It is also possible to alter
+   bonds between atoms straddling a boundary in bad ways.  E.g. by
+   converting a boundary from periodic to non-periodic.  It is also
+   possible when remapping atoms to put them (nearly) on top of each
+   other.  E.g. by converting a boundary from non-periodic to periodic.
+   All of these will typically lead to bad dynamics and/or generate error
+   messages.
+
+.. note::
+
+   The simulation box size/shape can be changed by arbitrarily
+   large amounts by this command.  This is not a problem, except that the
+   mapping of processors to the simulation box is not changed from its
+   initial 3d configuration; see the :doc:`processors <processors>`
+   command.  Thus, if the box size/shape changes dramatically, the
+   mapping of processors to the simulation box may not end up as optimal
+   as the initial mapping attempted to be.
+
+.. note::
+
+   Because the keywords used in this command are applied one at a
+   time to the simulation box and the atoms in it, care must be taken
+   with triclinic cells to avoid exceeding the limits on skew after each
+   transformation in the sequence.  If skew is exceeded before the final
+   transformation this can be avoided by changing the order of the
+   sequence, or breaking the transformation into two or more smaller
+   transformations.  For more information on the allowed limits for box
+   skew see the discussion on triclinic boxes on :doc:`Howto triclinic <Howto_triclinic>` doc page.
+
+
+----------
+
+
+For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their
+styles and values.
+
+For style *final*\ , the final lo and hi box boundaries of a dimension
+are specified.  The values can be in lattice or box distance units.
+See the discussion of the units keyword below.
+
+For style *delta*\ , plus or minus changes in the lo/hi box boundaries
+of a dimension are specified.  The values can be in lattice or box
+distance units.  See the discussion of the units keyword below.
+
+For style *scale*\ , a multiplicative factor to apply to the box length
+of a dimension is specified.  For example, if the initial box length
+is 10, and the factor is 1.1, then the final box length will be 11.  A
+factor less than 1.0 means compression.
+
+The *volume* style changes the specified dimension in such a way that
+the overall box volume remains constant with respect to the operation
+performed by the preceding keyword.  The *volume* style can only be
+used following a keyword that changed the volume, which is any of the
+*x*\ , *y*\ , *z* keywords.  If the preceding keyword "key" had a *volume*
+style, then both it and the current keyword apply to the keyword
+preceding "key".  I.e. this sequence of keywords is allowed:
+
+
+.. parsed-literal::
+
+   change_box all x scale 1.1 y volume z volume
+
+The *volume* style changes the associated dimension so that the
+overall box volume is unchanged relative to its value before the
+preceding keyword was invoked.
+
+If the following command is used, then the z box length will shrink by
+the same 1.1 factor the x box length was increased by:
+
+
+.. parsed-literal::
+
+   change_box all x scale 1.1 z volume
+
+If the following command is used, then the y,z box lengths will each
+shrink by sqrt(1.1) to keep the volume constant.  In this case, the
+y,z box lengths shrink so as to keep their relative aspect ratio
+constant:
+
+
+.. parsed-literal::
+
+   change_box all"x scale 1.1 y volume z volume
+
+If the following command is used, then the final box will be a factor
+of 10% larger in x and y, and a factor of 21% smaller in z, so as to
+keep the volume constant:
+
+
+.. parsed-literal::
+
+   change_box all x scale 1.1 z volume y scale 1.1 z volume
+
+.. note::
+
+   For solids or liquids, when one dimension of the box is
+   expanded, it may be physically undesirable to hold the other 2 box
+   lengths constant since that implies a density change.  For solids,
+   adjusting the other dimensions via the *volume* style may make
+   physical sense (just as for a liquid), but may not be correct for
+   materials and potentials whose Poisson ratio is not 0.5.
+
+For the *scale* and *volume* styles, the box length is expanded or
+compressed around its mid point.
+
+
+----------
+
+
+For the *xy*\ , *xz*\ , and *yz* parameters, this is the meaning of their
+styles and values.  Note that changing the tilt factors of a triclinic
+box does not change its volume.
+
+For style *final*\ , the final tilt factor is specified.  The value
+can be in lattice or box distance units.  See the discussion of the
+units keyword below.
+
+For style *delta*\ , a plus or minus change in the tilt factor is
+specified.  The value can be in lattice or box distance units.  See
+the discussion of the units keyword below.
+
+All of these styles change the xy, xz, yz tilt factors.  In LAMMPS,
+tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
+than half the distance of the parallel box length.  For example, if
+xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
+factor must be between -5 and 5.  Similarly, both xz and yz must be
+between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a
+limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are all equivalent.  Any tilt factor specified by this command
+must be within these limits.
+
+
+----------
+
+
+The *boundary* keyword takes arguments that have exactly the same
+meaning as they do for the :doc:`boundary <boundary>` command.  In each
+dimension, a single letter assigns the same style to both the lower
+and upper face of the box.  Two letters assigns the first style to the
+lower face and the second style to the upper face.
+
+The style *p* means the box is periodic; the other styles mean
+non-periodic. For style *f*\ , the position of the face is fixed.  For
+style *s*\ , the position of the face is set so as to encompass the
+atoms in that dimension (shrink-wrapping), no matter how far they
+move.  For style *m*\ , shrink-wrapping occurs, but is bounded by the
+current box edge in that dimension, so that the box will become no
+smaller.  See the :doc:`boundary <boundary>` command for more
+explanation of these style options.
+
+Note that the "boundary" command itself can only be used before the
+simulation box is defined via a :doc:`read\_data <read_data>` or
+:doc:`create\_box <create_box>` or :doc:`read\_restart <read_restart>`
+command.  This command allows the boundary conditions to be changed
+later in your input script.  Also note that the
+:doc:`read\_restart <read_restart>` will change boundary conditions to
+match what is stored in the restart file.  So if you wish to change
+them, you should use the change\_box command after the read\_restart
+command.
+
+
+----------
+
+
+The *ortho* and *triclinic* keywords convert the simulation box to be
+orthogonal or triclinic (non-orthogonal).
+
+The simulation box is defined as either orthogonal or triclinic when
+it is created via the :doc:`create\_box <create_box>`,
+:doc:`read\_data <read_data>`, or :doc:`read\_restart <read_restart>`
+commands.
+
+These keywords allow you to toggle the existing simulation box from
+orthogonal to triclinic and vice versa.  For example, an initial
+equilibration simulation can be run in an orthogonal box, the box can
+be toggled to triclinic, and then a :doc:`non-equilibrium MD (NEMD) simulation <Howto_nemd>` can be run with deformation via the :doc:`fix deform <fix_deform>` command.
+
+If the simulation box is currently triclinic and has non-zero tilt in
+xy, yz, or xz, then it cannot be converted to an orthogonal box.
+
+
+----------
+
+
+The *set* keyword saves the current box size/shape.  This can be
+useful if you wish to use the *remap* keyword more than once or if you
+wish it to be applied to an intermediate box size/shape in a sequence
+of keyword operations.  Note that the box size/shape is saved before
+any of the keywords are processed, i.e. the box size/shape at the time
+the create\_box command is encountered in the input script.
+
+The *remap* keyword remaps atom coordinates from the last saved box
+size/shape to the current box state.  For example, if you stretch the
+box in the x dimension or tilt it in the xy plane via the *x* and *xy*
+keywords, then the *remap* command will dilate or tilt the atoms to
+conform to the new box size/shape, as if the atoms moved with the box
+as it deformed.
+
+Note that this operation is performed without regard to periodic
+boundaries.  Also, any shrink-wrapping of non-periodic boundaries (see
+the :doc:`boundary <boundary>` command) occurs after all keywords,
+including this one, have been processed.
+
+Only atoms in the specified group are remapped.
+
+
+----------
+
+
+The *units* keyword determines the meaning of the distance units used
+to define various arguments.  A *box* value selects standard distance
+units as defined by the :doc:`units <units>` command, e.g. Angstroms for
+units = real or metal.  A *lattice* value means the distance units are
+in lattice spacings.  The :doc:`lattice <lattice>` command must have
+been previously used to define the lattice spacing.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+If you use the *ortho* or *triclinic* keywords, then at the point in
+the input script when this command is issued, no :doc:`dumps <dump>` can
+be active, nor can a :doc:`fix deform <fix_deform>` be active.  This is
+because these commands test whether the simulation box is orthogonal
+when they are first issued.  Note that these commands can be used in
+your script before a change\_box command is issued, so long as an
+:doc:`undump <undump>` or :doc:`unfix <unfix>` command is also used to
+turn them off.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix deform <fix_deform>`, :doc:`boundary <boundary>`
+
+Default
+"""""""
+
+The option default is units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/clear.rst b/doc/src/clear.rst
new file mode 100644
index 0000000000..dac4ba8fa4
--- /dev/null
+++ b/doc/src/clear.rst
@@ -0,0 +1,49 @@
+.. index:: clear
+
+clear command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   clear
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   (commands for 1st simulation)
+   clear
+   (commands for 2nd simulation)
+
+Description
+"""""""""""
+
+This command deletes all atoms, restores all settings to their default
+values, and frees all memory allocated by LAMMPS.  Once a clear
+command has been executed, it is almost as if LAMMPS were starting
+over, with only the exceptions noted below.  This command enables
+multiple jobs to be run sequentially from one input script.
+
+These settings are not affected by a clear command: the working
+directory (:doc:`shell <shell>` command), log file status
+(:doc:`log <log>` command), echo status (:doc:`echo <echo>` command), and
+input script variables (:doc:`variable <variable>` command).
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst
new file mode 100644
index 0000000000..9375bd60c9
--- /dev/null
+++ b/doc/src/comm_modify.rst
@@ -0,0 +1,187 @@
+.. index:: comm\_modify
+
+comm\_modify command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   comm_modify keyword value ...
+
+* zero or more keyword/value pairs may be appended
+* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel*
+  
+  .. parsed-literal::
+  
+       *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
+       *cutoff* value = Rcut (distance units) = communicate atoms from this far away
+       *cutoff/multi* type value
+          type = atom type or type range (supports asterisk notation)
+          value = Rcut (distance units) = communicate atoms for selected types from this far away
+       *group* value = group-ID = only communicate atoms in the group
+       *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   comm_modify mode multi
+   comm_modify mode multi group solvent
+   comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2\*4 15.0
+   comm_modify vel yes
+   comm_modify mode single cutoff 5.0 vel yes
+   comm_modify cutoff/multi \* 0.0
+
+Description
+"""""""""""
+
+This command sets parameters that affect the inter-processor
+communication of atom information that occurs each timestep as
+coordinates and other properties are exchanged between neighboring
+processors and stored as properties of ghost atoms.
+
+.. note::
+
+   These options apply to the currently defined comm style.  When
+   you specify a :doc:`comm\_style <comm_style>` or
+   :doc:`read\_restart <read_restart>` command, all communication settings
+   are restored to their default or stored values, including those
+   previously reset by a comm\_modify command.  Thus if your input script
+   specifies a comm\_style or read\_restart command, you should use the
+   comm\_modify command after it.
+
+The *mode* keyword determines whether a single or multiple cutoff
+distances are used to determine which atoms to communicate.
+
+The default mode is *single* which means each processor acquires
+information for ghost atoms that are within a single distance from its
+sub-domain.  The distance is by default the maximum of the neighbor
+cutoff across all atom type pairs.
+
+For many systems this is an efficient algorithm, but for systems with
+widely varying cutoffs for different type pairs, the *multi* mode can
+be faster.  In this case, each atom type is assigned its own distance
+cutoff for communication purposes, and fewer atoms will be
+communicated.  See the :doc:`neighbor multi <neighbor>` command for a
+neighbor list construction option that may also be beneficial for
+simulations of this kind.
+
+The *cutoff* keyword allows you to extend the ghost cutoff distance
+for communication mode *single*\ , which is the distance from the borders
+of a processor's sub-domain at which ghost atoms are acquired from other
+processors.  By default the ghost cutoff = neighbor cutoff = pairwise
+force cutoff + neighbor skin.  See the :doc:`neighbor <neighbor>` command
+for more information about the skin distance.  If the specified Rcut is
+greater than the neighbor cutoff, then extra ghost atoms will be acquired.
+If the provided cutoff is smaller, the provided value will be ignored,
+the ghost cutoff is set to the neighbor cutoff and a warning will be
+printed. Specifying a cutoff value of 0.0 will reset any previous value
+to the default. If bonded interactions exist and equilibrium bond length
+information is available, then also a heuristic based on that bond length
+is computed. It is used as communication cutoff, if there is no pair
+style present and no *comm\_modify cutoff* command used. Otherwise a
+warning is printed, if this bond based estimate is larger than the
+communication cutoff used. A
+
+The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
+communication mode *multi* instead. Since in this case the communication
+cutoffs are determined per atom type, a type specifier is needed and
+cutoff for one or multiple types can be extended. Also ranges of types
+using the usual asterisk notation can be given.
+
+These are simulation scenarios in which it may be useful or even
+necessary to set a ghost cutoff > neighbor cutoff:
+
+* a single polymer chain with bond interactions, but no pairwise interactions
+* bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff
+* ghost atoms beyond the pairwise cutoff are needed for some computation
+
+In the first scenario, a pairwise potential is not defined.  Thus the
+pairwise neighbor cutoff will be 0.0.  But ghost atoms are still
+needed for computing bond, angle, etc interactions between atoms on
+different processors, or when the interaction straddles a periodic
+boundary.
+
+The appropriate ghost cutoff depends on the :doc:`newton bond <newton>`
+setting.  For newton bond *off*\ , the distance needs to be the furthest
+distance between any two atoms in the bond, angle, etc.  E.g. the
+distance between 1-4 atoms in a dihedral.  For newton bond *on*\ , the
+distance between the central atom in the bond, angle, etc and any
+other atom is sufficient.  E.g. the distance between 2-4 atoms in a
+dihedral.
+
+In the second scenario, a pairwise potential is defined, but its
+neighbor cutoff is not sufficiently long enough to enable bond, angle,
+etc terms to be computed.  As in the previous scenario, an appropriate
+ghost cutoff should be set.
+
+In the last scenario, a :doc:`fix <fix>` or :doc:`compute <compute>` or
+:doc:`pairwise potential <pair_style>` needs to calculate with ghost
+atoms beyond the normal pairwise cutoff for some computation it
+performs (e.g. locate neighbors of ghost atoms in a multibody pair
+potential).  Setting the ghost cutoff appropriately can insure it will
+find the needed atoms.
+
+.. note::
+
+   In these scenarios, if you do not set the ghost cutoff long
+   enough, and if there is only one processor in a periodic dimension
+   (e.g. you are running in serial), then LAMMPS may "find" the atom it
+   is looking for (e.g. the partner atom in a bond), that is on the far
+   side of the simulation box, across a periodic boundary.  This will
+   typically lead to bad dynamics (i.e. the bond length is now the
+   simulation box length).  To detect if this is happening, see the
+   :doc:`neigh\_modify cluster <neigh_modify>` command.
+
+The *group* keyword will limit communication to atoms in the specified
+group.  This can be useful for models where no ghost atoms are needed
+for some kinds of particles.  All atoms (not just those in the
+specified group) will still migrate to new processors as they move.
+The group specified with this option must also be specified via the
+:doc:`atom\_modify first <atom_modify>` command.
+
+The *vel* keyword enables velocity information to be communicated with
+ghost particles.  Depending on the :doc:`atom\_style <atom_style>`,
+velocity info includes the translational velocity, angular velocity,
+and angular momentum of a particle.  If the *vel* option is set to
+*yes*\ , then ghost atoms store these quantities; if *no* then they do
+not.  The *yes* setting is needed by some pair styles which require
+the velocity state of both the I and J particles to compute a pairwise
+I,J interaction, as well as by some compute and fix commands.
+
+Note that if the :doc:`fix deform <fix_deform>` command is being used
+with its "remap v" option enabled, then the velocities for ghost atoms
+(in the fix deform group) mirrored across a periodic boundary will
+also include components due to any velocity shift that occurs across
+that boundary (e.g. due to dilation or shear).
+
+Restrictions
+""""""""""""
+
+
+Communication mode *multi* is currently only available for
+:doc:`comm\_style <comm_style>` *brick*\ .
+
+Related commands
+""""""""""""""""
+
+:doc:`comm\_style <comm_style>`, :doc:`neighbor <neighbor>`
+
+Default
+"""""""
+
+The option defaults are mode = single, group = all, cutoff = 0.0, vel =
+no.  The cutoff default of 0.0 means that ghost cutoff = neighbor
+cutoff = pairwise force cutoff + neighbor skin.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/comm_style.rst b/doc/src/comm_style.rst
new file mode 100644
index 0000000000..1d733b7c40
--- /dev/null
+++ b/doc/src/comm_style.rst
@@ -0,0 +1,78 @@
+.. index:: comm\_style
+
+comm\_style command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   comm_style style
+
+* style = *brick* or *tiled*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   comm_style brick
+   comm_style tiled
+
+Description
+"""""""""""
+
+This command sets the style of inter-processor communication of atom
+information that occurs each timestep as coordinates and other
+properties are exchanged between neighboring processors and stored as
+properties of ghost atoms.
+
+For the default *brick* style, the domain decomposition used by LAMMPS
+to partition the simulation box must be a regular 3d grid of bricks,
+one per processor.  Each processor communicates with its 6 Cartesian
+neighbors in the grid to acquire information for nearby atoms.
+
+For the *tiled* style, a more general domain decomposition can be
+used, as triggered by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.  The simulation box can be
+partitioned into non-overlapping rectangular-shaped "tiles" or varying
+sizes and shapes.  Again there is one tile per processor.  To acquire
+information for nearby atoms, communication must now be done with a
+more complex pattern of neighboring processors.
+
+Note that this command does not actually define a partitioning of the
+simulation box (a domain decomposition), rather it determines what
+kinds of decompositions are allowed and the pattern of communication
+used to enable the decomposition.  A decomposition is created when the
+simulation box is first created, via the :doc:`create\_box <create_box>`
+or :doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands.  For both the *brick* and *tiled* styles, the initial
+decomposition will be the same, as described by
+:doc:`create\_box <create_box>` and :doc:`processors <processors>`
+commands.  The decomposition can be changed via the
+:doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
+
+Restrictions
+""""""""""""
+
+
+Communication style *tiled* cannot be used with *triclinic* simulation
+cells.
+
+Related commands
+""""""""""""""""
+
+:doc:`comm\_modify <comm_modify>`, :doc:`processors <processors>`,
+:doc:`balance <balance>`, :doc:`fix balance <fix_balance>`
+
+Default
+"""""""
+
+The default style is brick.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst
new file mode 100644
index 0000000000..2eaa78d59c
--- /dev/null
+++ b/doc/src/commands_list.rst
@@ -0,0 +1,124 @@
+Commands
+########
+
+
+.. toctree::
+   :maxdepth: 1
+
+   angle_coeff
+   angle_style
+   atom_modify
+   atom_style
+   balance
+   bond_coeff
+   bond_style
+   bond_write
+   boundary
+   box
+   change_box
+   clear
+   comm_modify
+   comm_style
+   compute
+   compute_modify
+   create_atoms
+   create_bonds
+   create_box
+   delete_atoms
+   delete_bonds
+   dielectric
+   dihedral_coeff
+   dihedral_style
+   dimension
+   displace_atoms
+   dump
+   dump_adios
+   dump_cfg_uef
+   dump_h5md
+   dump_image
+   dump_modify
+   dump_molfile
+   dump_netcdf
+   dump_vtk
+   dynamical_matrix
+   echo
+   fix
+   fix_modify
+   group
+   group2ndx
+   hyper
+   if
+   improper_coeff
+   improper_style
+   include
+   info
+   jump
+   kim_commands
+   kspace_modify
+   kspace_style
+   label
+   lattice
+   log
+   mass
+   message
+   min_modify
+   min_spin
+   min_style
+   minimize
+   molecule
+   neb
+   neb_spin
+   neigh_modify
+   neighbor
+   newton
+   next
+   package
+   pair_coeff
+   pair_modify
+   pair_style
+   pair_write
+   partition
+   prd
+   print
+   processors
+   python
+   quit
+   read_data
+   read_dump
+   read_restart
+   region
+   replicate
+   rerun
+   reset_ids
+   reset_timestep
+   restart
+   run
+   run_style
+   server
+   server_mc
+   server_md
+   set
+   shell
+   special_bonds
+   suffix
+   tad
+   temper
+   temper_grem
+   temper_npt
+   thermo
+   thermo_modify
+   thermo_style
+   third_order
+   timer
+   timestep
+   uncompute
+   undump
+   unfix
+   units
+   variable
+   velocity
+   write_coeff
+   write_data
+   write_dump
+   write_restart
+
diff --git a/doc/src/compute.rst b/doc/src/compute.rst
new file mode 100644
index 0000000000..9c66c58bd9
--- /dev/null
+++ b/doc/src/compute.rst
@@ -0,0 +1,339 @@
+.. index:: compute
+
+compute command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID style args
+
+* ID = user-assigned name for the computation
+* group-ID = ID of the group of atoms to perform the computation on
+* style = one of a list of possible style names (see below)
+* args = arguments used by a particular style
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all temp
+   compute newtemp flow temp/partial 1 1 0
+   compute 3 all ke/atom
+
+Description
+"""""""""""
+
+Define a computation that will be performed on a group of atoms.
+Quantities calculated by a compute are instantaneous values, meaning
+they are calculated from information about atoms on the current
+timestep or iteration, though a compute may internally store some
+information about a previous state of the system.  Defining a compute
+does not perform a computation.  Instead computes are invoked by other
+LAMMPS commands as needed, e.g. to calculate a temperature needed for
+a thermostat fix or to generate thermodynamic or dump file output.
+See the :doc:`Howto output <Howto_output>` doc page for a summary of
+various LAMMPS output options, many of which involve computes.
+
+The ID of a compute can only contain alphanumeric characters and
+underscores.
+
+
+----------
+
+
+Computes calculate one of three styles of quantities: global,
+per-atom, or local.  A global quantity is one or more system-wide
+values, e.g. the temperature of the system.  A per-atom quantity is
+one or more values per atom, e.g. the kinetic energy of each atom.
+Per-atom values are set to 0.0 for atoms not in the specified compute
+group.  Local quantities are calculated by each processor based on the
+atoms it owns, but there may be zero or more per atom, e.g. a list of
+bond distances.  Computes that produce per-atom quantities have the
+word "atom" in their style, e.g. *ke/atom*\ .  Computes that produce
+local quantities have the word "local" in their style,
+e.g. *bond/local*\ .  Styles with neither "atom" or "local" in their
+style produce global quantities.
+
+Note that a single compute can produce either global or per-atom or
+local quantities, but not both global and per-atom.  It can produce
+local quantities in tandem with global or per-atom quantities.  The
+compute doc page will explain.
+
+Global, per-atom, and local quantities each come in three kinds: a
+single scalar value, a vector of values, or a 2d array of values.  The
+doc page for each compute describes the style and kind of values it
+produces, e.g. a per-atom vector.  Some computes produce more than one
+kind of a single style, e.g. a global scalar and a global vector.
+
+When a compute quantity is accessed, as in many of the output commands
+discussed below, it can be referenced via the following bracket
+notation, where ID is the ID of the compute:
+
++-------------+--------------------------------------------+
+| c\_ID       | entire scalar, vector, or array            |
++-------------+--------------------------------------------+
+| c\_ID[I]    | one element of vector, one column of array |
++-------------+--------------------------------------------+
+| c\_ID[I][J] | one element of array                       |
++-------------+--------------------------------------------+
+
+In other words, using one bracket reduces the dimension of the
+quantity once (vector -> scalar, array -> vector).  Using two brackets
+reduces the dimension twice (array -> scalar).  Thus a command that
+uses scalar compute values as input can also process elements of a
+vector or array.
+
+Note that commands and :doc:`variables <variable>` which use compute
+quantities typically do not allow for all kinds, e.g. a command may
+require a vector of values, not a scalar.  This means there is no
+ambiguity about referring to a compute quantity as c\_ID even if it
+produces, for example, both a scalar and vector.  The doc pages for
+various commands explain the details.
+
+
+----------
+
+
+In LAMMPS, the values generated by a compute can be used in several
+ways:
+
+* The results of computes that calculate a global temperature or
+  pressure can be used by fixes that do thermostatting or barostatting
+  or when atom velocities are created.
+* Global values can be output via the :doc:`thermo\_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
+  Or the values can be referenced in a :doc:`variable equal <variable>` or
+  :doc:`variable atom <variable>` command.
+* Per-atom values can be output via the :doc:`dump custom <dump>` command.
+  Or they can be time-averaged via the :doc:`fix ave/atom <fix_ave_atom>`
+  command or reduced by the :doc:`compute reduce <compute_reduce>`
+  command.  Or the per-atom values can be referenced in an :doc:`atom-style variable <variable>`.
+* Local values can be reduced by the :doc:`compute reduce <compute_reduce>` command, or histogrammed by the :doc:`fix ave/histo <fix_ave_histo>` command, or output by the :doc:`dump local <dump>` command.
+
+
+The results of computes that calculate global quantities can be either
+"intensive" or "extensive" values.  Intensive means the value is
+independent of the number of atoms in the simulation,
+e.g. temperature.  Extensive means the value scales with the number of
+atoms in the simulation, e.g. total rotational kinetic energy.
+:doc:`Thermodynamic output <thermo_style>` will normalize extensive
+values by the number of atoms in the system, depending on the
+"thermo\_modify norm" setting.  It will not normalize intensive values.
+If a compute value is accessed in another way, e.g. by a
+:doc:`variable <variable>`, you may want to know whether it is an
+intensive or extensive value.  See the doc page for individual
+computes for further info.
+
+
+----------
+
+
+LAMMPS creates its own computes internally for thermodynamic output.
+Three computes are always created, named "thermo\_temp",
+"thermo\_press", and "thermo\_pe", as if these commands had been invoked
+in the input script:
+
+
+.. parsed-literal::
+
+   compute thermo_temp all temp
+   compute thermo_press all pressure thermo_temp
+   compute thermo_pe all pe
+
+Additional computes for other quantities are created if the thermo
+style requires it.  See the documentation for the
+:doc:`thermo\_style <thermo_style>` command.
+
+Fixes that calculate temperature or pressure, i.e. for thermostatting
+or barostatting, may also create computes.  These are discussed in the
+documentation for specific :doc:`fix <fix>` commands.
+
+In all these cases, the default computes LAMMPS creates can be
+replaced by computes defined by the user in the input script, as
+described by the :doc:`thermo\_modify <thermo_modify>` and :doc:`fix modify <fix_modify>` commands.
+
+Properties of either a default or user-defined compute can be modified
+via the :doc:`compute\_modify <compute_modify>` command.
+
+Computes can be deleted with the :doc:`uncompute <uncompute>` command.
+
+Code for new computes can be added to LAMMPS; see the
+:doc:`Modify <Modify>` doc page for details.  The results of their
+calculations accessed in the various ways described above.
+
+
+----------
+
+
+Each compute style has its own doc page which describes its arguments
+and what it does.  Here is an alphabetic list of compute styles
+available in LAMMPS.  They are also listed in more compact form on the
+:doc:`Commands compute <Commands_compute>` doc page.
+
+There are also additional accelerated compute styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the :doc:`Commands compute <Commands_compute>` doc page are followed by one or more of
+(g,i,k,o,t) to indicate which accelerated styles exist.
+
+* :doc:`ackland/atom <compute_ackland_atom>` - determines the local lattice structure based on the Ackland formulation
+* :doc:`adf <compute_adf>` - angular distribution function of triples of atoms
+* :doc:`aggregate/atom <compute_cluster_atom>` - aggregate ID for each atom
+* :doc:`angle <compute_angle>` - energy of each angle sub-style
+* :doc:`angle/local <compute_angle_local>` - theta and energy of each angle
+* :doc:`angmom/chunk <compute_angmom_chunk>` - angular momentum for each chunk
+* :doc:`basal/atom <compute_basal_atom>` - calculates the hexagonal close-packed "c" lattice vector of each atom
+* :doc:`body/local <compute_body_local>` - attributes of body sub-particles
+* :doc:`bond <compute_bond>` - energy of each bond sub-style
+* :doc:`bond/local <compute_bond_local>` - distance and energy of each bond
+* :doc:`centro/atom <compute_centro_atom>` - centro-symmetry parameter for each atom
+* :doc:`centroid/stress/atom <compute_stress_atom>` - centroid based stress tensor for each atom
+* :doc:`chunk/atom <compute_chunk_atom>` - assign chunk IDs to each atom
+* :doc:`chunk/spread/atom <compute_chunk_spread_atom>` - spreads chunk values to each atom in chunk
+* :doc:`cluster/atom <compute_cluster_atom>` - cluster ID for each atom
+* :doc:`cna/atom <compute_cna_atom>` - common neighbor analysis (CNA) for each atom
+* :doc:`cnp/atom <compute_cnp_atom>` - common neighborhood parameter (CNP) for each atom
+* :doc:`com <compute_com>` - center-of-mass of group of atoms
+* :doc:`com/chunk <compute_com_chunk>` - center-of-mass for each chunk
+* :doc:`contact/atom <compute_contact_atom>` - contact count for each spherical particle
+* :doc:`coord/atom <compute_coord_atom>` - coordination number for each atom
+* :doc:`damage/atom <compute_damage_atom>` - Peridynamic damage for each atom
+* :doc:`dihedral <compute_dihedral>` - energy of each dihedral sub-style
+* :doc:`dihedral/local <compute_dihedral_local>` - angle of each dihedral
+* :doc:`dilatation/atom <compute_dilatation_atom>` - Peridynamic dilatation for each atom
+* :doc:`dipole/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk
+* :doc:`displace/atom <compute_displace_atom>` - displacement of each atom
+* :doc:`dpd <compute_dpd>` -
+* :doc:`dpd/atom <compute_dpd_atom>` -
+* :doc:`edpd/temp/atom <compute_edpd_temp_atom>` - per-atom temperature for each eDPD particle in a group
+* :doc:`entropy/atom <compute_entropy_atom>` - pair entropy fingerprint of each atom
+* :doc:`erotate/asphere <compute_erotate_asphere>` - rotational energy of aspherical particles
+* :doc:`erotate/rigid <compute_erotate_rigid>` - rotational energy of rigid bodies
+* :doc:`erotate/sphere <compute_erotate_sphere>` - rotational energy of spherical particles
+* :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` - rotational energy for each spherical particle
+* :doc:`event/displace <compute_event_displace>` - detect event on atom displacement
+* :doc:`fep <compute_fep>` -
+* :doc:`force/tally <compute_tally>` -
+* :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
+* :doc:`global/atom <compute_global_atom>` -
+* :doc:`group/group <compute_group_group>` - energy/force between two groups of atoms
+* :doc:`gyration <compute_gyration>` - radius of gyration of group of atoms
+* :doc:`gyration/chunk <compute_gyration_chunk>` - radius of gyration for each chunk
+* :doc:`gyration/shape <compute_gyration_shape>` - shape parameters from gyration tensor
+* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` - shape parameters from gyration tensor for each chunk
+* :doc:`heat/flux <compute_heat_flux>` - heat flux through a group of atoms
+* :doc:`heat/flux/tally <compute_tally>` -
+* :doc:`hexorder/atom <compute_hexorder_atom>` - bond orientational order parameter q6
+* :doc:`hma <compute_hma>` - harmonically mapped averaging for atomic crystals
+* :doc:`improper <compute_improper>` - energy of each improper sub-style
+* :doc:`improper/local <compute_improper_local>` - angle of each improper
+* :doc:`inertia/chunk <compute_inertia_chunk>` - inertia tensor for each chunk
+* :doc:`ke <compute_ke>` - translational kinetic energy
+* :doc:`ke/atom <compute_ke_atom>` - kinetic energy for each atom
+* :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model
+* :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model
+* :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies
+* :doc:`meso/e/atom <compute_meso_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
+* :doc:`meso/rho/atom <compute_meso_rho_atom>` - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
+* :doc:`meso/t/atom <compute_meso_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
+* :doc:`momentum <compute_momentum>` - translational momentum
+* :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms
+* :doc:`msd/chunk <compute_msd_chunk>` - mean-squared displacement for each chunk
+* :doc:`msd/nongauss <compute_msd_nongauss>` - MSD and non-Gaussian parameter of group of atoms
+* :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
+* :doc:`orientorder/atom <compute_orientorder_atom>` - Steinhardt bond orientational order parameters Ql
+* :doc:`pair <compute_pair>` - values computed by a pair style
+* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
+* :doc:`pe <compute_pe>` - potential energy
+* :doc:`pe/atom <compute_pe_atom>` - potential energy for each atom
+* :doc:`pe/mol/tally <compute_tally>` -
+* :doc:`pe/tally <compute_tally>` -
+* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
+* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
+* :doc:`pressure/cylinder <compute_pressure_cylinder>` - pressure tensor in cylindrical coordinates
+* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
+* :doc:`property/atom <compute_property_atom>` - convert atom attributes to per-atom vectors/arrays
+* :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
+* :doc:`property/local <compute_property_local>` - convert local attributes to localvectors/arrays
+* :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
+* :doc:`rdf <compute_rdf>` - radial distribution function g(r) histogram of group of atoms
+* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
+* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
+* :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
+* :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
+* :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
+* :doc:`slice <compute_slice>` - extract values from global vector or array
+* :doc:`smd/contact/radius <compute_smd_contact_radius>` -
+* :doc:`smd/damage <compute_smd_damage>` - damage status of SPH particles in Smooth Mach Dynamics
+* :doc:`smd/hourglass/error <compute_smd_hourglass_error>` -
+* :doc:`smd/internal/energy <compute_smd_internal_energy>` - per-particle enthalpy in Smooth Mach Dynamics
+* :doc:`smd/plastic/strain <compute_smd_plastic_strain>` - equivalent plastic strain per particle in Smooth Mach Dynamics
+* :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` - time rate of the equivalent plastic strain in Smooth Mach Dynamics
+* :doc:`smd/rho <compute_smd_rho>` - per-particle mass density in Smooth Mach Dynamics
+* :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` - deformation gradient in Smooth Mach Dynamics
+* :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>` - CFL-stable time increment per particle in Smooth Mach Dynamics
+* :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` -
+* :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` -
+* :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` -
+* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` -
+* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` - per-particle Cauchy stress tensor for SPH particles
+* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` -
+* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` -
+* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` -
+* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` -
+* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
+* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
+* :doc:`snap <compute_sna_atom>` - bispectrum components and related quantities for a group of atoms
+* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
+* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
+* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
+* :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
+* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
+* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
+* :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
+* :doc:`stress/tally <compute_tally>` -
+* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
+* :doc:`temp <compute_temp>` - temperature of group of atoms
+* :doc:`temp/asphere <compute_temp_asphere>` - temperature of aspherical particles
+* :doc:`temp/body <compute_temp_body>` - temperature of body particles
+* :doc:`temp/chunk <compute_temp_chunk>` - temperature of each chunk
+* :doc:`temp/com <compute_temp_com>` - temperature after subtracting center-of-mass velocity
+* :doc:`temp/cs <compute_temp_cs>` - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
+* :doc:`temp/deform <compute_temp_deform>` - temperature excluding box deformation velocity
+* :doc:`temp/deform/eff <compute_temp_deform_eff>` - temperature excluding box deformation velocity in the electron force field model
+* :doc:`temp/drude <compute_temp_drude>` - temperature of Core-Drude pairs
+* :doc:`temp/eff <compute_temp_eff>` - temperature of a group of nuclei and electrons in the electron force field model
+* :doc:`temp/partial <compute_temp_partial>` - temperature excluding one or more dimensions of velocity
+* :doc:`temp/profile <compute_temp_profile>` - temperature excluding a binned velocity profile
+* :doc:`temp/ramp <compute_temp_ramp>` - temperature excluding ramped velocity component
+* :doc:`temp/region <compute_temp_region>` - temperature of a region of atoms
+* :doc:`temp/region/eff <compute_temp_region_eff>` - temperature of a region of nuclei and electrons in the electron force field model
+* :doc:`temp/rotate <compute_temp_rotate>` - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities
+* :doc:`temp/sphere <compute_temp_sphere>` - temperature of spherical particles
+* :doc:`temp/uef <compute_temp_uef>` - kinetic energy tensor in the reference frame of an applied flow field
+* :doc:`ti <compute_ti>` - thermodynamic integration free energy values
+* :doc:`torque/chunk <compute_torque_chunk>` - torque applied on each chunk
+* :doc:`vacf <compute_vacf>` - velocity auto-correlation function of group of atoms
+* :doc:`vcm/chunk <compute_vcm_chunk>` - velocity of center-of-mass for each chunk
+* :doc:`voronoi/atom <compute_voronoi_atom>` - Voronoi volume and neighbors for each atom
+* :doc:`xrd <compute_xrd>` - x-ray diffraction intensity on a mesh of reciprocal lattice nodes
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`uncompute <uncompute>`, :doc:`compute\_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_ackland_atom.rst b/doc/src/compute_ackland_atom.rst
new file mode 100644
index 0000000000..c86ca121db
--- /dev/null
+++ b/doc/src/compute_ackland_atom.rst
@@ -0,0 +1,104 @@
+.. index:: compute ackland/atom
+
+compute ackland/atom command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID ackland/atom keyword/value
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* ackland/atom = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *legacy*
+  
+  .. parsed-literal::
+  
+       *legacy* yes/no = use (\ *yes*\ ) or do not use (\ *no*\ ) legacy ackland algorithm implementation
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all ackland/atom
+   compute 1 all ackland/atom legacy yes
+
+Description
+"""""""""""
+
+Defines a computation that calculates the local lattice structure
+according to the formulation given in :ref:`(Ackland) <Ackland>`.
+Historically, LAMMPS had two, slightly different implementations of
+the algorithm from the paper. With the *legacy* keyword, it is
+possible to switch between the pre-2015 (\ *legacy yes*\ ) and post-2015
+implementation (\ *legacy no*\ ). The post-2015 variant is the default.
+
+In contrast to the :doc:`centro-symmetry parameter <compute_centro_atom>` this method is stable against
+temperature boost, because it is based not on the distance between
+particles but the angles.  Therefore statistical fluctuations are
+averaged out a little more.  A comparison with the Common Neighbor
+Analysis metric is made in the paper.
+
+The result is a number which is mapped to the following different
+lattice structures:
+
+* 0 = UNKNOWN
+* 1 = BCC
+* 2 = FCC
+* 3 = HCP
+* 4 = ICO
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each of
+which computes this quantity.-
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The per-atom vector values will be unitless since they are the
+integers defined above.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute centro/atom <compute_centro_atom>`
+
+Default
+"""""""
+The keyword *legacy* defaults to *no*\ .
+
+
+----------
+
+
+.. _Ackland:
+
+
+
+**(Ackland)** Ackland, Jones, Phys Rev B, 73, 054104 (2006).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst
new file mode 100644
index 0000000000..3c8af03b10
--- /dev/null
+++ b/doc/src/compute_adf.rst
@@ -0,0 +1,234 @@
+.. index:: compute adf
+
+compute adf command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID adf Nbin itype1 jtype1 ktype1 Rjinner1 Rjouter1 Rkinner1 Rkouter1 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* adf = style name of this compute command
+* Nbin = number of ADF bins
+* itypeN = central atom type for Nth ADF histogram (see asterisk form below)
+* jtypeN = J atom type for Nth ADF histogram (see asterisk form below)
+* ktypeN = K atom type for Nth ADF histogram (see asterisk form below)
+* RjinnerN =  inner radius of J atom shell for Nth ADF histogram (distance units)
+* RjouterN =  outer radius of J atom shell for Nth ADF histogram (distance units)
+* RkinnerN = inner radius of K atom shell for Nth ADF histogram (distance units)
+* RkouterN =  outer radius of K atom shell for Nth ADF histogram (distance units)
+* zero or one keyword/value pairs may be appended
+* keyword = *ordinate*
+  
+  .. parsed-literal::
+  
+       *ordinate* value = *degree* or *radian* or *cosine*
+         Choose the ordinate parameter for the histogram
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 &
+                          1 1 2 0.0 1.2 0.0 1.5 &
+                          1 2 2 0.0 1.5 0.0 1.5 &
+                          2 1 1 0.0 1.2 0.0 1.2 &
+                          2 1 2 0.0 1.5 2.0 3.5 &
+                          2 2 2 2.0 3.5 2.0 3.5
+   compute 1 fluid adf 32 1\*2 1\*2 1\*2 0.5 3.5
+   compute 1 fluid adf 32
+
+Description
+"""""""""""
+
+Define a computation that calculates one or more angular distribution functions
+(ADF) for a group of particles.  Each ADF is calculated in histogram form
+by measuring the angle formed by a central atom and two neighbor atoms and
+binning these angles into *Nbin* bins.
+Only neighbors for which *Rinner* < *R* < *Router* are counted, where
+*Rinner* and *Router* are specified separately for the first and second
+neighbor atom in each requested ADF.
+
+.. note::
+
+   If you have a bonded system, then the settings of
+   :doc:`special\_bonds <special_bonds>` command can remove pairwise
+   interactions between atoms in the same bond, angle, or dihedral.  This
+   is the default setting for the :doc:`special\_bonds <special_bonds>`
+   command, and means those pairwise interactions do not appear in the
+   neighbor list.  Because this fix uses a neighbor list, it also means
+   those pairs will not be included in the ADF. This does not apply when
+   using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ ,
+   *coul/wolf* or similar.  One way to get around this would be to set
+   special\_bond scaling factors to very tiny numbers that are not exactly
+   zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
+   use the :doc:`rerun <rerun>` command to compute the ADF for snapshots in
+   the dump file.  The rerun script can use a
+   :doc:`special\_bonds <special_bonds>` command that includes all pairs in
+   the neighbor list.
+
+.. note::
+
+   If you request any outer cutoff *Router* > force cutoff, or if no
+   pair style is defined,  e.g. the :doc:`rerun <rerun>` command is being used to
+   post-process a dump file of snapshots you must insure ghost atom information
+   out to the largest value of *Router* + *skin* is communicated, via the
+   :doc:`comm\_modify cutoff <comm_modify>` command, else the ADF computation
+   cannot be performed, and LAMMPS will give an error message.  The *skin* value
+   is what is specified with the :doc:`neighbor <neighbor>` command.
+
+The *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN* settings can be specified in one of two
+ways.  An explicit numeric value can be used, as in the 1st example
+above.  Or a wild-card asterisk can be used to specify a range of atom
+types as in the 2nd example above.
+This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the 1st example
+above, this means that the ADF is computed where atoms of type *itypeN*
+are the central atom, and neighbor atoms of type *jtypeN* and *ktypeN*
+are forming the angle.  If any of *itypeN*\ , *jtypeN*\ , or *ktypeN*
+represent a range of values via
+the wild-card asterisk, as in the 2nd example above, this means that the
+ADF is computed where atoms of any of the range of types represented
+by *itypeN* are the central atom, and the angle is formed by two neighbors,
+one neighbor in the range of types represented by *jtypeN* and another neighbor
+in the range of types represented by *ktypeN*\ .
+
+If no *itypeN*\ , *jtypeN*\ , *ktypeN* settings are specified, then
+LAMMPS will generate a single ADF for all atoms in the group.
+The inner cutoff is set to zero and the outer cutoff is set
+to the force cutoff. If no pair\_style is specified, there is no
+force cutoff and LAMMPS will give an error message. Note that
+in most cases, generating an ADF for all atoms is not a good thing.
+Such an ADF is both uninformative and
+extremely expensive to compute.  For example, with liquid water
+with a 10 A force cutoff, there are 80,000 angles per atom.
+In addition, most of the interesting angular structure occurs for
+neighbors that are the closest to the central atom, involving
+just a few dozen angles.
+
+Angles for each ADF are generated by double-looping over the list of
+neighbors of each central atom I,
+just as they would be in the force calculation for
+a three-body potential such as :doc:`Stillinger-Weber <pair_sw>`.
+The angle formed by central atom I and neighbor atoms J and K is included in an
+ADF if the following criteria are met:
+
+* atoms I,J,K are all in the specified compute group
+* the distance between atoms I,J is between Rjinner and Rjouter
+* the distance between atoms I,K is between Rkinner and Rkouter
+* the type of the I atom matches itypeN (one or a range of types)
+* atoms I,J,K are distinct
+* the type of the J atom matches jtypeN (one or a range of types)
+* the type of the K atom matches ktypeN (one or a range of types)
+
+Each unique angle satisfying the above criteria is counted only once, regardless
+of whether either or both of the neighbor atoms making up the
+angle appear in both the J and K lists.
+It is OK if a particular angle is included in more than
+one individual histogram, due to the way the *itypeN*\ , *jtypeN*\ , *ktypeN*
+arguments are specified.
+
+The first ADF value for a bin is calculated from the histogram count by
+dividing by the total number of triples satisfying the criteria,
+so that the integral of the ADF w.r.t. angle is 1, i.e. the ADF
+is a probability density function.
+
+The second ADF value is reported as a cumulative sum of
+all bins up to the current bins, averaged
+over atoms of type *itypeN*\ . It represents the
+number of angles per central atom with angle less
+than or equal to the angle of the current bin,
+analogous to the coordination
+number radial distribution function.
+
+The *ordinate* optional keyword determines
+whether the bins are of uniform angular size from zero
+to 180 (\ *degree*\ ), zero to Pi (\ *radian*\ ), or the
+cosine of the angle uniform in the range [-1,1] (\ *cosine*\ ).
+*cosine* has the advantage of eliminating the *acos()* function
+call, which speeds up the compute by 2-3x, and it is also preferred
+on physical grounds, because the for uniformly distributed particles
+in 3D, the angular probability density w.r.t dtheta is
+sin(theta)/2, while for d(cos(theta)), it is 1/2,
+Regardless of which ordinate is chosen, the first column of ADF
+values is normalized w.r.t. the range of that ordinate, so that
+the integral is 1.
+
+The simplest way to output the results of the compute adf calculation
+to a file is to use the :doc:`fix ave/time <fix_ave_time>` command, for
+example:
+
+
+.. parsed-literal::
+
+   compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5
+   fix 1 all ave/time 100 1 100 c_myADF[\*] file tmp.adf mode vector
+
+**Output info:**
+
+This compute calculates a global array with the number of rows =
+*Nbins*\ , and the number of columns = 1 + 2\*Ntriples, where Ntriples is the
+number of I,J,K triples specified.  The first column has the bin
+coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has
+the two ADF values for a specific set of (\ *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN*\ )
+interactions, as described above.  These values can be used
+by any command that uses a global values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The array values calculated by this compute are all "intensive".
+
+The first column of array values is the angle-related ordinate, either
+the angle in degrees or radians, or the cosine of the angle.  Each
+subsequent pair of columns gives the first and second kinds of ADF
+for a specific set of (\ *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN*\ ). The values
+in the first ADF column are normalized numbers >= 0.0,
+whose integral w.r.t. the ordinate is 1,
+i.e. the first ADF is a normalized probability distribution.
+The values in the second ADF column are also numbers >= 0.0.
+They are the cumulative density distribution of angles per atom.
+By definition, this ADF is monotonically increasing from zero to
+a maximum value equal to the average total number of
+angles per atom satisfying the ADF criteria.
+
+Restrictions
+""""""""""""
+
+
+The ADF is not computed for neighbors outside the force cutoff,
+since processors (in parallel) don't know about atom coordinates for
+atoms further away than that distance.  If you want an ADF for larger
+distances, you can use the :doc:`rerun <rerun>` command to post-process
+a dump file and set the cutoff for the potential to be longer in the
+rerun script.  Note that in the rerun context, the force cutoff is
+arbitrary, since you aren't running dynamics and thus are not changing
+your model.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute rdf <compute_rdf>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`compute\_modify <compute_modify>`
+
+Default
+"""""""
+
+The keyword default is ordinate = degree.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst
new file mode 100644
index 0000000000..2b025ea217
--- /dev/null
+++ b/doc/src/compute_angle.rst
@@ -0,0 +1,62 @@
+.. index:: compute angle
+
+compute angle command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID angle
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* angle = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all angle
+
+Description
+"""""""""""
+
+Define a computation that extracts the angle energy calculated by each
+of the angle sub-styles used in the  "angle\_style
+hybrid" angle\_hybrid.html command.  These values are made accessible
+for output or further processing by other commands.  The group
+specified for this command is ignored.
+
+This compute is useful when using :doc:`angle\_style hybrid <angle_hybrid>` if you want to know the portion of the total
+energy contributed by one or more of the hybrid sub-styles.
+
+**Output info:**
+
+This compute calculates a global vector of length N where N is the
+number of sub\_styles defined by the :doc:`angle\_style hybrid <angle_style>` command, which can be accessed by indices
+1-N.  These values can be used by any command that uses global scalar
+or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector values are "extensive" and will be in energy
+:doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst
new file mode 100644
index 0000000000..3e93e90316
--- /dev/null
+++ b/doc/src/compute_angle_local.rst
@@ -0,0 +1,158 @@
+.. index:: compute angle/local
+
+compute angle/local command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID angle/local value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* angle/local = style name of this compute command
+* one or more values may be appended
+* value = *theta* or *eng* or *v\_name*
+  
+  .. parsed-literal::
+  
+       *theta* = tabulate angles
+       *eng* = tabulate angle energies
+       *v_name* = equal-style variable with name (see below)
+
+* zero or more keyword/args pairs may be appended
+* keyword = *set*
+  
+  .. parsed-literal::
+  
+       *set* args = theta name
+         theta = only currently allowed arg
+         name = name of variable to set with theta
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all angle/local theta
+   compute 1 all angle/local eng theta
+   compute 1 all angle/local theta v_cos set theta t
+
+Description
+"""""""""""
+
+Define a computation that calculates properties of individual angle
+interactions.  The number of datums generated, aggregated across all
+processors, equals the number of angles in the system, modified by the
+group parameter as explained below.
+
+The value *theta* is the angle for the 3 atoms in the interaction.
+
+The value *eng* is the interaction energy for the angle.
+
+The value *v\_name* can be used together with the *set* keyword to
+compute a user-specified function of the angle theta.  The *name*
+specified for the *v\_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
+variable which will store the angle theta.  This other variable must
+be an :doc:`internal-style variable <variable>` defined in the input
+script; its initial numeric value can be anything.  It must be an
+internal-style variable, because this command resets its value
+directly.  The *set* keyword is used to identify the name of this
+other variable associated with theta.
+
+Note that the value of theta for each angle which stored in the
+internal variable is in radians, not degrees.
+
+As an example, these commands can be added to the bench/in.rhodo
+script to compute the cosine and cosine\^2 of every angle in the system
+and output the statistics in various ways:
+
+
+.. parsed-literal::
+
+   variable t internal 0.0
+   variable cos equal cos(v_t)
+   variable cossq equal cos(v_t)\*cos(v_t)
+
+   compute 1 all property/local aatom1 aatom2 aatom3 atype
+   compute 2 all angle/local eng theta v_cos v_cossq set theta t
+   dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
+
+   compute 3 all reduce ave c_2**\***
+   thermo_style custom step temp press c_3**\***
+
+   fix 10 all ave/histo 10 10 100 -1 1 20 c_2\ **3** mode vector file tmp.histo
+
+The :doc:`dump local <dump>` command will output the energy, angle,
+cosine(angle), cosine\^2(angle) for every angle in the system.  The
+:doc:`thermo\_style <thermo_style>` command will print the average of
+those quantities via the :doc:`compute reduce <compute_reduce>` command
+with thermo output.  And the :doc:`fix ave/histo <fix_ave_histo>`
+command will histogram the cosine(angle) values and write them to a
+file.
+
+
+----------
+
+
+The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their angles.  An angle will only
+be included if all 3 atoms in the angle are in the specified compute
+group.  Any angles that have been broken (see the
+:doc:`angle\_style <angle_style>` command) by setting their angle type to
+0 are not included.  Angles that have been turned off (see the :doc:`fix shake <fix_shake>` or :doc:`delete\_bonds <delete_bonds>` commands) by
+setting their angle type negative are written into the file, but their
+energy will be 0.0.
+
+Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, angle output from the :doc:`compute property/local <compute_property_local>` command can be combined
+with data from this command and output by the :doc:`dump local <dump>`
+command in a consistent way.
+
+Here is an example of how to do this:
+
+
+.. parsed-literal::
+
+   compute 1 all property/local atype aatom1 aatom2 aatom3
+   compute 2 all angle/local theta eng
+   dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2]
+
+**Output info:**
+
+This compute calculates a local vector or local array depending on the
+number of values.  The length of the vector or number of rows in the
+array is the number of angles.  If a single value is specified, a
+local vector is produced.  If two or more values are specified, a
+local array is produced where the number of columns = the number of
+values.  The vector or array can be accessed by any command that uses
+local values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The output for *theta* will be in degrees.  The output for *eng* will
+be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst
new file mode 100644
index 0000000000..5da4adecac
--- /dev/null
+++ b/doc/src/compute_angmom_chunk.rst
@@ -0,0 +1,100 @@
+.. index:: compute angmom/chunk
+
+compute angmom/chunk command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID angmom/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* angmom/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid angmom/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the angular momentum of multiple
+chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates the 3 components of the angular momentum
+vector for each chunk, due to the velocity/momentum of the individual
+atoms in the chunk around the center-of-mass of the chunk.  The
+calculation includes all effects due to atoms passing through periodic
+boundaries.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+.. note::
+
+   The coordinates of an atom contribute to the chunk's angular
+   momentum in "unwrapped" form, by using the image flags associated with
+   each atom.  See the :doc:`dump custom <dump>` command for a discussion
+   of "unwrapped" coordinates.  See the Atoms section of the
+   :doc:`read\_data <read_data>` command for a discussion of image flags and
+   how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+The simplest way to output the results of the compute angmom/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all angmom/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+3 for the 3 xyz components of the angular momentum for each chunk.
+These values can be accessed by any command that uses global array
+values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The array values are "intensive".  The array values will be in
+mass-velocity-distance :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`variable angmom() function <variable>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst
new file mode 100644
index 0000000000..5c2cea3958
--- /dev/null
+++ b/doc/src/compute_basal_atom.rst
@@ -0,0 +1,90 @@
+.. index:: compute basal/atom
+
+compute basal/atom command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID basal/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* basal/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all basal/atom
+
+Description
+"""""""""""
+
+Defines a computation that calculates the hexagonal close-packed "c"
+lattice vector for each atom in the group.  It does this by
+calculating the normal unit vector to the basal plane for each atom.
+The results enable efficient identification and characterization of
+twins and grains in hexagonal close-packed structures.
+
+The output of the compute is thus the 3 components of a unit vector
+associated with each atom.  The components are set to 0.0 for
+atoms not in the group.
+
+Details of the calculation are given in :ref:`(Barrett) <Barrett>`.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each of
+which computes this quantity.
+
+An example input script that uses this compute is provided
+in examples/USER/misc/basal.
+
+**Output info:**
+
+This compute calculates a per-atom array with 3 columns, which can be
+accessed by indices 1-3 by any command that uses per-atom values from
+a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+The per-atom vector values are unitless since the 3 columns represent
+components of a unit vector.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The output of this compute will be meaningless unless the atoms are on
+(or near) hcp lattice sites, since the calculation assumes a
+well-defined basal plane.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute centro/atom <compute_centro_atom>`, :doc:`compute ackland/atom <compute_ackland_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Barrett:
+
+
+
+**(Barrett)** Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst
new file mode 100644
index 0000000000..eb431aafc2
--- /dev/null
+++ b/doc/src/compute_body_local.rst
@@ -0,0 +1,110 @@
+.. index:: compute body/local
+
+compute body/local command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID body/local input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* body/local = style name of this compute command
+* one or more keywords may be appended
+* keyword = *id* or *type* or *integer*
+  
+  .. parsed-literal::
+  
+       *id* = atom ID of the body particle
+       *type* = atom type of the body particle
+       *integer* = 1,2,3,etc = index of fields defined by body style
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all body/local type 1 2 3
+   compute 1 all body/local 3 6
+
+Description
+"""""""""""
+
+Define a computation that calculates properties of individual body
+sub-particles.  The number of datums generated, aggregated across all
+processors, equals the number of body sub-particles plus the number of
+non-body particles in the system, modified by the group parameter as
+explained below.  See the :doc:`Howto body <Howto_body>` doc page for
+more details on using body particles.
+
+The local data stored by this command is generated by looping over all
+the atoms.  An atom will only be included if it is in the group.  If
+the atom is a body particle, then its N sub-particles will be looped
+over, and it will contribute N datums to the count of datums.  If it
+is not a body particle, it will contribute 1 datum.
+
+For both body particles and non-body particles, the *id* keyword
+will store the ID of the particle.
+
+For both body particles and non-body particles, the *type* keyword
+will store the type of the particle.
+
+The *integer* keywords mean different things for body and non-body
+particles.  If the atom is not a body particle, only its *x*\ , *y*\ , *z*
+coordinates can be referenced, using the *integer* keywords 1,2,3.
+Note that this means that if you want to access more fields than this
+for body particles, then you cannot include non-body particles in the
+group.
+
+For a body particle, the *integer* keywords refer to fields calculated
+by the body style for each sub-particle.  The body style, as specified
+by the :doc:`atom\_style body <atom_style>`, determines how many fields
+exist and what they are.  See the :doc:`Howto\_body <Howto_body>` doc
+page for details of the different styles.
+
+Here is an example of how to output body information using the :doc:`dump local <dump>` command with this compute.  If fields 1,2,3 for the
+body sub-particles are x,y,z coordinates, then the dump file will be
+formatted similar to the output of a :doc:`dump atom or custom <dump>`
+command.
+
+
+.. parsed-literal::
+
+   compute 1 all body/local type 1 2 3
+   dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]
+
+**Output info:**
+
+This compute calculates a local vector or local array depending on the
+number of keywords.  The length of the vector or number of rows in the
+array is the number of datums as described above.  If a single keyword
+is specified, a local vector is produced.  If two or more keywords are
+specified, a local array is produced where the number of columns = the
+number of keywords.  The vector or array can be accessed by any
+command that uses local values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS
+output options.
+
+The :doc:`units <units>` for output values depend on the body style.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump local <dump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst
new file mode 100644
index 0000000000..74c1ccb262
--- /dev/null
+++ b/doc/src/compute_bond.rst
@@ -0,0 +1,62 @@
+.. index:: compute bond
+
+compute bond command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID bond
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* bond = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all bond
+
+Description
+"""""""""""
+
+Define a computation that extracts the bond energy calculated by each
+of the bond sub-styles used in the :doc:`bond\_style hybrid <bond_hybrid>` command.  These values are made accessible
+for output or further processing by other commands.  The group
+specified for this command is ignored.
+
+This compute is useful when using :doc:`bond\_style hybrid <bond_hybrid>`
+if you want to know the portion of the total energy contributed by one
+or more of the hybrid sub-styles.
+
+**Output info:**
+
+This compute calculates a global vector of length N where N is the
+number of sub\_styles defined by the :doc:`bond\_style hybrid <bond_style>` command, which can be accessed by indices 1-N.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector values are "extensive" and will be in energy
+:doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst
new file mode 100644
index 0000000000..1bca2ff439
--- /dev/null
+++ b/doc/src/compute_bond_local.rst
@@ -0,0 +1,214 @@
+.. index:: compute bond/local
+
+compute bond/local command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID bond/local value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* bond/local = style name of this compute command
+* one or more values may be appended
+* value = *dist* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v\_name*
+
+.. parsed-literal::
+
+     *dist* = bond distance
+     *engpot* = bond potential energy
+     *force* = bond force
+
+     *fx*\ ,\ *fy*\ ,\ *fz* = components of bond force
+     *engvib* = bond kinetic energy of vibration
+     *engrot* = bond kinetic energy of rotation
+     *engtrans* = bond kinetic energy of translation
+     *omega* = magnitude of bond angular velocity
+     *velvib* = vibrational velocity along the bond length
+     *v_name* = equal-style variable with name (see below)
+
+* zero or more keyword/args pairs may be appended
+* keyword = *set*
+
+.. parsed-literal::
+
+     *set* args = dist name
+       dist = only currently allowed arg
+       name = name of variable to set with distance (dist)
+
+
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all bond/local engpot
+   compute 1 all bond/local dist engpot force
+
+   compute 1 all bond/local dist fx fy fz
+
+   compute 1 all angle/local dist v_distsq set dist d
+
+Description
+"""""""""""
+
+Define a computation that calculates properties of individual bond
+interactions.  The number of datums generated, aggregated across all
+processors, equals the number of bonds in the system, modified by the
+group parameter as explained below.
+
+All these properties are computed for the pair of atoms in a bond,
+whether the 2 atoms represent a simple diatomic molecule, or are part
+of some larger molecule.
+
+The value *dist* is the current length of the bond.
+
+The value *engpot* is the potential energy for the bond,
+based on the current separation of the pair of atoms in the bond.
+
+The value *force* is the magnitude of the force acting between the
+pair of atoms in the bond.
+
+The values *fx*\ , *fy*\ , and *fz* are the xyz components of
+*force* between the pair of atoms in the bond.
+
+The remaining properties are all computed for motion of the two atoms
+relative to the center of mass (COM) velocity of the 2 atoms in the
+bond.
+
+The value *engvib* is the vibrational kinetic energy of the two atoms
+in the bond, which is simply 1/2 m1 v1\^2 + 1/2 m2 v2\^2, where v1 and
+v2 are the magnitude of the velocity of the 2 atoms along the bond
+direction, after the COM velocity has been subtracted from each.
+
+The value *engrot* is the rotational kinetic energy of the two atoms
+in the bond, which is simply 1/2 m1 v1\^2 + 1/2 m2 v2\^2, where v1 and
+v2 are the magnitude of the velocity of the 2 atoms perpendicular to
+the bond direction, after the COM velocity has been subtracted from
+each.
+
+The value *engtrans* is the translational kinetic energy associated
+with the motion of the COM of the system itself, namely 1/2 (m1+m2)
+Vcm\^2 where Vcm = magnitude of the velocity of the COM.
+
+Note that these 3 kinetic energy terms are simply a partitioning of
+the summed kinetic energy of the 2 atoms themselves.  I.e. total KE =
+1/2 m1 v1\^2 + 1/2 m2 v2\^2 = engvib + engrot + engtrans, where v1,v2
+are the magnitude of the velocities of the 2 atoms, without any
+adjustment for the COM velocity.
+
+The value *omega* is the magnitude of the angular velocity of the
+two atoms around their COM position.
+
+The value *velvib* is the magnitude of the relative velocity of the
+two atoms in the bond towards each other.  A negative value means the
+2 atoms are moving toward each other; a positive value means they are
+moving apart.
+
+The value *v\_name* can be used together with the *set* keyword to
+compute a user-specified function of the bond distance.  The *name*
+specified for the *v\_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
+variable which will store the bond distance.  This other variable must
+be an :doc:`internal-style variable <variable>` defined in the input
+script; its initial numeric value can be anything.  It must be an
+internal-style variable, because this command resets its value
+directly.  The *set* keyword is used to identify the name of this
+other variable associated with theta.
+
+As an example, these commands can be added to the bench/in.rhodo
+script to compute the distance\^2 of every bond in the system and
+output the statistics in various ways:
+
+
+.. parsed-literal::
+
+   variable d internal 0.0
+   variable dsq equal v_d\*v_d
+
+   compute 1 all property/local batom1 batom2 btype
+   compute 2 all bond/local engpot dist v_dsq set dist d
+   dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
+
+   compute 3 all reduce ave c_2**\***
+   thermo_style custom step temp press c_3**\***
+
+   fix 10 all ave/histo 10 10 100 0 6 20 c_2\ **3** mode vector file tmp.histo
+
+The :doc:`dump local <dump>` command will output the energy, distance,
+distance\^2 for every bond in the system.  The
+:doc:`thermo\_style <thermo_style>` command will print the average of
+those quantities via the :doc:`compute reduce <compute_reduce>` command
+with thermo output.  And the :doc:`fix ave/histo <fix_ave_histo>`
+command will histogram the distance\^2 values and write them to a file.
+
+
+----------
+
+
+The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their bonds.  A bond will only be
+included if both atoms in the bond are in the specified compute group.
+Any bonds that have been broken (see the :doc:`bond\_style <bond_style>`
+command) by setting their bond type to 0 are not included.  Bonds that
+have been turned off (see the :doc:`fix shake <fix_shake>` or
+:doc:`delete\_bonds <delete_bonds>` commands) by setting their bond type
+negative are written into the file, but their energy will be 0.0.
+
+Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, bond output from the :doc:`compute property/local <compute_property_local>` command can be combined
+with data from this command and output by the :doc:`dump local <dump>`
+command in a consistent way.
+
+Here is an example of how to do this:
+
+
+.. parsed-literal::
+
+   compute 1 all property/local btype batom1 batom2
+   compute 2 all bond/local dist engpot
+   dump 1 all local 1000 tmp.dump index c_1[\*] c_2[\*]
+
+**Output info:**
+
+This compute calculates a local vector or local array depending on the
+number of values.  The length of the vector or number of rows in the
+array is the number of bonds.  If a single value is specified, a local
+vector is produced.  If two or more values are specified, a local
+array is produced where the number of columns = the number of values.
+The vector or array can be accessed by any command that uses local
+values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The output for *dist* will be in distance :doc:`units <units>`. The
+output for *velvib* will be in velocity :doc:`units <units>`. The output
+for *omega* will be in velocity/distance :doc:`units <units>`. The
+output for *engtrans*\ , *engvib*\ , *engrot*\ , and *engpot* will be in
+energy :doc:`units <units>`. The output for *force* will be in force
+:doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_centro_atom.rst b/doc/src/compute_centro_atom.rst
new file mode 100644
index 0000000000..48a9ddd03c
--- /dev/null
+++ b/doc/src/compute_centro_atom.rst
@@ -0,0 +1,180 @@
+.. index:: compute centro/atom
+
+compute centro/atom command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID centro/atom lattice keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+  centro/atom = style name of this compute command
+  lattice = *fcc* or *bcc* or N = # of neighbors per atom to include
+* zero or more keyword/value pairs may be appended
+* keyword = *axes*
+
+.. parsed-literal::
+
+     *axes* value = *no* or *yes*
+       *no* = do not calculate 3 symmetry axes
+       *yes* = calculate 3 symmetry axes
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all centro/atom fcc
+
+   compute 1 all centro/atom 8
+
+Description
+"""""""""""
+
+Define a computation that calculates the centro-symmetry parameter for
+each atom in the group, for either FCC or BCC lattices, depending on
+the choice of the *lattice* argument.  In solid-state systems the
+centro-symmetry parameter is a useful measure of the local lattice
+disorder around an atom and can be used to characterize whether the
+atom is part of a perfect lattice, a local defect (e.g. a dislocation
+or stacking fault), or at a surface.
+
+The value of the centro-symmetry parameter will be 0.0 for atoms not
+in the specified compute group.
+
+This parameter is computed using the following formula from
+:ref:`(Kelchner) <Kelchner>`
+
+.. image:: Eqs/centro_symmetry.jpg
+   :align: center
+
+where the *N* nearest neighbors of each atom are identified and Ri and
+Ri+N/2 are vectors from the central atom to a particular pair of
+nearest neighbors.  There are N\*(N-1)/2 possible neighbor pairs that
+can contribute to this formula.  The quantity in the sum is computed
+for each, and the N/2 smallest are used.  This will typically be for
+pairs of atoms in symmetrically opposite positions with respect to the
+central atom; hence the i+N/2 notation.
+
+*N* is an input parameter, which should be set to correspond to the
+number of nearest neighbors in the underlying lattice of atoms.  If
+the keyword *fcc* or *bcc* is used, *N* is set to 12 and 8
+respectively.  More generally, *N* can be set to a positive, even
+integer.
+
+For an atom on a lattice site, surrounded by atoms on a perfect
+lattice, the centro-symmetry parameter will be 0.  It will be near 0
+for small thermal perturbations of a perfect lattice.  If a point
+defect exists, the symmetry is broken, and the parameter will be a
+larger positive value.  An atom at a surface will have a large
+positive parameter.  If the atom does not have *N* neighbors (within
+the potential cutoff), then its centro-symmetry parameter is set to
+0.0.
+
+If the keyword *axes* has the setting *yes*\ , then this compute also
+estimates three symmetry axes for each atom's local neighborhood.  The
+first two of these are the vectors joining the two pairs of neighbor
+atoms with smallest contributions to the centrosymmetry parameter,
+i.e. the two most symmetric pairs of atoms.  The third vector is
+normal to the first two by the right-hand rule.  All three vectors are
+normalized to unit length.  For FCC crystals, the first two vectors
+will lie along a <110> direction, while the third vector will lie
+along either a <100> or <111> direction.  For HCP crystals, the first
+two vectors will lie along <1000> directions, while the third vector
+will lie along <0001>.  This provides a simple way to measure local
+orientation in HCP structures.  In general, the *axes* keyword can be
+used to estimate the orientation of symmetry axes in the neighborhood
+of any atom.
+
+Only atoms within the cutoff of the pairwise neighbor list are
+considered as possible neighbors.  Atoms not in the compute group are
+included in the *N* neighbors used in this calculation.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+*centro/atom* style.
+
+**Output info:**
+
+By default, this compute calculates the centrosymmetry value for each
+atom as a per-atom vector, which can be accessed by any command that
+uses per-atom values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+If the *axes* keyword setting is *yes*\ , then a per-atom array is
+calculated. The first column is the centrosymmetry parameter.  The
+next three columns are the x, y, and z components of the first
+symmetry axis, followed by the second, and third symmetry axes in
+columns 5-7 and 8-10.
+
+The centrosymmetry values are unitless values >= 0.0.  Their magnitude
+depends on the lattice style due to the number of contributing neighbor
+pairs in the summation in the formula above.  And it depends on the
+local defects surrounding the central atom, as described above.  For
+the *axes yes* case, the vector components are also unitless, since
+they represent spatial directions.
+
+Here are typical centro-symmetry values, from a nanoindentation
+simulation into gold (FCC).  These were provided by Jon Zimmerman
+(Sandia):
+
+
+.. parsed-literal::
+
+   Bulk lattice = 0
+   Dislocation core ~ 1.0 (0.5 to 1.25)
+   Stacking faults ~ 5.0 (4.0 to 6.0)
+   Free surface ~ 23.0
+
+These values are \*not\* normalized by the square of the lattice
+parameter.  If they were, normalized values would be:
+
+
+.. parsed-literal::
+
+   Bulk lattice = 0
+   Dislocation core ~ 0.06 (0.03 to 0.075)
+   Stacking faults ~ 0.3 (0.24 to 0.36)
+   Free surface ~ 1.38
+
+For BCC materials, the values for dislocation cores and free surfaces
+would be somewhat different, due to their being only 8 neighbors instead
+of 12.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute cna/atom <compute_cna_atom>`
+
+Default
+"""""""
+
+The default value for the optional keyword is axes = no.
+
+
+----------
+
+
+.. _Kelchner:
+
+
+
+**(Kelchner)** Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst
new file mode 100644
index 0000000000..4cead81df8
--- /dev/null
+++ b/doc/src/compute_chunk_atom.rst
@@ -0,0 +1,707 @@
+.. index:: compute chunk/atom
+
+compute chunk/atom command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID chunk/atom style args keyword values ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* chunk/atom = style name of this compute command
+  
+  .. parsed-literal::
+  
+     style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *type* or *molecule* or c_ID, c_ID[I], f_ID, f_ID[I], v_name
+       *bin/1d* args = dim origin delta
+         dim = *x* or *y* or *z*
+         origin = *lower* or *center* or *upper* or coordinate value (distance units)
+         delta = thickness of spatial bins in dim (distance units)
+       *bin/2d* args = dim origin delta dim origin delta
+         dim = *x* or *y* or *z*
+         origin = *lower* or *center* or *upper* or coordinate value (distance units)
+         delta = thickness of spatial bins in dim (distance units)
+       *bin/3d* args = dim origin delta dim origin delta dim origin delta
+         dim = *x* or *y* or *z*
+         origin = *lower* or *center* or *upper* or coordinate value (distance units)
+         delta = thickness of spatial bins in dim (distance units)
+       *bin/sphere* args = xorig yorig zorig rmin rmax nsbin
+         xorig,yorig,zorig = center point of sphere
+         srmin,srmax = bin from sphere radius rmin to rmax
+         nsbin = # of spherical shell bins between rmin and rmax
+       *bin/cylinder* args = dim origin delta c1 c2 rmin rmax ncbin
+         dim = *x* or *y* or *z* = axis of cylinder axis
+         origin = *lower* or *center* or *upper* or coordinate value (distance units)
+         delta = thickness of spatial bins in dim (distance units)
+         c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
+         crmin,crmax = bin from cylinder radius rmin to rmax (distance units)
+         ncbin = # of concentric circle bins between rmin and rmax
+       *type* args = none
+       *molecule* args = none
+       c_ID, c_ID[I], f_ID, f_ID[I], v_name args = none
+         c_ID = per-atom vector calculated by a compute with ID
+         c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+         f_ID = per-atom vector calculated by a fix with ID
+         f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+         v_name = per-atom vector calculated by an atom-style variable with name
+
+* zero or more keyword/values pairs may be appended
+* keyword = *region* or *nchunk* or *static* or *compress* or *bound* or *discard* or *pbc* or *units*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region atoms must be in to be part of a chunk
+       *nchunk* value = *once* or *every*
+         once = only compute the number of chunks once
+         every = re-compute the number of chunks whenever invoked
+       *limit* values = 0 or Nc max or Nc exact
+         0 = no limit on the number of chunks
+         Nc max = limit number of chunks to be <= Nc
+         Nc exact = set number of chunks to exactly Nc
+       *ids* value = *once* or *nfreq* or *every*
+         once = assign chunk IDs to atoms only once, they persist thereafter
+         nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by :doc:`fix ave/chunk <fix_ave_chunk>` which sets Nfreq)
+         every = assign chunk IDs to atoms whenever invoked
+       *compress* value = *yes* or *no*
+         yes = compress chunk IDs to eliminate IDs with no atoms
+         no = do not compress chunk IDs even if some IDs have no atoms
+       *discard* value = *yes* or *no* or *mixed*
+         yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
+         no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
+         mixed = keep or discard such atoms according to spatial binning rule
+       *bound* values = x/y/z lo hi
+         x/y/z = *x* or *y* or *z* to bound sptial bins in this dimension
+         lo = *lower* or coordinate value (distance units)
+         hi = *upper* or coordinate value (distance units)
+       *pbc* value = *no* or *yes*
+         yes = use periodic distance for bin/sphere and bin/cylinder styles
+       *units* value = *box* or *lattice* or *reduced*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all chunk/atom type
+   compute 1 all chunk/atom bin/1d z lower 0.02 units reduced
+   compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5
+   compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes
+   compute 1 all chunk/atom bin/sphere 5 5 5 2.0 5.0 5 discard yes
+   compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes
+   compute 1 all chunk/atom c_cluster
+
+Description
+"""""""""""
+
+Define a computation that calculates an integer chunk ID from 1 to
+Nchunk for each atom in the group.  Values of chunk IDs are determined
+by the *style* of chunk, which can be based on atom type or molecule
+ID or spatial binning or a per-atom property or value calculated by
+another :doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`atom-style variable <variable>`.  Per-atom chunk IDs can be used by other
+computes with "chunk" in their style name, such as :doc:`compute com/chunk <compute_com_chunk>` or :doc:`compute msd/chunk <compute_msd_chunk>`.  Or they can be used by the :doc:`fix ave/chunk <fix_ave_chunk>` command to sum and time average a
+variety of per-atom properties over the atoms in each chunk.  Or they
+can simply be accessed by any command that uses per-atom values from a
+compute as input, as discussed on the :doc:`Howto output <Howto_output>`
+doc page.
+
+See the :doc:`Howto chunk <Howto_chunk>` doc page for an overview of how
+this compute can be used with a variety of other commands to tabulate
+properties of a simulation.  The page gives several examples of input
+script commands that can be used to calculate interesting properties.
+
+Conceptually it is important to realize that this compute does two
+simple things.  First, it sets the value of *Nchunk* = the number of
+chunks, which can be a constant value or change over time.  Second, it
+assigns each atom to a chunk via a chunk ID.  Chunk IDs range from 1
+to *Nchunk* inclusive; some chunks may have no atoms assigned to them.
+Atoms that do not belong to any chunk are assigned a value of 0.  Note
+that the two operations are not always performed together.  For
+example, spatial bins can be setup once (which sets *Nchunk*\ ), and
+atoms assigned to those bins many times thereafter (setting their
+chunk IDs).
+
+All other commands in LAMMPS that use chunk IDs assume there are
+*Nchunk* number of chunks, and that every atom is assigned to one of
+those chunks, or not assigned to any chunk.
+
+There are many options for specifying for how and when *Nchunk* is
+calculated, and how and when chunk IDs are assigned to atoms.  The
+details depend on the chunk *style* and its *args*\ , as well as
+optional keyword settings.  They can also depend on whether a :doc:`fix ave/chunk <fix_ave_chunk>` command is using this compute, since
+that command requires *Nchunk* to remain static across windows of
+timesteps it specifies, while it accumulates per-chunk averages.
+
+The details are described below.
+
+
+----------
+
+
+The different chunk styles operate as follows.  For each style, how it
+calculates *Nchunk* and assigns chunk IDs to atoms is explained.  Note
+that using the optional keywords can change both of those actions, as
+described further below where the keywords are discussed.
+
+
+----------
+
+
+The *binning* styles perform a spatial binning of atoms, and assign an
+atom the chunk ID corresponding to the bin number it is in.  *Nchunk*
+is set to the number of bins, which can change if the simulation box
+size changes.  This also depends on the setting of the *units*
+keyword; e.g. for *reduced* units the number of chunks may not change
+even if the box size does.
+
+The *bin/1d*\ , *bin/2d*\ , and *bin/3d* styles define bins as 1d layers
+(slabs), 2d pencils, or 3d boxes.  The *dim*\ , *origin*\ , and *delta*
+settings are specified 1, 2, or 3 times.  For 2d or 3d bins, there is
+no restriction on specifying dim = x before dim = y or z, or dim = y
+before dim = z.  Bins in a particular *dim* have a bin size in that
+dimension given by *delta*\ .  In each dimension, bins are defined
+relative to a specified *origin*\ , which may be the lower/upper edge of
+the simulation box (in that dimension), or its center point, or a
+specified coordinate value.  Starting at the origin, sufficient bins
+are created in both directions to completely span the simulation box
+or the bounds specified by the optional *bounds* keyword.
+
+For orthogonal simulation boxes, the bins are layers, pencils, or
+boxes aligned with the xyz coordinate axes.  For triclinic
+(non-orthogonal) simulation boxes, the bin faces are parallel to the
+tilted faces of the simulation box.  See the :doc:`Howto triclinic <Howto_triclinic>` doc page for a discussion of the
+geometry of triclinic boxes in LAMMPS.  As described there, a tilted
+simulation box has edge vectors a,b,c.  In that nomenclature, bins in
+the x dimension have faces with normals in the "b" cross "c"
+direction.  Bins in y have faces normal to the "a" cross "c"
+direction.  And bins in z have faces normal to the "a" cross "b"
+direction.  Note that in order to define the size and position of
+these bins in an unambiguous fashion, the *units* option must be set
+to *reduced* when using a triclinic simulation box, as noted below.
+
+The meaning of *origin* and *delta* for triclinic boxes is as follows.
+Consider a triclinic box with bins that are 1d layers or slabs in the
+x dimension.  No matter how the box is tilted, an *origin* of 0.0
+means start layers at the lower "b" cross "c" plane of the simulation
+box and an *origin* of 1.0 means to start layers at the upper "b"
+cross "c" face of the box.  A *delta* value of 0.1 in *reduced* units
+means there will be 10 layers from 0.0 to 1.0, regardless of the
+current size or shape of the simulation box.
+
+The *bin/sphere* style defines a set of spherical shell bins around
+the origin (\ *xorig*\ ,\ *yorig*\ ,\ *zorig*\ ), using *nsbin* bins with radii
+equally spaced between *srmin* and *srmax*\ .  This is effectively a 1d
+vector of bins.  For example, if *srmin* = 1.0 and *srmax* = 10.0 and
+*nsbin* = 9, then the first bin spans 1.0 < r < 2.0, and the last bin
+spans 9.0 < r 10.0.  The geometry of the bins is the same whether the
+simulation box is orthogonal or triclinic; i.e. the spherical shells
+are not tilted or scaled differently in different dimensions to
+transform them into ellipsoidal shells.
+
+The *bin/cylinder* style defines bins for a cylinder oriented along
+the axis *dim* with the axis coordinates in the other two radial
+dimensions at (\ *c1*\ ,\ *c2*\ ).  For dim = x, c1/c2 = y/z; for dim = y,
+c1/c2 = x/z; for dim = z, c1/c2 = x/y.  This is effectively a 2d array
+of bins.  The first dimension is along the cylinder axis, the second
+dimension is radially outward from the cylinder axis.  The bin size
+and positions along the cylinder axis are specified by the *origin*
+and *delta* values, the same as for the *bin/1d*\ , *bin/2d*\ , and
+*bin/3d* styles.  There are *ncbin* concentric circle bins in the
+radial direction from the cylinder axis with radii equally spaced
+between *crmin* and *crmax*\ .  For example, if *crmin* = 1.0 and
+*crmax* = 10.0 and *ncbin* = 9, then the first bin spans 1.0 < r <
+2.0, and the last bin spans 9.0 < r 10.0.  The geometry of the bins in
+the radial dimensions is the same whether the simulation box is
+orthogonal or triclinic; i.e. the concentric circles are not tilted or
+scaled differently in the two different dimensions to transform them
+into ellipses.
+
+The created bins (and hence the chunk IDs) are numbered consecutively
+from 1 to the number of bins = *Nchunk*\ .  For *bin2d* and *bin3d*\ , the
+numbering varies most rapidly in the first dimension (which could be
+x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
+3rd dimension.  For *bin/sphere*\ , the bin with smallest radii is chunk
+1 and the bni with largest radii is chunk Nchunk = *ncbin*\ .  For
+*bin/cylinder*\ , the numbering varies most rapidly in the dimension
+along the cylinder axis and most slowly in the radial direction.
+
+Each time this compute is invoked, each atom is mapped to a bin based
+on its current position.  Note that between reneighboring timesteps,
+atoms can move outside the current simulation box.  If the box is
+periodic (in that dimension) the atom is remapping into the periodic
+box for purposes of binning.  If the box in not periodic, the atom may
+have moved outside the bounds of all bins.  If an atom is not inside
+any bin, the *discard* keyword is used to determine how a chunk ID is
+assigned to the atom.
+
+
+----------
+
+
+The *type* style uses the atom type as the chunk ID.  *Nchunk* is set
+to the number of atom types defined for the simulation, e.g. via the
+:doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` commands.
+
+
+----------
+
+
+The *molecule* style uses the molecule ID of each atom as its chunk
+ID.  *Nchunk* is set to the largest chunk ID.  Note that this excludes
+molecule IDs for atoms which are not in the specified group or
+optional region.
+
+There is no requirement that all atoms in a particular molecule are
+assigned the same chunk ID (zero or non-zero), though you probably
+want that to be the case, if you wish to compute a per-molecule
+property.  LAMMPS will issue a warning if that is not the case, but
+only the first time that *Nchunk* is calculated.
+
+Note that atoms with a molecule ID = 0, which may be non-molecular
+solvent atoms, have an out-of-range chunk ID.  These atoms are
+discarded (not assigned to any chunk) or assigned to *Nchunk*\ ,
+depending on the value of the *discard* keyword.
+
+
+----------
+
+
+The *compute/fix/variable* styles set the chunk ID of each atom based
+on a quantity calculated and stored by a compute, fix, or variable.
+In each case, it must be a per-atom quantity.  In each case the
+referenced floating point values are converted to an integer chunk ID
+as follows.  The floating point value is truncated (rounded down) to
+an integer value.  If the integer value is <= 0, then a chunk ID of 0
+is assigned to the atom.  If the integer value is > 0, it becomes the
+chunk ID to the atom.  *Nchunk* is set to the largest chunk ID.  Note
+that this excludes atoms which are not in the specified group or
+optional region.
+
+If the style begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  If no bracketed integer is
+appended, the per-atom vector calculated by the compute is used.  If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the compute is used.  Users can also write code for
+their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+
+If the style begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  If no bracketed integer is
+appended, the per-atom vector calculated by the fix is used.  If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used.  Note that some fixes only produce
+their values on certain timesteps, which must be compatible with the
+timestep on which this compute accesses the fix, else an error
+results.  Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "v\_", a variable name for an *atom* or
+*atomfile* style :doc:`variable <variable>` must follow which has been
+previously defined in the input script.  Variables of style *atom* can
+reference thermodynamic keywords and various per-atom attributes, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of generating per-atom quantities to
+treat as a chunk ID.
+
+
+----------
+
+
+Normally, *Nchunk* = the number of chunks, is re-calculated every time
+this fix is invoked, though the value may or may not change.  As
+explained below, the *nchunk* keyword can be set to *once* which means
+*Nchunk* will never change.
+
+If a :doc:`fix ave/chunk <fix_ave_chunk>` command uses this compute, it
+can also turn off the re-calculation of *Nchunk* for one or more
+windows of timesteps.  The extent of the windows, during which Nchunk
+is held constant, are determined by the *Nevery*\ , *Nrepeat*\ , *Nfreq*
+values and the *ave* keyword setting that are used by the :doc:`fix ave/chunk <fix_ave_chunk>` command.
+
+Specifically, if *ave* = *one*\ , then for each span of *Nfreq*
+timesteps, *Nchunk* is held constant between the first timestep when
+averaging is done (within the Nfreq-length window), and the last
+timestep when averaging is done (multiple of Nfreq).  If *ave* =
+*running* or *window*\ , then *Nchunk* is held constant forever,
+starting on the first timestep when the :doc:`fix ave/chunk <fix_ave_chunk>` command invokes this compute.
+
+Note that multiple :doc:`fix ave/chunk <fix_ave_chunk>` commands can use
+the same compute chunk/atom compute.  However, the time windows they
+induce for holding *Nchunk* constant must be identical, else an error
+will be generated.
+
+
+----------
+
+
+The various optional keywords operate as follows.  Note that some of
+them function differently or are ignored by different chunk styles.
+Some of them also have different default values, depending on
+the chunk style, as listed below.
+
+The *region* keyword applies to all chunk styles.  If used, an atom
+must be in both the specified group and the specified geometric
+:doc:`region <region>` to be assigned to a chunk.
+
+
+----------
+
+
+The *nchunk* keyword applies to all chunk styles.  It specifies how
+often *Nchunk* is recalculated, which in turn can affect the chunk IDs
+assigned to individual atoms.
+
+If *nchunk* is set to *once*\ , then *Nchunk* is only calculated once,
+the first time this compute is invoked.  If *nchunk* is set to
+*every*\ , then *Nchunk* is re-calculated every time the compute is
+invoked.  Note that, as described above, the use of this compute
+by the :doc:`fix ave/chunk <fix_ave_chunk>` command can override
+the *every* setting.
+
+The default values for *nchunk* are listed below and depend on the
+chunk style and other system and keyword settings.  They attempt to
+represent typical use cases for the various chunk styles.  The
+*nchunk* value can always be set explicitly if desired.
+
+
+----------
+
+
+The *limit* keyword can be used to limit the calculated value of
+*Nchunk* = the number of chunks.  The limit is applied each time
+*Nchunk* is calculated, which also limits the chunk IDs assigned to
+any atom.  The *limit* keyword is used by all chunk styles except the
+*binning* styles, which ignore it.  This is because the number of bins
+can be tailored using the *bound* keyword (described below) which
+effectively limits the size of *Nchunk*\ .
+
+If *limit* is set to *Nc* = 0, then no limit is imposed on *Nchunk*\ ,
+though the *compress* keyword can still be used to reduce *Nchunk*\ , as
+described below.
+
+If *Nc* > 0, then the effect of the *limit* keyword depends on whether
+the *compress* keyword is also used with a setting of *yes*\ , and
+whether the *compress* keyword is specified before the *limit* keyword
+or after.
+
+In all cases, *Nchunk* is first calculated in the usual way for each
+chunk style, as described above.
+
+First, here is what occurs if *compress yes* is not set.  If *limit*
+is set to *Nc max*\ , then *Nchunk* is reset to the smaller of *Nchunk*
+and *Nc*\ .  If *limit* is set to *Nc exact*\ , then *Nchunk* is reset to
+*Nc*\ , whether the original *Nchunk* was larger or smaller than *Nc*\ .
+If *Nchunk* shrank due to the *limit* setting, then atom chunk IDs >
+*Nchunk* will be reset to 0 or *Nchunk*\ , depending on the setting of
+the *discard* keyword.  If *Nchunk* grew, there will simply be some
+chunks with no atoms assigned to them.
+
+If *compress yes* is set, and the *compress* keyword comes before the
+*limit* keyword, the compression operation is performed first, as
+described below, which resets *Nchunk*\ .  The *limit* keyword is then
+applied to the new *Nchunk* value, exactly as described in the
+preceding paragraph.  Note that in this case, all atoms will end up
+with chunk IDs <= *Nc*\ , but their original values (e.g. molecule ID or
+compute/fix/variable) may have been > *Nc*\ , because of the compression
+operation.
+
+If *compress yes* is set, and the *compress* keyword comes after the
+*limit* keyword, then the *limit* value of *Nc* is applied first to
+the uncompressed value of *Nchunk*\ , but only if *Nc* < *Nchunk*
+(whether *Nc max* or *Nc exact* is used).  This effectively means all
+atoms with chunk IDs > *Nc* have their chunk IDs reset to 0 or *Nc*\ ,
+depending on the setting of the *discard* keyword.  The compression
+operation is then performed, which may shrink *Nchunk* further.  If
+the new *Nchunk* < *Nc* and *limit* = *Nc exact* is specified, then
+*Nchunk* is reset to *Nc*\ , which results in extra chunks with no atoms
+assigned to them.  Note that in this case, all atoms will end up with
+chunk IDs <= *Nc*\ , and their original values (e.g. molecule ID or
+compute/fix/variable value) will also have been <= *Nc*\ .
+
+
+----------
+
+
+The *ids* keyword applies to all chunk styles.  If the setting is
+*once* then the chunk IDs assigned to atoms the first time this
+compute is invoked will be permanent, and never be re-computed.
+
+If the setting is *nfreq* and if a :doc:`fix ave/chunk <fix_ave_chunk>`
+command is using this compute, then in each of the *Nchunk* = constant
+time windows (discussed above), the chunk ID's assigned to atoms on
+the first step of the time window will persist until the end of the
+time window.
+
+If the setting is *every*\ , which is the default, then chunk IDs are
+re-calculated on any timestep this compute is invoked.
+
+.. note::
+
+   If you want the persistent chunk-IDs calculated by this compute
+   to be continuous when running from a :doc:`restart file <read_restart>`,
+   then you should use the same ID for this compute, as in the original
+   run.  This is so that the fix this compute creates to store per-atom
+   quantities will also have the same ID, and thus be initialized
+   correctly with chunk IDs from the restart file.
+
+
+----------
+
+
+The *compress* keyword applies to all chunk styles and affects how
+*Nchunk* is calculated, which in turn affects the chunk IDs assigned
+to each atom.  It is useful for converting a "sparse" set of chunk IDs
+(with many IDs that have no atoms assigned to them), into a "dense"
+set of IDs, where every chunk has one or more atoms assigned to it.
+
+Two possible use cases are as follows.  If a large simulation box is
+mostly empty space, then the *binning* style may produce many bins
+with no atoms.  If *compress* is set to *yes*\ , only bins with atoms
+will be contribute to *Nchunk*\ .  Likewise, the *molecule* or
+*compute/fix/variable* styles may produce large *Nchunk* values.  For
+example, the :doc:`compute cluster/atom <compute_cluster_atom>` command
+assigns every atom an atom ID for one of the atoms it is clustered
+with.  For a million-atom system with 5 clusters, there would only be
+5 unique chunk IDs, but the largest chunk ID might be 1 million,
+resulting in *Nchunk* = 1 million.  If *compress* is set to *yes*\ ,
+*Nchunk* will be reset to 5.
+
+If *compress* is set to *no*\ , which is the default, no compression is
+done.  If it is set to *yes*\ , all chunk IDs with no atoms are removed
+from the list of chunk IDs, and the list is sorted.  The remaining
+chunk IDs are renumbered from 1 to *Nchunk* where *Nchunk* is the new
+length of the list.  The chunk IDs assigned to each atom reflect
+the new renumbering from 1 to *Nchunk*\ .
+
+The original chunk IDs (before renumbering) can be accessed by the
+:doc:`compute property/chunk <compute_property_chunk>` command and its
+*id* keyword, or by the :doc:`fix ave/chunk <fix_ave_chunk>` command
+which outputs the original IDs as one of the columns in its global
+output array.  For example, using the "compute cluster/atom" command
+discussed above, the original 5 unique chunk IDs might be atom IDs
+(27,4982,58374,857838,1000000).  After compression, these will be
+renumbered to (1,2,3,4,5).  The original values (27,...,1000000) can
+be output to a file by the :doc:`fix ave/chunk <fix_ave_chunk>` command,
+or by using the :doc:`fix ave/time <fix_ave_time>` command in
+conjunction with the :doc:`compute property/chunk <compute_property_chunk>` command.
+
+.. note::
+
+   The compression operation requires global communication across
+   all processors to share their chunk ID values.  It can require large
+   memory on every processor to store them, even after they are
+   compressed, if there are a large number of unique chunk IDs with
+   atoms assigned to them.  It uses a STL map to find unique chunk IDs
+   and store them in sorted order.  Each time an atom is assigned a
+   compressed chunk ID, it must access the STL map.  All of this means
+   that compression can be expensive, both in memory and CPU time.  The
+   use of the *limit* keyword in conjunction with the *compress* keyword
+   can affect these costs, depending on which keyword is used first.  So
+   use this option with care.
+
+
+----------
+
+
+The *discard* keyword applies to all chunk styles.  It affects what
+chunk IDs are assigned to atoms that do not match one of the valid
+chunk IDs from 1 to *Nchunk*\ .  Note that it does not apply to atoms
+that are not in the specified group or optionally specified region.
+Those atoms are always assigned a chunk ID = 0.
+
+If the calculated chunk ID for an atom is not within the range 1 to
+*Nchunk* then it is a "discard" atom.  Note that *Nchunk* may have
+been shrunk by the *limit* keyword.  Or the *compress* keyword may
+have eliminated chunk IDs that were valid before the compression took
+place, and are now not in the compressed list.  Also note that for the
+*molecule* chunk style, if new molecules are added to the system,
+their chunk IDs may exceed a previously calculated *Nchunk*\ .
+Likewise, evaluation of a compute/fix/variable on a later timestep may
+return chunk IDs that are invalid for the previously calculated
+*Nchunk*\ .
+
+All the chunk styles except the *binning* styles, must use *discard*
+set to either *yes* or *no*\ .  If *discard* is set to *yes*\ , which is
+the default, then every "discard" atom has its chunk ID set to 0.  If
+*discard* is set to *no*\ , every "discard" atom has its chunk ID set to
+*Nchunk*\ .  I.e. it becomes part of the last chunk.
+
+The *binning* styles use the *discard* keyword to decide whether to
+discard atoms outside the spatial domain covered by bins, or to assign
+them to the bin they are nearest to.
+
+For the *bin/1d*\ , *bin/2d*\ , *bin/3d* styles the details are as
+follows.  If *discard* is set to *yes*\ , an out-of-domain atom will
+have its chunk ID set to 0.  If *discard* is set to *no*\ , the atom
+will have its chunk ID set to the first or last bin in that dimension.
+If *discard* is set to *mixed*\ , which is the default, it will only
+have its chunk ID set to the first or last bin if bins extend to the
+simulation box boundary in that dimension.  This is the case if the
+*bound* keyword settings are *lower* and *upper*\ , which is the
+default.  If the *bound* keyword settings are numeric values, then the
+atom will have its chunk ID set to 0 if it is outside the bounds of
+any bin.  Note that in this case, it is possible that the first or
+last bin extends beyond the numeric *bounds* settings, depending on
+the specified *origin*\ .  If this is the case, the chunk ID of the atom
+is only set to 0 if it is outside the first or last bin, not if it is
+simply outside the numeric *bounds* setting.
+
+For the *bin/sphere* style the details are as follows.  If *discard*
+is set to *yes*\ , an out-of-domain atom will have its chunk ID set to
+0.  If *discard* is set to *no* or *mixed*\ , the atom will have its
+chunk ID set to the first or last bin, i.e. the innermost or outermost
+spherical shell.  If the distance of the atom from the origin is less
+than *rmin*\ , it will be assigned to the first bin.  If the distance of
+the atom from the origin is greater than *rmax*\ , it will be assigned
+to the last bin.
+
+For the *bin/cylinder* style the details are as follows.  If *discard*
+is set to *yes*\ , an out-of-domain atom will have its chunk ID set to
+0.  If *discard* is set to *no*\ , the atom will have its chunk ID set
+to the first or last bin in both the radial and axis dimensions.  If
+*discard* is set to *mixed*\ , which is the default, the radial
+dimension is treated the same as for *discard* = no.  But for the axis
+dimension, it will only have its chunk ID set to the first or last
+bin if bins extend to the simulation box boundary in the axis
+dimension.  This is the case if the *bound* keyword settings are
+*lower* and *upper*\ , which is the default.  If the *bound* keyword
+settings are numeric values, then the atom will have its chunk ID set
+to 0 if it is outside the bounds of any bin.  Note that in this case,
+it is possible that the first or last bin extends beyond the numeric
+*bounds* settings, depending on the specified *origin*\ .  If this is
+the case, the chunk ID of the atom is only set to 0 if it is outside
+the first or last bin, not if it is simply outside the numeric
+*bounds* setting.
+
+If *discard* is set to *no* or *mixed*\ , the atom will have its
+chunk ID set to the first or last bin, i.e. the innermost or outermost
+spherical shell.  If the distance of the atom from the origin is less
+than *rmin*\ , it will be assigned to the first bin.  If the distance of
+the atom from the origin is greater than *rmax*\ , it will be assigned
+to the last bin.
+
+
+----------
+
+
+The *bound* keyword only applies to the *bin/1d*\ , *bin/2d*\ , *bin/3d*
+styles and to the axis dimension of the *bin/cylinder* style;
+otherwise it is ignored.  It can be used one or more times to limit
+the extent of bin coverage in a specified dimension, i.e. to only bin
+a portion of the box.  If the *lo* setting is *lower* or the *hi*
+setting is *upper*\ , the bin extent in that direction extends to the
+box boundary.  If a numeric value is used for *lo* and/or *hi*\ , then
+the bin extent in the *lo* or *hi* direction extends only to that
+value, which is assumed to be inside (or at least near) the simulation
+box boundaries, though LAMMPS does not check for this.  Note that
+using the *bound* keyword typically reduces the total number of bins
+and thus the number of chunks *Nchunk*\ .
+
+The *pbc* keyword only applies to the *bin/sphere* and *bin/cylinder*
+styles.  If set to *yes*\ , the distance an atom is from the sphere
+origin or cylinder axis is calculated in a minimum image sense with
+respect to periodic dimensions, when determining which bin the atom is
+in.  I.e. if x is a periodic dimension and the distance between the
+atom and the sphere center in the x dimension is greater than 0.5 \*
+simulation box length in x, then a box length is subtracted to give a
+distance < 0.5 \* simulation box length.  This allosws the sphere or
+cylinder center to be near a box edge, and atoms on the other side of
+the periodic box will still be close to the center point/axis.  Note
+that with a setting of *yes*\ , the outer sphere or cylinder radius must
+also be <= 0.5 \* simulation box length in any periodic dimension
+except for the cylinder axis dimension, or an error is generated.
+
+The *units* keyword only applies to the *binning* styles; otherwise it
+is ignored.  For the *bin/1d*\ , *bin/2d*\ , *bin/3d* styles, it
+determines the meaning of the distance units used for the bin sizes
+*delta* and for *origin* and *bounds* values if they are coordinate
+values.  For the *bin/sphere* style it determines the meaning of the
+distance units used for *xorig*\ ,\ *yorig*\ ,\ *zorig* and the radii *srmin*
+and *srmax*\ .  For the *bin/cylinder* style it determines the meaning
+of the distance units used for *delta*\ ,\ *c1*\ ,\ *c2* and the radii *crmin*
+and *crmax*\ .
+
+For orthogonal simulation boxes, any of the 3 options may
+be used.  For non-orthogonal (triclinic) simulation boxes, only the
+*reduced* option may be used.
+
+A *box* value selects standard distance units as defined by the
+:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
+A *lattice* value means the distance units are in lattice spacings.
+The :doc:`lattice <lattice>` command must have been previously used to
+define the lattice spacing.  A *reduced* value means normalized
+unitless values between 0 and 1, which represent the lower and upper
+faces of the simulation box respectively.  Thus an *origin* value of
+0.5 means the center of the box in any dimension.  A *delta* value of
+0.1 means 10 bins span the box in that dimension.
+
+Note that for the *bin/sphere* style, the radii *srmin* and *srmax* are
+scaled by the lattice spacing or reduced value of the *x* dimension.
+
+Note that for the *bin/cylinder* style, the radii *crmin* and *crmax*
+are scaled by the lattice spacing or reduced value of the 1st
+dimension perpendicular to the cylinder axis.  E.g. y for an x-axis
+cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values are unitless chunk IDs, ranging from 1 to
+*Nchunk* (inclusive) for atoms assigned to chunks, and 0 for atoms not
+belonging to a chunk.
+
+Restrictions
+""""""""""""
+
+
+Even if the *nchunk* keyword is set to *once*\ , the chunk IDs assigned
+to each atom are not stored in a restart files.  This means you cannot
+expect those assignments to persist in a restarted simulation.
+Instead you must re-specify this command and assign atoms to chunks when
+the restarted simulation begins.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ave/chunk <fix_ave_chunk>`,
+:doc:`compute global/atom <compute_global_atom>`
+
+Default
+"""""""
+
+The option defaults are as follows:
+
+* region = none
+* nchunk = every, if compress is yes, overriding other defaults listed here
+* nchunk = once, for type style
+* nchunk = once, for mol style if region is none
+* nchunk = every, for mol style if region is set
+* nchunk = once, for binning style if the simulation box size is static or units = reduced
+* nchunk = every, for binning style if the simulation box size is dynamic and units is lattice or box
+* nchunk = every, for compute/fix/variable style
+* limit = 0
+* ids = every
+* compress = no
+* discard = yes, for all styles except binning
+* discard = mixed, for binning styles
+* bound = lower and upper in all dimensions
+* pbc = no
+* units = lattice
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst
new file mode 100644
index 0000000000..7106c6ce0a
--- /dev/null
+++ b/doc/src/compute_chunk_spread_atom.rst
@@ -0,0 +1,237 @@
+.. index:: compute chunk/spread/atom
+
+compute chunk/spread/atom command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID chunk/spread/atom chunkID input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* chunk/spread/atom = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* one or more inputs can be listed
+* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N]
+  
+  .. parsed-literal::
+  
+       c_ID = global vector calculated by a compute with ID
+       c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = global vector calculated by a fix with ID
+       f_ID[I] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all chunk/spread/atom mychunk c_com**\*** c_gyration
+
+Description
+"""""""""""
+
+Define a calculation that "spreads" one or more per-chunk values to
+each atom in the chunk.  This can be useful in several scenarios:
+
+* For creating a :doc:`dump file <dump>` where each atom lists info about
+  the chunk it is in, e.g. for post-processing purposes.
+* To access chunk value in :doc:`atom-style variables <variable>` that
+  need info about the chunk each atom is in.
+* To use the :doc:`fix ave/chunk <fix_ave_chunk>` command to spatially
+  average per-chunk values calculated by a per-chunk compute.
+
+Examples are given below.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+For inputs that are computes, they must be a compute that calculates
+per-chunk values.  These are computes whose style names end in
+"/chunk".
+
+For inputs that are fixes, they should be a fix that calculates
+per-chunk values.  For example, :doc:`fix ave/chunk <fix_ave_chunk>` or
+:doc:`fix ave/time <fix_ave_time>` (assuming it is time-averaging
+per-chunk data).
+
+For each atom, this compute accesses its chunk ID from the specified
+*chunkID* compute, then accesses the per-chunk value in each input.
+Those values are copied to this compute to become the output for that
+atom.
+
+The values generated by this compute will be 0.0 for atoms not in the
+specified compute group *group-ID*\ .  They will also be 0.0 if the atom
+is not in a chunk, as assigned by the *chunkID* compute.  They will
+also be 0.0 if the current chunk ID for the atom is out-of-bounds with
+respect to the number of chunks stored by a particular input compute
+or fix.
+
+.. note::
+
+   LAMMPS does not check that a compute or fix which calculates
+   per-chunk values uses the same definition of chunks as this compute.
+   It's up to you to be consistent.  Likewise, for a fix input, LAMMPS
+   does not check that it is per-chunk data.  It only checks that the fix
+   produces a global vector or array.
+
+
+----------
+
+
+Each listed input is operated on independently.
+
+If a bracketed index I is used, it can be specified using a wildcard
+asterisk with the index to effectively specify multiple values.  This
+takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of
+columns in the array, then an asterisk with no numeric values means
+all indices from 1 to N.  A leading asterisk means all indices from 1
+to n (inclusive).  A trailing asterisk means all indices from n to N
+(inclusive).  A middle asterisk means all indices from m to n
+(inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 compute chunk/spread/atom
+commands are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>` command creates a per-atom array
+with 3 columns:
+
+
+.. parsed-literal::
+
+   compute com all com/chunk mychunk
+   compute 10 all chunk/spread/atom mychunk c_com[\*]
+   compute 10 all chunk/spread/atom mychunk c_com[1] c_com[2] c_com[3]
+
+
+----------
+
+
+Here is an example of writing a dump file the with the center-of-mass
+(COM) for the chunk each atom is in.  The commands below can be added
+to the bench/in.chain script.
+
+
+.. parsed-literal::
+
+   compute         cmol all chunk/atom molecule
+   compute         com all com/chunk cmol
+   compute         comchunk all chunk/spread/atom cmol c_com**\***
+   dump            1 all custom 50 tmp.dump id mol type x y z c_comchunk**\***
+   dump_modify     1 sort id
+
+The same per-chunk data for each atom could be used to define per-atom
+forces for the :doc:`fix addforce <fix_addforce>` command.  In this
+example the forces act to pull atoms of an extended polymer chain
+towards its COM in an attractive manner.
+
+
+.. parsed-literal::
+
+   compute         prop all property/atom xu yu zu
+   variable        k equal 0.1
+   variable        fx atom v_k\*(c_comchunk[1]-c_prop[1])
+   variable        fy atom v_k\*(c_comchunk[2]-c_prop[2])
+   variable        fz atom v_k\*(c_comchunk[3]-c_prop[3])
+   fix             3 all addforce v_fx v_fy v_fz
+
+Note that :doc:`compute property/atom <compute_property_atom>` is used
+to generate unwrapped coordinates for use in the per-atom force
+calculation, so that the effect of periodic boundaries is accounted
+for properly.
+
+Over time this applied force could shrink each polymer chain's radius
+of gyration in a polymer mixture simulation.  Here is output from the
+bench/in.chain script.  Thermo output is shown for 1000 steps, where
+the last column is the average radius of gyration over all 320 chains
+in the 32000 atom system:
+
+
+.. parsed-literal::
+
+   compute         gyr all gyration/chunk cmol
+   variable        ave equal ave(c_gyr)
+   thermo_style    custom step etotal press v_ave
+
+          0    22.394765    4.6721833     5.128278
+        100    22.445002    4.8166709    5.0348372
+        200    22.500128    4.8790392    4.9364875
+        300    22.534686    4.9183766    4.8590693
+        400    22.557196    4.9492211    4.7937849
+        500    22.571017    4.9161853    4.7412008
+        600    22.573944    5.0229708    4.6931243
+        700    22.581804    5.0541301    4.6440647
+        800    22.584683    4.9691734    4.6000016
+        900     22.59128    5.0247538    4.5611513
+       1000    22.586832      4.94697    4.5238362
+
+
+----------
+
+
+Here is an example for using one set of chunks, defined for molecules,
+to compute the dipole moment vector for each chunk.  E.g. for water
+molecules. Then spreading those values to each atom in each chunk.
+Then defining a second set of chunks based on spatial bins.  And
+finally, using the :doc:`fix ave/chunk <fix_ave_chunk>` command to
+calculate an average dipole moment vector per spatial bin.
+
+
+.. parsed-literal::
+
+   compute       cmol all chunk/atom molecule
+   compute       dipole all dipole/chunk cmol
+   compute       spread all chunk/spread/atom cmol c_dipole[1] c_dipole[2] c_dipole[3]
+   compute       cspatial all chunk/atom bin/1d z lower 0.1 units reduced
+   fix           ave all ave/chunk 100 10 1000 cspatial c_spread[\*]
+
+Note that the :doc:`fix ave/chunk <fix_ave_chunk>` command requires
+per-atom values as input.  That is why the compute chunk/spread/atom
+command is used to assign per-chunk values to each atom in the chunk.
+If a molecule straddles bin boundaries, each of its atoms contributes
+in a weighted manner to the average dipole moment of the spatial bin
+it is in.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a per-atom vector or array, which can be
+accessed by any command that uses per-atom values from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The output is a per-atom vector if a single input value is specified,
+otherwise a per-atom array is output.  The number of columns in the
+array is the number of inputs provided.  The per-atom values for the
+vector or each column of the array will be in whatever
+:doc:`units <units>` the corresponding input value is in.
+
+The vector or array values are "intensive".
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute reduce/chunk <compute_reduce_chunk>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst
new file mode 100644
index 0000000000..df1614858c
--- /dev/null
+++ b/doc/src/compute_cluster_atom.rst
@@ -0,0 +1,117 @@
+.. index:: compute cluster/atom
+
+compute cluster/atom command
+============================
+
+compute fragment/atom command
+=============================
+
+compute aggregate/atom command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID cluster/atom cutoff
+   compute ID group-ID fragment/atom
+   compute ID group-ID aggregate/atom cutoff
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* *cluster/atom* or *fragment/atom* or *aggregate/atom* = style name of this compute command
+* cutoff = distance within which to label atoms as part of same cluster (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all cluster/atom 3.5
+   compute 1 all fragment/atom
+
+   compute 1 all aggregate/atom 3.5
+
+Description
+"""""""""""
+
+Define a computation that assigns each atom a cluster, fragment,
+or aggregate ID.
+
+A cluster is defined as a set of atoms, each of which is within the
+cutoff distance from one or more other atoms in the cluster.  If an
+atom has no neighbors within the cutoff distance, then it is a 1-atom
+cluster.
+
+A fragment is similarly defined as a set of atoms, each of
+which has an explicit bond (i.e. defined via a :doc:`data file <read_data>`,
+the :doc:`create\_bonds <create_bonds>` command, or through fixes like
+:doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`,
+or :doc:`fix bond/break <fix_bond_break>`).  The cluster ID or fragment ID
+of every atom in the cluster will be set to the smallest atom ID of any atom
+in the cluster or fragment, respectively.
+
+An aggregate is defined by combining the rules for clusters and
+fragments, i.e. a set of atoms, where each of it is within the cutoff
+distance from one or more atoms within a fragment that is part of
+the same cluster. This measure can be used to track molecular assemblies
+like micelles.
+
+Only atoms in the compute group are clustered and assigned cluster
+IDs. Atoms not in the compute group are assigned a cluster ID = 0.
+For fragments, only bonds where **both** atoms of the bond are included
+in the compute group are assigned to fragments, so that only fragments
+are detected where **all** atoms are in the compute group. Thus atoms
+may be included in the compute group, yes still have a fragment ID of 0.
+
+For computes *cluster/atom* and *aggregate/atom* the neighbor list needed
+to compute this quantity is constructed each time the calculation is
+performed (i.e. each time a snapshot of atoms is dumped).  Thus it can be
+inefficient to compute/dump this quantity too frequently or to have
+multiple compute/dump commands, each of a *cluster/atom* or
+*aggregate/atom* style.
+
+.. note::
+
+   If you have a bonded system, then the settings of
+   :doc:`special\_bonds <special_bonds>` command can remove pairwise
+   interactions between atoms in the same bond, angle, or dihedral.  This
+   is the default setting for the :doc:`special\_bonds <special_bonds>`
+   command, and means those pairwise interactions do not appear in the
+   neighbor list.  Because this fix uses the neighbor list, it also means
+   those pairs will not be included when computing the clusters. This
+   does not apply when using long-range coulomb (\ *coul/long*\ , *coul/msm*\ ,
+   *coul/wolf* or similar.  One way to get around this would be to set
+   special\_bond scaling factors to very tiny numbers that are not exactly
+   zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
+   use the :doc:`rerun <rerun>` command to compute the clusters for
+   snapshots in the dump file.  The rerun script can use a
+   :doc:`special\_bonds <special_bonds>` command that includes all pairs in
+   the neighbor list.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be an ID > 0, as explained above.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute coord/atom <compute_coord_atom>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst
new file mode 100644
index 0000000000..f75506eb90
--- /dev/null
+++ b/doc/src/compute_cna_atom.rst
@@ -0,0 +1,119 @@
+.. index:: compute cna/atom
+
+compute cna/atom command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID cna/atom cutoff
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* cna/atom = style name of this compute command
+* cutoff = cutoff distance for nearest neighbors (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all cna/atom 3.08
+
+Description
+"""""""""""
+
+Define a computation that calculates the CNA (Common Neighbor
+Analysis) pattern for each atom in the group.  In solid-state systems
+the CNA pattern is a useful measure of the local crystal structure
+around an atom.  The CNA methodology is described in :ref:`(Faken) <Faken>`
+and :ref:`(Tsuzuki) <Tsuzuki1>`.
+
+Currently, there are five kinds of CNA patterns LAMMPS recognizes:
+
+* fcc = 1
+* hcp = 2
+* bcc = 3
+* icosahedral = 4
+* unknown = 5
+
+The value of the CNA pattern will be 0 for atoms not in the specified
+compute group.  Note that normally a CNA calculation should only be
+performed on mono-component systems.
+
+The CNA calculation can be sensitive to the specified cutoff value.
+You should insure the appropriate nearest neighbors of an atom are
+found within the cutoff distance for the presumed crystal structure.
+E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
+neighbors for perfect BCC crystals.  These formulas can be used to
+obtain a good cutoff distance:
+
+.. image:: Eqs/cna_cutoff1.jpg
+   :align: center
+
+where a is the lattice constant for the crystal structure concerned
+and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
+for HCP crystals.
+
+Also note that since the CNA calculation in LAMMPS uses the neighbors
+of an owned atom to find the nearest neighbors of a ghost atom, the
+following relation should also be satisfied:
+
+.. image:: Eqs/cna_cutoff2.jpg
+   :align: center
+
+where Rc is the cutoff distance of the potential, Rs is the skin
+distance as specified by the :doc:`neighbor <neighbor>` command, and
+cutoff is the argument used with the compute cna/atom command.  LAMMPS
+will issue a warning if this is not the case.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+*cna/atom* style.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be a number from 0 to 5, as explained
+above.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute centro/atom <compute_centro_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Faken:
+
+
+
+**(Faken)** Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
+
+.. _Tsuzuki1:
+
+
+
+**(Tsuzuki)** Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst
new file mode 100644
index 0000000000..ba31448776
--- /dev/null
+++ b/doc/src/compute_cnp_atom.rst
@@ -0,0 +1,133 @@
+.. index:: compute cnp/atom
+
+compute cnp/atom command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID cnp/atom cutoff
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* cnp/atom = style name of this compute command
+* cutoff = cutoff distance for nearest neighbors (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all cnp/atom 3.08
+
+Description
+"""""""""""
+
+Define a computation that calculates the Common Neighborhood
+Parameter (CNP) for each atom in the group.  In solid-state systems
+the CNP is a useful measure of the local crystal structure
+around an atom and can be used to characterize whether the
+atom is part of a perfect lattice, a local defect (e.g. a dislocation
+or stacking fault), or at a surface.
+
+The value of the CNP parameter will be 0.0 for atoms not in the
+specified compute group.  Note that normally a CNP calculation should
+only be performed on single component systems.
+
+This parameter is computed using the following formula from
+:ref:`(Tsuzuki) <Tsuzuki2>`
+
+.. image:: Eqs/cnp_eq.jpg
+   :align: center
+
+where the index *j* goes over the *n*\ i nearest neighbors of atom
+*i*\ , and the index *k* goes over the *n*\ ij common nearest neighbors
+between atom *i* and atom *j*\ . Rik and Rjk are the vectors connecting atom
+*k* to atoms *i* and *j*\ .  The quantity in the double sum is computed
+for each atom.
+
+The CNP calculation is sensitive to the specified cutoff value.
+You should ensure that the appropriate nearest neighbors of an atom are
+found within the cutoff distance for the presumed crystal structure.
+E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
+neighbors for perfect BCC crystals.  These formulas can be used to
+obtain a good cutoff distance:
+
+.. image:: Eqs/cnp_cutoff.jpg
+   :align: center
+
+where a is the lattice constant for the crystal structure concerned
+and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
+for HCP crystals.
+
+Also note that since the CNP calculation in LAMMPS uses the neighbors
+of an owned atom to find the nearest neighbors of a ghost atom, the
+following relation should also be satisfied:
+
+.. image:: Eqs/cnp_cutoff2.jpg
+   :align: center
+
+where Rc is the cutoff distance of the potential, Rs is the skin
+distance as specified by the :doc:`neighbor <neighbor>` command, and
+cutoff is the argument used with the compute cnp/atom command.  LAMMPS
+will issue a warning if this is not the case.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+*cnp/atom* style.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be real positive numbers. Some typical CNP
+values:
+
+
+.. parsed-literal::
+
+   FCC lattice = 0.0
+   BCC lattice = 0.0
+   HCP lattice = 4.4
+
+   FCC (111) surface ~ 13.0
+   FCC (100) surface ~ 26.5
+   FCC dislocation core ~ 11
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute cna/atom <compute_cna_atom>`
+:doc:`compute centro/atom <compute_centro_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Tsuzuki2:
+
+
+
+**(Tsuzuki)** Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst
new file mode 100644
index 0000000000..8a9381e37e
--- /dev/null
+++ b/doc/src/compute_com.rst
@@ -0,0 +1,69 @@
+.. index:: compute com
+
+compute com command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID com
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* com = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all com
+
+Description
+"""""""""""
+
+Define a computation that calculates the center-of-mass of the group
+of atoms, including all effects due to atoms passing through periodic
+boundaries.
+
+A vector of three quantities is calculated by this compute, which
+are the x,y,z coordinates of the center of mass.
+
+.. note::
+
+   The coordinates of an atom contribute to the center-of-mass in
+   "unwrapped" form, by using the image flags associated with each atom.
+   See the :doc:`dump custom <dump>` command for a discussion of
+   "unwrapped" coordinates.  See the Atoms section of the
+   :doc:`read\_data <read_data>` command for a discussion of image flags and
+   how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+**Output info:**
+
+This compute calculates a global vector of length 3, which can be
+accessed by indices 1-3 by any command that uses global vector values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The vector values are "intensive".  The vector values will be in
+distance :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute com/chunk <compute_com_chunk>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst
new file mode 100644
index 0000000000..d143f911f6
--- /dev/null
+++ b/doc/src/compute_com_chunk.rst
@@ -0,0 +1,98 @@
+.. index:: compute com/chunk
+
+compute com/chunk command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID com/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* com/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid com/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the center-of-mass for multiple
+chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates the x,y,z coordinates of the center-of-mass
+for each chunk, which includes all effects due to atoms passing through
+periodic boundaries.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+.. note::
+
+   The coordinates of an atom contribute to the chunk's
+   center-of-mass in "unwrapped" form, by using the image flags
+   associated with each atom.  See the :doc:`dump custom <dump>` command
+   for a discussion of "unwrapped" coordinates.  See the Atoms section of
+   the :doc:`read\_data <read_data>` command for a discussion of image flags
+   and how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+The simplest way to output the results of the compute com/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all com/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+3 for the x,y,z center-of-mass coordinates of each chunk.  These
+values can be accessed by any command that uses global array values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The array values are "intensive".  The array values will be in
+distance :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute com <compute_com>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst
new file mode 100644
index 0000000000..0d8563d2ce
--- /dev/null
+++ b/doc/src/compute_contact_atom.rst
@@ -0,0 +1,66 @@
+.. index:: compute contact/atom
+
+compute contact/atom command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID contact/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* contact/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all contact/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the number of contacts
+for each atom in a group.
+
+The contact number is defined for finite-size spherical particles as
+the number of neighbor atoms which overlap the central particle,
+meaning that their distance of separation is less than or equal to the
+sum of the radii of the two particles.
+
+The value of the contact number will be 0.0 for atoms not in the
+specified compute group.
+
+**Output info:**
+
+This compute calculates a per-atom vector, whose values can be
+accessed by any command that uses per-atom values from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The per-atom vector values will be a number >= 0.0, as explained
+above.
+
+Restrictions
+""""""""""""
+
+
+This compute requires that atoms store a radius as defined by the
+:doc:`atom\_style sphere <atom_style>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute coord/atom <compute_coord_atom>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst
new file mode 100644
index 0000000000..2e55d3a673
--- /dev/null
+++ b/doc/src/compute_coord_atom.rst
@@ -0,0 +1,162 @@
+.. index:: compute coord/atom
+
+compute coord/atom command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID coord/atom cstyle args ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* coord/atom = style name of this compute command
+* cstyle = *cutoff* or *orientorder*
+  
+  .. parsed-literal::
+  
+       *cutoff* args = cutoff [group group2-ID] typeN
+         cutoff = distance within which to count coordination neighbors (distance units)
+         group *group2-ID* = select group-ID to restrict which atoms to consider for coordination number (optional)
+         typeN = atom type for Nth coordination count (see asterisk form below)
+       *orientorder* args = orientorderID threshold
+         orientorderID = ID of an orientorder/atom compute
+         threshold = minimum value of the product of two "connected" atoms
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all coord/atom cutoff 2.0
+   compute 1 all coord/atom cutoff 6.0 1 2
+   compute 1 all coord/atom cutoff 6.0 2\*4 5\*8 \*
+   compute 1 solute coord/atom cutoff 2.0 group solvent
+   compute 1 all coord/atom orientorder 2 0.5
+
+Description
+"""""""""""
+
+This compute performs calculations between neighboring atoms to
+determine a coordination value.  The specific calculation and the
+meaning of the resulting value depend on the *cstyle* keyword used.
+
+The *cutoff* cstyle calculates one or more traditional coordination
+numbers for each atom.  A coordination number is defined as the number
+of neighbor atoms with specified atom type(s), and optionally within
+the specified group, that are within the specified cutoff distance from
+the central atom. The compute group selects only the central atoms; all
+neighboring atoms, unless selected by type, type range, or group option,
+are included in the coordination number tally.
+
+The optional *group* keyword allows to specify from which group atoms
+contribute to the coordination number. Default setting is group 'all'.
+
+The *typeN* keywords allow specification of which atom types
+contribute to each coordination number.  One coordination number is
+computed for each of the *typeN* keywords listed.  If no *typeN*
+keywords are listed, a single coordination number is calculated, which
+includes atoms of all types (same as the "\*" format, see below).
+
+The *typeN* keywords can be specified in one of two ways.  An explicit
+numeric value can be used, as in the 2nd example above.  Or a
+wild-card asterisk can be used to specify a range of atom types.  This
+takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of
+atom types, then an asterisk with no numeric values means all types
+from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The *orientorder* cstyle calculates the number of "connected" neighbor
+atoms J around each central atom I.  For this *cstyle*\ , connected is
+defined by the orientational order parameter calculated by the
+:doc:`compute orientorder/atom <compute_orientorder_atom>` command.
+This *cstyle* thus allows one to apply the ten Wolde's criterion to
+identify crystal-like atoms in a system, as discussed in :ref:`ten Wolde <tenWolde1>`.
+
+The ID of the previously specified :doc:`compute orientorder/atom <compute_orientorder_atom>` command is specified as
+*orientorderID*\ .  The compute must invoke its *components* option to
+calculate components of the *Ybar\_lm* vector for each atoms, as
+described in its documentation.  Note that orientorder/atom compute
+defines its own criteria for identifying neighboring atoms.  If the
+scalar product (*Ybar\_lm(i)*,*Ybar\_lm(j)*), calculated by the
+orientorder/atom compute is larger than the specified *threshold*\ ,
+then I and J are connected, and the coordination value of I is
+incremented by one.
+
+For all *cstyle* settings, all coordination values will be 0.0 for
+atoms not in the specified compute group.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently.
+
+.. note::
+
+   If you have a bonded system, then the settings of
+   :doc:`special\_bonds <special_bonds>` command can remove pairwise
+   interactions between atoms in the same bond, angle, or dihedral.  This
+   is the default setting for the :doc:`special\_bonds <special_bonds>`
+   command, and means those pairwise interactions do not appear in the
+   neighbor list.  Because this fix uses the neighbor list, it also means
+   those pairs will not be included in the coordination count.  One way
+   to get around this, is to write a dump file, and use the
+   :doc:`rerun <rerun>` command to compute the coordination for snapshots
+   in the dump file.  The rerun script can use a
+   :doc:`special\_bonds <special_bonds>` command that includes all pairs in
+   the neighbor list.
+
+**Output info:**
+
+For *cstyle* cutoff, this compute can calculate a per-atom vector or
+array.  If single *type1* keyword is specified (or if none are
+specified), this compute calculates a per-atom vector.  If multiple
+*typeN* keywords are specified, this compute calculates a per-atom
+array, with N columns.
+
+For *cstyle* orientorder, this compute calculates a per-atom vector.
+
+These values can be accessed by any command that uses per-atom values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The per-atom vector or array values will be a number >= 0.0, as
+explained above.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute cluster/atom <compute_cluster_atom>`
+:doc:`compute orientorder/atom <compute_orientorder_atom>`
+
+Default
+"""""""
+
+group = all
+
+
+----------
+
+
+.. _tenWolde1:
+
+
+
+**(tenWolde)** P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
+J. Chem. Phys. 104, 9932 (1996).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst
new file mode 100644
index 0000000000..2b498a3fb5
--- /dev/null
+++ b/doc/src/compute_damage_atom.rst
@@ -0,0 +1,72 @@
+.. index:: compute damage/atom
+
+compute damage/atom command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID damage/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* damage/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all damage/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom damage for each atom
+in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+for an overview of LAMMPS commands for Peridynamics modeling.
+
+The "damage" of a Peridynamics particles is based on the bond breakage
+between the particle and its neighbors.  If all the bonds are broken
+the particle is considered to be fully damaged.
+
+See the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
+definition of "damage" and more details about Peridynamics as it is
+implemented in LAMMPS.
+
+This command can be used with all the Peridynamic pair styles.
+
+The damage value will be 0.0 for atoms not in the specified compute
+group.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values are unitless numbers (damage) >= 0.0.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the PERI package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute dilatation/atom <compute_dilatation_atom>`,
+:doc:`compute plasticity/atom <compute_plasticity_atom>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst
new file mode 100644
index 0000000000..087b25c393
--- /dev/null
+++ b/doc/src/compute_dihedral.rst
@@ -0,0 +1,61 @@
+.. index:: compute dihedral
+
+compute dihedral command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID dihedral
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* dihedral = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all dihedral
+
+Description
+"""""""""""
+
+Define a computation that extracts the dihedral energy calculated by
+each of the dihedral sub-styles used in the :doc:`dihedral\_style hybrid <dihedral_hybrid>` command.  These values are made
+accessible for output or further processing by other commands.  The
+group specified for this command is ignored.
+
+This compute is useful when using :doc:`dihedral\_style hybrid <dihedral_hybrid>` if you want to know the portion of the
+total energy contributed by one or more of the hybrid sub-styles.
+
+**Output info:**
+
+This compute calculates a global vector of length N where N is the
+number of sub\_styles defined by the :doc:`dihedral\_style hybrid <dihedral_style>` command.  which can be accessed by indices
+1-N.  These values can be used by any command that uses global scalar
+or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector values are "extensive" and will be in energy
+:doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst
new file mode 100644
index 0000000000..f3908a9280
--- /dev/null
+++ b/doc/src/compute_dihedral_local.rst
@@ -0,0 +1,151 @@
+.. index:: compute dihedral/local
+
+compute dihedral/local command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID dihedral/local value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* dihedral/local = style name of this compute command
+* one or more values may be appended
+* value = *phi* or *v\_name*
+  
+  .. parsed-literal::
+  
+       *phi* = tabulate dihedral angles
+       *v_name* = equal-style variable with name (see below)
+
+* zero or more keyword/args pairs may be appended
+* keyword = *set*
+  
+  .. parsed-literal::
+  
+       *set* args = phi name
+         phi = only currently allowed arg
+         name = name of variable to set with phi
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all dihedral/local phi
+
+   compute 1 all dihedral/local phi v_cos set phi p
+
+Description
+"""""""""""
+
+Define a computation that calculates properties of individual dihedral
+interactions.  The number of datums generated, aggregated across all
+processors, equals the number of dihedral angles in the system, modified
+by the group parameter as explained below.
+
+The value *phi* is the dihedral angle, as defined in the diagram on
+the :doc:`dihedral\_style <dihedral_style>` doc page.
+
+The value *v\_name* can be used together with the *set* keyword to
+compute a user-specified function of the dihedral angle phi.  The
+*name* specified for the *v\_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
+variable which will store the angle phi.  This other variable must
+be an :doc:`internal-style variable <variable>` defined in the input
+script; its initial numeric value can be anything.  It must be an
+internal-style variable, because this command resets its value
+directly.  The *set* keyword is used to identify the name of this
+other variable associated with phi.
+
+Note that the value of phi for each angle which stored in the internal
+variable is in radians, not degrees.
+
+As an example, these commands can be added to the bench/in.rhodo
+script to compute the cosine and cosine\^2 of every dihedral angle in
+the system and output the statistics in various ways:
+
+
+.. parsed-literal::
+
+   variable p internal 0.0
+   variable cos equal cos(v_p)
+   variable cossq equal cos(v_p)\*cos(v_p)
+
+   compute 1 all property/local datom1 datom2 datom3 datom4 dtype
+   compute 2 all dihedral/local phi v_cos v_cossq set phi p
+   dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
+
+   compute 3 all reduce ave c_2**\***
+   thermo_style custom step temp press c_3**\***
+
+   fix 10 all ave/histo 10 10 100 -1 1 20 c_2\ **2** mode vector file tmp.histo
+
+The :doc:`dump local <dump>` command will output the angle,
+cosine(angle), cosine\^2(angle) for every dihedral in the system.  The
+:doc:`thermo\_style <thermo_style>` command will print the average of
+those quantities via the :doc:`compute reduce <compute_reduce>` command
+with thermo output.  And the :doc:`fix ave/histo <fix_ave_histo>`
+command will histogram the cosine(angle) values and write them to a
+file.
+
+
+----------
+
+
+The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their dihedrals.  A dihedral will
+only be included if all 4 atoms in the dihedral are in the specified
+compute group.
+
+Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, dihedral output from the :doc:`compute property/local <compute_property_local>` command can be combined
+with data from this command and output by the :doc:`dump local <dump>`
+command in a consistent way.
+
+Here is an example of how to do this:
+
+
+.. parsed-literal::
+
+   compute 1 all property/local dtype datom1 datom2 datom3 datom4
+   compute 2 all dihedral/local phi
+   dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
+
+**Output info:**
+
+This compute calculates a local vector or local array depending on the
+number of values.  The length of the vector or number of rows in the
+array is the number of dihedrals.  If a single value is specified, a
+local vector is produced.  If two or more values are specified, a
+local array is produced where the number of columns = the number of
+values.  The vector or array can be accessed by any command that uses
+local values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The output for *phi* will be in degrees.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst
new file mode 100644
index 0000000000..84e4d48a1c
--- /dev/null
+++ b/doc/src/compute_dilatation_atom.rst
@@ -0,0 +1,75 @@
+.. index:: compute dilatation/atom
+
+compute dilatation/atom command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID dilatation/atom
+
+* ID, group-ID are documented in compute command
+* dilation/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all dilatation/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom dilatation for each
+atom in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+for an overview of LAMMPS commands for Peridynamics modeling.
+
+For small deformation, dilatation of is the measure of the volumetric
+strain.
+
+The dilatation "theta" for each peridynamic particle I is calculated
+as a sum over its neighbors with unbroken bonds, where the
+contribution of the IJ pair is a function of the change in bond length
+(versus the initial length in the reference state), the volume
+fraction of the particles and an influence function.  See the
+`PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
+definition of dilatation.
+
+This command can only be used with a subset of the Peridynamic :doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps.
+
+The dilatation value will be 0.0 for atoms not in the specified
+compute group.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values are unitless numbers (theta) >= 0.0.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the PERI package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute damage/atom <compute_damage_atom>`,
+:doc:`compute plasticity/atom <compute_plasticity_atom>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst
new file mode 100644
index 0000000000..5c80b62faa
--- /dev/null
+++ b/doc/src/compute_dipole_chunk.rst
@@ -0,0 +1,103 @@
+.. index:: compute dipole/chunk
+
+compute dipole/chunk command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID dipole/chunk chunkID charge-correction
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* dipole/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* charge-correction = *mass* or *geometry*\ , use COM or geometric center for charged chunk correction (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid dipole/chunk molchunk
+   compute dw water dipole/chunk 1 geometry
+
+Description
+"""""""""""
+
+Define a computation that calculates the dipole vector and total dipole
+for multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates the x,y,z coordinates of the dipole vector
+and the total dipole moment for each chunk, which includes all effects
+due to atoms passing through periodic boundaries. For chunks with a net
+charge the resulting dipole is made position independent by subtracting
+the position vector of the center of mass or geometric center times the
+net charge from the computed dipole vector.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+.. note::
+
+   The coordinates of an atom contribute to the chunk's
+   dipole in "unwrapped" form, by using the image flags
+   associated with each atom.  See the :doc:`dump custom <dump>` command
+   for a discussion of "unwrapped" coordinates.  See the Atoms section of
+   the :doc:`read\_data <read_data>` command for a discussion of image flags
+   and how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+The simplest way to output the results of the compute com/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all dipole/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+4 for the x,y,z dipole vector components and the total dipole of each
+chunk. These values can be accessed by any command that uses global
+array values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The array values are "intensive".  The array values will be in
+dipole units, i.e. charge units times distance :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute com/chunk <compute_com_chunk>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst
new file mode 100644
index 0000000000..a5da397e99
--- /dev/null
+++ b/doc/src/compute_displace_atom.rst
@@ -0,0 +1,160 @@
+.. index:: compute displace/atom
+
+compute displace/atom command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID displace/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* displace/atom = style name of this compute command
+* zero or more keyword/arg pairs may be appended
+* keyword = *refresh*
+  
+  .. parsed-literal::
+  
+       *replace* arg = name of per-atom variable
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all displace/atom
+   compute 1 all displace/atom refresh myVar
+
+Description
+"""""""""""
+
+Define a computation that calculates the current displacement of each
+atom in the group from its original (reference) coordinates, including
+all effects due to atoms passing through periodic boundaries.
+
+A vector of four quantities per atom is calculated by this compute.
+The first 3 elements of the vector are the dx,dy,dz displacements.
+The 4th component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
+dz\*dz).
+
+The displacement of an atom is from its original position at the time
+the compute command was issued.  The value of the displacement will be
+0.0 for atoms not in the specified compute group.
+
+.. note::
+
+   Initial coordinates are stored in "unwrapped" form, by using the
+   image flags associated with each atom.  See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
+   See the Atoms section of the :doc:`read\_data <read_data>` command for a
+   discussion of image flags and how they are set for each atom.  You can
+   reset the image flags (e.g. to 0) before invoking this compute by
+   using the :doc:`set image <set>` command.
+
+.. note::
+
+   If you want the quantities calculated by this compute to be
+   continuous when running from a :doc:`restart file <read_restart>`, then
+   you should use the same ID for this compute, as in the original run.
+   This is so that the fix this compute creates to store per-atom
+   quantities will also have the same ID, and thus be initialized
+   correctly with time=0 atom coordinates from the restart file.
+
+
+----------
+
+
+The *refresh* option can be used in conjunction with the "dump\_modify
+refresh" command to generate incremental dump files.
+
+The definition and motivation of an incremental dump file is as
+follows.  Instead of outputting all atoms at each snapshot (with some
+associated values), you may only wish to output the subset of atoms
+with a value that has changed in some way compared to the value the
+last time that atom was output.  In some scenarios this can result in
+a dramatically smaller dump file.  If desired, by post-processing the
+sequence of snapshots, the values for all atoms at all timesteps can
+be inferred.
+
+A concrete example using this compute, is a simulation of atom
+diffusion in a solid, represented as atoms on a lattice.  Diffusive
+hops are rare.  Imagine that when a hop occurs an atom moves more than
+a distance *Dhop*\ .  For any snapshot we only want to output atoms that
+have hopped since the last snapshot.  This can be accomplished with
+something like the following commands:
+
+
+.. parsed-literal::
+
+   write_dump      all custom tmp.dump id type x y z    # see comment below
+
+   variable        Dhop equal 0.6
+   variable        check atom "c_dsp\ **4** > v_Dhop"
+   compute         dsp all displace/atom refresh check
+   dump            1 all custom 100 tmp.dump id type x y z
+   dump_modify     1 append yes thresh c_dsp\ **4** > $\ *Dhop* &
+                   refresh c_dsp delay 100
+
+The :doc:`dump\_modify thresh <dump_modify>` command will only output
+atoms that have displaced more than 0.6 Angstroms on each snapshot
+(assuming metal units).  The dump\_modify *refresh* option triggers a
+call to this compute at the end of every dump.
+
+The *refresh* argument for this compute is the ID of an :doc:`atom-style variable <variable>` which calculates a Boolean value (0 or 1)
+based on the same criterion used by dump\_modify thresh.  This compute
+evaluates the atom-style variable.  For each atom that returns 1
+(true), the original (reference) coordinates of the atom (stored by
+this compute) are updated.
+
+The effect of these commands is that a particular atom will only be
+output in the dump file on the snapshot after it makes a diffusive
+hop.  It will not be output again until it makes another hop.
+
+Note that in the first snapshot of a subsequent run, no atoms will be
+typically be output.  That is because the initial displacement for all
+atoms is 0.0.  If an initial dump snapshot is desired, containing the
+initial reference positions of all atoms, one way to do this is
+illustrated above.  An initial write\_dump command can be used before
+the first run.  It will contain the positions of all the atoms,
+Options in the :doc:`dump\_modify <dump_modify>` command above will
+append new output to that same file and delay the output until a later
+timestep.  The *delay* setting avoids a second time = 0 snapshot which
+would be empty.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a per-atom array with 4 columns, which can be
+accessed by indices 1-4 by any command that uses per-atom values from
+a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+The per-atom array values will be in distance :doc:`units <units>`.
+
+This compute supports the *refresh* option as explained above, for use
+in conjunction with :doc:`dump\_modify refresh <dump_modify>` to generate
+incremental dump files.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute msd <compute_msd>`, :doc:`dump custom <dump>`, :doc:`fix store/state <fix_store_state>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst
new file mode 100644
index 0000000000..f85c0259f8
--- /dev/null
+++ b/doc/src/compute_dpd.rst
@@ -0,0 +1,90 @@
+.. index:: compute dpd
+
+compute dpd command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID dpd
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* dpd = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all dpd
+
+Description
+"""""""""""
+
+Define a computation that accumulates the total internal conductive
+energy (U\_cond), the total internal mechanical energy (U\_mech), the
+total chemical energy (U\_chem) and the *harmonic* average of the internal
+temperature (dpdTheta) for the entire system of particles.  See the
+:doc:`compute dpd/atom <compute_dpd_atom>` command if you want
+per-particle internal energies and internal temperatures.
+
+The system internal properties are computed according to the following
+relations:
+
+.. image:: Eqs/compute_dpd.jpg
+   :align: center
+
+where N is the number of particles in the system
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global vector of length 5 (U\_cond, U\_mech,
+U\_chem, dpdTheta, N\_particles), which can be accessed by indices 1-5.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The vector values will be in energy and temperature :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command also requires use of the :doc:`atom\_style dpd <atom_style>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute dpd/atom <compute_dpd_atom>`,
+:doc:`thermo\_style <thermo_style>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Larentzos1:
+
+
+
+**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
+W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
+Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+Laboratory, Aberdeen Proving Ground, MD (2014).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst
new file mode 100644
index 0000000000..2970141a19
--- /dev/null
+++ b/doc/src/compute_dpd_atom.rst
@@ -0,0 +1,79 @@
+.. index:: compute dpd/atom
+
+compute dpd/atom command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID dpd/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* dpd/atom = style name of this compute command
+
+Examples
+""""""""
+
+compute 1 all dpd/atom
+
+Description
+"""""""""""
+
+Define a computation that accesses the per-particle internal
+conductive energy (u\_cond), internal mechanical energy (u\_mech),
+internal chemical energy (u\_chem) and
+internal temperatures (dpdTheta) for each particle in a group.  See
+the :doc:`compute dpd <compute_dpd>` command if you want the total
+internal conductive energy, the total internal mechanical energy, the
+total chemical energy and
+average internal temperature of the entire system or group of dpd
+particles.
+
+**Output info:**
+
+This compute calculates a per-particle array with 4 columns (u\_cond,
+u\_mech, u\_chem, dpdTheta), which can be accessed by indices 1-4 by any
+command that uses per-particle values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle array values will be in energy (u\_cond, u\_mech, u\_chem)
+and temperature (dpdTheta) :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command also requires use of the :doc:`atom\_style dpd <atom_style>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`, :doc:`compute dpd <compute_dpd>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Larentzos2:
+
+
+
+**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
+W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
+Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+Laboratory, Aberdeen Proving Ground, MD (2014).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst
new file mode 100644
index 0000000000..03dd4e9af5
--- /dev/null
+++ b/doc/src/compute_edpd_temp_atom.rst
@@ -0,0 +1,80 @@
+.. index:: compute edpd/temp/atom
+
+compute edpd/temp/atom command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID edpd/temp/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* edpd/temp/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all edpd/temp/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom temperature
+for each eDPD particle in a group.
+
+The temperature is a local temperature derived from the internal energy
+of each eDPD particle based on the local equilibrium hypothesis.
+For more details please see :ref:`(Espanol1997) <Espanol1997>` and
+:ref:`(Li2014) <Li2014a>`.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See the
+:doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS
+output options.
+
+The per-atom vector values will be in temperature :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MESO package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style edpd <pair_meso>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Espanol1997:
+
+
+
+**(Espanol1997)** Espanol, Europhys Lett, 40(6): 631-636 (1997).  DOI:
+10.1209/epl/i1997-00515-8
+
+.. _Li2014a:
+
+
+
+**(Li2014)** Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265:
+113-127 (2014).  DOI: 10.1016/j.jcp.2014.02.003.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst
new file mode 100644
index 0000000000..c43c73814c
--- /dev/null
+++ b/doc/src/compute_entropy_atom.rst
@@ -0,0 +1,164 @@
+.. index:: compute entropy/atom
+
+compute entropy/atom command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID entropy/atom sigma cutoff keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* entropy/atom = style name of this compute command
+* sigma = width of gaussians used in the g(r) smoothing
+* cutoff = cutoff for the g(r) calculation
+* one or more keyword/value pairs may be appended
+
+.. parsed-literal::
+
+   keyword = *avg* or *local*
+     *avg* values = *yes* or *no* cutoff2
+       *yes* = average the pair entropy over neighbors
+       *no* = do not average the pair entropy over neighbors
+       cutoff2 = cutoff for the averaging over neighbors
+     *local* values = *yes* or *no* = use the local density around each atom to normalize the g(r)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all entropy/atom 0.25 5.
+   compute 1 all entropy/atom 0.25 5. avg yes 5.
+   compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes
+
+Description
+"""""""""""
+
+Define a computation that calculates the pair entropy fingerprint for
+each atom in the group. The fingerprint is useful to distinguish between
+ordered and disordered environments, for instance liquid and solid-like
+environments, or glassy and crystalline-like environments. Some
+applications could be the identification of grain boundaries, a
+melt-solid interface, or a solid cluster emerging from the melt.
+The advantage of this parameter over others is that no a priori
+information about the solid structure is required.
+
+This parameter for atom i is computed using the following formula from
+:ref:`(Piaggi) <Piaggi>` and :ref:`(Nettleton) <Nettleton>` ,
+
+.. image:: Eqs/pair_entropy.jpg
+   :align: center
+
+where r is a distance, g(r) is the radial distribution function of atom
+i and rho is the density of the system. The g(r) computed for each
+atom i can be noisy and therefore it is smoothed using:
+
+.. image:: Eqs/pair_entropy2.jpg
+   :align: center
+
+where the sum in j goes through the neighbors of atom i, and sigma is a
+parameter to control the smoothing.
+
+The input parameters are *sigma* the smoothing parameter, and the
+*cutoff* for the calculation of g(r).
+
+If the keyword *avg* has the setting *yes*\ , then this compute also
+averages the parameter over the neighbors  of atom i according to:
+
+.. image:: Eqs/pair_entropy3.jpg
+   :align: center
+
+where the sum j goes over the neighbors of atom i and N is the number
+of neighbors. This procedure provides a sharper distinction between
+order and disorder environments. In this case the input parameter
+*cutoff2* is the cutoff for the averaging over the neighbors and
+must also be specified.
+
+If the *avg yes* option is used, the effective cutoff of the neighbor
+list should be *cutoff*\ +\ *cutoff2* and therefore it might be necessary
+to increase the skin of the neighbor list with:
+
+
+.. parsed-literal::
+
+   neighbor skin bin
+
+See :doc:`neighbor <neighbor>` for details.
+
+If the *local yes* option is used, the g(r) is normalized by the
+local density around each atom, that is to say the density around each
+atom  is the number of neighbors within the neighbor list cutoff divided
+by the corresponding volume. This option can be useful when dealing with
+inhomogeneous systems such as those that have surfaces.
+
+Here are typical input parameters for fcc aluminum (lattice
+constant 4.05 Angstroms),
+
+
+.. parsed-literal::
+
+   compute 1 all entropy/atom 0.25 5.7 avg yes 3.7
+
+and for bcc sodium (lattice constant 4.23 Angstroms),
+
+
+.. parsed-literal::
+
+   compute 1 all entropy/atom 0.25 7.3 avg yes 5.1
+
+**Output info:**
+
+By default, this compute calculates the pair entropy value for each
+atom as a per-atom vector, which can be accessed by any command that
+uses per-atom values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The pair entropy values have units of the Boltzmann constant. They are
+always negative, and lower values (lower entropy) correspond to more
+ordered environments.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute cna/atom <compute_cna_atom>`
+:doc:`compute centro/atom <compute_centro_atom>`
+
+Default
+"""""""
+
+The default values for the optional keywords are avg = no and local = no.
+
+
+----------
+
+
+.. _Piaggi:
+
+
+
+**(Piaggi)** Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017).
+
+.. _Nettleton:
+
+
+
+**(Nettleton)** Nettleton and Green, J Chem Phys, 29, 6 (1958).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst
new file mode 100644
index 0000000000..c50d21df99
--- /dev/null
+++ b/doc/src/compute_erotate_asphere.rst
@@ -0,0 +1,82 @@
+.. index:: compute erotate/asphere
+
+compute erotate/asphere command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID erotate/asphere
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* erotate/asphere = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all erotate/asphere
+
+Description
+"""""""""""
+
+Define a computation that calculates the rotational kinetic energy of
+a group of aspherical particles.  The aspherical particles can be
+ellipsoids, or line segments, or triangles.  See the
+:doc:`atom\_style <atom_style>` and :doc:`read\_data <read_data>` commands
+for descriptions of these options.
+
+For all 3 types of particles, the rotational kinetic energy is
+computed as 1/2 I w\^2, where I is the inertia tensor for the
+aspherical particle and w is its angular velocity, which is computed
+from its angular momentum if needed.
+
+.. note::
+
+   For :doc:`2d models <dimension>`, ellipsoidal particles are
+   treated as ellipsoids, not ellipses, meaning their moments of inertia
+   will be the same as in 3d.
+
+**Output info:**
+
+This compute calculates a global scalar (the KE).  This value can be
+used by any command that uses a global scalar value from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute requires that ellipsoidal particles atoms store a shape
+and quaternion orientation and angular momentum as defined by the
+:doc:`atom\_style ellipsoid <atom_style>` command.
+
+This compute requires that line segment particles atoms store a length
+and orientation and angular velocity as defined by the :doc:`atom\_style line <atom_style>` command.
+
+This compute requires that triangular particles atoms store a size and
+shape and quaternion orientation and angular momentum as defined by
+the :doc:`atom\_style tri <atom_style>` command.
+
+All particles in the group must be finite-size.  They cannot be point
+particles.
+
+**Related commands:** none
+
+:doc:`compute erotate/sphere <compute_erotate_sphere>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst
new file mode 100644
index 0000000000..2f74dd425c
--- /dev/null
+++ b/doc/src/compute_erotate_rigid.rst
@@ -0,0 +1,70 @@
+.. index:: compute erotate/rigid
+
+compute erotate/rigid command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID erotate/rigid fix-ID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* erotate/rigid = style name of this compute command
+* fix-ID = ID of rigid body fix
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all erotate/rigid myRigid
+
+Description
+"""""""""""
+
+Define a computation that calculates the rotational kinetic energy of
+a collection of rigid bodies, as defined by one of the :doc:`fix rigid <fix_rigid>` command variants.
+
+The rotational energy of each rigid body is computed as 1/2 I Wbody\^2,
+where I is the inertia tensor for the rigid body, and Wbody is its
+angular velocity vector.  Both I and Wbody are in the frame of
+reference of the rigid body, i.e. I is diagonalized.
+
+The *fix-ID* should be the ID of one of the :doc:`fix rigid <fix_rigid>`
+commands which defines the rigid bodies.  The group specified in the
+compute command is ignored.  The rotational energy of all the rigid
+bodies defined by the fix rigid command in included in the
+calculation.
+
+**Output info:**
+
+This compute calculates a global scalar (the summed rotational energy
+of all the rigid bodies).  This value can be used by any command that
+uses a global scalar value from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the RIGID package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute ke/rigid <compute_ke_rigid>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst
new file mode 100644
index 0000000000..fa1396681c
--- /dev/null
+++ b/doc/src/compute_erotate_sphere.rst
@@ -0,0 +1,71 @@
+.. index:: compute erotate/sphere
+
+compute erotate/sphere command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID erotate/sphere
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* erotate/sphere = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all erotate/sphere
+
+Description
+"""""""""""
+
+Define a computation that calculates the rotational kinetic energy of
+a group of spherical particles.
+
+The rotational energy is computed as 1/2 I w\^2, where I is the moment
+of inertia for a sphere and w is the particle's angular velocity.
+
+.. note::
+
+   For :doc:`2d models <dimension>`, particles are treated as
+   spheres, not disks, meaning their moment of inertia will be the same
+   as in 3d.
+
+**Output info:**
+
+This compute calculates a global scalar (the KE).  This value can be
+used by any command that uses a global scalar value from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute requires that atoms store a radius and angular velocity
+(omega) as defined by the :doc:`atom\_style sphere <atom_style>` command.
+
+All particles in the group must be finite-size spheres or point
+particles.  They cannot be aspherical.  Point particles will not
+contribute to the rotational energy.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute erotate/asphere <compute_erotate_asphere>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst
new file mode 100644
index 0000000000..31a90bc282
--- /dev/null
+++ b/doc/src/compute_erotate_sphere_atom.rst
@@ -0,0 +1,67 @@
+.. index:: compute erotate/sphere/atom
+
+compute erotate/sphere/atom command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID erotate/sphere/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* erotate/sphere/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all erotate/sphere/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the rotational kinetic energy for
+each particle in a group.
+
+The rotational energy is computed as 1/2 I w\^2, where I is the moment
+of inertia for a sphere and w is the particle's angular velocity.
+
+.. note::
+
+   For :doc:`2d models <dimension>`, particles are treated as
+   spheres, not disks, meaning their moment of inertia will be the same
+   as in 3d.
+
+The value of the rotational kinetic energy will be 0.0 for atoms not
+in the specified compute group or for point particles with a radius =
+0.0.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst
new file mode 100644
index 0000000000..55555c46bd
--- /dev/null
+++ b/doc/src/compute_event_displace.rst
@@ -0,0 +1,76 @@
+.. index:: compute event/displace
+
+compute event/displace command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID event/displace threshold
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* event/displace = style name of this compute command
+* threshold = minimum distance any particle must move to trigger an event (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all event/displace 0.5
+
+Description
+"""""""""""
+
+Define a computation that flags an "event" if any particle in the
+group has moved a distance greater than the specified threshold
+distance when compared to a previously stored reference state
+(i.e. the previous event).  This compute is typically used in
+conjunction with the :doc:`prd <prd>` and :doc:`tad <tad>` commands,
+to detect if a transition
+to a new minimum energy basin has occurred.
+
+This value calculated by the compute is equal to 0 if no particle has
+moved far enough, and equal to 1 if one or more particles have moved
+further than the threshold distance.
+
+.. note::
+
+   If the system is undergoing significant center-of-mass motion,
+   due to thermal motion, an external force, or an initial net momentum,
+   then this compute will not be able to distinguish that motion from
+   local atom displacements and may generate "false positives."
+
+**Output info:**
+
+This compute calculates a global scalar (the flag).  This value can be
+used by any command that uses a global scalar value from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "intensive".  The
+scalar value will be a 0 or 1 as explained above.
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`prd <prd>`, :doc:`tad <tad>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst
new file mode 100644
index 0000000000..c54d0ee8fa
--- /dev/null
+++ b/doc/src/compute_fep.rst
@@ -0,0 +1,349 @@
+.. index:: compute fep
+
+compute fep command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID fep temp attribute args ... keyword value ...
+
+* ID, group-ID are documented in the :doc:`compute <compute>` command
+* fep = name of this compute command
+* temp = external temperature (as specified for constant-temperature run)
+* one or more attributes with args may be appended
+* attribute = *pair* or *atom*
+  
+  .. parsed-literal::
+  
+       *pair* args = pstyle pparam I J v_delta
+         pstyle = pair style name, e.g. lj/cut
+         pparam = parameter to perturb
+         I,J = type pair(s) to set parameter for
+         v_delta = variable with perturbation to apply (in the units of the parameter)
+       *atom* args = aparam I v_delta
+         aparam = parameter to perturb
+         I = type to set parameter for
+         v_delta = variable with perturbation to apply (in the units of the parameter)
+
+* zero or more keyword/value pairs may be appended
+* keyword = *tail* or *volume*
+  
+  .. parsed-literal::
+  
+       *tail* value = *no* or *yes*
+         *no* = ignore tail correction to pair energies (usually small in fep)
+         *yes* = include tail correction to pair energies
+       *volume* value = *no* or *yes*
+         *no* = ignore volume changes (e.g. in *NVE* or *NVT* trajectories)
+         *yes* = include volume changes (e.g. in *NpT* trajectories)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all fep 298 pair lj/cut epsilon 1 \* v_delta pair lj/cut sigma 1 \* v_delta volume yes
+   compute 1 all fep 300 atom charge 2 v_delta
+
+Description
+"""""""""""
+
+Apply a perturbation to parameters of the interaction potential and
+recalculate the pair potential energy without changing the atomic
+coordinates from those of the reference, unperturbed system. This
+compute can be used to calculate free energy differences using several
+methods, such as free-energy perturbation (FEP), finite-difference
+thermodynamic integration (FDTI) or Bennet's acceptance ratio method
+(BAR).
+
+The potential energy of the system is decomposed in three terms: a
+background term corresponding to interaction sites whose parameters
+remain constant, a reference term :math:`U_0` corresponding to the
+initial interactions of the atoms that will undergo perturbation, and
+a term :math:`U_1` corresponding to the final interactions of
+these atoms:
+
+.. image:: Eqs/compute_fep_u.jpg
+   :align: center
+
+A coupling parameter :math:`\lambda` varying from 0 to 1 connects the
+reference and perturbed systems:
+
+.. image:: Eqs/compute_fep_lambda.jpg
+   :align: center
+
+It is possible but not necessary that the coupling parameter (or a
+function thereof) appears as a multiplication factor of the potential
+energy. Therefore, this compute can apply perturbations to interaction
+parameters that are not directly proportional to the potential energy
+(e.g. :math:`\sigma` in Lennard-Jones potentials).
+
+This command can be combined with :doc:`fix adapt <fix_adapt>` to
+perform multistage free-energy perturbation calculations along
+stepwise alchemical transformations during a simulation run:
+
+.. image:: Eqs/compute_fep_fep.jpg
+   :align: center
+
+This compute is suitable for the finite-difference thermodynamic
+integration (FDTI) method :ref:`(Mezei) <Mezei>`, which is based on an
+evaluation of the numerical derivative of the free energy by a
+perturbation method using a very small :math:`\delta`:
+
+.. image:: Eqs/compute_fep_fdti.jpg
+   :align: center
+
+where :math:`w_i` are weights of a numerical quadrature. The :doc:`fix adapt <fix_adapt>` command can be used to define the stages of
+:math:`\lambda` at which the derivative is calculated and averaged.
+
+The compute fep calculates the exponential Boltzmann term and also the
+potential energy difference :math:`U_1 -U_0`. By
+choosing a very small perturbation :math:`\delta` the thermodynamic
+integration method can be implemented using a numerical evaluation of
+the derivative of the potential energy with respect to :math:`\lambda`:
+
+.. image:: Eqs/compute_fep_ti.jpg
+   :align: center
+
+Another technique to calculate free energy differences is the
+acceptance ratio method :ref:`(Bennet) <Bennet>`, which can be implemented
+by calculating the potential energy differences with :math:`\delta` = 1.0 on
+both the forward and reverse routes:
+
+.. image:: Eqs/compute_fep_bar.jpg
+   :align: center
+
+The value of the free energy difference is determined by numerical
+root finding to establish the equality.
+
+Concerning the choice of how the atomic parameters are perturbed in
+order to setup an alchemical transformation route, several strategies
+are available, such as single-topology or double-topology strategies
+:ref:`(Pearlman) <Pearlman>`. The latter does not require modification of
+bond lengths, angles or other internal coordinates.
+
+NOTES: This compute command does not take kinetic energy into account,
+therefore the masses of the particles should not be modified between
+the reference and perturbed states, or along the alchemical
+transformation route.  This compute command does not change bond
+lengths or other internal coordinates :ref:`(Boresch, Karplus) <BoreschKarplus>`.
+
+
+----------
+
+
+The *pair* attribute enables various parameters of potentials defined
+by the :doc:`pair\_style <pair_style>` and :doc:`pair\_coeff <pair_coeff>`
+commands to be changed, if the pair style supports it.
+
+The *pstyle* argument is the name of the pair style. For example,
+*pstyle* could be specified as "lj/cut".  The *pparam* argument is the
+name of the parameter to change.  This is a list of
+pair styles and parameters that can be used with this compute.  See
+the doc pages for individual pair styles and their energy formulas for
+the meaning of these parameters:
+
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`born <pair_born>`                                             | a,b,c                   | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`buck <pair_buck>`                                             | a,c                     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`buck/mdf <pair_mdf>`                                          | a,c                     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/cut <pair_coul>`                                         | scale                   | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/cut/soft <pair_fep_soft>`                                | lambda                  | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/long, coul/msm <pair_coul>`                              | scale                   | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/long/soft <pair_fep_soft>`                               | scale, lambda           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`eam <pair_eam>`                                               | scale                   | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`gauss <pair_gauss>`                                           | a                       | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lennard/mdf <pair_mdf>`                                       | a,b                     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/class2 <pair_class2>`                                      | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>`        | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut <pair_lj>`                                             | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/soft <pair_fep_soft>`                                  | epsilon,sigma,lambda    | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj>` | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>`  | epsilon,sigma,lambda    | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long <pair_lj>`                | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>`                       | epsilon,sigma,lambda    | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/expand <pair_lj_expand>`                                   | epsilon,sigma,delta     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/mdf <pair_mdf>`                                            | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/sf/dipole/sf <pair_dipole>`                                | epsilon,sigma,scale     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`mie/cut <pair_mie>`                                           | epsilon,sigma,gamR,gamA | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`morse, morse/smooth/linear <pair_morse>`                      | d0,r0,alpha             | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`morse/soft <pair_morse>`                                      | d0,r0,alpha,lambda      | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`nm/cut <pair_nm>`                                             | e0,r0,nn,mm             | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>`                  | e0,r0,nn,mm             | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`ufm <pair_ufm>`                                               | epsilon,sigma,scale     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`soft <pair_soft>`                                             | a                       | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+
+Note that it is easy to add new potentials and their parameters to
+this list.  All it typically takes is adding an extract() method to
+the pair\_\*.cpp file associated with the potential.
+
+Similar to the :doc:`pair\_coeff <pair_coeff>` command, I and J can be
+specified in one of two ways.  Explicit numeric values can be used for
+each, as in the 1st example above.  I <= J is required.  LAMMPS sets
+the coefficients for the symmetric J,I interaction to the same
+values. A wild-card asterisk can be used in place of or in conjunction
+with the I,J arguments to set the coefficients for multiple pairs of
+atom types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+the number of atom types, then an asterisk with no numeric values
+means all types from 1 to N.  A leading asterisk means all types from
+1 to n (inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).  Note that only type pairs with I <= J are considered; if
+asterisks imply type pairs where J < I, they are ignored.
+
+If :doc:`pair\_style hybrid or hybrid/overlay <pair_hybrid>` is being
+used, then the *pstyle* will be a sub-style name.  You must specify
+I,J arguments that correspond to type pair values defined (via the
+:doc:`pair\_coeff <pair_coeff>` command) for that sub-style.
+
+The *v\_name* argument for keyword *pair* is the name of an
+:doc:`equal-style variable <variable>` which will be evaluated each time
+this compute is invoked.  It should be specified as v\_name, where name
+is the variable name.
+
+
+----------
+
+
+The *atom* attribute enables atom properties to be changed.  The
+*aparam* argument is the name of the parameter to change.  This is the
+current list of atom parameters that can be used with this compute:
+
+* charge = charge on particle
+
+The *v\_name* argument for keyword *pair* is the name of an
+:doc:`equal-style variable <variable>` which will be evaluated each time
+this compute is invoked.  It should be specified as v\_name, where name
+is the variable name.
+
+
+----------
+
+
+The *tail* keyword controls the calculation of the tail correction to
+"van der Waals" pair energies beyond the cutoff, if this has been
+activated via the :doc:`pair\_modify <pair_modify>` command. If the
+perturbation is small, the tail contribution to the energy difference
+between the reference and perturbed systems should be negligible.
+
+If the keyword *volume* = *yes*\ , then the Boltzmann term is multiplied
+by the volume so that correct ensemble averaging can be performed over
+trajectories during which the volume fluctuates or changes :ref:`(Allen and Tildesley) <AllenTildesley>`:
+
+.. image:: Eqs/compute_fep_vol.jpg
+   :align: center
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global vector of length 3 which contains the
+energy difference ( :math:`U_1-U_0` ) as c\_ID[1], the
+Boltzmann factor :math:`\exp(-(U_1-U_0)/kT)`, or
+:math:`V \exp(-(U_1-U_0)/kT)`, as c\_ID[2] and the
+volume of the simulation box :math:`V` as c\_ID[3]. :math:`U_1` is the
+pair potential energy obtained with the perturbed parameters and
+:math:`U_0` is the pair potential energy obtained with the
+unperturbed parameters. The energies include kspace terms if these
+are used in the simulation.
+
+These output results can be used by any command that uses a global
+scalar or vector from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
+
+The values calculated by this compute are "extensive".
+
+Restrictions
+""""""""""""
+
+
+This compute is distributed as the USER-FEP package.  It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix adapt/fep <fix_adapt_fep>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`pair\_fep\_soft <pair_fep_soft>`
+
+Default
+"""""""
+
+The option defaults are *tail* = *no*\ , *volume* = *no*\ .
+
+
+----------
+
+
+.. _Pearlman:
+
+
+
+**(Pearlman)** Pearlman, J Chem Phys, 98, 1487 (1994)
+
+.. _Mezei:
+
+
+
+**(Mezei)** Mezei, J Chem Phys, 86, 7084 (1987)
+
+.. _Bennet:
+
+
+
+**(Bennet)** Bennet, J Comput Phys, 22, 245 (1976)
+
+.. _BoreschKarplus:
+
+
+
+**(BoreschKarplus)** Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
+
+.. _AllenTildesley:
+
+
+
+**(AllenTildesley)** Allen and Tildesley, Computer Simulation of
+Liquids, Oxford University Press (1987)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst
new file mode 100644
index 0000000000..5ff6f1775f
--- /dev/null
+++ b/doc/src/compute_global_atom.rst
@@ -0,0 +1,250 @@
+.. index:: compute global/atom
+
+compute global/atom command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID style index input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* global/atom = style name of this compute command
+* index = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
+  
+  .. parsed-literal::
+  
+       c_ID = per-atom vector calculated by a compute with ID
+       c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+       f_ID = per-atom vector calculated by a fix with ID
+       f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+       v_name = per-atom vector calculated by an atom-style variable with name
+
+* one or more inputs can be listed
+* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
+  
+  .. parsed-literal::
+  
+       c_ID = global vector calculated by a compute with ID
+       c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = global vector calculated by a fix with ID
+       f_ID[I] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+       v_name = global vector calculated by a vector-style variable with name
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all global/atom c_chunk c_com[1\] c_com[2\] c_com[3\]
+   compute 1 all global/atom c_chunk c_com[\*\]
+
+Description
+"""""""""""
+
+Define a calculation that assigns global values to each atom from
+vectors or arrays of global values.  The specified *index* parameter
+is used to determine which global value is assigned to each atom.
+
+The *index* parameter must reference a per-atom vector or array from a
+:doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation of an
+atom-style :doc:`variable <variable>`.  Each *input* value must
+reference a global vector or array from a :doc:`compute <compute>` or
+:doc:`fix <fix>` or the evaluation of an vector-style
+:doc:`variable <variable>`.  Details are given below.
+
+The *index* value for an atom is used as a index I (from 1 to N) into
+the vector associated with each of the input values.  The Ith value
+from the input vector becomes one output value for that atom.  If the
+atom is not in the specified group, or the index I < 1 or I > M, where
+M is the actual length of the input vector, then an output value of
+0.0 is assigned to the atom.
+
+An example of how this command is useful, is in the context of
+"chunks" which are static or dynamic subsets of atoms.  The :doc:`compute chunk/atom <compute_chunk_atom>` command assigns unique chunk IDs
+to each atom.  It's output can be used as the *index* parameter for
+this command.  Various other computes with "chunk" in their style
+name, such as :doc:`compute com/chunk <compute_com_chunk>` or :doc:`compute msd/chunk <compute_msd_chunk>`, calculate properties for each
+chunk.  The output of these commands are global vectors or arrays,
+with one or more values per chunk, and can be used as input values for
+this command.  This command will then assign the global chunk value to
+each atom in the chunk, producing a per-atom vector or per-atom array
+as output.  The per-atom values can then be output to a dump file or
+used by any command that uses per-atom values from a compute as input,
+as discussed on the :doc:`Howto output <Howto_output>` doc page.
+
+As a concrete example, these commands will calculate the displacement
+of each atom from the center-of-mass of the molecule it is in, and
+dump those values to a dump file.  In this case, each molecule is a
+chunk.
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all com/chunk cc1
+   compute prop all property/atom xu yu zu
+   compute glob all global/atom c_cc1 c_myChunk[\*]
+   variable dx atom c_prop[1]-c_glob[1]
+   variable dy atom c_prop[2]-c_glob[2]
+   variable dz atom c_prop[3]-c_glob[3]
+   variable dist atom sqrt(v_dx\*v_dx+v_dy\*v_dy+v_dz\*v_dz)
+   dump 1 all custom 100 tmp.dump id xu yu zu c_glob[1] c_glob[2] c_glob[3] &
+        v_dx v_dy v_dz v_dist
+   dump_modify 1 sort id
+
+You can add these commands to the bench/in.chain script to see how
+they work.
+
+
+----------
+
+
+Note that for input values from a compute or fix, the bracketed index
+I can be specified using a wildcard asterisk with the index to
+effectively specify multiple values.  This takes the form "\*" or "\*n"
+or "n\*" or "m\*n".  If N = the size of the vector (for *mode* = scalar)
+or the number of columns in the array (for *mode* = vector), then an
+asterisk with no numeric values means all indices from 1 to N.  A
+leading asterisk means all indices from 1 to n (inclusive).  A
+trailing asterisk means all indices from n to N (inclusive).  A middle
+asterisk means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 compute global/atom commands
+are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>`
+command creates a global array with 3 columns:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute com all com/chunk cc1
+   compute 1 all global/atom c_cc1 c_com[1] c_com[2] c_com[3]
+   compute 1 all global/atom c_cc1 c_com[\*]
+
+
+----------
+
+
+This section explains the *index* parameter.  Note that it must
+reference per-atom values, as contrasted with the *input* values which
+must reference global values.
+
+Note that all of these options generate floating point values.  When
+they are used as an index into the specified input vectors, they
+simple rounded down to convert the value to integer indices.  The
+final values should range from 1 to N (inclusive), since they are used
+to access values from N-length vectors.
+
+If *index* begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  The compute must generate
+per-atom quantities.  See the individual :doc:`compute <compute>` doc
+page for details.  If no bracketed integer is appended, the per-atom
+vector calculated by the compute is used.  If a bracketed integer is
+appended, the Ith column of the per-atom array calculated by the
+compute is used.  Users can also write code for their own compute
+styles and :doc:`add them to LAMMPS <Modify>`.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If *index* begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  The Fix must generate
+per-atom quantities.  See the individual :doc:`fix <fix>` doc page for
+details.  Note that some fixes only produce their values on certain
+timesteps, which must be compatible with when compute global/atom
+references the values, else an error results.  If no bracketed integer
+is appended, the per-atom vector calculated by the fix is used.  If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used.  Users can also write code for their
+own fix style and :doc:`add them to LAMMPS <Modify>`.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If *index* begins with "v\_", a variable name must follow which has
+been previously defined in the input script.  It must be an
+:doc:`atom-style variable <variable>`.  Atom-style variables can
+reference thermodynamic keywords and various per-atom attributes, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of generating per-atom quantities to use
+as *index*\ .
+
+
+----------
+
+
+This section explains the kinds of *input* values that can be used.
+Note that inputs reference global values, as contrasted with the
+*index* parameter which must reference per-atom values.
+
+If a value begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  The compute must generate a
+global vector or array.  See the individual :doc:`compute <compute>` doc
+page for details.  If no bracketed integer is appended, the vector
+calculated by the compute is used.  If a bracketed integer is
+appended, the Ith column of the array calculated by the compute is
+used.  Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how
+I can be specified with a wildcard asterisk to effectively specify
+multiple values.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  The fix must generate a
+global vector or array.  See the individual :doc:`fix <fix>` doc page
+for details.  Note that some fixes only produce their values on
+certain timesteps, which must be compatible with when compute
+global/atom references the values, else an error results.  If no
+bracketed integer is appended, the vector calculated by the fix is
+used.  If a bracketed integer is appended, the Ith column of the array
+calculated by the fix is used.  Users can also write code for their
+own fix style and :doc:`add them to LAMMPS <Modify>`.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If a value begins with "v\_", a variable name must follow which has
+been previously defined in the input script.  It must be a
+:doc:`vector-style variable <variable>`.  Vector-style variables can
+reference thermodynamic keywords and various other attributes of
+atoms, or invoke other computes, fixes, or variables when they are
+evaluated, so this is a very general means of generating a vector of
+global quantities which the *index* parameter will reference for
+assignment of global values to atoms.
+
+
+----------
+
+
+**Output info:**
+
+If a single input is specified this compute produces a per-atom
+vector.  If multiple inputs are specified, this compute produces a
+per-atom array values, where the number of columns is equal to the
+number of inputs specified.  These values can be used by any command
+that uses per-atom vector or array values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector or array values will be in whatever units the
+corresponding input values are in.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`variable <variable>`,
+:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst
new file mode 100644
index 0000000000..7345bd1031
--- /dev/null
+++ b/doc/src/compute_group_group.rst
@@ -0,0 +1,187 @@
+.. index:: compute group/group
+
+compute group/group command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID group/group group2-ID keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* group/group = style name of this compute command
+* group2-ID = group ID of second (or same) group
+* zero or more keyword/value pairs may be appended
+* keyword = *pair* or *kspace* or *boundary* or *molecule*
+  
+  .. parsed-literal::
+  
+       *pair* value = *yes* or *no*
+       *kspace* value = *yes* or *no*
+       *boundary* value = *yes* or *no*
+       *molecule* value = *off* or *inter* or *intra*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 lower group/group upper
+   compute 1 lower group/group upper kspace yes
+   compute mine fluid group/group wall
+
+Description
+"""""""""""
+
+Define a computation that calculates the total energy and force
+interaction between two groups of atoms: the compute group and the
+specified group2.  The two groups can be the same.
+
+If the *pair* keyword is set to *yes*\ , which is the default, then the
+the interaction energy will include a pair component which is defined
+as the pairwise energy between all pairs of atoms where one atom in
+the pair is in the first group and the other is in the second group.
+Likewise, the interaction force calculated by this compute will
+include the force on the compute group atoms due to pairwise
+interactions with atoms in the specified group2.
+
+.. note::
+
+   The energies computed by the *pair* keyword do not include tail
+   corrections, even if they are enabled via the
+   :doc:`pair\_modify <pair_modify>` command.
+
+If the *molecule* keyword is set to *inter* or *intra* than an
+additional check is made based on the molecule IDs of the two atoms in
+each pair before including their pairwise interaction energy and
+force.  For the *inter* setting, the two atoms must be in different
+molecules.  For the *intra* setting, the two atoms must be in the same
+molecule.
+
+If the *kspace* keyword is set to *yes*\ , which is not the default, and
+if a :doc:`kspace\_style <kspace_style>` is defined, then the interaction
+energy will include a Kspace component which is the long-range
+Coulombic energy between all the atoms in the first group and all the
+atoms in the 2nd group.  Likewise, the interaction force calculated by
+this compute will include the force on the compute group atoms due to
+long-range Coulombic interactions with atoms in the specified group2.
+
+Normally the long-range Coulombic energy converges only when the net
+charge of the unit cell is zero.  However, one can assume the net
+charge of the system is neutralized by a uniform background plasma,
+and a correction to the system energy can be applied to reduce
+artifacts. For more information see :ref:`(Bogusz) <Bogusz>`.  If the
+*boundary* keyword is set to *yes*\ , which is the default, and *kspace*
+contributions are included, then this energy correction term will be
+added to the total group-group energy.  This correction term does not
+affect the force calculation and will be zero if one or both of the
+groups are charge neutral.  This energy correction term is the same as
+that included in the regular Ewald and PPPM routines.
+
+.. note::
+
+   The *molecule* setting only affects the group/group
+   contributions calculated by the *pair* keyword.  It does not affect
+   the group/group contributions calculated by the *kspace* keyword.
+
+This compute does not calculate any bond or angle or dihedral or
+improper interactions between atoms in the two groups.
+
+
+----------
+
+
+The pairwise contributions to the group-group interactions are
+calculated by looping over a neighbor list.  The Kspace contribution
+to the group-group interactions require essentially the same amount of
+work (FFTs, Ewald summation) as computing long-range forces for the
+entire system.  Thus it can be costly to invoke this compute too
+frequently.
+
+.. note::
+
+   If you have a bonded system, then the settings of
+   :doc:`special\_bonds <special_bonds>` command can remove pairwise
+   interactions between atoms in the same bond, angle, or dihedral.  This
+   is the default setting for the :doc:`special\_bonds <special_bonds>`
+   command, and means those pairwise interactions do not appear in the
+   neighbor list.  Because this compute uses a neighbor list, it also
+   means those pairs will not be included in the group/group interaction.
+   This does not apply when using long-range coulomb interactions
+   (\ *coul/long*\ , *coul/msm*\ , *coul/wolf* or similar.  One way to get
+   around this would be to set special\_bond scaling factors to very tiny
+   numbers that are not exactly zero (e.g. 1.0e-50). Another workaround
+   is to write a dump file, and use the :doc:`rerun <rerun>` command to
+   compute the group/group interactions for snapshots in the dump file.
+   The rerun script can use a :doc:`special\_bonds <special_bonds>` command
+   that includes all pairs in the neighbor list.
+
+If you desire a breakdown of the interactions into a pairwise and
+Kspace component, simply invoke the compute twice with the appropriate
+yes/no settings for the *pair* and *kspace* keywords.  This is no more
+costly than using a single compute with both keywords set to *yes*\ .
+The individual contributions can be summed in a
+:doc:`variable <variable>` if desired.
+
+This `document <PDF/kspace.pdf>`_ describes how the long-range
+group-group calculations are performed.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the energy) and a global
+vector of length 3 (force), which can be accessed by indices 1-3.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+Both the scalar and vector values calculated by this compute are
+"extensive".  The scalar value will be in energy :doc:`units <units>`.
+The vector values will be in force :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+Not all pair styles can be evaluated in a pairwise mode as required by
+this compute.  For example, 3-body and other many-body potentials,
+such as :doc:`Tersoff <pair_tersoff>` and
+:doc:`Stillinger-Weber <pair_sw>` cannot be used.  :doc:`EAM <pair_eam>`
+potentials will re-use previously computed embedding term contributions,
+so the computed pairwise forces and energies are based on the whole
+system and not valid if particles have been moved since.
+
+Not all :doc:`Kspace styles <kspace_style>` support the calculation of
+group/group interactions. The regular *ewald* and *pppm* styles do.
+
+**Related commands:** none
+
+Default
+"""""""
+
+The option defaults are pair = yes, kspace = no, boundary = yes,
+molecule = off.
+
+
+----------
+
+
+.. _Bogusz:
+
+
+
+Bogusz et al, J Chem Phys, 108, 7070 (1998)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst
new file mode 100644
index 0000000000..15636a9275
--- /dev/null
+++ b/doc/src/compute_gyration.rst
@@ -0,0 +1,86 @@
+.. index:: compute gyration
+
+compute gyration command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID gyration
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* gyration = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 molecule gyration
+
+Description
+"""""""""""
+
+Define a computation that calculates the radius of gyration Rg of the
+group of atoms, including all effects due to atoms passing through
+periodic boundaries.
+
+Rg is a measure of the size of the group of atoms, and is computed as
+the square root of the Rg\^2 value in this formula
+
+.. image:: Eqs/compute_gyration.jpg
+   :align: center
+
+where M is the total mass of the group, Rcm is the center-of-mass
+position of the group, and the sum is over all atoms in the group.
+
+A Rg\^2 tensor, stored as a 6-element vector, is also calculated by
+this compute.  The formula for the components of the tensor is the
+same as the above formula, except that (Ri - Rcm)\^2 is replaced by
+(Rix - Rcmx) \* (Riy - Rcmy) for the xy component, etc.  The 6
+components of the vector are ordered xx, yy, zz, xy, xz, yz.  Note
+that unlike the scalar Rg, each of the 6 values of the tensor is
+effectively a "squared" value, since the cross-terms may be negative
+and taking a sqrt() would be invalid.
+
+.. note::
+
+   The coordinates of an atom contribute to Rg in "unwrapped" form,
+   by using the image flags associated with each atom.  See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
+   See the Atoms section of the :doc:`read\_data <read_data>` command for a
+   discussion of image flags and how they are set for each atom.  You can
+   reset the image flags (e.g. to 0) before invoking this compute by
+   using the :doc:`set image <set>` command.
+
+**Output info:**
+
+This compute calculates a global scalar (Rg) and a global vector of
+length 6 (Rg\^2 tensor), which can be accessed by indices 1-6.  These
+values can be used by any command that uses a global scalar value or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar and vector values calculated by this compute are
+"intensive".  The scalar and vector values will be in distance and
+distance\^2 :doc:`units <units>` respectively.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute gyration/chunk <compute_gyration_chunk>`,
+:doc:`compute gyration/shape <compute_gyration_shape>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst
new file mode 100644
index 0000000000..4726a14d0e
--- /dev/null
+++ b/doc/src/compute_gyration_chunk.rst
@@ -0,0 +1,126 @@
+.. index:: compute gyration/chunk
+
+compute gyration/chunk command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID gyration/chunk chunkID keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* gyration/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* zero or more keyword/value pairs may be appended
+* keyword = *tensor*
+  
+  .. parsed-literal::
+  
+       *tensor* value = none
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 molecule gyration/chunk molchunk
+   compute 2 molecule gyration/chunk molchunk tensor
+
+Description
+"""""""""""
+
+Define a computation that calculates the radius of gyration Rg for
+multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates the radius of gyration Rg for each chunk,
+which includes all effects due to atoms passing through periodic
+boundaries.
+
+Rg is a measure of the size of a chunk, and is computed by this
+formula
+
+.. image:: Eqs/compute_gyration.jpg
+   :align: center
+
+where M is the total mass of the chunk, Rcm is the center-of-mass
+position of the chunk, and the sum is over all atoms in the
+chunk.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+If the *tensor* keyword is specified, then the scalar Rg value is not
+calculated, but an Rg tensor is instead calculated for each chunk.
+The formula for the components of the tensor is the same as the above
+formula, except that (Ri - Rcm)\^2 is replaced by (Rix - Rcmx) \* (Riy -
+Rcmy) for the xy component, etc.  The 6 components of the tensor are
+ordered xx, yy, zz, xy, xz, yz.
+
+.. note::
+
+   The coordinates of an atom contribute to Rg in "unwrapped" form,
+   by using the image flags associated with each atom.  See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
+   See the Atoms section of the :doc:`read\_data <read_data>` command for a
+   discussion of image flags and how they are set for each atom.  You can
+   reset the image flags (e.g. to 0) before invoking this compute by
+   using the :doc:`set image <set>` command.
+
+The simplest way to output the results of the compute gyration/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all gyration/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global vector if the *tensor* keyword is not
+specified and a global array if it is.  The length of the vector or
+number of rows in the array = the number of chunks *Nchunk* as
+calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  If the *tensor* keyword
+is specified, the global array has 6 columns.  The vector or array can
+be accessed by any command that uses global values from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+All the vector or array values calculated by this compute are
+"intensive".  The vector or array values will be in distance
+:doc:`units <units>`, since they are the square root of values
+represented by the formula above.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+:doc:`compute gyration <compute_gyration>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst
new file mode 100644
index 0000000000..5461825923
--- /dev/null
+++ b/doc/src/compute_gyration_shape.rst
@@ -0,0 +1,111 @@
+.. index:: compute gyration/shape
+
+compute gyration/shape command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID gyration/shape compute-ID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* gyration/shape = style name of this compute command
+* compute-ID = ID of :doc:`compute gyration <compute_gyration>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 molecule gyration/shape pe
+
+Description
+"""""""""""
+
+Define a computation that calculates the eigenvalues of the gyration tensor of a
+group of atoms and three shape parameters. The computation includes all effects
+due to atoms passing through periodic boundaries.
+
+The three computed shape parameters are the asphericity, b, the acylindricity, c,
+and the relative shape anisotropy, k:
+
+.. image:: Eqs/compute_shape_parameters.jpg
+   :align: center
+
+where lx <= ly <= lz are the three eigenvalues of the gyration tensor. A general description 
+of these parameters is provided in :ref:`(Mattice) <Mattice1>` while an application to polymer systems 
+can be found in :ref:`(Theodorou) <Theodorou1>`.
+The asphericity  is always non-negative and zero only when the three principal
+moments are equal. This zero condition is met when the distribution of particles
+is spherically symmetric (hence the name asphericity) but also whenever the particle
+distribution is symmetric with respect to the three coordinate axes, e.g.,
+when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
+solid. The acylindricity is always non-negative and zero only when the two principal
+moments are equal. This zero condition is met when the distribution of particles is
+cylindrically symmetric (hence the name, acylindricity), but also whenever the particle
+distribution is symmetric with respect to the two coordinate axes, e.g., when the
+particles are distributed uniformly on a regular prism. the relative shape anisotropy
+is bounded between zero (if all points are spherically symmetric) and one
+(if all points lie on a line).
+
+.. note::
+
+   The coordinates of an atom contribute to the gyration tensor in
+   "unwrapped" form, by using the image flags associated with each atom.
+   See the :doc:`dump custom <dump>` command for a discussion of "unwrapped"
+   coordinates. See the Atoms section of the :doc:`read\_data <read_data>`
+   command for a discussion of image flags and how they are set for each
+   atom.  You can reset the image flags (e.g. to 0) before invoking this
+   compute by using the :doc:`set image <set>` command.
+
+**Output info:**
+
+This compute calculates a global vector of
+length 6, which can be accessed by indices 1-6. The first three values are the
+eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
+and the relative shape anisotropy.  The computed values can be used by any command
+that uses global  vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector values calculated by this compute are
+"intensive".  The first five vector values will be in
+distance\^2 :doc:`units <units>` while the sixth one is dimensionless.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute gyration <compute_gyration>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Mattice1:
+
+
+
+**(Mattice)** Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.
+
+.. _Theodorou1:
+
+
+
+**(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst
new file mode 100644
index 0000000000..fa839aea35
--- /dev/null
+++ b/doc/src/compute_gyration_shape_chunk.rst
@@ -0,0 +1,113 @@
+.. index:: compute gyration/shape/chunk
+
+compute gyration/shape/chunk command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID gyration/shape/chunk compute-ID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* gyration/shape/chunk = style name of this compute command
+* compute-ID = ID of :doc:`compute gyration/chunk <compute_gyration_chunk>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 molecule gyration/shape/chunk pe
+
+Description
+"""""""""""
+
+Define a computation that calculates the eigenvalues of the gyration tensor and 
+three shape parameters of multiple chunks of atoms. The computation includes 
+all effects due to atoms passing through periodic boundaries.
+
+The three computed shape parameters are the asphericity, b, the acylindricity, c,
+and the relative shape anisotropy, k:
+
+.. image:: Eqs/compute_shape_parameters.jpg
+   :align: center
+
+where lx <= ly <= lz are the three eigenvalues of the gyration tensor. A general description 
+of these parameters is provided in :ref:`(Mattice) <Mattice2>` while an application to polymer systems 
+can be found in :ref:`(Theodorou) <Theodorou2>`. The asphericity  is always non-negative and zero 
+only when the three principal moments are equal. This zero condition is met when the distribution 
+of particles is spherically symmetric (hence the name asphericity) but also whenever the particle
+distribution is symmetric with respect to the three coordinate axes, e.g.,
+when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
+solid. The acylindricity is always non-negative and zero only when the two principal
+moments are equal. This zero condition is met when the distribution of particles is
+cylindrically symmetric (hence the name, acylindricity), but also whenever the particle
+distribution is symmetric with respect to the two coordinate axes, e.g., when the
+particles are distributed uniformly on a regular prism. the relative shape anisotropy
+is bounded between zero (if all points are spherically symmetric) and one
+(if all points lie on a line).
+
+The tensor keyword must be specified in the compute gyration/chunk command.
+
+.. note::
+
+   The coordinates of an atom contribute to the gyration tensor in
+   "unwrapped" form, by using the image flags associated with each atom.
+   See the :doc:`dump custom <dump>` command for a discussion of "unwrapped"
+   coordinates. See the Atoms section of the :doc:`read\_data <read_data>`
+   command for a discussion of image flags and how they are set for each
+   atom.  You can reset the image flags (e.g. to 0) before invoking this
+   compute by using the :doc:`set image <set>` command.
+
+**Output info:**
+
+This compute calculates a global array with six columns, 
+which can be accessed by indices 1-6. The first three columns are the
+eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
+and the relative shape anisotropy.  The computed values can be used by any command
+that uses global array values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The array calculated by this compute is
+"intensive".  The first five columns will be in
+distance\^2 :doc:`units <units>` while the sixth one is dimensionless.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute gyration/chunk <compute_gyration_chunk>`
+:doc:`compute gyration/shape <compute_gyration_shape>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Mattice2:
+
+
+
+**(Mattice)** Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.
+
+.. _Theodorou2:
+
+
+
+**(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst
new file mode 100644
index 0000000000..3b7058d3d3
--- /dev/null
+++ b/doc/src/compute_heat_flux.rst
@@ -0,0 +1,258 @@
+.. index:: compute heat/flux
+
+compute heat/flux command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID heat/flux ke-ID pe-ID stress-ID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* heat/flux = style name of this compute command
+* ke-ID = ID of a compute that calculates per-atom kinetic energy
+* pe-ID = ID of a compute that calculates per-atom potential energy
+* stress-ID = ID of a compute that calculates per-atom stress
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute myFlux all heat/flux myKE myPE myStress
+
+Description
+"""""""""""
+
+Define a computation that calculates the heat flux vector based on
+contributions from atoms in the specified group.  This can be used by
+itself to measure the heat flux through a set of atoms (e.g. a region
+between two thermostatted reservoirs held at different temperatures),
+or to calculate a thermal conductivity using the equilibrium
+Green-Kubo formalism.
+
+For other non-equilibrium ways to compute a thermal conductivity, see
+the :doc:`Howto kappa <Howto_kappa>` doc page..  These include use of
+the :doc:`fix thermal/conductivity <fix_thermal_conductivity>` command
+for the Muller-Plathe method.  Or the :doc:`fix heat <fix_heat>` command
+which can add or subtract heat from groups of atoms.
+
+The compute takes three arguments which are IDs of other
+:doc:`computes <compute>`.  One calculates per-atom kinetic energy
+(\ *ke-ID*\ ), one calculates per-atom potential energy (\ *pe-ID)*\ , and the
+third calculates per-atom stress (\ *stress-ID*\ ).
+
+.. note::
+
+   These other computes should provide values for all the atoms in
+   the group this compute specifies.  That means the other computes could
+   use the same group as this compute, or they can just use group "all"
+   (or any group whose atoms are superset of the atoms in this compute's
+   group).  LAMMPS does not check for this.
+
+In case of two-body interactions, the heat flux is defined as:
+
+.. math::
+   \mathbf{J} &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i - \sum_{i} \mathbf{S}_{i} \mathbf{v}_i \right] \\
+   &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \sum_{i<j} \left( \mathbf{F}_{ij} \cdot \mathbf{v}_j \right) \mathbf{r}_{ij} \right] \\
+   &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \frac{1}{2} \sum_{i<j} \left( \mathbf{F}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right)  \right) \mathbf{r}_{ij} \right]
+
+:math:`e_i` in the first term of the equation
+is the per-atom energy (potential and kinetic).
+This is calculated by the computes *ke-ID*
+and *pe-ID*. :math:`\mathbf{S}_i` in the second term is the
+per-atom stress tensor calculated by the compute *stress-ID*.
+See :doc:`compute stress/atom <compute_stress_atom>`
+and :doc:`compute centroid/stress/atom <compute_stress_atom>`
+for possible definitions of atomic stress :math:`\mathbf{S}_i`
+in the case of bonded and many-body interactions.
+The tensor multiplies :math:`\mathbf{v}_i` as a 3x3 matrix-vector multiply
+to yield a vector.
+Note that as discussed below, the 1/:math:`{V}` scaling factor in the
+equation for :math:`\mathbf{J}` is NOT included in the calculation performed by
+these computes; you need to add it for a volume appropriate to the atoms
+included in the calculation.
+
+.. note::
+
+   The :doc:`compute pe/atom <compute_pe_atom>` and
+   :doc:`compute stress/atom <compute_stress_atom>`
+   commands have options for which
+   terms to include in their calculation (pair, bond, etc).  The heat
+   flux calculation will thus include exactly the same terms. Normally
+   you should use :doc:`compute stress/atom virial <compute_stress_atom>`
+   or :doc:`compute centroid/stress/atom virial <compute_stress_atom>`
+   so as not to include a kinetic energy term in the heat flux.
+
+
+.. warning::
+
+   The compute *heat/flux* has been reported to produce unphysical
+   values for angle, dihedral and improper contributions
+   when used with :doc:`compute stress/atom <compute_stress_atom>`,
+   as discussed in :ref:`(Surblys) <Surblys2>` and :ref:`(Boone) <Boone>`.
+   You are strongly advised to
+   use :doc:`compute centroid/stress/atom <compute_stress_atom>`,
+   which has been implemented specifically for such cases.
+
+The Green-Kubo formulas relate the ensemble average of the
+auto-correlation of the heat flux :math:`\mathbf{J}`
+to the thermal conductivity :math:`\kappa`:
+
+.. math::
+   \kappa  = \frac{V}{k_B T^2} \int_0^\infty \langle J_x(0)  J_x(t) \rangle \, \mathrm{d} t = \frac{V}{3 k_B T^2} \int_0^\infty \langle \mathbf{J}(0) \cdot  \mathbf{J}(t)  \rangle \, \mathrm{d}t
+
+
+----------
+
+
+The heat flux can be output every so many timesteps (e.g. via the
+:doc:`thermo\_style custom <thermo_style>` command).  Then as a
+post-processing operation, an auto-correlation can be performed, its
+integral estimated, and the Green-Kubo formula above evaluated.
+
+The :doc:`fix ave/correlate <fix_ave_correlate>` command can calculate
+the auto-correlation.  The trap() function in the
+:doc:`variable <variable>` command can calculate the integral.
+
+An example LAMMPS input script for solid Ar is appended below.  The
+result should be: average conductivity ~0.29 in W/mK.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global vector of length 6.
+The first 3 components are the :math:`x`, :math:`y`, :math:`z`
+components of the full heat flux vector,
+i.e. (:math:`J_x`, :math:`J_y`, :math:`J_z`).
+The next 3 components are the :math:`x`, :math:`y`, :math:`z` components
+of just the convective portion of the flux, i.e. the
+first term in the equation for :math:`\mathbf{J}`.
+Each component can be
+accessed by indices 1-6. These values can be used by any command that
+uses global vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector values calculated by this compute are "extensive", meaning
+they scale with the number of atoms in the simulation.  They can be
+divided by the appropriate volume to get a flux, which would then be
+an "intensive" value, meaning independent of the number of atoms in
+the simulation.  Note that if the compute is "all", then the
+appropriate volume to divide by is the simulation box volume.
+However, if a sub-group is used, it should be the volume containing
+those atoms.
+
+The vector values will be in energy\*velocity :doc:`units <units>`.  Once
+divided by a volume the units will be that of flux, namely
+energy/area/time :doc:`units <units>`
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix thermal/conductivity <fix_thermal_conductivity>`,
+:doc:`fix ave/correlate <fix_ave_correlate>`,
+:doc:`variable <variable>`
+
+**Default:** none
+
+
+----------
+
+
+
+.. parsed-literal::
+
+   # Sample LAMMPS input script for thermal conductivity of solid Ar
+
+   units       real
+   variable    T equal 70
+   variable    V equal vol
+   variable    dt equal 4.0
+   variable    p equal 200     # correlation length
+   variable    s equal 10      # sample interval
+   variable    d equal $p\*$s   # dump interval
+
+   # convert from LAMMPS real units to SI
+
+   variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
+   variable    kCal2J equal 4186.0/6.02214e23
+   variable    A2m equal 1.0e-10
+   variable    fs2s equal 1.0e-15
+   variable    convert equal ${kCal2J}\*${kCal2J}/${fs2s}/${A2m}
+
+   # setup problem
+
+   dimension    3
+   boundary     p p p
+   lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+   region       box block 0 4 0 4 0 4
+   create_box   1 box
+   create_atoms 1 box
+   mass         1 39.948
+   pair_style   lj/cut 13.0
+   pair_coeff   \* \* 0.2381 3.405
+   timestep     ${dt}
+   thermo       $d
+
+   # equilibration and thermalization
+
+   velocity     all create $T 102486 mom yes rot yes dist gaussian
+   fix          NVT all nvt temp $T $T 10 drag 0.2
+   run          8000
+
+   # thermal conductivity calculation, switch to NVE if desired
+
+   #unfix       NVT
+   #fix         NVE all nve
+
+   reset_timestep 0
+   compute      myKE all ke/atom
+   compute      myPE all pe/atom
+   compute      myStress all stress/atom NULL virial
+   compute      flux all heat/flux myKE myPE myStress
+   variable     Jx equal c_flux[1]/vol
+   variable     Jy equal c_flux[2]/vol
+   variable     Jz equal c_flux[3]/vol
+   fix          JJ all ave/correlate $s $p $d &
+                c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running
+   variable     scale equal ${convert}/${kB}/$T/$T/$V\*$s\*${dt}
+   variable     k11 equal trap(f_JJ[3])\*${scale}
+   variable     k22 equal trap(f_JJ[4])\*${scale}
+   variable     k33 equal trap(f_JJ[5])\*${scale}
+   thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
+   run          100000
+   variable     k equal (v_k11+v_k22+v_k33)/3.0
+   variable     ndens equal count(all)/vol
+   print        "average conductivity: $k[W/mK] @ $T K, ${ndens} /A\^3"
+
+
+----------
+
+
+.. _Surblys2:
+
+
+
+**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
+
+.. _Boone:
+
+
+
+**(Boone)** Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt
deleted file mode 100644
index edd46f7587..0000000000
--- a/doc/src/compute_heat_flux.txt
+++ /dev/null
@@ -1,192 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-compute heat/flux command :h3
-
-[Syntax:]
-
-compute ID group-ID heat/flux ke-ID pe-ID stress-ID :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-heat/flux = style name of this compute command
-ke-ID = ID of a compute that calculates per-atom kinetic energy
-pe-ID = ID of a compute that calculates per-atom potential energy
-stress-ID = ID of a compute that calculates per-atom stress :ul
-
-[Examples:]
-
-compute myFlux all heat/flux myKE myPE myStress :pre
-
-[Description:]
-
-Define a computation that calculates the heat flux vector based on
-contributions from atoms in the specified group.  This can be used by
-itself to measure the heat flux through a set of atoms (e.g. a region
-between two thermostatted reservoirs held at different temperatures),
-or to calculate a thermal conductivity using the equilibrium
-Green-Kubo formalism.
-
-For other non-equilibrium ways to compute a thermal conductivity, see
-the "Howto kappa"_Howto_kappa.html doc page..  These include use of
-the "fix thermal/conductivity"_fix_thermal_conductivity.html command
-for the Muller-Plathe method.  Or the "fix heat"_fix_heat.html command
-which can add or subtract heat from groups of atoms.
-
-The compute takes three arguments which are IDs of other
-"computes"_compute.html.  One calculates per-atom kinetic energy
-({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
-third calculates per-atom stress ({stress-ID}).
-
-NOTE: These other computes should provide values for all the atoms in
-the group this compute specifies.  That means the other computes could
-use the same group as this compute, or they can just use group "all"
-(or any group whose atoms are superset of the atoms in this compute's
-group).  LAMMPS does not check for this.
-
-The Green-Kubo formulas relate the ensemble average of the
-auto-correlation of the heat flux J to the thermal conductivity kappa:
-
-:c,image(Eqs/heat_flux_J.jpg)
-
-:c,image(Eqs/heat_flux_k.jpg)
-
-Ei in the first term of the equation for J is the per-atom energy
-(potential and kinetic).  This is calculated by the computes {ke-ID}
-and {pe-ID}.  Si in the second term of the equation for J is the
-per-atom stress tensor calculated by the compute {stress-ID}.  The
-tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a
-vector.  Note that as discussed below, the 1/V scaling factor in the
-equation for J is NOT included in the calculation performed by this
-compute; you need to add it for a volume appropriate to the atoms
-included in the calculation.
-
-NOTE: The "compute pe/atom"_compute_pe_atom.html and "compute
-stress/atom"_compute_stress_atom.html commands have options for which
-terms to include in their calculation (pair, bond, etc).  The heat
-flux calculation will thus include exactly the same terms.  Normally
-you should use "compute stress/atom virial"_compute_stress_atom.html
-so as not to include a kinetic energy term in the heat flux.
-
-This compute calculates 6 quantities and stores them in a 6-component
-vector.  The first 3 components are the x, y, z components of the full
-heat flux vector, i.e. (Jx, Jy, Jz).  The next 3 components are the x,
-y, z components of just the convective portion of the flux, i.e. the
-first term in the equation for J above.
-
-:line
-
-The heat flux can be output every so many timesteps (e.g. via the
-"thermo_style custom"_thermo_style.html command).  Then as a
-post-processing operation, an auto-correlation can be performed, its
-integral estimated, and the Green-Kubo formula above evaluated.
-
-The "fix ave/correlate"_fix_ave_correlate.html command can calculate
-the auto-correlation.  The trap() function in the
-"variable"_variable.html command can calculate the integral.
-
-An example LAMMPS input script for solid Ar is appended below.  The
-result should be: average conductivity ~0.29 in W/mK.
-
-:line
-
-[Output info:]
-
-This compute calculates a global vector of length 6 (total heat flux
-vector, followed by convective heat flux vector), which can be
-accessed by indices 1-6.  These values can be used by any command that
-uses global vector values from a compute as input.  See the "Howto
-output"_Howto_output.html doc page for an overview of LAMMPS output
-options.
-
-The vector values calculated by this compute are "extensive", meaning
-they scale with the number of atoms in the simulation.  They can be
-divided by the appropriate volume to get a flux, which would then be
-an "intensive" value, meaning independent of the number of atoms in
-the simulation.  Note that if the compute is "all", then the
-appropriate volume to divide by is the simulation box volume.
-However, if a sub-group is used, it should be the volume containing
-those atoms.
-
-The vector values will be in energy*velocity "units"_units.html.  Once
-divided by a volume the units will be that of flux, namely
-energy/area/time "units"_units.html
-
-[Restrictions:] none
-
-[Related commands:]
-
-"fix thermal/conductivity"_fix_thermal_conductivity.html,
-"fix ave/correlate"_fix_ave_correlate.html,
-"variable"_variable.html
-
-[Default:] none
-
-:line
-
-# Sample LAMMPS input script for thermal conductivity of solid Ar :pre
-
-units       real
-variable    T equal 70
-variable    V equal vol
-variable    dt equal 4.0
-variable    p equal 200     # correlation length
-variable    s equal 10      # sample interval
-variable    d equal $p*$s   # dump interval :pre
-
-# convert from LAMMPS real units to SI :pre
-
-variable    kB equal 1.3806504e-23    # \[J/K\] Boltzmann
-variable    kCal2J equal 4186.0/6.02214e23
-variable    A2m equal 1.0e-10
-variable    fs2s equal 1.0e-15
-variable    convert equal $\{kCal2J\}*$\{kCal2J\}/$\{fs2s\}/$\{A2m\} :pre
-
-# setup problem :pre
-
-dimension    3
-boundary     p p p
-lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
-region       box block 0 4 0 4 0 4
-create_box   1 box
-create_atoms 1 box
-mass         1 39.948
-pair_style   lj/cut 13.0
-pair_coeff   * * 0.2381 3.405
-timestep     $\{dt\}
-thermo       $d :pre
-
-# equilibration and thermalization :pre
-
-velocity     all create $T 102486 mom yes rot yes dist gaussian
-fix          NVT all nvt temp $T $T 10 drag 0.2
-run          8000 :pre
-
-# thermal conductivity calculation, switch to NVE if desired :pre
-
-#unfix       NVT
-#fix         NVE all nve :pre
-
-reset_timestep 0
-compute      myKE all ke/atom
-compute      myPE all pe/atom
-compute      myStress all stress/atom NULL virial
-compute      flux all heat/flux myKE myPE myStress
-variable     Jx equal c_flux\[1\]/vol
-variable     Jy equal c_flux\[2\]/vol
-variable     Jz equal c_flux\[3\]/vol
-fix          JJ all ave/correlate $s $p $d &
-             c_flux\[1\] c_flux\[2\] c_flux\[3\] type auto file J0Jt.dat ave running
-variable     scale equal $\{convert\}/$\{kB\}/$T/$T/$V*$s*$\{dt\}
-variable     k11 equal trap(f_JJ\[3\])*$\{scale\}
-variable     k22 equal trap(f_JJ\[4\])*$\{scale\}
-variable     k33 equal trap(f_JJ\[5\])*$\{scale\}
-thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
-run          100000
-variable     k equal (v_k11+v_k22+v_k33)/3.0
-variable     ndens equal count(all)/vol
-print        "average conductivity: $k\[W/mK\] @ $T K, $\{ndens\} /A^3" :pre
diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst
new file mode 100644
index 0000000000..0807f2ff7f
--- /dev/null
+++ b/doc/src/compute_hexorder_atom.rst
@@ -0,0 +1,139 @@
+.. index:: compute hexorder/atom
+
+compute hexorder/atom command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID hexorder/atom keyword values ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* hexorder/atom = style name of this compute command
+* one or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *degree* or *nnn* or *cutoff*
+       *cutoff* value = distance cutoff
+       *nnn* value = number of nearest neighbors
+       *degree* value = degree *n* of order parameter
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all hexorder/atom
+   compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2
+
+Description
+"""""""""""
+
+Define a computation that calculates *qn* the bond-orientational
+order parameter for each atom in a group. The hexatic (\ *n* = 6) order
+parameter was introduced by :ref:`Nelson and Halperin <Nelson>` as a way to detect
+hexagonal symmetry in two-dimensional systems. For each atom, *qn*
+is a complex number (stored as two real numbers) defined as follows:
+
+.. image:: Eqs/hexorder.jpg
+   :align: center
+
+where the sum is over the *nnn* nearest neighbors
+of the central atom. The angle theta
+is formed by the bond vector rij and the *x* axis. theta is calculated
+only using the *x* and *y* components, whereas the distance from the
+central atom is calculated using all three
+*x*\ , *y*\ , and *z* components of the bond vector.
+Neighbor atoms not in the group
+are included in the order parameter of atoms in the group.
+
+The optional keyword *cutoff* defines the distance cutoff
+used when searching for neighbors. The default value, also
+the maximum allowable value, is the cutoff specified
+by the pair style.
+
+The optional keyword *nnn* defines the number of nearest
+neighbors used to calculate *qn*\ . The default value is 6.
+If the value is NULL, then all neighbors up to the
+distance cutoff are used.
+
+The optional keyword *degree* sets the degree *n* of the order parameter.
+The default value is 6. For a perfect hexagonal lattice with
+*nnn* = 6,
+*q*\ 6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3
+depends only on the orientation of the lattice relative to the *x* axis.
+In an isotropic liquid, local neighborhoods may still exhibit
+weak hexagonal symmetry, but because the orientational correlation
+decays quickly with distance, the value of phi will be different for
+different atoms, and so when *q*\ 6 is averaged over all the atoms
+in the system, \|<\ *q*\ 6>\| << 1.
+
+The value of *qn* is set to zero for atoms not in the
+specified compute group, as well as for atoms that have less than
+*nnn* neighbors within the distance cutoff.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently.
+
+.. note::
+
+   If you have a bonded system, then the settings of
+   :doc:`special\_bonds <special_bonds>` command can remove pairwise
+   interactions between atoms in the same bond, angle, or dihedral.  This
+   is the default setting for the :doc:`special\_bonds <special_bonds>`
+   command, and means those pairwise interactions do not appear in the
+   neighbor list.  Because this fix uses the neighbor list, it also means
+   those pairs will not be included in the order parameter.  This
+   difficulty can be circumvented by writing a dump file, and using the
+   :doc:`rerun <rerun>` command to compute the order parameter for
+   snapshots in the dump file.  The rerun script can use a
+   :doc:`special\_bonds <special_bonds>` command that includes all pairs in
+   the neighbor list.
+
+**Output info:**
+
+This compute calculates a per-atom array with 2 columns, giving the
+real and imaginary parts *qn*\ , a complex number restricted to the
+unit disk of the complex plane i.e. Re(\ *qn*\ )\^2 + Im(\ *qn*\ )\^2 <= 1 .
+
+These values can be accessed by any command that uses per-atom values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute orientorder/atom <compute_orientorder_atom>`, :doc:`compute coord/atom <compute_coord_atom>`, :doc:`compute centro/atom <compute_centro_atom>`
+
+Default
+"""""""
+
+The option defaults are *cutoff* = pair style cutoff, *nnn* = 6, *degree* = 6
+
+
+----------
+
+
+.. _Nelson:
+
+
+
+**(Nelson)** Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst
new file mode 100644
index 0000000000..d8e7a6b31a
--- /dev/null
+++ b/doc/src/compute_hma.rst
@@ -0,0 +1,209 @@
+.. index:: compute hma
+
+compute hma command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID hma temp-ID keyword ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* hma = style name of this compute command
+* temp-ID = ID of fix that specifies the set temperature during canonical simulation
+* keyword = *anharmonic* *u* *p Pharm* *cv*
+
+.. parsed-literal::
+
+     *anharmonic* = compute will return anharmonic property values
+     *u* = compute will return potential energy
+     *p* = compute will return pressure.  the following keyword must be the difference between the harmonic pressure and lattice pressure as described below
+     *cv* = compute will return the heat capacity
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 2 all hma 1 u
+   compute 2 all hma 1 anharmonic u p 0.9
+   compute 2 all hma 1 u cv
+
+Description
+"""""""""""
+
+Define a computation that calculates the properties of a solid (potential
+energy, pressure or heat capacity), using the harmonically-mapped averaging
+(HMA) method.
+This command yields much higher precision than the equivalent compute commands
+(:doc:`compute pe <compute_pe>`, :doc:`compute pressure <compute_pressure>`, etc.)
+commands during a canonical simulation of an atomic crystal. Specifically,
+near melting HMA can yield averages of a given precision an order of magnitude
+faster than conventional methods, and this only improves as the temperatures is
+lowered.  This is particularly important for evaluating the free energy by
+thermodynamic integration, where the low-temperature contributions are the
+greatest source of statistical uncertainty.  Moreover, HMA has other
+advantages, including smaller potential-truncation effects, finite-size
+effects, smaller timestep inaccuracy, faster equilibration and shorter
+decorrelation time.
+
+HMA should not be used if atoms are expected to diffuse.  It is also
+restricted to simulations in the NVT ensemble.  While this compute may be
+used with any potential in LAMMPS, it will provide inaccurate results
+for potentials that do not go to 0 at the truncation distance;
+:doc:`pair\_lj\_smooth\_linear <pair_lj_smooth_linear>` and Ewald summation should
+work fine, while :doc:`pair\_lj <pair_lj>` will perform poorly unless
+the potential is shifted (via :doc:`pair\_modify <pair_modify>` shift) or the cutoff is large.  Furthermore, computation of the heat capacity with
+this compute is restricted to those that implement the single\_hessian method
+in Pair.  Implementing single\_hessian in additional pair styles is simple.
+Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
+buffalo.edu) if your desired pair style does not have this method.  This is
+the list of pair styles that currently implement pair\_hessian:
+
+* :doc:`lj\_smooth\_linear <pair_lj_smooth_linear>`
+
+
+In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble
+averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination
+by noise produced by the already-known harmonic behavior.
+A detailed description of this method can be found in (:ref:`Moustafa <hma-Moustafa>`). The potential energy is computed by the formula:
+
+
+.. math::
+
+   \begin{equation}\left< U\right>_{HMA} = \frac{d}{2} (N-1) k_B T  + \left< U + \frac{1}{2} F\bullet\Delta r \right>\end{equation}
+
+where :math:`N` is the number of atoms in the system, :math:`k_B` is Boltzmann's
+constant, :math:`T` is the temperature, :math:`d` is the
+dimensionality of the system (2 or 3 for 2d/3d), :math:`F\bullet\Delta r` is the sum of dot products of the
+atomic force vectors and displacement (from lattice sites) vectors, and :math:`U` is the sum of
+pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies.
+
+The pressure is computed by the formula:
+
+
+.. math::
+
+   \begin{equation}\left< P\right>_{HMA} = \Delta \hat P + \left< P_{vir} + \frac{\beta \Delta \hat P - \rho}{d(N-1)} F\bullet\Delta r \right>\end{equation}
+
+where :math:`\rho` is the number density of the system, :math:`\Delta \hat P` is the
+difference between the harmonic and lattice pressure, :math:`P_{vir}` is
+the virial pressure computed as the sum of pair, bond, angle, dihedral,
+improper, kspace (long-range), and fix contributions to the force on each
+atom, and :math:`k_B=1/k_B T`.  Although the method will work for any value of :math:`\Delta \hat P`
+specified (use pressure :doc:`units <units>`), the precision of the resultant
+pressure is sensitive to :math:`\Delta \hat P`; the precision tends to be
+best when :math:`\Delta \hat P` is the actual the difference between the lattice
+pressure and harmonic pressure.
+
+
+.. math::
+
+   \begin{equation}\left<C_V \right>_{HMA} = \frac{d}{2} (N-1) k_B + \frac{1}{k_B T^2} \left( \left<
+   U_{HMA}^2 \right> - \left<U_{HMA}\right>^2 \right) + \frac{1}{4 T}
+   \left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right>\end{equation}
+
+where :math:`\Phi` is the Hessian matrix. The compute hma command
+computes the full expression for :math:`C_V` except for the
+:math:`\left<U_{HMA}^2\right>^2` in the variance term, which can be obtained by
+passing the *u* keyword; you must add this extra contribution to the :math:`C_V`
+value reported by this compute.  The variance term can cause significant
+round-off error when computing :math:`C_V`.  To address this, the *anharmonic*
+keyword can be passed and/or the output format can be specified with more
+digits.
+
+
+.. parsed-literal::
+
+   thermo_modify format float '%22.15e'
+
+The *anharmonic* keyword will instruct the compute to return anharmonic
+properties rather than the full properties, which include lattice, harmonic
+and anharmonic contributions.
+When using this keyword, the compute must be first active (it must be included
+via a :doc:`thermo\_style custom <thermo_style>` command) while the atoms are
+still at their lattice sites (before equilibration).
+
+The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover (:doc:`fix nvt <fix_nh>`) or
+Berendsen (:doc:`fix temp/berendsen <fix_temp_berendsen>`) thermostat used for the simulation. While using this command, Langevin thermostat
+(:doc:`fix langevin <fix_langevin>`)
+should be avoided as its extra forces interfere with the HMA implementation.
+
+.. note::
+
+   Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites.
+   The simulation should not be started before this command has been used in the input script.
+
+The following example illustrates the placement of this command in the input script:
+
+
+.. parsed-literal::
+
+   min_style cg
+   minimize 1e-35 1e-15 50000 500000
+   compute 1 all hma thermostatid u
+   fix thermostatid all nvt temp 600.0 600.0 100.0
+
+.. note::
+
+   Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation.
+
+.. note::
+
+   The :doc:`fix\_modify energy yes <fix_modify>` command must also be specified if a fix is to contribute potential energy to this command.
+
+An example input script that uses this compute is included in
+examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA
+properties fluctuate less than the corresponding conventional properties.
+
+**Output info:**
+
+This compute calculates a global vector that includes the n properties
+requested as arguments to the command (the potential energy, pressure and/or heat
+capacity).  The elements of the vector can be accessed by indices 1-n by any
+command that uses global vector values as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output options.
+
+The vector values calculated by this compute are "extensive".  The
+scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is enabled only
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Usage restricted to canonical (NVT) ensemble simulation only.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute pressure <compute_pressure>`
+
+:doc:`dynamical matrix <dynamical_matrix>` provides a finite difference
+formulation of the hessian provided by Pair's single\_hessian, which is used by
+this compute.
+
+**Default:** none
+
+
+----------
+
+
+.. _hma-Moustafa:
+
+
+
+**(Moustafa)** Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ ,
+`Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst
new file mode 100644
index 0000000000..27cd5f5902
--- /dev/null
+++ b/doc/src/compute_improper.rst
@@ -0,0 +1,61 @@
+.. index:: compute improper
+
+compute improper command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID improper
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* improper = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all improper
+
+Description
+"""""""""""
+
+Define a computation that extracts the improper energy calculated by
+each of the improper sub-styles used in the :doc:`improper\_style hybrid <improper_hybrid>` command.  These values are made
+accessible for output or further processing by other commands.  The
+group specified for this command is ignored.
+
+This compute is useful when using :doc:`improper\_style hybrid <improper_hybrid>` if you want to know the portion of the
+total energy contributed by one or more of the hybrid sub-styles.
+
+**Output info:**
+
+This compute calculates a global vector of length N where N is the
+number of sub\_styles defined by the :doc:`improper\_style hybrid <improper_style>` command.  which can be accessed by indices
+1-N.  These values can be used by any command that uses global scalar
+or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector values are "extensive" and will be in energy
+:doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst
new file mode 100644
index 0000000000..6daad705b5
--- /dev/null
+++ b/doc/src/compute_improper_local.rst
@@ -0,0 +1,95 @@
+.. index:: compute improper/local
+
+compute improper/local command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID improper/local value1 value2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* improper/local = style name of this compute command
+* one or more values may be appended
+* value = *chi*
+  
+  .. parsed-literal::
+  
+       *chi* = tabulate improper angles
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all improper/local chi
+
+Description
+"""""""""""
+
+Define a computation that calculates properties of individual improper
+interactions.  The number of datums generated, aggregated across all
+processors, equals the number of impropers in the system, modified by
+the group parameter as explained below.
+
+The value *chi* is the improper angle, as defined in the doc pages for
+the individual improper styles listed on
+:doc:`improper\_style <improper_style>` doc page.
+
+The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their impropers.  An improper will
+only be included if all 4 atoms in the improper are in the specified
+compute group.
+
+Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, improper output from the :doc:`compute property/local <compute_property_local>` command can be combined
+with data from this command and output by the :doc:`dump local <dump>`
+command in a consistent way.
+
+Here is an example of how to do this:
+
+
+.. parsed-literal::
+
+   compute 1 all property/local itype iatom1 iatom2 iatom3 iatom4
+   compute 2 all improper/local chi
+   dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
+
+**Output info:**
+
+This compute calculates a local vector or local array depending on the
+number of keywords.  The length of the vector or number of rows in the
+array is the number of impropers.  If a single keyword is specified, a
+local vector is produced.  If two or more keywords are specified, a
+local array is produced where the number of columns = the number of
+keywords.  The vector or array can be accessed by any command that
+uses local values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The output for *chi* will be in degrees.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst
new file mode 100644
index 0000000000..029245d883
--- /dev/null
+++ b/doc/src/compute_inertia_chunk.rst
@@ -0,0 +1,99 @@
+.. index:: compute inertia/chunk
+
+compute inertia/chunk command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID inertia/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* inertia/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid inertia/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the inertia tensor for multiple
+chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates the 6 components of the symmetric inertia
+tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz.  The
+calculation includes all effects due to atoms passing through periodic
+boundaries.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+.. note::
+
+   The coordinates of an atom contribute to the chunk's inertia
+   tensor in "unwrapped" form, by using the image flags associated with
+   each atom.  See the :doc:`dump custom <dump>` command for a discussion
+   of "unwrapped" coordinates.  See the Atoms section of the
+   :doc:`read\_data <read_data>` command for a discussion of image flags and
+   how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+The simplest way to output the results of the compute inertia/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all inertia/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+6 for the 6 components of the inertia tensor for each chunk, ordered
+as listed above.  These values can be accessed by any command that
+uses global array values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The array values are "intensive".  The array values will be in
+mass\*distance\^2 :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`variable inertia() function <variable>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst
new file mode 100644
index 0000000000..8d7fd3e5f4
--- /dev/null
+++ b/doc/src/compute_ke.rst
@@ -0,0 +1,71 @@
+.. index:: compute ke
+
+compute ke command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID ke
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* ke = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all ke
+
+Description
+"""""""""""
+
+Define a computation that calculates the translational kinetic energy
+of a group of particles.
+
+The kinetic energy of each particle is computed as 1/2 m v\^2, where m
+and v are the mass and velocity of the particle.
+
+There is a subtle difference between the quantity calculated by this
+compute and the kinetic energy calculated by the *ke* or *etotal*
+keyword used in thermodynamic output, as specified by the
+:doc:`thermo\_style <thermo_style>` command.  For this compute, kinetic
+energy is "translational" kinetic energy, calculated by the simple
+formula above.  For thermodynamic output, the *ke* keyword infers
+kinetic energy from the temperature of the system with 1/2 Kb T of
+energy for each degree of freedom.  For the default temperature
+computation via the :doc:`compute temp <compute_temp>` command, these
+are the same.  But different computes that calculate temperature can
+subtract out different non-thermal components of velocity and/or
+include different degrees of freedom (translational, rotational, etc).
+
+**Output info:**
+
+This compute calculates a global scalar (the summed KE).  This value
+can be used by any command that uses a global scalar value from a
+compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute erotate/sphere <compute_erotate_sphere>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst
new file mode 100644
index 0000000000..a377903866
--- /dev/null
+++ b/doc/src/compute_ke_atom.rst
@@ -0,0 +1,60 @@
+.. index:: compute ke/atom
+
+compute ke/atom command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID ke/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* ke/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all ke/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom translational
+kinetic energy for each atom in a group.
+
+The kinetic energy is simply 1/2 m v\^2, where m is the mass and v is
+the velocity of each atom.
+
+The value of the kinetic energy will be 0.0 for atoms not in the
+specified compute group.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst
new file mode 100644
index 0000000000..db08516b61
--- /dev/null
+++ b/doc/src/compute_ke_atom_eff.rst
@@ -0,0 +1,91 @@
+.. index:: compute ke/atom/eff
+
+compute ke/atom/eff command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID ke/atom/eff
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* ke/atom/eff = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all ke/atom/eff
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom translational
+(nuclei and electrons) and radial kinetic energy (electron only) in a
+group.  The particles are assumed to be nuclei and electrons modeled
+with the :doc:`electronic force field <pair_eff>`.
+
+The kinetic energy for each nucleus is computed as 1/2 m v\^2, where m
+corresponds to the corresponding nuclear mass, and the kinetic energy
+for each electron is computed as 1/2 (me v\^2 + 3/4 me s\^2), where me
+and v correspond to the mass and translational velocity of each
+electron, and s to its radial velocity, respectively.
+
+There is a subtle difference between the quantity calculated by this
+compute and the kinetic energy calculated by the *ke* or *etotal*
+keyword used in thermodynamic output, as specified by the
+:doc:`thermo\_style <thermo_style>` command. For this compute, kinetic
+energy is "translational" plus electronic "radial" kinetic energy,
+calculated by the simple formula above. For thermodynamic output, the
+*ke* keyword infers kinetic energy from the temperature of the system
+with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
+eFF.
+
+.. note::
+
+   The temperature in eFF should be monitored via the :doc:`compute temp/eff <compute_temp_eff>` command, which can be printed with
+   thermodynamic output by using the :doc:`thermo\_modify <thermo_modify>`
+   command, as shown in the following example:
+
+
+.. parsed-literal::
+
+   compute         effTemp all temp/eff
+   thermo_style    custom step etotal pe ke temp press
+   thermo_modify   temp effTemp
+
+The value of the kinetic energy will be 0.0 for atoms (nuclei or
+electrons) not in the specified compute group.
+
+**Output info:**
+
+This compute calculates a scalar quantity for each atom, which can be
+accessed by any command that uses per-atom computes as input.  See the
+:doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS
+output options.
+
+The per-atom vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst
new file mode 100644
index 0000000000..c635b9fecc
--- /dev/null
+++ b/doc/src/compute_ke_eff.rst
@@ -0,0 +1,90 @@
+.. index:: compute ke/eff
+
+compute ke/eff command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID ke/eff
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* ke/eff = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all ke/eff
+
+Description
+"""""""""""
+
+Define a computation that calculates the kinetic energy of motion of a
+group of eFF particles (nuclei and electrons), as modeled with the
+:doc:`electronic force field <pair_eff>`.
+
+The kinetic energy for each nucleus is computed as 1/2 m v\^2 and the
+kinetic energy for each electron is computed as 1/2(me v\^2 + 3/4 me
+s\^2), where m corresponds to the nuclear mass, me to the electron
+mass, v to the translational velocity of each particle, and s to the
+radial velocity of the electron, respectively.
+
+There is a subtle difference between the quantity calculated by this
+compute and the kinetic energy calculated by the *ke* or *etotal*
+keyword used in thermodynamic output, as specified by the
+:doc:`thermo\_style <thermo_style>` command.  For this compute, kinetic
+energy is "translational" and "radial" (only for electrons) kinetic
+energy, calculated by the simple formula above.  For thermodynamic
+output, the *ke* keyword infers kinetic energy from the temperature of
+the system with 1/2 Kb T of energy for each degree of freedom.  For
+the eFF temperature computation via the :doc:`compute temp\_eff <compute_temp_eff>` command, these are the same.  But
+different computes that calculate temperature can subtract out
+different non-thermal components of velocity and/or include other
+degrees of freedom.
+
+IMPRORTANT NOTE: The temperature in eFF models should be monitored via
+the :doc:`compute temp/eff <compute_temp_eff>` command, which can be
+printed with thermodynamic output by using the
+:doc:`thermo\_modify <thermo_modify>` command, as shown in the following
+example:
+
+
+.. parsed-literal::
+
+   compute         effTemp all temp/eff
+   thermo_style    custom step etotal pe ke temp press
+   thermo_modify   temp effTemp
+
+See :doc:`compute temp/eff <compute_temp_eff>`.
+
+**Output info:**
+
+This compute calculates a global scalar (the KE).  This value can be
+used by any command that uses a global scalar value from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst
new file mode 100644
index 0000000000..9d1b4fa9b6
--- /dev/null
+++ b/doc/src/compute_ke_rigid.rst
@@ -0,0 +1,69 @@
+.. index:: compute ke/rigid
+
+compute ke/rigid command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID ke/rigid fix-ID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* ke = style name of this compute command
+* fix-ID = ID of rigid body fix
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all ke/rigid myRigid
+
+Description
+"""""""""""
+
+Define a computation that calculates the translational kinetic energy
+of a collection of rigid bodies, as defined by one of the :doc:`fix rigid <fix_rigid>` command variants.
+
+The kinetic energy of each rigid body is computed as 1/2 M Vcm\^2,
+where M is the total mass of the rigid body, and Vcm is its
+center-of-mass velocity.
+
+The *fix-ID* should be the ID of one of the :doc:`fix rigid <fix_rigid>`
+commands which defines the rigid bodies.  The group specified in the
+compute command is ignored.  The kinetic energy of all the rigid
+bodies defined by the fix rigid command in included in the
+calculation.
+
+**Output info:**
+
+This compute calculates a global scalar (the summed KE of all the
+rigid bodies).  This value can be used by any command that uses a
+global scalar value from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the RIGID package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute erotate/rigid <compute_erotate_rigid>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_meso_e_atom.rst b/doc/src/compute_meso_e_atom.rst
new file mode 100644
index 0000000000..2417ab1265
--- /dev/null
+++ b/doc/src/compute_meso_e_atom.rst
@@ -0,0 +1,67 @@
+.. index:: compute meso/e/atom
+
+compute meso/e/atom command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID meso/e/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* meso/e/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all meso/e/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom internal energy
+for each atom in a group.
+
+The internal energy is the energy associated with the internal degrees
+of freedom of a mesoscopic particles, e.g. a Smooth-Particle
+Hydrodynamics particle.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The value of the internal energy will be 0.0 for atoms not in the
+specified compute group.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SPH package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_meso_rho_atom.rst b/doc/src/compute_meso_rho_atom.rst
new file mode 100644
index 0000000000..57fcd4e2fe
--- /dev/null
+++ b/doc/src/compute_meso_rho_atom.rst
@@ -0,0 +1,67 @@
+.. index:: compute meso/rho/atom
+
+compute meso/rho/atom command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID meso/rho/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* meso/rho/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all meso/rho/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom mesoscopic density
+for each atom in a group.
+
+The mesoscopic density is the mass density of a mesoscopic particle,
+calculated by kernel function interpolation using "pair style
+sph/rhosum".
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The value of the mesoscopic density will be 0.0 for atoms not in the
+specified compute group.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be in mass/volume :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SPH package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_meso_t_atom.rst b/doc/src/compute_meso_t_atom.rst
new file mode 100644
index 0000000000..b148516039
--- /dev/null
+++ b/doc/src/compute_meso_t_atom.rst
@@ -0,0 +1,69 @@
+.. index:: compute meso/t/atom
+
+compute meso/t/atom command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID meso/t/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* meso/t/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all meso/t/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom internal temperature
+for each atom in a group.
+
+The internal temperature is the ratio of internal energy over the heat
+capacity associated with the internal degrees of freedom of a mesoscopic
+particles, e.g. a Smooth-Particle Hydrodynamics particle.
+
+T\_\ *int* = E\_\ *int* / C\_\ *V, int*
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The value of the internal energy will be 0.0 for atoms not in the
+specified compute group.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be in temperature :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SPH package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst
new file mode 100644
index 0000000000..331887829e
--- /dev/null
+++ b/doc/src/compute_modify.rst
@@ -0,0 +1,87 @@
+.. index:: compute\_modify
+
+compute\_modify command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute_modify compute-ID keyword value ...
+
+* compute-ID = ID of the compute to modify
+* one or more keyword/value pairs may be listed
+* keyword = *extra/dof* or *extra* or *dynamic/dof* or *dynamic*
+  
+  .. parsed-literal::
+  
+       *extra/dof* value = N
+         N = # of extra degrees of freedom to subtract
+       *extra* syntax is identical to *extra/dof*\ , will be disabled at some point
+       *dynamic/dof* value = *yes* or *no*
+         yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
+       *dynamic* syntax is identical to *dynamic/dof*\ , will be disabled at some point
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute_modify myTemp extra/dof 0
+   compute_modify newtemp dynamic/dof yes extra/dof 600
+
+Description
+"""""""""""
+
+Modify one or more parameters of a previously defined compute.  Not
+all compute styles support all parameters.
+
+The *extra/dof* or *extra* keyword refers to how many
+degrees-of-freedom are subtracted (typically from 3N) as a normalizing
+factor in a temperature computation.  Only computes that compute a
+temperature use this option.  The default is 2 or 3 for :doc:`2d or 3d systems <dimension>` which is a correction factor for an ensemble
+of velocities with zero total linear momentum. For compute
+temp/partial, if one or more velocity components are excluded, the
+value used for *extra* is scaled accordingly. You can use a negative
+number for the *extra* parameter if you need to add
+degrees-of-freedom.  See the :doc:`compute temp/asphere <compute_temp_asphere>` command for an example.
+
+The *dynamic/dof* or *dynamic* keyword determines whether the number
+of atoms N in the compute group and their associated degrees of
+freedom are re-computed each time a temperature is computed.  Only
+compute styles that calculate a temperature use this option.  By
+default, N and their DOF are assumed to be constant.  If you are
+adding atoms or molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or expect atoms or molecules to be lost
+(e.g. due to exiting the simulation box or via :doc:`fix evaporate <fix_evaporate>`), then this option should be used to
+insure the temperature is correctly normalized.
+
+.. note::
+
+   The *extra* and *dynamic* keywords should not be used as they
+   are deprecated (March 2017) and will eventually be disabled.  Instead,
+   use the equivalent *extra/dof* and *dynamic/dof* keywords.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`
+
+Default
+"""""""
+
+The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
+dynamic/dof = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst
new file mode 100644
index 0000000000..d09c8a31eb
--- /dev/null
+++ b/doc/src/compute_momentum.rst
@@ -0,0 +1,59 @@
+.. index:: compute momentum
+
+compute momentum command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID momentum
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* momentum = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all momentum
+
+Description
+"""""""""""
+
+Define a computation that calculates the translational momentum
+of a group of particles.
+
+The momentum of each particles is computed as m v, where m and v are
+the mass and velocity of the particle.
+
+**Output info:**
+
+This compute calculates a global vector (the summed momentum) of
+length 3. This value can be used by any command that uses a global
+vector value from a compute as input. See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector value calculated by this compute is "extensive". The vector
+value will be in mass\*velocity :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst
new file mode 100644
index 0000000000..4d47d58cd0
--- /dev/null
+++ b/doc/src/compute_msd.rst
@@ -0,0 +1,129 @@
+.. index:: compute msd
+
+compute msd command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID msd keyword values ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* msd = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *com* or *average*
+  
+  .. parsed-literal::
+  
+       *com* value = *yes* or *no*
+       *average* value = *yes* or *no*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all msd
+   compute 1 upper msd com yes average yes
+
+Description
+"""""""""""
+
+Define a computation that calculates the mean-squared displacement
+(MSD) of the group of atoms, including all effects due to atoms
+passing through periodic boundaries.  For computation of the non-Gaussian
+parameter of mean-squared displacement, see the :doc:`compute msd/nongauss <compute_msd_nongauss>` command.
+
+A vector of four quantities is calculated by this compute.  The first 3
+elements of the vector are the squared dx,dy,dz displacements, summed
+and averaged over atoms in the group.  The 4th element is the total
+squared displacement, i.e. (dx\*dx + dy\*dy + dz\*dz), summed and
+averaged over atoms in the group.
+
+The slope of the mean-squared displacement (MSD) versus time is
+proportional to the diffusion coefficient of the diffusing atoms.
+
+The displacement of an atom is from its reference position. This is
+normally the original position at the time
+the compute command was issued, unless the *average* keyword is set to *yes*\ .
+The value of the displacement will be
+0.0 for atoms not in the specified compute group.
+
+If the *com* option is set to *yes* then the effect of any drift in
+the center-of-mass of the group of atoms is subtracted out before the
+displacement of each atom is calculated.
+
+If the *average* option is set to *yes* then the reference position of
+an atom is based on the average position of that atom, corrected for
+center-of-mass motion if requested.  The average position is a running
+average over all previous calls to the compute, including the current
+call. So on the first call it is current position, on the second call
+it is the arithmetic average of the current position and the position
+on the first call, and so on.  Note that when using this option, the
+precise value of the mean square displacement will depend on the
+number of times the compute is called. So, for example, changing the
+frequency of thermo output may change the computed displacement. Also,
+the precise values will be changed if a single simulation is broken up
+into two parts, using either multiple run commands or a restart
+file. It only makes sense to use this option if the atoms are not
+diffusing, so that their average positions relative to the center of
+mass of the system are stationary. The most common case is crystalline
+solids undergoing thermal motion.
+
+.. note::
+
+   Initial coordinates are stored in "unwrapped" form, by using the
+   image flags associated with each atom.  See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
+   See the Atoms section of the :doc:`read\_data <read_data>` command for a
+   discussion of image flags and how they are set for each atom.  You can
+   reset the image flags (e.g. to 0) before invoking this compute by
+   using the :doc:`set image <set>` command.
+
+.. note::
+
+   If you want the quantities calculated by this compute to be
+   continuous when running from a :doc:`restart file <read_restart>`, then
+   you should use the same ID for this compute, as in the original run.
+   This is so that the fix this compute creates to store per-atom
+   quantities will also have the same ID, and thus be initialized
+   correctly with atom reference positions from the restart file.  When
+   *average* is set to yes, then the atom reference positions are
+   restored correctly, but not the number of samples used obtain them. As
+   a result, the reference positions from the restart file are combined
+   with subsequent positions as if they were from a single sample,
+   instead of many, which will change the values of msd somewhat.
+
+**Output info:**
+
+This compute calculates a global vector of length 4, which can be
+accessed by indices 1-4 by any command that uses global vector values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The vector values are "intensive".  The vector values will be in
+distance\^2 :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute msd/nongauss <compute_msd_nongauss>`, :doc:`compute displace\_atom <compute_displace_atom>`, :doc:`fix store/state <fix_store_state>`, :doc:`compute msd/chunk <compute_msd_chunk>`
+
+Default
+"""""""
+
+The option default are com = no, average = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst
new file mode 100644
index 0000000000..18d1ae4440
--- /dev/null
+++ b/doc/src/compute_msd_chunk.rst
@@ -0,0 +1,137 @@
+.. index:: compute msd/chunk
+
+compute msd/chunk command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID msd/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* msd/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all msd/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the mean-squared displacement
+(MSD) for multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+Four quantities are calculated by this compute for each chunk.  The
+first 3 quantities are the squared dx,dy,dz displacements of the
+center-of-mass.  The 4th component is the total squared displacement,
+i.e. (dx\*dx + dy\*dy + dz\*dz) of the center-of-mass.  These
+calculations include all effects due to atoms passing through periodic
+boundaries.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+The slope of the mean-squared displacement (MSD) versus time is
+proportional to the diffusion coefficient of the diffusing chunks.
+
+The displacement of the center-of-mass of the chunk is from its
+original center-of-mass position, calculated on the timestep this
+compute command was first invoked.
+
+.. note::
+
+   The number of chunks *Nchunk* calculated by the :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant each
+   time this compute is invoked, so that the displacement for each chunk
+   from its original position can be computed consistently.  If *Nchunk*
+   does not remain constant, an error will be generated.  If needed, you
+   can enforce a constant *Nchunk* by using the *nchunk once* or *ids
+   once* options when specifying the :doc:`compute chunk/atom <compute_chunk_atom>` command.
+
+.. note::
+
+   This compute stores the original position (of the
+   center-of-mass) of each chunk.  When a displacement is calculated on a
+   later timestep, it is assumed that the same atoms are assigned to the
+   same chunk ID.  However LAMMPS has no simple way to insure this is the
+   case, though you can use the *ids once* option when specifying the
+   :doc:`compute chunk/atom <compute_chunk_atom>` command.  Note that if
+   this is not the case, the MSD calculation does not have a sensible
+   meaning.
+
+.. note::
+
+   The initial coordinates of the atoms in each chunk are stored in
+   "unwrapped" form, by using the image flags associated with each atom.
+   See the :doc:`dump custom <dump>` command for a discussion of
+   "unwrapped" coordinates.  See the Atoms section of the
+   :doc:`read\_data <read_data>` command for a discussion of image flags and
+   how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+.. note::
+
+   If you want the quantities calculated by this compute to be
+   continuous when running from a :doc:`restart file <read_restart>`, then
+   you should use the same ID for this compute, as in the original run.
+   This is so that the fix this compute creates to store per-chunk
+   quantities will also have the same ID, and thus be initialized
+   correctly with chunk reference positions from the restart file.
+
+The simplest way to output the results of the compute msd/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all msd/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+4 for dx,dy,dz and the total displacement.  These values can be
+accessed by any command that uses global array values from a compute
+as input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The array values are "intensive".  The array values will be in
+distance\^2 :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute msd <compute_msd>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst
new file mode 100644
index 0000000000..56407e1dde
--- /dev/null
+++ b/doc/src/compute_msd_nongauss.rst
@@ -0,0 +1,96 @@
+.. index:: compute msd/nongauss
+
+compute msd/nongauss command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID msd/nongauss keyword values ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* msd/nongauss = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *com*
+  
+  .. parsed-literal::
+  
+       *com* value = *yes* or *no*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all msd/nongauss
+   compute 1 upper msd/nongauss com yes
+
+Description
+"""""""""""
+
+Define a computation that calculates the mean-squared displacement
+(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
+including all effects due to atoms passing through periodic boundaries.
+
+A vector of three quantities is calculated by this compute.  The first
+element of the vector is the total squared dx,dy,dz displacements
+drsquared = (dx\*dx + dy\*dy + dz\*dz) of atoms, and the second is the
+fourth power of these displacements drfourth = (dx\*dx + dy\*dy +
+dz\*dz)\*(dx\*dx + dy\*dy + dz\*dz), summed and averaged over atoms in the
+group.  The 3rd component is the nonGaussian diffusion parameter NGP =
+3\*drfourth/(5\*drsquared\*drsquared), i.e.
+
+.. image:: Eqs/compute_msd_nongauss.jpg
+   :align: center
+
+The NGP is a commonly used quantity in studies of dynamical
+heterogeneity.  Its minimum theoretical value (-0.4) occurs when all
+atoms have the same displacement magnitude.  NGP=0 for Brownian
+diffusion, while NGP > 0 when some mobile atoms move faster than
+others.
+
+If the *com* option is set to *yes* then the effect of any drift in
+the center-of-mass of the group of atoms is subtracted out before the
+displacement of each atom is calculated.
+
+See the :doc:`compute msd <compute_msd>` doc page for further important
+NOTEs, which also apply to this compute.
+
+**Output info:**
+
+This compute calculates a global vector of length 3, which can be
+accessed by indices 1-3 by any command that uses global vector values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The vector values are "intensive".  The first vector value will be in
+distance\^2 :doc:`units <units>`, the second is in distance\^4 units, and
+the 3rd is dimensionless.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute msd <compute_msd>`
+
+Default
+"""""""
+
+The option default is com = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst
new file mode 100644
index 0000000000..bd0b8f91de
--- /dev/null
+++ b/doc/src/compute_omega_chunk.rst
@@ -0,0 +1,100 @@
+.. index:: compute omega/chunk
+
+compute omega/chunk command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID omega/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* omega/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid omega/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the angular velocity (omega) of
+multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates the 3 components of the angular velocity
+vector for each chunk, via the formula L = Iw where L is the angular
+momentum vector of the chunk, I is its moment of inertia tensor, and w
+is omega = angular velocity of the chunk.  The calculation includes
+all effects due to atoms passing through periodic boundaries.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+.. note::
+
+   The coordinates of an atom contribute to the chunk's angular
+   velocity in "unwrapped" form, by using the image flags associated with
+   each atom.  See the :doc:`dump custom <dump>` command for a discussion
+   of "unwrapped" coordinates.  See the Atoms section of the
+   :doc:`read\_data <read_data>` command for a discussion of image flags and
+   how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+The simplest way to output the results of the compute omega/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all omega/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+3 for the 3 xyz components of the angular velocity for each chunk.
+These values can be accessed by any command that uses global array
+values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The array values are "intensive".  The array values will be in
+velocity/distance :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`variable omega() function <variable>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst
new file mode 100644
index 0000000000..b7a1442a62
--- /dev/null
+++ b/doc/src/compute_orientorder_atom.rst
@@ -0,0 +1,197 @@
+.. index:: compute orientorder/atom
+
+compute orientorder/atom command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID orientorder/atom keyword values ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* orientorder/atom = style name of this compute command
+* one or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *cutoff* or *nnn* or *degrees* or *components*
+       *cutoff* value = distance cutoff
+       *nnn* value = number of nearest neighbors
+       *degrees* values = nlvalues, l1, l2,...
+       *wl* value = yes or no
+       *wl/hat* value = yes or no
+       *components* value = ldegree
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all orientorder/atom
+   compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
+   compute 1 all orientorder/atom wl/hat yes
+   compute 1 all orientorder/atom components 6
+
+Description
+"""""""""""
+
+Define a computation that calculates a set of bond-orientational
+order parameters *Ql* for each atom in a group. These order parameters
+were introduced by :ref:`Steinhardt et al. <Steinhardt>` as a way to
+characterize the local orientational order in atomic structures.
+For each atom, *Ql* is a real number defined as follows:
+
+.. image:: Eqs/orientorder.jpg
+   :align: center
+
+The first equation defines the spherical harmonic order parameters.
+These are complex number components of the 3D analog of the 2D order
+parameter *qn*\ , which is implemented as LAMMPS compute
+:doc:`hexorder/atom <compute_hexorder_atom>`.
+The summation is over the *nnn* nearest
+neighbors of the central atom.
+The angles theta and phi are the standard spherical polar angles
+defining the direction of the bond vector *rij*\ .
+The second equation defines *Ql*\ , which is a
+rotationally invariant non-negative amplitude obtained by summing
+over all the components of degree *l*\ .
+
+The optional keyword *cutoff* defines the distance cutoff
+used when searching for neighbors. The default value, also
+the maximum allowable value, is the cutoff specified
+by the pair style.
+
+The optional keyword *nnn* defines the number of nearest
+neighbors used to calculate *Ql*\ . The default value is 12.
+If the value is NULL, then all neighbors up to the
+specified distance cutoff are used.
+
+The optional keyword *degrees* defines the list of order parameters to
+be computed.  The first argument *nlvalues* is the number of order
+parameters. This is followed by that number of non-negative integers giving the
+degree of each order parameter. Because *Q*\ 2 and all odd-degree order
+parameters are zero for atoms in cubic crystals (see
+:ref:`Steinhardt <Steinhardt>`), the default order parameters are *Q*\ 4,
+*Q*\ 6, *Q*\ 8, *Q*\ 10, and *Q*\ 12. For the FCC crystal with *nnn* =12, *Q*\ 4
+= sqrt(7/3)/8 = 0.19094....  The numerical values of all order
+parameters up to *Q*\ 12 for a range of commonly encountered
+high-symmetry structures are given in Table I of :ref:`Mickel et al. <Mickel>`, and these can be reproduced with this compute
+
+The optional keyword *wl* will output the third-order invariants *Wl*
+(see Eq. 1.4 in :ref:`Steinhardt <Steinhardt>`) for the same degrees as
+for the *Ql* parameters. For the FCC crystal with *nnn* =12,
+*W*\ 4 = -sqrt(14/143).(49/4096)/Pi\^1.5 = -0.0006722136...
+
+The optional keyword *wl/hat* will output the normalized third-order
+invariants *Wlhat* (see Eq. 2.2 in :ref:`Steinhardt <Steinhardt>`)
+for the same degrees as for the *Ql* parameters. For the FCC crystal
+with *nnn* =12, *W*\ 4hat = -7/3\*sqrt(2/429) = -0.159317...The numerical
+values of *Wlhat* for a range of commonly encountered high-symmetry
+structures are given in Table I of :ref:`Steinhardt <Steinhardt>`, and these
+can be reproduced with this keyword.
+
+The optional keyword *components* will output the components of the
+normalized complex vector *Ybar\_lm* of degree *ldegree*\ , which must be
+explicitly included in the keyword *degrees*\ . This option can be used
+in conjunction with :doc:`compute coord\_atom <compute_coord_atom>` to
+calculate the ten Wolde's criterion to identify crystal-like
+particles, as discussed in :ref:`ten Wolde <tenWolde2>`.
+
+The value of *Ql* is set to zero for atoms not in the
+specified compute group, as well as for atoms that have less than
+*nnn* neighbors within the distance cutoff, unless *nnn* is NULL.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently.
+
+.. note::
+
+   If you have a bonded system, then the settings of
+   :doc:`special\_bonds <special_bonds>` command can remove pairwise
+   interactions between atoms in the same bond, angle, or dihedral.  This
+   is the default setting for the :doc:`special\_bonds <special_bonds>`
+   command, and means those pairwise interactions do not appear in the
+   neighbor list.  Because this fix uses the neighbor list, it also means
+   those pairs will not be included in the order parameter.  This
+   difficulty can be circumvented by writing a dump file, and using the
+   :doc:`rerun <rerun>` command to compute the order parameter for
+   snapshots in the dump file.  The rerun script can use a
+   :doc:`special\_bonds <special_bonds>` command that includes all pairs in
+   the neighbor list.
+
+**Output info:**
+
+This compute calculates a per-atom array with *nlvalues* columns,
+giving the *Ql* values for each atom, which are real numbers on the
+range 0 <= *Ql* <= 1.
+
+If the keyword *wl* is set to yes, then the *Wl* values for each
+atom will be added to the output array, which are real numbers.
+
+If the keyword *wl/hat* is set to yes, then the *Wl\_hat*
+values for each atom will be added to the output array, which are real numbers.
+
+If the keyword *components* is set, then the real and imaginary parts
+of each component of (normalized) *Ybar\_lm* will be added to the
+output array in the following order: Re(*Ybar\_-m*) Im(*Ybar\_-m*)
+Re(*Ybar\_-m+1*) Im(*Ybar\_-m+1*) ... Re(*Ybar\_m*) Im(*Ybar\_m*).  This
+way, the per-atom array will have a total of *nlvalues*\ +2\*(2\ *l*\ +1)
+columns.
+
+These values can be accessed by any command that uses per-atom values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute coord/atom <compute_coord_atom>`, :doc:`compute centro/atom <compute_centro_atom>`, :doc:`compute hexorder/atom <compute_hexorder_atom>`
+
+Default
+"""""""
+
+The option defaults are *cutoff* = pair style cutoff, *nnn* = 12,
+*degrees* = 5 4 6 8 10 12 i.e. *Q*\ 4, *Q*\ 6, *Q*\ 8, *Q*\ 10, and *Q*\ 12,
+*wl* = no, *wl/hat* = no, and *components* off
+
+
+----------
+
+
+.. _Steinhardt:
+
+
+
+**(Steinhardt)** P. Steinhardt, D. Nelson, and M. Ronchetti,
+Phys. Rev. B 28, 784 (1983).
+
+.. _Mickel:
+
+
+
+**(Mickel)** W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
+J. Chem. Phys. 138, 044501 (2013).
+
+.. _tenWolde2:
+
+
+
+**(tenWolde)** P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
+J. Chem. Phys. 104, 9932 (1996).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst
new file mode 100644
index 0000000000..924ddc7cca
--- /dev/null
+++ b/doc/src/compute_pair.rst
@@ -0,0 +1,107 @@
+.. index:: compute pair
+
+compute pair command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID pair pstyle [nstyle] [evalue]
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pair = style name of this compute command
+* pstyle = style name of a pair style that calculates additional values
+* nsub = *n*\ -instance of a sub-style, if a pair style is used multiple times in a hybrid style
+* *evalue* = *epair* or *evdwl* or *ecoul* or blank (optional)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all pair gauss
+   compute 1 all pair lj/cut/coul/cut ecoul
+   compute 1 all pair tersoff 2 epair
+   compute 1 all pair reax/c
+
+Description
+"""""""""""
+
+Define a computation that extracts additional values calculated by a
+pair style, and makes them accessible for output or further processing
+by other commands.
+
+.. note::
+
+   The group specified for this command is **ignored**\ .
+
+The specified *pstyle* must be a pair style used in your simulation
+either by itself or as a sub-style in a :doc:`pair\_style hybrid or hybrid/overlay <pair_hybrid>` command. If the sub-style is
+used more than once, an additional number *nsub* has to be specified
+in order to choose which instance of the sub-style will be used by
+the compute. Not specifying the number in this case will cause the
+compute to fail.
+
+The *evalue* setting is optional.  All
+pair styles tally a potential energy *epair* which may be broken into
+two parts: *evdwl* and *ecoul* such that *epair* = *evdwl* + *ecoul*\ .
+If the pair style calculates Coulombic interactions, their energy will
+be tallied in *ecoul*\ .  Everything else (whether it is a Lennard-Jones
+style van der Waals interaction or not) is tallied in *evdwl*\ .  If
+*evalue* is blank or specified as *epair*\ , then *epair* is stored
+as a global scalar by this compute.  This is useful when using
+:doc:`pair\_style hybrid <pair_hybrid>` if you want to know the portion
+of the total energy contributed by one sub-style.  If *evalue* is
+specified as *evdwl* or *ecoul*\ , then just that portion of the energy
+is stored as a global scalar.
+
+.. note::
+
+   The energy returned by the *evdwl* keyword does not include tail
+   corrections, even if they are enabled via the
+   :doc:`pair\_modify <pair_modify>` command.
+
+Some pair styles tally additional quantities, e.g. a breakdown of
+potential energy into 14 components is tallied by the :doc:`pair\_style reax/c <pair_reaxc>` command.  These values (1 or more)
+are stored as a global vector by this compute.  See the doc page for
+:doc:`individual pair styles <pair_style>` for info on these values.
+
+**Output info:**
+
+This compute calculates a global scalar which is *epair* or *evdwl* or
+*ecoul*\ .  If the pair style supports it, it also calculates a global
+vector of length >= 1, as determined by the pair style.  These values
+can be used by any command that uses global scalar or vector values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The scalar and vector values calculated by this compute are
+"extensive".
+
+The scalar value will be in energy :doc:`units <units>`.  The vector
+values will typically also be in energy :doc:`units <units>`, but see
+the doc page for the pair style for details.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`
+
+Default
+"""""""
+
+The keyword defaults are *evalue* = *epair*\ , nsub = 0.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst
new file mode 100644
index 0000000000..4e61852f2c
--- /dev/null
+++ b/doc/src/compute_pair_local.rst
@@ -0,0 +1,179 @@
+.. index:: compute pair/local
+
+compute pair/local command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID pair/local value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pair/local = style name of this compute command
+* one or more values may be appended
+* value = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
+  
+  .. parsed-literal::
+  
+       *dist* = pairwise distance
+       *eng* = pairwise energy
+       *force* = pairwise force
+       *fx*\ ,\ *fy*\ ,\ *fz* = components of pairwise force
+       *pN* = pair style specific quantities for allowed N values
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *cutoff*
+  
+  .. parsed-literal::
+  
+       *cutoff* arg = *type* or *radius*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all pair/local eng
+   compute 1 all pair/local dist eng force
+   compute 1 all pair/local dist eng fx fy fz
+   compute 1 all pair/local dist fx fy fz p1 p2 p3
+
+Description
+"""""""""""
+
+Define a computation that calculates properties of individual pairwise
+interactions.  The number of datums generated, aggregated across all
+processors, equals the number of pairwise interactions in the system.
+
+The local data stored by this command is generated by looping over the
+pairwise neighbor list.  Info about an individual pairwise interaction
+will only be included if both atoms in the pair are in the specified
+compute group, and if the current pairwise distance is less than the
+force cutoff distance for that interaction, as defined by the
+:doc:`pair\_style <pair_style>` and :doc:`pair\_coeff <pair_coeff>`
+commands.
+
+The value *dist* is the distance between the pair of atoms.
+
+The value *eng* is the interaction energy for the pair of atoms.
+
+The value *force* is the force acting between the pair of atoms, which
+is positive for a repulsive force and negative for an attractive
+force.  The values *fx*\ , *fy*\ , and *fz* are the xyz components of
+*force* on atom I.
+
+A pair style may define additional pairwise quantities which can be
+accessed as *p1* to *pN*\ , where N is defined by the pair style.  Most
+pair styles do not define any additional quantities, so N = 0.  An
+example of ones that do are the :doc:`granular pair styles <pair_gran>`
+which calculate the tangential force between two particles and return
+its components and magnitude acting on atom I for N = 1,2,3,4.  See
+individual pair styles for details.
+
+When using *pN* with pair style *hybrid*\ , the output will be the Nth
+quantity from the sub-style that computes the pairwise interaction
+(based on atom types).  If that sub-style does not define a *pN*\ ,
+the output will be 0.0.  The maximum allowed N is the maximum number
+of quantities provided by any sub-style.
+
+When using *pN* with pair style *hybrid/overlay* the quantities
+from all sub-styles that provide them are concatenated together
+into one long list. For example, if there are 3 sub-styles and
+2 of them have additional output (with 3 and 4 quantities,
+respectively), then 7 values (\ *p1* up to *p7*\ ) are defined.
+The values *p1* to *p3* refer to quantities defined by the first
+of the two sub-styles.  Values *p4* to *p7* refer to quantities
+from the second of the two sub-styles.  If the referenced *pN*
+is not computed for the specific pairwise interaction (based on
+atom types), then the output will be 0.0.
+
+The value *dist* will be in distance :doc:`units <units>`.  The value
+*eng* will be in energy :doc:`units <units>`.  The values *force*\ , *fx*\ ,
+*fy*\ , and *fz* will be in force :doc:`units <units>`.  The values *pN*
+will be in whatever units the pair style defines.
+
+The optional *cutoff* keyword determines how the force cutoff distance
+for an interaction is determined.  For the default setting of *type*\ ,
+the pairwise cutoff defined by the :doc:`pair\_style <pair_style>`
+command for the types of the two atoms is used.  For the *radius*
+setting, the sum of the radii of the two particles is used as a
+cutoff.  For example, this is appropriate for granular particles which
+only interact when they are overlapping, as computed by :doc:`granular pair styles <pair_gran>`.  Note that if a granular model defines atom
+types such that all particles of a specific type are monodisperse
+(same diameter), then the two settings are effectively identical.
+
+Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, pair output from the :doc:`compute property/local <compute_property_local>` command can be combined
+with data from this command and output by the :doc:`dump local <dump>`
+command in a consistent way.
+
+Here is an example of how to do this:
+
+
+.. parsed-literal::
+
+   compute 1 all property/local patom1 patom2
+   compute 2 all pair/local dist eng force
+   dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_2[1] c_2[2] c_2[3]
+
+.. note::
+
+   For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4
+   interactions within the molecular topology, their pairwise interaction
+   may be turned off, and thus they may not appear in the neighbor list,
+   and will not be part of the local data created by this command.  More
+   specifically, this will be true of I,J pairs with a weighting factor
+   of 0.0; pairs with a non-zero weighting factor are included.  The
+   weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set
+   by the :doc:`special\_bonds <special_bonds>` command.  An exception is if
+   long-range Coulombics are being computed via the
+   :doc:`kspace\_style <kspace_style>` command, then atom pairs with
+   weighting factors of zero are still included in the neighbor list, so
+   that a portion of the long-range interaction contribution can be
+   computed in the pair style.  Hence in that case, those atom pairs will
+   be part of the local data created by this command.
+
+**Output info:**
+
+This compute calculates a local vector or local array depending on the
+number of keywords.  The length of the vector or number of rows in the
+array is the number of pairs.  If a single keyword is specified, a
+local vector is produced.  If two or more keywords are specified, a
+local array is produced where the number of columns = the number of
+keywords.  The vector or array can be accessed by any command that
+uses local values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The output for *dist* will be in distance :doc:`units <units>`.  The
+output for *eng* will be in energy :doc:`units <units>`.  The output for
+*force*\ , *fx*\ , *fy*\ , and *fz* will be in force :doc:`units <units>`.
+The output for *pN* will be in whatever units the pair style defines.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
+
+Default
+"""""""
+
+The keyword default is cutoff = type.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst
new file mode 100644
index 0000000000..88f6b5f7f6
--- /dev/null
+++ b/doc/src/compute_pe.rst
@@ -0,0 +1,97 @@
+.. index:: compute pe
+
+compute pe command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID pe keyword ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pe = style name of this compute command
+* zero or more keywords may be appended
+* keyword = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *fix*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all pe
+   compute molPE all pe bond angle dihedral improper
+
+Description
+"""""""""""
+
+Define a computation that calculates the potential energy of the
+entire system of atoms.  The specified group must be "all".  See the
+:doc:`compute pe/atom <compute_pe_atom>` command if you want per-atom
+energies.  These per-atom values could be summed for a group of atoms
+via the :doc:`compute reduce <compute_reduce>` command.
+
+The energy is calculated by the various pair, bond, etc potentials
+defined for the simulation.  If no extra keywords are listed, then the
+potential energy is the sum of pair, bond, angle, dihedral, improper,
+kspace (long-range), and fix energy.  I.e. it is as if all the
+keywords were listed.  If any extra keywords are listed, then only
+those components are summed to compute the potential energy.
+
+The Kspace contribution requires 1 extra FFT each timestep the energy
+is calculated, if using the PPPM solver via the :doc:`kspace\_style pppm <kspace_style>` command.  Thus it can increase the cost of the
+PPPM calculation if it is needed on a large fraction of the simulation
+timesteps.
+
+Various fixes can contribute to the total potential energy of the
+system if the *fix* contribution is included.  See the doc pages for
+:doc:`individual fixes <fix>` for details of which ones compute a
+potential energy.
+
+.. note::
+
+   The :doc:`fix\_modify energy yes <fix_modify>` command must also be
+   specified if a fix is to contribute potential energy to this command.
+
+A compute of this style with the ID of "thermo\_pe" is created when
+LAMMPS starts up, as if this command were in the input script:
+
+
+.. parsed-literal::
+
+   compute thermo_pe all pe
+
+See the "thermo\_style" command for more details.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the potential energy).  This
+value can be used by any command that uses a global scalar value from
+a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe/atom <compute_pe_atom>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst
new file mode 100644
index 0000000000..bedc508d71
--- /dev/null
+++ b/doc/src/compute_pe_atom.rst
@@ -0,0 +1,123 @@
+.. index:: compute pe/atom
+
+compute pe/atom command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID pe/atom keyword ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pe/atom = style name of this compute command
+* zero or more keywords may be appended
+* keyword = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *fix*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all pe/atom
+   compute 1 all pe/atom pair
+   compute 1 all pe/atom pair bond
+
+Description
+"""""""""""
+
+Define a computation that computes the per-atom potential energy for
+each atom in a group.  See the :doc:`compute pe <compute_pe>` command if
+you want the potential energy of the entire system.
+
+The per-atom energy is calculated by the various pair, bond, etc
+potentials defined for the simulation.  If no extra keywords are
+listed, then the potential energy is the sum of pair, bond, angle,
+dihedral,improper, kspace (long-range), and fix energy.  I.e. it is as
+if all the keywords were listed.  If any extra keywords are listed,
+then only those components are summed to compute the potential energy.
+
+Note that the energy of each atom is due to its interaction with all
+other atoms in the simulation, not just with other atoms in the group.
+
+For an energy contribution produced by a small set of atoms (e.g. 4
+atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that
+energy is assigned in equal portions to each atom in the set.
+E.g. 1/4 of the dihedral energy to each of the 4 atoms.
+
+The :doc:`dihedral\_style charmm <dihedral_charmm>` style calculates
+pairwise interactions between 1-4 atoms.  The energy contribution of
+these terms is included in the pair energy, not the dihedral energy.
+
+The KSpace contribution is calculated using the method in
+:ref:`(Heyes) <Heyes1>` for the Ewald method and a related method for PPPM,
+as specified by the :doc:`kspace\_style pppm <kspace_style>` command.
+For PPPM, the calculation requires 1 extra FFT each timestep that
+per-atom energy is calculated.  This `document <PDF/kspace.pdf>`_
+describes how the long-range per-atom energy calculation is performed.
+
+Various fixes can contribute to the per-atom potential energy of the
+system if the *fix* contribution is included.  See the doc pages for
+:doc:`individual fixes <fix>` for details of which ones compute a
+per-atom potential energy.
+
+.. note::
+
+   The :doc:`fix\_modify energy yes <fix_modify>` command must also be
+   specified if a fix is to contribute per-atom potential energy to this
+   command.
+
+As an example of per-atom potential energy compared to total potential
+energy, these lines in an input script should yield the same result
+in the last 2 columns of thermo output:
+
+
+.. parsed-literal::
+
+   compute        peratom all pe/atom
+   compute        pe all reduce sum c_peratom
+   thermo_style   custom step temp etotal press pe c_pe
+
+.. note::
+
+   The per-atom energy does not include any Lennard-Jones tail
+   corrections to the energy added by the :doc:`pair\_modify tail yes <pair_modify>` command, since those are contributions to the
+   global system energy.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute stress/atom <compute_stress_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Heyes1:
+
+
+
+**(Heyes)** Heyes, Phys Rev B 49, 755 (1994),
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst
new file mode 100644
index 0000000000..10dc82df16
--- /dev/null
+++ b/doc/src/compute_plasticity_atom.rst
@@ -0,0 +1,82 @@
+.. index:: compute plasticity/atom
+
+compute plasticity/atom command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID plasticity/atom
+
+* ID, group-ID are documented in compute command
+* plasticity/atom = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all plasticity/atom
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom plasticity for each
+atom in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+for an overview of LAMMPS commands for Peridynamics modeling.
+
+The plasticity for a Peridynamic particle is the so-called consistency
+parameter (lambda).  For elastic deformation lambda = 0, otherwise
+lambda > 0 for plastic deformation.  For details, see
+:ref:`(Mitchell) <Mitchell>` and the PDF doc included in the LAMMPS
+distribution in `doc/PDF/PDLammps\_EPS.pdf <PDF/PDLammps_EPS.pdf>`_.
+
+This command can be invoked for one of the Peridynamic :doc:`pair styles <pair_peri>`: peri/eps.
+
+The plasticity value will be 0.0 for atoms not in the specified
+compute group.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-atom vector values are unitless numbers (lambda) >= 0.0.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the PERI package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute damage/atom <compute_damage_atom>`,
+:doc:`compute dilatation/atom <compute_dilatation_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Mitchell:
+
+
+
+**(Mitchell)** Mitchell, "A non-local, ordinary-state-based
+viscoelasticity model for peridynamics", Sandia National Lab Report,
+8064:1-28 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst
new file mode 100644
index 0000000000..d708b88ab0
--- /dev/null
+++ b/doc/src/compute_pressure.rst
@@ -0,0 +1,176 @@
+.. index:: compute pressure
+
+compute pressure command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID pressure temp-ID keyword ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pressure = style name of this compute command
+* temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+* zero or more keywords may be appended
+* keyword = *ke* or *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *fix* or *virial* or *pair/hybrid*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all pressure thermo_temp
+   compute 1 all pressure NULL pair bond
+   compute 1 all pressure NULL pair/hybrid lj/cut
+
+Description
+"""""""""""
+
+Define a computation that calculates the pressure of the entire system
+of atoms.  The specified group must be "all".  See the :doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom
+pressure (stress).  These per-atom values could be summed for a group
+of atoms via the :doc:`compute reduce <compute_reduce>` command.
+
+The pressure is computed by the formula
+
+.. image:: Eqs/pressure.jpg
+   :align: center
+
+where N is the number of atoms in the system (see discussion of DOF
+below), Kb is the Boltzmann constant, T is the temperature, d is the
+dimensionality of the system (2 or 3 for 2d/3d), and V is the system
+volume (or area in 2d).  The second term is the virial, equal to
+-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
+many-body, and long-range interactions, where r\_i and f\_i are the
+position and force vector of atom i, and the black dot indicates a dot
+product.  When periodic boundary conditions are used, N' necessarily
+includes periodic image (ghost) atoms outside the central box, and the
+position and force vectors of ghost atoms are thus included in the
+summation.  When periodic boundary conditions are not used, N' = N =
+the number of atoms in the system.  :doc:`Fixes <fix>` that impose
+constraints (e.g. the :doc:`fix shake <fix_shake>` command) also
+contribute to the virial term.
+
+A symmetric pressure tensor, stored as a 6-element vector, is also
+calculated by this compute.  The 6 components of the vector are
+ordered xx, yy, zz, xy, xz, yz.  The equation for the I,J components
+(where I and J = x,y,z) is similar to the above formula, except that
+the first term uses components of the kinetic energy tensor and the
+second term uses components of the virial tensor:
+
+.. image:: Eqs/pressure_tensor.jpg
+   :align: center
+
+If no extra keywords are listed, the entire equations above are
+calculated.  This includes a kinetic energy (temperature) term and the
+virial as the sum of pair, bond, angle, dihedral, improper, kspace
+(long-range), and fix contributions to the force on each atom.  If any
+extra keywords are listed, then only those components are summed to
+compute temperature or ke and/or the virial.  The *virial* keyword
+means include all terms except the kinetic energy *ke*\ .
+
+The *pair/hybrid* keyword means to only include contribution
+from a sub-style in a *hybrid* or *hybrid/overlay* pair style.
+
+Details of how LAMMPS computes the virial efficiently for the entire
+system, including for many-body potentials and accounting for the
+effects of periodic boundary conditions are discussed in
+:ref:`(Thompson) <Thompson1>`.
+
+The temperature and kinetic energy tensor is not calculated by this
+compute, but rather by the temperature compute specified with the
+command.  If the kinetic energy is not included in the pressure, than
+the temperature compute is not used and can be specified as NULL.
+Normally the temperature compute used by compute pressure should
+calculate the temperature of all atoms for consistency with the virial
+term, but any compute style that calculates temperature can be used,
+e.g. one that excludes frozen atoms or other degrees of freedom.
+
+Note that if desired the specified temperature compute can be one that
+subtracts off a bias to calculate a temperature using only the thermal
+velocity of the atoms, e.g. by subtracting a background streaming
+velocity.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.
+
+Also note that the N in the first formula above is really
+degrees-of-freedom divided by d = dimensionality, where the DOF value
+is calculated by the temperature compute.  See the various :doc:`compute temperature <compute>` styles for details.
+
+A compute of this style with the ID of "thermo\_press" is created when
+LAMMPS starts up, as if this command were in the input script:
+
+
+.. parsed-literal::
+
+   compute thermo_press all pressure thermo_temp
+
+where "thermo\_temp" is the ID of a similarly defined compute of style
+"temp".  See the "thermo\_style" command for more details.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the pressure) and a global
+vector of length 6 (pressure tensor), which can be accessed by indices
+1-6.  These values can be used by any command that uses global scalar
+or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar and vector values calculated by this compute are
+"intensive".  The scalar and vector values will be in pressure
+:doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`compute stress/atom <compute_stress_atom>`,
+:doc:`thermo\_style <thermo_style>`,
+
+**Default:** none
+
+
+----------
+
+
+.. _Thompson1:
+
+
+
+**(Thompson)** Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst
new file mode 100644
index 0000000000..d2ffb275ca
--- /dev/null
+++ b/doc/src/compute_pressure_cylinder.rst
@@ -0,0 +1,96 @@
+.. index:: compute pressure/cylinder
+
+compute pressure/cylinder command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pressure/cylinder = style name of this compute command
+* zlo = minimum z-boundary for cylinder
+* zhi = maximum z-boundary for cylinder
+* Rmax = maximum radius to perform calculation to
+* bin\_width = width of radial bins to use for calculation
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25
+
+Description
+"""""""""""
+
+Define a computation that calculates the pressure tensor of a system in
+cylindrical coordinates, as discussed in :ref:`(Addington) <Addington1>`.
+This is useful for systems with a single axis of rotational symmetry,
+such as cylindrical micelles or carbon nanotubes. The compute splits the
+system into radial, cylindrical-shell-type bins of width bin\_width,
+centered at x=0,y=0, and calculates the radial (P\_rhorho), azimuthal
+(P\_phiphi), and axial (P\_zz) components of the configurational pressure
+tensor. The local density is also calculated for each bin, so that the
+true pressure can be recovered as P\_kin+P\_conf=density\*k\*T+P\_conf.  The
+output is a global array with 5 columns; one each for bin radius, local
+number density, P\_rhorho, P\_phiphi, and P\_zz. The number of rows is
+governed by the values of Rmax and bin\_width. Pressure tensor values are
+output in pressure units.
+
+**Output info:**
+
+This compute calculates a global array with 5 columns and Rmax/bin\_width
+rows. The output columns are: R (distance units), number density (inverse
+volume units), configurational radial pressure (pressure units),
+configurational azimuthal pressure (pressure units), and configurational
+axial pressure (pressure units).
+
+The values calculated by this compute are
+"intensive".  The pressure values will be in pressure
+:doc:`units <units>`. The number density values will be in
+inverse volume :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute currently calculates the pressure tensor contributions
+for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
+and in the presence of bonded interactions, the result will be incorrect
+due to exclusions for special bonds)  and requires pair-wise force
+calculations not available for most many-body pair styles. K-space
+calculations are also excluded. Note that this pressure compute outputs
+the configurational terms only; the kinetic contribution is not included
+and may be calculated from the number density output by P\_kin=density\*k\*T.
+
+This compute is part of the USER-MISC package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`compute stress/atom <compute_stress_atom>`,
+:doc:`thermo\_style <thermo_style>`,
+
+**Default:** none
+
+
+----------
+
+
+.. _Addington1:
+
+
+
+**(Addington)** Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst
new file mode 100644
index 0000000000..f5a3d47945
--- /dev/null
+++ b/doc/src/compute_pressure_uef.rst
@@ -0,0 +1,70 @@
+.. index:: compute pressure/uef
+
+compute pressure/uef command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID pressure/uef temp-ID keyword ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pressure/uef = style name of this compute command
+* temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+* zero or more keywords may be appended
+* keyword = *ke* or *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *fix* or *virial*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all pressure/uef my_temp_uef
+   compute 2 all pressure/uef my_temp_uef virial
+
+Description
+"""""""""""
+
+This command is used to compute the pressure tensor in
+the reference frame of the applied flow field when
+:doc:`fix nvt/uef <fix_nh_uef>` or
+:doc:`fix npt/uef <fix_nh_uef>` is used.
+It is not necessary to use this command to compute the scalar
+value of the pressure. A :doc:`compute pressure <compute_pressure>`
+may be used for that purpose.
+
+The keywords and output information are documented in
+:doc:`compute\_pressure <compute_pressure>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`
+or :doc:`fix npt/uef <fix_nh_uef>` is active.
+
+The kinetic contribution to the pressure tensor
+will be accurate only when
+the compute specified by *temp-ID* is a
+:doc:`compute temp/uef <compute_temp_uef>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pressure <compute_pressure>`,
+:doc:`fix nvt/uef <fix_nh_uef>`,
+:doc:`compute temp/uef <compute_temp_uef>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst
new file mode 100644
index 0000000000..f78798e6f5
--- /dev/null
+++ b/doc/src/compute_property_atom.rst
@@ -0,0 +1,198 @@
+.. index:: compute property/atom
+
+compute property/atom command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID property/atom input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* property/atom = style name of this compute command
+* input = one or more atom attributes
+  
+  .. parsed-literal::
+  
+       possible attributes = id, mol, proc, type, mass,
+                             x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+                             vx, vy, vz, fx, fy, fz,
+                             q, mux, muy, muz, mu,
+                             sp, spx, spy, spz, fmx, fmy, fmz,
+                             radius, diameter, omegax, omegay, omegaz,
+                             angmomx, angmomy, angmomz,
+                             shapex,shapey, shapez,
+                             quatw, quati, quatj, quatk, tqx, tqy, tqz,
+                             end1x, end1y, end1z, end2x, end2y, end2z,
+                             corner1x, corner1y, corner1z,
+                             corner2x, corner2y, corner2z,
+                             corner3x, corner3y, corner3z,
+                             nbonds,
+                             vfrac, s0,
+                             spin, eradius, ervel, erforce,
+                             rho, drho, e, de, cv,
+                             i_name, d_name
+
+  
+  .. parsed-literal::
+  
+           id = atom ID
+           mol = molecule ID
+           proc = ID of processor that owns atom
+           type = atom type
+           mass = atom mass
+           x,y,z = unscaled atom coordinates
+           xs,ys,zs = scaled atom coordinates
+           xu,yu,zu = unwrapped atom coordinates
+           ix,iy,iz = box image that the atom is in
+           vx,vy,vz = atom velocities
+           fx,fy,fz = forces on atoms
+           q = atom charge
+           mux,muy,muz = orientation of dipole moment of atom
+           mu = magnitude of dipole moment of atom
+           sp = atomic magnetic spin moment
+           spx, spy, spz = direction of the atomic magnetic spin
+           fmx, fmy, fmz = magnetic force
+           radius,diameter = radius,diameter of spherical particle
+           omegax,omegay,omegaz = angular velocity of spherical particle
+           angmomx,angmomy,angmomz = angular momentum of aspherical particle
+           shapex,shapey,shapez = 3 diameters of aspherical particle
+           quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
+           tqx,tqy,tqz = torque on finite-size particles
+           end12x, end12y, end12z = end points of line segment
+           corner123x, corner123y, corner123z = corner points of triangle
+           nbonds = number of bonds assigned to an atom
+
+  
+  .. parsed-literal::
+  
+           PERI package per-atom properties:
+           vfrac = ???
+           s0 = ???
+
+  
+  .. parsed-literal::
+  
+           USER-EFF and USER-AWPMD package per-atom properties:
+           spin = electron spin
+           eradius = electron radius
+           ervel = electron radial velocity
+           erforce = electron radial force
+
+  
+  .. parsed-literal::
+  
+           USER-SPH package per-atom properties:
+           rho = ???
+           drho = ???
+           e = ???
+           de = ???
+           cv = ???
+
+  
+  .. parsed-literal::
+  
+           :doc:`fix property/atom <fix_property_atom>` per-atom properties:
+           i_name = custom integer vector with name
+           d_name = custom integer vector with name
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all property/atom xs vx fx mux
+   compute 2 all property/atom type
+   compute 1 all property/atom ix iy iz
+   compute 3 all property/atom sp spx spy spz
+
+Description
+"""""""""""
+
+Define a computation that simply stores atom attributes for each atom
+in the group.  This is useful so that the values can be used by other
+:doc:`output commands <Howto_output>` that take computes as inputs.  See
+for example, the :doc:`compute reduce <compute_reduce>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, and :doc:`atom-style variable <variable>`
+commands.
+
+The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some
+additional quantities that are only defined for certain :doc:`atom styles <atom_style>`.  Basically, this augmented list gives an
+input script access to any per-atom quantity stored by LAMMPS.
+
+The values are stored in a per-atom vector or array as discussed
+below.  Zeroes are stored for atoms not in the specified group or for
+quantities that are not defined for a particular particle in the group
+(e.g. *shapex* if the particle is not an ellipsoid).
+
+The additional quantities only accessible via this command, and not
+directly via the :doc:`dump custom <dump>` command, are as follows.
+
+*Shapex*\ , *shapey*\ , and *shapez* are defined for ellipsoidal particles
+and define the 3d shape of each particle.
+
+*Quatw*\ , *quati*\ , *quatj*\ , and *quatk* are defined for ellipsoidal
+particles and body particles and store the 4-vector quaternion
+representing the orientation of each particle.  See the :doc:`set <set>`
+command for an explanation of the quaternion vector.
+
+*End1x*\ , *end1y*\ , *end1z*\ , *end2x*\ , *end2y*\ , *end2z*\ , are defined for
+line segment particles and define the end points of each line segment.
+
+*Corner1x*\ , *corner1y*\ , *corner1z*\ , *corner2x*\ , *corner2y*\ ,
+*corner2z*\ , *corner3x*\ , *corner3y*\ , *corner3z*\ , are defined for
+triangular particles and define the corner points of each triangle.
+
+*Nbonds* is available for all molecular atom styles and refers to the
+number of explicit bonds assigned to an atom.  Note that if the
+:doc:`newton bond <newton>` command is set to *on*\ , which is the
+default, then every bond in the system is assigned to only one of the
+two atoms in the bond.  Thus a bond between atoms I,J may be tallied
+for either atom I or atom J.  If :doc:`newton bond off <newton>` is set,
+it will be tallied with both atom I and atom J.
+
+The *i\_name* and *d\_name* attributes refer to custom integer and
+floating-point properties that have been added to each atom via the
+:doc:`fix property/atom <fix_property_atom>` command.  When that command
+is used specific names are given to each attribute which are what is
+specified as the "name" portion of *i\_name* or *d\_name*.
+
+**Output info:**
+
+This compute calculates a per-atom vector or per-atom array depending
+on the number of input values.  If a single input is specified, a
+per-atom vector is produced.  If two or more inputs are specified, a
+per-atom array is produced where the number of columns = the number of
+inputs.  The vector or array can be accessed by any command that uses
+per-atom values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector or array values will be in whatever :doc:`units <units>` the
+corresponding attribute is in, e.g. velocity units for vx, charge
+units for q, etc.
+
+For the spin quantities, sp is in the units of the Bohr magneton, spx,
+spy, and spz are unitless quantities, and fmx, fmy and fmz are given
+in rad/THz.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
+:doc:`fix property/atom <fix_property_atom>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst
new file mode 100644
index 0000000000..a0832a33be
--- /dev/null
+++ b/doc/src/compute_property_chunk.rst
@@ -0,0 +1,129 @@
+.. index:: compute property/chunk
+
+compute property/chunk command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID property/chunk chunkID input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* property/chunk = style name of this compute command
+* input = one or more attributes
+  
+  .. parsed-literal::
+  
+       attributes = count, id, coord1, coord2, coord3
+         count = # of atoms in chunk
+         id = original chunk IDs before compression by :doc:`compute chunk/atom <compute_chunk_atom>`
+         coord123 = coordinates for spatial bins calculated by :doc:`compute chunk/atom <compute_chunk_atom>`
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all property/chunk count
+   compute 1 all property/chunk ID coord1
+
+Description
+"""""""""""
+
+Define a computation that stores the specified attributes of chunks of
+atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates and stores the specified attributes of chunks
+as global data so they can be accessed by other :doc:`output commands <Howto_output>` and used in conjunction with other
+commands that generate per-chunk data, such as :doc:`compute com/chunk <compute_com_chunk>` or :doc:`compute msd/chunk <compute_msd_chunk>`.
+
+Note that only atoms in the specified group contribute to the
+calculation of the *count* attribute.  The :doc:`compute chunk/atom <compute_chunk_atom>` command defines its own group;
+atoms will have a chunk ID = 0 if they are not in that group,
+signifying they are not assigned to a chunk, and will thus also not
+contribute to this calculation.  You can specify the "all" group for
+this command if you simply want to include atoms with non-zero chunk
+IDs.
+
+The *count* attribute is the number of atoms in the chunk.
+
+The *id* attribute stores the original chunk ID for each chunk.  It
+can only be used if the *compress* keyword was set to *yes* for the
+:doc:`compute chunk/atom <compute_chunk_atom>` command referenced by
+chunkID.  This means that the original chunk IDs (e.g. molecule IDs)
+will have been compressed to remove chunk IDs with no atoms assigned
+to them.  Thus a compressed chunk ID of 3 may correspond to an original
+chunk ID (molecule ID in this case) of 415.  The *id* attribute will
+then be 415 for the 3rd chunk.
+
+The *coordN* attributes can only be used if a *binning* style was used
+in the :doc:`compute chunk/atom <compute_chunk_atom>` command referenced
+by chunkID.  For *bin/1d*\ , *bin/2d*\ , and *bin/3d* styles the attribute
+is the center point of the bin in the corresponding dimension.  Style
+*bin/1d* only defines a *coord1* attribute.  Style *bin/2d* adds a
+*coord2* attribute.  Style *bin/3d* adds a *coord3* attribute.
+
+Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or *lattice*\ , the
+*coordN* attributes will be in distance :doc:`units <units>`.  If the
+value of the *units* keyword is *reduced*\ , the *coordN* attributes
+will be in unitless reduced units (0-1).
+
+The simplest way to output the results of the compute property/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk1 all property/chunk cc1 count
+   compute myChunk2 all com/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global vector or global array depending on
+the number of input values.  The length of the vector or number of
+rows in the array is the number of chunks.
+
+This compute calculates a global vector or global array where the
+number of rows = the number of chunks *Nchunk* as calculated by the
+specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  If a
+single input is specified, a global vector is produced.  If two or
+more inputs are specified, a global array is produced where the number
+of columns = the number of inputs.  The vector or array can be
+accessed by any command that uses global values from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The vector or array values are "intensive".  The values will be
+unitless or in the units discussed above.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ave/chunk <fix_ave_chunk>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst
new file mode 100644
index 0000000000..d388b4fc09
--- /dev/null
+++ b/doc/src/compute_property_local.rst
@@ -0,0 +1,179 @@
+.. index:: compute property/local
+
+compute property/local command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID property/local attribute1 attribute2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* property/local = style name of this compute command
+* one or more attributes may be appended
+  
+  .. parsed-literal::
+  
+       possible attributes = natom1 natom2 ntype1 ntype2
+                             patom1 patom2 ptype1 ptype2
+                             batom1 batom2 btype
+                             aatom1 aatom2 aatom3 atype
+                             datom1 datom2 datom3 datom4 dtype
+                             iatom1 iatom2 iatom3 iatom4 itype
+
+  
+  .. parsed-literal::
+  
+          natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
+          ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
+          patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
+          ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
+          batom1, batom2 = IDs of 2 atoms in each bond
+          btype = bond type of each bond
+          aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
+          atype = angle type of each angle
+          datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
+          dtype = dihedral type of each dihedral
+          iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
+          itype = improper type of each improper
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *cutoff*
+  
+  .. parsed-literal::
+  
+       *cutoff* arg = *type* or *radius*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all property/local btype batom1 batom2
+   compute 1 all property/local atype aatom2
+
+Description
+"""""""""""
+
+Define a computation that stores the specified attributes as local
+data so it can be accessed by other :doc:`output commands <Howto_output>`.  If the input attributes refer to bond
+information, then the number of datums generated, aggregated across
+all processors, equals the number of bonds in the system.  Ditto for
+pairs, angles, etc.
+
+If multiple attributes are specified then they must all generate the
+same amount of information, so that the resulting local array has the
+same number of rows for each column.  This means that only bond
+attributes can be specified together, or angle attributes, etc.  Bond
+and angle attributes can not be mixed in the same compute
+property/local command.
+
+If the inputs are pair attributes, the local data is generated by
+looping over the pairwise neighbor list.  Info about an individual
+pairwise interaction will only be included if both atoms in the pair
+are in the specified compute group.  For *natom1* and *natom2*\ , all
+atom pairs in the neighbor list are considered (out to the neighbor
+cutoff = force cutoff + :doc:`neighbor skin <neighbor>`).  For *patom1*
+and *patom2*\ , the distance between the atoms must be less than the
+force cutoff distance for that pair to be included, as defined by the
+:doc:`pair\_style <pair_style>` and :doc:`pair\_coeff <pair_coeff>`
+commands.
+
+The optional *cutoff* keyword determines how the force cutoff distance
+for an interaction is determined for the *patom1* and *patom2*
+attributes.  For the default setting of *type*\ , the pairwise cutoff
+defined by the :doc:`pair\_style <pair_style>` command for the types of
+the two atoms is used.  For the *radius* setting, the sum of the radii
+of the two particles is used as a cutoff.  For example, this is
+appropriate for granular particles which only interact when they are
+overlapping, as computed by :doc:`granular pair styles <pair_gran>`.
+Note that if a granular model defines atom types such that all
+particles of a specific type are monodisperse (same diameter), then
+the two settings are effectively identical.
+
+If the inputs are bond, angle, etc attributes, the local data is
+generated by looping over all the atoms owned on a processor and
+extracting bond, angle, etc info.  For bonds, info about an individual
+bond will only be included if both atoms in the bond are in the
+specified compute group.  Likewise for angles, dihedrals, etc.
+
+For bonds and angles, a bonds/angles that have been broken by setting
+their bond/angle type to 0 will not be included.  Bonds/angles that
+have been turned off (see the :doc:`fix shake <fix_shake>` or
+:doc:`delete\_bonds <delete_bonds>` commands) by setting their bond/angle
+type negative are written into the file.  This is consistent with the
+:doc:`compute bond/local <compute_bond_local>` and :doc:`compute angle/local <compute_angle_local>` commands
+
+Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, output from the :doc:`compute bond/local <compute_bond_local>` command can be combined with bond
+atom indices from this command and output by the :doc:`dump local <dump>` command in a consistent way.
+
+The *natom1* and *natom2*\ , or *patom1* and *patom2* attributes refer
+to the atom IDs of the 2 atoms in each pairwise interaction computed
+by the :doc:`pair\_style <pair_style>` command.  The *ntype1* and
+*ntype2*\ , or *ptype1* and *ptype2* attributes refer to the atom types
+of the 2 atoms in each pairwise interaction.
+
+.. note::
+
+   For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4
+   interactions within the molecular topology, their pairwise interaction
+   may be turned off, and thus they may not appear in the neighbor list,
+   and will not be part of the local data created by this command.  More
+   specifically, this may be true of I,J pairs with a weighting factor of
+   0.0; pairs with a non-zero weighting factor are included.  The
+   weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set
+   by the :doc:`special\_bonds <special_bonds>` command.
+
+The *batom1* and *batom2* attributes refer to the atom IDs of the 2
+atoms in each :doc:`bond <bond_style>`.  The *btype* attribute refers to
+the type of the bond, from 1 to Nbtypes = # of bond types.  The number
+of bond types is defined in the data file read by the
+:doc:`read\_data <read_data>` command.
+
+The attributes that start with "a", "d", "i", refer to similar values
+for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and
+:doc:`impropers <improper_style>`.
+
+**Output info:**
+
+This compute calculates a local vector or local array depending on the
+number of input values.  The length of the vector or number of rows in
+the array is the number of bonds, angles, etc.  If a single input is
+specified, a local vector is produced.  If two or more inputs are
+specified, a local array is produced where the number of columns = the
+number of inputs.  The vector or array can be accessed by any command
+that uses local values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector or array values will be integers that correspond to the
+specified attribute.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump local <dump>`, :doc:`compute reduce <compute_reduce>`
+
+Default
+"""""""
+
+The keyword default is cutoff = type.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst
new file mode 100644
index 0000000000..e414e8d2aa
--- /dev/null
+++ b/doc/src/compute_ptm_atom.rst
@@ -0,0 +1,135 @@
+.. index:: compute ptm/atom
+
+compute ptm/atom command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID ptm/atom structures threshold
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* ptm/atom = style name of this compute command
+* structures = structure types to search for
+* threshold = lattice distortion threshold (RMSD)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all ptm/atom default 0.1
+   compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
+   compute 1 all ptm/atom all 0
+
+Description
+"""""""""""
+
+Define a computation that determines the local lattice structure
+around an atom using the PTM (Polyhedral Template Matching) method.
+The PTM method is described in :ref:`(Larsen) <Larsen>`.
+
+Currently, there are seven lattice structures PTM recognizes:
+
+* fcc = 1
+* hcp = 2
+* bcc = 3
+* ico (icosahedral) = 4
+* sc (simple cubic) = 5
+* dcub (diamond cubic) = 6
+* dhex (diamond hexagonal) = 7
+* graphene = 8
+
+The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified
+compute group.  The choice of structures to search for can be specified using the "structures"
+argument, which is a hyphen-separated list of structure keywords.
+Two convenient pre-set options are provided:
+
+* default: fcc-hcp-bcc-ico
+* all: fcc-hcp-bcc-ico-sc-dcub-dhex-graphene
+
+The 'default' setting detects the same structures as the Common Neighbor Analysis method.
+The 'all' setting searches for all structure types.  A performance penalty is
+incurred for the diamond and graphene structures, so it is not recommended to use this option if
+it is known that the simulation does not contain these structures.
+
+PTM identifies structures using two steps.  First, a graph isomorphism test is used
+to identify potential structure matches.  Next, the deviation is computed between the
+local structure (in the simulation) and a template of the ideal lattice structure.
+The deviation is calculated as:
+
+.. image:: Eqs/ptm_rmsd.jpg
+   :align: center
+
+Here, u and v contain the coordinates of the local and ideal structures respectively,
+s is a scale factor, and Q is a rotation.  The best match is identified by the
+lowest RMSD value, using the optimal scaling, rotation, and correspondence between the
+points.
+
+The 'threshold' keyword sets an upper limit on the maximum permitted deviation before
+a local structure is identified as disordered.  Typical values are in the range 0.1-0.15,
+but larger values may be desirable at higher temperatures.
+A value of 0 is equivalent to infinity and can be used if no threshold is desired.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+*ptm/atom* style.
+
+**Output info:**
+
+This compute calculates a per-atom array, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+Results are stored in the per-atom array in the following order:
+
+* type
+* rmsd
+* interatomic distance
+* qw
+* qx
+* qy
+* qz
+
+The type is a number from -1 to 8.  The rmsd is a positive real number.
+The interatomic distance is computed from the scale factor in the RMSD equation.
+The (qw,qx,qy,qz) parameters represent the orientation of the local structure
+in quaternion form.  The reference coordinates for each template (from which the
+orientation is determined) can be found in the *ptm\_constants.h* file in the PTM source directory.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-PTM package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute centro/atom <compute_centro_atom>`
+:doc:`compute cna/atom <compute_cna_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Larsen:
+
+
+
+**(Larsen)** Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst
new file mode 100644
index 0000000000..19ab21475a
--- /dev/null
+++ b/doc/src/compute_rdf.rst
@@ -0,0 +1,224 @@
+.. index:: compute rdf
+
+compute rdf command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... keyword/value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* rdf = style name of this compute command
+* Nbin = number of RDF bins
+* itypeN = central atom type for Nth RDF histogram (see asterisk form below)
+* jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)
+* zero or more keyword/value pairs may be appended
+* keyword = *cutoff*
+  
+  .. parsed-literal::
+  
+       *cutoff* value = Rcut
+         Rcut = cutoff distance for RDF computation (distance units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all rdf 100
+   compute 1 all rdf 100 1 1
+   compute 1 all rdf 100 \* 3 cutoff 5.0
+   compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
+   compute 1 fluid rdf 500 1\*3 2 5 \*10 cutoff 3.5
+
+Description
+"""""""""""
+
+Define a computation that calculates the radial distribution function
+(RDF), also called g(r), and the coordination number for a group of
+particles.  Both are calculated in histogram form by binning pairwise
+distances into *Nbin* bins from 0.0 to the maximum force cutoff
+defined by the :doc:`pair\_style <pair_style>` command or the cutoff
+distance *Rcut* specified via the *cutoff* keyword.  The bins are of
+uniform size in radial distance.  Thus a single bin encompasses a thin
+shell of distances in 3d and a thin ring of distances in 2d.
+
+.. note::
+
+   If you have a bonded system, then the settings of
+   :doc:`special\_bonds <special_bonds>` command can remove pairwise
+   interactions between atoms in the same bond, angle, or dihedral.  This
+   is the default setting for the :doc:`special\_bonds <special_bonds>`
+   command, and means those pairwise interactions do not appear in the
+   neighbor list.  Because this fix uses a neighbor list, it also means
+   those pairs will not be included in the RDF. This does not apply when
+   using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ ,
+   *coul/wolf* or similar.  One way to get around this would be to set
+   special\_bond scaling factors to very tiny numbers that are not exactly
+   zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
+   use the :doc:`rerun <rerun>` command to compute the RDF for snapshots in
+   the dump file.  The rerun script can use a
+   :doc:`special\_bonds <special_bonds>` command that includes all pairs in
+   the neighbor list.
+
+By default the RDF is computed out to the maximum force cutoff defined
+by the :doc:`pair\_style <pair_style>` command.  If the *cutoff* keyword
+is used, then the RDF is computed accurately out to the *Rcut* > 0.0
+distance specified.
+
+.. note::
+
+   Normally, you should only use the *cutoff* keyword if no pair
+   style is defined, e.g. the :doc:`rerun <rerun>` command is being used to
+   post-process a dump file of snapshots.  Or if you really want the RDF
+   for distances beyond the pair\_style force cutoff and cannot easily
+   post-process a dump file to calculate it.  This is because using the
+   *cutoff* keyword incurs extra computation and possibly communication,
+   which may slow down your simulation.  If you specify a *Rcut* <= force
+   cutoff, you will force an additional neighbor list to be built at
+   every timestep this command is invoked (or every reneighboring
+   timestep, whichever is less frequent), which is inefficient.  LAMMPS
+   will warn you if this is the case.  If you specify a *Rcut* > force
+   cutoff, you must insure ghost atom information out to *Rcut* + *skin*
+   is communicated, via the :doc:`comm\_modify cutoff <comm_modify>`
+   command, else the RDF computation cannot be performed, and LAMMPS will
+   give an error message.  The *skin* value is what is specified with the
+   :doc:`neighbor <neighbor>` command.  In this case, you are forcing a
+   large neighbor list to be built just for the RDF computation, and
+   extra communication to be performed every timestep.
+
+The *itypeN* and *jtypeN* arguments are optional.  These arguments
+must come in pairs.  If no pairs are listed, then a single histogram
+is computed for g(r) between all atom types.  If one or more pairs are
+listed, then a separate histogram is generated for each
+*itype*\ ,\ *jtype* pair.
+
+The *itypeN* and *jtypeN* settings can be specified in one of two
+ways.  An explicit numeric value can be used, as in the 4th example
+above.  Or a wild-card asterisk can be used to specify a range of atom
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+If both *itypeN* and *jtypeN* are single values, as in the 4th example
+above, this means that a g(r) is computed where atoms of type *itypeN*
+are the central atom, and atoms of type *jtypeN* are the distribution
+atom.  If either *itypeN* and *jtypeN* represent a range of values via
+the wild-card asterisk, as in the 5th example above, this means that a
+g(r) is computed where atoms of any of the range of types represented
+by *itypeN* are the central atom, and atoms of any of the range of
+types represented by *jtypeN* are the distribution atom.
+
+Pairwise distances are generated by looping over a pairwise neighbor
+list, just as they would be in a :doc:`pair\_style <pair_style>`
+computation.  The distance between two atoms I and J is included in a
+specific histogram if the following criteria are met:
+
+* atoms I,J are both in the specified compute group
+* the distance between atoms I,J is less than the maximum force cutoff
+* the type of the I atom matches itypeN (one or a range of types)
+* the type of the J atom matches jtypeN (one or a range of types)
+
+It is OK if a particular pairwise distance is included in more than
+one individual histogram, due to the way the *itypeN* and *jtypeN*
+arguments are specified.
+
+The g(r) value for a bin is calculated from the histogram count by
+scaling it by the idealized number of how many counts there would be
+if atoms of type *jtypeN* were uniformly distributed.  Thus it
+involves the count of *itypeN* atoms, the count of *jtypeN* atoms, the
+volume of the entire simulation box, and the volume of the bin's thin
+shell in 3d (or the area of the bin's thin ring in 2d).
+
+A coordination number coord(r) is also calculated, which is the number
+of atoms of type *jtypeN* within the current bin or closer, averaged
+over atoms of type *itypeN*\ .  This is calculated as the area- or
+volume-weighted sum of g(r) values over all bins up to and including
+the current bin, multiplied by the global average volume density of
+atoms of type jtypeN.
+
+The simplest way to output the results of the compute rdf calculation
+to a file is to use the :doc:`fix ave/time <fix_ave_time>` command, for
+example:
+
+
+.. parsed-literal::
+
+   compute myRDF all rdf 50
+   fix 1 all ave/time 100 1 100 c_myRDF[\*] file tmp.rdf mode vector
+
+**Output info:**
+
+This compute calculates a global array with the number of rows =
+*Nbins*\ , and the number of columns = 1 + 2\*Npairs, where Npairs is the
+number of I,J pairings specified.  The first column has the bin
+coordinate (center of the bin), Each successive set of 2 columns has
+the g(r) and coord(r) values for a specific set of *itypeN* versus
+*jtypeN* interactions, as described above.  These values can be used
+by any command that uses a global values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The array values calculated by this compute are all "intensive".
+
+The first column of array values will be in distance
+:doc:`units <units>`.  The g(r) columns of array values are normalized
+numbers >= 0.0.  The coordination number columns of array values are
+also numbers >= 0.0.
+
+Restrictions
+""""""""""""
+
+
+The RDF is not computed for distances longer than the force cutoff,
+since processors (in parallel) don't know about atom coordinates for
+atoms further away than that distance.  If you want an RDF for larger
+distances, you can use the :doc:`rerun <rerun>` command to post-process
+a dump file and set the cutoff for the potential to be longer in the
+rerun script.  Note that in the rerun context, the force cutoff is
+arbitrary, since you aren't running dynamics and thus are not changing
+your model.  The definition of g(r) used by LAMMPS is only appropriate
+for characterizing atoms that are uniformly distributed throughout the
+simulation cell. In such cases, the coordination number is still
+correct and meaningful.  As an example, if a large simulation cell
+contains only one atom of type *itypeN* and one of *jtypeN*\ , then g(r)
+will register an arbitrarily large spike at whatever distance they
+happen to be at, and zero everywhere else.  Coord(r) will show a step
+change from zero to one at the location of the spike in g(r).
+
+.. note::
+
+   compute rdf can handle dynamic groups and systems where atoms
+   are added or removed, but this causes that certain normalization
+   parameters need to be re-computed in every step and include collective
+   communication operations. This will reduce performance and limit
+   parallel efficiency and scaling. For systems, where only the type
+   of atoms changes (e.g. when using :doc:`fix atom/swap <fix_atom_swap>`),
+   you need to explicitly request the dynamic normalization updates
+   via :doc:`compute\_modify dynamic yes <compute_modify>`
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ave/time <fix_ave_time>`, :doc:`compute\_modify <compute_modify>`,
+:doc:`compute adf <compute_adf>`
+
+Default
+"""""""
+
+The keyword defaults are cutoff = 0.0 (use the pairwise force cutoff).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst
new file mode 100644
index 0000000000..ff67fa9651
--- /dev/null
+++ b/doc/src/compute_reduce.rst
@@ -0,0 +1,244 @@
+.. index:: compute reduce
+
+compute reduce command
+======================
+
+compute reduce/region command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID style arg mode input1 input2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* style = *reduce* or *reduce/region*
+  
+  .. parsed-literal::
+  
+       *reduce* arg = none
+       *reduce/region* arg = region-ID
+         region-ID = ID of region to use for choosing atoms
+
+* mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq*
+* one or more inputs can be listed
+* input = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
+  
+  .. parsed-literal::
+  
+       x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+       c_ID = per-atom or local vector calculated by a compute with ID
+       c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = per-atom or local vector calculated by a fix with ID
+       f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
+       v_name = per-atom vector calculated by an atom-style variable with name
+
+* zero or more keyword/args pairs may be appended
+* keyword = *replace*
+  
+  .. parsed-literal::
+  
+       *replace* args = vec1 vec2
+         vec1 = reduced value from this input vector will be replaced
+         vec2 = replace it with vec1[N] where N is index of max/min value from vec2
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all reduce sum c_force
+   compute 1 all reduce/region subbox sum c_force
+   compute 2 all reduce min c_press[2] f_ave v_myKE
+   compute 2 all reduce min c_press[\*] f_ave v_myKE
+   compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
+
+Description
+"""""""""""
+
+Define a calculation that "reduces" one or more vector inputs into
+scalar values, one per listed input.  The inputs can be per-atom or
+local quantities; they cannot be global quantities.  Atom attributes
+are per-atom quantities, :doc:`computes <compute>` and :doc:`fixes <fix>`
+may generate any of the three kinds of quantities, and :doc:`atom-style variables <variable>` generate per-atom quantities.  See the
+:doc:`variable <variable>` command and its special functions which can
+perform the same operations as the compute reduce command on global
+vectors.
+
+The reduction operation is specified by the *mode* setting.  The *sum*
+option adds the values in the vector into a global total.  The *min*
+or *max* options find the minimum or maximum value across all vector
+values.  The *ave* setting adds the vector values into a global total,
+then divides by the number of values in the vector.  The *sumsq*
+option sums the square of the values in the vector into a global
+total.  The *avesq* setting does the same as *sumsq*\ , then divides the
+sum of squares by the number of values.  The last two options can be
+useful for calculating the variance of some quantity, e.g. variance =
+sumsq - ave\^2.
+
+Each listed input is operated on independently.  For per-atom inputs,
+the group specified with this command means only atoms within the
+group contribute to the result.  For per-atom inputs, if the compute
+reduce/region command is used, the atoms must also currently be within
+the region.  Note that an input that produces per-atom quantities may
+define its own group which affects the quantities it returns.  For
+example, if a compute is used as an input which generates a per-atom
+vector, it will generate values of 0.0 for atoms that are not in the
+group specified for that compute.
+
+Each listed input can be an atom attribute (position, velocity, force
+component) or can be the result of a :doc:`compute <compute>` or
+:doc:`fix <fix>` or the evaluation of an atom-style
+:doc:`variable <variable>`.
+
+Note that for values from a compute or fix, the bracketed index I can
+be specified using a wildcard asterisk with the index to effectively
+specify multiple values.  This takes the form "\*" or "\*n" or "n\*" or
+"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+number of columns in the array (for *mode* = vector), then an asterisk
+with no numeric values means all indices from 1 to N.  A leading
+asterisk means all indices from 1 to n (inclusive).  A trailing
+asterisk means all indices from n to N (inclusive).  A middle asterisk
+means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 compute reduce commands are
+equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
+command creates a per-atom array with 6 columns:
+
+
+.. parsed-literal::
+
+   compute myPress all stress/atom NULL
+   compute 2 all reduce min c_myPress[\*]
+   compute 2 all reduce min c_myPress[1] c_myPress[2] c_myPress[3] &
+                            c_myPress[4] c_myPress[5] c_myPress[6]
+
+
+----------
+
+
+The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+self-explanatory.  Note that other atom attributes can be used as
+inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+an input value from that compute.
+
+If a value begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  Computes can generate
+per-atom or local quantities.  See the individual
+:doc:`compute <compute>` doc page for details.  If no bracketed integer
+is appended, the vector calculated by the compute is used.  If a
+bracketed integer is appended, the Ith column of the array calculated
+by the compute is used.  Users can also write code for their own
+compute styles and :doc:`add them to LAMMPS <Modify>`.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  Fixes can generate per-atom
+or local quantities.  See the individual :doc:`fix <fix>` doc page for
+details.  Note that some fixes only produce their values on certain
+timesteps, which must be compatible with when compute reduce
+references the values, else an error results.  If no bracketed integer
+is appended, the vector calculated by the fix is used.  If a bracketed
+integer is appended, the Ith column of the array calculated by the fix
+is used.  Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how I can
+be specified with a wildcard asterisk to effectively specify multiple
+values.
+
+If a value begins with "v\_", a variable name must follow which has
+been previously defined in the input script.  It must be an
+:doc:`atom-style variable <variable>`.  Atom-style variables can
+reference thermodynamic keywords and various per-atom attributes, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of generating per-atom quantities to
+reduce.
+
+
+----------
+
+
+If the *replace* keyword is used, two indices *vec1* and *vec2* are
+specified, where each index ranges from 1 to the # of input values.
+The replace keyword can only be used if the *mode* is *min* or *max*\ .
+It works as follows.  A min/max is computed as usual on the *vec2*
+input vector.  The index N of that value within *vec2* is also stored.
+Then, instead of performing a min/max on the *vec1* input vector, the
+stored index is used to select the Nth element of the *vec1* vector.
+
+Thus, for example, if you wish to use this compute to find the bond
+with maximum stretch, you can do it as follows:
+
+
+.. parsed-literal::
+
+   compute 1 all property/local batom1 batom2
+   compute 2 all bond/local dist
+   compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
+   thermo_style custom step temp c_3[1] c_3[2] c_3[3]
+
+The first two input values in the compute reduce command are vectors
+with the IDs of the 2 atoms in each bond, using the :doc:`compute property/local <compute_property_local>` command.  The last input
+value is bond distance, using the :doc:`compute bond/local <compute_bond_local>` command.  Instead of taking the
+max of the two atom ID vectors, which does not yield useful
+information in this context, the *replace* keywords will extract the
+atom IDs for the two atoms in the bond of maximum stretch.  These atom
+IDs and the bond stretch will be printed with thermodynamic output.
+
+
+----------
+
+
+If a single input is specified this compute produces a global scalar
+value.  If multiple inputs are specified, this compute produces a
+global vector of values, the length of which is equal to the number of
+inputs specified.
+
+As discussed below, for the *sum* and *sumsq* modes, the value(s)
+produced by this compute are all "extensive", meaning their value
+scales linearly with the number of atoms involved.  If normalized
+values are desired, this compute can be accessed by the :doc:`thermo\_style custom <thermo_style>` command with :doc:`thermo\_modify norm yes <thermo_modify>` set as an option.  Or it can be accessed by a
+:doc:`variable <variable>` that divides by the appropriate atom count.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar if a single input value is
+specified or a global vector of length N where N is the number of
+inputs, and which can be accessed by indices 1 to N.  These values can
+be used by any command that uses global scalar or vector values from a
+compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+All the scalar or vector values calculated by this compute are
+"intensive", except when the *sum* or *sumsq* modes are used on
+per-atom or local vectors, in which case the calculated values are
+"extensive".
+
+The scalar or vector values will be in whatever :doc:`units <units>` the
+quantities being reduced are in.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`variable <variable>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst
new file mode 100644
index 0000000000..4f4384d91c
--- /dev/null
+++ b/doc/src/compute_reduce_chunk.rst
@@ -0,0 +1,205 @@
+.. index:: compute reduce/chunk
+
+compute reduce/chunk command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID reduce/chunk chunkID mode input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* reduce/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* mode = *sum* or *min* or *max*
+* one or more inputs can be listed
+* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_ID
+  
+  .. parsed-literal::
+  
+       c_ID = per-atom vector calculated by a compute with ID
+       c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = per-atom vector calculated by a fix with ID
+       f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+       v_name = per-atom vector calculated by an atom-style variable with name
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all reduce/chunk/atom mychunk min c_cluster
+
+Description
+"""""""""""
+
+Define a calculation that reduces one or more per-atom vectors into
+per-chunk values.  This can be useful for diagnostic output.  Or when
+used in conjunction with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can be
+used ot create per-atom values that induce a new set of chunks with a
+second :doc:`compute chunk/atom <compute_chunk_atom>` command.  An
+example is given below.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+For each atom, this compute accesses its chunk ID from the specified
+*chunkID* compute.  The per-atom value from an input contributes
+to a per-chunk value corresponding the the chunk ID.
+
+The reduction operation is specified by the *mode* setting and is
+performed over all the per-atom values from the atoms in each chunk.
+The *sum* option adds the pre-atom values to a per-chunk total.  The
+*min* or *max* options find the minimum or maximum value of the
+per-atom values for each chunk.
+
+Note that only atoms in the specified group contribute to the
+reduction operation.  If the *chunkID* compute returns a 0 for the
+chunk ID of an atom (i.e. the atom is not in a chunk defined by the
+:doc:`compute chunk/atom <compute_chunk_atom>` command), that atom will
+also not contribute to the reduction operation.  An input that is a
+compute or fix may define its own group which affects the quantities
+it returns.  For example, a compute with return a zero value for atoms
+that are not in the group specified for that compute.
+
+Each listed input is operated on independently.  Each input can be the
+result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation
+of an atom-style :doc:`variable <variable>`.
+
+Note that for values from a compute or fix, the bracketed index I can
+be specified using a wildcard asterisk with the index to effectively
+specify multiple values.  This takes the form "\*" or "\*n" or "n\*" or
+"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+number of columns in the array (for *mode* = vector), then an asterisk
+with no numeric values means all indices from 1 to N.  A leading
+asterisk means all indices from 1 to n (inclusive).  A trailing
+asterisk means all indices from n to N (inclusive).  A middle asterisk
+means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 compute reduce/chunk
+commands are equivalent, since the :doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
+array with 3 columns:
+
+
+.. parsed-literal::
+
+   compute prop all property/atom vx vy vz
+   compute 10 all reduce/chunk mychunk max c_prop[\*]
+   compute 10 all reduce/chunk mychunk max c_prop[1] c_prop[2] c_prop[3]
+
+
+----------
+
+
+Here is an example of using this compute, in conjunction with the
+compute chunk/spread/atom command to identify self-assembled micelles.
+The commands below can be added to the examples/in.micelle script.
+
+Imagine a collection of polymer chains or small molecules with
+hydrophobic end groups.  All the hydrophobic (HP) atoms are assigned
+to a group called "phobic".
+
+These commands will assign a unique cluster ID to all HP atoms within
+a specified distance of each other.  A cluster will contain all HP
+atoms in a single molecule, but also the HP atoms in nearby molecules,
+e.g. molecules that have clumped to form a micelle due to the
+attraction induced by the hydrophobicity.  The output of the
+chunk/reduce command will be a cluster ID per chunk (molecule).
+Molecules with the same cluster ID are in the same micelle.
+
+
+.. parsed-literal::
+
+   group phobic type 4     # specific to in.micelle model
+   compute cluster phobic cluster/atom 2.0
+   compute cmol all chunk/atom molecule
+   compute reduce phobic reduce/chunk cmol min c_cluster
+
+This per-chunk info could be output in at least two ways:
+
+
+.. parsed-literal::
+
+   fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector
+
+   compute spread all chunk/spread/atom cmol c_reduce
+   dump 1 all custom 1000 tmp.dump id type mol x y z c_cluster c_spread
+   dump_modify 1 sort id
+
+In the first case, each snapshot in the tmp.phobic file will contain
+one line per molecule.  Molecules with the same value are in the same
+micelle.  In the second case each dump snapshot contains all atoms,
+each with a final field with the cluster ID of the micelle that the HP
+atoms of that atom's molecule belong to.
+
+The result from compute chunk/spread/atom can be used to define a new
+set of chunks, where all the atoms in all the molecules in the same
+micelle are assigned to the same chunk, i.e. one chunk per micelle.
+
+
+.. parsed-literal::
+
+   compute micelle all chunk/atom c_spread compress yes
+
+Further analysis on a per-micelle basis can now be performed using any
+of the per-chunk computes listed on the :doc:`Howto chunk <Howto_chunk>`
+doc page.  E.g. count the number of atoms in each micelle, calculate
+its center or mass, shape (moments of inertia), radius of gyration,
+etc.
+
+
+.. parsed-literal::
+
+   compute prop all property/chunk micelle count
+   fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector
+
+Each snapshot in the tmp.micelle file will have one line per micelle
+with its count of atoms, plus a first line for a chunk with all the
+solvent atoms.  By the time 50000 steps have elapsed there are a
+handful of large micelles.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global vector if a single input value is
+specified, otherwise a global array is output.  The number of columns
+in the array is the number of inputs provided.  The length of the
+vector or the number of vector elements or array rows = the number of
+chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The vector or array can
+be accessed by any command that uses global values from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The per-atom values for the vector or each column of the array will be
+in whatever :doc:`units <units>` the corresponding input value is in.
+The vector or array values are "intensive".
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`, :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst
new file mode 100644
index 0000000000..1960814e0e
--- /dev/null
+++ b/doc/src/compute_rigid_local.rst
@@ -0,0 +1,205 @@
+.. index:: compute rigid/local
+
+compute rigid/local command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID rigid/local rigidID input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* rigid/local = style name of this compute command
+* rigidID = ID of fix rigid/small command or one of its variants
+* input = one or more rigid body attributes
+  
+  .. parsed-literal::
+  
+       possible attributes = id, mol, mass,
+                             x, y, z, xu, yu, zu, ix, iy, iz
+                             vx, vy, vz, fx, fy, fz,
+                             omegax, omegay, omegaz,
+                             angmomx, angmomy, angmomz,
+                             quatw, quati, quatj, quatk,
+                             tqx, tqy, tqz,
+                             inertiax, inertiay, inertiaz
+           id = atom ID of atom within body which owns body properties
+           mol = molecule ID used to define body in :doc:`fix rigid/small <fix_rigid>` command
+           mass = total mass of body
+           x,y,z = center of mass coords of body
+           xu,yu,zu = unwrapped center of mass coords of body
+           ix,iy,iz = box image that the center of mass is in
+           vx,vy,vz = center of mass velocities
+           fx,fy,fz = force of center of mass
+           omegax,omegay,omegaz = angular velocity of body
+           angmomx,angmomy,angmomz = angular momentum of body
+           quatw,quati,quatj,quatk = quaternion components for body
+           tqx,tqy,tqz = torque on body
+           inertiax,inertiay,inertiaz = diagonalized moments of inertia of body
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all rigid/local myRigid mol x y z
+
+Description
+"""""""""""
+
+Define a computation that simply stores rigid body attributes for
+rigid bodies defined by the :doc:`fix rigid/small <fix_rigid>` command
+or one of its NVE, NVT, NPT, NPH variants.  The data is stored as
+local data so it can be accessed by other :doc:`output commands <Howto_output>` that process local data, such as the
+:doc:`compute reduce <compute_reduce>` or :doc:`dump local <dump>`
+commands.
+
+Note that this command only works with the :doc:`fix rigid/small <fix_rigid>` command or its variants, not the fix rigid
+command and its variants.  The ID of the :doc:`fix rigid/small <fix_rigid>` command used to define rigid bodies must
+be specified as *rigidID*\ .  The :doc:`fix rigid <fix_rigid>` command is
+typically used to define a handful of (potentially very large) rigid
+bodies.  It outputs similar per-body information as this command
+directly from the fix as global data; see the :doc:`fix rigid <fix_rigid>` doc page for details
+
+The local data stored by this command is generated by looping over all
+the atoms owned on a processor.  If the atom is not in the specified
+*group-ID* or is not part of a rigid body it is skipped.  If it is not
+the atom within a body that is assigned to store the body information
+it is skipped (only one atom per body is so assigned).  If it is the
+assigned atom, then the info for that body is output.  This means that
+information for N bodies is generated.  N may be less than the # of
+bodies defined by the fix rigid command, if the atoms in some bodies
+are not in the *group-ID*\ .
+
+.. note::
+
+   Which atom in a body owns the body info is determined internal
+   to LAMMPS; it's the one nearest the geometric center of the body.
+   Typically you should avoid this complication, by defining the group
+   associated with this fix to include/exclude entire bodies.
+
+Note that as atoms and bodies migrate from processor to processor,
+there will be no consistent ordering of the entries within the local
+vector or array from one timestep to the next.
+
+Here is an example of how to use this compute to dump rigid body info
+to a file:
+
+
+.. parsed-literal::
+
+   compute 1 all rigid/local myRigid mol x y z fx fy fz
+   dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
+
+
+----------
+
+
+This section explains the rigid body attributes that can be specified.
+
+The *id* attribute is the atom-ID of the atom which owns the rigid body, which is
+assigned by the :doc:`fix rigid/small <fix_rigid>` command.
+
+The *mol* attribute is the molecule ID of the rigid body.  It should
+be the molecule ID which all of the atoms in the body belong to, since
+that is how the :doc:`fix rigid/small <fix_rigid>` command defines its
+rigid bodies.
+
+The *mass* attribute is the total mass of the rigid body.
+
+There are two options for outputting the coordinates of the center of
+mass (COM) of the body.  The *x*\ , *y*\ , *z* attributes write the COM
+"unscaled", in the appropriate distance :doc:`units <units>` (Angstroms,
+sigma, etc).  Use *xu*\ , *yu*\ , *zu* if you want the COM "unwrapped" by
+the image flags for each body.  Unwrapped means that if the body
+COM has passed through a periodic boundary one or more times, the value
+is generated what the COM coordinate would be if it had not been
+wrapped back into the periodic box.
+
+The image flags for the body can be generated directly using the *ix*\ ,
+*iy*\ , *iz* attributes.  For periodic dimensions, they specify which
+image of the simulation box the COM is considered to be in.  An image
+of 0 means it is inside the box as defined.  A value of 2 means add 2
+box lengths to get the true value.  A value of -1 means subtract 1 box
+length to get the true value.  LAMMPS updates these flags as the rigid
+body COMs cross periodic boundaries during the simulation.
+
+The *vx*\ , *vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz* attributes are components of
+the COM velocity and force on the COM of the body.
+
+The *omegax*\ , *omegay*\ , and *omegaz* attributes are the angular
+velocity components of the body around its COM.
+
+The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are the angular
+momentum components of the body around its COM.
+
+The *quatw*\ , *quati*\ , *quatj*\ , and *quatk* attributes are the
+components of the 4-vector quaternion representing the orientation of
+the rigid body.  See the :doc:`set <set>` command for an explanation of
+the quaternion vector.
+
+The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are the angular
+momentum components of the body around its COM.
+
+The *tqx*\ , *tqy*\ , *tqz* attributes are components of the torque acting
+on the body around its COM.
+
+The *inertiax*\ , *inertiay*\ , *inertiaz* attributes are components of
+diagonalized inertia tensor for the body, i.e the 3 moments of inertia
+for the body around its principal axes, as computed internally by
+LAMMPS.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a local vector or local array depending on the
+number of keywords.  The length of the vector or number of rows in the
+array is the number of rigid bodies.  If a single keyword is
+specified, a local vector is produced.  If two or more keywords are
+specified, a local array is produced where the number of columns = the
+number of keywords.  The vector or array can be accessed by any
+command that uses local values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS
+output options.
+
+The vector or array values will be in whatever :doc:`units <units>` the
+corresponding attribute is in:
+
+* id,mol = unitless
+* mass = mass units
+* x,y,z and xy,yu,zu = distance units
+* vx,vy,vz = velocity units
+* fx,fy,fz = force units
+* omegax,omegay,omegaz = radians/time units
+* angmomx,angmomy,angmomz = mass\*distance\^2/time units
+* quatw,quati,quatj,quatk = unitless
+* tqx,tqy,tqz = torque units
+* inertiax,inertiay,inertiaz = mass\*distance\^2 units
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the RIGID package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump local <dump>`, :doc:`compute reduce <compute_reduce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst
new file mode 100644
index 0000000000..d42c35abcd
--- /dev/null
+++ b/doc/src/compute_saed.rst
@@ -0,0 +1,214 @@
+.. index:: compute saed
+
+compute saed command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID saed lambda type1 type2 ... typeN keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* saed = style name of this compute command
+* lambda = wavelength of incident radiation (length units)
+* type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
+* zero or more keyword/value pairs may be appended
+* keyword = *Kmax* or *Zone* or *dR\_Ewald* or *c* or *manual* or *echo*
+  
+  .. parsed-literal::
+  
+       *Kmax* value = Maximum distance explored from reciprocal space origin
+                      (inverse length units)
+       *Zone* values = z1 z2 z3
+         z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
+                    reciprocal space will be meshed up to *Kmax*
+       *dR_Ewald* value = Thickness of Ewald sphere slice intercepting
+                          reciprocal space (inverse length units)
+       *c* values = c1 c2 c3
+         c1,c2,c3 = parameters to adjust the spacing of the reciprocal
+                    lattice nodes in the h, k, and l directions respectively
+       *manual* = flag to use manual spacing of reciprocal lattice points
+                  based on the values of the *c* parameters
+       *echo* = flag to provide extra output for debugging purposes
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+   compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+
+   fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+   fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+
+Description
+"""""""""""
+
+Define a computation that calculates electron diffraction intensity as
+described in :ref:`(Coleman) <saed-Coleman>` on a mesh of reciprocal lattice nodes
+defined by the entire simulation domain (or manually) using simulated
+radiation of wavelength lambda.
+
+The electron diffraction intensity I at each reciprocal lattice point
+is computed from the structure factor F using the equations:
+
+.. image:: Eqs/compute_saed1.jpg
+   :align: center
+
+.. image:: Eqs/compute_saed2.jpg
+   :align: center
+
+Here, K is the location of the reciprocal lattice node, rj is the
+position of each atom, fj are atomic scattering factors.
+
+Diffraction intensities are calculated on a three-dimensional mesh of
+reciprocal lattice nodes. The mesh spacing is defined either (a)  by
+the entire simulation domain or (b) manually using selected values as
+shown in the 2D diagram below.
+
+.. image:: JPG/saed_mesh_small.jpg
+   :target: JPG/saed_mesh.jpg
+   :align: center
+
+For a mesh defined by the simulation domain, a rectilinear grid is
+constructed with spacing *c*\ \*inv(A) along each reciprocal lattice
+axis. Where A are the vectors corresponding to the edges of the
+simulation cell. If one or two directions has non-periodic boundary
+conditions, then the spacing in these directions is defined from the
+average of the (inversed) box lengths with periodic boundary conditions.
+Meshes defined by the simulation domain must contain at least one periodic
+boundary.
+
+If the *manual* flag is included, the mesh of reciprocal lattice nodes
+will defined using the *c* values for the spacing along each reciprocal
+lattice axis. Note that manual mapping of the reciprocal space mesh is
+good for comparing diffraction results from  multiple simulations; however
+it can reduce the likelihood that Bragg reflections will be satisfied
+unless small spacing parameters <0.05 Angstrom\^(-1) are implemented.
+Meshes with manual spacing do not require a periodic boundary.
+
+The limits of the reciprocal lattice mesh are determined by the use of
+the *Kmax*\ , *Zone*\ , and *dR\_Ewald* parameters.  The rectilinear mesh
+created about the origin of reciprocal space is terminated at the
+boundary of a sphere of radius *Kmax* centered at the origin.  If
+*Zone* parameters z1=z2=z3=0 are used, diffraction intensities are
+computed throughout the entire spherical volume - note this can
+greatly increase the cost of computation.  Otherwise, *Zone*
+parameters will denote the z1=h, z2=k, and z3=l (in a global since)
+zone axis of an intersecting Ewald sphere.  Diffraction intensities
+will only be computed at the intersection of the reciprocal lattice
+mesh and a *dR\_Ewald* thick surface of the Ewald sphere.  See the
+example 3D intensity data and the intersection of a [010] zone axis
+in the below image.
+
+.. image:: JPG/saed_ewald_intersect_small.jpg
+   :target: JPG/saed_ewald_intersect.jpg
+   :align: center
+
+The atomic scattering factors, fj, accounts for the reduction in
+diffraction intensity due to Compton scattering.  Compute saed uses
+analytical approximations of the atomic scattering factors that vary
+for each atom type (type1 type2 ... typeN) and angle of diffraction.
+The analytic approximation is computed using the formula
+:ref:`(Brown) <Brown>`:
+
+.. image:: Eqs/compute_saed3.jpg
+   :align: center
+
+Coefficients parameterized by :ref:`(Fox) <Fox>` are assigned for each
+atom type designating the chemical symbol and charge of each atom
+type. Valid chemical symbols for compute saed are:
+
+H:       He:      Li:      Be:       B:
+C:        N:       O:       F:      Ne:
+Na:      Mg:      Al:      Si:       P:
+S:       Cl:      Ar:       K:      Ca:
+Sc:      Ti:       V:      Cr:      Mn:
+Fe:      Co:      Ni:      Cu:      Zn:
+Ga:      Ge:      As:      Se:      Br:
+Kr:      Rb:      Sr:       Y:      Zr:
+Nb:      Mo:      Tc:      Ru:      Rh:
+Pd:      Ag:      Cd:      In:      Sn:
+Sb:      Te:       I:      Xe:      Cs:
+Ba:      La:      Ce:      Pr:      Nd:
+Pm:      Sm:      Eu:      Gd:      Tb:
+Dy:      Ho:      Er:      Tm:      Yb:
+Lu:      Hf:      Ta:       W:      Re:
+Os:      Ir:      Pt:      Au:      Hg:
+Tl:      Pb:      Bi:      Po:      At:
+Rn:      Fr:      Ra:      Ac:      Th:
+Pa:       U:      Np:      Pu:      Am:
+Cm:      Bk:      Cf:tb(c=5,s=:)
+
+If the *echo* keyword is specified, compute saed will provide extra
+reporting information to the screen.
+
+**Output info:**
+
+This compute calculates a global vector.  The length of the vector is
+the number of reciprocal lattice nodes that are explored by the mesh.
+The entries of the global vector are the computed diffraction
+intensities as described above.
+
+The vector can be accessed by any command that uses global values from
+a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+All array values calculated by this compute are "intensive".
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-DIFFRACTION package.  It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The compute\_saed command does not work for triclinic cells.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix saed\_vtk <fix_saed_vtk>`, :doc:`compute xrd <compute_xrd>`
+
+Default
+"""""""
+
+The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR\_Ewald =
+0.01.
+
+
+----------
+
+
+.. _saed-Coleman:
+
+
+
+**(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020
+(2013).
+
+.. _Brown:
+
+
+
+**(Brown)** Brown et al. International Tables for Crystallography
+Volume C: Mathematical and Chemical Tables, 554-95 (2004).
+
+.. _Fox:
+
+
+
+**(Fox)** Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93
+(1989).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst
new file mode 100644
index 0000000000..e98048b912
--- /dev/null
+++ b/doc/src/compute_slice.rst
@@ -0,0 +1,137 @@
+.. index:: compute slice
+
+compute slice command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID slice Nstart Nstop Nskip input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* slice = style name of this compute command
+* Nstart = starting index within input vector(s)
+* Nstop = stopping index within input vector(s)
+* Nskip = extract every Nskip elements from input vector(s)
+* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N]
+  
+  .. parsed-literal::
+  
+       c_ID = global vector calculated by a compute with ID
+       c_ID[I] = Ith column of global array calculated by a compute with ID
+       f_ID = global vector calculated by a fix with ID
+       f_ID[I] = Ith column of global array calculated by a fix with ID
+       v_name = vector calculated by an vector-style variable with name
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all slice 1 100 10 c_msdmol[4]
+   compute 1 all slice 301 400 1 c_msdmol[4] v_myVec
+
+Description
+"""""""""""
+
+Define a calculation that "slices" one or more vector inputs into
+smaller vectors, one per listed input.  The inputs can be global
+quantities; they cannot be per-atom or local quantities.
+:doc:`Computes <compute>` and :doc:`fixes <fix>` and vector-style
+:doc:`variables <variable>` can generate such global quantities.  The
+group specified with this command is ignored.
+
+The values extracted from the input vector(s) are determined by the
+*Nstart*\ , *Nstop*\ , and *Nskip* parameters.  The elements of an input
+vector of length N are indexed from 1 to N.  Starting at element
+*Nstart*\ , every Mth element is extracted, where M = *Nskip*\ , until
+element *Nstop* is reached.  The extracted quantities are stored as a
+vector, which is typically shorter than the input vector.
+
+Each listed input is operated on independently to produce one output
+vector.  Each listed input must be a global vector or column of a
+global array calculated by another :doc:`compute <compute>` or
+:doc:`fix <fix>`.
+
+If an input value begins with "c\_", a compute ID must follow which has
+been previously defined in the input script and which generates a
+global vector or array.  See the individual :doc:`compute <compute>` doc
+page for details.  If no bracketed integer is appended, the vector
+calculated by the compute is used.  If a bracketed integer is
+appended, the Ith column of the array calculated by the compute is
+used.  Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script and which generates a global
+vector or array.  See the individual :doc:`fix <fix>` doc page for
+details.  Note that some fixes only produce their values on certain
+timesteps, which must be compatible with when compute slice references
+the values, else an error results.  If no bracketed integer is
+appended, the vector calculated by the fix is used.  If a bracketed
+integer is appended, the Ith column of the array calculated by the fix
+is used.  Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
+
+If an input value begins with "v\_", a variable name must follow which
+has been previously defined in the input script.  Only vector-style
+variables can be referenced.  See the :doc:`variable <variable>` command
+for details.  Note that variables of style *vector* define a formula
+which can reference individual atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+they are evaluated, so this is a very general means of specifying
+quantities to slice.
+
+If a single input is specified this compute produces a global vector,
+even if the length of the vector is 1.  If multiple inputs are
+specified, then a global array of values is produced, with the number
+of columns equal to the number of inputs specified.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global vector if a single input value is
+specified or a global array with N columns where N is the number of
+inputs.  The length of the vector or the number of rows in the array
+is equal to the number of values extracted from each input vector.
+These values can be used by any command that uses global vector or
+array values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector or array values calculated by this compute are simply
+copies of values generated by computes or fixes or variables that are
+input vectors to this compute.  If there is a single input vector of
+intensive and/or extensive values, then each value in the vector of
+values calculated by this compute will be "intensive" or "extensive",
+depending on the corresponding input value.  If there are multiple
+input vectors, and all the values in them are intensive, then the
+array values calculated by this compute are "intensive".  If there are
+multiple input vectors, and any value in them is extensive, then the
+array values calculated by this compute are "extensive".  Values
+produced by a variable are treated as intensive.
+
+The vector or array values will be in whatever :doc:`units <units>` the
+input quantities are in.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`compute reduce <compute_reduce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst
new file mode 100644
index 0000000000..82cb381692
--- /dev/null
+++ b/doc/src/compute_smd_contact_radius.rst
@@ -0,0 +1,66 @@
+.. index:: compute smd/contact/radius
+
+compute smd/contact/radius command
+==================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/contact/radius
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/contact/radius = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/contact/radius
+
+Description
+"""""""""""
+
+Define a computation which outputs the contact radius, i.e., the
+radius used to prevent particles from penetrating each other.  The
+contact radius is used only to prevent particles belonging to
+different physical bodies from penetrating each other. It is used by
+the contact pair styles, e.g., smd/hertz and smd/tri\_surface.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+The value of the contact radius will be 0.0 for particles not in the
+specified compute group.
+
+**Output info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle vector values will be in distance :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>` smd/hertz smd/tri\_surface
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst
new file mode 100644
index 0000000000..d828888b47
--- /dev/null
+++ b/doc/src/compute_smd_damage.rst
@@ -0,0 +1,59 @@
+.. index:: compute smd/damage
+
+compute smd/damage command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/damage
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/damage = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/damage
+
+Description
+"""""""""""
+
+Define a computation that calculates the damage status of SPH particles
+according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth Mach Dynamics in LAMMPS.
+
+**Output Info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle values are dimensionless an in the range of zero to one.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/plastic\_strain <compute_smd_plastic_strain>`, :doc:`smd/tlsph\_stress <compute_smd_tlsph_stress>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst
new file mode 100644
index 0000000000..e8ea6573c1
--- /dev/null
+++ b/doc/src/compute_smd_hourglass_error.rst
@@ -0,0 +1,72 @@
+.. index:: compute smd/hourglass/error
+
+compute smd/hourglass/error command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/hourglass/error
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/hourglass/error = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/hourglass/error
+
+Description
+"""""""""""
+
+Define a computation which outputs the error of the approximated
+relative separation with respect to the actual relative separation of
+the particles i and j. Ideally, if the deformation gradient is exact,
+and there exists a unique mapping between all particles' positions
+within the neighborhood of the central node and the deformation
+gradient, the approximated relative separation will coincide with the
+actual relative separation of the particles i and j in the deformed
+configuration.  This compute is only really useful for debugging the
+hourglass control mechanism which is part of the Total-Lagrangian SPH
+pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
+Mach Dynamics in LAMMPS.
+
+**Output Info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle vector values will are dimensionless. See
+:doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This quantity will be computed only for particles which interact with
+tlsph pair style.
+
+**Related Commands:**
+
+:doc:`smd/tlsph\_defgrad <compute_smd_tlsph_defgrad>`
+
+Default
+"""""""
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst
new file mode 100644
index 0000000000..b04494a415
--- /dev/null
+++ b/doc/src/compute_smd_internal_energy.rst
@@ -0,0 +1,60 @@
+.. index:: compute smd/internal/energy
+
+compute smd/internal/energy command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/internal/energy
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/smd/internal/energy = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/internal/energy
+
+Description
+"""""""""""
+
+Define a computation which outputs the per-particle enthalpy, i.e.,
+the sum of potential energy and heat.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
+Mach Dynamics in LAMMPS.
+
+**Output Info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle vector values will be given in :doc:`units <units>` of energy.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
+
+**Related Commands:**
+
+Default
+"""""""
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst
new file mode 100644
index 0000000000..8f27b039ca
--- /dev/null
+++ b/doc/src/compute_smd_plastic_strain.rst
@@ -0,0 +1,65 @@
+.. index:: compute smd/plastic/strain
+
+compute smd/plastic/strain command
+==================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/plastic/strain
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/plastic/strain = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/plastic/strain
+
+Description
+"""""""""""
+
+Define a computation that outputs the equivalent plastic strain per
+particle.  This command is only meaningful if a material model with
+plasticity is defined.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
+Mach Dynamics in LAMMPS.
+
+**Output Info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle values will be given dimensionless. See :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/plastic/strain/rate <compute_smd_tlsph_strain>`,
+:doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`,
+:doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst
new file mode 100644
index 0000000000..bf1b8a8530
--- /dev/null
+++ b/doc/src/compute_smd_plastic_strain_rate.rst
@@ -0,0 +1,65 @@
+.. index:: compute smd/plastic/strain/rate
+
+compute smd/plastic/strain/rate command
+=======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/plastic/strain/rate
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/plastic/strain/rate = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/plastic/strain/rate
+
+Description
+"""""""""""
+
+Define a computation that outputs the time rate of the equivalent
+plastic strain.  This command is only meaningful if a material model
+with plasticity is defined.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
+Mach Dynamics in LAMMPS.
+
+**Output Info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle values will be given in :doc:`units <units>` of one over time.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/plastic/strain <compute_smd_plastic_strain>`,
+:doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`,
+:doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst
new file mode 100644
index 0000000000..f3c2e1cc47
--- /dev/null
+++ b/doc/src/compute_smd_rho.rst
@@ -0,0 +1,62 @@
+.. index:: compute smd/rho
+
+compute smd/rho command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/rho
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/rho = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/rho
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-particle mass density.
+The mass density is the mass of a particle which is constant during
+the course of a simulation, divided by its volume, which can change
+due to mechanical deformation.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle values will be in :doc:`units <units>` of mass over volume.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute smd/vol <compute_smd_vol>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst
new file mode 100644
index 0000000000..ddff4ba4c2
--- /dev/null
+++ b/doc/src/compute_smd_tlsph_defgrad.rst
@@ -0,0 +1,67 @@
+.. index:: compute smd/tlsph/defgrad
+
+compute smd/tlsph/defgrad command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/tlsph/defgrad
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/tlsph/defgrad = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/tlsph/defgrad
+
+Description
+"""""""""""
+
+Define a computation that calculates the deformation gradient.  It is
+only meaningful for particles which interact according to the
+Total-Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute outputs a per-particle vector of vectors (tensors),
+which can be accessed by any command that uses per-particle values
+from a compute as input. See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The per-particle vector values will be given dimensionless. See
+:doc:`units <units>`.  The per-particle vector has 10 entries. The first
+nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz
+components of the asymmetric deformation gradient tensor. The tenth
+entry is the determinant of the deformation gradient.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. TThis compute can
+only be used for particles which interact via the total Lagrangian SPH
+pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/hourglass/error <compute_smd_hourglass_error>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst
new file mode 100644
index 0000000000..5a4f35e8b0
--- /dev/null
+++ b/doc/src/compute_smd_tlsph_dt.rst
@@ -0,0 +1,69 @@
+.. index:: compute smd/tlsph/dt
+
+compute smd/tlsph/dt command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/tlsph/dt
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/tlsph/dt = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/tlsph/dt
+
+Description
+"""""""""""
+
+Define a computation that outputs the CFL-stable time increment per
+particle.  This time increment is essentially given by the speed of
+sound, divided by the SPH smoothing length.  Because both the speed of
+sound and the smoothing length typically change during the course of a
+simulation, the stable time increment needs to be re-computed every
+time step.  This calculation is performed automatically in the
+relevant SPH pair styles and this compute only serves to make the
+stable time increment accessible for output purposes.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle values will be given in :doc:`units <units>` of time.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This compute can only be used for particles interacting with the
+Total-Lagrangian SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/adjust/dt <fix_smd_adjust_dt>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst
new file mode 100644
index 0000000000..cfa122aae6
--- /dev/null
+++ b/doc/src/compute_smd_tlsph_num_neighs.rst
@@ -0,0 +1,64 @@
+.. index:: compute smd/tlsph/num/neighs
+
+compute smd/tlsph/num/neighs command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/tlsph/num/neighs
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/tlsph/num/neighs = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/tlsph/num/neighs
+
+Description
+"""""""""""
+
+Define a computation that calculates the number of particles inside of
+the smoothing kernel radius for particles interacting via the
+Total-Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle values are dimensionless. See :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This quantity will be computed only for particles which interact with
+the Total-Lagrangian pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst
new file mode 100644
index 0000000000..0161e5e6e5
--- /dev/null
+++ b/doc/src/compute_smd_tlsph_shape.rst
@@ -0,0 +1,71 @@
+.. index:: compute smd/tlsph/shape
+
+compute smd/tlsph/shape command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/tlsph/shape
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/tlsph/shape = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/tlsph/shape
+
+Description
+"""""""""""
+
+Define a computation that outputs the current shape of the volume
+associated with a particle as a rotated ellipsoid.  It is only
+meaningful for particles which interact according to the
+Total-Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector of vectors, which can be
+accessed by any command that uses per-particle values from a compute
+as input. See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The per-particle vector has 7 entries. The first three entries
+correspond to the lengths of the ellipsoid's axes and have units of
+length.  These axis values are computed as the contact radius times the
+xx, yy, or zz components of the Green-Lagrange strain tensor
+associated with the particle.  The next 4 values are quaternions
+(order: q, x, y, z) which describe the spatial rotation of the
+particle relative to its initial state.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+This quantity will be computed only for particles which interact with
+the Total-Lagrangian SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/contact/radius <compute_smd_contact_radius>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst
new file mode 100644
index 0000000000..965d69a938
--- /dev/null
+++ b/doc/src/compute_smd_tlsph_strain.rst
@@ -0,0 +1,68 @@
+.. index:: compute smd/tlsph/strain
+
+compute smd/tlsph/strain command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/tlsph/strain
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/tlsph/strain = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/tlsph/strain
+
+Description
+"""""""""""
+
+Define a computation that calculates the Green-Lagrange strain tensor
+for particles interacting via the Total-Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector of vectors (tensors),
+which can be accessed by any command that uses per-particle values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The per-particle tensor values will be given dimensionless. See
+:doc:`units <units>`.
+
+The per-particle vector has 6 entries, corresponding to the xx, yy,
+zz, xy, xz, yz components of the symmetric strain tensor.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This quantity will be computed only for particles which interact with
+the Total-Lagrangian SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`,
+:doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst
new file mode 100644
index 0000000000..554706382a
--- /dev/null
+++ b/doc/src/compute_smd_tlsph_strain_rate.rst
@@ -0,0 +1,66 @@
+.. index:: compute smd/tlsph/strain/rate
+
+compute smd/tlsph/strain/rate command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/tlsph/strain/rate
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/tlsph/strain/rate = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/tlsph/strain/rate
+
+Description
+"""""""""""
+
+Define a computation that calculates the rate of the strain tensor for
+particles interacting via the Total-Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector of vectors (tensors),
+which can be accessed by any command that uses per-particle values
+from a compute as input. See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The values will be given in :doc:`units <units>` of one over time.
+
+The per-particle vector has 6 entries, corresponding to the xx, yy,
+zz, xy, xz, yz components of the symmetric strain rate tensor.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This quantity will be computed only for particles which interact with
+Total-Lagrangian SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute smd/tlsph/strain <compute_smd_tlsph_strain>`, :doc:`compute smd/tlsph/stress <compute_smd_tlsph_stress>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst
new file mode 100644
index 0000000000..db26b6b6b7
--- /dev/null
+++ b/doc/src/compute_smd_tlsph_stress.rst
@@ -0,0 +1,68 @@
+.. index:: compute smd/tlsph/stress
+
+compute smd/tlsph/stress command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/tlsph/stress
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/tlsph/stress = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/tlsph/stress
+
+Description
+"""""""""""
+
+Define a computation that outputs the Cauchy stress tensor for
+particles interacting via the Total-Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector of vectors (tensors),
+which can be accessed by any command that uses per-particle values
+from a compute as input. See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The values will be given in :doc:`units <units>` of pressure.
+
+The per-particle vector has 7 entries. The first six entries
+correspond to the xx, yy, zz, xy, xz and yz components of the
+symmetric Cauchy stress tensor. The seventh entry is the second
+invariant of the stress tensor, i.e., the von Mises equivalent stress.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This quantity will be computed only for particles which interact with
+the Total-Lagrangian SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute smd/tlsph/strain <compute_smd_tlsph_strain>`, :doc:`cmopute smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst
new file mode 100644
index 0000000000..61bd5ed97c
--- /dev/null
+++ b/doc/src/compute_smd_triangle_vertices.rst
@@ -0,0 +1,72 @@
+.. index:: compute smd/triangle/vertices
+
+compute smd/triangle/vertices command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/triangle/vertices
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/triangle/vertices = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/triangle/mesh/vertices
+
+Description
+"""""""""""
+
+Define a computation that returns the coordinates of the vertices
+corresponding to the triangle-elements of a mesh created by the :doc:`fix smd/wall\_surface <fix_smd_wall_surface>`.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute returns a per-particle vector of vectors, which can be
+accessed by any command that uses per-particle values from a compute
+as input. See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options.
+
+The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and
+(x3/y3/z3) corresponding to the first, second, and third vertex of
+each triangle.
+
+It is only meaningful to use this compute for a group of particles
+which is created via the :doc:`fix smd/wall\_surface <fix_smd_wall_surface>` command.
+
+The output of this compute can be used with the dump2vtk\_tris tool to
+generate a VTK representation of the smd/wall\_surface mesh for
+visualization purposes.
+
+The values will be given in :doc:`units <units>` of distance.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix smd/move/tri/surf <fix_smd_move_triangulated_surface>`,
+:doc:`fix smd/wall\_surface <fix_smd_wall_surface>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst
new file mode 100644
index 0000000000..fc98d03777
--- /dev/null
+++ b/doc/src/compute_smd_ulsph_num_neighs.rst
@@ -0,0 +1,63 @@
+.. index:: compute smd/ulsph/num/neighs
+
+compute smd/ulsph/num/neighs command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/ulsph/num/neighs
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/ulsph/num/neighs = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/ulsph/num/neighs
+
+Description
+"""""""""""
+
+Define a computation that returns the number of neighbor particles
+inside of the smoothing kernel radius for particles interacting via
+the updated Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute returns a per-particle vector, which can be accessed by
+any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle values will be given dimensionless, see :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst
new file mode 100644
index 0000000000..53a14e85fe
--- /dev/null
+++ b/doc/src/compute_smd_ulsph_strain.rst
@@ -0,0 +1,66 @@
+.. index:: compute smd/ulsph/strain
+
+compute smd/ulsph/strain command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/ulsph/strain
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/ulsph/strain = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/ulsph/strain
+
+Description
+"""""""""""
+
+Define a computation that outputs the logarithmic strain tensor.  for
+particles interacting via the updated Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle tensor, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle vector has 6 entries, corresponding to the xx, yy,
+zz, xy, xz, yz components of the symmetric strain rate tensor.
+
+The per-particle tensor values will be given dimensionless, see
+:doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute smd/tlsph/strain <compute_smd_tlsph_strain>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst
new file mode 100644
index 0000000000..0b8c6af19f
--- /dev/null
+++ b/doc/src/compute_smd_ulsph_strain_rate.rst
@@ -0,0 +1,67 @@
+.. index:: compute smd/ulsph/strain/rate
+
+compute smd/ulsph/strain/rate command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/ulsph/strain/rate
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/ulsph/strain/rate = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/ulsph/strain/rate
+
+Description
+"""""""""""
+
+Define a computation that outputs the rate of the logarithmic strain
+tensor for particles interacting via the updated Lagrangian SPH pair
+style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector of vectors (tensors),
+which can be accessed by any command that uses per-particle values
+from a compute as input. See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The values will be given in :doc:`units <units>` of one over time.
+
+The per-particle vector has 6 entries, corresponding to the xx, yy,
+zz, xy, xz, yz components of the symmetric strain rate tensor.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This compute can only be used for particles which interact with the
+updated Lagrangian SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst
new file mode 100644
index 0000000000..d3e3211250
--- /dev/null
+++ b/doc/src/compute_smd_ulsph_stress.rst
@@ -0,0 +1,66 @@
+.. index:: compute smd/ulsph/stress
+
+compute smd/ulsph/stress command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/ulsph/stress
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/ulsph/stress = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/ulsph/stress
+
+Description
+"""""""""""
+
+Define a computation that outputs the Cauchy stress tensor.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector of vectors (tensors),
+which can be accessed by any command that uses per-particle values
+from a compute as input. See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The values will be given in :doc:`units <units>` of pressure.
+
+The per-particle vector has 7 entries. The first six entries
+correspond to the xx, yy, zz, xy, xz, yz components of the symmetric
+Cauchy stress tensor. The seventh entry is the second invariant of the
+stress tensor, i.e., the von Mises equivalent stress.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute smd/ulsph/strain <compute_smd_ulsph_strain>`, :doc:`compute smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` :doc:`compute smd/tlsph/stress <compute_smd_tlsph_stress>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst
new file mode 100644
index 0000000000..a1b553ae6b
--- /dev/null
+++ b/doc/src/compute_smd_vol.rst
@@ -0,0 +1,64 @@
+.. index:: compute smd/vol
+
+compute smd/vol command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID smd/vol
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* smd/vol = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all smd/vol
+
+Description
+"""""""""""
+
+Define a computation that provides the per-particle volume and the sum
+of the per-particle volumes of the group for which the fix is defined.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
+Mach Dynamics in LAMMPS.
+
+**Output info:**
+
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+The per-particle vector values will be given in :doc:`units <units>` of
+volume.
+
+Additionally, the compute returns a scalar, which is the sum of the
+per-particle volumes of the group for which the fix is defined.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute smd/rho <compute_smd_rho>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst
new file mode 100644
index 0000000000..8556b3971b
--- /dev/null
+++ b/doc/src/compute_sna_atom.rst
@@ -0,0 +1,364 @@
+.. index:: compute sna/atom
+
+compute sna/atom command
+========================
+
+compute snad/atom command
+=========================
+
+compute snav/atom command
+=========================
+
+compute snap command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+   compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+   compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... 
+   compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* sna/atom = style name of this compute command
+* rcutfac = scale factor applied to all cutoff radii (positive real)
+* rfac0 = parameter in distance to angle conversion (0 < rcutfac < 1)
+* twojmax = band limit for bispectrum components (non-negative integer)
+* R\_1, R\_2,... = list of cutoff radii, one for each type (distance units)
+* w\_1, w\_2,... = list of neighbor weights, one for each type
+* zero or more keyword/value pairs may be appended
+* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag*
+  
+  .. parsed-literal::
+  
+       *rmin0* value = parameter in distance to angle conversion (distance units)
+       *switchflag* value = *0* or *1*
+          *0* = do not use switching function
+          *1* = use switching function
+       *bzeroflag* value = *0* or *1*
+          *0* = do not subtract B0
+          *1* = subtract B0
+       *quadraticflag* value = *0* or *1*
+          *0* = do not generate quadratic terms
+          *1* = generate quadratic terms
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
+   compute db all sna/atom 1.4 0.95 6 2.0 1.0
+   compute vb all sna/atom 1.4 0.95 6 2.0 1.0
+   compute snap all snap 1.4 0.95 6 2.0 1.0
+
+Description
+"""""""""""
+
+Define a computation that calculates a set of quantities related to the
+bispectrum components of the atoms in a group. These computes are
+used primarily for calculating the dependence of energy, force, and
+stress components on the linear coefficients in the 
+:doc:`snap pair\_style <pair_snap>`, which is useful when training a
+SNAP potential to match target data.
+
+Bispectrum components of an atom are order parameters characterizing
+the radial and angular distribution of neighbor atoms. The detailed
+mathematical definition is given in the paper by Thompson et
+al. :ref:`(Thompson) <Thompson20141>`
+
+The position of a neighbor atom *i'* relative to a central atom *i* is
+a point within the 3D ball of radius *R\_ii' = rcutfac\*(R\_i + R\_i')*
+
+Bartok et al. :ref:`(Bartok) <Bartok20101>`, proposed mapping this 3D ball
+onto the 3-sphere, the surface of the unit ball in a four-dimensional
+space.  The radial distance *r* within *R\_ii'* is mapped on to a third
+polar angle *theta0* defined by,
+
+.. image:: Eqs/compute_sna_atom1.jpg
+   :align: center
+
+In this way, all possible neighbor positions are mapped on to a subset
+of the 3-sphere.  Points south of the latitude *theta0max=rfac0\*Pi*
+are excluded.
+
+The natural basis for functions on the 3-sphere is formed by the 4D
+hyperspherical harmonics *U\^j\_m,m'(theta, phi, theta0).*  These
+functions are better known as *D\^j\_m,m',* the elements of the Wigner
+*D*\ -matrices :ref:`(Meremianin <Meremianin2006>`,
+:ref:`Varshalovich) <Varshalovich1987>`.
+
+The density of neighbors on the 3-sphere can be written as a sum of
+Dirac-delta functions, one for each neighbor, weighted by species and
+radial distance. Expanding this density function as a generalized
+Fourier series in the basis functions, we can write each Fourier
+coefficient as
+
+.. image:: Eqs/compute_sna_atom2.jpg
+   :align: center
+
+The *w\_i'* neighbor weights are dimensionless numbers that are chosen
+to distinguish atoms of different types, while the central atom is
+arbitrarily assigned a unit weight.  The function *fc(r)* ensures that
+the contribution of each neighbor atom goes smoothly to zero at
+*R\_ii'*:
+
+.. image:: Eqs/compute_sna_atom4.jpg
+   :align: center
+
+The expansion coefficients *u\^j\_m,m'* are complex-valued and they are
+not directly useful as descriptors, because they are not invariant
+under rotation of the polar coordinate frame. However, the following
+scalar triple products of expansion coefficients can be shown to be
+real-valued and invariant under rotation :ref:`(Bartok) <Bartok20101>`.
+
+.. image:: Eqs/compute_sna_atom3.jpg
+   :align: center
+
+The constants *H\^jmm'\_j1m1m1'\_j2m2m2'* are coupling coefficients,
+analogous to Clebsch-Gordan coefficients for rotations on the
+2-sphere. These invariants are the components of the bispectrum and
+these are the quantities calculated by the compute *sna/atom*\ . They
+characterize the strength of density correlations at three points on
+the 3-sphere. The j2=0 subset form the power spectrum, which
+characterizes the correlations of two points. The lowest-order
+components describe the coarsest features of the density function,
+while higher-order components reflect finer detail.  Note that the
+central atom is included in the expansion, so three point-correlations
+can be either due to three neighbors, or two neighbors and the central
+atom.
+
+Compute *snad/atom* calculates the derivative of the bispectrum components
+summed separately for each atom type:
+
+.. image:: Eqs/compute_sna_atom5.jpg
+   :align: center
+
+The sum is over all atoms *i'* of atom type *I*\ .  For each atom *i*\ ,
+this compute evaluates the above expression for each direction, each
+atom type, and each bispectrum component.  See section below on output
+for a detailed explanation.
+
+Compute *snav/atom* calculates the virial contribution due to the
+derivatives:
+
+.. image:: Eqs/compute_sna_atom6.jpg
+   :align: center
+
+Again, the sum is over all atoms *i'* of atom type *I*\ .  For each atom
+*i*\ , this compute evaluates the above expression for each of the six
+virial components, each atom type, and each bispectrum component.  See
+section below on output for a detailed explanation.
+
+Compute *snap* calculates a global array contains information related
+to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
+and *snav/atom*\ . The first row of the array contains the summation of 
+*sna/atom* over all atoms, but broken out by type. The last six rows
+of the array contain the summation of *snav/atom* over all atoms, broken
+out by type. In between these are 3\*\ *N* rows containing the same values
+computed by *snad/atom* (these are already summed over all atoms and
+broken out by type). The element in the last column of each row contains
+the potential energy, force, or stress, according to the row.
+These quantities correspond to the user-specified reference potential
+that must be subtracted from the target data when fitting SNAP.
+The potential energy calculation uses the built in compute *thermo\_pe*.
+The stress calculation uses a compute called *snap\_press* that is
+automatically created behind the scenes, according to the following
+command:
+
+
+.. parsed-literal::
+
+   compute snap_press all pressure NULL virial
+
+See section below on output for a detailed explanation of the data
+layout in the global array.
+
+The value of all bispectrum components will be zero for atoms not in
+the group. Neighbor atoms not in the group do not contribute to the
+bispectrum of atoms in the group.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently.
+
+The argument *rcutfac* is a scale factor that controls the ratio of
+atomic radius to radial cutoff distance.
+
+The argument *rfac0* and the optional keyword *rmin0* define the
+linear mapping from radial distance to polar angle *theta0* on the
+3-sphere.
+
+The argument *twojmax* defines which
+bispectrum components are generated. See section below on output for a
+detailed explanation of the number of bispectrum components and the
+ordered in which they are listed.
+
+The keyword *switchflag* can be used to turn off the switching
+function.
+
+The keyword *bzeroflag* determines whether or not *B0*\ , the bispectrum
+components of an atom with no neighbors, are subtracted from
+the calculated bispectrum components. This optional keyword
+normally only affects compute *sna/atom*\ . However, when
+*quadraticflag* is on, it also affects *snad/atom* and *snav/atom*\ .
+
+The keyword *quadraticflag* determines whether or not the
+quadratic analogs to the bispectrum quantities are generated.
+These are formed by taking the outer product of the vector
+of bispectrum components with itself.
+See section below on output for a
+detailed explanation of the number of quadratic terms and the
+ordered in which they are listed.
+
+.. note::
+
+   If you have a bonded system, then the settings of
+   :doc:`special\_bonds <special_bonds>` command can remove pairwise
+   interactions between atoms in the same bond, angle, or dihedral.  This
+   is the default setting for the :doc:`special\_bonds <special_bonds>`
+   command, and means those pairwise interactions do not appear in the
+   neighbor list.  Because this fix uses the neighbor list, it also means
+   those pairs will not be included in the calculation.  One way to get
+   around this, is to write a dump file, and use the :doc:`rerun <rerun>`
+   command to compute the bispectrum components for snapshots in the dump
+   file.  The rerun script can use a :doc:`special\_bonds <special_bonds>`
+   command that includes all pairs in the neighbor list.
+
+;line
+
+**Output info:**
+
+Compute *sna/atom* calculates a per-atom array, each column
+corresponding to a particular bispectrum component.  The total number
+of columns and the identity of the bispectrum component contained in
+each column depend of the value of *twojmax*\ , as
+described by the following piece of python code:
+
+
+.. parsed-literal::
+
+   for j1 in range(0,twojmax+1):
+       for j2 in range(0,j1+1):
+           for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+               if (j>=j1): print j1/2.,j2/2.,j/2.
+
+.. note::
+
+   the *diagonal* keyword allowing other possible choices
+   for the number of bispectrum components was removed in 2019,
+   since all potentials use the value of 3, corresponding to the
+   above set of bispectrum components.
+
+Compute *snad/atom* evaluates a per-atom array. The columns are
+arranged into *ntypes* blocks, listed in order of atom type *I*\ .  Each
+block contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z*
+components of the atom position.  Each of these sub-blocks contains
+one column for each bispectrum component, the same as for compute
+*sna/atom*
+
+Compute *snav/atom* evaluates a per-atom array. The columns are
+arranged into *ntypes* blocks, listed in order of atom type *I*\ .  Each
+block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
+*yz*\ , *xz*\ , and *xy* components of the virial tensor in Voigt
+notation.  Each of these sub-blocks contains one column for each
+bispectrum component, the same as for compute *sna/atom*
+
+Compute *snap* evaluates a global array. 
+The columns are arranged into
+*ntypes* blocks, listed in order of atom type *I*\ . Each block
+contains one column for each bispectrum component, the same as for compute
+*sna/atom*\ . A final column contains the corresponding energy, force component
+on an atom, or virial stress component. The rows of the array appear 
+in the following order:
+
+* 1 row: *sna/atom* quantities summed for all atoms of type *I*
+* 3\*\ *N* rows: *snad/atom* quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
+* 6 rows: *snav/atom* quantities summed for all atoms of type *I*
+
+For example, if *K* =30 and ntypes=1, the number of columns in the per-atom
+arrays generated by *sna/atom*\ , *snad/atom*\ , and *snav/atom*
+are 30, 90, and 180, respectively. With *quadratic* value=1,
+the numbers of columns are 930, 2790, and 5580, respectively.
+The number of columns in the global array generated by *snap*
+are 31, and 931, respectively, while the number of rows is
+1+3\*\ *N*\ +6, where *N* is the total number of atoms.
+
+If the *quadratic* keyword value is set to 1, then additional
+columns are generated, corresponding to
+the products of all distinct pairs of  bispectrum components. If the
+number of bispectrum components is *K*\ , then the number of distinct pairs
+is  *K*\ (\ *K*\ +1)/2.
+For compute *sna/atom* these columns are appended to existing *K* columns.
+The ordering of quadratic terms is upper-triangular,
+(1,1),(1,2)...(1,\ *K*\ ),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*\ ,\ *K*\ ).
+For computes *snad/atom* and *snav/atom* each set of *K*\ (\ *K*\ +1)/2
+additional columns is inserted directly after each of sub-block
+of linear terms i.e. linear and quadratic terms are contiguous.
+So the nesting order from inside to outside is bispectrum component,
+linear then quadratic, vector/tensor component, type.
+
+These values can be accessed by any command that uses per-atom values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+Restrictions
+""""""""""""
+
+
+These computes are part of the SNAP package.  They are only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style snap <pair_snap>`
+
+Default
+"""""""
+
+The optional keyword defaults are *rmin0* = 0,
+*switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0,
+
+
+----------
+
+
+.. _Thompson20141:
+
+
+
+**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
+available at `arXiv:1409.3880 <http://arxiv.org/abs/1409.3880>`_
+
+.. _Bartok20101:
+
+
+
+**(Bartok)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
+
+.. _Meremianin2006:
+
+
+
+**(Meremianin)** Meremianin, J. Phys. A,  39, 3099 (2006).
+
+.. _Varshalovich1987:
+
+
+
+**(Varshalovich)** Varshalovich, Moskalev, Khersonskii, Quantum Theory
+of Angular Momentum, World Scientific, Singapore (1987).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_spin.rst b/doc/src/compute_spin.rst
new file mode 100644
index 0000000000..034d2ab685
--- /dev/null
+++ b/doc/src/compute_spin.rst
@@ -0,0 +1,91 @@
+.. index:: compute spin
+
+compute spin command
+====================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID spin
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* spin = style name of this compute command
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   compute out_mag all spin
+
+Description
+"""""""""""
+
+Define a computation that calculates magnetic quantities for a system
+of atoms having spins.
+
+This compute calculates the following 6 magnetic quantities:
+
+* the three first quantities are the x,y and z coordinates of the total
+  magnetization,
+* the fourth quantity is the norm of the total magnetization,
+* The fifth quantity is the magnetic energy (in eV),
+* The sixth one is referred to as the spin temperature, according
+  to the work of :ref:`(Nurdin) <Nurdin1>`.
+
+
+The simplest way to output the results of the compute spin calculation
+is to define some of the quantities as variables, and to use the thermo and
+thermo\_style commands, for example:
+
+
+.. code-block:: LAMMPS
+
+   compute out_mag         all spin
+
+   variable mag_z          equal c_out_mag[3]
+   variable mag_norm       equal c_out_mag[4]
+   variable temp_mag       equal c_out_mag[6]
+
+   thermo                  10
+   thermo_style            custom step v_mag_z v_mag_norm v_temp_mag
+
+This series of commands evaluates the total magnetization along z, the norm of
+the total magnetization, and the magnetic temperature. Three variables are
+assigned to those quantities. The thermo and thermo\_style commands print them
+every 10 timesteps.
+
+**Output info:**
+
+The array values are "intensive".  The array values will be in
+metal units (:doc:`units <units>`).
+
+Restrictions
+""""""""""""
+
+
+The *spin* compute is part of the SPIN package.  This compute is only
+enabled if LAMMPS was built with this package.  See the :doc:`Build package <Build_package>` doc page for more info.  The atom\_style
+has to be "spin" for this compute to be valid.
+
+**Related commands:**
+
+none
+
+**Default:**
+
+none
+
+
+----------
+
+
+.. _Nurdin1:
+
+
+
+**(Nurdin)** Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
deleted file mode 100644
index d27e402972..0000000000
--- a/doc/src/compute_spin.txt
+++ /dev/null
@@ -1,77 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-compute spin command :h3
-
-[Syntax:]
-
-compute ID group-ID spin :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-spin = style name of this compute command :ul
-
-[Examples:]
-
-compute out_mag all spin :pre
-
-[Description:]
-
-Define a computation that calculates magnetic quantities for a system
-of atoms having spins.
-
-This compute calculates 6 magnetic quantities.
-
-The three first quantities are the x,y and z coordinates of the total
-magnetization.
-
-The fourth quantity is the norm of the total magnetization.
-
-The fifth quantity is the magnetic energy.
-
-The sixth one is referred to as the spin temperature, according
-to the work of "(Nurdin)"_#Nurdin1.
-
-The simplest way to output the results of the compute spin calculation
-is to define some of the quantities as variables, and to use the thermo and
-thermo_style commands, for example:
-
-compute out_mag		all spin :pre
-
-variable mag_z      	equal c_out_mag\[3\]
-variable mag_norm	equal c_out_mag\[4\]
-variable temp_mag      	equal c_out_mag\[6\] :pre
-
-thermo          	10
-thermo_style    	custom step v_mag_z v_mag_norm v_temp_mag :pre
-
-This series of commands evaluates the total magnetization along z, the norm of
-the total magnetization, and the magnetic temperature. Three variables are
-assigned to those quantities. The thermo and thermo_style commands print them
-every 10 timesteps.
-
-[Output info:]
-
-The array values are "intensive".  The array values will be in
-metal units ("units"_units.html).
-
-[Restrictions:]
-
-The {spin} compute is part of the SPIN package.  This compute is only
-enabled if LAMMPS was built with this package.  See the "Build
-package"_Build_package.html doc page for more info.  The atom_style
-has to be "spin" for this compute to be valid.
-
-[Related commands:] none
-
-[Default:] none
-
-:line
-
-:link(Nurdin1)
-[(Nurdin)] Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
-
diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst
new file mode 100644
index 0000000000..c37a8cc52d
--- /dev/null
+++ b/doc/src/compute_stress_atom.rst
@@ -0,0 +1,279 @@
+.. index:: compute stress/atom
+
+compute stress/atom command
+===========================
+compute centroid/stress/atom command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID style temp-ID keyword ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* style = *stress/atom* or *centroid/stress/atom*
+* temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+* zero or more keywords may be appended
+* keyword = *ke* or *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *fix* or *virial*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 mobile stress/atom NULL
+   compute 1 mobile stress/atom myRamp
+   compute 1 all stress/atom NULL pair bond
+   compute 1 all centroid/stress/atom NULL bond dihedral improper
+
+Description
+"""""""""""
+
+Define a computation that computes per-atom stress
+tensor for each atom in a group.  In case of compute *stress/atom*,
+the tensor for each atom is symmetric with 6
+components and is stored as a 6-element vector in the following order:
+:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
+In case of compute *centroid/stress/atom*,
+the tensor for each atom is asymmetric with 9 components
+and is stored as a 9-element vector in the following order:
+:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`,
+:math:`yx`, :math:`zx`, :math:`zy`.
+See the :doc:`compute pressure <compute_pressure>` command if you want the stress tensor
+(pressure) of the entire system.
+
+The stress tensor for atom :math:`I` is given by the following formula,
+where :math:`a` and :math:`b` take on values :math:`x`, :math:`y`, :math:`z`
+to generate the components of the tensor:
+
+.. math::
+
+   S_{ab}  =  - m v_a v_b - W_{ab}
+
+The first term is a kinetic energy contribution for atom :math:`I`.  See
+details below on how the specified *temp-ID* can affect the velocities
+used in this calculation. The second term is the virial
+contribution due to intra and intermolecular interactions,
+where the exact computation details are determined by the compute style.
+
+In case of compute *stress/atom*, the virial contribution is:
+
+.. math::
+
+   W_{ab} & = \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b})  \\
+  & + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\
+  & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
+
+The first term is a pairwise energy
+contribution where :math:`n` loops over the :math:`N_p`
+neighbors of atom :math:`I`, :math:`\mathbf{r}_1` and :math:`\mathbf{r}_2`
+are the positions of the 2 atoms in the pairwise interaction,
+and :math:`\mathbf{F}_1` and :math:`\mathbf{F}_2` are the forces
+on the 2 atoms resulting from the pairwise interaction.
+The second term is a bond contribution of
+similar form for the :math:`N_b` bonds which atom :math:`I` is part of.
+There are similar terms for the :math:`N_a` angle, :math:`N_d` dihedral,
+and :math:`N_i` improper interactions atom :math:`I` is part of.
+There is also a term for the KSpace
+contribution from long-range Coulombic interactions, if defined.
+Finally, there is a term for the :math:`N_f` :doc:`fixes <fix>` that apply
+internal constraint forces to atom :math:`I`. Currently, only the
+:doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>` commands
+contribute to this term.
+As the coefficients in the formula imply, a virial contribution
+produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
+atoms in a Tersoff 3-body interaction) is assigned in equal portions
+to each atom in the set.  E.g. 1/4 of the dihedral virial to each of
+the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
+to atoms in a water molecule via the :doc:`fix shake <fix_shake>`
+command.
+
+In case of compute *centroid/stress/atom*, the virial contribution is:
+
+.. math::
+
+   W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a}  F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\
+  & + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
+
+As with compute *stress/atom*, the first, second, third, fourth and fifth terms
+are pairwise, bond, angle, dihedral and improper contributions,
+but instead of assigning the virial contribution equally to each atom,
+only the force :math:`\mathbf{F}_I` acting on atom :math:`I`
+due to the interaction and the relative
+position :math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
+of the interacting atoms, i.e. centroid, is used.
+As the geometric center is different
+for each interaction, the :math:`\mathbf{r}_{I0}` also differs.
+The sixth and seventh terms, Kspace and :doc:`fix <fix>` contribution
+respectively, are computed identical to compute *stress/atom*.
+Although the total system virial is the same as compute *stress/atom*,
+compute *centroid/stress/atom* is know to result in more consistent
+heat flux values for angle, dihedrals and improper contributions
+when computed via :doc:`compute heat/flux <compute_heat_flux>`.
+
+If no extra keywords are listed, the kinetic contribution
+all of the virial contribution terms are
+included in the per-atom stress tensor.  If any extra keywords are
+listed, only those terms are summed to compute the tensor.  The
+*virial* keyword means include all terms except the kinetic energy
+*ke*\ .
+
+Note that the stress for each atom is due to its interaction with all
+other atoms in the simulation, not just with other atoms in the group.
+
+Details of how compute *stress/atom* obtains the virial for individual atoms for
+either pairwise or many-body potentials, and including the effects of
+periodic boundary conditions is discussed in :ref:`(Thompson) <Thompson2>`.
+The basic idea for many-body potentials is to treat each component of
+the force computation between a small cluster of atoms in the same
+manner as in the formula above for bond, angle, dihedral, etc
+interactions.  Namely the quantity :math:`\mathbf{r} \cdot \mathbf{F}`
+is summed over the atoms in
+the interaction, with the :math:`r` vectors unwrapped by periodic boundaries
+so that the cluster of atoms is close together.  The total
+contribution for the cluster interaction is divided evenly among those
+atoms. Details of how compute *centroid/stress/atom* obtains
+the virial for individual atoms
+is given in :ref:`(Surblys) <Surblys1>`,
+where the idea is that the virial of the atom :math:`I`
+is the result of only the force :math:`\mathbf{F}_I` on the atom due
+to the interaction
+and its positional vector :math:`\mathbf{r}_{I0}`,
+relative to the geometric center of the
+interacting atoms, regardless of the number of participating atoms.
+The periodic boundary treatment is identical to
+that of compute *stress/atom*, and both of them reduce to identical
+expressions for two-body interactions,
+i.e. computed values for contributions from bonds and two-body pair styles,
+such as :doc:`Lennard-Jones <pair_lj>`, will be the same,
+while contributions from angles, dihedrals and impropers will be different.
+
+The :doc:`dihedral\_style charmm <dihedral_charmm>` style calculates
+pairwise interactions between 1-4 atoms.  The virial contribution of
+these terms is included in the pair virial, not the dihedral virial.
+
+The KSpace contribution is calculated using the method in
+:ref:`(Heyes) <Heyes2>` for the Ewald method and by the methodology described
+in :ref:`(Sirk) <Sirk1>` for PPPM.  The choice of KSpace solver is specified
+by the :doc:`kspace\_style pppm <kspace_style>` command.  Note that for
+PPPM, the calculation requires 6 extra FFTs each timestep that
+per-atom stress is calculated.  Thus it can significantly increase the
+cost of the PPPM calculation if it is needed on a large fraction of
+the simulation timesteps.
+
+The *temp-ID* argument can be used to affect the per-atom velocities
+used in the kinetic energy contribution to the total stress.  If the
+kinetic energy is not included in the stress, than the temperature
+compute is not used and can be specified as NULL.  If the kinetic
+energy is included and you wish to use atom velocities as-is, then
+*temp-ID* can also be specified as NULL.  If desired, the specified
+temperature compute can be one that subtracts off a bias to leave each
+atom with only a thermal velocity to use in the formula above, e.g. by
+subtracting a background streaming velocity.  See the doc pages for
+individual :doc:`compute commands <compute>` to determine which ones
+include a bias.
+
+
+----------
+
+
+Note that as defined in the formula, per-atom stress is the negative
+of the per-atom pressure tensor.  It is also really a stress\*volume
+formulation, meaning the computed quantity is in units of
+pressure\*volume.  It would need to be divided by a per-atom volume to
+have units of stress (pressure), but an individual atom's volume is
+not well defined or easy to compute in a deformed solid or a liquid.
+See the :doc:`compute voronoi/atom <compute_voronoi_atom>` command for
+one possible way to estimate a per-atom volume.
+
+Thus, if the diagonal components of the per-atom stress tensor are
+summed for all atoms in the system and the sum is divided by :math:`dV`, where
+:math:`d` = dimension and :math:`V` is the volume of the system,
+the result should be :math:`-P`, where :math:`P`
+is the total pressure of the system.
+
+These lines in an input script for a 3d system should yield that
+result. I.e. the last 2 columns of thermo output will be the same:
+
+
+.. parsed-literal::
+
+   compute        peratom all stress/atom NULL
+   compute        p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+   variable       press equal -(c_p[1]+c_p[2]+c_p[3])/(3\*vol)
+   thermo_style   custom step temp etotal press v_press
+
+.. note::
+
+   The per-atom stress does not include any Lennard-Jones tail
+   corrections to the pressure added by the :doc:`pair\_modify tail yes <pair_modify>` command, since those are contributions to the
+   global system pressure.
+
+**Output info:**
+
+This compute *stress/atom* calculates a per-atom array with 6 columns, which can be
+accessed by indices 1-6 by any command that uses per-atom values from
+a compute as input.
+The compute *centroid/stress/atom* produces a per-atom array with 9 columns,
+but otherwise can be used in an identical manner to compute *stress/atom*.
+See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+The per-atom array values will be in pressure\*volume
+:doc:`units <units>` as discussed above.
+
+Restrictions
+""""""""""""
+Currently, compute *centroid/stress/atom* does not support
+pair styles with many-body interactions,
+such as :doc:`Tersoff <pair_tersoff>`,
+and LAMMPS will generate an error in such cases.
+In principal, equivalent formulation
+to that of angle, dihedral and improper contributions
+in the virial :math:`W_{ab}` formula
+can also be applied to the many-body pair styles,
+and is planned in the future.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute pressure <compute_pressure>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Heyes2:
+
+
+
+**(Heyes)** Heyes, Phys Rev B, 49, 755 (1994).
+
+.. _Sirk1:
+
+
+
+**(Sirk)** Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).
+
+.. _Thompson2:
+
+
+
+**(Thompson)** Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
+
+.. _Surblys1:
+
+
+
+**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt
deleted file mode 100644
index d81d97061c..0000000000
--- a/doc/src/compute_stress_atom.txt
+++ /dev/null
@@ -1,168 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-compute stress/atom command :h3
-
-[Syntax:]
-
-compute ID group-ID stress/atom temp-ID keyword ... :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-stress/atom = style name of this compute command
-temp-ID = ID of compute that calculates temperature, can be NULL if not needed
-zero or more keywords may be appended
-keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
-
-[Examples:]
-
-compute 1 mobile stress/atom NULL
-compute 1 mobile stress/atom myRamp
-compute 1 all stress/atom NULL pair bond :pre
-
-[Description:]
-
-Define a computation that computes the symmetric per-atom stress
-tensor for each atom in a group.  The tensor for each atom has 6
-components and is stored as a 6-element vector in the following order:
-xx, yy, zz, xy, xz, yz.  See the "compute
-pressure"_compute_pressure.html command if you want the stress tensor
-(pressure) of the entire system.
-
-The stress tensor for atom {I} is given by the following formula,
-where {a} and {b} take on values x,y,z to generate the 6 components of
-the symmetric tensor:
-
-:c,image(Eqs/stress_tensor.jpg)
-
-The first term is a kinetic energy contribution for atom {I}.  See
-details below on how the specified {temp-ID} can affect the velocities
-used in this calculation.  The second term is a pairwise energy
-contribution where {n} loops over the {Np} neighbors of atom {I}, {r1}
-and {r2} are the positions of the 2 atoms in the pairwise interaction,
-and {F1} and {F2} are the forces on the 2 atoms resulting from the
-pairwise interaction.  The third term is a bond contribution of
-similar form for the {Nb} bonds which atom {I} is part of.  There are
-similar terms for the {Na} angle, {Nd} dihedral, and {Ni} improper
-interactions atom {I} is part of.  There is also a term for the KSpace
-contribution from long-range Coulombic interactions, if defined.
-Finally, there is a term for the {Nf} "fixes"_fix.html that apply
-internal constraint forces to atom {I}.  Currently, only the "fix
-shake"_fix_shake.html and "fix rigid"_fix_rigid.html commands
-contribute to this term.
-
-As the coefficients in the formula imply, a virial contribution
-produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
-atoms in a Tersoff 3-body interaction) is assigned in equal portions
-to each atom in the set.  E.g. 1/4 of the dihedral virial to each of
-the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
-to atoms in a water molecule via the "fix shake"_fix_shake.html
-command.
-
-If no extra keywords are listed, all of the terms in this formula are
-included in the per-atom stress tensor.  If any extra keywords are
-listed, only those terms are summed to compute the tensor.  The
-{virial} keyword means include all terms except the kinetic energy
-{ke}.
-
-Note that the stress for each atom is due to its interaction with all
-other atoms in the simulation, not just with other atoms in the group.
-
-Details of how LAMMPS computes the virial for individual atoms for
-either pairwise or many-body potentials, and including the effects of
-periodic boundary conditions is discussed in "(Thompson)"_#Thompson2.
-The basic idea for many-body potentials is to treat each component of
-the force computation between a small cluster of atoms in the same
-manner as in the formula above for bond, angle, dihedral, etc
-interactions.  Namely the quantity R dot F is summed over the atoms in
-the interaction, with the R vectors unwrapped by periodic boundaries
-so that the cluster of atoms is close together.  The total
-contribution for the cluster interaction is divided evenly among those
-atoms.
-
-The "dihedral_style charmm"_dihedral_charmm.html style calculates
-pairwise interactions between 1-4 atoms.  The virial contribution of
-these terms is included in the pair virial, not the dihedral virial.
-
-The KSpace contribution is calculated using the method in
-"(Heyes)"_#Heyes2 for the Ewald method and by the methodology described
-in "(Sirk)"_#Sirk1 for PPPM.  The choice of KSpace solver is specified
-by the "kspace_style pppm"_kspace_style.html command.  Note that for
-PPPM, the calculation requires 6 extra FFTs each timestep that
-per-atom stress is calculated.  Thus it can significantly increase the
-cost of the PPPM calculation if it is needed on a large fraction of
-the simulation timesteps.
-
-The {temp-ID} argument can be used to affect the per-atom velocities
-used in the kinetic energy contribution to the total stress.  If the
-kinetic energy is not included in the stress, than the temperature
-compute is not used and can be specified as NULL.  If the kinetic
-energy is included and you wish to use atom velocities as-is, then
-{temp-ID} can also be specified as NULL.  If desired, the specified
-temperature compute can be one that subtracts off a bias to leave each
-atom with only a thermal velocity to use in the formula above, e.g. by
-subtracting a background streaming velocity.  See the doc pages for
-individual "compute commands"_compute.html to determine which ones
-include a bias.
-
-:line
-
-Note that as defined in the formula, per-atom stress is the negative
-of the per-atom pressure tensor.  It is also really a stress*volume
-formulation, meaning the computed quantity is in units of
-pressure*volume.  It would need to be divided by a per-atom volume to
-have units of stress (pressure), but an individual atom's volume is
-not well defined or easy to compute in a deformed solid or a liquid.
-See the "compute voronoi/atom"_compute_voronoi_atom.html command for
-one possible way to estimate a per-atom volume.
-
-Thus, if the diagonal components of the per-atom stress tensor are
-summed for all atoms in the system and the sum is divided by dV, where
-d = dimension and V is the volume of the system, the result should be
--P, where P is the total pressure of the system.
-
-These lines in an input script for a 3d system should yield that
-result.  I.e. the last 2 columns of thermo output will be the same:
-
-compute        peratom all stress/atom NULL
-compute        p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
-variable       press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
-thermo_style   custom step temp etotal press v_press :pre
-
-NOTE: The per-atom stress does not include any Lennard-Jones tail
-corrections to the pressure added by the "pair_modify tail
-yes"_pair_modify.html command, since those are contributions to the
-global system pressure.
-
-[Output info:]
-
-This compute calculates a per-atom array with 6 columns, which can be
-accessed by indices 1-6 by any command that uses per-atom values from
-a compute as input.  See the "Howto output"_Howto_output.html doc page
-for an overview of LAMMPS output options.
-
-The per-atom array values will be in pressure*volume
-"units"_units.html as discussed above.
-
-[Restrictions:] none
-
-[Related commands:]
-
-"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html
-
-[Default:] none
-
-:line
-
-:link(Heyes2)
-[(Heyes)] Heyes, Phys Rev B 49, 755 (1994),
-
-:link(Sirk1)
-[(Sirk)] Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).
-
-:link(Thompson2)
-[(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
new file mode 100644
index 0000000000..aadc78050c
--- /dev/null
+++ b/doc/src/compute_stress_mop.rst
@@ -0,0 +1,127 @@
+.. index:: compute stress/mop
+
+compute stress/mop command
+==========================
+
+compute stress/mop/profile command
+==================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID style dir args keywords ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* style = *stress/mop* or *stress/mop/profile*
+* dir = *x* or *y* or *z* is the direction normal to the plane
+* args = argument specific to the compute style
+* keywords = *kin* or *conf* or *total* (one of more can be specified)
+
+
+.. parsed-literal::
+
+     *stress/mop* args = pos
+       pos = *lower* or *center* or *upper* or coordinate value (distance units) is the position of the plane
+     *stress/mop/profile* args = origin delta
+       origin = *lower* or *center* or *upper* or coordinate value (distance units) is the position of the first plane
+       delta = value (distance units) is the distance between planes
+
+   compute 1 all stress/mop x lower total
+   compute 1 liquid stress/mop z 0.0 kin conf
+   fix 1 all ave/time 10 1000 10000 c_1[\*] file mop.time
+   fix 1 all ave/time 10 1000 10000 c_1[2] file mop.time
+
+   compute 1 all stress/mop/profile x lower 0.1 total
+   compute 1 liquid stress/mop/profile z 0.0 0.25 kin conf
+   fix 1 all ave/time 500 20 10000 c_1[\*] ave running overwrite file mopp.time mode vector
+
+Description
+"""""""""""
+
+Compute *stress/mop* and compute *stress/mop/profile* define computations that
+calculate components of the local stress tensor using the method of
+planes :ref:`(Todd) <mop-todd>`.  Specifically in compute *stress/mop* calculates 3
+components are computed in directions *dir*\ ,\ *x*\ ; *dir*\ ,\ *y*\ ; and
+*dir*\ ,\ *z*\ ; where *dir* is the direction normal to the plane, while
+in compute *stress/mop/profile* the profile of the stress is computed.
+
+Contrary to methods based on histograms of atomic stress (i.e. using
+:doc:`compute stress/atom <compute_stress_atom>`), the method of planes is
+compatible with mechanical balance in heterogeneous systems and at
+interfaces :ref:`(Todd) <mop-todd>`.
+
+The stress tensor is the sum of a kinetic term and a configurational
+term, which are given respectively by Eq. (21) and Eq. (16) in
+:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers that
+atoms have crossed the plane if their positions at times t-dt and t are
+one on either side of the plane, and uses the velocity at time t-dt/2
+given by the velocity-Verlet algorithm.
+
+Between one and three keywords can be used to indicate which
+contributions to the stress must be computed: kinetic stress (kin),
+configurational stress (conf), and/or total stress (total).
+
+NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
+
+NOTE 2: The local stress does not include any Lennard-Jones tail
+corrections to the pressure added by the :doc:`pair\_modify tail yes <pair_modify>` command, since those are contributions to the global system pressure.
+
+**Output info:**
+
+Compute *stress/mop* calculates a global vector (indices starting at 1), with 3
+values for each declared keyword (in the order the keywords have been
+declared). For each keyword, the stress tensor components are ordered as
+follows: stress\_dir,x, stress\_dir,y, and stress\_dir,z.
+
+Compute *stress/mop/profile* instead calculates a global array, with 1 column
+giving the position of the planes where the stress tensor was computed,
+and with 3 columns of values for each declared keyword (in the order the
+keywords have been declared). For each keyword, the profiles of stress
+tensor components are ordered as follows: stress\_dir,x; stress\_dir,y;
+and stress\_dir,z.
+
+The values are in pressure :doc:`units <units>`.
+
+The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`. For instance, the results can be written to a file using the :doc:`fix ave/time <fix_ave_time>` command. Please see the example in the examples/USER/mop folder.
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the USER-MISC package. They are only enabled if
+LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
+doc page on for more info.
+
+The method is only implemented for 3d orthogonal simulation boxes whose
+size does not change in time, and axis-aligned planes.
+
+The method only works with two-body pair interactions, because it
+requires the class method pair->single() to be implemented. In
+particular, it does not work with more than two-body pair interactions,
+intra-molecular interactions, and long range (kspace) interactions.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute stress/atom <compute_stress_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _mop-todd:
+
+
+
+**(Todd)** B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
+Phys. Rev. E 52, 1627 (1995).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst
new file mode 100644
index 0000000000..38ab176b7d
--- /dev/null
+++ b/doc/src/compute_tally.rst
@@ -0,0 +1,120 @@
+.. index:: compute force/tally
+
+compute force/tally command
+===========================
+
+compute heat/flux/tally command
+===============================
+
+compute pe/tally command
+========================
+
+compute pe/mol/tally command
+============================
+
+compute stress/tally command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID style group2-ID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* style = *force/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
+* group2-ID = group ID of second (or same) group
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 lower force/tally upper
+   compute 1 left pe/tally right
+   compute 1 lower stress/tally lower
+
+Description
+"""""""""""
+
+Define a computation that calculates properties between two groups of
+atoms by accumulating them from pairwise non-bonded computations.  The
+two groups can be the same. This is similar to :doc:`compute group/group <compute_group_group>` only that the data is
+accumulated directly during the non-bonded force computation. The
+computes *force/tally*\ , *pe/tally*\ , *stress/tally*\ , and
+*heat/flux/tally* are primarily provided as example how to program
+additional, more sophisticated computes using the tally callback
+mechanism. Compute *pe/mol/tally* is one such style, that can
+- through using this mechanism - separately tally intermolecular
+and intramolecular energies. Something that would otherwise be
+impossible without integrating this as a core functionality into
+the based classes of LAMMPS.
+
+
+----------
+
+
+The pairwise contributions are computing via a callback that the
+compute registers with the non-bonded pairwise force computation.
+This limits the use to systems that have no bonds, no Kspace, and no
+many-body interactions. On the other hand, the computation does not
+have to compute forces or energies a second time and thus can be much
+more efficient. The callback mechanism allows to write more complex
+pairwise property computations.
+
+
+----------
+
+
+**Output info:**
+
+Compute *pe/tally* calculates a global scalar (the energy) and a per
+atom scalar (the contributions of the single atom to the global
+scalar). Compute *pe/mol/tally* calculates a global 4-element vector
+containing (in this order): *evdwl* and *ecoul* for intramolecular pairs
+and *evdwl* and *ecoul* for intermolecular pairs. Since molecules are
+identified by their molecule IDs, the partitioning does not have to be
+related to molecules, but the energies are tallied into the respective
+slots depending on whether the molecule IDs of a pair are the same or
+different. Compute *force/tally* calculates a global scalar (the force
+magnitude) and a per atom 3-element vector (force contribution from
+each atom).  Compute *stress/tally* calculates a global scalar
+(average of the diagonal elements of the stress tensor) and a per atom
+vector (the 6 elements of stress tensor contributions from the
+individual atom).
+
+Both the scalar and vector values calculated by this compute are
+"extensive".
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-TALLY package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Not all pair styles can be evaluated in a pairwise mode as required by
+this compute.  For example, 3-body and other many-body potentials,
+such as :doc:`Tersoff <pair_tersoff>` and
+:doc:`Stillinger-Weber <pair_sw>` cannot be used.  :doc:`EAM <pair_eam>`
+potentials only include the pair potential portion of the EAM
+interaction when used by this compute, not the embedding term.  Also
+bonded or Kspace interactions do not contribute to this compute.
+
+The computes in this package are not compatible with dynamic groups.
+
+Related commands
+""""""""""""""""
+
+*compute group/group*\ \_compute\_group\_group.html, *compute
+heat/flux*\ \_compute\_heat\_flux.html
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst
new file mode 100644
index 0000000000..ed7af54d2a
--- /dev/null
+++ b/doc/src/compute_tdpd_cc_atom.rst
@@ -0,0 +1,75 @@
+.. index:: compute tdpd/cc/atom
+
+compute tdpd/cc/atom command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID tdpd/cc/atom index
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* tdpd/cc/atom = style name of this compute command
+* index = index of chemical species (1 to Nspecies)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all tdpd/cc/atom 2
+
+Description
+"""""""""""
+
+Define a computation that calculates the per-atom chemical
+concentration of a specified species for each tDPD particle in a
+group.
+
+The chemical concentration of each species is defined as the number of
+molecules carried by a tDPD particle for dilute solution.  For more
+details see :ref:`(Li2015) <Li2015a>`.
+
+**Output info:**
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See the
+:doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS
+output options.
+
+The per-atom vector values will be in the units of chemical species
+per unit mass.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MESO package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style tdpd <pair_meso>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Li2015a:
+
+
+
+**(Li2015)** Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143:
+014101 (2015).  DOI: 10.1063/1.4923254
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst
new file mode 100644
index 0000000000..052da705ac
--- /dev/null
+++ b/doc/src/compute_temp.rst
@@ -0,0 +1,127 @@
+.. index:: compute temp
+
+compute temp command
+====================
+
+compute temp/kk command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all temp
+   compute myTemp mobile temp
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms.  A compute of this style can be used by any command that
+computes a temperature, e.g. :doc:`thermo\_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+
+The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in the group, k = Boltzmann constant, and T = temperature.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute\_modify <compute_modify>` command.
+
+A compute of this style with the ID of "thermo\_temp" is created when
+LAMMPS starts up, as if this command were in the input script:
+
+
+.. parsed-literal::
+
+   compute thermo_temp all temp
+
+See the "thermo\_style" command for more details.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp/partial <compute_temp_partial>`, :doc:`compute temp/region <compute_temp_region>`, :doc:`compute pressure <compute_pressure>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst
new file mode 100644
index 0000000000..46743c780e
--- /dev/null
+++ b/doc/src/compute_temp_asphere.rst
@@ -0,0 +1,173 @@
+.. index:: compute temp/asphere
+
+compute temp/asphere command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/asphere keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/asphere = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *bias* or *dof*
+  
+  .. parsed-literal::
+  
+       *bias* value = bias-ID
+         bias-ID = ID of a temperature compute that removes a velocity bias
+       *dof* value = *all* or *rotate*
+         all = compute temperature of translational and rotational degrees of freedom
+         rotate = compute temperature of just rotational degrees of freedom
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all temp/asphere
+   compute myTemp mobile temp/asphere bias tempCOM
+   compute myTemp mobile temp/asphere dof rotate
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+aspherical particles, including a contribution from both their
+translational and rotational kinetic energy.  This differs from the
+usual :doc:`compute temp <compute_temp>` command, which assumes point
+particles with only translational kinetic energy.
+
+Only finite-size particles (aspherical or spherical) can be included
+in the group.  For 3d finite-size particles, each has 6 degrees of
+freedom (3 translational, 3 rotational).  For 2d finite-size
+particles, each has 3 degrees of freedom (2 translational, 1
+rotational).
+
+.. note::
+
+   This choice for degrees of freedom (dof) assumes that all
+   finite-size aspherical or spherical particles in your model will
+   freely rotate, sampling all their rotational dof.  It is possible to
+   use a combination of interaction potentials and fixes that induce no
+   torque or otherwise constrain some of all of your particles so that
+   this is not the case.  Then there are less dof and you should use the
+   :doc:`compute\_modify extra <compute_modify>` command to adjust the dof
+   accordingly.
+
+For example, an aspherical particle with all three of its shape
+parameters the same is a sphere.  If it does not rotate, then it
+should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d).  A
+uniaxial aspherical particle has two of its three shape parameters the
+same.  If it does not rotate around the axis perpendicular to its
+circular cross section, then it should have 5 dof instead of 6 in 3d.
+The latter is the case for uniaxial ellipsoids in a :doc:`GayBerne model <pair_gayberne>` since there is no induced torque around the
+optical axis.  It will also be the case for bi-axial ellipsoids when
+exactly two of the semiaxes have the same length and the corresponding
+relative well depths are equal.
+
+The translational kinetic energy is computed the same as is described
+by the :doc:`compute temp <compute_temp>` command.  The rotational
+kinetic energy is computed as 1/2 I w\^2, where I is the inertia tensor
+for the aspherical particle and w is its angular velocity, which is
+computed from its angular momentum.
+
+.. note::
+
+   For :doc:`2d models <dimension>`, particles are treated as
+   ellipsoids, not ellipses, meaning their moments of inertia will be the
+   same as in 3d.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute.  The formula for the components of the
+tensor is the same as the above formula, except that v\^2 and w\^2 are
+replaced by vx\*vy and wx\*wy for the xy component, and the appropriate
+elements of the inertia tensor are used.  The 6 components of the
+vector are ordered xx, yy, zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+This compute subtracts out translational degrees-of-freedom due to
+fixes that constrain molecular motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`.  This means the
+temperature of groups of atoms that include these constraints will be
+computed correctly.  If needed, the subtracted degrees-of-freedom can
+be altered using the *extra* option of the
+:doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+For the *bias* keyword, *bias-ID* refers to the ID of a temperature
+compute that removes a "bias" velocity from each atom.  This allows
+compute temp/sphere to compute its thermal temperature after the
+translational kinetic energy components have been altered in a
+prescribed way, e.g. to remove a flow velocity profile.  Thermostats
+that use this compute will work with this bias term.  See the doc
+pages for individual computes that calculate a temperature and the doc
+pages for fixes that perform thermostatting for more details.
+
+For the *dof* keyword, a setting of *all* calculates a temperature
+that includes both translational and rotational degrees of freedom.  A
+setting of *rotate* calculates a temperature that includes only
+rotational degrees of freedom.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the ASPHERE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This compute requires that atoms store angular momentum and a
+quaternion as defined by the :doc:`atom\_style ellipsoid <atom_style>`
+command.
+
+All particles in the group must be finite-size.  They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst
new file mode 100644
index 0000000000..e17227fe3e
--- /dev/null
+++ b/doc/src/compute_temp_body.rst
@@ -0,0 +1,149 @@
+.. index:: compute temp/body
+
+compute temp/body command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/body keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/body = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *bias* or *dof*
+  
+  .. parsed-literal::
+  
+       *bias* value = bias-ID
+         bias-ID = ID of a temperature compute that removes a velocity bias
+       *dof* value = *all* or *rotate*
+         all = compute temperature of translational and rotational degrees of freedom
+         rotate = compute temperature of just rotational degrees of freedom
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all temp/body
+   compute myTemp mobile temp/body bias tempCOM
+   compute myTemp mobile temp/body dof rotate
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+body particles, including a contribution from both their
+translational and rotational kinetic energy.  This differs from the
+usual :doc:`compute temp <compute_temp>` command, which assumes point
+particles with only translational kinetic energy.
+
+Only body particles can be included in the group.  For 3d particles,
+each has 6 degrees of freedom (3 translational, 3 rotational).  For 2d
+body particles, each has 3 degrees of freedom (2 translational, 1
+rotational).
+
+.. note::
+
+   This choice for degrees of freedom (dof) assumes that all body
+   particles in your model will freely rotate, sampling all their
+   rotational dof.  It is possible to use a combination of interaction
+   potentials and fixes that induce no torque or otherwise constrain some
+   of all of your particles so that this is not the case.  Then there are
+   less dof and you should use the :doc:`compute\_modify extra <compute_modify>` command to adjust the dof accordingly.
+
+The translational kinetic energy is computed the same as is described
+by the :doc:`compute temp <compute_temp>` command.  The rotational
+kinetic energy is computed as 1/2 I w\^2, where I is the inertia tensor
+for the aspherical particle and w is its angular velocity, which is
+computed from its angular momentum.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute.  The formula for the components of the
+tensor is the same as the above formula, except that v\^2 and w\^2 are
+replaced by vx\*vy and wx\*wy for the xy component, and the appropriate
+elements of the inertia tensor are used.  The 6 components of the
+vector are ordered xx, yy, zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+This compute subtracts out translational degrees-of-freedom due to
+fixes that constrain molecular motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`.  This means the
+temperature of groups of atoms that include these constraints will be
+computed correctly.  If needed, the subtracted degrees-of-freedom can
+be altered using the *extra* option of the
+:doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+For the *bias* keyword, *bias-ID* refers to the ID of a temperature
+compute that removes a "bias" velocity from each atom.  This allows
+compute temp/sphere to compute its thermal temperature after the
+translational kinetic energy components have been altered in a
+prescribed way, e.g. to remove a flow velocity profile.  Thermostats
+that use this compute will work with this bias term.  See the doc
+pages for individual computes that calculate a temperature and the doc
+pages for fixes that perform thermostatting for more details.
+
+For the *dof* keyword, a setting of *all* calculates a temperature
+that includes both translational and rotational degrees of freedom.  A
+setting of *rotate* calculates a temperature that includes only
+rotational degrees of freedom.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the BODY package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This compute requires that atoms store angular momentum and a
+quaternion as defined by the :doc:`atom\_style body <atom_style>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst
new file mode 100644
index 0000000000..cc9e70a0c5
--- /dev/null
+++ b/doc/src/compute_temp_chunk.rst
@@ -0,0 +1,260 @@
+.. index:: compute temp/chunk
+
+compute temp/chunk command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* zero or more values can be listed as value1,value2,etc
+* value = *temp* or *kecom* or *internal*
+  
+  .. parsed-literal::
+  
+       temp = temperature of each chunk
+       kecom = kinetic energy of each chunk based on velocity of center of mass
+       internal = internal kinetic energy of each chunk
+
+* zero or more keyword/value pairs may be appended
+* keyword = *com* or *bias* or *adof* or *cdof*
+  
+  .. parsed-literal::
+  
+       *com* value = *yes* or *no*
+         yes = subtract center-of-mass velocity from each chunk before calculating temperature
+         no = do not subtract center-of-mass velocity
+       *bias* value = bias-ID
+         bias-ID = ID of a temperature compute that removes a velocity bias
+       *adof* value = dof_per_atom
+         dof_per_atom = define this many degrees-of-freedom per atom
+       *cdof* value = dof_per_chunk
+         dof_per_chunk = define this many degrees-of-freedom per chunk
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid temp/chunk molchunk
+   compute 1 fluid temp/chunk molchunk temp internal
+   compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms that are also in chunks, after optionally subtracting out the
+center-of-mass velocity of each chunk.  By specifying optional values,
+it can also calculate the per-chunk temperature or energies of the
+multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+The temperature is calculated by the formula KE = DOF/2 k T, where KE =
+total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
+v\^2), DOF = the total number of degrees of freedom for those atoms, k
+= Boltzmann constant, and T = temperature.
+
+The DOF is calculated as N\*adof + Nchunk\*cdof, where N = number of
+atoms contributing to the KE, adof = degrees of freedom per atom, and
+cdof = degrees of freedom per chunk.  By default adof = 2 or 3 =
+dimensionality of system, as set via the :doc:`dimension <dimension>`
+command, and cdof = 0.0.  This gives the usual formula for
+temperature.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+Note that the number of atoms contributing to the temperature is
+calculated each time the temperature is evaluated since it is assumed
+the atoms may be dynamically assigned to chunks.  Thus there is no
+need to use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command for this compute style.
+
+If any optional values are specified, then per-chunk quantities are
+also calculated and stored in a global array, as described below.
+
+The *temp* value calculates the temperature for each chunk by the
+formula KE = DOF/2 k T, where KE = total kinetic energy of the chunk
+of atoms (sum of 1/2 m v\^2), DOF = the total number of degrees of
+freedom for all atoms in the chunk, k = Boltzmann constant, and T =
+temperature.
+
+The DOF in this case is calculated as N\*adof + cdof, where N = number
+of atoms in the chunk, adof = degrees of freedom per atom, and cdof =
+degrees of freedom per chunk.  By default adof = 2 or 3 =
+dimensionality of system, as set via the :doc:`dimension <dimension>`
+command, and cdof = 0.0.  This gives the usual formula for
+temperature.
+
+The *kecom* value calculates the kinetic energy of each chunk as if
+all its atoms were moving with the velocity of the center-of-mass of
+the chunk.
+
+The *internal* value calculates the internal kinetic energy of each
+chunk.  The interal KE is summed over the atoms in the chunk using an
+internal "thermal" velocity for each atom, which is its velocity minus
+the center-of-mass velocity of the chunk.
+
+
+----------
+
+
+Note that currently the global and per-chunk temperatures calculated
+by this compute only include translational degrees of freedom for each
+atom.  No rotational degrees of freedom are included for finite-size
+particles.  Also no degrees of freedom are subtracted for any velocity
+bias or constraints that are applied, such as :doc:`compute temp/partial <compute_temp_partial>`, or :doc:`fix shake <fix_shake>`
+or :doc:`fix rigid <fix_rigid>`.  This is because those degrees of
+freedom (e.g. a constrained bond) could apply to sets of atoms that
+are both included and excluded from a specific chunk, and hence the
+concept is somewhat ill-defined.  In some cases, you can use the
+*adof* and *cdof* keywords to adjust the calculated degrees of freedom
+appropriately, as explained below.
+
+Note that the per-chunk temperature calculated by this compute and the
+:doc:`fix ave/chunk temp <fix_ave_chunk>` command can be different.
+This compute calculates the temperature for each chunk for a single
+snapshot.  Fix ave/chunk can do that but can also time average those
+values over many snapshots, or it can compute a temperature as if the
+atoms in the chunk on different timesteps were collected together as
+one set of atoms to calculate their temperature.  This compute allows
+the center-of-mass velocity of each chunk to be subtracted before
+calculating the temperature; fix ave/chunk does not.
+
+.. note::
+
+   Only atoms in the specified group contribute to the calculations
+   performed by this compute.  The :doc:`compute chunk/atom <compute_chunk_atom>` command defines its own group;
+   atoms will have a chunk ID = 0 if they are not in that group,
+   signifying they are not assigned to a chunk, and will thus also not
+   contribute to this calculation.  You can specify the "all" group for
+   this command if you simply want to include atoms with non-zero chunk
+   IDs.
+
+The simplest way to output the per-chunk results of the compute
+temp/chunk calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>` command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all temp/chunk cc1 temp
+   fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+The *com* keyword can be used with a value of *yes* to subtract the
+velocity of the center-of-mass for each chunk from the velocity of the
+atoms in that chunk, before calculating either the global or per-chunk
+temperature.  This can be useful if the atoms are streaming or
+otherwise moving collectively, and you wish to calculate only the
+thermal temperature.
+
+For the *bias* keyword, *bias-ID* refers to the ID of a temperature
+compute that removes a "bias" velocity from each atom.  This also
+allows calculation of the global or per-chunk temperature using only
+the thermal temperature of atoms in each chunk after the translational
+kinetic energy components have been altered in a prescribed way,
+e.g. to remove a velocity profile.  It also applies to the calculation
+of the other per-chunk values, such as *kecom* or *internal*\ , which
+involve the center-of-mass velocity of each chunk, which is calculated
+after the velocity bias is removed from each atom.  Note that the
+temperature compute will apply its bias globally to the entire system,
+not on a per-chunk basis.
+
+The *adof* and *cdof* keywords define the values used in the degree of
+freedom (DOF) formulas used for the global or per-chunk temperature,
+as described above.  They can be used to calculate a more appropriate
+temperature for some kinds of chunks.  Here are 3 examples:
+
+If spatially binned chunks contain some number of water molecules and
+:doc:`fix shake <fix_shake>` is used to make each molecule rigid, then
+you could calculate a temperature with 6 degrees of freedom (DOF) (3
+translational, 3 rotational) per molecule by setting *adof* to 2.0.
+
+If :doc:`compute temp/partial <compute_temp_partial>` is used with the
+*bias* keyword to only allow the x component of velocity to contribute
+to the temperature, then *adof* = 1.0 would be appropriate.
+
+If each chunk consists of a large molecule, with some number of its
+bonds constrained by :doc:`fix shake <fix_shake>` or the entire molecule
+by :doc:`fix rigid/small <fix_rigid>`, *adof* = 0.0 and *cdof* could be
+set to the remaining degrees of freedom for the entire molecule
+(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
+molecule.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+This compute also optionally calculates a global array, if one or more
+of the optional values are specified.  The number of rows in the array
+= the number of chunks *Nchunk* as calculated by the specified
+:doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of
+columns is the number of specified values (1 or more).  These values
+can be accessed by any command that uses global array values from a
+compute as input.  Again, see the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".  The array values are "intensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.  The array values
+will be in temperature :doc:`units <units>` for the *temp* value, and in
+energy :doc:`units <units>` for the *kecom* and *internal* values.
+
+Restrictions
+""""""""""""
+
+
+The *com* and *bias* keywords cannot be used together.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`fix ave/chunk temp <fix_ave_chunk>`
+
+Default
+"""""""
+
+The option defaults are com no, no bias, adof = dimensionality of the
+system (2 or 3), and cdof = 0.0.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst
new file mode 100644
index 0000000000..083e9f652c
--- /dev/null
+++ b/doc/src/compute_temp_com.rst
@@ -0,0 +1,100 @@
+.. index:: compute temp/com
+
+compute temp/com command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/com
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/com = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all temp/com
+   compute myTemp mobile temp/com
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms, after subtracting out the center-of-mass velocity of the group.
+This is useful if the group is expected to have a non-zero net
+velocity for some reason.  A compute of this style can be used by any
+command that computes a temperature,
+e.g. :doc:`thermo\_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+
+After the center-of-mass velocity has been subtracted from each atom,
+the temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in the group, k = Boltzmann constant, and T = temperature.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+The removal of the center-of-mass velocity by this fix is essentially
+computing the temperature after a "bias" has been removed from the
+velocity of the atoms.  If this compute is used with a fix command
+that performs thermostatting then this bias will be subtracted from
+each atom, thermostatting of the remaining thermal velocity will be
+performed, and the bias will be added back in.  Thermostatting fixes
+that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst
new file mode 100644
index 0000000000..7d5843e1db
--- /dev/null
+++ b/doc/src/compute_temp_cs.rst
@@ -0,0 +1,131 @@
+.. index:: compute temp/cs
+
+compute temp/cs command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/cs group1 group2
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/cs = style name of this compute command
+* group1 = group-ID of either cores or shells
+* group2 = group-ID of either shells or cores
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute oxygen_c-s all temp/cs O_core O_shell
+   compute core_shells all temp/cs cores shells
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a system based
+on the center-of-mass velocity of atom pairs that are bonded to each
+other.  This compute is designed to be used with the adiabatic
+core/shell model of :ref:`(Mitchell and Finchham) <MitchellFinchham1>`.  See
+the :doc:`Howto coreshell <Howto_coreshell>` doc page for an overview of
+the model as implemented in LAMMPS.  Specifically, this compute
+enables correct temperature calculation and thermostatting of
+core/shell pairs where it is desirable for the internal degrees of
+freedom of the core/shell pairs to not be influenced by a thermostat.
+A compute of this style can be used by any command that computes a
+temperature via :doc:`fix\_modify <fix_modify>` e.g. :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+
+Note that this compute does not require all ions to be polarized,
+hence defined as core/shell pairs.  One can mix core/shell pairs and
+ions without a satellite particle if desired. The compute will
+consider the non-polarized ions according to the physical system.
+
+For this compute, core and shell particles are specified by two
+respective group IDs, which can be defined using the
+:doc:`group <group>` command.  The number of atoms in the two groups
+must be the same and there should be one bond defined between a pair
+of atoms in the two groups.  Non-polarized ions which might also be
+included in the treated system should not be included into either of
+these groups, they are taken into account by the *group-ID* (2nd
+argument) of the compute.
+
+The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in the group, k = Boltzmann constant, and T = temperature.  Note that
+the velocity of each core or shell atom used in the KE calculation is
+the velocity of the center-of-mass (COM) of the core/shell pair the
+atom is part of.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.  In contrast to the temperature, the velocity of
+each core or shell atom is taken individually.
+
+The change this fix makes to core/shell atom velocities is essentially
+computing the temperature after a "bias" has been removed from the
+velocity of the atoms.  This "bias" is the velocity of the atom
+relative to the COM velocity of the core/shell pair.  If this compute
+is used with a fix command that performs thermostatting then this bias
+will be subtracted from each atom, thermostatting of the remaining COM
+velocity will be performed, and the bias will be added back in.  This
+means the thermostatting will effectively be performed on the
+core/shell pairs, instead of on the individual core and shell atoms.
+Thermostatting fixes that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
+
+The internal energy of core/shell pairs can be calculated by the
+:doc:`compute temp/chunk <compute_temp_chunk>` command, if chunks are
+defined as core/shell pairs.  See the :doc:`Howto coreshell <Howto_coreshell>` doc page doc page for more discussion
+on how to do this.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+The number of core/shell pairs contributing to the temperature is
+assumed to be constant for the duration of the run.  No fixes should
+be used which generate new molecules or atoms during a simulation.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`compute temp/chunk <compute_temp_chunk>`
+
+**Default:** none
+
+
+----------
+
+
+.. _MitchellFinchham1:
+
+
+
+**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst
new file mode 100644
index 0000000000..88dbc62422
--- /dev/null
+++ b/doc/src/compute_temp_deform.rst
@@ -0,0 +1,142 @@
+.. index:: compute temp/deform
+
+compute temp/deform command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/deform
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/deform = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute myTemp all temp/deform
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms, after subtracting out a streaming velocity induced by the
+simulation box changing size and/or shape, for example in a
+non-equilibrium MD (NEMD) simulation.  The size/shape change is
+induced by use of the :doc:`fix deform <fix_deform>` command.  A compute
+of this style is created by the :doc:`fix nvt/sllod <fix_nvt_sllod>`
+command to compute the thermal temperature of atoms for thermostatting
+purposes.  A compute of this style can also be used by any command
+that computes a temperature, e.g. :doc:`thermo\_modify <thermo_modify>`,
+:doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+
+The deformation fix changes the box size and/or shape over time, so
+each atom in the simulation box can be thought of as having a
+"streaming" velocity.  For example, if the box is being sheared in x,
+relative to y, then atoms at the bottom of the box (low y) have a
+small x velocity, while atoms at the top of the box (hi y) have a
+large x velocity.  This position-dependent streaming velocity is
+subtracted from each atom's actual velocity to yield a thermal
+velocity which is used to compute the temperature.
+
+.. note::
+
+   :doc:`Fix deform <fix_deform>` has an option for remapping either
+   atom coordinates or velocities to the changing simulation box.  When
+   using this compute in conjunction with a deforming box, fix deform
+   should NOT remap atom positions, but rather should let atoms respond
+   to the changing box by adjusting their own velocities (or let :doc:`fix deform <fix_deform>` remap the atom velocities, see it's remap
+   option).  If fix deform does remap atom positions, then they appear to
+   move with the box but their velocity is not changed, and thus they do
+   NOT have the streaming velocity assumed by this compute.  LAMMPS will
+   warn you if fix deform is defined and its remap setting is not
+   consistent with this compute.
+
+After the streaming velocity has been subtracted from each atom, the
+temperature is calculated by the formula KE = dim/2 N k T, where KE =
+total kinetic energy of the group of atoms (sum of 1/2 m v\^2), dim = 2
+or 3 = dimensionality of the simulation, N = number of atoms in the
+group, k = Boltzmann constant, and T = temperature.  Note that v in
+the kinetic energy formula is the atom's thermal velocity.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+The removal of the box deformation velocity component by this fix is
+essentially computing the temperature after a "bias" has been removed
+from the velocity of the atoms.  If this compute is used with a fix
+command that performs thermostatting then this bias will be subtracted
+from each atom, thermostatting of the remaining thermal velocity will
+be performed, and the bias will be added back in.  Thermostatting
+fixes that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
+
+.. note::
+
+   The temperature calculated by this compute is only accurate if
+   the atoms are indeed moving with a stream velocity profile that
+   matches the box deformation.  If not, then the compute will subtract
+   off an incorrect stream velocity, yielding a bogus thermal
+   temperature.  You should NOT assume that your atoms are streaming at
+   the same rate the box is deforming.  Rather, you should monitor their
+   velocity profile, e.g. via the :doc:`fix ave/chunk <fix_ave_chunk>`
+   command.  And you can compare the results of this compute to :doc:`compute temp/profile <compute_temp_profile>`, which actually calculates the
+   stream profile before subtracting it.  If the two computes do not give
+   roughly the same temperature, then your atoms are not streaming
+   consistent with the box deformation.  See the :doc:`fix deform <fix_deform>` command for more details on ways to get atoms
+   to stream consistently with the box deformation.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp/ramp <compute_temp_ramp>`, :doc:`compute temp/profile <compute_temp_profile>`, :doc:`fix deform <fix_deform>`,
+:doc:`fix nvt/sllod <fix_nvt_sllod>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst
new file mode 100644
index 0000000000..98b28aa76a
--- /dev/null
+++ b/doc/src/compute_temp_deform_eff.rst
@@ -0,0 +1,80 @@
+.. index:: compute temp/deform/eff
+
+compute temp/deform/eff command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/deform/eff
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/deform/eff = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute myTemp all temp/deform/eff
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+nuclei and electrons in the :doc:`electron force field <pair_eff>`
+model, after subtracting out a streaming velocity induced by the
+simulation box changing size and/or shape, for example in a
+non-equilibrium MD (NEMD) simulation.  The size/shape change is
+induced by use of the :doc:`fix deform <fix_deform>` command.  A
+compute of this style is created by the :doc:`fix nvt/sllod/eff <fix_nvt_sllod_eff>` command to compute the thermal
+temperature of atoms for thermostatting purposes.  A compute of this
+style can also be used by any command that computes a temperature,
+e.g. :doc:`thermo\_modify <thermo_modify>`, :doc:`fix npt/eff <fix_nh_eff>`,
+etc.
+
+The calculation performed by this compute is exactly like that
+described by the :doc:`compute temp/deform <compute_temp_deform>`
+command, except that the formula for the temperature includes the
+radial electron velocity contributions, as discussed by the :doc:`compute temp/eff <compute_temp_eff>` command.  Note that only the
+translational degrees of freedom for each nuclei or electron are
+affected by the streaming velocity adjustment.  The radial velocity
+component of the electrons is not affected.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp/ramp <compute_temp_ramp>`, :doc:`fix deform <fix_deform>`,
+:doc:`fix nvt/sllod/eff <fix_nvt_sllod_eff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst
new file mode 100644
index 0000000000..fbebf02ea9
--- /dev/null
+++ b/doc/src/compute_temp_drude.rst
@@ -0,0 +1,87 @@
+.. index:: compute temp/drude
+
+compute temp/drude command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/drude
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/drude = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute TDRUDE all temp/drude
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperatures of core-Drude
+pairs. This compute is designed to be used with the :doc:`thermalized Drude oscillator model <Howto_drude>`.  Polarizable models in LAMMPS
+are described on the :doc:`Howto polarizable <Howto_polarizable>` doc
+page.
+
+Drude oscillators consist of a core particle and a Drude particle
+connected by a harmonic bond, and the relative motion of these Drude
+oscillators is usually maintained cold by a specific thermostat that
+acts on the relative motion of the core-Drude particle
+pairs. Therefore, because LAMMPS considers Drude particles as normal
+atoms in its default temperature compute (:doc:`compute temp <compute_temp>` command), the reduced temperature of the
+core-Drude particle pairs is not calculated correctly.
+
+By contrast, this compute calculates the temperature of the cores
+using center-of-mass velocities of the core-Drude pairs, and the
+reduced temperature of the Drude particles using the relative
+velocities of the Drude particles with respect to their cores.
+Non-polarizable atoms are considered as cores.  Their velocities
+contribute to the temperature of the cores.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6, which can be accessed by indices 1-6, whose components
+are
+
+1. temperature of the centers of mass (temperature units)
+2. temperature of the dipoles (temperature units)
+3. number of degrees of freedom of the centers of mass
+4. number of degrees of freedom of the dipoles
+5. kinetic energy of the centers of mass (energy units)
+6. kinetic energy of the dipoles (energy units)
+
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+Both the scalar value and the first two values of the vector
+calculated by this compute are "intensive".  The other 4 vector values
+are "extensive".
+
+Restrictions
+""""""""""""
+
+
+The number of degrees of freedom contributing to the temperature is
+assumed to be constant for the duration of the run unless the
+*fix\_modify* command sets the option *dynamic yes*\ .
+
+Related commands
+""""""""""""""""
+
+:doc:`fix drude <fix_drude>`, :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`pair\_style thole <pair_thole>`, :doc:`compute temp <compute_temp>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst
new file mode 100644
index 0000000000..b83a9cbec9
--- /dev/null
+++ b/doc/src/compute_temp_eff.rst
@@ -0,0 +1,108 @@
+.. index:: compute temp/eff
+
+compute temp/eff command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/eff
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/eff = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all temp/eff
+   compute myTemp mobile temp/eff
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+nuclei and electrons in the :doc:`electron force field <pair_eff>`
+model.  A compute of this style can be used by commands that compute a
+temperature, e.g. :doc:`thermo\_modify <thermo_modify>`, :doc:`fix npt/eff <fix_nh_eff>`, etc.
+
+The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2 for
+nuclei and sum of 1/2 (m v\^2 + 3/4 m s\^2) for electrons, where s
+includes the radial electron velocity contributions), dim = 2 or 3 =
+dimensionality of the simulation, N = number of atoms (only total
+number of nuclei in the eFF (see the :doc:`pair\_eff <pair_style>`
+command) in the group, k = Boltzmann constant, and T = temperature.
+This expression is summed over all nuclear and electronic degrees of
+freedom, essentially by setting the kinetic contribution to the heat
+capacity to 3/2k (where only nuclei contribute). This subtlety is
+valid for temperatures well below the Fermi temperature, which for
+densities two to five times the density of liquid H2 ranges from
+86,000 to 170,000 K.
+
+.. note::
+
+   For eFF models, in order to override the default temperature
+   reported by LAMMPS in the thermodynamic quantities reported via the
+   :doc:`thermo <thermo>` command, the user should apply a
+   :doc:`thermo\_modify <thermo_modify>` command, as shown in the following
+   example:
+
+
+.. parsed-literal::
+
+   compute         effTemp all temp/eff
+   thermo_style    custom step etotal pe ke temp press
+   thermo_modify   temp effTemp
+
+A 6-component kinetic energy tensor is also calculated by this compute
+for use in the computation of a pressure tensor.  The formula for the
+components of the tensor is the same as the above formula, except that
+v\^2 is replaced by vx \* vy for the xy component, etc.  For the eFF,
+again, the radial electronic velocities are also considered.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+**Output info:**
+
+The scalar value calculated by this compute is "intensive", meaning it
+is independent of the number of atoms in the simulation.  The vector
+values are "extensive", meaning they scale with the number of atoms in
+the simulation.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp/partial <compute_temp_partial>`, :doc:`compute temp/region <compute_temp_region>`, :doc:`compute pressure <compute_pressure>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst
new file mode 100644
index 0000000000..51e92dc4c4
--- /dev/null
+++ b/doc/src/compute_temp_partial.rst
@@ -0,0 +1,126 @@
+.. index:: compute temp/partial
+
+compute temp/partial command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/partial xflag yflag zflag
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/partial = style name of this compute command
+* xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute newT flow temp/partial 1 1 0
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms, after excluding one or more velocity components.  A compute of
+this style can be used by any command that computes a temperature,
+e.g. :doc:`thermo\_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+
+The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2),
+dim = dimensionality of the simulation, N = number of atoms in the
+group, k = Boltzmann constant, and T = temperature.  The calculation
+of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
+0.  The dim parameter is adjusted to give the correct number of
+degrees of freedom.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the calculation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+The removal of velocity components by this fix is essentially
+computing the temperature after a "bias" has been removed from the
+velocity of the atoms.  If this compute is used with a fix command
+that performs thermostatting then this bias will be subtracted from
+each atom, thermostatting of the remaining thermal velocity will be
+performed, and the bias will be added back in.  Thermostatting fixes
+that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`compute temp/region <compute_temp_region>`, :doc:`compute pressure <compute_pressure>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst
new file mode 100644
index 0000000000..67dcf3fd49
--- /dev/null
+++ b/doc/src/compute_temp_profile.rst
@@ -0,0 +1,202 @@
+.. index:: compute temp/profile
+
+compute temp/profile command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/profile xflag yflag zflag binstyle args
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/profile = style name of this compute command
+* xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
+* binstyle = *x* or *y* or *z* or *xy* or *yz* or *xz* or *xyz*
+  
+  .. parsed-literal::
+  
+       *x* arg = Nx
+       *y* arg = Ny
+       *z* arg = Nz
+       *xy* args = Nx Ny
+       *yz* args = Ny Nz
+       *xz* args = Nx Nz
+       *xyz* args = Nx Ny Nz
+         Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
+
+* zero or more keyword/value pairs may be appended
+* keyword = *out*
+  
+  .. parsed-literal::
+  
+       *out* value = *tensor* or *bin*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute myTemp flow temp/profile 1 1 1 x 10
+   compute myTemp flow temp/profile 1 1 1 x 10 out bin
+   compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms, after subtracting out a spatially-averaged center-of-mass
+velocity field, before computing the kinetic energy.  This can be
+useful for thermostatting a collection of atoms undergoing a complex
+flow, e.g. via a profile-unbiased thermostat (PUT) as described in
+:ref:`(Evans) <Evans1>`.  A compute of this style can be used by any command
+that computes a temperature, e.g. :doc:`thermo\_modify <thermo_modify>`,
+:doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+
+The *xflag*\ , *yflag*\ , *zflag* settings determine which components of
+average velocity are subtracted out.
+
+The *binstyle* setting and its *Nx*\ , *Ny*\ , *Nz* arguments determine
+how bins are setup to perform spatial averaging.  "Bins" can be 1d
+slabs, 2d pencils, or 3d bricks depending on which *binstyle* is used.
+The simulation box is partitioned conceptually into *Nx* by *Ny* by
+*Nz* bins.  Depending on the *binstyle*\ , you may only specify one or
+two of these values; the others are effectively set to 1 (no binning
+in that dimension).  For non-orthogonal (triclinic) simulation boxes,
+the bins are "tilted" slabs or pencils or bricks that are parallel to
+the tilted faces of the box.  See the :doc:`region prism <region>`
+command for a discussion of the geometry of tilted boxes in LAMMPS.
+
+When a temperature is computed, the center-of-mass velocity for the
+set of atoms that are both in the compute group and in the same
+spatial bin is calculated.  This bias velocity is then subtracted from
+the velocities of individual atoms in the bin to yield a thermal
+velocity for each atom.  Note that if there is only one atom in the
+bin, its thermal velocity will thus be 0.0.
+
+After the spatially-averaged velocity field has been subtracted from
+each atom, the temperature is calculated by the formula KE = (dim\*N
+- dim\*Nx\*Ny\*Nz) k T/2, where KE = total kinetic energy of the group of
+atoms (sum of 1/2 m v\^2), dim = 2 or 3 = dimensionality of the
+simulation, N = number of atoms in the group, k = Boltzmann constant,
+and T = temperature.  The dim\*Nx\*Ny\*Nz term are degrees of freedom
+subtracted to adjust for the removal of the center-of-mass velocity in
+each of Nx\*Ny\*Nz bins, as discussed in the :ref:`(Evans) <Evans1>` paper.
+
+If the *out* keyword is used with a *tensor* value, which is the
+default, a kinetic energy tensor, stored as a 6-element vector, is
+also calculated by this compute for use in the computation of a
+pressure tensor.  The formula for the components of the tensor is the
+same as the above formula, except that v\^2 is replaced by vx\*vy for
+the xy component, etc.  The 6 components of the vector are ordered xx,
+yy, zz, xy, xz, yz.
+
+If the *out* keyword is used with a *bin* value, the count of atoms
+and computed temperature for each bin are stored for output, as an
+array of values, as described below.  The temperature of each bin is
+calculated as described above, where the bias velocity is subtracted
+and only the remaining thermal velocity of atoms in the bin
+contributes to the temperature.  See the note below for how the
+temperature is normalized by the degrees-of-freedom of atoms in the
+bin.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+The removal of the spatially-averaged velocity field by this fix is
+essentially computing the temperature after a "bias" has been removed
+from the velocity of the atoms.  If this compute is used with a fix
+command that performs thermostatting then this bias will be subtracted
+from each atom, thermostatting of the remaining thermal velocity will
+be performed, and the bias will be added back in.  Thermostatting
+fixes that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute\_modify <compute_modify>` command.
+
+.. note::
+
+   When using the *out* keyword with a value of *bin*\ , the
+   calculated temperature for each bin does not include the
+   degrees-of-freedom adjustment described in the preceding paragraph,
+   for fixes that constrain molecular motion.  It does include the
+   adjustment due to the *extra* option, which is applied to each bin.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.  Using this compute in conjunction with a
+thermostatting fix, as explained there, will effectively implement a
+profile-unbiased thermostat (PUT), as described in :ref:`(Evans) <Evans1>`.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature).  Depending
+on the setting of the *out* keyword, it also calculates a global
+vector or array.  For *out* = *tensor*\ , it calculates a vector of
+length 6 (KE tensor), which can be accessed by indices 1-6.  For *out*
+= *bin* it calculates a global array which has 2 columns and N rows,
+where N is the number of bins.  The first column contains the number
+of atoms in that bin.  The second contains the temperature of that
+bin, calculated as described above.  The ordering of rows in the array
+is as follows.  Bins in x vary fastest, then y, then z.  Thus for a
+10x10x10 3d array of bins, there will be 1000 rows.  The bin with
+indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)\*10\*10 + (iy-1)\*10
++ ix = 322, where the rows are numbered from 1 to 1000 and the bin
+indices are numbered from 1 to 10 in each dimension.
+
+These values can be used by any command that uses global scalar or
+vector or array values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".  The array values are "intensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.  The first column
+of array values are counts; the values in the second column will be in
+temperature :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+You should not use too large a velocity-binning grid, especially in
+3d.  In the current implementation, the binned velocity averages are
+summed across all processors, so this will be inefficient if the grid
+is too large, and the operation is performed every timestep, as it
+will be for most thermostats.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`compute temp/ramp <compute_temp_ramp>`, :doc:`compute temp/deform <compute_temp_deform>`, :doc:`compute pressure <compute_pressure>`
+
+Default
+"""""""
+
+The option default is out = tensor.
+
+
+----------
+
+
+.. _Evans1:
+
+
+
+**(Evans)** Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst
new file mode 100644
index 0000000000..a4fc86d541
--- /dev/null
+++ b/doc/src/compute_temp_ramp.rst
@@ -0,0 +1,125 @@
+.. index:: compute temp/ramp
+
+compute temp/ramp command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/ramp = style name of this compute command
+* vdim = *vx* or *vy* or *vz*
+* vlo,vhi = subtract velocities between vlo and vhi (velocity units)
+* dim = *x* or *y* or *z*
+* clo,chi = lower and upper bound of domain to subtract from (distance units)
+* zero or more keyword/value pairs may be appended
+* keyword = *units*
+
+
+.. parsed-literal::
+
+     *units* value = *lattice* or *box*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms, after subtracting out an ramped velocity profile before
+computing the kinetic energy.  A compute of this style can be used by
+any command that computes a temperature,
+e.g. :doc:`thermo\_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+
+The meaning of the arguments for this command which define the
+velocity ramp are the same as for the :doc:`velocity ramp <velocity>`
+command which was presumably used to impose the velocity.
+
+After the ramp velocity has been subtracted from the specified
+dimension for each atom, the temperature is calculated by the formula
+KE = dim/2 N k T, where KE = total kinetic energy of the group of
+atoms (sum of 1/2 m v\^2), dim = 2 or 3 = dimensionality of the
+simulation, N = number of atoms in the group, k = Boltzmann constant,
+and T = temperature.
+
+The *units* keyword determines the meaning of the distance units used
+for coordinates (c1,c2) and velocities (vlo,vhi).  A *box* value
+selects standard distance units as defined by the :doc:`units <units>`
+command, e.g. Angstroms for units = real or metal.  A *lattice* value
+means the distance units are in lattice spacings; e.g. velocity =
+lattice spacings / tau.  The :doc:`lattice <lattice>` command must have
+been previously used to define the lattice spacing.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+The removal of the ramped velocity component by this fix is
+essentially computing the temperature after a "bias" has been removed
+from the velocity of the atoms.  If this compute is used with a fix
+command that performs thermostatting then this bias will be subtracted
+from each atom, thermostatting of the remaining thermal velocity will
+be performed, and the bias will be added back in.  Thermostatting
+fixes that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`compute temp/profie <compute_temp_profile>`, :doc:`compute temp/deform <compute_temp_deform>`, :doc:`compute pressure <compute_pressure>`
+
+Default
+"""""""
+
+The option default is units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst
new file mode 100644
index 0000000000..284b38d3b1
--- /dev/null
+++ b/doc/src/compute_temp_region.rst
@@ -0,0 +1,114 @@
+.. index:: compute temp/region
+
+compute temp/region command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/region region-ID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/region = style name of this compute command
+* region-ID = ID of region to use for choosing atoms
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute mine flow temp/region boundary
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms in a geometric region.  This can be useful for thermostatting
+one portion of the simulation box.  E.g. a McDLT simulation where one
+side is cooled, and the other side is heated.  A compute of this style
+can be used by any command that computes a temperature,
+e.g. :doc:`thermo\_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, etc.
+
+Note that a *region*\ -style temperature can be used to thermostat with
+:doc:`fix temp/rescale <fix_temp_rescale>` or :doc:`fix langevin <fix_langevin>`, but should probably not be used with
+Nose/Hoover style fixes (:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, or :doc:`fix nph <fix_nh>`), if the
+degrees-of-freedom included in the computed T varies with time.
+
+The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in both the group and region, k = Boltzmann constant, and T =
+temperature.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is calculated each
+time the temperature is evaluated since it is assumed atoms can
+enter/leave the region.  Thus there is no need to use the *dynamic*
+option of the :doc:`compute\_modify <compute_modify>` command for this
+compute style.
+
+The removal of atoms outside the region by this fix is essentially
+computing the temperature after a "bias" has been removed, which in
+this case is the velocity of any atoms outside the region.  If this
+compute is used with a fix command that performs thermostatting then
+this bias will be subtracted from each atom, thermostatting of the
+remaining thermal velocity will be performed, and the bias will be
+added back in.  Thermostatting fixes that work in this way include
+:doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.  This means that when this compute
+is used to calculate the temperature for any of the thermostatting
+fixes via the :doc:`fix modify temp <fix_modify>` command, the thermostat
+will operate only on atoms that are currently in the geometric
+region.
+
+Unlike other compute styles that calculate temperature, this compute
+does not subtract out degrees-of-freedom due to fixes that constrain
+motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`.  This is because those degrees of freedom
+(e.g. a constrained bond) could apply to sets of atoms that straddle
+the region boundary, and hence the concept is somewhat ill-defined.
+If needed the number of subtracted degrees-of-freedom can be set
+explicitly using the *extra* option of the
+:doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`compute pressure <compute_pressure>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst
new file mode 100644
index 0000000000..b09752a4e2
--- /dev/null
+++ b/doc/src/compute_temp_region_eff.rst
@@ -0,0 +1,71 @@
+.. index:: compute temp/region/eff
+
+compute temp/region/eff command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/region/eff region-ID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/region/eff = style name of this compute command
+* region-ID = ID of region to use for choosing atoms
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute mine flow temp/region/eff boundary
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+nuclei and electrons in the :doc:`electron force field <pair_eff>`
+model, within a geometric region using the electron force field.  A
+compute of this style can be used by commands that compute a
+temperature, e.g. :doc:`thermo\_modify <thermo_modify>`.
+
+The operation of this compute is exactly like that described by the
+:doc:`compute temp/region <compute_temp_region>` command, except that
+the formula for the temperature itself includes the radial electron
+velocity contributions, as discussed by the :doc:`compute temp/eff <compute_temp_eff>` command.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp/region <compute_temp_region>`, :doc:`compute temp/eff <compute_temp_eff>`, :doc:`compute pressure <compute_pressure>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst
new file mode 100644
index 0000000000..75912482d8
--- /dev/null
+++ b/doc/src/compute_temp_rotate.rst
@@ -0,0 +1,102 @@
+.. index:: compute temp/rotate
+
+compute temp/rotate command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/rotate
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/rotate = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute Tbead bead temp/rotate
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+atoms, after subtracting out the center-of-mass velocity and angular velocity of the group.
+This is useful if the group is expected to have a non-zero net
+velocity and/or global rotation motion for some reason.  A compute of this style can be used by any
+command that computes a temperature,
+e.g. :doc:`thermo\_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+
+After the center-of-mass velocity and angular velocity has been subtracted from each atom,
+the temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in the group, k = Boltzmann constant, and T = temperature.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor.  The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+The removal of the center-of-mass velocity and angular velocity by this fix is essentially
+computing the temperature after a "bias" has been removed from the
+velocity of the atoms.  If this compute is used with a fix command
+that performs thermostatting then this bias will be subtracted from
+each atom, thermostatting of the remaining thermal velocity will be
+performed, and the bias will be added back in.  Thermostatting fixes
+that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst
new file mode 100644
index 0000000000..6008874ce4
--- /dev/null
+++ b/doc/src/compute_temp_sphere.rst
@@ -0,0 +1,159 @@
+.. index:: compute temp/sphere
+
+compute temp/sphere command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/sphere keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/sphere = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *bias* or *dof*
+  
+  .. parsed-literal::
+  
+       *bias* value = bias-ID
+         bias-ID = ID of a temperature compute that removes a velocity bias
+       *dof* value = *all* or *rotate*
+         all = compute temperature of translational and rotational degrees of freedom
+         rotate = compute temperature of just rotational degrees of freedom
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all temp/sphere
+   compute myTemp mobile temp/sphere bias tempCOM
+   compute myTemp mobile temp/sphere dof rotate
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+spherical particles, including a contribution from both their
+translational and rotational kinetic energy.  This differs from the
+usual :doc:`compute temp <compute_temp>` command, which assumes point
+particles with only translational kinetic energy.
+
+Both point and finite-size particles can be included in the group.
+Point particles do not rotate, so they have only 3 translational
+degrees of freedom.  For 3d spherical particles, each has 6 degrees of
+freedom (3 translational, 3 rotational).  For 2d spherical particles,
+each has 3 degrees of freedom (2 translational, 1 rotational).
+
+.. note::
+
+   This choice for degrees of freedom (dof) assumes that all
+   finite-size spherical particles in your model will freely rotate,
+   sampling all their rotational dof.  It is possible to use a
+   combination of interaction potentials and fixes that induce no torque
+   or otherwise constrain some of all of your particles so that this is
+   not the case.  Then there are less dof and you should use the
+   :doc:`compute\_modify extra <compute_modify>` command to adjust the dof
+   accordingly.
+
+The translational kinetic energy is computed the same as is described
+by the :doc:`compute temp <compute_temp>` command.  The rotational
+kinetic energy is computed as 1/2 I w\^2, where I is the moment of
+inertia for a sphere and w is the particle's angular velocity.
+
+.. note::
+
+   For :doc:`2d models <dimension>`, particles are treated as
+   spheres, not disks, meaning their moment of inertia will be the same
+   as in 3d.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute.  The formula for the components of the
+tensor is the same as the above formulas, except that v\^2 and w\^2 are
+replaced by vx\*vy and wx\*wy for the xy component.  The 6 components of
+the vector are ordered xx, yy, zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute\_modify <compute_modify>` command if this is not the case.
+
+This compute subtracts out translational degrees-of-freedom due to
+fixes that constrain molecular motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`.  This means the
+temperature of groups of atoms that include these constraints will be
+computed correctly.  If needed, the subtracted degrees-of-freedom can
+be altered using the *extra* option of the
+:doc:`compute\_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+For the *bias* keyword, *bias-ID* refers to the ID of a temperature
+compute that removes a "bias" velocity from each atom.  This allows
+compute temp/sphere to compute its thermal temperature after the
+translational kinetic energy components have been altered in a
+prescribed way, e.g. to remove a flow velocity profile.  Thermostats
+that use this compute will work with this bias term.  See the doc
+pages for individual computes that calculate a temperature and the doc
+pages for fixes that perform thermostatting for more details.
+
+For the *dof* keyword, a setting of *all* calculates a temperature
+that includes both translational and rotational degrees of freedom.  A
+setting of *rotate* calculates a temperature that includes only
+rotational degrees of freedom.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the :doc:`atom\_style sphere <atom_style>`
+command.
+
+All particles in the group must be finite-size spheres, or point
+particles with radius = 0.0.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`, :doc:`compute temp/asphere <compute_temp>`
+
+Default
+"""""""
+
+The option defaults are no bias and dof = all.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst
new file mode 100644
index 0000000000..4512c08b6d
--- /dev/null
+++ b/doc/src/compute_temp_uef.rst
@@ -0,0 +1,62 @@
+.. index:: compute temp/uef
+
+compute temp/uef command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID temp/uef
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/uef = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all temp/uef
+   compute 2 sel temp/uef
+
+Description
+"""""""""""
+
+This command is used to compute the kinetic energy tensor in
+the reference frame of the applied flow field when
+:doc:`fix nvt/uef <fix_nh_uef>` or
+:doc:`fix npt/uef <fix_nh_uef>` is used.
+It is not necessary to use this command to compute the scalar
+value of the temperature. A :doc:`compute temp <compute_temp>`
+may be used for that purpose.
+
+Output information for this command can be found in the
+documentation for :doc:`compute temp <compute_temp>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`
+or :doc:`fix npt/uef <fix_nh_uef>` is active.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`,
+:doc:`fix nvt/uef <fix_nh_uef>`,
+:doc:`compute pressure/uef <compute_pressure_uef>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst
new file mode 100644
index 0000000000..e21e6caf6d
--- /dev/null
+++ b/doc/src/compute_ti.rst
@@ -0,0 +1,162 @@
+.. index:: compute ti
+
+compute ti command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group ti keyword args ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* ti = style name of this compute command
+* one or more attribute/arg pairs may be appended
+* keyword = pair style (lj/cut, gauss, born, etc) or *tail* or *kspace*
+  
+  .. parsed-literal::
+  
+       pair style args = atype v_name1 v_name2
+         atype = atom type (see asterisk form below)
+         v_name1 = variable with name1 that is energy scale factor and function of lambda
+         v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+       *tail* args = atype v_name1 v_name2
+         atype = atom type (see asterisk form below)
+         v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
+         v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+       *kspace* args = atype v_name1 v_name2
+         atype = atom type (see asterisk form below)
+         v_name1 = variable with name1 that is K-Space scale factor and function of lambda
+         v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
+   compute 1 all ti lj/cut 1\*3 v_lj v_dlj coul/long \* v_c v_dc kspace \* v_ks v_dks
+
+Description
+"""""""""""
+
+Define a computation that calculates the derivative of the interaction
+potential with respect to *lambda*\ , the coupling parameter used in a
+thermodynamic integration.  This derivative can be used to infer a
+free energy difference resulting from an alchemical simulation, as
+described in :ref:`Eike <Eike>`.
+
+Typically this compute will be used in conjunction with the :doc:`fix adapt <fix_adapt>` command which can perform alchemical
+transformations by adjusting the strength of an interaction potential
+as a simulation runs, as defined by one or more
+:doc:`pair\_style <pair_style>` or :doc:`kspace\_style <kspace_style>`
+commands.  This scaling is done via a prefactor on the energy, forces,
+virial calculated by the pair or K-Space style.  The prefactor is
+often a function of a *lambda* parameter which may be adjusted from 0
+to 1 (or vice versa) over the course of a :doc:`run <run>`.  The
+time-dependent adjustment is what the :doc:`fix adapt <fix_adapt>`
+command does.
+
+Assume that the unscaled energy of a pair\_style or kspace\_style is
+given by U.  Then the scaled energy is
+
+
+.. parsed-literal::
+
+   Us = f(lambda) U
+
+where f() is some function of lambda.  What this compute calculates is
+
+
+.. parsed-literal::
+
+   dUs / d(lambda) = U df(lambda)/dlambda = Us / f(lambda) df(lambda)/dlambda
+
+which is the derivative of the system's scaled potential energy Us
+with respect to *lambda*\ .
+
+To perform this calculation, you provide one or more atom types as
+*atype*\ .  *Atype* can be specified in one of two ways.  An explicit
+numeric values can be used, as in the 1st example above.  Or a
+wildcard asterisk can be used in place of or in conjunction with the
+*atype* argument to select multiple atom types.  This takes the form
+"\*" or "\*n" or "n\*" or "m\*n".  If N = the number of atom types, then
+an asterisk with no numeric values means all types from 1 to N.  A
+leading asterisk means all types from 1 to n (inclusive).  A trailing
+asterisk means all types from n to N (inclusive).  A middle asterisk
+means all types from m to n (inclusive).
+
+You also specify two functions, as :doc:`equal-style variables <variable>`.  The first is specified as *v\_name1*, where
+*name1* is the name of the variable, and is f(lambda) in the notation
+above.  The second is specified as *v\_name2*, where *name2* is the
+name of the variable, and is df(lambda) / dlambda in the notation
+above.  I.e. it is the analytic derivative of f() with respect to
+lambda.  Note that the *name1* variable is also typically given as an
+argument to the :doc:`fix adapt <fix_adapt>` command.
+
+An alchemical simulation may use several pair potentials together,
+invoked via the :doc:`pair\_style hybrid or hybrid/overlay <pair_hybrid>`
+command.  The total dUs/dlambda for the overall system is calculated
+as the sum of each contributing term as listed by the keywords in the
+compute ti command.  Individual pair potentials can be listed, which
+will be sub-styles in the hybrid case.  You can also include a K-space
+term via the *kspace* keyword.  You can also include a pairwise
+long-range tail correction to the energy via the *tail* keyword.
+
+For each term you can specify a different (or the same) scale factor
+by the two variables that you list.  Again, these will typically
+correspond toe the scale factors applied to these various potentials
+and the K-Space contribution via the :doc:`fix adapt <fix_adapt>`
+command.
+
+More details about the exact functional forms for the computation of
+du/dl can be found in the paper by :ref:`Eike <Eike>`.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar, namely dUs/dlambda.  This
+value can be used by any command that uses a global scalar value from
+a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "extensive".
+
+The scalar value will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix adapt <fix_adapt>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Eike:
+
+
+
+**(Eike)** Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst
new file mode 100644
index 0000000000..d673aee13e
--- /dev/null
+++ b/doc/src/compute_torque_chunk.rst
@@ -0,0 +1,99 @@
+.. index:: compute torque/chunk
+
+compute torque/chunk command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID torque/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* torque/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid torque/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the torque on multiple chunks of
+atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates the 3 components of the torque vector for eqch
+chunk, due to the forces on the individual atoms in the chunk around
+the center-of-mass of the chunk.  The calculation includes all effects
+due to atoms passing through periodic boundaries.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+.. note::
+
+   The coordinates of an atom contribute to the chunk's torque in
+   "unwrapped" form, by using the image flags associated with each atom.
+   See the :doc:`dump custom <dump>` command for a discussion of
+   "unwrapped" coordinates.  See the Atoms section of the
+   :doc:`read\_data <read_data>` command for a discussion of image flags and
+   how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+The simplest way to output the results of the compute torque/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all torque/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+3 for the 3 xyz components of the torque for each chunk.  These values
+can be accessed by any command that uses global array values from a
+compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+The array values are "intensive".  The array values will be in
+force-distance :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`variable torque() function <variable>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_vacf.rst b/doc/src/compute_vacf.rst
new file mode 100644
index 0000000000..9b2aa5e3bf
--- /dev/null
+++ b/doc/src/compute_vacf.rst
@@ -0,0 +1,87 @@
+.. index:: compute vacf
+
+compute vacf command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID vacf
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* vacf = style name of this compute command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all vacf
+   compute 1 upper vacf
+
+Description
+"""""""""""
+
+Define a computation that calculates the velocity auto-correlation
+function (VACF), averaged over a group of atoms.  Each atom's
+contribution to the VACF is its current velocity vector dotted into
+its initial velocity vector at the time the compute was specified.
+
+A vector of four quantities is calculated by this compute.  The first 3
+elements of the vector are vx \* vx0 (and similarly for the y and z
+components), summed and averaged over atoms in the group.  Vx is the
+current x-component of velocity for the atom, vx0 is the initial
+x-component of velocity for the atom.  The 4th element of the vector
+is the total VACF, i.e. (vx\*vx0 + vy\*vy0 + vz\*vz0), summed and
+averaged over atoms in the group.
+
+The integral of the VACF versus time is proportional to the diffusion
+coefficient of the diffusing atoms.  This can be computed in the
+following manner, using the :doc:`variable trap() <variable>` function:
+
+
+.. parsed-literal::
+
+   compute         2 all vacf
+   fix             5 all vector 1 c_2[4]
+   variable        diff equal dt\*trap(f_5)
+   thermo_style    custom step v_diff
+
+.. note::
+
+   If you want the quantities calculated by this compute to be
+   continuous when running from a :doc:`restart file <read_restart>`, then
+   you should use the same ID for this compute, as in the original run.
+   This is so that the fix this compute creates to store per-atom
+   quantities will also have the same ID, and thus be initialized
+   correctly with time=0 atom velocities from the restart file.
+
+**Output info:**
+
+This compute calculates a global vector of length 4, which can be
+accessed by indices 1-4 by any command that uses global vector values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+The vector values are "intensive".  The vector values will be in
+velocity\^2 :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute msd <compute_msd>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst
new file mode 100644
index 0000000000..f8718fe803
--- /dev/null
+++ b/doc/src/compute_vcm_chunk.rst
@@ -0,0 +1,86 @@
+.. index:: compute vcm/chunk
+
+compute vcm/chunk command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID vcm/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* vcm/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 fluid vcm/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the center-of-mass velocity for
+multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+This compute calculates the x,y,z components of the center-of-mass
+velocity for each chunk.  This is done by summing mass\*velocity for
+each atom in the chunk and dividing the sum by the total mass of the
+chunk.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+The simplest way to output the results of the compute vcm/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all vcm/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+3 for the x,y,z center-of-mass velocity coordinates of each chunk.
+These values can be accessed by any command that uses global array
+values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The array values are "intensive".  The array values will be in
+velocity :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst
new file mode 100644
index 0000000000..7474fe1a25
--- /dev/null
+++ b/doc/src/compute_voronoi_atom.rst
@@ -0,0 +1,256 @@
+.. index:: compute voronoi/atom
+
+compute voronoi/atom command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID voronoi/atom keyword arg ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* voronoi/atom = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *only\_group* or *surface* or *radius* or *edge\_histo* or *edge\_threshold*
+  or *face\_threshold* or *neighbors* or *peratom*
+  
+  .. parsed-literal::
+  
+       *only_group* = no arg
+       *occupation* = no arg
+       *surface* arg = sgroup-ID
+         sgroup-ID = compute the dividing surface between group-ID and sgroup-ID
+           this keyword adds a third column to the compute output
+       *radius* arg = v_r
+         v_r = radius atom style variable for a poly-disperse Voronoi tessellation
+       *edge_histo* arg = maxedge
+         maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
+       *edge_threshold* arg = minlength
+         minlength = minimum length for an edge to be counted
+       *face_threshold* arg = minarea
+         minarea = minimum area for a face to be counted
+       *neighbors* value = *yes* or *no* = store list of all neighbors or no
+       *peratom* value = *yes* or *no* = per-atom quantities accessible or no
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all voronoi/atom
+   compute 2 precipitate voronoi/atom surface matrix
+   compute 3b precipitate voronoi/atom radius v_r
+   compute 4 solute voronoi/atom only_group
+   compute 5 defects voronoi/atom occupation
+   compute 6 all voronoi/atom neighbors yes
+
+Description
+"""""""""""
+
+Define a computation that calculates the Voronoi tessellation of the
+atoms in the simulation box.  The tessellation is calculated using all
+atoms in the simulation, but non-zero values are only stored for atoms
+in the group.
+
+By default two per-atom quantities are calculated by this compute.
+The first is the volume of the Voronoi cell around each atom.  Any
+point in an atom's Voronoi cell is closer to that atom than any other.
+The second is the number of faces of the Voronoi cell. This is
+equal to the number of nearest neighbors of the central atom,
+plus any exterior faces (see note below). If the *peratom* keyword
+is set to "no", the per-atom quantities are still calculated,
+but they are not accessible.
+
+
+----------
+
+
+If the *only\_group* keyword is specified the tessellation is performed
+only with respect to the atoms contained in the compute group. This is
+equivalent to deleting all atoms not contained in the group prior to
+evaluating the tessellation.
+
+If the *surface* keyword is specified a third quantity per atom is
+computed: the Voronoi cell surface of the given atom. *surface* takes
+a group ID as an argument. If a group other than *all* is specified,
+only the Voronoi cell facets facing a neighbor atom from the specified
+group are counted towards the surface area.
+
+In the example above, a precipitate embedded in a matrix, only atoms
+at the surface of the precipitate will have non-zero surface area, and
+only the outward facing facets of the Voronoi cells are counted (the
+hull of the precipitate). The total surface area of the precipitate
+can be obtained by running a "reduce sum" compute on c\_2[3]
+
+If the *radius* keyword is specified with an atom style variable as
+the argument, a poly-disperse Voronoi tessellation is
+performed. Examples for radius variables are
+
+
+.. parsed-literal::
+
+   variable r1 atom (type==1)\*0.1+(type==2)\*0.4
+   compute radius all property/atom radius
+   variable r2 atom c_radius
+
+Here v\_r1 specifies a per-type radius of 0.1 units for type 1 atoms
+and 0.4 units for type 2 atoms, and v\_r2 accesses the radius property
+present in atom\_style sphere for granular models.
+
+The *edge\_histo* keyword activates the compilation of a histogram of
+number of edges on the faces of the Voronoi cells in the compute
+group. The argument *maxedge* of the this keyword is the largest number
+of edges on a single Voronoi cell face expected to occur in the
+sample. This keyword adds the generation of a global vector with
+*maxedge*\ +1 entries. The last entry in the vector contains the number of
+faces with more than *maxedge* edges. Since the polygon with the
+smallest amount of edges is a triangle, entries 1 and 2 of the vector
+will always be zero.
+
+The *edge\_threshold* and *face\_threshold* keywords allow the
+suppression of edges below a given minimum length and faces below a
+given minimum area. Ultra short edges and ultra small faces can occur
+as artifacts of the Voronoi tessellation. These keywords will affect
+the neighbor count and edge histogram outputs.
+
+If the *occupation* keyword is specified the tessellation is only
+performed for the first invocation of the compute and then stored.
+For all following invocations of the compute the number of atoms in
+each Voronoi cell in the stored tessellation is counted. In this mode
+the compute returns a per-atom array with 2 columns. The first column
+is the number of atoms currently in the Voronoi volume defined by this
+atom at the time of the first invocation of the compute (note that the
+atom may have moved significantly). The second column contains the
+total number of atoms sharing the Voronoi cell of the stored
+tessellation at the location of the current atom. Numbers in column
+one can be any positive integer including zero, while column two
+values will always be greater than zero. Column one data can be used
+to locate vacancies (the coordinates are given by the atom coordinates
+at the time step when the compute was first invoked), while column two
+data can be used to identify interstitial atoms.
+
+If the *neighbors* value is set to yes, then this compute creates a
+local array with 3 columns. There is one row for each face of each
+Voronoi cell. The 3 columns are the atom ID of the atom that owns the
+cell, the atom ID of the atom in the neighboring cell (or zero if the
+face is external), and the area of the face.  The array can be
+accessed by any command that uses local values from a compute as
+input.  See the :doc:`Howto output <Howto_output>` doc page for an
+overview of LAMMPS output options. More specifically, the array can be
+accessed by a :doc:`dump local <dump>` command to write a file
+containing all the Voronoi neighbors in a system:
+
+
+.. parsed-literal::
+
+   compute 6 all voronoi/atom neighbors yes
+   dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
+
+If the *face\_threshold* keyword is used, then only faces
+with areas greater than the threshold are stored.
+
+
+----------
+
+
+The Voronoi calculation is performed by the freely available `Voro++ package <voronoi_>`_, written by Chris Rycroft at UC Berkeley and LBL,
+which must be installed on your system when building LAMMPS for use
+with this compute.  See instructions on obtaining and installing the
+Voro++ software in the src/VORONOI/README file.
+
+.. _voronoi: http://math.lbl.gov/voro++/
+
+
+
+.. note::
+
+   The calculation of Voronoi volumes is performed by each
+   processor for the atoms it owns, and includes the effect of ghost
+   atoms stored by the processor.  This assumes that the Voronoi cells of
+   owned atoms are not affected by atoms beyond the ghost atom cut-off
+   distance.  This is usually a good assumption for liquid and solid
+   systems, but may lead to underestimation of Voronoi volumes in low
+   density systems.  By default, the set of ghost atoms stored by each
+   processor is determined by the cutoff used for
+   :doc:`pair\_style <pair_style>` interactions.  The cutoff can be set
+   explicitly via the :doc:`comm\_modify cutoff <comm_modify>` command.  The
+   Voronoi cells for atoms adjacent to empty regions will extend into
+   those regions up to the communication cutoff in x, y, or z.  In that
+   situation, an exterior face is created at the cutoff distance normal
+   to the x, y, or z direction.  For triclinic systems, the exterior face
+   is parallel to the corresponding reciprocal lattice vector.
+
+.. note::
+
+   The Voro++ package performs its calculation in 3d.  This will
+   still work for a 2d LAMMPS simulation, provided all the atoms have the
+   same z coordinate. The Voronoi cell of each atom will be a columnar
+   polyhedron with constant cross-sectional area along the z direction
+   and two exterior faces at the top and bottom of the simulation box. If
+   the atoms do not all have the same z coordinate, then the columnar
+   cells will be accordingly distorted. The cross-sectional area of each
+   Voronoi cell can be obtained by dividing its volume by the z extent of
+   the simulation box.  Note that you define the z extent of the
+   simulation box for 2d simulations when using the
+   :doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` commands.
+
+**Output info:**
+
+By default, this compute calculates a per-atom array with 2
+columns. In regular dynamic tessellation mode the first column is the
+Voronoi volume, the second is the neighbor count, as described above
+(read above for the output data in case the *occupation* keyword is
+specified).  These values can be accessed by any command that uses
+per-atom values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options. If the *peratom* keyword is set to "no", the per-atom array
+is still created, but it is not accessible.
+
+If the *edge\_histo* keyword is used, then this compute generates a
+global vector of length *maxedge*\ +1, containing a histogram of the
+number of edges per face.
+
+If the *neighbors* value is set to yes, then this compute calculates a
+local array with 3 columns. There is one row for each face of each
+Voronoi cell.
+
+.. note::
+
+   Some LAMMPS commands such as the :doc:`compute reduce <compute_reduce>` command can accept either a per-atom or
+   local quantity. If this compute produces both quantities, the command
+   may access the per-atom quantity, even if you want to access the local
+   quantity.  This effect can be eliminated by using the *peratom*
+   keyword to turn off the production of the per-atom quantities.  For
+   the default value *yes* both quantities are produced.  For the value
+   *no*\ , only the local array is produced.
+
+The Voronoi cell volume will be in distance :doc:`units <units>` cubed.
+The Voronoi face area will be in distance :doc:`units <units>` squared.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the VORONOI package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+It also requires you have a copy of the Voro++ library built and
+installed on your system.  See instructions on obtaining and
+installing the Voro++ software in the src/VORONOI/README file.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`, :doc:`dump local <dump>`
+
+**Default:** *neighbors* no, *peratom* yes
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst
new file mode 100644
index 0000000000..00466ed8ce
--- /dev/null
+++ b/doc/src/compute_xrd.rst
@@ -0,0 +1,278 @@
+.. index:: compute xrd
+
+compute xrd command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* xrd = style name of this compute command
+* lambda = wavelength of incident radiation (length units)
+* type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
+* zero or more keyword/value pairs may be appended
+* keyword = *2Theta* or *c* or *LP* or *manual* or *echo*
+  
+  .. parsed-literal::
+  
+       *2Theta* values = Min2Theta Max2Theta
+         Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
+         (radians or degrees)
+       *c* values = c1 c2 c3
+         c1,c2,c3 = parameters to adjust the spacing of the reciprocal
+                    lattice nodes in the h, k, and l directions respectively
+       *LP* value = switch to apply Lorentz-polarization factor
+         0/1 = off/on
+       *manual* = flag to use manual spacing of reciprocal lattice points
+                  based on the values of the *c* parameters
+       *echo* = flag to provide extra output for debugging purposes
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
+   compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual
+
+   fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
+   fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
+
+Description
+"""""""""""
+
+Define a computation that calculates x-ray diffraction intensity as described
+in :ref:`(Coleman) <xrd-Coleman>` on a mesh of reciprocal lattice nodes defined
+by the entire simulation domain (or manually) using a simulated radiation
+of wavelength lambda.
+
+The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
+is computed from the structure factor, F, using the equations:
+
+.. image:: Eqs/compute_xrd1.jpg
+   :align: center
+
+.. image:: Eqs/compute_xrd2.jpg
+   :align: center
+
+.. image:: Eqs/compute_xrd3.jpg
+   :align: center
+
+.. image:: Eqs/compute_xrd4.jpg
+   :align: center
+
+Here, K is the location of the reciprocal lattice node, rj is the
+position of each atom, fj are atomic scattering factors, LP is the
+Lorentz-polarization factor, and theta is the scattering angle of
+diffraction.  The Lorentz-polarization factor can be turned off using
+the optional *LP* keyword.
+
+Diffraction intensities are calculated on a three-dimensional mesh of
+reciprocal lattice nodes. The mesh spacing is defined either (a)
+by the entire simulation domain or (b) manually using selected values as
+shown in the 2D diagram below.
+
+.. image:: JPG/xrd_mesh_small.jpg
+   :target: JPG/xrd_mesh.jpg
+   :align: center
+
+For a mesh defined by the simulation domain, a rectilinear grid is
+constructed with spacing *c*\ \*inv(A) along each reciprocal lattice
+axis. Where A are the vectors corresponding to the edges of the
+simulation cell. If one or two directions has non-periodic boundary
+conditions, then the spacing in these directions is defined from the
+average of the (inversed) box lengths with periodic boundary conditions.
+Meshes defined by the simulation domain must contain at least one periodic
+boundary.
+
+If the *manual* flag is included, the mesh of reciprocal lattice nodes
+will defined using the *c* values for the spacing along each
+reciprocal lattice axis. Note that manual mapping of the reciprocal
+space mesh is good for comparing diffraction results from multiple
+simulations; however it can reduce the likelihood that Bragg
+reflections will be satisfied unless small spacing parameters (< 0.05
+Angstrom\^(-1)) are implemented.  Meshes with manual spacing do not
+require a periodic boundary.
+
+The limits of the reciprocal lattice mesh are determined by range of
+scattering angles explored.  The *2Theta* parameters allows the user
+to reduce the scattering angle range to only the region of interest
+which reduces the cost of the computation.
+
+The atomic scattering factors, fj, accounts for the reduction in
+diffraction intensity due to Compton scattering.  Compute xrd uses
+analytical approximations of the atomic scattering factors that vary
+for each atom type (type1 type2 ... typeN) and angle of diffraction.
+The analytic approximation is computed using the formula
+:ref:`(Colliex) <Colliex>`:
+
+.. image:: Eqs/compute_xrd5.jpg
+   :align: center
+
+Coefficients parameterized by :ref:`(Peng) <Peng>` are assigned for each
+atom type designating the chemical symbol and charge of each atom
+type. Valid chemical symbols for compute xrd are:
+
++------+------+------+-------+------+
+| H    | He1- | He   | Li    | Li1+ |
++------+------+------+-------+------+
+| Be   | Be2+ | B    | C     | Cval |
++------+------+------+-------+------+
+| N    | O    | O1-  | F     | F1-  |
++------+------+------+-------+------+
+| Ne   | Na   | Na1+ | Mg    | Mg2+ |
++------+------+------+-------+------+
+| Al   | Al3+ | Si   | Sival | Si4+ |
++------+------+------+-------+------+
+| P    | S    | Cl   | Cl1-  | Ar   |
++------+------+------+-------+------+
+| K    | Ca   | Ca2+ | Sc    | Sc3+ |
++------+------+------+-------+------+
+| Ti   | Ti2+ | Ti3+ | Ti4+  | V    |
++------+------+------+-------+------+
+| V2+  | V3+  | V5+  | Cr    | Cr2+ |
++------+------+------+-------+------+
+| Cr3+ | Mn   | Mn2+ | Mn3+  | Mn4+ |
++------+------+------+-------+------+
+| Fe   | Fe2+ | Fe3+ | Co    | Co2+ |
++------+------+------+-------+------+
+| Co   | Ni   | Ni2+ | Ni3+  | Cu   |
++------+------+------+-------+------+
+| Cu1+ | Cu2+ | Zn   | Zn2+  | Ga   |
++------+------+------+-------+------+
+| Ga3+ | Ge   | Ge4+ | As    | Se   |
++------+------+------+-------+------+
+| Br   | Br1- | Kr   | Rb    | Rb1+ |
++------+------+------+-------+------+
+| Sr   | Sr2+ | Y    | Y3+   | Zr   |
++------+------+------+-------+------+
+| Zr4+ | Nb   | Nb3+ | Nb5+  | Mo   |
++------+------+------+-------+------+
+| Mo3+ | Mo5+ | Mo6+ | Tc    | Ru   |
++------+------+------+-------+------+
+| Ru3+ | Ru4+ | Rh   | Rh3+  | Rh4+ |
++------+------+------+-------+------+
+| Pd   | Pd2+ | Pd4+ | Ag    | Ag1+ |
++------+------+------+-------+------+
+| Ag2+ | Cd   | Cd2+ | In    | In3+ |
++------+------+------+-------+------+
+| Sn   | Sn2+ | Sn4+ | Sb    | Sb3+ |
++------+------+------+-------+------+
+| Sb5+ | Te   | I    | I1-   | Xe   |
++------+------+------+-------+------+
+| Cs   | Cs1+ | Ba   | Ba2+  | La   |
++------+------+------+-------+------+
+| La3+ | Ce   | Ce3+ | Ce4+  | Pr   |
++------+------+------+-------+------+
+| Pr3+ | Pr4+ | Nd   | Nd3+  | Pm   |
++------+------+------+-------+------+
+| Pm3+ | Sm   | Sm3+ | Eu    | Eu2+ |
++------+------+------+-------+------+
+| Eu3+ | Gd   | Gd3+ | Tb    | Tb3+ |
++------+------+------+-------+------+
+| Dy   | Dy3+ | Ho   | Ho3+  | Er   |
++------+------+------+-------+------+
+| Er3+ | Tm   | Tm3+ | Yb    | Yb2+ |
++------+------+------+-------+------+
+| Yb3+ | Lu   | Lu3+ | Hf    | Hf4+ |
++------+------+------+-------+------+
+| Ta   | Ta5+ | W    | W6+   | Re   |
++------+------+------+-------+------+
+| Os   | Os4+ | Ir   | Ir3+  | Ir4+ |
++------+------+------+-------+------+
+| Pt   | Pt2+ | Pt4+ | Au    | Au1+ |
++------+------+------+-------+------+
+| Au3+ | Hg   | Hg1+ | Hg2+  | Tl   |
++------+------+------+-------+------+
+| Tl1+ | Tl3+ | Pb   | Pb2+  | Pb4+ |
++------+------+------+-------+------+
+| Bi   | Bi3+ | Bi5+ | Po    | At   |
++------+------+------+-------+------+
+| Rn   | Fr   | Ra   | Ra2+  | Ac   |
++------+------+------+-------+------+
+| Ac3+ | Th   | Th4+ | Pa    | U    |
++------+------+------+-------+------+
+| U3+  | U4+  | U6+  | Np    | Np3+ |
++------+------+------+-------+------+
+| Np4+ | Np6+ | Pu   | Pu3+  | Pu4+ |
++------+------+------+-------+------+
+| Pu6+ | Am   | Cm   | Bk    | Cf   |
++------+------+------+-------+------+
+
+If the *echo* keyword is specified, compute xrd will provide extra
+reporting information to the screen.
+
+**Output info:**
+
+This compute calculates a global array.  The number of rows in the
+array is the number of reciprocal lattice nodes that are explored
+which by the mesh.  The global array has 2 columns.
+
+The first column contains the diffraction angle in the units (radians
+or degrees) provided with the *2Theta* values. The second column contains
+the computed diffraction intensities as described above.
+
+The array can be accessed by any command that uses global values from
+a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
+
+All array values calculated by this compute are "intensive".
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-DIFFRACTION package.  It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The compute\_xrd command does not work for triclinic cells.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`compute saed <compute_saed>`
+
+Default
+"""""""
+
+The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
+no manual flag, no echo flag.
+
+
+----------
+
+
+.. _xrd-Coleman:
+
+
+
+**(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020
+(2013).
+
+.. _Colliex:
+
+
+
+**(Colliex)** Colliex et al. International Tables for Crystallography
+Volume C: Mathematical and Chemical Tables, 249-429 (2004).
+
+.. _Peng:
+
+
+
+**(Peng)** Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76
+(1996).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/computes.rst b/doc/src/computes.rst
new file mode 100644
index 0000000000..1c1819a444
--- /dev/null
+++ b/doc/src/computes.rst
@@ -0,0 +1,9 @@
+Computes
+########
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   compute_*
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
deleted file mode 100644
index b24387e856..0000000000
--- a/doc/src/computes.txt
+++ /dev/null
@@ -1,137 +0,0 @@
-Computes :h1
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   compute_ackland_atom
-   compute_adf
-   compute_angle
-   compute_angle_local
-   compute_angmom_chunk
-   compute_basal_atom
-   compute_body_local
-   compute_bond
-   compute_bond_local
-   compute_centro_atom
-   compute_chunk_atom
-   compute_chunk_spread_atom
-   compute_cluster_atom
-   compute_cna_atom
-   compute_cnp_atom
-   compute_com
-   compute_com_chunk
-   compute_contact_atom
-   compute_coord_atom
-   compute_damage_atom
-   compute_dihedral
-   compute_dihedral_local
-   compute_dilatation_atom
-   compute_dipole_chunk
-   compute_displace_atom
-   compute_dpd
-   compute_dpd_atom
-   compute_edpd_temp_atom
-   compute_entropy_atom
-   compute_erotate_asphere
-   compute_erotate_rigid
-   compute_erotate_sphere
-   compute_erotate_sphere_atom
-   compute_event_displace
-   compute_fep
-   compute_global_atom
-   compute_group_group
-   compute_gyration
-   compute_gyration_chunk
-   compute_gyration_shape
-   compute_heat_flux
-   compute_hexorder_atom
-   compute_hma
-   compute_improper
-   compute_improper_local
-   compute_inertia_chunk
-   compute_ke
-   compute_ke_atom
-   compute_ke_atom_eff
-   compute_ke_eff
-   compute_ke_rigid
-   compute_meso_e_atom
-   compute_meso_rho_atom
-   compute_meso_t_atom
-   compute_momentum
-   compute_msd
-   compute_msd_chunk
-   compute_msd_nongauss
-   compute_omega_chunk
-   compute_orientorder_atom
-   compute_pair
-   compute_pair_local
-   compute_pe
-   compute_pe_atom
-   compute_plasticity_atom
-   compute_pressure
-   compute_pressure_cylinder
-   compute_pressure_uef
-   compute_property_atom
-   compute_property_chunk
-   compute_property_local
-   compute_ptm_atom
-   compute_rdf
-   compute_reduce
-   compute_reduce_chunk
-   compute_rigid_local
-   compute_saed
-   compute_slice
-   compute_smd_contact_radius
-   compute_smd_damage
-   compute_smd_hourglass_error
-   compute_smd_internal_energy
-   compute_smd_plastic_strain
-   compute_smd_plastic_strain_rate
-   compute_smd_rho
-   compute_smd_tlsph_defgrad
-   compute_smd_tlsph_dt
-   compute_smd_tlsph_num_neighs
-   compute_smd_tlsph_shape
-   compute_smd_tlsph_strain
-   compute_smd_tlsph_strain_rate
-   compute_smd_tlsph_stress
-   compute_smd_triangle_vertices
-   compute_smd_ulsph_num_neighs
-   compute_smd_ulsph_strain
-   compute_smd_ulsph_strain_rate
-   compute_smd_ulsph_stress
-   compute_smd_vol
-   compute_sna_atom
-   compute_spin
-   compute_stress_atom
-   compute_stress_mop
-   compute_tally
-   compute_tdpd_cc_atom
-   compute_temp
-   compute_temp_asphere
-   compute_temp_body
-   compute_temp_chunk
-   compute_temp_com
-   compute_temp_cs
-   compute_temp_deform
-   compute_temp_deform_eff
-   compute_temp_drude
-   compute_temp_eff
-   compute_temp_partial
-   compute_temp_profile
-   compute_temp_ramp
-   compute_temp_region
-   compute_temp_region_eff
-   compute_temp_rotate
-   compute_temp_sphere
-   compute_temp_uef
-   compute_ti
-   compute_torque_chunk
-   compute_vacf
-   compute_vcm_chunk
-   compute_voronoi_atom
-   compute_xrd
-
-END_RST -->
diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst
new file mode 100644
index 0000000000..6a3dc8feaa
--- /dev/null
+++ b/doc/src/create_atoms.rst
@@ -0,0 +1,372 @@
+.. index:: create\_atoms
+
+create\_atoms command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   create_atoms type style args keyword values ...
+
+* type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
+* style = *box* or *region* or *single* or *random*
+  
+  .. parsed-literal::
+  
+       *box* args = none
+       *region* args = region-ID
+         region-ID = particles will only be created if contained in the region
+       *single* args = x y z
+         x,y,z = coordinates of a single particle (distance units)
+       *random* args = N seed region-ID
+         N = number of particles to create
+         seed = random # seed (positive integer)
+         region-ID = create atoms within this region, use NULL for entire simulation box
+
+* zero or more keyword/value pairs may be appended
+* keyword = *mol* or *basis* or *remap* or *var* or *set* or *units*
+  
+  .. parsed-literal::
+  
+       *mol* value = template-ID seed
+         template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
+         seed = random # seed (positive integer)
+       *basis* values = M itype
+         M = which basis atom
+         itype = atom type (1-N) to assign to this basis atom
+       *remap* value = *yes* or *no*
+       *var* value = name = variable name to evaluate for test of atom creation
+       *set* values = dim name
+         dim = *x* or *y* or *z*
+         name = name of variable to set with x, y, or z atom position
+       *rotate* values = theta Rx Ry Rz
+         theta = rotation angle for single molecule (degrees)
+         Rx,Ry,Rz = rotation vector for single molecule
+       *units* value = *lattice* or *box*
+         *lattice* = the geometry is defined in lattice units
+         *box* = the geometry is defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   create_atoms 1 box
+   create_atoms 3 region regsphere basis 2 3
+   create_atoms 3 single 0 0 5
+   create_atoms 1 box var v set x xpos set y ypos
+
+Description
+"""""""""""
+
+This command creates atoms (or molecules) on a lattice, or a single
+atom (or molecule), or a random collection of atoms (or molecules), as
+an alternative to reading in their coordinates explicitly via a
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+command.  A simulation box must already exist, which is typically
+created via the :doc:`create\_box <create_box>` command.  Before using
+this command, a lattice must also be defined using the
+:doc:`lattice <lattice>` command, unless you specify the *single* style
+with units = box or the *random* style.  For the remainder of this doc
+page, a created atom or molecule is referred to as a "particle".
+
+If created particles are individual atoms, they are assigned the
+specified atom *type*\ , though this can be altered via the *basis*
+keyword as discussed below.  If molecules are being created, the type
+of each atom in the created molecule is specified in the file read by
+the :doc:`molecule <molecule>` command, and those values are added to
+the specified atom *type*\ .  E.g. if *type* = 2, and the file specifies
+atom types 1,2,3, then each created molecule will have atom types
+3,4,5.
+
+For the *box* style, the create\_atoms command fills the entire
+simulation box with particles on the lattice.  If your simulation box
+is periodic, you should insure its size is a multiple of the lattice
+spacings, to avoid unwanted atom overlaps at the box boundaries.  If
+your box is periodic and a multiple of the lattice spacing in a
+particular dimension, LAMMPS is careful to put exactly one particle at
+the boundary (on either side of the box), not zero or two.
+
+For the *region* style, a geometric volume is filled with particles on
+the lattice.  This volume what is inside the simulation box and is
+also consistent with the region volume.  See the :doc:`region <region>`
+command for details.  Note that a region can be specified so that its
+"volume" is either inside or outside a geometric boundary.  Also note
+that if your region is the same size as a periodic simulation box (in
+some dimension), LAMMPS does not implement the same logic described
+above as for the *box* style, to insure exactly one particle at
+periodic boundaries.  if this is what you desire, you should either
+use the *box* style, or tweak the region size to get precisely the
+particles you want.
+
+For the *single* style, a single particle is added to the system at
+the specified coordinates.  This can be useful for debugging purposes
+or to create a tiny system with a handful of particles at specified
+positions.
+
+For the *random* style, N particles are added to the system at
+randomly generated coordinates, which can be useful for generating an
+amorphous system.  The particles are created one by one using the
+specified random number *seed*\ , resulting in the same set of particles
+coordinates, independent of how many processors are being used in the
+simulation.  If the *region-ID* argument is specified as NULL, then
+the created particles will be anywhere in the simulation box.  If a
+*region-ID* is specified, a geometric volume is filled which is both
+inside the simulation box and is also consistent with the region
+volume.  See the :doc:`region <region>` command for details.  Note that
+a region can be specified so that its "volume" is either inside or
+outside a geometric boundary.
+
+.. note::
+
+   Particles generated by the *random* style will typically be
+   highly overlapped which will cause many interatomic potentials to
+   compute large energies and forces.  Thus you should either perform an
+   :doc:`energy minimization <minimize>` or run dynamics with :doc:`fix nve/limit <fix_nve_limit>` to equilibrate such a system, before
+   running normal dynamics.
+
+Note that this command adds particles to those that already exist.
+This means it can be used to add particles to a system previously read
+in from a data or restart file.  Or the create\_atoms command can be
+used multiple times, to add multiple sets of particles to the
+simulation.  For example, grain boundaries can be created, by
+interleaving create\_atoms with :doc:`lattice <lattice>` commands
+specifying different orientations.  By using the create\_atoms command
+in conjunction with the :doc:`delete\_atoms <delete_atoms>` command,
+reasonably complex geometries can be created, or a protein can be
+solvated with a surrounding box of water molecules.
+
+In all these cases, care should be taken to insure that new atoms do
+not overlap existing atoms inappropriately, especially if molecules
+are being added.  The :doc:`delete\_atoms <delete_atoms>` command can be
+used to remove overlapping atoms or molecules.
+
+.. note::
+
+   You cannot use any of the styles explained above to create atoms
+   that are outside the simulation box; they will just be ignored by
+   LAMMPS.  This is true even if you are using shrink-wrapped box
+   boundaries, as specified by the :doc:`boundary <boundary>` command.
+   However, you can first use the :doc:`change\_box <change_box>` command to
+   temporarily expand the box, then add atoms via create\_atoms, then
+   finally use change\_box command again if needed to re-shrink-wrap the
+   new atoms.  See the :doc:`change\_box <change_box>` doc page for an
+   example of how to do this, using the create\_atoms *single* style to
+   insert a new atom outside the current simulation box.
+
+
+----------
+
+
+Individual atoms are inserted by this command, unless the *mol*
+keyword is used.  It specifies a *template-ID* previously defined
+using the :doc:`molecule <molecule>` command, which reads a file that
+defines the molecule.  The coordinates, atom types, charges, etc, as
+well as any bond/angle/etc and special neighbor information for the
+molecule can be specified in the molecule file.  See the
+:doc:`molecule <molecule>` command for details.  The only settings
+required to be in this file are the coordinates and types of atoms in
+the molecule.
+
+Using a lattice to add molecules, e.g. via the *box* or *region* or
+*single* styles, is exactly the same as adding atoms on lattice
+points, except that entire molecules are added at each point, i.e. on
+the point defined by each basis atom in the unit cell as it tiles the
+simulation box or region.  This is done by placing the geometric
+center of the molecule at the lattice point, and giving the molecule a
+random orientation about the point.  The random *seed* specified with
+the *mol* keyword is used for this operation, and the random numbers
+generated by each processor are different.  This means the coordinates
+of individual atoms (in the molecules) will be different when running
+on different numbers of processors, unlike when atoms are being
+created in parallel.
+
+Also note that because of the random rotations, it may be important to
+use a lattice with a large enough spacing that adjacent molecules will
+not overlap, regardless of their relative orientations.
+
+.. note::
+
+   If the :doc:`create\_box <create_box>` command is used to create
+   the simulation box, followed by the create\_atoms command with its
+   *mol* option for adding molecules, then you typically need to use the
+   optional keywords allowed by the :doc:`create\_box <create_box>` command
+   for extra bonds (angles,etc) or extra special neighbors.  This is
+   because by default, the :doc:`create\_box <create_box>` command sets up a
+   non-molecular system which doesn't allow molecules to be added.
+
+
+----------
+
+
+This is the meaning of the other allowed keywords.
+
+The *basis* keyword is only used when atoms (not molecules) are being
+created.  It specifies an atom type that will be assigned to specific
+basis atoms as they are created.  See the :doc:`lattice <lattice>`
+command for specifics on how basis atoms are defined for the unit cell
+of the lattice.  By default, all created atoms are assigned the
+argument *type* as their atom type.
+
+The *remap* keyword only applies to the *single* style.  If it is set
+to *yes*\ , then if the specified position is outside the simulation
+box, it will mapped back into the box, assuming the relevant
+dimensions are periodic.  If it is set to *no*\ , no remapping is done
+and no particle is created if its position is outside the box.
+
+The *var* and *set* keywords can be used together to provide a
+criterion for accepting or rejecting the addition of an individual
+atom, based on its coordinates.  The *name* specified for the *var*
+keyword is the name of an :doc:`equal-style variable <variable>` which
+should evaluate to a zero or non-zero value based on one or two or
+three variables which will store the x, y, or z coordinates of an atom
+(one variable per coordinate).  If used, these other variables must be
+:doc:`internal-style variables <variable>` defined in the input script;
+their initial numeric value can be anything.  They must be
+internal-style variables, because this command resets their values
+directly.  The *set* keyword is used to identify the names of these
+other variables, one variable for the x-coordinate of a created atom,
+one for y, and one for z.
+
+When an atom is created, its x,y,z coordinates become the values for
+any *set* variable that is defined.  The *var* variable is then
+evaluated.  If the returned value is 0.0, the atom is not created.  If
+it is non-zero, the atom is created.
+
+As an example, these commands can be used in a 2d simulation, to
+create a sinusoidal surface.  Note that the surface is "rough" due to
+individual lattice points being "above" or "below" the mathematical
+expression for the sinusoidal curve.  If a finer lattice were used,
+the sinusoid would appear to be "smoother".  Also note the use of the
+"xlat" and "ylat" :doc:`thermo\_style <thermo_style>` keywords which
+converts lattice spacings to distance.  Click on the image for a
+larger version.
+
+
+.. parsed-literal::
+
+   dimension       2
+   variable        x equal 100
+   variable        y equal 25
+   lattice         hex 0.8442
+   region          box block 0 $x 0 $y -0.5 0.5
+   create_box      1 box
+
+   variable        xx internal 0.0
+   variable        yy internal 0.0
+   variable        v equal "(0.2\*v_y\*ylat \* cos(v_xx/xlat \* 2.0\*PI\*4.0/v_x) + 0.5\*v_y\*ylat - v_yy) > 0.0"
+   create_atoms    1 box var v set x xx set y yy
+   write_dump      all atom sinusoid.lammpstrj
+
+.. image:: JPG/sinusoid_small.jpg
+   :target: JPG/sinusoid.jpg
+   :align: center
+
+The *rotate* keyword allows specification of the orientation
+at which molecules are inserted.  The axis of rotation is
+determined by the rotation vector (Rx,Ry,Rz) that goes through the
+insertion point.  The specified *theta* determines the angle of
+rotation around that axis.  Note that the direction of rotation for
+the atoms around the rotation axis is consistent with the right-hand
+rule: if your right-hand's thumb points along *R*\ , then your fingers
+wrap around the axis in the direction of rotation.
+
+The *units* keyword determines the meaning of the distance units used
+to specify the coordinates of the one particle created by the *single*
+style.  A *box* value selects standard distance units as defined by
+the :doc:`units <units>` command, e.g. Angstroms for units = real or
+metal.  A *lattice* value means the distance units are in lattice
+spacings.
+
+
+----------
+
+
+Atom IDs are assigned to created atoms in the following way.  The
+collection of created atoms are assigned consecutive IDs that start
+immediately following the largest atom ID existing before the
+create\_atoms command was invoked.  This is done by the processor's
+communicating the number of atoms they each own, the first processor
+numbering its atoms from 1 to N1, the second processor from N1+1 to
+N2, etc.  Where N1 = number of atoms owned by the first processor, N2
+= number owned by the second processor, etc.  Thus when the same
+simulation is performed on different numbers of processors, there is
+no guarantee a particular created atom will be assigned the same ID in
+both simulations.  If molecules are being created, molecule IDs are
+assigned to created molecules in a similar fashion.
+
+Aside from their ID, atom type, and xyz position, other properties of
+created atoms are set to default values, depending on which quantities
+are defined by the chosen :doc:`atom style <atom_style>`.  See the :doc:`atom style <atom_style>` command for more details.  See the
+:doc:`set <set>` and :doc:`velocity <velocity>` commands for info on how
+to change these values.
+
+* charge = 0.0
+* dipole moment magnitude = 0.0
+* diameter = 1.0
+* shape = 0.0 0.0 0.0
+* density = 1.0
+* volume = 1.0
+* velocity = 0.0 0.0 0.0
+* angular velocity = 0.0 0.0 0.0
+* angular momentum = 0.0 0.0 0.0
+* quaternion = (1,0,0,0)
+* bonds, angles, dihedrals, impropers = none
+
+If molecules are being created, these defaults can be overridden by
+values specified in the file read by the :doc:`molecule <molecule>`
+command.  E.g. the file typically defines bonds (angles,etc) between
+atoms in the molecule, and can optionally define charges on each atom.
+
+Note that the *sphere* atom style sets the default particle diameter
+to 1.0 as well as the density.  This means the mass for the particle
+is not 1.0, but is PI/6 \* diameter\^3 = 0.5236.
+
+Note that the *ellipsoid* atom style sets the default particle shape
+to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
+particle, not an ellipsoid, and has a mass of 1.0.
+
+Note that the *peri* style sets the default volume and density to 1.0
+and thus also set the mass for the particle to 1.0.
+
+The :doc:`set <set>` command can be used to override many of these
+default settings.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+An :doc:`atom\_style <atom_style>` must be previously defined to use this
+command.
+
+A rotation vector specified for a single molecule must be in
+the z-direction for a 2d model.
+
+Related commands
+""""""""""""""""
+
+:doc:`lattice <lattice>`, :doc:`region <region>`, :doc:`create\_box <create_box>`,
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`
+
+Default
+"""""""
+
+The default for the *basis* keyword is that all created atoms are
+assigned the argument *type* as their atom type (when single atoms are
+being created).  The other defaults are *remap* = no, *rotate* =
+random, and *units* = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst
new file mode 100644
index 0000000000..185c1ebfd7
--- /dev/null
+++ b/doc/src/create_bonds.rst
@@ -0,0 +1,239 @@
+.. index:: create\_bonds
+
+create\_bonds command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   create_bonds style args ... keyword value ...
+
+* style = *many* or *single/bond* or *single/angle* or *single/dihedral*
+
+
+.. parsed-literal::
+
+     *many* args = group-ID group2-ID btype rmin rmax
+       group-ID = ID of first group
+       group2-ID = ID of second group, bonds will be between atoms in the 2 groups
+       btype = bond type of created bonds
+       rmin = minimum distance between pair of atoms to bond together
+       rmax = maximum distance between pair of atoms to bond together
+     *single/bond* args = btype batom1 batom2
+       btype = bond type of new bond
+       batom1,batom2 = atom IDs for two atoms in bond
+     *single/angle* args = atype aatom1 aatom2 aatom3
+       atype = angle type of new angle
+       aatom1,aatom2,aatom3 = atom IDs for three atoms in angle
+     *single/dihedral* args = dtype datom1 datom2 datom3 datom4
+       dtype = dihedral type of new dihedral
+       datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral
+     *single/improper* args = itype iatom1 iatom2 iatom3 iatom4
+       itype = improper type of new improper
+       iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper
+
+* zero or more keyword/value pairs may be appended
+* keyword = *special*
+
+.. parsed-literal::
+
+     *special* value = *yes* or *no*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   create_bonds many all all 1 1.0 1.2
+   create_bonds many surf solvent 3 2.0 2.4
+   create_bonds single/bond 1 1 2
+   create_bonds single/angle 5 52 98 107 special no
+   create_bonds single/dihedral 2 4 19 27 101
+   create_bonds single/improper 3 23 26 31 57
+
+Description
+"""""""""""
+
+Create bonds between pairs of atoms that meet a specified distance
+criteria.  Or create a single bond, angle, dihedral or improper between 2, 3,
+or 4 specified atoms.
+
+The new bond (angle, dihedral, improper) interactions will then be computed
+during a simulation by the bond (angle, dihedral, improper) potential defined by
+the :doc:`bond\_style <bond_style>`, :doc:`bond\_coeff <bond_coeff>`,
+:doc:`angle\_style <angle_style>`, :doc:`angle\_coeff <angle_coeff>`,
+:doc:`dihedral\_style <dihedral_style>`,
+:doc:`dihedral\_coeff <dihedral_coeff>`, :doc:`improper\_style <improper_style>`,
+:doc:`improper\_coeff <improper_coeff>` commands.
+
+The *many* style is useful for adding bonds to a system, e.g. between
+nearest neighbors in a lattice of atoms, without having to enumerate
+all the bonds in the data file read by the :doc:`read\_data <read_data>`
+command.
+
+The *single* styles are useful for adding bonds, angles, dihedrals, impropers
+to a system incrementally, then continuing a simulation.
+
+Note that this command does not auto-create any angle, dihedral or improper
+interactions when a bond is added.  Nor does it auto-create any bonds
+when an angle, dihedral or improper is added.  Or auto-create any angles when a
+dihedral or improper is added.  Thus the flexibility of this command is limited.
+It can be used several times to create different types of bond at
+different distances.  But it cannot typically auto-create all the
+bonds or angles or dihedrals or impropers that would normally be defined in a
+data file for a complex system of molecules.
+
+.. note::
+
+   If the system has no bonds (angles, dihedrals, impropers) to begin with,
+   or if more bonds per atom are being added than currently exist, then you
+   must insure that the number of bond types and the maximum number of
+   bonds per atom are set to large enough values.  And similarly for
+   angles, dihedrals and impropers.  Otherwise an error may occur when too many
+   bonds (angles, dihedrals, impropers) are added to an atom.  If the
+   :doc:`read\_data <read_data>` command is used to define the system, these
+   parameters can be set via the "bond types" and "extra bond per atom"
+   fields in the header section of the data file.  If the
+   :doc:`create\_box <create_box>` command is used to define the system,
+   these 2 parameters can be set via its optional "bond/types" and
+   "extra/bond/per/atom" arguments.  And similarly for angles, dihedrals and
+   impropers.  See the doc pages for these 2 commands for details.
+
+
+----------
+
+
+The *many* style will create bonds between pairs of atoms I,J where I
+is in one of the two specified groups, and J is in the other.  The two
+groups can be the same, e.g. group "all".  The created bonds will be
+of bond type *btype*\ , where *btype* must be a value between 1 and the
+number of bond types defined.
+
+For a bond to be created, an I,J pair of atoms must be a distance D
+apart such that *rmin* <= D <= *rmax*\ .
+
+The following settings must have been made in an input script before
+this style is used:
+
+* special\_bonds weight for 1-2 interactions must be 0.0
+* a :doc:`pair\_style <pair_style>` must be defined
+* no :doc:`kspace\_style <kspace_style>` defined
+* minimum :doc:`pair\_style <pair_style>` cutoff + :doc:`neighbor <neighbor>` skin >= *rmax*
+
+These settings are required so that a neighbor list can be created to
+search for nearby atoms.  Pairs of atoms that are already bonded
+cannot appear in the neighbor list, to avoid creation of duplicate
+bonds.  The neighbor list for all atom type pairs must also extend to
+a distance that encompasses the *rmax* for new bonds to create.
+
+An additional requirement for this style is that your system must be
+ready to perform a simulation.  This means, for example, that all
+:doc:`pair\_style <pair_style>` coefficients be set via the
+:doc:`pair\_coeff <pair_coeff>` command.  A :doc:`bond\_style <bond_style>`
+command and all bond coefficients must also be set, even if no bonds
+exist before this command is invoked.  This is because the building of
+neighbor list requires initialization and setup of a simulation,
+similar to what a :doc:`run <run>` command would require.
+
+Note that you can change any of these settings after this command
+executes, e.g. if you wish to use long-range Coulombic interactions
+via the :doc:`kspace\_style <kspace_style>` command for your subsequent
+simulation.
+
+
+----------
+
+
+The *single/bond* style creates a single bond of type *btype* between
+two atoms with IDs *batom1* and *batom2*\ .  *Btype* must be a value
+between 1 and the number of bond types defined.
+
+The *single/angle* style creates a single angle of type *atype*
+between three atoms with IDs *aatom1*\ , *aatom2*\ , and *aatom3*\ .  The
+ordering of the atoms is the same as in the *Angles* section of a data
+file read by the :doc:`read\_data <read_data>` command.  I.e. the 3 atoms are
+ordered linearly within the angle; the central atom is *aatom2*\ .
+*Atype* must be a value between 1 and the number of angle types
+defined.
+
+The *single/dihedral* style creates a single dihedral of type *dtype*
+between four atoms with IDs *datom1*\ , *datom2*\ , *datom3*\ , and *datom4*\ .  The
+ordering of the atoms is the same as in the *Dihedrals* section of a data file
+read by the :doc:`read\_data <read_data>` command.  I.e. the 4 atoms are ordered
+linearly within the dihedral.  *dtype* must be a value between 1 and
+the number of dihedral types defined.
+
+The *single/improper* style creates a single improper of type *itype*
+between four atoms with IDs *iatom1*\ , *iatom2*\ , *iatom3*\ , and *iatom4*\ .  The
+ordering of the atoms is the same as in the *Impropers* section of a data file
+read by the :doc:`read\_data <read_data>` command.  I.e. the 4 atoms are ordered
+linearly within the improper.  *itype* must be a value between 1 and
+the number of improper types defined.
+
+
+----------
+
+
+The keyword *special* controls whether an internal list of special
+bonds is created after one or more bonds, or a single angle, dihedral or
+improper is added to the system.
+
+The default value is *yes*\ .  A value of *no* cannot be used
+with the *many* style.
+
+This is an expensive operation since the bond topology for the system
+must be walked to find all 1-2, 1-3, 1-4 interactions to store in an
+internal list, which is used when pairwise interactions are weighted;
+see the :doc:`special\_bonds <special_bonds>` command for details.
+
+Thus if you are adding a few bonds or a large list of angles all at
+the same time, by using this command repeatedly, it is more efficient
+to only trigger the internal list to be created once, after the last
+bond (or angle, or dihedral, or improper) is added:
+
+
+.. parsed-literal::
+
+   create_bonds single/bond 5 52 98 special no
+   create_bonds single/bond 5 73 74 special no
+   ...
+   create_bonds single/bond 5 17 386 special no
+   create_bonds single/bond 4 112 183 special yes
+
+Note that you MUST insure the internal list is re-built after the last
+bond (angle, dihedral, improper) is added, before performing a simulation.
+Otherwise pairwise interactions will not be properly excluded or
+weighted.  LAMMPS does NOT check that you have done this correctly.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command cannot be used with molecular systems defined using
+molecule template files via the :doc:`molecule <molecule>` and
+:doc:`atom\_style template <atom_style>` commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`create\_atoms <create_atoms>`, :doc:`delete\_bonds <delete_bonds>`
+
+Default
+"""""""
+
+The keyword default is special = yes.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst
new file mode 100644
index 0000000000..1bffab90b5
--- /dev/null
+++ b/doc/src/create_box.rst
@@ -0,0 +1,170 @@
+.. index:: create\_box
+
+create\_box command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   create_box N region-ID keyword value ...
+
+* N = # of atom types to use in this simulation
+* region-ID = ID of region to use as simulation domain
+* zero or more keyword/value pairs may be appended
+* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom*
+  
+  .. parsed-literal::
+  
+       *bond/types* value = # of bond types
+       *angle/types* value = # of angle types
+       *dihedral/types* value = # of dihedral types
+       *improper/types* value = # of improper types
+       *extra/bond/per/atom* value = # of bonds per atom
+       *extra/angle/per/atom* value = # of angles per atom
+       *extra/dihedral/per/atom* value = # of dihedrals per atom
+       *extra/improper/per/atom* value = # of impropers per atom
+       *extra/special/per/atom* value = # of special neighbors per atom
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   create_box 2 mybox
+   create_box 2 mybox bond/types 2 extra/bond/per/atom 1
+
+Description
+"""""""""""
+
+This command creates a simulation box based on the specified region.
+Thus a :doc:`region <region>` command must first be used to define a
+geometric domain.  It also partitions the simulation box into a
+regular 3d grid of rectangular bricks, one per processor, based on the
+number of processors being used and the settings of the
+:doc:`processors <processors>` command.  The partitioning can later be
+changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
+
+The argument N is the number of atom types that will be used in the
+simulation.
+
+If the region is not of style *prism*\ , then LAMMPS encloses the region
+(block, sphere, etc) with an axis-aligned orthogonal bounding box
+which becomes the simulation domain.
+
+If the region is of style *prism*\ , LAMMPS creates a non-orthogonal
+simulation domain shaped as a parallelepiped with triclinic symmetry.
+As defined by the :doc:`region prism <region>` command, the
+parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3
+edge vectors starting from the origin given by A = (xhi-xlo,0,0); B =
+(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo).  *Xy,xz,yz* can be 0.0 or
+positive or negative values and are called "tilt factors" because they
+are the amount of displacement applied to faces of an originally
+orthogonal box to transform it into the parallelepiped.
+
+By default, a *prism* region used with the create\_box command must
+have tilt factors (xy,xz,yz) that do not skew the box more than half
+the distance of the parallel box length.  For example, if xlo = 2 and
+xhi = 12, then the x box length is 10 and the xy tilt factor must be
+between -5 and 5.  Similarly, both xz and yz must be between
+-(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a limitation,
+since if the maximum tilt factor is 5 (as in this example), then
+configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
+geometrically equivalent.  If you wish to define a box with tilt
+factors that exceed these limits, you can use the :doc:`box tilt <box>`
+command, with a setting of *large*\ ; a setting of *small* is the
+default.
+
+See the :doc:`Howto triclinic <Howto_triclinic>` doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
+triclinic representations.
+
+When a prism region is used, the simulation domain should normally be
+periodic in the dimension that the tilt is applied to, which is given
+by the second dimension of the tilt factor (e.g. y for xy tilt).  This
+is so that pairs of atoms interacting across that boundary will have
+one of them shifted by the tilt factor.  Periodicity is set by the
+:doc:`boundary <boundary>` command.  For example, if the xy tilt factor
+is non-zero, then the y dimension should be periodic.  Similarly, the
+z dimension should be periodic if xz or yz is non-zero.  LAMMPS does
+not require this periodicity, but you may lose atoms if this is not
+the case.
+
+Also note that if your simulation will tilt the box, e.g. via the :doc:`fix deform <fix_deform>` command, the simulation box must be setup to
+be triclinic, even if the tilt factors are initially 0.0.  You can
+also change an orthogonal box to a triclinic box or vice versa by
+using the :doc:`change box <change_box>` command with its *ortho* and
+*triclinic* options.
+
+.. note::
+
+   If the system is non-periodic (in a dimension), then you should
+   not make the lo/hi box dimensions (as defined in your
+   :doc:`region <region>` command) radically smaller/larger than the extent
+   of the atoms you eventually plan to create, e.g. via the
+   :doc:`create\_atoms <create_atoms>` command.  For example, if your atoms
+   extend from 0 to 50, you should not specify the box bounds as -10000
+   and 10000. This is because as described above, LAMMPS uses the
+   specified box size to layout the 3d grid of processors.  A huge
+   (mostly empty) box will be sub-optimal for performance when using
+   "fixed" boundary conditions (see the :doc:`boundary <boundary>`
+   command).  When using "shrink-wrap" boundary conditions (see the
+   :doc:`boundary <boundary>` command), a huge (mostly empty) box may cause
+   a parallel simulation to lose atoms the first time that LAMMPS
+   shrink-wraps the box around the atoms.
+
+
+----------
+
+
+The optional keywords can be used to create a system that allows for
+bond (angle, dihedral, improper) interactions, or for molecules with
+special 1-2,1-3,1-4 neighbors to be added later.  These optional
+keywords serve the same purpose as the analogous keywords that can be
+used in a data file which are recognized by the
+:doc:`read\_data <read_data>` command when it sets up a system.
+
+Note that if these keywords are not used, then the create\_box command
+creates an atomic (non-molecular) simulation that does not allow bonds
+between pairs of atoms to be defined, or a :doc:`bond potential <bond_style>` to be specified, or for molecules with
+special neighbors to be added to the system by commands such as
+:doc:`create\_atoms mol <create_atoms>`, :doc:`fix deposit <fix_deposit>`
+or :doc:`fix pour <fix_pour>`.
+
+As an example, see the examples/deposit/in.deposit.molecule script,
+which deposits molecules onto a substrate.  Initially there are no
+molecules in the system, but they are added later by the :doc:`fix deposit <fix_deposit>` command.  The create\_box command in the
+script uses the bond/types and extra/bond/per/atom keywords to allow
+this.  If the added molecule contained more than 1 special bond
+(allowed by default), an extra/special/per/atom keyword would also
+need to be specified.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+An :doc:`atom\_style <atom_style>` and :doc:`region <region>` must have
+been previously defined to use this command.
+
+Related commands
+""""""""""""""""
+
+:doc:`read\_data <read_data>`, :doc:`create\_atoms <create_atoms>`,
+:doc:`region <region>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst
new file mode 100644
index 0000000000..f2db9aeb3a
--- /dev/null
+++ b/doc/src/delete_atoms.rst
@@ -0,0 +1,175 @@
+.. index:: delete\_atoms
+
+delete\_atoms command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   delete_atoms style args keyword value ...
+
+* style = *group* or *region* or *overlap* or *porosity*
+  
+  .. parsed-literal::
+  
+       *group* args = group-ID
+       *region* args = region-ID
+       *overlap* args = cutoff group1-ID group2-ID
+         cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
+         group1-ID = one atom in pair must be in this group
+         group2-ID = other atom in pair must be in this group
+       *porosity* args = region-ID fraction seed
+         region-ID = region within which to perform deletions
+         fraction = delete this fraction of atoms
+         seed = random number seed (positive integer)
+
+* zero or more keyword/value pairs may be appended
+* keyword = *compress* or *bond* or *mol*
+  
+  .. parsed-literal::
+  
+       *compress* value = *no* or *yes*
+       *bond* value = *no* or *yes*
+       *mol* value = *no* or *yes*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   delete_atoms group edge
+   delete_atoms region sphere compress no
+   delete_atoms overlap 0.3 all all
+   delete_atoms overlap 0.5 solvent colloid
+   delete_atoms porosity cube 0.1 482793 bond yes
+
+Description
+"""""""""""
+
+Delete the specified atoms.  This command can be used to carve out
+voids from a block of material or to delete created atoms that are too
+close to each other (e.g. at a grain boundary).
+
+For style *group*\ , all atoms belonging to the group are deleted.
+
+For style *region*\ , all atoms in the region volume are deleted.
+Additional atoms can be deleted if they are in a molecule for which
+one or more atoms were deleted within the region; see the *mol*
+keyword discussion below.
+
+For style *overlap* pairs of atoms whose distance of separation is
+within the specified cutoff distance are searched for, and one of the
+2 atoms is deleted.  Only pairs where one of the two atoms is in the
+first group specified and the other atom is in the second group are
+considered.  The atom that is in the first group is the one that is
+deleted.
+
+Note that it is OK for the two group IDs to be the same (e.g. group
+*all*\ ), or for some atoms to be members of both groups.  In these
+cases, either atom in the pair may be deleted.  Also note that if
+there are atoms which are members of both groups, the only guarantee
+is that at the end of the deletion operation, enough deletions will
+have occurred that no atom pairs within the cutoff will remain
+(subject to the group restriction).  There is no guarantee that the
+minimum number of atoms will be deleted, or that the same atoms will
+be deleted when running on different numbers of processors.
+
+For style *porosity* a specified *fraction* of atoms are deleted
+within the specified region.  For example, if fraction is 0.1, then
+10% of the atoms will be deleted.  The atoms to delete are chosen
+randomly.  There is no guarantee that the exact fraction of atoms will
+be deleted, or that the same atoms will be deleted when running on
+different numbers of processors.
+
+If the *compress* keyword is set to *yes*\ , then after atoms are
+deleted, then atom IDs are re-assigned so that they run from 1 to the
+number of atoms in the system.  Note that this is not done for
+molecular systems (see the :doc:`atom\_style <atom_style>` command),
+regardless of the *compress* setting, since it would foul up the bond
+connectivity that has already been assigned.  However, the
+:doc:`reset\_ids <reset_ids>` command can be used after this command to
+accomplish the same thing.
+
+Note that the re-assignment of IDs is not really a compression, where
+gaps in atom IDs are removed by decrementing atom IDs that are larger.
+Instead the IDs for all atoms are erased, and new IDs are assigned so
+that the atoms owned by individual processors have consecutive IDs, as
+the :doc:`create\_atoms <create_atoms>` command explains.
+
+A molecular system with fixed bonds, angles, dihedrals, or improper
+interactions, is one where the topology of the interactions is
+typically defined in the data file read by the
+:doc:`read\_data <read_data>` command, and where the interactions
+themselves are defined with the :doc:`bond\_style <bond_style>`,
+:doc:`angle\_style <angle_style>`, etc commands.  If you delete atoms
+from such a system, you must be careful not to end up with bonded
+interactions that are stored by remaining atoms but which include
+deleted atoms.  This will cause LAMMPS to generate a "missing atoms"
+error when the bonded interaction is computed.  The *bond* and *mol*
+keywords offer two ways to do that.
+
+It the *bond* keyword is set to *yes* then any bond or angle or
+dihedral or improper interaction that includes a deleted atom is also
+removed from the lists of such interactions stored by non-deleted
+atoms.  Note that simply deleting interactions due to dangling bonds
+(e.g. at a surface) may result in a inaccurate or invalid model for
+the remaining atoms.
+
+It the *mol* keyword is set to *yes*\ , then for every atom that is
+deleted, all other atoms in the same molecule (with the same molecule
+ID) will also be deleted.  This is not done for atoms with molecule ID
+= 0, since such an ID is assumed to flag isolated atoms that are not
+part of molecules.
+
+.. note::
+
+   The molecule deletion operation in invoked after all individual
+   atoms have been deleted using the rules described above for each
+   style.  This means additional atoms may be deleted that are not in the
+   group or region, that are not required by the overlap cutoff
+   criterion, or that will create a higher fraction of porosity than was
+   requested.
+
+Restrictions
+""""""""""""
+
+
+The *overlap* styles requires inter-processor communication to acquire
+ghost atoms and build a neighbor list.  This means that your system
+must be ready to perform a simulation before using this command (force
+fields setup, atom masses set, etc).  Since a neighbor list is used to
+find overlapping atom pairs, it also means that you must define a
+:doc:`pair style <pair_style>` with the minimum force cutoff distance
+between any pair of atoms types (plus the :doc:`neighbor <neighbor>`
+skin) >= the specified overlap cutoff.
+
+If the :doc:`special\_bonds <special_bonds>` command is used with a
+setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
+appear in the neighbor list, and thus will not be considered for
+deletion by the *overlap* styles.  You probably don't want to be
+deleting one atom in a bonded pair anyway.
+
+The *bond yes* option cannot be used with molecular systems defined
+using molecule template files via the :doc:`molecule <molecule>` and
+:doc:`atom\_style template <atom_style>` commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`create\_atoms <create_atoms>`, :doc:`reset\_ids <reset_ids>`
+
+Default
+"""""""
+
+The option defaults are compress = yes, bond = no, mol = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst
new file mode 100644
index 0000000000..f964d059a6
--- /dev/null
+++ b/doc/src/delete_bonds.rst
@@ -0,0 +1,168 @@
+.. index:: delete\_bonds
+
+delete\_bonds command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   delete_bonds group-ID style arg keyword ...
+
+* group-ID = group ID
+* style = *multi* or *atom* or *bond* or *angle* or *dihedral* or
+          *improper* or *stats*
+  
+  .. parsed-literal::
+  
+       *multi* arg = none
+       *atom* arg = an atom type or range of types (see below)
+       *bond* arg = a bond type or range of types (see below)
+       *angle* arg = an angle type or range of types (see below)
+       *dihedral* arg = a dihedral type or range of types (see below)
+       *improper* arg = an improper type or range of types (see below)
+       *stats* arg = none
+
+* zero or more keywords may be appended
+* keyword = *any* or *undo* or *remove* or *special*
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   delete_bonds frozen multi remove
+   delete_bonds all atom 4 special
+   delete_bonds all bond 0\*3 special
+   delete_bonds all stats
+
+Description
+"""""""""""
+
+Turn off (or on) molecular topology interactions, i.e. bonds, angles,
+dihedrals, impropers.  This command is useful for deleting
+interactions that have been previously turned off by bond-breaking
+potentials.  It is also useful for turning off topology interactions
+between frozen or rigid atoms.  Pairwise interactions can be turned
+off via the :doc:`neigh\_modify exclude <neigh_modify>` command.  The
+:doc:`fix shake <fix_shake>` command also effectively turns off certain
+bond and angle interactions.
+
+For all styles, by default, an interaction is only turned off (or on)
+if all the atoms involved are in the specified group.  See the *any*
+keyword to change the behavior.
+
+Several of the styles (\ *atom*\ , *bond*\ , *angle*\ , *dihedral*\ ,
+*improper*\ ) take a *type* as an argument.  The specified *type* should
+be an integer from 0 to N, where N is the number of relevant types
+(atom types, bond types, etc).  A value of 0 is only relevant for
+style *bond*\ ; see details below.  In all cases, a wildcard asterisk
+can be used in place of or in conjunction with the *type* argument to
+specify a range of types.  This takes the form "\*" or "\*n" or "n\*" or
+"m\*n".  If N = the number of types, then an asterisk with no numeric
+values means all types from 0 to N.  A leading asterisk means all
+types from 0 to n (inclusive).  A trailing asterisk means all types
+from n to N (inclusive).  A middle asterisk means all types from m to
+n (inclusive).  Note that it is fine to include a type of 0 for
+non-bond styles; it will simply be ignored.
+
+For style *multi* all bond, angle, dihedral, and improper interactions
+of any type, involving atoms in the group, are turned off.
+
+Style *atom* is the same as style *multi* except that in addition, one
+or more of the atoms involved in the bond, angle, dihedral, or
+improper interaction must also be of the specified atom type.
+
+For style *bond*\ , only bonds are candidates for turn-off, and the bond
+must also be of the specified type.  Styles *angle*\ , *dihedral*\ , and
+*improper* are treated similarly.
+
+For style *bond*\ , you can set the type to 0 to delete bonds that have
+been previously broken by a bond-breaking potential (which sets the
+bond type to 0 when a bond is broken); e.g. see the :doc:`bond\_style quartic <bond_style>` command.
+
+For style *stats* no interactions are turned off (or on); the status
+of all interactions in the specified group is simply reported.  This
+is useful for diagnostic purposes if bonds have been turned off by a
+bond-breaking potential during a previous run.
+
+The default behavior of the delete\_bonds command is to turn off
+interactions by toggling their type to a negative value, but not to
+permanently remove the interaction.  E.g. a bond\_type of 2 is set to
+-2.  The neighbor list creation routines will not include such an
+interaction in their interaction lists.  The default is also to not
+alter the list of 1-2, 1-3, 1-4 neighbors computed by the
+:doc:`special\_bonds <special_bonds>` command and used to weight pairwise
+force and energy calculations.  This means that pairwise computations
+will proceed as if the bond (or angle, etc) were still turned on.
+
+Several keywords can be appended to the argument list to alter the
+default behaviors.
+
+The *any* keyword changes the requirement that all atoms in the bond
+(angle, etc) must be in the specified group in order to turn-off the
+interaction.  Instead, if any of the atoms in the interaction are in
+the specified group, it will be turned off (or on if the *undo*
+keyword is used).
+
+The *undo* keyword inverts the delete\_bonds command so that the
+specified bonds, angles, etc are turned on if they are currently
+turned off.  This means a negative value is toggled to positive.  For
+example, for style *angle*\ , if *type* is specified as 2, then all
+angles with current type = -2, are reset to type = 2.  Note that the
+:doc:`fix shake <fix_shake>` command also sets bond and angle types
+negative, so this option should not be used on those interactions.
+
+The *remove* keyword is invoked at the end of the delete\_bonds
+operation.  It causes turned-off bonds (angles, etc) to be removed
+from each atom's data structure and then adjusts the global bond
+(angle, etc) counts accordingly.  Removal is a permanent change;
+removed bonds cannot be turned back on via the *undo* keyword.
+Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.
+
+The *special* keyword is invoked at the end of the delete\_bonds
+operation, after (optional) removal.  It re-computes the pairwise 1-2,
+1-3, 1-4 weighting list.  The weighting list computation treats
+turned-off bonds the same as turned-on.  Thus, turned-off bonds must
+be removed if you wish to change the weighting list.
+
+Note that the choice of *remove* and *special* options affects how
+1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that
+have been modified by the delete\_bonds command.
+
+Restrictions
+""""""""""""
+
+
+This command requires inter-processor communication to acquire ghost
+atoms, to coordinate the deleting of bonds, angles, etc between atoms
+shared by multiple processors.  This means that your system must be
+ready to perform a simulation before using this command (force fields
+setup, atom masses set, etc).  Just as would be needed to run
+dynamics, the force field you define should define a cutoff
+(e.g. through a :doc:`pair\_style <pair_style>` command) which is long
+enough for a processor to acquire the ghost atoms its needs to compute
+bond, angle, etc interactions.
+
+If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
+weighting list is not re-computed, this can cause a later :doc:`fix shake <fix_shake>` command to fail due to an atom's bonds being
+inconsistent with the weighting list.  This should only happen if the
+group used in the fix command includes both atoms in the bond, in
+which case you probably should be recomputing the weighting list.
+
+Related commands
+""""""""""""""""
+
+:doc:`neigh\_modify <neigh_modify>` exclude,
+:doc:`special\_bonds <special_bonds>`, :doc:`fix shake <fix_shake>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dielectric.rst b/doc/src/dielectric.rst
new file mode 100644
index 0000000000..96fc861d97
--- /dev/null
+++ b/doc/src/dielectric.rst
@@ -0,0 +1,55 @@
+.. index:: dielectric
+
+dielectric command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dielectric value
+
+* value = dielectric constant
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dielectric 2.0
+
+Description
+"""""""""""
+
+Set the dielectric constant for Coulombic interactions (pairwise and
+long-range) to this value.  The constant is unitless, since it is used
+to reduce the strength of the interactions.  The value is used in the
+denominator of the formulas for Coulombic interactions - e.g. a value
+of 4.0 reduces the Coulombic interactions to 25% of their default
+strength.  See the :doc:`pair\_style <pair_style>` command for more
+details.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style <pair_style>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   dielectric 1.0
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst
new file mode 100644
index 0000000000..52e636dd75
--- /dev/null
+++ b/doc/src/dihedral_charmm.rst
@@ -0,0 +1,197 @@
+.. index:: dihedral\_style charmm
+
+dihedral\_style charmm command
+==============================
+
+dihedral\_style charmm/intel command
+====================================
+
+dihedral\_style charmm/kk command
+=================================
+
+dihedral\_style charmm/omp command
+==================================
+
+dihedral\_style charmmfsw command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style style
+
+* style = *charmm* or *charmmfsw*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style charmm
+   dihedral_style charmmfsw
+   dihedral_coeff  1 0.2 1 180 1.0
+   dihedral_coeff  2 1.8 1   0 1.0
+   dihedral_coeff  1 3.1 2 180 0.5
+
+Description
+"""""""""""
+
+The *charmm* and *charmmfsw* dihedral styles use the potential
+
+.. image:: Eqs/dihedral_charmm.jpg
+   :align: center
+
+See :ref:`(MacKerell) <dihedral-MacKerell>` for a description of the CHARMM
+force field.  This dihedral style can also be used for the AMBER force
+field (see comment on weighting factors below).  See
+:ref:`(Cornell) <dihedral-Cornell>` for a description of the AMBER force
+field.
+
+.. note::
+
+   The newer *charmmfsw* style was released in March 2017.  We
+   recommend it be used instead of the older *charmm* style when running
+   a simulation with the CHARMM force field, either with long-range
+   Coulombics or a Coulombic cutoff, via the :doc:`pair\_style lj/charmmfsw/coul/long <pair_charmm>` and :doc:`pair\_style lj/charmmfsw/coul/charmmfsh <pair_charmm>` commands respectively.
+   Otherwise the older *charmm* style is fine to use.  See the discussion
+   below and more details on the :doc:`pair\_style charmm <pair_charmm>` doc
+   page.
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* K (energy)
+* n (integer >= 0)
+* d (integer value of degrees)
+* weighting factor (1.0, 0.5, or 0.0)
+
+The weighting factor is required to correct for double counting
+pairwise non-bonded Lennard-Jones interactions in cyclic systems or
+when using the CHARMM dihedral style with non-CHARMM force fields.
+With the CHARMM dihedral style, interactions between the 1st and 4th
+atoms in a dihedral are skipped during the normal non-bonded force
+computation and instead evaluated as part of the dihedral using
+special epsilon and sigma values specified with the
+:doc:`pair\_coeff <pair_charmm>` command of pair styles that contain
+"lj/charmm" (e.g. :doc:`pair\_style lj/charmm/coul/long <pair_charmm>`)
+In 6-membered rings, the same 1-4 interaction would be computed twice
+(once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the
+counterclockwise dihedral 1-6-5-4) and thus the weighting factor has
+to be 0.5 in this case.  In 4-membered or 5-membered rings, the 1-4
+dihedral also is counted as a 1-2 or 1-3 interaction when going around
+the ring in the opposite direction and thus the weighting factor is
+0.0, as the 1-2 and 1-3 exclusions take precedence.
+
+Note that this dihedral weighting factor is unrelated to the scaling
+factor specified by the :doc:`special bonds <special_bonds>` command
+which applies to all 1-4 interactions in the system.  For CHARMM force
+fields, the special\_bonds 1-4 interaction scaling factor should be set
+to 0.0. Since the corresponding 1-4 non-bonded interactions are
+computed with the dihedral.  This means that if any of the weighting
+factors defined as dihedral coefficients (4th coeff above) are
+non-zero, then you must use a pair style with "lj/charmm" and set the
+special\_bonds 1-4 scaling factor to 0.0 (which is the
+default). Otherwise 1-4 non-bonded interactions in dihedrals will be
+computed twice.
+
+For simulations using the CHARMM force field with a Coulombic cutoff,
+the difference between the *charmm* and *charmmfsw* styles is in the
+computation of the 1-4 non-bond interactions, though only if the
+distance between the two atoms is within the switching region of the
+pairwise potential defined by the corresponding CHARMM pair style,
+i.e. within the outer cutoff specified for the pair style.  The
+*charmmfsw* style should only be used when using the corresponding
+:doc:`pair\_style lj/charmmfsw/coul/charmmfsw <pair_charmm>` or
+:doc:`pair\_style lj/charmmfsw/coul/long <pair_charmm>` commands.  Use
+the *charmm* style with the older :doc:`pair\_style <pair_charmm>`
+commands that have just "charmm" in their style name.  See the
+discussion on the :doc:`CHARMM pair\_style <pair_charmm>` doc page for
+details.
+
+Note that for AMBER force fields, which use pair styles with "lj/cut",
+the special\_bonds 1-4 scaling factor should be set to the AMBER
+defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
+coeff above) must be set to 0.0. In this case, you can use any pair
+style you wish, since the dihedral does not need any Lennard-Jones
+parameter information and will not compute any 1-4 non-bonded
+interactions.  Likewise the *charmm* or *charmmfsw* styles are
+identical in this case since no 1-4 non-bonded interactions are
+computed.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+When using run\_style :doc:`respa <run_style>`, these dihedral styles
+must be assigned to the same r-RESPA level as *pair* or *outer*\ .
+
+When used in combination with CHARMM pair styles, the 1-4
+:doc:`special\_bonds <special_bonds>` scaling factors must be set to 0.0.
+Otherwise non-bonded contributions for these 1-4 pairs will be
+computed multiple times.
+
+These dihedral styles can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _dihedral-Cornell:
+
+
+
+**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+
+.. _dihedral-MacKerell:
+
+
+
+**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst
new file mode 100644
index 0000000000..f8f6a01bc4
--- /dev/null
+++ b/doc/src/dihedral_class2.rst
@@ -0,0 +1,202 @@
+.. index:: dihedral\_style class2
+
+dihedral\_style class2 command
+==============================
+
+dihedral\_style class2/omp command
+==================================
+
+dihedral\_style class2/kk command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style class2
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style class2
+   dihedral_coeff 1 100 75 100 70 80 60
+   dihedral_coeff \* mbt 3.5945 0.1704 -0.5490 1.5228
+   dihedral_coeff \* ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
+   dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
+   dihedral_coeff \* aat -13.5271 110.2453 105.1270
+   dihedral_coeff \* bb13 0.0 1.0119 1.1010
+
+Description
+"""""""""""
+
+The *class2* dihedral style uses the potential
+
+.. image:: Eqs/dihedral_class2.jpg
+   :align: center
+
+where Ed is the dihedral term, Embt is a middle-bond-torsion term,
+Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
+is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
+
+Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
+bond lengths.
+
+See :ref:`(Sun) <dihedral-Sun>` for a description of the COMPASS class2 force field.
+
+Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
+must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands.
+
+These are the 6 coefficients for the Ed formula:
+
+* K1 (energy)
+* phi1 (degrees)
+* K2 (energy)
+* phi2 (degrees)
+* K3 (energy)
+* phi3 (degrees)
+
+For the Embt formula, each line in a
+:doc:`dihedral\_coeff <dihedral_coeff>` command in the input script lists
+5 coefficients, the first of which is "mbt" to indicate they are
+MiddleBondTorsion coefficients.  In a data file, these coefficients
+should be listed under a "MiddleBondTorsion Coeffs" heading and you
+must leave out the "mbt", i.e. only list 4 coefficients after the
+dihedral type.
+
+* mbt
+* A1 (energy/distance)
+* A2 (energy/distance)
+* A3 (energy/distance)
+* r2 (distance)
+
+For the Eebt formula, each line in a
+:doc:`dihedral\_coeff <dihedral_coeff>` command in the input script lists
+9 coefficients, the first of which is "ebt" to indicate they are
+EndBondTorsion coefficients.  In a data file, these coefficients
+should be listed under a "EndBondTorsion Coeffs" heading and you must
+leave out the "ebt", i.e. only list 8 coefficients after the dihedral
+type.
+
+* ebt
+* B1 (energy/distance)
+* B2 (energy/distance)
+* B3 (energy/distance)
+* C1 (energy/distance)
+* C2 (energy/distance)
+* C3 (energy/distance)
+* r1 (distance)
+* r3 (distance)
+
+For the Eat formula, each line in a
+:doc:`dihedral\_coeff <dihedral_coeff>` command in the input script lists
+9 coefficients, the first of which is "at" to indicate they are
+AngleTorsion coefficients.  In a data file, these coefficients should
+be listed under a "AngleTorsion Coeffs" heading and you must leave out
+the "at", i.e. only list 8 coefficients after the dihedral type.
+
+* at
+* D1 (energy/radian)
+* D2 (energy/radian)
+* D3 (energy/radian)
+* E1 (energy/radian)
+* E2 (energy/radian)
+* E3 (energy/radian)
+* theta1 (degrees)
+* theta2 (degrees)
+
+Theta1 and theta2 are specified in degrees, but LAMMPS converts them
+to radians internally; hence the units of D and E are in
+energy/radian.
+
+For the Eaat formula, each line in a
+:doc:`dihedral\_coeff <dihedral_coeff>` command in the input script lists
+4 coefficients, the first of which is "aat" to indicate they are
+AngleAngleTorsion coefficients.  In a data file, these coefficients
+should be listed under a "AngleAngleTorsion Coeffs" heading and you
+must leave out the "aat", i.e. only list 3 coefficients after the
+dihedral type.
+
+* aat
+* M (energy/radian\^2)
+* theta1 (degrees)
+* theta2 (degrees)
+
+Theta1 and theta2 are specified in degrees, but LAMMPS converts them
+to radians internally; hence the units of M are in energy/radian\^2.
+
+For the Ebb13 formula, each line in a
+:doc:`dihedral\_coeff <dihedral_coeff>` command in the input script lists
+4 coefficients, the first of which is "bb13" to indicate they are
+BondBond13 coefficients.  In a data file, these coefficients should be
+listed under a "BondBond13 Coeffs" heading and you must leave out the
+"bb13", i.e. only list 3 coefficients after the dihedral type.
+
+* bb13
+* N (energy/distance\^2)
+* r1 (distance)
+* r3 (distance)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+CLASS2 package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _dihedral-Sun:
+
+
+
+**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst
new file mode 100644
index 0000000000..a2cddfa6e9
--- /dev/null
+++ b/doc/src/dihedral_coeff.rst
@@ -0,0 +1,119 @@
+.. index:: dihedral\_coeff
+
+dihedral\_coeff command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_coeff N args
+
+* N = dihedral type (see asterisk form below)
+* args = coefficients for one or more dihedral types
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_coeff 1 80.0 1 3
+   dihedral_coeff \* 80.0 1 3 0.5
+   dihedral_coeff 2\* 80.0 1 3 0.5
+
+Description
+"""""""""""
+
+Specify the dihedral force field coefficients for one or more dihedral types.
+The number and meaning of the coefficients depends on the dihedral style.
+Dihedral coefficients can also be set in the data file read by the
+:doc:`read\_data <read_data>` command or in a restart file.
+
+N can be specified in one of two ways.  An explicit numeric value can
+be used, as in the 1st example above.  Or a wild-card asterisk can be
+used to set the coefficients for multiple dihedral types.  This takes the
+form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of dihedral types,
+then an asterisk with no numeric values means all types from 1 to N.  A
+leading asterisk means all types from 1 to n (inclusive).  A trailing
+asterisk means all types from n to N (inclusive).  A middle asterisk
+means all types from m to n (inclusive).
+
+Note that using a dihedral\_coeff command can override a previous setting
+for the same dihedral type.  For example, these commands set the coeffs
+for all dihedral types, then overwrite the coeffs for just dihedral type 2:
+
+
+.. parsed-literal::
+
+   dihedral_coeff \* 80.0 1 3
+   dihedral_coeff 2 200.0 1 3
+
+A line in a data file that specifies dihedral coefficients uses the exact
+same format as the arguments of the dihedral\_coeff command in an input
+script, except that wild-card asterisks should not be used since
+coefficients for all N types must be listed in the file.  For example,
+under the "Dihedral Coeffs" section of a data file, the line that
+corresponds to the 1st example above would be listed as
+
+
+.. parsed-literal::
+
+   1 80.0 1 3
+
+The :doc:`dihedral\_style class2 <dihedral_class2>` is an exception to
+this rule, in that an additional argument is used in the input script
+to allow specification of the cross-term coefficients.  See its doc
+page for details.
+
+.. note::
+
+   When comparing the formulas and coefficients for various LAMMPS
+   dihedral styles with dihedral equations defined by other force fields,
+   note that some force field implementations divide/multiply the energy
+   prefactor *K* by the multiple number of torsions that contain the J-K
+   bond in an I-J-K-L torsion.  LAMMPS does not do this, i.e. the listed
+   dihedral equation applies to each individual dihedral.  Thus you need
+   to define *K* appropriately to account for this difference if
+   necessary.
+
+
+----------
+
+
+The list of all dihedral styles defined in LAMMPS is given on the
+:doc:`dihedral\_style <dihedral_style>` doc page.  They are also listed
+in more compact form on the :ref:`Commands dihedral <dihedral>` doc page.
+
+On either of those pages, click on the style to display the formula it
+computes and its coefficients as specified by the associated
+dihedral\_coeff command.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command must come after the simulation box is defined by a
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
+:doc:`create\_box <create_box>` command.
+
+A dihedral style must be defined before any dihedral coefficients are
+set, either in the input script or in a data file.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_style <dihedral_style>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst
new file mode 100644
index 0000000000..7a2f2bf2db
--- /dev/null
+++ b/doc/src/dihedral_cosine_shift_exp.rst
@@ -0,0 +1,102 @@
+.. index:: dihedral\_style cosine/shift/exp
+
+dihedral\_style cosine/shift/exp command
+========================================
+
+dihedral\_style cosine/shift/exp/omp command
+============================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style cosine/shift/exp
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style cosine/shift/exp
+   dihedral_coeff 1 10.0 45.0 2.0
+
+Description
+"""""""""""
+
+The *cosine/shift/exp* dihedral style uses the potential
+
+.. image:: Eqs/dihedral_cosine_shift_exp.jpg
+   :align: center
+
+where Umin, theta, and a are defined for each dihedral type.
+
+The potential is bounded between [-Umin:0] and the minimum is located
+at the angle theta0. The a parameter can be both positive or negative
+and is used to control the spring constant at the equilibrium.
+
+The spring constant is given by k=a exp(a) Umin/ [2 (Exp(a)-1)].
+For a>3 k/Umin = a/2 to better than 5% relative error. For negative
+values of the a parameter, the spring constant is essentially zero,
+and anharmonic terms takes over. The potential is furthermore well
+behaved in the limit a->0, where it has been implemented to linear
+order in a for a < 0.001.
+
+The following coefficients must be defined for each dihedral type via
+the :doc:`dihedral\_coeff <dihedral_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* umin (energy)
+* theta (angle)
+* A (real number)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`,
+:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst
new file mode 100644
index 0000000000..83f2349cd5
--- /dev/null
+++ b/doc/src/dihedral_fourier.rst
@@ -0,0 +1,95 @@
+.. index:: dihedral\_style fourier
+
+dihedral\_style fourier command
+===============================
+
+dihedral\_style fourier/intel command
+=====================================
+
+dihedral\_style fourier/omp command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style fourier
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style fourier
+   dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
+
+Description
+"""""""""""
+
+The *fourier* dihedral style uses the potential:
+
+.. image:: Eqs/dihedral_fourier.jpg
+   :align: center
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* m (integer >=1)
+* K1 (energy)
+* n1 (integer >= 0)
+* d1 (degrees)
+* [...]
+* Km (energy)
+* nm (integer >= 0)
+* dm (degrees)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst
new file mode 100644
index 0000000000..bdcfbf38ae
--- /dev/null
+++ b/doc/src/dihedral_harmonic.rst
@@ -0,0 +1,107 @@
+.. index:: dihedral\_style harmonic
+
+dihedral\_style harmonic command
+================================
+
+dihedral\_style harmonic/intel command
+======================================
+
+dihedral\_style harmonic/kk command
+===================================
+
+dihedral\_style harmonic/omp command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style harmonic
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style harmonic
+   dihedral_coeff 1 80.0 1 2
+
+Description
+"""""""""""
+
+The *harmonic* dihedral style uses the potential
+
+.. image:: Eqs/dihedral_harmonic.jpg
+   :align: center
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* K (energy)
+* d (+1 or -1)
+* n (integer >= 0)
+
+.. note::
+
+   Here are important points to take note of when defining LAMMPS
+   dihedral coefficients for the harmonic style, so that they are
+   compatible with how harmonic dihedrals are defined by other force
+   fields:
+
+* The LAMMPS convention is that the trans position = 180 degrees, while
+  in some force fields trans = 0 degrees.
+* Some force fields reverse the sign convention on *d*\ .
+* Some force fields let *n* be positive or negative which corresponds to
+  *d* = 1 or -1 for the harmonic style.
+
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst
new file mode 100644
index 0000000000..d348bf03de
--- /dev/null
+++ b/doc/src/dihedral_helix.rst
@@ -0,0 +1,105 @@
+.. index:: dihedral\_style helix
+
+dihedral\_style helix command
+=============================
+
+dihedral\_style helix/omp command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style helix
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style helix
+   dihedral_coeff 1 80.0 100.0 40.0
+
+Description
+"""""""""""
+
+The *helix* dihedral style uses the potential
+
+.. image:: Eqs/dihedral_helix.jpg
+   :align: center
+
+This coarse-grain dihedral potential is described in :ref:`(Guo) <Guo>`.
+For dihedral angles in the helical region, the energy function is
+represented by a standard potential consisting of three minima, one
+corresponding to the trans (t) state and the other to gauche states
+(g+ and g-).  The paper describes how the A,B,C parameters are chosen
+so as to balance secondary (largely driven by local interactions) and
+tertiary structure (driven by long-range interactions).
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* A (energy)
+* B (energy)
+* C (energy)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Guo:
+
+
+
+**(Guo)** Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst
new file mode 100644
index 0000000000..c878cbb9ca
--- /dev/null
+++ b/doc/src/dihedral_hybrid.rst
@@ -0,0 +1,111 @@
+.. index:: dihedral\_style hybrid
+
+dihedral\_style hybrid command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style hybrid style1 style2 ...
+
+* style1,style2 = list of one or more dihedral styles
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style hybrid harmonic helix
+   dihedral_coeff 1 harmonic 6.0 1 3
+   dihedral_coeff 2\* helix 10 10 10
+
+Description
+"""""""""""
+
+The *hybrid* style enables the use of multiple dihedral styles in one
+simulation.  An dihedral style is assigned to each dihedral type.  For
+example, dihedrals in a polymer flow (of dihedral type 1) could be
+computed with a *harmonic* potential and dihedrals in the wall
+boundary (of dihedral type 2) could be computed with a *helix*
+potential.  The assignment of dihedral type to style is made via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command or in the data file.
+
+In the dihedral\_coeff commands, the name of a dihedral style must be
+added after the dihedral type, with the remaining coefficients being
+those appropriate to that style.  In the example above, the 2
+dihedral\_coeff commands set dihedrals of dihedral type 1 to be
+computed with a *harmonic* potential with coefficients 6.0, 1, 3 for
+K, d, n.  All other dihedral types (2-N) are computed with a *helix*
+potential with coefficients 10, 10, 10 for A, B, C.
+
+If dihedral coefficients are specified in the data file read via the
+:doc:`read\_data <read_data>` command, then the same rule applies.
+E.g. "harmonic" or "helix", must be added after the dihedral type, for
+each line in the "Dihedral Coeffs" section, e.g.
+
+
+.. parsed-literal::
+
+   Dihedral Coeffs
+
+   1 harmonic 6.0 1 3
+   2 helix 10 10 10
+   ...
+
+If *class2* is one of the dihedral hybrid styles, the same rule holds
+for specifying additional AngleTorsion (and EndBondTorsion, etc)
+coefficients either via the input script or in the data file.
+I.e. *class2* must be added to each line after the dihedral type.  For
+lines in the AngleTorsion (or EndBondTorsion, etc) section of the data
+file for dihedral types that are not *class2*\ , you must use an
+dihedral style of *skip* as a placeholder, e.g.
+
+
+.. parsed-literal::
+
+   AngleTorsion Coeffs
+
+   1 skip
+   2 class2 1.0 1.0 1.0 3.0 3.0 3.0 30.0 50.0
+   ...
+
+Note that it is not necessary to use the dihedral style *skip* in the
+input script, since AngleTorsion (or EndBondTorsion, etc) coefficients
+need not be specified at all for dihedral types that are not *class2*\ .
+
+A dihedral style of *none* with no additional coefficients can be used
+in place of a dihedral style, either in a input script dihedral\_coeff
+command or in the data file, if you desire to turn off interactions
+for specific dihedral types.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Unlike other dihedral styles, the hybrid dihedral style does not store
+dihedral coefficient info for individual sub-styles in a :doc:`binary restart files <restart>`.  Thus when restarting a simulation from a
+restart file, you need to re-specify dihedral\_coeff commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst
new file mode 100644
index 0000000000..bd66014bd7
--- /dev/null
+++ b/doc/src/dihedral_multi_harmonic.rst
@@ -0,0 +1,89 @@
+.. index:: dihedral\_style multi/harmonic
+
+dihedral\_style multi/harmonic command
+======================================
+
+dihedral\_style multi/harmonic/omp command
+==========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style multi/harmonic
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style multi/harmonic
+   dihedral_coeff 1 20 20 20 20 20
+
+Description
+"""""""""""
+
+The *multi/harmonic* dihedral style uses the potential
+
+.. image:: Eqs/dihedral_multi_harmonic.jpg
+   :align: center
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* A1 (energy)
+* A2 (energy)
+* A3 (energy)
+* A4 (energy)
+* A5 (energy)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst
new file mode 100644
index 0000000000..51ddd6a109
--- /dev/null
+++ b/doc/src/dihedral_nharmonic.rst
@@ -0,0 +1,89 @@
+.. index:: dihedral\_style nharmonic
+
+dihedral\_style nharmonic command
+=================================
+
+dihedral\_style nharmonic/omp command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style nharmonic
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style nharmonic
+   dihedral_coeff \* 3 10.0 20.0 30.0
+
+Description
+"""""""""""
+
+The *nharmonic* dihedral style uses the potential:
+
+.. image:: Eqs/dihedral_nharmonic.jpg
+   :align: center
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* n (integer >=1)
+* A1 (energy)
+* A2 (energy)
+* ...
+* An (energy)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_none.rst b/doc/src/dihedral_none.rst
new file mode 100644
index 0000000000..ebae5c32d6
--- /dev/null
+++ b/doc/src/dihedral_none.rst
@@ -0,0 +1,46 @@
+.. index:: dihedral\_style none
+
+dihedral\_style none command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style none
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style none
+
+Description
+"""""""""""
+
+Using a dihedral style of none means dihedral forces and energies are
+not computed, even if quadruplets of dihedral atoms were listed in the
+data file read by the :doc:`read\_data <read_data>` command.
+
+See the :doc:`dihedral\_style zero <dihedral_zero>` command for a way to
+calculate dihedral statistics, but compute no dihedral interactions.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_style zero <dihedral_zero>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst
new file mode 100644
index 0000000000..4cd21423a2
--- /dev/null
+++ b/doc/src/dihedral_opls.rst
@@ -0,0 +1,111 @@
+.. index:: dihedral\_style opls
+
+dihedral\_style opls command
+============================
+
+dihedral\_style opls/intel command
+==================================
+
+dihedral\_style opls/kk command
+===============================
+
+dihedral\_style opls/omp command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style opls
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style opls
+   dihedral_coeff 1 1.740 -0.157 0.279 0.00   # CT-CT-CT-CT
+   dihedral_coeff 2 0.000 0.000 0.366 0.000   # CT-CT-CT-HC
+   dihedral_coeff 3 0.000 0.000 0.318 0.000   # HC-CT-CT-HC
+
+Description
+"""""""""""
+
+The *opls* dihedral style uses the potential
+
+.. image:: Eqs/dihedral_opls.jpg
+   :align: center
+
+Note that the usual 1/2 factor is not included in the K values.
+
+This dihedral potential is used in the OPLS force field and is
+described in :ref:`(Watkins) <Watkins>`.
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* K1 (energy)
+* K2 (energy)
+* K3 (energy)
+* K4 (energy)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Watkins:
+
+
+
+**(Watkins)** Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst
new file mode 100644
index 0000000000..d145d596ba
--- /dev/null
+++ b/doc/src/dihedral_quadratic.rst
@@ -0,0 +1,90 @@
+.. index:: dihedral\_style quadratic
+
+dihedral\_style quadratic command
+=================================
+
+dihedral\_style quadratic/omp command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style quadratic
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style quadratic
+   dihedral_coeff 100.0 80.0
+
+Description
+"""""""""""
+
+The *quadratic* dihedral style uses the potential:
+
+.. image:: Eqs/dihedral_quadratic.jpg
+   :align: center
+
+This dihedral potential can be used to keep a dihedral in a predefined
+value (cis=zero, right-hand convention is used).
+
+The following coefficients must be defined for each dihedral type via
+the :doc:`dihedral\_coeff <dihedral_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* K (energy/radian\^2)
+* phi0 (degrees)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst
new file mode 100644
index 0000000000..4c59e7297f
--- /dev/null
+++ b/doc/src/dihedral_spherical.rst
@@ -0,0 +1,104 @@
+.. index:: dihedral\_style spherical
+
+dihedral\_style spherical command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style spherical
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_coeff 1 1  286.1  1 124  1    1 90.0 0    1 90.0 0
+   dihedral_coeff 1 3  69.3   1 93.9 1    1 90   0    1 90   0  &
+                       49.1   0 0.00 0    1 74.4 1    0 0.00 0  &
+                       25.2   0 0.00 0    0 0.00 0    1 48.1 1
+
+Description
+"""""""""""
+
+The *spherical* dihedral style uses the potential:
+
+.. image:: JPG/dihedral_spherical_angles.jpg
+   :align: center
+
+.. image:: Eqs/dihedral_spherical.jpg
+   :align: center
+
+For this dihedral style, the energy can be any function that combines the
+4-body dihedral-angle (phi) and the two 3-body bond-angles (theta1, theta2).
+For this reason, there is usually no need to define 3-body "angle" forces
+separately for the atoms participating in these interactions.
+It is probably more efficient to incorporate 3-body angle forces into
+the dihedral interaction even if it requires adding additional terms to
+the expansion (as was done in the second example).  A careful choice of
+parameters can prevent singularities that occur with traditional
+force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
+
+The last example above corresponds to an interaction with a single energy
+minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains
+numerically stable at all angles (phi, theta1, theta2). In this example,
+the coefficients 49.1, and 25.2 can be physically interpreted as the
+harmonic spring constants for theta1 and theta2 around their minima.
+The coefficient 69.3 is the harmonic spring constant for phi after
+division by sin(74.4)\*sin(48.1) (the minima positions for theta1 and theta2).
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command as in the example above, or in
+the Dihedral Coeffs section of a data file read by the
+:doc:`read\_data <read_data>` command:
+
+* n (integer >= 1)
+* C1 (energy)
+* K1 (typically an integer)
+* a1 (degrees)
+* u1 (typically 0.0 or 1.0)
+* L1 (typically an integer)
+* b1 (degrees, typically 0.0 or 90.0)
+* v1 (typically 0.0 or 1.0)
+* M1 (typically an integer)
+* c1 (degrees, typically 0.0 or 90.0)
+* w1 (typically 0.0 or 1.0)
+* [...]
+* Cn (energy)
+* Kn (typically an integer)
+* an (degrees)
+* un (typically 0.0 or 1.0)
+* Ln (typically an integer)
+* bn (degrees, typically 0.0 or 90.0)
+* vn (typically 0.0 or 1.0)
+* Mn (typically an integer)
+* cn (degrees, typically 0.0 or 90.0)
+* wn (typically 0.0 or 1.0)
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+USER\_MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst
new file mode 100644
index 0000000000..553cfbde7c
--- /dev/null
+++ b/doc/src/dihedral_style.rst
@@ -0,0 +1,150 @@
+.. index:: dihedral\_style
+
+dihedral\_style command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style style
+
+* style = *none* or *hybrid* or *charmm* or *class2* or *harmonic* or *helix* or         *multi/harmonic* or *opls*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style harmonic
+   dihedral_style multi/harmonic
+   dihedral_style hybrid harmonic charmm
+
+Description
+"""""""""""
+
+Set the formula(s) LAMMPS uses to compute dihedral interactions
+between quadruplets of atoms, which remain in force for the duration
+of the simulation.  The list of dihedral quadruplets is read in by a
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` command
+from a data or restart file.
+
+Hybrid models where dihedrals are computed using different dihedral
+potentials can be setup using the *hybrid* dihedral style.
+
+The coefficients associated with a dihedral style can be specified in
+a data or restart file or via the :doc:`dihedral\_coeff <dihedral_coeff>`
+command.
+
+All dihedral potentials store their coefficient data in binary restart
+files which means dihedral\_style and
+:doc:`dihedral\_coeff <dihedral_coeff>` commands do not need to be
+re-specified in an input script that restarts a simulation.  See the
+:doc:`read\_restart <read_restart>` command for details on how to do
+this.  The one exception is that dihedral\_style *hybrid* only stores
+the list of sub-styles in the restart file; dihedral coefficients need
+to be re-specified.
+
+.. note::
+
+   When both a dihedral and pair style is defined, the
+   :doc:`special\_bonds <special_bonds>` command often needs to be used to
+   turn off (or weight) the pairwise interaction that would otherwise
+   exist between 4 bonded atoms.
+
+In the formulas listed for each dihedral style, *phi* is the torsional
+angle defined by the quadruplet of atoms.  This angle has a sign
+convention as shown in this diagram:
+
+.. image:: JPG/dihedral_sign.jpg
+   :align: center
+
+where the I,J,K,L ordering of the 4 atoms that define the dihedral
+is from left to right.
+
+This sign convention effects several of the dihedral styles listed
+below (e.g. charmm, helix) in the sense that the energy formula
+depends on the sign of phi, which may be reflected in the value of the
+coefficients you specify.
+
+.. note::
+
+   When comparing the formulas and coefficients for various LAMMPS
+   dihedral styles with dihedral equations defined by other force fields,
+   note that some force field implementations divide/multiply the energy
+   prefactor *K* by the multiple number of torsions that contain the J-K
+   bond in an I-J-K-L torsion.  LAMMPS does not do this, i.e. the listed
+   dihedral equation applies to each individual dihedral.  Thus you need
+   to define *K* appropriately via the
+   :doc:`dihedral\_coeff <dihedral_coeff>` command to account for this
+   difference if necessary.
+
+
+----------
+
+
+Here is an alphabetic list of dihedral styles defined in LAMMPS.  Click on
+the style to display the formula it computes and coefficients
+specified by the associated :doc:`dihedral\_coeff <dihedral_coeff>` command.
+
+Click on the style to display the formula it computes, any additional
+arguments specified in the dihedral\_style command, and coefficients
+specified by the associated :doc:`dihedral\_coeff <dihedral_coeff>`
+command.
+
+There are also additional accelerated pair styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the :ref:`Commands dihedral <dihedral>` doc page are followed by one or
+more of (g,i,k,o,t) to indicate which accelerated styles exist.
+
+* :doc:`none <dihedral_none>` - turn off dihedral interactions
+* :doc:`zero <dihedral_zero>` - topology but no interactions
+* :doc:`hybrid <dihedral_hybrid>` - define multiple styles of dihedral interactions
+
+* :doc:`charmm <dihedral_charmm>` - CHARMM dihedral
+* :doc:`charmmfsw <dihedral_charmm>` - CHARMM dihedral with force switching
+* :doc:`class2 <dihedral_class2>` - COMPASS (class 2) dihedral
+* :doc:`cosine/shift/exp <dihedral_cosine_shift_exp>` - dihedral with exponential in spring constant
+* :doc:`fourier <dihedral_fourier>` - dihedral with multiple cosine terms
+* :doc:`harmonic <dihedral_harmonic>` - harmonic dihedral
+* :doc:`helix <dihedral_helix>` - helix dihedral
+* :doc:`multi/harmonic <dihedral_multi_harmonic>` - dihedral with 5 harmonic terms
+* :doc:`nharmonic <dihedral_nharmonic>` - same as multi-harmonic with N terms
+* :doc:`opls <dihedral_opls>` - OPLS dihedral
+* :doc:`quadratic <dihedral_quadratic>` - dihedral with quadratic term in angle
+* :doc:`spherical <dihedral_spherical>` - dihedral which includes angle terms to avoid singularities
+* :doc:`table <dihedral_table>` - tabulated dihedral
+* :doc:`table/cut <dihedral_table_cut>` - tabulated dihedral with analytic cutoff
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Dihedral styles can only be set for atom styles that allow dihedrals
+to be defined.
+
+Most dihedral styles are part of the MOLECULE package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  The doc pages for
+individual dihedral potentials tell if it is part of a package.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+Default
+"""""""
+
+dihedral\_style none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst
new file mode 100644
index 0000000000..03c05f7893
--- /dev/null
+++ b/doc/src/dihedral_table.rst
@@ -0,0 +1,233 @@
+.. index:: dihedral\_style table
+
+dihedral\_style table command
+=============================
+
+dihedral\_style table/omp command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style table style Ntable
+
+* style = *linear* or *spline* = method of interpolation
+* Ntable = size of the internal lookup table
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style table spline 400
+   dihedral_style table linear 1000
+   dihedral_coeff 1 file.table DIH_TABLE1
+   dihedral_coeff 2 file.table DIH_TABLE2
+
+Description
+"""""""""""
+
+The *table* dihedral style creates interpolation tables of length
+*Ntable* from dihedral potential and derivative values listed in a
+file(s) as a function of the dihedral angle "phi".  The files are read
+by the :doc:`dihedral\_coeff <dihedral_coeff>` command.
+
+The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and derivative values at each of
+*Ntable* dihedral angles. During a simulation, these tables are used
+to interpolate energy and force values on individual atoms as
+needed. The interpolation is done in one of 2 styles: *linear* or
+*spline*\ .
+
+For the *linear* style, the dihedral angle (phi) is used to find 2
+surrounding table values from which an energy or its derivative is
+computed by linear interpolation.
+
+For the *spline* style, cubic spline coefficients are computed and
+stored at each of the *Ntable* evenly-spaced values in the
+interpolated table.  For a given dihedral angle (phi), the appropriate
+coefficients are chosen from this list, and a cubic polynomial is used
+to compute the energy and the derivative at this angle.
+
+The following coefficients must be defined for each dihedral type via
+the :doc:`dihedral\_coeff <dihedral_coeff>` command as in the example
+above.
+
+* filename
+* keyword
+
+The filename specifies a file containing tabulated energy and
+derivative values. The keyword specifies a section of the file.  The
+format of this file is described below.
+
+
+----------
+
+
+The format of a tabulated file is as follows (without the
+parenthesized comments).  It can begin with one or more comment
+or blank lines.
+
+
+.. parsed-literal::
+
+   # Table of the potential and its negative derivative
+
+   DIH_TABLE1                   (keyword is the first text on line)
+   N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
+                                (blank line)
+   1 -168.0 -1.40351172223 0.0423346818422
+   2 -156.0 -1.70447981034 0.00811786522531
+   3 -144.0 -1.62956100432 -0.0184129719987
+   ...
+   30 180.0 -0.707106781187 0.0719306095245
+
+   # Example 2: table of the potential. Forces omitted
+
+   DIH_TABLE2
+   N 30 NOF CHECKU testU.dat CHECKF testF.dat
+
+   1 -168.0 -1.40351172223
+   2 -156.0 -1.70447981034
+   3 -144.0 -1.62956100432
+   ...
+   30 180.0 -0.707106781187
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections. The first line begins with a keyword which
+identifies the section. The line can contain additional text, but the
+initial text must match the argument specified in the
+:doc:`dihedral\_coeff <dihedral_coeff>` command. The next line lists (in
+any order) one or more parameters for the table. Each parameter is a
+keyword followed by one or more numeric values.
+
+Following a blank line, the next N lines list the tabulated values. On
+each line, the 1st value is the index from 1 to N, the 2nd value is
+the angle value, the 3rd value is the energy (in energy units), and
+the 4th is -dE/d(phi) also in energy units). The 3rd term is the
+energy of the 4-atom configuration for the specified angle.  The 4th
+term (when present) is the negative derivative of the energy with
+respect to the angle (in degrees, or radians depending on whether the
+user selected DEGREES or RADIANS).  Thus the units of the last term
+are still energy, not force. The dihedral angle values must increase
+from one line to the next.
+
+Dihedral table splines are cyclic.  There is no discontinuity at 180
+degrees (or at any other angle).  Although in the examples above, the
+angles range from -180 to 180 degrees, in general, the first angle in
+the list can have any value (positive, zero, or negative).  However
+the *range* of angles represented in the table must be *strictly* less
+than 360 degrees (2pi radians) to avoid angle overlap.  (You may not
+supply entries in the table for both 180 and -180, for example.)  If
+the user's table covers only a narrow range of dihedral angles,
+strange numerical behavior can occur in the large remaining gap.
+
+**Parameters:**
+
+The parameter "N" is required and its value is the number of table
+entries that follow. Note that this may be different than the N
+specified in the :doc:`dihedral\_style table <dihedral_style>` command.
+Let *Ntable* is the number of table entries requested dihedral\_style
+command, and let *Nfile* be the parameter following "N" in the
+tabulated file ("30" in the sparse example above).  What LAMMPS does
+is a preliminary interpolation by creating splines using the *Nfile*
+tabulated values as nodal points.  It uses these to interpolate as
+needed to generate energy and derivative values at *Ntable* different
+points (which are evenly spaced over a 360 degree range, even if the
+angles in the file are not).  The resulting tables of length *Ntable*
+are then used as described above, when computing energy and force for
+individual dihedral angles and their atoms.  This means that if you
+want the interpolation tables of length *Ntable* to match exactly what
+is in the tabulated file (with effectively nopreliminary
+interpolation), you should set *Ntable* = *Nfile*\ .  To insure the
+nodal points in the user's file are aligned with the interpolated
+table entries, the angles in the table should be integer multiples of
+360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your
+choice of angle units).
+
+The optional "NOF" keyword allows the user to omit the forces
+(negative energy derivatives) from the table file (normally located in
+the 4th column).  In their place, forces will be calculated
+automatically by differentiating the potential energy function
+indicated by the 3rd column of the table (using either linear or
+spline interpolation).
+
+The optional "DEGREES" keyword allows the user to specify angles in
+degrees instead of radians (default).
+
+The optional "RADIANS" keyword allows the user to specify angles in
+radians instead of degrees.  (Note: This changes the way the forces
+are scaled in the 4th column of the data file.)
+
+The optional "CHECKU" keyword is followed by a filename.  This allows
+the user to save all of the *Ntable* different entries in the
+interpolated energy table to a file to make sure that the interpolated
+function agrees with the user's expectations.  (Note: You can
+temporarily increase the *Ntable* parameter to a high value for this
+purpose.  "\ *Ntable*\ " is explained above.)
+
+The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
+It is followed by a filename, and it allows the user to check the
+interpolated force table.  This option is available even if the user
+selected the "NOF" option.
+
+Note that one file can contain many sections, each with a tabulated
+potential. LAMMPS reads the file section by section until it finds one
+that matches the specified keyword.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart info:**
+
+This dihedral style writes the settings for the "dihedral\_style table"
+command to :doc:`binary restart files <restart>`, so a dihedral\_style
+command does not need to specified in an input script that reads a
+restart file.  However, the coefficient information is not stored in
+the restart file, since it is tabulated in the potential files.  Thus,
+dihedral\_coeff commands do need to be specified in the restart input
+script.
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst
new file mode 100644
index 0000000000..78b9346e61
--- /dev/null
+++ b/doc/src/dihedral_table_cut.rst
@@ -0,0 +1,236 @@
+.. index:: dihedral\_style table/cut
+
+dihedral\_style table/cut command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style table/cut style Ntable
+
+* style = *linear* or *spline* = method of interpolation
+* Ntable = size of the internal lookup table
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style table/cut spline 400
+   dihedral_style table/cut linear 1000
+   dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
+   dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
+
+Description
+"""""""""""
+
+The *table/cut* dihedral style creates interpolation tables of length
+*Ntable* from dihedral potential and derivative values listed in a
+file(s) as a function of the dihedral angle "phi".  In addition, an
+analytic cutoff that is quadratic in the bond-angle (theta) is applied
+in order to regularize the dihedral interaction.  The dihedral table
+files are read by the :doc:`dihedral\_coeff <dihedral_coeff>` command.
+
+The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and derivative values at each of
+*Ntable* dihedral angles. During a simulation, these tables are used
+to interpolate energy and force values on individual atoms as
+needed. The interpolation is done in one of 2 styles: *linear* or
+*spline*\ .
+
+For the *linear* style, the dihedral angle (phi) is used to find 2
+surrounding table values from which an energy or its derivative is
+computed by linear interpolation.
+
+For the *spline* style, cubic spline coefficients are computed and
+stored at each of the *Ntable* evenly-spaced values in the
+interpolated table.  For a given dihedral angle (phi), the appropriate
+coefficients are chosen from this list, and a cubic polynomial is used
+to compute the energy and the derivative at this angle.
+
+The following coefficients must be defined for each dihedral type via
+the :doc:`dihedral\_coeff <dihedral_coeff>` command as in the example
+above.
+
+* style (aat)
+* cutoff prefactor
+* cutoff angle1
+* cutoff angle2
+* filename
+* keyword
+
+The cutoff dihedral style uses a tabulated dihedral interaction with a
+cutoff function:
+
+.. image:: Eqs/dihedral_table_cut.jpg
+   :align: center
+
+The cutoff specifies an prefactor to the cutoff function.  While this value
+would ordinarily equal 1 there may be situations where the value should change.
+
+The cutoff angle1 specifies the angle (in degrees) below which the dihedral
+interaction is unmodified, i.e. the cutoff function is 1.
+
+The cutoff function is applied between angle1 and angle2, which is the angle at
+which the cutoff function drops to zero.  The value of zero effectively "turns
+off" the dihedral interaction.
+
+The filename specifies a file containing tabulated energy and
+derivative values. The keyword specifies a section of the file.  The
+format of this file is described below.
+
+
+----------
+
+
+The format of a tabulated file is as follows (without the
+parenthesized comments).  It can begin with one or more comment
+or blank lines.
+
+
+.. parsed-literal::
+
+   # Table of the potential and its negative derivative
+
+   DIH_TABLE1                   (keyword is the first text on line)
+   N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
+                                (blank line)
+   1 -168.0 -1.40351172223 0.0423346818422
+   2 -156.0 -1.70447981034 0.00811786522531
+   3 -144.0 -1.62956100432 -0.0184129719987
+   ...
+   30 180.0 -0.707106781187 0.0719306095245
+
+   # Example 2: table of the potential. Forces omitted
+
+   DIH_TABLE2
+   N 30 NOF CHECKU testU.dat CHECKF testF.dat
+
+   1 -168.0 -1.40351172223
+   2 -156.0 -1.70447981034
+   3 -144.0 -1.62956100432
+   ...
+   30 180.0 -0.707106781187
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections. The first line begins with a keyword which
+identifies the section. The line can contain additional text, but the
+initial text must match the argument specified in the
+:doc:`dihedral\_coeff <dihedral_coeff>` command. The next line lists (in
+any order) one or more parameters for the table. Each parameter is a
+keyword followed by one or more numeric values.
+
+Following a blank line, the next N lines list the tabulated values. On
+each line, the 1st value is the index from 1 to N, the 2nd value is
+the angle value, the 3rd value is the energy (in energy units), and
+the 4th is -dE/d(phi) also in energy units). The 3rd term is the
+energy of the 4-atom configuration for the specified angle.  The 4th
+term (when present) is the negative derivative of the energy with
+respect to the angle (in degrees, or radians depending on whether the
+user selected DEGREES or RADIANS).  Thus the units of the last term
+are still energy, not force. The dihedral angle values must increase
+from one line to the next.
+
+Dihedral table splines are cyclic.  There is no discontinuity at 180
+degrees (or at any other angle).  Although in the examples above, the
+angles range from -180 to 180 degrees, in general, the first angle in
+the list can have any value (positive, zero, or negative).  However
+the *range* of angles represented in the table must be *strictly* less
+than 360 degrees (2pi radians) to avoid angle overlap.  (You may not
+supply entries in the table for both 180 and -180, for example.)  If
+the user's table covers only a narrow range of dihedral angles,
+strange numerical behavior can occur in the large remaining gap.
+
+**Parameters:**
+
+The parameter "N" is required and its value is the number of table
+entries that follow. Note that this may be different than the N
+specified in the :doc:`dihedral\_style table <dihedral_style>` command.
+Let *Ntable* is the number of table entries requested dihedral\_style
+command, and let *Nfile* be the parameter following "N" in the
+tabulated file ("30" in the sparse example above).  What LAMMPS does
+is a preliminary interpolation by creating splines using the *Nfile*
+tabulated values as nodal points.  It uses these to interpolate as
+needed to generate energy and derivative values at *Ntable* different
+points (which are evenly spaced over a 360 degree range, even if the
+angles in the file are not).  The resulting tables of length *Ntable*
+are then used as described above, when computing energy and force for
+individual dihedral angles and their atoms.  This means that if you
+want the interpolation tables of length *Ntable* to match exactly what
+is in the tabulated file (with effectively nopreliminary
+interpolation), you should set *Ntable* = *Nfile*\ .  To insure the
+nodal points in the user's file are aligned with the interpolated
+table entries, the angles in the table should be integer multiples of
+360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your
+choice of angle units).
+
+The optional "NOF" keyword allows the user to omit the forces
+(negative energy derivatives) from the table file (normally located in
+the 4th column).  In their place, forces will be calculated
+automatically by differentiating the potential energy function
+indicated by the 3rd column of the table (using either linear or
+spline interpolation).
+
+The optional "DEGREES" keyword allows the user to specify angles in
+degrees instead of radians (default).
+
+The optional "RADIANS" keyword allows the user to specify angles in
+radians instead of degrees.  (Note: This changes the way the forces
+are scaled in the 4th column of the data file.)
+
+The optional "CHECKU" keyword is followed by a filename.  This allows
+the user to save all of the *Ntable* different entries in the
+interpolated energy table to a file to make sure that the interpolated
+function agrees with the user's expectations.  (Note: You can
+temporarily increase the *Ntable* parameter to a high value for this
+purpose.  "\ *Ntable*\ " is explained above.)
+
+The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
+It is followed by a filename, and it allows the user to check the
+interpolated force table.  This option is available even if the user
+selected the "NOF" option.
+
+Note that one file can contain many sections, each with a tabulated
+potential. LAMMPS reads the file section by section until it finds one
+that matches the specified keyword.
+
+**Restart info:**
+
+This dihedral style writes the settings for the "dihedral\_style table/cut"
+command to :doc:`binary restart files <restart>`, so a dihedral\_style
+command does not need to specified in an input script that reads a
+restart file.  However, the coefficient information is not stored in
+the restart file, since it is tabulated in the potential files.  Thus,
+dihedral\_coeff commands do need to be specified in the restart input
+script.
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral\_coeff <dihedral_coeff>`, :doc:`dihedral\_style table <dihedral_table>`
+
+**Default:** none
+
+.. _dihedralcut-Salerno:
+
+
+
+**(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst
new file mode 100644
index 0000000000..7edf15e213
--- /dev/null
+++ b/doc/src/dihedral_zero.rst
@@ -0,0 +1,58 @@
+.. index:: dihedral\_style zero
+
+dihedral\_style zero command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dihedral_style zero *nocoeff*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dihedral_style zero
+   dihedral_style zero nocoeff
+   dihedral_coeff \*
+
+Description
+"""""""""""
+
+Using a dihedral style of zero means dihedral forces and energies are
+not computed, but the geometry of dihedral quadruplets is still
+accessible to other commands.
+
+As an example, the :doc:`compute dihedral/local <compute_dihedral_local>` command can be used to
+compute the theta values for the list of quadruplets of dihedral atoms
+listed in the data file read by the :doc:`read\_data <read_data>`
+command.  If no dihedral style is defined, this command cannot be
+used.
+
+The optional *nocoeff* flag allows to read data files with a DihedralCoeff
+section for any dihedral style. Similarly, any dihedral\_coeff commands
+will only be checked for the dihedral type number and the rest ignored.
+
+Note that the :doc:`dihedral\_coeff <dihedral_coeff>` command must be
+used for all dihedral types, though no additional values are
+specified.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+:doc:`dihedral\_style none <dihedral_none>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dihedrals.rst b/doc/src/dihedrals.rst
new file mode 100644
index 0000000000..bab913f1c2
--- /dev/null
+++ b/doc/src/dihedrals.rst
@@ -0,0 +1,9 @@
+Dihedral Styles
+###############
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   dihedral_*
diff --git a/doc/src/dihedrals.txt b/doc/src/dihedrals.txt
deleted file mode 100644
index a862bf50a0..0000000000
--- a/doc/src/dihedrals.txt
+++ /dev/null
@@ -1,40 +0,0 @@
-Dihedral Styles :h1
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   dihedral_charmm
-   dihedral_class2
-   dihedral_cosine_shift_exp
-   dihedral_fourier
-   dihedral_harmonic
-   dihedral_helix
-   dihedral_hybrid
-   dihedral_multi_harmonic
-   dihedral_nharmonic
-   dihedral_none
-   dihedral_opls
-   dihedral_quadratic
-   dihedral_spherical
-   dihedral_table
-   dihedral_table_cut
-   dihedral_zero
-   dihedral_charmm
-   dihedral_class2
-   dihedral_cosine_shift_exp
-   dihedral_fourier
-   dihedral_harmonic
-   dihedral_helix
-   dihedral_hybrid
-   dihedral_multi_harmonic
-   dihedral_nharmonic
-   dihedral_none
-   dihedral_opls
-   dihedral_quadratic
-   dihedral_spherical
-   dihedral_table
-   dihedral_zero
-
-END_RST -->
diff --git a/doc/src/dimension.rst b/doc/src/dimension.rst
new file mode 100644
index 0000000000..c50d92c5f8
--- /dev/null
+++ b/doc/src/dimension.rst
@@ -0,0 +1,66 @@
+.. index:: dimension
+
+dimension command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dimension N
+
+* N = 2 or 3
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dimension 2
+
+Description
+"""""""""""
+
+Set the dimensionality of the simulation.  By default LAMMPS runs 3d
+simulations.  To run a 2d simulation, this command should be used
+prior to setting up a simulation box via the
+:doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` commands.
+Restart files also store this setting.
+
+See the discussion on the :doc:`Howto 2d <Howto_2d>` doc page for
+additional instructions on how to run 2d simulations.
+
+.. note::
+
+   Some models in LAMMPS treat particles as finite-size spheres or
+   ellipsoids, as opposed to point particles.  In 2d, the particles will
+   still be spheres or ellipsoids, not circular disks or ellipses,
+   meaning their moment of inertia will be the same as in 3d.
+
+Restrictions
+""""""""""""
+
+
+This command must be used before the simulation box is defined by a
+:doc:`read\_data <read_data>` or :doc:`create\_box <create_box>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix enforce2d <fix_enforce2d>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   dimension 3
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst
new file mode 100644
index 0000000000..2cf5849a10
--- /dev/null
+++ b/doc/src/displace_atoms.rst
@@ -0,0 +1,167 @@
+.. index:: displace\_atoms
+
+displace\_atoms command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   displace_atoms group-ID style args keyword value ...
+
+* group-ID = ID of group of atoms to displace
+* style = *move* or *ramp* or *random* or *rotate*
+  
+  .. parsed-literal::
+  
+       *move* args = delx dely delz
+         delx,dely,delz = distance to displace in each dimension (distance units)
+         any of delx,dely,delz can be a variable (see below)
+       *ramp* args = ddim dlo dhi dim clo chi
+         ddim = *x* or *y* or *z*
+         dlo,dhi = displacement distance between dlo and dhi (distance units)
+         dim = *x* or *y* or *z*
+         clo,chi = lower and upper bound of domain to displace (distance units)
+       *random* args = dx dy dz seed
+         dx,dy,dz = random displacement magnitude in each dimension (distance units)
+         seed = random # seed (positive integer)
+       *rotate* args = Px Py Pz Rx Ry Rz theta
+         Px,Py,Pz = origin point of axis of rotation (distance units)
+         Rx,Ry,Rz = axis of rotation vector
+         theta = angle of rotation (degrees)
+
+* zero or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+       keyword = *units*
+         value = *box* or *lattice*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   displace_atoms top move 0 -5 0 units box
+   displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
+
+Description
+"""""""""""
+
+Displace a group of atoms.  This can be used to move atoms a large
+distance before beginning a simulation or to randomize atoms initially
+on a lattice.  For example, in a shear simulation, an initial strain
+can be imposed on the system.  Or two groups of atoms can be brought
+into closer proximity.
+
+The *move* style displaces the group of atoms by the specified 3d
+displacement vector.  Any of the 3 quantities defining the vector
+components can be specified as an equal-style or atom-style
+:doc:`variable <variable>`.  If the value is a variable, it should be
+specified as v\_name, where name is the variable name.  In this case,
+the variable will be evaluated, and its value(s) used for the
+displacement(s).  The scale factor implied by the *units* keyword will
+also be applied to the variable result.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Atom-style variables can specify the same formulas as
+equal-style variables but can also include per-atom values, such as
+atom coordinates or per-atom values read from a file.  Note that if
+the variable references other :doc:`compute <compute>` or :doc:`fix <fix>`
+commands, those values must be up-to-date for the current timestep.
+See the "Variable Accuracy" section of the :doc:`variable <variable>`
+doc page for more details.
+
+The *ramp* style displaces atoms a variable amount in one dimension
+depending on the atom's coordinate in a (possibly) different
+dimension.  For example, the second example command displaces atoms in
+the x-direction an amount between 0.0 and 5.0 distance units.  Each
+atom's displacement depends on the fractional distance its y
+coordinate is between 2.0 and 20.5.  Atoms with y-coordinates outside
+those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
+
+The *random* style independently moves each atom in the group by a
+random displacement, uniformly sampled from a value between -dx and
++dx in the x dimension, and similarly for y and z.  Random numbers are
+used in such a way that the displacement of a particular atom is the
+same, regardless of how many processors are being used.
+
+The *rotate* style rotates each atom in the group by the angle *theta*
+around a rotation axis *R* = (Rx,Ry,Rz) that goes through a point *P* =
+(Px,Py,Pz).  The direction of rotation for the atoms around the
+rotation axis is consistent with the right-hand rule: if your
+right-hand thumb points along *R*\ , then your fingers wrap around the
+axis in the direction of positive theta.
+
+If the defined :doc:`atom\_style <atom_style>` assigns an orientation to
+each atom (:doc:`atom styles <atom_style>` ellipsoid, line, tri, body),
+then that property is also updated appropriately to correspond to the
+atom's rotation.
+
+Distance units for displacements and the origin point of the *rotate*
+style are determined by the setting of *box* or *lattice* for the
+*units* keyword.  *Box* means distance units as defined by the
+:doc:`units <units>` command - e.g. Angstroms for *real* units.
+*Lattice* means distance units are in lattice spacings.  The
+:doc:`lattice <lattice>` command must have been previously used to
+define the lattice spacing.
+
+
+----------
+
+
+.. note::
+
+   Care should be taken not to move atoms on top of other atoms.
+   After the move, atoms are remapped into the periodic simulation box if
+   needed, and any shrink-wrap boundary conditions (see the
+   :doc:`boundary <boundary>` command) are enforced which may change the
+   box size.  Other than this effect, this command does not change the
+   size or shape of the simulation box.  See the
+   :doc:`change\_box <change_box>` command if that effect is desired.
+
+.. note::
+
+   Atoms can be moved arbitrarily long distances by this command.
+   If the simulation box is non-periodic and shrink-wrapped (see the
+   :doc:`boundary <boundary>` command), this can change its size or shape.
+   This is not a problem, except that the mapping of processors to the
+   simulation box is not changed by this command from its initial 3d
+   configuration; see the :doc:`processors <processors>` command.  Thus, if
+   the box size/shape changes dramatically, the mapping of processors to
+   the simulation box may not end up as optimal as the initial mapping
+   attempted to be.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+For a 2d simulation, only rotations around the a vector parallel to
+the z-axis are allowed.
+
+Related commands
+""""""""""""""""
+
+:doc:`lattice <lattice>`, :doc:`change\_box <change_box>`,
+:doc:`fix move <fix_move>`
+
+Default
+"""""""
+
+The option defaults are units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump.rst b/doc/src/dump.rst
new file mode 100644
index 0000000000..e07100bb19
--- /dev/null
+++ b/doc/src/dump.rst
@@ -0,0 +1,729 @@
+.. index:: dump
+
+dump command
+============
+
+:doc:`dump vtk <dump_vtk>` command
+==================================
+
+:doc:`dump h5md <dump_h5md>` command
+====================================
+
+:doc:`dump molfile <dump_molfile>` command
+==========================================
+
+:doc:`dump netcdf <dump_netcdf>` command
+========================================
+
+:doc:`dump image <dump_image>` command
+======================================
+
+:doc:`dump movie <dump_image>` command
+======================================
+
+:doc:`dump adios <dump_adios>` command
+======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump ID group-ID style N file args
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be dumped
+* style = *atom* or *atom/gz* or *atom/mpiio* or *cfg* or *cfg/gz* or
+  *cfg/mpiio* or *custom* or *custom/gz* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/mpiio*
+* N = dump every this many timesteps
+* file = name of file to write dump info to
+* args = list of arguments for a particular style
+  
+  .. parsed-literal::
+  
+       *atom* args = none
+       *atom/gz* args = none
+       *atom/mpiio* args = none
+       *atom/adios* args = none,  discussed on :doc:`dump adios <dump_adios>` doc page
+       *cfg* args = same as *custom* args, see below
+       *cfg/gz* args = same as *custom* args, see below
+       *cfg/mpiio* args = same as *custom* args, see below
+       *custom*\ , *custom/gz*\ , *custom/mpiio* args = see below
+       *custom/adios* args = same as *custom* args, discussed on :doc:`dump adios <dump_adios>` doc page
+       *dcd* args = none
+       *h5md* args = discussed on :doc:`dump h5md <dump_h5md>` doc page
+       *image* args = discussed on :doc:`dump image <dump_image>` doc page
+       *local* args = see below
+       *molfile* args = discussed on :doc:`dump molfile <dump_molfile>` doc page
+       *movie* args = discussed on :doc:`dump image <dump_image>` doc page
+       *netcdf* args = discussed on :doc:`dump netcdf <dump_netcdf>` doc page
+       *netcdf/mpiio* args = discussed on :doc:`dump netcdf <dump_netcdf>` doc page
+       *vtk* args = same as *custom* args, see below, also :doc:`dump vtk <dump_vtk>` doc page
+       *xtc* args = none
+       *xyz* args = none
+       *xyz/gz* args = none
+       *xyz/mpiio* args = none
+
+* *custom* or *custom/gz* or *custom/mpiio* or *netcdf* or *netcdf/mpiio* args = list of atom attributes
+  
+  .. parsed-literal::
+  
+         possible attributes = id, mol, proc, procp1, type, element, mass,
+                               x, y, z, xs, ys, zs, xu, yu, zu,
+                               xsu, ysu, zsu, ix, iy, iz,
+                               vx, vy, vz, fx, fy, fz,
+                               q, mux, muy, muz, mu,
+                               radius, diameter, omegax, omegay, omegaz,
+                               angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                               c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+  
+  .. parsed-literal::
+  
+           id = atom ID
+           mol = molecule ID
+           proc = ID of processor that owns atom
+           procp1 = ID+1 of processor that owns atom
+           type = atom type
+           element = name of atom element, as defined by :doc:`dump_modify <dump_modify>` command
+           mass = atom mass
+           x,y,z = unscaled atom coordinates
+           xs,ys,zs = scaled atom coordinates
+           xu,yu,zu = unwrapped atom coordinates
+           xsu,ysu,zsu = scaled unwrapped atom coordinates
+           ix,iy,iz = box image that the atom is in
+           vx,vy,vz = atom velocities
+           fx,fy,fz = forces on atoms
+           q = atom charge
+           mux,muy,muz = orientation of dipole moment of atom
+           mu = magnitude of dipole moment of atom
+           radius,diameter = radius,diameter of spherical particle
+           omegax,omegay,omegaz = angular velocity of spherical particle
+           angmomx,angmomy,angmomz = angular momentum of aspherical particle
+           tqx,tqy,tqz = torque on finite-size particles
+           c_ID = per-atom vector calculated by a compute with ID
+           c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+           f_ID = per-atom vector calculated by a fix with ID
+           f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+           v_name = per-atom vector calculated by an atom-style variable with name
+           d_name = per-atom floating point vector with name, managed by fix property/atom
+           i_name = per-atom integer vector with name, managed by fix property/atom
+
+* *local* args = list of local attributes
+  
+  .. parsed-literal::
+  
+         possible attributes = index, c_ID, c_ID[I], f_ID, f_ID[I]
+           index = enumeration of local values
+           c_ID = local vector calculated by a compute with ID
+           c_ID[I] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
+           f_ID = local vector calculated by a fix with ID
+           f_ID[I] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump myDump all atom 100 dump.atom
+   dump myDump all atom/mpiio 100 dump.atom.mpiio
+   dump myDump all atom/gz 100 dump.atom.gz
+   dump 2 subgroup atom 50 dump.run.bin
+   dump 2 subgroup atom 50 dump.run.mpiio.bin
+   dump 4a all custom 100 dump.myforce.\* id type x y vx fx
+   dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
+   dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke
+   dump 2 inner cfg 10 dump.snap.\*.cfg mass type xs ys zs vx vy vz
+   dump snap all cfg 100 dump.config.\*.cfg mass type xs ys zs id type c_Stress[2]
+   dump 1 all xtc 1000 file.xtc
+
+Description
+"""""""""""
+
+Dump a snapshot of atom quantities to one or more files every N
+timesteps in one of several styles.  The *image* and *movie* styles are
+the exception: the *image* style renders a JPG, PNG, or PPM image file
+of the atom configuration every N timesteps while the *movie* style
+combines and compresses them into a movie file; both are discussed in
+detail on the :doc:`dump image <dump_image>` doc page.  The timesteps on
+which dump output is written can also be controlled by a variable.
+See the :doc:`dump\_modify every <dump_modify>` command.
+
+Only information for atoms in the specified group is dumped.  The
+:doc:`dump\_modify thresh and region and refresh <dump_modify>` commands
+can also alter what atoms are included.  Not all styles support
+these options; see details on the :doc:`dump\_modify <dump_modify>` doc
+page.
+
+As described below, the filename determines the kind of output (text
+or binary or gzipped, one big file or one per timestep, one big file
+or multiple smaller files).
+
+.. note::
+
+   Because periodic boundary conditions are enforced only on
+   timesteps when neighbor lists are rebuilt, the coordinates of an atom
+   written to a dump file may be slightly outside the simulation box.
+   Re-neighbor timesteps will not typically coincide with the timesteps
+   dump snapshots are written.  See the :doc:`dump\_modify pbc <dump_modify>` command if you with to force coordinates to be
+   strictly inside the simulation box.
+
+.. note::
+
+   Unless the :doc:`dump\_modify sort <dump_modify>` option is
+   invoked, the lines of atom information written to dump files
+   (typically one line per atom) will be in an indeterminate order for
+   each snapshot.  This is even true when running on a single processor,
+   if the :doc:`atom\_modify sort <atom_modify>` option is on, which it is
+   by default.  In this case atoms are re-ordered periodically during a
+   simulation, due to spatial sorting.  It is also true when running in
+   parallel, because data for a single snapshot is collected from
+   multiple processors, each of which owns a subset of the atoms.
+
+For the *atom*\ , *custom*\ , *cfg*\ , and *local* styles, sorting is off by
+default.  For the *dcd*\ , *xtc*\ , *xyz*\ , and *molfile* styles, sorting by
+atom ID is on by default. See the :doc:`dump\_modify <dump_modify>` doc
+page for details.
+
+The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , and *xyz/gz* styles are identical
+in command syntax to the corresponding styles without "gz", however,
+they generate compressed files using the zlib library. Thus the filename
+suffix ".gz" is mandatory. This is an alternative approach to writing
+compressed files via a pipe, as done by the regular dump styles, which
+may be required on clusters where the interface to the high-speed network
+disallows using the fork() library call (which is needed for a pipe).
+For the remainder of this doc page, you should thus consider the *atom*
+and *atom/gz* styles (etc) to be inter-changeable, with the exception
+of the required filename suffix.
+
+As explained below, the *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and
+*xyz/mpiio* styles are identical in command syntax and in the format
+of the dump files they create, to the corresponding styles without
+"mpiio", except the single dump file they produce is written in
+parallel via the MPI-IO library.  For the remainder of this doc page,
+you should thus consider the *atom* and *atom/mpiio* styles (etc) to
+be inter-changeable.  The one exception is how the filename is
+specified for the MPI-IO styles, as explained below.
+
+The precision of values output to text-based dump files can be
+controlled by the :doc:`dump\_modify format <dump_modify>` command and
+its options.
+
+
+----------
+
+
+The *style* keyword determines what atom quantities are written to the
+file and in what format.  Settings made via the
+:doc:`dump\_modify <dump_modify>` command can also alter the format of
+individual values and the file itself.
+
+The *atom*\ , *local*\ , and *custom* styles create files in a simple text
+format that is self-explanatory when viewing a dump file.  Some of the
+LAMMPS post-processing tools described on the :doc:`Tools <Tools>` doc
+page, including `Pizza.py <http://www.sandia.gov/~sjplimp/pizza.html>`_,
+work with this format, as does the :doc:`rerun <rerun>` command.
+
+For post-processing purposes the *atom*\ , *local*\ , and *custom* text
+files are self-describing in the following sense.
+
+The dimensions of the simulation box are included in each snapshot.
+For an orthogonal simulation box this information is formatted as:
+
+
+.. parsed-literal::
+
+   ITEM: BOX BOUNDS xx yy zz
+   xlo xhi
+   ylo yhi
+   zlo zhi
+
+where xlo,xhi are the maximum extents of the simulation box in the
+x-dimension, and similarly for y and z.  The "xx yy zz" represent 6
+characters that encode the style of boundary for each of the 6
+simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi).  Each of
+the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
+or m = shrink wrapped with a minimum value.  See the
+:doc:`boundary <boundary>` command for details.
+
+For triclinic simulation boxes (non-orthogonal), an orthogonal
+bounding box which encloses the triclinic simulation box is output,
+along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
+formatted as follows:
+
+
+.. parsed-literal::
+
+   ITEM: BOX BOUNDS xy xz yz xx yy zz
+   xlo_bound xhi_bound xy
+   ylo_bound yhi_bound xz
+   zlo_bound zhi_bound yz
+
+The presence of the text "xy xz yz" in the ITEM line indicates that
+the 3 tilt factors will be included on each of the 3 following lines.
+This bounding box is convenient for many visualization programs.  The
+meaning of the 6 character flags for "xx yy zz" is the same as above.
+
+Note that the first two numbers on each line are now xlo\_bound instead
+of xlo, etc, since they represent a bounding box.  See the :doc:`Howto triclinic <Howto_triclinic>` doc page for a geometric description
+of triclinic boxes, as defined by LAMMPS, simple formulas for how the
+6 bounding box extents (xlo\_bound,xhi\_bound,etc) are calculated from
+the triclinic parameters, and how to transform those parameters to and
+from other commonly used triclinic representations.
+
+The "ITEM: ATOMS" line in each snapshot lists column descriptors for
+the per-atom lines that follow.  For example, the descriptors would be
+"id type xs ys zs" for the default *atom* style, and would be the atom
+attributes you specify in the dump command for the *custom* style.
+
+For style *atom*\ , atom coordinates are written to the file, along with
+the atom ID and atom type.  By default, atom coords are written in a
+scaled format (from 0 to 1).  I.e. an x value of 0.25 means the atom
+is at a location 1/4 of the distance from xlo to xhi of the box
+boundaries.  The format can be changed to unscaled coords via the
+:doc:`dump\_modify <dump_modify>` settings.  Image flags can also be
+added for each atom via dump\_modify.
+
+Style *custom* allows you to specify a list of atom attributes to be
+written to the dump file for each atom.  Possible attributes are
+listed above and will appear in the order specified.  You cannot
+specify a quantity that is not defined for a particular simulation -
+such as *q* for atom style *bond*\ , since that atom style doesn't
+assign charges.  Dumps occur at the very end of a timestep, so atom
+attributes will include effects due to fixes that are applied during
+the timestep.  An explanation of the possible dump custom attributes
+is given below.
+
+For style *local*\ , local output generated by :doc:`computes <compute>`
+and :doc:`fixes <fix>` is used to generate lines of output that is
+written to the dump file.  This local data is typically calculated by
+each processor based on the atoms it owns, but there may be zero or
+more entities per atom, e.g. a list of bond distances.  An explanation
+of the possible dump local attributes is given below.  Note that by
+using input from the :doc:`compute property/local <compute_property_local>` command with dump local,
+it is possible to generate information on bonds, angles, etc that can
+be cut and pasted directly into a data file read by the
+:doc:`read\_data <read_data>` command.
+
+Style *cfg* has the same command syntax as style *custom* and writes
+extended CFG format files, as used by the
+`AtomEye <http://mt.seas.upenn.edu/Archive/Graphics/A>`_ visualization
+package.  Since the extended CFG format uses a single snapshot of the
+system per file, a wildcard "\*" must be included in the filename, as
+discussed below.  The list of atom attributes for style *cfg* must
+begin with either "mass type xs ys zs" or "mass type xsu ysu zsu"
+since these quantities are needed to write the CFG files in the
+appropriate format (though the "mass" and "type" fields do not appear
+explicitly in the file).  Any remaining attributes will be stored as
+"auxiliary properties" in the CFG files.  Note that you will typically
+want to use the :doc:`dump\_modify element <dump_modify>` command with
+CFG-formatted files, to associate element names with atom types, so
+that AtomEye can render atoms appropriately. When unwrapped
+coordinates *xsu*\ , *ysu*\ , and *zsu* are requested, the nominal AtomEye
+periodic cell dimensions are expanded by a large factor UNWRAPEXPAND =
+10.0, which ensures atoms that are displayed correctly for up to
+UNWRAPEXPAND/2 periodic boundary crossings in any direction.  Beyond
+this, AtomEye will rewrap the unwrapped coordinates.  The expansion
+causes the atoms to be drawn farther away from the viewer, but it is
+easy to zoom the atoms closer, and the interatomic distances are
+unaffected.
+
+The *dcd* style writes DCD files, a standard atomic trajectory format
+used by the CHARMM, NAMD, and XPlor molecular dynamics packages.  DCD
+files are binary and thus may not be portable to different machines.
+The number of atoms per snapshot cannot change with the *dcd* style.
+The *unwrap* option of the :doc:`dump\_modify <dump_modify>` command
+allows DCD coordinates to be written "unwrapped" by the image flags
+for each atom.  Unwrapped means that if the atom has passed through
+a periodic boundary one or more times, the value is printed for what
+the coordinate would be if it had not been wrapped back into the
+periodic box.  Note that these coordinates may thus be far outside
+the box size stored with the snapshot.
+
+The *xtc* style writes XTC files, a compressed trajectory format used
+by the GROMACS molecular dynamics package, and described
+`here <http://manual.gromacs.org/current/online/xtc.html>`_.
+The precision used in XTC files can be adjusted via the
+:doc:`dump\_modify <dump_modify>` command.  The default value of 1000
+means that coordinates are stored to 1/1000 nanometer accuracy.  XTC
+files are portable binary files written in the NFS XDR data format,
+so that any machine which supports XDR should be able to read them.
+The number of atoms per snapshot cannot change with the *xtc* style.
+The *unwrap* option of the :doc:`dump\_modify <dump_modify>` command allows
+XTC coordinates to be written "unwrapped" by the image flags for each
+atom.  Unwrapped means that if the atom has passed through a periodic
+boundary one or more times, the value is printed for what the
+coordinate would be if it had not been wrapped back into the periodic
+box.  Note that these coordinates may thus be far outside the box size
+stored with the snapshot.
+
+The *xyz* style writes XYZ files, which is a simple text-based
+coordinate format that many codes can read. Specifically it has
+a line with the number of atoms, then a comment line that is
+usually ignored followed by one line per atom with the atom type
+and the x-, y-, and z-coordinate of that atom. You can use the
+:doc:`dump\_modify element <dump_modify>` option to change the output
+from using the (numerical) atom type to an element name (or some
+other label). This will help many visualization programs to guess
+bonds and colors.
+
+Note that *atom*\ , *custom*\ , *dcd*\ , *xtc*\ , and *xyz* style dump files
+can be read directly by `VMD <http://www.ks.uiuc.edu/Research/vmd>`_, a
+popular molecular viewing program.
+
+
+----------
+
+
+Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges.  Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N.  This behavior can be
+changed via the :doc:`dump\_modify first <dump_modify>` command, which
+can also be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep.  N can be changed between runs by
+using the :doc:`dump\_modify every <dump_modify>` command (not allowed
+for *dcd* style).  The :doc:`dump\_modify every <dump_modify>` command
+also allows a variable to be used to determine the sequence of
+timesteps on which dump files are written.  In this mode a dump on the
+first timestep of a run will also not be written unless the
+:doc:`dump\_modify first <dump_modify>` command is used.
+
+The specified filename determines how the dump file(s) is written.
+The default is to write one large text file, which is opened when the
+dump command is invoked and closed when an :doc:`undump <undump>`
+command is used or when LAMMPS exits.  For the *dcd* and *xtc* styles,
+this is a single large binary file.
+
+Dump filenames can contain two wildcard characters.  If a "\*"
+character appears in the filename, then one file per snapshot is
+written and the "\*" character is replaced with the timestep value.
+For example, tmp.dump.\* becomes tmp.dump.0, tmp.dump.10000,
+tmp.dump.20000, etc.  This option is not available for the *dcd* and
+*xtc* styles.  Note that the :doc:`dump\_modify pad <dump_modify>`
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order with some post-processing tools.
+
+If a "%" character appears in the filename, then each of P processors
+writes a portion of the dump file, and the "%" character is replaced
+with the processor ID from 0 to P-1.  For example, tmp.dump.% becomes
+tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc.  This creates smaller
+files and can be a fast mode of output on parallel machines that
+support parallel I/O for output. This option is not available for the
+*dcd*\ , *xtc*\ , and *xyz* styles.
+
+By default, P = the number of processors meaning one file per
+processor, but P can be set to a smaller value via the *nfile* or
+*fileper* keywords of the :doc:`dump\_modify <dump_modify>` command.
+These options can be the most efficient way of writing out dump files
+when running on large numbers of processors.
+
+Note that using the "\*" and "%" characters together can produce a
+large number of small dump files!
+
+For the *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and *xyz/mpiio*
+styles, a single dump file is written in parallel via the MPI-IO
+library, which is part of the MPI standard for versions 2.0 and above.
+Using MPI-IO requires two steps.  First, build LAMMPS with its MPIIO
+package installed, e.g.
+
+
+.. parsed-literal::
+
+   make yes-mpiio    # installs the MPIIO package
+   make mpi          # build LAMMPS for your platform
+
+Second, use a dump filename which contains ".mpiio".  Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO restart files, which must be both written and read using
+MPI-IO, the dump files produced by these MPI-IO styles are identical
+in format to the files produced by their non-MPI-IO style
+counterparts.  This means you can write a dump file using MPI-IO and
+use the :doc:`read\_dump <read_dump>` command or perform other
+post-processing, just as if the dump file was not written using
+MPI-IO.
+
+Note that MPI-IO dump files are one large file which all processors
+write to.  You thus cannot use the "%" wildcard character described
+above in the filename since that specifies generation of multiple
+files.  You can use the ".bin" suffix described below in an MPI-IO
+dump file; again this file will be written in parallel and have the
+same binary format as if it were written without MPI-IO.
+
+If the filename ends with ".bin", the dump file (or files, if "\*" or
+"%" is also used) is written in binary format.  A binary dump file
+will be about the same size as a text version, but will typically
+write out much faster.  Of course, when post-processing, you will need
+to convert it back to text format (see the :ref:`binary2txt tool <binary>`) or write your own code to read the binary
+file.  The format of the binary file can be understood by looking at
+the tools/binary2txt.cpp file.  This option is only available for the
+*atom* and *custom* styles.
+
+If the filename ends with ".gz", the dump file (or files, if "\*" or "%"
+is also used) is written in gzipped format.  A gzipped dump file will
+be about 3x smaller than the text version, but will also take longer
+to write.  This option is not available for the *dcd* and *xtc*
+styles.
+
+
+----------
+
+
+Note that in the discussion which follows, for styles which can
+reference values from a compute or fix, like the *custom*\ , *cfg*\ , or
+*local* styles, the bracketed index I can be specified using a
+wildcard asterisk with the index to effectively specify multiple
+values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+size of the vector (for *mode* = scalar) or the number of columns in
+the array (for *mode* = vector), then an asterisk with no numeric
+values means all indices from 1 to N.  A leading asterisk means all
+indices from 1 to n (inclusive).  A trailing asterisk means all
+indices from n to N (inclusive).  A middle asterisk means all indices
+from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 dump commands are
+equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
+command creates a per-atom array with 6 columns:
+
+
+.. parsed-literal::
+
+   compute myPress all stress/atom NULL
+   dump 2 all custom 100 tmp.dump id myPress[\*]
+   dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
+                                     myPress[4] myPress[5] myPress[6]
+
+
+----------
+
+
+This section explains the local attributes that can be specified as
+part of the *local* style.
+
+The *index* attribute can be used to generate an index number from 1
+to N for each line written into the dump file, where N is the total
+number of local datums from all processors, or lines of output that
+will appear in the snapshot.  Note that because data from different
+processors depend on what atoms they currently own, and atoms migrate
+between processor, there is no guarantee that the same index will be
+used for the same info (e.g. a particular bond) in successive
+snapshots.
+
+The *c\_ID* and *c\_ID[I]* attributes allow local vectors or arrays
+calculated by a :doc:`compute <compute>` to be output.  The ID in the
+attribute should be replaced by the actual ID of the compute that has
+been defined previously in the input script.  See the
+:doc:`compute <compute>` command for details.  There are computes for
+calculating local information such as indices, types, and energies for
+bonds and angles.
+
+Note that computes which calculate global or per-atom quantities, as
+opposed to local quantities, cannot be output in a dump local command.
+Instead, global quantities can be output by the :doc:`thermo\_style custom <thermo_style>` command, and per-atom quantities can be
+output by the dump custom command.
+
+If *c\_ID* is used as a attribute, then the local vector calculated by
+the compute is printed.  If *c\_ID[I]* is used, then I must be in the
+range from 1-M, which will print the Ith column of the local array
+with M columns calculated by the compute.  See the discussion above
+for how I can be specified with a wildcard asterisk to effectively
+specify multiple values.
+
+The *f\_ID* and *f\_ID[I]* attributes allow local vectors or arrays
+calculated by a :doc:`fix <fix>` to be output.  The ID in the attribute
+should be replaced by the actual ID of the fix that has been defined
+previously in the input script.
+
+If *f\_ID* is used as a attribute, then the local vector calculated by
+the fix is printed.  If *f\_ID[I]* is used, then I must be in the
+range from 1-M, which will print the Ith column of the local with M
+columns calculated by the fix.  See the discussion above for how I can
+be specified with a wildcard asterisk to effectively specify multiple
+values.
+
+Here is an example of how to dump bond info for a system, including
+the distance and energy of each bond:
+
+
+.. parsed-literal::
+
+   compute 1 all property/local batom1 batom2 btype
+   compute 2 all bond/local dist eng
+   dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+
+
+----------
+
+
+This section explains the atom attributes that can be specified as
+part of the *custom* and *cfg* styles.
+
+The *id*\ , *mol*\ , *proc*\ , *procp1*\ , *type*\ , *element*\ , *mass*\ , *vx*\ ,
+*vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz*\ , *q* attributes are self-explanatory.
+
+*Id* is the atom ID.  *Mol* is the molecule ID, included in the data
+file for molecular systems.  *Proc* is the ID of the processor (0 to
+Nprocs-1) that currently owns the atom.  *Procp1* is the proc ID+1,
+which can be convenient in place of a *type* attribute (1 to Ntypes)
+for coloring atoms in a visualization program.  *Type* is the atom
+type (1 to Ntypes).  *Element* is typically the chemical name of an
+element, which you must assign to each type via the :doc:`dump\_modify element <dump_modify>` command.  More generally, it can be any
+string you wish to associated with an atom type.  *Mass* is the atom
+mass.  *Vx*\ , *vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz*\ , and *q* are components of
+atom velocity and force and atomic charge.
+
+There are several options for outputting atom coordinates.  The *x*\ ,
+*y*\ , *z* attributes write atom coordinates "unscaled", in the
+appropriate distance :doc:`units <units>` (Angstroms, sigma, etc).  Use
+*xs*\ , *ys*\ , *zs* if you want the coordinates "scaled" to the box size,
+so that each value is 0.0 to 1.0.  If the simulation box is triclinic
+(tilted), then all atom coords will still be between 0.0 and 1.0.
+I.e. actual unscaled (x,y,z) = xs\*A + ys\*B + zs\*C, where (A,B,C) are
+the non-orthogonal vectors of the simulation box edges, as discussed
+on the :doc:`Howto triclinic <Howto_triclinic>` doc page.
+
+Use *xu*\ , *yu*\ , *zu* if you want the coordinates "unwrapped" by the
+image flags for each atom.  Unwrapped means that if the atom has
+passed through a periodic boundary one or more times, the value is
+printed for what the coordinate would be if it had not been wrapped
+back into the periodic box.  Note that using *xu*\ , *yu*\ , *zu* means
+that the coordinate values may be far outside the box bounds printed
+with the snapshot.  Using *xsu*\ , *ysu*\ , *zsu* is similar to using
+*xu*\ , *yu*\ , *zu*\ , except that the unwrapped coordinates are scaled by
+the box size. Atoms that have passed through a periodic boundary will
+have the corresponding coordinate increased or decreased by 1.0.
+
+The image flags can be printed directly using the *ix*\ , *iy*\ , *iz*
+attributes.  For periodic dimensions, they specify which image of the
+simulation box the atom is considered to be in.  An image of 0 means
+it is inside the box as defined.  A value of 2 means add 2 box lengths
+to get the true value.  A value of -1 means subtract 1 box length to
+get the true value.  LAMMPS updates these flags as atoms cross
+periodic boundaries during the simulation.
+
+The *mux*\ , *muy*\ , *muz* attributes are specific to dipolar systems
+defined with an atom style of *dipole*\ .  They give the orientation of
+the atom's point dipole moment.  The *mu* attribute gives the
+magnitude of the atom's dipole moment.
+
+The *radius* and *diameter* attributes are specific to spherical
+particles that have a finite size, such as those defined with an atom
+style of *sphere*\ .
+
+The *omegax*\ , *omegay*\ , and *omegaz* attributes are specific to
+finite-size spherical particles that have an angular velocity.  Only
+certain atom styles, such as *sphere* define this quantity.
+
+The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are specific to
+finite-size aspherical particles that have an angular momentum.  Only
+the *ellipsoid* atom style defines this quantity.
+
+The *tqx*\ , *tqy*\ , *tqz* attributes are for finite-size particles that
+can sustain a rotational torque due to interactions with other
+particles.
+
+The *c\_ID* and *c\_ID[I]* attributes allow per-atom vectors or arrays
+calculated by a :doc:`compute <compute>` to be output.  The ID in the
+attribute should be replaced by the actual ID of the compute that has
+been defined previously in the input script.  See the
+:doc:`compute <compute>` command for details.  There are computes for
+calculating the per-atom energy, stress, centro-symmetry parameter,
+and coordination number of individual atoms.
+
+Note that computes which calculate global or local quantities, as
+opposed to per-atom quantities, cannot be output in a dump custom
+command.  Instead, global quantities can be output by the
+:doc:`thermo\_style custom <thermo_style>` command, and local quantities
+can be output by the dump local command.
+
+If *c\_ID* is used as a attribute, then the per-atom vector calculated
+by the compute is printed.  If *c\_ID[I]* is used, then I must be in
+the range from 1-M, which will print the Ith column of the per-atom
+array with M columns calculated by the compute.  See the discussion
+above for how I can be specified with a wildcard asterisk to
+effectively specify multiple values.
+
+The *f\_ID* and *f\_ID[I]* attributes allow vector or array per-atom
+quantities calculated by a :doc:`fix <fix>` to be output.  The ID in the
+attribute should be replaced by the actual ID of the fix that has been
+defined previously in the input script.  The :doc:`fix ave/atom <fix_ave_atom>` command is one that calculates per-atom
+quantities.  Since it can time-average per-atom quantities produced by
+any :doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style
+:doc:`variable <variable>`, this allows those time-averaged results to
+be written to a dump file.
+
+If *f\_ID* is used as a attribute, then the per-atom vector calculated
+by the fix is printed.  If *f\_ID[I]* is used, then I must be in the
+range from 1-M, which will print the Ith column of the per-atom array
+with M columns calculated by the fix.  See the discussion above for
+how I can be specified with a wildcard asterisk to effectively specify
+multiple values.
+
+The *v\_name* attribute allows per-atom vectors calculated by a
+:doc:`variable <variable>` to be output.  The name in the attribute
+should be replaced by the actual name of the variable that has been
+defined previously in the input script.  Only an atom-style variable
+can be referenced, since it is the only style that generates per-atom
+values.  Variables of style *atom* can reference individual atom
+attributes, per-atom attributes, thermodynamic keywords, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of creating quantities to output to a
+dump file.
+
+The *d\_name* and *i\_name* attributes allow to output custom per atom
+floating point or integer properties that are managed by
+:doc:`fix property/atom <fix_property_atom>`.
+
+See the :doc:`Modify <Modify>` doc page for information on how to add
+new compute and fix styles to LAMMPS to calculate per-atom quantities
+which could then be output into dump files.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+To write gzipped dump files, you must either compile LAMMPS with the
+-DLAMMPS\_GZIP option or use the styles from the COMPRESS package.
+See the :doc:`Build settings <Build_settings>` doc page for details.
+
+The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , and *xyz/gz* styles are part of
+the COMPRESS package.  They are only enabled if LAMMPS was built with
+that package.  See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+The *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and *xyz/mpiio* styles
+are part of the MPIIO package.  They are only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+The *xtc* style is part of the MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump adios <dump_adios>` :doc:`dump h5md <dump_h5md>`, :doc:`dump image <dump_image>`,
+:doc:`dump molfile <dump_molfile>`, :doc:`dump\_modify <dump_modify>`,
+:doc:`undump <undump>`
+
+Default
+"""""""
+
+The defaults for the *image* and *movie* styles are listed on the
+:doc:`dump image <dump_image>` doc page.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst
new file mode 100644
index 0000000000..b0db9f5aed
--- /dev/null
+++ b/doc/src/dump_adios.rst
@@ -0,0 +1,95 @@
+.. index:: dump atoms/adios 
+
+dump atoms/adios  command
+=========================
+
+dump custom/adios command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump ID group-ID atoms/adios N file.bp
+
+   dump ID group-ID custom/adios N file.bp args
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be imaged
+* adios = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* N = dump every this many timesteps
+* file.bp = name of file/stream to write to
+* args = same options as in :doc:`\ *dump custom*\ <dump>` command
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump adios1 all atom/adios   100 atoms.bp
+   dump 4a     all custom/adios 100 dump_adios.bp id v_p x y z
+   dump 2 subgroup custom/adios 100 dump_adios.bp mass type xs ys zs vx vy vz
+
+Description
+"""""""""""
+
+Dump a snapshot of atom coordinates every N timesteps in the
+`ADIOS <adios_>`_ based "BP" file format, or using different I/O solutions in ADIOS,
+to a stream that can be read on-line by another program.
+ADIOS-BP files are binary, portable and self-describing.
+
+.. _adios: https://github.com/ornladios/ADIOS2
+
+
+
+**Use from write\_dump:**
+
+It is possible to use these dump styles with the
+:doc:`write\_dump <write_dump>` command.  In this case, the sub-intervals
+must not be set at all.  The write\_dump command can be used to
+create a new file at each individual dump.
+
+
+.. parsed-literal::
+
+   dump 4     all atom/adios 100 dump.bp
+   write_dump all atom/adios singledump.bp
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The number of atoms per snapshot CAN change with the adios style.
+When using the ADIOS tool 'bpls' to list the content of a .bp file,
+bpls will print *\__* for the size of the output table indicating that
+its size is changing every step.
+
+The *atom/adios* and *custom/adios* dump styles are part of the USER-ADIOS
+package.  They are only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump\_modify <dump_modify>`, :doc:`undump <undump>`
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst
new file mode 100644
index 0000000000..28242b0871
--- /dev/null
+++ b/doc/src/dump_cfg_uef.rst
@@ -0,0 +1,67 @@
+.. index:: dump cfg/uef
+
+dump cfg/uef command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump ID group-ID cfg/uef N file mass type xs ys zs args
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be dumped
+* N = dump every this many timesteps
+* file = name of file to write dump info to
+  
+  .. parsed-literal::
+  
+     args = same as args for :doc:`dump custom <dump>`
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump 1 all cfg/uef 10 dump.\*.cfg mass type xs ys zs
+   dump 2 all cfg/uef 100 dump.\*.cfg mass type xs ys zs id c_stress
+
+Description
+"""""""""""
+
+This command is used to dump atomic coordinates in the
+reference frame of the applied flow field when
+:doc:`fix nvt/uef <fix_nh_uef>` or
+:doc:`fix npt/uef <fix_nh_uef>` or is used. Only the atomic
+coordinates and frame-invariant scalar quantities
+will be in the flow frame. If velocities are selected
+as output, for example, they will not be in the same
+reference frame as the atomic positions.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`
+or :doc:`fix npt/uef <fix_nh_uef>` is active.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`,
+:doc:`fix nvt/uef <fix_nh_uef>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst
new file mode 100644
index 0000000000..85a80e7d12
--- /dev/null
+++ b/doc/src/dump_h5md.rst
@@ -0,0 +1,158 @@
+.. index:: dump h5md
+
+dump h5md command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump ID group-ID h5md N file.h5 args
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be imaged
+* h5md = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* N = dump every this many timesteps
+* file.h5 = name of file to write to
+
+.. parsed-literal::
+
+   args = list of data elements to dump, with their dump "sub-intervals"
+     position options
+     image
+     velocity options
+     force options
+     species options
+     file_from ID: do not open a new file, re-use the already opened file from dump ID
+     box value = *yes* or *no*
+     create_group value = *yes* or *no*
+     author value = quoted string
+
+
+
+Note that at least one element must be specified and image may only be
+present if position is specified first.
+
+For the elements *position*\ , *velocity*\ , *force* and *species*\ , a
+sub-interval may be specified to write the data only every N\_element
+iterations of the dump (i.e. every N\*N\_element time steps). This is
+specified by this option directly following the element declaration:
+
+
+.. parsed-literal::
+
+   every N_element
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump h5md1 all h5md 100 dump_h5md.h5 position image
+   dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
+   dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"
+
+Description
+"""""""""""
+
+Dump a snapshot of atom coordinates every N timesteps in the
+`HDF5 <HDF5-ws_>`_ based `H5MD <h5md_>`_ file format :ref:`(de Buyl) <h5md_cpc>`.
+HDF5 files are binary, portable and self-describing.  This dump style
+will write only one file, on the root node.
+
+Several dumps may write to the same file, by using file\_from and
+referring to a previously defined dump.  Several groups may also be
+stored within the same file by defining several dumps.  A dump that
+refers (via *file\_from*) to an already open dump ID and that concerns
+another particle group must specify *create\_group yes*.
+
+.. _h5md: http://nongnu.org/h5md/
+
+
+
+Each data element is written every N\*N\_element steps. For *image*\ , no
+sub-interval is needed as it must be present at the same interval as
+*position*\ .  *image* must be given after *position* in any case.  The
+box information (edges in each dimension) is stored at the same
+interval than the *position* element, if present. Else it is stored
+every N steps.
+
+.. note::
+
+   Because periodic boundary conditions are enforced only on
+   timesteps when neighbor lists are rebuilt, the coordinates of an atom
+   written to a dump file may be slightly outside the simulation box.
+
+**Use from write\_dump:**
+
+It is possible to use this dump style with the
+:doc:`write\_dump <write_dump>` command.  In this case, the sub-intervals
+must not be set at all.  The write\_dump command can be used either to
+create a new file or to add current data to an existing dump file by
+using the *file\_from* keyword.
+
+Typically, the *species* data is fixed. The following two commands
+store the position data every 100 timesteps, with the image data, and
+store once the species data in the same file.
+
+
+.. parsed-literal::
+
+   dump h5md1 all h5md 100 dump.h5 position image
+   write_dump all h5md dump.h5 file_from h5md1 species
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The number of atoms per snapshot cannot change with the h5md style.
+The position data is stored wrapped (box boundaries not enforced, see
+note above).  Only orthogonal domains are currently supported. This is
+a limitation of the present dump h5md command and not of H5MD itself.
+
+The *h5md* dump style is part of the USER-H5MD package. It is only
+enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. It also requires
+(i) building the ch5md library provided with LAMMPS (See the :doc:`Build package <Build_package>` doc page for more info.) and (ii) having
+the `HDF5 <HDF5-ws_>`_ library installed (C bindings are sufficient) on
+your system.  The library ch5md is compiled with the h5cc wrapper
+provided by the HDF5 library.
+
+.. _HDF5-ws: http://www.hdfgroup.org/HDF5/
+
+
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump\_modify <dump_modify>`, :doc:`undump <undump>`
+
+
+----------
+
+
+.. _h5md\_cpc:
+
+
+
+**(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured,
+efficient, and portable file format for molecular data,
+Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
+`[arXiv:1308.6382] <http://arxiv.org/abs/1308.6382/>`_.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst
new file mode 100644
index 0000000000..84be993724
--- /dev/null
+++ b/doc/src/dump_image.rst
@@ -0,0 +1,753 @@
+.. index:: dump image
+
+dump image command
+==================
+
+dump movie command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump ID group-ID style N file color diameter keyword value ...
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be imaged
+* style = *image* or *movie* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* N = dump every this many timesteps
+* file = name of file to write image to
+* color = atom attribute that determines color of each atom
+* diameter = atom attribute that determines size of each atom
+* zero or more keyword/value pairs may be appended
+* keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *persp* or *box* or *axes* or *subbox* or *shiny* or *ssao*
+  
+  .. parsed-literal::
+  
+       *atom* = yes/no = do or do not draw atoms
+       *adiam* size = numeric value for atom diameter (distance units)
+       *bond* values = color width = color and width of bonds
+         color = *atom* or *type* or *none*
+         width = number or *atom* or *type* or *none*
+           number = numeric value for bond width (distance units)
+       *line* = color width
+         color = *type*
+         width = numeric value for line width (distance units)
+       *tri* = color tflag width
+         color = *type*
+         tflag = 1 for just triangle, 2 for just tri edges, 3 for both
+         width = numeric value for tringle edge width (distance units)
+       *body* = color bflag1 bflag2
+         color = *type*
+         bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
+       *fix* = fixID color fflag1 fflag2
+         fixID = ID of fix that generates objects to dray
+         color = *type*
+         fflag1,fflag2 = 2 numeric flags to affect how fix objects are drawn
+       *size* values = width height = size of images
+         width = width of image in # of pixels
+         height = height of image in # of pixels
+       *view* values = theta phi = view of simulation box
+         theta = view angle from +z axis (degrees)
+         phi = azimuthal view angle (degrees)
+         theta or phi can be a variable (see below)
+       *center* values = flag Cx Cy Cz = center point of image
+         flag = "s" for static, "d" for dynamic
+         Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
+         Cx,Cy,Cz can be variables (see below)
+       *up* values = Ux Uy Uz = direction that is "up" in image
+         Ux,Uy,Uz = components of up vector
+         Ux,Uy,Uz can be variables (see below)
+       *zoom* value = zfactor = size that simulation box appears in image
+         zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
+         zfactor can be a variable (see below)
+       *persp* value = pfactor = amount of "perspective" in image
+         pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
+         pfactor can be a variable (see below)
+       *box* values = yes/no diam = draw outline of simulation box
+         yes/no = do or do not draw simulation box lines
+         diam = diameter of box lines as fraction of shortest box length
+       *axes* values = yes/no length diam = draw xyz axes
+         yes/no = do or do not draw xyz axes lines next to simulation box
+         length = length of axes lines as fraction of respective box lengths
+         diam = diameter of axes lines as fraction of shortest box length
+       *subbox* values = yes/no diam = draw outline of processor sub-domains
+         yes/no = do or do not draw sub-domain lines
+         diam = diameter of sub-domain lines as fraction of shortest box length
+       *shiny* value = sfactor = shinyness of spheres and cylinders
+         sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
+       *ssao* value = yes/no seed dfactor = SSAO depth shading
+         yes/no = turn depth shading on/off
+         seed = random # seed (positive integer)
+         dfactor = strength of shading from 0.0 to 1.0
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump d0 all image 100 dump.\*.jpg type type
+   dump d1 mobile image 500 snap.\*.png element element ssao yes 4539 0.6
+   dump d2 all image 200 img-\*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
+   dump m0 all movie 1000 movie.mpg type type size 640 480
+   dump m1 all movie 1000 movie.avi type type size 640 480
+   dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
+
+Description
+"""""""""""
+
+Dump a high-quality rendered image of the atom configuration every N
+timesteps and save the images either as a sequence of JPEG or PNG or
+PPM files, or as a single movie file.  The options for this command as
+well as the :doc:`dump\_modify <dump_modify>` command control what is
+included in the image or movie and how it appears.  A series of such
+images can easily be manually converted into an animated movie of your
+simulation or the process can be automated without writing the
+intermediate files using the dump movie style; see further details
+below.  Other dump styles store snapshots of numerical data associated
+with atoms in various formats, as discussed on the :doc:`dump <dump>`
+doc page.
+
+Note that a set of images or a movie can be made after a simulation
+has been run, using the :doc:`rerun <rerun>` command to read snapshots
+from an existing dump file, and using these dump commands in the rerun
+script to generate the images/movie.
+
+Here are two sample images, rendered as 1024x1024 JPEG files.  Click
+to see the full-size images:
+
+.. raw:: html
+
+   <DIV ALIGN=center>
+
+.. image:: JPG/dump1_small.jpg
+   :target: JPG/dump1.jpg
+
+.. image:: JPG/dump2_small.jpg
+   :target: JPG/dump2.jpg
+
+.. raw:: html
+
+   </DIV>
+
+Only atoms in the specified group are rendered in the image.  The
+:doc:`dump\_modify region and thresh <dump_modify>` commands can also
+alter what atoms are included in the image.
+The filename suffix determines whether a JPEG, PNG, or PPM file is
+created with the *image* dump style.  If the suffix is ".jpg" or
+".jpeg", then a JPEG format file is created, if the suffix is ".png",
+then a PNG format is created, else a PPM (aka NETPBM) format file is
+created.  The JPEG and PNG files are binary; PPM has a text mode
+header followed by binary data. JPEG images have lossy compression;
+PNG has lossless compression; and PPM files are uncompressed but can
+be compressed with gzip, if LAMMPS has been compiled with
+-DLAMMPS\_GZIP and a ".gz" suffix is used.
+
+Similarly, the format of the resulting movie is chosen with the
+*movie* dump style. This is handled by the underlying FFmpeg converter
+and thus details have to be looked up in the FFmpeg documentation.
+Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
+Additional settings of the movie compression like bitrate and
+framerate can be set using the :doc:`dump\_modify <dump_modify>` command.
+
+To write out JPEG and PNG format files, you must build LAMMPS with
+support for the corresponding JPEG or PNG library. To convert images
+into movies, LAMMPS has to be compiled with the -DLAMMPS\_FFMPEG
+flag. See the :doc:`Build settings <Build_settings>` doc page for
+details.
+
+.. note::
+
+   Because periodic boundary conditions are enforced only on
+   timesteps when neighbor lists are rebuilt, the coordinates of an atom
+   in the image may be slightly outside the simulation box.
+
+
+----------
+
+
+Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges.  Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N.  This behavior can be
+changed via the :doc:`dump\_modify first <dump_modify>` command, which
+can be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep.  N can be changed between runs by
+using the :doc:`dump\_modify every <dump_modify>` command.
+
+Dump *image* filenames must contain a wildcard character "\*", so that
+one image file per snapshot is written.  The "\*" character is replaced
+with the timestep value.  For example, tmp.dump.\*.jpg becomes
+tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc.  Note
+that the :doc:`dump\_modify pad <dump_modify>` command can be used to
+insure all timestep numbers are the same length (e.g. 00010), which
+can make it easier to convert a series of images into a movie in the
+correct ordering.
+
+Dump *movie* filenames on the other hand, must not have any wildcard
+character since only one file combining all images into a single
+movie will be written by the movie encoder.
+
+
+----------
+
+
+The *color* and *diameter* settings determine the color and size of
+atoms rendered in the image.  They can be any atom attribute defined
+for the :doc:`dump custom <dump>` command, including *type* and
+*element*\ .  This includes per-atom quantities calculated by a
+:doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
+which are prefixed by "c\_", "f\_", or "v\_" respectively.  Note that the
+*diameter* setting can be overridden with a numeric value applied to
+all atoms by the optional *adiam* keyword.
+
+If *type* is specified for the *color* setting, then the color of each
+atom is determined by its atom type.  By default the mapping of types
+to colors is as follows:
+
+* type 1 = red
+* type 2 = green
+* type 3 = blue
+* type 4 = yellow
+* type 5 = aqua
+* type 6 = cyan
+
+and repeats itself for types > 6.  This mapping can be changed by the
+:doc:`dump\_modify acolor <dump_modify>` command.
+
+If *type* is specified for the *diameter* setting then the diameter of
+each atom is determined by its atom type.  By default all types have
+diameter 1.0.  This mapping can be changed by the :doc:`dump\_modify adiam <dump_modify>` command.
+
+If *element* is specified for the *color* and/or *diameter* setting,
+then the color and/or diameter of each atom is determined by which
+element it is, which in turn is specified by the element-to-type
+mapping specified by the "dump\_modify element" command.  By default
+every atom type is C (carbon).  Every element has a color and diameter
+associated with it, which is the same as the colors and sizes used by
+the `AtomEye <atomeye_>`_ visualization package.
+
+.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
+
+
+
+If other atom attributes are used for the *color* or *diameter*
+settings, they are interpreted in the following way.
+
+If "vx", for example, is used as the *color* setting, then the color
+of the atom will depend on the x-component of its velocity.  The
+association of a per-atom value with a specific color is determined by
+a "color map", which can be specified via the
+:doc:`dump\_modify <dump_modify>` command.  The basic idea is that the
+atom-attribute will be within a range of values, and every value
+within the range is mapped to a specific color.  Depending on how the
+color map is defined, that mapping can take place via interpolation so
+that a value of -3.2 is halfway between "red" and "blue", or
+discretely so that the value of -3.2 is "orange".
+
+If "vx", for example, is used as the *diameter* setting, then the atom
+will be rendered using the x-component of its velocity as the
+diameter.  If the per-atom value <= 0.0, them the atom will not be
+drawn.  Note that finite-size spherical particles, as defined by
+:doc:`atom\_style sphere <atom_style>` define a per-particle radius or
+diameter, which can be used as the *diameter* setting.
+
+
+----------
+
+
+The various keywords listed above control how the image is rendered.
+As listed below, all of the keywords have defaults, most of which you
+will likely not need to change.  The :doc:`dump modify <dump_modify>`
+also has options specific to the dump image style, particularly for
+assigning colors to atoms, bonds, and other image features.
+
+
+----------
+
+
+The *atom* keyword allow you to turn off the drawing of all atoms, if
+the specified value is *no*\ .  Note that this will not turn off the
+drawing of particles that are represented as lines, triangles, or
+bodies, as discussed below.  These particles can be drawn separately
+if the *line*\ , *tri*\ , or *body* keywords are used.
+
+The *adiam* keyword allows you to override the *diameter* setting to
+set a single numeric *size*\ .  All atoms will be drawn with that
+diameter, e.g. 1.5, which is in whatever distance :doc:`units <units>`
+the input script defines, e.g. Angstroms.
+
+
+----------
+
+
+The *bond* keyword allows to you to alter how bonds are drawn.  A bond
+is only drawn if both atoms in the bond are being drawn due to being
+in the specified group and due to other selection criteria
+(e.g. region, threshold settings of the
+:doc:`dump\_modify <dump_modify>` command).  By default, bonds are drawn
+if they are defined in the input data file as read by the
+:doc:`read\_data <read_data>` command.  Using *none* for both the bond
+*color* and *width* value will turn off the drawing of all bonds.
+
+If *atom* is specified for the bond *color* value, then each bond is
+drawn in 2 halves, with the color of each half being the color of the
+atom at that end of the bond.
+
+If *type* is specified for the *color* value, then the color of each
+bond is determined by its bond type.  By default the mapping of bond
+types to colors is as follows:
+
+* type 1 = red
+* type 2 = green
+* type 3 = blue
+* type 4 = yellow
+* type 5 = aqua
+* type 6 = cyan
+
+and repeats itself for bond types > 6.  This mapping can be changed by
+the :doc:`dump\_modify bcolor <dump_modify>` command.
+
+The bond *width* value can be a numeric value or *atom* or *type* (or
+*none* as indicated above).
+
+If a numeric value is specified, then all bonds will be drawn as
+cylinders with that diameter, e.g. 1.0, which is in whatever distance
+:doc:`units <units>` the input script defines, e.g. Angstroms.
+
+If *atom* is specified for the *width* value, then each bond
+will be drawn with a width corresponding to the minimum diameter
+of the 2 atoms in the bond.
+
+If *type* is specified for the *width* value then the diameter of each
+bond is determined by its bond type.  By default all types have
+diameter 0.5.  This mapping can be changed by the :doc:`dump\_modify bdiam <dump_modify>` command.
+
+
+----------
+
+
+The *line* keyword can be used when :doc:`atom\_style line <atom_style>`
+is used to define particles as line segments, and will draw them as
+lines.  If this keyword is not used, such particles will be drawn as
+spheres, the same as if they were regular atoms.  The only setting
+currently allowed for the *color* value is *type*\ , which will color
+the lines according to the atom type of the particle.  By default the
+mapping of types to colors is as follows:
+
+* type 1 = red
+* type 2 = green
+* type 3 = blue
+* type 4 = yellow
+* type 5 = aqua
+* type 6 = cyan
+
+and repeats itself for types > 6.  There is not yet an option to
+change this via the :doc:`dump\_modify <dump_modify>` command.
+
+The line *width* can only be a numeric value, which specifies that all
+lines will be drawn as cylinders with that diameter, e.g. 1.0, which
+is in whatever distance :doc:`units <units>` the input script defines,
+e.g. Angstroms.
+
+
+----------
+
+
+The *tri* keyword can be used when :doc:`atom\_style tri <atom_style>` is
+used to define particles as triangles, and will draw them as triangles
+or edges (3 lines) or both, depending on the setting for *tflag*\ .  If
+edges are drawn, the *width* setting determines the diameters of the
+line segments.  If this keyword is not used, triangle particles will
+be drawn as spheres, the same as if they were regular atoms.  The only
+setting currently allowed for the *color* value is *type*\ , which will
+color the triangles according to the atom type of the particle.  By
+default the mapping of types to colors is as follows:
+
+* type 1 = red
+* type 2 = green
+* type 3 = blue
+* type 4 = yellow
+* type 5 = aqua
+* type 6 = cyan
+
+and repeats itself for types > 6.  There is not yet an option to
+change this via the :doc:`dump\_modify <dump_modify>` command.
+
+
+----------
+
+
+The *body* keyword can be used when :doc:`atom\_style body <atom_style>`
+is used to define body particles with internal state
+(e.g. sub-particles), and will drawn them in a manner specific to the
+body style.  If this keyword is not used, such particles will be drawn
+as spheres, the same as if they were regular atoms.
+
+The :doc:`Howto body <Howto_body>` doc page describes the body styles
+LAMMPS currently supports, and provides more details as to the kind of
+body particles they represent and how they are drawn by this dump
+image command.  For all the body styles, individual atoms can be
+either a body particle or a usual point (non-body) particle.  Non-body
+particles will be drawn the same way they would be as a regular atom.
+The *bflag1* and *bflag2* settings are numerical values which are
+passed to the body style to affect how the drawing of a body particle
+is done.  See the :doc:`Howto body <Howto_body>` doc page for a
+description of what these parameters mean for each body style.
+
+The only setting currently allowed for the *color* value is *type*\ ,
+which will color the body particles according to the atom type of the
+particle.  By default the mapping of types to colors is as follows:
+
+* type 1 = red
+* type 2 = green
+* type 3 = blue
+* type 4 = yellow
+* type 5 = aqua
+* type 6 = cyan
+
+and repeats itself for types > 6.  There is not yet an option to
+change this via the :doc:`dump\_modify <dump_modify>` command.
+
+
+----------
+
+
+The *fix* keyword can be used with a :doc:`fix <fix>` that produces
+objects to be drawn.
+
+The *fflag1* and *fflag2* settings are numerical values which are
+passed to the fix to affect how the drawing of its objects is done.
+See the individual fix doc page for a description of what these
+parameters mean for a particular fix.
+
+The only setting currently allowed for the *color* value is *type*\ ,
+which will color the fix objects according to their type.  By default
+the mapping of types to colors is as follows:
+
+* type 1 = red
+* type 2 = green
+* type 3 = blue
+* type 4 = yellow
+* type 5 = aqua
+* type 6 = cyan
+
+and repeats itself for types > 6.  There is not yet an option to
+change this via the :doc:`dump\_modify <dump_modify>` command.
+
+
+----------
+
+
+The *size* keyword sets the width and height of the created images,
+i.e. the number of pixels in each direction.
+
+
+----------
+
+
+The *view*\ , *center*\ , *up*\ , *zoom*\ , and *persp* values determine how
+3d simulation space is mapped to the 2d plane of the image.  Basically
+they control how the simulation box appears in the image.
+
+All of the *view*\ , *center*\ , *up*\ , *zoom*\ , and *persp* values can be
+specified as numeric quantities, whose meaning is explained below.
+Any of them can also be specified as an :doc:`equal-style variable <variable>`, by using v\_name as the value, where "name" is
+the variable name.  In this case the variable will be evaluated on the
+timestep each image is created to create a new value.  If the
+equal-style variable is time-dependent, this is a means of changing
+the way the simulation box appears from image to image, effectively
+doing a pan or fly-by view of your simulation.
+
+The *view* keyword determines the viewpoint from which the simulation
+box is viewed, looking towards the *center* point.  The *theta* value
+is the vertical angle from the +z axis, and must be an angle from 0 to
+180 degrees.  The *phi* value is an azimuthal angle around the z axis
+and can be positive or negative.  A value of 0.0 is a view along the
++x axis, towards the *center* point.  If *theta* or *phi* are
+specified via variables, then the variable values should be in
+degrees.
+
+The *center* keyword determines the point in simulation space that
+will be at the center of the image.  *Cx*\ , *Cy*\ , and *Cz* are
+specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is
+the center of the simulation box.  These values do not have to be
+between 0.0 and 1.0, if you want the simulation box to be offset from
+the center of the image.  Note, however, that if you choose strange
+values for *Cx*\ , *Cy*\ , or *Cz* you may get a blank image.  Internally,
+*Cx*\ , *Cy*\ , and *Cz* are converted into a point in simulation space.
+If *flag* is set to "s" for static, then this conversion is done once,
+at the time the dump command is issued.  If *flag* is set to "d" for
+dynamic then the conversion is performed every time a new image is
+created.  If the box size or shape is changing, this will adjust the
+center point in simulation space.
+
+The *up* keyword determines what direction in simulation space will be
+"up" in the image.  Internally it is stored as a vector that is in the
+plane perpendicular to the view vector implied by the *theta* and
+*pni* values, and which is also in the plane defined by the view
+vector and user-specified up vector.  Thus this internal vector is
+computed from the user-specified *up* vector as
+
+
+.. parsed-literal::
+
+   up_internal = view cross (up cross view)
+
+This means the only restriction on the specified *up* vector is that
+it cannot be parallel to the *view* vector, implied by the *theta* and
+*phi* values.
+
+The *zoom* keyword scales the size of the simulation box as it appears
+in the image.  The default *zfactor* value of 1 should display an
+image mostly filled by the atoms in the simulation box.  A *zfactor* >
+1 will make the simulation box larger; a *zfactor* < 1 will make it
+smaller.  *Zfactor* must be a value > 0.0.
+
+The *persp* keyword determines how much depth perspective is present
+in the image.  Depth perspective makes lines that are parallel in
+simulation space appear non-parallel in the image.  A *pfactor* value
+of 0.0 means that parallel lines will meet at infinity (1.0/pfactor),
+which is an orthographic rendering with no perspective.  A *pfactor*
+value between 0.0 and 1.0 will introduce more perspective.  A *pfactor*
+value > 1 will create a highly skewed image with a large amount of
+perspective.
+
+.. note::
+
+   The *persp* keyword is not yet supported as an option.
+
+
+----------
+
+
+The *box* keyword determines if and how the simulation box boundaries
+are rendered as thin cylinders in the image.  If *no* is set, then the
+box boundaries are not drawn and the *diam* setting is ignored.  If
+*yes* is set, the 12 edges of the box are drawn, with a diameter that
+is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
+2d).  The color of the box boundaries can be set with the :doc:`dump\_modify boxcolor <dump_modify>` command.
+
+The *axes* keyword determines if and how the coordinate axes are
+rendered as thin cylinders in the image.  If *no* is set, then the
+axes are not drawn and the *length* and *diam* settings are ignored.
+If *yes* is set, 3 thin cylinders are drawn to represent the x,y,z
+axes in colors red,green,blue.  The origin of these cylinders will be
+offset from the lower left corner of the box by 10%.  The *length*
+setting determines how long the cylinders will be as a fraction of the
+respective box lengths.  The *diam* setting determines their thickness
+as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
+2d).
+
+The *subbox* keyword determines if and how processor sub-domain
+boundaries are rendered as thin cylinders in the image.  If *no* is
+set (default), then the sub-domain boundaries are not drawn and the
+*diam* setting is ignored.  If *yes* is set, the 12 edges of each
+processor sub-domain are drawn, with a diameter that is a fraction of
+the shortest box length in x,y,z (for 3d) or x,y (for 2d).  The color
+of the sub-domain boundaries can be set with the :doc:`dump\_modify boxcolor <dump_modify>` command.
+
+
+----------
+
+
+The *shiny* keyword determines how shiny the objects rendered in the
+image will appear.  The *sfactor* value must be a value 0.0 <=
+*sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface
+and *sfactor* = 0 is a rough non-shiny surface.
+
+The *ssao* keyword turns on/off a screen space ambient occlusion
+(SSAO) model for depth shading.  If *yes* is set, then atoms further
+away from the viewer are darkened via a randomized process, which is
+perceived as depth.  The calculation of this effect can increase the
+cost of computing the image by roughly 2x.  The strength of the effect
+can be scaled by the *dfactor* parameter.  If *no* is set, no depth
+shading is performed.
+
+
+----------
+
+
+A series of JPEG, PNG, or PPM images can be converted into a movie
+file and then played as a movie using commonly available tools. Using
+dump style *movie* automates this step and avoids the intermediate
+step of writing (many) image snapshot file. But LAMMPS has to be
+compiled with -DLAMMPS\_FFMPEG and an FFmpeg executable have to be
+installed.
+
+To manually convert JPEG, PNG or PPM files into an animated GIF or
+MPEG or other movie file you can use:
+
+* a) Use the ImageMagick convert program.
+  
+  .. parsed-literal::
+  
+     % convert \*.jpg foo.gif
+     % convert -loop 1 \*.ppm foo.mpg
+
+
+  Animated GIF files from ImageMagick are not optimized. You can use
+  a program like gifsicle to optimize and thus massively shrink them.
+  MPEG files created by ImageMagick are in MPEG-1 format with a rather
+  inefficient compression and low quality compared to more modern
+  compression styles like MPEG-4, H.264, VP8, VP9, H.265 and so on.
+
+* b) Use QuickTime.
+
+  Select "Open Image Sequence" under the File menu Load the images into
+  QuickTime to animate them Select "Export" under the File menu Save the
+  movie as a QuickTime movie (\*.mov) or in another format.  QuickTime
+  can generate very high quality and efficiently compressed movie
+  files. Some of the supported formats require to buy a license and some
+  are not readable on all platforms until specific runtime libraries are
+  installed.
+
+* c) Use FFmpeg
+
+  FFmpeg is a command line tool that is available on many platforms and
+  allows extremely flexible encoding and decoding of movies.
+
+  
+  .. parsed-literal::
+  
+     cat snap.\*.jpg \| ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
+     cat snap.\*.ppm \| ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
+
+
+  Front ends for FFmpeg exist for multiple platforms. For more
+  information see the `FFmpeg homepage <http://www.ffmpeg.org/>`_
+
+
+
+
+----------
+
+
+Play the movie:
+
+* a) Use your browser to view an animated GIF movie.
+
+  Select "Open File" under the File menu
+  Load the animated GIF file
+
+* b) Use the freely available mplayer or ffplay tool to view a
+  movie. Both are available for multiple OSes and support a large
+  variety of file formats and decoders.
+  
+  .. parsed-literal::
+  
+     % mplayer foo.mpg
+     % ffplay bar.avi
+
+* c) Use the `Pizza.py <http://www.sandia.gov/~sjplimp/pizza.html>`_
+  `animate tool <http://www.sandia.gov/~sjplimp/pizza/doc/animate.html>`_,
+  which works directly on a series of image files.
+  
+  .. parsed-literal::
+  
+     a = animate("foo\*.jpg")
+
+* d) QuickTime and other Windows- or MacOS-based media players can
+  obviously play movie files directly. Similarly for corresponding tools
+  bundled with Linux desktop environments.  However, due to licensing
+  issues with some file formats, the formats may require installing
+  additional libraries, purchasing a license, or may not be
+  supported.
+
+
+
+----------
+
+
+See the :doc:`Modify <Modify>` doc page for information on how to add
+new compute and fix styles to LAMMPS to calculate per-atom quantities
+which could then be output into dump files.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+To write JPEG images, you must use the -DLAMMPS\_JPEG switch when
+building LAMMPS and link with a JPEG library. To write PNG images, you
+must use the -DLAMMPS\_PNG switch when building LAMMPS and link with a
+PNG library.
+
+To write *movie* dumps, you must use the -DLAMMPS\_FFMPEG switch when
+building LAMMPS and have the FFmpeg executable available on the
+machine where LAMMPS is being run.  Typically it's name is lowercase,
+i.e. ffmpeg.
+
+See the :doc:`Build settings <Build_settings>` doc page for details.
+
+Note that since FFmpeg is run as an external program via a pipe,
+LAMMPS has limited control over its execution and no knowledge about
+errors and warnings printed by it. Those warnings and error messages
+will be printed to the screen only. Due to the way image data is
+communicated to FFmpeg, it will often print the message
+
+
+.. parsed-literal::
+
+   pipe:: Input/output error
+
+which can be safely ignored. Other warnings
+and errors have to be addressed according to the FFmpeg documentation.
+One known issue is that certain movie file formats (e.g. MPEG level 1
+and 2 format streams) have video bandwidth limits that can be crossed
+when rendering too large of image sizes. Typical warnings look like
+this:
+
+
+.. parsed-literal::
+
+   [mpeg @ 0x98b5e0] packet too large, ignoring buffer limits to mux it
+   [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
+   [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018
+
+In this case it is recommended to either reduce the size of the image
+or encode in a different format that is also supported by your copy of
+FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
+mp4).
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump\_modify <dump_modify>`, :doc:`undump <undump>`
+
+Default
+"""""""
+
+The defaults for the keywords are as follows:
+
+* adiam = not specified (use diameter setting)
+* atom = yes
+* bond = none none (if no bonds in system)
+* bond = atom 0.5 (if bonds in system)
+* size = 512 512
+* view = 60 30 (for 3d)
+* view = 0 0 (for 2d)
+* center = s 0.5 0.5 0.5
+* up = 0 0 1 (for 3d)
+* up = 0 1 0 (for 2d)
+* zoom = 1.0
+* persp = 0.0
+* box = yes 0.02
+* axes = no 0.0 0.0
+* subbox no 0.0
+* shiny = 1.0
+* ssao = no
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst
new file mode 100644
index 0000000000..1aa09c6092
--- /dev/null
+++ b/doc/src/dump_modify.rst
@@ -0,0 +1,1200 @@
+.. index:: dump\_modify
+
+dump\_modify command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump_modify dump-ID keyword values ...
+
+* dump-ID = ID of dump to modify
+* one or more keyword/value pairs may be appended
+* these keywords apply to various dump styles
+* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
+  
+  .. parsed-literal::
+  
+       *append* arg = *yes* or *no*
+       *at* arg = N
+         N = index of frame written upon first dump
+       *buffer* arg = *yes* or *no*
+       *delay* arg = Dstep
+         Dstep = delay output until this timestep
+       *element* args = E1 E2 ... EN, where N = # of atom types
+         E1,...,EN = element name, e.g. C or Fe or Ga
+       *every* arg = N
+         N = dump every this many timesteps
+         N can be a variable (see below)
+       *fileper* arg = Np
+         Np = write one file for every this many processors
+       *first* arg = *yes* or *no*
+       *flush* arg = *yes* or *no*
+       *format* args = *line* string, *int* string, *float* string, M string, or *none*
+         string = C-style format string
+         M = integer from 1 to N, where N = # of per-atom quantities being output
+       *image* arg = *yes* or *no*
+       *label* arg = string
+         string = character string (e.g. BONDS) to use in header of dump local file
+       *maxfiles* arg = Fmax
+         Fmax = keep only the most recent *Fmax* snapshots (one snapshot per file)
+       *nfile* arg = Nf
+         Nf = write this many files, one from each of Nf processors
+       *pad* arg = Nchar = # of characters to convert timestep to
+       *pbc* arg = *yes* or *no* = remap atoms via periodic boundary conditions
+       *precision* arg = power-of-10 value from 10 to 1000000
+       *region* arg = region-ID or "none"
+       *refresh* arg = c_ID = compute ID that supports a refresh operation
+       *scale* arg = *yes* or *no*
+       *sfactor* arg = coordinate scaling factor (> 0.0)
+       *sort* arg = *off* or *id* or N or -N
+          off = no sorting of per-atom lines within a snapshot
+          id = sort per-atom lines by atom ID
+          N = sort per-atom lines in ascending order by the Nth column
+          -N = sort per-atom lines in descending order by the Nth column
+       *tfactor* arg = time scaling factor (> 0.0)
+       *thermo* arg = *yes* or *no*
+       *time* arg = *yes* or *no*
+       *thresh* args = attribute operator value
+         attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
+         operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^"
+         value = numeric value to compare to, or LAST
+         these 3 args can be replaced by the word "none" to turn off thresholding
+       *units* arg = *yes* or *no*
+       *unwrap* arg = *yes* or *no*
+
+* these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>`
+* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
+  
+  .. parsed-literal::
+  
+       *acolor* args = type color
+         type = atom type or range of types (see below)
+         color = name of color or color1/color2/...
+       *adiam* args = type diam
+         type = atom type or range of types (see below)
+         diam = diameter of atoms of that type (distance units)
+       *amap* args = lo hi style delta N entry1 entry2 ... entryN
+         lo = number or *min* = lower bound of range of color map
+         hi = number or *max* = upper bound of range of color map
+         style = 2 letters = "c" or "d" or "s" plus "a" or "f"
+           "c" for continuous
+           "d" for discrete
+           "s" for sequential
+           "a" for absolute
+           "f" for fractional
+         delta = binsize (only used for style "s", otherwise ignored)
+           binsize = range is divided into bins of this width
+         N = # of subsequent entries
+         entry = value color (for continuous style)
+           value = number or *min* or *max* = single value within range
+           color = name of color used for that value
+         entry = lo hi color (for discrete style)
+           lo/hi = number or *min* or *max* = lower/upper bound of subset of range
+           color = name of color used for that subset of values
+         entry = color (for sequential style)
+           color = name of color used for a bin of values
+       *backcolor* arg = color
+         color = name of color for background
+       *bcolor* args = type color
+         type = bond type or range of types (see below)
+         color = name of color or color1/color2/...
+       *bdiam* args = type diam
+         type = bond type or range of types (see below)
+         diam = diameter of bonds of that type (distance units)
+       *boxcolor* arg = color
+         color = name of color for simulation box lines and processor sub-domain lines
+       *color* args = name R G B
+         name = name of color
+         R,G,B = red/green/blue numeric values from 0.0 to 1.0
+       *bitrate* arg = rate
+         rate = target bitrate for movie in kbps
+       *framerate* arg = fps
+         fps = frames per second for movie
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
+   dump_modify 1 format float %20.15g scale yes
+   dump_modify myDump image yes scale no flush yes
+   dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
+   dump_modify xtcdump precision 10000 sfactor 0.1
+   dump_modify 1 every 1000 nfile 20
+   dump_modify 1 every v_myVar
+   dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
+
+Description
+"""""""""""
+
+Modify the parameters of a previously defined dump command.  Not all
+parameters are relevant to all dump styles.
+
+As explained on the :doc:`dump <dump>` doc page, the *atom/mpiio*\ ,
+*custom/mpiio*\ , and *xyz/mpiio* dump styles are identical in command
+syntax and in the format of the dump files they create, to the
+corresponding styles without "mpiio", except the single dump file they
+produce is written in parallel via the MPI-IO library.  Thus if a
+dump\_modify option below is valid for the *atom* style, it is also
+valid for the *atom/mpiio* style, and similarly for the other styles
+which allow for use of MPI-IO.
+
+
+----------
+
+
+These keywords apply to various dump styles, including the :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>` styles.  The
+description gives details.
+
+
+----------
+
+
+The *append* keyword applies to all dump styles except *cfg* and *xtc*
+and *dcd*\ .  It also applies only to text output files, not to binary
+or gzipped or image/movie files.  If specified as *yes*\ , then dump
+snapshots are appended to the end of an existing dump file.  If
+specified as *no*\ , then a new dump file will be created which will
+overwrite an existing file with the same name.
+
+
+----------
+
+
+The *at* keyword only applies to the *netcdf* dump style.  It can only
+be used if the *append yes* keyword is also used.  The *N* argument is
+the index of which frame to append to.  A negative value can be
+specified for *N*\ , which means a frame counted from the end of the
+file.  The *at* keyword can only be used if the dump\_modify command is
+before the first command that causes dump snapshots to be output,
+e.g. a :doc:`run <run>` or :doc:`minimize <minimize>` command.  Once the
+dump file has been opened, this keyword has no further effect.
+
+
+----------
+
+
+The *buffer* keyword applies only to dump styles *atom*\ , *cfg*\ ,
+*custom*\ , *local*\ , and *xyz*\ .  It also applies only to text output
+files, not to binary or gzipped files.  If specified as *yes*\ , which
+is the default, then each processor writes its output into an internal
+text buffer, which is then sent to the processor(s) which perform file
+writes, and written by those processors(s) as one large chunk of text.
+If specified as *no*\ , each processor sends its per-atom data in binary
+format to the processor(s) which perform file wirtes, and those
+processor(s) format and write it line by line into the output file.
+
+The buffering mode is typically faster since each processor does the
+relatively expensive task of formatting the output for its own atoms.
+However it requires about twice the memory (per processor) for the
+extra buffering.
+
+
+----------
+
+
+The *delay* keyword applies to all dump styles.  No snapshots will be
+output until the specified *Dstep* timestep or later.  Specifying
+*Dstep* < 0 is the same as turning off the delay setting.  This is a
+way to turn off unwanted output early in a simulation, for example,
+during an equilibration phase.
+
+
+----------
+
+
+The *element* keyword applies only to the dump *cfg*\ , *xyz*\ , and
+*image* styles.  It associates element names (e.g. H, C, Fe) with
+LAMMPS atom types.  See the list of element names at the bottom of
+this page.
+
+In the case of dump *cfg*\ , this allows the `AtomEye <atomeye_>`_
+visualization package to read the dump file and render atoms with the
+appropriate size and color.
+
+In the case of dump *image*\ , the output images will follow the same
+`AtomEye <atomeye_>`_ convention.  An element name is specified for each
+atom type (1 to Ntype) in the simulation.  The same element name can
+be given to multiple atom types.
+
+In the case of *xyz* format dumps, there are no restrictions to what
+label can be used as an element name.  Any white-space separated text
+will be accepted.
+
+.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
+
+
+
+
+----------
+
+
+The *every* keyword changes the dump frequency originally specified by
+the :doc:`dump <dump>` command to a new value.  The every keyword can be
+specified in one of two ways.  It can be a numeric value in which case
+it must be > 0.  Or it can be an :doc:`equal-style variable <variable>`,
+which should be specified as v\_name, where name is the variable name.
+
+In this case, the variable is evaluated at the beginning of a run to
+determine the next timestep at which a dump snapshot will be written
+out.  On that timestep the variable will be evaluated again to
+determine the next timestep, etc.  Thus the variable should return
+timestep values.  See the stagger() and logfreq() and stride() math
+functions for :doc:`equal-style variables <variable>`, as examples of
+useful functions to use in this context.  Other similar math functions
+could easily be added as options for :doc:`equal-style variables <variable>`.  Also see the next() function, which allows
+use of a file-style variable which reads successive values from a
+file, each time the variable is evaluated.  Used with the *every*
+keyword, if the file contains a list of ascending timesteps, you can
+output snapshots whenever you wish.
+
+Note that when using the variable option with the *every* keyword, you
+need to use the *first* option if you want an initial snapshot written
+to the dump file.  The *every* keyword cannot be used with the dump
+*dcd* style.
+
+For example, the following commands will
+write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
+
+
+.. parsed-literal::
+
+   variable        s equal logfreq(10,3,10)
+   dump            1 all atom 100 tmp.dump
+   dump_modify     1 every v_s first yes
+
+The following commands would write snapshots at the timesteps listed
+in file tmp.times:
+
+
+.. parsed-literal::
+
+   variable        f file tmp.times
+   variable        s equal next(f)
+   dump            1 all atom 100 tmp.dump
+   dump_modify     1 every v_s
+
+.. note::
+
+   When using a file-style variable with the *every* keyword, the
+   file of timesteps must list a first timestep that is beyond the
+   current timestep (e.g. it cannot be 0).  And it must list one or more
+   timesteps beyond the length of the run you perform.  This is because
+   the dump command will generate an error if the next timestep it reads
+   from the file is not a value greater than the current timestep.  Thus
+   if you wanted output on steps 0,15,100 of a 100-timestep run, the file
+   should contain the values 15,100,101 and you should also use the
+   dump\_modify first command.  Any final value > 100 could be used in
+   place of 101.
+
+
+----------
+
+
+The *first* keyword determines whether a dump snapshot is written on
+the very first timestep after the dump command is invoked.  This will
+always occur if the current timestep is a multiple of N, the frequency
+specified in the :doc:`dump <dump>` command, including timestep 0.  But
+if this is not the case, a dump snapshot will only be written if the
+setting of this keyword is *yes*\ .  If it is *no*\ , which is the
+default, then it will not be written.
+
+
+----------
+
+
+The *flush* keyword determines whether a flush operation is invoked
+after a dump snapshot is written to the dump file.  A flush insures
+the output in that file is current (no buffering by the OS), even if
+LAMMPS halts before the simulation completes.  Flushes cannot be
+performed with dump style *xtc*\ .
+
+
+----------
+
+
+The *format* keyword can be used to change the default numeric format
+output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and
+*xyz* styles, and their MPIIO variants.  Only the *line* or *none*
+options can be used with the *atom* and *xyz* styles.
+
+All the specified format strings are C-style formats, e.g. as used by
+the C/C++ printf() command.  The *line* keyword takes a single
+argument which is the format string for an entire line of output for
+each atom (do not include a trailing "\n"), with N fields, which you
+must enclose in quotes if it is more than one field.  The *int* and
+*float* keywords take a single format argument and are applied to all
+integer or floating-point quantities output.  The setting for *M
+string* also takes a single format argument which is used for the Mth
+value output in each line, e.g. the 5th column is output in high
+precision for "format 5 %20.15g".
+
+.. note::
+
+   When using the *line* keyword for the *cfg* style, the first two
+   fields (atom ID and type) are not actually written into the CFG file,
+   however you must include formats for them in the format string.
+
+The *format* keyword can be used multiple times.  The precedence is
+that for each value in a line of output, the *M* format (if specified)
+is used, else the *int* or *float* setting (if specified) is used,
+else the *line* setting (if specified) for that value is used, else
+the default setting is used.  A setting of *none* clears all previous
+settings, reverting all values to their default format.
+
+.. note::
+
+   Atom and molecule IDs are stored internally as 4-byte or 8-byte
+   signed integers, depending on how LAMMPS was compiled.  When
+   specifying the *format int* option you can use a "%d"-style format
+   identifier in the format string and LAMMPS will convert this to the
+   corresponding 8-byte form if it is needed when outputting those
+   values.  However, when specifying the *line* option or *format M
+   string* option for those values, you should specify a format string
+   appropriate for an 8-byte signed integer, e.g. one with "%ld", if
+   LAMMPS was compiled with the -DLAMMPS\_BIGBIG option for 8-byte IDs.
+
+.. note::
+
+   Any value written to a text-based dump file that is a per-atom
+   quantity calculated by a :doc:`compute <compute>` or :doc:`fix <fix>` is
+   stored internally as a floating-point value.  If the value is actually
+   an integer and you wish it to appear in the text dump file as a
+   (large) integer, then you need to use an appropriate format.  For
+   example, these commands:
+
+
+.. parsed-literal::
+
+   compute     1 all property/local batom1 batom2
+   dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
+   dump_modify 1 format "%d %0.0f %0.0f"
+
+will output the two atom IDs for atoms in each bond as integers.  If
+the dump\_modify command were omitted, they would appear as
+floating-point values, assuming they were large integers (more than 6
+digits).  The "index" keyword should use the "%d" format since it is
+not generated by a compute or fix, and is stored internally as an
+integer.
+
+
+----------
+
+
+The *fileper* keyword is documented below with the *nfile* keyword.
+
+
+----------
+
+
+The *image* keyword applies only to the dump *atom* style.  If the
+image value is *yes*\ , 3 flags are appended to each atom's coords which
+are the absolute box image of the atom in each dimension.  For
+example, an x image flag of -2 with a normalized coord of 0.5 means
+the atom is in the center of the box, but has passed through the box
+boundary 2 times and is really 2 box lengths to the left of its
+current coordinate.  Note that for dump style *custom* these various
+values can be printed in the dump file by using the appropriate atom
+attributes in the dump command itself.
+
+
+----------
+
+
+The *label* keyword applies only to the dump *local* style.  When
+it writes local information, such as bond or angle topology
+to a dump file, it will use the specified *label* to format
+the header.  By default this includes 2 lines:
+
+
+.. parsed-literal::
+
+   ITEM: NUMBER OF ENTRIES
+   ITEM: ENTRIES ...
+
+The word "ENTRIES" will be replaced with the string specified,
+e.g. BONDS or ANGLES.
+
+
+----------
+
+
+The *maxfiles* keyword can only be used when a '\*' wildcard is
+included in the dump file name, i.e. when writing a new file(s) for
+each snapshot.  The specified *Fmax* is how many snapshots will be
+kept.  Once this number is reached, the file(s) containing the oldest
+snapshot is deleted before a new dump file is written.  If the
+specified *Fmax* <= 0, then all files are retained.
+
+This can be useful for debugging, especially if you don't know on what
+timestep something bad will happen, e.g. when LAMMPS will exit with an
+error.  You can dump every timestep, and limit the number of dump
+files produced, even if you run for 1000s of steps.
+
+
+----------
+
+
+The *nfile* or *fileper* keywords can be used in conjunction with the
+"%" wildcard character in the specified dump file name, for all dump
+styles except the *dcd*\ , *image*\ , *movie*\ , *xtc*\ , and *xyz* styles
+(for which "%" is not allowed).  As explained on the :doc:`dump <dump>`
+command doc page, the "%" character causes the dump file to be written
+in pieces, one piece for each of P processors.  By default P = the
+number of processors the simulation is running on.  The *nfile* or
+*fileper* keyword can be used to set P to a smaller value, which can
+be more efficient when running on a large number of processors.
+
+The *nfile* keyword sets P to the specified Nf value.  For example, if
+Nf = 4, and the simulation is running on 100 processors, 4 files will
+be written, by processors 0,25,50,75.  Each will collect information
+from itself and the next 24 processors and write it to a dump file.
+
+For the *fileper* keyword, the specified value of Np means write one
+file for every Np processors.  For example, if Np = 4, every 4th
+processor (0,4,8,12,etc) will collect information from itself and the
+next 3 processors and write it to a dump file.
+
+
+----------
+
+
+The *pad* keyword only applies when the dump filename is specified
+with a wildcard "\*" character which becomes the timestep.  If *pad* is
+0, which is the default, the timestep is converted into a string of
+unpadded length, e.g. 100 or 12000 or 2000000.  When *pad* is
+specified with *Nchar* > 0, the string is padded with leading zeroes
+so they are all the same length = *Nchar*\ .  For example, pad 7 would
+yield 0000100, 0012000, 2000000.  This can be useful so that
+post-processing programs can easily read the files in ascending
+timestep order.
+
+
+----------
+
+
+The *pbc* keyword applies to all the dump styles.  As explained on the
+:doc:`dump <dump>` doc page, atom coordinates in a dump file may be
+slightly outside the simulation box.  This is because periodic
+boundary conditions are enforced only on timesteps when neighbor lists
+are rebuilt, which will not typically coincide with the timesteps dump
+snapshots are written.  If the setting of this keyword is set to
+*yes*\ , then all atoms will be remapped to the periodic box before the
+snapshot is written, then restored to their original position.  If it
+is set to *no* they will not be.  The *no* setting is the default
+because it requires no extra computation.
+
+
+----------
+
+
+The *precision* keyword only applies to the dump *xtc* style.  A
+specified value of N means that coordinates are stored to 1/N
+nanometer accuracy, e.g. for N = 1000, the coordinates are written to
+1/1000 nanometer accuracy.
+
+
+----------
+
+
+The *refresh* keyword only applies to the dump *custom*\ , *cfg*\ ,
+*image*\ , and *movie* styles.  It allows an "incremental" dump file to
+be written, by refreshing a compute that is used as a threshold for
+determining which atoms are included in a dump snapshot.  The
+specified *c\_ID* gives the ID of the compute.  It is prefixed by "c\_"
+to indicate a compute, which is the only current option.  At some
+point, other options may be added, e.g. fixes or variables.
+
+.. note::
+
+   This keyword can only be specified once for a dump.  Refreshes
+   of multiple computes cannot yet be performed.
+
+The definition and motivation of an incremental dump file is as
+follows.  Instead of outputting all atoms at each snapshot (with some
+associated values), you may only wish to output the subset of atoms
+with a value that has changed in some way compared to the value the
+last time that atom was output.  In some scenarios this can result in
+a dramatically smaller dump file.  If desired, by post-processing the
+sequence of snapshots, the values for all atoms at all timesteps can
+be inferred.
+
+A concrete example is a simulation of atom diffusion in a solid,
+represented as atoms on a lattice.  Diffusive hops are rare.  Imagine
+that when a hop occurs an atom moves more than a distance *Dhop*\ .  For
+any snapshot we only want to output atoms that have hopped since the
+last snapshot.  This can be accomplished with something the following
+commands:
+
+
+.. parsed-literal::
+
+   variable        Dhop equal 0.6
+   variable        check atom "c_dsp[4] > v_Dhop"
+   compute         dsp all displace/atom refresh check
+   dump            1 all custom 20 tmp.dump id type x y z
+   dump_modify     1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp
+
+The :doc:`compute displace/atom <compute_displace_atom>` command
+calculates the displacement of each atom from its reference position.
+The "4" index is the scalar displacement; 1,2,3 are the xyz components
+of the displacement.  The :doc:`dump\_modify thresh <dump_modify>`
+command will cause only atoms that have displaced more than 0.6
+Angstroms to be output on a given snapshot (assuming metal units).
+However, note that when an atom is output, we also need to update the
+reference position for that atom to its new coordinates.  So that it
+will not be output in every snapshot thereafter.  That reference
+position is stored by :doc:`compute displace/atom <compute_displace_atom>`.  So the dump\_modify
+*refresh* option triggers a call to compute displace/atom at the end
+of every dump to perform that update.  The *refresh check* option
+shown as part of the :doc:`compute displace/atom <compute_displace_atom>` command enables the compute
+to respond to the call from the dump command, and update the
+appropriate reference positions.  This is done be defining an
+:doc:`atom-style variable <variable>`, *check* in this example, which
+calculates a Boolean value (0 or 1) for each atom, based on the same
+criterion used by dump\_modify thresh.
+
+See the :doc:`compute displace/atom <compute_displace_atom>` command for
+more details, including an example of how to produce output that
+includes an initial snapshot with the reference position of all atoms.
+
+Note that only computes with a *refresh* option will work with
+dump\_modify refresh.  See individual compute doc pages for details.
+Currently, only compute displace/atom supports this option.  Others
+may be added at some point.  If you use a compute that doesn't support
+refresh operations, LAMMPS will not complain; dump\_modify refresh will
+simply do nothing.
+
+
+----------
+
+
+The *region* keyword only applies to the dump *custom*\ , *cfg*\ ,
+*image*\ , and *movie* styles.  If specified, only atoms in the region
+will be written to the dump file or included in the image/movie.  Only
+one region can be applied as a filter (the last one specified).  See
+the :doc:`region <region>` command for more details.  Note that a region
+can be defined as the "inside" or "outside" of a geometric shape, and
+it can be the "union" or "intersection" of a series of simpler
+regions.
+
+
+----------
+
+
+The *scale* keyword applies only to the dump *atom* style.  A scale
+value of *yes* means atom coords are written in normalized units from
+0.0 to 1.0 in each box dimension.  If the simulation box is triclinic
+(tilted), then all atom coords will still be between 0.0 and 1.0.  A
+value of *no* means they are written in absolute distance units
+(e.g. Angstroms or sigma).
+
+
+----------
+
+
+The *sfactor* and *tfactor* keywords only apply to the dump *xtc*
+style.  They allow customization of the unit conversion factors used
+when writing to XTC files.  By default they are initialized for
+whatever :doc:`units <units>` style is being used, to write out
+coordinates in nanometers and time in picoseconds.  I.e. for *real*
+units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the
+Angstroms and fmsec used by *real* units are 0.1 nm and 0.001 psec
+respectively.  If you are using a units system with distance and time
+units far from nm and psec, you may wish to write XTC files with
+different units, since the compression algorithm used in XTC files is
+most effective when the typical magnitude of position data is between
+10.0 and 0.1.
+
+
+----------
+
+
+The *sort* keyword determines whether lines of per-atom output in a
+snapshot are sorted or not.  A sort value of *off* means they will
+typically be written in indeterminate order, either in serial or
+parallel.  This is the case even in serial if the :doc:`atom\_modify sort <atom_modify>` option is turned on, which it is by default, to
+improve performance.  A sort value of *id* means sort the output by
+atom ID.  A sort value of N or -N means sort the output by the value
+in the Nth column of per-atom info in either ascending or descending
+order.
+
+The dump *local* style cannot be sorted by atom ID, since there are
+typically multiple lines of output per atom.  Some dump styles, such
+as *dcd* and *xtc*\ , require sorting by atom ID to format the output
+file correctly.  If multiple processors are writing the dump file, via
+the "%" wildcard in the dump filename, then sorting cannot be
+performed.
+
+.. note::
+
+   Unless it is required by the dump style, sorting dump file
+   output requires extra overhead in terms of CPU and communication cost,
+   as well as memory, versus unsorted output.
+
+
+----------
+
+
+The *thermo* keyword only applies the dump *netcdf* style.  It
+triggers writing of :doc:`thermo <thermo>` information to the dump file
+alongside per-atom data.  The values included in the dump file are
+identical to the values specified by :doc:`thermo\_style <thermo_style>`.
+
+
+----------
+
+
+The *thresh* keyword only applies to the dump *custom*\ , *cfg*\ ,
+*image*\ , and *movie* styles.  Multiple thresholds can be specified.
+Specifying *none* turns off all threshold criteria.  If thresholds are
+specified, only atoms whose attributes meet all the threshold criteria
+are written to the dump file or included in the image.  The possible
+attributes that can be tested for are the same as those that can be
+specified in the :doc:`dump custom <dump>` command, with the exception
+of the *element* attribute, since it is not a numeric value.  Note
+that a different attributes can be used than those output by the :doc:`dump custom <dump>` command.  E.g. you can output the coordinates and
+stress of atoms whose energy is above some threshold.
+
+If an atom-style variable is used as the attribute, then it can
+produce continuous numeric values or effective Boolean 0/1 values
+which may be useful for the comparison operator.  Boolean values can
+be generated by variable formulas that use comparison or Boolean math
+operators or special functions like gmask() and rmask() and grmask().
+See the :doc:`variable <variable>` command doc page for details.
+
+The specified value must be a simple numeric value or the word LAST.
+If LAST is used, it refers to the value of the attribute the last time
+the dump command was invoked to produce a snapshot.  This is a way to
+only dump atoms whose attribute has changed (or not changed).
+Three examples follow.
+
+
+.. parsed-literal::
+
+   dump_modify ... thresh ix != LAST
+
+This will dump atoms which have crossed the periodic x boundary of the
+simulation box since the last dump.  (Note that atoms that crossed
+once and then crossed back between the two dump timesteps would not be
+included.)
+
+
+.. parsed-literal::
+
+   region foo sphere 10 20 10 15
+   variable inregion atom rmask(foo)
+   dump_modify ... thresh v_inregion \|\^ LAST
+
+This will dump atoms which crossed the boundary of the spherical
+region since the last dump.
+
+
+.. parsed-literal::
+
+   variable charge atom "(q > 0.5) \|\| (q < -0.5)"
+   dump_modify ... thresh v_charge \|\^ LAST
+
+This will dump atoms whose charge has changed from an absolute value
+less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
+E.g. due to reactions and subsequent charge equilibration in a
+reactive force field.
+
+The choice of operators listed above are the usual comparison
+operators.  The XOR operation (exclusive or) is also included as "\|\^".
+In this context, XOR means that if either the attribute or value is
+0.0 and the other is non-zero, then the result is "true" and the
+threshold criterion is met.  Otherwise it is not met.
+
+
+----------
+
+
+The *time* keyword only applies to the dump *atom*\ , *custom*\ , and
+*local* styles (and their COMPRESS package versions *atom/gz*\ ,
+*custom/gz* and *local/gz*\ ). If set to *yes*\ , each frame will will
+contain two extra lines before the "ITEM: TIMESTEP" entry:
+
+
+.. parsed-literal::
+
+   ITEM: TIME
+   \<elapsed time\>
+
+This will output the current elapsed simulation time in current
+time units equivalent to the :doc:`thermo keyword <thermo_style>` *time*\ .
+This is to simplify post-processing of trajectories using a variable time
+step, e.g. when using :doc:`fix dt/reset <fix_dt_reset>`.
+The default setting is *no*\ .
+
+
+----------
+
+
+The *units* keyword only applies to the dump *atom*\ , *custom*\ , and
+*local* styles (and their COMPRESS package versions *atom/gz*\ ,
+*custom/gz* and *local/gz*\ ). If set to *yes*\ , each individual dump
+file will contain two extra lines at the very beginning with:
+
+
+.. parsed-literal::
+
+   ITEM: UNITS
+   \<units style\>
+
+This will output the current selected :doc:`units <units>` style
+to the dump file and thus allows visualization and post-processing
+tools to determine the choice of units of the data in the dump file.
+The default setting is *no*\ .
+
+
+----------
+
+
+The *unwrap* keyword only applies to the dump *dcd* and *xtc* styles.
+If set to *yes*\ , coordinates will be written "unwrapped" by the image
+flags for each atom.  Unwrapped means that if the atom has passed through
+a periodic boundary one or more times, the value is printed for what
+the coordinate would be if it had not been wrapped back into the
+periodic box.  Note that these coordinates may thus be far outside the
+box size stored with the snapshot.
+
+
+----------
+
+
+These keywords apply only to the :doc:`dump image <dump_image>` and
+:doc:`dump movie <dump_image>` styles.  Any keyword that affects an
+image, also affects a movie, since the movie is simply a collection of
+images.  Some of the keywords only affect the :doc:`dump movie <dump_image>` style.  The descriptions give details.
+
+
+----------
+
+
+The *acolor* keyword can be used with the :doc:`dump image <dump_image>`
+command, when its atom color setting is *type*\ , to set the color that
+atoms of each type will be drawn in the image.
+
+The specified *type* should be an integer from 1 to Ntypes = the
+number of atom types.  A wildcard asterisk can be used in place of or
+in conjunction with the *type* argument to specify a range of atom
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The specified *color* can be a single color which is any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump\_modify color option.  Or it can be two or more colors separated
+by a "/" character, e.g. red/green/blue.  In the former case, that
+color is assigned to all the specified atom types.  In the latter
+case, the list of colors are assigned in a round-robin fashion to each
+of the specified atom types.
+
+
+----------
+
+
+The *adiam* keyword can be used with the :doc:`dump image <dump_image>`
+command, when its atom diameter setting is *type*\ , to set the size
+that atoms of each type will be drawn in the image.  The specified
+*type* should be an integer from 1 to Ntypes.  As with the *acolor*
+keyword, a wildcard asterisk can be used as part of the *type*
+argument to specify a range of atom types.  The specified *diam* is
+the size in whatever distance :doc:`units <units>` the input script is
+using, e.g. Angstroms.
+
+
+----------
+
+
+The *amap* keyword can be used with the :doc:`dump image <dump_image>`
+command, with its *atom* keyword, when its atom setting is an
+atom-attribute, to setup a color map.  The color map is used to assign
+a specific RGB (red/green/blue) color value to an individual atom when
+it is drawn, based on the atom's attribute, which is a numeric value,
+e.g. its x-component of velocity if the atom-attribute "vx" was
+specified.
+
+The basic idea of a color map is that the atom-attribute will be
+within a range of values, and that range is associated with a series
+of colors (e.g. red, blue, green).  An atom's specific value (vx =
+-3.2) can then mapped to the series of colors (e.g. halfway between
+red and blue), and a specific color is determined via an interpolation
+procedure.
+
+There are many possible options for the color map, enabled by the
+*amap* keyword.  Here are the details.
+
+The *lo* and *hi* settings determine the range of values allowed for
+the atom attribute.  If numeric values are used for *lo* and/or *hi*\ ,
+then values that are lower/higher than that value are set to the
+value.  I.e. the range is static.  If *lo* is specified as *min* or
+*hi* as *max* then the range is dynamic, and the lower and/or
+upper bound will be calculated each time an image is drawn, based
+on the set of atoms being visualized.
+
+The *style* setting is two letters, such as "ca".  The first letter is
+either "c" for continuous, "d" for discrete, or "s" for sequential.
+The second letter is either "a" for absolute, or "f" for fractional.
+
+A continuous color map is one in which the color changes continuously
+from value to value within the range.  A discrete color map is one in
+which discrete colors are assigned to sub-ranges of values within the
+range.  A sequential color map is one in which discrete colors are
+assigned to a sequence of sub-ranges of values covering the entire
+range.
+
+An absolute color map is one in which the values to which colors are
+assigned are specified explicitly as values within the range.  A
+fractional color map is one in which the values to which colors are
+assigned are specified as a fractional portion of the range.  For
+example if the range is from -10.0 to 10.0, and the color red is to be
+assigned to atoms with a value of 5.0, then for an absolute color map
+the number 5.0 would be used.  But for a fractional map, the number
+0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
+
+The *delta* setting must be specified for all styles, but is only used
+for the sequential style; otherwise the value is ignored.  It
+specifies the bin size to use within the range for assigning
+consecutive colors to.  For example, if the range is from -10.0 to
+10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
+the range.  The first will be from -10.0 <= color1 < -9.0, then 2nd
+from -9.0 <= color2 < -8.0, etc.
+
+The *N* setting is how many entries follow.  The format of the entries
+depends on whether the color map style is continuous, discrete or
+sequential.  In all cases the *color* setting can be any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump\_modify color option.
+
+For continuous color maps, each entry has a *value* and a *color*\ .
+The *value* is either a number within the range of values or *min* or
+*max*\ .  The *value* of the first entry must be *min* and the *value*
+of the last entry must be *max*\ .  Any entries in between must have
+increasing values.  Note that numeric values can be specified either
+as absolute numbers or as fractions (0.0 to 1.0) of the range,
+depending on the "a" or "f" in the style setting for the color map.
+
+Here is how the entries are used to determine the color of an
+individual atom, given the value X of its atom attribute.  X will fall
+between 2 of the entry values.  The color of the atom is linearly
+interpolated (in each of the RGB values) between the 2 colors
+associated with those entries.  For example, if X = -5.0 and the 2
+surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
+atom's color will be halfway between "red" and "blue", which happens
+to be "purple".
+
+For discrete color maps, each entry has a *lo* and *hi* value and a
+*color*\ .  The *lo* and *hi* settings are either numbers within the
+range of values or *lo* can be *min* or *hi* can be *max*\ .  The *lo*
+and *hi* settings of the last entry must be *min* and *max*\ .  Other
+entries can have any *lo* and *hi* values and the sub-ranges of
+different values can overlap.  Note that numeric *lo* and *hi* values
+can be specified either as absolute numbers or as fractions (0.0 to
+1.0) of the range, depending on the "a" or "f" in the style setting
+for the color map.
+
+Here is how the entries are used to determine the color of an
+individual atom, given the value X of its atom attribute.  The entries
+are scanned from first to last.  The first time that *lo* <= X <=
+*hi*\ , X is assigned the color associated with that entry.  You can
+think of the last entry as assigning a default color (since it will
+always be matched by X), and the earlier entries as colors that
+override the default.  Also note that no interpolation of a color RGB
+is done.  All atoms will be drawn with one of the colors in the list
+of entries.
+
+For sequential color maps, each entry has only a *color*\ .  Here is how
+the entries are used to determine the color of an individual atom,
+given the value X of its atom attribute.  The range is partitioned
+into N bins of width *binsize*\ .  Thus X will fall in a specific bin
+from 1 to N, say the Mth bin.  If it falls on a boundary between 2
+bins, it is considered to be in the higher of the 2 bins.  Each bin is
+assigned a color from the E entries.  If E < N, then the colors are
+repeated.  For example if 2 entries with colors red and green are
+specified, then the odd numbered bins will be red and the even bins
+green.  The color of the atom is the color of its bin.  Note that the
+sequential color map is really a shorthand way of defining a discrete
+color map without having to specify where all the bin boundaries are.
+
+Here is an example of using a sequential color map to color all the
+atoms in individual molecules with a different color.  See the
+examples/pour/in.pour.2d.molecule input script for an example of how
+this is used.
+
+
+.. parsed-literal::
+
+   variable        colors string &
+                   "red green blue yellow white &
+                   purple pink orange lime gray"
+   variable        mol atom mol%10
+   dump            1 all image 250 image.\*.jpg v_mol type &
+                   zoom 1.6 adiam 1.5
+   dump_modify     1 pad 5 amap 0 10 sa 1 10 ${colors}
+
+In this case, 10 colors are defined, and molecule IDs are
+mapped to one of the colors, even if there are 1000s of molecules.
+
+
+----------
+
+
+The *backcolor* sets the background color of the images.  The color
+name can be any of the 140 pre-defined colors (see below) or a color
+name defined by the dump\_modify color option.
+
+
+----------
+
+
+The *bcolor* keyword can be used with the :doc:`dump image <dump_image>`
+command, with its *bond* keyword, when its color setting is *type*\ , to
+set the color that bonds of each type will be drawn in the image.
+
+The specified *type* should be an integer from 1 to Nbondtypes = the
+number of bond types.  A wildcard asterisk can be used in place of or
+in conjunction with the *type* argument to specify a range of bond
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of bond types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The specified *color* can be a single color which is any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump\_modify color option.  Or it can be two or more colors separated
+by a "/" character, e.g. red/green/blue.  In the former case, that
+color is assigned to all the specified bond types.  In the latter
+case, the list of colors are assigned in a round-robin fashion to each
+of the specified bond types.
+
+
+----------
+
+
+The *bdiam* keyword can be used with the :doc:`dump image <dump_image>`
+command, with its *bond* keyword, when its diam setting is *type*\ , to
+set the diameter that bonds of each type will be drawn in the image.
+The specified *type* should be an integer from 1 to Nbondtypes.  As
+with the *bcolor* keyword, a wildcard asterisk can be used as part of
+the *type* argument to specify a range of bond types.  The specified
+*diam* is the size in whatever distance :doc:`units <units>` you are
+using, e.g. Angstroms.
+
+
+----------
+
+
+The *bitrate* keyword can be used with the :doc:`dump movie <dump_image>` command to define the size of the resulting
+movie file and its quality via setting how many kbits per second are
+to be used for the movie file. Higher bitrates require less
+compression and will result in higher quality movies.  The quality is
+also determined by the compression format and encoder.  The default
+setting is 2000 kbit/s, which will result in average quality with
+older compression formats.
+
+.. note::
+
+   Not all movie file formats supported by dump movie allow the
+   bitrate to be set.  If not, the setting is silently ignored.
+
+
+----------
+
+
+The *boxcolor* keyword sets the color of the simulation box drawn
+around the atoms in each image as well as the color of processor
+sub-domain boundaries.  See the "dump image box" command for how to
+specify that a box be drawn via the *box* keyword, and the sub-domain
+boundaries via the *subbox* keyword.  The color name can be any of the
+140 pre-defined colors (see below) or a color name defined by the
+dump\_modify color option.
+
+
+----------
+
+
+The *color* keyword allows definition of a new color name, in addition
+to the 140-predefined colors (see below), and associates 3
+red/green/blue RGB values with that color name.  The color name can
+then be used with any other dump\_modify keyword that takes a color
+name as a value.  The RGB values should each be floating point values
+between 0.0 and 1.0 inclusive.
+
+When a color name is converted to RGB values, the user-defined color
+names are searched first, then the 140 pre-defined color names.  This
+means you can also use the *color* keyword to overwrite one of the
+pre-defined color names with new RBG values.
+
+
+----------
+
+
+The *framerate* keyword can be used with the :doc:`dump movie <dump_image>` command to define the duration of the resulting
+movie file.  Movie files written by the dump *movie* command have a
+default frame rate of 24 frames per second and the images generated
+will be converted at that rate.  Thus a sequence of 1000 dump images
+will result in a movie of about 42 seconds.  To make a movie run
+longer you can either generate images more frequently or lower the
+frame rate.  To speed a movie up, you can do the inverse.  Using a
+frame rate higher than 24 is not recommended, as it will result in
+simply dropping the rendered images. It is more efficient to dump
+images less frequently.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump image <dump_image>`, :doc:`undump <undump>`
+
+Default
+"""""""
+
+The option defaults are
+
+* append = no
+* buffer = yes for dump styles *atom*\ , *custom*\ , *loca*\ , and *xyz*
+* element = "C" for every atom type
+* every = whatever it was set to via the :doc:`dump <dump>` command
+* fileper = # of processors
+* first = no
+* flush = yes
+* format = %d and %g for each integer or floating point value
+* image = no
+* label = ENTRIES
+* maxfiles = -1
+* nfile = 1
+* pad = 0
+* pbc = no
+* precision = 1000
+* region = none
+* scale = yes
+* sort = off for dump styles *atom*\ , *custom*\ , *cfg*\ , and *local*
+* sort = id for dump styles *dcd*\ , *xtc*\ , and *xyz*
+* thresh = none
+* units = no
+* unwrap = no
+
+* acolor = \* red/green/blue/yellow/aqua/cyan
+* adiam = \* 1.0
+* amap = min max cf 0.0 2 min blue max red
+* backcolor = black
+* bcolor = \* red/green/blue/yellow/aqua/cyan
+* bdiam = \* 0.5
+* bitrate = 2000
+* boxcolor = yellow
+* color = 140 color names are pre-defined as listed below
+* framerate = 24
+
+
+----------
+
+
+These are the standard 109 element names that LAMMPS pre-defines for
+use with the :doc:`dump image <dump_image>` and dump\_modify commands.
+
+* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
+* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
+* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
+* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
+* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
+* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
+* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
+* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
+* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
+* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
+* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
+
+
+----------
+
+
+These are the 140 colors that LAMMPS pre-defines for use with the
+:doc:`dump image <dump_image>` and dump\_modify commands.  Additional
+colors can be defined with the dump\_modify color command.  The 3
+numbers listed for each name are the RGB (red/green/blue) values.
+Divide each value by 255 to get the equivalent 0.0 to 1.0 value.
+
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| aliceblue = 240, 248, 255     | antiquewhite = 250, 235, 215         | aqua = 0, 255, 255              | aquamarine = 127, 255, 212     | azure = 240, 255, 255          |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| beige = 245, 245, 220         | bisque = 255, 228, 196               | black = 0, 0, 0                 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255               |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| blueviolet = 138, 43, 226     | brown = 165, 42, 42                  | burlywood = 222, 184, 135       | cadetblue = 95, 158, 160       | chartreuse = 127, 255, 0       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| chocolate = 210, 105, 30      | coral = 255, 127, 80                 | cornflowerblue = 100, 149, 237  | cornsilk = 255, 248, 220       | crimson = 220, 20, 60          |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| cyan = 0, 255, 255            | darkblue = 0, 0, 139                 | darkcyan = 0, 139, 139          | darkgoldenrod = 184, 134, 11   | darkgray = 169, 169, 169       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| darkgreen = 0, 100, 0         | darkkhaki = 189, 183, 107            | darkmagenta = 139, 0, 139       | darkolivegreen = 85, 107, 47   | darkorange = 255, 140, 0       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| darkorchid = 153, 50, 204     | darkred = 139, 0, 0                  | darksalmon = 233, 150, 122      | darkseagreen = 143, 188, 143   | darkslateblue = 72, 61, 139    |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| darkslategray = 47, 79, 79    | darkturquoise = 0, 206, 209          | darkviolet = 148, 0, 211        | deeppink = 255, 20, 147        | deepskyblue = 0, 191, 255      |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| dimgray = 105, 105, 105       | dodgerblue = 30, 144, 255            | firebrick = 178, 34, 34         | floralwhite = 255, 250, 240    | forestgreen = 34, 139, 34      |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| fuchsia = 255, 0, 255         | gainsboro = 220, 220, 220            | ghostwhite = 248, 248, 255      | gold = 255, 215, 0             | goldenrod = 218, 165, 32       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| gray = 128, 128, 128          | green = 0, 128, 0                    | greenyellow = 173, 255, 47      | honeydew = 240, 255, 240       | hotpink = 255, 105, 180        |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| indianred = 205, 92, 92       | indigo = 75, 0, 130                  | ivory = 255, 240, 240           | khaki = 240, 230, 140          | lavender = 230, 230, 250       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0              | lemonchiffon = 255, 250, 205    | lightblue = 173, 216, 230      | lightcoral = 240, 128, 128     |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| lightcyan = 224, 255, 255     | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144      | lightgrey = 211, 211, 211      | lightpink = 255, 182, 193      |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| lightsalmon = 255, 160, 122   | lightseagreen = 32, 178, 170         | lightskyblue = 135, 206, 250    | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| lightyellow = 255, 255, 224   | lime = 0, 255, 0                     | limegreen = 50, 205, 50         | linen = 250, 240, 230          | magenta = 255, 0, 255          |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| maroon = 128, 0, 0            | mediumaquamarine = 102, 205, 170     | mediumblue = 0, 0, 205          | mediumorchid = 186, 85, 211    | mediumpurple = 147, 112, 219   |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238      | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| midnightblue = 25, 25, 112    | mintcream = 245, 255, 250            | mistyrose = 255, 228, 225       | moccasin = 255, 228, 181       | navajowhite = 255, 222, 173    |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| navy = 0, 0, 128              | oldlace = 253, 245, 230              | olive = 128, 128, 0             | olivedrab = 107, 142, 35       | orange = 255, 165, 0           |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| orangered = 255, 69, 0        | orchid = 218, 112, 214               | palegoldenrod = 238, 232, 170   | palegreen = 152, 251, 152      | paleturquoise = 175, 238, 238  |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213           | peachpuff = 255, 239, 213       | peru = 205, 133, 63            | pink = 255, 192, 203           |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| plum = 221, 160, 221          | powderblue = 176, 224, 230           | purple = 128, 0, 128            | red = 255, 0, 0                | rosybrown = 188, 143, 143      |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| royalblue = 65, 105, 225      | saddlebrown = 139, 69, 19            | salmon = 250, 128, 114          | sandybrown = 244, 164, 96      | seagreen = 46, 139, 87         |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| seashell = 255, 245, 238      | sienna = 160, 82, 45                 | silver = 192, 192, 192          | skyblue = 135, 206, 235        | slateblue = 106, 90, 205       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| slategray = 112, 128, 144     | snow = 255, 250, 250                 | springgreen = 0, 255, 127       | steelblue = 70, 130, 180       | tan = 210, 180, 140            |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| teal = 0, 128, 128            | thistle = 216, 191, 216              | tomato = 253, 99, 71            | turquoise = 64, 224, 208       | violet = 238, 130, 238         |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| wheat = 245, 222, 179         | white = 255, 255, 255                | whitesmoke = 245, 245, 245      | yellow = 255, 255, 0           | yellowgreen = 154, 205, 50     |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst
new file mode 100644
index 0000000000..4c03def9b7
--- /dev/null
+++ b/doc/src/dump_molfile.rst
@@ -0,0 +1,145 @@
+.. index:: dump molfile
+
+dump molfile command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump ID group-ID molfile N file format path
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be imaged
+* molfile = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* N = dump every this many timesteps
+* file = name of file to write to
+* format = file format to be used
+* path = file path with plugins (optional)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump mf1 all molfile 10 melt1.xml hoomd
+   dump mf2 all molfile 10 melt2-\*.pdb pdb .
+   dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
+
+Description
+"""""""""""
+
+Dump a snapshot of atom coordinates and selected additional quantities
+to one or more files every N timesteps in one of several formats.
+Only information for atoms in the specified group is dumped.  This
+specific dump style uses molfile plugins that are bundled with the
+`VMD <http://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
+analysis program.
+
+Unless the filename contains a \* character, the output will be written
+to one single file with the specified format. Otherwise there will be
+one file per snapshot and the \* will be replaced by the time step number
+when the snapshot is written.
+
+.. note::
+
+   Because periodic boundary conditions are enforced only on
+   timesteps when neighbor lists are rebuilt, the coordinates of an atom
+   written to a dump file may be slightly outside the simulation box.
+
+The molfile plugin API has a few restrictions that have to be honored
+by this dump style: the number of atoms must not change, the atoms
+must be sorted, outside of the coordinates no change in atom properties
+(like type, mass, charge) will be recorded.
+
+
+----------
+
+
+The *format* keyword determines what format is used to write out the
+dump. For this to work, LAMMPS must be able to find and load a
+compatible molfile plugin that supports this format.  Settings made via
+the :doc:`dump\_modify <dump_modify>` command can alter per atom properties
+like element names.
+
+The *path* keyword determines which in directories. This is a "path"
+like other search paths, i.e. it can contain multiple directories
+separated by a colon (or semi-colon on windows). This keyword is
+optional and default to ".", the current directory.
+
+The *unwrap* option of the :doc:`dump\_modify <dump_modify>` command allows
+coordinates to be written "unwrapped" by the image flags for each atom.
+Unwrapped means that if the atom has passed through a periodic boundary
+one or more times, the value is printed for what the coordinate would be
+if it had not been wrapped back into the periodic box.  Note that these
+coordinates may thus be far outside the box size stored with the
+snapshot.
+
+
+----------
+
+
+Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges.  Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N.  This behavior can be
+changed via the :doc:`dump\_modify first <dump_modify>` command, which can
+be useful if the dump command is invoked after a minimization ended on
+an arbitrary timestep.  N can be changed between runs by using the
+:doc:`dump\_modify every <dump_modify>` command. The :doc:`dump\_modify every <dump_modify>` command also allows a variable to be used to
+determine the sequence of timesteps on which dump files are written.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *molfile* dump style is part of the USER-MOLFILE package.  It is
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Molfile plugins provide a consistent programming interface to read and
+write file formats commonly used in molecular simulations. The
+USER-MOLFILE package only provides the interface code, not the plugins.
+These can be obtained from a VMD installation which has to match the
+platform that you are using to compile LAMMPS for. By adding plugins
+to VMD, support for new file formats can be added to LAMMPS (or VMD
+or other programs that use them) without having to re-compile the
+application itself.  The plugins are installed in the directory:
+<VMDHOME>/plugins/<VMDARCH>/molfile
+
+.. note::
+
+   while the programming interface (API) to the plugins is backward
+   compatible, the binary interface (ABI) has been changing over time, so
+   it is necessary to compile this package with the plugin header files
+   from VMD that match the binary plugins.  These header files in the
+   directory: <VMDHOME>/plugins/include For convenience, the package ships
+   with a set of header files that are compatible with VMD 1.9 and 1.9.1
+   (June 2012)
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump\_modify <dump_modify>`, :doc:`undump <undump>`
+
+Default
+"""""""
+
+The default path is ".". All other properties have to be specified.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst
new file mode 100644
index 0000000000..f89faff0ca
--- /dev/null
+++ b/doc/src/dump_netcdf.rst
@@ -0,0 +1,97 @@
+.. index:: dump netcdf
+
+dump netcdf command
+===================
+
+dump netcdf/mpiio command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump ID group-ID netcdf N file args
+   dump ID group-ID netcdf/mpiio N file args
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be imaged
+* *netcdf* or *netcdf/mpiio*  = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* N = dump every this many timesteps
+* file = name of file to write dump info to
+* args = list of atom attributes, same as for :doc:`dump\_style custom <dump>`
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump 1 all netcdf 100 traj.nc type x y z vx vy vz
+   dump_modify 1 append yes at -1 thermo yes
+   dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
+   dump 1 all netcdf 1000 traj.\*.nc id type x y z
+
+Description
+"""""""""""
+
+Dump a snapshot of atom coordinates every N timesteps in Amber-style
+NetCDF file format.  NetCDF files are binary, portable and
+self-describing.  This dump style will write only one file on the root
+node.  The dump style *netcdf* uses the `standard NetCDF library <netcdf-home_>`_.  All data is collected on one processor and then
+written to the dump file.  Dump style *netcdf/mpiio* uses the
+`parallel NetCDF library <pnetcdf-home_>`_ and MPI-IO to write to the dump
+file in parallel; it has better performance on a larger number of
+processors.  Note that style *netcdf* outputs all atoms sorted by atom
+tag while style *netcdf/mpiio* outputs atoms in order of their MPI
+rank.
+
+NetCDF files can be directly visualized via the following tools:
+
+Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
+all extensions of this dump style.
+
+* VMD (http://www.ks.uiuc.edu/Research/vmd/).
+* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
+  contains a NetCDF reader that is not present in the standard
+  distribution of AtomEye.
+
+In addition to per-atom data, :doc:`thermo <thermo>` data can be included in the
+dump file. The data included in the dump file is identical to the data specified
+by :doc:`thermo\_style <thermo_style>`.
+
+.. _netcdf-home: http://www.unidata.ucar.edu/software/netcdf/
+
+
+
+.. _pnetcdf-home: http://trac.mcs.anl.gov/projects/parallel-netcdf/
+
+
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *netcdf* and *netcdf/mpiio* dump styles are part of the
+USER-NETCDF package.  They are only enabled if LAMMPS was built with
+that package. See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump\_modify <dump_modify>`, :doc:`undump <undump>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst
new file mode 100644
index 0000000000..2f229aaccc
--- /dev/null
+++ b/doc/src/dump_vtk.rst
@@ -0,0 +1,199 @@
+.. index:: dump vtk
+
+dump vtk command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dump ID group-ID vtk N file args
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be dumped
+* vtk = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* N = dump every this many timesteps
+* file = name of file to write dump info to
+* args = same as arguments for :doc:`dump\_style custom <dump>`
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dump dmpvtk all vtk 100 dump\*.myforce.vtk id type vx fx
+   dump dmpvtp flow vtk 100 dump\*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
+
+Description
+"""""""""""
+
+Dump a snapshot of atom quantities to one or more files every N
+timesteps in a format readable by the `VTK visualization toolkit <http://www.vtk.org>`_ or other visualization tools that use it,
+e.g. `ParaView <http://www.paraview.org>`_.  The timesteps on which dump
+output is written can also be controlled by a variable; see the
+:doc:`dump\_modify every <dump_modify>` command for details.
+
+This dump style is similar to :doc:`dump\_style custom <dump>` but uses
+the VTK library to write data to VTK simple legacy or XML format
+depending on the filename extension specified for the dump file.  This
+can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*,
+respectively, for XML format; see the `VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
+description of these formats.  Since this naming convention conflicts
+with the way binary output is usually specified (see below), the
+:doc:`dump\_modify binary <dump_modify>` command allows setting of a
+binary option for this dump style explicitly.
+
+Only information for atoms in the specified group is dumped.  The
+:doc:`dump\_modify thresh and region <dump_modify>` commands can also
+alter what atoms are included; see details below.
+
+As described below, special characters ("\*", "%") in the filename
+determine the kind of output.
+
+.. warning::
+
+   Because periodic boundary conditions are enforced only
+   on timesteps when neighbor lists are rebuilt, the coordinates of an
+   atom written to a dump file may be slightly outside the simulation
+   box.
+
+.. warning::
+
+   Unless the :doc:`dump\_modify sort <dump_modify>` option
+   is invoked, the lines of atom information written to dump files will
+   be in an indeterminate order for each snapshot.  This is even true
+   when running on a single processor, if the :doc:`atom\_modify sort <atom_modify>` option is on, which it is by default.  In this
+   case atoms are re-ordered periodically during a simulation, due to
+   spatial sorting.  It is also true when running in parallel, because
+   data for a single snapshot is collected from multiple processors, each
+   of which owns a subset of the atoms.
+
+For the *vtk* style, sorting is off by default. See the
+:doc:`dump\_modify <dump_modify>` doc page for details.
+
+
+----------
+
+
+The dimensions of the simulation box are written to a separate file
+for each snapshot (either in legacy VTK or XML format depending on the
+format of the main dump file) with the suffix *\_boundingBox* appended
+to the given dump filename.
+
+For an orthogonal simulation box this information is saved as a
+rectilinear grid (legacy .vtk or .vtr XML format).
+
+Triclinic simulation boxes (non-orthogonal) are saved as
+hexahedrons in either legacy .vtk or .vtu XML format.
+
+Style *vtk* allows you to specify a list of atom attributes to be
+written to the dump file for each atom.  The list of possible attributes
+is the same as for the :doc:`dump\_style custom <dump>` command; see
+its doc page for a listing and an explanation of each attribute.
+
+.. note::
+
+   Since position data is required to write VTK files the atom
+   attributes "x y z" do not have to be specified explicitly; they will
+   be included in the dump file regardless.  Also, in contrast to the
+   *custom* style, the specified *vtk* attributes are rearranged to
+   ensure correct ordering of vector components (except for computes and
+   fixes - these have to be given in the right order) and duplicate
+   entries are removed.
+
+The VTK format uses a single snapshot of the system per file, thus
+a wildcard "\*" must be included in the filename, as discussed below.
+Otherwise the dump files will get overwritten with the new snapshot
+each time.
+
+
+----------
+
+
+Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges.  Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N.  This behavior can be
+changed via the :doc:`dump\_modify first <dump_modify>` command, which
+can also be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep.  N can be changed between runs by
+using the :doc:`dump\_modify every <dump_modify>` command.
+The :doc:`dump\_modify every <dump_modify>` command
+also allows a variable to be used to determine the sequence of
+timesteps on which dump files are written.  In this mode a dump on the
+first timestep of a run will also not be written unless the
+:doc:`dump\_modify first <dump_modify>` command is used.
+
+Dump filenames can contain two wildcard characters.  If a "\*"
+character appears in the filename, then one file per snapshot is
+written and the "\*" character is replaced with the timestep value.
+For example, tmp.dump\*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
+tmp.dump20000.vtk, etc.  Note that the :doc:`dump\_modify pad <dump_modify>`
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order with some post-processing tools.
+
+If a "%" character appears in the filename, then each of P processors
+writes a portion of the dump file, and the "%" character is replaced
+with the processor ID from 0 to P-1 preceded by an underscore character.
+For example, tmp.dump%.vtp becomes tmp.dump\_0.vtp, tmp.dump\_1.vtp, ...
+tmp.dump\_P-1.vtp, etc.  This creates smaller files and can be a fast
+mode of output on parallel machines that support parallel I/O for output.
+
+By default, P = the number of processors meaning one file per
+processor, but P can be set to a smaller value via the *nfile* or
+*fileper* keywords of the :doc:`dump\_modify <dump_modify>` command.
+These options can be the most efficient way of writing out dump files
+when running on large numbers of processors.
+
+For the legacy VTK format "%" is ignored and P = 1, i.e., only
+processor 0 does write files.
+
+Note that using the "\*" and "%" characters together can produce a
+large number of small dump files!
+
+If *dump\_modify binary* is used, the dump file (or files, if "\*" or
+"%" is also used) is written in binary format.  A binary dump file
+will be about the same size as a text version, but will typically
+write out much faster.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *vtk* style does not support writing of gzipped dump files.
+
+The *vtk* dump style is part of the USER-VTK package. It is only
+enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+To use this dump style, you also must link to the VTK library.  See
+the info in lib/vtk/README and insure the Makefile.lammps file in that
+directory is appropriate for your machine.
+
+The *vtk* dump style supports neither buffering or custom format
+strings.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump image <dump_image>`,
+:doc:`dump\_modify <dump_modify>`, :doc:`undump <undump>`
+
+Default
+"""""""
+
+By default, files are written in ASCII format. If the file extension
+is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst
new file mode 100644
index 0000000000..0d4ccf7589
--- /dev/null
+++ b/doc/src/dynamical_matrix.rst
@@ -0,0 +1,88 @@
+.. index:: dynamical\_matrix
+
+dynamical\_matrix command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   dynamical_matrix group-ID style gamma args keyword value ...
+
+* group-ID = ID of group of atoms to displace
+* style = *regular* or *eskm*
+* gamma = finite different displacement length (distance units)
+* one or more keyword/arg pairs may be appended
+  
+  .. parsed-literal::
+  
+       keyword = *file* or *binary*
+         *file* name = name of output file for the dynamical matrix
+         *binary* arg = *yes* or *no* or *gzip*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   dynamical_matrix 1 regular 0.000001
+   dynamical_matrix 1 eskm 0.000001
+   dynamical_matrix 3 regular 0.00004 file dynmat.dat
+   dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes
+
+Description
+"""""""""""
+
+Calculate the dynamical matrix by finite difference of the selected group,
+
+.. image:: JPG/dynamical_matrix_dynmat.jpg
+   :align: center
+
+where D is the dynamical matrix and Phi is the force constant matrix defined by
+
+.. image:: JPG/dynamical_matrix_force_constant.jpg
+   :align: center
+
+The output for the dynamical matrix is printed three elements at a time. The
+three elements are the three beta elements for a respective i/alpha/j combination. 
+Each line is printed in order of j increasing first, alpha second, and i last.
+
+If the style eskm is selected, the dynamical matrix will be in units of inverse squared
+femtoseconds. These units will then conveniently leave frequencies in THz, where
+frequencies, represented as omega, can be calculated from
+
+:c, image(Eqs/dynamical\_matrix\_phonons.jpg)
+
+Restrictions
+""""""""""""
+
+
+The command collects an array of nine times the number of atoms in a group
+on every single MPI rank, so the memory requirements can be very significant
+for large systems.
+
+This command is part of the USER-PHONON package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix phonon <fix_phonon>`
+
+:doc:`compute hma <compute_hma>` uses an analytic formulation of the hessian
+provided by Pair's single\_hessian.
+
+Default
+"""""""
+
+The default settings are file = "dynmat.dyn", binary = no
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/echo.rst b/doc/src/echo.rst
new file mode 100644
index 0000000000..a88d821993
--- /dev/null
+++ b/doc/src/echo.rst
@@ -0,0 +1,53 @@
+.. index:: echo
+
+echo command
+============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   echo style
+
+* style = *none* or *screen* or *log* or *both*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   echo both
+   echo log
+
+Description
+"""""""""""
+
+This command determines whether LAMMPS echoes each input script
+command to the screen and/or log file as it is read and processed.  If
+an input script has errors, it can be useful to look at echoed output
+to see the last command processed.
+
+The :doc:`command-line switch <Run_options>` -echo can be used in place
+of this command.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   echo log
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix.rst b/doc/src/fix.rst
new file mode 100644
index 0000000000..cc99940f81
--- /dev/null
+++ b/doc/src/fix.rst
@@ -0,0 +1,411 @@
+.. index:: fix
+
+fix command
+===========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style args
+
+* ID = user-assigned name for the fix
+* group-ID = ID of the group of atoms to apply the fix to
+* style = one of a long list of possible style names (see below)
+* args = arguments used by a particular style
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve
+   fix 3 all nvt temp 300.0 300.0 0.01
+   fix mine top setforce 0.0 NULL 0.0
+
+Description
+"""""""""""
+
+Set a fix that will be applied to a group of atoms.  In LAMMPS, a
+"fix" is any operation that is applied to the system during
+timestepping or minimization.  Examples include updating of atom
+positions and velocities due to time integration, controlling
+temperature, applying constraint forces to atoms, enforcing boundary
+conditions, computing diagnostics, etc.  There are hundreds of fixes
+defined in LAMMPS and new ones can be added; see the
+:doc:`Modify <Modify>` doc page for details.
+
+Fixes perform their operations at different stages of the timestep.
+If 2 or more fixes operate at the same stage of the timestep, they are
+invoked in the order they were specified in the input script.
+
+The ID of a fix can only contain alphanumeric characters and
+underscores.
+
+Fixes can be deleted with the :doc:`unfix <unfix>` command.
+
+.. note::
+
+   The :doc:`unfix <unfix>` command is the only way to turn off a
+   fix; simply specifying a new fix with a similar style will not turn
+   off the first one.  This is especially important to realize for
+   integration fixes.  For example, using a :doc:`fix nve <fix_nve>`
+   command for a second run after using a :doc:`fix nvt <fix_nh>` command
+   for the first run, will not cancel out the NVT time integration
+   invoked by the "fix nvt" command.  Thus two time integrators would be
+   in place!
+
+If you specify a new fix with the same ID and style as an existing
+fix, the old fix is deleted and the new one is created (presumably
+with new settings).  This is the same as if an "unfix" command were
+first performed on the old fix, except that the new fix is kept in the
+same order relative to the existing fixes as the old one originally
+was.  Note that this operation also wipes out any additional changes
+made to the old fix via the :doc:`fix_modify <fix_modify>` command.
+
+The :doc:`fix modify <fix_modify>` command allows settings for some
+fixes to be reset.  See the doc page for individual fixes for details.
+
+Some fixes store an internal "state" which is written to binary
+restart files via the :doc:`restart <restart>` or
+:doc:`write_restart <write_restart>` commands.  This allows the fix to
+continue on with its calculations in a restarted simulation.  See the
+:doc:`read_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file.  See the doc pages
+for individual fixes for info on which ones can be restarted.
+
+
+----------
+
+
+Some fixes calculate one of three styles of quantities: global,
+per-atom, or local, which can be used by other commands or output as
+described below.  A global quantity is one or more system-wide values,
+e.g. the energy of a wall interacting with particles.  A per-atom
+quantity is one or more values per atom, e.g. the displacement vector
+for each atom since time 0.  Per-atom values are set to 0.0 for atoms
+not in the specified fix group.  Local quantities are calculated by
+each processor based on the atoms it owns, but there may be zero or
+more per atoms.
+
+Note that a single fix can produce either global or per-atom or local
+quantities (or none at all), but not both global and per-atom.  It can
+produce local quantities in tandem with global or per-atom quantities.
+The fix doc page will explain.
+
+Global, per-atom, and local quantities each come in three kinds: a
+single scalar value, a vector of values, or a 2d array of values.  The
+doc page for each fix describes the style and kind of values it
+produces, e.g. a per-atom vector.  Some fixes produce more than one
+kind of a single style, e.g. a global scalar and a global vector.
+
+When a fix quantity is accessed, as in many of the output commands
+discussed below, it can be referenced via the following bracket
+notation, where ID is the ID of the fix:
+
++-------------+--------------------------------------------+
+| f\_ID       | entire scalar, vector, or array            |
++-------------+--------------------------------------------+
+| f\_ID[I]    | one element of vector, one column of array |
++-------------+--------------------------------------------+
+| f\_ID[I][J] | one element of array                       |
++-------------+--------------------------------------------+
+
+In other words, using one bracket reduces the dimension of the
+quantity once (vector -> scalar, array -> vector).  Using two brackets
+reduces the dimension twice (array -> scalar).  Thus a command that
+uses scalar fix values as input can also process elements of a vector
+or array.
+
+Note that commands and :doc:`variables <variable>` which use fix
+quantities typically do not allow for all kinds, e.g. a command may
+require a vector of values, not a scalar.  This means there is no
+ambiguity about referring to a fix quantity as f\_ID even if it
+produces, for example, both a scalar and vector.  The doc pages for
+various commands explain the details.
+
+
+----------
+
+
+In LAMMPS, the values generated by a fix can be used in several ways:
+
+* Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
+  Or the values can be referenced in a :doc:`variable equal <variable>` or
+  :doc:`variable atom <variable>` command.
+* Per-atom values can be output via the :doc:`dump custom <dump>` command.
+  Or they can be time-averaged via the :doc:`fix ave/atom <fix_ave_atom>`
+  command or reduced by the :doc:`compute reduce <compute_reduce>`
+  command.  Or the per-atom values can be referenced in an :doc:`atom-style variable <variable>`.
+* Local values can be reduced by the :doc:`compute reduce <compute_reduce>` command, or histogrammed by the :doc:`fix ave/histo <fix_ave_histo>` command.
+
+
+See the :doc:`Howto output <Howto_output>` doc page for a summary of
+various LAMMPS output options, many of which involve fixes.
+
+The results of fixes that calculate global quantities can be either
+"intensive" or "extensive" values.  Intensive means the value is
+independent of the number of atoms in the simulation,
+e.g. temperature.  Extensive means the value scales with the number of
+atoms in the simulation, e.g. total rotational kinetic energy.
+:doc:`Thermodynamic output <thermo_style>` will normalize extensive
+values by the number of atoms in the system, depending on the
+"thermo\_modify norm" setting.  It will not normalize intensive values.
+If a fix value is accessed in another way, e.g. by a
+:doc:`variable <variable>`, you may want to know whether it is an
+intensive or extensive value.  See the doc page for individual fixes
+for further info.
+
+
+----------
+
+
+Each fix style has its own doc page which describes its arguments and
+what it does, as listed below.  Here is an alphabetic list of fix
+styles available in LAMMPS.  They are also listed in more compact form
+on the :doc:`Commands fix <Commands_fix>` doc page.
+
+There are also additional accelerated fix styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the :doc:`Commands fix <Commands_fix>` doc
+page are followed by one or more of (g,i,k,o,t) to indicate which
+accelerated styles exist.
+
+* :doc:`adapt <fix_adapt>` - change a simulation parameter over time
+* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
+* :doc:`addforce <fix_addforce>` - add a force to each atom
+* :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
+* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
+* :doc:`atc <fix_atc>` - initiates a coupled MD/FE simulation
+* :doc:`atom/swap <fix_atom_swap>` - Monte Carlo atom type swapping
+* :doc:`ave/atom <fix_ave_atom>` - compute per-atom time-averaged quantities
+* :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
+* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
+* :doc:`ave/correlate/long <fix_ave_correlate_long>` -
+* :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
+* :doc:`ave/histo/weight <fix_ave_histo>` - weighted version of fix ave/histo
+* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
+* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
+* :doc:`balance <fix_balance>` - perform dynamic load-balancing
+* :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
+* :doc:`bond/break <fix_bond_break>` - break bonds on the fly
+* :doc:`bond/create <fix_bond_create>` - create bonds on the fly
+* :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions
+* :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
+* :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
+* :doc:`client/md <fix_client_md>` - MD client for client/server simulations
+* :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
+* :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library
+* :doc:`controller <fix_controller>` - apply control loop feedback mechanism
+* :doc:`deform <fix_deform>` - change the simulation box size/shape
+* :doc:`deposit <fix_deposit>` - add new atoms above a surface
+* :doc:`dpd/energy <fix_dpd_energy>` - constant energy dissipative particle dynamics
+* :doc:`drag <fix_drag>` - drag atoms towards a defined coordinate
+* :doc:`drude <fix_drude>` - part of Drude oscillator polarization model
+* :doc:`drude/transform/direct <fix_drude_transform>` -  part of Drude oscillator polarization model
+* :doc:`drude/transform/inverse <fix_drude_transform>` -  part of Drude oscillator polarization model
+* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
+* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
+* :doc:`efield <fix_efield>` - impose electric field on system
+* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
+* :doc:`electron/stopping <fix_electron_stopping>` - electronic stopping power as a friction force
+* :doc:`enforce2d <fix_enforce2d>` - zero out z-dimension velocity and force
+* :doc:`eos/cv <fix_eos_cv>` -
+* :doc:`eos/table <fix_eos_table>` -
+* :doc:`eos/table/rx <fix_eos_table_rx>` -
+* :doc:`evaporate <fix_evaporate>` - remove atoms from simulation periodically
+* :doc:`external <fix_external>` - callback to an external driver program
+* :doc:`ffl <fix_ffl>` - apply a Fast-Forward Langevin equation thermostat
+* :doc:`filter/corotate <fix_filter_corotate>` - implement corotation filter to allow larger timesteps with r-RESPA
+* :doc:`flow/gauss <fix_flow_gauss>` - Gaussian dynamics for constant mass flux
+* :doc:`freeze <fix_freeze>` - freeze atoms in a granular simulation
+* :doc:`gcmc <fix_gcmc>` - grand canonical insertions/deletions
+* :doc:`gld <fix_gld>` - generalized Langevin dynamics integrator
+* :doc:`gle <fix_gle>` - generalized Langevin equation thermostat
+* :doc:`gravity <fix_gravity>` - add gravity to atoms in a granular simulation
+* :doc:`grem <fix_grem>` - implements the generalized replica exchange method
+* :doc:`halt <fix_halt>` - terminate a dynamics run or minimization
+* :doc:`heat <fix_heat>` - add/subtract momentum-conserving heat
+* :doc:`hyper/global <fix_hyper_global>` - global hyperdynamics
+* :doc:`hyper/local <fix_hyper_local>` - local hyperdynamics
+* :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol
+* :doc:`indent <fix_indent>` - impose force due to an indenter
+* :doc:`ipi <fix_ipi>` - enable LAMMPS to run as a client for i-PI path-integral simulations
+* :doc:`langevin <fix_langevin>` - Langevin temperature control
+* :doc:`langevin/drude <fix_langevin_drude>` - Langevin temperature control of Drude oscillators
+* :doc:`langevin/eff <fix_langevin_eff>` - Langevin temperature control for the electron force field model
+* :doc:`langevin/spin <fix_langevin_spin>` - Langevin temperature control for a spin or spin-lattice system
+* :doc:`latte <fix_latte>` - wrapper on LATTE density-functional tight-binding code
+* :doc:`lb/fluid <fix_lb_fluid>` -
+* :doc:`lb/momentum <fix_lb_momentum>` -
+* :doc:`lb/pc <fix_lb_pc>` -
+* :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` -
+* :doc:`lb/viscous <fix_lb_viscous>` -
+* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
+* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
+* :doc:`meso <fix_meso>` - time integration for SPH/DPDE particles
+* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
+* :doc:`meso/stationary <fix_meso_stationary>` -
+* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
+* :doc:`move <fix_move>` - move atoms in a prescribed fashion
+* :doc:`mscg <fix_mscg>` - apply MSCG method for force-matching to generate coarse grain models
+* :doc:`msst <fix_msst>` - multi-scale shock technique (MSST) integration
+* :doc:`mvv/dpd <fix_mvv_dpd>` - DPD using the modified velocity-Verlet integration algorithm
+* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm
+* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
+* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
+* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
+* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
+* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
+* :doc:`nph/body <fix_nph_body>` - NPH for body particles
+* :doc:`nph/eff <fix_nh_eff>` - NPH for  nuclei and electrons in the electron force field model
+* :doc:`nph/sphere <fix_nph_sphere>` - NPH for spherical particles
+* :doc:`nphug <fix_nphug>` - constant-stress Hugoniostat integration
+* :doc:`npt <fix_nh>` - constant NPT time integration via Nose/Hoover
+* :doc:`npt/asphere <fix_npt_asphere>` - NPT for aspherical particles
+* :doc:`npt/body <fix_npt_body>` - NPT for body particles
+* :doc:`npt/eff <fix_nh_eff>` - NPT for  nuclei and electrons in the electron force field model
+* :doc:`npt/sphere <fix_npt_sphere>` - NPT for spherical particles
+* :doc:`npt/uef <fix_nh_uef>` - NPT style time integration with diagonal flow
+* :doc:`nve <fix_nve>` - constant NVE time integration
+* :doc:`nve/asphere <fix_nve_asphere>` - NVE for aspherical particles
+* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` - NVE for aspherical particles without forces
+* :doc:`nve/awpmd <fix_nve_awpmd>` - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
+* :doc:`nve/body <fix_nve_body>` - NVE for body particles
+* :doc:`nve/dot <fix_nve_dot>` - rigid body constant energy time integrator for coarse grain models
+* :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>` - Langevin style rigid body time integrator for coarse grain models
+* :doc:`nve/eff <fix_nve_eff>` - NVE for  nuclei and electrons in the electron force field model
+* :doc:`nve/limit <fix_nve_limit>` - NVE with limited step length
+* :doc:`nve/line <fix_nve_line>` - NVE for line segments
+* :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` -
+* :doc:`nve/noforce <fix_nve_noforce>` - NVE without forces (v only)
+* :doc:`nve/sphere <fix_nve_sphere>` - NVE for spherical particles
+* :doc:`nve/spin <fix_nve_spin>` - NVE for a spin or spin-lattice system
+* :doc:`nve/tri <fix_nve_tri>` - NVE for triangles
+* :doc:`nvk <fix_nvk>` - constant kinetic energy time integration
+* :doc:`nvt <fix_nh>` - NVT time integration via Nose/Hoover
+* :doc:`nvt/asphere <fix_nvt_asphere>` - NVT for aspherical particles
+* :doc:`nvt/body <fix_nvt_body>` - NVT for body particles
+* :doc:`nvt/eff <fix_nh_eff>` - NVE for  nuclei and electrons in the electron force field model
+* :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>` -
+* :doc:`nvt/sllod <fix_nvt_sllod>` - NVT for NEMD with SLLOD equations
+* :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>` - NVT for NEMD with SLLOD equations for the electron force field model
+* :doc:`nvt/sphere <fix_nvt_sphere>` - NVT for spherical particles
+* :doc:`nvt/uef <fix_nh_uef>` - NVT style time integration with diagonal flow
+* :doc:`oneway <fix_oneway>` - constrain particles on move in one direction
+* :doc:`orient/bcc <fix_orient>` - add grain boundary migration force for BCC
+* :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
+* :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
+* :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
+* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
+* :doc:`plumed <fix_plumed>` - wrapper on PLUMED free energy library
+* :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies
+* :doc:`pour <fix_pour>` - pour new atoms/molecules into a granular simulation domain
+* :doc:`precession/spin <fix_precession_spin>` -
+* :doc:`press/berendsen <fix_press_berendsen>` - pressure control by Berendsen barostat
+* :doc:`print <fix_print>` - print text and variables during a simulation
+* :doc:`property/atom <fix_property_atom>` - add customized per-atom values
+* :doc:`python/invoke <fix_python_invoke>` - call a Python function during a simulation
+* :doc:`python/move <fix_python_move>` -  call a Python function during a simulation run
+* :doc:`qbmsst <fix_qbmsst>` - quantum bath multi-scale shock technique time integrator
+* :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential
+* :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method
+* :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
+* :doc:`qeq/point <fix_qeq>` - charge equilibration via point method
+* :doc:`qeq/reax <fix_qeq_reax>` - charge equilibration for ReaxFF potential
+* :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method
+* :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method
+* :doc:`qmmm <fix_qmmm>` - functionality to enable a quantum mechanics/molecular mechanics coupling
+* :doc:`qtb <fix_qtb>` - implement quantum thermal bath scheme
+* :doc:`rattle <fix_shake>` - RATTLE constraints on bonds and/or angles
+* :doc:`reax/c/bonds <fix_reaxc_bonds>` - write out ReaxFF bond information
+* :doc:`reax/c/species <fix_reaxc_species>` - write out ReaxFF molecule information
+* :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
+* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
+* :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems
+* :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
+* :doc:`rigid/meso <fix_rigid_meso>` - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
+* :doc:`rigid/nph <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NPH integration
+* :doc:`rigid/nph/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NPH integration
+* :doc:`rigid/npt <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NPT integration
+* :doc:`rigid/npt/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NPT integration
+* :doc:`rigid/nve <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
+* :doc:`rigid/nve/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
+* :doc:`rigid/nvt <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVT integration
+* :doc:`rigid/nvt/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVT integration
+* :doc:`rigid/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVE integration
+* :doc:`rx <fix_rx>` -
+* :doc:`saed/vtk <fix_saed_vtk>` -
+* :doc:`setforce <fix_setforce>` - set the force on each atom
+* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
+* :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
+* :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
+* :doc:`smd <fix_smd>` - applied a steered MD force to a group
+* :doc:`smd/adjust_dt <fix_smd_adjust_dt>` -
+* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>` -
+* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>` -
+* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
+* :doc:`smd/setvel <fix_smd_setvel>` -
+* :doc:`smd/wall_surface <fix_smd_wall_surface>` -
+* :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
+* :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
+* :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
+* :doc:`spring/self <fix_spring_self>` - spring from each atom to its origin
+* :doc:`srd <fix_srd>` - stochastic rotation dynamics (SRD)
+* :doc:`store/force <fix_store_force>` - store force on each atom
+* :doc:`store/state <fix_store_state>` - store attributes for each atom
+* :doc:`tdpd/source <fix_dpd_source>` -
+* :doc:`temp/berendsen <fix_temp_berendsen>` - temperature control by Berendsen thermostat
+* :doc:`temp/csld <fix_temp_csvr>` - canonical sampling thermostat with Langevin dynamics
+* :doc:`temp/csvr <fix_temp_csvr>` - canonical sampling thermostat with Hamiltonian dynamics
+* :doc:`temp/rescale <fix_temp_rescale>` - temperature control by velocity rescaling
+* :doc:`temp/rescale/eff <fix_temp_rescale_eff>` - temperature control by velocity rescaling in the electron force field model
+* :doc:`tfmc <fix_tfmc>` - perform force-bias Monte Carlo with time-stamped method
+* :doc:`thermal/conductivity <fix_thermal_conductivity>` - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
+* :doc:`ti/spring <fix_ti_spring>` -
+* :doc:`tmd <fix_tmd>` - guide a group of atoms to a new configuration
+* :doc:`ttm <fix_ttm>` - two-temperature model for electronic/atomic coupling
+* :doc:`ttm/mod <fix_ttm>` - enhanced two-temperature model with additional options
+* :doc:`tune/kspace <fix_tune_kspace>` - auto-tune KSpace parameters
+* :doc:`vector <fix_vector>` - accumulate a global vector every N timesteps
+* :doc:`viscosity <fix_viscosity>` - Muller-Plathe momentum exchange for viscosity calculation
+* :doc:`viscous <fix_viscous>` - viscous damping for granular simulations
+* :doc:`wall/body/polygon <fix_wall_body_polygon>` -
+* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` -
+* :doc:`wall/colloid <fix_wall>` - Lennard-Jones wall interacting with finite-size particles
+* :doc:`wall/ees <fix_wall_ees>` - wall for ellipsoidal particles
+* :doc:`wall/gran <fix_wall_gran>` - frictional wall(s) for granular simulations
+* :doc:`wall/gran/region <fix_wall_gran_region>` -
+* :doc:`wall/harmonic <fix_wall>` - harmonic spring wall
+* :doc:`wall/lj1043 <fix_wall>` - Lennard-Jones 10-4-3 wall
+* :doc:`wall/lj126 <fix_wall>` - Lennard-Jones 12-6 wall
+* :doc:`wall/lj93 <fix_wall>` - Lennard-Jones 9-3 wall
+* :doc:`wall/morse <fix_wall>` - Morse potential wall
+* :doc:`wall/piston <fix_wall_piston>` - moving reflective piston wall
+* :doc:`wall/reflect <fix_wall_reflect>` - reflecting wall(s)
+* :doc:`wall/region <fix_wall_region>` - use region surface as wall
+* :doc:`wall/region/ees <fix_wall_ees>` - use region surface as wall for ellipsoidal particles
+* :doc:`wall/srd <fix_wall_srd>` - slip/no-slip wall for SRD particles
+
+Restrictions
+""""""""""""
+
+
+Some fix styles are part of specific packages.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  The doc pages for
+individual fixes tell if it is part of a package.
+
+Related commands
+""""""""""""""""
+
+:doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst
new file mode 100644
index 0000000000..4d5cf59a39
--- /dev/null
+++ b/doc/src/fix_adapt.rst
@@ -0,0 +1,390 @@
+.. index:: fix adapt
+
+fix adapt command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID adapt N attribute args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* adapt = style name of this fix command
+* N = adapt simulation settings every this many timesteps
+* one or more attribute/arg pairs may be appended
+* attribute = *pair* or *kspace* or *atom*
+  
+  .. parsed-literal::
+  
+       *pair* args = pstyle pparam I J v_name
+         pstyle = pair style name, e.g. lj/cut
+         pparam = parameter to adapt over time
+         I,J = type pair(s) to set parameter for
+         v_name = variable with name that calculates value of pparam
+       *bond* args = bstyle bparam I v_name
+         bstyle = bond style name, e.g. harmonic
+         bparam = parameter to adapt over time
+         I = type bond to set parameter for
+         v_name = variable with name that calculates value of bparam
+       *kspace* arg = v_name
+         v_name = variable with name that calculates scale factor on K-space terms
+       *atom* args = aparam v_name
+         aparam = parameter to adapt over time
+         v_name = variable with name that calculates value of aparam
+
+* zero or more keyword/value pairs may be appended
+* keyword = *scale* or *reset*
+  
+  .. parsed-literal::
+  
+       *scale* value = *no* or *yes*
+         *no* = the variable value is the new setting
+         *yes* = the variable value multiplies the original setting
+       *reset* value = *no* or *yes*
+         *no* = values will remain altered at the end of a run
+         *yes* = reset altered values to their original values at the end of a run
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all adapt 1 pair soft a 1 1 v_prefactor
+   fix 1 all adapt 1 pair soft a 2\* 3 v_prefactor
+   fix 1 all adapt 1 pair lj/cut epsilon \* \* v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
+   fix 1 all adapt 10 atom diameter v_size
+
+   variable ramp_up equal "ramp(0.01,0.5)"
+   fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up
+
+Description
+"""""""""""
+
+Change or adapt one or more specific simulation attributes or settings
+over time as a simulation runs.  Pair potential and K-space and atom
+attributes which can be varied by this fix are discussed below.  Many
+other fixes can also be used to time-vary simulation parameters,
+e.g. the "fix deform" command will change the simulation box
+size/shape and the "fix move" command will change atom positions and
+velocities in a prescribed manner.  Also note that many commands allow
+variables as arguments for specific parameters, if described in that
+manner on their doc pages.  An equal-style variable can calculate a
+time-dependent quantity, so this is another way to vary a simulation
+parameter over time.
+
+If *N* is specified as 0, the specified attributes are only changed
+once, before the simulation begins.  This is all that is needed if the
+associated variables are not time-dependent.  If *N* > 0, then changes
+are made every *N* steps during the simulation, presumably with a
+variable that is time-dependent.
+
+Depending on the value of the *reset* keyword, attributes changed by
+this fix will or will not be reset back to their original values at
+the end of a simulation.  Even if *reset* is specified as *yes*\ , a
+restart file written during a simulation will contain the modified
+settings.
+
+If the *scale* keyword is set to *no*\ , then the value the parameter is
+set to will be whatever the variable generates.  If the *scale*
+keyword is set to *yes*\ , then the value of the altered parameter will
+be the initial value of that parameter multiplied by whatever the
+variable generates.  I.e. the variable is now a "scale factor" applied
+in (presumably) a time-varying fashion to the parameter.
+
+Note that whether scale is *no* or *yes*\ , internally, the parameters
+themselves are actually altered by this fix.  Make sure you use the
+*reset yes* option if you want the parameters to be restored to their
+initial values after the run.
+
+
+----------
+
+
+The *pair* keyword enables various parameters of potentials defined by
+the :doc:`pair\_style <pair_style>` command to be changed, if the pair
+style supports it.  Note that the :doc:`pair\_style <pair_style>` and
+:doc:`pair\_coeff <pair_coeff>` commands must be used in the usual manner
+to specify these parameters initially; the fix adapt command simply
+overrides the parameters.
+
+The *pstyle* argument is the name of the pair style.  If :doc:`pair\_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
+a sub-style name.  If there are multiple sub-styles using the same
+pair style, then *pstyle* should be specified as "style:N" where N is
+which instance of the pair style you wish to adapt, e.g. the first,
+second, etc.  For example, *pstyle* could be specified as "soft" or
+"lubricate" or "lj/cut:1" or "lj/cut:2".  The *pparam* argument is the
+name of the parameter to change.  This is the current list of pair
+styles and parameters that can be varied by this fix.  See the doc
+pages for individual pair styles and their energy formulas for the
+meaning of these parameters:
+
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`born <pair_born>`                                             | a,b,c                                            | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`born/coul/long, born/coul/msm <pair_born>`                    | coulombic\_cutoff                                | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`buck <pair_buck>`                                             | a,c                                              | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`buck/coul/long, buck/coul/msm <pair_buck>`                    | coulombic\_cutoff                                | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`buck/mdf <pair_mdf>`                                          | a,c                                              | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`coul/cut <pair_coul>`                                         | scale                                            | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`coul/cut/soft <pair_fep_soft>`                                | lambda                                           | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`coul/debye <pair_coul>`                                       | scale                                            | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`coul/dsf <pair_coul>`                                         | coulombic\_cutoff                                | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`coul/long, coul/msm <pair_coul>`                              | coulombic\_cutoff, scale                         | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`coul/long/soft <pair_fep_soft>`                               | scale, lambda, coulombic\_cutoff                 | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`eam, eam/alloy, eam/fs <pair_eam>`                            | scale                                            | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`gauss <pair_gauss>`                                           | a                                                | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lennard/mdf <pair_mdf>`                                       | A,B                                              | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/class2 <pair_class2>`                                      | epsilon,sigma                                    | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>`        | epsilon,sigma,coulombic\_cutoff                  | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/cut <pair_lj>`                                             | epsilon,sigma                                    | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj>` | epsilon,sigma,coulombic\_cutoff                  | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>`  | epsilon,sigma,lambda,coulombic\_cutoff           | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/cut/coul/dsf <pair_lj>`                                    | cutoff                                           | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/cut/tip4p/cut <pair_lj>`                                   | epsilon,sigma,coulombic\_cutoff                  | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/cut/soft <pair_fep_soft>`                                  | epsilon,sigma,lambda                             | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/expand <pair_lj_expand>`                                   | epsilon,sigma,delta                              | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/mdf <pair_mdf>`                                            | epsilon,sigma                                    | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/sf/dipole/sf <pair_dipole>`                                | epsilon,sigma,scale                              | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lubricate <pair_lubricate>`                                   | mu                                               | global      |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`mie/cut <pair_mie>`                                           | epsilon,sigma,gamma\_repulsive,gamma\_attractive | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`morse, morse/smooth/linear <pair_morse>`                      | D0,R0,alpha                                      | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`morse/soft <pair_morse>`                                      | D0,R0,alpha,lambda                               | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`nm/cut <pair_nm>`                                             | E0,R0,m,n                                        | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>`                  | E0,R0,m,n,coulombic\_cutoff                      | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`reax/c <pair_reaxc>`                                          | chi, eta, gamma                                  | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`spin/dmi <pair_spin_dmi>`                                     | coulombic\_cutoff                                | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`spin/exchange <pair_spin_exchange>`                           | coulombic\_cutoff                                | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`spin/magelec <pair_spin_magelec>`                             | coulombic\_cutoff                                | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`spin/neel <pair_spin_neel>`                                   | coulombic\_cutoff                                | type global |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`table <pair_table>`                                           | table\_cutoff                                    | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`ufm <pair_ufm>`                                               | epsilon,sigma                                    | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`soft <pair_soft>`                                             | a                                                | type pairs  |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+|                                                                     |                                                  |             |
++---------------------------------------------------------------------+--------------------------------------------------+-------------+
+
+.. note::
+
+   It is easy to add new pairwise potentials and their parameters
+   to this list.  All it typically takes is adding an extract() method to
+   the pair\_\*.cpp file associated with the potential.
+
+Some parameters are global settings for the pair style, e.g. the
+viscosity setting "mu" for :doc:`pair\_style lubricate <pair_lubricate>`.
+Other parameters apply to atom type pairs within the pair style,
+e.g. the prefactor "a" for :doc:`pair\_style soft <pair_soft>`.
+
+Note that for many of the potentials, the parameter that can be varied
+is effectively a prefactor on the entire energy expression for the
+potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"
+are exactly that, since the energy expression for the
+:doc:`coul/cut <pair_coul>` potential (for example) has no labeled
+prefactor in its formula.  To apply an effective prefactor to some
+potentials, multiple parameters need to be altered.  For example, the
+:doc:`Buckingham potential <pair_buck>` needs both the A and C terms
+altered together.  To scale the Buckingham potential, you should thus
+list the pair style twice, once for A and once for C.
+
+If a type pair parameter is specified, the *I* and *J* settings should
+be specified to indicate which type pairs to apply it to.  If a global
+parameter is specified, the *I* and *J* settings still need to be
+specified, but are ignored.
+
+Similar to the :doc:`pair\_coeff command <pair_coeff>`, I and J can be
+specified in one of two ways.  Explicit numeric values can be used for
+each, as in the 1st example above.  I <= J is required.  LAMMPS sets
+the coefficients for the symmetric J,I interaction to the same values.
+
+A wild-card asterisk can be used in place of or in conjunction with
+the I,J arguments to set the coefficients for multiple pairs of atom
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).  Note that only type pairs with I <= J are considered; if
+asterisks imply type pairs where J < I, they are ignored.
+
+IMPROTANT NOTE: If :doc:`pair\_style hybrid or hybrid/overlay <pair_hybrid>` is being used, then the *pstyle* will
+be a sub-style name.  You must specify I,J arguments that correspond
+to type pair values defined (via the :doc:`pair\_coeff <pair_coeff>`
+command) for that sub-style.
+
+The *v\_name* argument for keyword *pair* is the name of an
+:doc:`equal-style variable <variable>` which will be evaluated each time
+this fix is invoked to set the parameter to a new value.  It should be
+specified as v\_name, where name is the variable name.  Equal-style
+variables can specify formulas with various mathematical functions,
+and include :doc:`thermo\_style <thermo_style>` command keywords for the
+simulation box parameters and timestep and elapsed time.  Thus it is
+easy to specify parameters that change as a function of time or span
+consecutive runs in a continuous fashion.  For the latter, see the
+*start* and *stop* keywords of the :doc:`run <run>` command and the
+*elaplong* keyword of :doc:`thermo\_style custom <thermo_style>` for
+details.
+
+For example, these commands would change the prefactor coefficient of
+the :doc:`pair\_style soft <pair_soft>` potential from 10.0 to 30.0 in a
+linear fashion over the course of a simulation:
+
+
+.. parsed-literal::
+
+   variable prefactor equal ramp(10,30)
+   fix 1 all adapt 1 pair soft a \* \* v_prefactor
+
+
+----------
+
+
+The *bond* keyword uses the specified variable to change the value of
+a bond coefficient over time, very similar to how the *pair* keyword
+operates. The only difference is that now a bond coefficient for a
+given bond type is adapted.
+
+A wild-card asterisk can be used in place of or in conjunction with
+the bond type argument to set the coefficients for multiple bond types.
+This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of
+atom types, then an asterisk with no numeric values means all types
+from 1 to N.  A leading asterisk means all types from 1 to n (inclusive).
+A trailing asterisk means all types from n to N (inclusive).  A middle
+asterisk means all types from m to n (inclusive).
+
+Currently *bond* does not support bond\_style hybrid nor bond\_style
+hybrid/overlay as bond styles. The only bonds that currently are
+working with fix\_adapt are
+
++---------------------------------+-------+------------+
+| :doc:`gromos <bond_gromos>`     | k, r0 | type bonds |
++---------------------------------+-------+------------+
+| :doc:`harmonic <bond_harmonic>` | k,r0  | type bonds |
++---------------------------------+-------+------------+
+
+
+----------
+
+
+The *kspace* keyword used the specified variable as a scale factor on
+the energy, forces, virial calculated by whatever K-Space solver is
+defined by the :doc:`kspace\_style <kspace_style>` command.  If the
+variable has a value of 1.0, then the solver is unaltered.
+
+The *kspace* keyword works this way whether the *scale* keyword
+is set to *no* or *yes*\ .
+
+
+----------
+
+
+The *atom* keyword enables various atom properties to be changed.  The
+*aparam* argument is the name of the parameter to change.  This is the
+current list of atom parameters that can be varied by this fix:
+
+* charge = charge on particle
+* diameter = diameter of particle
+
+The *v\_name* argument of the *atom* keyword is the name of an
+:doc:`equal-style variable <variable>` which will be evaluated each time
+this fix is invoked to set the parameter to a new value.  It should be
+specified as v\_name, where name is the variable name.  See the
+discussion above describing the formulas associated with equal-style
+variables.  The new value is assigned to the corresponding attribute
+for all atoms in the fix group.
+
+.. note::
+
+   The *atom* keyword works this way whether the *scale* keyword is
+   set to *no* or *yes*\ .  I.e. the use of scale yes is not yet supported
+   by the *atom* keyword.
+
+If the atom parameter is *diameter* and per-atom density and per-atom
+mass are defined for particles (e.g. :doc:`atom\_style granular <atom_style>`), then the mass of each particle is also
+changed when the diameter changes (density is assumed to stay
+constant).
+
+For example, these commands would shrink the diameter of all granular
+particles in the "center" group from 1.0 to 0.1 in a linear fashion
+over the course of a 1000-step simulation:
+
+
+.. parsed-literal::
+
+   variable size equal ramp(1.0,0.1)
+   fix 1 center adapt 10 atom diameter v_size
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+For :doc:`rRESPA time integration <run_style>`, this fix changes
+parameters on the outermost rRESPA level.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute ti <compute_ti>`
+
+Default
+"""""""
+
+The option defaults are scale = no, reset = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst
new file mode 100644
index 0000000000..60c05ec796
--- /dev/null
+++ b/doc/src/fix_adapt_fep.rst
@@ -0,0 +1,332 @@
+.. index:: fix adapt/fep
+
+fix adapt/fep command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID adapt/fep N attribute args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* adapt/fep = style name of this fix command
+* N = adapt simulation settings every this many timesteps
+* one or more attribute/arg pairs may be appended
+* attribute = *pair* or *kspace* or *atom*
+  
+  .. parsed-literal::
+  
+       *pair* args = pstyle pparam I J v_name
+         pstyle = pair style name, e.g. lj/cut
+         pparam = parameter to adapt over time
+         I,J = type pair(s) to set parameter for
+         v_name = variable with name that calculates value of pparam
+       *kspace* arg = v_name
+         v_name = variable with name that calculates scale factor on K-space terms
+       *atom* args = aparam v_name
+         aparam = parameter to adapt over time
+         I = type(s) to set parameter for
+         v_name = variable with name that calculates value of aparam
+
+* zero or more keyword/value pairs may be appended
+* keyword = *scale* or *reset* or *after*
+  
+  .. parsed-literal::
+  
+       *scale* value = *no* or *yes*
+         *no* = the variable value is the new setting
+         *yes* = the variable value multiplies the original setting
+       *reset* value = *no* or *yes*
+         *no* = values will remain altered at the end of a run
+         *yes* = reset altered values to their original values at the end
+         of a run
+       *after* value = *no* or *yes*
+         *no* = parameters are adapted at timestep N
+         *yes* = parameters are adapted one timestep after N
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
+   fix 1 all adapt/fep 1 pair soft a 2\* 3 v_prefactor
+   fix 1 all adapt/fep 1 pair lj/cut epsilon \* \* v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
+   fix 1 all adapt/fep 10 atom diameter 1 v_size
+
+Description
+"""""""""""
+
+Change or adapt one or more specific simulation attributes or settings
+over time as a simulation runs.
+
+This is an enhanced version of the :doc:`fix adapt <fix_adapt>` command
+with two differences,
+
+* It is possible to modify the charges of chosen atom types only,
+  instead of scaling all the charges in the system.
+* There is a new option *after* for better compatibility with "fix
+  ave/time".
+
+
+This version is suited for free energy calculations using
+:doc:`compute ti <compute_ti>` or :doc:`compute fep <compute_fep>`.
+
+If *N* is specified as 0, the specified attributes are only changed
+once, before the simulation begins.  This is all that is needed if the
+associated variables are not time-dependent.  If *N* > 0, then changes
+are made every *N* steps during the simulation, presumably with a
+variable that is time-dependent.
+
+Depending on the value of the *reset* keyword, attributes changed by
+this fix will or will not be reset back to their original values at
+the end of a simulation.  Even if *reset* is specified as *yes*\ , a
+restart file written during a simulation will contain the modified
+settings.
+
+If the *scale* keyword is set to *no*\ , then the value the parameter is
+set to will be whatever the variable generates.  If the *scale*
+keyword is set to *yes*\ , then the value of the altered parameter will
+be the initial value of that parameter multiplied by whatever the
+variable generates.  I.e. the variable is now a "scale factor" applied
+in (presumably) a time-varying fashion to the parameter.  Internally,
+the parameters themselves are actually altered; make sure you use the
+*reset yes* option if you want the parameters to be restored to their
+initial values after the run.
+
+If the *after* keyword is set to *yes*\ , then the parameters are
+changed one timestep after the multiple of N. In this manner, if a fix
+such as "fix ave/time" is used to calculate averages at every N
+timesteps, all the contributions to the average will be obtained with
+the same values of the parameters.
+
+
+----------
+
+
+The *pair* keyword enables various parameters of potentials defined by
+the :doc:`pair\_style <pair_style>` command to be changed, if the pair
+style supports it.  Note that the :doc:`pair\_style <pair_style>` and
+:doc:`pair\_coeff <pair_coeff>` commands must be used in the usual manner
+to specify these parameters initially; the fix adapt command simply
+overrides the parameters.
+
+The *pstyle* argument is the name of the pair style.  If :doc:`pair\_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
+a sub-style name.  For example, *pstyle* could be specified as "soft"
+or "lubricate".  The *pparam* argument is the name of the parameter to
+change.  This is the current list of pair styles and parameters that
+can be varied by this fix.  See the doc pages for individual pair
+styles and their energy formulas for the meaning of these parameters:
+
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`born <pair_born>`                                             | a,b,c                   | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`buck <pair_buck>`                                             | a,c                     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`buck/mdf <pair_mdf>`                                          | a,c                     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/cut <pair_coul>`                                         | scale                   | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/cut/soft <pair_fep_soft>`                                | lambda                  | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/long, coul/msm <pair_coul>`                              | scale                   | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/long/soft <pair_fep_soft>`                               | scale, lambda           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`eam <pair_eam>`                                               | scale                   | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`gauss <pair_gauss>`                                           | a                       | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lennard/mdf <pair_mdf>`                                       | a,b                     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/class2 <pair_class2>`                                      | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>`        | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut <pair_lj>`                                             | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/soft <pair_fep_soft>`                                  | epsilon,sigma,lambda    | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj>` | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>`  | epsilon,sigma,lambda    | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long <pair_lj>`                | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>`                       | epsilon,sigma,lambda    | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/expand <pair_lj_expand>`                                   | epsilon,sigma,delta     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/mdf <pair_mdf>`                                            | epsilon,sigma           | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`lj/sf/dipole/sf <pair_dipole>`                                | epsilon,sigma,scale     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`mie/cut <pair_mie>`                                           | epsilon,sigma,gamR,gamA | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`morse, morse/smooth/linear <pair_morse>`                      | d0,r0,alpha             | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`morse/soft <pair_morse>`                                      | d0,r0,alpha,lambda      | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`nm/cut <pair_nm>`                                             | e0,r0,nn,mm             | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>`                  | e0,r0,nn,mm             | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`ufm <pair_ufm>`                                               | epsilon,sigma,scale     | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+| :doc:`soft <pair_soft>`                                             | a                       | type pairs |
++---------------------------------------------------------------------+-------------------------+------------+
+
+.. note::
+
+   It is easy to add new potentials and their parameters to this
+   list.  All it typically takes is adding an extract() method to the
+   pair\_\*.cpp file associated with the potential.
+
+Note that for many of the potentials, the parameter that can be varied
+is effectively a prefactor on the entire energy expression for the
+potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"
+are exactly that, since the energy expression for the
+:doc:`coul/cut <pair_coul>` potential (for example) has no labeled
+prefactor in its formula.  To apply an effective prefactor to some
+potentials, multiple parameters need to be altered.  For example, the
+:doc:`Buckingham potential <pair_buck>` needs both the A and C terms
+altered together.  To scale the Buckingham potential, you should thus
+list the pair style twice, once for A and once for C.
+
+If a type pair parameter is specified, the *I* and *J* settings should
+be specified to indicate which type pairs to apply it to.  If a global
+parameter is specified, the *I* and *J* settings still need to be
+specified, but are ignored.
+
+Similar to the :doc:`pair\_coeff command <pair_coeff>`, I and J can be
+specified in one of two ways.  Explicit numeric values can be used for
+each, as in the 1st example above.  I <= J is required.  LAMMPS sets
+the coefficients for the symmetric J,I interaction to the same values.
+
+A wild-card asterisk can be used in place of or in conjunction with
+the I,J arguments to set the coefficients for multiple pairs of atom
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).  Note that only type pairs with I <= J are considered; if
+asterisks imply type pairs where J < I, they are ignored.
+
+IMPROTANT NOTE: If :doc:`pair\_style hybrid or hybrid/overlay <pair_hybrid>` is being used, then the *pstyle* will
+be a sub-style name.  You must specify I,J arguments that correspond
+to type pair values defined (via the :doc:`pair\_coeff <pair_coeff>`
+command) for that sub-style.
+
+The *v\_name* argument for keyword *pair* is the name of an
+:doc:`equal-style variable <variable>` which will be evaluated each time
+this fix is invoked to set the parameter to a new value.  It should be
+specified as v\_name, where name is the variable name.  Equal-style
+variables can specify formulas with various mathematical functions,
+and include :doc:`thermo\_style <thermo_style>` command keywords for the
+simulation box parameters and timestep and elapsed time.  Thus it is
+easy to specify parameters that change as a function of time or span
+consecutive runs in a continuous fashion.  For the latter, see the
+*start* and *stop* keywords of the :doc:`run <run>` command and the
+*elaplong* keyword of :doc:`thermo\_style custom <thermo_style>` for
+details.
+
+For example, these commands would change the prefactor coefficient of
+the :doc:`pair\_style soft <pair_soft>` potential from 10.0 to 30.0 in a
+linear fashion over the course of a simulation:
+
+
+.. parsed-literal::
+
+   variable prefactor equal ramp(10,30)
+   fix 1 all adapt 1 pair soft a \* \* v_prefactor
+
+
+----------
+
+
+The *kspace* keyword used the specified variable as a scale factor on
+the energy, forces, virial calculated by whatever K-Space solver is
+defined by the :doc:`kspace\_style <kspace_style>` command.  If the
+variable has a value of 1.0, then the solver is unaltered.
+
+The *kspace* keyword works this way whether the *scale* keyword
+is set to *no* or *yes*\ .
+
+
+----------
+
+
+The *atom* keyword enables various atom properties to be changed.  The
+*aparam* argument is the name of the parameter to change.  This is the
+current list of atom parameters that can be varied by this fix:
+
+* charge = charge on particle
+* diameter = diameter of particle
+
+The *I* argument indicates which atom types are affected. A wild-card
+asterisk can be used in place of or in conjunction with the I argument
+to set the coefficients for multiple atom types.
+
+The *v\_name* argument of the *atom* keyword is the name of an
+:doc:`equal-style variable <variable>` which will be evaluated each time
+this fix is invoked to set the parameter to a new value.  It should be
+specified as v\_name, where name is the variable name.  See the
+discussion above describing the formulas associated with equal-style
+variables.  The new value is assigned to the corresponding attribute
+for all atoms in the fix group.
+
+If the atom parameter is *diameter* and per-atom density and per-atom
+mass are defined for particles (e.g. :doc:`atom\_style granular <atom_style>`), then the mass of each particle is also
+changed when the diameter changes (density is assumed to stay
+constant).
+
+For example, these commands would shrink the diameter of all granular
+particles in the "center" group from 1.0 to 0.1 in a linear fashion
+over the course of a 1000-step simulation:
+
+
+.. parsed-literal::
+
+   variable size equal ramp(1.0,0.1)
+   fix 1 center adapt 10 atom diameter \* v_size
+
+For :doc:`rRESPA time integration <run_style>`, this fix changes
+parameters on the outermost rRESPA level.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+
+Default
+"""""""
+
+The option defaults are scale = no, reset = no, after = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst
new file mode 100644
index 0000000000..91134eac12
--- /dev/null
+++ b/doc/src/fix_addforce.rst
@@ -0,0 +1,206 @@
+.. index:: fix addforce
+
+fix addforce command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID addforce fx fy fz keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* addforce = style name of this fix command
+* fx,fy,fz = force component values (force units)
+  
+  .. parsed-literal::
+  
+       any of fx,fy,fz can be a variable (see below)
+
+* zero or more keyword/value pairs may be appended to args
+* keyword = *every* or *region* or *energy*
+  
+  .. parsed-literal::
+  
+       *every* value = Nevery
+         Nevery = add force every this many timesteps
+       *region* value = region-ID
+         region-ID = ID of region atoms must be in to have added force
+       *energy* value = v_name
+         v_name = variable with name that calculates the potential energy of each atom in the added force field
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix kick flow addforce 1.0 0.0 0.0
+   fix kick flow addforce 1.0 0.0 v_oscillate
+   fix ff boundary addforce 0.0 0.0 v_push energy v_espace
+
+Description
+"""""""""""
+
+Add fx,fy,fz to the corresponding component of force for each atom in
+the group.  This command can be used to give an additional push to
+atoms in a simulation, such as for a simulation of Poiseuille flow in
+a channel.
+
+Any of the 3 quantities defining the force components can be specified
+as an equal-style or atom-style :doc:`variable <variable>`, namely *fx*\ ,
+*fy*\ , *fz*\ .  If the value is a variable, it should be specified as
+v\_name, where name is the variable name.  In this case, the variable
+will be evaluated each timestep, and its value(s) used to determine
+the force component.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent force field.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent force
+field with optional time-dependence as well.
+
+If the *every* keyword is used, the *Nevery* setting determines how
+often the forces are applied.  The default value is 1, for every
+timestep.
+
+If the *region* keyword is used, the atom must also be in the
+specified geometric :doc:`region <region>` in order to have force added
+to it.
+
+
+----------
+
+
+Adding a force to atoms implies a change in their potential energy as
+they move due to the applied force field.  For dynamics via the "run"
+command, this energy can be optionally added to the system's potential
+energy for thermodynamic output (see below).  For energy minimization
+via the "minimize" command, this energy must be added to the system's
+potential energy to formulate a self-consistent minimization problem
+(see below).
+
+The *energy* keyword is not allowed if the added force is a constant
+vector F = (fx,fy,fz), with all components defined as numeric
+constants and not as variables.  This is because LAMMPS can compute
+the energy for each atom directly as E = -x dot F = -(x\*fx + y\*fy +
+z\*fz), so that -Grad(E) = F.
+
+The *energy* keyword is optional if the added force is defined with
+one or more variables, and if you are performing dynamics via the
+:doc:`run <run>` command.  If the keyword is not used, LAMMPS will set
+the energy to 0.0, which is typically fine for dynamics.
+
+The *energy* keyword is required if the added force is defined with
+one or more variables, and you are performing energy minimization via
+the "minimize" command.  The keyword specifies the name of an
+atom-style :doc:`variable <variable>` which is used to compute the
+energy of each atom as function of its position.  Like variables used
+for *fx*\ , *fy*\ , *fz*\ , the energy variable is specified as v\_name,
+where name is the variable name.
+
+Note that when the *energy* keyword is used during an energy
+minimization, you must insure that the formula defined for the
+atom-style :doc:`variable <variable>` is consistent with the force
+variable formulas, i.e. that -Grad(E) = F.  For example, if the force
+were a spring-like F = kx, then the energy formula should be E =
+-0.5kx\^2.  If you don't do this correctly, the minimization will not
+converge properly.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential "energy" inferred by the added force to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+needed so that the :doc:`minimize <minimize>` command can include the
+forces added by this fix in a consistent manner.  I.e. there is a
+decrease in potential energy when atoms move in the direction of the
+added force.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to the added forces on atoms to the
+system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+The default is *virial no*
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost
+level.
+
+This fix computes a global scalar and a global 3-vector of forces,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar is the potential energy discussed above.  The vector is the
+total force on the group of atoms before the forces on individual
+atoms are changed by the fix.  The scalar and vector values calculated
+by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.  You should not
+specify force components with a variable that has time-dependence for
+use with a minimizer, since the minimizer increments the timestep as
+the iteration count during the minimization.
+
+.. note::
+
+   If you want the fictitious potential energy associated with the
+   added forces to be included in the total potential energy of the
+   system (the quantity being minimized), you MUST enable the
+   :doc:`fix\_modify <fix_modify>` *energy* option for this fix.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix setforce <fix_setforce>`, :doc:`fix aveforce <fix_aveforce>`
+
+Default
+"""""""
+
+The option default for the every keyword is every = 1.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst
new file mode 100644
index 0000000000..26493624ec
--- /dev/null
+++ b/doc/src/fix_addtorque.rst
@@ -0,0 +1,108 @@
+.. index:: fix addtorque
+
+fix addtorque command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID addtorque Tx Ty Tz
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* addtorque = style name of this fix command
+* Tx,Ty,Tz = torque component values (torque units)
+* any of Tx,Ty,Tz can be a variable (see below)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix kick bead addtorque 2.0 3.0 5.0
+   fix kick bead addtorque 0.0 0.0 v_oscillate
+
+Description
+"""""""""""
+
+Add a set of forces to each atom in
+the group such that:
+
+* the components of the total torque applied on the group (around its
+  center of mass) are Tx,Ty,Tz
+* the group would move as a rigid body in the absence of other
+  forces.
+
+
+This command can be used to drive a group of atoms into rotation.
+
+Any of the 3 quantities defining the torque components can be specified
+as an equal-style :doc:`variable <variable>`, namely *Tx*\ ,
+*Ty*\ , *Tz*\ .  If the value is a variable, it should be specified as
+v\_name, where name is the variable name.  In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+torque component.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent torque.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential "energy" inferred by the added forces to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+needed so that the :doc:`minimize <minimize>` command can include the
+forces added by this fix in a consistent manner.  I.e. there is a
+decrease in potential energy when atoms move in the direction of the
+added forces.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its torque. Default is the outermost level.
+
+This fix computes a global scalar and a global 3-vector, which can be
+accessed by various :doc:`output commands <Howto_output>`.  The scalar
+is the potential energy discussed above.  The vector is the total
+torque on the group of atoms before the forces on individual atoms are
+changed by the fix.  The scalar and vector values calculated by this
+fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.  You should not
+specify force components with a variable that has time-dependence for
+use with a minimizer, since the minimizer increments the timestep as
+the iteration count during the minimization.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix addforce <fix_addforce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst
new file mode 100644
index 0000000000..977e96a53a
--- /dev/null
+++ b/doc/src/fix_append_atoms.rst
@@ -0,0 +1,128 @@
+.. index:: fix append/atoms
+
+fix append/atoms command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID append/atoms face ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* append/atoms = style name of this fix command
+* face = *zhi*
+* zero or more keyword/value pairs may be appended
+* keyword = *basis* or *size* or *freq* or *temp* or *random* or *units*
+  
+  .. parsed-literal::
+  
+       *basis* values = M itype
+         M = which basis atom
+         itype = atom type (1-N) to assign to this basis atom
+       *size* args = Lz
+         Lz = z size of lattice region appended in a single event(distance units)
+       *freq* args = freq
+         freq = the number of timesteps between append events
+       *temp* args = target damp seed extent
+         target = target temperature for the region between zhi-extent and zhi (temperature units)
+         damp = damping parameter (time units)
+         seed = random number seed for langevin kicks
+         extent = extent of thermostatted region (distance units)
+       *random* args = xmax ymax zmax seed
+         *xmax*\ , *ymax*\ , *zmax* = maximum displacement in particular direction (distance units)
+         *seed* = random number seed for random displacement
+       *units* value = *lattice* or *box*
+         *lattice* = the wall position is defined in lattice units
+         *box* = the wall position is defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all append/atoms zhi size 5.0 freq 295 units lattice
+   fix 4 all append/atoms zhi size 15.0 freq 5 units box
+   fix A all append/atoms zhi size 1.0 freq 1000 units lattice
+
+Description
+"""""""""""
+
+This fix creates atoms on a lattice, appended on the zhi edge of the
+system box.  This can be useful when a shock or wave is propagating
+from zlo.  This allows the system to grow with time to accommodate an
+expanding wave.  A simulation box must already exist, which is
+typically created via the :doc:`create\_box <create_box>` command.
+Before using this command, a lattice must also be defined using the
+:doc:`lattice <lattice>` command.
+
+This fix will automatically freeze atoms on the zhi edge of the
+system, so that overlaps are avoided when new atoms are appended.
+
+The *basis* keyword specifies an atom type that will be assigned to
+specific basis atoms as they are created.  See the
+:doc:`lattice <lattice>` command for specifics on how basis atoms are
+defined for the unit cell of the lattice.  By default, all created
+atoms are assigned type = 1 unless this keyword specifies differently.
+
+The *size* keyword defines the size in z of the chunk of material to
+be added.
+
+The *random* keyword will give the atoms random displacements around
+their lattice points to simulate some initial temperature.
+
+The *temp* keyword will cause a region to be thermostatted with a
+Langevin thermostat on the zhi boundary.  The size of the region is
+measured from zhi and is set with the *extent* argument.
+
+The *units* keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant is used.
+A *box* value selects standard distance units as defined by the
+:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
+A *lattice* value means the distance units are in lattice spacings.
+The :doc:`lattice <lattice>` command must have been previously used to
+define the lattice spacings.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix style is part of the SHOCK package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+The boundary on which atoms are added with append/atoms must be
+shrink/minimum.  The opposite boundary may be any boundary type other
+than periodic.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall/piston <fix_wall_piston>` command
+
+Default
+"""""""
+
+The keyword defaults are size = 0.0, freq = 0, units = lattice.  All
+added atoms are of type 1 unless the basis keyword is used.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst
new file mode 100644
index 0000000000..b765efb30c
--- /dev/null
+++ b/doc/src/fix_atc.rst
@@ -0,0 +1,297 @@
+.. index:: fix atc
+
+fix atc command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix <fixID> <group> atc <type> <parameter_file>
+
+* fixID = name of fix
+* group = name of group fix is to be applied
+* type = *thermal* or *two\_temperature* or *hardy* or *field*
+
+.. parsed-literal::
+
+    *thermal* = thermal coupling with fields: temperature
+    *two_temperature* = electron-phonon coupling with field: temperature and electron_temperature
+    *hardy* = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
+    *field* = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
+
+* parameter\_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix AtC internal atc thermal Ar_thermal.dat
+   fix AtC internal atc two_temperature Ar_ttm.mat
+   fix AtC internal atc hardy
+   fix AtC internal atc field
+
+Description
+"""""""""""
+
+This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the post-processing does not. After instantiating this fix, several other fix\_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
+
+.. image:: JPG/atc_nanotube.jpg
+   :align: center
+
+
+.. parsed-literal::
+
+   The following coupling example is typical, but non-exhaustive:
+    # ... commands to create and initialize the MD system
+
+    # initial fix to designate coupling type and group to apply it to
+    # tag group physics material_file
+    fix AtC internal atc thermal Ar_thermal.mat
+
+    # create a uniform 12 x 2 x 2 mesh that covers region contain the group
+    # nx ny nz region periodicity
+    fix_modify AtC mesh create 12 2 2 mdRegion f p p
+
+    # specify the control method for the type of coupling
+    # physics control_type
+    fix_modify AtC thermal control flux
+
+    # specify the initial values for the empirical field "temperature"
+    # field node_group value
+    fix_modify AtC initial temperature all 30
+
+    # create an output stream for nodal fields
+    # filename output_frequency
+    fix_modify AtC output atc_fe_output 100
+
+    run 1000
+
+likewise for this post-processing example:
+
+
+.. parsed-literal::
+
+    # ... commands to create and initialize the MD system
+
+    # initial fix to designate post-processing and the group to apply it to
+    # no material file is allowed nor required
+    fix AtC internal atc hardy
+
+    # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
+    fix AtC kernel quartic_sphere 10.0
+
+    # create a uniform 1 x 1 x 1 mesh that covers region contain the group
+    # with periodicity this effectively creats a system average
+    fix_modify AtC mesh create 1 1 1 box p p p
+
+    # change from default lagrangian map to eulerian
+    # refreshed every 100 steps
+    fix_modify AtC atom_element_map eulerian 100
+
+    # start with no field defined
+    # add mass density, potential energy density, stress and temperature
+    fix_modify AtC fields add density energy stress temperature
+
+    # create an output stream for nodal fields
+    # filename output_frequency
+    fix_modify AtC output nvtFE 100 text
+
+    run 1000
+
+the mesh's linear interpolation functions can be used as the localization function
+by using the field option:
+
+
+.. parsed-literal::
+
+    fix AtC internal atc field
+    fix_modify AtC mesh create 1 1 1 box p p p
+    ...
+
+Note coupling and post-processing can be combined in the same simulations using separate fixes.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  The :doc:`fix\_modify <fix_modify>` options
+relevant to this fix are listed below.  No global scalar or vector or
+per-atom quantities are stored by this fix for access by various
+:doc:`output commands <Howto_output>`.  No parameter of this fix can be
+used with the *start/stop* keywords of the :doc:`run <run>` command.
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+Thermal and two\_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. In addition, currently:
+
+* the coupling is restricted to thermal physics
+* the FE computations are done in serial on each processor.
+
+Related commands
+""""""""""""""""
+
+After specifying this fix in your input script, several other :doc:`fix\_modify <fix_modify>` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
+
+fix\_modify commands for setup:
+
+* `fix\_modify AtC mesh create <USER/atc/man_mesh_create.html>`_
+* `fix\_modify AtC mesh quadrature <USER/atc/man_mesh_quadrature.html>`_
+* `fix\_modify AtC mesh read <USER/atc/man_mesh_read.html>`_
+* `fix\_modify AtC mesh write <USER/atc/man_mesh_write.html>`_
+* `fix\_modify AtC mesh create\_nodeset <USER/atc/man_mesh_create_nodeset.html>`_
+* `fix\_modify AtC mesh add\_to\_nodeset <USER/atc/man_mesh_add_to_nodeset.html>`_
+* `fix\_modify AtC mesh create\_faceset box <USER/atc/man_mesh_create_faceset_box.html>`_
+* `fix\_modify AtC mesh create\_faceset plane <USER/atc/man_mesh_create_faceset_plane.html>`_
+* `fix\_modify AtC mesh create\_elementset <USER/atc/man_mesh_create_elementset.html>`_
+* `fix\_modify AtC mesh delete\_elements <USER/atc/man_mesh_delete_elements.html>`_
+* `fix\_modify AtC mesh nodeset\_to\_elementset <USER/atc/man_mesh_nodeset_to_elementset.html>`_
+* `fix\_modify AtC boundary <USER/atc/man_boundary.html>`_
+* `fix\_modify AtC internal\_quadrature <USER/atc/man_internal_quadrature.html>`_
+* `fix\_modify AtC time\_integration (thermal) <USER/atc/man_thermal_time_integration.html>`_
+* `fix\_modify AtC time\_integration (momentum) <USER/atc/man_momentum_time_integration.html>`_
+* `fix\_modify AtC extrinsic electron\_integration <USER/atc/man_electron_integration.html>`_
+* `fix\_modify AtC internal\_element\_set <USER/atc/man_internal_element_set.html>`_
+* `fix\_modify AtC decomposition <USER/atc/man_decomposition.html>`_
+
+fix\_modify commands for boundary and initial conditions:
+
+* `fix\_modify AtC initial <USER/atc/man_initial.html>`_
+* `fix\_modify AtC fix <USER/atc/man_fix_nodes.html>`_
+* `fix\_modify AtC unfix <USER/atc/man_unfix_nodes.html>`_
+* `fix\_modify AtC fix\_flux <USER/atc/man_fix_flux.html>`_
+* `fix\_modify AtC unfix\_flux <USER/atc/man_unfix_flux.html>`_
+* `fix\_modify AtC source <USER/atc/man_source.html>`_
+* `fix\_modify AtC remove\_source <USER/atc/man_remove_source.html>`_
+
+fix\_modify commands for control and filtering:
+
+* `fix\_modify AtC control <USER/atc/man_control.html>`_
+* `fix\_modify AtC control thermal <USER/atc/man_control_thermal.html>`_
+* `fix\_modify AtC control thermal correction\_max\_iterations <USER/atc/man_control_thermal_correction_max_iterations.html>`_
+* `fix\_modify AtC control momentum <USER/atc/man_control_momentum.html>`_
+* `fix\_modify AtC control localized\_lambda <USER/atc/man_localized_lambda.html>`_
+* `fix\_modify AtC control lumped\_lambda\_solve <USER/atc/man_lumped_lambda_solve.html>`_
+* `fix\_modify AtC control mask\_direction <USER/atc/man_mask_direction.html>`_ control
+* `fix\_modify AtC filter <USER/atc/man_time_filter.html>`_
+* `fix\_modify AtC filter scale <USER/atc/man_filter_scale.html>`_
+* `fix\_modify AtC filter type <USER/atc/man_filter_type.html>`_
+* `fix\_modify AtC equilibrium\_start <USER/atc/man_equilibrium_start.html>`_
+* `fix\_modify AtC extrinsic exchange <USER/atc/man_extrinsic_exchange.html>`_
+* `fix\_modify AtC poisson\_solver <USER/atc/man_poisson_solver.html>`_
+
+fix\_modify commands for output:
+
+* `fix\_modify AtC output <USER/atc/man_output.html>`_
+* `fix\_modify AtC output nodeset <USER/atc/man_output_nodeset.html>`_
+* `fix\_modify AtC output elementset <USER/atc/man_output_elementset.html>`_
+* `fix\_modify AtC output boundary\_integral <USER/atc/man_boundary_integral.html>`_
+* `fix\_modify AtC output contour\_integral <USER/atc/man_contour_integral.html>`_
+* `fix\_modify AtC mesh output <USER/atc/man_mesh_output.html>`_
+* `fix\_modify AtC write\_restart <USER/atc/man_write_restart.html>`_
+* `fix\_modify AtC read\_restart <USER/atc/man_read_restart.html>`_
+
+fix\_modify commands for post-processing:
+
+* `fix\_modify AtC kernel <USER/atc/man_hardy_kernel.html>`_
+* `fix\_modify AtC fields <USER/atc/man_hardy_fields.html>`_
+* `fix\_modify AtC grdients <USER/atc/man_hardy_gradients.html>`_
+* `fix\_modify AtC rates <USER/atc/man_hardy_rates.html>`_
+* `fix\_modify AtC computes <USER/atc/man_hardy_computes.html>`_
+* `fix\_modify AtC on\_the\_fly <USER/atc/man_hardy_on_the_fly.html>`_
+* `fix\_modify AtC pair\_interactions/bond\_interactions <USER/atc/man_pair_interactions.html>`_
+* `fix\_modify AtC sample\_frequency <USER/atc/man_sample_frequency.html>`_
+* `fix\_modify AtC set <USER/atc/man_set.html>`_
+
+miscellaneous fix\_modify commands:
+
+* `fix\_modify AtC atom\_element\_map <USER/atc/man_atom_element_map.html>`_
+* `fix\_modify AtC atom\_weight <USER/atc/man_atom_weight.html>`_
+* `fix\_modify AtC write\_atom\_weights <USER/atc/man_write_atom_weights.html>`_
+* `fix\_modify AtC reset\_time <USER/atc/man_reset_time.html>`_
+* `fix\_modify AtC reset\_atomic\_reference\_positions <USER/atc/man_reset_atomic_reference_positions.html>`_
+* `fix\_modify AtC fe\_md\_boundary <USER/atc/man_fe_md_boundary.html>`_
+* `fix\_modify AtC boundary\_faceset <USER/atc/man_boundary_faceset.html>`_
+* `fix\_modify AtC consistent\_fe\_initialization <USER/atc/man_consistent_fe_initialization.html>`_
+* `fix\_modify AtC mass\_matrix <USER/atc/man_mass_matrix.html>`_
+* `fix\_modify AtC material <USER/atc/man_material.html>`_
+* `fix\_modify AtC atomic\_charge <USER/atc/man_atomic_charge.html>`_
+* `fix\_modify AtC source\_integration <USER/atc/man_source_integration.html>`_
+* `fix\_modify AtC temperature\_definition <USER/atc/man_temperature_definition.html>`_
+* `fix\_modify AtC track\_displacement <USER/atc/man_track_displacement.html>`_
+* `fix\_modify AtC boundary\_dynamics <USER/atc/man_boundary_dynamics.html>`_
+* `fix\_modify AtC add\_species <USER/atc/man_add_species.html>`_
+* `fix\_modify AtC add\_molecule <USER/atc/man_add_molecule.html>`_
+* `fix\_modify AtC remove\_species <USER/atc/man_remove_species.html>`_
+* `fix\_modify AtC remove\_molecule <USER/atc/man_remove_molecule.html>`_
+
+Note: a set of example input files with the attendant material files are included with this package
+
+Default
+"""""""
+None
+
+
+----------
+
+
+For detailed exposition of the theory and algorithms please see:
+
+.. _Wagner:
+
+
+
+**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
+
+.. _Zimmeman2004:
+
+
+
+**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
+
+.. _Zimmerman2010:
+
+
+
+**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
+
+.. _Templeton2010:
+
+
+
+**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
+
+.. _Jones:
+
+
+
+**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
+
+.. _Templeton2011:
+
+
+
+**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
+
+.. _Mandadapu:
+
+
+
+**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
+
+Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst
new file mode 100644
index 0000000000..e5851db353
--- /dev/null
+++ b/doc/src/fix_atom_swap.rst
@@ -0,0 +1,213 @@
+.. index:: fix atom/swap
+
+fix atom/swap command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID atom/swap N X seed T keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* atom/swap = style name of this fix command
+* N = invoke this fix every N steps
+* X = number of swaps to attempt every N steps
+* seed = random # seed (positive integer)
+* T = scaling temperature of the MC swaps (temperature units)
+* one or more keyword/value pairs may be appended to args
+* keyword = *types* or *mu* or *ke* or *semi-grand* or *region*
+  
+  .. parsed-literal::
+  
+       *types* values = two or more atom types
+       *mu* values = chemical potential of swap types (energy units)
+       *ke* value = *no* or *yes*
+         *no* = no conservation of kinetic energy after atom swaps
+         *yes* = kinetic energy is conserved after atom swaps
+       *semi-grand* value = *no* or *yes*
+         *no* = particle type counts and fractions conserved
+         *yes* = semi-grand canonical ensemble, particle fractions not conserved
+       *region* value = region-ID
+         region-ID = ID of region to use as an exchange/move volume
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
+   fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
+   fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
+
+Description
+"""""""""""
+
+This fix performs Monte Carlo swaps of atoms of one given atom type
+with atoms of the other given atom types. The specified T is used in
+the Metropolis criterion dictating swap probabilities.
+
+Perform X swaps of atoms of one type with atoms of another type
+according to a Monte Carlo probability. Swap candidates must be in the
+fix group, must be in the region (if specified), and must be of one of
+the listed types. Swaps are attempted between candidates that are
+chosen randomly with equal probability among the candidate
+atoms. Swaps are not attempted between atoms of the same type since
+nothing would happen.
+
+All atoms in the simulation domain can be moved using regular time
+integration displacements, e.g. via :doc:`fix nvt <fix_nh>`, resulting
+in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
+be needed when running such a hybrid simulation, especially if the
+swapped atoms are not well equilibrated.
+
+The *types* keyword is required. At least two atom types must be
+specified.
+
+The *ke* keyword can be set to *no* to turn off kinetic energy
+conservation for swaps. The default is *yes*\ , which means that swapped
+atoms have their velocities scaled by the ratio of the masses of the
+swapped atom types. This ensures that the kinetic energy of each atom
+is the same after the swap as it was before the swap, even though the
+atom masses have changed.
+
+The *semi-grand* keyword can be set to *yes* to switch to the
+semi-grand canonical ensemble as discussed in :ref:`(Sadigh) <Sadigh>`. This
+means that the total number of each particle type does not need to be
+conserved. The default is *no*\ , which means that the only kind of swap
+allowed exchanges an atom of one type with an atom of a different
+given type. In other words, the relative mole fractions of the swapped
+atoms remains constant. Whereas in the semi-grand canonical ensemble,
+the composition of the system can change. Note that when using
+*semi-grand*\ , atoms in the fix group whose type is not listed
+in the *types* keyword are ineligible for attempted
+conversion. An attempt is made to switch
+the selected atom (if eligible) to one of the other listed types
+with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
+
+The *mu* keyword allows users to specify chemical
+potentials. This is required and allowed only when using *semi-grand*\ .
+All chemical potentials are absolute, so there is one for
+each swap type listed following the *types* keyword.
+In semi-grand canonical ensemble simulations the chemical composition
+of the system is controlled by the difference in these values. So
+shifting all values by a constant amount will have no effect
+on the simulation.
+
+This command may optionally use the *region* keyword to define swap
+volume.  The specified region must have been previously defined with a
+:doc:`region <region>` command.  It must be defined with side = *in*\ .
+Swap attempts occur only between atoms that are both within the
+specified region. Swaps are not otherwise attempted.
+
+You should ensure you do not swap atoms belonging to a molecule, or
+LAMMPS will soon generate an error when it tries to find those atoms.
+LAMMPS will warn you if any of the atoms eligible for swapping have a
+non-zero molecule ID, but does not check for this at the time of
+swapping.
+
+If not using *semi-grand* this fix checks to ensure all atoms of the
+given types have the same atomic charge. LAMMPS doesn't enforce this
+in general, but it is needed for this fix to simplify the
+swapping procedure. Successful swaps will swap the atom type and charge
+of the swapped atoms. Conversely, when using *semi-grand*\ , it is assumed that all the atom
+types involved in switches have the same charge. Otherwise, charge
+would not be conserved. As a consequence, no checks on atomic charges are
+performed, and successful switches update the atom type but not the
+atom charge. While it is possible to use *semi-grand* with groups of
+atoms that have different charges, these charges will not be changed when the
+atom types change.
+
+Since this fix computes total potential energies before and after
+proposed swaps, so even complicated potential energy calculations are
+OK, including the following:
+
+* long-range electrostatics (kspace)
+* many body pair styles
+* hybrid pair styles
+* eam pair styles
+* triclinic systems
+* need to include potential energy contributions from other fixes
+
+Some fixes have an associated potential energy. Examples of such fixes
+include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
+:doc:`addforce <fix_addforce>`, :doc:`langevin <fix_langevin>`,
+:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen <fix_temp_berendsen>`,
+:doc:`temp/rescale <fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.
+For that energy to be included in the total potential energy of the
+system (the quantity used when performing GCMC moves),
+you MUST enable the :doc:`fix\_modify <fix_modify>` *energy* option for
+that fix.  The doc pages for individual :doc:`fix <fix>` commands
+specify if this should be done.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the fix to :doc:`binary restart files <restart>`.  This includes information about the random
+number generator seed, the next timestep for MC exchanges, the number
+of exchange attempts and successes etc.  See
+the :doc:`read\_restart <read_restart>` command for info on how to
+re-specify a fix in an input script that reads a restart file, so that
+the operation of the fix continues in an uninterrupted fashion.
+
+.. note::
+
+   For this to work correctly, the timestep must **not** be changed
+   after reading the restart with :doc:`reset\_timestep <reset_timestep>`.
+   The fix will try to detect it and stop with an error.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.
+
+This fix computes a global vector of length 2, which can be accessed
+by various :doc:`output commands <Howto_output>`.  The vector values are
+the following global cumulative quantities:
+
+* 1 = swap attempts
+* 2 = swap successes
+
+The vector values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MC package.  It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
+:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
+:doc:`delete\_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`
+
+Default
+"""""""
+
+The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
+all atom types.
+
+
+----------
+
+
+.. _Sadigh:
+
+
+
+**(Sadigh)** B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
+L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst
new file mode 100644
index 0000000000..3a066ab55b
--- /dev/null
+++ b/doc/src/fix_ave_atom.rst
@@ -0,0 +1,194 @@
+.. index:: fix ave/atom
+
+fix ave/atom command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ave/atom = style name of this fix command
+* Nevery = use input values every this many timesteps
+* Nrepeat = # of times to use input values for calculating averages
+* Nfreq = calculate averages every this many timesteps
+  one or more input values can be listed
+* value = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[i], f\_ID, f\_ID[i], v\_name
+  
+  .. parsed-literal::
+  
+       x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+       c_ID = per-atom vector calculated by a compute with ID
+       c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = per-atom vector calculated by a fix with ID
+       f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+       v_name = per-atom vector calculated by an atom-style variable with name
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all ave/atom 1 100 100 vx vy vz
+   fix 1 all ave/atom 10 20 1000 c_my_stress[1]
+   fix 1 all ave/atom 10 20 1000 c_my_stress[\*]
+
+Description
+"""""""""""
+
+Use one or more per-atom vectors as inputs every few timesteps, and
+average them atom by atom over longer timescales.  The resulting
+per-atom averages can be used by other :doc:`output commands <Howto_output>` such as the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` commands.
+
+The group specified with the command means only atoms within the group
+have their averages computed.  Results are set to 0.0 for atoms not in
+the group.
+
+Each input value can be an atom attribute (position, velocity, force
+component) or can be the result of a :doc:`compute <compute>` or
+:doc:`fix <fix>` or the evaluation of an atom-style
+:doc:`variable <variable>`.  In the latter cases, the compute, fix, or
+variable must produce a per-atom vector, not a global quantity or
+local quantity.  If you wish to time-average global quantities from a
+compute, fix, or variable, then see the :doc:`fix ave/time <fix_ave_time>` command.
+
+Each per-atom value of each input vector is averaged independently.
+
+:doc:`Computes <compute>` that produce per-atom vectors or arrays are
+those which have the word *atom* in their style name.  See the doc
+pages for individual :doc:`fixes <fix>` to determine which ones produce
+per-atom vectors or arrays.  :doc:`Variables <variable>` of style *atom*
+are the only ones that can be used with this fix since they produce
+per-atom vectors.
+
+Note that for values from a compute or fix, the bracketed index I can
+be specified using a wildcard asterisk with the index to effectively
+specify multiple values.  This takes the form "\*" or "\*n" or "n\*" or
+"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+number of columns in the array (for *mode* = vector), then an asterisk
+with no numeric values means all indices from 1 to N.  A leading
+asterisk means all indices from 1 to n (inclusive).  A trailing
+asterisk means all indices from n to N (inclusive).  A middle asterisk
+means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 fix ave/atom commands are
+equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
+command creates a per-atom array with 6 columns:
+
+
+.. parsed-literal::
+
+   compute my_stress all stress/atom NULL
+   fix 1 all ave/atom 10 20 1000 c_my_stress[\*]
+   fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[2] &
+                                 c_my_stress[3] c_my_stress[4] &
+                                 c_my_stress[5] c_my_stress[6]
+
+
+----------
+
+
+The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what
+timesteps the input values will be used in order to contribute to the
+average.  The final averaged quantities are generated on timesteps
+that are a multiple of *Nfreq*\ .  The average is over *Nrepeat*
+quantities, computed in the preceding portion of the simulation every
+*Nevery* timesteps.  *Nfreq* must be a multiple of *Nevery* and
+*Nevery* must be non-zero even if *Nrepeat* is 1.  Also, the timesteps
+contributing to the average value cannot overlap,
+i.e. Nrepeat\*Nevery can not exceed Nfreq.
+
+For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100.  Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc.
+
+
+----------
+
+
+The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+self-explanatory.  Note that other atom attributes can be used as
+inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+an input value from that compute.
+
+.. note::
+
+   The x,y,z attributes are values that are re-wrapped inside the
+   periodic box whenever an atom crosses a periodic boundary.  Thus if
+   you time average an atom that spends half its time on either side of
+   the periodic box, you will get a value in the middle of the box.  If
+   this is not what you want, consider averaging unwrapped coordinates,
+   which can be provided by the :doc:`compute property/atom <compute_property_atom>` command via its xu,yu,zu
+   attributes.
+
+If a value begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  If no bracketed term is
+appended, the per-atom vector calculated by the compute is used.  If a
+bracketed term containing an index I is appended, the Ith column of
+the per-atom array calculated by the compute is used.  Users can also
+write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how I can
+be specified with a wildcard asterisk to effectively specify multiple
+values.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  If no bracketed term is
+appended, the per-atom vector calculated by the fix is used.  If a
+bracketed term containing an index I is appended, the Ith column of
+the per-atom array calculated by the fix is used.  Note that some
+fixes only produce their values on certain timesteps, which must be
+compatible with *Nevery*\ , else an error will result.  Users can also
+write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how I can be
+specified with a wildcard asterisk to effectively specify multiple
+values.
+
+If a value begins with "v\_", a variable name must follow which has
+been previously defined in the input script as an :doc:`atom-style variable <variable>` Variables of style *atom* can reference
+thermodynamic keywords, or invoke other computes, fixes, or variables
+when they are evaluated, so this is a very general means of generating
+per-atom quantities to time average.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global scalar or vector quantities are
+stored by this fix for access by various :doc:`output commands <Howto_output>`.
+
+This fix produces a per-atom vector or array which can be accessed by
+various :doc:`output commands <Howto_output>`.  A vector is produced if
+only a single quantity is averaged by this fix.  If two or more
+quantities are averaged, then an array of values is produced.  The
+per-atom values can only be accessed on timesteps that are multiples
+of *Nfreq* since that is when averaging is performed.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`variable <variable>`,
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst
new file mode 100644
index 0000000000..981382e726
--- /dev/null
+++ b/doc/src/fix_ave_chunk.rst
@@ -0,0 +1,520 @@
+.. index:: fix ave/chunk
+
+fix ave/chunk command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ave/chunk = style name of this fix command
+* Nevery = use input values every this many timesteps
+* Nrepeat = # of times to use input values for calculating averages
+* Nfreq = calculate averages every this many timesteps
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* one or more input values can be listed
+* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c\_ID, c\_ID[I], f\_ID, f\_ID[I], v\_name
+  
+  .. parsed-literal::
+  
+       vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+       density/number, density/mass = number or mass density
+       temp = temperature
+       c_ID = per-atom vector calculated by a compute with ID
+       c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = per-atom vector calculated by a fix with ID
+       f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+       v_name = per-atom vector calculated by an atom-style variable with name
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *title1* or *title2* or *title3*
+  
+  .. parsed-literal::
+  
+       *norm* arg = *all* or *sample* or *none* = how output on *Nfreq* steps is normalized
+         all = output is sum of atoms across all *Nrepeat* samples, divided by atom count
+         sample = output is sum of *Nrepeat* sample averages, divided by *Nrepeat*
+         none = output is sum of *Nrepeat* sample sums, divided by *Nrepeat*
+       *ave* args = *one* or *running* or *window M*
+         one = output new average value every Nfreq steps
+         running = output cumulative average of all previous Nfreq steps
+         window M = output average of M most recent Nfreq steps
+       *bias* arg = bias-ID
+         bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
+       *adof* value = dof_per_atom
+         dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
+       *cdof* value = dof_per_chunk
+         dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
+       *file* arg = filename
+         filename = file to write results to
+       *overwrite* arg = none = overwrite output file with only latest output
+       *format* arg = string
+         string = C-style format string
+       *title1* arg = string
+         string = text to print as 1st line of output file
+       *title2* arg = string
+         string = text to print as 2nd line of output file
+       *title3* arg = string
+         string = text to print as 3rd line of output file
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
+   fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
+   fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+   fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+
+**NOTE:**
+
+If you are trying to replace a deprecated fix ave/spatial command
+with the newer, more flexible fix ave/chunk and :doc:`compute chunk/atom <compute_chunk_atom>` commands, you simply need to split
+the fix ave/spatial arguments across the two new commands.  For
+example, this command:
+
+
+.. parsed-literal::
+
+   fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
+
+could be replaced by:
+
+
+.. parsed-literal::
+
+   compute cc1 flow chunk/atom bin/1d y 0.0 1.0
+   fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile
+
+Description
+"""""""""""
+
+Use one or more per-atom vectors as inputs every few timesteps, sum
+the values over the atoms in each chunk at each timestep, then average
+the per-chunk values over longer timescales.  The resulting chunk
+averages can be used by other :doc:`output commands <Howto_output>` such
+as :doc:`thermo\_style custom <thermo_style>`, and can also be written to
+a file.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` doc page and the :doc:`Howto chunk <Howto_chunk>` doc page for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+
+Note that only atoms in the specified group contribute to the summing
+and averaging calculations.  The :doc:`compute chunk/atom <compute_chunk_atom>` command defines its own group as
+well as an optional region.  Atoms will have a chunk ID = 0, meaning
+they belong to no chunk, if they are not in that group or region.
+Thus you can specify the "all" group for this command if you simply
+want to use the chunk definitions provided by chunkID.
+
+Each specified per-atom value can be an atom attribute (position,
+velocity, force component), a mass or number density, or the result of
+a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation of an
+atom-style :doc:`variable <variable>`.  In the latter cases, the
+compute, fix, or variable must produce a per-atom quantity, not a
+global quantity.  Note that the :doc:`compute property/atom <compute_property_atom>` command provides access to
+any attribute defined and stored by atoms.  If you wish to
+time-average global quantities from a compute, fix, or variable, then
+see the :doc:`fix ave/time <fix_ave_time>` command.
+
+The per-atom values of each input vector are summed and averaged
+independently of the per-atom values in other input vectors.
+
+:doc:`Computes <compute>` that produce per-atom quantities are those
+which have the word *atom* in their style name.  See the doc pages for
+individual :doc:`fixes <fix>` to determine which ones produce per-atom
+quantities.  :doc:`Variables <variable>` of style *atom* are the only
+ones that can be used with this fix since all other styles of variable
+produce global quantities.
+
+Note that for values from a compute or fix, the bracketed index I can
+be specified using a wildcard asterisk with the index to effectively
+specify multiple values.  This takes the form "\*" or "\*n" or "n\*" or
+"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+number of columns in the array (for *mode* = vector), then an asterisk
+with no numeric values means all indices from 1 to N.  A leading
+asterisk means all indices from 1 to n (inclusive).  A trailing
+asterisk means all indices from n to N (inclusive).  A middle asterisk
+means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 fix ave/chunk commands are
+equivalent, since the :doc:`compute property/atom <compute_property_atom>` command creates, in this
+case, a per-atom array with 3 columns:
+
+
+.. parsed-literal::
+
+   compute myAng all property/atom angmomx angmomy angmomz
+   fix 1 all ave/chunk 100 1 100 cc1 c_myAng[\*] file tmp.angmom
+   fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
+
+.. note::
+
+   This fix works by creating an array of size *Nchunk* by Nvalues
+   on each processor.  *Nchunk* is the number of chunks which is defined
+   by the :doc:`compute chunk/atom <compute_chunk_atom>` command.
+   Nvalues is the number of input values specified.  Each processor loops
+   over its atoms, tallying its values to the appropriate chunk.  Then
+   the entire array is summed across all processors.  This means that
+   using a large number of chunks will incur an overhead in memory and
+   computational cost (summing across processors), so be careful to
+   define a reasonable number of chunks.
+
+
+----------
+
+
+The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what
+timesteps the input values will be accessed and contribute to the
+average.  The final averaged quantities are generated on timesteps
+that are a multiples of *Nfreq*\ .  The average is over *Nrepeat*
+quantities, computed in the preceding portion of the simulation every
+*Nevery* timesteps.  *Nfreq* must be a multiple of *Nevery* and
+*Nevery* must be non-zero even if *Nrepeat* is 1.  Also, the timesteps
+contributing to the average value cannot overlap, i.e. Nrepeat\*Nevery
+can not exceed Nfreq.
+
+For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100.  Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc.  If Nrepeat=1 and Nfreq = 100, then no time
+averaging is done; values are simply generated on timesteps
+100,200,etc.
+
+Each input value can also be averaged over the atoms in each chunk.
+The way the averaging is done across the *Nrepeat* timesteps to
+produce output on the *Nfreq* timesteps, and across multiple *Nfreq*
+outputs, is determined by the *norm* and *ave* keyword settings, as
+discussed below.
+
+.. note::
+
+   To perform per-chunk averaging within a *Nfreq* time window, the
+   number of chunks *Nchunk* defined by the :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant.  If
+   the *ave* keyword is set to *running* or *window* then *Nchunk* must
+   remain constant for the duration of the simulation.  This fix forces
+   the chunk/atom compute specified by chunkID to hold *Nchunk* constant
+   for the appropriate time windows, by not allowing it to re-calculate
+   *Nchunk*\ , which can also affect how it assigns chunk IDs to atoms.
+   This is particularly important to understand if the chunks defined by
+   the :doc:`compute chunk/atom <compute_chunk_atom>` command are spatial
+   bins.  If its *units* keyword is set to *box* or *lattice*\ , then the
+   number of bins *Nchunk* and size of each bin will be fixed over the
+   *Nfreq* time window, which can affect which atoms are discarded if the
+   simulation box size changes.  If its *units* keyword is set to
+   *reduced*\ , then the number of bins *Nchunk* will still be fixed, but
+   the size of each bin can vary at each timestep if the simulation box
+   size changes, e.g. for an NPT simulation.
+
+
+----------
+
+
+The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
+As noted above, any other atom attributes can be used as input values
+to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+an input value from that compute.
+
+The *density/number* value means the number density is computed for
+each chunk, i.e. number/volume.  The *density/mass* value means the
+mass density is computed for each chunk, i.e. total-mass/volume.  The
+output values are in units of 1/volume or density (mass/volume).  See
+the :doc:`units <units>` command doc page for the definition of density
+for each choice of units, e.g. gram/cm\^3.  If the chunks defined by
+the :doc:`compute chunk/atom <compute_chunk_atom>` command are spatial
+bins, the volume is the bin volume.  Otherwise it is the volume of the
+entire simulation box.
+
+The *temp* value means the temperature is computed for each chunk, by
+the formula KE = DOF/2 k T, where KE = total kinetic energy of the
+chunk of atoms (sum of 1/2 m v\^2), DOF = the total number of degrees
+of freedom for all atoms in the chunk, k = Boltzmann constant, and T =
+temperature.
+
+The DOF is calculated as N\*adof + cdof, where N = number of atoms in
+the chunk, adof = degrees of freedom per atom, and cdof = degrees of
+freedom per chunk.  By default adof = 2 or 3 = dimensionality of
+system, as set via the :doc:`dimension <dimension>` command, and cdof =
+0.0.  This gives the usual formula for temperature.
+
+Note that currently this temperature only includes translational
+degrees of freedom for each atom.  No rotational degrees of freedom
+are included for finite-size particles.  Also no degrees of freedom
+are subtracted for any velocity bias or constraints that are applied,
+such as :doc:`compute temp/partial <compute_temp_partial>`, or :doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`.  This is because
+those degrees of freedom (e.g. a constrained bond) could apply to sets
+of atoms that are both included and excluded from a specific chunk,
+and hence the concept is somewhat ill-defined.  In some cases, you can
+use the *adof* and *cdof* keywords to adjust the calculated degrees of
+freedom appropriately, as explained below.
+
+Also note that a bias can be subtracted from atom velocities before
+they are used in the above formula for KE, by using the *bias*
+keyword.  This allows, for example, a thermal temperature to be
+computed after removal of a flow velocity profile.
+
+Note that the per-chunk temperature calculated by this fix and the
+:doc:`compute temp/chunk <compute_temp_chunk>` command can be different.
+The compute calculates the temperature for each chunk for a single
+snapshot.  This fix can do that but can also time average those values
+over many snapshots, or it can compute a temperature as if the atoms
+in the chunk on different timesteps were collected together as one set
+of atoms to calculate their temperature.  The compute allows the
+center-of-mass velocity of each chunk to be subtracted before
+calculating the temperature; this fix does not.
+
+If a value begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  If no bracketed integer is
+appended, the per-atom vector calculated by the compute is used.  If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the compute is used.  Users can also write code for
+their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+See the discussion above for how I can be specified with a wildcard
+asterisk to effectively specify multiple values.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  If no bracketed integer is
+appended, the per-atom vector calculated by the fix is used.  If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used.  Note that some fixes only produce
+their values on certain timesteps, which must be compatible with
+*Nevery*\ , else an error results.  Users can also write code for their
+own fix styles and :doc:`add them to LAMMPS <Modify>`.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If a value begins with "v\_", a variable name must follow which has
+been previously defined in the input script.  Variables of style
+*atom* can reference thermodynamic keywords and various per-atom
+attributes, or invoke other computes, fixes, or variables when they
+are evaluated, so this is a very general means of generating per-atom
+quantities to average within chunks.
+
+
+----------
+
+
+Additional optional keywords also affect the operation of this fix
+and its outputs.
+
+The *norm* keyword affects how averaging is done for the per-chunk
+values that are output every *Nfreq* timesteps.
+
+It the *norm* setting is *all*\ , which is the default, a chunk value is
+summed over all atoms in all *Nrepeat* samples, as is the count of
+atoms in the chunk.  The averaged output value for the chunk on the
+*Nfreq* timesteps is Total-sum / Total-count.  In other words it is an
+average over atoms across the entire *Nfreq* timescale.  For the
+*density/number* and *density/mass* values, the volume (bin volume or
+system volume) used in the final normalization will be the volume at
+the final *Nfreq* timestep.
+
+If the *norm* setting is *sample*\ , the chunk value is summed over
+atoms for each sample, as is the count, and an "average sample value"
+is computed for each sample, i.e. Sample-sum / Sample-count.  The
+output value for the chunk on the *Nfreq* timesteps is the average of
+the *Nrepeat* "average sample values", i.e. the sum of *Nrepeat*
+"average sample values" divided by *Nrepeat*\ .  In other words it is an
+average of an average.  For the *density/number* and *density/mass*
+values, the volume (bin volume or system volume) used in the
+per-sample normalization will be the current volume at each sampling
+step.
+
+If the *norm* setting is *none*\ , a similar computation as for the
+*sample* setting is done, except the individual "average sample
+values" are "summed sample values".  A summed sample value is simply
+the chunk value summed over atoms in the sample, without dividing by
+the number of atoms in the sample.  The output value for the chunk on
+the *Nfreq* timesteps is the average of the *Nrepeat* "summed sample
+values", i.e. the sum of *Nrepeat* "summed sample values" divided by
+*Nrepeat*\ .  For the *density/number* and *density/mass* values, the
+volume (bin volume or system volume) used in the per-sample sum
+normalization will be the current volume at each sampling step.
+
+The *ave* keyword determines how the per-chunk values produced every
+*Nfreq* steps are averaged with values produced on previous steps that
+were multiples of *Nfreq*\ , before they are accessed by another output
+command or written to a file.
+
+If the *ave* setting is *one*\ , which is the default, then the chunk
+values produced on timesteps that are multiples of *Nfreq* are
+independent of each other; they are output as-is without further
+averaging.
+
+If the *ave* setting is *running*\ , then the chunk values produced on
+timesteps that are multiples of *Nfreq* are summed and averaged in a
+cumulative sense before being output.  Each output chunk value is thus
+the average of the chunk value produced on that timestep with all
+preceding values for the same chunk.  This running average begins when
+the fix is defined; it can only be restarted by deleting the fix via
+the :doc:`unfix <unfix>` command, or re-defining the fix by
+re-specifying it.
+
+If the *ave* setting is *window*\ , then the chunk values produced on
+timesteps that are multiples of *Nfreq* are summed and averaged within
+a moving "window" of time, so that the last M values for the same
+chunk are used to produce the output.  E.g. if M = 3 and Nfreq = 1000,
+then the output on step 10000 will be the average of the individual
+chunk values on steps 8000,9000,10000.  Outputs on early steps will
+average over less than M values if they are not available.
+
+The *bias* keyword specifies the ID of a temperature compute that
+removes a "bias" velocity from each atom, specified as *bias-ID*\ .  It
+is only used when the *temp* value is calculated, to compute the
+thermal temperature of each chunk after the translational kinetic
+energy components have been altered in a prescribed way, e.g.  to
+remove a flow velocity profile.  See the doc pages for individual
+computes that calculate a temperature to see which ones implement a
+bias.
+
+The *adof* and *cdof* keywords define the values used in the degree of
+freedom (DOF) formula described above for temperature calculation
+for each chunk.  They are only used when the *temp* value is
+calculated.  They can be used to calculate a more appropriate
+temperature for some kinds of chunks.  Here are 3 examples:
+
+If spatially binned chunks contain some number of water molecules and
+:doc:`fix shake <fix_shake>` is used to make each molecule rigid, then
+you could calculate a temperature with 6 degrees of freedom (DOF) (3
+translational, 3 rotational) per molecule by setting *adof* to 2.0.
+
+If :doc:`compute temp/partial <compute_temp_partial>` is used with the
+*bias* keyword to only allow the x component of velocity to contribute
+to the temperature, then *adof* = 1.0 would be appropriate.
+
+If each chunk consists of a large molecule, with some number of its
+bonds constrained by :doc:`fix shake <fix_shake>` or the entire molecule
+by :doc:`fix rigid/small <fix_rigid>`, *adof* = 0.0 and *cdof* could be
+set to the remaining degrees of freedom for the entire molecule
+(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
+molecule.
+
+The *file* keyword allows a filename to be specified.  Every *Nfreq*
+timesteps, a section of chunk info will be written to a text file in
+the following format.  A line with the timestep and number of chunks
+is written.  Then one line per chunk is written, containing the chunk
+ID (1-Nchunk), an optional original ID value, optional coordinate
+values for chunks that represent spatial bins, the number of atoms in
+the chunk, and one or more calculated values.  More explanation of the
+optional values is given below.  The number of values in each line
+corresponds to the number of values specified in the fix ave/chunk
+command.  The number of atoms and the value(s) are summed or average
+quantities, as explained above.
+
+The *overwrite* keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output.  This option can only be used with the *ave running* setting.
+
+The *format* keyword sets the numeric format of each value when it is
+printed to a file via the *file* keyword.  Note that all values are
+floating point quantities.  The default format is %g.  You can specify
+a higher precision if desired, e.g. %20.16g.
+
+The *title1* and *title2* and *title3* keywords allow specification of
+the strings that will be printed as the first 3 lines of the output
+file, assuming the *file* keyword was used.  LAMMPS uses default
+values for each of these, so they do not need to be specified.
+
+By default, these header lines are as follows:
+
+
+.. parsed-literal::
+
+   # Chunk-averaged data for fix ID and group name
+   # Timestep Number-of-chunks
+   # Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount value1 value2 ...
+
+In the first line, ID and name are replaced with the fix-ID and group
+name.  The second line describes the two values that are printed at
+the first of each section of output.  In the third line the values are
+replaced with the appropriate value names, e.g. fx or c\_myCompute\ **2**\ .
+
+The words in parenthesis only appear with corresponding columns if the
+chunk style specified for the :doc:`compute chunk/atom <compute_chunk_atom>` command supports them.  The OrigID
+column is only used if the *compress* keyword was set to *yes* for the
+:doc:`compute chunk/atom <compute_chunk_atom>` command.  This means that
+the original chunk IDs (e.g. molecule IDs) will have been compressed
+to remove chunk IDs with no atoms assigned to them.  Thus a compressed
+chunk ID of 3 may correspond to an original chunk ID or molecule ID of
+415.  The OrigID column will list 415 for the 3rd chunk.
+
+The CoordN columns only appear if a *binning* style was used in the
+:doc:`compute chunk/atom <compute_chunk_atom>` command.  For *bin/1d*\ ,
+*bin/2d*\ , and *bin/3d* styles the column values are the center point
+of the bin in the corresponding dimension.  Just Coord1 is used for
+*bin/1d*\ , Coord2 is added for *bin/2d*\ , Coord3 is added for *bin/3d*\ .
+For *bin/sphere*\ , just Coord1 is used, and it is the radial
+coordinate.  For *bin/cylinder*\ , Coord1 and Coord2 are used.  Coord1
+is the radial coordinate (away from the cylinder axis), and coord2 is
+the coordinate along the cylinder axis.
+
+Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or *lattice*\ , the
+coordinate values will be in distance :doc:`units <units>`.  If the
+value of the *units* keyword is *reduced*\ , the coordinate values will
+be in unitless reduced units (0-1).  This is not true for the Coord1 value
+of style *bin/sphere* or *bin/cylinder* which both represent radial
+dimensions.  Those values are always in distance :doc:`units <units>`.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global array of values which can be accessed by
+various :doc:`output commands <Howto_output>`.  The values can only be
+accessed on timesteps that are multiples of *Nfreq* since that is when
+averaging is performed.  The global array has # of rows = the number
+of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The # of columns =
+M+1+Nvalues, where M = 1 to 4, depending on whether the optional
+columns for OrigID and CoordN are used, as explained above.  Following
+the optional columns, the next column contains the count of atoms in
+the chunk, and the remaining columns are the Nvalue quantities.  When
+the array is accessed with a row I that exceeds the current number of
+chunks, than a 0.0 is returned by the fix instead of an error, since
+the number of chunks can vary as a simulation runs depending on how
+that value is computed by the compute chunk/atom command.
+
+The array values calculated by this fix are treated as "intensive",
+since they are typically already normalized by the count of atoms in
+each chunk.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`
+
+Default
+"""""""
+
+The option defaults are norm = all, ave = one, bias = none, no file output, and
+title 1,2,3 = strings as described above.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst
new file mode 100644
index 0000000000..9c7d27b761
--- /dev/null
+++ b/doc/src/fix_ave_correlate.rst
@@ -0,0 +1,393 @@
+.. index:: fix ave/correlate
+
+fix ave/correlate command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ave/correlate = style name of this fix command
+* Nevery = use input values every this many timesteps
+* Nrepeat = # of correlation time windows to accumulate
+* Nfreq = calculate time window averages every this many timesteps
+* one or more input values can be listed
+* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
+  
+  .. parsed-literal::
+  
+       c_ID = global scalar calculated by a compute with ID
+       c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = global scalar calculated by a fix with ID
+       f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
+       v_name = global value calculated by an equal-style variable with name
+       v_name[I] = Ith component of a vector-style variable with name
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *type* or *ave* or *start* or *prefactor* or *file* or *overwrite* or *title1* or *title2* or *title3*
+  
+  .. parsed-literal::
+  
+       *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full*
+         auto = correlate each value with itself
+         upper = correlate each value with each succeeding value
+         lower = correlate each value with each preceding value
+         auto/upper = auto + upper
+         auto/lower = auto + lower
+         full = correlate each value with every other value, including itself = auto + upper + lower
+       *ave* args = *one* or *running*
+         one = zero the correlation accumulation every Nfreq steps
+         running = accumulate correlations continuously
+       *start* args = Nstart
+         Nstart = start accumulating correlations on this timestep
+       *prefactor* args = value
+         value = prefactor to scale all the correlation data by
+       *file* arg = filename
+         filename = name of file to output correlation data to
+       *overwrite* arg = none = overwrite output file with only latest output
+       *title1* arg = string
+         string = text to print as 1st line of output file
+       *title2* arg = string
+         string = text to print as 2nd line of output file
+       *title3* arg = string
+         string = text to print as 3rd line of output file
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
+   fix 1 all ave/correlate 1 50 10000 &
+             c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+             type upper ave running title1 "My correlation data"
+
+fix 1 all ave/correlate 1 50 10000 c\_thermo\_press[\*]
+
+Description
+"""""""""""
+
+Use one or more global scalar values as inputs every few timesteps,
+calculate time correlations between them at varying time intervals,
+and average the correlation data over longer timescales.  The
+resulting correlation values can be time integrated by
+:doc:`variables <variable>` or used by other :doc:`output commands <Howto_output>` such as :doc:`thermo\_style custom <thermo_style>`, and can also be written to a file.  See the
+:doc:`fix ave/correlate/long <fix_ave_correlate_long>` command for an
+alternate method for computing correlation functions efficiently over
+very long time windows.
+
+The group specified with this command is ignored.  However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+
+Each listed value can be the result of a :doc:`compute <compute>` or
+:doc:`fix <fix>` or the evaluation of an equal-style or vector-style
+:doc:`variable <variable>`.  In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity.  If
+you wish to spatial- or time-average or histogram per-atom quantities
+from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
+:doc:`fix ave/histo <fix_ave_histo>` commands.  If you wish to convert a
+per-atom quantity into a single global value, see the :doc:`compute reduce <compute_reduce>` command.
+
+The input values must either be all scalars.  What kinds of
+correlations between input values are calculated is determined by the
+*type* keyword as discussed below.
+
+:doc:`Computes <compute>` that produce global quantities are those which
+do not have the word *atom* in their style name.  Only a few
+:doc:`fixes <fix>` produce global quantities.  See the doc pages for
+individual fixes for info on which ones produce such values.
+:doc:`Variables <variable>` of style *equal* and *vector* are the only
+ones that can be used with this fix.  Variables of style *atom* cannot
+be used, since they produce per-atom values.
+
+Note that for values from a compute or fix, the bracketed index I can
+be specified using a wildcard asterisk with the index to effectively
+specify multiple values.  This takes the form "\*" or "\*n" or "n\*" or
+"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+number of columns in the array (for *mode* = vector), then an asterisk
+with no numeric values means all indices from 1 to N.  A leading
+asterisk means all indices from 1 to n (inclusive).  A trailing
+asterisk means all indices from n to N (inclusive).  A middle asterisk
+means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual elements of the
+vector had been listed one by one.  E.g. these 2 fix ave/correlate
+commands are equivalent, since the :doc:`compute pressure <compute_pressure>` command creates a global vector with 6
+values.
+
+
+.. parsed-literal::
+
+   compute myPress all pressure NULL
+   fix 1 all ave/correlate 1 50 10000 c_myPress[\*]
+   fix 1 all ave/correlate 1 50 10000 &
+             c_myPress[1] c_myPress[2] c_myPress[3] &
+             c_myPress[4] c_myPress[5] c_myPress[6]
+
+
+----------
+
+
+The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what
+timesteps the input values will be used to calculate correlation data.
+The input values are sampled every *Nevery* timesteps.  The
+correlation data for the preceding samples is computed on timesteps
+that are a multiple of *Nfreq*\ .  Consider a set of samples from some
+initial time up to an output timestep.  The initial time could be the
+beginning of the simulation or the last output time; see the *ave*
+keyword for options.  For the set of samples, the correlation value
+Cij is calculated as:
+
+
+.. parsed-literal::
+
+   Cij(delta) = ave(Vi(t)\*Vj(t+delta))
+
+which is the correlation value between input values Vi and Vj,
+separated by time delta.  Note that the second value Vj in the pair is
+always the one sampled at the later time.  The ave() represents an
+average over every pair of samples in the set that are separated by
+time delta.  The maximum delta used is of size (\ *Nrepeat*\ -1)\*\ *Nevery*\ .
+Thus the correlation between a pair of input values yields *Nrepeat*
+correlation datums:
+
+
+.. parsed-literal::
+
+   Cij(0), Cij(Nevery), Cij(2\*Nevery), ..., Cij((Nrepeat-1)\*Nevery)
+
+For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
+timesteps 0,5,10,15,...,100 will be used to compute the final averages
+on timestep 100.  Six averages will be computed: Cij(0), Cij(5),
+Cij(10), Cij(15), Cij(20), and Cij(25).  Cij(10) on timestep 100 will
+be the average of 19 samples, namely Vi(0)\*Vj(10), Vi(5)\*Vj(15),
+Vi(10)\*V j20), Vi(15)\*Vj(25), ..., Vi(85)\*Vj(95), Vi(90)\*Vj(100).
+
+*Nfreq* must be a multiple of *Nevery*\ ; *Nevery* and *Nrepeat* must be
+non-zero.  Also, if the *ave* keyword is set to *one* which is the
+default, then *Nfreq* >= (\ *Nrepeat*\ -1)\*\ *Nevery* is required.
+
+
+----------
+
+
+If a value begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  If no bracketed term is
+appended, the global scalar calculated by the compute is used.  If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the compute is used.  See the discussion above for how I
+can be specified with a wildcard asterisk to effectively specify
+multiple values.
+
+Note that there is a :doc:`compute reduce <compute_reduce>` command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix ave/correlate.  Or it can be a compute
+defined not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
+or :doc:`fix temp/rescale <fix_temp_rescale>`.  See the doc pages for
+these commands which give the IDs of these computes.  Users can also
+write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  If no bracketed term is
+appended, the global scalar calculated by the fix is used.  If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the fix is used.  See the discussion above for how I can
+be specified with a wildcard asterisk to effectively specify multiple
+values.
+
+Note that some fixes only produce their values on certain timesteps,
+which must be compatible with *Nevery*\ , else an error will result.
+Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "v\_", a variable name must follow which has
+been previously defined in the input script.  Only equal-style or
+vector-style variables can be referenced; the latter requires a
+bracketed term to specify the Ith element of the vector calculated by
+the variable.  See the :doc:`variable <variable>` command for details.
+Note that variables of style *equal* or *vector* define a formula
+which can reference individual atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+they are evaluated, so this is a very general means of specifying
+quantities to time correlate.
+
+
+----------
+
+
+Additional optional keywords also affect the operation of this fix.
+
+The *type* keyword determines which pairs of input values are
+correlated with each other.  For N input values Vi, for i = 1 to N,
+let the number of pairs = Npair.  Note that the second value in the
+pair Vi(t)\*Vj(t+delta) is always the one sampled at the later time.
+
+* If *type* is set to *auto* then each input value is correlated with
+  itself.  I.e. Cii = Vi\*Vi, for i = 1 to N, so Npair = N.
+* If *type* is set
+  to *upper* then each input value is correlated with every succeeding
+  value.  I.e. Cij = Vi\*Vj, for i < j, so Npair = N\*(N-1)/2.
+* If *type* is set
+  to *lower* then each input value is correlated with every preceding
+  value.  I.e. Cij = Vi\*Vj, for i > j, so Npair = N\*(N-1)/2.
+* If *type* is set to *auto/upper* then each input value is correlated
+  with itself and every succeeding value.  I.e. Cij = Vi\*Vj, for i >= j,
+  so Npair = N\*(N+1)/2.
+* If *type* is set to *auto/lower* then each input value is correlated
+  with itself and every preceding value.  I.e. Cij = Vi\*Vj, for i <= j,
+  so Npair = N\*(N+1)/2.
+* If *type* is set to *full* then each input value is correlated with
+  itself and every other value.  I.e. Cij = Vi\*Vj, for i,j = 1,N so
+  Npair = N\^2.
+
+
+The *ave* keyword determines what happens to the accumulation of
+correlation samples every *Nfreq* timesteps.  If the *ave* setting is
+*one*\ , then the accumulation is restarted or zeroed every *Nfreq*
+timesteps.  Thus the outputs on successive *Nfreq* timesteps are
+essentially independent of each other.  The exception is that the
+Cij(0) = Vi(T)\*Vj(T) value at a timestep T, where T is a multiple of
+*Nfreq*\ , contributes to the correlation output both at time T and at
+time T+Nfreq.
+
+If the *ave* setting is *running*\ , then the accumulation is never
+zeroed.  Thus the output of correlation data at any timestep is the
+average over samples accumulated every *Nevery* steps since the fix
+was defined.  it can only be restarted by deleting the fix via the
+:doc:`unfix <unfix>` command, or by re-defining the fix by re-specifying
+it.
+
+The *start* keyword specifies what timestep the accumulation of
+correlation samples will begin on.  The default is step 0.  Setting it
+to a larger value can avoid adding non-equilibrated data to the
+correlation averages.
+
+The *prefactor* keyword specifies a constant which will be used as a
+multiplier on the correlation data after it is averaged.  It is
+effectively a scale factor on Vi\*Vj, which can be used to account for
+the size of the time window or other unit conversions.
+
+The *file* keyword allows a filename to be specified.  Every *Nfreq*
+steps, an array of correlation data is written to the file.  The
+number of rows is *Nrepeat*\ , as described above.  The number of
+columns is the Npair+2, also as described above.  Thus the file ends
+up to be a series of these array sections.
+
+The *overwrite* keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output.  This option can only be used with the *ave running* setting.
+
+The *title1* and *title2* and *title3* keywords allow specification of
+the strings that will be printed as the first 3 lines of the output
+file, assuming the *file* keyword was used.  LAMMPS uses default
+values for each of these, so they do not need to be specified.
+
+By default, these header lines are as follows:
+
+
+.. parsed-literal::
+
+   # Time-correlated data for fix ID
+   # TimeStep Number-of-time-windows
+   # Index TimeDelta Ncount valueI\*valueJ valueI\*valueJ ...
+
+In the first line, ID is replaced with the fix-ID.  The second line
+describes the two values that are printed at the first of each section
+of output.  In the third line the value pairs are replaced with the
+appropriate fields from the fix ave/correlate command.
+
+
+----------
+
+
+Let Sij = a set of time correlation data for input values I and J,
+namely the *Nrepeat* values:
+
+
+.. parsed-literal::
+
+   Sij = Cij(0), Cij(Nevery), Cij(2\*Nevery), ..., Cij(\*Nrepeat-1)\*Nevery)
+
+As explained below, these datums are output as one column of a global
+array, which is effectively the correlation matrix.
+
+The *trap* function defined for :doc:`equal-style variables <variable>`
+can be used to perform a time integration of this vector of datums,
+using a trapezoidal rule.  This is useful for calculating various
+quantities which can be derived from time correlation data.  If a
+normalization factor is needed for the time integration, it can be
+included in the variable formula or via the *prefactor* keyword.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global array of values which can be accessed by
+various :doc:`output commands <Howto_output>`.  The values can only be
+accessed on timesteps that are multiples of *Nfreq* since that is when
+averaging is performed.  The global array has # of rows = *Nrepeat*
+and # of columns = Npair+2.  The first column has the time delta (in
+timesteps) between the pairs of input values used to calculate the
+correlation, as described above.  The 2nd column has the number of
+samples contributing to the correlation average, as described above.
+The remaining Npair columns are for I,J pairs of the N input values,
+as determined by the *type* keyword, as described above.
+
+* For *type* = *auto*\ , the Npair = N columns are ordered: C11, C22, ...,
+  CNN.
+* For *type* = *upper*\ , the Npair = N\*(N-1)/2 columns are ordered: C12,
+  C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N.
+* For *type* = *lower*\ , the Npair = N\*(N-1)/2 columns are ordered: C21,
+  C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1.
+* For *type* = *auto/upper*\ , the Npair = N\*(N+1)/2 columns are ordered:
+  C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
+  CNN.
+* For *type* = *auto/lower*\ , the Npair = N\*(N+1)/2 columns are ordered:
+  C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
+  CNN.
+* For *type* = *full*\ , the Npair = N\^2 columns are ordered: C11, C12,
+  ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
+  CNN.
+
+
+The array values calculated by this fix are treated as intensive.  If
+you need to divide them by the number of atoms, you must do this in a
+later processing step, e.g. when using them in a
+:doc:`variable <variable>`.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ave/correlate/long <fix_ave_correlate_long>`,
+:doc:`compute <compute>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
+:doc:`fix ave/histo <fix_ave_histo>`, :doc:`variable <variable>`
+
+**Default:** none
+
+The option defaults are ave = one, type = auto, start = 0, no file
+output, title 1,2,3 = strings as described above, and prefactor = 1.0.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst
new file mode 100644
index 0000000000..a976061edc
--- /dev/null
+++ b/doc/src/fix_ave_correlate_long.rst
@@ -0,0 +1,162 @@
+.. index:: fix ave/correlate/long
+
+fix ave/correlate/long command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ave/correlate/long = style name of this fix command
+* Nevery = use input values every this many timesteps
+* Nfreq = save state of the time correlation functions every this many timesteps
+* one or more input values can be listed
+* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
+  
+  .. parsed-literal::
+  
+       c_ID = global scalar calculated by a compute with ID
+       c_ID[I] = Ith component of global vector calculated by a compute with ID
+       f_ID = global scalar calculated by a fix with ID
+       f_ID[I] = Ith component of global vector calculated by a fix with ID
+       v_name = global value calculated by an equal-style variable with name
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *p* or *m*
+  
+  .. parsed-literal::
+  
+       *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full*
+         auto = correlate each value with itself
+         upper = correlate each value with each succeeding value
+         lower = correlate each value with each preceding value
+         auto/upper = auto + upper
+         auto/lower = auto + lower
+         full = correlate each value with every other value, including itself = auto + upper + lower
+       *start* args = Nstart
+         Nstart = start accumulating correlations on this timestep
+       *file* arg = filename
+         filename = name of file to output correlation data to
+       *overwrite* arg = none = overwrite output file with only latest output
+       *title1* arg = string
+         string = text to print as 1st line of output file
+       *title2* arg = string
+         string = text to print as 2nd line of output file
+       *ncorr* arg = Ncorrelators
+         Ncorrelators = number of correlators to store
+       *nlen* args = Nlen
+         Nlen = length of each correlator
+       *ncount* args = Ncount
+         Ncount = number of values over which succesive correlators are averaged
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
+   fix 1 all ave/correlate/long 1 10000 &
+             c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+             type upper title1 "My correlation data" nlen 15 ncount 3
+
+Description
+"""""""""""
+
+This fix is similar in spirit and syntax to the :doc:`fix ave/correlate <fix_ave_correlate>`.  However, this fix allows the
+efficient calculation of time correlation functions on the fly over
+extremely long time windows without too much CPU overhead, using a
+multiple-tau method :ref:`(Ramirez) <Ramirez>` that decreases the resolution
+of the stored correlation function with time.
+
+The group specified with this command is ignored.  However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+
+Each listed value can be the result of a compute or fix or the
+evaluation of an equal-style variable. See the :doc:`fix ave/correlate <fix_ave_correlate>` doc page for details.
+
+The *Nevery* and *Nfreq* arguments specify on what timesteps the input
+values will be used to calculate correlation data, and the frequency
+with which the time correlation functions will be output to a file.
+Note that there is no *Nrepeat* argument, unlike the :doc:`fix ave/correlate <fix_ave_correlate>` command.
+
+The optional keywords *ncorr*\ , *nlen*\ , and *ncount* are unique to this
+command and determine the number of correlation points calculated and
+the memory and CPU overhead used by this calculation. *Nlen* and
+*ncount* determine the amount of averaging done at longer correlation
+times.  The default values *nlen=16*\ , *ncount=2* ensure that the
+systematic error of the multiple-tau correlator is always below the
+level of the statistical error of a typical simulation (which depends
+on the ensemble size and the simulation length).
+
+The maximum correlation time (in time steps) that can be reached is
+given by the formula (nlen-1) \* ncount\^(ncorr-1).  Longer correlation
+times are discarded and not calculated.  With the default values of
+the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to
+7864320 time steps.  If longer correlation times are needed, the value
+of ncorr should be increased. Using nlen=16 and ncount=2, with
+ncorr=30, the maximum number of steps that can be correlated is
+80530636808.  If ncorr=40, correlation times in excess of 8e12 time
+steps can be calculated.
+
+The total memory needed for each correlation pair is roughly
+4\*ncorr\*nlen\*8 bytes. With the default values of the parameters, this
+corresponds to about 10 KB.
+
+For the meaning of the additional optional keywords, see the :doc:`fix ave/correlate <fix_ave_correlate>` doc page.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Since this fix in intended for the calculation of time correlation
+functions over very long MD simulations, the information about this
+fix is written automatically to binary restart files, so that the time
+correlation calculation can continue in subsequent simulations. None
+of the fix\_modify options are relevant to this fix.
+
+No parameter of this fix can be used with the start/stop keywords of
+the run command. This fix is not invoked during energy minimization.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ave/correlate <fix_ave_correlate>`
+
+**Default:** none
+
+The option defaults for keywords that are also keywords for the :doc:`fix ave/correlate <fix_ave_correlate>` command are as follows: type =
+auto, start = 0, no file output, title 1,2 = strings as described on
+the :doc:`fix ave/correlate <fix_ave_correlate>` doc page.
+
+The option defaults for keywords unique to this command are as
+follows: ncorr=20, nlen=16, ncount=2.
+
+
+----------
+
+
+.. _Ramirez:
+
+
+
+**(Ramirez)** J. Ramirez, S.K. Sukumaran, B. Vorselaars and
+A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst
new file mode 100644
index 0000000000..4a2e73d7df
--- /dev/null
+++ b/doc/src/fix_ave_histo.rst
@@ -0,0 +1,395 @@
+.. index:: fix ave/histo
+
+fix ave/histo command
+=====================
+
+fix ave/histo/weight command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = *ave/histo* or *ave/histo/weight* = style name of this fix command
+* Nevery = use input values every this many timesteps
+* Nrepeat = # of times to use input values for calculating histogram
+* Nfreq = calculate histogram every this many timesteps
+* lo,hi = lo/hi bounds within which to histogram
+* Nbin = # of histogram bins
+* one or more input values can be listed
+* value = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
+  
+  .. parsed-literal::
+  
+       x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+       c_ID = scalar or vector calculated by a compute with ID
+       c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = scalar or vector calculated by a fix with ID
+       f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
+       v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
+       v_name[I] = value calculated by a vector-style variable with name
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *mode* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
+  
+  .. parsed-literal::
+  
+       *mode* arg = *scalar* or *vector*
+         scalar = all input values are scalars
+         vector = all input values are vectors
+       *kind* arg = *global* or *peratom* or *local*
+       *file* arg = filename
+         filename = name of file to output histogram(s) to
+       *ave* args = *one* or *running* or *window*
+         one = output a new average value every Nfreq steps
+         running = output cumulative average of all previous Nfreq steps
+         window M = output average of M most recent Nfreq steps
+       *start* args = Nstart
+         Nstart = start averaging on this timestep
+       *beyond* arg = *ignore* or *end* or *extra*
+         ignore = ignore values outside histogram lo/hi bounds
+         end = count values outside histogram lo/hi bounds in end bins
+         extra = create 2 extra bins for value outside histogram lo/hi bounds
+       *overwrite* arg = none = overwrite output file with only latest output
+       *title1* arg = string
+         string = text to print as 1st line of output file
+       *title2* arg = string
+         string = text to print as 2nd line of output file
+       *title3* arg = string
+         string = text to print as 3rd line of output file, only for vector mode
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
+   fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
+   fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[\*]
+   fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
+   fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
+
+Description
+"""""""""""
+
+Use one or more values as inputs every few timesteps to create a
+single histogram.  The histogram can then be averaged over longer
+timescales.  The resulting histogram can be used by other :doc:`output commands <Howto_output>`, and can also be written to a file.  The
+fix ave/histo/weight command has identical syntax to fix ave/histo,
+except that exactly two values must be specified.  See details below.
+
+The group specified with this command is ignored for global and local
+input values.  For per-atom input values, only atoms in the group
+contribute to the histogram.  Note that regardless of the specified
+group, specified values may represent calculations performed by
+computes and fixes which store their own "group" definition.
+
+A histogram is simply a count of the number of values that fall within
+a histogram bin.  *Nbins* are defined, with even spacing between *lo*
+and *hi*\ .  Values that fall outside the lo/hi bounds can be treated in
+different ways; see the discussion of the *beyond* keyword below.
+
+Each input value can be an atom attribute (position, velocity, force
+component) or can be the result of a :doc:`compute <compute>` or
+:doc:`fix <fix>` or the evaluation of an equal-style or vector-style or
+atom-style :doc:`variable <variable>`.  The set of input values can be
+either all global, all per-atom, or all local quantities.  Inputs of
+different kinds (e.g. global and per-atom) cannot be mixed.  Atom
+attributes are per-atom vector values.  See the doc page for
+individual "compute" and "fix" commands to see what kinds of
+quantities they generate.  See the optional *kind* keyword below for
+how to force the fix ave/histo command to disambiguate if necessary.
+
+Note that the output of this command is a single histogram for all
+input values combined together, not one histogram per input value.
+See below for details on the format of the output of this fix.
+
+The input values must either be all scalars or all vectors (or
+arrays), depending on the setting of the *mode* keyword.
+
+If *mode* = scalar, then the input values must be scalars, or vectors
+with a bracketed term appended, indicating the Ith value of the vector
+is used.
+
+If *mode* = vector, then the input values must be vectors, or arrays
+with a bracketed term appended, indicating the Ith column of the array
+is used.
+
+Note that for values from a compute or fix, the bracketed index I can
+be specified using a wildcard asterisk with the index to effectively
+specify multiple values.  This takes the form "\*" or "\*n" or "n\*" or
+"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+number of columns in the array (for *mode* = vector), then an asterisk
+with no numeric values means all indices from 1 to N.  A leading
+asterisk means all indices from 1 to n (inclusive).  A trailing
+asterisk means all indices from n to N (inclusive).  A middle asterisk
+means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual elements of the
+vector or columns of the array had been listed one by one.  E.g. these
+2 fix ave/histo commands are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>` command creates a global array with
+3 columns:
+
+
+.. parsed-literal::
+
+   compute myCOM all com/chunk
+   fix 1 all ave/histo 100 1 100 c_myCOM[\*] file tmp1.com mode vector
+   fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
+
+If the fix ave/histo/weight command is used, exactly two values must
+be specified.  If the values are vectors, they must be the same
+length.  The first value (a scalar or vector) is what is histogrammed
+into bins, in the same manner the fix ave/histo command operates.  The
+second value (a scalar or vector) is used as a "weight".  This means
+that instead of each value tallying a "1" to its bin, the
+corresponding weight is tallied.  E.g. The Nth entry (weight) in the
+second vector is tallied to the bin corresponding to the Nth entry in
+the first vector.
+
+
+----------
+
+
+The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what
+timesteps the input values will be used in order to contribute to the
+histogram.  The final histogram is generated on timesteps that are
+multiple of *Nfreq*\ .  It is averaged over *Nrepeat* histograms,
+computed in the preceding portion of the simulation every *Nevery*
+timesteps.  *Nfreq* must be a multiple of *Nevery* and *Nevery* must
+be non-zero even if *Nrepeat* is 1.  Also, the timesteps
+contributing to the histogram value cannot overlap,
+i.e. Nrepeat\*Nevery can not exceed Nfreq.
+
+For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
+on timesteps 90,92,94,96,98,100 will be used to compute the final
+histogram on timestep 100.  Similarly for timesteps
+190,192,194,196,198,200 on timestep 200, etc.  If Nrepeat=1 and Nfreq
+= 100, then no time averaging of the histogram is done; a histogram is
+simply generated on timesteps 100,200,etc.
+
+
+----------
+
+
+The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+self-explanatory.  Note that other atom attributes can be used as
+inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+an input value from that compute.
+
+If a value begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  If *mode* = scalar, then if
+no bracketed term is appended, the global scalar calculated by the
+compute is used.  If a bracketed term is appended, the Ith element of
+the global vector calculated by the compute is used.  If *mode* =
+vector, then if no bracketed term is appended, the global or per-atom
+or local vector calculated by the compute is used.  If a bracketed
+term is appended, the Ith column of the global or per-atom or local
+array calculated by the compute is used.  See the discussion above for
+how I can be specified with a wildcard asterisk to effectively specify
+multiple values.
+
+Note that there is a :doc:`compute reduce <compute_reduce>` command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix ave/histo.  Or it can be a compute defined
+not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
+or :doc:`fix temp/rescale <fix_temp_rescale>`.  See the doc pages for
+these commands which give the IDs of these computes.  Users can also
+write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  If *mode* = scalar, then if
+no bracketed term is appended, the global scalar calculated by the fix
+is used.  If a bracketed term is appended, the Ith element of the
+global vector calculated by the fix is used.  If *mode* = vector, then
+if no bracketed term is appended, the global or per-atom or local
+vector calculated by the fix is used.  If a bracketed term is
+appended, the Ith column of the global or per-atom or local array
+calculated by the fix is used.  See the discussion above for how I can
+be specified with a wildcard asterisk to effectively specify multiple
+values.
+
+Note that some fixes only produce their values on certain timesteps,
+which must be compatible with *Nevery*\ , else an error will result.
+Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "v\_", a variable name must follow which has
+been previously defined in the input script.  If *mode* = scalar, then
+only equal-style or vector-style variables can be used, which both
+produce global values.  In this mode, a vector-style variable requires
+a bracketed term to specify the Ith element of the vector calculated
+by the variable.  If *mode* = vector, then only vector-style or
+atom-style variables can be used, which produce a global or per-atom
+vector respectively.  The vector-style variable must be used without a
+bracketed term.  See the :doc:`variable <variable>` command for details.
+
+Note that variables of style *equal*\ , *vector*\ , and *atom* define a
+formula which can reference individual atom properties or
+thermodynamic keywords, or they can invoke other computes, fixes, or
+variables when they are evaluated, so this is a very general means of
+specifying quantities to histogram.
+
+
+----------
+
+
+Additional optional keywords also affect the operation of this fix.
+
+If the *mode* keyword is set to *scalar*\ , then all input values must
+be global scalars, or elements of global vectors.  If the *mode*
+keyword is set to *vector*\ , then all input values must be global or
+per-atom or local vectors, or columns of global or per-atom or local
+arrays.
+
+The *kind* keyword only needs to be set if a compute or fix produces
+more than one kind of output (global, per-atom, local).  If this is
+not the case, then LAMMPS will determine what kind of input is
+provided and whether all the input arguments are consistent.  If a
+compute or fix produces more than one kind of output, the *kind*
+keyword should be used to specify which output will be used.  The
+remaining input arguments must still be consistent.
+
+The *beyond* keyword determines how input values that fall outside the
+*lo* to *hi* bounds are treated.  Values such that *lo* <= value <=
+*hi* are assigned to one bin.  Values on a bin boundary are assigned
+to the lower of the 2 bins.  If *beyond* is set to *ignore* then
+values < *lo* and values > *hi* are ignored, i.e. they are not binned.
+If *beyond* is set to *end* then values < *lo* are counted in the
+first bin and values > *hi* are counted in the last bin.  If *beyond*
+is set to *extend* then two extra bins are created, so that there are
+Nbins+2 total bins.  Values < *lo* are counted in the first bin and
+values > *hi* are counted in the last bin (Nbins+2).  Values between
+*lo* and *hi* (inclusive) are counted in bins 2 through Nbins+1.  The
+"coordinate" stored and printed for these two extra bins is *lo* and
+*hi*\ .
+
+The *ave* keyword determines how the histogram produced every *Nfreq*
+steps are averaged with histograms produced on previous steps that
+were multiples of *Nfreq*\ , before they are accessed by another output
+command or written to a file.
+
+If the *ave* setting is *one*\ , then the histograms produced on
+timesteps that are multiples of *Nfreq* are independent of each other;
+they are output as-is without further averaging.
+
+If the *ave* setting is *running*\ , then the histograms produced on
+timesteps that are multiples of *Nfreq* are summed and averaged in a
+cumulative sense before being output.  Each bin value in the histogram
+is thus the average of the bin value produced on that timestep with
+all preceding values for the same bin.  This running average begins
+when the fix is defined; it can only be restarted by deleting the fix
+via the :doc:`unfix <unfix>` command, or by re-defining the fix by
+re-specifying it.
+
+If the *ave* setting is *window*\ , then the histograms produced on
+timesteps that are multiples of *Nfreq* are summed within a moving
+"window" of time, so that the last M histograms are used to produce
+the output.  E.g. if M = 3 and Nfreq = 1000, then the output on step
+10000 will be the combined histogram of the individual histograms on
+steps 8000,9000,10000.  Outputs on early steps will be sums over less
+than M histograms if they are not available.
+
+The *start* keyword specifies what timestep histogramming will begin
+on.  The default is step 0.  Often input values can be 0.0 at time 0,
+so setting *start* to a larger value can avoid including a 0.0 in
+a running or windowed histogram.
+
+The *file* keyword allows a filename to be specified.  Every *Nfreq*
+steps, one histogram is written to the file.  This includes a leading
+line that contains the timestep, number of bins, the total count of
+values contributing to the histogram, the count of values that were
+not histogrammed (see the *beyond* keyword), the minimum value
+encountered, and the maximum value encountered.  The min/max values
+include values that were not histogrammed.  Following the leading
+line, one line per bin is written into the file.  Each line contains
+the bin #, the coordinate for the center of the bin (between *lo* and
+*hi*\ ), the count of values in the bin, and the normalized count.  The
+normalized count is the bin count divided by the total count (not
+including values not histogrammed), so that the normalized values sum
+to 1.0 across all bins.
+
+The *overwrite* keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output.  This option can only be used with the *ave running* setting.
+
+The *title1* and *title2* and *title3* keywords allow specification of
+the strings that will be printed as the first 3 lines of the output
+file, assuming the *file* keyword was used.  LAMMPS uses default
+values for each of these, so they do not need to be specified.
+
+By default, these header lines are as follows:
+
+
+.. parsed-literal::
+
+   # Histogram for fix ID
+   # TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
+   # Bin Coord Count Count/Total
+
+In the first line, ID is replaced with the fix-ID.  The second line
+describes the six values that are printed at the first of each section
+of output.  The third describes the 4 values printed for each bin in
+the histogram.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix produces a global vector and global array which can be
+accessed by various :doc:`output commands <Howto_output>`.  The values
+can only be accessed on timesteps that are multiples of *Nfreq* since
+that is when a histogram is generated.  The global vector has 4
+values:
+
+* 1 = total counts in the histogram
+* 2 = values that were not histogrammed (see *beyond* keyword)
+* 3 = min value of all input values, including ones not histogrammed
+* 4 = max value of all input values, including ones not histogrammed
+
+The global array has # of rows = Nbins and # of columns = 3.  The
+first column has the bin coordinate, the 2nd column has the count of
+values in that histogram bin, and the 3rd column has the bin count
+divided by the total count (not including missing counts), so that the
+values in the 3rd column sum to 1.0.
+
+The vector and array values calculated by this fix are all treated as
+intensive.  If this is not the case, e.g. due to histogramming
+per-atom input values, then you will need to account for that when
+interpreting the values produced by this fix.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
+
+**Default:** none
+
+The option defaults are mode = scalar, kind = figured out from input
+arguments, ave = one, start = 0, no file output, beyond = ignore, and
+title 1,2,3 = strings as described above.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst
new file mode 100644
index 0000000000..3774379f19
--- /dev/null
+++ b/doc/src/fix_ave_time.rst
@@ -0,0 +1,375 @@
+.. index:: fix ave/time
+
+fix ave/time command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ave/time = style name of this fix command
+* Nevery = use input values every this many timesteps
+* Nrepeat = # of times to use input values for calculating averages
+* Nfreq = calculate averages every this many timesteps
+* one or more input values can be listed
+* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
+  
+  .. parsed-literal::
+  
+       c_ID = global scalar or vector calculated by a compute with ID
+       c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+       f_ID = global scalar or vector calculated by a fix with ID
+       f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+       v_name = value(s) calculated by an equal-style or vector-style variable with name
+       v_name[I] = value calculated by a vector-style variable with name
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *title1* or *title2* or *title3*
+  
+  .. parsed-literal::
+  
+       *mode* arg = *scalar* or *vector*
+         scalar = all input values are global scalars
+         vector = all input values are global vectors or global arrays
+       *ave* args = *one* or *running* or *window M*
+         one = output a new average value every Nfreq steps
+         running = output cumulative average of all previous Nfreq steps
+         window M = output average of M most recent Nfreq steps
+       *start* args = Nstart
+         Nstart = start averaging on this timestep
+       *off* arg = M = do not average this value
+         M = value # from 1 to Nvalues
+       *file* arg = filename
+         filename = name of file to output time averages to
+       *overwrite* arg = none = overwrite output file with only latest output
+       *format* arg = string
+         string = C-style format string
+       *title1* arg = string
+         string = text to print as 1st line of output file
+       *title2* arg = string
+         string = text to print as 2nd line of output file
+       *title3* arg = string
+         string = text to print as 3rd line of output file, only for vector mode
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
+   fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
+                                 title1 "My output values"
+   fix 1 all ave/time 100 5 1000 c_thermo_press[\*]
+   fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
+
+Description
+"""""""""""
+
+Use one or more global values as inputs every few timesteps, and
+average them over longer timescales.  The resulting averages can be
+used by other :doc:`output commands <Howto_output>` such as
+:doc:`thermo\_style custom <thermo_style>`, and can also be written to a
+file.  Note that if no time averaging is done, this command can be
+used as a convenient way to simply output one or more global values to
+a file.
+
+The group specified with this command is ignored.  However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+
+Each listed value can be the result of a :doc:`compute <compute>` or
+:doc:`fix <fix>` or the evaluation of an equal-style or vector-style
+:doc:`variable <variable>`.  In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity.  If
+you wish to spatial- or time-average or histogram per-atom quantities
+from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`,
+or :doc:`fix ave/histo <fix_ave_histo>` commands.  If you wish to sum a
+per-atom quantity into a single global quantity, see the :doc:`compute reduce <compute_reduce>` command.
+
+:doc:`Computes <compute>` that produce global quantities are those which
+do not have the word *atom* in their style name.  Only a few
+:doc:`fixes <fix>` produce global quantities.  See the doc pages for
+individual fixes for info on which ones produce such values.
+:doc:`Variables <variable>` of style *equal* and *vector* are the only
+ones that can be used with this fix.  Variables of style *atom* cannot
+be used, since they produce per-atom values.
+
+The input values must either be all scalars or all vectors depending
+on the setting of the *mode* keyword.  In both cases, the averaging is
+performed independently on each input value.  I.e. each input scalar
+is averaged independently or each element of each input vector is
+averaged independently.
+
+If *mode* = scalar, then the input values must be scalars, or vectors
+with a bracketed term appended, indicating the Ith value of the vector
+is used.
+
+If *mode* = vector, then the input values must be vectors, or arrays
+with a bracketed term appended, indicating the Ith column of the array
+is used.  All vectors must be the same length, which is the length of
+the vector or number of rows in the array.
+
+Note that for values from a compute or fix, the bracketed index I can
+be specified using a wildcard asterisk with the index to effectively
+specify multiple values.  This takes the form "\*" or "\*n" or "n\*" or
+"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+number of columns in the array (for *mode* = vector), then an asterisk
+with no numeric values means all indices from 1 to N.  A leading
+asterisk means all indices from 1 to n (inclusive).  A trailing
+asterisk means all indices from n to N (inclusive).  A middle asterisk
+means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual elements of the
+vector or columns of the array had been listed one by one.  E.g. these
+2 fix ave/time commands are equivalent, since the :doc:`compute rdf <compute_rdf>` command creates, in this case, a global array
+with 3 columns, each of length 50:
+
+
+.. parsed-literal::
+
+   compute myRDF all rdf 50 1 2
+   fix 1 all ave/time 100 1 100 c_myRDF[\*] file tmp1.rdf mode vector
+   fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
+
+
+----------
+
+
+The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what
+timesteps the input values will be used in order to contribute to the
+average.  The final averaged quantities are generated on timesteps
+that are a multiple of *Nfreq*\ .  The average is over *Nrepeat*
+quantities, computed in the preceding portion of the simulation every
+*Nevery* timesteps.  *Nfreq* must be a multiple of *Nevery* and
+*Nevery* must be non-zero even if *Nrepeat* is 1.  Also, the timesteps
+contributing to the average value cannot overlap,
+i.e. Nrepeat\*Nevery can not exceed Nfreq.
+
+For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100.  Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc.  If Nrepeat=1 and Nfreq = 100, then no time
+averaging is done; values are simply generated on timesteps
+100,200,etc.
+
+
+----------
+
+
+If a value begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  If *mode* = scalar, then if
+no bracketed term is appended, the global scalar calculated by the
+compute is used.  If a bracketed term is appended, the Ith element of
+the global vector calculated by the compute is used.  If *mode* =
+vector, then if no bracketed term is appended, the global vector
+calculated by the compute is used.  If a bracketed term is appended,
+the Ith column of the global array calculated by the compute is used.
+See the discussion above for how I can be specified with a wildcard
+asterisk to effectively specify multiple values.
+
+Note that there is a :doc:`compute reduce <compute_reduce>` command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix ave/time.  Or it can be a compute defined
+not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>`.  See
+the doc pages for these commands which give the IDs of these computes.
+Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  If *mode* = scalar, then if
+no bracketed term is appended, the global scalar calculated by the fix
+is used.  If a bracketed term is appended, the Ith element of the
+global vector calculated by the fix is used.  If *mode* = vector, then
+if no bracketed term is appended, the global vector calculated by the
+fix is used.  If a bracketed term is appended, the Ith column of the
+global array calculated by the fix is used.  See the discussion above
+for how I can be specified with a wildcard asterisk to effectively
+specify multiple values.
+
+Note that some fixes only produce their values on certain timesteps,
+which must be compatible with *Nevery*\ , else an error will result.
+Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "v\_", a variable name must follow which has
+been previously defined in the input script.  If *mode* = scalar, then
+only equal-style or vector-style variables can be used, which both
+produce global values.  In this mode, a vector-style variable requires
+a bracketed term to specify the Ith element of the vector calculated
+by the variable.  If *mode* = vector, then only a vector-style
+variable can be used, without a bracketed term.  See the
+:doc:`variable <variable>` command for details.
+
+Note that variables of style *equal* and *vector* define a formula
+which can reference individual atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+they are evaluated, so this is a very general means of specifying
+quantities to time average.
+
+
+----------
+
+
+Additional optional keywords also affect the operation of this fix.
+
+If the *mode* keyword is set to *scalar*\ , then all input values must
+be global scalars, or elements of global vectors.  If the *mode*
+keyword is set to *vector*\ , then all input values must be global
+vectors, or columns of global arrays.  They can also be global arrays,
+which are converted into a series of global vectors (one per column),
+as explained above.
+
+The *ave* keyword determines how the values produced every *Nfreq*
+steps are averaged with values produced on previous steps that were
+multiples of *Nfreq*\ , before they are accessed by another output
+command or written to a file.
+
+If the *ave* setting is *one*\ , then the values produced on timesteps
+that are multiples of *Nfreq* are independent of each other; they are
+output as-is without further averaging.
+
+If the *ave* setting is *running*\ , then the values produced on
+timesteps that are multiples of *Nfreq* are summed and averaged in a
+cumulative sense before being output.  Each output value is thus the
+average of the value produced on that timestep with all preceding
+values.  This running average begins when the fix is defined; it can
+only be restarted by deleting the fix via the :doc:`unfix <unfix>`
+command, or by re-defining the fix by re-specifying it.
+
+If the *ave* setting is *window*\ , then the values produced on
+timesteps that are multiples of *Nfreq* are summed and averaged within
+a moving "window" of time, so that the last M values are used to
+produce the output.  E.g. if M = 3 and Nfreq = 1000, then the output
+on step 10000 will be the average of the individual values on steps
+8000,9000,10000.  Outputs on early steps will average over less than M
+values if they are not available.
+
+The *start* keyword specifies what timestep averaging will begin on.
+The default is step 0.  Often input values can be 0.0 at time 0, so
+setting *start* to a larger value can avoid including a 0.0 in a
+running or windowed average.
+
+The *off* keyword can be used to flag any of the input values.  If a
+value is flagged, it will not be time averaged.  Instead the most
+recent input value will always be stored and output.  This is useful
+if one of more of the inputs produced by a compute or fix or variable
+are effectively constant or are simply current values.  E.g. they are
+being written to a file with other time-averaged values for purposes
+of creating well-formatted output.
+
+The *file* keyword allows a filename to be specified.  Every *Nfreq*
+steps, one quantity or vector of quantities is written to the file for
+each input value specified in the fix ave/time command.  For *mode* =
+scalar, this means a single line is written each time output is
+performed.  Thus the file ends up to be a series of lines, i.e. one
+column of numbers for each input value.  For *mode* = vector, an array
+of numbers is written each time output is performed.  The number of
+rows is the length of the input vectors, and the number of columns is
+the number of values.  Thus the file ends up to be a series of these
+array sections.
+
+The *overwrite* keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output.  This option can only be used with the *ave running* setting.
+
+The *format* keyword sets the numeric format of each value when it is
+printed to a file via the *file* keyword.  Note that all values are
+floating point quantities.  The default format is %g.  You can specify
+a higher precision if desired, e.g. %20.16g.
+
+The *title1* and *title2* and *title3* keywords allow specification of
+the strings that will be printed as the first 2 or 3 lines of the
+output file, assuming the *file* keyword was used.  LAMMPS uses
+default values for each of these, so they do not need to be specified.
+
+By default, these header lines are as follows for *mode* = scalar:
+
+
+.. parsed-literal::
+
+   # Time-averaged data for fix ID
+   # TimeStep value1 value2 ...
+
+In the first line, ID is replaced with the fix-ID.  In the second line
+the values are replaced with the appropriate fields from the fix
+ave/time command.  There is no third line in the header of the file,
+so the *title3* setting is ignored when *mode* = scalar.
+
+By default, these header lines are as follows for *mode* = vector:
+
+
+.. parsed-literal::
+
+   # Time-averaged data for fix ID
+   # TimeStep Number-of-rows
+   # Row value1 value2 ...
+
+In the first line, ID is replaced with the fix-ID.  The second line
+describes the two values that are printed at the first of each section
+of output.  In the third line the values are replaced with the
+appropriate fields from the fix ave/time command.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix produces a global scalar or global vector or global array
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The values can only be accessed on timesteps that are multiples of
+*Nfreq* since that is when averaging is performed.
+
+A scalar is produced if only a single input value is averaged and
+*mode* = scalar.  A vector is produced if multiple input values are
+averaged for *mode* = scalar, or a single input value for *mode* =
+vector.  In the first case, the length of the vector is the number of
+inputs.  In the second case, the length of the vector is the same as
+the length of the input vector.  An array is produced if multiple
+input values are averaged and *mode* = vector.  The global array has #
+of rows = length of the input vectors and # of columns = number of
+inputs.
+
+If the fix produces a scalar or vector, then the scalar and each
+element of the vector can be either "intensive" or "extensive",
+depending on whether the values contributing to the scalar or vector
+element are "intensive" or "extensive".  If the fix produces an array,
+then all elements in the array must be the same, either "intensive" or
+"extensive".  If a compute or fix provides the value being time
+averaged, then the compute or fix determines whether the value is
+intensive or extensive; see the doc page for that compute or fix for
+further info.  Values produced by a variable are treated as intensive.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
+
+Default
+"""""""
+
+The option defaults are mode = scalar, ave = one, start = 0, no file
+output, format = %g, title 1,2,3 = strings as described above, and no
+off settings for any input values.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst
new file mode 100644
index 0000000000..f786c043c9
--- /dev/null
+++ b/doc/src/fix_aveforce.rst
@@ -0,0 +1,139 @@
+.. index:: fix aveforce
+
+fix aveforce command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID aveforce fx fy fz keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* aveforce = style name of this fix command
+* fx,fy,fz = force component values (force units)
+  
+  .. parsed-literal::
+  
+       any of fx,fy,fz can be a variable (see below)
+
+* zero or more keyword/value pairs may be appended to args
+* keyword = *region*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region atoms must be in to have added force
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix pressdown topwall aveforce 0.0 -1.0 0.0
+   fix 2 bottomwall aveforce NULL -1.0 0.0 region top
+   fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
+
+Description
+"""""""""""
+
+Apply an additional external force to a group of atoms in such a way
+that every atom experiences the same force.  This is useful for
+pushing on wall or boundary atoms so that the structure of the wall
+does not change over time.
+
+The existing force is averaged for the group of atoms, component by
+component.  The actual force on each atom is then set to the average
+value plus the component specified in this command.  This means each
+atom in the group receives the same force.
+
+Any of the fx,fy,fz values can be specified as NULL which means the
+force in that dimension is not changed.  Note that this is not the
+same as specifying a 0.0 value, since that sets all forces to the same
+average value without adding in any additional force.
+
+Any of the 3 quantities defining the force components can be specified
+as an equal-style :doc:`variable <variable>`, namely *fx*\ , *fy*\ , *fz*\ .
+If the value is a variable, it should be specified as v\_name, where
+name is the variable name.  In this case, the variable will be
+evaluated each timestep, and its value used to determine the average
+force.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent average force.
+
+If the *region* keyword is used, the atom must also be in the
+specified geometric :doc:`region <region>` in order to have force added
+to it.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global 3-vector of forces, which can be accessed
+by various :doc:`output commands <Howto_output>`.  This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix.  The vector values calculated by this fix are
+"extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.  You should not
+specify force components with a variable that has time-dependence for
+use with a minimizer, since the minimizer increments the timestep as
+the iteration count during the minimization.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix setforce <fix_setforce>`, :doc:`fix addforce <fix_addforce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst
new file mode 100644
index 0000000000..93c2a5b33c
--- /dev/null
+++ b/doc/src/fix_balance.rst
@@ -0,0 +1,430 @@
+.. index:: fix balance
+
+fix balance command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID balance Nfreq thresh style args keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* balance = style name of this fix command
+* Nfreq = perform dynamic load balancing every this many steps
+* thresh = imbalance threshold that must be exceeded to perform a re-balance
+* style = *shift* or *rcb*
+  
+  .. parsed-literal::
+  
+       shift args = dimstr Niter stopthresh
+         dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
+         Niter = # of times to iterate within each dimension of dimstr sequence
+         stopthresh = stop balancing when this imbalance threshold is reached
+       *rcb* args = none
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *weight* or *out*
+  
+  .. parsed-literal::
+  
+       *weight* style args = use weighted particle counts for the balancing
+         *style* = *group* or *neigh* or *time* or *var* or *store*
+           *group* args = Ngroup group1 weight1 group2 weight2 ...
+             Ngroup = number of groups with assigned weights
+             group1, group2, ... = group IDs
+             weight1, weight2, ...   = corresponding weight factors
+           *neigh* factor = compute weight based on number of neighbors
+             factor = scaling factor (> 0)
+           *time* factor = compute weight based on time spend computing
+             factor = scaling factor (> 0)
+           *var* name = take weight from atom-style variable
+             name = name of the atom-style variable
+           *store* name = store weight in custom atom property defined by :doc:`fix property/atom <fix_property_atom>` command
+             name = atom property name (without d\_ prefix)
+       *out* arg = filename
+         filename = write each processor's sub-domain to a file, at each re-balancing
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 2 all balance 1000 1.05 shift x 10 1.05
+   fix 2 all balance 100 0.9 shift xy 20 1.1 out tmp.balance
+   fix 2 all balance 100 0.9 shift xy 20 1.1 weight group 3 substrate 3.0 solvent 1.0 solute 0.8 out tmp.balance
+   fix 2 all balance 100 1.0 shift x 10 1.1 weight time 0.8
+   fix 2 all balance 100 1.0 shift xy 5 1.1 weight var myweight weight neigh 0.6 weight store allweight
+   fix 2 all balance 1000 1.1 rcb
+
+Description
+"""""""""""
+
+This command adjusts the size and shape of processor sub-domains
+within the simulation box, to attempt to balance the number of
+particles and thus the computational cost (load) evenly across
+processors.  The load balancing is "dynamic" in the sense that
+re-balancing is performed periodically during the simulation.  To
+perform "static" balancing, before or between runs, see the
+:doc:`balance <balance>` command.
+
+Load-balancing is typically most useful if the particles in the
+simulation box have a spatially-varying density distribution or
+where the computational cost varies significantly between different
+atoms. E.g. a model of a vapor/liquid interface, or a solid with
+an irregular-shaped geometry containing void regions, or
+:doc:`hybrid pair style simulations <pair_hybrid>` which combine
+pair styles with different computational cost.  In these cases, the
+LAMMPS default of dividing the simulation box volume into a
+regular-spaced grid of 3d bricks, with one equal-volume sub-domain
+per processor, may assign numbers of particles per processor in a
+way that the computational effort varies significantly.  This can
+lead to poor performance when the simulation is run in parallel.
+
+The balancing can be performed with or without per-particle weighting.
+With no weighting, the balancing attempts to assign an equal number of
+particles to each processor.  With weighting, the balancing attempts
+to assign an equal aggregate computational weight to each processor,
+which typically induces a different number of atoms assigned to each
+processor.
+
+.. note::
+
+   The weighting options listed above are documented with the
+   :doc:`balance <balance>` command in :ref:`this section of the balance command <weighted_balance>` doc page.  That section
+   describes the various weighting options and gives a few examples of
+   how they can be used.  The weighting options are the same for both the
+   fix balance and :doc:`balance <balance>` commands.
+
+Note that the :doc:`processors <processors>` command allows some control
+over how the box volume is split across processors.  Specifically, for
+a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
+Pz, subject to the constraint that Px \* Py \* Pz = P, the total number
+of processors.  This is sufficient to achieve good load-balance for
+some problems on some processor counts.  However, all the processor
+sub-domains will still have the same shape and same volume.
+
+On a particular timestep, a load-balancing operation is only performed
+if the current "imbalance factor" in particles owned by each processor
+exceeds the specified *thresh* parameter.  The imbalance factor is
+defined as the maximum number of particles (or weight) owned by any
+processor, divided by the average number of particles (or weight) per
+processor.  Thus an imbalance factor of 1.0 is perfect balance.
+
+As an example, for 10000 particles running on 10 processors, if the
+most heavily loaded processor has 1200 particles, then the factor is
+1.2, meaning there is a 20% imbalance.  Note that re-balances can be
+forced even if the current balance is perfect (1.0) be specifying a
+*thresh* < 1.0.
+
+.. note::
+
+   This command attempts to minimize the imbalance factor, as
+   defined above.  But depending on the method a perfect balance (1.0)
+   may not be achieved.  For example, "grid" methods (defined below) that
+   create a logical 3d grid cannot achieve perfect balance for many
+   irregular distributions of particles.  Likewise, if a portion of the
+   system is a perfect lattice, e.g. the initial system is generated by
+   the :doc:`create\_atoms <create_atoms>` command, then "grid" methods may
+   be unable to achieve exact balance.  This is because entire lattice
+   planes will be owned or not owned by a single processor.
+
+.. note::
+
+   The imbalance factor is also an estimate of the maximum speed-up
+   you can hope to achieve by running a perfectly balanced simulation
+   versus an imbalanced one.  In the example above, the 10000 particle
+   simulation could run up to 20% faster if it were perfectly balanced,
+   versus when imbalanced.  However, computational cost is not strictly
+   proportional to particle count, and changing the relative size and
+   shape of processor sub-domains may lead to additional computational
+   and communication overheads, e.g. in the PPPM solver used via the
+   :doc:`kspace\_style <kspace_style>` command.  Thus you should benchmark
+   the run times of a simulation before and after balancing.
+
+
+----------
+
+
+The method used to perform a load balance is specified by one of the
+listed styles, which are described in detail below.  There are 2 kinds
+of styles.
+
+The *shift* style is a "grid" method which produces a logical 3d grid
+of processors.  It operates by changing the cutting planes (or lines)
+between processors in 3d (or 2d), to adjust the volume (area in 2d)
+assigned to each processor, as in the following 2d diagram where
+processor sub-domains are shown and atoms are colored by the processor
+that owns them.  The leftmost diagram is the default partitioning of
+the simulation box across processors (one sub-box for each of 16
+processors); the middle diagram is after a "grid" method has been
+applied.
+
+.. image:: JPG/balance_uniform_small.jpg
+   :target: JPG/balance_uniform.jpg
+.. image:: JPG/balance_nonuniform_small.jpg
+   :target: JPG/balance_nonuniform.jpg
+.. image:: JPG/balance_rcb_small.jpg
+   :target: JPG/balance_rcb.jpg
+
+
+The *rcb* style is a "tiling" method which does not produce a logical
+3d grid of processors.  Rather it tiles the simulation domain with
+rectangular sub-boxes of varying size and shape in an irregular
+fashion so as to have equal numbers of particles (or weight) in each
+sub-box, as in the rightmost diagram above.
+
+The "grid" methods can be used with either of the
+:doc:`comm\_style <comm_style>` command options, *brick* or *tiled*\ .  The
+"tiling" methods can only be used with :doc:`comm\_style tiled <comm_style>`.
+
+When a "grid" method is specified, the current domain partitioning can
+be either a logical 3d grid or a tiled partitioning.  In the former
+case, the current logical 3d grid is used as a starting point and
+changes are made to improve the imbalance factor.  In the latter case,
+the tiled partitioning is discarded and a logical 3d grid is created
+with uniform spacing in all dimensions.  This is the starting point
+for the balancing operation.
+
+When a "tiling" method is specified, the current domain partitioning
+("grid" or "tiled") is ignored, and a new partitioning is computed
+from scratch.
+
+
+----------
+
+
+The *group-ID* is ignored.  However the impact of balancing on
+different groups of atoms can be affected by using the *group* weight
+style as described below.
+
+The *Nfreq* setting determines how often a re-balance is performed.  If
+*Nfreq* > 0, then re-balancing will occur every *Nfreq* steps.  Each
+time a re-balance occurs, a reneighboring is triggered, so *Nfreq*
+should not be too small.  If *Nfreq* = 0, then re-balancing will be
+done every time reneighboring normally occurs, as determined by the
+the :doc:`neighbor <neighbor>` and :doc:`neigh\_modify <neigh_modify>`
+command settings.
+
+On re-balance steps, re-balancing will only be attempted if the current
+imbalance factor, as defined above, exceeds the *thresh* setting.
+
+
+----------
+
+
+The *shift* style invokes a "grid" method for balancing, as described
+above.  It changes the positions of cutting planes between processors
+in an iterative fashion, seeking to reduce the imbalance factor.
+
+The *dimstr* argument is a string of characters, each of which must be
+an "x" or "y" or "z".  Eacn character can appear zero or one time,
+since there is no advantage to balancing on a dimension more than
+once.  You should normally only list dimensions where you expect there
+to be a density variation in the particles.
+
+Balancing proceeds by adjusting the cutting planes in each of the
+dimensions listed in *dimstr*\ , one dimension at a time.  For a single
+dimension, the balancing operation (described below) is iterated on up
+to *Niter* times.  After each dimension finishes, the imbalance factor
+is re-computed, and the balancing operation halts if the *stopthresh*
+criterion is met.
+
+A re-balance operation in a single dimension is performed using a
+density-dependent recursive multisectioning algorithm, where the
+position of each cutting plane (line in 2d) in the dimension is
+adjusted independently.  This is similar to a recursive bisectioning
+for a single value, except that the bounds used for each bisectioning
+take advantage of information from neighboring cuts if possible, as
+well as counts of particles at the bounds on either side of each cuts,
+which themselves were cuts in previous iterations.  The latter is used
+to infer a density of particles near each of the current cuts.  At
+each iteration, the count of particles on either side of each plane is
+tallied.  If the counts do not match the target value for the plane,
+the position of the cut is adjusted based on the local density.  The
+low and high bounds are adjusted on each iteration, using new count
+information, so that they become closer together over time.  Thus as
+the recursion progresses, the count of particles on either side of the
+plane gets closer to the target value.
+
+The density-dependent part of this algorithm is often an advantage
+when you re-balance a system that is already nearly balanced.  It
+typically converges more quickly than the geometric bisectioning
+algorithm used by the :doc:`balance <balance>` command.  However, if can
+be a disadvantage if you attempt to re-balance a system that is far
+from balanced, and converge more slowly.  In this case you probably
+want to use the :doc:`balance <balance>` command before starting a run,
+so that you begin the run with a balanced system.
+
+Once the re-balancing is complete and final processor sub-domains
+assigned, particles migrate to their new owning processor as part of
+the normal reneighboring procedure.
+
+.. note::
+
+   At each re-balance operation, the bisectioning for each cutting
+   plane (line in 2d) typically starts with low and high bounds separated
+   by the extent of a processor's sub-domain in one dimension.  The size
+   of this bracketing region shrinks based on the local density, as
+   described above, which should typically be 1/2 or more every
+   iteration.  Thus if *Niter* is specified as 10, the cutting plane will
+   typically be positioned to better than 1 part in 1000 accuracy
+   (relative to the perfect target position).  For *Niter* = 20, it will
+   be accurate to better than 1 part in a million.  Thus there is no need
+   to set *Niter* to a large value.  This is especially true if you are
+   re-balancing often enough that each time you expect only an incremental
+   adjustment in the cutting planes is necessary.  LAMMPS will check if
+   the threshold accuracy is reached (in a dimension) is less iterations
+   than *Niter* and exit early.
+
+
+----------
+
+
+The *rcb* style invokes a "tiled" method for balancing, as described
+above.  It performs a recursive coordinate bisectioning (RCB) of the
+simulation domain. The basic idea is as follows.
+
+The simulation domain is cut into 2 boxes by an axis-aligned cut in
+the longest dimension, leaving one new box on either side of the cut.
+All the processors are also partitioned into 2 groups, half assigned
+to the box on the lower side of the cut, and half to the box on the
+upper side.  (If the processor count is odd, one side gets an extra
+processor.)  The cut is positioned so that the number of atoms in the
+lower box is exactly the number that the processors assigned to that
+box should own for load balance to be perfect.  This also makes load
+balance for the upper box perfect.  The positioning is done
+iteratively, by a bisectioning method.  Note that counting atoms on
+either side of the cut requires communication between all processors
+at each iteration.
+
+That is the procedure for the first cut.  Subsequent cuts are made
+recursively, in exactly the same manner.  The subset of processors
+assigned to each box make a new cut in the longest dimension of that
+box, splitting the box, the subset of processors, and the atoms in
+the box in two.  The recursion continues until every processor is
+assigned a sub-box of the entire simulation domain, and owns the atoms
+in that sub-box.
+
+
+----------
+
+
+The *out* keyword writes text to the specified *filename* with the
+results of each re-balancing operation.  The file contains the bounds
+of the sub-domain for each processor after the balancing operation
+completes.  The format of the file is compatible with the
+`Pizza.py <pizza_>`_ *mdump* tool which has support for manipulating and
+visualizing mesh files.  An example is shown here for a balancing by 4
+processors for a 2d problem:
+
+
+.. parsed-literal::
+
+   ITEM: TIMESTEP
+   0
+   ITEM: NUMBER OF NODES
+   16
+   ITEM: BOX BOUNDS
+   0 10
+   0 10
+   0 10
+   ITEM: NODES
+   1 1 0 0 0
+   2 1 5 0 0
+   3 1 5 5 0
+   4 1 0 5 0
+   5 1 5 0 0
+   6 1 10 0 0
+   7 1 10 5 0
+   8 1 5 5 0
+   9 1 0 5 0
+   10 1 5 5 0
+   11 1 5 10 0
+   12 1 10 5 0
+   13 1 5 5 0
+   14 1 10 5 0
+   15 1 10 10 0
+   16 1 5 10 0
+   ITEM: TIMESTEP
+   0
+   ITEM: NUMBER OF SQUARES
+   4
+   ITEM: SQUARES
+   1 1 1 2 3 4
+   2 1 5 6 7 8
+   3 1 9 10 11 12
+   4 1 13 14 15 16
+
+The coordinates of all the vertices are listed in the NODES section, 5
+per processor.  Note that the 4 sub-domains share vertices, so there
+will be duplicate nodes in the list.
+
+The "SQUARES" section lists the node IDs of the 4 vertices in a
+rectangle for each processor (1 to 4).
+
+For a 3d problem, the syntax is similar with 8 vertices listed for
+each processor, instead of 4, and "SQUARES" replaced by "CUBES".
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar which is the imbalance factor
+after the most recent re-balance and a global vector of length 3 with
+additional information about the most recent re-balancing.  The 3
+values in the vector are as follows:
+
+* 1 = max # of particles per processor
+* 2 = total # iterations performed in last re-balance
+* 3 = imbalance factor right before the last re-balance was performed
+
+As explained above, the imbalance factor is the ratio of the maximum
+number of particles (or total weight) on any processor to the average
+number of particles (or total weight) per processor.
+
+These quantities can be accessed by various :doc:`output commands <Howto_output>`.  The scalar and vector values calculated
+by this fix are "intensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+For 2d simulations, the *z* style cannot be used.  Nor can a "z"
+appear in *dimstr* for the *shift* style.
+
+Balancing through recursive bisectioning (\ *rcb* style) requires
+:doc:`comm\_style tiled <comm_style>`
+
+Related commands
+""""""""""""""""
+
+:doc:`group <group>`, :doc:`processors <processors>`, :doc:`balance <balance>`,
+:doc:`comm\_style <comm_style>`
+
+.. _pizza: http://pizza.sandia.gov
+
+**Default:** none
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst
new file mode 100644
index 0000000000..38e88ad1aa
--- /dev/null
+++ b/doc/src/fix_bocs.rst
@@ -0,0 +1,140 @@
+.. index:: fix bocs
+
+fix bocs command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix  ID group-ID bocs keyword values ...
+
+   keyword = *temp* or *cgiso* or *analytic* or *linear_spline* or *cubic_spline*
+     *temp* values = Tstart Tstop Tdamp
+     *cgiso* values = Pstart Pstop Pdamp
+     *basis set*
+       *analytic* values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
+       *linear_spline* values = input_filename
+       *cubic_spline* values = input_filename
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
+
+   fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat
+
+   thermo_modify press 1_press
+
+Description
+"""""""""""
+
+These commands incorporate a pressure correction as described by
+Dunn and Noid in :ref:`(Dunn1) <bocs-Dunn1>` to the standard MTTK
+barostat by Martyna et. al. in :ref:`(Martyna) <bocs-Martyna>` .
+The first half of the command mimics a standard fix npt command:
+
+
+.. parsed-literal::
+
+   fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp
+
+The two differences are replacing *npt* with *bocs*\ , and replacing
+*iso*\ /\ *aniso*\ /\ *etc* with *cgiso*\ .
+The rest of the command details what form you would like to use for
+the pressure correction equation. The choices are: *analytic*\ , *linear\_spline*,
+or *cubic\_spline*.
+
+With either spline method, the only argument that needs to follow it
+is the name of a file that contains the desired pressure correction
+as a function of volume. The file must be formatted so each line has:
+
+
+.. parsed-literal::
+
+   Volume_i, PressureCorrection_i
+
+Note both the COMMA and the SPACE separating the volume's
+value and its corresponding pressure correction. The volumes in the file
+must be uniformly spaced. Both the volumes and the pressure corrections
+should be provided in the proper units, e.g. if you are using *units real*\ ,
+the volumes should all be in cubic angstroms, and the pressure corrections
+should all be in atmospheres. Furthermore, the table should start/end at a
+volume considerably smaller/larger than you expect your system to sample
+during the simulation. If the system ever reaches a volume outside of the
+range provided, the simulation will stop.
+
+With the *analytic* option, the arguments are as follows:
+
+
+.. parsed-literal::
+
+   ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
+
+Note that *V\_avg* and *Coeff\_i* should all be in the proper units, e.g. if you
+are using *units real*\ , *V\_avg* should be in cubic angstroms, and the
+coefficients should all be in atmospheres \* cubic angstroms.
+
+Restrictions
+""""""""""""
+
+
+As this is computing a (modified) pressure, group-ID should be *all*\ .
+
+The pressure correction has only been tested for use with an isotropic
+pressure coupling in 3 dimensions.
+
+By default, LAMMPS will still report the normal value for the pressure
+if the pressure is printed via a *thermo* command, or if the pressures
+are written to a file every so often. In order to have LAMMPS report the
+modified pressure, you must include the *thermo\_modify* command given in
+the examples. For the last argument in the command, you should put
+XXXX\_press, where XXXX is the ID given to the fix bocs command (in the
+example, the ID of the fix bocs command is 1 ).
+
+This fix is part of the USER-BOCS package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+**Related:**
+
+For more details about the pressure correction and the entire BOCS software
+package, visit the `BOCS package on GitHub <bocsgithub_>`_ and read the release
+paper by Dunn et. al. :ref:`(Dunn2) <bocs-Dunn2>` .
+
+.. _bocsgithub: https://github.com/noid-group/BOCS
+
+
+
+
+----------
+
+
+.. _bocs-Dunn1:
+
+
+
+**(Dunn1)** Dunn and Noid, J Chem Phys, 143, 243148 (2015).
+
+.. _bocs-Martyna:
+
+
+
+**(Martyna)** Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
+
+.. _bocs-Dunn2:
+
+
+
+**(Dunn2)** Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst
new file mode 100644
index 0000000000..fa7aba3c6b
--- /dev/null
+++ b/doc/src/fix_bond_break.rst
@@ -0,0 +1,163 @@
+.. index:: fix bond/break
+
+fix bond/break command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID bond/break Nevery bondtype Rmax keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* bond/break = style name of this fix command
+* Nevery = attempt bond breaking every this many steps
+* bondtype = type of bonds to break
+* Rmax = bond longer than Rmax can break (distance units)
+* zero or more keyword/value pairs may be appended to args
+* keyword = *prob*
+  
+  .. parsed-literal::
+  
+       *prob* values = fraction seed
+         fraction = break a bond with this probability if otherwise eligible
+         seed = random number seed (positive integer)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 5 all bond/break 10 2 1.2
+   fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829
+
+Description
+"""""""""""
+
+Break bonds between pairs of atoms as a simulation runs according to
+specified criteria.  This can be used to model the dissolution of a
+polymer network due to stretching of the simulation box or other
+deformations.  In this context, a bond means an interaction between a
+pair of atoms computed by the :doc:`bond\_style <bond_style>` command.
+Once the bond is broken it will be permanently deleted, as will all
+angle, dihedral, and improper interactions that bond is part of.
+
+This is different than a :doc:`pairwise <pair_style>` bond-order
+potential such as Tersoff or AIREBO which infers bonds and many-body
+interactions based on the current geometry of a small cluster of atoms
+and effectively creates and destroys bonds and higher-order many-body
+interactions from timestep to timestep as atoms move.
+
+A check for possible bond breakage is performed every *Nevery*
+timesteps.  If two bonded atoms I,J are further than a distance *Rmax*
+of each other, if the bond is of type *bondtype*\ , and if both I and J
+are in the specified fix group, then I,J is labeled as a "possible"
+bond to break.
+
+If several bonds involving an atom are stretched, it may have multiple
+possible bonds to break.  Every atom checks its list of possible bonds
+to break and labels the longest such bond as its "sole" bond to break.
+After this is done, if atom I is bonded to atom J in its sole bond,
+and atom J is bonded to atom I in its sole bond, then the I,J bond is
+"eligible" to be broken.
+
+Note that these rules mean an atom will only be part of at most one
+broken bond on a given timestep.  It also means that if atom I chooses
+atom J as its sole partner, but atom J chooses atom K is its sole
+partner (due to Rjk > Rij), then this means atom I will not be part of
+a broken bond on this timestep, even if it has other possible bond
+partners.
+
+The *prob* keyword can effect whether an eligible bond is actually
+broken.  The *fraction* setting must be a value between 0.0 and 1.0.
+A uniform random number between 0.0 and 1.0 is generated and the
+eligible bond is only broken if the random number < fraction.
+
+When a bond is broken, data structures within LAMMPS that store bond
+topology are updated to reflect the breakage.  Likewise, if the bond
+is part of a 3-body (angle) or 4-body (dihedral, improper)
+interaction, that interaction is removed as well.  These changes
+typically affect pairwise interactions between atoms that used to be
+part of bonds, angles, etc.
+
+.. note::
+
+   One data structure that is not updated when a bond breaks are
+   the molecule IDs stored by each atom.  Even though one molecule
+   becomes two molecules due to the broken bond, all atoms in both new
+   molecules retain their original molecule IDs.
+
+Computationally, each timestep this fix operates, it loops over all
+the bonds in the system and computes distances between pairs of bonded
+atoms.  It also communicates between neighboring processors to
+coordinate which bonds are broken.  Moreover, if any bonds are broken,
+neighbor lists must be immediately updated on the same timestep.  This
+is to insure that any pairwise interactions that should be turned "on"
+due to a bond breaking, because they are no longer excluded by the
+presence of the bond and the settings of the
+:doc:`special\_bonds <special_bonds>` command, will be immediately
+recognized.  All of these operations increase the cost of a timestep.
+Thus you should be cautious about invoking this fix too frequently.
+
+You can dump out snapshots of the current bond topology via the :doc:`dump local <dump>` command.
+
+.. note::
+
+   Breaking a bond typically alters the energy of a system.  You
+   should be careful not to choose bond breaking criteria that induce a
+   dramatic change in energy.  For example, if you define a very stiff
+   harmonic bond and break it when 2 atoms are separated by a distance
+   far from the equilibrium bond length, then the 2 atoms will be
+   dramatically released when the bond is broken.  More generally, you
+   may need to thermostat your system to compensate for energy changes
+   resulting from broken bonds (and angles, dihedrals, impropers).
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes two statistics which it stores in a global vector of
+length 2, which can be accessed by various :doc:`output commands <Howto_output>`.  The vector values calculated by this fix
+are "intensive".
+
+These are the 2 quantities:
+
+* (1) # of bonds broken on the most recent breakage timestep
+* (2) cumulative # of bonds broken
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MC package.  It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/react <fix_bond_react>`, :doc:`fix bond/swap <fix_bond_swap>`,
+:doc:`dump local <dump>`, :doc:`special\_bonds <special_bonds>`
+
+Default
+"""""""
+
+The option defaults are prob = 1.0.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst
new file mode 100644
index 0000000000..9a11558e83
--- /dev/null
+++ b/doc/src/fix_bond_create.rst
@@ -0,0 +1,265 @@
+.. index:: fix bond/create
+
+fix bond/create command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* bond/create = style name of this fix command
+* Nevery = attempt bond creation every this many steps
+* itype,jtype = atoms of itype can bond to atoms of jtype
+* Rmin = 2 atoms separated by less than Rmin can bond (distance units)
+* bondtype = type of created bonds
+* zero or more keyword/value pairs may be appended to args
+* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype*
+  
+  .. parsed-literal::
+  
+       *iparam* values = maxbond, newtype
+         maxbond = max # of bonds of bondtype the itype atom can have
+         newtype = change the itype atom to this type when maxbonds exist
+       *jparam* values = maxbond, newtype
+         maxbond = max # of bonds of bondtype the jtype atom can have
+         newtype = change the jtype atom to this type when maxbonds exist
+       *prob* values = fraction seed
+         fraction = create a bond with this probability if otherwise eligible
+         seed = random number seed (positive integer)
+       *atype* value = angletype
+         angletype = type of created angles
+       *dtype* value = dihedraltype
+         dihedraltype = type of created dihedrals
+       *itype* value = impropertype
+         impropertype = type of created impropers
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 5 all bond/create 10 1 2 0.8 1
+   fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
+   fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
+
+Description
+"""""""""""
+
+Create bonds between pairs of atoms as a simulation runs according to
+specified criteria.  This can be used to model cross-linking of
+polymers, the formation of a percolation network, etc.  In this
+context, a bond means an interaction between a pair of atoms computed
+by the :doc:`bond\_style <bond_style>` command.  Once the bond is created
+it will be permanently in place.  Optionally, the creation of a bond
+can also create angle, dihedral, and improper interactions that bond
+is part of.  See the discussion of the *atype*\ , *dtype*\ , and *itype*
+keywords below.
+
+This is different than a :doc:`pairwise <pair_style>` bond-order
+potential such as Tersoff or AIREBO which infers bonds and many-body
+interactions based on the current geometry of a small cluster of atoms
+and effectively creates and destroys bonds and higher-order many-body
+interactions from timestep to timestep as atoms move.
+
+A check for possible new bonds is performed every *Nevery* timesteps.
+If two atoms I,J are within a distance *Rmin* of each other, if I is
+of atom type *itype*\ , if J is of atom type *jtype*\ , if both I and J
+are in the specified fix group, if a bond does not already exist
+between I and J, and if both I and J meet their respective *maxbond*
+requirement (explained below), then I,J is labeled as a "possible"
+bond pair.
+
+If several atoms are close to an atom, it may have multiple possible
+bond partners.  Every atom checks its list of possible bond partners
+and labels the closest such partner as its "sole" bond partner.  After
+this is done, if atom I has atom J as its sole partner, and atom J has
+atom I as its sole partner, then the I,J bond is "eligible" to be
+formed.
+
+Note that these rules mean an atom will only be part of at most one
+created bond on a given timestep.  It also means that if atom I
+chooses atom J as its sole partner, but atom J chooses atom K is its
+sole partner (due to Rjk < Rij), then this means atom I will not form
+a bond on this timestep, even if it has other possible bond partners.
+
+It is permissible to have *itype* = *jtype*\ .  *Rmin* must be <= the
+pairwise cutoff distance between *itype* and *jtype* atoms, as defined
+by the :doc:`pair\_style <pair_style>` command.
+
+The *iparam* and *jparam* keywords can be used to limit the bonding
+functionality of the participating atoms.  Each atom keeps track of
+how many bonds of *bondtype* it already has.  If atom I of
+itype already has *maxbond* bonds (as set by the *iparam*
+keyword), then it will not form any more.  Likewise for atom J.  If
+*maxbond* is set to 0, then there is no limit on the number of bonds
+that can be formed with that atom.
+
+The *newtype* value for *iparam* and *jparam* can be used to change
+the atom type of atom I or J when it reaches *maxbond* number of bonds
+of type *bondtype*\ .  This means it can now interact in a pairwise
+fashion with other atoms in a different way by specifying different
+:doc:`pair\_coeff <pair_coeff>` coefficients.  If you do not wish the
+atom type to change, simply specify *newtype* as *itype* or *jtype*\ .
+
+The *prob* keyword can also effect whether an eligible bond is
+actually created.  The *fraction* setting must be a value between 0.0
+and 1.0.  A uniform random number between 0.0 and 1.0 is generated and
+the eligible bond is only created if the random number < fraction.
+
+Any bond that is created is assigned a bond type of *bondtype*
+
+When a bond is created, data structures within LAMMPS that store bond
+topology are updated to reflect the creation.  If the bond is part of
+new 3-body (angle) or 4-body (dihedral, improper) interactions, you
+can choose to create new angles, dihedrals, impropers as well, using
+the *atype*\ , *dtype*\ , and *itype* keywords.  All of these changes
+typically affect pairwise interactions between atoms that are now part
+of new bonds, angles, etc.
+
+.. note::
+
+   One data structure that is not updated when a bond breaks are
+   the molecule IDs stored by each atom.  Even though two molecules
+   become one molecule due to the created bond, all atoms in the new
+   molecule retain their original molecule IDs.
+
+If the *atype* keyword is used and if an angle potential is defined
+via the :doc:`angle\_style <angle_style>` command, then any new 3-body
+interactions inferred by the creation of a bond will create new angles
+of type *angletype*\ , with parameters assigned by the corresponding
+:doc:`angle\_coeff <angle_coeff>` command.  Likewise, the *dtype* and
+*itype* keywords will create new dihedrals and impropers of type
+*dihedraltype* and *impropertype*\ .
+
+.. note::
+
+   To create a new bond, the internal LAMMPS data structures that
+   store this information must have space for it.  When LAMMPS is
+   initialized from a data file, the list of bonds is scanned and the
+   maximum number of bonds per atom is tallied.  If some atom will
+   acquire more bonds than this limit as this fix operates, then the
+   "extra bond per atom" parameter must be set to allow for it.  Ditto
+   for "extra angle per atom", "extra dihedral per atom", and "extra
+   improper per atom" if angles, dihedrals, or impropers are being added
+   when bonds are created.  See the :doc:`read\_data <read_data>` or
+   :doc:`create\_box <create_box>` command for more details.  Note that a
+   data file with no atoms can be used if you wish to add non-bonded
+   atoms via the :doc:`create atoms <create_atoms>` command, e.g. for a
+   percolation simulation.
+
+.. note::
+
+   LAMMPS stores and maintains a data structure with a list of the
+   1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
+   the system) for use in weighting pairwise interactions for bonded
+   atoms.  Note that adding a single bond always adds a new 1st neighbor
+   but may also induce \*many\* new 2nd and 3rd neighbors, depending on the
+   molecular topology of your system.  The "extra special per atom"
+   parameter must typically be set to allow for the new maximum total
+   size (1st + 2nd + 3rd neighbors) of this per-atom list.  There are 2
+   ways to do this.  See the :doc:`read\_data <read_data>` or
+   :doc:`create\_box <create_box>` commands for details.
+
+.. note::
+
+   Even if you do not use the *atype*\ , *dtype*\ , or *itype*
+   keywords, the list of topological neighbors is updated for atoms
+   affected by the new bond.  This in turn affects which neighbors are
+   considered for pairwise interactions, using the weighting rules set by
+   the :doc:`special\_bonds <special_bonds>` command.  Consider a new bond
+   created between atoms I,J.  If J has a bonded neighbor K, then K
+   becomes a 2nd neighbor of I.  Even if the *atype* keyword is not used
+   to create angle I-J-K, the pairwise interaction between I and K will
+   be potentially turned off or weighted by the 1-3 weighting specified
+   by the :doc:`special\_bonds <special_bonds>` command.  This is the case
+   even if the "angle yes" option was used with that command.  The same
+   is true for 3rd neighbors (1-4 interactions), the *dtype* keyword, and
+   the "dihedral yes" option used with the
+   :doc:`special\_bonds <special_bonds>` command.
+
+Note that even if your simulation starts with no bonds, you must
+define a :doc:`bond\_style <bond_style>` and use the
+:doc:`bond\_coeff <bond_coeff>` command to specify coefficients for the
+*bondtype*\ .  Similarly, if new atom types are specified by the
+*iparam* or *jparam* keywords, they must be within the range of atom
+types allowed by the simulation and pairwise coefficients must be
+specified for the new types.
+
+Computationally, each timestep this fix operates, it loops over
+neighbor lists and computes distances between pairs of atoms in the
+list.  It also communicates between neighboring processors to
+coordinate which bonds are created.  Moreover, if any bonds are
+created, neighbor lists must be immediately updated on the same
+timestep.  This is to insure that any pairwise interactions that
+should be turned "off" due to a bond creation, because they are now
+excluded by the presence of the bond and the settings of the
+:doc:`special\_bonds <special_bonds>` command, will be immediately
+recognized.  All of these operations increase the cost of a timestep.
+Thus you should be cautious about invoking this fix too frequently.
+
+You can dump out snapshots of the current bond topology via the :doc:`dump local <dump>` command.
+
+.. note::
+
+   Creating a bond typically alters the energy of a system.  You
+   should be careful not to choose bond creation criteria that induce a
+   dramatic change in energy.  For example, if you define a very stiff
+   harmonic bond and create it when 2 atoms are separated by a distance
+   far from the equilibrium bond length, then the 2 atoms will oscillate
+   dramatically when the bond is formed.  More generally, you may need to
+   thermostat your system to compensate for energy changes resulting from
+   created bonds (and angles, dihedrals, impropers).
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes two statistics which it stores in a global vector of
+length 2, which can be accessed by various :doc:`output commands <Howto_output>`.  The vector values calculated by this fix
+are "intensive".
+
+These are the 2 quantities:
+
+* (1) # of bonds created on the most recent creation timestep
+* (2) cumulative # of bonds created
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MC package.  It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix bond/break <fix_bond_break>`, :doc:`fix bond/react <fix_bond_react>`, :doc:`fix bond/swap <fix_bond_swap>`,
+:doc:`dump local <dump>`, :doc:`special\_bonds <special_bonds>`
+
+Default
+"""""""
+
+The option defaults are iparam = (0,itype), jparam = (0,jtype), and
+prob = 1.0.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst
new file mode 100644
index 0000000000..b2866eb9c7
--- /dev/null
+++ b/doc/src/fix_bond_react.rst
@@ -0,0 +1,548 @@
+.. index:: fix bond/react
+
+fix bond/react command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID bond/react common_keyword values ...
+     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+     ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command. Group-ID is ignored.
+* bond/react = style name of this fix command
+* the common keyword/values may be appended directly after 'bond/react'
+* this applies to all reaction specifications (below)
+* common\_keyword = *stabilization*
+
+  .. parsed-literal::
+
+       *stabilization* values = *no* or *yes* *group-ID* *xmax*
+         *no* = no reaction site stabilization
+         *yes* = perform reaction site stabilization
+           *group-ID* = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
+           *xmax* = xmax value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator
+
+* react = mandatory argument indicating new reaction specification
+* react-ID = user-assigned name for the reaction
+* react-group-ID = only atoms in this group are considered for the reaction
+* Nevery = attempt reaction every this many steps
+* Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units)
+* Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units)
+* template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology
+* template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
+* map\_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
+* zero or more individual keyword/value pairs may be appended to each react argument
+* individual\_keyword = *prob* or *max\_rxn* or *stabilize\_steps* or *update\_edges*
+
+  .. parsed-literal::
+
+         *prob* values = fraction seed
+           fraction = initiate reaction with this probability if otherwise eligible
+           seed = random number seed (positive integer)
+         *max_rxn* value = N
+           N = maximum number of reactions allowed to occur
+         *stabilize_steps* value = timesteps
+           timesteps = number of timesteps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms
+         *update_edges* value = *none* or *charges* or *custom*
+           none = do not update topology near the edges of reaction templates
+           charges = update atomic charges of all atoms in reaction templates
+           custom = force the update of user-specified atomic charges
+
+
+
+Examples
+""""""""
+
+For unabridged example scripts and files, see examples/USER/misc/bond\_react.
+
+
+.. parsed-literal::
+
+   molecule mol1 pre_reacted_topology.txt
+   molecule mol2 post_reacted_topology.txt
+   fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt
+
+   molecule mol1 pre_reacted_rxn1.txt
+   molecule mol2 post_reacted_rxn1.txt
+   molecule mol3 pre_reacted_rxn2.txt
+   molecule mol4 post_reacted_rxn2.txt
+   fix 5 all bond/react stabilization yes nvt_grp .03 &
+     react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
+     react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
+   fix 6 nvt_grp_REACT nvt temp 300 300 100 # set thermostat after bond/react
+
+Description
+"""""""""""
+
+Initiate complex covalent bonding (topology) changes. These topology
+changes will be referred to as 'reactions' throughout this
+documentation. Topology changes are defined in pre- and post-reaction
+molecule templates and can include creation and deletion of bonds,
+angles, dihedrals, impropers, bond types, angle types, dihedral types,
+atom types, or atomic charges. In addition, reaction by-products or
+other molecules can be identified and deleted.
+
+Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
+pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
+determine bonding changes a priori. Rather, it uses a distance-based
+probabilistic criteria to effect predetermined topology changes in
+simulations using standard force fields.
+
+This fix was created to facilitate the dynamic creation of polymeric,
+amorphous or highly cross-linked systems. A suggested workflow for
+using this fix is: 1) identify a reaction to be simulated 2) build a
+molecule template of the reaction site before the reaction has
+occurred 3) build a molecule template of the reaction site after the
+reaction has occurred 4) create a map that relates the
+template-atom-IDs of each atom between pre- and post-reaction molecule
+templates 5) fill a simulation box with molecules and run a simulation
+with fix bond/react.
+
+Only one 'fix bond/react' command can be used at a time. Multiple
+reactions can be simultaneously applied by specifying multiple *react*
+arguments to a single 'fix bond/react' command. This syntax is
+necessary because the 'common keywords' are applied to all reactions.
+
+The *stabilization* keyword enables reaction site stabilization.
+Reaction site stabilization is performed by including reacting atoms
+in an internally-created fix :doc:`nve/limit <fix_nve_limit>` time
+integrator for a set number of timesteps given by the
+*stabilize\_steps* keyword. While reacting atoms are being time
+integrated by the internal nve/limit, they are prevented from being
+involved in any new reactions. The *xmax* value keyword should
+typically be set to the maximum distance that non-reacting atoms move
+during the simulation.
+
+Fix bond/react creates and maintains two important dynamic groups of
+atoms when using the *stabilization* keyword. The first group contains
+all atoms currently involved in a reaction; this group is
+automatically thermostatted by an internally-created
+:doc:`nve/limit <fix_nve_limit>` integrator. The second group contains
+all atoms currently not involved in a reaction. This group should be
+used by a thermostat in order to time integrate the system. The name
+of this group of non-reacting atoms is created by appending '\_REACT'
+to the group-ID argument of the *stabilization* keyword, as shown in
+the second example above.
+
+.. note::
+
+   When using reaction stabilization, you should generally not have
+   a separate thermostat which acts on the 'all' group.
+
+The group-ID set using the *stabilization* keyword can be an existing
+static group or a previously-unused group-ID. It cannot be specified
+as 'all'. If the group-ID is previously unused, the fix bond/react
+command creates a :doc:`dynamic group <group>` that is initialized to
+include all atoms. If the group-ID is that of an existing static
+group, the group is used as the parent group of new,
+internally-created dynamic group. In both cases, this new dynamic
+group is named by appending '\_REACT' to the group-ID, e.g.
+nvt\_grp\_REACT. By specifying an existing group, you may thermostat
+constant-topology parts of your system separately. The dynamic group
+contains only atoms not involved in a reaction at a given timestep,
+and therefore should be used by a subsequent system-wide time
+integrator such as nvt, npt, or nve, as shown in the second example
+above (full examples can be found at examples/USER/misc/bond\_react).
+The time integration command should be placed after the fix bond/react
+command due to the internal dynamic grouping performed by fix
+bond/react.
+
+.. note::
+
+   If the group-ID is an existing static group, react-group-IDs
+   should also be specified as this static group, or a subset.
+
+The following comments pertain to each *react* argument (in other
+words, can be customized for each reaction, or reaction step):
+
+A check for possible new reaction sites is performed every *Nevery*
+timesteps.
+
+Three physical conditions must be met for a reaction to occur. First,
+a bonding atom pair must be identified within the reaction distance
+cutoffs. Second, the topology surrounding the bonding atom pair must
+match the topology of the pre-reaction template. Finally, any reaction
+constraints listed in the map file (see below) must be satisfied. If
+all of these conditions are met, the reaction site is eligible to be
+modified to match the post-reaction template.
+
+A bonding atom pair will be identified if several conditions are met.
+First, a pair of atoms I,J within the specified react-group-ID of type
+itype and jtype must be separated by a distance between *Rmin* and
+*Rmax*\ . It is possible that multiple bonding atom pairs are
+identified: if the bonding atoms in the pre-reacted template are  1-2
+neighbors, i.e. directly bonded, the farthest bonding atom partner is
+set as its bonding partner; otherwise, the closest potential partner
+is chosen. Then, if both an atom I and atom J have each other as their
+bonding partners, these two atoms are identified as the bonding atom
+pair of the reaction site. Once this unique bonding atom pair is
+identified for each reaction, there could two or more reactions that
+involve a given atom on the same timestep. If this is the case, only
+one such reaction is permitted to occur. This reaction is chosen
+randomly from all potential reactions. This capability allows e.g. for
+different reaction pathways to proceed from identical reaction sites
+with user-specified probabilities.
+
+The pre-reacted molecule template is specified by a molecule command.
+This molecule template file contains a sample reaction site and its
+surrounding topology. As described below, the bonding atom pairs of
+the pre-reacted template are specified by atom ID in the map file. The
+pre-reacted molecule template should contain as few atoms as possible
+while still completely describing the topology of all atoms affected
+by the reaction. For example, if the force field contains dihedrals,
+the pre-reacted template should contain any atom within three bonds of
+reacting atoms.
+
+Some atoms in the pre-reacted template that are not reacting may have
+missing topology with respect to the simulation. For example, the
+pre-reacted template may contain an atom that, in the simulation, is
+currently connected to the rest of a long polymer chain. These are
+referred to as edge atoms, and are also specified in the map file. All
+pre-reaction template atoms should be linked to a bonding atom, via at
+least one path that does not involve edge atoms. When the pre-reaction
+template contains edge atoms, not all atoms, bonds, charges, etc.
+specified in the reaction templates will be updated. Specifically,
+topology that involves only atoms that are 'too near' to template
+edges will not be updated. The definition of 'too near the edge'
+depends on which interactions are defined in the simulation. If the
+simulation has defined dihedrals, atoms within two bonds of edge atoms
+are considered 'too near the edge.' If the simulation defines angles,
+but not dihedrals, atoms within one bond of edge atoms are considered
+'too near the edge.' If just bonds are defined, only edge atoms are
+considered 'too near the edge.'
+
+.. note::
+
+   Small molecules, i.e. ones that have all their atoms contained
+   within the reaction templates, never have edge atoms.
+
+Note that some care must be taken when a building a molecule template
+for a given simulation. All atom types in the pre-reacted template
+must be the same as those of a potential reaction site in the
+simulation. A detailed discussion of matching molecule template atom
+types with the simulation is provided on the :doc:`molecule <molecule>`
+command page.
+
+The post-reacted molecule template contains a sample of the reaction
+site and its surrounding topology after the reaction has occurred. It
+must contain the same number of atoms as the pre-reacted template. A
+one-to-one correspondence between the atom IDs in the pre- and
+post-reacted templates is specified in the map file as described
+below. Note that during a reaction, an atom, bond, etc. type may
+change to one that was previously not present in the simulation. These
+new types must also be defined during the setup of a given simulation.
+A discussion of correctly handling this is also provided on the
+:doc:`molecule <molecule>` command page.
+
+.. note::
+
+   When a reaction occurs, it is possible that the resulting
+   topology/atom (e.g. special bonds, dihedrals, etc.) exceeds that of
+   the existing system and reaction templates. As when inserting
+   molecules, enough space for this increased topology/atom must be
+   reserved by using the relevant "extra" keywords to the
+   :doc:`read\_data <read_data>` or :doc:`create\_box <create_box>` commands.
+
+The map file is a text document with the following format:
+
+A map file has a header and a body. The header of map file the
+contains one mandatory keyword and five optional keywords. The
+mandatory keyword is 'equivalences':
+
+
+.. parsed-literal::
+
+   N *equivalences* = # of atoms N in the reaction molecule templates
+
+The optional keywords are 'edgeIDs', 'deleteIDs', 'customIDs' and
+'constraints':
+
+
+.. parsed-literal::
+
+   N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
+   N *deleteIDs* = # of atoms N that are specified for deletion
+   N *chiralIDs* = # of specified chiral centers N
+   N *customIDs* = # of atoms N that are specified for a custom update
+   N *constraints* = # of specified reaction constraints N
+
+The body of the map file contains two mandatory sections and five
+optional sections. The first mandatory section begins with the keyword
+'BondingIDs' and lists the atom IDs of the bonding atom pair in the
+pre-reacted molecule template. The second mandatory section begins
+with the keyword 'Equivalences' and lists a one-to-one correspondence
+between atom IDs of the pre- and post-reacted templates. The first
+column is an atom ID of the pre-reacted molecule template, and the
+second column is the corresponding atom ID of the post-reacted
+molecule template. The first optional section begins with the keyword
+'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
+molecule template. The second optional section begins with the keyword
+'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
+delete. The third optional section begins with the keyword 'ChiralIDs'
+lists the atom IDs of chiral atoms whose handedness should be
+enforced. The fourth optional section begins with the keyword 'Custom
+Edges' and allows for forcing the update of a specific atom's atomic
+charge. The first column is the ID of an atom near the edge of the
+pre-reacted molecule template, and the value of the second column is
+either 'none' or 'charges.' Further details are provided in the
+discussion of the 'update\_edges' keyword. The fifth optional section
+begins with the keyword 'Constraints' and lists additional criteria
+that must be satisfied in order for the reaction to occur. Currently,
+there are three types of constraints available, as discussed below.
+
+A sample map file is given below:
+
+
+----------
+
+
+
+.. parsed-literal::
+
+   # this is a map file
+
+   7 equivalences
+   2 edgeIDs
+
+   BondingIDs
+
+   3
+   5
+
+   EdgeIDs
+
+   1
+   7
+
+   Equivalences
+
+   1   1
+   2   2
+   3   3
+   4   4
+   5   5
+   6   6
+   7   7
+
+
+----------
+
+
+The handedness of atoms that are chiral centers can be enforced by
+listing their IDs in the ChiralIDs section. A chiral atom must be
+bonded to four atoms with mutually different atom types. This feature
+uses the coordinates and types of the involved atoms in the
+pre-reaction template to determine handedness. Three atoms bonded to
+the chiral center are arbitrarily chosen, to define an oriented plane,
+and the relative position of the fourth bonded atom determines the
+chiral center's handedness.
+
+Any number of additional constraints may be specified in the
+Constraints section of the map file. The constraint of type 'distance'
+has syntax as follows:
+
+
+.. parsed-literal::
+
+   distance *ID1* *ID2* *rmin* *rmax*
+
+where 'distance' is the required keyword, *ID1* and *ID2* are
+pre-reaction atom IDs, and these two atoms must be separated by a
+distance between *rmin* and *rmax* for the reaction to occur.
+
+The constraint of type 'angle' has the following syntax:
+
+
+.. parsed-literal::
+
+   angle *ID1* *ID2* *ID3* *amin* *amax*
+
+where 'angle' is the required keyword, *ID1*\ , *ID2* and *ID3* are
+pre-reaction atom IDs, and these three atoms must form an angle
+between *amin* and *amax* for the reaction to occur (where *ID2* is
+the central atom). Angles must be specified in degrees. This
+constraint can be used to enforce a certain orientation between
+reacting molecules.
+
+The constraint of type 'arrhenius' imposes an additional reaction
+probability according to the temperature-dependent Arrhenius equation:
+
+.. image:: Eqs/fix_bond_react.jpg
+   :align: center
+
+The Arrhenius constraint has the following syntax:
+
+
+.. parsed-literal::
+
+   arrhenius *A* *n* *E_a* *seed*
+
+where 'arrhenius' is the required keyword, *A* is the pre-exponential
+factor, *n* is the exponent of the temperature dependence, *E\_a* is
+the activation energy (:doc:`units <units>` of energy), and *seed* is a
+random number seed. The temperature is defined as the instantaneous
+temperature averaged over all atoms in the reaction site, and is
+calculated in the same manner as for example
+:doc:`compute\_temp\_chunk <compute_temp_chunk>`. Currently, there are no
+options for additional temperature averaging or velocity-biased
+temperature calculations. A uniform random number between 0 and 1 is
+generated using *seed*\ ; if this number is less than the result of the
+Arrhenius equation above, the reaction is permitted to occur.
+
+Once a reaction site has been successfully identified, data structures
+within LAMMPS that store bond topology are updated to reflect the
+post-reacted molecule template. All force fields with fixed bonds,
+angles, dihedrals or impropers are supported.
+
+A few capabilities to note: 1) You may specify as many *react*
+arguments as desired. For example, you could break down a complicated
+reaction mechanism into several reaction steps, each defined by its
+own *react* argument. 2) While typically a bond is formed or removed
+between the bonding atom pairs specified in the pre-reacted molecule
+template, this is not required. 3) By reversing the order of the pre-
+and post- reacted molecule templates in another *react* argument, you
+can allow for the possibility of one or more reverse reactions.
+
+The optional keywords deal with the probability of a given reaction
+occurring as well as the stable equilibration of each reaction site as
+it occurs:
+
+The *prob* keyword can affect whether or not an eligible reaction
+actually occurs. The fraction setting must be a value between 0.0 and
+1.0. A uniform random number between 0.0 and 1.0 is generated and the
+eligible reaction only occurs if the random number is less than the
+fraction. Up to N reactions are permitted to occur, as optionally
+specified by the *max\_rxn* keyword.
+
+The *stabilize\_steps* keyword allows for the specification of how many
+timesteps a reaction site is stabilized before being returned to the
+overall system thermostat. In order to produce the most physical
+behavior, this 'reaction site equilibration time' should be tuned to
+be as small as possible while retaining stability for a given system
+or reaction step. After a limited number of case studies, this number
+has been set to a default of 60 timesteps. Ideally, it should be
+individually tuned for each fix reaction step. Note that in some
+situations, decreasing rather than increasing this parameter will
+result in an increase in stability.
+
+The *update\_edges* keyword can increase the number of atoms whose
+atomic charges are updated, when the pre-reaction template contains
+edge atoms. When the value is set to 'charges,' all atoms' atomic
+charges are updated to those specified by the post-reaction template,
+including atoms near the edge of reaction templates. When the value is
+set to 'custom,' an additional section must be included in the map
+file that specifies whether or not to update charges, on a per-atom
+basis. The format of this section is detailed above. Listing a
+pre-reaction atom ID with a value of 'charges' will force the update
+of the atom's charge, even if it is near a template edge. Atoms not
+near a template edge are unaffected by this setting.
+
+A few other considerations:
+
+Many reactions result in one or more atoms that are considered
+unwanted by-products. Therefore, bond/react provides the option to
+delete a user-specified set of atoms. These pre-reaction atoms are
+identified in the map file. A deleted atom must still be included in
+the post-reaction molecule template, in which it cannot be bonded to
+an atom that is not deleted. In addition to deleting unwanted reaction
+by-products, this feature can be used to remove specific topologies,
+such as small rings, that may be otherwise indistinguishable.
+
+Optionally, you can enforce additional behaviors on reacting atoms.
+For example, it may be beneficial to force reacting atoms to remain at
+a certain temperature. For this, you can use the internally-created
+dynamic group named "bond\_react\_MASTER\_group", which consists of all
+atoms currently involved in a reaction. For example, adding the
+following command would add an additional thermostat to the group of
+all currently-reacting atoms:
+
+
+.. parsed-literal::
+
+   fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+.. note::
+
+   This command must be added after the fix bond/react command, and
+   will apply to all reactions.
+
+Computationally, each timestep this fix operates, it loops over
+neighbor lists (for bond-forming reactions) and computes distances
+between pairs of atoms in the list. It also communicates between
+neighboring processors to coordinate which bonds are created and/or
+removed. All of these operations increase the cost of a timestep. Thus
+you should be cautious about invoking this fix too frequently.
+
+You can dump out snapshots of the current bond topology via the dump
+local command.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Cumulative reaction counts for each reaction are written to :doc:`binary restart files <restart>`. These values are associated with the
+reaction name (react-ID). Additionally, internally-created per-atom
+properties are stored to allow for smooth restarts. None of the
+:doc:`fix\_modify <fix_modify>` options are relevant to this fix.
+
+This fix computes one statistic for each *react* argument that it
+stores in a global vector, of length 'number of react arguments', that
+can be accessed by various :doc:`output commands <Howto_output>`. The
+vector values calculated by this fix are "intensive".
+
+These is 1 quantity for each react argument:
+
+* (1) cumulative # of reactions occurred
+
+No parameter of this fix can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+When fix bond/react is 'unfixed,' all internally-created groups are
+deleted. Therefore, fix bond/react can only be unfixed after unfixing
+all other fixes that use any group created by fix bond/react.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix bond/create <fix_bond_create>`,
+:doc:`fix bond/break <fix_bond_break>`,
+:doc:`fix bond/swap <fix_bond_swap>`,
+:doc:`dump local <dump>`, :doc:`special\_bonds <special_bonds>`
+
+Default
+"""""""
+
+The option defaults are stabilization = no, prob = 1.0, stabilize\_steps = 60,
+update\_edges = none
+
+
+----------
+
+
+.. _Gissinger:
+
+
+
+**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst
new file mode 100644
index 0000000000..c4eb2a16b5
--- /dev/null
+++ b/doc/src/fix_bond_swap.rst
@@ -0,0 +1,216 @@
+.. index:: fix bond/swap
+
+fix bond/swap command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID bond/swap Nevery fraction cutoff seed
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* bond/swap = style name of this fix command
+* Nevery = attempt bond swapping every this many steps
+* fraction = fraction of group atoms to consider for swapping
+* cutoff = distance at which swapping will be considered (distance units)
+* seed = random # seed (positive integer)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all bond/swap 50 0.5 1.3 598934
+
+Description
+"""""""""""
+
+In a simulation of polymer chains, this command attempts to swap bonds
+between two different chains, effectively grafting the end of one
+chain onto another chain and vice versa.  This is done via Monte Carlo
+rules using the Boltzmann acceptance criterion.  The purpose is to
+equilibrate the polymer chain conformations more rapidly than dynamics
+alone would do it, by enabling instantaneous large conformational
+changes in a dense polymer melt.  The polymer chains should thus more
+rapidly converge to the proper end-to-end distances and radii of
+gyration.  It is designed for use with systems of
+:doc:`FENE <bond_fene>` or :doc:`harmonic <bond_harmonic>` bead-spring
+polymer chains where each polymer is a linear chain of monomers, but
+LAMMPS does not enforce this requirement, i.e. any
+:doc:`bond\_style <bond_style>` can be used.
+
+A schematic of the kinds of bond swaps that can occur is shown here:
+
+.. image:: JPG/bondswap.jpg
+   :align: center
+
+On the left, the red and blue chains have two monomers A1 and B1 close
+to each other, which are currently bonded to monomers A2 and B2
+respectively within their own chains.  The bond swap operation will
+attempt to delete the A1-A2 and B1-B2 bonds and replace them with
+A1-B2 and B1-A2 bonds.  If the swap is energetically favorable, the
+two chains on the right are the result and each polymer chain has
+undergone a dramatic conformational change.  This reference,
+:ref:`(Sides) <Sides>` provides more details on how the algorithm works and
+its application:
+
+The bond swapping operation is invoked every *Nevery* timesteps.  If
+any bond is swapped, a re-build of the neighbor lists is triggered,
+since a swap alters the list of which neighbors are considered for
+pairwise interaction.  At each invocation, each processor considers a
+random specified *fraction* of its atoms as potential swapping
+monomers for this timestep.  Choosing a small *fraction* value can
+reduce the likelihood of a reverse swap occurring soon after an
+initial swap.
+
+For each monomer A1, its neighbors are examined to find a possible B1
+monomer.  Both A1 and B1 must be in the fix group, their separation
+must be less than the specified *cutoff*\ , and the molecule IDs of A1
+and B1 must be the same (see below).  If a suitable partner is found,
+the energy change due to swapping the 2 bonds is computed.  This
+includes changes in pairwise, bond, and angle energies due to the
+altered connectivity of the 2 chains.  Dihedral and improper
+interactions are not allowed to be defined when this fix is used.
+
+If the energy decreases due to the swap operation, the bond swap is
+accepted.  If the energy increases it is accepted with probability
+exp(-delta/kT) where delta is the increase in energy, k is the
+Boltzmann constant, and T is the current temperature of the system.
+Whether the swap is accepted or rejected, no other swaps are attempted
+by this processor on this timestep.
+
+The criterion for matching molecule IDs is how bond swaps performed by
+this fix conserve chain length.  To use this features you must setup
+the molecule IDs for your polymer chains in a certain way, typically
+in the data file, read by the :doc:`read\_data <read_data>` command.
+Consider a system of 6-mer chains.  You have 2 choices.  If the
+molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
+swaps will conserve chain length.  For a particular monomer there will
+be only one other monomer on another chain which is a potential swap
+partner.  If the molecule IDs for monomers on each chain are set to
+1,2,3,3,2,1 then swaps will conserve chain length but swaps will be
+able to occur at either end of a chain.  Thus for a particular monomer
+there will be 2 possible swap partners on another chain.  In this
+scenario, swaps can also occur within a single chain, i.e. the two
+ends of a chain swap with each other.
+
+.. note::
+
+   If your simulation uses molecule IDs in the usual way, where all
+   monomers on a single chain are assigned the same ID (different for
+   each chain), then swaps will only occur within the same chain.  If you
+   assign the same molecule ID to all monomers in all chains then
+   inter-chain swaps will occur, but they will not conserve chain length.
+   Neither of these scenarios is probably what you want for this fix.
+
+.. note::
+
+   When a bond swap occurs the image flags of monomers in the new
+   polymer chains can become inconsistent.  See the :doc:`dump <dump>`
+   command for a discussion of image flags.  This is not an issue for
+   running dynamics, but can affect calculation of some diagnostic
+   quantities or the printing of unwrapped coordinates to a dump file.
+
+
+----------
+
+
+This fix computes a temperature each time it is invoked for use by the
+Boltzmann criterion.  To do this, the fix creates its own compute of
+style *temp*\ , as if this command had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp all temp
+
+See the :doc:`compute temp <compute_temp>` command for details.  Note
+that the ID of the new compute is the fix-ID with underscore + "temp"
+appended and the group for the new compute is "all", so that the
+temperature of the entire system is used.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* will have no
+effect on this fix.
+
+
+----------
+
+
+**Restart, fix\_modify, thermo output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place.  However, in a statistical sense, a
+restarted simulation should produce the same behavior.  Also note that
+each processor generates possible swaps independently of other
+processors.  Thus if you repeat the same simulation on a different number
+of processors, the specific swaps performed will be different.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a :doc:`compute <compute>` you have
+defined to this fix which will be used to compute the temperature for
+the Boltzmann criterion.
+
+This fix computes two statistical quantities as a global 2-vector of
+output, which can be accessed by various :doc:`output commands <Howto_output>`.  The first component of the vector is the
+cumulative number of swaps performed by all processors.  The second
+component of the vector is the cumulative number of swaps attempted
+(whether accepted or rejected).  Note that a swap "attempt" only
+occurs when swap partners meeting the criteria described above are
+found on a particular timestep.  The vector values calculated by this
+fix are "intensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MC package.  It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+The settings of the "special\_bond" command must be 0,1,1 in order to
+use this fix, which is typical of bead-spring chains with FENE or
+harmonic bonds.  This means that pairwise interactions between bonded
+atoms are turned off, but are turned on between atoms two or three
+hops away along the chain backbone.
+
+Currently, energy changes in dihedral and improper interactions due to
+a bond swap are not considered.  Thus a simulation that uses this fix
+cannot use a dihedral or improper potential.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix atom/swap <fix_atom_swap>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Sides:
+
+
+
+**(Sides)** Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,
+199-208 (2004).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst
new file mode 100644
index 0000000000..315846a943
--- /dev/null
+++ b/doc/src/fix_box_relax.rst
@@ -0,0 +1,422 @@
+.. index:: fix box/relax
+
+fix box/relax command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID box/relax keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* box/relax = style name of this fix command
+  
+  .. parsed-literal::
+  
+     one or more keyword value pairs may be appended
+     keyword = *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *nreset* or *vmax* or *dilate* or *scaleyz* or *scalexz* or *scalexy* or *fixedpoint*
+       *iso* or *aniso* or *tri* value = Ptarget = desired pressure (pressure units)
+       *x* or *y* or *z* or *xy* or *yz* or *xz* value = Ptarget = desired pressure (pressure units)
+       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *nreset* value = reset reference cell every this many minimizer iterations
+       *vmax* value = fraction = max allowed volume change in one iteration
+       *dilate* value = *all* or *partial*
+       *scaleyz* value = *yes* or *no* = scale yz with lz
+       *scalexz* value = *yes* or *no* = scale xz with lz
+       *scalexy* value = *yes* or *no* = scale xy with ly
+       *fixedpoint* values = x y z
+         x,y,z = perform relaxation dilation/contraction around this point (distance units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all box/relax iso 0.0 vmax 0.001
+   fix 2 water box/relax aniso 0.0 dilate partial
+   fix 2 ice box/relax tri 0.0 couple xy nreset 100
+
+Description
+"""""""""""
+
+Apply an external pressure or stress tensor to the simulation box
+during an :doc:`energy minimization <minimize>`.  This allows the box
+size and shape to vary during the iterations of the minimizer so that
+the final configuration will be both an energy minimum for the
+potential energy of the atoms, and the system pressure tensor will be
+close to the specified external tensor.  Conceptually, specifying a
+positive pressure is like squeezing on the simulation box; a negative
+pressure typically allows the box to expand.
+
+
+----------
+
+
+The external pressure tensor is specified using one or more of the
+*iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*\ , and *couple*
+keywords.  These keywords give you the ability to specify all 6
+components of an external stress tensor, and to couple various of
+these components together so that the dimensions they represent are
+varied together during the minimization.
+
+Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
+Triclinic (non-orthogonal) simulation boxes have 6 adjustable
+dimensions (x,y,z,xy,xz,yz).  The :doc:`create\_box <create_box>`, :doc:`read data <read_data>`, and :doc:`read\_restart <read_restart>` commands
+specify whether the simulation box is orthogonal or non-orthogonal
+(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
+
+The target pressures *Ptarget* for each of the 6 components of the
+stress tensor can be specified independently via the *x*\ , *y*\ , *z*\ ,
+*xy*\ , *xz*\ , *yz* keywords, which correspond to the 6 simulation box
+dimensions.  For example, if the *y* keyword is used, the y-box length
+will change during the minimization.  If the *xy* keyword is used, the
+xy tilt factor will change.  A box dimension will not change if that
+component is not specified.
+
+Note that in order to use the *xy*\ , *xz*\ , or *yz* keywords, the
+simulation box must be triclinic, even if its initial tilt factors are
+0.0.
+
+When the size of the simulation box changes, all atoms are re-scaled
+to new positions, unless the keyword *dilate* is specified with a
+value of *partial*\ , in which case only the atoms in the fix group are
+re-scaled.  This can be useful for leaving the coordinates of atoms in
+a solid substrate unchanged and controlling the pressure of a
+surrounding fluid.
+
+The *scaleyz*\ , *scalexz*\ , and *scalexy* keywords control whether or
+not the corresponding tilt factors are scaled with the associated box
+dimensions when relaxing triclinic periodic cells.  The default
+values *yes* will turn on scaling, which corresponds to adjusting the
+linear dimensions of the cell while preserving its shape.  Choosing
+*no* ensures that the tilt factors are not scaled with the box
+dimensions. See below for restrictions and default values in different
+situations. In older versions of LAMMPS, scaling of tilt factors was
+not performed. The old behavior can be recovered by setting all three
+scale keywords to *no*\ .
+
+The *fixedpoint* keyword specifies the fixed point for cell relaxation.
+By default, it is the center of the box.  Whatever point is
+chosen will not move during the simulation.  For example, if the lower
+periodic boundaries pass through (0,0,0), and this point is provided
+to *fixedpoint*\ , then the lower periodic boundaries will remain at
+(0,0,0), while the upper periodic boundaries will move twice as
+far. In all cases, the particle positions at each iteration are
+unaffected by the chosen value, except that all particles are
+displaced by the same amount, different on each iteration.
+
+.. note::
+
+   Applying an external pressure to tilt dimensions *xy*\ , *xz*\ , *yz*
+   can sometimes result in arbitrarily large values of the tilt factors,
+   i.e. a dramatically deformed simulation box.  This typically indicates
+   that there is something badly wrong with how the simulation was
+   constructed.  The two most common sources of this error are applying a
+   shear stress to a liquid system or specifying an external shear stress
+   tensor that exceeds the yield stress of the solid.  In either case the
+   minimization may converge to a bogus conformation or not converge at
+   all.  Also note that if the box shape tilts to an extreme shape,
+   LAMMPS will run less efficiently, due to the large volume of
+   communication needed to acquire ghost atoms around a processor's
+   irregular-shaped sub-domain.  For extreme values of tilt, LAMMPS may
+   also lose atoms and generate an error.
+
+.. note::
+
+   Performing a minimization with this fix is not a mathematically
+   well-defined minimization problem.  This is because the objective
+   function being minimized changes if the box size/shape changes.  In
+   practice this means the minimizer can get "stuck" before you have
+   reached the desired tolerance.  The solution to this is to restart the
+   minimizer from the new adjusted box size/shape, since that creates a
+   new objective function valid for the new box size/shape.  Repeat as
+   necessary until the box size/shape has reached its new equilibrium.
+
+
+----------
+
+
+The *couple* keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together.  The value specified
+with the keyword determines which are coupled.  For example, *xz*
+means the *Pxx* and *Pzz* components of the stress tensor are coupled.
+*Xyz* means all 3 diagonal components are coupled.  Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep.  The
+*Ptarget* values for any coupled dimensions must be identical.
+*Couple xyz* can be used for a 2d simulation; the *z* dimension is
+simply ignored.
+
+
+----------
+
+
+The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+
+The keyword *iso* means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together.  Using "iso Ptarget" is the same as specifying
+these 4 keywords:
+
+
+.. parsed-literal::
+
+   x Ptarget
+   y Ptarget
+   z Ptarget
+   couple xyz
+
+The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled
+independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure.  Using "aniso Ptarget" is the same as specifying these 4
+keywords:
+
+
+.. parsed-literal::
+
+   x Ptarget
+   y Ptarget
+   z Ptarget
+   couple none
+
+The keyword *tri* means *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , and *yz* dimensions
+are controlled independently using their individual stress components
+as the driving forces, and the specified scalar pressure as the
+external normal stress.  Using "tri Ptarget" is the same as specifying
+these 7 keywords:
+
+
+.. parsed-literal::
+
+   x Ptarget
+   y Ptarget
+   z Ptarget
+   xy 0.0
+   yz 0.0
+   xz 0.0
+   couple none
+
+
+----------
+
+
+The *vmax* keyword can be used to limit the fractional change in the
+volume of the simulation box that can occur in one iteration of the
+minimizer.  If the pressure is not settling down during the
+minimization this can be because the volume is fluctuating too much.
+The specified fraction must be greater than 0.0 and should be << 1.0.
+A value of 0.001 means the volume cannot change by more than 1/10 of a
+percent in one iteration when *couple xyz* has been specified.  For
+any other case it means no linear dimension of the simulation box can
+change by more than 1/10 of a percent.
+
+
+----------
+
+
+With this fix, the potential energy used by the minimizer is augmented
+by an additional energy provided by the fix. The overall objective
+function then is:
+
+.. image:: Eqs/fix_box_relax1.jpg
+   :align: center
+
+where *U* is the system potential energy, *P*\ \_t is the desired
+hydrostatic pressure, *V* and *V*\ \_0 are the system and reference
+volumes, respectively.  *E*\ \_\ *strain* is the strain energy expression
+proposed by Parrinello and Rahman :ref:`(Parrinello1981) <Parrinello1981>`.
+Taking derivatives of *E* w.r.t. the box dimensions, and setting these
+to zero, we find that at the minimum of the objective function, the
+global system stress tensor **P** will satisfy the relation:
+
+.. image:: Eqs/fix_box_relax2.jpg
+   :align: center
+
+where **I** is the identity matrix, **h**\ \_0 is the box dimension tensor of
+the reference cell, and **h**\ \_0\ *d* is the diagonal part of
+**h**\ \_0. **S**\ \_\ *t* is a symmetric stress tensor that is chosen by LAMMPS
+so that the upper-triangular components of **P** equal the stress tensor
+specified by the user.
+
+This equation only applies when the box dimensions are equal to those
+of the reference dimensions. If this is not the case, then the
+converged stress tensor will not equal that specified by the user.  We
+can resolve this problem by periodically resetting the reference
+dimensions. The keyword *nreset* controls how often this is done.  If
+this keyword is not used, or is given a value of zero, then the
+reference dimensions are set to those of the initial simulation domain
+and are never changed. A value of *nstep* means that every *nstep*
+minimization steps, the reference dimensions are set to those of the
+current simulation domain. Note that resetting the reference
+dimensions changes the objective function and gradients, which
+sometimes causes the minimization to fail. This can be resolved by
+changing the value of *nreset*\ , or simply continuing the minimization
+from a restart file.
+
+.. note::
+
+   As normally computed, pressure includes a kinetic- energy or
+   temperature-dependent component; see the :doc:`compute pressure <compute_pressure>` command.  However, atom velocities are
+   ignored during a minimization, and the applied pressure(s) specified
+   with this command are assumed to only be the virial component of the
+   pressure (the non-kinetic portion).  Thus if atoms have a non-zero
+   temperature and you print the usual thermodynamic pressure, it may not
+   appear the system is converging to your specified pressure.  The
+   solution for this is to either (a) zero the velocities of all atoms
+   before performing the minimization, or (b) make sure you are
+   monitoring the pressure without its kinetic component.  The latter can
+   be done by outputting the pressure from the pressure compute this
+   command creates (see below) or a pressure compute you define yourself.
+
+.. note::
+
+   Because pressure is often a very sensitive function of volume,
+   it can be difficult for the minimizer to equilibrate the system the
+   desired pressure with high precision, particularly for solids.  Some
+   techniques that seem to help are (a) use the "min\_modify line
+   quadratic" option when minimizing with box relaxations, (b) minimize
+   several times in succession if need be, to drive the pressure closer
+   to the target pressure, (c) relax the atom positions before relaxing
+   the box, and (d) relax the box to the target hydrostatic pressure
+   before relaxing to a target shear stress state. Also note that some
+   systems (e.g. liquids) will not sustain a non-hydrostatic applied
+   pressure, which means the minimizer will not converge.
+
+
+----------
+
+
+This fix computes a temperature and pressure each timestep.  The
+temperature is used to compute the kinetic contribution to the
+pressure, even though this is subsequently ignored by default.  To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp
+   compute fix-ID_press group-ID pressure fix-ID_temp virial
+
+See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press", and the group for the new computes is the same
+as the fix group.  Also note that the pressure compute does not
+include a kinetic component.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by this fix.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its temperature and pressure calculation, as described above.  Note
+that as described above, if you assign a pressure compute to this fix
+that includes a kinetic energy component it will affect the
+minimization, most likely in an undesirable way.
+
+.. note::
+
+   If both the *temp* and *press* keywords are used in a single
+   thermo\_modify command (or in two separate commands), then the order in
+   which the keywords are specified is important.  Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
+   an argument when it is specified.  The *temp* keyword will override
+   this (for the pressure compute being used by fix box/relax), but only if the
+   *temp* keyword comes after the *press* keyword.  If the *temp* keyword
+   comes before the *press* keyword, then the new pressure compute
+   specified by the *press* keyword will be unaffected by the *temp*
+   setting.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`. The scalar is the pressure-volume
+energy, plus the strain energy, if it exists, as described above.  The
+energy values reported at the end of a minimization run under
+"Minimization stats" include this energy, and so differ from what
+LAMMPS normally reports as potential energy. This fix does not support
+the :doc:`fix\_modify <fix_modify>` *energy* option, because that would
+result in double-counting of the fix energy in the minimization
+energy. Instead, the fix energy can be explicitly added to the
+potential energy using one of these two variants:
+
+
+.. parsed-literal::
+
+   variable emin equal pe+f_1
+
+   variable emin equal pe+f_1/atoms
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+This fix is invoked during :doc:`energy minimization <minimize>`, but
+not for the purpose of adding a contribution to the energy or forces
+being minimized.  Instead it alters the simulation box geometry as
+described above.
+
+Restrictions
+""""""""""""
+
+
+Only dimensions that are available can be adjusted by this fix.
+Non-periodic dimensions are not available.  *z*\ , *xz*\ , and *yz*\ , are
+not available for 2D simulations. *xy*\ , *xz*\ , and *yz* are only
+available if the simulation domain is non-orthogonal.  The
+:doc:`create\_box <create_box>`, :doc:`read data <read_data>`, and
+:doc:`read\_restart <read_restart>` commands specify whether the
+simulation box is orthogonal or non-orthogonal (triclinic) and explain
+the meaning of the xy,xz,yz tilt factors.
+
+The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
+for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
+can only be used if the 2nd dimension in the keyword is periodic,
+and if the tilt factor is not coupled to the barostat via keywords
+*tri*\ , *yz*\ , *xz*\ , and *xy*\ .
+
+Related commands
+""""""""""""""""
+
+:doc:`fix npt <fix_nh>`, :doc:`minimize <minimize>`
+
+Default
+"""""""
+
+The keyword defaults are dilate = all, vmax = 0.0001, nreset = 0.
+
+
+----------
+
+
+.. _Parrinello1981:
+
+
+
+**(Parrinello1981)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst
new file mode 100644
index 0000000000..853a09a9c4
--- /dev/null
+++ b/doc/src/fix_client_md.rst
@@ -0,0 +1,115 @@
+.. index:: fix client/md
+
+fix client/md command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID client/md
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* client/md = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all client/md
+
+Description
+"""""""""""
+
+This fix style enables LAMMPS to run as a "client" code and
+communicate each timestep with a separate "server" code to perform an
+MD simulation together.
+
+The :doc:`Howto client/server <Howto_client_server>` doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code.  The server responds to each request with a reply message.  This
+enables the two codes to work in tandem to perform a simulation.
+
+When using this fix, LAMMPS (as the client code) passes the current
+coordinates of all particles to the server code each timestep, which
+computes their interaction, and returns the energy, forces, and virial
+for the interacting particles to LAMMPS, so it can complete the
+timestep.
+
+The server code could be a quantum code, or another classical MD code
+which encodes a force field (pair\_style in LAMMPS lingo) which LAMMPS
+does not have.  In the quantum case, this fix is a mechanism for
+running *ab initio* MD with quantum forces.
+
+The group associated with this fix is ignored.
+
+The protocol and :doc:`units <units>` for message format and content
+that LAMMPS exchanges with the server code is defined on the :doc:`server md <server_md>` doc page.
+
+Note that when using LAMMPS as an MD client, your LAMMPS input script
+should not normally contain force field commands, like a
+:doc:`pair\_style <pair_style>`, :doc:`bond\_style <bond_style>`, or
+:doc:`kspace\_style <kspace_style>` command.  However it is possible for
+a server code to only compute a portion of the full force-field, while
+LAMMPS computes the remaining part.  Your LAMMPS script can also
+specify boundary conditions or force constraints in the usual way,
+which will be added to the per-atom forces returned by the server
+code.
+
+See the examples/message dir for example scripts where LAMMPS is both
+the "client" and/or "server" code for this kind of client/server MD
+simulation.  The examples/message/README file explains how to launch
+LAMMPS and another code in tandem to perform a coupled simulation.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential energy computed by the server application to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the server application's contribution to the system's
+virial as part of :doc:`thermodynamic output <thermo_style>`.  The
+default is *virial yes*
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the potential
+energy discussed above.  The scalar value calculated by this fix is
+"extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MESSAGE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+A script that uses this command must also use the
+:doc:`message <message>` command to setup the messaging protocol with
+the other server code.
+
+Related commands
+""""""""""""""""
+
+:doc:`message <message>`, :doc:`server <server>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst
new file mode 100644
index 0000000000..abdf095959
--- /dev/null
+++ b/doc/src/fix_cmap.rst
@@ -0,0 +1,172 @@
+.. index:: fix cmap
+
+fix cmap command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID cmap filename
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* cmap = style name of this fix command
+* filename = force-field file with CMAP coefficients
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix            myCMAP all cmap ../potentials/cmap36.data
+   read_data      proteinX.data fix myCMAP crossterm CMAP
+   fix_modify     myCMAP energy yes
+
+Description
+"""""""""""
+
+This command enables CMAP cross-terms to be added to simulations which
+use the CHARMM force field.  These are relevant for any CHARMM model
+of a peptide or protein sequences that is 3 or more amino-acid
+residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>` for details,
+including the analytic energy expressions for CMAP interactions.  The
+CMAP cross-terms add additional potential energy contributions to pairs
+of overlapping phi-psi dihedrals of amino-acids, which are important
+to properly represent their conformational behavior.
+
+The examples/cmap directory has a sample input script and data file
+for a small peptide, that illustrates use of the fix cmap command.
+
+As in the example above, this fix should be used before reading a data
+file that contains a listing of CMAP interactions.  The *filename*
+specified should contain the CMAP parameters for a particular version
+of the CHARMM force field.  Two such files are including in the
+lammps/potentials directory: charmm22.cmap and charmm36.cmap.
+
+The data file read by the "read\_data" must contain the topology of all
+the CMAP interactions, similar to the topology data for bonds, angles,
+dihedrals, etc.  Specially it should have a line like this
+in its header section:
+
+
+.. parsed-literal::
+
+   N crossterms
+
+where N is the number of CMAP cross-terms.  It should also have a section
+in the body of the data file like this with N lines:
+
+
+.. parsed-literal::
+
+   CMAP
+
+          1       1       8      10      12      18      20
+          2       5      18      20      22      25      27
+          [...]
+          N       3     314     315     317      318    330
+
+The first column is an index from 1 to N to enumerate the CMAP terms;
+it is ignored by LAMMPS.  The 2nd column is the "type" of the
+interaction; it is an index into the CMAP force field file.  The
+remaining 5 columns are the atom IDs of the atoms in the two 4-atom
+dihedrals that overlap to create the CMAP 5-body interaction.  Note
+that the "crossterm" and "CMAP" keywords for the header and body
+sections match those specified in the read\_data command following the
+data file name; see the :doc:`read\_data <read_data>` doc page for
+more details.
+
+A data file containing CMAP cross-terms can be generated from a PDB
+file using the charmm2lammps.pl script in the tools/ch2lmp directory
+of the LAMMPS distribution.  The script must be invoked with the
+optional "-cmap" flag to do this; see the tools/ch2lmp/README file for
+more information.
+
+The potential energy associated with CMAP interactions can be output
+as described below.  It can also be included in the total potential
+energy of the system, as output by the
+:doc:`thermo\_style <thermo_style>` command, if the :doc:`fix\_modify energy <fix_modify>` command is used, as in the example above.  See
+the note below about how to include the CMAP energy when performing an
+:doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the list of CMAP cross-terms to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>` command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential "energy" of the CMAP interactions system's
+potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to the interaction between atoms to
+the system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+The default is *virial yes*
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the potential
+energy discussed above.  The scalar value calculated by this fix is
+"extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the potential energy associated with the CMAP terms
+   forces to be included in the total potential energy of the system (the
+   quantity being minimized), you MUST enable the
+   :doc:`fix\_modify <fix_modify>` *energy* option for this fix.
+
+Restrictions
+""""""""""""
+
+
+To function as expected this fix command must be issued *before* a
+:doc:`read\_data <read_data>` command but *after* a
+:doc:`read\_restart <read_restart>` command.
+
+This fix can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix\_modify <fix_modify>`, :doc:`read\_data <read_data>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Buck:
+
+
+
+**(Buck)** Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
+(2006).
+
+.. _Brooks2:
+
+
+
+**(Brooks)** Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst
new file mode 100644
index 0000000000..bd29a394cb
--- /dev/null
+++ b/doc/src/fix_colvars.rst
@@ -0,0 +1,162 @@
+.. index:: fix colvars
+
+fix colvars command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID colvars configfile keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* colvars = style name of this fix command
+* configfile = the configuration file for the colvars module
+* keyword = *input* or *output* or *seed* or *tstat*
+  
+  .. parsed-literal::
+  
+       *input* arg = colvars.state file name or prefix or NULL (default: NULL)
+       *output* arg = output filename prefix (default: out)
+       *seed* arg = seed for random number generator (default: 1966)
+       *unwrap* arg = *yes* or *no*
+         use unwrapped coordinates in collective variables (default: yes)
+       *tstat* arg = fix id of a thermostat or NULL (default: NULL)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
+   fix abf all colvars colvars.inp tstat 1
+
+Description
+"""""""""""
+
+This fix interfaces LAMMPS to the collective variables "Colvars"
+library, which allows to calculate potentials of mean force
+(PMFs) for any set of colvars, using different sampling methods:
+currently implemented are the Adaptive Biasing Force (ABF) method,
+metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
+(US) via a flexible harmonic restraint bias.
+
+This documentation describes only the fix colvars command itself and
+LAMMPS specific parts of the code.  The full documentation of the
+colvars library is available as `this supplementary PDF document <PDF/colvars-refman-lammps.pdf>`_
+
+The Colvars library is developed at `https://github.com/colvars/colvars <https://github.com/colvars/colvars>`_
+A detailed discussion of its implementation is in :ref:`(Fiorin) <Fiorin>`.
+
+There are some example scripts for using this package with LAMMPS in the
+examples/USER/colvars directory.
+
+
+----------
+
+
+The only mandatory argument to the fix is the filename to the colvars
+input file that contains the input that is independent from the MD
+program in which the colvars library has been integrated.
+
+The *group-ID* entry is ignored. The collective variable module will
+always apply to the entire system and there can only be one instance
+of the colvars fix at a time. The colvars fix will only communicate
+the minimum information necessary and the colvars library supports
+multiple, completely independent collective variables, so there is
+no restriction to functionality by limiting the number of colvars fixes.
+
+The *input* keyword allows to specify a state file that would contain
+the restart information required in order to continue a calculation from
+a prerecorded state. Fix colvars records it state in :doc:`binary restart <restart>`
+files, so when using the :doc:`read\_restart <read_restart>` command,
+this is usually not needed.
+
+The *output* keyword allows to specify the output prefix. All output
+files generated will use this prefix followed by the ".colvars." and
+a word like "state" or "traj".
+
+The *seed* keyword contains the seed for the random number generator
+that will be used in the colvars module.
+
+The *unwrap* keyword controls whether wrapped or unwrapped coordinates
+are passed to the colvars library for calculation of the collective
+variables and the resulting forces. The default is *yes*\ , i.e. to use
+the image flags to reconstruct the absolute atom positions.
+Setting this to *no* will use the current local coordinates that are
+wrapped back into the simulation cell at each re-neighboring instead.
+
+The *tstat* keyword can be either NULL or the label of a thermostatting
+fix that thermostats all atoms in the fix colvars group. This will be
+used to provide the colvars module with the current thermostat target
+temperature.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the current status of the colvars module into
+:doc:`binary restart files <restart>`. This is in addition to the text
+mode status file that is written by the colvars module itself and the
+kind of information in both files is identical.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change from the biasing force added by the fix
+to the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The *fix\_modify configfile <config file>* option allows to add settings
+from an additional config file to the colvars module. This option can
+only be used, after the system has been initialized with a :doc:`run <run>`
+command.
+
+The *fix\_modify config <quoted string>* option allows to add settings
+from inline strings. Those have to fit on a single line when enclosed
+in a pair of double quotes ("), or can span multiple lines when bracketed
+by a pair of triple double quotes (""", like python embedded documentation).
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-COLVARS package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+There can only be one colvars fix active at a time. Since the interface
+communicates only the minimum amount of information and colvars module
+itself can handle an arbitrary number of collective variables, this is
+not a limitation of functionality.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix smd <fix_smd>`, :doc:`fix spring <fix_spring>`,
+:doc:`fix plumed <fix_plumed>`
+
+Default
+"""""""
+
+The default options are input = NULL, output = out, seed = 1966, unwrap yes,
+and tstat = NULL.
+
+
+----------
+
+
+.. _Fiorin:
+
+
+
+**(Fiorin)** Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst
new file mode 100644
index 0000000000..906be7ca7c
--- /dev/null
+++ b/doc/src/fix_controller.rst
@@ -0,0 +1,231 @@
+.. index:: fix controller
+
+fix controller command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID controller Nevery alpha Kp Ki Kd pvar setpoint cvar
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* controller = style name of this fix command
+* Nevery = invoke controller every this many timesteps
+* alpha = coupling constant for PID equation (see units discussion below)
+* Kp = proportional gain in PID equation (unitless)
+* Ki = integral gain in PID equation (unitless)
+* Kd = derivative gain in PID equation (unitless)
+* pvar = process variable of form c\_ID, c\_ID[I], f\_ID, f\_ID[I], or v\_name
+  
+  .. parsed-literal::
+  
+       c_ID = global scalar calculated by a compute with ID
+       c_ID[I] = Ith component of global vector calculated by a compute with ID
+       f_ID = global scalar calculated by a fix with ID
+       f_ID[I] = Ith component of global vector calculated by a fix with ID
+       v_name = value calculated by an equal-style variable with name
+
+* setpoint = desired value of process variable (same units as process variable)
+* cvar = name of control variable
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
+   fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
+   fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol
+
+Description
+"""""""""""
+
+This fix enables control of a LAMMPS simulation using a control loop
+feedback mechanism known as a proportional-integral-derivative (PID)
+controller.  The basic idea is to define a "process variable" which is
+a quantity that can be monitored during a running simulation.  A
+desired target value is chosen for the process variable.  A "control
+variable" is also defined which is an adjustable attribute of the
+running simulation, which the process variable will respond to.  The
+PID controller continuously adjusts the control variable based on the
+difference between the process variable and the target.
+
+Here are examples of ways in which this fix can be used.  The
+examples/pid directory contains a script that implements the simple
+thermostat.
+
++-----------------------------------------+---------------------+---------------------+
+| Goal                                    | process variable    | control variable    |
++-----------------------------------------+---------------------+---------------------+
+| Simple thermostat                       | instantaneous T     | thermostat target T |
++-----------------------------------------+---------------------+---------------------+
+| Find melting temperature                | average PE per atom | thermostat target T |
++-----------------------------------------+---------------------+---------------------+
+| Control pressure in non-periodic system | force on wall       | position of wall    |
++-----------------------------------------+---------------------+---------------------+
+|                                         |                     |                     |
++-----------------------------------------+---------------------+---------------------+
+
+.. note::
+
+   For this fix to work, the control variable must actually induce
+   a change in a running LAMMPS simulation.  Typically this will only
+   occur if there is some other command (e.g. a thermostat fix) which
+   uses the control variable as an input parameter.  This could be done
+   directly or indirectly, e.g. the other command uses a variable as
+   input whose formula uses the control variable.  The other command
+   should alter its behavior dynamically as the variable changes.
+
+.. note::
+
+   If there is a command you think could be used in this fashion,
+   but does not currently allow a variable as an input parameter, please
+   notify the LAMMPS developers.  It is often not difficult to enable a
+   command to use a variable as an input parameter.
+
+The group specified with this command is ignored.  However, note that
+the process variable may be defined by calculations performed by
+computes and fixes which store their own "group" definitions.
+
+The PID controller is invoked once each *Nevery* timesteps.
+
+The PID controller is implemented as a discretized version of
+the following dynamic equation:
+
+.. image:: Eqs/fix_controller1.jpg
+   :align: center
+
+where *c* is the continuous time analog of the control variable,
+*e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and
+*alpha*\ , *Kp*\ , *Ki*\ , and *Kd* are constants set by the corresponding
+keywords described above. The discretized version of this equation is:
+
+.. image:: Eqs/fix_controller2.jpg
+   :align: center
+
+where *tau* = *Nevery* \* *timestep* is the time interval between updates,
+and the subscripted variables indicate the values of *c* and *e* at
+successive updates.
+
+From the first equation, it is clear that if the three gain values
+*Kp*\ , *Ki*\ , *Kd* are dimensionless constants, then *alpha* must have
+units of [unit *cvar*\ ]/[unit *pvar*\ ]/[unit time] e.g. [ eV/K/ps
+]. The advantage of this unit scheme is that the value of the
+constants should be invariant under a change of either the MD timestep
+size or the value of *Nevery*\ . Similarly, if the LAMMPS :doc:`unit style <units>` is changed, it should only be necessary to change
+the value of *alpha* to reflect this, while leaving *Kp*\ , *Ki*\ , and
+*Kd* unaltered.
+
+When choosing the values of the four constants, it is best to first
+pick a value and sign for *alpha* that is consistent with the
+magnitudes and signs of *pvar* and *cvar*\ .  The magnitude of *Kp*
+should then be tested over a large positive range keeping *Ki* = *Kd* =0.
+A good value for *Kp* will produce a fast response in *pvar*\ , without
+overshooting the *setpoint*\ .  For many applications, proportional
+feedback is sufficient, and so *Ki* = *Kd* =0 can be used. In cases where
+there is a substantial lag time in the response of *pvar* to a change
+in *cvar*\ , this can be counteracted by increasing *Kd*\ . In situations
+where *pvar* plateaus without reaching *setpoint*\ , this can be
+counteracted by increasing *Ki*\ .  In the language of Charles Dickens,
+*Kp* represents the error of the present, *Ki* the error of the past,
+and *Kd* the error yet to come.
+
+Because this fix updates *cvar*\ , but does not initialize its value,
+the initial value is that assigned by the user in the input script via
+the :doc:`internal-style variable <variable>` command.  This value is
+used (by the other LAMMPS command that used the variable) until this
+fix performs its first update of *cvar* after *Nevery* timesteps.  On
+the first update, the value of the derivative term is set to zero,
+because the value of *e\_n-1* is not yet defined.
+
+
+----------
+
+
+The process variable *pvar* can be specified as the output of a
+:doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation of a
+:doc:`variable <variable>`.  In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity.
+
+If *pvar* begins with "c\_", a compute ID must follow which has been
+previously defined in the input script and which generates a global
+scalar or vector.  See the individual :doc:`compute <compute>` doc page
+for details.  If no bracketed integer is appended, the scalar
+calculated by the compute is used.  If a bracketed integer is
+appended, the Ith value of the vector calculated by the compute is
+used.  Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+
+If *pvar* begins with "f\_", a fix ID must follow which has been
+previously defined in the input script and which generates a global
+scalar or vector.  See the individual :doc:`fix <fix>` doc page for
+details.  Note that some fixes only produce their values on certain
+timesteps, which must be compatible with when fix controller
+references the values, or else an error results.  If no bracketed integer
+is appended, the scalar calculated by the fix is used.  If a bracketed
+integer is appended, the Ith value of the vector calculated by the fix
+is used.  Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
+
+If *pvar* begins with "v\_", a variable name must follow which has been
+previously defined in the input script.  Only equal-style variables
+can be referenced.  See the :doc:`variable <variable>` command for
+details.  Note that variables of style *equal* define a formula which
+can reference individual atom properties or thermodynamic keywords, or
+they can invoke other computes, fixes, or variables when they are
+evaluated, so this is a very general means of specifying the process
+variable.
+
+The target value *setpoint* for the process variable must be a numeric
+value, in whatever units *pvar* is defined for.
+
+The control variable *cvar* must be the name of an :doc:`internal-style variable <variable>` previously defined in the input script.  Note
+that it is not specified with a "v\_" prefix, just the name of the
+variable.  It must be an internal-style variable, because this fix
+updates its value directly.  Note that other commands can use an
+equal-style versus internal-style variable interchangeably.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Currently, no information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix produces a global vector with 3 values which can be accessed
+by various :doc:`output commands <Howto_output>`.  The values can be
+accessed on any timestep, though they are only updated on timesteps
+that are a multiple of *Nevery*\ .
+
+The three values are the most recent updates made to the control
+variable by each of the 3 terms in the PID equation above.  The first
+value is the proportional term, the second is the integral term, the
+third is the derivative term.
+
+The units of the vector values will be whatever units the control
+variable is in.  The vector values calculated by this fix are
+"extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix adapt <fix_adapt>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst
new file mode 100644
index 0000000000..dc0b566678
--- /dev/null
+++ b/doc/src/fix_deform.rst
@@ -0,0 +1,643 @@
+.. index:: fix deform
+
+fix deform command
+==================
+
+fix deform/kk command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID deform N parameter args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* deform = style name of this fix command
+* N = perform box deformation every this many timesteps
+* one or more parameter/arg pairs may be appended
+  
+  .. parsed-literal::
+  
+     parameter = *x* or *y* or *z* or *xy* or *xz* or *yz*
+       *x*\ , *y*\ , *z* args = style value(s)
+         style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable*
+           *final* values = lo hi
+             lo hi = box boundaries at end of run (distance units)
+           *delta* values = dlo dhi
+             dlo dhi = change in box boundaries at end of run (distance units)
+           *scale* values = factor
+             factor = multiplicative factor for change in box length at end of run
+           *vel* value = V
+             V = change box length at this velocity (distance/time units),
+                 effectively an engineering strain rate
+           *erate* value = R
+             R = engineering strain rate (1/time units)
+           *trate* value = R
+             R = true strain rate (1/time units)
+           *volume* value = none = adjust this dim to preserve volume of system
+           *wiggle* values = A Tp
+             A = amplitude of oscillation (distance units)
+             Tp = period of oscillation (time units)
+           *variable* values = v_name1 v_name2
+             v_name1 = variable with name1 for box length change as function of time
+             v_name2 = variable with name2 for change rate as function of time
+       *xy*\ , *xz*\ , *yz* args = style value
+         style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle*
+           *final* value = tilt
+             tilt = tilt factor at end of run (distance units)
+           *delta* value = dtilt
+             dtilt = change in tilt factor at end of run (distance units)
+           *vel* value = V
+             V = change tilt factor at this velocity (distance/time units),
+                 effectively an engineering shear strain rate
+           *erate* value = R
+             R = engineering shear strain rate (1/time units)
+           *trate* value = R
+             R = true shear strain rate (1/time units)
+           *wiggle* values = A Tp
+             A = amplitude of oscillation (distance units)
+             Tp = period of oscillation (time units)
+           *variable* values = v_name1 v_name2
+             v_name1 = variable with name1 for tilt change as function of time
+             v_name2 = variable with name2 for change rate as function of time
+
+* zero or more keyword/value pairs may be appended
+* keyword = *remap* or *flip* or *units*
+  
+  .. parsed-literal::
+  
+       *remap* value = *x* or *v* or *none*
+         x = remap coords of atoms in group into deforming box
+         v = remap velocities of all atoms when they cross periodic boundaries
+         none = no remapping of x or v
+       *flip* value = *yes* or *no*
+         allow or disallow box flips when it becomes highly skewed
+       *units* value = *lattice* or *box*
+         lattice = distances are defined in lattice units
+         box = distances are defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all deform 1 x final 0.0 9.0 z final 0.0 5.0 units box
+   fix 1 all deform 1 x trate 0.1 y volume z volume
+   fix 1 all deform 1 xy erate 0.001 remap v
+   fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
+
+Description
+"""""""""""
+
+Change the volume and/or shape of the simulation box during a dynamics
+run.  Orthogonal simulation boxes have 3 adjustable parameters
+(x,y,z).  Triclinic (non-orthogonal) simulation boxes have 6
+adjustable parameters (x,y,z,xy,xz,yz).  Any or all of them can be
+adjusted independently and simultaneously by this command.
+
+This fix can be used to perform non-equilibrium MD (NEMD) simulations
+of a continuously strained system.  See the :doc:`fix nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform <compute_temp_deform>` commands for more details.  Note
+that simulation of a continuously extended system (extensional flow)
+can be modeled using the :ref:`USER-UEF package <PKG-USER-UEF>` and its :doc:`fix commands <fix_nh_uef>`.
+
+For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be
+shrink-wrapped.  For the *xy*\ , *yz*\ , *xz* parameters, the associated
+2nd dimension cannot be shrink-wrapped.  Dimensions not varied by this
+command can be periodic or non-periodic.  Dimensions corresponding to
+unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
+
+The size and shape of the simulation box at the beginning of the
+simulation run were either specified by the
+:doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` or
+:doc:`read\_restart <read_restart>` command used to setup the simulation
+initially if it is the first run, or they are the values from the end
+of the previous run.  The :doc:`create\_box <create_box>`, :doc:`read data <read_data>`, and :doc:`read\_restart <read_restart>` commands
+specify whether the simulation box is orthogonal or non-orthogonal
+(triclinic) and explain the meaning of the xy,xz,yz tilt factors.  If
+fix deform changes the xy,xz,yz tilt factors, then the simulation box
+must be triclinic, even if its initial tilt factors are 0.0.
+
+As described below, the desired simulation box size and shape at the
+end of the run are determined by the parameters of the fix deform
+command.  Every Nth timestep during the run, the simulation box is
+expanded, contracted, or tilted to ramped values between the initial
+and final values.
+
+
+----------
+
+
+For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their
+styles and values.
+
+The *final*\ , *delta*\ , *scale*\ , *vel*\ , and *erate* styles all change
+the specified dimension of the box via "constant displacement" which
+is effectively a "constant engineering strain rate".  This means the
+box dimension changes linearly with time from its initial to final
+value.
+
+For style *final*\ , the final lo and hi box boundaries of a dimension
+are specified.  The values can be in lattice or box distance units.
+See the discussion of the units keyword below.
+
+For style *delta*\ , plus or minus changes in the lo/hi box boundaries
+of a dimension are specified.  The values can be in lattice or box
+distance units.  See the discussion of the units keyword below.
+
+For style *scale*\ , a multiplicative factor to apply to the box length
+of a dimension is specified.  For example, if the initial box length
+is 10, and the factor is 1.1, then the final box length will be 11.  A
+factor less than 1.0 means compression.
+
+For style *vel*\ , a velocity at which the box length changes is
+specified in units of distance/time.  This is effectively a "constant
+engineering strain rate", where rate = V/L0 and L0 is the initial box
+length.  The distance can be in lattice or box distance units.  See
+the discussion of the units keyword below.  For example, if the
+initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
+after 10 psec, the box length will have doubled.  After 20 psec, it
+will have tripled.
+
+The *erate* style changes a dimension of the box at a "constant
+engineering strain rate".  The units of the specified strain rate are
+1/time.  See the :doc:`units <units>` command for the time units
+associated with different choices of simulation units,
+e.g. picoseconds for "metal" units).  Tensile strain is unitless and
+is defined as delta/L0, where L0 is the original box length and delta
+is the change relative to the original length.  The box length L as a
+function of time will change as
+
+
+.. parsed-literal::
+
+   L(t) = L0 (1 + erate\*dt)
+
+where dt is the elapsed time (in time units).  Thus if *erate* R is
+specified as 0.1 and time units are picoseconds, this means the box
+length will increase by 10% of its original length every picosecond.
+I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc.  R =
+-0.01 means the box length will shrink by 1% of its original length
+every picosecond.  Note that for an "engineering" rate the change is
+based on the original box length, so running with R = 1 for 10
+picoseconds expands the box length by a factor of 11 (strain of 10),
+which is different that what the *trate* style would induce.
+
+The *trate* style changes a dimension of the box at a "constant true
+strain rate".  Note that this is not an "engineering strain rate", as
+the other styles are.  Rather, for a "true" rate, the rate of change
+is constant, which means the box dimension changes non-linearly with
+time from its initial to final value.  The units of the specified
+strain rate are 1/time.  See the :doc:`units <units>` command for the
+time units associated with different choices of simulation units,
+e.g. picoseconds for "metal" units).  Tensile strain is unitless and
+is defined as delta/L0, where L0 is the original box length and delta
+is the change relative to the original length.
+
+The box length L as a function of time will change as
+
+
+.. parsed-literal::
+
+   L(t) = L0 exp(trate\*dt)
+
+where dt is the elapsed time (in time units).  Thus if *trate* R is
+specified as ln(1.1) and time units are picoseconds, this means the
+box length will increase by 10% of its current (not original) length
+every picosecond.  I.e. strain after 1 psec = 0.1, strain after 2 psec
+= 0.21, etc.  R = ln(2) or ln(3) means the box length will double or
+triple every picosecond.  R = ln(0.99) means the box length will
+shrink by 1% of its current length every picosecond.  Note that for a
+"true" rate the change is continuous and based on the current length,
+so running with R = ln(2) for 10 picoseconds does not expand the box
+length by a factor of 11 as it would with *erate*\ , but by a factor of
+1024 since the box length will double every picosecond.
+
+Note that to change the volume (or cross-sectional area) of the
+simulation box at a constant rate, you can change multiple dimensions
+via *erate* or *trate*\ .  E.g. to double the box volume in a picosecond
+picosecond, you could set "x erate M", "y erate M", "z erate M", with
+M = pow(2,1/3) - 1 = 0.26, since if each box dimension grows by 26%,
+the box volume doubles.  Or you could set "x trate M", "y trate M", "z
+trate M", with M = ln(1.26) = 0.231, and the box volume would double
+every picosecond.
+
+The *volume* style changes the specified dimension in such a way that
+the box volume remains constant while other box dimensions are changed
+explicitly via the styles discussed above.  For example, "x scale 1.1
+y scale 1.1 z volume" will shrink the z box length as the x,y box
+lengths increase, to keep the volume constant (product of x,y,z
+lengths).  If "x scale 1.1 z volume" is specified and parameter *y* is
+unspecified, then the z box length will shrink as x increases to keep
+the product of x,z lengths constant.  If "x scale 1.1 y volume z
+volume" is specified, then both the y,z box lengths will shrink as x
+increases to keep the volume constant (product of x,y,z lengths).  In
+this case, the y,z box lengths shrink so as to keep their relative
+aspect ratio constant.
+
+For solids or liquids, note that when one dimension of the box is
+expanded via fix deform (i.e. tensile strain), it may be physically
+undesirable to hold the other 2 box lengths constant (unspecified by
+fix deform) since that implies a density change.  Using the *volume*
+style for those 2 dimensions to keep the box volume constant may make
+more physical sense, but may also not be correct for materials and
+potentials whose Poisson ratio is not 0.5.  An alternative is to use
+:doc:`fix npt aniso <fix_nh>` with zero applied pressure on those 2
+dimensions, so that they respond to the tensile strain dynamically.
+
+The *wiggle* style oscillates the specified box length dimension
+sinusoidally with the specified amplitude and period.  I.e. the box
+length L as a function of time is given by
+
+
+.. parsed-literal::
+
+   L(t) = L0 + A sin(2\*pi t/Tp)
+
+where L0 is its initial length.  If the amplitude A is a positive
+number the box initially expands, then contracts, etc.  If A is
+negative then the box initially contracts, then expands, etc.  The
+amplitude can be in lattice or box distance units.  See the discussion
+of the units keyword below.
+
+The *variable* style changes the specified box length dimension by
+evaluating a variable, which presumably is a function of time.  The
+variable with *name1* must be an :doc:`equal-style variable <variable>`
+and should calculate a change in box length in units of distance.
+Note that this distance is in box units, not lattice units; see the
+discussion of the *units* keyword below.  The formula associated with
+variable *name1* can reference the current timestep.  Note that it
+should return the "change" in box length, not the absolute box length.
+This means it should evaluate to 0.0 when invoked on the initial
+timestep of the run following the definition of fix deform.  It should
+evaluate to a value > 0.0 to dilate the box at future times, or a
+value < 0.0 to compress the box.
+
+The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of box length
+change, in units of distance/time, i.e. the time-derivative of the
+*name1* variable.  This quantity is used internally by LAMMPS to reset
+atom velocities when they cross periodic boundaries.  It is computed
+internally for the other styles, but you must provide it when using an
+arbitrary variable.
+
+Here is an example of using the *variable* style to perform the same
+box deformation as the *wiggle* style formula listed above, where we
+assume that the current timestep = 0.
+
+
+.. parsed-literal::
+
+   variable A equal 5.0
+   variable Tp equal 10.0
+   variable displace equal "v_A \* sin(2\*PI \* step\*dt/v_Tp)"
+   variable rate equal "2\*PI\*v_A/v_Tp \* cos(2\*PI \* step\*dt/v_Tp)"
+   fix 2 all deform 1 x variable v_displace v_rate remap v
+
+For the *scale*\ , *vel*\ , *erate*\ , *trate*\ , *volume*\ , *wiggle*\ , and
+*variable* styles, the box length is expanded or compressed around its
+mid point.
+
+
+----------
+
+
+For the *xy*\ , *xz*\ , and *yz* parameters, this is the meaning of their
+styles and values.  Note that changing the tilt factors of a triclinic
+box does not change its volume.
+
+The *final*\ , *delta*\ , *vel*\ , and *erate* styles all change the shear
+strain at a "constant engineering shear strain rate".  This means the
+tilt factor changes linearly with time from its initial to final
+value.
+
+For style *final*\ , the final tilt factor is specified.  The value
+can be in lattice or box distance units.  See the discussion of the
+units keyword below.
+
+For style *delta*\ , a plus or minus change in the tilt factor is
+specified.  The value can be in lattice or box distance units.  See
+the discussion of the units keyword below.
+
+For style *vel*\ , a velocity at which the tilt factor changes is
+specified in units of distance/time.  This is effectively an
+"engineering shear strain rate", where rate = V/L0 and L0 is the
+initial box length perpendicular to the direction of shear.  The
+distance can be in lattice or box distance units.  See the discussion
+of the units keyword below.  For example, if the initial tilt factor
+is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
+tilt factor will be 15 Angstroms.  After 2 psec, it will be 25
+Angstroms.
+
+The *erate* style changes a tilt factor at a "constant engineering
+shear strain rate".  The units of the specified shear strain rate are
+1/time.  See the :doc:`units <units>` command for the time units
+associated with different choices of simulation units,
+e.g. picoseconds for "metal" units).  Shear strain is unitless and is
+defined as offset/length, where length is the box length perpendicular
+to the shear direction (e.g. y box length for xy deformation) and
+offset is the displacement distance in the shear direction (e.g. x
+direction for xy deformation) from the unstrained orientation.
+
+The tilt factor T as a function of time will change as
+
+
+.. parsed-literal::
+
+   T(t) = T0 + L0\*erate\*dt
+
+where T0 is the initial tilt factor, L0 is the original length of the
+box perpendicular to the shear direction (e.g. y box length for xy
+deformation), and dt is the elapsed time (in time units).  Thus if
+*erate* R is specified as 0.1 and time units are picoseconds, this
+means the shear strain will increase by 0.1 every picosecond.  I.e. if
+the xy shear strain was initially 0.0, then strain after 1 psec = 0.1,
+strain after 2 psec = 0.2, etc.  Thus the tilt factor would be 0.0 at
+time 0, 0.1\*ybox at 1 psec, 0.2\*ybox at 2 psec, etc, where ybox is the
+original y box length.  R = 1 or 2 means the tilt factor will increase
+by 1 or 2 every picosecond.  R = -0.01 means a decrease in shear
+strain by 0.01 every picosecond.
+
+The *trate* style changes a tilt factor at a "constant true shear
+strain rate".  Note that this is not an "engineering shear strain
+rate", as the other styles are.  Rather, for a "true" rate, the rate
+of change is constant, which means the tilt factor changes
+non-linearly with time from its initial to final value.  The units of
+the specified shear strain rate are 1/time.  See the
+:doc:`units <units>` command for the time units associated with
+different choices of simulation units, e.g. picoseconds for "metal"
+units).  Shear strain is unitless and is defined as offset/length,
+where length is the box length perpendicular to the shear direction
+(e.g. y box length for xy deformation) and offset is the displacement
+distance in the shear direction (e.g. x direction for xy deformation)
+from the unstrained orientation.
+
+The tilt factor T as a function of time will change as
+
+
+.. parsed-literal::
+
+   T(t) = T0 exp(trate\*dt)
+
+where T0 is the initial tilt factor and dt is the elapsed time (in
+time units).  Thus if *trate* R is specified as ln(1.1) and time units
+are picoseconds, this means the shear strain or tilt factor will
+increase by 10% every picosecond.  I.e. if the xy shear strain was
+initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec =
+0.121, etc.  R = ln(2) or ln(3) means the tilt factor will double or
+triple every picosecond.  R = ln(0.99) means the tilt factor will
+shrink by 1% every picosecond.  Note that the change is continuous, so
+running with R = ln(2) for 10 picoseconds does not change the tilt
+factor by a factor of 10, but by a factor of 1024 since it doubles
+every picosecond.  Note that the initial tilt factor must be non-zero
+to use the *trate* option.
+
+Note that shear strain is defined as the tilt factor divided by the
+perpendicular box length.  The *erate* and *trate* styles control the
+tilt factor, but assume the perpendicular box length remains constant.
+If this is not the case (e.g. it changes due to another fix deform
+parameter), then this effect on the shear strain is ignored.
+
+The *wiggle* style oscillates the specified tilt factor sinusoidally
+with the specified amplitude and period.  I.e. the tilt factor T as a
+function of time is given by
+
+
+.. parsed-literal::
+
+   T(t) = T0 + A sin(2\*pi t/Tp)
+
+where T0 is its initial value.  If the amplitude A is a positive
+number the tilt factor initially becomes more positive, then more
+negative, etc.  If A is negative then the tilt factor initially
+becomes more negative, then more positive, etc.  The amplitude can be
+in lattice or box distance units.  See the discussion of the units
+keyword below.
+
+The *variable* style changes the specified tilt factor by evaluating a
+variable, which presumably is a function of time.  The variable with
+*name1* must be an :doc:`equal-style variable <variable>` and should
+calculate a change in tilt in units of distance.  Note that this
+distance is in box units, not lattice units; see the discussion of the
+*units* keyword below.  The formula associated with variable *name1*
+can reference the current timestep.  Note that it should return the
+"change" in tilt factor, not the absolute tilt factor.  This means it
+should evaluate to 0.0 when invoked on the initial timestep of the run
+following the definition of fix deform.
+
+The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of tilt change,
+in units of distance/time, i.e. the time-derivative of the *name1*
+variable.  This quantity is used internally by LAMMPS to reset atom
+velocities when they cross periodic boundaries.  It is computed
+internally for the other styles, but you must provide it when using an
+arbitrary variable.
+
+Here is an example of using the *variable* style to perform the same
+box deformation as the *wiggle* style formula listed above, where we
+assume that the current timestep = 0.
+
+
+.. parsed-literal::
+
+   variable A equal 5.0
+   variable Tp equal 10.0
+   variable displace equal "v_A \* sin(2\*PI \* step\*dt/v_Tp)"
+   variable rate equal "2\*PI\*v_A/v_Tp \* cos(2\*PI \* step\*dt/v_Tp)"
+   fix 2 all deform 1 xy variable v_displace v_rate remap v
+
+
+----------
+
+
+All of the tilt styles change the xy, xz, yz tilt factors during a
+simulation.  In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
+are normally bounded by half the distance of the parallel box length.
+See the discussion of the *flip* keyword below, to allow this bound to
+be exceeded, if desired.
+
+For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
+the xy tilt factor must be between -5 and 5.  Similarly, both xz and
+yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is
+not a limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are all equivalent.
+
+To obey this constraint and allow for large shear deformations to be
+applied via the *xy*\ , *xz*\ , or *yz* parameters, the following
+algorithm is used.  If *prd* is the associated parallel box length (10
+in the example above), then if the tilt factor exceeds the accepted
+range of -5 to 5 during the simulation, then the box is flipped to the
+other limit (an equivalent box) and the simulation continues.  Thus
+for this example, if the initial xy tilt factor was 0.0 and "xy final
+100.0" was specified, then during the simulation the xy tilt factor
+would increase from 0.0 to 5.0, the box would be flipped so that the
+tilt factor becomes -5.0, the tilt factor would increase from -5.0 to
+5.0, the box would be flipped again, etc.  The flip occurs 10 times
+and the final tilt factor at the end of the simulation would be 0.0.
+During each flip event, atoms are remapped into the new box in the
+appropriate manner.
+
+The one exception to this rule is if the 1st dimension in the tilt
+factor (x for xy) is non-periodic.  In that case, the limits on the
+tilt factor are not enforced, since flipping the box in that dimension
+does not change the atom positions due to non-periodicity.  In this
+mode, if you tilt the system to extreme angles, the simulation will
+simply become inefficient due to the highly skewed simulation box.
+
+
+----------
+
+
+Each time the box size or shape is changed, the *remap* keyword
+determines whether atom positions are remapped to the new box.  If
+*remap* is set to *x* (the default), atoms in the fix group are
+remapped; otherwise they are not.  Note that their velocities are not
+changed, just their positions are altered.  If *remap* is set to *v*\ ,
+then any atom in the fix group that crosses a periodic boundary will
+have a delta added to its velocity equal to the difference in
+velocities between the lo and hi boundaries.  Note that this velocity
+difference can include tilt components, e.g. a delta in the x velocity
+when an atom crosses the y periodic boundary.  If *remap* is set to
+*none*\ , then neither of these remappings take place.
+
+Conceptually, setting *remap* to *x* forces the atoms to deform via an
+affine transformation that exactly matches the box deformation.  This
+setting is typically appropriate for solids.  Note that though the
+atoms are effectively "moving" with the box over time, it is not due
+to their having a velocity that tracks the box change, but only due to
+the remapping.  By contrast, setting *remap* to *v* is typically
+appropriate for fluids, where you want the atoms to respond to the
+change in box size/shape on their own and acquire a velocity that
+matches the box change, so that their motion will naturally track the
+box without explicit remapping of their coordinates.
+
+.. note::
+
+   When non-equilibrium MD (NEMD) simulations are performed using
+   this fix, the option "remap v" should normally be used.  This is
+   because :doc:`fix nvt/sllod <fix_nvt_sllod>` adjusts the atom positions
+   and velocities to induce a velocity profile that matches the changing
+   box size/shape.  Thus atom coordinates should NOT be remapped by fix
+   deform, but velocities SHOULD be when atoms cross periodic boundaries,
+   since that is consistent with maintaining the velocity profile already
+   created by fix nvt/sllod.  LAMMPS will warn you if the *remap* setting
+   is not consistent with fix nvt/sllod.
+
+.. note::
+
+   For non-equilibrium MD (NEMD) simulations using "remap v" it is
+   usually desirable that the fluid (or flowing material, e.g. granular
+   particles) stream with a velocity profile consistent with the
+   deforming box.  As mentioned above, using a thermostat such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin <fix_langevin>`
+   (with a bias provided by :doc:`compute temp/deform <compute_temp_deform>`), will typically accomplish
+   that.  If you do not use a thermostat, then there is no driving force
+   pushing the atoms to flow in a manner consistent with the deforming
+   box.  E.g. for a shearing system the box deformation velocity may vary
+   from 0 at the bottom to 10 at the top of the box.  But the stream
+   velocity profile of the atoms may vary from -5 at the bottom to +5 at
+   the top.  You can monitor these effects using the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform <compute_temp_deform>`, and :doc:`compute temp/profile <compute_temp_profile>` commands.  One way to induce
+   atoms to stream consistent with the box deformation is to give them an
+   initial velocity profile, via the :doc:`velocity ramp <velocity>`
+   command, that matches the box deformation rate.  This also typically
+   helps the system come to equilibrium more quickly, even if a
+   thermostat is used.
+
+.. note::
+
+   If a :doc:`fix rigid <fix_rigid>` is defined for rigid bodies, and
+   *remap* is set to *x*\ , then the center-of-mass coordinates of rigid
+   bodies will be remapped to the changing simulation box.  This will be
+   done regardless of whether atoms in the rigid bodies are in the fix
+   deform group or not.  The velocity of the centers of mass are not
+   remapped even if *remap* is set to *v*\ , since :doc:`fix nvt/sllod <fix_nvt_sllod>` does not currently do anything special
+   for rigid particles.  If you wish to perform a NEMD simulation of
+   rigid particles, you can either thermostat them independently or
+   include a background fluid and thermostat the fluid via :doc:`fix nvt/sllod <fix_nvt_sllod>`.
+
+The *flip* keyword allows the tilt factors for a triclinic box to
+exceed half the distance of the parallel box length, as discussed
+above.  If the *flip* value is set to *yes*\ , the bound is enforced by
+flipping the box when it is exceeded.  If the *flip* value is set to
+*no*\ , the tilt will continue to change without flipping.  Note that if
+you apply large deformations, this means the box shape can tilt
+dramatically LAMMPS will run less efficiently, due to the large volume
+of communication needed to acquire ghost atoms around a processor's
+irregular-shaped sub-domain.  For extreme values of tilt, LAMMPS may
+also lose atoms and generate an error.
+
+The *units* keyword determines the meaning of the distance units used
+to define various arguments.  A *box* value selects standard distance
+units as defined by the :doc:`units <units>` command, e.g. Angstroms for
+units = real or metal.  A *lattice* value means the distance units are
+in lattice spacings.  The :doc:`lattice <lattice>` command must have
+been previously used to define the lattice spacing.  Note that the
+units choice also affects the *vel* style parameters since it is
+defined in terms of distance/time.  Also note that the units keyword
+does not affect the *variable* style.  You should use the *xlat*\ ,
+*ylat*\ , *zlat* keywords of the :doc:`thermo\_style <thermo_style>`
+command if you want to include lattice spacings in a variable formula.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix will restore the initial box settings from :doc:`binary restart files <restart>`, which allows the fix to be properly continue
+deformation, when using the start/stop options of the :doc:`run <run>`
+command.  None of the :doc:`fix\_modify <fix_modify>` options are
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
+
+This fix can perform deformation over multiple runs, using the *start*
+and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+You cannot apply x, y, or z deformations to a dimension that is
+shrink-wrapped via the :doc:`boundary <boundary>` command.
+
+You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
+xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`change\_box <change_box>`
+
+Default
+"""""""
+
+The option defaults are remap = x, flip = yes, and units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst
new file mode 100644
index 0000000000..45ae785f89
--- /dev/null
+++ b/doc/src/fix_deposit.rst
@@ -0,0 +1,318 @@
+.. index:: fix deposit
+
+fix deposit command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID deposit N type M seed keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* deposit = style name of this fix command
+* N = # of atoms or molecules to insert
+* type = atom type to assign to inserted atoms (offset for molecule insertion)
+* M = insert a single atom or molecule every M steps
+* seed = random # seed (positive integer)
+* one or more keyword/value pairs may be appended to args
+* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region to use as insertion volume
+       *id* value = *max* or *next*
+         max = atom ID for new atom(s) is max ID of all current atoms plus one
+         next = atom ID for new atom(s) increments by one for every deposition
+       *global* values = lo hi
+         lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
+       *local* values = lo hi delta
+         lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
+         delta = lateral distance within which a neighbor is considered "nearby" (distance units)
+       *near* value = R
+         R = only insert atom/molecule if further than R from existing particles (distance units)
+       *gaussian* values = xmid ymid zmid sigma
+         xmid,ymid,zmid = center of the gaussian distribution (distance units)
+         sigma = width of gaussian distribution (distance units)
+       *attempt* value = Q
+         Q = attempt a single insertion up to Q times
+       *rate* value = V
+         V = z velocity (y in 2d) at which insertion volume moves (velocity units)
+       *vx* values = vxlo vxhi
+         vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
+       *vy* values = vylo vyhi
+         vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
+       *vz* values = vzlo vzhi
+         vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
+       *target* values = tx ty tz
+         tx,ty,tz = location of target point (distance units)
+       *mol* value = template-ID
+         template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
+       *molfrac* values = f1 f2 ... fN
+         f1 to fN = relative probability of creating each of N molecules in template-ID
+       *rigid* value = fix-ID
+         fix-ID = ID of :doc:`fix rigid/small <fix_rigid>` command
+       *shake* value = fix-ID
+         fix-ID = ID of :doc:`fix shake <fix_shake>` command
+       *units* value = *lattice* or *box*
+         lattice = the geometry is defined in lattice units
+         box = the geometry is defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
+   fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
+   fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
+   fix 5 insert deposit 200 2 100 777 region disk gaussian 5.0 5.0 9.0 1.0 units box
+
+Description
+"""""""""""
+
+Insert a single atom or molecule into the simulation domain every M
+timesteps until N atoms or molecules have been inserted.  This is
+useful for simulating deposition onto a surface.  For the remainder of
+this doc page, a single inserted atom or molecule is referred to as a
+"particle".
+
+If inserted particles are individual atoms, they are assigned the
+specified atom type.  If they are molecules, the type of each atom in
+the inserted molecule is specified in the file read by the
+:doc:`molecule <molecule>` command, and those values are added to the
+specified atom type.  E.g. if the file specifies atom types 1,2,3, and
+those are the atom types you want for inserted molecules, then specify
+*type* = 0.  If you specify *type* = 2, the in the inserted molecule
+will have atom types 3,4,5.
+
+All atoms in the inserted particle are assigned to two groups: the
+default group "all" and the group specified in the fix deposit command
+(which can also be "all").
+
+If you are computing temperature values which include inserted
+particles, you will want to use the
+:doc:`compute\_modify <compute_modify>` dynamic option, which insures the
+current number of atoms is used as a normalizing factor each time the
+temperature is computed.
+
+Care must be taken that inserted particles are not too near existing
+atoms, using the options described below.  When inserting particles
+above a surface in a non-periodic box (see the
+:doc:`boundary <boundary>` command), the possibility of a particle
+escaping the surface and flying upward should be considered, since the
+particle may be lost or the box size may grow infinitely large.  A
+:doc:`fix wall/reflect <fix_wall_reflect>` command can be used to
+prevent this behavior.  Note that if a shrink-wrap boundary is used,
+it is OK to insert the new particle outside the box, however the box
+will immediately be expanded to include the new particle. When
+simulating a sputtering experiment it is probably more realistic to
+ignore those atoms using the :doc:`thermo\_modify <thermo_modify>`
+command with the *lost ignore* option and a fixed
+:doc:`boundary <boundary>`.
+
+The fix deposit command must use the *region* keyword to define an
+insertion volume.  The specified region must have been previously
+defined with a :doc:`region <region>` command.  It must be defined with
+side = *in*\ .
+
+.. note::
+
+   LAMMPS checks that the specified region is wholly inside the
+   simulation box.  It can do this correctly for orthonormal simulation
+   boxes.  However for :doc:`triclinic boxes <Howto_triclinic>`, it only
+   tests against the larger orthonormal box that bounds the tilted
+   simulation box.  If the specified region includes volume outside the
+   tilted box, then an insertion will likely fail, leading to a "lost
+   atoms" error.  Thus for triclinic boxes you should insure the
+   specified region is wholly inside the simulation box.
+
+The locations of inserted particles are taken from uniform distributed
+random numbers, unless the *gaussian* keyword is used. Then the
+individual coordinates are taken from a gaussian distribution of
+width *sigma* centered on *xmid,ymid,zmid*\ .
+
+Individual atoms are inserted, unless the *mol* keyword is used.  It
+specifies a *template-ID* previously defined using the
+:doc:`molecule <molecule>` command, which reads files that define one or
+more molecules.  The coordinates, atom types, charges, etc, as well as
+any bond/angle/etc and special neighbor information for the molecule
+can be specified in the molecule file.  See the
+:doc:`molecule <molecule>` command for details.  The only settings
+required to be in each file are the coordinates and types of atoms in
+the molecule.
+
+If the molecule template contains more than one molecule, the relative
+probability of depositing each molecule can be specified by the
+*molfrac* keyword.  N relative probabilities, each from 0.0 to 1.0, are
+specified, where N is the number of molecules in the template.  Each
+time a molecule is deposited, a random number is used to sample from
+the list of relative probabilities.  The N values must sum to 1.0.
+
+If you wish to insert molecules via the *mol* keyword, that will be
+treated as rigid bodies, use the *rigid* keyword, specifying as its
+value the ID of a separate :doc:`fix rigid/small <fix_rigid>`
+command which also appears in your input script.
+
+.. note::
+
+   If you wish the new rigid molecules (and other rigid molecules)
+   to be thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>`
+   or :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
+   "fix\_modify dynamic/dof yes" command for the rigid fix.  This is to
+   inform that fix that the molecule count will vary dynamically.
+
+If you wish to insert molecules via the *mol* keyword, that will have
+their bonds or angles constrained via SHAKE, use the *shake* keyword,
+specifying as its value the ID of a separate :doc:`fix shake <fix_shake>` command which also appears in your input script.
+
+Each timestep a particle is inserted, the coordinates for its atoms
+are chosen as follows.  For insertion of individual atoms, the
+"position" referred to in the following description is the coordinate
+of the atom.  For insertion of molecule, the "position" is the
+geometric center of the molecule; see the :doc:`molecule <molecule>` doc
+page for details.  A random rotation of the molecule around its center
+point is performed, which determines the coordinates all the
+individual atoms.
+
+A random position within the region insertion volume is generated.  If
+neither the *global* or *local* keyword is used, the random position
+is the trial position.  If the *global* keyword is used, the random
+x,y values are used, but the z position of the new particle is set
+above the highest current atom in the simulation by a distance
+randomly chosen between lo/hi.  (For a 2d simulation, this is done for
+the y position.)  If the *local* keyword is used, the z position is
+set a distance between lo/hi above the highest current atom in the
+simulation that is "nearby" the chosen x,y position.  In this context,
+"nearby" means the lateral distance (in x,y) between the new and old
+particles is less than the *delta* setting.
+
+Once a trial x,y,z position has been selected, the insertion is only
+performed if no current atom in the simulation is within a distance R
+of any atom in the new particle, including the effect of periodic
+boundary conditions if applicable.  R is defined by the *near*
+keyword.  Note that the default value for R is 0.0, which will allow
+atoms to strongly overlap if you are inserting where other atoms are
+present.  This distance test is performed independently for each atom
+in an inserted molecule, based on the randomly rotated configuration
+of the molecule.  If this test fails, a new random position within the
+insertion volume is chosen and another trial is made.  Up to Q
+attempts are made.  If the particle is not successfully inserted,
+LAMMPS prints a warning message.
+
+.. note::
+
+   If you are inserting finite size particles or a molecule or
+   rigid body consisting of finite-size particles, then you should
+   typically set R larger than the distance at which any inserted
+   particle may overlap with either a previously inserted particle or an
+   existing particle.  LAMMPS will issue a warning if R is smaller than
+   this value, based on the radii of existing and inserted particles.
+
+The *rate* option moves the insertion volume in the z direction (3d)
+or y direction (2d).  This enables particles to be inserted from a
+successively higher height over time.  Note that this parameter is
+ignored if the *global* or *local* keywords are used, since those
+options choose a z-coordinate for insertion independently.
+
+The vx, vy, and vz components of velocity for the inserted particle
+are set using the values specified for the *vx*\ , *vy*\ , and *vz*
+keywords.  Note that normally, new particles should be a assigned a
+negative vertical velocity so that they move towards the surface.  For
+molecules, the same velocity is given to every particle (no rotation
+or bond vibration).
+
+If the *target* option is used, the velocity vector of the inserted
+particle is changed so that it points from the insertion position
+towards the specified target point.  The magnitude of the velocity is
+unchanged.  This can be useful, for example, for simulating a
+sputtering process.  E.g. the target point can be far away, so that
+all incident particles strike the surface as if they are in an
+incident beam of particles at a prescribed angle.
+
+The *id* keyword determines how atom IDs and molecule IDs are assigned
+to newly deposited particles.  Molecule IDs are only assigned if
+molecules are being inserted.  For the *max* setting, the atom and
+molecule IDs of all current atoms are checked.  Atoms in the new
+particle are assigned IDs starting with the current maximum plus one.
+If a molecule is inserted it is assigned an ID = current maximum plus
+one.  This means that if particles leave the system, the new IDs may
+replace the lost ones.  For the *next* setting, the maximum ID of any
+atom and molecule is stored at the time the fix is defined.  Each time
+a new particle is added, this value is incremented to assign IDs to
+the new atom(s) or molecule.  Thus atom and molecule IDs for deposited
+particles will be consecutive even if particles leave the system over
+time.
+
+The *units* keyword determines the meaning of the distance units used
+for the other deposition parameters.  A *box* value selects standard
+distance units as defined by the :doc:`units <units>` command,
+e.g. Angstroms for units = real or metal.  A *lattice* value means the
+distance units are in lattice spacings.  The :doc:`lattice <lattice>`
+command must have been previously used to define the lattice spacing.
+Note that the units choice affects all the keyword values that have
+units of distance or velocity.
+
+.. note::
+
+   If you are monitoring the temperature of a system where the atom
+   count is changing due to adding particles, you typically should use
+   the :doc:`compute\_modify dynamic yes <compute_modify>` command for the
+   temperature compute you are using.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the deposition to :doc:`binary restart files <restart>`.  This includes information about how many
+particles have been deposited, the random number generator seed, the
+next timestep for deposition, etc.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+.. note::
+
+   For this to work correctly, the timestep must **not** be changed
+   after reading the restart with :doc:`reset\_timestep <reset_timestep>`.
+   The fix will try to detect it and stop with an error.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The specified insertion region cannot be a "dynamic" region, as
+defined by the :doc:`region <region>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix pour <fix_pour>`, :doc:`region <region>`
+
+Default
+"""""""
+
+Insertions are performed for individual atoms, i.e. no *mol* setting
+is defined.  If the *mol* keyword is used, the default for *molfrac*
+is an equal probabilities for all molecules in the template.
+Additional option defaults are id = max, delta = 0.0, near = 0.0,
+attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0,
+and units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst
new file mode 100644
index 0000000000..e2cedd0d9f
--- /dev/null
+++ b/doc/src/fix_dpd_energy.rst
@@ -0,0 +1,127 @@
+.. index:: fix dpd/energy
+
+fix dpd/energy command
+======================
+
+fix dpd/energy/kk command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID dpd/energy
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* dpd/energy = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all dpd/energy
+
+Description
+"""""""""""
+
+Perform constant energy dissipative particle dynamics (DPD-E)
+integration.  This fix updates the internal energies for particles in
+the group at each timestep.  It must be used in conjunction with a
+deterministic integrator (e.g. :doc:`fix nve <fix_nve>`) that updates
+the particle positions and velocities.
+
+For fix *dpd/energy*\ , the particle internal temperature is related to
+the particle internal energy through a mesoparticle equation of state.
+An additional fix must be specified that defines the equation of state
+for each particle, e.g. :doc:`fix eos/cv <fix_eos_cv>`.
+
+This fix must be used with the :doc:`pair\_style dpd/fdt/energy <pair_style>` command.
+
+Note that numerous variants of DPD can be specified by choosing an
+appropriate combination of the integrator and :doc:`pair\_style dpd/fdt/energy <pair_style>` command.  DPD under isoenergetic conditions
+can be specified by using fix *dpd/energy*\ , fix *nve* and pair\_style
+*dpd/fdt/energy*\ .  DPD under isoenthalpic conditions can
+be specified by using fix *dpd/energy*\ , fix *nph* and pair\_style
+*dpd/fdt/energy*\ .  Examples of each DPD variant are provided in the
+examples/USER/dpd directory.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix must be used with an additional fix that specifies time
+integration, e.g. :doc:`fix nve <fix_nve>`.
+
+The fix *dpd/energy* requires the *dpd* :doc:`atom\_style <atom_style>`
+to be used in order to properly account for the particle internal
+energies and temperature.
+
+The fix *dpd/energy* must be used with an additional fix that specifies the
+mesoparticle equation of state for each particle.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>` :doc:`fix eos/cv <fix_eos_cv>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Lisal1:
+
+
+
+**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
+particle dynamics at isothermal, isobaric, isoenergetic, and
+isoenthalpic conditions using Shardlow-like splitting algorithms.",
+J. Chem. Phys., 135, 204105 (2011).
+
+.. _Larentzos3:
+
+
+
+**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
+W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
+Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+Laboratory, Aberdeen Proving Ground, MD (2014).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst
new file mode 100644
index 0000000000..66895f2538
--- /dev/null
+++ b/doc/src/fix_dpd_source.rst
@@ -0,0 +1,124 @@
+.. index:: fix edpd/source
+
+fix edpd/source command
+=======================
+
+fix tdpd/source command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID edpd/source keyword values ...
+   fix ID group-ID tdpd/source cc_index keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* edpd/source or tdpd/source = style name of this fix command
+* index (only specified for tdpd/source) = index of chemical species (1 to Nspecies)
+* keyword = *sphere* or *cuboid*
+  
+  .. parsed-literal::
+  
+       *sphere* values = cx,cy,cz,radius,source
+         cx,cy,cz = x,y,z center of spherical domain (distance units)
+         radius = radius of a spherical domain (distance units)
+         source = heat source or concentration source (flux units, see below)
+       *cuboid* values = cx,cy,cz,dLx,dLy,dLz,source
+         cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units)
+         dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units)
+         source = heat source or concentration source (flux units, see below)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all edpd/source sphere 0.0 0.0 0.0 5.0 0.01
+   fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01
+   fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01
+   fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01
+
+Description
+"""""""""""
+
+Fix *edpd/source* adds a heat source as an external heat flux to each
+atom in a spherical or cuboid domain, where the *source* is in units
+of energy/time.  Fix *tdpd/source* adds an external concentration
+source of the chemical species specified by *index* as an external
+concentration flux for each atom in a spherical or cuboid domain,
+where the *source* is in units of mole/volume/time.
+
+This command can be used to give an additional heat/concentration
+source term to atoms in a simulation, such as for a simulation of a
+heat conduction with a source term (see Fig.12 in :ref:`(Li2014) <Li2014b>`)
+or diffusion with a source term (see Fig.1 in :ref:`(Li2015) <Li2015b>`), as
+an analog of a periodic Poiseuille flow problem.
+
+If the *sphere* keyword is used, the *cx,cy,cz,radius* defines a
+spherical domain to apply the source flux to.
+
+If the *cuboid* keyword is used, the *cx,cy,cz,dLx,dLy,dLz* defines a
+cuboid domain to apply the source flux to.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MESO package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Fix *edpd/source* must be used with the :doc:`pair\_style edpd <pair_meso>` command.  Fix *tdpd/source* must be used with the
+:doc:`pair\_style tdpd <pair_meso>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style edpd <pair_meso>`, :doc:`pair\_style tdpd <pair_meso>`,
+:doc:`compute edpd/temp/atom <compute_edpd_temp_atom>`, :doc:`compute tdpd/cc/atom <compute_tdpd_cc_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Li2014b:
+
+
+
+**(Li2014)** Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis,
+"Energy-conserving dissipative particle dynamics with
+temperature-dependent properties", J. Comput. Phys., 265: 113-127
+(2014). DOI: 10.1016/j.jcp.2014.02.003
+
+.. _Li2015b:
+
+
+
+**(Li2015)** Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis,
+"Transport dissipative particle dynamics model for mesoscopic
+advection-diffusion-reaction problems", J. Chem. Phys., 143: 014101
+(2015).  DOI: 10.1063/1.4923254
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst
new file mode 100644
index 0000000000..9490f58f01
--- /dev/null
+++ b/doc/src/fix_drag.rst
@@ -0,0 +1,74 @@
+.. index:: fix drag
+
+fix drag command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID drag x y z fmag delta
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* drag = style name of this fix command
+* x,y,z = coord to drag atoms towards
+* fmag = magnitude of force to apply to each atom (force units)
+* delta = cutoff distance inside of which force         is not applied (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix center small-molecule drag 0.0 10.0 0.0 5.0 2.0
+
+Description
+"""""""""""
+
+Apply a force to each atom in a group to drag it towards the point
+(x,y,z).  The magnitude of the force is specified by fmag.  If an atom
+is closer than a distance delta to the point, then the force is not
+applied.
+
+Any of the x,y,z values can be specified as NULL which means do not
+include that dimension in the distance calculation or force
+application.
+
+This command can be used to steer one or more atoms to a new location
+in the simulation.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global 3-vector of forces, which can be accessed
+by various :doc:`output commands <Howto_output>`.  This is the total
+force on the group of atoms by the drag force.  The vector values
+calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix spring <fix_spring>`, :doc:`fix spring/self <fix_spring_self>`,
+:doc:`fix spring/rg <fix_spring_rg>`, :doc:`fix smd <fix_smd>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst
new file mode 100644
index 0000000000..4a39c7abc8
--- /dev/null
+++ b/doc/src/fix_drude.rst
@@ -0,0 +1,59 @@
+.. index:: fix drude
+
+fix drude command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID drude flag1 flag2 ... flagN
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* drude = style name of this fix command
+* flag1 flag2 ... flagN = Drude flag for each atom type (1 to N) in the system
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all drude 1 1 0 1 0 2 2 2
+   fix 1 all drude C C N C N D D D
+
+Description
+"""""""""""
+
+Assign each atom type in the system to be one of 3 kinds of atoms
+within the Drude polarization model. This fix is designed to be used
+with the :doc:`thermalized Drude oscillator model <Howto_drude>`.
+Polarizable models in LAMMPS are described on the :doc:`Howto polarizable <Howto_polarizable>` doc page.
+
+The three possible types can be designated with an integer (0,1,2)
+or capital letter (N,C,D):
+
+* 0 or N = non-polarizable atom (not part of Drude model)
+* 1 or C = Drude core
+* 2 or D = Drude electron
+
+Restrictions
+""""""""""""
+
+
+This fix should be invoked before any other commands that implement
+the Drude oscillator model, such as :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair\_style thole <pair_thole>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair\_style thole <pair_thole>`
+
+**Default:** None
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst
new file mode 100644
index 0000000000..58c3628dce
--- /dev/null
+++ b/doc/src/fix_drude_transform.rst
@@ -0,0 +1,231 @@
+.. index:: fix drude/transform/direct
+
+fix drude/transform/direct command
+==================================
+
+fix drude/transform/inverse command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = *drude/transform/direct* or *drude/transform/inverse*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 all drude/transform/direct
+   fix 1 all drude/transform/inverse
+
+Description
+"""""""""""
+
+Transform the coordinates of Drude oscillators from real to reduced
+and back for thermalizing the Drude oscillators as described in
+:ref:`(Lamoureux) <Lamoureux1>` using a Nose-Hoover thermostat.  This fix is
+designed to be used with the :doc:`thermalized Drude oscillator model <Howto_drude>`.  Polarizable models in LAMMPS are described
+on the :doc:`Howto polarizable <Howto_polarizable>` doc page.
+
+Drude oscillators are a pair of atoms representing a single
+polarizable atom.  Ideally, the mass of Drude particles would vanish
+and their positions would be determined self-consistently by iterative
+minimization of the energy, the cores' positions being fixed.  It is
+however more efficient and it yields comparable results, if the Drude
+oscillators (the motion of the Drude particle relative to the core)
+are thermalized at a low temperature.  In that case, the Drude
+particles need a small mass.
+
+The thermostats act on the reduced degrees of freedom, which are
+defined by the following equations.  Note that in these equations
+upper case denotes atomic or center of mass values and lower case
+denotes Drude particle or dipole values. Primes denote the transformed
+(reduced) values, while bare letters denote the original values.
+
+Masses:
+
+.. math::
+
+   \begin{equation} M' = M + m \end{equation}
+
+
+.. math::
+
+   \begin{equation} m' = \frac {M\, m } {M'} \end{equation}
+
+Positions:
+
+.. math::
+
+   \begin{equation} X' = \frac {M\, X + m\, x} {M'}\end{equation}
+
+
+.. math::
+
+   \begin{equation} x' = x - X \end{equation}
+
+Velocities:
+
+.. math::
+
+   \begin{equation} V' = \frac {M\, V + m\, v} {M'}\end{equation}
+
+
+.. math::
+
+   \begin{equation} v' = v - V \end{equation}
+
+Forces:
+
+.. math::
+
+   \begin{equation} F' = F + f \end{equation}
+
+
+.. math::
+
+   \begin{equation} f' = \frac { M\, f - m\, F} {M'}\end{equation}
+
+This transform conserves the total kinetic energy
+
+.. math::
+
+   \begin{equation} \frac 1 2 \, (M\, V^2\ + m\, v^2)
+   = \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) \end{equation}
+
+and the virial defined with absolute positions
+
+.. math::
+
+   \begin{equation} X\, F + x\, f = X'\, F' + x'\, f' \end{equation}
+
+
+----------
+
+
+This fix requires each atom know whether it is a Drude particle or
+not.  You must therefore use the :doc:`fix drude <fix_drude>` command to
+specify the Drude status of each atom type.
+
+.. note::
+
+   only the Drude core atoms need to be in the group specified for
+   this fix. A Drude electron will be transformed together with its core
+   even if it is not itself in the group.  It is safe to include Drude
+   electrons or non-polarizable atoms in the group. The non-polarizable
+   atoms will simply not be transformed.
+
+
+----------
+
+
+This fix does NOT perform time integration. It only transform masses,
+coordinates, velocities and forces. Thus you must use separate time
+integration fixes, like :doc:`fix nve <fix_nve>` or :doc:`fix npt <fix_nh>` to actually update the velocities and positions of
+atoms.  In order to thermalize the reduced degrees of freedom at
+different temperatures, two Nose-Hoover thermostats must be defined,
+acting on two distinct groups.
+
+.. note::
+
+   The *fix drude/transform/direct* command must appear before any
+   Nose-Hoover thermostatting fixes.  The *fix drude/transform/inverse*
+   command must appear after any Nose-Hoover thermostatting fixes.
+
+Example:
+
+
+.. parsed-literal::
+
+   fix fDIRECT all drude/transform/direct
+   fix fNVT gCORES nvt temp 300.0 300.0 100
+   fix fNVT gDRUDES nvt temp 1.0 1.0 100
+   fix fINVERSE all drude/transform/inverse
+   compute TDRUDE all temp/drude
+   thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
+
+In this example, *gCORES* is the group of the atom cores and *gDRUDES*
+is the group of the Drude particles (electrons). The centers of mass
+of the Drude oscillators will be thermostatted at 300.0 and the
+internal degrees of freedom will be thermostatted at 1.0.  The
+temperatures of cores and Drude particles, in center-of-mass and
+relative coordinates, are calculated using :doc:`compute temp/drude <compute_temp_drude>`
+
+In addition, if you want to use a barostat to simulate a system at
+constant pressure, only one of the Nose-Hoover fixes must be *npt*\ ,
+the other one should be *nvt*\ . You must add a *compute temp/com* and a
+*fix\_modify* command so that the temperature of the *npt* fix be just
+that of its group (the Drude cores) but the pressure be the overall
+pressure *thermo\_press*.
+
+Example:
+
+
+.. parsed-literal::
+
+   compute cTEMP_CORE gCORES temp/com
+   fix fDIRECT all drude/transform/direct
+   fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500
+   fix_modify fNPT temp cTEMP_CORE press thermo_press
+   fix fNVT gDRUDES nvt temp 5.0 5.0 100
+   fix fINVERSE all drude/transform/inverse
+
+In this example, *gCORES* is the group of the atom cores and *gDRUDES*
+is the group of the Drude particles. The centers of mass of the Drude
+oscillators will be thermostatted at 298.0 and the internal degrees of
+freedom will be thermostatted at 5.0. The whole system will be
+barostatted at 1.0.
+
+In order to avoid the flying ice cube problem (irreversible transfer
+of linear momentum to the center of mass of the system), you may need
+to add a *fix momentum* command:
+
+
+.. parsed-literal::
+
+   fix fMOMENTUM all momentum 100 linear 1 1 1
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix drude <fix_drude>`,
+:doc:`fix langevin/drude <fix_langevin_drude>`,
+:doc:`compute temp/drude <compute_temp_drude>`,
+:doc:`pair\_style thole <pair_thole>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Lamoureux1:
+
+
+
+**(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst
new file mode 100644
index 0000000000..b99161934f
--- /dev/null
+++ b/doc/src/fix_dt_reset.rst
@@ -0,0 +1,118 @@
+.. index:: fix dt/reset
+
+fix dt/reset command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* dt/reset = style name of this fix command
+* N = re-compute dt every N timesteps
+* Tmin = minimum dt allowed which can be NULL (time units)
+* Tmax = maximum dt allowed which can be NULL (time units)
+* Xmax = maximum distance for an atom to move in one timestep (distance units)
+* zero or more keyword/value pairs may be appended
+* keyword = *emax* or *units*
+
+
+.. parsed-literal::
+
+     *emax* value = Emax
+       Emax = maximum kinetic energy change for an atom in one timestep (energy units)
+     *units* value = *lattice* or *box*
+       lattice = Xmax is defined in lattice units
+       box = Xmax is defined in simulation box units
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 5 all dt/reset 10 1.0e-5 0.01 0.1
+   fix 5 all dt/reset 10 0.01 2.0 0.2 units box
+   fix 5 all dt/reset 5 NULL 0.001 0.5 emax 30 units box
+
+Description
+"""""""""""
+
+Reset the timestep size every N steps during a run, so that no atom
+moves further than the specified *Xmax* distance, based on current
+atom velocities and forces.  Optionally an additional criterion is
+imposed by the *emax* keyword, so that no atom's kinetic energy
+changes by more than the specified *Emax*\ .
+
+This can be useful when starting from a configuration with overlapping
+atoms, where forces will be large.  Or it can be useful when running
+an impact simulation where one or more high-energy atoms collide with
+a solid, causing a damage cascade.
+
+This fix overrides the timestep size setting made by the
+:doc:`timestep <timestep>` command.  The new timestep size *dt* is
+computed in the following manner.
+
+For each atom, the timestep is computed that would cause it to
+displace *Xmax* on the next integration step, as a function of its
+current velocity and force.  Since performing this calculation exactly
+would require the solution to a quartic equation, a cheaper estimate
+is generated.  The estimate is conservative in that the atom's
+displacement is guaranteed not to exceed *Xmax*\ , though it may be
+smaller.
+
+In addition if the *emax* keyword is used, the specified *Emax* value
+is enforced as a limit on how much an atom's kinetic energy can
+change.  If the timestep required is even smaller than for the *Xmax*
+displacement, then the smaller timestep is used.
+
+Given this putative timestep for each atom, the minimum timestep value
+across all atoms is computed.  Then the *Tmin* and *Tmax* bounds are
+applied, if specified.  If one (or both) is specified as NULL, it is
+not applied.
+
+When the :doc:`run style <run_style>` is *respa*\ , this fix resets the
+outer loop (largest) timestep, which is the same timestep that the
+:doc:`timestep <timestep>` command sets.
+
+Note that the cumulative simulation time (in time units), which
+accounts for changes in the timestep size as a simulation proceeds,
+can be accessed by the :doc:`thermo\_style time <thermo_style>` keyword.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar stores the last
+timestep on which the timestep was reset to a new value.
+
+The scalar value calculated by this fix is "intensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`timestep <timestep>`
+
+Default
+"""""""
+
+The option defaults are units = lattice, and no emax kinetic energy
+limit.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst
new file mode 100644
index 0000000000..c5228a0cc3
--- /dev/null
+++ b/doc/src/fix_efield.rst
@@ -0,0 +1,186 @@
+.. index:: fix efield
+
+fix efield command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID efield ex ey ez keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* efield = style name of this fix command
+* ex,ey,ez = E-field component values (electric field units)
+* any of ex,ey,ez can be a variable (see below)
+* zero or more keyword/value pairs may be appended to args
+* keyword = *region* or *energy*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region atoms must be in to have added force
+       *energy* value = v_name
+         v_name = variable with name that calculates the potential energy of each atom in the added E-field
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix kick external-field efield 1.0 0.0 0.0
+   fix kick external-field efield 0.0 0.0 v_oscillate
+
+Description
+"""""""""""
+
+Add a force F = qE to each charged atom in the group due to an
+external electric field being applied to the system.  If the system
+contains point-dipoles, also add a torque on the dipoles due to the
+external electric field.
+
+For charges, any of the 3 quantities defining the E-field components
+can be specified as an equal-style or atom-style
+:doc:`variable <variable>`, namely *ex*\ , *ey*\ , *ez*\ .  If the value is a
+variable, it should be specified as v\_name, where name is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its value used to determine the E-field component.
+
+For point-dipoles, equal-style variables can be used, but atom-style
+variables are not currently supported, since they imply a spatial
+gradient in the electric field which means additional terms with
+gradients of the field are required for the force and torque on
+dipoles.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent E-field.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent E-field
+with optional time-dependence as well.
+
+If the *region* keyword is used, the atom must also be in the
+specified geometric :doc:`region <region>` in order to have force added
+to it.
+
+
+----------
+
+
+Adding a force or torque to atoms implies a change in their potential
+energy as they move or rotate due to the applied E-field.
+
+For dynamics via the "run" command, this energy can be optionally
+added to the system's potential energy for thermodynamic output (see
+below).  For energy minimization via the "minimize" command, this
+energy must be added to the system's potential energy to formulate a
+self-consistent minimization problem (see below).
+
+The *energy* keyword is not allowed if the added field is a constant
+vector (ex,ey,ez), with all components defined as numeric constants
+and not as variables.  This is because LAMMPS can compute the energy
+for each charged particle directly as E = -x dot qE = -q (x\*ex + y\*ey
++ z\*ez), so that -Grad(E) = F.  Similarly for point-dipole particles
+the energy can be computed as E = -mu dot E = -(mux\*ex + muy\*ey +
+muz\*ez).
+
+The *energy* keyword is optional if the added force is defined with
+one or more variables, and if you are performing dynamics via the
+:doc:`run <run>` command.  If the keyword is not used, LAMMPS will set
+the energy to 0.0, which is typically fine for dynamics.
+
+The *energy* keyword is required if the added force is defined with
+one or more variables, and you are performing energy minimization via
+the "minimize" command for charged particles.  It is not required for
+point-dipoles, but a warning is issued since the minimizer in LAMMPS
+does not rotate dipoles, so you should not expect to be able to
+minimize the orientation of dipoles in an applied electric field.
+
+The *energy* keyword specifies the name of an atom-style
+:doc:`variable <variable>` which is used to compute the energy of each
+atom as function of its position.  Like variables used for *ex*\ , *ey*\ ,
+*ez*\ , the energy variable is specified as v\_name, where name is the
+variable name.
+
+Note that when the *energy* keyword is used during an energy
+minimization, you must insure that the formula defined for the
+atom-style :doc:`variable <variable>` is consistent with the force
+variable formulas, i.e. that -Grad(E) = F.  For example, if the force
+due to the electric field were a spring-like F = kx, then the energy
+formula should be E = -0.5kx\^2.  If you don't do this correctly, the
+minimization will not converge properly.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential "energy" inferred by the added force due to
+the electric field to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`.  This is a fictitious
+quantity but is needed so that the :doc:`minimize <minimize>` command
+can include the forces added by this fix in a consistent manner.
+I.e. there is a decrease in potential energy when atoms move in the
+direction of the added force due to the electric field.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to the added forces on atoms to the
+system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+The default is *virial no*
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix adding its forces. Default is the outermost level.
+
+This fix computes a global scalar and a global 3-vector of forces,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar is the potential energy discussed above.  The vector is the
+total force added to the group of atoms.  The scalar and vector values
+calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.  You should not
+specify force components with a variable that has time-dependence for
+use with a minimizer, since the minimizer increments the timestep as
+the iteration count during the minimization.
+
+.. note::
+
+   If you want the fictitious potential energy associated with the
+   added forces to be included in the total potential energy of the
+   system (the quantity being minimized), you MUST enable the
+   :doc:`fix\_modify <fix_modify>` *energy* option for this fix.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix addforce <fix_addforce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst
new file mode 100644
index 0000000000..4c4487b11b
--- /dev/null
+++ b/doc/src/fix_ehex.rst
@@ -0,0 +1,209 @@
+.. index:: fix ehex
+
+fix ehex command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ehex nevery F keyword value
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ehex  = style name of this fix command
+* nevery = add/subtract heat every this many timesteps
+* F = energy flux into the reservoir (energy/time units)
+* zero or more keyword/value pairs may be appended to args
+* keyword = *region* or *constrain* or *com* or *hex*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region (reservoir) atoms must be in for added thermostatting force
+       *constrain* value = none
+         apply the constraint algorithm (SHAKE or RATTLE) again at the end of the timestep
+       *com* value = none
+         rescale all sites of a constrained cluster of atom if its COM is in the reservoir
+       *hex* value = none
+         omit the coordinate correction to recover the HEX algorithm
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   # Lennard-Jones, from examples/in.ehex.lj
+
+   fix fnve all nve
+   # specify regions rhot and rcold
+   ...
+   fix fhot all ehex 1 0.15 region rhot
+   fix fcold all ehex 1 -0.15 region rcold
+
+   # SPC/E water, from examples/in.ehex.spce
+   fix fnve all nve
+   # specify regions rhot and rcold
+   ...
+   fix fhot all ehex 1 0.075 region rhot constrain com
+   fix fcold all ehex 1 -0.075 region rcold constrain com
+   fix frattle all rattle 1e-10 400 0 b 1 a 1
+
+Description
+"""""""""""
+
+This fix implements the asymmetric version of the enhanced heat
+exchange algorithm :ref:`(Wirnsberger) <Wirnsberger>`. The eHEX algorithm is
+an extension of the heat exchange algorithm :ref:`(Ikeshoji) <Ikeshoji>` and
+adds an additional coordinate integration to account for higher-order
+truncation terms in the operator splitting.  The original HEX
+algorithm (implemented as :doc:`fix heat <fix_heat>`) is known to
+exhibit a slight energy drift limiting the accessible simulation times
+to a few nanoseconds.  This issue is greatly improved by the new
+algorithm decreasing the energy drift by at least a factor of a
+hundred (LJ and SPC/E water) with little computational overhead.
+
+In both algorithms (non-translational) kinetic energy is constantly
+swapped between regions (reservoirs) to impose a heat flux onto the
+system.  The equations of motion are therefore modified if a particle
+:math:`i` is located inside a reservoir :math:`\Gamma_k` where :math:`k>0`.  We
+use :math:`\Gamma_0` to label those parts of the simulation box which
+are not thermostatted.)  The input parameter *region-ID* of this fix
+corresponds to :math:`k`.  The energy swap is modelled by introducing an
+additional thermostatting force to the equations of motion, such that
+the time evolution of coordinates and momenta of particle :math:`i`
+becomes :ref:`(Wirnsberger) <Wirnsberger>`
+
+.. image:: Eqs/fix_ehex_eom.jpg
+   :align: center
+
+The thermostatting force is given by
+
+.. image:: Eqs/fix_ehex_f.jpg
+   :align: center
+
+where :math:`m_i` is the mass and :math:`k(\mathbf r_i)` maps the particle
+position to the respective reservoir. The quantity
+:math:`F_{\Gamma_{k(\mathbf r_i)}}` corresponds to the input parameter
+*F*\ , which is the energy flux into the reservoir. Furthermore,
+:math:`K_{\Gamma_{k(\mathbf r_i)}}` and :math:`v_{\Gamma_{k(\mathbf r_i)}}`
+denote the non-translational kinetic energy and the center of mass
+velocity of that reservoir. The thermostatting force does not affect
+the center of mass velocities of the individual reservoirs and the
+entire simulation box. A derivation of the equations and details on
+the numerical implementation with velocity Verlet in LAMMPS can be
+found in reference "(Wirnsberger)"#\_Wirnsberger.
+
+.. note::
+
+   This fix only integrates the thermostatting force and must be
+   combined with another integrator, such as :doc:`fix nve <fix_nve>`, to
+   solve the full equations of motion.
+
+This fix is different from a thermostat such as :doc:`fix nvt <fix_nh>`
+or :doc:`fix temp/rescale <fix_temp_rescale>` in that energy is
+added/subtracted continually.  Thus if there isn't another mechanism
+in place to counterbalance this effect, the entire system will heat or
+cool continuously.
+
+.. note::
+
+   If heat is subtracted from the system too aggressively so that
+   the group's kinetic energy would go to zero, then LAMMPS will halt
+   with an error message. Increasing the value of *nevery* means that
+   heat is added/subtracted less frequently but in larger portions.  The
+   resulting temperature profile will therefore be the same.
+
+This fix will default to :doc:`fix\_heat <fix_heat>` (HEX algorithm) if
+the keyword *hex* is specified.
+
+
+----------
+
+
+**Compatibility with SHAKE and RATTLE (rigid molecules)**\ :
+
+This fix is compatible with :doc:`fix shake <fix_shake>` and :doc:`fix rattle <fix_shake>`. If either of these constraining algorithms is
+specified in the input script and the keyword *constrain* is set, the
+bond distances will be corrected a second time at the end of the
+integration step.  It is recommended to specify the keyword *com* in
+addition to the keyword *constrain*\ . With this option all sites of a
+constrained cluster are rescaled, if its center of mass is located
+inside the region. Rescaling all sites of a cluster by the same factor
+does not introduce any velocity components along fixed bonds. No
+rescaling takes place if the center of mass lies outside the region.
+
+.. note::
+
+   You can only use the keyword *com* along with *constrain*\ .
+
+To achieve the highest accuracy it is recommended to use :doc:`fix rattle <fix_shake>` with the keywords *constrain* and *com* as
+shown in the second example. Only if RATTLE is employed, the velocity
+constraints will be satisfied.
+
+.. note::
+
+   Even if RATTLE is used and the keywords *com* and *constrain*
+   are both set, the coordinate constraints will not necessarily be
+   satisfied up to the target precision. The velocity constraints are
+   satisfied as long as all sites of a cluster are rescaled (keyword
+   *com*\ ) and the cluster does not span adjacent reservoirs. The current
+   implementation of the eHEX algorithm introduces a small error in the
+   bond distances, which goes to zero with order three in the
+   timestep. For example, in a simulation of SPC/E water with a timestep
+   of 2 fs the maximum relative error in the bond distances was found to
+   be on the order of :math:`10^{-7}` for relatively large
+   temperature gradients.  A higher precision can be achieved by
+   decreasing the timestep.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the RIGID package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix heat <fix_heat>`, :doc:`fix thermal/conductivity <fix_thermal_conductivity>`, :doc:`compute temp <compute_temp>`, :doc:`compute temp/region <compute_temp_region>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Ikeshoji:
+
+
+
+**(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
+
+.. _Wirnsberger:
+
+
+
+**(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143,
+124104 (2015).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst
new file mode 100644
index 0000000000..3329681333
--- /dev/null
+++ b/doc/src/fix_electron_stopping.rst
@@ -0,0 +1,210 @@
+.. index:: fix electron/stopping
+
+fix electron/stopping command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID electron/stopping Ecut file keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* electron/stopping = style name of this fix command
+* Ecut = minimum kinetic energy for electronic stopping (energy units)
+* file = name of the file containing the electronic stopping power table
+* zero or more keyword/value pairs may be appended to args
+* keyword = *region* or *minneigh*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = region, whose atoms will be affected by this fix
+       *minneigh* value = minneigh
+         minneigh = minimum number of neighbors an atom to have stopping applied
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix el all electron/stopping 10.0 elstop-table.txt
+   fix el all electron/stopping 10.0 elstop-table.txt minneigh 3
+   fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk
+
+Description
+"""""""""""
+
+This fix implements inelastic energy loss for fast projectiles in solids. It
+applies a friction force to fast moving atoms to slow them down due to
+:ref:`electronic stopping <elstopping>` (energy lost via electronic collisions per
+unit of distance). This fix should be used for simulation of irradiation
+damage or ion implantation, where the ions can lose noticeable amounts of
+energy from electron excitations. If the electronic stopping power is not
+considered, the simulated range of the ions can be severely overestimated
+(:ref:`Nordlund98 <Nordlund98>`, :ref:`Nordlund95 <Nordlund95>`).
+
+The electronic stopping is implemented by applying a friction force
+to each atom as:
+
+
+.. math::
+
+   \begin{equation}\vec{F}_i = \vec{F}^0_i - \frac{\vec{v}_i}{\|\vec{v}_i\|} \cdot S_e\end{equation}
+
+where :math:`\vec{F}_i` is the resulting total force on the atom.
+:math:`\vec{F}^0_i` is the original force applied to the atom, :math:`\vec{v}_i` is
+its velocity and :math:`S_e` is the stopping power of the ion.
+
+.. note::
+
+   In addition to electronic stopping, atomic cascades and irradiation
+   simulations require the use of an adaptive timestep (see
+   :doc:`fix dt/reset <fix_dt_reset>`) and the repulsive ZBL potential (see
+   :doc:`ZBL <pair_zbl>` potential) or similar. Without these settings the
+   interaction between the ion and the target atoms will be faulty. It is also
+   common to use in such simulations a thermostat (:doc:`fix\_nvt <fix_nh>`) in
+   the borders of the simulation cell.
+
+.. note::
+
+   This fix removes energy from fast projectiles without depositing it as a
+   heat to the simulation cell. Such implementation might lead to the unphysical
+   results when the amount of energy deposited to the electronic system is large,
+   e.g. simulations of Swift Heavy Ions (energy per nucleon of 100 keV/amu or
+   higher) or multiple projectiles. You could compensate energy loss by coupling
+   bulk atoms with some thermostat or control heat transfer between electronic and
+   atomic subsystems with the two-temperature model (:doc:`fix\_ttm <fix_ttm>`).
+
+At low velocities the electronic stopping is negligible. The electronic
+friction is not applied to atoms whose kinetic energy is smaller than *Ecut*\ ,
+or smaller than the lowest energy value given in the table in *file*\ .
+Electronic stopping should be applied only when a projectile reaches bulk
+material. This fix scans neighbor list and excludes atoms with fewer than
+*minneigh* neighbors (by default one). If the pair potential cutoff is large,
+minneigh should be increased, though not above the number of nearest neighbors
+in bulk material. An alternative is to disable the check for neighbors by
+setting *minneigh* to zero and using the *region* keyword. This is necessary
+when running simulations of cluster bombardment.
+
+If the *region* keyword is used, the atom must also be in the specified
+geometric :doc:`region <region>` in order to have electronic stopping applied to
+it. This is useful if the position of the bulk material is fixed. By default
+the electronic stopping is applied everywhere in the simulation cell.
+
+
+----------
+
+
+The energy ranges and stopping powers are read from the file *file*\ .
+Lines starting with *#* and empty lines are ignored. Otherwise each
+line must contain exactly **N+1** numbers, where **N** is the number of atom
+types in the simulation.
+
+The first column is the energy for which the stopping powers on that
+line apply. The energies must be sorted from the smallest to the largest.
+The other columns are the stopping powers :math:`S_e` for each atom type,
+in ascending order, in force :doc:`units <units>`. The stopping powers for
+intermediate energy values are calculated with linear interpolation between
+2 nearest points.
+
+For example:
+
+
+.. parsed-literal::
+
+   # This is a comment
+   #       atom-1    atom-2
+   # eV    eV/Ang    eV/Ang  # units metal
+    10        0        0
+   250       60       80
+   750      100      150
+
+If an atom which would have electronic stopping applied to it has a
+kinetic energy higher than the largest energy given in *file*\ , LAMMPS
+will exit with an error message.
+
+The stopping power depends on the energy of the ion and the target
+material. The electronic stopping table can be obtained from
+scientific publications, experimental databases or by using
+:ref:`SRIM <SRIM>` software. Other programs such as :ref:`CasP <CasP>` or
+:ref:`PASS <PASS>` can calculate the energy deposited as a function
+of the impact parameter of the ion; these results can be used
+to derive the stopping power.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` options are not supported.
+
+This fix computes a global scalar, which can be accessed by various
+:doc:`output commands <Howto_output>`. The scalar is the total energy
+loss from electronic stopping applied by this fix since the start of
+the latest run. It is considered "intensive".
+
+The *start/stop* keywords of the :doc:`run <run>` command have no effect
+on this fix.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Default
+"""""""
+
+The default is no limitation by region, and minneigh = 1.
+
+
+----------
+
+
+.. _elstopping:
+
+
+
+**(electronic stopping)** Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping\_power\_%28particle\_radiation%29
+
+.. _Nordlund98:
+
+
+
+**(Nordlund98)** Nordlund, Kai, et al.  Physical Review B 57.13 (1998): 7556.
+
+.. _Nordlund95:
+
+
+
+**(Nordlund95)** Nordlund, Kai. Computational materials science 3.4 (1995): 448-456.
+
+.. _SRIM:
+
+
+
+**(SRIM)** SRIM webpage: http://www.srim.org/
+
+.. _CasP:
+
+
+
+**(CasP)** CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp\_en.html
+
+.. _PASS:
+
+
+
+**(PASS)** PASS webpage: https://www.sdu.dk/en/DPASS
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst
new file mode 100644
index 0000000000..bef732a82d
--- /dev/null
+++ b/doc/src/fix_enforce2d.rst
@@ -0,0 +1,83 @@
+.. index:: fix enforce2d
+
+fix enforce2d command
+=====================
+
+fix enforce2d/kk command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID enforce2d
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* enforce2d = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 5 all enforce2d
+
+Description
+"""""""""""
+
+Zero out the z-dimension velocity and force on each atom in the group.
+This is useful when running a 2d simulation to insure that atoms do
+not move from their initial z coordinate.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst
new file mode 100644
index 0000000000..850d0ecde3
--- /dev/null
+++ b/doc/src/fix_eos_cv.rst
@@ -0,0 +1,79 @@
+.. index:: fix eos/cv
+
+fix eos/cv command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID eos/cv cv
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* eos/cv = style name of this fix command
+* cv = constant-volume heat capacity (energy/temperature units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all eos/cv 0.01
+
+Description
+"""""""""""
+
+Fix *eos/cv* applies a mesoparticle equation of state to relate the
+particle internal energy (u\_i) to the particle internal temperature
+(dpdTheta\_i).  The *eos/cv* mesoparticle equation of state requires
+the constant-volume heat capacity, and is defined as follows:
+
+.. image:: Eqs/fix_eos-cv.jpg
+   :align: center
+
+where Cv is the constant-volume heat capacity, u\_cond is the internal
+conductive energy, and u\_mech is the internal mechanical energy.  Note
+that alternative definitions of the mesoparticle equation of state are
+possible.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command also requires use of the :doc:`atom\_style dpd <atom_style>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix shardlow <fix_shardlow>`, :doc:`pair dpd/fdt <pair_dpd_fdt>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Larentzos4:
+
+
+
+**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
+W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
+Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+Laboratory, Aberdeen Proving Ground, MD (2014).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst
new file mode 100644
index 0000000000..3953d31f2d
--- /dev/null
+++ b/doc/src/fix_eos_table.rst
@@ -0,0 +1,134 @@
+.. index:: fix eos/table
+
+fix eos/table command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID eos/table style file N keyword
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* eos/table = style name of this fix command
+* style = *linear* = method of interpolation
+* file = filename containing the tabulated equation of state
+* N = use N values in *linear* tables
+* keyword = name of table keyword corresponding to table file
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all eos/table linear eos.table 100000 KEYWORD
+
+Description
+"""""""""""
+
+Fix *eos/table* applies a tabulated mesoparticle equation of state to
+relate the particle internal energy (u\_i) to the particle internal
+temperature (dpdTheta\_i).
+
+Fix *eos/table* creates interpolation tables of length *N* from
+internal energy values listed in a file as a function of internal
+temperature.
+
+The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy values at each of *N* internal
+temperatures, and vice versa.  During a simulation, these tables are
+used to interpolate internal energy or temperature values as needed.
+The interpolation is done with the *linear* style.
+
+For the *linear* style, the internal temperature is used to find 2
+surrounding table values from which an internal energy is computed by
+linear interpolation, and vice versa.
+
+The filename specifies a file containing tabulated internal
+temperature and internal energy values.  The keyword specifies a
+section of the file.  The format of this file is described below.
+
+
+----------
+
+
+The format of a tabulated file is as follows (without the
+parenthesized comments):
+
+
+.. parsed-literal::
+
+   # EOS TABLE                (one or more comment or blank lines)
+
+   KEYWORD                    (keyword is first text on line)
+   N 500                      (N  parameter)
+                              (blank)
+   1   1.00 0.000             (index, internal temperature, internal energy)
+   2   1.02 0.001
+   ...
+   500 10.0 0.500
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.  The first line begins with a keyword which
+identifies the section.  The line can contain additional text, but the
+initial text must match the argument specified in the fix command.
+
+The next line lists the number of table entries.  The parameter "N" is
+required and its value is the number of table entries that follow.
+Note that this may be different than the *N* specified in the :doc:`fix eos/table <fix_eos_table>` command.  Let Ntable = *N* in the fix
+command, and Nfile = "N" in the tabulated file.  What LAMMPS does is a
+preliminary interpolation by creating splines using the Nfile
+tabulated values as nodal points.  It uses these to interpolate as
+needed to generate energy and temperature values at Ntable different
+points.  The resulting tables of length Ntable are then used as
+described above, when computing energy and temperature relationships.
+This means that if you want the interpolation tables of length Ntable
+to match exactly what is in the tabulated file (with effectively no
+preliminary interpolation), you should set Ntable = Nfile.
+
+Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+the internal temperature (in temperature units), the 3rd value is the
+internal energy (in energy units).
+
+Note that the internal temperature and internal energy values must
+increase from one line to the next.
+
+Note that one file can contain many sections, each with a tabulated
+potential.  LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command also requires use of the :doc:`atom\_style dpd <atom_style>`
+command.
+
+The equation of state must be a monotonically increasing function.
+
+An error will occur if the internal temperature or internal energies
+are not within the table cutoffs.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix shardlow <fix_shardlow>`, :doc:`pair dpd/fdt <pair_dpd_fdt>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst
new file mode 100644
index 0000000000..622e24dd79
--- /dev/null
+++ b/doc/src/fix_eos_table_rx.rst
@@ -0,0 +1,232 @@
+.. index:: fix eos/table/rx
+
+fix eos/table/rx command
+========================
+
+fix eos/table/rx/kk command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID eos/table/rx style file1 N keyword ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* eos/table/rx = style name of this fix command
+* style = *linear* = method of interpolation
+* file1 = filename containing the tabulated equation of state
+* N = use N values in *linear* tables
+* keyword = name of table keyword corresponding to table file
+* file2 = filename containing the heats of formation of each species (optional)
+* deltaHf = heat of formation for a single species in energy units (optional)
+* energyCorr = energy correction in energy units (optional)
+* tempCorrCoeff = temperature correction coefficient (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table
+   fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5
+   fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 0.025 0.0
+
+Description
+"""""""""""
+
+Fix *eos/table/rx* applies a tabulated mesoparticle equation
+of state to relate the concentration-dependent particle internal
+energy (u\_i) to the particle internal temperature (dpdTheta\_i).
+
+The concentration-dependent particle internal energy (u\_i) is
+computed according to the following relation:
+
+.. image:: Eqs/fix_eos_table_rx.jpg
+   :align: center
+
+where *m* is the number of species, *c\_i,j* is the concentration of
+species *j* in particle *i*\ , *u\_j* is the internal energy of species j,
+*DeltaH\_f,j* is the heat of formation of species *j*\ , N is the number of
+molecules represented by the coarse-grained particle, kb is the
+Boltzmann constant, and T is the temperature of the system.  Additionally,
+it is possible to modify the concentration-dependent particle internal
+energy relation by adding an energy correction, temperature-dependent
+correction, and/or a molecule-dependent correction.  An energy correction can
+be specified as a constant (in energy units).  A temperature correction can be
+specified by multiplying a temperature correction coefficient by the
+internal temperature.  A molecular correction can be specified by
+by multiplying a molecule correction coefficient by the average number of
+product gas particles in the coarse-grain particle.
+
+Fix *eos/table/rx* creates interpolation tables of length *N* from *m*
+internal energy values of each species *u\_j* listed in a file as a
+function of internal temperature.  During a simulation, these tables
+are used to interpolate internal energy or temperature values as needed.
+The interpolation is done with the *linear* style.  For the *linear* style,
+the internal temperature is used to find 2 surrounding table values from
+which an internal energy is computed by linear interpolation.  A secant
+solver is used to determine the internal temperature from the internal energy.
+
+The first filename specifies a file containing tabulated internal
+temperature and *m* internal energy values for each species *u\_j*.
+The keyword specifies a section of the file.  The format of this
+file is described below.
+
+The second filename specifies a file containing heat of formation
+*DeltaH\_f,j* for each species.
+
+In cases where the coarse-grain particle represents a single molecular
+species (i.e., no reactions occur and fix *rx* is not present in the input file),
+fix *eos/table/rx* can be applied in a similar manner to fix *eos/table*
+within a non-reactive DPD simulation.  In this case, the heat of formation
+filename is replaced with the heat of formation value for the single species.
+Additionally, the energy correction and temperature correction coefficients may
+also be specified as fix arguments.
+
+
+----------
+
+
+The format of a tabulated file is as follows (without the
+parenthesized comments):
+
+
+.. parsed-literal::
+
+   # EOS TABLE                (one or more comment or blank lines)
+
+   KEYWORD                    (keyword is first text on line)
+   N 500 h2 no2 n2 ... no     (N  parameter species1 species2 ... speciesN)
+                              (blank)
+   1   1.00 0.000 ... 0.0000  (index, internal temperature, internal energy of species 1, ..., internal energy of species m)
+   2   1.02 0.001 ... 0.0002
+   ...
+   500 10.0 0.500 ... 1.0000
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.  The first line begins with a keyword which
+identifies the section.  The line can contain additional text, but the
+initial text must match the argument specified in the fix command.
+
+The next line lists the number of table entries and the species names
+that correspond with all the species listed in the reaction equations
+through the *fix rx* command.
+The parameter "N" is required and its value is the number of table
+entries that follow.  Let Nfile = "N" in the tabulated file.
+What LAMMPS does is a preliminary interpolation by creating splines
+using the Nfile tabulated values as nodal points.
+
+Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+the internal temperature (in temperature units), the 3rd value until
+the *m+3* value are the internal energies of the m species (in energy units).
+
+Note that all internal temperature and internal energy values must
+increase from one line to the next.
+
+Note that one file can contain many sections, each with a tabulated
+potential.  LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+
+
+----------
+
+
+The format of a heat of formation file is as follows (without the
+parenthesized comments):
+
+
+.. parsed-literal::
+
+   # HEAT OF FORMATION TABLE  (one or more comment or blank lines)
+
+                              (blank)
+   h2      0.00               (species name, heat of formation)
+   no2     0.34
+   n2      0.00
+   ...
+   no      0.93
+
+Note that the species can be listed in any order.  The tag that is
+used as the species name must correspond with the tags used to define
+the reactions with the :doc:`fix rx <fix_rx>` command.
+
+Alternatively, corrections to the EOS can be included by specifying
+three additional columns that correspond to the energy correction,
+the temperature correction coefficient and molecule correction
+coefficient.  In this case, the format of the file is as follows:
+
+
+.. parsed-literal::
+
+   # HEAT OF FORMATION TABLE     (one or more comment or blank lines)
+
+                                 (blank)
+   h2      0.00 1.23 0.025  0.0  (species name, heat of formation, energy correction, temperature correction coefficient, molecule correction coefficient)
+   no2     0.34 0.00 0.000 -1.76
+   n2      0.00 0.00 0.000 -1.76
+   ...
+   no      0.93 0.00 0.000 -1.76
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command also requires use of the :doc:`atom\_style dpd <atom_style>`
+command.
+
+The equation of state must be a monotonically increasing function.
+
+An error will occur if the internal temperature or internal energies
+are not within the table cutoffs.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix rx <fix_rx>`,
+:doc:`pair dpd/fdt <pair_dpd_fdt>`
+
+**Default:** none
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst
new file mode 100644
index 0000000000..24954ec3da
--- /dev/null
+++ b/doc/src/fix_evaporate.rst
@@ -0,0 +1,112 @@
+.. index:: fix evaporate
+
+fix evaporate command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID evaporate N M region-ID seed
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* evaporate = style name of this fix command
+* N = delete atoms every this many timesteps
+* M = number of atoms to delete each time
+* region-ID = ID of region within which to perform deletions
+* seed = random number seed to use for choosing atoms to delete
+* zero or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *molecule*
+       *molecule* value = *no* or *yes*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 solvent evaporate 1000 10 surface 49892
+   fix 1 solvent evaporate 1000 10 surface 38277 molecule yes
+
+Description
+"""""""""""
+
+Remove M atoms from the simulation every N steps.  This can be used,
+for example, to model evaporation of solvent particles or molecules
+(i.e. drying) of a system.  Every N steps, the number of atoms in the
+fix group and within the specified region are counted.  M of these are
+chosen at random and deleted.  If there are less than M eligible
+particles, then all of them are deleted.
+
+If the setting for the *molecule* keyword is *no*\ , then only single
+atoms are deleted.  In this case, you should insure you do not delete
+only a portion of a molecule (only some of its atoms), or LAMMPS will
+soon generate an error when it tries to find those atoms.  LAMMPS will
+warn you if any of the atoms eligible for deletion have a non-zero
+molecule ID, but does not check for this at the time of deletion.
+
+If the setting for the *molecule* keyword is *yes*\ , then when an atom
+is chosen for deletion, the entire molecule it is part of is deleted.
+The count of deleted atoms is incremented by the number of atoms in
+the molecule, which may make it exceed *M*\ .  If the molecule ID of the
+chosen atom is 0, then it is assumed to not be part of a molecule, and
+just the single atom is deleted.
+
+As an example, if you wish to delete 10 water molecules every *N*
+steps, you should set *M* to 30.  If only the water's oxygen atoms
+were in the fix group, then two hydrogen atoms would be deleted when
+an oxygen atom is selected for deletion, whether the hydrogen atoms
+are inside the evaporation region or not.
+
+Note that neighbor lists are re-built on timesteps that atoms are
+removed.  Thus you should not remove atoms too frequently or you will
+incur overhead due to the cost of building neighbor lists.
+
+.. note::
+
+   If you are monitoring the temperature of a system where the atom
+   count is changing due to evaporation, you typically should use the
+   :doc:`compute\_modify dynamic yes <compute_modify>` command for the
+   temperature compute you are using.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar, which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+number of deleted atoms.  The scalar value calculated by this fix is
+"intensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix deposit <fix_deposit>`
+
+Default
+"""""""
+
+The option defaults are molecule = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst
new file mode 100644
index 0000000000..fcd283ccc2
--- /dev/null
+++ b/doc/src/fix_external.rst
@@ -0,0 +1,187 @@
+.. index:: fix external
+
+fix external command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID external mode args
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* external = style name of this fix command
+* mode = *pf/callback* or *pf/array*
+  
+  .. parsed-literal::
+  
+       *pf/callback* args = Ncall Napply
+         Ncall = make callback every Ncall steps
+         Napply = apply callback forces every Napply steps
+       *pf/array* args = Napply
+         Napply = apply array forces every Napply steps
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all external pf/callback 1 1
+   fix 1 all external pf/callback 100 1
+   fix 1 all external pf/array 10
+
+Description
+"""""""""""
+
+This fix allows external programs that are running LAMMPS through its
+:doc:`library interface <Howto_library>` to modify certain LAMMPS
+properties on specific timesteps, similar to the way other fixes do.
+The external driver can be a :doc:`C/C++ or Fortran program <Howto_library>` or a :doc:`Python script <Python_head>`.
+
+
+----------
+
+
+If mode is *pf/callback* then the fix will make a callback every
+*Ncall* timesteps or minimization iterations to the external program.
+The external program computes forces on atoms by setting values in an
+array owned by the fix.  The fix then adds these forces to each atom
+in the group, once every *Napply* steps, similar to the way the :doc:`fix addforce <fix_addforce>` command works.  Note that if *Ncall* >
+*Napply*\ , the force values produced by one callback will persist, and
+be used multiple times to update atom forces.
+
+The callback function "foo" is invoked by the fix as:
+
+
+.. parsed-literal::
+
+   foo(void \*ptr, bigint timestep, int nlocal, int \*ids, double \*\*x, double \*\*fexternal);
+
+The arguments are as follows:
+
+* ptr = pointer provided by and simply passed back to external driver
+* timestep = current LAMMPS timestep
+* nlocal = # of atoms on this processor
+* ids = list of atom IDs on this processor
+* x = coordinates of atoms on this processor
+* fexternal = forces to add to atoms on this processor
+
+Note that timestep is a "bigint" which is defined in src/lmptype.h,
+typically as a 64-bit integer.
+
+Fexternal are the forces returned by the driver program.
+
+The fix has a set\_callback() method which the external driver can call
+to pass a pointer to its foo() function.  See the
+couple/lammps\_quest/lmpqst.cpp file in the LAMMPS distribution for an
+example of how this is done.  This sample application performs
+classical MD using quantum forces computed by a density functional
+code `Quest <quest_>`_.
+
+.. _quest: http://dft.sandia.gov/Quest
+
+
+
+
+----------
+
+
+If mode is *pf/array* then the fix simply stores force values in an
+array.  The fix adds these forces to each atom in the group, once
+every *Napply* steps, similar to the way the :doc:`fix addforce <fix_addforce>` command works.
+
+The name of the public force array provided by the FixExternal
+class is
+
+
+.. parsed-literal::
+
+   double \*\*fexternal;
+
+It is allocated by the FixExternal class as an (N,3) array where N is
+the number of atoms owned by a processor.  The 3 corresponds to the
+fx, fy, fz components of force.
+
+It is up to the external program to set the values in this array to
+the desired quantities, as often as desired.  For example, the driver
+program might perform an MD run in stages of 1000 timesteps each.  In
+between calls to the LAMMPS :doc:`run <run>` command, it could retrieve
+atom coordinates from LAMMPS, compute forces, set values in fexternal,
+etc.
+
+
+----------
+
+
+To use this fix during energy minimization, the energy corresponding
+to the added forces must also be set so as to be consistent with the
+added forces.  Otherwise the minimization will not converge correctly.
+
+This can be done from the external driver by calling this public
+method of the FixExternal class:
+
+
+.. parsed-literal::
+
+   void set_energy(double eng);
+
+where eng is the potential energy.  Eng is an extensive quantity,
+meaning it should be the sum over per-atom energies of all affected
+atoms.  It should also be provided in :doc:`energy units <units>`
+consistent with the simulation.  See the details below for how to
+insure this energy setting is used appropriately in a minimization.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential "energy" set by the external driver to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+needed so that the :doc:`minimize <minimize>` command can include the
+forces added by this fix in a consistent manner.  I.e. there is a
+decrease in potential energy when atoms move in the direction of the
+added force.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to the interactions computed by the
+external program to the system's virial as part of :doc:`thermodynamic output <thermo_style>`. The default is *virial yes*
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the potential
+energy discussed above.  The scalar stored by this fix is "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the fictitious potential energy associated with the
+   added forces to be included in the total potential energy of the
+   system (the quantity being minimized), you MUST enable the
+   :doc:`fix\_modify <fix_modify>` *energy* option for this fix.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst
new file mode 100644
index 0000000000..b914c23940
--- /dev/null
+++ b/doc/src/fix_ffl.rst
@@ -0,0 +1,142 @@
+.. index:: fix ffl
+
+fix ffl command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID id-group ffl tau Tstart Tstop seed [flip-type]
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ffl = style name of this fix command
+* tau = thermostat parameter (positive real)
+* Tstart, Tstop = temperature ramp during the run
+* seed = random number seed to use for generating noise (positive integer)
+* one more value may be appended
+  
+  .. parsed-literal::
+  
+         flip-type  = determines the flipping type, can be chosen between rescale - no_flip - hard - soft, if no flip type is given, rescale will be chosen by default
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 boundary ffl 10 300 300 31415
+   fix 1 all ffl 100 500 500 9265 soft
+
+Description
+"""""""""""
+
+Apply a Fast-Forward Langevin Equation (FFL) thermostat as described
+in :ref:`(Hijazi) <Hijazi>`. Contrary to
+:doc:`fix langevin <fix_langevin>`, this fix performs both
+thermostatting and evolution of the Hamiltonian equations of motion, so it
+should not be used together with :doc:`fix nve <fix_nve>` -- at least not
+on the same atom groups.
+
+The time-evolution of a single particle undergoing Langevin dynamics is described
+by the equations
+
+
+.. math::
+
+   \begin{equation} \frac {dq}{dt} = \frac{p}{m}, \end{equation}
+
+
+.. math::
+
+   \begin{equation} \frac {dp}{dt} = -\gamma p + W + F, \end{equation}
+
+where :math:`F` is the physical force, :math:`\gamma` is the friction coefficient, and :math:`W` is a
+Gaussian random force.
+
+The friction coefficient is the inverse of the thermostat parameter : :math:`\gamma = 1/\tau`, with :math:`\tau` the thermostat parameter *tau*\ .
+The thermostat parameter is given in the time units, :math:`\gamma` is in inverse time units.
+
+Equilibrium sampling a temperature T is obtained by specifying the
+target value as the *Tstart* and *Tstop* arguments, so that the internal
+constants depending on the temperature are computed automatically.
+
+The random number *seed* must be a positive integer.  A Marsaglia random
+number generator is used.  Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+The flipping type *flip-type* can be chosen between 4 types described in
+:ref:`(Hijazi) <Hijazi>`. The flipping operation occurs during the thermostatting
+step and it flips the momenta of the atoms. If no\_flip is chosen, no flip
+will be executed and the integration will be the same as a standard
+Langevin thermostat :ref:`(Bussi) <Bussi3>`. The other flipping types are : rescale - hard - soft.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+The instantaneous values of the extended variables are written to
+:doc:`binary restart files <restart>`.  Because the state of the random
+number generator is not saved in restart files, this means you cannot
+do "exact" restarts with this fix, where the simulation continues on
+the same as if no restart had taken place. However, in a statistical
+sense, a restarted simulation should produce the same behavior.
+Note however that you should use a different seed each time you
+restart, otherwise the same sequence of random numbers will be used
+each time, which might lead to stochastic synchronization and
+subtle artifacts in the sampling.
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".
+
+Restrictions
+""""""""""""
+
+
+In order to perform constant-pressure simulations please use
+:doc:`fix press/berendsen <fix_press_berendsen>`, rather than
+:doc:`fix npt <fix_nh>`, to avoid duplicate integration of the
+equations of motion.
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix viscous <fix_viscous>`, :doc:`fix nvt <fix_nh>`, :doc:`pair\_style dpd/tstat <pair_dpd>`, :doc:`fix gld <fix_gld>`, :doc:`fix gle <fix_gle>`
+
+
+----------
+
+
+.. _Hijazi:
+
+
+
+.. _Bussi3:
+
+**(Hijazi)** M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018)
+
+
+**(Bussi)** G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst
new file mode 100644
index 0000000000..50db945a37
--- /dev/null
+++ b/doc/src/fix_filter_corotate.rst
@@ -0,0 +1,104 @@
+.. index:: fix filter/corotate
+
+fix filter/corotate command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID filter/corotate keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* one or more constraint/value pairs are appended
+* constraint = *b* or *a* or *t* or *m*
+  
+  .. parsed-literal::
+  
+       *b* values = one or more bond types
+       *a* values = one or more angle types
+       *t* values = one or more atom types
+       *m* value = one or more mass values
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   timestep 8
+   run_style respa 3 2 8 bond 1 pair 2 kspace 3
+   fix cor all filter/corotate m 1.0
+
+   fix cor all filter/corotate b 4 19 a 3 5 2
+
+Description
+"""""""""""
+
+This fix implements a corotational filter for a mollified impulse
+method. In biomolecular simulations, it allows the usage of larger
+timesteps for long-range electrostatic interactions.  For details, see
+:ref:`(Fath) <Fath2017>`.
+
+When using :doc:`run\_style respa <run_style>` for a biomolecular
+simulation with high-frequency covalent bonds, the outer time-step is
+restricted to below ~ 4fs due to resonance problems. This fix filters
+the outer stage of the respa and thus a larger (outer) time-step can
+be used. Since in large biomolecular simulations the computation of
+the long-range electrostatic contributions poses a major bottleneck,
+this can significantly accelerate the simulation.
+
+The filter computes a cluster decomposition of the molecular structure
+following the criteria indicated by the options a, b, t and m. This
+process is similar to the approach in :doc:`fix shake <fix_shake>`,
+however, the clusters are not kept constrained. Instead, the position
+is slightly modified only for the computation of long-range forces. A
+good cluster decomposition constitutes in building clusters which
+contain the fastest covalent bonds inside clusters.
+
+If the clusters are chosen suitably, the :doc:`run\_style respa <run_style>` is stable for outer time-steps of at least 8fs.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about these fixes is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to these fixes.  No global or per-atom quantities are
+stored by these fixes for access by various :doc:`output commands <Howto_output>`.  No parameter of these fixes can be used
+with the *start/stop* keywords of the :doc:`run <run>` command.  These
+fixes are not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Currently, it does not support :doc:`molecule templates <molecule>`.
+
+Related commands
+""""""""""""""""
+
+**Default:** none
+
+
+----------
+
+
+.. _Fath2017:
+
+
+
+**(Fath)** Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst
new file mode 100644
index 0000000000..fa1d65c999
--- /dev/null
+++ b/doc/src/fix_flow_gauss.rst
@@ -0,0 +1,190 @@
+.. index:: fix flow/gauss
+
+fix flow/gauss command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID flow/gauss xflag yflag zflag keyword
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* flow/gauss = style name of this fix command
+* xflag,yflag,zflag = 0 or 1
+  
+  .. parsed-literal::
+  
+         0 = do not conserve current in this dimension
+         1 = conserve current in this dimension
+
+* zero or more keyword/value pairs may be appended
+* keyword = *energy*
+  
+  .. parsed-literal::
+  
+       *energy* value = no or yes
+         no = do not compute work done by this fix
+         yes = compute work done by this fix
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix GD fluid flow/gauss 1 0 0
+   fix GD fluid flow/gauss 1 1 1 energy yes
+
+Description
+"""""""""""
+
+This fix implements the Gaussian dynamics (GD) method to simulate a
+system at constant mass flux :ref:`(Strong) <Strong>`. GD is a
+nonequilibrium molecular dynamics simulation method that can be used
+to study fluid flows through pores, pipes, and channels. In its
+original implementation GD was used to compute the pressure required
+to achieve a fixed mass flux through an opening.  The flux can be
+conserved in any combination of the directions, x, y, or z, using
+xflag,yflag,zflag. This fix does not initialize a net flux through a
+system, it only conserves the center-of-mass momentum that is present
+when the fix is declared in the input script. Use the
+:doc:`velocity <velocity>` command to generate an initial center-of-mass
+momentum.
+
+GD applies an external fluctuating gravitational field that acts as a
+driving force to keep the system away from equilibrium. To maintain
+steady state, a profile-unbiased thermostat must be implemented to
+dissipate the heat that is added by the driving force. :doc:`Compute temp/profile <compute_temp_profile>` can be used to implement a
+profile-unbiased thermostat.
+
+A common use of this fix is to compute a pressure drop across a pipe,
+pore, or membrane. The pressure profile can be computed in LAMMPS with
+:doc:`compute stress/atom <compute_stress_atom>` and :doc:`fix ave/chunk <fix_ave_chunk>`, or with the hardy method in :doc:`fix atc <fix_atc>`. Note that the simple :doc:`compute stress/atom <compute_stress_atom>` method is only accurate away
+from inhomogeneities in the fluid, such as fixed wall atoms. Further,
+the computed pressure profile must be corrected for the acceleration
+applied by GD before computing a pressure drop or comparing it to
+other methods, such as the pump method :ref:`(Zhu) <Zhu>`. The pressure
+correction is discussed and described in :ref:`(Strong) <Strong>`.
+
+For a complete example including the considerations discussed
+above, see the examples/USER/flow\_gauss directory.
+
+.. note::
+
+   Only the flux of the atoms in group-ID will be conserved. If the
+   velocities of the group-ID atoms are coupled to the velocities of
+   other atoms in the simulation, the flux will not be conserved. For
+   example, in a simulation with fluid atoms and harmonically constrained
+   wall atoms, if a single thermostat is applied to group *all*\ , the
+   fluid atom velocities will be coupled to the wall atom velocities, and
+   the flux will not be conserved. This issue can be avoided by
+   thermostatting the fluid and wall groups separately.
+
+Adding an acceleration to atoms does work on the system. This added
+energy can be optionally subtracted from the potential energy for the
+thermodynamic output (see below) to check that the timestep is small
+enough to conserve energy. Since the applied acceleration is
+fluctuating in time, the work cannot be computed from a potential. As
+a result, computing the work is slightly more computationally
+expensive than usual, so it is not performed by default. To invoke the
+work calculation, use the *energy* keyword. The
+:doc:`fix\_modify <fix_modify>` *energy* option also invokes the work
+calculation, and overrides an *energy no* setting here. If neither
+*energy yes* or *fix\_modify energy yes* are set, the global scalar
+computed by the fix will return zero.
+
+.. note::
+
+   In order to check energy conservation, any other fixes that do
+   work on the system must have *fix\_modify energy yes* set as well. This
+   includes thermostat fixes and any constraints that hold the positions
+   of wall atoms fixed, such as :doc:`fix spring/self <fix_spring_self>`.
+
+If this fix is used in a simulation with the :doc:`rRESPA <run_style>`
+integrator, the applied acceleration must be computed and applied at the same
+rRESPA level as the interactions between the flowing fluid and the obstacle.
+The rRESPA level at which the acceleration is applied can be changed using
+the :doc:`fix\_modify <fix_modify>` *respa* option discussed below. If the
+flowing fluid and the obstacle interact through multiple interactions that are
+computed at different rRESPA levels, then there must be a separate flow/gauss
+fix for each level. For example, if the flowing fluid and obstacle interact
+through pairwise and long-range Coulomb interactions, which are computed at
+rRESPA levels 3 and 4, respectively, then there must be two separate
+flow/gauss fixes, one that specifies *fix\_modify respa 3* and one with
+*fix\_modify respa 4*.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to subtract the work done from the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows the user to set at which level of the :doc:`rRESPA <run_style>`
+integrator the fix computes and adds the external acceleration. Default is the
+outermost level.
+
+This fix computes a global scalar and a global 3-vector of forces,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar is the negative of the work done on the system, see above
+discussion.  The vector is the total force that this fix applied to
+the group of atoms on the current timestep.  The scalar and vector
+values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix addforce <fix_addforce>`, :doc:`compute temp/profile <compute_temp_profile>`, :doc:`velocity <velocity>`
+
+Default
+"""""""
+
+The option default for the *energy* keyword is energy = no.
+
+
+----------
+
+
+.. _Strong:
+
+
+
+**(Strong)** Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).
+
+.. _Evans2:
+
+
+
+**(Evans)** Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).
+
+.. _Zhu:
+
+
+
+**(Zhu)** Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst
new file mode 100644
index 0000000000..773eacf509
--- /dev/null
+++ b/doc/src/fix_freeze.rst
@@ -0,0 +1,101 @@
+.. index:: fix freeze
+
+fix freeze command
+==================
+
+fix freeze/kk command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID freeze
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* freeze = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 2 bottom freeze
+
+Description
+"""""""""""
+
+Zero out the force and torque on a granular particle.  This is useful
+for preventing certain particles from moving in a simulation.  The
+:doc:`granular pair styles <pair_gran>` also detect if this fix has been
+defined and compute interactions between frozen and non-frozen
+particles appropriately, as if the frozen particle has infinite mass.
+A similar functionality for normal (point) particles can be obtained
+using :doc:`fix setforce <fix_setforce>`.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global 3-vector of forces, which can be accessed
+by various :doc:`output commands <Howto_output>`.  This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix.  The vector values calculated by this fix are
+"extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the GRANULAR package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+There can only be a single freeze fix defined.  This is because other
+the :doc:`granular pair styles <pair_gran>` treat frozen particles
+differently and need to be able to reference a single group to which
+this fix is applied.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style sphere <atom_style>`, :doc:`fix setforce <fix_setforce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst
new file mode 100644
index 0000000000..9f64be8699
--- /dev/null
+++ b/doc/src/fix_gcmc.rst
@@ -0,0 +1,500 @@
+.. index:: fix gcmc
+
+fix gcmc command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* gcmc = style name of this fix command
+* N = invoke this fix every N steps
+* X = average number of GCMC exchanges to attempt every N steps
+* M = average number of MC moves to attempt every N steps
+* type = atom type for inserted atoms (must be 0 if mol keyword used)
+* seed = random # seed (positive integer)
+* T = temperature of the ideal gas reservoir (temperature units)
+* mu = chemical potential of the ideal gas reservoir (energy units)
+* displace = maximum Monte Carlo translation distance (length units)
+* zero or more keyword/value pairs may be appended to args
+  
+  .. parsed-literal::
+  
+     keyword = *mol*\ , *region*\ , *maxangle*\ , *pressure*\ , *fugacity_coeff*, *full_energy*, *charge*\ , *group*\ , *grouptype*\ , *intra_energy*, *tfac_insert*, or *overlap_cutoff*
+       *mol* value = template-ID
+         template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
+       *mcmoves* values = Patomtrans Pmoltrans Pmolrotate
+         Patomtrans = proportion of atom translation MC moves
+         Pmoltrans = proportion of molecule translation MC moves
+         Pmolrotate = proportion of molecule rotation MC moves
+       *rigid* value = fix-ID
+         fix-ID = ID of :doc:`fix rigid/small <fix_rigid>` command
+       *shake* value = fix-ID
+         fix-ID = ID of :doc:`fix shake <fix_shake>` command
+       *region* value = region-ID
+         region-ID = ID of region where GCMC exchanges and MC moves are allowed
+       *maxangle* value = maximum molecular rotation angle (degrees)
+       *pressure* value = pressure of the gas reservoir (pressure units)
+       *fugacity_coeff* value = fugacity coefficient of the gas reservoir (unitless)
+       *full_energy* = compute the entire system energy when performing GCMC exchanges and MC moves
+       *charge* value = charge of inserted atoms (charge units)
+       *group* value = group-ID
+         group-ID = group-ID for inserted atoms (string)
+       *grouptype* values = type group-ID
+         type = atom type (int)
+         group-ID = group-ID for inserted atoms (string)
+       *intra_energy* value = intramolecular energy (energy units)
+       *tfac_insert* value = scale up/down temperature of inserted atoms (unitless)
+       *overlap_cutoff* value = maximum pair distance for overlap rejection (distance units)
+       *max* value = Maximum number of molecules allowed in the system
+       *min* value = Minimum number of molecules allowed in the system
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
+   fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
+   fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
+
+Description
+"""""""""""
+
+This fix performs grand canonical Monte Carlo (GCMC) exchanges of
+atoms or molecules with an imaginary ideal gas
+reservoir at the specified T and chemical potential (mu) as discussed
+in :ref:`(Frenkel) <Frenkel>`. It also
+attempts  Monte Carlo (MC) moves (translations and molecule
+rotations) within the simulation cell or
+region. If used with the :doc:`fix nvt <fix_nh>`
+command, simulations in the grand canonical ensemble (muVT, constant
+chemical potential, constant volume, and constant temperature) can be
+performed.  Specific uses include computing isotherms in microporous
+materials, or computing vapor-liquid coexistence curves.
+
+Every N timesteps the fix attempts both GCMC exchanges
+(insertions or deletions) and MC moves of gas atoms or molecules.
+On those timesteps, the average number of attempted GCMC exchanges is X,
+while the average number of attempted MC moves is M.
+For GCMC exchanges of either molecular or atomic gasses,
+these exchanges can be either deletions or insertions,
+with equal probability.
+
+The possible choices for MC moves are translation of an atom,
+translation of a molecule, and rotation of a molecule.
+The relative amounts of each are determined by the optional
+*mcmoves* keyword (see below).
+The default behavior is as follows.
+If the *mol* keyword is used, only molecule translations
+and molecule rotations are performed with equal probability.
+Conversely, if the *mol* keyword is not used, only atom
+translations are performed.
+M should typically be
+chosen to be approximately equal to the expected number of gas atoms
+or molecules of the given type within the simulation cell or region,
+which will result in roughly one MC move per atom or molecule
+per MC cycle.
+
+All inserted particles are always added to two groups: the default
+group "all" and the fix group specified in the fix command.
+In addition, particles are also added to any groups
+specified by the *group* and *grouptype* keywords.  If inserted
+particles are individual atoms, they are assigned the atom type given
+by the type argument.  If they are molecules, the type argument has no
+effect and must be set to zero. Instead, the type of each atom in the
+inserted molecule is specified in the file read by the
+:doc:`molecule <molecule>` command.
+
+.. note::
+
+   Care should be taken to apply fix gcmc only to
+   a group that contains only those atoms and molecules
+   that you wish to manipulate using Monte Carlo.
+   Hence it is generally not a good idea to specify
+   the default group "all" in the fix command, although it is allowed.
+
+This fix cannot be used to perform GCMC insertions of gas atoms or
+molecules other than the exchanged type, but GCMC deletions,
+and MC translations, and rotations can be performed on any atom/molecule in
+the fix group.  All atoms in the simulation cell can be moved using
+regular time integration translations, e.g. via :doc:`fix nvt <fix_nh>`,
+resulting in a hybrid GCMC+MD simulation. A smaller-than-usual
+timestep size may be needed when running such a hybrid simulation,
+especially if the inserted molecules are not well equilibrated.
+
+This command may optionally use the *region* keyword to define an
+exchange and move volume.  The specified region must have been
+previously defined with a :doc:`region <region>` command.  It must be
+defined with side = *in*\ .  Insertion attempts occur only within the
+specified region. For non-rectangular regions, random trial points are
+generated within the rectangular bounding box until a point is found
+that lies inside the region. If no valid point is generated after 1000
+trials, no insertion is performed, but it is counted as an attempted
+insertion.  Move and deletion attempt candidates are selected from gas
+atoms or molecules within the region. If there are no candidates, no
+move or deletion is performed, but it is counted as an attempt move or
+deletion. If an attempted move places the atom or molecule
+center-of-mass outside the specified region, a new attempted move is
+generated. This process is repeated until the atom or molecule
+center-of-mass is inside the specified region.
+
+If used with :doc:`fix nvt <fix_nh>`, the temperature of the imaginary
+reservoir, T, should be set to be equivalent to the target temperature
+used in fix nvt. Otherwise, the imaginary reservoir will not be in
+thermal equilibrium with the simulation cell. Also, it is important
+that the temperature used by fix nvt be dynamic/dof, which can be
+achieved as follows:
+
+
+.. parsed-literal::
+
+   compute mdtemp mdatoms temp
+   compute_modify mdtemp dynamic/dof yes
+   fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
+   fix_modify mdnvt temp mdtemp
+
+Note that neighbor lists are re-built every timestep that this fix is
+invoked, so you should not set N to be too small.  However, periodic
+rebuilds are necessary in order to avoid dangerous rebuilds and missed
+interactions. Specifically, avoid performing so many MC translations
+per timestep that atoms can move beyond the neighbor list skin
+distance. See the :doc:`neighbor <neighbor>` command for details.
+
+When an atom or molecule is to be inserted, its coordinates are chosen
+at a random position within the current simulation cell or region, and
+new atom velocities are randomly chosen from the specified temperature
+distribution given by T. The effective temperature for new atom
+velocities can be increased or decreased using the optional keyword
+*tfac\_insert* (see below). Relative coordinates for atoms in a
+molecule are taken from the template molecule provided by the
+user. The center of mass of the molecule is placed at the insertion
+point. The orientation of the molecule is chosen at random by rotating
+about this point.
+
+Individual atoms are inserted, unless the *mol* keyword is used.  It
+specifies a *template-ID* previously defined using the
+:doc:`molecule <molecule>` command, which reads a file that defines the
+molecule.  The coordinates, atom types, charges, etc., as well as any
+bonding and special neighbor information for the molecule can
+be specified in the molecule file.  See the :doc:`molecule <molecule>`
+command for details.  The only settings required to be in this file
+are the coordinates and types of atoms in the molecule.
+
+When not using the *mol* keyword, you should ensure you do not delete
+atoms that are bonded to other atoms, or LAMMPS will soon generate an
+error when it tries to find bonded neighbors.  LAMMPS will warn you if
+any of the atoms eligible for deletion have a non-zero molecule ID,
+but does not check for this at the time of deletion.
+
+If you wish to insert molecules using the *mol* keyword that will be
+treated as rigid bodies, use the *rigid* keyword, specifying as its
+value the ID of a separate :doc:`fix rigid/small <fix_rigid>` command
+which also appears in your input script.
+
+.. note::
+
+   If you wish the new rigid molecules (and other rigid molecules)
+   to be thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>`
+   or :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
+   "fix\_modify dynamic/dof yes" command for the rigid fix.  This is to
+   inform that fix that the molecule count will vary dynamically.
+
+If you wish to insert molecules via the *mol* keyword, that will have
+their bonds or angles constrained via SHAKE, use the *shake* keyword,
+specifying as its value the ID of a separate :doc:`fix shake <fix_shake>` command which also appears in your input script.
+
+Optionally, users may specify the relative amounts of different MC
+moves using the *mcmoves* keyword. The values *Patomtrans*\ ,
+*Pmoltrans*\ , *Pmolrotate* specify the average proportion of
+atom translations, molecule translations, and molecule rotations,
+respectively. The values must be non-negative integers or real
+numbers, with at least one non-zero value. For example, (10,30,0)
+would result in 25% of the MC moves being atomic translations, 75%
+molecular translations, and no molecular rotations.
+
+Optionally, users may specify the maximum rotation angle for molecular
+rotations using the *maxangle* keyword and specifying the angle in
+degrees. Rotations are performed by generating a random point on the
+unit sphere and a random rotation angle on the range
+[0,maxangle). The molecule is then rotated by that angle about an
+axis passing through the molecule center of mass. The axis is parallel
+to the unit vector defined by the point on the unit sphere.  The same
+procedure is used for randomly rotating molecules when they are
+inserted, except that the maximum angle is 360 degrees.
+
+Note that fix gcmc does not use configurational bias MC or any other
+kind of sampling of intramolecular degrees of freedom.  Inserted
+molecules can have different orientations, but they will all have the
+same intramolecular configuration, which was specified in the molecule
+command input.
+
+For atomic gasses, inserted atoms have the specified atom type, but
+deleted atoms are any atoms that have been inserted or that already
+belong to the fix group. For molecular gasses, exchanged
+molecules use the same atom types as in the template molecule supplied
+by the user.  In both cases, exchanged atoms/molecules are assigned to
+two groups: the default group "all" and the fix group
+(which can also be "all").
+
+The chemical potential is a user-specified input parameter defined
+as:
+
+.. image:: Eqs/fix_gcmc1.jpg
+   :align: center
+
+The second term mu\_ex is the excess chemical potential due to
+energetic interactions and is formally zero for the fictitious gas
+reservoir but is non-zero for interacting systems. So, while the
+chemical potential of the reservoir and the simulation cell are equal,
+mu\_ex is not, and as a result, the densities of the two are generally
+quite different.  The first term mu\_id is the ideal gas contribution
+to the chemical potential.  mu\_id can be related to the density or
+pressure of the fictitious gas reservoir by:
+
+.. image:: Eqs/fix_gcmc2.jpg
+   :align: center
+
+where k is Boltzman's constant,
+T is the user-specified temperature, rho is the number density,
+P is the pressure, and phi is the fugacity coefficient.
+The constant Lambda is required for dimensional consistency.
+For all unit styles except *lj* it is defined as the thermal
+de Broglie wavelength
+
+.. image:: Eqs/fix_gcmc3.jpg
+   :align: center
+
+where h is Planck's constant, and m is the mass of the exchanged atom
+or molecule.  For unit style *lj*\ , Lambda is simply set to the
+unity. Note that prior to March 2017, lambda for unit style *lj* was
+calculated using the above formula with h set to the rather specific
+value of 0.18292026.  Chemical potential under the old definition can
+be converted to an equivalent value under the new definition by
+subtracting 3kTln(Lambda\_old).
+
+As an alternative to specifying mu directly, the ideal gas reservoir
+can be defined by its pressure P using the *pressure* keyword, in
+which case the user-specified chemical potential is ignored. The user
+may also specify the fugacity coefficient phi using the
+*fugacity\_coeff* keyword, which defaults to unity.
+
+The *full\_energy* option means that the fix calculates the total
+potential energy of the entire simulated system, instead of just
+the energy of the part that is changed. The total system
+energy before and after the proposed GCMC exchange or MC move
+is then used in the
+Metropolis criterion to determine whether or not to accept the
+proposed change. By default, this option is off,
+in which case only
+partial energies are computed to determine the energy difference
+due to the proposed change.
+
+The *full\_energy* option is needed for systems with complicated
+potential energy calculations, including the following:
+
+* long-range electrostatics (kspace)
+* many-body pair styles
+* hybrid pair styles
+* eam pair styles
+* tail corrections
+* need to include potential energy contributions from other fixes
+
+In these cases, LAMMPS will automatically apply the *full\_energy*
+keyword and issue a warning message.
+
+When the *mol* keyword is used, the *full\_energy* option also includes
+the intramolecular energy of inserted and deleted molecules, whereas
+this energy is not included when *full\_energy* is not used. If this
+is not desired, the *intra\_energy* keyword can be used to define an
+amount of energy that is subtracted from the final energy when a
+molecule is inserted, and subtracted from the initial energy when a molecule
+is deleted. For molecules that have a non-zero intramolecular energy,
+this will ensure roughly the same behavior whether or not the
+*full\_energy* option is used.
+
+Inserted atoms and molecules are assigned random velocities based on
+the specified temperature T. Because the relative velocity of all
+atoms in the molecule is zero, this may result in inserted molecules
+that are systematically too cold. In addition, the intramolecular
+potential energy of the inserted molecule may cause the kinetic energy
+of the molecule to quickly increase or decrease after insertion.  The
+*tfac\_insert* keyword allows the user to counteract these effects by
+changing the temperature used to assign velocities to inserted atoms
+and molecules by a constant factor. For a particular application, some
+experimentation may be required to find a value of *tfac\_insert* that
+results in inserted molecules that equilibrate quickly to the correct
+temperature.
+
+Some fixes have an associated potential energy. Examples of such fixes
+include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
+:doc:`addforce <fix_addforce>`, :doc:`langevin <fix_langevin>`,
+:doc:`restrain <fix_restrain>`,
+:doc:`temp/berendsen <fix_temp_berendsen>`,
+:doc:`temp/rescale <fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.
+For that energy to be included in the total potential energy of the
+system (the quantity used when performing GCMC exchange and MC moves),
+you MUST enable
+the :doc:`fix\_modify <fix_modify>` *energy* option for that fix.  The
+doc pages for individual :doc:`fix <fix>` commands specify if this
+should be done.
+
+Use the *charge* option to insert atoms with a user-specified point
+charge. Note that doing so will cause the system to become
+non-neutral.  LAMMPS issues a warning when using long-range
+electrostatics (kspace) with non-neutral systems. See the :doc:`compute group/group <compute_group_group>` documentation for more details
+about simulating non-neutral systems with kspace on.
+
+Use of this fix typically will cause the number of atoms to fluctuate,
+therefore, you will want to use the
+:doc:`compute\_modify dynamic/dof <compute_modify>` command to insure that the
+current number of atoms is used as a normalizing factor each time
+temperature is computed. A simple example of this is:
+
+
+.. parsed-literal::
+
+   compute_modify thermo_temp dynamic yes
+
+A more complicated example is listed earlier on this page
+in the context of NVT dynamics.
+
+.. note::
+
+   If the density of the cell is initially very small or zero, and
+   increases to a much larger density after a period of equilibration,
+   then certain quantities that are only calculated once at the start
+   (kspace parameters) may no longer be accurate.  The
+   solution is to start a new simulation after the equilibrium density
+   has been reached.
+
+With some pair\_styles, such as :doc:`Buckingham <pair_buck>`,
+:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxc>`, two
+atoms placed close to each other may have an arbitrary large, negative
+potential energy due to the functional form of the potential.  While
+these unphysical configurations are inaccessible to typical dynamical
+trajectories, they can be generated by Monte Carlo moves. The
+*overlap\_cutoff* keyword suppresses these moves by effectively
+assigning an infinite positive energy to all new configurations that
+place any pair of atoms closer than the specified overlap cutoff
+distance.
+
+The *max* and *min* keywords allow for the restriction of the number
+of atoms in the simulation. They automatically reject all insertion 
+or deletion moves that would take the system beyond the set boundaries.
+Should the system already be beyond the boundary, only moves that bring 
+the system closer to the bounds may be accepted.
+
+The *group* keyword adds all inserted atoms to the
+:doc:`group <group>` of the group-ID value. The *grouptype* keyword
+adds all inserted atoms of the specified type to the
+:doc:`group <group>` of the group-ID value.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the fix to :doc:`binary restart files <restart>`.  This includes information about the random
+number generator seed, the next timestep for MC exchanges,  the number
+of MC step attempts and successes etc.  See
+the :doc:`read\_restart <read_restart>` command for info on how to
+re-specify a fix in an input script that reads a restart file, so that
+the operation of the fix continues in an uninterrupted fashion.
+
+.. note::
+
+   For this to work correctly, the timestep must **not** be changed
+   after reading the restart with :doc:`reset\_timestep <reset_timestep>`.
+   The fix will try to detect it and stop with an error.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.
+
+This fix computes a global vector of length 8, which can be accessed
+by various :doc:`output commands <Howto_output>`.  The vector values are
+the following global cumulative quantities:
+
+* 1 = translation attempts
+* 2 = translation successes
+* 3 = insertion attempts
+* 4 = insertion successes
+* 5 = deletion attempts
+* 6 = deletion successes
+* 7 = rotation attempts
+* 8 = rotation successes
+
+The vector values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MC package.  It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Do not set "neigh\_modify once yes" or else this fix will never be
+called.  Reneighboring is required.
+
+Can be run in parallel, but aspects of the GCMC part will not scale
+well in parallel. Only usable for 3D simulations.
+
+When using fix gcmc in combination with fix shake or fix rigid,
+only GCMC exchange moves are supported, so the argument
+*M* must be zero.
+
+Note that very lengthy simulations involving insertions/deletions of
+billions of gas molecules may run out of atom or molecule IDs and
+trigger an error, so it is better to run multiple shorter-duration
+simulations. Likewise, very large molecules have not been tested and
+may turn out to be problematic.
+
+Use of multiple fix gcmc commands in the same input script can be
+problematic if using a template molecule. The issue is that the
+user-referenced template molecule in the second fix gcmc command may
+no longer exist since it might have been deleted by the first fix gcmc
+command. An existing template molecule will need to be referenced by
+the user for each subsequent fix gcmc command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix atom/swap <fix_atom_swap>`,
+:doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
+:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
+:doc:`delete\_atoms <delete_atoms>`
+
+Default
+"""""""
+
+The option defaults are mol = no, maxangle = 10, overlap\_cutoff = 0.0,
+fugacity\_coeff = 1.0, intra\_energy = 0.0, tfac\_insert = 1.0.
+(Patomtrans, Pmoltrans, Pmolrotate) = (1, 0, 0) for mol = no and
+(0, 1, 1) for mol = yes. full\_energy = no,
+except for the situations where full\_energy is required, as
+listed above.
+
+
+----------
+
+
+.. _Frenkel:
+
+
+
+**(Frenkel)** Frenkel and Smit, Understanding Molecular Simulation,
+Academic Press, London, 2002.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst
new file mode 100644
index 0000000000..03b5aa418b
--- /dev/null
+++ b/doc/src/fix_gld.rst
@@ -0,0 +1,181 @@
+.. index:: fix gld
+
+fix gld command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* gld = style name of this fix command
+* Tstart,Tstop = desired temperature at start/end of run (temperature units)
+* N\_k = number of terms in the Prony series representation of the memory kernel
+* seed = random number seed to use for white noise (positive integer)
+* series = *pprony* is presently the only available option
+* c\_k = the weight of the kth term in the Prony series (mass per time units)
+* tau\_k = the time constant of the kth term in the Prony series (time units)
+* zero or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *frozen* or *zero*
+       *frozen* value = *no* or *yes*
+         *no* = initialize extended variables using values drawn from equilibrium distribution at Tstart
+         *yes* = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
+       *zero* value = *no* or *yes*
+         *no* = do not set total random force to zero
+         *yes* = set total random force to zero
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all gld 1.0 1.0 2 82885 pprony 0.5 1.0 1.0 2.0 frozen yes zero yes
+   fix 3 rouse gld 7.355 7.355 4 48823 pprony 107.1 0.02415 186.0 0.04294 428.6 0.09661 1714 0.38643
+
+Description
+"""""""""""
+
+Applies Generalized Langevin Dynamics to a group of atoms, as
+described in :ref:`(Baczewski) <Baczewski>`.  This is intended to model the
+effect of an implicit solvent with a temporally non-local dissipative
+force and a colored Gaussian random force, consistent with the
+Fluctuation-Dissipation Theorem.  The functional form of the memory
+kernel associated with the temporally non-local force is constrained
+to be a Prony series.
+
+.. note::
+
+   While this fix bears many similarities to :doc:`fix langevin <fix_langevin>`, it has one significant
+   difference. Namely, :doc:`fix gld <fix_gld>` performs time integration,
+   whereas :doc:`fix langevin <fix_langevin>` does NOT. To this end, the
+   specification of another fix to perform time integration, such as :doc:`fix nve <fix_nve>`, is NOT necessary.
+
+With this fix active, the force on the *j*\ th atom is given as
+
+.. image:: Eqs/fix_gld1.jpg
+   :align: center
+
+Here, the first term is representative of all conservative (pairwise,
+bonded, etc) forces external to this fix, the second is the temporally
+non-local dissipative force given as a Prony series, and the third is
+the colored Gaussian random force.
+
+The Prony series form of the memory kernel is chosen to enable an
+extended variable formalism, with a number of exemplary mathematical
+features discussed in :ref:`(Baczewski) <Baczewski>`. In particular, 3N\_k
+extended variables are added to each atom, which effect the action of
+the memory kernel without having to explicitly evaluate the integral
+over time in the second term of the force. This also has the benefit
+of requiring the generation of uncorrelated random forces, rather than
+correlated random forces as specified in the third term of the force.
+
+Presently, the Prony series coefficients are limited to being greater
+than or equal to zero, and the time constants are limited to being
+greater than zero. To this end, the value of series MUST be set to
+*pprony*\ , for now. Future updates will allow for negative coefficients
+and other representations of the memory kernel. It is with these
+updates in mind that the series option was included.
+
+The units of the Prony series coefficients are chosen to be mass per
+time to ensure that the numerical integration scheme stably approaches
+the Newtonian and Langevin limits. Details of these limits, and the
+associated numerical concerns are discussed in
+:ref:`(Baczewski) <Baczewski>`.
+
+The desired temperature at each timestep is ramped from *Tstart* to
+*Tstop* over the course of the next run.
+
+The random # *seed* must be a positive integer. A Marsaglia random
+number generator is used. Each processor uses the input seed to
+generate its own unique seed and its own stream of random
+numbers. Thus the dynamics of the system will not be identical on two
+runs on different numbers of processors.
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+The keyword *frozen* can be used to specify how the extended variables
+associated with the GLD memory kernel are initialized. Specifying no
+(the default), the initial values are drawn at random from an
+equilibrium distribution at *Tstart*\ , consistent with the
+Fluctuation-Dissipation Theorem. Specifying yes, initializes the
+extended variables to zero.
+
+The keyword *zero* can be used to eliminate drift due to the
+thermostat. Because the random forces on different atoms are
+independent, they do not sum exactly to zero. As a result, this fix
+applies a small random force to the entire system, and the
+center-of-mass of the system undergoes a slow random walk. If the
+keyword *zero* is set to *yes*\ , the total random force is set exactly
+to zero by subtracting off an equal part of it from each atom in the
+group. As a result, the center-of-mass of a system with zero initial
+momentum will not drift over time.
+
+
+----------
+
+
+**Restart, run start/stop, minimize info:**
+
+The instantaneous values of the extended variables are written to
+:doc:`binary restart files <restart>`.  Because the state of the random
+number generator is not saved in restart files, this means you cannot
+do "exact" restarts with this fix, where the simulation continues on
+the same as if no restart had taken place. However, in a statistical
+sense, a restarted simulation should produce the same behavior.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix langevin <fix_langevin>`, :doc:`fix viscous <fix_viscous>`,
+:doc:`pair\_style dpd/tstat <pair_dpd>`
+
+Default
+"""""""
+
+The option defaults are frozen = no, zero = no.
+
+
+----------
+
+
+.. _Baczewski:
+
+
+
+**(Baczewski)** A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst
new file mode 100644
index 0000000000..ecb03618f5
--- /dev/null
+++ b/doc/src/fix_gle.rst
@@ -0,0 +1,182 @@
+.. index:: fix gle
+
+fix gle command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID id-group gle Ns Tstart Tstop seed Amatrix [noneq Cmatrix] [every stride]
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* gle = style name of this fix command
+* Ns = number of additional fictitious momenta
+* Tstart, Tstop = temperature ramp during the run
+* Amatrix = file to read the drift matrix A from
+* seed = random number seed to use for generating noise (positive integer)
+* zero or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+       keyword = *noneq* or *every*
+         *noneq* Cmatrix  = file to read the non-equilibrium covariance matrix from
+         *every* stride   = apply the GLE once every time steps. Reduces the accuracy
+             of the integration of the GLE, but has \*no effect\* on the accuracy of equilibrium
+             sampling. It might change sampling properties when used together with *noneq*\ .
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 boundary gle 6 300 300 31415 smart.A
+   fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C
+
+Description
+"""""""""""
+
+Apply a Generalized Langevin Equation (GLE) thermostat as described
+in :ref:`(Ceriotti) <Ceriotti>`. The formalism allows one to obtain a number
+of different effects ranging from efficient sampling of all
+vibrational modes in the system to inexpensive (approximate)
+modelling of nuclear quantum effects. Contrary to
+:doc:`fix langevin <fix_langevin>`, this fix performs both
+thermostatting and evolution of the Hamiltonian equations of motion, so it
+should not be used together with :doc:`fix nve <fix_nve>` -- at least not
+on the same atom groups.
+
+Each degree of freedom in the thermostatted group is supplemented
+with Ns additional degrees of freedom s, and the equations of motion
+become
+
+
+.. parsed-literal::
+
+   dq/dt=p/m
+   d(p,s)/dt=(F,0) - A(p,s) + B dW/dt
+
+where F is the physical force, A is the drift matrix (that generalizes
+the friction in Langevin dynamics), B is the diffusion term and dW/dt
+un-correlated Gaussian random forces. The A matrix couples the physical
+(q,p) dynamics with that of the additional degrees of freedom,
+and makes it possible to obtain effectively a history-dependent
+noise and friction kernel.
+
+The drift matrix should be given as an external file *Afile*\ ,
+as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
+optimal for a given application and the system of choice can be
+obtained from :ref:`(GLE4MD) <GLE4MD>`.
+
+Equilibrium sampling a temperature T is obtained by specifying the
+target value as the *Tstart* and *Tstop* arguments, so that the diffusion
+matrix that gives canonical sampling for a given A is computed automatically.
+However, the GLE framework also allow for non-equilibrium sampling, that
+can be used for instance to model inexpensively zero-point energy
+effects :ref:`(Ceriotti2) <Ceriotti2>`. This is achieved specifying the *noneq*
+keyword followed by the name of the file that contains the static covariance
+matrix for the non-equilibrium dynamics.  Please note, that the covariance
+matrix is expected to be given in **temperature units**\ .
+
+Since integrating GLE dynamics can be costly when used together with
+simple potentials, one can use the *every* optional keyword to
+apply the Langevin terms only once every several MD steps, in a
+multiple time-step fashion. This should be used with care when doing
+non-equilibrium sampling, but should have no effect on equilibrium
+averages when using canonical sampling.
+
+The random number *seed* must be a positive integer.  A Marsaglia random
+number generator is used.  Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+Note also that the Generalized Langevin Dynamics scheme that is
+implemented by the :doc:`fix gld <fix_gld>` scheme is closely related
+to the present one. In fact, it should be always possible to cast the
+Prony series form of the memory kernel used by GLD into an appropriate
+input matrix for :doc:`fix gle <fix_gle>`. While the GLE scheme is more
+general, the form used by :doc:`fix gld <fix_gld>` can be more directly
+related to the representation of an implicit solvent environment.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+The instantaneous values of the extended variables are written to
+:doc:`binary restart files <restart>`.  Because the state of the random
+number generator is not saved in restart files, this means you cannot
+do "exact" restarts with this fix, where the simulation continues on
+the same as if no restart had taken place. However, in a statistical
+sense, a restarted simulation should produce the same behavior.
+Note however that you should use a different seed each time you
+restart, otherwise the same sequence of random numbers will be used
+each time, which might lead to stochastic synchronization and
+subtle artifacts in the sampling.
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".
+
+Restrictions
+""""""""""""
+
+
+The GLE thermostat in its current implementation should not be used
+with rigid bodies, SHAKE or RATTLE. It is expected that all the
+thermostatted degrees of freedom are fully flexible, and the sampled
+ensemble will not be correct otherwise.
+
+In order to perform constant-pressure simulations please use
+:doc:`fix press/berendsen <fix_press_berendsen>`, rather than
+:doc:`fix npt <fix_nh>`, to avoid duplicate integration of the
+equations of motion.
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix viscous <fix_viscous>`, :doc:`fix nvt <fix_nh>`, :doc:`pair\_style dpd/tstat <pair_dpd>`, :doc:`fix gld <fix_gld>`
+
+
+----------
+
+
+.. _Ceriotti:
+
+
+
+**(Ceriotti)** Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
+1170-80 (2010)
+
+.. _GLE4MD:
+
+
+
+**(GLE4MD)** `http://gle4md.org/ <http://gle4md.org/>`_
+
+.. _Ceriotti2:
+
+
+
+**(Ceriotti2)** Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
+030603 (2009)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst
new file mode 100644
index 0000000000..e8aae5a910
--- /dev/null
+++ b/doc/src/fix_gravity.rst
@@ -0,0 +1,163 @@
+.. index:: fix gravity
+
+fix gravity command
+===================
+
+fix gravity/omp command
+=======================
+
+fix gravity/kk command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group gravity magnitude style args
+
+* ID, group are documented in :doc:`fix <fix>` command
+* gravity = style name of this fix command
+* magnitude = size of acceleration (force/mass units)
+* magnitude can be a variable (see below)
+* style = *chute* or *spherical* or *gradient* or *vector*
+  
+  .. parsed-literal::
+  
+       *chute* args = angle
+         angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
+         angle can be a variable (see below)
+       *spherical* args = phi theta
+         phi = azimuthal angle from +x axis (in degrees)
+         theta = angle from +z or +y axis in 3d/2d (in degrees)
+         phi or theta can be a variable (see below)
+       *vector* args = x y z
+         x y z = vector direction to apply the acceleration
+         x or y or z can be a variable (see below)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all gravity 1.0 chute 24.0
+   fix 1 all gravity v_increase chute 24.0
+   fix 1 all gravity 1.0 spherical 0.0 -180.0
+   fix 1 all gravity 10.0 spherical v_phi v_theta
+   fix 1 all gravity 100.0 vector 1 1 0
+
+Description
+"""""""""""
+
+Impose an additional acceleration on each particle in the group.  This
+fix is typically used with granular systems to include a "gravity"
+term acting on the macroscopic particles.  More generally, it can
+represent any kind of driving field, e.g. a pressure gradient inducing
+a Poiseuille flow in a fluid.  Note that this fix operates differently
+than the :doc:`fix addforce <fix_addforce>` command.  The addforce fix
+adds the same force to each atom, independent of its mass.  This
+command imparts the same acceleration to each atom (force/mass).
+
+The *magnitude* of the acceleration is specified in force/mass units.
+For granular systems (LJ units) this is typically 1.0.  See the
+:doc:`units <units>` command for details.
+
+Style *chute* is typically used for simulations of chute flow where
+the specified *angle* is the chute angle, with flow occurring in the +x
+direction.  For 3d systems, the tilt is away from the z axis; for 2d
+systems, the tilt is away from the y axis.
+
+Style *spherical* allows an arbitrary 3d direction to be specified for
+the acceleration vector.  *Phi* and *theta* are defined in the usual
+spherical coordinates.  Thus for acceleration acting in the -z
+direction, *theta* would be 180.0 (or -180.0).  *Theta* = 90.0 and
+*phi* = -90.0 would mean acceleration acts in the -y direction.  For
+2d systems, *phi* is ignored and *theta* is an angle in the xy plane
+where *theta* = 0.0 is the y-axis.
+
+Style *vector* imposes an acceleration in the vector direction given
+by (x,y,z).  Only the direction of the vector is important; it's
+length is ignored.  For 2d systems, the *z* component is ignored.
+
+Any of the quantities *magnitude*\ , *angle*\ , *phi*\ , *theta*\ , *x*\ , *y*\ ,
+*z* which define the gravitational magnitude and direction, can be
+specified as an equal-style :doc:`variable <variable>`.  If the value is
+a variable, it should be specified as v\_name, where name is the
+variable name.  In this case, the variable will be evaluated each
+timestep, and its value used to determine the quantity.  You should
+insure that the variable calculates a result in the appropriate units,
+e.g. force/mass or degrees.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent gravitational
+field.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the gravitational potential energy of the system to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  This scalar is the gravitational
+potential energy of the particles in the defined field, namely mass \*
+(g dot x) for each particles, where x and mass are the particles
+position and mass, and g is the gravitational field.  The scalar value
+calculated by this fix is "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style sphere <atom_style>`, :doc:`fix addforce <fix_addforce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst
new file mode 100644
index 0000000000..598131a935
--- /dev/null
+++ b/doc/src/fix_grem.rst
@@ -0,0 +1,131 @@
+.. index:: fix grem
+
+fix grem command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID grem lambda eta H0 thermostat-ID
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* grem = style name of this fix command
+* lambda = intercept parameter of linear effective temperature function
+* eta = slope parameter of linear effective temperature function
+* H0 = shift parameter of linear effective temperature function
+* thermostat-ID = ID of Nose-Hoover thermostat or barostat used in simulation
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix             fxgREM all grem 400 -0.01 -30000 fxnpt
+   thermo_modify   press fxgREM_press
+
+   fix             fxgREM all grem 502 -0.15 -80000 fxnvt
+
+Description
+"""""""""""
+
+This fix implements the molecular dynamics version of the generalized
+replica exchange method (gREM) originally developed by :ref:`(Kim) <Kim2010>`,
+which uses non-Boltzmann ensembles to sample over first order phase
+transitions. The is done by defining replicas with an enthalpy
+dependent effective temperature
+
+.. image:: Eqs/fix_grem.jpg
+   :align: center
+
+with *eta* negative and steep enough to only intersect the
+characteristic microcanonical temperature (Ts) of the system once,
+ensuring a unimodal enthalpy distribution in that replica. *Lambda* is
+the intercept and effects the generalized ensemble similar to how
+temperature effects a Boltzmann ensemble. *H0* is a reference
+enthalpy, and is typically set as the lowest desired sampled enthalpy.
+Further explanation can be found in our recent papers
+:ref:`(Malolepsza) <Malolepsza>`.
+
+This fix requires a Nose-Hoover thermostat fix reference passed to the
+grem as *thermostat-ID*\ . Two distinct temperatures exist in this
+generalized ensemble, the effective temperature defined above, and a
+kinetic temperature that controls the velocity distribution of
+particles as usual. Either constant volume or constant pressure
+algorithms can be used.
+
+The fix enforces a generalized ensemble in a single replica
+only. Typically, this ideology is combined with replica exchange with
+replicas differing by *lambda* only for simplicity, but this is not
+required. A multi-replica simulation can be run within the LAMMPS
+environment using the :doc:`temper/grem <temper_grem>` command. This
+utilizes LAMMPS partition mode and requires the number of available
+processors be on the order of the number of desired replicas. A
+100-replica simulation would require at least 100 processors (1 per
+world at minimum). If a many replicas are needed on a small number of
+processors, multi-replica runs can be run outside of LAMMPS.  An
+example of this can be found in examples/USER/misc/grem and has no
+limit on the number of replicas per processor. However, this is very
+inefficient and error prone and should be avoided if possible.
+
+In general, defining the generalized ensembles is unique for every
+system. When starting a many-replica simulation without any knowledge
+of the underlying microcanonical temperature, there are several tricks
+we have utilized to optimize the process.  Choosing a less-steep *eta*
+yields broader distributions, requiring fewer replicas to map the
+microcanonical temperature.  While this likely struggles from the same
+sampling problems gREM was built to avoid, it provides quick insight
+to Ts.  Initially using an evenly-spaced *lambda* distribution
+identifies regions where small changes in enthalpy lead to large
+temperature changes. Replicas are easily added where needed.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`thermo\_modify <thermo_modify>` *press* option is supported
+by this fix to add the rescaled kinetic pressure as part of
+:doc:`thermodynamic output <thermo_style>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`temper/grem <temper_grem>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`thermo\_modify <thermo_modify>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Kim2010:
+
+
+
+**(Kim)** Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).
+
+.. _Malolepsza:
+
+
+
+**(Malolepsza)** Malolepsza, Secor, Keyes, J Phys Chem B 119 (42),
+13379-13384 (2015).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst
new file mode 100644
index 0000000000..4eaa75abb8
--- /dev/null
+++ b/doc/src/fix_halt.rst
@@ -0,0 +1,174 @@
+.. index:: fix halt
+
+fix halt command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID halt N attribute operator avalue keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* halt = style name of this fix command
+* N = check halt condition every N steps
+* attribute = *bondmax* or *tlimit* or v\_name
+  
+  .. parsed-literal::
+  
+       bondmax = length of longest bond in the system
+       tlimit = elapsed CPU time
+       v_name = name of :doc:`equal-style variable <variable>`
+
+* operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^"
+* avalue = numeric value to compare attribute to
+* zero or more keyword/value pairs may be appended
+* keyword = *error* or *message*
+  
+  .. parsed-literal::
+  
+       *error* value = *hard* or *soft* or *continue*
+       *message* value = *yes* or *no*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 10 all halt 1 bondmax > 1.5
+   fix 10 all print 10 v_myCheck != 0 error soft
+
+Description
+"""""""""""
+
+Check a condition every N steps during a simulation run.  N must be >=
+1.  If the condition is met, exit the run immediately.  In this
+context a "run" can be dynamics or minimization iterations, as
+specified by the :doc:`run <run>` or :doc:`minimize <minimize>` command.
+
+The specified group-ID is ignored by this fix.
+
+The specified *attribute* can be one of the options listed above,
+namely *bondmax* or *tlimit*\ , or an :doc:`equal-style variable <variable>` referenced as *v\_name*, where "name" is the
+name of a variable that has been defined previously in the input
+script.
+
+The *bondmax* attribute will loop over all bonds in the system,
+compute their current lengths, and set *attribute* to the longest bond
+distance.
+
+The *tlimit* attribute queries the elapsed CPU time (in seconds) since
+the current run began, and sets *attribute* to that value.  This is an
+alternative way to limit the length of a simulation run, similar to
+the :doc:`timer <timer>` timeout command.  There are two differences in
+using this method versus the timer command option.  The first is that
+the clock starts at the beginning of the current run (not when the
+timer or fix command is specified), so that any setup time for the run
+is not included in the elapsed time.  The second is that the timer
+invocation and syncing across all processors (via MPI\_Allreduce) is
+not performed once every *N* steps by this command.  Instead it is
+performed (typically) only a small number of times and the elapsed
+times are used to predict when the end-of-the-run will be.  Both of
+these attributes can be useful when performing benchmark calculations
+for a desired length of time with minimal overhead.  For example, if
+a run is performing 1000s of timesteps/sec, the overhead for syncing
+the timer frequently across a large number of processors may be
+non-negligible.
+
+Equal-style variables evaluate to a numeric value.  See the
+:doc:`variable <variable>` command for a description.  They calculate
+formulas which can involve mathematical operations, atom properties,
+group properties, thermodynamic properties, global values calculated
+by a :doc:`compute <compute>` or :doc:`fix <fix>`, or references to other
+:doc:`variables <variable>`.  Thus they are a very general means of
+computing some attribute of the current system.  For example, the
+following "bondmax" variable will calculate the same quantity as the
+hstyle = bondmax option.
+
+
+.. parsed-literal::
+
+   compute         bdist all bond/local dist
+   compute         bmax all reduce max c_bdist
+   variable        bondmax equal c_bmax
+
+Thus these two versions of a fix halt command will do the same thing:
+
+
+.. parsed-literal::
+
+   fix 10 all halt 1 bondmax > 1.5
+   fix 10 all halt 1 v_bondmax > 1.5
+
+The version with "bondmax" will just run somewhat faster, due to less
+overhead in computing bond lengths and not storing them in a separate
+compute.
+
+The choice of operators listed above are the usual comparison
+operators.  The XOR operation (exclusive or) is also included as "\|\^".
+In this context, XOR means that if either the attribute or avalue is
+0.0 and the other is non-zero, then the result is "true".  Otherwise
+it is "false".
+
+The specified *avalue* must be a numeric value.
+
+
+----------
+
+
+The optional *error* keyword determines how the current run is halted.
+If its value is *hard*\ , then LAMMPS will stop with an error message.
+
+If its value is *soft*\ , LAMMPS will exit the current run, but continue
+to execute subsequent commands in the input script.  However,
+additional :doc:`run <run>` or :doc:`minimize <minimize>` commands will be
+skipped.  For example, this allows a script to output the current
+state of the system, e.g. via a :doc:`write\_dump <write_dump>` or
+:doc:`write\_restart <write_restart>` command.
+
+If its value is *continue*\ , the behavior is the same as for *soft*\ ,
+except subsequent :doc:`run <run>` or :doc:`minimize <minimize>` commands
+are executed.  This allows your script to remedy the condition that
+triggered the halt, if necessary.  Note that you may wish use the
+:doc:`unfix <unfix>` command on the fix halt ID, so that the same
+condition is not immediately triggered in a subsequent run.
+
+The optional *message* keyword determines whether a message is printed
+to the screen and logfile when the halt condition is triggered.  If
+*message* is set to yes, a one line message with the values that
+triggered the halt is printed.  If *message* is set to no, no message
+is printed; the run simply exits.  The latter may be desirable for
+post-processing tools that extract thermodynamic information from log
+files.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`variable <variable>`
+
+Default
+"""""""
+
+The option defaults are error = hard and message = yes.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst
new file mode 100644
index 0000000000..1972eb2b03
--- /dev/null
+++ b/doc/src/fix_heat.rst
@@ -0,0 +1,144 @@
+.. index:: fix heat
+
+fix heat command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID heat N eflux
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* heat = style name of this fix command
+* N = add/subtract heat every this many timesteps
+* eflux = rate of heat addition or subtraction (energy/time units)
+* eflux can be a variable (see below)
+* zero or more keyword/value pairs may be appended to args
+* keyword = *region*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region atoms must be in to have added force
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 qin heat 1 1.0
+   fix 3 qin heat 10 v_flux
+   fix 4 qout heat 1 -1.0 region top
+
+Description
+"""""""""""
+
+Add non-translational kinetic energy (heat) to a group of atoms in a
+manner that conserves their aggregate momentum.  Two of these fixes
+can be used to establish a temperature gradient across a simulation
+domain by adding heat (energy) to one group of atoms (hot reservoir)
+and subtracting heat from another (cold reservoir).  E.g. a simulation
+sampling from the McDLT ensemble.
+
+If the *region* keyword is used, the atom must be in both the group
+and the specified geometric :doc:`region <region>` in order to have
+energy added or subtracted to it.  If not specified, then the atoms in
+the group are affected wherever they may move to.
+
+Heat addition/subtraction is performed every N timesteps.  The *eflux*
+parameter can be specified as a numeric constant or as a variable (see
+below).  If it is a numeric constant or equal-style variable which
+evaluates to a scalar value, then the *eflux* determines the change in
+aggregate energy of the entire group of atoms per unit time, e.g. in
+eV/psec for :doc:`metal units <units>`.  In this case it is an
+"extensive" quantity, meaning its magnitude should be scaled with the
+number of atoms in the group.  Note that since *eflux* has per-time
+units (i.e. it is a flux), this means that a larger value of N will
+add/subtract a larger amount of energy each time the fix is invoked.
+
+.. note::
+
+   The heat-exchange (HEX) algorithm implemented by this fix is
+   known to exhibit a pronounced energy drift. An improved algorithm
+   (eHEX) is available as a :doc:`fix ehex <fix_ehex>` command and might be
+   preferable if energy conservation is important.
+
+If *eflux* is specified as an atom-style variable (see below), then
+the variable computes one value per atom.  In this case, each value is
+the energy flux for a single atom, again in units of energy per unit
+time.  In this case, each value is an "intensive" quantity, which need
+not be scaled with the number of atoms in the group.
+
+As mentioned above, the *eflux* parameter can be specified as an
+equal-style or atom\_style :doc:`variable <variable>`.  If the value is a
+variable, it should be specified as v\_name, where name is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its value(s) used to determine the flux.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent flux.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent flux
+with optional time-dependence as well.
+
+.. note::
+
+   If heat is subtracted from the system too aggressively so that
+   the group's kinetic energy would go to zero, or any individual atom's
+   kinetic energy would go to zero for the case where *eflux* is an
+   atom-style variable, then LAMMPS will halt with an error message.
+
+Fix heat is different from a thermostat such as :doc:`fix nvt <fix_nh>`
+or :doc:`fix temp/rescale <fix_temp_rescale>` in that energy is
+added/subtracted continually.  Thus if there isn't another mechanism
+in place to counterbalance this effect, the entire system will heat or
+cool continuously.  You can use multiple heat fixes so that the net
+energy change is 0.0 or use :doc:`fix viscous <fix_viscous>` to drain
+energy from the system.
+
+This fix does not change the coordinates of its atoms; it only scales
+their velocities.  Thus you must still use an integration fix
+(e.g. :doc:`fix nve <fix_nve>`) on the affected atoms.  This fix should
+not normally be used on atoms that have their temperature controlled
+by another fix - e.g. :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` fix.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  This scalar is the most recent
+value by which velocities were scaled.  The scalar value calculated by
+this fix is "intensive".  If *eflux* is specified as an atom-style
+variable, this fix computes the average value by which the velocities
+were scaled for all of the atoms that had their velocities scaled.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ehex <fix_ehex>`, :doc:`compute temp <compute_temp>`, :doc:`compute temp/region <compute_temp_region>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst
new file mode 100644
index 0000000000..7aa5891e25
--- /dev/null
+++ b/doc/src/fix_hyper_global.rst
@@ -0,0 +1,301 @@
+.. index:: fix hyper/global
+
+fix hyper/global command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID hyper/global cutbond qfactor Vmax Tequil
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* hyper/global = style name of this fix command
+* cutbond = max distance at which a pair of atoms is considered bonded (distance units)
+* qfactor = max strain at which bias potential goes to 0.0 (unitless)
+* Vmax = height of bias potential (energy units)
+* Tequil = equilibration temperature (temperature units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all hyper/global 1.0 0.3 0.8 300.0
+
+Description
+"""""""""""
+
+This fix is meant to be used with the :doc:`hyper <hyper>` command to
+perform a bond-boost global hyperdynamics (GHD) simulation.  The role
+of this fix is to a select a single pair of atoms in the system at
+each timestep to add a global bias potential to, which will alter the
+dynamics of the system in a manner that effectively accelerates time.
+This is in contrast to the :doc:`fix hyper/local <fix_hyper_local>`
+command, which can be user to perform a local hyperdynamics (LHD)
+simulation, by adding a local bias potential to multiple pairs of
+atoms at each timestep.  GHD can time accelerate a small simulation
+with up to a few 100 atoms.  For larger systems, LHD is needed to
+achieve good time acceleration.
+
+For a system that undergoes rare transition events, where one or more
+atoms move over an energy barrier to a new potential energy basin, the
+effect of the bias potential is to induce more rapid transitions.
+This can lead to a dramatic speed-up in the rate at which events
+occurs, without altering their relative frequencies, thus leading to
+an overall increase in the elapsed real time of the simulation as
+compared to running for the same number of timesteps with normal MD.
+See the :doc:`hyper <hyper>` doc page for a more general discussion of
+hyperdynamics and citations that explain both GHD and LHD.
+
+The equations and logic used by this fix and described here to perform
+GHD follow the description given in :ref:`(Voter2013) <Voter2013ghd>`.  The
+bond-boost form of a bias potential for HD is due to Miron and
+Fichthorn as described in :ref:`(Miron) <Mironghd>`.  In LAMMPS we use a
+simplified version of bond-boost GHD where a single bond in the system
+is biased at any one timestep.
+
+Bonds are defined between each pair of I,J atoms whose R0ij distance
+is less than *cutbond*\ , when the system is in a quenched state
+(minimum) energy.  Note that these are not "bonds" in a covalent
+sense.  A bond is simply any pair of atoms that meet the distance
+criterion.  *Cutbond* is an argument to this fix; it is discussed
+below.  A bond is only formed if one or both of the I.J atoms are in
+the specified group.
+
+The current strain of bond IJ (when running dynamics) is defined as
+
+
+.. parsed-literal::
+
+   Eij = (Rij - R0ij) / R0ij
+
+where Rij is the current distance between atoms I,J, and R0ij is the
+equilibrium distance in the quenched state.
+
+The bias energy Vij of any bond IJ is defined as
+
+
+.. parsed-literal::
+
+   Vij = Vmax \* (1 - (Eij/q)\^2) for abs(Eij) < qfactor
+       = 0 otherwise
+
+where the prefactor *Vmax* and the cutoff *qfactor* are arguments to
+this fix; they are discussed below.  This functional form is an
+inverse parabola centered at 0.0 with height Vmax and which goes to
+0.0 at +/- qfactor.
+
+Let Emax = the maximum of abs(Eij) for all IJ bonds in the system on a
+given timestep.  On that step, Vij is added as a bias potential to
+only the single bond with strain Emax, call it Vij(max).  Note that
+Vij(max) will be 0.0 if Emax >= qfactor on that timestep.  Also note
+that Vij(max) is added to the normal interatomic potential that is
+computed between all atoms in the system at every step.
+
+The derivative of Vij(max) with respect to the position of each atom
+in the Emax bond gives a bias force Fij(max) acting on the bond as
+
+
+.. parsed-literal::
+
+   Fij(max) = - dVij(max)/dEij = 2 Vmax Eij / qfactor\^2   for abs(Eij) < qfactor
+            = 0 otherwise
+
+which can be decomposed into an equal and opposite force acting on
+only the two I,J atoms in the Emax bond.
+
+The time boost factor for the system is given each timestep I by
+
+
+.. parsed-literal::
+
+   Bi = exp(beta \* Vij(max))
+
+where beta = 1/kTequil, and *Tequil* is the temperature of the system
+and an argument to this fix.  Note that Bi >= 1 at every step.
+
+.. note::
+
+   To run a GHD simulation, the input script must also use the :doc:`fix langevin <fix_langevin>` command to thermostat the atoms at the
+   same *Tequil* as specified by this fix, so that the system is running
+   constant-temperature (NVT) dynamics.  LAMMPS does not check that this
+   is done.
+
+The elapsed time t\_hyper for a GHD simulation running for *N*
+timesteps is simply
+
+
+.. parsed-literal::
+
+   t_hyper = Sum (i = 1 to N) Bi \* dt
+
+where dt is the timestep size defined by the :doc:`timestep <timestep>`
+command.  The effective time acceleration due to GHD is thus t\_hyper /
+N\*dt, where N\*dt is elapsed time for a normal MD run of N timesteps.
+
+Note that in GHD, the boost factor varies from timestep to timestep.
+Likewise, which bond has Emax strain and thus which pair of atoms the
+bias potential is added to, will also vary from timestep to timestep.
+This is in contrast to local hyperdynamics (LHD) where the boost
+factor is an input parameter; see the :doc:`fix hyper/local <fix_hyper_local>` doc page for details.
+
+
+----------
+
+
+Here is additional information on the input parameters for GHD.
+
+The *cutbond* argument is the cutoff distance for defining bonds
+between pairs of nearby atoms.  A pair of I,J atoms in their
+equilibrium, minimum-energy configuration, which are separated by a
+distance Rij < *cutbond*\ , are flagged as a bonded pair.  Setting
+*cubond* to be ~25% larger than the nearest-neighbor distance in a
+crystalline lattice is a typical choice for solids, so that bonds
+exist only between nearest neighbor pairs.
+
+The *qfactor* argument is the limiting strain at which the bias
+potential goes to 0.0.  It is dimensionless, so a value of 0.3 means a
+bond distance can be up to 30% larger or 30% smaller than the
+equilibrium (quenched) R0ij distance and the two atoms in the bond
+could still experience a non-zero bias force.
+
+If *qfactor* is set too large, then transitions from one energy basin
+to another are affected because the bias potential is non-zero at the
+transition state (e.g. saddle point).  If *qfactor* is set too small
+than little boost is achieved because the Eij strain of some bond in
+the system will (nearly) always exceed *qfactor*\ .  A value of 0.3 for
+*qfactor* is typically reasonable.
+
+The *Vmax* argument is the prefactor on the bias potential.  Ideally,
+tt should be set to a value slightly less than the smallest barrier
+height for an event to occur.  Otherwise the applied bias potential
+may be large enough (when added to the interatomic potential) to
+produce a local energy basin with a maxima in the center.  This can
+produce artificial energy minima in the same basin that trap an atom.
+Or if *Vmax* is even larger, it may induce an atom(s) to rapidly
+transition to another energy basin.  Both cases are "bad dynamics"
+which violate the assumptions of GHD that guarantee an accelerated
+time-accurate trajectory of the system.
+
+Note that if *Vmax* is set too small, the GHD simulation will run
+correctly.  There will just be fewer events because the hyper time
+(t\_hyper equation above) will be shorter.
+
+.. note::
+
+   If you have no physical intuition as to the smallest barrier
+   height in your system, a reasonable strategy to determine the largest
+   *Vmax* you can use for a GHD model, is to run a sequence of
+   simulations with smaller and smaller *Vmax* values, until the event
+   rate does not change (as a function of hyper time).
+
+The *Tequil* argument is the temperature at which the system is
+simulated; see the comment above about the :doc:`fix langevin <fix_langevin>` thermostatting.  It is also part of the
+beta term in the exponential factor that determines how much boost is
+achieved as a function of the bias potential.
+
+In general, the lower the value of *Tequil* and the higher the value
+of *Vmax*\ , the more time boost will be achievable by the GHD
+algorithm.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy of the bias potential to the system's
+potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar and global vector of length 12, which
+can be accessed by various :doc:`output commands <Howto_output>`.  The
+scalar is the magnitude of the bias potential (energy units) applied on
+the current timestep.  The vector stores the following quantities:
+
+* 1 = boost factor on this step (unitless)
+* 2 = max strain Eij of any bond on this step (absolute value, unitless)
+* 3 = ID of first atom in the max-strain bond
+* 4 = ID of second atom in the max-strain bond
+* 5 = average # of bonds/atom on this step
+
+* 6 = fraction of timesteps where the biased bond has bias = 0.0 during this run
+* 7 = fraction of timesteps where the biased bond has negative strain during this run
+* 8 = max drift distance of any atom during this run (distance units)
+* 9 = max bond length during this run (distance units)
+
+* 10 = cumulative hyper time since fix was defined (time units)
+* 11 = cumulative count of event timesteps since fix was defined
+* 12 = cumulative count of atoms in events since fix was defined
+
+The first 5 quantities are for the current timestep.  Quantities 6-9
+are for the current hyper run.  They are reset each time a new hyper
+run is performed.  Quantities 19-12 are cumulative across multiple
+runs (since the point in the input script the fix was defined).
+
+For value 8, drift is the distance an atom moves between two quenched
+states when the second quench determines an event has occurred.  Atoms
+involved in an event will typically move the greatest distance since
+others typically remain near their original quenched position.
+
+For value 11, events are checked for by the :doc:`hyper <hyper>` command
+once every *Nevent* timesteps.  This value is the count of those
+timesteps on which one (or more) events was detected.  It is NOT the
+number of distinct events, since more than one event may occur in the
+same *Nevent* time window.
+
+For value 12, each time the :doc:`hyper <hyper>` command checks for an
+event, it invokes a compute to flag zero or more atoms as
+participating in one or more events.  E.g. atoms that have displaced
+more than some distance from the previous quench state.  Value 11 is
+the cumulative count of the number of atoms participating in any of
+the events that were found.
+
+The scalar and vector values calculated by this fix are all
+"intensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`hyper <hyper>`, :doc:`fix hyper/local <fix_hyper_local>`
+
+**Default:** None
+
+
+----------
+
+
+.. _Voter2013ghd:
+
+
+
+**(Voter2013)** S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
+144110 (2013).
+
+.. _Mironghd:
+
+
+
+**(Miron)** R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst
new file mode 100644
index 0000000000..14bdff77d1
--- /dev/null
+++ b/doc/src/fix_hyper_local.rst
@@ -0,0 +1,516 @@
+.. index:: fix hyper/local
+
+fix hyper/local command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID hyper/local cutbond qfactor Vmax Tequil Dcut alpha Btarget
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* hyper/local = style name of this fix command
+* cutbond = max distance at which a pair of atoms is considered bonded (distance units)
+* qfactor = max strain at which bias potential goes to 0.0 (unitless)
+* Vmax = estimated height of bias potential (energy units)
+* Tequil = equilibration temperature (temperature units)
+* Dcut = minimum distance between boosted bonds (distance units)
+* alpha = boostostat relaxation time (time units)
+* Btarget = desired time boost factor (unitless)
+* zero or more keyword/value pairs may be appended
+* keyword = *check/ghost* or *check/bias*
+  
+  .. parsed-literal::
+  
+       *check/ghost* values = none
+       *check/bias* values = Nevery error/warn/ignore
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all hyper/local 1.0 0.3 0.8 300.0
+
+Description
+"""""""""""
+
+This fix is meant to be used with the :doc:`hyper <hyper>` command to
+perform a bond-boost local hyperdynamics (LHD) simulation.  The role
+of this fix is to a select multiple pairs of atoms in the system at
+each timestep to add a local bias potential to, which will alter the
+dynamics of the system in a manner that effectively accelerates time.
+This is in contrast to the :doc:`fix hyper/global <fix_hyper_global>`
+command, which can be user to perform a global hyperdynamics (GHD)
+simulation, by adding a global bias potential to a single pair of
+atoms at each timestep.  GHD can time accelerate a small simulation
+with up to a few 100 atoms.  For larger systems, LHD is needed to
+achieve good time acceleration.
+
+For a system that undergoes rare transition events, where one or more
+atoms move over an energy barrier to a new potential energy basin, the
+effect of the bias potential is to induce more rapid transitions.
+This can lead to a dramatic speed-up in the rate at which events
+occurs, without altering their relative frequencies, thus leading to
+an overall increase in the elapsed real time of the simulation as
+compared to running for the same number of timesteps with normal MD.
+See the :doc:`hyper <hyper>` doc page for a more general discussion of
+hyperdynamics and citations that explain both GHD and LHD.
+
+The equations and logic used by this fix and described here to perform
+LHD follow the description given in :ref:`(Voter2013) <Voter2013lhd>`.  The
+bond-boost form of a bias potential for HD is due to Miron and
+Fichthorn as described in :ref:`(Miron) <Mironlhd>`.
+
+To understand this description, you should first read the description
+of the GHD algorithm on the :doc:`fix hyper/global <fix_hyper_global>`
+doc page.  This description of LHD builds on the GHD description.
+
+The definition of bonds and Eij are the same for GHD and LHD.  The
+formulas for Vij(max) and Fij(max) are also the same except for a
+pre-factor Cij, explained below.
+
+The bias energy Vij applied to a bond IJ with maximum strain is
+
+
+.. parsed-literal::
+
+   Vij(max) = Cij \* Vmax \* (1 - (Eij/q)\^2) for abs(Eij) < qfactor
+            = 0 otherwise
+
+The derivative of Vij(max) with respect to the position of each atom
+in the IJ bond gives a bias force Fij(max) acting on the bond as
+
+
+.. parsed-literal::
+
+   Fij(max) = - dVij(max)/dEij = 2 Cij Vmax Eij / qfactor\^2   for abs(Eij) < qfactor
+            = 0 otherwise
+
+which can be decomposed into an equal and opposite force acting on
+only the two I,J atoms in the IJ bond.
+
+The key difference is that in GHD a bias energy and force is added (on
+a particular timestep) to only one bond (pair of atoms) in the system,
+which is the bond with maximum strain Emax.
+
+In LHD, a bias energy and force can be added to multiple bonds
+separated by the specified *Dcut* distance or more.  A bond IJ is
+biased if it is the maximum strain bond within its local
+"neighborhood", which is defined as the bond IJ plus any neighbor
+bonds within a distance *Dcut* from IJ.  The "distance" between bond
+IJ and bond KL is the minimum distance between any of the IK, IL, JK,
+JL pairs of atoms.
+
+For a large system, multiple bonds will typically meet this
+requirement, and thus a bias potential Vij(max) will be applied to
+many bonds on the same timestep.
+
+In LHD, all bonds store a Cij prefactor which appears in the Vij(max)
+and Fij(max) equations above.  Note that the Cij factor scales the
+strength of the bias energy and forces whenever bond IJ is the maximum
+strain bond in its neighborhood.
+
+Cij is initialized to 1.0 when a bond between the I,J atoms is first
+defined.  The specified *Btarget* factor is then used to adjust the
+Cij prefactors for each bond every timestep in the following manner.
+
+An instantaneous boost factor Bij is computed each timestep
+for each bond, as
+
+
+.. parsed-literal::
+
+   Bij = exp(beta \* Vkl(max))
+
+where Vkl(max) is the bias energy of the maxstrain bond KL within bond
+IJ's neighborhood, beta = 1/kTequil, and *Tequil* is the temperature
+of the system and an argument to this fix.
+
+.. note::
+
+   To run an LHD simulation, the input script must also use the
+   :doc:`fix langevin <fix_langevin>` command to thermostat the atoms at
+   the same *Tequil* as specified by this fix, so that the system is
+   running constant-temperature (NVT) dynamics.  LAMMPS does not check
+   that this is done.
+
+Note that if IJ = KL, then bond IJ is a biased bond on that timestep,
+otherwise it is not.  But regardless, the boost factor Bij can be
+thought of an estimate of time boost currently being applied within a
+local region centered on bond IJ.  For LHD, we want this to be the
+specified *Btarget* value everywhere in the simulation domain.
+
+To accomplish this, if Bij < Btarget, the Cij prefactor for bond IJ is
+incremented on the current timestep by an amount proportional to the
+inverse of the specified *alpha* and the difference (Bij - Btarget).
+Conversely if Bij > Btarget, Cij is decremented by the same amount.
+This procedure is termed "boostostatting" in
+:ref:`(Voter2013) <Voter2013lhd>`.  It drives all of the individual Cij to
+values such that when Vij\ *max* is applied as a bias to bond IJ, the
+resulting boost factor Bij will be close to *Btarget* on average.
+Thus the LHD time acceleration factor for the overall system is
+effectively *Btarget*\ .
+
+Note that in LHD, the boost factor *Btarget* is specified by the user.
+This is in contrast to global hyperdynamics (GHD) where the boost
+factor varies each timestep and is computed as a function of *Vmax*\ ,
+Emax, and *Tequil*\ ; see the :doc:`fix hyper/global <fix_hyper_global>`
+doc page for details.
+
+
+----------
+
+
+Here is additional information on the input parameters for LHD.
+
+Note that the *cutbond*\ , *qfactor*\ , and *Tequil* arguments have the
+same meaning as for GHD.  The *Vmax* argument is slightly different.
+The *Dcut*\ , *alpha*\ , and *Btarget* parameters are unique to LHD.
+
+The *cutbond* argument is the cutoff distance for defining bonds
+between pairs of nearby atoms.  A pair of I,J atoms in their
+equilibrium, minimum-energy configuration, which are separated by a
+distance Rij < *cutbond*\ , are flagged as a bonded pair.  Setting
+*cubond* to be ~25% larger than the nearest-neighbor distance in a
+crystalline lattice is a typical choice for solids, so that bonds
+exist only between nearest neighbor pairs.
+
+The *qfactor* argument is the limiting strain at which the bias
+potential goes to 0.0.  It is dimensionless, so a value of 0.3 means a
+bond distance can be up to 30% larger or 30% smaller than the
+equilibrium (quenched) R0ij distance and the two atoms in the bond
+could still experience a non-zero bias force.
+
+If *qfactor* is set too large, then transitions from one energy basin
+to another are affected because the bias potential is non-zero at the
+transition state (e.g. saddle point).  If *qfactor* is set too small
+than little boost can be achieved because the Eij strain of some bond in
+the system will (nearly) always exceed *qfactor*\ .  A value of 0.3 for
+*qfactor* is typically a reasonable value.
+
+The *Vmax* argument is a fixed prefactor on the bias potential.  There
+is a also a dynamic prefactor Cij, driven by the choice of *Btarget*
+as discussed above.  The product of these should be a value less than
+the smallest barrier height for an event to occur.  Otherwise the
+applied bias potential may be large enough (when added to the
+interatomic potential) to produce a local energy basin with a maxima
+in the center.  This can produce artificial energy minima in the same
+basin that trap an atom.  Or if Cij\*\ *Vmax* is even larger, it may
+induce an atom(s) to rapidly transition to another energy basin.  Both
+cases are "bad dynamics" which violate the assumptions of LHD that
+guarantee an accelerated time-accurate trajectory of the system.
+
+.. note::
+
+   It may seem that *Vmax* can be set to any value, and Cij will
+   compensate to reduce the overall prefactor if necessary.  However the
+   Cij are initialized to 1.0 and the boostostatting procedure typically
+   operates slowly enough that there can be a time period of bad dynamics
+   if *Vmax* is set too large.  A better strategy is to set *Vmax* to the
+   smallest barrier height for an event (the same as for GHD), so that
+   the Cij remain near unity.
+
+The *Tequil* argument is the temperature at which the system is
+simulated; see the comment above about the :doc:`fix langevin <fix_langevin>` thermostatting.  It is also part of the
+beta term in the exponential factor that determines how much boost is
+achieved as a function of the bias potential.  See the discussion of
+the *Btarget* argument below.
+
+As discussed above, the *Dcut* argument is the distance required
+between two locally maxstrain bonds for them to both be selected as
+biased bonds on the same timestep.  Computationally, the larger *Dcut*
+is, the more work (computation and communication) must be done each
+timestep within the LHD algorithm.  And the fewer bonds can be
+simultaneously biased, which may mean the specified *Btarget* time
+acceleration cannot be achieved.
+
+Physically *Dcut* should be a long enough distance that biasing two
+pairs of atoms that close together will not influence the dynamics of
+each pair.  E.g. something like 2x the cutoff of the interatomic
+potential.  In practice a *Dcut* value of ~10 Angstroms seems to work
+well for many solid-state systems.
+
+.. note::
+
+   You should insure that ghost atom communication is performed for
+   a distance of at least *Dcut* + *cutevent* = the distance one or more
+   atoms move (between quenched states) to be considered an "event".  It
+   is an argument to the "compute event/displace" command used to detect
+   events.  By default the ghost communication distance is set by the
+   pair\_style cutoff, which will typically be < *Dcut*\ .  The :doc:`comm\_modify cutoff <comm_modify>` command should be used to override the ghost
+   cutoff explicitly, e.g.
+
+
+.. parsed-literal::
+
+   comm_modify cutoff 12.0
+
+Note that this fix does not know the *cutevent* parameter, but uses
+half the *cutbond* parameter as an estimate to warn if the ghost
+cutoff is not long enough.
+
+As described above the *alpha* argument is a pre-factor in the
+boostostat update equation for each bond's Cij prefactor.  *Alpha* is
+specified in time units, similar to other thermostat or barostat
+damping parameters.  It is roughly the physical time it will take the
+boostostat to adjust a Cij value from a too high (or too low) value to
+a correct one.  An *alpha* setting of a few ps is typically good for
+solid-state systems.  Note that the *alpha* argument here is the
+inverse of the alpha parameter discussed in
+:ref:`(Voter2013) <Voter2013lhd>`.
+
+The *Btarget* argument is the desired time boost factor (a value > 1)
+that all the atoms in the system will experience.  The elapsed time
+t\_hyper for an LHD simulation running for *N* timesteps is simply
+
+
+.. parsed-literal::
+
+   t_hyper = Btarget \* N\*dt
+
+where dt is the timestep size defined by the :doc:`timestep <timestep>`
+command.  The effective time acceleration due to LHD is thus t\_hyper /
+N\*dt = Btarget, where N\*dt is elapsed time for a normal MD run
+of N timesteps.
+
+You cannot choose an arbitrarily large setting for *Btarget*\ .  The
+maximum value you should choose is
+
+
+.. parsed-literal::
+
+   Btarget = exp(beta \* Vsmall)
+
+where Vsmall is the smallest event barrier height in your system, beta
+= 1/kTequil, and *Tequil* is the specified temperature of the system
+(both by this fix and the Langevin thermostat).
+
+Note that if *Btarget* is set smaller than this, the LHD simulation
+will run correctly.  There will just be fewer events because the hyper
+time (t\_hyper equation above) will be shorter.
+
+.. note::
+
+   If you have no physical intuition as to the smallest barrier
+   height in your system, a reasonable strategy to determine the largest
+   *Btarget* you can use for an LHD model, is to run a sequence of
+   simulations with smaller and smaller *Btarget* values, until the event
+   rate does not change (as a function of hyper time).
+
+
+----------
+
+
+Here is additional information on the optional keywords for this fix.
+
+The *check/ghost* keyword turns on extra computation each timestep to
+compute statistics about ghost atoms used to determine which bonds to
+bias.  The output of these stats are the vector values 14 and 15,
+described below.  If this keyword is not enabled, the output
+of the stats will be zero.
+
+The *check/bias* keyword turns on extra computation and communication
+to check if any biased bonds are closer than *Dcut* to each other,
+which should not be the case if LHD is operating correctly.  Thus it
+is a debugging check.  The *Nevery* setting determines how often the
+check is made.  The *error*\ , *warn*\ , or *ignore* setting determines
+what is done if the count of too-close bonds is not zero.  Either the
+code will exit, or issue a warning, or silently tally the count.  The
+count can be output as vector value 17, as described below.  If this
+keyword is not enabled, the output of that statistic will be 0.
+
+Note that both of these computations are costly, hence they are only
+enabled by these keywords.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy of the bias potential to the system's
+potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar and global vector of length 21,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar is the magnitude of the bias potential (energy units)
+applied on the current timestep, summed over all biased bonds.  The
+vector stores the following quantities:
+
+* 1 = # of biased bonds on this step
+* 2 = max strain Eij of any bond on this step (absolute value, unitless)
+* 3 = average bias coeff for all bonds on this step (unitless)
+* 4 = average # of bonds/atom on this step
+* 5 = average neighbor bonds/bond on this step within *Dcut*
+
+* 6 = max bond length during this run (distance units)
+* 7 = average # of biased bonds/step during this run
+* 8 = fraction of biased bonds with no bias during this run
+* 9 = fraction of biased bonds with negative strain during this run
+* 10 = average bias coeff for all bonds during this run (unitless)
+* 11 = min bias coeff for any bond during this run (unitless)
+* 12 = max bias coeff for any bond during this run (unitless)
+
+* 13 = max drift distance of any bond atom during this run (distance units)
+* 14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
+* 15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
+* 16 = count of ghost atoms that could not be found on reneighbor steps during this run
+* 17 = count of bias overlaps (< Dcut) found during this run
+
+* 18 = cumulative hyper time since fix created (time units)
+* 19 = cumulative count of event timesteps since fix created
+* 20 = cumulative count of atoms in events since fix created
+* 21 = cumulative # of new bonds formed since fix created
+
+The first quantities (1-5) are for the current timestep.  Quantities
+6-17 are for the current hyper run.  They are reset each time a new
+hyper run is performed.  Quantities 18-21 are cumulative across
+multiple runs (since the point in the input script the fix was
+defined).
+
+For value 8, the numerator is a count of all biased bonds on each
+timestep whose bias energy = 0.0 due to Eij >= *qfactor*\ .  The
+denominator is the count of all biased bonds on all timesteps.
+
+For value 9, the numerator is a count of all biased bonds on each
+timestep with negative strain.  The denominator is the count of all
+biased bonds on all timesteps.
+
+Values 13-17 are mostly useful for debugging and diagnostic purposes.
+
+For value 13, drift is the distance an atom moves between two quenched
+states when the second quench determines an event has occurred.  Atoms
+involved in an event will typically move the greatest distance since
+others typically remain near their original quenched position.
+
+For values 14-16, neighbor atoms in the full neighbor list with cutoff
+*Dcut* may be ghost atoms outside a processor's sub-box.  Before the
+next event occurs they may move further than *Dcut* away from the
+sub-box boundary.  Value 14 is the furthest (from the sub-box) any
+ghost atom in the neighbor list with maxstrain < *qfactor* was
+accessed during the run.  Value 15 is the same except that the ghost
+atom's maxstrain may be >= *qfactor*\ , which may mean it is about to
+participate in an event.  Value 16 is a count of how many ghost atoms
+could not be found on reneighbor steps, presumably because they moved
+too far away due to their participation in an event (which will likely
+be detected at the next quench).
+
+Typical values for 14 and 15 should be slightly larger than *Dcut*\ ,
+which accounts for ghost atoms initially at a *Dcut* distance moving
+thermally before the next event takes place.
+
+Note that for values 14 and 15 to be computed, the optional keyword
+*check/ghost* must be specified.  Otherwise these values will be zero.
+This is because computing them incurs overhead, so the values are only
+computed if requested.
+
+Value 16 should be zero or small.  As explained above a small count
+likely means some ghost atoms were participating in their own events
+and moved a longer distance.  If the value is large, it likely means
+the communication cutoff for ghosts is too close to *Dcut* leading to
+many not-found ghost atoms before the next event.  This may lead to a
+reduced number of bonds being selected for biasing, since the code
+assumes those atoms are part of highly strained bonds.  As explained
+above, the :doc:`comm\_modify cutoff <comm_modify>` command can be used
+to set a longer cutoff.
+
+For value 17, no two bonds should be biased if they are within a
+*Dcut* distance of each other.  This value should be zero, indicating
+that no pair of biased bonds are closer than *Dcut* from each other.
+
+Note that for values 17 to be computed, the optional keyword
+*check/bias* must be specified and it determines how often this check
+is performed.  This is because performing the check incurs overhead,
+so if only computed as often as requested.
+
+The result at the end of the run is the cumulative total from every
+timestep the check was made.  Note that the value is a count of atoms
+in bonds which found other atoms in bonds too close, so it is almost
+always an over-count of the number of too-close bonds.
+
+Value 18 is simply the specified *boost* factor times the number of
+timesteps times the timestep size.
+
+For value 19, events are checked for by the :doc:`hyper <hyper>` command
+once every *Nevent* timesteps.  This value is the count of those
+timesteps on which one (or more) events was detected.  It is NOT the
+number of distinct events, since more than one event may occur in the
+same *Nevent* time window.
+
+For value 20, each time the :doc:`hyper <hyper>` command checks for an
+event, it invokes a compute to flag zero or more atoms as
+participating in one or more events.  E.g. atoms that have displaced
+more than some distance from the previous quench state.  Value 20 is
+the cumulative count of the number of atoms participating in any of
+the events that were found.
+
+Value 21 tallies the number of new bonds created by the bond reset
+operation.  Bonds between a specific I,J pair of atoms may persist for
+the entire hyperdynamics simulation if neither I or J are involved in
+an event.
+
+The scalar and vector values calculated by this fix are all
+"intensive".
+
+This fix also computes a local vector of length the number of bonds
+currently in the system.  The value for each bond is its Cij prefactor
+(bias coefficient).  These values can be can be accessed by various
+:doc:`output commands <Howto_output>`.  A particularly useful one is the
+:doc:`fix ave/histo <fix_ave_histo>` command which can be used to
+histogram the Cij values to see if they are distributed reasonably
+close to 1.0, which indicates a good choice of *Vmax*\ .
+
+The local values calculated by this fix are unitless.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the REPLICA package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`hyper <hyper>`, :doc:`fix hyper/global <fix_hyper_global>`
+
+Default
+"""""""
+
+The check/ghost and check/bias keywords are not enabled by default.
+
+
+----------
+
+
+.. _Voter2013lhd:
+
+
+
+**(Voter2013)** S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
+144110 (2013).
+
+.. _Mironlhd:
+
+
+
+**(Miron)** R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst
new file mode 100644
index 0000000000..b688316546
--- /dev/null
+++ b/doc/src/fix_imd.rst
@@ -0,0 +1,182 @@
+.. index:: fix imd
+
+fix imd command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID imd trate port keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* imd = style name of this fix command
+* port = port number on which the fix listens for an IMD client
+* keyword = *unwrap* or *fscale* or *trate*
+  
+  .. parsed-literal::
+  
+       *unwrap* arg = *on* or *off*
+         off = coordinates are wrapped back into the principal unit cell (default)
+         on = "unwrapped" coordinates using the image flags used
+       *fscale* arg = factor
+         factor = floating point number to scale IMD forces (default: 1.0)
+       *trate* arg = transmission rate of coordinate data sets (default: 1)
+       *nowait* arg = *on* or *off*
+         off = LAMMPS waits to be connected to an IMD client before continuing (default)
+         on = LAMMPS listens for an IMD client, but continues with the run
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix vmd all imd 5678
+   fix comm all imd 8888 trate 5 unwrap on fscale 10.0
+
+Description
+"""""""""""
+
+This fix implements the "Interactive MD" (IMD) protocol which allows
+realtime visualization and manipulation of MD simulations through the
+IMD protocol, as initially implemented in VMD and NAMD.  Specifically
+it allows LAMMPS to connect an IMD client, for example the `VMD visualization program <VMD_>`_, so that it can monitor the progress of the
+simulation and interactively apply forces to selected atoms.
+
+If LAMMPS is compiled with the pre-processor flag -DLAMMPS\_ASYNC\_IMD
+then fix imd will use POSIX threads to spawn a IMD communication
+thread on MPI rank 0 in order to offload data reading and writing
+from the main execution thread and potentially lower the inferred
+latencies for slow communication links. This feature has only been
+tested under linux.
+
+There are example scripts for using this package with LAMMPS in
+examples/USER/imd. Additional examples and a driver for use with the
+Novint Falcon game controller as haptic device can be found at:
+http://sites.google.com/site/akohlmey/software/vrpn-icms.
+
+The source code for this fix includes code developed by the
+Theoretical and Computational Biophysics Group in the Beckman
+Institute for Advanced Science and Technology at the University of
+Illinois at Urbana-Champaign.  We thank them for providing a software
+interface that allows codes like LAMMPS to hook to `VMD <VMD_>`_.
+
+Upon initialization of the fix, it will open a communication port on
+the node with MPI task 0 and wait for an incoming connection.  As soon
+as an IMD client is connected, the simulation will continue and the
+fix will send the current coordinates of the fix's group to the IMD
+client at every trate MD step. When using r-RESPA, trate applies to
+the steps of the outmost RESPA level.  During a run with an active IMD
+connection also the IMD client can request to apply forces to selected
+atoms of the fix group.
+
+The port number selected must be an available network port number.  On
+many machines, port numbers < 1024 are reserved for accounts with
+system manager privilege and specific applications. If multiple imd
+fixes would be active at the same time, each needs to use a different
+port number.
+
+The *nowait* keyword controls the behavior of the fix when no IMD
+client is connected. With the default setting of *off*\ , LAMMPS will
+wait until a connection is made before continuing with the
+execution. Setting *nowait* to *on* will have the LAMMPS code be ready
+to connect to a client, but continue with the simulation. This can for
+example be used to monitor the progress of an ongoing calculation
+without the need to be permanently connected or having to download a
+trajectory file.
+
+The *trate* keyword allows to select how often the coordinate data is
+sent to the IMD client. It can also be changed on request of the IMD
+client through an IMD protocol message.  The *unwrap* keyword allows
+to send "unwrapped" coordinates to the IMD client that undo the
+wrapping back of coordinates into the principle unit cell, as done by
+default in LAMMPS.  The *fscale* keyword allows to apply a scaling
+factor to forces transmitted by the IMD client. The IMD protocols
+stipulates that forces are transferred in kcal/mol/angstrom under the
+assumption that coordinates are given in angstrom. For LAMMPS runs
+with different units or as a measure to tweak the forces generated by
+the manipulation of the IMD client, this option allows to make
+adjustments.
+
+To connect VMD to a listening LAMMPS simulation on the same machine
+with fix imd enabled, one needs to start VMD and load a coordinate or
+topology file that matches the fix group.  When the VMD command
+prompts appears, one types the command line:
+
+
+.. parsed-literal::
+
+   imd connect localhost 5678
+
+This assumes that *fix imd* was started with 5678 as a port
+number for the IMD protocol.
+
+The steps to do interactive manipulation of a running simulation in
+VMD are the following:
+
+In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
+Atom".  You may alternately select "Residue", or "Fragment" to apply
+forces to whole residues or fragments. Your mouse can now be used to
+apply forces to your simulation. Click on an atom, residue, or
+fragment and drag to apply a force. Click quickly without moving the
+mouse to turn the force off. You can also use a variety of 3D position
+trackers to apply forces to your simulation. Game controllers or haptic
+devices with force-feedback such as the Novint Falcon or Sensable
+PHANTOM allow you to feel the resistance due to inertia or interactions
+with neighbors that the atoms experience you are trying to move, as if
+they were real objects. See the `VMD IMD Homepage <imdvmd_>`_ and the
+`VRPN-ICMS Homepage <vrpnicms_>`_ for more details.
+
+If IMD control messages are received, a line of text describing the
+message and its effect will be printed to the LAMMPS output screen, if
+screen output is active.
+
+.. _VMD: http://www.ks.uiuc.edu/Research/vmd
+
+
+
+.. _imdvmd: http://www.ks.uiuc.edu/Research/vmd/imd/
+
+
+
+.. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms
+
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global scalar or vector or per-atom
+quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`.  No parameter of this fix can be used
+with the *start/stop* keywords of the :doc:`run <run>` command.  This
+fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+When used in combination with VMD, a topology or coordinate file has
+to be loaded, which matches (in number and ordering of atoms) the
+group the fix is applied to. The fix internally sorts atom IDs by
+ascending integer value; in VMD (and thus the IMD protocol) those will
+be assigned 0-based consecutive index numbers.
+
+When using multiple active IMD connections at the same time, each
+needs to use a different port number.
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst
new file mode 100644
index 0000000000..c130ede009
--- /dev/null
+++ b/doc/src/fix_indent.rst
@@ -0,0 +1,234 @@
+.. index:: fix indent
+
+fix indent command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID indent K keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* indent = style name of this fix command
+* K = force constant for indenter surface (force/distance\^2 units)
+* one or more keyword/value pairs may be appended
+* keyword = *sphere* or *cylinder* or *plane* or *side* or *units*
+  
+  .. parsed-literal::
+  
+       *sphere* args = x y z R
+         x,y,z = initial position of center of indenter (distance units)
+         R = sphere radius of indenter (distance units)
+         any of x,y,z,R can be a variable (see below)
+       *cylinder* args = dim c1 c2 R
+         dim = *x* or *y* or *z* = axis of cylinder
+         c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
+         R = cylinder radius of indenter (distance units)
+         any of c1,c2,R can be a variable (see below)
+       *plane* args = dim pos side
+         dim = *x* or *y* or *z* = plane perpendicular to this dimension
+         pos = position of plane in dimension x, y, or z (distance units)
+         pos can be a variable (see below)
+         side = *lo* or *hi*
+       *side* value = *in* or *out*
+         *in* = the indenter acts on particles inside the sphere or cylinder
+         *out* = the indenter acts on particles outside the sphere or cylinder
+       *units* value = *lattice* or *box*
+         lattice = the geometry is defined in lattice units
+         box = the geometry is defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
+   fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
+   fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
+
+Description
+"""""""""""
+
+Insert an indenter within a simulation box.  The indenter repels all
+atoms in the group that touch it, so it can be used to push into a
+material or as an obstacle in a flow.  Or it can be used as a
+constraining wall around a simulation; see the discussion of the
+*side* keyword below.
+
+The indenter can either be spherical or cylindrical or planar.  You
+must set one of those 3 keywords.
+
+A spherical indenter exerts a force of magnitude
+
+
+.. parsed-literal::
+
+   F(r) = - K (r - R)\^2
+
+on each atom where *K* is the specified force constant, *r* is the
+distance from the atom to the center of the indenter, and *R* is the
+radius of the indenter.  The force is repulsive and F(r) = 0 for *r* >
+*R*\ .
+
+A cylindrical indenter exerts the same force, except that *r* is the
+distance from the atom to the center axis of the cylinder.  The
+cylinder extends infinitely along its axis.
+
+Spherical and cylindrical indenters account for periodic boundaries in
+two ways.  First, the center point of a spherical indenter (x,y,z) or
+axis of a cylindrical indenter (c1,c2) is remapped back into the
+simulation box, if the box is periodic in a particular dimension.
+This occurs every timestep if the indenter geometry is specified with
+a variable (see below), e.g. it is moving over time.  Second, the
+calculation of distance to the indenter center or axis accounts for
+periodic boundaries.  Both of these mean that an indenter can
+effectively move through and straddle one or more periodic boundaries.
+
+A planar indenter is really an axis-aligned infinite-extent wall
+exerting the same force on atoms in the system, where *R* is the
+position of the plane and *r-R* is the distance from the plane.  If
+the *side* parameter of the plane is specified as *lo* then it will
+indent from the lo end of the simulation box, meaning that atoms with
+a coordinate less than the plane's current position will be pushed
+towards the hi end of the box and atoms with a coordinate higher than
+the plane's current position will feel no force.  Vice versa if *side*
+is specified as *hi*\ .
+
+Any of the 4 quantities defining a spherical indenter's geometry can
+be specified as an equal-style :doc:`variable <variable>`, namely *x*\ ,
+*y*\ , *z*\ , or *R*\ .  Similarly, for a cylindrical indenter, any of *c1*\ ,
+*c2*\ , or *R*\ , can be a variable.  For a planar indenter, *pos* can be
+a variable.  If the value is a variable, it should be specified as
+v\_name, where name is the variable name.  In this case, the variable
+will be evaluated each timestep, and its value used to define the
+indenter geometry.
+
+Note that equal-style variables can specify formulas with various
+mathematical functions, and include :doc:`thermo\_style <thermo_style>`
+command keywords for the simulation box parameters and timestep and
+elapsed time.  Thus it is easy to specify indenter properties that
+change as a function of time or span consecutive runs in a continuous
+fashion.  For the latter, see the *start* and *stop* keywords of the
+:doc:`run <run>` command and the *elaplong* keyword of :doc:`thermo\_style custom <thermo_style>` for details.
+
+For example, if a spherical indenter's x-position is specified as v\_x,
+then this variable definition will keep it's center at a relative
+position in the simulation box, 1/4 of the way from the left edge to
+the right edge, even if the box size changes:
+
+
+.. parsed-literal::
+
+   variable x equal "xlo + 0.25\*lx"
+
+Similarly, either of these variable definitions will move the indenter
+from an initial position at 2.5 at a constant velocity of 5:
+
+
+.. parsed-literal::
+
+   variable x equal "2.5 + 5\*elaplong\*dt"
+   variable x equal vdisplace(2.5,5)
+
+If a spherical indenter's radius is specified as v\_r, then these
+variable definitions will grow the size of the indenter at a specified
+rate.
+
+
+.. parsed-literal::
+
+   variable r0 equal 0.0
+   variable rate equal 1.0
+   variable r equal "v_r0 + step\*dt\*v_rate"
+
+If the *side* keyword is specified as *out*\ , which is the default,
+then particles outside the indenter are pushed away from its outer
+surface, as described above.  This only applies to spherical or
+cylindrical indenters.  If the *side* keyword is specified as *in*\ ,
+the action of the indenter is reversed.  Particles inside the indenter
+are pushed away from its inner surface.  In other words, the indenter
+is now a containing wall that traps the particles inside it.  If the
+radius shrinks over time, it will squeeze the particles.
+
+The *units* keyword determines the meaning of the distance units used
+to define the indenter geometry.  A *box* value selects standard
+distance units as defined by the :doc:`units <units>` command,
+e.g. Angstroms for units = real or metal.  A *lattice* value means the
+distance units are in lattice spacings.  The :doc:`lattice <lattice>`
+command must have been previously used to define the lattice spacing.
+The (x,y,z) coords of the indenter position are scaled by the x,y,z
+lattice spacings respectively.  The radius of a spherical or
+cylindrical indenter is scaled by the x lattice spacing.
+
+Note that the units keyword only affects indenter geometry parameters
+specified directly with numbers, not those specified as variables.  In
+the latter case, you should use the *xlat*\ , *ylat*\ , *zlat* keywords of
+the :doc:`thermo\_style <thermo_style>` command if you want to include
+lattice spacings in a variable formula.
+
+The force constant *K* is not affected by the *units* keyword.  It is
+always in force/distance\^2 units where force and distance are defined
+by the :doc:`units <units>` command.  If you wish K to be scaled by the
+lattice spacing, you can define K with a variable whose formula
+contains *xlat*\ , *ylat*\ , *zlat* keywords of the
+:doc:`thermo\_style <thermo_style>` command, e.g.
+
+
+.. parsed-literal::
+
+   variable k equal 100.0/xlat/xlat
+   fix 1 all indent $k sphere ...
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy of interaction between atoms and the indenter to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  The energy of each particle interacting
+with the indenter is K/3 (r - R)\^3.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global scalar energy and a global 3-vector of
+forces (on the indenter), which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar and vector values calculated
+by this fix are "extensive".
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.  Note that if you
+define the indenter geometry with a variable using a time-dependent
+formula, LAMMPS uses the iteration count in the minimizer as the
+timestep.  But it is almost certainly a bad idea to have the indenter
+change its position or size during a minimization.  LAMMPS does not
+check if you have done this.
+
+.. note::
+
+   If you want the atom/indenter interaction energy to be included
+   in the total potential energy of the system (the quantity being
+   minimized), you must enable the :doc:`fix\_modify <fix_modify>` *energy*
+   option for this fix.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+Default
+"""""""
+
+The option defaults are side = out and units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst
new file mode 100644
index 0000000000..1dc89c4174
--- /dev/null
+++ b/doc/src/fix_ipi.rst
@@ -0,0 +1,117 @@
+.. index:: fix ipi
+
+fix ipi command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ipi address port [unix] [reset]
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ipi = style name of this fix command
+* address = internet address (FQDN or IP), or UNIX socket name
+* port = port number (ignored for UNIX sockets)
+* optional keyword = *unix*\ , if present uses a unix socket
+* optional keyword = *reset*\ , if present reset electrostatics at each call
+
+Examples
+""""""""
+
+fix 1 all ipi my.server.com 12345
+fix 1 all ipi mysocket 666 unix reset
+
+Description
+"""""""""""
+
+This fix enables LAMMPS to be run as a client for the i-PI Python
+wrapper :ref:`(IPI) <ipihome>` for performing a path integral molecular dynamics
+(PIMD) simulation.  The philosophy behind i-PI is described in the
+following publication :ref:`(IPI-CPC) <IPICPC>`.
+
+A version of the i-PI package, containing only files needed for use
+with LAMMPS, is provided in the tools/i-pi directory.  See the
+tools/i-pi/manual.pdf for an introduction to i-PI.  The
+examples/USER/i-pi directory contains example scripts for using i-PI
+with LAMMPS.
+
+In brief, the path integral molecular dynamics is performed by the
+Python wrapper, while the client (LAMMPS in this case) simply computes
+forces and energy for each configuration. The communication between
+the two components takes place using sockets, and is reduced to the
+bare minimum. All the parameters of the dynamics are specified in the
+input of i-PI, and all the parameters of the force field must be
+specified as LAMMPS inputs, preceding the *fix ipi* command.
+
+The server address must be specified by the *address* argument, and
+can be either the IP address, the fully-qualified name of the server,
+or the name of a UNIX socket for local, faster communication. In the
+case of internet sockets, the *port* argument specifies the port
+number on which i-PI is listening, while the *unix* optional switch
+specifies that the socket is a UNIX socket.
+
+Note that there is no check of data integrity, or that the atomic
+configurations make sense. It is assumed that the species in the i-PI
+input are listed in the same order as in the data file of LAMMPS. The
+initial configuration is ignored, as it will be substituted with the
+coordinates received from i-PI before forces are ever evaluated.
+
+A note of caution when using potentials that contain long-range
+electrostatics, or that contain parameters that depend on box size:
+all of these options will be initialized based on the cell size in the
+LAMMPS-side initial configuration and kept constant during the run.
+This is required to e.g. obtain reproducible and conserved forces.
+If the cell varies too wildly, it may be advisable to re-initialize
+these interactions at each call. This behavior can be requested by
+setting the *reset* switch.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+There is no restart information associated with this fix, since all
+the dynamical parameters are dealt with by i-PI.
+
+Restrictions
+""""""""""""
+
+
+Using this fix on anything other than all atoms requires particular
+care, since i-PI will know nothing on atoms that are not those whose
+coordinates are transferred. However, one could use this strategy to
+define an external potential acting on the atoms that are moved by
+i-PI.
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  Because of the
+use of UNIX domain sockets, this fix will only work in a UNIX
+environment.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`
+
+
+----------
+
+
+.. _IPICPC:
+
+
+
+**(IPI-CPC)** Ceriotti, More and Manolopoulos, Comp Phys Comm, 185,
+1019-1026 (2014).
+
+.. _ipihome:
+
+
+
+**(IPI)**
+`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst
new file mode 100644
index 0000000000..d6f52084f5
--- /dev/null
+++ b/doc/src/fix_langevin.rst
@@ -0,0 +1,386 @@
+.. index:: fix langevin
+
+fix langevin command
+====================
+
+fix langevin/kk command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID langevin Tstart Tstop damp seed keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* langevin = style name of this fix command
+* Tstart,Tstop = desired temperature at start/end of run (temperature units)
+* Tstart can be a variable (see below)
+* damp = damping parameter (time units)
+* seed = random number seed to use for white noise (positive integer)
+* zero or more keyword/value pairs may be appended
+* keyword = *angmom* or *omega* or *scale* or *tally* or *zero*
+  
+  .. parsed-literal::
+  
+       *angmom* value = *no* or factor
+         *no* = do not thermostat rotational degrees of freedom via the angular momentum
+         factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
+       *gjf* value = *no* or *vfull* or *vhalf*
+         *no* = use standard formulation
+         *vfull* = use Gronbech-Jensen/Farago formulation
+         *vhalf* = use 2GJ formulation
+       *omega* value = *no* or *yes*
+         *no* = do not thermostat rotational degrees of freedom via the angular velocity
+         *yes* = do thermostat rotational degrees of freedom via the angular velocity
+       *scale* values = type ratio
+         type = atom type (1-N)
+         ratio = factor by which to scale the damping coefficient
+       *tally* value = *no* or *yes*
+         *no* = do not tally the energy added/subtracted to atoms
+         *yes* = do tally the energy added/subtracted to atoms
+       *zero* value = *no* or *yes*
+         *no* = do not set total random force to zero
+         *yes* = set total random force to zero
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 boundary langevin 1.0 1.0 1000.0 699483
+   fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5
+   fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333
+
+Description
+"""""""""""
+
+Apply a Langevin thermostat as described in :ref:`(Schneider) <Schneider1>`
+to a group of atoms which models an interaction with a background
+implicit solvent.  Used with :doc:`fix nve <fix_nve>`, this command
+performs Brownian dynamics (BD), since the total force on each atom
+will have the form:
+
+
+.. parsed-literal::
+
+   F = Fc + Ff + Fr
+   Ff = - (m / damp) v
+   Fr is proportional to sqrt(Kb T m / (dt damp))
+
+Fc is the conservative force computed via the usual inter-particle
+interactions (:doc:`pair\_style <pair_style>`,
+:doc:`bond\_style <bond_style>`, etc).
+
+The Ff and Fr terms are added by this fix on a per-particle basis.
+See the :doc:`pair\_style dpd/tstat <pair_dpd>` command for a
+thermostatting option that adds similar terms on a pairwise basis to
+pairs of interacting particles.
+
+Ff is a frictional drag or viscous damping term proportional to the
+particle's velocity.  The proportionality constant for each atom is
+computed as m/damp, where m is the mass of the particle and damp is
+the damping factor specified by the user.
+
+Fr is a force due to solvent atoms at a temperature T randomly bumping
+into the particle.  As derived from the fluctuation/dissipation
+theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
+dt damp), where Kb is the Boltzmann constant, T is the desired
+temperature, m is the mass of the particle, dt is the timestep size,
+and damp is the damping factor.  Random numbers are used to randomize
+the direction and magnitude of this force as described in
+:ref:`(Dunweg) <Dunweg1>`, where a uniform random number is used (instead of
+a Gaussian random number) for speed.
+
+Note that unless you use the *omega* or *angmom* keywords, the
+thermostat effect of this fix is applied to only the translational
+degrees of freedom for the particles, which is an important
+consideration for finite-size particles, which have rotational degrees
+of freedom, are being thermostatted.  The translational degrees of
+freedom can also have a bias velocity removed from them before
+thermostatting takes place; see the description below.
+
+.. note::
+
+   Unlike the :doc:`fix nvt <fix_nh>` command which performs
+   Nose/Hoover thermostatting AND time integration, this fix does NOT
+   perform time integration.  It only modifies forces to effect
+   thermostatting.  Thus you must use a separate time integration fix,
+   like :doc:`fix nve <fix_nve>` to actually update the velocities and
+   positions of atoms using the modified forces.  Likewise, this fix
+   should not normally be used on atoms that also have their temperature
+   controlled by another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>` commands.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+
+The desired temperature at each timestep is a ramped value during the
+run from *Tstart* to *Tstop*\ .
+
+*Tstart* can be specified as an equal-style or atom-style
+:doc:`variable <variable>`.  In this case, the *Tstop* setting is
+ignored.  If the value is a variable, it should be specified as
+v\_name, where name is the variable name.  In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+target temperature.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent temperature.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent
+temperature with optional time-dependence as well.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that remove a "bias" from the
+atom velocities.  E.g. removing the center-of-mass velocity from a
+group of atoms or removing the x-component of velocity from the
+calculation.  This is not done by default, but only if the
+:doc:`fix\_modify <fix_modify>` command is used to assign a temperature
+compute to this fix that includes such a bias term.  See the doc pages
+for individual :doc:`compute commands <compute>` to determine which ones
+include a bias.  In this case, the thermostat works in the following
+manner: bias is removed from each atom, thermostatting is performed on
+the remaining thermal degrees of freedom, and the bias is added back
+in.
+
+The *damp* parameter is specified in time units and determines how
+rapidly the temperature is relaxed.  For example, a value of 100.0
+means to relax the temperature in a timespan of (roughly) 100 time
+units (tau or fmsec or psec - see the :doc:`units <units>` command).
+The damp factor can be thought of as inversely related to the
+viscosity of the solvent.  I.e. a small relaxation time implies a
+hi-viscosity solvent and vice versa.  See the discussion about gamma
+and viscosity in the documentation for the :doc:`fix viscous <fix_viscous>` command for more details.
+
+The random # *seed* must be a positive integer.  A Marsaglia random
+number generator is used.  Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+The keyword *angmom* and *omega* keywords enable thermostatting of
+rotational degrees of freedom in addition to the usual translational
+degrees of freedom.  This can only be done for finite-size particles.
+
+A simulation using atom\_style sphere defines an omega for finite-size
+spheres.  A simulation using atom\_style ellipsoid defines a finite
+size and shape for aspherical particles and an angular momentum.
+The Langevin formulas for thermostatting the rotational degrees of
+freedom are the same as those above, where force is replaced by
+torque, m is replaced by the moment of inertia I, and v is replaced by
+omega (which is derived from the angular momentum in the case of
+aspherical particles).
+
+The rotational temperature of the particles can be monitored by the
+:doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute temp/asphere <compute_temp_asphere>` commands with their rotate
+options.
+
+For the *omega* keyword there is also a scale factor of 10.0/3.0 that
+is applied as a multiplier on the Ff (damping) term in the equation
+above and of sqrt(10.0/3.0) as a multiplier on the Fr term.  This does
+not affect the thermostatting behavior of the Langevin formalism but
+insures that the randomized rotational diffusivity of spherical
+particles is correct.
+
+For the *angmom* keyword a similar scale factor is needed which is
+10.0/3.0 for spherical particles, but is anisotropic for aspherical
+particles (e.g. ellipsoids).  Currently LAMMPS only applies an
+isotropic scale factor, and you can choose its magnitude as the
+specified value of the *angmom* keyword.  If your aspherical particles
+are (nearly) spherical than a value of 10.0/3.0 = 3.333 is a good
+choice.  If they are highly aspherical, a value of 1.0 is as good a
+choice as any, since the effects on rotational diffusivity of the
+particles will be incorrect regardless.  Note that for any reasonable
+scale factor, the thermostatting effect of the *angmom* keyword on the
+rotational temperature of the aspherical particles should still be
+valid.
+
+The keyword *scale* allows the damp factor to be scaled up or down by
+the specified factor for atoms of that type.  This can be useful when
+different atom types have different sizes or masses.  It can be used
+multiple times to adjust damp for several atom types.  Note that
+specifying a ratio of 2 increases the relaxation time which is
+equivalent to the solvent's viscosity acting on particles with 1/2 the
+diameter.  This is the opposite effect of scale factors used by the
+:doc:`fix viscous <fix_viscous>` command, since the damp factor in fix
+*langevin* is inversely related to the gamma factor in fix *viscous*\ .
+Also note that the damping factor in fix *langevin* includes the
+particle mass in Ff, unlike fix *viscous*\ .  Thus the mass and size of
+different atom types should be accounted for in the choice of ratio
+values.
+
+The keyword *tally* enables the calculation of the cumulative energy
+added/subtracted to the atoms as they are thermostatted.  Effectively
+it is the energy exchanged between the infinite thermal reservoir and
+the particles.  As described below, this energy can then be printed
+out or added to the potential energy of the system to monitor energy
+conservation.
+
+.. note::
+
+   this accumulated energy does NOT include kinetic energy removed
+   by the *zero* flag. LAMMPS will print a warning when both options are
+   active.
+
+The keyword *zero* can be used to eliminate drift due to the
+thermostat. Because the random forces on different atoms are
+independent, they do not sum exactly to zero.  As a result, this fix
+applies a small random force to the entire system, and the
+center-of-mass of the system undergoes a slow random walk.  If the
+keyword *zero* is set to *yes*\ , the total random force is set exactly
+to zero by subtracting off an equal part of it from each atom in the
+group.  As a result, the center-of-mass of a system with zero initial
+momentum will not drift over time.
+
+The keyword *gjf* can be used to run the :ref:`Gronbech-Jensen/Farago <Gronbech-Jensen>` time-discretization of the Langevin model.  As
+described in the papers cited below, the purpose of this method is to
+enable longer timesteps to be used (up to the numerical stability
+limit of the integrator), while still producing the correct Boltzmann
+distribution of atom positions.
+
+The current implementation provides the user with the option to output
+the velocity in one of two forms: *vfull* or *vhalf*\ , which replaces
+the outdated option *yes*\ . The *gjf* option *vfull* outputs the on-site
+velocity given in :ref:`Gronbech-Jensen/Farago <Gronbech-Jensen>`; this velocity
+is shown to be systematically lower than the target temperature by a small
+amount, which grows quadratically with the timestep.
+The *gjf* option *vhalf* outputs the 2GJ half-step velocity given in
+:ref:`Gronbech Jensen/Gronbech-Jensen <2Gronbech-Jensen>`; for linear systems,
+this velocity is shown to not have any statistical errors for any stable time step.
+An overview of statistically correct Boltzmann and Maxwell-Boltzmann
+sampling of true on-site and true half-step velocities is given in
+:ref:`Gronbech-Jensen <1Gronbech-Jensen>`.
+Regardless of the choice of output velocity, the sampling of the configurational
+distribution of atom positions is the same, and linearly consistent with the
+target temperature.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place.  However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  Note that use of this option requires
+setting the *tally* keyword to *yes*\ .
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".  Note that calculation of this quantity requires
+setting the *tally* keyword to *yes*\ .
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+For *gjf* do not choose damp=dt/2. *gjf* is not compatible
+with run\_style respa.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix viscous <fix_viscous>`, :doc:`fix nvt <fix_nh>`, :doc:`pair\_style dpd/tstat <pair_dpd>`
+
+Default
+"""""""
+
+The option defaults are angmom = no, omega = no, scale = 1.0 for all
+types, tally = no, zero = no, gjf = no.
+
+
+----------
+
+
+.. _Dunweg1:
+
+
+
+**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
+
+.. _Schneider1:
+
+
+
+**(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
+
+.. _Gronbech-Jensen:
+
+
+
+**(Gronbech-Jensen)** Gronbech-Jensen and Farago, Mol Phys, 111, 983
+(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
+
+.. _2Gronbech-Jensen:
+
+
+
+**(Gronbech-Jensen)** Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019)
+
+.. _1Gronbech-Jensen:
+
+
+
+**(Gronbech-Jensen)** Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst
new file mode 100644
index 0000000000..16de2eba8b
--- /dev/null
+++ b/doc/src/fix_langevin_drude.rst
@@ -0,0 +1,326 @@
+.. index:: fix langevin/drude
+
+fix langevin/drude command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* langevin/drude = style name of this fix command
+* Tcom = desired temperature of the centers of mass (temperature units)
+* damp\_com = damping parameter for the thermostat on centers of mass (time units)
+* seed\_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer)
+* Tdrude = desired temperature of the Drude oscillators (temperature units)
+* damp\_drude = damping parameter for the thermostat on Drude oscillators (time units)
+* seed\_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer)
+* zero or more keyword/value pairs may be appended
+* keyword = *zero*
+  
+  .. parsed-literal::
+  
+       *zero* value = *no* or *yes*
+         *no* = do not set total random force on centers of mass to zero
+         *yes* = set total random force on centers of mass to zero
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
+   fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
+
+Description
+"""""""""""
+
+Apply two Langevin thermostats as described in :ref:`(Jiang) <Jiang1>` for
+thermalizing the reduced degrees of freedom of Drude oscillators.
+This link describes how to use the :doc:`thermalized Drude oscillator model <Howto_drude>` in LAMMPS and polarizable models in LAMMPS
+are discussed on the :doc:`Howto polarizable <Howto_polarizable>` doc
+page.
+
+Drude oscillators are a way to simulate polarizables atoms, by
+splitting them into a core and a Drude particle bound by a harmonic
+bond.  The thermalization works by transforming the particles degrees
+of freedom by these equations.  In these equations upper case denotes
+atomic or center of mass values and lower case denotes Drude particle
+or dipole values. Primes denote the transformed (reduced) values,
+while bare letters denote the original values.
+
+Velocities:
+
+.. math::
+
+   \begin{equation} V' = \frac {M\, V + m\, v} {M'} \end{equation}
+
+
+.. math::
+
+   \begin{equation} v' = v - V \end{equation}
+
+Masses:
+
+.. math::
+
+   \begin{equation} M' = M + m \end{equation}
+
+
+.. math::
+
+   \begin{equation} m' = \frac {M\, m } {M'} \end{equation}
+
+The Langevin forces are computed as
+
+.. math::
+
+   \begin{equation} F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' \end{equation}
+
+
+.. math::
+
+   \begin{equation} f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' \end{equation}
+
+:math:`F_r'` is a random force proportional to
+:math:`\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'}                  {\mathrm dt\, \mathtt{damp\_com} }         }`.
+:math:`f_r'` is a random force proportional to
+:math:`\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'}                  {\mathrm dt\, \mathtt{damp\_drude} }         }`.
+Then the real forces acting on the particles are computed from the inverse
+transform:
+
+.. math::
+
+   \begin{equation} F = \frac M {M'}\, F' - f' \end{equation}
+
+
+.. math::
+
+   \begin{equation} f = \frac m {M'}\, F' + f' \end{equation}
+
+This fix also thermostats non-polarizable atoms in the group at
+temperature *Tcom*\ , as if they had a massless Drude partner.  The
+Drude particles themselves need not be in the group. The center of
+mass and the dipole are thermostatted iff the core atom is in the
+group.
+
+Note that the thermostat effect of this fix is applied to only the
+translational degrees of freedom of the particles, which is an
+important consideration if finite-size particles, which have
+rotational degrees of freedom, are being thermostatted. The
+translational degrees of freedom can also have a bias velocity removed
+from them before thermostatting takes place; see the description below.
+
+.. note::
+
+   Like the :doc:`fix langevin <fix_langevin>` command, this fix does
+   NOT perform time integration. It only modifies forces to effect
+   thermostatting. Thus you must use a separate time integration fix, like
+   :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>` to actually update the
+   velocities and positions of atoms using the modified forces.
+   Likewise, this fix should not normally be used on atoms that also have
+   their temperature controlled by another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>` commands.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+
+----------
+
+
+This fix requires each atom know whether it is a Drude particle or
+not.  You must therefore use the :doc:`fix drude <fix_drude>` command to
+specify the Drude status of each atom type.
+
+.. note::
+
+   only the Drude core atoms need to be in the group specified for
+   this fix. A Drude electron will be transformed together with its cores
+   even if it is not itself in the group.  It is safe to include Drude
+   electrons or non-polarizable atoms in the group. The non-polarizable
+   atoms will simply be thermostatted as if they had a massless Drude
+   partner (electron).
+
+.. note::
+
+   Ghost atoms need to know their velocity for this fix to act
+   correctly.  You must use the :doc:`comm\_modify <comm_modify>` command to
+   enable this, e.g.
+
+
+.. parsed-literal::
+
+   comm_modify vel yes
+
+
+----------
+
+
+*Tcom* is the target temperature of the centers of mass, which would
+be used to thermostat the non-polarizable atoms.  *Tdrude* is the
+(normally low) target temperature of the core-Drude particle pairs
+(dipoles).  *Tcom* and *Tdrude* can be specified as an equal-style
+:doc:`variable <variable>`.  If the value is a variable, it should be
+specified as v\_name, where name is the variable name. In this case,
+the variable will be evaluated each timestep, and its value used to
+determine the target temperature.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent temperature.
+
+Like other fixes that perform thermostatting, this fix can be used with
+:doc:`compute commands <compute>` that remove a "bias" from the atom
+velocities.  E.g. removing the center-of-mass velocity from a group of
+atoms.  This is not done by default, but only if the
+:doc:`fix\_modify <fix_modify>` command is used to assign a temperature
+compute to this fix that includes such a bias term.  See the doc pages
+for individual :doc:`compute commands <compute>` to determine which ones
+include a bias.  In this case, the thermostat works in the following
+manner: bias is removed from each atom, thermostatting is performed on
+the remaining thermal degrees of freedom, and the bias is added back
+in.  NOTE: this feature has not been tested.
+
+Note: The temperature thermostatting the core-Drude particle pairs
+should be chosen low enough, so as to mimic as closely as possible the
+self-consistent minimization. It must however be high enough, so that
+the dipoles can follow the local electric field exerted by the
+neighboring atoms. The optimal value probably depends on the
+temperature of the centers of mass and on the mass of the Drude
+particles.
+
+*damp\_com* is the characteristic time for reaching thermal equilibrium
+of the centers of mass.  For example, a value of 100.0 means to relax
+the temperature of the centers of mass in a timespan of (roughly) 100
+time units (tau or fmsec or psec - see the :doc:`units <units>`
+command).  *damp\_drude* is the characteristic time for reaching
+thermal equilibrium of the dipoles. It is typically a few timesteps.
+
+The number *seed\_com* and *seed\_drude* are positive integers. They set
+the seeds of the Marsaglia random number generators used for
+generating the random forces on centers of mass and on the
+dipoles. Each processor uses the input seed to generate its own unique
+seed and its own stream of random numbers.  Thus the dynamics of the
+system will not be identical on two runs on different numbers of
+processors.
+
+The keyword *zero* can be used to eliminate drift due to the
+thermostat on centers of mass. Because the random forces on different
+centers of mass are independent, they do not sum exactly to zero.  As
+a result, this fix applies a small random force to the entire system,
+and the momentum of the total center of mass of the system undergoes a
+slow random walk.  If the keyword *zero* is set to *yes*\ , the total
+random force on the centers of mass is set exactly to zero by
+subtracting off an equal part of it from each center of mass in the
+group. As a result, the total center of mass of a system with zero
+initial momentum will not drift over time.
+
+The actual temperatures of cores and Drude particles, in
+center-of-mass and relative coordinates, respectively, can be
+calculated using the :doc:`compute temp/drude <compute_temp_drude>`
+command.
+
+
+----------
+
+
+Usage example for rigid bodies in the NPT ensemble:
+
+
+.. parsed-literal::
+
+   comm_modify vel yes
+   fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
+   fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
+   fix NVE DRUDES nve
+   compute TDRUDE all temp/drude
+   thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
+
+Comments:
+
+* Drude particles should not be in the rigid group, otherwise the Drude
+  oscillators will be frozen and the system will lose its
+  polarizability.
+* *zero yes* avoids a drift of the center of mass of
+  the system, but is a bit slower.
+* Use two different random seeds to avoid unphysical correlations.
+* Temperature is controlled by the fix *langevin/drude*\ , so the
+  time-integration fixes do not thermostat.  Don't forget to
+  time-integrate both cores and Drude particles.
+* Pressure is time-integrated only once by using *nve* for Drude
+  particles and *nph* for atoms/cores (or vice versa). Do not use *nph*
+  for both.
+* The temperatures of cores and Drude particles are calculated by
+  :doc:`compute temp/drude <compute_temp_drude>`
+* Contrary to the alternative thermostatting using Nose-Hoover thermostat
+  fix *npt* and :doc:`fix drude/transform <fix_drude_transform>`, the
+  *fix\_modify* command is not required here, because the fix *nph*
+  computes the global pressure even if its group is *ATOMS*\ . This is
+  what we want. If we thermostatted *ATOMS* using *npt*\ , the pressure
+  should be the global one, but the temperature should be only that of
+  the cores. That's why the command *fix\_modify* should be called in
+  that case.
+
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place.  However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above. For consistency, the group used by the
+compute should include the group of this fix and the Drude particles.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix langevin <fix_langevin>`,
+:doc:`fix drude <fix_drude>`,
+:doc:`fix drude/transform <fix_drude_transform>`,
+:doc:`compute temp/drude <compute_temp_drude>`,
+:doc:`pair\_style thole <pair_thole>`
+
+Default
+"""""""
+
+The option defaults are zero = no.
+
+
+----------
+
+
+.. _Jiang1:
+
+
+
+**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
+Phys Chem Lett, 2, 87-92 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst
new file mode 100644
index 0000000000..0de23c65ab
--- /dev/null
+++ b/doc/src/fix_langevin_eff.rst
@@ -0,0 +1,140 @@
+.. index:: fix langevin/eff
+
+fix langevin/eff command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* langevin/eff = style name of this fix command
+* Tstart,Tstop = desired temperature at start/end of run (temperature units)
+* damp = damping parameter (time units)
+* seed = random number seed to use for white noise (positive integer)
+* zero or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *scale* or *tally* or *zero*
+       *scale* values = type ratio
+         type = atom type (1-N)
+         ratio = factor by which to scale the damping coefficient
+       *tally* values = *no* or *yes*
+         *no* = do not tally the energy added/subtracted to atoms
+         *yes* = do tally the energy added/subtracted to atoms
+
+  
+  .. parsed-literal::
+  
+       *zero* value = *no* or *yes*
+         *no* = do not set total random force to zero
+         *yes* = set total random force to zero
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
+   fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5
+
+Description
+"""""""""""
+
+Apply a Langevin thermostat as described in :ref:`(Schneider) <Schneider2>`
+to a group of nuclei and electrons in the :doc:`electron force field <pair_eff>` model.  Used with :doc:`fix nve/eff <fix_nve_eff>`,
+this command performs Brownian dynamics (BD), since the total force on
+each atom will have the form:
+
+
+.. parsed-literal::
+
+   F = Fc + Ff + Fr
+   Ff = - (m / damp) v
+   Fr is proportional to sqrt(Kb T m / (dt damp))
+
+Fc is the conservative force computed via the usual inter-particle
+interactions (:doc:`pair\_style <pair_style>`).
+
+The Ff and Fr terms are added by this fix on a per-particle basis.
+
+The operation of this fix is exactly like that described by the :doc:`fix langevin <fix_langevin>` command, except that the thermostatting
+is also applied to the radial electron velocity for electron
+particles.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place.  However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  Note that use of this option requires
+setting the *tally* keyword to *yes*\ .
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".  Note that calculation of this quantity requires
+setting the *tally* keyword to *yes*\ .
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+This fix is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix langevin <fix_langevin>`
+
+Default
+"""""""
+
+The option defaults are scale = 1.0 for all types and tally = no.
+
+
+----------
+
+
+.. _Dunweg2:
+
+
+
+**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
+
+.. _Schneider2:
+
+
+
+**(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst
new file mode 100644
index 0000000000..2902c8fb24
--- /dev/null
+++ b/doc/src/fix_langevin_spin.rst
@@ -0,0 +1,126 @@
+.. index:: fix langevin/spin
+
+fix langevin/spin command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID langevin/spin T Tdamp seed
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* langevin/spin = style name of this fix command
+* T = desired temperature of the bath (temperature units, K in metal units)
+* Tdamp = transverse magnetic damping parameter (adim)
+* seed = random number seed to use for white noise (positive integer)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 2 all langevin/spin 300.0 0.01 21
+
+Description
+"""""""""""
+
+Apply a Langevin thermostat as described in :ref:`(Mayergoyz) <Mayergoyz1>` to the
+magnetic spins associated to the atoms.
+Used with :doc:`fix nve/spin <fix_nve_spin>`, this command performs
+Brownian dynamics (BD).
+A random torque and a transverse dissipation are applied to each spin i according to
+the following stochastic differential equation:
+
+.. image:: Eqs/fix_langevin_spin_sLLG.jpg
+   :align: center
+
+with lambda the transverse damping, and eta a random vector.
+This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG)
+equation.
+
+The components of eta are drawn from a Gaussian probability law. Their amplitude
+is defined as a proportion of the temperature of the external thermostat T (in K
+in metal units).
+
+More details about this implementation are reported in :ref:`(Tranchida) <Tranchida2>`.
+
+Note: due to the form of the sLLG equation, this fix has to be defined just
+before the nve/spin fix (and after all other magnetic fixes).
+As an example:
+
+
+.. parsed-literal::
+
+   fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
+   fix 2 all langevin/spin 300.0 0.01 21
+   fix 3 all nve/spin lattice moving
+
+is correct, but defining a force/spin command after the langevin/spin command
+would give an error message.
+
+Note: The random # *seed* must be a positive integer.  A Marsaglia random
+number generator is used.  Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place.  However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+The *langevin/spin* fix is part of the SPIN package.  This style is
+only enabled if LAMMPS was built with this package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The numerical integration has to be performed with *fix nve/spin*
+when *fix langevin/spin* is enabled.
+
+This fix has to be the last defined magnetic fix before the time
+integration fix (e.g. *fix nve/spin*\ ).
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve/spin <fix_nve_spin>`, :doc:`fix precession/spin <fix_precession_spin>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Mayergoyz1:
+
+
+
+**(Mayergoyz)** I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009)
+
+.. _Tranchida2:
+
+
+
+**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, 372, 406-425, (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst
new file mode 100644
index 0000000000..a13df3f40a
--- /dev/null
+++ b/doc/src/fix_latte.rst
@@ -0,0 +1,259 @@
+.. index:: fix latte
+
+fix latte command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID latte peID
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* latte = style name of this fix command
+* peID = NULL or ID of compute used to calculate per-atom energy
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix dftb all latte NULL
+
+Description
+"""""""""""
+
+This fix style is a wrapper on the self-consistent charge transfer
+density functional based tight binding (DFTB) code LATTE. If you
+download and build LATTE, it can be called as a library by LAMMPS via
+this fix to run dynamics or perform energy minimization using DFTB
+forces and energies computed by LATTE.
+
+LATTE is principally developed and supported by Marc Cawkwell and
+co-workers at Los Alamos National Laboratory (LANL).  See the full
+list of contributors in the src/LATTE/README file.
+
+To use this fix, the LATTE program needs to be compiled as a library
+and linked with LAMMPS.  LATTE can be downloaded (or cloned) from
+`https://github.com/lanl/LATTE <https://github.com/lanl/LATTE>`_.
+Instructions on how to download and build LATTE on your system can be
+found in the lib/latte/README.  Note that you can also use the "make
+lib-latte" command from the LAMMPS src directory to automate this
+process.
+
+Once LAMMPS is built with the LATTE package, you can run the example
+input scripts for molecular dynamics or energy minimization that are
+found in examples/latte.
+
+A step-by-step tutorial can be followed at: `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_
+
+The *peID* argument is not yet supported by fix latte, so it must be
+specified as NULL.  Eventually it will be used to enable LAMMPS to
+calculate a Coulomb potential as an alternative to LATTE performing
+the calculation.
+
+
+----------
+
+
+LATTE is a code for performing self-consistent charge transfer
+tight-binding (SC-TB) calculations of total energies and the forces
+acting on atoms in molecules and solids. This tight-binding method is
+becoming more and more popular and widely used in chemistry,
+biochemistry, material science, etc.
+
+The SC-TB formalism is derived from an expansion of the Kohn-Sham
+density functional to second order in charge fluctuations about a
+reference charge of overlapping atom-centered densities and bond
+integrals are parameterized using a Slater-Koster tight-binding
+approach. This procedure, which usually is referred to as the DFTB
+method has been described in detail by (:ref:`Elstner <Elstner>`) and
+(:ref:`Finnis <Finnis2>`) and coworkers.
+
+The work of the LATTE developers follows that of Elstner closely with
+respect to the physical model.  However, the development of LATTE is
+geared principally toward large-scale, long duration, microcanonical
+quantum-based Born-Oppenheimer molecular dynamics (QMD) simulations.
+One of the main bottlenecks of an electronic structure calculation is
+the solution of the generalized eigenvalue problem which scales with
+the cube of the system size O(N\^3).
+
+The Theoretical and Computer sciences divisions at Los Alamos National
+Laboratory have accumulated large experience addressing this issue by
+calculating the density matrix directly instead of using
+diagonalization. We typically use a recursive sparse Fermi-operator
+expansion using second-order spectral projection functions
+(SP2-algorithm), which was introduced by Niklasson in 2002
+(:ref:`Niklasson2002 <Niklasson2002>`), (:ref:`Rubensson <Rubensson>`),
+(:ref:`Mniszewski <Mniszewski>`).  When the matrices involved in the
+recursive expansion are sufficiently sparse, the calculation of the
+density matrix scales linearly as a function of the system size O(N).
+
+Another important feature is the extended Lagrangian framework for
+Born-Oppenheimer molecular dynamics (XL-BOMD)
+(:ref:`Niklasson2008 <Niklasson2008>`) (:ref:`Niklasson2014 <Niklasson2014>`),
+(:ref:`Niklasson2017 <Niklasson2017>`) that allows for a drastic reduction
+or even a complete removal of the iterative self-consistent field
+optimization.  Often only a single density matrix calculation per
+molecular dynamics time step is required, yet total energy stability
+is well maintained.  The SP2 and XL-BOMD techniques enables stable
+linear scaling MD simulations with a very small computational
+overhead.  This opens a number of opportunities in many different
+areas of chemistry and materials science, as we now can simulate
+larger system sizes and longer time scales
+(:ref:`Cawkwell2012 <Cawkwell2012>`), (:ref:`Negre2016 <Negre2016>`).
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential energy computed by LATTE to the system's
+potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the LATTE DFTB contribution to the system's virial as part
+of :doc:`thermodynamic output <thermo_style>`.  The default is *virial
+yes*
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the potential
+energy discussed above.  The scalar value calculated by this fix is
+"extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The DFTB forces computed by LATTE via this fix are imposed during an
+energy minimization, invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the potential energy associated with the DFTB
+   forces to be included in the total potential energy of the system (the
+   quantity being minimized), you MUST enable the
+   :doc:`fix\_modify <fix_modify>` *energy* option for this fix.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the LATTE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You must use metal units, as set by the :doc:`units <units>` command to
+use this fix.
+
+LATTE does not currently compute per-atom energy or per-atom virial
+contributions.  So they will not show up as part of the calculations
+performed by the :doc:`compute pe/atom <compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>` commands.
+
+Currently, LAMMPS must be run in serial or as a single MPI task, to
+use this fix.  This is typically not a bottleneck, since LATTE will be
+doing 99% or more of the work to compute quantum-accurate forces.
+
+.. note::
+
+   NEB calculations can be done using this fix using multiple
+   replicas and running LAMMPS in parallel.  However, each replica must
+   be run on a single MPI task.  For details, see the :doc:`neb <neb>`
+   command doc page and the :doc:`-partition command-line switch <Run_options>`
+
+**Related commands:** none
+
+**Default:** none
+
+
+----------
+
+
+.. _Elstner:
+
+
+
+**(Elstner)** M. Elstner, D. Poresag, G. Jungnickel, J. Elsner,
+M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
+7260 (1998).
+
+.. _Elstner1:
+
+
+
+**(Elstner)** M. Elstner, D. Poresag, G. Jungnickel, J. Elsner,
+M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
+7260 (1998).
+
+.. _Finnis2:
+
+
+
+**(Finnis)** M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
+Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).
+
+.. _Mniszewski:
+
+
+
+**(Mniszewski)** S. M. Mniszewski, M. J. Cawkwell, M. E. Wall,
+J. Mohd-Yusof, N. Bock, T. C.  Germann, and A. M. N. Niklasson,
+J. Chem. Theory Comput., 11, 4644 (2015).
+
+.. _Niklasson2002:
+
+
+
+**(Niklasson2002)** A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
+
+.. _Rubensson:
+
+
+
+**(Rubensson)** E. H. Rubensson, A. M. N. Niklasson, SIAM
+J. Sci. Comput. 36 (2), 147-170, (2014).
+
+.. _Niklasson2008:
+
+
+
+**(Niklasson2008)** A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004
+(2008).
+
+.. _Niklasson2014:
+
+
+
+**(Niklasson2014)** A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
+141, 164123, (2014).
+
+.. _Niklasson2017:
+
+
+
+**(Niklasson2017)** A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
+
+.. _Cawkwell2012:
+
+
+
+**(Cawkwell2012)** A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
+(17), 174308 (2012).
+
+.. _Negre2016:
+
+
+
+**(Negre2016)** C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell,
+N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp.,
+12, 3063 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst
new file mode 100644
index 0000000000..cd177b7f32
--- /dev/null
+++ b/doc/src/fix_lb_fluid.rst
@@ -0,0 +1,412 @@
+.. index:: fix lb/fluid
+
+fix lb/fluid command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID lb/fluid nevery LBtype viscosity density keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* lb/fluid = style name of this fix command
+* nevery = update the lattice-Boltzmann fluid every this many timesteps
+* LBtype = 1 to use the standard finite difference LB integrator,
+  2 to use the LB integrator of :ref:`Ollila et al. <Ollila>`
+* viscosity = the fluid viscosity (units of mass/(time\*length)).
+* density = the fluid density.
+* zero or more keyword/value pairs may be appended
+* keyword = *setArea* or *setGamma* or *scaleGamma* or *dx* or *dm* or *a0* or *noise* or *calcforce* or *trilinear* or *D3Q19* or *read\_restart* or *write\_restart* or *zwall\_velocity* or *bodyforce* or *printfluid*
+  
+  .. parsed-literal::
+  
+       *setArea* values = type node_area
+           type = atom type (1-N)
+           node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
+       *setGamma* values = gamma
+           gamma = user set value for the force coupling constant.
+       *scaleGamma* values = type gammaFactor
+           type = atom type (1-N)
+           gammaFactor = factor to scale the *setGamma* gamma value by, for the specified atom type.
+       *dx* values = dx_LB = the lattice spacing.
+       *dm* values = dm_LB = the lattice-Boltzmann mass unit.
+       *a0* values = a_0_real = the square of the speed of sound in the fluid.
+       *noise* values = Temperature seed
+           Temperature = fluid temperature.
+           seed = random number generator seed (positive integer)
+       *calcforce* values = N forcegroup-ID
+           N = output the force and torque every N timesteps
+           forcegroup-ID = ID of the particle group to calculate the force and torque of
+       *trilinear* values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
+       *D3Q19* values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
+       *read_restart* values = restart file = name of the restart file to use to restart a fluid run.
+       *write_restart* values = N = write a restart file every N MD timesteps.
+       *zwall_velocity* values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
+       *bodyforce* values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
+       *printfluid* values = N = print the fluid density and velocity at each grid point every N timesteps.
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1
+   fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873
+
+Description
+"""""""""""
+
+Implement a lattice-Boltzmann fluid on a uniform mesh covering the LAMMPS
+simulation domain.  The MD particles described by *group-ID* apply a velocity
+dependent force to the fluid.
+
+The lattice-Boltzmann algorithm solves for the fluid motion governed by
+the Navier Stokes equations,
+
+.. image:: Eqs/fix_lb_fluid_navierstokes.jpg
+   :align: center
+
+with,
+
+.. image:: Eqs/fix_lb_fluid_viscosity.jpg
+   :align: center
+
+where rho is the fluid density, u is the local fluid velocity, sigma
+is the stress tensor, F is a local external force, and eta and Lambda
+are the shear and bulk viscosities respectively.  Here, we have
+implemented
+
+.. image:: Eqs/fix_lb_fluid_stress.jpg
+   :align: center
+
+with a\_0 set to 1/3 (dx/dt)\^2 by default.
+
+The algorithm involves tracking the time evolution of a set of partial
+distribution functions which evolve according to a velocity
+discretized version of the Boltzmann equation,
+
+.. image:: Eqs/fix_lb_fluid_boltzmann.jpg
+   :align: center
+
+where the first term on the right hand side represents a single time
+relaxation towards the equilibrium distribution function, and tau is a
+parameter physically related to the viscosity.  On a technical note,
+we have implemented a 15 velocity model (D3Q15) as default; however,
+the user can switch to a 19 velocity model (D3Q19) through the use of
+the *D3Q19* keyword.  This fix provides the user with the choice of
+two algorithms to solve this equation, through the specification of
+the keyword *LBtype*\ .  If *LBtype* is set equal to 1, the standard
+finite difference LB integrator is used.  If *LBtype* is set equal to
+2, the algorithm of :ref:`Ollila et al. <Ollila>` is used.
+
+Physical variables are then defined in terms of moments of the distribution
+functions,
+
+.. image:: Eqs/fix_lb_fluid_properties.jpg
+   :align: center
+
+Full details of the lattice-Boltzmann algorithm used can be found in
+:ref:`Mackay et al. <fluid-Mackay>`.
+
+The fluid is coupled to the MD particles described by *group-ID*
+through a velocity dependent force.  The contribution to the fluid
+force on a given lattice mesh site j due to MD particle alpha is
+calculated as:
+
+.. image:: Eqs/fix_lb_fluid_fluidforce.jpg
+   :align: center
+
+where v\_n is the velocity of the MD particle, u\_f is the fluid
+velocity interpolated to the particle location, and gamma is the force
+coupling constant.  Zeta is a weight assigned to the grid point,
+obtained by distributing the particle to the nearest lattice sites.
+For this, the user has the choice between a trilinear stencil, which
+provides a support of 8 lattice sites, or the immersed boundary method
+Peskin stencil, which provides a support of 64 lattice sites.  While
+the Peskin stencil is seen to provide more stable results, the
+trilinear stencil may be better suited for simulation of objects close
+to walls, due to its smaller support.  Therefore, by default, the
+Peskin stencil is used; however the user may switch to the trilinear
+stencil by specifying the keyword, *trilinear*\ .
+
+By default, the force coupling constant, gamma, is calculated according to
+
+.. image:: Eqs/fix_lb_fluid_gammadefault.jpg
+   :align: center
+
+Here, m\_v is the mass of the MD particle, m\_u is a representative
+fluid mass at the particle location, and dt\_collision is a collision
+time, chosen such that tau/dt\_collision = 1 (see :ref:`Mackay and Denniston <Mackay2>` for full details).  In order to calculate m\_u, the
+fluid density is interpolated to the MD particle location, and
+multiplied by a volume, node\_area\*dx\_lb, where node\_area represents
+the portion of the surface area of the composite object associated
+with a given MD particle.  By default, node\_area is set equal to
+dx\_lb\*dx\_lb; however specific values for given atom types can be set
+using the *setArea* keyword.
+
+The user also has the option of specifying their own value for the
+force coupling constant, for all the MD particles associated with the
+fix, through the use of the *setGamma* keyword.  This may be useful
+when modelling porous particles.  See :ref:`Mackay et al. <fluid-Mackay>` for a
+detailed description of the method by which the user can choose an
+appropriate gamma value.
+
+.. note::
+
+   while this fix applies the force of the particles on the fluid,
+   it does not apply the force of the fluid to the particles.  When the
+   force coupling constant is set using the default method, there is only
+   one option to include this hydrodynamic force on the particles, and
+   that is through the use of the :doc:`lb/viscous <fix_lb_viscous>` fix.
+   This fix adds the hydrodynamic force to the total force acting on the
+   particles, after which any of the built-in LAMMPS integrators can be
+   used to integrate the particle motion.  However, if the user specifies
+   their own value for the force coupling constant, as mentioned in
+   :ref:`Mackay et al. <fluid-Mackay>`, the built-in LAMMPS integrators may prove to
+   be unstable.  Therefore, we have included our own integrators :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and :doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
+   cases.  These integrators should not be used with the
+   :doc:`lb/viscous <fix_lb_viscous>` fix, as they add hydrodynamic forces
+   to the particles directly.  In addition, they can not be used if the
+   force coupling constant has been set the default way.
+
+.. note::
+
+   if the force coupling constant is set using the default method,
+   and the :doc:`lb/viscous <fix_lb_viscous>` fix is NOT used to add the
+   hydrodynamic force to the total force acting on the particles, this
+   physically corresponds to a situation in which an infinitely massive
+   particle is moving through the fluid (since collisions between the
+   particle and the fluid do not act to change the particle's velocity).
+   Therefore, the user should set the mass of the particle to be
+   significantly larger than the mass of the fluid at the particle
+   location, in order to approximate an infinitely massive particle (see
+   the dragforce test run for an example).
+
+
+----------
+
+
+Inside the fix, parameters are scaled by the lattice-Boltzmann
+timestep, dt, grid spacing, dx, and mass unit, dm.  dt is set equal to
+(nevery\*dt\_MD), where dt\_MD is the MD timestep.  By default, dm is set
+equal to 1.0, and dx is chosen so that tau/(dt) =
+(3\*eta\*dt)/(rho\*dx\^2) is approximately equal to 1.  However, the user
+has the option of specifying their own values for dm, and dx, by using
+the optional keywords *dm*\ , and *dx* respectively.
+
+.. note::
+
+   Care must be taken when choosing both a value for dx, and a
+   simulation domain size.  This fix uses the same subdivision of the
+   simulation domain among processors as the main LAMMPS program.  In
+   order to uniformly cover the simulation domain with lattice sites, the
+   lengths of the individual LAMMPS sub-domains must all be evenly
+   divisible by dx.  If the simulation domain size is cubic, with equal
+   lengths in all dimensions, and the default value for dx is used, this
+   will automatically be satisfied.
+
+Physical parameters describing the fluid are specified through
+*viscosity*\ , *density*\ , and *a0*\ . If the force coupling constant is
+set the default way, the surface area associated with the MD particles
+is specified using the *setArea* keyword.  If the user chooses to
+specify a value for the force coupling constant, this is set using the
+*setGamma* keyword.  These parameters should all be given in terms of
+the mass, distance, and time units chosen for the main LAMMPS run, as
+they are scaled by the LB timestep, lattice spacing, and mass unit,
+inside the fix.
+
+
+----------
+
+
+The *setArea* keyword allows the user to associate a surface area with
+a given atom type.  For example if a spherical composite object of
+radius R is represented as a spherical shell of N evenly distributed
+MD particles, all of the same type, the surface area per particle
+associated with that atom type should be set equal to 4\*pi\*R\^2/N.
+This keyword should only be used if the force coupling constant,
+gamma, is set the default way.
+
+The *setGamma* keyword allows the user to specify their own value for
+the force coupling constant, gamma, instead of using the default
+value.
+
+The *scaleGamma* keyword should be used in conjunction with the
+*setGamma* keyword, when the user wishes to specify different gamma
+values for different atom types.  This keyword allows the user to
+scale the *setGamma* gamma value by a factor, gammaFactor, for a given
+atom type.
+
+The *dx* keyword allows the user to specify a value for the LB grid
+spacing.
+
+The *dm* keyword allows the user to specify the LB mass unit.
+
+If the *a0* keyword is used, the value specified is used for the
+square of the speed of sound in the fluid.  If this keyword is not
+present, the speed of sound squared is set equal to (1/3)\*(dx/dt)\^2.
+Setting a0 > (dx/dt)\^2 is not allowed, as this may lead to
+instabilities.
+
+If the *noise* keyword is used, followed by a positive temperature
+value, and a positive integer random number seed, a thermal
+lattice-Boltzmann algorithm is used.  If *LBtype* is set equal to 1
+(i.e. the standard LB integrator is chosen), the thermal LB algorithm
+of :ref:`Adhikari et al. <Adhikari>` is used; however if *LBtype* is set
+equal to 2 both the LB integrator, and thermal LB algorithm described
+in :ref:`Ollila et al. <Ollila>` are used.
+
+If the *calcforce* keyword is used, both the fluid force and torque
+acting on the specified particle group are printed to the screen every
+N timesteps.
+
+If the keyword *trilinear* is used, the trilinear stencil is used to
+interpolate the particle nodes onto the fluid mesh.  By default, the
+immersed boundary method, Peskin stencil is used.  Both of these
+interpolation methods are described in :ref:`Mackay et al. <fluid-Mackay>`.
+
+If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
+used by the lattice-Boltzmann algorithm.  By default, the 15 velocity
+(D3Q15) lattice is used.
+
+If the keyword *write\_restart* is used, followed by a positive
+integer, N, a binary restart file is printed every N LB timesteps.
+This restart file only contains information about the fluid.
+Therefore, a LAMMPS restart file should also be written in order to
+print out full details of the simulation.
+
+.. note::
+
+   When a large number of lattice grid points are used, the restart
+   files may become quite large.
+
+In order to restart the fluid portion of the simulation, the keyword
+*read\_restart* is specified, followed by the name of the binary
+lb\_fluid restart file to be used.
+
+If the *zwall\_velocity* keyword is used y-velocities are assigned to
+the lower and upper walls.  This keyword requires the presence of
+walls in the z-direction.  This is set by assigning fixed boundary
+conditions in the z-direction.  If fixed boundary conditions are
+present in the z-direction, and this keyword is not used, the walls
+are assumed to be stationary.
+
+If the *bodyforce* keyword is used, a constant body force is added to
+the fluid, defined by it's x, y and z components.
+
+If the *printfluid* keyword is used, followed by a positive integer, N,
+the fluid densities and velocities at each lattice site are printed to the
+screen every N timesteps.
+
+
+----------
+
+
+For further details, as well as descriptions and results of several
+test runs, see :ref:`Mackay et al. <fluid-Mackay>`.  Please include a citation to
+this paper if the lb\_fluid fix is used in work contributing to
+published research.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Due to the large size of the fluid data, this fix writes it's own
+binary restart files, if requested, independent of the main LAMMPS
+:doc:`binary restart files <restart>`; no information about *lb\_fluid*
+is written to the main LAMMPS :doc:`binary restart files <restart>`.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-LB package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix can only be used with an orthogonal simulation domain.
+
+Walls have only been implemented in the z-direction.  Therefore, the
+boundary conditions, as specified via the main LAMMPS boundary command
+must be periodic for x and y, and either fixed or periodic for z.
+Shrink-wrapped boundary conditions are not permitted with this fix.
+
+This fix must be used before any of :doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and/ or :doc:`fix lb/pc <fix_lb_pc>` , as the fluid needs to be initialized before
+any of these routines try to access its properties.  In addition, in
+order for the hydrodynamic forces to be added to the particles, this
+fix must be used in conjunction with the
+:doc:`lb/viscous <fix_lb_viscous>` fix if the force coupling constant is
+set by default, or either the :doc:`lb/viscous <fix_lb_viscous>` fix or
+one of the :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` or
+:doc:`lb/pc <fix_lb_pc>` integrators, if the user chooses to specify
+their own value for the force coupling constant.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, :doc:`fix lb/pc <fix_lb_pc>`
+
+Default
+"""""""
+
+By default, the force coupling constant is set according to
+
+.. image:: Eqs/fix_lb_fluid_gammadefault.jpg
+   :align: center
+
+and an area of dx\_lb\^2 per node, used to calculate the fluid mass at
+the particle node location, is assumed.
+
+dx is chosen such that tau/(delta t\_LB) =
+(3 eta dt\_LB)/(rho dx\_lb\^2) is approximately equal to 1.
+dm is set equal to 1.0.
+a0 is set equal to (1/3)\*(dx\_lb/dt\_lb)\^2.
+The Peskin stencil is used as the default interpolation method.
+The D3Q15 lattice is used for the lattice-Boltzmann algorithm.
+If walls are present, they are assumed to be stationary.
+
+
+----------
+
+
+.. _Ollila:
+
+
+
+**(Ollila et al.)** Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902.
+
+.. _fluid-Mackay:
+
+
+
+**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
+
+.. _Mackay2:
+
+
+
+**(Mackay and Denniston)** Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298.
+
+.. _Adhikari:
+
+
+
+**(Adhikari et al.)** Adhikari, R., Stratford, K.,  Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst
new file mode 100644
index 0000000000..2f1b953db3
--- /dev/null
+++ b/doc/src/fix_lb_momentum.rst
@@ -0,0 +1,89 @@
+.. index:: fix lb/momentum
+
+fix lb/momentum command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID lb/momentum nevery keyword values ...
+
+* ID, group-ID are documented in the :doc:`fix <fix>` command
+* lb/momentum = style name of this fix command
+* nevery = adjust the momentum every this many timesteps
+* zero or more keyword/value pairs may be appended
+* keyword = *linear*
+  
+  .. parsed-literal::
+  
+       *linear* values = xflag yflag zflag
+         xflag,yflag,zflag = 0/1 to exclude/include each dimension.
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 sphere lb/momentum
+   fix 1 all lb/momentum linear 1 1 0
+
+Description
+"""""""""""
+
+This fix is based on the :doc:`fix momentum <fix_momentum>` command, and
+was created to be used in place of that command, when a
+lattice-Boltzmann fluid is present.
+
+Zero the total linear momentum of the system, including both the atoms
+specified by group-ID and the lattice-Boltzmann fluid every nevery
+timesteps.  This is accomplished by adjusting the particle velocities
+and the fluid velocities at each lattice site.
+
+.. note::
+
+   This fix only considers the linear momentum of the system.
+
+By default, the subtraction is performed for each dimension.  This can
+be changed by specifying the keyword *linear*\ , along with a set of
+three flags set to 0/1 in order to exclude/ include the corresponding
+dimension.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+Can only be used if a lattice-Boltzmann fluid has been created via the
+:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
+command.
+
+This fix is part of the USER-LB package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix momentum <fix_momentum>`, :doc:`fix lb/fluid <fix_lb_fluid>`
+
+Default
+"""""""
+
+Zeros the total system linear momentum in each dimension.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst
new file mode 100644
index 0000000000..f490b82981
--- /dev/null
+++ b/doc/src/fix_lb_pc.rst
@@ -0,0 +1,73 @@
+.. index:: fix lb/pc
+
+fix lb/pc command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID lb/pc
+
+* ID, group-ID are documented in the :doc:`fix <fix>` command
+* lb/pc = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all lb/pc
+
+Description
+"""""""""""
+
+Update the positions and velocities of the individual particles
+described by *group-ID*\ , experiencing velocity-dependent hydrodynamic
+forces, using the integration algorithm described in :ref:`Mackay et al. <Mackay1>`.  This integration algorithm should only be used if a
+user-specified value for the force-coupling constant used in :doc:`fix lb/fluid <fix_lb_fluid>` has been set; do not use this integration
+algorithm if the force coupling constant has been set by default.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-LB package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Can only be used if a lattice-Boltzmann fluid has been created via the
+:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix lb/fluid <fix_lb_fluid>` :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
+
+**Default:** None.
+
+
+----------
+
+
+.. _Mackay1:
+
+
+
+**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst
new file mode 100644
index 0000000000..dfa7cf0663
--- /dev/null
+++ b/doc/src/fix_lb_rigid_pc_sphere.rst
@@ -0,0 +1,173 @@
+.. index:: fix lb/rigid/pc/sphere
+
+fix lb/rigid/pc/sphere command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID lb/rigid/pc/sphere bodystyle args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* lb/rigid/pc/sphere = style name of this fix command
+* bodystyle = *single* or *molecule* or *group*
+  
+  .. parsed-literal::
+  
+       *single* args = none
+       *molecule* args = none
+       *group* args = N groupID1 groupID2 ...
+         N = # of groups
+
+* zero or more keyword/value pairs may be appended
+* keyword = *force* or *torque* or *innerNodes*
+  
+  .. parsed-literal::
+  
+       *force* values = M xflag yflag zflag
+         M = which rigid body from 1-Nbody (see asterisk form below)
+         xflag,yflag,zflag = off/on if component of center-of-mass force is active
+       *torque* values = M xflag yflag zflag
+         M = which rigid body from 1-Nbody (see asterisk form below)
+         xflag,yflag,zflag = off/on if component of center-of-mass torque is active
+       *innerNodes* values = innergroup-ID
+         innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 spheres lb/rigid/pc/sphere
+   fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms
+
+Description
+"""""""""""
+
+This fix is based on the :doc:`fix rigid <fix_rigid>` command, and was
+created to be used in place of that fix, to integrate the equations of
+motion of spherical rigid bodies when a lattice-Boltzmann fluid is
+present with a user-specified value of the force-coupling constant.
+The fix uses the integration algorithm described in :ref:`Mackay et al. <Mackay>` to update the positions, velocities, and orientations of
+a set of spherical rigid bodies experiencing velocity dependent
+hydrodynamic forces.  The spherical bodies are assumed to rotate as
+solid, uniform density spheres, with moments of inertia calculated
+using the combined sum of the masses of all the constituent particles
+(which are assumed to be point particles).
+
+
+----------
+
+
+By default, all of the atoms that this fix acts on experience a
+hydrodynamic force due to the presence of the lattice-Boltzmann fluid.
+However, the *innerNodes* keyword allows the user to specify atoms
+belonging to a rigid object which do not interact with the
+lattice-Boltzmann fluid (i.e. these atoms do not feel a hydrodynamic
+force from the lattice-Boltzmann fluid).  This can be used to
+distinguish between atoms on the surface of a non-porous object, and
+those on the inside.
+
+This feature can be used, for example, when implementing a hard sphere
+interaction between two spherical objects.  Instead of interactions
+occurring between the particles on the surfaces of the two spheres, it
+is desirable simply to place an atom at the center of each sphere,
+which does not contribute to the hydrodynamic force, and have these
+central atoms interact with one another.
+
+
+----------
+
+
+Apart from the features described above, this fix is very similar to
+the rigid fix (although it includes fewer optional arguments, and
+assumes the constituent atoms are point particles); see
+:doc:`fix rigid <fix_rigid>` for a complete documentation.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about the *rigid* and *rigid/nve* fixes are written to
+:doc:`binary restart files <restart>`.
+
+Similar to the :doc:`fix rigid <fix_rigid>` command: The rigid fix
+computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar value calculated by these
+fixes is "intensive".  The scalar is the current temperature of the
+collection of rigid bodies.  This is averaged over all rigid bodies
+and their translational and rotational degrees of freedom.  The
+translational energy of a rigid body is 1/2 m v\^2, where m = total
+mass of the body and v = the velocity of its center of mass.  The
+rotational energy of a rigid body is 1/2 I w\^2, where I = the moment
+of inertia tensor of the body and w = its angular velocity.  Degrees
+of freedom constrained by the *force* and *torque* keywords are
+removed from this calculation.
+
+All of these fixes compute a global array of values which can be
+accessed by various :doc:`output commands <Howto_output>`.  The number
+of rows in the array is equal to the number of rigid bodies.  The
+number of columns is 15.  Thus for each rigid body, 15 values are
+stored: the xyz coords of the center of mass (COM), the xyz components
+of the COM velocity, the xyz components of the force acting on the
+COM, the xyz components of the torque acting on the COM, and the xyz
+image flags of the COM, which have the same meaning as image flags for
+atom positions (see the "dump" command).  The force and torque values
+in the array are not affected by the *force* and *torque* keywords in
+the fix rigid command; they reflect values before any changes are made
+by those keywords.
+
+The ordering of the rigid bodies (by row in the array) is as follows.
+For the *single* keyword there is just one rigid body.  For the
+*molecule* keyword, the bodies are ordered by ascending molecule ID.
+For the *group* keyword, the list of group IDs determines the ordering
+of bodies.
+
+The array values calculated by these fixes are "intensive", meaning
+they are independent of the number of atoms in the simulation.
+
+No parameter of these fixes can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.  These fixes are not invoked during
+:doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-LB package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Can only be used if a lattice-Boltzmann fluid has been created via the
+:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
+command.  Should only be used if the force coupling constant used in
+:doc:`fix lb/fluid <fix_lb_fluid>` has been set by the user; this
+integration fix cannot be used if the force coupling constant is set
+by default.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix lb/fluid <fix_lb_fluid>`, :doc:`fix lb/pc <fix_lb_pc>`
+
+Default
+"""""""
+
+The defaults are force \* on on on, and torque \* on on on.
+
+
+----------
+
+
+.. _Mackay:
+
+
+
+**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst
new file mode 100644
index 0000000000..ee962dfd75
--- /dev/null
+++ b/doc/src/fix_lb_viscous.rst
@@ -0,0 +1,108 @@
+.. index:: fix lb/viscous
+
+fix lb/viscous command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID lb/viscous
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* lb/viscous = style name of this fix command
+
+Examples
+""""""""
+
+fix 1 flow lb/viscous
+
+Description
+"""""""""""
+
+This fix is similar to the :doc:`fix viscous <fix_viscous>` command, and
+is to be used in place of that command when a lattice-Boltzmann fluid
+is present, and the user wishes to integrate the particle motion using
+one of the built in LAMMPS integrators.
+
+This fix adds a force, F = - Gamma\*(velocity-fluid\_velocity), to each
+atom, where Gamma is the force coupling constant described in the :doc:`fix lb/fluid <fix_lb_fluid>` command (which applies an equal and
+opposite force to the fluid).
+
+.. note::
+
+   This fix should only be used in conjunction with one of the
+   built in LAMMPS integrators; it should not be used with the :doc:`fix lb/pc <fix_lb_pc>` or :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` integrators, which
+   already include the hydrodynamic forces.  These latter fixes should
+   only be used if the force coupling constant has been set by the user
+   (instead of using the default value); if the default force coupling
+   value is used, then this fix provides the only method for adding the
+   hydrodynamic forces to the particles.
+
+
+----------
+
+
+For further details, as well as descriptions and results of several
+test runs, see :ref:`Mackay et al. <Mackay3>`.  Please include a citation to
+this paper if this fix is used in work contributing to published
+research.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+As described in the :doc:`fix viscous <fix_viscous>` documentation:
+
+"No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.  This fix should only
+be used with damped dynamics minimizers that allow for
+non-conservative forces.  See the :doc:`min\_style <min_style>` command
+for details."
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-LB package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Can only be used if a lattice-Boltzmann fluid has been created via the
+:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
+command.
+
+This fix should not be used if either the :doc:`fix lb/pc <fix_lb_pc>`
+or :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` integrator is
+used.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix lb/fluid <fix_lb_fluid>`, :doc:`fix lb/pc <fix_lb_pc>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Mackay3:
+
+
+
+**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst
new file mode 100644
index 0000000000..ef365eb75c
--- /dev/null
+++ b/doc/src/fix_lineforce.rst
@@ -0,0 +1,62 @@
+.. index:: fix lineforce
+
+fix lineforce command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID lineforce x y z
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* lineforce = style name of this fix command
+* x y z = direction of line as a 3-vector
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix hold boundary lineforce 0.0 1.0 1.0
+
+Description
+"""""""""""
+
+Adjust the forces on each atom in the group so that only the component
+of force along the linear direction specified by the vector (x,y,z)
+remains.  This is done by subtracting out components of force in the
+plane perpendicular to the line.
+
+If the initial velocity of the atom is 0.0 (or along the line), then
+it should continue to move along the line thereafter.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix planeforce <fix_planeforce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst
new file mode 100644
index 0000000000..58f98762dc
--- /dev/null
+++ b/doc/src/fix_manifoldforce.rst
@@ -0,0 +1,74 @@
+.. index:: fix manifoldforce
+
+fix manifoldforce command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID manifoldforce manifold manifold-args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* manifold = name of the manifold
+* manifold-args = parameters for the manifold
+
+
+Examples
+""""""""
+
+fix constrain all manifoldforce sphere 5.0
+
+Description
+"""""""""""
+
+This fix subtracts each time step from the force the component along
+the normal of the specified :doc:`manifold <Howto_manifold>`.  This can be
+used in combination with :doc:`minimize <minimize>` to remove overlap
+between particles while keeping them (roughly) constrained to the
+given manifold, e.g. to set up a run with :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`.  I have found that
+only *hftn* and *quickmin* with a very small time step perform
+adequately though.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Only use this with *min\_style hftn* or *min\_style quickmin*. If not,
+the constraints will not be satisfied very well at all. A warning is
+generated if the *min\_style* is incompatible but no error.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`, :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_meso.rst b/doc/src/fix_meso.rst
new file mode 100644
index 0000000000..6be247101e
--- /dev/null
+++ b/doc/src/fix_meso.rst
@@ -0,0 +1,61 @@
+.. index:: fix meso
+
+fix meso command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID meso
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* meso = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all meso
+
+Description
+"""""""""""
+
+Perform time integration to update position, velocity, internal energy
+and local density for atoms in the group each timestep. This fix is
+needed to time-integrate mesoscopic systems where particles carry
+internal variables such as SPH or DPDE.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SPH package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+"fix meso/stationary"
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst
new file mode 100644
index 0000000000..79d9f499e5
--- /dev/null
+++ b/doc/src/fix_meso_move.rst
@@ -0,0 +1,273 @@
+.. index:: fix meso/move
+
+fix meso/move command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID meso/move style args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* meso/move = style name of this fix command
+* style = *linear* or *wiggle* or *rotate* or *variable*
+  
+  .. parsed-literal::
+  
+       *linear* args = Vx Vy Vz
+         Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+       *wiggle* args = Ax Ay Az period
+         Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
+         period = period of oscillation (time units)
+       *rotate* args = Px Py Pz Rx Ry Rz period
+         Px,Py,Pz = origin point of axis of rotation (distance units)
+         Rx,Ry,Rz = axis of rotation vector
+         period = period of rotation (time units)
+       *variable* args = v_dx v_dy v_dz v_vx v_vy v_vz
+         v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
+         v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
+
+* zero or more keyword/value pairs may be appended
+* keyword = *units*
+  
+  .. parsed-literal::
+  
+       *units* value = *box* or *lattice*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box
+   fix 2 boundary meso/move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+   fix 2 boundary meso/move variable v_myx v_myy NULL v_VX v_VY NULL
+
+Description
+"""""""""""
+
+Perform updates of position, velocity, internal energy and local
+density for mesoscopic particles in the group each timestep using the
+specified settings or formulas, without regard to forces on the
+particles. This can be useful for boundary, solid bodies or other
+particles, whose movement can influence nearby particles.
+
+The operation of this fix is exactly like that described by the
+:doc:`fix move <fix_move>` command, except that particles' density,
+internal energy and extrapolated velocity are also updated.
+
+.. note::
+
+   The particles affected by this fix should not be time integrated
+   by other fixes (e.g. :doc:`fix meso <fix_meso>`, :doc:`fix meso/stationary <fix_meso_stationary>`), since that will change their
+   positions and velocities twice.
+
+.. note::
+
+   As particles move due to this fix, they will pass through periodic
+   boundaries and be remapped to the other side of the simulation box,
+   just as they would during normal time integration (e.g. via the :doc:`fix meso <fix_meso>` command).  It is up to you to decide whether periodic
+   boundaries are appropriate with the kind of particle motion you are
+   prescribing with this fix.
+
+.. note::
+
+   As discussed below, particles are moved relative to their initial
+   position at the time the fix is specified.  These initial coordinates
+   are stored by the fix in "unwrapped" form, by using the image flags
+   associated with each particle.  See the :doc:`dump custom <dump>` command
+   for a discussion of "unwrapped" coordinates.  See the Atoms section of
+   the :doc:`read\_data <read_data>` command for a discussion of image flags
+   and how they are set for each particle.  You can reset the image flags
+   (e.g. to 0) before invoking this fix by using the :doc:`set image <set>`
+   command.
+
+
+----------
+
+
+The *linear* style moves particles at a constant velocity, so that their
+position *X* = (x,y,z) as a function of time is given in vector
+notation as
+
+
+.. parsed-literal::
+
+   X(t) = X0 + V \* delta
+
+where *X0* = (x0,y0,z0) is their position at the time the fix is
+specified, *V* is the specified velocity vector with components
+(Vx,Vy,Vz), and *delta* is the time elapsed since the fix was
+specified.  This style also sets the velocity of each particle to V =
+(Vx,Vy,Vz).  If any of the velocity components is specified as NULL,
+then the position and velocity of that component is time integrated
+the same as the :doc:`fix meso <fix_meso>` command would perform, using
+the corresponding force component on the particle.
+
+Note that the *linear* style is identical to using the *variable*
+style with an :doc:`equal-style variable <variable>` that uses the
+vdisplace() function.  E.g.
+
+
+.. parsed-literal::
+
+   variable V equal 10.0
+   variable x equal vdisplace(0.0,$V)
+   fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
+
+The *wiggle* style moves particles in an oscillatory fashion, so that
+their position *X* = (x,y,z) as a function of time is given in vector
+notation as
+
+
+.. parsed-literal::
+
+   X(t) = X0 + A sin(omega\*delta)
+
+where *X0* = (x0,y0,z0) is their position at the time the fix is
+specified, *A* is the specified amplitude vector with components
+(Ax,Ay,Az), *omega* is 2 PI / *period*\ , and *delta* is the time
+elapsed since the fix was specified.  This style also sets the
+velocity of each particle to the time derivative of this expression.
+If any of the amplitude components is specified as NULL, then the
+position and velocity of that component is time integrated the same as
+the :doc:`fix meso <fix_meso>` command would perform, using the
+corresponding force component on the particle.
+
+Note that the *wiggle* style is identical to using the *variable*
+style with :doc:`equal-style variables <variable>` that use the
+swiggle() and cwiggle() functions.  E.g.
+
+
+.. parsed-literal::
+
+   variable A equal 10.0
+   variable T equal 5.0
+   variable omega equal 2.0\*PI/$T
+   variable x equal swiggle(0.0,$A,$T)
+   variable v equal v_omega\*($A-cwiggle(0.0,$A,$T))
+   fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
+
+The *rotate* style rotates particles around a rotation axis *R* =
+(Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz).  The *period* of
+the rotation is also specified.  The direction of rotation for the
+particles around the rotation axis is consistent with the right-hand
+rule: if your right-hand thumb points along *R*\ , then your fingers wrap
+around the axis in the direction of rotation.
+
+This style also sets the velocity of each particle to (omega cross
+Rperp) where omega is its angular velocity around the rotation axis and
+Rperp is a perpendicular vector from the rotation axis to the particle.
+
+The *variable* style allows the position and velocity components of
+each particle to be set by formulas specified via the
+:doc:`variable <variable>` command.  Each of the 6 variables is
+specified as an argument to the fix as v\_name, where name is the
+variable name that is defined elsewhere in the input script.
+
+Each variable must be of either the *equal* or *atom* style.
+*Equal*\ -style variables compute a single numeric quantity, that can be
+a function of the timestep as well as of other simulation values.
+*Atom*\ -style variables compute a numeric quantity for each particle, that
+can be a function per-atom quantities, such as the particle's position, as
+well as of the timestep and other simulation values.  Note that this
+fix stores the original coordinates of each particle (see note below) so
+that per-atom quantity can be used in an atom-style variable formula.
+See the :doc:`variable <variable>` command for details.
+
+The first 3 variables (v\_dx,v\_dy,v\_dz) specified for the *variable*
+style are used to calculate a displacement from the particle's original
+position at the time the fix was specified.  The second 3 variables
+(v\_vx,v\_vy,v\_vz) specified are used to compute a velocity for each
+particle.
+
+Any of the 6 variables can be specified as NULL.  If both the
+displacement and velocity variables for a particular x,y,z component
+are specified as NULL, then the position and velocity of that
+component is time integrated the same as the :doc:`fix meso <fix_meso>`
+command would perform, using the corresponding force component on the
+particle.  If only the velocity variable for a component is specified as
+NULL, then the displacement variable will be used to set the position
+of the particle, and its velocity component will not be changed. If only
+the displacement variable for a component is specified as NULL, then
+the velocity variable will be used to set the velocity of the particle,
+and the position of the particle will be time integrated using that
+velocity.
+
+The *units* keyword determines the meaning of the distance units used
+to define the *linear* velocity and *wiggle* amplitude and *rotate*
+origin.  This setting is ignored for the *variable* style.  A *box*
+value selects standard units as defined by the :doc:`units <units>`
+command, e.g. velocity in Angstroms/fmsec and amplitude and position
+in Angstroms for units = real.  A *lattice* value means the velocity
+units are in lattice spacings per time and the amplitude and position
+are in lattice spacings.  The :doc:`lattice <lattice>` command must have
+been previously used to define the lattice spacing.  Each of these 3
+quantities may be dependent on the x,y,z dimension, since the lattice
+spacings can be different in x,y,z.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the original coordinates of moving particles to :doc:`binary restart files <restart>`, as well as the initial timestep, so that
+the motion can be continuous in a restarted simulation.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+.. note::
+
+   Because the move positions are a function of the current
+   timestep and the initial timestep, you cannot reset the timestep to a
+   different value after reading a restart file, if you expect a fix move
+   command to work in an uninterrupted fashion.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.
+
+This fix produces a per-atom array which can be accessed by various
+:doc:`output commands <Howto_output>`.  The number of columns for each
+atom is 3, and the columns store the original unwrapped x,y,z coords
+of each particle.  The per-atom values can be accessed on any timestep.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SDPD package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store density and internal energy as
+defined by the :doc:`atom\_style meso <atom_style>` command.
+
+All particles in the group must be mesoscopic SPH/SDPD particles.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix move <fix_move>`, :doc:`fix meso <fix_meso>`,
+:doc:`displace\_atoms <displace_atoms>`
+
+Default
+"""""""
+
+The option default is units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_meso_stationary.rst b/doc/src/fix_meso_stationary.rst
new file mode 100644
index 0000000000..5a39661cb6
--- /dev/null
+++ b/doc/src/fix_meso_stationary.rst
@@ -0,0 +1,62 @@
+.. index:: fix meso/stationary
+
+fix meso/stationary command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID meso/stationary
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* meso = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 boundary meso/stationary
+
+Description
+"""""""""""
+
+Perform time integration to update internal energy and local density,
+but not position or velocity for atoms in the group each timestep.
+This fix is needed for SPH simulations to correctly time-integrate
+fixed boundary particles which constrain a fluid to a given region in
+space.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SPH package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+"fix meso"
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst
new file mode 100644
index 0000000000..ed9f82988e
--- /dev/null
+++ b/doc/src/fix_modify.rst
@@ -0,0 +1,174 @@
+.. index:: fix\_modify
+
+fix\_modify command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix_modify fix-ID keyword value ...
+
+* fix-ID = ID of the fix to modify
+* one or more keyword/value pairs may be appended
+* keyword = *temp* or *press* or *energy* or *virial* or *respa* or *dynamic/dof* or *bodyforces*
+  
+  .. parsed-literal::
+  
+       *temp* value = compute ID that calculates a temperature
+       *press* value = compute ID that calculates a pressure
+       *energy* value = *yes* or *no*
+       *virial* value = *yes* or *no*
+       *respa* value = *1* to *max respa level* or *0* (for outermost level)
+       *dynamic/dof* value = *yes* or *no*
+         yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
+       *bodyforces* value = *early* or *late*
+         early/late = compute rigid-body forces/torques early or late in the timestep
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix_modify 3 temp myTemp press myPress
+   fix_modify 1 energy yes
+   fix_modify tether respa 2
+
+Description
+"""""""""""
+
+Modify one or more parameters of a previously defined fix.  Only
+specific fix styles support specific parameters.  See the doc pages
+for individual fix commands for info on which ones support which
+fix\_modify parameters.
+
+The *temp* keyword is used to determine how a fix computes
+temperature.  The specified compute ID must have been previously
+defined by the user via the :doc:`compute <compute>` command and it must
+be a style of compute that calculates a temperature.  All fixes that
+compute temperatures define their own compute by default, as described
+in their documentation.  Thus this option allows the user to override
+the default method for computing T.
+
+The *press* keyword is used to determine how a fix computes pressure.
+The specified compute ID must have been previously defined by the user
+via the :doc:`compute <compute>` command and it must be a style of
+compute that calculates a pressure.  All fixes that compute pressures
+define their own compute by default, as described in their
+documentation.  Thus this option allows the user to override the
+default method for computing P.
+
+The *energy* keyword can be used with fixes that support it.
+*energy yes* adds a contribution to the potential energy of the
+system. The fix's global and per-atom
+energy is included in the calculation performed by the :doc:`compute pe <compute_pe>` or :doc:`compute pe/atom <compute_pe_atom>`
+commands.  See the :doc:`thermo\_style <thermo_style>` command for info
+on how potential energy is output.  For fixes that tally a global
+energy, it can be printed by using the keyword f\_ID in the
+thermo\_style custom command, where ID is the fix-ID of the appropriate
+fix.
+
+.. note::
+
+   You must also specify the *energy yes* setting for a fix if you
+   are using it when performing an :doc:`energy minimization <minimize>`
+   and if you want the energy and forces it produces to be part of the
+   optimization criteria.
+
+The *virial* keyword can be used with fixes that support it.
+*virial yes* adds a contribution to the virial of the
+system. The fix's global and per-atom
+virial is included in the calculation performed by the :doc:`compute pressure <compute_pressure>` or
+:doc:`compute stress/atom <compute_stress_atom>`
+commands.  See the :doc:`thermo\_style <thermo_style>` command for info
+on how pressure is output.
+
+.. note::
+
+   You must specify the *virial yes* setting for a fix if you
+   are doing :doc:`box relaxation <fix_box_relax>` and
+   if you want virial contribution of the fix to be part of the
+   relaxation criteria, although this seems unlikely.
+
+.. note::
+
+   This option is only supported by fixes that explicitly say
+   so. For some of these (e.g. the :doc:`fix shake <fix_shake>` command)
+   the default setting is *virial yes*\ , for others it is *virial no*\ .
+
+For fixes that set or modify forces, it may be possible to select at
+which :doc:`r-RESPA <run_style>` level the fix operates via the *respa*
+keyword. The RESPA level at which the fix is active can be selected.
+This is a number ranging from 1 to the number of levels. If the RESPA
+level is larger than the current maximum, the outermost level will be
+used, which is also the default setting. This default can be restored
+using a value of *0* for the RESPA level. The affected fix has to be
+enabled to support this feature; if not, *fix\_modify* will report an
+error. Active fixes with a custom RESPA level setting are reported
+with their specified level at the beginning of a r-RESPA run.
+
+The *dynamic/dof* keyword determines whether the number of atoms N in
+the fix group and their associated degrees of freedom are re-computed
+each time a temperature is computed.  Only fix styles that calculate
+their own internal temperature use this option.  Currently this is
+only the :doc:`fix rigid/nvt/small <fix_rigid>` and :doc:`fix rigid/npt/small <fix_rigid>` commands for the purpose of
+thermostatting rigid body translation and rotation.  By default, N and
+their DOF are assumed to be constant.  If you are adding atoms or
+molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
+expect atoms or molecules to be lost (e.g. due to exiting the
+simulation box or via :doc:`fix evaporate <fix_evaporate>`), then
+this option should be used to insure the temperature is correctly
+normalized.
+
+.. note::
+
+   Other thermostatting fixes, such as :doc:`fix nvt <fix_nh>`, do
+   not use the *dynamic/dof* keyword because they use a temperature
+   compute to calculate temperature.  See the :doc:`compute\_modify dynamic/dof <compute_modify>` command for a similar way to insure
+   correct temperature normalization for those thermostats.
+
+The *bodyforces* keyword determines whether the forces and torques
+acting on rigid bodies are computed *early* at the post-force stage of
+each timestep (right after per-atom forces have been computed and
+communicated among processors), or *late* at the final-integrate stage
+of each timestep (after any other fixes have finished their post-force
+tasks).  Only the rigid-body integration fixes use this option, which
+includes :doc:`fix rigid <fix_rigid>` and :doc:`fix rigid/small <fix_rigid>`, and their variants, and also :doc:`fix poems <fix_poems>`.
+
+The default is *late*\ .  If there are other fixes that add forces to
+individual atoms, then the rigid-body constraints will include these
+forces when time-integrating the rigid bodies.  If *early* is
+specified, then new fixes can be written that use or modify the
+per-body force and torque, before time-integration of the rigid bodies
+occurs.  Note however this has the side effect, that fixes such as
+:doc:`fix addforce <fix_addforce>`, :doc:`fix setforce <fix_setforce>`,
+:doc:`fix spring <fix_spring>`, which add forces to individual atoms
+will have no effect on the motion of the rigid bodies if they are
+specified in the input script after the fix rigid command.  LAMMPS
+will give a warning if that is the case.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix <fix>`, :doc:`compute temp <compute_temp>`, :doc:`compute pressure <compute_pressure>`, :doc:`thermo\_style <thermo_style>`
+
+Default
+"""""""
+
+The option defaults are temp = ID defined by fix, press = ID defined
+by fix, energy = no, virial = different for each fix style, respa = 0,
+bodyforce = late.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst
new file mode 100644
index 0000000000..e3ace5a60e
--- /dev/null
+++ b/doc/src/fix_momentum.rst
@@ -0,0 +1,117 @@
+.. index:: fix momentum
+
+fix momentum command
+====================
+
+fix momentum/kk command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID momentum N keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* momentum = style name of this fix command
+* N = adjust the momentum every this many timesteps
+  one or more keyword/value pairs may be appended
+* keyword = *linear* or *angular* or *rescale*
+  
+  .. parsed-literal::
+  
+       *linear* values = xflag yflag zflag
+         xflag,yflag,zflag = 0/1 to exclude/include each dimension
+       *angular* values = none
+
+  
+  .. parsed-literal::
+  
+       *rescale* values = none
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all momentum 1 linear 1 1 0
+   fix 1 all momentum 1 linear 1 1 1 rescale
+   fix 1 all momentum 100 linear 1 1 1 angular
+
+Description
+"""""""""""
+
+Zero the linear and/or angular momentum of the group of atoms every N
+timesteps by adjusting the velocities of the atoms.  One (or both) of
+the *linear* or *angular* keywords must be specified.
+
+If the *linear* keyword is used, the linear momentum is zeroed by
+subtracting the center-of-mass velocity of the group from each atom.
+This does not change the relative velocity of any pair of atoms.  One
+or more dimensions can be excluded from this operation by setting the
+corresponding flag to 0.
+
+If the *angular* keyword is used, the angular momentum is zeroed by
+subtracting a rotational component from each atom.
+
+This command can be used to insure the entire collection of atoms (or
+a subset of them) does not drift or rotate during the simulation due
+to random perturbations (e.g. :doc:`fix langevin <fix_langevin>`
+thermostatting).
+
+The *rescale* keyword enables conserving the kinetic energy of the group
+of atoms by rescaling the velocities after the momentum was removed.
+
+Note that the :doc:`velocity <velocity>` command can be used to create
+initial velocities with zero aggregate linear and/or angular momentum.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix recenter <fix_recenter>`, :doc:`velocity <velocity>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst
new file mode 100644
index 0000000000..6994d9aa7c
--- /dev/null
+++ b/doc/src/fix_move.rst
@@ -0,0 +1,263 @@
+.. index:: fix move
+
+fix move command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID move style args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* move = style name of this fix command
+* style = *linear* or *wiggle* or *rotate* or *variable*
+  
+  .. parsed-literal::
+  
+       *linear* args = Vx Vy Vz
+         Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+       *wiggle* args = Ax Ay Az period
+         Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
+         period = period of oscillation (time units)
+       *rotate* args = Px Py Pz Rx Ry Rz period
+         Px,Py,Pz = origin point of axis of rotation (distance units)
+         Rx,Ry,Rz = axis of rotation vector
+         period = period of rotation (time units)
+       *variable* args = v_dx v_dy v_dz v_vx v_vy v_vz
+         v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
+         v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
+
+* zero or more keyword/value pairs may be appended
+* keyword = *units*
+  
+  .. parsed-literal::
+  
+       *units* value = *box* or *lattice*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
+   fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+   fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
+
+Description
+"""""""""""
+
+Perform updates of position and velocity for atoms in the group each
+timestep using the specified settings or formulas, without regard to
+forces on the atoms.  This can be useful for boundary or other atoms,
+whose movement can influence nearby atoms.
+
+.. note::
+
+   The atoms affected by this fix should not normally be time
+   integrated by other fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`), since that will change their positions and
+   velocities twice.
+
+.. note::
+
+   As atoms move due to this fix, they will pass through periodic
+   boundaries and be remapped to the other side of the simulation box,
+   just as they would during normal time integration (e.g. via the :doc:`fix nve <fix_nve>` command).  It is up to you to decide whether
+   periodic boundaries are appropriate with the kind of atom motion you
+   are prescribing with this fix.
+
+.. note::
+
+   As discussed below, atoms are moved relative to their initial
+   position at the time the fix is specified.  These initial coordinates
+   are stored by the fix in "unwrapped" form, by using the image flags
+   associated with each atom.  See the :doc:`dump custom <dump>` command
+   for a discussion of "unwrapped" coordinates.  See the Atoms section of
+   the :doc:`read\_data <read_data>` command for a discussion of image flags
+   and how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this fix by using the :doc:`set image <set>`
+   command.
+
+
+----------
+
+
+The *linear* style moves atoms at a constant velocity, so that their
+position *X* = (x,y,z) as a function of time is given in vector
+notation as
+
+
+.. parsed-literal::
+
+   X(t) = X0 + V \* delta
+
+where *X0* = (x0,y0,z0) is their position at the time the fix is
+specified, *V* is the specified velocity vector with components
+(Vx,Vy,Vz), and *delta* is the time elapsed since the fix was
+specified.  This style also sets the velocity of each atom to V =
+(Vx,Vy,Vz).  If any of the velocity components is specified as NULL,
+then the position and velocity of that component is time integrated
+the same as the :doc:`fix nve <fix_nve>` command would perform, using
+the corresponding force component on the atom.
+
+Note that the *linear* style is identical to using the *variable*
+style with an :doc:`equal-style variable <variable>` that uses the
+vdisplace() function.  E.g.
+
+
+.. parsed-literal::
+
+   variable V equal 10.0
+   variable x equal vdisplace(0.0,$V)
+   fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
+
+The *wiggle* style moves atoms in an oscillatory fashion, so that
+their position *X* = (x,y,z) as a function of time is given in vector
+notation as
+
+
+.. parsed-literal::
+
+   X(t) = X0 + A sin(omega\*delta)
+
+where *X0* = (x0,y0,z0) is their position at the time the fix is
+specified, *A* is the specified amplitude vector with components
+(Ax,Ay,Az), *omega* is 2 PI / *period*\ , and *delta* is the time
+elapsed since the fix was specified.  This style also sets the
+velocity of each atom to the time derivative of this expression.  If
+any of the amplitude components is specified as NULL, then the
+position and velocity of that component is time integrated the same as
+the :doc:`fix nve <fix_nve>` command would perform, using the
+corresponding force component on the atom.
+
+Note that the *wiggle* style is identical to using the *variable*
+style with :doc:`equal-style variables <variable>` that use the
+swiggle() and cwiggle() functions.  E.g.
+
+
+.. parsed-literal::
+
+   variable A equal 10.0
+   variable T equal 5.0
+   variable omega equal 2.0\*PI/$T
+   variable x equal swiggle(0.0,$A,$T)
+   variable v equal v_omega\*($A-cwiggle(0.0,$A,$T))
+   fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
+
+The *rotate* style rotates atoms around a rotation axis *R* =
+(Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz).  The *period* of
+the rotation is also specified.  The direction of rotation for the
+atoms around the rotation axis is consistent with the right-hand rule:
+if your right-hand thumb points along *R*\ , then your fingers wrap
+around the axis in the direction of rotation.
+
+This style also sets the velocity of each atom to (omega cross Rperp)
+where omega is its angular velocity around the rotation axis and Rperp
+is a perpendicular vector from the rotation axis to the atom.  If the
+defined :doc:`atom\_style <atom_style>` assigns an angular velocity or
+angular momentum or orientation to each atom (:doc:`atom styles <atom_style>` sphere, ellipsoid, line, tri, body), then
+those properties are also updated appropriately to correspond to the
+atom's motion and rotation over time.
+
+The *variable* style allows the position and velocity components of
+each atom to be set by formulas specified via the
+:doc:`variable <variable>` command.  Each of the 6 variables is
+specified as an argument to the fix as v\_name, where name is the
+variable name that is defined elsewhere in the input script.
+
+Each variable must be of either the *equal* or *atom* style.
+*Equal*\ -style variables compute a single numeric quantity, that can be
+a function of the timestep as well as of other simulation values.
+*Atom*\ -style variables compute a numeric quantity for each atom, that
+can be a function per-atom quantities, such as the atom's position, as
+well as of the timestep and other simulation values.  Note that this
+fix stores the original coordinates of each atom (see note below) so
+that per-atom quantity can be used in an atom-style variable formula.
+See the :doc:`variable <variable>` command for details.
+
+The first 3 variables (v\_dx,v\_dy,v\_dz) specified for the *variable*
+style are used to calculate a displacement from the atom's original
+position at the time the fix was specified.  The second 3 variables
+(v\_vx,v\_vy,v\_vz) specified are used to compute a velocity for each
+atom.
+
+Any of the 6 variables can be specified as NULL.  If both the
+displacement and velocity variables for a particular x,y,z component
+are specified as NULL, then the position and velocity of that
+component is time integrated the same as the :doc:`fix nve <fix_nve>`
+command would perform, using the corresponding force component on the
+atom.  If only the velocity variable for a component is specified as
+NULL, then the displacement variable will be used to set the position
+of the atom, and its velocity component will not be changed.  If only
+the displacement variable for a component is specified as NULL, then
+the velocity variable will be used to set the velocity of the atom,
+and the position of the atom will be time integrated using that
+velocity.
+
+The *units* keyword determines the meaning of the distance units used
+to define the *linear* velocity and *wiggle* amplitude and *rotate*
+origin.  This setting is ignored for the *variable* style.  A *box*
+value selects standard units as defined by the :doc:`units <units>`
+command, e.g. velocity in Angstroms/fmsec and amplitude and position
+in Angstroms for units = real.  A *lattice* value means the velocity
+units are in lattice spacings per time and the amplitude and position
+are in lattice spacings.  The :doc:`lattice <lattice>` command must have
+been previously used to define the lattice spacing.  Each of these 3
+quantities may be dependent on the x,y,z dimension, since the lattice
+spacings can be different in x,y,z.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the original coordinates of moving atoms to :doc:`binary restart files <restart>`, as well as the initial timestep, so that
+the motion can be continuous in a restarted simulation.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+.. note::
+
+   Because the move positions are a function of the current
+   timestep and the initial timestep, you cannot reset the timestep to a
+   different value after reading a restart file, if you expect a fix move
+   command to work in an uninterrupted fashion.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.
+
+This fix produces a per-atom array which can be accessed by various
+:doc:`output commands <Howto_output>`.  The number of columns for each
+atom is 3, and the columns store the original unwrapped x,y,z coords
+of each atom.  The per-atom values can be accessed on any timestep.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+For :doc:`rRESPA time integration <run_style>`, this fix adjusts the
+position and velocity of atoms on the outermost rRESPA level.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`displace\_atoms <displace_atoms>`
+
+**Default:** none
+
+The option default is units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst
new file mode 100644
index 0000000000..b6f776677e
--- /dev/null
+++ b/doc/src/fix_mscg.rst
@@ -0,0 +1,155 @@
+.. index:: fix mscg
+
+fix mscg command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID mscg N keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* mscg = style name of this fix command
+* N = envoke this fix every this many timesteps
+* zero or more keyword/value pairs may be appended
+* keyword = *range* or *name* or *max*
+  
+  .. parsed-literal::
+  
+       *range* arg = *on* or *off*
+         *on* = range finding functionality is performed
+         *off* = force matching functionality is performed
+       *name* args = name1 ... nameN
+         name1,...,nameN = string names for each atom type (1-Ntype)
+       *max* args = maxb maxa maxd
+         maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all mscg 1
+   fix 1 all mscg 1 range name A B
+   fix 1 all mscg 1 max 4 8 20
+
+Description
+"""""""""""
+
+This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
+snapshots from a dump file to generate potentials for coarse-grained
+simulations from all-atom simulations, using a force-matching
+technique (:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
+
+It makes use of the MS-CG library, written and maintained by Greg
+Voth's group at the University of Chicago, which is freely available
+on their `MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.  See instructions
+on obtaining and installing the MS-CG library in the src/MSCG/README
+file, which must be done before you build LAMMPS with this fix command
+and use the command in a LAMMPS input script.
+
+An example script using this fix is provided the examples/mscg
+directory.
+
+The general workflow for using LAMMPS in conjunction with the MS-CG
+library to create a coarse-grained model and run coarse-grained
+simulations is as follows:
+
+1. Perform all-atom simulations on the system to be coarse grained.
+2. Generate a trajectory mapped to the coarse-grained model.
+3. Create input files for the MS-CG library.
+4. Run the range finder functionality of the MS-CG library.
+5. Run the force matching functionality of the MS-CG library.
+6. Check the results of the force matching.
+7. Run coarse-grained simulations using the new coarse-grained potentials.
+
+This fix can perform the range finding and force matching steps 4 and
+5 of the above workflow when used in conjunction with the
+:doc:`rerun <rerun>` command.  It does not perform steps 1-3 and 6-7.
+
+Step 2 can be performed using a Python script (what is the name?)
+provided with the MS-CG library which defines the coarse-grained model
+and converts a standard LAMMPS dump file for an all-atom simulation
+(step 1) into a LAMMPS dump file which has the positions of and forces
+on the coarse-grained beads.
+
+In step 3, an input file named "control.in" is needed by the MS-CG
+library which sets parameters for the range finding and force matching
+functionalities.  See the examples/mscg/control.in file as an example.
+And see the documentation provided with the MS-CG library for more
+info on this file.
+
+When this fix is used to perform steps 4 and 5, the MS-CG library also
+produces additional output files.  The range finder functionality
+(step 4) outputs files defining pair and bonded interaction ranges.
+The force matching functionality (step 5) outputs tabulated force
+files for every interaction in the system. Other diagnostic files can
+also be output depending on the parameters in the MS-CG library input
+script.  Again, see the documentation provided with the MS-CG library
+for more info.
+
+
+----------
+
+
+The *range* keyword specifies which MS-CG library functionality should
+be invoked. If *on*\ , the step 4 range finder functionality is invoked.
+*off*\ , the step 5 force matching functionality is invoked.
+
+If the *name* keyword is used, string names are defined to associate
+with the integer atom types in LAMMPS.  *Ntype* names must be
+provided, one for each atom type (1-Ntype).
+
+The *max* keyword specifies the maximum number of bonds, angles, and
+dihedrals a bead can have in the coarse-grained model.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MSCG package. It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+The MS-CG library uses C++11, which may not be supported by older
+compilers. The MS-CG library also has some additional numeric library
+dependencies, which are described in its documentation.
+
+Currently, the MS-CG library is not setup to run in parallel with MPI,
+so this fix can only be used in a serial LAMMPS build and run
+on a single processor.
+
+**Related commands:** none
+
+Default
+"""""""
+
+The default keyword settings are range off, max 4 12 36.
+
+
+----------
+
+
+.. _Izvekov:
+
+
+
+**(Izvekov)** Izvekov, Voth, J Chem Phys 123, 134105 (2005).
+
+.. _Noid:
+
+
+
+**(Noid)** Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
+Chem Phys 128, 134105 (2008).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst
new file mode 100644
index 0000000000..85fb9049c3
--- /dev/null
+++ b/doc/src/fix_msst.rst
@@ -0,0 +1,228 @@
+.. index:: fix msst
+
+fix msst command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID msst dir shockvel keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* msst = style name of this fix
+* dir = *x* or *y* or *z*
+* shockvel = shock velocity (strictly positive, distance/time units)
+* zero or more keyword value pairs may be appended
+* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *beta* or *dftb*
+  
+  .. parsed-literal::
+  
+       *q* value = cell mass-like parameter (mass\^2/distance\^4 units)
+       *mu* value = artificial viscosity (mass/length/time units)
+       *p0* value = initial pressure in the shock equations (pressure units)
+       *v0* value = initial simulation cell volume in the shock equations (distance\^3 units)
+       *e0* value = initial total energy (energy units)
+       *tscale* value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
+       *dftb* value = *yes* or *no* for whether using MSST in conjunction with DFTB+
+       *beta* value = scale factor for improved energy conservation
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
+   fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4  v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01
+   fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 dftb yes beta 0.5
+
+Description
+"""""""""""
+
+This command performs the Multi-Scale Shock Technique (MSST)
+integration to update positions and velocities each timestep to mimic
+a compressive shock wave passing over the system. See :ref:`(Reed) <Reed>`
+for a detailed description of this method.  The MSST varies the cell
+volume and temperature in such a way as to restrain the system to the
+shock Hugoniot and the Rayleigh line. These restraints correspond to
+the macroscopic conservation laws dictated by a shock
+front. *shockvel* determines the steady shock velocity that will be
+simulated.
+
+To perform a simulation, choose a value of *q* that provides volume
+compression on the timescale of 100 fs to 1 ps.  If the volume is not
+compressing, either the shock speed is chosen to be below the material
+sound speed or *p0* has been chosen inaccurately.  Volume compression
+at the start can be sped up by using a non-zero value of *tscale*\ . Use
+the smallest value of *tscale* that results in compression.
+
+Under some special high-symmetry conditions, the pressure (volume)
+and/or temperature of the system may oscillate for many cycles even
+with an appropriate choice of mass-like parameter *q*\ . Such
+oscillations have physical significance in some cases.  The optional
+*mu* keyword adds an artificial viscosity that helps break the system
+symmetry to equilibrate to the shock Hugoniot and Rayleigh line more
+rapidly in such cases.
+
+The keyword *tscale* is a factor between 0 and 1 that determines what
+fraction of thermal kinetic energy is converted to compressive strain
+kinetic energy at the start of the simulation.  Setting this parameter
+to a non-zero value may assist in compression at the start of
+simulations where it is slow to occur.
+
+If keywords *e0*\ , *p0*\ ,or *v0* are not supplied, these quantities will
+be calculated on the first step, after the energy specified by
+*tscale* is removed.  The value of *e0* is not used in the dynamical
+equations, but is used in calculating the deviation from the Hugoniot.
+
+The keyword *beta* is a scaling term that can be added to the MSST
+ionic equations of motion to account for drift in the conserved
+quantity during long timescale simulations, similar to a Berendsen
+thermostat. See :ref:`(Reed) <Reed>` and :ref:`(Goldman) <Goldman2>` for more
+details.  The value of *beta* must be between 0.0 and 1.0 inclusive.
+A value of 0.0 means no contribution, a value of 1.0 means a full
+contribution.
+
+Values of shockvel less than a critical value determined by the
+material response will not have compressive solutions. This will be
+reflected in lack of significant change of the volume in the MSST.
+
+For all pressure styles, the simulation box stays orthogonal in shape.
+Parrinello-Rahman boundary conditions (tilted box) are supported by
+LAMMPS, but are not implemented for MSST.
+
+This fix computes a temperature and pressure and potential energy each
+timestep. To do this, the fix creates its own computes of style "temp"
+"pressure", and "pe", as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_MSST_temp all temp
+   compute fix-ID_MSST_press all pressure fix-ID_MSST_temp
+
+   compute fix-ID_MSST_pe all pe
+
+See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + "_MSST\_temp`or <MSST_press">`_
+or "_MSST\_pe".  The group for the new computes is "all".
+
+
+----------
+
+
+The *dftb* keyword is to allow this fix to be used when LAMMPS is
+being driven by DFTB+, a density-functional tight-binding code. If the
+keyword *dftb* is used with a value of *yes*\ , then the MSST equations
+are altered to account for the electron entropy contribution to the
+Hugonio relations and total energy.  See :ref:`(Reed2) <Reed2>` and
+:ref:`(Goldman) <Goldman2>` for details on this contribution.  In this case,
+you must define a :doc:`fix external <fix_external>` command in your
+input script, which is used to callback to DFTB+ during the LAMMPS
+timestepping.  DFTB+ will communicate its info to LAMMPS via that fix.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of all internal variables to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>` command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The progress of the MSST can be monitored by printing the global
+scalar and global vector quantities computed by the fix.
+
+The scalar is the cumulative energy change due to the fix. This is
+also the energy added to the potential energy by the
+:doc:`fix\_modify <fix_modify>` *energy* command.  With this command, the
+thermo keyword *etotal* prints the conserved quantity of the MSST
+dynamic equations. This can be used to test if the MD timestep is
+sufficiently small for accurate integration of the dynamic
+equations. See also :doc:`thermo\_style <thermo_style>` command.
+
+The global vector contains four values in this order:
+
+[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian\_speed*, *lagrangian\_position*]
+
+1. *dhugoniot* is the departure from the Hugoniot (temperature units).
+2. *drayleigh* is the departure from the Rayleigh line (pressure units).
+3. *lagrangian\_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
+4. *lagrangian\_position* is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front.
+
+To print these quantities to the log file with descriptive column
+headers, the following LAMMPS commands are suggested:
+
+
+.. parsed-literal::
+
+   fix              msst all msst z
+   fix_modify       msst energy yes
+   variable dhug    equal f_msst[1]
+   variable dray    equal f_msst[2]
+   variable lgr_vel equal f_msst[3]
+   variable lgr_pos equal f_msst[4]
+   thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+
+These fixes compute a global scalar and a global vector of 4
+quantities, which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar values calculated by this fix
+are "extensive"; the vector values are "intensive".
+
+Restrictions
+""""""""""""
+
+
+This fix style is part of the SHOCK package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+All cell dimensions must be periodic. This fix can not be used with a
+triclinic cell.  The MSST fix has been tested only for the group-ID
+all.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nphug <fix_nphug>`, :doc:`fix deform <fix_deform>`
+
+Default
+"""""""
+
+The keyword defaults are q = 10, mu = 0, tscale = 0.01, dftb = no,
+beta = 0.0.  Note that p0, v0, and e0 are calculated on the first
+timestep.
+
+
+----------
+
+
+.. _Reed:
+
+
+
+**(Reed)** Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503
+(2003).
+
+.. _Reed2:
+
+
+
+**(Reed2)** Reed, J. Phys. Chem. C, 116, 2205 (2012).
+
+.. _Goldman2:
+
+
+
+**(Goldman)** Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner,
+J. Phys. Chem. C, 117, 7885 (2013).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst
new file mode 100644
index 0000000000..9c9471fd71
--- /dev/null
+++ b/doc/src/fix_mvv_dpd.rst
@@ -0,0 +1,119 @@
+.. index:: fix mvv/dpd
+
+fix mvv/dpd command
+===================
+
+fix mvv/edpd command
+====================
+
+fix mvv/tdpd command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID mvv/dpd lambda
+
+   fix ID group-ID mvv/edpd lambda
+
+   fix ID group-ID mvv/tdpd lambda
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* mvv/dpd, mvv/edpd, mvv/tdpd = style name of this fix command
+* lambda = (optional) relaxation parameter (unitless)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all mvv/dpd
+   fix 1 all mvv/dpd 0.5
+   fix 1 all mvv/edpd
+   fix 1 all mvv/edpd 0.5
+   fix 1 all mvv/tdpd
+   fix 1 all mvv/tdpd 0.5
+
+Description
+"""""""""""
+
+Perform time integration using the modified velocity-Verlet (MVV)
+algorithm to update position and velocity (fix mvv/dpd), or position,
+velocity and temperature (fix mvv/edpd), or position, velocity and
+concentration (fix mvv/tdpd) for particles in the group each timestep.
+
+The modified velocity-Verlet (MVV) algorithm aims to improve the
+stability of the time integrator by using an extrapolated version of
+the velocity for the force evaluation:
+
+.. image:: Eqs/fix_mvv_dpd.jpg
+   :align: center
+
+where the parameter <font size="4">&lambda;</font> depends on the
+specific choice of DPD parameters, and needs to be tuned on a
+case-by-case basis.  Specification of a *lambda* value is optional.
+If specified, the setting must be from 0.0 to 1.0.  If not specified,
+a default value of 0.5 is used, which effectively reproduces the
+standard velocity-Verlet (VV) scheme.  For more details, see
+:ref:`Groot <Groot2>`.
+
+Fix *mvv/dpd* updates the position and velocity of each atom.  It can
+be used with the :doc:`pair\_style mdpd <pair_meso>` command or other
+pair styles such as :doc:`pair dpd <pair_dpd>`.
+
+Fix *mvv/edpd* updates the per-atom temperature, in addition to
+position and velocity, and must be used with the :doc:`pair\_style edpd <pair_meso>` command.
+
+Fix *mvv/tdpd* updates the per-atom chemical concentration, in
+addition to position and velocity, and must be used with the
+:doc:`pair\_style tdpd <pair_meso>` command.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MESO package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style mdpd <pair_meso>`, :doc:`pair\_style edpd <pair_meso>`,
+:doc:`pair\_style tdpd <pair_meso>`
+
+Default
+"""""""
+
+The default value for the optional *lambda* parameter is 0.5.
+
+
+----------
+
+
+.. _Groot2:
+
+
+
+**(Groot)** Groot and Warren, J Chem Phys, 107: 4423-4435 (1997).  DOI:
+10.1063/1.474784
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst
new file mode 100644
index 0000000000..5dded81f55
--- /dev/null
+++ b/doc/src/fix_neb.rst
@@ -0,0 +1,292 @@
+.. index:: fix neb
+
+fix neb command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID neb Kspring keyword value
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* neb = style name of this fix command
+* Kspring = spring constant for parallel nudging force (force/distance units or force units, see parallel keyword)
+* zero or more keyword/value pairs may be appended
+* keyword = *parallel* or *perp* or *end*
+
+.. parsed-literal::
+
+     *parallel* value = *neigh* or *ideal*
+       *neigh* = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units)
+       *ideal* = parallel nudging force based on interpolated ideal position (Kspring = force units)
+     *perp* value = *Kspring2*
+       *Kspring2* = spring constant for perpendicular nudging force (force/distance units)
+     *end* values = estyle Kspring3
+       *estyle* = *first* or *last* or *last/efirst* or *last/efirst/middle*
+         *first* = apply force to first replica
+         *last* = apply force to last replica
+         *last/efirst* = apply force to last replica and set its target energy to that of first replica
+         *last/efirst/middle* = same as *last/efirst* plus prevent middle replicas having lower energy than first replica
+       *Kspring3* = spring constant for target energy term (1/distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 active neb 10.0
+   fix 2 all neb 1.0 perp 1.0 end last
+   fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
+   fix 1 all neb 1.0 parallel ideal end last/efirst 1
+
+Description
+"""""""""""
+
+Add nudging forces to atoms in the group for a multi-replica
+simulation run via the :doc:`neb <neb>` command to perform a nudged
+elastic band (NEB) calculation for finding the transition state.
+Hi-level explanations of NEB are given with the :doc:`neb <neb>` command
+and on the :doc:`Howto replica <Howto_replica>` doc page.  The fix neb
+command must be used with the "neb" command and defines how
+inter-replica nudging forces are computed.  A NEB calculation is
+divided in two stages. In the first stage n replicas are relaxed
+toward a MEP until convergence.  In the second stage, the climbing
+image scheme (see :ref:`(Henkelman2) <Henkelman2>`) is enabled, so that the
+replica having the highest energy relaxes toward the saddle point
+(i.e. the point of highest energy along the MEP), and a second
+relaxation is performed.
+
+A key purpose of the nudging forces is to keep the replicas equally
+spaced.  During the NEB calculation, the 3N-length vector of
+interatomic force Fi = -Grad(V) for each replica I is altered.  For
+all intermediate replicas (i.e. for 1 < I < N, except the climbing
+replica) the force vector becomes:
+
+
+.. parsed-literal::
+
+   Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp
+
+T' is the unit "tangent" vector for replica I and is a function of Ri,
+Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
+roughly in the direction of (Ri+i - Ri-1); see the
+:ref:`(Henkelman1) <Henkelman1>` paper for details.  Ri are the atomic
+coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its
+neighbor replicas.  The term (Grad(V) dot T') is used to remove the
+component of the gradient parallel to the path which would tend to
+distribute the replica unevenly along the path.  Fnudge\_parallel is an
+artificial nudging force which is applied only in the tangent
+direction and which maintains the equal spacing between replicas (see
+below for more information).  Fnudge\_perp is an optional artificial
+spring which is applied in a direction perpendicular to the tangent
+direction and which prevent the paths from forming acute kinks (see
+below for more information).
+
+In the second stage of the NEB calculation, the interatomic force Fi
+for the climbing replica (the replica of highest energy after the
+first stage) is changed to:
+
+
+.. parsed-literal::
+
+   Fi = -Grad(V) + 2 (Grad(V) dot T') T'
+
+and the relaxation procedure is continued to a new converged MEP.
+
+
+----------
+
+
+The keyword *parallel* specifies how the parallel nudging force is
+computed.  With a value of *neigh*\ , the parallel nudging force is
+computed as in :ref:`(Henkelman1) <Henkelman1>` by connecting each
+intermediate replica with the previous and the next image:
+
+
+.. parsed-literal::
+
+   Fnudge_parallel = *Kspring* \* (\|Ri+1 - Ri\| - \|Ri - Ri-1\|)
+
+Note that in this case the specified *Kspring* is in force/distance
+units.
+
+With a value of *ideal*\ , the spring force is computed as suggested in
+ref`(WeinanE) <WeinanE>` 
+
+
+.. parsed-literal::
+
+   Fnudge_parallel = -\ *Kspring* \* (RD-RDideal) / (2 \* meanDist)
+
+where RD is the "reaction coordinate" see :doc:`neb <neb>` section, and
+RDideal is the ideal RD for which all the images are equally spaced.
+I.e. RDideal = (I-1)\*meanDist when the climbing replica is off, where
+I is the replica number).  The meanDist is the average distance
+between replicas.  Note that in this case the specified *Kspring* is
+in force units.
+
+Note that the *ideal* form of nudging can often be more effective at
+keeping the replicas equally spaced.
+
+
+----------
+
+
+The keyword *perp* specifies if and how a perpendicular nudging force
+is computed.  It adds a spring force perpendicular to the path in
+order to prevent the path from becoming too strongly kinked.  It can
+significantly improve the convergence of the NEB calculation when the
+resolution is poor.  I.e. when few replicas are used; see
+:ref:`(Maras) <Maras1>` for details.
+
+The perpendicular spring force is given by
+
+
+.. parsed-literal::
+
+   Fnudge_perp = *Kspring2* \* F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri)
+
+where *Kspring2* is the specified value.  F(Ri-1 Ri R+1) is a smooth
+scalar function of the angle Ri-1 Ri Ri+1.  It is equal to 0.0 when
+the path is straight and is equal to 1 when the angle Ri-1 Ri Ri+1 is
+acute.  F(Ri-1 Ri R+1) is defined in :ref:`(Jonsson) <Jonsson>`.
+
+If *Kspring2* is set to 0.0 (the default) then no perpendicular spring
+force is added.
+
+
+----------
+
+
+By default, no additional forces act on the first and last replicas
+during the NEB relaxation, so these replicas simply relax toward their
+respective local minima.  By using the key word *end*\ , additional
+forces can be applied to the first and/or last replicas, to enable
+them to relax toward a MEP while constraining their energy E to the
+target energy ETarget.
+
+If ETarget>E, the interatomic force Fi for the specified replica becomes:
+
+
+.. parsed-literal::
+
+   Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)\*Kspring3) T',  *when* Grad(V) dot T' < 0
+   Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)\*Kspring3) T', *when* Grad(V) dot T' > 0
+
+The "spring" constant on the difference in energies is the specified
+*Kspring3* value.
+
+When *estyle* is specified as *first*\ , the force is applied to the
+first replica.  When *estyle* is specified as *last*\ , the force is
+applied to the last replica.  Note that the *end* keyword can be used
+twice to add forces to both the first and last replicas.
+
+For both these *estyle* settings, the target energy *ETarget* is set
+to the initial energy of the replica (at the start of the NEB
+calculation).
+
+If the *estyle* is specified as *last/efirst* or *last/efirst/middle*\ ,
+force is applied to the last replica, but the target energy *ETarget*
+is continuously set to the energy of the first replica, as it evolves
+during the NEB relaxation.
+
+The difference between these two *estyle* options is as follows.  When
+*estyle* is specified as *last/efirst*\ , no change is made to the
+inter-replica force applied to the intermediate replicas (neither
+first or last).  If the initial path is too far from the MEP, an
+intermediate replica may relax "faster" and reach a lower energy than
+the last replica.  In this case the intermediate replica will be
+relaxing toward its own local minima.  This behavior can be prevented
+by specifying *estyle* as *last/efirst/middle* which will alter the
+inter-replica force applied to intermediate replicas by removing the
+contribution of the gradient to the inter-replica force.  This will
+only be done if a particular intermediate replica has a lower energy
+than the first replica.  This should effectively prevent the
+intermediate replicas from over-relaxing.
+
+After converging a NEB calculation using an *estyle* of
+*last/efirst/middle*\ , you should check that all intermediate replicas
+have a larger energy than the first replica. If this is not the case,
+the path is probably not a MEP.
+
+Finally, note that the last replica may never reach the target energy
+if it is stuck in a local minima which has a larger energy than the
+target energy.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+as invoked by the :doc:`minimize <minimize>` command via the
+:doc:`neb <neb>` command.
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`neb <neb>`
+
+Default
+"""""""
+
+The option defaults are parallel = neigh, perp = 0.0, ends is not
+specified (no inter-replica force on the end replicas).
+
+
+----------
+
+
+.. _Henkelman1:
+
+
+
+**(Henkelman1)** Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
+
+.. _Henkelman2:
+
+
+
+**(Henkelman2)** Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+9901-9904 (2000).
+
+.. _WeinanE:
+
+
+
+**(WeinanE)** E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
+
+.. _Jonsson:
+
+
+
+**(Jonsson)** Jonsson, Mills and Jacobsen, in Classical and Quantum
+Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti,
+and Coker World Scientific, Singapore, 1998, p 385.
+
+.. _Maras1:
+
+
+
+**(Maras)** Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
+Comp Phys Comm, 205, 13-21 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst
new file mode 100644
index 0000000000..5b316f0009
--- /dev/null
+++ b/doc/src/fix_neb_spin.rst
@@ -0,0 +1,93 @@
+.. index:: fix neb/spin
+
+fix neb/spin command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID neb/spin Kspring
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* neb/spin = style name of this fix command
+
+.. parsed-literal::
+
+   Kspring = spring constant for parallel nudging force
+   (force/distance units or force units, see parallel keyword)
+
+Examples
+""""""""
+
+fix 1 active neb/spin 1.0
+
+Description
+"""""""""""
+
+Add nudging forces to spins in the group for a multi-replica
+simulation run via the :doc:`neb/spin <neb_spin>` command to perform a
+geodesic nudged elastic band (GNEB) calculation for finding the
+transition state.
+Hi-level explanations of GNEB are given with the
+:doc:`neb/spin <neb_spin>` command and on the
+:doc:`Howto replica <Howto_replica>` doc page.
+The fix neb/spin command must be used with the "neb/spin" command and
+defines how inter-replica nudging forces are computed.  A GNEB
+calculation is divided in two stages. In the first stage n replicas
+are relaxed toward a MEP until convergence.  In the second stage, the
+climbing image scheme is enabled, so that the replica having the highest
+energy relaxes toward the saddle point (i.e. the point of highest energy
+along the MEP), and a second relaxation is performed.
+
+The nudging forces are calculated as explained in
+:ref:`(BessarabB) <BessarabB>`).
+See this reference for more explanation about their expression.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+as invoked by the :doc:`minimize <minimize>` command via the
+:doc:`neb/spin <neb_spin>` command.
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the SPIN
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`neb\_spin <neb_spin>`
+
+Default
+"""""""
+
+none
+
+
+----------
+
+
+.. _BessarabB:
+
+
+
+**(BessarabB)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+335-347 (2015).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst
new file mode 100644
index 0000000000..6f3d31b9cf
--- /dev/null
+++ b/doc/src/fix_nh.rst
@@ -0,0 +1,743 @@
+.. index:: fix nvt
+
+fix nvt command
+===============
+
+fix nvt/intel command
+=====================
+
+fix nvt/kk command
+==================
+
+fix nvt/omp command
+===================
+
+fix npt command
+===============
+
+fix npt/intel command
+=====================
+
+fix npt/kk command
+==================
+
+fix npt/omp command
+===================
+
+fix nph command
+===============
+
+fix nph/kk command
+==================
+
+fix nph/omp command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style_name keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style\_name = *nvt* or *npt* or *nph*
+* one or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*
+       *temp* values = Tstart Tstop Tdamp
+         Tstart,Tstop = external temperature at start/end of run
+         Tdamp = temperature damping parameter (time units)
+       *iso* or *aniso* or *tri* values = Pstart Pstop Pdamp
+         Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+         Pdamp = pressure damping parameter (time units)
+       *x* or *y* or *z* or *xy* or *yz* or *xz* values = Pstart Pstop Pdamp
+         Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+         Pdamp = stress damping parameter (time units)
+       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *tchain* value = N
+         N = length of thermostat chain (1 = single thermostat)
+       *pchain* values = N
+         N length of thermostat chain on barostat (0 = no thermostat)
+       *mtk* value = *yes* or *no* = add in MTK adjustment term or not
+       *tloop* value = M
+         M = number of sub-cycles to perform on thermostat
+       *ploop* value = M
+         M = number of sub-cycles to perform on barostat thermostat
+       *nreset* value = reset reference cell every this many timesteps
+       *drag* value = Df
+         Df = drag factor added to barostat/thermostat (0.0 = no drag)
+       *dilate* value = dilate-group-ID
+         dilate-group-ID = only dilate atoms in this group due to barostat volume changes
+       *scalexy* value = *yes* or *no* = scale xy with ly
+       *scaleyz* value = *yes* or *no* = scale yz with lz
+       *scalexz* value = *yes* or *no* = scale xz with lz
+       *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed
+       *fixedpoint* values = x y z
+         x,y,z = perform barostat dilation/contraction around this point (distance units)
+       *update* value = *dipole* or *dipole/dlm*
+         dipole = update dipole orientation (only for sphere variants)
+         dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nvt temp 300.0 300.0 100.0
+   fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
+   fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
+   fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
+
+Description
+"""""""""""
+
+These commands perform time integration on Nose-Hoover style
+non-Hamiltonian equations of motion which are designed to generate
+positions and velocities sampled from the canonical (nvt),
+isothermal-isobaric (npt), and isenthalpic (nph) ensembles.  This
+updates the position and velocity for atoms in the group each
+timestep.
+
+The thermostatting and barostatting is achieved by adding some dynamic
+variables which are coupled to the particle velocities
+(thermostatting) and simulation domain dimensions (barostatting).  In
+addition to basic thermostatting and barostatting, these fixes can
+also create a chain of thermostats coupled to the particle thermostat,
+and another chain of thermostats coupled to the barostat
+variables. The barostat can be coupled to the overall box volume, or
+to individual dimensions, including the *xy*\ , *xz* and *yz* tilt
+dimensions. The external pressure of the barostat can be specified as
+either a scalar pressure (isobaric ensemble) or as components of a
+symmetric stress tensor (constant stress ensemble).  When used
+correctly, the time-averaged temperature and stress tensor of the
+particles will match the target values specified by Tstart/Tstop and
+Pstart/Pstop.
+
+The equations of motion used are those of Shinoda et al in
+:ref:`(Shinoda) <nh-Shinoda>`, which combine the hydrostatic equations of
+Martyna, Tobias and Klein in :ref:`(Martyna) <nh-Martyna>` with the strain
+energy proposed by Parrinello and Rahman in
+:ref:`(Parrinello) <nh-Parrinello>`.  The time integration schemes closely
+follow the time-reversible measure-preserving Verlet and rRESPA
+integrators derived by Tuckerman et al in :ref:`(Tuckerman) <nh-Tuckerman>`.
+
+
+----------
+
+
+The thermostat parameters for fix styles *nvt* and *npt* is specified
+using the *temp* keyword.  Other thermostat-related keywords are
+*tchain*\ , *tloop* and *drag*\ , which are discussed below.
+
+The thermostat is applied to only the translational degrees of freedom
+for the particles.  The translational degrees of freedom can also have
+a bias velocity removed before thermostatting takes place; see the
+description below.  The desired temperature at each timestep is a
+ramped value during the run from *Tstart* to *Tstop*\ .  The *Tdamp*
+parameter is specified in time units and determines how rapidly the
+temperature is relaxed.  For example, a value of 10.0 means to relax
+the temperature in a timespan of (roughly) 10 time units (e.g. tau or
+fmsec or psec - see the :doc:`units <units>` command).  The atoms in the
+fix group are the only ones whose velocities and positions are updated
+by the velocity/position update portion of the integration.
+
+.. note::
+
+   A Nose-Hoover thermostat will not work well for arbitrary values
+   of *Tdamp*\ .  If *Tdamp* is too small, the temperature can fluctuate
+   wildly; if it is too large, the temperature will take a very long time
+   to equilibrate.  A good choice for many models is a *Tdamp* of around
+   100 timesteps.  Note that this is NOT the same as 100 time units for
+   most :doc:`units <units>` settings. A simple way to ensure this, is
+   via using an :doc:`immediate variable <variable>` expression accessing
+   the thermo property 'dt', which is the length of the time step. Example:
+
+
+.. parsed-literal::
+
+   fix 1 all nvt temp 300.0 300.0 $(100.0\*dt)
+
+
+----------
+
+
+The barostat parameters for fix styles *npt* and *nph* is specified
+using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ ,
+*xz*\ , *yz*\ , and *couple* keywords.  These keywords give you the
+ability to specify all 6 components of an external stress tensor, and
+to couple various of these components together so that the dimensions
+they represent are varied together during a constant-pressure
+simulation.
+
+Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ ,
+*nreset*\ , *drag*\ , and *dilate*\ , which are discussed below.
+
+Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
+Triclinic (non-orthogonal) simulation boxes have 6 adjustable
+dimensions (x,y,z,xy,xz,yz).  The :doc:`create\_box <create_box>`, :doc:`read data <read_data>`, and :doc:`read\_restart <read_restart>` commands
+specify whether the simulation box is orthogonal or non-orthogonal
+(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
+
+The target pressures for each of the 6 components of the stress tensor
+can be specified independently via the *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*
+keywords, which correspond to the 6 simulation box dimensions.  For
+each component, the external pressure or tensor component at each
+timestep is a ramped value during the run from *Pstart* to *Pstop*\ .
+If a target pressure is specified for a component, then the
+corresponding box dimension will change during a simulation.  For
+example, if the *y* keyword is used, the y-box length will change.  If
+the *xy* keyword is used, the xy tilt factor will change.  A box
+dimension will not change if that component is not specified, although
+you have the option to change that dimension via the :doc:`fix deform <fix_deform>` command.
+
+Note that in order to use the *xy*\ , *xz*\ , or *yz* keywords, the
+simulation box must be triclinic, even if its initial tilt factors are
+0.0.
+
+For all barostat keywords, the *Pdamp* parameter operates like the
+*Tdamp* parameter, determining the time scale on which pressure is
+relaxed.  For example, a value of 10.0 means to relax the pressure in
+a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+the :doc:`units <units>` command).
+
+.. note::
+
+   A Nose-Hoover barostat will not work well for arbitrary values
+   of *Pdamp*\ .  If *Pdamp* is too small, the pressure and volume can
+   fluctuate wildly; if it is too large, the pressure will take a very
+   long time to equilibrate.  A good choice for many models is a *Pdamp*
+   of around 1000 timesteps.  However, note that *Pdamp* is specified in
+   time units, and that timesteps are NOT the same as time units for most
+   :doc:`units <units>` settings.
+
+Regardless of what atoms are in the fix group (the only atoms which
+are time integrated), a global pressure or stress tensor is computed
+for all atoms.  Similarly, when the size of the simulation box is
+changed, all atoms are re-scaled to new positions, unless the keyword
+*dilate* is specified with a *dilate-group-ID* for a group that
+represents a subset of the atoms.  This can be useful, for example, to
+leave the coordinates of atoms in a solid substrate unchanged and
+controlling the pressure of a surrounding fluid.  This option should
+be used with care, since it can be unphysical to dilate some atoms and
+not others, because it can introduce large, instantaneous
+displacements between a pair of atoms (one dilated, one not) that are
+far from the dilation origin.  Also note that for atoms not in the fix
+group, a separate time integration fix like :doc:`fix nve <fix_nve>` or
+:doc:`fix nvt <fix_nh>` can be used on them, independent of whether they
+are dilated or not.
+
+
+----------
+
+
+The *couple* keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together.  The value specified
+with the keyword determines which are coupled.  For example, *xz*
+means the *Pxx* and *Pzz* components of the stress tensor are coupled.
+*Xyz* means all 3 diagonal components are coupled.  Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep.  The
+*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must
+be identical.  *Couple xyz* can be used for a 2d simulation; the *z*
+dimension is simply ignored.
+
+
+----------
+
+
+The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+
+The keyword *iso* means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together.  Using "iso Pstart Pstop Pdamp" is the same as
+specifying these 4 keywords:
+
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   couple xyz
+
+The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled
+independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure.  Using "aniso Pstart Pstop Pdamp" is the same as specifying
+these 4 keywords:
+
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   couple none
+
+The keyword *tri* means *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , and *yz* dimensions
+are controlled independently using their individual stress components
+as the driving forces, and the specified scalar pressure as the
+external normal stress.  Using "tri Pstart Pstop Pdamp" is the same as
+specifying these 7 keywords:
+
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   xy 0.0 0.0 Pdamp
+   yz 0.0 0.0 Pdamp
+   xz 0.0 0.0 Pdamp
+   couple none
+
+
+----------
+
+
+In some cases (e.g. for solids) the pressure (volume) and/or
+temperature of the system can oscillate undesirably when a Nose/Hoover
+barostat and thermostat is applied.  The optional *drag* keyword will
+damp these oscillations, although it alters the Nose/Hoover equations.
+A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
+A non-zero value adds a drag term; the larger the value specified, the
+greater the damping effect.  Performing a short run and monitoring the
+pressure and temperature is the best way to determine if the drag term
+is working.  Typically a value between 0.2 to 2.0 is sufficient to
+damp oscillations after a few periods. Note that use of the drag
+keyword will interfere with energy conservation and will also change
+the distribution of positions and velocities so that they do not
+correspond to the nominal NVT, NPT, or NPH ensembles.
+
+An alternative way to control initial oscillations is to use chain
+thermostats. The keyword *tchain* determines the number of thermostats
+in the particle thermostat. A value of 1 corresponds to the original
+Nose-Hoover thermostat. The keyword *pchain* specifies the number of
+thermostats in the chain thermostatting the barostat degrees of
+freedom. A value of 0 corresponds to no thermostatting of the
+barostat variables.
+
+The *mtk* keyword controls whether or not the correction terms due to
+Martyna, Tuckerman, and Klein are included in the equations of motion
+:ref:`(Martyna) <nh-Martyna>`.  Specifying *no* reproduces the original
+Hoover barostat, whose volume probability distribution function
+differs from the true NPT and NPH ensembles by a factor of 1/V.  Hence
+using *yes* is more correct, but in many cases the difference is
+negligible.
+
+The keyword *tloop* can be used to improve the accuracy of integration
+scheme at little extra cost.  The initial and final updates of the
+thermostat variables are broken up into *tloop* sub-steps, each of
+length *dt*\ /\ *tloop*\ . This corresponds to using a first-order
+Suzuki-Yoshida scheme :ref:`(Tuckerman) <nh-Tuckerman>`.  The keyword *ploop*
+does the same thing for the barostat thermostat.
+
+The keyword *nreset* controls how often the reference dimensions used
+to define the strain energy are reset.  If this keyword is not used,
+or is given a value of zero, then the reference dimensions are set to
+those of the initial simulation domain and are never changed. If the
+simulation domain changes significantly during the simulation, then
+the final average pressure tensor will differ significantly from the
+specified values of the external stress tensor.  A value of *nstep*
+means that every *nstep* timesteps, the reference dimensions are set
+to those of the current simulation domain.
+
+The *scaleyz*\ , *scalexz*\ , and *scalexy* keywords control whether or
+not the corresponding tilt factors are scaled with the associated box
+dimensions when barostatting triclinic periodic cells.  The default
+values *yes* will turn on scaling, which corresponds to adjusting the
+linear dimensions of the cell while preserving its shape.  Choosing
+*no* ensures that the tilt factors are not scaled with the box
+dimensions. See below for restrictions and default values in different
+situations. In older versions of LAMMPS, scaling of tilt factors was
+not performed. The old behavior can be recovered by setting all three
+scale keywords to *no*\ .
+
+The *flip* keyword allows the tilt factors for a triclinic box to
+exceed half the distance of the parallel box length, as discussed
+below.  If the *flip* value is set to *yes*\ , the bound is enforced by
+flipping the box when it is exceeded.  If the *flip* value is set to
+*no*\ , the tilt will continue to change without flipping.  Note that if
+applied stress induces large deformations (e.g. in a liquid), this
+means the box shape can tilt dramatically and LAMMPS will run less
+efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped sub-domain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+
+The *fixedpoint* keyword specifies the fixed point for barostat volume
+changes. By default, it is the center of the box.  Whatever point is
+chosen will not move during the simulation.  For example, if the lower
+periodic boundaries pass through (0,0,0), and this point is provided
+to *fixedpoint*\ , then the lower periodic boundaries will remain at
+(0,0,0), while the upper periodic boundaries will move twice as
+far. In all cases, the particle trajectories are unaffected by the
+chosen value, except for a time-dependent constant translation of
+positions.
+
+If the *update* keyword is used with the *dipole* value, then the
+orientation of the dipole moment of each particle is also updated
+during the time integration.  This option should be used for models
+where a dipole moment is assigned to finite-size particles,
+e.g. spheroids via use of the :doc:`atom\_style hybrid sphere dipole <atom_style>` command.
+
+The default dipole orientation integrator can be changed to the
+Dullweber-Leimkuhler-McLachlan integration scheme
+:ref:`(Dullweber) <nh-Dullweber>` when using *update* with the value
+*dipole/dlm*\ . This integrator is symplectic and time-reversible,
+giving better energy conservation and allows slightly longer timesteps
+at only a small additional computational cost.
+
+
+----------
+
+
+.. note::
+
+   Using a barostat coupled to tilt dimensions *xy*\ , *xz*\ , *yz* can
+   sometimes result in arbitrarily large values of the tilt dimensions,
+   i.e. a dramatically deformed simulation box.  LAMMPS allows the tilt
+   factors to grow a small amount beyond the normal limit of half the box
+   length (0.6 times the box length), and then performs a box "flip" to
+   an equivalent periodic cell.  See the discussion of the *flip* keyword
+   above, to allow this bound to be exceeded, if desired.
+
+The flip operation is described in more detail in the doc page for
+:doc:`fix deform <fix_deform>`.  Both the barostat dynamics and the atom
+trajectories are unaffected by this operation.  However, if a tilt
+factor is incremented by a large amount (1.5 times the box length) on
+a single timestep, LAMMPS can not accommodate this event and will
+terminate the simulation with an error. This error typically indicates
+that there is something badly wrong with how the simulation was
+constructed, such as specifying values of *Pstart* that are too far
+from the current stress value, or specifying a timestep that is too
+large. Triclinic barostatting should be used with care. This also is
+true for other barostat styles, although they tend to be more
+forgiving of insults. In particular, it is important to recognize that
+equilibrium liquids can not support a shear stress and that
+equilibrium solids can not support shear stresses that exceed the
+yield stress.
+
+One exception to this rule is if the 1st dimension in the tilt factor
+(x for xy) is non-periodic.  In that case, the limits on the tilt
+factor are not enforced, since flipping the box in that dimension does
+not change the atom positions due to non-periodicity.  In this mode,
+if you tilt the system to extreme angles, the simulation will simply
+become inefficient due to the highly skewed simulation box.
+
+.. note::
+
+   Unlike the :doc:`fix temp/berendsen <fix_temp_berendsen>` command
+   which performs thermostatting but NO time integration, these fixes
+   perform thermostatting/barostatting AND time integration.  Thus you
+   should not use any other time integration fix, such as :doc:`fix nve <fix_nve>` on atoms to which this fix is applied.  Likewise,
+   fix nvt and fix npt should not normally be used on atoms that also
+   have their temperature controlled by another fix - e.g. by :doc:`fix langevin <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>`
+   commands.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` and :doc:`Howto barostat <Howto_barostat>` doc pages for a discussion of different
+ways to compute temperature and perform thermostatting and
+barostatting.
+
+
+----------
+
+
+These fixes compute a temperature and pressure each timestep.  To do
+this, the thermostat and barostat fixes create their own computes of
+style "temp" and "pressure", as if one of these sets of commands had
+been issued:
+
+For fix nvt:
+compute fix-ID\_temp group-ID temp
+
+
+.. parsed-literal::
+
+   For fix npt and fix nph:
+   compute fix-ID_temp all temp
+   compute fix-ID_press all pressure fix-ID_temp
+
+For fix nvt, the group for the new temperature compute is the same as
+the fix group.  For fix npt and fix nph, the group for both the new
+temperature and pressure compute is "all" since pressure is computed
+for the entire system.  In the case of fix nph, the temperature
+compute is not used for thermostatting, but just for a kinetic-energy
+contribution to the pressure.  See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>`
+commands for details.  Note that the IDs of the new computes are the
+fix-ID + underscore + "temp" or fix\_ID + underscore + "press".
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of these
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command.  Or you can print this
+temperature or pressure during thermodynamic output via the
+:doc:`thermo\_style custom <thermo_style>` command using the appropriate
+compute-ID.  It also means that changing attributes of *thermo\_temp*
+or *thermo\_press* will have no effect on this fix.
+
+Like other fixes that perform thermostatting, fix nvt and fix npt can
+be used with :doc:`compute commands <compute>` that calculate a
+temperature after removing a "bias" from the atom velocities.
+E.g. removing the center-of-mass velocity from a group of atoms or
+only calculating temperature on the x-component of velocity or only
+calculating temperature for atoms in a geometric region.  This is not
+done by default, but only if the :doc:`fix\_modify <fix_modify>` command
+is used to assign a temperature compute to this fix that includes such
+a bias term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+These fixes can be used with either the *verlet* or *respa*
+:doc:`integrators <run_style>`. When using one of the barostat fixes
+with *respa*\ , LAMMPS uses an integrator constructed
+according to the following factorization of the Liouville propagator
+(for two rRESPA levels):
+
+.. image:: Eqs/fix_nh1.jpg
+   :align: center
+
+This factorization differs somewhat from that of Tuckerman et al, in
+that the barostat is only updated at the outermost rRESPA level,
+whereas Tuckerman's factorization requires splitting the pressure into
+pieces corresponding to the forces computed at each rRESPA level. In
+theory, the latter method will exhibit better numerical stability. In
+practice, because Pdamp is normally chosen to be a large multiple of
+the outermost rRESPA timestep, the barostat dynamics are not the
+limiting factor for numerical stability. Both factorizations are
+time-reversible and can be shown to preserve the phase space measure
+of the underlying non-Hamiltonian equations of motion.
+
+.. note::
+
+   This implementation has been shown to conserve linear momentum
+   up to machine precision under NVT dynamics. Under NPT dynamics,
+   for a system with zero initial total linear momentum, the total
+   momentum fluctuates close to zero. It may occasionally undergo brief
+   excursions to non-negligible values, before returning close to zero.
+   Over long simulations, this has the effect of causing the center-of-mass
+   to undergo a slow random walk. This can be mitigated by resetting
+   the momentum at infrequent intervals using the
+   :doc:`fix momentum <fix_momentum>` command.
+
+
+----------
+
+
+The fix npt and fix nph commands can be used with rigid bodies or
+mixtures of rigid bodies and non-rigid particles (e.g. solvent).  But
+there are also :doc:`fix rigid/npt <fix_rigid>` and :doc:`fix rigid/nph <fix_rigid>` commands, which are typically a more natural
+choice.  See the doc page for those commands for more discussion of
+the various ways to do this.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+These fixes writes the state of all the thermostat and barostat
+variables to :doc:`binary restart files <restart>`.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by these fixes.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure, as described above.
+If you do this, note that the kinetic energy derived from the compute
+temperature should be consistent with the virial term computed using
+all atoms for the pressure.  LAMMPS will warn you if you choose to
+compute temperature on a subset of atoms.
+
+.. note::
+
+   If both the *temp* and *press* keywords are used in a single
+   thermo\_modify command (or in two separate commands), then the order in
+   which the keywords are specified is important.  Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
+   an argument when it is specified.  The *temp* keyword will override
+   this (for the pressure compute being used by fix npt), but only if the
+   *temp* keyword comes after the *press* keyword.  If the *temp* keyword
+   comes before the *press* keyword, then the new pressure compute
+   specified by the *press* keyword will be unaffected by the *temp*
+   setting.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by these
+fixes to add the energy change induced by Nose/Hoover thermostatting
+and barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`.
+
+These fixes compute a global scalar and a global vector of quantities,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar value calculated by these fixes is "extensive"; the vector
+values are "intensive".
+
+The scalar is the cumulative energy change due to the fix.
+
+The vector stores internal Nose/Hoover thermostat and barostat
+variables.  The number and meaning of the vector values depends on
+which fix is used and the settings for keywords *tchain* and *pchain*\ ,
+which specify the number of Nose/Hoover chains for the thermostat and
+barostat.  If no thermostatting is done, then *tchain* is 0.  If no
+barostatting is done, then *pchain* is 0.  In the following list,
+"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
+the barostat.  Its value is 0 if no barostat is used, else its value
+is 6 if any off-diagonal stress tensor component is barostatted, else
+its value is 1 if *couple xyz* is used or *couple xy* for a 2d
+simulation, otherwise its value is 3.
+
+The order of values in the global vector and their meaning is as
+follows.  The notation means there are tchain values for eta, followed
+by tchain for eta\_dot, followed by ndof for omega, etc:
+
+* eta[tchain] = particle thermostat displacements (unitless)
+* eta\_dot[tchain] = particle thermostat velocities (1/time units)
+* omega[ndof] = barostat displacements (unitless)
+* omega\_dot[ndof] = barostat velocities (1/time units)
+* etap[pchain] = barostat thermostat displacements (unitless)
+* etap\_dot[pchain] = barostat thermostat velocities (1/time units)
+* PE\_eta[tchain] = potential energy of each particle thermostat displacement (energy units)
+* KE\_eta\_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units)
+* PE\_omega[ndof] = potential energy of each barostat displacement (energy units)
+* KE\_omega\_dot[ndof] = kinetic energy of each barostat velocity (energy units)
+* PE\_etap[pchain] = potential energy of each barostat thermostat displacement (energy units)
+* KE\_etap\_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units)
+* PE\_strain[1] = scalar strain energy (energy units)
+
+These fixes can ramp their external temperature and pressure over
+multiple runs, using the *start* and *stop* keywords of the
+:doc:`run <run>` command.  See the :doc:`run <run>` command for details of
+how to do this.
+
+These fixes are not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
+periodic.  *Xy*\ , *xz*\ , and *yz* can only be barostatted if the
+simulation domain is triclinic and the 2nd dimension in the keyword
+(\ *y* dimension in *xy*\ ) is periodic.  *Z*\ , *xz*\ , and *yz*\ , cannot be
+barostatted for 2D simulations.  The :doc:`create\_box <create_box>`,
+:doc:`read data <read_data>`, and :doc:`read\_restart <read_restart>`
+commands specify whether the simulation box is orthogonal or
+non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz
+tilt factors.
+
+For the *temp* keyword, the final Tstop cannot be 0.0 since it would
+make the external T = 0.0 at some timestep during the simulation which
+is not allowed in the Nose/Hoover formulation.
+
+The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
+for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
+can only be used if the 2nd dimension in the keyword is periodic,
+and if the tilt factor is not coupled to the barostat via keywords
+*tri*\ , *yz*\ , *xz*\ , and *xy*\ .
+
+These fixes can be used with dynamic groups as defined by the
+:doc:`group <group>` command.  Likewise they can be used with groups to
+which atoms are added or deleted over time, e.g. a deposition
+simulation.  However, the conservation properties of the thermostat
+and barostat are defined for systems with a static set of atoms.  You
+may observe odd behavior if the atoms in a group vary dramatically
+over time or the atom count becomes very small.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix\_modify <fix_modify>`,
+:doc:`run\_style <run_style>`
+
+Default
+"""""""
+
+The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
+ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
+flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
+dimension and not coupled to barostat, otherwise no.
+
+
+----------
+
+
+.. _nh-Martyna:
+
+
+
+**(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
+
+.. _nh-Parrinello:
+
+
+
+**(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
+
+.. _nh-Tuckerman:
+
+
+
+**(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
+Martyna, J Phys A: Math Gen, 39, 5629 (2006).
+
+.. _nh-Shinoda:
+
+
+
+**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
+
+.. _nh-Dullweber:
+
+
+
+**(Dullweber)** Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107,
+5840 (1997).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst
new file mode 100644
index 0000000000..cf6a65352f
--- /dev/null
+++ b/doc/src/fix_nh_eff.rst
@@ -0,0 +1,181 @@
+.. index:: fix nvt/eff
+
+fix nvt/eff command
+===================
+
+fix npt/eff command
+===================
+
+fix nph/eff command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style_name keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style\_name = *nvt/eff* or *npt/eff* or *nph/eff*
+  
+  .. parsed-literal::
+  
+     one or more keyword value pairs may be appended
+     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate*
+       *temp* values = Tstart Tstop Tdamp
+         Tstart,Tstop = external temperature at start/end of run
+         Tdamp = temperature damping parameter (time units)
+       *iso* or *aniso* or *tri* values = Pstart Pstop Pdamp
+         Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+         Pdamp = pressure damping parameter (time units)
+       *x* or *y* or *z* or *xy* or *yz* or *xz* values = Pstart Pstop Pdamp
+         Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+         Pdamp = stress damping parameter (time units)
+       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *tchain* value = length of thermostat chain (1 = single thermostat)
+       *pchain* values = length of thermostat chain on barostat (0 = no thermostat)
+       *mtk* value = *yes* or *no* = add in MTK adjustment term or not
+       *tloop* value = number of sub-cycles to perform on thermostat
+       *ploop* value = number of sub-cycles to perform on barostat thermostat
+       *nreset* value = reset reference cell every this many timesteps
+       *drag* value = drag factor added to barostat/thermostat (0.0 = no drag)
+       *dilate* value = *all* or *partial*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nvt/eff temp 300.0 300.0 0.1
+   fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
+   fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
+   fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
+
+Description
+"""""""""""
+
+These commands perform time integration on Nose-Hoover style
+non-Hamiltonian equations of motion for nuclei and electrons in the
+group for the :doc:`electron force field <pair_eff>` model.  The fixes
+are designed to generate positions and velocities sampled from the
+canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
+ensembles.  This is achieved by adding some dynamic variables which
+are coupled to the particle velocities (thermostatting) and simulation
+domain dimensions (barostatting).  In addition to basic thermostatting
+and barostatting, these fixes can also create a chain of thermostats
+coupled to the particle thermostat, and another chain of thermostats
+coupled to the barostat variables. The barostat can be coupled to the
+overall box volume, or to individual dimensions, including the *xy*\ ,
+*xz* and *yz* tilt dimensions. The external pressure of the barostat
+can be specified as either a scalar pressure (isobaric ensemble) or as
+components of a symmetric stress tensor (constant stress ensemble).
+When used correctly, the time-averaged temperature and stress tensor
+of the particles will match the target values specified by
+Tstart/Tstop and Pstart/Pstop.
+
+The operation of these fixes is exactly like that described by the
+:doc:`fix nvt, npt, and nph <fix_nh>` commands, except that the radius
+and radial velocity of electrons are also updated.  Likewise the
+temperature and pressure calculated by the fix, using the computes it
+creates (as discussed in the :doc:`fix nvt, npt, and nph <fix_nh>`
+doc page), are performed with computes that include the eFF contribution
+to the temperature or kinetic energy from the electron radial velocity.
+
+.. note::
+
+   there are two different pressures that can be reported for eFF
+   when defining the pair\_style (see :doc:`pair eff/cut <pair_eff>` to
+   understand these settings), one (default) that considers electrons do
+   not contribute radial virial components (i.e. electrons treated as
+   incompressible 'rigid' spheres) and one that does.  The radial
+   electronic contributions to the virials are only tallied if the
+   flexible pressure option is set, and this will affect both global and
+   per-atom quantities.  In principle, the true pressure of a system is
+   somewhere in between the rigid and the flexible eFF pressures, but,
+   for most cases, the difference between these two pressures will not be
+   significant over long-term averaged runs (i.e. even though the energy
+   partitioning changes, the total energy remains similar).
+
+.. note::
+
+   currently, there is no available option for the user to set or
+   create temperature distributions that include the radial electronic
+   degrees of freedom with the :doc:`velocity <velocity>` command, so the
+   the user must allow for these degrees of freedom to equilibrate
+   (i.e. equi-partitioning of energy) through time integration.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+See the doc page for the :doc:`fix nvt, npt, and nph <fix_nh>` commands
+for details.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Other restriction discussed on the doc page for the :doc:`fix nvt, npt, and nph <fix_nh>` commands also apply.
+
+.. note::
+
+   The temperature for systems (regions or groups) with only
+   electrons and no nuclei is 0.0 (i.e. not defined) in the current
+   temperature calculations, a practical example would be a uniform
+   electron gas or a very hot plasma, where electrons remain delocalized
+   from the nuclei.  This is because, even though electron virials are
+   included in the temperature calculation, these are averaged over the
+   nuclear degrees of freedom only.  In such cases a corrective term must
+   be added to the pressure to get the correct kinetic contribution.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix nph <fix_nh>`, :doc:`fix npt <fix_nh>`,
+:doc:`fix\_modify <fix_modify>`, :doc:`run\_style <run_style>`
+
+Default
+"""""""
+
+The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
+ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
+
+
+----------
+
+
+.. _Martyna1:
+
+
+
+**(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
+
+.. _Parrinello:
+
+
+
+**(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
+
+.. _Tuckerman1:
+
+
+
+**(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
+Martyna, J Phys A: Math Gen, 39, 5629 (2006).
+
+.. _Shinoda2:
+
+
+
+**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst
new file mode 100644
index 0000000000..35110d9cce
--- /dev/null
+++ b/doc/src/fix_nh_uef.rst
@@ -0,0 +1,279 @@
+.. index:: fix nvt/uef
+
+fix nvt/uef command
+===================
+
+fix npt/uef command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style\_name = *nvt/uef* or *npt/uef*
+* *Tstart*\ , *Tstop*\ , and *Tdamp* are documented in the :doc:`fix npt <fix_nh>` command
+* *edot\_x* and *edot\_y* are the strain rates in the x and y directions (1/(time units))
+* one or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *ext* or *strain* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk*
+       *ext* value = *x* or *y* or *z* or *xy* or *yz* or *xz* = external dimensions
+         sets the external dimensions used to calculate the scalar pressure
+       *strain* values = e_x e_y = initial strain
+         usually not needed, but may be needed to resume a run with a data file.
+       *iso*\ , *x*\ , *y*\ , *z*\ , *tchain*\ , *pchain*\ , *tloop*\ , *ploop*\ , *mtk* keywords
+         documented by the :doc:`fix npt <fix_nh>` command
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005
+   fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005
+   fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz
+   fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000
+
+Description
+"""""""""""
+
+This fix can be used to simulate non-equilibrium molecular dynamics
+(NEMD) under diagonal flow fields, including uniaxial and bi-axial
+flow.  Simulations under continuous extensional flow may be carried
+out for an indefinite amount of time.  It is an implementation of the
+boundary conditions from :ref:`(Dobson) <Dobson>`, and also uses numerical
+lattice reduction as was proposed by :ref:`(Hunt) <Hunt>`. The lattice
+reduction algorithm is from :ref:`(Semaev) <Semaev>`. The fix is intended for
+simulations of homogeneous flows, and integrates the SLLOD equations
+of motion, originally proposed by Hoover and Ladd (see :ref:`(Evans and Morriss) <Sllod>`).  Additional detail about this implementation can be
+found in :ref:`(Nicholson and Rutledge) <Nicholson>`.
+
+Note that NEMD simulations of a continuously strained system can be
+performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>` commands.
+
+The applied flow field is set by the *eps* keyword. The values
+*edot\_x* and *edot\_y* correspond to the strain rates in the xx and yy
+directions.  It is implicitly assumed that the flow field is
+traceless, and therefore the strain rate in the zz direction is eqal
+to -(*edot\_x* + *edot\_y*).
+
+.. note::
+
+   Due to an instability in the SLLOD equations under extension,
+   :doc:`fix momentum <fix_momentum>` should be used to regularly reset the
+   linear momentum.
+
+The boundary conditions require a simulation box that does not have a
+consistent alignment relative to the applied flow field. Since LAMMPS
+utilizes an upper-triangular simulation box, it is not possible to
+express the evolving simulation box in the same coordinate system as
+the flow field.  This fix keeps track of two coordinate systems: the
+flow frame, and the upper triangular LAMMPS frame. The coordinate
+systems are related to each other through the QR decomposition, as is
+illustrated in the image below.
+
+.. image:: JPG/uef_frames.jpg
+   :align: center
+
+During most molecular dynamics operations, the system is represented
+in the LAMMPS frame. Only when the positions and velocities are
+updated is the system rotated to the flow frame, and it is rotated
+back to the LAMMPS frame immediately afterwards. For this reason, all
+vector-valued quantities (except for the tensors from
+:doc:`compute\_pressure/uef <compute_pressure_uef>` and
+:doc:`compute\_temp/uef <compute_temp_uef>`) will be computed in the
+LAMMPS frame. Rotationally invariant scalar quantities like the
+temperature and hydrostatic pressure are frame-invariant and will be
+computed correctly. Additionally, the system is in the LAMMPS frame
+during all of the output steps, and therefore trajectory files made
+using the dump command will be in the LAMMPS frame unless the
+:doc:`dump\_cfg/uef <dump_cfg_uef>` command is used.
+
+
+----------
+
+
+Temperature control is achieved with the default Nose-Hoover style
+thermostat documented in :doc:`fix npt <fix_nh>`. When this fix is
+active, only the peculiar velocity of each atom is stored, defined as
+the velocity relative to the streaming velocity. This is in contrast
+to :doc:`fix nvt/sllod <fix_nvt_sllod>`, which uses a lab-frame
+velocity, and removes the contribution from the streaming velocity in
+order to compute the temperature.
+
+Pressure control is achieved using the default Nose-Hoover barostat
+documented in :doc:`fix npt <fix_nh>`. There are two ways to control the
+pressure using this fix. The first method involves using the *ext*
+keyword along with the *iso* pressure style. With this method, the
+pressure is controlled by scaling the simulation box isotropically to
+achieve the average pressure only in the directions specified by
+*ext*\ .  For example, if the *ext* value is set to *xy*\ , the average
+pressure (Pxx+Pyy)/2 will be controlled.
+
+This example command will control the total hydrostatic pressure under
+uniaxial tension:
+
+
+.. parsed-literal::
+
+   fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz
+
+This example command will control the average stress in compression
+directions, which would typically correspond to free surfaces under
+drawing with uniaxial tension:
+
+
+.. parsed-literal::
+
+   fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy
+
+The second method for pressure control involves setting the normal
+stresses using the *x*\ , *y* , and/or *z* keywords. When using this
+method, the same pressure must be specified via *Pstart* and *Pstop*
+for all dimensions controlled. Any choice of pressure conditions that
+would cause LAMMPS to compute a deviatoric stress are not permissible
+and will result in an error. Additionally, all dimensions with
+controlled stress must have the same applied strain rate. The *ext*
+keyword must be set to the default value (\ *xyz*\ ) when using this
+method.
+
+For example, the following commands will work:
+
+
+.. parsed-literal::
+
+   fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5
+   fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5
+
+The following commands will not work:
+
+
+.. parsed-literal::
+
+   fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5
+   fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5
+
+
+----------
+
+
+These fix computes a temperature and pressure each timestep.  To do
+this, it creates its own computes of style "temp/uef" and
+"pressure/uef", as if one of these two sets of commands had been
+issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp/uef
+   compute fix-ID_press group-ID pressure/uef fix-ID_temp
+
+   compute fix-ID_temp all temp/uef
+   compute fix-ID_press all pressure/uef fix-ID_temp
+
+See the :doc:`compute temp/uef <compute_temp_uef>` and :doc:`compute pressure/uef <compute_pressure_uef>` commands for details.  Note
+that the IDs of the new computes are the fix-ID + underscore + "temp"
+or fix\_ID + underscore + "press".
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+The fix writes the state of all the thermostat and barostat variables,
+as well as the cumulative strain applied, to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>` command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+.. note::
+
+   It is not necessary to set the *strain* keyword when resuming a
+   run from a restart file. Only for resuming from data files, which do
+   not contain the cumulative applied strain, will this keyword be
+   necessary.
+
+This fix can be used with the :doc:`fix\_modify <fix_modify>` *temp* and
+*press* options. The temperature and pressure computes used must be of
+type *temp/uef* and *pressure/uef*\ .
+
+This fix computes the same global scalar and vector quantities as :doc:`fix npt <fix_nh>`.
+
+The fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Due to requirements of the boundary conditions, when the *strain*
+keyword is set to zero (or unset), the initial simulation box must be
+cubic and have style triclinic. If the box is initially of type ortho,
+use :doc:`change\_box <change_box>` before invoking the fix.
+
+.. note::
+
+   When resuming from restart files, you may need to use :doc:`box tilt large <box>` since lammps has internal criteria from lattice
+   reduction that are not the same as the criteria in the numerical
+   lattice reduction algorithm.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, :doc:`compute temp/uef <compute_temp_uef>`, :doc:`compute pressure/uef <compute_pressure_uef>`, :doc:`dump cfg/uef <dump_cfg_uef>`
+
+Default
+"""""""
+
+The default keyword values specific to this fix are exy = xyz, strain
+= 0 0.  The remaining defaults are the same as for *fix
+npt*\ \_fix\_nh.html except tchain = 1.  The reason for this change is
+given in :doc:`fix nvt/sllod <fix_nvt_sllod>`.
+
+
+----------
+
+
+.. _Dobson:
+
+
+
+**(Dobson)** Dobson, J Chem Phys, 141, 184103 (2014).
+
+.. _Hunt:
+
+
+
+**(Hunt)** Hunt, Mol Simul, 42, 347 (2016).
+
+.. _Semaev:
+
+
+
+**(Semaev)** Semaev, Cryptography and Lattices, 181 (2001).
+
+.. _Sllod:
+
+
+
+**(Evans and Morriss)** Evans and Morriss, Phys Rev A, 30, 1528 (1984).
+
+.. _Nicholson:
+
+
+
+**(Nicholson and Rutledge)** Nicholson and Rutledge, J Chem Phys, 145,
+244903 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst
new file mode 100644
index 0000000000..cea1ee71b3
--- /dev/null
+++ b/doc/src/fix_nph_asphere.rst
@@ -0,0 +1,164 @@
+.. index:: fix nph/asphere
+
+fix nph/asphere command
+=======================
+
+fix nph/asphere/omp command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nph/asphere args keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nph/asphere = style name of this fix command
+* additional barostat related keyword/value pairs from the :doc:`fix nph <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nph/asphere iso 0.0 0.0 1000.0
+   fix 2 all nph/asphere x 5.0 5.0 1000.0
+   fix 2 all nph/asphere x 5.0 5.0 1000.0 drag 0.2
+   fix 2 water nph/asphere aniso 0.0 0.0 1000.0 dilate partial
+
+Description
+"""""""""""
+
+Perform constant NPH integration to update position, velocity,
+orientation, and angular velocity each timestep for aspherical or
+ellipsoidal particles in the group using a Nose/Hoover pressure
+barostat.  P is pressure; H is enthalpy.  This creates a system
+trajectory consistent with the isenthalpic ensemble.
+
+This fix differs from the :doc:`fix nph <fix_nh>` command, which assumes
+point particles and only updates their position and velocity.
+
+Additional parameters affecting the barostat are specified by keywords
+and values documented with the :doc:`fix nph <fix_nh>` command.  See,
+for example, discussion of the *aniso*\ , and *dilate* keywords.
+
+The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPH integration.
+
+Regardless of what particles are in the fix group, a global pressure is
+computed for all particles.  Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword *dilate* is specified with a value of *partial*\ , in which case
+only the particles in the fix group are re-scaled.  The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+
+
+----------
+
+
+This fix computes a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp/asphere" and
+"pressure", as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp all temp/asphere
+   compute fix-ID_press all pressure fix-ID_temp
+
+See the :doc:`compute temp/asphere <compute_temp_asphere>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by this fix.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover barostatting to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix nph <fix_nh>` command.
+
+This fix can ramp its target pressure over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style ellipsoid <atom_style>`
+command.
+
+All particles in the group must be finite-size.  They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nph <fix_nh>`, :doc:`fix nve\_asphere <fix_nve_asphere>`, :doc:`fix nvt\_asphere <fix_nvt_asphere>`, :doc:`fix npt\_asphere <fix_npt_asphere>`, :doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst
new file mode 100644
index 0000000000..8ce3009700
--- /dev/null
+++ b/doc/src/fix_nph_body.rst
@@ -0,0 +1,157 @@
+.. index:: fix nph/body
+
+fix nph/body command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nph/body args keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nph/body = style name of this fix command
+* additional barostat related keyword/value pairs from the :doc:`fix nph <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nph/body iso 0.0 0.0 1000.0
+   fix 2 all nph/body x 5.0 5.0 1000.0
+   fix 2 all nph/body x 5.0 5.0 1000.0 drag 0.2
+   fix 2 water nph/body aniso 0.0 0.0 1000.0 dilate partial
+
+Description
+"""""""""""
+
+Perform constant NPH integration to update position, velocity,
+orientation, and angular velocity each timestep for body
+particles in the group using a Nose/Hoover pressure
+barostat.  P is pressure; H is enthalpy.  This creates a system
+trajectory consistent with the isenthalpic ensemble.
+
+This fix differs from the :doc:`fix nph <fix_nh>` command, which assumes
+point particles and only updates their position and velocity.
+
+Additional parameters affecting the barostat are specified by keywords
+and values documented with the :doc:`fix nph <fix_nh>` command.  See,
+for example, discussion of the *aniso*\ , and *dilate* keywords.
+
+The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPH integration.
+
+Regardless of what particles are in the fix group, a global pressure is
+computed for all particles.  Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword *dilate* is specified with a value of *partial*\ , in which case
+only the particles in the fix group are re-scaled.  The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+
+
+----------
+
+
+This fix computes a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp/body" and
+"pressure", as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp all temp/body
+   compute fix-ID_press all pressure fix-ID_temp
+
+See the :doc:`compute temp/body <compute_temp_body>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by this fix.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover barostatting to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix nph <fix_nh>` command.
+
+This fix can ramp its target pressure over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the BODY package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style body <atom_style>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nph <fix_nh>`, :doc:`fix nve\_body <fix_nve_body>`, :doc:`fix nvt\_body <fix_nvt_body>`, :doc:`fix npt\_body <fix_npt_body>`, :doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst
new file mode 100644
index 0000000000..af45b6babc
--- /dev/null
+++ b/doc/src/fix_nph_sphere.rst
@@ -0,0 +1,177 @@
+.. index:: fix nph/sphere
+
+fix nph/sphere command
+======================
+
+fix nph/sphere/omp command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nph/sphere args keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nph/sphere = style name of this fix command
+* keyword = *disc*
+  
+  .. parsed-literal::
+  
+       *disc* value = none = treat particles as 2d discs, not spheres
+
+* additional barostat related keyword/value pairs from the :doc:`fix nph <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nph/sphere iso 0.0 0.0 1000.0
+   fix 2 all nph/sphere x 5.0 5.0 1000.0
+   fix 2 all nph/sphere x 5.0 5.0 1000.0 disc
+   fix 2 all nph/sphere x 5.0 5.0 1000.0 drag 0.2
+   fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial
+
+Description
+"""""""""""
+
+Perform constant NPH integration to update position, velocity, and
+angular velocity each timestep for finite-size spherical particles in
+the group using a Nose/Hoover pressure barostat.  P is pressure; H is
+enthalpy.  This creates a system trajectory consistent with the
+isenthalpic ensemble.
+
+This fix differs from the :doc:`fix nph <fix_nh>` command, which assumes
+point particles and only updates their position and velocity.
+
+If the *disc* keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the :doc:`dimension <dimension>` keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
+Additional parameters affecting the barostat are specified by keywords
+and values documented with the :doc:`fix nph <fix_nh>` command.  See,
+for example, discussion of the *aniso*\ , and *dilate* keywords.
+
+The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPH integration.
+
+Regardless of what particles are in the fix group, a global pressure is
+computed for all particles.  Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword *dilate* is specified with a value of *partial*\ , in which case
+only the particles in the fix group are re-scaled.  The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+
+
+----------
+
+
+This fix computes a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp/sphere" and
+"pressure", as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp all temp/sphere
+   compute fix-ID_press all pressure fix-ID_temp
+
+See the :doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by this fix.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover barostatting to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix nph <fix_nh>` command.
+
+This fix can ramp its target pressure over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the :doc:`atom\_style sphere <atom_style>`
+command.
+
+All particles in the group must be finite-size spheres.  They cannot
+be point particles.
+
+Use of the *disc* keyword is only allowed for 2d simulations, as
+defined by the :doc:`dimension <dimension>` keyword.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nph <fix_nh>`, :doc:`fix nve\_sphere <fix_nve_sphere>`, :doc:`fix nvt\_sphere <fix_nvt_sphere>`, :doc:`fix npt\_sphere <fix_npt_sphere>`,
+:doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst
new file mode 100644
index 0000000000..be0a28b8b4
--- /dev/null
+++ b/doc/src/fix_nphug.rst
@@ -0,0 +1,259 @@
+.. index:: fix nphug
+
+fix nphug command
+=================
+
+fix nphug/omp command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nphug keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+  
+  .. parsed-literal::
+  
+     one or more keyword value pairs may be appended
+     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scaleyz* or *scalexz* or *scalexy*
+       *temp* values = Value1 Value2 Tdamp
+         Value1, Value2 = Nose-Hoover target temperatures, ignored by Hugoniostat
+         Tdamp = temperature damping parameter (time units)
+       *iso* or *aniso* or *tri* values = Pstart Pstop Pdamp
+         Pstart,Pstop = scalar external pressures, must be equal (pressure units)
+         Pdamp = pressure damping parameter (time units)
+       *x* or *y* or *z* or *xy* or *yz* or *xz* values = Pstart Pstop Pdamp
+         Pstart,Pstop = external stress tensor components, must be equal (pressure units)
+         Pdamp = stress damping parameter (time units)
+       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *tchain* value = length of thermostat chain (1 = single thermostat)
+       *pchain* values = length of thermostat chain on barostat (0 = no thermostat)
+       *mtk* value = *yes* or *no* = add in MTK adjustment term or not
+       *tloop* value = number of sub-cycles to perform on thermostat
+       *ploop* value = number of sub-cycles to perform on barostat thermostat
+       *nreset* value = reset reference cell every this many timesteps
+       *drag* value = drag factor added to barostat/thermostat (0.0 = no drag)
+       *dilate* value = *all* or *partial*
+       *scaleyz* value = *yes* or *no* = scale yz with lz
+       *scalexz* value = *yes* or *no* = scale xz with lz
+       *scalexy* value = *yes* or *no* = scale xy with ly
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
+   fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
+
+Description
+"""""""""""
+
+This command is a variant of the Nose-Hoover
+:doc:`fix npt <fix_nh>` fix style.
+It performs time integration of the Hugoniostat equations
+of motion developed by Ravelo et al. :ref:`(Ravelo) <Ravelo1>`.
+These equations compress the system to a state with average
+axial stress or pressure equal to the specified target value
+and that satisfies the Rankine-Hugoniot (RH)
+jump conditions for steady shocks.
+
+The compression can be performed
+either
+hydrostatically (using keyword *iso*\ , *aniso*\ , or *tri*\ ) or uniaxially
+(using keywords *x*\ , *y*\ , or *z*\ ).  In the hydrostatic case,
+the cell dimensions change dynamically so that the average axial stress
+in all three directions converges towards the specified target value.
+In the uniaxial case, the chosen cell dimension changes dynamically
+so that the average
+axial stress in that direction converges towards the target value. The
+other two cell dimensions are kept fixed (zero lateral strain).
+
+This leads to the following additional restrictions on the keywords:
+
+* One and only one of the following keywords should be used: *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*
+* The specified initial and final target pressures must be the same.
+* The keywords *xy*\ , *xz*\ , *yz* may not be used.
+* The only admissible value for the couple keyword is *xyz*\ , which has the same effect as keyword *iso*
+* The *temp* keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored.
+
+Essentially, a Hugoniostat simulation is an NPT simulation in which the
+user-specified target temperature is replaced with a time-dependent
+target temperature Tt obtained from the following equation:
+
+.. image:: Eqs/fix_nphug.jpg
+   :align: center
+
+where T and Tt are the instantaneous and target temperatures,
+P and P0 are the instantaneous and reference pressures or axial stresses,
+depending on whether hydrostatic or uniaxial compression is being
+performed, V and V0 are the instantaneous and reference volumes,
+E and E0 are the instantaneous and reference internal energy (potential
+plus kinetic), Ndof is the number of degrees of freedom used in the
+definition of temperature, and kB is the Boltzmann constant. Delta is the
+negative deviation of the instantaneous temperature from the target temperature.
+When the system reaches a stable equilibrium, the value of Delta should
+fluctuate about zero.
+
+The values of E0, V0, and P0 are the instantaneous values at the start of
+the simulation. These can be overridden using the fix\_modify keywords *e0*\ ,
+*v0*\ , and *p0* described below.
+
+
+----------
+
+
+.. note::
+
+   Unlike the :doc:`fix temp/berendsen <fix_temp_berendsen>` command
+   which performs thermostatting but NO time integration, this fix
+   performs thermostatting/barostatting AND time integration.  Thus you
+   should not use any other time integration fix, such as :doc:`fix nve <fix_nve>` on atoms to which this fix is applied.  Likewise,
+   this fix should not be used on atoms that have their temperature
+   controlled by another fix - e.g. by :doc:`fix langevin <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>` commands.
+
+
+----------
+
+
+This fix computes a temperature and pressure at each timestep.  To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if one of these two sets of commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp
+   compute fix-ID_press group-ID pressure fix-ID_temp
+
+   compute fix-ID_temp all temp
+   compute fix-ID_press all pressure fix-ID_temp
+
+See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press".  The group for
+the new computes is "all" since pressure is computed for the entire
+system.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the values of E0, V0, and P0, as well as the
+state of all the thermostat and barostat
+variables to :doc:`binary restart files <restart>`.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *e0*\ , *v0* and *p0* keywords
+can be used to define the values of E0, V0, and P0. Note the
+the values for *e0* and *v0* are extensive, and so must correspond
+to the total energy and volume of the entire system, not energy and
+volume per atom. If any of these quantities are not specified, then the
+instantaneous value in the system at the start of the simulation is used.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by these fixes.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure, as described above.
+If you do this, note that the kinetic energy derived from the compute
+temperature should be consistent with the virial term computed using
+all atoms for the pressure.  LAMMPS will warn you if you choose to
+compute temperature on a subset of atoms.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by these
+fixes to add the energy change induced by Nose/Hoover thermostatting
+and barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`. Either way, this energy is \*not\*
+included in the definition of internal energy E when calculating the value
+of Delta in the above equation.
+
+These fixes compute a global scalar and a global vector of quantities,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar value calculated by these fixes is "extensive"; the vector
+values are "intensive".
+
+The scalar is the cumulative energy change due to the fix.
+
+The vector stores three quantities unique to this fix (Delta, Us, and up),
+followed by all the internal Nose/Hoover thermostat and barostat
+variables defined for :doc:`fix npt <fix_nh>`. Delta is the deviation
+of the temperature from the target temperature, given by the above equation.
+Us and up are the shock and particle velocity corresponding to a steady
+shock calculated from the RH conditions. They have units of distance/time.
+
+Restrictions
+""""""""""""
+
+
+This fix style is part of the SHOCK package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+All the usual restrictions for :doc:`fix npt <fix_nh>` apply,
+plus the additional ones mentioned above.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix msst <fix_msst>`, :doc:`fix npt <fix_nh>`, :doc:`fix\_modify <fix_modify>`
+
+Default
+"""""""
+
+The keyword defaults are the same as those for :doc:`fix npt <fix_nh>`
+
+
+----------
+
+
+.. _Ravelo1:
+
+
+
+**(Ravelo)** Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst
new file mode 100644
index 0000000000..a728128aa3
--- /dev/null
+++ b/doc/src/fix_npt_asphere.rst
@@ -0,0 +1,189 @@
+.. index:: fix npt/asphere
+
+fix npt/asphere command
+=======================
+
+fix npt/asphere/omp command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID npt/asphere keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* npt/asphere = style name of this fix command
+* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
+   fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
+   fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
+   fix 2 water npt/asphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
+
+Description
+"""""""""""
+
+Perform constant NPT integration to update position, velocity,
+orientation, and angular velocity each timestep for aspherical or
+ellipsoidal particles in the group using a Nose/Hoover temperature
+thermostat and Nose/Hoover pressure barostat.  P is pressure; T is
+temperature.  This creates a system trajectory consistent with the
+isothermal-isobaric ensemble.
+
+This fix differs from the :doc:`fix npt <fix_nh>` command, which
+assumes point particles and only updates their position and velocity.
+
+The thermostat is applied to both the translational and rotational
+degrees of freedom for the aspherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below).  The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+Additional parameters affecting the thermostat and barostat are
+specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command.  See, for example, discussion of the *temp*\ ,
+*iso*\ , *aniso*\ , and *dilate* keywords.
+
+The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPT integration.
+
+Regardless of what particles are in the fix group, a global pressure is
+computed for all particles.  Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword *dilate* is specified with a value of *partial*\ , in which case
+only the particles in the fix group are re-scaled.  The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+
+
+----------
+
+
+This fix computes a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp/asphere" and
+"pressure", as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp all temp/asphere
+   compute fix-ID_press all pressure fix-ID_temp
+
+See the :doc:`compute temp/asphere <compute_temp_asphere>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover thermostat and barostat
+to :doc:`binary restart files <restart>`.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by this fix.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix npt <fix_nh>` command.
+
+This fix can ramp its target temperature and pressure over multiple
+runs, using the *start* and *stop* keywords of the :doc:`run <run>`
+command.  See the :doc:`run <run>` command for details of how to do
+this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style ellipsoid <atom_style>`
+command.
+
+All particles in the group must be finite-size.  They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix npt <fix_nh>`, :doc:`fix nve\_asphere <fix_nve_asphere>`, :doc:`fix nvt\_asphere <fix_nvt_asphere>`, :doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst
new file mode 100644
index 0000000000..64ae261e31
--- /dev/null
+++ b/doc/src/fix_npt_body.rst
@@ -0,0 +1,182 @@
+.. index:: fix npt/body
+
+fix npt/body command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID npt/body keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* npt/body = style name of this fix command
+* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all npt/body temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
+   fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
+   fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
+   fix 2 water npt/body temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
+
+Description
+"""""""""""
+
+Perform constant NPT integration to update position, velocity,
+orientation, and angular velocity each timestep for body
+particles in the group using a Nose/Hoover temperature
+thermostat and Nose/Hoover pressure barostat.  P is pressure; T is
+temperature.  This creates a system trajectory consistent with the
+isothermal-isobaric ensemble.
+
+This fix differs from the :doc:`fix npt <fix_nh>` command, which
+assumes point particles and only updates their position and velocity.
+
+The thermostat is applied to both the translational and rotational
+degrees of freedom for the body particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below).  The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+Additional parameters affecting the thermostat and barostat are
+specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command.  See, for example, discussion of the *temp*\ ,
+*iso*\ , *aniso*\ , and *dilate* keywords.
+
+The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPT integration.
+
+Regardless of what particles are in the fix group, a global pressure is
+computed for all particles.  Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword *dilate* is specified with a value of *partial*\ , in which case
+only the particles in the fix group are re-scaled.  The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+
+
+----------
+
+
+This fix computes a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp/body" and
+"pressure", as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp all temp/body
+   compute fix-ID_press all pressure fix-ID_temp
+
+See the :doc:`compute temp/body <compute_temp_body>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover thermostat and barostat
+to :doc:`binary restart files <restart>`.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by this fix.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix npt <fix_nh>` command.
+
+This fix can ramp its target temperature and pressure over multiple
+runs, using the *start* and *stop* keywords of the :doc:`run <run>`
+command.  See the :doc:`run <run>` command for details of how to do
+this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the BODY package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style body <atom_style>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix npt <fix_nh>`, :doc:`fix nve\_body <fix_nve_body>`, :doc:`fix nvt\_body <fix_nvt_body>`, :doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst
new file mode 100644
index 0000000000..9fe7b93633
--- /dev/null
+++ b/doc/src/fix_npt_sphere.rst
@@ -0,0 +1,201 @@
+.. index:: fix npt/sphere
+
+fix npt/sphere command
+======================
+
+fix npt/sphere/omp command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID npt/sphere keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+  npt/sphere = style name of this fix command
+  zero or more keyword/value pairs may be appended
+* keyword = *disc*
+
+.. parsed-literal::
+
+     *disc* value = none = treat particles as 2d discs, not spheres
+
+* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
+   fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
+   fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc
+   fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
+   fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
+
+Description
+"""""""""""
+
+Perform constant NPT integration to update position, velocity, and
+angular velocity each timestep for finite-sizex spherical particles in
+the group using a Nose/Hoover temperature thermostat and Nose/Hoover
+pressure barostat.  P is pressure; T is temperature.  This creates a
+system trajectory consistent with the isothermal-isobaric ensemble.
+
+This fix differs from the :doc:`fix npt <fix_nh>` command, which
+assumes point particles and only updates their position and velocity.
+
+The thermostat is applied to both the translational and rotational
+degrees of freedom for the spherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below).  The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+If the *disc* keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the :doc:`dimension <dimension>` keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
+Additional parameters affecting the thermostat and barostat are
+specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command.  See, for example, discussion of the *temp*\ ,
+*iso*\ , *aniso*\ , and *dilate* keywords.
+
+The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPT integration.
+
+Regardless of what particles are in the fix group, a global pressure is
+computed for all particles.  Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword *dilate* is specified with a value of *partial*\ , in which case
+only the particles in the fix group are re-scaled.  The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+
+
+----------
+
+
+This fix computes a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp/sphere" and
+"pressure", as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp all temp/sphere
+   compute fix-ID_press all pressure fix-ID_temp
+
+See the :doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover thermostat and barostat
+to :doc:`binary restart files <restart>`.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by this fix.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix npt <fix_nh>` command.
+
+This fix can ramp its target temperature and pressure over multiple
+runs, using the *start* and *stop* keywords of the :doc:`run <run>`
+command.  See the :doc:`run <run>` command for details of how to do
+this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the :doc:`atom\_style sphere <atom_style>`
+command.
+
+All particles in the group must be finite-size spheres.  They cannot
+be point particles.
+
+Use of the *disc* keyword is only allowed for 2d simulations, as
+defined by the :doc:`dimension <dimension>` keyword.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix npt <fix_nh>`, :doc:`fix nve\_sphere <fix_nve_sphere>`, :doc:`fix nvt\_sphere <fix_nvt_sphere>`, :doc:`fix npt\_asphere <fix_npt_asphere>`, :doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst
new file mode 100644
index 0000000000..bae6f8a95c
--- /dev/null
+++ b/doc/src/fix_nve.rst
@@ -0,0 +1,90 @@
+.. index:: fix nve
+
+fix nve command
+===============
+
+fix nve/intel command
+=====================
+
+fix nve/kk command
+==================
+
+fix nve/omp command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position and velocity for
+atoms in the group each timestep.  V is volume; E is energy.  This
+creates a system trajectory consistent with the microcanonical
+ensemble.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst
new file mode 100644
index 0000000000..4ac734c468
--- /dev/null
+++ b/doc/src/fix_nve_asphere.rst
@@ -0,0 +1,98 @@
+.. index:: fix nve/asphere
+
+fix nve/asphere command
+=======================
+
+fix nve/asphere/intel command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/asphere
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/asphere = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/asphere
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position, velocity,
+orientation, and angular velocity for aspherical particles in the
+group each timestep.  V is volume; E is energy.  This creates a system
+trajectory consistent with the microcanonical ensemble.
+
+This fix differs from the :doc:`fix nve <fix_nve>` command, which
+assumes point particles and only updates their position and velocity.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style ellipsoid <atom_style>`
+command.
+
+All particles in the group must be finite-size.  They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nve/sphere <fix_nve_sphere>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst
new file mode 100644
index 0000000000..309928f582
--- /dev/null
+++ b/doc/src/fix_nve_asphere_noforce.rst
@@ -0,0 +1,72 @@
+.. index:: fix nve/asphere/noforce
+
+fix nve/asphere/noforce command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/asphere/noforce
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/asphere/noforce = style name of this fix command
+
+Examples
+""""""""
+
+fix 1 all nve/asphere/noforce
+
+Description
+"""""""""""
+
+Perform updates of position and orientation, but not velocity or
+angular momentum for atoms in the group each timestep.  In other
+words, the force and torque on the atoms is ignored and their velocity
+and angular momentum are not updated.  The atom velocities and
+angular momenta are used to update their positions and orientation.
+
+This is useful as an implicit time integrator for Fast Lubrication
+Dynamics, since the velocity and angular momentum are updated by the
+:doc:`pair\_style lubricuteU <pair_lubricateU>` command.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style ellipsoid <atom_style>`
+command.
+
+All particles in the group must be finite-size.  They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve/noforce <fix_nve_noforce>`, :doc:`fix nve/asphere <fix_nve_asphere>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst
new file mode 100644
index 0000000000..e44f78c25c
--- /dev/null
+++ b/doc/src/fix_nve_awpmd.rst
@@ -0,0 +1,65 @@
+.. index:: fix nve/awpmd
+
+fix nve/awpmd command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/awpmd
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/awpmd = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/awpmd
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position and velocity for
+nuclei and electrons in the group for the :doc:`Antisymmetrized Wave Packet Molecular Dynamics <pair_awpmd>` model.  V is volume; E is energy.
+This creates a system trajectory consistent with the microcanonical
+ensemble.
+
+The operation of this fix is exactly like that described by the :doc:`fix nve <fix_nve>` command, except that the width and width-velocity of
+the electron wave functions are also updated.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-AWPMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst
new file mode 100644
index 0000000000..1d75b3ac34
--- /dev/null
+++ b/doc/src/fix_nve_body.rst
@@ -0,0 +1,69 @@
+.. index:: fix nve/body
+
+fix nve/body command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/body
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/body = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/body
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position, velocity,
+orientation, and angular velocity for body particles in the group each
+timestep.  V is volume; E is energy.  This creates a system trajectory
+consistent with the microcanonical ensemble.  See the :doc:`Howto body <Howto_body>` doc page for more details on using body
+particles.
+
+This fix differs from the :doc:`fix nve <fix_nve>` command, which
+assumes point particles and only updates their position and velocity.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the BODY package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style body <atom_style>`
+command.
+
+All particles in the group must be body particles.  They cannot be
+point particles.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nve/asphere <fix_nve_asphere>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst
new file mode 100644
index 0000000000..5fc6a46ab5
--- /dev/null
+++ b/doc/src/fix_nve_dot.rst
@@ -0,0 +1,84 @@
+.. index:: fix nve/dot
+
+fix nve/dot command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/dot
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/dot = style name of this fix command
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/dot
+
+Description
+"""""""""""
+
+Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack4>`
+to a group of atoms, but without Langevin dynamics.
+This command performs Molecular dynamics (MD)
+via a velocity-Verlet algorithm and an evolution operator that rotates
+the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller4>`.
+
+This command is the equivalent of the :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+without damping and noise and can be used to determine the stability range
+in a NVE ensemble prior to using the Langevin-type DOTC-integrator
+(see also :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`).
+The command is equivalent to the :doc:`fix nve <fix_nve>`.
+The particles are always considered to have a finite size.
+
+An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
+Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich4>`.
+The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles can only be used if LAMMPS was built with the
+:ref:`USER-CGDNA <PKG-USER-CGDNA>` package and the MOLECULE and ASPHERE package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`fix nve <fix_nve>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Davidchack4:
+
+**(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
+
+.. _Miller4:
+
+**(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
+
+.. _Henrich4:
+
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt
deleted file mode 100644
index fcd8926c13..0000000000
--- a/doc/src/fix_nve_dot.txt
+++ /dev/null
@@ -1,63 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix nve/dot command :h3
-
-[Syntax:]
-
-fix ID group-ID nve/dot :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-nve/dot = style name of this fix command :l
-:ule
-
-[Examples:]
-
-fix 1 all nve/dot :pre
-
-[Description:]
-
-Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
-to a group of atoms, but without Langevin dynamics.
-This command performs Molecular dynamics (MD)
-via a velocity-Verlet algorithm and an evolution operator that rotates
-the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
-
-This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-without damping and noise and can be used to determine the stability range
-in a NVE ensemble prior to using the Langevin-type DOTC-integrator
-(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
-The command is equivalent to the "fix nve"_fix_nve.html.
-The particles are always considered to have a finite size.
-
-An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
-Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html
-
-[Default:] none
-
-:line
-
-:link(Davidchack1)
-[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller1)
-[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
-:link(Henrich3)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst
new file mode 100644
index 0000000000..3143db968f
--- /dev/null
+++ b/doc/src/fix_nve_dotc_langevin.rst
@@ -0,0 +1,176 @@
+.. index:: fix nve/dotc/langevin
+
+fix nve/dotc/langevin command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/dotc/langevin = style name of this fix command
+* Tstart,Tstop = desired temperature at start/end of run (temperature units)
+* damp = damping parameter (time units)
+* seed = random number seed to use for white noise (positive integer)
+* keyword = *angmom*
+  
+  .. parsed-literal::
+  
+       *angmom* value = factor
+         factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
+   fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10
+
+Description
+"""""""""""
+
+Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
+as described in :ref:`(Davidchack) <Davidchack5>`
+to a group of atoms, which models an interaction with an implicit background
+solvent.  This command performs Brownian dynamics (BD)
+via a technique that splits the integration into a deterministic Hamiltonian
+part and the Ornstein-Uhlenbeck process for noise and damping.
+The quaternion degrees of freedom are updated though an evolution
+operator which performs a rotation in quaternion space, preserves
+the quaternion norm and is akin to :ref:`(Miller) <Miller5>`.
+
+In terms of syntax this command has been closely modelled on the
+:doc:`fix langevin <fix_langevin>` and its *angmom* option. But it combines
+the :doc:`fix nve <fix_nve>` and the :doc:`fix langevin <fix_langevin>` in
+one single command. The main feature is improved stability
+over the standard integrator, permitting slightly larger timestep sizes.
+
+.. note::
+
+   Unlike the :doc:`fix langevin <fix_langevin>` this command performs
+   also time integration of the translational and quaternion degrees of freedom.
+
+The total force on each atom will have the form:
+
+
+.. parsed-literal::
+
+   F = Fc + Ff + Fr
+   Ff = - (m / damp) v
+   Fr is proportional to sqrt(Kb T m / (dt damp))
+
+Fc is the conservative force computed via the usual inter-particle
+interactions (:doc:`pair\_style <pair_style>`,
+:doc:`bond\_style <bond_style>`, etc).
+
+The Ff and Fr terms are implicitly taken into account by this fix
+on a per-particle basis.
+
+Ff is a frictional drag or viscous damping term proportional to the
+particle's velocity.  The proportionality constant for each atom is
+computed as m/damp, where m is the mass of the particle and damp is
+the damping factor specified by the user.
+
+Fr is a force due to solvent atoms at a temperature T randomly bumping
+into the particle.  As derived from the fluctuation/dissipation
+theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
+dt damp), where Kb is the Boltzmann constant, T is the desired
+temperature, m is the mass of the particle, dt is the timestep size,
+and damp is the damping factor.  Random numbers are used to randomize
+the direction and magnitude of this force as described in
+:ref:`(Dunweg) <Dunweg5>`, where a uniform random number is used (instead of
+a Gaussian random number) for speed.
+
+
+----------
+
+
+*Tstart* and *Tstop* have to be constant values, i.e. they cannot
+be variables. If used together with the oxDNA force field for
+coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
+corresponds to T = 300 K.
+
+The *damp* parameter is specified in time units and determines how
+rapidly the temperature is relaxed.  For example, a value of 0.03
+means to relax the temperature in a timespan of (roughly) 0.03 time
+units tau (see the :doc:`units <units>` command).
+The damp factor can be thought of as inversely related to the
+viscosity of the solvent, i.e. a small relaxation time implies a
+hi-viscosity solvent and vice versa.  See the discussion about gamma
+and viscosity in the documentation for the :doc:`fix viscous <fix_viscous>` command for more details.
+Note that the value 78.9375 in the second example above corresponds
+to a diffusion constant, which is about an order of magnitude larger
+than realistic ones. This has been used to sample configurations faster
+in Brownian dynamics simulations.
+
+The random # *seed* must be a positive integer. A Marsaglia random
+number generator is used.  Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+The keyword/value option has to be used in the following way:
+
+This fix has to be used together with the *angmom* keyword. The
+particles are always considered to have a finite size.
+The keyword *angmom* enables thermostatting of the rotational degrees of
+freedom in addition to the usual translational degrees of freedom.
+
+The scale factor after the *angmom* keyword gives the ratio of the rotational to
+the translational friction coefficient.
+
+An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
+Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
+The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles can only be used if LAMMPS was built with the
+:ref:`USER-CGDNA <PKG-USER-CGDNA>` package and the MOLECULE and ASPHERE package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix nve/dot <fix_nve_dot>`, :doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Davidchack5:
+
+**(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
+
+.. _Miller5:
+
+**(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
+
+.. _Dunweg5:
+
+**(Dunweg)** B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
+
+.. _Henrich5:
+
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt
deleted file mode 100644
index 898ca5132b..0000000000
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ /dev/null
@@ -1,143 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix nve/dotc/langevin command :h3
-
-[Syntax:]
-
-fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-nve/dotc/langevin = style name of this fix command :l
-Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
-damp = damping parameter (time units) :l
-seed = random number seed to use for white noise (positive integer) :l
-keyword = {angmom} :l
-  {angmom} value = factor
-    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
-:ule
-
-[Examples:]
-
-fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
-fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
-
-[Description:]
-
-Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
-as described in "(Davidchack)"_#Davidchack2
-to a group of atoms, which models an interaction with an implicit background
-solvent.  This command performs Brownian dynamics (BD)
-via a technique that splits the integration into a deterministic Hamiltonian
-part and the Ornstein-Uhlenbeck process for noise and damping.
-The quaternion degrees of freedom are updated though an evolution
-operator which performs a rotation in quaternion space, preserves
-the quaternion norm and is akin to "(Miller)"_#Miller2.
-
-In terms of syntax this command has been closely modelled on the
-"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
-the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
-one single command. The main feature is improved stability
-over the standard integrator, permitting slightly larger timestep sizes.
-
-NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
-also time integration of the translational and quaternion degrees of freedom.
-
-The total force on each atom will have the form:
-
-F = Fc + Ff + Fr
-Ff = - (m / damp) v
-Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
-
-Fc is the conservative force computed via the usual inter-particle
-interactions ("pair_style"_pair_style.html,
-"bond_style"_bond_style.html, etc).
-
-The Ff and Fr terms are implicitly taken into account by this fix
-on a per-particle basis.
-
-Ff is a frictional drag or viscous damping term proportional to the
-particle's velocity.  The proportionality constant for each atom is
-computed as m/damp, where m is the mass of the particle and damp is
-the damping factor specified by the user.
-
-Fr is a force due to solvent atoms at a temperature T randomly bumping
-into the particle.  As derived from the fluctuation/dissipation
-theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
-dt damp), where Kb is the Boltzmann constant, T is the desired
-temperature, m is the mass of the particle, dt is the timestep size,
-and damp is the damping factor.  Random numbers are used to randomize
-the direction and magnitude of this force as described in
-"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of
-a Gaussian random number) for speed.
-
-:line
-
-{Tstart} and {Tstop} have to be constant values, i.e. they cannot
-be variables. If used together with the oxDNA force field for
-coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
-corresponds to T = 300 K.
-
-The {damp} parameter is specified in time units and determines how
-rapidly the temperature is relaxed.  For example, a value of 0.03
-means to relax the temperature in a timespan of (roughly) 0.03 time
-units tau (see the "units"_units.html command).
-The damp factor can be thought of as inversely related to the
-viscosity of the solvent, i.e. a small relaxation time implies a
-hi-viscosity solvent and vice versa.  See the discussion about gamma
-and viscosity in the documentation for the "fix
-viscous"_fix_viscous.html command for more details.
-Note that the value 78.9375 in the second example above corresponds
-to a diffusion constant, which is about an order of magnitude larger
-than realistic ones. This has been used to sample configurations faster
-in Brownian dynamics simulations.
-
-The random # {seed} must be a positive integer. A Marsaglia random
-number generator is used.  Each processor uses the input seed to
-generate its own unique seed and its own stream of random numbers.
-Thus the dynamics of the system will not be identical on two runs on
-different numbers of processors.
-
-The keyword/value option has to be used in the following way:
-
-This fix has to be used together with the {angmom} keyword. The
-particles are always considered to have a finite size.
-The keyword {angmom} enables thermostatting of the rotational degrees of
-freedom in addition to the usual translational degrees of freedom.
-
-The scale factor after the {angmom} keyword gives the ratio of the rotational to
-the translational friction coefficient.
-
-An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
-
-[Default:] none
-
-:line
-
-:link(Davidchack2)
-[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller2)
-[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
-:link(Dunweg3)
-[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
-:link(Henrich4)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst
new file mode 100644
index 0000000000..a7346f1ed2
--- /dev/null
+++ b/doc/src/fix_nve_eff.rst
@@ -0,0 +1,60 @@
+.. index:: fix nve/eff
+
+fix nve/eff command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/eff
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/eff = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/eff
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position and velocity for
+nuclei and electrons in the group for the :doc:`electron force field <pair_eff>` model.  V is volume; E is energy.  This creates a
+system trajectory consistent with the microcanonical ensemble.
+
+The operation of this fix is exactly like that described by the :doc:`fix nve <fix_nve>` command, except that the radius and radial velocity
+of electrons are also updated.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nvt/eff <fix_nh_eff>`, :doc:`fix npt/eff <fix_nh_eff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst
new file mode 100644
index 0000000000..f637db54d1
--- /dev/null
+++ b/doc/src/fix_nve_limit.rst
@@ -0,0 +1,98 @@
+.. index:: fix nve/limit
+
+fix nve/limit command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/limit xmax
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve = style name of this fix command
+* xmax = maximum distance an atom can move in one timestep (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/limit 0.1
+
+Description
+"""""""""""
+
+Perform constant NVE updates of position and velocity for atoms in the
+group each timestep.  A limit is imposed on the maximum distance an
+atom can move in one timestep.  This is useful when starting a
+simulation with a configuration containing highly overlapped atoms.
+Normally this would generate huge forces which would blow atoms out of
+the simulation box, causing LAMMPS to stop with an error.
+
+Using this fix can overcome that problem.  Forces on atoms must still
+be computable (which typically means 2 atoms must have a separation
+distance > 0.0).  But large velocities generated by large forces are
+reset to a value that corresponds to a displacement of length *xmax*
+in a single timestep.  *Xmax* is specified in distance units; see the
+:doc:`units <units>` command for details.  The value of *xmax* should be
+consistent with the neighbor skin distance and the frequency of
+neighbor list re-building, so that pairwise interactions are not
+missed on successive timesteps as atoms move.  See the
+:doc:`neighbor <neighbor>` and :doc:`neigh\_modify <neigh_modify>` commands
+for details.
+
+Note that if a velocity reset occurs the integrator will not conserve
+energy.  On steps where no velocity resets occur, this integrator is
+exactly like the :doc:`fix nve <fix_nve>` command.  Since forces are
+unaltered, pressures computed by thermodynamic output will still be
+very large for overlapped configurations.
+
+.. note::
+
+   You should not use :doc:`fix shake <fix_shake>` in conjunction
+   with this fix.  That is because fix shake applies constraint forces
+   based on the predicted positions of atoms after the next timestep.
+   It has no way of knowing the timestep may change due to this fix,
+   which will cause the constraint forces to be invalid.  A better
+   strategy is to turn off fix shake when performing initial dynamics
+   that need this fix, then turn fix shake on when doing normal dynamics
+   with a fixed-size timestep.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the count of how
+many updates of atom's velocity/position were limited by the maximum
+distance criterion.  This should be roughly the number of atoms so
+affected, except that updates occur at both the beginning and end of a
+timestep in a velocity Verlet timestepping algorithm.  This is a
+cumulative quantity for the current run, but is re-initialized to zero
+each time a run is performed.  The scalar value calculated by this fix
+is "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nve/noforce <fix_nve_noforce>`,
+:doc:`pair\_style soft <pair_soft>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst
new file mode 100644
index 0000000000..8f77e8481e
--- /dev/null
+++ b/doc/src/fix_nve_line.rst
@@ -0,0 +1,65 @@
+.. index:: fix nve/line
+
+fix nve/line command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/line
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/line = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/line
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position, velocity,
+orientation, and angular velocity for line segment particles in the
+group each timestep.  V is volume; E is energy.  This creates a system
+trajectory consistent with the microcanonical ensemble.  See :doc:`Howto spherical <Howto_spherical>` doc page for an overview of using line
+segment particles.
+
+This fix differs from the :doc:`fix nve <fix_nve>` command, which
+assumes point particles and only updates their position and velocity.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that particles be line segments as defined by the
+:doc:`atom\_style line <atom_style>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nve/asphere <fix_nve_asphere>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst
new file mode 100644
index 0000000000..5836dc005c
--- /dev/null
+++ b/doc/src/fix_nve_manifold_rattle.rst
@@ -0,0 +1,129 @@
+.. index:: fix nve/manifold/rattle
+
+fix nve/manifold/rattle command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/manifold/rattle = style name of this fix command
+* tol = tolerance to which Newton iteration must converge
+* maxit = maximum number of iterations to perform
+* manifold = name of the manifold
+* manifold-args = parameters for the manifold
+* one or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *every*
+       *every* values = N
+         N = print info about iteration every N steps. N = 0 means no output
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/manifold/rattle 1e-4 10 sphere 5.0
+   fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position and velocity for
+atoms constrained to a curved surface (manifold) in the group each
+timestep. The constraint is handled by RATTLE :ref:`(Andersen) <Andersen1>`
+written out for the special case of single-particle constraints as
+explained in :ref:`(Paquay) <Paquay2>`.  V is volume; E is energy. This way,
+the dynamics of particles constrained to curved surfaces can be
+studied. If combined with :doc:`fix langevin <fix_langevin>`, this
+generates Brownian motion of particles constrained to a curved
+surface. For a list of currently supported manifolds and their
+parameters, see the :doc:`Howto manifold <Howto_manifold>` doc page.
+
+Note that the particles must initially be close to the manifold in
+question. If not, RATTLE will not be able to iterate until the
+constraint is satisfied, and an error is generated. For simple
+manifolds this can be achieved with *region* and *create\_atoms*
+commands, but for more complex surfaces it might be more useful to
+write a script.
+
+The manifold args may be equal-style variables, like so:
+
+
+.. parsed-literal::
+
+   variable R equal "ramp(5.0,3.0)"
+   fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
+
+In this case, the manifold parameter will change in time according to
+the variable.  This is not a problem for the time integrator as long
+as the change of the manifold is slow with respect to the dynamics of
+the particles.  Note that if the manifold has to exert work on the
+particles because of these changes, the total energy might not be
+conserved.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`, :doc:`fix manifoldforce <fix_manifoldforce>`
+
+**Default:** every = 0, tchain = 3
+
+
+----------
+
+
+.. _Andersen1:
+
+
+
+**(Andersen)** Andersen, J. Comp. Phys. 52, 24, (1983).
+
+.. _Paquay2:
+
+
+
+**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
+preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst
new file mode 100644
index 0000000000..07caefca16
--- /dev/null
+++ b/doc/src/fix_nve_noforce.rst
@@ -0,0 +1,64 @@
+.. index:: fix nve/noforce
+
+fix nve/noforce command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/noforce = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 wall nve/noforce
+
+Description
+"""""""""""
+
+Perform updates of position, but not velocity for atoms in the group
+each timestep.  In other words, the force on the atoms is ignored and
+their velocity is not updated.  The atom velocities are used to update
+their positions.
+
+This can be useful for wall atoms, when you set their velocities, and
+want the wall to move (or stay stationary) in a prescribed fashion.
+
+This can also be accomplished via the :doc:`fix setforce <fix_setforce>`
+command, but with fix nve/noforce, the forces on the wall atoms are
+unchanged, and can thus be printed by the :doc:`dump <dump>` command or
+queried with an equal-style :doc:`variable <variable>` that uses the
+fcm() group function to compute the total force on the group of atoms.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst
new file mode 100644
index 0000000000..1789a9e119
--- /dev/null
+++ b/doc/src/fix_nve_sphere.rst
@@ -0,0 +1,146 @@
+.. index:: fix nve/sphere
+
+fix nve/sphere command
+======================
+
+fix nve/sphere/omp command
+==========================
+
+fix nve/sphere/kk command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/sphere
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/sphere = style name of this fix command
+* zero or more keyword/value pairs may be appended
+* keyword = *update* or *disc*
+  
+  .. parsed-literal::
+  
+       *update* value = *dipole* or *dipole/dlm*
+         dipole = update orientation of dipole moment during integration
+         dipole/dlm = use DLM integrator to update dipole orientation
+       *disc* value = none = treat particles as 2d discs, not spheres
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/sphere
+   fix 1 all nve/sphere update dipole
+   fix 1 all nve/sphere disc
+   fix 1 all nve/sphere update dipole/dlm
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position, velocity, and
+angular velocity for finite-size spherical particles in the group each
+timestep.  V is volume; E is energy.  This creates a system trajectory
+consistent with the microcanonical ensemble.
+
+This fix differs from the :doc:`fix nve <fix_nve>` command, which
+assumes point particles and only updates their position and velocity.
+
+If the *update* keyword is used with the *dipole* value, then the
+orientation of the dipole moment of each particle is also updated
+during the time integration.  This option should be used for models
+where a dipole moment is assigned to finite-size particles,
+e.g. spheroids via use of the :doc:`atom\_style hybrid sphere dipole <atom_style>` command.
+
+The default dipole orientation integrator can be changed to the
+Dullweber-Leimkuhler-McLachlan integration scheme
+:ref:`(Dullweber) <nh-Dullweber>` when using *update* with the value
+*dipole/dlm*\ . This integrator is symplectic and time-reversible,
+giving better energy conservation and allows slightly longer timesteps
+at only a small additional computational cost.
+
+If the *disc* keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the :doc:`dimension <dimension>` keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the :doc:`atom\_style sphere <atom_style>`
+command.  If the *dipole* keyword is used, then they must also store a
+dipole moment as defined by the :doc:`atom\_style dipole <atom_style>`
+command.
+
+All particles in the group must be finite-size spheres.  They cannot
+be point particles.
+
+Use of the *disc* keyword is only allowed for 2d simulations, as
+defined by the :doc:`dimension <dimension>` keyword.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nve/asphere <fix_nve_asphere>`
+
+**Default:** none
+
+
+----------
+
+
+.. _nve-Dullweber:
+
+
+
+**(Dullweber)** Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107,
+5840 (1997).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst
new file mode 100644
index 0000000000..5f1b1a648f
--- /dev/null
+++ b/doc/src/fix_nve_spin.rst
@@ -0,0 +1,113 @@
+.. index:: fix nve/spin
+
+fix nve/spin command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/spin keyword values
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/spin = style name of this fix command
+* keyword = *lattice*
+  
+  .. parsed-literal::
+  
+       *lattice* value = *moving* or *frozen*
+         moving = integrate both spin and atomic degress of freedom
+         frozen = integrate spins on a fixed lattice
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 all nve/spin lattice moving
+   fix 1 all nve/spin lattice frozen
+
+Description
+"""""""""""
+
+Perform a symplectic integration for the spin or spin-lattice system.
+
+The *lattice* keyword defines if the spins are integrated on a lattice
+of fixed atoms (lattice = frozen), or if atoms are moving
+(lattice = moving).
+The first case corresponds to a spin dynamics calculation, and
+the second to a spin-lattice calculation.
+By default a spin-lattice integration is performed (lattice = moving).
+
+The *nve/spin* fix applies a Suzuki-Trotter decomposition to
+the equations of motion of the spin lattice system, following the scheme:
+
+.. image:: Eqs/fix_integration_spin_stdecomposition.jpg
+   :align: center
+
+according to the implementation reported in :ref:`(Omelyan) <Omelyan1>`.
+
+A sectoring method enables this scheme for parallel calculations.
+The implementation of this sectoring algorithm is reported
+in :ref:`(Tranchida) <Tranchida1>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix style can only be used if LAMMPS was built with the SPIN
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+To use the spin algorithm, it is necessary to define a map with
+the atom\_modify command. Typically, by adding the command:
+
+
+.. parsed-literal::
+
+   atom_modify map array
+
+before you create the simulation box. Note that the keyword "hash"
+instead of "array" is also valid.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style spin <atom_style>`, :doc:`fix nve <fix_nve>`
+
+Default
+"""""""
+
+The option default is lattice = moving.
+
+
+----------
+
+
+.. _Omelyan1:
+
+
+
+**(Omelyan)** Omelyan, Mryglod, and Folk. Phys. Rev. Lett.
+86(5), 898. (2001).
+
+.. _Tranchida1:
+
+
+
+**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, 372, 406-425, (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst
new file mode 100644
index 0000000000..4e71a69c5a
--- /dev/null
+++ b/doc/src/fix_nve_tri.rst
@@ -0,0 +1,66 @@
+.. index:: fix nve/tri
+
+fix nve/tri command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nve/tri
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/tri = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve/tri
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position, velocity,
+orientation, and angular momentum for triangular particles in the
+group each timestep.  V is volume; E is energy.  This creates a system
+trajectory consistent with the microcanonical ensemble.  See the
+:doc:`Howto spherical <Howto_spherical>` doc page for an overview of
+using triangular particles.
+
+This fix differs from the :doc:`fix nve <fix_nve>` command, which
+assumes point particles and only updates their position and velocity.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that particles be triangles as defined by the
+:doc:`atom\_style tri <atom_style>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nve/asphere <fix_nve_asphere>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst
new file mode 100644
index 0000000000..c153ab6ff2
--- /dev/null
+++ b/doc/src/fix_nvk.rst
@@ -0,0 +1,89 @@
+.. index:: fix nvk
+
+fix nvk command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nvk
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nvk = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nvk
+
+Description
+"""""""""""
+
+Perform constant kinetic energy integration using the Gaussian
+thermostat to update position and velocity for atoms in the group each
+timestep.  V is volume; K is kinetic energy. This creates a system
+trajectory consistent with the isokinetic ensemble.
+
+The equations of motion used are those of Minary et al in
+:ref:`(Minary) <nvk-Minary>`, a variant of those initially given by Zhang in
+:ref:`(Zhang) <nvk-Zhang>`.
+
+The kinetic energy will be held constant at its value given when fix
+nvk is initiated. If a different kinetic energy is desired, the
+:doc:`velocity <velocity>` command should be used to change the kinetic
+energy prior to this fix.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+The Gaussian thermostat only works when it is applied to all atoms in
+the simulation box. Therefore, the group must be set to all.
+
+This fix has not yet been implemented to work with the RESPA integrator.
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+**Related commands:** none
+
+**Default:** none
+
+
+----------
+
+
+.. _nvk-Minary:
+
+
+
+**(Minary)** Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003).
+
+.. _nvk-Zhang:
+
+
+
+**(Zhang)** Zhang, J Chem Phys, 106, 6102 (1997).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst
new file mode 100644
index 0000000000..9df4c9e84f
--- /dev/null
+++ b/doc/src/fix_nvt_asphere.rst
@@ -0,0 +1,163 @@
+.. index:: fix nvt/asphere
+
+fix nvt/asphere command
+=======================
+
+fix nvt/asphere/omp command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nvt/asphere keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nvt/asphere = style name of this fix command
+* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nvt/asphere temp 300.0 300.0 100.0
+   fix 1 all nvt/asphere temp 300.0 300.0 100.0 drag 0.2
+
+Description
+"""""""""""
+
+Perform constant NVT integration to update position, velocity,
+orientation, and angular velocity each timestep for aspherical or
+ellipsoidal particles in the group using a Nose/Hoover temperature
+thermostat.  V is volume; T is temperature.  This creates a system
+trajectory consistent with the canonical ensemble.
+
+This fix differs from the :doc:`fix nvt <fix_nh>` command, which
+assumes point particles and only updates their position and velocity.
+
+The thermostat is applied to both the translational and rotational
+degrees of freedom for the aspherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below).  The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+Additional parameters affecting the thermostat are specified by
+keywords and values documented with the :doc:`fix nvt <fix_nh>`
+command.  See, for example, discussion of the *temp* and *drag*
+keywords.
+
+This fix computes a temperature each timestep.  To do this, the fix
+creates its own compute of style "temp/asphere", as if this command
+had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp/asphere
+
+See the :doc:`compute temp/asphere <compute_temp_asphere>` command for
+details.  Note that the ID of the new compute is the fix-ID +
+underscore + "temp", and the group for the new compute is the same as
+the fix group.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* will have no
+effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a :doc:`compute <compute>` you have
+defined to this fix which will be used in its thermostatting
+procedure.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix nvt <fix_nh>` command.
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style ellipsoid <atom_style>`
+command.
+
+All particles in the group must be finite-size.  They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix nve\_asphere <fix_nve_asphere>`, :doc:`fix npt\_asphere <fix_npt_asphere>`, :doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst
new file mode 100644
index 0000000000..f94c1850da
--- /dev/null
+++ b/doc/src/fix_nvt_body.rst
@@ -0,0 +1,156 @@
+.. index:: fix nvt/body
+
+fix nvt/body command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nvt/body keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nvt/body = style name of this fix command
+* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nvt/body temp 300.0 300.0 100.0
+   fix 1 all nvt/body temp 300.0 300.0 100.0 drag 0.2
+
+Description
+"""""""""""
+
+Perform constant NVT integration to update position, velocity,
+orientation, and angular velocity each timestep for body
+particles in the group using a Nose/Hoover temperature
+thermostat.  V is volume; T is temperature.  This creates a system
+trajectory consistent with the canonical ensemble.
+
+This fix differs from the :doc:`fix nvt <fix_nh>` command, which
+assumes point particles and only updates their position and velocity.
+
+The thermostat is applied to both the translational and rotational
+degrees of freedom for the body particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below).  The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+Additional parameters affecting the thermostat are specified by
+keywords and values documented with the :doc:`fix nvt <fix_nh>`
+command.  See, for example, discussion of the *temp* and *drag*
+keywords.
+
+This fix computes a temperature each timestep.  To do this, the fix
+creates its own compute of style "temp/body", as if this command
+had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp/body
+
+See the :doc:`compute temp/body <compute_temp_body>` command for
+details.  Note that the ID of the new compute is the fix-ID +
+underscore + "temp", and the group for the new compute is the same as
+the fix group.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* will have no
+effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a :doc:`compute <compute>` you have
+defined to this fix which will be used in its thermostatting
+procedure.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix nvt <fix_nh>` command.
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the BODY package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store torque and angular momentum and a
+quaternion as defined by the :doc:`atom\_style body <atom_style>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix nve\_body <fix_nve_body>`, :doc:`fix npt\_body <fix_npt_body>`, :doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst
new file mode 100644
index 0000000000..4b9c063caf
--- /dev/null
+++ b/doc/src/fix_nvt_manifold_rattle.rst
@@ -0,0 +1,103 @@
+.. index:: fix nvt/manifold/rattle
+
+fix nvt/manifold/rattle command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nvt/manifold/rattle = style name of this fix command
+* tol = tolerance to which Newton iteration must converge
+* maxit = maximum number of iterations to perform
+* manifold = name of the manifold
+* manifold-args = parameters for the manifold
+* one or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *temp* or *tchain* or *every*
+       *temp* values = Tstart Tstop Tdamp
+         Tstart, Tstop = external temperature at start/end of run
+         Tdamp = temperature damping parameter (time units)
+       *tchain* value = N
+         N = length of thermostat chain (1 = single thermostat)
+       *every* value = N
+         N = print info about iteration every N steps. N = 0 means no output
+
+
+
+Examples
+""""""""
+
+fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0
+
+Description
+"""""""""""
+
+This fix combines the RATTLE-based :ref:`(Andersen) <Andersen2>` time
+integrator of :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
+:ref:`(Paquay) <Paquay3>` with a Nose-Hoover-chain thermostat to sample the
+canonical ensemble of particles constrained to a curved surface
+(manifold). This sampling does suffer from discretization bias of
+O(dt).  For a list of currently supported manifolds and their
+parameters, see the :doc:`Howto manifold <Howto_manifold>` doc page.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve/manifold/rattle <fix_nvt_manifold_rattle>`, :doc:`fix manifoldforce <fix_manifoldforce>` **Default:** every = 0
+
+
+----------
+
+
+.. _Andersen2:
+
+
+
+**(Andersen)** Andersen, J. Comp. Phys. 52, 24, (1983).
+
+.. _Paquay3:
+
+
+
+**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
+preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst
new file mode 100644
index 0000000000..aa4197e19b
--- /dev/null
+++ b/doc/src/fix_nvt_sllod.rst
@@ -0,0 +1,215 @@
+.. index:: fix nvt/sllod
+
+fix nvt/sllod command
+=====================
+
+fix nvt/sllod/intel command
+===========================
+
+fix nvt/sllod/omp command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nvt/sllod keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nvt/sllod = style name of this fix command
+* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nvt/sllod temp 300.0 300.0 100.0
+   fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2
+
+Description
+"""""""""""
+
+Perform constant NVT integration to update positions and velocities
+each timestep for atoms in the group using a Nose/Hoover temperature
+thermostat.  V is volume; T is temperature.  This creates a system
+trajectory consistent with the canonical ensemble.
+
+This thermostat is used for a simulation box that is changing size
+and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
+The size/shape change is induced by use of the :doc:`fix deform <fix_deform>` command, so each point in the simulation box
+can be thought of as having a "streaming" velocity.  This
+position-dependent streaming velocity is subtracted from each atom's
+actual velocity to yield a thermal velocity which is used for
+temperature computation and thermostatting.  For example, if the box
+is being sheared in x, relative to y, then points at the bottom of the
+box (low y) have a small x velocity, while points at the top of the
+box (hi y) have a large x velocity.  These velocities do not
+contribute to the thermal "temperature" of the atom.
+
+.. note::
+
+   :doc:`Fix deform <fix_deform>` has an option for remapping either
+   atom coordinates or velocities to the changing simulation box.  To use
+   fix nvt/sllod, fix deform should NOT remap atom positions, because fix
+   nvt/sllod adjusts the atom positions and velocities to create a
+   velocity profile that matches the changing box size/shape.  Fix deform
+   SHOULD remap atom velocities when atoms cross periodic boundaries
+   since that is consistent with maintaining the velocity profile created
+   by fix nvt/sllod.  LAMMPS will give an error if this setting is not
+   consistent.
+
+The SLLOD equations of motion, originally proposed by Hoover and Ladd
+(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be equivalent to
+Newton's equations of motion for shear flow by :ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate the desired
+velocity gradient and the correct production of work by stresses for
+all forms of homogeneous flow by :ref:`(Daivis and Todd) <Daivis>`.  As
+implemented in LAMMPS, they are coupled to a Nose/Hoover chain
+thermostat in a velocity Verlet formulation, closely following the
+implementation used for the :doc:`fix nvt <fix_nh>` command.
+
+.. note::
+
+   A recent (2017) book by :ref:`(Daivis and Todd) <Daivis-sllod>`
+   discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+   thermostatting generally, for both simple and complex fluids,
+   e.g. molecular systems.  The latter can be tricky to do correctly.
+
+Additional parameters affecting the thermostat are specified by
+keywords and values documented with the :doc:`fix nvt <fix_nh>`
+command.  See, for example, discussion of the *temp* and *drag*
+keywords.
+
+This fix computes a temperature each timestep.  To do this, the fix
+creates its own compute of style "temp/deform", as if this command had
+been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp/deform
+
+See the :doc:`compute temp/deform <compute_temp_deform>` command for
+details.  Note that the ID of the new compute is the fix-ID +
+underscore + "temp", and the group for the new compute is the same as
+the fix group.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* will have no
+effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a :doc:`compute <compute>` you have
+defined to this fix which will be used in its thermostatting
+procedure.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix nvt <fix_nh>` command.
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix works best without Nose-Hoover chain thermostats, i.e. using
+tchain = 1.  Setting tchain to larger values can result in poor
+equilibration.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix langevin <fix_langevin>`,
+:doc:`fix\_modify <fix_modify>`, :doc:`compute temp/deform <compute_temp_deform>`
+
+Default
+"""""""
+
+Same as :doc:`fix nvt <fix_nh>`, except tchain = 1.
+
+
+----------
+
+
+.. _Evans3:
+
+
+
+**(Evans and Morriss)** Evans and Morriss, Phys Rev A, 30, 1528 (1984).
+
+.. _Daivis:
+
+
+
+**(Daivis and Todd)** Daivis and Todd, J Chem Phys, 124, 194103 (2006).
+
+.. _Daivis-sllod:
+
+
+
+**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst
new file mode 100644
index 0000000000..0e8b005176
--- /dev/null
+++ b/doc/src/fix_nvt_sllod_eff.rst
@@ -0,0 +1,103 @@
+.. index:: fix nvt/sllod/eff
+
+fix nvt/sllod/eff command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nvt/sllod/eff keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nvt/sllod/eff = style name of this fix command
+* additional thermostat related keyword/value pairs from the :doc:`fix nvt/eff <fix_nh_eff>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1
+   fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2
+
+Description
+"""""""""""
+
+Perform constant NVT integration to update positions and velocities
+each timestep for nuclei and electrons in the group for the :doc:`electron force field <pair_eff>` model, using a Nose/Hoover temperature
+thermostat.  V is volume; T is temperature.  This creates a system
+trajectory consistent with the canonical ensemble.
+
+The operation of this fix is exactly like that described by the :doc:`fix nvt/sllod <fix_nvt_sllod>` command, except that the radius and
+radial velocity of electrons are also updated and thermostatted.
+Likewise the temperature calculated by the fix, using the compute it
+creates (as discussed in the :doc:`fix nvt, npt, and nph <fix_nh>` doc
+page), is performed with a :doc:`compute temp/deform/eff <compute_temp_deform_eff>` command that includes
+the eFF contribution to the temperature from the electron radial
+velocity.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a :doc:`compute <compute>` you have
+defined to this fix which will be used in its thermostatting
+procedure.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix nvt/eff <fix_nh_eff>` command.
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix works best without Nose-Hoover chain thermostats, i.e. using
+tchain = 1.  Setting tchain to larger values can result in poor
+equilibration.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve/eff <fix_nve_eff>`, :doc:`fix nvt/eff <fix_nh_eff>`, :doc:`fix langevin/eff <fix_langevin_eff>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, :doc:`fix\_modify <fix_modify>`, :doc:`compute temp/deform/eff <compute_temp_deform_eff>`
+
+Default
+"""""""
+
+Same as :doc:`fix nvt/eff <fix_nh_eff>`, except tchain = 1.
+
+
+----------
+
+
+.. _Tuckerman2:
+
+
+
+**(Tuckerman)** Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
+106, 5615 (1997).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst
new file mode 100644
index 0000000000..eedf21f69b
--- /dev/null
+++ b/doc/src/fix_nvt_sphere.rst
@@ -0,0 +1,176 @@
+.. index:: fix nvt/sphere
+
+fix nvt/sphere command
+======================
+
+fix nvt/sphere/omp command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID nvt/sphere keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nvt/sphere = style name of this fix command
+* zero or more keyword/value pairs may be appended
+* keyword = *disc*
+  
+  .. parsed-literal::
+  
+       *disc* value = none = treat particles as 2d discs, not spheres
+
+* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nvt/sphere temp 300.0 300.0 100.0
+   fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc
+   fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2
+
+Description
+"""""""""""
+
+Perform constant NVT integration to update position, velocity, and
+angular velocity each timestep for finite-size spherical particles in
+the group using a Nose/Hoover temperature thermostat.  V is volume; T
+is temperature.  This creates a system trajectory consistent with the
+canonical ensemble.
+
+This fix differs from the :doc:`fix nvt <fix_nh>` command, which
+assumes point particles and only updates their position and velocity.
+
+The thermostat is applied to both the translational and rotational
+degrees of freedom for the spherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below).  The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+If the *disc* keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the :doc:`dimension <dimension>` keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
+Additional parameters affecting the thermostat are specified by
+keywords and values documented with the :doc:`fix nvt <fix_nh>`
+command.  See, for example, discussion of the *temp* and *drag*
+keywords.
+
+This fix computes a temperature each timestep.  To do this, the fix
+creates its own compute of style "temp/sphere", as if this command
+had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp/sphere
+
+See the :doc:`compute temp/sphere <compute_temp_sphere>` command for
+details.  Note that the ID of the new compute is the fix-ID +
+underscore + "temp", and the group for the new compute is the same as
+the fix group.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* will have no
+effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a :doc:`compute <compute>` you have
+defined to this fix which will be used in its thermostatting
+procedure.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes the same global scalar and global vector of
+quantities as does the :doc:`fix nvt <fix_nh>` command.
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the :doc:`atom\_style sphere <atom_style>`
+command.
+
+All particles in the group must be finite-size spheres.  They cannot
+be point particles.
+
+Use of the *disc* keyword is only allowed for 2d simulations, as
+defined by the :doc:`dimension <dimension>` keyword.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix nve\_sphere <fix_nve_sphere>`, :doc:`fix nvt\_asphere <fix_nvt_asphere>`, :doc:`fix npt\_sphere <fix_npt_sphere>`, :doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst
new file mode 100644
index 0000000000..9d1f40ef5f
--- /dev/null
+++ b/doc/src/fix_oneway.rst
@@ -0,0 +1,73 @@
+.. index:: fix oneway
+
+fix oneway command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID oneway N region-ID direction
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* oneway = style name of this fix command
+* N = apply this fix every this many timesteps
+* region-ID = ID of region where fix is active
+* direction = *x* or *-x* or *y* or *-y* or *z* or *-z* = coordinate and direction of the oneway constraint
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix ions oneway 10 semi -x
+   fix all oneway 1 left -z
+   fix all oneway 1 right z
+
+Description
+"""""""""""
+
+Enforce that particles in the group and in a given region can only
+move in one direction.  This is done by reversing a particle's
+velocity component, if it has the wrong sign in the specified
+dimension.  The effect is that the particle moves in one direction
+only.
+
+This can be used, for example, as a simple model of a semi-permeable
+membrane, or as an implementation of Maxwell's demon.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall/reflect <fix_wall_reflect>` command
+
+**Default:** none
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst
new file mode 100644
index 0000000000..dcce12eb91
--- /dev/null
+++ b/doc/src/fix_orient.rst
@@ -0,0 +1,231 @@
+.. index:: fix orient/fcc
+
+fix orient/fcc command
+======================
+
+fix orient/bcc command
+======================
+
+
+.. parsed-literal::
+
+   fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1
+   fix ID group-ID orient/bcc nstats dir alat dE cutlo cuthi file0 file1
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nstats = print stats every this many steps, 0 = never
+* dir = 0/1 for which crystal is used as reference
+* alat = fcc/bcc cubic lattice constant (distance units)
+* dE = energy added to each atom (energy units)
+* cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi
+* file0,file1 = files that specify orientation of each grain
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec
+   fix gb all orient/bcc 0 1 2.882 0.001 0.25 0.75 ngb.left ngb.right
+
+Description
+"""""""""""
+
+The fix applies an orientation-dependent force to atoms near a planar
+grain boundary which can be used to induce grain boundary migration
+(in the direction perpendicular to the grain boundary plane).  The
+motivation and explanation of this force and its application are
+described in :ref:`(Janssens) <Janssens>`. The adaptation to bcc crystals
+is described in :ref:`(Wicaksono1) <Wicaksono1>`. The computed force is only
+applied to atoms in the fix group.
+
+The basic idea is that atoms in one grain (on one side of the
+boundary) have a potential energy dE added to them.  Atoms in the
+other grain have 0.0 potential energy added.  Atoms near the boundary
+(whose neighbor environment is intermediate between the two grain
+orientations) have an energy between 0.0 and dE added.  This creates
+an effective driving force to reduce the potential energy of atoms
+near the boundary by pushing them towards one of the grain
+orientations.  For dir = 1 and dE > 0, the boundary will thus move so
+that the grain described by file0 grows and the grain described by
+file1 shrinks.  Thus this fix is designed for simulations of two-grain
+systems, either with one grain boundary and free surfaces parallel to
+the boundary, or a system with periodic boundary conditions and two
+equal and opposite grain boundaries.  In either case, the entire
+system can displace during the simulation, and such motion should be
+accounted for in measuring the grain boundary velocity.
+
+The potential energy added to atom I is given by these formulas
+
+.. image:: Eqs/fix_orient_fcc.jpg
+   :align: center
+
+which are fully explained in :ref:`(Janssens) <Janssens>`.  For fcc crystals
+this order parameter Xi for atom I in equation (1) is a sum over the
+12 nearest neighbors of atom I. For bcc crystals it is the
+corresponding sum of the 8 nearest neighbors. Rj is the vector from
+atom I to its neighbor J, and RIj is a vector in the reference
+(perfect) crystal.  That is, if dir = 0/1, then RIj is a vector to an
+atom coord from file 0/1.  Equation (2) gives the expected value of
+the order parameter XiIJ in the other grain.  Hi and lo cutoffs are
+defined in equations (3) and (4), using the input parameters *cutlo*
+and *cuthi* as thresholds to avoid adding grain boundary energy when
+the deviation in the order parameter from 0 or 1 is small (e.g. due to
+thermal fluctuations in a perfect crystal).  The added potential
+energy Ui for atom I is given in equation (6) where it is interpolated
+between 0 and dE using the two threshold Xi values and the Wi value of
+equation (5).
+
+The derivative of this energy expression gives the force on each atom
+which thus depends on the orientation of its neighbors relative to the
+2 grain orientations.  Only atoms near the grain boundary feel a net
+force which tends to drive them to one of the two grain orientations.
+
+In equation (1), the reference vector used for each neighbor is the
+reference vector closest to the actual neighbor position.  This means
+it is possible two different neighbors will use the same reference
+vector.  In such cases, the atom in question is far from a perfect
+orientation and will likely receive the full dE addition, so the
+effect of duplicate reference vector usage is small.
+
+The *dir* parameter determines which grain wants to grow at the
+expense of the other.  A value of 0 means the first grain will shrink;
+a value of 1 means it will grow.  This assumes that *dE* is positive.
+The reverse will be true if *dE* is negative.
+
+The *alat* parameter is the cubic lattice constant for the fcc or bcc
+material and is only used to compute a cutoff distance of 1.57 \* alat
+/ sqrt(2) for finding the 12 or 8 nearest neighbors of each atom
+(which should be valid for an fcc or bcc crystal).  A longer/shorter
+cutoff can be imposed by adjusting *alat*\ .  If a particular atom has
+less than 12 or 8 neighbors within the cutoff, the order parameter of
+equation (1) is effectively multiplied by 12 or 8 divided by the
+actual number of neighbors within the cutoff.
+
+The *dE* parameter is the maximum amount of additional energy added to
+each atom in the grain which wants to shrink.
+
+The *cutlo* and *cuthi* parameters are used to reduce the force added
+to bulk atoms in each grain far away from the boundary.  An atom in
+the bulk surrounded by neighbors at the ideal grain orientation would
+compute an order parameter of 0 or 1 and have no force added.
+However, thermal vibrations in the solid will cause the order
+parameters to be greater than 0 or less than 1.  The cutoff parameters
+mask this effect, allowing forces to only be added to atoms with
+order-parameters between the cutoff values.
+
+*File0* and *file1* are filenames for the two grains which each
+contain 6 vectors (6 lines with 3 values per line) which specify the
+grain orientations.  Each vector is a displacement from a central atom
+(0,0,0) to a nearest neighbor atom in an fcc lattice at the proper
+orientation.  The vector lengths should all be identical since an fcc
+lattice has a coordination number of 12.  Only 6 are listed due to
+symmetry, so the list must include one from each pair of
+equal-and-opposite neighbors.  A pair of orientation files for a
+Sigma=5 tilt boundary are shown below. A tutorial that can help for
+writing the orientation files is given in :ref:`(Wicaksono2) <Wicaksono2>`
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential energy of atom interactions with the grain
+boundary driving force to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by these
+fixes. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator a fix is adding its forces. Default is the outermost level.
+
+This fix calculates a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the potential
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".
+
+This fix also calculates a per-atom array which can be accessed by
+various :doc:`output commands <Howto_output>`.  The array stores the
+order parameter Xi and normalized order parameter (0 to 1) for each
+atom.  The per-atom values can be accessed on any timestep.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix should only be used with fcc or bcc lattices.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Janssens:
+
+
+
+**(Janssens)** Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature
+Materials, 5, 124-127 (2006).
+
+.. _Wicaksono1:
+
+
+
+**(Wicaksono1)** Wicaksono, Sinclair, Militzer, Computational Materials
+Science, 117, 397-405 (2016).
+
+.. _Wicaksono2:
+
+
+
+**(Wicaksono2)** Wicaksono, figshare,
+https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015).
+
+
+----------
+
+
+For illustration purposes, here are example files that specify a
+Sigma=5 <100> tilt boundary.  This is for a lattice constant of 3.5706
+Angs.
+
+file0:
+
+
+.. parsed-literal::
+
+        0.798410432046075    1.785300000000000    1.596820864092150
+       -0.798410432046075    1.785300000000000   -1.596820864092150
+        2.395231296138225    0.000000000000000    0.798410432046075
+        0.798410432046075    0.000000000000000   -2.395231296138225
+        1.596820864092150    1.785300000000000   -0.798410432046075
+        1.596820864092150   -1.785300000000000   -0.798410432046075
+
+file1:
+
+
+.. parsed-literal::
+
+       -0.798410432046075    1.785300000000000    1.596820864092150
+        0.798410432046075    1.785300000000000   -1.596820864092150
+        0.798410432046075    0.000000000000000    2.395231296138225
+        2.395231296138225    0.000000000000000   -0.798410432046075
+        1.596820864092150    1.785300000000000    0.798410432046075
+        1.596820864092150   -1.785300000000000    0.798410432046075
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst
new file mode 100644
index 0000000000..ca71595664
--- /dev/null
+++ b/doc/src/fix_phonon.rst
@@ -0,0 +1,245 @@
+.. index:: fix phonon
+
+fix phonon command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* phonon = style name of this fix command
+* N = measure the Green's function every this many timesteps
+* Noutput = output the dynamical matrix every this many measurements
+* Nwait = wait this many timesteps before measuring
+* map\_file = *file* or *GAMMA*
+  
+  .. parsed-literal::
+  
+       *file* is the file that contains the mapping info between atom ID and the lattice indices.
+
+  
+  .. parsed-literal::
+  
+       *GAMMA* flags to treate the whole simulation box as a unit cell, so that the mapping
+       info can be generated internally. In this case, dynamical matrix at only the gamma-point
+       will/can be evaluated.
+
+* prefix = prefix for output files
+* one or none keyword/value pairs may be appended
+* keyword = *sysdim* or *nasr*
+  
+  .. parsed-literal::
+  
+       *sysdim* value = d
+         d = dimension of the system, usually the same as the MD model dimension
+       *nasr* value = n
+         n = number of iterations to enforce the acoustic sum rule
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1
+   fix 1 all phonon 20 5000 200000 map.in EAM3D
+   fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100
+
+Description
+"""""""""""
+
+Calculate the dynamical matrix from molecular dynamics simulations
+based on fluctuation-dissipation theory for a group of atoms.
+
+Consider a crystal with :math:`N` unit cells in three dimensions labeled
+:math:`l = (l_1, l_2, l_3)` where :math:`l_i` are integers.  Each unit cell is
+defined by three linearly independent vectors :math:`\mathbf{a}_1`,
+:math:`\mathbf{a}_2`, :math:`\mathbf{a}_3` forming a parallelepiped,
+containing :math:`K` basis atoms labeled :math:`k`.
+
+Based on fluctuation-dissipation theory, the force constant
+coefficients of the system in reciprocal space are given by
+(:ref:`Campana <Campana>` , :ref:`Kong <Kong>`)
+
+
+.. math::
+
+   \begin{equation}\mathbf{\Phi}_{k\alpha,k^\prime \beta}(\mathbf{q}) = k_B T \mathbf{G}^{-1}_{k\alpha,k^\prime \beta}(\mathbf{q})\end{equation}
+
+where :math:`\mathbf{G}` is the Green's functions coefficients given by
+
+
+.. math::
+
+   \begin{equation}\mathbf{G}_{k\alpha,k^\prime \beta}(\mathbf{q}) = \left< \mathbf{u}_{k\alpha}(\mathbf{q}) \bullet \mathbf{u}_{k^\prime \beta}^*(\mathbf{q}) \right>\end{equation}
+
+where :math:`\left< \ldots \right>` denotes the ensemble average, and
+
+
+.. math::
+
+   \begin{equation}\mathbf{u}_{k\alpha}(\mathbf{q}) = \sum_l \mathbf{u}_{l k \alpha} \exp{(i\mathbf{qr}_l)}\end{equation}
+
+is the :math:`\alpha` component of the atomic displacement for the :math:`k`
+th atom in the unit cell in reciprocal space at :math:`\mathbf{q}`. In
+practice, the Green's functions coefficients can also be measured
+according to the following formula,
+
+
+.. math::
+
+   \begin{equation}\mathbf{G}_{k\alpha,k^\prime \beta}(\mathbf{q}) =
+   \left< \mathbf{R}_{k \alpha}(\mathbf{q}) \bullet \mathbf{R}^*_{k^\prime \beta}(\mathbf{q}) \right>
+   - \left<\mathbf{R}\right>_{k \alpha}(\mathbf{q}) \bullet \left<\mathbf{R}\right>^*_{k^\prime \beta}(\mathbf{q})\end{equation}
+
+where :math:`\mathbf{R}` is the instantaneous positions of atoms, and
+:math:`\left<\mathbf{R}\right>` is the averaged atomic positions. It
+gives essentially the same results as the displacement method and is
+easier to implement in an MD code.
+
+Once the force constant matrix is known, the dynamical matrix
+:math:`\mathbf{D}` can then be obtained by
+
+
+.. math::
+
+   \begin{equation}\mathbf{D}_{k\alpha, k^\prime\beta}(\mathbf{q}) =
+   (m_k m_{k^\prime})^{-\frac{1}{2}} \mathbf{\Phi}_{k \alpha, k^\prime \beta}(\mathbf{q})\end{equation}
+
+whose eigenvalues are exactly the phonon frequencies at :math:`\mathbf{q}`.
+
+This fix uses positions of atoms in the specified group and calculates
+two-point correlations.  To achieve this. the positions of the atoms
+are examined every *Nevery* steps and are Fourier-transformed into
+reciprocal space, where the averaging process and correlation
+computation is then done.  After every *Noutput* measurements, the
+matrix :math:`\mathbf{G}(\mathbf{q})` is calculated and inverted to
+obtain the elastic stiffness coefficients.  The dynamical matrices are
+then constructed and written to *prefix*\ .bin.timestep files in binary
+format and to the file *prefix*\ .log for each wave-vector
+:math:`\mathbf{q}`.
+
+A detailed description of this method can be found in
+(:ref:`Kong2011 <Kong2011>`).
+
+The *sysdim* keyword is optional.  If specified with a value smaller
+than the dimensionality of the LAMMPS simulation, its value is used
+for the dynamical matrix calculation.  For example, using LAMMPS ot
+model a 2D or 3D system, the phonon dispersion of a 1D atomic chain
+can be computed using *sysdim* = 1.
+
+The *nasr* keyword is optional.  An iterative procedure is employed to
+enforce the acoustic sum rule on :math:`\Phi` at :math:`\Gamma`, and the number
+provided by keyword *nasr* gives the total number of iterations. For a
+system whose unit cell has only one atom, *nasr* = 1 is sufficient;
+for other systems, *nasr* = 10 is typically sufficient.
+
+The *map\_file* contains the mapping information between the lattice
+indices and the atom IDs, which tells the code which atom sits at
+which lattice point; the lattice indices start from 0. An auxiliary
+code, `latgen <http://code.google.com/p/latgen>`_, can be employed to
+generate the compatible map file for various crystals.
+
+In case one simulates a non-periodic system, where the whole simulation
+box is treated as a unit cell, one can set *map\_file* as *GAMMA*\ , so
+that the mapping info will be generated internally and a file is not
+needed. In this case, the dynamical matrix at only the gamma-point
+will/can be evaluated. Please keep in mind that fix-phonon is designed
+for cyrstals, it will be inefficient and even degrade the performance
+of lammps in case the unit cell is too large.
+
+The calculated dynamical matrix elements are written out in
+:doc:`energy/distance\^2/mass <units>` units.  The coordinates for *q*
+points in the log file is in the units of the basis vectors of the
+corresponding reciprocal lattice.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix. You can use it to change the temperature compute from thermo\_temp
+to the one that reflects the true temperature of atoms in the group.
+
+No global scalar or vector or per-atom quantities are stored by this
+fix for access by various :doc:`output commands <Howto_output>`.
+
+Instead, this fix outputs its initialization information (including
+mapping information) and the calculated dynamical matrices to the file
+*prefix*\ .log, with the specified *prefix*\ .  The dynamical matrices are
+also written to files *prefix*\ .bin.timestep in binary format.  These
+can be read by the post-processing tool in tools/phonon to compute the
+phonon density of states and/or phonon dispersion curves.
+
+No parameter of this fix can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix assumes a crystalline system with periodical lattice. The
+temperature of the system should not exceed the melting temperature to
+keep the system in its solid state.
+
+This fix is part of the USER-PHONON package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires LAMMPS be built with an FFT library.  See the :doc:`Build settings <Build_settings>` doc page for details.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute msd <compute_msd>`,
+:doc:`dynamical\_matrix <dynamical_matrix>`
+
+Default
+"""""""
+
+The option defaults are sysdim = the same dimension as specified by
+the :doc:`dimension <dimension>` command, and nasr = 20.
+
+
+----------
+
+
+.. _Campana:
+
+
+
+**(Campana)** C. Campana and
+M. H. Muser, *Practical Green's function approach to the
+simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <http://dx.doi.org/10.1103/PhysRevB.74.075420>`_
+
+.. _Kong:
+
+
+
+**(Kong)** L.T. Kong, G. Bartels, C. Campana,
+C. Denniston, and Martin H. Muser, *Implementation of Green's
+function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). <http://dx.doi.org/10.1016/j.cpc.2008.12.035>`_
+
+L.T. Kong, C. Denniston, and Martin H. Muser,
+*An improved version of the Green's function molecular dynamics
+method*\ , `Computer Physics Communications [182](2):540-541 (2011). <http://dx.doi.org/10.1016/j.cpc.2010.10.006>`_
+
+.. _Kong2011:
+
+
+
+**(Kong2011)** L.T. Kong, *Phonon dispersion measured directly from
+molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). <http://dx.doi.org/10.1016/j.cpc.2011.04.019>`_
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
new file mode 100644
index 0000000000..2639150bd4
--- /dev/null
+++ b/doc/src/fix_pimd.rst
@@ -0,0 +1,228 @@
+.. index:: fix pimd
+
+fix pimd command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID pimd keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* pimd = style name of this fix command
+* zero or more keyword/value pairs may be appended
+* keyword = *method* or *fmass* or *sp* or *temp* or *nhc*
+  
+  .. parsed-literal::
+  
+       *method* value = *pimd* or *nmpimd* or *cmd*
+       *fmass* value = scaling factor on mass
+       *sp* value = scaling factor on Planck constant
+       *temp* value = temperature (temperarate units)
+       *nhc* value = Nc = number of chains in Nose-Hoover thermostat
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
+
+Description
+"""""""""""
+
+This command performs quantum molecular dynamics simulations based on
+the Feynman path integral to include effects of tunneling and
+zero-point motion.  In this formalism, the isomorphism of a quantum
+partition function for the original system to a classical partition
+function for a ring-polymer system is exploited, to efficiently sample
+configurations from the canonical ensemble :ref:`(Feynman) <Feynman>`.
+The classical partition function and its components are given
+by the following equations:
+
+.. image:: Eqs/fix_pimd.jpg
+   :align: center
+
+The interested user is referred to any of the numerous references on
+this methodology, but briefly, each quantum particle in a path
+integral simulation is represented by a ring-polymer of P quasi-beads,
+labeled from 1 to P.  During the simulation, each quasi-bead interacts
+with beads on the other ring-polymers with the same imaginary time
+index (the second term in the effective potential above).  The
+quasi-beads also interact with the two neighboring quasi-beads through
+the spring potential in imaginary-time space (first term in effective
+potential).  To sample the canonical ensemble, a Nose-Hoover massive
+chain thermostat is applied :ref:`(Tuckerman) <pimd-Tuckerman>`.  With the
+massive chain algorithm, a chain of NH thermostats is coupled to each
+degree of freedom for each quasi-bead.  The keyword *temp* sets the
+target temperature for the system and the keyword *nhc* sets the
+number *Nc* of thermostats in each chain.  For example, for a
+simulation of N particles with P beads in each ring-polymer, the total
+number of NH thermostats would be 3 x N x P x Nc.
+
+.. note::
+
+   This fix implements a complete velocity-verlet integrator
+   combined with NH massive chain thermostat, so no other time
+   integration fix should be used.
+
+The *method* keyword determines what style of PIMD is performed.  A
+value of *pimd* is standard PIMD.  A value of *nmpimd* is for
+normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
+(CMD).  The difference between the styles is as follows.
+
+In standard PIMD, the value used for a bead's fictitious mass is
+arbitrary.  A common choice is to use Mi = m/P, which results in the
+mass of the entire ring-polymer being equal to the real quantum
+particle.  But it can be difficult to efficiently integrate the
+equations of motion for the stiff harmonic interactions in the ring
+polymers.
+
+A useful way to resolve this issue is to integrate the equations of
+motion in a normal mode representation, using Normal Mode
+Path-Integral Molecular Dynamics (NMPIMD) :ref:`(Cao1) <Cao1>`.  In NMPIMD,
+the NH chains are attached to each normal mode of the ring-polymer and
+the fictitious mass of each mode is chosen as Mk = the eigenvalue of
+the Kth normal mode for k > 0. The k = 0 mode, referred to as the
+zero-frequency mode or centroid, corresponds to overall translation of
+the ring-polymer and is assigned the mass of the real particle.
+
+Motion of the centroid can be effectively uncoupled from the other
+normal modes by scaling the fictitious masses to achieve a partial
+adiabatic separation.  This is called a Centroid Molecular Dynamics
+(CMD) approximation :ref:`(Cao2) <Cao2>`.  The time-evolution (and resulting
+dynamics) of the quantum particles can be used to obtain centroid time
+correlation functions, which can be further used to obtain the true
+quantum correlation function for the original system.  The CMD method
+also uses normal modes to evolve the system, except only the k > 0
+modes are thermostatted, not the centroid degrees of freedom.
+
+The keyword *fmass* sets a further scaling factor for the fictitious
+masses of beads, which can be used for the Partial Adiabatic CMD
+:ref:`(Hone) <Hone>`, or to be set as P, which results in the fictitious
+masses to be equal to the real particle masses.
+
+The keyword *sp* is a scaling factor on Planck's constant, which can
+be useful for debugging or other purposes.  The default value of 1.0
+is appropriate for most situations.
+
+The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
+as described in :ref:`(Calhoun) <Calhoun>`.  In LAMMPS this is done by using
+:doc:`multi-replica feature <Howto_replica>` in LAMMPS, where each
+quasi-particle system is stored and simulated on a separate partition
+of processors.  The following diagram illustrates this approach.  The
+original system with 2 ring polymers is shown in red.  Since each ring
+has 4 quasi-beads (imaginary time slices), there are 4 replicas of the
+system, each running on one of the 4 partitions of processors.  Each
+replica (shown in green) owns one quasi-bead in each ring.
+
+.. image:: JPG/pimd.jpg
+   :align: center
+
+To run a PIMD simulation with M quasi-beads in each ring polymer using
+N MPI tasks for each partition's domain-decomposition, you would use P
+= MxN processors (cores) and run the simulation as follows:
+
+
+.. parsed-literal::
+
+   mpirun -np P lmp_mpi -partition MxN -in script
+
+Note that in the LAMMPS input script for a multi-partition simulation,
+it is often very useful to define a :doc:`uloop-style variable <variable>` such as
+
+
+.. parsed-literal::
+
+   variable ibead uloop M pad
+
+where M is the number of quasi-beads (partitions) used in the
+calculation.  The uloop variable can then be used to manage I/O
+related tasks for each of the partitions, e.g.
+
+
+.. parsed-literal::
+
+   dump dcd all dcd 10 system_${ibead}.dcd
+   restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
+   read_restart system_${ibead}.restart2
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+A PIMD simulation can be initialized with a single data file read via
+the :doc:`read\_data <read_data>` command.  However, this means all
+quasi-beads in a ring polymer will have identical positions and
+velocities, resulting in identical trajectories for all quasi-beads.
+To avoid this, users can simply initialize velocities with different
+random number seeds assigned to each partition, as defined by the
+uloop variable, e.g.
+
+
+.. parsed-literal::
+
+   velocity all create 300.0 1234${ibead} rot yes dist gaussian
+
+Default
+"""""""
+
+The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0,
+and nhc = 2.
+
+
+----------
+
+
+.. _Feynman:
+
+
+
+**(Feynman)** R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and
+Path Integrals, McGraw-Hill, New York (1965).
+
+.. _pimd-Tuckerman:
+
+
+
+**(Tuckerman)** M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).
+
+.. _Cao1:
+
+
+
+**(Cao1)** J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
+
+.. _Cao2:
+
+
+
+**(Cao2)** J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994).
+
+.. _Hone:
+
+
+
+**(Hone)** T. Hone, P. Rossky, G. Voth, J Chem Phys, 124,
+154103 (2006).
+
+.. _Calhoun:
+
+
+
+**(Calhoun)** A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262,
+415 (1996).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst
new file mode 100644
index 0000000000..1cac0f8be8
--- /dev/null
+++ b/doc/src/fix_planeforce.rst
@@ -0,0 +1,62 @@
+.. index:: fix planeforce
+
+fix planeforce command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID planeforce x y z
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* planeforce = style name of this fix command
+* x y z = 3-vector that is normal to the plane
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix hold boundary planeforce 1.0 0.0 0.0
+
+Description
+"""""""""""
+
+Adjust the forces on each atom in the group so that only the
+components of force in the plane specified by the normal vector
+(x,y,z) remain.  This is done by subtracting out the component of
+force perpendicular to the plane.
+
+If the initial velocity of the atom is 0.0 (or in the plane), then it
+should continue to move in the plane thereafter.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix lineforce <fix_lineforce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst
new file mode 100644
index 0000000000..93a3ac0638
--- /dev/null
+++ b/doc/src/fix_plumed.rst
@@ -0,0 +1,142 @@
+.. index:: fix plumed
+
+fix plumed command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID plumed keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* plumed = style name of this fix command
+* keyword = *plumedfile* or *outfile*
+  
+  .. parsed-literal::
+  
+       *plumedfile* arg = name of PLUMED input file to use (default: NULL)
+       *outfile* arg = name of file on which to write the PLUMED log (default: NULL)
+
+
+
+Examples
+""""""""
+
+fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
+
+Description
+"""""""""""
+
+This fix instructs LAMMPS to call the `PLUMED <plumedhome_>`_ library, which
+allows one to perform various forms of trajectory analysis on the fly
+and to also use methods such as umbrella sampling and metadynamics to
+enhance the sampling of phase space.
+
+The documentation included here only describes the fix plumed command
+itself.  This command is LAMMPS specific, whereas most of the
+functionality implemented in PLUMED will work with a range of MD codes,
+and when PLUMED is used as a stand alone code for analysis.  The full
+`documentation for PLUMED <plumeddocs_>`_ is available online and included
+in the PLUMED source code.  The PLUMED library development is hosted at
+`https://github.com/plumed/plumed2 <https://github.com/plumed/plumed2>`_
+A detailed discussion of the code can be found in :ref:`(PLUMED) <PLUMED>`.
+
+There is an example input for using this package with LAMMPS in the
+examples/USER/plumed directory.
+
+
+----------
+
+
+The command to make LAMMPS call PLUMED during a run requires two keyword
+value pairs pointing to the PLUMED input file and an output file for the
+PLUMED log. The user must specify these arguments every time PLUMED is
+to be used.  Furthermore, the fix plumed command should appear in the
+LAMMPS input file **after** relevant input parameters (e.g. the timestep)
+have been set.
+
+The *group-ID* entry is ignored. LAMMPS will always pass all the atoms
+to PLUMED and there can only be one instance of the plumed fix at a
+time. The way the plumed fix is implemented ensures that the minimum
+amount of information required is communicated.  Furthermore, PLUMED
+supports multiple, completely independent collective variables, multiple
+independent biases and multiple independent forms of analysis.  There is
+thus really no restriction in functionality by only allowing only one
+plumed fix in the LAMMPS input.
+
+The *plumedfile* keyword allows the user to specify the name of the
+PLUMED input file.  Instructions as to what should be included in a
+plumed input file can be found in the `documentation for PLUMED <plumeddocs_>`_
+
+The *outfile* keyword allows the user to specify the name of a file in
+which to output the PLUMED log.  This log file normally just repeats the
+information that is contained in the input file to confirm it was
+correctly read and parsed.  The names of the files in which the results
+are stored from the various analysis options performed by PLUMED will
+be specified by the user in the PLUMED input file.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+When performing a restart of a calculation that involves PLUMED you must
+include a RESTART command in the PLUMED input file as detailed in the
+`PLUMED documentation <plumeddocs_>`_.  When the restart command is found in
+the PLUMED input PLUMED will append to the files that were generated in
+the run that was performed previously.  No part of the PLUMED restart
+data is included in the LAMMPS restart files.  Furthermore, any history
+dependent bias potentials that were accumulated in previous calculations
+will be read in when the RESTART command is included in the PLUMED
+input.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is not supported by
+this fix.
+
+Nothing is computed by this fix that can be accessed by any of the
+:doc:`output commands <Howto_output>` within LAMMPS.  All the quantities
+of interest can be output by commands that are native to PLUMED,
+however.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-PLUMED package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+There can only be one plumed fix active at a time.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix smd <fix_smd>`
+:doc:`fix colvars <fix_colvars>`
+
+Default
+"""""""
+
+The default options are plumedfile = NULL and outfile = NULL
+
+
+----------
+
+
+.. _PLUMED:
+
+
+
+**(PLUMED)** G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
+
+.. _plumeddocs: http://www.plumed.org/doc.html
+
+
+
+.. _plumedhome: http://www.plumed.org/
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst
new file mode 100644
index 0000000000..816568b537
--- /dev/null
+++ b/doc/src/fix_poems.rst
@@ -0,0 +1,159 @@
+.. index:: fix poems
+
+fix poems command
+=================
+
+Syntax:
+
+
+.. parsed-literal::
+
+   fix ID group-ID poems keyword values
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* poems = style name of this fix command
+* keyword = *group* or *file* or *molecule*
+  
+  .. parsed-literal::
+  
+       *group* values = list of group IDs
+       *molecule* values = none
+       *file* values = filename
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 fluid poems group clump1 clump2 clump3
+   fix 3 fluid poems file cluster.list
+
+Description
+"""""""""""
+
+Treats one or more sets of atoms as coupled rigid bodies.  This means
+that each timestep the total force and torque on each rigid body is
+computed and the coordinates and velocities of the atoms are updated
+so that the collection of bodies move as a coupled set.  This can be
+useful for treating a large biomolecule as a collection of connected,
+coarse-grained particles.
+
+The coupling, associated motion constraints, and time integration is
+performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS) <poems_>`_ which computes the
+constrained rigid-body motion of articulated (jointed) multibody
+systems :ref:`(Anderson) <Anderson>`.  POEMS was written and is distributed
+by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
+and other members of his group at Rensselaer Polytechnic Institute
+(RPI).  Rudranarayan developed the LAMMPS/POEMS interface.  For
+copyright information on POEMS and other details, please refer to the
+documents in the poems directory distributed with LAMMPS.
+
+.. _poems: http://www.rpi.edu/~anderk5/lab
+
+
+
+This fix updates the positions and velocities of the rigid atoms with
+a constant-energy time integration, so you should not update the same
+atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
+
+Each body must have a non-degenerate inertia tensor, which means if
+must contain at least 3 non-collinear atoms.  Which atoms are in which
+bodies can be defined via several options.
+
+For option *group*\ , each of the listed groups is treated as a rigid
+body.  Note that only atoms that are also in the fix group are
+included in each rigid body.
+
+For option *molecule*\ , each set of atoms in the group with a different
+molecule ID is treated as a rigid body.
+
+For option *file*\ , sets of atoms are read from the specified file and
+each set is treated as a rigid body.  Each line of the file specifies
+a rigid body in the following format:
+
+ID type atom1-ID atom2-ID atom3-ID ...
+
+ID as an integer from 1 to M (the number of rigid bodies).  Type is
+any integer; it is not used by the fix poems command.  The remaining
+arguments are IDs of atoms in the rigid body, each typically from 1 to
+N (the number of atoms in the system).  Only atoms that are also in
+the fix group are included in each rigid body.  Blank lines and lines
+that begin with '#' are skipped.
+
+A connection between a pair of rigid bodies is inferred if one atom is
+common to both bodies.  The POEMS solver treats that atom as a
+spherical joint with 3 degrees of freedom.  Currently, a collection of
+bodies can only be connected by joints as a linear chain.  The entire
+collection of rigid bodies can represent one or more chains.  Other
+connection topologies (tree, ring) are not allowed, but will be added
+later.  Note that if no joints exist, it is more efficient to use the
+:doc:`fix rigid <fix_rigid>` command to simulate the system.
+
+When the poems fix is defined, it will print out statistics on the
+total # of clusters, bodies, joints, atoms involved.  A cluster in
+this context means a set of rigid bodies connected by joints.
+
+For computational efficiency, you should turn off pairwise and bond
+interactions within each rigid body, as they no longer contribute to
+the motion.  The "neigh\_modify exclude" and "delete\_bonds" commands
+can be used to do this if each rigid body is a group.
+
+For computational efficiency, you should only define one fix poems
+which includes all the desired rigid bodies.  LAMMPS will allow
+multiple poems fixes to be defined, but it is more expensive.
+
+The degrees-of-freedom removed by coupled rigid bodies are accounted
+for in temperature and pressure computations.  Similarly, the rigid
+body contribution to the pressure virial is also accounted for.  The
+latter is only correct if forces within the bodies have been turned
+off, and there is only a single fix poems defined.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *bodyforces* option is supported by
+this fix style to set whether per-body forces and torques are computed
+early or late in a timestep, i.e. at the post-force stage or at the
+final-integrate stage, respectively.
+
+No global or per-atom quantities are stored by this fix for access by
+various :doc:`output commands <Howto_output>`.  No parameter of this fix
+can be used with the *start/stop* keywords of the :doc:`run <run>`
+command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the POEMS package.  It is only enabled if LAMMPS
+was built with that package, which also requires the POEMS library be
+built and linked with LAMMPS.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix rigid <fix_rigid>`, :doc:`delete\_bonds <delete_bonds>`,
+:doc:`neigh\_modify <neigh_modify>` exclude
+
+**Default:** none
+
+
+----------
+
+
+.. _Anderson:
+
+
+
+**(Anderson)** Anderson, Mukherjee, Critchley, Ziegler, and Lipton
+"POEMS: Parallelizable Open-source Efficient Multibody Software ",
+Engineering With Computers (2006). (`link to paper <http://dx.doi.org/10.1007/s00366-006-0026-x>`_)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst
new file mode 100644
index 0000000000..8deeb6e885
--- /dev/null
+++ b/doc/src/fix_pour.rst
@@ -0,0 +1,291 @@
+.. index:: fix pour
+
+fix pour command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID pour N type seed keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* pour = style name of this fix command
+* N = # of particles to insert
+* type = atom type to assign to inserted particles (offset for molecule insertion)
+* seed = random # seed (positive integer)
+* one or more keyword/value pairs may be appended to args
+* keyword = *region* or *diam* or *vol* or *rate* or *dens* or *vel* or *mol* or *rigid* or *shake* or *ignore*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region to use as insertion volume
+       *diam* values = dstyle args
+         dstyle = *one* or *range* or *poly*
+           *one* args = D
+             D = single diameter for inserted particles (distance units)
+           *range* args = Dlo Dhi
+             Dlo,Dhi = range of diameters for inserted particles (distance units)
+           *poly* args = Npoly D1 P1 D2 P2 ...
+             Npoly = # of (D,P) pairs
+             D1,D2,... = diameter for subset of inserted particles (distance units)
+             P1,P2,... = percentage of inserted particles with this diameter (0-1)
+       *id* values = idflag
+         idflag = *max* or *next* = how to choose IDs for inserted particles and molecules
+       *vol* values = fraction Nattempt
+         fraction = desired volume fraction for filling insertion volume
+         Nattempt = max # of insertion attempts per particle
+       *rate* value = V
+         V = z velocity (3d) or y velocity (2d) at which
+             insertion volume moves (velocity units)
+       *dens* values = Rholo Rhohi
+         Rholo,Rhohi = range of densities for inserted particles (mass/volume units)
+       *vel* values (3d) = vxlo vxhi vylo vyhi vz
+       *vel* values (2d) = vxlo vxhi vy
+         vxlo,vxhi = range of x velocities for inserted particles (velocity units)
+         vylo,vyhi = range of y velocities for inserted particles (velocity units)
+         vz = z velocity (3d) assigned to inserted particles (velocity units)
+         vy = y velocity (2d) assigned to inserted particles (velocity units)
+       *mol* value = template-ID
+         template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
+       *molfrac* values = f1 f2 ... fN
+         f1 to fN = relative probability of creating each of N molecules in template-ID
+       *rigid* value = fix-ID
+         fix-ID = ID of :doc:`fix rigid/small <fix_rigid>` command
+       *shake* value = fix-ID
+         fix-ID = ID of :doc:`fix shake <fix_shake>` command
+       *ignore* value = none
+         skip any line or triangle particles when detecting possible
+           overlaps with inserted particles
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 all pour 1000 2 29494 region myblock
+   fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1
+   fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6
+   fix ins all pour 500 1 4767548 vol 0.8 10 region slab mol object rigid myRigid
+
+Description
+"""""""""""
+
+Insert finite-size particles or molecules into the simulation box
+every few timesteps within a specified region until N particles or
+molecules have been inserted.  This is typically used to model the
+pouring of granular particles into a container under the influence of
+gravity.  For the remainder of this doc page, a single inserted atom
+or molecule is referred to as a "particle".
+
+If inserted particles are individual atoms, they are assigned the
+specified atom type.  If they are molecules, the type of each atom in
+the inserted molecule is specified in the file read by the
+:doc:`molecule <molecule>` command, and those values are added to the
+specified atom type.  E.g. if the file specifies atom types 1,2,3, and
+those are the atom types you want for inserted molecules, then specify
+*type* = 0.  If you specify *type* = 2, the in the inserted molecule
+will have atom types 3,4,5.
+
+All atoms in the inserted particle are assigned to two groups: the
+default group "all" and the group specified in the fix pour command
+(which can also be "all").
+
+This command must use the *region* keyword to define an insertion
+volume.  The specified region must have been previously defined with a
+:doc:`region <region>` command.  It must be of type *block* or a z-axis
+*cylinder* and must be defined with side = *in*\ .  The cylinder style
+of region can only be used with 3d simulations.
+
+Individual atoms are inserted, unless the *mol* keyword is used.  It
+specifies a *template-ID* previously defined using the
+:doc:`molecule <molecule>` command, which reads a file that defines the
+molecule.  The coordinates, atom types, center-of-mass, moments of
+inertia, etc, as well as any bond/angle/etc and special neighbor
+information for the molecule can be specified in the molecule file.
+See the :doc:`molecule <molecule>` command for details.  The only
+settings required to be in this file are the coordinates and types of
+atoms in the molecule.
+
+If the molecule template contains more than one molecule, the relative
+probability of depositing each molecule can be specified by the
+*molfrac* keyword.  N relative probabilities, each from 0.0 to 1.0, are
+specified, where N is the number of molecules in the template.  Each
+time a molecule is inserted, a random number is used to sample from
+the list of relative probabilities.  The N values must sum to 1.0.
+
+If you wish to insert molecules via the *mol* keyword, that will be
+treated as rigid bodies, use the *rigid* keyword, specifying as its
+value the ID of a separate :doc:`fix rigid/small <fix_rigid>`
+command which also appears in your input script.
+
+.. note::
+
+   If you wish the new rigid molecules (and other rigid molecules)
+   to be thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>`
+   or :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
+   "fix\_modify dynamic/dof yes" command for the rigid fix.  This is to
+   inform that fix that the molecule count will vary dynamically.
+
+If you wish to insert molecules via the *mol* keyword, that will have
+their bonds or angles constrained via SHAKE, use the *shake* keyword,
+specifying as its value the ID of a separate :doc:`fix shake <fix_shake>` command which also appears in your input script.
+
+Each timestep particles are inserted, they are placed randomly inside
+the insertion volume so as to mimic a stream of poured particles.  If
+they are molecules they are also oriented randomly.  Each atom in the
+particle is tested for overlaps with existing particles, including
+effects due to periodic boundary conditions if applicable.  If an
+overlap is detected, another random insertion attempt is made; see the
+*vol* keyword discussion below.  The larger the volume of the
+insertion region, the more particles that can be inserted at any one
+timestep.  Particles are inserted again after enough time has elapsed
+that the previously inserted particles fall out of the insertion
+volume under the influence of gravity.  Insertions continue every so
+many timesteps until the desired # of particles has been inserted.
+
+.. note::
+
+   If you are monitoring the temperature of a system where the
+   particle count is changing due to adding particles, you typically
+   should use the :doc:`compute\_modify dynamic yes <compute_modify>`
+   command for the temperature compute you are using.
+
+
+----------
+
+
+All other keywords are optional with defaults as shown below.
+
+The *diam* option is only used when inserting atoms and specifies the
+diameters of inserted particles.  There are 3 styles: *one*\ , *range*\ ,
+or *poly*\ .  For *one*\ , all particles will have diameter *D*\ .  For
+*range*\ , the diameter of each particle will be chosen randomly and
+uniformly between the specified *Dlo* and *Dhi* bounds.  For *poly*\ , a
+series of *Npoly* diameters is specified.  For each diameter a
+percentage value from 0.0 to 1.0 is also specified.  The *Npoly*
+percentages must sum to 1.0.  For the example shown above with "diam 2
+0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7
+or 1.5.  40% of the particles will be small; 60% will be large.
+
+Note that for molecule insertion, the diameters of individual atoms in
+the molecule can be specified in the file read by the
+:doc:`molecule <molecule>` command.  If not specified, the diameter of
+each atom in the molecule has a default diameter of 1.0.
+
+The *id* option has two settings which are used to determine the atom
+or molecule IDs to assign to inserted particles/molecules.  In both
+cases a check is done of the current system to find the maximum
+current atom and molecule ID of any existing particle.  Newly inserted
+particles and molecules are assigned IDs that increment those max
+values.  For the *max* setting, which is the default, this check is
+done at every insertion step, which allows for particles to leave the
+system, and their IDs to potentially be re-used.  For the *next*
+setting this check is done only once when the fix is specified, which
+can be more efficient if you are sure particles will not be added in
+some other way.
+
+The *vol* option specifies what volume fraction of the insertion
+volume will be filled with particles.  For particles with a size
+specified by the *diam range* keyword, they are assumed to all be of
+maximum diameter *Dhi* for purposes of computing their contribution to
+the volume fraction.
+
+The higher the volume fraction value, the more particles are inserted
+each timestep.  Since inserted particles cannot overlap, the maximum
+volume fraction should be no higher than about 0.6.  Each timestep
+particles are inserted, LAMMPS will make up to a total of M tries to
+insert the new particles without overlaps, where M = # of inserted
+particles \* Nattempt.  If LAMMPS is unsuccessful at completing all
+insertions, it prints a warning.
+
+The *dens* and *vel* options enable inserted particles to have a range
+of densities or xy velocities.  The specific values for a particular
+inserted particle will be chosen randomly and uniformly between the
+specified bounds.  Internally, the density value for a particle is
+converted to a mass, based on the radius (volume) of the particle.
+The *vz* or *vy* value for option *vel* assigns a z-velocity (3d) or
+y-velocity (2d) to each inserted particle.
+
+The *rate* option moves the insertion volume in the z direction (3d)
+or y direction (2d).  This enables pouring particles from a
+successively higher height over time.
+
+The *ignore* option is useful when running a simulation that used line
+segment (2d) or triangle (3d) particles, typically to define
+boundaries for spherical granular particles to interact with.  See the
+:doc:`atom\_style line or tri <atom_style>` command for details.  Lines
+and triangles store their size, and if the size is large it may
+overlap (in a spherical sense) with the insertion region, even if the
+line/triangle is oriented such that there is no actual overlap.  This
+can prevent particles from being inserted.  The *ignore* keyword
+causes the overlap check to skip any line or triangle particles.
+Obviously you should only use it if there is in fact no overlap of the
+line or triangle particles with the insertion region.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  This means you must be careful when restarting a
+pouring simulation, when the restart file was written in the middle of
+the pouring operation.  Specifically, you should use a new fix pour
+command in the input script for the restarted simulation that
+continues the operation.  You will need to adjust the arguments of the
+original fix pour command to do this.
+
+Also note that because the state of the random number generator is not
+saved in restart files, you cannot do "exact" restarts with this fix,
+where the simulation continues on the same as if no restart had taken
+place.  However, in a statistical sense, a restarted simulation should
+produce the same behavior if you adjust the fix pour parameters
+appropriately.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the GRANULAR package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+For 3d simulations, a gravity fix in the -z direction must be defined
+for use in conjunction with this fix.  For 2d simulations, gravity
+must be defined in the -y direction.
+
+The specified insertion region cannot be a "dynamic" region, as
+defined by the :doc:`region <region>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix deposit <fix_deposit>`, :doc:`fix gravity <fix_gravity>`,
+:doc:`region <region>`
+
+Default
+"""""""
+
+Insertions are performed for individual particles, i.e. no *mol*
+setting is defined.  If the *mol* keyword is used, the default for
+*molfrac* is an equal probabilities for all molecules in the template.
+Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol =
+0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0 (for 3d), vel = 0.0 0.0 0.0
+(for 2d), and id = max.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst
new file mode 100644
index 0000000000..2c84eaa304
--- /dev/null
+++ b/doc/src/fix_precession_spin.rst
@@ -0,0 +1,185 @@
+.. index:: fix precession/spin
+
+fix precession/spin command
+===========================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   fix ID group precession/spin style args
+
+* ID, group are documented in :doc:`fix <fix>` command
+* precession/spin = style name of this fix command
+* style = *zeeman* or *anisotropy* or *cubic*
+  
+  .. parsed-literal::
+  
+       *zeeman* args = H x y z
+         H = intensity of the magnetic field (in Tesla)
+         x y z = vector direction of the field
+       *anisotropy* args = K x y z
+         K = intensity of the magnetic anisotropy (in eV)
+         x y z = vector direction of the anisotropy
+
+  
+  .. parsed-literal::
+  
+       *cubic* args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z
+         K1 and K2c = intensity of the magnetic anisotropy (in eV)
+         n1x to n3z = three direction vectors of the cubic anisotropy
+
+
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
+   fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
+   fix 1 iron precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+   fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0
+
+Description
+"""""""""""
+
+This fix applies a precession torque to each magnetic spin in the group.
+
+Style *zeeman* is used for the simulation of the interaction
+between the magnetic spins in the defined group and an external
+magnetic field:
+
+.. math::
+
+   H_{Zeeman} = -g \sum_{i=0}^{N}\mu_{i}\, \vec{s}_{i} \cdot\vec{B}_{ext}
+
+with:
+
+* :math:`\vec{B}_{ext}` the external magnetic field (in T)
+* :math:`g` the Lande factor (hard-coded as :math:`g=2.0`)
+* :math:`\vec{s}_i` the unitary vector describing the orientation of spin :math:`i`
+* :math:`\mu_i` the atomic moment of spin :math:`i` given as a multiple of the
+  Bohr magneton :math:`\mu_B` (for example, :math:`\mu_i \approx 2.2` in bulk iron).
+
+
+The field value in Tesla is multiplied by the gyromagnetic
+ratio, :math:`g \cdot \mu_B/\hbar`, converting it into a precession frequency in
+rad.THz (in metal units and with :math:`\mu_B = 5.788 eV/T`).
+
+As a comparison, the figure below displays the simulation of a
+single spin (of norm :math:`\mu_i = 1.0`) submitted to an external
+magnetic field of :math:`\vert B_{ext}\vert = 10.0\; \mathrm{Tesla}` (and oriented along the z
+axis). 
+The upper plot shows the average magnetization along the
+external magnetic field axis and the lower plot the Zeeman
+energy, both as a function of temperature.
+The reference result is provided by the plot of the Langevin 
+function for the same parameters.
+
+.. image:: JPG/zeeman_langevin.jpg
+   :align: center
+
+The temperature effects are accounted for by connecting the spin
+:math:`i` to a thermal bath using a Langevin thermostat (see
+:doc:`fix\_langevin\_spin <fix_langevin_spin>` for the definition of 
+this thermostat).
+
+Style *anisotropy* is used to simulate an easy axis or an easy plane
+for the magnetic spins in the defined group:
+
+.. math::
+
+   H_{aniso}  = -\sum_{{ i}=1}^{N} K_{an}(\mathbf{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2
+
+with :math:`n` defining the direction of the anisotropy, and :math:`K` (in eV) its intensity.
+If :math:`K > 0`, an easy axis is defined, and if :math:`K < 0`, an easy plane is defined.
+
+Style *cubic* is used to simulate a cubic anisotropy, with three
+possible easy axis for the magnetic spins in the defined group:
+
+.. math::
+
+   H_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
+   \Big[
+   \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2 +
+   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2 +
+   \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2 \Big]
+   +K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2
+
+with :math:`K_1` and :math:`K_{2c}` (in eV) the intensity coefficients and
+:math:`\vec{n}_1`, :math:`\vec{n}_2` and :math:`\vec{n}_3` defining the three anisotropic directions
+defined by the command (from *n1x* to *n3z*).
+For :math:`\vec{n}_1 = (1 0 0)`, :math:`\vec{n}_2 = (0 1 0)`, and :math:`\vec{n}_3 = (0 0 1)`, :math:`K_1 < 0` defines an
+iron type anisotropy (easy axis along the :math:`(0 0 1)`-type cube
+edges), and :math:`K_1 > 0` defines a nickel type anisotropy (easy axis
+along the :math:`(1 1 1)`-type cube diagonals).
+:math:`K_2^c > 0` also defines easy axis along the :math:`(1 1 1)`-type cube
+diagonals.
+See chapter 2 of :ref:`(Skomski) <Skomski1>` for more details on cubic
+anisotropies.
+
+In all cases, the choice of :math:`(x y z)` only imposes the vector
+directions for the forces. Only the direction of the vector is
+important; its length is ignored (the entered vectors are
+normalized).
+
+Those styles can be combined within one single command line.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+By default, the energy associated to this fix is not added to the potential
+energy of the system.
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this fix
+to add this magnetic potential energy to the potential energy of the system,
+
+
+.. code-block:: LAMMPS
+
+   fix             1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+   fix_modify      1 energy yes
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+Restrictions
+""""""""""""
+
+
+The *precession/spin* style is part of the SPIN package.  This style
+is only enabled if LAMMPS was built with this package, and if the
+atom\_style "spin" was declared.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style spin <atom_style>`
+
+**Default:**
+
+none
+
+
+----------
+
+
+.. _Skomski1:
+
+
+
+**(Skomski)** Skomski, R. (2008). Simple models of magnetism.
+Oxford University Press.
diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt
deleted file mode 100644
index 708b2bd7aa..0000000000
--- a/doc/src/fix_precession_spin.txt
+++ /dev/null
@@ -1,116 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix precession/spin command :h3
-
-[Syntax:]
-
-fix ID group precession/spin style args :pre
-
-ID, group are documented in "fix"_fix.html command :ulb,l
-precession/spin = style name of this fix command :l
-style = {zeeman} or {anisotropy} or {cubic} :l
-  {zeeman} args = H x y z
-    H = intensity of the magnetic field (in Tesla)
-    x y z = vector direction of the field
-  {anisotropy} args = K x y z
-    K = intensity of the magnetic anisotropy (in eV)
-    x y z = vector direction of the anisotropy :pre
-  {cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z 
-    K1 and K2c = intensity of the magnetic anisotropy (in eV)
-    n1x to n3z = three direction vectors of the cubic anisotropy :pre
-:ule
-
-[Examples:]
-
-fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
-fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
-fix 1 iron precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
-fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre
-
-[Description:]
-
-This fix applies a precession torque to each magnetic spin in the group.
-
-Style {zeeman} is used for the simulation of the interaction
-between the magnetic spins in the defined group and an external
-magnetic field:
-
-:c,image(Eqs/force_spin_zeeman.jpg)
-
-with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T
-in metal units).
-
-Style {anisotropy} is used to simulate an easy axis or an easy plane
-for the magnetic spins in the defined group:
-
-:c,image(Eqs/force_spin_aniso.jpg)
-
-with n defining the direction of the anisotropy, and K (in eV) its intensity.
-If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
-
-Style {cubic} is used to simulate a cubic anisotropy, with three
-possible easy axis for the magnetic spins in the defined group: 
-
-:c,image(Eqs/fix_spin_cubic.jpg)
-
-with K1 and K2c (in eV) the intensity coefficients and 
-n1, n2 and n3 defining the three anisotropic directions
-defined by the command (from n1x to n3z). 
-For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an 
-iron type anisotropy (easy axis along the (001)-type cube
-edges), and K1 > 0 defines a nickel type anisotropy (easy axis
-along the (111)-type cube diagonals). 
-K2^c > 0 also defines easy axis along the (111)-type cube
-diagonals.
-See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic
-anisotropies.
-
-In all cases, the choice of (x y z) only imposes the vector
-directions for the forces. Only the direction of the vector is 
-important; it's length is ignored (the entered vectors are
-normalized).
-
-Those styles can be combined within one single command line.
-
-:line
-
-[Restart, fix_modify, output, run start/stop, minimize info:]
-
-By default, the energy associated to this fix is not added to the potential
-energy of the system.
-The "fix_modify"_fix_modify.html {energy} option is supported by this fix
-to add this magnetic potential energy to the potential energy of the system,
-
-fix             1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix_modify      1 energy yes :pre
-
-This fix computes a global scalar which can be accessed by various
-"output commands"_Howto_output.html.
-
-No information about this fix is written to "binary restart
-files"_restart.html.
-
-[Restrictions:]
-
-The {precession/spin} style is part of the SPIN package.  This style
-is only enabled if LAMMPS was built with this package, and if the
-atom_style "spin" was declared.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"atom_style spin"_atom_style.html
-
-[Default:] none
-
-:line
-
-:link(Skomski1)
-[(Skomski)] Skomski, R. (2008). Simple models of magnetism.
-Oxford University Press.
diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst
new file mode 100644
index 0000000000..4237d06228
--- /dev/null
+++ b/doc/src/fix_press_berendsen.rst
@@ -0,0 +1,262 @@
+.. index:: fix press/berendsen
+
+fix press/berendsen command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID press/berendsen keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* press/berendsen = style name of this fix command
+  
+  .. parsed-literal::
+  
+     one or more keyword value pairs may be appended
+     keyword = *iso* or *aniso* or *x* or *y* or *z* or *couple* or *dilate* or *modulus*
+       *iso* or *aniso* values = Pstart Pstop Pdamp
+         Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+         Pdamp = pressure damping parameter (time units)
+       *x* or *y* or *z* values = Pstart Pstop Pdamp
+         Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+         Pdamp = stress damping parameter (time units)
+       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *modulus* value = bulk modulus of system (pressure units)
+       *dilate* value = *all* or *partial*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all press/berendsen iso 0.0 0.0 1000.0
+   fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial
+
+Description
+"""""""""""
+
+Reset the pressure of the system by using a Berendsen barostat
+:ref:`(Berendsen) <Berendsen1>`, which rescales the system volume and
+(optionally) the atoms coordinates within the simulation box every
+timestep.
+
+Regardless of what atoms are in the fix group, a global pressure is
+computed for all atoms.  Similarly, when the size of the simulation
+box is changed, all atoms are re-scaled to new positions, unless the
+keyword *dilate* is specified with a value of *partial*\ , in which case
+only the atoms in the fix group are re-scaled.  The latter can be
+useful for leaving the coordinates of atoms in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+
+.. note::
+
+   Unlike the :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>`
+   commands which perform Nose/Hoover barostatting AND time integration,
+   this fix does NOT perform time integration.  It only modifies the box
+   size and atom coordinates to effect barostatting.  Thus you must use a
+   separate time integration fix, like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` to actually update the positions and velocities of
+   atoms.  This fix can be used in conjunction with thermostatting fixes
+   to control the temperature, such as :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` or :doc:`fix temp/berendsen <fix_temp_berendsen>`.
+
+See the :doc:`Howto baroostat <Howto_barostat>` doc page for a
+discussion of different ways to perform barostatting.
+
+
+----------
+
+
+The barostat is specified using one or more of the *iso*\ , *aniso*\ ,
+*x*\ , *y*\ , *z*\ , and *couple* keywords.  These keywords give you the
+ability to specify the 3 diagonal components of an external stress
+tensor, and to couple various of these components together so that the
+dimensions they represent are varied together during a
+constant-pressure simulation.  Unlike the :doc:`fix npt <fix_nh>` and
+:doc:`fix nph <fix_nh>` commands, this fix cannot be used with triclinic
+(non-orthogonal) simulation boxes to control all 6 components of the
+general pressure tensor.
+
+The target pressures for each of the 3 diagonal components of the
+stress tensor can be specified independently via the *x*\ , *y*\ , *z*\ ,
+keywords, which correspond to the 3 simulation box dimensions.  For
+each component, the external pressure or tensor component at each
+timestep is a ramped value during the run from *Pstart* to *Pstop*\ .
+If a target pressure is specified for a component, then the
+corresponding box dimension will change during a simulation.  For
+example, if the *y* keyword is used, the y-box length will change.  A
+box dimension will not change if that component is not specified,
+although you have the option to change that dimension via the :doc:`fix deform <fix_deform>` command.
+
+For all barostat keywords, the *Pdamp* parameter determines the time
+scale on which pressure is relaxed.  For example, a value of 10.0
+means to relax the pressure in a timespan of (roughly) 10 time units
+(tau or fmsec or psec - see the :doc:`units <units>` command).
+
+.. note::
+
+   A Berendsen barostat will not work well for arbitrary values of
+   *Pdamp*\ .  If *Pdamp* is too small, the pressure and volume can
+   fluctuate wildly; if it is too large, the pressure will take a very
+   long time to equilibrate.  A good choice for many models is a *Pdamp*
+   of around 1000 timesteps.  However, note that *Pdamp* is specified in
+   time units, and that timesteps are NOT the same as time units for most
+   :doc:`units <units>` settings.
+
+.. note::
+
+   The relaxation time is actually also a function of the bulk
+   modulus of the system (inverse of isothermal compressibility).  The
+   bulk modulus has units of pressure and is the amount of pressure that
+   would need to be applied (isotropically) to reduce the volume of the
+   system by a factor of 2 (assuming the bulk modulus was a constant,
+   independent of density, which it's not).  The bulk modulus can be set
+   via the keyword *modulus*\ .  The *Pdamp* parameter is effectively
+   multiplied by the bulk modulus, so if the pressure is relaxing faster
+   than expected or desired, increasing the bulk modulus has the same
+   effect as increasing *Pdamp*\ .  The converse is also true.  LAMMPS does
+   not attempt to guess a correct value of the bulk modulus; it just uses
+   10.0 as a default value which gives reasonable relaxation for a
+   Lennard-Jones liquid, but will be way off for other materials and way
+   too small for solids.  Thus you should experiment to find appropriate
+   values of *Pdamp* and/or the *modulus* when using this fix.
+
+
+----------
+
+
+The *couple* keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together.  The value specified
+with the keyword determines which are coupled.  For example, *xz*
+means the *Pxx* and *Pzz* components of the stress tensor are coupled.
+*Xyz* means all 3 diagonal components are coupled.  Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep.  The
+*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must
+be identical.  *Couple xyz* can be used for a 2d simulation; the *z*
+dimension is simply ignored.
+
+
+----------
+
+
+The *iso* and *aniso* keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+
+The keyword *iso* means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together.  Using "iso Pstart Pstop Pdamp" is the same as
+specifying these 4 keywords:
+
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   couple xyz
+
+The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled
+independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure.  Using "aniso Pstart Pstop Pdamp" is the same as specifying
+these 4 keywords:
+
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   couple none
+
+
+----------
+
+
+This fix computes a temperature and pressure each timestep.  To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if these commands had been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp
+   compute fix-ID_press group-ID pressure fix-ID_temp
+
+See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID
++ underscore + "press", and the group for the new computes is the same
+as the fix group.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*
+and *thermo\_press*.  This means you can change the attributes of this
+fix's temperature or pressure via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+or pressure during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* or
+*thermo\_press* will have no effect on this fix.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by this fix.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its temperature and pressure calculations.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+No global or per-atom quantities are stored by this fix for access by
+various :doc:`output commands <Howto_output>`.
+
+This fix can ramp its target pressure over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+Any dimension being adjusted by this fix must be periodic.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`,
+:doc:`fix\_modify <fix_modify>`
+
+Default
+"""""""
+
+The keyword defaults are dilate = all, modulus = 10.0 in units of
+pressure for whatever :doc:`units <units>` are defined.
+
+
+----------
+
+
+.. _Berendsen1:
+
+
+
+**(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
+Phys, 81, 3684 (1984).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst
new file mode 100644
index 0000000000..865d3d9741
--- /dev/null
+++ b/doc/src/fix_print.rst
@@ -0,0 +1,124 @@
+.. index:: fix print
+
+fix print command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID print N string keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* print = style name of this fix command
+* N = print every N steps; N can be a variable (see below)
+* string = text string to print with optional variable names
+* zero or more keyword/value pairs may be appended
+* keyword = *file* or *append* or *screen* or *title*
+  
+  .. parsed-literal::
+  
+       *file* value = filename
+       *append* value = filename
+       *screen* value = *yes* or *no*
+       *title* value = string
+         string =  text to print as 1st line of output file
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix extra all print 100 "Coords of marker atom = $x $y $z"
+   fix extra all print 100 "Coords of marker atom = $x $y $z" file coord.txt
+
+Description
+"""""""""""
+
+Print a text string every N steps during a simulation run.  This can
+be used for diagnostic purposes or as a debugging tool to monitor some
+quantity during a run.  The text string must be a single argument, so
+it should be enclosed in double quotes if it is more than one word.
+If it contains variables it must be enclosed in double quotes to
+insure they are not evaluated when the input script line is read, but
+will instead be evaluated each time the string is printed.
+
+Instead of a numeric value, N can be specified as an :doc:`equal-style variable <variable>`, which should be specified as v\_name, where
+name is the variable name.  In this case, the variable is evaluated at
+the beginning of a run to determine the **next** timestep at which the
+string will be written out.  On that timestep, the variable will be
+evaluated again to determine the next timestep, etc.
+Thus the variable should return timestep values.  See the stagger()
+and logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
+this context. For example, the following commands will print output at
+timesteps 10,20,30,100,200,300,1000,2000,etc:
+
+
+.. parsed-literal::
+
+   variable        s equal logfreq(10,3,10)
+   fix extra all print v_s "Coords of marker atom = $x $y $z"
+
+The specified group-ID is ignored by this fix.
+
+See the :doc:`variable <variable>` command for a description of *equal*
+style variables which are the most useful ones to use with the fix
+print command, since they are evaluated afresh each timestep that the
+fix print line is output.  Equal-style variables calculate formulas
+involving mathematical operations, atom properties, group properties,
+thermodynamic properties, global values calculated by a
+:doc:`compute <compute>` or :doc:`fix <fix>`, or references to other
+:doc:`variables <variable>`.
+
+If the *file* or *append* keyword is used, a filename is specified to
+which the output generated by this fix will be written.  If *file* is
+used, then the filename is overwritten if it already exists.  If
+*append* is used, then the filename is appended to if it already
+exists, or created if it does not exist.
+
+If the *screen* keyword is used, output by this fix to the screen and
+logfile can be turned on or off as desired.
+
+The *title* keyword allow specification of the string that will be
+printed as the first line of the output file, assuming the *file*
+keyword was used.  By default, the title line is as follows:
+
+
+.. parsed-literal::
+
+   # Fix print output for fix ID
+
+where ID is replaced with the fix-ID.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`variable <variable>`, :doc:`print <print>`
+
+Default
+"""""""
+
+The option defaults are no file output, screen = yes, and title string
+as described above.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst
new file mode 100644
index 0000000000..645bc13452
--- /dev/null
+++ b/doc/src/fix_property_atom.rst
@@ -0,0 +1,343 @@
+.. index:: fix property/atom
+
+fix property/atom command
+=========================
+
+fix property/atom/kk command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID property/atom vec1 vec2 ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* property/atom = style name of this fix command
+* vec1,vec2,... = *mol* or *q* or *rmass* or *i\_name* or *d\_name*
+  
+  .. parsed-literal::
+  
+       *mol* = molecule IDs
+       *q* = charge
+       *rmass* = per-atom mass
+       *i_name* = new integer vector referenced by name
+       *d_name* = new floating-point vector referenced by name
+
+* zero of more keyword/value pairs may be appended
+* keyword = *ghost*
+  
+  .. parsed-literal::
+  
+       *ghost* value = *no* or *yes* for whether ghost atom info in communicated
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all property/atom mol
+   fix 1 all property/atom i_myflag1 i_myflag2
+   fix 1 all property/atom d_sx d_sy d_sz
+
+Description
+"""""""""""
+
+Create one or more additional per-atom vectors to store information
+about atoms and to use during a simulation.  The specified *group-ID*
+is ignored by this fix.
+
+The atom style used for a simulation defines a set of per-atom
+properties, as explained on the :doc:`atom\_style <atom_style>` and
+:doc:`read\_data <read_data>` doc pages.  The latter command allows these
+properties to be defined for each atom in the system when a data file
+is read.  This fix will augment the set of properties with new custom
+ones. This can be useful in several scenarios.
+
+If the atom style does not define molecule IDs, per-atom charge,
+or per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
+keywords.  This can be useful, e.g, to define "molecules" to use as
+rigid bodies with the :doc:`fix rigid <fix_rigid>` command, or just to
+carry around an extra flag with the atoms (stored as a molecule ID)
+that can be used to group atoms without having to use the group
+command (which is limited to a total of 32 groups including *all*\ ).
+
+Another application would be to use the *rmass* flag in order to have
+per-atom masses instead of per-type masses, for example this can be
+useful to study isotope effects with partial isotope substitution.
+Please :ref:`see below <isotopes>` for an example of simulating a mixture
+of light and heavy water with the TIP4P water potential.
+
+An alternative to using fix *property/atom* in these ways is to
+use an atom style that does define molecule IDs or charge or per-atom
+mass (indirectly via diameter and density) or to use a hybrid atom
+style that combines two or more atom styles
+to provide the union of all atom properties. However, this has two
+practical drawbacks:  first, it typically necessitates changing the
+format of the data file, which can be tedious for large systems;
+and second, it may define additional properties that are not needed
+such as bond lists, which has some overhead when there are no bonds.
+
+In the future, we may add additional per-atom properties similar to
+*mol*\ , *q* or *rmass*\ , which "turn-on" specific properties defined
+by some atom styles, so they can be used by atom styles that do not
+define them.
+
+More generally, the *i\_name* and *d\_name* vectors allow one or more
+new custom per-atom properties to be defined.  Each name must be
+unique and can use alphanumeric or underscore characters.  These
+vectors can store whatever values you decide are useful in your
+simulation.  As explained below there are several ways to initialize
+and access and output these values, both via input script commands and
+in new code that you add to LAMMPS.
+
+This is effectively a simple way to add per-atom properties to a model
+without needing to write code for a new :doc:`atom style <atom_style>`
+that defines the properties.  Note however that implementing a new
+atom style allows new atom properties to be more tightly and
+seamlessly integrated with the rest of the code.
+
+The new atom properties encode values that migrate with atoms to new
+processors and are written to restart files.  If you want the new
+properties to also be defined for ghost atoms, then use the *ghost*
+keyword with a value of *yes*\ .  This will invoke extra communication
+when ghost atoms are created (at every re-neighboring) to insure the
+new properties are also defined for the ghost atoms.
+
+.. note::
+
+   If you use this command with the *mol*\ , *q* or *rmass* vectors,
+   then you most likely want to set *ghost* yes, since these properties
+   are stored with ghost atoms if you use an :doc:`atom\_style <atom_style>`
+   that defines them, and many LAMMPS operations that use molecule IDs or
+   charge, such as neighbor lists and pair styles, will expect ghost
+   atoms to have these values.  LAMMPS will issue a warning it you define
+   those vectors but do not set *ghost* yes.
+
+.. note::
+
+   The properties for ghost atoms are not updated every timestep,
+   but only once every few steps when neighbor lists are re-built.  Thus
+   the *ghost* keyword is suitable for static properties, like molecule
+   IDs, but not for dynamic properties that change every step.  For the
+   latter, the code you add to LAMMPS to change the properties will also
+   need to communicate their new values to/from ghost atoms, an operation
+   that can be invoked from within a :doc:`pair style <pair_style>` or
+   :doc:`fix <fix>` or :doc:`compute <compute>` that you write.
+
+.. note::
+
+   If this fix is defined **after** the simulation box is created,
+   a 'run 0' command should be issued to properly initialize the storage
+   created by this fix.
+
+
+----------
+
+
+This fix is one of a small number that can be defined in an input
+script before the simulation box is created or atoms are defined.
+This is so it can be used with the :doc:`read\_data <read_data>` command
+as described below.
+
+Per-atom properties that are defined by the :doc:`atom style <atom_style>` are initialized when atoms are created, e.g. by
+the :doc:`read\_data <read_data>` or :doc:`create\_atoms <create_atoms>`
+commands.  The per-atom properties defined by this fix are not.  So
+you need to initialize them explicitly.  This can be done by the
+:doc:`read\_data <read_data>` command, using its *fix* keyword and
+passing it the fix-ID of this fix.
+
+Thus these commands:
+
+
+.. parsed-literal::
+
+   fix prop all property/atom mol d_flag
+   read_data data.txt fix prop NULL Molecules
+
+would allow a data file to have a section like this:
+
+
+.. parsed-literal::
+
+   Molecules
+
+   1 4 1.5
+   2 4 3.0
+   3 10 1.0
+   4 10 1.0
+   5 10 1.0
+   ...
+   N 763 4.5
+
+where N is the number of atoms, and the first field on each line is
+the atom-ID, followed by a molecule-ID and a floating point value that
+will be stored in a new property called "flag".  Note that the list of
+per-atom properties can be in any order.
+
+Another way of initializing the new properties is via the
+:doc:`set <set>` command.  For example, if you wanted molecules
+defined for every set of 10 atoms, based on their atom-IDs,
+these commands could be used:
+
+
+.. parsed-literal::
+
+   fix prop all property/atom mol
+   variable cluster atom ((id-1)/10)+1
+   set atom \* mol v_cluster
+
+The :doc:`atom-style variable <variable>` will create values for atoms
+with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9.  When the
+:doc:`set <set>` commands assigns them to the molecule ID for each atom,
+they will be truncated to an integer value, so atoms 31-40 will all be
+assigned a molecule ID of 4.
+
+Note that :doc:`atomfile-style variables <variable>` can also be used in
+place of atom-style variables, which means in this case that the
+molecule IDs could be read-in from a separate file and assigned by the
+:doc:`set <set>` command.  This allows you to initialize new per-atom
+properties in a completely general fashion.
+
+
+----------
+
+
+For new atom properties specified as *i\_name* or *d\_name*, the
+:doc:`compute property/atom <compute_property_atom>` command can access
+their values.  This means that the values can be output via the :doc:`dump custom <dump>` command, accessed by fixes like :doc:`fix ave/atom <fix_ave_atom>`, accessed by other computes like :doc:`compute reduce <compute_reduce>`, or used in :doc:`atom-style variables <variable>`.
+
+For example, these commands will output two new properties to a custom
+dump file:
+
+
+.. parsed-literal::
+
+   fix prop all property/atom i_flag1 d_flag2
+   compute 1 all property/atom i_flag1 d_flag2
+   dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
+
+
+----------
+
+
+If you wish to add new :doc:`pair styles <pair_style>`,
+:doc:`fixes <fix>`, or :doc:`computes <compute>` that use the per-atom
+properties defined by this fix, see the :doc:`Modify atom <Modify_atom>`
+doc page which has details on how the properties can be accessed from
+added classes.
+
+
+----------
+
+
+.. _isotopes:
+
+
+
+Example for using per-atom masses with TIP4P water to
+study isotope effects. When setting up simulations with the :doc:`TIP4P pair styles <Howto_tip4p>` for water, you have to provide exactly
+one atom type each to identify the water oxygen and hydrogen
+atoms. Since the atom mass is normally tied to the atom type, this
+makes it impossible to study multiple isotopes in the same simulation.
+With *fix property/atom rmass* however, the per-type masses are
+replaced by per-atom masses. Asumming you have a working input deck
+for regular TIP4P water, where water oxygen is atom type 1 and water
+hydrogen is atom type 2, the following lines of input script convert
+this to using per-atom masses:
+
+
+.. parsed-literal::
+
+   fix Isotopes all property/atom rmass ghost yes
+   set type 1 mass 15.9994
+   set type 2 mass 1.008
+
+When writing out the system data with the :doc:`write\_data <write_data>`
+command, there will be a new section named with the fix-ID
+(i.e. *Isotopes* in this case). Alternatively, you can take an
+existing data file and just add this *Isotopes* section with
+one line per atom containing atom-ID and mass. Either way, the
+extended data file can be read back with:
+
+
+.. parsed-literal::
+
+   fix Isotopes all property/atom rmass ghost yes
+   read_data tip4p-isotopes.data fix Isotopes NULL Isotopes
+
+Please note that the first *Isotopes* refers to the fix-ID
+and the second to the name of the section. The following input
+script code will now change the first 100 water molecules in this
+example to heavy water:
+
+
+.. parsed-literal::
+
+   group hwat id 2:300:3
+   group hwat id 3:300:3
+   set group hwat mass 2.0141018
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a
+simulation is restarted.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`read\_data <read_data>`, :doc:`set <set>`, :doc:`compute property/atom <compute_property_atom>`
+
+Default
+"""""""
+
+The default keyword values are ghost = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst
new file mode 100644
index 0000000000..0ee101198b
--- /dev/null
+++ b/doc/src/fix_python_invoke.rst
@@ -0,0 +1,93 @@
+.. index:: fix python/invoke
+
+fix python/invoke command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID python/invoke N callback function_name
+
+* ID, group-ID are ignored by this fix
+* python/invoke = style name of this fix command
+* N = execute every N steps
+* callback = *post\_force* or *end\_of\_step*
+  
+  .. parsed-literal::
+  
+       *post_force* = callback after force computations on atoms every N time steps
+       *end_of_step* = callback after every N time steps
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   python post_force_callback here """
+   from lammps import lammps
+
+   def post_force_callback(lammps_ptr, vflag):
+       lmp = lammps(ptr=lammps_ptr)
+       # access LAMMPS state using Python interface
+   """
+
+   python end_of_step_callback here """
+   def end_of_step_callback(lammps_ptr):
+       lmp = lammps(ptr=lammps_ptr)
+       # access LAMMPS state using Python interface
+   """
+
+   fix pf  all python/invoke 50 post_force post_force_callback
+   fix eos all python/invoke 50 end_of_step end_of_step_callback
+
+Description
+"""""""""""
+
+This fix allows you to call a Python function during a simulation run.
+The callback is either executed after forces have been applied to atoms
+or at the end of every N time steps.
+
+Callback functions must be declared in the global scope of the
+active Python interpreter. This can either be done by defining it
+inline using the python command or by importing functions from other
+Python modules. If LAMMPS is driven using the library interface from
+Python, functions defined in the driving Python interpreter can also
+be executed.
+
+Each callback is given a pointer object as first argument. This can be
+used to initialize an instance of the lammps Python interface, which
+gives access to the LAMMPS state from Python.
+
+.. warning::
+
+   While you can access the state of LAMMPS via library functions
+   from these callbacks, trying to execute input script commands will in the best
+   case not work or in the worst case result in undefined behavior.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the PYTHON package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Building LAMMPS with the PYTHON package will link LAMMPS with the
+Python library on your system.  Settings to enable this are in the
+lib/python/Makefile.lammps file.  See the lib/python/README file for
+information on those settings.
+
+Related commands
+""""""""""""""""
+
+:doc:`python command <python>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst
new file mode 100644
index 0000000000..0d59cf82c0
--- /dev/null
+++ b/doc/src/fix_python_move.rst
@@ -0,0 +1,117 @@
+.. index:: fix python/move
+
+fix python/move command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix python/move pymodule.CLASS
+
+pymodule.CLASS = use class **CLASS** in module/file **pymodule** to compute how to move atoms
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix  1 all python/move py_nve.NVE
+   fix  1 all python/move py_nve.NVE_OPT
+
+Description
+"""""""""""
+
+The *python/move* fix style provides a way to define ways how particles
+are moved during an MD run from python script code, that is loaded from
+a file into LAMMPS and executed at the various steps where other fixes
+can be executed. This python script must contain specific python class
+definitions.
+
+This allows to implement complex position updates and also modified
+time integration methods. Due to python being an interpreted language,
+however, the performance of this fix can be moderately to significantly
+slower than the corresponding C++ code. For specific cases, this
+performance penalty can be limited through effective use of NumPy.
+
+
+----------
+
+
+The python module file has to start with the following code:
+
+
+.. parsed-literal::
+
+   from __future_\_ import print_function
+   import lammps
+   import ctypes
+   import traceback
+   import numpy as np
+   #
+   class LAMMPSFix(object):
+       def __init__(self, ptr, group_name="all"):
+           self.lmp = lammps.lammps(ptr=ptr)
+           self.group_name = group_name
+   #
+   class LAMMPSFixMove(LAMMPSFix):
+       def __init__(self, ptr, group_name="all"):
+           super(LAMMPSFixMove, self).__init__(ptr, group_name)
+   #
+       def init(self):
+           pass
+   #
+       def initial_integrate(self, vflag):
+           pass
+   #
+       def final_integrate(self):
+           pass
+   #
+       def initial_integrate_respa(self, vflag, ilevel, iloop):
+           pass
+   #
+       def final_integrate_respa(self, ilevel, iloop):
+           pass
+   #
+       def reset_dt(self):
+           pass
+
+Any classes implementing new atom motion functionality have to be
+derived from the **LAMMPSFixMove** class, overriding the available
+methods as needed.
+
+Examples for how to do this are in the *examples/python* folder.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the PYTHON package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix python/invoke <fix_python_invoke>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst
new file mode 100644
index 0000000000..84ab2abc91
--- /dev/null
+++ b/doc/src/fix_qbmsst.rst
@@ -0,0 +1,256 @@
+.. index:: fix qbmsst
+
+fix qbmsst command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID qbmsst dir shockvel keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* qbmsst = style name of this fix
+* dir = *x* or *y* or *z*
+* shockvel = shock velocity (strictly positive, velocity units)
+* zero or more keyword/value pairs may be appended
+* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed*\ or *f\_max* or *N\_f* or *eta* or *beta* or *T\_init*
+  
+  .. parsed-literal::
+  
+       *q* value = cell mass-like parameter (mass\^2/distance\^4 units)
+       *mu* value = artificial viscosity (mass/distance/time units)
+       *p0* value = initial pressure in the shock equations (pressure units)
+       *v0* value = initial simulation cell volume in the shock equations (distance\^3 units)
+       *e0* value = initial total energy (energy units)
+       *tscale* value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
+       *damp* value = damping parameter (time units) inverse of friction <i>&gamma;</i>
+       *seed* value = random number seed (positive integer)
+       *f_max* value = upper cutoff frequency of the vibration spectrum (1/time units)
+       *N_f* value = number of frequency bins (positive integer)
+       *eta* value = coupling constant between the shock system and the quantum thermal bath (positive unitless)
+       *beta* value = the quantum temperature is updated every beta time steps (positive integer)
+       *T_init* value = quantum temperature for the initial state (temperature units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
+   fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
+
+Two example input scripts are given, including shocked alpha quartz
+and shocked liquid methane. The input script first equilibrate an
+initial state with the quantum thermal bath at the target temperature
+and then apply the qbmsst to simulate shock compression with quantum
+nuclear correction.  The following two figures plot related quantities
+for shocked alpha quartz.
+
+.. image:: JPG/qbmsst_init.jpg
+   :align: center
+
+Figure 1. Classical temperature <i>T</i><sup>cl</sup> = &sum;
+<i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub> vs. time
+for coupling the alpha quartz initial state with the quantum thermal
+bath at target quantum temperature <i>T</i><sup>qm</sup> = 300 K. The
+NpH ensemble is used for time integration while QTB provides the
+colored random force. <i>T</i><sup>cl</sup> converges at the timescale
+of *damp* which is set to be 1 ps.
+
+.. image:: JPG/qbmsst_shock.jpg
+   :align: center
+
+Figure 2. Quantum temperature and pressure vs. time for simulating
+shocked alpha quartz with the QBMSST. The shock propagates along the z
+direction. Restart of the QBMSST command is demonstrated in the
+example input script. Thermodynamic quantities stay continuous before
+and after the restart.
+
+Description
+"""""""""""
+
+This command performs the Quantum-Bath coupled Multi-Scale Shock
+Technique (QBMSST) integration. See :ref:`(Qi) <Qi>` for a detailed
+description of this method.  The QBMSST provides description of the
+thermodynamics and kinetics of shock processes while incorporating
+quantum nuclear effects.  The *shockvel* setting determines the steady
+shock velocity that will be simulated along direction *dir*\ .
+
+Quantum nuclear effects :doc:`(fix qtb) <fix_qtb>` can be crucial
+especially when the temperature of the initial state is below the
+classical limit or there is a great change in the zero point energies
+between the initial and final states. Theoretical post processing
+quantum corrections of shock compressed water and methane have been
+reported as much as 30% of the temperatures :ref:`(Goldman) <Goldman1>`.  A
+self-consistent method that couples the shock to a quantum thermal
+bath described by a colored noise Langevin thermostat has been
+developed by Qi et al :ref:`(Qi) <Qi>` and applied to shocked methane.  The
+onset of chemistry is reported to be at a pressure on the shock
+Hugoniot that is 40% lower than observed with classical molecular
+dynamics.
+
+It is highly recommended that the system be already in an equilibrium
+state with a quantum thermal bath at temperature of *T\_init*.  The fix
+command :doc:`fix qtb <fix_qtb>` at constant temperature *T\_init* could
+be used before applying this command to introduce self-consistent
+quantum nuclear effects into the initial state.
+
+The parameters *q*\ , *mu*\ , *e0*\ , *p0*\ , *v0* and *tscale* are described
+in the command :doc:`fix msst <fix_msst>`. The values of *e0*\ , *p0*\ , or
+*v0* will be calculated on the first step if not specified.  The
+parameter of *damp*\ , *f\_max*, and *N\_f* are described in the command
+:doc:`fix qtb <fix_qtb>`.
+
+The fix qbmsst command couples the shock system to a quantum thermal
+bath with a rate that is proportional to the change of the total
+energy of the shock system, <i>etot</i> - <i>etot</i><sub>0</sub>.
+Here <i>etot</i> consists of both the system energy and a thermal
+term, see :ref:`(Qi) <Qi>`, and <i>etot</i><sub>0</sub> = *e0* is the
+initial total energy.
+
+The *eta* (<i>&eta;</i>) parameter is a unitless coupling constant
+between the shock system and the quantum thermal bath. A small *eta*
+value cannot adjust the quantum temperature fast enough during the
+temperature ramping period of shock compression while large *eta*
+leads to big temperature oscillation. A value of *eta* between 0.3 and
+1 is usually appropriate for simulating most systems under shock
+compression. We observe that different values of *eta* lead to almost
+the same final thermodynamic state behind the shock, as expected.
+
+The quantum temperature is updated every *beta* (<i>&beta;</i>) steps
+with an integration time interval *beta* times longer than the
+simulation time step. In that case, <i>etot</i> is taken as its
+average over the past *beta* steps. The temperature of the quantum
+thermal bath <i>T</i><sup>qm</sup> changes dynamically according to
+the following equation where &Delta;<i>t</i> is the MD time step and
+<i>&gamma;</i> is the friction constant which is equal to the inverse
+of the *damp* parameter.
+
+.. raw:: html
+
+   <center><font size="4"> <i>dT</i><sup>qm</sup>/<i>dt =
+   &gamma;&eta;</i>&sum;<i><sup>&beta;</sup><sub>l =
+   1</sub></i>[<i>etot</i>(<i>t-l</i>&Delta;<i>t</i>)-<i>etot</i><sub>0</sub>]/<i>3&beta;Nk</i><sub>B</sub>
+   </font></center>
+
+The parameter *T\_init* is the initial temperature of the quantum
+thermal bath and the system before shock loading.
+
+For all pressure styles, the simulation box stays orthorhombic in
+shape. Parrinello-Rahman boundary conditions (tilted box) are
+supported by LAMMPS, but are not implemented for QBMSST.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Because the state of the random number generator is not written to
+:doc:`binary restart files <restart>`, this fix cannot be restarted
+"exactly" in an uninterrupted fashion. However, in a statistical
+sense, a restarted simulation should produce similar behaviors of the
+system as if it is not interrupted.  To achieve such a restart, one
+should write explicitly the same value for *q*\ , *mu*\ , *damp*\ , *f\_max*,
+*N\_f*, *eta*\ , and *beta* and set *tscale* = 0 if the system is
+compressed during the first run.
+
+The progress of the QBMSST can be monitored by printing the global
+scalar and global vector quantities computed by the fix.  The global
+vector contains five values in this order:
+
+[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian\_speed*, *lagrangian\_position*,
+*quantum\_temperature*]
+
+1. *dhugoniot* is the departure from the Hugoniot (temperature units).
+2. *drayleigh* is the departure from the Rayleigh line (pressure units).
+3. *lagrangian\_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
+4. *lagrangian\_position* is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front.
+5. *quantum\_temperature* is the temperature of the quantum thermal bath <i>T</i><sup>qm</sup>.
+
+To print these quantities to the log file with descriptive column
+headers, the following LAMMPS commands are suggested. Here the
+:doc:`fix\_modify <fix_modify>` energy command is also enabled to allow
+the thermo keyword *etotal* to print the quantity <i>etot</i>.  See
+also the :doc:`thermo\_style <thermo_style>` command.
+
+
+.. parsed-literal::
+
+   fix             fix_id all msst z
+   fix_modify      fix_id energy yes
+   variable        dhug    equal f_fix_id[1]
+   variable        dray    equal f_fix_id[2]
+   variable        lgr_vel equal f_fix_id[3]
+   variable        lgr_pos equal f_fix_id[4]
+   variable        T_qm    equal f_fix_id[5]
+   thermo_style    custom  step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
+
+The global scalar under the entry f\_fix\_id is the quantity of thermo
+energy as an extra part of <i>etot</i>. This global scalar and the
+vector of 5 quantities can be accessed by various :doc:`output commands <Howto_output>`. It is worth noting that the temp keyword
+under the :doc:`thermo\_style <thermo_style>` command print the
+instantaneous classical temperature <i>T</i><sup>cl</sup> as described
+in the command :doc:`fix qtb <fix_qtb>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix style is part of the USER-QTB package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+All cell dimensions must be periodic. This fix can not be used with a
+triclinic cell.  The QBMSST fix has been tested only for the group-ID
+all.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`fix qtb <fix_qtb>`, :doc:`fix msst <fix_msst>`
+
+
+----------
+
+
+Default
+"""""""
+
+The keyword defaults are q = 10, mu = 0, tscale = 0.01, damp = 1, seed
+= 880302, f\_max = 200.0, N\_f = 100, eta = 1.0, beta = 100, and
+T\_init=300.0. e0, p0, and v0 are calculated on the first step.
+
+
+----------
+
+
+.. _Goldman1:
+
+
+
+**(Goldman)** Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)
+
+.. _Qi:
+
+
+
+**(Qi)** Qi and Reed, J. Phys. Chem. A 116, 10451 (2012).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst
new file mode 100644
index 0000000000..8875c22af6
--- /dev/null
+++ b/doc/src/fix_qeq.rst
@@ -0,0 +1,270 @@
+.. index:: fix qeq/point
+
+fix qeq/point command
+=====================
+
+fix qeq/shielded command
+========================
+
+fix qeq/slater command
+======================
+
+fix qeq/dynamic command
+=======================
+
+fix qeq/fire command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/dynamic* or *qeq/fire*
+* Nevery = perform charge equilibration every this many steps
+* cutoff = global cutoff for charge-charge interactions (distance unit)
+* tolerance = precision to which charges will be equilibrated
+* maxiter = maximum iterations to perform charge equilibration
+* qfile = a filename with QEq parameters or *coul/streitz* or *reax/c*
+* zero or more keyword/value pairs may be appended
+* keyword = *alpha* or *qdamp* or *qstep*
+  
+  .. parsed-literal::
+  
+       *alpha* value = Slater type orbital exponent (qeq/slater only)
+       *qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
+       *qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
+   fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
+   fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
+   fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
+   fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
+
+Description
+"""""""""""
+
+Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano) <Nakano1>` (also known
+as the matrix inversion method) and in :ref:`(Rick and Stuart) <Rick1>` (also
+known as the extended Lagrangian method) based on the
+electronegativity equilization principle.
+
+These fixes can be used with any :doc:`pair style <pair_style>` in
+LAMMPS, so long as per-atom charges are defined.  The most typical
+use-case is in conjunction with a :doc:`pair style <pair_style>` that
+performs charge equilibration periodically (e.g. every timestep), such
+as the ReaxFF or Streitz-Mintmire potential.
+But these fixes can also be used with
+potentials that normally assume per-atom charges are fixed, e.g. a
+:doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>` potential.
+
+Because the charge equilibration calculation is effectively
+independent of the pair style, these fixes can also be used to perform
+a one-time assignment of charges to atoms.  For example, you could
+define the QEq fix, perform a zero-timestep run via the :doc:`run <run>`
+command without any pair style defined which would set per-atom
+charges (based on the current atom configuration), then remove the fix
+via the :doc:`unfix <unfix>` command before performing further dynamics.
+
+.. note::
+
+   Computing and using charge values different from published
+   values defined for a fixed-charge potential like Buckingham or CHARMM
+   or AMBER, can have a strong effect on energies and forces, and
+   produces a different model than the published versions.
+
+.. note::
+
+   The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used
+   to perform charge equilibration with the :doc:`COMB potential <pair_comb>`.  The :doc:`fix qeq/reax <fix_qeq_reax>`
+   command can be used to perform charge equilibration with the :doc:`ReaxFF force field <pair_reaxc>`, although fix qeq/shielded yields the
+   same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
+   are the same.  Eventually the fix qeq/reax command will be deprecated.
+
+The QEq method minimizes the electrostatic energy of the system (or
+equalizes the derivative of energy with respect to charge of all the
+atoms) by adjusting the partial charge on individual atoms based on
+interactions with their neighbors within *cutoff*\ .  It requires a few
+parameters, in *metal* units, for each atom type which provided in a
+file specified by *qfile*\ .  The file has the following format
+
+
+.. parsed-literal::
+
+   1 chi eta gamma zeta qcore
+   2 chi eta gamma zeta qcore
+   ...
+   Ntype chi eta gamma zeta qcore
+
+There have to be parameters given for every atom type. Wildcard entries
+are possible using the same syntax as elsewhere in LAMMPS
+(i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones.
+Empty lines or any text following the pound sign (#) are ignored.
+Each line starts with the atom type followed by five parameters.
+Only a subset of the parameters is used by each QEq style as described
+below, thus the others can be set to 0.0 if desired, but all five
+entries per line are required.
+
+* *chi* = electronegativity in energy units
+* *eta* = self-Coulomb potential in energy units
+* *gamma* = shielded Coulomb constant defined by :ref:`ReaxFF force field <vanDuin>` in distance units
+* *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire <Streitz1>` potential in reverse distance units
+* *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential <Streitz1>` potential in charge units
+
+The *qeq/point* style describes partial charges on atoms as point
+charges.  Interaction between a pair of charged particles is 1/r,
+which is the simplest description of the interaction between charges.
+Only the *chi* and *eta* parameters from the *qfile* file are used.
+Note that Coulomb catastrophe can occur if repulsion between the pair
+of charged particles is too weak.  This style solves partial charges
+on atoms via the matrix inversion method.  A tolerance of 1.0e-6 is
+usually a good number.
+
+The *qeq/shielded* style describes partial charges on atoms also as
+point charges, but uses a shielded Coulomb potential to describe the
+interaction between a pair of charged particles.  Interaction through
+the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field <vanDuin>` paper.  The shielding accounts for charge overlap
+between charged particles at small separation.  This style is the same
+as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with :doc:`pair\_style reax/c <pair_reaxc>`.  Only the *chi*\ , *eta*\ , and *gamma*
+parameters from the *qfile* file are used. When using the string
+*reax/c* as filename, these parameters are extracted directly from
+an active *reax/c* pair style.  This style solves partial
+charges on atoms via the matrix inversion method.  A tolerance of
+1.0e-6 is usually a good number.
+
+The *qeq/slater* style describes partial charges on atoms as spherical
+charge densities centered around atoms via the Slater 1\ *s* orbital, so
+that the interaction between a pair of charged particles is the
+product of two Slater 1\ *s* orbitals.  The expression for the Slater
+1\ *s* orbital is given under equation (6) of the
+:ref:`Streitz-Mintmire <Streitz1>` paper.  Only the *chi*\ , *eta*\ , *zeta*\ , and
+*qcore* parameters from the *qfile* file are used. When using the string
+*coul/streitz* as filename, these parameters are extracted directly from
+an active *coul/streitz* pair style.  This style solves
+partial charges on atoms via the matrix inversion method.  A tolerance
+of 1.0e-6 is usually a good number.  Keyword *alpha* can be used to
+change the Slater type orbital exponent.
+
+The *qeq/dynamic* style describes partial charges on atoms as point
+charges that interact through 1/r, but the extended Lagrangian method
+is used to solve partial charges on atoms.  Only the *chi* and *eta*
+parameters from the *qfile* file are used.  Note that Coulomb
+catastrophe can occur if repulsion between the pair of charged
+particles is too weak.  A tolerance of 1.0e-3 is usually a good
+number.  Keyword *qdamp* can be used to change the damping factor, while
+keyword *qstep* can be used to change the time step size.
+
+The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model and charge
+solver as the *qeq/dynamic* style, but employs a FIRE minimization
+algorithm to solve for equilibrium charges.
+Keyword *qdamp* can be used to change the damping factor, while
+keyword *qstep* can be used to change the time step size.
+
+Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe
+different charge models, whereas the matrix inversion method and the
+extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
+different solvers.
+
+Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all describe
+charges as point charges that interact through 1/r relationship, but
+solve partial charges on atoms using different solvers.  These three
+styles should yield comparable results if
+the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the
+same.  Style *qeq/point* is typically faster, *qeq/dynamic* scales
+better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
+
+.. note::
+
+   To avoid the evaluation of the derivative of charge with respect
+   to position, which is typically ill-defined, the system should have a
+   zero net charge.
+
+.. note::
+
+   Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is
+   non-trivial.  Charges on atoms are not guaranteed to equilibrate with
+   arbitrary choices of these parameters.  We do not develop these QEq
+   parameters.  See the examples/qeq directory for some examples.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about these fixes is written to :doc:`binary restart files <restart>`.  No global scalar or vector or per-atom
+quantities are stored by these fixes for access by various :doc:`output commands <Howto_output>`.  No parameter of these fixes can be used
+with the *start/stop* keywords of the :doc:`run <run>` command.
+
+Thexe fixes are invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+These fixes are part of the QEQ package.  They are only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix qeq/reax <fix_qeq_reax>`, :doc:`fix qeq/comb <fix_qeq_comb>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Rappe1:
+
+
+
+**(Rappe and Goddard)** A. K. Rappe and W. A. Goddard III, J Physical
+Chemistry, 95, 3358-3363 (1991).
+
+.. _Nakano1:
+
+
+
+**(Nakano)** A. Nakano, Computer Physics Communications, 104, 59-69 (1997).
+
+.. _Rick1:
+
+
+
+**(Rick and Stuart)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics
+101, 16141 (1994).
+
+.. _Streitz1:
+
+
+
+**(Streitz-Mintmire)** F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
+16, 11996 (1994)
+
+.. _vanDuin:
+
+
+
+**(ReaxFF)** A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J
+Physical Chemistry, 105, 9396-9049 (2001)
+
+.. _Shan:
+
+
+
+**(QEq/Fire)** T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst
new file mode 100644
index 0000000000..35eb514a75
--- /dev/null
+++ b/doc/src/fix_qeq_comb.rst
@@ -0,0 +1,165 @@
+.. index:: fix qeq/comb
+
+fix qeq/comb command
+====================
+
+fix qeq/comb/omp command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID qeq/comb Nevery precision keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* qeq/comb = style name of this fix command
+* Nevery = perform charge equilibration every this many steps
+* precision = convergence criterion for charge equilibration
+* zero or more keyword/value pairs may be appended
+* keyword = *file*
+  
+  .. parsed-literal::
+  
+       *file* value = filename
+         filename = name of file to write QEQ equilibration info to
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 surface qeq/comb 10 0.0001
+
+Description
+"""""""""""
+
+Perform charge equilibration (QeQ) in conjunction with the COMB
+(Charge-Optimized Many-Body) potential as described in
+:ref:`(COMB\_1) <COMB_1>` and :ref:`(COMB\_2) <COMB_2>`.  It performs the charge
+equilibration portion of the calculation using the so-called QEq
+method, whereby the charge on each atom is adjusted to minimize the
+energy of the system.  This fix can only be used with the COMB
+potential; see the :doc:`fix qeq/reax <fix_qeq_reax>` command for a QeQ
+calculation that can be used with any potential.
+
+Only charges on the atoms in the specified group are equilibrated.
+The fix relies on the pair style (COMB in this case) to calculate the
+per-atom electronegativity (effective force on the charges).  An
+electronegativity equalization calculation (or QEq) is performed in an
+iterative fashion, which in parallel requires communication at each
+iteration for processors to exchange charge information about nearby
+atoms with each other.  See :ref:`Rappe\_and\_Goddard <Rappe_and_Goddard>` and
+:ref:`Rick\_and\_Stuart <Rick_and_Stuart>` for details.
+
+During a run, charge equilibration is performed every *Nevery* time
+steps.  Charge equilibration is also always enforced on the first step
+of each run.  The *precision* argument controls the tolerance for the
+difference in electronegativity for all atoms during charge
+equilibration.  *Precision* is a trade-off between the cost of
+performing charge equilibration (more iterations) and accuracy.
+
+If the *file* keyword is used, then information about each
+equilibration calculation is written to the specified file.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is performing charge equilibration. Default is
+the outermost level.
+
+This fix produces a per-atom vector which can be accessed by various
+:doc:`output commands <Howto_output>`.  The vector stores the gradient
+of the charge on each atom.  The per-atom values be accessed on any
+timestep.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+This fix can be invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix command currently only supports :doc:`pair style *comb*\ <pair_comb>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style comb <pair_comb>`
+
+Default
+"""""""
+
+No file output is performed.
+
+
+----------
+
+
+.. _COMB\_1:
+
+
+
+**(COMB\_1)** J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
+
+.. _COMB\_2:
+
+
+
+**(COMB\_2)** T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R.
+Phillpot, Phys Rev B, 81, 125328 (2010).
+
+.. _Rappe\_and\_Goddard:
+
+
+
+**(Rappe\_and\_Goddard)** A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358
+(1991).
+
+.. _Rick\_and\_Stuart:
+
+
+
+**(Rick\_and\_Stuart)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys
+101, 16141 (1994).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst
new file mode 100644
index 0000000000..4371e7a1a1
--- /dev/null
+++ b/doc/src/fix_qeq_reax.rst
@@ -0,0 +1,156 @@
+.. index:: fix qeq/reax
+
+fix qeq/reax command
+====================
+
+fix qeq/reax/kk command
+=======================
+
+fix qeq/reax/omp command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* qeq/reax = style name of this fix command
+* Nevery = perform QEq every this many steps
+* cutlo,cuthi = lo and hi cutoff for Taper radius
+* tolerance = precision to which charges will be equilibrated
+* params = reax/c or a filename
+* args   = *dual* (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+   fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
+
+Description
+"""""""""""
+
+Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) <Rappe2>` and formulated in :ref:`(Nakano) <Nakano2>`.  It is
+typically used in conjunction with the ReaxFF force field model as
+implemented in the :doc:`pair\_style reax/c <pair_reaxc>` command, but
+it can be used with any potential in LAMMPS, so long as it defines and
+uses charges on each atom.  The :doc:`fix qeq/comb <fix_qeq_comb>`
+command should be used to perform charge equilibration with the :doc:`COMB potential <pair_comb>`.  For more technical details about the
+charge equilibration performed by fix qeq/reax, see the
+:ref:`(Aktulga) <qeq-Aktulga>` paper.
+
+The QEq method minimizes the electrostatic energy of the system by
+adjusting the partial charge on individual atoms based on interactions
+with their neighbors.  It requires some parameters for each atom type.
+If the *params* setting above is the word "reax/c", then these are
+extracted from the :doc:`pair\_style reax/c <pair_reaxc>` command and
+the ReaxFF force field file it reads in.  If a file name is specified
+for *params*\ , then the parameters are taken from the specified file
+and the file must contain one line for each atom type.  The latter
+form must be used when performing QeQ with a non-ReaxFF potential.
+Each line should be formatted as follows:
+
+
+.. parsed-literal::
+
+   itype chi eta gamma
+
+where *itype* is the atom type from 1 to Ntypes, *chi* denotes the
+electronegativity in eV, *eta* denotes the self-Coulomb
+potential in eV, and *gamma* denotes the valence orbital
+exponent.  Note that these 3 quantities are also in the ReaxFF
+potential file, except that eta is defined here as twice the eta value
+in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
+of this fix are hard-coded to be A, eV, and electronic charge.
+
+The optional *dual* keyword allows to perform the optimization
+of the S and T matrices in parallel. This is only supported for
+the *qeq/reax/omp* style. Otherwise they are processed separately.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  No global scalar or vector or per-atom
+quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`.  No parameter of this fix can be used
+with the *start/stop* keywords of the :doc:`run <run>` command.
+
+This fix is invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-REAXC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix does not correctly handle interactions
+involving multiple periodic images of the same atom. Hence, it should not
+be used for periodic cell dimensions less than 10 angstroms.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style reax/c <pair_reaxc>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Rappe2:
+
+
+
+**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95,
+3358-3363 (1991).
+
+.. _Nakano2:
+
+
+
+**(Nakano)** Nakano, Computer Physics Communications, 104, 59-69 (1997).
+
+.. _qeq-Aktulga:
+
+
+
+**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
+245-259 (2012).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst
new file mode 100644
index 0000000000..ee08cd1d15
--- /dev/null
+++ b/doc/src/fix_qmmm.rst
@@ -0,0 +1,73 @@
+.. index:: fix qmmm
+
+fix qmmm command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID qmmm
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* qmmm = style name of this fix command
+
+Examples
+""""""""
+
+fix 1 qmol qmmm
+
+Description
+"""""""""""
+
+This fix provides functionality to enable a quantum
+mechanics/molecular mechanics (QM/MM) coupling of LAMMPS to a quantum
+mechanical code.  The current implementation only supports an ONIOM
+style mechanical coupling to the `Quantum ESPRESSO <espresso_>`_ plane
+wave DFT package.  Electrostatic coupling is in preparation and the
+interface has been written in a manner that coupling to other QM codes
+should be possible without changes to LAMMPS itself.
+
+.. _espresso: http://www.quantum-espresso.org
+
+
+
+The interface code for this is in the lib/qmmm directory of the LAMMPS
+distribution and is being made available at this early stage of
+development in order to encourage contributions for interfaces to
+other QM codes.  This will allow the LAMMPS side of the implementation
+to be adapted if necessary before being finalized.
+
+Details about how to use this fix are currently documented in the
+description of the QM/MM interface code itself in lib/qmmm/README.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global scalar or vector or per-atom
+quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`.  No parameter of this fix can be used
+with the *start/stop* keywords of the :doc:`run <run>` command.  This
+fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-QMMM package.  It is only enabled if
+LAMMPS was built with that package. It also requires building a
+library provided with LAMMPS.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The fix is only functional when LAMMPS is built as a library and
+linked with a compatible QM program and a QM/MM front end into a QM/MM
+executable.  See the lib/qmmm/README file for details.
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst
new file mode 100644
index 0000000000..a940dd1833
--- /dev/null
+++ b/doc/src/fix_qtb.rst
@@ -0,0 +1,218 @@
+.. index:: fix qtb
+
+fix qtb command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID qtb keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* qtb = style name of this fix
+* zero or more keyword/value pairs may be appended
+* keyword = *temp* or *damp* or *seed* or *f\_max* or *N\_f*
+  
+  .. parsed-literal::
+  
+       *temp* value = target quantum temperature (temperature units)
+       *damp* value = damping parameter (time units) inverse of friction <i>&gamma</i>;
+       *seed* value = random number seed (positive integer)
+       *f_max* value = upper cutoff frequency of the vibration spectrum (1/time units)
+       *N_f* value = number of frequency bins (positive integer)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve
+   fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
+   fix 2 all nph iso 1.01325 1.01325 1
+   fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
+
+Description
+"""""""""""
+
+This command performs the quantum thermal bath scheme proposed by
+:ref:`(Dammak) <Dammak>` to include self-consistent quantum nuclear effects,
+when used in conjunction with the :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>` commands.
+
+Classical molecular dynamics simulation does not include any quantum
+nuclear effect. Quantum treatment of the vibrational modes will
+introduce zero point energy into the system, alter the energy power
+spectrum and bias the heat capacity from the classical limit. Missing
+all the quantum nuclear effects, classical MD cannot model systems at
+temperatures lower than their classical limits. This effect is
+especially important for materials with a large population of hydrogen
+atoms and thus higher classical limits.
+
+The equation of motion implemented by this command follows a Langevin
+form:
+
+.. raw:: html
+
+   <center><font size="4"><i> m<sub>i</sub>a<sub>i</sub> = f<sub>i</sub>
+   + R<sub>i</sub> -
+   m<sub>i</sub>&gamma;v<sub>i</sub>. </i></font></center>
+
+Here <i>m<sub>i</sub></i>, <i>a<sub>i</sub></i>, <i>f<sub>i</sub>
+</i>, <i>R<sub>i</sub></i>, <i>&gamma;</i> and <i>v<sub>i</sub> </i>
+represent mass, acceleration, force exerted by all other atoms, random
+force, frictional coefficient (the inverse of damping parameter damp),
+and velocity. The random force <i>R<sub>i</sub></i> is "colored" so
+that any vibrational mode with frequency <i>&omega;</i> will have a
+temperature-sensitive energy <i>&theta;</i>(<i>&omega;,T</i>) which
+resembles the energy expectation for a quantum harmonic oscillator
+with the same natural frequency:
+
+.. raw:: html
+
+   <center><font size="4"> <i>&theta;</i>(<i>&omega;,T</i>) =
+   &#8463;&omega;/2 +
+   &#8463;&omega;[</i>exp(<i>&#8463;&omega;/k</i><sub>B</sub><i>T</i>)<i>-1</i>]<i><sup>-1</sup></i>
+   </font></center>
+
+To efficiently generate the random forces, we employ the method
+of :ref:`(Barrat) <Barrat>`, that circumvents the need to generate all
+random forces for all times before the simulation. The memory
+requirement of this approach is less demanding and independent
+of the simulation duration. Since the total random force <i>R</i><sub>tot</sub>
+does not necessarily vanish for a finite number of atoms,
+<i>R<sub>i</sub></i> is replaced by <i>R<sub>i</sub></i> - <i>R</i><sub>tot</sub>/<i>N</i><sub>tot</sub>
+to avoid collective motion of the system.
+
+The *temp* parameter sets the target quantum temperature. LAMMPS will
+still have an output temperature in its thermo style. That is the
+instantaneous classical temperature <i>T</i><sup>cl</sup> derived from
+the atom velocities at thermal equilibrium. A non-zero
+<i>T</i><sup>cl</sup> will be present even when the quantum
+temperature approaches zero. This is associated with zero-point energy
+at low temperatures.
+
+.. raw:: html
+
+   <center><font size="4"> <i>T</i><sup>cl</sup> = &sum;
+   <i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub>
+   </font></center>
+
+The *damp* parameter is specified in time units, and it equals the
+inverse of the frictional coefficient <i>&gamma;</i>. <i>&gamma;</i>
+should be as small as possible but slightly larger than the timescale
+of anharmonic coupling in the system which is about 10 ps to 100
+ps. When <i>&gamma;</i> is too large, it gives an energy spectrum that
+differs from the desired Bose-Einstein spectrum. When <i>&gamma;</i>
+is too small, the quantum thermal bath coupling to the system will be
+less significant than anharmonic effects, reducing to a classical
+limit. We find that setting <i>&gamma;</i> between 5 THz and 1 THz
+could be appropriate depending on the system.
+
+The random number *seed* is a positive integer used to initiate a
+Marsaglia random number generator. Each processor uses the input seed
+to generate its own unique seed and its own stream of random
+numbers. Thus the dynamics of the system will not be identical on two
+runs on different numbers of processors.
+
+The *f\_max* parameter truncate the noise frequency domain so that
+vibrational modes with frequencies higher than *f\_max* will not be
+modulated. If we denote &Delta;<i>t</i> as the time interval for the
+MD integration, *f\_max* is always reset by the code to make
+<i>&alpha;</i> = (int)(2*f\_max*&Delta;<i>t</i>)<sup><i>-1</i></sup> a
+positive integer and print out relative information. An appropriate
+value for the cutoff frequency *f\_max* would be around 2~3
+<i>f</i><sub>D</sub>, where <i>f</i><sub>D</sub> is the Debye
+frequency.
+
+The *N\_f* parameter is the frequency grid size, the number of points
+from 0 to *f\_max* in the frequency domain that will be
+sampled. <i>3&times;2</i> *N\_f* per-atom random numbers are required
+in the random force generation and there could be as many atoms as in
+the whole simulation that can migrate into every individual
+processor. A larger *N\_f* provides a more accurate sampling of the
+spectrum while consumes more memory.  With fixed *f\_max* and
+<i>&gamma;</i>, *N\_f* should be big enough to converge the classical
+temperature <i>T</i><sup>cl</sup> as a function of target quantum bath
+temperature. Memory usage per processor could be from 10 to 100
+Mbytes.
+
+.. note::
+
+   Unlike the :doc:`fix nvt <fix_nh>` command which performs
+   Nose/Hoover thermostatting AND time integration, this fix does NOT
+   perform time integration. It only modifies forces to a colored
+   thermostat. Thus you must use a separate time integration fix, like
+   :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>` to actually update the
+   velocities and positions of atoms (as shown in the
+   examples). Likewise, this fix should not normally be used with other
+   fixes or commands that also specify system temperatures , e.g. :doc:`fix nvt <fix_nh>` and :doc:`fix temp/rescale <fix_temp_rescale>`.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimizie info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix. However, in a statistical sense, a restarted
+simulation should produce similar behaviors of the system.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix style is part of the USER-QTB package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix qbmsst <fix_qbmsst>`
+
+
+----------
+
+
+Default
+"""""""
+
+The keyword defaults are temp = 300, damp = 1, seed = 880302,
+f\_max=200.0 and N\_f = 100.
+
+
+----------
+
+
+.. _Dammak:
+
+
+
+**(Dammak)** Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev
+Lett, 103, 190601 (2009).
+
+.. _Barrat:
+
+
+
+**(Barrat)** Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst
new file mode 100644
index 0000000000..b6c15a2dd3
--- /dev/null
+++ b/doc/src/fix_reaxc_bonds.rst
@@ -0,0 +1,122 @@
+.. index:: fix reax/c/bonds
+
+fix reax/c/bonds command
+========================
+
+fix reax/c/bonds/kk command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID reaxc/bonds Nevery filename
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* reax/bonds = style name of this fix command
+* Nevery = output interval in timesteps
+* filename = name of output file
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all reax/c/bonds 100 bonds.reaxc
+
+Description
+"""""""""""
+
+Write out the bond information computed by the ReaxFF potential specified
+by :doc:`pair\_style reax/c <pair_reaxc>` in the exact same format as the
+original stand-alone ReaxFF code of Adri van Duin.  The bond information
+is written to *filename* on timesteps that are multiples of *Nevery*\ ,
+including timestep 0.  For time-averaged chemical species analysis,
+please see the :doc:`fix reaxc/c/species <fix_reaxc_species>` command.
+
+The specified group-ID is ignored by this fix.
+
+The format of the output file should be reasonably self-explanatory.
+The meaning of the column header abbreviations is as follows:
+
+* id = atom id
+* type = atom type
+* nb = number of bonds
+* id\_1 = atom id of first bond
+* id\_nb = atom id of Nth bond
+* mol = molecule id
+* bo\_1 = bond order of first bond
+* bo\_nb = bond order of Nth bond
+* abo = atom bond order (sum of all bonds)
+* nlp = number of lone pairs
+* q = atomic charge
+
+If the filename ends with ".gz", the output file is written in gzipped
+format.  A gzipped dump file will be about 3x smaller than the text
+version, but will also take longer to write.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in :doc:`Speed <Speed>`
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See :doc:`Speed <Speed>` of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The fix reax/c/bonds command requires that the :doc:`pair\_style reax/c <pair_reaxc>` is invoked.  This fix is part of the
+USER-REAXC package.  It is only enabled if LAMMPS was built with that
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+To write gzipped bond files, you must compile LAMMPS with the
+-DLAMMPS\_GZIP option.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style reax/c <pair_reaxc>`, :doc:`fix reax/c/species <fix_reaxc_species>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst
new file mode 100644
index 0000000000..210f6fe5cc
--- /dev/null
+++ b/doc/src/fix_reaxc_species.rst
@@ -0,0 +1,204 @@
+.. index:: fix reax/c/species
+
+fix reax/c/species command
+==========================
+
+fix reax/c/species/kk command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* reax/c/species = style name of this command
+* Nevery = sample bond-order every this many timesteps
+* Nrepeat = # of bond-order samples used for calculating averages
+* Nfreq = calculate average bond-order every this many timesteps
+* filename = name of output file
+* zero or more keyword/value pairs may be appended
+* keyword = *cutoff* or *element* or *position*
+  
+  .. parsed-literal::
+  
+       *cutoff* value = I J Cutoff
+         I, J = atom types
+         Cutoff = Bond-order cutoff value for this pair of atom types
+       *element* value = Element1, Element2, ...
+       *position* value = posfreq filepos
+         posfreq = write position files every this many timestep
+         filepos = name of position output file
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all reax/c/species 10 10 100 species.out
+   fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
+   fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
+
+Description
+"""""""""""
+
+Write out the chemical species information computed by the ReaxFF
+potential specified by :doc:`pair\_style reax/c <pair_reaxc>`.
+Bond-order values (either averaged or instantaneous, depending on
+value of *Nrepeat*\ ) are used to determine chemical bonds.  Every
+*Nfreq* timesteps, chemical species information is written to
+*filename* as a two line output.  The first line is a header
+containing labels. The second line consists of the following:
+timestep, total number of molecules, total number of distinct species,
+number of molecules of each species.  In this context, "species" means
+a unique molecule.  The chemical formula of each species is given in
+the first line.
+
+If the filename ends with ".gz", the output file is written in gzipped
+format.  A gzipped dump file will be about 3x smaller than the text version,
+but will also take longer to write.
+
+Optional keyword *cutoff* can be assigned to change the minimum
+bond-order values used in identifying chemical bonds between pairs of
+atoms.  Bond-order cutoffs should be carefully chosen, as bond-order
+cutoffs that are too small may include too many bonds (which will
+result in an error), while cutoffs that are too large will result in
+fragmented molecules.  The default cutoff of 0.3 usually gives good
+results.
+
+The optional keyword *element* can be used to specify the chemical
+symbol printed for each LAMMPS atom type. The number of symbols must
+match the number of LAMMPS atom types and each symbol must consist of
+1 or 2 alphanumeric characters. Normally, these symbols should be
+chosen to match the chemical identity of each LAMMPS atom type, as
+specified using the :doc:`reax/c pair\_coeff <pair_reaxc>` command and
+the ReaxFF force field file.
+
+The optional keyword *position* writes center-of-mass positions of
+each identified molecules to file *filepos* every *posfreq* timesteps.
+The first line contains information on timestep, total number of
+molecules, total number of distinct species, and box dimensions.  The
+second line is a header containing labels.  From the third line
+downward, each molecule writes a line of output containing the
+following information: molecule ID, number of atoms in this molecule,
+chemical formula, total charge, and center-of-mass xyz positions of
+this molecule.  The xyz positions are in fractional coordinates
+relative to the box dimensions.
+
+For the keyword *position*\ , the *filepos* is the name of the output
+file.  It can contain the wildcard character "\*".  If the "\*"
+character appears in *filepos*\ , then one file per snapshot is written
+at *posfreq* and the "\*" character is replaced with the timestep
+value.  For example, AuO.pos.\* becomes AuO.pos.0, AuO.pos.1000, etc.
+
+
+----------
+
+
+The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what
+timesteps the bond-order values are sampled to get the average bond
+order.  The species analysis is performed using the average bond-order
+on timesteps that are a multiple of *Nfreq*\ .  The average is over
+*Nrepeat* bond-order samples, computed in the preceding portion of the
+simulation every *Nevery* timesteps.  *Nfreq* must be a multiple of
+*Nevery* and *Nevery* must be non-zero even if *Nrepeat* is 1.
+Also, the timesteps
+contributing to the average bond-order cannot overlap,
+i.e. Nrepeat\*Nevery can not exceed Nfreq.
+
+For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
+values on timesteps 90,92,94,96,98,100 will be used to compute the
+average bond-order for the species analysis output on timestep 100.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes both a global vector of length 2 and a per-atom
+vector, either of which can be accessed by various :doc:`output commands <Howto_output>`.  The values in the global vector are
+"intensive".
+
+The 2 values in the global vector are as follows:
+
+* 1 = total number of molecules
+* 2 = total number of distinct species
+
+The per-atom vector stores the molecule ID for each atom as identified
+by the fix.  If an atom is not in a molecule, its ID will be 0.
+For atoms in the same molecule, the molecule ID for all of them
+will be the same and will be equal to the smallest atom ID of
+any atom in the molecule.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in :doc:`Speed <Speed>`
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See :doc:`Speed <Speed>` of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The "fix reax/c/species" currently only works with :doc:`pair\_style reax/c <pair_reaxc>` and it requires that the :doc:`pair\_style reax/c <pair_reaxc>` be invoked.  This fix is part of the
+USER-REAXC package.  It is only enabled if LAMMPS was built with that
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+To write gzipped species files, you must compile LAMMPS with the
+-DLAMMPS\_GZIP option.
+
+It should be possible to extend it to other reactive pair\_styles (such as
+:doc:`rebo <pair_airebo>`, :doc:`airebo <pair_airebo>`,
+:doc:`comb <pair_comb>`, and :doc:`bop <pair_bop>`), but this has not yet been done.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style reax/c <pair_reaxc>`, :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
+
+Default
+"""""""
+
+The default values for bond-order cutoffs are 0.3 for all I-J pairs.  The
+default element symbols are C, H, O, N.  Position files are not written
+by default.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst
new file mode 100644
index 0000000000..0a33bbaea3
--- /dev/null
+++ b/doc/src/fix_recenter.rst
@@ -0,0 +1,143 @@
+.. index:: fix recenter
+
+fix recenter command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID recenter x y z keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* recenter = style name of this fix command
+* x,y,z = constrain center-of-mass to these coords (distance units),         any coord can also be NULL or INIT (see below)
+* zero or more keyword/value pairs may be appended
+* keyword = *shift* or *units*
+  
+  .. parsed-literal::
+  
+       *shift* value = group-ID
+         group-ID = group of atoms whose coords are shifted
+       *units* value = *box* or *lattice* or *fraction*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all recenter 0.0 0.5 0.0
+   fix 1 all recenter INIT INIT NULL
+   fix 1 all recenter INIT 0.0 0.0 units box
+
+Description
+"""""""""""
+
+Constrain the center-of-mass position of a group of atoms by adjusting
+the coordinates of the atoms every timestep.  This is simply a small
+shift that does not alter the dynamics of the system or change the
+relative coordinates of any pair of atoms in the group.  This can be
+used to insure the entire collection of atoms (or a portion of them)
+do not drift during the simulation due to random perturbations
+(e.g. :doc:`fix langevin <fix_langevin>` thermostatting).
+
+Distance units for the x,y,z values are determined by the setting of
+the *units* keyword, as discussed below.  One or more x,y,z values can
+also be specified as NULL, which means exclude that dimension from
+this operation.  Or it can be specified as INIT which means to
+constrain the center-of-mass to its initial value at the beginning of
+the run.
+
+The center-of-mass (COM) is computed for the group specified by the
+fix.  If the current COM is different than the specified x,y,z, then a
+group of atoms has their coordinates shifted by the difference.  By
+default the shifted group is also the group specified by the fix.  A
+different group can be shifted by using the *shift* keyword.  For
+example, the COM could be computed on a protein to keep it in the
+center of the simulation box.  But the entire system (protein + water)
+could be shifted.
+
+If the *units* keyword is set to *box*\ , then the distance units of
+x,y,z are defined by the :doc:`units <units>` command - e.g. Angstroms
+for *real* units.  A *lattice* value means the distance units are in
+lattice spacings.  The :doc:`lattice <lattice>` command must have been
+previously used to define the lattice spacing.  A *fraction* value
+means a fractional distance between the lo/hi box boundaries, e.g. 0.5
+= middle of the box.  The default is to use lattice units.
+
+Note that the :doc:`velocity <velocity>` command can be used to create
+velocities with zero aggregate linear and/or angular momentum.
+
+.. note::
+
+   This fix performs its operations at the same point in the
+   timestep as other time integration fixes, such as :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, or :doc:`fix npt <fix_nh>`.
+   Thus fix recenter should normally be the last such fix specified in
+   the input script, since the adjustments it makes to atom coordinates
+   should come after the changes made by time integration.  LAMMPS will
+   warn you if your fixes are not ordered this way.
+
+.. note::
+
+   If you use this fix on a small group of atoms (e.g. a molecule
+   in solvent) without using the *shift* keyword to adjust the positions
+   of all atoms in the system, then the results can be unpredictable.
+   For example, if the molecule is pushed consistently in one direction
+   by a flowing solvent, its velocity will increase.  But its coordinates
+   will be re-centered, meaning it is moved back towards the force.  Thus
+   over time, the velocity and effective temperature of the molecule
+   could become very large, though it won't actually be moving due to the
+   re-centering.  If you are thermostatting the entire system, then the
+   solvent would be cooled to compensate.  A better solution for this
+   simulation scenario is to use the :doc:`fix spring <fix_spring>` command
+   to tether the molecule in place.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the distance the
+group is moved by fix recenter.
+
+This fix also computes global 3-vector which can be accessed by
+various :doc:`output commands <Howto_output>`.  The 3 quantities in the
+vector are xyz components of displacement applied to the group of
+atoms by the fix.
+
+The scalar and vector values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix should not be used with an x,y,z setting that causes a large
+shift in the system on the 1st timestep, due to the requested COM
+being very different from the initial COM.  This could cause atoms to
+be lost, especially in parallel.  Instead, use the
+:doc:`displace\_atoms <displace_atoms>` command, which can be used to
+move atoms a large distance.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix momentum <fix_momentum>`, :doc:`velocity <velocity>`
+
+Default
+"""""""
+
+The option defaults are shift = fix group-ID, and units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst
new file mode 100644
index 0000000000..0fc0ccee77
--- /dev/null
+++ b/doc/src/fix_restrain.rst
@@ -0,0 +1,240 @@
+.. index:: fix restrain
+
+fix restrain command
+====================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID restrain keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* restrain = style name of this fix command
+* one or more keyword/arg pairs may be appended
+* keyword = *bond* or *angle* or *dihedral*
+  
+  .. parsed-literal::
+  
+       *bond* args = atom1 atom2 Kstart Kstop r0
+         atom1,atom2 = IDs of 2 atoms in bond
+         Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+         r0 = equilibrium bond distance (distance units)
+       *angle* args = atom1 atom2 atom3 Kstart Kstop theta0
+         atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
+         Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+         theta0 = equilibrium angle theta (degrees)
+       *dihedral* args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
+         atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
+         Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+         phi0 = equilibrium dihedral angle phi (degrees)
+         keyword/value = optional keyword value pairs. supported keyword/value pairs:
+           *mult* n = dihedral multiplicity n (integer >= 0, default = 1)
+
+
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
+   fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
+   fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
+   fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
+
+Description
+"""""""""""
+
+Restrain the motion of the specified sets of atoms by making them part
+of a bond or angle or dihedral interaction whose strength can vary
+over time during a simulation.  This is functionally similar to
+creating a bond or angle or dihedral for the same atoms in a data
+file, as specified by the :doc:`read\_data <read_data>` command, albeit
+with a time-varying pre-factor coefficient, and except for exclusion
+rules, as explained below.
+
+For the purpose of force field parameter-fitting or mapping a molecular
+potential energy surface, this fix reduces the hassle and risk
+associated with modifying data files.  In other words, use this fix to
+temporarily force a molecule to adopt a particular conformation.  To
+create a permanent bond or angle or dihedral, you should modify the
+data file.
+
+.. note::
+
+   Adding a bond/angle/dihedral with this command does not apply
+   the exclusion rules and weighting factors specified by the
+   :doc:`special\_bonds <special_bonds>` command to atoms in the restraint
+   that are now bonded (1-2,1-3,1-4 neighbors) as a result.  If they are
+   close enough to interact in a :doc:`pair\_style <pair_style>` sense
+   (non-bonded interaction), then the bond/angle/dihedral restraint
+   interaction will simply be superposed on top of that interaction.
+
+The group-ID specified by this fix is ignored.
+
+The second example above applies a restraint to hold the dihedral
+angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
+restraint coefficient.  The fourth example applies similar restraints
+to multiple dihedral angles using a restraint coefficient that
+increases from 0.0 to 2000.0 over the course of the run.
+
+.. note::
+
+   Adding a force to atoms implies a change in their potential
+   energy as they move due to the applied force field.  For dynamics via
+   the :doc:`run <run>` command, this energy can be added to the system's
+   potential energy for thermodynamic output (see below).  For energy
+   minimization via the :doc:`minimize <minimize>` command, this energy
+   must be added to the system's potential energy to formulate a
+   self-consistent minimization problem (see below).
+
+In order for a restraint to be effective, the restraint force must
+typically be significantly larger than the forces associated with
+conventional force field terms.  If the restraint is applied during a
+dynamics run (as opposed to during an energy minimization), a large
+restraint coefficient can significantly reduce the stable timestep
+size, especially if the atoms are initially far from the preferred
+conformation.  You may need to experiment to determine what value of :math:`K`
+works best for a given application.
+
+For the case of finding a minimum energy structure for a single
+molecule with particular restraints (e.g. for fitting force field
+parameters or constructing a potential energy surface), commands such
+as the following may be useful:
+
+
+.. code-block:: LAMMPS
+
+   # minimize molecule energy with restraints
+   velocity all create 600.0 8675309 mom yes rot yes dist gaussian
+   fix NVE all nve
+   fix TFIX all langevin 600.0 0.0 100 24601
+   fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2}
+   fix_modify REST energy yes
+   run 10000
+   fix TFIX all langevin 0.0 0.0 100 24601
+   fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2}
+   fix_modify REST energy yes
+   run 10000
+   # sanity check for convergence
+   minimize 1e-6 1e-9 1000 100000
+   # report unrestrained energies
+   unfix REST
+   run 0
+
+
+----------
+
+
+The *bond* keyword applies a bond restraint to the specified atoms
+using the same functional form used by the :doc:`bond\_style harmonic <bond_harmonic>` command.  The potential associated with
+the restraint is
+
+.. math::
+
+   E = K (r - r_0)^2
+
+
+with the following coefficients:
+
+* :math:`K` (energy/distance\^2)
+* :math:`r_0` (distance)
+
+:math:`K` and :math:`r_0` are specified with the fix.  Note that the usual 1/2 factor
+is included in :math:`K`.
+
+
+----------
+
+
+The *angle* keyword applies an angle restraint to the specified atoms
+using the same functional form used by the :doc:`angle\_style harmonic <angle_harmonic>` command.  The potential associated with
+the restraint is
+
+.. math::
+
+   E = K (\theta - \theta_0)^2
+
+with the following coefficients:
+
+* :math:`K` (energy/radian\^2)
+* :math:`\theta_0` (degrees)
+
+:math:`K` and :math:`\theta_0` are specified with the fix.  Note that the usual 1/2
+factor is included in :math:`K`.
+
+
+----------
+
+
+The *dihedral* keyword applies a dihedral restraint to the specified
+atoms using a simplified form of the function used by the
+:doc:`dihedral\_style charmm <dihedral_charmm>` command.  The potential
+associated with the restraint is
+
+.. math::
+
+   E = K [ 1 + \cos (n \phi - d) ]
+
+
+with the following coefficients:
+
+* :math:`K` (energy)
+* :math:`n` (multiplicity, >= 0)
+* :math:`d` (degrees) = :math:`\phi_0 + 180`
+
+:math:`K` and :math:`\phi_0` are specified with the fix.  Note that the value of the
+dihedral multiplicity :math:`n` is set by default to 1. You can use the
+optional *mult* keyword to set it to a different positive integer.
+Also note that the energy will be a minimum when the
+current dihedral angle :math:`\phi` is equal to :math:`\phi_0`.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the potential energy associated with this fix to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+.. note::
+
+   If you want the fictitious potential energy associated with the
+   added forces to be included in the total potential energy of the
+   system (the quantity being minimized), you MUST enable the
+   :doc:`fix\_modify <fix_modify>` *energy* option for this fix.
+
+This fix computes a global scalar and a global vector of length 3,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar is the total potential energy for *all* the restraints as
+discussed above. The vector values are the sum of contributions to the
+following individual categories:
+
+* 1 = bond energy
+* 2 = angle energy
+* 3 = dihedral energy
+
+The scalar and vector values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+**Default:** none
diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt
deleted file mode 100644
index 8e962f4cc9..0000000000
--- a/doc/src/fix_restrain.txt
+++ /dev/null
@@ -1,209 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix restrain command :h3
-
-[Syntax:]
-
-fix ID group-ID restrain keyword args ... :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-restrain = style name of this fix command :l
-one or more keyword/arg pairs may be appended :l
-keyword = {bond} or {angle} or {dihedral} :l
-  {bond} args = atom1 atom2 Kstart Kstop r0
-    atom1,atom2 = IDs of 2 atoms in bond
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    r0 = equilibrium bond distance (distance units)
-  {angle} args = atom1 atom2 atom3 Kstart Kstop theta0
-    atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    theta0 = equilibrium angle theta (degrees)
-  {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
-    atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    phi0 = equilibrium dihedral angle phi (degrees)
-    keyword/value = optional keyword value pairs. supported keyword/value pairs:
-      {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre
-:ule
-
-[Examples:]
-
-fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
-fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
-fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
-fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 :pre
-
-[Description:]
-
-Restrain the motion of the specified sets of atoms by making them part
-of a bond or angle or dihedral interaction whose strength can vary
-over time during a simulation.  This is functionally similar to
-creating a bond or angle or dihedral for the same atoms in a data
-file, as specified by the "read_data"_read_data.html command, albeit
-with a time-varying pre-factor coefficient, and except for exclusion
-rules, as explained below.
-
-For the purpose of force field parameter-fitting or mapping a molecular
-potential energy surface, this fix reduces the hassle and risk
-associated with modifying data files.  In other words, use this fix to
-temporarily force a molecule to adopt a particular conformation.  To
-create a permanent bond or angle or dihedral, you should modify the
-data file.
-
-NOTE: Adding a bond/angle/dihedral with this command does not apply
-the exclusion rules and weighting factors specified by the
-"special_bonds"_special_bonds.html command to atoms in the restraint
-that are now bonded (1-2,1-3,1-4 neighbors) as a result.  If they are
-close enough to interact in a "pair_style"_pair_style.html sense
-(non-bonded interaction), then the bond/angle/dihedral restraint
-interaction will simply be superposed on top of that interaction.
-
-The group-ID specified by this fix is ignored.
-
-The second example above applies a restraint to hold the dihedral
-angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
-restraint coefficient.  The fourth example applies similar restraints
-to multiple dihedral angles using a restraint coefficient that
-increases from 0.0 to 2000.0 over the course of the run.
-
-NOTE: Adding a force to atoms implies a change in their potential
-energy as they move due to the applied force field.  For dynamics via
-the "run"_run.html command, this energy can be added to the system's
-potential energy for thermodynamic output (see below).  For energy
-minimization via the "minimize"_minimize.html command, this energy
-must be added to the system's potential energy to formulate a
-self-consistent minimization problem (see below).
-
-In order for a restraint to be effective, the restraint force must
-typically be significantly larger than the forces associated with
-conventional force field terms.  If the restraint is applied during a
-dynamics run (as opposed to during an energy minimization), a large
-restraint coefficient can significantly reduce the stable timestep
-size, especially if the atoms are initially far from the preferred
-conformation.  You may need to experiment to determine what value of K
-works best for a given application.
-
-For the case of finding a minimum energy structure for a single
-molecule with particular restraints (e.g. for fitting force field
-parameters or constructing a potential energy surface), commands such
-as the following may be useful:
-
-# minimize molecule energy with restraints
-velocity all create 600.0 8675309 mom yes rot yes dist gaussian
-fix NVE all nve
-fix TFIX all langevin 600.0 0.0 100 24601
-fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $\{angle1\} dihedral 3 1 2 9 0.0 5000.0 $\{angle2\}
-fix_modify REST energy yes
-run 10000
-fix TFIX all langevin 0.0 0.0 100 24601
-fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $\{angle1\} dihedral 3 1 2 9 5000.0 5000.0 $\{angle2\}
-fix_modify REST energy yes
-run 10000
-# sanity check for convergence
-minimize 1e-6 1e-9 1000 100000
-# report unrestrained energies
-unfix REST
-run 0 :pre
-
-:line
-
-The {bond} keyword applies a bond restraint to the specified atoms
-using the same functional form used by the "bond_style
-harmonic"_bond_harmonic.html command.  The potential associated with
-the restraint is
-
-:c,image(Eqs/bond_harmonic.jpg)
-
-with the following coefficients:
-
-K (energy/distance^2)
-r0 (distance) :ul
-
-K and r0 are specified with the fix.  Note that the usual 1/2 factor
-is included in K.
-
-:line
-
-The {angle} keyword applies an angle restraint to the specified atoms
-using the same functional form used by the "angle_style
-harmonic"_angle_harmonic.html command.  The potential associated with
-the restraint is
-
-:c,image(Eqs/angle_harmonic.jpg)
-
-with the following coefficients:
-
-K (energy/radian^2)
-theta0 (degrees) :ul
-
-K and theta0 are specified with the fix.  Note that the usual 1/2
-factor is included in K.
-
-:line
-
-The {dihedral} keyword applies a dihedral restraint to the specified
-atoms using a simplified form of the function used by the
-"dihedral_style charmm"_dihedral_charmm.html command.  The potential
-associated with the restraint is
-
-:c,image(Eqs/dihedral_charmm.jpg)
-
-with the following coefficients:
-
-K (energy)
-n (multiplicity, >= 0)
-d (degrees) = phi0 + 180 :ul
-
-K and phi0 are specified with the fix.  Note that the value of the
-dihedral multiplicity {n} is set by default to 1. You can use the
-optional {mult} keyword to set it to a different positive integer.
-Also note that the energy will be a minimum when the
-current dihedral angle phi is equal to phi0.
-
-:line
-
-[Restart, fix_modify, output, run start/stop, minimize info:]
-
-No information about this fix is written to "binary restart
-files"_restart.html.
-
-The "fix_modify"_fix_modify.html {energy} option is supported by this
-fix to add the potential energy associated with this fix to the
-system's potential energy as part of "thermodynamic
-output"_thermo_style.html.
-
-The "fix_modify"_fix_modify.html {respa} option is supported by this
-fix. This allows to set at which level of the "r-RESPA"_run_style.html
-integrator the fix is adding its forces. Default is the outermost level.
-
-NOTE: If you want the fictitious potential energy associated with the
-added forces to be included in the total potential energy of the
-system (the quantity being minimized), you MUST enable the
-"fix_modify"_fix_modify.html {energy} option for this fix.
-
-This fix computes a global scalar and a global vector of length 3,
-which can be accessed by various "output commands"_Howto_output.html.
-The scalar is the total potential energy for {all} the restraints as
-discussed above. The vector values are the sum of contributions to the
-following individual categories:
-
-1 = bond energy
-2 = angle energy
-3 = dihedral energy :ul
-
-The scalar and vector values calculated by this fix are "extensive".
-
-No parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command.
-
-[Restrictions:] none
-
-[Related commands:] none
-
-[Default:] none
diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst
new file mode 100644
index 0000000000..7f18b03966
--- /dev/null
+++ b/doc/src/fix_rhok.rst
@@ -0,0 +1,71 @@
+.. index:: fix rhok
+
+fix rhok command
+================
+
+
+.. parsed-literal::
+
+   fix ID group-ID rhok nx ny nz K a
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nx, ny, nz = k-vector of collective density field
+* K = spring constant of bias potential
+* a = anchor point of bias potential
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix bias all rhok 16 0 0 4.0 16.0
+   fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0
+   # output of 4 values from fix rhok: U_bias rho_k_RE  rho_k_IM  \|rho_k\|
+   thermo_style custom step temp pzz lz f_bias f_bias[1] f_bias[2] f_bias[3]
+
+Description
+"""""""""""
+
+The fix applies a force to atoms given by the potential
+
+.. image:: Eqs/fix_rhok.jpg
+   :align: center
+
+as described in :ref:`(Pedersen) <Pedersen>`.
+
+This field, which biases configurations with long-range order, can be
+used to study crystal-liquid interfaces and determine melting
+temperatures :ref:`(Pedersen) <Pedersen>`.
+
+An example of using the interface pinning method is located in the
+*examples/USER/misc/rhok* directory.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`thermo\_style <thermo_style>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Pedersen:
+
+
+
+**(Pedersen)** Pedersen, J. Chem. Phys., 139, 104102 (2013).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst
new file mode 100644
index 0000000000..1f16d33a19
--- /dev/null
+++ b/doc/src/fix_rigid.rst
@@ -0,0 +1,958 @@
+.. index:: fix rigid
+
+fix rigid command
+=================
+
+fix rigid/omp command
+=====================
+
+fix rigid/nve command
+=====================
+
+fix rigid/nve/omp command
+=========================
+
+fix rigid/nvt command
+=====================
+
+fix rigid/nvt/omp command
+=========================
+
+fix rigid/npt command
+=====================
+
+fix rigid/npt/omp command
+=========================
+
+fix rigid/nph command
+=====================
+
+fix rigid/nph/omp command
+=========================
+
+fix rigid/small command
+=======================
+
+fix rigid/small/omp command
+===========================
+
+fix rigid/nve/small command
+===========================
+
+fix rigid/nvt/small command
+===========================
+
+fix rigid/npt/small command
+===========================
+
+fix rigid/nph/small command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style bodystyle args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = *rigid* or *rigid/nve* or *rigid/nvt* or *rigid/npt* or *rigid/nph* or *rigid/small* or *rigid/nve/small* or *rigid/nvt/small* or *rigid/npt/small* or *rigid/nph/small*
+* bodystyle = *single* or *molecule* or *group*
+  
+  .. parsed-literal::
+  
+       *single* args = none
+       *molecule* args = none
+       *custom* args = *i_propname* or *v_varname*
+         i_propname = an integer property defined via fix property/atom
+         v_varname  = an atom-style or atomfile-style variable
+       *group* args = N groupID1 groupID2 ...
+         N = # of groups
+         groupID1, groupID2, ... = list of N group IDs
+
+* zero or more keyword/value pairs may be appended
+* keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile*
+  
+  .. parsed-literal::
+  
+       *langevin* values = Tstart Tstop Tperiod seed
+         Tstart,Tstop = desired temperature at start/stop of run (temperature units)
+         Tdamp = temperature damping parameter (time units)
+         seed = random number seed to use for white noise (positive integer)
+       *reinit* = *yes* or *no*
+       *temp* values = Tstart Tstop Tdamp
+         Tstart,Tstop = desired temperature at start/stop of run (temperature units)
+         Tdamp = temperature damping parameter (time units)
+       *iso* or *aniso* values = Pstart Pstop Pdamp
+         Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+         Pdamp = pressure damping parameter (time units)
+       *x* or *y* or *z* values = Pstart Pstop Pdamp
+         Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+         Pdamp = stress damping parameter (time units)
+       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *tparam* values = Tchain Titer Torder
+         Tchain = length of Nose/Hoover thermostat chain
+         Titer = number of thermostat iterations performed
+         Torder = 3 or 5 = Yoshida-Suzuki integration parameters
+       *pchain* values = Pchain
+         Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
+       *dilate* value = dilate-group-ID
+         dilate-group-ID = only dilate atoms in this group due to barostat volume changes
+       *force* values = M xflag yflag zflag
+         M = which rigid body from 1-Nbody (see asterisk form below)
+         xflag,yflag,zflag = off/on if component of center-of-mass force is active
+       *torque* values = M xflag yflag zflag
+         M = which rigid body from 1-Nbody (see asterisk form below)
+         xflag,yflag,zflag = off/on if component of center-of-mass torque is active
+       *infile* filename
+         filename = file with per-body values of mass, center-of-mass, moments of inertia
+       *mol* value = template-ID
+         template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 clump rigid single reinit yes
+   fix 1 clump rigid/small molecule
+   fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
+   fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 reinit no
+   fix 1 polychains rigid molecule force 1\*5 off off off force 6\*10 off off on
+   fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
+   fix 2 fluid rigid group 3 clump1 clump2 clump3 torque \* off off off
+   fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
+   fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
+   fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
+   fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0
+
+   variable bodyid atom 1.0\*gmask(clump1)+2.0\*gmask(clump2)+3.0\*gmask(clump3)
+   fix 1 clump rigid custom v_bodyid
+
+   variable bodyid atomfile bodies.txt
+   fix 1 clump rigid custom v_bodyid
+
+   fix 0 all property/atom i_bodyid
+   read_restart data.rigid fix 0 NULL Bodies
+   fix 1 clump rigid/small custom i_bodyid
+
+Description
+"""""""""""
+
+Treat one or more sets of atoms as independent rigid bodies.  This
+means that each timestep the total force and torque on each rigid body
+is computed as the sum of the forces and torques on its constituent
+particles.  The coordinates, velocities, and orientations of the atoms
+in each body are then updated so that the body moves and rotates as a
+single entity.  This is implemented by creating internal data structures
+for each rigid body and performing time integration on these data
+structures.  Positions, velocities, and orientations of the constituent
+particles are regenerated from the rigid body data structures in every
+time step. This restricts which operations and fixes can be applied to
+rigid bodies. See below for a detailed discussion.
+
+Examples of large rigid bodies are a colloidal particle, or portions
+of a biomolecule such as a protein.
+
+Example of small rigid bodies are patchy nanoparticles, such as those
+modeled in :ref:`this paper <Zhang1>` by Sharon Glotzer's group, clumps of
+granular particles, lipid molecules consisting of one or more point
+dipoles connected to other spheroids or ellipsoids, irregular
+particles built from line segments (2d) or triangles (3d), and
+coarse-grain models of nano or colloidal particles consisting of a
+small number of constituent particles.  Note that the :doc:`fix shake <fix_shake>` command can also be used to rigidify small
+molecules of 2, 3, or 4 atoms, e.g. water molecules.  That fix treats
+the constituent atoms as point masses.
+
+These fixes also update the positions and velocities of the atoms in
+each rigid body via time integration, in the NVE, NVT, NPT, or NPH
+ensemble, as described below.
+
+There are two main variants of this fix, fix rigid and fix
+rigid/small.  The NVE/NVT/NPT/NHT versions belong to one of the two
+variants, as their style names indicate.
+
+.. note::
+
+   Not all of the *bodystyle* options and keyword/value options are
+   available for both the *rigid* and *rigid/small* variants.  See
+   details below.
+
+The *rigid* styles are typically the best choice for a system with a
+small number of large rigid bodies, each of which can extend across
+the domain of many processors.  It operates by creating a single
+global list of rigid bodies, which all processors contribute to.
+MPI\_Allreduce operations are performed each timestep to sum the
+contributions from each processor to the force and torque on all the
+bodies.  This operation will not scale well in parallel if large
+numbers of rigid bodies are simulated.
+
+The *rigid/small* styles are typically best for a system with a large
+number of small rigid bodies.  Each body is assigned to the atom
+closest to the geometrical center of the body.  The fix operates using
+local lists of rigid bodies owned by each processor and information is
+exchanged and summed via local communication between neighboring
+processors when ghost atom info is accumulated.
+
+.. note::
+
+   To use the *rigid/small* styles the ghost atom cutoff must be
+   large enough to span the distance between the atom that owns the body
+   and every other atom in the body.  This distance value is printed out
+   when the rigid bodies are defined.  If the
+   :doc:`pair\_style <pair_style>` cutoff plus neighbor skin does not span
+   this distance, then you should use the :doc:`comm\_modify cutoff <comm_modify>` command with a setting epsilon larger than
+   the distance.
+
+Which of the two variants is faster for a particular problem is hard
+to predict.  The best way to decide is to perform a short test run.
+Both variants should give identical numerical answers for short runs.
+Long runs should give statistically similar results, but round-off
+differences may accumulate to produce divergent trajectories.
+
+.. note::
+
+   You should not update the atoms in rigid bodies via other
+   time-integration fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix move <fix_move>`),
+   or you will have conflicting updates to positions and velocities
+   resulting in unphysical behavior in most cases. When performing a hybrid
+   simulation with some atoms in rigid bodies, and some not, a separate
+   time integration fix like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` should be used for the non-rigid particles.
+
+.. note::
+
+   These fixes are overkill if you simply want to hold a collection
+   of atoms stationary or have them move with a constant velocity.  A
+   simpler way to hold atoms stationary is to not include those atoms in
+   your time integration fix.  E.g. use "fix 1 mobile nve" instead of
+   "fix 1 all nve", where "mobile" is the group of atoms that you want to
+   move.  You can move atoms with a constant velocity by assigning them
+   an initial velocity (via the :doc:`velocity <velocity>` command),
+   setting the force on them to 0.0 (via the :doc:`fix setforce <fix_setforce>` command), and integrating them as usual
+   (e.g. via the :doc:`fix nve <fix_nve>` command).
+
+.. warning::
+
+   The aggregate properties of each rigid body are
+   calculated at the start of a simulation run and are maintained in
+   internal data structures. The properties include the position and
+   velocity of the center-of-mass of the body, its moments of inertia, and
+   its angular momentum.  This is done using the properties of the
+   constituent atoms of the body at that point in time (or see the *infile*
+   keyword option).  Thereafter, changing these properties of individual
+   atoms in the body will have no effect on a rigid body's dynamics, unless
+   they effect any computation of per-atom forces or torques. If the
+   keyword *reinit* is set to *yes* (the default), the rigid body data
+   structures will be recreated at the beginning of each *run* command;
+   if the keyword *reinit* is set to *no*\ , the rigid body data structures
+   will be built only at the very first *run* command and maintained for
+   as long as the rigid fix is defined. For example, you might think you
+   could displace the atoms in a body or add a large velocity to each atom
+   in a body to make it move in a desired direction before a 2nd run is
+   performed, using the :doc:`set <set>` or
+   :doc:`displace\_atoms <displace_atoms>` or :doc:`velocity <velocity>`
+   commands.  But these commands will not affect the internal attributes
+   of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no*
+   (or using the *infile* option, which implies *reinit* *no*\ ) the position
+   and velocity of individual atoms in the body will be reset when time
+   integration starts again.
+
+
+----------
+
+
+Each rigid body must have two or more atoms.  An atom can belong to at
+most one rigid body.  Which atoms are in which bodies can be defined
+via several options.
+
+.. note::
+
+   With the *rigid/small* styles, which require that *bodystyle* be
+   specified as *molecule* or *custom*\ , you can define a system that has
+   no rigid bodies initially.  This is useful when you are using the
+   *mol* keyword in conjunction with another fix that is adding rigid
+   bodies on-the-fly as molecules, such as :doc:`fix deposit <fix_deposit>`
+   or :doc:`fix pour <fix_pour>`.
+
+For bodystyle *single* the entire fix group of atoms is treated as one
+rigid body.  This option is only allowed for the *rigid* styles.
+
+For bodystyle *molecule*\ , atoms are grouped into rigid bodies by their
+respective molecule IDs: each set of atoms in the fix group with the
+same molecule ID is treated as a different rigid body.  This option is
+allowed for both the *rigid* and *rigid/small* styles.  Note that
+atoms with a molecule ID = 0 will be treated as a single rigid body.
+For a system with atomic solvent (typically this is atoms with
+molecule ID = 0) surrounding rigid bodies, this may not be what you
+want.  Thus you should be careful to use a fix group that only
+includes atoms you want to be part of rigid bodies.
+
+Bodystyle *custom* is similar to bodystyle *molecule* except that it
+is more flexible in using other per-atom properties to define the sets
+of atoms that form rigid bodies.  An integer vector defined by the
+:doc:`fix property/atom <fix_property_atom>` command can be used.  Or an
+:doc:`atom-style or atomfile-style variable <variable>` can be used; the
+floating-point value produced by the variable is rounded to an
+integer.  As with bodystyle *molecule*\ , each set of atoms in the fix
+groups with the same integer value is treated as a different rigid
+body.  Since fix property/atom vectors and atom-style variables
+produce values for all atoms, you should be careful to use a fix group
+that only includes atoms you want to be part of rigid bodies.
+
+.. note::
+
+   To compute the initial center-of-mass position and other
+   properties of each rigid body, the image flags for each atom in the
+   body are used to "unwrap" the atom coordinates.  Thus you must insure
+   that these image flags are consistent so that the unwrapping creates a
+   valid rigid body (one where the atoms are close together),
+   particularly if the atoms in a single rigid body straddle a periodic
+   boundary.  This means the input data file or restart file must define
+   the image flags for each atom consistently or that you have used the
+   :doc:`set <set>` command to specify them correctly.  If a dimension is
+   non-periodic then the image flag of each atom must be 0 in that
+   dimension, else an error is generated.
+
+The *force* and *torque* keywords discussed next are only allowed for
+the *rigid* styles.
+
+By default, each rigid body is acted on by other atoms which induce an
+external force and torque on its center of mass, causing it to
+translate and rotate.  Components of the external center-of-mass force
+and torque can be turned off by the *force* and *torque* keywords.
+This may be useful if you wish a body to rotate but not translate, or
+vice versa, or if you wish it to rotate or translate continuously
+unaffected by interactions with other particles.  Note that if you
+expect a rigid body not to move or rotate by using these keywords, you
+must insure its initial center-of-mass translational or angular
+velocity is 0.0.  Otherwise the initial translational or angular
+momentum the body has will persist.
+
+An xflag, yflag, or zflag set to *off* means turn off the component of
+force of torque in that dimension.  A setting of *on* means turn on
+the component, which is the default.  Which rigid body(s) the settings
+apply to is determined by the first argument of the *force* and
+*torque* keywords.  It can be an integer M from 1 to Nbody, where
+Nbody is the number of rigid bodies defined.  A wild-card asterisk can
+be used in place of, or in conjunction with, the M argument to set the
+flags for multiple rigid bodies.  This takes the form "\*" or "\*n" or
+"n\*" or "m\*n".  If N = the number of rigid bodies, then an asterisk
+with no numeric values means all bodies from 1 to N.  A leading
+asterisk means all bodies from 1 to n (inclusive).  A trailing
+asterisk means all bodies from n to N (inclusive).  A middle asterisk
+means all types from m to n (inclusive).  Note that you can use the
+*force* or *torque* keywords as many times as you like.  If a
+particular rigid body has its component flags set multiple times, the
+settings from the final keyword are used.
+
+.. note::
+
+   For computational efficiency, you may wish to turn off pairwise
+   and bond interactions within each rigid body, as they no longer
+   contribute to the motion.  The :doc:`neigh\_modify exclude <neigh_modify>` and :doc:`delete\_bonds <delete_bonds>`
+   commands are used to do this.  If the rigid bodies have strongly
+   overlapping atoms, you may need to turn off these interactions to
+   avoid numerical problems due to large equal/opposite intra-body forces
+   swamping the contribution of small inter-body forces.
+
+For computational efficiency, you should typically define one fix
+rigid or fix rigid/small command which includes all the desired rigid
+bodies.  LAMMPS will allow multiple rigid fixes to be defined, but it
+is more expensive.
+
+
+----------
+
+
+The constituent particles within a rigid body can be point particles
+(the default in LAMMPS) or finite-size particles, such as spheres or
+ellipsoids or line segments or triangles.  See the :doc:`atom\_style sphere and ellipsoid and line and tri <atom_style>` commands for more
+details on these kinds of particles.  Finite-size particles contribute
+differently to the moment of inertia of a rigid body than do point
+particles.  Finite-size particles can also experience torque (e.g. due
+to :doc:`frictional granular interactions <pair_gran>`) and have an
+orientation.  These contributions are accounted for by these fixes.
+
+Forces between particles within a body do not contribute to the
+external force or torque on the body.  Thus for computational
+efficiency, you may wish to turn off pairwise and bond interactions
+between particles within each rigid body.  The :doc:`neigh\_modify exclude <neigh_modify>` and :doc:`delete\_bonds <delete_bonds>`
+commands are used to do this.  For finite-size particles this also
+means the particles can be highly overlapped when creating the rigid
+body.
+
+
+----------
+
+
+The *rigid*\ , *rigid/nve*\ , *rigid/small*\ , and *rigid/small/nve* styles
+perform constant NVE time integration.  They are referred to below as
+the 4 NVE rigid styles.  The only difference is that the *rigid* and
+*rigid/small* styles use an integration technique based on Richardson
+iterations.  The *rigid/nve* and *rigid/small/nve* styles uses the
+methods described in the paper by :ref:`Miller <Miller3>`, which are thought
+to provide better energy conservation than an iterative approach.
+
+The *rigid/nvt* and *rigid/nvt/small* styles performs constant NVT
+integration using a Nose/Hoover thermostat with chains as described
+originally in :ref:`(Hoover) <Hoover>` and :ref:`(Martyna) <Martyna2>`, which
+thermostats both the translational and rotational degrees of freedom
+of the rigid bodies.  They are referred to below as the 2 NVT rigid
+styles.  The rigid-body algorithm used by *rigid/nvt* is described in
+the paper by :ref:`Kamberaj <Kamberaj>`.
+
+The *rigid/npt*\ , *rigid/nph*\ , *rigid/npt/small*\ , and *rigid/nph/small*
+styles perform constant NPT or NPH integration using a Nose/Hoover
+barostat with chains.  They are referred to below as the 4 NPT and NPH
+rigid styles.  For the NPT case, the same Nose/Hoover thermostat is
+also used as with *rigid/nvt* and *rigid/nvt/small*\ .
+
+The barostat parameters are specified using one or more of the *iso*\ ,
+*aniso*\ , *x*\ , *y*\ , *z* and *couple* keywords.  These keywords give you
+the ability to specify 3 diagonal components of the external stress
+tensor, and to couple these components together so that the dimensions
+they represent are varied together during a constant-pressure
+simulation.  The effects of these keywords are similar to those
+defined in :doc:`fix npt/nph <fix_nh>`
+
+.. note::
+
+   Currently the *rigid/npt*\ , *rigid/nph*\ , *rigid/npt/small*\ , and
+   *rigid/nph/small* styles do not support triclinic (non-orthogonal)
+   boxes.
+
+The target pressures for each of the 6 components of the stress tensor
+can be specified independently via the *x*\ , *y*\ , *z* keywords, which
+correspond to the 3 simulation box dimensions.  For each component,
+the external pressure or tensor component at each timestep is a ramped
+value during the run from *Pstart* to *Pstop*\ . If a target pressure is
+specified for a component, then the corresponding box dimension will
+change during a simulation.  For example, if the *y* keyword is used,
+the y-box length will change.  A box dimension will not change if that
+component is not specified, although you have the option to change
+that dimension via the :doc:`fix deform <fix_deform>` command.
+
+For all barostat keywords, the *Pdamp* parameter operates like the
+*Tdamp* parameter, determining the time scale on which pressure is
+relaxed.  For example, a value of 10.0 means to relax the pressure in
+a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+the :doc:`units <units>` command).
+
+Regardless of what atoms are in the fix group (the only atoms which
+are time integrated), a global pressure or stress tensor is computed
+for all atoms.  Similarly, when the size of the simulation box is
+changed, all atoms are re-scaled to new positions, unless the keyword
+*dilate* is specified with a *dilate-group-ID* for a group that
+represents a subset of the atoms.  This can be useful, for example, to
+leave the coordinates of atoms in a solid substrate unchanged and
+controlling the pressure of a surrounding fluid.  Another example is a
+system consisting of rigid bodies and point particles where the
+barostat is only coupled with the rigid bodies.  This option should be
+used with care, since it can be unphysical to dilate some atoms and
+not others, because it can introduce large, instantaneous
+displacements between a pair of atoms (one dilated, one not) that are
+far from the dilation origin.
+
+The *couple* keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together.  The value specified
+with the keyword determines which are coupled.  For example, *xz*
+means the *Pxx* and *Pzz* components of the stress tensor are coupled.
+*Xyz* means all 3 diagonal components are coupled.  Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep.  The
+*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must
+be identical.  *Couple xyz* can be used for a 2d simulation; the *z*
+dimension is simply ignored.
+
+The *iso* and *aniso* keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+
+The keyword *iso* means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together.  Using "iso Pstart Pstop Pdamp" is the same as
+specifying these 4 keywords:
+
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   couple xyz
+
+The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled
+independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure.  Using "aniso Pstart Pstop Pdamp" is the same as specifying
+these 4 keywords:
+
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   couple none
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+The *reinit* keyword determines, whether the rigid body properties
+are re-initialized between run commands. With the option *yes* (the
+default) this is done, with the option *no* this is not done. Turning
+off the re-initialization can be helpful to protect rigid bodies against
+unphysical manipulations between runs or when properties cannot be
+easily re-computed (e.g. when read from a file). When using the *infile*
+keyword, the *reinit* option is automatically set to *no*\ .
+
+The *langevin* and *temp* and *tparam* keywords perform thermostatting
+of the rigid bodies, altering both their translational and rotational
+degrees of freedom.  What is meant by "temperature" of a collection of
+rigid bodies and how it can be monitored via the fix output is
+discussed below.
+
+The *langevin* keyword applies a Langevin thermostat to the constant
+NVE time integration performed by any of the 4 NVE rigid styles:
+*rigid*\ , *rigid/nve*\ , *rigid/small*\ , *rigid/small/nve*\ .  It cannot be
+used with the 2 NVT rigid styles: *rigid/nvt*\ , *rigid/small/nvt*\ .  The
+desired temperature at each timestep is a ramped value during the run
+from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in time
+units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+:doc:`units <units>` command).  The random # *seed* must be a positive
+integer.
+
+The way that Langevin thermostatting operates is explained on the :doc:`fix langevin <fix_langevin>` doc page.  If you wish to simply viscously
+damp the rotational motion without thermostatting, you can set
+*Tstart* and *Tstop* to 0.0, which means only the viscous drag term in
+the Langevin thermostat will be applied.  See the discussion on the
+:doc:`fix viscous <fix_viscous>` doc page for details.
+
+.. note::
+
+   When the *langevin* keyword is used with fix rigid versus fix
+   rigid/small, different dynamics will result for parallel runs.  This
+   is because of the way random numbers are used in the two cases.  The
+   dynamics for the two cases should be statistically similar, but will
+   not be identical, even for a single timestep.
+
+The *temp* and *tparam* keywords apply a Nose/Hoover thermostat to the
+NVT time integration performed by the 2 NVT rigid styles.  They cannot
+be used with the 4 NVE rigid styles.  The desired temperature at each
+timestep is a ramped value during the run from *Tstart* to *Tstop*\ .
+The *Tdamp* parameter is specified in time units and determines how
+rapidly the temperature is relaxed.  For example, a value of 100.0
+means to relax the temperature in a timespan of (roughly) 100 time
+units (tau or fmsec or psec - see the :doc:`units <units>` command).
+
+Nose/Hoover chains are used in conjunction with this thermostat.  The
+*tparam* keyword can optionally be used to change the chain settings
+used.  *Tchain* is the number of thermostats in the Nose Hoover chain.
+This value, along with *Tdamp* can be varied to dampen undesirable
+oscillations in temperature that can occur in a simulation.  As a rule
+of thumb, increasing the chain length should lead to smaller
+oscillations. The keyword *pchain* specifies the number of
+thermostats in the chain thermostatting the barostat degrees of
+freedom.
+
+.. note::
+
+   There are alternate ways to thermostat a system of rigid bodies.
+   You can use :doc:`fix langevin <fix_langevin>` to treat the individual
+   particles in the rigid bodies as effectively immersed in an implicit
+   solvent, e.g. a Brownian dynamics model.  For hybrid systems with both
+   rigid bodies and solvent particles, you can thermostat only the
+   solvent particles that surround one or more rigid bodies by
+   appropriate choice of groups in the compute and fix commands for
+   temperature and thermostatting.  The solvent interactions with the
+   rigid bodies should then effectively thermostat the rigid body
+   temperature as well without use of the Langevin or Nose/Hoover options
+   associated with the fix rigid commands.
+
+
+----------
+
+
+The *mol* keyword can only be used with the *rigid/small* styles.  It
+must be used when other commands, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`, add rigid
+bodies on-the-fly during a simulation.  You specify a *template-ID*
+previously defined using the :doc:`molecule <molecule>` command, which
+reads a file that defines the molecule.  You must use the same
+*template-ID* that the other fix which is adding rigid bodies uses.
+The coordinates, atom types, atom diameters, center-of-mass, and
+moments of inertia can be specified in the molecule file.  See the
+:doc:`molecule <molecule>` command for details.  The only settings
+required to be in this file are the coordinates and types of atoms in
+the molecule, in which case the molecule command calculates the other
+quantities itself.
+
+Note that these other fixes create new rigid bodies, in addition to
+those defined initially by this fix via the *bodystyle* setting.
+
+Also note that when using the *mol* keyword, extra restart information
+about all rigid bodies is written out whenever a restart file is
+written out.  See the NOTE in the next section for details.
+
+
+----------
+
+
+The *infile* keyword allows a file of rigid body attributes to be read
+in from a file, rather then having LAMMPS compute them.  There are 5
+such attributes: the total mass of the rigid body, its center-of-mass
+position, its 6 moments of inertia, its center-of-mass velocity, and
+the 3 image flags of the center-of-mass position.  For rigid bodies
+consisting of point particles or non-overlapping finite-size
+particles, LAMMPS can compute these values accurately.  However, for
+rigid bodies consisting of finite-size particles which overlap each
+other, LAMMPS will ignore the overlaps when computing these 4
+attributes.  The amount of error this induces depends on the amount of
+overlap.  To avoid this issue, the values can be pre-computed
+(e.g. using Monte Carlo integration).
+
+The format of the file is as follows.  Note that the file does not
+have to list attributes for every rigid body integrated by fix rigid.
+Only bodies which the file specifies will have their computed
+attributes overridden.  The file can contain initial blank lines or
+comment lines starting with "#" which are ignored.  The first
+non-blank, non-comment line should list N = the number of lines to
+follow.  The N successive lines contain the following information:
+
+
+.. parsed-literal::
+
+   ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+   ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+   ...
+   IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+
+The rigid body IDs are all positive integers.  For the *single*
+bodystyle, only an ID of 1 can be used.  For the *group* bodystyle,
+IDs from 1 to Ng can be used where Ng is the number of specified
+groups.  For the *molecule* bodystyle, use the molecule ID for the
+atoms in a specific rigid body as the rigid body ID.
+
+The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
+self-explanatory.  The center-of-mass should be consistent with what
+is calculated for the position of the rigid body with all its atoms
+unwrapped by their respective image flags.  If this produces a
+center-of-mass that is outside the simulation box, LAMMPS wraps it
+back into the box.
+
+The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
+values consistent with the current orientation of the rigid body
+around its center of mass.  The values are with respect to the
+simulation box XYZ axes, not with respect to the principal axes of the
+rigid body itself.  LAMMPS performs the latter calculation internally.
+
+The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
+The (lx,ly,lz) values are the angular momentum of the body.  The
+(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
+wish the body to have no initial motion.
+
+The (ixcm,iycm,izcm) values are the image flags of the center of mass
+of the body.  For periodic dimensions, they specify which image of the
+simulation box the body is considered to be in.  An image of 0 means
+it is inside the box as defined.  A value of 2 means add 2 box lengths
+to get the true value.  A value of -1 means subtract 1 box length to
+get the true value.  LAMMPS updates these flags as the rigid bodies
+cross periodic boundaries during the simulation.
+
+.. note::
+
+   If you use the *infile* or *mol* keywords and write restart
+   files during a simulation, then each time a restart file is written,
+   the fix also write an auxiliary restart file with the name
+   rfile.rigid, where "rfile" is the name of the restart file,
+   e.g. tmp.restart.10000 and tmp.restart.10000.rigid.  This auxiliary
+   file is in the same format described above.  Thus it can be used in a
+   new input script that restarts the run and re-specifies a rigid fix
+   using an *infile* keyword and the appropriate filename.  Note that the
+   auxiliary file will contain one line for every rigid body, even if the
+   original file only listed a subset of the rigid bodies.
+
+
+----------
+
+
+If you use a :doc:`temperature compute <compute>` with a group that
+includes particles in rigid bodies, the degrees-of-freedom removed by
+each rigid body are accounted for in the temperature (and pressure)
+computation, but only if the temperature group includes all the
+particles in a particular rigid body.
+
+A 3d rigid body has 6 degrees of freedom (3 translational, 3
+rotational), except for a collection of point particles lying on a
+straight line, which has only 5, e.g a dimer.  A 2d rigid body has 3
+degrees of freedom (2 translational, 1 rotational).
+
+.. note::
+
+   You may wish to explicitly subtract additional
+   degrees-of-freedom if you use the *force* and *torque* keywords to
+   eliminate certain motions of one or more rigid bodies.  LAMMPS does
+   not do this automatically.
+
+The rigid body contribution to the pressure of the system (virial) is
+also accounted for by this fix.
+
+
+----------
+
+
+If your simulation is a hybrid model with a mixture of rigid bodies
+and non-rigid particles (e.g. solvent) there are several ways these
+rigid fixes can be used in tandem with :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph <fix_nh>`.
+
+If you wish to perform NVE dynamics (no thermostatting or
+barostatting), use one of 4 NVE rigid styles to integrate the rigid
+bodies, and :doc:`fix nve <fix_nve>` to integrate the non-rigid
+particles.
+
+If you wish to perform NVT dynamics (thermostatting, but no
+barostatting), you can use one of the 2 NVT rigid styles for the rigid
+bodies, and any thermostatting fix for the non-rigid particles (:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`).  You can also use one of the
+4 NVE rigid styles for the rigid bodies and thermostat them using :doc:`fix langevin <fix_langevin>` on the group that contains all the
+particles in the rigid bodies.  The net force added by :doc:`fix langevin <fix_langevin>` to each rigid body effectively thermostats
+its translational center-of-mass motion.  Not sure how well it does at
+thermostatting its rotational motion.
+
+If you with to perform NPT or NPH dynamics (barostatting), you cannot
+use both :doc:`fix npt <fix_nh>` and the NPT or NPH rigid styles.  This
+is because there can only be one fix which monitors the global
+pressure and changes the simulation box dimensions.  So you have 3
+choices:
+
+* Use one of the 4 NPT or NPH styles for the rigid bodies.  Use the
+  *dilate* all option so that it will dilate the positions of the
+  non-rigid particles as well.  Use :doc:`fix nvt <fix_nh>` (or any other
+  thermostat) for the non-rigid particles.
+* Use :doc:`fix npt <fix_nh>` for the group of non-rigid particles.  Use
+  the *dilate* all option so that it will dilate the center-of-mass
+  positions of the rigid bodies as well.  Use one of the 4 NVE or 2 NVT
+  rigid styles for the rigid bodies.
+* Use :doc:`fix press/berendsen <fix_press_berendsen>` to compute the
+  pressure and change the box dimensions.  Use one of the 4 NVE or 2 NVT
+  rigid styles for the rigid bodies.  Use :doc:`fix nvt <fix_nh>` (or any
+  other thermostat) for the non-rigid particles.
+
+
+In all case, the rigid bodies and non-rigid particles both contribute
+to the global pressure and the box is scaled the same by any of the
+barostatting fixes.
+
+You could even use the 2nd and 3rd options for a non-hybrid simulation
+consisting of only rigid bodies, assuming you give :doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to do.  The
+barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) will monitor the pressure
+and change the box dimensions, but not time integrate any particles.
+The integration of the rigid bodies will be performed by fix
+rigid/nvt.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about the 4 NVE rigid styles is written to :doc:`binary restart files <restart>`.  The exception is if the *infile* or
+*mol* keyword is used, in which case an auxiliary file is written out
+with rigid body information each time a restart file is written, as
+explained above for the *infile* keyword.  For the 2 NVT rigid styles,
+the state of the Nose/Hoover thermostat is written to :doc:`binary restart files <restart>`.  Ditto for the 4 NPT and NPH rigid styles, and
+the state of the Nose/Hoover barostat.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by the 6
+NVT, NPT, NPH rigid styles to add the energy change induced by the
+thermostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to keeping the objects rigid to the
+system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+The default is *virial yes*
+
+The :doc:`fix\_modify <fix_modify>` *temp* and *press* options are
+supported by the 4 NPT and NPH rigid styles to change the computes
+used to calculate the instantaneous pressure tensor.  Note that the 2
+NVT rigid fixes do not use any external compute to compute
+instantaneous temperature.
+
+The :doc:`fix\_modify <fix_modify>` *bodyforces* option is supported by
+all rigid styles to set whether per-body forces and torques are
+computed early or late in a timestep, i.e. at the post-force stage or
+at the final-integrate stage or the timestep, respectively.
+
+The 2 NVE rigid fixes compute a global scalar which can be accessed by
+various :doc:`output commands <Howto_output>`.  The scalar value
+calculated by these fixes is "intensive".  The scalar is the current
+temperature of the collection of rigid bodies.  This is averaged over
+all rigid bodies and their translational and rotational degrees of
+freedom.  The translational energy of a rigid body is 1/2 m v\^2, where
+m = total mass of the body and v = the velocity of its center of mass.
+The rotational energy of a rigid body is 1/2 I w\^2, where I = the
+moment of inertia tensor of the body and w = its angular velocity.
+Degrees of freedom constrained by the *force* and *torque* keywords
+are removed from this calculation, but only for the *rigid* and
+*rigid/nve* fixes.
+
+The 6 NVT, NPT, NPH rigid fixes compute a global scalar which can be
+accessed by various :doc:`output commands <Howto_output>`.  The scalar
+value calculated by these fixes is "extensive".  The scalar is the
+cumulative energy change due to the thermostatting and barostatting
+the fix performs.
+
+All of the *rigid* styles (not the *rigid/small* styles) compute a
+global array of values which can be accessed by various :doc:`output commands <Howto_output>`.  Similar information about the bodies
+defined by the *rigid/small* styles can be accessed via the :doc:`compute rigid/local <compute_rigid_local>` command.
+
+The number of rows in the array is equal to the number of rigid
+bodies.  The number of columns is 15.  Thus for each rigid body, 15
+values are stored: the xyz coords of the center of mass (COM), the xyz
+components of the COM velocity, the xyz components of the force acting
+on the COM, the xyz components of the torque acting on the COM, and
+the xyz image flags of the COM.
+
+The center of mass (COM) for each body is similar to unwrapped
+coordinates written to a dump file.  It will always be inside (or
+slightly outside) the simulation box.  The image flags have the same
+meaning as image flags for atom positions (see the "dump" command).
+This means you can calculate the unwrapped COM by applying the image
+flags to the COM, the same as when unwrapped coordinates are written
+to a dump file.
+
+The force and torque values in the array are not affected by the
+*force* and *torque* keywords in the fix rigid command; they reflect
+values before any changes are made by those keywords.
+
+The ordering of the rigid bodies (by row in the array) is as follows.
+For the *single* keyword there is just one rigid body.  For the
+*molecule* keyword, the bodies are ordered by ascending molecule ID.
+For the *group* keyword, the list of group IDs determines the ordering
+of bodies.
+
+The array values calculated by these fixes are "intensive", meaning
+they are independent of the number of atoms in the simulation.
+
+No parameter of these fixes can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.  These fixes are not invoked during
+:doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These fixes are all part of the RIGID package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Assigning a temperature via the :doc:`velocity create <velocity>`
+command to a system with :doc:`rigid bodies <fix_rigid>` may not have
+the desired outcome for two reasons.  First, the velocity command can
+be invoked before the rigid-body fix is invoked or initialized and the
+number of adjusted degrees of freedom (DOFs) is known.  Thus it is not
+possible to compute the target temperature correctly.  Second, the
+assigned velocities may be partially canceled when constraints are
+first enforced, leading to a different temperature than desired.  A
+workaround for this is to perform a :doc:`run 0 <run>` command, which
+insures all DOFs are accounted for properly, and then rescale the
+temperature to the desired value before performing a simulation.  For
+example:
+
+
+.. parsed-literal::
+
+   velocity all create 300.0 12345
+   run 0                             # temperature may not be 300K
+   velocity all scale 300.0          # now it should be
+
+Related commands
+""""""""""""""""
+
+:doc:`delete\_bonds <delete_bonds>`, :doc:`neigh\_modify <neigh_modify>`
+exclude, :doc:`fix shake <fix_shake>`
+
+Default
+"""""""
+
+The option defaults are force \* on on on and torque \* on on on,
+meaning all rigid bodies are acted on by center-of-mass force and
+torque.  Also Tchain = Pchain = 10, Titer = 1, Torder = 3, reinit = yes.
+
+
+----------
+
+
+.. _Hoover:
+
+
+
+**(Hoover)** Hoover, Phys Rev A, 31, 1695 (1985).
+
+.. _Kamberaj:
+
+
+
+**(Kamberaj)** Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
+
+.. _Martyna2:
+
+
+
+**(Martyna)** Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
+Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
+
+.. _Miller3:
+
+
+
+**(Miller)** Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
+J Chem Phys, 116, 8649 (2002).
+
+.. _Zhang1:
+
+
+
+**(Zhang)** Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst
new file mode 100644
index 0000000000..c7835e83fb
--- /dev/null
+++ b/doc/src/fix_rigid_meso.rst
@@ -0,0 +1,396 @@
+.. index:: fix rigid/meso
+
+fix rigid/meso command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID rigid/meso bodystyle args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rigid/meso = style name of this fix command
+* bodystyle = *single* or *molecule* or *group*
+  
+  .. parsed-literal::
+  
+       *single* args = none
+       *molecule* args = none
+       *custom* args = *i_propname* or *v_varname*
+         i_propname = an integer property defined via fix property/atom
+         v_varname  = an atom-style or atomfile-style variable
+       *group* args = N groupID1 groupID2 ...
+         N = # of groups
+         groupID1, groupID2, ... = list of N group IDs
+
+* zero or more keyword/value pairs may be appended
+* keyword = *reinit* or *force* or *torque* or *infile*
+  
+  .. parsed-literal::
+  
+       *reinit* = *yes* or *no*
+       *force* values = M xflag yflag zflag
+         M = which rigid body from 1-Nbody (see asterisk form below)
+         xflag,yflag,zflag = off/on if component of center-of-mass force is active
+       *torque* values = M xflag yflag zflag
+         M = which rigid body from 1-Nbody (see asterisk form below)
+         xflag,yflag,zflag = off/on if component of center-of-mass torque is active
+       *infile* filename
+         filename = file with per-body values of mass, center-of-mass, moments of inertia
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 ellipsoid rigid/meso single
+   fix 1 rods      rigid/meso molecule
+   fix 1 spheres   rigid/meso single force 1 off off on
+   fix 1 particles rigid/meso molecule force 1\*5 off off off force 6\*10 off off on
+   fix 2 spheres   rigid/meso group 3 sphere1 sphere2 sphere3 torque \* off off off
+
+Description
+"""""""""""
+
+Treat one or more sets of mesoscopic SPH/SDPD particles as independent
+rigid bodies.  This means that each timestep the total force and torque
+on each rigid body is computed as the sum of the forces and torques on
+its constituent particles.  The coordinates and velocities of the
+particles in each body are then updated so that the body moves and
+rotates as a single entity using the methods described in the paper by
+:ref:`(Miller) <Miller>`. Density and internal energy of the particles will
+also be updated. This is implemented by creating internal data structures
+for each rigid body and performing time integration on these data
+structures.  Positions and velocities of the constituent particles are
+regenerated from the rigid body data structures in every time step. This
+restricts which operations and fixes can be applied to rigid bodies. See
+below for a detailed discussion.
+
+The operation of this fix is exactly like that described by the
+:doc:`fix rigid/nve <fix_rigid>` command, except that particles' density,
+internal energy and extrapolated velocity are also updated.
+
+.. note::
+
+   You should not update the particles in rigid bodies via other
+   time-integration fixes (e.g. :doc:`fix meso <fix_meso>`,
+   :doc:`fix meso/stationary <fix_meso_stationary>`), or you will have conflicting
+   updates to positions and velocities resulting in unphysical behavior in most
+   cases. When performing a hybrid simulation with some atoms in rigid bodies,
+   and some not, a separate time integration fix like :doc:`fix meso <fix_meso>`
+   should be used for the non-rigid particles.
+
+.. note::
+
+   These fixes are overkill if you simply want to hold a collection
+   of particles stationary or have them move with a constant velocity. To
+   hold particles stationary use :doc:`fix meso/stationary <fix_meso_stationary>` instead. If you would like to
+   move particles with a constant velocity use :doc:`fix meso/move <fix_meso_move>`.
+
+.. warning::
+
+   The aggregate properties of each rigid body are
+   calculated at the start of a simulation run and are maintained in
+   internal data structures. The properties include the position and
+   velocity of the center-of-mass of the body, its moments of inertia, and
+   its angular momentum.  This is done using the properties of the
+   constituent particles of the body at that point in time (or see the *infile*
+   keyword option).  Thereafter, changing these properties of individual
+   particles in the body will have no effect on a rigid body's dynamics, unless
+   they effect any computation of per-particle forces or torques. If the
+   keyword *reinit* is set to *yes* (the default), the rigid body data
+   structures will be recreated at the beginning of each *run* command;
+   if the keyword *reinit* is set to *no*\ , the rigid body data structures
+   will be built only at the very first *run* command and maintained for
+   as long as the rigid fix is defined. For example, you might think you
+   could displace the particles in a body or add a large velocity to each particle
+   in a body to make it move in a desired direction before a 2nd run is
+   performed, using the :doc:`set <set>` or
+   :doc:`displace\_atoms <displace_atoms>` or :doc:`velocity <velocity>`
+   commands.  But these commands will not affect the internal attributes
+   of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no*
+   (or using the *infile* option, which implies *reinit* *no*\ ) the position
+   and velocity of individual particles in the body will be reset when time
+   integration starts again.
+
+
+----------
+
+
+Each rigid body must have two or more particles.  A particle can belong
+to at most one rigid body.  Which particles are in which bodies can be
+defined via several options.
+
+For bodystyle *single* the entire fix group of particles is treated as
+one rigid body.
+
+For bodystyle *molecule*\ , particles are grouped into rigid bodies by their
+respective molecule IDs: each set of particles in the fix group with the
+same molecule ID is treated as a different rigid body.  Note that particles
+with a molecule ID = 0 will be treated as a single rigid body. For a
+system with solvent (typically this is particles with molecule ID = 0)
+surrounding rigid bodies, this may not be what you want.  Thus you
+should be careful to use a fix group that only includes particles you
+want to be part of rigid bodies.
+
+Bodystyle *custom* is similar to bodystyle *molecule* except that it
+is more flexible in using other per-atom properties to define the sets
+of particles that form rigid bodies.  An integer vector defined by the
+:doc:`fix property/atom <fix_property_atom>` command can be used.  Or an
+:doc:`atom-style or atomfile-style variable <variable>` can be used; the
+floating-point value produced by the variable is rounded to an
+integer.  As with bodystyle *molecule*\ , each set of particles in the fix
+groups with the same integer value is treated as a different rigid
+body.  Since fix property/atom vectors and atom-style variables
+produce values for all particles, you should be careful to use a fix group
+that only includes particles you want to be part of rigid bodies.
+
+For bodystyle *group*\ , each of the listed groups is treated as a
+separate rigid body.  Only particles that are also in the fix group are
+included in each rigid body.
+
+.. note::
+
+   To compute the initial center-of-mass position and other
+   properties of each rigid body, the image flags for each particle in the
+   body are used to "unwrap" the particle coordinates.  Thus you must
+   insure that these image flags are consistent so that the unwrapping
+   creates a valid rigid body (one where the particles are close together)
+   , particularly if the particles in a single rigid body straddle a
+   periodic boundary.  This means the input data file or restart file must
+   define the image flags for each particle consistently or that you have
+   used the :doc:`set <set>` command to specify them correctly.  If a
+   dimension is non-periodic then the image flag of each particle must be
+   0 in that dimension, else an error is generated.
+
+By default, each rigid body is acted on by other particles which induce
+an external force and torque on its center of mass, causing it to
+translate and rotate.  Components of the external center-of-mass force
+and torque can be turned off by the *force* and *torque* keywords.
+This may be useful if you wish a body to rotate but not translate, or
+vice versa, or if you wish it to rotate or translate continuously
+unaffected by interactions with other particles.  Note that if you
+expect a rigid body not to move or rotate by using these keywords, you
+must insure its initial center-of-mass translational or angular
+velocity is 0.0. Otherwise the initial translational or angular
+momentum, the body has, will persist.
+
+An xflag, yflag, or zflag set to *off* means turn off the component of
+force or torque in that dimension.  A setting of *on* means turn on
+the component, which is the default.  Which rigid body(s) the settings
+apply to is determined by the first argument of the *force* and
+*torque* keywords.  It can be an integer M from 1 to Nbody, where
+Nbody is the number of rigid bodies defined.  A wild-card asterisk can
+be used in place of, or in conjunction with, the M argument to set the
+flags for multiple rigid bodies.  This takes the form "\*" or "\*n" or
+"n\*" or "m\*n".  If N = the number of rigid bodies, then an asterisk
+with no numeric values means all bodies from 1 to N.  A leading
+asterisk means all bodies from 1 to n (inclusive).  A trailing
+asterisk means all bodies from n to N (inclusive).  A middle asterisk
+means all bodies from m to n (inclusive).  Note that you can use the
+*force* or *torque* keywords as many times as you like.  If a
+particular rigid body has its component flags set multiple times, the
+settings from the final keyword are used.
+
+For computational efficiency, you should typically define one fix
+rigid/meso command which includes all the desired rigid bodies. LAMMPS
+will allow multiple rigid/meso fixes to be defined, but it is more
+expensive.
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+The *reinit* keyword determines, whether the rigid body properties
+are re-initialized between run commands. With the option *yes* (the
+default) this is done, with the option *no* this is not done. Turning
+off the re-initialization can be helpful to protect rigid bodies against
+unphysical manipulations between runs or when properties cannot be
+easily re-computed (e.g. when read from a file). When using the *infile*
+keyword, the *reinit* option is automatically set to *no*\ .
+
+
+----------
+
+
+The *infile* keyword allows a file of rigid body attributes to be read
+in from a file, rather then having LAMMPS compute them.  There are 5
+such attributes: the total mass of the rigid body, its center-of-mass
+position, its 6 moments of inertia, its center-of-mass velocity, and
+the 3 image flags of the center-of-mass position.  For rigid bodies
+consisting of point particles or non-overlapping finite-size
+particles, LAMMPS can compute these values accurately.  However, for
+rigid bodies consisting of finite-size particles which overlap each
+other, LAMMPS will ignore the overlaps when computing these 4
+attributes.  The amount of error this induces depends on the amount of
+overlap.  To avoid this issue, the values can be pre-computed
+(e.g. using Monte Carlo integration).
+
+The format of the file is as follows.  Note that the file does not
+have to list attributes for every rigid body integrated by fix rigid.
+Only bodies which the file specifies will have their computed
+attributes overridden.  The file can contain initial blank lines or
+comment lines starting with "#" which are ignored.  The first
+non-blank, non-comment line should list N = the number of lines to
+follow.  The N successive lines contain the following information:
+
+
+.. parsed-literal::
+
+   ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+   ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+   ...
+   IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+
+The rigid body IDs are all positive integers.  For the *single*
+bodystyle, only an ID of 1 can be used.  For the *group* bodystyle,
+IDs from 1 to Ng can be used where Ng is the number of specified
+groups.  For the *molecule* bodystyle, use the molecule ID for the
+atoms in a specific rigid body as the rigid body ID.
+
+The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
+self-explanatory.  The center-of-mass should be consistent with what
+is calculated for the position of the rigid body with all its atoms
+unwrapped by their respective image flags.  If this produces a
+center-of-mass that is outside the simulation box, LAMMPS wraps it
+back into the box.
+
+The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
+values consistent with the current orientation of the rigid body
+around its center of mass.  The values are with respect to the
+simulation box XYZ axes, not with respect to the principal axes of the
+rigid body itself.  LAMMPS performs the latter calculation internally.
+
+The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
+The (lx,ly,lz) values are the angular momentum of the body.  The
+(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
+wish the body to have no initial motion.
+
+The (ixcm,iycm,izcm) values are the image flags of the center of mass
+of the body.  For periodic dimensions, they specify which image of the
+simulation box the body is considered to be in.  An image of 0 means
+it is inside the box as defined.  A value of 2 means add 2 box lengths
+to get the true value.  A value of -1 means subtract 1 box length to
+get the true value.  LAMMPS updates these flags as the rigid bodies
+cross periodic boundaries during the simulation.
+
+.. note::
+
+   If you use the *infile* keyword and write restart
+   files during a simulation, then each time a restart file is written,
+   the fix also write an auxiliary restart file with the name
+   rfile.rigid, where "rfile" is the name of the restart file,
+   e.g. tmp.restart.10000 and tmp.restart.10000.rigid.  This auxiliary
+   file is in the same format described above.  Thus it can be used in a
+   new input script that restarts the run and re-specifies a rigid fix
+   using an *infile* keyword and the appropriate filename.  Note that the
+   auxiliary file will contain one line for every rigid body, even if the
+   original file only listed a subset of the rigid bodies.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information is written to :doc:`binary restart files <restart>`.
+If the *infile* keyword is used, an auxiliary file is written out
+with rigid body information each time a restart file is written, as
+explained above for the *infile* keyword.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.
+
+This fix computes a global array of values which can be accessed by
+various :doc:`output commands <Howto_output>`.
+
+The number of rows in the array is equal to the number of rigid
+bodies.  The number of columns is 28.  Thus for each rigid body, 28
+values are stored: the xyz coords of the center of mass (COM), the xyz
+components of the COM velocity, the xyz components of the force acting
+on the COM, the components of the 4-vector quaternion representing the
+orientation of the rigid body, the xyz components of the angular velocity
+of the body around its COM, the xyz components of the torque acting on the
+COM, the 3 principal components of the moment of inertia, the xyz components
+of the angular momentum of the body around its COM, and the xyz image
+flags of the COM.
+
+The center of mass (COM) for each body is similar to unwrapped
+coordinates written to a dump file.  It will always be inside (or
+slightly outside) the simulation box.  The image flags have the same
+meaning as image flags for particle positions (see the "dump" command).
+This means you can calculate the unwrapped COM by applying the image
+flags to the COM, the same as when unwrapped coordinates are written
+to a dump file.
+
+The force and torque values in the array are not affected by the
+*force* and *torque* keywords in the fix rigid command; they reflect
+values before any changes are made by those keywords.
+
+The ordering of the rigid bodies (by row in the array) is as follows.
+For the *single* keyword there is just one rigid body.  For the
+*molecule* keyword, the bodies are ordered by ascending molecule ID.
+For the *group* keyword, the list of group IDs determines the ordering
+of bodies.
+
+The array values calculated by this fix are "intensive", meaning they
+are independent of the number of particles in the simulation.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SDPD package and also depends on the RIGID
+package.  It is only enabled if LAMMPS was built with both packages. See
+the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms store density and internal energy as
+defined by the :doc:`atom\_style meso <atom_style>` command.
+
+All particles in the group must be mesoscopic SPH/SDPD particles.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix meso/move <fix_meso_move>`, :doc:`fix rigid <fix_rigid>`,
+:doc:`neigh\_modify exclude <neigh_modify>`
+
+Default
+"""""""
+
+The option defaults are force \* on on on and torque \* on on on,
+meaning all rigid bodies are acted on by center-of-mass force and
+torque. Also reinit = yes.
+
+
+----------
+
+
+.. _Miller:
+
+
+
+**(Miller)** Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
+J Chem Phys, 116, 8649 (2002).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst
new file mode 100644
index 0000000000..b9df24f5a9
--- /dev/null
+++ b/doc/src/fix_rx.rst
@@ -0,0 +1,253 @@
+.. index:: fix rx
+
+fix rx command
+==============
+
+fix rx/kk command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID rx file localTemp matrix solver minSteps ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rx = style name of this fix command
+* file = filename containing the reaction kinetic equations and Arrhenius parameters
+* localTemp = *none,lucy* = no local temperature averaging or local temperature defined through Lucy weighting function
+* matrix = *sparse, dense* format for the stoichiometric matrix
+* solver = *lammps\_rk4,rkf45* = rk4 is an explicit 4th order Runge-Kutta method; rkf45 is an adaptive 4th-order Runge-Kutta-Fehlberg method
+* minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45)
+* maxSteps = maximum number of steps for the rkf45 solver (rkf45 only)
+* relTol = relative tolerance for the rkf45 solver (rkf45 only)
+* absTol = absolute tolerance for the rkf45 solver (rkf45 only)
+* diag   = Diagnostics frequency for the rkf45 solver (optional, rkf45 only)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all rx kinetics.rx none dense lammps_rk4
+   fix 1 all rx kinetics.rx none sparse lammps_rk4 1
+   fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10
+   fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8
+   fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1
+
+Description
+"""""""""""
+
+Fix *rx* solves the reaction kinetic ODEs for a given reaction set that is
+defined within the file associated with this command.
+
+For a general reaction such that
+
+.. image:: Eqs/fix_rx_reaction.jpg
+   :align: center
+
+the reaction rate equation is defined to be of the form
+
+.. image:: Eqs/fix_rx_reactionRate.jpg
+   :align: center
+
+In the current implementation, the exponents are defined to be equal
+to the stoichiometric coefficients.  A given reaction set consisting
+of *n* reaction equations will contain a total of *m* species.  A set
+of *m* ordinary differential equations (ODEs) that describe the change
+in concentration of a given species as a function of time are then
+constructed based on the *n* reaction rate equations.
+
+The ODE systems are solved over the full DPD timestep *dt* using either a 4th
+order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified
+by the *lammps\_rk4* keyword, or a 4th order Runge-Kutta-Fehlberg (rkf45) method
+with an adaptive step-size for *h*\ . The number of ODE steps per DPD timestep
+for the rk4 method is optionally specified immediately after the rk4
+keyword. The ODE step-size is set as *dt/num\_steps*. Smaller
+step-sizes tend to yield more accurate results but there is not
+control on the error. For error control, use the rkf45 ODE solver.
+
+The rkf45 method adjusts the step-size so that the local truncation error is held
+within the specified absolute and relative tolerances. The initial step-size *h0*
+can be specified by the user or estimated internally. It is recommended that the user
+specify *h0* since this will generally reduced the number of ODE integration steps
+required. *h0* is defined as *dt / min\_steps* if min\_steps >= 1. If min\_steps == 0,
+*h0* is estimated such that an explicit Euler method would likely produce
+an acceptable solution. This is generally overly conservative for the 4th-order
+method and users are advised to specify *h0* as some fraction of the DPD timestep.
+For small DPD timesteps, only one step may be necessary depending upon the tolerances.
+Note that more than min\_steps ODE steps may be taken depending upon the ODE stiffness
+but no more than max\_steps will be taken. If max\_steps is reached, an error warning
+is printed and the simulation is stopped.
+
+After each ODE step, the solution error *e* is tested and weighted using the absTol
+and relTol values. The error vector is weighted as *e* / (relTol \* \|\ *u*\ \| + absTol)
+where *u* is the solution vector. If the norm of the error is <= 1, the solution is
+accepted, *h* is increased by a proportional amount, and the next ODE step is begun.
+Otherwise, *h* is shrunk and the ODE step is repeated.
+
+Run-time diagnostics are available for the rkf45 ODE solver. The frequency
+(in time-steps) that diagnostics are reported is controlled by the last (optional)
+12th argument. A negative frequency means that diagnostics are reported once at the
+end of each run. A positive value N means that the diagnostics are reported once
+per N time-steps.
+
+The diagnostics report the average # of integrator steps and RHS function evaluations
+and run-time per ODE as well as the average/RMS/min/max per process. If the
+reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE
+statistics can be used to adjust the tolerance and min/max step parameters. The
+statistics per MPI process can be useful to examine any load imbalance caused by the
+adaptive ODE solver. (Some DPD particles can take longer to solve than others. This
+can lead to an imbalance across the MPI processes.)
+
+
+----------
+
+
+The filename specifies a file that contains the entire set of reaction
+kinetic equations and corresponding Arrhenius parameters.  The format of
+this file is described below.
+
+There is no restriction on the total number or reaction equations that
+are specified.  The species names are arbitrary string names that are
+associated with the species concentrations.  Each species in a given
+reaction must be preceded by it's stoichiometric coefficient.  The
+only delimiters that are recognized between the species are either a
+*+* or *=* character.  The *=* character corresponds to an
+irreversible reaction.  After specifying the reaction, the reaction
+rate constant is determined through the temperature dependent
+Arrhenius equation:
+
+.. image:: Eqs/fix_rx.jpg
+   :align: center
+
+where *A* is the Arrhenius factor in time units or concentration/time
+units, *n* is the unitless exponent of the temperature dependence, and
+*E\_a* is the activation energy in energy units.  The temperature
+dependence can be removed by specifying the exponent as zero.
+
+The internal temperature of the coarse-grained particles can be used
+in constructing the reaction rate constants at every DPD timestep by
+specifying the keyword *none*\ .  Alternatively, the keyword *lucy* can
+be specified to compute a local-average particle internal temperature
+for use in the reaction rate constant expressions.  The local-average
+particle internal temperature is defined as:
+
+.. image:: Eqs/fix_rx_localTemp.jpg
+   :align: center
+
+where the Lucy function is expressed as:
+
+.. image:: Eqs/fix_rx_localTemp2.jpg
+   :align: center
+
+The self-particle interaction is included in the above equation.
+
+The stoichiometric coefficients for the reaction mechanism are stored
+in either a sparse or dense matrix format. The dense matrix should only be
+used for small reaction mechanisms. The sparse matrix should be used when there
+are many reactions (e.g., more than 5). This allows the number of reactions and
+species to grow while keeping the computational cost tractable. The matrix
+format can be specified as using either the *sparse* or *dense* keywords.
+If all stoichiometric coefficients for a reaction are small integers (whole
+numbers <= 3), a fast exponential function is used. This can save significant
+computational time so users are encouraged to use integer coefficients
+where possible.
+
+
+----------
+
+
+The format of a tabulated file is as follows (without the
+parenthesized comments):
+
+
+.. parsed-literal::
+
+   # Rxn equations and parameters                                               (one or more comment or blank lines)
+
+   1.0 hcn + 1.0 no2 = 1.0  no + 0.5 n2  + 0.5 h2 + 1.0 co   2.49E+01 0.0 1.34  (rxn equation, A, n, Ea)
+   1.0 hcn + 1.0  no = 1.0  co + 1.0 n2  + 0.5 h2            2.16E+00 0.0 1.52
+   ...
+   1.0  no + 1.0  co = 0.5  n2 + 1.0 co2                     1.66E+06 0.0 0.69
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.
+
+Following a blank line, the next N lines list the N reaction
+equations.  Each species within the reaction equation is specified
+through its stoichiometric coefficient and a species tag.  Reactant
+species are specified on the left-hand side of the equation and
+product species are specified on the right-hand side of the equation.
+After specifying the reactant and product species, the final three
+arguments of each line represent the Arrhenius parameter *A*\ , the
+temperature exponent *n*\ , and the activation energy *Ea*\ .
+
+Note that the species tags that are defined in the reaction equations
+are used by the :doc:`fix eos/table/rx <fix_eos_table_rx>` command to
+define the thermodynamic properties of each species.  Furthermore, the
+number of species molecules (i.e., concentration) can be specified
+either with the :doc:`set <set>` command using the "d\_" prefix or by
+reading directly the concentrations from a data file.  For the latter
+case, the :doc:`read\_data <read_data>` command with the fix keyword
+should be specified, where the fix-ID will be the "fix rx`ID with a <SPECIES">`_ suffix, e.g.
+
+fix          foo all rx reaction.file ...
+read\_data    data.dpd fix foo\_SPECIES NULL Species
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This command also requires use of the :doc:`atom\_style dpd <atom_style>`
+command.
+
+This command can only be used with a constant energy or constant
+enthalpy DPD simulation.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix eos/table/rx <fix_eos_table_rx>`,
+:doc:`fix shardlow <fix_shardlow>`,
+:doc:`pair dpd/fdt/energy <pair_dpd_fdt>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst
new file mode 100644
index 0000000000..8b11f71e62
--- /dev/null
+++ b/doc/src/fix_saed_vtk.rst
@@ -0,0 +1,219 @@
+.. index:: fix saed/vtk
+
+fix saed/vtk command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* saed/vtk = style name of this fix command
+* Nevery = use input values every this many timesteps
+* Nrepeat = # of times to use input values for calculating averages
+* Nfreq = calculate averages every this many timesteps
+* c\_ID = saed compute ID
+  
+  .. parsed-literal::
+  
+     keyword = *file* or *ave* or *start* or *file* or *overwrite*\ :l
+       *ave* args = *one* or *running* or *window M*
+         one = output a new average value every Nfreq steps
+         running = output cumulative average of all previous Nfreq steps
+         window M = output average of M most recent Nfreq steps
+       *start* args = Nstart
+         Nstart = start averaging on this timestep
+       *file* arg = filename
+         filename = name of file to output time averages to
+       *overwrite* arg = none = overwrite output file with only latest output
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+   compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+
+   fix 1 all saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+   fix 2 all saed/vtk 1 1 1 c_2 file Ni_000.saed
+
+Description
+"""""""""""
+
+Time average computed intensities from :doc:`compute saed <compute_saed>` and
+write output to a file in the 3rd generation vtk image data format for
+visualization directly in parallelized visualization software packages
+like ParaView and VisIt. Note that if no time averaging is done, this
+command can be used as a convenient way to simply output diffraction
+intensities at a single snapshot.
+
+To produce output in the image data vtk format ghost data is added
+outside the *Kmax* range assigned in the compute saed. The ghost data is
+assigned a value of -1 and can be removed setting a minimum isovolume
+of 0 within the visualization software. SAED images can be created by
+visualizing a spherical slice of the data that is centered at
+R\_Ewald\*[h k l]/norm([h k l]), where R\_Ewald=1/lambda.
+
+The group specified within this command is ignored. However, note that
+specified values may represent calculations performed by saed computes
+which store their own "group" definitions.
+
+Fix saed/vtk is designed to work only with :doc:`compute saed <compute_saed>`
+values, e.g.
+
+
+.. parsed-literal::
+
+   compute 3 top saed 0.0251 Al O
+   fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
+
+
+----------
+
+
+The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what
+timesteps the input values will be used in order to contribute to the
+average.  The final averaged quantities are generated on timesteps
+that are a multiple of *Nfreq*\ .  The average is over *Nrepeat*
+quantities, computed in the preceding portion of the simulation every
+*Nevery* timesteps.  *Nfreq* must be a multiple of *Nevery* and
+*Nevery* must be non-zero even if *Nrepeat* is 1.
+Also, the timesteps
+contributing to the average value cannot overlap,
+i.e. Nrepeat\*Nevery can not exceed Nfreq.
+
+For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100.  Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc.  If Nrepeat=1 and Nfreq = 100, then no time
+averaging is done; values are simply generated on timesteps
+100,200,etc.
+
+
+----------
+
+
+The output for fix ave/time/saed is a file written with the 3rd generation
+vtk image data formatting.  The filename assigned by the *file* keyword is
+appended with \_N.vtk where N is an index (0,1,2...) to account for multiple
+diffraction intensity outputs.
+
+By default the header contains the following information (with example data):
+
+
+.. parsed-literal::
+
+   # vtk DataFile Version 3.0 c_SAED
+   Image data set
+   ASCII
+   DATASET STRUCTURED_POINTS
+   DIMENSIONS 337 219 209
+   ASPECT_RATIO 0.00507953 0.00785161 0.00821458
+   ORIGIN -0.853361 -0.855826 -0.854316
+   POINT_DATA 15424827
+   SCALARS intensity float
+   LOOKUP_TABLE default
+   ...data
+
+In this example, kspace is sampled across a 337 x 219 x 209 point mesh
+where the mesh spacing is approximately 0.005, 0.007, and 0.008
+inv(length) units in the k1, k2, and k3 directions, respectively.
+The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that
+the origin will lie at 0, 0, 0.   Here, 15,424,827 kspace points are
+sampled in total.
+
+
+----------
+
+
+Additional optional keywords also affect the operation of this fix.
+
+The *ave* keyword determines how the values produced every *Nfreq*
+steps are averaged with values produced on previous steps that were
+multiples of *Nfreq*\ , before they are accessed by another output
+command or written to a file.
+
+If the *ave* setting is *one*\ , then the values produced on timesteps
+that are multiples of *Nfreq* are independent of each other; they are
+output as-is without further averaging.
+
+If the *ave* setting is *running*\ , then the values produced on
+timesteps that are multiples of *Nfreq* are summed and averaged in a
+cumulative sense before being output.  Each output value is thus the
+average of the value produced on that timestep with all preceding
+values.  This running average begins when the fix is defined; it can
+only be restarted by deleting the fix via the :doc:`unfix <unfix>`
+command, or by re-defining the fix by re-specifying it.
+
+If the *ave* setting is *window*\ , then the values produced on
+timesteps that are multiples of *Nfreq* are summed and averaged within
+a moving "window" of time, so that the last M values are used to
+produce the output.  E.g. if M = 3 and Nfreq = 1000, then the output
+on step 10000 will be the average of the individual values on steps
+8000,9000,10000.  Outputs on early steps will average over less than M
+values if they are not available.
+
+The *start* keyword specifies what timestep averaging will begin on.
+The default is step 0.  Often input values can be 0.0 at time 0, so
+setting *start* to a larger value can avoid including a 0.0 in a
+running or windowed average.
+
+The *file* keyword allows a filename to be specified.  Every *Nfreq*
+steps, the vector of saed intensity data is written to a new file using
+the 3rd generation vtk format.  The base of each file is assigned by
+the *file* keyword and this string is appended with \_N.vtk where N is
+an index (0,1,2...) to account for situations with multiple diffraction
+intensity outputs.
+
+The *overwrite* keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output.  This option can only be used with the *ave running* setting.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+The attributes for fix\_saed\_vtk must match the values assigned in the
+associated :doc:`compute\_saed <compute_saed>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute\_saed <compute_saed>`
+
+Default
+"""""""
+
+The option defaults are ave = one, start = 0, no file output.
+
+
+----------
+
+
+.. _Coleman:
+
+
+
+**(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020
+(2013).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst
new file mode 100644
index 0000000000..a01fb7dc00
--- /dev/null
+++ b/doc/src/fix_setforce.rst
@@ -0,0 +1,167 @@
+.. index:: fix setforce
+
+fix setforce command
+====================
+
+fix setforce/kk command
+=======================
+
+fix setforce/spin command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID setforce fx fy fz keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* setforce = style name of this fix command
+* fx,fy,fz = force component values
+* any of fx,fy,fz can be a variable (see below)
+* zero or more keyword/value pairs may be appended to args
+* keyword = *region*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region atoms must be in to have added force
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix freeze indenter setforce 0.0 0.0 0.0
+   fix 2 edge setforce NULL 0.0 0.0
+   fix 1 edge setforce/spin 0.0 0.0 0.0
+   fix 2 edge setforce NULL 0.0 v_oscillate
+
+Description
+"""""""""""
+
+Set each component of force on each atom in the group to the specified
+values fx,fy,fz.  This erases all previously computed forces on the
+atom, though additional fixes could add new forces.  This command can
+be used to freeze certain atoms in the simulation by zeroing their
+force, either for running dynamics or performing an energy
+minimization.  For dynamics, this assumes their initial velocity is
+also zero.
+
+Any of the fx,fy,fz values can be specified as NULL which means do not
+alter the force component in that dimension.
+
+Any of the 3 quantities defining the force components can be specified
+as an equal-style or atom-style :doc:`variable <variable>`, namely *fx*\ ,
+*fy*\ , *fz*\ .  If the value is a variable, it should be specified as
+v\_name, where name is the variable name.  In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+force component.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent force field.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent force
+field with optional time-dependence as well.
+
+If the *region* keyword is used, the atom must also be in the
+specified geometric :doc:`region <region>` in order to have force added
+to it.
+
+
+----------
+
+
+Style *spin* suffix sets the components of the magnetic precession
+vectors instead of the mechanical forces. This also erases all
+previously computed magnetic precession vectors on the atom, though
+additional magnetic fixes could add new forces.
+
+This command can be used to freeze the magnetic moment of certain
+atoms in the simulation by zeroing their precession vector.
+
+All options defined above remain valid, they just apply to the magnetic
+precession vectors instead of the forces.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+The region keyword is also supported by Kokkos, but a Kokkos-enabled
+region must be used. See the region :doc:`region <region>` command for
+more information.
+
+These accelerated styles are part of the r Kokkos package.  They are
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is setting the forces to the desired values; on all
+other levels, the force is set to 0.0 for the atoms in the fix group,
+so that setforce values are not counted multiple times. Default is to
+to override forces at the outermost level.
+
+This fix computes a global 3-vector of forces, which can be accessed
+by various :doc:`output commands <Howto_output>`.  This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix.  The vector values calculated by this fix are
+"extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command, but you cannot set
+forces to any value besides zero when performing a minimization.  Use
+the :doc:`fix addforce <fix_addforce>` command if you want to apply a
+non-zero force to atoms during a minimization.
+
+Restrictions
+""""""""""""
+
+
+The fix *setforce/spin* only makes sense when LAMMPS was built with the
+SPIN package.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix addforce <fix_addforce>`, :doc:`fix aveforce <fix_aveforce>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst
new file mode 100644
index 0000000000..28a50e6754
--- /dev/null
+++ b/doc/src/fix_shake.rst
@@ -0,0 +1,270 @@
+.. index:: fix shake
+
+fix shake command
+=================
+
+fix rattle command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style tol iter N constraint values ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = shake or rattle = style name of this fix command
+* tol = accuracy tolerance of SHAKE solution
+* iter = max # of iterations in each SHAKE solution
+* N = print SHAKE statistics every this many timesteps (0 = never)
+* one or more constraint/value pairs are appended
+* constraint = *b* or *a* or *t* or *m*
+  
+  .. parsed-literal::
+  
+       *b* values = one or more bond types
+       *a* values = one or more angle types
+       *t* values = one or more atom types
+       *m* value = one or more mass values
+
+* zero or more keyword/value pairs may be appended
+* keyword = *mol*
+  
+  .. parsed-literal::
+  
+       *mol* value = template-ID
+         template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
+   fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
+   fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
+   fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31
+   fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
+
+Description
+"""""""""""
+
+Apply bond and angle constraints to specified bonds and angles in the
+simulation by either the SHAKE or RATTLE algorithms.  This typically
+enables a longer timestep.
+
+**SHAKE vs RATTLE:**
+
+The SHAKE algorithm was invented for schemes such as standard Verlet
+timestepping, where only the coordinates are integrated and the
+velocities are approximated as finite differences to the trajectories
+(:ref:`Ryckaert et al. (1977) <Ryckaert>`).  If the velocities are
+integrated explicitly, as with velocity Verlet which is what LAMMPS
+uses as an integration method, a second set of constraining forces is
+required in order to eliminate velocity components along the bonds
+(:ref:`Andersen (1983) <Andersen3>`).
+
+In order to formulate individual constraints for SHAKE and RATTLE,
+focus on a single molecule whose bonds are constrained.  Let Ri and Vi
+be the position and velocity of atom *i* at time *n*\ , for
+*i* =1,...,\ *N*\ , where *N* is the number of sites of our reference
+molecule. The distance vector between sites *i* and *j* is given by
+
+.. image:: Eqs/fix_rattle_rij.jpg
+   :align: center
+
+The constraints can then be formulated as
+
+.. image:: Eqs/fix_rattle_constraints.jpg
+   :align: center
+
+The SHAKE algorithm satisfies the first condition, i.e. the sites at
+time *n+1* will have the desired separations Dij immediately after the
+coordinates are integrated.  If we also enforce the second condition,
+the velocity components along the bonds will vanish.  RATTLE satisfies
+both conditions.  As implemented in LAMMPS, fix rattle uses fix shake
+for satisfying the coordinate constraints. Therefore the settings and
+optional keywords are the same for both fixes, and all the information
+below about SHAKE is also relevant for RATTLE.
+
+**SHAKE:**
+
+Each timestep the specified bonds and angles are reset to their
+equilibrium lengths and angular values via the SHAKE algorithm
+(:ref:`Ryckaert et al. (1977) <Ryckaert>`).  This is done by applying an
+additional constraint force so that the new positions preserve the
+desired atom separations.  The equations for the additional force are
+solved via an iterative method that typically converges to an accurate
+solution in a few iterations.  The desired tolerance (e.g. 1.0e-4 = 1
+part in 10000) and maximum # of iterations are specified as arguments.
+Setting the N argument will print statistics to the screen and log
+file about regarding the lengths of bonds and angles that are being
+constrained.  Small delta values mean SHAKE is doing a good job.
+
+In LAMMPS, only small clusters of atoms can be constrained.  This is
+so the constraint calculation for a cluster can be performed by a
+single processor, to enable good parallel performance.  A cluster is
+defined as a central atom connected to others in the cluster by
+constrained bonds.  LAMMPS allows for the following kinds of clusters
+to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
+one central atom bonded to 2 others and the angle between the 3 atoms
+also constrained.  This means water molecules or CH2 or CH3 groups may
+be constrained, but not all the C-C backbone bonds of a long polymer
+chain.
+
+The *b* constraint lists bond types that will be constrained.  The *t*
+constraint lists atom types.  All bonds connected to an atom of the
+specified type will be constrained.  The *m* constraint lists atom
+masses.  All bonds connected to atoms of the specified masses will be
+constrained (within a fudge factor of MASSDELTA specified in
+fix\_shake.cpp).  The *a* constraint lists angle types.  If both bonds
+in the angle are constrained then the angle will also be constrained
+if its type is in the list.
+
+For all constraints, a particular bond is only constrained if both
+atoms in the bond are in the group specified with the SHAKE fix.
+
+The degrees-of-freedom removed by SHAKE bonds and angles are accounted
+for in temperature and pressure computations.  Similarly, the SHAKE
+contribution to the pressure of the system (virial) is also accounted
+for.
+
+.. note::
+
+   This command works by using the current forces on atoms to
+   calculate an additional constraint force which when added will leave
+   the atoms in positions that satisfy the SHAKE constraints (e.g. bond
+   length) after the next time integration step.  If you define fixes
+   (e.g. :doc:`fix efield <fix_efield>`) that add additional force to the
+   atoms after fix shake operates, then this fix will not take them into
+   account and the time integration will typically not satisfy the SHAKE
+   constraints.  The solution for this is to make sure that fix shake is
+   defined in your input script after any other fixes which add or change
+   forces (to atoms that fix shake operates on).
+
+
+----------
+
+
+The *mol* keyword should be used when other commands, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`, add molecules
+on-the-fly during a simulation, and you wish to constrain the new
+molecules via SHAKE.  You specify a *template-ID* previously defined
+using the :doc:`molecule <molecule>` command, which reads a file that
+defines the molecule.  You must use the same *template-ID* that the
+command adding molecules uses.  The coordinates, atom types, special
+bond restrictions, and SHAKE info can be specified in the molecule
+file.  See the :doc:`molecule <molecule>` command for details.  The only
+settings required to be in this file (by this command) are the SHAKE
+info of atoms in the molecule.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**RATTLE:**
+
+The velocity constraints lead to a linear system of equations which
+can be solved analytically.  The implementation of the algorithm in
+LAMMPS closely follows (:ref:`Andersen (1983) <Andersen3>`).
+
+.. note::
+
+   The fix rattle command modifies forces and velocities and thus
+   should be defined after all other integration fixes in your input
+   script.  If you define other fixes that modify velocities or forces
+   after fix rattle operates, then fix rattle will not take them into
+   account and the overall time integration will typically not satisfy
+   the RATTLE constraints.  You can check whether the constraints work
+   correctly by setting the value of RATTLE\_DEBUG in src/fix\_rattle.cpp
+   to 1 and recompiling LAMMPS.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to keeping the constraints to the
+system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+The default is *virial yes*
+
+No information about these fixes is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to these fixes.  No global or per-atom quantities are
+stored by these fixes for access by various :doc:`output commands <Howto_output>`.  No parameter of these fixes can be used
+with the *start/stop* keywords of the :doc:`run <run>` command.  These
+fixes are not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+These fixes are part of the RIGID package.  They are only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+For computational efficiency, there can only be one shake or rattle
+fix defined in a simulation.
+
+If you use a tolerance that is too large or a max-iteration count that
+is too small, the constraints will not be enforced very strongly,
+which can lead to poor energy conservation.  You can test for this in
+your system by running a constant NVE simulation with a particular set
+of SHAKE parameters and monitoring the energy versus time.
+
+SHAKE or RATTLE should not be used to constrain an angle at 180
+degrees (e.g. linear CO2 molecule).  This causes numeric difficulties.
+You can use :doc:`fix rigid or fix rigid/small <fix_rigid>` instead to
+make a linear molecule rigid.
+
+**Related commands:** none
+
+**Default:** none
+
+
+----------
+
+
+.. _Ryckaert:
+
+
+
+**(Ryckaert)** J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen,
+J of Comp Phys, 23, 327-341 (1977).
+
+.. _Andersen3:
+
+
+
+**(Andersen)** H. Andersen, J of Comp Phys, 52, 24-34 (1983).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst
new file mode 100644
index 0000000000..b1f3cb0745
--- /dev/null
+++ b/doc/src/fix_shardlow.rst
@@ -0,0 +1,141 @@
+.. index:: fix shardlow
+
+fix shardlow command
+====================
+
+fix shardlow/kk command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID shardlow
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* shardlow = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all shardlow
+
+Description
+"""""""""""
+
+Specifies that the Shardlow splitting algorithm (SSA) is to be used to
+integrate the DPD equations of motion.  The SSA splits the integration
+into a stochastic and deterministic integration step.  The fix
+*shardlow* performs the stochastic integration step and must be used
+in conjunction with a deterministic integrator (e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`).  The stochastic
+integration of the dissipative and random forces is performed prior to
+the deterministic integration of the conservative force. Further
+details regarding the method are provided in :ref:`(Lisal) <Lisal>` and
+:ref:`(Larentzos1) <Larentzos1sh>`.
+
+The fix *shardlow* must be used with the :doc:`pair\_style dpd/fdt <pair_style>` or :doc:`pair\_style dpd/fdt/energy <pair_style>` command to properly initialize the
+fluctuation-dissipation theorem parameter(s) sigma (and kappa, if
+necessary).
+
+Note that numerous variants of DPD can be specified by choosing an
+appropriate combination of the integrator and :doc:`pair\_style dpd/fdt <pair_style>` command.  DPD under isothermal conditions can
+be specified by using fix *shardlow*\ , fix *nve* and pair\_style
+*dpd/fdt*\ .  DPD under isoenergetic conditions can be specified by
+using fix *shardlow*\ , fix *nve* and pair\_style *dpd/fdt/energy*\ .  DPD
+under isobaric conditions can be specified by using fix shardlow, fix
+*nph* and pair\_style *dpd/fdt*\ .  DPD under isoenthalpic conditions can
+be specified by using fix shardlow, fix *nph* and pair\_style
+*dpd/fdt/energy*\ .  Examples of each DPD variant are provided in the
+examples/USER/dpd directory.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix is currently limited to orthogonal simulation cell
+geometries.
+
+This fix must be used with an additional fix that specifies time
+integration, e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`.
+
+The Shardlow splitting algorithm requires the sizes of the sub-domain
+lengths to be larger than twice the cutoff+skin.  Generally, the
+domain decomposition is dependent on the number of processors
+requested.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style dpd/fdt <pair_dpd_fdt>`, :doc:`fix eos/cv <fix_eos_cv>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Lisal:
+
+
+
+**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
+particle dynamics as isothermal, isobaric, isoenergetic, and
+isoenthalpic conditions using Shardlow-like splitting algorithms.",
+J. Chem. Phys., 135, 204105 (2011).
+
+.. _Larentzos1sh:
+
+
+
+**(Larentzos1)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and
+W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic
+Dissipative Particle Dynamics Using Shardlow-Like Splitting
+Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014).
+
+.. _Larentzos2sh:
+
+
+
+**(Larentzos2)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
+W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
+Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+Laboratory, Aberdeen Proving Ground, MD (2014).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst
new file mode 100644
index 0000000000..7473cb07a9
--- /dev/null
+++ b/doc/src/fix_smd.rst
@@ -0,0 +1,184 @@
+.. index:: fix smd
+
+fix smd command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID smd type values keyword values
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* smd  = style name of this fix command
+* mode = *cvel* or *cfor* to select constant velocity or constant force SMD
+  
+  .. parsed-literal::
+  
+       *cvel* values = K vel
+         K = spring constant (force/distance units)
+         vel = velocity of pulling (distance/time units)
+       *cfor* values = force
+         force = pulling force (force units)
+
+* keyword = *tether* or *couple*
+  
+  .. parsed-literal::
+  
+       *tether* values = x y z R0
+         x,y,z = point to which spring is tethered
+         R0 = distance of end of spring from tether point (distance units)
+       *couple* values = group-ID2 x y z R0
+         group-ID2 = 2nd group to couple to fix group with a spring
+         x,y,z = direction of spring, automatically computed with 'auto'
+         R0 = distance of end of spring (distance units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix  pull    cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
+   fix  pull    cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
+   fix  stretch cterm smd cvel 20.0  0.0001 couple nterm auto auto auto 0.0
+   fix  pull    cterm smd cfor  5.0 tether 25.0 25.0 25.0 0.0
+
+Description
+"""""""""""
+
+This fix implements several options of steered MD (SMD) as reviewed in
+:ref:`(Izrailev) <Izrailev>`, which allows to induce conformational changes
+in systems and to compute the potential of mean force (PMF) along the
+assumed reaction coordinate :ref:`(Park) <Park>` based on Jarzynski's
+equality :ref:`(Jarzynski) <Jarzynski>`.  This fix borrows a lot from :doc:`fix spring <fix_spring>` and :doc:`fix setforce <fix_setforce>`.
+
+You can apply a moving spring force to a group of atoms (\ *tether*
+style) or between two groups of atoms (\ *couple* style).  The spring
+can then be used in either constant velocity (\ *cvel*\ ) mode or in
+constant force (\ *cfor*\ ) mode to induce transitions in your systems.
+When running in *tether* style, you may need some way to fix some
+other part of the system (e.g. via :doc:`fix spring/self <fix_spring_self>`)
+
+The *tether* style attaches a spring between a point at a distance of
+R0 away from a fixed point *x,y,z* and the center of mass of the fix
+group of atoms.  A restoring force of magnitude K (R - R0) Mi / M is
+applied to each atom in the group where *K* is the spring constant, Mi
+is the mass of the atom, and M is the total mass of all atoms in the
+group.  Note that *K* thus represents the total force on the group of
+atoms, not a per-atom force.
+
+In *cvel* mode the distance R is incremented or decremented
+monotonously according to the pulling (or pushing) velocity.
+In *cfor* mode a constant force is added and the actual distance
+in direction of the spring is recorded.
+
+The *couple* style links two groups of atoms together.  The first
+group is the fix group; the second is specified by group-ID2.  The
+groups are coupled together by a spring that is at equilibrium when
+the two groups are displaced by a vector in direction *x,y,z* with
+respect to each other and at a distance R0 from that displacement.
+Note that *x,y,z* only provides a direction and will be internally
+normalized. But since it represents the *absolute* displacement of
+group-ID2 relative to the fix group, (1,1,0) is a different spring
+than (-1,-1,0).  For each vector component, the displacement can be
+described with the *auto* parameter. In this case the direction is
+re-computed in every step, which can be useful for steering a local
+process where the whole object undergoes some other change.  When the
+relative positions and distance between the two groups are not in
+equilibrium, the same spring force described above is applied to atoms
+in each of the two groups.
+
+For both the *tether* and *couple* styles, any of the x,y,z values can
+be specified as NULL which means do not include that dimension in the
+distance calculation or force application.
+
+For constant velocity pulling (\ *cvel* mode), the running integral
+over the pulling force in direction of the spring is recorded and
+can then later be used to compute the potential of mean force (PMF)
+by averaging over multiple independent trajectories along the same
+pulling path.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+The fix stores the direction of the spring, current pulling target
+distance and the running PMF to :doc:`binary restart files <restart>`.
+See the :doc:`read\_restart <read_restart>` command for info on how to
+re-specify a fix in an input script that reads a restart file, so that
+the operation of the fix continues in an uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to the added forces on atoms to the
+system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+The default is *virial no*
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a vector list of 7 quantities, which can be accessed
+by various :doc:`output commands <Howto_output>`.  The quantities in the
+vector are in this order: the x-, y-, and z-component of the pulling
+force, the total force in direction of the pull, the equilibrium
+distance of the spring, the distance between the two reference points,
+and finally the accumulated PMF (the sum of pulling forces times
+displacement).
+
+The force is the total force on the group of atoms by the spring.  In
+the case of the *couple* style, it is the force on the fix group
+(group-ID) or the negative of the force on the 2nd group (group-ID2).
+The vector values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix drag <fix_drag>`, :doc:`fix spring <fix_spring>`,
+:doc:`fix spring/self <fix_spring_self>`,
+:doc:`fix spring/rg <fix_spring_rg>`,
+:doc:`fix colvars <fix_colvars>`, :doc:`fix plumed <fix_plumed>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Izrailev:
+
+
+
+**(Izrailev)** Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
+Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
+Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
+Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
+
+.. _Park:
+
+
+
+**(Park)** Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
+
+.. _Jarzynski:
+
+
+
+**(Jarzynski)** Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst
new file mode 100644
index 0000000000..5176e158fe
--- /dev/null
+++ b/doc/src/fix_smd_adjust_dt.rst
@@ -0,0 +1,74 @@
+.. index:: fix smd/adjust\_dt
+
+fix smd/adjust\_dt command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID smd/adjust_dt arg
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* smd/adjust\_dt = style name of this fix command
+* arg = *s\_fact*
+  
+  .. parsed-literal::
+  
+       *s_fact* = safety factor
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all smd/adjust_dt 0.1
+
+Description
+"""""""""""
+
+The fix calculates a new stable time increment for use with the SMD
+time integrators.
+
+The stable time increment is based on multiple conditions. For the SPH
+pair styles, a CFL criterion (Courant, Friedrichs & Lewy, 1928) is
+evaluated, which determines the speed of sound cannot propagate
+further than a typical spacing between particles within a single time
+step to ensure no information is lost. For the contact pair styles, a
+linear analysis of the pair potential determines a stable maximum time
+step.
+
+This fix inquires the minimum stable time increment across all
+particles contained in the group for which this fix is defined. An
+additional safety factor *s\_fact* is applied to the time increment.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth Mach
+Dynamics in LAMMPS.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Currently, no part of USER-SMD supports restarting nor minimization.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/tlsph\_dt <compute_smd_tlsph_dt>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst
new file mode 100644
index 0000000000..32aba62dd9
--- /dev/null
+++ b/doc/src/fix_smd_integrate_tlsph.rst
@@ -0,0 +1,69 @@
+.. index:: fix smd/integrate\_tlsph
+
+fix smd/integrate\_tlsph command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID smd/integrate_tlsph keyword values
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* smd/integrate\_tlsph = style name of this fix command
+* zero or more keyword/value pairs may be appended
+* keyword = *limit\_velocity*
+
+
+.. parsed-literal::
+
+     *limit_velocity* value = max_vel
+       max_vel = maximum allowed velocity
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all smd/integrate_tlsph
+   fix 1 all smd/integrate_tlsph limit_velocity 1000
+
+Description
+"""""""""""
+
+The fix performs explicit time integration for particles which
+interact according with the Total-Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth Mach
+Dynamics in LAMMPS.
+
+The *limit\_velocity* keyword will control the velocity, scaling the
+norm of the velocity vector to max\_vel in case it exceeds this
+velocity limit.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst
new file mode 100644
index 0000000000..216e8652bd
--- /dev/null
+++ b/doc/src/fix_smd_integrate_ulsph.rst
@@ -0,0 +1,73 @@
+.. index:: fix smd/integrate\_ulsph
+
+fix smd/integrate\_ulsph command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID smd/integrate_ulsph keyword
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* smd/integrate\_ulsph = style name of this fix command
+* zero or more keyword/value pairs may be appended
+* keyword = adjust\_radius or limit\_velocity
+
+adjust\_radius values = adjust\_radius\_factor min\_nn max\_nn
+      adjust\_radius\_factor = factor which scale the smooth/kernel radius
+      min\_nn = minimum number of neighbors
+      max\_nn = maximum number of neighbors
+limit\_velocity values = max\_velocity
+      max\_velocity = maximum allowed velocity.
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
+   fix 1 all smd/integrate_ulsph limit_velocity 1000
+
+Description
+"""""""""""
+
+The fix performs explicit time integration for particles which
+interact with the updated Lagrangian SPH pair style.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth Mach
+Dynamics in LAMMPS.
+
+The *adjust\_radius* keyword activates dynamic adjustment of the
+per-particle SPH smoothing kernel radius such that the number of
+neighbors per particles remains within the interval *min\_nn* to
+*max\_nn*. The parameter *adjust\_radius\_factor* determines the amount
+of adjustment per timestep. Typical values are *adjust\_radius\_factor*
+=1.02, *min\_nn* =15, and *max\_nn* =20.
+
+The *limit\_velocity* keyword will control the velocity, scaling the norm of
+the velocity vector to max\_vel in case it exceeds this velocity limit.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst
new file mode 100644
index 0000000000..866a799d45
--- /dev/null
+++ b/doc/src/fix_smd_move_triangulated_surface.rst
@@ -0,0 +1,93 @@
+.. index:: fix smd/move\_tri\_surf
+
+fix smd/move\_tri\_surf command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID smd/move_tri_surf keyword
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* smd/move\_tri\_surf keyword = style name of this fix command
+* keyword = *\*LINEAR* or *\*WIGGLE* or *\*ROTATE*
+  
+  .. parsed-literal::
+  
+        *\*LINEAR* args = Vx Vy Vz
+           Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+        *\*WIGGLE* args = Vx Vy Vz max_travel
+           vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
+           max_travel = wiggle amplitude
+        *\*ROTATE* args = Px Py Pz Rx Ry Rz period
+           Px,Py,Pz = origin point of axis of rotation (distance units)
+           Rx,Ry,Rz = axis of rotation vector
+           period = period of rotation (time units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 tool smd/move_tri_surf \*LINEAR 20 20 10
+   fix 2 tool smd/move_tri_surf \*WIGGLE 20 20 10
+   fix 2 tool smd/move_tri_surf \*ROTATE 0 0 0 5 2 1
+
+Description
+"""""""""""
+
+This fix applies only to rigid surfaces read from .STL files via fix
+:doc:`smd/wall\_surface <fix_smd_wall_surface>` .  It updates position
+and velocity for the particles in the group each timestep without
+regard to forces on the particles.  The rigid surfaces can thus be
+moved along simple trajectories during the simulation.
+
+The *\*LINEAR* style moves particles with the specified constant velocity
+vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
+to V = (Vx,Vy,Vz).
+
+The *\*WIGGLE* style moves particles in an oscillatory fashion.
+Particles are moved along (vx, vy, vz) with constant velocity until a
+displacement of max\_travel is reached. Then, the velocity vector is
+reversed. This process is repeated.
+
+The *\*ROTATE* style rotates particles around a rotation axis R =
+(Rx,Ry,Rz) that goes through a point P = (Px,Py,Pz). The period of the
+rotation is also specified. This style also sets the velocity of each
+particle to (omega cross Rperp) where omega is its angular velocity
+around the rotation axis and Rperp is a perpendicular vector from the
+rotation axis to the particle.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth Mach
+Dynamics in LAMMPS.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/triangle\_mesh\_vertices <compute_smd_triangle_vertices>`,
+:doc:`smd/wall\_surface <fix_smd_wall_surface>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst
new file mode 100644
index 0000000000..6a8eb80ade
--- /dev/null
+++ b/doc/src/fix_smd_setvel.rst
@@ -0,0 +1,100 @@
+.. index:: fix smd/setvel
+
+fix smd/setvel command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID smd/setvel vx vy vz keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* smd/setvel = style name of this fix command
+* vx,vy,vz = velocity component values
+* any of vx,vy,vz can be a variable (see below)
+* zero or more keyword/value pairs may be appended to args
+* keyword = *region*
+  
+  .. parsed-literal::
+  
+       *region* value = region-ID
+         region-ID = ID of region particles must be in to have their velocities set
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix top_velocity top_group setvel 1.0 0.0 0.0
+
+Description
+"""""""""""
+
+Set each component of velocity on each particle in the group to the specified
+values vx,vy,vz, regardless of the forces acting on the particle.  This command can
+be used to impose velocity boundary conditions.
+
+Any of the vx,vy,vz values can be specified as NULL which means do not
+alter the velocity component in that dimension.
+
+This fix is indented to be used together with a time integration fix.
+
+Any of the 3 quantities defining the velocity components can be specified
+as an equal-style or atom-style :doc:`variable <variable>`, namely *vx*\ ,
+*vy*\ , *vz*\ .  If the value is a variable, it should be specified as
+v\_name, where name is the variable name.  In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+force component.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent velocity field.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent velocity
+field with optional time-dependence as well.
+
+If the *region* keyword is used, the particle must also be in the
+specified geometric :doc:`region <region>` in order to have its velocity set by this command.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Currently, no part of USER-SMD supports restarting nor minimization
+None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global 3-vector of forces, which can be accessed
+by various :doc:`output commands <Howto_output>`.  This is the total
+force on the group of atoms.  The vector values calculated by this fix
+are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst
new file mode 100644
index 0000000000..d3c98e3088
--- /dev/null
+++ b/doc/src/fix_smd_wall_surface.rst
@@ -0,0 +1,86 @@
+.. index:: fix smd/wall\_surface
+
+fix smd/wall\_surface command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID smd/wall_surface arg type mol-ID
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* smd/wall\_surface = style name of this fix command
+* arg = *file*
+  
+  .. parsed-literal::
+  
+        *file* = file name of a triangular mesh in stl format
+
+* type = particle type to be given to the new particles created by this fix
+* mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix stl_surf all smd/wall_surface tool.stl 2 65535
+
+Description
+"""""""""""
+
+This fix creates reads a triangulated surface from a file in .STL
+format.  For each triangle, a new particle is created which stores the
+barycenter of the triangle and the vertex positions.  The radius of
+the new particle is that of the minimum circle which encompasses the
+triangle vertices.
+
+The triangulated surface can be used as a complex rigid wall via the
+:doc:`smd/tri\_surface <pair_smd_triangulated_surface>` pair style.  It
+is possible to move the triangulated surface via the
+:doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` fix style.
+
+Immediately after a .STL file has been read, the simulation needs to
+be run for 0 timesteps in order to properly register the new particles
+in the system. See the "funnel\_flow" example in the USER-SMD examples
+directory.
+
+See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth Mach
+Dynamics in LAMMPS.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The molecule ID given to the particles created by this fix have to be
+equal to or larger than 65535.
+
+Within each .STL file, only a single triangulated object must be
+present, even though the STL format allows for the possibility of
+multiple objects in one file.
+
+Related commands
+""""""""""""""""
+
+:doc:`smd/triangle\_mesh\_vertices <compute_smd_triangle_vertices>`,
+:doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>`,
+:doc:`smd/tri\_surface <pair_smd_triangulated_surface>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst
new file mode 100644
index 0000000000..2d874e4b23
--- /dev/null
+++ b/doc/src/fix_spring.rst
@@ -0,0 +1,161 @@
+.. index:: fix spring
+
+fix spring command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID spring keyword values
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* spring = style name of this fix command
+* keyword = *tether* or *couple*
+  
+  .. parsed-literal::
+  
+       *tether* values = K x y z R0
+         K = spring constant (force/distance units)
+         x,y,z = point to which spring is tethered
+         R0 = equilibrium distance from tether point (distance units)
+       *couple* values = group-ID2 K x y z R0
+         group-ID2 = 2nd group to couple to fix group with a spring
+         K = spring constant (force/distance units)
+         x,y,z = direction of spring
+         R0 = equilibrium distance of spring (distance units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0
+   fix pull ligand spring tether 50.0 0.0 0.0 0.0 5.0
+   fix pull ligand spring tether 50.0 NULL NULL 2.0 3.0
+   fix 5 bilayer1 spring couple bilayer2 100.0 NULL NULL 10.0 0.0
+   fix longitudinal pore spring couple ion 100.0 NULL NULL -20.0 0.0
+   fix radial pore spring couple ion 100.0 0.0 0.0 NULL 5.0
+
+Description
+"""""""""""
+
+Apply a spring force to a group of atoms or between two groups of
+atoms.  This is useful for applying an umbrella force to a small
+molecule or lightly tethering a large group of atoms (e.g. all the
+solvent or a large molecule) to the center of the simulation box so
+that it doesn't wander away over the course of a long simulation.  It
+can also be used to hold the centers of mass of two groups of atoms at
+a given distance or orientation with respect to each other.
+
+The *tether* style attaches a spring between a fixed point *x,y,z* and
+the center of mass of the fix group of atoms.  The equilibrium
+position of the spring is R0.  At each timestep the distance R from
+the center of mass of the group of atoms to the tethering point is
+computed, taking account of wrap-around in a periodic simulation box.
+A restoring force of magnitude K (R - R0) Mi / M is applied to each
+atom in the group where *K* is the spring constant, Mi is the mass of
+the atom, and M is the total mass of all atoms in the group.  Note
+that *K* thus represents the spring constant for the total force on
+the group of atoms, not for a spring applied to each atom.
+
+The *couple* style links two groups of atoms together.  The first
+group is the fix group; the second is specified by group-ID2.  The
+groups are coupled together by a spring that is at equilibrium when
+the two groups are displaced by a vector *x,y,z* with respect to each
+other and at a distance R0 from that displacement.  Note that *x,y,z*
+is the equilibrium displacement of group-ID2 relative to the fix
+group.  Thus (1,1,0) is a different spring than (-1,-1,0).  When the
+relative positions and distance between the two groups are not in
+equilibrium, the same spring force described above is applied to atoms
+in each of the two groups.
+
+For both the *tether* and *couple* styles, any of the x,y,z values can
+be specified as NULL which means do not include that dimension in the
+distance calculation or force application.
+
+The first example above pulls the ligand towards the point (0,0,0).
+The second example holds the ligand near the surface of a sphere of
+radius 5 around the point (0,0,0).  The third example holds the ligand
+a distance 3 away from the z=2 plane (on either side).
+
+The fourth example holds 2 bilayers a distance 10 apart in z.  For the
+last two examples, imagine a pore (a slab of atoms with a cylindrical
+hole cut out) oriented with the pore axis along z, and an ion moving
+within the pore.  The fifth example holds the ion a distance of -20
+below the z = 0 center plane of the pore (umbrella sampling).  The
+last example holds the ion a distance 5 away from the pore axis
+(assuming the center-of-mass of the pore in x,y is the pore axis).
+
+.. note::
+
+   The center of mass of a group of atoms is calculated in
+   "unwrapped" coordinates using atom image flags, which means that the
+   group can straddle a periodic boundary.  See the :doc:`dump <dump>` doc
+   page for a discussion of unwrapped coordinates.  It also means that a
+   spring connecting two groups or a group and the tether point can cross
+   a periodic boundary and its length be calculated correctly.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy stored in the spring to the system's potential
+energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the spring energy
+= 0.5 \* K \* r\^2.
+
+This fix also computes global 4-vector which can be accessed by
+various :doc:`output commands <Howto_output>`.  The first 3 quantities
+in the vector are xyz components of the total force added to the group
+of atoms by the spring.  In the case of the *couple* style, it is the
+force on the fix group (group-ID) or the negative of the force on the
+2nd group (group-ID2).  The 4th quantity in the vector is the
+magnitude of the force added by the spring, as a positive value if
+(r-R0) > 0 and a negative value if (r-R0) < 0.  This sign convention
+can be useful when using the spring force to compute a potential of
+mean force (PMF).
+
+The scalar and vector values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the spring energy to be included in the total
+   potential energy of the system (the quantity being minimized), you
+   MUST enable the :doc:`fix\_modify <fix_modify>` *energy* option for this
+   fix.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix drag <fix_drag>`, :doc:`fix spring/self <fix_spring_self>`,
+:doc:`fix spring/rg <fix_spring_rg>`, :doc:`fix smd <fix_smd>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst
new file mode 100644
index 0000000000..9f6182df8e
--- /dev/null
+++ b/doc/src/fix_spring_chunk.rst
@@ -0,0 +1,99 @@
+.. index:: fix spring/chunk
+
+fix spring/chunk command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID spring/chunk K chunkID comID
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* spring/chunk = style name of this fix command
+* K = spring constant for each chunk (force/distance units)
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* comID = ID of :doc:`compute com/chunk <compute_com_chunk>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix restrain all spring/chunk 100 chunkID comID
+
+Description
+"""""""""""
+
+Apply a spring force to the center-of-mass (COM) of chunks of atoms as
+defined by the :doc:`compute chunk/atom <compute_chunk_atom>` command.
+Chunks can be molecules or spatial bins or other groupings of atoms.
+This is a way of tethering each chunk to its initial COM coordinates.
+
+The *chunkID* is the ID of a compute chunk/atom command defined in the
+input script.  It is used to define the chunks.  The *comID* is the ID
+of a compute com/chunk command defined in the input script.  It is
+used to compute the COMs of each chunk.
+
+At the beginning of the first :doc:`run <run>` or
+:doc:`minimize <minimize>` command after this fix is defined, the
+initial COM of each chunk is calculated and stored as R0m, where M is
+the chunk number.  Thereafter, at every timestep (or minimization
+iteration), the current COM of each chunk is calculated as Rm.  A
+restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each
+atom in each chunk where *K* is the specified spring constant, Mi is
+the mass of the atom, and Mm is the total mass of all atoms in the
+chunk.  Note that *K* thus represents the spring constant for the
+total force on each chunk of atoms, not for a spring applied to each
+atom.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy stored in all the springs to the system's potential
+energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the energy of all
+the springs, i.e. 0.5 \* K \* r\^2 per-spring.
+
+The scalar value calculated by this fix is "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the spring energies to be included in the total
+   potential energy of the system (the quantity being minimized), you
+   MUST enable the :doc:`fix\_modify <fix_modify>` *energy* option for this
+   fix.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix spring <fix_spring>`, :doc:`fix spring/self <fix_spring_self>`,
+:doc:`fix spring/rg <fix_spring_rg>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst
new file mode 100644
index 0000000000..b2573483e0
--- /dev/null
+++ b/doc/src/fix_spring_rg.rst
@@ -0,0 +1,85 @@
+.. index:: fix spring/rg
+
+fix spring/rg command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID spring/rg K RG0
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* spring/rg = style name of this fix command
+* K = harmonic force constant (force/distance units)
+* RG0 = target radius of gyration to constrain to (distance units)
+
+
+.. parsed-literal::
+
+     if RG0 = NULL, use the current RG as the target value
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 protein spring/rg 5.0 10.0
+   fix 2 micelle spring/rg 5.0 NULL
+
+Description
+"""""""""""
+
+Apply a harmonic restraining force to atoms in the group to affect
+their central moment about the center of mass (radius of gyration).
+This fix is useful to encourage a protein or polymer to fold/unfold
+and also when sampling along the radius of gyration as a reaction
+coordinate (i.e. for protein folding).
+
+The radius of gyration is defined as RG in the first formula.  The
+energy of the constraint and associated force on each atom is given by
+the second and third formulas, when the group is at a different RG
+than the target value RG0.
+
+.. image:: Eqs/fix_spring_rg.jpg
+   :align: center
+
+The (xi - center-of-mass) term is computed taking into account
+periodic boundary conditions, m\_i is the mass of the atom, and M is
+the mass of the entire group.  Note that K is thus a force constant
+for the aggregate force on the group of atoms, not a per-atom force.
+
+If RG0 is specified as NULL, then the RG of the group is computed at
+the time the fix is specified, and that value is used as the target.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix spring <fix_spring>`, :doc:`fix spring/self <fix_spring_self>`
+:doc:`fix drag <fix_drag>`, :doc:`fix smd <fix_smd>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst
new file mode 100644
index 0000000000..d061c96eba
--- /dev/null
+++ b/doc/src/fix_spring_self.rst
@@ -0,0 +1,96 @@
+.. index:: fix spring/self
+
+fix spring/self command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID spring/self K dir
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* spring/self = style name of this fix command
+* K = spring constant (force/distance units)
+* dir = xyz, xy, xz, yz, x, y, or z (optional, default: xyz)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix tether boundary-atoms spring/self 10.0
+   fix zrest  move spring/self 10.0 z
+
+Description
+"""""""""""
+
+Apply a spring force independently to each atom in the group to tether
+it to its initial position.  The initial position for each atom is its
+location at the time the fix command was issued.  At each timestep,
+the magnitude of the force on each atom is -Kr, where r is the
+displacement of the atom from its current position to its initial
+position.  The distance r correctly takes into account any crossings
+of periodic boundary by the atom since it was in its initial
+position.
+
+With the (optional) dir flag, one can select in which direction the
+spring force is applied. By default, the restraint is applied in all
+directions, but it can be limited to the xy-, xz-, yz-plane and the
+x-, y-, or z-direction, thus restraining the atoms to a line or a
+plane, respectively.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the original coordinates of tethered atoms to :doc:`binary restart files <restart>`, so that the spring effect will be the
+same in a restarted simulation.  See the
+:doc:`read\_restart <read_restart>` command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy stored in the per-atom springs to the system's
+potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is an energy which is
+the sum of the spring energy for each atom, where the per-atom energy
+is 0.5 \* K \* r\^2.  The scalar value calculated by this fix is
+"extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the per-atom spring energy to be included in the
+   total potential energy of the system (the quantity being minimized),
+   you MUST enable the :doc:`fix\_modify <fix_modify>` *energy* option for
+   this fix.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix drag <fix_drag>`, :doc:`fix spring <fix_spring>`,
+:doc:`fix smd <fix_smd>`, :doc:`fix spring/rg <fix_spring_rg>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst
new file mode 100644
index 0000000000..51c1b25930
--- /dev/null
+++ b/doc/src/fix_srd.rst
@@ -0,0 +1,432 @@
+.. index:: fix srd
+
+fix srd command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* srd = style name of this fix command
+* N = reset SRD particle velocities every this many timesteps
+* groupbig-ID = ID of group of large particles that SRDs interact with
+* Tsrd = temperature of SRD particles (temperature units)
+* hgrid = grid spacing for SRD grouping (distance units)
+* seed = random # seed (positive integer)
+
+* zero or more keyword/value pairs may be appended
+* keyword = *lamda* or *collision* or *overlap* or *inside* or *exact* or *radius* or *bounce* or *search* or *cubic* or *shift* or *tstat* or *rescale*
+  
+  .. parsed-literal::
+  
+       *lamda* value = mean free path of SRD particles (distance units)
+       *collision* value = *noslip* or *slip* = collision model
+       *overlap* value = *yes* or *no* = whether big particles may overlap
+       *inside* value = *error* or *warn* or *ignore* = how SRD particles which end up inside a big particle are treated
+       *exact* value = *yes* or *no*
+       *radius* value = rfactor = scale collision radius by this factor
+       *bounce* value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
+       *search* value = sgrid = grid spacing for collision partner searching (distance units)
+       *cubic* values = style tolerance
+         style = *error* or *warn*
+         tolerance = fractional difference allowed (0 <= tol <= 1)
+       *shift* values = flag shiftseed
+         flag = *yes* or *no* or *possible* = SRD bin shifting for better statistics
+           *yes* = perform bin shifting each time SRD velocities are rescaled
+           *no* = no shifting
+           *possible* = shift depending on mean free path and bin size
+         shiftseed = random # seed (positive integer)
+       *tstat* value = *yes* or *no* = thermostat SRD particles or not
+       *rescale* value = *yes* or *no* or *rotate* or *collide* = rescaling of SRD velocities
+         *yes* = rescale during velocity rotation and collisions
+         *no* = no rescaling
+         *rotate* = rescale during velocity rotation, but not collisions
+         *collide* = rescale during collisions, but not velocity rotation
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 srd srd 10 big 1.0 0.25 482984
+   fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5
+
+Description
+"""""""""""
+
+Treat a group of particles as stochastic rotation dynamics (SRD)
+particles that serve as a background solvent when interacting with big
+(colloidal) particles in groupbig-ID.  The SRD formalism is described
+in :ref:`(Hecht) <Hecht>`.  The key idea behind using SRD particles as a
+cheap coarse-grained solvent is that SRD particles do not interact
+with each other, but only with the solute particles, which in LAMMPS
+can be spheroids, ellipsoids, or line segments, or triangles, or rigid
+bodies containing multiple spheroids or ellipsoids or line segments
+or triangles.  The collision and rotation properties of the model
+imbue the SRD particles with fluid-like properties, including an
+effective viscosity.  Thus simulations with large solute particles can
+be run more quickly, to measure solute properties like diffusivity
+and viscosity in a background fluid.  The usual LAMMPS fixes for such
+simulations, such as :doc:`fix deform <fix_deform>`, :doc:`fix viscosity <fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`,
+can be used in conjunction with the SRD model.
+
+For more details on how the SRD model is implemented in LAMMPS, :ref:`this paper <Petersen1>` describes the implementation and usage of pure SRD
+fluids.  :ref:`This paper <Lechman>`, which is nearly complete, describes
+the implementation and usage of mixture systems (solute particles in
+an SRD fluid).  See the examples/srd directory for sample input
+scripts using SRD particles in both settings.
+
+This fix does 2 things:
+
+(1) It advects the SRD particles, performing collisions between SRD
+and big particles or walls every timestep, imparting force and torque
+to the big particles.  Collisions also change the position and
+velocity of SRD particles.
+
+(2) It resets the velocity distribution of SRD particles via random
+rotations every N timesteps.
+
+SRD particles have a mass, temperature, characteristic timestep
+dt\_SRD, and mean free path between collisions (lamda).  The
+fundamental equation relating these 4 quantities is
+
+
+.. parsed-literal::
+
+   lamda = dt_SRD \* sqrt(Kboltz \* Tsrd / mass)
+
+The mass of SRD particles is set by the :doc:`mass <mass>` command
+elsewhere in the input script.  The SRD timestep dt\_SRD is N times the
+step dt defined by the :doc:`timestep <timestep>` command.  Big
+particles move in the normal way via a time integration :doc:`fix <fix>`
+with a short timestep dt.  SRD particles advect with a large timestep
+dt\_SRD >= dt.
+
+If the *lamda* keyword is not specified, the SRD temperature
+*Tsrd* is used in the above formula to compute lamda.  If the *lamda*
+keyword is specified, then the *Tsrd* setting is ignored and the above
+equation is used to compute the SRD temperature.
+
+The characteristic length scale for the SRD fluid is set by *hgrid*
+which is used to bin SRD particles for purposes of resetting their
+velocities.  Normally hgrid is set to be 1/4 of the big particle
+diameter or smaller, to adequately resolve fluid properties around the
+big particles.
+
+Lamda cannot be smaller than 0.6 \* hgrid, else an error is generated
+(unless the *shift* keyword is used, see below).  The velocities of
+SRD particles are bounded by Vmax, which is set so that an SRD
+particle will not advect further than Dmax = 4\*lamda in dt\_SRD.  This
+means that roughly speaking, Dmax should not be larger than a big
+particle diameter, else SRDs may pass through big particles without
+colliding.  A warning is generated if this is the case.
+
+Collisions between SRD particles and big particles or walls are
+modeled as a lightweight SRD point particle hitting a heavy big
+particle of given diameter or a wall at a point on its surface and
+bouncing off with a new velocity.  The collision changes the momentum
+of the SRD particle.  It imparts a force and torque to the big
+particle.  It imparts a force to a wall.  Static or moving SRD walls
+are setup via the :doc:`fix wall/srd <fix_wall_srd>` command.  For the
+remainder of this doc page, a collision of an SRD particle with a wall
+can be viewed as a collision with a big particle of infinite radius
+and mass.
+
+The *collision* keyword sets the style of collisions.  The *slip*
+style means that the tangential component of the SRD particle momentum
+is preserved.  Thus a force is imparted to a big particle, but no
+torque.  The normal component of the new SRD velocity is sampled from
+a Gaussian distribution at temperature *Tsrd*\ .
+
+For the *noslip* style, both the normal and tangential components of
+the new SRD velocity are sampled from a Gaussian distribution at
+temperature *Tsrd*\ .  Additionally, a new tangential direction for the
+SRD velocity is chosen randomly.  This collision style imparts torque
+to a big particle.  Thus a time integrator :doc:`fix <fix>` that rotates
+the big particles appropriately should be used.
+
+
+----------
+
+
+The *overlap* keyword should be set to *yes* if two (or more) big
+particles can ever overlap.  This depends on the pair potential
+interaction used for big-big interactions, or could be the case if
+multiple big particles are held together as rigid bodies via the :doc:`fix rigid <fix_rigid>` command.  If the *overlap* keyword is *no* and
+big particles do in fact overlap, then SRD/big collisions can generate
+an error if an SRD ends up inside two (or more) big particles at once.
+How this error is treated is determined by the *inside* keyword.
+Running with *overlap* set to *no* allows for faster collision
+checking, so it should only be set to *yes* if needed.
+
+The *inside* keyword determines how a collision is treated if the
+computation determines that the timestep started with the SRD particle
+already inside a big particle.  If the setting is *error* then this
+generates an error message and LAMMPS stops.  If the setting is *warn*
+then this generates a warning message and the code continues.  If the
+setting is *ignore* then no message is generated.  One of the output
+quantities logged by the fix (see below) tallies the number of such
+events, so it can be monitored.  Note that once an SRD particle is
+inside a big particle, it may remain there for several steps until it
+drifts outside the big particle.
+
+The *exact* keyword determines how accurately collisions are computed.
+A setting of *yes* computes the time and position of each collision as
+SRD and big particles move together.  A setting of *no* estimates the
+position of each collision based on the end-of-timestep positions of
+the SRD and big particle.  If *overlap* is set to yes, the setting of
+the *exact* keyword is ignored since time-accurate collisions are
+needed.
+
+The *radius* keyword scales the effective size of big particles.  If
+big particles will overlap as they undergo dynamics, then this keyword
+can be used to scale down their effective collision radius by an
+amount *rfactor*\ , so that SRD particle will only collide with one big
+particle at a time.  For example, in a Lennard-Jones system at a
+temperature of 1.0 (in reduced LJ units), the minimum separation
+between two big particles is as small as about 0.88 sigma.  Thus an
+*rfactor* value of 0.85 should prevent dual collisions.
+
+The *bounce* keyword can be used to limit the maximum number of
+collisions an SRD particle undergoes in a single timestep as it
+bounces between nearby big particles.  Note that if the limit is
+reached, the SRD can be left inside a big particle.  A setting of 0 is
+the same as no limit.
+
+
+----------
+
+
+There are 2 kinds of bins created and maintained when running an SRD
+simulation.  The first are "SRD bins" which are used to bin SRD
+particles and reset their velocities, as discussed above.  The second
+are "search bins" which are used to identify SRD/big particle
+collisions.
+
+The *search* keyword can be used to choose a search bin size for
+identifying SRD/big particle collisions.  The default is to use the
+*hgrid* parameter for SRD bins as the search bin size.  Choosing a
+smaller or large value may be more efficient, depending on the
+problem.  But, in a statistical sense, it should not change the
+simulation results.
+
+The *cubic* keyword can be used to generate an error or warning when
+the bin size chosen by LAMMPS creates SRD bins that are non-cubic or
+different than the requested value of *hgrid* by a specified
+*tolerance*\ .  Note that using non-cubic SRD bins can lead to
+undetermined behavior when rotating the velocities of SRD particles,
+hence LAMMPS tries to protect you from this problem.
+
+LAMMPS attempts to set the SRD bin size to exactly *hgrid*\ .  However,
+there must be an integer number of bins in each dimension of the
+simulation box.  Thus the actual bin size will depend on the size and
+shape of the overall simulation box.  The actual bin size is printed
+as part of the SRD output when a simulation begins.
+
+If the actual bin size in non-cubic by an amount exceeding the
+tolerance, an error or warning is printed, depending on the style of
+the *cubic* keyword.  Likewise, if the actual bin size differs from
+the requested *hgrid* value by an amount exceeding the tolerance, then
+an error or warning is printed.  The *tolerance* is a fractional
+difference.  E.g. a tolerance setting of 0.01 on the shape means that
+if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an
+error or warning is generated.  Similarly, if the ratio of any bin
+dimension with *hgrid* exceeds (1 +/- tolerance), then an error or
+warning is generated.
+
+.. note::
+
+   The fix srd command can be used with simulations the size and/or
+   shape of the simulation box changes.  This can be due to non-periodic
+   boundary conditions or the use of fixes such as the :doc:`fix deform <fix_deform>` or :doc:`fix wall/srd <fix_wall_srd>` commands
+   to impose a shear on an SRD fluid or an interaction with an external
+   wall.  If the box size changes then the size of SRD bins must be
+   recalculated every reneighboring.  This is not necessary if only the
+   box shape changes.  This re-binning is always done so as to fit an
+   integer number of bins in the current box dimension, whether it be a
+   fixed, shrink-wrapped, or periodic boundary, as set by the
+   :doc:`boundary <boundary>` command.  If the box size or shape changes,
+   then the size of the search bins must be recalculated every
+   reneighboring.  Note that changing the SRD bin size may alter the
+   properties of the SRD fluid, such as its viscosity.
+
+The *shift* keyword determines whether the coordinates of SRD
+particles are randomly shifted when binned for purposes of rotating
+their velocities.  When no shifting is performed, SRD particles are
+binned and the velocity distribution of the set of SRD particles in
+each bin is adjusted via a rotation operator.  This is a statistically
+valid operation if SRD particles move sufficiently far between
+successive rotations.  This is determined by their mean-free path
+lamda.  If lamda is less than 0.6 of the SRD bin size, then shifting
+is required.  A shift means that all of the SRD particles are shifted
+by a vector whose coordinates are chosen randomly in the range [-1/2
+bin size, 1/2 bin size].  Note that all particles are shifted by the
+same vector.  The specified random number *shiftseed* is used to
+generate these vectors.  This operation sufficiently randomizes which
+SRD particles are in the same bin, even if lamda is small.
+
+If the *shift* flag is set to *no*\ , then no shifting is performed, but
+bin data will be communicated if bins overlap processor boundaries.
+An error will be generated if lamda < 0.6 of the SRD bin size.  If the
+*shift* flag is set to *possible*\ , then shifting is performed only if
+lamda < 0.6 of the SRD bin size.  A warning is generated to let you
+know this is occurring.  If the *shift* flag is set to *yes* then
+shifting is performed regardless of the magnitude of lamda.  Note that
+the *shiftseed* is not used if the *shift* flag is set to *no*\ , but
+must still be specified.
+
+Note that shifting of SRD coordinates requires extra communication,
+hence it should not normally be enabled unless required.
+
+The *tstat* keyword will thermostat the SRD particles to the specified
+*Tsrd*\ .  This is done every N timesteps, during the velocity rotation
+operation, by rescaling the thermal velocity of particles in each SRD
+bin to the desired temperature.  If there is a streaming velocity
+associated with the system, e.g. due to use of the :doc:`fix deform <fix_deform>` command to perform a simulation undergoing
+shear, then that is also accounted for.  The mean velocity of each bin
+of SRD particles is set to the position-dependent streaming velocity,
+based on the coordinates of the center of the SRD bin.  Note that
+collisions of SRD particles with big particles or walls has a
+thermostatting effect on the colliding particles, so it may not be
+necessary to thermostat the SRD particles on a bin by bin basis in
+that case.  Also note that for streaming simulations, if no
+thermostatting is performed (the default), then it may take a long
+time for the SRD fluid to come to equilibrium with a velocity profile
+that matches the simulation box deformation.
+
+The *rescale* keyword enables rescaling of an SRD particle's velocity
+if it would travel more than 4 mean-free paths in an SRD timestep.  If
+an SRD particle exceeds this velocity it is possible it will be lost
+when migrating to other processors or that collisions with big
+particles will be missed, either of which will generate errors.  Thus
+the safest mode is to run with rescaling enabled.  However rescaling
+removes kinetic energy from the system (the particle's velocity is
+reduced).  The latter will not typically be a problem if
+thermostatting is enabled via the *tstat* keyword or if SRD collisions
+with big particles or walls effectively thermostat the system.  If you
+wish to turn off rescaling (on is the default), e.g. for a pure SRD
+system with no thermostatting so that the temperature does not decline
+over time, the *rescale* keyword can be used.  The *no* value turns
+rescaling off during collisions and the per-bin velocity rotation
+operation.  The *collide* and *rotate* values turn it on for
+one of the operations and off for the other.
+
+
+----------
+
+
+.. note::
+
+   This fix is normally used for simulations with a huge number of
+   SRD particles relative to the number of big particles, e.g. 100 to 1.
+   In this scenario, computations that involve only big particles
+   (neighbor list creation, communication, time integration) can slow
+   down dramatically due to the large number of background SRD particles.
+
+Three other input script commands will largely overcome this effect,
+speeding up an SRD simulation by a significant amount.  These are the
+:doc:`atom\_modify first <atom_modify>`, :doc:`neigh\_modify include <neigh_modify>`, and :doc:`comm\_modify group <comm_modify>`
+commands.  Each takes a group-ID as an argument, which in this case
+should be the group-ID of the big solute particles.
+
+Additionally, when a :doc:`pair\_style <pair_style>` for big/big particle
+interactions is specified, the :doc:`pair\_coeff <pair_coeff>` command
+should be used to turn off big/SRD interactions, e.g. by setting their
+epsilon or cutoff length to 0.0.
+
+The "delete\_atoms overlap" command may be useful in setting up an SRD
+simulation to insure there are no initial overlaps between big and SRD
+particles.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix tabulates several SRD statistics which are stored in a vector
+of length 12, which can be accessed by various :doc:`output commands <Howto_output>`.  The vector values calculated by this fix
+are "intensive", meaning they do not scale with the size of the
+simulation.  Technically, the first 8 do scale with the size of the
+simulation, but treating them as intensive means they are not scaled
+when printed as part of thermodynamic output.
+
+These are the 12 quantities.  All are values for the current timestep,
+except for quantity 5 and the last three, each of which are
+cumulative quantities since the beginning of the run.
+
+* (1) # of SRD/big collision checks performed
+* (2) # of SRDs which had a collision
+* (3) # of SRD/big collisions (including multiple bounces)
+* (4) # of SRD particles inside a big particle
+* (5) # of SRD particles whose velocity was rescaled to be < Vmax
+* (6) # of bins for collision searching
+* (7) # of bins for SRD velocity rotation
+* (8) # of bins in which SRD temperature was computed
+* (9) SRD temperature
+* (10) # of SRD particles which have undergone max # of bounces
+* (11) max # of bounces any SRD particle has had in a single step
+* (12) # of reneighborings due to SRD particles moving too far
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the SRD
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall/srd <fix_wall_srd>`
+
+Default
+"""""""
+
+The option defaults are lamda inferred from Tsrd, collision = noslip,
+overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
+search = hgrid, cubic = error 0.01, shift = no, tstat = no, and
+rescale = yes.
+
+
+----------
+
+
+.. _Hecht:
+
+
+
+**(Hecht)** Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).
+
+.. _Petersen1:
+
+
+
+**(Petersen)** Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
+Chem Phys, 132, 174106 (2010).
+
+.. _Lechman:
+
+
+
+**(Lechman)** Lechman, et al, in preparation (2010).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst
new file mode 100644
index 0000000000..4578f39f87
--- /dev/null
+++ b/doc/src/fix_store_force.rst
@@ -0,0 +1,81 @@
+.. index:: fix store/force
+
+fix store/force command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID store/force
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* store/force = style name of this fix command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all store/force
+
+Description
+"""""""""""
+
+Store the forces on atoms in the group at the point during each
+timestep when the fix is invoked, as described below.  This is useful
+for storing forces before constraints or other boundary conditions are
+computed which modify the forces, so that unmodified forces can be
+:doc:`written to a dump file <dump>` or accessed by other :doc:`output commands <Howto_output>` that use per-atom quantities.
+
+This fix is invoked at the point in the velocity-Verlet timestepping
+immediately after :doc:`pair <pair_style>`, :doc:`bond <bond_style>`,
+:doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`,
+:doc:`improper <improper_style>`, and :doc:`long-range <kspace_style>`
+forces have been calculated.  It is the point in the timestep when
+various fixes that compute constraint forces are calculated and
+potentially modify the force on each atom.  Examples of such fixes are
+:doc:`fix shake <fix_shake>`, :doc:`fix wall <fix_wall>`, and :doc:`fix indent <fix_indent>`.
+
+.. note::
+
+   The order in which various fixes are applied which operate at
+   the same point during the timestep, is the same as the order they are
+   specified in the input script.  Thus normally, if you want to store
+   per-atom forces due to force field interactions, before constraints
+   are applied, you should list this fix first within that set of fixes,
+   i.e. before other fixes that apply constraints.  However, if you wish
+   to include certain constraints (e.g. fix shake) in the stored force,
+   then it could be specified after some fixes and before others.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix produces a per-atom array which can be accessed by various
+:doc:`output commands <Howto_output>`.  The number of columns for each
+atom is 3, and the columns store the x,y,z forces on each atom.  The
+per-atom values be accessed on any timestep.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix store\_state <fix_store_state>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst
new file mode 100644
index 0000000000..131ba5d0b1
--- /dev/null
+++ b/doc/src/fix_store_state.rst
@@ -0,0 +1,148 @@
+.. index:: fix store/state
+
+fix store/state command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID store/state N input1 input2 ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* store/state = style name of this fix command
+* N = store atom attributes every N steps, N = 0 for initial store only
+* input = one or more atom attributes
+  
+  .. parsed-literal::
+  
+       possible attributes = id, mol, type, mass,
+                             x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
+                             vx, vy, vz, fx, fy, fz,
+                             q, mux, muy, muz, mu,
+                             radius, diameter, omegax, omegay, omegaz,
+                             angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                             c_ID, c_ID[N], f_ID, f_ID[N], v_name,
+                             d_name, i_name
+
+  
+  .. parsed-literal::
+  
+           id = atom ID
+           mol = molecule ID
+           type = atom type
+           mass = atom mass
+           x,y,z = unscaled atom coordinates
+           xs,ys,zs = scaled atom coordinates
+           xu,yu,zu = unwrapped atom coordinates
+           xsu,ysu,zsu = scaled unwrapped atom coordinates
+           ix,iy,iz = box image that the atom is in
+           vx,vy,vz = atom velocities
+           fx,fy,fz = forces on atoms
+           q = atom charge
+           mux,muy,muz = orientation of dipolar atom
+           mu = magnitued of dipole moment of atom
+           radius,diameter = radius.diameter of spherical particle
+           omegax,omegay,omegaz = angular velocity of spherical particle
+           angmomx,angmomy,angmomz = angular momentum of aspherical particle
+           tqx,tqy,tqz = torque on finite-size particles
+           c_ID = per-atom vector calculated by a compute with ID
+           c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+           f_ID = per-atom vector calculated by a fix with ID
+           f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+           v_name = per-atom vector calculated by an atom-style variable with name
+           d_name = per-atom floating point vector name, managed by fix property/atom
+           i_name = per-atom integer vector name, managed by fix property/atom
+
+* zero or more keyword/value pairs may be appended
+* keyword = *com*
+  
+  .. parsed-literal::
+  
+       *com* value = *yes* or *no*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all store/state 0 x y z
+   fix 1 all store/state 0 xu yu zu com yes
+   fix 2 all store/state 1000 vx vy vz
+
+Description
+"""""""""""
+
+Define a fix that stores attributes for each atom in the group at the
+time the fix is defined.  If *N* is 0, then the values are never
+updated, so this is a way of archiving an atom attribute at a given
+time for future use in a calculation or output.  See the discussion of
+:doc:`output commands <Howto_output>` that take fixes as inputs.
+
+If *N* is not zero, then the attributes will be updated every *N*
+steps.
+
+.. note::
+
+   Actually, only atom attributes specified by keywords like *xu*
+   or *vy* or *radius* are initially stored immediately at the point in
+   your input script when the fix is defined.  Attributes specified by a
+   compute, fix, or variable are not initially stored until the first run
+   following the fix definition begins.  This is because calculating
+   those attributes may require quantities that are not defined in
+   between runs.
+
+The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning.
+
+If the *com* keyword is set to *yes* then the *xu*\ , *yu*\ , and *zu*
+inputs store the position of each atom relative to the center-of-mass
+of the group of atoms, instead of storing the absolute position.
+
+The requested values are stored in a per-atom vector or array as
+discussed below.  Zeroes are stored for atoms not in the specified
+group.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a
+simulation is restarted.  See the :doc:`read\_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.
+
+If a single input is specified, this fix produces a per-atom vector.
+If multiple inputs are specified, a per-atom array is produced where
+the number of columns for each atom is the number of inputs.  These
+can be accessed by various :doc:`output commands <Howto_output>`.  The
+per-atom values be accessed on any timestep.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`, :doc:`compute property/atom <compute_property_atom>`,
+:doc:`fix property/atom <fix_property_atom>`, :doc:`variable <variable>`
+
+Default
+"""""""
+
+The option default is com = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst
new file mode 100644
index 0000000000..8d0959cd96
--- /dev/null
+++ b/doc/src/fix_temp_berendsen.rst
@@ -0,0 +1,186 @@
+.. index:: fix temp/berendsen
+
+fix temp/berendsen command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID temp/berendsen Tstart Tstop Tdamp
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* temp/berendsen = style name of this fix command
+* Tstart,Tstop = desired temperature at start/end of run
+  
+  .. parsed-literal::
+  
+       Tstart can be a variable (see below)
+
+* Tdamp = temperature damping parameter (time units)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all temp/berendsen 300.0 300.0 100.0
+
+Description
+"""""""""""
+
+Reset the temperature of a group of atoms by using a Berendsen
+thermostat :ref:`(Berendsen) <Berendsen2>`, which rescales their velocities
+every timestep.
+
+The thermostat is applied to only the translational degrees of freedom
+for the particles, which is an important consideration for finite-size
+particles which have rotational degrees of freedom are being
+thermostatted with this fix.  The translational degrees of freedom can
+also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+The desired temperature at each timestep is a ramped value during the
+run from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+:doc:`units <units>` command).
+
+*Tstart* can be specified as an equal-style :doc:`variable <variable>`.
+In this case, the *Tstop* setting is ignored.  If the value is a
+variable, it should be specified as v\_name, where name is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its value used to determine the target temperature.
+
+.. note::
+
+   This thermostat will generate an error if the current
+   temperature is zero at the end of a timestep.  It cannot rescale a
+   zero temperature.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent temperature.
+
+.. note::
+
+   Unlike the :doc:`fix nvt <fix_nh>` command which performs
+   Nose/Hoover thermostatting AND time integration, this fix does NOT
+   perform time integration.  It only modifies velocities to effect
+   thermostatting.  Thus you must use a separate time integration fix,
+   like :doc:`fix nve <fix_nve>` to actually update the positions of atoms
+   using the modified velocities.  Likewise, this fix should not normally
+   be used on atoms that also have their temperature controlled by
+   another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` commands.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+This fix computes a temperature each timestep.  To do this, the fix
+creates its own compute of style "temp", as if this command had been
+issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp
+
+See the :doc:`compute temp <compute_temp>` command for details.  Note
+that the ID of the new compute is the fix-ID + underscore + "temp",
+and the group for the new compute is the same as the fix group.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* will have no
+effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change implied by a velocity rescaling to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix can be used with dynamic groups as defined by the
+:doc:`group <group>` command.  Likewise it can be used with groups to
+which atoms are added or deleted over time, e.g. a deposition
+simulation.  However, the conservation properties of the thermostat
+and barostat are defined for systems with a static set of atoms.  You
+may observe odd behavior if the atoms in a group vary dramatically
+over time or the atom count becomes very small.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix langevin <fix_langevin>`,
+:doc:`fix\_modify <fix_modify>`, :doc:`compute temp <compute_temp>`,
+:doc:`fix press/berendsen <fix_press_berendsen>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Berendsen2:
+
+
+
+**(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
+Phys, 81, 3684 (1984).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst
new file mode 100644
index 0000000000..6494c9e981
--- /dev/null
+++ b/doc/src/fix_temp_csvr.rst
@@ -0,0 +1,198 @@
+.. index:: fix temp/csvr
+
+fix temp/csvr command
+=====================
+
+fix temp/csld command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID temp/csvr Tstart Tstop Tdamp seed
+
+   fix ID group-ID temp/csld Tstart Tstop Tdamp seed
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* temp/csvr or temp/csld = style name of this fix command
+* Tstart,Tstop = desired temperature at start/end of run
+  
+  .. parsed-literal::
+  
+       Tstart can be a variable (see below)
+
+* Tdamp = temperature damping parameter (time units)
+* seed = random number seed to use for white noise (positive integer)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all temp/csvr 300.0 300.0 100.0 54324
+
+   fix 1 all temp/csld 100.0 300.0 10.0 123321
+
+Description
+"""""""""""
+
+Adjust the temperature with a canonical sampling thermostat that uses
+global velocity rescaling with Hamiltonian dynamics (\ *temp/csvr*\ )
+:ref:`(Bussi1) <Bussi1>`, or Langevin dynamics (\ *temp/csld*\ )
+:ref:`(Bussi2) <Bussi2>`.  In the case of *temp/csvr* the thermostat is
+similar to the empirical Berendsen thermostat in
+:doc:`temp/berendsen <fix_temp_berendsen>`, but chooses the actual
+scaling factor from a suitably chosen (gaussian) distribution rather
+than having it determined from the time constant directly. In the case
+of *temp/csld* the velocities are updated to a linear combination of
+the current velocities with a gaussian distribution of velocities at
+the desired temperature.  Both thermostats are applied every timestep.
+
+The thermostat is applied to only the translational degrees of freedom
+for the particles, which is an important consideration for finite-size
+particles which have rotational degrees of freedom are being
+thermostatted with these fixes.  The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+The desired temperature at each timestep is a ramped value during the
+run from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+:doc:`units <units>` command).
+
+*Tstart* can be specified as an equal-style :doc:`variable <variable>`.
+In this case, the *Tstop* setting is ignored.  If the value is a
+variable, it should be specified as v\_name, where name is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its value used to determine the target temperature.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent temperature.
+
+.. note::
+
+   Unlike the :doc:`fix nvt <fix_nh>` command which performs
+   Nose/Hoover thermostatting AND time integration, these fixes do NOT
+   perform time integration. They only modify velocities to effect
+   thermostatting.  Thus you must use a separate time integration fix,
+   like :doc:`fix nve <fix_nve>` to actually update the positions of atoms
+   using the modified velocities.  Likewise, these fixes should not
+   normally be used on atoms that also have their temperature controlled
+   by another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` commands.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+These fixes compute a temperature each timestep.  To do this, the fix
+creates its own compute of style "temp", as if this command had been
+issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp
+
+See the :doc:`compute temp <compute_temp>` command for details.  Note
+that the ID of the new compute is the fix-ID + underscore + "temp",
+and the group for the new compute is the same as the fix group.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* will have no
+effect on this fix.
+
+Like other fixes that perform thermostatting, these fixes can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about these fixes are written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by these
+fixes.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to these fixes which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+these fixes and by the compute should be the same.
+
+These fixes can ramp its target temperature over multiple runs, using
+the *start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+These fixes are not invoked during :doc:`energy minimization <minimize>`.
+
+These fixes compute a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to the fix.  The scalar value calculated by this fix
+is "extensive".
+
+Restrictions
+""""""""""""
+
+
+These fixes are not compatible with :doc:`fix shake <fix_shake>`.
+
+The fix can be used with dynamic groups as defined by the
+:doc:`group <group>` command.  Likewise it can be used with groups to
+which atoms are added or deleted over time, e.g. a deposition
+simulation.  However, the conservation properties of the thermostat
+and barostat are defined for systems with a static set of atoms.  You
+may observe odd behavior if the atoms in a group vary dramatically
+over time or the atom count becomes very small.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix langevin <fix_langevin>`,
+:doc:`fix\_modify <fix_modify>`, :doc:`compute temp <compute_temp>`,
+:doc:`fix temp/berendsen <fix_temp_berendsen>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Bussi1:
+
+
+
+.. _Bussi2:
+
+**(Bussi1)** Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
+
+
+**(Bussi2)** Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst
new file mode 100644
index 0000000000..80f03a3018
--- /dev/null
+++ b/doc/src/fix_temp_rescale.rst
@@ -0,0 +1,173 @@
+.. index:: fix temp/rescale
+
+fix temp/rescale command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID temp/rescale N Tstart Tstop window fraction
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* temp/rescale = style name of this fix command
+* N = perform rescaling every N steps
+* Tstart,Tstop = desired temperature at start/end of run (temperature units)
+  
+  .. parsed-literal::
+  
+       Tstart can be a variable (see below)
+
+* window = only rescale if temperature is outside this window (temperature units)
+* fraction = rescale to target temperature by this fraction
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
+   fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
+   fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
+
+Description
+"""""""""""
+
+Reset the temperature of a group of atoms by explicitly rescaling
+their velocities.
+
+The rescaling is applied to only the translational degrees of freedom
+for the particles, which is an important consideration if finite-size
+particles which have rotational degrees of freedom are being
+thermostatted with this fix.  The translational degrees of freedom can
+also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+
+Rescaling is performed every N timesteps.  The target temperature is a
+ramped value between the *Tstart* and *Tstop* temperatures at the
+beginning and end of the run.
+
+.. note::
+
+   This thermostat will generate an error if the current
+   temperature is zero at the end of a timestep it is invoked on.  It
+   cannot rescale a zero temperature.
+
+*Tstart* can be specified as an equal-style :doc:`variable <variable>`.
+In this case, the *Tstop* setting is ignored.  If the value is a
+variable, it should be specified as v\_name, where name is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its value used to determine the target temperature.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent temperature.
+
+Rescaling is only performed if the difference between the current and
+desired temperatures is greater than the *window* value.  The amount
+of rescaling that is applied is a *fraction* (from 0.0 to 1.0) of the
+difference between the actual and desired temperature.  E.g. if
+*fraction* = 1.0, the temperature is reset to exactly the desired
+value.
+
+.. note::
+
+   Unlike the :doc:`fix nvt <fix_nh>` command which performs
+   Nose/Hoover thermostatting AND time integration, this fix does NOT
+   perform time integration.  It only modifies velocities to effect
+   thermostatting.  Thus you must use a separate time integration fix,
+   like :doc:`fix nve <fix_nve>` to actually update the positions of atoms
+   using the modified velocities.  Likewise, this fix should not normally
+   be used on atoms that also have their temperature controlled by
+   another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` commands.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+This fix computes a temperature each timestep.  To do this, the fix
+creates its own compute of style "temp", as if one of this command had
+been issued:
+
+
+.. parsed-literal::
+
+   compute fix-ID_temp group-ID temp
+
+See the :doc:`compute temp <compute_temp>` for details.  Note that the
+ID of the new compute is the fix-ID + underscore + "temp", and the
+group for the new compute is the same as the fix group.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the :doc:`thermo\_style <thermo_style>` command) with ID = *thermo\_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute\_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo\_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo\_temp* will have no
+effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix\_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change implied by a velocity rescaling to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix langevin <fix_langevin>`, :doc:`fix nvt <fix_nh>`,
+:doc:`fix\_modify <fix_modify>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst
new file mode 100644
index 0000000000..e60459a29b
--- /dev/null
+++ b/doc/src/fix_temp_rescale_eff.rst
@@ -0,0 +1,83 @@
+.. index:: fix temp/rescale/eff
+
+fix temp/rescale/eff command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* temp/rescale/eff = style name of this fix command
+* N = perform rescaling every N steps
+* Tstart,Tstop = desired temperature at start/end of run (temperature units)
+* window = only rescale if temperature is outside this window (temperature units)
+* fraction = rescale to target temperature by this fraction
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0
+
+Description
+"""""""""""
+
+Reset the temperature of a group of nuclei and electrons in the
+:doc:`electron force field <pair_eff>` model by explicitly rescaling
+their velocities.
+
+The operation of this fix is exactly like that described by the :doc:`fix temp/rescale <fix_temp_rescale>` command, except that the rescaling
+is also applied to the radial electron velocity for electron
+particles.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy change implied by a velocity rescaling to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-EFF package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix langevin/eff <fix_langevin_eff>`, :doc:`fix nvt/eff <fix_nh_eff>`, :doc:`fix\_modify <fix_modify>`,
+:doc:`fix temp rescale <fix_temp_rescale>`,
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst
new file mode 100644
index 0000000000..ab407ba7b1
--- /dev/null
+++ b/doc/src/fix_tfmc.rst
@@ -0,0 +1,181 @@
+.. index:: fix tfmc
+
+fix tfmc command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID tfmc Delta Temp seed keyword value
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* tfmc = style name of this fix command
+* Delta = maximal displacement length (distance units)
+* Temp = imposed temperature of the system
+* seed = random number seed (positive integer)
+* zero or more keyword/arg pairs may be appended
+* keyword = *com* or *rot*
+  
+  .. parsed-literal::
+  
+       *com* args = xflag yflag zflag
+         xflag,yflag,zflag = 0/1 to exclude/include each dimension
+       *rot* args = none
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all tfmc 0.1 1000.0 159345
+   fix 1 all tfmc 0.05 600.0 658943 com 1 1 0
+   fix 1 all tfmc 0.1 750.0 387068 com 1 1 1 rot
+
+Description
+"""""""""""
+
+Perform uniform-acceptance force-bias Monte Carlo (fbMC) simulations,
+using the time-stamped force-bias Monte Carlo (tfMC) algorithm
+described in :ref:`(Mees) <Mees>` and :ref:`(Bal) <Bal>`.
+
+One successful use case of force-bias Monte Carlo methods is that they
+can be used to extend the time scale of atomistic simulations, in
+particular when long time scale relaxation effects must be considered;
+some interesting examples are given in the review by :ref:`(Neyts) <Neyts>`.
+An example of a typical use case would be the modelling of chemical
+vapor deposition (CVD) processes on a surface, in which impacts by
+gas-phase species can be performed using MD, but subsequent relaxation
+of the surface is too slow to be done using MD only. Using tfMC can
+allow for a much faster relaxation of the surface, so that higher
+fluxes can be used, effectively extending the time scale of the
+simulation. (Such an alternating simulation approach could be set up
+using a :doc:`loop <jump>`.)
+
+The initial version of tfMC algorithm in :ref:`(Mees) <Mees>` contained an
+estimation of the effective time scale of such a simulation, but it
+was later shown that the speed-up one can gain from a tfMC simulation
+is system- and process-dependent, ranging from none to several orders
+of magnitude. In general, solid-state processes such as
+(re)crystallization or growth can be accelerated by up to two or three
+orders of magnitude, whereas diffusion in the liquid phase is not
+accelerated at all. The observed pseudodynamics when using the tfMC
+method is not the actual dynamics one would obtain using MD, but the
+relative importance of processes can match the actual relative
+dynamics of the system quite well, provided *Delta* is chosen with
+care. Thus, the system's equilibrium is reached faster than in MD,
+along a path that is generally roughly similar to a typical MD
+simulation (but not necessarily so). See :ref:`(Bal) <Bal>` for details.
+
+Each step, all atoms in the selected group are displaced using the
+stochastic tfMC algorithm, which is designed to sample the canonical
+(NVT) ensemble at the temperature *Temp*\ . Although tfMC is a Monte
+Carlo algorithm and thus strictly speaking does not perform time
+integration, it is similar in the sense that it uses the forces on all
+atoms in order to update their positions. Therefore, it is implemented
+as a time integration fix, and no other fixes of this type (such as
+:doc:`fix nve <fix_nve>`) should be used at the same time. Because
+velocities do not play a role in this kind of Monte Carlo simulations,
+instantaneous temperatures as calculated by :doc:`temperature computes <compute_temp>` or :doc:`thermodynamic output <thermo_style>` have no meaning: the only relevant
+temperature is the sampling temperature *Temp*\ .  Similarly, performing
+tfMC simulations does not require setting a :doc:`timestep <timestep>`
+and the :doc:`simulated time <thermo_style>` as calculated by LAMMPS is
+meaningless.
+
+The critical parameter determining the success of a tfMC simulation is
+*Delta*\ , the maximal displacement length of the lightest element in
+the system: the larger it is, the longer the effective time scale of
+the simulation will be (there is an approximately quadratic
+dependence). However, *Delta* must also be chosen sufficiently small
+in order to comply with detailed balance; in general values between 5
+and 10 % of the nearest neighbor distance are found to be a good
+choice. For a more extensive discussion with specific examples, please
+refer to :ref:`(Bal) <Bal>`, which also describes how the code calculates
+element-specific maximal displacements from *Delta*\ , based on the
+fourth root of their mass.
+
+Because of the uncorrelated movements of the atoms, the center-of-mass
+of the fix group will not necessarily be stationary, just like its
+orientation. When the *com* keyword is used, all atom positions will
+be shifted (after every tfMC iteration) in order to fix the position
+of the center-of-mass along the included directions, by setting the
+corresponding flag to 1. The *rot* keyword does the same for the
+rotational component of the tfMC displacements after every iteration.
+
+.. note::
+
+   the *com* and *rot* keywords should not be used if an external
+   force is acting on the specified fix group, along the included
+   directions. This can be either a true external force (e.g.  through
+   :doc:`fix wall <fix_wall>`) or forces due to the interaction with atoms
+   not included in the fix group. This is because in such cases,
+   translations or rotations of the fix group could be induced by these
+   external forces, and removing them will lead to a violation of
+   detailed balance.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MC package.  It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+This fix is not compatible with :doc:`fix shake <fix_shake>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix gcmc <fix_gcmc>`, :doc:`fix nvt <fix_nh>`
+
+Default
+"""""""
+
+The option default is com = 0 0 0
+
+
+----------
+
+
+.. _Bal:
+
+
+
+**(Bal)** K. M Bal and E. C. Neyts, J. Chem. Phys. 141, 204104 (2014).
+
+.. _Mees:
+
+
+
+**(Mees)** M. J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and
+A. Stesmans, Phys. Rev. B 85, 134301 (2012).
+
+.. _Neyts:
+
+
+
+**(Neyts)** E. C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320
+(2013).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst
new file mode 100644
index 0000000000..05552c1b37
--- /dev/null
+++ b/doc/src/fix_thermal_conductivity.rst
@@ -0,0 +1,188 @@
+.. index:: fix thermal/conductivity
+
+fix thermal/conductivity command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID thermal/conductivity N edim Nbin keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* thermal/conductivity = style name of this fix command
+* N = perform kinetic energy exchange every N steps
+* edim = *x* or *y* or *z* = direction of kinetic energy transfer
+* Nbin = # of layers in edim direction (must be even number)
+* zero or more keyword/value pairs may be appended
+* keyword = *swap*
+  
+  .. parsed-literal::
+  
+       *swap* value = Nswap = number of swaps to perform every N steps
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all thermal/conductivity 100 z 20
+   fix 1 all thermal/conductivity 50 z 20 swap 2
+
+Description
+"""""""""""
+
+Use the Muller-Plathe algorithm described in :ref:`this paper <Muller-Plathe1>` to exchange kinetic energy between two particles
+in different regions of the simulation box every N steps.  This
+induces a temperature gradient in the system.  As described below this
+enables the thermal conductivity of a material to be calculated.  This
+algorithm is sometimes called a reverse non-equilibrium MD (reverse
+NEMD) approach to computing thermal conductivity.  This is because the
+usual NEMD approach is to impose a temperature gradient on the system
+and measure the response as the resulting heat flux.  In the
+Muller-Plathe method, the heat flux is imposed, and the temperature
+gradient is the system's response.
+
+See the :doc:`compute heat/flux <compute_heat_flux>` command for details
+on how to compute thermal conductivity in an alternate way, via the
+Green-Kubo formalism.
+
+The simulation box is divided into *Nbin* layers in the *edim*
+direction, where the layer 1 is at the low end of that dimension and
+the layer *Nbin* is at the high end.  Every N steps, Nswap pairs of
+atoms are chosen in the following manner.  Only atoms in the fix group
+are considered.  The hottest Nswap atoms in layer 1 are selected.
+Similarly, the coldest Nswap atoms in the "middle" layer (see below)
+are selected.  The two sets of Nswap atoms are paired up and their
+velocities are exchanged.  This effectively swaps their kinetic
+energies, assuming their masses are the same.  If the masses are
+different, an exchange of velocities relative to center of mass motion
+of the 2 atoms is performed, to conserve kinetic energy.  Over time,
+this induces a temperature gradient in the system which can be
+measured using commands such as the following, which writes the
+temperature profile (assuming z = edim) to the file tmp.profile:
+
+
+.. parsed-literal::
+
+   compute   ke all ke/atom
+   variable  temp atom c_ke/1.5
+   compute   layers all chunk/atom bin/1d z lower 0.05 units reduced
+   fix       3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
+
+Note that by default, Nswap = 1, though this can be changed by the
+optional *swap* keyword.  Setting this parameter appropriately, in
+conjunction with the swap rate N, allows the heat flux to be adjusted
+across a wide range of values, and the kinetic energy to be exchanged
+in large chunks or more smoothly.
+
+The "middle" layer for velocity swapping is defined as the *Nbin*\ /2 +
+1 layer.  Thus if *Nbin* = 20, the two swapping layers are 1 and 11.
+This should lead to a symmetric temperature profile since the two
+layers are separated by the same distance in both directions in a
+periodic sense.  This is why *Nbin* is restricted to being an even
+number.
+
+As described below, the total kinetic energy transferred by these
+swaps is computed by the fix and can be output.  Dividing this
+quantity by time and the cross-sectional area of the simulation box
+yields a heat flux.  The ratio of heat flux to the slope of the
+temperature profile is proportional to the thermal conductivity of the
+fluid, in appropriate units.  See the :ref:`Muller-Plathe paper <Muller-Plathe1>` for details.
+
+.. note::
+
+   If your system is periodic in the direction of the heat flux,
+   then the flux is going in 2 directions.  This means the effective heat
+   flux in one direction is reduced by a factor of 2.  You will see this
+   in the equations for thermal conductivity (kappa) in the Muller-Plathe
+   paper.  LAMMPS is simply tallying kinetic energy which does not
+   account for whether or not your system is periodic; you must use the
+   value appropriately to yield a kappa for your system.
+
+.. note::
+
+   After equilibration, if the temperature gradient you observe is
+   not linear, then you are likely swapping energy too frequently and are
+   not in a regime of linear response.  In this case you cannot
+   accurately infer a thermal conductivity and should try increasing the
+   Nevery parameter.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+kinetic energy transferred between the bottom and middle of the
+simulation box (in the *edim* direction) is stored as a scalar
+quantity by this fix.  This quantity is zeroed when the fix is defined
+and accumulates thereafter, once every N steps.  The units of the
+quantity are energy; see the :doc:`units <units>` command for details.
+The scalar value calculated by this fix is "intensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Swaps conserve both momentum and kinetic energy, even if the masses of
+the swapped atoms are not equal.  Thus you should not need to
+thermostat the system.  If you do use a thermostat, you may want to
+apply it only to the non-swapped dimensions (other than *vdim*\ ).
+
+LAMMPS does not check, but you should not use this fix to swap the
+kinetic energy of atoms that are in constrained molecules, e.g. via
+:doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`.  This is
+because application of the constraints will alter the amount of
+transferred momentum.  You should, however, be able to use flexible
+molecules.  See the :ref:`Zhang paper <Zhang2>` for a discussion and results
+of this idea.
+
+When running a simulation with large, massive particles or molecules
+in a background solvent, you may want to only exchange kinetic energy
+between solvent particles.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ehex <fix_ehex>`, :doc:`fix heat <fix_heat>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix viscosity <fix_viscosity>`,
+:doc:`compute heat/flux <compute_heat_flux>`
+
+Default
+"""""""
+
+The option defaults are swap = 1.
+
+
+----------
+
+
+.. _Muller-Plathe1:
+
+
+
+**(Muller-Plathe)** Muller-Plathe, J Chem Phys, 106, 6082 (1997).
+
+.. _Zhang2:
+
+
+
+**(Zhang)** Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B,
+109, 15060-15067 (2005).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst
new file mode 100644
index 0000000000..807f89b172
--- /dev/null
+++ b/doc/src/fix_ti_spring.rst
@@ -0,0 +1,189 @@
+.. index:: fix ti/spring
+
+fix ti/spring command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ti/spring k t_s t_eq keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* ti/spring = style name of this fix command
+* k = spring constant (force/distance units)
+* t\_eq = number of steps for the equilibration procedure
+* t\_s = number of steps for the switching procedure
+* zero or more keyword/value pairs may be appended to args
+* keyword = *function*
+  
+  .. parsed-literal::
+  
+       *function* value = function-ID
+         function-ID = ID of the switching function (1 or 2)
+
+
+
+**Example:**
+
+
+.. parsed-literal::
+
+   fix 1 all ti/spring 50.0 2000 1000 function 2
+
+Description
+"""""""""""
+
+This fix allows you to compute the free energy of crystalline solids
+by performing a nonequilibrium thermodynamic integration between the
+solid of interest and an Einstein crystal. A detailed explanation of
+how to use this command and choose its parameters for optimal
+performance and accuracy is given in the paper by
+:ref:`Freitas <Freitas1>`. The paper also presents a short summary of the
+theory of nonequilibrium thermodynamic integration.
+
+The thermodynamic integration procedure is performed by rescaling the
+force on each atom. Given an atomic configuration the force (F) on
+each atom is given by
+
+.. image:: Eqs/fix_ti_spring_force.jpg
+   :align: center
+
+where F\_solid is the force that acts on an atom due to an interatomic
+potential (\ *e.g.* EAM potential), F\_harm is the force due to the
+Einstein crystal harmonic spring, and lambda is the coupling parameter
+of the thermodynamic integration. An Einstein crystal is a solid where
+each atom is attached to its equilibrium position by a harmonic spring
+with spring constant *k*\ . With this fix a spring force is applied
+independently to each atom in the group defined by the fix to tether
+it to its initial position. The initial position of each atom is its
+position at the time the fix command was issued.
+
+The fix acts as follows: during the first *t\_eq* steps after the fix
+is defined the value of lambda is zero. This is the period to
+equilibrate the system in the lambda = 0 state. After this the value
+of lambda changes dynamically during the simulation from 0 to 1
+according to the function defined using the keyword *function*
+(described below), this switching from lambda from 0 to 1 is done in
+*t\_s* steps. Then comes the second equilibration period of *t\_eq* to
+equilibrate the system in the lambda = 1 state. After that, the
+switching back to the lambda = 0 state is made using *t\_s* timesteps
+and following the same switching function. After this period the value
+of lambda is kept equal to zero and the fix has no other effect on the
+dynamics of the system.
+
+The processes described above is known as nonequilibrium thermodynamic
+integration and is has been shown (:ref:`Freitas <Freitas1>`) to present a
+much superior efficiency when compared to standard equilibrium
+methods. The reason why the switching it is made in both directions
+(potential to Einstein crystal and back) is to eliminate the
+dissipated heat due to the nonequilibrium process. Further details
+about nonequilibrium thermodynamic integration and its implementation
+in LAMMPS is available in :ref:`Freitas <Freitas1>`.
+
+The *function* keyword allows the use of two different lambda
+paths. Option *1* results in a constant rate of change of lambda with
+time:
+
+.. image:: Eqs/fix_ti_spring_function_1.jpg
+   :align: center
+
+where tau is the scaled time variable *t/t\_s*. The option *2* performs
+the lambda switching at a rate defined by the following switching
+function
+
+.. image:: Eqs/fix_ti_spring_function_2.jpg
+   :align: center
+
+This function has zero slope as lambda approaches its extreme values
+(0 and 1), according to :ref:`de Koning <deKoning96>` this results in
+smaller fluctuations on the integral to be computed on the
+thermodynamic integration. The use of option *2* is recommended since
+it results in better accuracy and less dissipation without any
+increase in computational resources cost.
+
+.. note::
+
+   As described in :ref:`Freitas <Freitas1>`, it is important to keep the
+   center-of-mass fixed during the thermodynamic integration. A nonzero
+   total velocity will result in divergences during the integration due
+   to the fact that the atoms are 'attached' to their equilibrium
+   positions by the Einstein crystal. Check the option *zero* of :doc:`fix langevin <fix_langevin>` and :doc:`velocity <velocity>`. The use of
+   the Nose-Hoover thermostat (:doc:`fix nvt <fix_nh>`) is *NOT*
+   recommended due to its well documented issues with the canonical
+   sampling of harmonic degrees of freedom (notice that the *chain*
+   option will *NOT* solve this problem). The Langevin thermostat (:doc:`fix langevin <fix_langevin>`) correctly thermostats the system and we
+   advise its usage with ti/spring command.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the original coordinates of tethered atoms to :doc:`binary restart files <restart>`, so that the spring effect will be the
+same in a restarted simulation. See the :doc:`read restart <read_restart>` command for info on how to re-specify a fix
+in an input script that reads a restart file, so that the operation of
+the fix continues in an uninterrupted fashion.
+
+The :doc:`fix modify <fix_modify>` *energy* option is supported by this
+fix to add the energy stored in the per-atom springs to the system's
+potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar and a global vector quantities which
+can be accessed by various :doc:`output commands <Howto_output>`. The
+scalar is an energy which is the sum of the spring energy for each
+atom, where the per-atom energy is 0.5 \* k \* r\^2. The vector has 2
+positions, the first one is the coupling parameter lambda and the
+second one is the time derivative of lambda. The scalar and vector
+values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the per-atom spring energy to be included in the
+   total potential energy of the system (the quantity being minimized),
+   you MUST enable the :doc:`fix modify <fix_modify>` *energy* option for
+   this fix.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix spring <fix_spring>`, :doc:`fix adapt <fix_adapt>`
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Default
+"""""""
+
+The keyword default is function = 1.
+
+
+----------
+
+
+.. _Freitas1:
+
+
+
+**(Freitas)** Freitas, Asta, and de Koning, Computational Materials
+Science, 112, 333 (2016).
+
+.. _deKoning96:
+
+
+
+**(de Koning)** de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst
new file mode 100644
index 0000000000..ed31733196
--- /dev/null
+++ b/doc/src/fix_tmd.rst
@@ -0,0 +1,151 @@
+.. index:: fix tmd
+
+fix tmd command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID tmd rho_final file1 N file2
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* tmd = style name of this fix command
+* rho\_final = desired value of rho at the end of the run (distance units)
+* file1 = filename to read target structure from
+* N = dump TMD statistics every this many timesteps, 0 = no dump
+* file2 = filename to write TMD statistics to (only needed if N > 0)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all nve
+   fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
+
+Description
+"""""""""""
+
+Perform targeted molecular dynamics (TMD) on a group of atoms.  A
+holonomic constraint is used to force the atoms to move towards (or
+away from) the target configuration.  The parameter "rho" is
+monotonically decreased (or increased) from its initial value to
+rho\_final at the end of the run.
+
+Rho has distance units and is a measure of the root-mean-squared
+distance (RMSD) between the current configuration of the atoms in the
+group and the target coordinates listed in file1.  Thus a value of
+rho\_final = 0.0 means move the atoms all the way to the final
+structure during the course of the run.
+
+The target file1 can be ASCII text or a gzipped text file (detected by
+a .gz suffix).  The format of the target file1 is as follows:
+
+
+.. parsed-literal::
+
+   0.0 25.0 xlo xhi
+   0.0 25.0 ylo yhi
+   0.0 25.0 zlo zhi
+   125     24.97311   1.69005     23.46956 0 0 -1
+   126     1.94691    2.79640     1.92799  1 0 0
+   127     0.15906    3.46099     0.79121  1 0 0
+   ...
+
+The first 3 lines may or may not be needed, depending on the format of
+the atoms to follow.  If image flags are included with the atoms, the
+1st 3 lo/hi lines must appear in the file.  If image flags are not
+included, the 1st 3 lines should not appear.  The 3 lines contain the
+simulation box dimensions for the atom coordinates, in the same format
+as in a LAMMPS data file (see the :doc:`read\_data <read_data>` command).
+
+The remaining lines each contain an atom ID and its target x,y,z
+coordinates.  The atom lines (all or none of them) can optionally be
+followed by 3 integer values: nx,ny,nz.  For periodic dimensions, they
+specify which image of the box the atom is considered to be in, i.e. a
+value of N (positive or negative) means add N times the box length to
+the coordinate to get the true value.
+
+The atom lines can be listed in any order, but every atom in the group
+must be listed in the file.  Atoms not in the fix group may also be
+listed; they will be ignored.
+
+TMD statistics are written to file2 every N timesteps, unless N is
+specified as 0, which means no statistics.
+
+The atoms in the fix tmd group should be integrated (via a fix nve,
+nvt, npt) along with other atoms in the system.
+
+Restarts can be used with a fix tmd command.  For example, imagine a
+10000 timestep run with a rho\_initial = 11 and a rho\_final = 1.  If a
+restart file was written after 2000 time steps, then the configuration
+in the file would have a rho value of 9.  A new 8000 time step run
+could be performed with the same rho\_final = 1 to complete the
+conformational change at the same transition rate.  Note that for
+restarted runs, the name of the TMD statistics file should be changed
+to prevent it being overwritten.
+
+For more information about TMD, see :ref:`(Schlitter1) <Schlitter1>` and
+:ref:`(Schlitter2) <Schlitter2>`.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+
+This fix can ramp its rho parameter over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+All TMD fixes must be listed in the input script after all integrator
+fixes (nve, nvt, npt) are applied.  This ensures that atoms are moved
+before their positions are corrected to comply with the constraint.
+
+Atoms that have a TMD fix applied should not be part of a group to
+which a SHAKE fix is applied.  This is because LAMMPS assumes there
+are not multiple competing holonomic constraints applied to the same
+atoms.
+
+To read gzipped target files, you must compile LAMMPS with the
+-DLAMMPS\_GZIP option.  See the :doc:`Build settings <Build_settings>`
+doc page for details.
+
+**Related commands:** none
+
+**Default:** none
+
+
+----------
+
+
+.. _Schlitter1:
+
+
+
+**(Schlitter1)** Schlitter, Swegat, Mulders, "Distance-type reaction
+coordinates for modelling activated processes", J Molecular Modeling,
+7, 171-177 (2001).
+
+.. _Schlitter2:
+
+
+
+**(Schlitter2)** Schlitter and Klahn, "The free energy of a reaction
+coordinate at multiple constraints: a concise formulation", Molecular
+Physics, 101, 3439-3443 (2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst
new file mode 100644
index 0000000000..b6bc43ecd3
--- /dev/null
+++ b/doc/src/fix_ttm.rst
@@ -0,0 +1,383 @@
+.. index:: fix ttm
+
+fix ttm command
+===============
+
+fix ttm/mod command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile
+   fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = *ttm* or *ttm\_mod*
+* seed = random number seed to use for white noise (positive integer)
+* remaining arguments for fix ttm:
+  
+  .. parsed-literal::
+  
+       C_e  = electronic specific heat (energy/(electron\*temperature) units)
+       rho_e = electronic density (electrons/volume units)
+       kappa_e = electronic thermal conductivity (energy/(time\*distance\*temperature) units)
+       gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
+       gamma_s = friction coefficient due to electronic stopping (mass/time units)
+       v_0 = electronic stopping critical velocity (velocity units)
+       Nx = number of thermal solve grid points in the x-direction (positive integer)
+       Ny = number of thermal solve grid points in the y-direction (positive integer)
+       Nz = number of thermal solve grid points in the z-direction (positive integer)
+       T_infile = filename to read initial electronic temperature from
+       N = dump TTM temperatures every this many timesteps, 0 = no dump
+       T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+
+* remaining arguments for fix ttm/mod:
+  
+  .. parsed-literal::
+  
+       init_file = file with the parameters to TTM
+       Nx = number of thermal solve grid points in the x-direction (positive integer)
+       Ny = number of thermal solve grid points in the y-direction (positive integer)
+       Nz = number of thermal solve grid points in the z-direction (positive integer)
+       T_infile = filename to read initial electronic temperature from
+       N = dump TTM temperatures every this many timesteps, 0 = no dump
+       T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
+   fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out
+   fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out
+
+Description
+"""""""""""
+
+Use a two-temperature model (TTM) to represent heat transfer through
+and between electronic and atomic subsystems.  LAMMPS models the
+atomic subsystem as usual with a molecular dynamics model and the
+classical force field specified by the user, but the electronic
+subsystem is modeled as a continuum, or a background "gas", on a
+regular grid.  Energy can be transferred spatially within the grid
+representing the electrons.  Energy can also be transferred between
+the electronic and the atomic subsystems.  The algorithm underlying
+this fix was derived by D. M.  Duffy and A. M. Rutherford and is
+discussed in two J Physics: Condensed Matter papers: :ref:`(Duffy) <Duffy>`
+and :ref:`(Rutherford) <Rutherford>`.  They used this algorithm in cascade
+simulations where a primary knock-on atom (PKA) was initialized with a
+high velocity to simulate a radiation event.
+
+The description in this sub-section applies to both fix ttm and fix
+ttm/mod.  Fix ttm/mod adds options to account for external heat
+sources (e.g. at a surface) and for specifying parameters that allow
+the electronic heat capacity to depend strongly on electronic
+temperature.  It is more expensive computationally than fix ttm
+because it treats the thermal diffusion equation as non-linear.  More
+details on fix ttm/mod are given below.
+
+Heat transfer between the electronic and atomic subsystems is carried
+out via an inhomogeneous Langevin thermostat.  This thermostat differs
+from the regular Langevin thermostat (:doc:`fix langevin <fix_langevin>`) in three important ways.  First, the
+Langevin thermostat is applied uniformly to all atoms in the
+user-specified group for a single target temperature, whereas the TTM
+fix applies Langevin thermostatting locally to atoms within the
+volumes represented by the user-specified grid points with a target
+temperature specific to that grid point.  Second, the Langevin
+thermostat couples the temperature of the atoms to an infinite heat
+reservoir, whereas the heat reservoir for fix TTM is finite and
+represents the local electrons.  Third, the TTM fix allows users to
+specify not just one friction coefficient, but rather two independent
+friction coefficients: one for the electron-ion interactions
+(*gamma\_p*), and one for electron stopping (*gamma\_s*).
+
+When the friction coefficient due to electron stopping, *gamma\_s*, is
+non-zero, electron stopping effects are included for atoms moving
+faster than the electron stopping critical velocity, *v\_0*.  For
+further details about this algorithm, see :ref:`(Duffy) <Duffy>` and
+:ref:`(Rutherford) <Rutherford>`.
+
+Energy transport within the electronic subsystem is solved according
+to the heat diffusion equation with added source terms for heat
+transfer between the subsystems:
+
+.. image:: Eqs/fix_ttm.jpg
+   :align: center
+
+where C\_e is the specific heat, rho\_e is the density, kappa\_e is the
+thermal conductivity, T is temperature, the "e" and "a" subscripts
+represent electronic and atomic subsystems respectively, g\_p is the
+coupling constant for the electron-ion interaction, and g\_s is the
+electron stopping coupling parameter.  C\_e, rho\_e, and kappa\_e are
+specified as parameters to the fix.  The other quantities are derived.
+The form of the heat diffusion equation used here is almost the same
+as that in equation 6 of :ref:`(Duffy) <Duffy>`, with the exception that the
+electronic density is explicitly represented, rather than being part
+of the specific heat parameter.
+
+Currently, fix ttm assumes that none of the user-supplied parameters
+will vary with temperature. Note that :ref:`(Duffy) <Duffy>` used a tanh()
+functional form for the temperature dependence of the electronic
+specific heat, but ignored temperature dependencies of any of the
+other parameters.  See more discussion below for fix ttm/mod.
+
+These fixes require use of periodic boundary conditions and a 3D
+simulation.  Periodic boundary conditions are also used in the heat
+equation solve for the electronic subsystem.  This varies from the
+approach of :ref:`(Rutherford) <Rutherford>` where the atomic subsystem was
+embedded within a larger continuum representation of the electronic
+subsystem.
+
+The initial electronic temperature input file, *T\_infile*, is a text
+file LAMMPS reads in with no header and with four numeric columns
+(ix,iy,iz,Temp) and with a number of rows equal to the number of
+user-specified grid points (Nx by Ny by Nz).  The ix,iy,iz are node
+indices from 0 to nxnodes-1, etc.  For example, the initial electronic
+temperatures on a 1 by 2 by 3 grid could be specified in a *T\_infile*
+as follows:
+
+
+.. parsed-literal::
+
+   0 0 0 1.0
+   0 0 1 1.0
+   0 0 2 1.0
+   0 1 0 2.0
+   0 1 1 2.0
+   0 1 2 2.0
+
+where the electronic temperatures along the y=0 plane have been set to
+1.0, and the electronic temperatures along the y=1 plane have been set
+to 2.0.  The order of lines in this file is no important.  If all the
+nodal values are not specified, LAMMPS will generate an error.
+
+The temperature output file, *T\_oufile*, is created and written by
+this fix.  Temperatures for both the electronic and atomic subsystems
+at every node and every N timesteps are output.  If N is specified as
+zero, no output is generated, and no output filename is needed.  The
+format of the output is as follows.  One long line is written every
+output timestep.  The timestep itself is given in the first column.
+The next Nx\*Ny\*Nz columns contain the temperatures for the atomic
+subsystem, and the final Nx\*Ny\*Nz columns contain the temperatures for
+the electronic subsystem.  The ordering of the Nx\*Ny\*Nz columns is
+with the z index varying fastest, y the next fastest, and x the
+slowest.
+
+These fixes do not change the coordinates of their atoms; they only
+scales their velocities.  Thus a time integration fix (e.g. :doc:`fix nve <fix_nve>`) should still be used to time integrate the affected
+atoms.  The fixes should not normally be used on atoms that have their
+temperature controlled by another fix - e.g. :doc:`fix nvt <fix_nh>` or
+:doc:`fix langevin <fix_langevin>`.
+
+.. note::
+
+   The current implementations of these fixes create a copy of the
+   electron grid that overlays the entire simulation domain, for each
+   processor.  Values on the grid are summed across all processors.  Thus
+   you should insure that this grid is not too large, else your
+   simulation could incur high memory and communication costs.
+
+
+----------
+
+
+**Additional details for fix ttm/mod**
+
+Fix ttm/mod uses the heat diffusion equation with possible external
+heat sources (e.g. laser heating in ablation simulations):
+
+.. image:: Eqs/fix_ttm_mod.jpg
+   :align: center
+
+where theta is the Heaviside step function, I\_0 is the (absorbed)
+laser pulse intensity for ablation simulations, l\_skin is the depth
+of skin-layer, and all other designations have the same meaning as in
+the former equation. The duration of the pulse is set by the parameter
+*tau* in the *init\_file*.
+
+Fix ttm/mod also allows users to specify the dependencies of C\_e and
+kappa\_e on the electronic temperature. The specific heat is expressed
+as
+
+.. image:: Eqs/fix_ttm_ce.jpg
+   :align: center
+
+where *X* = T\_e/1000, and the thermal conductivity is defined as
+kappa\_e = D\_e\*rho\_e\*C\_e, where D\_e is the thermal diffusion
+coefficient.
+
+Electronic pressure effects are included in the TTM model to account
+for the blast force acting on ions because of electronic pressure
+gradient (see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`).  The total force
+acting on an ion is:
+
+.. image:: Eqs/fix_ttm_blast.jpg
+   :align: center
+
+where F\_langevin is a force from Langevin thermostat simulating
+electron-phonon coupling, and nabla P\_e/n\_ion is the electron blast
+force.
+
+The electronic pressure is taken to be P\_e = B\*rho\_e\*C\_e\*T\_e
+
+The current fix ttm/mod implementation allows TTM simulations with a
+vacuum. The vacuum region is defined as the grid cells with zero
+electronic temperature. The numerical scheme does not allow energy
+exchange with such cells. Since the material can expand to previously
+unoccupied region in some simulations, the vacuum border can be
+allowed to move. It is controlled by the *surface\_movement* parameter
+in the *init\_file*. If it is set to 1, then "vacuum" cells can be
+changed to "electron-filled" cells with the temperature *T\_e_min* if
+atoms move into them (currently only implemented for the case of
+1-dimensional motion of flat surface normal to the X axis). The
+initial borders of vacuum can be set in the *init\_file* via *lsurface*
+and *rsurface* parameters. In this case, electronic pressure gradient
+is calculated as
+
+.. image:: Eqs/fix_ttm_blast1.jpg
+   :align: center
+
+where lambda is the electron mean free path (see :ref:`(Norman) <Norman>`,
+:ref:`(Pisarev) <Pisarev>`)
+
+The fix ttm/mod parameter file *init\_file* has the following syntax/
+Every line with the odd number is considered as a comment and
+ignored. The lines with the even numbers are treated as follows:
+
+
+.. parsed-literal::
+
+   a_0, energy/(temperature\*electron) units
+   a_1, energy/(temperature\^2\*electron) units
+   a_2, energy/(temperature\^3\*electron) units
+   a_3, energy/(temperature\^4\*electron) units
+   a_4, energy/(temperature\^5\*electron) units
+   C_0, energy/(temperature\*electron) units
+   A, 1/temperature units
+   rho_e, electrons/volume units
+   D_e, length\^2/time units
+   gamma_p, mass/time units
+   gamma_s, mass/time units
+   v_0, length/time units
+   I_0, energy/(time\*length\^2) units
+   lsurface, electron grid units (positive integer)
+   rsurface, electron grid units (positive integer)
+   l_skin, length units
+   tau, time units
+   B, dimensionless
+   lambda, length units
+   n_ion, ions/volume units
+   surface_movement: 0 to disable tracking of surface motion, 1 to enable
+   T_e_min, temperature units
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+These fixes write the state of the electronic subsystem and the energy
+exchange between the subsystems to :doc:`binary restart files <restart>`.  See the :doc:`read\_restart <read_restart>` command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+Because the state of the random number generator is not saved in the
+restart files, this means you cannot do "exact" restarts with this
+fix, where the simulation continues on the same as if no restart had
+taken place.  However, in a statistical sense, a restarted simulation
+should produce the same behavior.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to these
+fixes.
+
+Both fixes compute 2 output quantities stored in a vector of length 2,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The first quantity is the total energy of the electronic
+subsystem. The second quantity is the energy transferred from the
+electronic to the atomic subsystem on that timestep. Note that the
+velocity verlet integrator applies the fix ttm forces to the atomic
+subsystem as two half-step velocity updates: one on the current
+timestep and one on the subsequent timestep.  Consequently, the change
+in the atomic subsystem energy is lagged by half a timestep relative
+to the change in the electronic subsystem energy. As a result of this,
+users may notice slight fluctuations in the sum of the atomic and
+electronic subsystem energies reported at the end of the timestep.
+
+The vector values calculated are "extensive".
+
+No parameter of the fixes can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.  The fixes are not invoked during
+:doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+Fix *ttm* is part of the MISC package. It is only enabled if LAMMPS
+was built with that package.  Fix *ttm/mod* is part of the USER-MISC
+package. It is only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+These fixes can only be used for 3d simulations and orthogonal
+simulation boxes.  You must also use periodic
+:doc:`boundary <boundary>` conditions.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix langevin <fix_langevin>`, :doc:`fix dt/reset <fix_dt_reset>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Duffy:
+
+
+
+**(Duffy)** D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19,
+016207-016218 (2007).
+
+.. _Rutherford:
+
+
+
+**(Rutherford)** A M Rutherford and D M Duffy, J. Phys.:
+Condens. Matter, 19, 496201-496210 (2007).
+
+.. _Chen:
+
+
+
+**(Chen)** J Chen, D Tzou and J Beraun, Int. J. Heat
+Mass Transfer, 49, 307-316 (2006).
+
+.. _Norman:
+
+
+
+**(Norman)** G E Norman, S V Starikov, V V Stegailov et al., Contrib.
+Plasma Phys., 53, 129-139 (2013).
+
+.. _Pisarev:
+
+
+
+**(Pisarev)** V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26,
+475401 (2014).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst
new file mode 100644
index 0000000000..1dc6c2befd
--- /dev/null
+++ b/doc/src/fix_tune_kspace.rst
@@ -0,0 +1,109 @@
+.. index:: fix tune/kspace
+
+fix tune/kspace command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID tune/kspace N
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* tune/kspace = style name of this fix command
+* N = invoke this fix every N steps
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 2 all tune/kspace 100
+
+Description
+"""""""""""
+
+This fix tests each kspace style (Ewald, PPPM, and MSM), and
+automatically selects the fastest style to use for the remainder
+of the run. If the fastest style is Ewald or PPPM, the fix also
+adjusts the Coulombic cutoff towards optimal speed. Future versions
+of this fix will automatically select other kspace parameters
+to use for maximum simulation speed. The kspace parameters may
+include the style, cutoff, grid points in each direction, order,
+Ewald parameter, MSM parallelization cut-point, MPI tasks to use, etc.
+
+The rationale for this fix is to provide the user with
+as-fast-as-possible simulations that include long-range electrostatics
+(kspace) while meeting the user-prescribed accuracy requirement. A
+simple heuristic could never capture the optimal combination of
+parameters for every possible run-time scenario. But by performing
+short tests of various kspace parameter sets, this fix allows
+parameters to be tailored specifically to the user's machine, MPI
+ranks, use of threading or accelerators, the simulated system, and the
+simulation details. In addition, it is possible that parameters could
+be evolved with the simulation on-the-fly, which is useful for systems
+that are dynamically evolving (e.g. changes in box size/shape or
+number of particles).
+
+When this fix is invoked, LAMMPS will perform short timed tests of
+various parameter sets to determine the optimal parameters. Tests are
+performed on-the-fly, with a new test initialized every N steps. N should
+be chosen large enough so that adequate CPU time lapses between tests,
+thereby providing statistically significant timings. But N should not be
+chosen to be so large that an unfortunate parameter set test takes an
+inordinate amount of wall time to complete. An N of 100 for most problems
+seems reasonable. Once an optimal parameter set is found, that set is
+used for the remainder of the run.
+
+This fix uses heuristics to guide it's selection of parameter sets to test,
+but the actual timed results will be used to decide which set to use in the
+simulation.
+
+It is not necessary to discard trajectories produced using sub-optimal
+parameter sets, or a mix of various parameter sets, since the user-prescribed
+accuracy will have been maintained throughout. However, some users may prefer
+to use this fix only to discover the optimal parameter set for a given setup
+that can then be used on subsequent production runs.
+
+This fix starts with kspace parameters that are set by the user with the
+:doc:`kspace\_style <kspace_style>` and :doc:`kspace\_modify <kspace_modify>`
+commands. The prescribed accuracy will be maintained by this fix throughout
+the simulation.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the KSPACE package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Do not set "neigh\_modify once yes" or else this fix will never be
+called.  Reneighboring is required.
+
+This fix is not compatible with a hybrid pair style, long-range dispersion,
+TIP4P water support, or long-range point dipole support.
+
+Related commands
+""""""""""""""""
+
+:doc:`kspace\_style <kspace_style>`, :doc:`boundary <boundary>`
+:doc:`kspace\_modify <kspace_modify>`, :doc:`pair\_style lj/cut/coul/long <pair_lj>`, :doc:`pair\_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair\_style lj/long <pair_lj_long>`, :doc:`pair\_style lj/long/coul/long <pair_lj_long>`,
+:doc:`pair\_style buck/coul/long <pair_buck>`
+
+Default
+"""""""
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst
new file mode 100644
index 0000000000..3d7fb85274
--- /dev/null
+++ b/doc/src/fix_vector.rst
@@ -0,0 +1,181 @@
+.. index:: fix vector
+
+fix vector command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID vector Nevery value1 value2 ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* vector = style name of this fix command
+* Nevery = use input values every this many timesteps
+* one or more input values can be listed
+* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
+  
+  .. parsed-literal::
+  
+       c_ID = global scalar calculated by a compute with ID
+       c_ID[I] = Ith component of global vector calculated by a compute with ID
+       f_ID = global scalar calculated by a fix with ID
+       f_ID[I] = Ith component of global vector calculated by a fix with ID
+       v_name = value calculated by an equal-style variable with name
+       v_name[I] = Ith component of vector-style variable with name
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all vector 100 c_myTemp
+   fix 1 all vector 5 c_myTemp v_integral
+
+Description
+"""""""""""
+
+Use one or more global values as inputs every few timesteps, and
+simply store them.  For a single specified value, the values are
+stored as a global vector of growing length.  For multiple specified
+values, they are stored as rows in a global array, whose number of
+rows is growing.  The resulting vector or array can be used by other
+:doc:`output commands <Howto_output>`.
+
+One way to to use this command is to accumulate a vector that is
+time-integrated using the :doc:`variable trap() <variable>` function.
+For example the velocity auto-correlation function (VACF) can be
+time-integrated, to yield a diffusion coefficient, as follows:
+
+
+.. parsed-literal::
+
+   compute         2 all vacf
+   fix             5 all vector 1 c_2[4]
+   variable        diff equal dt\*trap(f_5)
+   thermo_style    custom step v_diff
+
+The group specified with this command is ignored.  However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+
+Each listed value can be the result of a :doc:`compute <compute>` or
+:doc:`fix <fix>` or the evaluation of an equal-style or vector-style
+:doc:`variable <variable>`.  In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity.  And
+the global quantity must be a scalar, not a vector or array.
+
+:doc:`Computes <compute>` that produce global quantities are those which
+do not have the word *atom* in their style name.  Only a few
+:doc:`fixes <fix>` produce global quantities.  See the doc pages for
+individual fixes for info on which ones produce such values.
+:doc:`Variables <variable>` of style *equal* or *vector* are the only
+ones that can be used with this fix.  Variables of style *atom* cannot
+be used, since they produce per-atom values.
+
+The *Nevery* argument specifies on what timesteps the input values
+will be used in order to be stored.  Only timesteps that are a
+multiple of *Nevery*\ , including timestep 0, will contribute values.
+
+Note that if you perform multiple runs, using the "pre no" option of
+the :doc:`run <run>` command to avoid initialization on subsequent runs,
+then you need to use the *stop* keyword with the first :doc:`run <run>`
+command with a timestep value that encompasses all the runs.  This is
+so that the vector or array stored by this fix can be allocated to a
+sufficient size.
+
+
+----------
+
+
+If a value begins with "c\_", a compute ID must follow which has been
+previously defined in the input script.  If no bracketed term is
+appended, the global scalar calculated by the compute is used.  If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the compute is used.
+
+Note that there is a :doc:`compute reduce <compute_reduce>` command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix vector.  Or it can be a compute defined
+not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
+or :doc:`fix temp/rescale <fix_temp_rescale>`.  See the doc pages for
+these commands which give the IDs of these computes.  Users can also
+write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "f\_", a fix ID must follow which has been
+previously defined in the input script.  If no bracketed term is
+appended, the global scalar calculated by the fix is used.  If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the fix is used.
+
+Note that some fixes only produce their values on certain timesteps,
+which must be compatible with *Nevery*\ , else an error will result.
+Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
+
+If a value begins with "v\_", a variable name must follow which has
+been previously defined in the input script.  An equal-style or
+vector-style variable can be referenced; the latter requires a
+bracketed term to specify the Ith element of the vector calculated by
+the variable.  See the :doc:`variable <variable>` command for details.
+Note that variables of style *equal* and *vector* define a formula
+which can reference individual atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+they are evaluated, so this is a very general means of specifying
+quantities to be stored by fix vector.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix produces a global vector or global array which can be
+accessed by various :doc:`output commands <Howto_output>`.  The values
+can only be accessed on timesteps that are multiples of *Nevery*\ .
+
+A vector is produced if only a single input value is specified.
+An array is produced if multiple input values are specified.
+The length of the vector or the number of rows in the array grows
+by 1 every *Nevery* timesteps.
+
+If the fix produces a vector, then the entire vector will be either
+"intensive" or "extensive", depending on whether the values stored in
+the vector are "intensive" or "extensive".  If the fix produces an
+array, then all elements in the array must be the same, either
+"intensive" or "extensive".  If a compute or fix provides the value
+stored, then the compute or fix determines whether the value is
+intensive or extensive; see the doc page for that compute or fix for
+further info.  Values produced by a variable are treated as intensive.
+
+This fix can allocate storage for stored values accumulated over
+multiple runs, using the *start* and *stop* keywords of the
+:doc:`run <run>` command.  See the :doc:`run <run>` command for details of
+how to do this.  If using the :doc:`run pre no <run>` command option,
+this is required to allow the fix to allocate sufficient storage for
+stored values.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`, :doc:`variable <variable>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst
new file mode 100644
index 0000000000..637551b1e4
--- /dev/null
+++ b/doc/src/fix_viscosity.rst
@@ -0,0 +1,191 @@
+.. index:: fix viscosity
+
+fix viscosity command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID viscosity N vdim pdim Nbin keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* viscosity = style name of this fix command
+* N = perform momentum exchange every N steps
+* vdim = *x* or *y* or *z* = which momentum component to exchange
+* pdim = *x* or *y* or *z* = direction of momentum transfer
+* Nbin = # of layers in pdim direction (must be even number)
+* zero or more keyword/value pairs may be appended
+* keyword = *swap* or *target*
+  
+  .. parsed-literal::
+  
+       *swap* value = Nswap = number of swaps to perform every N steps
+       *vtarget* value = V or INF = target velocity of swap partners (velocity units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all viscosity 100 x z 20
+   fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5
+
+Description
+"""""""""""
+
+Use the Muller-Plathe algorithm described in :ref:`this paper <Muller-Plathe2>` to exchange momenta between two particles in
+different regions of the simulation box every N steps.  This induces a
+shear velocity profile in the system.  As described below this enables
+a viscosity of the fluid to be calculated.  This algorithm is
+sometimes called a reverse non-equilibrium MD (reverse NEMD) approach
+to computing viscosity.  This is because the usual NEMD approach is to
+impose a shear velocity profile on the system and measure the response
+via an off-diagonal component of the stress tensor, which is
+proportional to the momentum flux.  In the Muller-Plathe method, the
+momentum flux is imposed, and the shear velocity profile is the
+system's response.
+
+The simulation box is divided into *Nbin* layers in the *pdim*
+direction, where the layer 1 is at the low end of that dimension and
+the layer *Nbin* is at the high end.  Every N steps, Nswap pairs of
+atoms are chosen in the following manner.  Only atoms in the fix group
+are considered.  Nswap atoms in layer 1 with positive velocity
+components in the *vdim* direction closest to the target value *V* are
+selected.  Similarly, Nswap atoms in the "middle" layer (see below) with
+negative velocity components in the *vdim* direction closest to the
+negative of the target value *V* are selected.  The two sets of Nswap
+atoms are paired up and their *vdim* momenta components are swapped
+within each pair.  This resets their velocities, typically in opposite
+directions.  Over time, this induces a shear velocity profile in the
+system which can be measured using commands such as the following,
+which writes the profile to the file tmp.profile:
+
+
+.. parsed-literal::
+
+   compute layers all chunk/atom bin/1d z lower 0.05 units reduced
+   fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile
+
+Note that by default, Nswap = 1 and vtarget = INF, though this can be
+changed by the optional *swap* and *vtarget* keywords.  When vtarget =
+INF, one or more atoms with the most positive and negative velocity
+components are selected.  Setting these parameters appropriately, in
+conjunction with the swap rate N, allows the momentum flux rate to be
+adjusted across a wide range of values, and the momenta to be
+exchanged in large chunks or more smoothly.
+
+The "middle" layer for momenta swapping is defined as the *Nbin*\ /2 + 1
+layer.  Thus if *Nbin* = 20, the two swapping layers are 1 and 11.
+This should lead to a symmetric velocity profile since the two layers
+are separated by the same distance in both directions in a periodic
+sense.  This is why *Nbin* is restricted to being an even number.
+
+As described below, the total momentum transferred by these velocity
+swaps is computed by the fix and can be output.  Dividing this
+quantity by time and the cross-sectional area of the simulation box
+yields a momentum flux.  The ratio of momentum flux to the slope of
+the shear velocity profile is proportional to the viscosity of the
+fluid, in appropriate units.  See the :ref:`Muller-Plathe paper <Muller-Plathe2>` for details.
+
+.. note::
+
+   If your system is periodic in the direction of the momentum
+   flux, then the flux is going in 2 directions.  This means the
+   effective momentum flux in one direction is reduced by a factor of 2.
+   You will see this in the equations for viscosity in the Muller-Plathe
+   paper.  LAMMPS is simply tallying momentum which does not account for
+   whether or not your system is periodic; you must use the value
+   appropriately to yield a viscosity for your system.
+
+.. note::
+
+   After equilibration, if the velocity profile you observe is not
+   linear, then you are likely swapping momentum too frequently and are
+   not in a regime of linear response.  In this case you cannot
+   accurately infer a viscosity and should try increasing the Nevery
+   parameter.
+
+An alternative method for calculating a viscosity is to run a NEMD
+simulation, as described on the :doc:`Howto nemd <Howto_nemd>` doc page.
+NEMD simulations deform the simulation box via the :doc:`fix deform <fix_deform>` command.  Thus they cannot be run on a charged
+system using a :doc:`PPPM solver <kspace_style>` since PPPM does not
+currently support non-orthogonal boxes.  Using fix viscosity keeps the
+box orthogonal; thus it does not suffer from this limitation.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+momentum transferred between the bottom and middle of the simulation
+box (in the *pdim* direction) is stored as a scalar quantity by this
+fix.  This quantity is zeroed when the fix is defined and accumulates
+thereafter, once every N steps.  The units of the quantity are
+momentum = mass\*velocity.  The scalar value calculated by this fix is
+"intensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Swaps conserve both momentum and kinetic energy, even if the masses of
+the swapped atoms are not equal.  Thus you should not need to
+thermostat the system.  If you do use a thermostat, you may want to
+apply it only to the non-swapped dimensions (other than *vdim*\ ).
+
+LAMMPS does not check, but you should not use this fix to swap
+velocities of atoms that are in constrained molecules, e.g. via :doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`.  This is because
+application of the constraints will alter the amount of transferred
+momentum.  You should, however, be able to use flexible molecules.
+See the :ref:`Maginn paper <Maginn>` for an example of using this algorithm
+in a computation of alcohol molecule properties.
+
+When running a simulation with large, massive particles or molecules
+in a background solvent, you may want to only exchange momenta between
+solvent particles.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix thermal/conductivity <fix_thermal_conductivity>`
+
+Default
+"""""""
+
+The option defaults are swap = 1 and vtarget = INF.
+
+
+----------
+
+
+.. _Muller-Plathe2:
+
+
+
+**(Muller-Plathe)** Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
+
+.. _Maginn:
+
+
+
+**(Maginn)** Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
+260, 218-231 (2007).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst
new file mode 100644
index 0000000000..247600db93
--- /dev/null
+++ b/doc/src/fix_viscous.rst
@@ -0,0 +1,122 @@
+.. index:: fix viscous
+
+fix viscous command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID viscous gamma keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* viscous = style name of this fix command
+* gamma = damping coefficient (force/velocity units)
+* zero or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *scale*
+       *scale* values = type ratio
+         type = atom type (1-N)
+         ratio = factor to scale the damping coefficient by
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 flow viscous 0.1
+   fix 1 damp viscous 0.5 scale 3 2.5
+
+Description
+"""""""""""
+
+Add a viscous damping force to atoms in the group that is proportional
+to the velocity of the atom.  The added force can be thought of as a
+frictional interaction with implicit solvent, i.e. the no-slip Stokes
+drag on a spherical particle.  In granular simulations this can be
+useful for draining the kinetic energy from the system in a controlled
+fashion.  If used without additional thermostatting (to add kinetic
+energy to the system), it has the effect of slowly (or rapidly)
+freezing the system; hence it can also be used as a simple energy
+minimization technique.
+
+The damping force F is given by F = - gamma \* velocity.  The larger
+the coefficient, the faster the kinetic energy is reduced.  If the
+optional keyword *scale* is used, gamma can scaled up or down by the
+specified factor for atoms of that type.  It can be used multiple
+times to adjust gamma for several atom types.
+
+.. note::
+
+   You should specify gamma in force/velocity units.  This is not
+   the same as mass/time units, at least for some of the LAMMPS
+   :doc:`units <units>` options like "real" or "metal" that are not
+   self-consistent.
+
+In a Brownian dynamics context, gamma = Kb T / D, where Kb =
+Boltzmann's constant, T = temperature, and D = particle diffusion
+coefficient.  D can be written as Kb T / (3 pi eta d), where eta =
+dynamic viscosity of the frictional fluid and d = diameter of
+particle.  This means gamma = 3 pi eta d, and thus is proportional to
+the viscosity of the fluid and the particle diameter.
+
+In the current implementation, rather than have the user specify a
+viscosity, gamma is specified directly in force/velocity units.  If
+needed, gamma can be adjusted for atoms of different sizes
+(i.e. sigma) by using the *scale* keyword.
+
+Note that Brownian dynamics models also typically include a randomized
+force term to thermostat the system at a chosen temperature.  The :doc:`fix langevin <fix_langevin>` command does this.  It has the same
+viscous damping term as fix viscous and adds a random force to each
+atom.  The random force term is proportional to the sqrt of the chosen
+thermostatting temperature.  Thus if you use fix langevin with a
+target T = 0, its random force term is zero, and you are essentially
+performing the same operation as fix viscous.  Also note that the
+gamma of fix viscous is related to the damping parameter of :doc:`fix langevin <fix_langevin>`, however the former is specified in units
+of force/velocity and the latter in units of time, so that it can more
+easily be used as a thermostat.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is modifying forces. Default is the outermost level.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.  This fix should only
+be used with damped dynamics minimizers that allow for
+non-conservative forces.  See the :doc:`min\_style <min_style>` command
+for details.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix langevin <fix_langevin>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst
new file mode 100644
index 0000000000..b31ee4a663
--- /dev/null
+++ b/doc/src/fix_wall.rst
@@ -0,0 +1,415 @@
+.. index:: fix wall/lj93
+
+fix wall/lj93 command
+=====================
+
+fix wall/lj93/kk command
+========================
+
+fix wall/lj126 command
+======================
+
+fix wall/lj1043 command
+=======================
+
+fix wall/colloid command
+========================
+
+fix wall/harmonic command
+=========================
+
+fix wall/morse command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style face args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = *wall/lj93* or *wall/lj126* or *wall/lj1043* or *wall/colloid* or *wall/harmonic* or *wall/morse*
+* one or more face/arg pairs may be appended
+* face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi*
+* args for styles *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic*
+  
+  .. parsed-literal::
+  
+         args = coord epsilon sigma cutoff
+         coord = position of wall = EDGE or constant or variable
+           EDGE = current lo or hi edge of simulation box
+           constant = number like 0.0 or -30.0 (distance units)
+           variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
+         epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units)
+           epsilon can be a variable (see below)
+         sigma = size factor for wall-particle interaction (distance units)
+           sigma can be a variable (see below)
+         cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
+
+* args for style *morse*
+  
+  .. parsed-literal::
+  
+         args = coord D_0 alpha r_0 cutoff
+         coord = position of wall = EDGE or constant or variable
+           EDGE = current lo or hi edge of simulation box
+           constant = number like 0.0 or -30.0 (distance units)
+           variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
+         D_0 = depth of the potential (energy units)
+           D_0 can be a variable (see below)
+         alpha = width factor for wall-particle interaction (1/distance units)
+           alpha can be a variable (see below)
+         r_0 = distance of the potential minimum from the face of region (distance units)
+           r_0 can be a variable (see below)
+         cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
+
+* zero or more keyword/value pairs may be appended
+* keyword = *units* or *fld*
+  
+  .. parsed-literal::
+  
+       *units* value = *lattice* or *box*
+         *lattice* = the wall position is defined in lattice units
+         *box* = the wall position is defined in simulation box units
+       *fld* value = *yes* or *no*
+         *yes* = invoke the wall constraint to be compatible with implicit FLD
+         *no* = invoke the wall constraint in the normal way
+       *pbc* value = *yes* or *no*
+         *yes* = allow periodic boundary in a wall dimension
+         *no* = require non-perioidic boundaries in any wall dimension
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
+   fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
+   fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box
+   fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
+   fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
+
+Description
+"""""""""""
+
+Bound the simulation domain on one or more of its faces with a flat
+wall that interacts with the atoms in the group by generating a force
+on the atom in a direction perpendicular to the wall.  The energy of
+wall-particle interactions depends on the style.
+
+For style *wall/lj93*\ , the energy E is given by the 9/3 potential:
+
+.. image:: Eqs/fix_wall_lj93.jpg
+   :align: center
+
+For style *wall/lj126*\ , the energy E is given by the 12/6 potential:
+
+.. image:: Eqs/pair_lj.jpg
+   :align: center
+
+For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential:
+
+.. image:: Eqs/fix_wall_lj1043.jpg
+   :align: center
+
+For style *wall/colloid*\ , the energy E is given by an integrated form
+of the :doc:`pair\_style colloid <pair_colloid>` potential:
+
+.. image:: Eqs/fix_wall_colloid.jpg
+   :align: center
+
+For style *wall/harmonic*\ , the energy E is given by a harmonic spring
+potential:
+
+.. image:: Eqs/fix_wall_harmonic.jpg
+   :align: center
+
+For style *wall/morse*\ , the energy E is given by a Morse potential:
+
+.. image:: Eqs/pair_morse.jpg
+   :align: center
+
+In all cases, *r* is the distance from the particle to the wall at
+position *coord*\ , and Rc is the *cutoff* distance at which the
+particle and wall no longer interact.  The energy of the wall
+potential is shifted so that the wall-particle interaction energy is
+0.0 at the cutoff distance.
+
+Up to 6 walls or faces can be specified in a single command: *xlo*\ ,
+*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ .  A *lo* face interacts with
+particles near the lower side of the simulation box in that dimension.
+A *hi* face interacts with particles near the upper side of the
+simulation box in that dimension.
+
+The position of each wall can be specified in one of 3 ways: as the
+EDGE of the simulation box, as a constant value, or as a variable.  If
+EDGE is used, then the corresponding boundary of the current
+simulation box is used.  If a numeric constant is specified then the
+wall is placed at that position in the appropriate dimension (x, y, or
+z).  In both the EDGE and constant cases, the wall will never move.
+If the wall position is a variable, it should be specified as v\_name,
+where name is an :doc:`equal-style variable <variable>` name.  In this
+case the variable is evaluated each timestep and the result becomes
+the current position of the reflecting wall.  Equal-style variables
+can specify formulas with various mathematical functions, and include
+:doc:`thermo\_style <thermo_style>` command keywords for the simulation
+box parameters and timestep and elapsed time.  Thus it is easy to
+specify a time-dependent wall position.  See examples below.
+
+For the *wall/lj93* and *wall/lj126* and *wall/lj1043* styles,
+*epsilon* and *sigma* are the usual Lennard-Jones parameters, which
+determine the strength and size of the particle as it interacts with
+the wall.  Epsilon has energy units.  Note that this *epsilon* and
+*sigma* may be different than any *epsilon* or *sigma* values defined
+for a pair style that computes particle-particle interactions.
+
+The *wall/lj93* interaction is derived by integrating over a 3d
+half-lattice of Lennard-Jones 12/6 particles.  The *wall/lj126*
+interaction is effectively a harder, more repulsive wall interaction.
+The *wall/lj1043* interaction is yet a different form of wall
+interaction, described in Magda et al in :ref:`(Magda) <Magda>`.
+
+For the *wall/colloid* style, *R* is the radius of the colloid
+particle, *D* is the distance from the surface of the colloid particle
+to the wall (r-R), and *sigma* is the size of a constituent LJ
+particle inside the colloid particle and wall.  Note that the cutoff
+distance Rc in this case is the distance from the colloid particle
+center to the wall.  The prefactor *epsilon* can be thought of as an
+effective Hamaker constant with energy units for the strength of the
+colloid-wall interaction.  More specifically, the *epsilon* pre-factor
+= 4 \* pi\^2 \* rho\_wall \* rho\_colloid \* epsilon \* sigma\^6, where epsilon
+and sigma are the LJ parameters for the constituent LJ
+particles. Rho\_wall and rho\_colloid are the number density of the
+constituent particles, in the wall and colloid respectively, in units
+of 1/volume.
+
+The *wall/colloid* interaction is derived by integrating over
+constituent LJ particles of size *sigma* within the colloid particle
+and a 3d half-lattice of Lennard-Jones 12/6 particles of size *sigma*
+in the wall.  As mentioned in the preceding paragraph, the density of
+particles in the wall and colloid can be different, as specified by
+the *epsilon* pre-factor.
+
+For the *wall/harmonic* style, *epsilon* is effectively the spring
+constant K, and has units (energy/distance\^2).  The input parameter
+*sigma* is ignored.  The minimum energy position of the harmonic
+spring is at the *cutoff*\ .  This is a repulsive-only spring since the
+interaction is truncated at the *cutoff*
+
+For the *wall/morse* style, the three parameters are in this order:
+*D\_0* the depth of the potential, *alpha* the width parameter, and
+*r\_0* the location of the minimum.  *D\_0* has energy units, *alpha*
+inverse distance units, and *r\_0* distance units.
+
+For any wall, the *epsilon* and/or *sigma* and/or *alpha* parameter can
+be specified
+as an :doc:`equal-style variable <variable>`, in which case it should be
+specified as v\_name, where name is the variable name.  As with a
+variable wall position, the variable is evaluated each timestep and
+the result becomes the current epsilon or sigma of the wall.
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent wall interaction.
+
+.. note::
+
+   For all of the styles, you must insure that r is always > 0 for
+   all particles in the group, or LAMMPS will generate an error.  This
+   means you cannot start your simulation with particles at the wall
+   position *coord* (r = 0) or with particles on the wrong side of the
+   wall (r < 0).  For the *wall/lj93* and *wall/lj126* styles, the energy
+   of the wall/particle interaction (and hence the force on the particle)
+   blows up as r -> 0.  The *wall/colloid* style is even more
+   restrictive, since the energy blows up as D = r-R -> 0.  This means
+   the finite-size particles of radius R must be a distance larger than R
+   from the wall position *coord*\ .  The *harmonic* style is a softer
+   potential and does not blow up as r -> 0, but you must use a large
+   enough *epsilon* that particles always reamin on the correct side of
+   the wall (r > 0).
+
+The *units* keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant or
+variable is used.  It is not relevant when EDGE is used to specify a
+face position.  In the variable case, the variable is assumed to
+produce a value compatible with the *units* setting you specify.
+
+A *box* value selects standard distance units as defined by the
+:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
+A *lattice* value means the distance units are in lattice spacings.
+The :doc:`lattice <lattice>` command must have been previously used to
+define the lattice spacings.
+
+The *fld* keyword can be used with a *yes* setting to invoke the wall
+constraint before pairwise interactions are computed.  This allows an
+implicit FLD model using :doc:`pair\_style lubricateU <pair_lubricateU>`
+to include the wall force in its calculations.  If the setting is
+*no*\ , wall forces are imposed after pairwise interactions, in the
+usual manner.
+
+The *pbc* keyword can be used with a *yes* setting to allow walls to
+be specified in a periodic dimension.  See the
+:doc:`boundary <boundary>` command for options on simulation box
+boundaries.  The default for *pbc* is *no*\ , which means the system
+must be non-periodic when using a wall.  But you may wish to use a
+periodic box.  E.g. to allow some particles to interact with the wall
+via the fix group-ID, and others to pass through it and wrap around a
+periodic box.  In this case you should insure that the wall if
+sufficiently far enough away from the box boundary.  If you do not,
+then particles may interact with both the wall and with periodic
+images on the other side of the box, which is probably not what you
+want.
+
+
+----------
+
+
+Here are examples of variable definitions that move the wall position
+in a time-dependent fashion using equal-style
+:doc:`variables <variable>`.  The wall interaction parameters (epsilon,
+sigma) could be varied with additional variable definitions.
+
+
+.. parsed-literal::
+
+   variable ramp equal ramp(0,10)
+   fix 1 all wall xlo v_ramp 1.0 1.0 2.5
+
+   variable linear equal vdisplace(0,20)
+   fix 1 all wall xlo v_linear 1.0 1.0 2.5
+
+   variable wiggle equal swiggle(0.0,5.0,3.0)
+   fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
+
+   variable wiggle equal cwiggle(0.0,5.0,3.0)
+   fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
+
+The ramp(lo,hi) function adjusts the wall position linearly from lo to
+hi over the course of a run.  The vdisplace(c0,velocity) function does
+something similar using the equation position = c0 + velocity\*delta,
+where delta is the elapsed time.
+
+The swiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, where omega = 2 PI
+/ period:
+
+
+.. parsed-literal::
+
+   position = c0 + A sin(omega\*delta)
+
+The cwiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, which will have an
+initial wall velocity of 0.0, and thus may impose a gentler
+perturbation on the particles:
+
+
+.. parsed-literal::
+
+   position = c0 + A (1 - cos(omega\*delta))
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy of interaction between atoms and each wall to
+the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to the interaction between
+atoms and each wall to the system's virial as part of :doc:`thermodynamic output <thermo_style>`. The default is *virial no*
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global scalar energy and a global vector of
+forces, which can be accessed by various :doc:`output commands <Howto_output>`.  Note that the scalar energy is the sum
+of interactions with all defined walls.  If you want the energy on a
+per-wall basis, you need to use multiple fix wall commands.  The
+length of the vector is equal to the number of walls defined by the
+fix.  Each vector value is the normal force on a specific wall.  Note
+that an outward force on a wall will be a negative value for *lo*
+walls and a positive value for *hi* walls.  The scalar and vector
+values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the atom/wall interaction energy to be included in
+   the total potential energy of the system (the quantity being
+   minimized), you MUST enable the :doc:`fix\_modify <fix_modify>` *energy*
+   option for this fix.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall/reflect <fix_wall_reflect>`,
+:doc:`fix wall/gran <fix_wall_gran>`,
+:doc:`fix wall/region <fix_wall_region>`
+
+Default
+"""""""
+
+The option defaults units = lattice, fld = no, and pbc = no.
+
+
+----------
+
+
+.. _Magda:
+
+
+
+**(Magda)** Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985);
+erratum in JCP 84, 2901 (1986).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst
new file mode 100644
index 0000000000..840338db5c
--- /dev/null
+++ b/doc/src/fix_wall_body_polygon.rst
@@ -0,0 +1,119 @@
+.. index:: fix wall/body/polygon
+
+fix wall/body/polygon command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID wall/body/polygon k_n c_n c_t wallstyle args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/body/polygon = style name of this fix command
+* k\_n = normal repulsion strength (force/distance or pressure units)
+* c\_n = normal damping coefficient (force/distance or pressure units)
+* c\_t = tangential damping coefficient (force/distance or pressure units)
+* wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder*
+* args = list of arguments for a particular style
+  
+  .. parsed-literal::
+  
+       *xplane* or *yplane* args = lo hi
+         lo,hi = position of lower and upper plane (distance units), either can be NULL)
+       *zcylinder* args = radius
+         radius = cylinder radius (distance units)
+
+* zero or more keyword/value pairs may be appended to args
+* keyword = *wiggle*
+  
+  .. parsed-literal::
+  
+       *wiggle* values = dim amplitude period
+         dim = *x* or *y* or *z*
+         amplitude = size of oscillation (distance units)
+         period = time of oscillation (time units)
+
+
+
+Examples
+""""""""
+
+fix 1 all wall/body/polygon 1000.0 20.0 5.0 xplane -10.0 10.0
+
+Description
+"""""""""""
+
+This fix is for use with 2d models of body particles of style
+*rounded/polygon*\ .  It bounds the simulation domain with wall(s).  All
+particles in the group interact with the wall when they are close
+enough to touch it.  The nature of the interaction between the wall
+and the polygon particles is the same as that between the polygon
+particles themselves, which is similar to a Hookean potential.  See
+the :doc:`Howto body <Howto_body>` doc page for more details on using
+body particles.
+
+The parameters *k\_n*, *c\_n*, *c\_t* have the same meaning and units as
+those specified with the :doc:`pair\_style body/rounded/polygon <pair_body_rounded_polygon>` command.
+
+The *wallstyle* can be planar or cylindrical.  The 2 planar options
+specify a pair of walls in a dimension.  Wall positions are given by
+*lo* and *hi*\ .  Either of the values can be specified as NULL if a
+single wall is desired.  For a *zcylinder* wallstyle, the cylinder's
+axis is at x = y = 0.0, and the radius of the cylinder is specified.
+
+Optionally, the wall can be moving, if the *wiggle* keyword is
+appended.
+
+For the *wiggle* keyword, the wall oscillates sinusoidally, similar to
+the oscillations of particles which can be specified by the :doc:`fix move <fix_move>` command.  This is useful in packing simulations of
+particles.  The arguments to the *wiggle* keyword specify a dimension
+for the motion, as well as it's *amplitude* and *period*\ .  Note that
+if the dimension is in the plane of the wall, this is effectively a
+shearing motion.  If the dimension is perpendicular to the wall, it is
+more of a shaking motion.  A *zcylinder* wall can only be wiggled in
+the z dimension.
+
+Each timestep, the position of a wiggled wall in the appropriate *dim*
+is set according to this equation:
+
+
+.. parsed-literal::
+
+   position = coord + A - A cos (omega \* delta)
+
+where *coord* is the specified initial position of the wall, *A* is
+the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time
+elapsed since the fix was specified.  The velocity of the wall is set
+to the derivative of this expression.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the BODY package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Any dimension (xy) that has a wall must be non-periodic.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style body <atom_style>`, :doc:`pair\_style body/rounded/polygon <pair_body_rounded_polygon>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst
new file mode 100644
index 0000000000..6c3e3f5e6d
--- /dev/null
+++ b/doc/src/fix_wall_body_polyhedron.rst
@@ -0,0 +1,118 @@
+.. index:: fix wall/body/polyhedron
+
+fix wall/body/polyhedron command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID wall/body/polyhedron k_n c_n c_t wallstyle args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/body/polyhedron = style name of this fix command
+* k\_n = normal repulsion strength (force/distance units or pressure units - see discussion below)
+* c\_n = normal damping coefficient (force/distance units or pressure units - see discussion below)
+* c\_t = tangential damping coefficient (force/distance units or pressure units - see discussion below)
+* wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder*
+* args = list of arguments for a particular style
+  
+  .. parsed-literal::
+  
+       *xplane* or *yplane* args = lo hi
+         lo,hi = position of lower and upper plane (distance units), either can be NULL)
+       *zcylinder* args = radius
+         radius = cylinder radius (distance units)
+
+* zero or more keyword/value pairs may be appended to args
+* keyword = *wiggle*
+  
+  .. parsed-literal::
+  
+       *wiggle* values = dim amplitude period
+         dim = *x* or *y* or *z*
+         amplitude = size of oscillation (distance units)
+         period = time of oscillation (time units)
+
+
+
+Examples
+""""""""
+
+fix 1 all wall/body/polyhedron 1000.0 20.0 5.0 xplane -10.0 10.0
+
+Description
+"""""""""""
+
+This fix is for use with 3d models of body particles of style
+*rounded/polyhedron*\ .  It bounds the simulation domain with wall(s).
+All particles in the group interact with the wall when they are close
+enough to touch it.  The nature of the interaction between the wall
+and the polygon particles is the same as that between the polygon
+particles themselves, which is similar to a Hookean potential.  See
+the :doc:`Howto body <Howto_body>` doc page for more details on using
+body particles.
+
+The parameters *k\_n*, *c\_n*, *c\_t* have the same meaning and units as
+those specified with the :doc:`pair\_style body/rounded/polyhedron <pair_body_rounded_polyhedron>` command.
+
+The *wallstyle* can be planar or cylindrical.  The 3 planar options
+specify a pair of walls in a dimension.  Wall positions are given by
+*lo* and *hi*\ .  Either of the values can be specified as NULL if a
+single wall is desired.  For a *zcylinder* wallstyle, the cylinder's
+axis is at x = y = 0.0, and the radius of the cylinder is specified.
+
+Optionally, the wall can be moving, if the *wiggle* keyword is appended.
+
+For the *wiggle* keyword, the wall oscillates sinusoidally, similar to
+the oscillations of particles which can be specified by the :doc:`fix move <fix_move>` command.  This is useful in packing simulations of
+particles.  The arguments to the *wiggle* keyword specify a dimension
+for the motion, as well as it's *amplitude* and *period*\ .  Note that
+if the dimension is in the plane of the wall, this is effectively a
+shearing motion.  If the dimension is perpendicular to the wall, it is
+more of a shaking motion.  A *zcylinder* wall can only be wiggled in
+the z dimension.
+
+Each timestep, the position of a wiggled wall in the appropriate *dim*
+is set according to this equation:
+
+
+.. parsed-literal::
+
+   position = coord + A - A cos (omega \* delta)
+
+where *coord* is the specified initial position of the wall, *A* is
+the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time
+elapsed since the fix was specified.  The velocity of the wall is set
+to the derivative of this expression.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the BODY package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Any dimension (xyz) that has a wall must be non-periodic.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style body <atom_style>`, :doc:`pair\_style body/rounded/polyhedron <pair_body_rounded_polyhedron>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst
new file mode 100644
index 0000000000..559f1958d9
--- /dev/null
+++ b/doc/src/fix_wall_ees.rst
@@ -0,0 +1,145 @@
+.. index:: fix wall/ees
+
+fix wall/ees command
+====================
+
+fix wall/region/ees command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID style args
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = *wall/ees* or *wall/region/ees*
+  
+  .. parsed-literal::
+  
+       args for style *wall/ees*\ : one or more *face parameters* groups may be appended
+       face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi*
+       parameters = coord epsilon sigma cutoff
+         coord = position of wall = EDGE or constant or variable
+           EDGE = current lo or hi edge of simulation box
+           constant = number like 0.0 or -30.0 (distance units)
+           variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
+         epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units)
+           epsilon can be a variable (see below)
+         sigma = size factor for wall-particle interaction (distance units)
+           sigma can be a variable (see below)
+         cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
+
+  
+  .. parsed-literal::
+  
+       args for style *wall/region/ees*\ : *region-ID* *epsilon* *sigma* *cutoff*
+         region-ID = region whose boundary will act as wall
+         epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units)
+         sigma = size factor for wall-particle interaction (distance units)
+         cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box
+   fix wallhi all wall/ees xhi EDGE 1.0 1.0 2.5
+   fix wallhi all wall/ees v_wiggle 23.2 1.0 1.0 2.5
+   fix zwalls all wall/ees zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
+
+   fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5
+
+Description
+"""""""""""
+
+Fix *wall/ees* bounds the simulation domain on one or more of its
+faces with a flat wall that interacts with the ellipsoidal atoms in the
+group by generating a force on the atom in a direction perpendicular to
+the wall and a torque parallel with the wall.  The energy of
+wall-particle interactions E is given by:
+
+.. image:: Eqs/fix_wall_ees.jpg
+   :align: center
+
+Introduced by Babadi and Ejtehadi in :ref:`(Babadi) <BabadiEjtehadi>`. Here,
+*r* is the distance from the particle to the wall at position *coord*\ ,
+and Rc is the *cutoff* distance at which the particle and wall no
+longer interact. Also, sigma\_n is the distance between center of
+ellipsoid and the nearest point of its surface to the wall. The energy
+of the wall is:
+
+.. image:: JPG/fix_wall_ees_image.jpg
+   :align: center
+
+Details of using this command and specifications are the same as
+fix/wall command. You can also find an example in USER/ees/ under
+examples/ directory.
+
+The prefactor *epsilon* can be thought of as an
+effective Hamaker constant with energy units for the strength of the
+ellipsoid-wall interaction.  More specifically, the *epsilon* pre-factor
+= 8 \* pi\^2 \* rho\_wall \* rho\_ellipsoid \* epsilon
+\* sigma\_a \* sigma\_b \* sigma\_c, where epsilon is the LJ parameters for
+the constituent LJ particles and sigma\_a, sigma\_b, and sigma\_c are radii
+of ellipsoidal particles. Rho\_wall and rho\_ellipsoid are the number
+density of the constituent particles, in the wall and ellipsoid
+respectively, in units of 1/volume.
+
+.. note::
+
+   You must insure that r is always bigger than sigma\_n for
+   all particles in the group, or LAMMPS will generate an error.  This
+   means you cannot start your simulation with particles touching the wall
+   position *coord* (r = sigma\_n) or with particles penetrating the wall
+   (0 =< r < sigma\_n) or with particles on the wrong side of the
+   wall (r < 0).
+
+Fix *wall/region/ees* treats the surface of the geometric region defined
+by the *region-ID* as a bounding wall which interacts with nearby
+ellipsoidal particles according to the EES potential introduced above.
+
+Other details of this command are the same as for the :doc:`fix wall/region <fix_wall_region>` command.  One may also find an example
+of using this fix in the examples/USER/misc/ees/ directory.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This fix requires that atoms be ellipsoids as defined by the
+:doc:`atom\_style ellipsoid <atom_style>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall <fix_wall>`,
+:doc:`pair resquared <pair_resquared>`
+
+Default
+"""""""
+
+none
+
+
+----------
+
+
+.. _BabadiEjtehadi:
+
+
+
+**(Babadi)** Babadi and Ejtehadi, EPL, 77 (2007) 23002.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst
new file mode 100644
index 0000000000..5c9c476a44
--- /dev/null
+++ b/doc/src/fix_wall_gran.rst
@@ -0,0 +1,216 @@
+.. index:: fix wall/gran
+
+fix wall/gran command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID wall/gran fstyle fstyle_params wallstyle args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/gran = style name of this fix command
+* fstyle = style of force interactions between particles and wall
+  
+  .. parsed-literal::
+  
+       possible choices: hooke, hooke/history, hertz/history, granular
+
+* fstyle\_params = parameters associated with force interaction style
+  
+  .. parsed-literal::
+  
+       For *hooke*\ , *hooke/history*\ , and *hertz/history*\ , *fstyle_params* are:
+             Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+             Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+             gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+             gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
+             xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
+             dampflag = 0 or 1 if tangential damping force is excluded or included
+
+  
+  .. parsed-literal::
+  
+       For *granular*\ , *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular <pair_granular>`
+
+* wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder*
+* args = list of arguments for a particular style
+  
+  .. parsed-literal::
+  
+       *xplane* or *yplane* or *zplane* args = lo hi
+         lo,hi = position of lower and upper plane (distance units), either can be NULL)
+       *zcylinder* args = radius
+         radius = cylinder radius (distance units)
+
+* zero or more keyword/value pairs may be appended to args
+* keyword = *wiggle* or *shear*
+  
+  .. parsed-literal::
+  
+       *wiggle* values = dim amplitude period
+         dim = *x* or *y* or *z*
+         amplitude = size of oscillation (distance units)
+         period = time of oscillation (time units)
+       *shear* values = dim vshear
+         dim = *x* or *y* or *z*
+         vshear = magnitude of shear velocity (velocity units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
+   fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
+   fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
+   fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
+   fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+   fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
+
+Description
+"""""""""""
+
+Bound the simulation domain of a granular system with a frictional
+wall.  All particles in the group interact with the wall when they are
+close enough to touch it.
+
+The nature of the wall/particle interactions are determined by the
+*fstyle* setting.  It can be any of the styles defined by the
+:doc:`pair\_style gran/\* <pair_gran>` or the more general `pair\_style granular <pair_granular.html">`_ commands.  Currently the options are
+*hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and
+*granular* with all the possible options of the associated
+*pair\_coeff* command for the latter.  The equation for the force
+between the wall and particles touching it is the same as the
+corresponding equation on the :doc:`pair\_style gran/\* <pair_gran>` and
+:doc:`pair\_style\_granular <pair_granular>` doc pages, in the limit of
+one of the two particles going to infinite radius and mass (flat
+wall).  Specifically, delta = radius - r = overlap of particle with
+wall, m\_eff = mass of particle, and the effective radius of contact =
+RiRj/Ri+Rj is set to the radius of the particle.
+
+The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag*
+have the same meaning and units as those specified with the
+:doc:`pair\_style gran/\* <pair_gran>` commands.  This means a NULL can be
+used for either *Kt* or *gamma\_t* as described on that page.  If a
+NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7
+*Kn*\ .  If a NULL is used for *gamma\_t*, then a default value is used
+where *gamma\_t* = 1/2 *gamma\_n*.
+
+All the model choices for cohesion, tangential friction, rolling
+friction and twisting friction supported by the :doc:`pair\_style granular <pair_granular>` through its *pair\_coeff* command are also
+supported for walls. These are discussed in greater detail on the doc
+page for :doc:`pair\_style granular <pair_granular>`.
+
+Note that you can choose a different force styles and/or different
+values for the wall/particle coefficients than for particle/particle
+interactions.  E.g. if you wish to model the wall as a different
+material.
+
+.. note::
+
+   As discussed on the doc page for :doc:`pair\_style gran/\* <pair_gran>`, versions of LAMMPS before 9Jan09 used a
+   different equation for Hertzian interactions.  This means Hertizian
+   wall/particle interactions have also changed.  They now include a
+   sqrt(radius) term which was not present before.  Also the previous
+   versions used Kn and Kt from the pairwise interaction and hardwired
+   dampflag to 1, rather than letting them be specified directly.  This
+   means you can set the values of the wall/particle coefficients
+   appropriately in the current code to reproduce the results of a
+   previous Hertzian monodisperse calculation.  For example, for the
+   common case of a monodisperse system with particles of diameter 1, Kn,
+   Kt, gamma\_n, and gamma\_s should be set sqrt(2.0) larger than they were
+   previously.
+
+The effective mass *m\_eff* in the formulas listed on the :doc:`pair\_style granular <pair_gran>` doc page is the mass of the particle for
+particle/wall interactions (mass of wall is infinite).  If the
+particle is part of a rigid body, its mass is replaced by the mass of
+the rigid body in those formulas.  This is determined by searching for
+a :doc:`fix rigid <fix_rigid>` command (or its variants).
+
+The *wallstyle* can be planar or cylindrical.  The 3 planar options
+specify a pair of walls in a dimension.  Wall positions are given by
+*lo* and *hi*\ .  Either of the values can be specified as NULL if a
+single wall is desired.  For a *zcylinder* wallstyle, the cylinder's
+axis is at x = y = 0.0, and the radius of the cylinder is specified.
+
+Optionally, the wall can be moving, if the *wiggle* or *shear*
+keywords are appended.  Both keywords cannot be used together.
+
+For the *wiggle* keyword, the wall oscillates sinusoidally, similar to
+the oscillations of particles which can be specified by the :doc:`fix move <fix_move>` command.  This is useful in packing simulations of
+granular particles.  The arguments to the *wiggle* keyword specify a
+dimension for the motion, as well as it's *amplitude* and *period*\ .
+Note that if the dimension is in the plane of the wall, this is
+effectively a shearing motion.  If the dimension is perpendicular to
+the wall, it is more of a shaking motion.  A *zcylinder* wall can only
+be wiggled in the z dimension.
+
+Each timestep, the position of a wiggled wall in the appropriate *dim*
+is set according to this equation:
+
+
+.. parsed-literal::
+
+   position = coord + A - A cos (omega \* delta)
+
+where *coord* is the specified initial position of the wall, *A* is
+the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time
+elapsed since the fix was specified.  The velocity of the wall is set
+to the derivative of this expression.
+
+For the *shear* keyword, the wall moves continuously in the specified
+dimension with velocity *vshear*\ .  The dimension must be tangential to
+walls with a planar *wallstyle*\ , e.g. in the *y* or *z* directions for
+an *xplane* wall.  For *zcylinder* walls, a dimension of *z* means the
+cylinder is moving in the z-direction along it's axis.  A dimension of
+*x* or *y* means the cylinder is spinning around the z-axis, either in
+the clockwise direction for *vshear* > 0 or counter-clockwise for
+*vshear* < 0.  In this case, *vshear* is the tangential velocity of
+the wall at whatever *radius* has been defined.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+This fix writes the shear friction state of atoms interacting with the
+wall to :doc:`binary restart files <restart>`, so that a simulation can
+continue correctly if granular potentials with shear "history" effects
+are being used.  See the :doc:`read\_restart <read_restart>` command for
+info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the GRANULAR package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Any dimension (xyz) that has a granular wall must be non-periodic.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix move <fix_move>`,
+:doc:`fix wall/gran/region <fix_wall_gran_region>`,
+:doc:`pair\_style gran/\* <pair_gran>`
+:doc:`pair\_style granular <pair_granular>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst
new file mode 100644
index 0000000000..cdd6c7445b
--- /dev/null
+++ b/doc/src/fix_wall_gran_region.rst
@@ -0,0 +1,249 @@
+.. index:: fix wall/gran/region
+
+fix wall/gran/region command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/region = style name of this fix command
+* fstyle = style of force interactions between particles and wall
+  
+  .. parsed-literal::
+  
+       possible choices: hooke, hooke/history, hertz/history, granular
+
+* fstyle\_params = parameters associated with force interaction style
+  
+  .. parsed-literal::
+  
+       For *hooke*\ , *hooke/history*\ , and *hertz/history*\ , *fstyle_params* are:
+             Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+             Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+             gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+             gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
+             xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
+             dampflag = 0 or 1 if tangential damping force is excluded or included
+
+  
+  .. parsed-literal::
+  
+       For *granular*\ , *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular <pair_granular>`
+
+* wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
+* region-ID = region whose boundary will act as wall
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone
+   fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
+   fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+   fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
+
+Description
+"""""""""""
+
+Treat the surface of the geometric region defined by the *region-ID*
+as a bounding frictional wall which interacts with nearby finite-size
+granular particles when they are close enough to touch the wall.  See
+the :doc:`fix wall/region <fix_wall_region>` and :doc:`fix wall/gran <fix_wall_gran>` commands for related kinds of walls for
+non-granular particles and simpler wall geometries, respectively.
+
+Here are snapshots of example models using this command.
+Corresponding input scripts can be found in examples/granregion.
+Click on the images to see a bigger picture.  Movies of these
+simulations are `here on the Movies page <http://lammps.sandia.gov/movies.html#granregion>`_ of the LAMMPS
+web site.
+
+.. image:: JPG/gran_funnel_small.jpg
+   :target: JPG/gran_funnel.png
+
+.. image:: JPG/gran_mixer_small.jpg
+   :target: JPG/gran_mixer.png
+
+
+----------
+
+
+The distance between a particle and the region boundary is the
+distance to the nearest point on the region surface.  The force the
+wall exerts on the particle is along the direction between that point
+and the particle center, which is the direction normal to the surface
+at that point.  Note that if the region surface is comprised of
+multiple "faces", then each face can exert a force on the particle if
+it is close enough.  E.g. for :doc:`region\_style block <region>`, a
+particle in the interior, near a corner of the block, could feel wall
+forces from 1, 2, or 3 faces of the block.
+
+Regions are defined using the :doc:`region <region>` command.  Note that
+the region volume can be interior or exterior to the bounding surface,
+which will determine in which direction the surface interacts with
+particles, i.e. the direction of the surface normal. The exception to
+this is if one or more *open* options are specified for the region
+command, in which case particles interact with both the interior and
+exterior surfaces of regions.
+
+Regions can either be primitive shapes (block, sphere, cylinder, etc)
+or combinations of primitive shapes specified via the *union* or
+*intersect* region styles.  These latter styles can be used to
+construct particle containers with complex shapes.
+
+Regions can also move dynamically via the :doc:`region <region>` command
+keywords (move) and *rotate*\ , or change their shape by use of variables
+as inputs to the :doc:`region <region>` command.  If such a region is used
+with this fix, then the region surface will move in time in the
+corresponding manner.
+
+.. note::
+
+   As discussed on the :doc:`region <region>` command doc page,
+   regions in LAMMPS do not get wrapped across periodic boundaries.  It
+   is up to you to ensure that the region location with respect to
+   periodic or non-periodic boundaries is specified appropriately via the
+   :doc:`region <region>` and :doc:`boundary <boundary>` commands when using
+   a region as a wall that bounds particle motion.
+
+.. note::
+
+   For primitive regions with sharp corners and/or edges (e.g. a
+   block or cylinder), wall/particle forces are computed accurately for
+   both interior and exterior regions.  For *union* and *intersect*
+   regions, additional sharp corners and edges may be present due to the
+   intersection of the surfaces of 2 or more primitive volumes.  These
+   corners and edges can be of two types: concave or convex.  Concave
+   points/edges are like the corners of a cube as seen by particles in
+   the interior of a cube.  Wall/particle forces around these features
+   are computed correctly.  Convex points/edges are like the corners of a
+   cube as seen by particles exterior to the cube, i.e. the points jut
+   into the volume where particles are present.  LAMMPS does NOT compute
+   the location of these convex points directly, and hence wall/particle
+   forces in the cutoff volume around these points suffer from
+   inaccuracies.  The basic problem is that the outward normal of the
+   surface is not continuous at these points.  This can cause particles
+   to feel no force (they don't "see" the wall) when in one location,
+   then move a distance epsilon, and suddenly feel a large force because
+   they now "see" the wall.  In a worst-case scenario, this can blow
+   particles out of the simulation box.  Thus, as a general rule you
+   should not use the fix wall/gran/region command with *union* or
+   *interesect* regions that have convex points or edges resulting from
+   the union/intersection (convex points/edges in the union/intersection
+   due to a single sub-region are still OK).
+
+.. note::
+
+   Similarly, you should not define *union* or *intersert* regions
+   for use with this command that share an overlapping common face that
+   is part of the overall outer boundary (interior boundary is OK), even
+   if the face is smooth.  E.g. two regions of style block in a *union*
+   region, where the two blocks overlap on one or more of their faces.
+   This is because LAMMPS discards points that are part of multiple
+   sub-regions when calculating wall/particle interactions, to avoid
+   double-counting the interaction.  Having two coincident faces could
+   cause the face to become invisible to the particles.  The solution is
+   to make the two faces differ by epsilon in their position.
+
+The nature of the wall/particle interactions are determined by the
+*fstyle* setting.  It can be any of the styles defined by the
+:doc:`pair\_style gran/\* <pair_gran>` or the more general `pair\_style granular <pair_granular.html">`_ commands.  Currently the options are
+*hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and
+*granular* with all the possible options of the associated
+*pair\_coeff* command for the latter.  The equation for the force
+between the wall and particles touching it is the same as the
+corresponding equation on the :doc:`pair\_style gran/\* <pair_gran>` and
+:doc:`pair\_style\_granular <pair_granular>` doc pages, but the effective
+radius is calculated using the radius of the particle and the radius
+of curvature of the wall at the contact point.
+
+Specifically, delta = radius - r = overlap of particle with wall,
+m\_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with
+Rj replaced by the radius of curvature of the wall at the contact
+point.  The radius of curvature can be negative for a concave wall
+section, e.g. the interior of cylinder.  For a flat wall, delta =
+radius - r = overlap of particle with wall, m\_eff = mass of particle,
+and the effective radius of contact is just the radius of the
+particle.
+
+The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag*
+have the same meaning and units as those specified with the
+:doc:`pair\_style gran/\* <pair_gran>` commands.  This means a NULL can be
+used for either *Kt* or *gamma\_t* as described on that page.  If a
+NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7
+*Kn*\ .  If a NULL is used for *gamma\_t*, then a default value is used
+where *gamma\_t* = 1/2 *gamma\_n*.
+
+All the model choices for cohesion, tangential friction, rolling
+friction and twisting friction supported by the :doc:`pair\_style granular <pair_granular>` through its *pair\_coeff* command are also
+supported for walls. These are discussed in greater detail on the doc
+page for :doc:`pair\_style granular <pair_granular>`.
+
+Note that you can choose a different force styles and/or different
+values for the 6 wall/particle coefficients than for particle/particle
+interactions.  E.g. if you wish to model the wall as a different
+material.
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+Similar to :doc:`fix wall/gran <fix_wall_gran>` command, this fix writes
+the shear friction state of atoms interacting with the wall to :doc:`binary restart files <restart>`, so that a simulation can continue
+correctly if granular potentials with shear "history" effects are
+being used.  This fix also includes info about a moving region in the
+restart file.  See the :doc:`read\_restart <read_restart>` command for
+info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+.. note::
+
+   Information about region definitions is NOT included in restart
+   files, as discussed on the :doc:`read\_restart <read_restart>` doc page.
+   So you must re-define your region and if it is a moving region, define
+   its motion attributes in a way that is consistent with the simulation
+   that wrote the restart file.  In particular, if you want to change the
+   region motion attributes (e.g. its velocity), then you should ensure
+   the position/orientation of the region at the initial restart timestep
+   is the same as it was on the timestep the restart file was written.
+   If this is not possible, you may need to ignore info in the restart
+   file by defining a new fix wall/gran/region command in your restart
+   script, e.g. with a different fix ID.  Or if you want to keep the
+   shear history info but discard the region motion information, you can
+   use the same fix ID for fix wall/gran/region, but assign it a region
+   with a different region ID.
+
+None of the :doc:`fix\_modify <fix_modify>` options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the GRANULAR package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix\_move <fix_move>`,
+:doc:`fix wall/gran <fix_wall_gran>`,
+:doc:`fix wall/region <fix_wall_region>`,
+:doc:`pair\_style granular <pair_gran>`,
+:doc:`region <region>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst
new file mode 100644
index 0000000000..c38057915b
--- /dev/null
+++ b/doc/src/fix_wall_piston.rst
@@ -0,0 +1,135 @@
+.. index:: fix wall/piston
+
+fix wall/piston command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID wall/piston face ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/piston = style name of this fix command
+* face = *zlo*
+* zero or more keyword/value pairs may be appended
+* keyword = *pos* or *vel* or *ramp* or *units*
+  
+  .. parsed-literal::
+  
+       *pos* args = z
+         z = z coordinate at which the piston begins (distance units)
+       *vel* args = vz
+         vz = final velocity of the piston (velocity units)
+       *ramp* = use a linear velocity ramp from 0 to vz
+       *temp* args = target damp seed extent
+         target = target velocity for region immediately ahead of the piston
+         damp = damping parameter (time units)
+         seed = random number seed for langevin kicks
+         extent = extent of thermostatted region (distance units)
+       *units* value = *lattice* or *box*
+         *lattice* = the wall position is defined in lattice units
+         *box* = the wall position is defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix xwalls all wall/piston zlo
+   fix walls all wall/piston zlo pos 1.0 vel 10.0 units box
+   fix top all wall/piston zlo vel 10.0 ramp
+
+Description
+"""""""""""
+
+Bound the simulation with a moving wall which reflect particles in the
+specified group and drive the system with an effective infinite-mass
+piston capable of driving shock waves.
+
+A momentum mirror technique is used, which means that if an atom (or
+the wall) moves such that an atom is outside the wall on a timestep by
+a distance delta (e.g. due to :doc:`fix nve <fix_nve>`), then it is put
+back inside the face by the same delta, and the velocity relative to
+the moving wall is flipped in z.  For instance, a stationary particle
+hit with a piston wall with velocity vz, will end the timestep with a
+velocity of 2\*vz.
+
+Currently the *face* keyword can only be *zlo*\ .  This creates a piston
+moving in the positive z direction.  Particles with z coordinate less
+than the wall position are reflected to a z coordinate greater than
+the wall position.  If the piston velocity is vpz and the particle
+velocity before reflection is vzi, the particle velocity after
+reflection is -vzi + 2\*vpz.
+
+The initial position of the wall can be specified by the *pos* keyword.
+
+The final velocity of the wall can be specified by the *vel* keyword
+
+The *ramp* keyword will cause the wall/piston to adjust the velocity
+linearly from zero velocity to *vel* over the course of the run. If
+the *ramp* keyword is omitted then the wall/piston moves at a constant
+velocity defined by *vel*\ .
+
+The *temp* keyword will cause the region immediately in front of the
+wall/piston to be thermostatted with a Langevin thermostat.  This
+region moves with the piston.  The damping and kicking are measured in
+the reference frame of the piston.  So, a temperature of zero would
+mean all particles were moving at exactly the speed of the
+wall/piston.
+
+The *units* keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant is used.
+
+A *box* value selects standard distance units as defined by the
+:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
+A *lattice* value means the distance units are in lattice spacings.
+The :doc:`lattice <lattice>` command must have been previously used to
+define the lattice spacings.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+This fix style is part of the SHOCK package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+The face that has the wall/piston must be boundary type 's'
+(shrink-wrapped). The opposing face can be
+any boundary type other than periodic.
+
+A wall/piston should not be used with rigid bodies such as those
+defined by a "fix rigid" command.  This is because the wall/piston
+displaces atoms directly rather than exerting a force on them.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall/reflect <fix_wall>` command, :doc:`fix append/atoms <fix_append_atoms>` command
+
+Default
+"""""""
+
+The keyword defaults are pos = 0, vel = 0, units = lattice.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst
new file mode 100644
index 0000000000..8fba2d8e2b
--- /dev/null
+++ b/doc/src/fix_wall_reflect.rst
@@ -0,0 +1,219 @@
+.. index:: fix wall/reflect
+
+fix wall/reflect command
+========================
+
+fix wall/reflect/kk command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID wall/reflect face arg ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/reflect = style name of this fix command
+* one or more face/arg pairs may be appended
+* face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi*
+  
+  .. parsed-literal::
+  
+       *xlo*\ ,\ *ylo*\ ,\ *zlo* arg = EDGE or constant or variable
+         EDGE = current lo edge of simulation box
+         constant = number like 0.0 or -30.0 (distance units)
+         variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
+       *xhi*\ ,\ *yhi*\ ,\ *zhi* arg = EDGE or constant or variable
+         EDGE = current hi edge of simulation box
+         constant = number like 50.0 or 100.3 (distance units)
+         variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
+
+* zero or more keyword/value pairs may be appended
+* keyword = *units*
+  
+  .. parsed-literal::
+  
+       *units* value = *lattice* or *box*
+         *lattice* = the wall position is defined in lattice units
+         *box* = the wall position is defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix xwalls all wall/reflect xlo EDGE xhi EDGE
+   fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
+   fix top all wall/reflect zhi v_pressdown
+
+Description
+"""""""""""
+
+Bound the simulation with one or more walls which reflect particles
+in the specified group when they attempt to move through them.
+
+Reflection means that if an atom moves outside the wall on a timestep
+by a distance delta (e.g. due to :doc:`fix nve <fix_nve>`), then it is
+put back inside the face by the same delta, and the sign of the
+corresponding component of its velocity is flipped.
+
+When used in conjunction with :doc:`fix nve <fix_nve>` and :doc:`run\_style verlet <run_style>`, the resultant time-integration algorithm is
+equivalent to the primitive splitting algorithm (PSA) described by
+:ref:`Bond <Bond1>`.  Because each reflection event divides
+the corresponding timestep asymmetrically, energy conservation is only
+satisfied to O(dt), rather than to O(dt\^2) as it would be for
+velocity-Verlet integration without reflective walls.
+
+Up to 6 walls or faces can be specified in a single command: *xlo*\ ,
+*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ .  A *lo* face reflects particles
+that move to a coordinate less than the wall position, back in the
+*hi* direction.  A *hi* face reflects particles that move to a
+coordinate higher than the wall position, back in the *lo* direction.
+
+The position of each wall can be specified in one of 3 ways: as the
+EDGE of the simulation box, as a constant value, or as a variable.  If
+EDGE is used, then the corresponding boundary of the current
+simulation box is used.  If a numeric constant is specified then the
+wall is placed at that position in the appropriate dimension (x, y, or
+z).  In both the EDGE and constant cases, the wall will never move.
+If the wall position is a variable, it should be specified as v\_name,
+where name is an :doc:`equal-style variable <variable>` name.  In this
+case the variable is evaluated each timestep and the result becomes
+the current position of the reflecting wall.  Equal-style variables
+can specify formulas with various mathematical functions, and include
+:doc:`thermo\_style <thermo_style>` command keywords for the simulation
+box parameters and timestep and elapsed time.  Thus it is easy to
+specify a time-dependent wall position.
+
+The *units* keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant or
+variable is used.  It is not relevant when EDGE is used to specify a
+face position.  In the variable case, the variable is assumed to
+produce a value compatible with the *units* setting you specify.
+
+A *box* value selects standard distance units as defined by the
+:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
+A *lattice* value means the distance units are in lattice spacings.
+The :doc:`lattice <lattice>` command must have been previously used to
+define the lattice spacings.
+
+
+----------
+
+
+Here are examples of variable definitions that move the wall position
+in a time-dependent fashion using equal-style
+:doc:`variables <variable>`.
+
+
+.. parsed-literal::
+
+   variable ramp equal ramp(0,10)
+   fix 1 all wall/reflect xlo v_ramp
+
+   variable linear equal vdisplace(0,20)
+   fix 1 all wall/reflect xlo v_linear
+
+   variable wiggle equal swiggle(0.0,5.0,3.0)
+   fix 1 all wall/reflect xlo v_wiggle
+
+   variable wiggle equal cwiggle(0.0,5.0,3.0)
+   fix 1 all wall/reflect xlo v_wiggle
+
+The ramp(lo,hi) function adjusts the wall position linearly from lo to
+hi over the course of a run.  The vdisplace(c0,velocity) function does
+something similar using the equation position = c0 + velocity\*delta,
+where delta is the elapsed time.
+
+The swiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, where omega = 2 PI
+/ period:
+
+
+.. parsed-literal::
+
+   position = c0 + A sin(omega\*delta)
+
+The cwiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, which will have an
+initial wall velocity of 0.0, and thus may impose a gentler
+perturbation on the particles:
+
+
+.. parsed-literal::
+
+   position = c0 + A (1 - cos(omega\*delta))
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+Any dimension (xyz) that has a reflecting wall must be non-periodic.
+
+A reflecting wall should not be used with rigid bodies such as those
+defined by a "fix rigid" command.  This is because the wall/reflect
+displaces atoms directly rather than exerts a force on them.  For
+rigid bodies, use a soft wall instead, such as :doc:`fix wall/lj93 <fix_wall>`.  LAMMPS will flag the use of a rigid
+fix with fix wall/reflect with a warning, but will not generate an
+error.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall/lj93 <fix_wall>`, :doc:`fix oneway <fix_oneway>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Bond1:
+
+
+
+**(Bond)** Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst
new file mode 100644
index 0000000000..36b2dffde9
--- /dev/null
+++ b/doc/src/fix_wall_region.rst
@@ -0,0 +1,232 @@
+.. index:: fix wall/region
+
+fix wall/region command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID wall/region region-ID style args ... cutoff
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/region = style name of this fix command
+* region-ID = region whose boundary will act as wall
+* style = *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic* or *morse*
+* args for styles *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic* =
+  
+  .. parsed-literal::
+  
+        epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units)
+        sigma = size factor for wall-particle interaction (distance units)
+
+* args for style *morse* =
+  
+  .. parsed-literal::
+  
+        D_0 = depth of the potential (energy units)
+        alpha = width parameter (1/distance units)
+        r_0 = distance of the potential minimum from wall position (distance units)
+
+* cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix wall all wall/region mySphere lj93 1.0 1.0 2.5
+   fix wall all wall/region mySphere harmonic 1.0 0.0 2.5
+   fix wall all wall/region box_top morse 1.0 1.0 1.5 3.0
+
+Description
+"""""""""""
+
+Treat the surface of the geometric region defined by the *region-ID*
+as a bounding wall which interacts with nearby particles according to
+the specified style.
+
+The distance between a particle and the surface is the distance to the
+nearest point on the surface and the force the wall exerts on the
+particle is along the direction between that point and the particle,
+which is the direction normal to the surface at that point.  Note that
+if the region surface is comprised of multiple "faces", then each face
+can exert a force on the particle if it is close enough.  E.g. for
+:doc:`region\_style block <region>`, a particle in the interior, near a
+corner of the block, could feel wall forces from 1, 2, or 3 faces of
+the block.
+
+Regions are defined using the :doc:`region <region>` command.  Note that
+the region volume can be interior or exterior to the bounding surface,
+which will determine in which direction the surface interacts with
+particles, i.e. the direction of the surface normal.  The surface of
+the region only exerts forces on particles "inside" the region; if a
+particle is "outside" the region it will generate an error, because it
+has moved through the wall.
+
+Regions can either be primitive shapes (block, sphere, cylinder, etc)
+or combinations of primitive shapes specified via the *union* or
+*intersect* region styles.  These latter styles can be used to
+construct particle containers with complex shapes.  Regions can also
+change over time via the :doc:`region <region>` command keywords (move)
+and *rotate*\ .  If such a region is used with this fix, then the of
+region surface will move over time in the corresponding manner.
+
+.. note::
+
+   As discussed on the :doc:`region <region>` command doc page,
+   regions in LAMMPS do not get wrapped across periodic boundaries.  It
+   is up to you to insure that periodic or non-periodic boundaries are
+   specified appropriately via the :doc:`boundary <boundary>` command when
+   using a region as a wall that bounds particle motion.  This also means
+   that if you embed a region in your simulation box and want it to
+   repulse particles from its surface (using the "side out" option in the
+   :doc:`region <region>` command), that its repulsive force will not be
+   felt across a periodic boundary.
+
+.. note::
+
+   For primitive regions with sharp corners and/or edges (e.g. a
+   block or cylinder), wall/particle forces are computed accurately for
+   both interior and exterior regions.  For *union* and *intersect*
+   regions, additional sharp corners and edges may be present due to the
+   intersection of the surfaces of 2 or more primitive volumes.  These
+   corners and edges can be of two types: concave or convex.  Concave
+   points/edges are like the corners of a cube as seen by particles in
+   the interior of a cube.  Wall/particle forces around these features
+   are computed correctly.  Convex points/edges are like the corners of a
+   cube as seen by particles exterior to the cube, i.e. the points jut
+   into the volume where particles are present.  LAMMPS does NOT compute
+   the location of these convex points directly, and hence wall/particle
+   forces in the cutoff volume around these points suffer from
+   inaccuracies.  The basic problem is that the outward normal of the
+   surface is not continuous at these points.  This can cause particles
+   to feel no force (they don't "see" the wall) when in one location,
+   then move a distance epsilon, and suddenly feel a large force because
+   they now "see" the wall.  In a worst-case scenario, this can blow
+   particles out of the simulation box.  Thus, as a general rule you
+   should not use the fix wall/gran/region command with *union* or
+   *interesect* regions that have convex points or edges resulting from
+   the union/intersection (convex points/edges in the union/intersection
+   due to a single sub-region are still OK).
+
+.. note::
+
+   Similarly, you should not define *union* or *intersert* regions
+   for use with this command that share an overlapping common face that
+   is part of the overall outer boundary (interior boundary is OK), even
+   if the face is smooth.  E.g. two regions of style block in a *union*
+   region, where the two blocks overlap on one or more of their faces.
+   This is because LAMMPS discards points that are part of multiple
+   sub-regions when calculating wall/particle interactions, to avoid
+   double-counting the interaction.  Having two coincident faces could
+   cause the face to become invisible to the particles.  The solution is
+   to make the two faces differ by epsilon in their position.
+
+The energy of wall-particle interactions depends on the specified
+style.
+
+For style *lj93*\ , the energy E is given by the 9/3 potential:
+
+.. image:: Eqs/fix_wall_lj93.jpg
+   :align: center
+
+For style *lj126*\ , the energy E is given by the 12/6 potential:
+
+.. image:: Eqs/pair_lj.jpg
+   :align: center
+
+For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential:
+
+.. image:: Eqs/fix_wall_lj1043.jpg
+   :align: center
+
+For style *colloid*\ , the energy E is given by an integrated form of
+the :doc:`pair\_style colloid <pair_colloid>` potential:
+
+.. image:: Eqs/fix_wall_colloid.jpg
+   :align: center
+
+For style *wall/harmonic*\ , the energy E is given by a harmonic spring
+potential (the distance parameter is ignored):
+
+.. image:: Eqs/fix_wall_harmonic.jpg
+   :align: center
+
+For style *wall/morse*\ , the energy E is given by the Morse potential:
+
+.. image:: Eqs/pair_morse.jpg
+   :align: center
+
+Unlike other styles, this requires three parameters (*D\_0*, *alpha*\ , *r\_0*
+in this order) instead of two like for the other wall styles.
+
+In all cases, *r* is the distance from the particle to the region
+surface, and Rc is the *cutoff* distance at which the particle and
+surface no longer interact.  The cutoff is always the last argument.
+The energy of the wall potential is shifted so that the wall-particle
+interaction energy is 0.0 at the cutoff distance.
+
+For a full description of these wall styles, see fix\_style
+:doc:`wall <fix_wall>`
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this
+fix to add the energy of interaction between atoms and the wall to the
+system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+The :doc:`fix\_modify <fix_modify>` *virial* option is supported by this
+fix to add the contribution due to the interaction between
+atoms and each wall to the system's virial as part of :doc:`thermodynamic output <thermo_style>`. The default is *virial no*
+
+The :doc:`fix\_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
+This fix computes a global scalar energy and a global 3-length vector
+of forces, which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar energy is the sum of energy
+interactions for all particles interacting with the wall represented
+by the region surface.  The 3 vector quantities are the x,y,z
+components of the total force acting on the wall due to the particles.
+The scalar and vector values calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the atom/wall interaction energy to be included in
+   the total potential energy of the system (the quantity being
+   minimized), you MUST enable the :doc:`fix\_modify <fix_modify>` *energy*
+   option for this fix.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall/lj93 <fix_wall>`,
+:doc:`fix wall/lj126 <fix_wall>`,
+:doc:`fix wall/lj1043 <fix_wall>`,
+:doc:`fix wall/colloid <fix_wall>`,
+:doc:`fix wall/harmonic <fix_wall>`,
+:doc:`fix wall/gran <fix_wall_gran>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst
new file mode 100644
index 0000000000..c302539f3c
--- /dev/null
+++ b/doc/src/fix_wall_srd.rst
@@ -0,0 +1,225 @@
+.. index:: fix wall/srd
+
+fix wall/srd command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID wall/srd face arg ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/srd = style name of this fix command
+* one or more face/arg pairs may be appended
+* face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi*
+  
+  .. parsed-literal::
+  
+       *xlo*\ ,\ *ylo*\ ,\ *zlo* arg = EDGE or constant or variable
+         EDGE = current lo edge of simulation box
+         constant = number like 0.0 or -30.0 (distance units)
+         variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
+       *xhi*\ ,\ *yhi*\ ,\ *zhi* arg = EDGE or constant or variable
+         EDGE = current hi edge of simulation box
+         constant = number like 50.0 or 100.3 (distance units)
+         variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
+
+* zero or more keyword/value pairs may be appended
+* keyword = *units*
+  
+  .. parsed-literal::
+  
+       *units* value = *lattice* or *box*
+         *lattice* = the wall position is defined in lattice units
+         *box* = the wall position is defined in simulation box units
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix xwalls all wall/srd xlo EDGE xhi EDGE
+   fix walls all wall/srd xlo 0.0 ylo 10.0 units box
+   fix top all wall/srd zhi v_pressdown
+
+Description
+"""""""""""
+
+Bound the simulation with one or more walls which interact with
+stochastic reaction dynamics (SRD) particles as slip (smooth) or
+no-slip (rough) flat surfaces.  The wall interaction is actually
+invoked via the :doc:`fix srd <fix_srd>` command, only on the group of
+SRD particles it defines, so the group setting for the fix wall/srd
+command is ignored.
+
+A particle/wall collision occurs if an SRD particle moves outside the
+wall on a timestep.  This alters the position and velocity of the SRD
+particle and imparts a force to the wall.
+
+The *collision* and *Tsrd* settings specified via the :doc:`fix srd <fix_srd>` command affect the SRD/wall collisions.  A *slip*
+setting for the *collision* keyword means that the tangential
+component of the SRD particle momentum is preserved.  Thus only a
+normal force is imparted to the wall.  The normal component of the new
+SRD velocity is sampled from a Gaussian distribution at temperature
+*Tsrd*\ .
+
+For a *noslip* setting of the *collision* keyword, both the normal and
+tangential components of the new SRD velocity are sampled from a
+Gaussian distribution at temperature *Tsrd*\ .  Additionally, a new
+tangential direction for the SRD velocity is chosen randomly.  This
+collision style imparts both a normal and tangential force to the
+wall.
+
+Up to 6 walls or faces can be specified in a single command: *xlo*\ ,
+*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ .  A *lo* face reflects particles
+that move to a coordinate less than the wall position, back in the
+*hi* direction.  A *hi* face reflects particles that move to a
+coordinate higher than the wall position, back in the *lo* direction.
+
+The position of each wall can be specified in one of 3 ways: as the
+EDGE of the simulation box, as a constant value, or as a variable.  If
+EDGE is used, then the corresponding boundary of the current
+simulation box is used.  If a numeric constant is specified then the
+wall is placed at that position in the appropriate dimension (x, y, or
+z).  In both the EDGE and constant cases, the wall will never move.
+If the wall position is a variable, it should be specified as v\_name,
+where name is an :doc:`equal-style variable <variable>` name.  In this
+case the variable is evaluated each timestep and the result becomes
+the current position of the reflecting wall.  Equal-style variables
+can specify formulas with various mathematical functions, and include
+:doc:`thermo\_style <thermo_style>` command keywords for the simulation
+box parameters and timestep and elapsed time.  Thus it is easy to
+specify a time-dependent wall position.
+
+.. note::
+
+   Because the trajectory of the SRD particle is tracked as it
+   collides with the wall, you must insure that r = distance of the
+   particle from the wall, is always > 0 for SRD particles, or LAMMPS
+   will generate an error.  This means you cannot start your simulation
+   with SRD particles at the wall position *coord* (r = 0) or with
+   particles on the wrong side of the wall (r < 0).
+
+.. note::
+
+   If you have 2 or more walls that come together at an edge or
+   corner (e.g. walls in the x and y dimensions), then be sure to set the
+   *overlap* keyword to *yes* in the :doc:`fix srd <fix_srd>` command,
+   since the walls effectively overlap when SRD particles collide with
+   them.  LAMMPS will issue a warning if you do not do this.
+
+.. note::
+
+   The walls of this fix only interact with SRD particles, as
+   defined by the :doc:`fix srd <fix_srd>` command.  If you are simulating
+   a mixture containing other kinds of particles, then you should
+   typically use :doc:`another wall command <fix_wall>` to act on the other
+   particles.  Since SRD particles will be colliding both with the walls
+   and the other particles, it is important to insure that the other
+   particle's finite extent does not overlap an SRD wall.  If you do not
+   do this, you may generate errors when SRD particles end up "inside"
+   another particle or a wall at the beginning of a collision step.
+
+The *units* keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant is used.
+It is not relevant when EDGE or a variable is used to specify a face
+position.
+
+A *box* value selects standard distance units as defined by the
+:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
+A *lattice* value means the distance units are in lattice spacings.
+The :doc:`lattice <lattice>` command must have been previously used to
+define the lattice spacings.
+
+
+----------
+
+
+Here are examples of variable definitions that move the wall position
+in a time-dependent fashion using equal-style
+:doc:`variables <variable>`.
+
+
+.. parsed-literal::
+
+   variable ramp equal ramp(0,10)
+   fix 1 all wall/srd xlo v_ramp
+
+   variable linear equal vdisplace(0,20)
+   fix 1 all wall/srd xlo v_linear
+
+   variable wiggle equal swiggle(0.0,5.0,3.0)
+   fix 1 all wall/srd xlo v_wiggle
+
+   variable wiggle equal cwiggle(0.0,5.0,3.0)
+   fix 1 all wall/srd xlo v_wiggle
+
+The ramp(lo,hi) function adjusts the wall position linearly from lo to
+hi over the course of a run.  The displace(c0,velocity) function does
+something similar using the equation position = c0 + velocity\*delta,
+where delta is the elapsed time.
+
+The swiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, where omega = 2 PI
+/ period:
+
+
+.. parsed-literal::
+
+   position = c0 + A sin(omega\*delta)
+
+The cwiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, which will have an
+initial wall velocity of 0.0, and thus may impose a gentler
+perturbation on the particles:
+
+
+.. parsed-literal::
+
+   position = c0 + A (1 - cos(omega\*delta))
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix\_modify <fix_modify>` options
+are relevant to this fix.
+
+This fix computes a global array of values which can be accessed by
+various :doc:`output commands <Howto_output>`.  The number of rows in
+the array is equal to the number of walls defined by the fix.  The
+number of columns is 3, for the x,y,z components of force on each
+wall.
+
+Note that an outward normal force on a wall will be a negative value
+for *lo* walls and a positive value for *hi* walls.  The array values
+calculated by this fix are "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+Any dimension (xyz) that has an SRD wall must be non-periodic.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix srd <fix_srd>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/fixes.rst b/doc/src/fixes.rst
new file mode 100644
index 0000000000..5a85738c45
--- /dev/null
+++ b/doc/src/fixes.rst
@@ -0,0 +1,9 @@
+Fixes
+#####
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   fix_*
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
deleted file mode 100644
index d966b9a225..0000000000
--- a/doc/src/fixes.txt
+++ /dev/null
@@ -1,190 +0,0 @@
-Fixes :h1
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   fix_adapt
-   fix_adapt_fep
-   fix_addforce
-   fix_addtorque
-   fix_append_atoms
-   fix_atc
-   fix_atom_swap
-   fix_ave_atom
-   fix_ave_chunk
-   fix_ave_correlate
-   fix_ave_correlate_long
-   fix_ave_histo
-   fix_ave_time
-   fix_aveforce
-   fix_balance
-   fix_bocs
-   fix_bond_break
-   fix_bond_create
-   fix_bond_swap
-   fix_bond_react
-   fix_box_relax
-   fix_client_md
-   fix_cmap
-   fix_colvars
-   fix_controller
-   fix_deform
-   fix_deposit
-   fix_drag
-   fix_drude
-   fix_drude_transform
-   fix_dpd_energy
-   fix_dpd_source
-   fix_dt_reset
-   fix_efield
-   fix_ehex
-   fix_electron_stopping
-   fix_enforce2d
-   fix_eos_cv
-   fix_eos_table
-   fix_eos_table_rx
-   fix_evaporate
-   fix_external
-   fix_ffl
-   fix_filter_corotate
-   fix_flow_gauss
-   fix_freeze
-   fix_gcmc
-   fix_gld
-   fix_gle
-   fix_gravity
-   fix_grem
-   fix_halt
-   fix_heat
-   fix_hyper_global
-   fix_hyper_local
-   fix_imd
-   fix_indent
-   fix_ipi
-   fix_langevin
-   fix_langevin_drude
-   fix_langevin_eff
-   fix_langevin_spin
-   fix_latte
-   fix_lb_fluid
-   fix_lb_momentum
-   fix_lb_pc
-   fix_lb_rigid_pc_sphere
-   fix_lb_viscous
-   fix_lineforce
-   fix_manifoldforce
-   fix_meso
-   fix_meso_move
-   fix_meso_stationary
-   fix_momentum
-   fix_move
-   fix_mscg
-   fix_msst
-   fix_mvv_dpd
-   fix_neb
-   fix_neb_spin
-   fix_nh
-   fix_nh_eff
-   fix_nh_uef
-   fix_nph_asphere
-   fix_nph_body
-   fix_nph_sphere
-   fix_nphug
-   fix_npt_asphere
-   fix_npt_body
-   fix_npt_sphere
-   fix_nve
-   fix_nve_asphere
-   fix_nve_asphere_noforce
-   fix_nve_awpmd
-   fix_nve_body
-   fix_nve_dot
-   fix_nve_dotc_langevin
-   fix_nve_eff
-   fix_nve_limit
-   fix_nve_line
-   fix_nve_manifold_rattle
-   fix_nve_noforce
-   fix_nve_sphere
-   fix_nve_spin
-   fix_nve_tri
-   fix_nvk
-   fix_nvt_asphere
-   fix_nvt_body
-   fix_nvt_manifold_rattle
-   fix_nvt_sllod
-   fix_nvt_sllod_eff
-   fix_nvt_sphere
-   fix_oneway
-   fix_orient
-   fix_phonon
-   fix_pimd
-   fix_planeforce
-   fix_plumed
-   fix_poems
-   fix_pour
-   fix_precession_spin
-   fix_press_berendsen
-   fix_print
-   fix_property_atom
-   fix_python_invoke
-   fix_python_move
-   fix_qbmsst
-   fix_qeq
-   fix_qeq_comb
-   fix_qeq_reax
-   fix_qmmm
-   fix_qtb
-   fix_reaxc_bonds
-   fix_reaxc_species
-   fix_recenter
-   fix_restrain
-   fix_rhok
-   fix_rigid
-   fix_rigid_meso
-   fix_rx
-   fix_saed_vtk
-   fix_setforce
-   fix_shake
-   fix_shardlow
-   fix_smd
-   fix_smd_adjust_dt
-   fix_smd_integrate_tlsph
-   fix_smd_integrate_ulsph
-   fix_smd_move_triangulated_surface
-   fix_smd_setvel
-   fix_smd_wall_surface
-   fix_spring
-   fix_spring_chunk
-   fix_spring_rg
-   fix_spring_self
-   fix_srd
-   fix_store_force
-   fix_store_state
-   fix_temp_berendsen
-   fix_temp_csvr
-   fix_temp_rescale
-   fix_temp_rescale_eff
-   fix_tfmc
-   fix_thermal_conductivity
-   fix_ti_spring
-   fix_tmd
-   fix_ttm
-   fix_tune_kspace
-   fix_vector
-   fix_viscosity
-   fix_viscous
-   fix_wall
-   fix_wall_body_polygon
-   fix_wall_body_polyhedron
-   fix_wall_ees
-   fix_wall_gran
-   fix_wall_gran_region
-   fix_wall_piston
-   fix_wall_reflect
-   fix_wall_region
-   fix_wall_srd
-
-END_RST -->
diff --git a/doc/src/group.rst b/doc/src/group.rst
new file mode 100644
index 0000000000..6868dfd268
--- /dev/null
+++ b/doc/src/group.rst
@@ -0,0 +1,328 @@
+.. index:: group
+
+group command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   group ID style args
+
+* ID = user-defined name of the group
+* style = *delete* or *clear* or *empty* or *region* or         *type* or *id* or *molecule* or *variable* or         *include* or *subtract* or *union* or *intersect* or         *dynamic* or *static*
+  
+  .. parsed-literal::
+  
+       *delete* = no args
+       *clear* = no args
+       *empty* = no args
+       *region* args = region-ID
+       *type* or *id* or *molecule*
+         args = list of one or more atom types, atom IDs, or molecule IDs
+           any entry in list can be a sequence formatted as A:B or A:B:C where
+           A = starting index, B = ending index,
+           C = increment between indices, 1 if not specified
+         args = logical value
+           logical = "<" or "<=" or ">" or ">=" or "==" or "!="
+           value = an atom type or atom ID or molecule ID (depending on *style*\ )
+         args = logical value1 value2
+           logical = "<>"
+           value1,value2 = atom types or atom IDs or molecule IDs (depending on *style*\ )
+       *variable* args = variable-name
+       *include* args = molecule
+         molecule = add atoms to group with same molecule ID as atoms already in group
+       *subtract* args = two or more group IDs
+       *union* args = one or more group IDs
+       *intersect* args = two or more group IDs
+       *dynamic* args = parent-ID keyword value ...
+         one or more keyword/value pairs may be appended
+         keyword = *region* or *var* or *every*
+           *region* value = region-ID
+           *var* value = name of variable
+           *property* value = name of per-atom property
+           *every* value = N = update group every this many timesteps
+       *static* = no args
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   group edge region regstrip
+   group water type 3 4
+   group sub id 10 25 50
+   group sub id 10 25 50 500:1000
+   group sub id 100:10000:10
+   group sub id <= 150
+   group polyA molecule <> 50 250
+   group hienergy variable eng
+   group hienergy include molecule
+   group boundary subtract all a2 a3
+   group boundary union lower upper
+   group boundary intersect upper flow
+   group boundary delete
+   group mine dynamic all region myRegion every 100
+
+Description
+"""""""""""
+
+Identify a collection of atoms as belonging to a group.  The group ID
+can then be used in other commands such as :doc:`fix <fix>`,
+:doc:`compute <compute>`, :doc:`dump <dump>`, or :doc:`velocity <velocity>`
+to act on those atoms together.
+
+If the group ID already exists, the group command adds the specified
+atoms to the group.
+
+.. note::
+
+   By default groups are static, meaning the atoms are permanently
+   assigned to the group.  For example, if the *region* style is used to
+   assign atoms to a group, the atoms will remain in the group even if
+   they later move out of the region.  As explained below, the *dynamic*
+   style can be used to make a group dynamic so that a periodic
+   determination is made as to which atoms are in the group.  Since many
+   LAMMPS commands operate on groups of atoms, you should think carefully
+   about whether making a group dynamic makes sense for your model.
+
+A group with the ID *all* is predefined.  All atoms belong to this
+group.  This group cannot be deleted, or made dynamic.
+
+The *delete* style removes the named group and un-assigns all atoms
+that were assigned to that group.  Since there is a restriction (see
+below) that no more than 32 groups can be defined at any time, the
+*delete* style allows you to remove groups that are no longer needed,
+so that more can be specified.  You cannot delete a group if it has
+been used to define a current :doc:`fix <fix>` or :doc:`compute <compute>`
+or :doc:`dump <dump>`.
+
+The *clear* style un-assigns all atoms that were assigned to that
+group.  This may be dangerous to do during a simulation run,
+e.g. using the :doc:`run every <run>` command if a fix or compute or
+other operation expects the atoms in the group to remain constant, but
+LAMMPS does not check for this.
+
+The *empty* style creates an empty group, which is useful for commands
+like :doc:`fix gcmc <fix_gcmc>` or with complex scripts that add atoms
+to a group.
+
+The *region* style puts all atoms in the region volume into the group.
+Note that this is a static one-time assignment.  The atoms remain
+assigned (or not assigned) to the group even in they later move out of
+the region volume.
+
+The *type*\ , *id*\ , and *molecule* styles put all atoms with the
+specified atom types, atom IDs, or molecule IDs into the group.  These
+3 styles can use arguments specified in one of two formats.
+
+The first format is a list of values (types or IDs).  For example, the
+2nd command in the examples above puts all atoms of type 3 or 4 into
+the group named *water*\ .  Each entry in the list can be a
+colon-separated sequence A:B or A:B:C, as in two of the examples
+above.  A "sequence" generates a sequence of values (types or IDs),
+with an optional increment.  The first example with 500:1000 has the
+default increment of 1 and would add all atom IDs from 500 to 1000
+(inclusive) to the group sub, along with 10,25,50 since they also
+appear in the list of values.  The second example with 100:10000:10
+uses an increment of 10 and would thus would add atoms IDs
+100,110,120, ... 9990,10000 to the group sub.
+
+The second format is a *logical* followed by one or two values (type
+or ID).  The 7 valid logicals are listed above.  All the logicals
+except <> take a single argument.  The 3rd example above adds all
+atoms with IDs from 1 to 150 to the group named *sub*\ .  The logical <>
+means "between" and takes 2 arguments.  The 4th example above adds all
+atoms belonging to molecules with IDs from 50 to 250 (inclusive) to
+the group named polyA.
+
+The *variable* style evaluates a variable to determine which atoms to
+add to the group.  It must be an :doc:`atom-style variable <variable>`
+previously defined in the input script.  If the variable evaluates
+to a non-zero value for a particular atom, then that atom is added
+to the specified group.
+
+Atom-style variables can specify formulas that include thermodynamic
+quantities, per-atom values such as atom coordinates, or per-atom
+quantities calculated by computes, fixes, or other variables.  They
+can also include Boolean logic where 2 numeric values are compared to
+yield a 1 or 0 (effectively a true or false).  Thus using the
+*variable* style, is a general way to flag specific atoms to include
+or exclude from a group.
+
+For example, these lines define a variable "eatom" that calculates the
+potential energy of each atom and includes it in the group if its
+potential energy is above the threshold value -3.0.
+
+
+.. parsed-literal::
+
+   compute         1 all pe/atom
+   compute         2 all reduce sum c_1
+   thermo_style    custom step temp pe c_2
+   run             0
+
+   variable        eatom atom "c_1 > -3.0"
+   group           hienergy variable eatom
+
+Note that these lines
+
+
+.. parsed-literal::
+
+   compute         2 all reduce sum c_1
+   thermo_style    custom step temp pe c_2
+   run             0
+
+are necessary to insure that the "eatom" variable is current when the
+group command invokes it.  Because the eatom variable computes the
+per-atom energy via the pe/atom compute, it will only be current if a
+run has been performed which evaluated pairwise energies, and the
+pe/atom compute was actually invoked during the run.  Printing the
+thermodynamic info for compute 2 insures that this is the case, since
+it sums the pe/atom compute values (in the reduce compute) to output
+them to the screen.  See the "Variable Accuracy" section of the
+:doc:`variable <variable>` doc page for more details on insuring that
+variables are current when they are evaluated between runs.
+
+The *include* style with its arg *molecule* adds atoms to a group that
+have the same molecule ID as atoms already in the group.  The molecule
+ID = 0 is ignored in this operation, since it is assumed to flag
+isolated atoms that are not part of molecules.  An example of where
+this operation is useful is if the *region* style has been used
+previously to add atoms to a group that are within a geometric region.
+If molecules straddle the region boundary, then atoms outside the
+region that are part of molecules with atoms inside the region will
+not be in the group.  Using the group command a 2nd time with *include
+molecule* will add those atoms that are outside the region to the
+group.
+
+.. note::
+
+   The *include molecule* operation is relatively expensive in a
+   parallel sense.  This is because it requires communication of relevant
+   molecule IDs between all the processors and each processor to loop
+   over its atoms once per processor, to compare its atoms to the list of
+   molecule IDs from every other processor.  Hence it scales as N, rather
+   than N/P as most of the group operations do, where N is the number of
+   atoms, and P is the number of processors.
+
+The *subtract* style takes a list of two or more existing group names
+as arguments.  All atoms that belong to the 1st group, but not to any
+of the other groups are added to the specified group.
+
+The *union* style takes a list of one or more existing group names as
+arguments.  All atoms that belong to any of the listed groups are
+added to the specified group.
+
+The *intersect* style takes a list of two or more existing group names
+as arguments.  Atoms that belong to every one of the listed groups are
+added to the specified group.
+
+
+----------
+
+
+The *dynamic* style flags an existing or new group as dynamic.  This
+means atoms will be (re)assigned to the group periodically as a
+simulation runs.  This is in contrast to static groups where atoms are
+permanently assigned to the group.  The way the assignment occurs is
+as follows.  Only atoms in the group specified as the parent group via
+the parent-ID are assigned to the dynamic group before the following
+conditions are applied.  If the *region* keyword is used, atoms not in
+the specified region are removed from the dynamic group.  If the *var*
+keyword is used, the variable name must be an atom-style or
+atomfile-style variable.  The variable is evaluated and atoms whose
+per-atom values are 0.0, are removed from the dynamic group. If the *property*
+keyword is used, the per-atom property name must be a previously defined
+per-atom property.  The per-atom property is evaluated and atoms whose
+values are 0.0 are removed from the dynamic group.
+
+The assignment of atoms to a dynamic group is done at the beginning of
+each run and on every timestep that is a multiple of *N*\ , which is the
+argument for the *every* keyword (N = 1 is the default).  For an
+energy minimization, via the :doc:`minimize <minimize>` command, an
+assignment is made at the beginning of the minimization, but not
+during the iterations of the minimizer.
+
+The point in the timestep at which atoms are assigned to a dynamic
+group is after the initial stage of velocity Verlet time integration
+has been performed, and before neighbor lists or forces are computed.
+This is the point in the timestep where atom positions have just
+changed due to the time integration, so the region criterion should be
+accurate, if applied.
+
+.. note::
+
+   If the *region* keyword is used to determine what atoms are in
+   the dynamic group, atoms can move outside of the simulation box
+   between reneighboring events.  Thus if you want to include all atoms
+   on the left side of the simulation box, you probably want to set the
+   left boundary of the region to be outside the simulation box by some
+   reasonable amount (e.g. up to the cutoff of the potential), else they
+   may be excluded from the dynamic region.
+
+Here is an example of using a dynamic group to shrink the set of atoms
+being integrated by using a spherical region with a variable radius
+(shrinking from 18 to 5 over the course of the run).  This could be
+used to model a quench of the system, freezing atoms outside the
+shrinking sphere, then converting the remaining atoms to a static
+group and running further.
+
+
+.. parsed-literal::
+
+   variable        nsteps equal 5000
+   variable        rad equal 18-(step/v_nsteps)\*(18-5)
+   region          ss sphere 20 20 0 v_rad
+   group           mobile dynamic all region ss
+   fix             1 mobile nve
+   run             ${nsteps}
+   group           mobile static
+   run             ${nsteps}
+
+.. note::
+
+   All fixes and computes take a group ID as an argument, but they
+   do not all allow for use of a dynamic group.  If you get an error
+   message that this is not allowed, but feel that it should be for the
+   fix or compute in question, then please post your reasoning to the
+   LAMMPS mail list and we can change it.
+
+The *static* style removes the setting for a dynamic group, converting
+it to a static group (the default).  The atoms in the static group are
+those currently in the dynamic group.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+There can be no more than 32 groups defined at one time, including
+"all".
+
+The parent group of a dynamic group cannot itself be a dynamic group.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`fix <fix>`, :doc:`region <region>`,
+:doc:`velocity <velocity>`
+
+Default
+"""""""
+
+All atoms belong to the "all" group.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst
new file mode 100644
index 0000000000..03ce1d6d4a
--- /dev/null
+++ b/doc/src/group2ndx.rst
@@ -0,0 +1,79 @@
+.. index:: group2ndx
+
+group2ndx command
+=================
+
+ndx2group command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   group2ndx file group-ID ...
+   ndx2group file group-ID ...
+
+* file = name of index file to write out or read in
+* zero or more group IDs may be appended
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   group2ndx allindex.ndx
+   group2ndx someindex.ndx upper lower mobile
+   ndx2group someindex.ndx
+   ndx2group someindex.ndx mobile
+
+Description
+"""""""""""
+
+Write or read a Gromacs style index file in text format that associates
+atom IDs with the corresponding group definitions. This index file can be
+used with in combination with Gromacs analysis tools or to import group
+definitions into the :doc:`fix colvars <fix_colvars>` input file. It can
+also be used to save and restore group definitions for static groups.
+
+The *group2ndx* command will write group definitions to an index file.
+Without specifying any group IDs, all groups will be written to the index
+file. When specifying group IDs, only those groups will be written to the
+index file. In order to follow the Gromacs conventions, the group *all*
+will be renamed to *System* in the index file.
+
+The *ndx2group* command will create of update group definitions from those
+stored in an index file. Without specifying any group IDs, all groups except
+*System* will be read from the index file and the corresponding groups
+recreated. If a group of the same name already exists, it will be completely
+reset. When specifying group IDs, those groups, if present, will be read
+from the index file and restored.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command requires that atoms have atom IDs, since this is the
+information that is written to the index file.
+
+These commands are part of the USER-COLVARS package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`group <group>`, :doc:`dump <dump>`, :doc:`fix colvars <fix_colvars>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst
new file mode 100644
index 0000000000..bf1e884cda
--- /dev/null
+++ b/doc/src/hyper.rst
@@ -0,0 +1,219 @@
+.. index:: hyper
+
+hyper command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   hyper N Nevent fix-ID compute-ID keyword values ...
+
+* N = # of timesteps to run
+* Nevent = check for events every this many steps
+* fix-ID = ID of a fix that applies a global or local bias potential, can be NULL
+* compute-ID = ID of a compute that identifies when an event has occurred
+* zero or more keyword/value pairs may be appended
+* keyword = *min* or *dump* or *rebond*
+  
+  .. parsed-literal::
+  
+       *min* values = etol ftol maxiter maxeval
+         etol = stopping tolerance for energy, used in quenching
+         ftol = stopping tolerance for force, used in quenching
+         maxiter = max iterations of minimize, used in quenching
+         maxeval = max number of force/energy evaluations, used in quenching
+       *dump* value = dump-ID
+         dump-ID = ID of dump to trigger whenever an event takes place
+       *rebond* value = Nrebond
+         Nrebond = frequency at which to reset bonds, even if no event has occurred
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   compute event all event/displace 1.0
+   fix HG mobile hyper/global 3.0 0.3 0.4 800.0
+   hyper 5000 100 HG event min 1.0e-6 1.0e-6 100 100 dump 1 dump 5
+
+Description
+"""""""""""
+
+Run a bond-boost hyperdynamics (HD) simulation where time is
+accelerated by application of a bias potential to one or more pairs of
+nearby atoms in the system.  This command can be used to run both
+global and local hyperdynamics.  In global HD a single bond within the
+system is biased on each timestep.  In local HD multiple bonds
+(separated by a sufficient distance) can be biased simultaneously at
+each timestep.  In the bond-boost hyperdynamics context, a "bond" is
+not a covalent bond between a pair of atoms in a molecule.  Rather it
+is simply a pair of nearby atoms as discussed below.
+
+Both global and local HD are described in :ref:`(Voter2013) <Voter2013>` by
+Art Voter and collaborators.  Similar to parallel replica dynamics
+(PRD), global and local HD are methods for performing accelerated
+dynamics that are suitable for infrequent-event systems that obey
+first-order kinetics.  A good overview of accelerated dynamics methods
+for such systems in given in :ref:`(Voter2002) <Voter2002hd>` from the same
+group.  To quote from the review paper: "The dynamical evolution is
+characterized by vibrational excursions within a potential basin,
+punctuated by occasional transitions between basins."  The transition
+probability is characterized by p(t) = k\*exp(-kt) where k is the rate
+constant.  Running multiple replicas gives an effective enhancement in
+the timescale spanned by the multiple simulations, while waiting for
+an event to occur.
+
+Both HD and PRD produce a time-accurate trajectory that effectively
+extends the timescale over which a system can be simulated, but they
+do it differently.  HD uses a single replica of the system and
+accelerates time by biasing the interaction potential in a manner such
+that each timestep is effectively longer.  PRD creates Nr replicas of
+the system and runs dynamics on each independently with a normal
+unbiased potential until an event occurs in one of the replicas.  The
+time between events is reduced by a factor of Nr replicas.  For both
+methods, per CPU second, more physical time elapses and more events
+occur.  See the :doc:`prd <prd>` doc page for more info about PRD.
+
+An HD run has several stages, which are repeated each time an event
+occurs, as explained below.  The logic for an HD run is as follows:
+
+
+.. parsed-literal::
+
+   quench
+   create initial list of bonds
+
+   while (time remains):
+     run dynamics for Nevent steps
+     quench
+     check for an event
+     if event occurred: reset list of bonds
+     restore pre-quench state
+
+The list of bonds is the list of atom pairs of atoms that are within a
+short cutoff distance of each other after the system energy is
+minimized (quenched).  This list is created and reset by a :doc:`fix hyper/global <fix_hyper_global>` or :doc:`fix hyper/local <fix_hyper_local>` command specified as *fix-ID*\ .  At
+every dynamics timestep, the same fix selects one of more bonds to
+apply a bias potential to.
+
+.. note::
+
+   The style of fix associated with the specified *fix-ID*
+   determines whether you are running the global versus local
+   hyperdynamics algorithm.
+
+Dynamics (with the bias potential) is run continuously, stopping every
+*Nevent* steps to check if a transition event has occurred.  The
+specified *N* for total steps must be a multiple of *Nevent*\ .  check
+is performed by quenching the system and comparing the resulting atom
+coordinates to the coordinates from the previous basin.
+
+A quench is an energy minimization and is performed by whichever
+algorithm has been defined by the :doc:`min\_style <min_style>` command.
+Minimization parameters may be set via the
+:doc:`min\_modify <min_modify>` command and by the *min* keyword of the
+hyper command.  The latter are the settings that would be used with
+the :doc:`minimize <minimize>` command.  Note that typically, you do not
+need to perform a highly-converged minimization to detect a transition
+event, though you may need to in order to prevent a set of atoms in
+the system from relaxing to a saddle point.
+
+The event check is performed by a compute with the specified
+*compute-ID*\ .  Currently there is only one compute that works with the
+hyper command, which is the :doc:`compute event/displace <compute_event_displace>` command.  Other
+event-checking computes may be added.  :doc:`Compute event/displace <compute_event_displace>` checks whether any atom in
+the compute group has moved further than a specified threshold
+distance.  If so, an event has occurred.
+
+If this happens, the list of bonds is reset, since some bond pairs
+are likely now too far apart, and new pairs are likely close enough
+to be considered a bond.  The pre-quenched state of the
+system (coordinates and velocities) is restored, and dynamics continue.
+
+At the end of the hyper run, a variety of statistics are output to the
+screen and logfile.  These include info relevant to both global and
+local hyperdynamics, such as the number of events and the elapsed
+hyper time (accelerated time), And it includes info specific to one or
+the other, depending on which style of fix was specified by *fix-ID*\ .
+
+
+----------
+
+
+The optional keywords operate as follows.
+
+As explained above, the *min* keyword can be used to specify
+parameters for the quench.  Their meaning is the same
+as for the :doc:`minimize <minimize>` command
+
+The *dump* keyword can be used to trigger a specific dump command with
+the specified *dump-ID* to output a snapshot each time an event is
+detected.  It can be specified multiple times with different *dump-ID*
+values, as in the example above.  These snapshots will be for the
+quenched state of the system on a timestep that is a multiple of
+*Nevent*\ , i.e. a timestep after the event has occurred.  Note that any
+dump command in the input script will also output snapshots at
+whatever timestep interval it defines via its *N* argument; see the
+:doc:`dump <dump>` command for details.  This means if you only want a
+particular dump to output snapshots when events are detected, you
+should specify its *N* as a value larger than the length of the
+hyperdynamics run.
+
+As in the code logic above, the bond list is normally only reset when
+an event occurs.  The *rebond* keyword will force a reset of the bond
+list every *Nrebond* steps, even if an event has not occurred.
+*Nrebond* must be a multiple of *Nevent*\ .  This can be useful to check
+if more frequent resets alter event statistics, perhaps because the
+parameters chosen for defining what is a bond and what is an event are
+producing bad dynamics in the presence of the bias potential.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix hyper/global <fix_hyper_global>`, :doc:`fix hyper/local <fix_hyper_local>`, :doc:`compute event/displace <compute_event_displace>`, :doc:`prd <prd>`
+
+Default
+"""""""
+
+The option defaults are min = 0.1 0.1 40 50 and time = steps.
+
+
+----------
+
+
+.. _Voter2013:
+
+
+
+**(Voter2013)** S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
+144110 (2013).
+
+.. _Voter2002hd:
+
+
+
+**(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials
+Research 32, 321 (2002).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/if.rst b/doc/src/if.rst
new file mode 100644
index 0000000000..3886d35f9c
--- /dev/null
+++ b/doc/src/if.rst
@@ -0,0 +1,223 @@
+.. index:: if
+
+if command
+==========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   if boolean then t1 t2 ... elif boolean f1 f2 ... elif boolean f1 f2 ... else e1 e2 ...
+
+* boolean = a Boolean expression evaluated as TRUE or FALSE (see below)
+* then = required word
+* t1,t2,...,tN = one or more LAMMPS commands to execute if condition is met, each enclosed in quotes
+* elif = optional word, can appear multiple times
+* f1,f2,...,fN = one or more LAMMPS commands to execute if elif condition is met, each enclosed in quotes (optional arguments)
+* else = optional argument
+* e1,e2,...,eN = one or more LAMMPS commands to execute if no condition is met, each enclosed in quotes (optional arguments)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   if "${steps} > 1000" then quit
+   if "${myString} == a10" then quit
+   if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
+   if "(${eng} > 0.0) \|\| ($n < 1000)" then &
+     "timestep 0.005" &
+   elif $n<10000 &
+     "timestep 0.01" &
+   else &
+     "timestep 0.02" &
+     "print 'Max step reached'"
+   if "${eng} > ${eng_previous}" then "jump file1" else "jump file2"
+
+Description
+"""""""""""
+
+This command provides an if-then-else capability within an input
+script.  A Boolean expression is evaluated and the result is TRUE or
+FALSE.  Note that as in the examples above, the expression can contain
+variables, as defined by the :doc:`variable <variable>` command, which
+will be evaluated as part of the expression.  Thus a user-defined
+formula that reflects the current state of the simulation can be used
+to issue one or more new commands.
+
+If the result of the Boolean expression is TRUE, then one or more
+commands (t1, t2, ..., tN) are executed.  If it is FALSE, then Boolean
+expressions associated with successive elif keywords are evaluated
+until one is found to be true, in which case its commands (f1, f2,
+..., fN) are executed.  If no Boolean expression is TRUE, then the
+commands associated with the else keyword, namely (e1, e2, ..., eN),
+are executed.  The elif and else keywords and their associated
+commands are optional.  If they aren't specified and the initial
+Boolean expression is FALSE, then no commands are executed.
+
+The syntax for Boolean expressions is described below.
+
+Each command (t1, f1, e1, etc) can be any valid LAMMPS input script
+command.  If the command is more than one word, it must enclosed in
+quotes, so it will be treated as a single argument, as in the examples
+above.
+
+.. note::
+
+   If a command itself requires a quoted argument (e.g. a
+   :doc:`print <print>` command), then double and single quotes can be used
+   and nested in the usual manner, as in the examples above and below.
+   The :doc:`Commands parse <Commands_parse>` doc page has more details on
+   using quotes in arguments.  Only one of level of nesting is allowed,
+   but that should be sufficient for most use cases.
+
+Note that by using the line continuation character "&", the if command
+can be spread across many lines, though it is still a single command:
+
+
+.. parsed-literal::
+
+   if "$a < $b" then &
+     "print 'Minimum value = $a'" &
+     "run 1000" &
+   else &
+     'print "Minimum value = $b"' &
+     "minimize 0.001 0.001 1000 10000"
+
+Note that if one of the commands to execute is :doc:`quit <quit>`, as in
+the first example above, then executing the command will cause LAMMPS
+to halt.
+
+Note that by jumping to a label in the same input script, the if
+command can be used to break out of a loop.  See the :doc:`variable delete <variable>` command for info on how to delete the associated
+loop variable, so that it can be re-used later in the input script.
+
+Here is an example of a loop which checks every 1000 steps if the
+system temperature has reached a certain value, and if so, breaks out
+of the loop to finish the run.  Note that any variable could be
+checked, so long as it is current on the timestep when the run
+completes.  As explained on the :doc:`variable <variable>` doc page,
+this can be insured by including the variable in thermodynamic output.
+
+
+.. parsed-literal::
+
+   variable myTemp equal temp
+   label loop
+   variable a loop 1000
+   run 1000
+   if "${myTemp} < 300.0" then "jump SELF break"
+   next a
+   jump SELF loop
+   label break
+   print "ALL DONE"
+
+Here is an example of a double loop which uses the if and
+:doc:`jump <jump>` commands to break out of the inner loop when a
+condition is met, then continues iterating through the outer loop.
+
+
+.. parsed-literal::
+
+   label       loopa
+   variable    a loop 5
+     label     loopb
+     variable  b loop 5
+     print     "A,B = $a,$b"
+     run       10000
+     if        "$b > 2" then "jump SELF break"
+     next      b
+     jump      in.script loopb
+   label       break
+   variable    b delete
+   next        a
+   jump        SELF loopa
+
+
+----------
+
+
+The Boolean expressions for the if and elif keywords have a C-like
+syntax.  Note that each expression is a single argument within the if
+command.  Thus if you want to include spaces in the expression for
+clarity, you must enclose the entire expression in quotes.
+
+An expression is built out of numbers (which start with a digit or
+period or minus sign) or strings (which start with a letter and can
+contain alphanumeric characters or underscores):
+
+
+.. parsed-literal::
+
+   0.2, 100, 1.0e20, -15.4, etc
+   InP, myString, a123, ab_23_cd, etc
+
+and Boolean operators:
+
+
+.. parsed-literal::
+
+   A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A \|\| B, A \|\^ B, !A
+
+Each A and B is a number or string or a variable reference like $a or
+${abc}, or A or B can be another Boolean expression.
+
+If a variable is used it can produce a number when evaluated, like an
+:doc:`equal-style variable <variable>`.  Or it can produce a string,
+like an :doc:`index-style variable <variable>`.  For an individual
+Boolean operator, A and B must both be numbers or must both be
+strings.  You cannot compare a number to a string.
+
+Expressions are evaluated left to right and have the usual C-style
+precedence: the unary logical NOT operator "!" has the highest
+precedence, the 4 relational operators "<", "<=", ">", and ">=" are
+next; the two remaining relational operators "==" and "!=" are next;
+then the logical AND operator "&&"; and finally the logical OR
+operator "\|\|" and logical XOR (exclusive or) operator "\|\^" have the
+lowest precedence.  Parenthesis can be used to group one or more
+portions of an expression and/or enforce a different order of
+evaluation than what would occur with the default precedence.
+
+When the 6 relational operators (first 6 in list above) compare 2
+numbers, they return either a 1.0 or 0.0 depending on whether the
+relationship between A and B is TRUE or FALSE.  When the 6 relational
+operators compare 2 strings, they also return a 1.0 or 0.0 for TRUE or
+FALSE, but the comparison is done by the C function strcmp().
+
+When the 3 logical operators (last 3 in list above) compare 2 numbers,
+they also return either a 1.0 or 0.0 depending on whether the
+relationship between A and B is TRUE or FALSE (or just A).  The
+logical AND operator will return 1.0 if both its arguments are
+non-zero, else it returns 0.0.  The logical OR operator will return
+1.0 if either of its arguments is non-zero, else it returns 0.0.  The
+logical XOR operator will return 1.0 if one of its arguments is zero
+and the other non-zero, else it returns 0.0.  The logical NOT operator
+returns 1.0 if its argument is 0.0, else it returns 0.0.  The 3
+logical operators can only be used to operate on numbers, not on
+strings.
+
+The overall Boolean expression produces a TRUE result if the result is
+non-zero.  If the result is zero, the expression result is FALSE.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`variable <variable>`, :doc:`print <print>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst
new file mode 100644
index 0000000000..d6f23e761c
--- /dev/null
+++ b/doc/src/improper_class2.rst
@@ -0,0 +1,148 @@
+.. index:: improper\_style class2
+
+improper\_style class2 command
+==============================
+
+improper\_style class2/omp command
+==================================
+
+improper\_style class2/kk command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style class2
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style class2
+   improper_coeff 1 100.0 0
+   improper_coeff \* aa 0.0 0.0 0.0 115.06 130.01 115.06
+
+Description
+"""""""""""
+
+The *class2* improper style uses the potential
+
+.. image:: Eqs/improper_class2.jpg
+   :align: center
+
+where Ei is the improper term and Eaa is an angle-angle term.  The 3 X
+terms in Ei are an average over 3 out-of-plane angles.
+
+The 4 atoms in an improper quadruplet (listed in the data file read by
+the :doc:`read\_data <read_data>` command) are ordered I,J,K,L.  X\_IJKL
+refers to the angle between the plane of I,J,K and the plane of J,K,L,
+and the bond JK lies in both planes.  Similarly for X\_KJLI and X\_LJIK.
+Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X
+terms.  Thus J (the 2nd atom in the quadruplet) is the atom of
+symmetry in the 3 X angles.
+
+The subscripts on the various theta's refer to different combinations
+of 3 atoms (I,J,K,L) used to form a particular angle.  E.g. Theta\_IJL
+is the angle formed by atoms I,J,L with J in the middle.  Theta1,
+theta2, theta3 are the equilibrium positions of those angles.  Again,
+atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the
+theta angles, since it is always the center atom.
+
+Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L
+would exist for an improper to be defined between the 4 atoms, but
+this is not required.
+
+See :ref:`(Sun) <improper-Sun>` for a description of the COMPASS class2 force field.
+
+Coefficients for the Ei and Eaa formulas must be defined for each
+improper type via the :doc:`improper\_coeff <improper_coeff>` command as
+in the example above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands.
+
+These are the 2 coefficients for the Ei formula:
+
+* K (energy/radian\^2)
+* X0 (degrees)
+
+X0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian\^2.
+
+For the Eaa formula, each line in a
+:doc:`improper\_coeff <improper_coeff>` command in the input script lists
+7 coefficients, the first of which is "aa" to indicate they are
+AngleAngle coefficients.  In a data file, these coefficients should be
+listed under a "AngleAngle Coeffs" heading and you must leave out the
+"aa", i.e. only list 6 coefficients after the improper type.
+
+* aa
+* M1 (energy/distance)
+* M2 (energy/distance)
+* M3 (energy/distance)
+* theta1 (degrees)
+* theta2 (degrees)
+* theta3 (degrees)
+
+The theta values are specified in degrees, but LAMMPS converts them to
+radians internally; hence the units of M are in energy/radian\^2.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+CLASS2 package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _improper-Sun:
+
+
+
+**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst
new file mode 100644
index 0000000000..b71469523f
--- /dev/null
+++ b/doc/src/improper_coeff.rst
@@ -0,0 +1,110 @@
+.. index:: improper\_coeff
+
+improper\_coeff command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_coeff N args
+
+* N = improper type (see asterisk form below)
+* args = coefficients for one or more improper types
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_coeff 1 300.0 0.0
+   improper_coeff \* 80.2 -1 2
+   improper_coeff \*4 80.2 -1 2
+
+Description
+"""""""""""
+
+Specify the improper force field coefficients for one or more improper
+types.  The number and meaning of the coefficients depends on the
+improper style.  Improper coefficients can also be set in the data
+file read by the :doc:`read\_data <read_data>` command or in a restart
+file.
+
+N can be specified in one of two ways.  An explicit numeric value can
+be used, as in the 1st example above.  Or a wild-card asterisk can be
+used to set the coefficients for multiple improper types.  This takes
+the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of improper
+types, then an asterisk with no numeric values means all types from 1
+to N.  A leading asterisk means all types from 1 to n (inclusive).  A
+trailing asterisk means all types from n to N (inclusive).  A middle
+asterisk means all types from m to n (inclusive).
+
+Note that using an improper\_coeff command can override a previous
+setting for the same improper type.  For example, these commands set
+the coeffs for all improper types, then overwrite the coeffs for just
+improper type 2:
+
+
+.. parsed-literal::
+
+   improper_coeff \* 300.0 0.0
+   improper_coeff 2 50.0 0.0
+
+A line in a data file that specifies improper coefficients uses the
+exact same format as the arguments of the improper\_coeff command in an
+input script, except that wild-card asterisks should not be used since
+coefficients for all N types must be listed in the file.  For example,
+under the "Improper Coeffs" section of a data file, the line that
+corresponds to the 1st example above would be listed as
+
+
+.. parsed-literal::
+
+   1 300.0 0.0
+
+The :doc:`improper\_style class2 <improper_class2>` is an exception to
+this rule, in that an additional argument is used in the input script
+to allow specification of the cross-term coefficients.  See its doc
+page for details.
+
+
+----------
+
+
+The list of all improper styles defined in LAMMPS is given on the
+:doc:`improper\_style <improper_style>` doc page.  They are also listed
+in more compact form on the :ref:`Commands improper <improper>` doc page.
+
+On either of those pages, click on the style to display the formula it
+computes and its coefficients as specified by the associated
+improper\_coeff command.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command must come after the simulation box is defined by a
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
+:doc:`create\_box <create_box>` command.
+
+An improper style must be defined before any improper coefficients are
+set, either in the input script or in a data file.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_style <improper_style>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst
new file mode 100644
index 0000000000..803f6d9e6a
--- /dev/null
+++ b/doc/src/improper_cossq.rst
@@ -0,0 +1,102 @@
+.. index:: improper\_style cossq
+
+improper\_style cossq command
+=============================
+
+improper\_style cossq/omp command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style cossq
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style cossq
+   improper_coeff 1 4.0 0.0
+
+Description
+"""""""""""
+
+The *cossq* improper style uses the potential
+
+.. image:: Eqs/improper_cossq.jpg
+   :align: center
+
+where x is the improper angle, x0 is its equilibrium value, and K is a
+prefactor.
+
+If the 4 atoms in an improper quadruplet (listed in the data file read
+by the :doc:`read\_data <read_data>` command) are ordered I,J,K,L then X
+is the angle between the plane of I,J,K and the plane of J,K,L.
+Alternatively, you can think of atoms J,K,L as being in a plane, and
+atom I above the plane, and X as a measure of how far out-of-plane I
+is with respect to the other 3 atoms.
+
+Note that defining 4 atoms to interact in this way, does not mean that
+bonds necessarily exist between I-J, J-K, or K-L, as they would in a
+linear dihedral.  Normally, the bonds I-J, I-K, I-L would exist for an
+improper to be defined between the 4 atoms.
+
+The following coefficients must be defined for each improper type via
+the :doc:`improper\_coeff <improper_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* K (energy)
+* X0 (degrees)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst
new file mode 100644
index 0000000000..43cd36f60a
--- /dev/null
+++ b/doc/src/improper_cvff.rst
@@ -0,0 +1,105 @@
+.. index:: improper\_style cvff
+
+improper\_style cvff command
+============================
+
+improper\_style cvff/intel command
+==================================
+
+improper\_style cvff/omp command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style cvff
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style cvff
+   improper_coeff 1 80.0 -1 4
+
+Description
+"""""""""""
+
+The *cvff* improper style uses the potential
+
+.. image:: Eqs/improper_cvff.jpg
+   :align: center
+
+where phi is the improper dihedral angle.
+
+If the 4 atoms in an improper quadruplet (listed in the data file read
+by the :doc:`read\_data <read_data>` command) are ordered I,J,K,L then
+the improper dihedral angle is between the plane of I,J,K and the
+plane of J,K,L.  Note that because this is effectively a dihedral
+angle, the formula for this improper style is the same as for
+:doc:`dihedral\_style harmonic <dihedral_harmonic>`.
+
+Note that defining 4 atoms to interact in this way, does not mean that
+bonds necessarily exist between I-J, J-K, or K-L, as they would in a
+linear dihedral.  Normally, the bonds I-J, I-K, I-L would exist for an
+improper to be defined between the 4 atoms.
+
+The following coefficients must be defined for each improper type via
+the :doc:`improper\_coeff <improper_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* K (energy)
+* d (+1 or -1)
+* n (0,1,2,3,4,6)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst
new file mode 100644
index 0000000000..4efc9a2261
--- /dev/null
+++ b/doc/src/improper_distance.rst
@@ -0,0 +1,71 @@
+.. index:: improper\_style distance
+
+improper\_style distance command
+================================
+
+Syntax
+""""""
+
+improper\_style distance
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style distance
+   improper_coeff 1 80.0 100.0
+
+Description
+"""""""""""
+
+The *distance* improper style uses the potential
+
+.. image:: Eqs/improper_dist-1.jpg
+   :align: center
+
+where d is the distance between the central atom and the plane formed
+by the other three atoms.  If the 4 atoms in an improper quadruplet
+(listed in the data file read by the :doc:`read\_data <read_data>`
+command) are ordered I,J,K,L then the I-atom is assumed to be the
+central atom.
+
+.. image:: JPG/improper_distance.jpg
+   :align: center
+
+Note that defining 4 atoms to interact in this way, does not mean that
+bonds necessarily exist between I-J, J-K, or K-L, as they would in a
+linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
+improper to be defined between the 4 atoms.
+
+The following coefficients must be defined for each improper type via
+the improper\_coeff command as in the example above, or in the data
+file or restart files read by the read\_data or read\_restart commands:
+
+* K\_2 (energy/distance\^2)
+* K\_4 (energy/distance\^4)
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst
new file mode 100644
index 0000000000..8fb74129ec
--- /dev/null
+++ b/doc/src/improper_distharm.rst
@@ -0,0 +1,65 @@
+.. index:: improper\_style distharm
+
+improper\_style distharm command
+================================
+
+Syntax
+""""""
+
+improper\_style distharm
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style distharm
+   improper_coeff 1 25.0 0.5
+
+Description
+"""""""""""
+
+The *distharm* improper style uses the potential
+
+.. image:: Eqs/improper_distharm.jpg
+   :align: center
+
+where d is the oriented distance between the central atom and the plane formed
+by the other three atoms.  If the 4 atoms in an improper quadruplet
+(listed in the data file read by the :doc:`read\_data <read_data>`
+command) are ordered I,J,K,L then the L-atom is assumed to be the
+central atom. Note that this is different from the convention used
+in the improper\_style distance. The distance d is oriented and can take
+on negative values. This may lead to unwanted behavior if d0 is not equal to zero.
+
+The following coefficients must be defined for each improper type via
+the improper\_coeff command as in the example above, or in the data
+file or restart files read by the read\_data or read\_restart commands:
+
+* K (energy/distance\^2)
+* d0 (distance)
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+USER-YAFF package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst
new file mode 100644
index 0000000000..227b02d275
--- /dev/null
+++ b/doc/src/improper_fourier.rst
@@ -0,0 +1,98 @@
+.. index:: improper\_style fourier
+
+improper\_style fourier command
+===============================
+
+improper\_style fourier/omp command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style fourier
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style fourier
+   improper_coeff 1 100.0 0.0 1.0 0.5 1
+
+Description
+"""""""""""
+
+The *fourier* improper style uses the following potential:
+
+.. image:: Eqs/improper_fourier.jpg
+   :align: center
+
+where K is the force constant, C0, C1, C2 are dimensionless coefficients,
+and omega is the angle between the IL axis and the IJK plane:
+
+.. image:: JPG/umbrella.jpg
+   :align: center
+
+If all parameter (see below) is not zero, the all the three possible angles will taken in account.
+
+The following coefficients must be defined for each improper type via
+the :doc:`improper\_coeff <improper_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* K (energy)
+* C0 (unitless)
+* C1 (unitless)
+* C2 (unitless)
+* all  (0 or 1, optional)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This angle style can only be used if LAMMPS was built with the
+USER\_MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst
new file mode 100644
index 0000000000..6eb205f8e7
--- /dev/null
+++ b/doc/src/improper_harmonic.rst
@@ -0,0 +1,111 @@
+.. index:: improper\_style harmonic
+
+improper\_style harmonic command
+================================
+
+improper\_style harmonic/intel command
+======================================
+
+improper\_style harmonic/kk command
+===================================
+
+improper\_style harmonic/omp command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style harmonic
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style harmonic
+   improper_coeff 1 100.0 0
+
+Description
+"""""""""""
+
+The *harmonic* improper style uses the potential
+
+.. image:: Eqs/improper_harmonic.jpg
+   :align: center
+
+where X is the improper angle, X0 is its equilibrium value, and K is a
+prefactor.  Note that the usual 1/2 factor is included in K.
+
+If the 4 atoms in an improper quadruplet (listed in the data file read
+by the :doc:`read\_data <read_data>` command) are ordered I,J,K,L then X
+is the angle between the plane of I,J,K and the plane of J,K,L.
+Alternatively, you can think of atoms J,K,L as being in a plane, and
+atom I above the plane, and X as a measure of how far out-of-plane I
+is with respect to the other 3 atoms.
+
+Note that defining 4 atoms to interact in this way, does not mean that
+bonds necessarily exist between I-J, J-K, or K-L, as they would in a
+linear dihedral.  Normally, the bonds I-J, I-K, I-L would exist for an
+improper to be defined between the 4 atoms.
+
+The following coefficients must be defined for each improper type via
+the :doc:`improper\_coeff <improper_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* K (energy/radian\^2)
+* X0 (degrees)
+
+X0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian\^2.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst
new file mode 100644
index 0000000000..7272cb2abc
--- /dev/null
+++ b/doc/src/improper_hybrid.rst
@@ -0,0 +1,83 @@
+.. index:: improper\_style hybrid
+
+improper\_style hybrid command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style hybrid style1 style2 ...
+
+* style1,style2 = list of one or more improper styles
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style hybrid harmonic helix
+   improper_coeff 1 harmonic 120.0 30
+   improper_coeff 2 cvff 20.0 -1 2
+
+Description
+"""""""""""
+
+The *hybrid* style enables the use of multiple improper styles in one
+simulation.  An improper style is assigned to each improper type.  For
+example, impropers in a polymer flow (of improper type 1) could be
+computed with a *harmonic* potential and impropers in the wall
+boundary (of improper type 2) could be computed with a *cvff*
+potential.  The assignment of improper type to style is made via the
+:doc:`improper\_coeff <improper_coeff>` command or in the data file.
+
+In the improper\_coeff command, the first coefficient sets the improper
+style and the remaining coefficients are those appropriate to that
+style.  In the example above, the 2 improper\_coeff commands would set
+impropers of improper type 1 to be computed with a *harmonic*
+potential with coefficients 120.0, 30 for K, X0.  Improper type 2
+would be computed with a *cvff* potential with coefficients 20.0, -1,
+2 for K, d, n.
+
+If the improper *class2* potential is one of the hybrid styles, it
+requires additional AngleAngle coefficients be specified in the data
+file.  These lines must also have an additional "class2" argument
+added after the improper type.  For improper types which are assigned
+to other hybrid styles, use the style name (e.g. "harmonic")
+appropriate to that style.  The AngleAngle coeffs for that improper
+type will then be ignored.
+
+An improper style of *none* can be specified as the 2nd argument to
+the improper\_coeff command, if you desire to turn off certain improper
+types.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Unlike other improper styles, the hybrid improper style does not store
+improper coefficient info for individual sub-styles in a :doc:`binary restart files <restart>`.  Thus when restarting a simulation from a
+restart file, you need to re-specify improper\_coeff commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst
new file mode 100644
index 0000000000..11832d2754
--- /dev/null
+++ b/doc/src/improper_inversion_harmonic.rst
@@ -0,0 +1,82 @@
+.. index:: improper\_style inversion/harmonic
+
+improper\_style inversion/harmonic command
+==========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style inversion/harmonic
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style inversion/harmonic
+   improper_coeff 1 18.776340 0.000000
+
+Description
+"""""""""""
+
+The *inversion/harmonic* improper style follows the Wilson-Decius
+out-of-plane angle definition and uses an harmonic potential:
+
+.. image:: Eqs/improper_inversion_harmonic.jpg
+   :align: center
+
+where K is the force constant and omega is the angle evaluated for
+all three axis-plane combinations centered around the atom I.  For
+the IL axis and the IJK plane omega looks as follows:
+
+.. image:: JPG/umbrella.jpg
+   :align: center
+
+Note that the *inversion/harmonic* angle term evaluation differs to
+the :doc:`improper\_umbrella <improper_umbrella>` due to the cyclic
+evaluation of all possible angles omega.
+
+The following coefficients must be defined for each improper type via
+the :doc:`improper\_coeff <improper_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* K (energy)
+* omega0 (degrees)
+
+If omega0 = 0 the potential term has a minimum for the planar
+structure.  Otherwise it has two minima at +/- omega0, with a barrier
+in between.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+USER-MOFFF package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_none.rst b/doc/src/improper_none.rst
new file mode 100644
index 0000000000..83622b4f11
--- /dev/null
+++ b/doc/src/improper_none.rst
@@ -0,0 +1,46 @@
+.. index:: improper\_style none
+
+improper\_style none command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style none
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style none
+
+Description
+"""""""""""
+
+Using an improper style of none means improper forces and energies are
+not computed, even if quadruplets of improper atoms were listed in the
+data file read by the :doc:`read\_data <read_data>` command.
+
+See the :doc:`improper\_style zero <improper_zero>` command for a way to
+calculate improper statistics, but compute no improper interactions.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_style zero <improper_zero>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst
new file mode 100644
index 0000000000..374b64fcd7
--- /dev/null
+++ b/doc/src/improper_ring.rst
@@ -0,0 +1,111 @@
+.. index:: improper\_style ring
+
+improper\_style ring command
+============================
+
+improper\_style ring/omp command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style ring
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style ring
+   improper_coeff 1 8000 70.5
+
+Description
+"""""""""""
+
+The *ring* improper style uses the potential
+
+.. image:: Eqs/improper_ring.jpg
+   :align: center
+
+where K is a prefactor, theta is the angle formed by the atoms
+specified by (i,j,k,l) indices and theta0 its equilibrium value.
+
+If the 4 atoms in an improper quadruplet (listed in the data file read
+by the :doc:`read\_data <read_data>` command) are ordered i,j,k,l then
+theta\_\ *ijl* is the angle between atoms i,j and l, theta\_\ *ijk* is the
+angle between atoms i,j and k, theta\_\ *kjl* is the angle between atoms
+j,k, and l.
+
+The "ring" improper style implements the improper potential introduced
+by Destree et al., in Equation (9) of :ref:`(Destree) <Destree>`.  This
+potential does not affect small amplitude vibrations but is used in an
+ad-hoc way to prevent the onset of accidentally large amplitude
+fluctuations leading to the occurrence of a planar conformation of the
+three bonds i-j, j-k and j-l, an intermediate conformation toward the
+chiral inversion of a methine carbon.  In the "Impropers" section of
+data file four atoms: i, j, k and l are specified with i,j and l lying
+on the backbone of the chain and k specifying the chirality of j.
+
+The following coefficients must be defined for each improper type via
+the :doc:`improper\_coeff <improper_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* K (energy)
+* theta0 (degrees)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+.. _Destree:
+
+
+
+**(Destree)** M. Destree, F. Laupretre, A. Lyulin, and J.-P.  Ryckaert,
+J Chem Phys, 112, 9632 (2000).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst
new file mode 100644
index 0000000000..94e9c12fca
--- /dev/null
+++ b/doc/src/improper_sqdistharm.rst
@@ -0,0 +1,66 @@
+.. index:: improper\_style sqdistharm
+
+improper\_style sqdistharm command
+==================================
+
+Syntax
+""""""
+
+improper\_style sqdistharm
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style sqdistharm
+   improper_coeff 1 50.0 0.1
+
+Description
+"""""""""""
+
+The *sqdistharm* improper style uses the potential
+
+.. image:: Eqs/improper_sqdistharm.jpg
+   :align: center
+
+where d is the distance between the central atom and the plane formed
+by the other three atoms.  If the 4 atoms in an improper quadruplet
+(listed in the data file read by the :doc:`read\_data <read_data>`
+command) are ordered I,J,K,L then the L-atom is assumed to be the
+central atom. Note that this is different from the convention used
+in the improper\_style distance.
+
+The following coefficients must be defined for each improper type via
+the improper\_coeff command as in the example above, or in the data
+file or restart files read by the read\_data or read\_restart commands:
+
+* K (energy/distance\^4)
+* d0\^2 (distance\^2)
+
+Note that d0\^2 (in units distance\^2) has be provided and not d0.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst
new file mode 100644
index 0000000000..e49818981a
--- /dev/null
+++ b/doc/src/improper_style.rst
@@ -0,0 +1,128 @@
+.. index:: improper\_style
+
+improper\_style command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style style
+
+* style = *none* or *hybrid* or *class2* or *cvff* or *harmonic*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style harmonic
+   improper_style cvff
+   improper_style hybrid cvff harmonic
+
+Description
+"""""""""""
+
+Set the formula(s) LAMMPS uses to compute improper interactions
+between quadruplets of atoms, which remain in force for the duration
+of the simulation.  The list of improper quadruplets is read in by a
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` command
+from a data or restart file.  Note that the ordering of the 4 atoms in
+an improper quadruplet determines the definition of the improper
+angle used in the formula for each style.  See the doc pages of
+individual styles for details.
+
+Hybrid models where impropers are computed using different improper
+potentials can be setup using the *hybrid* improper style.
+
+The coefficients associated with an improper style can be specified in
+a data or restart file or via the :doc:`improper\_coeff <improper_coeff>`
+command.
+
+All improper potentials store their coefficient data in binary restart
+files which means improper\_style and
+:doc:`improper\_coeff <improper_coeff>` commands do not need to be
+re-specified in an input script that restarts a simulation.  See the
+:doc:`read\_restart <read_restart>` command for details on how to do
+this.  The one exception is that improper\_style *hybrid* only stores
+the list of sub-styles in the restart file; improper coefficients need
+to be re-specified.
+
+.. note::
+
+   When both an improper and pair style is defined, the
+   :doc:`special\_bonds <special_bonds>` command often needs to be used to
+   turn off (or weight) the pairwise interaction that would otherwise
+   exist between a group of 4 bonded atoms.
+
+
+----------
+
+
+Here is an alphabetic list of improper styles defined in LAMMPS.
+Click on the style to display the formula it computes and coefficients
+specified by the associated :doc:`improper\_coeff <improper_coeff>`
+command.
+
+Click on the style to display the formula it computes, any additional
+arguments specified in the improper\_style command, and coefficients
+specified by the associated :doc:`improper\_coeff <improper_coeff>`
+command.
+
+There are also additional accelerated pair styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the :ref:`Commands improper <improper>` doc page are followed by one or
+more of (g,i,k,o,t) to indicate which accelerated styles exist.
+
+* :doc:`none <improper_none>` - turn off improper interactions
+* :doc:`zero <improper_zero>` - topology but no interactions
+* :doc:`hybrid <improper_hybrid>` - define multiple styles of improper interactions
+
+* :doc:`class2 <improper_class2>` - COMPASS (class 2) improper
+* :doc:`cossq <improper_cossq>` - improper with a cosine squared term
+* :doc:`cvff <improper_cvff>` - CVFF improper
+* :doc:`distance <improper_distance>` - improper based on distance between atom planes
+* :doc:`distharm <improper_distharm>` - improper that is harmonic in the out-of-plane distance
+* :doc:`fourier <improper_fourier>` - improper with multiple cosine terms
+* :doc:`harmonic <improper_harmonic>` - harmonic improper
+* :doc:`inversion/harmonic <improper_inversion_harmonic>` - harmonic improper with Wilson-Decius out-of-plane definition
+* :doc:`ring <improper_ring>` - improper which prevents planar conformations
+* :doc:`umbrella <improper_umbrella>` - DREIDING improper
+
+:doc:`sqdistharm <improper_sqdistharm>` - improper that is harmonic in the square of the out-of-plane distance
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Improper styles can only be set for atom\_style choices that allow
+impropers to be defined.
+
+Most improper styles are part of the MOLECULE package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  The doc pages for
+individual improper potentials tell if it is part of a package.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   improper_style none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst
new file mode 100644
index 0000000000..785d3ce7dd
--- /dev/null
+++ b/doc/src/improper_umbrella.rst
@@ -0,0 +1,112 @@
+.. index:: improper\_style umbrella
+
+improper\_style umbrella command
+================================
+
+improper\_style umbrella/omp command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style umbrella
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style umbrella
+   improper_coeff 1 100.0 180.0
+
+Description
+"""""""""""
+
+The *umbrella* improper style uses the following potential, which is
+commonly referred to as a classic inversion and used in the
+:doc:`DREIDING <Howto_bioFF>` force field:
+
+.. image:: Eqs/improper_umbrella.jpg
+   :align: center
+
+where K is the force constant and omega is the angle between the IL
+axis and the IJK plane:
+
+.. image:: JPG/umbrella.jpg
+   :align: center
+
+If omega0 = 0 the potential term has a minimum for the planar
+structure.  Otherwise it has two minima at +/- omega0, with a barrier
+in between.
+
+See :ref:`(Mayo) <umbrella-Mayo>` for a description of the DREIDING force field.
+
+The following coefficients must be defined for each improper type via
+the :doc:`improper\_coeff <improper_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* K (energy)
+* omega0 (degrees)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This improper style can only be used if LAMMPS was built with the
+MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`improper\_coeff <improper_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _umbrella-Mayo:
+
+
+
+**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990),
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst
new file mode 100644
index 0000000000..145146e6f6
--- /dev/null
+++ b/doc/src/improper_zero.rst
@@ -0,0 +1,58 @@
+.. index:: improper\_style zero
+
+improper\_style zero command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   improper_style zero *nocoeff*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   improper_style zero
+   improper_style zero nocoeff
+   improper_coeff \*
+
+Description
+"""""""""""
+
+Using an improper style of zero means improper forces and energies are
+not computed, but the geometry of improper quadruplets is still
+accessible to other commands.
+
+As an example, the :doc:`compute improper/local <compute_improper_local>` command can be used to
+compute the chi values for the list of quadruplets of improper atoms
+listed in the data file read by the :doc:`read\_data <read_data>`
+command.  If no improper style is defined, this command cannot be
+used.
+
+The optional *nocoeff* flag allows to read data files with a ImproperCoeff
+section for any improper style. Similarly, any improper\_coeff commands
+will only be checked for the improper type number and the rest ignored.
+
+Note that the :doc:`improper\_coeff <improper_coeff>` command must be
+used for all improper types, though no additional values are
+specified.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+:doc:`improper\_style none <improper_none>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/impropers.rst b/doc/src/impropers.rst
new file mode 100644
index 0000000000..93b4776d2c
--- /dev/null
+++ b/doc/src/impropers.rst
@@ -0,0 +1,9 @@
+Improper Styles
+###############
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   improper_*
diff --git a/doc/src/impropers.txt b/doc/src/impropers.txt
deleted file mode 100644
index ce829197fe..0000000000
--- a/doc/src/impropers.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-Improper Styles :h1
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   improper_class2
-   improper_cossq
-   improper_cvff
-   improper_distance
-   improper_distharm
-   improper_fourier
-   improper_harmonic
-   improper_hybrid
-   improper_inversion_harmonic
-   improper_none
-   improper_ring
-   improper_umbrella
-   improper_sqdistharm
-   improper_zero
-
-END_RST -->
diff --git a/doc/src/include.rst b/doc/src/include.rst
new file mode 100644
index 0000000000..9f1a11e8f7
--- /dev/null
+++ b/doc/src/include.rst
@@ -0,0 +1,52 @@
+.. index:: include
+
+include command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   include file
+
+* file = filename of new input script to switch to
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   include newfile
+   include in.run2
+
+Description
+"""""""""""
+
+This command opens a new input script file and begins reading LAMMPS
+commands from that file.  When the new file is finished, the original
+file is returned to.  Include files can be nested as deeply as
+desired.  If input script A includes script B, and B includes A, then
+LAMMPS could run for a long time.
+
+If the filename is a variable (see the :doc:`variable <variable>`
+command), different processor partitions can run different input
+scripts.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`variable <variable>`, :doc:`jump <jump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/info.rst b/doc/src/info.rst
new file mode 100644
index 0000000000..cc41b49f29
--- /dev/null
+++ b/doc/src/info.rst
@@ -0,0 +1,135 @@
+.. index:: info
+
+info command
+============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   info args
+
+* args = one or more of the following keywords: *out*\ , *all*\ , *system*\ , *memory*\ , *communication*\ , *computes*\ , *dumps*\ , *fixes*\ , *groups*\ , *regions*\ , *variables*\ , *coeffs*\ , *styles*\ , *time*\ , or *configuration*
+* *out* values = *screen*\ , *log*\ , *append* filename, *overwrite* filename
+* *styles* values = *all*\ , *angle*\ , *atom*\ , *bond*\ , *compute*\ , *command*\ , *dump*\ , *dihedral*\ , *fix*\ , *improper*\ , *integrate*\ , *kspace*\ , *minimize*\ , *pair*\ , *region*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   info system
+   info groups computes variables
+   info all out log
+   info all out append info.txt
+   info styles all
+   info styles atom
+
+Description
+"""""""""""
+
+Print out information about the current internal state of the running
+LAMMPS process. This can be helpful when debugging or validating
+complex input scripts.  Several output categories are available and
+one or more output category may be requested.
+
+The *out* flag controls where the output is sent. It can only be sent
+to one target. By default this is the screen, if it is active. The
+*log* argument selects the log file instead. With the *append* and
+*overwrite* option, followed by a filename, the output is written
+to that file, which is either appended to or overwritten, respectively.
+
+The *all* flag activates printing all categories listed below.
+
+The *configuration* category prints some information about the
+LAMMPS version as well as architecture and OS it is run on.
+
+The *memory* category prints some information about the current
+memory allocation of MPI rank 0 (this the amount of dynamically
+allocated memory reported by LAMMPS classes). Where supported,
+also some OS specific information about the size of the reserved
+memory pool size (this is where malloc() and the new operator
+request memory from) and the maximum resident set size is reported
+(this is the maximum amount of physical memory occupied so far).
+
+The *system* category prints a general system overview listing.  This
+includes the unit style, atom style, number of atoms, bonds, angles,
+dihedrals, and impropers and the number of the respective types, box
+dimensions and properties, force computing styles and more.
+
+The *communication* category prints a variety of information about
+communication and parallelization: the MPI library version level,
+the number of MPI ranks and OpenMP threads, the communication style
+and layout, the processor grid dimensions, ghost atom communication
+mode, cutoff, and related settings.
+
+The *computes* category prints a list of all currently defined
+computes, their IDs and styles and groups they operate on.
+
+The *dumps* category prints a list of all currently active dumps,
+their IDs, styles, filenames, groups, and dump frequencies.
+
+The *fixes* category prints a list of all currently defined fixes,
+their IDs and styles and groups they operate on.
+
+The *groups* category prints a list of all currently defined groups.
+
+The *regions* category prints a list of all currently defined regions,
+their IDs and styles and whether "inside" or "outside" atoms are
+selected.
+
+The *variables* category prints a list of all currently defined
+variables, their names, styles, definition and last computed value, if
+available.
+
+The *coeffs* category prints a list for each defined force style
+(pair, bond, angle, dihedral, improper) indicating which of the
+corresponding coefficients have been set. This can be very helpful
+to debug error messages like "All pair coeffs are not set".
+
+The *styles* category prints the list of styles available in the
+current LAMMPS binary. It supports one of the following options
+to control which category of styles is printed out:
+
+* all
+* angle
+* atom
+* bond
+* compute
+* command
+* dump
+* dihedral
+* fix
+* improper
+* integrate
+* kspace
+* minimize
+* pair
+* region
+
+The *time* category prints the accumulated CPU and wall time for the
+process that writes output (usually MPI rank 0).
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`print <print>`
+
+Default
+"""""""
+
+The *out* option has the default *screen*\ .
+
+The *styles* option has the default *all*\ .
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/jump.rst b/doc/src/jump.rst
new file mode 100644
index 0000000000..bd16c9109f
--- /dev/null
+++ b/doc/src/jump.rst
@@ -0,0 +1,163 @@
+.. index:: jump
+
+jump command
+============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   jump file label
+
+* file = filename of new input script to switch to
+* label = optional label within file to jump to
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   jump newfile
+   jump in.run2 runloop
+   jump SELF runloop
+
+Description
+"""""""""""
+
+This command closes the current input script file, opens the file with
+the specified name, and begins reading LAMMPS commands from that file.
+Unlike the :doc:`include <include>` command, the original file is not
+returned to, although by using multiple jump commands it is possible
+to chain from file to file or back to the original file.
+
+If the word "SELF" is used for the filename, then the current input
+script is re-opened and read again.
+
+.. note::
+
+   The SELF option is not guaranteed to work when the current input
+   script is being read through stdin (standard input), e.g.
+
+
+.. parsed-literal::
+
+   lmp_g++ < in.script
+
+since the SELF option invokes the C-library rewind() call, which may
+not be supported for stdin on some systems or by some MPI
+implementations.  This can be worked around by using the :doc:`-in command-line switch <Run_options>`, e.g.
+
+
+.. parsed-literal::
+
+   lmp_g++ -in in.script
+
+or by using the :doc:`-var command-line switch <Run_options>` to pass
+the script name as a variable to the input script.  In the latter
+case, a :doc:`variable <variable>` called "fname" could be used in place
+of SELF, e.g.
+
+
+.. parsed-literal::
+
+   lmp_g++ -var fname in.script < in.script
+
+The 2nd argument to the jump command is optional.  If specified, it is
+treated as a label and the new file is scanned (without executing
+commands) until the label is found, and commands are executed from
+that point forward.  This can be used to loop over a portion of the
+input script, as in this example.  These commands perform 10 runs,
+each of 10000 steps, and create 10 dump files named file.1, file.2,
+etc.  The :doc:`next <next>` command is used to exit the loop after 10
+iterations.  When the "a" variable has been incremented for the tenth
+time, it will cause the next jump command to be skipped.
+
+
+.. parsed-literal::
+
+   variable a loop 10
+   label loop
+   dump 1 all atom 100 file.$a
+   run 10000
+   undump 1
+   next a
+   jump in.lj loop
+
+If the jump *file* argument is a variable, the jump command can be
+used to cause different processor partitions to run different input
+scripts.  In this example, LAMMPS is run on 40 processors, with 4
+partitions of 10 procs each.  An in.file containing the example
+variable and jump command will cause each partition to run a different
+simulation.
+
+
+.. parsed-literal::
+
+   mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
+
+   variable f world script.1 script.2 script.3 script.4
+   jump $f
+
+Here is an example of a loop which checks every 1000 steps if the
+system temperature has reached a certain value, and if so, breaks out
+of the loop to finish the run.  Note that any variable could be
+checked, so long as it is current on the timestep when the run
+completes.  As explained on the :doc:`variable <variable>` doc page,
+this can be insured by including the variable in thermodynamic output.
+
+
+.. parsed-literal::
+
+   variable myTemp equal temp
+   label loop
+   variable a loop 1000
+   run 1000
+   if "${myTemp} < 300.0" then "jump SELF break"
+   next a
+   jump SELF loop
+   label break
+   print "ALL DONE"
+
+Here is an example of a double loop which uses the if and
+:doc:`jump <jump>` commands to break out of the inner loop when a
+condition is met, then continues iterating through the outer loop.
+
+
+.. parsed-literal::
+
+   label       loopa
+   variable    a loop 5
+     label     loopb
+     variable  b loop 5
+     print     "A,B = $a,$b"
+     run       10000
+     if        "$b > 2" then "jump SELF break"
+     next      b
+     jump      in.script loopb
+   label       break
+   variable    b delete
+   next        a
+   jump        SELF loopa
+
+Restrictions
+""""""""""""
+
+
+If you jump to a file and it does not contain the specified label,
+LAMMPS will come to the end of the file and exit.
+
+Related commands
+""""""""""""""""
+
+:doc:`variable <variable>`, :doc:`include <include>`, :doc:`label <label>`,
+:doc:`next <next>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst
new file mode 100644
index 0000000000..9f0b5a6775
--- /dev/null
+++ b/doc/src/kim_commands.rst
@@ -0,0 +1,920 @@
+.. index:: kim\_init
+
+kim\_init command
+=================
+
+kim\_interactions command
+=========================
+
+kim\_query command
+==================
+
+kim\_param command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   kim_init model user_units unitarg
+   kim_interactions typeargs
+   kim_query variable formatarg query_function queryargs
+   kim_param get param_name index_range variables formatarg
+   kim_param set param_name index_range values
+
+.. _formatarg\_options:
+
+
+
+* model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM)
+* user\_units = the LAMMPS :doc:`units <units>` style assumed in the LAMMPS input script
+* unitarg = *unit\_conversion\_mode* (optional)
+* typeargs = atom type to species mapping (one entry per atom type) or *fixed\_types* for models with a preset fixed mapping
+* variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command.
+* formatarg = *list, split, or explicit* (optional):
+  
+  .. parsed-literal::
+  
+     *list* = returns a single string with a list of space separated values
+            (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as
+            defined by the *variable* argument. [default for *kim_query*]
+     *split* = returns the values separately in new variables with names based
+            on the prefix specified in *variable* and a number appended to
+            indicate which element in the list of values is in the variable.
+     *explicit* = returns the values separately in one more more variable names
+            provided as arguments that preceed *formatarg*\ . [default for *kim_param*]
+
+* query\_function = name of the OpenKIM web API query function to be used
+* queryargs = a series of *keyword=value* pairs that represent the web query; supported keywords depend on the query function
+* param\_name = name of a KIM portable model parameter
+* index\_range = KIM portable model parameter index range (an integer for a single element, or pair of integers separated by a colon for a range of elements)
+* values = new value(s) to replace the current value(s) of a KIM portable model parameter
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+   kim_interactions Si
+   kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+   kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode
+   kim_interactions C H O
+   kim_init Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolventsPolymers__SM_039297821658_000 real
+   kim_interactions fixed_types
+   kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Al"] units=["angstrom"]
+   kim_param get gamma 1 varGamma
+   kim_param set gamma 1 3.0
+
+Description
+"""""""""""
+
+The set of *kim\_commands* provide a high-level wrapper around the
+`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
+repository of interatomic models (IMs) (potentials and force fields),
+so that they can be used by LAMMPS scripts.  These commands do not implement
+any computations directly, but rather generate LAMMPS input commands based
+on the information retrieved from the OpenKIM repository to initialize and
+activate OpenKIM IMs and query their predictions for use in the LAMMPS script.
+All LAMMPS input commands generated and executed by *kim\_commands* are
+echoed to the LAMMPS log file.
+
+Benefits of Using OpenKIM IMs
+-----------------------------
+
+Employing OpenKIM IMs provides LAMMPS users with multiple benefits:
+
+Reliability
+^^^^^^^^^^^
+
+* All content archived in OpenKIM is reviewed by the `KIM Editor <https://openkim.org/governance/>`_ for quality.
+* IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded.
+* IMs in OpenKIM are exhaustively tested using `KIM Tests <https://openkim.org/doc/evaluation/kim-tests/>`_ that compute a host of material properties, and `KIM Verification Checks <https://openkim.org/doc/evaluation/kim-verification-checks/>`_ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the  `OpenKIM browse interface <https://openkim.org/browse>`_.
+
+Reproducibility
+^^^^^^^^^^^^^^^
+
+* Each IM in OpenKIM is issued a unique identifier (`KIM ID <https://openkim.org/doc/schema/kim-ids/>`_), which includes a version number (last three digits).  Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID.
+* OpenKIM is a member organization of `DataCite <https://datacite.org/>`_ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility.
+
+Convenience
+^^^^^^^^^^^
+
+* IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the *kim\_init* command documented on this page.
+* The *kim\_query* web query tool provides the ability to use the predictions of IMs for supported material properties (computed via `KIM Tests <https://openkim.org/doc/evaluation/kim-tests/>`_) as part of a LAMMPS input script setup and analysis.
+* Support is provided for unit conversion between the :doc:`unit style <units>` used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units.
+
+.. _IM\_types:
+
+
+
+Types of IMs in OpenKIM
+-----------------------
+
+There are two types of IMs archived in OpenKIM:
+
+.. _PM\_type:
+
+
+
+1. The first type is called a *KIM Portable Model* (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface (`KIM API <https://openkim.org/kim-api/>`_) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see `complete list of supported codes <https://openkim.org/projects-using-kim/>`_).
+2. The second type is called a *KIM Simulator Model* (SM). A KIM SM is an IM that is implemented natively within a simulation code (\ *simulator*\ ) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS.
+
+With these two IM types, OpenKIM can archive and test almost all IMs that
+can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see
+the `upload instructions <https://openkim.org/doc/repository/adding-content/>`_.)
+
+OpenKIM IMs are uniquely identified by a
+`KIM ID <https://openkim.org/doc/schema/kim-ids/>`_.
+The extended KIM ID consists of
+a human-readable prefix identifying the type of IM, authors, publication year,
+and supported species, separated by two underscores from the KIM ID itself,
+which begins with an IM code
+(\ *MO* for a KIM Portable Model, and *SM* for a KIM Simulator Model)
+followed by a unique 12-digit code and a 3-digit version identifier.
+By convention SM prefixes begin with *Sim\_* to readily identify them.
+
+
+.. parsed-literal::
+
+   SW_StillingerWeber_1985_Si__MO_405512056662_005
+   Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+
+Each OpenKIM IM has a dedicated "Model Page" on `OpenKIM <https://openkim.org>`_
+providing all the information on the IM including a title, description,
+authorship and citation information, test and verification check results,
+visualizations of results, a wiki with documentation and user comments, and
+access to raw files, and other information.
+The URL for the Model Page is constructed from the
+`extended KIM ID <https://openkim.org/doc/schema/kim-ids/>`_ of the IM:
+
+
+.. parsed-literal::
+
+   https://openkim.org/id/extended_KIM_ID
+
+For example, for the Stillinger--Weber potential
+listed above the Model Page is located at:
+
+
+.. parsed-literal::
+
+   `https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 <https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005>`_
+
+See the `current list of KIM PMs and SMs archived in OpenKIM <https://openkim.org/browse/models/by-species>`_.
+This list is sorted by species and can be filtered to display only
+IMs for certain species combinations.
+
+See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+
+.. note::
+
+   It is also possible to locally install IMs not archived in OpenKIM,
+   in which case their names do not have to conform to the KIM ID format.
+
+Using OpenKIM IMs with LAMMPS
+-----------------------------
+
+Two commands are employed when using OpenKIM IMs, one to select the
+IM and perform necessary initialization (*kim\_init*), and the second
+to set up the IM for use by executing any necessary LAMMPS commands
+(*kim\_interactions*). Both are required.
+
+See the *examples/kim* directory for example input scripts that use KIM PMs
+and KIM SMs.
+
+OpenKIM IM Initialization (*kim\_init*)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The *kim\_init* mode command must be issued **before**
+the simulation box is created (normally at the top of the file).
+This command sets the OpenKIM IM that will be used and may issue
+additional commands changing LAMMPS default settings that are required
+for using the selected IM (such as :doc:`units <units>` or
+:doc:`atom\_style <atom_style>`). If needed, those settings can be overridden,
+however, typically a script containing a *kim\_init* command
+would not include *units* and *atom\_style* commands.
+
+The required arguments of *kim\_init* are the *model* name of the
+IM to be used in the simulation (for an IM archived in OpenKIM this is
+its `extended KIM ID <https://openkim.org/doc/schema/kim-ids/>`_, and
+the *user\_units*, which are the LAMMPS :doc:`units style <units>` used
+in the input script.  (Any dimensioned numerical values in the input
+script and values read in from files are expected to be in the
+*user\_units* system.)
+
+The selected IM can be either a :ref:`KIM PM or a KIM SM <IM_types>`.
+For a KIM SM, the *kim\_init* command verifies that the SM is designed
+to work with LAMMPS (and not another simulation code).
+In addition, the LAMMPS version used for defining
+the SM and the LAMMPS version being currently run are
+printed to help diagnose any incompatible changes to input script or
+command syntax between the two LAMMPS versions.
+
+Based on the selected model *kim\_init* may modify the
+:doc:`atom\_style <atom_style>`.
+Some SMs have requirements for this setting. If this is the case, then
+*atom\_style* will be set to the required style. Otherwise, the value is left
+unchanged (which in the absence of an *atom\_style* command in the input script
+is the :doc:`default atom\_style value <atom_style>`).
+
+Regarding units, the *kim\_init* command behaves in different ways depending
+on whether or not *unit conversion mode* is activated as indicated by the
+optional *unitarg* argument.
+If unit conversion mode is **not** active, then *user\_units* must
+either match the required units of the IM or the IM must be able
+to adjust its units to match. (The latter is only possible with some KIM PMs;
+SMs can never adjust their units.) If a match is possible, the LAMMPS
+:doc:`units <units>` command is called to set the units to
+*user\_units*. If the match fails, the simulation is terminated with
+an error.
+
+Here is an example of a LAMMPS script to compute the cohesive energy
+of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994)
+potential for Al:
+
+
+.. parsed-literal::
+
+   kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+   boundary         p p p
+   lattice          fcc 4.032
+   region           simbox block 0 1 0 1 0 1 units lattice
+   create_box       1 simbox
+   create_atoms     1 box
+   mass             1 26.981539
+   kim_interactions Al
+   run              0
+   variable         Ec equal (pe/count(all))/${_u_energy}
+   print            "Cohesive Energy = ${EcJ} eV"
+
+The above script will end with an error in the *kim\_init* line if the
+IM is changed to another potential for Al that does not work with *metal*
+units. To address this *kim\_init* offers the *unit\_conversion\_mode*
+as shown below.
+If unit conversion mode *is* active, then *kim\_init* calls the LAMMPS
+:doc:`units <units>` command to set the units to the IM's required or
+preferred units. Conversion factors between the IM's units and the *user\_units*
+are defined for all :doc:`physical quantities <units>` (mass, distance, etc.).
+(Note that converting to or from the "lj" unit style is not supported.)
+These factors are stored as :doc:`internal style variables <variable>` with
+the following standard names:
+
+
+.. parsed-literal::
+
+   _u_mass
+   _u_distance
+   _u_time
+   _u_energy
+   _u_velocity
+   _u_force
+   _u_torque
+   _u_temperature
+   _u_pressure
+   _u_viscosity
+   _u_charge
+   _u_dipole
+   _u_efield
+   _u_density
+
+If desired, the input script can be designed to work with these conversion
+factors so that the script will work without change with any OpenKIM IM.
+(This approach is used in the
+`OpenKIM Testing Framework <https://openkim.org/doc/evaluation/kim-tests/>`_.)
+For example, the script given above for the cohesive energy of fcc Al
+can be rewritten to work with any IM regardless of units. The following
+script constructs an fcc lattice with a lattice parameter defined in
+meters, computes the total energy, and prints the cohesive energy in
+Joules regardless of the units of the IM.
+
+
+.. parsed-literal::
+
+   kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode
+   boundary         p p p
+   lattice          fcc 4.032e-10\*${_u_distance}
+   region           simbox block 0 1 0 1 0 1 units lattice
+   create_box       1 simbox
+   create_atoms     1 box
+   mass             1 4.480134e-26\*${_u_mass}
+   kim_interactions Al
+   run              0
+   variable         Ec_in_J equal (pe/count(all))/${_u_energy}
+   print            "Cohesive Energy = ${Ec_in_J} J"
+
+Note the multiplication by ${\_u_distance} and ${\_u_mass} to convert
+from SI units (specified in the *kim\_init* command) to whatever units the
+IM uses (metal in this case), and the division by ${\_u_energy}
+to convert from the IM's energy units to SI units (Joule). This script
+will work correctly for any IM for Al (KIM PM or SM) selected by the
+*kim\_init* command.
+
+Care must be taken to apply unit conversion to dimensional variables read in
+from a file. For example, if a configuration of atoms is read in from a
+dump file using the :doc:`read\_dump <read_dump>` command, the following can
+be done to convert the box and all atomic positions to the correct units:
+
+
+.. parsed-literal::
+
+   variable xyfinal equal xy\*${_u_distance}
+   variable xzfinal equal xz\*${_u_distance}
+   variable yzfinal equal yz\*${_u_distance}
+   change_box all x scale ${_u_distance} &
+                          y scale ${_u_distance} &
+                          z scale ${_u_distance} &
+                          xy final ${xyfinal} &
+                          xz final ${xzfinal} &
+                          yz final ${yzfinal} &
+                          remap
+
+.. note::
+
+   Unit conversion will only work if the conversion factors are placed in
+   all appropriate places in the input script. It is up to the user to do this
+   correctly.
+
+OpenKIM IM Execution (*kim\_interactions*)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The second and final step in using an OpenKIM IM is to execute the
+*kim\_interactions* command. This command must be preceded by a *kim\_init*
+command and a command that defines the number of atom types *N* (such as
+:doc:`create\_box <create_box>`).
+The *kim\_interactions* command has one argument *typeargs*\ . This argument
+contains either a list of *N* chemical species, which defines a mapping between
+atom types in LAMMPS to the available species in the OpenKIM IM, or the
+keyword *fixed\_types* for models that have a preset fixed mapping (i.e.
+the mapping between LAMMPS atom types and chemical species is defined by
+the model and cannot be changed). In the latter case, the user must consult
+the model documentation to see how many atom types there are and how they
+map to the chemical species.
+
+For example, consider an OpenKIM IM that supports Si and C species.
+If the LAMMPS simulation has four atom types, where the first three are Si,
+and the fourth is C, the following *kim\_interactions* command would be used:
+
+
+.. parsed-literal::
+
+   kim_interactions Si Si Si C
+
+Alternatively, for a model with a fixed mapping the command would be:
+
+
+.. parsed-literal::
+
+   kim_interactions fixed_types
+
+The *kim\_interactions* command performs all the necessary steps to set up
+the OpenKIM IM selected in the *kim\_init* command. The specific actions depend
+on whether the IM is a KIM PM or a KIM SM.  For a KIM PM,
+a :doc:`pair\_style kim <pair_kim>` command is executed followed by
+the appropriate *pair\_coeff* command. For example, for the
+Ercolessi and Adams (1994) KIM PM for Al set by the following commands:
+
+
+.. parsed-literal::
+
+   kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+   ...
+   ...  box specification lines skipped
+   ...
+   kim_interactions Al
+
+the *kim\_interactions* command executes the following LAMMPS input commands:
+
+
+.. parsed-literal::
+
+   pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005
+   pair_coeff \* \* Al
+
+For a KIM SM, the generated input commands may be more complex
+and require that LAMMPS is built with the required packages included
+for the type of potential being used. The set of commands to be executed
+is defined in the SM specification file, which is part of the SM package.
+For example, for the Strachan et al. (2003) ReaxFF SM
+set by the following commands:
+
+
+.. parsed-literal::
+
+   kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+   ...
+   ...  box specification lines skipped
+   ...
+   kim_interactions C H N O
+
+the *kim\_interactions* command executes the following LAMMPS input commands:
+
+
+.. parsed-literal::
+
+   pair_style reax/c lmp_control safezone 2.0 mincap 100
+   pair_coeff \* \* ffield.reax.rdx C H N O
+   fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
+
+Note that the files *lmp\_control*, *ffield.reax.rdx* and *param.qeq*
+are specific to the Strachan et al. (2003) ReaxFF parameterization
+and are archived as part of the SM package in OpenKIM.
+Note also that parameters like cutoff radii and charge tolerances,
+which have an effect on IM predictions, are also included in the
+SM definition ensuring reproducibility.
+
+.. note::
+
+   When using *kim\_init* and *kim\_interactions* to select
+   and set up an OpenKIM IM, other LAMMPS commands
+   for the same functions (such as pair\_style, pair\_coeff, bond\_style,
+   bond\_coeff, fixes related to charge equilibration, etc.) should normally
+   not appear in the input script.
+
+Using OpenKIM Web Queries in LAMMPS (*kim\_query*)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The *kim\_query* command performs a web query to retrieve the predictions
+of an IM set by *kim\_init* for material properties archived in
+`OpenKIM <https://openkim.org>`_.
+
+.. note::
+
+   The *kim\_query* command must be preceded by a *kim\_init* command.
+
+The syntax for the *kim\_query* command is as follows:
+
+
+.. parsed-literal::
+
+   kim_query variable formatarg query_function queryargs
+
+The result of the query is stored in one or more
+:doc:`string style variables <variable>` as determined by the
+optional *formatarg* argument :ref:`documented above <formatarg_options>`.
+For the "list" setting of *formatarg* (or if *formatarg* is not
+specified), the result is returned as a space-separated list of
+values in *variable*\ .
+The *formatarg* keyword "split" separates the result values into
+individual variables of the form *prefix\_I*, where *prefix* is set to the
+*kim\_query* *variable* argument and *I* ranges from 1 to the number of
+returned values. The number and order of the returned values is determined
+by the type of query performed.  (Note that the "explicit" setting of
+*formatarg* is not supported by *kim\_query*.)
+
+.. note::
+
+   *kim\_query* only supports queries that return a single result or
+   an array of values. More complex queries that return a JSON structure
+   are not currently supported. An attempt to use *kim\_query* in such
+   cases will generate an error.
+
+The second required argument *query\_function* is the name of the
+query function to be called (e.g. *get\_lattice\_constant\_cubic*).
+All following :doc:`arguments <Commands_parse>` are parameters handed over to
+the web query in the format *keyword=value*\ , where *value* is always
+an array of one or more comma-separated items in brackets.
+The list of supported keywords and the type and format of their values
+depend on the query function used. The current list of query functions
+is available on the OpenKIM webpage at
+`https://openkim.org/doc/usage/kim-query <https://openkim.org/doc/usage/kim-query>`_.
+
+.. note::
+
+   All query functions require the *model* keyword, which identifies
+   the IM whose predictions are being queried. This keyword is automatically
+   generated by *kim\_query* based on the IM set in *kim\_init* and must not
+   be specified as an argument to *kim\_query*.
+
+.. note::
+
+   Each *query\_function* is associated with a default method (implemented
+   as a `KIM Test <https://openkim.org/doc/evaluation/kim-tests/>`_)
+   used to compute this property. In cases where there are multiple
+   methods in OpenKIM for computing a property, a *method* keyword can
+   be provided to select the method of choice.  See the
+   `query documentation <https://openkim.org/doc/repository/kim-query>`_
+   to see which methods are available for a given *query function*\ .
+
+*kim\_query* Usage Examples and Further Clarifications
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The data obtained by *kim\_query* commands can be used as part of the setup
+or analysis phases of LAMMPS simulations. Some examples are given below.
+
+**Define an equilibrium fcc crystal**
+
+
+.. parsed-literal::
+
+   kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+   boundary         p p p
+   kim_query        a0 get_lattice_constant_cubic crystal=["fcc"] species=["Al"] units=["angstrom"]
+   lattice          fcc ${a0}
+   ...
+
+The *kim\_query* command retrieves from `OpenKIM <https://openkim.org>`_
+the equilibrium lattice constant predicted by the Ercolessi and Adams (1994)
+potential for the fcc structure and places it in
+variable *a0*\ . This variable is then used on the next line to set up the
+crystal. By using *kim\_query*, the user is saved the trouble and possible
+error of tracking this value down, or of having to perform an energy
+minimization to find the equilibrium lattice constant.
+
+Note that in *unit\_conversion\_mode* the results obtained from a
+*kim\_query* would need to be converted to the appropriate units system.
+For example, in the above script, the lattice command would need to be
+changed to: "lattice fcc ${a0}\*${\_u_distance}".
+
+**Define an equilibrium hcp crystal**
+
+
+.. parsed-literal::
+
+   kim_init         EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal
+   boundary         p p p
+   kim_query        latconst split get_lattice_constant_hexagonal crystal=["hcp"] species=["Zr"] units=["angstrom"]
+   variable         a0 equal latconst_1
+   variable         c0 equal latconst_2
+   variable         c_to_a equal ${c0}/${a0}
+   lattice          custom ${a0} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 ${c_to_a} &
+                    basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75
+   ...
+
+In this case the *kim\_query* returns two arguments (since the hexagonal
+close packed (hcp) structure has two independent lattice constants).
+The *formatarg* keyword "split" places the two values into
+the variables *latconst\_1* and *latconst\_2*. (These variables are
+created if they do not already exist.) For convenience the variables
+*a0* and *c0* are created in order to make the remainder of the
+input script more readable.
+
+**Define a crystal at finite temperature accounting for thermal expansion**
+
+
+.. parsed-literal::
+
+   kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+   boundary         p p p
+   kim_query        a0 get_lattice_constant_cubic crystal=["fcc"] species=["Al"] units=["angstrom"]
+   kim_query        alpha get_linear_thermal_expansion_coefficient_cubic  crystal=["fcc"] species=["Al"] units=["1/K"] temperature=[293.15] temperature_units=["K"]
+   variable         DeltaT equal 300
+   lattice          fcc ${a0}\*${alpha}\*${DeltaT}
+   ...
+
+As in the previous example, the equilibrium lattice constant is obtained
+for the Ercolessi and Adams (1994) potential. However, in this case the
+crystal is scaled to the appropriate lattice constant at room temperature
+(293.15 K) by using the linear thermal expansion constant predicted by the
+potential.
+
+.. note::
+
+   When passing numerical values as arguments (as in the case
+   of the temperature in the above example) it is also possible to pass a
+   tolerance indicating how close to the value is considered a match.
+   If no tolerance is passed a default value is used. If multiple results
+   are returned (indicating that the tolerance is too large), *kim\_query*
+   will return an error. See the
+   `query documentation <https://openkim.org/doc/repository/kim-query>`_
+   to see which numerical arguments and tolerances are available for a
+   given *query function*\ .
+
+**Compute defect formation energy**
+
+
+.. parsed-literal::
+
+   kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+   ...
+   ... Build fcc crystal containing some defect and compute the total energy
+   ... which is stored in the variable *Etot*
+   ...
+   kim_query        Ec get_cohesive_energy_cubic crystal=["fcc"] species=["Al"] units=["eV"]
+   variable         Eform equal ${Etot} - count(all)\*${Ec}
+   ...
+
+The defect formation energy *Eform* is computed by subtracting from *Etot* the
+ideal fcc cohesive energy of the atoms in the system obtained from
+`OpenKIM <https://openkim.org>`_ for the Ercolessi and Adams (1994) potential.
+
+.. note::
+
+   *kim\_query* commands return results archived in
+   `OpenKIM <https://openkim.org>`_. These results are obtained
+   using programs for computing material properties
+   (KIM Tests and KIM Test Drivers) that were contributed to OpenKIM.
+   In order to give credit to Test developers, the number of times results
+   from these programs are queried is tracked. No other information about
+   the nature of the query or its source is recorded.
+
+Accessing KIM Model Parameters from LAMMPS (*kim\_param*)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+All IMs are functional forms containing a set of
+parameters.  The values of these parameters are typically
+selected to best reproduce a training set of quantum mechanical
+calculations or available experimental data.  For example, a
+Lennard-Jones potential intended to model argon might have the values of
+its two parameters, epsilon and sigma, fit to the
+dimer dissociation energy or thermodynamic properties at a critical point
+of the phase diagram.
+
+Normally a user employing an IM should not modify its parameters since,
+as noted above, these are selected to reproduce material properties.
+However, there are cases where accessing and modifying IM parameters
+is desired, such as for assessing uncertainty, fitting an IM,
+or working with an ensemble of IMs. As explained :ref:`above <IM_types>`,
+IMs archived in OpenKIM are either Portable Models (PMs) or
+Simulator Models (SMs). KIM PMs are complete independent implementations
+of an IM, whereas KIM SMs are wrappers to an IM implemented within LAMMPS.
+Two different mechanisms are provided for accessing IM parameters in these
+two cases:
+
+* For a KIM PM, the *kim\_param* command can be used to *get* and *set* the values of the PM's parameters as explained below.
+* For a KIM SM, the user should consult the documentation page for the specific IM and follow instructions there for how to modify its parameters (if possible).
+
+The *kim\_param get* and *kim\_param set* commands provide an interface
+to access and change the parameters of a KIM PM that "publishes" its
+parameters and makes them publicly available (see the
+`KIM API documentation <https://kim-api.readthedocs.io/en/devel/features.html>`_
+for details).
+
+.. note::
+
+   The *kim\_param get/set* commands must be preceded by *kim\_init*.
+   The *kim\_param set* command must additionally be preceded by a
+   *kim\_interactions* command (or alternatively by a *pair\_style kim*
+   and *pair\_coeff* commands).  The *kim\_param set* command may be used wherever a *pair\_coeff* command may occur.
+
+The syntax for the *kim\_param* command is as follows:
+
+
+.. parsed-literal::
+
+   kim_param get param_name index_range variable formatarg
+   kim_param set param_name index_range values
+
+Here, *param\_name* is the name of a KIM PM parameter (which is published
+by the PM and available for access). The specific string used to identify
+a parameter is defined by the PM. For example, for the
+`Stillinger--Weber (SW) potential in OpenKIM <https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005>`_,
+the parameter names are *A, B, p, q, sigma, gamma, cutoff, lambda, costheta0*\ .
+
+.. note::
+
+   The list of all the parameters that a PM exposes for access/mutation are
+   automatically written to the lammps log file when *kim\_init* is called.
+
+Each published parameter of a KIM PM takes the form of an array of
+numerical values. The array can contain one element for a single-valued
+parameter, or a set of values. For example, the
+`multispecies SW potential for the Zn-Cd-Hg-S-Se-Te system <https://openkim.org/id/SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002>`_
+has the same parameter names as the
+`single-species SW potential <https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005>`_,
+but each parameter array contains 21 entries that correspond to the parameter
+values used for each pairwise combination of the model's six supported species
+(this model does not have parameters specific to individual ternary
+combinations of its supported species).
+
+The *index\_range* argument may either be an integer referring to
+a specific element within the array associated with the parameter
+specified by *param\_name*, or a pair of integers separated by a colon
+that refer to a slice of this array.  In both cases, one-based indexing is
+used to refer to the entries of the array.
+
+The result of a *get* operation for a specific *index\_range* is stored in
+one or more :doc:`LAMMPS string style variables <variable>` as determined
+by the optional *formatarg* argument :ref:`documented above. <formatarg_options>`
+If not specified, the default for *formatarg* is "explicit" for the
+*kim\_param* command.
+
+For the case where the result is an array with multiple values
+(i.e. *index\_range* contains a range), the optional "split" or "explicit"
+*formatarg* keywords can be used to separate the results into multiple
+variables; see the examples below.
+Multiple parameters can be retrieved with a single call to *kim\_param get*
+by repeating the argument list following *get*\ .
+
+For a *set* operation, the *values* argument contains the new value(s)
+for the element(s) of the parameter specified by *index\_range*. For the case
+where multiple values are being set, *values* contains a set of values
+separated by spaces. Multiple parameters can be set with a single call to
+*kim\_param set* by repeating the argument list following *set*\ .
+
+*kim\_param* Usage Examples and Further Clarifications
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Examples of getting and setting KIM PM parameters with further
+clarifications are provided below.
+
+**Getting a scalar parameter**
+
+
+.. parsed-literal::
+
+   kim_init         SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+   ...
+   kim_param        get A 1 VARA
+
+In this case, the value of the SW *A* parameter is retrieved and placed
+in the LAMMPS variable *VARA*\ . The variable *VARA* can be used
+in the remainder of the input script in the same manner as any other
+LAMMPS variable.
+
+**Getting multiple scalar parameters with a single call**
+
+
+.. parsed-literal::
+
+   kim_init         SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+   ...
+   kim_param        get A 1 VARA B 1 VARB
+
+This retrieves the *A* and *B* parameters of the SW potential and stores
+them in the LAMMPS variables *VARA* and *VARB*\ .
+
+**Getting a range of values from a parameter**
+
+There are several options when getting a range of values from a parameter
+determined by the *formatarg* argument.
+
+
+.. parsed-literal::
+
+   kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+   ...
+   kim_param        get lambda 7:9 LAM_TeTe LAM_TeZn LAM_TeSe
+
+In this case, *formatarg* is not specified and therefore the default
+"explicit" mode is used. (The behavior would be the same if the word
+*explicit* were added after *LAM\_TeSe*.) Elements 7, 8 and 9 of parameter
+lambda retrieved by the *get* operation are placed in the LAMMPS variables
+*LAM\_TeTe*, *LAM\_TeZn* and *LAM\_TeSe*, respectively.
+
+.. note::
+
+   In the above example, elements 7--9 of the lambda parameter correspond
+   to Te-Te, Te-Zm and Te-Se interactions. This can be determined by visiting
+   the `model page for the specified potential <https://openkim.org/id/SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002>`_
+   and looking at its parameter file linked to at the bottom of the page
+   (file with .param ending) and consulting the README documentation
+   provided with the driver for the PM being used. A link to the driver
+   is provided at the top of the model page.
+
+
+.. parsed-literal::
+
+   kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+   ...
+   kim_param        get lambda 15:17 LAMS list
+   variable         LAM_VALUE index ${LAMS}
+   label            loop_on_lambda
+   ...
+   ... do something with current value of lambda
+   ...
+   next             LAM_VALUE
+   jump             SELF loop_on_lambda
+
+In this case, the "list" mode of *formatarg* is used.
+The result of the *get* operation is stored in the LAMMPS variable
+*LAMS* as a string containing the three retrieved values separated
+by spaces, e.g "1.0 2.0 3.0". This can be used in LAMMPS with an
+*index* variable to access the values one at a time within a loop
+as shown in the example. At each iteration of the loop *LAM\_VALUE*
+contains the current value of lambda.
+
+
+.. parsed-literal::
+
+   kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+   ...
+   kim_param        get lambda 15:17 LAM split
+
+In this case, the "split" mode of *formatarg* is used.
+The three values retrieved by the *get* operation are stored in
+the three LAMMPS variables *LAM\_15*, *LAM\_16* and *LAM\_17*.
+The provided name "LAM" is used as prefix and the location in
+the lambda array is appended to create the variable names.
+
+**Setting a scalar parameter**
+
+
+.. parsed-literal::
+
+   kim_init         SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+   ...
+   kim_interactions Si
+   kim_param        set gamma 1 2.6
+
+Here, the SW potential's gamma parameter is set to 2.6.  Note that the *get*
+and *set* commands work together, so that a *get* following a *set*
+operation will return the new value that was set. For example:
+
+
+.. parsed-literal::
+
+   ...
+   kim_interactions Si
+   kim_param        get gamma 1 ORIG_GAMMA
+   kim_param        set gamma 1 2.6
+   kim_param        get gamma 1 NEW_GAMMA
+   ...
+   print            "original gamma = ${ORIG_GAMMA}, new gamma = ${NEW_GAMMA}"
+
+Here, *ORIG\_GAMMA* will contain the original gamma value for the SW
+potential, while *NEW\_GAMMA* will contain the value 2.6.
+
+**Setting multiple scalar parameters with a single call**
+
+
+.. parsed-literal::
+
+   kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+   ...
+   kim_interactions Cd Te
+   variable        VARG equal 2.6
+   variable        VARS equal 2.0951
+   kim_param       set gamma 1 ${VARG} sigma 3 ${VARS}
+
+In this case, the first element of the *gamma* parameter and
+third element of the *sigma* parameter are set to 2.6 and 2.0951,
+respectively. This example also shows how LAMMPS variables can
+be used when setting parameters.
+
+**Setting a range of values of a parameter**
+
+
+.. parsed-literal::
+
+   kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+   ...
+   kim_interactions Cd Te Zn Se Hg S
+   kim_param        set sigma 2:6 2.35214 2.23869 2.04516 2.43269 1.80415
+
+In this case, elements 2 through 6 of the parameter *sigma*
+are set to the values 2.35214, 2.23869, 2.04516, 2.43269 and 1.80415 in
+order.
+
+Citation of OpenKIM IMs
+-----------------------
+
+When publishing results obtained using OpenKIM IMs researchers are requested
+to cite the OpenKIM project :ref:`(Tadmor) <kim-mainpaper>`, KIM API
+:ref:`(Elliott) <kim-api>`, and the specific IM codes used in the simulations,
+in addition to the relevant scientific references for the IM.
+The citation format for an IM is displayed on its page on
+`OpenKIM <https://openkim.org>`_ along with the corresponding BibTex file,
+and is automatically added to the LAMMPS *log.cite* file.
+
+Citing the IM software (KIM infrastructure and specific PM or SM codes)
+used in the simulation gives credit to the researchers who developed them
+and enables open source efforts like OpenKIM to function.
+
+Restrictions
+""""""""""""
+
+
+The set of *kim\_commands* is part of the KIM package.  It is only enabled if
+LAMMPS is built with that package. A requirement for the KIM package,
+is the KIM API library that must be downloaded from the
+`OpenKIM website <https://openkim.org/kim-api/>`_ and installed before
+LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed. See the KIM
+section of the :doc:`Packages details <Packages_details>` for details.
+
+Furthermore, when using *kim\_commands* to run KIM SMs, any packages required
+by the native potential being used or other commands or fixes that it invokes
+must be installed.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style kim <pair_kim>`
+
+
+----------
+
+
+.. _kim-mainpaper:
+
+
+
+**(Tadmor)** Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011).
+doi: `https://doi.org/10.1007/s11837-011-0102-6 <https://doi.org/10.1007/s11837-011-0102-6>`_
+
+.. _kim-api:
+
+
+
+**(Elliott)** Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011)
+doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst
new file mode 100644
index 0000000000..5f4dad4dcd
--- /dev/null
+++ b/doc/src/kspace_modify.rst
@@ -0,0 +1,567 @@
+.. index:: kspace\_modify
+
+kspace\_modify command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   kspace_modify keyword value ...
+
+* one or more keyword/value pairs may be listed
+* keyword = *collective* or *compute* or *cutoff/adjust* or *diff* or *disp/auto* or *fftbench* or *force/disp/kspace* or *force/disp/real* or *force* or *gewald/disp* or *gewald* or *kmax/ewald* or *mesh* or *minorder* or *mix/disp* or *order/disp* or *order* or *overlap* or *scafacos* or *slab* or *splittol*
+  
+  .. parsed-literal::
+  
+       *collective* value = *yes* or *no*
+       *compute* value = *yes* or *no*
+       *cutoff/adjust* value = *yes* or *no*
+       *diff* value = *ad* or *ik* = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
+       *disp/auto* value = yes or no
+       *fftbench* value = *yes* or *no*
+       *force/disp/real* value = accuracy (force units)
+       *force/disp/kspace* value = accuracy (force units)
+       *force* value = accuracy (force units)
+       *gewald* value = rinv (1/distance units)
+         rinv = G-ewald parameter for Coulombics
+       *gewald/disp* value = rinv (1/distance units)
+         rinv = G-ewald parameter for dispersion
+       *kmax/ewald* value = kx ky kz
+         kx,ky,kz = number of Ewald sum kspace vectors in each dimension
+       *mesh* value = x y z
+         x,y,z = grid size in each dimension for long-range Coulombics
+       *mesh/disp* value = x y z
+         x,y,z = grid size in each dimension for 1/r\^6 dispersion
+       *minorder* value = M
+         M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
+       *mix/disp* value = *pair* or *geom* or *none*
+       *order* value = N
+         N = extent of Gaussian for PPPM or MSM mapping of charge to grid
+       *order/disp* value = N
+         N = extent of Gaussian for PPPM mapping of dispersion term to grid
+       *overlap* = *yes* or *no* = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
+       *pressure/scalar* value = *yes* or *no*
+       *scafacos* values = option value1 value2 ...
+         option = *tolerance*
+           value = *energy* or *energy_rel* or *field* or *field_rel* or *potential* or *potential_rel*
+         option = *fmm_tuning*
+           value = *0* or *1*
+       *slab* value = volfactor or *nozforce*
+         volfactor = ratio of the total extended volume used in the
+           2d approximation compared with the volume of the simulation domain
+         *nozforce* turns off kspace forces in the z direction
+       *splittol* value = tol
+         tol = relative size of two eigenvalues (see discussion below)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   kspace_modify mesh 24 24 30 order 6
+   kspace_modify slab 3.0
+   kspace_modify scafacos tolerance energy
+
+Description
+"""""""""""
+
+Set parameters used by the kspace solvers defined by the
+:doc:`kspace\_style <kspace_style>` command.  Not all parameters are
+relevant to all kspace styles.
+
+
+----------
+
+
+The *collective* keyword applies only to PPPM.  It is set to *no* by
+default, except on IBM BlueGene machines.  If this option is set to
+*yes*\ , LAMMPS will use MPI collective operations to remap data for
+3d-FFT operations instead of the default point-to-point communication.
+This is faster on IBM BlueGene machines, and may also be faster on
+other machines if they have an efficient implementation of MPI
+collective operations and adequate hardware.
+
+
+----------
+
+
+The *compute* keyword allows Kspace computations to be turned off,
+even though a :doc:`kspace\_style <kspace_style>` is defined.  This is
+not useful for running a real simulation, but can be useful for
+debugging purposes or for computing only partial forces that do not
+include the Kspace contribution.  You can also do this by simply not
+defining a :doc:`kspace\_style <kspace_style>`, but a Kspace-compatible
+:doc:`pair\_style <pair_style>` requires a kspace style to be defined.
+This keyword gives you that option.
+
+
+----------
+
+
+The *cutoff/adjust* keyword applies only to MSM. If this option is
+turned on, the Coulombic cutoff will be automatically adjusted at the
+beginning of the run to give the desired estimated error. Other
+cutoffs such as LJ will not be affected. If the grid is not set using
+the *mesh* command, this command will also attempt to use the optimal
+grid that minimizes cost using an estimate given by
+:ref:`(Hardy) <Hardy1>`. Note that this cost estimate is not exact, somewhat
+experimental, and still may not yield the optimal parameters.
+
+
+----------
+
+
+The *diff* keyword specifies the differentiation scheme used by the
+PPPM method to compute forces on particles given electrostatic
+potentials on the PPPM mesh.  The *ik* approach is the default for
+PPPM and is the original formulation used in :ref:`(Hockney) <Hockney1>`.  It
+performs differentiation in Kspace, and uses 3 FFTs to transfer each
+component of the computed fields back to real space for total of 4
+FFTs per timestep.
+
+The analytic differentiation *ad* approach uses only 1 FFT to transfer
+information back to real space for a total of 2 FFTs per timestep.  It
+then performs analytic differentiation on the single quantity to
+generate the 3 components of the electric field at each grid point.
+This is sometimes referred to as "smoothed" PPPM.  This approach
+requires a somewhat larger PPPM mesh to achieve the same accuracy as
+the *ik* method. Currently, only the *ik* method (default) can be
+used for a triclinic simulation cell with PPPM. The *ad* method is
+always used for MSM.
+
+.. note::
+
+   Currently, not all PPPM styles support the *ad* option.  Support
+   for those PPPM variants will be added later.
+
+
+----------
+
+
+The *disp/auto* option controls whether the pppm/disp is allowed to
+generate PPPM parameters automatically. If set to *no*\ , parameters have
+to be specified using the *gewald/disp*\ , *mesh/disp*\ ,
+*force/disp/real* or *force/disp/kspace* keywords, or
+the code will stop with an error message. When this option is set to
+*yes*\ , the error message will not appear and the simulation will start.
+For a typical application, using the automatic parameter generation
+will provide simulations that are either inaccurate or slow. Using this
+option is thus not recommended. For guidelines on how to obtain good
+parameters, see the :doc:`How-To <Howto_dispersion>` discussion.
+
+
+----------
+
+
+The *fftbench* keyword applies only to PPPM. It is off by default. If
+this option is turned on, LAMMPS will perform a short FFT benchmark
+computation and report its timings, and will thus finish a some seconds
+later than it would if this option were off.
+
+
+----------
+
+
+The *force/disp/real* and *force/disp/kspace* keywords set the force
+accuracy for the real and space computations for the dispersion part
+of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`, optimal
+performance and accuracy in the results is obtained when these values
+are different.
+
+
+----------
+
+
+The *force* keyword overrides the relative accuracy parameter set by
+the :doc:`kspace\_style <kspace_style>` command with an absolute
+accuracy.  The accuracy determines the RMS error in per-atom forces
+calculated by the long-range solver and is thus specified in force
+units.  A negative value for the accuracy setting means to use the
+relative accuracy parameter.  The accuracy setting is used in
+conjunction with the pairwise cutoff to determine the number of
+K-space vectors for style *ewald*\ , the FFT grid size for style
+*pppm*\ , or the real space grid size for style *msm*\ .
+
+
+----------
+
+
+The *gewald* keyword sets the value of the Ewald or PPPM G-ewald
+parameter for charge as *rinv* in reciprocal distance units.  Without
+this setting, LAMMPS chooses the parameter automatically as a function
+of cutoff, precision, grid spacing, etc.  This means it can vary from
+one simulation to the next which may not be desirable for matching a
+KSpace solver to a pre-tabulated pairwise potential.  This setting can
+also be useful if Ewald or PPPM fails to choose a good grid spacing
+and G-ewald parameter automatically.  If the value is set to 0.0,
+LAMMPS will choose the G-ewald parameter automatically.  MSM does not
+use the *gewald* parameter.
+
+
+----------
+
+
+The *gewald/disp* keyword sets the value of the Ewald or PPPM G-ewald
+parameter for dispersion as *rinv* in reciprocal distance units.  It
+has the same meaning as the *gewald* setting for Coulombics.
+
+
+----------
+
+
+The *kmax/ewald* keyword sets the number of kspace vectors in each
+dimension for kspace style *ewald*\ .  The three values must be positive
+integers, or else (0,0,0), which unsets the option.  When this option
+is not set, the Ewald sum scheme chooses its own kspace vectors,
+consistent with the user-specified accuracy and pairwise cutoff. In
+any case, if kspace style *ewald* is invoked, the values used are
+printed to the screen and the log file at the start of the run.
+
+
+----------
+
+
+The *mesh* keyword sets the grid size for kspace style *pppm* or
+*msm*\ .  In the case of PPPM, this is the FFT mesh, and each dimension
+must be factorizable into powers of 2, 3, and 5.  In the case of MSM,
+this is the finest scale real-space mesh, and each dimension must be
+factorizable into powers of 2.  When this option is not set, the PPPM
+or MSM solver chooses its own grid size, consistent with the
+user-specified accuracy and pairwise cutoff.  Values for x,y,z of
+0,0,0 unset the option.
+
+
+----------
+
+
+The *mesh/disp* keyword sets the grid size for kspace style
+*pppm/disp*\ .  This is the FFT mesh for long-range dispersion and ach
+dimension must be factorizable into powers of 2, 3, and 5.  When this
+option is not set, the PPPM solver chooses its own grid size,
+consistent with the user-specified accuracy and pairwise cutoff.
+Values for x,y,z of 0,0,0 unset the option.
+
+
+----------
+
+
+The *minorder* keyword allows LAMMPS to reduce the *order* setting if
+necessary to keep the communication of ghost grid point limited to
+exchanges between nearest-neighbor processors.  See the discussion of
+the *overlap* keyword for details.  If the *overlap* keyword is set to
+*yes*\ , which is the default, this is never needed.  If it set to *no*
+and overlap occurs, then LAMMPS will reduce the order setting, one
+step at a time, until the ghost grid overlap only extends to nearest
+neighbor processors.  The *minorder* keyword limits how small the
+*order* setting can become.  The minimum allowed value for PPPM is 2,
+which is the default.  If *minorder* is set to the same value as
+*order* then no reduction is allowed, and LAMMPS will generate an
+error if the grid communication is non-nearest-neighbor and *overlap*
+is set to *no*\ . The *minorder* keyword is not currently supported in
+MSM.
+
+
+----------
+
+
+The *mix/disp* keyword selects the mixing rule for the dispersion
+coefficients.  With *pair*\ , the dispersion coefficients of unlike
+types are computed as indicated with :doc:`pair\_modify <pair_modify>`.
+With *geom*\ , geometric mixing is enforced on the dispersion
+coefficients in the kspace coefficients. When using the arithmetic
+mixing rule, this will speed-up the simulations but introduces some
+error in the force computations, as shown in :ref:`(Wennberg) <Wennberg>`.
+With *none*\ , it is assumed that no mixing rule is
+applicable. Splitting of the dispersion coefficients will be performed
+as described in :ref:`(Isele-Holder) <Isele-Holder1>`.
+
+This splitting can be influenced with the *splittol* keywords.  Only
+the eigenvalues that are larger than tol compared to the largest
+eigenvalues are included. Using this keywords the original matrix of
+dispersion coefficients is approximated. This leads to faster
+computations, but the accuracy in the reciprocal space computations of
+the dispersion part is decreased.
+
+
+----------
+
+
+The *order* keyword determines how many grid spacings an atom's charge
+extends when it is mapped to the grid in kspace style *pppm* or *msm*\ .
+The default for this parameter is 5 for PPPM and 8 for MSM, which
+means each charge spans 5 or 8 grid cells in each dimension,
+respectively.  For the LAMMPS implementation of MSM, the order can
+range from 4 to 10 and must be even. For PPPM, the minimum allowed
+setting is 2 and the maximum allowed setting is 7.  The larger the
+value of this parameter, the smaller that LAMMPS will set the grid
+size, to achieve the requested accuracy.  Conversely, the smaller the
+order value, the larger the grid size will be.  Note that there is an
+inherent trade-off involved: a small grid will lower the cost of FFTs
+or MSM direct sum, but a larger order parameter will increase the cost
+of interpolating charge/fields to/from the grid.
+
+The PPPM order parameter may be reset by LAMMPS when it sets up the
+FFT grid if the implied grid stencil extends beyond the grid cells
+owned by neighboring processors.  Typically this will only occur when
+small problems are run on large numbers of processors.  A warning will
+be generated indicating the order parameter is being reduced to allow
+LAMMPS to run the problem. Automatic adjustment of the order parameter
+is not supported in MSM.
+
+
+----------
+
+
+The *order/disp* keyword determines how many grid spacings an atom's
+dispersion term extends when it is mapped to the grid in kspace style
+*pppm/disp*\ .  It has the same meaning as the *order* setting for
+Coulombics.
+
+
+----------
+
+
+The *overlap* keyword can be used in conjunction with the *minorder*
+keyword with the PPPM styles to adjust the amount of communication
+that occurs when values on the FFT grid are exchanged between
+processors.  This communication is distinct from the communication
+inherent in the parallel FFTs themselves, and is required because
+processors interpolate charge and field values using grid point values
+owned by neighboring processors (i.e. ghost point communication).  If
+the *overlap* keyword is set to *yes* then this communication is
+allowed to extend beyond nearest-neighbor processors, e.g. when using
+lots of processors on a small problem.  If it is set to *no* then the
+communication will be limited to nearest-neighbor processors and the
+*order* setting will be reduced if necessary, as explained by the
+*minorder* keyword discussion. The *overlap* keyword is always set to
+*yes* in MSM.
+
+
+----------
+
+
+The *pressure/scalar* keyword applies only to MSM. If this option is
+turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
+be computed, which can be used, for example, to run an isotropic barostat.
+Computing the full pressure tensor with MSM is expensive, and this option
+provides a faster alternative. The scalar pressure is computed using a
+relationship between the Coulombic energy and pressure :ref:`(Hummer) <Hummer>`
+instead of using the virial equation. This option cannot be used to access
+individual components of the pressure tensor, to compute per-atom virial,
+or with suffix kspace/pair styles of MSM, like OMP or GPU.
+
+
+----------
+
+
+The *scafacos* keyword is used for settings that are passed to the
+ScaFaCoS library when using :doc:`kspace\_style scafacos <kspace_style>`.
+
+The *tolerance* option affects how the *accuracy* specified with the
+:doc:`kspace\_style <kspace_style>` command is interpreted by ScaFaCoS.
+The following values may be used:
+
+* energy = absolute accuracy in total Coulombic energy
+* energy\_rel = relative accuracy in total Coulombic energy
+* potential = absolute accuracy in total Coulombic potential
+* potential\_rel = relative accuracy in total Coulombic potential
+* field = absolute accuracy in electric field
+* field\_rel = relative accuracy in electric field
+
+The values with suffix \_rel indicate the tolerance is a relative
+tolerance; the other values impose an absolute tolerance on the given
+quantity. Absolute tolerance in this case means, that for a given
+quantity q and a given absolute tolerance of t\_a the result should
+be between q-t\_a and q+t\_a. For a relative tolerance t\_r the relative
+error should not be greater than t\_r, i.e. abs(1 - (result/q)) < t\_r.
+As a consequence of this, the tolerance type should be checked, when
+performing computations with a high absolute field / energy. E.g.
+if the total energy in the system is 1000000.0 an absolute tolerance
+of 1e-3 would mean that the result has to be between 999999.999 and
+1000000.001, which would be equivalent to a relative tolerance of
+1e-9.
+
+The energy and energy\_rel values, set a tolerance based on the total
+Coulombic energy of the system.  The potential and potential\_rel set a
+tolerance based on the per-atom Coulombic energy.  The field and
+field\_rel tolerance types set a tolerance based on the electric field
+values computed by ScaFaCoS.  Since per-atom forces are derived from
+the per-atom electric field, this effectively sets a tolerance on the
+forces, similar to other LAMMPS KSpace styles, as explained on the
+:doc:`kspace\_style <kspace_style>` doc page.
+
+Note that not all ScaFaCoS solvers support all tolerance types.
+These are the allowed values for each method:
+
+* fmm = energy and energy\_rel
+* p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic)
+* p3m = field
+* ewald = field
+* direct = has no tolerance tuning
+
+If the tolerance type is not changed, the default values for the
+tolerance type are the first values in the above list, e.g. energy
+is the default tolerance type for the fmm solver.
+
+The *fmm\_tuning* option is only relevant when using the FMM method.
+It activates (value=1) or deactivates (value=0) an internal tuning
+mechanism for the FMM solver.  The tuning operation runs sequentially
+and can be very time-consuming.  Usually it is not needed for systems
+with a homogeneous charge distribution. The default for this option is
+therefore *0*\ . The FMM internal tuning is performed once, when the
+solver is set up.
+
+
+----------
+
+
+The *slab* keyword allows an Ewald or PPPM solver to be used for a
+systems that are periodic in x,y but non-periodic in z - a
+:doc:`boundary <boundary>` setting of "boundary p p f".  This is done by
+treating the system as if it were periodic in z, but inserting empty
+volume between atom slabs and removing dipole inter-slab interactions
+so that slab-slab interactions are effectively turned off.  The
+volfactor value sets the ratio of the extended dimension in z divided
+by the actual dimension in z.  The recommended value is 3.0.  A larger
+value is inefficient; a smaller value introduces unwanted slab-slab
+interactions.  The use of fixed boundaries in z means that the user
+must prevent particle migration beyond the initial z-bounds, typically
+by providing a wall-style fix.  The methodology behind the *slab*
+option is explained in the paper by :ref:`(Yeh) <Yeh>`.  The *slab* option
+is also extended to non-neutral systems :ref:`(Ballenegger) <Ballenegger>`.
+
+An alternative slab option can be invoked with the *nozforce* keyword
+in lieu of the volfactor.  This turns off all kspace forces in the z
+direction.  The *nozforce* option is not supported by MSM. For MSM,
+any combination of periodic, non-periodic, or shrink-wrapped
+boundaries can be set using :doc:`boundary <boundary>` (the slab
+approximation in not needed).  The *slab* keyword is not currently
+supported by Ewald or PPPM when using a triclinic simulation cell. The
+slab correction has also been extended to point dipole interactions
+:ref:`(Klapp) <Klapp>` in :doc:`kspace\_style <kspace_style>` *ewald/disp*\ ,
+*ewald/dipole*\ , and *pppm/dipole*\ .
+
+.. note::
+
+   If you wish to apply an electric field in the Z-direction, in
+   conjunction with the *slab* keyword, you should do it by adding
+   explicit charged particles to the +/- Z surfaces.  If you do it via
+   the :doc:`fix efield <fix_efield>` command, it will not give the correct
+   dielectric constant due to the Yeh/Berkowitz :ref:`(Yeh) <Yeh>` correction
+   not being compatible with how :doc:`fix efield <fix_efield>` works.
+
+
+----------
+
+
+The *force/disp/real* and *force/disp/kspace* keywords set the force
+accuracy for the real and space computations for the dispersion part
+of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`, optimal
+performance and accuracy in the results is obtained when these values
+are different.
+
+The *disp/auto* option controls whether the pppm/disp is allowed to
+generate PPPM parameters automatically. If set to *no*\ , parameters
+have to be specified using the *gewald/disp*\ , *mesh/disp*\ ,
+*force/disp/real* or *force/disp/kspace* keywords, or the code will
+stop with an error message. When this option is set to *yes*\ , the
+error message will not appear and the simulation will start.  For a
+typical application, using the automatic parameter generation will
+provide simulations that are either inaccurate or slow. Using this
+option is thus not recommended.  For guidelines on how to obtain good
+parameters, see the :doc:`Howto dispersion <Howto_dispersion>` doc page.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`kspace\_style <kspace_style>`, :doc:`boundary <boundary>`
+
+Default
+"""""""
+
+The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
+5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
+gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
+yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff =
+ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace
+= -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel,
+order = order/disp = 7.  For scafacos settings, the scafacos tolerance
+option depends on the method chosen, as documented above.  The
+scafacos fmm\_tuning default = 0.
+
+
+----------
+
+
+.. _Hockney1:
+
+
+
+**(Hockney)** Hockney and Eastwood, Computer Simulation Using Particles,
+Adam Hilger, NY (1989).
+
+.. _Yeh:
+
+
+
+**(Yeh)** Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
+
+.. _Ballenegger:
+
+
+
+**(Ballenegger)** Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
+(2009).
+
+.. _Klapp:
+
+
+
+**(Klapp)** Klapp, Schoen, J Chem Phys, 117, 8050 (2002).
+
+.. _Hardy1:
+
+
+
+**(Hardy)** David Hardy thesis: Multilevel Summation for the Fast
+Evaluation of Forces for the Simulation of Biomolecules, University of
+Illinois at Urbana-Champaign, (2006).
+
+.. _Hummer:
+
+
+
+**(Hummer)** Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)
+
+.. _Isele-Holder1:
+
+
+
+**(Isele-Holder)** Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
+Chem Theory Comput, 9, 5412 (2013).
+
+.. _Wennberg:
+
+
+
+**(Wennberg)** Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
+9, 3527 (2013).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst
new file mode 100644
index 0000000000..32179f8be0
--- /dev/null
+++ b/doc/src/kspace_style.rst
@@ -0,0 +1,597 @@
+.. index:: kspace\_style
+
+kspace\_style command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   kspace_style style value
+
+* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
+
+  .. parsed-literal::
+
+       *none* value = none
+       *ewald* value = accuracy
+         accuracy = desired relative error in forces
+       *ewald/dipole* value = accuracy
+         accuracy = desired relative error in forces
+       *ewald/dipole/spin* value = accuracy
+         accuracy = desired relative error in forces
+       *ewald/disp* value = accuracy
+         accuracy = desired relative error in forces
+       *ewald/omp* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/cg* values = accuracy (smallq)
+         accuracy = desired relative error in forces
+         smallq = cutoff for charges to be considered (optional) (charge units)
+       *pppm/dipole* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/dipole/spin* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/disp* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/tip4p* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/disp/tip4p* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/gpu* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/intel* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/disp/intel* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/kk* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/omp* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/cg/omp* values = accuracy (smallq)
+         accuracy = desired relative error in forces
+         smallq = cutoff for charges to be considered (optional) (charge units)
+       *pppm/disp/omp* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/tip4p/omp* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/disp/tip4p/omp* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/stagger* value = accuracy
+         accuracy = desired relative error in forces
+       *msm* value = accuracy
+         accuracy = desired relative error in forces
+       *msm/cg* value = accuracy (smallq)
+         accuracy = desired relative error in forces
+         smallq = cutoff for charges to be considered (optional) (charge units)
+       *msm/omp* value = accuracy
+         accuracy = desired relative error in forces
+       *msm/cg/omp* value = accuracy (smallq)
+         accuracy = desired relative error in forces
+         smallq = cutoff for charges to be considered (optional) (charge units)
+       *scafacos* values = method accuracy
+         method = fmm or p2nfft or p3m or ewald or direct
+         accuracy = desired relative error in forces
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   kspace_style pppm 1.0e-4
+   kspace_style pppm/cg 1.0e-5 1.0e-6
+   kspace style msm 1.0e-4
+   kspace style scafacos fmm 1.0e-4
+   kspace_style none
+
+Description
+"""""""""""
+
+Define a long-range solver for LAMMPS to use each timestep to compute
+long-range Coulombic interactions or long-range 1/r\^6 interactions.
+Most of the long-range solvers perform their computation in K-space,
+hence the name of this command.
+
+When such a solver is used in conjunction with an appropriate pair
+style, the cutoff for Coulombic or 1/r\^N interactions is effectively
+infinite.  If the Coulombic case, this means each charge in the system
+interacts with charges in an infinite array of periodic images of the
+simulation domain.
+
+Note that using a long-range solver requires use of a matching :doc:`pair style <pair_style>` to perform consistent short-range pairwise
+calculations.  This means that the name of the pair style contains a
+matching keyword to the name of the KSpace style, as in this table:
+
++----------------------+-----------------------+
+| Pair style           | KSpace style          |
++----------------------+-----------------------+
+| coul/long            | ewald or pppm         |
++----------------------+-----------------------+
+| coul/msm             | msm                   |
++----------------------+-----------------------+
+| lj/long or buck/long | disp (for dispersion) |
++----------------------+-----------------------+
+| tip4p/long           | tip4p                 |
++----------------------+-----------------------+
+
+
+----------
+
+
+The *ewald* style performs a standard Ewald summation as described in
+any solid-state physics text.
+
+The *ewald/disp* style adds a long-range dispersion sum option for
+1/r\^6 potentials and is useful for simulation of interfaces
+:ref:`(Veld) <Veld>`.  It also performs standard Coulombic Ewald summations,
+but in a more efficient manner than the *ewald* style.  The 1/r\^6
+capability means that Lennard-Jones or Buckingham potentials can be
+used without a cutoff, i.e. they become full long-range potentials.
+The *ewald/disp* style can also be used with point-dipoles, see
+:ref:`(Toukmaji) <Toukmaji>`.
+
+The *ewald/dipole* style adds long-range standard Ewald summations
+for dipole-dipole interactions, see :ref:`(Toukmaji) <Toukmaji>`.
+
+The *ewald/dipole/spin* style adds long-range standard Ewald
+summations for magnetic dipole-dipole interactions between
+magnetic spins.
+
+
+----------
+
+
+The *pppm* style invokes a particle-particle particle-mesh solver
+:ref:`(Hockney) <Hockney>` which maps atom charge to a 3d mesh, uses 3d FFTs
+to solve Poisson's equation on the mesh, then interpolates electric
+fields on the mesh points back to the atoms.  It is closely related to
+the particle-mesh Ewald technique (PME) :ref:`(Darden) <Darden>` used in
+AMBER and CHARMM.  The cost of traditional Ewald summation scales as
+N\^(3/2) where N is the number of atoms in the system.  The PPPM solver
+scales as Nlog(N) due to the FFTs, so it is almost always a faster
+choice :ref:`(Pollock) <Pollock>`.
+
+The *pppm/cg* style is identical to the *pppm* style except that it
+has an optimization for systems where most particles are uncharged.
+Similarly the *msm/cg* style implements the same optimization for *msm*\ .
+The optional *smallq* argument defines the cutoff for the absolute
+charge value which determines whether a particle is considered charged
+or not.  Its default value is 1.0e-5.
+
+The *pppm/dipole* style invokes a particle-particle particle-mesh solver
+for dipole-dipole interactions, following the method of :ref:`(Cerda) <Cerda2008>`.
+
+The *pppm/dipole/spin* style invokes a particle-particle particle-mesh solver
+for magnetic dipole-dipole interactions between magnetic spins.
+
+The *pppm/tip4p* style is identical to the *pppm* style except that it
+adds a charge at the massless 4th site in each TIP4P water molecule.
+It should be used with :doc:`pair styles <pair_style>` with a
+*tip4p/long* in their style name.
+
+The *pppm/stagger* style performs calculations using two different
+meshes, one shifted slightly with respect to the other.  This can
+reduce force aliasing errors and increase the accuracy of the method
+for a given mesh size.  Or a coarser mesh can be used for the same
+target accuracy, which saves CPU time.  However, there is a trade-off
+since FFTs on two meshes are now performed which increases the
+computation required.  See :ref:`(Cerutti) <Cerutti>`, :ref:`(Neelov) <Neelov>`,
+and :ref:`(Hockney) <Hockney>` for details of the method.
+
+For high relative accuracy, using staggered PPPM allows the mesh size
+to be reduced by a factor of 2 in each dimension as compared to
+regular PPPM (for the same target accuracy).  This can give up to a 4x
+speedup in the KSpace time (8x less mesh points, 2x more expensive).
+However, for low relative accuracy, the staggered PPPM mesh size may
+be essentially the same as for regular PPPM, which means the method
+will be up to 2x slower in the KSpace time (simply 2x more expensive).
+For more details and timings, see the :doc:`Speed tips <Speed_tips>` doc
+page.
+
+.. note::
+
+   Using *pppm/stagger* may not give the same increase in the
+   accuracy of energy and pressure as it does in forces, so some caution
+   must be used if energy and/or pressure are quantities of interest,
+   such as when using a barostat.
+
+
+----------
+
+
+The *pppm/disp* and *pppm/disp/tip4p* styles add a mesh-based long-range
+dispersion sum option for 1/r\^6 potentials :ref:`(Isele-Holder) <Isele-Holder2012>`,
+similar to the *ewald/disp* style. The 1/r\^6 capability means
+that Lennard-Jones or Buckingham potentials can be used without a cutoff,
+i.e. they become full long-range potentials.
+
+For these styles, you will possibly want to adjust the default choice
+of parameters by using the :doc:`kspace\_modify <kspace_modify>` command.
+This can be done by either choosing the Ewald and grid parameters, or
+by specifying separate accuracies for the real and kspace
+calculations. When not making any settings, the simulation will stop
+with an error message. Further information on the influence of the
+parameters and how to choose them is described in
+:ref:`(Isele-Holder) <Isele-Holder2012>`,
+:ref:`(Isele-Holder2) <Isele-Holder2013>` and the :doc:`Howto dispersion <Howto_dispersion>` doc page.
+
+
+----------
+
+
+.. note::
+
+   All of the PPPM styles can be used with single-precision FFTs by
+   using the compiler switch -DFFT\_SINGLE for the FFT\_INC setting in your
+   lo-level Makefile.  This setting also changes some of the PPPM
+   operations (e.g. mapping charge to mesh and interpolating electric
+   fields to particles) to be performed in single precision.  This option
+   can speed-up long-range calculations, particularly in parallel or on
+   GPUs.  The use of the -DFFT\_SINGLE flag is discussed on the :doc:`Build settings <Build_settings>` doc page. MSM does not currently support
+   the -DFFT\_SINGLE compiler switch.
+
+
+----------
+
+
+The *msm* style invokes a multi-level summation method MSM solver,
+:ref:`(Hardy) <Hardy2006>` or :ref:`(Hardy2) <Hardy2009>`, which maps atom charge
+to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
+meshes on which direct Coulomb solvers are done.  This method does not
+use FFTs and scales as N. It may therefore be faster than the other
+K-space solvers for relatively large problems when running on large
+core counts. MSM can also be used for non-periodic boundary conditions
+and for mixed periodic and non-periodic boundaries.
+
+MSM is most competitive versus Ewald and PPPM when only relatively
+low accuracy forces, about 1e-4 relative error or less accurate,
+are needed. Note that use of a larger Coulombic cutoff (i.e. 15
+angstroms instead of 10 angstroms) provides better MSM accuracy for
+both the real space and grid computed forces.
+
+Currently calculation of the full pressure tensor in MSM is expensive.
+Using the :doc:`kspace\_modify <kspace_modify>` *pressure/scalar yes*
+command provides a less expensive way to compute the scalar pressure
+(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
+to run an isotropic barostat. If the full pressure tensor is needed,
+then calculating the pressure at every timestep or using a fixed
+pressure simulation with MSM will cause the code to run slower.
+
+
+----------
+
+
+The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_ which provides a variety of solver
+methods which can be used with LAMMPS.  The paper by :ref:`(Who) <Who2012>`
+gives an overview of ScaFaCoS.
+
+ScaFaCoS was developed by a consortium of German research facilities
+with a BMBF (German Ministry of Science and Education) funded project
+in 2009-2012. Participants of the consortium were the Universities of
+Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
+Forschungszentrum Juelich.
+
+The library is available for download at "http://scafacos.de" or can
+be cloned from the git-repository
+"git://github.com/scafacos/scafacos.git".
+
+In order to use this KSpace style, you must download and build the
+ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package
+installed package which links LAMMPS to the ScaFaCoS library.
+See details on :ref:`this page <USER-SCAFACOS>`.
+
+.. note::
+
+   Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
+   Coulombic interactions, both short- and long-range.  Thus you should
+   NOT use a Coulombic pair style when using kspace\_style scafacos.  This
+   also means the total Coulombic energy (short- and long-range) will be
+   tallied for :doc:`thermodynamic output <thermo_style>` command as part
+   of the *elong* keyword; the *ecoul* keyword will be zero.
+
+.. note::
+
+   See the current restriction below about use of ScaFaCoS in
+   LAMMPS with molecular charged systems or the TIP4P water model.
+
+The specified *method* determines which ScaFaCoS algorithm is used.
+These are the ScaFaCoS methods currently available from LAMMPS:
+
+* *fmm* = Fast Multi-Pole method
+* *p2nfft* = FFT-based Coulomb solver
+* *ewald* = Ewald summation
+* *direct* = direct O(N\^2) summation
+* *p3m* = PPPM
+
+We plan to support additional ScaFaCoS solvers from LAMMPS in the
+future.  For an overview of the included solvers, refer to
+:ref:`(Sutmann) <Sutmann2013>`
+
+The specified *accuracy* is similar to the accuracy setting for other
+LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
+it in different ways for different methods it supports.  Within the
+ScaFaCoS library the *accuracy* is treated as a tolerance level
+(either absolute or relative) for the chosen quantity, where the
+quantity can be either the Columic field values, the per-atom Columic
+energy or the total Columic energy.  To select from these options, see
+the :doc:`kspace\_modify scafacos accuracy <kspace_modify>` doc page.
+
+The :doc:`kspace\_modify scafacos <kspace_modify>` command also explains
+other ScaFaCoS options currently exposed to LAMMPS.
+
+
+----------
+
+
+The specified *accuracy* determines the relative RMS error in per-atom
+forces calculated by the long-range solver.  It is set as a
+dimensionless number, relative to the force that two unit point
+charges (e.g. 2 monovalent ions) exert on each other at a distance of
+1 Angstrom.  This reference value was chosen as representative of the
+magnitude of electrostatic forces in atomic systems.  Thus an accuracy
+value of 1.0e-4 means that the RMS error will be a factor of 10000
+smaller than the reference force.
+
+The accuracy setting is used in conjunction with the pairwise cutoff
+to determine the number of K-space vectors for style *ewald* or the
+grid size for style *pppm* or *msm*\ .
+
+Note that style *pppm* only computes the grid size at the beginning of
+a simulation, so if the length or triclinic tilt of the simulation
+cell increases dramatically during the course of the simulation, the
+accuracy of the simulation may degrade.  Likewise, if the
+:doc:`kspace\_modify slab <kspace_modify>` option is used with
+shrink-wrap boundaries in the z-dimension, and the box size changes
+dramatically in z.  For example, for a triclinic system with all three
+tilt factors set to the maximum limit, the PPPM grid should be
+increased roughly by a factor of 1.5 in the y direction and 2.0 in the
+z direction as compared to the same system using a cubic orthogonal
+simulation cell.  One way to handle this issue if you have a long
+simulation where the box size changes dramatically, is to break it
+into shorter simulations (multiple :doc:`run <run>` commands).  This
+works because the grid size is re-computed at the beginning of each
+run.  Another way to ensure the described accuracy requirement is met
+is to run a short simulation at the maximum expected tilt or length,
+note the required grid size, and then use the
+:doc:`kspace\_modify <kspace_modify>` *mesh* command to manually set the
+PPPM grid size to this value for the long run.  The simulation then
+will be "too accurate" for some portion of the run.
+
+RMS force errors in real space for *ewald* and *pppm* are estimated
+using equation 18 of :ref:`(Kolafa) <Kolafa>`, which is also referenced as
+equation 9 of :ref:`(Petersen) <Petersen>`. RMS force errors in K-space for
+*ewald* are estimated using equation 11 of :ref:`(Petersen) <Petersen>`,
+which is similar to equation 32 of :ref:`(Kolafa) <Kolafa>`. RMS force
+errors in K-space for *pppm* are estimated using equation 38 of
+:ref:`(Deserno) <Deserno>`. RMS force errors for *msm* are estimated
+using ideas from chapter 3 of :ref:`(Hardy) <Hardy2006>`, with equation 3.197
+of particular note. When using *msm* with non-periodic boundary
+conditions, it is expected that the error estimation will be too
+pessimistic. RMS force errors for dipoles when using *ewald/disp*
+or *ewald/dipole* are estimated using equations 33 and 46 of
+:ref:`(Wang) <Wang>`. The RMS force errors for *pppm/dipole* are estimated
+using the equations in :ref:`(Cerda) <Cerda2008>`.
+
+See the :doc:`kspace\_modify <kspace_modify>` command for additional
+options of the K-space solvers that can be set, including a *force*
+option for setting an absolute RMS error in forces, as opposed to a
+relative RMS error.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+More specifically, the *pppm/gpu* style performs charge assignment and
+force interpolation calculations on the GPU.  These processes are
+performed either in single or double precision, depending on whether
+the -DFFT\_SINGLE setting was specified in your lo-level Makefile, as
+discussed above.  The FFTs themselves are still calculated on the CPU.
+If *pppm/gpu* is used with a GPU-enabled pair style, part of the PPPM
+calculation can be performed concurrently on the GPU while other
+calculations for non-bonded and bonded force calculation are performed
+on the CPU.
+
+The *pppm/kk* style also performs charge assignment and force
+interpolation calculations on the GPU while the FFTs themselves are
+calculated on the CPU in non-threaded mode.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP, and OPT packages respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Note that the long-range electrostatic solvers in LAMMPS assume conducting
+metal (tinfoil) boundary conditions for both charge and dipole
+interactions. Vacuum boundary conditions are not currently supported.
+
+The *ewald/disp*\ , *ewald*\ , *pppm*\ , and *msm* styles support
+non-orthogonal (triclinic symmetry) simulation boxes. However,
+triclinic simulation cells may not yet be supported by suffix versions
+of these styles.
+
+All of the kspace styles are part of the KSPACE package.  They are
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+For MSM, a simulation must be 3d and one can use any combination of
+periodic, non-periodic, or shrink-wrapped boundaries (specified using
+the :doc:`boundary <boundary>` command).
+
+For Ewald and PPPM, a simulation must be 3d and periodic in all
+dimensions.  The only exception is if the slab option is set with
+:doc:`kspace\_modify <kspace_modify>`, in which case the xy dimensions
+must be periodic and the z dimension must be non-periodic.
+
+The scafacos KSpace style will only be enabled if LAMMPS is built with
+the USER-SCAFACOS package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+The use of ScaFaCos in LAMMPS does not yet support molecular charged
+systems where the short-range Coulombic interactions between atoms in
+the same bond/angle/dihedral are weighted by the
+:doc:`special\_bonds <special_bonds>` command.  Likewise it does not
+support the "TIP4P water style" where a fictitious charge site is
+introduced in each water molecule.
+Finally, the methods *p3m* and *ewald* do not support computing the
+virial, so this contribution is not included.
+
+Related commands
+""""""""""""""""
+
+:doc:`kspace\_modify <kspace_modify>`, :doc:`pair\_style lj/cut/coul/long <pair_lj>`, :doc:`pair\_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair\_style lj/long/coul/long <pair_lj_long>`, :doc:`pair\_style buck/coul/long <pair_buck>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   kspace_style none
+
+
+----------
+
+
+.. _Darden:
+
+
+
+**(Darden)** Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
+
+.. _Deserno:
+
+
+
+**(Deserno)** Deserno and Holm, J Chem Phys, 109, 7694 (1998).
+
+.. _Hockney:
+
+
+
+**(Hockney)** Hockney and Eastwood, Computer Simulation Using Particles,
+Adam Hilger, NY (1989).
+
+.. _Kolafa:
+
+
+
+**(Kolafa)** Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
+
+.. _Petersen:
+
+
+
+**(Petersen)** Petersen, J Chem Phys, 103, 3668 (1995).
+
+.. _Wang:
+
+
+
+**(Wang)** Wang and Holm, J Chem Phys, 115, 6277 (2001).
+
+.. _Pollock:
+
+
+
+**(Pollock)** Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
+
+.. _Cerutti:
+
+
+
+**(Cerutti)** Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
+and Computation 5, 2322 (2009)
+
+.. _Neelov:
+
+
+
+**(Neelov)** Neelov, Holm, J Chem Phys 132, 234103 (2010)
+
+.. _Veld:
+
+
+
+**(Veld)** In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
+
+.. _Toukmaji:
+
+
+
+**(Toukmaji)** Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
+10913 (2000).
+
+.. _Isele-Holder2012:
+
+
+
+**(Isele-Holder)** Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
+174107 (2012).
+
+.. _Isele-Holder2013:
+
+
+
+**(Isele-Holder2)** Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
+J Chem Theory Comput 9, 5412 (2013).
+
+.. _Hardy2006:
+
+
+
+**(Hardy)** David Hardy thesis: Multilevel Summation for the Fast
+Evaluation of Forces for the Simulation of Biomolecules, University of
+Illinois at Urbana-Champaign, (2006).
+
+.. _Hardy2009:
+
+
+
+**(Hardy2)** Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
+(2009).
+
+.. _Sutmann2013:
+
+
+
+**(Sutmann)** Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
+
+.. _Cerda2008:
+
+
+
+**(Cerda)** Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
+
+.. _Who2012:
+
+
+
+**(Who)** Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
+(2012).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
deleted file mode 100644
index 98ec1e64e6..0000000000
--- a/doc/src/kspace_style.txt
+++ /dev/null
@@ -1,495 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-kspace_style command :h3
-
-[Syntax:]
-
-kspace_style style value :pre
-
-style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l
-  {none} value = none
-  {ewald} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/disp} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/dipole} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/dipole/spin} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/cg} values = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {pppm/disp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/tip4p} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/disp/tip4p} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/gpu} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/intel} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/kk} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/cg/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/disp/intel} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/tip4p/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/stagger} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/dipole} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/dipole/spin} value = accuracy
-    accuracy = desired relative error in forces
-  {msm} value = accuracy
-    accuracy = desired relative error in forces
-  {msm/cg} value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {msm/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {msm/cg/omp} value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {scafacos} values = method accuracy
-    method = fmm or p2nfft or p3m or ewald or direct
-    accuracy = desired relative error in forces :pre
-:ule
-
-[Examples:]
-
-kspace_style pppm 1.0e-4
-kspace_style pppm/cg 1.0e-5 1.0e-6
-kspace style msm 1.0e-4
-kspace style scafacos fmm 1.0e-4
-kspace_style none :pre
-
-[Description:]
-
-Define a long-range solver for LAMMPS to use each timestep to compute
-long-range Coulombic interactions or long-range 1/r^6 interactions.
-Most of the long-range solvers perform their computation in K-space,
-hence the name of this command.
-
-When such a solver is used in conjunction with an appropriate pair
-style, the cutoff for Coulombic or 1/r^N interactions is effectively
-infinite.  If the Coulombic case, this means each charge in the system
-interacts with charges in an infinite array of periodic images of the
-simulation domain.
-
-Note that using a long-range solver requires use of a matching "pair
-style"_pair_style.html to perform consistent short-range pairwise
-calculations.  This means that the name of the pair style contains a
-matching keyword to the name of the KSpace style, as in this table:
-
-Pair style : KSpace style
-coul/long : ewald or pppm
-coul/msm : msm
-lj/long or buck/long : disp (for dispersion)
-tip4p/long : tip4p :tb(s=:,ea=c)
-
-:line
-
-The {ewald} style performs a standard Ewald summation as described in
-any solid-state physics text.
-
-The {ewald/disp} style adds a long-range dispersion sum option for
-1/r^6 potentials and is useful for simulation of interfaces
-"(Veld)"_#Veld.  It also performs standard Coulombic Ewald summations,
-but in a more efficient manner than the {ewald} style.  The 1/r^6
-capability means that Lennard-Jones or Buckingham potentials can be
-used without a cutoff, i.e. they become full long-range potentials.
-The {ewald/disp} style can also be used with point-dipoles, see
-"(Toukmaji)"_#Toukmaji.
-
-The {ewald/dipole} style adds long-range standard Ewald summations 
-for dipole-dipole interactions, see "(Toukmaji)"_#Toukmaji.
-
-The {ewald/dipole/spin} style adds long-range standard Ewald 
-summations for magnetic dipole-dipole interactions between
-magnetic spins.
-
-:line
-
-The {pppm} style invokes a particle-particle particle-mesh solver
-"(Hockney)"_#Hockney which maps atom charge to a 3d mesh, uses 3d FFTs
-to solve Poisson's equation on the mesh, then interpolates electric
-fields on the mesh points back to the atoms.  It is closely related to
-the particle-mesh Ewald technique (PME) "(Darden)"_#Darden used in
-AMBER and CHARMM.  The cost of traditional Ewald summation scales as
-N^(3/2) where N is the number of atoms in the system.  The PPPM solver
-scales as Nlog(N) due to the FFTs, so it is almost always a faster
-choice "(Pollock)"_#Pollock.
-
-The {pppm/cg} style is identical to the {pppm} style except that it
-has an optimization for systems where most particles are uncharged.
-Similarly the {msm/cg} style implements the same optimization for {msm}.
-The optional {smallq} argument defines the cutoff for the absolute
-charge value which determines whether a particle is considered charged
-or not.  Its default value is 1.0e-5.
-
-The {pppm/dipole} style invokes a particle-particle particle-mesh solver 
-for dipole-dipole interactions, following the method of "(Cerda)"_#Cerda2008.
-
-The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver 
-for magnetic dipole-dipole interactions between magnetic spins. 
-
-The {pppm/tip4p} style is identical to the {pppm} style except that it
-adds a charge at the massless 4th site in each TIP4P water molecule.
-It should be used with "pair styles"_pair_style.html with a
-{tip4p/long} in their style name.
-
-The {pppm/stagger} style performs calculations using two different
-meshes, one shifted slightly with respect to the other.  This can
-reduce force aliasing errors and increase the accuracy of the method
-for a given mesh size.  Or a coarser mesh can be used for the same
-target accuracy, which saves CPU time.  However, there is a trade-off
-since FFTs on two meshes are now performed which increases the
-computation required.  See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov,
-and "(Hockney)"_#Hockney for details of the method.
-
-For high relative accuracy, using staggered PPPM allows the mesh size
-to be reduced by a factor of 2 in each dimension as compared to
-regular PPPM (for the same target accuracy).  This can give up to a 4x
-speedup in the KSpace time (8x less mesh points, 2x more expensive).
-However, for low relative accuracy, the staggered PPPM mesh size may
-be essentially the same as for regular PPPM, which means the method
-will be up to 2x slower in the KSpace time (simply 2x more expensive).
-For more details and timings, see the "Speed tips"_Speed_tips.html doc
-page.
-
-NOTE: Using {pppm/stagger} may not give the same increase in the
-accuracy of energy and pressure as it does in forces, so some caution
-must be used if energy and/or pressure are quantities of interest,
-such as when using a barostat.
-
-:line
-
-The {pppm/disp} and {pppm/disp/tip4p} styles add a mesh-based long-range
-dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder2012,
-similar to the {ewald/disp} style. The 1/r^6 capability means
-that Lennard-Jones or Buckingham potentials can be used without a cutoff,
-i.e. they become full long-range potentials.
-
-For these styles, you will possibly want to adjust the default choice
-of parameters by using the "kspace_modify"_kspace_modify.html command.
-This can be done by either choosing the Ewald and grid parameters, or
-by specifying separate accuracies for the real and kspace
-calculations. When not making any settings, the simulation will stop
-with an error message. Further information on the influence of the
-parameters and how to choose them is described in
-"(Isele-Holder)"_#Isele-Holder2012,
-"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto
-dispersion"_Howto_dispersion.html doc page.
-
-:line
-
-NOTE: All of the PPPM styles can be used with single-precision FFTs by
-using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
-lo-level Makefile.  This setting also changes some of the PPPM
-operations (e.g. mapping charge to mesh and interpolating electric
-fields to particles) to be performed in single precision.  This option
-can speed-up long-range calculations, particularly in parallel or on
-GPUs.  The use of the -DFFT_SINGLE flag is discussed on the "Build
-settings"_Build_settings.html doc page. MSM does not currently support
-the -DFFT_SINGLE compiler switch.
-
-:line
-
-The {msm} style invokes a multi-level summation method MSM solver,
-"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge
-to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
-meshes on which direct Coulomb solvers are done.  This method does not
-use FFTs and scales as N. It may therefore be faster than the other
-K-space solvers for relatively large problems when running on large
-core counts. MSM can also be used for non-periodic boundary conditions
-and for mixed periodic and non-periodic boundaries.
-
-MSM is most competitive versus Ewald and PPPM when only relatively
-low accuracy forces, about 1e-4 relative error or less accurate,
-are needed. Note that use of a larger Coulombic cutoff (i.e. 15
-angstroms instead of 10 angstroms) provides better MSM accuracy for
-both the real space and grid computed forces.
-
-Currently calculation of the full pressure tensor in MSM is expensive.
-Using the "kspace_modify"_kspace_modify.html {pressure/scalar yes}
-command provides a less expensive way to compute the scalar pressure
-(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
-to run an isotropic barostat. If the full pressure tensor is needed,
-then calculating the pressure at every timestep or using a fixed
-pressure simulation with MSM will cause the code to run slower.
-
-:line
-
-The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver
-library"_http://www.scafacos.de which provides a variety of solver
-methods which can be used with LAMMPS.  The paper by "(Who)"_#Who2012
-gives an overview of ScaFaCoS.
-
-ScaFaCoS was developed by a consortium of German research facilities
-with a BMBF (German Ministry of Science and Education) funded project
-in 2009-2012. Participants of the consortium were the Universities of
-Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
-Forschungszentrum Juelich.
-
-The library is available for download at "http://scafacos.de" or can
-be cloned from the git-repository
-"git://github.com/scafacos/scafacos.git".
-
-In order to use this KSpace style, you must download and build the
-ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package
-installed package which links LAMMPS to the ScaFaCoS library.
-See details on "this page"_Section_packages.html#USER-SCAFACOS.
-
-NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
-Coulombic interactions, both short- and long-range.  Thus you should
-NOT use a Coulombic pair style when using kspace_style scafacos.  This
-also means the total Coulombic energy (short- and long-range) will be
-tallied for "thermodynamic output"_thermo_style.html command as part
-of the {elong} keyword; the {ecoul} keyword will be zero.
-
-NOTE: See the current restriction below about use of ScaFaCoS in
-LAMMPS with molecular charged systems or the TIP4P water model.
-
-The specified {method} determines which ScaFaCoS algorithm is used.
-These are the ScaFaCoS methods currently available from LAMMPS:
-
-{fmm} = Fast Multi-Pole method
-{p2nfft} = FFT-based Coulomb solver
-{ewald} = Ewald summation
-{direct} = direct O(N^2) summation
-{p3m} = PPPM :ul
-
-We plan to support additional ScaFaCoS solvers from LAMMPS in the
-future.  For an overview of the included solvers, refer to
-"(Sutmann)"_#Sutmann2013
-
-The specified {accuracy} is similar to the accuracy setting for other
-LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
-it in different ways for different methods it supports.  Within the
-ScaFaCoS library the {accuracy} is treated as a tolerance level
-(either absolute or relative) for the chosen quantity, where the
-quantity can be either the Columic field values, the per-atom Columic
-energy or the total Columic energy.  To select from these options, see
-the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
-
-The "kspace_modify scafacos"_kspace_modify.html command also explains
-other ScaFaCoS options currently exposed to LAMMPS.
-
-:line
-
-The specified {accuracy} determines the relative RMS error in per-atom
-forces calculated by the long-range solver.  It is set as a
-dimensionless number, relative to the force that two unit point
-charges (e.g. 2 monovalent ions) exert on each other at a distance of
-1 Angstrom.  This reference value was chosen as representative of the
-magnitude of electrostatic forces in atomic systems.  Thus an accuracy
-value of 1.0e-4 means that the RMS error will be a factor of 10000
-smaller than the reference force.
-
-The accuracy setting is used in conjunction with the pairwise cutoff
-to determine the number of K-space vectors for style {ewald} or the
-grid size for style {pppm} or {msm}.
-
-Note that style {pppm} only computes the grid size at the beginning of
-a simulation, so if the length or triclinic tilt of the simulation
-cell increases dramatically during the course of the simulation, the
-accuracy of the simulation may degrade.  Likewise, if the
-"kspace_modify slab"_kspace_modify.html option is used with
-shrink-wrap boundaries in the z-dimension, and the box size changes
-dramatically in z.  For example, for a triclinic system with all three
-tilt factors set to the maximum limit, the PPPM grid should be
-increased roughly by a factor of 1.5 in the y direction and 2.0 in the
-z direction as compared to the same system using a cubic orthogonal
-simulation cell.  One way to handle this issue if you have a long
-simulation where the box size changes dramatically, is to break it
-into shorter simulations (multiple "run"_run.html commands).  This
-works because the grid size is re-computed at the beginning of each
-run.  Another way to ensure the described accuracy requirement is met
-is to run a short simulation at the maximum expected tilt or length,
-note the required grid size, and then use the
-"kspace_modify"_kspace_modify.html {mesh} command to manually set the
-PPPM grid size to this value for the long run.  The simulation then
-will be "too accurate" for some portion of the run.
-
-RMS force errors in real space for {ewald} and {pppm} are estimated
-using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
-equation 9 of "(Petersen)"_#Petersen. RMS force errors in K-space for
-{ewald} are estimated using equation 11 of "(Petersen)"_#Petersen,
-which is similar to equation 32 of "(Kolafa)"_#Kolafa. RMS force
-errors in K-space for {pppm} are estimated using equation 38 of
-"(Deserno)"_#Deserno. RMS force errors for {msm} are estimated
-using ideas from chapter 3 of "(Hardy)"_#Hardy2006, with equation 3.197
-of particular note. When using {msm} with non-periodic boundary
-conditions, it is expected that the error estimation will be too
-pessimistic. RMS force errors for dipoles when using {ewald/disp}
-or {ewald/dipole} are estimated using equations 33 and 46 of
-"(Wang)"_#Wang. The RMS force errors for {pppm/dipole} are estimated
-using the equations in "(Cerda)"_#Cerda2008.
-
-
-See the "kspace_modify"_kspace_modify.html command for additional
-options of the K-space solvers that can be set, including a {force}
-option for setting an absolute RMS error in forces, as opposed to a
-relative RMS error.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-More specifically, the {pppm/gpu} style performs charge assignment and
-force interpolation calculations on the GPU.  These processes are
-performed either in single or double precision, depending on whether
-the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
-discussed above.  The FFTs themselves are still calculated on the CPU.
-If {pppm/gpu} is used with a GPU-enabled pair style, part of the PPPM
-calculation can be performed concurrently on the GPU while other
-calculations for non-bonded and bonded force calculation are performed
-on the CPU.
-
-The {pppm/kk} style also performs charge assignment and force
-interpolation calculations on the GPU while the FFTs themselves are
-calculated on the CPU in non-threaded mode.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP, and OPT packages respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-Note that the long-range electrostatic solvers in LAMMPS assume conducting
-metal (tinfoil) boundary conditions for both charge and dipole
-interactions. Vacuum boundary conditions are not currently supported.
-
-The {ewald/disp}, {ewald}, {pppm}, and {msm} styles support
-non-orthogonal (triclinic symmetry) simulation boxes. However,
-triclinic simulation cells may not yet be supported by suffix versions
-of these styles.
-
-All of the kspace styles are part of the KSPACE package.  They are
-only enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-For MSM, a simulation must be 3d and one can use any combination of
-periodic, non-periodic, or shrink-wrapped boundaries (specified using
-the "boundary"_boundary.html command).
-
-For Ewald and PPPM, a simulation must be 3d and periodic in all
-dimensions.  The only exception is if the slab option is set with
-"kspace_modify"_kspace_modify.html, in which case the xy dimensions
-must be periodic and the z dimension must be non-periodic.
-
-The scafacos KSpace style will only be enabled if LAMMPS is built with
-the USER-SCAFACOS package.  See the "Build package"_Build_package.html
-doc page for more info.
-
-The use of ScaFaCos in LAMMPS does not yet support molecular charged
-systems where the short-range Coulombic interactions between atoms in
-the same bond/angle/dihedral are weighted by the
-"special_bonds"_special_bonds.html command.  Likewise it does not
-support the "TIP4P water style" where a fictitious charge site is
-introduced in each water molecule.
-Finally, the methods {p3m} and {ewald} do not support computing the
-virial, so this contribution is not included.
-
-[Related commands:]
-
-"kspace_modify"_kspace_modify.html, "pair_style
-lj/cut/coul/long"_pair_lj.html, "pair_style
-lj/charmm/coul/long"_pair_charmm.html, "pair_style
-lj/long/coul/long"_pair_lj_long.html, "pair_style
-buck/coul/long"_pair_buck.html
-
-[Default:]
-
-kspace_style none :pre
-
-:line
-
-:link(Darden)
-[(Darden)] Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
-
-:link(Deserno)
-[(Deserno)] Deserno and Holm, J Chem Phys, 109, 7694 (1998).
-
-:link(Hockney)
-[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
-Adam Hilger, NY (1989).
-
-:link(Kolafa)
-[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
-
-:link(Petersen)
-[(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995).
-
-:link(Wang)
-[(Wang)] Wang and Holm, J Chem Phys, 115, 6277 (2001).
-
-:link(Pollock)
-[(Pollock)] Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
-
-:link(Cerutti)
-[(Cerutti)] Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
-and Computation 5, 2322 (2009)
-
-:link(Neelov)
-[(Neelov)] Neelov, Holm, J Chem Phys 132, 234103 (2010)
-
-:link(Veld)
-[(Veld)] In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
-
-:link(Toukmaji)
-[(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
-10913 (2000).
-
-:link(Isele-Holder2012)
-[(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
-174107 (2012).
-
-:link(Isele-Holder2013)
-[(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
-J Chem Theory Comput 9, 5412 (2013).
-
-:link(Hardy2006)
-[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
-Evaluation of Forces for the Simulation of Biomolecules, University of
-Illinois at Urbana-Champaign, (2006).
-
-:link(Hardy2009)
-[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
-(2009).
-
-:link(Sutmann2013)
-[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
-
-:link(Cerda2008)
-[(Cerda)] Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
-
-:link(Who2012)
-[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
-(2012).
diff --git a/doc/src/label.rst b/doc/src/label.rst
new file mode 100644
index 0000000000..31ebbfe0cb
--- /dev/null
+++ b/doc/src/label.rst
@@ -0,0 +1,47 @@
+.. index:: label
+
+label command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   label ID
+
+* ID = string used as label name
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   label xyz
+   label loop
+
+Description
+"""""""""""
+
+Label this line of the input script with the chosen ID.  Unless a jump
+command was used previously, this does nothing.  But if a
+:doc:`jump <jump>` command was used with a label argument to begin
+invoking this script file, then all command lines in the script prior
+to this line will be ignored.  I.e. execution of the script will begin
+at this line.  This is useful for looping over a section of the input
+script as discussed in the :doc:`jump <jump>` command.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst
new file mode 100644
index 0000000000..bf5dec5453
--- /dev/null
+++ b/doc/src/lattice.rst
@@ -0,0 +1,335 @@
+.. index:: lattice
+
+lattice command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   lattice style scale keyword values ...
+
+* style = *none* or *sc* or *bcc* or *fcc* or *hcp* or *diamond* or         *sq* or *sq2* or *hex* or *custom*
+* scale = scale factor between lattice and simulation box
+  
+  .. parsed-literal::
+  
+       scale = reduced density rho\* (for LJ units)
+       scale = lattice constant in distance units (for all other units)
+
+* zero or more keyword/value pairs may be appended
+* keyword = *origin* or *orient* or *spacing* or *a1* or *a2* or *a3* or *basis*
+  
+  .. parsed-literal::
+  
+       *origin* values = x y z
+         x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
+       *orient* values = dim i j k
+         dim = *x* or *y* or *z*
+         i,j,k = integer lattice directions
+       *spacing* values = dx dy dz
+         dx,dy,dz = lattice spacings in the x,y,z box directions
+       *a1*\ ,\ *a2*\ ,\ *a3* values = x y z
+         x,y,z = primitive vector components that define unit cell
+       *basis* values = x y z
+         x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   lattice fcc 3.52
+   lattice hex 0.85
+   lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
+   lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
+                       basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
+   lattice none 2.0
+
+Description
+"""""""""""
+
+Define a lattice for use by other commands.  In LAMMPS, a lattice is
+simply a set of points in space, determined by a unit cell with basis
+atoms, that is replicated infinitely in all dimensions.  The arguments
+of the lattice command can be used to define a wide variety of
+crystallographic lattices.
+
+A lattice is used by LAMMPS in two ways.  First, the
+:doc:`create\_atoms <create_atoms>` command creates atoms on the lattice
+points inside the simulation box.  Note that the
+:doc:`create\_atoms <create_atoms>` command allows different atom types
+to be assigned to different basis atoms of the lattice.  Second, the
+lattice spacing in the x,y,z dimensions implied by the lattice, can be
+used by other commands as distance units
+(e.g. :doc:`create\_box <create_box>`, :doc:`region <region>` and
+:doc:`velocity <velocity>`), which are often convenient to use when the
+underlying problem geometry is atoms on a lattice.
+
+The lattice style must be consistent with the dimension of the
+simulation - see the :doc:`dimension <dimension>` command.  Styles *sc*
+or *bcc* or *fcc* or *hcp* or *diamond* are for 3d problems.  Styles
+*sq* or *sq2* or *hex* are for 2d problems.  Style *custom* can be
+used for either 2d or 3d problems.
+
+A lattice consists of a unit cell, a set of basis atoms within that
+cell, and a set of transformation parameters (scale, origin, orient)
+that map the unit cell into the simulation box.  The vectors a1,a2,a3
+are the edge vectors of the unit cell.  This is the nomenclature for
+"primitive" vectors in solid-state crystallography, but in LAMMPS the
+unit cell they determine does not have to be a "primitive cell" of
+minimum volume.
+
+Note that the lattice command can be used multiple times in an input
+script.  Each time it is invoked, the lattice attributes are
+re-defined and are used for all subsequent commands (that use lattice
+attributes).  For example, a sequence of lattice,
+:doc:`region <region>`, and :doc:`create\_atoms <create_atoms>` commands
+can be repeated multiple times to build a poly-crystalline model with
+different geometric regions populated with atoms in different lattice
+orientations.
+
+
+----------
+
+
+A lattice of style *none* does not define a unit cell and basis set,
+so it cannot be used with the :doc:`create\_atoms <create_atoms>`
+command.  However it does define a lattice spacing via the specified
+scale parameter.  As explained above the lattice spacings in x,y,z can
+be used by other commands as distance units.  No additional
+keyword/value pairs can be specified for the *none* style.  By
+default, a "lattice none 1.0" is defined, which means the lattice
+spacing is the same as one distance unit, as defined by the
+:doc:`units <units>` command.
+
+Lattices of style *sc*\ , *fcc*\ , *bcc*\ , and *diamond* are 3d lattices
+that define a cubic unit cell with edge length = 1.0.  This means a1 =
+1 0 0, a2 = 0 1 0, and a3 = 0 0 1.  Style *hcp* has a1 = 1 0 0, a2 = 0
+sqrt(3) 0, and a3 = 0 0 sqrt(8/3).  The placement of the basis atoms
+within the unit cell are described in any solid-state physics text.  A
+*sc* lattice has 1 basis atom at the lower-left-bottom corner of the
+cube.  A *bcc* lattice has 2 basis atoms, one at the corner and one at
+the center of the cube.  A *fcc* lattice has 4 basis atoms, one at the
+corner and 3 at the cube face centers.  A *hcp* lattice has 4 basis
+atoms, two in the z = 0 plane and 2 in the z = 0.5 plane.  A *diamond*
+lattice has 8 basis atoms.
+
+Lattices of style *sq* and *sq2* are 2d lattices that define a square
+unit cell with edge length = 1.0.  This means a1 = 1 0 0 and a2 = 0 1
+0.  A *sq* lattice has 1 basis atom at the lower-left corner of the
+square.  A *sq2* lattice has 2 basis atoms, one at the corner and one
+at the center of the square.  A *hex* style is also a 2d lattice, but
+the unit cell is rectangular, with a1 = 1 0 0 and a2 = 0 sqrt(3) 0.
+It has 2 basis atoms, one at the corner and one at the center of the
+rectangle.
+
+A lattice of style *custom* allows you to specify a1, a2, a3, and a
+list of basis atoms to put in the unit cell.  By default, a1 and a2
+and a3 are 3 orthogonal unit vectors (edges of a unit cube).  But you
+can specify them to be of any length and non-orthogonal to each other,
+so that they describe a tilted parallelepiped.  Via the *basis*
+keyword you add atoms, one at a time, to the unit cell.  Its arguments
+are fractional coordinates (0.0 <= x,y,z < 1.0).  The position vector
+x of a basis atom within the unit cell is thus a linear combination of
+the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
+where bx,by,bz are the 3 values specified for the *basis* keyword.
+
+
+----------
+
+
+This sub-section discusses the arguments that determine how the
+idealized unit cell is transformed into a lattice of points within the
+simulation box.
+
+The *scale* argument determines how the size of the unit cell will be
+scaled when mapping it into the simulation box.  I.e. it determines a
+multiplicative factor to apply to the unit cell, to convert it to a
+lattice of the desired size and distance units in the simulation box.
+The meaning of the *scale* argument depends on the :doc:`units <units>`
+being used in your simulation.
+
+For all unit styles except *lj*\ , the scale argument is specified in
+the distance units defined by the unit style.  For example, in *real*
+or *metal* units, if the unit cell is a unit cube with edge length
+1.0, specifying scale = 3.52 would create a cubic lattice with a
+spacing of 3.52 Angstroms.  In *cgs* units, the spacing would be 3.52
+cm.
+
+For unit style *lj*\ , the scale argument is the Lennard-Jones reduced
+density, typically written as rho\*.  LAMMPS converts this value into
+the multiplicative factor via the formula "factor\^dim = rho/rho\*",
+where rho = N/V with V = the volume of the lattice unit cell and N =
+the number of basis atoms in the unit cell (described below), and dim
+= 2 or 3 for the dimensionality of the simulation.  Effectively, this
+means that if LJ particles of size sigma = 1.0 are used in the
+simulation, the lattice of particles will be at the desired reduced
+density.
+
+The *origin* option specifies how the unit cell will be shifted or
+translated when mapping it into the simulation box.  The x,y,z values
+are fractional values (0.0 <= x,y,z < 1.0) meaning shift the lattice
+by a fraction of the lattice spacing in each dimension.  The meaning
+of "lattice spacing" is discussed below.
+
+The *orient* option specifies how the unit cell will be rotated when
+mapping it into the simulation box.  The *dim* argument is one of the
+3 coordinate axes in the simulation box.  The other 3 arguments are
+the crystallographic direction in the lattice that you want to orient
+along that axis, specified as integers.  E.g. "orient x 2 1 0" means
+the x-axis in the simulation box will be the [210] lattice
+direction, and similarly for y and z.  The 3 lattice directions you
+specify do not have to be unit vectors, but they must be mutually
+orthogonal and obey the right-hand rule, i.e. (X cross Y) points in
+the Z direction.
+
+.. note::
+
+   The preceding paragraph describing lattice directions is only
+   valid for orthogonal cubic unit cells (or square in 2d).  If you are
+   using a *hcp* or *hex* lattice or the more general lattice style
+   *custom* with non-orthogonal a1,a2,a3 vectors, then you should think
+   of the 3 *orient* vectors as creating a 3x3 rotation matrix which is
+   applied to a1,a2,a3 to rotate the original unit cell to a new
+   orientation in the simulation box.
+
+
+----------
+
+
+Several LAMMPS commands have the option to use distance units that are
+inferred from "lattice spacings" in the x,y,z box directions.
+E.g. the :doc:`region <region>` command can create a block of size
+10x20x20, where 10 means 10 lattice spacings in the x direction.
+
+.. note::
+
+   Though they are called lattice spacings, all the commands that
+   have a "units lattice" option, simply use the 3 values as scale
+   factors on the distance units defined by the :doc:`units <units>`
+   command.  Thus if you do not like the lattice spacings computed by
+   LAMMPS (e.g. for a non-orthogonal or rotated unit cell), you can
+   define the 3 values to be whatever you wish, via the *spacing* option.
+
+If the *spacing* option is not specified, the lattice spacings are
+computed by LAMMPS in the following way.  A unit cell of the lattice
+is mapped into the simulation box (scaled and rotated), so that it now
+has (perhaps) a modified size and orientation.  The lattice spacing in
+X is defined as the difference between the min/max extent of the x
+coordinates of the 8 corner points of the modified unit cell (4 in
+2d).  Similarly, the Y and Z lattice spacings are defined as the
+difference in the min/max of the y and z coordinates.
+
+Note that if the unit cell is orthogonal with axis-aligned edges (no
+rotation via the *orient* keyword), then the lattice spacings in each
+dimension are simply the scale factor (described above) multiplied by
+the length of a1,a2,a3.  Thus a *hex* style lattice with a scale
+factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
+3\*sqrt(3.0) in y.
+
+.. note::
+
+   For non-orthogonal unit cells and/or when a rotation is applied
+   via the *orient* keyword, then the lattice spacings computed by LAMMPS
+   are typically less intuitive.  In particular, in these cases, there is
+   no guarantee that a particular lattice spacing is an integer multiple
+   of the periodicity of the lattice in that direction.  Thus, if you
+   create an orthogonal periodic simulation box whose size in a dimension
+   is a multiple of the lattice spacing, and then fill it with atoms via
+   the :doc:`create\_atoms <create_atoms>` command, you will NOT necessarily
+   create a periodic system.  I.e. atoms may overlap incorrectly at the
+   faces of the simulation box.
+
+The *spacing* option sets the 3 lattice spacings directly.  All must
+be non-zero (use 1.0 for dz in a 2d simulation).  The specified values
+are multiplied by the multiplicative factor described above that is
+associated with the scale factor.  Thus a spacing of 1.0 means one
+unit cell edge length independent of the scale factor.  As mentioned
+above, this option can be useful if the spacings LAMMPS computes are
+inconvenient to use in subsequent commands, which can be the case for
+non-orthogonal or rotated lattices.
+
+Note that whenever the lattice command is used, the values of the
+lattice spacings LAMMPS calculates are printed out.  Thus their effect
+in commands that use the spacings should be decipherable.
+
+
+----------
+
+
+Example commands for generating a Wurtzite crystal (courtesy
+of Aidan Thompson), with its 8 atom unit cell.
+
+
+.. parsed-literal::
+
+   variable a equal  4.340330
+   variable b equal  $a\*sqrt(3.0)
+   variable c equal  $a\*sqrt(8.0/3.0)
+
+   variable 1_3 equal 1.0/3.0
+   variable 2_3 equal 2.0/3.0
+   variable 1_6 equal 1.0/6.0
+   variable 5_6 equal 5.0/6.0
+   variable 1_12 equal 1.0/12.0
+   variable 5_12 equal 5.0/12.0
+
+   lattice custom    1.0     &
+           a1      $a      0.0     0.0     &
+           a2      0.0     $b      0.0     &
+           a3      0.0     0.0     $c      &
+           basis   0.0     0.0     0.0     &
+           basis   0.5     0.5     0.0     &
+           basis   ${1_3}  0.0     0.5     &
+           basis   ${5_6}  0.5     0.5     &
+           basis   0.0     0.0     0.625   &
+           basis   0.5     0.5     0.625   &
+           basis   ${1_3}  0.0     0.125   &
+           basis   ${5_6}  0.5     0.125
+
+   region myreg block 0 1 0 1 0 1
+   create_box      2 myreg
+   create_atoms    1 box      &
+           basis   5       2       &
+           basis   6       2       &
+           basis   7       2       &
+           basis   8       2
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *a1,a2,a3,basis* keywords can only be used with style *custom*\ .
+
+Related commands
+""""""""""""""""
+
+:doc:`dimension <dimension>`, :doc:`create\_atoms <create_atoms>`,
+:doc:`region <region>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   lattice none 1.0
+
+For other lattice styles, the option defaults are origin = 0.0 0.0
+0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1 0 0,
+a2 = 0 1 0, and a3 = 0 0 1.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/log.rst b/doc/src/log.rst
new file mode 100644
index 0000000000..0f53040c13
--- /dev/null
+++ b/doc/src/log.rst
@@ -0,0 +1,56 @@
+.. index:: log
+
+log command
+===========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   log file keyword
+
+* file = name of new logfile
+* keyword = *append* if output should be appended to logfile (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   log log.equil
+   log log.equil append
+
+Description
+"""""""""""
+
+This command closes the current LAMMPS log file, opens a new file with
+the specified name, and begins logging information to it.  If the
+specified file name is *none*\ , then no new log file is opened.  If the
+optional keyword *append* is specified, then output will be appended
+to an existing log file, instead of overwriting it.
+
+If multiple processor partitions are being used, the file name should
+be a variable, so that different processors do not attempt to write to
+the same log file.
+
+The file "log.lammps" is the default log file for a LAMMPS run.  The
+name of the initial log file can also be set by the :doc:`-log command-line switch <Run_options>`.
+
+Restrictions
+""""""""""""
+ none
+
+**Related commands:** none
+
+Default
+"""""""
+
+The default LAMMPS log file is named log.lammps
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/mass.rst b/doc/src/mass.rst
new file mode 100644
index 0000000000..05cef2e3b2
--- /dev/null
+++ b/doc/src/mass.rst
@@ -0,0 +1,95 @@
+.. index:: mass
+
+mass command
+============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   mass I value
+
+* I = atom type (see asterisk form below)
+* value = mass
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   mass 1 1.0
+   mass \* 62.5
+   mass 2\* 62.5
+
+Description
+"""""""""""
+
+Set the mass for all atoms of one or more atom types.  Per-type mass
+values can also be set in the :doc:`read\_data <read_data>` data file
+using the "Masses" keyword.  See the :doc:`units <units>` command for
+what mass units to use.
+
+The I index can be specified in one of two ways.  An explicit numeric
+value can be used, as in the 1st example above.  Or a wild-card
+asterisk can be used to set the mass for multiple atom types.  This
+takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of
+atom types, then an asterisk with no numeric values means all types
+from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+A line in a :doc:`data file <read_data>` that follows the "Masses"
+keyword specifies mass using the same format as the arguments of the
+mass command in an input script, except that no wild-card asterisk can
+be used.  For example, under the "Masses" section of a data file, the
+line that corresponds to the 1st example above would be listed as
+
+
+.. parsed-literal::
+
+   1 1.0
+
+Note that the mass command can only be used if the :doc:`atom style <atom_style>` requires per-type atom mass to be set.
+Currently, all but the *sphere* and *ellipsoid* and *peri* styles do.
+They require mass to be set for individual particles, not types.
+Per-atom masses are defined in the data file read by the
+:doc:`read\_data <read_data>` command, or set to default values by the
+:doc:`create\_atoms <create_atoms>` command.  Per-atom masses can also be
+set to new values by the :doc:`set mass <set>` or :doc:`set density <set>`
+commands.
+
+Also note that :doc:`pair\_style eam <pair_eam>` and :doc:`pair\_style bop <pair_bop>` commands define the masses of atom types in their
+respective potential files, in which case the mass command is normally
+not used.
+
+If you define a :doc:`hybrid atom style <atom_style>` which includes one
+(or more) sub-styles which require per-type mass and one (or more)
+sub-styles which require per-atom mass, then you must define both.
+However, in this case the per-type mass will be ignored; only the
+per-atom mass will be used by LAMMPS.
+
+Restrictions
+""""""""""""
+
+
+This command must come after the simulation box is defined by a
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
+:doc:`create\_box <create_box>` command.
+
+All masses must be defined before a simulation is run.  They must also
+all be defined before a :doc:`velocity <velocity>` or :doc:`fix shake <fix_shake>` command is used.
+
+The mass assigned to any type or atom must be > 0.0.
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/message.rst b/doc/src/message.rst
new file mode 100644
index 0000000000..f81b498152
--- /dev/null
+++ b/doc/src/message.rst
@@ -0,0 +1,195 @@
+.. index:: message
+
+message command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   message which protocol mode arg
+
+* which = *client* or *server*
+* protocol = *md* or *mc*
+* mode = *file* or *zmq* or *mpi/one* or *mpi/two*
+  
+  .. parsed-literal::
+  
+       *file* arg = filename
+         filename = file used for message exchanges
+       *zmq* arg = socket-ID
+         socket-ID for client = localhost:5555, see description below
+         socket-ID for server = \*:5555, see description below
+       *mpi/one* arg = none
+       *mpi/two* arg = filename
+         filename = file used to establish communication between 2 MPI jobs
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   message client md file tmp.couple
+   message server md file tmp.couple
+
+   message client md zmq localhost:5555
+   message server md zmq \*:5555
+
+   message client md mpi/one
+   message server md mpi/one
+
+   message client md mpi/two tmp.couple
+   message server md mpi/two tmp.couple
+
+Description
+"""""""""""
+
+Establish a messaging protocol between LAMMPS and another code for the
+purpose of client/server coupling.
+
+The :doc:`Howto client/server <Howto_client_server>` doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code.  The server responds to each request with a reply message.  This
+enables the two codes to work in tandem to perform a simulation.
+
+
+----------
+
+
+The *which* argument defines LAMMPS to be the client or the server.
+
+
+----------
+
+
+The *protocol* argument defines the format and content of messages
+that will be exchanged between the two codes.  The current options
+are:
+
+* md = run dynamics with another code
+* mc = perform Monte Carlo moves with another code
+
+For protocol *md*\ , LAMMPS can be either a client or server.  See the
+:doc:`server md <server_md>` doc page for details on the protocol.
+
+For protocol *mc*\ , LAMMPS can be the server.  See the :doc:`server mc <server_mc>` doc page for details on the protocol.
+
+
+----------
+
+
+The *mode* argument specifies how messages are exchanged between the
+client and server codes.  Both codes must use the same mode and use
+consistent parameters.
+
+For mode *file*\ , the 2 codes communicate via binary files.  They must
+use the same filename, which is actually a file prefix.  Several files
+with that prefix will be created and deleted as a simulation runs.
+The filename can include a path.  Both codes must be able to access
+the path/file in a common filesystem.
+
+For mode *zmq*\ , the 2 codes communicate via a socket on the server
+code's machine.  Support for socket messaging is provided by the
+open-source `ZeroMQ library <http://zeromq.org>`_, which must be
+installed on your system.  The client specifies an IP address (IPv4
+format) or the DNS name of the machine the server code is running on,
+followed by a 4-digit port ID for the socket, separated by a colon.
+E.g.
+
+
+.. parsed-literal::
+
+   localhost:5555        # client and server running on same machine
+   192.168.1.1:5555      # server is 192.168.1.1
+   deptbox.uni.edu:5555  # server is deptbox.uni.edu
+
+The server specifies "\*:5555" where "\*" represents all available
+interfaces on the server's machine, and the port ID must match
+what the client specifies.
+
+.. note::
+
+   What are allowed port IDs?
+
+.. note::
+
+   Additional explanation is needed here about how to use the *zmq*
+   mode on a parallel machine, e.g. a cluster with many nodes.
+
+For mode *mpi/one*\ , the 2 codes communicate via MPI and are launched
+by the same mpirun command, e.g. with this syntax for OpenMPI:
+
+
+.. parsed-literal::
+
+   mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args  # LAMMPS is client
+   mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server  # LAMMPS is server
+
+Note the use of the "-mpicolor color" command-line argument with
+LAMMPS.  See the :doc:`command-line args <Run_options>` doc page for
+further explanation.
+
+For mode *mpi/two*\ , the 2 codes communicate via MPI, but are launched
+be 2 separate mpirun commands.  The specified *filename* argument is a
+file the 2 MPI processes will use to exchange info so that an MPI
+inter-communicator can be established to enable the 2 codes to send
+MPI messages to each other.  Both codes must be able to access the
+path/file in a common filesystem.
+
+
+----------
+
+
+Normally, the message command should be used at the top of a LAMMPS
+input script.  It performs an initial handshake with the other code to
+setup messaging and to verify that both codes are using the same
+message protocol and mode.  Assuming both codes are launched at
+(nearly) the same time, the other code should perform the same kind of
+initialization.
+
+If LAMMPS is the client code, it will begin sending messages when a
+LAMMPS client command begins its operation.  E.g. for the :doc:`fix client/md <fix_client_md>` command, it is when a :doc:`run <run>`
+command is executed.
+
+If LAMMPS is the server code, it will begin receiving messages when
+the :doc:`server <server>` command is invoked.
+
+A fix client command will terminate its messaging with the server when
+LAMMPS ends, or the fix is deleted via the :doc:`unfix <unfix>` command.
+The server command will terminate its messaging with the client when the
+client signals it.  Then the remainder of the LAMMPS input script will
+be processed.
+
+If both codes do something similar, this means a new round of
+client/server messaging can be initiated after termination by re-using
+a 2nd message command in your LAMMPS input script, followed by a new
+fix client or server command.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the MESSAGE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`server <server>`, :doc:`fix client/md <fix_client_md>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst
new file mode 100644
index 0000000000..6b25a1d32d
--- /dev/null
+++ b/doc/src/min_modify.rst
@@ -0,0 +1,155 @@
+.. index:: min\_modify
+
+min\_modify command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   min_modify keyword values ...
+
+* one or more keyword/value pairs may be listed
+  
+  .. parsed-literal::
+  
+     keyword = *dmax* or *line* or *norm* or *alpha_damp* or *discrete_factor*
+       *dmax* value = max
+         max = maximum distance for line search to move (distance units)
+       *line* value = *backtrack* or *quadratic* or *forcezero* or *spin_cubic* or *spin_none*
+         backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use 
+       *norm* value = *two* or *max*
+         two = Euclidean two-norm (length of 3N vector)
+         inf = max force component across all 3-vectors
+         max = max force norm across all 3-vectors
+       *alpha_damp* value = damping
+         damping = fictitious Gilbert damping for spin minimization (adim)
+       *discrete_factor* value = factor
+         factor = discretization factor for adaptive spin timestep (adim)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   min_modify dmax 0.2
+
+Description
+"""""""""""
+
+This command sets parameters that affect the energy minimization
+algorithms selected by the :doc:`min\_style <min_style>` command.  The
+various settings may affect the convergence rate and overall number of
+force evaluations required by a minimization, so users can experiment
+with these parameters to tune their minimizations.
+
+The *cg* and *sd* minimization styles have an outer iteration and an
+inner iteration which is steps along a one-dimensional line search in
+a particular search direction.  The *dmax* parameter is how far any
+atom can move in a single line search in any dimension (x, y, or z).
+For the *quickmin* and *fire* minimization styles, the *dmax* setting
+is how far any atom can move in a single iteration (timestep).  Thus a
+value of 0.1 in real :doc:`units <units>` means no atom will move
+further than 0.1 Angstroms in a single outer iteration.  This prevents
+highly overlapped atoms from being moved long distances (e.g. through
+another atom) due to large forces.
+
+The choice of line search algorithm for the *cg* and *sd* minimization
+styles can be selected via the *line* keyword.
+The default *quadratic* line search algorithm starts out using
+the robust backtracking method described below. However, once
+the system gets close to a local
+minimum and the linesearch steps get small, so that the energy
+is approximately quadratic in the step length, it uses the
+estimated location of zero gradient as the linesearch step,
+provided the energy change is downhill.
+This becomes more efficient than backtracking
+for highly-converged relaxations. The *forcezero*
+line search algorithm is similar to *quadratic*\ .
+It may be more efficient than *quadratic* on some systems.
+
+The backtracking search is robust and should always find a local energy
+minimum.  However, it will "converge" when it can no longer reduce the
+energy of the system.  Individual atom forces may still be larger than
+desired at this point, because the energy change is measured as the
+difference of two large values (energy before and energy after) and
+that difference may be smaller than machine epsilon even if atoms
+could move in the gradient direction to reduce forces further.
+
+The choice of a norm can be modified for the min styles *cg*\ , *sd*\ , 
+*quickmin*\ , *fire*\ , *spin*\ , *spin/cg* and *spin/lbfgs* using 
+the *norm* keyword.
+The default *two* norm computes the 2-norm (Euclidean length) of the
+global force vector:
+
+.. image:: Eqs/norm_two.jpg
+   :align: center
+
+The *max* norm computes the length of the 3-vector force 
+for each atom  (2-norm), and takes the maximum value of those across 
+all atoms
+
+.. image:: Eqs/norm_max.jpg
+   :align: center
+
+The *inf* norm takes the maximum component across the forces of
+all atoms in the system:
+
+.. image:: Eqs/norm_inf.jpg
+   :align: center
+
+For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force
+norm is replaced by the spin-torque norm.
+
+Keywords *alpha\_damp* and *discrete\_factor* only make sense when
+a :doc:`min\_spin <min_spin>` command is declared.
+Keyword *alpha\_damp* defines an analog of a magnetic Gilbert
+damping. It defines a relaxation rate toward an equilibrium for
+a given magnetic system.
+Keyword *discrete\_factor* defines a discretization factor for the
+adaptive timestep used in the *spin* minimization.
+See :doc:`min\_spin <min_spin>` for more information about those
+quantities.
+
+The choice of a line search algorithm for the *spin/cg* and
+*spin/lbfgs* styles can be specified via the *line* keyword.
+The *spin\_cubic* and  *spin\_none* only make sense when one of those 
+two minimization styles is declared.
+The *spin\_cubic* performs the line search based on a cubic interpolation
+of the energy along the search direction. The *spin\_none* keyword
+deactivates the line search procedure.
+The *spin\_none* is a default value for *line* keyword for both *spin/lbfgs*
+and *spin/cg*\ . Convergence of *spin/lbfgs* can be more robust if
+*spin\_cubic* line search is used.
+
+Restrictions
+""""""""""""
+
+
+For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used
+when styles *spin/cg* and *spin/lbfgs* are employed.
+See :doc:`neb/spin <neb_spin>` for more explanation.
+
+Related commands
+""""""""""""""""
+
+:doc:`min\_style <min_style>`, :doc:`minimize <minimize>`
+
+Default
+"""""""
+
+The option defaults are dmax = 0.1, line = quadratic and norm = two.
+
+For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the
+option defaults are alpha\_damp = 1.0, discrete\_factor = 10.0,
+line = spin\_none, and norm = euclidean.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst
new file mode 100644
index 0000000000..1535a1067f
--- /dev/null
+++ b/doc/src/min_spin.rst
@@ -0,0 +1,133 @@
+.. index:: min\_style spin
+
+min\_style spin command
+=======================
+
+min\_style spin/cg command
+==========================
+
+min\_style spin/lbfgs command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   min_style spin 
+   min_style spin/cg 
+   min_style spin/lbfgs
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   min_style  spin/lbfgs
+   min_modify line spin_cubic discrete_factor 10.0
+
+Description
+"""""""""""
+
+Apply a minimization algorithm to use when a :doc:`minimize <minimize>`
+command is performed.
+
+Style *spin* defines a damped spin dynamics with an adaptive
+timestep, according to:
+
+.. image:: Eqs/min_spin_damping.jpg
+   :align: center
+
+with lambda a damping coefficient (similar to a Gilbert
+damping).
+Lambda can be defined by setting the *alpha\_damp* keyword with the
+:doc:`min\_modify <min_modify>` command.
+
+The minimization procedure solves this equation using an
+adaptive timestep. The value of this timestep is defined
+by the largest precession frequency that has to be solved in the
+system:
+
+.. image:: Eqs/min_spin_timestep.jpg
+   :align: center
+
+with *\|omega\|\_\ *max*\ * the norm of the largest precession frequency
+in the system (across all processes, and across all replicas if a
+spin/neb calculation is performed).
+
+Kappa defines a discretization factor *discrete\_factor* for the
+definition of this timestep.
+*discrete\_factor* can be defined with the :doc:`min\_modify <min_modify>`
+command.
+
+Style *spin/cg* defines an orthogonal spin optimization
+(OSO) combined to a conjugate gradient (CG) algorithm. 
+The :doc:`min\_modify <min_modify>` command can be used to
+couple the *spin/cg* to a line search procedure, and to modify the 
+discretization factor *discrete\_factor*.
+By default, style *spin/cg* does not employ the line search procedure 
+and uses the adaptive time-step technique in the same way as style *spin*\ .
+
+Style *spin/lbfgs* defines an orthogonal spin optimization
+(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno 
+(L-BFGS) algorithm.
+By default, style *spin/lbfgs* does not employ line search procedure.
+If the line search procedure is not used then the discrete factor defines
+the maximum root mean squared rotation angle of spins by equation *pi/(5\*Kappa)*.
+The default value for Kappa is 10.
+The *spin\_cubic* line search can improve the convergence of the 
+*spin/lbfgs* algorithm.
+
+The :doc:`min\_modify <min_modify>` command can be used to
+activate the line search procedure, and to modify the
+discretization factor *discrete\_factor*.
+
+For more information about styles *spin/cg* and *spin/lbfgs*\ , 
+see their implementation reported in :ref:`(Ivanov) <Ivanov1>`.
+
+.. note::
+
+   All the *spin* styles replace the force tolerance by a torque
+   tolerance. See :doc:`minimize <minimize>` for more explanation.
+
+.. note::
+
+   The *spin/cg* and *spin/lbfgs* styles can be used
+   for magnetic NEB calculations only if the line search procedure
+   is deactivated. See :doc:`neb/spin <neb_spin>` for more explanation.
+
+Restrictions
+""""""""""""
+
+
+This minimization procedure is only applied to spin degrees of
+freedom for a frozen lattice configuration.
+
+Related commands
+""""""""""""""""
+
+:doc:`min\_style <min_style>`, :doc:`minimize <minimize>`,
+:doc:`min\_modify <min_modify>`
+
+Default
+"""""""
+
+The option defaults are *alpha\_damp* = 1.0, *discrete\_factor* =
+10.0, *line* = spin\_none and *norm* = euclidean.
+
+
+----------
+
+
+.. _Ivanov1:
+
+
+
+**(Ivanov)** Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/min_spin.txt b/doc/src/min_spin.txt
deleted file mode 100644
index 890e324aca..0000000000
--- a/doc/src/min_spin.txt
+++ /dev/null
@@ -1,65 +0,0 @@
-"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-:line
-
-min_style spin command :h3
-
-[Syntax:]
-
-min_style spin :pre
-
-[Examples:]
-
-min_style 	spin :pre 
-
-[Description:]
-
-Apply a minimization algorithm to use when a "minimize"_minimize.html
-command is performed.
-
-Style {spin} defines a damped spin dynamics with an adaptive
-timestep, according to:
-
-:c,image(Eqs/min_spin_damping.jpg)
-
-with lambda a damping coefficient (similar to a Gilbert
-damping).
-Lambda can be defined by setting the {alpha_damp} keyword with the 
-"min_modify"_min_modify.html command. 
-
-The minimization procedure solves this equation using an
-adaptive timestep. The value of this timestep is defined 
-by the largest precession frequency that has to be solved in the 
-system:
-
-:c,image(Eqs/min_spin_timestep.jpg)
-
-with {|omega|_{max}} the norm of the largest precession frequency
-in the system (across all processes, and across all replicas if a
-spin/neb calculation is performed). 
-
-Kappa defines a discretization factor {discrete_factor} for the 
-definition of this timestep. 
-{discrete_factor} can be defined with the "min_modify"_min_modify.html
-command.
-
-NOTE: The {spin} style replaces the force tolerance by a torque
-tolerance. See "minimize"_minimize.html for more explanation. 
-
-[Restrictions:] 
-
-This minimization procedure is only applied to spin degrees of
-freedom for a frozen lattice configuration.
-
-[Related commands:]
-
-"min_style"_min_style.html, "minimize"_minimize.html, 
-"min_modify"_min_modify.html
-
-[Default:]
-
-The option defaults are {alpha_damp} = 1.0 and {discrete_factor} =
-10.0.
diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst
new file mode 100644
index 0000000000..91accc7967
--- /dev/null
+++ b/doc/src/min_style.rst
@@ -0,0 +1,170 @@
+.. index:: min\_style
+
+min\_style command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   min_style style
+
+* style = *cg* or *hftn* or *sd* or *quickmin* or *fire* or *spin* or *spin/cg* or *spin/lbfgs*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   min_style cg
+   min_style spin
+   min_style fire
+
+Description
+"""""""""""
+
+Choose a minimization algorithm to use when a :doc:`minimize <minimize>`
+command is performed.
+
+Style *cg* is the Polak-Ribiere version of the conjugate gradient (CG)
+algorithm.  At each iteration the force gradient is combined with the
+previous iteration information to compute a new search direction
+perpendicular (conjugate) to the previous search direction.  The PR
+variant affects how the direction is chosen and how the CG method is
+restarted when it ceases to make progress.  The PR variant is thought
+to be the most effective CG choice for most problems.
+
+Style *hftn* is a Hessian-free truncated Newton algorithm.  At each
+iteration a quadratic model of the energy potential is solved by a
+conjugate gradient inner iteration.  The Hessian (second derivatives)
+of the energy is not formed directly, but approximated in each
+conjugate search direction by a finite difference directional
+derivative.  When close to an energy minimum, the algorithm behaves
+like a Newton method and exhibits a quadratic convergence rate to high
+accuracy.  In most cases the behavior of *hftn* is similar to *cg*\ ,
+but it offers an alternative if *cg* seems to perform poorly.  This
+style is not affected by the :doc:`min\_modify <min_modify>` command.
+
+Style *sd* is a steepest descent algorithm.  At each iteration, the
+search direction is set to the downhill direction corresponding to the
+force vector (negative gradient of energy).  Typically, steepest
+descent will not converge as quickly as CG, but may be more robust in
+some situations.
+
+Style *quickmin* is a damped dynamics method described in
+:ref:`(Sheppard) <Sheppard>`, where the damping parameter is related to the
+projection of the velocity vector along the current force vector for
+each atom.  The velocity of each atom is initialized to 0.0 by this
+style, at the beginning of a minimization.
+
+Style *fire* is a damped dynamics method described in
+:ref:`(Bitzek) <Bitzek>`, which is similar to *quickmin* but adds a variable
+timestep and alters the projection operation to maintain components of
+the velocity non-parallel to the current force vector.  The velocity
+of each atom is initialized to 0.0 by this style, at the beginning of
+a minimization.
+
+Style *spin* is a damped spin dynamics with an adaptive
+timestep.
+
+Style *spin/cg* uses an orthogonal spin optimization (OSO)
+combined to a conjugate gradient (CG) approach to minimize spin
+configurations.
+
+Style *spin/lbfgs* uses an orthogonal spin optimization (OSO)
+combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
+(LBFGS) approach to minimize spin configurations.
+
+See the :doc:`min/spin <min_spin>` doc page for more information
+about the *spin*\ , *spin/cg* and *spin/lbfgs* styles.
+
+Either the *quickmin* and *fire* styles are useful in the context of
+nudged elastic band (NEB) calculations via the :doc:`neb <neb>` command.
+
+Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful 
+in the context of magnetic geodesic nudged elastic band (GNEB) calculations 
+via the :doc:`neb/spin <neb_spin>` command.
+
+.. note::
+
+   The damped dynamic minimizers use whatever timestep you have
+   defined via the :doc:`timestep <timestep>` command.  Often they will
+   converge more quickly if you use a timestep about 10x larger than you
+   would normally use for dynamics simulations.
+
+.. note::
+
+   The *quickmin*\ , *fire*\ , *hftn*\ , and *cg/kk* styles do not yet
+   support the use of the :doc:`fix box/relax <fix_box_relax>` command or
+   minimizations involving the electron radius in :doc:`eFF <pair_eff>`
+   models.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`min\_modify <min_modify>`, :doc:`minimize <minimize>`, :doc:`neb <neb>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   min_style cg
+
+
+----------
+
+
+.. _Sheppard:
+
+
+
+**(Sheppard)** Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106
+(2008).  See ref 1 in this paper for original reference to Qmin in
+Jonsson, Mills, Jacobsen.
+
+.. _Bitzek:
+
+
+
+**(Bitzek)** Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
+97, 170201 (2006).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst
new file mode 100644
index 0000000000..668759401e
--- /dev/null
+++ b/doc/src/minimize.rst
@@ -0,0 +1,344 @@
+.. index:: minimize
+
+minimize command
+================
+
+minimize/kk command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   minimize etol ftol maxiter maxeval
+
+* etol = stopping tolerance for energy (unitless)
+* ftol = stopping tolerance for force (force units)
+* maxiter = max iterations of minimizer
+* maxeval = max number of force/energy evaluations
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   minimize 1.0e-4 1.0e-6 100 1000
+   minimize 0.0 1.0e-8 1000 100000
+
+Description
+"""""""""""
+
+Perform an energy minimization of the system, by iteratively adjusting
+atom coordinates.  Iterations are terminated when one of the stopping
+criteria is satisfied.  At that point the configuration will hopefully
+be in local potential energy minimum.  More precisely, the
+configuration should approximate a critical point for the objective
+function (see below), which may or may not be a local minimum.
+
+The minimization algorithm used is set by the
+:doc:`min\_style <min_style>` command.  Other options are set by the
+:doc:`min\_modify <min_modify>` command.  Minimize commands can be
+interspersed with :doc:`run <run>` commands to alternate between
+relaxation and dynamics.  The minimizers bound the distance atoms move
+in one iteration, so that you can relax systems with highly overlapped
+atoms (large energies and forces) by pushing the atoms off of each
+other.
+
+Alternate means of relaxing a system are to run dynamics with a small
+or :doc:`limited timestep <fix_nve_limit>`.  Or dynamics can be run
+using :doc:`fix viscous <fix_viscous>` to impose a damping force that
+slowly drains all kinetic energy from the system.  The :doc:`pair\_style soft <pair_soft>` potential can be used to un-overlap atoms while
+running dynamics.
+
+Note that you can minimize some atoms in the system while holding the
+coordinates of other atoms fixed by applying :doc:`fix setforce <fix_setforce>` to the other atoms.  See a fuller
+discussion of using fixes while minimizing below.
+
+The :doc:`minimization styles <min_style>` *cg*\ , *sd*\ , and *hftn*
+involves an outer iteration loop which sets the search direction along
+which atom coordinates are changed.  An inner iteration is then
+performed using a line search algorithm.  The line search typically
+evaluates forces and energies several times to set new coordinates.
+Currently, a backtracking algorithm is used which may not be optimal
+in terms of the number of force evaluations performed, but appears to
+be more robust than previous line searches we've tried.  The
+backtracking method is described in Nocedal and Wright's Numerical
+Optimization (Procedure 3.1 on p 41).
+
+The :doc:`minimization styles <min_style>` *quickmin* and *fire* perform
+damped dynamics using an Euler integration step.  Thus they require a
+:doc:`timestep <timestep>` be defined.
+
+.. note::
+
+   The damped dynamic minimizers use whatever timestep you have
+   defined via the :doc:`timestep <timestep>` command.  Often they will
+   converge more quickly if you use a timestep about 10x larger than you
+   would normally use for dynamics simulations.
+
+
+----------
+
+
+In all cases, the objective function being minimized is the total
+potential energy of the system as a function of the N atom
+coordinates:
+
+.. image:: Eqs/min_energy.jpg
+   :align: center
+
+where the first term is the sum of all non-bonded :doc:`pairwise interactions <pair_style>` including :doc:`long-range Coulombic interactions <kspace_style>`, the 2nd through 5th terms are
+:doc:`bond <bond_style>`, :doc:`angle <angle_style>`,
+:doc:`dihedral <dihedral_style>`, and :doc:`improper <improper_style>`
+interactions respectively, and the last term is energy due to
+:doc:`fixes <fix>` which can act as constraints or apply force to atoms,
+such as through interaction with a wall.  See the discussion below about
+how fix commands affect minimization.
+
+The starting point for the minimization is the current configuration
+of the atoms.
+
+
+----------
+
+
+The minimization procedure stops if any of several criteria are met:
+
+* the change in energy between outer iterations is less than *etol*
+* the 2-norm (length) of the global force vector is less than the *ftol*
+* the line search fails because the step distance backtracks to 0.0
+* the number of outer iterations or timesteps exceeds *maxiter*
+* the number of total force evaluations exceeds *maxeval*
+
+.. note::
+
+   the :doc:`minimization style <min_style>` *spin*\ ,
+   *spin/cg*\ , and *spin/lbfgs* replace
+   the force tolerance *ftol* by a torque tolerance.
+   The minimization procedure stops if the 2-norm (length) of the torque vector on atom
+   (defined as the cross product between the
+   atomic spin and its precession vectors omega) is less than *ftol*\ ,
+   or if any of the other criteria are met. Torque have the same units as the energy.
+
+.. note::
+
+   You can also use the :doc:`fix halt <fix_halt>` command to specify
+   a general criterion for exiting a minimization, that is a calculation
+   performed on the state of the current system, as defined by an
+   :doc:`equal-style variable <variable>`.
+
+For the first criterion, the specified energy tolerance *etol* is
+unitless; it is met when the energy change between successive
+iterations divided by the energy magnitude is less than or equal to
+the tolerance.  For example, a setting of 1.0e-4 for *etol* means an
+energy tolerance of one part in 10\^4.  For the damped dynamics
+minimizers this check is not performed for a few steps after
+velocities are reset to 0, otherwise the minimizer would prematurely
+converge.
+
+For the second criterion, the specified force tolerance *ftol* is in
+force units, since it is the length of the global force vector for all
+atoms, e.g. a vector of size 3N for N atoms.  Since many of the
+components will be near zero after minimization, you can think of
+*ftol* as an upper bound on the final force on any component of any
+atom.  For example, a setting of 1.0e-4 for *ftol* means no x, y, or z
+component of force on any atom will be larger than 1.0e-4 (in force
+units) after minimization.
+
+Either or both of the *etol* and *ftol* values can be set to 0.0, in
+which case some other criterion will terminate the minimization.
+
+During a minimization, the outer iteration count is treated as a
+timestep.  Output is triggered by this timestep, e.g. thermodynamic
+output or dump and restart files.
+
+Using the :doc:`thermo\_style custom <thermo_style>` command with the
+*fmax* or *fnorm* keywords can be useful for monitoring the progress
+of the minimization.  Note that these outputs will be calculated only
+from forces on the atoms, and will not include any extra degrees of
+freedom, such as from the :doc:`fix box/relax <fix_box_relax>` command.
+
+Following minimization, a statistical summary is printed that lists
+which convergence criterion caused the minimizer to stop, as well as
+information about the energy, force, final line search, and
+iteration counts.  An example is as follows:
+
+
+.. parsed-literal::
+
+   Minimization stats:
+     Stopping criterion = max iterations
+     Energy initial, next-to-last, final =
+          -0.626828169302     -2.82642039062     -2.82643549739
+     Force two-norm initial, final = 2052.1 91.9642
+     Force max component initial, final = 346.048 9.78056
+     Final line search alpha, max atom move = 2.23899e-06 2.18986e-05
+     Iterations, force evaluations = 2000 12724
+
+The 3 energy values are for before and after the minimization and on
+the next-to-last iteration.  This is what the *etol* parameter checks.
+
+The two-norm force values are the length of the global force vector
+before and after minimization.  This is what the *ftol* parameter
+checks.
+
+The max-component force values are the absolute value of the largest
+component (x,y,z) in the global force vector, i.e. the infinity-norm
+of the force vector.
+
+The alpha parameter for the line-search, when multiplied by the max
+force component (on the last iteration), gives the max distance any
+atom moved during the last iteration.  Alpha will be 0.0 if the line
+search could not reduce the energy.  Even if alpha is non-zero, if the
+"max atom move" distance is tiny compared to typical atom coordinates,
+then it is possible the last iteration effectively caused no atom
+movement and thus the evaluated energy did not change and the
+minimizer terminated.  Said another way, even with non-zero forces,
+it's possible the effect of those forces is to move atoms a distance
+less than machine precision, so that the energy cannot be further
+reduced.
+
+The iterations and force evaluation values are what is checked by the
+*maxiter* and *maxeval* parameters.
+
+
+----------
+
+
+.. note::
+
+   There are several force fields in LAMMPS which have
+   discontinuities or other approximations which may prevent you from
+   performing an energy minimization to high tolerances.  For example,
+   you should use a :doc:`pair style <pair_style>` that goes to 0.0 at the
+   cutoff distance when performing minimization (even if you later change
+   it when running dynamics).  If you do not do this, the total energy of
+   the system will have discontinuities when the relative distance
+   between any pair of atoms changes from cutoff+epsilon to
+   cutoff-epsilon and the minimizer may behave poorly.  Some of the
+   many-body potentials use splines and other internal cutoffs that
+   inherently have this problem.  The :doc:`long-range Coulombic styles <kspace_style>` (PPPM, Ewald) are approximate to within the
+   user-specified tolerance, which means their energy and forces may not
+   agree to a higher precision than the Kspace-specified tolerance.  In
+   all these cases, the minimizer may give up and stop before finding a
+   minimum to the specified energy or force tolerance.
+
+Note that a cutoff Lennard-Jones potential (and others) can be shifted
+so that its energy is 0.0 at the cutoff via the
+:doc:`pair\_modify <pair_modify>` command.  See the doc pages for
+individual :doc:`pair styles <pair_style>` for details.  Note that
+Coulombic potentials always have a cutoff, unless versions with a
+long-range component are used (e.g. :doc:`pair\_style lj/cut/coul/long <pair_lj>`).  The CHARMM potentials go to 0.0 at
+the cutoff (e.g. :doc:`pair\_style lj/charmm/coul/charmm <pair_charmm>`),
+as do the GROMACS potentials (e.g. :doc:`pair\_style lj/gromacs <pair_gromacs>`).
+
+If a soft potential (:doc:`pair\_style soft <pair_soft>`) is used the
+Astop value is used for the prefactor (no time dependence).
+
+The :doc:`fix box/relax <fix_box_relax>` command can be used to apply an
+external pressure to the simulation box and allow it to shrink/expand
+during the minimization.
+
+Only a few other fixes (typically those that add forces) are invoked
+during minimization.  See the doc pages for individual :doc:`fix <fix>`
+commands to see which ones are relevant.  Current examples of fixes
+that can be used include:
+
+* :doc:`fix addforce <fix_addforce>`
+* :doc:`fix addtorque <fix_addtorque>`
+* :doc:`fix efield <fix_efield>`
+* :doc:`fix enforce2d <fix_enforce2d>`
+* :doc:`fix indent <fix_indent>`
+* :doc:`fix lineforce <fix_lineforce>`
+* :doc:`fix planeforce <fix_planeforce>`
+* :doc:`fix setforce <fix_setforce>`
+* :doc:`fix spring <fix_spring>`
+* :doc:`fix spring/self <fix_spring_self>`
+* :doc:`fix viscous <fix_viscous>`
+* :doc:`fix wall <fix_wall>`
+* :doc:`fix wall/region <fix_wall_region>`
+
+.. note::
+
+   Some fixes which are invoked during minimization have an
+   associated potential energy.  For that energy to be included in the
+   total potential energy of the system (the quantity being minimized),
+   you MUST enable the :doc:`fix\_modify <fix_modify>` *energy* option for
+   that fix.  The doc pages for individual :doc:`fix <fix>` commands
+   specify if this should be done.
+
+.. note::
+
+   The minimizers in LAMMPS do not allow for bonds (or angles, etc)
+   to be held fixed while atom coordinates are being relaxed, e.g. via
+   :doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`.  See more
+   info in the Restrictions section below.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Features that are not yet implemented are listed here, in case someone
+knows how they could be coded:
+
+It is an error to use :doc:`fix shake <fix_shake>` with minimization
+because it turns off bonds that should be included in the potential
+energy of the system.  The effect of a fix shake can be approximated
+during a minimization by using stiff spring constants for the bonds
+and/or angles that would normally be constrained by the SHAKE
+algorithm.
+
+:doc:`Fix rigid <fix_rigid>` is also not supported by minimization.  It
+is not an error to have it defined, but the energy minimization will
+not keep the defined body(s) rigid during the minimization.  Note that
+if bonds, angles, etc internal to a rigid body have been turned off
+(e.g. via :doc:`neigh\_modify exclude <neigh_modify>`), they will not
+contribute to the potential energy which is probably not what is
+desired.
+
+Pair potentials that produce torque on a particle (e.g. :doc:`granular potentials <pair_gran>` or the :doc:`GayBerne potential <pair_gayberne>` for ellipsoidal particles) are not
+relaxed by a minimization.  More specifically, radial relaxations are
+induced, but no rotations are induced by a minimization, so such a
+system will not fully relax.
+
+Related commands
+""""""""""""""""
+
+:doc:`min\_modify <min_modify>`, :doc:`min\_style <min_style>`,
+:doc:`run\_style <run_style>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst
new file mode 100644
index 0000000000..e4a8a40468
--- /dev/null
+++ b/doc/src/molecule.rst
@@ -0,0 +1,518 @@
+.. index:: molecule
+
+molecule command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   molecule ID file1 keyword values ... file2 keyword values ... fileN ...
+
+* ID = user-assigned name for the molecule template
+* file1,file2,... = names of files containing molecule descriptions
+* zero or more keyword/value pairs may be appended after each file
+* keyword = *offset* or *toff* or *boff* or *aoff* or *doff* or *ioff* or *scale*
+  
+  .. parsed-literal::
+  
+       *offset* values = Toff Boff Aoff Doff Ioff
+         Toff = offset to add to atom types
+         Boff = offset to add to bond types
+         Aoff = offset to add to angle types
+         Doff = offset to add to dihedral types
+         Ioff = offset to add to improper types
+       *toff* value = Toff
+         Toff = offset to add to atom types
+       *boff* value = Boff
+         Boff = offset to add to bond types
+       *aoff* value = Aoff
+         Aoff = offset to add to angle types
+       *doff* value = Doff
+         Doff = offset to add to dihedral types
+       *ioff* value = Ioff
+         Ioff = offset to add to improper types
+       *scale* value = sfactor
+         sfactor = scale factor to apply to the size and mass of the molecule
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   molecule 1 mymol.txt
+   molecule 1 co2.txt h2o.txt
+   molecule CO2 co2.txt boff 3 aoff 2
+   molecule 1 mymol.txt offset 6 9 18 23 14
+   molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3
+
+Description
+"""""""""""
+
+Define a molecule template that can be used as part of other LAMMPS
+commands, typically to define a collection of particles as a bonded
+molecule or a rigid body.  Commands that currently use molecule
+templates include:
+
+* :doc:`fix deposit <fix_deposit>`
+* :doc:`fix pour <fix_pour>`
+* :doc:`fix rigid/small <fix_rigid>`
+* :doc:`fix shake <fix_shake>`
+* :doc:`fix gcmc <fix_gcmc>`
+* :doc:`create\_atoms <create_atoms>`
+* :doc:`atom\_style template <atom_style>`
+
+The ID of a molecule template can only contain alphanumeric characters
+and underscores.
+
+A single template can contain multiple molecules, listed one per file.
+Some of the commands listed above currently use only the first
+molecule in the template, and will issue a warning if the template
+contains multiple molecules.  The :doc:`atom\_style template <atom_style>` command allows multiple-molecule templates
+to define a system with more than one templated molecule.
+
+Each filename can be followed by optional keywords which are applied
+only to the molecule in the file as used in this template.  This is to
+make it easy to use the same molecule file in different molecule
+templates or in different simulations.  You can specify the same file
+multiple times with different optional keywords.
+
+The *offset*\ , *toff*\ , *aoff*\ , *doff*\ , *ioff* keywords add the
+specified offset values to the atom types, bond types, angle types,
+dihedral types, and/or improper types as they are read from the
+molecule file.  E.g. if *toff* = 2, and the file uses atom types
+1,2,3, then each created molecule will have atom types 3,4,5.  For the
+*offset* keyword, all five offset values must be specified, but
+individual values will be ignored if the molecule template does not
+use that attribute (e.g. no bonds).
+
+The *scale* keyword scales the size of the molecule.  This can be
+useful for modeling polydisperse granular rigid bodies.  The scale
+factor is applied to each of these properties in the molecule file, if
+they are defined: the individual particle coordinates (Coords
+section), the individual mass of each particle (Masses section), the
+individual diameters of each particle (Diameters section), the total
+mass of the molecule (header keyword = mass), the center-of-mass of
+the molecule (header keyword = com), and the moments of inertia of the
+molecule (header keyword = inertia).
+
+.. note::
+
+   The molecule command can be used to define molecules with bonds,
+   angles, dihedrals, impropers, or special bond lists of neighbors
+   within a molecular topology, so that you can later add the molecules
+   to your simulation, via one or more of the commands listed above.
+   Since this topology-related information requires that suitable storage
+   is reserved when LAMMPS creates the simulation box (e.g. when using
+   the :doc:`create\_box <create_box>` command or the
+   :doc:`read\_data <read_data>` command) suitable space has to be reserved
+   so you do not overflow those pre-allocated data structures when adding
+   molecules later.  Both the :doc:`create\_box <create_box>` command and
+   the :doc:`read\_data <read_data>` command have "extra" options which
+   insure space is allocated for storing topology info for molecules that
+   are added later.
+
+The format of an individual molecule file is similar but
+(not identical) to the data file read by the :doc:`read\_data <read_data>`
+commands, and is as follows.
+
+A molecule file has a header and a body.  The header appears first.
+The first line of the header is always skipped; it typically contains
+a description of the file.  Then lines are read one at a time.  Lines
+can have a trailing comment starting with '#' that is ignored.  If the
+line is blank (only white-space after comment is deleted), it is
+skipped.  If the line contains a header keyword, the corresponding
+value(s) is read from the line.  If it doesn't contain a header
+keyword, the line begins the body of the file.
+
+The body of the file contains zero or more sections.  The first line
+of a section has only a keyword.  The next line is skipped.  The
+remaining lines of the section contain values.  The number of lines
+depends on the section keyword as described below.  Zero or more blank
+lines can be used between sections.  Sections can appear in any order,
+with a few exceptions as noted below.
+
+These are the recognized header keywords.  Header lines can come in
+any order.  The numeric value(s) are read from the beginning of the
+line.  The keyword should appear at the end of the line.  All these
+settings have default values, as explained below.  A line need only
+appear if the value(s) are different than the default.
+
+* N *atoms* = # of atoms N in molecule, default = 0
+* Nb *bonds* = # of bonds Nb in molecule, default = 0
+* Na *angles* = # of angles Na in molecule, default = 0
+* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
+* Ni *impropers* = # of impropers Ni in molecule, default = 0
+* Mtotal *mass* = total mass of molecule
+* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
+* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
+
+For *mass*\ , *com*\ , and *inertia*\ , the default is for LAMMPS to
+calculate this quantity itself if needed, assuming the molecules
+consists of a set of point particles or finite-size particles (with a
+non-zero diameter) that do not overlap.  If finite-size particles in
+the molecule do overlap, LAMMPS will not account for the overlap
+effects when calculating any of these 3 quantities, so you should
+pre-compute them yourself and list the values in the file.
+
+The mass and center-of-mass coordinates (Xc,Yc,Zc) are
+self-explanatory.  The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
+should be the values consistent with the current orientation of the
+rigid body around its center of mass.  The values are with respect to
+the simulation box XYZ axes, not with respect to the principal axes of
+the rigid body itself.  LAMMPS performs the latter calculation
+internally.
+
+These are the allowed section keywords for the body of the file.
+
+* *Coords, Types, Charges, Diameters, Masses* = atom-property sections
+* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
+* *Special Bond Counts, Special Bonds* = special neighbor info
+* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
+
+If a Bonds section is specified then the Special Bond Counts and
+Special Bonds sections can also be used, if desired, to explicitly
+list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
+details below).  This is optional since if these sections are not
+included, LAMMPS will auto-generate this information.  Note that
+LAMMPS uses this info to properly exclude or weight bonded pairwise
+interactions between bonded atoms.  See the
+:doc:`special\_bonds <special_bonds>` command for more details.  One
+reason to list the special bond info explicitly is for the
+:doc:`thermalized Drude oscillator model <Howto_drude>` which treats the
+bonds between nuclear cores and Drude electrons in a different manner.
+
+.. note::
+
+   Whether a section is required depends on how the molecule
+   template is used by other LAMMPS commands.  For example, to add a
+   molecule via the :doc:`fix deposit <fix_deposit>` command, the Coords
+   and Types sections are required.  To add a rigid body via the :doc:`fix pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
+   required, since the molecule will be treated as a rigid body.  Some
+   sections are optional.  For example, the :doc:`fix pour <fix_pour>`
+   command can be used to add "molecules" which are clusters of
+   finite-size granular particles.  If the Diameters section is not
+   specified, each particle in the molecule will have a default diameter
+   of 1.0.  See the doc pages for LAMMPS commands that use molecule
+   templates for more details.
+
+Each section is listed below in alphabetic order.  The format of each
+section is described including the number of lines it must contain and
+rules (if any) for whether it can appear in the data file.  In each
+case the ID is ignored; it is simply included for readability, and
+should be a number from 1 to Nlines for the section, indicating which
+atom (or bond, etc) the entry applies to.  The lines are assumed to be
+listed in order from 1 to Nlines, but LAMMPS does not check for this.
+
+
+----------
+
+
+*Coords* section:
+
+* one line per atom
+* line syntax: ID x y z
+* x,y,z = coordinate of atom
+
+
+----------
+
+
+*Types* section:
+
+* one line per atom
+* line syntax: ID type
+* type = atom type of atom
+
+
+----------
+
+
+*Charges* section:
+
+* one line per atom
+* line syntax: ID q
+* q = charge on atom
+
+This section is only allowed for :doc:`atom styles <atom_style>` that
+support charge.  If this section is not included, the default charge
+on each atom in the molecule is 0.0.
+
+
+----------
+
+
+*Diameters* section:
+
+* one line per atom
+* line syntax: ID diam
+* diam = diameter of atom
+
+This section is only allowed for :doc:`atom styles <atom_style>` that
+support finite-size spherical particles, e.g. atom\_style sphere.  If
+not listed, the default diameter of each atom in the molecule is 1.0.
+
+
+----------
+
+
+*Masses* section:
+
+* one line per atom
+* line syntax: ID mass
+* mass = mass of atom
+
+This section is only allowed for :doc:`atom styles <atom_style>` that
+support per-atom mass, as opposed to per-type mass.  See the
+:doc:`mass <mass>` command for details.  If this section is not
+included, the default mass for each atom is derived from its volume
+(see Diameters section) and a default density of 1.0, in
+:doc:`units <units>` of mass/volume.
+
+
+----------
+
+
+*Bonds* section:
+
+* one line per bond
+* line syntax: ID type atom1 atom2
+* type = bond type (1-Nbondtype)
+* atom1,atom2 = IDs of atoms in bond
+
+The IDs for the two atoms in each bond should be values
+from 1 to Natoms, where Natoms = # of atoms in the molecule.
+
+
+----------
+
+
+*Angles* section:
+
+* one line per angle
+* line syntax: ID type atom1 atom2 atom3
+* type = angle type (1-Nangletype)
+* atom1,atom2,atom3 = IDs of atoms in angle
+
+The IDs for the three atoms in each angle should be values from 1 to
+Natoms, where Natoms = # of atoms in the molecule.  The 3 atoms are
+ordered linearly within the angle.  Thus the central atom (around
+which the angle is computed) is the atom2 in the list.
+
+
+----------
+
+
+*Dihedrals* section:
+
+* one line per dihedral
+* line syntax: ID type atom1 atom2 atom3 atom4
+* type = dihedral type (1-Ndihedraltype)
+* atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
+
+The IDs for the four atoms in each dihedral should be values from 1 to
+Natoms, where Natoms = # of atoms in the molecule.  The 4 atoms are
+ordered linearly within the dihedral.
+
+
+----------
+
+
+*Impropers* section:
+
+* one line per improper
+* line syntax: ID type atom1 atom2 atom3 atom4
+* type = improper type (1-Nimpropertype)
+* atom1,atom2,atom3,atom4 = IDs of atoms in improper
+
+The IDs for the four atoms in each improper should be values from 1 to
+Natoms, where Natoms = # of atoms in the molecule.  The ordering of
+the 4 atoms determines the definition of the improper angle used in
+the formula for the defined :doc:`improper style <improper_style>`.  See
+the doc pages for individual styles for details.
+
+
+----------
+
+
+*Special Bond Counts* section:
+
+* one line per atom
+* line syntax: ID N1 N2 N3
+* N1 = # of 1-2 bonds
+* N2 = # of 1-3 bonds
+* N3 = # of 1-4 bonds
+
+N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
+this atom within the topology of the molecule.  See the
+:doc:`special\_bonds <special_bonds>` doc page for more discussion of
+1-2, 1-3, 1-4 neighbors.  If this section appears, the Special Bonds
+section must also appear.
+
+As explained above, LAMMPS will auto-generate this information if this
+section is not specified.  If specified, this section will
+override what would be auto-generated.
+
+
+----------
+
+
+*Special Bonds* section:
+
+* one line per atom
+* line syntax: ID a b c d ...
+* a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds
+
+A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
+1-4 neighbors of this atom.  The IDs should be values from 1 to
+Natoms, where Natoms = # of atoms in the molecule.  The first N1
+values should be the 1-2 neighbors, the next N2 should be the 1-3
+neighbors, the last N3 should be the 1-4 neighbors.  No atom ID should
+appear more than once.  See the :doc:`special\_bonds <special_bonds>` doc
+page for more discussion of 1-2, 1-3, 1-4 neighbors.  If this section
+appears, the Special Bond Counts section must also appear.
+
+As explained above, LAMMPS will auto-generate this information if this
+section is not specified.  If specified, this section will override
+what would be auto-generated.
+
+
+----------
+
+
+*Shake Flags* section:
+
+* one line per atom
+* line syntax: ID flag
+* flag = 0,1,2,3,4
+
+This section is only needed when molecules created using the template
+will be constrained by SHAKE via the "fix shake" command.  The other
+two Shake sections must also appear in the file, following this one.
+
+The meaning of the flag for each atom is as follows.  See the :doc:`fix shake <fix_shake>` doc page for a further description of SHAKE
+clusters.
+
+* 0 = not part of a SHAKE cluster
+* 1 = part of a SHAKE angle cluster (two bonds and the angle they form)
+* 2 = part of a 2-atom SHAKE cluster with a single bond
+* 3 = part of a 3-atom SHAKE cluster with two bonds
+* 4 = part of a 4-atom SHAKE cluster with three bonds
+
+
+----------
+
+
+*Shake Atoms* section:
+
+* one line per atom
+* line syntax: ID a b c d
+* a,b,c,d = IDs of atoms in cluster
+
+This section is only needed when molecules created using the template
+will be constrained by SHAKE via the "fix shake" command.  The other
+two Shake sections must also appear in the file.
+
+The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
+in the SHAKE cluster that this atom belongs to.  The number of values
+that must appear is determined by the shake flag for the atom (see the
+Shake Flags section above).  All atoms in a particular cluster should
+list their a,b,c,d values identically.
+
+If flag = 0, no a,b,c,d values are listed on the line, just the
+(ignored) ID.
+
+If flag = 1, a,b,c are listed, where a = ID of central atom in the
+angle, and b,c the other two atoms in the angle.
+
+If flag = 2, a,b are listed, where a = ID of atom in bond with the
+lowest ID, and b = ID of atom in bond with the highest ID.
+
+If flag = 3, a,b,c are listed, where a = ID of central atom,
+and b,c = IDs of other two atoms bonded to the central atom.
+
+If flag = 4, a,b,c,d are listed, where a = ID of central atom,
+and b,c,d = IDs of other three atoms bonded to the central atom.
+
+See the :doc:`fix shake <fix_shake>` doc page for a further description
+of SHAKE clusters.
+
+
+----------
+
+
+*Shake Bond Types* section:
+
+* one line per atom
+* line syntax: ID a b c
+* a,b,c = bond types (or angle type) of bonds (or angle) in cluster
+
+This section is only needed when molecules created using the template
+will be constrained by SHAKE via the "fix shake" command.  The other
+two Shake sections must also appear in the file.
+
+The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
+in the SHAKE cluster that this atom belongs to.  The number of values
+that must appear is determined by the shake flag for the atom (see the
+Shake Flags section above).  All atoms in a particular cluster should
+list their a,b,c values identically.
+
+If flag = 0, no a,b,c values are listed on the line, just the
+(ignored) ID.
+
+If flag = 1, a,b,c are listed, where a = bondtype of the bond between
+the central atom and the first non-central atom (value b in the Shake
+Atoms section), b = bondtype of the bond between the central atom and
+the 2nd non-central atom (value c in the Shake Atoms section), and c =
+the angle type (1 to Nangletypes) of the angle between the 3 atoms.
+
+If flag = 2, only a is listed, where a = bondtype of the bond between
+the 2 atoms in the cluster.
+
+If flag = 3, a,b are listed, where a = bondtype of the bond between
+the central atom and the first non-central atom (value b in the Shake
+Atoms section), and b = bondtype of the bond between the central atom
+and the 2nd non-central atom (value c in the Shake Atoms section).
+
+If flag = 4, a,b,c are listed, where a = bondtype of the bond between
+the central atom and the first non-central atom (value b in the Shake
+Atoms section), b = bondtype of the bond between the central atom and
+the 2nd non-central atom (value c in the Shake Atoms section), and c =
+bondtype of the bond between the central atom and the 3rd non-central
+atom (value d in the Shake Atoms section).
+
+See the :doc:`fix shake <fix_shake>` doc page for a further description
+of SHAKE clusters.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command must come after the simulation box is define by a
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
+:doc:`create\_box <create_box>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix deposit <fix_deposit>`, :doc:`fix pour <fix_pour>`,
+:doc:`fix gcmc <fix_gcmc>`
+
+Default
+"""""""
+
+The default keywords values are offset 0 0 0 0 0 and scale = 1.0.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/neb.rst b/doc/src/neb.rst
new file mode 100644
index 0000000000..ef14739301
--- /dev/null
+++ b/doc/src/neb.rst
@@ -0,0 +1,478 @@
+.. index:: neb
+
+neb command
+===========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   neb etol ftol N1 N2 Nevery file-style arg keyword
+
+* etol = stopping tolerance for energy (energy units)
+* ftol = stopping tolerance for force (force units)
+* N1 = max # of iterations (timesteps) to run initial NEB
+* N2 = max # of iterations (timesteps) to run barrier-climbing NEB
+* Nevery = print replica energies and reaction coordinates every this many timesteps
+* file-style = *final* or *each* or *none*
+  
+  .. parsed-literal::
+  
+       *final* arg = filename
+         filename = file with initial coords for final replica
+           coords for intermediate replicas are linearly interpolated
+           between first and last replica
+       *each* arg = filename
+         filename = unique filename for each replica (except first)
+           with its initial coords
+       *none* arg = no argument all replicas assumed to already have
+           their initial coords
+
+keyword = *verbose*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   neb 0.1 0.0 1000 500 50 final coords.final
+   neb 0.0 0.001 1000 500 50 each coords.initial.$i
+   neb 0.0 0.001 1000 500 50 none verbose
+
+Description
+"""""""""""
+
+Perform a nudged elastic band (NEB) calculation using multiple
+replicas of a system.  Two or more replicas must be used; the first
+and last are the end points of the transition path.
+
+NEB is a method for finding both the atomic configurations and height
+of the energy barrier associated with a transition state, e.g. for an
+atom to perform a diffusive hop from one energy basin to another in a
+coordinated fashion with its neighbors.  The implementation in LAMMPS
+follows the discussion in these 4 papers: :ref:`(HenkelmanA) <HenkelmanA>`,
+:ref:`(HenkelmanB) <HenkelmanB>`, :ref:`(Nakano) <Nakano3>` and :ref:`(Maras) <Maras2>`.
+
+Each replica runs on a partition of one or more processors.  Processor
+partitions are defined at run-time using the :doc:`-partition command-line switch <Run_options>`.  Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on just one or two processors.  You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica.  See the :doc:`Howto replica <Howto_replica>`
+doc page for further discussion.
+
+.. note::
+
+   As explained below, a NEB calculation performs a damped dynamics
+   minimization across all the replicas.  The minimizer uses whatever
+   timestep you have defined in your input script, via the
+   :doc:`timestep <timestep>` command.  Often NEB will converge more
+   quickly if you use a timestep about 10x larger than you would normally
+   use for dynamics simulations.
+
+When a NEB calculation is performed, it is assumed that each replica
+is running the same system, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of atoms, the interaction
+potentials, and the starting configuration when the neb command is
+issued should be the same for every replica.
+
+In a NEB calculation each replica is connected to other replicas by
+inter-replica nudging forces.  These forces are imposed by the :doc:`fix neb <fix_neb>` command, which must be used in conjunction with the
+neb command.  The group used to define the fix neb command defines the
+NEB atoms which are the only ones that inter-replica springs are
+applied to.  If the group does not include all atoms, then non-NEB
+atoms have no inter-replica springs and the forces they feel and their
+motion is computed in the usual way due only to other atoms within
+their replica.  Conceptually, the non-NEB atoms provide a background
+force field for the NEB atoms.  They can be allowed to move during the
+NEB minimization procedure (which will typically induce different
+coordinates for non-NEB atoms in different replicas), or held fixed
+using other LAMMPS commands such as :doc:`fix setforce <fix_setforce>`.
+Note that the :doc:`partition <partition>` command can be used to invoke
+a command on a subset of the replicas, e.g. if you wish to hold NEB or
+non-NEB atoms fixed in only the end-point replicas.
+
+The initial atomic configuration for each of the replicas can be
+specified in different manners via the *file-style* setting, as
+discussed below.  Only atoms whose initial coordinates should differ
+from the current configuration need be specified.
+
+Conceptually, the initial and final configurations for the first
+replica should be states on either side of an energy barrier.
+
+As explained below, the initial configurations of intermediate
+replicas can be atomic coordinates interpolated in a linear fashion
+between the first and last replicas.  This is often adequate for
+simple transitions.  For more complex transitions, it may lead to slow
+convergence or even bad results if the minimum energy path (MEP, see
+below) of states over the barrier cannot be correctly converged to
+from such an initial path.  In this case, you will want to generate
+initial states for the intermediate replicas that are geometrically
+closer to the MEP and read them in.
+
+
+----------
+
+
+For a *file-style* setting of *final*\ , a filename is specified which
+contains atomic coordinates for zero or more atoms, in the format
+described below.  For each atom that appears in the file, the new
+coordinates are assigned to that atom in the final replica.  Each
+intermediate replica also assigns a new position to that atom in an
+interpolated manner.  This is done by using the current position of
+the atom as the starting point and the read-in position as the final
+point.  The distance between them is calculated, and the new position
+is assigned to be a fraction of the distance.  E.g. if there are 10
+replicas, the 2nd replica will assign a position that is 10% of the
+distance along a line between the starting and final point, and the
+9th replica will assign a position that is 90% of the distance along
+the line.  Note that for this procedure to produce consistent
+coordinates across all the replicas, the current coordinates need to
+be the same in all replicas.  LAMMPS does not check for this, but
+invalid initial configurations will likely result if it is not the
+case.
+
+.. note::
+
+   The "distance" between the starting and final point is
+   calculated in a minimum-image sense for a periodic simulation box.
+   This means that if the two positions are on opposite sides of a box
+   (periodic in that dimension), the distance between them will be small,
+   because the periodic image of one of the atoms is close to the other.
+   Similarly, even if the assigned position resulting from the
+   interpolation is outside the periodic box, the atom will be wrapped
+   back into the box when the NEB calculation begins.
+
+For a *file-style* setting of *each*\ , a filename is specified which is
+assumed to be unique to each replica.  This can be done by using a
+variable in the filename, e.g.
+
+
+.. parsed-literal::
+
+   variable i equal part
+   neb 0.0 0.001 1000 500 50 each coords.initial.$i
+
+which in this case will substitute the partition ID (0 to N-1) for the
+variable I, which is also effectively the replica ID.  See the
+:doc:`variable <variable>` command for other options, such as using
+world-, universe-, or uloop-style variables.
+
+Each replica (except the first replica) will read its file, formatted
+as described below, and for any atom that appears in the file, assign
+the specified coordinates to its atom.  The various files do not need
+to contain the same set of atoms.
+
+For a *file-style* setting of *none*\ , no filename is specified.  Each
+replica is assumed to already be in its initial configuration at the
+time the neb command is issued.  This allows each replica to define
+its own configuration by reading a replica-specific data or restart or
+dump file, via the :doc:`read\_data <read_data>`,
+:doc:`read\_restart <read_restart>`, or :doc:`read\_dump <read_dump>`
+commands.  The replica-specific names of these files can be specified
+as in the discussion above for the *each* file-style.  Also see the
+section below for how a NEB calculation can produce restart files, so
+that a long calculation can be restarted if needed.
+
+.. note::
+
+   None of the *file-style* settings change the initial
+   configuration of any atom in the first replica.  The first replica
+   must thus be in the correct initial configuration at the time the neb
+   command is issued.
+
+
+----------
+
+
+A NEB calculation proceeds in two stages, each of which is a
+minimization procedure, performed via damped dynamics.  To enable
+this, you must first define a damped dynamics
+:doc:`min\_style <min_style>`, such as *quickmin* or *fire*\ .  The *cg*\ ,
+*sd*\ , and *hftn* styles cannot be used, since they perform iterative
+line searches in their inner loop, which cannot be easily synchronized
+across multiple replicas.
+
+The minimizer tolerances for energy and force are set by *etol* and
+*ftol*\ , the same as for the :doc:`minimize <minimize>` command.
+
+A non-zero *etol* means that the NEB calculation will terminate if the
+energy criterion is met by every replica.  The energies being compared
+to *etol* do not include any contribution from the inter-replica
+nudging forces, since these are non-conservative.  A non-zero *ftol*
+means that the NEB calculation will terminate if the force criterion
+is met by every replica.  The forces being compared to *ftol* include
+the inter-replica nudging forces.
+
+The maximum number of iterations in each stage is set by *N1* and
+*N2*\ .  These are effectively timestep counts since each iteration of
+damped dynamics is like a single timestep in a dynamics
+:doc:`run <run>`.  During both stages, the potential energy of each
+replica and its normalized distance along the reaction path (reaction
+coordinate RD) will be printed to the screen and log file every
+*Nevery* timesteps.  The RD is 0 and 1 for the first and last replica.
+For intermediate replicas, it is the cumulative distance (normalized
+by the total cumulative distance) between adjacent replicas, where
+"distance" is defined as the length of the 3N-vector of differences in
+atomic coordinates, where N is the number of NEB atoms involved in the
+transition.  These outputs allow you to monitor NEB's progress in
+finding a good energy barrier.  *N1* and *N2* must both be multiples
+of *Nevery*\ .
+
+In the first stage of NEB, the set of replicas should converge toward
+a minimum energy path (MEP) of conformational states that transition
+over a barrier.  The MEP for a transition is defined as a sequence of
+3N-dimensional states, each of which has a potential energy gradient
+parallel to the MEP itself.  The configuration of highest energy along
+a MEP corresponds to a saddle point.  The replica states will also be
+roughly equally spaced along the MEP due to the inter-replica nudging
+force added by the :doc:`fix neb <fix_neb>` command.
+
+In the second stage of NEB, the replica with the highest energy is
+selected and the inter-replica forces on it are converted to a force
+that drives its atom coordinates to the top or saddle point of the
+barrier, via the barrier-climbing calculation described in
+:ref:`(HenkelmanB) <HenkelmanB>`.  As before, the other replicas rearrange
+themselves along the MEP so as to be roughly equally spaced.
+
+When both stages are complete, if the NEB calculation was successful,
+the configurations of the replicas should be along (close to) the MEP
+and the replica with the highest energy should be an atomic
+configuration at (close to) the saddle point of the transition. The
+potential energies for the set of replicas represents the energy
+profile of the transition along the MEP.
+
+
+----------
+
+
+A few other settings in your input script are required or advised to
+perform a NEB calculation.  See the NOTE about the choice of timestep
+at the beginning of this doc page.
+
+An atom map must be defined which it is not by default for :doc:`atom\_style atomic <atom_style>` problems.  The :doc:`atom\_modify map <atom_modify>` command can be used to do this.
+
+The minimizers in LAMMPS operate on all atoms in your system, even
+non-NEB atoms, as defined above.  To prevent non-NEB atoms from moving
+during the minimization, you should use the :doc:`fix setforce <fix_setforce>` command to set the force on each of those
+atoms to 0.0.  This is not required, and may not even be desired in
+some cases, but if those atoms move too far (e.g. because the initial
+state of your system was not well-minimized), it can cause problems
+for the NEB procedure.
+
+The damped dynamics :doc:`minimizers <min_style>`, such as *quickmin*
+and *fire*\ ), adjust the position and velocity of the atoms via an
+Euler integration step.  Thus you must define an appropriate
+:doc:`timestep <timestep>` to use with NEB.  As mentioned above, NEB
+will often converge more quickly if you use a timestep about 10x
+larger than you would normally use for dynamics simulations.
+
+
+----------
+
+
+Each file read by the neb command containing atomic coordinates used
+to initialize one or more replicas must be formatted as follows.
+
+The file can be ASCII text or a gzipped text file (detected by a .gz
+suffix).  The file can contain initial blank lines or comment lines
+starting with "#" which are ignored.  The first non-blank, non-comment
+line should list N = the number of lines to follow.  The N successive
+lines contain the following information:
+
+
+.. parsed-literal::
+
+   ID1 x1 y1 z1
+   ID2 x2 y2 z2
+   ...
+   IDN xN yN zN
+
+The fields are the atom ID, followed by the x,y,z coordinates.  The
+lines can be listed in any order.  Additional trailing information on
+the line is OK, such as a comment.
+
+Note that for a typical NEB calculation you do not need to specify
+initial coordinates for very many atoms to produce differing starting
+and final replicas whose intermediate replicas will converge to the
+energy barrier.  Typically only new coordinates for atoms
+geometrically near the barrier need be specified.
+
+Also note there is no requirement that the atoms in the file
+correspond to the NEB atoms in the group defined by the :doc:`fix neb <fix_neb>` command.  Not every NEB atom need be in the file,
+and non-NEB atoms can be listed in the file.
+
+
+----------
+
+
+Four kinds of output can be generated during a NEB calculation: energy
+barrier statistics, thermodynamic output by each replica, dump files,
+and restart files.
+
+When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file
+contains a line of output, printed once every *Nevery* timesteps.  It
+contains the timestep, the maximum force per replica, the maximum
+force per atom (in any replica), potential gradients in the initial,
+final, and climbing replicas, the forward and backward energy
+barriers, the total reaction coordinate (RDT), and the normalized
+reaction coordinate and potential energy of each replica.
+
+The "maximum force per replica" is the two-norm of the 3N-length force
+vector for the atoms in each replica, maximized across replicas, which
+is what the *ftol* setting is checking against.  In this case, N is
+all the atoms in each replica.  The "maximum force per atom" is the
+maximum force component of any atom in any replica.  The potential
+gradients are the two-norm of the 3N-length force vector solely due to
+the interaction potential i.e.  without adding in inter-replica
+forces.
+
+The "reaction coordinate" (RD) for each replica is the two-norm of the
+3N-length vector of distances between its atoms and the preceding
+replica's atoms, added to the RD of the preceding replica. The RD of
+the first replica RD1 = 0.0; the RD of the final replica RDN = RDT,
+the total reaction coordinate.  The normalized RDs are divided by RDT,
+so that they form a monotonically increasing sequence from zero to
+one. When computing RD, N only includes the atoms being operated on by
+the fix neb command.
+
+The forward (reverse) energy barrier is the potential energy of the
+highest replica minus the energy of the first (last) replica.
+
+Supplementary information for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. This
+information include the following.  The "path angle" (pathangle) for
+the replica i which is the angle between the 3N-length vectors (Ri-1 -
+Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
+i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
+aligned.  "angletangrad" is the angle between the 3N-length tangent
+vector and the 3N-length force vector at image i. The tangent vector
+is calculated as in :ref:`(HenkelmanA) <HenkelmanA>` for all intermediate
+replicas and at R2 - R1 and RM - RM-1 for the first and last replica,
+respectively.  "anglegrad" is the angle between the 3N-length energy
+gradient vector of replica i and that of replica i+1. It is not
+defined for the final replica and reads nan.  gradV is the norm of the
+energy gradient of image i.  ReplicaForce is the two-norm of the
+3N-length force vector (including nudging forces) for replica i.
+MaxAtomForce is the maximum force component of any atom in replica i.
+
+When a NEB calculation does not converge properly, the supplementary
+information can help understanding what is going wrong. For instance
+when the path angle becomes acute, the definition of tangent used in
+the NEB calculation is questionable and the NEB cannot may diverge
+:ref:`(Maras) <Maras2>`.
+
+When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
+NEB calculation, these contain the thermodynamic output for each
+replica.
+
+If :doc:`dump <dump>` commands in the input script define a filename
+that includes a *universe* or *uloop* style :doc:`variable <variable>`,
+then one dump file (per dump command) will be created for each
+replica.  At the end of the NEB calculation, the final snapshot in
+each file will contain the sequence of snapshots that transition the
+system over the energy barrier.  Earlier snapshots will show the
+convergence of the replicas to the MEP.
+
+Likewise, :doc:`restart <restart>` filenames can be specified with a
+*universe* or *uloop* style :doc:`variable <variable>`, to generate
+restart files for each replica.  These may be useful if the NEB
+calculation fails to converge properly to the MEP, and you wish to
+restart the calculation from an intermediate point with altered
+parameters.
+
+There are 2 Python scripts provided in the tools/python directory,
+neb\_combine.py and neb\_final.py, which are useful in analyzing output
+from a NEB calculation.  Assume a NEB simulation with M replicas, and
+the NEB atoms labeled with a specific atom type.
+
+The neb\_combine.py script extracts atom coords for the NEB atoms from
+all M dump files and creates a single dump file where each snapshot
+contains the NEB atoms from all the replicas and one copy of non-NEB
+atoms from the first replica (presumed to be identical in other
+replicas).  This can be visualized/animated to see how the NEB atoms
+relax as the NEB calculation proceeds.
+
+The neb\_final.py script extracts the final snapshot from each of the M
+dump files to create a single dump file with M snapshots.  This can be
+visualized to watch the system make its transition over the energy
+barrier.
+
+To illustrate, here are images from the final snapshot produced by the
+neb\_combine.py script run on the dump files produced by the two
+example input scripts in examples/neb.  Click on them to see a larger
+image.
+
+.. image:: JPG/hop1_small.jpg
+   :target: JPG/hop1.jpg
+
+.. image:: JPG/hop2_small.jpg
+   :target: JPG/hop2.jpg
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`prd <prd>`, :doc:`temper <temper>`, :doc:`fix langevin <fix_langevin>`,
+:doc:`fix viscous <fix_viscous>`
+
+Default
+"""""""
+
+none
+
+
+----------
+
+
+.. _HenkelmanA:
+
+
+
+**(HenkelmanA)** Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
+
+.. _HenkelmanB:
+
+
+
+**(HenkelmanB)** Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+9901-9904 (2000).
+
+.. _Nakano3:
+
+
+
+**(Nakano)** Nakano, Comp Phys Comm, 178, 280-289 (2008).
+
+.. _Maras2:
+
+
+
+**(Maras)** Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
+Comp Phys Comm, 205, 13-21 (2016)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst
new file mode 100644
index 0000000000..161348e97c
--- /dev/null
+++ b/doc/src/neb_spin.rst
@@ -0,0 +1,423 @@
+.. index:: neb/spin
+
+neb/spin command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   neb/spin etol ttol N1 N2 Nevery file-style arg keyword
+
+* etol = stopping tolerance for energy (energy units)
+* ttol = stopping tolerance for torque ( units)
+* N1 = max # of iterations (timesteps) to run initial NEB
+* N2 = max # of iterations (timesteps) to run barrier-climbing NEB
+* Nevery = print replica energies and reaction coordinates every this many timesteps
+* file-style = *final* or *each* or *none*
+  
+  .. parsed-literal::
+  
+       *final* arg = filename
+         filename = file with initial coords for final replica
+           coords for intermediate replicas are linearly interpolated
+           between first and last replica
+       *each* arg = filename
+         filename = unique filename for each replica (except first)
+           with its initial coords
+       *none* arg = no argument all replicas assumed to already have
+           their initial coords
+
+keyword = *verbose*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   neb/spin 0.1 0.0 1000 500 50 final coords.final
+   neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i
+   neb/spin 0.0 0.001 1000 500 50 none verbose
+
+Description
+"""""""""""
+
+Perform a geodesic nudged elastic band (GNEB) calculation using multiple
+replicas of a system.  Two or more replicas must be used; the first
+and last are the end points of the transition path.
+
+GNEB is a method for finding both the spin configurations and height
+of the energy barrier associated with a transition state, e.g.
+spins to perform a collective rotation from one energy basin to
+another.
+The implementation in LAMMPS follows the discussion in the
+following paper: :ref:`(BessarabA) <BessarabA>`.
+
+Each replica runs on a partition of one or more processors.  Processor
+partitions are defined at run-time using the :doc:`-partition command-line switch <Run_options>`.  Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on just one or two processors.  You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica.  See the :doc:`Howto replica <Howto_replica>`
+doc page for further discussion.
+
+.. note::
+
+   As explained below, a GNEB calculation performs a
+   minimization across all the replicas. One of the :doc:`spin <min_spin>`
+   style minimizers has to be defined in your input script.
+
+When a GNEB calculation is performed, it is assumed that each replica
+is running the same system, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of magnetic atoms, the
+interaction potentials, and the starting configuration when the neb
+command is issued should be the same for every replica.
+
+In a GNEB calculation each replica is connected to other replicas by
+inter-replica nudging forces.  These forces are imposed by the :doc:`fix neb/spin <fix_neb_spin>` command, which must be used in conjunction
+with the neb command.
+The group used to define the fix neb/spin command defines the
+GNEB magnetic atoms which are the only ones that inter-replica springs
+are applied to.
+If the group does not include all magnetic atoms, then non-GNEB
+magnetic atoms have no inter-replica springs and the torques they feel
+and their precession motion is computed in the usual way due only
+to other magnetic atoms within their replica.
+Conceptually, the non-GNEB atoms provide a background force field for
+the GNEB atoms.
+Their magnetic spins can be allowed to evolve during the GNEB
+minimization procedure.
+
+The initial spin configuration for each of the replicas can be
+specified in different manners via the *file-style* setting, as
+discussed below.  Only atomic spins whose initial coordinates should
+differ from the current configuration need to be specified.
+
+Conceptually, the initial and final configurations for the first
+replica should be states on either side of an energy barrier.
+
+As explained below, the initial configurations of intermediate
+replicas can be spin coordinates interpolated in a linear fashion
+between the first and last replicas.  This is often adequate for
+simple transitions.  For more complex transitions, it may lead to slow
+convergence or even bad results if the minimum energy path (MEP, see
+below) of states over the barrier cannot be correctly converged to
+from such an initial path.  In this case, you will want to generate
+initial states for the intermediate replicas that are geometrically
+closer to the MEP and read them in.
+
+
+----------
+
+
+For a *file-style* setting of *final*\ , a filename is specified which
+contains atomic and spin coordinates for zero or more atoms, in the
+format described below.
+For each atom that appears in the file, the new coordinates are
+assigned to that atom in the final replica.  Each intermediate replica
+also assigns a new spin to that atom in an interpolated manner.
+This is done by using the current direction of the spin at the starting
+point and the read-in direction as the final point.
+The "angular distance" between them is calculated, and the new direction
+is assigned to be a fraction of the angular distance.
+
+.. note::
+
+   The "angular distance" between the starting and final point is
+   evaluated in the geodesic sense, as described in
+   :ref:`(BessarabA) <BessarabA>`.
+
+.. note::
+
+   The angular interpolation between the starting and final point
+   is achieved using Rodrigues formula:
+
+.. image:: Eqs/neb_spin_rodrigues_formula.jpg
+   :align: center
+
+where m\_i\^I is the initial spin configuration for the spin i,
+omega\_i\^nu is a rotation angle defined as:
+
+.. image:: Eqs/neb_spin_angle.jpg
+   :align: center
+
+with nu the image number, Q the total number of images, and
+omega\_i the total rotation between the initial and final spins.
+k\_i defines a rotation axis such as:
+
+.. image:: Eqs/neb_spin_k.jpg
+   :align: center
+
+if the initial and final spins are not aligned.
+If the initial and final spins are aligned, then their cross
+product is null, and the expression above does not apply.
+If they point toward the same direction, the intermediate images
+conserve the same orientation.
+If the initial and final spins are aligned, but point toward
+opposite directions, an arbitrary rotation vector belonging to
+the plane perpendicular to initial and final spins is chosen.
+In this case, a warning message is displayed.
+
+For a *file-style* setting of *each*\ , a filename is specified which is
+assumed to be unique to each replica.
+See the :doc:`neb <neb>` documentation page for more information about this
+option.
+
+For a *file-style* setting of *none*\ , no filename is specified.  Each
+replica is assumed to already be in its initial configuration at the
+time the neb command is issued.  This allows each replica to define
+its own configuration by reading a replica-specific data or restart or
+dump file, via the :doc:`read\_data <read_data>`,
+:doc:`read\_restart <read_restart>`, or :doc:`read\_dump <read_dump>`
+commands.  The replica-specific names of these files can be specified
+as in the discussion above for the *each* file-style.  Also see the
+section below for how a NEB calculation can produce restart files, so
+that a long calculation can be restarted if needed.
+
+.. note::
+
+   None of the *file-style* settings change the initial
+   configuration of any atom in the first replica.  The first replica
+   must thus be in the correct initial configuration at the time the neb
+   command is issued.
+
+
+----------
+
+
+A NEB calculation proceeds in two stages, each of which is a
+minimization procedure.  To enable
+this, you must first define a
+:doc:`min\_style <min_style>`, using either the *spin*\ ,
+*spin/cg*\ , or *spin/lbfgs* style (see
+:doc:`min\_spin <min_spin>` for more information).  
+The other styles cannot be used, since they relax the lattice
+degrees of freedom instead of the spins.
+
+The minimizer tolerances for energy and force are set by *etol* and
+*ttol*\ , the same as for the :doc:`minimize <minimize>` command.
+
+A non-zero *etol* means that the GNEB calculation will terminate if the
+energy criterion is met by every replica.  The energies being compared
+to *etol* do not include any contribution from the inter-replica
+nudging forces, since these are non-conservative.  A non-zero *ttol*
+means that the GNEB calculation will terminate if the torque criterion
+is met by every replica.  The torques being compared to *ttol* include
+the inter-replica nudging forces.
+
+The maximum number of iterations in each stage is set by *N1* and
+*N2*\ .  These are effectively timestep counts since each iteration of
+damped dynamics is like a single timestep in a dynamics
+:doc:`run <run>`.  During both stages, the potential energy of each
+replica and its normalized distance along the reaction path (reaction
+coordinate RD) will be printed to the screen and log file every
+*Nevery* timesteps.  The RD is 0 and 1 for the first and last replica.
+For intermediate replicas, it is the cumulative angular distance
+(normalized by the total cumulative angular distance) between adjacent
+replicas, where "distance" is defined as the length of the 3N-vector of
+the geodesic distances in spin coordinates, with N the number of
+GNEB spins involved (see equation (13) in :ref:`(BessarabA) <BessarabA>`).
+These outputs allow you to monitor NEB's progress in
+finding a good energy barrier.  *N1* and *N2* must both be multiples
+of *Nevery*\ .
+
+In the first stage of GNEB, the set of replicas should converge toward
+a minimum energy path (MEP) of conformational states that transition
+over a barrier.  The MEP for a transition is defined as a sequence of
+3N-dimensional spin states, each of which has a potential energy
+gradient parallel to the MEP itself.
+The configuration of highest energy along a MEP corresponds to a saddle
+point.  The replica states will also be roughly equally spaced along
+the MEP due to the inter-replica nudging force added by the
+:doc:`fix neb <fix_neb>` command.
+
+In the second stage of GNEB, the replica with the highest energy is
+selected and the inter-replica forces on it are converted to a force
+that drives its spin coordinates to the top or saddle point of the
+barrier, via the barrier-climbing calculation described in
+:ref:`(BessarabA) <BessarabA>`.  As before, the other replicas rearrange
+themselves along the MEP so as to be roughly equally spaced.
+
+When both stages are complete, if the GNEB calculation was successful,
+the configurations of the replicas should be along (close to) the MEP
+and the replica with the highest energy should be a spin
+configuration at (close to) the saddle point of the transition. The
+potential energies for the set of replicas represents the energy
+profile of the transition along the MEP.
+
+
+----------
+
+
+An atom map must be defined which it is not by default for :doc:`atom\_style atomic <atom_style>` problems.  The :doc:`atom\_modify map <atom_modify>` command can be used to do this.
+
+An initial value can be defined for the timestep. Although, the *spin*
+minimization algorithm is an adaptive timestep methodology, so that
+this timestep is likely to evolve during the calculation.
+
+The minimizers in LAMMPS operate on all spins in your system, even
+non-GNEB atoms, as defined above.
+
+
+----------
+
+
+Each file read by the neb/spin command containing spin coordinates used
+to initialize one or more replicas must be formatted as follows.
+
+The file can be ASCII text or a gzipped text file (detected by a .gz
+suffix).  The file can contain initial blank lines or comment lines
+starting with "#" which are ignored.  The first non-blank, non-comment
+line should list N = the number of lines to follow.  The N successive
+lines contain the following information:
+
+
+.. parsed-literal::
+
+   ID1 g1 x1 y1 z1 sx1 sy1 sz1
+   ID2 g2 x2 y2 z2 sx2 sy2 sz2
+   ...
+   IDN gN yN zN sxN syN szN
+
+The fields are the atom ID, the norm of the associated magnetic spin,
+followed by the *x,y,z* coordinates and the *sx,sy,sz* spin coordinates.
+The lines can be listed in any order.  Additional trailing information on
+the line is OK, such as a comment.
+
+Note that for a typical GNEB calculation you do not need to specify
+initial spin coordinates for very many atoms to produce differing starting
+and final replicas whose intermediate replicas will converge to the
+energy barrier.  Typically only new spin coordinates for atoms
+geometrically near the barrier need be specified.
+
+Also note there is no requirement that the atoms in the file
+correspond to the GNEB atoms in the group defined by the :doc:`fix neb <fix_neb>` command.  Not every GNEB atom need be in the file,
+and non-GNEB atoms can be listed in the file.
+
+
+----------
+
+
+Four kinds of output can be generated during a GNEB calculation: energy
+barrier statistics, thermodynamic output by each replica, dump files,
+and restart files.
+
+When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file
+contains a line of output, printed once every *Nevery* timesteps.  It
+contains the timestep, the maximum torque per replica, the maximum
+torque per atom (in any replica), potential gradients in the initial,
+final, and climbing replicas, the forward and backward energy
+barriers, the total reaction coordinate (RDT), and the normalized
+reaction coordinate and potential energy of each replica.
+
+The "maximum torque per replica" is the two-norm of the
+3N-length vector given by the cross product of a spin by its
+precession vector omega, in each replica, maximized across replicas,
+which is what the *ttol* setting is checking against.  In this case, N is
+all the atoms in each replica.  The "maximum torque per atom" is the
+maximum torque component of any atom in any replica.  The potential
+gradients are the two-norm of the 3N-length magnetic precession vector
+solely due to the interaction potential i.e. without adding in
+inter-replica forces, and projected along the path tangent (as detailed
+in Appendix D of :ref:`(BessarabA) <BessarabA>`).
+
+The "reaction coordinate" (RD) for each replica is the two-norm of the
+3N-length vector of geodesic distances between its spins and the preceding
+replica's spins (see equation (13) of :ref:`(BessarabA) <BessarabA>`), added to
+the RD of the preceding replica. The RD of the first replica RD1 = 0.0;
+the RD of the final replica RDN = RDT, the total reaction coordinate.
+The normalized RDs are divided by RDT, so that they form a monotonically
+increasing sequence from zero to one. When computing RD, N only includes
+the spins being operated on by the fix neb/spin command.
+
+The forward (reverse) energy barrier is the potential energy of the
+highest replica minus the energy of the first (last) replica.
+
+Supplementary information for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. This
+information include the following.
+The "GradVidottan" are the projections of the potential gradient for
+the replica i on its tangent vector (as detailed in Appendix D of
+:ref:`(BessarabA) <BessarabA>`).
+The "DNi" are the non normalized geodesic distances (see equation (13)
+of :ref:`(BessarabA) <BessarabA>`), between a replica i and the next replica
+i+1. For the last replica, this distance is not defined and a "NAN"
+value is the corresponding output.
+
+When a NEB calculation does not converge properly, the supplementary
+information can help understanding what is going wrong.
+
+When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
+GNEB calculation, these contain the thermodynamic output for each
+replica.
+
+If :doc:`dump <dump>` commands in the input script define a filename
+that includes a *universe* or *uloop* style :doc:`variable <variable>`,
+then one dump file (per dump command) will be created for each
+replica.  At the end of the GNEB calculation, the final snapshot in
+each file will contain the sequence of snapshots that transition the
+system over the energy barrier.  Earlier snapshots will show the
+convergence of the replicas to the MEP.
+
+Likewise, :doc:`restart <restart>` filenames can be specified with a
+*universe* or *uloop* style :doc:`variable <variable>`, to generate
+restart files for each replica.  These may be useful if the GNEB
+calculation fails to converge properly to the MEP, and you wish to
+restart the calculation from an intermediate point with altered
+parameters.
+
+A c file script in provided in the tool/spin/interpolate\_gneb
+directory, that interpolates the MEP given the information provided
+by the verbose output option (as detailed in Appendix D of
+:ref:`(BessarabA) <BessarabA>`).
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the SPIN
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used
+when styles *spin/cg* and *spin/lbfgs* are employed.
+
+
+----------
+
+
+Related commands
+""""""""""""""""
+
+:doc:`min/spin <min_spin>`, :doc:`fix neb/spin <fix_neb_spin>`
+
+Default
+"""""""
+
+none
+
+
+----------
+
+
+.. _BessarabA:
+
+
+
+**(BessarabA)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+335-347 (2015).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst
new file mode 100644
index 0000000000..9035690a00
--- /dev/null
+++ b/doc/src/neigh_modify.rst
@@ -0,0 +1,234 @@
+.. index:: neigh\_modify
+
+neigh\_modify command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   neigh_modify keyword values ...
+
+* one or more keyword/value pairs may be listed
+  
+  .. parsed-literal::
+  
+     keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize*
+       *delay* value = N
+         N = delay building until this many steps since last build
+       *every* value = M
+         M = build neighbor list every this many steps
+       *check* value = *yes* or *no*
+         *yes* = only build if some atom has moved half the skin distance or more
+         *no* = always build on 1st step that *every* and *delay* are satisfied
+       *once*
+         *yes* = only build neighbor list once at start of run and never rebuild
+         *no* = rebuild neighbor list according to other settings
+       *cluster*
+         *yes* = check bond,angle,etc neighbor list for nearby clusters
+         *no* = do not check bond,angle,etc neighbor list for nearby clusters
+       *include* value = group-ID
+         group-ID = only build pair neighbor lists for atoms in this group
+       *exclude* values:
+         type M N
+           M,N = exclude if one atom in pair is type M, other is type N
+         group group1-ID group2-ID
+           group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd
+         molecule/intra group-ID
+           group-ID = exclude if both atoms are in the same molecule and in group
+         molecule/inter group-ID
+           group-ID = exclude if both atoms are in different molecules and in group
+         none
+           delete all exclude settings
+       *page* value = N
+         N = number of pairs stored in a single neighbor page
+       *one* value = N
+         N = max number of neighbors of one atom
+       *binsize* value = size
+         size = bin size for neighbor list construction (distance units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   neigh_modify every 2 delay 10 check yes page 100000
+   neigh_modify exclude type 2 3
+   neigh_modify exclude group frozen frozen check no
+   neigh_modify exclude group residue1 chain3
+   neigh_modify exclude molecule/intra rigid
+
+Description
+"""""""""""
+
+This command sets parameters that affect the building and use of
+pairwise neighbor lists.  Depending on what pair interactions and
+other commands are defined, a simulation may require one or more
+neighbor lists.
+
+The *every*\ , *delay*\ , *check*\ , and *once* options affect how often
+lists are built as a simulation runs.  The *delay* setting means never
+build new lists until at least N steps after the previous build.  The
+*every* setting means build lists every M steps (after the delay has
+passed).  If the *check* setting is *no*\ , the lists are built on the
+first step that satisfies the *delay* and *every* settings.  If the
+*check* setting is *yes*\ , then the *every* and *delay* settings
+determine when a build may possibly be performed, but an actual build
+only occurs if some atom has moved more than half the skin distance
+(specified in the :doc:`neighbor <neighbor>` command) since the last
+build.
+
+If the *once* setting is yes, then the neighbor list is only built
+once at the beginning of each run, and never rebuilt, except on steps
+when a restart file is written, or steps when a fix forces a rebuild
+to occur (e.g. fixes that create or delete atoms, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix evaporate <fix_evaporate>`).
+This setting should only be made if you are certain atoms will not
+move far enough that the neighbor list should be rebuilt, e.g. running
+a simulation of a cold crystal.  Note that it is not that expensive to
+check if neighbor lists should be rebuilt.
+
+When the rRESPA integrator is used (see the :doc:`run\_style <run_style>`
+command), the *every* and *delay* parameters refer to the longest
+(outermost) timestep.
+
+The *cluster* option does a sanity test every time neighbor lists are
+built for bond, angle, dihedral, and improper interactions, to check
+that each set of 2, 3, or 4 atoms is a cluster of nearby atoms.  It
+does this by computing the distance between pairs of atoms in the
+interaction and insuring they are not further apart than half the
+periodic box length.  If they are, an error is generated, since the
+interaction would be computed between far-away atoms instead of their
+nearby periodic images.  The only way this should happen is if the
+pairwise cutoff is so short that atoms that are part of the same
+interaction are not communicated as ghost atoms.  This is an unusual
+model (e.g. no pair interactions at all) and the problem can be fixed
+by use of the :doc:`comm\_modify cutoff <comm_modify>` command.  Note
+that to save time, the default *cluster* setting is *no*\ , so that this
+check is not performed.
+
+The *include* option limits the building of pairwise neighbor lists to
+atoms in the specified group.  This can be useful for models where a
+large portion of the simulation is particles that do not interact with
+other particles or with each other via pairwise interactions.  The
+group specified with this option must also be specified via the
+:doc:`atom\_modify first <atom_modify>` command.  Note that specifying
+"all" as the group-ID effectively turns off the *include* option.
+
+The *exclude* option turns off pairwise interactions between certain
+pairs of atoms, by not including them in the neighbor list.  These are
+sample scenarios where this is useful:
+
+* In crack simulations, pairwise interactions can be shut off between 2
+  slabs of atoms to effectively create a crack.
+* When a large collection of atoms is treated as frozen, interactions
+  between those atoms can be turned off to save needless
+  computation. E.g. Using the :doc:`fix setforce <fix_setforce>` command
+  to freeze a wall or portion of a bio-molecule.
+* When one or more rigid bodies are specified, interactions within each
+  body can be turned off to save needless computation.  See the :doc:`fix rigid <fix_rigid>` command for more details.
+
+
+The *exclude type* option turns off the pairwise interaction if one
+atom is of type M and the other of type N.  M can equal N.  The
+*exclude group* option turns off the interaction if one atom is in the
+first group and the other is the second.  Group1-ID can equal
+group2-ID.  The *exclude molecule/intra* option turns off the
+interaction if both atoms are in the specified group and in the same
+molecule, as determined by their molecule ID.  The *exclude
+molecule/inter* turns off the interaction between pairs of atoms that
+have different molecule IDs and are both in the specified group.
+
+Each of the exclude options can be specified multiple times.  The
+*exclude type* option is the most efficient option to use; it requires
+only a single check, no matter how many times it has been specified.
+The other exclude options are more expensive if specified multiple
+times; they require one check for each time they have been specified.
+
+Note that the exclude options only affect pairwise interactions; see
+the :doc:`delete\_bonds <delete_bonds>` command for information on
+turning off bond interactions.
+
+.. note::
+
+   Excluding pairwise interactions will not work correctly when
+   also using a long-range solver via the
+   :doc:`kspace\_style <kspace_style>` command.  LAMMPS will give a warning
+   to this effect.  This is because the short-range pairwise interaction
+   needs to subtract off a term from the total energy for pairs whose
+   short-range interaction is excluded, to compensate for how the
+   long-range solver treats the interaction.  This is done correctly for
+   pairwise interactions that are excluded (or weighted) via the
+   :doc:`special\_bonds <special_bonds>` command.  But it is not done for
+   interactions that are excluded via these neigh\_modify exclude options.
+
+The *page* and *one* options affect how memory is allocated for the
+neighbor lists.  For most simulations the default settings for these
+options are fine, but if a very large problem is being run or a very
+long cutoff is being used, these parameters can be tuned.  The indices
+of neighboring atoms are stored in "pages", which are allocated one
+after another as they fill up.  The size of each page is set by the
+*page* value.  A new page is allocated when the next atom's neighbors
+could potentially overflow the list.  This threshold is set by the
+*one* value which tells LAMMPS the maximum number of neighbor's one
+atom can have.
+
+.. note::
+
+   LAMMPS can crash without an error message if the number of
+   neighbors for a single particle is larger than the *page* setting,
+   which means it is much, much larger than the *one* setting.  This is
+   because LAMMPS doesn't error check these limits for every pairwise
+   interaction (too costly), but only after all the particle's neighbors
+   have been found.  This problem usually means something is very wrong
+   with the way you've setup your problem (particle spacing, cutoff
+   length, neighbor skin distance, etc).  If you really expect that many
+   neighbors per particle, then boost the *one* and *page* settings
+   accordingly.
+
+The *binsize* option allows you to specify what size of bins will be
+used in neighbor list construction to sort and find neighboring atoms.
+By default, for :doc:`neighbor style bin <neighbor>`, LAMMPS uses bins
+that are 1/2 the size of the maximum pair cutoff.  For :doc:`neighbor style multi <neighbor>`, the bins are 1/2 the size of the minimum pair
+cutoff.  Typically these are good values for minimizing the time for
+neighbor list construction.  This setting overrides the default.
+If you make it too big, there is little overhead due to
+looping over bins, but more atoms are checked.  If you make it too
+small, the optimal number of atoms is checked, but bin overhead goes
+up.  If you set the binsize to 0.0, LAMMPS will use the default
+binsize of 1/2 the cutoff.
+
+Restrictions
+""""""""""""
+
+
+If the "delay" setting is non-zero, then it must be a multiple of the
+"every" setting.
+
+The molecule/intra and molecule/inter exclude options can only be used
+with atom styles that define molecule IDs.
+
+The value of the *page* setting must be at least 10x larger than the
+*one* setting.  This insures neighbor pages are not mostly empty
+space.
+
+Related commands
+""""""""""""""""
+
+:doc:`neighbor <neighbor>`, :doc:`delete\_bonds <delete_bonds>`
+
+Default
+"""""""
+
+The option defaults are delay = 10, every = 1, check = yes, once = no,
+cluster = no, include = all (same as no include option defined),
+exclude = none, page = 100000, one = 2000, and binsize = 0.0.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst
new file mode 100644
index 0000000000..ae21232609
--- /dev/null
+++ b/doc/src/neighbor.rst
@@ -0,0 +1,95 @@
+.. index:: neighbor
+
+neighbor command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   neighbor skin style
+
+* skin = extra distance beyond force cutoff (distance units)
+* style = *bin* or *nsq* or *multi*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   neighbor 0.3 bin
+   neighbor 2.0 nsq
+
+Description
+"""""""""""
+
+This command sets parameters that affect the building of pairwise
+neighbor lists.  All atom pairs within a neighbor cutoff distance
+equal to the their force cutoff plus the *skin* distance are stored in
+the list.  Typically, the larger the skin distance, the less often
+neighbor lists need to be built, but more pairs must be checked for
+possible force interactions every timestep.  The default value for
+*skin* depends on the choice of units for the simulation; see the
+default values below.
+
+The *skin* distance is also used to determine how often atoms migrate
+to new processors if the *check* option of the
+:doc:`neigh\_modify <neigh_modify>` command is set to *yes*\ .  Atoms are
+migrated (communicated) to new processors on the same timestep that
+neighbor lists are re-built.
+
+The *style* value selects what algorithm is used to build the list.
+The *bin* style creates the list by binning which is an operation that
+scales linearly with N/P, the number of atoms per processor where N =
+total number of atoms and P = number of processors.  It is almost
+always faster than the *nsq* style which scales as (N/P)\^2.  For
+unsolvated small molecules in a non-periodic box, the *nsq* choice can
+sometimes be faster.  Either style should give the same answers.
+
+The *multi* style is a modified binning algorithm that is useful for
+systems with a wide range of cutoff distances, e.g. due to different
+size particles.  For the *bin* style, the bin size is set to 1/2 of
+the largest cutoff distance between any pair of atom types and a
+single set of bins is defined to search over for all atom types.  This
+can be inefficient if one pair of types has a very long cutoff, but
+other type pairs have a much shorter cutoff.  For style *multi* the
+bin size is set to 1/2 of the shortest cutoff distance and multiple
+sets of bins are defined to search over for different atom types.
+This imposes some extra setup overhead, but the searches themselves
+may be much faster for the short-cutoff cases.  See the :doc:`comm\_modify mode multi <comm_modify>` command for a communication option
+that may also be beneficial for simulations of this kind.
+
+The :doc:`neigh\_modify <neigh_modify>` command has additional options
+that control how often neighbor lists are built and which pairs are
+stored in the list.
+
+When a run is finished, counts of the number of neighbors stored in
+the pairwise list and the number of times neighbor lists were built
+are printed to the screen and log file.  See the :doc:`Run output <Run_output>` doc page for details.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`neigh\_modify <neigh_modify>`, :doc:`units <units>`,
+:doc:`comm\_modify <comm_modify>`
+
+Default
+"""""""
+
+| 0.3 bin for units = lj, skin = 0.3 sigma
+| 2.0 bin for units = real or metal, skin = 2.0 Angstroms
+| 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
+| 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm 
+| 
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/newton.rst b/doc/src/newton.rst
new file mode 100644
index 0000000000..6c1f600224
--- /dev/null
+++ b/doc/src/newton.rst
@@ -0,0 +1,78 @@
+.. index:: newton
+
+newton command
+==============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   newton flag
+   newton flag1 flag2
+
+* flag = *on* or *off* for both pairwise and bonded interactions
+* flag1 = *on* or *off* for pairwise interactions
+* flag2 = *on* or *off* for bonded interactions
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   newton off
+   newton on off
+
+Description
+"""""""""""
+
+This command turns Newton's 3rd law *on* or *off* for pairwise and
+bonded interactions.  For most problems, setting Newton's 3rd law to
+*on* means a modest savings in computation at the cost of two times
+more communication.  Whether this is faster depends on problem size,
+force cutoff lengths, a machine's compute/communication ratio, and how
+many processors are being used.
+
+Setting the pairwise newton flag to *off* means that if two
+interacting atoms are on different processors, both processors compute
+their interaction and the resulting force information is not
+communicated.  Similarly, for bonded interactions, newton *off* means
+that if a bond, angle, dihedral, or improper interaction contains
+atoms on 2 or more processors, the interaction is computed by each
+processor.
+
+LAMMPS should produce the same answers for any newton flag settings,
+except for round-off issues.
+
+With :doc:`run\_style <run_style>` *respa* and only bonded interactions
+(bond, angle, etc) computed in the innermost timestep, it may be
+faster to turn newton *off* for bonded interactions, to avoid extra
+communication in the innermost loop.
+
+Restrictions
+""""""""""""
+
+
+The newton bond setting cannot be changed after the simulation box is
+defined by a :doc:`read\_data <read_data>` or
+:doc:`create\_box <create_box>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`run\_style <run_style>` respa
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   newton on
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/next.rst b/doc/src/next.rst
new file mode 100644
index 0000000000..e4446de48d
--- /dev/null
+++ b/doc/src/next.rst
@@ -0,0 +1,163 @@
+.. index:: next
+
+next command
+============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   next variables
+
+* variables = one or more variable names
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   next x
+   next a t x myTemp
+
+Description
+"""""""""""
+
+This command is used with variables defined by the
+:doc:`variable <variable>` command.  It assigns the next value to the
+variable from the list of values defined for that variable by the
+:doc:`variable <variable>` command.  Thus when that variable is
+subsequently substituted for in an input script command, the new value
+is used.
+
+See the :doc:`variable <variable>` command for info on how to define and
+use different kinds of variables in LAMMPS input scripts.  If a
+variable name is a single lower-case character from "a" to "z", it can
+be used in an input script command as $a or $z.  If it is multiple
+letters, it can be used as ${myTemp}.
+
+If multiple variables are used as arguments to the *next* command,
+then all must be of the same variable style: *index*\ , *loop*\ , *file*\ ,
+*universe*\ , or *uloop*\ .  An exception is that *universe*\ - and
+*uloop*\ -style variables can be mixed in the same *next* command.
+
+All the variables specified with the next command are incremented by
+one value from their respective list of values.  A *file*\ -style
+variable reads the next line from its associated file.  An
+*atomfile*\ -style variable reads the next set of lines (one per atom)
+from its associated file.  *String-* or *atom*\ - or *equal*\ - or
+*world*\ -style variables cannot be used with the next command,
+since they only store a single value.
+
+When any of the variables in the next command has no more values, a
+flag is set that causes the input script to skip the next
+:doc:`jump <jump>` command encountered.  This enables a loop containing
+a next command to exit.  As explained in the :doc:`variable <variable>`
+command, the variable that has exhausted its values is also deleted.
+This allows it to be used and re-defined later in the input script.
+*File*\ -style and *atomfile*\ -style variables are exhausted when the
+end-of-file is reached.
+
+When the next command is used with *index*\ - or *loop*\ -style variables,
+the next value is assigned to the variable for all processors.  When
+the next command is used with *file*\ -style variables, the next line is
+read from its file and the string assigned to the variable.  When the
+next command is used with *atomfile*\ -style variables, the next set of
+per-atom values is read from its file and assigned to the variable.
+
+When the next command is used with *universe*\ - or *uloop*\ -style
+variables, all *universe*\ - or *uloop*\ -style variables must be listed
+in the next command.  This is because of the manner in which the
+incrementing is done, using a single lock file for all variables.  The
+next value (for each variable) is assigned to whichever processor
+partition executes the command first.  All processors in the partition
+are assigned the same value(s).  Running LAMMPS on multiple partitions
+of processors via the :doc:`-partition command-line switch <Run_options>`.  *Universe*\ - and *uloop*\ -style variables are
+incremented using the files "tmp.lammps.variable" and
+"tmp.lammps.variable.lock" which you will see in your directory during
+and after such a LAMMPS run.
+
+Here is an example of running a series of simulations using the next
+command with an *index*\ -style variable.  If this input script is named
+in.polymer, 8 simulations would be run using data files from
+directories run1 through run8.
+
+
+.. parsed-literal::
+
+   variable d index run1 run2 run3 run4 run5 run6 run7 run8
+   shell cd $d
+   read_data data.polymer
+   run 10000
+   shell cd ..
+   clear
+   next d
+   jump in.polymer
+
+If the variable "d" were of style *universe*\ , and the same in.polymer
+input script were run on 3 partitions of processors, then the first 3
+simulations would begin, one on each set of processors.  Whichever
+partition finished first, it would assign variable "d" the 4th value
+and run another simulation, and so forth until all 8 simulations were
+finished.
+
+Jump and next commands can also be nested to enable multi-level loops.
+For example, this script will run 15 simulations in a double loop.
+
+
+.. parsed-literal::
+
+   variable i loop 3
+     variable j loop 5
+     clear
+     ...
+     read_data data.polymer.$i$j
+     print Running simulation $i.$j
+     run 10000
+     next j
+     jump in.script
+   next i
+   jump in.script
+
+Here is an example of a double loop which uses the :doc:`if <if>` and
+:doc:`jump <jump>` commands to break out of the inner loop when a
+condition is met, then continues iterating through the outer loop.
+
+
+.. parsed-literal::
+
+   label       loopa
+   variable    a loop 5
+     label     loopb
+     variable  b loop 5
+     print     "A,B = $a,$b"
+     run       10000
+     if        $b > 2 then "jump in.script break"
+     next      b
+     jump      in.script loopb
+   label       break
+   variable    b delete
+
+   next        a
+   jump        in.script loopa
+
+Restrictions
+""""""""""""
+
+
+As described above.
+
+Related commands
+""""""""""""""""
+
+:doc:`jump <jump>`, :doc:`include <include>`, :doc:`shell <shell>`,
+:doc:`variable <variable>`,
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/package.rst b/doc/src/package.rst
new file mode 100644
index 0000000000..06cebea6c4
--- /dev/null
+++ b/doc/src/package.rst
@@ -0,0 +1,689 @@
+.. index:: package
+
+package command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   package style args
+
+* style = *gpu* or *intel* or *kokkos* or *omp*
+* args = arguments specific to the style
+  
+  .. parsed-literal::
+  
+       *gpu* args = Ngpu keyword value ...
+         Ngpu = # of GPUs per node
+         zero or more keyword/value pairs may be appended
+         keywords = *neigh* or *newton* or *binsize* or *split* or *gpuID* or *tpa* or *device* or *blocksize*
+           *neigh* value = *yes* or *no*
+             yes = neighbor list build on GPU (default)
+             no = neighbor list build on CPU
+           *newton* = *off* or *on*
+             off = set Newton pairwise flag off (default and required)
+             on = set Newton pairwise flag on (currently not allowed)
+           *binsize* value = size
+             size = bin size for neighbor list construction (distance units)
+           *split* = fraction
+             fraction = fraction of atoms assigned to GPU (default = 1.0)
+           *gpuID* values = first last
+             first = ID of first GPU to be used on each node
+             last = ID of last GPU to be used on each node
+           *tpa* value = Nthreads
+             Nthreads = # of GPU threads used per atom
+           *device* value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13
+             platform_id = numerical OpenCL platform id (default: -1)
+             device_type = *kepler* or *fermi* or *cypress* or *intel* or *phi* or *generic* or *custom*
+             val1,val2,... = custom OpenCL tune parameters (see below for details)
+           *blocksize* value = size
+             size = thread block size for pair force computation
+       *intel* args = NPhi keyword value ...
+         Nphi = # of co-processors per node
+         zero or more keyword/value pairs may be appended
+         keywords = *mode* or *omp* or *lrt* or *balance* or *ghost* or *tpc* or *tptask* or *no_affinity*
+           *mode* value = *single* or *mixed* or *double*
+             single = perform force calculations in single precision
+             mixed = perform force calculations in mixed precision
+             double = perform force calculations in double precision
+           *omp* value = Nthreads
+             Nthreads = number of OpenMP threads to use on CPU (default = 0)
+           *lrt* value = *yes* or *no*
+             yes = use additional thread dedicated for some PPPM calculations
+             no = do not dedicate an extra thread for some PPPM calculations
+           *balance* value = split
+             split = fraction of work to offload to co-processor, -1 for dynamic
+           *ghost* value = *yes* or *no*
+             yes = include ghost atoms for offload
+             no = do not include ghost atoms for offload
+           *tpc* value = Ntpc
+             Ntpc = max number of co-processor threads per co-processor core (default = 4)
+           *tptask* value = Ntptask
+             Ntptask = max number of co-processor threads per MPI task (default = 240)
+           *no_affinity* values = none
+       *kokkos* args = keyword value ...
+         zero or more keyword/value pairs may be appended
+         keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/reverse* or *cuda/aware*
+           *neigh* value = *full* or *half*
+             full = full neighbor list
+             half = half neighbor list built in thread-safe manner
+           *neigh/qeq* value = *full* or *half*
+             full = full neighbor list
+             half = half neighbor list built in thread-safe manner
+           *neigh/thread* value = *off* or *on*
+             off = thread only over atoms
+             on = thread over both atoms and neighbors
+           *newton* = *off* or *on*
+             off = set Newton pairwise and bonded flags off
+             on = set Newton pairwise and bonded flags on
+           *binsize* value = size
+             size = bin size for neighbor list construction (distance units)
+           *comm* value = *no* or *host* or *device*
+             use value for comm/exchange and comm/forward and comm/reverse
+           *comm/exchange* value = *no* or *host* or *device*
+           *comm/forward* value = *no* or *host* or *device*
+           *comm/reverse* value = *no* or *host* or *device*
+             no = perform communication pack/unpack in non-KOKKOS mode
+             host = perform pack/unpack on host (e.g. with OpenMP threading)
+             device = perform pack/unpack on device (e.g. on GPU)
+           *cuda/aware* = *off* or *on*
+             off = do not use CUDA-aware MPI
+             on = use CUDA-aware MPI (default)
+       *omp* args = Nthreads keyword value ...
+         Nthread = # of OpenMP threads to associate with each MPI process
+         zero or more keyword/value pairs may be appended
+         keywords = *neigh*
+           *neigh* value = *yes* or *no*
+             yes = threaded neighbor list build (default)
+             no = non-threaded neighbor list build
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   package gpu 1
+   package gpu 1 split 0.75
+   package gpu 2 split -1.0
+   package gpu 1 device kepler
+   package gpu 1 device 2:generic
+   package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128
+   package kokkos neigh half comm device
+   package omp 0 neigh no
+   package omp 4
+   package intel 1
+   package intel 2 omp 4 mode mixed balance 0.5
+
+Description
+"""""""""""
+
+This command invokes package-specific settings for the various
+accelerator packages available in LAMMPS.  Currently the following
+packages use settings from this command: GPU, USER-INTEL, KOKKOS, and
+USER-OMP.
+
+If this command is specified in an input script, it must be near the
+top of the script, before the simulation box has been defined.  This
+is because it specifies settings that the accelerator packages use in
+their initialization, before a simulation is defined.
+
+This command can also be specified from the command-line when
+launching LAMMPS, using the "-pk" :doc:`command-line switch <Run_options>`.  The syntax is exactly the same as when used
+in an input script.
+
+Note that all of the accelerator packages require the package command
+to be specified (except the OPT package), if the package is to be used
+in a simulation (LAMMPS can be built with an accelerator package
+without using it in a particular simulation).  However, in all cases,
+a default version of the command is typically invoked by other
+accelerator settings.
+
+The KOKKOS package requires a "-k on" :doc:`command-line switch <Run_options>` respectively, which invokes a "package
+kokkos" command with default settings.
+
+For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
+intel" or "-sf omp" :doc:`command-line switch <Run_options>` is used to
+auto-append accelerator suffixes to various styles in the input
+script, then those switches also invoke a "package gpu", "package
+intel", or "package omp" command with default settings.
+
+.. note::
+
+   A package command for a particular style can be invoked multiple
+   times when a simulation is setup, e.g. by the :doc:`-c on, -k on, -sf, and -pk command-line switches <Run_options>`, and by using this command
+   in an input script.  Each time it is used all of the style options are
+   set, either to default values or to specified settings.  I.e. settings
+   from previous invocations do not persist across multiple invocations.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more details
+about using the various accelerator packages for speeding up LAMMPS
+simulations.
+
+
+----------
+
+
+The *gpu* style invokes settings associated with the use of the GPU
+package.
+
+The *Ngpu* argument sets the number of GPUs per node.  There must be
+at least as many MPI tasks per node as GPUs, as set by the mpirun or
+mpiexec command.  If there are more MPI tasks (per node)
+than GPUs, multiple MPI tasks will share each GPU.
+
+Optional keyword/value pairs can also be specified.  Each has a
+default value as listed below.
+
+The *neigh* keyword specifies where neighbor lists for pair style
+computation will be built.  If *neigh* is *yes*\ , which is the default,
+neighbor list building is performed on the GPU.  If *neigh* is *no*\ ,
+neighbor list building is performed on the CPU.  GPU neighbor list
+building currently cannot be used with a triclinic box.  GPU neighbor
+lists are not compatible with commands that are not GPU-enabled.  When
+a non-GPU enabled command requires a neighbor list, it will also be
+built on the CPU.  In these cases, it will typically be more efficient
+to only use CPU neighbor list builds.
+
+The *newton* keyword sets the Newton flags for pairwise (not bonded)
+interactions to *off* or *on*\ , the same as the :doc:`newton <newton>`
+command allows.  Currently, only an *off* value is allowed, since all
+the GPU package pair styles require this setting.  This means more
+computation is done, but less communication.  In the future a value of
+*on* may be allowed, so the *newton* keyword is included as an option
+for compatibility with the package command for other accelerator
+styles.  Note that the newton setting for bonded interactions is not
+affected by this keyword.
+
+The *binsize* keyword sets the size of bins used to bin atoms in
+neighbor list builds performed on the GPU, if *neigh* = *yes* is set.
+If *binsize* is set to 0.0 (the default), then bins = the size of the
+pairwise cutoff + neighbor skin distance.  This is 2x larger than the
+LAMMPS default used for neighbor list building on the CPU.  This will
+be close to optimal for the GPU, so you do not normally need to use
+this keyword.  Note that if you use a longer-than-usual pairwise
+cutoff, e.g. to allow for a smaller fraction of KSpace work with a
+:doc:`long-range Coulombic solver <kspace_style>` because the GPU is
+faster at performing pairwise interactions, then it may be optimal to
+make the *binsize* smaller than the default.  For example, with a
+cutoff of 20\*sigma in LJ :doc:`units <units>` and a neighbor skin
+distance of sigma, a *binsize* = 5.25\*sigma can be more efficient than
+the default.
+
+The *split* keyword can be used for load balancing force calculations
+between CPU and GPU cores in GPU-enabled pair styles. If 0 < *split* <
+1.0, a fixed fraction of particles is offloaded to the GPU while force
+calculation for the other particles occurs simultaneously on the CPU.
+If *split* < 0.0, the optimal fraction (based on CPU and GPU timings)
+is calculated every 25 timesteps, i.e. dynamic load-balancing across
+the CPU and GPU is performed.  If *split* = 1.0, all force
+calculations for GPU accelerated pair styles are performed on the GPU.
+In this case, other :doc:`hybrid <pair_hybrid>` pair interactions,
+:doc:`bond <bond_style>`, :doc:`angle <angle_style>`,
+:doc:`dihedral <dihedral_style>`, :doc:`improper <improper_style>`, and
+:doc:`long-range <kspace_style>` calculations can be performed on the
+CPU while the GPU is performing force calculations for the GPU-enabled
+pair style.  If all CPU force computations complete before the GPU
+completes, LAMMPS will block until the GPU has finished before
+continuing the timestep.
+
+As an example, if you have two GPUs per node and 8 CPU cores per node,
+and would like to run on 4 nodes (32 cores) with dynamic balancing of
+force calculation across CPU and GPU cores, you could specify
+
+
+.. parsed-literal::
+
+   mpirun -np 32 -sf gpu -in in.script    # launch command
+   package gpu 2 split -1                 # input script command
+
+In this case, all CPU cores and GPU devices on the nodes would be
+utilized.  Each GPU device would be shared by 4 CPU cores. The CPU
+cores would perform force calculations for some fraction of the
+particles at the same time the GPUs performed force calculation for
+the other particles.
+
+The *gpuID* keyword allows selection of which GPUs on each node will
+be used for a simulation.  The *first* and *last* values specify the
+GPU IDs to use (from 0 to Ngpu-1).  By default, first = 0 and last =
+Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number
+of physical GPUs.  If you only wish to use a subset, set Ngpu to a
+smaller number and first/last to a sub-range of the available GPUs.
+
+The *tpa* keyword sets the number of GPU thread per atom used to
+perform force calculations.  With a default value of 1, the number of
+threads will be chosen based on the pair style, however, the value can
+be set explicitly with this keyword to fine-tune performance.  For
+large cutoffs or with a small number of particles per GPU, increasing
+the value can improve performance. The number of threads per atom must
+be a power of 2 and currently cannot be greater than 32.
+
+The *device* keyword can be used to tune parameters optimized for a
+specific accelerator and platform when using OpenCL. OpenCL supports
+the concept of a **platform**\ , which represents one or more devices that
+share the same driver (e.g. there would be a different platform for
+GPUs from different vendors or for CPU based accelerator support).
+In LAMMPS only one platform can be active at a time and by default
+the first platform with an accelerator is selected. This is equivalent
+to using a platform ID of -1. The platform ID is a number corresponding
+to the output of the ocl\_get\_devices tool. The platform ID is passed
+to the GPU library, by prefixing the *device* keyword with that number
+separated by a colon. For CUDA, the *device* keyword is ignored.
+Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA
+Fermi, AMD Cypress, Intel x86\_64 CPU, Intel Xeon Phi, or a generic device.
+More devices may be added later.  The default device type can be
+specified when building LAMMPS with the GPU library, via setting a
+variable in the lib/gpu/Makefile that is used.
+
+In addition, a device type *custom* is available, which is followed by
+13 comma separated numbers, which allows to set those tweakable parameters
+from the package command. It can be combined with the (colon separated)
+platform id. The individual settings are:
+
+* MEM\_THREADS
+* THREADS\_PER\_ATOM
+* THREADS\_PER\_CHARGE
+* BLOCK\_PAIR
+* MAX\_SHARED\_TYPES
+* BLOCK\_NBOR\_BUILD
+* BLOCK\_BIO\_PAIR
+* BLOCK\_ELLIPSE
+* WARP\_SIZE
+* PPPM\_BLOCK\_1D
+* BLOCK\_CELL\_2D
+* BLOCK\_CELL\_ID
+* MAX\_BIO\_SHARED\_TYPES
+
+The *blocksize* keyword allows you to tweak the number of threads used
+per thread block. This number should be a multiple of 32 (for GPUs)
+and its maximum depends on the specific GPU hardware. Typical choices
+are 64, 128, or 256. A larger block size increases occupancy of
+individual GPU cores, but reduces the total number of thread blocks,
+thus may lead to load imbalance.
+
+
+----------
+
+
+The *intel* style invokes settings associated with the use of the
+USER-INTEL package.  All of its settings, except the *omp* and *mode*
+keywords, are ignored if LAMMPS was not built with Xeon Phi
+co-processor support.  All of its settings, including the *omp* and
+*mode* keyword are applicable if LAMMPS was built with co-processor
+support.
+
+The *Nphi* argument sets the number of co-processors per node.
+This can be set to any value, including 0, if LAMMPS was not
+built with co-processor support.
+
+Optional keyword/value pairs can also be specified.  Each has a
+default value as listed below.
+
+The *omp* keyword determines the number of OpenMP threads allocated
+for each MPI task when any portion of the interactions computed by a
+USER-INTEL pair style are run on the CPU.  This can be the case even
+if LAMMPS was built with co-processor support; see the *balance*
+keyword discussion below.  If you are running with less MPI tasks/node
+than there are CPUs, it can be advantageous to use OpenMP threading on
+the CPUs.
+
+.. note::
+
+   The *omp* keyword has nothing to do with co-processor threads on
+   the Xeon Phi; see the *tpc* and *tptask* keywords below for a
+   discussion of co-processor threads.
+
+The *Nthread* value for the *omp* keyword sets the number of OpenMP
+threads allocated for each MPI task.  Setting *Nthread* = 0 (the
+default) instructs LAMMPS to use whatever value is the default for the
+given OpenMP environment. This is usually determined via the
+*OMP\_NUM\_THREADS* environment variable or the compiler runtime, which
+is usually a value of 1.
+
+For more details, including examples of how to set the OMP\_NUM\_THREADS
+environment variable, see the discussion of the *Nthreads* setting on
+this doc page for the "package omp" command.  Nthreads is a required
+argument for the USER-OMP package.  Its meaning is exactly the same
+for the USER-INTEL package.
+
+.. note::
+
+   If you build LAMMPS with both the USER-INTEL and USER-OMP
+   packages, be aware that both packages allow setting of the *Nthreads*
+   value via their package commands, but there is only a single global
+   *Nthreads* value used by OpenMP.  Thus if both package commands are
+   invoked, you should insure the two values are consistent.  If they are
+   not, the last one invoked will take precedence, for both packages.
+   Also note that if the :doc:`-sf hybrid intel omp command-line switch <Run_options>` is used, it invokes a "package intel"
+   command, followed by a "package omp" command, both with a setting of
+   *Nthreads* = 0.
+
+The *mode* keyword determines the precision mode to use for
+computing pair style forces, either on the CPU or on the co-processor,
+when using a USER-INTEL supported :doc:`pair style <pair_style>`.  It
+can take a value of *single*\ , *mixed* which is the default, or
+*double*\ .  *Single* means single precision is used for the entire
+force calculation.  *Mixed* means forces between a pair of atoms are
+computed in single precision, but accumulated and stored in double
+precision, including storage of forces, torques, energies, and virial
+quantities.  *Double* means double precision is used for the entire
+force calculation.
+
+The *lrt* keyword can be used to enable "Long Range Thread (LRT)"
+mode. It can take a value of *yes* to enable and *no* to disable.
+LRT mode generates an extra thread (in addition to any OpenMP threads
+specified with the OMP\_NUM\_THREADS environment variable or the *omp*
+keyword). The extra thread is dedicated for performing part of the
+:doc:`PPPM solver <kspace_style>` computations and communications. This
+can improve parallel performance on processors supporting
+Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel
+processors. In this mode, one additional thread is generated per MPI
+process. LAMMPS will generate a warning in the case that more threads
+are used than available in SMT hardware on a node. If the PPPM solver
+from the USER-INTEL package is not used, then the LRT setting is
+ignored and no extra threads are generated. Enabling LRT will replace
+the :doc:`run\_style <run_style>` with the *verlet/lrt/intel* style that
+is identical to the default *verlet* style aside from supporting the
+LRT feature. This feature requires setting the pre-processor flag
+-DLMP\_INTEL\_USELRT in the makefile when compiling LAMMPS.
+
+The *balance* keyword sets the fraction of :doc:`pair style <pair_style>` work offloaded to the co-processor for split
+values between 0.0 and 1.0 inclusive.  While this fraction of work is
+running on the co-processor, other calculations will run on the host,
+including neighbor and pair calculations that are not offloaded, as
+well as angle, bond, dihedral, kspace, and some MPI communications.
+If *split* is set to -1, the fraction of work is dynamically adjusted
+automatically throughout the run.  This typically give performance
+within 5 to 10 percent of the optimal fixed fraction.
+
+The *ghost* keyword determines whether or not ghost atoms, i.e. atoms
+at the boundaries of processor sub-domains, are offloaded for neighbor
+and force calculations.  When the value = "no", ghost atoms are not
+offloaded.  This option can reduce the amount of data transfer with
+the co-processor and can also overlap MPI communication of forces with
+computation on the co-processor when the :doc:`newton pair <newton>`
+setting is "on".  When the value = "yes", ghost atoms are offloaded.
+In some cases this can provide better performance, especially if the
+*balance* fraction is high.
+
+The *tpc* keyword sets the max # of co-processor threads *Ntpc* that
+will run on each core of the co-processor.  The default value = 4,
+which is the number of hardware threads per core supported by the
+current generation Xeon Phi chips.
+
+The *tptask* keyword sets the max # of co-processor threads (Ntptask*
+assigned to each MPI task.  The default value = 240, which is the
+total # of threads an entire current generation Xeon Phi chip can run
+(240 = 60 cores \* 4 threads/core).  This means each MPI task assigned
+to the Phi will enough threads for the chip to run the max allowed,
+even if only 1 MPI task is assigned.  If 8 MPI tasks are assigned to
+the Phi, each will run with 30 threads.  If you wish to limit the
+number of threads per MPI task, set *tptask* to a smaller value.
+E.g. for *tptask* = 16, if 8 MPI tasks are assigned, each will run
+with 16 threads, for a total of 128.
+
+Note that the default settings for *tpc* and *tptask* are fine for
+most problems, regardless of how many MPI tasks you assign to a Phi.
+
+The *no\_affinity* keyword will turn off automatic setting of core
+affinity for MPI tasks and OpenMP threads on the host when using
+offload to a co-processor. Affinity settings are used when possible
+to prevent MPI tasks and OpenMP threads from being on separate NUMA
+domains and to prevent offload threads from interfering with other
+processes/threads used for LAMMPS.
+
+
+----------
+
+
+The *kokkos* style invokes settings associated with the use of the
+KOKKOS package.
+
+All of the settings are optional keyword/value pairs. Each has a default
+value as listed below.
+
+The *neigh* keyword determines how neighbor lists are built. A value of
+*half* uses a thread-safe variant of half-neighbor lists, the same as
+used by most pair styles in LAMMPS, which is the default when running on
+CPUs (i.e. the Kokkos CUDA back end is not enabled).
+
+A value of *full* uses a full neighbor lists and is the default when
+running on GPUs. This performs twice as much computation as the *half*
+option, however that is often a win because it is thread-safe and
+doesn't require atomic operations in the calculation of pair forces. For
+that reason, *full* is the default setting for GPUs. However, when
+running on CPUs, a *half* neighbor list is the default because it are
+often faster, just as it is for non-accelerated pair styles. Similarly,
+the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`. If not explicitly set, the value of
+*neigh/qeq* will match *neigh*\ .
+
+If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package
+threads only over atoms. However, for small systems, this may not expose
+enough parallelism to keep a GPU busy. When this keyword is set to *on*\ ,
+the KOKKOS package threads over both atoms and neighbors of atoms. When
+using *neigh/thread* *on*\ , a full neighbor list must also be used. Using
+*neigh/thread* *on* may be slower for large systems, so this this option
+is turned on by default only when there are 16K atoms or less owned by
+an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
+potentials support this keyword yet, and only thread over atoms. Many
+simple pair-wise potentials such as Lennard-Jones do support threading
+over both atoms and neighbors.
+
+The *newton* keyword sets the Newton flags for pairwise and bonded
+interactions to *off* or *on*\ , the same as the :doc:`newton <newton>`
+command allows. The default for GPUs is *off* because this will almost
+always give better performance for the KOKKOS package. This means more
+computation is done, but less communication. However, when running on
+CPUs a value of *on* is the default since it can often be faster, just
+as it is for non-accelerated pair styles
+
+The *binsize* keyword sets the size of bins used to bin atoms in
+neighbor list builds. The same value can be set by the :doc:`neigh\_modify binsize <neigh_modify>` command. Making it an option in the package
+kokkos command allows it to be set from the command line. The default
+value for CPUs is 0.0, which means the LAMMPS default will be used,
+which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
+distance. This is fine when neighbor lists are built on the CPU. For GPU
+builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin
+is often faster, which is the default. Note that if you use a
+longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction
+of KSpace work with a :doc:`long-range Coulombic solver <kspace_style>`
+because the GPU is faster at performing pairwise interactions, then this
+rule of thumb may give too large a binsize and the default should be
+overridden with a smaller value.
+
+The *comm* and *comm/exchange* and *comm/forward* and *comm/reverse*
+keywords determine whether the host or device performs the packing and
+unpacking of data when communicating per-atom data between processors.
+"Exchange" communication happens only on timesteps that neighbor lists
+are rebuilt. The data is only for atoms that migrate to new processors.
+"Forward" communication happens every timestep. "Reverse" communication
+happens every timestep if the *newton* option is on. The data is for
+atom coordinates and any other atom properties that needs to be updated
+for ghost atoms owned by each processor.
+
+The *comm* keyword is simply a short-cut to set the same value for both
+the *comm/exchange* and *comm/forward* and *comm/reverse* keywords.
+
+The value options for all 3 keywords are *no* or *host* or *device*\ . A
+value of *no* means to use the standard non-KOKKOS method of
+packing/unpacking data for the communication. A value of *host* means to
+use the host, typically a multi-core CPU, and perform the
+packing/unpacking in parallel with threads. A value of *device* means to
+use the device, typically a GPU, to perform the packing/unpacking
+operation.
+
+The optimal choice for these keywords depends on the input script and
+the hardware used. The *no* value is useful for verifying that the
+Kokkos-based *host* and *device* values are working correctly. It is the
+default when running on CPUs since it is usually the fastest.
+
+When running on CPUs or Xeon Phi, the *host* and *device* values work
+identically. When using GPUs, the *device* value is the default since it
+will typically be optimal if all of your styles used in your input
+script are supported by the KOKKOS package. In this case data can stay
+on the GPU for many timesteps without being moved between the host and
+GPU, if you use the *device* value. If your script uses styles (e.g.
+fixes) which are not yet supported by the KOKKOS package, then data has
+to be move between the host and device anyway, so it is typically faster
+to let the host handle communication, by using the *host* value. Using
+*host* instead of *no* will enable use of multiple threads to
+pack/unpack communicated data. When running small systems on a GPU,
+performing the exchange pack/unpack on the host CPU can give speedup
+since it reduces the number of CUDA kernel launches.
+
+The *cuda/aware* keyword chooses whether CUDA-aware MPI will be used. When
+this keyword is set to *on*\ , buffers in GPU memory are passed directly
+through MPI send/receive calls. This reduces overhead of first copying
+the data to the host CPU. However CUDA-aware MPI is not supported on all
+systems, which can lead to segmentation faults and would require using a
+value of *off*\ . If LAMMPS can safely detect that CUDA-aware MPI is not
+available (currently only possible with OpenMPI v2.0.0 or later), then
+the *cuda/aware* keyword is automatically set to *off* by default. When
+the *cuda/aware* keyword is set to *off* while any of the *comm*
+keywords are set to *device*\ , the value for these *comm* keywords will
+be automatically changed to *host*\ . This setting has no effect if not
+running on GPUs or if using only one MPI rank. CUDA-aware MPI is available
+for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the
+"MV2\_USE\_CUDA" environment variable is set to "1", CrayMPI, and IBM
+Spectrum MPI when the "-gpu" flag is used.
+
+
+----------
+
+
+The *omp* style invokes settings associated with the use of the
+USER-OMP package.
+
+The *Nthread* argument sets the number of OpenMP threads allocated for
+each MPI task.  For example, if your system has nodes with dual
+quad-core processors, it has a total of 8 cores per node.  You could
+use two MPI tasks per node (e.g. using the -ppn option of the mpirun
+command in MPICH or -npernode in OpenMPI), and set *Nthreads* = 4.
+This would use all 8 cores on each node.  Note that the product of MPI
+tasks \* threads/task should not exceed the physical number of cores
+(on a node), otherwise performance will suffer.
+
+Setting *Nthread* = 0 instructs LAMMPS to use whatever value is the
+default for the given OpenMP environment. This is usually determined
+via the *OMP\_NUM\_THREADS* environment variable or the compiler
+runtime.  Note that in most cases the default for OpenMP capable
+compilers is to use one thread for each available CPU core when
+*OMP\_NUM\_THREADS* is not explicitly set, which can lead to poor
+performance.
+
+Here are examples of how to set the environment variable when
+launching LAMMPS:
+
+
+.. parsed-literal::
+
+   env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
+   env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
+   mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
+
+or you can set it permanently in your shell's start-up script.
+All three of these examples use a total of 4 CPU cores.
+
+Note that different MPI implementations have different ways of passing
+the OMP\_NUM\_THREADS environment variable to all MPI processes.  The
+2nd example line above is for MPICH; the 3rd example line with -x is
+for OpenMPI.  Check your MPI documentation for additional details.
+
+What combination of threads and MPI tasks gives the best performance
+is difficult to predict and can depend on many components of your
+input.  Not all features of LAMMPS support OpenMP threading via the
+USER-OMP package and the parallel efficiency can be very different,
+too.
+
+Optional keyword/value pairs can also be specified.  Each has a
+default value as listed below.
+
+The *neigh* keyword specifies whether neighbor list building will be
+multi-threaded in addition to force calculations.  If *neigh* is set
+to *no* then neighbor list calculation is performed only by MPI tasks
+with no OpenMP threading.  If *mode* is *yes* (the default), a
+multi-threaded neighbor list build is used.  Using *neigh* = *yes* is
+almost always faster and should produce identical neighbor lists at the
+expense of using more memory.  Specifically, neighbor list pages are
+allocated for all threads at the same time and each thread works
+within its own pages.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command cannot be used after the simulation box is defined by a
+:doc:`read\_data <read_data>` or :doc:`create\_box <create_box>` command.
+
+The gpu style of this command can only be invoked if LAMMPS was built
+with the GPU package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+The intel style of this command can only be invoked if LAMMPS was
+built with the USER-INTEL package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The kk style of this command can only be invoked if LAMMPS was built
+with the KOKKOS package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+The omp style of this command can only be invoked if LAMMPS was built
+with the USER-OMP package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`suffix <suffix>`, :doc:`-pk command-line switch <Run_options>`
+
+Default
+"""""""
+
+For the GPU package, the default is Ngpu = 1 and the option defaults
+are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
+to Ngpu-1, tpa = 1, and device = not used.  These settings are made
+automatically if the "-sf gpu" :doc:`command-line switch <Run_options>`
+is used.  If it is not used, you must invoke the package gpu command
+in your input script or via the "-pk gpu" :doc:`command-line switch <Run_options>`.
+
+For the USER-INTEL package, the default is Nphi = 1 and the option
+defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
+tptask = 240.  The default ghost option is determined by the pair
+style being used.  This value is output to the screen in the offload
+report at the end of each run.  Note that all of these settings,
+except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
+Phi co-processor support.  These settings are made automatically if the
+"-sf intel" :doc:`command-line switch <Run_options>` is used.  If it is
+not used, you must invoke the package intel command in your input
+script or via the "-pk intel" :doc:`command-line switch <Run_options>`.
+
+For the KOKKOS package, the option defaults for GPUs are neigh = full,
+neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
+value, comm = device, cuda/aware = on. When LAMMPS can safely detect
+that CUDA-aware MPI is not available, the default value of cuda/aware
+becomes "off". For CPUs or Xeon Phis, the option defaults are neigh =
+half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The
+option neigh/thread = on when there are 16K atoms or less on an MPI
+rank, otherwise it is "off". These settings are made automatically by
+the required "-k on" :doc:`command-line switch <Run_options>`. You can
+change them by using the package kokkos command in your input script or
+via the :doc:`-pk kokkos command-line switch <Run_options>`.
+
+For the OMP package, the default is Nthreads = 0 and the option
+defaults are neigh = yes.  These settings are made automatically if
+the "-sf omp" :doc:`command-line switch <Run_options>` is used.  If it
+is not used, you must invoke the package omp command in your input
+script or via the "-pk omp" :doc:`command-line switch <Run_options>`.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/package.txt b/doc/src/package.txt
deleted file mode 100644
index edd409a842..0000000000
--- a/doc/src/package.txt
+++ /dev/null
@@ -1,660 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-package command :h3
-
-[Syntax:]
-
-package style args :pre
-
-style = {gpu} or {intel} or {kokkos} or {omp} :ulb,l
-args = arguments specific to the style :l
-  {gpu} args = Ngpu keyword value ...
-    Ngpu = # of GPUs per node
-    zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {newton} or {binsize} or {split} or {gpuID} or {tpa} or {device} or {blocksize}
-      {neigh} value = {yes} or {no}
-        yes = neighbor list build on GPU (default)
-        no = neighbor list build on CPU
-      {newton} = {off} or {on}
-        off = set Newton pairwise flag off (default and required)
-        on = set Newton pairwise flag on (currently not allowed)
-      {binsize} value = size
-        size = bin size for neighbor list construction (distance units)
-      {split} = fraction
-        fraction = fraction of atoms assigned to GPU (default = 1.0)
-      {gpuID} values = first last
-        first = ID of first GPU to be used on each node
-        last = ID of last GPU to be used on each node
-      {tpa} value = Nthreads
-        Nthreads = # of GPU threads used per atom
-      {device} value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13
-        platform_id = numerical OpenCL platform id (default: -1)
-        device_type = {kepler} or {fermi} or {cypress} or {intel} or {phi} or {generic} or {custom}
-        val1,val2,... = custom OpenCL tune parameters (see below for details)
-      {blocksize} value = size
-        size = thread block size for pair force computation
-  {intel} args = NPhi keyword value ...
-    Nphi = # of co-processors per node
-    zero or more keyword/value pairs may be appended
-    keywords = {mode} or {omp} or {lrt} or {balance} or {ghost} or {tpc} or {tptask} or {no_affinity}
-      {mode} value = {single} or {mixed} or {double}
-        single = perform force calculations in single precision
-        mixed = perform force calculations in mixed precision
-        double = perform force calculations in double precision
-      {omp} value = Nthreads
-        Nthreads = number of OpenMP threads to use on CPU (default = 0)
-      {lrt} value = {yes} or {no}
-        yes = use additional thread dedicated for some PPPM calculations
-        no = do not dedicate an extra thread for some PPPM calculations
-      {balance} value = split
-        split = fraction of work to offload to co-processor, -1 for dynamic
-      {ghost} value = {yes} or {no}
-        yes = include ghost atoms for offload
-        no = do not include ghost atoms for offload
-      {tpc} value = Ntpc
-        Ntpc = max number of co-processor threads per co-processor core (default = 4)
-      {tptask} value = Ntptask
-        Ntptask = max number of co-processor threads per MPI task (default = 240)
-      {no_affinity} values = none
-  {kokkos} args = keyword value ...
-    zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {cuda/aware}
-      {neigh} value = {full} or {half}
-        full = full neighbor list
-        half = half neighbor list built in thread-safe manner
-      {neigh/qeq} value = {full} or {half}
-        full = full neighbor list
-        half = half neighbor list built in thread-safe manner
-      {neigh/thread} value = {off} or {on}
-        off = thread only over atoms
-        on = thread over both atoms and neighbors
-      {newton} = {off} or {on}
-        off = set Newton pairwise and bonded flags off
-        on = set Newton pairwise and bonded flags on
-      {binsize} value = size
-        size = bin size for neighbor list construction (distance units)
-      {comm} value = {no} or {host} or {device}
-        use value for comm/exchange and comm/forward and comm/reverse
-      {comm/exchange} value = {no} or {host} or {device}
-      {comm/forward} value = {no} or {host} or {device}
-      {comm/reverse} value = {no} or {host} or {device}
-        no = perform communication pack/unpack in non-KOKKOS mode
-        host = perform pack/unpack on host (e.g. with OpenMP threading)
-        device = perform pack/unpack on device (e.g. on GPU)
-      {cuda/aware} = {off} or {on}
-        off = do not use CUDA-aware MPI
-        on = use CUDA-aware MPI (default)
-  {omp} args = Nthreads keyword value ...
-    Nthread = # of OpenMP threads to associate with each MPI process
-    zero or more keyword/value pairs may be appended
-    keywords = {neigh}
-      {neigh} value = {yes} or {no}
-        yes = threaded neighbor list build (default)
-        no = non-threaded neighbor list build :pre
-:ule
-
-[Examples:]
-
-package gpu 1
-package gpu 1 split 0.75
-package gpu 2 split -1.0
-package gpu 1 device kepler
-package gpu 1 device 2:generic
-package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128
-package kokkos neigh half comm device
-package omp 0 neigh no
-package omp 4
-package intel 1
-package intel 2 omp 4 mode mixed balance 0.5 :pre
-
-[Description:]
-
-This command invokes package-specific settings for the various
-accelerator packages available in LAMMPS.  Currently the following
-packages use settings from this command: GPU, USER-INTEL, KOKKOS, and
-USER-OMP.
-
-If this command is specified in an input script, it must be near the
-top of the script, before the simulation box has been defined.  This
-is because it specifies settings that the accelerator packages use in
-their initialization, before a simulation is defined.
-
-This command can also be specified from the command-line when
-launching LAMMPS, using the "-pk" "command-line
-switch"_Run_options.html.  The syntax is exactly the same as when used
-in an input script.
-
-Note that all of the accelerator packages require the package command
-to be specified (except the OPT package), if the package is to be used
-in a simulation (LAMMPS can be built with an accelerator package
-without using it in a particular simulation).  However, in all cases,
-a default version of the command is typically invoked by other
-accelerator settings.
-
-The KOKKOS package requires a "-k on" "command-line
-switch"_Run_options.html respectively, which invokes a "package
-kokkos" command with default settings.
-
-For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
-intel" or "-sf omp" "command-line switch"_Run_options.html is used to
-auto-append accelerator suffixes to various styles in the input
-script, then those switches also invoke a "package gpu", "package
-intel", or "package omp" command with default settings.
-
-NOTE: A package command for a particular style can be invoked multiple
-times when a simulation is setup, e.g. by the "-c on, -k on, -sf, and
--pk command-line switches"_Run_options.html, and by using this command
-in an input script.  Each time it is used all of the style options are
-set, either to default values or to specified settings.  I.e. settings
-from previous invocations do not persist across multiple invocations.
-
-See the "Speed packages"_Speed_packages.html doc page for more details
-about using the various accelerator packages for speeding up LAMMPS
-simulations.
-
-:line
-
-The {gpu} style invokes settings associated with the use of the GPU
-package.
-
-The {Ngpu} argument sets the number of GPUs per node.  There must be
-at least as many MPI tasks per node as GPUs, as set by the mpirun or
-mpiexec command.  If there are more MPI tasks (per node)
-than GPUs, multiple MPI tasks will share each GPU.
-
-Optional keyword/value pairs can also be specified.  Each has a
-default value as listed below.
-
-The {neigh} keyword specifies where neighbor lists for pair style
-computation will be built.  If {neigh} is {yes}, which is the default,
-neighbor list building is performed on the GPU.  If {neigh} is {no},
-neighbor list building is performed on the CPU.  GPU neighbor list
-building currently cannot be used with a triclinic box.  GPU neighbor
-lists are not compatible with commands that are not GPU-enabled.  When
-a non-GPU enabled command requires a neighbor list, it will also be
-built on the CPU.  In these cases, it will typically be more efficient
-to only use CPU neighbor list builds.
-
-The {newton} keyword sets the Newton flags for pairwise (not bonded)
-interactions to {off} or {on}, the same as the "newton"_newton.html
-command allows.  Currently, only an {off} value is allowed, since all
-the GPU package pair styles require this setting.  This means more
-computation is done, but less communication.  In the future a value of
-{on} may be allowed, so the {newton} keyword is included as an option
-for compatibility with the package command for other accelerator
-styles.  Note that the newton setting for bonded interactions is not
-affected by this keyword.
-
-The {binsize} keyword sets the size of bins used to bin atoms in
-neighbor list builds performed on the GPU, if {neigh} = {yes} is set.
-If {binsize} is set to 0.0 (the default), then bins = the size of the
-pairwise cutoff + neighbor skin distance.  This is 2x larger than the
-LAMMPS default used for neighbor list building on the CPU.  This will
-be close to optimal for the GPU, so you do not normally need to use
-this keyword.  Note that if you use a longer-than-usual pairwise
-cutoff, e.g. to allow for a smaller fraction of KSpace work with a
-"long-range Coulombic solver"_kspace_style.html because the GPU is
-faster at performing pairwise interactions, then it may be optimal to
-make the {binsize} smaller than the default.  For example, with a
-cutoff of 20*sigma in LJ "units"_units.html and a neighbor skin
-distance of sigma, a {binsize} = 5.25*sigma can be more efficient than
-the default.
-
-The {split} keyword can be used for load balancing force calculations
-between CPU and GPU cores in GPU-enabled pair styles. If 0 < {split} <
-1.0, a fixed fraction of particles is offloaded to the GPU while force
-calculation for the other particles occurs simultaneously on the CPU.
-If {split} < 0.0, the optimal fraction (based on CPU and GPU timings)
-is calculated every 25 timesteps, i.e. dynamic load-balancing across
-the CPU and GPU is performed.  If {split} = 1.0, all force
-calculations for GPU accelerated pair styles are performed on the GPU.
-In this case, other "hybrid"_pair_hybrid.html pair interactions,
-"bond"_bond_style.html, "angle"_angle_style.html,
-"dihedral"_dihedral_style.html, "improper"_improper_style.html, and
-"long-range"_kspace_style.html calculations can be performed on the
-CPU while the GPU is performing force calculations for the GPU-enabled
-pair style.  If all CPU force computations complete before the GPU
-completes, LAMMPS will block until the GPU has finished before
-continuing the timestep.
-
-As an example, if you have two GPUs per node and 8 CPU cores per node,
-and would like to run on 4 nodes (32 cores) with dynamic balancing of
-force calculation across CPU and GPU cores, you could specify
-
-mpirun -np 32 -sf gpu -in in.script    # launch command
-package gpu 2 split -1                 # input script command :pre
-
-In this case, all CPU cores and GPU devices on the nodes would be
-utilized.  Each GPU device would be shared by 4 CPU cores. The CPU
-cores would perform force calculations for some fraction of the
-particles at the same time the GPUs performed force calculation for
-the other particles.
-
-The {gpuID} keyword allows selection of which GPUs on each node will
-be used for a simulation.  The {first} and {last} values specify the
-GPU IDs to use (from 0 to Ngpu-1).  By default, first = 0 and last =
-Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number
-of physical GPUs.  If you only wish to use a subset, set Ngpu to a
-smaller number and first/last to a sub-range of the available GPUs.
-
-The {tpa} keyword sets the number of GPU thread per atom used to
-perform force calculations.  With a default value of 1, the number of
-threads will be chosen based on the pair style, however, the value can
-be set explicitly with this keyword to fine-tune performance.  For
-large cutoffs or with a small number of particles per GPU, increasing
-the value can improve performance. The number of threads per atom must
-be a power of 2 and currently cannot be greater than 32.
-
-The {device} keyword can be used to tune parameters optimized for a
-specific accelerator and platform when using OpenCL. OpenCL supports
-the concept of a [platform], which represents one or more devices that
-share the same driver (e.g. there would be a different platform for
-GPUs from different vendors or for CPU based accelerator support).
-In LAMMPS only one platform can be active at a time and by default
-the first platform with an accelerator is selected. This is equivalent
-to using a platform ID of -1. The platform ID is a number corresponding
-to the output of the ocl_get_devices tool. The platform ID is passed
-to the GPU library, by prefixing the {device} keyword with that number
-separated by a colon. For CUDA, the {device} keyword is ignored.
-Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA
-Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device.
-More devices may be added later.  The default device type can be
-specified when building LAMMPS with the GPU library, via setting a
-variable in the lib/gpu/Makefile that is used.
-
-In addition, a device type {custom} is available, which is followed by
-13 comma separated numbers, which allows to set those tweakable parameters
-from the package command. It can be combined with the (colon separated)
-platform id. The individual settings are:
-
-MEM_THREADS
-THREADS_PER_ATOM
-THREADS_PER_CHARGE
-BLOCK_PAIR
-MAX_SHARED_TYPES
-BLOCK_NBOR_BUILD
-BLOCK_BIO_PAIR
-BLOCK_ELLIPSE
-WARP_SIZE
-PPPM_BLOCK_1D
-BLOCK_CELL_2D
-BLOCK_CELL_ID
-MAX_BIO_SHARED_TYPES :ul
-
-The {blocksize} keyword allows you to tweak the number of threads used
-per thread block. This number should be a multiple of 32 (for GPUs)
-and its maximum depends on the specific GPU hardware. Typical choices
-are 64, 128, or 256. A larger block size increases occupancy of
-individual GPU cores, but reduces the total number of thread blocks,
-thus may lead to load imbalance.
-
-:line
-
-The {intel} style invokes settings associated with the use of the
-USER-INTEL package.  All of its settings, except the {omp} and {mode}
-keywords, are ignored if LAMMPS was not built with Xeon Phi
-co-processor support.  All of its settings, including the {omp} and
-{mode} keyword are applicable if LAMMPS was built with co-processor
-support.
-
-The {Nphi} argument sets the number of co-processors per node.
-This can be set to any value, including 0, if LAMMPS was not
-built with co-processor support.
-
-Optional keyword/value pairs can also be specified.  Each has a
-default value as listed below.
-
-The {omp} keyword determines the number of OpenMP threads allocated
-for each MPI task when any portion of the interactions computed by a
-USER-INTEL pair style are run on the CPU.  This can be the case even
-if LAMMPS was built with co-processor support; see the {balance}
-keyword discussion below.  If you are running with less MPI tasks/node
-than there are CPUs, it can be advantageous to use OpenMP threading on
-the CPUs.
-
-NOTE: The {omp} keyword has nothing to do with co-processor threads on
-the Xeon Phi; see the {tpc} and {tptask} keywords below for a
-discussion of co-processor threads.
-
-The {Nthread} value for the {omp} keyword sets the number of OpenMP
-threads allocated for each MPI task.  Setting {Nthread} = 0 (the
-default) instructs LAMMPS to use whatever value is the default for the
-given OpenMP environment. This is usually determined via the
-{OMP_NUM_THREADS} environment variable or the compiler runtime, which
-is usually a value of 1.
-
-For more details, including examples of how to set the OMP_NUM_THREADS
-environment variable, see the discussion of the {Nthreads} setting on
-this doc page for the "package omp" command.  Nthreads is a required
-argument for the USER-OMP package.  Its meaning is exactly the same
-for the USER-INTEL package.
-
-NOTE: If you build LAMMPS with both the USER-INTEL and USER-OMP
-packages, be aware that both packages allow setting of the {Nthreads}
-value via their package commands, but there is only a single global
-{Nthreads} value used by OpenMP.  Thus if both package commands are
-invoked, you should insure the two values are consistent.  If they are
-not, the last one invoked will take precedence, for both packages.
-Also note that if the "-sf hybrid intel omp command-line
-switch"_Run_options.html is used, it invokes a "package intel"
-command, followed by a "package omp" command, both with a setting of
-{Nthreads} = 0.
-
-The {mode} keyword determines the precision mode to use for
-computing pair style forces, either on the CPU or on the co-processor,
-when using a USER-INTEL supported "pair style"_pair_style.html.  It
-can take a value of {single}, {mixed} which is the default, or
-{double}.  {Single} means single precision is used for the entire
-force calculation.  {Mixed} means forces between a pair of atoms are
-computed in single precision, but accumulated and stored in double
-precision, including storage of forces, torques, energies, and virial
-quantities.  {Double} means double precision is used for the entire
-force calculation.
-
-The {lrt} keyword can be used to enable "Long Range Thread (LRT)"
-mode. It can take a value of {yes} to enable and {no} to disable.
-LRT mode generates an extra thread (in addition to any OpenMP threads
-specified with the OMP_NUM_THREADS environment variable or the {omp}
-keyword). The extra thread is dedicated for performing part of the
-"PPPM solver"_kspace_style.html computations and communications. This
-can improve parallel performance on processors supporting
-Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel
-processors. In this mode, one additional thread is generated per MPI
-process. LAMMPS will generate a warning in the case that more threads
-are used than available in SMT hardware on a node. If the PPPM solver
-from the USER-INTEL package is not used, then the LRT setting is
-ignored and no extra threads are generated. Enabling LRT will replace
-the "run_style"_run_style.html with the {verlet/lrt/intel} style that
-is identical to the default {verlet} style aside from supporting the
-LRT feature. This feature requires setting the pre-processor flag
--DLMP_INTEL_USELRT in the makefile when compiling LAMMPS.
-
-The {balance} keyword sets the fraction of "pair
-style"_pair_style.html work offloaded to the co-processor for split
-values between 0.0 and 1.0 inclusive.  While this fraction of work is
-running on the co-processor, other calculations will run on the host,
-including neighbor and pair calculations that are not offloaded, as
-well as angle, bond, dihedral, kspace, and some MPI communications.
-If {split} is set to -1, the fraction of work is dynamically adjusted
-automatically throughout the run.  This typically give performance
-within 5 to 10 percent of the optimal fixed fraction.
-
-The {ghost} keyword determines whether or not ghost atoms, i.e. atoms
-at the boundaries of processor sub-domains, are offloaded for neighbor
-and force calculations.  When the value = "no", ghost atoms are not
-offloaded.  This option can reduce the amount of data transfer with
-the co-processor and can also overlap MPI communication of forces with
-computation on the co-processor when the "newton pair"_newton.html
-setting is "on".  When the value = "yes", ghost atoms are offloaded.
-In some cases this can provide better performance, especially if the
-{balance} fraction is high.
-
-The {tpc} keyword sets the max # of co-processor threads {Ntpc} that
-will run on each core of the co-processor.  The default value = 4,
-which is the number of hardware threads per core supported by the
-current generation Xeon Phi chips.
-
-The {tptask} keyword sets the max # of co-processor threads (Ntptask}
-assigned to each MPI task.  The default value = 240, which is the
-total # of threads an entire current generation Xeon Phi chip can run
-(240 = 60 cores * 4 threads/core).  This means each MPI task assigned
-to the Phi will enough threads for the chip to run the max allowed,
-even if only 1 MPI task is assigned.  If 8 MPI tasks are assigned to
-the Phi, each will run with 30 threads.  If you wish to limit the
-number of threads per MPI task, set {tptask} to a smaller value.
-E.g. for {tptask} = 16, if 8 MPI tasks are assigned, each will run
-with 16 threads, for a total of 128.
-
-Note that the default settings for {tpc} and {tptask} are fine for
-most problems, regardless of how many MPI tasks you assign to a Phi.
-
-The {no_affinity} keyword will turn off automatic setting of core
-affinity for MPI tasks and OpenMP threads on the host when using
-offload to a co-processor. Affinity settings are used when possible
-to prevent MPI tasks and OpenMP threads from being on separate NUMA
-domains and to prevent offload threads from interfering with other
-processes/threads used for LAMMPS.
-
-:line
-
-The {kokkos} style invokes settings associated with the use of the 
-KOKKOS package. 
-
-All of the settings are optional keyword/value pairs. Each has a default 
-value as listed below. 
-
-The {neigh} keyword determines how neighbor lists are built. A value of 
-{half} uses a thread-safe variant of half-neighbor lists, the same as 
-used by most pair styles in LAMMPS, which is the default when running on 
-CPUs (i.e. the Kokkos CUDA back end is not enabled). 
-
-A value of {full} uses a full neighbor lists and is the default when 
-running on GPUs. This performs twice as much computation as the {half} 
-option, however that is often a win because it is thread-safe and 
-doesn't require atomic operations in the calculation of pair forces. For 
-that reason, {full} is the default setting for GPUs. However, when 
-running on CPUs, a {half} neighbor list is the default because it are 
-often faster, just as it is for non-accelerated pair styles. Similarly, 
-the {neigh/qeq} keyword determines how neighbor lists are built for "fix 
-qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of 
-{neigh/qeq} will match {neigh}.
-
-If the {neigh/thread} keyword is set to {off}, then the KOKKOS package 
-threads only over atoms. However, for small systems, this may not expose 
-enough parallelism to keep a GPU busy. When this keyword is set to {on}, 
-the KOKKOS package threads over both atoms and neighbors of atoms. When 
-using {neigh/thread} {on}, a full neighbor list must also be used. Using 
-{neigh/thread} {on} may be slower for large systems, so this this option 
-is turned on by default only when there are 16K atoms or less owned by 
-an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled 
-potentials support this keyword yet, and only thread over atoms. Many 
-simple pair-wise potentials such as Lennard-Jones do support threading 
-over both atoms and neighbors.
-
-The {newton} keyword sets the Newton flags for pairwise and bonded 
-interactions to {off} or {on}, the same as the "newton"_newton.html 
-command allows. The default for GPUs is {off} because this will almost 
-always give better performance for the KOKKOS package. This means more 
-computation is done, but less communication. However, when running on 
-CPUs a value of {on} is the default since it can often be faster, just 
-as it is for non-accelerated pair styles 
-
-The {binsize} keyword sets the size of bins used to bin atoms in 
-neighbor list builds. The same value can be set by the "neigh_modify 
-binsize"_neigh_modify.html command. Making it an option in the package 
-kokkos command allows it to be set from the command line. The default 
-value for CPUs is 0.0, which means the LAMMPS default will be used, 
-which is bins = 1/2 the size of the pairwise cutoff + neighbor skin 
-distance. This is fine when neighbor lists are built on the CPU. For GPU 
-builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin 
-is often faster, which is the default. Note that if you use a 
-longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction 
-of KSpace work with a "long-range Coulombic solver"_kspace_style.html 
-because the GPU is faster at performing pairwise interactions, then this 
-rule of thumb may give too large a binsize and the default should be 
-overridden with a smaller value. 
-
-The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} 
-keywords determine whether the host or device performs the packing and 
-unpacking of data when communicating per-atom data between processors. 
-"Exchange" communication happens only on timesteps that neighbor lists 
-are rebuilt. The data is only for atoms that migrate to new processors. 
-"Forward" communication happens every timestep. "Reverse" communication 
-happens every timestep if the {newton} option is on. The data is for 
-atom coordinates and any other atom properties that needs to be updated 
-for ghost atoms owned by each processor.
-
-The {comm} keyword is simply a short-cut to set the same value for both 
-the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
-
-The value options for all 3 keywords are {no} or {host} or {device}. A 
-value of {no} means to use the standard non-KOKKOS method of 
-packing/unpacking data for the communication. A value of {host} means to 
-use the host, typically a multi-core CPU, and perform the 
-packing/unpacking in parallel with threads. A value of {device} means to 
-use the device, typically a GPU, to perform the packing/unpacking 
-operation.
-
-The optimal choice for these keywords depends on the input script and 
-the hardware used. The {no} value is useful for verifying that the 
-Kokkos-based {host} and {device} values are working correctly. It is the 
-default when running on CPUs since it is usually the fastest.
-
-When running on CPUs or Xeon Phi, the {host} and {device} values work 
-identically. When using GPUs, the {device} value is the default since it 
-will typically be optimal if all of your styles used in your input 
-script are supported by the KOKKOS package. In this case data can stay 
-on the GPU for many timesteps without being moved between the host and 
-GPU, if you use the {device} value. If your script uses styles (e.g. 
-fixes) which are not yet supported by the KOKKOS package, then data has 
-to be move between the host and device anyway, so it is typically faster 
-to let the host handle communication, by using the {host} value. Using 
-{host} instead of {no} will enable use of multiple threads to 
-pack/unpack communicated data. When running small systems on a GPU, 
-performing the exchange pack/unpack on the host CPU can give speedup 
-since it reduces the number of CUDA kernel launches.
-
-The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When 
-this keyword is set to {on}, buffers in GPU memory are passed directly 
-through MPI send/receive calls. This reduces overhead of first copying 
-the data to the host CPU. However CUDA-aware MPI is not supported on all 
-systems, which can lead to segmentation faults and would require using a 
-value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not 
-available (currently only possible with OpenMPI v2.0.0 or later), then 
-the {cuda/aware} keyword is automatically set to {off} by default. When 
-the {cuda/aware} keyword is set to {off} while any of the {comm} 
-keywords are set to {device}, the value for these {comm} keywords will 
-be automatically changed to {host}. This setting has no effect if not 
-running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later 
-versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment
-variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu"
-flag is used.
-
-:line
-
-The {omp} style invokes settings associated with the use of the
-USER-OMP package.
-
-The {Nthread} argument sets the number of OpenMP threads allocated for
-each MPI task.  For example, if your system has nodes with dual
-quad-core processors, it has a total of 8 cores per node.  You could
-use two MPI tasks per node (e.g. using the -ppn option of the mpirun
-command in MPICH or -npernode in OpenMPI), and set {Nthreads} = 4.
-This would use all 8 cores on each node.  Note that the product of MPI
-tasks * threads/task should not exceed the physical number of cores
-(on a node), otherwise performance will suffer.
-
-Setting {Nthread} = 0 instructs LAMMPS to use whatever value is the
-default for the given OpenMP environment. This is usually determined
-via the {OMP_NUM_THREADS} environment variable or the compiler
-runtime.  Note that in most cases the default for OpenMP capable
-compilers is to use one thread for each available CPU core when
-{OMP_NUM_THREADS} is not explicitly set, which can lead to poor
-performance.
-
-Here are examples of how to set the environment variable when
-launching LAMMPS:
-
-env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
-env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
-mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script :pre
-
-or you can set it permanently in your shell's start-up script.
-All three of these examples use a total of 4 CPU cores.
-
-Note that different MPI implementations have different ways of passing
-the OMP_NUM_THREADS environment variable to all MPI processes.  The
-2nd example line above is for MPICH; the 3rd example line with -x is
-for OpenMPI.  Check your MPI documentation for additional details.
-
-What combination of threads and MPI tasks gives the best performance
-is difficult to predict and can depend on many components of your
-input.  Not all features of LAMMPS support OpenMP threading via the
-USER-OMP package and the parallel efficiency can be very different,
-too.
-
-Optional keyword/value pairs can also be specified.  Each has a
-default value as listed below.
-
-The {neigh} keyword specifies whether neighbor list building will be
-multi-threaded in addition to force calculations.  If {neigh} is set
-to {no} then neighbor list calculation is performed only by MPI tasks
-with no OpenMP threading.  If {mode} is {yes} (the default), a
-multi-threaded neighbor list build is used.  Using {neigh} = {yes} is
-almost always faster and should produce identical neighbor lists at the
-expense of using more memory.  Specifically, neighbor list pages are
-allocated for all threads at the same time and each thread works
-within its own pages.
-
-:line
-
-[Restrictions:]
-
-This command cannot be used after the simulation box is defined by a
-"read_data"_read_data.html or "create_box"_create_box.html command.
-
-The gpu style of this command can only be invoked if LAMMPS was built
-with the GPU package.  See the "Build package"_Build_package.html doc
-page for more info.
-
-The intel style of this command can only be invoked if LAMMPS was
-built with the USER-INTEL package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-The kk style of this command can only be invoked if LAMMPS was built
-with the KOKKOS package.  See the "Build package"_Build_package.html
-doc page for more info.
-
-The omp style of this command can only be invoked if LAMMPS was built
-with the USER-OMP package.  See the "Build package"_Build_package.html
-doc page for more info.
-
-[Related commands:]
-
-"suffix"_suffix.html, "-pk command-line switch"_Run_options.html
-
-[Default:]
-
-For the GPU package, the default is Ngpu = 1 and the option defaults
-are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
-to Ngpu-1, tpa = 1, and device = not used.  These settings are made
-automatically if the "-sf gpu" "command-line switch"_Run_options.html
-is used.  If it is not used, you must invoke the package gpu command
-in your input script or via the "-pk gpu" "command-line
-switch"_Run_options.html.
-
-For the USER-INTEL package, the default is Nphi = 1 and the option
-defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
-tptask = 240.  The default ghost option is determined by the pair
-style being used.  This value is output to the screen in the offload
-report at the end of each run.  Note that all of these settings,
-except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
-Phi co-processor support.  These settings are made automatically if the
-"-sf intel" "command-line switch"_Run_options.html is used.  If it is
-not used, you must invoke the package intel command in your input
-script or via the "-pk intel" "command-line
-switch"_Run_options.html.
-
-For the KOKKOS package, the option defaults for GPUs are neigh = full, 
-neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default 
-value, comm = device, cuda/aware = on. When LAMMPS can safely detect 
-that CUDA-aware MPI is not available, the default value of cuda/aware 
-becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = 
-half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The 
-option neigh/thread = on when there are 16K atoms or less on an MPI 
-rank, otherwise it is "off". These settings are made automatically by 
-the required "-k on" "command-line switch"_Run_options.html. You can 
-change them by using the package kokkos command in your input script or 
-via the "-pk kokkos command-line switch"_Run_options.html.
-
-For the OMP package, the default is Nthreads = 0 and the option
-defaults are neigh = yes.  These settings are made automatically if
-the "-sf omp" "command-line switch"_Run_options.html is used.  If it
-is not used, you must invoke the package omp command in your input
-script or via the "-pk omp" "command-line switch"_Run_options.html.
diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst
new file mode 100644
index 0000000000..36311f738d
--- /dev/null
+++ b/doc/src/pair_adp.rst
@@ -0,0 +1,211 @@
+.. index:: pair\_style adp
+
+pair\_style adp command
+=======================
+
+pair\_style adp/omp command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style adp
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style adp
+   pair_coeff \* \* Ta.adp Ta
+   pair_coeff \* \* ../potentials/AlCu.adp Al Al Cu
+
+Description
+"""""""""""
+
+Style *adp* computes pairwise interactions for metals and metal alloys
+using the angular dependent potential (ADP) of :ref:`(Mishin) <Mishin>`,
+which is a generalization of the :doc:`embedded atom method (EAM) potential <pair_eam>`.  The LAMMPS implementation is discussed in
+:ref:`(Singh) <Singh>`.  The total energy Ei of an atom I is given by
+
+.. image:: Eqs/pair_adp.jpg
+   :align: center
+
+where F is the embedding energy which is a function of the atomic
+electron density rho, phi is a pair potential interaction, alpha and
+beta are the element types of atoms I and J, and s and t = 1,2,3 and
+refer to the cartesian coordinates.  The mu and lambda terms represent
+the dipole and quadruple distortions of the local atomic environment
+which extend the original EAM framework by introducing angular forces.
+
+Note that unlike for other potentials, cutoffs for ADP potentials are
+not set in the pair\_style or pair\_coeff command; they are specified in
+the ADP potential files themselves.  Likewise, the ADP potential files
+list atomic masses; thus you do not need to use the :doc:`mass <mass>`
+command to specify them.
+
+**ADP potentials are available from:**
+
+* The NIST WWW site at http://www.ctcms.nist.gov/potentials.
+  Note that ADP potentials obtained from NIST must be converted
+  into the extended DYNAMO *setfl* format discussed below.
+* The OpenKIM Project at https://openkim.org/browse/models/by-type provides
+  ADP potentials that can be used directly in LAMMPS with the :doc:`kim\_commands interface <kim_commands>`.
+
+----------
+
+
+Only a single pair\_coeff command is used with the *adp* style which
+specifies an extended DYNAMO *setfl* file, which contains information
+for M elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of extended *setfl* elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways to
+specify the path for the potential file.
+
+As an example, the potentials/AlCu.adp file, included in the
+potentials directory of the LAMMPS distribution, is an extended *setfl*
+file which has tabulated ADP values for w elements and their alloy
+interactions: Cu and Al.  If your LAMMPS simulation has 4 atoms types
+and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
+the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* AlCu.adp Al Al Al Cu
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
+element in the extended *setfl* file.  The final Cu argument maps
+LAMMPS atom type 4 to the Al element in the extended *setfl* file.
+Note that there is no requirement that your simulation use all the
+elements specified by the extended *setfl* file.
+
+If a mapping value is specified as NULL, the mapping is not performed.
+This can be used when an *adp* potential is used as part of the
+*hybrid* pair style.  The NULL values are placeholders for atom types
+that will be used with other potentials.
+
+*Adp* files in the *potentials* directory of the LAMMPS distribution
+have an ".adp" suffix.  A DYNAMO *setfl* file extended for ADP is
+formatted as follows.  Basically it is the standard *setfl* format
+with additional tabulated functions u and w added to the file after
+the tabulated pair potentials.  See the :doc:`pair\_eam <pair_eam>`
+command for further details on the *setfl* format.
+
+* lines 1,2,3 = comments (ignored)
+* line 4: Nelements Element1 Element2 ... ElementN
+* line 5: Nrho, drho, Nr, dr, cutoff
+
+Following the 5 header lines are Nelements sections, one for each
+element, each with the following format:
+
+* line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
+* embedding function F(rho) (Nrho values)
+* density function rho(r) (Nr values)
+
+Following the Nelements sections, Nr values for each pair potential
+phi(r) array are listed for all i,j element pairs in the same format
+as other arrays.  Since these interactions are symmetric (i,j = j,i)
+only phi arrays with i >= j are listed, in the following order: i,j =
+(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
+Nelements).  The tabulated values for each phi function are listed as
+r\*phi (in units of eV-Angstroms), since they are for atom pairs, the
+same as for :doc:`other EAM files <pair_eam>`.
+
+After the phi(r) arrays, each of the u(r) arrays are listed in the
+same order with the same assumptions of symmetry.  Directly following
+the u(r), the w(r) arrays are listed.  Note that phi(r) is the only
+array tabulated with a scaling by r.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, no special mixing rules are needed, since
+the ADP potential files specify alloy interactions explicitly.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in tabulated potential files.
+Thus, you need to re-specify the pair\_style and pair\_coeff commands in
+an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_eam <pair_eam>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Mishin:
+
+
+
+**(Mishin)** Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029
+(2005).
+
+.. _Singh:
+
+
+
+**(Singh)** Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst
new file mode 100644
index 0000000000..96bcf5eccd
--- /dev/null
+++ b/doc/src/pair_agni.rst
@@ -0,0 +1,157 @@
+.. index:: pair\_style agni
+
+pair\_style agni command
+========================
+
+pair\_style agni/omp command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style agni
+
+Examples
+""""""""
+pair\_style      agni
+pair\_coeff      \* \* Al.agni Al
+
+Description
+"""""""""""
+
+Style *agni* style computes the many-body vectorial force components for
+an atom as
+
+.. image:: Eqs/pair_agni.jpg
+   :align: center
+
+*u* labels the individual components, i.e. x, y or z, and *V* is the
+corresponding atomic fingerprint. *d* is the Euclidean distance between
+any two atomic fingerprints. A total of N\_t reference atomic
+environments are considered to construct the force field file. *alpha\_t*
+and *l* are the weight coefficients and length scale parameter of the
+non-linear regression model.
+
+The method implements the recently proposed machine learning access to
+atomic forces as discussed extensively in the following publications -
+:ref:`(Botu1) <Botu2015adaptive>` and :ref:`(Botu2) <Botu2015learning>`. The premise
+of the method is to map the atomic environment numerically into a
+fingerprint, and use machine learning methods to create a mapping to the
+vectorial atomic forces.
+
+Only a single pair\_coeff command is used with the *agni* style which
+specifies an AGNI potential file containing the parameters of the
+force field for the needed elements. These are mapped to LAMMPS atom
+types by specifying N additional arguments after the filename in the
+pair\_coeff command, where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of AGNI elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the force field file.
+
+An AGNI force field is fully specified by the filename which contains the
+parameters of the force field, i.e., the reference training environments
+used to construct the machine learning force field. Example force field
+and input files are provided in the examples/USER/misc/agni directory.
+
+
+----------
+
+
+Styles with *omp* suffix is functionally the same as the corresponding
+style without the suffix. They have been optimized to run faster,
+depending on your available hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc page.  The accelerated style takes
+the same arguments and should produce the same results, except for
+round-off and precision issues.
+
+The accelerated style is part of the USER-OMP.  They are only enabled
+if LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated style explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Currently, only elemental systems are implemented. Also, the method
+only provides access to the forces and not energies or stresses.
+The lack of potential energy data makes this pair style incompatible with
+several of the :doc:`minimizer algorthms <min_style>` like *cg* or *sd*\ .
+It should work with damped dynamics based minimizers like *fire* or
+*quickmin*\ .  However, one can access the energy via thermodynamic
+integration of the forces as discussed in
+:ref:`(Botu3) <Botu2016construct>`.  This pair style is part of the
+USER-MISC package. It is only enabled if LAMMPS was built with that
+package. See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+The AGNI force field files provided with LAMMPS (see the
+potentials directory) are parameterized for metal :doc:`units <units>`.
+You can use the AGNI potential with any LAMMPS units, but you would need
+to create your own AGNI potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Botu2015adaptive:
+
+
+
+**(Botu1)** V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
+
+.. _Botu2015learning:
+
+
+
+**(Botu2)** V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015).
+
+.. _Botu2016construct:
+
+
+
+**(Botu3)** V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst
new file mode 100644
index 0000000000..66dc56c7a6
--- /dev/null
+++ b/doc/src/pair_airebo.rst
@@ -0,0 +1,293 @@
+.. index:: pair\_style airebo
+
+pair\_style airebo command
+==========================
+
+pair\_style airebo/intel command
+================================
+
+pair\_style airebo/omp command
+==============================
+
+pair\_style airebo/morse command
+================================
+
+pair\_style airebo/morse/intel command
+======================================
+
+pair\_style airebo/morse/omp command
+====================================
+
+pair\_style rebo command
+========================
+
+pair\_style rebo/intel command
+==============================
+
+pair\_style rebo/omp command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style cutoff LJ_flag TORSION_flag cutoff_min
+
+* style = *airebo* or *airebo/morse* or *rebo*
+* cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)
+* LJ\_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional)
+* TORSION\_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional)
+* cutoff\_min = Start of the transition region of cutoff (sigma scale factor) (AIREBO and AIREBO-M only, optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style airebo 3.0
+   pair_style airebo 2.5 1 0
+   pair_coeff \* \* ../potentials/CH.airebo H C
+
+   pair_style airebo/morse 3.0
+   pair_coeff \* \* ../potentials/CH.airebo-m H C
+
+   pair_style rebo
+   pair_coeff \* \* ../potentials/CH.rebo H C
+
+Description
+"""""""""""
+
+The *airebo* pair style computes the Adaptive Intermolecular Reactive
+Empirical Bond Order (AIREBO) Potential of :ref:`(Stuart) <Stuart>` for a
+system of carbon and/or hydrogen atoms.  Note that this is the initial
+formulation of AIREBO from 2000, not the later formulation.
+
+The *airebo/morse* pair style computes the AIREBO-M potential, which
+is equivalent to AIREBO, but replaces the LJ term with a Morse potential.
+The Morse potentials are parameterized by high-quality quantum chemistry
+(MP2) calculations and do not diverge as quickly as particle density
+increases. This allows AIREBO-M to retain accuracy to much higher pressures
+than AIREBO (up to 40 GPa for Polyethylene). Details for this potential
+and its parameterization are given in :ref:`(O'Conner) <OConnor>`.
+
+The *rebo* pair style computes the Reactive Empirical Bond Order (REBO)
+Potential of :ref:`(Brenner) <Brenner>`. Note that this is the so-called
+2nd generation REBO from 2002, not the original REBO from 1990.
+As discussed below, 2nd generation REBO is closely related to the
+initial AIREBO; it is just a subset of the potential energy terms
+with a few slightly different parameters
+
+The AIREBO potential consists of three terms:
+
+.. image:: Eqs/pair_airebo.jpg
+   :align: center
+
+By default, all three terms are included.  For the *airebo* style, if
+the first two optional flag arguments to the pair\_style command are
+included, the LJ and torsional terms can be turned off.  Note that
+both or neither of the flags must be included.  If both of the LJ an
+torsional terms are turned off, it becomes the 2nd-generation REBO
+potential, with a small caveat on the spline fitting procedure
+mentioned below.  This can be specified directly as pair\_style *rebo*
+with no additional arguments.
+
+The detailed formulas for this potential are given in
+:ref:`(Stuart) <Stuart>`; here we provide only a brief description.
+
+The E\_REBO term has the same functional form as the hydrocarbon REBO
+potential developed in :ref:`(Brenner) <Brenner>`.  The coefficients for
+E\_REBO in AIREBO are essentially the same as Brenner's potential, but
+a few fitted spline values are slightly different.  For most cases the
+E\_REBO term in AIREBO will produce the same energies, forces and
+statistical averages as the original REBO potential from which it was
+derived.  The E\_REBO term in the AIREBO potential gives the model its
+reactive capabilities and only describes short-ranged C-C, C-H and H-H
+interactions (r < 2 Angstroms). These interactions have strong
+coordination-dependence through a bond order parameter, which adjusts
+the attraction between the I,J atoms based on the position of other
+nearby atoms and thus has 3- and 4-body dependence.
+
+The E\_LJ term adds longer-ranged interactions (2 < r < cutoff) using a
+form similar to the standard :doc:`Lennard Jones potential <pair_lj>`.
+The E\_LJ term in AIREBO contains a series of switching functions so
+that the short-ranged LJ repulsion (1/r\^12) does not interfere with
+the energetics captured by the E\_REBO term.  The extent of the E\_LJ
+interactions is determined by the *cutoff* argument to the pair\_style
+command which is a scale factor.  For each type pair (C-C, C-H, H-H)
+the cutoff is obtained by multiplying the scale factor by the sigma
+value defined in the potential file for that type pair.  In the
+standard AIREBO potential, sigma\_CC = 3.4 Angstroms, so with a scale
+factor of 3.0 (the argument in pair\_style), the resulting E\_LJ cutoff
+would be 10.2 Angstroms.
+
+By default, the longer-ranged interaction is smoothly switched off
+between 2.16 and 3.0 sigma. By specifying *cutoff\_min* in addition
+to *cutoff*\ , the switching can be configured to take place between
+*cutoff\_min* and *cutoff*\ . *cutoff\_min* can only be specified if all
+optional arguments are given.
+
+The E\_TORSION term is an explicit 4-body potential that describes
+various dihedral angle preferences in hydrocarbon configurations.
+
+
+----------
+
+
+Only a single pair\_coeff command is used with the *airebo*\ , *airebo*
+or *rebo* style which specifies an AIREBO, REBO, or AIREBO-M potential
+file with parameters for C and H.  Note that as of LAMMPS version
+15 May 2019 the *rebo* style in LAMMPS uses its own potential
+file (CH.rebo).  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of AIREBO elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, if your LAMMPS simulation has 4 atom types and you want
+the 1st 3 to be C, and the 4th to be H, you would use the following
+pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* CH.airebo C C C H
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three C arguments map LAMMPS atom types 1,2,3 to the C
+element in the AIREBO file.  The final H argument maps LAMMPS atom
+type 4 to the H element in the SW file.  If a mapping value is
+specified as NULL, the mapping is not performed.  This can be used
+when a *airebo* potential is used as part of the *hybrid* pair style.
+The NULL values are placeholders for atom types that will be used with
+other potentials.
+
+The parameters/coefficients for the AIREBO potentials are listed in
+the CH.airebo file to agree with the original :ref:`(Stuart) <Stuart>`
+paper.  Thus the parameters are specific to this potential and the way
+it was fit, so modifying the file should be done cautiously.
+
+Similarly the parameters/coefficients for the AIREBO-M potentials are
+listed in the CH.airebo-m file to agree with the :ref:`(O'Connor) <OConnor>`
+paper. Thus the parameters are specific to this potential and the way
+it was fit, so modifying the file should be done cautiously. The
+AIREBO-M Morse potentials were parameterized using a cutoff of
+3.0 (sigma). Modifying this cutoff may impact simulation accuracy.
+
+This pair style tallies a breakdown of the total AIREBO potential
+energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 3.
+The 3 values correspond to the following sub-categories:
+
+1. *E\_REBO* = REBO energy
+2. *E\_LJ* = Lennard-Jones energy
+3. *E\_TORSION* = Torsion energy
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+
+.. parsed-literal::
+
+   compute 0 all pair airebo
+   variable REBO     equal c_0[1]
+   variable LJ       equal c_0[2]
+   variable TORSION  equal c_0[3]
+   thermo_style custom step temp epair v_REBO v_LJ v_TORSION
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+These pair styles do not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+These pair styles do not write their information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+These pair styles are part of the MANYBODY package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+These pair potentials require the :doc:`newton <newton>` setting to be
+"on" for pair interactions.
+
+The CH.airebo and CH.airebo-m potential files provided with LAMMPS
+(see the potentials directory) are parameterized for metal :doc:`units <units>`.
+You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
+but you would need to create your own AIREBO or AIREBO-M potential file
+with coefficients listed in the appropriate units, if your simulation
+doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Stuart:
+
+
+
+**(Stuart)** Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486
+(2000).
+
+.. _Brenner:
+
+
+
+**(Brenner)** Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
+Physics: Condensed Matter, 14, 783-802 (2002).
+
+.. _OConnor:
+
+
+
+**(O'Connor)** O'Connor et al., J. Chem. Phys. 142, 024903 (2015).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_atm.rst b/doc/src/pair_atm.rst
new file mode 100644
index 0000000000..1f22ca01c3
--- /dev/null
+++ b/doc/src/pair_atm.rst
@@ -0,0 +1,197 @@
+.. index:: pair\_style atm
+
+pair\_style atm command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style atm cutoff cutoff_triple
+
+* cutoff = cutoff for each pair in 3-body interaction (distance units)
+* cutoff\_triple = additional cutoff applied to product of 3 pairwise distances (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style atm 4.5 2.5
+   pair_coeff \* \* \* 0.072
+
+   pair_style hybrid/overlay lj/cut 6.5 atm 4.5 2.5
+   pair_coeff \* \* lj/cut 1.0 1.0
+   pair_coeff 1 1 atm 1 0.064
+   pair_coeff 1 1 atm 2 0.080
+   pair_coeff 1 2 atm 2 0.100
+   pair_coeff 2 2 atm 2 0.125
+
+Description
+"""""""""""
+
+The *atm* style computes a 3-body :ref:`Axilrod-Teller-Muto <Axilrod>`
+potential for the energy E of a system of atoms as
+
+.. image:: Eqs/pair_atm.jpg
+   :align: center
+
+where nu is the three-body interaction strength.  The distances
+between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2,
+gamma3 are as shown in this diagram:
+
+.. image:: JPG/pair_atm_dia.jpg
+   :align: center
+
+Note that for the interaction between a triplet of atoms I,J,K, there
+is no "central" atom.  The interaction is symmetric with respect to
+permutation of the three atoms. Thus the nu value is
+the same for all those permutations of the atom types of I,J,K
+and needs to be specified only once, as discussed below.
+
+The *atm* potential is typically used in combination with a two-body
+potential using the :doc:`pair\_style hybrid/overlay <pair_hybrid>`
+command as in the example above.
+
+The potential for a triplet of atom is calculated only if all 3
+distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
+In addition, the product of the 3 distances r12\*r23\*r31 <
+cutoff\_triple\^3 is required, which excludes from calculation the
+triplets with small contribution to the interaction.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the restart files read by the
+:doc:`read\_restart <read_restart>` commands:
+
+* K = atom type of the third atom (1 to Ntypes)
+* nu = prefactor (energy/distance\^9 units)
+
+K can be specified in one of two ways.  An explicit numeric value can
+be used, as in the 2nd example above.  J <= K is required.  LAMMPS
+sets the coefficients for the other 5 symmetric interactions to the
+same values.  E.g. if I = 1, J = 2, K = 3, then these 6 values are set
+to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321.  This
+enforces the symmetry discussed above.
+
+A wildcard asterisk can be used for K to set the coefficients for
+multiple triplets of atom types.  This takes the form "\*" or "\*n" or
+"n\*" or "m\*n".  If N = the number of atom types, then an asterisk with
+no numeric values means all types from 1 to N.  A leading asterisk
+means all types from 1 to n (inclusive).  A trailing asterisk means
+all types from n to N (inclusive).  A middle asterisk means all types
+from m to n (inclusive).  Note that only type triplets with J <= K are
+considered; if asterisks imply type triplets where K < J, they are
+ignored.
+
+Note that a pair\_coeff command can override a previous setting for the
+same I,J,K triplet.  For example, these commands set nu for all I,J.K
+triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* \* 0.25
+   pair_coeff 2 3 4 0.1
+
+Note that for a simulation with a single atom type, only a single
+entry is required, e.g.
+
+
+.. parsed-literal::
+
+   pair_coeff 1 1 1 0.25
+
+For a simulation with two atom types, four pair\_coeff commands will
+specify all possible nu values:
+
+
+.. parsed-literal::
+
+   pair_coeff 1 1 1 nu1
+   pair_coeff 1 1 2 nu2
+   pair_coeff 1 2 2 nu3
+   pair_coeff 2 2 2 nu4
+
+For a simulation with three atom types, ten pair\_coeff commands will
+specify all possible nu values:
+
+
+.. parsed-literal::
+
+   pair_coeff 1 1 1 nu1
+   pair_coeff 1 1 2 nu2
+   pair_coeff 1 1 3 nu3
+   pair_coeff 1 2 2 nu4
+   pair_coeff 1 2 3 nu5
+   pair_coeff 1 3 3 nu6
+   pair_coeff 2 2 2 nu7
+   pair_coeff 2 2 3 nu8
+   pair_coeff 2 3 3 nu9
+   pair_coeff 3 3 3 nu10
+
+By default the nu value for all triplets is set to 0.0.  Thus it is
+not required to provide pair\_coeff commands that enumerate triplet
+interactions for all K types.  If some I,J,K combination is not
+specified, then there will be no 3-body ATM interactions for that
+combination and all its permutations.  However, as with all pair
+styles, it is required to specify a pair\_coeff command for all I,J
+combinations, else an error will result.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair styles do not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+However, if the *atm* potential is used in combination with other
+potentials using the :doc:`pair\_style hybrid/overlay <pair_hybrid>`
+command then pair\_coeff commands need to be re-specified
+in the restart input script.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Axilrod:
+
+
+
+**(Axilrod)**
+Axilrod and Teller, J Chem Phys, 11, 299 (1943);
+Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst
new file mode 100644
index 0000000000..0076f50684
--- /dev/null
+++ b/doc/src/pair_awpmd.rst
@@ -0,0 +1,140 @@
+.. index:: pair\_style awpmd/cut
+
+pair\_style awpmd/cut command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style awpmd/cut Rc keyword value ...
+
+* Rc = global cutoff, -1 means cutoff of half the shortest box length
+* zero or more keyword/value pairs may be appended
+* keyword = *hartree* or *dproduct* or *uhf* or *free* or *pbc* or *fix* or *harm* or *ermscale* or *flex\_press*
+  
+  .. parsed-literal::
+  
+       *hartree* value = none
+       *dproduct* value = none
+       *uhf* value = none
+       *free* value = none
+       *pbc* value = Plen
+         Plen = periodic width of electron = -1 or positive value (distance units)
+       *fix* value = Flen
+         Flen = fixed width of electron = -1 or positive value (distance units)
+       *harm* value = width
+         width = harmonic width constraint
+       *ermscale* value = factor
+         factor = scaling between electron mass and width variable mass
+       *flex_press* value = none
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style awpmd/cut -1
+   pair_style awpmd/cut 40.0 uhf free
+   pair_coeff \* \*
+   pair_coeff 2 2 20.0
+
+Description
+"""""""""""
+
+This pair style contains an implementation of the Antisymmetrized Wave
+Packet Molecular Dynamics (AWPMD) method.  Need citation here.  Need
+basic formulas here.  Could be links to other documents.
+
+Rc is the cutoff.
+
+The pair\_style command allows for several optional keywords
+to be specified.
+
+The *hartree*\ , *dproduct*\ , and *uhf* keywords specify the form of the
+initial trial wave function for the system.  If the *hartree* keyword
+is used, then a Hartree multielectron trial wave function is used.  If
+the *dproduct* keyword is used, then a trial function which is a
+product of two determinants for each spin type is used.  If the *uhf*
+keyword is used, then an unrestricted Hartree-Fock trial wave function
+is used.
+
+The *free*\ , *pbc*\ , and *fix* keywords specify a width constraint on
+the electron wave packets.  If the *free* keyword is specified, then there is no
+constraint.  If the *pbc* keyword is used and *Plen* is specified as
+-1, then the maximum width is half the shortest box length.  If *Plen*
+is a positive value, then the value is the maximum width.  If the
+*fix* keyword is used and *Flen* is specified as -1, then electrons
+have a constant width that is read from the data file.  If *Flen* is a
+positive value, then the constant width for all electrons is set to
+*Flen*\ .
+
+The *harm* keyword allow oscillations in the width of the
+electron wave packets.  More details are needed.
+
+The *ermscale* keyword specifies a unitless scaling factor
+between the electron masses and the width variable mass.  More
+details needed.
+
+If the *flex\_press* keyword is used, then a contribution from the
+electrons is added to the total virial and pressure of the system.
+
+This potential is designed to be used with :doc:`atom\_style wavepacket <atom_style>` definitions, in order to handle the
+description of systems with interacting nuclei and explicit electrons.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cutoff (distance units)
+
+For *awpmd/cut*\ , the cutoff coefficient is optional.  If it is not
+used (as in some of the examples above), the default global value
+specified in the pair\_style command is used.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+The :doc:`pair\_modify <pair_modify>` mix, shift, table, and tail options
+are not relevant for this pair style.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+Default
+"""""""
+
+These are the defaults for the pair\_style keywords: *hartree* for the
+initial wave function, *free* for the wave packet width.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst
new file mode 100644
index 0000000000..96f6d5d3f5
--- /dev/null
+++ b/doc/src/pair_beck.rst
@@ -0,0 +1,133 @@
+.. index:: pair\_style beck
+
+pair\_style beck command
+========================
+
+pair\_style beck/gpu command
+============================
+
+pair\_style beck/omp command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style beck Rc
+
+* Rc = cutoff for interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style beck 8.0
+   pair_coeff \* \* 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
+   pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0
+
+Description
+"""""""""""
+
+Style *beck* computes interactions based on the potential by
+:ref:`(Beck) <Beck>`, originally designed for simulation of Helium.  It
+includes truncation at a cutoff distance Rc.
+
+.. image:: Eqs/pair_beck.jpg
+   :align: center
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands.
+
+* A (energy units)
+* B (energy-distance\^6 units)
+* a (distance units)
+* alpha (1/distance units)
+* beta  (1/distance\^6 units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global cutoff
+Rc is used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, coefficients must be specified.
+No default mixing rules are used.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Beck:
+
+
+
+**(Beck)** Beck, Molecular Physics, 14, 311 (1968).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_body_nparticle.rst b/doc/src/pair_body_nparticle.rst
new file mode 100644
index 0000000000..5d6b2a500b
--- /dev/null
+++ b/doc/src/pair_body_nparticle.rst
@@ -0,0 +1,133 @@
+.. index:: pair\_style body/nparticle
+
+pair\_style body/nparticle command
+==================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style body/nparticle cutoff
+
+cutoff = global cutoff for interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style body/nparticle 3.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 1 1 1.0 1.5 2.5
+
+Description
+"""""""""""
+
+Style *body/nparticle* is for use with body particles and calculates
+pairwise body/body interactions as well as interactions between body
+and point-particles.  See the :doc:`Howto body <Howto_body>` doc page
+for more details on using body particles.
+
+This pair style is designed for use with the "nparticle" body style,
+which is specified as an argument to the "atom-style body" command.
+See the :doc:`Howto body <Howto_body>` doc page for more details about
+the body styles LAMMPS supports.  The "nparticle" style treats a body
+particle as a rigid body composed of N sub-particles.
+
+The coordinates of a body particle are its center-of-mass (COM).  If
+the COMs of a pair of body particles are within the cutoff (global or
+type-specific, as specified above), then all interactions between
+pairs of sub-particles in the two body particles are computed.
+E.g. if the first body particle has 3 sub-particles, and the second
+has 10, then 30 interactions are computed and summed to yield the
+total force and torque on each body particle.
+
+.. note::
+
+   In the example just described, all 30 interactions are computed
+   even if the distance between a particular pair of sub-particles is
+   greater than the cutoff.  Likewise, no interaction between two body
+   particles is computed if the two COMs are further apart than the
+   cutoff, even if the distance between some pairs of their sub-particles
+   is within the cutoff.  Thus care should be used in defining the cutoff
+   distances for body particles, depending on their shape and size.
+
+Similar rules apply for a body particle interacting with a point
+particle.  The distance between the two particles is calculated using
+the COM of the body particle and the position of the point particle.
+If the distance is within the cutoff and the body particle has N
+sub-particles, then N interactions with the point particle are
+computed and summed.  If the distance is not within the cutoff, no
+interactions between the body and point particle are computed.
+
+The interaction between two sub-particles, or a sub-particle and point
+particle, or between two point particles is computed as a Lennard-Jones
+interaction, using the standard formula
+
+.. image:: Eqs/pair_lj.jpg
+   :align: center
+
+where Rc is the cutoff.  As explained above, an interaction involving
+one or two body sub-particles may be computed even for r > Rc.
+
+For style *body*\ , the following coefficients must be defined for each
+pair of atoms types via the :doc:`pair\_coeff <pair_coeff>` command as in
+the examples above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global cutoff
+is used.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of this pair style can be mixed.  The
+default mix value is *geometric*\ .  See the "pair\_modify" command for
+details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the BODY package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Defining particles to be bodies so they participate in body/body or
+body/particle interactions requires the use of the :doc:`atom\_style body <atom_style>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix rigid <fix_rigid>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst
new file mode 100644
index 0000000000..237a792344
--- /dev/null
+++ b/doc/src/pair_body_rounded_polygon.rst
@@ -0,0 +1,147 @@
+.. index:: pair\_style body/rounded/polygon
+
+pair\_style body/rounded/polygon command
+========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style body/rounded/polygon c_n c_t mu delta_ua cutoff
+
+   c_n = normal damping coefficient
+   c_t = tangential damping coefficient
+   mu = normal friction coefficient during gross sliding
+   delta_ua = multiple contact scaling factor
+   cutoff = global separation cutoff for interactions (distance units), see below for definition
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style body/rounded/polygon 20.0 5.0 0.0 1.0 0.5
+   pair_coeff \* \* 100.0 1.0
+   pair_coeff 1 1 100.0 1.0
+
+Description
+"""""""""""
+
+Style *body/rounded/polygon* is for use with 2d models of body
+particles of style *rounded/polygon*\ .  It calculates pairwise
+body/body interactions which can include body particles modeled as
+1-vertex circular disks with a specified diameter.  See the :doc:`Howto body <Howto_body>` doc page for more details on using body
+rounded/polygon particles.
+
+This pairwise interaction between rounded polygons is described in
+:ref:`Fraige <pair-Fraige>`, where a polygon does not have sharp corners,
+but is rounded at its vertices by circles centered on each vertex with
+a specified diameter.  The edges of the polygon are defined between
+pairs of adjacent vertices.  The circle diameter for each polygon is
+specified in the data file read by the :doc:`read data <read_data>`
+command.  This is a 2d discrete element model (DEM) which allows for
+multiple contact points.
+
+Note that when two particles interact, the effective surface of each
+polygon particle is displaced outward from each of its vertices and
+edges by half its circle diameter (as in the diagram below of a gray
+and yellow square particle).  The interaction forces and energies
+between two particles are defined with respect to the separation of
+their respective rounded surfaces, not by the separation of the
+vertices and edges themselves.
+
+This means that the specified cutoff in the pair\_style command is the
+cutoff distance, r\_c, for the surface separation, \delta\_n (see figure
+below).  This is the distance at which two particles no longer
+interact.  If r\_c is specified as 0.0, then it is a contact-only
+interaction.  I.e. the two particles must overlap in order to exert a
+repulsive force on each other.  If r\_c > 0.0, then the force between
+two particles will be attractive for surface separations from 0 to
+r\_c, and repulsive once the particles overlap.
+
+Note that unlike for other pair styles, the specified cutoff is not
+the distance between the centers of two particles at which they stop
+interacting.  This center-to-center distance depends on the shape and
+size of the two particles and their relative orientation.  LAMMPS
+takes that into account when computing the surface separation distance
+and applying the r\_c cutoff.
+
+The forces between vertex-vertex, vertex-edge, and edge-edge overlaps
+are given by:
+
+.. image:: Eqs/pair_body_rounded.jpg
+   :align: center
+
+.. image:: JPG/pair_body_rounded.jpg
+   :align: center
+
+Note that F\_n and F\_t are functions of the surface separation \delta\_n
+= d - (R\_i + R\_j).  In this model, when (R\_i + R\_j) < d < (R\_i + R\_j)
++ r\_c, that is, 0 < \delta\_n < r\_c, the cohesive region of the two
+surfaces overlap and the two surfaces are attractive to each other.
+
+In :ref:`Fraige <pair-Fraige>`, the tangential friction force between two
+particles that are in contact is modeled differently prior to gross
+sliding (i.e. static friction) and during gross-sliding (kinetic
+friction).  The latter takes place when the tangential deformation
+exceeds the Coulomb frictional limit.  In the current implementation,
+however, we do not take into account frictional history, i.e. we do
+not keep track of how many time steps the two particles have been in
+contact nor calculate the tangential deformation.  Instead, we assume
+that gross sliding takes place as soon as two particles are in
+contact.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the data file read by the :doc:`read\_data <read_data>` command:
+
+* k\_n (energy/distance\^2 units)
+* k\_na (energy/distance\^2 units)
+
+Effectively, k\_n and k\_na are the slopes of the red lines in the plot
+above for force versus surface separation, for \delta\_n < 0 and 0 <
+\delta\_n < r\_c respectively.
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+These pair styles are part of the BODY package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+.. _pair-Fraige:
+
+
+
+**(Fraige)** F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
+Particuology, 6, 455 (2008).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst
new file mode 100644
index 0000000000..1334756908
--- /dev/null
+++ b/doc/src/pair_body_rounded_polyhedron.rst
@@ -0,0 +1,142 @@
+.. index:: pair\_style body/rounded/polyhedron
+
+pair\_style body/rounded/polyhedron command
+===========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff
+
+   c_n = normal damping coefficient
+   c_t = tangential damping coefficient
+   mu = normal friction coefficient during gross sliding
+   delta_ua = multiple contact scaling factor
+   cutoff = global separation cutoff for interactions (distance units), see below for definition
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5
+   pair_coeff \* \* 100.0 1.0
+   pair_coeff 1 1 100.0 1.0
+
+Description
+"""""""""""
+
+Style *body/rounded/polygon* is for use with 3d models of body
+particles of style *rounded/polyhedron*\ .  It calculates pairwise
+body/body interactions which can include body particles modeled as
+1-vertex spheres with a specified diameter.  See the :doc:`Howto body <Howto_body>` doc page for more details on using body
+rounded/polyhedron particles.
+
+This pairwise interaction between the rounded polyhedra is described
+in :ref:`Wang <pair-Wang>`, where a polyhedron does not have sharp corners
+and edges, but is rounded at its vertices and edges by spheres
+centered on each vertex with a specified diameter.  The edges if the
+polyhedron are defined between pairs of adjacent vertices.  Its faces
+are defined by a loop of edges.  The sphere diameter for each polygon
+is specified in the data file read by the :doc:`read data <read_data>`
+command.  This is a discrete element model (DEM) which allows for
+multiple contact points.
+
+Note that when two particles interact, the effective surface of each
+polyhedron particle is displaced outward from each of its vertices,
+edges, and faces by half its sphere diameter.  The interaction forces
+and energies between two particles are defined with respect to the
+separation of their respective rounded surfaces, not by the separation
+of the vertices, edges, and faces themselves.
+
+This means that the specified cutoff in the pair\_style command is the
+cutoff distance, r\_c, for the surface separation, \delta\_n (see figure
+below).  This is the distance at which two particles no longer
+interact.  If r\_c is specified as 0.0, then it is a contact-only
+interaction.  I.e. the two particles must overlap in order to exert a
+repulsive force on each other.  If r\_c > 0.0, then the force between
+two particles will be attractive for surface separations from 0 to
+r\_c, and repulsive once the particles overlap.
+
+Note that unlike for other pair styles, the specified cutoff is not
+the distance between the centers of two particles at which they stop
+interacting.  This center-to-center distance depends on the shape and
+size of the two particles and their relative orientation.  LAMMPS
+takes that into account when computing the surface separation distance
+and applying the r\_c cutoff.
+
+The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge,
+and edge-face overlaps are given by:
+
+.. image:: Eqs/pair_body_rounded.jpg
+   :align: center
+
+.. image:: JPG/pair_body_rounded.jpg
+   :align: center
+
+In :ref:`Wang <pair-Wang>`, the tangential friction force between two
+particles that are in contact is modeled differently prior to gross
+sliding (i.e. static friction) and during gross-sliding (kinetic
+friction).  The latter takes place when the tangential deformation
+exceeds the Coulomb frictional limit.  In the current implementation,
+however, we do not take into account frictional history, i.e. we do
+not keep track of how many time steps the two particles have been in
+contact nor calculate the tangential deformation.  Instead, we assume
+that gross sliding takes place as soon as two particles are in
+contact.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the data file read by the :doc:`read\_data <read_data>` command:
+
+* k\_n (energy/distance\^2 units)
+* k\_na (energy/distance\^2 units)
+
+Effectively, k\_n and k\_na are the slopes of the red lines in the plot
+above for force versus surface separation, for \delta\_n < 0 and 0 <
+\delta\_n < r\_c respectively.
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+These pair styles are part of the BODY package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+.. _pair-Wang:
+
+
+
+**(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
+Matter, 13, 1 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst
new file mode 100644
index 0000000000..75446ded3c
--- /dev/null
+++ b/doc/src/pair_bop.rst
@@ -0,0 +1,480 @@
+.. index:: pair\_style bop
+
+pair\_style bop command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style bop keyword ...
+
+* zero or more keywords may be appended
+* keyword = *save*
+
+.. parsed-literal::
+
+     save = pre-compute and save some values
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style bop
+   pair_coeff \* \* ../potentials/CdTe_bop Cd Te
+   pair_style bop save
+   pair_coeff \* \* ../potentials/CdTe.bop.table Cd Te Te
+   comm_modify cutoff 14.70
+
+Description
+"""""""""""
+
+The *bop* pair style computes Bond-Order Potentials (BOP) based on
+quantum mechanical theory incorporating both sigma and pi bonding.
+By analytically deriving the BOP from quantum mechanical theory its
+transferability to different phases can approach that of quantum
+mechanical methods.  This potential is similar to the original BOP
+developed by Pettifor (:ref:`Pettifor\_1 <Pettifor_1>`,
+:ref:`Pettifor\_2 <Pettifor_2>`, :ref:`Pettifor\_3 <Pettifor_3>`) and later updated
+by Murdick, Zhou, and Ward (:ref:`Murdick <Murdick>`, :ref:`Ward <Ward>`).
+Currently, BOP potential files for these systems are provided with
+LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs.  A system with
+only a subset of these elements, including a single element (e.g. C or
+Cu or Al or Ga or Zn or CdZn), can also be modeled by using the
+appropriate alloy file and assigning all atom types to the
+single element or subset of elements via the pair\_coeff command, as
+discussed below.
+
+The BOP potential consists of three terms:
+
+.. image:: Eqs/pair_bop.jpg
+   :align: center
+
+where phi\_ij(r\_ij) is a short-range two-body function representing the
+repulsion between a pair of ion cores, beta\_(sigma,ij)(r\_ij) and
+beta\_(sigma,ij)(r\_ij) are respectively sigma and pi bond integrals,
+THETA\_(sigma,ij) and THETA\_(pi,ij) are sigma and pi bond-orders, and
+U\_prom is the promotion energy for sp-valent systems.
+
+The detailed formulas for this potential are given in Ward
+(:ref:`Ward <Ward>`); here we provide only a brief description.
+
+The repulsive energy phi\_ij(r\_ij) and the bond integrals
+beta\_(sigma,ij)(r\_ij) and beta\_(phi,ij)(r\_ij) are functions of the
+interatomic distance r\_ij between atom i and j.  Each of these
+potentials has a smooth cutoff at a radius of r\_(cut,ij).  These
+smooth cutoffs ensure stable behavior at situations with high sampling
+near the cutoff such as melts and surfaces.
+
+The bond-orders can be viewed as environment-dependent local variables
+that are ij bond specific.  The maximum value of the sigma bond-order
+(THETA\_sigma) is 1, while that of the pi bond-order (THETA\_pi) is 2,
+attributing to a maximum value of the total bond-order
+(THETA\_sigma+THETA\_pi) of 3.  The sigma and pi bond-orders reflect the
+ubiquitous single-, double-, and triple- bond behavior of
+chemistry. Their analytical expressions can be derived from tight-
+binding theory by recursively expanding an inter-site Green's function
+as a continued fraction. To accurately represent the bonding with a
+computationally efficient potential formulation suitable for MD
+simulations, the derived BOP only takes (and retains) the first two
+levels of the recursive representations for both the sigma and the pi
+bond-orders. Bond-order terms can be understood in terms of molecular
+orbital hopping paths based upon the Cyrot-Lackmann theorem
+(:ref:`Pettifor\_1 <Pettifor_1>`).  The sigma bond-order with a half-full
+valence shell is used to interpolate the bond-order expression that
+incorporated explicit valance band filling.  This pi bond-order
+expression also contains also contains a three-member ring term that
+allows implementation of an asymmetric density of states, which helps
+to either stabilize or destabilize close-packed structures.  The pi
+bond-order includes hopping paths of length 4.  This enables the
+incorporation of dihedral angles effects.
+
+.. note::
+
+   Note that unlike for other potentials, cutoffs for BOP
+   potentials are not set in the pair\_style or pair\_coeff command; they
+   are specified in the BOP potential files themselves.  Likewise, the
+   BOP potential files list atomic masses; thus you do not need to use
+   the :doc:`mass <mass>` command to specify them.  Note that for BOP
+   potentials with hydrogen, you will likely want to set the mass of H
+   atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
+   You can do this by using the :doc:`mass <mass>` command after using the
+   :doc:`pair\_coeff <pair_coeff>` command to read the BOP potential
+   file.
+
+One option can be specified as a keyword with the pair\_style command.
+
+The *save* keyword gives you the option to calculate in advance and
+store a set of distances, angles, and derivatives of angles.  The
+default is to not do this, but to calculate them on-the-fly each time
+they are needed.  The former may be faster, but takes more memory.
+The latter requires less memory, but may be slower.  It is best to
+test this option to optimize the speed of BOP for your particular
+system configuration.
+
+
+----------
+
+
+Only a single pair\_coeff command is used with the *bop* style which
+specifies a BOP potential file, with parameters for all needed
+elements.  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of BOP elements to atom types
+
+As an example, imagine the CdTe.bop file has BOP values for Cd
+and Te.  If your LAMMPS simulation has 4 atoms types and you want the
+1st 3 to be Cd, and the 4th to be Te, you would use the following
+pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* CdTe Cd Cd Cd Te
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd
+element in the BOP file.  The final Te argument maps LAMMPS atom type
+4 to the Te element in the BOP file.
+
+BOP files in the *potentials* directory of the LAMMPS distribution
+have a ".bop" suffix.  The potentials are in tabulated form containing
+pre-tabulated pair functions for phi\_ij(r\_ij), beta\_(sigma,ij)(r\_ij),
+and beta\_pi,ij)(r\_ij).
+
+The parameters/coefficients format for the different kinds of BOP
+files are given below with variables matching the formulation of Ward
+(:ref:`Ward <Ward>`) and Zhou (:ref:`Zhou <Zhou1>`). Each header line containing a
+":" is preceded by a blank line.
+
+
+----------
+
+
+**No angular table file format**\ :
+
+The parameters/coefficients format for the BOP potentials input file
+containing pre-tabulated functions of g is given below with variables
+matching the formulation of Ward (:ref:`Ward <Ward>`).  This format also
+assumes the angular functions have the formulation of (:ref:`Ward <Ward>`).
+
+* Line 1: # elements N
+
+The first line is followed by N lines containing the atomic
+number, mass, and element symbol of each element.
+
+Following the definition of the elements several global variables for
+the tabulated functions are given.
+
+* Line 1: nr, nBOt (nr is the number of divisions the radius is broken
+  into for function tables and MUST be a factor of 5; nBOt is the number
+  of divisions for the tabulated values of THETA\_(S,ij)
+* Line 2: delta\_1-delta\_7 (if all are not used in the particular
+* formulation, set unused values to 0.0)
+
+
+Following this N lines for e\_1-e\_N containing p\_pi.
+
+* Line 3: p\_pi (for e\_1)
+* Line 4: p\_pi (for e\_2 and continues to e\_N)
+
+The next section contains several pair constants for the number of
+interaction types e\_i-e\_j, with i=1->N, j=i->N
+
+* Line 1: r\_cut (for e\_1-e\_1 interactions)
+* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi
+* Line 3: delta\_sigma, delta\_pi
+* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of
+  the previous section but is interaction type dependent)
+
+
+The next section contains a line for each three body interaction type
+e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N
+
+* Line 1: g\_(sigma0), g\_(sigma1), g\_(sigma2) (These are coefficients for
+  g\_(sigma,jik)(THETA\_ijk) for e\_1-e\_1-e\_1 interaction. :ref:`Ward <Ward>`
+  contains the full expressions for the constants as functions of
+  b\_(sigma,ijk), p\_(sigma,ijk), u\_(sigma,ijk))
+* Line 2: g\_(sigma0), g\_(sigma1), g\_(sigma2) (for e\_1-e\_1-e\_2)
+
+
+The next section contains a block for each interaction type for the
+phi\_ij(r\_ij).  Each block has nr entries with 5 entries per line.
+
+* Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e\_1-e\_1
+  interaction type)
+* Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues
+  until nr)
+* ...
+* Line nr/5\_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the
+  e\_1-e\_1 interaction type)
+
+
+The next section contains a block for each interaction type for the
+beta\_(sigma,ij)(r\_ij).  Each block has nr entries with 5 entries per
+line.
+
+* Line 1: beta\_sigma(r1), beta\_sigma(r2), beta\_sigma(r3), beta\_sigma(r4),
+  beta\_sigma(r5) (for the e\_1-e\_1 interaction type)
+* Line 2: beta\_sigma(r6), beta\_sigma(r7), beta\_sigma(r8), beta\_sigma(r9),
+  beta\_sigma(r10) (this continues until nr)
+* ...
+* Line nr/5+1: beta\_sigma(r1), beta\_sigma(r2), beta\_sigma(r3),
+  beta\_sigma(r4), beta\_sigma(r5) (for the e\_1-e\_2 interaction type)
+
+
+The next section contains a block for each interaction type for
+beta\_(pi,ij)(r\_ij).  Each block has nr entries with 5 entries per line.
+
+* Line 1: beta\_pi(r1), beta\_pi(r2), beta\_pi(r3), beta\_pi(r4), beta\_pi(r5)
+  (for the e\_1-e\_1 interaction type)
+* Line 2: beta\_pi(r6), beta\_pi(r7), beta\_pi(r8), beta\_pi(r9),
+  beta\_pi(r10) (this continues until nr)
+* ...
+* Line nr/5+1: beta\_pi(r1), beta\_pi(r2), beta\_pi(r3), beta\_pi(r4),
+  beta\_pi(r5) (for the e\_1-e\_2 interaction type)
+
+
+The next section contains a block for each interaction type for the
+THETA\_(S,ij)((THETA\_(sigma,ij))\^(1/2), f\_(sigma,ij)).  Each block has
+nBOt entries with 5 entries per line.
+
+* Line 1: THETA\_(S,ij)(r1), THETA\_(S,ij)(r2), THETA\_(S,ij)(r3),
+  THETA\_(S,ij)(r4), THETA\_(S,ij)(r5) (for the e\_1-e\_2 interaction type)
+* Line 2: THETA\_(S,ij)(r6), THETA\_(S,ij)(r7), THETA\_(S,ij)(r8),
+  THETA\_(S,ij)(r9), THETA\_(S,ij)(r10) (this continues until nBOt)
+* ...
+* Line nBOt/5+1: THETA\_(S,ij)(r1), THETA\_(S,ij)(r2), THETA\_(S,ij)(r3),
+  THETA\_(S,ij)(r4), THETA\_(S,ij)(r5) (for the e\_1-e\_2 interaction type)
+
+
+The next section contains a block of N lines for e\_1-e\_N
+
+* Line 1: delta\^mu (for e\_1)
+* Line 2: delta\^mu (for e\_2 and repeats to e\_N)
+
+The last section contains more constants for e\_i-e\_j interactions with
+i=0->N, j=i->N
+
+* Line 1: (A\_ij)\^(mu\*nu) (for e1-e1)
+* Line 2: (A\_ij)\^(mu\*nu) (for e1-e2 and repeats as above)
+
+
+----------
+
+
+**Angular spline table file format**\ :
+
+The parameters/coefficients format for the BOP potentials input file
+containing pre-tabulated functions of g is given below with variables
+matching the formulation of Ward (:ref:`Ward <Ward>`).  This format also
+assumes the angular functions have the formulation of (:ref:`Zhou <Zhou1>`).
+
+* Line 1: # elements N
+
+The first line is followed by N lines containing the atomic
+number, mass, and element symbol of each element.
+
+Following the definition of the elements several global variables for
+the tabulated functions are given.
+
+* Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken
+  into for function tables and MUST be a factor of 5; ntheta is the power of the
+  power of the spline used to fit the angular function; nBOt is the number
+  of divisions for the tabulated values of THETA\_(S,ij)
+* Line 2: delta\_1-delta\_7 (if all are not used in the particular
+* formulation, set unused values to 0.0)
+
+
+Following this N lines for e\_1-e\_N containing p\_pi.
+
+* Line 3: p\_pi (for e\_1)
+* Line 4: p\_pi (for e\_2 and continues to e\_N)
+
+The next section contains several pair constants for the number of
+interaction types e\_i-e\_j, with i=1->N, j=i->N
+
+* Line 1: r\_cut (for e\_1-e\_1 interactions)
+* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi
+* Line 3: delta\_sigma, delta\_pi
+* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of
+  the previous section but is interaction type dependent)
+
+
+The next section contains a line for each three body interaction type
+e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N
+
+* Line 1: g0, g1, g2... (These are coefficients for the angular spline
+  of the g\_(sigma,jik)(THETA\_ijk) for e\_1-e\_1-e\_1 interaction.  The
+  function can contain up to 10 term thus 10 constants.  The first line
+  can contain up to five constants.  If the spline has more than five
+  terms the second line will contain the remaining constants The
+  following lines will then contain the constants for the remaining g0,
+  g1, g2... (for e\_1-e\_1-e\_2) and the other three body
+  interactions
+
+
+The rest of the table has the same structure as the previous section
+(see above).
+
+
+----------
+
+
+**Angular no-spline table file format**\ :
+
+The parameters/coefficients format for the BOP potentials input file
+containing pre-tabulated functions of g is given below with variables
+matching the formulation of Ward (:ref:`Ward <Ward>`).  This format also
+assumes the angular functions have the formulation of (:ref:`Zhou <Zhou1>`).
+
+* Line 1: # elements N
+
+The first two lines are followed by N lines containing the atomic
+number, mass, and element symbol of each element.
+
+Following the definition of the elements several global variables for
+the tabulated functions are given.
+
+* Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken
+  into for function tables and MUST be a factor of 5; ntheta is the number of
+  divisions for the tabulated values of the g angular function; nBOt is the number
+  of divisions for the tabulated values of THETA\_(S,ij)
+* Line 2: delta\_1-delta\_7 (if all are not used in the particular
+* formulation, set unused values to 0.0)
+
+
+Following this N lines for e\_1-e\_N containing p\_pi.
+
+* Line 3: p\_pi (for e\_1)
+* Line 4: p\_pi (for e\_2 and continues to e\_N)
+
+The next section contains several pair constants for the number of
+interaction types e\_i-e\_j, with i=1->N, j=i->N
+
+* Line 1: r\_cut (for e\_1-e\_1 interactions)
+* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi
+* Line 3: delta\_sigma, delta\_pi
+* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of
+  the previous section but is interaction type dependent)
+
+
+The next section contains a line for each three body interaction type
+e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N
+
+* Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e\_1-e\_1-e\_1
+  interaction type)
+* Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues
+  until ntheta)
+* ...
+* Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the
+  e\_1-e\_1-e\_2 interaction type)
+
+
+The rest of the table has the same structure as the previous section (see above).
+
+
+----------
+
+
+**Mixing, shift, table tail correction, restart**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles are part of the MANYBODY package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+These pair potentials require the :doc:`newtion <newton>` setting to be
+"on" for pair interactions.
+
+The CdTe.bop and GaAs.bop potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal :doc:`units <units>`.
+You can use the BOP potential with any LAMMPS units, but you would need
+to create your own BOP potential file with coefficients listed in the
+appropriate units if your simulation does not use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+Default
+"""""""
+
+non-tabulated potential file, a\_0 is non-zero.
+
+
+----------
+
+
+.. _Pettifor\_1:
+
+
+
+**(Pettifor\_1)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487
+(1999).
+
+.. _Pettifor\_2:
+
+
+
+**(Pettifor\_2)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84,
+4124 (2000).
+
+.. _Pettifor\_3:
+
+
+
+**(Pettifor\_3)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103
+(2002).
+
+.. _Murdick:
+
+
+
+**(Murdick)** D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R.
+Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006).
+
+.. _Ward:
+
+
+
+**(Ward)** D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A.
+Zimmerman, Phys. Rev. B, 85,115206 (2012).
+
+.. _Zhou1:
+
+
+
+**(Zhou)** X.W. Zhou, D.K. Ward, M. Foster (TBP).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst
new file mode 100644
index 0000000000..3a9191cfd7
--- /dev/null
+++ b/doc/src/pair_born.rst
@@ -0,0 +1,238 @@
+.. index:: pair\_style born
+
+pair\_style born command
+========================
+
+pair\_style born/omp command
+============================
+
+pair\_style born/gpu command
+============================
+
+pair\_style born/coul/long command
+==================================
+
+pair\_style born/coul/long/gpu command
+======================================
+
+pair\_style born/coul/long/omp command
+======================================
+
+pair\_style born/coul/msm command
+=================================
+
+pair\_style born/coul/msm/omp command
+=====================================
+
+pair\_style born/coul/wolf command
+==================================
+
+pair\_style born/coul/wolf/gpu command
+======================================
+
+pair\_style born/coul/wolf/omp command
+======================================
+
+pair\_style born/coul/dsf command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *born* or *born/coul/long* or *born/coul/msm* or *born/coul/wolf*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *born* args = cutoff
+       cutoff = global cutoff for non-Coulombic interactions (distance units)
+     *born/coul/long* args = cutoff (cutoff2)
+       cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *born/coul/msm* args = cutoff (cutoff2)
+       cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *born/coul/wolf* args = alpha cutoff (cutoff2)
+       alpha = damping parameter (inverse distance units)
+       cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *born/coul/dsf* args = alpha cutoff (cutoff2)
+       alpha = damping parameter (inverse distance units)
+       cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style born 10.0
+   pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51
+   pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
+   pair_style born/coul/long 10.0
+   pair_style born/coul/long 10.0 8.
+   pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51
+   pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
+   pair_style born/coul/msm 10.0
+   pair_style born/coul/msm 10.0 8.0
+   pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51
+   pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
+   pair_style born/coul/wolf 0.25 10.0
+   pair_style born/coul/wolf 0.25 10.0 9.0
+   pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51
+   pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
+   pair_style born/coul/dsf 0.1 10.0 12.0
+   pair_coeff \* \*   0.0 1.00 0.00 0.00 0.00
+   pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
+
+Description
+"""""""""""
+
+The *born* style computes the Born-Mayer-Huggins or Tosi/Fumi
+potential described in :ref:`(Fumi and Tosi) <FumiTosi>`, given by
+
+.. image:: Eqs/pair_born.jpg
+   :align: center
+
+where sigma is an interaction-dependent length parameter, rho is an
+ionic-pair dependent length parameter, and Rc is the cutoff.
+
+The styles with *coul/long* or *coul/msm* add a Coulombic term as
+described for the :doc:`lj/cut <pair_lj>` pair styles.  An additional
+damping factor is applied to the Coulombic term so it can be used in
+conjunction with the :doc:`kspace\_style <kspace_style>` command and its
+*ewald* or *pppm* of *msm* option.  The Coulombic cutoff specified for
+this style means that pairwise interactions within this distance are
+computed directly; interactions outside that distance are computed in
+reciprocal space.
+
+If one cutoff is specified for the *born/coul/long* and
+*born/coul/msm* style, it is used for both the A,C,D and Coulombic
+terms.  If two cutoffs are specified, the first is used as the cutoff
+for the A,C,D terms, and the second is the cutoff for the Coulombic
+term.
+
+The *born/coul/wolf* style adds a Coulombic term as described for the
+Wolf potential in the :doc:`coul/wolf <pair_coul>` pair style.
+
+The *born/coul/dsf* style computes the Coulomb contribution with the
+damped shifted force model as in the :doc:`coul/dsf <pair_coul>` style.
+
+Note that these potentials are related to the :doc:`Buckingham potential <pair_buck>`.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* A (energy units)
+* rho (distance units)
+* sigma (distance units)
+* C (energy units \* distance units\^6)
+* D (energy units \* distance units\^8)
+* cutoff (distance units)
+
+The second coefficient, rho, must be greater than zero.
+
+The last coefficient is optional.  If not specified, the global A,C,D
+cutoff specified in the pair\_style command is used.
+
+For *born/coul/long*\ , *born/coul/wolf* and *born/coul/dsf* no
+Coulombic cutoff can be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair\_style command.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+These pair styles do not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+These styles support the :doc:`pair\_modify <pair_modify>` shift option
+for the energy of the exp(), 1/r\^6, and 1/r\^8 portion of the pair
+interaction.
+
+The *born/coul/long* pair style supports the
+:doc:`pair\_modify <pair_modify>` table option to tabulate the
+short-range portion of the long-range Coulombic interaction.
+
+These styles support the pair\_modify tail option for adding long-range
+tail corrections to energy and pressure.
+
+Thess styles writes thei information to binary :doc:`restart <restart>`
+files, so pair\_style and pair\_coeff commands do not need to be
+specified in an input script that reads a restart file.
+
+These styles can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  They do not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *born/coul/long* style is part of the KSPACE package.  It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style buck <pair_buck>`
+
+**Default:** none
+
+
+----------
+
+
+.. _FumiTosi:
+
+
+
+Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964),
+Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst
new file mode 100644
index 0000000000..a05043d141
--- /dev/null
+++ b/doc/src/pair_brownian.rst
@@ -0,0 +1,161 @@
+.. index:: pair\_style brownian
+
+pair\_style brownian command
+============================
+
+pair\_style brownian/omp command
+================================
+
+pair\_style brownian/poly command
+=================================
+
+pair\_style brownian/poly/omp command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
+
+* style = *brownian* or *brownian/poly*
+* mu = dynamic viscosity (dynamic viscosity units)
+* flaglog = 0/1 log terms in the lubrication approximation on/off
+* flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects
+* cutinner = inner cutoff distance (distance units)
+* cutoff = outer cutoff for interactions (distance units)
+* t\_target = target temp of the system (temperature units)
+* seed = seed for the random number generator (positive integer)
+* flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
+* flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
+   pair_coeff 1 1 2.05 2.8
+   pair_coeff \* \*
+
+Description
+"""""""""""
+
+Styles *brownian* and *brownian/poly* compute Brownian forces and
+torques on finite-size spherical particles.  The former requires
+monodisperse spherical particles; the latter allows for polydisperse
+spherical particles.
+
+These pair styles are designed to be used with either the :doc:`pair\_style lubricate <pair_lubricate>` or :doc:`pair\_style lubricateU <pair_lubricateU>` commands to provide thermostatting
+when dissipative lubrication forces are acting.  Thus the parameters
+*mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , and *cutoff* should be
+specified consistent with the settings in the lubrication pair styles.
+For details, refer to either of the lubrication pair styles.
+
+The *t\_target* setting is used to specify the target temperature of
+the system.  The random number *seed* is used to generate random
+numbers for the thermostatting procedure.
+
+The *flagHI* and *flagVF* settings are optional.  Neither should be
+used, or both must be defined.
+
+
+----------
+
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cutinner (distance units)
+* cutoff (distance units)
+
+The two coefficients are optional.  If neither is specified, the two
+cutoffs specified in the pair\_style command are used.  Otherwise both
+must be specified.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in :doc:`this section <Speed>` of
+the manual.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See :doc:`this section <Speed>` of the manual for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the two cutoff distances for this
+pair style can be mixed.  The default mix value is *geometric*\ .  See
+the "pair\_modify" command for details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the COLLOID package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Only spherical monodisperse particles are allowed for pair\_style
+brownian.
+
+Only spherical particles are allowed for pair\_style brownian/poly.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style lubricate <pair_lubricate>`, :doc:`pair\_style lubricateU <pair_lubricateU>`
+
+Default
+"""""""
+
+The default settings for the optional args are flagHI = 1 and flagVF =
+1.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst
new file mode 100644
index 0000000000..7c559001b8
--- /dev/null
+++ b/doc/src/pair_buck.rst
@@ -0,0 +1,242 @@
+.. index:: pair\_style buck
+
+pair\_style buck command
+========================
+
+pair\_style buck/gpu command
+============================
+
+pair\_style buck/intel command
+==============================
+
+pair\_style buck/kk command
+===========================
+
+pair\_style buck/omp command
+============================
+
+pair\_style buck/coul/cut command
+=================================
+
+pair\_style buck/coul/cut/gpu command
+=====================================
+
+pair\_style buck/coul/cut/intel command
+=======================================
+
+pair\_style buck/coul/cut/kk command
+====================================
+
+pair\_style buck/coul/cut/omp command
+=====================================
+
+pair\_style buck/coul/long command
+==================================
+
+pair\_style buck/coul/long/gpu command
+======================================
+
+pair\_style buck/coul/long/intel command
+========================================
+
+pair\_style buck/coul/long/kk command
+=====================================
+
+pair\_style buck/coul/long/omp command
+======================================
+
+pair\_style buck/coul/msm command
+=================================
+
+pair\_style buck/coul/msm/omp command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *buck* or *buck/coul/cut* or *buck/coul/long* or *buck/coul/msm*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *buck* args = cutoff
+       cutoff = global cutoff for Buckingham interactions (distance units)
+     *buck/coul/cut* args = cutoff (cutoff2)
+       cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *buck/coul/long* args = cutoff (cutoff2)
+       cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *buck/coul/msm* args = cutoff (cutoff2)
+       cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style buck 2.5
+   pair_coeff \* \* 100.0 1.5 200.0
+   pair_coeff \* \* 100.0 1.5 200.0 3.0
+
+   pair_style buck/coul/cut 10.0
+   pair_style buck/coul/cut 10.0 8.0
+   pair_coeff \* \* 100.0 1.5 200.0
+   pair_coeff 1 1 100.0 1.5 200.0 9.0
+   pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
+
+   pair_style buck/coul/long 10.0
+   pair_style buck/coul/long 10.0 8.0
+   pair_coeff \* \* 100.0 1.5 200.0
+   pair_coeff 1 1 100.0 1.5 200.0 9.0
+
+   pair_style buck/coul/msm 10.0
+   pair_style buck/coul/msm 10.0 8.0
+   pair_coeff \* \* 100.0 1.5 200.0
+   pair_coeff 1 1 100.0 1.5 200.0 9.0
+
+Description
+"""""""""""
+
+The *buck* style computes a Buckingham potential (exp/6 instead of
+Lennard-Jones 12/6) given by
+
+.. image:: Eqs/pair_buck.jpg
+   :align: center
+
+where rho is an ionic-pair dependent length parameter, and Rc is the
+cutoff on both terms.
+
+The styles with *coul/cut* or *coul/long* or *coul/msm* add a
+Coulombic term as described for the :doc:`lj/cut <pair_lj>` pair styles.
+For *buck/coul/long* and *buc/coul/msm*\ , an additional damping factor
+is applied to the Coulombic term so it can be used in conjunction with
+the :doc:`kspace\_style <kspace_style>` command and its *ewald* or *pppm*
+or *msm* option.  The Coulombic cutoff specified for this style means
+that pairwise interactions within this distance are computed directly;
+interactions outside that distance are computed in reciprocal space.
+
+If one cutoff is specified for the *born/coul/cut* and
+*born/coul/long* and *born/coul/msm* styles, it is used for both the
+A,C and Coulombic terms.  If two cutoffs are specified, the first is
+used as the cutoff for the A,C terms, and the second is the cutoff for
+the Coulombic term.
+
+Note that these potentials are related to the :doc:`Born-Mayer-Huggins potential <pair_born>`.
+
+.. note::
+
+   For all these pair styles, the terms with A and C are always
+   cutoff.  The additional Coulombic term can be cutoff or long-range (no
+   cutoff) depending on whether the style name includes coul/cut or
+   coul/long or coul/msm.  If you wish the C/r\^6 term to be long-range
+   (no cutoff), then see the :doc:`pair\_style buck/long/coul/long <pair_buck_long>` command.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* A (energy units)
+* rho (distance units)
+* C (energy-distance\^6 units)
+* cutoff (distance units)
+* cutoff2 (distance units)
+
+The second coefficient, rho, must be greater than zero.
+The coefficients A, rho, and C can be written as analytical expressions
+of epsilon and sigma, in analogy to the Lennard-Jones potential
+:ref:`(Khrapak) <Khrapak>`.
+
+The latter 2 coefficients are optional.  If not specified, the global
+A,C and Coulombic cutoffs are used.  If only one cutoff is specified,
+it is used as the cutoff for both A,C and Coulombic interactions for
+this type pair.  If both coefficients are specified, they are used as
+the A,C and Coulombic cutoffs for this type pair.  You cannot specify
+2 cutoffs for style *buck*\ , since it has no Coulombic terms.
+For *buck/coul/long* only the LJ cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair\_style command.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+These pair styles do not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+These styles support the :doc:`pair\_modify <pair_modify>` shift option
+for the energy of the exp() and 1/r\^6 portion of the pair interaction.
+
+The *buck/coul/long* pair style supports the
+:doc:`pair\_modify <pair_modify>` table option to tabulate the
+short-range portion of the long-range Coulombic interaction.
+
+These styles support the pair\_modify tail option for adding long-range
+tail corrections to energy and pressure for the A,C terms in the
+pair interaction.
+
+These styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These styles can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  They do not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+The *buck/coul/long* style is part of the KSPACE package.  They are
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style born <pair_born>`
+
+**Default:** none
+
+.. _Khrapak:
+
+
+
+**(Khrapak)** Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst
new file mode 100644
index 0000000000..94351f5152
--- /dev/null
+++ b/doc/src/pair_buck6d_coul_gauss.rst
@@ -0,0 +1,164 @@
+.. index:: pair\_style buck6d/coul/gauss/dsf
+
+pair\_style buck6d/coul/gauss/dsf command
+=========================================
+
+pair\_style buck6d/coul/gauss/long command
+==========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *buck6d/coul/gauss/dsf* or *buck6d/coul/gauss/long*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *buck6d/coul/gauss/dsf* args = smooth cutoff (cutoff2)
+       smooth  = smoothing onset within Buckingham cutoff (ratio)
+       cutoff  = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *buck6d/coul/gauss/long* args = smooth smooth2 cutoff (cutoff2)
+       smooth   = smoothing onset within Buckingham cutoff (ratio)
+       smooth2  = smoothing onset within Coulombic cutoff (ratio)
+       cutoff   = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+       cutoff2  = global cutoff for Coulombic (optional) (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style buck6d/coul/gauss/dsf    0.9000    12.0000
+   pair_coeff 1  1  1030.  3.061  457.179  4.521  0.608
+
+   pair_style buck6d/coul/gauss/long   0.9000  1.0000  12.0000
+   pair_coeff 1  1  1030.  3.061  457.179  4.521  0.608
+
+Description
+"""""""""""
+
+The *buck6d/coul/gauss* styles evaluate vdW and Coulomb
+interactions following the MOF-FF force field after
+:ref:`(Schmid) <Schmid>`. The vdW term of the *buck6d* styles
+computes a dispersion damped Buckingham potential:
+
+.. image:: Eqs/pair_buck6d.jpg
+   :align: center
+
+where A and C are a force constant, kappa is an ionic-pair dependent
+reciprocal length parameter, D is a dispersion correction parameter,
+and the cutoff Rc truncates the interaction distance.
+The first term in the potential corresponds to the Buckingham
+repulsion term and the second term to the dispersion attraction with
+a damping correction analog to the Grimme correction used in DFT.
+The latter corrects for artifacts occurring at short distances which
+become an issue for soft vdW potentials.
+
+The *buck6d* styles include a smoothing function which is invoked
+according to the global smoothing parameter within the specified
+cutoff.  Hereby a parameter of i.e. 0.9 invokes the smoothing
+within 90% of the cutoff.  No smoothing is applied at a value
+of 1.0. For the *gauss/dsf* style this smoothing is only applicable
+for the dispersion damped Buckingham potential. For the *gauss/long*
+styles the smoothing function can also be invoked for the real
+space coulomb interactions which enforce continuous energies and
+forces at the cutoff.
+
+Both styles *buck6d/coul/gauss/dsf* and *buck6d/coul/gauss/long*
+evaluate a Coulomb potential using spherical Gaussian type charge
+distributions which effectively dampen electrostatic interactions
+for high charges at close distances.  The electrostatic potential
+is thus evaluated as:
+
+.. image:: Eqs/pair_coul_gauss.jpg
+   :align: center
+
+where C is an energy-conversion constant, Qi and Qj are the
+charges on the 2 atoms, epsilon is the dielectric constant which
+can be set by the :doc:`dielectric <dielectric>` command, alpha is
+ion pair dependent damping parameter and erf() is the error-function.
+The cutoff Rc truncates the interaction distance.
+
+The style *buck6d/coul/gauss/dsf* computes the Coulomb interaction
+via the damped shifted force model described in :ref:`(Fennell) <Fennell>`
+approximating an Ewald sum similar to the :doc:`pair coul/dsf <pair_coul>`
+styles. In *buck6d/coul/gauss/long* an additional damping factor is
+applied to the Coulombic term so it can be used in conjunction with the
+:doc:`kspace\_style <kspace_style>` command and its *ewald* or *pppm*
+options. The Coulombic cutoff in this case separates the real and
+reciprocal space evaluation of the Ewald sum.
+
+If one cutoff is specified it is used for both the vdW and Coulomb
+terms.  If two cutoffs are specified, the first is used as the cutoff
+for the vdW terms, and the second is the cutoff for the Coulombic term.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* A (energy units)
+* rho (distance\^-1 units)
+* C (energy-distance\^6 units)
+* D (distance\^14 units)
+* alpha (distance\^-1 units)
+* cutoff (distance units)
+
+The second coefficient, rho, must be greater than zero. The latter
+coefficient is optional.  If not specified, the global vdW cutoff
+is used.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+These pair styles do not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+These styles do not support the :doc:`pair\_modify <pair_modify>` shift
+option for the energy. Instead the smoothing function should be applied
+by setting the global smoothing parameter to a value < 1.0.
+
+These styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the USER-MOFFF package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+.. _Schmid:
+
+
+
+.. _Fennell:
+
+**(Schmid)** S. Bureekaew, S. Amirjalayer, M. Tafipolsky, C. Spickermann, T.K. Roy and R. Schmid, Phys. Status Solidi B, 6, 1128 (2013).
+
+
+**(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst
new file mode 100644
index 0000000000..3871e554ce
--- /dev/null
+++ b/doc/src/pair_buck_long.rst
@@ -0,0 +1,199 @@
+.. index:: pair\_style buck/long/coul/long
+
+pair\_style buck/long/coul/long command
+=======================================
+
+pair\_style buck/long/coul/long/omp command
+===========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2)
+
+* flag\_buck = *long* or *cut*
+  
+  .. parsed-literal::
+  
+       *long* = use Kspace long-range summation for the dispersion term 1/r\^6
+       *cut* = use a cutoff
+
+* flag\_coul = *long* or *off*
+  
+  .. parsed-literal::
+  
+       *long* = use Kspace long-range summation for the Coulombic term 1/r
+       *off* = omit the Coulombic term
+
+* cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units)
+* cutoff2 = global cutoff for Coulombic (optional) (distance units)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style buck/long/coul/long cut off 2.5
+   pair_style buck/long/coul/long cut long 2.5 4.0
+   pair_style buck/long/coul/long long long 4.0
+   pair_coeff \* \* 1 1
+   pair_coeff 1 1 1 3 4
+
+Description
+"""""""""""
+
+The *buck/long/coul/long* style computes a Buckingham potential (exp/6
+instead of Lennard-Jones 12/6) and Coulombic potential, given by
+
+.. image:: Eqs/pair_buck.jpg
+   :align: center
+
+.. image:: Eqs/pair_coulomb.jpg
+   :align: center
+
+Rc is the cutoff.  If one cutoff is specified in the pair\_style
+command, it is used for both the Buckingham and Coulombic terms.  If
+two cutoffs are specified, they are used as cutoffs for the Buckingham
+and Coulombic terms respectively.
+
+The purpose of this pair style is to capture long-range interactions
+resulting from both attractive 1/r\^6 Buckingham and Coulombic 1/r
+interactions.  This is done by use of the *flag\_buck* and *flag\_coul*
+settings.  The :ref:`Ismail <Ismail>` paper has more details on when it is
+appropriate to include long-range 1/r\^6 interactions, using this
+potential.
+
+If *flag\_buck* is set to *long*\ , no cutoff is used on the Buckingham
+1/r\^6 dispersion term.  The long-range portion can be calculated by
+using the :doc:`kspace\_style ewald/disp or pppm/disp <kspace_style>`
+commands.  The specified Buckingham cutoff then determines which
+portion of the Buckingham interactions are computed directly by the
+pair potential versus which part is computed in reciprocal space via
+the Kspace style.  If *flag\_buck* is set to *cut*\ , the Buckingham
+interactions are simply cutoff, as with :doc:`pair\_style buck <pair_buck>`.
+
+If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic
+interactions.  The long-range portion can calculated by using any of
+several :doc:`kspace\_style <kspace_style>` command options such as
+*pppm* or *ewald*\ .  Note that if *flag\_buck* is also set to long, then
+the *ewald/disp* or *pppm/disp* Kspace style needs to be used to
+perform the long-range calculations for both the Buckingham and
+Coulombic interactions.  If *flag\_coul* is set to *off*\ , Coulombic
+interactions are not computed.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* A (energy units)
+* rho (distance units)
+* C (energy-distance\^6 units)
+* cutoff (distance units)
+* cutoff2 (distance units)
+
+The second coefficient, rho, must be greater than zero.
+
+The latter 2 coefficients are optional.  If not specified, the global
+Buckingham and Coulombic cutoffs specified in the pair\_style command
+are used.  If only one cutoff is specified, it is used as the cutoff
+for both Buckingham and Coulombic interactions for this type pair.  If
+both coefficients are specified, they are used as the Buckingham and
+Coulombic cutoffs for this type pair.  Note that if you are using
+*flag\_buck* set to *long*\ , you cannot specify a Buckingham cutoff for
+an atom type pair, since only one global Buckingham cutoff is allowed.
+Similarly, if you are using *flag\_coul* set to *long*\ , you cannot
+specify a Coulombic cutoff for an atom type pair, since only one
+global Coulombic cutoff is allowed.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair styles does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the exp() and 1/r\^6 portion of the pair
+interaction, assuming *flag\_buck* is *cut*\ .
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the Buckingham portion of the pair
+interaction.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` table and
+table/disp options since they can tabulate the short-range portion of
+the long-range Coulombic and dispersion interactions.
+
+This pair style write its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style supports the use of the *inner*\ , *middle*\ , and *outer*
+keywords of the :doc:`run\_style respa <run_style>` command, meaning the
+pairwise forces can be partitioned by distance at different levels of
+the rRESPA hierarchy.  See the :doc:`run\_style <run_style>` command for
+details.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the KSPACE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Ismail:
+
+
+
+**(Ismail)** Ismail, Tsige, In 't Veld, Grest, Molecular Physics
+(accepted) (2007).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst
new file mode 100644
index 0000000000..cd3e5dbc70
--- /dev/null
+++ b/doc/src/pair_charmm.rst
@@ -0,0 +1,336 @@
+.. index:: pair\_style lj/charmm/coul/charmm
+
+pair\_style lj/charmm/coul/charmm command
+=========================================
+
+pair\_style lj/charmm/coul/charmm/intel command
+===============================================
+
+pair\_style lj/charmm/coul/charmm/kk command
+============================================
+
+pair\_style lj/charmm/coul/charmm/omp command
+=============================================
+
+pair\_style lj/charmm/coul/charmm/implicit command
+==================================================
+
+pair\_style lj/charmm/coul/charmm/implicit/kk command
+=====================================================
+
+pair\_style lj/charmm/coul/charmm/implicit/omp command
+======================================================
+
+pair\_style lj/charmm/coul/long command
+=======================================
+
+pair\_style lj/charmm/coul/long/gpu command
+===========================================
+
+pair\_style lj/charmm/coul/long/intel command
+=============================================
+
+pair\_style lj/charmm/coul/long/kk command
+==========================================
+
+pair\_style lj/charmm/coul/long/opt command
+===========================================
+
+pair\_style lj/charmm/coul/long/omp command
+===========================================
+
+pair\_style lj/charmm/coul/msm command
+======================================
+
+pair\_style lj/charmm/coul/msm/omp command
+==========================================
+
+pair\_style lj/charmmfsw/coul/charmmfsh command
+===============================================
+
+pair\_style lj/charmmfsw/coul/long command
+==========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/charmm/coul/charmm* or *lj/charmm/coul/charmm/implicit* or *lj/charmm/coul/long* or *lj/charmm/coul/msm* or *lj/charmmfsw/coul/charmmfsh* or *lj/charmmfsw/coul/long*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *lj/charmm/coul/charmm* args = inner outer (inner2) (outer2)
+       inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
+       inner2, outer2 = global switching cutoffs for Coulombic (optional)
+     *lj/charmm/coul/charmm/implicit* args = inner outer (inner2) (outer2)
+       inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+       inner2, outer2 = global switching cutoffs for Coulombic (optional)
+     *lj/charmm/coul/long* args = inner outer (cutoff)
+       inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+       cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+     *lj/charmm/coul/msm* args = inner outer (cutoff)
+       inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+       cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+     *lj/charmmfsw/coul/charmmfsh* args = inner outer (cutoff)
+       inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
+       cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+     *lj/charmmfsw/coul/long* args = inner outer (cutoff)
+       inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
+       cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/charmm/coul/charmm 8.0 10.0
+   pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
+   pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0
+   pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0
+   pair_coeff \* \* 100.0 2.0
+   pair_coeff 1 1 100.0 2.0 150.0 3.5
+
+   pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
+   pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
+   pair_coeff \* \* 100.0 2.0
+   pair_coeff 1 1 100.0 2.0 150.0 3.5
+
+   pair_style lj/charmm/coul/long 8.0 10.0
+   pair_style lj/charmm/coul/long 8.0 10.0 9.0
+   pair_style lj/charmmfsw/coul/long 8.0 10.0
+   pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0
+   pair_coeff \* \* 100.0 2.0
+   pair_coeff 1 1 100.0 2.0 150.0 3.5
+
+   pair_style lj/charmm/coul/msm 8.0 10.0
+   pair_style lj/charmm/coul/msm 8.0 10.0 9.0
+   pair_coeff \* \* 100.0 2.0
+   pair_coeff 1 1 100.0 2.0 150.0 3.5
+
+Description
+"""""""""""
+
+These pair styles compute Lennard Jones (LJ) and Coulombic
+interactions with additional switching or shifting functions that ramp
+the energy and/or force smoothly to zero between an inner and outer
+cutoff.  They are implementations of the widely used CHARMM force
+field used in the `CHARMM <http://www.scripps.edu/brooks>`_ MD code (and
+others).  See :ref:`(MacKerell) <pair-MacKerell>` for a description of the
+CHARMM force field.
+
+The styles with *charmm* (not *charmmfsw* or *charmmfsh*\ ) in their
+name are the older, original LAMMPS implementations.  They compute the
+LJ and Coulombic interactions with an energy switching function (esw,
+shown in the formula below as S(r)), which ramps the energy smoothly
+to zero between the inner and outer cutoff.  This can cause
+irregularities in pair-wise forces (due to the discontinuous 2nd
+derivative of energy at the boundaries of the switching region), which
+in some cases can result in detectable artifacts in an MD simulation.
+
+The newer styles with *charmmfsw* or *charmmfsh* in their name replace
+the energy switching with force switching (fsw) and force shifting
+(fsh) functions, for LJ and Coulombic interactions respectively.
+These follow the formulas and description given in
+:ref:`(Steinbach) <Steinbach>` and :ref:`(Brooks) <Brooks1>` to minimize these
+artifacts.
+
+.. note::
+
+   The newer *charmmfsw* or *charmmfsh* styles were released in
+   March 2017.  We recommend they be used instead of the older *charmm*
+   styles.  This includes the newer :doc:`dihedral\_style charmmfsw <dihedral_charmm>` command.  Eventually code from the new
+   styles will propagate into the related pair styles (e.g. implicit,
+   accelerator, free energy variants).
+
+.. note::
+
+   The newest CHARMM pair styles reset the Coulombic energy
+   conversion factor used internally in the code, from the LAMMPS value
+   to the CHARMM value, as if it were effectively a parameter of the
+   force field.  This is because the CHARMM code uses a slightly
+   different value for the this conversion factor in :doc:`real units <units>` (Kcal/mole), namely CHARMM = 332.0716, LAMMPS =
+   332.06371.  This is to enable more precise agreement by LAMMPS with
+   the CHARMM force field energies and forces, when using one of these
+   two CHARMM pair styles.
+
+.. image:: Eqs/pair_charmm.jpg
+   :align: center
+
+where S(r) is the energy switching function mentioned above for the
+*charmm* styles.  See the :ref:`(Steinbach) <Steinbach>` paper for the
+functional forms of the force switching and force shifting functions
+used in the *charmmfsw* and *charmmfsh* styles.
+
+When using the *lj/charmm/coul/charmm styles*\ , both the LJ and
+Coulombic terms require an inner and outer cutoff. They can be the
+same for both formulas or different depending on whether 2 or 4
+arguments are used in the pair\_style command.  For the
+*lj/charmmfsw/coul/charmmfsh* style, the LJ term requires both an
+inner and outer cutoff, while the Coulombic term requires only one
+cutoff.  If the Coulombic cutoff is not specified (2 instead of 3
+arguments), the LJ outer cutoff is used for the Coulombic cutoff.  In
+all cases where an inner and outer cutoff are specified, the inner
+cutoff distance must be less than the outer cutoff.  It is typical to
+make the difference between the inner and outer cutoffs about 2.0
+Angstroms.
+
+Style *lj/charmm/coul/charmm/implicit* computes the same formulas as
+style *lj/charmm/coul/charmm* except that an additional 1/r term is
+included in the Coulombic formula.  The Coulombic energy thus varies
+as 1/r\^2.  This is effectively a distance-dependent dielectric term
+which is a simple model for an implicit solvent with additional
+screening.  It is designed for use in a simulation of an unsolvated
+biomolecule (no explicit water molecules).
+
+Styles *lj/charmm/coul/long* and *lj/charmm/coul/msm* compute the same
+formulas as style *lj/charmm/coul/charmm* and style
+*lj/charmmfsw/coul/long* computes the same formulas as style
+*lj/charmmfsw/coul/charmmfsh*\ , except that an additional damping
+factor is applied to the Coulombic term, so it can be used in
+conjunction with the :doc:`kspace\_style <kspace_style>` command and its
+*ewald* or *pppm* or *msm* option.  Only one Coulombic cutoff is
+specified for these styles; if only 2 arguments are used in the
+pair\_style command, then the outer LJ cutoff is used as the single
+Coulombic cutoff.  The Coulombic cutoff specified for these styles
+means that pairwise interactions within this distance are computed
+directly; interactions outside that distance are computed in
+reciprocal space.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* epsilon\_14 (energy units)
+* sigma\_14 (distance units)
+
+Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum at 2\^(1/6)
+sigma.
+
+The latter 2 coefficients are optional.  If they are specified, they
+are used in the LJ formula between 2 atoms of these types which are
+also first and fourth atoms in any dihedral.  No cutoffs are specified
+because the CHARMM force field does not allow varying cutoffs for
+individual atom pairs; all pairs use the global cutoff(s) specified in
+the pair\_style command.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon, sigma, epsilon\_14,
+and sigma\_14 coefficients for all of the lj/charmm pair styles can be
+mixed.  The default mix value is *arithmetic* to coincide with the
+usual settings for the CHARMM force field.  See the "pair\_modify"
+command for details.
+
+None of the *lj/charmm* or *lj/charmmfsw* pair styles support the
+:doc:`pair\_modify <pair_modify>` shift option, since the Lennard-Jones
+portion of the pair interaction is smoothed to 0.0 at the cutoff.
+
+The *lj/charmm/coul/long* and *lj/charmmfsw/coul/long* styles support
+the :doc:`pair\_modify <pair_modify>` table option since they can
+tabulate the short-range portion of the long-range Coulombic
+interaction.
+
+None of the *lj/charmm* or *lj/charmmfsw* pair styles support the
+:doc:`pair\_modify <pair_modify>` tail option for adding long-range tail
+corrections to energy and pressure, since the Lennard-Jones portion of
+the pair interaction is smoothed to 0.0 at the cutoff.
+
+All of the *lj/charmm* and *lj/charmmfsw* pair styles write their
+information to :doc:`binary restart files <restart>`, so pair\_style and
+pair\_coeff commands do not need to be specified in an input script
+that reads a restart file.
+
+The *lj/charmm/coul/long* and *lj/charmmfsw/coul/long* pair styles
+support the use of the *inner*\ , *middle*\ , and *outer* keywords of the
+:doc:`run\_style respa <run_style>` command, meaning the pairwise forces
+can be partitioned by distance at different levels of the rRESPA
+hierarchy.  The other styles only support the *pair* keyword of
+run\_style respa.  See the :doc:`run\_style <run_style>` command for
+details.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All the styles with *coul/charmm* or *coul/charmmfsh* styles are part
+of the MOLECULE package.  All the styles with *coul/long* style are
+part of the KSPACE package.  They are only enabled if LAMMPS was built
+with those packages.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Brooks1:
+
+
+
+**(Brooks)** Brooks, et al, J Comput Chem, 30, 1545 (2009).
+
+.. _pair-MacKerell:
+
+
+
+**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
+.. _Steinbach:
+
+
+
+**(Steinbach)** Steinbach, Brooks, J Comput Chem, 15, 667 (1994).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst
new file mode 100644
index 0000000000..985e6688f3
--- /dev/null
+++ b/doc/src/pair_class2.rst
@@ -0,0 +1,223 @@
+.. index:: pair\_style lj/class2
+
+pair\_style lj/class2 command
+=============================
+
+pair\_style lj/class2/gpu command
+=================================
+
+pair\_style lj/class2/kk command
+================================
+
+pair\_style lj/class2/omp command
+=================================
+
+pair\_style lj/class2/coul/cut command
+======================================
+
+pair\_style lj/class2/coul/cut/kk command
+=========================================
+
+pair\_style lj/class2/coul/cut/omp command
+==========================================
+
+pair\_style lj/class2/coul/long command
+=======================================
+
+pair\_style lj/class2/coul/long/gpu command
+===========================================
+
+pair\_style lj/class2/coul/long/kk command
+==========================================
+
+pair\_style lj/class2/coul/long/omp command
+===========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/class2* or *lj/class2/coul/cut* or *lj/class2/coul/long*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *lj/class2* args = cutoff
+       cutoff = global cutoff for class 2 interactions (distance units)
+     *lj/class2/coul/cut* args = cutoff (cutoff2)
+       cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/class2/coul/long* args = cutoff (cutoff2)
+       cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/class2 10.0
+   pair_coeff \* \* 100.0 2.5
+   pair_coeff 1 2\* 100.0 2.5 9.0
+
+   pair_style lj/class2/coul/cut 10.0
+   pair_style lj/class2/coul/cut 10.0 8.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+   pair_coeff 1 1 100.0 3.5 9.0 9.0
+
+   pair_style lj/class2/coul/long 10.0
+   pair_style lj/class2/coul/long 10.0 8.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+
+Description
+"""""""""""
+
+The *lj/class2* styles compute a 6/9 Lennard-Jones potential given by
+
+.. image:: Eqs/pair_class2.jpg
+   :align: center
+
+Rc is the cutoff.
+
+The *lj/class2/coul/cut* and *lj/class2/coul/long* styles add a
+Coulombic term as described for the :doc:`lj/cut <pair_lj>` pair styles.
+
+See :ref:`(Sun) <pair-Sun>` for a description of the COMPASS class2 force field.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff1 (distance units)
+* cutoff2 (distance units)
+
+The latter 2 coefficients are optional.  If not specified, the global
+class 2 and Coulombic cutoffs are used.  If only one cutoff is
+specified, it is used as the cutoff for both class 2 and Coulombic
+interactions for this type pair.  If both coefficients are specified,
+they are used as the class 2 and Coulombic cutoffs for this type pair.
+You cannot specify 2 cutoffs for style *lj/class2*\ , since it has no
+Coulombic terms.
+
+For *lj/class2/coul/long* only the class 2 cutoff can be specified
+since a Coulombic cutoff cannot be specified for an individual I,J
+type pair.  All type pairs use the same global Coulombic cutoff
+specified in the pair\_style command.
+
+
+----------
+
+
+If the pair\_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule for epsilon and sigma for
+all class2 potentials is to use the *sixthpower* formulas documented
+by the :doc:`pair\_modify <pair_modify>` command.  The :doc:`pair\_modify mix <pair_modify>` setting is thus ignored for class2 potentials
+for epsilon and sigma.  However it is still followed for mixing the
+cutoff distance.
+
+
+----------
+
+
+A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
+free energy calculations, is part of the USER-FEP package and is documented with
+the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/class2 pair styles can be mixed.
+Epsilon and sigma are always mixed with the value *sixthpower*\ .  The
+cutoff distance is mixed by whatever option is set by the pair\_modify
+command (default = geometric).  See the "pair\_modify" command for
+details.
+
+All of the lj/class2 pair styles support the
+:doc:`pair\_modify <pair_modify>` shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+
+The *lj/class2/coul/long* pair style does not support the
+:doc:`pair\_modify <pair_modify>` table option since a tabulation
+capability has not yet been added to this potential.
+
+All of the lj/class2 pair styles support the
+:doc:`pair\_modify <pair_modify>` tail option for adding a long-range
+tail correction to the energy and pressure of the Lennard-Jones
+portion of the pair interaction.
+
+All of the lj/class2 pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+Only the *lj/class2* and *lj/class2/coul/long* pair styles support the use of the
+*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa <run_style>` command, meaning the pairwise forces can be
+partitioned by distance at different levels of the rRESPA hierarchy.
+The other styles only support the *pair* keyword of run\_style respa.
+See the :doc:`run\_style <run_style>` command for details.
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the CLASS2 package.  They are only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+
+**Default:** none
+
+
+----------
+
+
+.. _pair-Sun:
+
+
+
+**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst
new file mode 100644
index 0000000000..424b8c3242
--- /dev/null
+++ b/doc/src/pair_coeff.rst
@@ -0,0 +1,165 @@
+.. index:: pair\_coeff
+
+pair\_coeff command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_coeff I J args
+
+* I,J = atom types (see asterisk form below)
+* args = coefficients for one or more pairs of atom types
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_coeff 1 2 1.0 1.0 2.5
+   pair_coeff 2 \* 1.0 1.0
+   pair_coeff 3\* 1\*2 1.0 1.0 2.5
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff \* \* nialhjea 1 1 2
+   pair_coeff \* 3 morse.table ENTRY1
+   pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
+
+Description
+"""""""""""
+
+Specify the pairwise force field coefficients for one or more pairs of
+atom types.  The number and meaning of the coefficients depends on the
+pair style.  Pair coefficients can also be set in the data file read
+by the :doc:`read\_data <read_data>` command or in a restart file.
+
+I and J can be specified in one of two ways.  Explicit numeric values
+can be used for each, as in the 1st example above.  I <= J is
+required.  LAMMPS sets the coefficients for the symmetric J,I
+interaction to the same values.
+
+A wildcard asterisk can be used in place of or in conjunction with the
+I,J arguments to set the coefficients for multiple pairs of atom
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of atom types, then an asterisk with no numeric values means all
+types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).  Note that only type pairs with I <= J are considered; if
+asterisks imply type pairs where J < I, they are ignored.
+
+Note that a pair\_coeff command can override a previous setting for the
+same I,J pair.  For example, these commands set the coeffs for all I,J
+pairs, then overwrite the coeffs for just the I,J = 2,3 pair:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* 1.0 1.0 2.5
+   pair_coeff 2 3 2.0 1.0 1.12
+
+A line in a data file that specifies pair coefficients uses the exact
+same format as the arguments of the pair\_coeff command in an input
+script, with the exception of the I,J type arguments.  In each line of
+the "Pair Coeffs" section of a data file, only a single type I is
+specified, which sets the coefficients for type I interacting with
+type I.  This is because the section has exactly N lines, where N =
+the number of atom types.  For this reason, the wild-card asterisk
+should also not be used as part of the I argument.  Thus in a data
+file, the line corresponding to the 1st example above would be listed
+as
+
+
+.. parsed-literal::
+
+   2 1.0 1.0 2.5
+
+For many potentials, if coefficients for type pairs with I != J are
+not set explicitly by a pair\_coeff command, the values are inferred
+from the I,I and J,J settings by mixing rules; see the
+:doc:`pair\_modify <pair_modify>` command for a discussion.  Details on
+this option as it pertains to individual potentials are described on
+the doc page for the potential.
+
+Many pair styles, typically for many-body potentials, use tabulated
+potential files as input, when specifying the pair\_coeff command.
+Potential files provided with LAMMPS are in the potentials directory
+of the distribution.  For some potentials, such as EAM, other archives
+of suitable files can be found on the Web.  They can be used with
+LAMMPS so long as they are in the format LAMMPS expects, as discussed
+on the individual doc pages.
+
+When a pair\_coeff command using a potential file is specified, LAMMPS
+looks for the potential file in 2 places.  First it looks in the
+location specified.  E.g. if the file is specified as "niu3.eam", it
+is looked for in the current working directory.  If it is specified as
+"../potentials/niu3.eam", then it is looked for in the potentials
+directory, assuming it is a sister directory of the current working
+directory.  If the file is not found, it is then looked for in the
+directory specified by the LAMMPS\_POTENTIALS environment variable.
+Thus if this is set to the potentials directory in the LAMMPS distribution,
+then you can use those files from anywhere on your system, without
+copying them into your working directory.  Environment variables are
+set in different ways for different shells.  Here are example settings
+for
+
+csh, tcsh:
+
+
+.. parsed-literal::
+
+   % setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
+
+bash:
+
+
+.. parsed-literal::
+
+   % export LAMMPS_POTENTIALS=/path/to/lammps/potentials
+
+Windows:
+
+
+.. parsed-literal::
+
+   % set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials"
+
+
+----------
+
+
+The alphabetic list of pair styles defined in LAMMPS is given on the
+:doc:`pair\_style <pair_style>` doc page.  They are also listed in more
+compact form on the :doc:`Commands pair <Commands_pair>` doc page.
+
+Click on the style to display the formula it computes and its
+coefficients as specified by the associated pair\_coeff command.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command must come after the simulation box is defined by a
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
+:doc:`create\_box <create_box>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style <pair_style>`, :doc:`pair\_modify <pair_modify>`,
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`,
+:doc:`pair\_write <pair_write>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst
new file mode 100644
index 0000000000..fb9c92989f
--- /dev/null
+++ b/doc/src/pair_colloid.rst
@@ -0,0 +1,230 @@
+.. index:: pair\_style colloid
+
+pair\_style colloid command
+===========================
+
+pair\_style colloid/gpu command
+===============================
+
+pair\_style colloid/omp command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style colloid cutoff
+
+* cutoff = global cutoff for colloidal interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style colloid 10.0
+   pair_coeff \* \*  25 1.0 10.0 10.0
+   pair_coeff 1 1 144 1.0 0.0 0.0 3.0
+   pair_coeff 1 2  75.398 1.0 0.0 10.0 9.0
+   pair_coeff 2 2  39.478 1.0 10.0 10.0 25.0
+
+Description
+"""""""""""
+
+Style *colloid* computes pairwise interactions between large colloidal
+particles and small solvent particles using 3 formulas.  A colloidal
+particle has a size > sigma; a solvent particle is the usual
+Lennard-Jones particle of size sigma.
+
+The colloid-colloid interaction energy is given by
+
+.. image:: Eqs/pair_colloid_cc.jpg
+   :align: center
+
+where A\_cc is the Hamaker constant, a1 and a2 are the radii of the two
+colloidal particles, and Rc is the cutoff.  This equation results from
+describing each colloidal particle as an integrated collection of
+Lennard-Jones particles of size sigma and is derived in
+:ref:`(Everaers) <Everaers1>`.
+
+The colloid-solvent interaction energy is given by
+
+.. image:: Eqs/pair_colloid_cs.jpg
+   :align: center
+
+where A\_cs is the Hamaker constant, a is the radius of the colloidal
+particle, and Rc is the cutoff.  This formula is derived from the
+colloid-colloid interaction, letting one of the particle sizes go to
+zero.
+
+The solvent-solvent interaction energy is given by the usual
+Lennard-Jones formula
+
+.. image:: Eqs/pair_colloid_ss.jpg
+   :align: center
+
+with A\_ss set appropriately, which results from letting both particle
+sizes go to zero.
+
+When used in combination with :doc:`pair\_style yukawa/colloid <pair_colloid>`, the two terms become the so-called
+DLVO potential, which combines electrostatic repulsion and van der
+Waals attraction.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* A (energy units)
+* sigma (distance units)
+* d1 (distance units)
+* d2 (distance units)
+* cutoff (distance units)
+
+A is the Hamaker energy prefactor and should typically be set as
+follows:
+
+* A\_cc = colloid/colloid = 4 pi\^2 = 39.5
+* A\_cs = colloid/solvent = sqrt(A\_cc\*A\_ss)
+* A\_ss = solvent/solvent = 144 (assuming epsilon = 1, so that 144/36 = 4)
+
+Sigma is the size of the solvent particle or the constituent particles
+integrated over in the colloidal particle and should typically be set
+as follows:
+
+* Sigma\_cc = colloid/colloid = 1.0
+* Sigma\_cs = colloid/solvent = arithmetic mixing between colloid sigma and solvent sigma
+* Sigma\_ss = solvent/solvent = 1.0 or whatever size the solvent particle is
+
+Thus typically Sigma\_cs = 1.0, unless the solvent particle's size !=
+1.0.
+
+D1 and d2 are particle diameters, so that d1 = 2\*a1 and d2 = 2\*a2 in
+the formulas above.  Both d1 and d2 must be values >= 0.  If d1 > 0
+and d2 > 0, then the pair interacts via the colloid-colloid formula
+above.  If d1 = 0 and d2 = 0, then the pair interacts via the
+solvent-solvent formula.  I.e. a d value of 0 is a Lennard-Jones
+particle of size sigma.  If either d1 = 0 or d2 = 0 and the other is
+larger, then the pair interacts via the colloid-solvent formula.
+
+Note that the diameter of a particular particle type may appear in
+multiple pair\_coeff commands, as it interacts with other particle
+types.  You should insure the particle diameter is specified
+consistently each time it appears.
+
+The last coefficient is optional.  If not specified, the global cutoff
+specified in the pair\_style command is used.  However, you typically
+want different cutoffs for interactions between different particle
+sizes.  E.g. if colloidal particles of diameter 10 are used with
+solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5
+would correspond to a colloid-colloid cutoff of 25.  A good
+rule-of-thumb is to use a colloid-solvent cutoff that is half the big
+diameter + 4 times the small diameter.  I.e. 9 = 5 + 4 for the
+colloid-solvent cutoff in this case.
+
+.. note::
+
+   When using pair\_style colloid for a mixture with 2 (or more)
+   widely different particles sizes (e.g. sigma=10 colloids in a
+   background sigma=1 LJ fluid), you will likely want to use these
+   commands for efficiency: :doc:`neighbor multi <neighbor>` and
+   :doc:`comm\_modify multi <comm_modify>`.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the A, sigma, d1, and d2
+coefficients and cutoff distance for this pair style can be mixed.  A
+is an energy value mixed like a LJ epsilon.  D1 and d2 are distance
+values and are mixed like sigma.  The default mix value is
+*geometric*\ .  See the "pair\_modify" command for details.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the COLLOID package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Normally, this pair style should be used with finite-size particles
+which have a diameter, e.g. see the :doc:`atom\_style sphere <atom_style>` command.  However, this is not a requirement,
+since the only definition of particle size is via the pair\_coeff
+parameters for each type.  In other words, the physical radius of the
+particle is ignored.  Thus you should insure that the d1,d2 parameters
+you specify are consistent with the physical size of the particles of
+that type.
+
+Per-particle polydispersity is not yet supported by this pair style;
+only per-type polydispersity is enabled via the pair\_coeff parameters.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Everaers1:
+
+
+
+**(Everaers)** Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst
new file mode 100644
index 0000000000..ece536a011
--- /dev/null
+++ b/doc/src/pair_comb.rst
@@ -0,0 +1,227 @@
+.. index:: pair\_style comb
+
+pair\_style comb command
+========================
+
+pair\_style comb/omp command
+============================
+
+pair\_style comb3 command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style comb
+   pair_style comb3 keyword
+
+   keyword = *polar*
+     *polar* value = *polar_on* or *polar_off* = whether or not to include atomic polarization
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style comb
+   pair_coeff \* \* ../potentials/ffield.comb Si
+   pair_coeff \* \* ../potentials/ffield.comb Hf Si O
+
+   pair_style comb3 polar_off
+   pair_coeff \* \* ../potentials/ffield.comb3 O Cu N C O
+
+Description
+"""""""""""
+
+Style *comb* computes the second-generation variable charge COMB
+(Charge-Optimized Many-Body) potential.  Style *comb3* computes the
+third-generation COMB potential.  These COMB potentials are described
+in :ref:`(COMB) <COMB>` and :ref:`(COMB3) <COMB3>`.  Briefly, the total energy
+*E<sub>T</sub>* of a system of atoms is given by
+
+.. image:: Eqs/pair_comb1.jpg
+   :align: center
+
+where *E<sub>i</sub><sup>self</sup>* is the self-energy of atom *i*
+(including atomic ionization energies and electron affinities),
+*E<sub>ij</sub><sup>short</sup>* is the bond-order potential between
+atoms *i* and *j*\ ,
+*E<sub>ij</sub><sup>Coul</sup>* is the Coulomb interactions,
+*E<sup>polar</sup>* is the polarization term for organic systems
+(style *comb3* only),
+*E<sup>vdW</sup>* is the van der Waals energy (style *comb3* only),
+*E<sup>barr</sup>* is a charge barrier function, and
+*E<sup>corr</sup>* are angular correction terms.
+
+The COMB potentials (styles *comb* and *comb3*\ ) are variable charge
+potentials.  The equilibrium charge on each atom is calculated by the
+electronegativity equalization (QEq) method.  See :ref:`Rick <Rick2>` for
+further details.  This is implemented by the :doc:`fix qeq/comb <fix_qeq_comb>` command, which should normally be
+specified in the input script when running a model with the COMB
+potential.  The :doc:`fix qeq/comb <fix_qeq_comb>` command has options
+that determine how often charge equilibration is performed, its
+convergence criterion, and which atoms are included in the
+calculation.
+
+Only a single pair\_coeff command is used with the *comb* and *comb3*
+styles which specifies the COMB potential file with parameters for all
+needed elements.  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the potential file in the pair\_coeff
+command, where N is the number of LAMMPS atom types.
+
+For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
+HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
+last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
+use the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* ../potentials/ffield.comb Si Hf O Si
+
+The first two arguments must be \* \* so as to span all LAMMPS atom
+types.  The first and last Si arguments map LAMMPS atom types 1 and 4
+to the Si element in the *ffield.comb* file.  The second Hf argument
+maps LAMMPS atom type 2 to the Hf element, and the third O argument
+maps LAMMPS atom type 3 to the O element in the potential file.  If a
+mapping value is specified as NULL, the mapping is not performed.
+This can be used when a *comb* potential is used as part of the
+*hybrid* pair style.  The NULL values are placeholders for atom types
+that will be used with other potentials.
+
+For style *comb*\ , the provided potential file *ffield.comb* contains
+all currently-available 2nd generation COMB parameterizations: for Si,
+Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals.  For style
+*comb3*\ , the potential file *ffield.comb3* contains all
+currently-available 3rd generation COMB parameterizations: O, Cu, N, C,
+H, Ti, Zn and Zr.  The status of the optimization of the compounds, for
+example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
+following table:
+
+.. image:: Eqs/pair_comb2.jpg
+   :align: center
+
+For style *comb3*\ , in addition to ffield.comb3, a special parameter
+file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be
+automatically loaded if carbon atom is detected in LAMMPS input
+structure.  This file must be in your working directory or in the
+directory pointed to by the environment variable LAMMPS\_POTENTIALS, as
+described on the :doc:`pair\_coeff <pair_coeff>` command doc page.
+
+Keyword *polar* indicates whether the force field includes
+the atomic polarization.  Since the equilibration of the polarization
+has not yet been implemented, it can only set polar\_off at present.
+
+.. note::
+
+   You can not use potential file *ffield.comb* with style *comb3*\ ,
+   nor file *ffield.comb3* with style *comb*\ .
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+These pair styles does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+These pair styles do not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style, pair\_coeff, and :doc:`fix qeq/comb <fix_qeq_comb>` commands in an input script that reads a
+restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles are part of the MANYBODY package.  It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+These pair styles requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The COMB potentials in the *ffield.comb* and *ffield.comb3* files provided
+with LAMMPS (see the potentials directory) are parameterized for metal
+:doc:`units <units>`.  You can use the COMB potential with any LAMMPS
+units, but you would need to create your own COMB potential file with
+coefficients listed in the appropriate units if your simulation
+doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style <pair_style>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`fix qeq/comb <fix_qeq_comb>`
+
+**Default:** none
+
+
+----------
+
+
+.. _COMB:
+
+
+
+**(COMB)**  T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
+S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
+
+.. _COMB3:
+
+
+
+**(COMB3)** T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
+Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
+255-279 (2013).
+
+.. _Rick2:
+
+
+
+**(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
+(1994).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst
new file mode 100644
index 0000000000..f08ddc38e0
--- /dev/null
+++ b/doc/src/pair_cosine_squared.rst
@@ -0,0 +1,134 @@
+.. index:: pair\_style cosine/squared
+
+pair\_style cosine/squared command
+==================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style cosine/squared cutoff
+
+* cutoff = global cutoff for cosine-squared interactions (distance units)
+
+
+.. parsed-literal::
+
+   pair_coeff i j eps sigma
+   pair_coeff i j eps sigma cutoff
+   pair_coeff i j eps sigma wca
+   pair_coeff i j eps sigma cutoff wca
+
+* i,j = a particle type
+* eps = interaction strength, i.e. the depth of the potential minimum (energy units)
+* sigma = distance of the potential minimum from 0
+* cutoff = the cutoff distance for this pair type, if different from global (distance units)
+* wca = if specified a Weeks-Chandler-Andersen potential (with eps strength and minimum at sigma) is added, otherwise not
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style cosine/squared 3.0
+   pair_coeff \* \* 1.0 1.3
+   pair_coeff 1 3 1.0 1.3 2.0
+   pair_coeff 1 3 1.0 1.3 wca
+   pair_coeff 1 3 1.0 1.3 2.0 wca
+
+Description
+"""""""""""
+
+Style *cosine/squared* computes a potential of the form
+
+.. image:: Eqs/pair_cosine_squared.jpg
+   :align: center
+
+between two point particles, where (sigma, -epsilon) is the location of
+the (rightmost) minimum of the potential, as explained in the syntax
+section above.
+
+This potential was first used in (Cooke)\_#CKD for a coarse-grained lipid
+membrane model.  It is generally very useful as a non-specific
+interaction potential because it is fully adjustable in depth and width
+while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0)
+smoothly, requiring no shifting and causing no related artifacts, tail
+energy calculations etc. This evidently requires *cutoff* to be larger
+than *sigma*\ .
+
+If the *wca* option is used then a Weeks-Chandler-Andersen potential
+(Weeks)\_#WCA is added to the above specified cosine-squared potential,
+specifically the following:
+
+.. image:: Eqs/pair_cosine_squared_wca.jpg
+   :align: center
+
+In this case, and this case only, the *sigma* parameter can be equal to
+*cutoff* (sigma = cutoff) which will result in ONLY the WCA potential
+being used (and print a warning), so the minimum will be attained at
+(sigma, 0). This is a convenience feature that enables a purely
+repulsive potential to be used without a need to define an additional
+pair style and use the hybrid styles.
+
+The energy and force of this pair style for parameters epsilon = 1.0,
+sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown
+in the graphs below:
+
+.. image:: JPG/pair_cosine_squared_graphs.jpg
+   :align: center
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+Mixing is not supported for this style.
+
+The *shift*\ , *table* and *tail* options are not relevant for this style.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *cosine/squared* style is part of the "USER-MISC" package. It is only
+enabled if LAMMPS is build with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_style lj/cut <pair_lj>`
+
+**Default:** none
+
+.. _CKD:
+
+
+
+**(Cooke)** "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"
+
+.. _WCA:
+
+
+
+**(Weeks)** "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)"
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst
new file mode 100644
index 0000000000..fda9ae4069
--- /dev/null
+++ b/doc/src/pair_coul.rst
@@ -0,0 +1,434 @@
+.. index:: pair\_style coul/cut
+
+pair\_style coul/cut command
+============================
+
+pair\_style coul/cut/gpu command
+================================
+
+pair\_style coul/cut/kk command
+===============================
+
+pair\_style coul/cut/omp command
+================================
+
+pair\_style coul/debye command
+==============================
+
+pair\_style coul/debye/gpu command
+==================================
+
+pair\_style coul/debye/kk command
+=================================
+
+pair\_style coul/debye/omp command
+==================================
+
+pair\_style coul/dsf command
+============================
+
+pair\_style coul/dsf/gpu command
+================================
+
+pair\_style coul/dsf/kk command
+===============================
+
+pair\_style coul/dsf/omp command
+================================
+
+pair\_style coul/long command
+=============================
+
+pair\_style coul/long/omp command
+=================================
+
+pair\_style coul/long/gpu command
+=================================
+
+pair\_style coul/long/kk command
+================================
+
+pair\_style coul/msm command
+============================
+
+pair\_style coul/msm/omp command
+================================
+
+pair\_style coul/streitz command
+================================
+
+pair\_style coul/wolf command
+=============================
+
+pair\_style coul/wolf/kk command
+================================
+
+pair\_style coul/wolf/omp command
+=================================
+
+pair\_style tip4p/cut command
+=============================
+
+pair\_style tip4p/long command
+==============================
+
+pair\_style tip4p/cut/omp command
+=================================
+
+pair\_style tip4p/long/omp command
+==================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style coul/cut cutoff
+   pair_style coul/debye kappa cutoff
+   pair_style coul/dsf alpha cutoff
+   pair_style coul/long cutoff
+   pair_style coul/long/gpu cutoff
+   pair_style coul/wolf alpha cutoff
+   pair_style coul/streitz cutoff keyword alpha
+   pair_style tip4p/cut otype htype btype atype qdist cutoff
+   pair_style tip4p/long otype htype btype atype qdist cutoff
+
+* cutoff = global cutoff for Coulombic interactions
+* kappa = Debye length (inverse distance units)
+* alpha = damping parameter (inverse distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style coul/cut 2.5
+   pair_coeff \* \*
+   pair_coeff 2 2 3.5
+
+   pair_style coul/debye 1.4 3.0
+   pair_coeff \* \*
+   pair_coeff 2 2 3.5
+
+   pair_style coul/dsf 0.05 10.0
+   pair_coeff \* \*
+
+   pair_style coul/long 10.0
+   pair_coeff \* \*
+
+   pair_style coul/msm 10.0
+   pair_coeff \* \*
+
+   pair_style coul/wolf 0.2 9.0
+   pair_coeff \* \*
+
+   pair_style coul/streitz 12.0 ewald
+   pair_style coul/streitz 12.0 wolf 0.30
+   pair_coeff \* \* AlO.streitz Al O
+
+   pair_style tip4p/cut 1 2 7 8 0.15 12.0
+   pair_coeff \* \*
+
+   pair_style tip4p/long 1 2 7 8 0.15 10.0
+   pair_coeff \* \*
+
+Description
+"""""""""""
+
+The *coul/cut* style computes the standard Coulombic interaction
+potential given by
+
+.. image:: Eqs/pair_coulomb.jpg
+   :align: center
+
+where C is an energy-conversion constant, Qi and Qj are the charges on
+the 2 atoms, and epsilon is the dielectric constant which can be set
+by the :doc:`dielectric <dielectric>` command.  The cutoff Rc truncates
+the interaction distance.
+
+
+----------
+
+
+Style *coul/debye* adds an additional exp() damping factor to the
+Coulombic term, given by
+
+.. image:: Eqs/pair_debye.jpg
+   :align: center
+
+where kappa is the Debye length.  This potential is another way to
+mimic the screening effect of a polar solvent.
+
+
+----------
+
+
+Style *coul/dsf* computes Coulombic interactions via the damped
+shifted force model described in :ref:`Fennell <Fennell1>`, given by:
+
+.. image:: Eqs/pair_coul_dsf.jpg
+   :align: center
+
+where *alpha* is the damping parameter and erfc() is the
+complementary error-function. The potential corrects issues in the
+Wolf model (described below) to provide consistent forces and energies
+(the Wolf potential is not differentiable at the cutoff) and smooth
+decay to zero.
+
+
+----------
+
+
+Style *coul/wolf* computes Coulombic interactions via the Wolf
+summation method, described in :ref:`Wolf <Wolf1>`, given by:
+
+.. image:: Eqs/pair_coul_wolf.jpg
+   :align: center
+
+where *alpha* is the damping parameter, and erc() and erfc() are
+error-function and complementary error-function terms.  This potential
+is essentially a short-range, spherically-truncated,
+charge-neutralized, shifted, pairwise *1/r* summation.  With a
+manipulation of adding and subtracting a self term (for i = j) to the
+first and second term on the right-hand-side, respectively, and a
+small enough *alpha* damping parameter, the second term shrinks and
+the potential becomes a rapidly-converging real-space summation.  With
+a long enough cutoff and small enough alpha parameter, the energy and
+forces calculated by the Wolf summation method approach those of the
+Ewald sum.  So it is a means of getting effective long-range
+interactions with a short-range potential.
+
+
+----------
+
+
+Style *coul/streitz* is the Coulomb pair interaction defined as part
+of the Streitz-Mintmire potential, as described in :ref:`this paper <Streitz2>`, in which charge distribution about an atom is modeled
+as a Slater 1\ *s* orbital.  More details can be found in the referenced
+paper.  To fully reproduce the published Streitz-Mintmire potential,
+which is a variable charge potential, style *coul/streitz* must be
+used with :doc:`pair\_style eam/alloy <pair_eam>` (or some other
+short-range potential that has been parameterized appropriately) via
+the :doc:`pair\_style hybrid/overlay <pair_hybrid>` command.  Likewise,
+charge equilibration must be performed via the :doc:`fix qeq/slater <fix_qeq>` command. For example:
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
+   pair_coeff \* \* coul/streitz AlO.streitz Al O
+   pair_coeff \* \* eam/alloy AlO.eam.alloy Al O
+   fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
+
+The keyword *wolf* in the coul/streitz command denotes computing
+Coulombic interactions via Wolf summation.  An additional damping
+parameter is required for the Wolf summation, as described for the
+coul/wolf potential above.  Alternatively, Coulombic interactions can
+be computed via an Ewald summation.  For example:
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
+   kspace_style ewald 1e-6
+
+Keyword *ewald* does not need a damping parameter, but a
+:doc:`kspace\_style <kspace_style>` must be defined, which can be style
+*ewald* or *pppm*\ .  The Ewald method was used in Streitz and
+Mintmire's original paper, but a Wolf summation offers a speed-up in
+some cases.
+
+For the fix qeq/slater command, the *qfile* can be a filename that
+contains QEq parameters as discussed on the :doc:`fix qeq <fix_qeq>`
+command doc page.  Alternatively *qfile* can be replaced by
+"coul/streitz", in which case the fix will extract QEq parameters from
+the coul/streitz pair style itself.
+
+See the examples/strietz directory for an example input script that
+uses the Streitz-Mintmire potential.  The potentials directory has the
+AlO.eam.alloy and AlO.streitz potential files used by the example.
+
+Note that the Streiz-Mintmire potential is generally used for oxides,
+but there is no conceptual problem with extending it to nitrides and
+carbides (such as SiC, TiN).  Pair coul/strietz used by itself or with
+any other pair style such as EAM, MEAM, Tersoff, or LJ in
+hybrid/overlay mode.  To do this, you would need to provide a
+Streitz-Mintmire parameterization for the material being modeled.
+
+
+----------
+
+
+Styles *coul/long* and *coul/msm* compute the same Coulombic
+interactions as style *coul/cut* except that an additional damping
+factor is applied so it can be used in conjunction with the
+:doc:`kspace\_style <kspace_style>` command and its *ewald* or *pppm*
+option.  The Coulombic cutoff specified for this style means that
+pairwise interactions within this distance are computed directly;
+interactions outside that distance are computed in reciprocal space.
+
+Styles *tip4p/cut* and *tip4p/long* implement the Coulomb part of
+the TIP4P water model of :ref:`(Jorgensen) <Jorgensen3>`, which introduces
+a massless site located a short distance away from the oxygen atom
+along the bisector of the HOH angle.  The atomic types of the oxygen and
+hydrogen atoms, the bond and angle types for OH and HOH interactions,
+and the distance to the massless charge site are specified as
+pair\_style arguments.  Style *tip4p/cut* uses a global cutoff for
+Coulomb interactions; style *tip4p/long* is for use with a long-range
+Coulombic solver (Ewald or PPPM).
+
+.. note::
+
+   For each TIP4P water molecule in your system, the atom IDs for
+   the O and 2 H atoms must be consecutive, with the O atom first.  This
+   is to enable LAMMPS to "find" the 2 H atoms associated with each O
+   atom.  For example, if the atom ID of an O atom in a TIP4P water
+   molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+
+See the :doc:`Howto tip4p <Howto_tip4p>` doc page for more information
+on how to use the TIP4P pair styles and lists of parameters to set.
+Note that the neighbor list cutoff for Coulomb interactions is
+effectively extended by a distance 2\*qdist when using the TIP4P pair
+style, to account for the offset distance of the fictitious charges on
+O atoms in water molecules.  Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
+shrink the size of the neighbor list.  This leads to slightly larger
+cost for the long-range calculation, so you can test the trade-off for
+your model.
+
+
+----------
+
+
+Note that these potentials are designed to be combined with other pair
+potentials via the :doc:`pair\_style hybrid/overlay <pair_hybrid>`
+command.  This is because they have no repulsive core.  Hence if they
+are used by themselves, there will be no repulsion to keep two
+oppositely charged particles from moving arbitrarily close to each
+other.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cutoff (distance units)
+
+For *coul/cut* and *coul/debye*\ , the cutoff coefficient is optional.
+If it is not used (as in some of the examples above), the default
+global value specified in the pair\_style command is used.
+
+For *coul/long* and *coul/msm* no cutoff can be specified for an
+individual I,J type pair via the pair\_coeff command.  All type pairs
+use the same global Coulombic cutoff specified in the pair\_style
+command.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the cutoff distance for the
+*coul/cut* style can be mixed.  The default mix value is *geometric*\ .
+See the "pair\_modify" command for details.
+
+The :doc:`pair\_modify <pair_modify>` shift option is not relevant
+for these pair styles.
+
+The *coul/long* style supports the :doc:`pair\_modify <pair_modify>`
+table option for tabulation of the short-range portion of the
+long-range Coulombic interaction.
+
+These pair styles do not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *coul/long*\ , *coul/msm* and *tip4p/long* styles are part of the
+KSPACE package.  They are only enabled if LAMMPS was built with that
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace\_style <kspace_style>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Wolf1:
+
+
+
+**(Wolf)** D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
+Phys, 110, 8254 (1999).
+
+.. _Fennell1:
+
+
+
+**(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
+234104 (2006).
+
+.. _Streitz2:
+
+
+
+**(Streitz)** F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003
+(1994).
+
+.. _Jorgensen3:
+
+
+
+**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst
new file mode 100644
index 0000000000..2e86ab41b4
--- /dev/null
+++ b/doc/src/pair_coul_diel.rst
@@ -0,0 +1,139 @@
+.. index:: pair\_style coul/diel
+
+pair\_style coul/diel command
+=============================
+
+pair\_style coul/diel/omp command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style coul/diel cutoff
+
+cutoff = global cutoff (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style coul/diel 3.5
+   pair_coeff 1 4 78. 1.375 0.112
+
+Description
+"""""""""""
+
+Style *coul/diel* computes a Coulomb correction for implicit solvent
+ion interactions in which the dielectric permittivity is distance dependent.
+The dielectric permittivity epsilon\_D(r) connects to limiting regimes:
+One limit is defined by a small dielectric permittivity (close to vacuum)
+at or close to contact separation between the ions. At larger separations
+the dielectric permittivity reaches a bulk value used in the regular Coulomb
+interaction coul/long or coul/cut.
+The transition is modeled by a hyperbolic function which is incorporated
+in the Coulomb correction term for small ion separations as follows
+
+.. image:: Eqs/pair_coul_diel.jpg
+   :align: center
+
+where r\_me is the inflection point of epsilon\_D(r) and sigma\_e is a slope
+defining length scale. C is the same Coulomb conversion factor as in the
+pair\_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb
+interaction between ions is corrected at small distances r. The lower
+limit of epsilon\_D(r->0)=5.2 due to dielectric saturation :ref:`(Stiles) <Stiles>`
+while the Coulomb interaction reaches its bulk limit by setting
+epsilon\_D(r->\infty)=epsilon, the bulk value of the solvent which is 78
+for water at 298K.
+
+Examples of the use of this type of Coulomb interaction include implicit
+solvent simulations of salt ions
+:ref:`(Lenart) <Lenart1>` and of ionic surfactants :ref:`(Jusufi) <Jusufi1>`.
+Note that this potential is only reasonable for implicit solvent simulations
+and in combination with coul/cut or coul/long. It is also usually combined
+with gauss/cut, see :ref:`(Lenart) <Lenart1>` or :ref:`(Jusufi) <Jusufi1>`.
+
+The following coefficients must be defined for each pair of atom
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the example
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* epsilon (no units)
+* r\_me (distance units)
+* sigma\_e (distance units)
+
+The global cutoff (r\_c) specified in the pair\_style command is used.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support parameter mixing. Coefficients must
+be given explicitly for each type of particle pairs.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the Gauss-potential portion of the pair
+interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This style is part of the "USER-MISC" package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+:doc:`pair\_style gauss/cut <pair_gauss>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Stiles:
+
+
+
+**(Stiles)** Stiles , Hubbard, and Kayser, J Chem Phys, 77,
+6189 (1982).
+
+.. _Lenart1:
+
+
+
+**(Lenart)** Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
+044509 (2007).
+
+.. _Jusufi1:
+
+
+
+**(Jusufi)** Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
+13783 (2008).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst
new file mode 100644
index 0000000000..c6d306b2eb
--- /dev/null
+++ b/doc/src/pair_coul_shield.rst
@@ -0,0 +1,119 @@
+.. index:: pair\_style coul/shield
+
+pair\_style coul/shield command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style coul/shield cutoff tap_flag
+
+* cutoff = global cutoff (distance units)
+* tap\_flag = 0/1 to turn off/on the taper function
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style coul/shield 16.0 1
+   pair_coeff 1 2 0.70
+
+Description
+"""""""""""
+
+Style *coul/shield* computes a Coulomb interaction for boron and
+nitrogen atoms located in different layers of hexagonal boron
+nitride. This potential is designed be used in combination with
+the pair style :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
+
+.. note::
+
+   This potential is intended for electrostatic interactions between
+   two different layers of hexagonal boron nitride. Therefore, to avoid
+   interaction within the same layers, each layer should have a separate
+   molecule id and is recommended to use the "full" atom style, so that
+   charge and molecule ID information is included.
+
+.. image:: Eqs/pair_coul_shield.jpg
+   :align: center
+
+Where Tap(r\_ij) is the taper function which provides a continuous cutoff
+(up to third derivative) for inter-atomic separations larger than r\_c
+:ref:`(Leven1) <Leven3>`, :ref:`(Leven2) <Leven4>` and :ref:`(Maaravi) <Maaravi1>`.
+Here *lambda* is the shielding parameter that
+eliminates the short-range singularity of the classical mono-polar
+electrostatic interaction expression :ref:`(Maaravi) <Maaravi1>`.
+
+The shielding parameter *lambda* (1/distance units) must be defined for
+each pair of atom types via the :doc:`pair\_coeff <pair_coeff>` command as
+in the example above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` commands:
+
+The global cutoff (r\_c) specified in the pair\_style command is used.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support parameter mixing. Coefficients must
+be given explicitly for each type of particle pairs.
+
+The :doc:`pair\_modify <pair_modify>` *table* option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+*tail* option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This style is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+:doc:`pair\_style ilp/graphene/hbn <pair_ilp_graphene_hbn>`
+
+**Default:** tap\_flag = 1
+
+
+----------
+
+
+.. _Leven3:
+
+
+
+**(Leven1)** I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
+
+.. _Leven4:
+
+
+
+**(Leven2)** I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
+
+.. _Maaravi1:
+
+
+
+**(Maaravi)** T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst
new file mode 100644
index 0000000000..3667aa6e2f
--- /dev/null
+++ b/doc/src/pair_cs.rst
@@ -0,0 +1,218 @@
+.. index:: pair\_style born/coul/dsf/cs
+
+pair\_style born/coul/dsf/cs command
+====================================
+
+pair\_style born/coul/long/cs command
+=====================================
+
+pair\_style born/coul/long/cs/gpu command
+=========================================
+
+pair\_style born/coul/wolf/cs command
+=====================================
+
+pair\_style born/coul/wolf/cs/gpu command
+=========================================
+
+pair\_style buck/coul/long/cs command
+=====================================
+
+pair\_style coul/long/cs command
+================================
+
+pair\_style coul/long/cs/gpu command
+====================================
+
+pair\_style coul/wolf/cs command
+================================
+
+pair\_style lj/cut/coul/long/cs command
+=======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *born/coul/dsf/cs* or *born/coul/long/cs* or *born/coul/wolf/cs* or *buck/coul/long/cs* or *coul/long/cs* or *coul/wolf/cs* or *lj/cut/coul/long/cs*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *born/coul/dsf/cs* args = alpha cutoff (cutoff2)
+       alpha = damping parameter (inverse distance units)
+       cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (distance units)
+     *born/coul/long/cs* args = cutoff (cutoff2)
+       cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *born/coul/wolf/cs* args = alpha cutoff (cutoff2)
+       alpha = damping parameter (inverse distance units)
+       cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *buck/coul/long/cs* args = cutoff (cutoff2)
+       cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *coul/long* args = cutoff
+       cutoff = global cutoff for Coulombic (distance units)
+     *coul/wolf* args = alpha cutoff
+       alpha = damping parameter (inverse distance units)
+       cutoff = global cutoff for Coulombic (distance units)
+     *lj/cut/coul/long/cs* args = cutoff (cutoff2)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style born/coul/dsf/cs 0.1 10.0 12.0
+   pair_coeff \* \*   0.0 1.00 0.00 0.00 0.00
+   pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
+
+   pair_style born/coul/long/cs 10.0 8.0
+   pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
+   pair_style born/coul/wolf/cs 0.25 10.0 12.0
+   pair_coeff \* \*   0.0 1.00 0.00 0.00 0.00
+   pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
+
+   pair_style buck/coul/long/cs 10.0
+   pair_style buck/coul/long/cs 10.0 8.0
+   pair_coeff \* \* 100.0 1.5 200.0
+   pair_coeff 1 1 100.0 1.5 200.0 9.0
+
+   pair_style coul/long/cs 10.0
+   pair_coeff \* \*
+
+   pair_style coul/wolf/cs 0.2 9.0
+   pair_coeff \* \*
+
+   pair_style lj/cut/coul/long/cs 10.0
+   pair_style lj/cut/coul/long/cs 10.0 8.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+
+Description
+"""""""""""
+
+These pair styles are designed to be used with the adiabatic
+core/shell model of :ref:`(Mitchell and Finchham) <MitchellFinchham2>`.  See
+the :doc:`Howto coreshell <Howto_coreshell>` doc page for an overview of
+the model as implemented in LAMMPS.
+
+All the styles are identical to the corresponding pair style without
+the "/cs" in the name:
+
+* :doc:`pair\_style born/coul/dsf <pair_born>`
+* :doc:`pair\_style born/coul/long <pair_born>`
+* :doc:`pair\_style born/coul/wolf <pair_born>`
+* :doc:`pair\_style buck/coul/long <pair_buck>`
+* :doc:`pair\_style coul/long <pair_coul>`
+* :doc:`pair\_style coul/wolf <pair_coul>`
+* :doc:`pair\_style lj/cut/coul/long <pair_lj>`
+
+except that they correctly treat the special case where the distance
+between two charged core and shell atoms in the same core/shell pair
+approach r = 0.0.
+
+Styles with a "/long" in the name are used with a long-range solver
+for Coulombic interactions via the :doc:`kspace\_style <kspace_style>`
+command.  They require special treatment of the short-range Coulombic
+interactions within the cor/shell model.
+
+Specifically, the short-range Coulomb interaction between a core and
+its shell should be turned off using the
+:doc:`special\_bonds <special_bonds>` command by setting the 1-2 weight
+to 0.0, which works because the core and shell atoms are bonded to
+each other.  This induces a long-range correction approximation which
+fails at small distances (~< 10e-8). Therefore, the Coulomb term which
+is used to calculate the correction factor is extended by a minimal
+distance (r\_min = 1.0-6) when the interaction between a core/shell
+pair is treated, as follows
+
+.. image:: Eqs/pair_cs.jpg
+   :align: center
+
+where C is an energy-conversion constant, Qi and Qj are the charges on
+the core and shell, epsilon is the dielectric constant and r\_min is the
+minimal distance.
+
+For styles that are not used with a long-range solver, i.e. those with
+"/dsf" or "/wolf" in the name, the only correction is the addition of
+a minimal distance to avoid the possible r = 0.0 case for a core/shell
+pair.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+See the corresponding doc pages for pair styles without the "cs"
+suffix to see how mixing, shifting, tabulation, tail correction,
+restarting, and rRESPA are handled by theses pair styles.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles are part of the CORESHELL package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style born <pair_born>`,
+:doc:`pair\_style buck <pair_buck>`
+
+**Default:** none
+
+
+----------
+
+
+.. _MitchellFinchham2:
+
+
+
+**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst
new file mode 100644
index 0000000000..fc7de92900
--- /dev/null
+++ b/doc/src/pair_dipole.rst
@@ -0,0 +1,321 @@
+.. index:: pair\_style lj/cut/dipole/cut
+
+pair\_style lj/cut/dipole/cut command
+=====================================
+
+pair\_style lj/cut/dipole/cut/gpu command
+=========================================
+
+pair\_style lj/cut/dipole/cut/omp command
+=========================================
+
+pair\_style lj/sf/dipole/sf command
+===================================
+
+pair\_style lj/sf/dipole/sf/gpu command
+=======================================
+
+pair\_style lj/sf/dipole/sf/omp command
+=======================================
+
+pair\_style lj/cut/dipole/long command
+======================================
+
+pair\_style lj/cut/dipole/long/gpu command
+==========================================
+
+pair\_style lj/long/dipole/long command
+=======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/dipole/cut cutoff (cutoff2)
+   pair_style lj/sf/dipole/sf cutoff (cutoff2)
+   pair_style lj/cut/dipole/long cutoff (cutoff2)
+   pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)
+
+* cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)
+* cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units)
+* flag\_lj = *long* or *cut* or *off*
+  
+  .. parsed-literal::
+  
+       *long* = use long-range damping on dispersion 1/r\^6 term
+       *cut* = use a cutoff on dispersion 1/r\^6 term
+       *off* = omit disperion 1/r\^6 term entirely
+
+* flag\_coul = *long* or *off*
+  
+  .. parsed-literal::
+  
+       *long* = use long-range damping on Coulombic 1/r and point-dipole terms
+       *off* = omit Coulombic and point-dipole terms entirely
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/dipole/cut 10.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 2 3 1.0 1.0 2.5 4.0
+
+   pair_style lj/sf/dipole/sf 9.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
+   pair_coeff 2 3 1.0 1.0 2.5 4.0
+
+   pair_style lj/cut/dipole/long 10.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 2 3 1.0 1.0 2.5 4.0
+
+   pair_style lj/long/dipole/long long long 3.5 10.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 2 3 1.0 1.0 2.5 4.0
+
+Description
+"""""""""""
+
+Style *lj/cut/dipole/cut* computes interactions between pairs of particles
+that each have a charge and/or a point dipole moment.  In addition to
+the usual Lennard-Jones interaction between the particles (Elj) the
+charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp)
+interactions are computed by these formulas for the energy (E), force
+(F), and torque (T) between particles I and J.
+
+.. image:: Eqs/pair_dipole.jpg
+   :align: center
+
+where qi and qj are the charges on the two particles, pi and pj are
+the dipole moment vectors of the two particles, r is their separation
+distance, and the vector r = Ri - Rj is the separation vector between
+the two particles.  Note that Eqq and Fqq are simply Coulombic energy
+and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
+torques do not act symmetrically.  These formulas are discussed in
+:ref:`(Allen) <Allen2>` and in :ref:`(Toukmaji) <Toukmaji2>`.
+
+Also note, that in the code, all of these terms (except Elj) have a
+C/epsilon prefactor, the same as the Coulombic term in the LJ +
+Coulombic pair styles discussed :doc:`here <pair_lj>`.  C is an
+energy-conversion constant and epsilon is the dielectric constant
+which can be set by the :doc:`dielectric <dielectric>` command.  The
+same is true of the equations that follow for other dipole pair
+styles.
+
+Style *lj/sf/dipole/sf* computes "shifted-force" interactions between
+pairs of particles that each have a charge and/or a point dipole
+moment. In general, a shifted-force potential is a (slightly) modified
+potential containing extra terms that make both the energy and its
+derivative go to zero at the cutoff distance; this removes
+(cutoff-related) problems in energy conservation and any numerical
+instability in the equations of motion :ref:`(Allen) <Allen2>`. Shifted-force
+interactions for the Lennard-Jones (E\_LJ), charge-charge (Eqq),
+charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp)
+potentials are computed by these formulas for the energy (E), force
+(F), and torque (T) between particles I and J:
+
+.. image:: Eqs/pair_dipole_sf.jpg
+   :align: center
+
+.. image:: Eqs/pair_dipole_sf2.jpg
+   :align: center
+
+where epsilon and sigma are the standard LJ parameters, r\_c is the
+cutoff, qi and qj are the charges on the two particles, pi and pj are
+the dipole moment vectors of the two particles, r is their separation
+distance, and the vector r = Ri - Rj is the separation vector between
+the two particles.  Note that Eqq and Fqq are simply Coulombic energy
+and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
+torques do not act symmetrically.  The shifted-force formula for the
+Lennard-Jones potential is reported in :ref:`(Stoddard) <Stoddard>`.  The
+original (non-shifted) formulas for the electrostatic potentials,
+forces and torques can be found in :ref:`(Price) <Price2>`. The shifted-force
+electrostatic potentials have been obtained by applying equation 5.13
+of :ref:`(Allen) <Allen2>`. The formulas for the corresponding forces and
+torques have been obtained by applying the 'chain rule' as in appendix
+C.3 of :ref:`(Allen) <Allen2>`.
+
+If one cutoff is specified in the pair\_style command, it is used for
+both the LJ and Coulombic (q,p) terms.  If two cutoffs are specified,
+they are used as cutoffs for the LJ and Coulombic (q,p) terms
+respectively. This pair style also supports an optional *scale* keyword
+as part of a pair\_coeff statement, where the interactions can be
+scaled according to this factor. This scale factor is also made available
+for use with fix adapt.
+
+Style *lj/cut/dipole/long* computes long-range point-dipole
+interactions as discussed in :ref:`(Toukmaji) <Toukmaji2>`. Dipole-dipole,
+dipole-charge, and charge-charge interactions are all supported, along
+with the standard 12/6 Lennard-Jones interactions, which are computed
+with a cutoff.  A :doc:`kspace\_style <kspace_style>` must be defined to
+use this pair style.  Currently, only :doc:`kspace\_style ewald/disp <kspace_style>` support long-range point-dipole
+interactions.
+
+Style *lj/long/dipole/long* also computes point-dipole interactions as
+discussed in :ref:`(Toukmaji) <Toukmaji2>`. Long-range dipole-dipole,
+dipole-charge, and charge-charge interactions are all supported, along
+with the standard 12/6 Lennard-Jones interactions.  LJ interactions
+can be cutoff or long-ranged.
+
+For style *lj/long/dipole/long*\ , if *flag\_lj* is set to *long*\ , no
+cutoff is used on the LJ 1/r\^6 dispersion term.  The long-range
+portion is calculated by using the :doc:`kspace\_style ewald\_disp <kspace_style>` command.  The specified LJ cutoff then
+determines which portion of the LJ interactions are computed directly
+by the pair potential versus which part is computed in reciprocal
+space via the Kspace style.  If *flag\_lj* is set to *cut*\ , the LJ
+interactions are simply cutoff, as with :doc:`pair\_style lj/cut <pair_lj>`.  If *flag\_lj* is set to *off*\ , LJ interactions
+are not computed at all.
+
+If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic or
+dipole interactions.  The long-range portion is calculated by using
+*ewald\_disp* of the :doc:`kspace\_style <kspace_style>` command. If
+*flag\_coul* is set to *off*\ , Coulombic and dipole interactions are not
+computed at all.
+
+Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere update dipole <fix_nve_sphere>` or the :doc:`fix nvt/sphere update dipole <fix_nvt_sphere>` command to rotate the
+dipole moments.  The *omega* option on the :doc:`fix langevin <fix_langevin>` command can be used to thermostat the
+rotational motion.  The :doc:`compute temp/sphere <compute_temp_sphere>`
+command can be used to monitor the temperature, since it includes
+rotational degrees of freedom.  The :doc:`atom\_style hybrid dipole sphere <atom_style>` command should be used since
+it defines the point dipoles and their rotational state.
+The magnitude and orientation of the dipole moment for each particle
+can be defined by the :doc:`set <set>` command or in the "Atoms" section
+of the data file read in by the :doc:`read\_data <read_data>` command.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff1 (distance units)
+* cutoff2 (distance units)
+
+The latter 2 coefficients are optional.  If not specified, the global
+LJ and Coulombic cutoffs specified in the pair\_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair.  If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distances for this pair style can be mixed.  The default
+mix value is *geometric*\ .  See the "pair\_modify" command for details.
+
+For atom type pairs I,J and I != J, the A, sigma, d1, and d2
+coefficients and cutoff distance for this pair style can be mixed.  A
+is an energy value mixed like a LJ epsilon.  D1 and d2 are distance
+values and are mixed like sigma.  The default mix value is
+*geometric*\ .  See the "pair\_modify" command for details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the Lennard-Jones portion of the pair
+interaction; such energy goes to zero at the cutoff by construction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+The *lj/cut/dipole/cut*\ , *lj/cut/dipole/long*\ , and
+*lj/long/dipole/long* styles are part of the DIPOLE package.  They are
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The *lj/sf/dipole/sf* style is part of the USER-MISC package.  It is
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Using dipole pair styles with *electron* :doc:`units <units>` is not
+currently supported.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`set <set>`, :doc:`read\_data <read_data>`,
+:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Allen2:
+
+
+
+**(Allen)** Allen and Tildesley, Computer Simulation of Liquids,
+Clarendon Press, Oxford, 1987.
+
+.. _Toukmaji2:
+
+
+
+**(Toukmaji)** Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
+10913 (2000).
+
+.. _Stoddard:
+
+
+
+**(Stoddard)** Stoddard and Ford, Phys Rev A, 8, 1504 (1973).
+
+.. _Price2:
+
+
+
+**(Price)** Price, Stone and Alderton, Mol Phys, 52, 987 (1984).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst
new file mode 100644
index 0000000000..439e41d93b
--- /dev/null
+++ b/doc/src/pair_dpd.rst
@@ -0,0 +1,248 @@
+.. index:: pair\_style dpd
+
+pair\_style dpd command
+=======================
+
+pair\_style dpd/gpu command
+===========================
+
+pair\_style dpd/intel command
+=============================
+
+pair\_style dpd/omp command
+===========================
+
+pair\_style dpd/tstat command
+=============================
+
+pair\_style dpd/tstat/gpu command
+=================================
+
+pair\_style dpd/tstat/omp command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style dpd T cutoff seed
+   pair_style dpd/tstat Tstart Tstop cutoff seed
+
+* T = temperature (temperature units)
+* Tstart,Tstop = desired temperature at start/end of run (temperature units)
+* cutoff = global cutoff for DPD interactions (distance units)
+* seed = random # seed (positive integer)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style dpd 1.0 2.5 34387
+   pair_coeff \* \* 3.0 1.0
+   pair_coeff 1 1 3.0 1.0 1.0
+
+   pair_style dpd/tstat 1.0 1.0 2.5 34387
+   pair_coeff \* \* 1.0
+   pair_coeff 1 1 1.0 1.0
+
+Description
+"""""""""""
+
+Style *dpd* computes a force field for dissipative particle dynamics
+(DPD) following the exposition in :ref:`(Groot) <Groot1>`.
+
+Style *dpd/tstat* invokes a DPD thermostat on pairwise interactions,
+which is equivalent to the non-conservative portion of the DPD force
+field.  This pair-wise thermostat can be used in conjunction with any
+:doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
+like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
+Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`.  To use
+*dpd/tstat* as a thermostat for another pair style, use the :doc:`pair\_style hybrid/overlay <pair_hybrid>` command to compute both the desired
+pair interaction and the thermostat for each pair of particles.
+
+For style *dpd*\ , the force on atom I due to atom J is given as a sum
+of 3 terms
+
+.. image:: Eqs/pair_dpd.jpg
+   :align: center
+
+where Fc is a conservative force, Fd is a dissipative force, and Fr is
+a random force.  Rij is a unit vector in the direction Ri - Rj, Vij is
+the vector difference in velocities of the two atoms = Vi - Vj, alpha
+is a Gaussian random number with zero mean and unit variance, dt is
+the timestep size, and w(r) is a weighting factor that varies between
+0 and 1.  Rc is the cutoff.  Sigma is set equal to sqrt(2 Kb T gamma),
+where Kb is the Boltzmann constant and T is the temperature parameter
+in the pair\_style command.
+
+For style *dpd/tstat*\ , the force on atom I due to atom J is the same
+as the above equation, except that the conservative Fc term is
+dropped.  Also, during the run, T is set each timestep to a ramped
+value from Tstart to Tstop.
+
+For style *dpd*\ , the pairwise energy associated with style *dpd* is
+only due to the conservative force term Fc, and is shifted to be zero
+at the cutoff distance Rc.  The pairwise virial is calculated using
+all 3 terms.  For style *dpd/tstat* there is no pairwise energy, but
+the last two terms of the formula make a contribution to the virial.
+
+For style *dpd*\ , the following coefficients must be defined for each
+pair of atoms types via the :doc:`pair\_coeff <pair_coeff>` command as in
+the examples above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* A (force units)
+* gamma (force/velocity units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global DPD
+cutoff is used.  Note that sigma is set equal to sqrt(2 T gamma),
+where T is the temperature set by the :doc:`pair\_style <pair_style>`
+command so it does not need to be specified.
+
+For style *dpd/tstat*\ , the coefficients defined for each pair of
+atoms types via the :doc:`pair\_coeff <pair_coeff>` command is the same,
+except that A is not included.
+
+The GPU-accelerated versions of these styles are implemented based on
+the work of :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`.
+
+.. note::
+
+   If you are modeling DPD polymer chains, you may want to use the
+   :doc:`pair\_style srp <pair_srp>` command in conjunction with these pair
+   styles.  It is a soft segmental repulsive potential (SRP) that can
+   prevent DPD polymer chains from crossing each other.
+
+.. note::
+
+   The virial calculation for pressure when using this pair style
+   includes all the components of force listed above, including the
+   random force.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+These pair styles do not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+These pair styles do not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the pair interaction.  Note that as
+discussed above, the energy due to the conservative Fc term is already
+shifted to be 0.0 at the cutoff distance Rc.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for these pair styles.
+
+These pair style do not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+These pair styles writes their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.  Note
+that the user-specified random number seed is stored in the restart
+file, so when a simulation is restarted, each processor will
+re-initialize its random number generator the same way it did
+initially.  This means the random forces will be random, but will not
+be the same as they would have been if the original simulation had
+continued past the restart time.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+The *dpd/tstat* style can ramp its target temperature over multiple
+runs, using the *start* and *stop* keywords of the :doc:`run <run>`
+command.  See the :doc:`run <run>` command for details of how to do
+this.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The default frequency for rebuilding neighbor lists is every 10 steps
+(see the :doc:`neigh\_modify <neigh_modify>` command). This may be too
+infrequent for style *dpd* simulations since particles move rapidly
+and can overlap by large amounts.  If this setting yields a non-zero
+number of "dangerous" reneighborings (printed at the end of a
+simulation), you should experiment with forcing reneighboring more
+often and see if system energies/trajectories change.
+
+These pair styles requires you to use the :doc:`comm\_modify vel yes <comm_modify>` command so that velocities are stored by ghost
+atoms.
+
+These pair styles will not restart exactly when using the
+:doc:`read\_restart <read_restart>` command, though they should provide
+statistically similar results.  This is because the forces they
+compute depend on atom velocities.  See the
+:doc:`read\_restart <read_restart>` command for more details.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`pair\_style srp <pair_srp>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Groot1:
+
+
+
+**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
+
+.. _Afshar:
+
+
+
+**(Afshar)** Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys
+Comm, 184, 1119-1128 (2013).
+
+.. _Phillips:
+
+
+
+**(Phillips)** C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput
+Phys Comm, 230, 7191-7201 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst
new file mode 100644
index 0000000000..c0d4f8c0c4
--- /dev/null
+++ b/doc/src/pair_dpd_fdt.rst
@@ -0,0 +1,207 @@
+.. index:: pair\_style dpd/fdt
+
+pair\_style dpd/fdt command
+===========================
+
+pair\_style dpd/fdt/energy command
+==================================
+
+pair\_style dpd/fdt/energy/kk command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *dpd/fdt* or *dpd/fdt/energy*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *dpd/fdt* args = T cutoff seed
+       T = temperature (temperature units)
+       cutoff = global cutoff for DPD interactions (distance units)
+       seed = random # seed (positive integer)
+     *dpd/fdt/energy* args = cutoff seed
+       cutoff = global cutoff for DPD interactions (distance units)
+       seed = random # seed (positive integer)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style dpd/fdt 300.0 2.5 34387
+   pair_coeff \* \* 3.0 1.0 2.5
+
+   pair_style dpd/fdt/energy 2.5 34387
+   pair_coeff \* \* 3.0 1.0 0.1 2.5
+
+Description
+"""""""""""
+
+Styles *dpd/fdt* and *dpd/fdt/energy* compute the force for dissipative
+particle dynamics (DPD) simulations.  The *dpd/fdt* style is used to
+perform DPD simulations under isothermal and isobaric conditions,
+while the *dpd/fdt/energy* style is used to perform DPD simulations
+under isoenergetic and isoenthalpic conditions (see :ref:`(Lisal) <Lisal3>`).
+For DPD simulations in general, the force on atom I due to atom J is
+given as a sum of 3 terms
+
+.. image:: Eqs/pair_dpd.jpg
+   :align: center
+
+where Fc is a conservative force, Fd is a dissipative force, and Fr is
+a random force.  Rij is a unit vector in the direction Ri - Rj, Vij is
+the vector difference in velocities of the two atoms = Vi - Vj, alpha
+is a Gaussian random number with zero mean and unit variance, dt is
+the timestep size, and w(r) is a weighting factor that varies between
+0 and 1.  Rc is the cutoff.  The weighting factor, omega\_ij, varies
+between 0 and 1, and is chosen to have the following functional form:
+
+.. image:: Eqs/pair_dpd_omega.jpg
+   :align: center
+
+Note that alternative definitions of the weighting function exist, but
+would have to be implemented as a separate pair style command.
+
+For style *dpd/fdt*\ , the fluctuation-dissipation theorem defines gamma
+to be set equal to sigma\*sigma/(2 T), where T is the set point
+temperature specified as a pair style parameter in the above examples.
+The following coefficients must be defined for each pair of atoms types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` commands:
+
+* A (force units)
+* sigma (force\*time\^(1/2) units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global DPD
+cutoff is used.
+
+Style *dpd/fdt/energy* is used to perform DPD simulations
+under isoenergetic and isoenthalpic conditions.  The fluctuation-dissipation
+theorem defines gamma to be set equal to sigma\*sigma/(2 dpdTheta), where
+dpdTheta is the average internal temperature for the pair. The particle
+internal temperature is related to the particle internal energy through
+a mesoparticle equation of state (see :doc:`fix eos <fix>`). The
+differential internal conductive and mechanical energies are computed
+within style *dpd/fdt/energy* as:
+
+.. image:: Eqs/pair_dpd_energy.jpg
+   :align: center
+
+where
+
+.. image:: Eqs/pair_dpd_energy_terms.jpg
+   :align: center
+
+Zeta\_ij\^q is a second Gaussian random number with zero mean and unit
+variance that is used to compute the internal conductive energy. The
+fluctuation-dissipation theorem defines alpha\*alpha to be set
+equal to 2\*kB\*kappa, where kappa is the mesoparticle thermal
+conductivity parameter.   The following coefficients must be defined for
+each pair of atoms types via the :doc:`pair\_coeff <pair_coeff>`
+command as in the examples above, or in the data file or restart files
+read by the :doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* A (force units)
+* sigma (force\*time\^(1/2) units)
+* kappa (energy\*temperature/time units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global DPD
+cutoff is used.
+
+The pairwise energy associated with styles *dpd/fdt* and
+*dpd/fdt/energy* is only due to the conservative force term Fc, and is
+shifted to be zero at the cutoff distance Rc.  The pairwise virial is
+calculated using only the conservative term.
+
+The forces computed through the *dpd/fdt* and *dpd/fdt/energy* styles
+can be integrated with the velocity-Verlet integration scheme or the
+Shardlow splitting integration scheme described by :ref:`(Lisal) <Lisal3>`.
+In the cases when these pair styles are combined with the
+:doc:`fix shardlow <fix_shardlow>`, these pair styles differ from the
+other dpd styles in that the dissipative and random forces are split
+from the force calculation and are not computed within the pair style.
+Thus, only the conservative force is computed by the pair style,
+while the stochastic integration of the dissipative and random forces
+are handled through the Shardlow splitting algorithm approach.  The
+Shardlow splitting algorithm is advantageous, especially when
+performing DPD under isoenergetic conditions, as it allows
+significantly larger timesteps to be taken.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These commands are part of the USER-DPD package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Pair styles *dpd/fdt* and *dpd/fdt/energy* require use of the
+:doc:`comm\_modify vel yes <comm_modify>` option so that velocities are
+stored by ghost atoms.
+
+Pair style *dpd/fdt/energy* requires :doc:`atom\_style dpd <atom_style>`
+to be used in order to properly account for the particle internal
+energies and temperatures.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix shardlow <fix_shardlow>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Lisal3:
+
+
+
+**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
+particle dynamics at isothermal, isobaric, isoenergetic, and
+isoenthalpic conditions using Shardlow-like splitting algorithms.",
+J. Chem. Phys., 135, 204105 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst
new file mode 100644
index 0000000000..270afb8dbd
--- /dev/null
+++ b/doc/src/pair_drip.rst
@@ -0,0 +1,167 @@
+.. index:: pair\_style drip
+
+pair\_style drip command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay drip [styles ...]
+
+* styles = other styles to be overlayed with drip (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay drip
+   pair_coeff \* \* none
+   pair_coeff \* \* drip  C.drip  C
+
+   pair_style hybrid/overlay drip rebo
+   pair_coeff \* \* drip  C.drip     C
+   pair_coeff \* \* rebo  CH.airebo  C
+
+   pair_style hybrid/overlay drip rebo
+   pair_coeff \* \* drip  C.drip     C NULL
+   pair_coeff \* \* rebo  CH.airebo  C H
+
+Description
+"""""""""""
+
+Style *drip* computes the interlayer interactions of layered materials using
+the dihedral-angle-corrected registry-dependent (DRIP) potential as described
+in :ref:`(Wen) <Wen2018>`, which is based on the :ref:`(Kolmogorov) <Kolmogorov2005>`
+potential and provides an improved prediction for forces.
+The total potential energy of a system is
+
+.. image:: Eqs/pair_drip.jpg
+   :align: center
+
+where the *r\^-6* term models the attractive London dispersion,
+the exponential term is designed to capture the registry effect due to
+overlapping *pi* bonds, and *fc* is a cutoff function.
+
+This potential (DRIP) only provides the interlayer interactions between
+graphene layers. So, to perform a realistic simulation, it should be used in
+combination with an intralayer potential such as :doc:`REBO <pair_airebo>` and
+:doc:`Tersoff <pair_tersoff>`.
+To keep the intralayer interactions unaffected, we should avoid applying DRIP
+to contribute energy to intralayer interactions. This can be achieved by
+assigning different molecular IDs to atoms in different layers, and DRIP is
+implemented such that only atoms with different molecular ID can interact with
+each other. For this purpose, :doc:`atom style <atom_style>` "molecular" or
+"full" has to be used.
+
+On the other way around, :doc:`REBO <pair_airebo>` (:doc:`Tersoff <pair_tersoff>`
+or any other potential used to provide the intralayer interactions) should not
+interfere with the interlayer interactions described by DRIP. This is typically
+automatically achieved using the commands provided in the *Examples* section
+above, since the cutoff distance for carbon-carbon interaction in the intralayer
+potentials (e.g. 2 Angstrom for :doc:`REBO <pair_airebo>`) is much smaller than
+the equilibrium layer distance of graphene layers (about 3.4 Angstrom).
+If you want, you can enforce this by assigning different atom types to atoms in
+different layers, and apply an intralayer potential to one atom type.
+See :doc:`pair\_hybrid <pair_hybrid>` for details.
+
+
+----------
+
+
+The :doc:`pair\_coeff <pair_coeff>` command for DRIP takes *4+N* arguments, where
+*N* is the number of LAMMPS atom types. The fist three arguments must be fixed
+to be *\* \* drip*, the fourth argument is the path to the DRIP parameter file,
+and the remaining N arguments specifying the mapping between element in the
+parameter file and atom types. For example, if your LAMMPS simulation has 3 atom
+types and you want all of them to be C, you would use the following pair\_coeff
+command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* drip  C.drip  C C C
+
+If a mapping value is specified as NULL, the mapping is not performed. This
+could be useful when DRIP is used to model part of the system where other
+element exists. Suppose you have a hydrocarbon system, with C of atom type 1
+and H of atom type 2, you can use the following command to inform DRIP not to
+model H atoms:
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay drip rebo
+   pair_coeff \* \* drip  C.drip     C NULL
+   pair_coeff \* \* rebo  CH.airebo  C H
+
+.. note::
+
+   The potential parameters developed in :ref:`(Wen) <Wen2018>` are provided with
+   LAMMPS (see the "potentials" directory). Besides those in :ref:`Wen <Wen2018>`, an
+   additional parameter "normal\_cutoff", specific to the LAMMPS implementation, is
+   used to find the three nearest neighbors of an atom to construct the normal.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, and restart info**\ :
+
+This pair style does not support the pair\_modify mix, shift, table,
+and tail options.
+
+This pair style does not write their information to binary restart files, since
+it is stored in potential files. Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-MISC package. It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+This pair potential requires the :doc:`newton <newton>` setting to be "on" for
+pair interactions.
+
+The *C.drip* parameter file provided with LAMMPS (see the "potentials"
+directory) is parameterized for metal :doc:`units <units>`. You can use the DRIP
+potential with any LAMMPS units, but you would need to create your own custom
+parameter file with coefficients listed in the appropriate units, if your
+simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style lebedeva\_z <pair_lebedeva_z>`,
+:doc:`pair\_style kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`,
+:doc:`pair\_style kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`,
+:doc:`pair\_style ilp/graphene/hbn <pair_ilp_graphene_hbn>`.
+
+
+----------
+
+
+.. _Wen2018:
+
+
+
+**(Wen)** M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B,
+98, 235404 (2018)
+
+.. _Kolmogorov2005:
+
+
+
+**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst
new file mode 100644
index 0000000000..38093d00e8
--- /dev/null
+++ b/doc/src/pair_dsmc.rst
@@ -0,0 +1,178 @@
+.. index:: pair\_style dsmc
+
+pair\_style dsmc command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
+
+* max\_cell\_size = global maximum cell size for DSMC interactions (distance units)
+* seed = random # seed (positive integer)
+* weighting = macroparticle weighting
+* Tref = reference temperature (temperature units)
+* Nrecompute = re-compute v\*sigma\_max every this many timesteps (timesteps)
+* Nsample = sample this many times in recomputing v\*sigma\_max
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style dsmc 2.5 34387 10 1.0 100 20
+   pair_coeff \* \* 1.0
+   pair_coeff 1 1 1.0
+
+Description
+"""""""""""
+
+Style *dsmc* computes collisions between pairs of particles for a
+direct simulation Monte Carlo (DSMC) model following the exposition in
+:ref:`(Bird) <Bird>`.  Each collision resets the velocities of the two
+particles involved.  The number of pairwise collisions for each pair
+or particle types and the length scale within which they occur are
+determined by the parameters of the pair\_style and pair\_coeff
+commands.
+
+Stochastic collisions are performed using the variable hard sphere
+(VHS) approach, with the user-defined *max\_cell\_size* value used as
+the maximum DSMC cell size, and reference cross-sections for
+collisions given using the pair\_coeff command.
+
+There is no pairwise energy or virial contributions associated with
+this pair style.
+
+The following coefficient must be defined for each pair of atoms types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* sigma (area units, i.e. distance-squared)
+
+The global DSMC *max\_cell\_size* determines the maximum cell length
+used in the DSMC calculation.  A structured mesh is overlayed on the
+simulation box such that an integer number of cells are created in
+each direction for each processor's sub-domain.  Cell lengths are
+adjusted up to the user-specified maximum cell size.
+
+
+----------
+
+
+To perform a DSMC simulation with LAMMPS, several additional options
+should be set in your input script, though LAMMPS does not check for
+these settings.
+
+Since this pair style does not compute particle forces, you should use
+the "fix nve/noforce" time integration fix for the DSMC particles,
+e.g.
+
+
+.. parsed-literal::
+
+   fix 1 all nve/noforce
+
+This pair style assumes that all particles will communicated to
+neighboring processors every timestep as they move.  This makes it
+possible to perform all collisions between pairs of particles that are
+on the same processor.  To ensure this occurs, you should use
+these commands:
+
+
+.. parsed-literal::
+
+   neighbor 0.0 bin
+   neigh_modify every 1 delay 0 check no
+   atom_modify sort 0 0.0
+   communicate single cutoff 0.0
+
+These commands ensure that LAMMPS communicates particles to
+neighboring processors every timestep and that no ghost atoms are
+created.  The output statistics for a simulation run should indicate
+there are no ghost particles or neighbors.
+
+In order to get correct DSMC collision statistics, users should
+specify a Gaussian velocity distribution when populating the
+simulation domain. Note that the default velocity distribution is
+uniform, which will not give good DSMC collision rates. Specify
+"dist gaussian" when using the :doc:`velocity <velocity>` command
+as in the following:
+
+
+.. parsed-literal::
+
+   velocity all create 594.6 87287 loop geom dist gaussian
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.  Note
+that the user-specified random number seed is stored in the restart
+file, so when a simulation is restarted, each processor will
+re-initialize its random number generator the same way it did
+initially.  This means the random forces will be random, but will not
+be the same as they would have been if the original simulation had
+continued past the restart time.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the MC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix nve/noforce <fix_nve_noforce>`,
+:doc:`neigh\_modify <neigh_modify>`, :doc:`neighbor <neighbor>`,
+:doc:`comm\_modify <comm_modify>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Bird:
+
+
+
+**(Bird)** G. A. Bird, "Molecular Gas Dynamics and the Direct Simulation
+of Gas Flows" (1994).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst
new file mode 100644
index 0000000000..73afdd7f53
--- /dev/null
+++ b/doc/src/pair_e3b.rst
@@ -0,0 +1,176 @@
+.. index:: pair\_style e3b
+
+pair\_style e3b command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style e3b Otype
+
+* Otype = atom type for oxygen
+
+.. parsed-literal::
+
+   pair_coeff \* \* keyword
+
+* one or more keyword/value pairs must be appended.
+* keyword = *preset* or *Ea* or *Eb* or *Ec* or *E2* or *K3* or *K2* or *Rs* or *Rc3* or *Rc2* or *bondL* or *neigh*
+* If the *preset* keyword is given, no others are needed.
+  Otherwise, all are mandatory except for *neigh*\ .
+  The *neigh* keyword is always optional.
+
+.. parsed-literal::
+
+     *preset* arg = *2011* or *2015* = which set of predefined parameters to use
+              2011 = use the potential parameters from :ref:`(Tainter 2011) <Tainter2011>`
+              2015 = use the potential parameters from :ref:`(Tainter 2015) <Tainter2015>`
+     *Ea* arg = three-body energy for type A hydrogen bonding interactions (energy units)
+     *Eb* arg = three-body energy for type B hydrogen bonding interactions (energy units)
+     *Ec* arg = three-body energy for type C hydrogen bonding interactions (energy units)
+     *E2* arg = two-body energy correction (energy units)
+     *K3* arg = three-body exponential constant (inverse distance units)
+     *K2* arg = two-body exponential constant (inverse distance units)
+     *Rc3* arg = three-body cutoff (distance units)
+     *Rc2* arg = two-body cutoff (distance units)
+     *Rs* arg = three-body switching function cutoff (distance units)
+     *bondL* arg = intramolecular OH bond length (distance units)
+     *neigh* arg = approximate integer number of molecules within Rc3 of an oxygen atom
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style e3b 1
+   pair_coeff \* \* Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572
+
+   pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
+   pair_coeff \* \* e3b preset 2011
+
+Description
+"""""""""""
+
+The *e3b* style computes an \"explicit three-body\" (E3B) potential for water :ref:`(Kumar 2008) <Kumar>`.
+
+.. image:: Eqs/e3b.jpg
+   :align: center
+
+This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly.
+To use it in this way, it must be applied in conjunction with a conventional two-body water model, through *pair\_style hybrid/overlay*.
+The three body interactions are split into three types: A, B, and C.
+Type A corresponds to anti-cooperative double hydrogen bond donor interactions.
+Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond.
+Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions.
+The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3.
+The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential.
+The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2.
+See :ref:`(Kumar 2008) <Kumar>` for more details.
+
+Only a single *pair\_coeff* command is used with the *e3b* style.
+The 1st two arguments must be \* \*.
+The oxygen atom type for the pair style is passed as the only argument to the *pair\_style* command, not in the *pair\_coeff* command.
+The hydrogen atom type is inferred by the ordering of the atoms.
+
+.. note::
+
+   Every atom of type Otype must be part of a water molecule.
+   Each water molecule must have consecutive IDs with the oxygen first.
+   This pair style does not test that this criteria is met.
+
+The *pair\_coeff* command must have at least one keyword/value pair, as described above.
+The *preset* keyword sets the potential parameters to the values used in :ref:`(Tainter 2011) <Tainter2011>` or :ref:`(Tainter 2015) <Tainter2015>`.
+To use the water models defined in those references, the *e3b* style should always be used in conjunction with an *lj/cut/tip4p/long* style through *pair\_style hybrid/overlay*, as demonstrated in the second example above.
+The *preset 2011* option should be used with the :doc:`TIP4P water model <Howto_tip4p>`.
+The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model <Howto_tip4p>`.
+If the *preset* keyword is used, no other keyword is needed.
+Changes to the preset parameters can be made by specifying the *preset* keyword followed by the specific parameter to change, like *Ea*\ .
+Note that the other keywords must come after *preset* in the pair\_style command.
+The *e3b* style can also be used to implement any three-body potential of the same form by specifying all the keywords except *neigh*\ : *Ea*\ , *Eb*\ , *Ec*\ , *E2*\ , *K3*\ , *K2*\ , *Rc3*\ , *Rc2*\ , *Rs*\ , and *bondL*\ .
+The keyword *bondL* specifies the intramolecular OH bond length of the water model being used.
+This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not.
+
+This pair style allocates arrays sized according to the number of pairwise interactions within Rc3.
+To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom.
+This estimate defaults to 10 and can be changed using the *neigh* keyword, which takes an integer as an argument.
+If the neigh setting is too small, the simulation will fail with the error "neigh is too small".
+If the neigh setting is too large, the pair style will use more memory than necessary.
+
+This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 4.
+The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
+
+See the examples/USER/e3b directory for a complete example script.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style is incompatible with :doc:`respa <run_style>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-MISC package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+This pair style requires a fixed number of atoms in the simulation, so it is incompatible with fixes like :doc:`fix deposit <fix_deposit>`.
+If the number of atoms changes between runs, this pair style must be re-initialized by calling the *pair\_style* and *pair\_coeffs* commands.
+This is not a fundamental limitation of the pair style, but the code currently does not support a variable number of atoms.
+
+The *preset* keyword currently only works with real, metal, si, and cgs :doc:`units <units>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`compute pair <compute_pair>`
+
+Default
+"""""""
+
+The option default for the *neigh* keyword is 10.
+
+
+----------
+
+
+.. _Kumar:
+
+
+
+.. _Tainter2011:
+
+**(Kumar)** Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
+
+
+.. _Tainter2015:
+
+**(Tainter 2011)** Tainter, Pieniazek, Lin, and Skinner, J. Chem. Phys., 134, 184501 (2011)
+
+
+**(Tainter 2015)** Tainter, Shi, and Skinner, 11, 2268 (2015)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst
new file mode 100644
index 0000000000..b367f00eb5
--- /dev/null
+++ b/doc/src/pair_eam.rst
@@ -0,0 +1,555 @@
+.. index:: pair\_style eam
+
+pair\_style eam command
+=======================
+
+pair\_style eam/gpu command
+===========================
+
+pair\_style eam/intel command
+=============================
+
+pair\_style eam/kk command
+==========================
+
+pair\_style eam/omp command
+===========================
+
+pair\_style eam/opt command
+===========================
+
+pair\_style eam/alloy command
+=============================
+
+pair\_style eam/alloy/gpu command
+=================================
+
+pair\_style eam/alloy/intel command
+===================================
+
+pair\_style eam/alloy/kk command
+================================
+
+pair\_style eam/alloy/omp command
+=================================
+
+pair\_style eam/alloy/opt command
+=================================
+
+pair\_style eam/cd command
+==========================
+
+pair\_style eam/cd/omp command
+==============================
+
+pair\_style eam/cd/old command
+==============================
+
+pair\_style eam/cd/old/omp command
+==================================
+
+pair\_style eam/fs command
+==========================
+
+pair\_style eam/fs/gpu command
+==============================
+
+pair\_style eam/fs/intel command
+================================
+
+pair\_style eam/fs/kk command
+=============================
+
+pair\_style eam/fs/omp command
+==============================
+
+pair\_style eam/fs/opt command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style
+
+* style = *eam* or *eam/alloy* or *eam/cd* or *eam/cd/old* or *eam/fs*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style eam
+   pair_coeff \* \* cuu3
+   pair_coeff 1\*3 1\*3 niu3.eam
+
+   pair_style eam/alloy
+   pair_coeff \* \* ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
+
+   pair_style eam/cd
+   pair_coeff \* \* ../potentials/FeCr.cdeam Fe Cr
+
+   pair_style eam/fs
+   pair_coeff \* \* NiAlH_jea.eam.fs Ni Al Ni Ni
+
+Description
+"""""""""""
+
+Style *eam* computes pairwise interactions for metals and metal alloys
+using embedded-atom method (EAM) potentials :ref:`(Daw) <Daw>`.  The total
+energy Ei of an atom I is given by
+
+.. image:: Eqs/pair_eam.jpg
+   :align: center
+
+where F is the embedding energy which is a function of the atomic
+electron density rho, phi is a pair potential interaction, and alpha
+and beta are the element types of atoms I and J.  The multi-body
+nature of the EAM potential is a result of the embedding energy term.
+Both summations in the formula are over all neighbors J of atom I
+within the cutoff distance.
+
+The cutoff distance and the tabulated values of the functionals F,
+rho, and phi are listed in one or more files which are specified by
+the :doc:`pair\_coeff <pair_coeff>` command.  These are ASCII text files
+in a DYNAMO-style format which is described below.  DYNAMO was the
+original serial EAM MD code, written by the EAM originators.  Several
+DYNAMO potential files for different metals are included in the
+"potentials" directory of the LAMMPS distribution.  All of these files
+are parameterized in terms of LAMMPS :doc:`metal units <units>`.
+
+.. note::
+
+   The *eam* style reads single-element EAM potentials in the
+   DYNAMO *funcfl* format.  Either single element or alloy systems can be
+   modeled using multiple *funcfl* files and style *eam*\ .  For the alloy
+   case LAMMPS mixes the single-element potentials to produce alloy
+   potentials, the same way that DYNAMO does.  Alternatively, a single
+   DYNAMO *setfl* file or Finnis/Sinclair EAM file can be used by LAMMPS
+   to model alloy systems by invoking the *eam/alloy* or *eam/cd* or
+   *eam/fs* styles as described below.  These files require no mixing
+   since they specify alloy interactions explicitly.
+
+.. note::
+
+   Note that unlike for other potentials, cutoffs for EAM
+   potentials are not set in the pair\_style or pair\_coeff command; they
+   are specified in the EAM potential files themselves.  Likewise, the
+   EAM potential files list atomic masses; thus you do not need to use
+   the :doc:`mass <mass>` command to specify them.
+
+There are several WWW sites that distribute and document EAM
+potentials stored in DYNAMO or other formats:
+
+
+.. parsed-literal::
+
+   http://www.ctcms.nist.gov/potentials
+   http://cst-www.nrl.navy.mil/ccm6/ap
+   http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
+
+These potentials should be usable with LAMMPS, though the alternate
+formats would need to be converted to the DYNAMO format used by LAMMPS
+and described on this page.  The NIST site is maintained by Chandler
+Becker (cbecker at nist.gov) who is good resource for info on
+interatomic potentials and file formats.
+
+
+----------
+
+
+For style *eam*\ , potential values are read from a file that is in the
+DYNAMO single-element *funcfl* format.  If the DYNAMO file was created
+by a Fortran program, it cannot have "D" values in it for exponents.
+C only recognizes "e" or "E" for scientific notation.
+
+Note that unlike for other potentials, cutoffs for EAM potentials are
+not set in the pair\_style or pair\_coeff command; they are specified in
+the EAM potential files themselves.
+
+For style *eam* a potential file must be assigned to each I,I pair of
+atom types by using one or more pair\_coeff commands, each with a
+single argument:
+
+* filename
+
+Thus the following command
+
+
+.. parsed-literal::
+
+   pair_coeff \*2 1\*2 cuu3.eam
+
+will read the cuu3 potential file and use the tabulated Cu values for
+F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
+1,2 and 2,1 are ignored).  See the :doc:`pair\_coeff <pair_coeff>` doc
+page for alternate ways to specify the path for the potential file.
+In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms.
+Different single-element files can be assigned to different atom types
+to model an alloy system.  The mixing to create alloy potentials for
+type pairs with I != J is done automatically the same way that the
+serial DYNAMO code originally did it; you do not need to specify
+coefficients for these type pairs.
+
+*Funcfl* files in the *potentials* directory of the LAMMPS
+distribution have an ".eam" suffix.  A DYNAMO single-element *funcfl*
+file is formatted as follows:
+
+* line 1: comment (ignored)
+* line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
+* line 3: Nrho, drho, Nr, dr, cutoff
+
+On line 2, all values but the mass are ignored by LAMMPS.  The mass is
+in mass :doc:`units <units>`, e.g. mass number or grams/mole for metal
+units.  The cubic lattice constant is in Angstroms.  On line 3, Nrho
+and Nr are the number of tabulated values in the subsequent arrays,
+drho and dr are the spacing in density and distance space for the
+values in those arrays, and the specified cutoff becomes the pairwise
+cutoff used by LAMMPS for the potential.  The units of dr are
+Angstroms; I'm not sure of the units for drho - some measure of
+electron density.
+
+Following the three header lines are three arrays of tabulated values:
+
+* embedding function F(rho) (Nrho values)
+* effective charge function Z(r) (Nr values)
+* density function rho(r) (Nr values)
+
+The values for each array can be listed as multiple values per line,
+so long as each array starts on a new line.  For example, the
+individual Z(r) values are for r = 0,dr,2\*dr, ... (Nr-1)\*dr.
+
+The units for the embedding function F are eV.  The units for the
+density function rho are the same as for drho (see above, electron
+density).  The units for the effective charge Z are "atomic charge" or
+sqrt(Hartree \* Bohr-radii).  For two interacting atoms i,j this is used
+by LAMMPS to compute the pair potential term in the EAM energy
+expression as r\*phi, in units of eV-Angstroms, via the formula
+
+
+.. parsed-literal::
+
+   r\*phi = 27.2 \* 0.529 \* Zi \* Zj
+
+where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
+
+
+----------
+
+
+Style *eam/alloy* computes pairwise interactions using the same
+formula as style *eam*\ .  However the associated
+:doc:`pair\_coeff <pair_coeff>` command reads a DYNAMO *setfl* file
+instead of a *funcfl* file.  *Setfl* files can be used to model a
+single-element or alloy system.  In the alloy case, as explained
+above, *setfl* files contain explicit tabulated values for alloy
+interactions.  Thus they allow more generality than *funcfl* files for
+modeling alloys.
+
+For style *eam/alloy*\ , potential values are read from a file that is
+in the DYNAMO multi-element *setfl* format, except that element names
+(Ni, Cu, etc) are added to one of the lines in the file.  If the
+DYNAMO file was created by a Fortran program, it cannot have "D"
+values in it for exponents.  C only recognizes "e" or "E" for
+scientific notation.
+
+Only a single pair\_coeff command is used with the *eam/alloy* style
+which specifies a DYNAMO *setfl* file, which contains information for
+M elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of *setfl* elements to atom types
+
+As an example, the potentials/NiAlH\_jea.eam.alloy file is a *setfl*
+file which has tabulated EAM values for 3 elements and their alloy
+interactions: Ni, Al, and H.  See the :doc:`pair\_coeff <pair_coeff>` doc
+page for alternate ways to specify the path for the potential file.
+If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to
+be Ni, and the 4th to be Al, you would use the following pair\_coeff
+command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* NiAlH_jea.eam.alloy Ni Ni Ni Al
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
+element in the *setfl* file.  The final Al argument maps LAMMPS atom
+type 4 to the Al element in the *setfl* file.  Note that there is no
+requirement that your simulation use all the elements specified by the
+*setfl* file.
+
+If a mapping value is specified as NULL, the mapping is not performed.
+This can be used when an *eam/alloy* potential is used as part of the
+*hybrid* pair style.  The NULL values are placeholders for atom types
+that will be used with other potentials.
+
+*Setfl* files in the *potentials* directory of the LAMMPS distribution
+have an ".eam.alloy" suffix.  A DYNAMO multi-element *setfl* file is
+formatted as follows:
+
+* lines 1,2,3 = comments (ignored)
+* line 4: Nelements Element1 Element2 ... ElementN
+* line 5: Nrho, drho, Nr, dr, cutoff
+
+In a DYNAMO *setfl* file, line 4 only lists Nelements = the # of
+elements in the *setfl* file.  For LAMMPS, the element name (Ni, Cu,
+etc) of each element must be added to the line, in the order the
+elements appear in the file.
+
+The meaning and units of the values in line 5 is the same as for the
+*funcfl* file described above.  Note that the cutoff (in Angstroms) is
+a global value, valid for all pairwise interactions for all element
+pairings.
+
+Following the 5 header lines are Nelements sections, one for each
+element, each with the following format:
+
+* line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
+* embedding function F(rho) (Nrho values)
+* density function rho(r) (Nr values)
+
+As with the *funcfl* files, only the mass (in mass :doc:`units <units>`,
+e.g. mass number or grams/mole for metal units) is used by LAMMPS from
+the 1st line.  The cubic lattice constant is in Angstroms.  The F and
+rho arrays are unique to a single element and have the same format and
+units as in a *funcfl* file.
+
+Following the Nelements sections, Nr values for each pair potential
+phi(r) array are listed for all i,j element pairs in the same format
+as other arrays.  Since these interactions are symmetric (i,j = j,i)
+only phi arrays with i >= j are listed, in the following order: i,j =
+(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
+Nelements).  Unlike the effective charge array Z(r) in *funcfl* files,
+the tabulated values for each phi function are listed in *setfl* files
+directly as r\*phi (in units of eV-Angstroms), since they are for atom
+pairs.
+
+
+----------
+
+
+Style *eam/cd* is similar to the *eam/alloy* style, except that it
+computes alloy pairwise interactions using the concentration-dependent
+embedded-atom method (CD-EAM).  This model can reproduce the enthalpy
+of mixing of alloys over the full composition range, as described in
+:ref:`(Stukowski) <Stukowski>`. Style *eam/cd/old* is an older, slightly
+different and slower two-site formulation of the model :ref:`(Caro) <Caro>`.
+
+The pair\_coeff command is specified the same as for the *eam/alloy*
+style.  However the DYNAMO *setfl* file must has two
+lines added to it, at the end of the file:
+
+* line 1: Comment line (ignored)
+* line 2: N Coefficient0 Coefficient1 ... CoefficientN
+
+The last line begins with the degree *N* of the polynomial function
+*h(x)* that modifies the cross interaction between A and B elements.
+Then *N+1* coefficients for the terms of the polynomial are then
+listed.
+
+Modified EAM *setfl* files used with the *eam/cd* style must contain
+exactly two elements, i.e. in the current implementation the *eam/cd*
+style only supports binary alloys.  The first and second elements in
+the input EAM file are always taken as the *A* and *B* species.
+
+*CD-EAM* files in the *potentials* directory of the LAMMPS
+distribution have a ".cdeam" suffix.
+
+
+----------
+
+
+Style *eam/fs* computes pairwise interactions for metals and metal
+alloys using a generalized form of EAM potentials due to Finnis and
+Sinclair :ref:`(Finnis) <Finnis1>`.  The total energy Ei of an atom I is
+given by
+
+.. image:: Eqs/pair_eam_fs.jpg
+   :align: center
+
+This has the same form as the EAM formula above, except that rho is
+now a functional specific to the atomic types of both atoms I and J,
+so that different elements can contribute differently to the total
+electron density at an atomic site depending on the identity of the
+element at that atomic site.
+
+The associated :doc:`pair\_coeff <pair_coeff>` command for style *eam/fs*
+reads a DYNAMO *setfl* file that has been extended to include
+additional rho\_alpha\_beta arrays of tabulated values.  A discussion of
+how FS EAM differs from conventional EAM alloy potentials is given in
+:ref:`(Ackland1) <Ackland1>`.  An example of such a potential is the same
+author's Fe-P FS potential :ref:`(Ackland2) <Ackland2>`.  Note that while FS
+potentials always specify the embedding energy with a square root
+dependence on the total density, the implementation in LAMMPS does not
+require that; the user can tabulate any functional form desired in the
+FS potential files.
+
+For style *eam/fs*\ , the form of the pair\_coeff command is exactly the
+same as for style *eam/alloy*\ , e.g.
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* NiAlH_jea.eam.fs Ni Ni Ni Al
+
+where there are N additional arguments after the filename, where N is
+the number of LAMMPS atom types.  See the :doc:`pair\_coeff <pair_coeff>`
+doc page for alternate ways to specify the path for the potential
+file.  The N values determine the mapping of LAMMPS atom types to EAM
+elements in the file, as described above for style *eam/alloy*\ .  As
+with *eam/alloy*\ , if a mapping value is NULL, the mapping is not
+performed.  This can be used when an *eam/fs* potential is used as
+part of the *hybrid* pair style.  The NULL values are used as
+placeholders for atom types that will be used with other potentials.
+
+FS EAM files include more information than the DYNAMO *setfl* format
+files read by *eam/alloy*\ , in that i,j density functionals for all
+pairs of elements are included as needed by the Finnis/Sinclair
+formulation of the EAM.
+
+FS EAM files in the *potentials* directory of the LAMMPS distribution
+have an ".eam.fs" suffix.  They are formatted as follows:
+
+* lines 1,2,3 = comments (ignored)
+* line 4: Nelements Element1 Element2 ... ElementN
+* line 5: Nrho, drho, Nr, dr, cutoff
+
+The 5-line header section is identical to an EAM *setfl* file.
+
+Following the header are Nelements sections, one for each element I,
+each with the following format:
+
+* line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
+* embedding function F(rho) (Nrho values)
+* density function rho(r) for element I at element 1 (Nr values)
+* density function rho(r) for element I at element 2
+* ...
+* density function rho(r) for element I at element Nelement
+
+The units of these quantities in line 1 are the same as for *setfl*
+files.  Note that the rho(r) arrays in Finnis/Sinclair can be
+asymmetric (i,j != j,i) so there are Nelements\^2 of them listed in the
+file.
+
+Following the Nelements sections, Nr values for each pair potential
+phi(r) array are listed in the same manner (r\*phi, units of
+eV-Angstroms) as in EAM *setfl* files.  Note that in Finnis/Sinclair,
+the phi(r) arrays are still symmetric, so only phi arrays for i >= j
+are listed.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above with the individual styles.  You never need to specify
+a pair\_coeff command with I != J arguments for the eam styles.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+The eam pair styles do not write their information to :doc:`binary restart files <restart>`, since it is stored in tabulated potential files.
+Thus, you need to re-specify the pair\_style and pair\_coeff commands in
+an input script that reads a restart file.
+
+The eam pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All of these styles are part of the MANYBODY package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Ackland1:
+
+
+
+**(Ackland1)** Ackland, Condensed Matter (2005).
+
+.. _Ackland2:
+
+
+
+**(Ackland2)** Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
+of Physics: Condensed Matter, 16, S2629 (2004).
+
+.. _Daw:
+
+
+
+**(Daw)** Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
+Daw, Baskes, Phys Rev B, 29, 6443 (1984).
+
+.. _Finnis1:
+
+
+
+**(Finnis)** Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
+
+.. _Stukowski:
+
+
+
+**(Stukowski)** Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
+Materials Science & Engineering, 7, 075005 (2009).
+
+.. _Caro:
+
+
+
+**(Caro)** A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst
new file mode 100644
index 0000000000..a976baaf61
--- /dev/null
+++ b/doc/src/pair_edip.rst
@@ -0,0 +1,194 @@
+.. index:: pair\_style edip
+
+pair\_style edip command
+========================
+
+pair\_style edip/omp command
+============================
+
+pair\_style edip/multi command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style
+
+* style = *edip* or *edip/multi*
+
+Examples
+""""""""
+
+pair\_style edip
+pair\_coeff \* \* Si.edip Si
+
+Description
+"""""""""""
+
+The *edip* and *edip/multi* styles compute a 3-body :ref:`EDIP <EDIP>`
+potential which is popular for modeling silicon materials where
+it can have advantages over other models such as the
+:doc:`Stillinger-Weber <pair_sw>` or :doc:`Tersoff <pair_tersoff>`
+potentials. The *edip* style has been programmed for single element
+potentials, while *edip/multi* supports multi-element EDIP runs.
+
+In EDIP, the energy E of a system of atoms is
+
+.. image:: Eqs/pair_edip.jpg
+   :align: center
+
+where phi2 is a two-body term and phi3 is a three-body term.  The
+summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance = a.
+Both terms depend on the local environment of atom I through its
+effective coordination number defined by Z, which is unity for a
+cutoff distance < c and gently goes to 0 at distance = a.
+
+Only a single pair\_coeff command is used with the *edip* style which
+specifies a EDIP potential file with parameters for all
+needed elements.  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of EDIP elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine a file Si.edip has EDIP values for Si.
+
+EDIP files in the *potentials* directory of the LAMMPS
+distribution have a ".edip" suffix.  Lines that are not blank or
+comments (starting with #) define parameters for a triplet of
+elements.  The parameters in a single entry correspond to the two-body
+and three-body coefficients in the formula above:
+
+* element 1 (the center atom in a 3-body interaction)
+* element 2
+* element 3
+* A (energy units)
+* B (distance units)
+* cutoffA (distance units)
+* cutoffC (distance units)
+* alpha
+* beta
+* eta
+* gamma (distance units)
+* lambda (energy units)
+* mu
+* tho
+* sigma (distance units)
+* Q0
+* u1
+* u2
+* u3
+* u4
+
+The A, B, beta, sigma parameters are used only for two-body interactions.
+The eta, gamma, lambda, mu, Q0 and all u1 to u4 parameters are used only
+for three-body interactions. The alpha and cutoffC parameters are used
+for the coordination environment function only.
+
+The EDIP potential file must contain entries for all the
+elements listed in the pair\_coeff command.  It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. SiSiSi).  For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify EDIP parameters for all permutations of the two elements
+interacting in three-body configurations.  Thus for 3 elements, 27
+entries would be required, etc.
+
+At the moment, only a single element parameterization is
+implemented. However, the author is not aware of other
+multi-element EDIP parameterization. If you know any and
+you are interest in that, please contact the author of
+the EDIP package.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The EDIP potential files provided with LAMMPS (see the potentials directory)
+are parameterized for metal :doc:`units <units>`.
+You can use the EDIP potential with any LAMMPS units, but you would need
+to create your own EDIP potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _EDIP:
+
+
+
+**(EDIP)** J F Justo et al, Phys Rev B 58, 2539 (1998).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst
new file mode 100644
index 0000000000..438ced6785
--- /dev/null
+++ b/doc/src/pair_eff.rst
@@ -0,0 +1,358 @@
+.. index:: pair\_style eff/cut
+
+pair\_style eff/cut command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style eff/cut cutoff keyword args ...
+
+* cutoff = global cutoff for Coulombic interactions
+* zero or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *limit/eradius* or *pressure/evirials* or *ecp*
+       *limit/eradius* args = none
+       *pressure/evirials* args = none
+       *ecp* args = type element type element ...
+         type = LAMMPS atom type (1 to Ntypes)
+         element = element symbol (e.g. H, Si)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style eff/cut 39.7
+   pair_style eff/cut 40.0 limit/eradius
+   pair_style eff/cut 40.0 limit/eradius pressure/evirials
+   pair_style eff/cut 40.0 ecp 1 Si 3 C
+   pair_coeff \* \*
+   pair_coeff 2 2 20.0
+   pair_coeff 1 s 0.320852 2.283269 0.814857
+   pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
+
+Description
+"""""""""""
+
+This pair style contains a LAMMPS implementation of the electron Force
+Field (eFF) potential currently under development at Caltech, as
+described in :ref:`(Jaramillo-Botero) <Jaramillo-Botero>`.  The eFF for Z<6
+was first introduced by :ref:`(Su) <Su>` in 2007. It has been extended to
+higher Zs by using effective core potentials (ECPs) that now cover up
+to 2nd and 3rd row p-block elements of the periodic table.
+
+eFF can be viewed as an approximation to QM wave packet dynamics and
+Fermionic molecular dynamics, combining the ability of electronic
+structure methods to describe atomic structure, bonding, and chemistry
+in materials, and of plasma methods to describe nonequilibrium
+dynamics of large systems with a large number of highly excited
+electrons.  Yet, eFF relies on a simplification of the electronic
+wave function in which electrons are described as floating Gaussian
+wave packets whose position and size respond to the various dynamic
+forces between interacting classical nuclear particles and spherical
+Gaussian electron wave packets.  The wave function is taken to be a
+Hartree product of the wave packets.  To compensate for the lack of
+explicit antisymmetry in the resulting wave function, a spin-dependent
+Pauli potential is included in the Hamiltonian.  Substituting this
+wave function into the time-dependent Schrodinger equation produces
+equations of motion that correspond - to second order - to classical
+Hamiltonian relations between electron position and size, and their
+conjugate momenta.  The N-electron wave function is described as a
+product of one-electron Gaussian functions, whose size is a dynamical
+variable and whose position is not constrained to a nuclear
+center. This form allows for straightforward propagation of the
+wave function, with time, using a simple formulation from which the
+equations of motion are then integrated with conventional MD
+algorithms. In addition to this spin-dependent Pauli repulsion
+potential term between Gaussians, eFF includes the electron kinetic
+energy from the Gaussians.  These two terms are based on
+first-principles quantum mechanics.  On the other hand, nuclei are
+described as point charges, which interact with other nuclei and
+electrons through standard electrostatic potential forms.
+
+The full Hamiltonian (shown below), contains then a standard
+description for electrostatic interactions between a set of
+delocalized point and Gaussian charges which include, nuclei-nuclei
+(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a
+mixed QM-classical mechanics method rather than a conventional force
+field method (in which electron motions are averaged out into ground
+state nuclear motions, i.e a single electronic state, and particle
+interactions are described via empirically parameterized interatomic
+potential functions). This makes eFF uniquely suited to simulate
+materials over a wide range of temperatures and pressures where
+electronically excited and ionized states of matter can occur and
+coexist.  Furthermore, the interactions between particles -nuclei and
+electrons- reduce to the sum of a set of effective pairwise potentials
+in the eFF formulation.  The *eff/cut* style computes the pairwise
+Coulomb interactions between nuclei and electrons (E\_NN,E\_Ne,E\_ee),
+and the quantum-derived Pauli (E\_PR) and Kinetic energy interactions
+potentials between electrons (E\_KE) for a total energy expression
+given as,
+
+.. image:: Eqs/eff_energy_expression.jpg
+   :align: center
+
+The individual terms are defined as follows:
+
+.. image:: Eqs/eff_KE.jpg
+   :align: center
+
+.. image:: Eqs/eff_NN.jpg
+   :align: center
+
+.. image:: Eqs/eff_Ne.jpg
+   :align: center
+
+.. image:: Eqs/eff_ee.jpg
+   :align: center
+
+.. image:: Eqs/eff_Pauli.jpg
+   :align: center
+
+where, s\_i correspond to the electron sizes, the sigmas i's to the
+fixed spins of the electrons, Z\_i to the charges on the nuclei, R\_ij
+to the distances between the nuclei or the nuclei and electrons, and
+r\_ij to the distances between electrons.  For additional details see
+:ref:`(Jaramillo-Botero) <Jaramillo-Botero>`.
+
+The overall electrostatics energy is given in Hartree units of energy
+by default and can be modified by an energy-conversion constant,
+according to the units chosen (see :doc:`electron\_units <units>`).  The
+cutoff Rc, given in Bohrs (by default), truncates the interaction
+distance.  The recommended cutoff for this pair style should follow
+the minimum image criterion, i.e. half of the minimum unit cell
+length.
+
+Style *eff/long* (not yet available) computes the same interactions as
+style *eff/cut* except that an additional damping factor is applied so
+it can be used in conjunction with the
+:doc:`kspace\_style <kspace_style>` command and its *ewald* or *pppm*
+option.  The Coulombic cutoff specified for this style means that
+pairwise interactions within this distance are computed directly;
+interactions outside that distance are computed in reciprocal space.
+
+This potential is designed to be used with :doc:`atom\_style electron <atom_style>` definitions, in order to handle the
+description of systems with interacting nuclei and explicit electrons.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cutoff (distance units)
+
+For *eff/cut*\ , the cutoff coefficient is optional.  If it is not used
+(as in some of the examples above), the default global value specified
+in the pair\_style command is used.
+
+For *eff/long* (not yet available) no cutoff will be specified for an
+individual I,J type pair via the :doc:`pair\_coeff <pair_coeff>` command.
+All type pairs use the same global cutoff specified in the pair\_style
+command.
+
+
+----------
+
+
+The *limit/eradius* and *pressure/evirials* keywords are optional.
+Neither or both must be specified.  If not specified they are unset.
+
+The *limit/eradius* keyword is used to restrain electron size from
+becoming excessively diffuse at very high temperatures were the
+Gaussian wave packet representation breaks down, and from expanding as
+free particles to infinite size.  If unset, electron radius is free to
+increase without bounds.  If set, a restraining harmonic potential of
+the form E = 1/2k\_ss\^2 for s > L\_box/2, where k\_s = 1 Hartrees/Bohr\^2,
+is applied on the electron radius.
+
+The *pressure/evirials* keyword is used to control between two types
+of pressure computation: if unset, the computed pressure does not
+include the electronic radial virials contributions to the total
+pressure (scalar or tensor).  If set, the computed pressure will
+include the electronic radial virial contributions to the total
+pressure (scalar and tensor).
+
+The *ecp* keyword is used to associate an ECP representation for a
+particular atom type.  The ECP captures the orbital overlap between a
+core pseudo particle and valence electrons within the Pauli repulsion.
+A list of type:element-symbol pairs may be provided for all ECP
+representations, after the "ecp" keyword.
+
+.. note::
+
+   Default ECP parameters are provided for C, N, O, Al, and Si.
+   Users can modify these using the pair\_coeff command as exemplified
+   above.  For this, the User must distinguish between two different
+   functional forms supported, one that captures the orbital overlap
+   assuming the s-type core interacts with an s-like valence electron
+   (s-s) and another that assumes the interaction is s-p.  For systems
+   that exhibit significant p-character (e.g. C, N, O) the s-p form is
+   recommended. The "s" ECP form requires 3 parameters and the "p" 5
+   parameters.
+
+.. note::
+
+   there are two different pressures that can be reported for eFF
+   when defining this pair\_style, one (default) that considers electrons
+   do not contribute radial virial components (i.e. electrons treated as
+   incompressible 'rigid' spheres) and one that does.  The radial
+   electronic contributions to the virials are only tallied if the
+   flexible pressure option is set, and this will affect both global and
+   per-atom quantities.  In principle, the true pressure of a system is
+   somewhere in between the rigid and the flexible eFF pressures, but,
+   for most cases, the difference between these two pressures will not be
+   significant over long-term averaged runs (i.e. even though the energy
+   partitioning changes, the total energy remains similar).
+
+
+----------
+
+
+.. note::
+
+   This implementation of eFF gives a reasonably accurate description
+   for systems containing nuclei from Z = 1-6 in "all electron"
+   representations.  For systems with increasingly non-spherical
+   electrons, Users should use the ECP representations.  ECPs are now
+   supported and validated for most of the 2nd and 3rd row elements of
+   the p-block.  Predefined parameters are provided for C, N, O, Al, and
+   Si.  The ECP captures the orbital overlap between the core and valence
+   electrons (i.e. Pauli repulsion) with one of the functional forms:
+
+.. image:: Eqs/eff_ECP1.jpg
+   :align: center
+
+.. image:: Eqs/eff_ECP2.jpg
+   :align: center
+
+Where the 1st form correspond to core interactions with s-type valence
+electrons and the 2nd to core interactions with p-type valence
+electrons.
+
+The current version adds full support for models with fixed-core and
+ECP definitions.  to enable larger timesteps (i.e. by avoiding the
+high frequency vibrational modes -translational and radial- of the 2 s
+electrons), and in the ECP case to reduce the increased orbital
+complexity in higher Z elements (up to Z<18).  A fixed-core should be
+defined with a mass that includes the corresponding nuclear mass plus
+the 2 s electrons in atomic mass units (2x5.4857990943e-4), and a
+radius equivalent to that of minimized 1s electrons (see examples
+under /examples/USER/eff/fixed-core).  An pseudo-core should be
+described with a mass that includes the corresponding nuclear mass,
+plus all the core electrons (i.e no outer shell electrons), and a
+radius equivalent to that of a corresponding minimized full-electron
+system.  The charge for a pseudo-core atom should be given by the
+number of outer shell electrons.
+
+In general, eFF excels at computing the properties of materials in
+extreme conditions and tracing the system dynamics over multi-picosecond
+timescales; this is particularly relevant where electron excitations
+can change significantly the nature of bonding in the system. It can
+capture with surprising accuracy the behavior of such systems because
+it describes consistently and in an unbiased manner many different
+kinds of bonds, including covalent, ionic, multicenter, ionic, and
+plasma, and how they interconvert and/or change when they become
+excited.  eFF also excels in computing the relative thermochemistry of
+isodemic reactions and conformational changes, where the bonds of the
+reactants are of the same type as the bonds of the products.  eFF
+assumes that kinetic energy differences dominate the overall exchange
+energy, which is true when the electrons present are nearly spherical
+and nodeless and valid for covalent compounds such as dense hydrogen,
+hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth
+metals (e.g. beryllium) and semimetals such as boron; and various
+compounds containing ionic and/or multicenter bonds, such as boron
+dihydride.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the cutoff distance for the
+*eff/cut* style can be mixed.  The default mix value is *geometric*\ .
+See the "pair\_modify" command for details.
+
+The :doc:`pair\_modify <pair_modify>` shift option is not relevant for
+these pair styles.
+
+The *eff/long* (not yet available) style supports the
+:doc:`pair\_modify <pair_modify>` table option for tabulation of the
+short-range portion of the long-range Coulombic interaction.
+
+These pair styles do not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles will only be enabled if LAMMPS is built with the
+USER-EFF package.  It will only be enabled if LAMMPS was built with
+that package.  See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+These pair styles require that particles store electron attributes
+such as radius, radial velocity, and radial force, as defined by the
+:doc:`atom\_style <atom_style>`.  The *electron* atom style does all of
+this.
+
+Thes pair styles require you to use the :doc:`comm\_modify vel yes <comm_modify>` command so that velocities are stored by ghost
+atoms.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+Default
+"""""""
+
+If not specified, limit\_eradius = 0 and pressure\_with\_evirials = 0.
+
+
+----------
+
+
+.. _Su:
+
+
+
+**(Su)** Su and Goddard, Excited Electron Dynamics Modeling of Warm
+Dense Matter, Phys Rev Lett, 99:185003 (2007).
+
+.. _Jaramillo-Botero:
+
+
+
+**(Jaramillo-Botero)** Jaramillo-Botero, Su, Qi, Goddard, Large-scale,
+Long-term Non-adiabatic Electron Molecular Dynamics for Describing
+Material Properties and Phenomena in Extreme Environments, J Comp
+Chem, 32, 497-512 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst
new file mode 100644
index 0000000000..001f314443
--- /dev/null
+++ b/doc/src/pair_eim.rst
@@ -0,0 +1,204 @@
+.. index:: pair\_style eim
+
+pair\_style eim command
+=======================
+
+pair\_style eim/omp command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style
+
+* style = *eim*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style eim
+   pair_coeff \* \* Na Cl ../potentials/ffield.eim Na Cl
+   pair_coeff \* \* Na Cl ffield.eim  Na Na Na Cl
+   pair_coeff \* \* Na Cl ../potentials/ffield.eim Cl NULL Na
+
+Description
+"""""""""""
+
+Style *eim* computes pairwise interactions for ionic compounds
+using embedded-ion method (EIM) potentials :ref:`(Zhou) <Zhou2>`.  The
+energy of the system E is given by
+
+.. image:: Eqs/pair_eim1.jpg
+   :align: center
+
+The first term is a double pairwise sum over the J neighbors of all I
+atoms, where phi\_ij is a pair potential.  The second term sums over
+the embedding energy E\_i of atom I, which is a function of its charge
+q\_i and the electrical potential sigma\_i at its location.  E\_i, q\_i,
+and sigma\_i are calculated as
+
+.. image:: Eqs/pair_eim2.jpg
+   :align: center
+
+where eta\_ji is a pairwise function describing electron flow from atom
+I to atom J, and psi\_ij is another pairwise function.  The multi-body
+nature of the EIM potential is a result of the embedding energy term.
+A complete list of all the pair functions used in EIM is summarized
+below
+
+.. image:: Eqs/pair_eim3.jpg
+   :align: center
+
+Here E\_b, r\_e, r\_(c,phi), alpha, beta, A\_(psi), zeta, r\_(s,psi),
+r\_(c,psi), A\_(eta), r\_(s,eta), r\_(c,eta), chi, and pair function type
+p are parameters, with subscripts ij indicating the two species of
+atoms in the atomic pair.
+
+.. note::
+
+   Even though the EIM potential is treating atoms as charged ions,
+   you should not use a LAMMPS :doc:`atom\_style <atom_style>` that stores a
+   charge on each atom and thus requires you to assign a charge to each
+   atom, e.g. the *charge* or *full* atom styles.  This is because the
+   EIM potential infers the charge on an atom from the equation above for
+   q\_i; you do not assign charges explicitly.
+
+
+----------
+
+
+All the EIM parameters are listed in a potential file which is
+specified by the :doc:`pair\_coeff <pair_coeff>` command.  This is an
+ASCII text file in a format described below.  The "ffield.eim" file
+included in the "potentials" directory of the LAMMPS distribution
+currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I.
+A system with any combination of these elements can be modeled.  This
+file is parameterized in terms of LAMMPS :doc:`metal units <units>`.
+
+Note that unlike other potentials, cutoffs for EIM potentials are not
+set in the pair\_style or pair\_coeff command; they are specified in the
+EIM potential file itself.  Likewise, the EIM potential file lists
+atomic masses; thus you do not need to use the :doc:`mass <mass>`
+command to specify them.
+
+Only a single pair\_coeff command is used with the *eim* style which
+specifies an EIM potential file and the element(s) to extract
+information for.  The EIM elements are mapped to LAMMPS atom types by
+specifying N additional arguments after the filename in the pair\_coeff
+command, where N is the number of LAMMPS atom types:
+
+* Elem1, Elem2, ...
+* EIM potential file
+* N element names = mapping of EIM elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example like one of those above, suppose you want to model a
+system with Na and Cl atoms.  If your LAMMPS simulation has 4 atoms
+types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
+use the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* Na Cl ffield.eim Na Na Na Cl
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The filename is the EIM potential file.  The Na and Cl arguments
+(before the file name) are the two elements for which info will be
+extracted from the potential file.  The first three trailing Na
+arguments map LAMMPS atom types 1,2,3 to the EIM Na element.  The
+final Cl argument maps LAMMPS atom type 4 to the EIM Cl element.
+
+If a mapping value is specified as NULL, the mapping is not performed.
+This can be used when an *eim* potential is used as part of the
+*hybrid* pair style.  The NULL values are placeholders for atom types
+that will be used with other potentials.
+
+The ffield.eim file in the *potentials* directory of the LAMMPS
+distribution is formatted as follows:
+
+Lines starting with # are comments and are ignored by LAMMPS.  Lines
+starting with "global:" include three global values. The first value
+divides the cations from anions, i.e., any elements with
+electronegativity above this value are viewed as anions, and any
+elements with electronegativity below this value are viewed as
+cations. The second and third values are related to the cutoff
+function - i.e. the 0.510204, 1.64498, and 0.010204 shown in the above
+equation can be derived from these values.
+
+Lines starting with "element:" are formatted as follows: name of
+element, atomic number, atomic mass, electronic negativity, atomic
+radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive
+energy (LAMMPS ignores it), and q0 (must be 0).
+
+Lines starting with "pair:" are entered as: element 1, element 2,
+r\_(c,phi), r\_(c,phi) (redundant for historical reasons), E\_b, r\_e,
+alpha, beta, r\_(c,eta), A\_(eta), r\_(s,eta), r\_(c,psi), A\_(psi), zeta,
+r\_(s,psi), and p.
+
+The lines in the file can be in any order; LAMMPS extracts the info it
+needs.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the MANYBODY package.  It is only enabled if
+LAMMPS was built with that package.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Zhou2:
+
+
+
+**(Zhou)** Zhou, submitted for publication (2010).  Please contact
+Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst
new file mode 100644
index 0000000000..d8262e0712
--- /dev/null
+++ b/doc/src/pair_exp6_rx.rst
@@ -0,0 +1,214 @@
+.. index:: pair\_style exp6/rx
+
+pair\_style exp6/rx command
+===========================
+
+pair\_style exp6/rx/kk command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style exp6/rx cutoff ...
+
+* cutoff = global cutoff for DPD interactions (distance units)
+* weighting = fractional or molecular (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style exp6/rx 10.0
+   pair_style exp6/rx 10.0 fractional
+   pair_style exp6/rx 10.0 molecular
+   pair_coeff \* \* exp6.params h2o h2o exponent 1.0 1.0 10.0
+   pair_coeff \* \* exp6.params h2o 1fluid exponent 1.0 1.0 10.0
+   pair_coeff \* \* exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0
+   pair_coeff \* \* exp6.params 1fluid 1fluid none 10.0
+   pair_coeff \* \* exp6.params 1fluid 1fluid polynomial filename 10.0
+
+Description
+"""""""""""
+
+Style *exp6/rx* is used in reaction DPD simulations, where the
+coarse-grained (CG) particles are composed of *m* species whose
+reaction rate kinetics are determined from a set of *n* reaction rate
+equations through the :doc:`fix rx <fix_rx>` command.  The species of
+one CG particle can interact with a species in a neighboring CG
+particle through a site-site interaction potential model.  The
+*exp6/rx* style computes an exponential-6 potential given by
+
+.. image:: Eqs/pair_exp6_rx.jpg
+   :align: center
+
+where the *epsilon* parameter determines the depth of the potential
+minimum located at *Rm*\ , and *alpha* determines the softness of the repulsion.
+
+The coefficients must be defined for each species in a given particle
+type via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, where the first argument is the filename that includes the
+exponential-6 parameters for each species.  The file includes the
+species tag followed by the *alpha*\ , *epsilon* and *Rm*
+parameters. The format of the file is described below.
+
+The second and third arguments specify the site-site interaction
+potential between two species contained within two different
+particles.  The species tags must either correspond to the species
+defined in the reaction kinetics files specified with the :doc:`fix rx <fix_rx>` command or they must correspond to the tag "1fluid",
+signifying interaction with a product species mixture determined
+through a one-fluid approximation.  The interaction potential is
+weighted by the geometric average of either the mole fraction concentrations
+or the number of molecules associated with the interacting coarse-grained
+particles (see the *fractional* or *molecular* weighting pair style options).
+The coarse-grained potential is stored before and after the
+reaction kinetics solver is applied, where the difference is defined
+to be the internal chemical energy (uChem).
+
+The fourth argument specifies the type of scaling that will be used
+to scale the EXP-6 parameters as reactions occur.  Currently, there
+are three scaling options:  *exponent*\ , *polynomial* and *none*\ .
+
+Exponent scaling requires two additional arguments for scaling
+the *Rm* and *epsilon* parameters, respectively.  The scaling factor
+is computed by phi\^exponent, where phi is the number of molecules
+represented by the coarse-grain particle and exponent is specified
+as a pair coefficient argument for *Rm* and *epsilon*\ , respectively.
+The *Rm* and *epsilon* parameters are multiplied by the scaling
+factor to give the scaled interaction parameters for the CG particle.
+
+Polynomial scaling requires a filename to be specified as a pair
+coeff argument.  The file contains the coefficients to a fifth order
+polynomial for the *alpha*\ , *epsilon* and *Rm* parameters that depend
+upon phi (the number of molecules represented by the CG particle).
+The format of a polynomial file is provided below.
+
+The *none* option to the scaling does not have any additional pair coeff
+arguments.  This is equivalent to specifying the *exponent* option with
+*Rm* and *epsilon* exponents of 0.0 and 0.0, respectively.
+
+The final argument specifies the interaction cutoff (optional).
+
+
+----------
+
+
+The format of a tabulated file is as follows (without the
+parenthesized comments):
+
+
+.. parsed-literal::
+
+   # exponential-6 parameters for various species      (one or more comment or blank lines)
+
+   h2o  exp6  11.00 0.02 3.50                          (species, exp6, alpha, Rm, epsilon)
+   no2  exp6  13.60 0.01 3.70
+   ...
+   co2  exp6  13.00 0.03 3.20
+
+The format of the polynomial scaling file as follows (without the
+parenthesized comments):
+
+
+.. parsed-literal::
+
+   # POLYNOMIAL FILE          (one or more comment or blank lines)
+
+   #  General Functional Form:
+   #  A\*phi\^5 + B\*phi\^4 + C\*phi\^3 + D\*phi\^2 + E\*phi + F
+   #
+   #  Parameter  A        B         C        D         E        F
+                              (blank)
+   alpha        0.0000   0.00000   0.00008  0.04955  -0.73804  13.63201
+   epsilon      0.0000   0.00478  -0.06283  0.24486  -0.33737   2.60097
+   rm           0.0001  -0.00118  -0.00253  0.05812  -0.00509   1.50106
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.
+
+Following a blank line, the next N lines list the species and their
+corresponding parameters.  The first argument is the species tag, the
+second argument is the exp6 tag, the 3rd argument is the *alpha*
+parameter (energy units), the 4th argument is the *epsilon* parameter
+(energy-distance\^6 units), and the 5th argument is the *Rm* parameter
+(distance units).  If a species tag of "1fluid" is listed as a pair
+coefficient, a one-fluid approximation is specified where a
+concentration-dependent combination of the parameters is computed
+through the following equations:
+
+.. image:: Eqs/pair_exp6_rx_oneFluid.jpg
+   :align: center
+
+where
+
+.. image:: Eqs/pair_exp6_rx_oneFluid2.jpg
+   :align: center
+
+and xa and xb are the mole fractions of a and b, respectively, which
+comprise the gas mixture.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the :doc:`pair\_modify <pair_modify>` shift option
+for the energy of the exp() and 1/r\^6 portion of the pair interaction.
+
+This style does not support the pair\_modify tail option for adding long-range
+tail corrections to energy and pressure for the A,C terms in the
+pair interaction.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** fractional weighting
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_extep.rst b/doc/src/pair_extep.rst
new file mode 100644
index 0000000000..8d5da3d974
--- /dev/null
+++ b/doc/src/pair_extep.rst
@@ -0,0 +1,59 @@
+.. index:: pair\_style extep
+
+pair\_style extep command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style extep
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style extep
+   pair_coeff \* \* BN.extep B N
+
+Description
+"""""""""""
+
+Style *extep* computes the Extended Tersoff Potential (ExTeP)
+interactions as described in :ref:`(Los2017) <Los2017>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+"pair\_tersoff" pair\_tersoff.html
+
+**Default:** none
+
+
+----------
+
+
+.. _Los2017:
+
+
+
+**(Los2017)** J. H. Los et al. "Extended Tersoff potential for boron nitride:
+Energetics and elastic properties of pristine and defective h-BN",
+Phys. Rev. B 96 (184108), 2017.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst
new file mode 100644
index 0000000000..90dbfeb612
--- /dev/null
+++ b/doc/src/pair_fep_soft.rst
@@ -0,0 +1,433 @@
+.. index:: pair\_style lj/cut/soft
+
+pair\_style lj/cut/soft command
+===============================
+
+pair\_style lj/cut/soft/omp command
+===================================
+
+pair\_style lj/cut/coul/cut/soft command
+========================================
+
+pair\_style lj/cut/coul/cut/soft/omp command
+============================================
+
+pair\_style lj/cut/coul/long/soft command
+=========================================
+
+pair\_style lj/cut/coul/long/soft/omp command
+=============================================
+
+pair\_style lj/cut/tip4p/long/soft command
+==========================================
+
+pair\_style lj/cut/tip4p/long/soft/omp command
+==============================================
+
+pair\_style lj/charmm/coul/long/soft command
+============================================
+
+pair\_style lj/charmm/coul/long/soft/omp command
+================================================
+
+pair\_style lj/class2/soft command
+==================================
+
+pair\_style lj/class2/coul/cut/soft command
+===========================================
+
+pair\_style lj/class2/coul/long/soft command
+============================================
+
+pair\_style coul/cut/soft command
+=================================
+
+pair\_style coul/cut/soft/omp command
+=====================================
+
+pair\_style coul/long/soft command
+==================================
+
+pair\_style coul/long/soft/omp command
+======================================
+
+pair\_style tip4p/long/soft command
+===================================
+
+pair\_style tip4p/long/soft/omp command
+=======================================
+
+pair\_style morse/soft command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/cut/soft* or *lj/cut/coul/cut/soft* or *lj/cut/coul/long/soft* or *lj/cut/tip4p/long/soft* or *lj/charmm/coul/long/soft* or *lj/class2/soft* or *lj/class2/coul/cut/soft* or *lj/class2/coul/long/soft* or *coul/cut/soft* or *coul/long/soft* or *tip4p/long/soft* or *morse/soft*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *lj/cut/soft* args = n alpha_lj cutoff
+       n, alpha_LJ = parameters of soft-core potential
+       cutoff = global cutoff for Lennard-Jones interactions (distance units)
+     *lj/cut/coul/cut/soft* args = n alpha_LJ alpha_C cutoff (cutoff2)
+       n, alpha_LJ, alpha_C = parameters of soft-core potential
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/cut/coul/long/soft* args = n alpha_LJ alpha_C cutoff
+       n, alpha_LJ, alpha_C = parameters of the soft-core potential
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/cut/tip4p/long/soft* args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
+       otype,htype = atom types for TIP4P O and H
+       btype,atype = bond and angle types for TIP4P waters
+       qdist = distance from O atom to massless charge (distance units)
+       n, alpha_LJ, alpha_C = parameters of the soft-core potential
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/charmm/coul/long/soft* args = n alpha_LJ alpha_C inner outer (cutoff)
+       n, alpha_LJ, alpha_C = parameters of the soft-core potential
+       inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
+       cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
+     *lj/class2/soft* args = n alpha_lj cutoff
+       n, alpha_LJ = parameters of soft-core potential
+       cutoff = global cutoff for Lennard-Jones interactions (distance units)
+     *lj/class2/coul/cut/soft* args = n alpha_LJ alpha_C cutoff (cutoff2)
+       n, alpha_LJ, alpha_C = parameters of soft-core potential
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/class2/coul/long/soft* args = n alpha_LJ alpha_C cutoff (cutoff2)
+       n, alpha_LJ, alpha_C = parameters of soft-core potential
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *coul/cut/soft* args = n alpha_C cutoff
+       n, alpha_C = parameters of the soft-core potential
+       cutoff = global cutoff for Coulomb interactions (distance units)
+     *coul/long/soft* args = n alpha_C cutoff
+       n, alpha_C = parameters of the soft-core potential
+       cutoff = global cutoff for Coulomb interactions (distance units)
+     *tip4p/long/soft* args = otype htype btype atype qdist n alpha_C cutoff
+       otype,htype = atom types for TIP4P O and H
+       btype,atype = bond and angle types for TIP4P waters
+       qdist = distance from O atom to massless charge (distance units)
+       n, alpha_C = parameters of the soft-core potential
+       cutoff = global cutoff for Coulomb interactions (distance units)
+     *morse/soft* args = n lf cutoff
+       n = soft-core parameter
+       lf = transformation range is lf < lambda < 1
+       cutoff = global cutoff for Morse interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/soft 2.0 0.5 9.5
+   pair_coeff \* \* 0.28 3.1 1.0
+   pair_coeff 1 1 0.28 3.1 1.0 9.5
+
+   pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
+   pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
+   pair_coeff \* \* 0.28 3.1 1.0
+   pair_coeff 1 1 0.28 3.1 0.5 10.0
+   pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
+
+   pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
+   pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
+   pair_coeff \* \* 0.28 3.1 1.0
+   pair_coeff 1 1 0.28 3.1 0.0 10.0
+   pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
+
+   pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
+   pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
+   pair_coeff \* \* 0.155 3.1536 1.0
+   pair_coeff 1 1 0.155 3.1536 1.0 9.5
+
+   pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
+   pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
+   pair_coeff \* \* 0.28 3.1 1.0
+   pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
+
+   pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5
+   pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 9.5
+   pair_coeff \* \* 0.28 3.1 1.0
+   pair_coeff 1 1 0.28 3.1 0.0 10.0
+   pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
+
+   pair_style coul/long/soft 1.0 10.0 9.5
+   pair_coeff \* \* 1.0
+   pair_coeff 1 1 1.0 9.5
+
+   pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
+   pair_coeff \* \* 1.0
+   pair_coeff 1 1 1.0 9.5
+
+   pair_style morse/soft 4 0.9 10.0
+   pair_coeff \* \* 100.0 2.0 1.5 1.0
+   pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
+
+Description
+"""""""""""
+
+These pair styles have a soft repulsive core, tunable by a parameter lambda,
+in order to avoid singularities during free energy calculations when sites are
+created or annihilated :ref:`(Beutler) <Beutler>`.  When lambda tends to 0 the pair
+interaction vanishes with a soft repulsive core.  When lambda tends to 1, the pair
+interaction approaches the normal, non-soft potential. These pair styles
+are suited for "alchemical" free energy calculations using the :doc:`fix adapt/fep <fix_adapt_fep>` and :doc:`compute fep <compute_fep>` commands.
+
+The *lj/cut/soft* style and related sub-styles compute the 12-6 Lennard-Jones
+and Coulomb potentials modified by a soft core, with the functional form
+
+.. image:: Eqs/pair_lj_soft.jpg
+   :align: center
+
+The *lj/class2/soft* style is a 9-6 potential with the exponent of the
+denominator of the first term in brackets taking the value 1.5 instead of 2
+(other details differ, see the form of the potential in
+:doc:`pair\_class2 <pair_class2>`).
+
+Coulomb interactions can also be damped with a soft core at short distance,
+
+.. image:: Eqs/pair_coul_soft.jpg
+   :align: center
+
+In the Coulomb part C is an energy-conversion constant, q\_i and q\_j
+are the charges on the 2 atoms, and epsilon is the dielectric constant
+which can be set by the :doc:`dielectric <dielectric>` command.
+
+The coefficient lambda is an activation parameter. When lambda = 1 the pair
+potential is identical to a Lennard-Jones term or a Coulomb term or a
+combination of both. When lambda = 0 the interactions are deactivated. The
+transition between these two extrema is smoothed by a soft repulsive core in
+order to avoid singularities in potential energy and forces when sites are
+created or annihilated and can overlap :ref:`(Beutler) <Beutler>`.
+
+The parameters n, alpha\_LJ and alpha\_C are set in the
+:doc:`pair\_style <pair_style>` command, before the cutoffs.  Usual choices for the
+exponent are n = 2 or n = 1. For the remaining coefficients alpha\_LJ = 0.5 and
+alpha\_C = 10 Angstrom\^2 are appropriate choices. Plots of the 12/6 LJ and
+Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1.
+
+.. image:: JPG/lj_soft.jpg
+.. image:: JPG/coul_soft.jpg
+
+
+For the *lj/cut/coul/cut/soft* or *lj/cut/coul/long/soft* pair styles, as well
+as for the equivalent *class2* versions, the following coefficients must be
+defined for each pair of atoms types via the :doc:`pair\_coeff <pair_coeff>`
+command as in the examples above, or in the data file or restart files read by
+the :doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` commands, or
+by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* lambda (activation parameter, between 0 and 1)
+* cutoff1 (distance units)
+* cutoff2 (distance units)
+
+The latter two coefficients are optional.  If not specified, the global
+LJ and Coulombic cutoffs specified in the pair\_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair.  If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair.  You cannot specify 2 cutoffs for style *lj/cut/soft*\ ,
+since it has no Coulombic terms. For the *coul/cut/soft* and
+*coul/long/soft* only lambda and the optional cutoff2 are to be
+specified.
+
+Style *lj/cut/tip4p/long/soft* implements a soft-core version of the TIP4P water
+model. The usage of the TIP4P pair style is documented in the
+:doc:`pair\_lj <pair_lj>` styles. In the soft version the parameters n, alpha\_LJ
+and alpha\_C are set in the :doc:`pair\_style <pair_style>` command, after the
+specific parameters of the TIP4P water model and before the cutoffs. The
+activation parameter lambda is supplied as an argument of the
+:doc:`pair\_coeff <pair_coeff>` command, after epsilon and sigma and before the
+optional cutoffs.
+
+Style *lj/charmm/coul/long/soft* implements a soft-core version of the modified
+12-6 LJ potential used in CHARMM and documented in the
+:doc:`pair\_lj\_charmm <pair_charmm>` style. In the soft version the parameters n,
+alpha\_LJ and alpha\_C are set in the :doc:`pair\_style <pair_style>` command, before
+the global cutoffs. The activation parameter lambda is introduced as an argument
+of the :doc:`pair\_coeff <pair_coeff>` command, after epsilon and sigma and
+before the optional eps14 and sigma14.
+
+Style *lj/class2/soft* implements a soft-core version of the 9-6 potential in
+:doc:`pair\_class2 <pair_class2>`. In the soft version the parameters n, alpha\_LJ
+and alpha\_C are set in the :doc:`pair\_style <pair_style>` command, before the
+global cutoffs. The activation parameter lambda is introduced as an argument of
+the the :doc:`pair\_coeff <pair_coeff>` command, after epsilon and sigma and before
+the optional cutoffs.
+
+The *coul/cut/soft*\ , *coul/long/soft* and *tip4p/long/soft* sub-styles
+are designed to be combined with other pair potentials via the
+:doc:`pair\_style hybrid/overlay <pair_hybrid>` command.  This is because
+they have no repulsive core.  Hence, if used by themselves, there will
+be no repulsion to keep two oppositely charged particles from
+overlapping each other. In this case, if lambda = 1, a singularity may
+occur.  These sub-styles are suitable to represent charges embedded in
+the Lennard-Jones radius of another site (for example hydrogen atoms
+in several water models).
+
+.. note::
+
+   When using the soft-core Coulomb potentials with long-range
+   solvers (\ *coul/long/soft*\ , *lj/cut/coul/long/soft*\ , etc.)  in a free
+   energy calculation in which sites holding electrostatic charges are
+   being created or annihilated (using :doc:`fix adapt/fep <fix_adapt_fep>`
+   and :doc:`compute fep <compute_fep>`) it is important to adapt both the
+   lambda activation parameter (from 0 to 1, or the reverse) and the
+   value of the charge (from 0 to its final value, or the reverse). This
+   ensures that long-range electrostatic terms (kspace) are correct. It
+   is not necessary to use soft-core Coulomb potentials if the van der
+   Waals site is present during the free-energy route, thus avoiding
+   overlap of the charges. Examples are provided in the LAMMPS source
+   directory tree, under examples/USER/fep.
+
+.. note::
+
+   To avoid division by zero do not set sigma = 0 in the *lj/cut/soft* and
+   related styles; use the lambda parameter instead to activate/deactivate
+   interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not
+   interact though the Lennard-Jones term the *coul/long/soft* or similar sub-style
+   can be used via the :doc:`pair\_style hybrid/overlay <pair_hybrid>` command.
+
+
+----------
+
+
+The *morse/soft* variant modifies the :doc:`pair\_morse <pair_morse>` style at
+short range to have a soft core. The functional form differs from that of the
+*lj/soft* styles, and is instead given by:
+
+.. image:: Eqs/pair_morse_soft.jpg
+   :align: center
+
+The *morse/soft* style requires the following pair coefficients:
+
+* D0 (energy units)
+* alpha (1/distance units)
+* r0 (distance units)
+* lambda (unitless, between 0.0 and 1.0)
+* cutoff (distance units)
+
+The last coefficient is optional. If not specified, the global morse cutoff is
+used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, tail correction, restart info**\ :
+
+The different versions of the *lj/cut/soft* pair styles support mixing.  For atom
+type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff
+distance for these pair style can be mixed.  The default mix value is
+*geometric* for 12-6 styles.
+
+The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to use the
+*sixthpower* formulas. The :doc:`pair\_modify mix <pair_modify>` setting is thus
+ignored for class2 potentials for epsilon and sigma. However it is still
+followed for mixing the cutoff distance. See the :doc:`pair\_modify <pair_modify>`
+command for details.
+
+The *morse/soft* pair style does not support mixing. Thus, coefficients for all
+LJ pairs must be specified explicitly.
+
+All of the pair styles with soft core support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the Lennard-Jones portion of the pair
+interaction.
+
+The different versions of the *lj/cut/soft* pair styles support the
+:doc:`pair\_modify <pair_modify>` tail option for adding a long-range tail
+correction to the energy and pressure for the Lennard-Jones portion of the pair
+interaction.
+
+.. note::
+
+   The analytical form of the tail corrections for energy and pressure used
+   in the *lj/cut/soft* potentials are approximate, being identical to that of the
+   corresponding non-soft potentials scaled by a factor lambda\^n. The errors due to
+   this approximation should be negligible. For example, for a cutoff of 2.5 sigma
+   this approximation leads to maximum relative errors in tail corrections of the
+   order of 1e-4 for energy and virial (alpha\_LJ = 0.5, n = 2). The error vanishes
+   when lambda approaches 0 or 1. Note that these are the errors affecting the
+   long-range tail (itself a correction to the interaction energy) which includes
+   other approximations, namely that the system is homogeneous (local density equal
+   the average density) beyond the cutoff.
+
+The *morse/soft* pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and pressure.
+
+All of these pair styles write information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need to be
+specified in an input script that reads a restart file.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The pair styles with soft core are only enabled if LAMMPS was built with the
+USER-FEP package. The *long* versions also require the KSPACE package to be
+installed. The soft *tip4p* versions also require the MOLECULE package to be
+installed. These styles are only enabled if LAMMPS was built with those
+packages.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix adapt <fix_adapt>`,
+:doc:`fix adapt/fep <fix_adapt_fep>`, :doc:`compute fep <compute_fep>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Beutler:
+
+
+
+**(Beutler)** Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem
+Phys Lett, 222, 529 (1994).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst
new file mode 100644
index 0000000000..e5252afe2b
--- /dev/null
+++ b/doc/src/pair_gauss.rst
@@ -0,0 +1,217 @@
+.. index:: pair\_style gauss
+
+pair\_style gauss command
+=========================
+
+pair\_style gauss/gpu command
+=============================
+
+pair\_style gauss/omp command
+=============================
+
+pair\_style gauss/cut command
+=============================
+
+pair\_style gauss/cut/omp command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style gauss cutoff
+   pair_style gauss/cut cutoff
+
+* cutoff = global cutoff for Gauss interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style gauss 12.0
+   pair_coeff \* \* 1.0 0.9
+   pair_coeff 1 4 1.0 0.9 10.0
+
+   pair_style gauss/cut 3.5
+   pair_coeff 1 4 0.2805 1.45 0.112
+
+Description
+"""""""""""
+
+Style *gauss* computes a tethering potential of the form
+
+.. image:: Eqs/pair_gauss.jpg
+   :align: center
+
+between an atom and its corresponding tether site which will typically
+be a frozen atom in the simulation.  Rc is the cutoff.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* A (energy units)
+* B (1/distance\^2 units)
+* cutoff (distance units)
+
+The last coefficient is optional. If not specified, the global cutoff
+is used.
+
+Style *gauss/cut* computes a generalized Gaussian interaction potential
+between pairs of particles:
+
+.. image:: Eqs/pair_gauss_cut.jpg
+   :align: center
+
+where H determines together with the standard deviation sigma\_h the
+peak height of the Gaussian function, and r\_mh the peak position.
+Examples of the use of the Gaussian potentials include implicit
+solvent simulations of salt ions :ref:`(Lenart) <Lenart2>` and of surfactants
+:ref:`(Jusufi) <Jusufi2>`.  In these instances the Gaussian potential mimics
+the hydration barrier between a pair of particles. The hydration
+barrier is located at r\_mh and has a width of sigma\_h. The prefactor
+determines the height of the potential barrier.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the example above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* H (energy \* distance units)
+* r\_mh (distance units)
+* sigma\_h (distance units)
+* cutoff (distance units)
+
+The last coefficient is optional. If not specified, the global cutoff
+is used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the A, B, H, sigma\_h, r\_mh
+parameters, and the cutoff distance for these pair styles can be mixed:
+A (energy units)
+sqrt(1/B) (distance units, see below)
+H (energy units)
+sigma\_h (distance units)
+r\_mh (distance units)
+cutoff (distance units):ul
+
+The default mix value is *geometric*\ .
+Only *arithmetic* and *geometric* mix values are supported.
+See the "pair\_modify" command for details.
+
+The A and H parameters are mixed using the same rules normally
+used to mix the "epsilon" parameter in a Lennard Jones interaction.
+The sigma\_h, r\_mh, and the cutoff distance are mixed using the same
+rules used to mix the "sigma" parameter in a Lennard Jones interaction.
+The B parameter is converted to a distance (sigma), before mixing
+(using sigma=B\^-0.5), and converted back to a coefficient
+afterwards (using B=sigma\^2).
+Negative A values are converted to positive A values (using abs(A))
+before mixing, and converted back after mixing
+(by multiplying by min(sign(Ai),sign(Aj))).
+This way, if either particle is repulsive (if Ai<0 or Aj<0),
+then the default interaction between both particles will be repulsive.
+
+The *gauss* style does not support the :doc:`pair\_modify <pair_modify>`
+shift option. There is no effect due to the Gaussian well beyond the
+cutoff; hence reasonable cutoffs need to be specified.
+
+The *gauss/cut* style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the Gauss-potential portion of the pair
+interaction.
+
+The :doc:`pair\_modify <pair_modify>` table and tail options are not
+relevant for these pair styles.
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+The *gauss* pair style tallies an "occupancy" count of how many Gaussian-well
+sites have an atom within the distance at which the force is a maximum
+= sqrt(0.5/b).  This quantity can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 1.
+
+To print this quantity to the log file (with a descriptive column
+heading) the following commands could be included in an input script:
+
+
+.. parsed-literal::
+
+   compute gauss all pair gauss
+   variable occ equal c_gauss[1]
+   thermo_style custom step temp epair v_occ
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *gauss/cut* style is part of the "user-misc" package. It is only
+enabled if LAMMPS is build with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_style coul/diel <pair_coul_diel>`
+
+**Default:** none
+
+.. _Lenart2:
+
+
+
+**(Lenart)** Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
+044509 (2007).
+
+.. _Jusufi2:
+
+
+
+**(Jusufi)** Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
+13783 (2008).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst
new file mode 100644
index 0000000000..47b7b5564e
--- /dev/null
+++ b/doc/src/pair_gayberne.rst
@@ -0,0 +1,264 @@
+.. index:: pair\_style gayberne
+
+pair\_style gayberne command
+============================
+
+pair\_style gayberne/gpu command
+================================
+
+pair\_style gayberne/intel command
+==================================
+
+pair\_style gayberne/omp command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style gayberne gamma upsilon mu cutoff
+
+* gamma = shift for potential minimum (typically 1)
+* upsilon = exponent for eta orientation-dependent energy function
+* mu = exponent for chi orientation-dependent energy function
+* cutoff = global cutoff for interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style gayberne 1.0 1.0 1.0 10.0
+   pair_coeff \* \* 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
+
+Description
+"""""""""""
+
+The *gayberne* styles compute a Gay-Berne anisotropic LJ interaction
+:ref:`(Berardi) <Berardi>` between pairs of ellipsoidal particles or an
+ellipsoidal and spherical particle via the formulas
+
+.. image:: Eqs/pair_gayberne.jpg
+   :align: center
+
+where A1 and A2 are the transformation matrices from the simulation
+box frame to the body frame and r12 is the center to center vector
+between the particles.  Ur controls the shifted distance dependent
+interaction based on the distance of closest approach of the two
+particles (h12) and the user-specified shift parameter gamma.  When
+both particles are spherical, the formula reduces to the usual
+Lennard-Jones interaction (see details below for when Gay-Berne treats
+a particle as "spherical").
+
+For large uniform molecules it has been shown that the energy
+parameters are approximately representable in terms of local contact
+curvatures :ref:`(Everaers) <Everaers2>`:
+
+.. image:: Eqs/pair_gayberne2.jpg
+   :align: center
+
+The variable names utilized as potential parameters are for the most
+part taken from :ref:`(Everaers) <Everaers2>` in order to be consistent with
+the :doc:`RE-squared pair potential <pair_resquared>`.  Details on the
+upsilon and mu parameters are given
+`here <PDF/pair_resquared_extra.pdf>`_.
+
+More details of the Gay-Berne formulation are given in the references
+listed below and in `this supplementary document <PDF/pair_gayberne_extra.pdf>`_.
+
+Use of this pair style requires the NVE, NVT, or NPT fixes with the
+*asphere* extension (e.g. :doc:`fix nve/asphere <fix_nve_asphere>`) in
+order to integrate particle rotation.  Additionally, :doc:`atom\_style ellipsoid <atom_style>` should be used since it defines the
+rotational state and the size and shape of each ellipsoidal particle.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon = well depth (energy units)
+* sigma = minimum effective particle radii (distance units)
+* epsilon\_i_a = relative well depth of type I for side-to-side interactions
+* epsilon\_i_b = relative well depth of type I for face-to-face interactions
+* epsilon\_i_c = relative well depth of type I for end-to-end interactions
+* epsilon\_j_a = relative well depth of type J for side-to-side interactions
+* epsilon\_j_b = relative well depth of type J for face-to-face interactions
+* epsilon\_j_c = relative well depth of type J for end-to-end interactions
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global
+cutoff specified in the pair\_style command is used.
+
+It is typical with the Gay-Berne potential to define *sigma* as the
+minimum of the 3 shape diameters of the particles involved in an I,I
+interaction, though this is not required.  Note that this is a
+different meaning for *sigma* than the :doc:`pair\_style resquared <pair_resquared>` potential uses.
+
+The epsilon\_i and epsilon\_j coefficients are actually defined for atom
+types, not for pairs of atom types.  Thus, in a series of pair\_coeff
+commands, they only need to be specified once for each atom type.
+
+Specifically, if any of epsilon\_i_a, epsilon\_i_b, epsilon\_i_c are
+non-zero, the three values are assigned to atom type I.  If all the
+epsilon\_i values are zero, they are ignored.  If any of epsilon\_j_a,
+epsilon\_j_b, epsilon\_j_c are non-zero, the three values are assigned
+to atom type J.  If all three epsilon\_j values are zero, they are
+ignored.  Thus the typical way to define the epsilon\_i and epsilon\_j
+coefficients is to list their values in "pair\_coeff I J" commands when
+I = J, but set them to 0.0 when I != J.  If you do list them when I !=
+J, you should insure they are consistent with their values in other
+pair\_coeff commands, since only the last setting will be in effect.
+
+Note that if this potential is being used as a sub-style of
+:doc:`pair\_style hybrid <pair_hybrid>`, and there is no "pair\_coeff I I"
+setting made for Gay-Berne for a particular type I (because I-I
+interactions are computed by another hybrid pair potential), then you
+still need to insure the epsilon a,b,c coefficients are assigned to
+that type. e.g. in a "pair\_coeff I J" command.
+
+.. note::
+
+   If the epsilon a = b = c for an atom type, and if the shape of
+   the particle itself is spherical, meaning its 3 shape parameters are
+   all the same, then the particle is treated as an LJ sphere by the
+   Gay-Berne potential.  This is significant because if two LJ spheres
+   interact, then the simple Lennard-Jones formula is used to compute
+   their interaction energy/force using the specified epsilon and sigma
+   as the standard LJ parameters.  This is much cheaper to compute than
+   the full Gay-Berne formula.  To treat the particle as a LJ sphere with
+   sigma = D, you should normally set epsilon a = b = c = 1.0, set the
+   pair\_coeff sigma = D, and also set the 3 shape parameters for the
+   particle to D.  The one exception is that if the 3 shape parameters
+   are set to 0.0, which is a valid way in LAMMPS to specify a point
+   particle, then the Gay-Berne potential will treat that as shape
+   parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
+   requires finite-size particles.  In this case you should still set the
+   pair\_coeff sigma to 1.0 as well.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for this pair style can be mixed.  The default mix
+value is *geometric*\ .  See the "pair\_modify" command for details.
+
+This pair styles supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction, but only for sphere-sphere interactions.  There is no
+shifting performed for ellipsoidal interactions due to the anisotropic
+dependence of the interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *gayberne* style is part of the ASPHERE package.  It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+These pair style require that atoms store torque and a quaternion to
+represent their orientation, as defined by the
+:doc:`atom\_style <atom_style>`.  It also require they store a per-type
+:doc:`shape <set>`.  The particles cannot store a per-particle
+diameter.
+
+This pair style requires that atoms be ellipsoids as defined by the
+:doc:`atom\_style ellipsoid <atom_style>` command.
+
+Particles acted on by the potential can be finite-size aspherical or
+spherical particles, or point particles.  Spherical particles have all
+3 of their shape parameters equal to each other.  Point particles have
+all 3 of their shape parameters equal to 0.0.
+
+The Gay-Berne potential does not become isotropic as r increases
+:ref:`(Everaers) <Everaers2>`.  The distance-of-closest-approach
+approximation used by LAMMPS becomes less accurate when high-aspect
+ratio ellipsoids are used.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix nve/asphere <fix_nve_asphere>`,
+:doc:`compute temp/asphere <compute_temp_asphere>`, :doc:`pair\_style resquared <pair_resquared>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Everaers2:
+
+
+
+**(Everaers)** Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
+
+.. _Berardi:
+
+
+
+**(Berardi)** Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
+Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
+
+.. _Perram:
+
+
+
+**(Perram)** Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
+
+.. _Allen3:
+
+
+
+**(Allen)** Allen and Germano, Mol Phys 104, 3225-3235 (2006).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst
new file mode 100644
index 0000000000..7f03519f35
--- /dev/null
+++ b/doc/src/pair_gran.rst
@@ -0,0 +1,315 @@
+.. index:: pair\_style gran/hooke
+
+pair\_style gran/hooke command
+==============================
+
+pair\_style gran/hooke/omp command
+==================================
+
+pair\_style gran/hooke/history command
+======================================
+
+pair\_style gran/hooke/history/omp command
+==========================================
+
+pair\_style gran/hooke/history/kk command
+=========================================
+
+pair\_style gran/hertz/history command
+======================================
+
+pair\_style gran/hertz/history/omp command
+==========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style Kn Kt gamma_n gamma_t xmu dampflag
+
+* style = *gran/hooke* or *gran/hooke/history* or *gran/hertz/history*
+* Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+* Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+* gamma\_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+* gamma\_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
+* xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
+* dampflag = 0 or 1 if tangential damping force is excluded or included
+
+
+.. note::
+
+   Versions of LAMMPS before 9Jan09 had different style names for
+   granular force fields.  This is to emphasize the fact that the
+   Hertzian equation has changed to model polydispersity more accurately.
+   A side effect of the change is that the Kn, Kt, gamma\_n, and gamma\_t
+   coefficients in the pair\_style command must be specified with
+   different values in order to reproduce calculations made with earlier
+   versions of LAMMPS, even for monodisperse systems.  See the NOTE below
+   for details.
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
+   pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
+
+Description
+"""""""""""
+
+The *gran* styles use the following formulas for the frictional force
+between two granular particles, as described in
+:ref:`(Brilliantov) <Brilliantov>`, :ref:`(Silbert) <Silbert>`, and
+:ref:`(Zhang) <Zhang3>`, when the distance r between two particles of radii
+Ri and Rj is less than their contact distance d = Ri + Rj.  There is
+no force between the particles when r > d.
+
+The two Hookean styles use this formula:
+
+.. image:: Eqs/pair_gran_hooke.jpg
+   :align: center
+
+The Hertzian style uses this formula:
+
+.. image:: Eqs/pair_gran_hertz.jpg
+   :align: center
+
+In both equations the first parenthesized term is the normal force
+between the two particles and the second parenthesized term is the
+tangential force.  The normal force has 2 terms, a contact force and a
+damping force.  The tangential force also has 2 terms: a shear force
+and a damping force.  The shear force is a "history" effect that
+accounts for the tangential displacement between the particles for the
+duration of the time they are in contact.  This term is included in
+pair styles *hooke/history* and *hertz/history*\ , but is not included
+in pair style *hooke*\ .  The tangential damping force term is included
+in all three pair styles if *dampflag* is set to 1; it is not included
+if *dampflag* is set to 0.
+
+The other quantities in the equations are as follows:
+
+* delta = d - r = overlap distance of 2 particles
+* Kn = elastic constant for normal contact
+* Kt = elastic constant for tangential contact
+* gamma\_n = viscoelastic damping constant for normal contact
+* gamma\_t = viscoelastic damping constant for tangential contact
+* m\_eff = Mi Mj / (Mi + Mj) = effective mass of 2 particles of mass Mi and Mj
+* Delta St = tangential displacement vector between 2 particles       which is truncated to satisfy a frictional yield criterion
+* n\_ij = unit vector along the line connecting the centers of the 2 particles
+* Vn = normal component of the relative velocity of the 2 particles
+* Vt = tangential component of the relative velocity of the 2 particles
+
+The Kn, Kt, gamma\_n, and gamma\_t coefficients are specified as
+parameters to the pair\_style command.  If a NULL is used for Kt, then
+a default value is used where Kt = 2/7 Kn.  If a NULL is used for
+gamma\_t, then a default value is used where gamma\_t = 1/2 gamma\_n.
+
+The interpretation and units for these 4 coefficients are different in
+the Hookean versus Hertzian equations.
+
+The Hookean model is one where the normal push-back force for two
+overlapping particles is a linear function of the overlap distance.
+Thus the specified Kn is in units of (force/distance).  Note that this
+push-back force is independent of absolute particle size (in the
+monodisperse case) and of the relative sizes of the two particles (in
+the polydisperse case).  This model also applies to the other terms in
+the force equation so that the specified gamma\_n is in units of
+(1/time), Kt is in units of (force/distance), and gamma\_t is in units
+of (1/time).
+
+The Hertzian model is one where the normal push-back force for two
+overlapping particles is proportional to the area of overlap of the
+two particles, and is thus a non-linear function of overlap distance.
+Thus Kn has units of force per area and is thus specified in units of
+(pressure).  The effects of absolute particle size (monodispersity)
+and relative size (polydispersity) are captured in the radii-dependent
+pre-factors.  When these pre-factors are carried through to the other
+terms in the force equation it means that the specified gamma\_n is in
+units of (1/(time\*distance)), Kt is in units of (pressure), and
+gamma\_t is in units of (1/(time\*distance)).
+
+Note that in the Hookean case, Kn can be thought of as a linear spring
+constant with units of force/distance.  In the Hertzian case, Kn is
+like a non-linear spring constant with units of force/area or
+pressure, and as shown in the :ref:`(Zhang) <Zhang3>` paper, Kn = 4G /
+(3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E /
+(2(1+nu)), and E = Young's modulus.  Similarly, Kt = 4G / (2-nu).
+(NOTE: in an earlier version of the manual, we incorrectly stated that
+Kt = 8G / (2-nu).)
+
+Thus in the Hertzian case Kn and Kt can be set to values that
+corresponds to properties of the material being modeled.  This is also
+true in the Hookean case, except that a spring constant must be chosen
+that is appropriate for the absolute size of particles in the model.
+Since relative particle sizes are not accounted for, the Hookean
+styles may not be a suitable model for polydisperse systems.
+
+.. note::
+
+   In versions of LAMMPS before 9Jan09, the equation for Hertzian
+   interactions did not include the sqrt(RiRj/Ri+Rj) term and thus was
+   not as accurate for polydisperse systems.  For monodisperse systems,
+   sqrt(RiRj/Ri+Rj) is a constant factor that effectively scales all 4
+   coefficients: Kn, Kt, gamma\_n, gamma\_t.  Thus you can set the values
+   of these 4 coefficients appropriately in the current code to reproduce
+   the results of a previous Hertzian monodisperse calculation.  For
+   example, for the common case of a monodisperse system with particles
+   of diameter 1, all 4 of these coefficients should now be set 2x larger
+   than they were previously.
+
+Xmu is also specified in the pair\_style command and is the upper limit
+of the tangential force through the Coulomb criterion Ft = xmu\*Fn,
+where Ft and Fn are the total tangential and normal force components
+in the formulas above.  Thus in the Hookean case, the tangential force
+between 2 particles grows according to a tangential spring and
+dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn\*xmu until
+the particles lose contact.  In the Hertzian case, a similar analogy
+holds, though the spring is no longer linear.
+
+.. note::
+
+   Normally, xmu should be specified as a fractional value between
+   0.0 and 1.0, however LAMMPS allows large values (up to 1.0e4) to allow
+   for modeling of systems which can sustain very large tangential
+   forces.
+
+The effective mass *m\_eff* is given by the formula above for two
+isolated particles.  If either particle is part of a rigid body, its
+mass is replaced by the mass of the rigid body in the formula above.
+This is determined by searching for a :doc:`fix rigid <fix_rigid>`
+command (or its variants).
+
+For granular styles there are no additional coefficients to set for
+each pair of atom types via the :doc:`pair\_coeff <pair_coeff>` command.
+All settings are global and are made via the pair\_style command.
+However you must still use the :doc:`pair\_coeff <pair_coeff>` for all
+pairs of granular atom types.  For example the command
+
+
+.. parsed-literal::
+
+   pair_coeff \* \*
+
+should be used if all atoms in the simulation interact via a granular
+potential (i.e. one of the pair styles above is used).  If a granular
+potential is used as a sub-style of :doc:`pair\_style hybrid <pair_hybrid>`, then specific atom types can be used in the
+pair\_coeff command to determine which atoms interact via a granular
+potential.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+The :doc:`pair\_modify <pair_modify>` mix, shift, table, and tail options
+are not relevant for granular pair styles.
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so a pair\_style command does not need to be
+specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+The single() function of these pair styles returns 0.0 for the energy
+of a pairwise interaction, since energy is not conserved in these
+dissipative potentials.  It also returns only the normal component of
+the pairwise interaction force.  However, the single() function also
+calculates 10 extra pairwise quantities.  The first 3 are the
+components of the tangential force between particles I and J, acting
+on particle I.  The 4th is the magnitude of this tangential force.
+The next 3 (5-7) are the components of the relative velocity in the
+normal direction (along the line joining the 2 sphere centers).  The
+last 3 (8-10) the components of the relative velocity in the
+tangential direction.
+
+These extra quantities can be accessed by the :doc:`compute pair/local <compute_pair_local>` command, as *p1*\ , *p2*\ , ...,
+*p10*\ .
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All the granular pair styles are part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+These pair styles require that atoms store torque and angular velocity
+(omega) as defined by the :doc:`atom\_style <atom_style>`.  They also
+require a per-particle radius is stored.  The *sphere* atom style does
+all of this.
+
+This pair style requires you to use the :doc:`comm\_modify vel yes <comm_modify>` command so that velocities are stored by ghost
+atoms.
+
+These pair styles will not restart exactly when using the
+:doc:`read\_restart <read_restart>` command, though they should provide
+statistically similar results.  This is because the forces they
+compute depend on atom velocities.  See the
+:doc:`read\_restart <read_restart>` command for more details.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Brilliantov:
+
+
+
+**(Brilliantov)** Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53,
+p 5382-5392 (1996).
+
+.. _Silbert:
+
+
+
+**(Silbert)** Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev
+E, 64, p 051302 (2001).
+
+.. _Zhang3:
+
+
+
+**(Zhang)** Zhang and Makse, Phys Rev E, 72, p 011301 (2005).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst
new file mode 100644
index 0000000000..294bec9b8c
--- /dev/null
+++ b/doc/src/pair_granular.rst
@@ -0,0 +1,878 @@
+.. index:: pair\_style granular
+
+pair\_style granular command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style granular cutoff
+
+* cutoff = global cutoff (optional).  See discussion below.
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style granular
+   pair_coeff \* \* hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity
+
+   pair_style granular
+   pair_coeff \* \* hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity
+
+   pair_style granular
+   pair_coeff \* \* hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4
+
+   pair_style granular
+   pair_coeff \* \* hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji
+
+   pair_style granular
+   pair_coeff 1 \* jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+   pair_coeff 2 2 hertz 200.0 100.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
+
+   pair_style granular
+   pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+   pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall
+
+Description
+"""""""""""
+
+The *granular* styles support a variety of options for the normal,
+tangential, rolling and twisting forces resulting from contact between
+two granular particles. This expands on the options offered by the
+:doc:`pair gran/\* <pair_gran>` pair styles. The total computed forces
+and torques are the sum of various models selected for the normal,
+tangential, rolling and twisting modes of motion.
+
+All model choices and parameters are entered in the
+:doc:`pair\_coeff <pair_coeff>` command, as described below.  Unlike
+e.g. :doc:`pair gran/hooke <pair_gran>`, coefficient values are not
+global, but can be set to different values for different combinations
+of particle types, as determined by the :doc:`pair\_coeff <pair_coeff>`
+command.  If the contact model choice is the same for two particle
+types, the mixing for the cross-coefficients can be carried out
+automatically. This is shown in the last example, where model
+choices are the same for type 1 - type 1 as for type 2 - type2
+interactions, but coefficients are different. In this case, the
+mixed coefficients for type 1 - type 2 interactions can be determined from
+mixing rules discussed below.  For additional flexibility,
+coefficients as well as model forms can vary between particle types,
+as shown in the fourth example: type 1 - type 1 interactions are based
+on a Johnson-Kendall-Roberts normal contact model and 2-2 interactions
+are based on a DMT cohesive model (see below).  In that example, 1-1
+and 2-2 interactions have different model forms, in which case mixing of
+coefficients cannot be determined, so 1-2 interactions must be
+explicitly defined via the *pair\_coeff 1 \** command, otherwise an
+error would result.
+
+
+----------
+
+
+The first required keyword for the *pair\_coeff* command is the normal
+contact model. Currently supported options for normal contact models
+and their required arguments are:
+
+1. *hooke* : :math:`k_n`, :math:`\eta_{n0}` (or :math:`e`)
+2. *hertz* : :math:`k_n`, :math:`\eta_{n0}` (or :math:`e`)
+3. *hertz/material* : E, :math:`\eta_{n0}` (or :math:`e`), :math:`\nu`
+4. *dmt* : E, :math:`\eta_{n0}` (or :math:`e`), :math:`\nu`, :math:`\gamma`
+5. *jkr* : E, :math:`\eta_{n0}` (or :math:`e`), :math:`\nu`, :math:`\gamma`
+
+Here, :math:`k_n` is spring stiffness (with units that depend on model
+choice, see below); :math:`\eta_{n0}` is a damping prefactor (or, in its
+place a coefficient of restitution :math:`e`, depending on the choice of
+damping mode, see below); E is Young's modulus in units of
+*force*\ /\ *length*\ \^2, i.e. *pressure*\ ; :math:`\nu` is Poisson's ratio and
+:math:`\gamma` is a surface energy density, in units of
+*energy*\ /\ *length*\ \^2.
+
+For the *hooke* model, the normal, elastic component of force acting
+on particle *i* due to contact with particle *j* is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_{ne, Hooke} = k_N \delta_{ij} \mathbf{n}\end{equation}
+
+Where :math:`\delta_{ij} = R_i + R_j - \|\mathbf{r}_{ij}\|` is the particle
+overlap, :math:`R_i, R_j` are the particle radii, :math:`\mathbf{r}_{ij} = \mathbf{r}_i - \mathbf{r}_j` is the vector separating the two
+particle centers (note the i-j ordering so that :math:`F_{ne}` is
+positive for repulsion), and :math:`\mathbf{n} = \frac{\mathbf{r}_{ij}}{\|\mathbf{r}_{ij}\|}`.  Therefore,
+for *hooke*\ , the units of the spring constant :math:`k_n` are
+*force*\ /\ *distance*\ , or equivalently *mass*\ /*time\^2*.
+
+For the *hertz* model, the normal component of force is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_{ne, Hertz} = k_N R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}\end{equation}
+
+Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective
+radius, denoted for simplicity as *R* from here on.  For *hertz*\ , the
+units of the spring constant :math:`k_n` are *force*\ /\ *length*\ \^2, or
+equivalently *pressure*\ .
+
+For the *hertz/material* model, the force is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}\end{equation}
+
+Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}` is the effective Young's
+modulus, with :math:`\nu_i, \nu_j` the Poisson ratios of the particles of
+types *i* and *j*\ . Note that if the elastic modulus and the shear
+modulus of the two particles are the same, the *hertz/material* model
+is equivalent to the *hertz* model with :math:`k_N = 4/3 E_{eff}`
+
+The *dmt* model corresponds to the
+:ref:`(Derjaguin-Muller-Toporov) <DMT1975>` cohesive model, where the force
+is simply Hertz with an additional attractive cohesion term:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_{ne, dmt} = \left(\frac{4}{3} E R^{1/2}\delta_{ij}^{3/2} - 4\pi\gamma R\right)\mathbf{n}\end{equation}
+
+The *jkr* model is the :ref:`(Johnson-Kendall-Roberts) <JKR1971>` model,
+where the force is computed as:
+
+
+.. math::
+
+   \begin{equation}\label{eq:force_jkr}
+   \mathbf{F}_{ne, jkr} = \left(\frac{4Ea^3}{3R} - 2\pi a^2\sqrt{\frac{4\gamma E}{\pi a}}\right)\mathbf{n}\end{equation}
+
+Here, *a* is the radius of the contact zone, related to the overlap
+:math:`\delta` according to:
+
+
+.. math::
+
+   \begin{equation}\delta = a^2/R - 2\sqrt{\pi \gamma a/E}\end{equation}
+
+LAMMPS internally inverts the equation above to solve for *a* in terms
+of :math:`\delta`, then solves for the force in the previous
+equation. Additionally, note that the JKR model allows for a tensile
+force beyond contact (i.e. for :math:`\delta < 0`), up to a maximum of
+:math:`3\pi\gamma R` (also known as the 'pull-off' force).  Note that this
+is a hysteretic effect, where particles that are not contacting
+initially will not experience force until they come into contact
+:math:`\delta \geq 0`; as they move apart and (:math:`\delta < 0`), they
+experience a tensile force up to :math:`3\pi\gamma R`, at which point they
+lose contact.
+
+
+----------
+
+
+In addition, the normal force is augmented by a damping term of the
+following general form:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_{n,damp} = -\eta_n \mathbf{v}_{n,rel}\end{equation}
+
+Here, :math:`\mathbf{v}_{n,rel} = (\mathbf{v}_j - \mathbf{v}_i) \cdot \mathbf{n} \mathbf{n}` is the component of relative velocity along
+:math:`\mathbf{n}`.
+
+The optional *damping* keyword to the *pair\_coeff* command followed by
+a keyword determines the model form of the damping factor :math:`\eta_n`,
+and the interpretation of the :math:`\eta_{n0}` or :math:`e` coefficients
+specified as part of the normal contact model settings. The *damping*
+keyword and corresponding model form selection may be appended
+anywhere in the *pair coeff* command.  Note that the choice of damping
+model affects both the normal and tangential damping (and depending on
+other settings, potentially also the twisting damping).  The options
+for the damping model currently supported are:
+
+1. *velocity*
+2. *mass\_velocity*
+3. *viscoelastic*
+4. *tsuji*
+
+If the *damping* keyword is not specified, the *viscoelastic* model is
+used by default.
+
+For *damping velocity*\ , the normal damping is simply equal to the
+user-specified damping coefficient in the *normal* model:
+
+
+.. math::
+
+   \begin{equation}\eta_n = \eta_{n0}\end{equation}
+
+Here, :math:`\eta_{n0}` is the damping coefficient specified for the normal
+contact model, in units of *mass*\ /\ *time*\ .
+
+For *damping mass\_velocity*, the normal damping is given by:
+
+
+.. math::
+
+   \begin{equation}\eta_n = \eta_{n0} m_{eff}\end{equation}
+
+Here, :math:`\eta_{n0}` is the damping coefficient specified for the normal
+contact model, in units of *mass*\ /\ *time* and
+:math:`m_{eff} = m_i m_j/(m_i + m_j)` is the effective mass.
+Use *damping mass\_velocity* to reproduce the damping behavior of
+*pair gran/hooke/\**.
+
+The *damping viscoelastic* model is based on the viscoelastic
+treatment of :ref:`(Brilliantov et al) <Brill1996>`, where the normal
+damping is given by:
+
+
+.. math::
+
+   \begin{equation}\eta_n = \eta_{n0}\ a m_{eff}\end{equation}
+
+Here, *a* is the contact radius, given by :math:`a =\sqrt{R\delta}`
+for all models except *jkr*\ , for which it is given implicitly according
+to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`.  For *damping viscoelastic*\ ,
+:math:`\eta_{n0}` is in units of 1/(\ *time*\ \*\ *distance*\ ).
+
+The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`. Here, the damping coefficient specified as part of
+the normal model is interpreted as a restitution coefficient
+:math:`e`. The damping constant :math:`\eta_n` is given by:
+
+
+.. math::
+
+   \begin{equation}\eta_n = \alpha (m_{eff}k_n)^{1/2}\end{equation}
+
+For normal contact models based on material parameters, :math:`k_n = 4/3Ea`.  The parameter :math:`\alpha` is related to the restitution
+coefficient *e* according to:
+
+
+.. math::
+
+   \begin{equation}\alpha = 1.2728-4.2783e+11.087e^2-22.348e^3+27.467e^4-18.022e^5+4.8218e^6\end{equation}
+
+The dimensionless coefficient of restitution :math:`e` specified as part
+of the normal contact model parameters should be between 0 and 1, but
+no error check is performed on this.
+
+The total normal force is computed as the sum of the elastic and
+damping components:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_n = \mathbf{F}_{ne} + \mathbf{F}_{n,damp}\end{equation}
+
+
+----------
+
+
+The *pair\_coeff* command also requires specification of the tangential
+contact model. The required keyword *tangential* is expected, followed
+by the model choice and associated parameters. Currently supported
+tangential model choices and their expected parameters are as follows:
+
+1. *linear\_nohistory* : :math:`x_{\gamma,t}`, :math:`\mu_s`
+2. *linear\_history* : :math:`k_t`, :math:`x_{\gamma,t}`, :math:`\mu_s`
+3. *mindlin* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s`
+4. *mindlin\_rescale* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s`
+
+Here, :math:`x_{\gamma,t}` is a dimensionless multiplier for the normal
+damping :math:`\eta_n` that determines the magnitude of the tangential
+damping, :math:`\mu_t` is the tangential (or sliding) friction
+coefficient, and :math:`k_t` is the tangential stiffness coefficient.
+
+For *tangential linear\_nohistory*, a simple velocity-dependent Coulomb
+friction criterion is used, which mimics the behavior of the *pair
+gran/hooke* style. The tangential force (\mathbf{F}\_t\) is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_t =  -min(\mu_t F_{n0}, \|\mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}\end{equation}
+
+The tangential damping force :math:`\mathbf{F}_\mathrm{t,damp}` is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_\mathrm{t,damp} = -\eta_t \mathbf{v}_{t,rel}\end{equation}
+
+The tangential damping prefactor :math:`\eta_t` is calculated by scaling
+the normal damping :math:`\eta_n` (see above):
+
+
+.. math::
+
+   \begin{equation}\eta_t = -x_{\gamma,t} \eta_n\end{equation}
+
+The normal damping prefactor :math:`\eta_n` is determined by the choice
+of the *damping* keyword, as discussed above.  Thus, the *damping*
+keyword also affects the tangential damping.  The parameter
+:math:`x_{\gamma,t}` is a scaling coefficient. Several works in the
+literature use :math:`x_{\gamma,t} = 1` (:ref:`Marshall <Marshall2009>`,
+:ref:`Tsuji et al <Tsuji1992>`, :ref:`Silbert et al <Silbert2001>`).  The relative
+tangential velocity at the point of contact is given by
+:math:`\mathbf{v}_{t, rel} = \mathbf{v}_{t} - (R_i\Omega_i + R_j\Omega_j) \times \mathbf{n}`, where :math:`\mathbf{v}_{t} = \mathbf{v}_r - \mathbf{v}_r\cdot\mathbf{n}{n}`,
+:math:`\mathbf{v}_r = \mathbf{v}_j - \mathbf{v}_i`.
+The direction of the applied force is :math:`\mathbf{t} = \mathbf{v_{t,rel}}/\|\mathbf{v_{t,rel}}\|` .
+
+The normal force value :math:`F_{n0}` used to compute the critical force
+depends on the form of the contact model. For non-cohesive models
+(\ *hertz*\ , *hertz/material*\ , *hooke*\ ), it is given by the magnitude of
+the normal force:
+
+
+.. math::
+
+   \begin{equation}F_{n0} = \|\mathbf{F}_n\|\end{equation}
+
+For cohesive models such as *jkr* and *dmt*\ , the critical force is
+adjusted so that the critical tangential force approaches :math:`\mu_t F_{pulloff}`, see :ref:`Marshall <Marshall2009>`, equation 43, and
+:ref:`Thornton <Thornton1991>`.  For both models, :math:`F_{n0}` takes the
+form:
+
+
+.. math::
+
+   \begin{equation}F_{n0} = \|\mathbf{F}_ne + 2 F_{pulloff}\|\end{equation}
+
+Where :math:`F_{pulloff} = 3\pi \gamma R` for *jkr*\ , and
+:math:`F_{pulloff} = 4\pi \gamma R` for *dmt*\ .
+
+The remaining tangential options all use accumulated tangential
+displacement (i.e. contact history). This is discussed below in the
+context of the *linear\_history* option, but the same treatment of the
+accumulated displacement applies to the other options as well.
+
+For *tangential linear\_history*, the tangential force is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_t =  -min(\mu_t F_{n0}, \|-k_t\mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}\end{equation}
+
+Here, :math:`\mathbf{\xi}` is the tangential displacement accumulated
+during the entire duration of the contact:
+
+
+.. math::
+
+   \begin{equation}\mathbf{\xi} = \int_{t0}^t \mathbf{v}_{t,rel}(\tau) \mathrm{d}\tau\end{equation}
+
+This accumulated tangential displacement must be adjusted to account
+for changes in the frame of reference of the contacting pair of
+particles during contact. This occurs due to the overall motion of the
+contacting particles in a rigid-body-like fashion during the duration
+of the contact. There are two modes of motion that are relevant: the
+'tumbling' rotation of the contacting pair, which changes the
+orientation of the plane in which tangential displacement occurs; and
+'spinning' rotation of the contacting pair about the vector connecting
+their centers of mass (:math:`\mathbf{n}`).  Corrections due to the
+former mode of motion are made by rotating the accumulated
+displacement into the plane that is tangential to the contact vector
+at each step, or equivalently removing any component of the tangential
+displacement that lies along :math:`\mathbf{n}`, and rescaling to
+preserve the magnitude.  This follows the discussion in
+:ref:`Luding <Luding2008>`, see equation 17 and relevant discussion in that
+work:
+
+
+.. math::
+
+   \begin{equation}\mathbf{\xi} = \left(\mathbf{\xi'} - (\mathbf{n} \cdot \mathbf{\xi'})\mathbf{n}\right) \frac{\|\mathbf{\xi'}\|}{\|\mathbf{\xi'}\| - \mathbf{n}\cdot\mathbf{\xi'}}
+   \label{eq:rotate_displacements}\end{equation}
+
+Here, :math:`\mathbf{\xi'}` is the accumulated displacement prior to the
+current time step and :math:`\mathbf{\xi}` is the corrected
+displacement. Corrections to the displacement due to the second mode
+of motion described above (rotations about :math:`\mathbf{n}`) are not
+currently implemented, but are expected to be minor for most
+simulations.
+
+Furthermore, when the tangential force exceeds the critical force, the
+tangential displacement is re-scaled to match the value for the
+critical force (see :ref:`Luding <Luding2008>`, equation 20 and related
+discussion):
+
+
+.. math::
+
+   \begin{equation}\mathbf{\xi} = -\frac{1}{k_t}\left(\mu_t F_{n0}\mathbf{t} + \mathbf{F}_{t,damp}\right)\end{equation}
+
+The tangential force is added to the total normal force (elastic plus
+damping) to produce the total force on the particle. The tangential
+force also acts at the contact point (defined as the center of the
+overlap region) to induce a torque on each particle according to:
+
+
+.. math::
+
+   \begin{equation}\mathbf{\tau}_i = -(R_i - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t\end{equation}
+
+
+.. math::
+
+   \begin{equation}\mathbf{\tau}_j = -(R_j - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t\end{equation}
+
+For *tangential mindlin*\ , the :ref:`Mindlin <Mindlin1949>` no-slip solution is used, which differs from the *linear\_history*
+option by an additional factor of *a*\ , the radius of the contact region. The tangential force is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_t =  -min(\mu_t F_{n0}, \|-k_t a \mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}\end{equation}
+
+Here, *a* is the radius of the contact region, given by :math:`a =\sqrt{R\delta}`
+for all normal contact models, except for *jkr*\ , where it is given
+implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see
+discussion above. To match the Mindlin solution, one should set :math:`k_t = 4G/(2-\nu)`, where :math:`G` is the shear modulus, related to Young's modulus
+:math:`E` by :math:`G = E/(2(1+\nu))`, where :math:`\nu` is Poisson's ratio. This
+can also be achieved by specifying *NULL* for :math:`k_t`, in which case a
+normal contact model that specifies material parameters :math:`E` and
+:math:`\nu` is required (e.g. *hertz/material*\ , *dmt* or *jkr*\ ). In this
+case, mixing of the shear modulus for different particle types *i* and
+*j* is done according to:
+
+
+.. math::
+
+   \begin{equation}1/G = 2(2-\nu_i)(1+\nu_i)/E_i + 2(2-\nu_j)(1+\nu_j)/E_j\end{equation}
+
+The *mindlin\_rescale* option uses the same form as *mindlin*\ , but the
+magnitude of the tangential displacement is re-scaled as the contact
+unloads, i.e. if :math:`a < a_{t_{n-1}}`:
+
+
+.. math::
+
+   \begin{equation}\mathbf{\xi} = \mathbf{\xi_{t_{n-1}}} \frac{a}{a_{t_{n-1}}}\end{equation}
+
+Here, :math:`t_{n-1}` indicates the value at the previous time
+step. This rescaling accounts for the fact that a decrease in the
+contact area upon unloading leads to the contact being unable to
+support the previous tangential loading, and spurious energy is
+created without the rescaling above (:ref:`Walton <WaltonPC>` ). See also
+discussion in :ref:`Thornton et al, 2013 <Thornton2013>` , particularly
+equation 18(b) of that work and associated discussion.
+
+
+----------
+
+
+The optional *rolling* keyword enables rolling friction, which resists
+pure rolling motion of particles. The options currently supported are:
+
+1. *none*
+2. *sds* : :math:`k_{roll}`, :math:`\gamma_{roll}`, :math:`\mu_{roll}`
+
+If the *rolling* keyword is not specified, the model defaults to *none*\ .
+
+For *rolling sds*\ , rolling friction is computed via a
+spring-dashpot-slider, using a 'pseudo-force' formulation, as detailed
+by :ref:`Luding <Luding2008>`. Unlike the formulation in
+:ref:`Marshall <Marshall2009>`, this allows for the required adjustment of
+rolling displacement due to changes in the frame of reference of the
+contacting pair.  The rolling pseudo-force is computed analogously to
+the tangential force:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_{roll,0} =  k_{roll} \mathbf{\xi}_{roll}  - \gamma_{roll} \mathbf{v}_{roll}\end{equation}
+
+Here, :math:`\mathbf{v}_{roll} = -R(\mathbf{\Omega}_i - \mathbf{\Omega}_j) \times \mathbf{n}` is the relative rolling
+velocity, as given in :ref:`Wang et al <Wang2015>` and
+:ref:`Luding <Luding2008>`. This differs from the expressions given by :ref:`Kuhn and Bagi <Kuhn2004>` and used in :ref:`Marshall <Marshall2009>`; see :ref:`Wang et al <Wang2015>` for details. The rolling displacement is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{\xi}_{roll} = \int_{t_0}^t \mathbf{v}_{roll} (\tau) \mathrm{d} \tau\end{equation}
+
+A Coulomb friction criterion truncates the rolling pseudo-force if it
+exceeds a critical value:
+
+
+.. math::
+
+   \begin{equation}\mathbf{F}_{roll} =  min(\mu_{roll} F_{n,0}, \|\mathbf{F}_{roll,0}\|)\mathbf{k}\end{equation}
+
+Here, :math:`\mathbf{k} = \mathbf{v}_{roll}/\|\mathbf{v}_{roll}\|` is the direction of
+the pseudo-force.  As with tangential displacement, the rolling
+displacement is rescaled when the critical force is exceeded, so that
+the spring length corresponds the critical force. Additionally, the
+displacement is adjusted to account for rotations of the frame of
+reference of the two contacting particles in a manner analogous to the
+tangential displacement.
+
+The rolling pseudo-force does not contribute to the total force on
+either particle (hence 'pseudo'), but acts only to induce an equal and
+opposite torque on each particle, according to:
+
+
+.. math::
+
+   \begin{equation}\tau_{roll,i} =  R_{eff} \mathbf{n} \times \mathbf{F}_{roll}\end{equation}
+
+
+.. math::
+
+   \begin{equation}\tau_{roll,j} =  -\tau_{roll,i}\end{equation}
+
+
+----------
+
+
+The optional *twisting* keyword enables twisting friction, which
+resists rotation of two contacting particles about the vector
+:math:`\mathbf{n}` that connects their centers. The options currently
+supported are:
+
+1. *none*
+2. *sds* : :math:`k_{twist}`, :math:`\gamma_{twist}`, :math:`\mu_{twist}`
+3. *marshall*
+
+If the *twisting* keyword is not specified, the model defaults to *none*\ .
+
+For both *twisting sds* and *twisting marshall*\ , a history-dependent
+spring-dashpot-slider is used to compute the twisting torque. Because
+twisting displacement is a scalar, there is no need to adjust for
+changes in the frame of reference due to rotations of the particle
+pair. The formulation in :ref:`Marshall <Marshall2009>` therefore provides
+the most straightforward treatment:
+
+
+.. math::
+
+   \begin{equation}\tau_{twist,0} = -k_{twist}\xi_{twist} - \gamma_{twist}\Omega_{twist}\end{equation}
+
+Here :math:`\xi_{twist} = \int_{t_0}^t \Omega_{twist} (\tau) \mathrm{d}\tau` is the twisting angular displacement, and
+:math:`\Omega_{twist} = (\mathbf{\Omega}_i - \mathbf{\Omega}_j) \cdot \mathbf{n}` is the relative twisting angular velocity. The torque
+is then truncated according to:
+
+
+.. math::
+
+   \begin{equation}\tau_{twist} = min(\mu_{twist} F_{n,0}, \tau_{twist,0})\end{equation}
+
+Similar to the sliding and rolling displacement, the angular
+displacement is rescaled so that it corresponds to the critical value
+if the twisting torque exceeds this critical value:
+
+
+.. math::
+
+   \begin{equation}\xi_{twist} = \frac{1}{k_{twist}} (\mu_{twist} F_{n,0}sgn(\Omega_{twist}) - \gamma_{twist}\Omega_{twist})\end{equation}
+
+For *twisting sds*\ , the coefficients :math:`k_{twist}, \gamma_{twist}`
+and :math:`\mu_{twist}` are simply the user input parameters that follow
+the *twisting sds* keywords in the *pair\_coeff* command.
+
+For *twisting\_marshall*, the coefficients are expressed in terms of
+sliding friction coefficients, as discussed in
+:ref:`Marshall <Marshall2009>` (see equations 32 and 33 of that work):
+
+
+.. math::
+
+   \begin{equation}k_{twist} = 0.5k_ta^2\end{equation}
+
+
+.. math::
+
+   \begin{equation}\eta_{twist} = 0.5\eta_ta^2\end{equation}
+
+
+.. math::
+
+   \begin{equation}\mu_{twist} = \frac{2}{3}a\mu_t\end{equation}
+
+Finally, the twisting torque on each particle is given by:
+
+
+.. math::
+
+   \begin{equation}\mathbf{\tau}_{twist,i} = \tau_{twist}\mathbf{n}\end{equation}
+
+
+.. math::
+
+   \begin{equation}\mathbf{\tau}_{twist,j} = -\mathbf{\tau}_{twist,i}\end{equation}
+
+
+----------
+
+
+The *granular* pair style can reproduce the behavior of the
+*pair gran/\** styles with the appropriate settings (some very
+minor differences can be expected due to corrections in
+displacement history frame-of-reference, and the application
+of the torque at the center of the contact rather than
+at each particle). The first example above
+is equivalent to *pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1*\ .
+The second example is equivalent to
+*pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
+The third example is equivalent to
+*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
+
+
+----------
+
+
+LAMMPS automatically sets pairwise cutoff values for *pair\_style
+granular* based on particle radii (and in the case of *jkr* pull-off
+distances). In the vast majority of situations, this is adequate.
+However, a cutoff value can optionally be appended to the *pair\_style
+granular* command to specify a global cutoff (i.e. a cutoff for all
+atom types). Additionally, the optional *cutoff* keyword can be passed
+to the *pair\_coeff* command, followed by a cutoff value.  This will
+set a pairwise cutoff for the atom types in the *pair\_coeff* command.
+These options may be useful in some rare cases where the automatic
+cutoff determination is not sufficient, e.g.  if particle diameters
+are being modified via the *fix adapt* command. In that case, the
+global cutoff specified as part of the *pair\_style granular* command
+is applied to all atom types, unless it is overridden for a given atom
+type combination by the *cutoff* value specified in the *pair coeff*
+command.  If *cutoff* is only specified in the *pair coeff* command
+and no global cutoff is appended to the *pair\_style granular* command,
+then LAMMPS will use that cutoff for the specified atom type
+combination, and automatically set pairwise cutoffs for the remaining
+atom types.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+The :doc:`pair\_modify <pair_modify>` mix, shift, table, and tail options
+are not relevant for granular pair styles.
+
+Mixing of coefficients is carried out using geometric averaging for
+most quantities, e.g. if friction coefficient for type 1-type 1
+interactions is set to :math:`\mu_1`, and friction coefficient for type
+2-type 2 interactions is set to :math:`\mu_2`, the friction coefficient
+for type1-type2 interactions is computed as :math:`\sqrt{\mu_1\mu_2}`
+(unless explicitly specified to a different value by a *pair\_coeff 1 2
+...* command). The exception to this is elastic modulus, only
+applicable to *hertz/material*\ , *dmt* and *jkr* normal contact
+models. In that case, the effective elastic modulus is computed as:
+
+
+.. math::
+
+   \begin{equation}E_{eff,ij} = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}\end{equation}
+
+If the *i-j* coefficients :math:`E_{ij}` and :math:`\nu_{ij}` are
+explicitly specified, the effective modulus is computed as:
+
+
+.. math::
+
+   \begin{equation}E_{eff,ij} = \left(\frac{1-\nu_{ij}^2}{E_{ij}} + \frac{1-\nu_{ij}^2}{E_{ij}}\right)^{-1}\end{equation}
+
+or
+
+
+.. math::
+
+   \begin{equation}E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij})}\end{equation}
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so a pair\_style command does not need to be
+specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+The single() function of these pair styles returns 0.0 for the energy
+of a pairwise interaction, since energy is not conserved in these
+dissipative potentials.  It also returns only the normal component of
+the pairwise interaction force.  However, the single() function also
+calculates 12 extra pairwise quantities.  The first 3 are the
+components of the tangential force between particles I and J, acting
+on particle I.  The 4th is the magnitude of this tangential force.
+The next 3 (5-7) are the components of the rolling torque acting on
+particle I. The next entry (8) is the magnitude of the rolling torque.
+The next entry (9) is the magnitude of the twisting torque acting
+about the vector connecting the two particle centers.
+The last 3 (10-12) are the components of the vector connecting
+the centers of the two particles (x\_I - x\_J).
+
+These extra quantities can be accessed by the :doc:`compute pair/local <compute_pair_local>` command, as *p1*\ , *p2*\ , ...,
+*p12*\ .
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All the granular pair styles are part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+These pair styles require that atoms store torque and angular velocity
+(omega) as defined by the :doc:`atom\_style <atom_style>`.  They also
+require a per-particle radius is stored.  The *sphere* atom style does
+all of this.
+
+This pair style requires you to use the :doc:`comm\_modify vel yes <comm_modify>` command so that velocities are stored by ghost
+atoms.
+
+These pair styles will not restart exactly when using the
+:doc:`read\_restart <read_restart>` command, though they should provide
+statistically similar results.  This is because the forces they
+compute depend on atom velocities.  See the
+:doc:`read\_restart <read_restart>` command for more details.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+:doc:`pair gran/\* <pair_gran>`
+
+Default
+"""""""
+
+For the *pair\_coeff* settings: *damping viscoelastic*\ , *rolling none*\ ,
+*twisting none*\ .
+
+**References:**
+
+.. _Brill1996:
+
+
+
+**(Brilliantov et al, 1996)** Brilliantov, N. V., Spahn, F., Hertzsch,
+J. M., & Poschel, T. (1996).  Model for collisions in granular
+gases. Physical review E, 53(5), 5382.
+
+.. _Tsuji1992:
+
+
+
+**(Tsuji et al, 1992)** Tsuji, Y., Tanaka, T., & Ishida,
+T. (1992). Lagrangian numerical simulation of plug flow of
+cohesionless particles in a horizontal pipe. Powder technology, 71(3),
+239-250.
+
+.. _JKR1971:
+
+
+
+**(Johnson et al, 1971)** Johnson, K. L., Kendall, K., & Roberts,
+A. D. (1971).  Surface energy and the contact of elastic
+solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
+
+.. _DMT1975:
+
+
+
+**Derjaguin et al, 1975)** Derjaguin, B. V., Muller, V. M., & Toporov,
+Y. P. (1975). Effect of contact deformations on the adhesion of
+particles. Journal of Colloid and interface science, 53(2), 314-326.
+
+.. _Luding2008:
+
+
+
+**(Luding, 2008)** Luding, S. (2008). Cohesive, frictional powders:
+contact models for tension. Granular matter, 10(4), 235.
+
+.. _Marshall2009:
+
+
+
+**(Marshall, 2009)** Marshall, J. S. (2009). Discrete-element modeling
+of particulate aerosol flows.  Journal of Computational Physics,
+228(5), 1541-1561.
+
+.. _Silbert2001:
+
+
+
+**(Silbert, 2001)** Silbert, L. E., Ertas, D., Grest, G. S., Halsey,
+T. C., Levine, D., & Plimpton, S. J. (2001).  Granular flow down an
+inclined plane: Bagnold scaling and rheology. Physical Review E,
+64(5), 051302.
+
+.. _Kuhn2004:
+
+
+
+**(Kuhn and Bagi, 2005)** Kuhn, M. R., & Bagi, K. (2004). Contact
+rolling and deformation in granular media.  International journal of
+solids and structures, 41(21), 5793-5820.
+
+.. _Wang2015:
+
+
+
+**(Wang et al, 2015)** Wang, Y., Alonso-Marroquin, F., & Guo,
+W. W. (2015).  Rolling and sliding in 3-D discrete element
+models. Particuology, 23, 49-55.
+
+.. _Thornton1991:
+
+
+
+**(Thornton, 1991)** Thornton, C. (1991). Interparticle sliding in the
+presence of adhesion.  J. Phys. D: Appl. Phys. 24 1942
+
+.. _Mindlin1949:
+
+
+
+**(Mindlin, 1949)** Mindlin, R. D. (1949). Compliance of elastic bodies
+in contact.  J. Appl. Mech., ASME 16, 259-268.
+
+.. _Thornton2013:
+
+
+
+**(Thornton et al, 2013)** Thornton, C., Cummins, S. J., & Cleary,
+P. W. (2013).  An investigation of the comparative behaviour of
+alternative contact force models during inelastic collisions. Powder
+Technology, 233, 30-46.
+
+.. _WaltonPC:
+
+
+
+**(Otis R. Walton)** Walton, O.R., Personal Communication
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst
new file mode 100644
index 0000000000..9bc803bc55
--- /dev/null
+++ b/doc/src/pair_gromacs.rst
@@ -0,0 +1,193 @@
+.. index:: pair\_style lj/gromacs
+
+pair\_style lj/gromacs command
+==============================
+
+pair\_style lj/gromacs/gpu command
+==================================
+
+pair\_style lj/gromacs/kk command
+=================================
+
+pair\_style lj/gromacs/omp command
+==================================
+
+pair\_style lj/gromacs/coul/gromacs command
+===========================================
+
+pair\_style lj/gromacs/coul/gromacs/kk command
+==============================================
+
+pair\_style lj/gromacs/coul/gromacs/omp command
+===============================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/gromacs* or *lj/gromacs/coul/gromacs*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *lj/gromacs* args = inner outer
+       inner, outer = global switching cutoffs for Lennard Jones
+     *lj/gromacs/coul/gromacs* args = inner outer (inner2) (outer2)
+       inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
+       inner2, outer2 = global switching cutoffs for Coulombic (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/gromacs 9.0 12.0
+   pair_coeff \* \* 100.0 2.0
+   pair_coeff 2 2 100.0 2.0 8.0 10.0
+
+   pair_style lj/gromacs/coul/gromacs 9.0 12.0
+   pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
+   pair_coeff \* \* 100.0 2.0
+
+Description
+"""""""""""
+
+The *lj/gromacs* styles compute shifted LJ and Coulombic interactions
+with an additional switching function S(r) that ramps the energy and force
+smoothly to zero between an inner and outer cutoff.  It is a commonly
+used potential in the `GROMACS <http://www.gromacs.org>`_ MD code and for
+the coarse-grained models of :ref:`(Marrink) <Marrink>`.
+
+.. image:: Eqs/pair_gromacs.jpg
+   :align: center
+
+r1 is the inner cutoff; rc is the outer cutoff.  The coefficients A, B,
+and C are computed by LAMMPS to perform the shifting and smoothing.
+The function
+S(r) is actually applied once to each term of the LJ formula and once
+to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
+depending on which pair\_style is used.  The boundary conditions
+applied to the smoothing function are as follows: S'(r1) = S''(r1) = 0,
+S(rc) = -E(rc), S'(rc) = -E'(rc), and S''(rc) = -E''(rc),
+where E(r) is the corresponding term
+in the LJ or Coulombic potential energy function.
+Single and double primes denote first and second
+derivatives with respect to r, respectively.
+
+The inner and outer cutoff for the LJ and Coulombic terms can be the
+same or different depending on whether 2 or 4 arguments are used in
+the pair\_style command.  The inner LJ cutoff must be > 0, but the
+inner Coulombic cutoff can be >= 0.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* inner (distance units)
+* outer (distance units)
+
+Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum at 2\^(1/6)
+sigma.
+
+The last 2 coefficients are optional inner and outer cutoffs for style
+*lj/gromacs*\ .  If not specified, the global *inner* and *outer* values
+are used.
+
+The last 2 coefficients cannot be used with style
+*lj/gromacs/coul/gromacs* because this force field does not allow
+varying cutoffs for individual atom pairs; all pairs use the global
+cutoff(s) specified in the pair\_style command.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is *geometric*\ .  See the "pair\_modify" command
+for details.
+
+None of the GROMACS pair styles support the
+:doc:`pair\_modify <pair_modify>` shift option, since the Lennard-Jones
+portion of the pair interaction is already smoothed to 0.0 at the
+cutoff.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+None of the GROMACS pair styles support the
+:doc:`pair\_modify <pair_modify>` tail option for adding long-range tail
+corrections to energy and pressure, since there are no corrections for
+a potential that goes to 0.0 at the cutoff.
+
+All of the GROMACS pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+All of the GROMACS pair styles can only be used via the *pair*
+keyword of the :doc:`run\_style respa <run_style>` command.  They do not
+support the *inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Marrink:
+
+
+
+**(Marrink)** Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst
new file mode 100644
index 0000000000..d1c89eaee8
--- /dev/null
+++ b/doc/src/pair_gw.rst
@@ -0,0 +1,145 @@
+.. index:: pair\_style gw
+
+pair\_style gw command
+======================
+
+pair\_style gw/zbl command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style
+
+* style = *gw* or *gw/zbl*
+
+Examples
+""""""""
+
+pair\_style gw
+pair\_coeff \* \* SiC.gw Si C C
+
+
+.. parsed-literal::
+
+   pair_style gw/zbl
+   pair_coeff \* \* SiC.gw.zbl C Si
+
+Description
+"""""""""""
+
+The *gw* style computes a 3-body :ref:`Gao-Weber <Gao>` potential;
+similarly *gw/zbl* combines this potential with a modified
+repulsive ZBL core function in a similar fashion as implemented
+in the :doc:`tersoff/zbl <pair_tersoff_zbl>` pair style.
+
+Unfortunately the author of this contributed code has not been
+able to submit a suitable documentation explaining the details
+of the potentials. The LAMMPS developers thus have finally decided
+to release the code anyway with only the technical explanations.
+For details of the model and the parameters, please refer to the
+linked publication.
+
+Only a single pair\_coeff command is used with the *gw* and *gw/zbl*
+styles which specifies a Gao-Weber potential file with parameters
+for all needed elements.  These are mapped to LAMMPS atom types by
+specifying N additional arguments after the filename in the pair\_coeff
+command, where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of GW elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine a file SiC.gw has Gao-Weber values for Si and C.
+If your LAMMPS simulation has 4 atoms types and you want the first 3 to
+be Si, and the 4th to be C, you would use the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* SiC.gw Si Si Si C
+
+The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the GW file.  The final C argument maps LAMMPS atom type 4
+to the C element in the GW file.  If a mapping value is specified as
+NULL, the mapping is not performed.  This can be used when a *gw*
+potential is used as part of the *hybrid* pair style.  The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+
+Gao-Weber files in the *potentials* directory of the LAMMPS
+distribution have a ".gw" suffix.  Gao-Weber with ZBL files
+have a ".gz.zbl" suffix. The structure of the potential files
+is similar to other many-body potentials supported by LAMMPS.
+You have to refer to the comments in the files and the literature
+to learn more details.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the MANYBODY package. It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The Gao-Weber potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal :doc:`units <units>`.
+You can use the GW potential with any LAMMPS units, but you would need
+to create your own GW potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Gao:
+
+
+
+**(Gao)** Gao and Weber, Nuclear Instruments and Methods in Physics
+Research B 191 (2012) 504.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst
new file mode 100644
index 0000000000..f87f0c45e2
--- /dev/null
+++ b/doc/src/pair_hbond_dreiding.rst
@@ -0,0 +1,286 @@
+.. index:: pair\_style hbond/dreiding/lj
+
+pair\_style hbond/dreiding/lj command
+=====================================
+
+pair\_style hbond/dreiding/lj/omp command
+=========================================
+
+pair\_style hbond/dreiding/morse command
+========================================
+
+pair\_style hbond/dreiding/morse/omp command
+============================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
+
+* style = *hbond/dreiding/lj* or *hbond/dreiding/morse*
+* n = cosine angle periodicity
+* inner\_distance\_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units)
+* outer\_distance\_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
+* angle\_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
+* interactions (degrees)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
+   pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
+
+   pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
+   pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
+
+Description
+"""""""""""
+
+The *hbond/dreiding* styles compute the Acceptor-Hydrogen-Donor (AHD)
+3-body hydrogen bond interaction for the :doc:`DREIDING <Howto_bioFF>`
+force field, given by:
+
+.. image:: Eqs/pair_hbond_dreiding.jpg
+   :align: center
+
+where Rin is the inner spline distance cutoff, Rout is the outer
+distance cutoff, theta\_c is the angle cutoff, and n is the cosine
+periodicity.
+
+Here, *r* is the radial distance between the donor (D) and acceptor
+(A) atoms and *theta* is the bond angle between the acceptor, the
+hydrogen (H) and the donor atoms:
+
+.. image:: JPG/dreiding_hbond.jpg
+   :align: center
+
+These 3-body interactions can be defined for pairs of acceptor and
+donor atoms, based on atom types.  For each donor/acceptor atom pair,
+the 3rd atom in the interaction is a hydrogen permanently bonded to
+the donor atom, e.g. in a bond list read in from a data file via the
+:doc:`read\_data <read_data>` command.  The atom types of possible
+hydrogen atoms for each donor/acceptor type pair are specified by the
+:doc:`pair\_coeff <pair_coeff>` command (see below).
+
+Style *hbond/dreiding/lj* is the original DREIDING potential of
+:ref:`(Mayo) <pair-Mayo>`.  It uses a LJ 12/10 functional for the Donor-Acceptor
+interactions. To match the results in the original paper, use n = 4.
+
+Style *hbond/dreiding/morse* is an improved version using a Morse
+potential for the Donor-Acceptor interactions. :ref:`(Liu) <Liu>` showed
+that the Morse form gives improved results for Dendrimer simulations,
+when n = 2.
+
+See the :doc:`Howto bioFF <Howto_bioFF>` doc page for more information
+on the DREIDING force field.
+
+.. note::
+
+   Because the Dreiding hydrogen bond potential is only one portion
+   of an overall force field which typically includes other pairwise
+   interactions, it is common to use it as a sub-style in a :doc:`pair\_style hybrid/overlay <pair_hybrid>` command, where another pair style
+   provides the repulsive core interaction between pairs of atoms, e.g. a
+   1/r\^12 Lennard-Jones repulsion.
+
+.. note::
+
+   When using the hbond/dreiding pair styles with :doc:`pair\_style hybrid/overlay <pair_hybrid>`, you should explicitly define pair
+   interactions between the donor atom and acceptor atoms, (as well as
+   between these atoms and ALL other atoms in your system).  Whenever
+   :doc:`pair\_style hybrid/overlay <pair_hybrid>` is used, ordinary mixing
+   rules are not applied to atoms like the donor and acceptor atoms
+   because they are typically referenced in multiple pair styles.
+   Neglecting to do this can cause difficult-to-detect physics problems.
+
+.. note::
+
+   In the original Dreiding force field paper 1-4 non-bonded
+   interactions ARE allowed.  If this is desired for your model, use the
+   special\_bonds command (e.g. "special\_bonds lj 0.0 0.0 1.0") to turn
+   these interactions on.
+
+
+----------
+
+
+The following coefficients must be defined for pairs of eligible
+donor/acceptor types via the :doc:`pair\_coeff <pair_coeff>` command as
+in the examples above.
+
+.. note::
+
+   Unlike other pair styles and their associated
+   :doc:`pair\_coeff <pair_coeff>` commands, you do not need to specify
+   pair\_coeff settings for all possible I,J type pairs.  Only I,J type
+   pairs for atoms which act as joint donors/acceptors need to be
+   specified; all other type pairs are assumed to be inactive.
+
+.. note::
+
+   A :doc:`pair\_coeff <pair_coeff>` command can be specified multiple
+   times for the same donor/acceptor type pair.  This enables multiple
+   hydrogen types to be assigned to the same donor/acceptor type pair.
+   For other pair\_styles, if the pair\_coeff command is re-used for the
+   same I.J type pair, the settings for that type pair are overwritten.
+   For the hydrogen bond potentials this is not the case; the settings
+   are cumulative.  This means the only way to turn off a previous
+   setting, is to re-use the pair\_style command and start over.
+
+For the *hbond/dreiding/lj* style the list of coefficients is as
+follows:
+
+* K = hydrogen atom type = 1 to Ntypes
+* donor flag = *i* or *j*
+* epsilon (energy units)
+* sigma (distance units)
+* n = exponent in formula above
+* distance cutoff Rin (distance units)
+* distance cutoff Rout (distance units)
+* angle cutoff (degrees)
+
+For the *hbond/dreiding/morse* style the list of coefficients is as
+follows:
+
+* K = hydrogen atom type = 1 to Ntypes
+* donor flag = *i* or *j*
+* D0 (energy units)
+* alpha (1/distance units)
+* r0 (distance units)
+* n = exponent in formula above
+* distance cutoff Rin (distance units)
+* distance cutoff Rout (distance units)
+* angle cutoff (degrees)
+
+A single hydrogen atom type K can be specified, or a wild-card asterisk
+can be used in place of or in conjunction with the K arguments to
+select multiple types as hydrogen atoms.  This takes the form
+"\*" or "\*n" or "n\*" or "m\*n".  See the :doc:`pair\_coeff <pair_coeff>`
+command doc page for details.
+
+If the donor flag is *i*\ , then the atom of type I in the pair\_coeff
+command is treated as the donor, and J is the acceptor.  If the donor
+flag is *j*\ , then the atom of type J in the pair\_coeff command is
+treated as the donor and I is the donor.  This option is required
+because the :doc:`pair\_coeff <pair_coeff>` command requires that I <= J.
+
+Epsilon and sigma are settings for the hydrogen bond potential based
+on a Lennard-Jones functional form.  Note that sigma is defined as the
+zero-crossing distance for the potential, not as the energy minimum at
+2\^(1/6) sigma.
+
+D0 and alpha and r0 are settings for the hydrogen bond potential based
+on a Morse functional form.
+
+The last 3 coefficients for both styles are optional.  If not
+specified, the global n, distance cutoff, and angle cutoff specified
+in the pair\_style command are used.  If you wish to only override the
+2nd or 3rd optional parameter, you must also specify the preceding
+optional parameters.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+These pair styles do not support mixing. You must explicitly identify
+each donor/acceptor type pair.
+
+These styles do not support the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the interactions.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant for
+these pair styles.
+
+These pair styles do not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+These pair styles do not write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands need to be
+re-specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+These pair styles tally a count of how many hydrogen bonding
+interactions they calculate each timestep and the hbond energy.  These
+quantities can be accessed via the :doc:`compute pair <compute_pair>`
+command as a vector of values of length 2.
+
+To print these quantities to the log file (with a descriptive column
+heading) the following commands could be included in an input script:
+
+
+.. parsed-literal::
+
+   compute hb all pair hbond/dreiding/lj
+   variable n_hbond equal c_hb[1] #number hbonds
+   variable E_hbond equal c_hb[2] #hbond energy
+   thermo_style custom step temp epair v_E_hbond
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _pair-Mayo:
+
+
+
+**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
+
+.. _Liu:
+
+
+
+**(Liu)** Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
+2798 (2009)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst
new file mode 100644
index 0000000000..3ee9c19428
--- /dev/null
+++ b/doc/src/pair_hybrid.rst
@@ -0,0 +1,444 @@
+.. index:: pair\_style hybrid
+
+pair\_style hybrid command
+==========================
+
+pair\_style hybrid/kk command
+=============================
+
+pair\_style hybrid/overlay command
+==================================
+
+pair\_style hybrid/overlay/kk command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid style1 args style2 args ...
+   pair_style hybrid/overlay style1 args style2 args ...
+
+* style1,style2 = list of one or more pair styles and their arguments
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
+   pair_coeff 1\*2 1\*2 eam niu3
+   pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+   pair_coeff 1\*2 3 lj/cut 0.5 1.2
+
+   pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
+   pair_coeff \* \* lj/cut 1.0 1.0
+   pair_coeff \* \* coul/long
+
+Description
+"""""""""""
+
+The *hybrid* and *hybrid/overlay* styles enable the use of multiple
+pair styles in one simulation.  With the *hybrid* style, exactly one
+pair style is assigned to each pair of atom types.  With the
+*hybrid/overlay* style, one or more pair styles can be assigned to
+each pair of atom types.  The assignment of pair styles to type pairs
+is made via the :doc:`pair\_coeff <pair_coeff>` command.
+
+Here are two examples of hybrid simulations.  The *hybrid* style could
+be used for a simulation of a metal droplet on a LJ surface.  The
+metal atoms interact with each other via an *eam* potential, the
+surface atoms interact with each other via a *lj/cut* potential, and
+the metal/surface interaction is also computed via a *lj/cut*
+potential.  The *hybrid/overlay* style could be used as in the 2nd
+example above, where multiple potentials are superposed in an additive
+fashion to compute the interaction between atoms.  In this example,
+using *lj/cut* and *coul/long* together gives the same result as if
+the *lj/cut/coul/long* potential were used by itself.  In this case,
+it would be more efficient to use the single combined potential, but
+in general any combination of pair potentials can be used together in
+to produce an interaction that is not encoded in any single pair\_style
+file, e.g. adding Coulombic forces between granular particles.
+
+All pair styles that will be used are listed as "sub-styles" following
+the *hybrid* or *hybrid/overlay* keyword, in any order.  Each
+sub-style's name is followed by its usual arguments, as illustrated in
+the example above.  See the doc pages of individual pair styles for a
+listing and explanation of the appropriate arguments.
+
+Note that an individual pair style can be used multiple times as a
+sub-style.  For efficiency this should only be done if your model
+requires it.  E.g. if you have different regions of Si and C atoms and
+wish to use a Tersoff potential for pure Si for one set of atoms, and
+a Tersoff potential for pure C for the other set (presumably with some
+3rd potential for Si-C interactions), then the sub-style *tersoff*
+could be listed twice.  But if you just want to use a Lennard-Jones or
+other pairwise potential for several different atom type pairs in your
+model, then you should just list the sub-style once and use the
+pair\_coeff command to assign parameters for the different type pairs.
+
+.. note::
+
+   There is one exception to this option to list an individual
+   pair style multiple times: GPU-enabled pair styles in the GPU package.
+   This is because the GPU package currently assumes that only one
+   instance of a pair style is being used.
+
+In the pair\_coeff commands, the name of a pair style must be added
+after the I,J type specification, with the remaining coefficients
+being those appropriate to that style.  If the pair style is used
+multiple times in the pair\_style command, then an additional numeric
+argument must also be specified which is a number from 1 to M where M
+is the number of times the sub-style was listed in the pair style
+command.  The extra number indicates which instance of the sub-style
+these coefficients apply to.
+
+For example, consider a simulation with 3 atom types: types 1 and 2
+are Ni atoms, type 3 are LJ atoms with charges.  The following
+commands would set up a hybrid simulation:
+
+
+.. parsed-literal::
+
+   pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
+   pair_coeff \* \* eam/alloy nialhjea Ni Ni NULL
+   pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+   pair_coeff 1\*2 3 lj/cut 0.8 1.3
+
+As an example of using the same pair style multiple times, consider a
+simulation with 2 atom types.  Type 1 is Si, type 2 is C.  The
+following commands would model the Si atoms with Tersoff, the C atoms
+with Tersoff, and the cross-interactions with Lennard-Jones:
+
+
+.. parsed-literal::
+
+   pair_style hybrid lj/cut 2.5 tersoff tersoff
+   pair_coeff \* \* tersoff 1 Si.tersoff Si NULL
+   pair_coeff \* \* tersoff 2 C.tersoff NULL C
+   pair_coeff 1 2 lj/cut 1.0 1.5
+
+If pair coefficients are specified in the data file read via the
+:doc:`read\_data <read_data>` command, then the same rule applies.
+E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for
+each line in the "Pair Coeffs" section, e.g.
+
+
+.. parsed-literal::
+
+   Pair Coeffs
+
+   1 lj/cut/coul/cut 1.0 1.0
+   ...
+
+Note that the pair\_coeff command for some potentials such as
+:doc:`pair\_style eam/alloy <pair_eam>` includes a mapping specification
+of elements to all atom types, which in the hybrid case, can include
+atom types not assigned to the *eam/alloy* potential.  The NULL
+keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO,
+etc), to denote an atom type that will be assigned to a different
+sub-style.
+
+For the *hybrid* style, each atom type pair I,J is assigned to exactly
+one sub-style.  Just as with a simulation using a single pair style,
+if you specify the same atom type pair in a second pair\_coeff command,
+the previous assignment will be overwritten.
+
+For the *hybrid/overlay* style, each atom type pair I,J can be
+assigned to one or more sub-styles.  If you specify the same atom type
+pair in a second pair\_coeff command with a new sub-style, then the
+second sub-style is added to the list of potentials that will be
+calculated for two interacting atoms of those types.  If you specify
+the same atom type pair in a second pair\_coeff command with a
+sub-style that has already been defined for that pair of atoms, then
+the new pair coefficients simply override the previous ones, as in the
+normal usage of the pair\_coeff command.  E.g. these two sets of
+commands are the same:
+
+
+.. parsed-literal::
+
+   pair_style lj/cut 2.5
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 2 2 1.5 0.8
+
+   pair_style hybrid/overlay lj/cut 2.5
+   pair_coeff \* \* lj/cut 1.0 1.0
+   pair_coeff 2 2 lj/cut 1.5 0.8
+
+Coefficients must be defined for each pair of atoms types via the
+:doc:`pair\_coeff <pair_coeff>` command as described above, or in the
+data file or restart files read by the :doc:`read\_data <read_data>` or
+:doc:`read\_restart <read_restart>` commands, or by mixing as described
+below.
+
+For both the *hybrid* and *hybrid/overlay* styles, every atom type
+pair I,J (where I <= J) must be assigned to at least one sub-style via
+the :doc:`pair\_coeff <pair_coeff>` command as in the examples above, or
+in the data file read by the :doc:`read\_data <read_data>`, or by mixing
+as described below.
+
+If you want there to be no interactions between a particular pair of
+atom types, you have 3 choices.  You can assign the type pair to some
+sub-style and use the :doc:`neigh\_modify exclude type <neigh_modify>`
+command.  You can assign it to some sub-style and set the coefficients
+so that there is effectively no interaction (e.g. epsilon = 0.0 in a
+LJ potential).  Or, for *hybrid* and *hybrid/overlay* simulations, you
+can use this form of the pair\_coeff command in your input script:
+
+
+.. parsed-literal::
+
+   pair_coeff        2 3 none
+
+or this form in the "Pair Coeffs" section of the data file:
+
+
+.. parsed-literal::
+
+   3 none
+
+If an assignment to *none* is made in a simulation with the
+*hybrid/overlay* pair style, it wipes out all previous assignments of
+that atom type pair to sub-styles.
+
+Note that you may need to use an :doc:`atom\_style <atom_style>` hybrid
+command in your input script, if atoms in the simulation will need
+attributes from several atom styles, due to using multiple pair
+potentials.
+
+
+----------
+
+
+Different force fields (e.g. CHARMM vs AMBER) may have different rules
+for applying weightings that change the strength of pairwise
+interactions between pairs of atoms that are also 1-2, 1-3, and 1-4
+neighbors in the molecular bond topology, as normally set by the
+:doc:`special\_bonds <special_bonds>` command.  Different weights can be
+assigned to different pair hybrid sub-styles via the :doc:`pair\_modify special <pair_modify>` command. This allows multiple force fields
+to be used in a model of a hybrid system, however, there is no consistent
+approach to determine parameters automatically for the interactions
+between the two force fields, this is only recommended when particles
+described by the different force fields do not mix.
+
+Here is an example for mixing CHARMM and AMBER: The global *amber*
+setting sets the 1-4 interactions to non-zero scaling factors and
+then overrides them with 0.0 only for CHARMM:
+
+
+.. parsed-literal::
+
+   special_bonds amber
+   pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+   pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+
+The this input achieves the same effect:
+
+
+.. parsed-literal::
+
+   special_bonds 0.0 0.0 0.1
+   pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+   pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
+   pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
+   pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+
+Here is an example for mixing Tersoff with OPLS/AA based on
+a data file that defines bonds for all atoms where for the
+Tersoff part of the system the force constants for the bonded
+interactions have been set to 0. Note the global settings are
+effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA:
+
+
+.. parsed-literal::
+
+   special_bonds lj/coul 1e-20 1e-20 0.5
+   pair_hybrid tersoff lj/cut/coul/long 12.0
+   pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
+
+For use with the various :doc:`compute \*/tally <compute_tally>`
+computes, the :doc:`pair\_modify compute/tally <pair_modify>`
+command can be used to selectively turn off processing of
+the compute tally styles, for example, if those pair styles
+(e.g. many-body styles) do not support this feature.
+
+See the :doc:`pair\_modify <pair_modify>` doc page for details on
+the specific syntax, requirements and restrictions.
+
+
+----------
+
+
+The potential energy contribution to the overall system due to an
+individual sub-style can be accessed and output via the :doc:`compute pair <compute_pair>` command.
+
+
+----------
+
+
+.. note::
+
+   Several of the potentials defined via the pair\_style command in
+   LAMMPS are really many-body potentials, such as Tersoff, AIREBO, MEAM,
+   ReaxFF, etc.  The way to think about using these potentials in a
+   hybrid setting is as follows.
+
+A subset of atom types is assigned to the many-body potential with a
+single :doc:`pair\_coeff <pair_coeff>` command, using "\* \*" to include
+all types and the NULL keywords described above to exclude specific
+types not assigned to that potential.  If types 1,3,4 were assigned in
+that way (but not type 2), this means that all many-body interactions
+between all atoms of types 1,3,4 will be computed by that potential.
+Pair\_style hybrid allows interactions between type pairs 2-2, 1-2,
+2-3, 2-4 to be specified for computation by other pair styles.  You
+could even add a second interaction for 1-1 to be computed by another
+pair style, assuming pair\_style hybrid/overlay is used.
+
+But you should not, as a general rule, attempt to exclude the
+many-body interactions for some subset of the type pairs within the
+set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions.  That
+is not conceptually well-defined for many-body interactions, since the
+potential will typically calculate energies and foces for small groups
+of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to
+find the additional atoms in the group.  It is typically non-physical
+to think of excluding an interaction between a particular pair of
+atoms when the potential computes 3-body or 4-body interactions.
+
+However, you can still use the pair\_coeff none setting or the
+:doc:`neigh\_modify exclude <neigh_modify>` command to exclude certain
+type pairs from the neighbor list that will be passed to a many-body
+sub-style.  This will alter the calculations made by a many-body
+potential, since it builds its list of 3-body, 4-body, etc
+interactions from the pair list.  You will need to think carefully as
+to whether it produces a physically meaningful result for your model.
+
+For example, imagine you have two atom types in your model, type 1 for
+atoms in one surface, and type 2 for atoms in the other, and you wish
+to use a Tersoff potential to compute interactions within each
+surface, but not between surfaces.  Then either of these two command
+sequences would implement that model:
+
+
+.. parsed-literal::
+
+   pair_style hybrid tersoff
+   pair_coeff \* \* tersoff SiC.tersoff C C
+   pair_coeff 1 2 none
+
+   pair_style tersoff
+   pair_coeff \* \* SiC.tersoff C C
+   neigh_modify exclude type 1 2
+
+Either way, only neighbor lists with 1-1 or 2-2 interactions would be
+passed to the Tersoff potential, which means it would compute no
+3-body interactions containing both type 1 and 2 atoms.
+
+Here is another example, using hybrid/overlay, to use 2 many-body
+potentials together, in an overlapping manner.  Imagine you have CNT
+(C atoms) on a Si surface.  You want to use Tersoff for Si/Si and Si/C
+interactions, and AIREBO for C/C interactions.  Si atoms are type 1; C
+atoms are type 2.  Something like this will work:
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay tersoff airebo 3.0
+   pair_coeff \* \* tersoff SiC.tersoff.custom Si C
+   pair_coeff \* \* airebo CH.airebo NULL C
+
+Note that to prevent the Tersoff potential from computing C/C
+interactions, you would need to modify the SiC.tersoff file to turn
+off C/C interaction, i.e. by setting the appropriate coefficients to
+0.0.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.
+
+Since the *hybrid* and *hybrid/overlay* styles delegate computation to
+the individual sub-styles, the suffix versions of the *hybrid* and
+*hybrid/overlay* styles are used to propagate the corresponding suffix
+to all sub-styles, if those versions exist. Otherwise the
+non-accelerated version will be used.
+
+The individual accelerated sub-styles are part of the GPU, USER-OMP
+and OPT packages, respectively.  They are only enabled if LAMMPS was
+built with those packages.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+Any pair potential settings made via the
+:doc:`pair\_modify <pair_modify>` command are passed along to all
+sub-styles of the hybrid potential.
+
+For atom type pairs I,J and I != J, if the sub-style assigned to I,I
+and J,J is the same, and if the sub-style allows for mixing, then the
+coefficients for I,J can be mixed.  This means you do not have to
+specify a pair\_coeff command for I,J since the I,J type pair will be
+assigned automatically to the sub-style defined for both I,I and J,J
+and its coefficients generated by the mixing rule used by that
+sub-style.  For the *hybrid/overlay* style, there is an additional
+requirement that both the I,I and J,J pairs are assigned to a single
+sub-style.  See the "pair\_modify" command for details of mixing rules.
+See the See the doc page for the sub-style to see if allows for
+mixing.
+
+The hybrid pair styles supports the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options for an I,J pair interaction, if the
+associated sub-style supports it.
+
+For the hybrid pair styles, the list of sub-styles and their
+respective settings are written to :doc:`binary restart files <restart>`, so a :doc:`pair\_style <pair_style>` command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file.  Thus, pair\_coeff commands need to be re-specified in the
+restart input script.
+
+These pair styles support the use of the *inner*\ , *middle*\ , and
+*outer* keywords of the :doc:`run\_style respa <run_style>` command, if
+their sub-styles do.
+
+Restrictions
+""""""""""""
+
+
+When using a long-range Coulombic solver (via the
+:doc:`kspace\_style <kspace_style>` command) with a hybrid pair\_style,
+one or more sub-styles will be of the "long" variety,
+e.g. *lj/cut/coul/long* or *buck/coul/long*\ .  You must insure that the
+short-range Coulombic cutoff used by each of these long pair styles is
+the same or else LAMMPS will generate an error.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst
new file mode 100644
index 0000000000..696cd83ace
--- /dev/null
+++ b/doc/src/pair_ilp_graphene_hbn.rst
@@ -0,0 +1,197 @@
+.. index:: pair\_style ilp/graphene/hbn
+
+pair\_style ilp/graphene/hbn command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style [hybrid/overlay ...] ilp/graphene/hbn cutoff tap_flag
+
+* cutoff = global cutoff (distance units)
+* tap\_flag = 0/1 to turn off/on the taper function
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style  hybrid/overlay ilp/graphene/hbn 16.0 1
+   pair_coeff  \* \* ilp/graphene/hbn  BNCH.ILP B N C
+
+   pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+   pair_coeff  \* \* rebo              CH.rebo     NULL NULL C
+   pair_coeff  \* \* tersoff           BNC.tersoff B    N    NULL
+   pair_coeff  \* \* ilp/graphene/hbn  BNCH.ILP    B    N    C
+   pair_coeff  1 1 coul/shield 0.70
+   pair_coeff  1 2 coul/shield 0.695
+   pair_coeff  2 2 coul/shield 0.69
+
+Description
+"""""""""""
+
+The *ilp/graphene/hbn* style computes the registry-dependent interlayer
+potential (ILP) potential as described in :ref:`(Leven1) <Leven1>`,
+:ref:`(Leven2) <Leven2>` and :ref:`(Maaravi) <Maaravi2>`.
+The normals are calculated in the way as described
+in :ref:`(Kolmogorov) <Kolmogorov2>`.
+
+.. image:: Eqs/pair_ilp_graphene_hbn.jpg
+   :align: center
+
+Where Tap(r\_ij) is the taper function which provides a continuous
+cutoff (up to third derivative) for interatomic separations larger than
+r\_c :ref:`(Maaravi) <Maaravi2>`. The definitions of each parameter in the above
+equation can be found in :ref:`(Leven1) <Leven1>` and :ref:`(Maaravi) <Maaravi2>`.
+
+It is important to include all the pairs to build the neighbor list for
+calculating the normals.
+
+.. note::
+
+   This potential (ILP) is intended for interlayer interactions between two
+   different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.
+   To perform a realistic simulation, this potential must be used in combination with
+   intralayer potential, such as :doc:`AIREBO <pair_airebo>` or :doc:`Tersoff <pair_tersoff>` potential.
+   To keep the intralayer properties unaffected, the interlayer interaction
+   within the same layers should be avoided. Hence, each atom has to have a layer
+   identifier such that atoms residing on the same layer interact via the
+   appropriate intralayer potential and atoms residing on different layers
+   interact via the ILP. Here, the molecule id is chosen as the layer identifier,
+   thus a data file with the "full" atom style is required to use this potential.
+
+The parameter file (e.g. BNCH.ILP), is intended for use with *metal*
+:doc:`units <units>`, with energies in meV. Two additional parameters,
+*S*\ , and *rcut* are included in the parameter file. *S* is designed to
+facilitate scaling of energies. *rcut* is designed to build the neighbor
+list for calculating the normals for each atom pair.
+
+.. note::
+
+   The parameters presented in the parameter file (e.g. BNCH.ILP),
+   are fitted with taper function by setting the cutoff equal to 16.0
+   Angstrom.  Using different cutoff or taper function should be careful.
+   The parameters for atoms pairs between Boron and Nitrogen are fitted with
+   a screened Coulomb interaction :doc:`coul/shield <pair_coul_shield>`. Therefore,
+   to simulated the properties of h-BN correctly, this potential must be used in
+   combination with the pair style :doc:`coul/shield <pair_coul_shield>`.
+
+.. note::
+
+   Two new sets of parameters of ILP for two-dimensional hexagonal
+   Materials are presented in :ref:`(Ouyang) <Ouyang>`.  These parameters provide
+   a good description in both short- and long-range interaction regimes.
+   While the old ILP parameters published in :ref:`(Leven2) <Leven2>` and
+   :ref:`(Maaravi) <Maaravi2>` are only suitable for long-range interaction
+   regime. This feature is essential for simulations in high pressure
+   regime (i.e., the interlayer distance is smaller than the equilibrium
+   distance).  The benchmark tests and comparison of these parameters can
+   be found in :ref:`(Ouyang) <Ouyang>`.
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair\_style *none*\ .
+
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+1. *E\_vdW* = vdW (attractive) energy
+2. *E\_Rep* = Repulsive energy
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+
+.. parsed-literal::
+
+   compute 0 all pair ilp/graphene/hbn
+   variable Evdw  equal c_0[1]
+   variable Erep  equal c_0[2]
+   thermo_style custom step temp epair v_Erep v_Evdw
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the pair\_modify mix, shift, table, and
+tail options.
+
+This pair style does not write their information to binary restart
+files, since it is stored in potential files. Thus, you need to
+re-specify the pair\_style and pair\_coeff commands in an input script
+that reads a restart file.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair potential requires the newton setting to be *on* for pair
+interactions.
+
+The BNCH.ILP potential file provided with LAMMPS (see the potentials
+directory) are parameterized for *metal* units.  You can use this
+potential with any LAMMPS units, but you would need to create your
+BNCH.ILP potential file with coefficients listed in the appropriate
+units, if your simulation does not use *metal* units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_none <pair_none>`,
+:doc:`pair\_style hybrid/overlay <pair_hybrid>`,
+:doc:`pair\_style drip <pair_drip>`,
+:doc:`pair\_style pair\_kolmogorov\_crespi\_z <pair_kolmogorov_crespi_z>`,
+:doc:`pair\_style pair\_kolmogorov\_crespi\_full <pair_kolmogorov_crespi_full>`,
+:doc:`pair\_style pair\_lebedeva\_z <pair_lebedeva_z>`,
+:doc:`pair\_style pair\_coul\_shield <pair_coul_shield>`.
+
+**Default:** tap\_flag = 1
+
+
+----------
+
+
+.. _Leven1:
+
+
+
+**(Leven1)** I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
+
+.. _Leven2:
+
+
+
+**(Leven2)** I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
+
+.. _Maaravi2:
+
+
+
+**(Maaravi)** T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
+
+.. _Kolmogorov2:
+
+
+
+**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
+
+.. _Ouyang:
+
+
+
+**(Ouyang)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst
new file mode 100644
index 0000000000..768ac3fa9b
--- /dev/null
+++ b/doc/src/pair_kim.rst
@@ -0,0 +1,135 @@
+.. index:: pair\_style kim
+
+pair\_style kim command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style kim model
+
+model = name of a KIM model (the KIM ID for models archived in OpenKIM)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
+   pair_coeff \* \* Si
+
+Description
+"""""""""""
+
+This pair style is a wrapper on the `Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_ repository of interatomic
+potentials to enable their use in LAMMPS scripts.
+
+The preferred interface for using interatomic models archived in
+OpenKIM is the :doc:`kim\_commands interface <kim_commands>`. That
+interface supports both "KIM Portable Models" (PMs) that conform to the
+KIM API Portable Model Interface (PMI) and can be used by any
+simulation code that conforms to the KIM API/PMI, and
+"KIM Simulator Models" that are natively implemented within a single
+simulation code (like LAMMPS) and can only be used with it.
+The *pair\_style kim* command is limited to KIM PMs. It is
+used by the :doc:`kim\_commands interface <kim_commands>` as needed.
+
+.. note::
+
+   Since *pair\_style kim* is called by *kim\_interactions* as needed,
+   is not recommended to be directly used in input scripts.
+
+
+----------
+
+
+The argument *model* is the name of the KIM PM.
+For potentials archived in OpenKIM
+this is the extended KIM ID (see :doc:`kim\_commands <kim_commands>`
+for details). LAMMPS can invoke any KIM PM, however there can
+be incompatibilities (for example due to unit matching issues).
+In the event of an incompatibility, the code will terminate with
+an error message. Check both the LAMMPS and KIM log files for details.
+
+Only a single *pair\_coeff* command is used with the *kim* style, which
+specifies the mapping of LAMMPS atom types to the species supported by
+the KIM PM.  This is done by specifying *N* additional arguments
+after the \* \* in the *pair\_coeff* command, where *N* is the number of
+LAMMPS atom types:
+
+* N element names = mapping of KIM elements to atom types
+
+For example, consider a KIM PM that supports Si and C species.
+If the LAMMPS simulation has four atom types, where the first three are Si,
+and the fourth is C, the following *pair\_coeff* command would be used:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* Si Si Si C
+
+The first two arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as
+defined within KIM PM.  The final C argument maps LAMMPS atom type 4 to C.
+
+
+----------
+
+
+In addition to the usual LAMMPS error messages, the KIM library itself
+may generate errors, which should be printed to the screen.  In this
+case it is also useful to check the *kim.log* file for additional error
+information.  The file *kim.log* should be generated in the same
+directory where LAMMPS is running.
+
+To download, build, and install the KIM library on your system, see
+the *lib/kim/README* file.  Once you have done this and built LAMMPS
+with the KIM package installed you can run the example input scripts
+in *examples/kim*\ .
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since KIM stores the potential parameters.
+Thus, you need to re-specify the pair\_style and pair\_coeff commands in
+an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the KIM package. See details on
+restrictions in :doc:`kim\_commands <kim_commands>`.
+
+This current version of pair\_style kim is compatible with the
+kim-api package version 2.0.0 and higher.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`kim\_commands <kim_commands>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst
new file mode 100644
index 0000000000..8fe76c6b71
--- /dev/null
+++ b/doc/src/pair_kolmogorov_crespi_full.rst
@@ -0,0 +1,166 @@
+.. index:: pair\_style kolmogorov/crespi/full
+
+pair\_style kolmogorov/crespi/full command
+==========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag
+
+* cutoff = global cutoff (distance units)
+* tap\_flag = 0/1 to turn off/on the taper function
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
+   pair_coeff \* \* none
+   pair_coeff \* \* kolmogorov/crespi/full  CH.KC   C C
+
+   pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
+   pair_coeff \* \* rebo                    CH.rebo      C H
+   pair_coeff \* \* kolmogorov/crespi/full  CH_taper.KC  C H
+
+Description
+"""""""""""
+
+The *kolmogorov/crespi/full* style computes the Kolmogorov-Crespi (KC)
+interaction potential as described in :ref:`(Kolmogorov) <Kolmogorov1>`.
+No simplification is made,
+
+.. image:: Eqs/pair_kolmogorov_crespi_full.jpg
+   :align: center
+
+It is important to have a sufficiently large cutoff to ensure smooth
+forces and to include all the pairs to build the neighbor list for
+calculating the normals.  Energies are shifted so that they go
+continuously to zero at the cutoff assuming that the exponential part of
+*Vij* (first term) decays sufficiently fast.  This shift is achieved by
+the last term in the equation for *Vij* above. This is essential only
+when the tapper function is turned off. The formula of taper function
+can be found in pair style :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`.
+
+.. note::
+
+   This potential (ILP) is intended for interlayer interactions between two
+   different layers of graphene. To perform a realistic simulation, this potential
+   must be used in combination with intralayer potential, such as
+   :doc:`AIREBO <pair_airebo>` or :doc:`Tersoff <pair_tersoff>` potential.
+   To keep the intralayer properties unaffected, the interlayer interaction
+   within the same layers should be avoided. Hence, each atom has to have a layer
+   identifier such that atoms residing on the same layer interact via the
+   appropriate intralayer potential and atoms residing on different layers
+   interact via the ILP. Here, the molecule id is chosen as the layer identifier,
+   thus a data file with the "full" atom style is required to use this potential.
+
+The parameter file (e.g. CH.KC), is intended for use with *metal*
+:doc:`units <units>`, with energies in meV. Two additional parameters, *S*\ ,
+and *rcut* are included in the parameter file. *S* is designed to
+facilitate scaling of energies. *rcut* is designed to build the neighbor
+list for calculating the normals for each atom pair.
+
+.. note::
+
+   Two new sets of parameters of KC potential for hydrocarbons, CH.KC
+   (without the taper function) and CH\_taper.KC (with the taper function)
+   are presented in :ref:`(Ouyang) <Ouyang1>`.  The energy for the KC potential
+   with the taper function goes continuously to zero at the cutoff.  The
+   parameters in both CH.KC and CH\_taper.KC provide a good description in
+   both short- and long-range interaction regimes. While the original
+   parameters (CC.KC) published in :ref:`(Kolmogorov) <Kolmogorov1>` are only
+   suitable for long-range interaction regime.  This feature is essential
+   for simulations in high pressure regime (i.e., the interlayer distance
+   is smaller than the equilibrium distance).  The benchmark tests and
+   comparison of these parameters can be found in :ref:`(Ouyang) <Ouyang1>`.
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair\_style *none*\ .
+
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+1. *E\_vdW* = vdW (attractive) energy
+2. *E\_Rep* = Repulsive energy
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+
+.. parsed-literal::
+
+   compute 0 all pair kolmogorov/crespi/full
+   variable Evdw  equal c_0[1]
+   variable Erep  equal c_0[2]
+   thermo_style custom step temp epair v_Erep v_Evdw
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the pair\_modify mix, shift, table,
+and tail options.
+
+This pair style does not write their information to binary restart
+files, since it is stored in potential files. Thus, you need to
+re-specify the pair\_style and pair\_coeff commands in an input script
+that reads a restart file.
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair potential requires the newton setting to be *on* for pair
+interactions.
+
+The CH.KC potential file provided with LAMMPS (see the potentials
+folder) are parameterized for metal units.  You can use this potential
+with any LAMMPS units, but you would need to create your own custom
+CC.KC potential file with all coefficients converted to the appropriate
+units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_none <pair_none>`,
+:doc:`pair\_style hybrid/overlay <pair_hybrid>`,
+:doc:`pair\_style drip <pair_drip>`,
+:doc:`pair\_style pair\_lebedeva\_z <pair_lebedeva_z>`,
+:doc:`pair\_style kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`,
+:doc:`pair\_style ilp/graphene/hbn <pair_ilp_graphene_hbn>`.
+
+**Default:** tap\_flag = 0
+
+
+----------
+
+
+.. _Kolmogorov1:
+
+
+
+**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+
+.. _Ouyang1:
+
+
+
+**(Ouyang)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst
new file mode 100644
index 0000000000..a1e6c1afad
--- /dev/null
+++ b/doc/src/pair_kolmogorov_crespi_z.rst
@@ -0,0 +1,96 @@
+.. index:: pair\_style kolmogorov/crespi/z
+
+pair\_style kolmogorov/crespi/z command
+=======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style [hybrid/overlay ...] kolmogorov/crespi/z cutoff
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay kolmogorov/crespi/z 20.0
+   pair_coeff \* \* none
+   pair_coeff 1 2 kolmogorov/crespi/z  CC.KC   C C
+
+   pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
+   pair_coeff \* \* rebo                 CH.rebo    C C
+   pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C
+
+Description
+"""""""""""
+
+The *kolmogorov/crespi/z* style computes the Kolmogorov-Crespi interaction
+potential as described in :ref:`(Kolmogorov) <KC05>`. An important simplification is made,
+which is to take all normals along the z-axis.
+
+.. image:: Eqs/pair_kolmogorov_crespi_z.jpg
+   :align: center
+
+It is important to have a sufficiently large cutoff to ensure smooth forces.
+Energies are shifted so that they go continuously to zero at the cutoff assuming
+that the exponential part of *Vij* (first term) decays sufficiently fast.
+This shift is achieved by the last term in the equation for *Vij* above.
+
+This potential is intended for interactions between two layers of graphene.
+Therefore, to avoid interaction between layers in multi-layered materials,
+each layer should have a separate atom type and interactions should only
+be computed between atom types of neighboring layers.
+
+The parameter file (e.g. CC.KC), is intended for use with metal
+:doc:`units <units>`, with energies in meV. An additional parameter, *S*\ ,
+is available to facilitate scaling of energies in accordance with
+:ref:`(vanWijk) <vanWijk>`.
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair\_style *none*\ .
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_none <pair_none>`,
+:doc:`pair\_style hybrid/overlay <pair_hybrid>`,
+:doc:`pair\_style drip <pair_drip>`,
+:doc:`pair\_style ilp/graphene/hbn <pair_ilp_graphene_hbn>`.
+:doc:`pair\_style kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`,
+:doc:`pair\_style lebedeva/z <pair_lebedeva_z>`
+
+**Default:** none
+
+
+----------
+
+
+.. _KC05:
+
+
+
+**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+
+.. _vanWijk:
+
+
+
+**(vanWijk)** M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino,
+Physical Review Letters, 113, 135504 (2014)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst
new file mode 100644
index 0000000000..8f667bf918
--- /dev/null
+++ b/doc/src/pair_lcbop.rst
@@ -0,0 +1,116 @@
+.. index:: pair\_style lcbop
+
+pair\_style lcbop command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style lcbop
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lcbop
+   pair_coeff \* \* ../potentials/C.lcbop C
+
+Description
+"""""""""""
+
+The *lcbop* pair style computes the long-range bond-order potential
+for carbon (LCBOP) of :ref:`(Los and Fasolino) <Los>`.  See section II in
+that paper for the analytic equations associated with the potential.
+
+Only a single pair\_coeff command is used with the *lcbop* style which
+specifies an LCBOP potential file with parameters for specific
+elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of LCBOP elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, if your LAMMPS simulation has 4 atom types and you want
+the 1st 3 to be C you would use the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* C.lcbop C C C NULL
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first C argument maps LAMMPS atom type 1 to the C element in the
+LCBOP file. If a mapping value is specified as NULL, the mapping is
+not performed.  This can be used when a *lcbop* potential is used as
+part of the *hybrid* pair style.  The NULL values are placeholders for
+atom types that will be used with other potentials.
+
+The parameters/coefficients for the LCBOP potential as applied to C
+are listed in the C.lcbop file to agree with the original :ref:`(Los and Fasolino) <Los>` paper.  Thus the parameters are specific to this
+potential and the way it was fit, so modifying the file should be done
+carefully.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This pair styles is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair potential requires the :doc:`newton <newton>` setting to be
+"on" for pair interactions.
+
+The C.lcbop potential file provided with LAMMPS (see the potentials
+directory) is parameterized for metal :doc:`units <units>`.  You can use
+the LCBOP potential with any LAMMPS units, but you would need to
+create your own LCBOP potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_airebo <pair_airebo>`, :doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Los:
+
+
+
+**(Los and Fasolino)** J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107
+(2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst
new file mode 100644
index 0000000000..78e21ca616
--- /dev/null
+++ b/doc/src/pair_lebedeva_z.rst
@@ -0,0 +1,83 @@
+.. index:: pair\_style lebedeva/z
+
+pair\_style lebedeva/z command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style [hybrid/overlay ...] lebedeva/z cutoff
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay lebedeva/z 20.0
+   pair_coeff \* \* none
+   pair_coeff 1 2 lebedeva/z  CC.Lebedeva   C C
+
+   pair_style hybrid/overlay rebo lebedeva/z 14.0
+   pair_coeff \* \* rebo        CH.rebo       C C
+   pair_coeff 1 2 lebedeva/z  CC.Lebedeva   C C
+
+Description
+"""""""""""
+
+The *lebedeva/z* style computes the Lebedeva interaction
+potential as described in :ref:`(Lebedeva et al.) <Leb01>`. An important simplification is made,
+which is to take all normals along the z-axis.
+
+.. image:: Eqs/pair_lebedeva.png
+   :align: center
+
+It is important to have a sufficiently large cutoff to ensure smooth forces.
+Energies are shifted so that they go continuously to zero at the cutoff assuming
+that the exponential part of *Vij* (first term) decays sufficiently fast.
+This shift is achieved by the last term in the equation for *Vij* above.
+
+The parameter file (e.g. CC.Lebedeva), is intended for use with metal
+:doc:`units <units>`, with energies in meV. An additional parameter, *S*\ ,
+is available to facilitate scaling of energies.
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair\_style *none*\ .
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_style none <pair_none>`,
+:doc:`pair\_style hybrid/overlay <pair_hybrid>`,
+:doc:`pair\_style drip <pair_drip>`,
+:doc:`pair\_style ilp/graphene/hbd <pair_ilp_graphene_hbn>`,
+:doc:`pair\_style kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`,
+:doc:`pair\_style kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`.
+
+**Default:** none
+
+
+----------
+
+
+.. _Leb01:
+
+
+
+**(Lebedeva et al.)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst
new file mode 100644
index 0000000000..e8b1a9850f
--- /dev/null
+++ b/doc/src/pair_line_lj.rst
@@ -0,0 +1,159 @@
+.. index:: pair\_style line/lj
+
+pair\_style line/lj command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style line/lj cutoff
+
+cutoff = global cutoff for interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style line/lj 3.0
+   pair_coeff \* \* 1.0 1.0 1.0 0.8 1.12
+   pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
+   pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
+
+Description
+"""""""""""
+
+Style *line/lj* treats particles which are line segments as a set of
+small spherical particles that tile the line segment length as
+explained below.  Interactions between two line segments, each with N1
+and N2 spherical particles, are calculated as the pairwise sum of
+N1\*N2 Lennard-Jones interactions.  Interactions between a line segment
+with N spherical particles and a point particle are treated as the
+pairwise sum of N Lennard-Jones interactions.  See the :doc:`pair\_style lj/cut <pair_lj>` doc page for the definition of Lennard-Jones
+interactions.
+
+The set of non-overlapping spherical sub-particles that represent a
+line segment are generated in the following manner.  Their size is a
+function of the line segment length and the specified sub-particle
+size for that particle type.  If a line segment has a length L and is
+of type I, then the number of spheres N that represent the segment is
+calculated as N = L/sizeI, rounded up to an integer value.  Thus if L
+is not evenly divisible by sizeI, N is incremented to include one
+extra sphere.  The centers of the spheres are spaced equally along the
+line segment.  Imagine N+1 equally-space points, which include the 2
+end points of the segment.  The sphere centers are halfway between
+each pair of points.
+
+The LJ interaction between 2 spheres on different line segments (or a
+sphere on a line segment and a point particles) is computed with
+sub-particle epsilon, sigma, and cutoff values that are set by the
+pair\_coeff command, as described below.  If the distance between the 2
+spheres is greater than the sub-particle cutoff, there is no
+interaction.  This means that some pairs of sub-particles on 2 line
+segments may interact, but others may not.
+
+For purposes of creating the neighbor list for pairs of interacting
+line segments or lines/point particles, a regular particle-particle
+cutoff is used, as defined by the *cutoff* setting above in the
+pair\_style command or overridden with an optional argument in the
+pair\_coeff command for a type pair as discussed below.  The distance
+between the centers of 2 line segments, or the center of a line
+segment and a point particle, must be less than this distance (plus
+the neighbor skin; see the :doc:`neighbor <neighbor>` command), for
+the pair of particles to be included in the neighbor list.
+
+.. note::
+
+   This means that a too-short value for the *cutoff* setting can
+   exclude a pair of particles from the neighbor list even if pairs of
+   their sub-particle spheres would interact, based on the sub-particle
+   cutoff specified in the pair\_coeff command.  E.g. sub-particles at the
+   ends of the line segments that are close to each other.  Which may not
+   be what you want, since it means the ends of 2 line segments could
+   pass through each other.  It is up to you to specify a *cutoff*
+   setting that is consistent with the length of the line segments you
+   are using and the sub-particle cutoff settings.
+
+For style *line/lj*\ , the following coefficients must be defined for
+each pair of atom types via the :doc:`pair\_coeff <pair_coeff>` command
+as in the examples above, or in the data file or restart files read by
+the :doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* sizeI (distance units)
+* sizeJ (distance units)
+* epsilon (energy units)
+* sigma (distance units)
+* subcutoff (distance units)
+* cutoff (distance units)
+
+The *sizeI* and *sizeJ* coefficients are the sub-particle sizes for
+line particles of type I and type J.  They are used to define the N
+sub-particles per segment as described above.  These coefficients are
+actually stored on a per-type basis.  Thus if there are multiple
+pair\_coeff commands that involve type I, as either the first or
+second atom type, you should use consistent values for sizeI or sizeJ
+in all of them.  If you do not do this, the last value specified for
+sizeI will apply to all segments of type I.  If typeI or typeJ refers
+to point particles, the corresponding sizeI or sizeJ is ignored; it
+can be set to 0.0.
+
+The *epsilon*\ , *sigma*\ , and *subcutoff* coefficients are used to
+compute an LJ interactions between a pair of sub-particles on 2 line
+segments (of type I and J), or between a sub particle/point particle
+pair.  As discussed above, the *subcutoff* and *cutoff* params are
+different.  The latter is only used for building the neighbor list
+when the distance between centers of two line segments or one segment
+and a point particle is calculated.
+
+The *cutoff* coefficient is optional.  If not specified, the global
+cutoff is used.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, coefficients must be specified.
+No default mixing rules are used.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the ASPHERE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Defining particles to be line segments so they participate in
+line/line or line/particle interactions requires the use the
+:doc:`atom\_style line <atom_style>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style tri/lj <pair_tri_lj>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst
new file mode 100644
index 0000000000..b74070c4d3
--- /dev/null
+++ b/doc/src/pair_list.rst
@@ -0,0 +1,168 @@
+.. index:: pair_style list
+
+pair_style list command
+=======================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style list listfile cutoff keyword
+
+* listfile = name of file with list of pairwise interactions
+* cutoff = global cutoff (distance units)
+* keyword = optional flag *nocheck* or *check* (default is *check*\ )
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style list restraints.txt 200.0
+   pair_coeff * *
+
+   pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
+   pair_coeff * * lj/cut 1.0 1.0
+   pair_coeff 3* 3* list
+
+Description
+"""""""""""
+
+Style *list* computes interactions between explicitly listed pairs of
+atoms with the option to select functional form and parameters for
+each individual pair.  Because the parameters are set in the list
+file, the pair\_coeff command has no parameters (but still needs to be
+provided).  The *check* and *nocheck* keywords enable/disable a test
+that checks whether all listed bonds were present and computed.
+
+This pair style can be thought of as a hybrid between bonded,
+non-bonded, and restraint interactions.  It will typically be used as
+an additional interaction within the *hybrid/overlay* pair style.  It
+currently supports three interaction styles: a 12-6 Lennard-Jones, a
+Morse and a harmonic potential.
+
+The format of the list file is as follows:
+
+* one line per pair of atoms
+* empty lines will be ignored
+* comment text starts with a '#' character
+* line syntax: *ID1 ID2 style coeffs cutoff*
+  
+  .. parsed-literal::
+  
+       ID1 = atom ID of first atom
+       ID2 = atom ID of second atom
+       style = style of interaction
+       coeffs = list of coeffs
+       cutoff = cutoff for interaction (optional)
+
+
+
+The cutoff parameter is optional. If not specified, the global cutoff
+is used.
+
+Here is an example file:
+
+
+.. parsed-literal::
+
+   # this is a comment
+
+   15 259 lj126     1.0 1.0      50.0
+   15 603 morse    10.0 1.2 2.0  10.0 # and another comment
+   18 470 harmonic 50.0 1.2       5.0
+
+The style *lj126* computes pairwise interactions with the formula
+
+.. math::
+
+   E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c
+
+
+and the coefficients:
+
+* :math:`\epsilon` (energy units)
+* :math:`\sigma` (distance units)
+
+The style *morse* computes pairwise interactions with the formula
+
+.. math::
+
+   E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c
+
+
+and the coefficients:
+
+* :math:`D_0` (energy units)
+* :math:`\alpha` (1/distance units)
+* :math:`r_0` (distance units)
+
+The style *harmonic* computes pairwise interactions with the formula
+
+.. math::
+
+   E = K (r - r_0)^2
+
+and the coefficients:
+
+* :math:`K` (energy units)
+* :math:`r_0` (distance units)
+
+Note that the usual 1/2 factor is included in :math:`K`.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support mixing since all parameters are
+explicit for each pair.
+
+The :doc:`pair\_modify <pair_modify>` shift option is supported by this
+pair style.
+
+The :doc:`pair\_modify <pair_modify>` table and tail options are not
+relevant for this pair style.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style does not use a neighbor list and instead identifies
+atoms by their IDs. This has two consequences: 1) The cutoff has to be
+chosen sufficiently large, so that the second atom of a pair has to be
+a ghost atom on the same node on which the first atom is local;
+otherwise the interaction will be skipped. You can use the *check*
+option to detect, if interactions are missing. 2) Unlike other pair
+styles in LAMMPS, an atom I will not interact with multiple images of
+atom J (assuming the images are within the cutoff distance), but only
+with the nearest image.
+
+This style is part of the USER-MISC package. It is only enabled if
+LAMMPS is build with that package. See the :doc:`Build package <Build_package>` doc page on for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_style hybrid/overlay <pair_hybrid>`,
+:doc:`pair\_style lj/cut <pair_lj>`,
+:doc:`pair\_style morse <pair_morse>`,
+:doc:`bond\_style harmonic <bond_harmonic>`
+
+**Default:** none
diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt
deleted file mode 100644
index 9500a4c508..0000000000
--- a/doc/src/pair_list.txt
+++ /dev/null
@@ -1,144 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style list command :h3
-
-[Syntax:]
-
-pair_style list listfile cutoff keyword :pre
-
-listfile = name of file with list of pairwise interactions
-cutoff = global cutoff (distance units)
-keyword = optional flag {nocheck} or {check} (default is {check}) :ul
-
-[Examples:]
-
-pair_style list restraints.txt 200.0
-pair_coeff * * :pre
-
-pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff 3* 3* list :pre
-
-[Description:]
-
-Style {list} computes interactions between explicitly listed pairs of
-atoms with the option to select functional form and parameters for
-each individual pair.  Because the parameters are set in the list
-file, the pair_coeff command has no parameters (but still needs to be
-provided).  The {check} and {nocheck} keywords enable/disable a test
-that checks whether all listed bonds were present and computed.
-
-This pair style can be thought of as a hybrid between bonded,
-non-bonded, and restraint interactions.  It will typically be used as
-an additional interaction within the {hybrid/overlay} pair style.  It
-currently supports three interaction styles: a 12-6 Lennard-Jones, a
-Morse and a harmonic potential.
-
-The format of the list file is as follows:
-
-one line per pair of atoms :ulb,l
-empty lines will be ignored :l
-comment text starts with a '#' character :l
-line syntax: {ID1 ID2 style coeffs cutoff} :l
-  ID1 = atom ID of first atom
-  ID2 = atom ID of second atom
-  style = style of interaction
-  coeffs = list of coeffs
-  cutoff = cutoff for interaction (optional) :pre
-:ule
-
-The cutoff parameter is optional. If not specified, the global cutoff
-is used.
-
-Here is an example file:
-
-# this is a comment :pre
-
-15 259 lj126     1.0 1.0      50.0
-15 603 morse    10.0 1.2 2.0  10.0 # and another comment
-18 470 harmonic 50.0 1.2       5.0  :pre
-
-The style {lj126} computes pairwise interactions with the formula
-
-:c,image(Eqs/pair_lj.jpg)
-
-and the coefficients:
-
-epsilon (energy units)
-sigma (distance units) :ul
-
-The style {morse} computes pairwise interactions with the formula
-
-:c,image(Eqs/pair_morse.jpg)
-
-and the coefficients:
-
-D0 (energy units)
-alpha (1/distance units)
-r0 (distance units) :ul
-
-The style {harmonic} computes pairwise interactions with the formula
-
-:c,image(Eqs/bond_harmonic.jpg)
-
-and the coefficients:
-
-K (energy units)
-r0 (distance units) :ul
-
-Note that the usual 1/2 factor is included in K.
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-This pair style does not support mixing since all parameters are
-explicit for each pair.
-
-The "pair_modify"_pair_modify.html shift option is supported by this
-pair style.
-
-The "pair_modify"_pair_modify.html table and tail options are not
-relevant for this pair style.
-
-This pair style does not write its information to "binary restart
-files"_restart.html, so pair_style and pair_coeff commands need
-to be specified in an input script that reads a restart file.
-
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
-
-:line
-
-[Restrictions:]
-
-This pair style does not use a neighbor list and instead identifies
-atoms by their IDs. This has two consequences: 1) The cutoff has to be
-chosen sufficiently large, so that the second atom of a pair has to be
-a ghost atom on the same node on which the first atom is local;
-otherwise the interaction will be skipped. You can use the {check}
-option to detect, if interactions are missing. 2) Unlike other pair
-styles in LAMMPS, an atom I will not interact with multiple images of
-atom J (assuming the images are within the cutoff distance), but only
-with the nearest image.
-
-This style is part of the USER-MISC package. It is only enabled if
-LAMMPS is build with that package. See the "Build
-package"_Build_package.html doc page on for more info.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html,
-"pair_style hybrid/overlay"_pair_hybrid.html,
-"pair_style lj/cut"_pair_lj.html,
-"pair_style morse"_pair_morse.html,
-"bond_style harmonic"_bond_harmonic.html
-
-[Default:] none
diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst
new file mode 100644
index 0000000000..7a46f0a0db
--- /dev/null
+++ b/doc/src/pair_lj.rst
@@ -0,0 +1,451 @@
+.. index:: pair\_style lj/cut
+
+pair\_style lj/cut command
+==========================
+
+pair\_style lj/cut/gpu command
+==============================
+
+pair\_style lj/cut/intel command
+================================
+
+pair\_style lj/cut/kk command
+=============================
+
+pair\_style lj/cut/opt command
+==============================
+
+pair\_style lj/cut/omp command
+==============================
+
+pair\_style lj/cut/coul/cut command
+===================================
+
+pair\_style lj/cut/coul/cut/gpu command
+=======================================
+
+pair\_style lj/cut/coul/cut/kk command
+======================================
+
+pair\_style lj/cut/coul/cut/omp command
+=======================================
+
+pair\_style lj/cut/coul/debye command
+=====================================
+
+pair\_style lj/cut/coul/debye/gpu command
+=========================================
+
+pair\_style lj/cut/coul/debye/kk command
+========================================
+
+pair\_style lj/cut/coul/debye/omp command
+=========================================
+
+pair\_style lj/cut/coul/dsf command
+===================================
+
+pair\_style lj/cut/coul/dsf/gpu command
+=======================================
+
+pair\_style lj/cut/coul/dsf/kk command
+======================================
+
+pair\_style lj/cut/coul/dsf/omp command
+=======================================
+
+pair\_style lj/cut/coul/long command
+====================================
+
+pair\_style lj/cut/coul/long/gpu command
+========================================
+
+pair\_style lj/cut/coul/long/kk command
+=======================================
+
+pair\_style lj/cut/coul/long/intel command
+==========================================
+
+pair\_style lj/cut/coul/long/opt command
+========================================
+
+pair\_style lj/cut/coul/long/omp command
+========================================
+
+pair\_style lj/cut/coul/msm command
+===================================
+
+pair\_style lj/cut/coul/msm/gpu command
+=======================================
+
+pair\_style lj/cut/coul/msm/omp command
+=======================================
+
+pair\_style lj/cut/coul/wolf command
+====================================
+
+pair\_style lj/cut/coul/wolf/omp command
+========================================
+
+pair\_style lj/cut/tip4p/cut command
+====================================
+
+pair\_style lj/cut/tip4p/cut/gpu command
+========================================
+
+pair\_style lj/cut/tip4p/cut/omp command
+========================================
+
+pair\_style lj/cut/tip4p/long command
+=====================================
+
+pair\_style lj/cut/tip4p/long/omp command
+=========================================
+
+pair\_style lj/cut/tip4p/long/opt command
+=========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/cut* or *lj/cut/coul/cut* or *lj/cut/coul/debye* or *lj/cut/coul/dsf* or *lj/cut/coul/long* *lj/cut/coul/msm* or *lj/cut/tip4p/long*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *lj/cut* args = cutoff
+       cutoff = global cutoff for Lennard Jones interactions (distance units)
+     *lj/cut/coul/cut* args = cutoff (cutoff2)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/cut/coul/debye* args = kappa cutoff (cutoff2)
+       kappa = inverse of the Debye length (inverse distance units)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/cut/coul/dsf* args = alpha cutoff (cutoff2)
+       alpha = damping parameter (inverse distance units)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (distance units)
+     *lj/cut/coul/long* args = cutoff (cutoff2)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/cut/coul/msm* args = cutoff (cutoff2)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/cut/coul/wolf* args = alpha cutoff (cutoff2)
+       alpha = damping parameter (inverse distance units)
+       cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/cut/tip4p/cut* args = otype htype btype atype qdist cutoff (cutoff2)
+       otype,htype = atom types for TIP4P O and H
+       btype,atype = bond and angle types for TIP4P waters
+       qdist = distance from O atom to massless charge (distance units)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/cut/tip4p/long* args = otype htype btype atype qdist cutoff (cutoff2)
+       otype,htype = atom types for TIP4P O and H
+       btype,atype = bond and angle types for TIP4P waters
+       qdist = distance from O atom to massless charge (distance units)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/cut 2.5
+   pair_coeff \* \* 1 1
+   pair_coeff 1 1 1 1.1 2.8
+
+   pair_style lj/cut/coul/cut 10.0
+   pair_style lj/cut/coul/cut 10.0 8.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+   pair_coeff 1 1 100.0 3.5 9.0 9.0
+
+   pair_style lj/cut/coul/debye 1.5 3.0
+   pair_style lj/cut/coul/debye 1.5 2.5 5.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 1 1 1.0 1.5 2.5
+   pair_coeff 1 1 1.0 1.5 2.5 5.0
+
+   pair_style lj/cut/coul/dsf 0.05 2.5 10.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 1 1 1.0 1.0 2.5
+
+   pair_style lj/cut/coul/long 10.0
+   pair_style lj/cut/coul/long 10.0 8.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+
+   pair_style lj/cut/coul/msm 10.0
+   pair_style lj/cut/coul/msm 10.0 8.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+
+   pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
+   pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+
+   pair_style lj/cut/coul/wolf 0.2 5. 10.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 1 1 1.0 1.0 2.5
+
+   pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
+   pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+
+Description
+"""""""""""
+
+The *lj/cut* styles compute the standard 12/6 Lennard-Jones potential,
+given by
+
+.. image:: Eqs/pair_lj.jpg
+   :align: center
+
+Rc is the cutoff.
+
+Style *lj/cut/coul/cut* adds a Coulombic pairwise interaction given by
+
+.. image:: Eqs/pair_coulomb.jpg
+   :align: center
+
+where C is an energy-conversion constant, Qi and Qj are the charges on
+the 2 atoms, and epsilon is the dielectric constant which can be set
+by the :doc:`dielectric <dielectric>` command.  If one cutoff is
+specified in the pair\_style command, it is used for both the LJ and
+Coulombic terms.  If two cutoffs are specified, they are used as
+cutoffs for the LJ and Coulombic terms respectively.
+
+Style *lj/cut/coul/debye* adds an additional exp() damping factor
+to the Coulombic term, given by
+
+.. image:: Eqs/pair_debye.jpg
+   :align: center
+
+where kappa is the inverse of the Debye length.  This potential is
+another way to mimic the screening effect of a polar solvent.
+
+Style *lj/cut/coul/dsf* computes the Coulombic term via the damped
+shifted force model described in :ref:`Fennell <Fennell2>`, given by:
+
+.. image:: Eqs/pair_coul_dsf.jpg
+   :align: center
+
+where *alpha* is the damping parameter and erfc() is the complementary
+error-function. This potential is essentially a short-range,
+spherically-truncated, charge-neutralized, shifted, pairwise *1/r*
+summation.  The potential is based on Wolf summation, proposed as an
+alternative to Ewald summation for condensed phase systems where
+charge screening causes electrostatic interactions to become
+effectively short-ranged. In order for the electrostatic sum to be
+absolutely convergent, charge neutralization within the cutoff radius
+is enforced by shifting the potential through placement of image
+charges on the cutoff sphere. Convergence can often be improved by
+setting *alpha* to a small non-zero value.
+
+Styles *lj/cut/coul/long* and *lj/cut/coul/msm* compute the same
+Coulombic interactions as style *lj/cut/coul/cut* except that an
+additional damping factor is applied to the Coulombic term so it can
+be used in conjunction with the :doc:`kspace\_style <kspace_style>`
+command and its *ewald* or *pppm* option.  The Coulombic cutoff
+specified for this style means that pairwise interactions within this
+distance are computed directly; interactions outside that distance are
+computed in reciprocal space.
+
+Style *coul/wolf* adds a Coulombic pairwise interaction via the Wolf
+summation method, described in :ref:`Wolf <Wolf1>`, given by:
+
+.. image:: Eqs/pair_coul_wolf.jpg
+   :align: center
+
+where *alpha* is the damping parameter, and erfc() is the
+complementary error-function terms.  This potential
+is essentially a short-range, spherically-truncated,
+charge-neutralized, shifted, pairwise *1/r* summation.  With a
+manipulation of adding and subtracting a self term (for i = j) to the
+first and second term on the right-hand-side, respectively, and a
+small enough *alpha* damping parameter, the second term shrinks and
+the potential becomes a rapidly-converging real-space summation.  With
+a long enough cutoff and small enough alpha parameter, the energy and
+forces calculated by the Wolf summation method approach those of the
+Ewald sum.  So it is a means of getting effective long-range
+interactions with a short-range potential.
+
+Styles *lj/cut/tip4p/cut* and *lj/cut/tip4p/long* implement the TIP4P
+water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
+site located a short distance away from the oxygen atom along the
+bisector of the HOH angle.  The atomic types of the oxygen and
+hydrogen atoms, the bond and angle types for OH and HOH interactions,
+and the distance to the massless charge site are specified as
+pair\_style arguments.  Style *lj/cut/tip4p/cut* uses a cutoff for
+Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
+long-range Coulombic solver (Ewald or PPPM).
+
+.. note::
+
+   For each TIP4P water molecule in your system, the atom IDs for
+   the O and 2 H atoms must be consecutive, with the O atom first.  This
+   is to enable LAMMPS to "find" the 2 H atoms associated with each O
+   atom.  For example, if the atom ID of an O atom in a TIP4P water
+   molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+
+See the :doc:`Howto tip4p <Howto_tip4p>` doc page for more information
+on how to use the TIP4P pair styles and lists of parameters to set.
+Note that the neighbor list cutoff for Coulomb interactions is
+effectively extended by a distance 2\*qdist when using the TIP4P pair
+style, to account for the offset distance of the fictitious charges on
+O atoms in water molecules.  Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
+shrink the size of the neighbor list.  This leads to slightly larger
+cost for the long-range calculation, so you can test the trade-off for
+your model.
+
+For all of the *lj/cut* pair styles, the following coefficients must
+be defined for each pair of atoms types via the
+:doc:`pair\_coeff <pair_coeff>` command as in the examples above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands, or by mixing as
+described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff1 (distance units)
+* cutoff2 (distance units)
+
+Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum at 2\^(1/6)
+sigma.
+
+The latter 2 coefficients are optional.  If not specified, the global
+LJ and Coulombic cutoffs specified in the pair\_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair.  If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair.  You cannot specify 2 cutoffs for style *lj/cut*\ , since it
+has no Coulombic terms.
+
+For *lj/cut/coul/long* and *lj/cut/coul/msm* and *lj/cut/tip4p/cut*
+and *lj/cut/tip4p/long* only the LJ cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair\_style command.
+
+
+----------
+
+
+A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
+free energy calculations, is part of the USER-FEP package and is documented with
+the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is *geometric*\ .  See the "pair\_modify" command
+for details.
+
+All of the *lj/cut* pair styles support the
+:doc:`pair\_modify <pair_modify>` shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+
+The *lj/cut/coul/long* and *lj/cut/tip4p/long* pair styles support the
+:doc:`pair\_modify <pair_modify>` table option since they can tabulate
+the short-range portion of the long-range Coulombic interaction.
+
+All of the *lj/cut* pair styles support the
+:doc:`pair\_modify <pair_modify>` tail option for adding a long-range
+tail correction to the energy and pressure for the Lennard-Jones
+portion of the pair interaction.
+
+All of the *lj/cut* pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+The *lj/cut* and *lj/cut/coul/long* pair styles support the use of the
+*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa <run_style>` command, meaning the pairwise forces can be
+partitioned by distance at different levels of the rRESPA hierarchy.
+The other styles only support the *pair* keyword of run\_style respa.
+See the :doc:`run\_style <run_style>` command for details.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *lj/cut/coul/long* and *lj/cut/tip4p/long* styles are part of the
+KSPACE package. The *lj/cut/tip4p/cut* style is part of the MOLECULE
+package. These styles are only enabled if LAMMPS was built with those
+packages.  See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Jorgensen2:
+
+
+
+**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+
+.. _Fennell2:
+
+
+
+**(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
+234104 (2006).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst
new file mode 100644
index 0000000000..814eac69f9
--- /dev/null
+++ b/doc/src/pair_lj96.rst
@@ -0,0 +1,126 @@
+.. index:: pair\_style lj96/cut
+
+pair\_style lj96/cut command
+============================
+
+pair\_style lj96/cut/gpu command
+================================
+
+pair\_style lj96/cut/omp command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style lj96/cut cutoff
+
+* cutoff = global cutoff for lj96/cut interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj96/cut 2.5
+   pair_coeff \* \* 1.0 1.0 4.0
+   pair_coeff 1 1 1.0 1.0
+
+Description
+"""""""""""
+
+The *lj96/cut* style compute a 9/6 Lennard-Jones potential, instead
+of the standard 12/6 potential, given by
+
+.. image:: Eqs/pair_lj96.jpg
+   :align: center
+
+Rc is the cutoff.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global LJ
+cutoff specified in the pair\_style command is used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is *geometric*\ .  See the "pair\_modify" command
+for details.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` tail
+option for adding a long-range tail correction to the energy and
+pressure of the pair interaction.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style supports the use of the *inner*\ , *middle*\ , and *outer*
+keywords of the :doc:`run\_style respa <run_style>` command, meaning the
+pairwise forces can be partitioned by distance at different levels of
+the rRESPA hierarchy.  See the :doc:`run\_style <run_style>` command for
+details.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst
new file mode 100644
index 0000000000..e03e70cb6b
--- /dev/null
+++ b/doc/src/pair_lj_cubic.rst
@@ -0,0 +1,156 @@
+.. index:: pair\_style lj/cubic
+
+pair\_style lj/cubic command
+============================
+
+pair\_style lj/cubic/gpu command
+================================
+
+pair\_style lj/cubic/omp command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/cubic
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/cubic
+   pair_coeff \* \* 1.0 0.8908987
+
+Description
+"""""""""""
+
+The *lj/cubic* style computes a truncated LJ interaction potential
+whose energy and force are continuous everywhere.  Inside the
+inflection point the interaction is identical to the standard 12/6
+:doc:`Lennard-Jones <pair_lj>` potential.  The LJ function outside the
+inflection point is replaced with a cubic function of distance. The
+energy, force, and second derivative are continuous at the inflection
+point.  The cubic coefficient A3 is chosen so that both energy and
+force go to zero at the cutoff distance.  Outside the cutoff distance
+the energy and force are zero.
+
+.. image:: Eqs/pair_lj_cubic.jpg
+   :align: center
+
+The location of the inflection point rs is defined
+by the LJ diameter, rs/sigma = (26/7)\^1/6. The cutoff distance
+is defined by rc/rs = 67/48 or rc/sigma = 1.737....
+The analytic expression for the
+the cubic coefficient
+A3\*rmin\^3/epsilon = 27.93... is given in the paper by
+Holian and Ravelo :ref:`(Holian) <Holian>`.
+
+This potential is commonly used to study the shock mechanics of FCC
+solids, as in Ravelo et al. :ref:`(Ravelo) <Ravelo2>`.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the example above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+
+Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum, which is
+located at rmin = 2\^(1/6)\*sigma. In the above example, sigma =
+0.8908987, so rmin = 1.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is *geometric*\ .  See the "pair\_modify" command
+for details.
+
+The lj/cubic pair style does not support the
+:doc:`pair\_modify <pair_modify>` shift option,
+since pair interaction is already smoothed to 0.0 at the
+cutoff.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+The lj/cubic pair style does not support the
+:doc:`pair\_modify <pair_modify>` tail option for adding long-range tail
+corrections to energy and pressure, since there are no corrections for
+a potential that goes to 0.0 at the cutoff.
+
+The lj/cubic pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+The lj/cubic pair style can only be used via the *pair*
+keyword of the :doc:`run\_style respa <run_style>` command.  It does not
+support the *inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Holian:
+
+
+
+.. _Ravelo2:
+
+**(Holian)** Holian and Ravelo, Phys Rev B, 51, 11275 (1995).
+
+
+**(Ravelo)** Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst
new file mode 100644
index 0000000000..45a56219c4
--- /dev/null
+++ b/doc/src/pair_lj_expand.rst
@@ -0,0 +1,150 @@
+.. index:: pair\_style lj/expand
+
+pair\_style lj/expand command
+=============================
+
+pair\_style lj/expand/gpu command
+=================================
+
+pair\_style lj/expand/kk command
+================================
+
+pair\_style lj/expand/omp command
+=================================
+
+pair\_style lj/expand/coul/long command
+=======================================
+
+pair\_style lj/expand/coul/long/gpu command
+===========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/expand cutoff
+
+* cutoff = global cutoff for lj/expand interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/expand 2.5
+   pair_coeff \* \* 1.0 1.0 0.5
+   pair_coeff 1 1 1.0 1.0 -0.2 2.0
+
+   pair_style lj/expand/coul/long 2.5
+   pair_style lj/expand/coul/long 2.5 4.0
+   pair_coeff \* \* 1.0 1.0 0.5
+   pair_coeff 1 1 1.0 1.0 -0.2 3.0
+
+Description
+"""""""""""
+
+Style *lj/expand* computes a LJ interaction with a distance shifted by
+delta which can be useful when particles are of different sizes, since
+it is different that using different sigma values in a standard LJ
+formula:
+
+.. image:: Eqs/pair_lj_expand.jpg
+   :align: center
+
+Rc is the cutoff which does not include the delta distance.  I.e. the
+actual force cutoff is the sum of cutoff + delta.
+
+For all of the *lj/expand* pair styles, the following coefficients must
+be defined for each pair of atoms types via the
+:doc:`pair\_coeff <pair_coeff>` command as in the examples above, or in
+the data file or restart files read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands, or by mixing as
+described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* delta (distance units)
+* cutoff (distance units)
+
+The delta values can be positive or negative.  The last coefficient is
+optional.  If not specified, the global LJ cutoff is used.
+
+For *lj/expand/coul/long* only the LJ cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair\_style command.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon, sigma, and shift
+coefficients and cutoff distance for this pair style can be mixed.
+Shift is always mixed via an *arithmetic* rule.  The other
+coefficients are mixed according to the pair\_modify mix value.  The
+default mix value is *geometric*\ .  See the "pair\_modify" command for
+details.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` tail
+option for adding a long-range tail correction to the energy and
+pressure of the pair interaction.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst
new file mode 100644
index 0000000000..c6f17e2eb8
--- /dev/null
+++ b/doc/src/pair_lj_long.rst
@@ -0,0 +1,278 @@
+.. index:: pair\_style lj/long/coul/long
+
+pair\_style lj/long/coul/long command
+=====================================
+
+pair\_style lj/long/coul/long/intel command
+===========================================
+
+pair\_style lj/long/coul/long/omp command
+=========================================
+
+pair\_style lj/long/coul/long/opt command
+=========================================
+
+pair\_style lj/long/tip4p/long command
+======================================
+
+pair\_style lj/long/tip4p/long/omp command
+==========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/long/coul/long* or *lj/long/tip4p/long*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *lj/long/coul/long* args = flag_lj flag_coul cutoff (cutoff2)
+       flag_lj = *long* or *cut* or *off*
+         *long* = use Kspace long-range summation for dispersion 1/r\^6 term
+         *cut* = use a cutoff on dispersion 1/r\^6 term
+         *off* = omit disperion 1/r\^6 term entirely
+       flag_coul = *long* or *off*
+         *long* = use Kspace long-range summation for Coulombic 1/r term
+         *off* = omit Coulombic term
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+     *lj/long/tip4p/long* args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
+       flag_lj = *long* or *cut*
+         *long* = use Kspace long-range summation for dispersion 1/r\^6 term
+         *cut* = use a cutoff
+       flag_coul = *long* or *off*
+         *long* = use Kspace long-range summation for Coulombic 1/r term
+         *off* = omit Coulombic term
+       otype,htype = atom types for TIP4P O and H
+       btype,atype = bond and angle types for TIP4P waters
+       qdist = distance from O atom to massless charge (distance units)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/long/coul/long cut off 2.5
+   pair_style lj/long/coul/long cut long 2.5 4.0
+   pair_style lj/long/coul/long long long 2.5 4.0
+   pair_coeff \* \* 1 1
+   pair_coeff 1 1 1 3 4
+
+   pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
+   pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
+   pair_coeff \* \* 100.0 3.0
+   pair_coeff 1 1 100.0 3.5 9.0
+
+Description
+"""""""""""
+
+Style *lj/long/coul/long* computes the standard 12/6 Lennard-Jones and
+Coulombic potentials, given by
+
+.. image:: Eqs/pair_lj.jpg
+   :align: center
+
+.. image:: Eqs/pair_coulomb.jpg
+   :align: center
+
+where C is an energy-conversion constant, Qi and Qj are the charges on
+the 2 atoms, epsilon is the dielectric constant which can be set by
+the :doc:`dielectric <dielectric>` command, and Rc is the cutoff.  If
+one cutoff is specified in the pair\_style command, it is used for both
+the LJ and Coulombic terms.  If two cutoffs are specified, they are
+used as cutoffs for the LJ and Coulombic terms respectively.
+
+The purpose of this pair style is to capture long-range interactions
+resulting from both attractive 1/r\^6 Lennard-Jones and Coulombic 1/r
+interactions.  This is done by use of the *flag\_lj* and *flag\_coul*
+settings.  The :ref:`In 't Veld <Veld2>` paper has more details on when it is
+appropriate to include long-range 1/r\^6 interactions, using this
+potential.
+
+Style *lj/long/tip4p/long* implements the TIP4P water model of
+:ref:`(Jorgensen) <Jorgensen4>`, which introduces a massless site located a
+short distance away from the oxygen atom along the bisector of the HOH
+angle.  The atomic types of the oxygen and hydrogen atoms, the bond
+and angle types for OH and HOH interactions, and the distance to the
+massless charge site are specified as pair\_style arguments.
+
+.. note::
+
+   For each TIP4P water molecule in your system, the atom IDs for
+   the O and 2 H atoms must be consecutive, with the O atom first.  This
+   is to enable LAMMPS to "find" the 2 H atoms associated with each O
+   atom.  For example, if the atom ID of an O atom in a TIP4P water
+   molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+
+See the :doc:`Howto tip4p <Howto_tip4p>` doc page for more
+information on how to use the TIP4P pair style.  Note that the
+neighbor list cutoff for Coulomb interactions is effectively extended
+by a distance 2\*qdist when using the TIP4P pair style, to account for
+the offset distance of the fictitious charges on O atoms in water
+molecules.  Thus it is typically best in an efficiency sense to use a
+LJ cutoff >= Coulombic cutoff + 2\*qdist, to shrink the size of the
+neighbor list.  This leads to slightly larger cost for the long-range
+calculation, so you can test the trade-off for your model.
+
+If *flag\_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6
+dispersion term.  The long-range portion can be calculated by using
+the :doc:`kspace\_style ewald/disp or pppm/disp <kspace_style>` commands.
+The specified LJ cutoff then determines which portion of the LJ
+interactions are computed directly by the pair potential versus which
+part is computed in reciprocal space via the Kspace style.  If
+*flag\_lj* is set to *cut*\ , the LJ interactions are simply cutoff, as
+with :doc:`pair\_style lj/cut <pair_lj>`.
+
+If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic
+interactions.  The long-range portion can calculated by using any of
+several :doc:`kspace\_style <kspace_style>` command options such as
+*pppm* or *ewald*\ .  Note that if *flag\_lj* is also set to long, then
+the *ewald/disp* or *pppm/disp* Kspace style needs to be used to
+perform the long-range calculations for both the LJ and Coulombic
+interactions.  If *flag\_coul* is set to *off*\ , Coulombic interactions
+are not computed.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff1 (distance units)
+* cutoff2 (distance units)
+
+Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum at 2\^(1/6)
+sigma.
+
+The latter 2 coefficients are optional.  If not specified, the global
+LJ and Coulombic cutoffs specified in the pair\_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair.  If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair.
+
+Note that if you are using *flag\_lj* set to *long*\ , you
+cannot specify a LJ cutoff for an atom type pair, since only one
+global LJ cutoff is allowed.  Similarly, if you are using *flag\_coul*
+set to *long*\ , you cannot specify a Coulombic cutoff for an atom type
+pair, since only one global Coulombic cutoff is allowed.
+
+For *lj/long/tip4p/long* only the LJ cutoff can be specified
+since a Coulombic cutoff cannot be specified for an individual I,J
+type pair.  All type pairs use the same global Coulombic cutoff
+specified in the pair\_style command.
+
+
+----------
+
+
+A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
+free energy calculations, is part of the USER-FEP package and is documented with
+the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/long pair styles can be mixed.
+The default mix value is *geometric*\ .  See the "pair\_modify" command
+for details.
+
+These pair styles support the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction, assuming *flag\_lj* is *cut*\ .
+
+These pair styles support the :doc:`pair\_modify <pair_modify>` table and
+table/disp options since they can tabulate the short-range portion of
+the long-range Coulombic and dispersion interactions.
+
+Thes pair styles do not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding a long-range tail correction to the
+Lennard-Jones portion of the energy and pressure.
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+The pair lj/long/coul/long styles support the use of the *inner*\ ,
+*middle*\ , and *outer* keywords of the :doc:`run\_style respa <run_style>`
+command, meaning the pairwise forces can be partitioned by distance at
+different levels of the rRESPA hierarchy.  See the
+:doc:`run\_style <run_style>` command for details.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the KSPACE package.  They are only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Veld2:
+
+
+
+**(In 't Veld)** In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
+
+.. _Jorgensen4:
+
+
+
+**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst
new file mode 100644
index 0000000000..6120faa24a
--- /dev/null
+++ b/doc/src/pair_lj_smooth.rst
@@ -0,0 +1,140 @@
+.. index:: pair\_style lj/smooth
+
+pair\_style lj/smooth command
+=============================
+
+pair\_style lj/smooth/omp command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/smooth Rin Rc
+
+* Rin = inner cutoff beyond which force smoothing will be applied (distance units)
+* Rc = outer cutoff for lj/smooth interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/smooth 8.0 10.0
+   pair_coeff \* \* 10.0 1.5
+   pair_coeff 1 1 20.0 1.3 7.0 9.0
+
+Description
+"""""""""""
+
+Style *lj/smooth* computes a LJ interaction with a force smoothing
+applied between the inner and outer cutoff.
+
+.. image:: Eqs/pair_lj_smooth.jpg
+   :align: center
+
+The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to
+cause the force to vary smoothly from the inner cutoff Rin to the
+outer cutoff Rc.
+
+At the inner cutoff the force and its 1st derivative
+will match the non-smoothed LJ formula.  At the outer cutoff the force
+and its 1st derivative will be 0.0.  The inner cutoff cannot be 0.0.
+
+.. note::
+
+   this force smoothing causes the energy to be discontinuous both
+   in its values and 1st derivative.  This can lead to poor energy
+   conservation and may require the use of a thermostat.  Plot the energy
+   and force resulting from this formula via the
+   :doc:`pair\_write <pair_write>` command to see the effect.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* inner (distance units)
+* outer (distance units)
+
+The last 2 coefficients are optional inner and outer cutoffs.  If not
+specified, the global values for Rin and Rc are used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon, sigma, Rin
+coefficients and the cutoff distance for this pair style can be mixed.
+Rin is a cutoff value and is mixed like the cutoff.  The other
+coefficients are mixed according to the pair\_modify mix option.  The
+default mix value is *geometric*\ .  See the "pair\_modify" command for
+details.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair lj/smooth/linear <pair_lj_smooth_linear>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst
new file mode 100644
index 0000000000..13dc334719
--- /dev/null
+++ b/doc/src/pair_lj_smooth_linear.rst
@@ -0,0 +1,133 @@
+.. index:: pair\_style lj/smooth/linear
+
+pair\_style lj/smooth/linear command
+====================================
+
+pair\_style lj/smooth/linear/omp command
+========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/smooth/linear cutoff
+
+* cutoff = global cutoff for Lennard-Jones interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/smooth/linear 2.5
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 1 1 0.3 3.0 9.0
+
+Description
+"""""""""""
+
+Style *lj/smooth/linear* computes a truncated and force-shifted LJ
+interaction (aka Shifted Force Lennard-Jones) that combines the
+standard 12/6 Lennard-Jones function and subtracts a linear term based
+on the cutoff distance, so that both, the potential and the force, go
+continuously to zero at the cutoff Rc :ref:`(Toxvaerd) <Toxvaerd>`:
+
+.. image:: Eqs/pair_lj_smooth_linear.jpg
+   :align: center
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff (distance units)
+
+The last coefficient is optional. If not specified, the global
+LJ cutoff specified in the pair\_style command is used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance can be mixed. The default mix value is geometric.
+See the "pair\_modify" command for details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the pair interaction, since it goes
+to 0.0 at the cutoff by construction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair lj/smooth <pair_lj_smooth>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Toxvaerd:
+
+
+
+**(Toxvaerd)** Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst
new file mode 100644
index 0000000000..dd4040c595
--- /dev/null
+++ b/doc/src/pair_lj_switch3_coulgauss_long.rst
@@ -0,0 +1,104 @@
+.. index:: pair\_style lj/switch3/coulgauss/long
+
+pair\_style lj/switch3/coulgauss/long command
+=============================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/switch3/coulgauss/long*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *lj/switch3/coulgauss/long* args = cutoff (cutoff2) width
+       cutoff  = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+       width  = width parameter of the smoothing function (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/switch3/coulgauss/long    12.0 3.0
+   pair_coeff 1  0.2 2.5 1.2
+
+   pair_style lj/switch3/coulgauss/long   12.0 10.0 3.0
+   pair_coeff 1  0.2 2.5 1.2
+
+Description
+"""""""""""
+
+The *lj/switch3/coulgauss* style evaluates the LJ
+vdW potential
+
+.. image:: Eqs/pair_lj_switch3.jpg
+   :align: center
+
+, which goes smoothly to zero at the cutoff r\_c as defined
+by the switching function
+
+.. image:: Eqs/pair_switch3.jpg
+   :align: center
+
+where w is the width defined in the arguments. This potential
+is combined with Coulomb interaction between Gaussian charge densities:
+
+.. image:: Eqs/pair_coulgauss.jpg
+   :align: center
+
+where qi and qj are the
+charges on the 2 atoms, epsilon is the dielectric constant which
+can be set by the :doc:`dielectric <dielectric>` command, gamma\_i and gamma\_j
+are the widths of the Gaussian charge distribution and erf() is the error-function.
+This style has to be used in conjunction with the :doc:`kspace\_style <kspace_style>` command
+
+If one cutoff is specified it is used for both the vdW and Coulomb
+terms.  If two cutoffs are specified, the first is used as the cutoff
+for the vdW terms, and the second is the cutoff for the Coulombic term.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* epsilon (energy)
+* sigma (distance)
+* gamma (distance)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+Shifting the potential energy is not necessary because the switching
+function ensures that the potential is zero at the cut-off.
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the USER-YAFF package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst
new file mode 100644
index 0000000000..2a9d4068b7
--- /dev/null
+++ b/doc/src/pair_local_density.rst
@@ -0,0 +1,253 @@
+.. index:: pair\_style local/density
+
+pair\_style local/density command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style arg
+
+* style = *local/density*
+* arg = name of file containing tabulated values of local density and the potential
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style local/density benzene_water.localdensity.table
+
+   pair_style hybrid/overlay table spline 500 local/density 
+   pair_coeff \* \* local/density  benzene_water.localdensity.table
+
+Description
+"""""""""""
+
+The local density (LD) potential is a mean-field manybody potential, and, in some 
+sense,a generalization of embedded atom models (EAM). The name "local density 
+potential" arises from the fact that it assigns an energy to an atom depending 
+on the number of neighboring atoms of given type around it within a predefined 
+spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
+literature suggests that such potentials can be widely useful  in capturing 
+effective multibody forces in a computationally efficient manner so as to 
+improve the quality of CG models of implicit solvation:ref:`(Sanyal1) <Sanyal1>` and 
+phase-segregation in liquid mixtures:ref:`(Sanyal2) <Sanyal2>`, and provide guidelines 
+to determine the extent of manybody correlations present in a CG 
+model.:ref:`(Rosenberger) <Rosenberger>` The LD potential in LAMMPS is primarily 
+intended to be used as a corrective potential over traditional pair potentials 
+in bottom-up CG models, i.e., as a hybrid pair style with 
+other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.). 
+Because the LD potential is not a pair potential per se,  it is implemented 
+simply as a single auxiliary file with all specifications that will be read 
+upon initialization.
+
+.. note::
+
+   Thus when used as the only interaction in the system, there is no 
+   corresponding pair\_coeff command and when used with other pair styles using the 
+   hybrid/overlay option, the corresponding pair\_coeff command must be supplied
+   \*  \* as placeholders for the atom types.
+
+
+----------
+
+
+**System with a single CG atom type:**
+
+A system of a single atom type (e.g., LJ argon) with a single local density (LD)
+potential would have an energy given by:
+
+.. image:: Eqs/pair_local_density_energy.jpg
+   :align: center
+
+where rho\_i is the LD at atom i and F(rho) is similar in spirit to the 
+embedding function used in EAM potentials. The LD at atom i is given by the sum
+
+.. image:: Eqs/pair_local_density_ld.jpg
+   :align: center
+
+where phi is an indicator function that is one at r=0 and zero beyond a cutoff 
+distance R2. The choice of the functional form of phi is somewhat arbitrary, 
+but the following piecewise cubic function has proven sufficiently general: 
+:ref:`(Sanyal1) <Sanyal1>`, :ref:`(Sanyal2) <Sanyal2>` :ref:`(Rosenberger) <Rosenberger>`
+
+.. image:: Eqs/pair_local_density_indicator_func.jpg
+   :align: center
+
+The constants *c* are chosen so that the indicator function smoothly 
+interpolates between 1 and 0 between the distances R1 and R2, which are 
+called the inner and outer cutoffs, respectively. Thus phi satisfies 
+phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) =  dphi/dr @ (r=R2) = 0. The embedding 
+function F(rho) may or may not have a closed-form expression. To maintain 
+generality, it is practically represented with a spline-interpolated table 
+over a predetermined range of rho. Outside of that range it simply adopts zero 
+values at the endpoints.
+
+It can be shown that the total force between two atoms due to the LD potential 
+takes the form of a pair force, which motivates its designation as a LAMMPS 
+pair style. Please see :ref:`(Sanyal1) <Sanyal1>` for details of the derivation.
+
+
+----------
+
+
+**Systems with arbitrary numbers of atom types:**
+
+The potential is easily generalized to systems involving multiple atom types:
+
+.. image:: Eqs/pair_local_density_energy_multi.jpg
+   :align: center
+
+with the LD expressed as
+
+.. image:: Eqs/pair_local_density_ld_multi.jpg
+   :align: center
+
+where alpha gives the type of atom i, beta the type of atom j, and the 
+coefficients a and b filter for atom types as specified by the user. a is 
+called the central atom filter as it determines to which atoms the 
+potential applies; a\_alpha = 1 if the LD potential applies to atom type alpha 
+else zero. On the other hand, b is called the neighbor atom filter because it 
+specifies which atom types to use in the calculation of the LD; b\_beta = 1 if 
+atom type beta contributes to the LD and zero otherwise.
+
+.. note::
+
+   Note that the potentials need not be symmetric with respect to atom types, 
+   which is the reason for two distinct sets of coefficients a and b. An atom type 
+   may contribute to the LD but not the potential, or to the potential but not the 
+   LD. Such decisions are made by the user and should (ideally) be motivated on 
+   physical grounds for the problem at hand.
+
+
+----------
+
+
+**General form for implementation in LAMMPS:**
+
+Of course, a system with many atom types may have many different possible LD 
+potentials, each with their own atom type filters, cutoffs, and embedding 
+functions. The most general form of this potential as implemented in the 
+pair\_style local/density is:
+
+.. image:: Eqs/pair_local_density_energy_implement.jpg
+   :align: center
+
+where, k is an index that spans the (arbitrary) number of applied LD potentials 
+N\_LD. Each LD is calculated as before with:
+
+.. image:: Eqs/pair_local_density_ld_implement.jpg
+   :align: center
+
+The superscript on the indicator function phi simply indicates that it is 
+associated with specific values of the cutoff distances R1(k) and R2(k). In 
+summary, there may be N\_LD distinct LD potentials. With each potential type (k), 
+one must specify:
+
+* the inner and outer cutoffs as R1 and R2
+* the central type filter a(k), where k = 1,2,...N\_LD
+* the neighbor type filter b(k), where k = 1,2,...N\_LD
+* the LD potential function F(k)(rho), typically as a table that is later spline-interpolated
+
+
+----------
+
+
+**Tabulated input file format:**
+
+
+.. parsed-literal::
+
+   Line 1:             comment or blank (ignored)
+   Line 2:             comment or blank (ignored)
+   Line 3:             N_LD N_rho (# of LD potentials and # of tabulated values, single space separated)
+   Line 4:             blank (ignored)
+   Line 5:             R1(k) R2(k) (lower and upper cutoffs, single space separated)
+   Line 6:             central-types (central atom types, single space separated)
+   Line 7:             neighbor-types (neighbor atom types single space separated)
+   Line 8:             rho_min rho_max drho (min, max and diff. in tabulated rho values, single space separated)
+   Line 9:             F(k)(rho_min + 0.drho)
+   Line 10:            F(k)(rho_min + 1.drho)
+   Line 11:            F(k)(rho_min + 2.drho)
+   ...
+   Line 9+N_rho:       F(k)(rho_min + N_rho . drho)
+   Line 10+N_rho:      blank (ignored)
+
+   Block 2
+
+   Block 3
+
+   Block N_LD
+
+Lines 5 to 9+N\_rho constitute the first block. Thus the input file is separated 
+(by blank lines) into N\_LD blocks each representing a separate LD potential and 
+each specifying its own upper and lower cutoffs, central and neighbor atoms, 
+and potential.  In general, blank lines anywhere are ignored.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, info**\ :
+This pair style does not support automatic mixing. For atom type pairs alpha,
+beta and alpha != beta, even if LD potentials of type (alpha, alpha) and 
+(beta, beta) are provided, you will need to explicitly provide LD potential 
+types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha,
+beta) means that alpha is the central atom to which the LD potential is applied
+and beta is the neighbor atom which contributes to the LD potential on alpha).
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+The local/density pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in tabulated potential files.
+Thus, you need to re-specify the pair\_style and pair\_coeff commands in
+an input script that reads a restart file.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The local/density pair style is a part of the USER-MISC package. It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Sanyal1:
+
+
+
+.. _Sanyal2:
+
+**(Sanyal1)** Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109.
+
+
+**(Sanyal2)** Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
+
+.. _Rosenberger:
+
+
+
+**(Rosenberger)** Rosenberger, Sanyal, Shell and van der Vegt,  Journal of Chemical Physics, 2019, 151 (4), 044111.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst
new file mode 100644
index 0000000000..b9033be48d
--- /dev/null
+++ b/doc/src/pair_lubricate.rst
@@ -0,0 +1,258 @@
+.. index:: pair\_style lubricate
+
+pair\_style lubricate command
+=============================
+
+pair\_style lubricate/omp command
+=================================
+
+pair\_style lubricate/poly command
+==================================
+
+pair\_style lubricate/poly/omp command
+======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF
+
+* style = *lubricate* or *lubricate/poly*
+* mu = dynamic viscosity (dynamic viscosity units)
+* flaglog = 0/1 to exclude/include log terms in the lubrication approximation
+* flagfld = 0/1 to exclude/include Fast Lubrication Dynamics (FLD) effects
+* cutinner = inner cutoff distance (distance units)
+* cutoff = outer cutoff for interactions (distance units)
+* flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
+* flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
+
+**Examples:** (all assume radius = 1)
+
+
+.. parsed-literal::
+
+   pair_style lubricate 1.5 1 1 2.01 2.5
+   pair_coeff 1 1 2.05 2.8
+   pair_coeff \* \*
+
+   pair_style lubricate 1.5 1 1 2.01 2.5
+   pair_coeff \* \*
+   variable mu equal ramp(1,2)
+   fix 1 all adapt 1 pair lubricate mu \* \* v_mu
+
+Description
+"""""""""""
+
+Styles *lubricate* and *lubricate/poly* compute hydrodynamic
+interactions between mono-disperse finite-size spherical particles in
+a pairwise fashion.  The interactions have 2 components.  The first is
+Ball-Melrose lubrication terms via the formulas in :ref:`(Ball and Melrose) <Ball1>`
+
+.. image:: Eqs/pair_lubricate.jpg
+   :align: center
+
+which represents the dissipation W between two nearby particles due to
+their relative velocities in the presence of a background solvent with
+viscosity *mu*\ .  Note that this is dynamic viscosity which has units of
+mass/distance/time, not kinematic viscosity.
+
+The Asq (squeeze) term is the strongest and is included if *flagHI* is
+set to 1 (default). It scales as 1/gap where gap is the separation
+between the surfaces of the 2 particles. The Ash (shear) and Apu
+(pump) terms are only included if *flaglog* is set to 1. They are the
+next strongest interactions, and the only other singular interaction,
+and scale as log(gap). Note that *flaglog* = 1 and *flagHI* = 0 is
+invalid, and will result in a warning message, after which *flagHI* will
+be set to 1. The Atw (twist) term is currently not included. It is
+typically a very small contribution to the lubrication forces.
+
+The *flagHI* and *flagVF* settings are optional.  Neither should be
+used, or both must be defined.
+
+*Cutinner* sets the minimum center-to-center separation that will be
+used in calculations irrespective of the actual separation.  *Cutoff*
+is the maximum center-to-center separation at which an interaction is
+computed.  Using a *cutoff* less than 3 radii is recommended if
+*flaglog* is set to 1.
+
+The other component is due to the Fast Lubrication Dynamics (FLD)
+approximation, described in :ref:`(Kumar) <Kumar1>`, which can be
+represented by the following equation
+
+.. image:: Eqs/fld.jpg
+   :align: center
+
+where U represents the velocities and angular velocities of the
+particles, U\^\ *infty* represents the velocity and the angular velocity
+of the undisturbed fluid, and E\^\ *infty* represents the rate of strain
+tensor of the undisturbed fluid with viscosity *mu*\ . Again, note that
+this is dynamic viscosity which has units of mass/distance/time, not
+kinematic viscosity. Volume fraction corrections to R\_FU are included
+as long as *flagVF* is set to 1 (default).
+
+.. note::
+
+   When using the FLD terms, these pair styles are designed to be
+   used with explicit time integration and a correspondingly small
+   timestep.  Thus either :doc:`fix nve/sphere <fix_nve_sphere>` or :doc:`fix nve/asphere <fix_nve_asphere>` should be used for time integration.
+   To perform implicit FLD, see the :doc:`pair\_style lubricateU <pair_lubricateU>` command.
+
+Style *lubricate* requires monodisperse spherical particles; style
+*lubricate/poly* allows for polydisperse spherical particles.
+
+The viscosity *mu* can be varied in a time-dependent manner over the
+course of a simulation, in which case in which case the pair\_style
+setting for *mu* will be overridden.  See the :doc:`fix adapt <fix_adapt>`
+command for details.
+
+If the suspension is sheared via the :doc:`fix deform <fix_deform>`
+command then the pair style uses the shear rate to adjust the
+hydrodynamic interactions accordingly. Volume changes due to fix
+deform are accounted for when computing the volume fraction
+corrections to R\_FU.
+
+When computing the volume fraction corrections to R\_FU, the presence
+of walls (whether moving or stationary) will affect the volume
+fraction available to colloidal particles. This is currently accounted
+for with the following types of walls: :doc:`wall/lj93 <fix_wall>`,
+:doc:`wall/lj126 <fix_wall>`, :doc:`wall/colloid <fix_wall>`, and
+:doc:`wall/harmonic <fix_wall>`.  For these wall styles, the correct
+volume fraction will be used when walls do not coincide with the box
+boundary, as well as when walls move and thereby cause a change in the
+volume fraction. Other wall styles will still work, but they will
+result in the volume fraction being computed based on the box
+boundaries.
+
+Since lubrication forces are dissipative, it is usually desirable to
+thermostat the system at a constant temperature. If Brownian motion
+(at a constant temperature) is desired, it can be set using the
+:doc:`pair\_style brownian <pair_brownian>` command. These pair styles
+and the brownian style should use consistent parameters for *mu*\ ,
+*flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ .
+
+
+----------
+
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cutinner (distance units)
+* cutoff (distance units)
+
+The two coefficients are optional.  If neither is specified, the two
+cutoffs specified in the pair\_style command are used.  Otherwise both
+must be specified.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in :doc:`this section <Speed>` of
+the manual.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See :doc:`this section <Speed>` of the manual for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the two cutoff distances for this
+pair style can be mixed.  The default mix value is *geometric*\ .  See
+the "pair\_modify" command for details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the COLLOID package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Only spherical monodisperse particles are allowed for pair\_style
+lubricate.
+
+Only spherical particles are allowed for pair\_style lubricate/poly.
+
+These pair styles will not restart exactly when using the
+:doc:`read\_restart <read_restart>` command, though they should provide
+statistically similar results.  This is because the forces they
+compute depend on atom velocities.  See the
+:doc:`read\_restart <read_restart>` command for more details.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style lubricateU <pair_lubricateU>`
+
+Default
+"""""""
+
+The default settings for the optional args are flagHI = 1 and flagVF =
+1.
+
+
+----------
+
+
+.. _Ball1:
+
+
+
+**(Ball)** Ball and Melrose, Physica A, 247, 444-472 (1997).
+
+.. _Kumar1:
+
+
+
+**(Kumar)** Kumar and Higdon, Phys Rev E, 82, 051401 (2010).  See also
+his thesis for more details: A. Kumar, "Microscale Dynamics in
+Suspensions of Non-spherical Particles", Thesis, University of
+Illinois Urbana-Champaign,
+(2010). (`https://www.ideals.illinois.edu/handle/2142/16032 <https://www.ideals.illinois.edu/handle/2142/16032>`_)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst
new file mode 100644
index 0000000000..bf0a39c56e
--- /dev/null
+++ b/doc/src/pair_lubricateU.rst
@@ -0,0 +1,242 @@
+.. index:: pair\_style lubricateU
+
+pair\_style lubricateU command
+==============================
+
+pair\_style lubricateU/poly command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF
+
+* style = *lubricateU* or *lubricateU/poly*
+* mu = dynamic viscosity (dynamic viscosity units)
+* flaglog = 0/1 to exclude/include log terms in the lubrication approximation
+* cutinner = inner cut off distance (distance units)
+* cutoff = outer cutoff for interactions (distance units)
+* gdot = shear rate (1/time units)
+* flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
+* flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
+
+**Examples:** (all assume radius = 1)
+
+
+.. parsed-literal::
+
+   pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
+   pair_coeff 1 1 2.05 2.8
+   pair_coeff \* \*
+
+Description
+"""""""""""
+
+Styles *lubricateU* and *lubricateU/poly* compute velocities and
+angular velocities for finite-size spherical particles such that the
+hydrodynamic interaction balances the force and torque due to all
+other types of interactions.
+
+The interactions have 2 components.  The first is
+Ball-Melrose lubrication terms via the formulas in :ref:`(Ball and Melrose) <Ball2>`
+
+.. image:: Eqs/pair_lubricate.jpg
+   :align: center
+
+which represents the dissipation W between two nearby particles due to
+their relative velocities in the presence of a background solvent with
+viscosity *mu*\ .  Note that this is dynamic viscosity which has units of
+mass/distance/time, not kinematic viscosity.
+
+The Asq (squeeze) term is the strongest and is included as long as
+*flagHI* is set to 1 (default). It scales as 1/gap where gap is the
+separation between the surfaces of the 2 particles. The Ash (shear)
+and Apu (pump) terms are only included if *flaglog* is set to 1. They
+are the next strongest interactions, and the only other singular
+interaction, and scale as log(gap). Note that *flaglog* = 1 and
+*flagHI* = 0 is invalid, and will result in a warning message, after
+which *flagHI* will be set to 1. The Atw (twist) term is currently not
+included. It is typically a very small contribution to the lubrication
+forces.
+
+The *flagHI* and *flagVF* settings are optional.  Neither should be
+used, or both must be defined.
+
+*Cutinner* sets the minimum center-to-center separation that will be
+used in calculations irrespective of the actual separation.  *Cutoff*
+is the maximum center-to-center separation at which an interaction is
+computed.  Using a *cutoff* less than 3 radii is recommended if
+*flaglog* is set to 1.
+
+The other component is due to the Fast Lubrication Dynamics (FLD)
+approximation, described in :ref:`(Kumar) <Kumar2>`.  The equation being
+solved to balance the forces and torques is
+
+.. image:: Eqs/fld2.jpg
+   :align: center
+
+where U represents the velocities and angular velocities of the
+particles, U\^\ *infty* represents the velocities and the angular
+velocities of the undisturbed fluid, and E\^\ *infty* represents the rate
+of strain tensor of the undisturbed fluid flow with viscosity
+*mu*\ . Again, note that this is dynamic viscosity which has units of
+mass/distance/time, not kinematic viscosity.  Volume fraction
+corrections to R\_FU are included if *flagVF* is set to 1 (default).
+
+F\ *rest* represents the forces and torques due to all other types of
+interactions, e.g. Brownian, electrostatic etc.  Note that this
+algorithm neglects the inertial terms, thereby removing the
+restriction of resolving the small interial time scale, which may not
+be of interest for colloidal particles.  This pair style solves for
+the velocity such that the hydrodynamic force balances all other types
+of forces, thereby resulting in a net zero force (zero inertia limit).
+When defining this pair style, it must be defined last so that when
+this style is invoked all other types of forces have already been
+computed.  For the same reason, it won't work if additional non-pair
+styles are defined (such as bond or Kspace forces) as they are
+calculated in LAMMPS after the pairwise interactions have been
+computed.
+
+.. note::
+
+   When using these styles, the these pair styles are designed to
+   be used with implicit time integration and a correspondingly larger
+   timestep.  Thus either :doc:`fix nve/noforce <fix_nve_noforce>` should
+   be used for spherical particles defined via :doc:`atom\_style sphere <atom_style>` or :doc:`fix nve/asphere/noforce <fix_nve_asphere_noforce>` should be used for
+   spherical particles defined via :doc:`atom\_style ellipsoid <atom_style>`.  This is because the velocity and angular
+   momentum of each particle is set by the pair style, and should not be
+   reset by the time integration fix.
+
+Style *lubricateU* requires monodisperse spherical particles; style
+*lubricateU/poly* allows for polydisperse spherical particles.
+
+If the suspension is sheared via the :doc:`fix deform <fix_deform>`
+command then the pair style uses the shear rate to adjust the
+hydrodynamic interactions accordingly. Volume changes due to fix
+deform are accounted for when computing the volume fraction
+corrections to R\_FU.
+
+When computing the volume fraction corrections to R\_FU, the presence
+of walls (whether moving or stationary) will affect the volume
+fraction available to colloidal particles. This is currently accounted
+for with the following types of walls: :doc:`wall/lj93 <fix_wall>`,
+:doc:`wall/lj126 <fix_wall>`, :doc:`wall/colloid <fix_wall>`, and
+:doc:`wall/harmonic <fix_wall>`.  For these wall styles, the correct
+volume fraction will be used when walls do not coincide with the box
+boundary, as well as when walls move and thereby cause a change in the
+volume fraction. To use these wall styles with pair\_style *lubricateU*
+or *lubricateU/poly*\ , the *fld yes* option must be specified in the
+fix wall command.
+
+Since lubrication forces are dissipative, it is usually desirable to
+thermostat the system at a constant temperature. If Brownian motion
+(at a constant temperature) is desired, it can be set using the
+:doc:`pair\_style brownian <pair_brownian>` command. These pair styles
+and the brownian style should use consistent parameters for *mu*\ ,
+*flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ .
+
+
+----------
+
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cutinner (distance units)
+* cutoff (distance units)
+
+The two coefficients are optional.  If neither is specified, the two
+cutoffs specified in the pair\_style command are used.  Otherwise both
+must be specified.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the two cutoff distances for this
+pair style can be mixed.  The default mix value is *geometric*\ .  See
+the "pair\_modify" command for details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the COLLOID package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Currently, these pair styles assume that all other types of
+forces/torques on the particles have been already been computed when
+it is invoked.  This requires this style to be defined as the last of
+the pair styles, and that no fixes apply additional constraint forces.
+One exception is the :doc:`fix wall/colloid <fix_wall>` commands, which
+has an "fld" option to apply their wall forces correctly.
+
+Only spherical monodisperse particles are allowed for pair\_style
+lubricateU.
+
+Only spherical particles are allowed for pair\_style lubricateU/poly.
+
+For sheared suspensions, it is assumed that the shearing is done in
+the xy plane, with x being the velocity direction and y being the
+velocity-gradient direction. In this case, one must use :doc:`fix deform <fix_deform>` with the same rate of shear (erate).
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style lubricate <pair_lubricate>`
+
+Default
+"""""""
+
+The default settings for the optional args are flagHI = 1 and flagVF =
+1.
+
+
+----------
+
+
+.. _Ball2:
+
+
+
+**(Ball)** Ball and Melrose, Physica A, 247, 444-472 (1997).
+
+.. _Kumar2:
+
+
+
+**(Kumar)** Kumar and Higdon, Phys Rev E, 82, 051401 (2010).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst
new file mode 100644
index 0000000000..181b7929a7
--- /dev/null
+++ b/doc/src/pair_mdf.rst
@@ -0,0 +1,196 @@
+.. index:: pair\_style lj/mdf
+
+pair\_style lj/mdf command
+==========================
+
+pair\_style buck/mdf command
+============================
+
+pair\_style lennard/mdf command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/mdf* or *buck/mdf* or *lennard/mdf*
+* args = list of arguments for a particular style
+  
+  .. parsed-literal::
+  
+       *lj/mdf* args = cutoff1 cutoff2
+         cutoff1 = inner cutoff for the start of the tapering function
+         cutoff1 = out cutoff for the end of the tapering function
+       *buck/mdf* args = cutoff1 cutoff2
+         cutoff1 = inner cutoff for the start of the tapering function
+         cutoff1 = out cutoff for the end of the tapering function
+       *lennard/mdf* args = cutoff1 cutoff2
+         cutoff1 = inner cutoff for the start of the tapering function
+         cutoff1 = out cutoff for the end of the tapering function
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/mdf 2.5 3.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 1 1 1.1 2.8 3.0 3.2
+
+   pair_style buck 2.5 3.0
+   pair_coeff \* \* 100.0 1.5 200.0
+   pair_coeff \* \* 100.0 1.5 200.0 3.0 3.5
+
+   pair_style lennard/mdf 2.5 3.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2
+
+Description
+"""""""""""
+
+The *lj/mdf*\ , *buck/mdf* and *lennard/mdf* compute the standard 12-6
+Lennard-Jones and Buckingham potential with the addition of a taper
+function that ramps the energy and force smoothly to zero between an
+inner and outer cutoff.
+
+.. image:: Eqs/pair_mdf-1.jpg
+   :align: center
+
+The tapering, *f(r)*\ , is done by using the Mei, Davenport, Fernando
+function :ref:`(Mei) <Mei>`.
+
+.. image:: Eqs/pair_mdf-2.jpg
+   :align: center
+
+where
+
+.. image:: Eqs/pair_mdf-3.jpg
+   :align: center
+
+Here *r\_m* is the inner cutoff radius and *r\_cut* is the outer cutoff
+radius.
+
+
+----------
+
+
+For the *lj/mdf* pair\_style, the potential energy, *E(r)*\ , is the
+standard 12-6 Lennard-Jones written in the epsilon/sigma form:
+
+.. image:: Eqs/pair_mdf-4.jpg
+   :align: center
+
+Either the first two or all of the following coefficients must be
+defined for each pair of atoms types via the pair\_coeff command as
+in the examples above, or in the data file read by the
+:doc:`read\_data <read_data>`. The two cutoffs default to the global
+values and epsilon and sigma can also be determined by mixing as
+described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* r\_m (distance units)
+* r\_\ *cut* (distance units)
+
+
+----------
+
+
+For the *buck/mdf* pair\_style, the potential energy, *E(r)*\ , is the
+standard Buckingham potential with three required coefficients.
+The two cutoffs can be omitted and default to the corresponding
+global values:
+
+.. image:: Eqs/pair_mdf-5.jpg
+   :align: center
+
+* A (energy units)
+* \rho (distance units)
+* C (energy-distance\^6 units)
+* r\_m (distance units)
+* r\_\ *cut* (distance units)
+
+
+----------
+
+
+For the *lennard/mdf* pair\_style, the potential energy, *E(r)*\ , is the
+standard 12-6 Lennard-Jones written in the A/B form:
+
+.. image:: Eqs/pair_mdf-6.jpg
+   :align: center
+
+The following coefficients must be defined for each pair of atoms
+types via the pair\_coeff command as in the examples above, or in the
+data file read by the read\_data commands, or by mixing as described below.
+The two cutoffs default to their global values and must be either both
+given or both left out:
+
+* A (energy-distance\^12 units)
+* B (energy-distance\^6 units)
+* r\_m (distance units)
+* r\_\ *cut* (distance units)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distances for the lj/mdf pair style can be mixed.
+The default mix value is *geometric*\ .  See the "pair\_modify" command
+for details. The other two pair styles buck/mdf and lennard/mdf do not
+support mixing, so all I,J pairs of coefficients must be specified
+explicitly.
+
+None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports
+the :doc:`pair\_modify <pair_modify>` shift option or long-range
+tail corrections to pressure and energy.
+
+These styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These styles can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  They do not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Mei:
+
+
+
+**(Mei)** Mei, Davenport, Fernando, Phys Rev B, 43 4653 (1991)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst
new file mode 100644
index 0000000000..68ccc829c9
--- /dev/null
+++ b/doc/src/pair_meam_spline.rst
@@ -0,0 +1,200 @@
+.. index:: pair\_style meam/spline
+
+pair\_style meam/spline command
+===============================
+
+pair\_style meam/spline/omp command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style meam/spline
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style meam/spline
+   pair_coeff \* \* Ti.meam.spline Ti
+   pair_coeff \* \* Ti.meam.spline Ti Ti Ti
+
+Description
+"""""""""""
+
+The *meam/spline* style computes pairwise interactions for metals
+using a variant of modified embedded-atom method (MEAM) potentials
+:ref:`(Lenosky) <Lenosky1>`.  For a single species ("old-style") MEAM,
+the total energy E is given by
+
+.. image:: Eqs/pair_meam_spline.jpg
+   :align: center
+
+where rho\_i is the density at atom I, theta\_jik is the angle between
+atoms J, I, and K centered on atom I. The five functions Phi, U, rho,
+f, and g are represented by cubic splines.
+
+The *meam/spline* style also supports a new style multicomponent
+modified embedded-atom method (MEAM) potential :ref:`(Zhang) <Zhang4>`, where
+the total energy E is given by
+
+.. image:: Eqs/pair_meam_spline_multicomponent.jpg
+   :align: center
+
+where the five functions Phi, U, rho, f, and g depend on the chemistry
+of the atoms in the interaction.  In particular, if there are N different
+chemistries, there are N different U, rho, and f functions, while there
+are N(N+1)/2 different Phi and g functions.  The new style multicomponent
+MEAM potential files are indicated by the second line in the file starts
+with "meam/spline" followed by the number of elements and the name of each
+element.
+
+The cutoffs and the coefficients for these spline functions are listed
+in a parameter file which is specified by the
+:doc:`pair\_coeff <pair_coeff>` command.  Parameter files for different
+elements are included in the "potentials" directory of the LAMMPS
+distribution and have a ".meam.spline" file suffix.  All of these
+files are parameterized in terms of LAMMPS :doc:`metal units <units>`.
+
+Note that unlike for other potentials, cutoffs for spline-based MEAM
+potentials are not set in the pair\_style or pair\_coeff command; they
+are specified in the potential files themselves.
+
+Unlike the EAM pair style, which retrieves the atomic mass from the
+potential file, the spline-based MEAM potentials do not include mass
+information; thus you need to use the :doc:`mass <mass>` command to
+specify it.
+
+Only a single pair\_coeff command is used with the *meam/spline* style
+which specifies a potential file with parameters for all needed
+elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of spline-based MEAM elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine the Ti.meam.spline file has values for Ti (old style).  If
+your LAMMPS simulation has 3 atoms types and they are all to be
+treated with this potentials, you would use the following pair\_coeff
+command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* Ti.meam.spline Ti Ti Ti
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
+in the potential file.  If a mapping value is specified as NULL, the
+mapping is not performed.  This can be used when a *meam/spline*
+potential is used as part of the *hybrid* pair style.  The NULL values
+are placeholders for atom types that will be used with other
+potentials. The old-style potential maps any non-NULL species named
+on the command line to that single type.
+
+An example with a two component spline (new style) is TiO.meam.spline, where
+the command
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* TiO.meam.spline Ti O
+
+will map the 1st atom type to Ti and the second atom type to O. Note
+in this case that the species names need to match exactly with the
+names of the elements in the TiO.meam.spline file; otherwise an
+error will be raised. This behavior is different than the old style
+MEAM files.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+The *meam/spline* pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in an external
+potential parameter file.  Thus, you need to re-specify the pair\_style
+and pair\_coeff commands in an input script that reads a restart file.
+
+The *meam/spline* pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+This pair style is only enabled if LAMMPS was built with the USER-MISC
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style meam/c <pair_meamc>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Lenosky1:
+
+
+
+**(Lenosky)** Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter,
+Kress, Modelling Simulation Materials Science Engineering, 8, 825
+(2000).
+
+.. _Zhang4:
+
+
+
+**(Zhang)** Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst
new file mode 100644
index 0000000000..9331b5f36a
--- /dev/null
+++ b/doc/src/pair_meam_sw_spline.rst
@@ -0,0 +1,167 @@
+.. index:: pair\_style meam/sw/spline
+
+pair\_style meam/sw/spline command
+==================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style meam/sw/spline
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style meam/sw/spline
+   pair_coeff \* \* Ti.meam.sw.spline Ti
+   pair_coeff \* \* Ti.meam.sw.spline Ti Ti Ti
+
+Description
+"""""""""""
+
+The *meam/sw/spline* style computes pairwise interactions for metals
+using a variant of modified embedded-atom method (MEAM) potentials
+:ref:`(Lenosky) <Lenosky2>` with an additional Stillinger-Weber (SW) term
+:ref:`(Stillinger) <Stillinger1>` in the energy.  This form of the potential
+was first proposed by Nicklas, Fellinger, and Park
+:ref:`(Nicklas) <Nicklas>`.  We refer to it as MEAM+SW.  The total energy E
+is given by
+
+.. image:: Eqs/pair_meam_sw_spline.jpg
+   :align: center
+
+where rho\_I is the density at atom I, theta\_JIK is the angle between
+atoms J, I, and K centered on atom I. The seven functions
+Phi, F, G, U, rho, f, and g are represented by cubic splines.
+
+The cutoffs and the coefficients for these spline functions are listed
+in a parameter file which is specified by the
+:doc:`pair\_coeff <pair_coeff>` command.  Parameter files for different
+elements are included in the "potentials" directory of the LAMMPS
+distribution and have a ".meam.sw.spline" file suffix.  All of these
+files are parameterized in terms of LAMMPS :doc:`metal units <units>`.
+
+Note that unlike for other potentials, cutoffs for spline-based
+MEAM+SW potentials are not set in the pair\_style or pair\_coeff
+command; they are specified in the potential files themselves.
+
+Unlike the EAM pair style, which retrieves the atomic mass from the
+potential file, the spline-based MEAM+SW potentials do not include
+mass information; thus you need to use the :doc:`mass <mass>` command to
+specify it.
+
+Only a single pair\_coeff command is used with the meam/sw/spline style
+which specifies a potential file with parameters for all needed
+elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of spline-based MEAM+SW elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine the Ti.meam.sw.spline file has values for Ti.
+If your LAMMPS simulation has 3 atoms types and they are all to be
+treated with this potential, you would use the following pair\_coeff
+command:
+
+pair\_coeff \* \* Ti.meam.sw.spline Ti Ti Ti
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
+in the potential file. If a mapping value is specified as NULL, the
+mapping is not performed. This can be used when a *meam/sw/spline*
+potential is used as part of the hybrid pair style. The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+
+.. note::
+
+   The *meam/sw/spline* style currently supports only
+   single-element MEAM+SW potentials.  It may be extended for alloy
+   systems in the future.
+
+Example input scripts that use this pair style are provided
+in the examples/USER/misc/meam\_sw\_spline directory.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+The pair style does not support multiple element types or mixing.
+It has been designed for pure elements only.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+The *meam/sw/spline* pair style does not write its information to
+:doc:`binary restart files <restart>`, since it is stored in an external
+potential parameter file.  Thus, you need to re-specify the pair\_style
+and pair\_coeff commands in an input script that reads a restart file.
+
+The *meam/sw/spline* pair style can only be used via the *pair*
+keyword of the :doc:`run\_style respa <run_style>` command.  They do not
+support the *inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+This pair style is only enabled if LAMMPS was built with the USER-MISC
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style meam/c <pair_meamc>`,
+:doc:`pair\_style meam/spline <pair_meam_spline>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Lenosky2:
+
+
+
+**(Lenosky)** Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter,
+Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000).
+
+.. _Stillinger1:
+
+
+
+**(Stillinger)** Stillinger, Weber, Phys. Rev. B 31, 5262 (1985).
+
+.. _Nicklas:
+
+
+
+**(Nicklas)**
+The spline-based MEAM+SW format was first devised and used to develop
+potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
+and Hyoungki Park at The Ohio State University.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst
new file mode 100644
index 0000000000..ac858ce24b
--- /dev/null
+++ b/doc/src/pair_meamc.rst
@@ -0,0 +1,478 @@
+.. index:: pair\_style meam/c
+
+pair\_style meam/c command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style
+
+style = *meam/c*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style meam/c
+   pair_coeff \* \* ../potentials/library.meam Si ../potentials/si.meam Si
+   pair_coeff \* \* ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
+
+Description
+"""""""""""
+
+.. note::
+
+   The behavior of the MEAM potential for alloy systems has changed
+   as of November 2010; see description below of the mixture\_ref\_t
+   parameter
+
+Style *meam/c* computes pairwise interactions for a variety of materials
+using modified embedded-atom method (MEAM) potentials
+:ref:`(Baskes) <Baskes>`.  Conceptually, it is an extension to the original
+:doc:`EAM potentials <pair_eam>` which adds angular forces.  It is
+thus suitable for modeling metals and alloys with fcc, bcc, hcp and
+diamond cubic structures, as well as covalently bonded materials like
+silicon and carbon. Style *meam/c* is a translation of the (now obsolete)
+*meam* code from Fortran to C++. It is functionally equivalent to *meam*
+but more efficient, and thus *meam* has been removed from LAMMPS after
+the 12 December 2018 release.
+
+In the MEAM formulation, the total energy E of a system of atoms is
+given by:
+
+.. image:: Eqs/pair_meam.jpg
+   :align: center
+
+where F is the embedding energy which is a function of the atomic
+electron density rho, and phi is a pair potential interaction.  The
+pair interaction is summed over all neighbors J of atom I within the
+cutoff distance.  As with EAM, the multi-body nature of the MEAM
+potential is a result of the embedding energy term.  Details of the
+computation of the embedding and pair energies, as implemented in
+LAMMPS, are given in :ref:`(Gullet) <Gullet>` and references therein.
+
+The various parameters in the MEAM formulas are listed in two files
+which are specified by the :doc:`pair\_coeff <pair_coeff>` command.
+These are ASCII text files in a format consistent with other MD codes
+that implement MEAM potentials, such as the serial DYNAMO code and
+Warp.  Several MEAM potential files with parameters for different
+materials are included in the "potentials" directory of the LAMMPS
+distribution with a ".meam" suffix.  All of these are parameterized in
+terms of LAMMPS :doc:`metal units <units>`.
+
+Note that unlike for other potentials, cutoffs for MEAM potentials are
+not set in the pair\_style or pair\_coeff command; they are specified in
+the MEAM potential files themselves.
+
+Only a single pair\_coeff command is used with the *meam* style which
+specifies two MEAM files and the element(s) to extract information
+for.  The MEAM elements are mapped to LAMMPS atom types by specifying
+N additional arguments after the 2nd filename in the pair\_coeff
+command, where N is the number of LAMMPS atom types:
+
+* MEAM library file
+* Elem1, Elem2, ...
+* MEAM parameter file
+* N element names = mapping of MEAM elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential files.
+
+As an example, the potentials/library.meam file has generic MEAM
+settings for a variety of elements.  The potentials/SiC.meam file has
+specific parameter settings for a Si and C alloy system.  If your
+LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
+and the 4th to be C, you would use the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* library.meam Si C sic.meam Si Si Si C
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The two filenames are for the library and parameter file respectively.
+The Si and C arguments (between the file names) are the two elements
+for which info will be extracted from the library file.  The first
+three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si
+element.  The final C argument maps LAMMPS atom type 4 to the MEAM C
+element.
+
+If the 2nd filename is specified as NULL, no parameter file is read,
+which simply means the generic parameters in the library file are
+used.  Use of the NULL specification for the parameter file is
+discouraged for systems with more than a single element type
+(e.g. alloys), since the parameter file is expected to set element
+interaction terms that are not captured by the information in the
+library file.
+
+If a mapping value is specified as NULL, the mapping is not performed.
+This can be used when a *meam* potential is used as part of the
+*hybrid* pair style.  The NULL values are placeholders for atom types
+that will be used with other potentials.
+
+.. note::
+
+   If the 2nd filename is NULL, the element names between the two
+   filenames can appear in any order, e.g. "Si C" or "C Si" in the
+   example above.  However, if the 2nd filename is not NULL (as in the
+   example above), it contains settings that are Fortran-indexed for the
+   elements that preceed it.  Thus you need to insure you list the
+   elements between the filenames in an order consistent with how the
+   values in the 2nd filename are indexed.  See details below on the
+   syntax for settings in the 2nd file.
+
+The MEAM library file provided with LAMMPS has the name
+potentials/library.meam.  It is the "meamf" file used by other MD
+codes.  Aside from blank and comment lines (start with #) which can
+appear anywhere, it is formatted as a series of entries, each of which
+has 19 parameters and can span multiple lines:
+
+elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub,
+t0, t1, t2, t3, rozero, ibar
+
+The "elt" and "lat" parameters are text strings, such as elt = Si or
+Cu and lat = dia or fcc.  Because the library file is used by Fortran
+MD codes, these strings may be enclosed in single quotes, but this is
+not required.  The other numeric parameters match values in the
+formulas above.  The value of the "elt" string is what is used in the
+pair\_coeff command to identify which settings from the library file
+you wish to read in.  There can be multiple entries in the library
+file with the same "elt" value; LAMMPS reads the 1st matching entry it
+finds and ignores the rest.
+
+Other parameters in the MEAM library file correspond to single-element
+potential parameters:
+
+
+.. parsed-literal::
+
+   lat      = lattice structure of reference configuration
+   z        = number of nearest neighbors in the reference structure
+   ielement = atomic number
+   atwt     = atomic weight
+   alat     = lattice constant of reference structure
+   esub     = energy per atom (eV) in the reference structure at equilibrium
+   asub     = "A" parameter for MEAM (see e.g. :ref:`(Baskes) <Baskes>`)
+
+The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
+standard MEAM parameters in the literature :ref:`(Baskes) <Baskes>` (the b
+parameters are the standard beta parameters). Note that only parameters
+normalized to t0 = 1.0 are supported.  The rozero parameter is
+an element-dependent density scaling that weights the reference
+background density (see e.g. equation 4.5 in :ref:`(Gullet) <Gullet>`) and
+is typically 1.0 for single-element systems.  The ibar parameter
+selects the form of the function G(Gamma) used to compute the electron
+density; options are
+
+
+.. parsed-literal::
+
+      0 => G = sqrt(1+Gamma)
+      1 => G = exp(Gamma/2)
+      2 => not implemented
+      3 => G = 2/(1+exp(-Gamma))
+      4 => G = sqrt(1+Gamma)
+     -5 => G = +-sqrt(abs(1+Gamma))
+
+If used, the MEAM parameter file contains settings that override or
+complement the library file settings.  Examples of such parameter
+files are in the potentials directory with a ".meam" suffix.  Their
+format is the same as is read by other Fortran MD codes.  Aside from
+blank and comment lines (start with #) which can appear anywhere, each
+line has one of the following forms.  Each line can also have a
+trailing comment (starting with #) which is ignored.
+
+
+.. parsed-literal::
+
+   keyword = value
+   keyword(I) = value
+   keyword(I,J) = value
+   keyword(I,J,K) = value
+
+The indices I, J, K correspond to the elements selected from the
+MEAM library file numbered in the order of how those elements were
+selected starting from 1. Thus for the example given below
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* library.meam Si C sic.meam Si Si Si C
+
+an index of 1 would refer to Si and an index of 2 to C.
+
+The recognized keywords for the parameter file are as follows:
+
+Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,
+augt1, gsmooth\_factor, re
+
+where
+
+
+.. parsed-literal::
+
+   rc          = cutoff radius for cutoff function; default = 4.0
+   delr        = length of smoothing distance for cutoff function; default = 0.1
+   rho0(I)     = relative density for element I (overwrites value
+                 read from meamf file)
+   Ec(I,J)     = cohesive energy of reference structure for I-J mixture
+   delta(I,J)  = heat of formation for I-J alloy; if Ec_IJ is input as
+                 zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
+   alpha(I,J)  = alpha parameter for pair potential between I and J (can
+                 be computed from bulk modulus of reference structure
+   re(I,J)     = equilibrium distance between I and J in the reference
+                 structure
+   Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened
+                 by K (I<=J); default = 2.8
+   Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
+                 by K (I<=J); default = 2.0
+   lattce(I,J) = lattice structure of I-J reference structure:
+                   fcc = face centered cubic
+                   bcc = body centered cubic
+                   hcp = hexagonal close-packed
+                   dim = dimer
+                   dia = diamond (interlaced fcc for alloy)
+                   dia3= diamond structure with primary 1NN and secondary 3NN interation
+                   b1  = rock salt (NaCl structure)
+                   c11 = MoSi2 structure
+                   l12 = Cu3Au structure (lower case L, followed by 12)
+                   b2  = CsCl structure (interpenetrating simple cubic)
+                   ch4 = methane-like structure, only for binary system
+                   lin = linear structure (180 degree angle)
+                   zig = zigzag structure with a uniform angle
+                   tri = H2O-like structure that has an angle
+   nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for
+                 I-J pair (see for example :ref:`(Lee) <Lee>`).
+                   0 = second-nearest neighbor formulation off
+                   1 = second-nearest neighbor formulation on
+                   default = 0
+   attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
+                   default = 0
+   repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
+                   default = 0
+   zbl(I,J)    = blend the MEAM I-J pair potential with the ZBL potential for small
+                 atom separations :ref:`(ZBL) <ZBL>`
+                   default = 1
+   theta(I,J)  = angle between three atoms in line, zigzag, and trimer reference structures in degrees
+                   default = 180
+   gsmooth_factor  = factor determining the length of the G-function smoothing
+                     region; only significant for ibar=0 or ibar=4.
+                         99.0 = short smoothing region, sharp step
+                         0.5  = long smoothing region, smooth step
+                         default = 99.0
+   augt1           = integer flag for whether to augment t1 parameter by
+                     3/5\*t3 to account for old vs. new meam formulations;
+                       0 = don't augment t1
+                       1 = augment t1
+                       default = 1
+   ialloy          = integer flag to use alternative averaging rule for t parameters,
+                     for comparison with the DYNAMO MEAM code
+                       0 = standard averaging (matches ialloy=0 in DYNAMO)
+                       1 = alternative averaging (matches ialloy=1 in DYNAMO)
+                       2 = no averaging of t (use single-element values)
+                       default = 0
+   mixture_ref_t   = integer flag to use mixture average of t to compute the background
+                     reference density for alloys, instead of the single-element values
+                     (see description and warning elsewhere in this doc page)
+                       0 = do not use mixture averaging for t in the reference density
+                       1 = use mixture averaging for t in the reference density
+                       default = 0
+   erose_form      = integer value to select the form of the Rose energy function
+                     (see description below).
+                       default = 0
+   emb_lin_neg     = integer value to select embedding function for negative densities
+                       0 = F(rho)=0
+                       1 = F(rho) = -asub\*esub\*rho (linear in rho, matches DYNAMO)
+                       default = 0
+   bkgd_dyn        = integer value to select background density formula
+                       0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
+                       1 = rho_bkgd = rho0_meam(a)\*Z_meam(a) (matches DYNAMO)
+                       default = 0
+
+Rc, delr, re are in distance units (Angstroms in the case of metal
+units).  Ec and delta are in energy units (eV in the case of metal
+units).
+
+Each keyword represents a quantity which is either a scalar, vector,
+2d array, or 3d array and must be specified with the correct
+corresponding array syntax.  The indices I,J,K each run from 1 to N
+where N is the number of MEAM elements being used.
+
+Thus these lines
+
+
+.. parsed-literal::
+
+   rho0(2) = 2.25
+   alpha(1,2) = 4.37
+
+set rho0 for the 2nd element to the value 2.25 and set alpha for the
+alloy interaction between elements 1 and 2 to 4.37.
+
+The augt1 parameter is related to modifications in the MEAM
+formulation of the partial electron density function.  In recent
+literature, an extra term is included in the expression for the
+third-order density in order to make the densities orthogonal (see for
+example :ref:`(Wang) <Wang2>`, equation 3d); this term is included in the
+MEAM implementation in lammps.  However, in earlier published work
+this term was not included when deriving parameters, including most of
+those provided in the library.meam file included with lammps, and to
+account for this difference the parameter t1 must be augmented by
+3/5\*t3.  If augt1=1, the default, this augmentation is done
+automatically.  When parameter values are fit using the modified
+density function, as in more recent literature, augt1 should be set to
+0.
+
+The mixture\_ref\_t parameter is available to match results with those
+of previous versions of lammps (before January 2011).  Newer versions
+of lammps, by default, use the single-element values of the t
+parameters to compute the background reference density.  This is the
+proper way to compute these parameters.  Earlier versions of lammps
+used an alloy mixture averaged value of t to compute the background
+reference density.  Setting mixture\_ref\_t=1 gives the old behavior.
+WARNING: using mixture\_ref\_t=1 will give results that are demonstrably
+incorrect for second-neighbor MEAM, and non-standard for
+first-neighbor MEAM; this option is included only for matching with
+previous versions of lammps and should be avoided if possible.
+
+The parameters attrac and repuls, along with the integer selection
+parameter erose\_form, can be used to modify the Rose energy function
+used to compute the pair potential.  This function gives the energy of
+the reference state as a function of interatomic spacing.  The form of
+this function is:
+
+
+.. parsed-literal::
+
+   astar = alpha \* (r/re - 1.d0)
+   if erose_form = 0: erose = -Ec\*(1+astar+a3\*(astar\*\*3)/(r/re))\*exp(-astar)
+   if erose_form = 1: erose = -Ec\*(1+astar+(-attrac+repuls/r)\*(astar\*\*3))\*exp(-astar)
+   if erose_form = 2: erose = -Ec\*(1 +astar + a3\*(astar\*\*3))\*exp(-astar)
+   a3 = repuls, astar < 0
+   a3 = attrac, astar >= 0
+
+Most published MEAM parameter sets use the default values attrac=repulse=0.
+Setting repuls=attrac=delta corresponds to the form used in several
+recent published MEAM parameter sets, such as :ref:`(Valone) <Valone>`
+
+.. note::
+
+   The default form of the erose expression in LAMMPS was corrected
+   in March 2009.  The current version is correct, but may show different
+   behavior compared with earlier versions of lammps with the attrac
+   and/or repuls parameters are non-zero.  To obtain the previous default
+   form, use erose\_form = 1 (this form does not seem to appear in the
+   literature).  An alternative form (see e.g. :ref:`(Lee2) <Lee2>`) is
+   available using erose\_form = 2.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above.  You never need to
+specify a pair\_coeff command with I != J arguments for this style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *meam/c* style is provided in the USER-MEAMC package. It is
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+The maximum number of elements, that can be read from the MEAM
+library file, is determined at compile time. The default is 5.
+If you need support for more elements, you have to change the
+define for the constant 'maxelt' at the beginning of the file
+src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no
+limit on the number of atoms types.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style eam <pair_eam>`,
+:doc:`pair\_style meam/spline <pair_meam_spline>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Baskes:
+
+
+
+**(Baskes)** Baskes, Phys Rev B, 46, 2727-2742 (1992).
+
+.. _Gullet:
+
+
+
+**(Gullet)** Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
+This report may be accessed on-line via `this link <sandreport_>`_.
+
+.. _sandreport: http://infoserve.sandia.gov/sand\_doc/2003/038782.pdf
+
+
+
+.. _Lee:
+
+
+
+**(Lee)** Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
+
+.. _Lee2:
+
+
+
+**(Lee2)** Lee, Baskes, Kim, Cho.  Phys. Rev. B, 64, 184102 (2001).
+
+.. _Valone:
+
+
+
+**(Valone)** Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
+
+.. _Wang2:
+
+
+
+**(Wang)** Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).
+
+.. _ZBL:
+
+
+
+**(ZBL)** J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges
+of Ions in Matter", Vol 1, 1985, Pergamon Press.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_meamc.txt b/doc/src/pair_meamc.txt
deleted file mode 100644
index 7c42e9d2f2..0000000000
--- a/doc/src/pair_meamc.txt
+++ /dev/null
@@ -1,400 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style meam/c command :h3
-
-[Syntax:]
-
-pair_style style :pre
-
-style = {meam/c}
-
-[Examples:]
-
-pair_style meam/c
-pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
-pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
-
-[Description:]
-
-NOTE: The behavior of the MEAM potential for alloy systems has changed
-as of November 2010; see description below of the mixture_ref_t
-parameter
-
-Style {meam/c} computes pairwise interactions for a variety of materials
-using modified embedded-atom method (MEAM) potentials
-"(Baskes)"_#Baskes.  Conceptually, it is an extension to the original
-"EAM potentials"_pair_eam.html which adds angular forces.  It is
-thus suitable for modeling metals and alloys with fcc, bcc, hcp and
-diamond cubic structures, as well as covalently bonded materials like
-silicon and carbon. Style {meam/c} is a translation of the (now obsolete)
-{meam} code from Fortran to C++. It is functionally equivalent to {meam}
-but more efficient, and thus {meam} has been removed from LAMMPS after
-the 12 December 2018 release.
-
-In the MEAM formulation, the total energy E of a system of atoms is
-given by:
-
-:c,image(Eqs/pair_meam.jpg)
-
-where F is the embedding energy which is a function of the atomic
-electron density rho, and phi is a pair potential interaction.  The
-pair interaction is summed over all neighbors J of atom I within the
-cutoff distance.  As with EAM, the multi-body nature of the MEAM
-potential is a result of the embedding energy term.  Details of the
-computation of the embedding and pair energies, as implemented in
-LAMMPS, are given in "(Gullet)"_#Gullet and references therein.
-
-The various parameters in the MEAM formulas are listed in two files
-which are specified by the "pair_coeff"_pair_coeff.html command.
-These are ASCII text files in a format consistent with other MD codes
-that implement MEAM potentials, such as the serial DYNAMO code and
-Warp.  Several MEAM potential files with parameters for different
-materials are included in the "potentials" directory of the LAMMPS
-distribution with a ".meam" suffix.  All of these are parameterized in
-terms of LAMMPS "metal units"_units.html.
-
-Note that unlike for other potentials, cutoffs for MEAM potentials are
-not set in the pair_style or pair_coeff command; they are specified in
-the MEAM potential files themselves.
-
-Only a single pair_coeff command is used with the {meam} style which
-specifies two MEAM files and the element(s) to extract information
-for.  The MEAM elements are mapped to LAMMPS atom types by specifying
-N additional arguments after the 2nd filename in the pair_coeff
-command, where N is the number of LAMMPS atom types:
-
-MEAM library file
-Elem1, Elem2, ...
-MEAM parameter file
-N element names = mapping of MEAM elements to atom types :ul
-
-See the "pair_coeff"_pair_coeff.html doc page for alternate ways
-to specify the path for the potential files.
-
-As an example, the potentials/library.meam file has generic MEAM
-settings for a variety of elements.  The potentials/SiC.meam file has
-specific parameter settings for a Si and C alloy system.  If your
-LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
-and the 4th to be C, you would use the following pair_coeff command:
-
-pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre
-
-The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
-The two filenames are for the library and parameter file respectively.
-The Si and C arguments (between the file names) are the two elements
-for which info will be extracted from the library file.  The first
-three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si
-element.  The final C argument maps LAMMPS atom type 4 to the MEAM C
-element.
-
-If the 2nd filename is specified as NULL, no parameter file is read,
-which simply means the generic parameters in the library file are
-used.  Use of the NULL specification for the parameter file is
-discouraged for systems with more than a single element type
-(e.g. alloys), since the parameter file is expected to set element
-interaction terms that are not captured by the information in the
-library file.
-
-If a mapping value is specified as NULL, the mapping is not performed.
-This can be used when a {meam} potential is used as part of the
-{hybrid} pair style.  The NULL values are placeholders for atom types
-that will be used with other potentials.
-
-NOTE: If the 2nd filename is NULL, the element names between the two
-filenames can appear in any order, e.g. "Si C" or "C Si" in the
-example above.  However, if the 2nd filename is not NULL (as in the
-example above), it contains settings that are Fortran-indexed for the
-elements that preceed it.  Thus you need to insure you list the
-elements between the filenames in an order consistent with how the
-values in the 2nd filename are indexed.  See details below on the
-syntax for settings in the 2nd file.
-
-The MEAM library file provided with LAMMPS has the name
-potentials/library.meam.  It is the "meamf" file used by other MD
-codes.  Aside from blank and comment lines (start with #) which can
-appear anywhere, it is formatted as a series of entries, each of which
-has 19 parameters and can span multiple lines:
-
-elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub,
-t0, t1, t2, t3, rozero, ibar
-
-The "elt" and "lat" parameters are text strings, such as elt = Si or
-Cu and lat = dia or fcc.  Because the library file is used by Fortran
-MD codes, these strings may be enclosed in single quotes, but this is
-not required.  The other numeric parameters match values in the
-formulas above.  The value of the "elt" string is what is used in the
-pair_coeff command to identify which settings from the library file
-you wish to read in.  There can be multiple entries in the library
-file with the same "elt" value; LAMMPS reads the 1st matching entry it
-finds and ignores the rest.
-
-Other parameters in the MEAM library file correspond to single-element
-potential parameters:
-
-lat      = lattice structure of reference configuration
-z        = number of nearest neighbors in the reference structure
-ielement = atomic number
-atwt     = atomic weight
-alat     = lattice constant of reference structure
-esub     = energy per atom (eV) in the reference structure at equilibrium
-asub     = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre
-
-The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
-standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b
-parameters are the standard beta parameters). Note that only parameters
-normalized to t0 = 1.0 are supported.  The rozero parameter is
-an element-dependent density scaling that weights the reference
-background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and
-is typically 1.0 for single-element systems.  The ibar parameter
-selects the form of the function G(Gamma) used to compute the electron
-density; options are
-
-   0 => G = sqrt(1+Gamma)
-   1 => G = exp(Gamma/2)
-   2 => not implemented
-   3 => G = 2/(1+exp(-Gamma))
-   4 => G = sqrt(1+Gamma)
-  -5 => G = +-sqrt(abs(1+Gamma)) :pre
-
-If used, the MEAM parameter file contains settings that override or
-complement the library file settings.  Examples of such parameter
-files are in the potentials directory with a ".meam" suffix.  Their
-format is the same as is read by other Fortran MD codes.  Aside from
-blank and comment lines (start with #) which can appear anywhere, each
-line has one of the following forms.  Each line can also have a
-trailing comment (starting with #) which is ignored.
-
-keyword = value
-keyword(I) = value
-keyword(I,J) = value
-keyword(I,J,K) = value :pre
-
-The indices I, J, K correspond to the elements selected from the
-MEAM library file numbered in the order of how those elements were
-selected starting from 1. Thus for the example given below
-
-pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre
-
-an index of 1 would refer to Si and an index of 2 to C.
-
-The recognized keywords for the parameter file are as follows:
-
-Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,
-augt1, gsmooth_factor, re
-
-where
-
-rc          = cutoff radius for cutoff function; default = 4.0
-delr        = length of smoothing distance for cutoff function; default = 0.1
-rho0(I)     = relative density for element I (overwrites value
-              read from meamf file)
-Ec(I,J)     = cohesive energy of reference structure for I-J mixture
-delta(I,J)  = heat of formation for I-J alloy; if Ec_IJ is input as
-              zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
-alpha(I,J)  = alpha parameter for pair potential between I and J (can
-              be computed from bulk modulus of reference structure
-re(I,J)     = equilibrium distance between I and J in the reference
-              structure
-Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened
-              by K (I<=J); default = 2.8
-Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
-              by K (I<=J); default = 2.0
-lattce(I,J) = lattice structure of I-J reference structure:
-                dia = diamond (interlaced fcc for alloy)
-                fcc = face centered cubic
-                bcc = body centered cubic
-                dim = dimer
-                b1  = rock salt (NaCl structure)
-                hcp = hexagonal close-packed
-                c11 = MoSi2 structure
-                l12 = Cu3Au structure (lower case L, followed by 12)
-                b2  = CsCl structure (interpenetrating simple cubic)
-nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for
-              I-J pair (see for example "(Lee)"_#Lee).
-                0 = second-nearest neighbor formulation off
-                1 = second-nearest neighbor formulation on
-                default = 0
-attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
-                default = 0
-repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
-                default = 0
-zbl(I,J)    = blend the MEAM I-J pair potential with the ZBL potential for small
-              atom separations "(ZBL)"_#ZBL
-                default = 1
-gsmooth_factor  = factor determining the length of the G-function smoothing
-                  region; only significant for ibar=0 or ibar=4.
-                      99.0 = short smoothing region, sharp step
-                      0.5  = long smoothing region, smooth step
-                      default = 99.0
-augt1           = integer flag for whether to augment t1 parameter by
-                  3/5*t3 to account for old vs. new meam formulations;
-                    0 = don't augment t1
-                    1 = augment t1
-                    default = 1
-ialloy          = integer flag to use alternative averaging rule for t parameters,
-                  for comparison with the DYNAMO MEAM code
-                    0 = standard averaging (matches ialloy=0 in DYNAMO)
-                    1 = alternative averaging (matches ialloy=1 in DYNAMO)
-                    2 = no averaging of t (use single-element values)
-                    default = 0
-mixture_ref_t   = integer flag to use mixture average of t to compute the background
-                  reference density for alloys, instead of the single-element values
-                  (see description and warning elsewhere in this doc page)
-                    0 = do not use mixture averaging for t in the reference density
-                    1 = use mixture averaging for t in the reference density
-                    default = 0
-erose_form      = integer value to select the form of the Rose energy function
-                  (see description below).
-                    default = 0
-emb_lin_neg     = integer value to select embedding function for negative densities
-                    0 = F(rho)=0
-                    1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO)
-                    default = 0
-bkgd_dyn        = integer value to select background density formula
-                    0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
-                    1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO)
-                    default = 0 :pre
-
-Rc, delr, re are in distance units (Angstroms in the case of metal
-units).  Ec and delta are in energy units (eV in the case of metal
-units).
-
-Each keyword represents a quantity which is either a scalar, vector,
-2d array, or 3d array and must be specified with the correct
-corresponding array syntax.  The indices I,J,K each run from 1 to N
-where N is the number of MEAM elements being used.
-
-Thus these lines
-
-rho0(2) = 2.25
-alpha(1,2) = 4.37 :pre
-
-set rho0 for the 2nd element to the value 2.25 and set alpha for the
-alloy interaction between elements 1 and 2 to 4.37.
-
-The augt1 parameter is related to modifications in the MEAM
-formulation of the partial electron density function.  In recent
-literature, an extra term is included in the expression for the
-third-order density in order to make the densities orthogonal (see for
-example "(Wang)"_#Wang2, equation 3d); this term is included in the
-MEAM implementation in lammps.  However, in earlier published work
-this term was not included when deriving parameters, including most of
-those provided in the library.meam file included with lammps, and to
-account for this difference the parameter t1 must be augmented by
-3/5*t3.  If augt1=1, the default, this augmentation is done
-automatically.  When parameter values are fit using the modified
-density function, as in more recent literature, augt1 should be set to
-0.
-
-The mixture_ref_t parameter is available to match results with those
-of previous versions of lammps (before January 2011).  Newer versions
-of lammps, by default, use the single-element values of the t
-parameters to compute the background reference density.  This is the
-proper way to compute these parameters.  Earlier versions of lammps
-used an alloy mixture averaged value of t to compute the background
-reference density.  Setting mixture_ref_t=1 gives the old behavior.
-WARNING: using mixture_ref_t=1 will give results that are demonstrably
-incorrect for second-neighbor MEAM, and non-standard for
-first-neighbor MEAM; this option is included only for matching with
-previous versions of lammps and should be avoided if possible.
-
-The parameters attrac and repuls, along with the integer selection
-parameter erose_form, can be used to modify the Rose energy function
-used to compute the pair potential.  This function gives the energy of
-the reference state as a function of interatomic spacing.  The form of
-this function is:
-
-astar = alpha * (r/re - 1.d0)
-if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
-if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
-if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
-a3 = repuls, astar < 0
-a3 = attrac, astar >= 0 :pre
-
-Most published MEAM parameter sets use the default values attrac=repulse=0.
-Setting repuls=attrac=delta corresponds to the form used in several
-recent published MEAM parameter sets, such as "(Valone)"_#Valone
-
-NOTE: The default form of the erose expression in LAMMPS was corrected
-in March 2009.  The current version is correct, but may show different
-behavior compared with earlier versions of lammps with the attrac
-and/or repuls parameters are non-zero.  To obtain the previous default
-form, use erose_form = 1 (this form does not seem to appear in the
-literature).  An alternative form (see e.g. "(Lee2)"_#Lee2) is
-available using erose_form = 2.
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-For atom type pairs I,J and I != J, where types I and J correspond to
-two different element types, mixing is performed by LAMMPS with
-user-specifiable parameters as described above.  You never need to
-specify a pair_coeff command with I != J arguments for this style.
-
-This pair style does not support the "pair_modify"_pair_modify.html
-shift, table, and tail options.
-
-This pair style does not write its information to "binary restart
-files"_restart.html, since it is stored in potential files.  Thus, you
-need to re-specify the pair_style and pair_coeff commands in an input
-script that reads a restart file.
-
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
-
-:line
-
-[Restrictions:]
-
-The {meam/c} style is provided in the USER-MEAMC package. It is
-only enabled if LAMMPS was built with that package.
-See the "Build package"_Build_package.html doc page for more info.
-
-The maximum number of elements, that can be read from the MEAM
-library file, is determined at compile time. The default is 5.
-If you need support for more elements, you have to change the
-define for the constant 'maxelt' at the beginning of the file
-src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no
-limit on the number of atoms types.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html,
-"pair_style meam/spline"_pair_meam_spline.html
-
-[Default:] none
-
-:line
-
-:link(Baskes)
-[(Baskes)] Baskes, Phys Rev B, 46, 2727-2742 (1992).
-
-:link(Gullet)
-[(Gullet)] Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
-This report may be accessed on-line via "this link"_sandreport.
-
-:link(sandreport,http://infoserve.sandia.gov/sand_doc/2003/038782.pdf)
-
-:link(Lee)
-[(Lee)] Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
-
-:link(Lee2)
-[(Lee2)] Lee, Baskes, Kim, Cho.  Phys. Rev. B, 64, 184102 (2001).
-
-:link(Valone)
-[(Valone)] Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
-
-:link(Wang2)
-[(Wang)] Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).
-
-:link(ZBL)
-[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges
-of Ions in Matter", Vol 1, 1985, Pergamon Press.
diff --git a/doc/src/pair_meso.rst b/doc/src/pair_meso.rst
new file mode 100644
index 0000000000..b4a945409d
--- /dev/null
+++ b/doc/src/pair_meso.rst
@@ -0,0 +1,337 @@
+.. index:: pair\_style edpd
+
+pair\_style edpd command
+========================
+
+pair\_style mdpd command
+========================
+
+pair\_style mdpd/rhosum command
+===============================
+
+pair\_style tdpd command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *edpd* or *mdpd* or *mdpd/rhosum* or *tdpd*
+* args = list of arguments for a particular style
+  
+  .. parsed-literal::
+  
+       *edpd* args = cutoff seed
+         cutoff = global cutoff for eDPD interactions (distance units)
+         seed = random # seed (integer) (if <= 0, eDPD will use current time as the seed)
+       *mdpd* args = T cutoff seed
+         T = temperature (temperature units)
+         cutoff = global cutoff for mDPD interactions (distance units)
+         seed = random # seed (integer) (if <= 0, mDPD will use current time as the seed)
+       *mdpd/rhosum* args =
+       *tdpd* args = T cutoff seed
+         T = temperature (temperature units)
+         cutoff = global cutoff for tDPD interactions (distance units)
+         seed = random # seed (integer) (if <= 0, tDPD will use current time as the seed)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style edpd 1.58 9872598
+   pair_coeff \* \* 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58
+   pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10
+   pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
+
+   pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 65689
+   pair_coeff 1 1 mdpd/rhosum  0.75
+   pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75
+
+   pair_style tdpd 1.0 1.58 935662
+   pair_coeff \* \* 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0
+   pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
+
+Description
+"""""""""""
+
+The *edpd* style computes the pairwise interactions and heat fluxes
+for eDPD particles following the formulations in
+:ref:`(Li2014\_JCP) <Li2014_JCP>` and :ref:`Li2015\_CC <Li2015_CC>`. The time
+evolution of an eDPD particle is governed by the conservation of
+momentum and energy given by
+
+.. image:: Eqs/pair_edpd_gov.jpg
+   :align: center
+
+where the three components of <font size="4">F<sub>i</sub></font>
+including the conservative force <font
+size="4">F<sub>ij</sub><sup>C</sup></font>, dissipative force <font
+size="4">F<sub>ij</sub><sup>D</sup></font> and random force <font
+size="4">F<sub>ij</sub><sup>R</sup></font> are expressed as
+
+.. image:: Eqs/pair_edpd_force.jpg
+   :align: center
+
+in which the exponent of the weighting function <font
+size="4"><i>s</i></font> can be defined as a temperature-dependent
+variable. The heat flux between particles accounting for the
+collisional heat flux <font size="4">q<sup>C</sup></font>, viscous
+heat flux <font size="4">q<sup>V</sup></font>, and random heat flux
+<font size="4">q<sup>R</sup></font> are given by
+
+.. image:: Eqs/pair_edpd_heat.jpg
+   :align: center
+
+where the mesoscopic heat friction <font size="4">&kappa;</font> is given by
+
+.. image:: Eqs/pair_edpd_kappa.jpg
+   :align: center
+
+with <font size="4">&upsilon;</font> being the kinematic
+viscosity. For more details, see Eq.(15) in :ref:`(Li2014\_JCP) <Li2014_JCP>`.
+
+The following coefficients must be defined in eDPD system for each
+pair of atom types via the :doc:`pair\_coeff <pair_coeff>` command as in
+the examples above.
+
+* A (force units)
+* gamma (force/velocity units)
+* power\_f (positive real)
+* cutoff (distance units)
+* kappa (thermal conductivity units)
+* power\_T (positive real)
+* cutoff\_T (distance units)
+* optional keyword = power or kappa
+
+The keyword *power* or *kappa* is optional. Both "power" and "kappa"
+require 4 parameters <font size="4">c<sub>1</sub>, c<sub>2</sub>,
+c<sub>4</sub>, c<sub>4</sub></font> showing the temperature dependence
+of the exponent <center><font size="4"> <i>s</i>(<i>T</i>) =
+power\_f\*(1+c<sub>1</sub>\*(T-1)+c<sub>2</sub>\*(T-1)<sup>2</sup>
++c<sub>3</sub>\*(T-1)<sup>3</sup>+c<sub>4</sub>\*(T-1)<sup>4</sup>)</font></center>
+and of the mesoscopic heat friction <center><font size="4">
+<i>s<sub>T</sub>(T)</i> =
+kappa\*(1+c<sub>1</sub>\*(T-1)+c<sub>2</sub>\*(T-1)<sup>2</sup>
++c<sub>3</sub>\*(T-1)<sup>3</sup>+c<sub>4</sub>\*(T-1)<sup>4</sup>)</font></center>
+If the keyword *power* or *kappa* is not specified, the eDPD system
+will use constant power\_f and kappa, which is independent to
+temperature changes.
+
+
+----------
+
+
+The *mdpd/rhosum* style computes the local particle mass density rho
+for mDPD particles by kernel function interpolation.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above.
+
+* cutoff (distance units)
+
+
+----------
+
+
+The *mdpd* style computes the many-body interactions between mDPD
+particles following the formulations in
+:ref:`(Li2013\_POF) <Li2013_POF>`. The dissipative and random forces are in
+the form same as the classical DPD, but the conservative force is
+local density dependent, which are given by
+
+.. image:: Eqs/pair_mdpd_force.jpg
+   :align: center
+
+where the first term in <font size="4">F<sup>C</sup></font> with a
+negative coefficient A < 0 stands for an attractive force within an
+interaction range <font size="4">r<sub>c</sub></font>, and the second
+term with B > 0 is the density-dependent repulsive force within an
+interaction range <font size="4">r<sub>d</sub></font>.
+
+The following coefficients must be defined for each pair of atom types via the
+:doc:`pair\_coeff <pair_coeff>` command as in the examples above.
+
+* A (force units)
+* B (force units)
+* gamma (force/velocity units)
+* cutoff\_c (distance units)
+* cutoff\_d (distance units)
+
+
+----------
+
+
+The *tdpd* style computes the pairwise interactions and chemical
+concentration fluxes for tDPD particles following the formulations in
+:ref:`(Li2015\_JCP) <Li2015_JCP>`.  The time evolution of a tDPD particle is
+governed by the conservation of momentum and concentration given by
+
+.. image:: Eqs/pair_tdpd_gov.jpg
+   :align: center
+
+where the three components of <font size="4">F<sub>i</sub></font>
+including the conservative force <font
+size="4">F<sub>ij</sub><sup>C</sup></font>, dissipative force <font
+size="4">F<sub>ij</sub><sup>D</sup></font> and random force <font
+size="4">F<sub>ij</sub><sup>R</sup></font> are expressed as
+
+.. image:: Eqs/pair_tdpd_force.jpg
+   :align: center
+
+The concentration flux between two tDPD particles includes the Fickian
+flux <font size="4">Q<sub>ij</sub><sup>D</sup></font> and random flux
+<font size="4">Q<sub>ij</sub><sup>R</sup></font>, which are given by
+
+.. image:: Eqs/pair_tdpd_flux.jpg
+   :align: center
+
+where the parameters kappa and epsilon determine the strength of the
+Fickian and random fluxes. <font size="4"><i>m</i><sub>s</sub></font>
+is the mass of a single solute molecule.  In general, <font
+size="4"><i>m</i><sub>s</sub></font> is much smaller than the mass of
+a tDPD particle <font size="4"><i>m</i></font>. For more details, see
+:ref:`(Li2015\_JCP) <Li2015_JCP>`.
+
+The following coefficients must be defined for each pair of atom types via the
+:doc:`pair\_coeff <pair_coeff>` command as in the examples above.
+
+* A (force units)
+* gamma (force/velocity units)
+* power\_f (positive real)
+* cutoff (distance units)
+* cutoff\_CC (distance units)
+* kappa\_i (diffusivity units)
+* epsilon\_i (diffusivity units)
+* power\_cc\_i (positive real)
+
+The last 3 values must be repeated Nspecies times, so that values for
+each of the Nspecies chemical species are specified, as indicated by
+the "I" suffix.  In the first pair\_coeff example above for pair\_style
+tdpd, Nspecies = 1.  In the second example, Nspecies = 2, so 3
+additional coeffs are specified (for species 2).
+
+
+----------
+
+
+**Example scripts**
+
+There are example scripts for using all these pair styles in
+examples/USER/meso.  The example for an eDPD simulation models heat
+conduction with source terms analog of periodic Poiseuille flow
+problem. The setup follows Fig.12 in :ref:`(Li2014\_JCP) <Li2014_JCP>`. The
+output of the short eDPD simulation (about 2 minutes on a single core)
+gives a temperature and density profiles as
+
+.. image:: JPG/examples_edpd.jpg
+   :align: center
+
+The example for a mDPD simulation models the oscillations of a liquid
+droplet started from a liquid film. The mDPD parameters are adopted
+from :ref:`(Li2013\_POF) <Li2013_POF>`.  The short mDPD run (about 2 minutes
+on a single core) generates a particle trajectory which can
+be visualized as follows.
+
+.. image:: JPG/examples_mdpd_first.jpg
+   :target: JPG/examples_mdpd.gif
+   :align: center
+
+.. image:: JPG/examples_mdpd_last.jpg
+   :align: center
+
+The first image is the initial state of the simulation.  If you
+click it a GIF movie should play in your browser.  The second image
+is the final state of the simulation.
+
+The example for a tDPD simulation computes the effective diffusion
+coefficient of a tDPD system using a method analogous to the periodic
+Poiseuille flow.  The tDPD system is specified with two chemical
+species, and the setup follows Fig.1 in
+:ref:`(Li2015\_JCP) <Li2015_JCP>`. The output of the short tDPD simulation
+(about one and a half minutes on a single core) gives the
+concentration profiles of the two chemical species as
+
+.. image:: JPG/examples_tdpd.jpg
+   :align: center
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support
+mixing. Thus, coefficients for all I,J pairs must be specified explicitly.
+
+The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support
+the :doc:`pair\_modify <pair_modify>` shift, table, and tail options.
+
+The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not write
+information to :doc:`binary restart files <restart>`. Thus, you need
+to re-specify the pair\_style and pair\_coeff commands in an input script
+that reads a restart file.
+
+Restrictions
+""""""""""""
+
+
+The pair styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* are part of
+the USER-MESO package. It is only enabled if LAMMPS was built with
+that package.  See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix mvv/dpd <fix_mvv_dpd>`,
+:doc:`fix mvv/edpd <fix_mvv_dpd>`, :doc:`fix mvv/tdpd <fix_mvv_dpd>`,
+:doc:`fix edpd/source <fix_dpd_source>`, :doc:`fix tdpd/source <fix_dpd_source>`,
+:doc:`compute edpd/temp/atom <compute_edpd_temp_atom>`,
+:doc:`compute tdpd/cc/atom <compute_tdpd_cc_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Li2014\_JCP:
+
+
+
+**(Li2014\_JCP)** Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys,
+265: 113-127 (2014).  DOI: 10.1016/j.jcp.2014.02.003.
+
+.. _Li2015\_CC:
+
+
+
+**(Li2015\_CC)** Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040
+(2015).  DOI: 10.1039/C5CC01684C.
+
+.. _Li2013\_POF:
+
+
+
+**(Li2013\_POF)** Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013).
+DOI: 10.1063/1.4812366.
+
+.. _Li2015\_JCP:
+
+
+
+**(Li2015\_JCP)** Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys,
+143: 014101 (2015).  DOI: 10.1063/1.4923254.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst
new file mode 100644
index 0000000000..1c43d47b00
--- /dev/null
+++ b/doc/src/pair_mgpt.rst
@@ -0,0 +1,254 @@
+.. index:: pair\_style mgpt
+
+pair\_style mgpt command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style mgpt
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style mgpt
+   pair_coeff \* \* Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
+   cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
+   cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
+   pair_coeff \* \* parmin potin Omega volpress yes nbody 1234 precision double
+   pair_coeff \* \* parmin potin Omega volpress yes nbody 12
+
+Description
+"""""""""""
+
+Within DFT quantum mechanics, generalized pseudopotential theory (GPT)
+(:ref:`Moriarty1 <Moriarty1>`) provides a first-principles approach to
+multi-ion interatomic potentials in d-band transition metals, with a
+volume-dependent, real-space total-energy functional for the N-ion
+elemental bulk material in the form
+
+.. image:: Eqs/pair_mgpt.jpg
+   :align: center
+
+where the prime on each summation sign indicates the exclusion of all
+self-interaction terms from the summation.  The leading volume term
+E\_vol as well as the two-ion central-force pair potential v\_2 and the
+three- and four-ion angular-force potentials, v\_3 and v\_4, depend
+explicitly on the atomic volume Omega, but are structure independent
+and transferable to all bulk ion configurations, either ordered or
+disordered, and with of without the presence of point and line
+defects.  The simplified model GPT or MGPT (:ref:`Moriarty2 <Moriarty2>`,
+:ref:`Moriarty3 <Moriarty3>`), which retains the form of E\_tot and permits
+more efficient large-scale atomistic simulations, derives from the GPT
+through a series of systematic approximations applied to E\_vol and the
+potentials v\_n that are valid for mid-period transition metals with
+nearly half-filled d bands.
+
+Both analytic (:ref:`Moriarty2 <Moriarty2>`) and matrix
+(:ref:`Moriarty3 <Moriarty3>`) representations of MGPT have been developed.
+In the more general matrix representation, which can also be applied
+to f-band actinide metals and permits both canonical and non-canonical
+d/f bands, the multi-ion potentials are evaluated on the fly during a
+simulation through d- or f-state matrix multiplication, and the forces
+that move the ions are determined analytically.  Fast matrix-MGPT
+algorithms have been developed independently by Glosli
+(:ref:`Glosli <Glosli>`, :ref:`Moriarty3 <Moriarty3>`) and by Oppelstrup
+(:ref:`Oppelstrup <Oppelstrup>`)
+
+The *mgpt* pair style calculates forces, energies, and the total
+energy per atom, E\_tot/N, using the Oppelstrup matrix-MGPT algorithm.
+Input potential and control data are entered through the
+:doc:`pair\_coeff <pair_coeff>` command.  Each material treated requires
+input parmin and potin potential files, as shown in the above
+examples, as well as specification by the user of the initial atomic
+volume Omega through pair\_coeff.  At the beginning of a time step in
+any simulation, the total volume of the simulation cell V should
+always be equal to Omega\*N, where N is the number of metal ions
+present, taking into account the presence of any vacancies and/or
+interstitials in the case of a solid.  In a constant-volume
+simulation, which is the normal mode of operation for the *mgpt* pair
+style, Omega, V and N all remain constant throughout the simulation
+and thus are equal to their initial values.  In a constant-stress
+simulation, the cell volume V will change (slowly) as the simulation
+proceeds.  After each time step, the atomic volume should be updated
+by the code as Omega = V/N.  In addition, the volume term E\_vol and
+the potentials v\_2, v\_3 and v\_4 have to be removed at the end of the
+time step, and then respecified at the new value of Omega.  In all
+simulations, Omega must remain within the defined volume range for
+E\_vol and the potentials for the given material.
+
+The default option volpress yes in the :doc:`pair\_coeff <pair_coeff>`
+command includes all volume derivatives of E\_tot required to calculate
+the stress tensor and pressure correctly.  The option volpress no
+disregards the pressure contribution resulting from the volume term
+E\_vol, and can be used for testing and analysis purposes.  The
+additional optional variable nbody controls the specific terms in
+E\_tot that are calculated.  The default option and the normal option
+for mid-period transition and actinide metals is nbody 1234 for which
+all four terms in E\_tot are retained.  The option nbody 12, for
+example, retains only the volume term and the two-ion pair potential
+term and can be used for GPT series-end transition metals that can be
+well described without v\_3 and v\_4.  The nbody option can also be used
+to test or analyze the contribution of any of the four terms in E\_tot
+to a given calculated property.
+
+The *mgpt* pair style makes extensive use of matrix algebra and
+includes optimized kernels for the BlueGene/Q architecture and the
+Intel/AMD (x86) architectures.  When compiled with the appropriate
+compiler and compiler switches (-msse3 on x86, and using the IBM XL
+compiler on BG/Q), these optimized routines are used automatically.
+For BG/Q machines, building with the default Makefile for that
+architecture (e.g., "make bgq") should enable the optimized algebra
+routines.  For x-86 machines, there is a provided Makefile.mgptfast
+which enables the fast algebra routines, i.e. build LAMMPS with "make
+mgptfast".  The user will be informed in the output files of the
+matrix kernels in use. To further improve speed, on x86 the option
+precision single can be added to the :doc:`pair\_coeff <pair_coeff>`
+command line, which improves speed (up to a factor of two) at the cost
+of doing matrix calculations with 7 digit precision instead of the
+default 16. For consistency the default option can be specified
+explicitly by the option precision double.
+
+All remaining potential and control data are contained with the parmin
+and potin files, including cutoffs, atomic mass, and other basic MGPT
+variables.  Specific MGPT potential data for the transition metals
+tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials),
+and vanadium (V6.1 potentials) are contained in the LAMMPS potentials
+directory.  The stored files are, respectively, Ta4.mgpt.parmin,
+Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin,
+Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and
+V6.1.mgpt.potin .  Useful corresponding informational "README" files
+on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the
+potentials directory.  These latter files indicate the volume mesh and
+range for each potential and give appropriate references for the
+potentials.  It is expected that MGPT potentials for additional
+materials will be added over time.
+
+Useful example MGPT scripts are given in the examples/USER/mgpt
+directory.  These scripts show the necessary steps to perform
+constant-volume calculations and simulations.  It is strongly
+recommended that the user work through and understand these examples
+before proceeding to more complex simulations.
+
+.. note::
+
+   For good performance, LAMMPS should be built with the compiler
+   flags "-O3 -msse3 -funroll-loops" when including this pair style.  The
+   src/MAKE/OPTIONS/Makefile.mgptfast is an example machine Makefile with
+   these options included as part of a standard MPI build.  Note that it
+   as provided, it will build with whatever low-level compiler (g++, icc,
+   etc) is the default for your MPI installation.
+
+
+----------
+
+
+**Mixing, shift, table tail correction, restart**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+needs to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-MGPT package and is only enabled
+if LAMMPS is built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The MGPT potentials require the :doc:`newtion <newton>` setting to be
+"on" for pair style interactions.
+
+The stored parmin and potin potential files provided with LAMMPS in
+the "potentials" directory are written in Rydberg atomic units, with
+energies in Rydbergs and distances in Bohr radii. The *mgpt* pair
+style converts Rydbergs to Hartrees to make the potential files
+compatible with LAMMPS electron :doc:`units <units>`.
+
+The form of E\_tot used in the *mgpt* pair style is only appropriate
+for elemental bulk solids and liquids.  This includes solids with
+point and extended defects such as vacancies, interstitials, grain
+boundaries and dislocations.  Alloys and free surfaces, however,
+require significant modifications, which are not included in the
+*mgpt* pair style.  Likewise, the *hybrid* pair style is not allowed,
+where MGPT would be used for some atoms but not for others.
+
+Electron-thermal effects are not included in the standard MGPT
+potentials provided in the "potentials" directory, where the
+potentials have been constructed at zero electron temperature.
+Physically, electron-thermal effects may be important in 3d (e.g., V)
+and 4d (e.g., Mo) transition metals at high temperatures near melt and
+above.  It is expected that temperature-dependent MGPT potentials for
+such cases will be added over time.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+Default
+"""""""
+
+The options defaults for the :doc:`pair\_coeff <pair_coeff>` command are
+volpress yes, nbody 1234, and precision double.
+
+
+----------
+
+
+.. _Moriarty1:
+
+
+
+**(Moriarty1)** Moriarty, Physical Review B, 38, 3199 (1988).
+
+.. _Moriarty2:
+
+
+
+**(Moriarty2)** Moriarty, Physical Review B, 42, 1609 (1990).
+Moriarty, Physical Review B 49, 12431 (1994).
+
+.. _Moriarty3:
+
+
+
+**(Moriarty3)** Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang,
+Journal of Materials Research, 21, 563 (2006).
+
+.. _Glosli:
+
+
+
+**(Glosli)** Glosli, unpublished, 2005.
+Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference
+Series, 46, 254 (2006).
+
+.. _Oppelstrup:
+
+
+
+**(Oppelstrup)** Oppelstrup, unpublished, 2015.
+Oppelstrup and Moriarty, to be published.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst
new file mode 100644
index 0000000000..ba94830475
--- /dev/null
+++ b/doc/src/pair_mie.rst
@@ -0,0 +1,126 @@
+.. index:: pair\_style mie/cut
+
+pair\_style mie/cut command
+===========================
+
+pair\_style mie/cut/gpu command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style mie/cut cutoff
+
+* cutoff = global cutoff for mie/cut interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style mie/cut 10.0
+   pair_coeff 1 1 0.72 3.40 23.00 6.66
+   pair_coeff 2 2 0.30 3.55 12.65 6.00
+   pair_coeff 1 2 0.46 3.32 16.90 6.31
+
+Description
+"""""""""""
+
+The *mie/cut* style computes the Mie potential, given by
+
+.. image:: Eqs/pair_mie.jpg
+   :align: center
+
+Rc is the cutoff and C is a function that depends on the repulsive and
+attractive exponents, given by:
+
+.. image:: Eqs/pair_mie2.jpg
+   :align: center
+
+Note that for 12/6 exponents, C is equal to 4 and the formula is the
+same as the standard Lennard-Jones potential.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* gammaR
+* gammaA
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global
+cutoff specified in the pair\_style command is used.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the mie/cut pair styles can be mixed.
+If not explicitly defined, both the repulsive and attractive gamma
+exponents for different atoms will be calculated following the same
+mixing rule defined for distances.  The default mix value is
+*geometric*\ . See the "pair\_modify" command for details.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` tail
+option for adding a long-range tail correction to the energy and
+pressure of the pair interaction.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style supports the use of the *inner*\ , *middle*\ , and *outer*
+keywords of the :doc:`run\_style respa <run_style>` command, meaning the
+pairwise forces can be partitioned by distance at different levels of
+the rRESPA hierarchy.  See the :doc:`run\_style <run_style>` command for
+details.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Mie:
+
+
+
+**(Mie)** G. Mie, Ann Phys, 316, 657 (1903).
+
+.. _Avendano:
+
+
+
+**(Avendano)** C. Avendano, T. Lafitte, A. Galindo, C. S. Adjiman,
+G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_mm3_switch3_coulgauss.txt b/doc/src/pair_mm3_switch3_coulgauss.txt
deleted file mode 100644
index 3e0e24150e..0000000000
--- a/doc/src/pair_mm3_switch3_coulgauss.txt
+++ /dev/null
@@ -1,88 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style mm3/switch3/coulgauss/long command :h3
-
-[Syntax:]
-
-pair_style style args :pre
-
-style = {mm3/switch3/coulgauss/long}
-args = list of arguments for a particular style :ul
-  {mm3/switch3/coulgauss/long} args = cutoff (cutoff2) width
-    cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-    width  = width parameter of the smoothing function (distance units) :pre
-
-[Examples:]
-
-pair_style mm3/switch3/coulgauss/long    12.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-[Description:]
-
-The {mm3/switch3/coulgauss} style evaluates the MM3
-vdW potential "(Allinger)"_#mm3-allinger1989
-
-:c,image(Eqs/pair_mm3_switch3.jpg)
-
-, which goes smoothly to zero at the cutoff r_c as defined
-by the switching function
-
-:c,image(Eqs/pair_switch3.jpg)
-
-where w is the width defined in the arguments. This potential
-is combined with Coulomb interaction between Gaussian charge densities:
-
-:c,image(Eqs/pair_coulgauss.jpg)
-
-where qi and qj are the
-charges on the 2 atoms, epsilon is the dielectric constant which
-can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
-are the widths of the Gaussian charge distribution and erf() is the error-function.
-This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
-
-If one cutoff is specified it is used for both the vdW and Coulomb
-terms.  If two cutoffs are specified, the first is used as the cutoff
-for the vdW terms, and the second is the cutoff for the Coulombic term.
-
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-epsilon (energy)
-r_v (distance)
-gamma (distance) :ul
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-Mixing rules are fixed for this style as defined above. 
-
-Shifting the potential energy is not necessary because the switching
-function ensures that the potential is zero at the cut-off.
-
-
-[Restrictions:]
-
-These styles are part of the USER-YAFF package.  They are only
-enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html
-
-[Default:] none
-
diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst
new file mode 100644
index 0000000000..3f3a7cbc72
--- /dev/null
+++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst
@@ -0,0 +1,106 @@
+.. index:: pair\_style mm3/switch3/coulgauss/long
+
+pair\_style mm3/switch3/coulgauss/long command
+==============================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *mm3/switch3/coulgauss/long*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
+       cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+       width  = width parameter of the smoothing function (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style mm3/switch3/coulgauss/long    12.0 3.0
+   pair_coeff 1  0.2 2.5 1.2
+
+   pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
+   pair_coeff 1  0.2 2.5 1.2
+
+Description
+"""""""""""
+
+The *mm3/switch3/coulgauss/long* style evaluates the MM3
+vdW potential :ref:`(Allinger) <mm3-allinger1989>`
+
+.. image:: Eqs/pair_mm3_switch3.jpg
+   :align: center
+
+, which goes smoothly to zero at the cutoff r\_c as defined
+by the switching function
+
+.. image:: Eqs/pair_switch3.jpg
+   :align: center
+
+where w is the width defined in the arguments. This potential
+is combined with Coulomb interaction between Gaussian charge densities:
+
+.. image:: Eqs/pair_coulgauss.jpg
+   :align: center
+
+where qi and qj are the
+charges on the 2 atoms, epsilon is the dielectric constant which
+can be set by the :doc:`dielectric <dielectric>` command, gamma\_i and gamma\_j
+are the widths of the Gaussian charge distribution and erf() is the error-function.
+This style has to be used in conjunction with the :doc:`kspace\_style <kspace_style>` command
+
+If one cutoff is specified it is used for both the vdW and Coulomb
+terms.  If two cutoffs are specified, the first is used as the cutoff
+for the vdW terms, and the second is the cutoff for the Coulombic term.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* epsilon (energy)
+* r\_v (distance)
+* gamma (distance)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+Mixing rules are fixed for this style as defined above.
+
+Shifting the potential energy is not necessary because the switching
+function ensures that the potential is zero at the cut-off.
+
+Restrictions
+""""""""""""
+
+
+These styles are part of the USER-YAFF package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst
new file mode 100644
index 0000000000..b45a50573a
--- /dev/null
+++ b/doc/src/pair_modify.rst
@@ -0,0 +1,324 @@
+.. index:: pair\_modify
+
+pair\_modify command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_modify keyword values ...
+
+* one or more keyword/value pairs may be listed
+* keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner*
+  or *tabinner/disp* or *tail* or *compute* or *nofdotr*
+  
+  .. parsed-literal::
+  
+       *pair* values = sub-style N *special* which wt1 wt2 wt3
+                    or sub-style N *compute/tally* flag
+         sub-style = sub-style of :doc:`pair hybrid <pair_hybrid>`
+         N = which instance of sub-style (only if sub-style is used multiple times)
+           *special* which wt1 wt2 wt3 = override *special_bonds* settings (optional)
+             which = *lj/coul* or *lj* or *coul*
+             w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
+           *compute/tally* flag = *yes* or *no*
+       *mix* value = *geometric* or *arithmetic* or *sixthpower*
+       *shift* value = *yes* or *no*
+       *table* value = N
+         2\^N = # of values in table
+       *table/disp* value = N
+         2\^N = # of values in table
+       *tabinner* value = cutoff
+         cutoff = inner cutoff at which to begin table (distance units)
+       *tabinner/disp* value = cutoff
+         cutoff = inner cutoff at which to begin table (distance units)
+       *tail* value = *yes* or *no*
+       *compute* value = *yes* or *no*
+       *nofdotr*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_modify shift yes mix geometric
+   pair_modify tail yes
+   pair_modify table 12
+   pair_modify pair lj/cut compute no
+   pair_modify pair tersoff compute/tally no
+   pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
+
+Description
+"""""""""""
+
+Modify the parameters of the currently defined pair style.  Not all
+parameters are relevant to all pair styles.
+
+If used, the *pair* keyword must appear first in the list of keywords.
+It can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles.  It means that all the
+following parameters will only be modified for the specified
+sub-style.  If the sub-style is defined multiple times, then an
+additional numeric argument *N* must also be specified, which is a
+number from 1 to M where M is the number of times the sub-style was
+listed in the :doc:`pair\_style hybrid <pair_hybrid>` command.  The extra
+number indicates which instance of the sub-style the remaining
+keywords will be applied to.  Note that if the *pair* keyword is not
+used, and the pair style is *hybrid* or *hybrid/overlay*\ , then all the
+specified keywords will be applied to all sub-styles.
+
+The *special* and *compute/tally* keywords can **only** be used in
+conjunction with the *pair* keyword and must directly follow it.
+*special* allows to override the
+:doc:`special\_bonds <special_bonds>` settings for the specified sub-style.
+*compute/tally* allows to disable or enable registering
+:doc:`compute \*/tally <compute_tally>` computes for a given sub-style.
+More details are given below.
+
+The *mix* keyword affects pair coefficients for interactions between
+atoms of type I and J, when I != J and the coefficients are not
+explicitly set in the input script.  Note that coefficients for I = J
+must be set explicitly, either in the input script via the
+"pair\_coeff" command or in the "Pair Coeffs" section of the :doc:`data file <read_data>`.  For some pair styles it is not necessary to
+specify coefficients when I != J, since a "mixing" rule will create
+them from the I,I and J,J settings.  The pair\_modify *mix* value
+determines what formulas are used to compute the mixed coefficients.
+In each case, the cutoff distance is mixed the same way as sigma.
+
+Note that not all pair styles support mixing.  Also, some mix options
+are not available for certain pair styles.  See the doc page for
+individual pair styles for those restrictions.  Note also that the
+:doc:`pair\_coeff <pair_coeff>` command also can be to directly set
+coefficients for a specific I != J pairing, in which case no mixing is
+performed.
+
+mix *geometric*
+
+
+.. parsed-literal::
+
+   epsilon_ij = sqrt(epsilon_i \* epsilon_j)
+   sigma_ij = sqrt(sigma_i \* sigma_j)
+
+mix *arithmetic*
+
+
+.. parsed-literal::
+
+   epsilon_ij = sqrt(epsilon_i \* epsilon_j)
+   sigma_ij = (sigma_i + sigma_j) / 2
+
+mix *sixthpower*
+
+
+.. parsed-literal::
+
+   epsilon_ij = (2 \* sqrt(epsilon_i\*epsilon_j) \* sigma_i\^3 \* sigma_j\^3) /
+                (sigma_i\^6 + sigma_j\^6)
+   sigma_ij = ((sigma_i\*\*6 + sigma_j\*\*6) / 2) \^ (1/6)
+
+The *shift* keyword determines whether a Lennard-Jones potential is
+shifted at its cutoff to 0.0.  If so, this adds an energy term to each
+pairwise interaction which will be included in the thermodynamic
+output, but does not affect pair forces or atom trajectories.  See the
+doc page for individual pair styles to see which ones support this
+option.
+
+The *table* and *table/disp* keywords apply to pair styles with a
+long-range Coulombic term or long-range dispersion term respectively;
+see the doc page for individual styles to see which potentials support
+these options.  If N is non-zero, a table of length 2\^N is
+pre-computed for forces and energies, which can shrink their
+computational cost by up to a factor of 2.  The table is indexed via a
+bit-mapping technique :ref:`(Wolff) <Wolff1>` and a linear interpolation is
+performed between adjacent table values.  In our experiments with
+different table styles (lookup, linear, spline), this method typically
+gave the best performance in terms of speed and accuracy.
+
+The choice of table length is a tradeoff in accuracy versus speed.  A
+larger N yields more accurate force computations, but requires more
+memory which can slow down the computation due to cache misses.  A
+reasonable value of N is between 8 and 16.  The default value of 12
+(table of length 4096) gives approximately the same accuracy as the
+no-table (N = 0) option.  For N = 0, forces and energies are computed
+directly, using a polynomial fit for the needed erfc() function
+evaluation, which is what earlier versions of LAMMPS did.  Values
+greater than 16 typically slow down the simulation and will not
+improve accuracy; values from 1 to 8 give unreliable results.
+
+The *tabinner* and *tabinner/disp* keywords set an inner cutoff above
+which the pairwise computation is done by table lookup (if tables are
+invoked), for the corresponding Coulombic and dispersion tables
+discussed with the *table* and *table/disp* keywords.  The smaller the
+cutoff is set, the less accurate the table becomes (for a given number
+of table values), which can require use of larger tables.  The default
+cutoff value is sqrt(2.0) distance units which means nearly all
+pairwise interactions are computed via table lookup for simulations
+with "real" units, but some close pairs may be computed directly
+(non-table) for simulations with "lj" units.
+
+When the *tail* keyword is set to *yes*\ , certain pair styles will add
+a long-range VanderWaals tail "correction" to the energy and pressure.
+These corrections are bookkeeping terms which do not affect dynamics,
+unless a constant-pressure simulation is being performed.  See the doc
+page for individual styles to see which support this option.  These
+corrections are included in the calculation and printing of
+thermodynamic quantities (see the :doc:`thermo\_style <thermo_style>`
+command).  Their effect will also be included in constant NPT or NPH
+simulations where the pressure influences the simulation box
+dimensions (e.g. the :doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`
+commands).  The formulas used for the long-range corrections come from
+equation 5 of :ref:`(Sun) <Sun>`.
+
+.. note::
+
+   The tail correction terms are computed at the beginning of each
+   run, using the current atom counts of each atom type.  If atoms are
+   deleted (or lost) or created during a simulation, e.g. via the :doc:`fix gcmc <fix_gcmc>` command, the correction factors are not
+   re-computed.  If you expect the counts to change dramatically, you can
+   break a run into a series of shorter runs so that the correction
+   factors are re-computed more frequently.
+
+Several additional assumptions are inherent in using tail corrections,
+including the following:
+
+* The simulated system is a 3d bulk homogeneous liquid. This option
+  should not be used for systems that are non-liquid, 2d, have a slab
+  geometry (only 2d periodic), or inhomogeneous.
+* G(r), the radial distribution function (rdf), is unity beyond the
+  cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
+  LJ fluid), and it is probably a good idea to verify this assumption by
+  checking the rdf.  The rdf is not exactly unity beyond the cutoff for
+  each pair of interaction types, so the tail correction is necessarily
+  an approximation.
+
+  The tail corrections are computed at the beginning of each simulation
+  run.  If the number of atoms changes during the run, e.g. due to atoms
+  leaving the simulation domain, or use of the :doc:`fix gcmc <fix_gcmc>`
+  command, then the corrections are not updated to reflect the changed
+  atom count.  If this is a large effect in your simulation, you should
+  break the long run into several short runs, so that the correction
+  factors are re-computed multiple times.
+
+* Thermophysical properties obtained from calculations with this option
+  enabled will not be thermodynamically consistent with the truncated
+  force-field that was used.  In other words, atoms do not feel any LJ
+  pair interactions beyond the cutoff, but the energy and pressure
+  reported by the simulation include an estimated contribution from
+  those interactions.
+
+
+The *compute* keyword allows pairwise computations to be turned off,
+even though a :doc:`pair\_style <pair_style>` is defined.  This is not
+useful for running a real simulation, but can be useful for debugging
+purposes or for performing a :doc:`rerun <rerun>` simulation, when you
+only wish to compute partial forces that do not include the pairwise
+contribution.
+
+Two examples are as follows.  First, this option allows you to perform
+a simulation with :doc:`pair\_style hybrid <pair_hybrid>` with only a
+subset of the hybrid sub-styles enabled.  Second, this option allows
+you to perform a simulation with only long-range interactions but no
+short-range pairwise interactions.  Doing this by simply not defining
+a pair style will not work, because the
+:doc:`kspace\_style <kspace_style>` command requires a Kspace-compatible
+pair style be defined.
+
+The *nofdotr* keyword allows to disable an optimization that computes
+the global stress tensor from the total forces and atom positions rather
+than from summing forces between individual pairs of atoms.
+
+
+----------
+
+
+The *special* keyword allows to override the 1-2, 1-3, and 1-4
+exclusion settings for individual sub-styles of a
+:doc:`hybrid pair style <pair_hybrid>`. It requires 4 arguments similar
+to the :doc:`special\_bonds <special_bonds>` command, *which* and
+wt1,wt2,wt3.  The *which* argument can be *lj* to change the
+Lennard-Jones settings, *coul* to change the Coulombic settings,
+or *lj/coul* to change both to the same set of 3 values.  The wt1,wt2,wt3
+values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
+1-3, and 1-4 bond topology neighbors, respectively. The *special*
+keyword can only be used in conjunction with the *pair* keyword
+and has to directly follow it.  This option is not compatible with
+pair styles from the GPU or the USER-INTEL package and attempting
+it will cause an error.
+
+.. note::
+
+   The global settings specified by the
+   :doc:`special\_bonds <special_bonds>` command affect the construction of
+   neighbor lists.  Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
+   exclude those pairs from the neighbor list entirely.  Weights of 1.0
+   store the neighbor with no weighting applied. Thus only global values
+   different from exactly 0.0 or 1.0 can be overridden and an error is
+   generated if the requested setting is not compatible with the global
+   setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
+   usually a sufficient workaround in this case without causing a
+   significant error.
+
+The *compute/tally* keyword takes exactly 1 argument (\ *no* or *yes*\ ),
+and allows to selectively disable or enable processing of the various
+:doc:`compute \*/tally <compute_tally>` styles for a given
+:doc:`pair hybrid or hybrid/overlay <pair_hybrid>` sub-style.
+
+.. note::
+
+   Any "pair\_modify pair compute/tally" command must be issued
+   **before** the corresponding compute style is defined.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+You cannot use *shift* yes with *tail* yes, since those are
+conflicting options.  You cannot use *tail* yes with 2d simulations.
+You cannot use *special* with pair styles from the GPU or
+USER-INTEL package.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style <pair_style>`, :doc:`pair\_style hybrid <pair_hybrid>`,
+pair\_coeff"_pair\_coeff.html, :doc:`thermo\_style <thermo_style>`,
+:doc:`compute \*/tally <compute_tally>`
+
+Default
+"""""""
+
+The option defaults are mix = geometric, shift = no, table = 12,
+tabinner = sqrt(2.0), tail = no, and compute = yes.
+
+Note that some pair styles perform mixing, but only a certain style of
+mixing.  See the doc pages for individual pair styles for details.
+
+
+----------
+
+
+.. _Wolff1:
+
+
+
+**(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
+
+.. _Sun:
+
+
+
+**(Sun)** Sun, J Phys Chem B, 102, 7338-7364 (1998).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt
deleted file mode 100644
index c446aa29d0..0000000000
--- a/doc/src/pair_modify.txt
+++ /dev/null
@@ -1,281 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_modify command :h3
-
-[Syntax:]
-
-pair_modify keyword values ... :pre
-
-one or more keyword/value pairs may be listed :ulb,l
-keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner}
-or {tabinner/disp} or {tail} or {compute} or {nofdotr} :l
-  {pair} values = sub-style N {special} which wt1 wt2 wt3
-               or sub-style N {compute/tally} flag
-    sub-style = sub-style of "pair hybrid"_pair_hybrid.html
-    N = which instance of sub-style (only if sub-style is used multiple times)
-      {special} which wt1 wt2 wt3 = override {special_bonds} settings (optional)
-        which = {lj/coul} or {lj} or {coul}
-        w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
-      {compute/tally} flag = {yes} or {no}
-  {mix} value = {geometric} or {arithmetic} or {sixthpower}
-  {shift} value = {yes} or {no}
-  {table} value = N
-    2^N = # of values in table
-  {table/disp} value = N
-    2^N = # of values in table
-  {tabinner} value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  {tabinner/disp} value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  {tail} value = {yes} or {no}
-  {compute} value = {yes} or {no}
-  {nofdotr} :pre
-:ule
-
-[Examples:]
-
-pair_modify shift yes mix geometric
-pair_modify tail yes
-pair_modify table 12
-pair_modify pair lj/cut compute no
-pair_modify pair tersoff compute/tally no
-pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0 :pre
-
-[Description:]
-
-Modify the parameters of the currently defined pair style.  Not all
-parameters are relevant to all pair styles.
-
-If used, the {pair} keyword must appear first in the list of keywords.
-It can only be used with the "hybrid and
-hybrid/overlay"_pair_hybrid.html pair styles.  It means that all the
-following parameters will only be modified for the specified
-sub-style.  If the sub-style is defined multiple times, then an
-additional numeric argument {N} must also be specified, which is a
-number from 1 to M where M is the number of times the sub-style was
-listed in the "pair_style hybrid"_pair_hybrid.html command.  The extra
-number indicates which instance of the sub-style the remaining
-keywords will be applied to.  Note that if the {pair} keyword is not
-used, and the pair style is {hybrid} or {hybrid/overlay}, then all the
-specified keywords will be applied to all sub-styles.
-
-The {special} and {compute/tally} keywords can [only] be used in
-conjunction with the {pair} keyword and must directly follow it.
-{special} allows to override the
-"special_bonds"_special_bonds.html settings for the specified sub-style.
-{compute/tally} allows to disable or enable registering
-"compute */tally"_compute_tally.html computes for a given sub-style.
-More details are given below.
-
-The {mix} keyword affects pair coefficients for interactions between
-atoms of type I and J, when I != J and the coefficients are not
-explicitly set in the input script.  Note that coefficients for I = J
-must be set explicitly, either in the input script via the
-"pair_coeff" command or in the "Pair Coeffs" section of the "data
-file"_read_data.html.  For some pair styles it is not necessary to
-specify coefficients when I != J, since a "mixing" rule will create
-them from the I,I and J,J settings.  The pair_modify {mix} value
-determines what formulas are used to compute the mixed coefficients.
-In each case, the cutoff distance is mixed the same way as sigma.
-
-Note that not all pair styles support mixing.  Also, some mix options
-are not available for certain pair styles.  See the doc page for
-individual pair styles for those restrictions.  Note also that the
-"pair_coeff"_pair_coeff.html command also can be to directly set
-coefficients for a specific I != J pairing, in which case no mixing is
-performed.
-
-mix {geometric}
-
-epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = sqrt(sigma_i * sigma_j) :pre
-
-mix {arithmetic}
-
-epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = (sigma_i + sigma_j) / 2 :pre
-
-mix {sixthpower}
-
-epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
-             (sigma_i^6 + sigma_j^6)
-sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
-
-The {shift} keyword determines whether a Lennard-Jones potential is
-shifted at its cutoff to 0.0.  If so, this adds an energy term to each
-pairwise interaction which will be included in the thermodynamic
-output, but does not affect pair forces or atom trajectories.  See the
-doc page for individual pair styles to see which ones support this
-option.
-
-The {table} and {table/disp} keywords apply to pair styles with a
-long-range Coulombic term or long-range dispersion term respectively;
-see the doc page for individual styles to see which potentials support
-these options.  If N is non-zero, a table of length 2^N is
-pre-computed for forces and energies, which can shrink their
-computational cost by up to a factor of 2.  The table is indexed via a
-bit-mapping technique "(Wolff)"_#Wolff1 and a linear interpolation is
-performed between adjacent table values.  In our experiments with
-different table styles (lookup, linear, spline), this method typically
-gave the best performance in terms of speed and accuracy.
-
-The choice of table length is a tradeoff in accuracy versus speed.  A
-larger N yields more accurate force computations, but requires more
-memory which can slow down the computation due to cache misses.  A
-reasonable value of N is between 8 and 16.  The default value of 12
-(table of length 4096) gives approximately the same accuracy as the
-no-table (N = 0) option.  For N = 0, forces and energies are computed
-directly, using a polynomial fit for the needed erfc() function
-evaluation, which is what earlier versions of LAMMPS did.  Values
-greater than 16 typically slow down the simulation and will not
-improve accuracy; values from 1 to 8 give unreliable results.
-
-The {tabinner} and {tabinner/disp} keywords set an inner cutoff above
-which the pairwise computation is done by table lookup (if tables are
-invoked), for the corresponding Coulombic and dispersion tables
-discussed with the {table} and {table/disp} keywords.  The smaller the
-cutoff is set, the less accurate the table becomes (for a given number
-of table values), which can require use of larger tables.  The default
-cutoff value is sqrt(2.0) distance units which means nearly all
-pairwise interactions are computed via table lookup for simulations
-with "real" units, but some close pairs may be computed directly
-(non-table) for simulations with "lj" units.
-
-When the {tail} keyword is set to {yes}, certain pair styles will add
-a long-range VanderWaals tail "correction" to the energy and pressure.
-These corrections are bookkeeping terms which do not affect dynamics,
-unless a constant-pressure simulation is being performed.  See the doc
-page for individual styles to see which support this option.  These
-corrections are included in the calculation and printing of
-thermodynamic quantities (see the "thermo_style"_thermo_style.html
-command).  Their effect will also be included in constant NPT or NPH
-simulations where the pressure influences the simulation box
-dimensions (e.g. the "fix npt"_fix_nh.html and "fix nph"_fix_nh.html
-commands).  The formulas used for the long-range corrections come from
-equation 5 of "(Sun)"_#Sun.
-
-NOTE: The tail correction terms are computed at the beginning of each
-run, using the current atom counts of each atom type.  If atoms are
-deleted (or lost) or created during a simulation, e.g. via the "fix
-gcmc"_fix_gcmc.html command, the correction factors are not
-re-computed.  If you expect the counts to change dramatically, you can
-break a run into a series of shorter runs so that the correction
-factors are re-computed more frequently.
-
-Several additional assumptions are inherent in using tail corrections,
-including the following:
-
-The simulated system is a 3d bulk homogeneous liquid. This option
-should not be used for systems that are non-liquid, 2d, have a slab
-geometry (only 2d periodic), or inhomogeneous. :ulb,l
-
-G(r), the radial distribution function (rdf), is unity beyond the
-cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
-LJ fluid), and it is probably a good idea to verify this assumption by
-checking the rdf.  The rdf is not exactly unity beyond the cutoff for
-each pair of interaction types, so the tail correction is necessarily
-an approximation. :l
-
-The tail corrections are computed at the beginning of each simulation
-run.  If the number of atoms changes during the run, e.g. due to atoms
-leaving the simulation domain, or use of the "fix gcmc"_fix_gcmc.html
-command, then the corrections are not updated to reflect the changed
-atom count.  If this is a large effect in your simulation, you should
-break the long run into several short runs, so that the correction
-factors are re-computed multiple times.
-
-Thermophysical properties obtained from calculations with this option
-enabled will not be thermodynamically consistent with the truncated
-force-field that was used.  In other words, atoms do not feel any LJ
-pair interactions beyond the cutoff, but the energy and pressure
-reported by the simulation include an estimated contribution from
-those interactions. :l
-:ule
-
-The {compute} keyword allows pairwise computations to be turned off,
-even though a "pair_style"_pair_style.html is defined.  This is not
-useful for running a real simulation, but can be useful for debugging
-purposes or for performing a "rerun"_rerun.html simulation, when you
-only wish to compute partial forces that do not include the pairwise
-contribution.
-
-Two examples are as follows.  First, this option allows you to perform
-a simulation with "pair_style hybrid"_pair_hybrid.html with only a
-subset of the hybrid sub-styles enabled.  Second, this option allows
-you to perform a simulation with only long-range interactions but no
-short-range pairwise interactions.  Doing this by simply not defining
-a pair style will not work, because the
-"kspace_style"_kspace_style.html command requires a Kspace-compatible
-pair style be defined.
-
-The {nofdotr} keyword allows to disable an optimization that computes
-the global stress tensor from the total forces and atom positions rather
-than from summing forces between individual pairs of atoms.
-
-:line
-
-The {special} keyword allows to override the 1-2, 1-3, and 1-4
-exclusion settings for individual sub-styles of a
-"hybrid pair style"_pair_hybrid.html. It requires 4 arguments similar
-to the "special_bonds"_special_bonds.html command, {which} and
-wt1,wt2,wt3.  The {which} argument can be {lj} to change the
-Lennard-Jones settings, {coul} to change the Coulombic settings,
-or {lj/coul} to change both to the same set of 3 values.  The wt1,wt2,wt3
-values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
-1-3, and 1-4 bond topology neighbors, respectively. The {special}
-keyword can only be used in conjunction with the {pair} keyword
-and has to directly follow it.
-
-NOTE: The global settings specified by the
-"special_bonds"_special_bonds.html command affect the construction of
-neighbor lists.  Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
-exclude those pairs from the neighbor list entirely.  Weights of 1.0
-store the neighbor with no weighting applied. Thus only global values
-different from exactly 0.0 or 1.0 can be overridden and an error is
-generated if the requested setting is not compatible with the global
-setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
-usually a sufficient workaround in this case without causing a
-significant error.
-
-The {compute/tally} keyword takes exactly 1 argument ({no} or {yes}),
-and allows to selectively disable or enable processing of the various
-"compute */tally"_compute_tally.html styles for a given
-"pair hybrid or hybrid/overlay"_pair_hybrid.html sub-style.
-
-NOTE: Any "pair_modify pair compute/tally" command must be issued
-[before] the corresponding compute style is defined.
-
-:line
-
-[Restrictions:] none
-
-You cannot use {shift} yes with {tail} yes, since those are
-conflicting options.  You cannot use {tail} yes with 2d simulations.
-
-[Related commands:]
-
-"pair_style"_pair_style.html, "pair_style hybrid"_pair_hybrid.html,
-pair_coeff"_pair_coeff.html, "thermo_style"_thermo_style.html,
-"compute */tally"_compute_tally.html
-
-[Default:]
-
-The option defaults are mix = geometric, shift = no, table = 12,
-tabinner = sqrt(2.0), tail = no, and compute = yes.
-
-Note that some pair styles perform mixing, but only a certain style of
-mixing.  See the doc pages for individual pair styles for details.
-
-:line
-
-:link(Wolff1)
-[(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
-
-:link(Sun)
-[(Sun)] Sun, J Phys Chem B, 102, 7338-7364 (1998).
diff --git a/doc/src/pair_momb.rst b/doc/src/pair_momb.rst
new file mode 100644
index 0000000000..e318d285a3
--- /dev/null
+++ b/doc/src/pair_momb.rst
@@ -0,0 +1,96 @@
+.. index:: pair\_style momb
+
+pair\_style momb command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style momb cutoff s6 d
+
+* cutoff = global cutoff (distance units)
+* s6 = global scaling factor of the exchange-correlation functional used (unitless)
+* d = damping scaling factor of Grimme's method (unitless)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style momb 12.0 0.75 20.0
+   pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
+
+   pair_coeff 1 2 momb 0.0 1.0 1.0 10.2847 2.361
+
+Description
+"""""""""""
+
+Style *momb* computes pairwise van der Waals (vdW) and short-range
+interactions using the Morse potential and :ref:`(Grimme) <Grimme>` method
+implemented in the Many-Body Metal-Organic (MOMB) force field
+described comprehensively in :ref:`(Fichthorn) <Fichthorn>` and
+:ref:`(Zhou) <Zhou4>`. Grimme's method is widely used to correct for
+dispersion in density functional theory calculations.
+
+.. image:: Eqs/pair_momb.jpg
+   :align: center
+
+For the *momb* pair style, the following coefficients must be defined
+for each pair of atoms types via the :doc:`pair\_coeff <pair_coeff>`
+command as in the examples above, or in the data file or restart files
+read by the :doc:`read\_data <read_data>` as described below:
+
+* D0 (energy units)
+* alpha (1/distance units)
+* r0 (distance units)
+* C6 (energy\*distance\^6 units)
+* Rr (distance units, typically sum of atomic vdW radii)
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the USER-MISC package. It is only enabled if
+LAMMPS is built with that package. See the :doc:`Build package <Build_package>` doc page on for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style morse <pair_morse>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Grimme:
+
+
+
+**(Grimme)** Grimme, J Comput Chem, 27(15), 1787-1799 (2006).
+
+.. _Fichthorn:
+
+
+
+**(Fichthorn)** Fichthorn, Balankura, Qi, CrystEngComm, 18(29), 5410-5417 (2016).
+
+.. _Zhou4:
+
+
+
+**(Zhou)** Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst
new file mode 100644
index 0000000000..61f2e08904
--- /dev/null
+++ b/doc/src/pair_morse.rst
@@ -0,0 +1,170 @@
+.. index:: pair\_style morse
+
+pair\_style morse command
+=========================
+
+pair\_style morse/gpu command
+=============================
+
+pair\_style morse/omp command
+=============================
+
+pair\_style morse/opt command
+=============================
+
+pair\_style morse/smooth/linear command
+=======================================
+
+pair\_style morse/smooth/linear/omp command
+===========================================
+
+pair\_style morse/kk command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *morse* or *morse/smooth/linear* or *morse/soft*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+    *morse* args = cutoff
+      cutoff = global cutoff for Morse interactions (distance units)
+    *morse/smooth/linear* args = cutoff
+      cutoff = global cutoff for Morse interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style morse 2.5
+   pair_style morse/smooth/linear 2.5
+   pair_coeff \* \* 100.0 2.0 1.5
+   pair_coeff 1 1 100.0 2.0 1.5 3.0
+
+Description
+"""""""""""
+
+Style *morse* computes pairwise interactions with the formula
+
+.. image:: Eqs/pair_morse.jpg
+   :align: center
+
+Rc is the cutoff.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* D0 (energy units)
+* alpha (1/distance units)
+* r0 (distance units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global morse
+cutoff is used.
+
+
+----------
+
+
+The *morse/smooth/linear* variant is similar to the lj/smooth/linear
+variant in that it adds to the potential a shift and a linear term
+so that both, potential energy and force, go to zero at the cut-off:
+
+.. image:: Eqs/pair_morse_smooth_linear.jpg
+   :align: center
+
+The syntax of the pair\_style and pair\_coeff commands are the same for
+the *morse* and *morse/smooth/linear* styles.
+
+
+----------
+
+
+A version of the *morse* style with a soft core, *morse/soft*\ , suitable for use in
+free energy calculations, is part of the USER-FEP package and is documented with
+the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is only
+available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+None of these pair styles support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+All of these pair styles support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table options is not relevant for
+the Morse pair styles.
+
+None of these pair styles support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+All of these pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *morse/smooth/linear* pair style is only enabled if LAMMPS was
+built with the USER-MISC package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst
new file mode 100644
index 0000000000..cd2032c799
--- /dev/null
+++ b/doc/src/pair_multi_lucy.rst
@@ -0,0 +1,234 @@
+.. index:: pair\_style multi/lucy
+
+pair\_style multi/lucy command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style multi/lucy style N keyword ...
+
+* style = *lookup* or *linear* = method of interpolation
+* N = use N values in *lookup*\ , *linear* tables
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style multi/lucy linear 1000
+   pair_coeff \* \* multibody.table ENTRY1 7.0
+
+Description
+"""""""""""
+
+Style *multi/lucy* computes a density-dependent force following from
+the many-body form described in :ref:`(Moore) <Moore1>` and
+:ref:`(Warren) <Warren1>` as
+
+.. image:: Eqs/pair_multi_lucy.jpg
+   :align: center
+
+which consists of a density-dependent function, A(rho), and a
+radial-dependent weight function, omegaDD(rij).  The radial-dependent
+weight function, omegaDD(rij), is taken as the Lucy function:
+
+.. image:: Eqs/pair_multi_lucy2.jpg
+   :align: center
+
+The density-dependent energy for a given particle is given by:
+
+.. image:: Eqs/pair_multi_lucy_energy.jpg
+   :align: center
+
+See the supporting information of :ref:`(Brennan) <Brennan1>` or the
+publication by :ref:`(Moore) <Moore1>` for more details on the functional
+form.
+
+An interpolation table is used to evaluate the density-dependent
+energy (Integral(A(rho)drho) and force (A(rho)).  Note that the
+pre-factor to the energy is computed after the interpolation, thus the
+Integral(A(rho)drho will have units of energy / length\^4.
+
+The interpolation table is created as a pre-computation by fitting
+cubic splines to the file values and interpolating the
+density-dependent energy and force at each of *N* densities.  During a
+simulation, the tables are used to interpolate the density-dependent
+energy and force as needed for each pair of particles separated by a
+distance *R*\ .  The interpolation is done in one of 2 styles: *lookup*
+and *linear*\ .
+
+For the *lookup* style, the density is used to find the nearest table
+entry, which is the density-dependent energy and force.
+
+For the *linear* style, the density is used to find the 2 surrounding
+table values from which the density-dependent energy and force are
+computed by linear interpolation.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* filename
+* keyword
+* cutoff (distance units)
+
+The filename specifies a file containing the tabulated
+density-dependent energy and force.  The keyword specifies a section
+of the file.  The cutoff is an optional coefficient.  If not
+specified, the outer cutoff in the table itself (see below) will be
+used to build an interpolation table that extend to the largest
+tabulated distance.  If specified, only file values up to the cutoff
+are used to create the interpolation table.  The format of this file
+is described below.
+
+
+----------
+
+
+The format of a tabulated file is a series of one or more sections,
+defined as follows (without the parenthesized comments):
+
+
+.. parsed-literal::
+
+   # Density-dependent function (one or more comment or blank lines)
+
+   DD-FUNCTION                (keyword is first text on line)
+   N 500 R 1.0 10.0           (N, R, RSQ parameters)
+                              (blank)
+   1 1.0 25.5 102.34          (index, density, energy/r\^4, force)
+   2 1.02 23.4 98.5
+   ...
+   500 10.0 0.001 0.003
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.  The first line begins with a keyword which
+identifies the section.  The line can contain additional text, but the
+initial text must match the argument specified in the pair\_coeff
+command.  The next line lists (in any order) one or more parameters
+for the table.  Each parameter is a keyword followed by one or more
+numeric values.
+
+The parameter "N" is required and its value is the number of table
+entries that follow.  Note that this may be different than the *N*
+specified in the :doc:`pair\_style multi/lucy <pair_multi_lucy>` command.
+Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the
+tabulated file.  What LAMMPS does is a preliminary interpolation by
+creating splines using the Nfile tabulated values as nodal points.  It
+uses these to interpolate the density-dependent energy and force at
+Ntable different points.  The resulting tables of length Ntable are
+then used as described above, when computing the density-dependent
+energy and force.  This means that if you want the interpolation
+tables of length Ntable to match exactly what is in the tabulated file
+(with effectively no preliminary interpolation), you should set Ntable
+= Nfile, and use the "RSQ" parameter.  This is because the internal
+table abscissa is always RSQ (separation distance squared), for
+efficient lookup.
+
+All other parameters are optional.  If "R" or "RSQ" does
+not appear, then the distances in each line of the table are used
+as-is to perform spline interpolation.  In this case, the table values
+can be spaced in *density* uniformly or however you wish to position table
+values in regions of large gradients.
+
+If used, the parameters "R" or "RSQ" are followed by 2 values *rlo*
+and *rhi*\ .  If specified, the density associated with each density-dependent
+energy and force value is computed from these 2 values (at high accuracy), rather
+than using the (low-accuracy) value listed in each line of the table.
+The density values in the table file are ignored in this case.
+For "R", distances uniformly spaced between *rlo* and *rhi* are
+computed; for "RSQ", squared distances uniformly spaced between
+*rlo\*rlo* and *rhi\*rhi* are computed.
+
+.. note::
+
+   If you use "R" or "RSQ", the tabulated distance values in the
+   file are effectively ignored, and replaced by new values as described
+   in the previous paragraph.  If the density value in the table is not
+   very close to the new value (i.e. round-off difference), then you will
+   be assigning density-dependent energy and force values to a different density,
+   which is probably not what you want.  LAMMPS will warn if this is occurring.
+
+Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+r (in density units), the 3rd value is the density-dependent function value
+(in energy units / length\^4), and the 4th is the force (in force units).  The
+density values must increase from one line to the next.
+
+Note that one file can contain many sections, each with a tabulated
+potential.  LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+The :doc:`pair\_modify <pair_modify>` shift, table, and tail options are
+not relevant for this pair style.
+
+This pair style writes the settings for the "pair\_style multi/lucy" command
+to :doc:`binary restart files <restart>`, so a pair\_style command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file, since it is tabulated in the potential files.  Thus, pair\_coeff
+commands do need to be specified in the restart input script.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Warren1:
+
+
+
+**(Warren)** Warren, Phys Rev E, 68, 066702 (2003).
+
+.. _Brennan1:
+
+
+
+**(Brennan)** Brennan, J Chem Phys Lett, 5, 2144-2149 (2014).
+
+.. _Moore1:
+
+
+
+**(Moore)** Moore, J Chem Phys, 144, 104501 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst
new file mode 100644
index 0000000000..977309e311
--- /dev/null
+++ b/doc/src/pair_multi_lucy_rx.rst
@@ -0,0 +1,285 @@
+.. index:: pair\_style multi/lucy/rx
+
+pair\_style multi/lucy/rx command
+=================================
+
+pair\_style multi/lucy/rx/kk command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style multi/lucy/rx style N keyword ...
+
+* style = *lookup* or *linear* = method of interpolation
+* N = use N values in *lookup*\ , *linear* tables
+* weighting = fractional or molecular (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style multi/lucy/rx linear 1000
+   pair_style multi/lucy/rx linear 1000 fractional
+   pair_style multi/lucy/rx linear 1000 molecular
+   pair_coeff \* \* multibody.table ENTRY1 h2o h2o 7.0
+   pair_coeff \* \* multibody.table ENTRY1 h2o 1fluid 7.0
+
+Description
+"""""""""""
+
+Style *multi/lucy/rx* is used in reaction DPD simulations, where the
+coarse-grained (CG) particles are composed of *m* species whose
+reaction rate kinetics are determined from a set of *n* reaction rate
+equations through the :doc:`fix rx <fix_rx>` command.  The species of
+one CG particle can interact with a species in a neighboring CG
+particle through a site-site interaction potential model.  Style
+*multi/lucy/rx* computes the site-site density-dependent force
+following from the many-body form described in :ref:`(Moore) <Moore2>` and
+:ref:`(Warren) <Warren2>` as
+
+.. image:: Eqs/pair_multi_lucy.jpg
+   :align: center
+
+which consists of a density-dependent function, A(rho), and a
+radial-dependent weight function, omegaDD(rij).  The radial-dependent
+weight function, omegaDD(rij), is taken as the Lucy function:
+
+.. image:: Eqs/pair_multi_lucy2.jpg
+   :align: center
+
+The density-dependent energy for a given particle is given by:
+
+.. image:: Eqs/pair_multi_lucy_energy.jpg
+   :align: center
+
+See the supporting information of :ref:`(Brennan) <Brennan2>` or the
+publication by :ref:`(Moore) <Moore2>` for more details on the functional
+form.
+
+An interpolation table is used to evaluate the density-dependent
+energy (Integral(A(rho)drho) and force (A(rho)).  Note that the
+pre-factor to the energy is computed after the interpolation, thus the
+Integral(A(rho)drho will have units of energy / length\^4.
+
+The interpolation table is created as a pre-computation by fitting
+cubic splines to the file values and interpolating the
+density-dependent energy and force at each of *N* densities.  During a
+simulation, the tables are used to interpolate the density-dependent
+energy and force as needed for each pair of particles separated by a
+distance *R*\ .  The interpolation is done in one of 2 styles: *lookup*
+and *linear*\ .
+
+For the *lookup* style, the density is used to find the nearest table
+entry, which is the density-dependent energy and force.
+
+For the *linear* style, the density is used to find the 2 surrounding
+table values from which the density-dependent energy and force are
+computed by linear interpolation.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* filename
+* keyword
+* species1
+* species2
+* cutoff (distance units)
+
+The filename specifies a file containing the tabulated
+density-dependent energy and force.  The keyword specifies a section
+of the file.  The cutoff is an optional coefficient.  If not
+specified, the outer cutoff in the table itself (see below) will be
+used to build an interpolation table that extend to the largest
+tabulated distance.  If specified, only file values up to the cutoff
+are used to create the interpolation table.  The format of this file
+is described below.
+
+The species tags define the site-site interaction potential between
+two species contained within two different particles.  The species
+tags must either correspond to the species defined in the reaction
+kinetics files specified with the :doc:`fix rx <fix_rx>` command or they
+must correspond to the tag "1fluid", signifying interaction with a
+product species mixture determined through a one-fluid approximation.
+The interaction potential is weighted by the geometric average of
+either the mole fraction concentrations or the number of molecules
+associated with the interacting coarse-grained particles (see the
+*fractional* or *molecular* weighting pair style options). The coarse-grained potential is
+stored before and after the reaction kinetics solver is applied, where
+the difference is defined to be the internal chemical energy (uChem).
+
+
+----------
+
+
+The format of a tabulated file is a series of one or more sections,
+defined as follows (without the parenthesized comments):
+
+
+.. parsed-literal::
+
+   # Density-dependent function (one or more comment or blank lines)
+
+   DD-FUNCTION                (keyword is first text on line)
+   N 500 R 1.0 10.0           (N, R, RSQ parameters)
+                              (blank)
+   1 1.0 25.5 102.34          (index, density, energy/r\^4, force)
+   2 1.02 23.4 98.5
+   ...
+   500 10.0 0.001 0.003
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.  The first line begins with a keyword which
+identifies the section.  The line can contain additional text, but the
+initial text must match the argument specified in the pair\_coeff
+command.  The next line lists (in any order) one or more parameters
+for the table.  Each parameter is a keyword followed by one or more
+numeric values.
+
+The parameter "N" is required and its value is the number of table
+entries that follow.  Note that this may be different than the *N*
+specified in the :doc:`pair\_style multi/lucy/rx <pair_multi_lucy_rx>`
+command.  Let Ntable = *N* in the pair\_style command, and Nfile = "N"
+in the tabulated file.  What LAMMPS does is a preliminary
+interpolation by creating splines using the Nfile tabulated values as
+nodal points.  It uses these to interpolate the density-dependent
+energy and force at Ntable different points.  The resulting tables of
+length Ntable are then used as described above, when computing the
+density-dependent energy and force.  This means that if you want the
+interpolation tables of length Ntable to match exactly what is in the
+tabulated file (with effectively no preliminary interpolation), you
+should set Ntable = Nfile, and use the "RSQ" parameter.  This is
+because the internal table abscissa is always RSQ (separation distance
+squared), for efficient lookup.
+
+All other parameters are optional.  If "R" or "RSQ" does not appear,
+then the distances in each line of the table are used as-is to perform
+spline interpolation.  In this case, the table values can be spaced in
+*density* uniformly or however you wish to position table values in
+regions of large gradients.
+
+If used, the parameters "R" or "RSQ" are followed by 2 values *rlo*
+and *rhi*\ .  If specified, the density associated with each
+density-dependent energy and force value is computed from these 2
+values (at high accuracy), rather than using the (low-accuracy) value
+listed in each line of the table.  The density values in the table
+file are ignored in this case.  For "R", distances uniformly spaced
+between *rlo* and *rhi* are computed; for "RSQ", squared distances
+uniformly spaced between *rlo\*rlo* and *rhi\*rhi* are computed.
+
+.. note::
+
+   If you use "R" or "RSQ", the tabulated distance values in the
+   file are effectively ignored, and replaced by new values as described
+   in the previous paragraph.  If the density value in the table is not
+   very close to the new value (i.e. round-off difference), then you will
+   be assigning density-dependent energy and force values to a different
+   density, which is probably not what you want.  LAMMPS will warn if
+   this is occurring.
+
+Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+r (in density units), the 3rd value is the density-dependent function
+value (in energy units / length\^4), and the 4th is the force (in force
+units).  The density values must increase from one line to the next.
+
+Note that one file can contain many sections, each with a tabulated
+potential.  LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+The :doc:`pair\_modify <pair_modify>` shift, table, and tail options are
+not relevant for this pair style.
+
+This pair style writes the settings for the "pair\_style multi/lucy/rx" command
+to :doc:`binary restart files <restart>`, so a pair\_style command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file, since it is tabulated in the potential files.  Thus, pair\_coeff
+commands do need to be specified in the restart input script.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** fractional weighting
+
+
+----------
+
+
+.. _Warren2:
+
+
+
+**(Warren)** Warren, Phys Rev E, 68, 066702 (2003).
+
+.. _Brennan2:
+
+
+
+**(Brennan)** Brennan, J Chem Phys Lett, 5, 2144-2149 (2014).
+
+.. _Moore2:
+
+
+
+**(Moore)** Moore, J Chem Phys, 144, 104501 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst
new file mode 100644
index 0000000000..ef00dec25a
--- /dev/null
+++ b/doc/src/pair_nb3b_harmonic.rst
@@ -0,0 +1,119 @@
+.. index:: pair\_style nb3b/harmonic
+
+pair\_style nb3b/harmonic command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style nb3b/harmonic
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style nb3b/harmonic
+   pair_coeff \* \* MgOH.nb3bharmonic Mg O H
+
+Description
+"""""""""""
+
+This pair style computes a non-bonded 3-body harmonic potential for the
+energy E of a system of atoms as
+
+.. image:: Eqs/pair_nb3b_harmonic.jpg
+   :align: center
+
+where *theta\_0* is the equilibrium value of the angle and *K* is a
+prefactor. Note that the usual 1/2 factor is included in *K*\ . The form
+of the potential is identical to that used in angle\_style *harmonic*\ ,
+but in this case, the atoms do not need to be explicitly bonded.
+
+Only a single pair\_coeff command is used with this style which
+specifies a potential file with parameters for specified elements.
+These are mapped to LAMMPS atom types by specifying N additional
+arguments after the filename in the pair\_coeff command, where N is the
+number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine a file SiC.nb3b.harmonic has potential values
+for Si and C.  If your LAMMPS simulation has 4 atoms types and you
+want the 1st 3 to be Si, and the 4th to be C, you would use the
+following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* SiC.nb3b.harmonic Si Si Si C
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the potential file.  The final C argument maps LAMMPS atom
+type 4 to the C element in the potential file.  If a mapping value is
+specified as NULL, the mapping is not performed.  This can be used
+when the potential is used as part of the *hybrid* pair style.  The
+NULL values are placeholders for atom types that will be used with
+other potentials. An example of a pair\_coeff command for use with the
+*hybrid* pair style is:
+
+pair\_coeff \* \* nb3b/harmonic MgOH.nb3b.harmonic Mg O H
+
+Three-body non-bonded harmonic files in the *potentials* directory of
+the LAMMPS distribution have a ".nb3b.harmonic" suffix.  Lines that
+are not blank or comments (starting with #) define parameters for a
+triplet of elements.
+
+Each entry has six arguments. The first three are atom types as
+referenced in the LAMMPS input file. The first argument specifies the
+central atom. The fourth argument indicates the *K* parameter. The
+fifth argument indicates *theta\_0*. The sixth argument indicates a
+separation cutoff in Angstroms.
+
+For a given entry, if the second and third arguments are identical,
+then the entry is for a cutoff for the distance between types 1 and 2
+(values for *K* and *theta\_0* are irrelevant in this case).
+
+For a given entry, if the first three arguments are all different,
+then the entry is for the *K* and *theta\_0* parameters (the cutoff in
+this case is irrelevant).
+
+It is required that the potential file contains entries for *all*
+permutations of the elements listed in the pair\_coeff command.
+If certain combinations are not parameterized the corresponding
+parameters should be set to zero. The potential file can also
+contain entries for additional elements which are not used in
+a particular simulation; LAMMPS ignores those entries.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style can only be used if LAMMPS was built with the MANYBODY
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst
new file mode 100644
index 0000000000..e188ce1d1f
--- /dev/null
+++ b/doc/src/pair_nm.rst
@@ -0,0 +1,201 @@
+.. index:: pair\_style nm/cut
+
+pair\_style nm/cut command
+==========================
+
+pair\_style nm/cut/coul/cut command
+===================================
+
+pair\_style nm/cut/coul/long command
+====================================
+
+pair\_style nm/cut/omp command
+==============================
+
+pair\_style nm/cut/coul/cut/omp command
+=======================================
+
+pair\_style nm/cut/coul/long/omp command
+========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *nm/cut* or *nm/cut/coul/cut* or *nm/cut/coul/long*
+* args = list of arguments for a particular style
+  
+  .. parsed-literal::
+  
+       *nm/cut* args = cutoff
+         cutoff = global cutoff for Pair interactions (distance units)
+       *nm/cut/coul/cut* args = cutoff (cutoff2)
+         cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
+         cutoff2 = global cutoff for Coulombic (optional) (distance units)
+       *nm/cut/coul/long* args = cutoff (cutoff2)
+         cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
+         cutoff2 = global cutoff for Coulombic (optional) (distance units)
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style nm/cut 12.0
+   pair_coeff \* \* 0.01 5.4 8.0 7.0
+   pair_coeff 1 1 0.01 4.4 7.0 6.0
+
+   pair_style nm/cut/coul/cut 12.0 15.0
+   pair_coeff \* \* 0.01 5.4 8.0 7.0
+   pair_coeff 1 1 0.01 4.4 7.0 6.0
+
+   pair_style nm/cut/coul/long 12.0 15.0
+   pair_coeff \* \* 0.01 5.4 8.0 7.0
+   pair_coeff 1 1 0.01 4.4 7.0 6.0
+
+Description
+"""""""""""
+
+Style *nm* computes site-site interactions based on the N-M potential
+by :ref:`Clarke <Clarke>`, mainly used for ionic liquids.  A site can
+represent a single atom or a united-atom site.  The energy of an
+interaction has the following form:
+
+.. image:: Eqs/pair_nm.jpg
+   :align: center
+
+Rc is the cutoff.
+
+Style *nm/cut/coul/cut* adds a Coulombic pairwise interaction given by
+
+.. image:: Eqs/pair_coulomb.jpg
+   :align: center
+
+where C is an energy-conversion constant, Qi and Qj are the charges on
+the 2 atoms, and epsilon is the dielectric constant which can be set
+by the :doc:`dielectric <dielectric>` command.  If one cutoff is
+specified in the pair\_style command, it is used for both the NM and
+Coulombic terms.  If two cutoffs are specified, they are used as
+cutoffs for the NM and Coulombic terms respectively.
+
+Styles *nm/cut/coul/long* compute the same
+Coulombic interactions as style *nm/cut/coul/cut* except that an
+additional damping factor is applied to the Coulombic term so it can
+be used in conjunction with the :doc:`kspace\_style <kspace_style>`
+command and its *ewald* or *pppm* option.  The Coulombic cutoff
+specified for this style means that pairwise interactions within this
+distance are computed directly; interactions outside that distance are
+computed in reciprocal space.
+
+For all of the *nm* pair styles, the following coefficients must
+be defined for each pair of atoms types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the
+examples above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands.
+
+* E0 (energy units)
+* r0 (distance units)
+* n (unitless)
+* m (unitless)
+* cutoff1 (distance units)
+* cutoff2 (distance units)
+
+The latter 2 coefficients are optional.  If not specified, the global
+NM and Coulombic cutoffs specified in the pair\_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both NM
+and Coulombic interactions for this type pair.  If both coefficients
+are specified, they are used as the NM and Coulombic cutoffs for this
+type pair.  You cannot specify 2 cutoffs for style *nm*\ , since it
+has no Coulombic terms.
+
+For *nm/cut/coul/long* only the NM cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair\_style command.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+These pair styles do not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+All of the *nm* pair styles supports the
+:doc:`pair\_modify <pair_modify>` shift option for the energy of the pair
+interaction.
+
+The *nm/cut/coul/long* pair styles support the
+:doc:`pair\_modify <pair_modify>` table option since they can tabulate
+the short-range portion of the long-range Coulombic interaction.
+
+All of the *nm* pair styles support the :doc:`pair\_modify <pair_modify>`
+tail option for adding a long-range tail correction to the energy and
+pressure for the NM portion of the pair interaction.
+
+All of the *nm* pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+All of the *nm* pair styles can only be used via the *pair* keyword of
+the :doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+Restrictions
+""""""""""""
+
+
+These pair styles are part of the MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Clarke:
+
+
+
+**(Clarke)** Clarke and Smith, J Chem Phys, 84, 2290 (1986).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_none.rst b/doc/src/pair_none.rst
new file mode 100644
index 0000000000..080bb1168a
--- /dev/null
+++ b/doc/src/pair_none.rst
@@ -0,0 +1,58 @@
+.. index:: pair\_style none
+
+pair\_style none command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style none
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style none
+
+Description
+"""""""""""
+
+Using a pair style of none means pair forces and energies are not
+computed.
+
+With this choice, the force cutoff is 0.0, which means that only atoms
+within the neighbor skin distance (see the :doc:`neighbor <neighbor>`
+command) are communicated between processors.  You must insure the
+skin distance is large enough to acquire atoms needed for computing
+bonds, angles, etc.
+
+A pair style of *none* will also prevent pairwise neighbor lists from
+being built.  However if the :doc:`neighbor <neighbor>` style is *bin*\ ,
+data structures for binning are still allocated.  If the neighbor skin
+distance is small, then these data structures can consume a large
+amount of memory.  So you should either set the neighbor style to
+*nsq* or set the skin distance to a larger value.
+
+See the :doc:`pair\_style zero <pair_zero>` for a way to trigger the
+building of a neighbor lists, but compute no pairwise interactions.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style zero <pair_zero>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst
new file mode 100644
index 0000000000..727f19c327
--- /dev/null
+++ b/doc/src/pair_oxdna.rst
@@ -0,0 +1,150 @@
+.. index:: pair\_style oxdna/excv
+
+pair\_style oxdna/excv command
+==============================
+
+pair\_style oxdna/stk command
+=============================
+
+pair\_style oxdna/hbond command
+===============================
+
+pair\_style oxdna/xstk command
+==============================
+
+pair\_style oxdna/coaxstk command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style1
+
+   pair_coeff \* \* style2 args
+
+* style1 = *hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk*
+
+* style2 = *oxdna/excv* or *oxdna/stk* or *oxdna/hbond* or *oxdna/xstk* or *oxdna/coaxstk*
+* args = list of arguments for these particular styles
+
+
+.. parsed-literal::
+
+     *oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+       seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
+       T = temperature (oxDNA units, 0.1 = 300 K)
+       xi = 1.3448 (temperature-independent coefficient in stacking strength)
+       kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
+     *oxdna/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+       seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+       eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+   pair_coeff \* \* oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+   pair_coeff \* \* oxdna/stk     seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+   pair_coeff \* \* oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff \* \* oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+   pair_coeff \* \* oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+Description
+"""""""""""
+
+The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA force field
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
+excluded volume interaction *oxdna/excv*\ , the stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk*
+and coaxial stacking interaction *oxdna/coaxstk* as well
+as the hydrogen-bonding interaction *oxdna/hbond* between complementary pairs of nucleotides on
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported :ref:`(Sulc) <Sulc1>`. Quasi-unique base-pairing between nucleotides can be achieved by using 
+more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
+This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
+up and down along the backbone.
+
+The exact functional form of the pair styles is rather complex.
+The individual potentials consist of products of modulation factors,
+which themselves are constructed from a number of more basic potentials
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
+We refer to :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>` and :ref:`(Ouldridge) <Ouldridge1>`
+for a detailed description of the oxDNA force field.
+
+.. note::
+
+   These pair styles have to be used together with the related oxDNA bond style
+   *oxdna/fene* for the connectivity of the phosphate backbone (see also documentation of
+   :doc:`bond\_style oxdna/fene <bond_oxdna>`). Most of the coefficients
+   in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
+   Exceptions are the first four coefficients after *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
+   and the first coefficient after *oxdna/hbond* (seq=seqdep in the above example).
+   When using a Langevin thermostat, e.g. through :doc:`fix langevin <fix_langevin>`
+   or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+   the temperature coefficients have to be matched to the one used in the fix.
+
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
+A simple python setup tool which creates single straight or helical DNA strands,
+DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
+
+Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
+this implementation.  The article contains general information
+on the model, its implementation and performance as well as the structure of
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA publications
+:ref:`(Ouldridge) <Ouldridge1>`, 
+:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
+and :ref:`(Sulc) <Sulc1>`.
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+:doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
+:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+ 
+**Default:** none
+
+
+----------
+
+.. _Henrich1:
+
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
+.. _Ouldridge-DPhil1:
+
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+.. _Ouldridge1:
+
+**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+
+.. _Sulc1:
+
+**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
deleted file mode 100644
index dfcd93c9a8..0000000000
--- a/doc/src/pair_oxdna.txt
+++ /dev/null
@@ -1,109 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style oxdna/excv command :h3
-pair_style oxdna/stk command :h3
-pair_style oxdna/hbond command :h3
-pair_style oxdna/xstk command :h3
-pair_style oxdna/coaxstk command :h3
-
-[Syntax:]
-
-pair_style style1 :pre
-
-pair_coeff * * style2 args :pre
-
-style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
-
-style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
-args = list of arguments for these particular styles :ul
-
-  {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    xi = temperature-independent coefficient in stacking strength
-    kappa = coefficient of linear temperature dependence in stacking strength
-  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
-    eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
-
-[Examples:]
-
-pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
-pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
-
-[Description:]
-
-The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
-excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
-and coaxial stacking interaction {oxdna/coaxstk} as well
-as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
-opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported "(Sulc)"_#Sulc1.
-
-The exact functional form of the pair styles is rather complex.
-The individual potentials consist of products of modulation factors,
-which themselves are constructed from a number of more basic potentials
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
-for a detailed description of the oxDNA force field.
-
-NOTE: These pair styles have to be used together with the related oxDNA bond style
-{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
-in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
-Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
-and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
-When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
-or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-the temperature coefficients have to be matched to the one used in the fix.
-
-Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
-A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-
-Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
-"Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
-"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
-
-[Default:] none
-
-:line
-
-:link(Henrich1)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
-
-:link(Sulc1)
-[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
-:link(Ouldridge-DPhil1)
-[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
-
-:link(Ouldridge1)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst
new file mode 100644
index 0000000000..77052da666
--- /dev/null
+++ b/doc/src/pair_oxdna2.rst
@@ -0,0 +1,160 @@
+.. index:: pair\_style oxdna2/excv
+
+pair\_style oxdna2/excv command
+===============================
+
+pair\_style oxdna2/stk command
+==============================
+
+pair\_style oxdna2/hbond command
+================================
+
+pair\_style oxdna2/xstk command
+===============================
+
+pair\_style oxdna2/coaxstk command
+==================================
+
+pair\_style oxdna2/dh command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style1
+
+   pair_coeff \* \* style2 args
+
+* style1 = *hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh*
+
+* style2 = *oxdna2/excv* or *oxdna2/stk* or *oxdna2/hbond* or *oxdna2/xstk* or *oxdna2/coaxstk* or *oxdna2/dh*
+* args = list of arguments for these particular styles
+
+
+.. parsed-literal::
+
+     *oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+       seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
+       T = temperature (oxDNA units, 0.1 = 300 K)
+       xi = 1.3523 (temperature-independent coefficient in stacking strength)
+       kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
+     *oxdna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+       seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+       eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
+     *oxdna2/dh* args = T rhos qeff
+       T = temperature (oxDNA units, 0.1 = 300 K)
+       rhos = salt concentration (mole per litre)
+       qeff = 0.815 (effective charge in elementary charges)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+   pair_coeff \* \* oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+   pair_coeff \* \* oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+   pair_coeff \* \* oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff \* \* oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+   pair_coeff \* \* oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+   pair_coeff \* \* oxdna2/dh      0.1 0.5 0.815
+
+Description
+"""""""""""
+
+The *oxdna2* pair styles compute the pairwise-additive parts of the oxDNA force field
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
+excluded volume interaction *oxdna2/excv*\ , the stacking *oxdna2/stk*\ , cross-stacking *oxdna2/xstk*
+and coaxial stacking interaction *oxdna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxdna2/dh*
+as well as the hydrogen-bonding interaction *oxdna2/hbond* between complementary pairs of nucleotides on
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported :ref:`(Sulc) <Sulc2>`. Quasi-unique base-pairing between nucleotides can be achieved by using 
+more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
+This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
+up and down along the backbone.
+
+The exact functional form of the pair styles is rather complex.
+The individual potentials consist of products of modulation factors,
+which themselves are constructed from a number of more basic potentials
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
+We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
+and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
+
+.. note::
+
+   These pair styles have to be used together with the related oxDNA2 bond style
+   *oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of
+   :doc:`bond\_style oxdna2/fene <bond_oxdna>`). Most of the coefficients
+   in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
+   Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
+   the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
+   after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat
+   e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+   the temperature coefficients have to be matched to the one used in the fix.
+
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
+A simple python setup tool which creates single straight or helical DNA strands,
+DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
+
+Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
+this implementation.  The article contains general information
+on the model, its implementation and performance as well as the structure of
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxDNA2 publications
+:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+:doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
+:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+
+**Default:** none
+
+
+----------
+
+.. _Henrich2:
+
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
+.. _Snodin2:
+
+**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
+
+.. _Sulc2:
+
+**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
+.. _Ouldridge-DPhil2:
+
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+.. _Ouldridge2:
+
+**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
deleted file mode 100644
index 3e462f384d..0000000000
--- a/doc/src/pair_oxdna2.txt
+++ /dev/null
@@ -1,118 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style oxdna2/excv command :h3
-pair_style oxdna2/stk command :h3
-pair_style oxdna2/hbond command :h3
-pair_style oxdna2/xstk command :h3
-pair_style oxdna2/coaxstk command :h3
-pair_style oxdna2/dh command :h3
-
-[Syntax:]
-
-pair_style style1 :pre
-
-pair_coeff * * style2 args :pre
-
-style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
-
-style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
-args = list of arguments for these particular styles :ul
-
-  {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    xi = temperature-independent coefficient in stacking strength 
-    kappa = coefficient of linear temperature dependence in stacking strength 
-  {oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
-    eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
-  {oxdna2/dh} args = T rhos qeff
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    rhos = salt concentration (mole per litre)
-    qeff = effective charge (elementary charges) :pre
-
-[Examples:]
-
-pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
-pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
-pair_coeff * * oxdna2/dh      0.1 1.0 0.815 :pre
-
-[Description:]
-
-The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
-excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
-and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
-as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
-opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported "(Sulc)"_#Sulc2.
-
-The exact functional form of the pair styles is rather complex.
-The individual potentials consist of products of modulation factors,
-which themselves are constructed from a number of more basic potentials
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
-and  "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
-
-NOTE: These pair styles have to be used together with the related oxDNA2 bond style
-{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
-in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
-Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
-the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients
-after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
-e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-the temperature coefficients have to be matched to the one used in the fix.
-
-Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
-A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-
-Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
-"Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
-"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
-
-[Default:] none
-
-:line
-
-:link(Henrich)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
-
-:link(Sulc2)
-[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
-:link(Snodin)
-[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
-
-:link(Ouldridge-DPhil2)
-[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
-
-:link(Ouldridge2)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst
new file mode 100644
index 0000000000..3cc6e7f4a6
--- /dev/null
+++ b/doc/src/pair_oxrna2.rst
@@ -0,0 +1,158 @@
+.. index:: pair_style oxrna2/excv
+
+pair_style oxrna2/excv command
+==============================
+
+pair_style oxrna2/stk command
+=============================
+
+pair_style oxrna2/hbond command
+===============================
+
+pair_style oxrna2/xstk command
+==============================
+
+pair_style oxrna2/coaxstk command
+=================================
+
+pair_style oxrna2/dh command
+============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style style1
+
+   pair_coeff * * style2 args
+
+* style1 = *hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh*
+
+* style2 = *oxrna2/excv* or *oxrna2/stk* or *oxrna2/hbond* or *oxrna2/xstk* or *oxrna2/coaxstk* or *oxrna2/dh*
+* args = list of arguments for these particular styles
+
+
+.. parsed-literal::
+
+     *oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+       seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
+       T = temperature (oxDNA units, 0.1 = 300 K)
+       xi = 1.40206 (temperature-independent coefficient in stacking strength)
+       kappa = 2.77 (coefficient of linear temperature dependence in stacking strength)
+     *oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 
+       seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+       eps = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs)
+     *oxrna2/dh* args = T rhos qeff
+       T = temperature (oxDNA units, 0.1 = 300 K)
+       rhos = salt concentration (mole per litre)
+       qeff = 1.02455 (effective charge in elementary charges)
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+   pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+   pair_coeff * * oxrna2/stk     seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+   pair_coeff * * oxrna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 1 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 2 3 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff 3 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+   pair_coeff * * oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
+   pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+   pair_coeff * * oxrna2/dh      0.1 0.5 1.02455
+
+Description
+"""""""""""
+
+The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
+excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-stacking *oxrna2/xstk*
+and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh*
+as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported :ref:`(Sulc2) <Sulc32>`. Quasi-unique base-pairing between nucleotides can be achieved by using 
+more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
+This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
+up and down along the backbone.
+
+The exact functional form of the pair styles is rather complex.
+The individual potentials consist of products of modulation factors,
+which themselves are constructed from a number of more basic potentials
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
+We refer to :ref:`(Sulc1) <Sulc31>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil3>`
+and  :ref:`(Ouldridge) <Ouldridge3>` for a detailed description of the oxRNA2 force field.
+
+.. note::
+
+   These pair styles have to be used together with the related oxDNA2 bond style
+   *oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of
+   :doc:`bond\_style oxrna2/fene <bond_oxdna>`). Most of the coefficients
+   in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
+   Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example),
+   the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients
+   after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat
+   e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+   the temperature coefficients have to be matched to the one used in the fix.
+
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
+A simple python setup tool which creates single straight or helical DNA strands,
+DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
+
+Please cite :ref:`(Henrich) <Henrich3>` in any publication that uses
+this implementation.  The article contains general information
+on the model, its implementation and performance as well as the structure of
+the data and input file. The preprint version of the article can be found
+`here <PDF/USER-CGDNA.pdf>`_.
+Please cite also the relevant oxRNA2 publications
+:ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair styles can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+:doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
+:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
+:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+
+**Default:**
+
+none
+
+
+----------
+
+.. _Henrich3:
+
+**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
+.. _Sulc31:
+
+**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
+
+.. _Sulc32:
+
+**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
+.. _Ouldridge-DPhil3:
+
+**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+.. _Ouldridge3:
+
+**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst
new file mode 100644
index 0000000000..284f3de32a
--- /dev/null
+++ b/doc/src/pair_peri.rst
@@ -0,0 +1,254 @@
+.. index:: pair\_style peri/pmb
+
+pair\_style peri/pmb command
+============================
+
+pair\_style peri/pmb/omp command
+================================
+
+pair\_style peri/lps command
+============================
+
+pair\_style peri/lps/omp command
+================================
+
+pair\_style peri/ves command
+============================
+
+pair\_style peri/eps command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style
+
+* style = *peri/pmb* or *peri/lps* or *peri/ves* or *peri/eps*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style peri/pmb
+   pair_coeff \* \* 1.6863e22 0.0015001 0.0005 0.25
+
+   pair_style peri/lps
+   pair_coeff \* \* 14.9e9 14.9e9 0.0015001 0.0005 0.25
+
+   pair_style peri/ves
+   pair_coeff \* \* 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
+
+   pair_style peri/eps
+   pair_coeff \* \* 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
+
+Description
+"""""""""""
+
+The peridynamic pair styles implement material models that can be used
+at the mesoscopic and macroscopic scales.  See `this document <PDF/PDLammps_overview.pdf>`_ for an overview of LAMMPS commands
+for Peridynamics modeling.
+
+Style *peri/pmb* implements the Peridynamic bond-based prototype
+microelastic brittle (PMB) model.
+
+Style *peri/lps* implements the Peridynamic state-based linear
+peridynamic solid (LPS) model.
+
+Style *peri/ves* implements the Peridynamic state-based linear
+peridynamic viscoelastic solid (VES) model.
+
+Style *peri/eps* implements the Peridynamic state-based elastic-plastic
+solid (EPS) model.
+
+The canonical papers on Peridynamics are :ref:`(Silling 2000) <Silling2000>`
+and :ref:`(Silling 2007) <Silling2007>`.  The implementation of Peridynamics
+in LAMMPS is described in :ref:`(Parks) <Parks>`.  Also see the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
+more details about its implementation.
+
+The peridynamic VES and EPS models in PDLAMMPS were implemented by
+R. Rahman and J. T. Foster at University of Texas at San Antonio.  The
+original VES formulation is described in "(Mitchell2011)" and the
+original EPS formulation is in "(Mitchell2011a)".  Additional PDF docs
+that describe the VES and EPS implementations are include in the
+LAMMPS distribution in `doc/PDF/PDLammps\_VES.pdf <PDF/PDLammps_VES.pdf>`_ and
+`doc/PDF/PDLammps\_EPS.pdf <PDF/PDLammps_EPS.pdf>`_.  For questions
+regarding the VES and EPS models in LAMMPS you can contact R. Rahman
+(rezwanur.rahman at utsa.edu).
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below.
+
+For the *peri/pmb* style:
+
+* c (energy/distance/volume\^2 units)
+* horizon (distance units)
+* s00 (unitless)
+* alpha (unitless)
+
+C is the effectively a spring constant for Peridynamic bonds, the
+horizon is a cutoff distance for truncating interactions, and s00 and
+alpha are used as a bond breaking criteria.  The units of c are such
+that c/distance = stiffness/volume\^2, where stiffness is
+energy/distance\^2 and volume is distance\^3.  See the users guide for
+more details.
+
+For the *peri/lps* style:
+
+* K (force/area units)
+* G (force/area units)
+* horizon (distance units)
+* s00 (unitless)
+* alpha (unitless)
+
+K is the bulk modulus and G is the shear modulus.  The horizon is a
+cutoff distance for truncating interactions, and s00 and alpha are
+used as a bond breaking criteria. See the users guide for more
+details.
+
+For the *peri/ves* style:
+
+* K (force/area units)
+* G (force/area units)
+* horizon (distance units)
+* s00 (unitless)
+* alpha (unitless)
+* m\_lambdai (unitless)
+* m\_taubi (unitless)
+
+K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance for truncating interactions, and s00 and alpha are
+used as a bond breaking criteria. m\_lambdai and m\_taubi are the
+viscoelastic relaxation parameter and time constant,
+respectively. m\_lambdai varies within zero to one. For very small
+values of m\_lambdai the viscoelastic model responds very similar to a
+linear elastic model. For details please see the description in
+"(Mtchell2011)".
+
+For the *peri/eps* style:
+
+* K (force/area units)
+* G (force/area units)
+* horizon (distance units)
+* s00 (unitless)
+* alpha (unitless)
+* m\_yield\_stress (force/area units)
+
+K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance and s00 and alpha are used as a bond breaking
+criteria.  m\_yield\_stress is the yield stress of the material. For
+details please see the description in "(Mtchell2011a)".
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+These pair styles do not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+These pair styles do not support the :doc:`pair\_modify <pair_modify>`
+shift option.
+
+The :doc:`pair\_modify <pair_modify>` table and tail options are not
+relevant for these pair styles.
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All of these styles are part of the PERI package. They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Parks:
+
+
+
+**(Parks)** Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11),
+777-783 (2008).
+
+.. _Silling2000:
+
+
+
+**(Silling 2000)** Silling, J Mech Phys Solids, 48, 175-209 (2000).
+
+.. _Silling2007:
+
+
+
+**(Silling 2007)** Silling, Epton, Weckner, Xu, Askari, J Elasticity,
+88, 151-184 (2007).
+
+.. _Mitchell2011:
+
+
+
+**(Mitchell2011)** Mitchell. A non-local, ordinary-state-based
+viscoelasticity model for peridynamics. Sandia National Lab Report,
+8064:1-28 (2011).
+
+.. _Mitchell2011a:
+
+
+
+**(Mitchell2011a)** Mitchell. A Nonlocal, Ordinary, State-Based
+Plasticity Model for Peridynamics. Sandia National Lab Report,
+3166:1-34 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst
new file mode 100644
index 0000000000..e9ab595011
--- /dev/null
+++ b/doc/src/pair_polymorphic.rst
@@ -0,0 +1,288 @@
+.. index:: pair\_style polymorphic
+
+pair\_style polymorphic command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style polymorphic
+
+style = *polymorphic*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style polymorphic
+   pair_coeff \* \* TlBr_msw.polymorphic Tl Br
+   pair_coeff \* \* AlCu_eam.polymorphic Al Cu
+   pair_coeff \* \* GaN_tersoff.polymorphic Ga N
+   pair_coeff \* \* GaN_sw.polymorphic GaN
+
+Description
+"""""""""""
+
+The *polymorphic* pair style computes a 3-body free-form potential
+(:ref:`Zhou <Zhou3>`) for the energy E of a system of atoms as
+
+.. image:: Eqs/polymorphic1.jpg
+   :align: center
+
+.. image:: Eqs/polymorphic2.jpg
+   :align: center
+
+.. image:: Eqs/polymorphic3.jpg
+   :align: center
+
+where I, J, K represent species of atoms i, j, and k, i\_1, ..., i\_N
+represents a list of i's neighbors, delta\_ij is a Direc constant
+(i.e., delta\_ij = 1 when i = j, and delta\_ij = 0 otherwise), eta\_ij is
+similar constant that can be set either to eta\_ij = delta\_ij or eta\_ij
+= 1 - delta\_ij depending on the potential type, U\_IJ(r\_ij),
+V\_IJ(r\_ij), W\_IK(r\_ik) are pair functions, G\_JIK(cos(theta)) is an
+angular function, P\_IK(delta r\_jik) is a function of atomic spacing
+differential delta r\_jik = r\_ij - xi\_IJ\*r\_ik with xi\_IJ being a
+pair-dependent parameter, and F\_IJ(X\_ij) is a function of the local
+environment variable X\_ij. This generic potential is fully defined
+once the constants eta\_ij and xi\_IJ, and the six functions U\_IJ(r\_ij),
+V\_IJ(r\_ij), W\_IK(r\_ik), G\_JIK(cos(theta)), P\_IK(delta r\_jik), and
+F\_IJ(X\_ij) are given. Note that these six functions are all one
+dimensional, and hence can be provided in an analytic or tabular
+form. This allows users to design different potentials solely based on
+a manipulation of these functions. For instance, the potential reduces
+to Stillinger-Weber potential (:ref:`SW <SW>`) if we set
+
+.. image:: Eqs/polymorphic4.jpg
+   :align: center
+
+The potential reduces to Tersoff types of potential
+(:ref:`Tersoff <Tersoff>` or :ref:`Albe <poly-Albe>`) if we set
+
+.. image:: Eqs/polymorphic5.jpg
+   :align: center
+
+.. image:: Eqs/polymorphic6.jpg
+   :align: center
+
+The potential reduces to Rockett-Tersoff (:ref:`Wang <Wang3>`) type if we set
+
+.. image:: Eqs/polymorphic7.jpg
+   :align: center
+
+.. image:: Eqs/polymorphic6.jpg
+   :align: center
+
+.. image:: Eqs/polymorphic8.jpg
+   :align: center
+
+The potential becomes embedded atom method (:ref:`Daw <poly-Daw>`) if we set
+
+.. image:: Eqs/polymorphic9.jpg
+   :align: center
+
+In the embedded atom method case, phi\_IJ(r\_ij) is the pair energy,
+F\_I(X) is the embedding energy, X is the local electron density, and
+f\_K(r) is the atomic electron density function.
+
+If the tabulated functions are created using the parameters of sw,
+tersoff, and eam potentials, the polymorphic pair style will produce
+the same global properties (energies and stresses) and the same forces
+as the sw, tersoff, and eam pair styles. The polymorphic pair style
+also produces the same atom properties (energies and stresses) as the
+corresponding tersoff and eam pair styles. However, due to a different
+partition of global properties to atom properties, the polymorphic
+pair style will produce different atom properties (energies and
+stresses) as the sw pair style. This does not mean that polymorphic
+pair style is different from the sw pair style in this case. It just
+means that the definitions of the atom energies and atom stresses are
+different.
+
+Only a single pair\_coeff command is used with the polymorphic style
+which specifies an potential file for all needed elements. These are
+mapped to LAMMPS atom types by specifying N additional arguments after
+the filename in the pair\_coeff command, where N is the number of
+LAMMPS atom types:
+
+* filename
+* N element names = mapping of Tersoff elements to atom types
+
+See the pair\_coeff doc page for alternate ways to specify the path for
+the potential file.  Several files for polymorphic potentials are
+included in the potentials dir of the LAMMPS distribution.  They have a
+"poly" suffix.
+
+As an example, imagine the SiC\_tersoff.polymorphic file has tabulated
+functions for Si-C tersoff potential. If your LAMMPS simulation has 4
+atoms types and you want the 1st 3 to be Si, and the 4th to be C, you
+would use the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* SiC_tersoff.polymorphic Si Si Si C
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom
+types. The first three Si arguments map LAMMPS atom types 1,2,3 to the
+Si element in the polymorphic file. The final C argument maps LAMMPS
+atom type 4 to the C element in the polymorphic file. If a mapping
+value is specified as NULL, the mapping is not performed. This can be
+used when an polymorphic potential is used as part of the hybrid pair
+style. The NULL values are placeholders for atom types that will be
+used with other potentials.
+
+Potential files in the potentials directory of the LAMMPS distribution
+have a ".poly" suffix. At the beginning of the files, an unlimited
+number of lines starting with '#' are used to describe the potential
+and are ignored by LAMMPS. The next line lists two numbers:
+
+
+.. parsed-literal::
+
+   ntypes eta
+
+Here ntypes represent total number of species defined in the potential
+file, and eta = 0 or 1. The number ntypes must equal the total number
+of different species defined in the pair\_coeff command. When eta = 1,
+eta\_ij defined in the potential functions above is set to 1 -
+delta\_ij, otherwise eta\_ij is set to delta\_ij. The next ntypes lines
+each lists two numbers and a character string representing atomic
+number, atomic mass, and name of the species of the ntypes elements:
+
+
+.. parsed-literal::
+
+   atomic_number atomic-mass element (1)
+   atomic_number atomic-mass element (2)
+   ...
+   atomic_number atomic-mass element (ntypes)
+
+The next ntypes\*(ntypes+1)/2 lines contain two numbers:
+
+
+.. parsed-literal::
+
+   cut xi (1)
+   cut xi (2)
+   ...
+   cut xi (ntypes\*(ntypes+1)/2)
+
+Here cut means the cutoff distance of the pair functions, xi is the
+same as defined in the potential functions above. The
+ntypes\*(ntypes+1)/2 lines are related to the pairs according to the
+sequence of first ii (self) pairs, i = 1, 2, ..., ntypes, and then
+then ij (cross) pairs, i = 1, 2, ..., ntypes-1, and j = i+1, i+2, ...,
+ntypes (i.e., the sequence of the ij pairs follows 11, 22, ..., 12,
+13, 14, ..., 23, 24, ...).
+
+The final blocks of the potential file are the U, V, W, P, G, and F
+functions are listed sequentially. First, U functions are given for
+each of the ntypes\*(ntypes+1)/2 pairs according to the sequence
+described above. For each of the pairs, nr values are listed. Next,
+similar arrays are given for V, W, and P functions. Then G functions
+are given for all the ntypes\*ntypes\*ntypes ijk triplets in a natural
+sequence i from 1 to ntypes, j from 1 to ntypes, and k from 1 to
+ntypes (i.e., ijk = 111, 112, 113, ..., 121, 122, 123 ..., 211, 212,
+...). Each of the ijk functions contains ng values. Finally, the F
+functions are listed for all ntypes\*(ntypes+1)/2 pairs, each
+containing nx values. Either analytic or tabulated functions can be
+specified. Currently, constant, exponential, sine and cosine analytic
+functions are available which are specified with: constant c1 , where
+f(x) = c1 exponential c1 c2 , where f(x) = c1 exp(c2\*x) sine c1 c2 ,
+where f(x) = c1 sin(c2\*x) cos c1 c2 , where f(x) = c1 cos(c2\*x)
+Tabulated functions are specified by spline n x1 x2, where n=number of
+point, (x1,x2)=range and then followed by n values evaluated uniformly
+over these argument ranges.  The valid argument ranges of the
+functions are between 0 <= r <= cut for the U(r), V(r), W(r)
+functions, -cutmax <= delta\_r <= cutmax for the P(delta\_r) functions,
+-1 <= costheta <= 1 for the G(costheta) functions, and 0 <= X <= maxX
+for the F(X) functions.
+
+**Mixing, shift, table tail correction, restart**\ :
+
+This pair styles does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write their information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+If using create\_atoms command, atomic masses must be defined in the
+input script. If using read\_data, atomic masses must be defined in the
+atomic structure data file.
+
+This pair style is part of the MANYBODY package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair potential requires the :doc:`newtion <newton>` setting to be
+"on" for pair interactions.
+
+The potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal :doc:`units <units>`. You can use
+any LAMMPS units, but you would need to create your own potential
+files.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+
+----------
+
+
+.. _Zhou3:
+
+
+
+**(Zhou)** X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and
+F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).
+
+.. _SW:
+
+
+
+**(SW)** F. H. Stillinger-Weber, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985).
+
+.. _Tersoff:
+
+
+
+**(Tersoff)** J. Tersoff, Phys. Rev. B, 39, 5566 (1989).
+
+.. _poly-Albe:
+
+
+
+**(Albe)** K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B,
+66, 035205 (2002).
+
+.. _Wang3:
+
+
+
+**(Wang)** J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991).
+
+.. _poly-Daw:
+
+
+
+**(Daw)** M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst
new file mode 100644
index 0000000000..53480ff286
--- /dev/null
+++ b/doc/src/pair_python.rst
@@ -0,0 +1,255 @@
+.. index:: pair\_style python
+
+pair\_style python command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style python cutoff
+
+cutoff = global cutoff for interactions in python potential classes
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style python 2.5
+   pair_coeff \* \* py_pot.LJCutMelt lj
+
+   pair_style hybrid/overlay coul/long 12.0 python 12.0
+   pair_coeff \* \* coul/long
+   pair_coeff \* \* python py_pot.LJCutSPCE OW NULL
+
+Description
+"""""""""""
+
+The *python* pair style provides a way to define pairwise additive
+potential functions as python script code that is loaded into LAMMPS
+from a python file which must contain specific python class definitions.
+This allows to rapidly evaluate different potential functions without
+having to modify and re-compile LAMMPS. Due to python being an
+interpreted language, however, the performance of this pair style is
+going to be significantly slower (often between 20x and 100x) than
+corresponding compiled code. This penalty can be significantly reduced
+through generating tabulations from the python code through the
+:doc:`pair\_write <pair_write>` command, which is supported by this style.
+
+Only a single pair\_coeff command is used with the *python* pair style
+which specifies a python class inside a python module or file that
+LAMMPS will look up in the current directory, the folder pointed to by
+the LAMMPS\_POTENTIALS environment variable or somewhere in your python
+path.  A single python module can hold multiple python pair class
+definitions. The class definitions itself have to follow specific
+rules that are explained below.
+
+Atom types in the python class are specified through symbolic
+constants, typically strings. These are mapped to LAMMPS atom types by
+specifying N additional arguments after the class name in the
+pair\_coeff command, where N must be the number of currently defined
+atom types:
+
+As an example, imagine a file *py\_pot.py* has a python potential class
+names *LJCutMelt* with parameters and potential functions for a two
+Lennard-Jones atom types labeled as 'LJ1' and 'LJ2'. In your LAMMPS
+input and you would have defined 3 atom types, out of which the first
+two are supposed to be using the 'LJ1' parameters and the third the
+'LJ2' parameters, then you would use the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* py_pot.LJCutMelt LJ1 LJ1 LJ2
+
+The first two arguments **must** be \* \* so as to span all LAMMPS atom
+types.  The first two LJ1 arguments map LAMMPS atom types 1 and 2 to
+the LJ1 atom type in the LJCutMelt class of the py\_pot.py file.  The
+final LJ2 argument maps LAMMPS atom type 3 to the LJ2 atom type the
+python file.  If a mapping value is specified as NULL, the mapping is
+not performed, any pair interaction with this atom type will be
+skipped. This can be used when a *python* potential is used as part of
+the *hybrid* or *hybrid/overlay* pair style. The NULL values are then
+placeholders for atom types that will be used with other potentials.
+
+
+----------
+
+
+The python potential file has to start with the following code:
+
+
+.. parsed-literal::
+
+   from __future_\_ import print_function
+   #
+   class LAMMPSPairPotential(object):
+       def __init__(self):
+           self.pmap=dict()
+           self.units='lj'
+       def map_coeff(self,name,ltype):
+           self.pmap[ltype]=name
+       def check_units(self,units):
+           if (units != self.units):
+              raise Exception("Conflicting units: %s vs. %s" % (self.units,units))
+
+Any classes with definitions of specific potentials have to be derived
+from this class and should be initialize in a similar fashion to the
+example given below.
+
+.. note::
+
+   The class constructor has to set up a data structure containing
+   the potential parameters supported by this class.  It should also
+   define a variable *self.units* containing a string matching one of the
+   options of LAMMPS' :doc:`units <units>` command, which is used to
+   verify, that the potential definition in the python class and in the
+   LAMMPS input match.
+
+Here is an example for a single type Lennard-Jones potential class
+*LJCutMelt* in reduced units, which defines an atom type *lj* for
+which the parameters epsilon and sigma are both 1.0:
+
+
+.. parsed-literal::
+
+   class LJCutMelt(LAMMPSPairPotential):
+       def __init__(self):
+           super(LJCutMelt,self).__init__()
+           # set coeffs: 48\*eps\*sig\*\*12, 24\*eps\*sig\*\*6,
+           #              4\*eps\*sig\*\*12,  4\*eps\*sig\*\*6
+           self.units = 'lj'
+           self.coeff = {'lj'  : {'lj'  : (48.0,24.0,4.0,4.0)}}
+
+The class also has to provide two methods for the computation of the
+potential energy and forces, which have be named *compute\_force*,
+and *compute\_energy*, which both take 3 numerical arguments:
+
+* rsq   = the square of the distance between a pair of atoms (float)
+* itype = the (numerical) type of the first atom
+* jtype = the (numerical) type of the second atom
+
+This functions need to compute the force and the energy, respectively,
+and use the result as return value. The functions need to use the
+*pmap* dictionary to convert the LAMMPS atom type number to the symbolic
+value of the internal potential parameter data structure. Following
+the *LJCutMelt* example, here are the two functions:
+
+
+.. parsed-literal::
+
+      def compute_force(self,rsq,itype,jtype):
+           coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
+           r2inv  = 1.0/rsq
+           r6inv  = r2inv\*r2inv\*r2inv
+           lj1 = coeff[0]
+           lj2 = coeff[1]
+           return (r6inv \* (lj1\*r6inv - lj2))\*r2inv
+
+       def compute_energy(self,rsq,itype,jtype):
+           coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
+           r2inv  = 1.0/rsq
+           r6inv  = r2inv\*r2inv\*r2inv
+           lj3 = coeff[2]
+           lj4 = coeff[3]
+           return (r6inv \* (lj3\*r6inv - lj4))
+
+.. note::
+
+   for consistency with the C++ pair styles in LAMMPS, the
+   *compute\_force* function follows the conventions of the Pair::single()
+   methods and does not return the full force, but the force scaled by
+   the distance between the two atoms, so this value only needs to be
+   multiplied by delta x, delta y, and delta z to conveniently obtain the
+   three components of the force vector between these two atoms.
+
+
+----------
+
+
+.. note::
+
+   The evaluation of scripted python code will slow down the
+   computation pair-wise interactions quite significantly. However, this
+   can be largely worked around through using the python pair style not
+   for the actual simulation, but to generate tabulated potentials on the
+   fly using the :doc:`pair\_write <pair_write>` command. Please see below
+   for an example LAMMPS input of how to build a table file:
+
+
+.. parsed-literal::
+
+   pair_style python 2.5
+   pair_coeff \* \* py_pot.LJCutMelt lj
+   shell rm -f melt.table
+   pair_write  1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj
+
+Note that it is strongly recommended to try to **delete** the potential
+table file before generating it. Since the *pair\_write* command will
+always **append** to a table file, while pair style table will use the
+**first match**\ . Thus when changing the potential function in the python
+class, the table pair style will still read the old variant unless the
+table file is first deleted.
+
+After switching the pair style to *table*\ , the potential tables need
+to be assigned to the LAMMPS atom types like this:
+
+
+.. parsed-literal::
+
+   pair_style      table linear 2000
+   pair_coeff      1  1  melt.table lj
+
+This can also be done for more complex systems.  Please see the
+*examples/python* folders for a few more examples.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+Mixing of potential parameters has to be handled inside the provided
+python module. The python pair style simply assumes that force and
+energy computation can be correctly performed for all pairs of atom
+types as they are mapped to the atom type labels inside the python
+potential class.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the PYTHON package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_write <pair_write>`,
+:doc:`pair style table <pair_table>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst
new file mode 100644
index 0000000000..3e953afebc
--- /dev/null
+++ b/doc/src/pair_quip.rst
@@ -0,0 +1,124 @@
+.. index:: pair\_style quip
+
+pair\_style quip command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style quip
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style      quip
+   pair_coeff      \* \* gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
+   pair_coeff      \* \* sw_example.xml "IP SW" 14
+
+Description
+"""""""""""
+
+Style *quip* provides an interface for calling potential routines from
+the QUIP package. QUIP is built separately, and then linked to
+LAMMPS. The most recent version of the QUIP package can be downloaded
+from GitHub:
+`https://github.com/libAtoms/QUIP <https://github.com/libAtoms/QUIP>`_. The
+interface is chiefly intended to be used to run Gaussian Approximation
+Potentials (GAP), which are described in the following publications:
+:ref:`(Bartok et al) <Bartok_2010>` and :ref:`(PhD thesis of Bartok) <Bartok_PhD>`.
+
+Only a single pair\_coeff command is used with the *quip* style that
+specifies a QUIP potential file containing the parameters of the
+potential for all needed elements in XML format. This is followed by a
+QUIP initialization string. Finally, the QUIP elements are mapped to
+LAMMPS atom types by specifying N atomic numbers, where N is the
+number of LAMMPS atom types:
+
+* QUIP filename
+* QUIP initialization string
+* N atomic numbers = mapping of QUIP elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+A QUIP potential is fully specified by the filename which contains the
+parameters of the potential in XML format, the initialization string,
+and the map of atomic numbers.
+
+GAP potentials can be obtained from the Data repository section of
+`http://www.libatoms.org <http://www.libatoms.org>`_, where the
+appropriate initialization strings are also advised. The list of
+atomic numbers must be matched to the LAMMPS atom types specified in
+the LAMMPS data file or elsewhere.
+
+Two examples input scripts are provided in the examples/USER/quip
+directory.
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-QUIP package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+QUIP potentials are parameterized in electron-volts and Angstroms and
+therefore should be used with LAMMPS metal :doc:`units <units>`.
+
+QUIP potentials are generally not designed to work with the scaling
+factors set by the :doc:`special\_bonds <special_bonds>` command.  The
+recommended setting in molecular systems is to include all
+interactions, i.e. to use *special\_bonds lj/coul 1.0 1.0 1.0*. Scaling
+factors > 0.0 will be ignored and treated as 1.0. The only exception
+to this rule is if you know that your QUIP potential needs to exclude
+bonded, 1-3, or 1-4 interactions and does not already do this exclusion
+within QUIP. Then a factor 0.0 needs to be used which will remove such
+pairs from the neighbor list. This needs to be very carefully tested,
+because it may remove pairs from the neighbor list that are still
+required.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+
+----------
+
+
+.. _Bartok\_2010:
+
+
+
+**(Bartok\_2010)** AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical
+Review Letters 104, 136403 (2010).
+
+.. _Bartok\_PhD:
+
+
+
+**(Bartok\_PhD)** A Bartok-Partay, PhD Thesis, University of Cambridge,
+(2010).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst
new file mode 100644
index 0000000000..b670711e8c
--- /dev/null
+++ b/doc/src/pair_reaxc.rst
@@ -0,0 +1,401 @@
+.. index:: pair\_style reax/c
+
+pair\_style reax/c command
+==========================
+
+pair\_style reax/c/kk command
+=============================
+
+pair\_style reax/c/omp command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style reax/c cfile keyword value
+
+* cfile = NULL or name of a control file
+* zero or more keyword/value pairs may be appended
+  
+  .. parsed-literal::
+  
+     keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap*
+       *checkqeq* value = *yes* or *no* = whether or not to require qeq/reax fix
+       *enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
+       *lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
+       *safezone* = factor used for array allocation
+       *mincap* = minimum size for array allocation
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style reax/c NULL
+   pair_style reax/c controlfile checkqeq no
+   pair_style reax/c NULL lgvdw yes
+   pair_style reax/c NULL safezone 1.6 mincap 100
+   pair_coeff \* \* ffield.reax C H O N
+
+Description
+"""""""""""
+
+Style *reax/c* computes the ReaxFF potential of van Duin, Goddard and
+co-workers.  ReaxFF uses distance-dependent bond-order functions to
+represent the contributions of chemical bonding to the potential
+energy. There is more than one version of ReaxFF. The version
+implemented in LAMMPS uses the functional forms documented in the
+supplemental information of the following paper: :ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`.  The version integrated into LAMMPS matches
+the most up-to-date version of ReaxFF as of summer 2010.  For more
+technical details about the pair reax/c implementation of ReaxFF, see
+the :ref:`(Aktulga) <Aktulga>` paper. The *reax/c* style was initially
+implemented as a stand-alone C code and is now integrated into LAMMPS
+as a package.
+
+The *reax/c/kk* style is a Kokkos version of the ReaxFF potential that
+is derived from the *reax/c* style. The Kokkos version can run on GPUs
+and can also use OpenMP multithreading. For more information about the
+Kokkos package, see :doc:`Packages details <Packages_details>` and
+:doc:`Speed kokkos <Speed_kokkos>` doc pages.  One important
+consideration when using the *reax/c/kk* style is the choice of either
+half or full neighbor lists. This setting can be changed using the
+Kokkos :doc:`package <package>` command.
+
+The *reax/c* style differs from the (obsolete) "pair\_style reax"
+command in the implementation details.  The *reax* style was a
+Fortran library, linked to LAMMPS.  The *reax* style has been removed
+from LAMMPS after the 12 December 2018 version.
+
+LAMMPS provides several different versions of ffield.reax in its
+potentials dir, each called potentials/ffield.reax.label.  These are
+documented in potentials/README.reax.  The default ffield.reax
+contains parameterizations for the following elements: C, H, O, N.
+
+The format of these files is identical to that used originally by van
+Duin.  We have tested the accuracy of *pair\_style reax/c* potential
+against the original ReaxFF code for the systems mentioned above.  You
+can use other ffield files for specific chemical systems that may be
+available elsewhere (but note that their accuracy may not have been
+tested).
+
+.. note::
+
+   We do not distribute a wide variety of ReaxFF force field files
+   with LAMMPS.  Adri van Duin's group at PSU is the central repository
+   for this kind of data as they are continuously deriving and updating
+   parameterizations for different classes of materials.  You can submit
+   a contact request at the Materials Computation Center (MCC) website
+   `https://www.mri.psu.edu/materials-computation-center/connect-mcc <https://www.mri.psu.edu/materials-computation-center/connect-mcc>`_,
+   describing the material(s) you are interested in modeling with ReaxFF.
+   They can tell you what is currently available or what it would take to
+   create a suitable ReaxFF parameterization.
+
+The *cfile* setting can be specified as NULL, in which case default
+settings are used. A control file can be specified which defines
+values of control variables. Some control variables are
+global parameters for the ReaxFF potential. Others define certain
+performance and output settings.
+Each line in the control file specifies the value for
+a control variable.  The format of the control file is described
+below.
+
+.. note::
+
+   The LAMMPS default values for the ReaxFF global parameters
+   correspond to those used by Adri van Duin's stand-alone serial
+   code. If these are changed by setting control variables in the control
+   file, the results from LAMMPS and the serial code will not agree.
+
+Examples using *pair\_style reax/c* are provided in the examples/reax
+sub-directory.
+
+Use of this pair style requires that a charge be defined for every
+atom.  See the :doc:`atom\_style <atom_style>` and
+:doc:`read\_data <read_data>` commands for details on how to specify
+charges.
+
+The ReaxFF parameter files provided were created using a charge
+equilibration (QEq) model for handling the electrostatic interactions.
+Therefore, by default, LAMMPS requires that the :doc:`fix qeq/reax <fix_qeq_reax>` command be used with *pair\_style reax/c*
+when simulating a ReaxFF model, to equilibrate charge each timestep.
+Using the keyword *checkqeq* with the value *no*
+turns off the check for *fix qeq/reax*\ ,
+allowing a simulation to be run without charge equilibration.
+In this case, the static charges you
+assign to each atom will be used for computing the electrostatic
+interactions in the system.
+See the :doc:`fix qeq/reax <fix_qeq_reax>` command for details.
+
+Using the optional keyword *lgvdw* with the value *yes* turns on the
+low-gradient correction of the ReaxFF/C for long-range London
+Dispersion, as described in the :ref:`(Liu) <Liu_2011>` paper. Force field
+file *ffield.reax.lg* is designed for this correction, and is trained
+for several energetic materials (see "Liu"). When using lg-correction,
+recommended value for parameter *thb* is 0.01, which can be set in the
+control file.  Note: Force field files are different for the original
+or lg corrected pair styles, using wrong ffield file generates an
+error message.
+
+Using the optional keyword *enobonds* with the value *yes*\ , the energy
+of atoms with no bonds (i.e. isolated atoms) is included in the total
+potential energy and the per-atom energy of that atom.  If the value
+*no* is specified then the energy of atoms with no bonds is set to
+zero.  The latter behavior is usual not desired, as it causes
+discontinuities in the potential energy when the bonding of an atom
+drops to zero.
+
+Optional keywords *safezone* and *mincap* are used for allocating
+reax/c arrays.  Increasing these values can avoid memory problems,
+such as segmentation faults and bondchk failed errors, that could
+occur under certain conditions. These keywords aren't used by the
+Kokkos version, which instead uses a more robust memory allocation
+scheme that checks if the sizes of the arrays have been exceeded and
+automatically allocates more memory.
+
+The thermo variable *evdwl* stores the sum of all the ReaxFF potential
+energy contributions, with the exception of the Coulombic and charge
+equilibration contributions which are stored in the thermo variable
+*ecoul*\ .  The output of these quantities is controlled by the
+:doc:`thermo <thermo>` command.
+
+This pair style tallies a breakdown of the total ReaxFF potential
+energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 14.
+The 14 values correspond to the following sub-categories (the variable
+names in italics match those used in the original FORTRAN ReaxFF
+code):
+
+1. *eb* = bond energy
+2. *ea* = atom energy
+3. *elp* = lone-pair energy
+4. *emol* = molecule energy (always 0.0)
+5. *ev* = valence angle energy
+6. *epen* = double-bond valence angle penalty
+7. *ecoa* = valence angle conjugation energy
+8. *ehb* = hydrogen bond energy
+9. *et* = torsion energy
+10. *eco* = conjugation energy
+11. *ew* = van der Waals energy
+12. *ep* = Coulomb energy
+13. *efi* = electric field energy (always 0.0)
+14. *eqeq* = charge equilibration energy
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+
+.. parsed-literal::
+
+   compute reax all pair reax/c
+   variable eb      equal c_reax[1]
+   variable ea      equal c_reax[2]
+   [...]
+   variable eqeq    equal c_reax[14]
+   thermo_style custom step temp epair v_eb v_ea [...] v_eqeq
+
+Only a single pair\_coeff command is used with the *reax/c* style which
+specifies a ReaxFF potential file with parameters for all needed
+elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N indices = ReaxFF elements
+
+The filename is the ReaxFF potential file.
+
+In the ReaxFF potential file, near the top, after the general
+parameters, is the atomic parameters section that contains element
+names, each with a couple dozen numeric parameters.  If there are M
+elements specified in the *ffield* file, think of these as numbered 1
+to M. Each of the N indices you specify for the N atom types of LAMMPS
+atoms must be an integer from 1 to M.  Atoms with LAMMPS type 1 will
+be mapped to whatever element you specify as the first index value,
+etc.  If a mapping value is specified as NULL, the mapping is not
+performed.  This can be used when the *reax/c* style is used as part
+of the *hybrid* pair style.  The NULL values are placeholders for atom
+types that will be used with other potentials.
+
+As an example, say your LAMMPS simulation has 4 atom types and the
+elements are ordered as C, H, O, N in the *ffield* file.  If you want
+the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
+H, you would use the following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* ffield.reax C C N H
+
+
+----------
+
+
+The format of a line in the control file is as follows:
+
+
+.. parsed-literal::
+
+   variable_name value
+
+and it may be followed by an "!" character and a trailing comment.
+
+If the value of a control variable is not specified, then default
+values are used.  What follows is the list of variables along with a
+brief description of their use and default values.
+
+simulation\_name: Output files produced by *pair\_style reax/c* carry
+this name + extensions specific to their contents.  Partial energies
+are reported with a ".pot" extension, while the trajectory file has
+".trj" extension.
+
+tabulate\_long\_range: To improve performance, long range interactions
+can optionally be tabulated (0 means no tabulation). Value of this
+variable denotes the size of the long range interaction table.  The
+range from 0 to long range cutoff (defined in the *ffield* file) is
+divided into *tabulate\_long\_range* points.  Then at the start of
+simulation, we fill in the entries of the long range interaction table
+by computing the energies and forces resulting from van der Waals and
+Coulomb interactions between every possible atom type pairs present in
+the input system.  During the simulation we consult to the long range
+interaction table to estimate the energy and forces between a pair of
+atoms. Linear interpolation is used for estimation. (default value =
+0)
+
+energy\_update\_freq: Denotes the frequency (in number of steps) of
+writes into the partial energies file. (default value = 0)
+
+nbrhood\_cutoff: Denotes the near neighbors cutoff (in Angstroms)
+regarding the bonded interactions. (default value = 5.0)
+
+hbond\_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
+bond interactions.(default value = 7.5. A value of 0.0 turns off
+hydrogen bonds)
+
+bond\_graph\_cutoff: is the threshold used in determining what is a
+physical bond, what is not. Bonds and angles reported in the
+trajectory file rely on this cutoff. (default value = 0.3)
+
+thb\_cutoff: cutoff value for the strength of bonds to be considered in
+three body interactions. (default value = 0.001)
+
+thb\_cutoff\_sq: cutoff value for the strength of bond order products
+to be considered in three body interactions. (default value = 0.00001)
+
+write\_freq: Frequency of writes into the trajectory file. (default
+value = 0)
+
+traj\_title: Title of the trajectory - not the name of the trajectory
+file.
+
+atom\_info: 1 means print only atomic positions + charge (default = 0)
+
+atom\_forces: 1 adds net forces to atom lines in the trajectory file
+(default = 0)
+
+atom\_velocities: 1 adds atomic velocities to atoms line (default = 0)
+
+bond\_info: 1 prints bonds in the trajectory file (default = 0)
+
+angle\_info: 1 prints angles in the trajectory file (default = 0)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-REAXC package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+The ReaxFF potential files provided with LAMMPS in the potentials
+directory are parameterized for real :doc:`units <units>`.  You can use
+the ReaxFF potential with any LAMMPS units, but you would need to
+create your own potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "real" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix qeq/reax <fix_qeq_reax>`, :doc:`fix reax/c/bonds <fix_reaxc_bonds>`, :doc:`fix reax/c/species <fix_reaxc_species>`
+
+Default
+"""""""
+
+The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no,
+safezone = 1.2, mincap = 50.
+
+
+----------
+
+
+.. _Chenoweth\_20082:
+
+
+
+**(Chenoweth\_2008)** Chenoweth, van Duin and Goddard,
+Journal of Physical Chemistry A, 112, 1040-1053 (2008).
+
+.. _Aktulga:
+
+
+
+(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
+245-259 (2012).
+
+.. _Liu\_2011:
+
+
+
+**(Liu)** L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal
+of Physical Chemistry A, 115, 11016-11022 (2011).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst
new file mode 100644
index 0000000000..2ddf7fb24d
--- /dev/null
+++ b/doc/src/pair_resquared.rst
@@ -0,0 +1,260 @@
+.. index:: pair\_style resquared
+
+pair\_style resquared command
+=============================
+
+pair\_style resquared/gpu command
+=================================
+
+pair\_style resquared/omp command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style resquared cutoff
+
+* cutoff = global cutoff for interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style resquared 10.0
+   pair_coeff \* \* 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
+
+Description
+"""""""""""
+
+Style *resquared* computes the RE-squared anisotropic interaction
+:ref:`(Everaers) <Everaers3>`, :ref:`(Babadi) <Babadi>` between pairs of
+ellipsoidal and/or spherical Lennard-Jones particles.  For ellipsoidal
+interactions, the potential considers the ellipsoid as being comprised
+of small spheres of size sigma.  LJ particles are a single sphere of
+size sigma.  The distinction is made to allow the pair style to make
+efficient calculations of ellipsoid/solvent interactions.
+
+Details for the equations used are given in the references below and
+in `this supplementary document <PDF/pair_resquared_extra.pdf>`_.
+
+Use of this pair style requires the NVE, NVT, or NPT fixes with the
+*asphere* extension (e.g. :doc:`fix nve/asphere <fix_nve_asphere>`) in
+order to integrate particle rotation.  Additionally, :doc:`atom\_style ellipsoid <atom_style>` should be used since it defines the
+rotational state and the size and shape of each ellipsoidal particle.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* A12 = Energy Prefactor/Hamaker constant (energy units)
+* sigma = atomic interaction diameter (distance units)
+* epsilon\_i_a = relative well depth of type I for side-to-side interactions
+* epsilon\_i_b = relative well depth of type I for face-to-face interactions
+* epsilon\_i_c = relative well depth of type I for end-to-end interactions
+* epsilon\_j_a = relative well depth of type J for side-to-side interactions
+* epsilon\_j_b = relative well depth of type J for face-to-face interactions
+* epsilon\_j_c = relative well depth of type J for end-to-end interactions
+* cutoff (distance units)
+
+The parameters used depend on the type of the interacting particles,
+i.e. ellipsoids or LJ spheres.  The type of a particle is determined
+by the diameters specified for its 3 shape parameters.  If all 3 shape
+parameters = 0.0, then the particle is treated as an LJ sphere.  The
+epsilon\_i_\* or epsilon\_j_\* parameters are ignored for LJ spheres.  If
+the 3 shape parameters are > 0.0, then the particle is treated as an
+ellipsoid (even if the 3 parameters are equal to each other).
+
+A12 specifies the energy prefactor which depends on the types of the
+two interacting particles.
+
+For ellipsoid/ellipsoid interactions, the interaction is computed by
+the formulas in the supplementary document referenced above.  A12 is
+the Hamaker constant as described in :ref:`(Everaers) <Everaers3>`. In LJ
+units:
+
+.. image:: Eqs/pair_resquared.jpg
+   :align: center
+
+where rho gives the number density of the spherical particles
+composing the ellipsoids and epsilon\_LJ determines the interaction
+strength of the spherical particles.
+
+For ellipsoid/LJ sphere interactions, the interaction is also computed
+by the formulas in the supplementary document referenced above.  A12
+has a modified form (see `here <PDF/pair_resquared_extra.pdf>`_ for
+details):
+
+.. image:: Eqs/pair_resquared2.jpg
+   :align: center
+
+For ellipsoid/LJ sphere interactions, a correction to the distance-
+of-closest approach equation has been implemented to reduce the error
+from two particles of disparate sizes; see `this supplementary document <PDF/pair_resquared_extra.pdf>`_.
+
+For LJ sphere/LJ sphere interactions, the interaction is computed
+using the standard Lennard-Jones formula, which is much cheaper to
+compute than the ellipsoidal formulas.  A12 is used as epsilon in the
+standard LJ formula:
+
+.. image:: Eqs/pair_resquared3.jpg
+   :align: center
+
+and the specified *sigma* is used as the sigma in the standard LJ
+formula.
+
+When one of both of the interacting particles are ellipsoids, then
+*sigma* specifies the diameter of the continuous distribution of
+constituent particles within each ellipsoid used to model the
+RE-squared potential.  Note that this is a different meaning for
+*sigma* than the :doc:`pair\_style gayberne <pair_gayberne>` potential
+uses.
+
+The epsilon\_i and epsilon\_j coefficients are defined for atom types,
+not for pairs of atom types.  Thus, in a series of pair\_coeff
+commands, they only need to be specified once for each atom type.
+
+Specifically, if any of epsilon\_i_a, epsilon\_i_b, epsilon\_i_c are
+non-zero, the three values are assigned to atom type I.  If all the
+epsilon\_i values are zero, they are ignored.  If any of epsilon\_j_a,
+epsilon\_j_b, epsilon\_j_c are non-zero, the three values are assigned
+to atom type J.  If all three epsilon\_i values are zero, they are
+ignored.  Thus the typical way to define the epsilon\_i and epsilon\_j
+coefficients is to list their values in "pair\_coeff I J" commands when
+I = J, but set them to 0.0 when I != J.  If you do list them when I !=
+J, you should insure they are consistent with their values in other
+pair\_coeff commands.
+
+Note that if this potential is being used as a sub-style of
+:doc:`pair\_style hybrid <pair_hybrid>`, and there is no "pair\_coeff I I"
+setting made for RE-squared for a particular type I (because I-I
+interactions are computed by another hybrid pair potential), then you
+still need to insure the epsilon a,b,c coefficients are assigned to
+that type in a "pair\_coeff I J" command.
+
+For large uniform molecules it has been shown that the epsilon\_\*\_\*
+energy parameters are approximately representable in terms of local
+contact curvatures :ref:`(Everaers) <Everaers3>`:
+
+.. image:: Eqs/pair_resquared4.jpg
+   :align: center
+
+where a, b, and c give the particle diameters.
+
+The last coefficient is optional.  If not specified, the global cutoff
+specified in the pair\_style command is used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance can be mixed, but only for sphere pairs.  The
+default mix value is *geometric*\ .  See the "pair\_modify" command for
+details.  Other type pairs cannot be mixed, due to the different
+meanings of the energy prefactors used to calculate the interactions
+and the implicit dependence of the ellipsoid-sphere interaction on the
+equation for the Hamaker constant presented here.  Mixing of sigma and
+epsilon followed by calculation of the energy prefactors using the
+equations above is recommended.
+
+This pair styles supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction, but only for sphere-sphere interactions.  There is no
+shifting performed for ellipsoidal interactions due to the anisotropic
+dependence of the interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords of the :doc:`run\_style command <run_style>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the ASPHERE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires that atoms be ellipsoids as defined by the
+:doc:`atom\_style ellipsoid <atom_style>` command.
+
+Particles acted on by the potential can be finite-size aspherical or
+spherical particles, or point particles.  Spherical particles have all
+3 of their shape parameters equal to each other.  Point particles have
+all 3 of their shape parameters equal to 0.0.
+
+The distance-of-closest-approach approximation used by LAMMPS becomes
+less accurate when high-aspect ratio ellipsoids are used.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix nve/asphere <fix_nve_asphere>`,
+:doc:`compute temp/asphere <compute_temp_asphere>`, :doc:`pair\_style gayberne <pair_gayberne>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Everaers3:
+
+
+
+**(Everaers)** Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
+
+.. _Babadi:
+
+
+
+**(Berardi)** Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst
new file mode 100644
index 0000000000..17694067c8
--- /dev/null
+++ b/doc/src/pair_sdk.rst
@@ -0,0 +1,203 @@
+.. index:: pair\_style lj/sdk
+
+pair\_style lj/sdk command
+==========================
+
+pair\_style lj/sdk/gpu command
+==============================
+
+pair\_style lj/sdk/kk command
+=============================
+
+pair\_style lj/sdk/omp command
+==============================
+
+pair\_style lj/sdk/coul/long command
+====================================
+
+pair\_style lj/sdk/coul/long/gpu command
+========================================
+
+pair\_style lj/sdk/coul/long/omp command
+========================================
+
+pair\_style lj/sdk/coul/msm command
+===================================
+
+pair\_style lj/sdk/coul/msm/omp command
+=======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *lj/sdk* or *lj/sdk/coul/long*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *lj/sdk* args = cutoff
+       cutoff = global cutoff for Lennard Jones interactions (distance units)
+     *lj/sdk/coul/long* args = cutoff (cutoff2)
+       cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/sdk 2.5
+   pair_coeff 1 1 lj12_6 1 1.1 2.8
+
+   pair_style lj/sdk/coul/long 10.0
+   pair_style lj/sdk/coul/long 10.0 12.0
+   pair_coeff 1 1 lj9_6 100.0 3.5 12.0
+
+   pair_style lj/sdk/coul/msm 10.0
+   pair_style lj/sdk/coul/msm 10.0 12.0
+   pair_coeff 1 1 lj9_6 100.0 3.5 12.0
+
+Description
+"""""""""""
+
+The *lj/sdk* styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
+given by
+
+.. image:: Eqs/pair_cmm.jpg
+   :align: center
+
+as required for the SDK Coarse-grained MD parameterization discussed in
+:ref:`(Shinoda) <Shinoda3>` and :ref:`(DeVane) <DeVane>`.  Rc is the cutoff.
+
+Style *lj/sdk/coul/long* computes the adds Coulombic interactions
+with an additional damping factor applied so it can be used in
+conjunction with the :doc:`kspace\_style <kspace_style>` command and
+its *ewald* or *pppm* or *pppm/cg* option.  The Coulombic cutoff
+specified for this style means that pairwise interactions within
+this distance are computed directly; interactions outside that
+distance are computed in reciprocal space.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cg\_type (lj9\_6, lj12\_4, or lj12\_6)
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff1 (distance units)
+
+Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum. The prefactors
+are chosen so that the potential minimum is at -epsilon.
+
+The latter 2 coefficients are optional.  If not specified, the global
+LJ and Coulombic cutoffs specified in the pair\_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair.  If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair.
+
+For *lj/sdk/coul/long* and *lj/sdk/coul/msm* only the LJ cutoff can be
+specified since a Coulombic cutoff cannot be specified for an
+individual I,J type pair.  All type pairs use the same global
+Coulombic cutoff specified in the pair\_style command.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp* or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP, and OPT packages respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, and rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed,
+since different pairs may have different exponents. So all parameters
+for all pairs have to be specified explicitly through the "pair\_coeff"
+command. Defining then in a data file is also not supported, due to
+limitations of that file format.
+
+All of the lj/sdk pair styles support the
+:doc:`pair\_modify <pair_modify>` shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+
+The *lj/sdk/coul/long* pair styles support the
+:doc:`pair\_modify <pair_modify>` table option since they can tabulate
+the short-range portion of the long-range Coulombic interaction.
+
+All of the lj/sdk pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+The lj/sdk and lj/cut/coul/long pair styles do not support
+the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa <run_style>` command.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All of the lj/sdk pair styles are part of the USER-CGSDK package.  The
+*lj/sdk/coul/long* style also requires the KSPACE package to be built
+(which is enabled by default).  They are only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`angle\_style sdk <angle_sdk>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Shinoda3:
+
+
+
+**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
+
+.. _DeVane:
+
+
+
+**(DeVane)**  Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst
new file mode 100644
index 0000000000..ec4ada108b
--- /dev/null
+++ b/doc/src/pair_sdpd_taitwater_isothermal.rst
@@ -0,0 +1,130 @@
+.. index:: pair\_style sdpd/taitwater/isothermal
+
+pair\_style sdpd/taitwater/isothermal command
+=============================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style sdpd/taitwater/isothermal temperature viscosity seed
+
+* temperature = temperature of the fluid (temperature units)
+* viscosity = dynamic viscosity of the fluid (mass\*distance/time units)
+* seed = random number generator seed (positive integer, optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style sdpd/taitwater/isothermal 300. 1. 28681
+   pair_coeff \* \* 1000.0 1430.0 2.4
+
+Description
+"""""""""""
+
+The sdpd/taitwater/isothermal style computes forces between mesoscopic
+particles according to the Smoothed Dissipative Particle Dynamics model
+described in this paper by :ref:`(Espanol and Revenga) <Espanol_Revenga>` under
+the following assumptions:
+
+
+
+#. The temperature is constant and uniform.
+#. The shear viscosity is constant and uniform.
+#. The volume viscosity is negligible before the shear viscosity.
+#. The Boltzmann constant is negligible before the heat capacity of a
+   single mesoscopic particle of fluid.
+
+The third assumption is true for water in nearly incompressible flows.
+The fourth holds true for water for any reasonable size one can
+imagine for a mesoscopic particle.
+
+The pressure forces between particles will be computed according to
+Tait's equation of state:
+
+.. image:: Eqs/pair_sph_tait.jpg
+   :align: center
+
+where gamma = 7 and B = c\_0\^2 rho\_0 / gamma, with rho\_0 being the
+reference density and c\_0 the reference speed of sound.
+
+The laminar viscosity and the random forces will be computed according
+to formulas described in :ref:`(Espanol and Revenga) <Espanol_Revenga>`.
+
+.. warning::
+
+   Similar to :doc:`brownian <pair_brownian>` and
+   :doc:`dpd <pair_dpd>` styles, the :doc:`newton <newton>` setting for
+   pairwise interactions needs to be on when running LAMMPS in parallel
+   if you want to ensure linear momentum conservation. Otherwise random
+   forces generated for pairs straddling processor boundary will not be
+   equal and opposite.
+
+.. note::
+
+   The actual random seed used will be a mix of what you specify
+   and other parameters like the MPI ranks. This is to ensure that
+   different MPI tasks have distinct seeds.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* rho0 reference density (mass/volume units)
+* c0 reference soundspeed (distance/time units)
+* h kernel function cutoff (distance units)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  It does not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-SDPD package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair coeff <pair_coeff>`, :doc:`pair sph/rhosum <pair_sph_rhosum>`
+
+Default
+"""""""
+
+The default seed is 0 (before mixing).
+
+
+----------
+
+
+.. _Espanol\_Revenga:
+
+
+
+**(Espanol and Revenga)** Espanol, Revenga, Physical Review E, 67, 026705 (2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst
new file mode 100644
index 0000000000..5af530aabb
--- /dev/null
+++ b/doc/src/pair_smd_hertz.rst
@@ -0,0 +1,73 @@
+.. index:: pair\_style smd/hertz
+
+pair\_style smd/hertz command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style smd/hertz scale_factor
+
+Examples
+""""""""
+
+pair\_style smd/hertz 1.0
+pair\_coeff 1 1 <contact\_stiffness>
+
+Description
+"""""""""""
+
+The *smd/hertz* style calculates contact forces between SPH particles
+belonging to different physical bodies.
+
+The contact forces are calculated using a Hertz potential, which
+evaluates the overlap between two particles (whose spatial extents are
+defined via its contact radius).  The effect is that a particles
+cannot penetrate into each other.  The parameter <contact\_stiffness>
+has units of pressure and should equal roughly one half of the Young's
+modulus (or bulk modulus in the case of fluids) of the material model
+associated with the SPH particles.
+
+The parameter *scale\_factor* can be used to scale the particles'
+contact radii. This can be useful to control how close particles can
+approach each other. Usually, *scale\_factor* =1.0.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+No mixing is performed automatically.  Currently, no part of USER-SMD
+supports restarting nor minimization.  rRESPA does not apply to this
+pair style.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst
new file mode 100644
index 0000000000..02343b678f
--- /dev/null
+++ b/doc/src/pair_smd_tlsph.rst
@@ -0,0 +1,89 @@
+.. index:: pair\_style smd/tlsph
+
+pair\_style smd/tlsph command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style smd/tlsph args
+
+Examples
+""""""""
+
+pair\_style smd/tlsph
+
+Description
+"""""""""""
+
+The *smd/tlsph* style computes particle interactions according to
+continuum mechanics constitutive laws and a Total-Lagrangian
+Smooth-Particle Hydrodynamics algorithm.
+
+This pair style is invoked with the following command:
+
+
+.. parsed-literal::
+
+   pair_style smd/tlsph
+   pair_coeff i j \*COMMON rho0 E nu Q1 Q2 hg Cp &
+                  \*END
+
+Here, *i* and *j* denote the *LAMMPS* particle types for which this
+pair style is defined. Note that *i* and *j* must be equal, i.e., no
+*tlsph* cross interactions between different particle types are
+allowed.  In contrast to the usual *LAMMPS* *pair coeff* definitions,
+which are given solely a number of floats and integers, the *tlsph*
+*pair coeff* definition is organized using keywords. These keywords
+mark the beginning of different sets of parameters for particle
+properties, material constitutive models, and damage models. The *pair
+coeff* line must be terminated with the *\*END* keyword. The use the
+line continuation operator *&* is recommended. A typical invocation of
+the *tlsph* for a solid body would consist of an equation of state for
+computing the pressure (the diagonal components of the stress tensor),
+and a material model to compute shear stresses (the off-diagonal
+components of the stress tensor). Damage and failure models can also
+be added.
+
+Please see the `SMD user guide <PDF/SMD_LAMMPS_userguide.pdf>`_ for a
+complete listing of the possible keywords and material models.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+No mixing is performed automatically.  Currently, no part of USER-SMD
+supports restarting nor minimization.  rRESPA does not apply to this
+pair style.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst
new file mode 100644
index 0000000000..07b08a95f2
--- /dev/null
+++ b/doc/src/pair_smd_triangulated_surface.rst
@@ -0,0 +1,74 @@
+.. index:: pair\_style smd/tri\_surface
+
+pair\_style smd/tri\_surface command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style smd/tri_surface scale_factor
+
+Examples
+""""""""
+
+pair\_style smd/tri\_surface 1.0
+pair\_coeff 1 1 <contact\_stiffness>
+
+Description
+"""""""""""
+
+The *smd/tri\_surface* style calculates contact forces between SPH
+particles and a rigid wall boundary defined via the
+:doc:`smd/wall\_surface <fix_smd_wall_surface>` fix.
+
+The contact forces are calculated using a Hertz potential, which
+evaluates the overlap between a particle (whose spatial extents are
+defined via its contact radius) and the triangle.  The effect is that
+a particle cannot penetrate into the triangular surface.  The
+parameter <contact\_stiffness> has units of pressure and should equal
+roughly one half of the Young's modulus (or bulk modulus in the case
+of fluids) of the material model associated with the SPH particle
+
+The parameter *scale\_factor* can be used to scale the particles'
+contact radii. This can be useful to control how close particles can
+approach the triangulated surface. Usually, *scale\_factor* =1.0.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+No mixing is performed automatically.
+Currently, no part of USER-SMD supports restarting nor minimization.
+rRESPA does not apply to this pair style.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst
new file mode 100644
index 0000000000..cd97a799a3
--- /dev/null
+++ b/doc/src/pair_smd_ulsph.rst
@@ -0,0 +1,104 @@
+.. index:: pair\_style smd/ulsph
+
+pair\_style smd/ulsph command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style smd/ulsph args
+
+* these keywords must be given
+
+
+.. parsed-literal::
+
+   keyword = *\*DENSITY_SUMMATION* or *\*DENSITY_CONTINUITY* and *\*VELOCITY_GRADIENT* or *\*NO_VELOCITY_GRADIENT* and *\*GRADIENT_CORRECTION* or *\*NO_GRADIENT_CORRECTION*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style smd/ulsph \*DENSITY_CONTINUITY \*VELOCITY_GRADIENT \*NO_GRADIENT_CORRECTION
+
+Description
+"""""""""""
+
+The *smd/ulsph* style computes particle interactions according to
+continuum mechanics constitutive laws and an updated Lagrangian
+Smooth-Particle Hydrodynamics algorithm.
+
+This pair style is invoked similar to the following command:
+
+
+.. parsed-literal::
+
+   pair_style smd/ulsph \*DENSITY_CONTINUITY \*VELOCITY_GRADIENT \*NO_GRADIENT_CORRECTION
+   pair_coeff i j \*COMMON rho0 c0 Q1 Cp hg &
+                  \*END
+
+Here, *i* and *j* denote the *LAMMPS* particle types for which this
+pair style is defined. Note that *i* and *j* can be different, i.e.,
+*ulsph* cross interactions between different particle types are
+allowed. However, *i*\ --\ *i* respectively *j*\ --\ *j* pair\_coeff lines have
+to precede a cross interaction.  In contrast to the usual *LAMMPS*
+*pair coeff* definitions, which are given solely a number of floats
+and integers, the *ulsph* *pair coeff* definition is organized using
+keywords. These keywords mark the beginning of different sets of
+parameters for particle properties, material constitutive models, and
+damage models. The *pair coeff* line must be terminated with the
+*\*END* keyword. The use the line continuation operator *&* is
+recommended. A typical invocation of the *ulsph* for a solid body
+would consist of an equation of state for computing the pressure (the
+diagonal components of the stress tensor), and a material model to
+compute shear stresses (the off-diagonal components of the stress
+tensor).
+
+Note that the use of \*GRADIENT\_CORRECTION can lead to severe numerical
+instabilities. For a general fluid simulation, \*NO\_GRADIENT\_CORRECTION
+is recommended.
+
+Please see the `SMD user guide <PDF/SMD_LAMMPS_userguide.pdf>`_ for a
+complete listing of the possible keywords and material models.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+No mixing is performed automatically.  Currently, no part of USER-SMD
+supports restarting nor minimization.  rRESPA does not apply to this
+pair style.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This fix is part of the USER-SMD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst
new file mode 100644
index 0000000000..cb57f6ba98
--- /dev/null
+++ b/doc/src/pair_smtbq.rst
@@ -0,0 +1,300 @@
+.. index:: pair\_style smtbq
+
+pair\_style smtbq command
+=========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style smtbq
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style smtbq
+   pair_coeff \* \* ffield.smtbq.Al2O3 O Al
+
+Description
+"""""""""""
+
+This pair style computes a variable charge SMTB-Q (Second-Moment
+tight-Binding QEq) potential as described in :ref:`SMTB-Q\_1 <SMTB-Q_1>` and
+:ref:`SMTB-Q\_2 <SMTB-Q_2>`. Briefly, the energy of metallic-oxygen systems
+is given by three contributions:
+
+.. image:: Eqs/pair_smtbq1.jpg
+   :align: center
+
+where *E<sub>tot</sub>* is the total potential energy of the system,
+*E<sub>ES</sub>* is the electrostatic part of the total energy,
+*E<sub>OO</sub>* is the interaction between oxygen atoms and
+*E<sub>MO</sub>* is a short-range interaction between metal and oxygen
+atoms. This interactions depend on interatomic distance
+*r<sub>ij</sub>* and/or the charge *Q<sub>i</sub>* of atoms
+*i*\ . Cut-off function enables smooth convergence to zero interaction.
+
+The parameters appearing in the upper expressions are set in the
+ffield.SMTBQ.Syst file where Syst corresponds to the selected system
+(e.g. field.SMTBQ.Al2O3). Examples for TiO<sub>2</sub>,
+Al<sub>2</sub>O<sub>3</sub> are provided.  A single pair\_coeff command
+is used with the SMTBQ styles which provides the path to the potential
+file with parameters for needed elements. These are mapped to LAMMPS
+atom types by specifying additional arguments after the potential
+filename in the pair\_coeff command. Note that atom type 1 must always
+correspond to oxygen atoms. As an example, to simulate a TiO2 system,
+atom type 1 has to be oxygen and atom type 2 Ti. The following
+pair\_coeff command should then be used:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
+
+The electrostatic part of the energy consists of two components 
+
+self-energy of atom *i* in the form of a second order charge dependent
+polynomial and a long-range Coulombic electrostatic interaction. The
+latter uses the wolf summation method described in :ref:`Wolf <Wolf2>`,
+spherically truncated at a longer cutoff, *R<sub>coul</sub>*\ . The
+charge of each ion is modeled by an orbital Slater which depends on
+the principal quantum number (\ *n*\ ) of the outer orbital shared by the
+ion.
+
+Interaction between oxygen, *E<sub>OO</sub>*\ , consists of two parts,
+an attractive and a repulsive part. The attractive part is effective
+only at short range (< r<sub>2</sub><sup>OO</sup>). The attractive
+contribution was optimized to study surfaces reconstruction
+(e.g. :ref:`SMTB-Q\_2 <SMTB-Q_2>` in TiO<sub>2</sub>) and is not necessary
+for oxide bulk modeling. The repulsive part is the Pauli interaction
+between the electron clouds of oxygen. The Pauli repulsion and the
+coulombic electrostatic interaction have same cut off value. In the
+ffield.SMTBQ.Syst, the keyword *'buck'* allows to consider only the
+repulsive O-O interactions. The keyword *'buckPlusAttr'* allows to
+consider the repulsive and the attractive O-O interactions.
+
+The short-range interaction between metal-oxygen, *E<sub>MO</sub>* is
+based on the second moment approximation of the density of states with
+a N-body potential for the band energy term,
+*E<sup>i</sup><sub>cov</sub>*\ , and a Born-Mayer type repulsive terms
+as indicated by the keyword *'second\_moment'* in the
+ffield.SMTBQ.Syst. The energy band term is given by:
+
+.. image:: Eqs/pair_smtbq2.jpg
+   :align: center
+
+where *&#951<sub>i</sub>* is the stoichiometry of atom *i*\ ,
+*&#948Q<sub>i</sub>* is the charge delocalization of atom *i*\ ,
+compared to its formal charge
+*Q<sup>F</sup><sub>i</sub>*\ . n<sub>0</sub>, the number of hybridized
+orbitals, is calculated with to the atomic orbitals shared
+*d<sub>i</sub>* and the stoichiometry
+*&#951<sub>i</sub>*\ . *r<sub>c1</sub>* and *r<sub>c2</sub>* are the two
+cutoff radius around the fourth neighbors in the cutoff function.
+
+In the formalism used here, *&#958<sup>0</sup>* is the energy
+parameter. *&#958<sup>0</sup>* is in tight-binding approximation the
+hopping integral between the hybridized orbitals of the cation and the
+anion. In the literature we find many ways to write the hopping
+integral depending on whether one takes the point of view of the anion
+or cation. These are equivalent vision. The correspondence between the
+two visions is explained in appendix A of the article in the
+SrTiO<sub>3</sub> :ref:`SMTB-Q\_3 <SMTB-Q_3>` (parameter *&#946* shown in
+this article is in fact the *&#946<sub>O</sub>*\ ). To summarize the
+relationship between the hopping integral *&#958<sup>0</sup>* and the
+others, we have in an oxide C<sub>n</sub>O<sub>m</sub> the following
+relationship:
+
+.. image:: Eqs/pair_smtbq3.jpg
+   :align: center
+
+Thus parameter &#956, indicated above, is given by : &#956 = (&#8730n
++ &#8730m) &#8260 2
+
+The potential offers the possibility to consider the polarizability of
+the electron clouds of oxygen by changing the slater radius of the
+charge density around the oxygen atoms through the parameters *rBB, rB and
+rS* in the ffield.SMTBQ.Syst. This change in radius is performed
+according to the method developed by E. Maras
+:ref:`SMTB-Q\_2 <SMTB-Q_2>`. This method needs to determine the number of
+nearest neighbors around the oxygen. This calculation is based on
+first (\ *r<sub>1n</sub>*\ ) and second (\ *r<sub>2n</sub>*\ ) distances
+neighbors.
+
+The SMTB-Q potential is a variable charge potential. The equilibrium
+charge on each atom is calculated by the electronegativity
+equalization (QEq) method. See :ref:`Rick <Rick3>` for further detail. One
+can adjust the frequency, the maximum number of iterative loop and the
+convergence of the equilibrium charge calculation. To obtain the
+energy conservation in NVE thermodynamic ensemble, we recommend to use
+a convergence parameter in the interval 10<sup>-5</sup> -
+10<sup>-6</sup> eV.
+
+The ffield.SMTBQ.Syst files are provided for few systems. They consist
+of nine parts and the lines beginning with '#' are comments (note that
+the number of comment lines matter). The first sections are on the
+potential parameters and others are on the simulation options and
+might be modified. Keywords are character type and must be enclosed in
+quotation marks ('').
+
+1) Number of different element in the oxide:
+
+* N<sub>elem</sub>= 2 or 3
+* Divided line
+
+2) Atomic parameters
+
+For the anion (oxygen) 
+
+* Name of element (char) and stoichiometry in oxide
+* Formal charge and mass of element
+* Principal quantum number of outer orbital (\ *n*\ ), electronegativity (\ *&#967<sup>0</sup><sub>i</simulationub>*\ ) and hardness (\ *J<sup>0</sup><sub>i</sub>*\ )
+* Ionic radius parameters  : max coordination number (\ *coordBB* = 6 by default), bulk coordination number *(coordB)*\ , surface coordination number  *(coordS)* and *rBB, rB and rS*  the slater radius for each coordination number. (<b>note : If you don't want to change the slater radius, use three identical radius values</b>)
+* Number of orbital shared by the element in the oxide (\ *d<sub>i</sub>*\ )
+* Divided line
+
+For each cations (metal):
+
+* Name of element (char) and stoichiometry in oxide
+* Formal charge and mass of element
+* Number of electron in outer orbital *(ne)*\ , electronegativity (\ *&#967<sup>0</sup><sub>i</simulationub>*\ ), hardness (\ *J<sup>0</sup><sub>i</sub>*\ ) and *r<sub>Salter</sub>* the slater radius for the cation.
+* Number of orbitals shared by the elements in the oxide (\ *d<sub>i</sub>*\ )
+* Divided line
+
+3) Potential parameters:
+
+* Keyword for element1, element2 and interaction potential ('second\_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2.  If the potential is 'second\_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
+* Potential parameter: <pre><br/> If type of potential is 'second\_moment' : *A (eV)*\ , *p*\ , *&#958<sup>0</sup>* (eV) and *q* <br/> *r<sub>c1</sub>* (&#197), *r<sub>c2</sub>* (&#197) and *r<sub>0</sub>* (&#197) <br/> If type of potential is 'buck' : *C* (eV) and *&#961* (&#197) <br/> If type of potential is 'buckPlusAttr' : *C* (eV) and *&#961* (&#197) <br/> *D* (eV), *B* (&#197<sup>-1</sup>), *r<sub>1</sub><sup>OO</sup>* (&#197) and *r<sub>2</sub><sup>OO</sup>* (&#197) </pre>
+* Divided line
+
+4) Tables parameters:
+
+* Cutoff radius for the Coulomb interaction (\ *R<sub>coul</sub>*\ )
+* Starting radius  (\ *r<sub>min</sub>* = 1,18845 &#197) and increments (\ *dr* = 0,001 &#197) for creating the potential table.
+* Divided line
+
+5) Rick model parameter:
+
+* *Nevery* : parameter to set the frequency (\ *1/Nevery*\ ) of the charge resolution. The charges are evaluated each *Nevery* time steps.
+* Max number of iterative loop (\ *loopmax*\ ) and precision criterion (\ *prec*\ ) in eV of the charge resolution
+* Divided line
+
+6) Coordination parameter:
+
+* First (\ *r<sub>1n</sub>*\ ) and second (\ *r<sub>2n</sub>*\ ) neighbor distances in &#197
+* Divided line
+
+7) Charge initialization mode:
+
+* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Q<sub>init</sub>*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Q<sub>init</sub>*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create\_atom"#create\_atom command or the charge specified in the file structure using :doc:`read\_data <read_data>` command.
+* Divided line
+
+8) Mode for the electronegativity equalization (Qeq) 
+
+* Keyword mode: <pre> <br/> QEqAll  (one QEq group) \|   no parameters <br/> QEqAllParallel (several QEq groups) \|   no parameters <br/> Surface \|   zlim   (QEq only for z>zlim)   </pre>
+* Parameter if necessary
+* Divided line
+
+9) Verbose 
+
+* If you want the code to work in verbose mode or not : 'true' or 'false'
+* If you want to print or not in file 'Energy\_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and *N<sub>Energy</sub>*\ . This option writes in file every *N<sub>Energy</sub>* time step. If the value is 'false' then *N<sub>Energy</sub>* = 0. The file take into account the possibility to have several QEq group *g* then it writes: time step, number of atoms in group *g*\ , electrostatic part of energy, *E<sub>ES</sub>*\ , the interaction between oxygen, *E<sub>OO</sub>*\ , and short range metal-oxygen interaction, *E<sub>MO</sub>*\ .
+* If you want to print in file 'Electroneg\_component.txt' the electronegativity component (\ *&#8706E<sub>tot</sub> &#8260&#8706Q<sub>i</sub>*\ ) or not: 'true' or 'false' and *N<sub>Electroneg</sub>*\ .This option writes in file every *N<sub>Electroneg</sub>* time step. If the value is 'false' then *N<sub>Electroneg</sub>* = 0.  The file consist in atom number *i*\ , atom type (1 for oxygen and # higher than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge of atom *i*\ , electrostatic part of atom *i* electronegativity, covalent part of atom *i* electronegativity, the hopping integral of atom *i* *(Z&#946<sup>2</sup>)<sub>i<sub>* and box electronegativity.
+
+.. note::
+
+   This last option slows down the calculation dramatically.  Use
+   only with a single processor simulation.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info:**
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+needs to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+**Restriction:**
+
+This pair style is part of the USER-SMTBQ package and is only enabled
+if LAMMPS is built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This potential requires using atom type 1 for oxygen and atom type
+higher than 1 for metal atoms.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The SMTB-Q potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal :doc:`units <units>`.
+
+
+----------
+
+
+**Citing this work:**
+
+Please cite related publication: N. Salles, O. Politano, E. Amzallag
+and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
+
+
+----------
+
+
+.. _SMTB-Q\_1:
+
+
+
+**(SMTB-Q\_1)** N. Salles, O. Politano, E. Amzallag, R. Tetot,
+Comput. Mater. Sci. 111 (2016) 181-189
+
+.. _SMTB-Q\_2:
+
+
+
+**(SMTB-Q\_2)** E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
+H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399
+
+.. _SMTB-Q\_3:
+
+
+
+**(SMTB-Q\_3)** R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
+Science 616, 19-8722 28 (2013)
+
+.. _Wolf2:
+
+
+
+**(Wolf)** D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
+Phys, 110, 8254 (1999).
+
+.. _Rick3:
+
+
+
+**(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
+(1994).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst
new file mode 100644
index 0000000000..1b0fb0f385
--- /dev/null
+++ b/doc/src/pair_snap.rst
@@ -0,0 +1,252 @@
+.. index:: pair\_style snap
+
+pair\_style snap command
+========================
+
+pair\_style snap/kk command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style snap
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style snap
+   pair_coeff \* \* InP.snapcoeff InP.snapparam In In P P
+
+Description
+"""""""""""
+
+Pair style *snap* computes interactions using the spectral
+neighbor analysis potential (SNAP) :ref:`(Thompson) <Thompson20142>`.
+Like the GAP framework of Bartok et al. :ref:`(Bartok2010) <Bartok20102>`,
+:ref:`(Bartok2013) <Bartok2013>` which uses bispectrum components
+to characterize the local neighborhood of each atom
+in a very general way. The mathematical definition of the
+bispectrum calculation used by SNAP is identical
+to that used by :doc:`compute sna/atom <compute_sna_atom>`.
+In SNAP, the total energy is decomposed into a sum over
+atom energies. The energy of atom *i* is
+expressed as a weighted sum over bispectrum components.
+
+.. image:: Eqs/pair_snap.jpg
+   :align: center
+
+where *B\_k\^i* is the *k*\ -th bispectrum component of atom *i*\ ,
+and *beta\_k\^alpha\_i* is the corresponding linear coefficient
+that depends on *alpha\_i*, the SNAP element of atom *i*\ . The
+number of bispectrum components used and their definitions
+depend on the value of *twojmax*
+defined in the SNAP parameter file described below.
+The bispectrum calculation is described in more detail
+in :doc:`compute sna/atom <compute_sna_atom>`.
+
+Note that unlike for other potentials, cutoffs for SNAP potentials are
+not set in the pair\_style or pair\_coeff command; they are specified in
+the SNAP potential files themselves.
+
+Only a single pair\_coeff command is used with the *snap* style which
+specifies a SNAP coefficient file followed by a SNAP parameter file
+and then N additional arguments specifying the mapping of SNAP
+elements to LAMMPS atom types, where N is the number of
+LAMMPS atom types:
+
+* SNAP coefficient file
+* SNAP parameter file
+* N element names = mapping of SNAP elements to atom types
+
+As an example, if a LAMMPS indium phosphide simulation has 4 atoms
+types, with the first two being indium and the 3rd and 4th being
+phophorous, the pair\_coeff command would look like this:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* snap InP.snapcoeff InP.snapparam In In P P
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The two filenames are for the coefficient and parameter files, respectively.
+The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
+SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
+3 and 4 to the SNAP 'P' element.
+
+If a SNAP mapping value is
+specified as NULL, the mapping is not performed.
+This can be used when a *snap* potential is used as part of the
+*hybrid* pair style.  The NULL values are placeholders for atom types
+that will be used with other potentials.
+
+The name of the SNAP coefficient file usually ends in the
+".snapcoeff" extension. It may contain coefficients
+for many SNAP elements. The only requirement is that it
+contain at least those element names appearing in the
+LAMMPS mapping list.
+The name of the SNAP parameter file usually ends in the ".snapparam"
+extension. It contains a small number
+of parameters that define the overall form of the SNAP potential.
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for these files.
+
+Quite commonly,
+SNAP potentials are combined with one or more other LAMMPS pair styles
+using the *hybrid/overlay* pair style. As an example, the SNAP
+tantalum potential provided in the LAMMPS potentials directory
+combines the *snap* and *zbl* pair styles. It is invoked
+by the following commands:
+
+
+.. parsed-literal::
+
+           variable zblcutinner equal 4
+           variable zblcutouter equal 4.8
+           variable zblz equal 73
+           pair_style hybrid/overlay &
+           zbl ${zblcutinner} ${zblcutouter} snap
+           pair_coeff \* \* zbl 0.0
+           pair_coeff 1 1 zbl ${zblz}
+           pair_coeff \* \* snap Ta06A.snapcoeff Ta06A.snapparam Ta
+
+It is convenient to keep these commands in a separate file that can
+be inserted in any LAMMPS input script using the :doc:`include <include>`
+command.
+
+The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict
+format after that. The first non-blank non-comment
+line must contain two integers:
+
+* nelem  = Number of elements
+* ncoeff = Number of coefficients
+
+This is followed by one block for each of the *nelem* elements.
+The first line of each block contains three entries:
+
+* Element symbol (text string)
+* R = Element radius (distance units)
+* w = Element weight (dimensionless)
+
+This line is followed by *ncoeff* coefficients, one per line.
+
+The SNAP parameter file can contain blank and comment lines (start
+with #) anywhere. Each non-blank non-comment line must contain one
+keyword/value pair. The required keywords are *rcutfac* and
+*twojmax*\ . Optional keywords are *rfac0*\ , *rmin0*\ ,
+*switchflag*\ , and *bzeroflag*\ .
+
+The default values for these keywords are
+
+* *rfac0* = 0.99363
+* *rmin0* = 0.0
+* *switchflag* = 0
+* *bzeroflag* = 1
+* *quadraticflag* = 1
+
+Detailed definitions for all the keywords are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page.
+If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term,
+0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
+The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
+for each element, the upper-triangular elements of alpha.
+
+.. note::
+
+   The previously used *diagonalstyle* keyword was removed in 2019,
+   since all known SNAP potentials use the default value of 3.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above.  You never need to
+specify a pair\_coeff command with I != J arguments for this style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the SNAP package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute sna/atom <compute_sna_atom>`,
+:doc:`compute snad/atom <compute_sna_atom>`,
+:doc:`compute snav/atom <compute_sna_atom>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Thompson20142:
+
+
+
+**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).
+
+.. _Bartok20102:
+
+
+
+**(Bartok2010)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
+
+.. _Bartok2013:
+
+
+
+**(Bartok2013)** Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst
new file mode 100644
index 0000000000..9e81b26c10
--- /dev/null
+++ b/doc/src/pair_soft.rst
@@ -0,0 +1,158 @@
+.. index:: pair\_style soft
+
+pair\_style soft command
+========================
+
+pair\_style soft/gpu command
+============================
+
+pair\_style soft/omp command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style soft cutoff
+
+* cutoff = global cutoff for soft interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style soft 1.0
+   pair_coeff \* \* 10.0
+   pair_coeff 1 1 10.0 3.0
+
+   pair_style soft 1.0
+   pair_coeff \* \* 0.0
+   variable prefactor equal ramp(0,30)
+   fix 1 all adapt 1 pair soft a \* \* v_prefactor
+
+Description
+"""""""""""
+
+Style *soft* computes pairwise interactions with the formula
+
+.. image:: Eqs/pair_soft.jpg
+   :align: center
+
+It is useful for pushing apart overlapping atoms, since it does not
+blow up as r goes to 0.  A is a pre-factor that can be made to vary in
+time from the start to the end of the run (see discussion below),
+e.g. to start with a very soft potential and slowly harden the
+interactions over time.  Rc is the cutoff.  See the :doc:`fix nve/limit <fix_nve_limit>` command for another way to push apart
+overlapping atoms.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* A (energy units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global soft
+cutoff is used.
+
+.. note::
+
+   The syntax for :doc:`pair\_coeff <pair_coeff>` with a single A
+   coeff is different in the current version of LAMMPS than in older
+   versions which took two values, Astart and Astop, to ramp between
+   them.  This functionality is now available in a more general form
+   through the :doc:`fix adapt <fix_adapt>` command, as explained below.
+   Note that if you use an old input script and specify Astart and Astop
+   without a cutoff, then LAMMPS will interpret that as A and a cutoff,
+   which is probably not what you want.
+
+The :doc:`fix adapt <fix_adapt>` command can be used to vary A for one
+or more pair types over the course of a simulation, in which case
+pair\_coeff settings for A must still be specified, but will be
+overridden.  For example these commands will vary the prefactor A for
+all pairwise interactions from 0.0 at the beginning to 30.0 at the end
+of a run:
+
+
+.. parsed-literal::
+
+   variable prefactor equal ramp(0,30)
+   fix 1 all adapt 1 pair soft a \* \* v_prefactor
+
+Note that a formula defined by an :doc:`equal-style variable <variable>`
+can use the current timestep, elapsed time in the current run, elapsed
+time since the beginning of a series of runs, as well as access other
+variables.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed.  A is always mixed via a
+*geometric* rule.  The cutoff is mixed according to the pair\_modify
+mix value.  The default mix value is *geometric*\ .  See the
+"pair\_modify" command for details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option, since the pair interaction goes to 0.0 at the cutoff.
+
+The :doc:`pair\_modify <pair_modify>` table and tail options are not
+relevant for this pair style.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix nve/limit <fix_nve_limit>`, :doc:`fix adapt <fix_adapt>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst
new file mode 100644
index 0000000000..741cfe4368
--- /dev/null
+++ b/doc/src/pair_sph_heatconduction.rst
@@ -0,0 +1,74 @@
+.. index:: pair\_style sph/heatconduction
+
+pair\_style sph/heatconduction command
+======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/heatconduction
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/heatconduction
+   pair_coeff \* \* 1.0 2.4
+
+Description
+"""""""""""
+
+The sph/heatconduction style computes heat transport between SPH particles.
+The transport model is the diffusion equation for the internal energy.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* D diffusion coefficient (length\^2/time units)
+* h kernel function cutoff (distance units)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  It does not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-SPH package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, pair\_sph/rhosum
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst
new file mode 100644
index 0000000000..9267186e7d
--- /dev/null
+++ b/doc/src/pair_sph_idealgas.rst
@@ -0,0 +1,93 @@
+.. index:: pair\_style sph/idealgas
+
+pair\_style sph/idealgas command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/idealgas
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/idealgas
+   pair_coeff \* \* 1.0 2.4
+
+Description
+"""""""""""
+
+The sph/idealgas style computes pressure forces between particles
+according to the ideal gas equation of state:
+
+.. image:: Eqs/pair_sph_ideal.jpg
+   :align: center
+
+where gamma = 1.4 is the heat capacity ratio, rho is the local
+density, and e is the internal energy per unit mass.  This pair style
+also computes Monaghan's artificial viscosity to prevent particles
+from interpenetrating :ref:`(Monaghan) <ideal-Monoghan>`.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* nu artificial viscosity (no units)
+* h kernel function cutoff (distance units)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  It does not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-SPH package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, pair\_sph/rhosum
+
+**Default:** none
+
+
+----------
+
+
+.. _ideal-Monoghan:
+
+
+
+**(Monaghan)** Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst
new file mode 100644
index 0000000000..cf9d145121
--- /dev/null
+++ b/doc/src/pair_sph_lj.rst
@@ -0,0 +1,98 @@
+.. index:: pair\_style sph/lj
+
+pair\_style sph/lj command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/lj
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/lj
+   pair_coeff \* \* 1.0 2.4
+
+Description
+"""""""""""
+
+The sph/lj style computes pressure forces between particles according
+to the Lennard-Jones equation of state, which is computed according to
+Ree's 1980 polynomial fit :ref:`(Ree) <Ree>`. The Lennard-Jones parameters
+epsilon and sigma are set to unity.  This pair style also computes
+Monaghan's artificial viscosity to prevent particles from
+interpenetrating :ref:`(Monaghan) <Monoghan>`.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* nu artificial viscosity (no units)
+* h kernel function cutoff (distance units)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  It does not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+As noted above, the Lennard-Jones parameters epsilon and sigma are set
+to unity.
+
+This pair style is part of the USER-SPH package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, pair\_sph/rhosum
+
+**Default:** none
+
+
+----------
+
+
+.. _Ree:
+
+
+
+**(Ree)** Ree, Journal of Chemical Physics, 73, 5401 (1980).
+
+.. _Monoghan:
+
+
+
+**(Monaghan)** Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst
new file mode 100644
index 0000000000..2ba1ad010a
--- /dev/null
+++ b/doc/src/pair_sph_rhosum.rst
@@ -0,0 +1,75 @@
+.. index:: pair\_style sph/rhosum
+
+pair\_style sph/rhosum command
+==============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/rhosum Nstep
+
+* Nstep = timestep interval
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/rhosum 10
+   pair_coeff \* \* 2.4
+
+Description
+"""""""""""
+
+The sph/rhosum style computes the local particle mass density rho for
+SPH particles by kernel function interpolation, every Nstep timesteps.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* h (distance units)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  It does not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-SPH package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, pair\_sph/taitwater
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst
new file mode 100644
index 0000000000..ede4d4b115
--- /dev/null
+++ b/doc/src/pair_sph_taitwater.rst
@@ -0,0 +1,96 @@
+.. index:: pair\_style sph/taitwater
+
+pair\_style sph/taitwater command
+=================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/taitwater
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/taitwater
+   pair_coeff \* \* 1000.0 1430.0 1.0 2.4
+
+Description
+"""""""""""
+
+The sph/taitwater style computes pressure forces between SPH particles
+according to Tait's equation of state:
+
+.. image:: Eqs/pair_sph_tait.jpg
+   :align: center
+
+where gamma = 7 and B = c\_0\^2 rho\_0 / gamma, with rho\_0 being the
+reference density and c\_0 the reference speed of sound.
+
+This pair style also computes Monaghan's artificial viscosity to
+prevent particles from interpenetrating :ref:`(Monaghan) <Monaghan>`.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* rho0 reference density (mass/volume units)
+* c0 reference soundspeed (distance/time units)
+* nu artificial viscosity (no units)
+* h kernel function cutoff (distance units)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  It does not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-SPH package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, pair\_sph/rhosum
+
+**Default:** none
+
+
+----------
+
+
+.. _Monaghan:
+
+
+
+**(Monaghan)** Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst
new file mode 100644
index 0000000000..8637faf188
--- /dev/null
+++ b/doc/src/pair_sph_taitwater_morris.rst
@@ -0,0 +1,94 @@
+.. index:: pair\_style sph/taitwater/morris
+
+pair\_style sph/taitwater/morris command
+========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/taitwater/morris
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style sph/taitwater/morris
+   pair_coeff \* \* 1000.0 1430.0 1.0 2.4
+
+Description
+"""""""""""
+
+The sph/taitwater/morris style computes pressure forces between SPH
+particles according to Tait's equation of state:
+
+.. image:: Eqs/pair_sph_tait.jpg
+   :align: center
+
+where gamma = 7 and B = c\_0\^2 rho\_0 / gamma, with rho\_0 being the
+reference density and c\_0 the reference speed of sound.
+
+This pair style also computes laminar viscosity :ref:`(Morris) <Morris>`.
+
+See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* rho0 reference density (mass/volume units)
+* c0 reference soundspeed (distance/time units)
+* nu dynamic viscosity (mass\*distance/time units)
+* h kernel function cutoff (distance units)
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair\_style and
+pair\_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the :doc:`run\_style respa <run_style>` command.  It does not support the *inner*\ ,
+*middle*\ , *outer* keywords.
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-SPH package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, pair\_sph/rhosum
+
+**Default:** none
+
+
+----------
+
+
+.. _Morris:
+
+
+
+**(Morris)** Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst
new file mode 100644
index 0000000000..87a3f7e424
--- /dev/null
+++ b/doc/src/pair_spin_dipole.rst
@@ -0,0 +1,96 @@
+.. index:: pair\_style spin/dipole/cut
+
+pair\_style spin/dipole/cut command
+===================================
+
+pair\_style spin/dipole/long command
+====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style spin/dipole/cut cutoff
+   pair_style spin/dipole/long cutoff
+
+* cutoff = global cutoff for magnetic dipole energy and forces
+  (optional) (distance units)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style spin/dipole/cut 10.0
+   pair_coeff \* \* 10.0
+   pair_coeff 2 3 8.0
+
+   pair_style spin/dipole/long 9.0
+   pair_coeff \* \* 10.0
+   pair_coeff 2 3 6.0
+
+Description
+"""""""""""
+
+Style *spin/dipole/cut* computes a short-range dipole-dipole
+interaction between pairs of magnetic particles that each
+have a magnetic spin.
+The magnetic dipole-dipole interactions are computed by the
+following formulas for the magnetic energy, magnetic precession
+vector omega and mechanical force between particles I and J.
+
+.. image:: Eqs/pair_spin_dipole.jpg
+   :align: center
+
+where si and sj are the spin on two magnetic particles,
+r is their separation distance, and the vector e = (Ri - Rj)/\|Ri - Rj\|
+is the direction vector between the two particles.
+
+Style *spin/dipole/long* computes long-range magnetic dipole-dipole
+interaction.
+A :doc:`kspace\_style <kspace_style>` must be defined to
+use this pair style.  Currently, :doc:`kspace\_style ewald/dipole/spin <kspace_style>` and :doc:`kspace\_style pppm/dipole/spin <kspace_style>` support long-range magnetic
+dipole-dipole interactions.
+
+
+----------
+
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+Restrictions
+""""""""""""
+
+
+The *spin/dipole/cut* and *spin/dipole/long* styles are part of
+the SPIN package.  They are only enabled if LAMMPS was built with that
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+Using dipole/spin pair styles with *electron* :doc:`units <units>` is not
+currently supported.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`kspace\_style <kspace_style>`
+:doc:`fix nve/spin <fix_nve_spin>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst
new file mode 100644
index 0000000000..166885d29d
--- /dev/null
+++ b/doc/src/pair_spin_dmi.rst
@@ -0,0 +1,113 @@
+.. index:: pair\_style spin/dmi
+
+pair\_style spin/dmi command
+============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style spin/dmi cutoff
+
+* cutoff = global cutoff pair (distance in metal units)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style spin/dmi 4.0
+   pair_coeff \* \* dmi 2.6 0.001 1.0 0.0 0.0
+   pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0
+
+Description
+"""""""""""
+
+Style *spin/dmi* computes the Dzyaloshinskii-Moriya (DM) interaction
+between pairs of magnetic spins.
+According to the expression reported in :ref:`(Rohart) <Rohart>`, one has
+the following DM energy:
+
+.. image:: Eqs/pair_spin_dmi_interaction.jpg
+   :align: center
+
+where si and sj are two neighboring magnetic spins of two particles,
+eij = (ri - rj)/\|ri-rj\| is the unit vector between sites i and j,
+and D is the DM vector defining the intensity (in eV) and the direction
+of the interaction.
+
+In :ref:`(Rohart) <Rohart>`, D is defined as the direction normal to the film oriented
+from the high spin-orbit layer to the magnetic ultra-thin film.
+
+The application of a spin-lattice Poisson bracket to this energy (as described
+in :ref:`(Tranchida) <Tranchida5>`) allows to derive a magnetic torque omega, and a
+mechanical force F (for spin-lattice calculations only) for each magnetic
+particle i:
+
+.. image:: Eqs/pair_spin_dmi_forces.jpg
+   :align: center
+
+More details about the derivation of these torques/forces are reported in
+:ref:`(Tranchida) <Tranchida5>`.
+
+For the *spin/dmi* pair style, the following coefficients must be defined for
+each pair of atoms types via the :doc:`pair\_coeff <pair_coeff>` command as in
+the examples above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` commands, and
+set in the following order:
+
+* rc (distance units)
+* \|D\| (energy units)
+* Dx, Dy, Dz  (direction of D)
+
+Note that rc is the radius cutoff of the considered DM interaction, \|D\| is
+the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction.
+
+None of those coefficients is optional.  If not specified, the *spin/dmi*
+pair style cannot be used.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All the *pair/spin* styles are part of the SPIN package.  These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom\_style "spin" was declared.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style spin <atom_style>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_eam <pair_eam>`,
+
+**Default:** none
+
+
+----------
+
+
+.. _Rohart:
+
+
+
+.. _Tranchida5:
+
+**(Rohart)** Rohart and Thiaville,
+Physical Review B, 88(18), 184422. (2013).
+
+
+**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, 372, 406-425, (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst
new file mode 100644
index 0000000000..3bbbed421b
--- /dev/null
+++ b/doc/src/pair_spin_exchange.rst
@@ -0,0 +1,123 @@
+.. index:: pair\_style spin/exchange
+
+pair\_style spin/exchange command
+=================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style spin/exchange cutoff
+
+* cutoff = global cutoff pair (distance in metal units)
+
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style spin/exchange 4.0
+   pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
+   pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965
+
+Description
+"""""""""""
+
+Style *spin/exchange* computes the exchange interaction between
+pairs of magnetic spins:
+
+.. math::
+
+   H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j 
+
+where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two neighboring magnetic spins of two particles,
+:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance between the two
+particles. The summation is over pairs of nearest neighbors. 
+:math:`J(r_{ij})` is a function defining the intensity and the sign of the exchange
+interaction for different neighboring shells. This function is defined as:
+
+.. math::
+
+    {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
+
+where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the associated
+"pair\_coeff" command, and :math:`R_c` is the radius cutoff associated to
+the pair interaction (see below for more explanations).
+
+The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function above matches with
+the value of the exchange interaction for the :math:`N` neighbor shells taken into account.
+Examples and more explanations about this function and its parameterization are reported
+in :ref:`(Tranchida) <Tranchida3>`.
+
+From this exchange interaction, each spin :math:`i` will be submitted
+to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
+force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
+such as:
+
+.. math::
+
+   \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} 
+   \left(r_{ij} \right)\,\vec{s}_{j} 
+   ~~{\rm and}~~ 
+   \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}  
+
+with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij} = \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
+vector between sites :math:`i` and :math:`j`.
+
+More details about the derivation of these torques/forces are reported in
+:ref:`(Tranchida) <Tranchida3>`.
+
+For the *spin/exchange* pair style, the following coefficients must be defined
+for each pair of atoms types via the :doc:`pair\_coeff <pair_coeff>` command as in
+the examples above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` commands, and
+set in the following order:
+
+* :math:`R_c` (distance units)
+* :math:`a`  (energy units)
+* :math:`b`  (adim parameter)
+* :math:`d`  (distance units)
+
+Note that :math:`R_c` is the radius cutoff of the considered exchange interaction,
+and :math:`a`, :math:`b` and :math:`d` are the three coefficients performing the parameterization
+of the function :math:`J(r_{ij})` defined above.
+
+None of those coefficients is optional. If not specified, the
+*spin/exchange* pair style cannot be used.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All the *pair/spin* styles are part of the SPIN package.  These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom\_style "spin" was declared.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style spin <atom_style>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_eam <pair_eam>`,
+
+**Default:**
+
+none
+
+
+----------
+
+
+.. _Tranchida3:
+
+
+
+**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, 372, 406-425, (2018).
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
deleted file mode 100644
index 76a6d508d2..0000000000
--- a/doc/src/pair_spin_exchange.txt
+++ /dev/null
@@ -1,98 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style spin/exchange command :h3
-
-[Syntax:]
-
-pair_style spin/exchange cutoff :pre
-
-cutoff = global cutoff pair (distance in metal units) :ulb,l
-
-:ule
-
-[Examples:]
-
-pair_style spin/exchange 4.0
-pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
-pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre
-
-[Description:]
-
-Style {spin/exchange} computes the exchange interaction between
-pairs of magnetic spins:
-
-:c,image(Eqs/pair_spin_exchange_interaction.jpg)
-
-where si and sj are two neighboring magnetic spins of two particles,
-rij = ri - rj is the inter-atomic distance between the two particles,
-and J(rij) is a function defining the intensity and the sign of the exchange
-interaction for different neighboring shells. This function is defined as:
-
-:c,image(Eqs/pair_spin_exchange_function.jpg)
-
-where a, b and d are the three constant coefficients defined in the associated
-"pair_coeff" command (see below for more explanations).
-
-The coefficients a, b, and d need to be fitted so that the function above matches with
-the value of the exchange interaction for the N neighbor shells taken into account.
-Examples and more explanations about this function and its parameterization are reported
-in "(Tranchida)"_#Tranchida3.
-
-From this exchange interaction, each spin i will be submitted
-to a magnetic torque omega, and its associated atom can be submitted to a
-force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html),
-such as:
-
-:c,image(Eqs/pair_spin_exchange_forces.jpg)
-
-with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit
-vector between sites i and j.
-
-More details about the derivation of these torques/forces are reported in
-"(Tranchida)"_#Tranchida3.
-
-For the {spin/exchange} pair style, the following coefficients must be defined
-for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
-the examples above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html commands, and
-set in the following order:
-
-rc (distance units)
-a  (energy units)
-b  (adim parameter)
-d  (distance units) :ul
-
-Note that rc is the radius cutoff of the considered exchange interaction,
-and a, b and d are the three coefficients performing the parameterization
-of the function J(rij) defined above.
-
-None of those coefficients is optional. If not specified, the
-{spin/exchange} pair style cannot be used.
-
-:line
-
-[Restrictions:]
-
-All the {pair/spin} styles are part of the SPIN package.  These styles
-are only enabled if LAMMPS was built with this package, and if the
-atom_style "spin" was declared.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
-"pair_eam"_pair_eam.html,
-
-[Default:] none
-
-:line
-
-:link(Tranchida3)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, 372, 406-425, (2018).
diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst
new file mode 100644
index 0000000000..679e13e628
--- /dev/null
+++ b/doc/src/pair_spin_magelec.rst
@@ -0,0 +1,95 @@
+.. index:: pair\_style spin/magelec
+
+pair\_style spin/magelec command
+================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style spin/magelec cutoff
+
+* cutoff = global cutoff pair (distance in metal units)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style spin/magelec 4.5
+   pair_coeff \* \* magelec 4.5 0.00109 1.0 1.0 1.0
+
+Description
+"""""""""""
+
+Style *spin/me* computes a magneto-electric interaction between
+pairs of magnetic spins. According to the derivation reported in
+:ref:`(Katsura) <Katsura1>`, this interaction is defined as:
+
+.. image:: Eqs/pair_spin_me_interaction.jpg
+   :align: center
+
+where si and sj are neighboring magnetic spins of two particles,
+eij = (ri - rj)/\|ri-rj\| is the normalized separation vector between the
+two particles, and E is an electric polarization vector.
+The norm and direction of E are giving the intensity and the
+direction of a screened dielectric atomic polarization (in eV).
+
+From this magneto-electric interaction, each spin i will be submitted
+to a magnetic torque omega, and its associated atom can be submitted to a
+force F for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
+such as:
+
+.. image:: Eqs/pair_spin_me_forces.jpg
+   :align: center
+
+with h the Planck constant (in metal units).
+
+More details about the derivation of these torques/forces are reported in
+:ref:`(Tranchida) <Tranchida4>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All the *pair/spin* styles are part of the SPIN package.  These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom\_style "spin" was declared.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style spin <atom_style>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_spin\_exchange <pair_spin_exchange>`, :doc:`pair\_eam <pair_eam>`,
+
+**Default:** none
+
+
+----------
+
+
+.. _Katsura1:
+
+
+
+**(Katsura)** H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005)
+
+.. _Tranchida4:
+
+
+
+**(Tranchida)** Tranchida, Plimpton, Thibaudeau, and Thompson,
+Journal of Computational Physics, 372, 406-425, (2018).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst
new file mode 100644
index 0000000000..ecdb8f30f6
--- /dev/null
+++ b/doc/src/pair_spin_neel.rst
@@ -0,0 +1,110 @@
+.. index:: pair_style spin/neel
+
+pair_style spin/neel command
+============================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style spin/neel cutoff
+
+* cutoff = global cutoff pair (distance in metal units)
+
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style spin/neel 4.0
+   pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+   pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0
+
+Description
+"""""""""""
+
+Style *spin/neel* computes the Neel pair anisotropy model
+between pairs of magnetic spins:
+
+.. math::
+
+   \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})({\mathbf{e}}_{ij}
+   \cdot {\mathbf{s}}_{j})-\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3} \right)
+   +q_1(r_{ij})\left( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^2 -\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3}\right)
+   \left( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^2 -\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3} \right)
+   + q_2(r_{ij}) \Big( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i}) ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{j})^3 + ({\mathbf{e}}_{ij}\cdot
+   {\mathbf{s}}_{j}) ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^3\Big)
+
+where :math:`\mathbf{s}_i` and :math:`\mathbf{s}_j` are two neighboring magnetic spins of two particles,
+:math:`r_{ij} = \vert \mathbf{r}_i - \mathbf{r}_j \vert` is the inter-atomic distance between the two particles,
+:math:`\mathbf{e}_{ij} = \frac{\mathbf{r}_i - \mathbf{r}_j}{\vert \mathbf{r}_i - \mathbf{r}_j\vert}` is their normalized separation vector and :math:`g_1`,
+:math:`q_1` and :math:`q_2` are three functions defining the intensity of the dipolar
+and quadrupolar contributions, with:
+
+.. math::
+
+   g_1(r_{ij}) &= g(r_{ij}) + \frac{12}{35} q(r_{ij}) \\
+   q_1(r_{ij}) &= \frac{9}{5} q(r_{ij}) \\
+   q_2(r_{ij}) &= - \frac{2}{5} q(r_{ij})
+
+With the functions :math:`g(r_{ij})` and :math:`q(r_{ij})` defined and fitted according to
+the same Bethe-Slater function used to fit the exchange interaction:
+
+.. math::
+
+   {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
+
+where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the
+associated "pair\_coeff" command.
+
+The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function
+above matches with the values of the magneto-elastic constant of the
+materials at stake.
+
+Examples and more explanations about this function and its
+parameterization are reported in :ref:`(Tranchida) <Tranchida6>`. More
+examples of parameterization will be provided in future work.
+
+From this DM interaction, each spin :math:`i` will be submitted to a magnetic
+torque :math:`\mathbf{\omega}` and its associated atom to a force :math:`\mathbf{F}` (for spin-lattice
+calculations only).
+
+More details about the derivation of these torques/forces are reported
+in :ref:`(Tranchida) <Tranchida6>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All the *pair/spin* styles are part of the SPIN package.  These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom\_style "spin" was declared.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`atom\_style spin <atom_style>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair\_eam <pair_eam>`,
+
+**Default:**
+
+none
+
+
+----------
+
+
+.. _Tranchida6:
+
+
+
+**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, 372, 406-425, (2018).
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
deleted file mode 100644
index 009ef7947d..0000000000
--- a/doc/src/pair_spin_neel.txt
+++ /dev/null
@@ -1,83 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style spin/neel command :h3
-
-[Syntax:]
-
-pair_style spin/neel cutoff :pre
-
-cutoff = global cutoff pair (distance in metal units) :ulb,l
-
-:ule
-	
-[Examples:]
-
-pair_style spin/neel 4.0
-pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
-pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre
-
-[Description:]
-
-Style {spin/neel} computes the Neel pair anisotropy model
-between pairs of magnetic spins:
-
-:c,image(Eqs/pair_spin_neel_interaction.jpg)
-
-where si and sj are two neighboring magnetic spins of two particles,
-rij = ri - rj is the inter-atomic distance between the two particles,
-eij = (ri - rj)/|ri-rj| is their normalized separation vector and g1,
-q1 and q2 are three functions defining the intensity of the dipolar
-and quadrupolar contributions, with:
-
-:c,image(Eqs/pair_spin_neel_functions.jpg)
-
-With the functions g(rij) and q(rij) defined and fitted according to
-the same Bethe-Slater function used to fit the exchange interaction:
-
-:c,image(Eqs/pair_spin_exchange_function.jpg)
-
-where a, b and d are the three constant coefficients defined in the
-associated "pair_coeff" command.
-
-The coefficients a, b, and d need to be fitted so that the function
-above matches with the values of the magneto-elastic constant of the
-materials at stake.
-
-Examples and more explanations about this function and its
-parameterization are reported in "(Tranchida)"_#Tranchida6. More
-examples of parameterization will be provided in future work.
-
-From this DM interaction, each spin i will be submitted to a magnetic
-torque omega and its associated atom to a force F (for spin-lattice
-calculations only).
-
-More details about the derivation of these torques/forces are reported
-in "(Tranchida)"_#Tranchida6.
-
-:line
-
-[Restrictions:]
-
-All the {pair/spin} styles are part of the SPIN package.  These styles
-are only enabled if LAMMPS was built with this package, and if the
-atom_style "spin" was declared.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
-"pair_eam"_pair_eam.html,
-
-[Default:] none
-
-:line
-
-:link(Tranchida6)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, 372, 406-425, (2018).
diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst
new file mode 100644
index 0000000000..1b4e6d3031
--- /dev/null
+++ b/doc/src/pair_srp.rst
@@ -0,0 +1,190 @@
+.. index:: pair\_style srp
+
+pair\_style srp command
+=======================
+
+Syntax
+""""""
+
+pair\_style srp cutoff btype dist keyword value ...
+
+* cutoff = global cutoff for SRP interactions (distance units)
+* btype = bond type to apply SRP interactions to (can be wildcard, see below)
+* distance = *min* or *mid*
+* zero or more keyword/value pairs may be appended
+* keyword = *exclude*
+  
+  .. parsed-literal::
+  
+       *bptype* value = atom type for bond particles
+       *exclude* value = *yes* or *no*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
+   pair_coeff 1 1 dpd 60.0 4.5 1.0
+   pair_coeff 1 2 none
+   pair_coeff 2 2 srp 100.0 0.8
+
+   pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 \* min exclude yes
+   pair_coeff 1 1 dpd 60.0 50 1.0
+   pair_coeff 1 2 none
+   pair_coeff 2 2 srp 40.0
+
+   pair_style hybrid srp 0.8 2 mid
+   pair_coeff 1 1 none
+   pair_coeff 1 2 none
+   pair_coeff 2 2 srp 100.0 0.8
+
+Description
+"""""""""""
+
+Style *srp* computes a soft segmental repulsive potential (SRP) that
+acts between pairs of bonds. This potential is useful for preventing
+bonds from passing through one another when a soft non-bonded
+potential acts between beads in, for example, DPD polymer chains.  An
+example input script that uses this command is provided in
+examples/USER/srp.
+
+Bonds of specified type *btype* interact with one another through a
+bond-pairwise potential, such that the force on bond *i* due to bond
+*j* is as follows
+
+.. image:: Eqs/pair_srp1.jpg
+   :align: center
+
+where *r* and *rij* are the distance and unit vector between the two
+bonds.  Note that *btype* can be specified as an asterisk "\*", which
+case the interaction is applied to all bond types.  The *mid* option
+computes *r* and *rij* from the midpoint distance between bonds. The
+*min* option computes *r* and *rij* from the minimum distance between
+bonds. The force acting on a bond is mapped onto the two bond atoms
+according to the lever rule,
+
+.. image:: Eqs/pair_srp2.jpg
+   :align: center
+
+where *L* is the normalized distance from the atom to the point of
+closest approach of bond *i* and *j*\ . The *mid* option takes *L* as
+0.5 for each interaction as described in :ref:`(Sirk) <Sirk2>`.
+
+The following coefficients must be defined via the
+:doc:`pair\_coeff <pair_coeff>` command as in the examples above, or in
+the data file or restart file read by the :doc:`read\_data <read_data>`
+or :doc:`read\_restart <read_restart>` commands:
+
+* *C* (force units)
+* *rc* (distance units)
+
+The last coefficient is optional. If not specified, the global cutoff
+is used.
+
+.. note::
+
+   Pair style srp considers each bond of type *btype* to be a
+   fictitious "particle" of type *bptype*\ , where *bptype* is either the
+   largest atom type in the system, or the type set by the *bptype* flag.
+   Any actual existing particles with this atom type will be deleted at
+   the beginning of a run. This means you must specify the number of
+   types in your system accordingly; usually to be one larger than what
+   would normally be the case, e.g. via the :doc:`create\_box <create_box>`
+   or by changing the header in your :doc:`data file <read_data>`.  The
+   fictitious "bond particles" are inserted at the beginning of the run,
+   and serve as placeholders that define the position of the bonds.  This
+   allows neighbor lists to be constructed and pairwise interactions to
+   be computed in almost the same way as is done for actual particles.
+   Because bonds interact only with other bonds, :doc:`pair\_style hybrid <pair_hybrid>` should be used to turn off interactions
+   between atom type *bptype* and all other types of atoms.  An error
+   will be flagged if :doc:`pair\_style hybrid <pair_hybrid>` is not used.
+
+The optional *exclude* keyword determines if forces are computed
+between first neighbor (directly connected) bonds.  For a setting of
+*no*\ , first neighbor forces are computed; for *yes* they are not
+computed. A setting of *no* cannot be used with the *min* option for
+distance calculation because the minimum distance between directly
+connected bonds is zero.
+
+Pair style *srp* turns off normalization of thermodynamic properties
+by particle number, as if the command :doc:`thermo\_modify norm no <thermo_modify>` had been issued.
+
+The pairwise energy associated with style *srp* is shifted to be zero
+at the cutoff distance *rc*\ .
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair styles does not support mixing.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option for the energy of the pair interaction. Note that as
+discussed above, the energy term is already shifted to be 0.0 at the
+cutoff distance *rc*\ .
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant for
+this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes global and per-atom information to :doc:`binary restart files <restart>`. Pair srp should be used with :doc:`pair\_style hybrid <pair_hybrid>`, thus the pair\_coeff commands need to be
+specified in the input script when reading a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the USER-MISC package. It is only enabled
+if LAMMPS was built with that package. See the Making LAMMPS section
+for more info.
+
+This pair style must be used with :doc:`pair\_style hybrid <pair_hybrid>`.
+
+This pair style requires the :doc:`newton <newton>` command to be *on*
+for non-bonded interactions.
+
+This pair style is not compatible with :doc:`rigid body integrators <fix_rigid>`
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style hybrid <pair_hybrid>`, :doc:`pair\_coeff <pair_coeff>`,
+:doc:`pair dpd <pair_dpd>`
+
+Default
+"""""""
+
+The default keyword value is exclude = yes.
+
+
+----------
+
+
+.. _Sirk2:
+
+
+
+**(Sirk)** Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
+Chem Phys, 136 (13) 134903, 2012.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst
new file mode 100644
index 0000000000..9b23266ca8
--- /dev/null
+++ b/doc/src/pair_style.rst
@@ -0,0 +1,363 @@
+.. index:: pair\_style
+
+pair\_style command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = one of the styles from the list below
+* args = arguments used by a particular style
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style lj/cut 2.5
+   pair_style eam/alloy
+   pair_style hybrid lj/charmm/coul/long 10.0 eam
+   pair_style table linear 1000
+   pair_style none
+
+Description
+"""""""""""
+
+Set the formula(s) LAMMPS uses to compute pairwise interactions.  In
+LAMMPS, pair potentials are defined between pairs of atoms that are
+within a cutoff distance and the set of active interactions typically
+changes over time.  See the :doc:`bond_style <bond_style>` command to
+define potentials between pairs of bonded atoms, which typically
+remain in place for the duration of a simulation.
+
+In LAMMPS, pairwise force fields encompass a variety of interactions,
+some of which include many-body effects, e.g. EAM, Stillinger-Weber,
+Tersoff, REBO potentials.  They are still classified as "pairwise"
+potentials because the set of interacting atoms changes with time
+(unlike molecular bonds) and thus a neighbor list is used to find
+nearby interacting atoms.
+
+Hybrid models where specified pairs of atom types interact via
+different pair potentials can be setup using the *hybrid* pair style.
+
+The coefficients associated with a pair style are typically set for
+each pair of atom types, and are specified by the
+:doc:`pair_coeff <pair_coeff>` command or read from a file by the
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+commands.
+
+The :doc:`pair_modify <pair_modify>` command sets options for mixing of
+type I-J interaction coefficients and adding energy offsets or tail
+corrections to Lennard-Jones potentials.  Details on these options as
+they pertain to individual potentials are described on the doc page
+for the potential.  Likewise, info on whether the potential
+information is stored in a :doc:`restart file <write_restart>` is listed
+on the potential doc page.
+
+In the formulas listed for each pair style, *E* is the energy of a
+pairwise interaction between two atoms separated by a distance *r*\ .
+The force between the atoms is the negative derivative of this
+expression.
+
+If the pair\_style command has a cutoff argument, it sets global
+cutoffs for all pairs of atom types.  The distance(s) can be smaller
+or larger than the dimensions of the simulation box.
+
+Typically, the global cutoff value can be overridden for a specific
+pair of atom types by the :doc:`pair_coeff <pair_coeff>` command.  The
+pair style settings (including global cutoffs) can be changed by a
+subsequent pair\_style command using the same style.  This will reset
+the cutoffs for all atom type pairs, including those previously set
+explicitly by a :doc:`pair_coeff <pair_coeff>` command.  The exceptions
+to this are that pair\_style *table* and *hybrid* settings cannot be
+reset.  A new pair\_style command for these styles will wipe out all
+previously specified pair\_coeff values.
+
+
+----------
+
+
+Here is an alphabetic list of pair styles defined in LAMMPS.  They are
+also listed in more compact form on the :doc:`Commands pair <Commands_pair>` doc page.
+
+Click on the style to display the formula it computes, any additional
+arguments specified in the pair\_style command, and coefficients
+specified by the associated :doc:`pair_coeff <pair_coeff>` command.
+
+There are also additional accelerated pair styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the :doc:`Commands pair <Commands_pair>`
+doc page are followed by one or more of (g,i,k,o,t) to indicate which
+accelerated styles exist.
+
+* :doc:`none <pair_none>` - turn off pairwise interactions
+* :doc:`hybrid <pair_hybrid>` - multiple styles of pairwise interactions
+* :doc:`hybrid/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions
+* :doc:`zero <pair_zero>` - neighbor list but no interactions
+
+* :doc:`adp <pair_adp>` - angular dependent potential (ADP) of Mishin
+* :doc:`agni <pair_agni>` - machine learned potential mapping atomic environment to forces
+* :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
+* :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
+* :doc:`atm <pair_atm>` - Axilrod-Teller-Muto potential
+* :doc:`awpmd/cut <pair_awpmd>` - Antisymmetrized Wave Packet MD potential for atoms and electrons
+* :doc:`beck <pair_beck>` - Beck potential
+* :doc:`body/nparticle <pair_body_nparticle>` - interactions between body particles
+* :doc:`body/rounded/polygon <pair_body_rounded_polygon>` - granular-style 2d polygon potential
+* :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>` - granular-style 3d polyhedron potential
+* :doc:`bop <pair_bop>` - BOP potential of Pettifor
+* :doc:`born <pair_born>` - Born-Mayer-Huggins potential
+* :doc:`born/coul/dsf <pair_born>` - Born with damped-shifted-force model
+* :doc:`born/coul/dsf/cs <pair_cs>` - Born with damped-shifted-force and core/shell model
+* :doc:`born/coul/long <pair_born>` - Born with long-range Coulombics
+* :doc:`born/coul/long/cs <pair_cs>` - Born with long-range Coulombics and core/shell
+* :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulombics
+* :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulombics
+* :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulombics and core/shell model
+* :doc:`brownian <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics
+* :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity
+* :doc:`buck <pair_buck>` - Buckingham potential
+* :doc:`buck/coul/cut <pair_buck>` - Buckingham with cutoff Coulomb
+* :doc:`buck/coul/long <pair_buck>` - Buckingham with long-range Coulombics
+* :doc:`buck/coul/long/cs <pair_cs>` - Buckingham with long-range Coulombics and core/shell
+* :doc:`buck/coul/msm <pair_buck>` - Buckingham with long-range MSM Coulombics
+* :doc:`buck/long/coul/long <pair_buck_long>` - long-range Buckingham with long-range Coulombics
+* :doc:`buck/mdf <pair_mdf>` - Buckingham with a taper function
+* :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>` - dispersion-damped Buckingham with damped-shift-force model
+* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>` - dispersion-damped Buckingham with long-range Coulombics
+* :doc:`colloid <pair_colloid>` - integrated colloidal potential
+* :doc:`comb <pair_comb>` - charge-optimized many-body (COMB) potential
+* :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential
+* :doc:`cosine/squared <pair_cosine_squared>` - Cooke-Kremer-Deserno membrane model potential
+* :doc:`coul/cut <pair_coul>` - cutoff Coulombic potential
+* :doc:`coul/cut/soft <pair_fep_soft>` - Coulombic potential with a soft core
+* :doc:`coul/debye <pair_coul>` - cutoff Coulombic potential with Debye screening
+* :doc:`coul/diel <pair_coul_diel>` - Coulomb potential with dielectric permittivity
+* :doc:`coul/dsf <pair_coul>` - Coulombics with damped-shifted-force model
+* :doc:`coul/long <pair_coul>` - long-range Coulombic potential
+* :doc:`coul/long/cs <pair_cs>` - long-range Coulombic potential and core/shell
+* :doc:`coul/long/soft <pair_fep_soft>` - long-range Coulombic potential with a soft core
+* :doc:`coul/msm <pair_coul>` - long-range MSM Coulombics
+* :doc:`coul/shield <pair_coul_shield>` - Coulombics for boron nitride for use with :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` potential
+* :doc:`coul/streitz <pair_coul>` - Coulombics via Streitz/Mintmire Slater orbitals
+* :doc:`coul/wolf <pair_coul>` - Coulombics via Wolf potential
+* :doc:`coul/wolf/cs <pair_cs>` - ditto with core/shell adjustments
+* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
+* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
+* :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
+* :doc:`dpd/tstat <pair_dpd>` - pair-wise DPD thermostatting
+* :doc:`dsmc <pair_dsmc>` - Direct Simulation Monte Carlo (DSMC)
+* :doc:`e3b <pair_e3b>` - Explicit-three body (E3B) water model
+* :doc:`drip <pair_drip>` - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
+* :doc:`eam <pair_eam>` - embedded atom method (EAM)
+* :doc:`eam/alloy <pair_eam>` - alloy EAM
+* :doc:`eam/cd <pair_eam>` - concentration-dependent EAM
+* :doc:`eam/cd/old <pair_eam>` - older two-site model for concentration-dependent EAM
+* :doc:`eam/fs <pair_eam>` - Finnis-Sinclair EAM
+* :doc:`edip <pair_edip>` - three-body EDIP potential
+* :doc:`edip/multi <pair_edip>` - multi-element EDIP potential
+* :doc:`edpd <pair_meso>` - eDPD particle interactions
+* :doc:`eff/cut <pair_eff>` - electron force field with a cutoff
+* :doc:`eim <pair_eim>` - embedded ion method (EIM)
+* :doc:`exp6/rx <pair_exp6_rx>` - reactive DPD potential
+* :doc:`extep <pair_extep>` - extended Tersoff potential
+* :doc:`gauss <pair_gauss>` - Gaussian potential
+* :doc:`gauss/cut <pair_gauss>` - generalized Gaussian potential
+* :doc:`gayberne <pair_gayberne>` - Gay-Berne ellipsoidal potential
+* :doc:`granular <pair_granular>` - Generalized granular potential
+* :doc:`gran/hertz/history <pair_gran>` - granular potential with Hertzian interactions
+* :doc:`gran/hooke <pair_gran>` - granular potential with history effects
+* :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects
+* :doc:`gw <pair_gw>` - Gao-Weber potential
+* :doc:`gw/zbl <pair_gw>` - Gao-Weber potential with a repulsive ZBL core
+* :doc:`hbond/dreiding/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
+* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
+* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
+* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
+* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications
+* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` - Kolmogorov-Crespi (KC) potential with normals along z-axis
+* :doc:`lcbop <pair_lcbop>` - long-range bond-order potential (LCBOP)
+* :doc:`lebedeva/z <pair_lebedeva_z>` - Lebedeva interlayer potential for graphene with normals along z-axis
+* :doc:`lennard/mdf <pair_mdf>` - LJ potential in A/B form with a taper function
+* :doc:`line/lj <pair_line_lj>` - LJ potential between line segments
+* :doc:`list <pair_list>` - potential between pairs of atoms explicitly listed in an input file
+* :doc:`lj/charmm/coul/charmm <pair_charmm>` - CHARMM potential with cutoff Coulomb
+* :doc:`lj/charmm/coul/charmm/implicit <pair_charmm>` - CHARMM for implicit solvent
+* :doc:`lj/charmm/coul/long <pair_charmm>` - CHARMM with long-range Coulomb
+* :doc:`lj/charmm/coul/long/soft <pair_fep_soft>` - CHARMM with long-range Coulomb and a soft core
+* :doc:`lj/charmm/coul/msm <pair_charmm>` - CHARMM with long-range MSM Coulombics
+* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>` - CHARMM with force switching and shifting
+* :doc:`lj/charmmfsw/coul/long <pair_charmm>` - CHARMM with force switching and long-rnage Coulombics
+* :doc:`lj/class2 <pair_class2>` - COMPASS (class 2) force field with no Coulomb
+* :doc:`lj/class2/coul/cut <pair_class2>` - COMPASS with cutoff Coulomb
+* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>` - COMPASS with cutoff Coulomb with a soft core
+* :doc:`lj/class2/coul/long <pair_class2>` - COMPASS with long-range Coulomb
+* :doc:`lj/class2/coul/long/soft <pair_fep_soft>` - COMPASS with long-range Coulomb with a soft core
+* :doc:`lj/class2/soft <pair_fep_soft>` - COMPASS (class 2) force field with no Coulomb with a soft core
+* :doc:`lj/cubic <pair_lj_cubic>` - LJ with cubic after inflection point
+* :doc:`lj/cut <pair_lj>` - cutoff Lennard-Jones potential with no Coulomb
+* :doc:`lj/cut/coul/cut <pair_lj>` - LJ with cutoff Coulomb
+* :doc:`lj/cut/coul/cut/soft <pair_fep_soft>` - LJ with cutoff Coulomb with a soft core
+* :doc:`lj/cut/coul/debye <pair_lj>` - LJ with Debye screening added to Coulomb
+* :doc:`lj/cut/coul/dsf <pair_lj>` - LJ with Coulombics via damped shifted forces
+* :doc:`lj/cut/coul/long <pair_lj>` - LJ with long-range Coulombics
+* :doc:`lj/cut/coul/long/cs <pair_cs>` - ditto with core/shell adjustments
+* :doc:`lj/cut/coul/long/soft <pair_fep_soft>` - LJ with long-range Coulombics with a soft core
+* :doc:`lj/cut/coul/msm <pair_lj>` - LJ with long-range MSM Coulombics
+* :doc:`lj/cut/coul/wolf <pair_lj>` - LJ with Coulombics via Wolf potential
+* :doc:`lj/cut/dipole/cut <pair_dipole>` - point dipoles with cutoff
+* :doc:`lj/cut/dipole/long <pair_dipole>` - point dipoles with long-range Ewald
+* :doc:`lj/cut/soft <pair_fep_soft>` - LJ with a soft core
+* :doc:`lj/cut/thole/long <pair_thole>` - LJ with Coulombics with thole damping
+* :doc:`lj/cut/tip4p/cut <pair_lj>` - LJ with cutoff Coulomb for TIP4P water
+* :doc:`lj/cut/tip4p/long <pair_lj>` - LJ with long-range Coulomb for TIP4P water
+* :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` - LJ with cutoff Coulomb for TIP4P water with a soft core
+* :doc:`lj/expand <pair_lj_expand>` - Lennard-Jones for variable size particles
+* :doc:`lj/expand/coul/long <pair_lj_expand>` - Lennard-Jones for variable size particles with long-range Coulombics
+* :doc:`lj/gromacs <pair_gromacs>` - GROMACS-style Lennard-Jones potential
+* :doc:`lj/gromacs/coul/gromacs <pair_gromacs>` - GROMACS-style LJ and Coulombic potential
+* :doc:`lj/long/coul/long <pair_lj_long>` - long-range LJ and long-range Coulombics
+* :doc:`lj/long/dipole/long <pair_dipole>` - long-range LJ and long-range point dipoles
+* :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulombics for TIP4P water
+* :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
+* :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining
+* :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulombics
+* :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulombics via MSM
+* :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
+* :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
+* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
+* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed LJ vdW potential with Gaussian electrostatics
+* :doc:`lj96/cut <pair_lj96>` - Lennard-Jones 9/6 potential
+* :doc:`local/density <pair_local_density>` - generalized basic local density potential
+* :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces
+* :doc:`lubricate/poly <pair_lubricate>` - hydrodynamic lubrication forces with polydispersity
+* :doc:`lubricateU <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication Dynamics
+* :doc:`lubricateU/poly <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
+* :doc:`mdpd <pair_meso>` - mDPD particle interactions
+* :doc:`mdpd/rhosum <pair_meso>` - mDPD particle interactions for mass density
+* :doc:`meam/c <pair_meamc>` - modified embedded atom method (MEAM) in C
+* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
+* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
+* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
+* :doc:`mie/cut <pair_mie>` - Mie potential
+* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
+* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
+* :doc:`morse <pair_morse>` - Morse potential
+* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential
+* :doc:`morse/soft <pair_morse>` - Morse potential with a soft core
+* :doc:`multi/lucy <pair_multi_lucy>` - DPD potential with density-dependent force
+* :doc:`multi/lucy/rx <pair_multi_lucy_rx>` - reactive DPD potential with density-dependent force
+* :doc:`nb3b/harmonic <pair_nb3b_harmonic>` - non-bonded 3-body harmonic potential
+* :doc:`nm/cut <pair_nm>` - N-M potential
+* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
+* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulombics
+* :doc:`oxdna/coaxstk <pair_oxdna>` -
+* :doc:`oxdna/excv <pair_oxdna>` -
+* :doc:`oxdna/hbond <pair_oxdna>` -
+* :doc:`oxdna/stk <pair_oxdna>` -
+* :doc:`oxdna/xstk <pair_oxdna>` -
+* :doc:`oxdna2/coaxstk <pair_oxdna2>` -
+* :doc:`oxdna2/dh <pair_oxdna2>` -
+* :doc:`oxdna2/excv <pair_oxdna2>` -
+* :doc:`oxdna2/hbond <pair_oxdna2>` -
+* :doc:`oxdna2/stk <pair_oxdna2>` -
+* :doc:`oxdna2/xstk <pair_oxdna2>` -
+* :doc:`oxrna2/coaxstk <pair_oxrna2>` -
+* :doc:`oxrna2/dh <pair_oxrna2>` -
+* :doc:`oxrna2/excv <pair_oxrna2>` -
+* :doc:`oxrna2/hbond <pair_oxrna2>` -
+* :doc:`oxrna2/stk <pair_oxrna2>` -
+* :doc:`oxrna2/xstk <pair_oxrna2>` -
+* :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
+* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
+* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
+* :doc:`peri/ves <pair_peri>` - peridynamic VES potential
+* :doc:`polymorphic <pair_polymorphic>` - polymorphic 3-body potential
+* :doc:`python <pair_python>` -
+* :doc:`quip <pair_quip>` -
+* :doc:`reax/c <pair_reaxc>` - ReaxFF potential in C
+* :doc:`rebo <pair_airebo>` - 2nd generation REBO potential of Brenner
+* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
+* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
+* :doc:`smd/hertz <pair_smd_hertz>` -
+* :doc:`smd/tlsph <pair_smd_tlsph>` -
+* :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
+* :doc:`smd/ulsph <pair_smd_ulsph>` -
+* :doc:`smtbq <pair_smtbq>` -
+* :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
+* :doc:`soft <pair_soft>` - Soft (cosine) potential
+* :doc:`sph/heatconduction <pair_sph_heatconduction>` -
+* :doc:`sph/idealgas <pair_sph_idealgas>` -
+* :doc:`sph/lj <pair_sph_lj>` -
+* :doc:`sph/rhosum <pair_sph_rhosum>` -
+* :doc:`sph/taitwater <pair_sph_taitwater>` -
+* :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` -
+* :doc:`spin/dipole/cut <pair_spin_dipole>` -
+* :doc:`spin/dipole/long <pair_spin_dipole>` -
+* :doc:`spin/dmi <pair_spin_dmi>` -
+* :doc:`spin/exchange <pair_spin_exchange>` -
+* :doc:`spin/magelec <pair_spin_magelec>` -
+* :doc:`spin/neel <pair_spin_neel>` -
+* :doc:`srp <pair_srp>` -
+* :doc:`sw <pair_sw>` - Stillinger-Weber 3-body potential
+* :doc:`table <pair_table>` - tabulated pair potential
+* :doc:`table/rx <pair_table_rx>` -
+* :doc:`tdpd <pair_meso>` - tDPD particle interactions
+* :doc:`tersoff <pair_tersoff>` - Tersoff 3-body potential
+* :doc:`tersoff/mod <pair_tersoff_mod>` - modified Tersoff 3-body potential
+* :doc:`tersoff/mod/c <pair_tersoff_mod>` -
+* :doc:`tersoff/table <pair_tersoff>` -
+* :doc:`tersoff/zbl <pair_tersoff_zbl>` - Tersoff/ZBL 3-body potential
+* :doc:`thole <pair_thole>` - Coulomb interactions with thole damping
+* :doc:`tip4p/cut <pair_coul>` - Coulomb for TIP4P water w/out LJ
+* :doc:`tip4p/long <pair_coul>` - long-range Coulombics for TIP4P water w/out LJ
+* :doc:`tip4p/long/soft <pair_fep_soft>` -
+* :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles
+* :doc:`ufm <pair_ufm>` -
+* :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential
+* :doc:`vashishta/table <pair_vashishta>` -
+* :doc:`yukawa <pair_yukawa>` - Yukawa potential
+* :doc:`yukawa/colloid <pair_yukawa_colloid>` - screened Yukawa potential for finite-size particles
+* :doc:`zbl <pair_zbl>` - Ziegler-Biersack-Littmark potential
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command must be used before any coefficients are set by the
+:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`, or
+:doc:`read_restart <read_restart>` commands.
+
+Some pair styles are part of specific packages.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  The doc pages for
+individual pair potentials tell if it is part of a package.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`,
+:doc:`pair_modify <pair_modify>`, :doc:`kspace_style <kspace_style>`,
+:doc:`dielectric <dielectric>`, :doc:`pair_write <pair_write>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   pair_style none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
deleted file mode 100644
index 1b8e6d46ec..0000000000
--- a/doc/src/pair_style.txt
+++ /dev/null
@@ -1,337 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style command :h3
-
-[Syntax:]
-
-pair_style style args :pre
-
-style = one of the styles from the list below
-args = arguments used by a particular style :ul
-
-[Examples:]
-
-pair_style lj/cut 2.5
-pair_style eam/alloy
-pair_style hybrid lj/charmm/coul/long 10.0 eam
-pair_style table linear 1000
-pair_style none :pre
-
-[Description:]
-
-Set the formula(s) LAMMPS uses to compute pairwise interactions.  In
-LAMMPS, pair potentials are defined between pairs of atoms that are
-within a cutoff distance and the set of active interactions typically
-changes over time.  See the "bond_style"_bond_style.html command to
-define potentials between pairs of bonded atoms, which typically
-remain in place for the duration of a simulation.
-
-In LAMMPS, pairwise force fields encompass a variety of interactions,
-some of which include many-body effects, e.g. EAM, Stillinger-Weber,
-Tersoff, REBO potentials.  They are still classified as "pairwise"
-potentials because the set of interacting atoms changes with time
-(unlike molecular bonds) and thus a neighbor list is used to find
-nearby interacting atoms.
-
-Hybrid models where specified pairs of atom types interact via
-different pair potentials can be setup using the {hybrid} pair style.
-
-The coefficients associated with a pair style are typically set for
-each pair of atom types, and are specified by the
-"pair_coeff"_pair_coeff.html command or read from a file by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands.
-
-The "pair_modify"_pair_modify.html command sets options for mixing of
-type I-J interaction coefficients and adding energy offsets or tail
-corrections to Lennard-Jones potentials.  Details on these options as
-they pertain to individual potentials are described on the doc page
-for the potential.  Likewise, info on whether the potential
-information is stored in a "restart file"_write_restart.html is listed
-on the potential doc page.
-
-In the formulas listed for each pair style, {E} is the energy of a
-pairwise interaction between two atoms separated by a distance {r}.
-The force between the atoms is the negative derivative of this
-expression.
-
-If the pair_style command has a cutoff argument, it sets global
-cutoffs for all pairs of atom types.  The distance(s) can be smaller
-or larger than the dimensions of the simulation box.
-
-Typically, the global cutoff value can be overridden for a specific
-pair of atom types by the "pair_coeff"_pair_coeff.html command.  The
-pair style settings (including global cutoffs) can be changed by a
-subsequent pair_style command using the same style.  This will reset
-the cutoffs for all atom type pairs, including those previously set
-explicitly by a "pair_coeff"_pair_coeff.html command.  The exceptions
-to this are that pair_style {table} and {hybrid} settings cannot be
-reset.  A new pair_style command for these styles will wipe out all
-previously specified pair_coeff values.
-
-:line
-
-Here is an alphabetic list of pair styles defined in LAMMPS.  They are
-also listed in more compact form on the "Commands
-pair"_Commands_pair.html doc page.
-
-Click on the style to display the formula it computes, any additional
-arguments specified in the pair_style command, and coefficients
-specified by the associated "pair_coeff"_pair_coeff.html command.
-
-There are also additional accelerated pair styles included in the
-LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
-The individual style names on the "Commands pair"_Commands_pair.html
-doc page are followed by one or more of (g,i,k,o,t) to indicate which
-accelerated styles exist.
-
-"none"_pair_none.html - turn off pairwise interactions
-"hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
-"hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions
-"zero"_pair_zero.html - neighbor list but no interactions :ul
-
-"adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
-"agni"_pair_agni.html - machine learned potential mapping atomic environment to forces
-"airebo"_pair_airebo.html - AIREBO potential of Stuart
-"airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
-"atm"_pair_atm.html - Axilrod-Teller-Muto potential
-"awpmd/cut"_pair_awpmd.html - Antisymmetrized Wave Packet MD potential for atoms and electrons
-"beck"_pair_beck.html - Beck potential
-"body/nparticle"_pair_body_nparticle.html - interactions between body particles
-"body/rounded/polygon"_pair_body_rounded_polygon.html - granular-style 2d polygon potential
-"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - granular-style 3d polyhedron potential
-"bop"_pair_bop.html - BOP potential of Pettifor
-"born"_pair_born.html - Born-Mayer-Huggins potential
-"born/coul/dsf"_pair_born.html - Born with damped-shifted-force model
-"born/coul/dsf/cs"_pair_cs.html - Born with damped-shifted-force and core/shell model
-"born/coul/long"_pair_born.html - Born with long-range Coulombics
-"born/coul/long/cs"_pair_cs.html - Born with long-range Coulombics and core/shell
-"born/coul/msm"_pair_born.html - Born with long-range MSM Coulombics
-"born/coul/wolf"_pair_born.html - Born with Wolf potential for Coulombics
-"born/coul/wolf/cs"_pair_cs.html - Born with Wolf potential for Coulombics and core/shell model
-"brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
-"brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
-"buck"_pair_buck.html - Buckingham potential
-"buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
-"buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics
-"buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell
-"buck/coul/msm"_pair_buck.html - Buckingham with long-range MSM Coulombics
-"buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics
-"buck/mdf"_pair_mdf.html - Buckingham with a taper function
-"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with damped-shift-force model
-"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with long-range Coulombics
-"colloid"_pair_colloid.html - integrated colloidal potential
-"comb"_pair_comb.html - charge-optimized many-body (COMB) potential
-"comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
-"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential
-"coul/cut"_pair_coul.html - cutoff Coulombic potential
-"coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
-"coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
-"coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity
-"coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model
-"coul/long"_pair_coul.html - long-range Coulombic potential
-"coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell
-"coul/long/soft"_pair_fep_soft.html - long-range Coulombic potential with a soft core
-"coul/msm"_pair_coul.html - long-range MSM Coulombics
-"coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential
-"coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals
-"coul/wolf"_pair_coul.html - Coulombics via Wolf potential
-"coul/wolf/cs"_pair_cs.html - ditto with core/shell adjustments
-"dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
-"dpd/fdt"_pair_dpd_fdt.html - DPD for constant temperature and pressure
-"dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy
-"dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting
-"dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
-"e3b"_pair_e3b.html - Explicit-three body (E3B) water model
-"drip"_pair_drip.html - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
-"eam"_pair_eam.html - embedded atom method (EAM)
-"eam/alloy"_pair_eam.html - alloy EAM
-"eam/cd"_pair_eam.html - concentration-dependent EAM
-"eam/cd/old"_pair_eam.html - older two-site model for concentration-dependent EAM
-"eam/fs"_pair_eam.html - Finnis-Sinclair EAM
-"edip"_pair_edip.html - three-body EDIP potential
-"edip/multi"_pair_edip.html - multi-element EDIP potential
-"edpd"_pair_meso.html - eDPD particle interactions
-"eff/cut"_pair_eff.html - electron force field with a cutoff
-"eim"_pair_eim.html - embedded ion method (EIM)
-"exp6/rx"_pair_exp6_rx.html - reactive DPD potential
-"extep"_pair_extep.html - extended Tersoff potential
-"gauss"_pair_gauss.html - Gaussian potential
-"gauss/cut"_pair_gauss.html - generalized Gaussian potential
-"gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
-"gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
-"gran/hooke"_pair_gran.html - granular potential with history effects
-"gran/hooke/history"_pair_gran.html - granular potential without history effects
-"gw"_pair_gw.html - Gao-Weber potential
-"gw/zbl"_pair_gw.html - Gao-Weber potential with a repulsive ZBL core
-"hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
-"hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
-"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - registry-dependent interlayer potential (ILP)
-"kim"_pair_kim.html - interface to potentials provided by KIM project
-"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
-"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
-"lebedeva/z"_pair_lebedeva_z.html - Lebedeva interlayer potential for graphene with normals along z-axis
-"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
-"line/lj"_pair_line_lj.html - LJ potential between line segments
-"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file
-"lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
-"lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
-"lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
-"lj/charmm/coul/long/soft"_pair_fep_soft.html - CHARMM with long-range Coulomb and a soft core
-"lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - CHARMM with force switching and shifting
-"lj/charmmfsw/coul/long"_pair_charmm.html - CHARMM with force switching and long-rnage Coulombics
-"lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
-"lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
-"lj/class2/coul/cut/soft"_pair_fep_soft.html - COMPASS with cutoff Coulomb with a soft core
-"lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
-"lj/class2/coul/long/soft"_pair_fep_soft.html - COMPASS with long-range Coulomb with a soft core
-"lj/class2/soft"_pair_fep_soft.html - COMPASS (class 2) force field with no Coulomb with a soft core
-"lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point
-"lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
-"lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
-"lj/cut/coul/cut/soft"_pair_fep_soft.html - LJ with cutoff Coulomb with a soft core
-"lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
-"lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
-"lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
-"lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments
-"lj/cut/coul/long/soft"_pair_fep_soft.html - LJ with long-range Coulombics with a soft core
-"lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
-"lj/cut/coul/wolf"_pair_lj.html - LJ with Coulombics via Wolf potential
-"lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff
-"lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald
-"lj/cut/soft"_pair_fep_soft.html - LJ with a soft core
-"lj/cut/thole/long"_pair_thole.html - LJ with Coulombics with thole damping
-"lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
-"lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
-"lj/cut/tip4p/long/soft"_pair_fep_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core
-"lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
-"lj/expand/coul/long"_pair_lj_expand.html - Lennard-Jones for variable size particles with long-range Coulombics
-"lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
-"lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
-"lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics
-"lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles
-"lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulombics for TIP4P water
-"lj/mdf"_pair_mdf.html - LJ potential with a taper function
-"lj/sdk"_pair_sdk.html - LJ for SDK coarse-graining
-"lj/sdk/coul/long"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics
-"lj/sdk/coul/msm"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics via MSM
-"lj/sf/dipole/sf"_pair_dipole.html - LJ with dipole interaction with shifted forces
-"lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
-"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential
-"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
-"lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
-"lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
-"lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
-"lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics
-"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
-"mdpd"_pair_meso.html - mDPD particle interactions
-"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
-"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
-"meam/spline"_pair_meam_spline.html - splined version of MEAM
-"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
-"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
-"mie/cut"_pair_mie.html - Mie potential
-"mm3/switch3/coulgauss"_pair_mm3_switch3_coulgauss - smoothed MM3 vdW potential with Gaussian electrostatics
-"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field
-"morse"_pair_morse.html - Morse potential
-"morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential
-"morse/soft"_pair_morse.html - Morse potential with a soft core
-"multi/lucy"_pair_multi_lucy.html - DPD potential with density-dependent force
-"multi/lucy/rx"_pair_multi_lucy_rx.html - reactive DPD potential with density-dependent force
-"nb3b/harmonic"_pair_nb3b_harmonic.html - non-bonded 3-body harmonic potential
-"nm/cut"_pair_nm.html - N-M potential
-"nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb
-"nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics
-"oxdna/coaxstk"_pair_oxdna.html -
-"oxdna/excv"_pair_oxdna.html -
-"oxdna/hbond"_pair_oxdna.html -
-"oxdna/stk"_pair_oxdna.html -
-"oxdna/xstk"_pair_oxdna.html -
-"oxdna2/coaxstk"_pair_oxdna2.html -
-"oxdna2/dh"_pair_oxdna2.html -
-"oxdna2/excv"_pair_oxdna2.html -
-"oxdna2/hbond"_pair_oxdna2.html -
-"oxdna2/stk"_pair_oxdna2.html -
-"oxdna2/xstk"_pair_oxdna2.html -
-"peri/eps"_pair_peri.html - peridynamic EPS potential
-"peri/lps"_pair_peri.html - peridynamic LPS potential
-"peri/pmb"_pair_peri.html - peridynamic PMB potential
-"peri/ves"_pair_peri.html - peridynamic VES potential
-"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
-"python"_pair_python.html -
-"quip"_pair_quip.html -
-"reax/c"_pair_reaxc.html - ReaxFF potential in C
-"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
-"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
-"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions
-"smd/hertz"_pair_smd_hertz.html -
-"smd/tlsph"_pair_smd_tlsph.html -
-"smd/tri_surface"_pair_smd_triangulated_surface.html -
-"smd/ulsph"_pair_smd_ulsph.html -
-"smtbq"_pair_smtbq.html -
-"snap"_pair_snap.html - SNAP quantum-accurate potential
-"soft"_pair_soft.html - Soft (cosine) potential
-"sph/heatconduction"_pair_sph_heatconduction.html -
-"sph/idealgas"_pair_sph_idealgas.html -
-"sph/lj"_pair_sph_lj.html -
-"sph/rhosum"_pair_sph_rhosum.html -
-"sph/taitwater"_pair_sph_taitwater.html -
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html -
-"spin/dipole/cut"_pair_spin_dipole.html -
-"spin/dipole/long"_pair_spin_dipole.html -
-"spin/dmi"_pair_spin_dmi.html -
-"spin/exchange"_pair_spin_exchange.html -
-"spin/magelec"_pair_spin_magelec.html -
-"spin/neel"_pair_spin_neel.html -
-"srp"_pair_srp.html -
-"sw"_pair_sw.html - Stillinger-Weber 3-body potential
-"table"_pair_table.html - tabulated pair potential
-"table/rx"_pair_table_rx.html -
-"tdpd"_pair_meso.html - tDPD particle interactions
-"tersoff"_pair_tersoff.html - Tersoff 3-body potential
-"tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential
-"tersoff/mod/c"_pair_tersoff_mod.html -
-"tersoff/table"_pair_tersoff.html -
-"tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential
-"thole"_pair_thole.html - Coulomb interactions with thole damping
-"tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
-"tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
-"tip4p/long/soft"_pair_fep_soft.html -
-"tri/lj"_pair_tri_lj.html - LJ potential between triangles
-"ufm"_pair_ufm.html -
-"vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential
-"vashishta/table"_pair_vashishta.html -
-"yukawa"_pair_yukawa.html - Yukawa potential
-"yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles
-"zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul
-
-:line
-
-[Restrictions:]
-
-This command must be used before any coefficients are set by the
-"pair_coeff"_pair_coeff.html, "read_data"_read_data.html, or
-"read_restart"_read_restart.html commands.
-
-Some pair styles are part of specific packages.  They are only enabled
-if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  The doc pages for
-individual pair potentials tell if it is part of a package.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html, "read_data"_read_data.html,
-"pair_modify"_pair_modify.html, "kspace_style"_kspace_style.html,
-"dielectric"_dielectric.html, "pair_write"_pair_write.html
-
-[Default:]
-
-pair_style none :pre
diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst
new file mode 100644
index 0000000000..ae09daf919
--- /dev/null
+++ b/doc/src/pair_sw.rst
@@ -0,0 +1,246 @@
+.. index:: pair\_style sw
+
+pair\_style sw command
+======================
+
+pair\_style sw/gpu command
+==========================
+
+pair\_style sw/intel command
+============================
+
+pair\_style sw/kk command
+=========================
+
+pair\_style sw/omp command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style sw
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style sw
+   pair_coeff \* \* si.sw Si
+   pair_coeff \* \* GaN.sw Ga N Ga
+
+Description
+"""""""""""
+
+The *sw* style computes a 3-body :ref:`Stillinger-Weber <Stillinger2>`
+potential for the energy E of a system of atoms as
+
+.. image:: Eqs/pair_sw.jpg
+   :align: center
+
+where phi2 is a two-body term and phi3 is a three-body term.  The
+summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance = a\*sigma.
+
+Only a single pair\_coeff command is used with the *sw* style which
+specifies a Stillinger-Weber potential file with parameters for all
+needed elements.  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of SW elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine a file SiC.sw has Stillinger-Weber values for
+Si and C.  If your LAMMPS simulation has 4 atoms types and you want
+the 1st 3 to be Si, and the 4th to be C, you would use the following
+pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* SiC.sw Si Si Si C
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the SW file.  The final C argument maps LAMMPS atom type 4
+to the C element in the SW file.  If a mapping value is specified as
+NULL, the mapping is not performed.  This can be used when a *sw*
+potential is used as part of the *hybrid* pair style.  The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+
+Stillinger-Weber files in the *potentials* directory of the LAMMPS
+distribution have a ".sw" suffix.  Lines that are not blank or
+comments (starting with #) define parameters for a triplet of
+elements.  The parameters in a single entry correspond to the two-body
+and three-body coefficients in the formula above:
+
+* element 1 (the center atom in a 3-body interaction)
+* element 2
+* element 3
+* epsilon (energy units)
+* sigma (distance units)
+* a
+* lambda
+* gamma
+* costheta0
+* A
+* B
+* p
+* q
+* tol
+
+The A, B, p, and q parameters are used only for two-body
+interactions.  The lambda and costheta0 parameters are used only for
+three-body interactions. The epsilon, sigma and a parameters are used
+for both two-body and three-body interactions. gamma is used only in the
+three-body interactions, but is defined for pairs of atoms.
+The non-annotated parameters are unitless.
+
+LAMMPS introduces an additional performance-optimization parameter tol
+that is used for both two-body and three-body interactions.  In the
+Stillinger-Weber potential, the interaction energies become negligibly
+small at atomic separations substantially less than the theoretical
+cutoff distances.  LAMMPS therefore defines a virtual cutoff distance
+based on a user defined tolerance tol.  The use of the virtual cutoff
+distance in constructing atom neighbor lists can significantly reduce
+the neighbor list sizes and therefore the computational cost.  LAMMPS
+provides a *tol* value for each of the three-body entries so that they
+can be separately controlled. If tol = 0.0, then the standard
+Stillinger-Weber cutoff is used.
+
+The Stillinger-Weber potential file must contain entries for all the
+elements listed in the pair\_coeff command.  It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. SiSiSi).  For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify SW parameters for all permutations of the two elements
+interacting in three-body configurations.  Thus for 3 elements, 27
+entries would be required, etc.
+
+As annotated above, the first element in the entry is the center atom
+in a three-body interaction.  Thus an entry for SiCC means a Si atom
+with 2 C atoms as neighbors.  The parameter values used for the
+two-body interaction come from the entry where the 2nd and 3rd
+elements are the same.  Thus the two-body parameters for Si
+interacting with C, comes from the SiCC entry.  The three-body
+parameters can in principle be specific to the three elements of the
+configuration. In the literature, however, the three-body parameters
+are usually defined by simple formulas involving two sets of pair-wise
+parameters, corresponding to the ij and ik pairs, where i is the
+center atom. The user must ensure that the correct combining rule is
+used to calculate the values of the three-body parameters for
+alloys. Note also that the function phi3 contains two exponential
+screening factors with parameter values from the ij pair and ik
+pairs. So phi3 for a C atom bonded to a Si atom and a second C atom
+will depend on the three-body parameters for the CSiC entry, and also
+on the two-body parameters for the CCC and CSiSi entries. Since the
+order of the two neighbors is arbitrary, the three-body parameters for
+entries CSiC and CCSi should be the same.  Similarly, the two-body
+parameters for entries SiCC and CSiSi should also be the same.  The
+parameters used only for two-body interactions (A, B, p, and q) in
+entries whose 2nd and 3rd element are different (e.g. SiCSi) are not
+used for anything and can be set to 0.0 if desired.
+This is also true for the parameters in phi3 that are
+taken from the ij and ik pairs (sigma, a, gamma)
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+When using the USER-INTEL package with this style, there is an
+additional 5 to 10 percent performance improvement when the
+Stillinger-Weber parameters p and q are set to 4 and 0 respectively.
+These parameters are common for modeling silicon and water.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The Stillinger-Weber potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal :doc:`units <units>`.
+You can use the SW potential with any LAMMPS units, but you would need
+to create your own SW potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Stillinger2:
+
+
+
+**(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst
new file mode 100644
index 0000000000..202832dfe7
--- /dev/null
+++ b/doc/src/pair_table.rst
@@ -0,0 +1,301 @@
+.. index:: pair\_style table
+
+pair\_style table command
+=========================
+
+pair\_style table/gpu command
+=============================
+
+pair\_style table/kk command
+============================
+
+pair\_style table/omp command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style table style N keyword ...
+
+* style = *lookup* or *linear* or *spline* or *bitmap* = method of interpolation
+* N = use N values in *lookup*\ , *linear*\ , *spline* tables
+* N = use 2\^N values in *bitmap* tables
+* zero or more keywords may be appended
+* keyword = *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style table linear 1000
+   pair_style table linear 1000 pppm
+   pair_style table bitmap 12
+   pair_coeff \* 3 morse.table ENTRY1
+   pair_coeff \* 3 morse.table ENTRY1 7.0
+
+Description
+"""""""""""
+
+Style *table* creates interpolation tables from potential energy and
+force values listed in a file(s) as a function of distance.  When
+performing dynamics or minimization, the interpolation tables are used
+to evaluate energy and forces for pairwise interactions between
+particles, similar to how analytic formulas are used for other pair
+styles.
+
+The interpolation tables are created as a pre-computation by fitting
+cubic splines to the file values and interpolating energy and force
+values at each of *N* distances.  During a simulation, the tables are
+used to interpolate energy and force values as needed for each pair of
+particles separated by a distance *R*\ .  The interpolation is done in
+one of 4 styles: *lookup*\ , *linear*\ , *spline*\ , or *bitmap*\ .
+
+For the *lookup* style, the distance *R* is used to find the nearest
+table entry, which is the energy or force.
+
+For the *linear* style, the distance *R* is used to find the 2
+surrounding table values from which an energy or force is computed by
+linear interpolation.
+
+For the *spline* style, a cubic spline coefficients are computed and
+stored for each of the *N* values in the table, one set of splines for
+energy, another for force.  Note that these splines are different than
+the ones used to pre-compute the *N* values.  Those splines were fit
+to the *Nfile* values in the tabulated file, where often *Nfile* <
+*N*\ .  The distance *R* is used to find the appropriate set of spline
+coefficients which are used to evaluate a cubic polynomial which
+computes the energy or force.
+
+For the *bitmap* style, the specified *N* is used to create
+interpolation tables that are 2\^N in length.  The distance *R* is used
+to index into the table via a fast bit-mapping technique due to
+:ref:`(Wolff) <Wolff2>`, and a linear interpolation is performed between
+adjacent table values.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* filename
+* keyword
+* cutoff (distance units)
+
+The filename specifies a file containing tabulated energy and force
+values.  The keyword specifies a section of the file.  The cutoff is
+an optional coefficient.  If not specified, the outer cutoff in the
+table itself (see below) will be used to build an interpolation table
+that extend to the largest tabulated distance.  If specified, only
+file values up to the cutoff are used to create the interpolation
+table.  The format of this file is described below.
+
+If your tabulated potential(s) are designed to be used as the
+short-range part of one of the long-range solvers specified by the
+:doc:`kspace\_style <kspace_style>` command, then you must use one or
+more of the optional keywords listed above for the pair\_style command.
+These are *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*\ .  This
+is so LAMMPS can insure the short-range potential and long-range
+solver are compatible with each other, as it does for other
+short-range pair styles, such as :doc:`pair\_style lj/cut/coul/long <pair_lj>`.  Note that it is up to you to insure
+the tabulated values for each pair of atom types has the correct
+functional form to be compatible with the matching long-range solver.
+
+
+----------
+
+
+Here are some guidelines for using the pair\_style table command to
+best effect:
+
+* Vary the number of table points; you may need to use more than you think
+  to get good resolution.
+* Always use the :doc:`pair\_write <pair_write>` command to produce a plot
+  of what the final interpolated potential looks like.  This can show up
+  interpolation "features" you may not like.
+* Start with the linear style; it's the style least likely to have problems.
+* Use *N* in the pair\_style command equal to the "N" in the tabulation
+  file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation
+  is not needed.  See discussion below.
+* Make sure that your tabulated forces and tabulated energies are
+  consistent (dE/dr = -F) over the entire range of r values.  LAMMPS
+  will warn if this is not the case.
+* Use as large an inner cutoff as possible.  This avoids fitting splines
+  to very steep parts of the potential.
+
+
+
+----------
+
+
+The format of a tabulated file is a series of one or more sections,
+defined as follows (without the parenthesized comments):
+
+
+.. parsed-literal::
+
+   # Morse potential for Fe   (one or more comment or blank lines)
+
+   MORSE_FE                   (keyword is first text on line)
+   N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
+                              (blank)
+   1 1.0 25.5 102.34          (index, r, energy, force)
+   2 1.02 23.4 98.5
+   ...
+   500 10.0 0.001 0.003
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.  The first line begins with a keyword which
+identifies the section.  The line can contain additional text, but the
+initial text must match the argument specified in the pair\_coeff
+command.  The next line lists (in any order) one or more parameters
+for the table.  Each parameter is a keyword followed by one or more
+numeric values.
+
+The parameter "N" is required and its value is the number of table
+entries that follow.  Note that this may be different than the *N*
+specified in the :doc:`pair\_style table <pair_style>` command.  Let
+Ntable = *N* in the pair\_style command, and Nfile = "N" in the
+tabulated file.  What LAMMPS does is a preliminary interpolation by
+creating splines using the Nfile tabulated values as nodal points.  It
+uses these to interpolate energy and force values at Ntable different
+points.  The resulting tables of length Ntable are then used as
+described above, when computing energy and force for individual pair
+distances.  This means that if you want the interpolation tables of
+length Ntable to match exactly what is in the tabulated file (with
+effectively no preliminary interpolation), you should set Ntable =
+Nfile, and use the "RSQ" or "BITMAP" parameter.  This is because the
+internal table abscissa is always RSQ (separation distance squared),
+for efficient lookup.
+
+All other parameters are optional.  If "R" or "RSQ" or "BITMAP" does
+not appear, then the distances in each line of the table are used
+as-is to perform spline interpolation.  In this case, the table values
+can be spaced in *r* uniformly or however you wish to position table
+values in regions of large gradients.
+
+If used, the parameters "R" or "RSQ" are followed by 2 values *rlo*
+and *rhi*\ .  If specified, the distance associated with each energy and
+force value is computed from these 2 values (at high accuracy), rather
+than using the (low-accuracy) value listed in each line of the table.
+The distance values in the table file are ignored in this case.
+For "R", distances uniformly spaced between *rlo* and *rhi* are
+computed; for "RSQ", squared distances uniformly spaced between
+*rlo\*rlo* and *rhi\*rhi* are computed.
+
+.. note::
+
+   If you use "R" or "RSQ", the tabulated distance values in the
+   file are effectively ignored, and replaced by new values as described
+   in the previous paragraph.  If the distance value in the table is not
+   very close to the new value (i.e. round-off difference), then you will
+   be assigning energy/force values to a different distance, which is
+   probably not what you want.  LAMMPS will warn if this is occurring.
+
+If used, the parameter "BITMAP" is also followed by 2 values *rlo* and
+*rhi*\ .  These values, along with the "N" value determine the ordering
+of the N lines that follow and what distance is associated with each.
+This ordering is complex, so it is not documented here, since this
+file is typically produced by the :doc:`pair\_write <pair_write>` command
+with its *bitmap* option.  When the table is in BITMAP format, the "N"
+parameter in the file must be equal to 2\^M where M is the value
+specified in the pair\_style command.  Also, a cutoff parameter cannot
+be used as an optional 3rd argument in the pair\_coeff command; the
+entire table extent as specified in the file must be used.
+
+If used, the parameter "FPRIME" is followed by 2 values *fplo* and
+*fphi* which are the derivative of the force at the innermost and
+outermost distances listed in the table.  These values are needed by
+the spline construction routines.  If not specified by the "FPRIME"
+parameter, they are estimated (less accurately) by the first 2 and
+last 2 force values in the table.  This parameter is not used by
+BITMAP tables.
+
+Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+r (in distance units), the 3rd value is the energy (in energy units),
+and the 4th is the force (in force units).  The r values must increase
+from one line to the next (unless the BITMAP parameter is specified).
+
+Note that one file can contain many sections, each with a tabulated
+potential.  LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+The :doc:`pair\_modify <pair_modify>` shift, table, and tail options are
+not relevant for this pair style.
+
+This pair style writes the settings for the "pair\_style table" command
+to :doc:`binary restart files <restart>`, so a pair\_style command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file, since it is tabulated in the potential files.  Thus, pair\_coeff
+commands do need to be specified in the restart input script.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_write <pair_write>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Wolff2:
+
+
+
+**(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst
new file mode 100644
index 0000000000..e04f12e715
--- /dev/null
+++ b/doc/src/pair_table_rx.rst
@@ -0,0 +1,288 @@
+.. index:: pair\_style table/rx
+
+pair\_style table/rx command
+============================
+
+pair\_style table/rx/kk command
+===============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style table style N ...
+
+* style = *lookup* or *linear* or *spline* or *bitmap* = method of interpolation
+* N = use N values in *lookup*\ , *linear*\ , *spline* tables
+* weighting = fractional or molecular (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style table/rx linear 1000
+   pair_style table/rx linear 1000 fractional
+   pair_style table/rx linear 1000 molecular
+   pair_coeff \* \* rxn.table ENTRY1 h2o h2o 10.0
+   pair_coeff \* \* rxn.table ENTRY1 1fluid 1fluid 10.0
+   pair_coeff \* 3 rxn.table ENTRY1 h2o no2 10.0
+
+Description
+"""""""""""
+
+Style *table/rx* is used in reaction DPD simulations,where the
+coarse-grained (CG) particles are composed of *m* species whose
+reaction rate kinetics are determined from a set of *n* reaction rate
+equations through the :doc:`fix rx <fix_rx>` command.  The species of
+one CG particle can interact with a species in a neighboring CG
+particle through a site-site interaction potential model. Style
+*table/rx* creates interpolation tables of length *N* from pair
+potential and force values listed in a file(s) as a function of
+distance.  The files are read by the :doc:`pair\_coeff <pair_coeff>`
+command.
+
+The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and force values at each of *N*
+distances.  During a simulation, these tables are used to interpolate
+energy and force values as needed.  The interpolation is done in one
+of 4 styles: *lookup*\ , *linear*\ , *spline*\ , or *bitmap*\ .
+
+For the *lookup* style, the distance between 2 atoms is used to find
+the nearest table entry, which is the energy or force.
+
+For the *linear* style, the pair distance is used to find 2
+surrounding table values from which an energy or force is computed by
+linear interpolation.
+
+For the *spline* style, a cubic spline coefficients are computed and
+stored at each of the *N* values in the table.  The pair distance is
+used to find the appropriate set of coefficients which are used to
+evaluate a cubic polynomial which computes the energy or force.
+
+For the *bitmap* style, the N means to create interpolation tables
+that are 2\^N in length.  The pair distance is used to index into the
+table via a fast bit-mapping technique :ref:`(Wolff) <Wolff>` and a linear
+interpolation is performed between adjacent table values.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above.
+
+* filename
+* keyword
+* species1
+* species2
+* cutoff (distance units)
+
+The filename specifies a file containing tabulated energy and force
+values.  The keyword specifies a section of the file.  The cutoff is
+an optional coefficient.  If not specified, the outer cutoff in the
+table itself (see below) will be used to build an interpolation table
+that extend to the largest tabulated distance.  If specified, only
+file values up to the cutoff are used to create the interpolation
+table.  The format of this file is described below.
+
+The species tags define the site-site interaction potential between
+two species contained within two different particles.  The species
+tags must either correspond to the species defined in the reaction
+kinetics files specified with the :doc:`fix rx <fix_rx>` command or they
+must correspond to the tag "1fluid", signifying interaction with a
+product species mixture determined through a one-fluid approximation.
+The interaction potential is weighted by the geometric average of
+either the mole fraction concentrations or the number of molecules
+associated with the interacting coarse-grained particles (see the
+*fractional* or *molecular* weighting pair style options). The coarse-grained potential is
+stored before and after the reaction kinetics solver is applied, where
+the difference is defined to be the internal chemical energy (uChem).
+
+
+----------
+
+
+Here are some guidelines for using the pair\_style table/rx command to
+best effect:
+
+* Vary the number of table points; you may need to use more than you think
+  to get good resolution.
+* Always use the :doc:`pair\_write <pair_write>` command to produce a plot
+  of what the final interpolated potential looks like.  This can show up
+  interpolation "features" you may not like.
+* Start with the linear style; it's the style least likely to have problems.
+* Use *N* in the pair\_style command equal to the "N" in the tabulation
+  file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation
+  is not needed.  See discussion below.
+* Make sure that your tabulated forces and tabulated energies are consistent
+  (dE/dr = -F) along the entire range of r values.
+* Use as large an inner cutoff as possible.  This avoids fitting splines
+  to very steep parts of the potential.
+
+
+
+----------
+
+
+The format of a tabulated file is a series of one or more sections,
+defined as follows (without the parenthesized comments):
+
+
+.. parsed-literal::
+
+   # Morse potential for Fe   (one or more comment or blank lines)
+
+   MORSE_FE                   (keyword is first text on line)
+   N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
+                              (blank)
+   1 1.0 25.5 102.34          (index, r, energy, force)
+   2 1.02 23.4 98.5
+   ...
+   500 10.0 0.001 0.003
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.  The first line begins with a keyword which
+identifies the section.  The line can contain additional text, but the
+initial text must match the argument specified in the pair\_coeff
+command.  The next line lists (in any order) one or more parameters
+for the table.  Each parameter is a keyword followed by one or more
+numeric values.
+
+The parameter "N" is required and its value is the number of table
+entries that follow.  Note that this may be different than the *N*
+specified in the :doc:`pair\_style table/rx <pair_style>` command.  Let
+Ntable = *N* in the pair\_style command, and Nfile = "N" in the
+tabulated file.  What LAMMPS does is a preliminary interpolation by
+creating splines using the Nfile tabulated values as nodal points.  It
+uses these to interpolate as needed to generate energy and force
+values at Ntable different points.  The resulting tables of length
+Ntable are then used as described above, when computing energy and
+force for individual pair distances.  This means that if you want the
+interpolation tables of length Ntable to match exactly what is in the
+tabulated file (with effectively no preliminary interpolation), you
+should set Ntable = Nfile, and use the "RSQ" or "BITMAP" parameter.
+The internal table abscissa is RSQ (separation distance squared).
+
+All other parameters are optional.  If "R" or "RSQ" or "BITMAP" does
+not appear, then the distances in each line of the table are used
+as-is to perform spline interpolation.  In this case, the table values
+can be spaced in *r* uniformly or however you wish to position table
+values in regions of large gradients.
+
+If used, the parameters "R" or "RSQ" are followed by 2 values *rlo*
+and *rhi*\ .  If specified, the distance associated with each energy and
+force value is computed from these 2 values (at high accuracy), rather
+than using the (low-accuracy) value listed in each line of the table.
+The distance values in the table file are ignored in this case.
+For "R", distances uniformly spaced between *rlo* and *rhi* are
+computed; for "RSQ", squared distances uniformly spaced between
+*rlo\*rlo* and *rhi\*rhi* are computed.
+
+If used, the parameter "BITMAP" is also followed by 2 values *rlo* and
+*rhi*\ .  These values, along with the "N" value determine the ordering
+of the N lines that follow and what distance is associated with each.
+This ordering is complex, so it is not documented here, since this
+file is typically produced by the :doc:`pair\_write <pair_write>` command
+with its *bitmap* option.  When the table is in BITMAP format, the "N"
+parameter in the file must be equal to 2\^M where M is the value
+specified in the pair\_style command.  Also, a cutoff parameter cannot
+be used as an optional 3rd argument in the pair\_coeff command; the
+entire table extent as specified in the file must be used.
+
+If used, the parameter "FPRIME" is followed by 2 values *fplo* and
+*fphi* which are the derivative of the force at the innermost and
+outermost distances listed in the table.  These values are needed by
+the spline construction routines.  If not specified by the "FPRIME"
+parameter, they are estimated (less accurately) by the first 2 and
+last 2 force values in the table.  This parameter is not used by
+BITMAP tables.
+
+Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+r (in distance units), the 3rd value is the energy (in energy units),
+and the 4th is the force (in force units).  The r values must increase
+from one line to the next (unless the BITMAP parameter is specified).
+
+Note that one file can contain many sections, each with a tabulated
+potential.  LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+The :doc:`pair\_modify <pair_modify>` shift, table, and tail options are
+not relevant for this pair style.
+
+This pair style writes the settings for the "pair\_style table/rx" command
+to :doc:`binary restart files <restart>`, so a pair\_style command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file, since it is tabulated in the potential files.  Thus, pair\_coeff
+commands do need to be specified in the restart input script.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the USER-DPD package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** fractional weighting
+
+
+----------
+
+
+.. _Wolff:
+
+
+
+**(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst
new file mode 100644
index 0000000000..773ee649df
--- /dev/null
+++ b/doc/src/pair_tersoff.rst
@@ -0,0 +1,294 @@
+.. index:: pair\_style tersoff
+
+pair\_style tersoff command
+===========================
+
+pair\_style tersoff/table command
+=================================
+
+pair\_style tersoff/gpu command
+===============================
+
+pair\_style tersoff/intel command
+=================================
+
+pair\_style tersoff/kk command
+==============================
+
+pair\_style tersoff/omp command
+===============================
+
+pair\_style tersoff/table/omp command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style
+
+* style = *tersoff* or *tersoff/table* or *tersoff/gpu* or *tersoff/omp* or *tersoff/table/omp*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style tersoff
+   pair_coeff \* \* Si.tersoff Si
+   pair_coeff \* \* SiC.tersoff Si C Si
+
+   pair_style tersoff/table
+   pair_coeff \* \* SiCGe.tersoff Si(D)
+
+Description
+"""""""""""
+
+The *tersoff* style computes a 3-body Tersoff potential
+:ref:`(Tersoff\_1) <Tersoff_11>` for the energy E of a system of atoms as
+
+.. image:: Eqs/pair_tersoff_1.jpg
+   :align: center
+
+where f\_R is a two-body term and f\_A includes three-body interactions.
+The summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance = R + D.
+
+The *tersoff/table* style uses tabulated forms for the two-body,
+environment and angular functions. Linear interpolation is performed
+between adjacent table entries. The table length is chosen to be
+accurate within 10\^-6 with respect to the *tersoff* style energy.
+The *tersoff/table* should give better performance in terms of speed.
+
+Only a single pair\_coeff command is used with the *tersoff* style
+which specifies a Tersoff potential file with parameters for all
+needed elements.  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of Tersoff elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine the SiC.tersoff file has Tersoff values for Si
+and C.  If your LAMMPS simulation has 4 atoms types and you want the
+1st 3 to be Si, and the 4th to be C, you would use the following
+pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* SiC.tersoff Si Si Si C
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the Tersoff file.  The final C argument maps LAMMPS atom
+type 4 to the C element in the Tersoff file.  If a mapping value is
+specified as NULL, the mapping is not performed.  This can be used
+when a *tersoff* potential is used as part of the *hybrid* pair style.
+The NULL values are placeholders for atom types that will be used with
+other potentials.
+
+Tersoff files in the *potentials* directory of the LAMMPS distribution
+have a ".tersoff" suffix.  Lines that are not blank or comments
+(starting with #) define parameters for a triplet of elements.  The
+parameters in a single entry correspond to coefficients in the formula
+above:
+
+* element 1 (the center atom in a 3-body interaction)
+* element 2 (the atom bonded to the center atom)
+* element 3 (the atom influencing the 1-2 bond in a bond-order sense)
+* m
+* gamma
+* lambda3 (1/distance units)
+* c
+* d
+* costheta0 (can be a value < -1 or > 1)
+* n
+* beta
+* lambda2 (1/distance units)
+* B (energy units)
+* R (distance units)
+* D (distance units)
+* lambda1 (1/distance units)
+* A (energy units)
+
+The n, beta, lambda2, B, lambda1, and A parameters are only used for
+two-body interactions.  The m, gamma, lambda3, c, d, and costheta0
+parameters are only used for three-body interactions. The R and D
+parameters are used for both two-body and three-body interactions. The
+non-annotated parameters are unitless.  The value of m must be 3 or 1.
+
+The Tersoff potential file must contain entries for all the elements
+listed in the pair\_coeff command.  It can also contain entries for
+additional elements not being used in a particular simulation; LAMMPS
+ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. SiSiSi).  For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify Tersoff parameters for all permutations of the two elements
+interacting in three-body configurations.  Thus for 3 elements, 27
+entries would be required, etc.
+
+As annotated above, the first element in the entry is the center atom
+in a three-body interaction and it is bonded to the 2nd atom and the
+bond is influenced by the 3rd atom.  Thus an entry for SiCC means Si
+bonded to a C with another C atom influencing the bond.  Thus
+three-body parameters for SiCSi and SiSiC entries will not, in
+general, be the same.  The parameters used for the two-body
+interaction come from the entry where the 2nd element is repeated.
+Thus the two-body parameters for Si interacting with C, comes from the
+SiCC entry.
+
+The parameters used for a particular
+three-body interaction come from the entry with the corresponding
+three elements.  The parameters used only for two-body interactions
+(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
+element are different (e.g. SiCSi) are not used for anything and can
+be set to 0.0 if desired.
+
+Note that the twobody parameters in entries such as SiCC and CSiSi
+are often the same, due to the common use of symmetric mixing rules,
+but this is not always the case. For example, the beta and n parameters in
+Tersoff\_2 :ref:`(Tersoff\_2) <Tersoff_21>` are not symmetric.
+
+We chose the above form so as to enable users to define all commonly
+used variants of the Tersoff potential.  In particular, our form
+reduces to the original Tersoff form when m = 3 and gamma = 1, while
+it reduces to the form of :ref:`Albe et al. <Albe>` when beta = 1 and m = 1.
+Note that in the current Tersoff implementation in LAMMPS, m must be
+specified as either 3 or 1.  Tersoff used a slightly different but
+equivalent form for alloys, which we will refer to as Tersoff\_2
+potential :ref:`(Tersoff\_2) <Tersoff_21>`. The *tersoff/table* style implements
+Tersoff\_2 parameterization only.
+
+LAMMPS parameter values for Tersoff\_2 can be obtained as follows:
+gamma\_ijk = omega\_ik, lambda3 = 0 and the value of
+m has no effect.  The parameters for species i and j can be calculated
+using the Tersoff\_2 mixing rules:
+
+.. image:: Eqs/pair_tersoff_2.jpg
+   :align: center
+
+Tersoff\_2 parameters R and S must be converted to the LAMMPS
+parameters R and D (R is different in both forms), using the following
+relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
+Tersoff\_2 parameters.
+
+In the potentials directory, the file SiCGe.tersoff provides the
+LAMMPS parameters for Tersoff's various versions of Si, as well as his
+alloy parameters for Si, C, and Ge. This file can be used for pure Si,
+(three different versions), pure C, pure Ge, binary SiC, and binary
+SiGe.  LAMMPS will generate an error if this file is used with any
+combination involving C and Ge, since there are no entries for the GeC
+interactions (Tersoff did not publish parameters for this
+cross-interaction.)  Tersoff files are also provided for the SiC alloy
+(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
+
+Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
+for helping clarify how Tersoff parameters for alloys have been
+defined in various papers.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The Tersoff potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal :doc:`units <units>`.  You can
+use the Tersoff potential with any LAMMPS units, but you would need to
+create your own Tersoff potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Tersoff\_11:
+
+
+
+**(Tersoff\_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988).
+
+.. _Albe:
+
+
+
+**(Albe)** J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.:
+Condens. Matter, 15, 5649(2003).
+
+.. _Tersoff\_21:
+
+
+
+**(Tersoff\_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst
new file mode 100644
index 0000000000..15cce523f7
--- /dev/null
+++ b/doc/src/pair_tersoff_mod.rst
@@ -0,0 +1,252 @@
+.. index:: pair\_style tersoff/mod
+
+pair\_style tersoff/mod command
+===============================
+
+pair\_style tersoff/mod/c command
+=================================
+
+pair\_style tersoff/mod/gpu command
+===================================
+
+pair\_style tersoff/mod/kk command
+==================================
+
+pair\_style tersoff/mod/omp command
+===================================
+
+pair\_style tersoff/mod/c/omp command
+=====================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style tersoff/mod
+
+   pair_style tersoff/mod/c
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style tersoff/mod
+   pair_coeff \* \* Si.tersoff.mod Si Si
+
+   pair_style tersoff/mod/c
+   pair_coeff \* \* Si.tersoff.modc Si Si
+
+Description
+"""""""""""
+
+The *tersoff/mod* and *tersoff/mod/c* styles computes a bond-order type
+interatomic potential :ref:`(Kumagai) <Kumagai>` based on a 3-body Tersoff
+potential :ref:`(Tersoff\_1) <Tersoff_12>`, :ref:`(Tersoff\_2) <Tersoff_22>` with
+modified cutoff function and angular-dependent term, giving the energy
+E of a system of atoms as
+
+.. image:: Eqs/pair_tersoff_mod.jpg
+   :align: center
+
+where f\_R is a two-body term and f\_A includes three-body interactions.
+The summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance = R + D.
+The *tersoff/mod/c* style differs from *tersoff/mod* only in the
+formulation of the V\_ij term, where it contains an additional c0 term.
+
+.. image:: Eqs/pair_tersoff_mod_c.jpg
+   :align: center
+
+The modified cutoff function f\_C proposed by :ref:`(Murty) <Murty>` and
+having a continuous second-order differential is employed. The
+angular-dependent term g(theta) was modified to increase the
+flexibility of the potential.
+
+The *tersoff/mod* potential is fitted to both the elastic constants
+and melting point by employing the modified Tersoff potential function
+form in which the angular-dependent term is improved. The model
+performs extremely well in describing the crystalline, liquid, and
+amorphous phases :ref:`(Schelling) <Schelling>`.
+
+Only a single pair\_coeff command is used with the *tersoff/mod* style
+which specifies a Tersoff/MOD potential file with parameters for all
+needed elements.  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of Tersoff/MOD elements to atom types
+
+As an example, imagine the Si.tersoff\_mod file has Tersoff values for Si.
+If your LAMMPS simulation has 3 Si atoms types, you would use the following
+pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* Si.tersoff_mod Si Si Si
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
+in the Tersoff/MOD file. If a mapping value is specified as NULL, the
+mapping is not performed.  This can be used when a *tersoff/mod*
+potential is used as part of the *hybrid* pair style. The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+
+Tersoff/MOD file in the *potentials* directory of the LAMMPS
+distribution have a ".tersoff.mod" suffix. Potential files for the
+*tersoff/mod/c* style have the suffix ".tersoff.modc". Lines that are
+not blank or comments (starting with #) define parameters for a triplet
+of elements.  The parameters in a single entry correspond to
+coefficients in the formulae above:
+
+element 1 (the center atom in a 3-body interaction)
+element 2 (the atom bonded to the center atom)
+element 3 (the atom influencing the 1-2 bond in a bond-order sense)
+beta
+alpha
+h
+eta
+beta\_ters = 1 (dummy parameter)
+lambda2 (1/distance units)
+B (energy units)
+R (distance units)
+D (distance units)
+lambda1 (1/distance units)
+A (energy units)
+n
+c1
+c2
+c3
+c4
+c5
+c0 (energy units, tersoff/mod/c only):ul
+
+The n, eta, lambda2, B, lambda1, and A parameters are only used for
+two-body interactions.  The beta, alpha, c1, c2, c3, c4, c5, h
+parameters are only used for three-body interactions. The R and D
+parameters are used for both two-body and three-body interactions.
+The c0 term applies to *tersoff/mod/c* only. The non-annotated
+parameters are unitless.
+
+The Tersoff/MOD potential file must contain entries for all the elements
+listed in the pair\_coeff command.  It can also contain entries for
+additional elements not being used in a particular simulation; LAMMPS
+ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. SiSiSi). As annotated above, the first element in the entry is
+the center atom in a three-body interaction and it is bonded to the
+2nd atom and the bond is influenced by the 3rd atom.  Thus an entry
+for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The Tersoff/MOD potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal :doc:`units <units>`.  You can
+use the Tersoff/MOD potential with any LAMMPS units, but you would need to
+create your own Tersoff/MOD potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Kumagai:
+
+
+
+**(Kumagai)** T. Kumagai, S. Izumi, S. Hara, S. Sakai,
+Comp. Mat. Science, 39, 457 (2007).
+
+.. _Tersoff\_12:
+
+
+
+**(Tersoff\_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988).
+
+.. _Tersoff\_22:
+
+
+
+**(Tersoff\_2)** J. Tersoff, Phys Rev B, 38, 9902 (1988).
+
+.. _Murty:
+
+
+
+**(Murty)** M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).
+
+.. _Schelling:
+
+
+
+**(Schelling)** Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst
new file mode 100644
index 0000000000..fecc22c31a
--- /dev/null
+++ b/doc/src/pair_tersoff_zbl.rst
@@ -0,0 +1,306 @@
+.. index:: pair\_style tersoff/zbl
+
+pair\_style tersoff/zbl command
+===============================
+
+pair\_style tersoff/zbl/gpu command
+===================================
+
+pair\_style tersoff/zbl/kk command
+==================================
+
+pair\_style tersoff/zbl/omp command
+===================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style tersoff/zbl
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style tersoff/zbl
+   pair_coeff \* \* SiC.tersoff.zbl Si C Si
+
+Description
+"""""""""""
+
+The *tersoff/zbl* style computes a 3-body Tersoff potential
+:ref:`(Tersoff\_1) <zbl-Tersoff_1>` with a close-separation pairwise modification
+based on a Coulomb potential and the Ziegler-Biersack-Littmark
+universal screening function :ref:`(ZBL) <zbl-ZBL>`, giving the energy E of a
+system of atoms as
+
+.. image:: Eqs/pair_tersoff_zbl.jpg
+   :align: center
+
+The f\_F term is a fermi-like function used to smoothly connect the ZBL
+repulsive potential with the Tersoff potential.  There are 2
+parameters used to adjust it: A\_F and r\_C.  A\_F controls how "sharp"
+the transition is between the two, and r\_C is essentially the cutoff
+for the ZBL potential.
+
+For the ZBL portion, there are two terms. The first is the Coulomb
+repulsive term, with Z1, Z2 as the number of protons in each nucleus,
+e as the electron charge (1 for metal and real units) and epsilon0 as
+the permittivity of vacuum.  The second part is the ZBL universal
+screening function, with a0 being the Bohr radius (typically 0.529
+Angstroms), and the remainder of the coefficients provided by the
+original paper.  This screening function should be applicable to most
+systems.  However, it is only accurate for small separations
+(i.e. less than 1 Angstrom).
+
+For the Tersoff portion, f\_R is a two-body term and f\_A includes
+three-body interactions. The summations in the formula are over all
+neighbors J and K of atom I within a cutoff distance = R + D.
+
+Only a single pair\_coeff command is used with the *tersoff/zbl* style
+which specifies a Tersoff/ZBL potential file with parameters for all
+needed elements.  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of Tersoff/ZBL elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values
+for Si and C.  If your LAMMPS simulation has 4 atoms types and you
+want the 1st 3 to be Si, and the 4th to be C, you would use the
+following pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* SiC.tersoff Si Si Si C
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the Tersoff/ZBL file.  The final C argument maps LAMMPS
+atom type 4 to the C element in the Tersoff/ZBL file.  If a mapping
+value is specified as NULL, the mapping is not performed.  This can be
+used when a *tersoff/zbl* potential is used as part of the *hybrid*
+pair style.  The NULL values are placeholders for atom types that will
+be used with other potentials.
+
+Tersoff/ZBL files in the *potentials* directory of the LAMMPS
+distribution have a ".tersoff.zbl" suffix.  Lines that are not blank
+or comments (starting with #) define parameters for a triplet of
+elements.  The parameters in a single entry correspond to coefficients
+in the formula above:
+
+* element 1 (the center atom in a 3-body interaction)
+* element 2 (the atom bonded to the center atom)
+* element 3 (the atom influencing the 1-2 bond in a bond-order sense)
+* m
+* gamma
+* lambda3 (1/distance units)
+* c
+* d
+* costheta0 (can be a value < -1 or > 1)
+* n
+* beta
+* lambda2 (1/distance units)
+* B (energy units)
+* R (distance units)
+* D (distance units)
+* lambda1 (1/distance units)
+* A (energy units)
+* Z\_i
+* Z\_j
+* ZBLcut (distance units)
+* ZBLexpscale (1/distance units)
+
+The n, beta, lambda2, B, lambda1, and A parameters are only used for
+two-body interactions.  The m, gamma, lambda3, c, d, and costheta0
+parameters are only used for three-body interactions. The R and D
+parameters are used for both two-body and three-body interactions. The
+Z\_i,Z\_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive
+portion of the potential and in the Fermi-like function.  The
+non-annotated parameters are unitless.  The value of m must be 3 or 1.
+
+The Tersoff/ZBL potential file must contain entries for all the
+elements listed in the pair\_coeff command.  It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. SiSiSi).  For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify Tersoff parameters for all permutations of the two elements
+interacting in three-body configurations.  Thus for 3 elements, 27
+entries would be required, etc.
+
+As annotated above, the first element in the entry is the center atom
+in a three-body interaction and it is bonded to the 2nd atom and the
+bond is influenced by the 3rd atom.  Thus an entry for SiCC means Si
+bonded to a C with another C atom influencing the bond.  Thus
+three-body parameters for SiCSi and SiSiC entries will not, in
+general, be the same.  The parameters used for the two-body
+interaction come from the entry where the 2nd element is repeated.
+Thus the two-body parameters for Si interacting with C, comes from the
+SiCC entry.
+
+The parameters used for a particular
+three-body interaction come from the entry with the corresponding
+three elements.  The parameters used only for two-body interactions
+(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
+element are different (e.g. SiCSi) are not used for anything and can
+be set to 0.0 if desired.
+
+Note that the twobody parameters in entries such as SiCC and CSiSi
+are often the same, due to the common use of symmetric mixing rules,
+but this is not always the case. For example, the beta and n parameters in
+Tersoff\_2 :ref:`(Tersoff\_2) <zbl-Tersoff_2>` are not symmetric.
+
+We chose the above form so as to enable users to define all commonly
+used variants of the Tersoff portion of the potential.  In particular,
+our form reduces to the original Tersoff form when m = 3 and gamma =
+1, while it reduces to the form of :ref:`Albe et al. <zbl-Albe>` when beta = 1
+and m = 1.  Note that in the current Tersoff implementation in LAMMPS,
+m must be specified as either 3 or 1.  Tersoff used a slightly
+different but equivalent form for alloys, which we will refer to as
+Tersoff\_2 potential :ref:`(Tersoff\_2) <zbl-Tersoff_2>`.
+
+LAMMPS parameter values for Tersoff\_2 can be obtained as follows:
+gamma = omega\_ijk, lambda3 = 0 and the value of
+m has no effect.  The parameters for species i and j can be calculated
+using the Tersoff\_2 mixing rules:
+
+.. image:: Eqs/pair_tersoff_2.jpg
+   :align: center
+
+Tersoff\_2 parameters R and S must be converted to the LAMMPS
+parameters R and D (R is different in both forms), using the following
+relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
+Tersoff\_2 parameters.
+
+In the potentials directory, the file SiCGe.tersoff provides the
+LAMMPS parameters for Tersoff's various versions of Si, as well as his
+alloy parameters for Si, C, and Ge. This file can be used for pure Si,
+(three different versions), pure C, pure Ge, binary SiC, and binary
+SiGe.  LAMMPS will generate an error if this file is used with any
+combination involving C and Ge, since there are no entries for the GeC
+interactions (Tersoff did not publish parameters for this
+cross-interaction.)  Tersoff files are also provided for the SiC alloy
+(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
+
+Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
+for helping clarify how Tersoff parameters for alloys have been
+defined in various papers.  Also thanks to Ram Devanathan for
+providing the base ZBL implementation.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This pair style is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The Tersoff/ZBL potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal :doc:`units <units>`.
+You can use the Tersoff potential with any LAMMPS units, but you would
+need to create your own Tersoff potential file with coefficients
+listed in the appropriate units if your simulation doesn't use "metal"
+units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _zbl-Tersoff\_1:
+
+
+
+**(Tersoff\_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988).
+
+.. _zbl-ZBL:
+
+
+
+**(ZBL)** J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
+of Ions in Matter' Vol 1, 1985, Pergamon Press.
+
+.. _zbl-Albe:
+
+
+
+**(Albe)** J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.:
+Condens. Matter, 15, 5649(2003).
+
+.. _zbl-Tersoff\_2:
+
+
+
+**(Tersoff\_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst
new file mode 100644
index 0000000000..8f4bac0182
--- /dev/null
+++ b/doc/src/pair_thole.rst
@@ -0,0 +1,220 @@
+.. index:: pair\_style thole
+
+pair\_style thole command
+=========================
+
+pair\_style lj/cut/thole/long command
+=====================================
+
+pair\_style lj/cut/thole/long/omp command
+=========================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *thole* or *lj/cut/thole/long* or *lj/cut/thole/long/omp*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *thole* args = damp cutoff
+       damp = global damping parameter
+       cutoff = global cutoff (distance units)
+     *lj/cut/thole/long* or *lj/cut/thole/long/omp* args = damp cutoff (cutoff2)
+       damp = global damping parameter
+       cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Thole (optional) (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style hybrid/overlay ... thole 2.6 12.0
+   pair_coeff 1 1 thole 1.0
+   pair_coeff 1 2 thole 1.0 2.6 10.0
+   pair_coeff \* 2 thole 1.0 2.6
+
+   pair_style lj/cut/thole/long 2.6 12.0
+
+Description
+"""""""""""
+
+The *thole* pair styles are meant to be used with force fields that
+include explicit polarization through Drude dipoles.  This link
+describes how to use the :doc:`thermalized Drude oscillator model <Howto_drude>` in LAMMPS and polarizable models in LAMMPS are
+discussed on the :doc:`Howto polarizable <Howto_polarizable>` doc page.
+
+The *thole* pair style should be used as a sub-style within in the
+:doc:`pair\_hybrid/overlay <pair_hybrid>` command, in conjunction with a
+main pair style including Coulomb interactions, i.e. any pair style
+containing *coul/cut* or *coul/long* in its style name.
+
+The *lj/cut/thole/long* pair style is equivalent to, but more convenient that
+the frequent combination *hybrid/overlay lj/cut/coul/long cutoff thole damp
+cutoff2*\ . It is not only a shorthand for this pair\_style combination, but
+it also allows for mixing pair coefficients instead of listing them all.
+The *lj/cut/thole/long* pair style is also a bit faster because it avoids an
+overlay and can benefit from OMP acceleration. Moreover, it uses a more
+precise approximation of the direct Coulomb interaction at short range similar
+to :doc:`coul/long/cs <pair_cs>`, which stabilizes the temperature of
+Drude particles.
+
+The *thole* pair styles compute the Coulomb interaction damped at
+short distances by a function
+
+
+.. math::
+
+   \begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 +
+   \frac{s_{ij} r_{ij} }{2} \right)
+   \exp \left( - s_{ij} r_{ij} \right) \end{equation}
+
+This function results from an adaptation to point charges
+:ref:`(Noskov) <Noskov1>` of the dipole screening scheme originally proposed
+by :ref:`Thole <Thole1>`. The scaling coefficient :math:`s_{ij}` is determined
+by the polarizability of the atoms, :math:`\alpha_i`, and by a Thole
+damping parameter :math:`a`.  This Thole damping parameter usually takes
+a value of 2.6, but in certain force fields the value can depend upon
+the atom types. The mixing rule for Thole damping parameters is the
+arithmetic average, and for polarizabilities the geometric average
+between the atom-specific values.
+
+
+.. math::
+
+   \begin{equation} s_{ij} = \frac{ a_{ij} }{
+   (\alpha_{ij})^{1/3} } = \frac{ (a_i + a_j)/2 }{
+   [(\alpha_i\alpha_j)^{1/2}]^{1/3} } \end{equation}
+
+The damping function is only applied to the interactions between the
+point charges representing the induced dipoles on polarizable sites,
+that is, charges on Drude particles, :math:`q_{D,i}`, and opposite
+charges, :math:`-q_{D,i}`, located on the respective core particles
+(to which each Drude particle is bonded). Therefore, Thole screening
+is not applied to the full charge of the core particle :math:`q_i`, but
+only to the :math:`-q_{D,i}` part of it.
+
+The interactions between core charges are subject to the weighting
+factors set by the :doc:`special\_bonds <special_bonds>` command. The
+interactions between Drude particles and core charges or
+non-polarizable atoms are also subject to these weighting factors. The
+Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
+their respective cores.
+
+For pair\_style *thole*\ , the following coefficients must be defined for
+each pair of atoms types via the :doc:`pair\_coeff <pair_coeff>` command
+as in the example above.
+
+* alpha (distance units\^3)
+* damp
+* cutoff (distance units)
+
+The last two coefficients are optional.  If not specified the global
+Thole damping parameter or global cutoff specified in the pair\_style
+command are used. In order to specify a cutoff (third argument) a damp
+parameter (second argument) must also be specified.
+
+For pair style *lj/cut/thole/long*\ , the following coefficients must be
+defined for each pair of atoms types via the :doc:`pair\_coeff <pair_coeff>`
+command.
+
+* epsilon (energy units)
+* sigma (length units)
+* alpha (distance units\^3)
+* damps
+* LJ cutoff (distance units)
+
+The last two coefficients are optional and default to the global values from
+the *pair\_style* command line.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+**Mixing**\ :
+
+The *thole* pair style does not support mixing.  Thus, coefficients
+for all I,J pairs must be specified explicitly.
+
+The *lj/cut/thole/long* pair style does support mixing. Mixed coefficients
+are defined using
+
+
+.. math::
+
+   \begin{equation} \alpha_{ij} = \sqrt{\alpha_i\alpha_j}\end{equation}
+
+
+.. math::
+
+   \begin{equation} a_{ij} = \frac 1 2 (a_i + a_j)\end{equation}
+
+Restrictions
+""""""""""""
+
+
+These pair styles are part of the USER-DRUDE package. They are only
+enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair\_style should currently not be used with the :doc:`charmm dihedral style <dihedral_charmm>` if the latter has non-zero 1-4 weighting
+factors. This is because the *thole* pair style does not know which
+pairs are 1-4 partners of which dihedrals.
+
+The *lj/cut/thole/long* pair style should be used with a :doc:`Kspace solver <kspace_style>`
+like PPPM or Ewald, which is only enabled if LAMMPS was built with the kspace
+package.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix drude <fix_drude>`, :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`
+:doc:`pair\_style lj/cut/coul/long <pair_lj>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Noskov1:
+
+
+
+**(Noskov)** Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).
+
+.. _Thole1:
+
+
+
+**(Thole)** Chem Phys, 59, 341 (1981).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst
new file mode 100644
index 0000000000..350f9c0617
--- /dev/null
+++ b/doc/src/pair_tri_lj.rst
@@ -0,0 +1,128 @@
+.. index:: pair\_style tri/lj
+
+pair\_style tri/lj command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style tri/lj cutoff
+
+cutoff = global cutoff for interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style tri/lj 3.0
+   pair_coeff \* \* 1.0 1.0
+   pair_coeff 1 1 1.0 1.5 2.5
+
+Description
+"""""""""""
+
+Style *tri/lj* treats particles which are triangles as a set of small
+spherical particles that tile the triangle surface as explained below.
+Interactions between two triangles, each with N1 and N2 spherical
+particles, are calculated as the pairwise sum of N1\*N2 Lennard-Jones
+interactions.  Interactions between a triangle with N spherical
+particles and a point particle are treated as the pairwise sum of N
+Lennard-Jones interactions.  See the :doc:`pair\_style lj/cut <pair_lj>`
+doc page for the definition of Lennard-Jones interactions.
+
+The cutoff distance for an interaction between 2 triangles, or between
+a triangle and a point particle, is calculated from the position of
+the triangle (its centroid), not between pairs of individual spheres
+comprising the triangle.  Thus an interaction is either calculated in
+its entirety or not at all.
+
+The set of non-overlapping spherical particles that represent a
+triangle, for purposes of this pair style, are generated in the
+following manner.  Assume the triangle is of type I, and sigma\_II has
+been specified.  We want a set of spheres with centers in the plane of
+the triangle, none of them larger in diameter than sigma\_II, which
+completely cover the triangle's area, but with minimal overlap and a
+minimal total number of spheres.  This is done in a recursive manner.
+Place a sphere at the centroid of the original triangle.  Calculate
+what diameter it must have to just cover all 3 corner points of the
+triangle.  If that diameter is equal to or smaller than sigma\_II, then
+include a sphere of the calculated diameter in the set of covering
+spheres.  It the diameter is larger than sigma\_II, then split the
+triangle into 2 triangles by bisecting its longest side.  Repeat the
+process on each sub-triangle, recursing as far as needed to generate a
+set of covering spheres.  When finished, the original criteria are
+met, and the set of covering spheres should be near minimal in number
+and overlap, at least for input triangles with a reasonable
+aspect-ratio.
+
+The LJ interaction between 2 spheres on different triangles of types
+I,J is computed with an arithmetic mixing of the sigma values of the 2
+spheres and using the specified epsilon value for I,J atom types.
+Note that because the sigma values for triangles spheres is computed
+using only sigma\_II values, specific to the triangles's type, this
+means that any specified sigma\_IJ values (for I != J) are effectively
+ignored.
+
+For style *tri/lj*\ , the following coefficients must be defined for
+each pair of atoms types via the :doc:`pair\_coeff <pair_coeff>` command
+as in the examples above, or in the data file or restart files read by
+the :doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global cutoff
+is used.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of this pair style can be mixed.  The
+default mix value is *geometric*\ .  See the "pair\_modify" command for
+details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the ASPHERE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Defining particles to be triangles so they participate in tri/tri or
+tri/particle interactions requires the use the :doc:`atom\_style tri <atom_style>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`pair\_style line/lj <pair_line_lj>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst
new file mode 100644
index 0000000000..318762bb4b
--- /dev/null
+++ b/doc/src/pair_ufm.rst
@@ -0,0 +1,167 @@
+.. index:: pair\_style ufm
+
+pair\_style ufm command
+=======================
+
+pair\_style ufm/gpu command
+===========================
+
+pair\_style ufm/omp command
+===========================
+
+pair\_style ufm/opt command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style ufm cutoff
+
+* cutoff = global cutoff for *ufm* interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style ufm 4.0
+   pair_coeff 1 1 100.0 1.0 2.5
+   pair_coeff \* \* 100.0 1.0
+
+   pair_style ufm 4.0
+   pair_coeff \* \* 10.0 1.0
+   variable prefactor equal ramp(10,100)
+   fix 1 all adapt 1 pair ufm epsilon \* \* v_prefactor
+
+Description
+"""""""""""
+
+Style *ufm* computes pairwise interactions using the Uhlenbeck-Ford model (UFM) potential :ref:`(Paula Leite2016) <PL2>` which is given by
+
+.. image:: Eqs/pair_ufm.jpg
+   :align: center
+
+where rc is the cutoff, sigma is a distance-scale and epsilon is an energy-scale, i.e., a product of Boltzmann constant kB, temperature T and the Uhlenbeck-Ford p-parameter which is responsible
+to control the softness of the interactions :ref:`(Paula Leite2017) <PL1>`.
+This model is useful as a reference system for fluid-phase free-energy calculations :ref:`(Paula Leite2016) <PL2>`.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* epsilon (energy units)
+* sigma (distance units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global *ufm*
+cutoff is used.
+
+The :doc:`fix adapt <fix_adapt>` command can be used to vary epsilon and sigma for this pair style over the course of a simulation, in which case
+pair\_coeff settings for epsilon and sigma must still be specified, but will be
+overridden.  For example these commands will vary the prefactor epsilon for
+all pairwise interactions from 10.0 at the beginning to 100.0 at the end
+of a run:
+
+
+.. parsed-literal::
+
+   variable prefactor equal ramp(10,100)
+   fix 1 all adapt 1 pair ufm epsilon \* \* v_prefactor
+
+.. note::
+
+   The thermodynamic integration procedure can be performed with this potential using :doc:`fix adapt <fix_adapt>`. This command will rescale the force on each atom by varying a scale variable, which always starts with value 1.0. The syntax is the same described above, however, changing epsilon to scale. A detailed explanation of how to use this command and perform nonequilibrium thermodynamic integration in LAMMPS is given in the paper by :ref:`(Freitas) <Freitas2>`.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed.  A is always mixed via a
+*geometric* rule.  The cutoff is mixed according to the pair\_modify
+mix value.  The default mix value is *geometric*\ .  See the
+"pair\_modify" command for details.
+
+This pair style support the :doc:`pair\_modify <pair_modify>` shift option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table and tail are not relevant for this
+pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>` tail option for adding long-range tail corrections to energy and pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`, :doc:`fix adapt <fix_adapt>`
+
+**Default:** none
+
+.. _PL1:
+
+
+
+**(Paula Leite2017)** Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96,
+32115 (2017).
+
+.. _PL2:
+
+
+
+**(Paula Leite2016)** Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126,
+044509 (2016).
+
+.. _Freitas2:
+
+
+
+**(Freitas)** Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst
new file mode 100644
index 0000000000..c4c8a6c9f5
--- /dev/null
+++ b/doc/src/pair_vashishta.rst
@@ -0,0 +1,289 @@
+.. index:: pair\_style vashishta
+
+pair\_style vashishta command
+=============================
+
+pair\_style vashishta/gpu command
+=================================
+
+pair\_style vashishta/omp command
+=================================
+
+pair\_style vashishta/kk command
+================================
+
+pair\_style vashishta/table command
+===================================
+
+pair\_style vashishta/table/omp command
+=======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style style args
+
+* style = *vashishta* or *vashishta/table* or *vashishta/omp* or *vashishta/table/omp*
+* args = list of arguments for a particular style
+
+
+.. parsed-literal::
+
+     *vashishta* or *vashishta/omp* args = none
+     *vashishta/table* or *vashishta/table/omp* args = Ntable cutinner
+       Ntable = # of tabulation points
+       cutinner = tablulate from cutinner to cutoff
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style vashishta
+   pair_coeff \* \* SiC.vashishta Si C
+
+   pair_style vashishta/table 100000 0.2
+   pair_coeff \* \* SiC.vashishta Si C
+
+Description
+"""""""""""
+
+The *vashishta* and *vashishta/table* styles compute the combined
+2-body and 3-body family of potentials developed in the group of Priya
+Vashishta and collaborators.  By combining repulsive, screened
+Coulombic, screened charge-dipole, and dispersion interactions with a
+bond-angle energy based on the Stillinger-Weber potential, this
+potential has been used to describe a variety of inorganic compounds,
+including SiO2 :ref:`Vashishta1990 <Vashishta1990>`, SiC
+:ref:`Vashishta2007 <Vashishta2007>`, and InP :ref:`Branicio2009 <Branicio2009>`.
+
+The potential for the energy U of a system of atoms is
+
+.. image:: Eqs/pair_vashishta.jpg
+   :align: center
+
+where we follow the notation used in :ref:`Branicio2009 <Branicio2009>`.
+U2 is a two-body term and U3 is a three-body term.  The
+summation over two-body terms is over all neighbors J within
+a cutoff distance = *rc*\ .  The twobody terms are shifted and
+tilted by a linear function so that the energy and force are
+both zero at *rc*\ . The summation over three-body terms
+is over all neighbors J and K within a cut-off distance = *r0*\ ,
+where the exponential screening function becomes zero.
+
+The *vashishta* style computes these formulas analytically.  The
+*vashishta/table* style tabulates the analytic values for *Ntable*
+points from cutinner to the cutoff of the potential.  The points are
+equally spaced in R\^2 space from cutinner\^2 to cutoff\^2.  For the
+two-body term in the above equation, a linear interpolation for each
+pairwise distance between adjacent points in the table.  In practice
+the tabulated version can run 3-5x faster than the analytic version
+with moderate to little loss of accuracy for Ntable values
+between 10000 and 1000000. It is not recommended to use less than
+5000 tabulation points.
+
+Only a single pair\_coeff command is used with either style which
+specifies a Vashishta potential file with parameters for all needed
+elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair\_coeff command,
+where N is the number of LAMMPS atom types:
+
+* filename
+* N element names = mapping of Vashishta elements to atom types
+
+See the :doc:`pair\_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine a file SiC.vashishta has parameters for
+Si and C.  If your LAMMPS simulation has 4 atoms types and you want
+the 1st 3 to be Si, and the 4th to be C, you would use the following
+pair\_coeff command:
+
+
+.. parsed-literal::
+
+   pair_coeff \* \* SiC.vashishta Si Si Si C
+
+The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the file.  The final C argument maps LAMMPS atom type 4
+to the C element in the file.  If a mapping value is specified as
+NULL, the mapping is not performed.  This can be used when a *vashishta*
+potential is used as part of the *hybrid* pair style.  The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+
+Vashishta files in the *potentials* directory of the LAMMPS
+distribution have a ".vashishta" suffix.  Lines that are not blank or
+comments (starting with #) define parameters for a triplet of
+elements.  The parameters in a single entry correspond to the two-body
+and three-body coefficients in the formulae above:
+
+* element 1 (the center atom in a 3-body interaction)
+* element 2
+* element 3
+* H (energy units)
+* eta
+* Zi (electron charge units)
+* Zj (electron charge units)
+* lambda1 (distance units)
+* D (energy units)
+* lambda4 (distance units)
+* W (energy units)
+* rc (distance units)
+* B (energy units)
+* gamma
+* r0 (distance units)
+* C
+* costheta0
+
+The non-annotated parameters are unitless.  The Vashishta potential
+file must contain entries for all the elements listed in the
+pair\_coeff command.  It can also contain entries for additional
+elements not being used in a particular simulation; LAMMPS ignores
+those entries.  For a single-element simulation, only a single entry
+is required (e.g. SiSiSi).  For a two-element simulation, the file
+must contain 8 entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC,
+CCSi, CCC), that specify parameters for all permutations of the two
+elements interacting in three-body configurations.  Thus for 3
+elements, 27 entries would be required, etc.
+
+Depending on the particular version of the Vashishta potential, the
+values of these parameters may be keyed to the identities of zero,
+one, two, or three elements.  In order to make the input file format
+unambiguous, general, and simple to code, LAMMPS uses a slightly
+confusing method for specifying parameters.  All parameters are
+divided into two classes: two-body and three-body.  Two-body and
+three-body parameters are handled differently, as described below.
+The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma,
+and r0.  They appear in the above formulae with two subscripts.  The
+parameters Zi and Zj are also classified as two-body parameters, even
+though they only have 1 subscript.  The three-body parameters are B,
+C, costheta0.  They appear in the above formulae with three
+subscripts.  Two-body and three-body parameters are handled
+differently, as described below.
+
+The first element in each entry is the center atom in a three-body
+interaction, while the second and third elements are two neighbor
+atoms. Three-body parameters for a central atom I and two neighbors J
+and K are taken from the IJK entry.  Note that even though three-body
+parameters do not depend on the order of J and K, LAMMPS stores
+three-body parameters for both IJK and IKJ.  The user must ensure that
+these values are equal.  Two-body parameters for an atom I interacting
+with atom J are taken from the IJJ entry, where the 2nd and 3rd
+elements are the same. Thus the two-body parameters for Si interacting
+with C come from the SiCC entry. Note that even though two-body
+parameters (except possibly gamma and r0 in U3) do not depend on the
+order of the two elements, LAMMPS will get the Si-C value from the
+SiCC entry and the C-Si value from the CSiSi entry. The user must
+ensure that these values are equal. Two-body parameters appearing in
+entries where the 2nd and 3rd elements are different are stored but
+never used. It is good practice to enter zero for these values. Note
+that the three-body function U3 above contains the two-body parameters
+gamma and r0. So U3 for a central C atom bonded to an Si atom and a
+second C atom will take three-body parameters from the CSiC entry, but
+two-body parameters from the CCC and CSiSi entries.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair\_style and pair\_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+These pair style are part of the MANYBODY package.  They is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+These pair styles requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+The Vashishta potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal :doc:`units <units>`.  You can
+use the Vashishta potential with any LAMMPS units, but you would need
+to create your own potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Vashishta1990:
+
+
+
+**(Vashishta1990)** P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B
+41, 12197 (1990).
+
+.. _Vashishta2007:
+
+
+
+**(Vashishta2007)** P. Vashishta, R. K. Kalia, A. Nakano,
+J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
+
+.. _Branicio2009:
+
+
+
+**(Branicio2009)** Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed
+Matter 21 (2009) 095002
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst
new file mode 100644
index 0000000000..17be08f29a
--- /dev/null
+++ b/doc/src/pair_write.rst
@@ -0,0 +1,91 @@
+.. index:: pair\_write
+
+pair\_write command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_write itype jtype N style inner outer file keyword Qi Qj
+
+* itype,jtype = 2 atom types
+* N = # of values
+* style = *r* or *rsq* or *bitmap*
+* inner,outer = inner and outer cutoff (distance units)
+* file = name of file to write values to
+* keyword = section name in file for this set of tabulated values
+* Qi,Qj = 2 atom charges (charge units) (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_write 1 3 500 r 1.0 10.0 table.txt LJ
+   pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5
+
+Description
+"""""""""""
+
+Write energy and force values to a file as a function of distance for
+the currently defined pair potential.  This is useful for plotting the
+potential function or otherwise debugging its values.  If the file
+already exists, the table of values is appended to the end of the file
+to allow multiple tables of energy and force to be included in one
+file.
+
+The energy and force values are computed at distances from inner to
+outer for 2 interacting atoms of type itype and jtype, using the
+appropriate :doc:`pair\_coeff <pair_coeff>` coefficients.  If the style
+is *r*\ , then N distances are used, evenly spaced in r; if the style is
+*rsq*\ , N distances are used, evenly spaced in r\^2.
+
+For example, for N = 7, style = *r*\ , inner = 1.0, and outer = 4.0,
+values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
+
+If the style is *bitmap*\ , then 2\^N values are written to the file in a
+format and order consistent with how they are read in by the
+:doc:`pair\_coeff <pair_coeff>` command for pair style *table*\ .  For
+reasonable accuracy in a bitmapped table, choose N >= 12, an *inner*
+value that is smaller than the distance of closest approach of 2
+atoms, and an *outer* value <= cutoff of the potential.
+
+If the pair potential is computed between charged atoms, the charges
+of the pair of interacting atoms can optionally be specified.  If not
+specified, values of Qi = Qj = 1.0 are used.
+
+The file is written in the format used as input for the
+:doc:`pair\_style <pair_style>` *table* option with *keyword* as the
+section name.  Each line written to the file lists an index number
+(1-N), a distance (in distance units), an energy (in energy units),
+and a force (in force units).
+
+Restrictions
+""""""""""""
+
+
+All force field coefficients for pair and other kinds of interactions
+must be set before this command can be invoked.
+
+Due to how the pairwise force is computed, an inner value > 0.0 must
+be specified even if the potential has a finite value at r = 0.0.
+
+For EAM potentials, the pair\_write command only tabulates the
+pairwise portion of the potential, not the embedding portion.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style table <pair_table>`,
+:doc:`pair\_style <pair_style>`, :doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst
new file mode 100644
index 0000000000..14cec88d2e
--- /dev/null
+++ b/doc/src/pair_yukawa.rst
@@ -0,0 +1,126 @@
+.. index:: pair\_style yukawa
+
+pair\_style yukawa command
+==========================
+
+pair\_style yukawa/gpu command
+==============================
+
+pair\_style yukawa/omp command
+==============================
+
+pair\_style yukawa/kk command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style yukawa kappa cutoff
+
+* kappa = screening length (inverse distance units)
+* cutoff = global cutoff for Yukawa interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style yukawa 2.0 2.5
+   pair_coeff 1 1 100.0 2.3
+   pair_coeff \* \* 100.0
+
+Description
+"""""""""""
+
+Style *yukawa* computes pairwise interactions with the formula
+
+.. image:: Eqs/pair_yukawa.jpg
+   :align: center
+
+Rc is the cutoff.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* A (energy\*distance units)
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global yukawa
+cutoff is used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed.  A is an energy value mixed
+like a LJ epsilon.  The default mix value is *geometric*\ .  See the
+"pair\_modify" command for details.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst
new file mode 100644
index 0000000000..b46f8fc704
--- /dev/null
+++ b/doc/src/pair_yukawa_colloid.rst
@@ -0,0 +1,181 @@
+.. index:: pair\_style yukawa/colloid
+
+pair\_style yukawa/colloid command
+==================================
+
+pair\_style yukawa/colloid/gpu command
+======================================
+
+pair\_style yukawa/colloid/omp command
+======================================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style yukawa/colloid kappa cutoff
+
+* kappa = screening length (inverse distance units)
+* cutoff = global cutoff for colloidal Yukawa interactions (distance units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style yukawa/colloid 2.0 2.5
+   pair_coeff 1 1 100.0 2.3
+   pair_coeff \* \* 100.0
+
+Description
+"""""""""""
+
+Style *yukawa/colloid* computes pairwise interactions with the formula
+
+.. image:: Eqs/pair_yukawa_colloid.jpg
+   :align: center
+
+where Ri and Rj are the radii of the two particles and Rc is the
+cutoff.
+
+In contrast to :doc:`pair\_style yukawa <pair_yukawa>`, this functional
+form arises from the Coulombic interaction between two colloid
+particles, screened due to the presence of an electrolyte, see the
+book by :ref:`Safran <Safran>` for a derivation in the context of DLVO
+theory.  :doc:`Pair\_style yukawa <pair_yukawa>` is a screened Coulombic
+potential between two point-charges and uses no such approximation.
+
+This potential applies to nearby particle pairs for which the Derjagin
+approximation holds, meaning h << Ri + Rj, where h is the
+surface-to-surface separation of the two particles.
+
+When used in combination with :doc:`pair\_style colloid <pair_colloid>`,
+the two terms become the so-called DLVO potential, which combines
+electrostatic repulsion and van der Waals attraction.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* A (energy/distance units)
+* cutoff (distance units)
+
+The prefactor A is determined from the relationship between surface
+charge and surface potential due to the presence of electrolyte.  Note
+that the A for this potential style has different units than the A
+used in :doc:`pair\_style yukawa <pair_yukawa>`.  For low surface
+potentials, i.e. less than about 25 mV, A can be written as:
+
+
+.. parsed-literal::
+
+   A = 2 \* PI \* R\*eps\*eps0 \* kappa \* psi\^2
+
+where
+
+* R = colloid radius (distance units)
+* eps0 = permittivity of free space (charge\^2/energy/distance units)
+* eps = relative permittivity of fluid medium (dimensionless)
+* kappa = inverse screening length (1/distance units)
+* psi = surface potential (energy/charge units)
+
+The last coefficient is optional.  If not specified, the global
+yukawa/colloid cutoff is used.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed.  A is an energy value mixed
+like a LJ epsilon.  The default mix value is *geometric*\ .  See the
+"pair\_modify" command for details.
+
+This pair style supports the :doc:`pair\_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This style is part of the COLLOID package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+This pair style requires that atoms be finite-size spheres with a
+diameter, as defined by the :doc:`atom\_style sphere <atom_style>`
+command.
+
+Per-particle polydispersity is not yet supported by this pair style;
+per-type polydispersity is allowed.  This means all particles of the
+same type must have the same diameter.  Each type can have a different
+diameter.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Safran:
+
+
+
+**(Safran)** Safran, Statistical Thermodynamics of Surfaces, Interfaces,
+And Membranes, Westview Press, ISBN: 978-0813340791 (2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst
new file mode 100644
index 0000000000..6bb485ee8a
--- /dev/null
+++ b/doc/src/pair_zbl.rst
@@ -0,0 +1,169 @@
+.. index:: pair\_style zbl
+
+pair\_style zbl command
+=======================
+
+pair\_style zbl/gpu command
+===========================
+
+pair\_style zbl/kk command
+==========================
+
+pair\_style zbl/omp command
+===========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style zbl inner outer
+
+* inner = distance where switching function begins
+* outer = global cutoff for ZBL interaction
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style zbl 3.0 4.0
+   pair_coeff \* \* 73.0 73.0
+   pair_coeff 1 1 14.0 14.0
+
+Description
+"""""""""""
+
+Style *zbl* computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear
+repulsion for describing high-energy collisions between atoms.
+:ref:`(Ziegler) <Ziegler>`. It includes an additional switching function
+that ramps the energy, force, and curvature smoothly to zero
+between an inner and outer cutoff. The potential
+energy due to a pair of atoms at a distance r\_ij is given by:
+
+.. image:: Eqs/pair_zbl.jpg
+   :align: center
+
+where e is the electron charge, epsilon\_0 is the electrical
+permittivity of vacuum, and Z\_i and Z\_j are the nuclear charges of the
+two atoms.  The switching function S(r) is identical to that used by
+:doc:`pair\_style lj/gromacs <pair_gromacs>`.  Here, the inner and outer
+cutoff are the same for all pairs of atom types.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair\_coeff <pair_coeff>` command as in the examples above,
+or in the LAMMPS data file.
+
+* Z\_i (atomic number for first atom type, e.g. 13.0 for aluminum)
+
+* Z\_j (ditto for second atom type)
+
+The values of Z\_i and Z\_j are normally equal to the atomic
+numbers of the two atom types. Thus, the user may optionally
+specify only the coefficients for each I==I pair, and rely
+on the obvious mixing rule for cross interactions (see below).
+Note that when I==I it is required that Z\_i == Z\_j. When used
+with :doc:`hybrid/overlay <pair_hybrid>` and pairs are assigned
+to more than one sub-style, the mixing rule is not used and
+each pair of types interacting with the ZBL sub-style must
+be included in a pair\_coeff command.
+
+.. note::
+
+   The numerical values of the exponential decay constants in the
+   screening function depend on the unit of distance. In the above
+   equation they are given for units of angstroms. LAMMPS will
+   automatically convert these values to the distance unit of the
+   specified LAMMPS :doc:`units <units>` setting.  The values of Z should
+   always be given as multiples of a proton's charge, e.g. 29.0 for
+   copper.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, the Z\_i and Z\_j coefficients
+can be mixed by taking Z\_i and Z\_j from the values specified for
+I == I and J == J cases. When used
+with :doc:`hybrid/overlay <pair_hybrid>` and pairs are assigned
+to more than one sub-style, the mixing rule is not used and
+each pair of types interacting with the ZBL sub-style
+must be included in a pair\_coeff command.
+The :doc:`pair\_modify <pair_modify>` mix option has no effect on
+the mixing behavior
+
+The ZBL pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift option, since the ZBL interaction is already smoothed to 0.0 at
+the cutoff.
+
+The :doc:`pair\_modify <pair_modify>` table option is not relevant for
+this pair style.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure, since there are no corrections for a potential that goes to
+0.0 at the cutoff.
+
+This pair style does not write information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands must be
+specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run\_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_coeff <pair_coeff>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Ziegler:
+
+
+
+**(Ziegler)** J.F. Ziegler, J. P. Biersack and U. Littmark, "The
+Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst
new file mode 100644
index 0000000000..6afafc2017
--- /dev/null
+++ b/doc/src/pair_zero.rst
@@ -0,0 +1,99 @@
+.. index:: pair\_style zero
+
+pair\_style zero command
+========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   pair_style zero cutoff *nocoeff*
+
+* zero = style name of this pair style
+* cutoff = global cutoff (distance units)
+* nocoeff = ignore all pair\_coeff parameters (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   pair_style zero 10.0
+   pair_style zero 5.0 nocoeff
+   pair_coeff \* \*
+   pair_coeff 1 2\*4 3.0
+
+Description
+"""""""""""
+
+Define a global or per-type cutoff length for the purpose of
+building a neighbor list and acquiring ghost atoms, but do
+not compute any pairwise forces or energies.
+
+This can be useful for fixes or computes which require a neighbor list
+to enumerate pairs of atoms within some cutoff distance, but when
+pairwise forces are not otherwise needed.  Examples are the :doc:`fix bond/create <fix_bond_create>`, :doc:`compute rdf <compute_rdf>`,
+:doc:`compute voronoi/atom <compute_voronoi_atom>` commands.
+
+Note that the :doc:`comm\_modify cutoff <comm_modify>` command can be
+used to insure communication of ghost atoms even when a pair style is
+not defined, but it will not trigger neighbor list generation.
+
+The optional *nocoeff* flag allows to read data files with a PairCoeff
+section for any pair style. Similarly, any pair\_coeff commands
+will only be checked for the atom type numbers and the rest ignored.
+In this case, only the global cutoff will be used.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cutoff (distance units)
+
+This coefficient is optional.  If not specified, the global cutoff
+specified in the pair\_style command is used. If the pair\_style has
+been specified with the optional *nocoeff* flag, then a cutoff
+pair coefficient is ignored.
+
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+The cutoff distance for this pair style can be mixed.  The default mix
+value is *geometric*\ .  See the "pair\_modify" command for details.
+
+This pair style does not support the :doc:`pair\_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style writes its information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+This pair style supports the use of the *inner*\ , *middle*\ ,
+and *outer* keywords of the :doc:`run\_style respa <run_style>` command.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair\_style none <pair_none>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/pairs.rst b/doc/src/pairs.rst
new file mode 100644
index 0000000000..4fdf2b2c69
--- /dev/null
+++ b/doc/src/pairs.rst
@@ -0,0 +1,9 @@
+Pair Styles
+###########
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   pair_*
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
deleted file mode 100644
index f36a87dea3..0000000000
--- a/doc/src/pairs.txt
+++ /dev/null
@@ -1,130 +0,0 @@
-Pair Styles :h1
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   pair_adp
-   pair_agni
-   pair_airebo
-   pair_atm
-   pair_awpmd
-   pair_beck
-   pair_body_nparticle
-   pair_body_rounded_polygon
-   pair_body_rounded_polyhedron
-   pair_bop
-   pair_born
-   pair_brownian
-   pair_buck
-   pair_buck_long
-   pair_buck6d_coul_gauss
-   pair_charmm
-   pair_class2
-   pair_colloid
-   pair_comb
-   pair_cosine_squared
-   pair_coul
-   pair_coul_diel
-   pair_coul_shield
-   pair_cs
-   pair_dipole
-   pair_dpd
-   pair_dpd_fdt
-   pair_drip
-   pair_dsmc
-   pair_e3b
-   pair_eam
-   pair_edip
-   pair_eff
-   pair_eim
-   pair_exp6_rx
-   pair_extep
-   pair_fep_soft
-   pair_gauss
-   pair_gayberne
-   pair_gran
-   pair_granular
-   pair_gromacs
-   pair_gw
-   pair_hbond_dreiding
-   pair_hybrid
-   pair_ilp_graphene_hbn
-   pair_kim
-   pair_kolmogorov_crespi_full
-   pair_kolmogorov_crespi_z
-   pair_lcbop
-   pair_lebedeva_z
-   pair_line_lj
-   pair_list
-   pair_lj
-   pair_lj96
-   pair_lj_cubic
-   pair_lj_expand
-   pair_lj_long
-   pair_lj_smooth
-   pair_lj_smooth_linear
-   pair_lj_switch3_coulgauss
-   pair_lubricate
-   pair_lubricateU
-   pair_mdf
-   pair_meamc
-   pair_meam_spline
-   pair_meam_sw_spline
-   pair_meso
-   pair_mgpt
-   pair_mie
-   pair_mm3_switch3_coulgauss
-   pair_momb
-   pair_morse
-   pair_multi_lucy
-   pair_multi_lucy_rx
-   pair_nb3b_harmonic
-   pair_nm
-   pair_none
-   pair_oxdna
-   pair_oxdna2
-   pair_peri
-   pair_polymorphic
-   pair_python
-   pair_quip
-   pair_reaxc
-   pair_resquared
-   pair_sdk
-   pair_sdpd_taitwater_isothermal
-   pair_smd_hertz
-   pair_smd_tlsph
-   pair_smd_triangulated_surface
-   pair_smd_ulsph
-   pair_smtbq
-   pair_snap
-   pair_soft
-   pair_sph_heatconduction
-   pair_sph_idealgas
-   pair_sph_lj
-   pair_sph_rhosum
-   pair_sph_taitwater
-   pair_sph_taitwater_morris
-   pair_spin_dipole
-   pair_spin_dmi
-   pair_spin_exchange
-   pair_spin_magelec
-   pair_spin_neel
-   pair_srp
-   pair_sw
-   pair_table
-   pair_table_rx
-   pair_tersoff
-   pair_tersoff_mod
-   pair_tersoff_zbl
-   pair_thole
-   pair_tri_lj
-   pair_ufm
-   pair_vashishta
-   pair_yukawa
-   pair_yukawa_colloid
-   pair_zbl
-   pair_zero
-
-END_RST -->
diff --git a/doc/src/partition.rst b/doc/src/partition.rst
new file mode 100644
index 0000000000..e238e7c60d
--- /dev/null
+++ b/doc/src/partition.rst
@@ -0,0 +1,82 @@
+.. index:: partition
+
+partition command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   partition style N command ...
+
+* style = *yes* or *no*
+* N = partition number (see asterisk form below)
+* command = any LAMMPS command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   partition yes 1 processors 4 10 6
+   partition no 5 print "Active partition"
+   partition yes \*5 fix all nve
+   partition yes 6\* fix all nvt temp 1.0 1.0 0.1
+
+Description
+"""""""""""
+
+This command invokes the specified command on a subset of the
+partitions of processors you have defined via the :doc:`-partition command-line switch <Run_options>`.
+
+Normally, every input script command in your script is invoked by
+every partition.  This behavior can be modified by defining world- or
+universe-style :doc:`variables <variable>` that have different values
+for each partition.  This mechanism can be used to cause your script
+to jump to different input script files on different partitions, if
+such a variable is used in a :doc:`jump <jump>` command.
+
+The "partition" command is another mechanism for having as input
+script operate differently on different partitions.  It is basically a
+prefix on any LAMMPS command.  The command will only be invoked on
+the partition(s) specified by the *style* and *N* arguments.
+
+If the *style* is *yes*\ , the command will be invoked on any partition
+which matches the *N* argument.  If the *style* is *no* the command
+will be invoked on all the partitions which do not match the Np
+argument.
+
+Partitions are numbered from 1 to Np, where Np is the number of
+partitions specified by the :doc:`-partition command-line switch <Run_options>`.
+
+*N* can be specified in one of two ways.  An explicit numeric value
+can be used, as in the 1st example above.  Or a wild-card asterisk can
+be used to span a range of partition numbers.  This takes the form "\*"
+or "\*n" or "n\*" or "m\*n".  An asterisk with no numeric values means
+all partitions from 1 to Np.  A leading asterisk means all partitions
+from 1 to n (inclusive).  A trailing asterisk means all partitions
+from n to Np (inclusive).  A middle asterisk means all partitions from
+m to n (inclusive).
+
+This command can be useful for the "run\_style verlet/split" command
+which imposed requirements on how the :doc:`processors <processors>`
+command lays out a 3d grid of processors in each of 2 partitions.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`run\_style verlet/split <run_style>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/prd.rst b/doc/src/prd.rst
new file mode 100644
index 0000000000..5ea3db6121
--- /dev/null
+++ b/doc/src/prd.rst
@@ -0,0 +1,371 @@
+.. index:: prd
+
+prd command
+===========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
+
+* N = # of timesteps to run (not including dephasing/quenching)
+* t\_event = timestep interval between event checks
+* n\_dephase = number of velocity randomizations to perform in each dephase run
+* t\_dephase = number of timesteps to run dynamics after each velocity randomization during dephase
+* t\_correlate = number of timesteps within which 2 consecutive events are considered to be correlated
+* compute-ID = ID of the compute used for event detection
+* random\_seed = random # seed (positive integer)
+* zero or more keyword/value pairs may be appended
+* keyword = *min* or *temp* or *vel*
+  
+  .. parsed-literal::
+  
+       *min* values = etol ftol maxiter maxeval
+         etol = stopping tolerance for energy, used in quenching
+         ftol = stopping tolerance for force, used in quenching
+         maxiter = max iterations of minimize, used in quenching
+         maxeval = max number of force/energy evaluations, used in quenching
+       *temp* value = Tdephase
+         Tdephase = target temperature for velocity randomization, used in dephasing
+       *vel* values = loop dist
+         loop = *all* or *local* or *geom*\ , used in dephasing
+         dist = *uniform* or *gaussian*\ , used in dephasing
+       *time* value = *steps* or *clock*
+         *steps* = simulation runs for N timesteps on each replica (default)
+         *clock* = simulation runs for N timesteps across all replicas
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   prd 5000 100 10 10 100 1 54982
+   prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200
+
+Description
+"""""""""""
+
+Run a parallel replica dynamics (PRD) simulation using multiple
+replicas of a system.  One or more replicas can be used.  The total
+number of steps *N* to run can be interpreted in one of two ways; see
+discussion of the *time* keyword below.
+
+PRD is described in :ref:`(Voter1998) <Voter1998>` by Art Voter.  Similar to
+global or local hyperdynamics (HD), PRD is a method for performing
+accelerated dynamics that is suitable for infrequent-event systems
+that obey first-order kinetics.  A good overview of accelerated
+dynamics methods for such systems in given in this review paper
+:ref:`(Voter2002) <Voter2002prd>` from Art's group.  To quote from the
+paper: "The dynamical evolution is characterized by vibrational
+excursions within a potential basin, punctuated by occasional
+transitions between basins."  The transition probability is
+characterized by p(t) = k\*exp(-kt) where k is the rate constant.
+Running multiple replicas gives an effective enhancement in the
+timescale spanned by the multiple simulations, while waiting for an
+event to occur.
+
+Both PRD and HD produce a time-accurate trajectory that effectively
+extends the timescale over which a system can be simulated, but they
+do it differently.  PRD creates Nr replicas of the system and runs
+dynamics on each independently with a normal unbiased potential until
+an event occurs in one of the replicas.  The time between events is
+reduced by a factor of Nr replicas.  HD uses a single replica of the
+system and accelerates time by biasing the interaction potential in a
+manner such that each timestep is effectively longer.  For both
+methods, per CPU second, more physical time elapses and more events
+occur.  See the :doc:`hyper <hyper>` doc page for more info about HD.
+
+In PRD, each replica runs on a partition of one or more processors.
+Processor partitions are defined at run-time using the :doc:`-partition command-line switch <Run_options>`.  Note that if you have MPI
+installed, you can run a multi-replica simulation with more replicas
+(partitions) than you have physical processors, e.g you can run a
+10-replica simulation on one or two processors.  However for PRD, this
+makes little sense, since running a replica on virtual instead of
+physical processors,offers no effective parallel speed-up in searching
+for infrequent events.  See the :doc:`Howto replica <Howto_replica>` doc
+page for further discussion.
+
+When a PRD simulation is performed, it is assumed that each replica is
+running the same model, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of atoms, the interaction
+potentials, etc should be the same for every replica.
+
+A PRD run has several stages, which are repeated each time an "event"
+occurs in one of the replicas, as explained below.  The logic for a
+PRD run is as follows:
+
+
+.. parsed-literal::
+
+   while (time remains):
+     dephase for n_dephase\*t_dephase steps
+     until (event occurs on some replica):
+       run dynamics for t_event steps
+       quench
+       check for uncorrelated event on any replica
+     until (no correlated event occurs):
+       run dynamics for t_correlate steps
+       quench
+       check for correlated event on this replica
+     event replica shares state with all replicas
+
+Before this loop begins, the state of the system on replica 0 is
+shared with all replicas, so that all replicas begin from the same
+initial state. The first potential energy basin is identified by
+quenching (an energy minimization, see below) the initial state and
+storing the resulting coordinates for reference.
+
+In the first stage, dephasing is performed by each replica
+independently to eliminate correlations between replicas.  This is
+done by choosing a random set of velocities, based on the
+*random\_seed* that is specified, and running *t\_dephase* timesteps of
+dynamics.  This is repeated *n\_dephase* times.  At each of the
+*n\_dephase* stages, if an event occurs during the *t\_dephase* steps of
+dynamics for a particular replica, the replica repeats the stage until
+no event occurs.
+
+If the *temp* keyword is not specified, the target temperature for
+velocity randomization for each replica is the current temperature of
+that replica.  Otherwise, it is the specified *Tdephase* temperature.
+The style of velocity randomization is controlled using the keyword
+*vel* with arguments that have the same meaning as their counterparts
+in the :doc:`velocity <velocity>` command.
+
+In the second stage, each replica runs dynamics continuously, stopping
+every *t\_event* steps to check if a transition event has occurred.
+This check is performed by quenching the system and comparing the
+resulting atom coordinates to the coordinates from the previous basin.
+The first time through the PRD loop, the "previous basin" is the set
+of quenched coordinates from the initial state of the system.
+
+A quench is an energy minimization and is performed by whichever
+algorithm has been defined by the :doc:`min\_style <min_style>` command.
+Minimization parameters may be set via the
+:doc:`min\_modify <min_modify>` command and by the *min* keyword of the
+PRD command.  The latter are the settings that would be used with the
+:doc:`minimize <minimize>` command.  Note that typically, you do not
+need to perform a highly-converged minimization to detect a transition
+event, though you may need to in order to prevent a set of atoms in
+the system from relaxing to a saddle point.
+
+The event check is performed by a compute with the specified
+*compute-ID*\ .  Currently there is only one compute that works with the
+PRD command, which is the :doc:`compute event/displace <compute_event_displace>` command.  Other
+event-checking computes may be added.  :doc:`Compute event/displace <compute_event_displace>` checks whether any atom in
+the compute group has moved further than a specified threshold
+distance.  If so, an "event" has occurred.
+
+In the third stage, the replica on which the event occurred (event
+replica) continues to run dynamics to search for correlated events.
+This is done by running dynamics for *t\_correlate* steps, quenching
+every *t\_event* steps, and checking if another event has occurred.
+
+The first time no correlated event occurs, the final state of the
+event replica is shared with all replicas, the new basin reference
+coordinates are updated with the quenched state, and the outer loop
+begins again. While the replica event is searching for correlated
+events, all the other replicas also run dynamics and event checking
+with the same schedule, but the final states are always overwritten by
+the state of the event replica.
+
+The outer loop of the pseudo-code above continues until *N* steps of
+dynamics have been performed.  Note that *N* only includes the
+dynamics of stages 2 and 3, not the steps taken during dephasing or
+the minimization iterations of quenching.  The specified *N* is
+interpreted in one of two ways, depending on the *time* keyword.  If
+the *time* value is *steps*\ , which is the default, then each replica
+runs for *N* timesteps.  If the *time* value is *clock*\ , then the
+simulation runs until *N* aggregate timesteps across all replicas have
+elapsed.  This aggregate time is the "clock" time defined below, which
+typically advances nearly M times faster than the timestepping on a
+single replica, where M is the number of replicas.
+
+
+----------
+
+
+Four kinds of output can be generated during a PRD run: event
+statistics, thermodynamic output by each replica, dump files, and
+restart files.
+
+When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file is
+limited to event statistics.  Note that if a PRD run is performed on
+only a single replica then the event statistics will be intermixed
+with the usual thermodynamic output discussed below.
+
+The quantities printed each time an event occurs are the timestep, CPU
+time, clock, event number, a correlation flag, the number of
+coincident events, and the replica number of the chosen event.
+
+The timestep is the usual LAMMPS timestep, except that time does not
+advance during dephasing or quenches, but only during dynamics.  Note
+that are two kinds of dynamics in the PRD loop listed above that
+contribute to this timestepping.  The first is when all replicas are
+performing independent dynamics, waiting for an event to occur.  The
+second is when correlated events are being searched for, but only one
+replica is running dynamics.
+
+The CPU time is the total elapsed time on each processor, since the
+start of the PRD run.
+
+The clock is the same as the timestep except that it advances by M
+steps per timestep during the first kind of dynamics when the M
+replicas are running independently.  The clock advances by only 1 step
+per timestep during the second kind of dynamics, when only a single
+replica is checking for a correlated event.  Thus "clock" time
+represents the aggregate time (in steps) that has effectively elapsed
+during a PRD simulation on M replicas.  If most of the PRD run is
+spent in the second stage of the loop above, searching for infrequent
+events, then the clock will advance nearly M times faster than it
+would if a single replica was running.  Note the clock time between
+successive events should be drawn from p(t).
+
+The event number is a counter that increments with each event, whether
+it is uncorrelated or correlated.
+
+The correlation flag will be 0 when an uncorrelated event occurs
+during the second stage of the loop listed above, i.e. when all
+replicas are running independently.  The correlation flag will be 1
+when a correlated event occurs during the third stage of the loop
+listed above, i.e. when only one replica is running dynamics.
+
+When more than one replica detects an event at the end of the same
+event check (every *t\_event* steps) during the second stage, then
+one of them is chosen at random.  The number of coincident events is
+the number of replicas that detected an event.  Normally, this value
+should be 1.  If it is often greater than 1, then either the number of
+replicas is too large, or *t\_event* is too large.
+
+The replica number is the ID of the replica (from 0 to M-1) in which
+the event occurred.
+
+
+----------
+
+
+When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For
+the PRD command, these contain the thermodynamic output for each
+replica.  You will see short runs and minimizations corresponding to
+the dynamics and quench operations of the loop listed above.  The
+timestep will be reset appropriately depending on whether the
+operation advances time or not.
+
+After the PRD command completes, timing statistics for the PRD run are
+printed in each replica's log file, giving a breakdown of how much CPU
+time was spent in each stage (dephasing, dynamics, quenching, etc).
+
+
+----------
+
+
+Any :doc:`dump files <dump>` defined in the input script, will be
+written to during a PRD run at timesteps corresponding to both
+uncorrelated and correlated events.  This means the requested dump
+frequency in the :doc:`dump <dump>` command is ignored.  There will be
+one dump file (per dump command) created for all partitions.
+
+The atom coordinates of the dump snapshot are those of the minimum
+energy configuration resulting from quenching following a transition
+event.  The timesteps written into the dump files correspond to the
+timestep at which the event occurred and NOT the clock.  A dump
+snapshot corresponding to the initial minimum state used for event
+detection is written to the dump file at the beginning of each PRD
+run.
+
+
+----------
+
+
+If the :doc:`restart <restart>` command is used, a single restart file
+for all the partitions is generated, which allows a PRD run to be
+continued by a new input script in the usual manner.
+
+The restart file is generated at the end of the loop listed above.  If
+no correlated events are found, this means it contains a snapshot of
+the system at time T + *t\_correlate*, where T is the time at which the
+uncorrelated event occurred.  If correlated events were found, then it
+contains a snapshot of the system at time T + *t\_correlate*, where T
+is the time of the last correlated event.
+
+The restart frequency specified in the :doc:`restart <restart>` command
+is interpreted differently when performing a PRD run.  It does not
+mean the timestep interval between restart files.  Instead it means an
+event interval for uncorrelated events.  Thus a frequency of 1 means
+write a restart file every time an uncorrelated event occurs.  A
+frequency of 10 means write a restart file every 10th uncorrelated
+event.
+
+When an input script reads a restart file from a previous PRD run, the
+new script can be run on a different number of replicas or processors.
+However, it is assumed that *t\_correlate* in the new PRD command is
+the same as it was previously.  If not, the calculation of the "clock"
+value for the first event in the new run will be slightly off.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+The *N* and *t\_correlate* settings must be integer multiples of
+*t\_event*.
+
+Runs restarted from restart file written during a PRD run will not
+produce identical results due to changes in the random numbers used
+for dephasing.
+
+This command cannot be used when any fixes are defined that keep track
+of elapsed time to perform time-dependent operations.  Examples
+include the "ave" fixes such as :doc:`fix ave/chunk <fix_ave_chunk>`.
+Also :doc:`fix dt/reset <fix_dt_reset>` and :doc:`fix deposit <fix_deposit>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute event/displace <compute_event_displace>`,
+:doc:`min\_modify <min_modify>`, :doc:`min\_style <min_style>`,
+:doc:`run\_style <run_style>`, :doc:`minimize <minimize>`,
+:doc:`velocity <velocity>`, :doc:`temper <temper>`, :doc:`neb <neb>`,
+:doc:`tad <tad>`, :doc:`hyper <hyper>`
+
+Default
+"""""""
+
+The option defaults are min = 0.1 0.1 40 50, no temp setting, vel =
+geom gaussian, and time = steps.
+
+
+----------
+
+
+.. _Voter1998:
+
+
+
+**(Voter1998)** Voter, Phys Rev B, 57, 13985 (1998).
+
+.. _Voter2002prd:
+
+
+
+**(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials
+Research 32, 321 (2002).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/print.rst b/doc/src/print.rst
new file mode 100644
index 0000000000..93b1224993
--- /dev/null
+++ b/doc/src/print.rst
@@ -0,0 +1,101 @@
+.. index:: print
+
+print command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   print string keyword value
+
+* string = text string to print, which may contain variables
+* zero or more keyword/value pairs may be appended
+* keyword = *file* or *append* or *screen* or *universe*
+  
+  .. parsed-literal::
+  
+       *file* value = filename
+       *append* value = filename
+       *screen* value = *yes* or *no*
+       *universe* value = *yes* or *no*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   print "Done with equilibration" file info.dat
+   print Vol=$v append info.dat screen no
+   print "The system volume is now $v"
+   print 'The system volume is now $v'
+   print "NEB calculation 1 complete" screen no universe yes
+   print """
+   System volume = $v
+   System temperature = $t
+   """
+
+Description
+"""""""""""
+
+Print a text string to the screen and logfile.  The text string must
+be a single argument, so if it is one line but more than one word, it
+should be enclosed in single or double quotes.  To generate multiple
+lines of output, the string can be enclosed in triple quotes, as in
+the last example above.  If the text string contains variables, they
+will be evaluated and their current values printed.
+
+If the *file* or *append* keyword is used, a filename is specified to
+which the output will be written.  If *file* is used, then the
+filename is overwritten if it already exists.  If *append* is used,
+then the filename is appended to if it already exists, or created if
+it does not exist.
+
+If the *screen* keyword is used, output to the screen and logfile can
+be turned on or off as desired.
+
+If the *universe* keyword is used, output to the global screen and
+logfile can be turned on or off as desired. In multi-partition
+calculations, the *screen* option and the corresponding output only
+apply to the screen and logfile of the individual partition.
+
+If you want the print command to be executed multiple times (with
+changing variable values), there are 3 options.  First, consider using
+the :doc:`fix print <fix_print>` command, which will print a string
+periodically during a simulation.  Second, the print command can be
+used as an argument to the *every* option of the :doc:`run <run>`
+command.  Third, the print command could appear in a section of the
+input script that is looped over (see the :doc:`jump <jump>` and
+:doc:`next <next>` commands).
+
+See the :doc:`variable <variable>` command for a description of *equal*
+style variables which are typically the most useful ones to use with
+the print command.  Equal-style variables can calculate formulas
+involving mathematical operations, atom properties, group properties,
+thermodynamic properties, global values calculated by a
+:doc:`compute <compute>` or :doc:`fix <fix>`, or references to other
+:doc:`variables <variable>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix print <fix_print>`, :doc:`variable <variable>`
+
+Default
+"""""""
+
+The option defaults are no file output, screen = yes, and universe = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/processors.rst b/doc/src/processors.rst
new file mode 100644
index 0000000000..a13b44330c
--- /dev/null
+++ b/doc/src/processors.rst
@@ -0,0 +1,385 @@
+.. index:: processors
+
+processors command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   processors Px Py Pz keyword args ...
+
+* Px,Py,Pz = # of processors in each dimension of 3d grid overlaying the simulation domain
+* zero or more keyword/arg pairs may be appended
+* keyword = *grid* or *map* or *part* or *file*
+  
+  .. parsed-literal::
+  
+       *grid* arg = gstyle params ...
+         gstyle = *onelevel* or *twolevel* or *numa* or *custom*
+           onelevel params = none
+           twolevel params = Nc Cx Cy Cz
+             Nc = number of cores per node
+             Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
+           numa params = none
+           custom params = infile
+             infile = file containing grid layout
+       *map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx*
+          cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
+          cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
+          xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering
+       *numa* arg = none
+       *part* args = Psend Precv cstyle
+         Psend = partition # (1 to Np) which will send its processor layout
+         Precv = partition # (1 to Np) which will recv the processor layout
+         cstyle = *multiple*
+           *multiple* = Psend grid will be multiple of Precv grid in each dimension
+       *file* arg = outfile
+         outfile = name of file to write 3d grid of processors to
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   processors \* \* 5
+   processors 2 4 4
+   processors \* \* 8 map xyz
+   processors \* \* \* grid numa
+   processors \* \* \* grid twolevel 4 \* \* 1
+   processors 4 8 16 grid custom myfile
+   processors \* \* \* part 1 2 multiple
+
+Description
+"""""""""""
+
+Specify how processors are mapped as a regular 3d grid to the global
+simulation box.  The mapping involves 2 steps.  First if there are P
+processors it means choosing a factorization P = Px by Py by Pz so
+that there are Px processors in the x dimension, and similarly for the
+y and z dimensions.  Second, the P processors are mapped to the
+regular 3d grid.  The arguments to this command control each of these
+2 steps.
+
+The Px, Py, Pz parameters affect the factorization.  Any of the 3
+parameters can be specified with an asterisk "\*", which means LAMMPS
+will choose the number of processors in that dimension of the grid.
+It will do this based on the size and shape of the global simulation
+box so as to minimize the surface-to-volume ratio of each processor's
+sub-domain.
+
+Choosing explicit values for Px or Py or Pz can be used to override
+the default manner in which LAMMPS will create the regular 3d grid of
+processors, if it is known to be sub-optimal for a particular problem.
+E.g. a problem where the extent of atoms will change dramatically in a
+particular dimension over the course of the simulation.
+
+The product of Px, Py, Pz must equal P, the total # of processors
+LAMMPS is running on.  For a :doc:`2d simulation <dimension>`, Pz must
+equal 1.
+
+Note that if you run on a prime number of processors P, then a grid
+such as 1 x P x 1 will be required, which may incur extra
+communication costs due to the high surface area of each processor's
+sub-domain.
+
+Also note that if multiple partitions are being used then P is the
+number of processors in this partition; see the :doc:`-partition command-line switch <Run_options>` doc page for details.  Also note
+that you can prefix the processors command with the
+:doc:`partition <partition>` command to easily specify different
+Px,Py,Pz values for different partitions.
+
+You can use the :doc:`partition <partition>` command to specify
+different processor grids for different partitions, e.g.
+
+
+.. parsed-literal::
+
+   partition yes 1 processors 4 4 4
+   partition yes 2 processors 2 3 2
+
+.. note::
+
+   This command only affects the initial regular 3d grid created
+   when the simulation box is first specified via a
+   :doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` or
+   :doc:`read\_restart <read_restart>` command.  Or if the simulation box is
+   re-created via the :doc:`replicate <replicate>` command.  The same
+   regular grid is initially created, regardless of which
+   :doc:`comm\_style <comm_style>` command is in effect.
+
+If load-balancing is never invoked via the :doc:`balance <balance>` or
+:doc:`fix balance <fix_balance>` commands, then the initial regular grid
+will persist for all simulations.  If balancing is performed, some of
+the methods invoked by those commands retain the logical topology of
+the initial 3d grid, and the mapping of processors to the grid
+specified by the processors command.  However the grid spacings in
+different dimensions may change, so that processors own sub-domains of
+different sizes.  If the :doc:`comm\_style tiled <comm_style>` command is
+used, methods invoked by the balancing commands may discard the 3d
+grid of processors and tile the simulation domain with sub-domains of
+different sizes and shapes which no longer have a logical 3d
+connectivity.  If that occurs, all the information specified by the
+processors command is ignored.
+
+
+----------
+
+
+The *grid* keyword affects the factorization of P into Px,Py,Pz and it
+can also affect how the P processor IDs are mapped to the 3d grid of
+processors.
+
+The *onelevel* style creates a 3d grid that is compatible with the
+Px,Py,Pz settings, and which minimizes the surface-to-volume ratio of
+each processor's sub-domain, as described above.  The mapping of
+processors to the grid is determined by the *map* keyword setting.
+
+The *twolevel* style can be used on machines with multicore nodes to
+minimize off-node communication.  It insures that contiguous
+sub-sections of the 3d grid are assigned to all the cores of a node.
+For example if *Nc* is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of
+the 3d grid will correspond to the cores of each node.  This affects
+both the factorization and mapping steps.
+
+The *Cx*\ , *Cy*\ , *Cz* settings are similar to the *Px*\ , *Py*\ , *Pz*
+settings, only their product should equal *Nc*\ .  Any of the 3
+parameters can be specified with an asterisk "\*", which means LAMMPS
+will choose the number of cores in that dimension of the node's
+sub-grid.  As with Px,Py,Pz, it will do this based on the size and
+shape of the global simulation box so as to minimize the
+surface-to-volume ratio of each processor's sub-domain.
+
+.. note::
+
+   For the *twolevel* style to work correctly, it assumes the MPI
+   ranks of processors LAMMPS is running on are ordered by core and then
+   by node.  E.g. if you are running on 2 quad-core nodes, for a total of
+   8 processors, then it assumes processors 0,1,2,3 are on node 1, and
+   processors 4,5,6,7 are on node 2.  This is the default rank ordering
+   for most MPI implementations, but some MPIs provide options for this
+   ordering, e.g. via environment variable settings.
+
+The *numa* style operates similar to the *twolevel* keyword except
+that it auto-detects which cores are running on which nodes.
+Currently, it does this in only 2 levels, but it may be extended in
+the future to account for socket topology and other non-uniform memory
+access (NUMA) costs.  It also uses a different algorithm than the
+*twolevel* keyword for doing the two-level factorization of the
+simulation box into a 3d processor grid to minimize off-node
+communication, and it does its own MPI-based mapping of nodes and
+cores to the regular 3d grid.  Thus it may produce a different layout
+of the processors than the *twolevel* options.
+
+The *numa* style will give an error if the number of MPI processes is
+not divisible by the number of cores used per node, or any of the Px
+or Py of Pz values is greater than 1.
+
+.. note::
+
+   Unlike the *twolevel* style, the *numa* style does not require
+   any particular ordering of MPI ranks i norder to work correctly.  This
+   is because it auto-detects which processes are running on which nodes.
+
+The *custom* style uses the file *infile* to define both the 3d
+factorization and the mapping of processors to the grid.
+
+The file should have the following format.  Any number of initial
+blank or comment lines (starting with a "#" character) can be present.
+The first non-blank, non-comment line should have
+3 values:
+
+
+.. parsed-literal::
+
+   Px Py Py
+
+These must be compatible with the total number of processors
+and the Px, Py, Pz settings of the processors command.
+
+This line should be immediately followed by
+P = Px\*Py\*Pz lines of the form:
+
+
+.. parsed-literal::
+
+   ID I J K
+
+where ID is a processor ID (from 0 to P-1) and I,J,K are the
+processors location in the 3d grid.  I must be a number from 1 to Px
+(inclusive) and similarly for J and K.  The P lines can be listed in
+any order, but no processor ID should appear more than once.
+
+
+----------
+
+
+The *map* keyword affects how the P processor IDs (from 0 to P-1) are
+mapped to the 3d grid of processors.  It is only used by the
+*onelevel* and *twolevel* grid settings.
+
+The *cart* style uses the family of MPI Cartesian functions to perform
+the mapping, namely MPI\_Cart\_create(), MPI\_Cart\_get(),
+MPI\_Cart\_shift(), and MPI\_Cart\_rank().  It invokes the
+MPI\_Cart\_create() function with its reorder flag = 0, so that MPI is
+not free to reorder the processors.
+
+The *cart/reorder* style does the same thing as the *cart* style
+except it sets the reorder flag to 1, so that MPI can reorder
+processors if it desires.
+
+The *xyz*\ , *xzy*\ , *yxz*\ , *yzx*\ , *zxy*\ , and *zyx* styles are all
+similar.  If the style is IJK, then it maps the P processors to the
+grid so that the processor ID in the I direction varies fastest, the
+processor ID in the J direction varies next fastest, and the processor
+ID in the K direction varies slowest.  For example, if you select
+style *xyz* and you have a 2x2x2 grid of 8 processors, the assignments
+of the 8 octants of the simulation domain will be:
+
+
+.. parsed-literal::
+
+   proc 0 = lo x, lo y, lo z octant
+   proc 1 = hi x, lo y, lo z octant
+   proc 2 = lo x, hi y, lo z octant
+   proc 3 = hi x, hi y, lo z octant
+   proc 4 = lo x, lo y, hi z octant
+   proc 5 = hi x, lo y, hi z octant
+   proc 6 = lo x, hi y, hi z octant
+   proc 7 = hi x, hi y, hi z octant
+
+Note that, in principle, an MPI implementation on a particular machine
+should be aware of both the machine's network topology and the
+specific subset of processors and nodes that were assigned to your
+simulation.  Thus its MPI\_Cart calls can optimize the assignment of
+MPI processes to the 3d grid to minimize communication costs.  In
+practice, however, few if any MPI implementations actually do this.
+So it is likely that the *cart* and *cart/reorder* styles simply give
+the same result as one of the IJK styles.
+
+Also note, that for the *twolevel* grid style, the *map* setting is
+used to first map the nodes to the 3d grid, then again to the cores
+within each node.  For the latter step, the *cart* and *cart/reorder*
+styles are not supported, so an *xyz* style is used in their place.
+
+
+----------
+
+
+The *part* keyword affects the factorization of P into Px,Py,Pz.
+
+It can be useful when running in multi-partition mode, e.g. with the
+:doc:`run\_style verlet/split <run_style>` command.  It specifies a
+dependency between a sending partition *Psend* and a receiving
+partition *Precv* which is enforced when each is setting up their own
+mapping of their processors to the simulation box.  Each of *Psend*
+and *Precv* must be integers from 1 to Np, where Np is the number of
+partitions you have defined via the :doc:`-partition command-line switch <Run_options>`.
+
+A "dependency" means that the sending partition will create its
+regular 3d grid as Px by Py by Pz and after it has done this, it will
+send the Px,Py,Pz values to the receiving partition.  The receiving
+partition will wait to receive these values before creating its own
+regular 3d grid and will use the sender's Px,Py,Pz values as a
+constraint.  The nature of the constraint is determined by the
+*cstyle* argument.
+
+For a *cstyle* of *multiple*\ , each dimension of the sender's processor
+grid is required to be an integer multiple of the corresponding
+dimension in the receiver's processor grid.  This is a requirement of
+the :doc:`run\_style verlet/split <run_style>` command.
+
+For example, assume the sending partition creates a 4x6x10 grid = 240
+processor grid.  If the receiving partition is running on 80
+processors, it could create a 4x2x10 grid, but it will not create a
+2x4x10 grid, since in the y-dimension, 6 is not an integer multiple of
+4.
+
+.. note::
+
+   If you use the :doc:`partition <partition>` command to invoke
+   different "processors" commands on different partitions, and you also
+   use the *part* keyword, then you must insure that both the sending and
+   receiving partitions invoke the "processors" command that connects the
+   2 partitions via the *part* keyword.  LAMMPS cannot easily check for
+   this, but your simulation will likely hang in its setup phase if this
+   error has been made.
+
+
+----------
+
+
+The *file* keyword writes the mapping of the factorization of P
+processors and their mapping to the 3d grid to the specified file
+*outfile*\ .  This is useful to check that you assigned physical
+processors in the manner you desired, which can be tricky to figure
+out, especially when running on multiple partitions or on, a multicore
+machine or when the processor ranks were reordered by use of the
+:doc:`-reorder command-line switch <Run_options>` or due to use of
+MPI-specific launch options such as a config file.
+
+If you have multiple partitions you should insure that each one writes
+to a different file, e.g. using a :doc:`world-style variable <variable>`
+for the filename.  The file has a self-explanatory header, followed by
+one-line per processor in this format:
+
+world-ID universe-ID original-ID: I J K: name
+
+The IDs are the processor's rank in this simulation (the world), the
+universe (of multiple simulations), and the original MPI communicator
+used to instantiate LAMMPS, respectively.  The world and universe IDs
+will only be different if you are running on more than one partition;
+see the :doc:`-partition command-line switch <Run_options>`.  The
+universe and original IDs will only be different if you used the
+:doc:`-reorder command-line switch <Run_options>` to reorder the
+processors differently than their rank in the original communicator
+LAMMPS was instantiated with.
+
+I,J,K are the indices of the processor in the regular 3d grid, each
+from 1 to Nd, where Nd is the number of processors in that dimension
+of the grid.
+
+The *name* is what is returned by a call to MPI\_Get\_processor\_name()
+and should represent an identifier relevant to the physical processors
+in your machine.  Note that depending on the MPI implementation,
+multiple cores can have the same *name*\ .
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command cannot be used after the simulation box is defined by a
+:doc:`read\_data <read_data>` or :doc:`create\_box <create_box>` command.
+It can be used before a restart file is read to change the 3d
+processor grid from what is specified in the restart file.
+
+The *grid numa* keyword only currently works with the *map cart*
+option.
+
+The *part* keyword (for the receiving partition) only works with the
+*grid onelevel* or *grid twolevel* options.
+
+Related commands
+""""""""""""""""
+
+:doc:`partition <partition>`, :doc:`-reorder command-line switch <Run_options>`
+
+Default
+"""""""
+
+The option defaults are Px Py Pz = \* \* \*, grid = onelevel, and map =
+cart.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/python.rst b/doc/src/python.rst
new file mode 100644
index 0000000000..20c22a60ae
--- /dev/null
+++ b/doc/src/python.rst
@@ -0,0 +1,556 @@
+.. index:: python
+
+python command
+==============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   python func keyword args ...
+
+* func = name of Python function
+* one or more keyword/args pairs must be appended
+  
+  .. parsed-literal::
+  
+     keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists* or *source*
+       *invoke* arg = none = invoke the previously defined Python function
+       *input* args = N i1 i2 ... iN
+         N = # of inputs to function
+         i1,...,iN = value, SELF, or LAMMPS variable name
+           value = integer number, floating point number, or string
+           SELF = reference to LAMMPS itself which can be accessed by Python function
+           variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
+       *return* arg = varReturn
+         varReturn = v_name  = LAMMPS variable name which return value of function will be assigned to
+       *format* arg = fstring with M characters
+         M = N if no return value, where N = # of inputs
+         M = N+1 if there is a return value
+         fstring = each character (i,f,s,p) corresponds in order to an input or return value
+         'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
+       *length* arg = Nlen
+         Nlen = max length of string returned from Python function
+       *file* arg = filename
+         filename = file of Python code, which defines func
+       *here* arg = inline
+         inline = one or more lines of Python code which defines func
+                  must be a single argument, typically enclosed between triple quotes
+       *exists* arg = none = Python code has been loaded by previous python command
+       *source* arg = *filename* or *inline*
+         filename = file of Python code which will be executed immediately
+         inline = one or more lines of Python code which will be executed immediately
+                  must be a single argument, typically enclosed between triple quotes
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   python pForce input 2 v_x 20.0 return v_f format fff file force.py
+   python pForce invoke
+
+   python factorial input 1 myN return v_fac format ii here """
+   def factorial(n):
+     if n == 1: return n
+     return n \* factorial(n-1)
+    """
+
+   python loop input 1 SELF return v_value format pf here """
+   def loop(lmpptr,N,cut0):
+     from lammps import lammps
+     lmp = lammps(ptr=lmpptr)
+
+     # loop N times, increasing cutoff each time
+
+     for i in range(N):
+       cut = cut0 + i\*0.1
+       lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
+       lmp.command("pair_style lj/cut ${cut}")   # LAMMPS commands
+       lmp.command("pair_coeff \* \* 1.0 1.0")
+       lmp.command("run 100")
+    """
+
+Description
+"""""""""""
+
+Define a Python function or execute a previously defined function or
+execute some arbitrary python code.
+Arguments, including LAMMPS variables, can be passed to the function
+from the LAMMPS input script and a value returned by the Python
+function to a LAMMPS variable.  The Python code for the function can
+be included directly in the input script or in a separate Python file.
+The function can be standard Python code or it can make "callbacks" to
+LAMMPS through its library interface to query or set internal values
+within LAMMPS.  This is a powerful mechanism for performing complex
+operations in a LAMMPS input script that are not possible with the
+simple input script and variable syntax which LAMMPS defines.  Thus
+your input script can operate more like a true programming language.
+
+Use of this command requires building LAMMPS with the PYTHON package
+which links to the Python library so that the Python interpreter is
+embedded in LAMMPS.  More details about this process are given below.
+
+There are two ways to invoke a Python function once it has been
+defined.  One is using the *invoke* keyword.  The other is to assign
+the function to a :doc:`python-style variable <variable>` defined in
+your input script.  Whenever the variable is evaluated, it will
+execute the Python function to assign a value to the variable.  Note
+that variables can be evaluated in many different ways within LAMMPS.
+They can be substituted for directly in an input script.  Or they can
+be passed to various commands as arguments, so that the variable is
+evaluated during a simulation run.
+
+A broader overview of how Python can be used with LAMMPS is given on
+the :doc:`Python <Python_head>` doc page.  There is an examples/python
+directory which illustrates use of the python command.
+
+
+----------
+
+
+The *func* setting specifies the name of the Python function.  The
+code for the function is defined using the *file* or *here* keywords
+as explained below. In case of the *source* keyword, the name of
+the function is ignored.
+
+If the *invoke* keyword is used, no other keywords can be used, and a
+previous python command must have defined the Python function
+referenced by this command.  This invokes the Python function with the
+previously defined arguments and return value processed as explained
+below.  You can invoke the function as many times as you wish in your
+input script.
+
+If the *source* keyword is used, no other keywords can be used.
+The argument can be a filename or a string with python commands,
+either on a single line enclosed in quotes, or as multiple lines
+enclosed in triple quotes. These python commands will be passed
+to the python interpreter and executed immediately without registering
+a python function for future execution.
+
+The *input* keyword defines how many arguments *N* the Python function
+expects.  If it takes no arguments, then the *input* keyword should
+not be used.  Each argument can be specified directly as a value,
+e.g. 6 or 3.14159 or abc (a string of characters).  The type of each
+argument is specified by the *format* keyword as explained below, so
+that Python will know how to interpret the value.  If the word SELF is
+used for an argument it has a special meaning.  A pointer is passed to
+the Python function which it converts into a reference to LAMMPS
+itself.  This enables the function to call back to LAMMPS through its
+library interface as explained below.  This allows the Python function
+to query or set values internal to LAMMPS which can affect the
+subsequent execution of the input script.  A LAMMPS variable can also
+be used as an argument, specified as v\_name, where "name" is the name
+of the variable.  Any style of LAMMPS variable can be used, as defined
+by the :doc:`variable <variable>` command.  Each time the Python
+function is invoked, the LAMMPS variable is evaluated and its value is
+passed to the Python function.
+
+The *return* keyword is only needed if the Python function returns a
+value.  The specified *varReturn* must be of the form v\_name, where
+"name" is the name of a python-style LAMMPS variable, defined by the
+:doc:`variable <variable>` command.  The Python function can return a
+numeric or string value, as specified by the *format* keyword.
+
+As explained on the :doc:`variable <variable>` doc page, the definition
+of a python-style variable associates a Python function name with the
+variable.  This must match the *func* setting for this command.  For
+example these two commands would be self-consistent:
+
+
+.. parsed-literal::
+
+   variable foo python myMultiply
+   python myMultiply return v_foo format f file funcs.py
+
+The two commands can appear in either order in the input script so
+long as both are specified before the Python function is invoked for
+the first time.
+
+The *format* keyword must be used if the *input* or *return* keyword
+is used.  It defines an *fstring* with M characters, where M = sum of
+number of inputs and outputs.  The order of characters corresponds to
+the N inputs, followed by the return value (if it exists).  Each
+character must be one of the following: "i" for integer, "f" for
+floating point, "s" for string, or "p" for SELF.  Each character
+defines the type of the corresponding input or output value of the
+Python function and affects the type conversion that is performed
+internally as data is passed back and forth between LAMMPS and Python.
+Note that it is permissible to use a :doc:`python-style variable <variable>` in a LAMMPS command that allows for an
+equal-style variable as an argument, but only if the output of the
+Python function is flagged as a numeric value ("i" or "f") via the
+*format* keyword.
+
+If the *return* keyword is used and the *format* keyword specifies the
+output as a string, then the default maximum length of that string is
+63 characters (64-1 for the string terminator).  If you want to return
+a longer string, the *length* keyword can be specified with its *Nlen*
+value set to a larger number (the code allocates space for Nlen+1 to
+include the string terminator).  If the Python function generates a
+string longer than the default 63 or the specified *Nlen*\ , it will be
+truncated.
+
+
+----------
+
+
+Either the *file*\ , *here*\ , or *exists* keyword must be used, but only
+one of them.  These keywords specify what Python code to load into the
+Python interpreter.  The *file* keyword gives the name of a file,
+which should end with a ".py" suffix, which contains Python code.  The
+code will be immediately loaded into and run in the "main" module of
+the Python interpreter.  Note that Python code which contains a
+function definition does not "execute" the function when it is run; it
+simply defines the function so that it can be invoked later.
+
+The *here* keyword does the same thing, except that the Python code
+follows as a single argument to the *here* keyword.  This can be done
+using triple quotes as delimiters, as in the examples above.  This
+allows Python code to be listed verbatim in your input script, with
+proper indentation, blank lines, and comments, as desired.  See the
+:doc:`Commands parse <Commands_parse>` doc page, for an explanation of
+how triple quotes can be used as part of input script syntax.
+
+The *exists* keyword takes no argument.  It means that Python code
+containing the required Python function defined by the *func* setting,
+is assumed to have been previously loaded by another python command.
+
+Note that the Python code that is loaded and run must contain a
+function with the specified *func* name.  To operate properly when
+later invoked, the function code must match the *input* and
+*return* and *format* keywords specified by the python command.
+Otherwise Python will generate an error.
+
+
+----------
+
+
+This section describes how Python code can be written to work with
+LAMMPS.
+
+Whether you load Python code from a file or directly from your input
+script, via the *file* and *here* keywords, the code can be identical.
+It must be indented properly as Python requires.  It can contain
+comments or blank lines.  If the code is in your input script, it
+cannot however contain triple-quoted Python strings, since that will
+conflict with the triple-quote parsing that the LAMMPS input script
+performs.
+
+All the Python code you specify via one or more python commands is
+loaded into the Python "main" module, i.e. \__main\__.  The code can
+define global variables or statements that are outside of function
+definitions.  It can contain multiple functions, only one of which
+matches the *func* setting in the python command.  This means you can
+use the *file* keyword once to load several functions, and the
+*exists* keyword thereafter in subsequent python commands to access
+the other functions previously loaded.
+
+A Python function you define (or more generally, the code you load)
+can import other Python modules or classes, it can make calls to other
+system functions or functions you define, and it can access or modify
+global variables (in the "main" module) which will persist between
+successive function calls.  The latter can be useful, for example, to
+prevent a function from being invoke multiple times per timestep by
+different commands in a LAMMPS input script that access the returned
+python-style variable associated with the function.  For example,
+consider this function loaded with two global variables defined
+outside the function:
+
+
+.. parsed-literal::
+
+   nsteplast = -1
+   nvaluelast = 0
+
+   def expensive(nstep):
+     global nsteplast,nvaluelast
+     if nstep == nsteplast: return nvaluelast
+     nsteplast = nstep
+     # perform complicated calculation
+     nvalue = ...
+     nvaluelast = nvalue
+     return nvalue
+
+Nsteplast stores the previous timestep the function was invoked
+(passed as an argument to the function).  Nvaluelast stores the return
+value computed on the last function invocation.  If the function is
+invoked again on the same timestep, the previous value is simply
+returned, without re-computing it.  The "global" statement inside the
+Python function allows it to overwrite the global variables.
+
+Note that if you load Python code multiple times (via multiple python
+commands), you can overwrite previously loaded variables and functions
+if you are not careful.  E.g. if the code above were loaded twice, the
+global variables would be re-initialized, which might not be what you
+want.  Likewise, if a function with the same name exists in two chunks
+of Python code you load, the function loaded second will override the
+function loaded first.
+
+It's important to realize that if you are running LAMMPS in parallel,
+each MPI task will load the Python interpreter and execute a local
+copy of the Python function(s) you define.  There is no connection
+between the Python interpreters running on different processors.
+This implies three important things.
+
+First, if you put a print statement in your Python function, you will
+see P copies of the output, when running on P processors.  If the
+prints occur at (nearly) the same time, the P copies of the output may
+be mixed together.  Welcome to the world of parallel programming and
+debugging.
+
+Second, if your Python code loads modules that are not pre-loaded by
+the Python library, then it will load the module from disk.  This may
+be a bottleneck if 1000s of processors try to load a module at the
+same time.  On some large supercomputers, loading of modules from disk
+by Python may be disabled.  In this case you would need to pre-build a
+Python library that has the required modules pre-loaded and link
+LAMMPS with that library.
+
+Third, if your Python code calls back to LAMMPS (discussed in the
+next section) and causes LAMMPS to perform an MPI operation requires
+global communication (e.g. via MPI\_Allreduce), such as computing the
+global temperature of the system, then you must insure all your Python
+functions (running independently on different processors) call back to
+LAMMPS.  Otherwise the code may hang.
+
+
+----------
+
+
+Your Python function can "call back" to LAMMPS through its
+library interface, if you use the SELF input to pass Python
+a pointer to LAMMPS.  The mechanism for doing this in your
+Python function is as follows:
+
+
+.. parsed-literal::
+
+   def foo(lmpptr,...):
+     from lammps import lammps
+     lmp = lammps(ptr=lmpptr)
+     lmp.command('print "Hello from inside Python"')
+     ...
+
+The function definition must include a variable (lmpptr in this case)
+which corresponds to SELF in the python command.  The first line of
+the function imports the Python module lammps.py in the python dir of
+the distribution.  The second line creates a Python object "lmp" which
+wraps the instance of LAMMPS that called the function.  The
+"ptr=lmpptr" argument is what makes that happen.  The third line
+invokes the command() function in the LAMMPS library interface.  It
+takes a single string argument which is a LAMMPS input script command
+for LAMMPS to execute, the same as if it appeared in your input
+script.  In this case, LAMMPS should output
+
+
+.. parsed-literal::
+
+   Hello from inside Python
+
+to the screen and log file.  Note that since the LAMMPS print command
+itself takes a string in quotes as its argument, the Python string
+must be delimited with a different style of quotes.
+
+The :doc:`Pytnon library <Python_library>` doc page describes the syntax
+for how Python wraps the various functions included in the LAMMPS
+library interface.
+
+A more interesting example is in the examples/python/in.python script
+which loads and runs the following function from examples/python/funcs.py:
+
+
+.. parsed-literal::
+
+   def loop(N,cut0,thresh,lmpptr):
+     print "LOOP ARGS",N,cut0,thresh,lmpptr
+     from lammps import lammps
+     lmp = lammps(ptr=lmpptr)
+     natoms = lmp.get_natoms()
+
+     for i in range(N):
+       cut = cut0 + i\*0.1
+
+       lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
+       lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
+       #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
+
+       lmp.command("pair_coeff \* \* 1.0 1.0")       # ditto
+       lmp.command("run 10")                       # ditto
+       pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
+       print "PE",pe/natoms,thresh
+       if pe/natoms < thresh: return
+
+with these input script commands:
+
+
+.. parsed-literal::
+
+   python          loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
+   python          loop invoke
+
+This has the effect of looping over a series of 10 short runs (10
+timesteps each) where the pair style cutoff is increased from a value
+of 1.0 in distance units, in increments of 0.1.  The looping stops
+when the per-atom potential energy falls below a threshold of -4.0 in
+energy units.  More generally, Python can be used to implement a loop
+with complex logic, much more so than can be created using the LAMMPS
+:doc:`jump <jump>` and :doc:`if <if>` commands.
+
+Several LAMMPS library functions are called from the loop function.
+Get\_natoms() returns the number of atoms in the simulation, so that it
+can be used to normalize the potential energy that is returned by
+extract\_compute() for the "thermo\_pe" compute that is defined by
+default for LAMMPS thermodynamic output.  Set\_variable() sets the
+value of a string variable defined in LAMMPS.  This library function
+is a useful way for a Python function to return multiple values to
+LAMMPS, more than the single value that can be passed back via a
+return statement.  This cutoff value in the "cut" variable is then
+substituted (by LAMMPS) in the pair\_style command that is executed
+next.  Alternatively, the "LAMMPS command option" line could be used
+in place of the 2 preceding lines, to have Python insert the value
+into the LAMMPS command string.
+
+.. note::
+
+   When using the callback mechanism just described, recognize that
+   there are some operations you should not attempt because LAMMPS cannot
+   execute them correctly.  If the Python function is invoked between
+   runs in the LAMMPS input script, then it should be OK to invoke any
+   LAMMPS input script command via the library interface command() or
+   file() functions, so long as the command would work if it were
+   executed in the LAMMPS input script directly at the same point.
+
+However, a Python function can also be invoked during a run, whenever
+an associated LAMMPS variable it is assigned to is evaluated.  If the
+variable is an input argument to another LAMMPS command (e.g. :doc:`fix setforce <fix_setforce>`), then the Python function will be invoked
+inside the class for that command, in one of its methods that is
+invoked in the middle of a timestep.  You cannot execute arbitrary
+input script commands from the Python function (again, via the
+command() or file() functions) at that point in the run and expect it
+to work.  Other library functions such as those that invoke computes
+or other variables may have hidden side effects as well.  In these
+cases, LAMMPS has no simple way to check that something illogical is
+being attempted.
+
+The same applies to Python functions called during a simulation run at
+each time step using :doc:`fix python/invoke <fix_python_invoke>`.
+
+
+----------
+
+
+If you run Python code directly on your workstation, either
+interactively or by using Python to launch a Python script stored in a
+file, and your code has an error, you will typically see informative
+error messages.  That is not the case when you run Python code from
+LAMMPS using an embedded Python interpreter.  The code will typically
+fail silently.  LAMMPS will catch some errors but cannot tell you
+where in the Python code the problem occurred.  For example, if the
+Python code cannot be loaded and run because it has syntax or other
+logic errors, you may get an error from Python pointing to the
+offending line, or you may get one of these generic errors from
+LAMMPS:
+
+
+.. parsed-literal::
+
+   Could not process Python file
+   Could not process Python string
+
+When the Python function is invoked, if it does not return properly,
+you will typically get this generic error from LAMMPS:
+
+
+.. parsed-literal::
+
+   Python function evaluation failed
+
+Here are three suggestions for debugging your Python code while
+running it under LAMMPS.
+
+First, don't run it under LAMMPS, at least to start with!  Debug it
+using plain Python.  Load and invoke your function, pass it arguments,
+check return values, etc.
+
+Second, add Python print statements to the function to check how far
+it gets and intermediate values it calculates.  See the discussion
+above about printing from Python when running in parallel.
+
+Third, use Python exception handling.  For example, say this statement
+in your Python function is failing, because you have not initialized the
+variable foo:
+
+
+.. parsed-literal::
+
+   foo += 1
+
+If you put one (or more) statements inside a "try" statement,
+like this:
+
+
+.. parsed-literal::
+
+   import exceptions
+   print "Inside simple function"
+   try:
+     foo += 1      # one or more statements here
+   except Exception, e:
+     print "FOO error:",e
+
+then you will get this message printed to the screen:
+
+
+.. parsed-literal::
+
+   FOO error: local variable 'foo' referenced before assignment
+
+If there is no error in the try statements, then nothing is printed.
+Either way the function continues on (unless you put a return or
+sys.exit() in the except clause).
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the PYTHON package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Building LAMMPS with the PYTHON package will link LAMMPS with the
+Python library on your system.  Settings to enable this are in the
+lib/python/Makefile.lammps file.  See the lib/python/README file for
+information on those settings.
+
+If you use Python code which calls back to LAMMPS, via the SELF input
+argument explained above, there is an extra step required when
+building LAMMPS.  LAMMPS must also be built as a shared library and
+your Python function must be able to load the Python module in
+python/lammps.py that wraps the LAMMPS library interface.  These are
+the same steps required to use Python by itself to wrap LAMMPS.
+Details on these steps are explained on the :doc:`Python <Python_head>`
+doc page.  Note that it is important that the stand-alone LAMMPS
+executable and the LAMMPS shared library be consistent (built from the
+same source code files) in order for this to work.  If the two have
+been built at different times using different source files, problems
+may occur.
+
+Related commands
+""""""""""""""""
+
+:doc:`shell <shell>`, :doc:`variable <variable>`, :doc:`fix python/invoke <fix_python_invoke>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/quit.rst b/doc/src/quit.rst
new file mode 100644
index 0000000000..2129920022
--- /dev/null
+++ b/doc/src/quit.rst
@@ -0,0 +1,58 @@
+.. index:: quit
+
+quit command
+============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   quit status
+
+status = numerical exit status (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   quit
+   if "$n > 10000" then "quit 1"
+
+Description
+"""""""""""
+
+This command causes LAMMPS to exit, after shutting down all output
+cleanly.
+
+It can be used as a debug statement in an input script, to terminate
+the script at some intermediate point.
+
+It can also be used as an invoked command inside the "then" or "else"
+portion of an :doc:`if <if>` command.
+
+The optional status argument is an integer which signals the return
+status to a program calling LAMMPS.  A return status of 0 usually
+indicates success.  A status != 0 is failure, where the specified
+value can be used to distinguish the kind of error, e.g. where in the
+input script the quit was invoked.  If not specified, a status of 0 is
+returned.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`if <if>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst
new file mode 100644
index 0000000000..798f95e5ec
--- /dev/null
+++ b/doc/src/read_data.rst
@@ -0,0 +1,1445 @@
+.. index:: read\_data
+
+read\_data command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   read_data file keyword args ...
+
+* file = name of data file to read in
+* zero or more keyword/arg pairs may be appended
+* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *group* or *nocoeff* or *fix*
+  
+  .. parsed-literal::
+  
+       *add* arg = *append* or *IDoffset* or *IDoffset MOLoffset* or *merge*
+         append = add new atoms with atom IDs appended to current IDs
+         IDoffset = add new atoms with atom IDs having IDoffset added
+         MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled)
+         merge = add new atoms with their atom IDs (and molecule IDs) unchanged
+       *offset* args = toff boff aoff doff ioff
+         toff = offset to add to atom types
+         boff = offset to add to bond types
+         aoff = offset to add to angle types
+         doff = offset to add to dihedral types
+         ioff = offset to add to improper types
+       *shift* args = Sx Sy Sz
+         Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
+       *extra/atom/types* arg = # of extra atom types
+       *extra/bond/types* arg = # of extra bond types
+       *extra/angle/types* arg = # of extra angle types
+       *extra/dihedral/types* arg = # of extra dihedral types
+       *extra/improper/types* arg = # of extra improper types
+       *extra/bond/per/atom* arg = leave space for this many new bonds per atom
+       *extra/angle/per/atom* arg = leave space for this many new angles per atom
+       *extra/dihedral/per/atom* arg = leave space for this many new dihedrals per atom
+       *extra/improper/per/atom* arg = leave space for this many new impropers per atom
+       *extra/special/per/atom* arg = leave space for extra 1-2,1-3,1-4 interactions per atom
+       *group* args = groupID
+         groupID = add atoms in data file to this group
+       *nocoeff* = ignore force field parameters
+       *fix* args = fix-ID header-string section-string
+         fix-ID = ID of fix to process header lines and sections of data file
+         header-string = header lines containing this string will be passed to fix
+         section-string = section names with this string will be passed to fix
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   read_data data.lj
+   read_data ../run7/data.polymer.gz
+   read_data data.protein fix mycmap crossterm CMAP
+   read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
+   read_data data.water add merge 1 group solvent
+
+Description
+"""""""""""
+
+Read in a data file containing information LAMMPS needs to run a
+simulation.  The file can be ASCII text or a gzipped text file
+(detected by a .gz suffix).  This is one of 3 ways to specify initial
+atom coordinates; see the :doc:`read\_restart <read_restart>` and
+:doc:`create\_atoms <create_atoms>` commands for alternative methods.
+Also see the explanation of the :doc:`-restart command-line switch <Run_options>` which can convert a restart file to a data
+file.
+
+This command can be used multiple times to add new atoms and their
+properties to an existing system by using the *add*\ , *offset*\ , and
+*shift* keywords.  See more details below, which includes the use case
+for the *extra* keywords.
+
+The *group* keyword adds all the atoms in the data file to the
+specified group-ID.  The group will be created if it does not already
+exist.  This is useful if you are reading multiple data files and wish
+to put sets of atoms into different groups so they can be operated on
+later.  E.g. a group of added atoms can be moved to new positions via
+the :doc:`displace\_atoms <displace_atoms>` command.  Note that atoms
+read from the data file are also always added to the "all" group.  The
+:doc:`group <group>` command discusses atom groups, as used in LAMMPS.
+
+The *nocoeff* keyword tells read\_data to ignore force field parameters.
+The various Coeff sections are still read and have to have the correct
+number of lines, but they are not applied. This also allows to read a
+data file without having any pair, bond, angle, dihedral or improper
+styles defined, or to read a data file for a different force field.
+
+The use of the *fix* keyword is discussed below.
+
+
+----------
+
+
+**Reading multiple data files**
+
+The read\_data command can be used multiple times with the same or
+different data files to build up a complex system from components
+contained in individual data files.  For example one data file could
+contain fluid in a confined domain; a second could contain wall atoms,
+and the second file could be read a third time to create a wall on the
+other side of the fluid.  The third set of atoms could be rotated to
+an opposing direction using the :doc:`displace\_atoms <displace_atoms>`
+command, after the third read\_data command is used.
+
+The *add*\ , *offset*\ , *shift*\ , *extra*\ , and *group* keywords are
+useful in this context.
+
+If a simulation box does not yet exist, the *add* keyword
+cannot be used; the read\_data command is being used for the first
+time.  If a simulation box does exist, due to using the
+:doc:`create\_box <create_box>` command, or a previous read\_data command,
+then the *add* keyword must be used.
+
+.. note::
+
+   The simulation box size (xlo to xhi, ylo to yhi, zlo to zhi) in
+   the new data file will be merged with the existing simulation box to
+   create a large enough box in each dimension to contain both the
+   existing and new atoms.  Each box dimension never shrinks due to this
+   merge operation, it only stays the same or grows. Care must be used if
+   you are growing the existing simulation box in a periodic dimension.
+   If there are existing atoms with bonds that straddle that periodic
+   boundary, then the atoms may become far apart if the box size grows.
+   This will separate the atoms in the bond, which can lead to "lost"
+   bond atoms or bad dynamics.
+
+The three choices for the *add* argument affect how the atom IDs and
+molecule IDs of atoms in the data file are treated.  If *append* is
+specified, atoms in the data file are added to the current system,
+with their atom IDs reset so that an atom-ID = M in the data file
+becomes atom-ID = N+M, where N is the largest atom ID in the current
+system.  This rule is applied to all occurrences of atom IDs in the
+data file, e.g. in the Velocity or Bonds section. This is also done
+for molecule IDs, if the atom style does support molecule IDs or
+they are enabled via fix property/atom. If *IDoffset* is specified,
+then *IDoffset* is a numeric value is given, e.g. 1000, so that an
+atom-ID = M in the data file becomes atom-ID = 1000+M. For systems
+with enabled molecule IDs, another numerical argument *MOLoffset*
+is required representing the equivalent offset for molecule IDs.
+If *merge* is specified, the data file atoms
+are added to the current system without changing their IDs.  They are
+assumed to merge (without duplication) with the currently defined
+atoms.  It is up to you to insure there are no multiply defined atom
+IDs, as LAMMPS only performs an incomplete check that this is the case
+by insuring the resulting max atom-ID >= the number of atoms. For
+molecule IDs, there is no check done at all.
+
+The *offset* and *shift* keywords can only be used if the *add*
+keyword is also specified.
+
+The *offset* keyword adds the specified offset values to the atom
+types, bond types, angle types, dihedral types, and improper types as
+they are read from the data file.  E.g. if *toff* = 2, and the file
+uses atom types 1,2,3, then the added atoms will have atom types
+3,4,5.  These offsets apply to all occurrences of types in the data
+file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
+sections.  This makes it easy to use atoms and molecules and their
+attributes from a data file in different simulations, where you want
+their types (atom, bond, angle, etc) to be different depending on what
+other types already exist.  All five offset values must be specified,
+but individual values will be ignored if the data file does not use
+that attribute (e.g. no bonds).
+
+The *shift* keyword can be used to specify an (Sx, Sy, Sz)
+displacement applied to the coordinates of each atom.  Sz must be 0.0
+for a 2d simulation.  This is a mechanism for adding structured
+collections of atoms at different locations within the simulation box,
+to build up a complex geometry.  It is up to you to insure atoms do
+not end up overlapping unphysically which would lead to bad dynamics.
+Note that the :doc:`displace\_atoms <displace_atoms>` command can be used
+to move a subset of atoms after they have been read from a data file.
+Likewise, the :doc:`delete\_atoms <delete_atoms>` command can be used to
+remove overlapping atoms.  Note that the shift values (Sx, Sy, Sz) are
+also added to the simulation box information (xlo, xhi, ylo, yhi, zlo,
+zhi) in the data file to shift its boundaries.  E.g. xlo\_new = xlo +
+Sx, xhi\_new = xhi + Sx.
+
+The *extra* keywords can only be used the first time the read\_data
+command is used.  They are useful if you intend to add new atom, bond,
+angle, etc types later with additional read\_data commands.  This is
+because the maximum number of allowed atom, bond, angle, etc types is
+set by LAMMPS when the system is first initialized.  If you do not use
+the *extra* keywords, then the number of these types will be limited
+to what appears in the first data file you read.  For example, if the
+first data file is a solid substrate of Si, it will likely specify a
+single atom type.  If you read a second data file with a different
+material (water molecules) that sit on top of the substrate, you will
+want to use different atom types for those atoms.  You can only do
+this if you set the *extra/atom/types* keyword to a sufficiently large
+value when reading the substrate data file.  Note that use of the
+*extra* keywords also allows each data file to contain sections like
+Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for
+the number of types in that data file.  If the *offset* keyword is
+used appropriately when each data file is read, the values in those
+sections will be stored correctly in the larger data structures
+allocated by the use of the *extra* keywords.  E.g. the substrate file
+can list mass and pair coefficients for type 1 silicon atoms.  The
+water file can list mass and pair coefficients for type 1 and type 2
+hydrogen and oxygen atoms.  Use of the *extra* and *offset* keywords
+will store those mass and pair coefficient values appropriately in
+data structures that allow for 3 atom types (Si, H, O).  Of course,
+you would still need to specify coefficients for H/Si and O/Si
+interactions in your input script to have a complete pairwise
+interaction model.
+
+An alternative to using the *extra* keywords with the read\_data
+command, is to use the :doc:`create\_box <create_box>` command to
+initialize the simulation box and all the various type limits you need
+via its *extra* keywords.  Then use the read\_data command one or more
+times to populate the system with atoms, bonds, angles, etc, using the
+*offset* keyword if desired to alter types used in the various data
+files you read.
+
+
+----------
+
+
+**Format of a data file**
+
+The structure of the data file is important, though many settings and
+sections are optional or can come in any order.  See the examples
+directory for sample data files for different problems.
+
+A data file has a header and a body.  The header appears first.  The
+first line of the header is always skipped; it typically contains a
+description of the file.  Then lines are read one at a time.  Lines
+can have a trailing comment starting with '#' that is ignored.  If the
+line is blank (only white-space after comment is deleted), it is
+skipped.  If the line contains a header keyword, the corresponding
+value(s) is read from the line.  If it doesn't contain a header
+keyword, the line begins the body of the file.
+
+The body of the file contains zero or more sections.  The first line
+of a section has only a keyword.  This line can have a trailing
+comment starting with '#' that is either ignored or can be used to
+check for a style match, as described below.  The next line is
+skipped.  The remaining lines of the section contain values.  The
+number of lines depends on the section keyword as described below.
+Zero or more blank lines can be used between sections.  Sections can
+appear in any order, with a few exceptions as noted below.
+
+The keyword *fix* can be used one or more times.  Each usage specifies
+a fix that will be used to process a specific portion of the data
+file.  Any header line containing *header-string* and any section with
+a name containing *section-string* will be passed to the specified
+fix.  See the :doc:`fix property/atom <fix_property_atom>` command for
+an example of a fix that operates in this manner.  The doc page for
+the fix defines the syntax of the header line(s) and section(s) that
+it reads from the data file.  Note that the *header-string* can be
+specified as NULL, in which case no header lines are passed to the
+fix.  This means that it can infer the length of its Section from
+standard header settings, such as the number of atoms.
+
+The formatting of individual lines in the data file (indentation,
+spacing between words and numbers) is not important except that header
+and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must
+be capitalized as shown and can't have extra white-space between their
+words - e.g. two spaces or a tab between the 2 words in "xlo xhi" or
+the 2 words in "Bond Coeffs", is not valid.
+
+
+----------
+
+
+**Format of the header of a data file**
+
+These are the recognized header keywords.  Header lines can come in
+any order.  The value(s) are read from the beginning of the line.
+Thus the keyword *atoms* should be in a line like "1000 atoms"; the
+keyword *ylo yhi* should be in a line like "-10.0 10.0 ylo yhi"; the
+keyword *xy xz yz* should be in a line like "0.0 5.0 6.0 xy xz yz".
+All these settings have a default value of 0, except the lo/hi box
+size defaults are -0.5 and 0.5.  A line need only appear if the value
+is different than the default.
+
+* *atoms* = # of atoms in system
+* *bonds* = # of bonds in system
+* *angles* = # of angles in system
+* *dihedrals* = # of dihedrals in system
+* *impropers* = # of impropers in system
+* *atom types* = # of atom types in system
+* *bond types* = # of bond types in system
+* *angle types* = # of angle types in system
+* *dihedral types* = # of dihedral types in system
+* *improper types* = # of improper types in system
+* *extra bond per atom* = leave space for this many new bonds per atom (deprecated, use extra/bond/per/atom keyword)
+* *extra angle per atom* = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword)
+* *extra dihedral per atom* = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword)
+* *extra improper per atom* = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword)
+* *extra special per atom* = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword)
+* *ellipsoids* = # of ellipsoids in system
+* *lines* = # of line segments in system
+* *triangles* = # of triangles in system
+* *bodies* = # of bodies in system
+* *xlo xhi* = simulation box boundaries in x dimension
+* *ylo yhi* = simulation box boundaries in y dimension
+* *zlo zhi* = simulation box boundaries in z dimension
+* *xy xz yz* = simulation box tilt factors for triclinic system
+
+The initial simulation box size is determined by the lo/hi settings.
+In any dimension, the system may be periodic or non-periodic; see the
+:doc:`boundary <boundary>` command.  When the simulation box is created
+it is also partitioned into a regular 3d grid of rectangular bricks,
+one per processor, based on the number of processors being used and
+the settings of the :doc:`processors <processors>` command.  The
+partitioning can later be changed by the :doc:`balance <balance>` or
+:doc:`fix balance <fix_balance>` commands.
+
+If the *xy xz yz* line does not appear, LAMMPS will set up an
+axis-aligned (orthogonal) simulation box.  If the line does appear,
+LAMMPS creates a non-orthogonal simulation domain shaped as a
+parallelepiped with triclinic symmetry.  The parallelepiped has its
+"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
+from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
+(xz,yz,zhi-zlo).  *Xy,xz,yz* can be 0.0 or positive or negative values
+and are called "tilt factors" because they are the amount of
+displacement applied to faces of an originally orthogonal box to
+transform it into the parallelepiped.
+
+By default, the tilt factors (xy,xz,yz) can not skew the box more than
+half the distance of the corresponding parallel box length.  For
+example, if xlo = 2 and xhi = 12, then the x box length is 10 and the
+xy tilt factor must be between -5 and 5.  Similarly, both xz and yz
+must be between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not
+a limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are all geometrically equivalent.  If you wish to define a box
+with tilt factors that exceed these limits, you can use the :doc:`box tilt <box>` command, with a setting of *large*\ ; a setting of
+*small* is the default.
+
+See the :doc:`Howto triclinic <Howto_triclinic>` doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
+triclinic representations.
+
+When a triclinic system is used, the simulation domain should normally
+be periodic in the dimension that the tilt is applied to, which is
+given by the second dimension of the tilt factor (e.g. y for xy tilt).
+This is so that pairs of atoms interacting across that boundary will
+have one of them shifted by the tilt factor.  Periodicity is set by
+the :doc:`boundary <boundary>` command.  For example, if the xy tilt
+factor is non-zero, then the y dimension should be periodic.
+Similarly, the z dimension should be periodic if xz or yz is non-zero.
+LAMMPS does not require this periodicity, but you may lose atoms if
+this is not the case.
+
+Also note that if your simulation will tilt the box, e.g. via the :doc:`fix deform <fix_deform>` command, the simulation box must be setup to
+be triclinic, even if the tilt factors are initially 0.0.  You can
+also change an orthogonal box to a triclinic box or vice versa by
+using the :doc:`change box <change_box>` command with its *ortho* and
+*triclinic* options.
+
+For 2d simulations, the *zlo zhi* values should be set to bound the z
+coords for atoms that appear in the file; the default of -0.5 0.5 is
+valid if all z coords are 0.0.  For 2d triclinic simulations, the xz
+and yz tilt factors must be 0.0.
+
+If the system is periodic (in a dimension), then atom coordinates can
+be outside the bounds (in that dimension); they will be remapped (in a
+periodic sense) back inside the box.  Note that if the *add* option is
+being used to add atoms to a simulation box that already exists, this
+periodic remapping will be performed using simulation box bounds that
+are the union of the existing box and the box boundaries in the new
+data file.
+
+.. note::
+
+   If the system is non-periodic (in a dimension), then all atoms
+   in the data file must have coordinates (in that dimension) that are
+   "greater than or equal to" the lo value and "less than or equal to"
+   the hi value.  If the non-periodic dimension is of style "fixed" (see
+   the :doc:`boundary <boundary>` command), then the atom coords must be
+   strictly "less than" the hi value, due to the way LAMMPS assign atoms
+   to processors.  Note that you should not make the lo/hi values
+   radically smaller/larger than the extent of the atoms.  For example,
+   if your atoms extend from 0 to 50, you should not specify the box
+   bounds as -10000 and 10000.  This is because LAMMPS uses the specified
+   box size to layout the 3d grid of processors.  A huge (mostly empty)
+   box will be sub-optimal for performance when using "fixed" boundary
+   conditions (see the :doc:`boundary <boundary>` command).  When using
+   "shrink-wrap" boundary conditions (see the :doc:`boundary <boundary>`
+   command), a huge (mostly empty) box may cause a parallel simulation to
+   lose atoms when LAMMPS shrink-wraps the box around the atoms.  The
+   read\_data command will generate an error in this case.
+
+The "extra bond per atom" setting (angle, dihedral, improper) is only
+needed if new bonds (angles, dihedrals, impropers) will be added to
+the system when a simulation runs, e.g. by using the :doc:`fix bond/create <fix_bond_create>` command. Using this header flag
+is deprecated; please use the *extra/bond/per/atom* keyword (and
+correspondingly for angles, dihedrals and impropers) in the read\_data
+command instead. Either will pre-allocate space in LAMMPS data
+structures for storing the new bonds (angles, dihedrals, impropers).
+
+The "extra special per atom" setting is typically only needed if new
+bonds/angles/etc will be added to the system, e.g. by using the :doc:`fix bond/create <fix_bond_create>` command.  Or if entire new molecules
+will be added to the system, e.g. by using the
+:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` commands,
+which will have more special 1-2,1-3,1-4 neighbors than any other
+molecules defined in the data file.  Using this header flag is
+deprecated; please use the *extra/special/per/atom* keyword instead.
+Using this setting will pre-allocate space in the LAMMPS data
+structures for storing these neighbors.  See the
+:doc:`special\_bonds <special_bonds>` and :doc:`molecule <molecule>` doc
+pages for more discussion of 1-2,1-3,1-4 neighbors.
+
+.. note::
+
+   All of the "extra" settings are only applied in the first data
+   file read and when no simulation box has yet been created; as soon as
+   the simulation box is created (and read\_data implies that), these
+   settings are *locked* and cannot be changed anymore. Please see the
+   description of the *add* keyword above for reading multiple data files.
+   If they appear in later data files, they are ignored.
+
+The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
+only used with :doc:`atom\_style ellipsoid or line or tri or body <atom_style>` and specify how many of the atoms are
+finite-size ellipsoids or lines or triangles or bodies; the remainder
+are point particles.  See the discussion of ellipsoidflag and the
+*Ellipsoids* section below.  See the discussion of lineflag and the
+*Lines* section below.  See the discussion of triangleflag and the
+*Triangles* section below.  See the discussion of bodyflag and the
+*Bodies* section below.
+
+.. note::
+
+   For :doc:`atom\_style template <atom_style>`, the molecular
+   topology (bonds,angles,etc) is contained in the molecule templates
+   read-in by the :doc:`molecule <molecule>` command.  This means you
+   cannot set the *bonds*\ , *angles*\ , etc header keywords in the data
+   file, nor can you define *Bonds*\ , *Angles*\ , etc sections as discussed
+   below.  You can set the *bond types*\ , *angle types*\ , etc header
+   keywords, though it is not necessary.  If specified, they must match
+   the maximum values defined in any of the template molecules.
+
+
+----------
+
+
+**Format of the body of a data file**
+
+These are the section keywords for the body of the file.
+
+* *Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies* = atom-property sections
+* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
+* *Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs,    Improper Coeffs* = force field sections
+* *BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs,    EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs,    BondBond13 Coeffs, AngleAngle Coeffs* = class 2 force field sections
+
+These keywords will check an appended comment for a match with the
+currently defined style:
+
+* *Atoms, Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs*
+
+For example, these lines:
+
+
+.. parsed-literal::
+
+   Atoms # sphere
+   Pair Coeffs # lj/cut
+
+will check if the currently-defined :doc:`atom\_style <atom_style>` is
+*sphere*\ , and the current :doc:`pair\_style <pair_style>` is *lj/cut*\ .
+If not, LAMMPS will issue a warning to indicate that the data file
+section likely does not contain the correct number or type of
+parameters expected for the currently-defined style.
+
+Each section is listed below in alphabetic order.  The format of each
+section is described including the number of lines it must contain and
+rules (if any) for where it can appear in the data file.
+
+Any individual line in the various sections can have a trailing
+comment starting with "#" for annotation purposes.  E.g. in the
+Atoms section:
+
+
+.. parsed-literal::
+
+   10 1 17 -1.0 10.0 5.0 6.0   # salt ion
+
+
+----------
+
+
+*Angle Coeffs* section:
+
+* one line per angle type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = angle type (1-N)
+       coeffs = list of coeffs
+
+* example:
+  
+  .. parsed-literal::
+  
+       6 70 108.5 0 0
+
+
+
+The number and meaning of the coefficients are specific to the defined
+angle style.  See the :doc:`angle\_style <angle_style>` and
+:doc:`angle\_coeff <angle_coeff>` commands for details.  Coefficients can
+also be set via the :doc:`angle\_coeff <angle_coeff>` command in the
+input script.
+
+
+----------
+
+
+*AngleAngle Coeffs* section:
+
+* one line per improper type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = improper type (1-N)
+       coeffs = list of coeffs (see :doc:`improper_coeff <improper_coeff>`)
+
+
+
+
+----------
+
+
+*AngleAngleTorsion Coeffs* section:
+
+* one line per dihedral type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = dihedral type (1-N)
+       coeffs = list of coeffs (see :doc:`dihedral_coeff <dihedral_coeff>`)
+
+
+
+
+----------
+
+
+*Angles* section:
+
+* one line per angle
+* line syntax: ID type atom1 atom2 atom3
+  
+  .. parsed-literal::
+  
+       ID = number of angle (1-Nangles)
+       type = angle type (1-Nangletype)
+       atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
+
+example:
+  
+  .. parsed-literal::
+  
+       2 2 17 29 430
+
+
+
+The 3 atoms are ordered linearly within the angle.  Thus the central
+atom (around which the angle is computed) is the atom2 in the list.
+E.g. H,O,H for a water molecule.  The *Angles* section must appear
+after the *Atoms* section.  All values in this section must be
+integers (1, not 1.0).
+
+
+----------
+
+
+*AngleTorsion Coeffs* section:
+
+* one line per dihedral type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = dihedral type (1-N)
+       coeffs = list of coeffs (see :doc:`dihedral_coeff <dihedral_coeff>`)
+
+
+
+
+----------
+
+
+*Atoms* section:
+
+* one line per atom
+* line syntax: depends on atom style
+
+An *Atoms* section must appear in the data file if natoms > 0 in the
+header section.  The atoms can be listed in any order.  These are the
+line formats for each :doc:`atom style <atom_style>` in LAMMPS.  As
+discussed below, each line can optionally have 3 flags (nx,ny,nz)
+appended to it, which indicate which image of a periodic simulation
+box the atom is in.  These may be important to include for some kinds
+of analysis.
+
++------------+---------------------------------------------------------------------------+
+| angle      | atom-ID molecule-ID atom-type x y z                                       |
++------------+---------------------------------------------------------------------------+
+| atomic     | atom-ID atom-type x y z                                                   |
++------------+---------------------------------------------------------------------------+
+| body       | atom-ID atom-type bodyflag mass x y z                                     |
++------------+---------------------------------------------------------------------------+
+| bond       | atom-ID molecule-ID atom-type x y z                                       |
++------------+---------------------------------------------------------------------------+
+| charge     | atom-ID atom-type q x y z                                                 |
++------------+---------------------------------------------------------------------------+
+| dipole     | atom-ID atom-type q x y z mux muy muz                                     |
++------------+---------------------------------------------------------------------------+
+| dpd        | atom-ID atom-type theta x y z                                             |
++------------+---------------------------------------------------------------------------+
+| edpd       | atom-ID atom-type edpd\_temp edpd\_cv x y z                               |
++------------+---------------------------------------------------------------------------+
+| mdpd       | atom-ID atom-type rho x y z                                               |
++------------+---------------------------------------------------------------------------+
+| tdpd       | atom-ID atom-type x y z cc1 cc2 ... ccNspecies                            |
++------------+---------------------------------------------------------------------------+
+| electron   | atom-ID atom-type q spin eradius x y z                                    |
++------------+---------------------------------------------------------------------------+
+| ellipsoid  | atom-ID atom-type ellipsoidflag density x y z                             |
++------------+---------------------------------------------------------------------------+
+| full       | atom-ID molecule-ID atom-type q x y z                                     |
++------------+---------------------------------------------------------------------------+
+| line       | atom-ID molecule-ID atom-type lineflag density x y z                      |
++------------+---------------------------------------------------------------------------+
+| meso       | atom-ID atom-type rho e cv x y z                                          |
++------------+---------------------------------------------------------------------------+
+| molecular  | atom-ID molecule-ID atom-type x y z                                       |
++------------+---------------------------------------------------------------------------+
+| peri       | atom-ID atom-type volume density x y z                                    |
++------------+---------------------------------------------------------------------------+
+| smd        | atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z |
++------------+---------------------------------------------------------------------------+
+| sphere     | atom-ID atom-type diameter density x y z                                  |
++------------+---------------------------------------------------------------------------+
+| spin       | atom-ID atom-type sp x y z spx spy spz                                    |
++------------+---------------------------------------------------------------------------+
+| template   | atom-ID molecule-ID template-index template-atom atom-type x y z          |
++------------+---------------------------------------------------------------------------+
+| tri        | atom-ID molecule-ID atom-type triangleflag density x y z                  |
++------------+---------------------------------------------------------------------------+
+| wavepacket | atom-ID atom-type charge spin eradius etag cs\_re cs\_im x y z            |
++------------+---------------------------------------------------------------------------+
+| hybrid     | atom-ID atom-type x y z sub-style1 sub-style2 ...                         |
++------------+---------------------------------------------------------------------------+
+
+The per-atom values have these meanings and units, listed alphabetically:
+
+* atom-ID = integer ID of atom
+* atom-type = type of atom (1-Ntype)
+* bodyflag = 1 for body particles, 0 for point particles
+* cc = chemical concentration for tDPD particles for each species (mole/volume units)
+* contact-radius = ??? (distance units)
+* cs\_re,cs\_im = real/imaginary parts of wave packet coefficients
+* cv = heat capacity (need units) for SPH particles
+* density = density of particle (mass/distance\^3 or mass/distance\^2 or mass/distance units, depending on dimensionality of particle)
+* diameter = diameter of spherical atom (distance units)
+* e = energy (need units) for SPH particles
+* edpd\_temp = temperature for eDPD particles (temperature units)
+* edpd\_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units)
+* ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
+* eradius = electron radius (or fixed-core radius)
+* etag = integer ID of electron that each wave packet belongs to
+* kernel-radius = ??? (distance units)
+* lineflag = 1 for line segment particles, 0 for point or spherical particles
+* mass = mass of particle (mass units)
+* molecule-ID = integer ID of molecule the atom belongs to
+* mux,muy,muz = components of dipole moment of atom (dipole units)
+* q = charge on atom (charge units)
+* rho = density (need units) for SPH particles
+* spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
+* sp = norm of magnetic spin of atom (in number of Bohr magnetons)
+* spx,spy,spz = components of magnetic spin of atom (adim normalized vector)
+* template-atom = which atom within a template molecule the atom is
+* template-index = which molecule within the molecule template the atom is part of
+* theta = internal temperature of a DPD particle
+* triangleflag = 1 for triangular particles, 0 for point or spherical particles
+* volume = volume of Peridynamic particle (distance\^3 units)
+* x,y,z = coordinates of atom (distance units)
+
+The units for these quantities depend on the unit style; see the
+:doc:`units <units>` command for details.
+
+For 2d simulations specify z as 0.0, or a value within the *zlo zhi*
+setting in the data file header.
+
+The atom-ID is used to identify the atom throughout the simulation and
+in dump files.  Normally, it is a unique value from 1 to Natoms for
+each atom.  Unique values larger than Natoms can be used, but they
+will cause extra memory to be allocated on each processor, if an atom
+map array is used, but not if an atom map hash is used; see the
+:doc:`atom\_modify <atom_modify>` command for details.  If an atom map is
+not used (e.g. an atomic system with no bonds), and you don't care if
+unique atom IDs appear in dump files, then the atom-IDs can all be set
+to 0.
+
+The molecule ID is a 2nd identifier attached to an atom.  Normally, it
+is a number from 1 to N, identifying which molecule the atom belongs
+to.  It can be 0 if it is a non-bonded atom or if you don't care to
+keep track of molecule assignments.
+
+The diameter specifies the size of a finite-size spherical particle.
+It can be set to 0.0, which means that atom is a point particle.
+
+The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
+whether the particle is a finite-size ellipsoid or line or triangle or
+body of finite size, or whether the particle is a point particle.
+Additional attributes must be defined for each ellipsoid, line,
+triangle, or body in the corresponding *Ellipsoids*\ , *Lines*\ ,
+*Triangles*\ , or *Bodies* section.
+
+The *template-index* and *template-atom* are only defined used by
+:doc:`atom\_style template <atom_style>`.  In this case the
+:doc:`molecule <molecule>` command is used to define a molecule template
+which contains one or more molecules.  If an atom belongs to one of
+those molecules, its *template-index* and *template-atom* are both set
+to positive integers; if not the values are both 0.  The
+*template-index* is which molecule (1 to Nmols) the atom belongs to.
+The *template-atom* is which atom (1 to Natoms) within the molecule
+the atom is.
+
+Some pair styles and fixes and computes that operate on finite-size
+particles allow for a mixture of finite-size and point particles.  See
+the doc pages of individual commands for details.
+
+For finite-size particles, the density is used in conjunction with the
+particle volume to set the mass of each particle as mass = density \*
+volume.  In this context, volume can be a 3d quantity (for spheres or
+ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
+segments).  If the volume is 0.0, meaning a point particle, then the
+density value is used as the mass.  One exception is for the body atom
+style, in which case the mass of each particle (body or point
+particle) is specified explicitly.  This is because the volume of the
+body is unknown.
+
+Note that for 2d simulations of spheres, this command will treat them
+as spheres when converting density to mass.  However, they can also be
+modeled as 2d discs (circles) if the :doc:`set density/disc <set>`
+command is used to reset their mass after the read\_data command is
+used.  A *disc* keyword can also be used with time integration fixes,
+such as :doc:`fix nve/sphere <fix_nve_sphere>` and :doc:`fix nvt/sphere <fix_nve_sphere>` to time integrate their motion as 2d
+discs (not 3d spheres), by changing their moment of inertia.
+
+For atom\_style hybrid, following the 5 initial values (ID,type,x,y,z),
+specific values for each sub-style must be listed.  The order of the
+sub-styles is the same as they were listed in the
+:doc:`atom\_style <atom_style>` command.  The sub-style specific values
+are those that are not the 5 standard ones (ID,type,x,y,z).  For
+example, for the "charge" sub-style, a "q" value would appear.  For
+the "full" sub-style, a "molecule-ID" and "q" would appear.  These are
+listed in the same order they appear as listed above.  Thus if
+
+
+.. parsed-literal::
+
+   atom_style hybrid charge sphere
+
+were used in the input script, each atom line would have these fields:
+
+
+.. parsed-literal::
+
+   atom-ID atom-type x y z q diameter density
+
+Note that if a non-standard value is defined by multiple sub-styles,
+it must appear multiple times in the atom line.  E.g. the atom line
+for atom\_style hybrid dipole full would list "q" twice:
+
+
+.. parsed-literal::
+
+   atom-ID atom-type x y z q mux muy myz molecule-ID q
+
+Atom lines specify the (x,y,z) coordinates of atoms.  These can be
+inside or outside the simulation box.  When the data file is read,
+LAMMPS wraps coordinates outside the box back into the box for
+dimensions that are periodic.  As discussed above, if an atom is
+outside the box in a non-periodic dimension, it will be lost.
+
+LAMMPS always stores atom coordinates as values which are inside the
+simulation box.  It also stores 3 flags which indicate which image of
+the simulation box (in each dimension) the atom would be in if its
+coordinates were unwrapped across periodic boundaries.  An image flag
+of 0 means the atom is still inside the box when unwrapped.  A value
+of 2 means add 2 box lengths to get the unwrapped coordinate.  A value
+of -1 means subtract 1 box length to get the unwrapped coordinate.
+LAMMPS updates these flags as atoms cross periodic boundaries during
+the simulation.  The :doc:`dump <dump>` command can output atom
+coordinates in wrapped or unwrapped form, as well as the 3 image
+flags.
+
+In the data file, atom lines (all lines or none of them) can
+optionally list 3 trailing integer values (nx,ny,nz), which are used
+to initialize the atom's image flags.  If nx,ny,nz values are not
+listed in the data file, LAMMPS initializes them to 0.  Note that the
+image flags are immediately updated if an atom's coordinates need to
+wrapped back into the simulation box.
+
+It is only important to set image flags correctly in a data file if a
+simulation model relies on unwrapped coordinates for some calculation;
+otherwise they can be left unspecified.  Examples of LAMMPS commands
+that use unwrapped coordinates internally are as follows:
+
+* Atoms in a rigid body (see :doc:`fix rigid <fix_rigid>`, :doc:`fix rigid/small <fix_rigid>`) must have consistent image flags, so that
+  when the atoms are unwrapped, they are near each other, i.e. as a
+  single body.
+* If the :doc:`replicate <replicate>` command is used to generate a larger
+  system, image flags must be consistent for bonded atoms when the bond
+  crosses a periodic boundary.  I.e. the values of the image flags
+  should be different by 1 (in the appropriate dimension) for the two
+  atoms in such a bond.
+* If you plan to :doc:`dump <dump>` image flags and perform post-analysis
+  that will unwrap atom coordinates, it may be important that a
+  continued run (restarted from a data file) begins with image flags
+  that are consistent with the previous run.
+
+
+.. note::
+
+   If your system is an infinite periodic crystal with bonds then
+   it is impossible to have fully consistent image flags.  This is because
+   some bonds will cross periodic boundaries and connect two atoms with the
+   same image flag.
+
+Atom velocities and other atom quantities not defined above are set to
+0.0 when the *Atoms* section is read.  Velocities can be set later by
+a *Velocities* section in the data file or by a
+:doc:`velocity <velocity>` or :doc:`set <set>` command in the input
+script.
+
+
+----------
+
+
+*Bodies* section:
+
+* one or more lines per body
+* first line syntax: atom-ID Ninteger Ndouble
+  
+  .. parsed-literal::
+  
+       Ninteger = # of integer quantities for this particle
+       Ndouble = # of floating-point quantities for this particle
+
+* 0 or more integer lines with total of Ninteger values
+* 0 or more double lines with total of Ndouble values
+* example:
+  
+  .. parsed-literal::
+  
+       12 3 6
+       2 3 2
+       1.0 2.0 3.0 1.0 2.0 4.0
+
+* example:
+  
+  .. parsed-literal::
+  
+       12 0 14
+       1.0 2.0 3.0 1.0 2.0 4.0 1.0
+       2.0 3.0 1.0 2.0 4.0 4.0 2.0
+
+
+
+The *Bodies* section must appear if :doc:`atom\_style body <atom_style>`
+is used and any atoms listed in the *Atoms* section have a bodyflag =
+1.  The number of bodies should be specified in the header section via
+the "bodies" keyword.
+
+Each body can have a variable number of integer and/or floating-point
+values.  The number and meaning of the values is defined by the body
+style, as described in the :doc:`Howto body <Howto_body>` doc page.  The
+body style is given as an argument to the :doc:`atom\_style body <atom_style>` command.
+
+The Ninteger and Ndouble values determine how many integer and
+floating-point values are specified for this particle.  Ninteger and
+Ndouble can be as large as needed and can be different for every body.
+Integer values are then listed next on subsequent lines.  Lines are
+read one at a time until Ninteger values are read.  Floating-point
+values follow on subsequent lines, Again lines are read one at a time
+until Ndouble values are read.  Note that if there are no values of a
+particular type, no lines appear for that type.
+
+The *Bodies* section must appear after the *Atoms* section.
+
+
+----------
+
+
+*Bond Coeffs* section:
+
+* one line per bond type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = bond type (1-N)
+       coeffs = list of coeffs
+
+* example:
+  
+  .. parsed-literal::
+  
+       4 250 1.49
+
+
+
+The number and meaning of the coefficients are specific to the defined
+bond style.  See the :doc:`bond\_style <bond_style>` and
+:doc:`bond\_coeff <bond_coeff>` commands for details.  Coefficients can
+also be set via the :doc:`bond\_coeff <bond_coeff>` command in the input
+script.
+
+
+----------
+
+
+*BondAngle Coeffs* section:
+
+* one line per angle type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = angle type (1-N)
+       coeffs = list of coeffs (see class 2 section of :doc:`angle_coeff <angle_coeff>`)
+
+
+
+
+----------
+
+
+*BondBond Coeffs* section:
+
+* one line per angle type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = angle type (1-N)
+       coeffs = list of coeffs (see class 2 section of :doc:`angle_coeff <angle_coeff>`)
+
+
+
+
+----------
+
+
+*BondBond13 Coeffs* section:
+
+* one line per dihedral type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = dihedral type (1-N)
+       coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff <dihedral_coeff>`)
+
+
+
+
+----------
+
+
+*Bonds* section:
+
+* one line per bond
+* line syntax: ID type atom1 atom2
+  
+  .. parsed-literal::
+  
+       ID = bond number (1-Nbonds)
+       type = bond type (1-Nbondtype)
+       atom1,atom2 = IDs of 1st,2nd atoms in bond
+
+* example:
+  
+  .. parsed-literal::
+  
+       12 3 17 29
+
+
+
+The *Bonds* section must appear after the *Atoms* section.  All values
+in this section must be integers (1, not 1.0).
+
+
+----------
+
+
+*Dihedral Coeffs* section:
+
+* one line per dihedral type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = dihedral type (1-N)
+       coeffs = list of coeffs
+
+* example:
+  
+  .. parsed-literal::
+  
+       3 0.6 1 0 1
+
+
+
+The number and meaning of the coefficients are specific to the defined
+dihedral style.  See the :doc:`dihedral\_style <dihedral_style>` and
+:doc:`dihedral\_coeff <dihedral_coeff>` commands for details.
+Coefficients can also be set via the
+:doc:`dihedral\_coeff <dihedral_coeff>` command in the input script.
+
+
+----------
+
+
+*Dihedrals* section:
+
+* one line per dihedral
+* line syntax: ID type atom1 atom2 atom3 atom4
+  
+  .. parsed-literal::
+  
+       ID = number of dihedral (1-Ndihedrals)
+       type = dihedral type (1-Ndihedraltype)
+       atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
+
+* example:
+  
+  .. parsed-literal::
+  
+       12 4 17 29 30 21
+
+
+
+The 4 atoms are ordered linearly within the dihedral.  The *Dihedrals*
+section must appear after the *Atoms* section.  All values in this
+section must be integers (1, not 1.0).
+
+
+----------
+
+
+*Ellipsoids* section:
+
+* one line per ellipsoid
+* line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk
+  
+  .. parsed-literal::
+  
+       atom-ID = ID of atom which is an ellipsoid
+       shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
+       quatw,quati,quatj,quatk = quaternion components for orientation of atom
+
+* example:
+  
+  .. parsed-literal::
+  
+       12 1 2 1 1 0 0 0
+
+
+
+The *Ellipsoids* section must appear if :doc:`atom\_style ellipsoid <atom_style>` is used and any atoms are listed in the
+*Atoms* section with an ellipsoidflag = 1.  The number of ellipsoids
+should be specified in the header section via the "ellipsoids"
+keyword.
+
+The 3 shape values specify the 3 diameters or aspect ratios of a
+finite-size ellipsoidal particle, when it is oriented along the 3
+coordinate axes.  They must all be non-zero values.
+
+The values *quatw*\ , *quati*\ , *quatj*\ , and *quatk* set the orientation
+of the atom as a quaternion (4-vector).  Note that the shape
+attributes specify the aspect ratios of an ellipsoidal particle, which
+is oriented by default with its x-axis along the simulation box's
+x-axis, and similarly for y and z.  If this body is rotated (via the
+right-hand rule) by an angle theta around a unit vector (a,b,c), then
+the quaternion that represents its new orientation is given by
+(cos(theta/2), a\*sin(theta/2), b\*sin(theta/2), c\*sin(theta/2)).  These
+4 components are quatw, quati, quatj, and quatk as specified above.
+LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
+specified as a unit vector.
+
+The *Ellipsoids* section must appear after the *Atoms* section.
+
+
+----------
+
+
+*EndBondTorsion Coeffs* section:
+
+* one line per dihedral type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = dihedral type (1-N)
+       coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff <dihedral_coeff>`)
+
+
+
+
+----------
+
+
+*Improper Coeffs* section:
+
+* one line per improper type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = improper type (1-N)
+       coeffs = list of coeffs
+
+* example:
+  
+  .. parsed-literal::
+  
+       2 20 0.0548311
+
+
+
+The number and meaning of the coefficients are specific to the defined
+improper style.  See the :doc:`improper\_style <improper_style>` and
+:doc:`improper\_coeff <improper_coeff>` commands for details.
+Coefficients can also be set via the
+:doc:`improper\_coeff <improper_coeff>` command in the input script.
+
+
+----------
+
+
+*Impropers* section:
+
+* one line per improper
+* line syntax: ID type atom1 atom2 atom3 atom4
+  
+  .. parsed-literal::
+  
+       ID = number of improper (1-Nimpropers)
+       type = improper type (1-Nimpropertype)
+       atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
+
+* example:
+  
+  .. parsed-literal::
+  
+       12 3 17 29 13 100
+
+
+
+The ordering of the 4 atoms determines the definition of the improper
+angle used in the formula for each :doc:`improper style <improper_style>`.  See the doc pages for individual styles
+for details.
+
+The *Impropers* section must appear after the *Atoms* section.  All
+values in this section must be integers (1, not 1.0).
+
+
+----------
+
+
+*Lines* section:
+
+* one line per line segment
+* line syntax: atom-ID x1 y1 x2 y2
+  
+  .. parsed-literal::
+  
+       atom-ID = ID of atom which is a line segment
+       x1,y1 = 1st end point
+       x2,y2 = 2nd end point
+
+* example:
+  
+  .. parsed-literal::
+  
+       12 1.0 0.0 2.0 0.0
+
+
+
+The *Lines* section must appear if :doc:`atom\_style line <atom_style>`
+is used and any atoms are listed in the *Atoms* section with a
+lineflag = 1.  The number of lines should be specified in the header
+section via the "lines" keyword.
+
+The 2 end points are the end points of the line segment.  The ordering
+of the 2 points should be such that using a right-hand rule to cross
+the line segment with a unit vector in the +z direction, gives an
+"outward" normal vector perpendicular to the line segment.
+I.e. normal = (c2-c1) x (0,0,1).  This orientation may be important
+for defining some interactions.
+
+The *Lines* section must appear after the *Atoms* section.
+
+
+----------
+
+
+*Masses* section:
+
+* one line per atom type
+* line syntax: ID mass
+  
+  .. parsed-literal::
+  
+       ID = atom type (1-N)
+       mass = mass value
+
+* example:
+  
+  .. parsed-literal::
+  
+       3 1.01
+
+
+
+This defines the mass of each atom type.  This can also be set via the
+:doc:`mass <mass>` command in the input script.  This section cannot be
+used for atom styles that define a mass for individual atoms -
+e.g. :doc:`atom\_style sphere <atom_style>`.
+
+
+----------
+
+
+*MiddleBondTorsion Coeffs* section:
+
+* one line per dihedral type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = dihedral type (1-N)
+       coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff <dihedral_coeff>`)
+
+
+
+
+----------
+
+
+*Pair Coeffs* section:
+
+* one line per atom type
+* line syntax: ID coeffs
+  
+  .. parsed-literal::
+  
+       ID = atom type (1-N)
+       coeffs = list of coeffs
+
+* example:
+  
+  .. parsed-literal::
+  
+       3 0.022 2.35197 0.022 2.35197
+
+
+
+The number and meaning of the coefficients are specific to the defined
+pair style.  See the :doc:`pair\_style <pair_style>` and
+:doc:`pair\_coeff <pair_coeff>` commands for details.  Since pair
+coefficients for types I != J are not specified, these will be
+generated automatically by the pair style's mixing rule.  See the
+individual pair\_style doc pages and the :doc:`pair\_modify mix <pair_modify>` command for details.  Pair coefficients can also
+be set via the :doc:`pair\_coeff <pair_coeff>` command in the input
+script.
+
+
+----------
+
+
+*PairIJ Coeffs* section:
+
+* one line per pair of atom types for all I,J with I <= J
+* line syntax: ID1 ID2 coeffs
+  
+  .. parsed-literal::
+  
+       ID1 = atom type I = 1-N
+       ID2 = atom type J = I-N, with I <= J
+       coeffs = list of coeffs
+
+* examples:
+  
+  .. parsed-literal::
+  
+       3 3 0.022 2.35197 0.022 2.35197
+       3 5 0.022 2.35197 0.022 2.35197
+
+
+
+This section must have N\*(N+1)/2 lines where N = # of atom types.  The
+number and meaning of the coefficients are specific to the defined
+pair style.  See the :doc:`pair\_style <pair_style>` and
+:doc:`pair\_coeff <pair_coeff>` commands for details.  Since pair
+coefficients for types I != J are all specified, these values will
+turn off the default mixing rule defined by the pair style.  See the
+individual pair\_style doc pages and the :doc:`pair\_modify mix <pair_modify>` command for details.  Pair coefficients can also
+be set via the :doc:`pair\_coeff <pair_coeff>` command in the input
+script.
+
+
+----------
+
+
+*Triangles* section:
+
+* one line per triangle
+* line syntax: atom-ID x1 y1 z1 x2 y2 z2 x3 y3 z3
+  
+  .. parsed-literal::
+  
+       atom-ID = ID of atom which is a line segment
+       x1,y1,z1 = 1st corner point
+       x2,y2,z2 = 2nd corner point
+       x3,y3,z3 = 3rd corner point
+
+* example:
+  
+  .. parsed-literal::
+  
+       12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0
+
+
+
+The *Triangles* section must appear if :doc:`atom\_style tri <atom_style>` is used and any atoms are listed in the *Atoms*
+section with a triangleflag = 1.  The number of lines should be
+specified in the header section via the "triangles" keyword.
+
+The 3 corner points are the corner points of the triangle.  The
+ordering of the 3 points should be such that using a right-hand rule
+to go from point1 to point2 to point3 gives an "outward" normal vector
+to the face of the triangle.  I.e. normal = (c2-c1) x (c3-c1).  This
+orientation may be important for defining some interactions.
+
+The *Triangles* section must appear after the *Atoms* section.
+
+
+----------
+
+
+*Velocities* section:
+
+* one line per atom
+* line syntax: depends on atom style
+
++--------------------------------+--------------------------------------------+
+| all styles except those listed | atom-ID vx vy vz                           |
++--------------------------------+--------------------------------------------+
+| electron                       | atom-ID vx vy vz ervel                     |
++--------------------------------+--------------------------------------------+
+| ellipsoid                      | atom-ID vx vy vz lx ly lz                  |
++--------------------------------+--------------------------------------------+
+| sphere                         | atom-ID vx vy vz wx wy wz                  |
++--------------------------------+--------------------------------------------+
+| hybrid                         | atom-ID vx vy vz sub-style1 sub-style2 ... |
++--------------------------------+--------------------------------------------+
+
+where the keywords have these meanings:
+
+vx,vy,vz = translational velocity of atom
+lx,ly,lz = angular momentum of aspherical atom
+wx,wy,wz = angular velocity of spherical atom
+ervel = electron radial velocity (0 for fixed-core):ul
+
+The velocity lines can appear in any order.  This section can only be
+used after an *Atoms* section.  This is because the *Atoms* section
+must have assigned a unique atom ID to each atom so that velocities
+can be assigned to them.
+
+Vx, vy, vz, and ervel are in :doc:`units <units>` of velocity.  Lx, ly,
+lz are in units of angular momentum (distance-velocity-mass).  Wx, Wy,
+Wz are in units of angular velocity (radians/time).
+
+For atom\_style hybrid, following the 4 initial values (ID,vx,vy,vz),
+specific values for each sub-style must be listed.  The order of the
+sub-styles is the same as they were listed in the
+:doc:`atom\_style <atom_style>` command.  The sub-style specific values
+are those that are not the 5 standard ones (ID,vx,vy,vz).  For
+example, for the "sphere" sub-style, "wx", "wy", "wz" values would
+appear.  These are listed in the same order they appear as listed
+above.  Thus if
+
+
+.. parsed-literal::
+
+   atom_style hybrid electron sphere
+
+were used in the input script, each velocity line would have these
+fields:
+
+
+.. parsed-literal::
+
+   atom-ID vx vy vz ervel wx wy wz
+
+Translational velocities can also be set by the
+:doc:`velocity <velocity>` command in the input script.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+To read gzipped data files, you must compile LAMMPS with the
+-DLAMMPS\_GZIP option.  See the :doc:`Build settings <Build_settings>`
+doc page for details.
+
+Related commands
+""""""""""""""""
+
+:doc:`read\_dump <read_dump>`, :doc:`read\_restart <read_restart>`,
+:doc:`create\_atoms <create_atoms>`, :doc:`write\_data <write_data>`
+
+Default
+"""""""
+
+The default for all the *extra* keywords is 0.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst
new file mode 100644
index 0000000000..d8f6a5015d
--- /dev/null
+++ b/doc/src/read_dump.rst
@@ -0,0 +1,380 @@
+.. index:: read\_dump
+
+read\_dump command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   read_dump file Nstep field1 field2 ... keyword values ...
+
+* file = name of dump file to read
+* Nstep = snapshot timestep to read from file
+* one or more fields may be appended
+  
+  .. parsed-literal::
+  
+     field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz*
+       *x*\ ,\ *y*\ ,\ *z* = atom coordinates
+       *vx*\ ,\ *vy*\ ,\ *vz* = velocity components
+       *q* = charge
+       *ix*\ ,\ *iy*\ ,\ *iz* = image flags in each dimension
+       *fx*\ ,\ *fy*\ ,\ *fz* = force components
+
+* zero or more keyword/value pairs may be appended
+* keyword = *nfile* or *box* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*
+  
+  .. parsed-literal::
+  
+       *nfile* value = Nfiles = how many parallel dump files exist
+       *box* value = *yes* or *no* = replace simulation box with dump box
+       *replace* value = *yes* or *no* = overwrite atoms with dump atoms
+       *purge* value = *yes* or *no* = delete all atoms before adding dump atoms
+       *trim* value = *yes* or *no* = trim atoms not in dump snapshot
+       *add* value = *yes* or *keep* or *no* = add new dump atoms to system
+       *label* value = field column
+         field = one of the listed fields or *id* or *type*
+         column = label on corresponding column in dump file
+       *scaled* value = *yes* or *no* = coords in dump file are scaled/unscaled
+       *wrapped* value = *yes* or *no* = coords in dump file are wrapped/unwrapped
+       *format* values = format of dump file, must be last keyword if used
+         *native* = native LAMMPS dump file
+         *xyz* = XYZ file
+         *molfile* style path = VMD molfile plugin interface
+           style = *dcd* or *xyz* or others supported by molfile plugins
+           path = optional path for location of molfile plugins
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   read_dump dump.file 5000 x y z
+   read_dump dump.xyz 5 x y z box no format xyz
+   read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins"
+   read_dump dump.dcd 0 x y z box yes format molfile dcd
+   read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+   read_dump dump.file 5000 x y vx vy trim yes
+   read_dump ../run7/dump.file.gz 10000 x y z box yes
+   read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
+   read_dump dump.dcd 0 x y z format molfile dcd
+   read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+
+Description
+"""""""""""
+
+Read atom information from a dump file to overwrite the current atom
+coordinates, and optionally the atom velocities and image flags and
+the simulation box dimensions.  This is useful for restarting a run
+from a particular snapshot in a dump file.  See the
+:doc:`read\_restart <read_restart>` and :doc:`read\_data <read_data>`
+commands for alternative methods to do this.  Also see the
+:doc:`rerun <rerun>` command for a means of reading multiple snapshots
+from a dump file.
+
+Note that a simulation box must already be defined before using the
+read\_dump command.  This can be done by the
+:doc:`create\_box <create_box>`, :doc:`read\_data <read_data>`, or
+:doc:`read\_restart <read_restart>` commands.  The read\_dump command can
+reset the simulation box dimensions, as explained below.
+
+Also note that reading per-atom information from a dump snapshot is
+limited to the atom coordinates, velocities and image flags, as
+explained below.  Other atom properties, which may be necessary to run
+a valid simulation, such as atom charge, or bond topology information
+for a molecular system, are not read from (or even contained in) dump
+files.  Thus this auxiliary information should be defined in the usual
+way, e.g. in a data file read in by a :doc:`read\_data <read_data>`
+command, before using the read\_dump command, or by the :doc:`set <set>`
+command, after the dump snapshot is read.
+
+
+----------
+
+
+If the dump filename specified as *file* ends with ".gz", the dump
+file is read in gzipped format.  You cannot (yet) read a dump file
+that was written in binary format with a ".bin" suffix.
+
+You can read dump files that were written (in parallel) to multiple
+files via the "%" wild-card character in the dump file name.  If any
+specified dump file name contains a "%", they must all contain it.
+See the :doc:`dump <dump>` command for details.
+The "%" wild-card character is only supported by the *native* format
+for dump files, described next.
+
+If reading parallel dump files, you must also use the *nfile* keyword
+to tell LAMMPS how many parallel files exist, via its specified
+*Nfiles* value.
+
+The format of the dump file is selected through the *format* keyword.
+If specified, it must be the last keyword used, since all remaining
+arguments are passed on to the dump reader.  The *native* format is
+for native LAMMPS dump files, written with a :doc:`dump atom <dump>` or
+:doc:`dump custom <dump>` command.  The *xyz* format is for generic XYZ
+formatted dump files.  These formats take no additional values.
+
+The *molfile* format supports reading data through using the `VMD <vmd_>`_
+molfile plugin interface. This dump reader format is only available,
+if the USER-MOLFILE package has been installed when compiling
+LAMMPS.
+
+The *molfile* format takes one or two additional values.  The *style*
+value determines the file format to be used and can be any format that
+the molfile plugins support, such as DCD or XYZ.  Note that DCD dump
+files can be written by LAMMPS via the :doc:`dump dcd <dump>` command.
+The *path* value specifies a list of directories which LAMMPS will
+search for the molfile plugins appropriate to the specified *style*\ .
+The syntax of the *path* value is like other search paths: it can
+contain multiple directories separated by a colon (or semi-colon on
+windows).  The *path* keyword is optional and defaults to ".",
+i.e. the current directory.
+
+Support for other dump format readers may be added in the future.
+
+
+----------
+
+
+Global information is first read from the dump file, namely timestep
+and box information.
+
+The dump file is scanned for a snapshot with a timestamp that matches
+the specified *Nstep*\ .  This means the LAMMPS timestep the dump file
+snapshot was written on for the *native* format.  Note that the *xyz*
+and *molfile* formats do not store the timestep.  For these formats,
+timesteps are numbered logically, in a sequential manner, starting
+from 0.  Thus to access the 10th snapshot in an *xyz* or *mofile*
+formatted dump file, use *Nstep* = 9.
+
+The dimensions of the simulation box for the selected snapshot are
+also read; see the *box* keyword discussion below.  For the *native*
+format, an error is generated if the snapshot is for a triclinic box
+and the current simulation box is orthogonal or vice versa.  A warning
+will be generated if the snapshot box boundary conditions (periodic,
+shrink-wrapped, etc) do not match the current simulation boundary
+conditions, but the boundary condition information in the snapshot is
+otherwise ignored.  See the "boundary" command for more details.
+
+For the *xyz* format, no information about the box is available, so
+you must set the *box* flag to *no*\ .  See details below.
+
+For the *molfile* format, reading simulation box information is
+typically supported, but the location of the simulation box origin is
+lost and no explicit information about periodicity or
+orthogonal/triclinic box shape is available.  The USER-MOLFILE package
+makes a best effort to guess based on heuristics, but this may not
+always work perfectly.
+
+
+----------
+
+
+Per-atom information from the dump file snapshot is then read from the
+dump file snapshot.  This corresponds to the specified *fields* listed
+in the read\_dump command.  It is an error to specify a z-dimension
+field, namely *z*\ , *vz*\ , or *iz*\ , for a 2d simulation.
+
+For dump files in *native* format, each column of per-atom data has a
+text label listed in the file.  A matching label for each field must
+appear, e.g. the label "vy" for the field *vy*\ .  For the *x*\ , *y*\ , *z*
+fields any of the following labels are considered a match:
+
+
+.. parsed-literal::
+
+   x, xs, xu, xsu for field *x*
+   y, ys, yu, ysu for field *y*
+   z, zs, zu, zsu for field *z*
+
+The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and
+unwrapped) is explained on the :doc:`dump <dump>` command doc page.
+These labels are searched for in the list of column labels in the dump
+file, in order, until a match is found.
+
+The dump file must also contain atom IDs, with a column label of "id".
+
+If the *add* keyword is specified with a value of *yes* or *keep*\ , as
+discussed below, the dump file must contain atom types, with a column
+label of "type".
+
+If a column label you want to read from the dump file is not a match
+to a specified field, the *label* keyword can be used to specify the
+specific column label from the dump file to associate with that field.
+An example is if a time-averaged coordinate is written to the dump
+file via the :doc:`fix ave/atom <fix_ave_atom>` command.  The column
+will then have a label corresponding to the fix-ID rather than "x" or
+"xs".  The *label* keyword can also be used to specify new column
+labels for fields *id* and *type*\ .
+
+For dump files in *xyz* format, only the *x*\ , *y*\ , and *z* fields are
+supported.  The dump file does not store atom IDs, so these are
+assigned consecutively to the atoms as they appear in the dump file,
+starting from 1.  Thus you should insure that order of atoms is
+consistent from snapshot to snapshot in the XYZ dump file.  See
+the :doc:`dump\_modify sort <dump_modify>` command if the XYZ dump file
+was written by LAMMPS.
+
+For dump files in *molfile* format, the *x*\ , *y*\ , *z*\ , *vx*\ , *vy*\ , and
+*vz* fields can be specified.  However, not all molfile formats store
+velocities, or their respective plugins may not support reading of
+velocities.  The molfile dump files do not store atom IDs, so these
+are assigned consecutively to the atoms as they appear in the dump
+file, starting from 1.  Thus you should insure that order of atoms are
+consistent from snapshot to snapshot in the molfile dump file.
+See the :doc:`dump\_modify sort <dump_modify>` command if the dump file
+was written by LAMMPS.
+
+
+----------
+
+
+Information from the dump file snapshot is used to overwrite or
+replace properties of the current system.  There are various options
+for how this is done, determined by the specified fields and optional
+keywords.
+
+The timestep of the snapshot becomes the current timestep for the
+simulation.  See the :doc:`reset\_timestep <reset_timestep>` command if
+you wish to change this after the dump snapshot is read.
+
+If the *box* keyword is specified with a *yes* value, then the current
+simulation box dimensions are replaced by the dump snapshot box
+dimensions.  If the *box* keyword is specified with a *no* value, the
+current simulation box is unchanged.
+
+If the *purge* keyword is specified with a *yes* value, then all
+current atoms in the system are deleted before any of the operations
+invoked by the *replace*\ , *trim*\ , or *add* keywords take place.
+
+If the *replace* keyword is specified with a *yes* value, then atoms
+with IDs that are in both the current system and the dump snapshot
+have their properties overwritten by field values.  If the *replace*
+keyword is specified with a *no* value, atoms with IDs that are in
+both the current system and the dump snapshot are not modified.
+
+If the *trim* keyword is specified with a *yes* value, then atoms with
+IDs that are in the current system but not in the dump snapshot are
+deleted.  These atoms are unaffected if the *trim* keyword is
+specified with a *no* value.
+
+If the *add* keyword is specified with a *no* value (default), then
+dump file atoms with IDs that are not in the current system are not
+added to the system.  They are simply ignored.
+
+If a *yes* value is specified, the atoms with new IDs are added to the
+system but their atom IDs are not preserved.  Instead, after all the
+atoms are added, new IDs are assigned to them in the same manner as is
+described for the :doc:`create\_atoms <create_atoms>` command.  Basically
+the largest existing atom ID in the system is identified, and all the
+added atoms are assigned IDs that consecutively follow the largest ID.
+
+If a *keep* value is specified, the atoms with new IDs are added to
+the system and their atom IDs are preserved.  This may lead to
+non-contiguous IDs for the combined system.
+
+Note that atoms added via the *add* keyword will only have the
+attributes read from the dump file due to the *field* arguments.  For
+example, if *x* or *y* or *z* or *q* is not specified as a field, a
+value of 0.0 is used for added atoms.  Added atoms must have an atom
+type, so this value must appear in the dump file.
+
+Any other attributes (e.g. charge or particle diameter for spherical
+particles) will be set to default values, the same as if the
+:doc:`create\_atoms <create_atoms>` command were used.
+
+
+----------
+
+
+Atom coordinates read from the dump file are first converted into
+unscaled coordinates, relative to the box dimensions of the snapshot.
+These coordinates are then be assigned to an existing or new atom in
+the current simulation.  The coordinates will then be remapped to the
+simulation box, whether it is the original box or the dump snapshot
+box.  If periodic boundary conditions apply, this means the atom will
+be remapped back into the simulation box if necessary.  If shrink-wrap
+boundary conditions apply, the new coordinates may change the
+simulation box dimensions.  If fixed boundary conditions apply, the
+atom will be lost if it is outside the simulation box.
+
+For *native* format dump files, the 3 xyz image flags for an atom in
+the dump file are set to the corresponding values appearing in the
+dump file if the *ix*\ , *iy*\ , *iz* fields are specified.  If not
+specified, the image flags for replaced atoms are not changed and
+image flags for new atoms are set to default values.  If coordinates
+read from the dump file are in unwrapped format (e.g. *xu*\ ) then the
+image flags for read-in atoms are also set to default values.  The
+remapping procedure described in the previous paragraph will then
+change images flags for all atoms (old and new) if periodic boundary
+conditions are applied to remap an atom back into the simulation box.
+
+.. note::
+
+   If you get a warning about inconsistent image flags after
+   reading in a dump snapshot, it means one or more pairs of bonded atoms
+   now have inconsistent image flags.  As discussed on the :doc:`Errors common <Errors_common>` doc page this may or may not cause problems
+   for subsequent simulations.  One way this can happen is if you read
+   image flag fields from the dump file but do not also use the dump file
+   box parameters.
+
+LAMMPS knows how to compute unscaled and remapped coordinates for the
+snapshot column labels discussed above, e.g. *x*\ , *xs*\ , *xu*\ , *xsu*\ .
+If another column label is assigned to the *x* or *y* or *z* field via
+the *label* keyword, e.g. for coordinates output by the :doc:`fix ave/atom <fix_ave_atom>` command, then LAMMPS needs to know whether
+the coordinate information in the dump file is scaled and/or wrapped.
+This can be set via the *scaled* and *wrapped* keywords.  Note that
+the value of the *scaled* and *wrapped* keywords is ignored for fields
+*x* or *y* or *z* if the *label* keyword is not used to assign a
+column label to that field.
+
+The scaled/unscaled and wrapped/unwrapped setting must be identical
+for any of the *x*\ , *y*\ , *z* fields that are specified.  Thus you
+cannot read *xs* and *yu* from the dump file.  Also, if the dump file
+coordinates are scaled and the simulation box is triclinic, then all 3
+of the *x*\ , *y*\ , *z* fields must be specified, since they are all
+needed to generate absolute, unscaled coordinates.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+To read gzipped dump files, you must compile LAMMPS with the
+-DLAMMPS\_GZIP option.  See the :doc:`Build settings <Build_settings>`
+doc page for details.
+
+The *molfile* dump file formats are part of the USER-MOLFILE package.
+They are only enabled if LAMMPS was built with that packages.  See the
+:doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump molfile <dump_molfile>`,
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`,
+:doc:`rerun <rerun>`
+
+Default
+"""""""
+
+The option defaults are box = yes, replace = yes, purge = no, trim =
+no, add = no, scaled = no, wrapped = yes, and format = native.
+
+.. _vmd: http://www.ks.uiuc.edu/Research/vmd
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst
new file mode 100644
index 0000000000..44210a3a70
--- /dev/null
+++ b/doc/src/read_restart.rst
@@ -0,0 +1,288 @@
+.. index:: read\_restart
+
+read\_restart command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   read_restart file flag
+
+* file = name of binary restart file to read in
+* flag = remap (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   read_restart save.10000
+   read_restart save.10000 remap
+   read_restart restart.\*
+   read_restart restart.\*.mpiio
+   read_restart poly.\*.% remap
+
+Description
+"""""""""""
+
+Read in a previously saved system configuration from a restart file.
+This allows continuation of a previous run.  Details about what
+information is stored (and not stored) in a restart file is given
+below.  Basically this operation will re-create the simulation box
+with all its atoms and their attributes as well as some related global
+settings, at the point in time it was written to the restart file by a
+previous simulation.  The simulation box will be partitioned into a
+regular 3d grid of rectangular bricks, one per processor, based on the
+number of processors in the current simulation and the settings of the
+:doc:`processors <processors>` command.  The partitioning can later be
+changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
+
+.. note::
+
+   Normally, restart files are written by the
+   :doc:`restart <restart>` or :doc:`write\_restart <write_restart>` commands
+   so that all atoms in the restart file are inside the simulation box.
+   If this is not the case, the read\_restart command will print an error
+   that atoms were "lost" when the file is read.  This error should be
+   reported to the LAMMPS developers so the invalid writing of the
+   restart file can be fixed.  If you still wish to use the restart file,
+   the optional *remap* flag can be appended to the read\_restart command.
+   This should avoid the error, by explicitly remapping each atom back
+   into the simulation box, updating image flags for the atom
+   appropriately.
+
+Restart files are saved in binary format to enable exact restarts,
+meaning that the trajectories of a restarted run will precisely match
+those produced by the original run had it continued on.
+
+Several things can prevent exact restarts due to round-off effects, in
+which case the trajectories in the 2 runs will slowly diverge.  These
+include running on a different number of processors or changing
+certain settings such as those set by the :doc:`newton <newton>` or
+:doc:`processors <processors>` commands.  LAMMPS will issue a warning in
+these cases.
+
+Certain fixes will not restart exactly, though they should provide
+statistically similar results.  These include :doc:`fix shake <fix_shake>` and :doc:`fix langevin <fix_langevin>`.
+
+Certain pair styles will not restart exactly, though they should
+provide statistically similar results.  This is because the forces
+they compute depend on atom velocities, which are used at half-step
+values every timestep when forces are computed.  When a run restarts,
+forces are initially evaluated with a full-step velocity, which is
+different than if the run had continued.  These pair styles include
+:doc:`granular pair styles <pair_gran>`, :doc:`pair dpd <pair_dpd>`, and
+:doc:`pair lubricate <pair_lubricate>`.
+
+If a restarted run is immediately different than the run which
+produced the restart file, it could be a LAMMPS bug, so consider
+:doc:`reporting it <Errors_bugs>` if you think the behavior is a bug.
+
+Because restart files are binary, they may not be portable to other
+machines.  In this case, you can use the :doc:`-restart command-line switch <Run_options>` to convert a restart file to a data file.
+
+Similar to how restart files are written (see the
+:doc:`write\_restart <write_restart>` and :doc:`restart <restart>`
+commands), the restart filename can contain two wild-card characters.
+If a "\*" appears in the filename, the directory is searched for all
+filenames that match the pattern where "\*" is replaced with a timestep
+value.  The file with the largest timestep value is read in.  Thus,
+this effectively means, read the latest restart file.  It's useful if
+you want your script to continue a run from where it left off.  See
+the :doc:`run <run>` command and its "upto" option for how to specify
+the run command so it doesn't need to be changed either.
+
+If a "%" character appears in the restart filename, LAMMPS expects a
+set of multiple files to exist.  The :doc:`restart <restart>` and
+:doc:`write\_restart <write_restart>` commands explain how such sets are
+created.  Read\_restart will first read a filename where "%" is
+replaced by "base".  This file tells LAMMPS how many processors
+created the set and how many files are in it.  Read\_restart then reads
+the additional files.  For example, if the restart file was specified
+as save.% when it was written, then read\_restart reads the files
+save.base, save.0, save.1, ... save.P-1, where P is the number of
+processors that created the restart file.
+
+Note that P could be the total number of processors in the previous
+simulation, or some subset of those processors, if the *fileper* or
+*nfile* options were used when the restart file was written; see the
+:doc:`restart <restart>` and :doc:`write\_restart <write_restart>` commands
+for details.  The processors in the current LAMMPS simulation share
+the work of reading these files; each reads a roughly equal subset of
+the files.  The number of processors which created the set can be
+different the number of processors in the current LAMMPS simulation.
+This can be a fast mode of input on parallel machines that support
+parallel I/O.
+
+A restart file can also be read in parallel as one large binary file
+via the MPI-IO library, assuming it was also written with MPI-IO.
+MPI-IO is part of the MPI standard for versions 2.0 and above.  Using
+MPI-IO requires two steps.  First, build LAMMPS with its MPIIO package
+installed, e.g.
+
+
+.. parsed-literal::
+
+   make yes-mpiio    # installs the MPIIO package
+   make mpi          # build LAMMPS for your platform
+
+Second, use a restart filename which contains ".mpiio".  Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO dump files, a particular restart file must be both
+written and read using MPI-IO.
+
+
+----------
+
+
+Here is the list of information included in a restart file, which
+means these quantities do not need to be re-specified in the input
+script that reads the restart file, though you can redefine many of
+these settings after the restart file is read.
+
+* :doc:`units <units>`
+* :doc:`newton bond <newton>` (see discussion of newton command below)
+* :doc:`atom style <atom_style>` and :doc:`atom\_modify <atom_modify>` settings id, map, sort
+* :doc:`comm style <comm_style>` and :doc:`comm\_modify <comm_modify>` settings mode, cutoff, vel
+* :doc:`timestep <timestep>`
+* simulation box size and shape and :doc:`boundary <boundary>` settings
+* atom :doc:`group <group>` definitions
+* per-type atom settings such as :doc:`mass <mass>`
+* per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc)
+* force field styles (:doc:`pair <pair_style>`, :doc:`bond <bond_style>`, :doc:`angle <angle_style>`, etc)
+* force field coefficients (:doc:`pair <pair_coeff>`, :doc:`bond <bond_coeff>`, :doc:`angle <angle_coeff>`, etc) in some cases (see below)
+* :doc:`pair\_modify <pair_modify>` settings, except the compute option
+* :doc:`special\_bonds <special_bonds>` settings
+
+Here is a list of information not stored in a restart file, which
+means you must re-issue these commands in your input script, after
+reading the restart file.
+
+* :doc:`newton pair <newton>` (see discussion of newton command below)
+* :doc:`fix <fix>` commands (see below)
+* :doc:`compute <compute>` commands (see below)
+* :doc:`variable <variable>` commands
+* :doc:`region <region>` commands
+* :doc:`neighbor list <neighbor>` criteria including :doc:`neigh\_modify <neigh_modify>` settings
+* :doc:`kspace\_style <kspace_style>` and :doc:`kspace\_modify <kspace_modify>` settings
+* info for :doc:`thermodynamic <thermo_style>`, :doc:`dump <dump>`, or :doc:`restart <restart>` output
+
+The :doc:`newton <newton>` command has two settings, one for pairwise
+interactions, the other for bonded.  Both settings are stored in the
+restart file.  For the bond setting, the value in the file will
+overwrite the current value (at the time the read\_restart command is
+issued) and warn if the two values are not the same and the current
+value is not the default.  For the pair setting, the value in the file
+will not overwrite the current value (so that you can override the
+previous run's value), but a warning is issued if the two values are
+not the same and the current value is not the default.
+
+Note that some force field styles (pair, bond, angle, etc) do not
+store their coefficient info in restart files.  Typically these are
+many-body or tabulated potentials which read their parameters from
+separate files.  In these cases you will need to re-specify the
+:doc:`pair\_coeff <pair_coeff>`, :doc:`bond\_coeff <bond_coeff>`, etc
+commands in your restart input script.  The doc pages for individual
+force field styles mention if this is the case.  This is also true of
+:doc:`pair\_style hybrid <pair_hybrid>` (bond hybrid, angle hybrid, etc)
+commands; they do not store coefficient info.
+
+As indicated in the above list, the :doc:`fixes <fix>` used for a
+simulation are not stored in the restart file.  This means the new
+input script should specify all fixes it will use.  However, note that
+some fixes store an internal "state" which is written to the restart
+file.  This allows the fix to continue on with its calculations in a
+restarted simulation.  To re-enable such a fix, the fix command in the
+new input script must be of the same style and use the same fix-ID as
+was used in the input script that wrote the restart file.
+
+If a match is found, LAMMPS prints a message indicating that the fix
+is being re-enabled.  If no match is found before the first run or
+minimization is performed by the new script, the "state" information
+for the saved fix is discarded.  At the time the discard occurs,
+LAMMPS will also print a list of fixes for which the information is
+being discarded.  See the doc pages for individual fixes for info on
+which ones can be restarted in this manner.  Note that fixes which are
+created internally by other LAMMPS commands (computes, fixes, etc)
+will have style names which are all-capitalized, and IDs which are
+generated internally.
+
+Likewise, the :doc:`computes <fix>` used for a simulation are not stored
+in the restart file.  This means the new input script should specify
+all computes it will use.  However, some computes create a fix
+internally to store "state" information that persists from timestep to
+timestep.  An example is the :doc:`compute msd <compute_msd>` command
+which uses a fix to store a reference coordinate for each atom, so
+that a displacement can be calculated at any later time.  If the
+compute command in the new input script uses the same compute-ID and
+group-ID as was used in the input script that wrote the restart file,
+then it will create the same fix in the restarted run.  This means the
+re-created fix will be re-enabled with the stored state information as
+described in the previous paragraph, so that the compute can continue
+its calculations in a consistent manner.
+
+.. note::
+
+   There are a handful of commands which can be used before or
+   between runs which may require a system initialization.  Examples
+   include the "balance", "displace\_atoms", "delete\_atoms", "set" (some
+   options), and "velocity" (some options) commands.  This is because
+   they can migrate atoms to new processors.  Thus they will also discard
+   unused "state" information from fixes.  You will know the discard has
+   occurred because a list of discarded fixes will be printed to the
+   screen and log file, as explained above.  This means that if you wish
+   to retain that info in a restarted run, you must re-specify the
+   relevant fixes and computes (which create fixes) before those commands
+   are used.
+
+Some pair styles, like the :doc:`granular pair styles <pair_gran>`, also
+use a fix to store "state" information that persists from timestep to
+timestep.  In the case of granular potentials, it is contact
+information between pairs of touching particles.  This info will also
+be re-enabled in the restart script, assuming you re-use the same
+granular pair style.
+
+LAMMPS allows bond interactions (angle, etc) to be turned off or
+deleted in various ways, which can affect how their info is stored in
+a restart file.
+
+If bonds (angles, etc) have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete\_bonds <delete_bonds>` command,
+their info will be written to a restart file as if they are turned on.
+This means they will need to be turned off again in a new run after
+the restart file is read.
+
+Bonds that are broken (e.g. by a bond-breaking potential) are written
+to the restart file as broken bonds with a type of 0.  Thus these
+bonds will still be broken when the restart file is read.
+
+Bonds that have been broken by the :doc:`fix bond/break <fix_bond_break>` command have disappeared from the
+system.  No information about these bonds is written to the restart
+file.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+To write and read restart files in parallel with MPI-IO, the MPIIO
+package must be installed.
+
+Related commands
+""""""""""""""""
+
+:doc:`read\_data <read_data>`, :doc:`read\_dump <read_dump>`,
+:doc:`write\_restart <write_restart>`, :doc:`restart <restart>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/region.rst b/doc/src/region.rst
new file mode 100644
index 0000000000..3eaaae30ac
--- /dev/null
+++ b/doc/src/region.rst
@@ -0,0 +1,435 @@
+.. index:: region
+
+region command
+==============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   region ID style args keyword arg ...
+
+* ID = user-assigned name for the region
+* style = *delete* or *block* or *cone* or *cylinder* or *plane* or *prism* or *sphere* or *union* or *intersect*
+  
+  .. parsed-literal::
+  
+       *delete* = no args
+       *block* args = xlo xhi ylo yhi zlo zhi
+         xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
+       *cone* args = dim c1 c2 radlo radhi lo hi
+         dim = *x* or *y* or *z* = axis of cone
+         c1,c2 = coords of cone axis in other 2 dimensions (distance units)
+         radlo,radhi = cone radii at lo and hi end (distance units)
+         lo,hi = bounds of cone in dim (distance units)
+       *cylinder* args = dim c1 c2 radius lo hi
+         dim = *x* or *y* or *z* = axis of cylinder
+         c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
+         radius = cylinder radius (distance units)
+           c1,c2, and radius can be a variable (see below)
+         lo,hi = bounds of cylinder in dim (distance units)
+       *plane* args = px py pz nx ny nz
+         px,py,pz = point on the plane (distance units)
+         nx,ny,nz = direction normal to plane (distance units)
+       *prism* args = xlo xhi ylo yhi zlo zhi xy xz yz
+         xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
+         xy = distance to tilt y in x direction (distance units)
+         xz = distance to tilt z in x direction (distance units)
+         yz = distance to tilt z in y direction (distance units)
+       *sphere* args = x y z radius
+         x,y,z = center of sphere (distance units)
+         radius = radius of sphere (distance units)
+           x,y,z, and radius can be a variable (see below)
+       *union* args = N reg-ID1 reg-ID2 ...
+         N = # of regions to follow, must be 2 or greater
+         reg-ID1,reg-ID2, ... = IDs of regions to join together
+       *intersect* args = N reg-ID1 reg-ID2 ...
+         N = # of regions to follow, must be 2 or greater
+         reg-ID1,reg-ID2, ... = IDs of regions to intersect
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *side* or *units* or *move* or *rotate* or *open*
+  
+  .. parsed-literal::
+  
+       *side* value = *in* or *out*
+         *in* = the region is inside the specified geometry
+         *out* = the region is outside the specified geometry
+       *units* value = *lattice* or *box*
+         *lattice* = the geometry is defined in lattice units
+         *box* = the geometry is defined in simulation box units
+       *move* args = v_x v_y v_z
+         v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
+       *rotate* args = v_theta Px Py Pz Rx Ry Rz
+         v_theta = equal-style variable for rotaton of region over time (in radians)
+         Px,Py,Pz = origin for axis of rotation (distance units)
+         Rx,Ry,Rz = axis of rotation vector
+       *open* value = integer from 1-6 corresponding to face index (see below)
+
+* accelerated styles (with same args) = *block/kk*
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   region 1 block -3.0 5.0 INF 10.0 INF INF
+   region 2 sphere 0.0 0.0 0.0 5 side out
+   region void cylinder y 2 3 5 -5.0 EDGE units box
+   region 1 prism 0 10 0 10 0 10 2 0 0
+   region outside union 4 side1 side2 side3 side4
+   region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL
+   region openbox block 0 10 0 10 0 10 open 5 open 6 units box
+   region funnel cone z 10 10 2 5 0 10 open 1 units box
+
+Description
+"""""""""""
+
+This command defines a geometric region of space.  Various other
+commands use regions.  For example, the region can be filled with
+atoms via the :doc:`create\_atoms <create_atoms>` command.  Or a bounding
+box around the region, can be used to define the simulation box via
+the :doc:`create\_box <create_box>` command.  Or the atoms in the region
+can be identified as a group via the :doc:`group <group>` command, or
+deleted via the :doc:`delete\_atoms <delete_atoms>` command.  Or the
+surface of the region can be used as a boundary wall via the :doc:`fix wall/region <fix_wall_region>` command.
+
+Commands which use regions typically test whether an atom's position
+is contained in the region or not.  For this purpose, coordinates
+exactly on the region boundary are considered to be interior to the
+region.  This means, for example, for a spherical region, an atom on
+the sphere surface would be part of the region if the sphere were
+defined with the *side in* keyword, but would not be part of the
+region if it were defined using the *side out* keyword.  See more
+details on the *side* keyword below.
+
+Normally, regions in LAMMPS are "static", meaning their geometric
+extent does not change with time.  If the *move* or *rotate* keyword
+is used, as described below, the region becomes "dynamic", meaning
+it's location or orientation changes with time.  This may be useful,
+for example, when thermostatting a region, via the compute temp/region
+command, or when the fix wall/region command uses a region surface as
+a bounding wall on particle motion, i.e. a rotating container.
+
+The *delete* style removes the named region.  Since there is little
+overhead to defining extra regions, there is normally no need to do
+this, unless you are defining and discarding large numbers of regions
+in your input script.
+
+The lo/hi values for *block* or *cone* or *cylinder* or *prism* styles
+can be specified as EDGE or INF.  EDGE means they extend all the way
+to the global simulation box boundary.  Note that this is the current
+box boundary; if the box changes size during a simulation, the region
+does not.  INF means a large negative or positive number (1.0e20), so
+it should encompass the simulation box even if it changes size.  If a
+region is defined before the simulation box has been created (via
+:doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` or
+:doc:`read\_restart <read_restart>` commands), then an EDGE or INF
+parameter cannot be used.  For a *prism* region, a non-zero tilt
+factor in any pair of dimensions cannot be used if both the lo/hi
+values in either of those dimensions are INF.  E.g. if the xy tilt is
+non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi.
+
+.. note::
+
+   Regions in LAMMPS do not get wrapped across periodic boundaries,
+   as specified by the :doc:`boundary <boundary>` command.  For example, a
+   spherical region that is defined so that it overlaps a periodic
+   boundary is not treated as 2 half-spheres, one on either side of the
+   simulation box.
+
+.. note::
+
+   Regions in LAMMPS are always 3d geometric objects, regardless of
+   whether the :doc:`dimension <dimension>` of a simulation is 2d or 3d.
+   Thus when using regions in a 2d simulation, you should be careful to
+   define the region so that its intersection with the 2d x-y plane of
+   the simulation has the 2d geometric extent you want.
+
+For style *cone*\ , an axis-aligned cone is defined which is like a
+*cylinder* except that two different radii (one at each end) can be
+defined.  Either of the radii (but not both) can be 0.0.
+
+For style *cone* and *cylinder*\ , the c1,c2 params are coordinates in
+the 2 other dimensions besides the cylinder axis dimension.  For dim =
+x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y.
+Thus the third example above specifies a cylinder with its axis in the
+y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
+extending in the y-direction from -5.0 to the upper box boundary.
+
+For style *plane*\ , a plane is defined which contain the point
+(px,py,pz) and has a normal vector (nx,ny,nz).  The normal vector does
+not have to be of unit length.  The "inside" of the plane is the
+half-space in the direction of the normal vector; see the discussion
+of the *side* option below.
+
+For style *prism*\ , a parallelepiped is defined (it's too hard to spell
+parallelepiped in an input script!).  The parallelepiped has its
+"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
+from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
+(xz,yz,zhi-zlo).  *Xy,xz,yz* can be 0.0 or positive or negative values
+and are called "tilt factors" because they are the amount of
+displacement applied to faces of an originally orthogonal box to
+transform it into the parallelepiped.
+
+A prism region that will be used with the :doc:`create\_box <create_box>`
+command to define a triclinic simulation box must have tilt factors
+(xy,xz,yz) that do not skew the box more than half the distance of
+corresponding the parallel box length.  For example, if xlo = 2 and
+xhi = 12, then the x box length is 10 and the xy tilt factor must be
+between -5 and 5.  Similarly, both xz and yz must be between
+-(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a limitation,
+since if the maximum tilt factor is 5 (as in this example), then
+configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
+geometrically equivalent.
+
+The *radius* value for style *sphere* and *cylinder* can be specified
+as an equal-style :doc:`variable <variable>`.  If the value is a
+variable, it should be specified as v\_name, where name is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its value used to determine the radius of the region. For style *sphere*
+also the x-, y-, and z- coordinate of the center of the sphere and for
+style *cylinder* the two center positions c1 and c2 for the location of
+the cylinder axes can be a variable with the same kind of effect and
+requirements than for the radius.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent radius or have
+a time dependent position of the sphere or cylinder region.
+
+See the :doc:`Howto tricilinc <Howto_triclinic>` doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
+triclinic representations.
+
+The *union* style creates a region consisting of the volume of all the
+listed regions combined.  The *intersect* style creates a region
+consisting of the volume that is common to all the listed regions.
+
+.. note::
+
+   The *union* and *intersect* regions operate by invoking methods
+   from their list of sub-regions.  Thus you cannot delete the
+   sub-regions after defining a *union* or *intersection* region.
+
+
+----------
+
+
+The *side* keyword determines whether the region is considered to be
+inside or outside of the specified geometry.  Using this keyword in
+conjunction with *union* and *intersect* regions, complex geometries
+can be built up.  For example, if the interior of two spheres were
+each defined as regions, and a *union* style with *side* = out was
+constructed listing the region-IDs of the 2 spheres, the resulting
+region would be all the volume in the simulation box that was outside
+both of the spheres.
+
+The *units* keyword determines the meaning of the distance units used
+to define the region for any argument above listed as having distance
+units.  It also affects the scaling of the velocity vector specified
+with the *vel* keyword, the amplitude vector specified with the
+*wiggle* keyword, and the rotation point specified with the *rotate*
+keyword, since they each involve a distance metric.
+
+A *box* value selects standard distance units as defined by the
+:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
+A *lattice* value means the distance units are in lattice spacings.
+The :doc:`lattice <lattice>` command must have been previously used to
+define the lattice spacings which are used as follows:
+
+* For style *block*\ , the lattice spacing in dimension x is applied to
+  xlo and xhi, similarly the spacings in dimensions y,z are applied to
+  ylo/yhi and zlo/zhi.
+* For style *cone*\ , the lattice spacing in argument *dim* is applied to
+  lo and hi.  The spacings in the two radial dimensions are applied to
+  c1 and c2.  The two cone radii are scaled by the lattice
+  spacing in the dimension corresponding to c1.
+* For style *cylinder*\ , the lattice spacing in argument *dim* is applied
+  to lo and hi.  The spacings in the two radial dimensions are applied
+  to c1 and c2.  The cylinder radius is scaled by the lattice
+  spacing in the dimension corresponding to c1.
+* For style *plane*\ , the lattice spacing in dimension x is applied to
+  px and nx, similarly the spacings in dimensions y,z are applied to
+  py/ny and pz/nz.
+* For style *prism*\ , the lattice spacing in dimension x is applied to
+  xlo and xhi, similarly for ylo/yhi and zlo/zhi.  The lattice spacing
+  in dimension x is applied to xy and xz, and the spacing in dimension y
+  to yz.
+* For style *sphere*\ , the lattice spacing in dimensions x,y,z are
+  applied to the sphere center x,y,z.  The spacing in dimension x is
+  applied to the sphere radius.
+
+
+----------
+
+
+If the *move* or *rotate* keywords are used, the region is "dynamic",
+meaning its location or orientation changes with time.  These keywords
+cannot be used with a *union* or *intersect* style region.  Instead,
+the keywords should be used to make the individual sub-regions of the
+*union* or *intersect* region dynamic.  Normally, each sub-region
+should be "dynamic" in the same manner (e.g. rotate around the same
+point), though this is not a requirement.
+
+The *move* keyword allows one or more :doc:`equal-style variables <variable>` to be used to specify the x,y,z displacement
+of the region, typically as a function of time.  A variable is
+specified as v\_name, where name is the variable name.  Any of the
+three variables can be specified as NULL, in which case no
+displacement is calculated in that dimension.
+
+Note that equal-style variables can specify formulas with various
+mathematical functions, and include :doc:`thermo\_style <thermo_style>`
+command keywords for the simulation box parameters and timestep and
+elapsed time.  Thus it is easy to specify a region displacement that
+change as a function of time or spans consecutive runs in a continuous
+fashion.  For the latter, see the *start* and *stop* keywords of the
+:doc:`run <run>` command and the *elaplong* keyword of :doc:`thermo\_style custom <thermo_style>` for details.
+
+For example, these commands would displace a region from its initial
+position, in the positive x direction, effectively at a constant
+velocity:
+
+
+.. parsed-literal::
+
+   variable dx equal ramp(0,10)
+   region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
+
+Note that the initial displacement is 0.0, though that is not required.
+
+Either of these variables would "wiggle" the region back and forth in
+the y direction:
+
+
+.. parsed-literal::
+
+   variable dy equal swiggle(0,5,100)
+   variable dysame equal 5\*sin(2\*PI\*elaplong\*dt/100)
+   region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
+
+The *rotate* keyword rotates the region around a rotation axis *R* =
+(Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz).  The rotation
+angle is calculated, presumably as a function of time, by a variable
+specified as v\_theta, where theta is the variable name.  The variable
+should generate its result in radians.  The direction of rotation for
+the region around the rotation axis is consistent with the right-hand
+rule: if your right-hand thumb points along *R*\ , then your fingers
+wrap around the axis in the direction of rotation.
+
+The *move* and *rotate* keywords can be used together.  In this case,
+the displacement specified by the *move* keyword is applied to the *P*
+point of the *rotate* keyword.
+
+
+----------
+
+
+The *open* keyword can be used (multiple times) to indicate that one
+or more faces of the region are ignored for purposes of particle/wall
+interactions.  This keyword is only relevant for regions used by the
+*fix wall/region* and *fix wall/gran/region* commands.  It can be used
+to create "open" containers where only some of the region faces are
+walls.  For example, a funnel can be created with a *cone* style
+region that has an open face at the smaller radius for particles to
+flow out, or at the larger radius for pouring particles into the cone,
+or both.
+
+Note that using the *open* keyword partly overrides the *side*
+keyword, since both exterior and interior surfaces of an open region
+are tested for particle contacts.  The exception to this is a *union*
+or *intersect* region which includes an open sub-region.  In that case
+the *side* keyword is still used to define the union/intersect region
+volume, and the *open* settings are only applied to the individual
+sub-regions that use them.
+
+The indices specified as part of the *open* keyword have the following
+meanings:
+
+For style *block*\ , indices 1-6 correspond to the xlo, xhi, ylo, yhi,
+zlo, zhi surfaces of the block.  I.e. 1 is the yz plane at x = xlo, 2
+is the yz-plane at x = xhi, 3 is the xz plane at y = ylo, 4 is the xz
+plane at y = yhi, 5 is the xy plane at z = zlo, 6 is the xy plane at z
+= zhi).  In the second-to-last example above, the region is a box open
+at both xy planes.
+
+For style *prism*\ , values 1-6 have the same mapping as for style
+*block*\ .  I.e. in an untilted *prism*\ , *open* indices correspond to
+the xlo, xhi, ylo, yhi, zlo, zhi surfaces.
+
+For style *cylinder*\ , index 1 corresponds to the flat end cap at the
+low coordinate along the cylinder axis, index 2 corresponds to the
+high-coordinate flat end cap along the cylinder axis, and index 3 is
+the curved cylinder surface.  For example, a *cylinder* region with
+*open 1 open 2* keywords will be open at both ends (e.g. a section of
+pipe), regardless of the cylinder orientation.
+
+For style *cone*\ , the mapping is the same as for style *cylinder*\ .
+Index 1 is the low-coordinate flat end cap, index 2 is the
+high-coordinate flat end cap, and index 3 is the curved cone surface.
+In the last example above, a *cone* region is defined along the z-axis
+that is open at the zlo value (e.g. for use as a funnel).
+
+For all other styles, the *open* keyword is ignored.  As indicated
+above, this includes the *intersect* and *union* regions, though their
+sub-regions can be defined with the *open* keyword.
+
+
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+The code using the region (such as a fix or compute) must also be supported
+by Kokkos or no acceleration will occur. Currently, only *block* style
+regions are supported by Kokkos.
+
+These accelerated styles are part of the Kokkos package.  They are
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+A prism cannot be of 0.0 thickness in any dimension; use a small z
+thickness for 2d simulations.  For 2d simulations, the xz and yz
+parameters must be 0.0.
+
+Related commands
+""""""""""""""""
+
+:doc:`lattice <lattice>`, :doc:`create\_atoms <create_atoms>`,
+:doc:`delete\_atoms <delete_atoms>`, :doc:`group <group>`
+
+Default
+"""""""
+
+The option defaults are side = in, units = lattice, and no move or
+rotation.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/replicate.rst b/doc/src/replicate.rst
new file mode 100644
index 0000000000..f7682c3d54
--- /dev/null
+++ b/doc/src/replicate.rst
@@ -0,0 +1,116 @@
+.. index:: replicate
+
+replicate command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   replicate nx ny nz *keyword*
+
+nx,ny,nz = replication factors in each dimension 
+
+* optional *keyword* = *bbox*
+  
+  .. parsed-literal::
+  
+       *bbox* = only check atoms in replicas that overlap with a processor's sub-domain
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   replicate 2 3 2
+
+Description
+"""""""""""
+
+Replicate the current simulation one or more times in each dimension.
+For example, replication factors of 2,2,2 will create a simulation
+with 8x as many atoms by doubling the simulation domain in each
+dimension.  A replication factor of 1 in a dimension leaves the
+simulation domain unchanged.  When the new simulation box is created
+it is also partitioned into a regular 3d grid of rectangular bricks,
+one per processor, based on the number of processors being used and
+the settings of the :doc:`processors <processors>` command.  The
+partitioning can later be changed by the :doc:`balance <balance>` or
+:doc:`fix balance <fix_balance>` commands.
+
+All properties of the atoms are replicated, including their
+velocities, which may or may not be desirable.  New atom IDs are
+assigned to new atoms, as are molecule IDs.  Bonds and other topology
+interactions are created between pairs of new atoms as well as between
+old and new atoms.  This is done by using the image flag for each atom
+to "unwrap" it out of the periodic box before replicating it.
+
+This means that any molecular bond you specify in the original data
+file that crosses a periodic boundary should be between two atoms with
+image flags that differ by 1.  This will allow the bond to be
+unwrapped appropriately.
+
+The optional keyword *bbox* uses a bounding box to only check atoms in
+replicas that overlap with a processor's sub-domain when assigning
+atoms to processors.  It typically results in a substantial speedup
+when using the replicate command on a large number of processors.  It
+does require temporary use of more memory, specifically that each
+processor can store all atoms in the entire system before it is
+replicated.
+
+Restrictions
+""""""""""""
+
+
+A 2d simulation cannot be replicated in the z dimension.
+
+If a simulation is non-periodic in a dimension, care should be used
+when replicating it in that dimension, as it may put atoms nearly on
+top of each other.
+
+.. note::
+
+   You cannot use the replicate command on a system which has a
+   molecule that spans the box and is bonded to itself across a periodic
+   boundary, so that the molecule is effectively a loop.  A simple
+   example would be a linear polymer chain that spans the simulation box
+   and bonds back to itself across the periodic boundary.  More realistic
+   examples would be a CNT (meant to be an infinitely long CNT) or a
+   graphene sheet or a bulk periodic crystal where there are explicit
+   bonds specified between near neighbors.  (Note that this only applies
+   to systems that have permanent bonds as specified in the data file.  A
+   CNT that is just atoms modeled with the :doc:`AIREBO potential <pair_airebo>` has no such permanent bonds, so it can be
+   replicated.)  The reason replication does not work with those systems
+   is that the image flag settings described above cannot be made
+   consistent.  I.e. it is not possible to define images flags so that
+   when every pair of bonded atoms is unwrapped (using the image flags),
+   they will be close to each other.  The only way the replicate command
+   could work in this scenario is for it to break a bond, insert more
+   atoms, and re-connect the loop for the larger simulation box.  But it
+   is not clever enough to do this.  So you will have to construct a
+   larger version of your molecule as a pre-processing step and input a
+   new data file to LAMMPS.
+
+If the current simulation was read in from a restart file (before a
+run is performed), there must not be any fix information stored in
+the file for individual atoms.  Similarly, no fixes can be defined at
+the time the replicate command is used that require vectors of atom
+information to be stored.  This is because the replicate command does
+not know how to replicate that information for new atoms it creates.
+To work around this restriction, restart files may be converted into
+data files and fixes may be undefined via the :doc:`unfix <unfix>`
+command before and redefined after the replicate command.
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst
new file mode 100644
index 0000000000..9b5fdc5ff5
--- /dev/null
+++ b/doc/src/rerun.rst
@@ -0,0 +1,237 @@
+.. index:: rerun
+
+rerun command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   rerun file1 file2 ... keyword args ...
+
+* file1,file2,... = dump file(s) to read
+* one or more keywords may be appended, keyword *dump* must appear and be last
+  
+  .. parsed-literal::
+  
+     keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *dump*
+      *first* args = Nfirst
+        Nfirst = dump timestep to start on
+      *last* args = Nlast
+        Nlast = dumptimestep to stop on
+      *every* args = Nevery
+        Nevery = read snapshots matching every this many timesteps
+      *skip* args = Nskip
+        Nskip = read one out of every Nskip snapshots
+      *start* args = Nstart
+        Nstart = timestep on which pseudo run will start
+      *stop* args = Nstop
+        Nstop = timestep to which pseudo run will end
+      *dump* args = same as :doc:`read_dump <read_dump>` command starting with its field arguments
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   rerun dump.file dump x y z vx vy vz
+   rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z
+   rerun dump.vels dump x y z vx vy vz box yes format molfile lammpstrj
+   rerun dump.dcd dump x y z box no format molfile dcd
+   rerun ../run7/dump.file.gz skip 2 dump x y z box yes
+
+Description
+"""""""""""
+
+Perform a pseudo simulation run where atom information is read one
+snapshot at a time from a dump file(s), and energies and forces are
+computed on the shapshot to produce thermodynamic or other output.
+
+This can be useful in the following kinds of scenarios, after an
+initial simulation produced the dump file:
+
+* Compute the energy and forces of snaphots using a different potential.
+* Calculate one or more diagnostic quantities on the snapshots that
+  weren't computed in the initial run.  These can also be computed with
+  settings not used in the initial run, e.g. computing an RDF via the
+  :doc:`compute rdf <compute_rdf>` command with a longer cutoff than was
+  used initially.
+* Calculate the portion of per-atom forces resulting from a subset of
+  the potential.  E.g. compute only Coulombic forces.  This can be done
+  by only defining only a Coulombic pair style in the rerun script.
+  Doing this in the original script would result in different (bad)
+  dynamics.
+
+
+Conceptually, using the rerun command is like running an input script
+that has a loop in it (see the :doc:`next <next>` and :doc:`jump <jump>`
+commands).  Each iteration of the loop reads one snapshot from the
+dump file via the :doc:`read\_dump <read_dump>` command, sets the
+timestep to the appropriate value, and then invokes a :doc:`run <run>`
+command for zero timesteps to simply compute energy and forces, and
+any other :doc:`thermodynamic output <thermo_style>` or diagnostic info
+you have defined.  This computation also invokes any fixes you have
+defined that apply constraints to the system, such as :doc:`fix shake <fix_shake>` or :doc:`fix indent <fix_indent>`.
+
+Note that a simulation box must already be defined before using the
+rerun command.  This can be done by the :doc:`create\_box <create_box>`,
+:doc:`read\_data <read_data>`, or :doc:`read\_restart <read_restart>`
+commands.
+
+Also note that reading per-atom information from dump snapshots is
+limited to the atom coordinates, velocities and image flags as
+explained in the :doc:`read\_dump <read_dump>` command.  Other atom
+properties, which may be necessary to compute energies and forces,
+such as atom charge, or bond topology information for a molecular
+system, are not read from (or even contained in) dump files.  Thus
+this auxiliary information should be defined in the usual way, e.g. in
+a data file read in by a :doc:`read\_data <read_data>` command, before
+using the rerun command.
+
+Also note that the frequency of thermodynamic or dump output from the
+rerun simulation will depend on settings made in the rerun script, the
+same as for output from any LAMMPS simulation.  See further info below
+as to what that means if the timesteps for snapshots read from dump
+files do not match the specified output frequency.
+
+
+----------
+
+
+If more than one dump file is specified, the dump files are read one
+after the other.  It is assumed that snapshot timesteps will be in
+ascending order.  If a snapshot is encountered that is not in
+ascending order, it will skip the snapshot until it reads one that is.
+This allows skipping of a duplicate snapshot (same timestep),
+e.g. that appeared at the end of one file and beginning of the next.
+However if you specify a series of dump files in an incorrect order
+(with respect to the timesteps they contain), you may skip large
+numbers of snapshots
+
+Note that the dump files specified as part of the *dump* keyword can
+be parallel files, i.e. written as multiple files either per processor
+and/or per snapshot.  If that is the case they will also be read in
+parallel which can make the rerun command operate dramatically faster
+for large systems.  See the doc page for the `read\_dump <read_dump>`_ and
+:doc:`dump <dump>` commands which describe how to read and write
+parallel dump files.
+
+The *first*\ , *last*\ , *every*\ , *skip* keywords determine which
+snapshots are read from the dump file(s).  Snapshots are skipped until
+they have a timestamp >= *Nfirst*\ .  When a snapshot with a timestamp >
+*Nlast* is encountered, the rerun command finishes.  Note below that
+the defaults for *first* and *last* are to read all snapshots.  If the
+*every* keyword is set to a value > 0, then only snapshots with
+timestamps that are a multiple of *Nevery* are read (the first
+snapshot is always read).  If *Nevery* = 0, then this criterion is
+ignored, i.e. every snapshot is read that meets the other criteria.
+If the *skip* keyword is used, then after the first snapshot is read,
+every Nth snapshot is read, where N = *Nskip*\ .  E.g. if *Nskip* = 3,
+then only 1 out of every 3 snapshots is read, assuming the snapshot
+timestamp is also consistent with the other criteria.
+
+The *start* and *stop* keywords do not affect which snapshots are read
+from the dump file(s).  Rather, they have the same meaning that they
+do for the :doc:`run <run>` command.  They only need to be defined if
+(a) you are using a :doc:`fix <fix>` command that changes some value
+over time, and (b) you want the reference point for elapsed time (from
+start to stop) to be different than the *first* and *last* settings.
+See the doc page for individual fixes to see which ones can be used
+with the *start/stop* keywords.  Note that if you define neither of
+the *start*\ /\ *stop* or *first*\ /\ *last* keywords, then LAMMPS treats the
+pseudo run as going from 0 to a huge value (effectively infinity).
+This means that any quantity that a fix scales as a fraction of
+elapsed time in the run, will essentially remain at its initial value.
+Also note that an error will occur if you read a snapshot from the
+dump file with a timestep value larger than the *stop* setting you
+have specified.
+
+The *dump* keyword is required and must be the last keyword specified.
+Its arguments are passed internally to the :doc:`read\_dump <read_dump>`
+command.  The first argument following the *dump* keyword should be
+the *field1* argument of the :doc:`read\_dump <read_dump>` command.  See
+the :doc:`read\_dump <read_dump>` doc page for details on the various
+options it allows for extracting information from the dump file
+snapshots, and for using that information to alter the LAMMPS
+simulation.
+
+
+----------
+
+
+In general, a LAMMPS input script that uses a rerun command can
+include and perform all the usual operations of an input script that
+uses the :doc:`run <run>` command.  There are a few exceptions and
+points to consider, as discussed here.
+
+Fixes that perform time integration, such as :doc:`fix nve <fix_nve>` or
+:doc:`fix npt <fix_nh>` are not invoked, since no time integration is
+performed.  Fixes that perturb or constrain the forces on atoms will
+be invoked, just as they would during a normal run.  Examples are :doc:`fix indent <fix_indent>` and :doc:`fix langevin <fix_langevin>`.  So you
+should think carefully as to whether that makes sense for the manner
+in which you are reprocessing the dump snapshots.
+
+If you only want the rerun script to perform an analysis that does
+not involve pair interactions, such as use compute msd to calculated
+displacements over time, you do not need to define a :doc:`pair style <pair_style>`, which may also mean neighbor lists will not
+need to be calculated which saves time.  The :doc:`comm\_modify cutoff <comm_modify>` command can also be used to insure ghost
+atoms are acquired from far enough away for operations like bond and
+angle evaluations, if no pair style is being used.
+
+Every time a snapshot is read, the timestep for the simulation is
+reset, as if the :doc:`reset\_timestep <reset_timestep>` command were
+used.  This command has some restrictions as to what fixes can be
+defined.  See its doc page for details.  For example, the :doc:`fix deposit <fix_deposit>` and :doc:`fix dt/reset <fix_dt_reset>` fixes
+are in this category.  They also make no sense to use with a rerun
+command.
+
+If time-averaging fixes like :doc:`fix ave/time <fix_ave_time>` are
+used, they are invoked on timesteps that are a function of their
+*Nevery*\ , *Nrepeat*\ , and *Nfreq* settings.  As an example, see the
+:doc:`fix ave/time <fix_ave_time>` doc page for details.  You must
+insure those settings are consistent with the snapshot timestamps that
+are read from the dump file(s).  If an averaging fix is not invoked on
+a timestep it expects to be, LAMMPS will flag an error.
+
+The various forms of LAMMPS output, as defined by the
+:doc:`thermo\_style <thermo_style>`, :doc:`thermo <thermo>`,
+:doc:`dump <dump>`, and :doc:`restart <restart>` commands occur with
+specified frequency, e.g. every N steps.  If the timestep for a dump
+snapshot is not a multiple of N, then it will be read and processed,
+but no output will be produced.  If you want output for every dump
+snapshot, you can simply use N=1 for an output frequency, e.g. for
+thermodynamic output or new dump file output.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+To read gzipped dump files, you must compile LAMMPS with the
+-DLAMMPS\_GZIP option.  See the :doc:`Build settings <Build_settings>`
+doc page for details.
+
+Related commands
+""""""""""""""""
+
+:doc:`read\_dump <read_dump>`
+
+Default
+"""""""
+
+The option defaults are first = 0, last = a huge value (effectively
+infinity), start = same as first, stop = same as last, every = 0, skip
+= 1;
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/reset_ids.rst b/doc/src/reset_ids.rst
new file mode 100644
index 0000000000..774b9d4628
--- /dev/null
+++ b/doc/src/reset_ids.rst
@@ -0,0 +1,69 @@
+.. index:: reset\_ids
+
+reset\_ids command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   reset_ids
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   reset_ids
+
+Description
+"""""""""""
+
+Reset atom IDs for the system, including all the global IDs stored
+for bond, angle, dihedral, improper topology data.  This will
+create a set of IDs that are numbered contiguously from 1 to N
+for a N atoms system.
+
+This can be useful to do after performing a "delete\_atoms" command for
+a molecular system.  The delete\_atoms compress yes option will not
+perform this operation due to the existence of bond topology.  It can
+also be useful to do after any simulation which has lost atoms,
+e.g. due to atoms moving outside a simulation box with fixed
+boundaries (see the "boundary command"), or due to evaporation (see
+the "fix evaporate" command).
+
+Note that the resetting of IDs is not really a compression, where gaps
+in atom IDs are removed by decrementing atom IDs that are larger.
+Instead the IDs for all atoms are erased, and new IDs are assigned so
+that the atoms owned by an individual processor have consecutive IDs,
+as the :doc:`create\_atoms <create_atoms>` command explains.
+
+.. note::
+
+   If this command is used before a :doc:`pair style <pair_style>` is
+   defined, an error about bond topology atom IDs not being found may
+   result.  This is because the cutoff distance for ghost atom
+   communication was not sufficient to find atoms in bonds, angles, etc
+   that are owned by other processors.  The :doc:`comm\_modify cutoff <comm_modify>` command can be used to correct this issue.
+   Or you can define a pair style before using this command.  If you do
+   the former, you should unset the comm\_modify cutoff after using
+   reset\_ids so that subsequent communication is not inefficient.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`delete\_atoms <delete_atoms>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/reset_timestep.rst b/doc/src/reset_timestep.rst
new file mode 100644
index 0000000000..f898bf2453
--- /dev/null
+++ b/doc/src/reset_timestep.rst
@@ -0,0 +1,72 @@
+.. index:: reset\_timestep
+
+reset\_timestep command
+=======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   reset_timestep N
+
+* N = timestep number
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   reset_timestep 0
+   reset_timestep 4000000
+
+Description
+"""""""""""
+
+Set the timestep counter to the specified value.  This command
+normally comes after the timestep has been set by reading a restart
+file via the :doc:`read\_restart <read_restart>` command, or a previous
+simulation advanced the timestep.
+
+The :doc:`read\_data <read_data>` and :doc:`create\_box <create_box>`
+commands set the timestep to 0; the :doc:`read\_restart <read_restart>`
+command sets the timestep to the value it had when the restart file
+was written.
+
+Restrictions
+""""""""""""
+ none
+
+This command cannot be used when any fixes are defined that keep track
+of elapsed time to perform certain kinds of time-dependent operations.
+Examples are the :doc:`fix deposit <fix_deposit>` and :doc:`fix dt/reset <fix_dt_reset>` commands.  The former adds atoms on
+specific timesteps.  The latter keeps track of accumulated time.
+
+Various fixes use the current timestep to calculate related
+quantities.  If the timestep is reset, this may produce unexpected
+behavior, but LAMMPS allows the fixes to be defined even if the
+timestep is reset.  For example, commands which thermostat the system,
+e.g. :doc:`fix nvt <fix_nh>`, allow you to specify a target temperature
+which ramps from Tstart to Tstop which may persist over several runs.
+If you change the timestep, you may induce an instantaneous change in
+the target temperature.
+
+Resetting the timestep clears flags for :doc:`computes <compute>` that
+may have calculated some quantity from a previous run.  This means
+these quantity cannot be accessed by a variable in between runs until
+a new run is performed.  See the :doc:`variable <variable>` command for
+more details.
+
+Related commands
+""""""""""""""""
+
+:doc:`rerun <rerun>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/restart.rst b/doc/src/restart.rst
new file mode 100644
index 0000000000..e061adece3
--- /dev/null
+++ b/doc/src/restart.rst
@@ -0,0 +1,204 @@
+.. index:: restart
+
+restart command
+===============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   restart 0
+   restart N root keyword value ...
+   restart N file1 file2 keyword value ...
+
+* N = write a restart file every this many timesteps
+* N can be a variable (see below)
+* root = filename to which timestep # is appended
+* file1,file2 = two full filenames, toggle between them when writing file
+* zero or more keyword/value pairs may be appended
+* keyword = *fileper* or *nfile*
+  
+  .. parsed-literal::
+  
+       *fileper* arg = Np
+         Np = write one file for every this many processors
+       *nfile* arg = Nf
+         Nf = write this many files, one from each of Nf processors
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   restart 0
+   restart 1000 poly.restart
+   restart 1000 poly.restart.mpiio
+   restart 1000 restart.\*.equil
+   restart 10000 poly.%.1 poly.%.2 nfile 10
+   restart v_mystep poly.restart
+
+Description
+"""""""""""
+
+Write out a binary restart file with the current state of the
+simulation every so many timesteps, in either or both of two modes, as
+a run proceeds.  A value of 0 means do not write out any restart
+files.  The two modes are as follows.  If one filename is specified, a
+series of filenames will be created which include the timestep in the
+filename.  If two filenames are specified, only 2 restart files will
+be created, with those names.  LAMMPS will toggle between the 2 names
+as it writes successive restart files.
+
+Note that you can specify the restart command twice, once with a
+single filename and once with two filenames.  This would allow you,
+for example, to write out archival restart files every 100000 steps
+using a single filename, and more frequent temporary restart files
+every 1000 steps, using two filenames.  Using restart 0 will turn off
+both modes of output.
+
+Similar to :doc:`dump <dump>` files, the restart filename(s) can contain
+two wild-card characters.
+
+If a "\*" appears in the single filename, it is replaced with the
+current timestep value.  This is only recognized when a single
+filename is used (not when toggling back and forth).  Thus, the 3rd
+example above creates restart files as follows: restart.1000.equil,
+restart.2000.equil, etc.  If a single filename is used with no "\*",
+then the timestep value is appended.  E.g. the 2nd example above
+creates restart files as follows: poly.restart.1000,
+poly.restart.2000, etc.
+
+If a "%" character appears in the restart filename(s), then one file
+is written for each processor and the "%" character is replaced with
+the processor ID from 0 to P-1.  An additional file with the "%"
+replaced by "base" is also written, which contains global information.
+For example, the files written on step 1000 for filename restart.%
+would be restart.base.1000, restart.0.1000, restart.1.1000, ...,
+restart.P-1.1000.  This creates smaller files and can be a fast mode
+of output and subsequent input on parallel machines that support
+parallel I/O.  The optional *fileper* and *nfile* keywords discussed
+below can alter the number of files written.
+
+The restart file can also be written in parallel as one large binary
+file via the MPI-IO library, which is part of the MPI standard for
+versions 2.0 and above.  Using MPI-IO requires two steps.  First,
+build LAMMPS with its MPIIO package installed, e.g.
+
+
+.. parsed-literal::
+
+   make yes-mpiio    # installs the MPIIO package
+   make mpi          # build LAMMPS for your platform
+
+Second, use a restart filename which contains ".mpiio".  Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO dump files, a particular restart file must be both
+written and read using MPI-IO.
+
+Restart files are written on timesteps that are a multiple of N but
+not on the first timestep of a run or minimization.  You can use the
+:doc:`write\_restart <write_restart>` command to write a restart file
+before a run begins.  A restart file is not written on the last
+timestep of a run unless it is a multiple of N.  A restart file is
+written on the last timestep of a minimization if N > 0 and the
+minimization converges.
+
+Instead of a numeric value, N can be specified as an :doc:`equal-style variable <variable>`, which should be specified as v\_name, where
+name is the variable name.  In this case, the variable is evaluated at
+the beginning of a run to determine the next timestep at which a
+restart file will be written out.  On that timestep, the variable will
+be evaluated again to determine the next timestep, etc.  Thus the
+variable should return timestep values.  See the stagger() and
+logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
+this context.  Other similar math functions could easily be added as
+options for :doc:`equal-style variables <variable>`.
+
+For example, the following commands will write restart files
+every step from 1100 to 1200, and could be useful for debugging
+a simulation where something goes wrong at step 1163:
+
+
+.. parsed-literal::
+
+   variable       s equal stride(1100,1200,1)
+   restart        v_s tmp.restart
+
+
+----------
+
+
+See the :doc:`read\_restart <read_restart>` command for information about
+what is stored in a restart file.
+
+Restart files can be read by a :doc:`read\_restart <read_restart>`
+command to restart a simulation from a particular state.  Because the
+file is binary (to enable exact restarts), it may not be readable on
+another machine.  In this case, you can use the :doc:`-r command-line switch <Run_options>` to convert a restart file to a data file.
+
+.. note::
+
+   Although the purpose of restart files is to enable restarting a
+   simulation from where it left off, not all information about a
+   simulation is stored in the file.  For example, the list of fixes that
+   were specified during the initial run is not stored, which means the
+   new input script must specify any fixes you want to use.  Even when
+   restart information is stored in the file, as it is for some fixes,
+   commands may need to be re-specified in the new input script, in order
+   to re-use that information.  See the :doc:`read\_restart <read_restart>`
+   command for information about what is stored in a restart file.
+
+
+----------
+
+
+The optional *nfile* or *fileper* keywords can be used in conjunction
+with the "%" wildcard character in the specified restart file name(s).
+As explained above, the "%" character causes the restart file to be
+written in pieces, one piece for each of P processors.  By default P =
+the number of processors the simulation is running on.  The *nfile* or
+*fileper* keyword can be used to set P to a smaller value, which can
+be more efficient when running on a large number of processors.
+
+The *nfile* keyword sets P to the specified Nf value.  For example, if
+Nf = 4, and the simulation is running on 100 processors, 4 files will
+be written, by processors 0,25,50,75.  Each will collect information
+from itself and the next 24 processors and write it to a restart file.
+
+For the *fileper* keyword, the specified value of Np means write one
+file for every Np processors.  For example, if Np = 4, every 4th
+processor (0,4,8,12,etc) will collect information from itself and the
+next 3 processors and write it to a restart file.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+To write and read restart files in parallel with MPI-IO, the MPIIO
+package must be installed.
+
+Related commands
+""""""""""""""""
+
+:doc:`write\_restart <write_restart>`, :doc:`read\_restart <read_restart>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   restart 0
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/run.rst b/doc/src/run.rst
new file mode 100644
index 0000000000..1399c6a963
--- /dev/null
+++ b/doc/src/run.rst
@@ -0,0 +1,241 @@
+.. index:: run
+
+run command
+===========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   run N keyword values ...
+
+* N = # of timesteps
+* zero or more keyword/value pairs may be appended
+* keyword = *upto* or *start* or *stop* or *pre* or *post* or *every*
+  
+  .. parsed-literal::
+  
+       *upto* value = none
+       *start* value = N1
+         N1 = timestep at which 1st run started
+       *stop* value = N2
+         N2 = timestep at which last run will end
+       *pre* value = *no* or *yes*
+       *post* value = *no* or *yes*
+       *every* values = M c1 c2 ...
+         M = break the run into M-timestep segments and invoke one or more commands between each segment
+         c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes
+         c1 = NULL means no command will be invoked
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   run 10000
+   run 1000000 upto
+   run 100 start 0 stop 1000
+   run 1000 pre no post yes
+   run 100000 start 0 stop 1000000 every 1000 "print 'Protein Rg = $r'"
+   run 100000 every 1000 NULL
+
+Description
+"""""""""""
+
+Run or continue dynamics for a specified number of timesteps.
+
+When the :doc:`run style <run_style>` is *respa*\ , N refers to outer
+loop (largest) timesteps.
+
+A value of N = 0 is acceptable; only the thermodynamics of the system
+are computed and printed without taking a timestep.
+
+The *upto* keyword means to perform a run starting at the current
+timestep up to the specified timestep.  E.g. if the current timestep
+is 10,000 and "run 100000 upto" is used, then an additional 90,000
+timesteps will be run.  This can be useful for very long runs on a
+machine that allocates chunks of time and terminate your job when time
+is exceeded.  If you need to restart your script multiple times
+(reading in the last restart file), you can keep restarting your
+script with the same run command until the simulation finally
+completes.
+
+The *start* or *stop* keywords can be used if multiple runs are being
+performed and you want a :doc:`fix <fix>` command that changes some
+value over time (e.g. temperature) to make the change across the
+entire set of runs and not just a single run.  See the doc page for
+individual fixes to see which ones can be used with the *start/stop*
+keywords.
+
+For example, consider this fix followed by 10 run commands:
+
+
+.. parsed-literal::
+
+   fix         1 all nvt 200.0 300.0 1.0
+   run         1000 start 0 stop 10000
+   run         1000 start 0 stop 10000
+   ...
+   run         1000 start 0 stop 10000
+
+The NVT fix ramps the target temperature from 200.0 to 300.0 during a
+run.  If the run commands did not have the start/stop keywords (just
+"run 1000"), then the temperature would ramp from 200.0 to 300.0
+during the 1000 steps of each run.  With the start/stop keywords, the
+ramping takes place over the 10000 steps of all runs together.
+
+The *pre* and *post* keywords can be used to streamline the setup,
+clean-up, and associated output to the screen that happens before and
+after a run.  This can be useful if you wish to do many short runs in
+succession (e.g. LAMMPS is being called as a library which is doing
+other computations between successive short LAMMPS runs).
+
+By default (pre and post = yes), LAMMPS creates neighbor lists,
+computes forces, and imposes fix constraints before every run.  And
+after every run it gathers and prints timings statistics.  If a run is
+just a continuation of a previous run (i.e. no settings are changed),
+the initial computation is not necessary; the old neighbor list is
+still valid as are the forces.  So if *pre* is specified as "no" then
+the initial setup is skipped, except for printing thermodynamic info.
+Note that if *pre* is set to "no" for the very 1st run LAMMPS
+performs, then it is overridden, since the initial setup computations
+must be done.
+
+.. note::
+
+   If your input script changes the system between 2 runs, then the
+   initial setup must be performed to insure the change is recognized by
+   all parts of the code that are affected.  Examples are adding a
+   :doc:`fix <fix>` or :doc:`dump <dump>` or :doc:`compute <compute>`, changing
+   a :doc:`neighbor <neigh_modify>` list parameter, or writing restart file
+   which can migrate atoms between processors.  LAMMPS has no easy way to
+   check if this has happened, but it is an error to use the *pre no*
+   option in this case.
+
+If *post* is specified as "no", the full timing summary is skipped;
+only a one-line summary timing is printed.
+
+The *every* keyword provides a means of breaking a LAMMPS run into a
+series of shorter runs.  Optionally, one or more LAMMPS commands (c1,
+c2, ..., cN) will be executed in between the short runs.  If used, the
+*every* keyword must be the last keyword, since it has a variable
+number of arguments.  Each of the trailing arguments is a single
+LAMMPS command, and each command should be enclosed in quotes, so that
+the entire command will be treated as a single argument.  This will
+also prevent any variables in the command from being evaluated until
+it is executed multiple times during the run.  Note that if a command
+itself needs one of its arguments quoted (e.g. the :doc:`print <print>`
+command), then you can use a combination of single and double quotes,
+as in the example above or below.
+
+The *every* keyword is a means to avoid listing a long series of runs
+and interleaving commands in your input script.  For example, a
+:doc:`print <print>` command could be invoked or a :doc:`fix <fix>` could
+be redefined, e.g. to reset a thermostat temperature.  Or this could
+be useful for invoking a command you have added to LAMMPS that wraps
+some other code (e.g. as a library) to perform a computation
+periodically during a long LAMMPS run.  See the :doc:`Modify <Modify>`
+doc page for info about how to add new commands to LAMMPS.  See the
+:doc:`Howto couple <Howto_couple>` doc page for ideas about how to
+couple LAMMPS to other codes.
+
+With the *every* option, N total steps are simulated, in shorter runs
+of M steps each.  After each M-length run, the specified commands are
+invoked.  If only a single command is specified as NULL, then no
+command is invoked.  Thus these lines:
+
+
+.. parsed-literal::
+
+   variable q equal x[100]
+   run 6000 every 2000 "print 'Coord = $q'"
+
+are the equivalent of:
+
+
+.. parsed-literal::
+
+   variable q equal x[100]
+   run 2000
+   print "Coord = $q"
+   run 2000
+   print "Coord = $q"
+   run 2000
+   print "Coord = $q"
+
+which does 3 runs of 2000 steps and prints the x-coordinate of a
+particular atom between runs.  Note that the variable "$q" will
+be evaluated afresh each time the print command is executed.
+
+Note that by using the line continuation character "&", the run every
+command can be spread across many lines, though it is still a single
+command:
+
+
+.. parsed-literal::
+
+   run 100000 every 1000 &
+     "print 'Minimum value = $a'" &
+     "print 'Maximum value = $b'" &
+     "print 'Temp = $c'" &
+     "print 'Press = $d'"
+
+If the *pre* and *post* options are set to "no" when used with the
+*every* keyword, then the 1st run will do the full setup and the last
+run will print the full timing summary, but these operations will be
+skipped for intermediate runs.
+
+.. note::
+
+   You might wish to specify a command that exits the run by
+   jumping out of the loop, e.g.
+
+
+.. parsed-literal::
+
+   variable t equal temp
+   run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'"
+
+However, this will not work.  The run command simply executes each
+command one at a time each time it pauses, then continues the run.
+
+Instead, you should use the :doc:`fix halt <fix_halt>` command, which
+has additional options for how to exit the run.
+
+Restrictions
+""""""""""""
+
+
+When not using the *upto* keyword, the number of specified timesteps N
+must fit in a signed 32-bit integer, so you are limited to slightly
+more than 2 billion steps (2\^31) in a single run.  When using *upto*\ ,
+N can be larger than a signed 32-bit integer, however the difference
+between N and the current timestep must still be no larger than
+2\^31 steps.
+
+However, with or without the *upto* keyword, you can perform
+successive runs to run a simulation for any number of steps (ok, up to
+2\^63 total steps).  I.e. the timestep counter within LAMMPS is a
+64-bit signed integer.
+
+Related commands
+""""""""""""""""
+
+:doc:`minimize <minimize>`, :doc:`run\_style <run_style>`,
+:doc:`temper <temper>`, :doc:`fix halt <fix_halt>`
+
+Default
+"""""""
+
+The option defaults are start = the current timestep, stop = current
+timestep + N, pre = yes, and post = yes.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst
new file mode 100644
index 0000000000..5dd51f7f1a
--- /dev/null
+++ b/doc/src/run_style.rst
@@ -0,0 +1,374 @@
+.. index:: run\_style
+
+run\_style command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   run_style style args
+
+* style = *verlet* or *verlet/split* or *respa* or *respa/omp*
+  
+  .. parsed-literal::
+  
+       *verlet* args = none
+       *verlet/split* args = none
+       *respa* args = N n1 n2 ... keyword values ...
+         N = # of levels of rRESPA
+         n1, n2, ... = loop factors between rRESPA levels (N-1 values)
+         zero or more keyword/value pairings may be appended to the loop factors
+         keyword = *bond* or *angle* or *dihedral* or *improper* or
+                   *pair* or *inner* or *middle* or *outer* or *hybrid* or *kspace*
+           *bond* value = M
+             M = which level (1-N) to compute bond forces in
+           *angle* value = M
+             M = which level (1-N) to compute angle forces in
+           *dihedral* value = M
+             M = which level (1-N) to compute dihedral forces in
+           *improper* value = M
+             M = which level (1-N) to compute improper forces in
+           *pair* value = M
+             M = which level (1-N) to compute pair forces in
+           *inner* values = M cut1 cut2
+             M = which level (1-N) to compute pair inner forces in
+             cut1 = inner cutoff between pair inner and
+                    pair middle or outer  (distance units)
+             cut2 = outer cutoff between pair inner and
+                    pair middle or outer  (distance units)
+           *middle* values = M cut1 cut2
+             M = which level (1-N) to compute pair middle forces in
+             cut1 = inner cutoff between pair middle and pair outer (distance units)
+             cut2 = outer cutoff between pair middle and pair outer (distance units)
+           *outer* value = M
+             M = which level (1-N) to compute pair outer forces in
+           *hybrid* values = M1 M2 ... (as many values as there are hybrid sub-styles
+             M1 = which level (1-N) to compute the first pair_style hybrid sub-style in
+             M2 = which level (1-N) to compute the second pair_style hybrid sub-style in
+             M3,etc
+           *kspace* value = M
+             M = which level (1-N) to compute kspace forces in
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   run_style verlet
+   run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
+   run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
+   run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
+
+Description
+"""""""""""
+
+Choose the style of time integrator used for molecular dynamics
+simulations performed by LAMMPS.
+
+The *verlet* style is a standard velocity-Verlet integrator.
+
+
+----------
+
+
+The *verlet/split* style is also a velocity-Verlet integrator, but it
+splits the force calculation within each timestep over 2 partitions of
+processors.  See the :doc:`-partition command-line switch <Run_options>`
+for info on how to run LAMMPS with multiple partitions.
+
+Specifically, this style performs all computation except the
+:doc:`kspace\_style <kspace_style>` portion of the force field on the 1st
+partition.  This include the :doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`, :doc:`neighbor list building <neighbor>`,
+:doc:`fixes <fix>` including time integration, and output.  The
+:doc:`kspace\_style <kspace_style>` portion of the calculation is
+performed on the 2nd partition.
+
+This is most useful for the PPPM kspace\_style when its performance on
+a large number of processors degrades due to the cost of communication
+in its 3d FFTs.  In this scenario, splitting your P total processors
+into 2 subsets of processors, P1 in the 1st partition and P2 in the
+2nd partition, can enable your simulation to run faster.  This is
+because the long-range forces in PPPM can be calculated at the same
+time as pair-wise and bonded forces are being calculated, and the FFTs
+can actually speed up when running on fewer processors.
+
+To use this style, you must define 2 partitions where P1 is a multiple
+of P2.  Typically having P1 be 3x larger than P2 is a good choice.
+The 3d processor layouts in each partition must overlay in the
+following sense.  If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by
+Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly
+for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
+
+Typically the best way to do this is to let the 1st partition choose
+its onn optimal layout, then require the 2nd partition's layout to
+match the integer multiple constraint.  See the
+:doc:`processors <processors>` command with its *part* keyword for a way
+to control this, e.g.
+
+
+.. parsed-literal::
+
+   procssors \* \* \* part 1 2 multiple
+
+You can also use the :doc:`partition <partition>` command to explicitly
+specify the processor layout on each partition.  E.g. for 2 partitions
+of 60 and 15 processors each:
+
+
+.. parsed-literal::
+
+   partition yes 1 processors 3 4 5
+   partition yes 2 processors 3 1 5
+
+When you run in 2-partition mode with the *verlet/split* style, the
+thermodynamic data for the entire simulation will be output to the log
+and screen file of the 1st partition, which are log.lammps.0 and
+screen.0 by default; see the :doc:`-plog and -pscreen command-line switches <Run_options>` to change this.  The log and screen file
+for the 2nd partition will not contain thermodynamic output beyond the
+1st timestep of the run.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for performance
+details of the speed-up offered by the *verlet/split* style.  One
+important performance consideration is the assignment of logical
+processors in the 2 partitions to the physical cores of a parallel
+machine.  The :doc:`processors <processors>` command has options to
+support this, and strategies are discussed in :doc:`Section 5 <Speed>` of the manual.
+
+
+----------
+
+
+The *respa* style implements the rRESPA multi-timescale integrator
+:ref:`(Tuckerman) <Tuckerman3>` with N hierarchical levels, where level 1 is
+the innermost loop (shortest timestep) and level N is the outermost
+loop (largest timestep).  The loop factor arguments specify what the
+looping factor is between levels.  N1 specifies the number of
+iterations of level 1 for a single iteration of level 2, N2 is the
+iterations of level 2 per iteration of level 3, etc.  N-1 looping
+parameters must be specified.
+
+Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors,
+you could choose to have bond interactions computed 8x per large
+timestep, angle interactions computed 4x, pair interactions computed
+2x, and long-range interactions once per large timestep.
+
+The :doc:`timestep <timestep>` command sets the large timestep for the
+outermost rRESPA level.  Thus if the 3 loop factors are "2 2 2" for
+4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the
+inner timestep would be 8x smaller or 0.5 fmsec.  All other LAMMPS
+commands that specify number of timesteps (e.g. :doc:`thermo <thermo>`
+for thermo output every N steps, :doc:`neigh\_modify delay/every <neigh_modify>` parameters, :doc:`dump <dump>` every N
+steps, etc) refer to the outermost timesteps.
+
+The rRESPA keywords enable you to specify at what level of the
+hierarchy various forces will be computed.  If not specified, the
+defaults are that bond forces are computed at level 1 (innermost
+loop), angle forces are computed where bond forces are, dihedral
+forces are computed where angle forces are, improper forces are
+computed where dihedral forces are, pair forces are computed at the
+outermost level, and kspace forces are computed where pair forces are.
+The inner, middle, outer forces have no defaults.
+
+For fixes that support it, the rRESPA level at which a given fix is
+active, can be selected through the :doc:`fix\_modify <fix_modify>` command.
+
+The *inner* and *middle* keywords take additional arguments for
+cutoffs that are used by the pairwise force computations.  If the 2
+cutoffs for *inner* are 5.0 and 6.0, this means that all pairs up to
+6.0 apart are computed by the inner force.  Those between 5.0 and 6.0
+have their force go ramped to 0.0 so the overlap with the next regime
+(middle or outer) is smooth.  The next regime (middle or outer) will
+compute forces for all pairs from 5.0 outward, with those from 5.0 to
+6.0 having their value ramped in an inverse manner.
+
+Note that you can use *inner* and *outer* without using *middle* to
+split the pairwise computations into two portions instead of three.
+Unless you are using a very long pairwise cutoff, a 2-way split is
+often faster than a 3-way split, since it avoids too much duplicate
+computation of pairwise interactions near the intermediate cutoffs.
+
+Also note that only a few pair potentials support the use of the
+*inner* and *middle* and *outer* keywords.  If not, only the *pair*
+keyword can be used with that pair style, meaning all pairwise forces
+are computed at the same rRESPA level.  See the doc pages for
+individual pair styles for details.
+
+Another option for using pair potentials with rRESPA is with the
+*hybrid* keyword, which requires the use of the :doc:`pair\_style hybrid or hybrid/overlay <pair_hybrid>` command.  In this scenario, different
+sub-styles of the hybrid pair style are evaluated at different rRESPA
+levels.  This can be useful, for example, to set different timesteps
+for hybrid coarse-grained/all-atom models.  The *hybrid* keyword
+requires as many level assignments as there are hybrid sub-styles,
+which assigns each sub-style to a rRESPA level, following their order
+of definition in the pair\_style command. Since the *hybrid* keyword
+operates on pair style computations, it is mutually exclusive with
+either the *pair* or the *inner*\ /\ *middle*\ /\ *outer* keywords.
+
+When using rRESPA (or for any MD simulation) care must be taken to
+choose a timestep size(s) that insures the Hamiltonian for the chosen
+ensemble is conserved.  For the constant NVE ensemble, total energy
+must be conserved.  Unfortunately, it is difficult to know *a priori*
+how well energy will be conserved, and a fairly long test simulation
+(~10 ps) is usually necessary in order to verify that no long-term
+drift in energy occurs with the trial set of parameters.
+
+With that caveat, a few rules-of-thumb may be useful in selecting
+*respa* settings.  The following applies mostly to biomolecular
+simulations using the CHARMM or a similar all-atom force field, but
+the concepts are adaptable to other problems.  Without SHAKE, bonds
+involving hydrogen atoms exhibit high-frequency vibrations and require
+a timestep on the order of 0.5 fmsec in order to conserve energy.  The
+relatively inexpensive force computations for the bonds, angles,
+impropers, and dihedrals can be computed on this innermost 0.5 fmsec
+step.  The outermost timestep cannot be greater than 4.0 fmsec without
+risking energy drift.  Smooth switching of forces between the levels
+of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2
+angstrom "healing distance" (the distance between the outer and inner
+cutoffs) works reasonably well.  We thus recommend the following
+settings for use of the *respa* style without SHAKE in biomolecular
+simulations:
+
+
+.. parsed-literal::
+
+   timestep  4.0
+   run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
+
+With these settings, users can expect good energy conservation and
+roughly a 2.5 fold speedup over the *verlet* style with a 0.5 fmsec
+timestep.
+
+If SHAKE is used with the *respa* style, time reversibility is lost,
+but substantially longer time steps can be achieved.  For biomolecular
+simulations using the CHARMM or similar all-atom force field, bonds
+involving hydrogen atoms exhibit high frequency vibrations and require
+a time step on the order of 0.5 fmsec in order to conserve energy.
+These high frequency modes also limit the outer time step sizes since
+the modes are coupled.  It is therefore desirable to use SHAKE with
+respa in order to freeze out these high frequency motions and increase
+the size of the time steps in the respa hierarchy.  The following
+settings can be used for biomolecular simulations with SHAKE and
+rRESPA:
+
+
+.. parsed-literal::
+
+   fix             2 all shake 0.000001 500 0 m 1.0 a 1
+   timestep        4.0
+   run_style       respa 2 2 inner 1 4.0 5.0 outer 2
+
+With these settings, users can expect good energy conservation and
+roughly a 1.5 fold speedup over the *verlet* style with SHAKE and a
+2.0 fmsec timestep.
+
+For non-biomolecular simulations, the *respa* style can be
+advantageous if there is a clear separation of time scales - fast and
+slow modes in the simulation.  For example, a system of slowly-moving
+charged polymer chains could be setup as follows:
+
+
+.. parsed-literal::
+
+   timestep 4.0
+   run_style respa 2 8
+
+This is two-level rRESPA with an 8x difference between the short and
+long timesteps.  The bonds, angles, dihedrals will be computed every
+0.5 fs (assuming real units), while the pair and kspace interactions
+will be computed once every 4 fs.  These are the default settings for
+each kind of interaction, so no additional keywords are necessary.
+
+Even a LJ system can benefit from rRESPA if the interactions are
+divided by the inner, middle and outer keywords.  A 2-fold or more
+speedup can be obtained while maintaining good energy conservation.
+In real units, for a pure LJ fluid at liquid density, with a sigma of
+3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings
+seem to work well:
+
+
+.. parsed-literal::
+
+   timestep  36.0
+   run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
+
+
+----------
+
+
+The *respa/omp* style is a variant of *respa* adapted for use with
+pair, bond, angle, dihedral, improper, or kspace styles with an *omp*
+suffix. It is functionally equivalent to *respa* but performs
+additional operations required for managing *omp* styles.  For more on
+*omp* styles see the :doc:`Speed omp <Speed_omp>` doc page.  Accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
+
+You can specify *respa/omp* explicitly in your input script, or you
+can use the :doc:`-suffix command-line switch <Run_options>` when you
+invoke LAMMPS, or you can use the :doc:`suffix <suffix>` command in your
+input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *verlet/split* style can only be used if LAMMPS was built with the
+REPLICA package. Correspondingly the *respa/omp* style is available
+only if the USER-OMP package was included. See the :doc:`Build package <Build_package>` doc page for more info.
+
+Whenever using rRESPA, the user should experiment with trade-offs in
+speed and accuracy for their system, and verify that they are
+conserving energy to adequate precision.
+
+Related commands
+""""""""""""""""
+
+:doc:`timestep <timestep>`, :doc:`run <run>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   run_style verlet
+
+For run\_style respa, the default assignment of interactions
+to rRESPA levels is as follows:
+
+* bond forces = level 1 (innermost loop)
+* angle forces = same level as bond forces
+* dihedral forces = same level as angle forces
+* improper forces = same level as dihedral forces
+* pair forces = level N (outermost level)
+* kspace forces = same level as pair forces
+* inner, middle, outer forces = no default
+
+
+----------
+
+
+.. _Tuckerman3:
+
+
+
+**(Tuckerman)** Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
+(1992).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/server.rst b/doc/src/server.rst
new file mode 100644
index 0000000000..463a67d356
--- /dev/null
+++ b/doc/src/server.rst
@@ -0,0 +1,81 @@
+.. index:: server
+
+server command
+==============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   server protocol
+
+* protocol = *md* or *mc*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   server md
+
+Description
+"""""""""""
+
+This command starts LAMMPS running in "server" mode, where it receives
+messages from a separate "client" code and responds by sending a reply
+message back to the client.  The specified *protocol* determines the
+format and content of messages LAMMPS expects to receive and how it
+responds.
+
+The :doc:`Howto client/server <Howto_client_server>` doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code.  The server responds to each request with a reply message.  This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code.  The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The *protocol* argument defines the format and content of messages
+that will be exchanged between the two codes.  The current options
+are:
+
+* :doc:`md <server_md>` = run dynamics with another code
+* :doc:`mc <server_mc>` = perform Monte Carlo moves with another code
+
+For protocol *md*\ , LAMMPS can be either a client (via the :doc:`fix client/md <fix_client_md>` command) or server.  See the :doc:`server md <server_md>` doc page for details on the protocol.
+
+For protocol *mc*\ , LAMMPS can be the server.  See the :doc:`server mc <server_mc>` doc page for details on the protocol.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the MESSAGE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+A script that uses this command must also use the
+:doc:`message <message>` command to setup the messaging protocol with
+the other client code.
+
+Related commands
+""""""""""""""""
+
+:doc:`message <message>`, :doc:`fix client/md <fix_client_md>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/server_mc.rst b/doc/src/server_mc.rst
new file mode 100644
index 0000000000..850eceb008
--- /dev/null
+++ b/doc/src/server_mc.rst
@@ -0,0 +1,137 @@
+.. index:: server mc
+
+server mc command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   server mc
+
+mc = the protocol argument to the :doc:`server <server>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   server mc
+
+Description
+"""""""""""
+
+This command starts LAMMPS running in "server" mode, where it will
+expect messages from a separate "client" code that match the *mc*
+protocol for format and content explained below.  For each message
+LAMMPS receives it will send a message back to the client.
+
+The :doc:`Howto client/server <Howto_client_server>` doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code.  The server responds to each request with a reply message.  This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code.  The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The :doc:`server <server>` doc page gives other options for using LAMMPS
+See an example of how this command is used in
+examples/COUPLE/lammps\_mc/in.server.
+
+
+----------
+
+
+When using this command, LAMMPS (as the server code) receives
+instructions from a Monte Carlo (MC) driver to displace random atoms,
+compute the energy before and after displacement, and run dynamics to
+equilibrate the system.
+
+The MC driver performs the random displacements on random atoms,
+accepts or rejects the move in an MC sense, and orchestrates the MD
+runs.
+
+The format and content of the exchanged messages are explained here in
+a conceptual sense.  Python-style pseudo code for the library calls to
+the CSlib is shown, which performs the actual message exchange between
+the two codes.  See the `CSlib website <http://cslib.sandia.gov>`_ doc
+pages for more details on the actual library syntax.  The "cs" object
+in this pseudo code is a pointer to an instance of the CSlib.
+
+See the src/MESSAGE/server\_mc.cpp file for details on how LAMMPS uses
+these messages.  See the examples/COUPLE/lammps\_mc/mc.cpp file for an
+example of how an MC driver code can use these messages.
+
+Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
+
+**Client sends one of these kinds of message**\ :
+
+
+.. parsed-literal::
+
+   cs->send(NATOMS,0)      # msgID = 1 with no fields
+
+   cs->send(EINIT,0)       # msgID = 2 with no fields
+
+   cs->send(DISPLACE,2)    # msgID = 3 with 2 fields
+   cs->pack_int(1,ID)        # 1st field = ID of atom to displace
+   cs->pack(2,3,xnew)      # 2nd field = new xyz coords of displaced atom
+
+   cs->send(ACCEPT,1)      # msgID = 4 with 1 field
+   cs->pack_int(1,flag)    # 1st field = accept/reject flag
+
+   cs->send(RUN,1)         # msgID = 5 with 1 field
+   cs->pack_int(1,nsteps)  # 1st field = # of timesteps to run MD
+
+**Server replies**\ :
+
+
+.. parsed-literal::
+
+   cs->send(NATOMS,1)      # msgID = 1 with 1 field
+   cs->pack_int(1,natoms)  # 1st field = number of atoms
+
+   cs->send(EINIT,2)         # msgID = 2 with 2 fields
+   cs->pack_double(1,poteng) # 1st field = potential energy of system
+   cs->pack(2,3\*natoms,x)    # 2nd field = 3N coords of Natoms
+
+   cs->send(DISPLACE,1)      # msgID = 3 with 1 field
+   cs->pack_double(1,poteng) # 1st field = new potential energy of system
+
+   cs->send(ACCEPT,0)      # msgID = 4 with no fields
+
+   cs->send(RUN,0)         # msgID = 5 with no fields
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the MESSAGE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+A script that uses this command must also use the
+:doc:`message <message>` command to setup the messaging protocol with
+the other client code.
+
+Related commands
+""""""""""""""""
+
+:doc:`message <message>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/server_md.rst b/doc/src/server_md.rst
new file mode 100644
index 0000000000..26fd65a797
--- /dev/null
+++ b/doc/src/server_md.rst
@@ -0,0 +1,174 @@
+.. index:: server md
+
+server md command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   server md
+
+md = the protocol argument to the :doc:`server <server>` command
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   server md
+
+Description
+"""""""""""
+
+This command starts LAMMPS running in "server" mode, where it will
+expect messages from a separate "client" code that match the *md*
+protocol for format and content explained below.  For each message
+LAMMPS receives it will send a message back to the client.
+
+The :doc:`Howto client/server <Howto_client_server>` doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code.  The server responds to each request with a reply message.  This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code.  The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The :doc:`server <server>` doc page gives other options for using LAMMPS
+in server mode.  See an example of how this command is used in
+examples/message/in.message.server.
+
+
+----------
+
+
+When using this command, LAMMPS (as the server code) receives the
+current coordinates of all particles from the client code each
+timestep, computes their interaction, and returns the energy, forces,
+and pressure for the interacting particles to the client code, so it
+can complete the timestep.  This command could also be used with a
+client code that performs energy minimization, using the server to
+compute forces and energy each iteration of its minimizer.
+
+When using the :doc:`fix client/md <fix_client_md>` command, LAMMPS (as
+the client code) does the timestepping and receives needed energy,
+forces, and pressure values from the server code.
+
+The format and content of the exchanged messages are explained here in
+a conceptual sense.  Python-style pseudo code for the library calls to
+the CSlib is shown, which performs the actual message exchange between
+the two codes.  See the `CSlib website <http://cslib.sandia.gov>`_ doc
+pages for more details on the actual library syntax.  The "cs" object
+in this pseudo code is a pointer to an instance of the CSlib.
+
+See the src/MESSAGE/server\_md.cpp and src/MESSAGE/fix\_client\_md.cpp
+files for details on how LAMMPS uses these messages.  See the
+examples/COUPLE/lammps\_vasp/vasp\_wrapper.py file for an example of how
+a quantum code (VASP) can use these messages.
+
+The following pseudo-code uses these values, defined as enums.
+
+Define:
+
+
+.. parsed-literal::
+
+   SETUP=1, STEP=2
+   DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10
+   FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4
+
+**Client sends 2 kinds of messages**\ :
+
+
+.. parsed-literal::
+
+   # required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
+   # optional fields: UNITS, CHARGE
+
+   cs->send(SETUP,nfields)        # msgID with nfields
+
+   cs->pack_int(DIM,dim)          # dimension (2,3) of simulation
+   cs->pack(PERIODICITY,3,xyz)    # periodicity flags in 3 dims
+   cs->pack(ORIGIN,3,origin)      # lower-left corner of simulation box
+   cs->pack(BOX,9,box)            # 3 edge vectors of simulation box
+   cs->pack_int(NATOMS,natoms)    # total number of atoms
+   cs->pack_int(NTYPES,ntypes)    # number of atom types
+   cs->pack(TYPES,natoms,type)    # vector of per-atom types
+   cs->pack(COORDS,3\*natoms,x)    # vector of 3N atom coords
+   cs->pack_string(UNITS,units)   # units = "lj", "real", "metal", etc
+   cs->pack(CHARGE,natoms,q)      # vector of per-atom charge
+
+   # required fields: COORDS
+   # optional fields: ORIGIN, BOX
+
+   cs->send(STEP,nfields)         # msgID with nfields
+
+   cs->pack(COORDS,3\*natoms,x)    # vector of 3N atom coords
+   cs->pack(ORIGIN,3,origin)      # lower-left corner of simulation box
+   cs->pack(BOX,9,box)            # 3 edge vectors of simulation box
+
+**Server replies to either kind of message**\ :
+
+
+.. parsed-literal::
+
+   # required fields: FORCES, ENERGY, PRESSURE
+   # optional fields: ERROR
+
+   cs->send(msgID,nfields)      # msgID with nfields
+   cs->pack(FORCES,3\*Natoms,f)  # vector of 3N forces on atoms
+   cs->pack(ENERGY,1,poteng)    # total potential energy of system
+   cs->pack(PRESSURE,6,press)   # global pressure tensor (6-vector)
+   cs->pack_int(ERROR,flag)     # server had an error (e.g. DFT non-convergence)
+
+
+----------
+
+
+The units for various quantities that are sent and received iva
+messages are defined for atomic-scale simulations in the table below.
+The client and server codes (including LAMMPS) can use internal units
+different than these (e.g. :doc:`real units <units>` in LAMMPS), so long
+as they convert to these units for messaging.
+
+* COORDS, ORIGIN, BOX = Angstroms
+* CHARGE = multiple of electron charge (1.0 is a proton)
+* ENERGY = eV
+* FORCES = eV/Angstrom
+* PRESSURE = bars
+
+Note that these are :doc:`metal units <units>` in LAMMPS.
+
+If you wish to run LAMMPS in another its non-atomic units, e.g. :doc:`lj units <units>`, then the client and server should exchange a UNITS
+message as indicated above, and both the client and server should
+agree on the units for the data they exchange.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command is part of the MESSAGE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`message <message>`, :doc:`fix client/md <fix_client_md>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/set.rst b/doc/src/set.rst
new file mode 100644
index 0000000000..7a9bb4662c
--- /dev/null
+++ b/doc/src/set.rst
@@ -0,0 +1,491 @@
+.. index:: set
+
+set command
+===========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   set style ID keyword values ...
+
+* style = *atom* or *type* or *mol* or *group* or *region*
+* ID = atom ID range or type range or mol ID range or group ID or region ID
+* one or more keyword/value pairs may be appended
+* keyword = *type* or *type/fraction* or *mol* or *x* or *y* or *z* or           *charge* or *dipole* or *dipole/random* or *quat* or           *spin* or *spin/random* or *quat* or           *quat/random* or *diameter* or *shape* or           *length* or *tri* or *theta* or *theta/random* or           *angmom* or *omega* or           *mass* or *density* or *density/disc* or *volume* or *image* or           *bond* or *angle* or *dihedral* or *improper* or           *meso/e* or *meso/cv* or *meso/rho* or           *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or           *edpd/temp* or *edpd/cv* or *cc* or *i\_name* or *d\_name*
+  
+  .. parsed-literal::
+  
+       *type* value = atom type
+         value can be an atom-style variable (see below)
+       *type/fraction* values = type fraction seed
+         type = new atom type
+         fraction = fraction of selected atoms to set to new atom type
+         seed = random # seed (positive integer)
+       *mol* value = molecule ID
+         value can be an atom-style variable (see below)
+       *x*\ ,\ *y*\ ,\ *z* value = atom coordinate (distance units)
+         value can be an atom-style variable (see below)
+       *vx*\ ,\ *vy*\ ,\ *vz* value = atom velocity (velocity units)
+         value can be an atom-style variable (see below)
+       *charge* value = atomic charge (charge units)
+         value can be an atom-style variable (see below)
+       *dipole* values = x y z
+         x,y,z = orientation of dipole moment vector
+         any of x,y,z can be an atom-style variable (see below)
+       *dipole/random* value = seed Dlen
+         seed = random # seed (positive integer) for dipole moment orientations
+         Dlen = magnitude of dipole moment (dipole units)
+       *spin* values = g x y z
+         g = magnitude of magnetic spin vector (in Bohr magneton's unit)
+         x,y,z = orientation of magnetic spin vector
+         any of x,y,z can be an atom-style variable (see below)
+       *spin/random* value = seed Dlen
+         seed = random # seed (positive integer) for magnetic spin orientations
+         Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit)
+       *quat* values = a b c theta
+         a,b,c = unit vector to rotate particle around via right-hand rule
+         theta = rotation angle (degrees)
+         any of a,b,c,theta can be an atom-style variable (see below)
+       *quat/random* value = seed
+         seed = random # seed (positive integer) for quaternion orientations
+       *diameter* value = diameter of spherical particle (distance units)
+         value can be an atom-style variable (see below)
+       *shape* value = Sx Sy Sz
+         Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
+       *length* value = len
+         len = length of line segment (distance units)
+         len can be an atom-style variable (see below)
+       *tri* value = side
+         side = side length of equilateral triangle (distance units)
+         side can be an atom-style variable (see below)
+       *theta* value = angle (degrees)
+         angle = orientation of line segment with respect to x-axis
+         angle can be an atom-style variable (see below)
+       *theta/random* value = seed
+         seed = random # seed (positive integer) for line segment orienations
+       *angmom* values = Lx Ly Lz
+         Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
+         any of Lx,Ly,Lz can be an atom-style variable (see below)
+       *omega* values = Wx Wy Wz
+         Wx,Wy,Wz = components of angular velocity vector (radians/time units)
+         any of wx,wy,wz can be an atom-style variable (see below)
+       *mass* value = per-atom mass (mass units)
+         value can be an atom-style variable (see below)
+       *density* value = particle density for a sphere or ellipsoid (mass/distance\^3 units), or for a triangle (mass/distance\^2 units) or line (mass/distance units) particle
+         value can be an atom-style variable (see below)
+       *density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
+         value can be an atom-style variable (see below)
+       *volume* value = particle volume for Peridynamic particle (distance\^3 units)
+         value can be an atom-style variable (see below)
+       *image* nx ny nz
+         nx,ny,nz = which periodic image of the simulation box the atom is in
+         any of nx,ny,nz can be an atom-style variable (see below)
+       *bond* value = bond type for all bonds between selected atoms
+       *angle* value = angle type for all angles between selected atoms
+       *dihedral* value = dihedral type for all dihedrals between selected atoms
+       *improper* value = improper type for all impropers between selected atoms
+       *meso/e* value = energy of SPH particles (need units)
+         value can be an atom-style variable (see below)
+       *meso/cv* value = heat capacity of SPH particles (need units)
+         value can be an atom-style variable (see below)
+       *meso/rho* value = density of SPH particles (need units)
+         value can be an atom-style variable (see below)
+       *smd/contact/radius* = radius for short range interactions, i.e. contact and friction
+         value can be an atom-style variable (see below)
+       *smd/mass/density* = set particle mass based on volume by providing a mass density
+         value can be an atom-style variable (see below)
+       *dpd/theta* value = internal temperature of DPD particles (temperature units)
+         value can be an atom-style variable (see below)
+         value can be NULL which sets internal temp of each particle to KE temp
+       *edpd/temp* value = temperature of eDPD particles (temperature units)
+         value can be an atom-style variable (see below)
+       *edpd/cv* value = volumetric heat capacity of eDPD particles (energy/temperature/volume units)
+         value can be an atom-style variable (see below)
+       *cc* values = index cc
+         index = index of a chemical species (1 to Nspecies)
+         cc = chemical concentration of tDPD particles for a species (mole/volume units)
+       *i_name* value = value for custom integer vector with name
+       *d_name* value = value for custom floating-point vector with name
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   set group solvent type 2
+   set group solvent type/fraction 2 0.5 12393
+   set group edge bond 4
+   set region half charge 0.5
+   set type 3 charge 0.5
+   set type 1\*3 charge 0.5
+   set atom \* charge v_atomfile
+   set atom 100\*200 x 0.5 y 1.0
+   set atom 100 vx 0.0 vy 0.0 vz -1.0
+   set atom 1492 type 3
+
+Description
+"""""""""""
+
+Set one or more properties of one or more atoms.  Since atom
+properties are initially assigned by the :doc:`read\_data <read_data>`,
+:doc:`read\_restart <read_restart>` or :doc:`create\_atoms <create_atoms>`
+commands, this command changes those assignments.  This can be useful
+for overriding the default values assigned by the
+:doc:`create\_atoms <create_atoms>` command (e.g. charge = 0.0).  It can
+be useful for altering pairwise and molecular force interactions,
+since force-field coefficients are defined in terms of types.  It can
+be used to change the labeling of atoms by atom type or molecule ID
+when they are output in :doc:`dump <dump>` files.  It can also be useful
+for debugging purposes; i.e. positioning an atom at a precise location
+to compute subsequent forces or energy.
+
+Note that the *style* and *ID* arguments determine which atoms have
+their properties reset.  The remaining keywords specify which
+properties to reset and what the new values are.  Some strings like
+*type* or *mol* can be used as a style and/or a keyword.
+
+
+----------
+
+
+This section describes how to select which atoms to change
+the properties of, via the *style* and *ID* arguments.
+
+The style *atom* selects all the atoms in a range of atom IDs.  The
+style *type* selects all the atoms in a range of types.  The style
+*mol* selects all the atoms in a range of molecule IDs.
+
+In each of the range cases, the range can be specified as a single
+numeric value, or a wildcard asterisk can be used to specify a range
+of values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  For
+example, for the style *type*\ , if N = the number of atom types, then
+an asterisk with no numeric values means all types from 1 to N.  A
+leading asterisk means all types from 1 to n (inclusive).  A trailing
+asterisk means all types from n to N (inclusive).  A middle asterisk
+means all types from m to n (inclusive).  For all the styles except
+*mol*\ , the lowest value for the wildcard is 1; for *mol* it is 0.
+
+The style *group* selects all the atoms in the specified group.  The
+style *region* selects all the atoms in the specified geometric
+region.  See the :doc:`group <group>` and :doc:`region <region>` commands
+for details of how to specify a group or region.
+
+
+----------
+
+
+This section describes the keyword options for which properties to
+change, for the selected atoms.
+
+Note that except where explicitly prohibited below, all of the
+keywords allow an :doc:`atom-style or atomfile-style variable <variable>` to be used as the specified value(s).  If the
+value is a variable, it should be specified as v\_name, where name is
+the variable name.  In this case, the variable will be evaluated, and
+its resulting per-atom value used to determine the value assigned to
+each selected atom.  Note that the per-atom value from the variable
+will be ignored for atoms that are not selected via the *style* and
+*ID* settings explained above.  A simple way to use per-atom values
+from the variable to reset a property for all atoms is to use style
+*atom* with *ID* = "\*"; this selects all atom IDs.
+
+Atom-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  They can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a time-dependent or
+spatially-dependent set of per-atom values.  As explained on the
+:doc:`variable <variable>` doc page, atomfile-style variables can be
+used in place of atom-style variables, and thus as arguments to the
+set command.  Atomfile-style variables read their per-atoms values
+from a file.
+
+.. note::
+
+   Atom-style and atomfile-style variables return floating point
+   per-atom values.  If the values are assigned to an integer variable,
+   such as the molecule ID, then the floating point value is truncated to
+   its integer portion, e.g. a value of 2.6 would become 2.
+
+Keyword *type* sets the atom type for all selected atoms.  The
+specified value must be from 1 to ntypes, where ntypes was set by the
+:doc:`create\_box <create_box>` command or the *atom types* field in the
+header of the data file read by the :doc:`read\_data <read_data>`
+command.
+
+Keyword *type/fraction* sets the atom type for a fraction of the
+selected atoms.  The actual number of atoms changed is not guaranteed
+to be exactly the requested fraction, but should be statistically
+close.  Random numbers are used in such a way that a particular atom
+is changed or not changed, regardless of how many processors are being
+used.  This keyword does not allow use of an atom-style variable.
+
+Keyword *mol* sets the molecule ID for all selected atoms.  The :doc:`atom style <atom_style>` being used must support the use of molecule
+IDs.
+
+Keywords *x*\ , *y*\ , *z*\ , and *charge* set the coordinates or charge of
+all selected atoms.  For *charge*\ , the :doc:`atom style <atom_style>`
+being used must support the use of atomic charge. Keywords *vx*\ , *vy*\ ,
+and *vz* set the velocities of all selected atoms.
+
+Keyword *dipole* uses the specified x,y,z values as components of a
+vector to set as the orientation of the dipole moment vectors of the
+selected atoms.  The magnitude of the dipole moment is set
+by the length of this orientation vector.
+
+Keyword *dipole/random* randomizes the orientation of the dipole
+moment vectors for the selected atoms and sets the magnitude of each
+to the specified *Dlen* value.  For 2d systems, the z component of the
+orientation is set to 0.0.  Random numbers are used in such a way that
+the orientation of a particular atom is the same, regardless of how
+many processors are being used.  This keyword does not allow use of an
+atom-style variable.
+
+Keyword *spin* uses the specified g value to set the magnitude of the
+magnetic spin vectors, and the x,y,z values as components of a vector
+to set as the orientation of the magnetic spin vectors of the selected
+atoms.
+
+Keyword *spin/random* randomizes the orientation of the magnetic spin
+vectors for the selected atoms and sets the magnitude of each to the
+specified *Dlen* value.
+
+Keyword *quat* uses the specified values to create a quaternion
+(4-vector) that represents the orientation of the selected atoms.  The
+particles must define a quaternion for their orientation
+(e.g. ellipsoids, triangles, body particles) as defined by the
+:doc:`atom\_style <atom_style>` command.  Note that particles defined by
+:doc:`atom\_style ellipsoid <atom_style>` have 3 shape parameters.  The 3
+values must be non-zero for each particle set by this command.  They
+are used to specify the aspect ratios of an ellipsoidal particle,
+which is oriented by default with its x-axis along the simulation
+box's x-axis, and similarly for y and z.  If this body is rotated (via
+the right-hand rule) by an angle theta around a unit rotation vector
+(a,b,c), then the quaternion that represents its new orientation is
+given by (cos(theta/2), a\*sin(theta/2), b\*sin(theta/2),
+c\*sin(theta/2)).  The theta and a,b,c values are the arguments to the
+*quat* keyword.  LAMMPS normalizes the quaternion in case (a,b,c) was
+not specified as a unit vector.  For 2d systems, the a,b,c values are
+ignored, since a rotation vector of (0,0,1) is the only valid choice.
+
+Keyword *quat/random* randomizes the orientation of the quaternion for
+the selected atoms.  The particles must define a quaternion for their
+orientation (e.g. ellipsoids, triangles, body particles) as defined by
+the :doc:`atom\_style <atom_style>` command.  Random numbers are used in
+such a way that the orientation of a particular atom is the same,
+regardless of how many processors are being used.  For 2d systems,
+only orientations in the xy plane are generated.  As with keyword
+*quat*\ , for ellipsoidal particles, the 3 shape values must be non-zero
+for each particle set by this command.  This keyword does not allow
+use of an atom-style variable.
+
+Keyword *diameter* sets the size of the selected atoms.  The particles
+must be finite-size spheres as defined by the :doc:`atom\_style sphere <atom_style>` command.  The diameter of a particle can be
+set to 0.0, which means they will be treated as point particles.  Note
+that this command does not adjust the particle mass, even if it was
+defined with a density, e.g. via the :doc:`read\_data <read_data>`
+command.
+
+Keyword *shape* sets the size and shape of the selected atoms.  The
+particles must be ellipsoids as defined by the :doc:`atom\_style ellipsoid <atom_style>` command.  The *Sx*\ , *Sy*\ , *Sz* settings are
+the 3 diameters of the ellipsoid in each direction.  All 3 can be set
+to the same value, which means the ellipsoid is effectively a sphere.
+They can also all be set to 0.0 which means the particle will be
+treated as a point particle.  Note that this command does not adjust
+the particle mass, even if it was defined with a density, e.g. via the
+:doc:`read\_data <read_data>` command.
+
+Keyword *length* sets the length of selected atoms.  The particles
+must be line segments as defined by the :doc:`atom\_style line <atom_style>` command.  If the specified value is non-zero the
+line segment is (re)set to a length = the specified value, centered
+around the particle position, with an orientation along the x-axis.
+If the specified value is 0.0, the particle will become a point
+particle.  Note that this command does not adjust the particle mass,
+even if it was defined with a density, e.g. via the
+:doc:`read\_data <read_data>` command.
+
+Keyword *tri* sets the size of selected atoms.  The particles must be
+triangles as defined by the :doc:`atom\_style tri <atom_style>` command.
+If the specified value is non-zero the triangle is (re)set to be an
+equilateral triangle in the xy plane with side length = the specified
+value, with a centroid at the particle position, with its base
+parallel to the x axis, and the y-axis running from the center of the
+base to the top point of the triangle.  If the specified value is 0.0,
+the particle will become a point particle.  Note that this command
+does not adjust the particle mass, even if it was defined with a
+density, e.g. via the :doc:`read\_data <read_data>` command.
+
+Keyword *theta* sets the orientation of selected atoms.  The particles
+must be line segments as defined by the :doc:`atom\_style line <atom_style>` command.  The specified value is used to set the
+orientation angle of the line segments with respect to the x axis.
+
+Keyword *theta/random* randomizes the orientation of theta for the
+selected atoms.  The particles must be line segments as defined by the
+:doc:`atom\_style line <atom_style>` command.  Random numbers are used in
+such a way that the orientation of a particular atom is the same,
+regardless of how many processors are being used.  This keyword does
+not allow use of an atom-style variable.
+
+Keyword *angmom* sets the angular momentum of selected atoms.  The
+particles must be ellipsoids as defined by the :doc:`atom\_style ellipsoid <atom_style>` command or triangles as defined by the
+:doc:`atom\_style tri <atom_style>` command.  The angular momentum vector
+of the particles is set to the 3 specified components.
+
+Keyword *omega* sets the angular velocity of selected atoms.  The
+particles must be spheres as defined by the "atom\_style sphere"_
+atom\_style.html command.  The angular velocity vector of the particles
+is set to the 3 specified components.
+
+Keyword *mass* sets the mass of all selected particles.  The particles
+must have a per-atom mass attribute, as defined by the
+:doc:`atom\_style <atom_style>` command.  See the "mass" command for how
+to set mass values on a per-type basis.
+
+Keyword *density* or *density/disc* also sets the mass of all selected
+particles, but in a different way.  The particles must have a per-atom
+mass attribute, as defined by the :doc:`atom\_style <atom_style>`
+command.  If the atom has a radius attribute (see :doc:`atom\_style sphere <atom_style>`) and its radius is non-zero, its mass is set
+from the density and particle volume for 3d systems (the input density
+is assumed to be in mass/distance\^3 units).  For 2d, the default is
+for LAMMPS to model particles with a radius attribute as spheres.
+However, if the *density/disc* keyword is used, then they can be
+modeled as 2d discs (circles).  Their mass is set from the density and
+particle area (the input density is assumed to be in mass/distance\^2
+units).
+
+If the atom has a shape attribute (see :doc:`atom\_style ellipsoid <atom_style>`) and its 3 shape parameters are non-zero,
+then its mass is set from the density and particle volume (the input
+density is assumed to be in mass/distance\^3 units).  The
+*density/disc* keyword has no effect; it does not (yet) treat 3d
+ellipsoids as 2d ellipses.
+
+If the atom has a length attribute (see :doc:`atom\_style line <atom_style>`) and its length is non-zero, then its mass is
+set from the density and line segment length (the input density is
+assumed to be in mass/distance units).  If the atom has an area
+attribute (see :doc:`atom\_style tri <atom_style>`) and its area is
+non-zero, then its mass is set from the density and triangle area (the
+input density is assumed to be in mass/distance\^2 units).
+
+If none of these cases are valid, then the mass is set to the density
+value directly (the input density is assumed to be in mass units).
+
+Keyword *volume* sets the volume of all selected particles.
+Currently, only the :doc:`atom\_style peri <atom_style>` command defines
+particles with a volume attribute.  Note that this command does not
+adjust the particle mass.
+
+Keyword *image* sets which image of the simulation box the atom is
+considered to be in.  An image of 0 means it is inside the box as
+defined.  A value of 2 means add 2 box lengths to get the true value.
+A value of -1 means subtract 1 box length to get the true value.
+LAMMPS updates these flags as atoms cross periodic boundaries during
+the simulation.  The flags can be output with atom snapshots via the
+:doc:`dump <dump>` command.  If a value of NULL is specified for any of
+nx,ny,nz, then the current image value for that dimension is unchanged.
+For non-periodic dimensions only a value of 0 can be specified.
+This command can be useful after a system has been equilibrated and
+atoms have diffused one or more box lengths in various directions.
+This command can then reset the image values for atoms so that they
+are effectively inside the simulation box, e.g if a diffusion
+coefficient is about to be measured via the :doc:`compute msd <compute_msd>` command.  Care should be taken not to reset the
+image flags of two atoms in a bond to the same value if the bond
+straddles a periodic boundary (rather they should be different by +/-
+1).  This will not affect the dynamics of a simulation, but may mess
+up analysis of the trajectories if a LAMMPS diagnostic or your own
+analysis relies on the image flags to unwrap a molecule which
+straddles the periodic box.
+
+Keywords *bond*\ , *angle*\ , *dihedral*\ , and *improper*\ , set the bond
+type (angle type, etc) of all bonds (angles, etc) of selected atoms to
+the specified value from 1 to nbondtypes (nangletypes, etc).  All
+atoms in a particular bond (angle, etc) must be selected atoms in
+order for the change to be made.  The value of nbondtype (nangletypes,
+etc) was set by the *bond types* (\ *angle types*\ , etc) field in the
+header of the data file read by the :doc:`read\_data <read_data>`
+command.  These keywords do not allow use of an atom-style variable.
+
+Keywords *meso/e*\ , *meso/cv*\ , and *meso/rho* set the energy, heat
+capacity, and density of smoothed particle hydrodynamics (SPH)
+particles.  See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to
+using SPH in LAMMPS.
+
+Keyword *smd/mass/density* sets the mass of all selected particles,
+but it is only applicable to the Smooth Mach Dynamics package
+USER-SMD.  It assumes that the particle volume has already been
+correctly set and calculates particle mass from the provided mass
+density value.
+
+Keyword *smd/contact/radius* only applies to simulations with the
+Smooth Mach Dynamics package USER-SMD.  Itsets an interaction radius
+for computing short-range interactions, e.g. repulsive forces to
+prevent different individual physical bodies from penetrating each
+other. Note that the SPH smoothing kernel diameter used for computing
+long range, nonlocal interactions, is set using the *diameter*
+keyword.
+
+Keyword *dpd/theta* sets the internal temperature of a DPD particle as
+defined by the USER-DPD package.  If the specified value is a number
+it must be >= 0.0.  If the specified value is NULL, then the kinetic
+temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2
+m v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz).  Each particle's internal
+temperature is set to Tkin.  If the specified value is an atom-style
+variable, then the variable is evaluated for each particle.  If a
+value >= 0.0, the internal temperature is set to that value.  If it is
+< 0.0, the computation of Tkin is performed and the internal
+temperature is set to that value.
+
+Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric
+heat capacity of an eDPD particle as defined by the USER-MESO package.
+Currently, only :doc:`atom\_style edpd <atom_style>` defines particles
+with these attributes. The values for the temperature and heat
+capacity must be positive.
+
+Keyword *cc* sets the chemical concentration of a tDPD particle for a
+specified species as defined by the USER-MESO package. Currently, only
+:doc:`atom\_style tdpd <atom_style>` defines particles with this
+attribute. An integer for "index" selects a chemical species (1 to
+Nspecies) where Nspecies is set by the atom\_style command. The value
+for the chemical concentration must be >= 0.0.
+
+Keywords *i\_name* and *d\_name* refer to custom integer and
+floating-point properties that have been added to each atom via the
+:doc:`fix property/atom <fix_property_atom>` command.  When that command
+is used specific names are given to each attribute which are what is
+specified as the "name" portion of *i\_name* or *d\_name*.
+
+Restrictions
+""""""""""""
+
+
+You cannot set an atom attribute (e.g. *mol* or *q* or *volume*\ ) if
+the :doc:`atom\_style <atom_style>` does not have that attribute.
+
+This command requires inter-processor communication to coordinate the
+setting of bond types (angle types, etc).  This means that your system
+must be ready to perform a simulation before using one of these
+keywords (force fields set, atom mass set, etc).  This is not
+necessary for other keywords.
+
+Using the *region* style with the bond (angle, etc) keywords can give
+unpredictable results if there are bonds (angles, etc) that straddle
+periodic boundaries.  This is because the region may only extend up to
+the boundary and partner atoms in the bond (angle, etc) may have
+coordinates outside the simulation box if they are ghost atoms.
+
+Related commands
+""""""""""""""""
+
+:doc:`create\_box <create_box>`, :doc:`create\_atoms <create_atoms>`,
+:doc:`read\_data <read_data>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/shell.rst b/doc/src/shell.rst
new file mode 100644
index 0000000000..59ff9e42fb
--- /dev/null
+++ b/doc/src/shell.rst
@@ -0,0 +1,128 @@
+.. index:: shell
+
+shell command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   shell cmd args
+
+* cmd = *cd* or *mkdir* or *mv* or *rm* or *rmdir* or *putenv* or arbitrary command
+  
+  .. parsed-literal::
+  
+       *cd* arg = dir
+         dir = directory to change to
+       *mkdir* args = dir1 dir2 ...
+         dir1,dir2 = one or more directories to create
+       *mv* args = old new
+         old = old filename
+         new = new filename
+       *rm* args = file1 file2 ...
+         file1,file2 = one or more filenames to delete
+       *rmdir* args = dir1 dir2 ...
+         dir1,dir2 = one or more directories to delete
+       *putenv* args = var1=value1 var2=value2
+         var=value = one of more definitions of environment variables
+       anything else is passed as a command to the shell for direct execution
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   shell cd sub1
+   shell cd ..
+   shell mkdir tmp1 tmp2 tmp3
+   shell rmdir tmp1
+   shell mv log.lammps hold/log.1
+   shell rm TMP/file1 TMP/file2
+   shell putenv LAMMPS_POTENTIALS=../../potentials
+   shell my_setup file1 10 file2
+   shell my_post_process 100 dump.out
+
+Description
+"""""""""""
+
+Execute a shell command.  A few simple file-based shell commands are
+supported directly, in Unix-style syntax.  Any command not listed
+above is passed as-is to the C-library system() call, which invokes
+the command in a shell.
+
+This is means to invoke other commands from your input script.  For
+example, you can move files around in preparation for the next section
+of the input script.  Or you can run a program that pre-processes data
+for input into LAMMPS.  Or you can run a program that post-processes
+LAMMPS output data.
+
+With the exception of *cd*\ , all commands, including ones invoked via a
+system() call, are executed by only a single processor, so that
+files/directories are not being manipulated by multiple processors.
+
+The *cd* cmd executes the Unix "cd" command to change the working
+directory.  All subsequent LAMMPS commands that read/write files will
+use the new directory.  All processors execute this command.
+
+The *mkdir* cmd executes the Unix "mkdir" command to create one or
+more directories.
+
+The *mv* cmd executes the Unix "mv" command to rename a file and/or
+move it to a new directory.
+
+The *rm* cmd executes the Unix "rm" command to remove one or more
+files.
+
+The *rmdir* cmd executes the Unix "rmdir" command to remove one or
+more directories.  A directory must be empty to be successfully
+removed.
+
+The *putenv* cmd defines or updates an environment variable directly.
+Since this command does not pass through the shell, no shell variable
+expansion or globbing is performed, only the usual substitution for
+LAMMPS variables defined with the :doc:`variable <variable>` command is
+performed.  The resulting string is then used literally.
+
+Any other cmd is passed as-is to the shell along with its arguments as
+one string, invoked by the C-library system() call.  For example,
+these lines in your input script:
+
+
+.. parsed-literal::
+
+   variable n equal 10
+   variable foo string file2
+   shell my_setup file1 $n ${foo}
+
+would be the same as invoking
+
+
+.. parsed-literal::
+
+   % my_setup file1 10 file2
+
+from a command-line prompt.  The executable program "my\_setup" is run
+with 3 arguments: file1 10 file2.
+
+Restrictions
+""""""""""""
+
+
+LAMMPS does not detect errors or print warnings when any of these
+commands execute.  E.g. if the specified directory does not exist,
+executing the *cd* command will silently do nothing.
+
+**Related commands:** none
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst
new file mode 100644
index 0000000000..1e30dc2761
--- /dev/null
+++ b/doc/src/special_bonds.rst
@@ -0,0 +1,300 @@
+.. index:: special\_bonds
+
+special\_bonds command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   special_bonds keyword values ...
+
+* one or more keyword/value pairs may be appended
+* keyword = *amber* or *charmm* or *dreiding* or *fene* or *lj/coul* or *lj* or *coul* or *angle* or *dihedral*
+  
+  .. parsed-literal::
+  
+       *amber* values = none
+       *charmm* values = none
+       *dreiding* values = none
+       *fene* values = none
+       *lj/coul* values = w1,w2,w3
+         w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
+       *lj* values = w1,w2,w3
+         w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
+       *coul* values = w1,w2,w3
+         w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
+       *angle* value = *yes* or *no*
+       *dihedral* value = *yes* or *no*
+
+
+
+Examples:
+
+
+.. parsed-literal::
+
+   special_bonds amber
+   special_bonds charmm
+   special_bonds fene dihedral no
+   special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
+   special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
+
+Description
+"""""""""""
+
+Set weighting coefficients for pairwise energy and force contributions
+between pairs of atoms that are also permanently bonded to each other,
+either directly or via one or two intermediate bonds.  These weighting
+factors are used by nearly all :doc:`pair styles <pair_style>` in LAMMPS
+that compute simple pairwise interactions.  Permanent bonds between
+atoms are specified by defining the bond topology in the data file
+read by the :doc:`read\_data <read_data>` command.  Typically a
+:doc:`bond\_style <bond_style>` command is also used to define a bond
+potential.  The rationale for using these weighting factors is that
+the interaction between a pair of bonded atoms is all (or mostly)
+specified by the bond, angle, dihedral potentials, and thus the
+non-bonded Lennard-Jones or Coulombic interaction between the pair of
+atoms should be excluded (or reduced by a weighting factor).
+
+.. note::
+
+   These weighting factors are NOT used by :doc:`pair styles <pair_style>` that compute many-body interactions, since the
+   "bonds" that result from such interactions are not permanent, but are
+   created and broken dynamically as atom conformations change.  Examples
+   of pair styles in this category are EAM, MEAM, Stillinger-Weber,
+   Tersoff, COMB, AIREBO, and ReaxFF.  In fact, it generally makes no
+   sense to define permanent bonds between atoms that interact via these
+   potentials, though such bonds may exist elsewhere in your system,
+   e.g. when using the :doc:`pair\_style hybrid <pair_hybrid>` command.
+   Thus LAMMPS ignores special\_bonds settings when many-body potentials
+   are calculated.  Please note, that the existence of explicit bonds
+   for atoms that are described by a many-body potential will alter the
+   neighbor list and thus can render the computation of those interactions
+   invalid, since those pairs are not only used to determine direct
+   pairwise interactions but also neighbors of neighbors and more.
+   The recommended course of action is to remove such bonds, or - if
+   that is not possible - use a special bonds setting of 1.0 1.0 1.0.
+
+.. note::
+
+   Unlike some commands in LAMMPS, you cannot use this command
+   multiple times in an incremental fashion: e.g. to first set the LJ
+   settings and then the Coulombic ones.  Each time you use this command
+   it sets all the coefficients to default values and only overrides the
+   one you specify, so you should set all the options you need each time
+   you use it.  See more details at the bottom of this page.
+
+The Coulomb factors are applied to any Coulomb (charge interaction)
+term that the potential calculates.  The LJ factors are applied to the
+remaining terms that the potential calculates, whether they represent
+LJ interactions or not.  The weighting factors are a scaling
+pre-factor on the energy and force between the pair of atoms.  A value
+of 1.0 means include the full interaction; a value of 0.0 means
+exclude it completely.
+
+The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
+factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
+each other.  The 2nd coefficient is the weighting factor on 1-3 atom
+pairs which are those separated by 2 bonds (e.g. the two H atoms in a
+water molecule).  The 3rd coefficient is the weighting factor on 1-4
+atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
+atoms in a dihedral interaction).  Thus if the 1-2 coefficient is set
+to 0.0, then the pairwise interaction is effectively turned off for
+all pairs of atoms bonded to each other.  If it is set to 1.0, then
+that interaction will be at full strength.
+
+.. note::
+
+   For purposes of computing weighted pairwise interactions, 1-3
+   and 1-4 interactions are not defined from the list of angles or
+   dihedrals used by the simulation.  Rather, they are inferred
+   topologically from the set of bonds specified when the simulation is
+   defined from a data or restart file (see :doc:`read\_data <read_data>` or
+   :doc:`read\_restart <read_restart>` commands).  Thus the set of
+   1-2,1-3,1-4 interactions that the weights apply to is the same whether
+   angle and dihedral potentials are computed or not, and remains the
+   same even if bonds are constrained, or turned off, or removed during a
+   simulation.
+
+The two exceptions to this rule are (a) if the *angle* or *dihedral*
+keywords are set to *yes* (see below), or (b) if the
+:doc:`delete\_bonds <delete_bonds>` command is used with the *special*
+option that re-computes the 1-2,1-3,1-4 topologies after bonds are
+deleted; see the :doc:`delete\_bonds <delete_bonds>` command for more
+details.
+
+The *amber* keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
+interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
+is the default for a commonly used version of the AMBER force field,
+where the last value is really 5/6.  See :ref:`(Cornell) <Cornell>` for a
+description of the AMBER force field.
+
+The *charmm* keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
+LJ and Coulombic interactions, which is the default for a commonly
+used version of the CHARMM force field.  Note that in pair styles
+*lj/charmm/coul/charmm* and *lj/charmm/coul/long* the 1-4 coefficients
+are defined explicitly, and these pairwise contributions are computed
+as part of the charmm dihedral style - see the
+:doc:`pair\_coeff <pair_coeff>` and :doc:`dihedral\_style <dihedral_style>`
+commands for more information.  See :ref:`(MacKerell) <MacKerell>` for a
+description of the CHARMM force field.
+
+The *dreiding* keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
+LJ and Coulombic interactions, which is the default for the Dreiding
+force field, as discussed in :ref:`(Mayo) <Mayo>`.
+
+The *fene* keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
+LJ and Coulombic interactions, which is consistent with a
+coarse-grained polymer model with :doc:`FENE bonds <bond_fene>`.  See
+:ref:`(Kremer) <Kremer>` for a description of FENE bonds.
+
+The *lj/coul*\ , *lj*\ , and *coul* keywords allow the 3 coefficients to
+be set explicitly.  The *lj/coul* keyword sets both the LJ and
+Coulombic coefficients to the same 3 values.  The *lj* and *coul*
+keywords only set either the LJ or Coulombic coefficients.  Use both
+of them if you wish to set the LJ coefficients to different values
+than the Coulombic coefficients.
+
+The *angle* keyword allows the 1-3 weighting factor to be ignored for
+individual atom pairs if they are not listed as the first and last
+atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in
+any dihedral defined in the simulation.  For example, imagine the 1-3
+weighting factor is set to 0.5 and you have a linear molecule with 4
+atoms and bonds as follows: 1-2-3-4.  If your data file defines 1-2-3
+as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a
+dihedral, then the pairwise interaction between atoms 1 and 3 will
+always be weighted by 0.5, but different force fields use different
+rules for weighting the pairwise interaction between atoms 2 and 4.
+If the *angle* keyword is specified as *yes*\ , then the pairwise
+interaction between atoms 2 and 4 will be unaffected (full weighting
+of 1.0).  If the *angle* keyword is specified as *no* which is the
+default, then the 2,4 interaction will also be weighted by 0.5.
+
+The *dihedral* keyword allows the 1-4 weighting factor to be ignored
+for individual atom pairs if they are not listed as the first and last
+atoms in any dihedral defined in the simulation.  For example, imagine
+the 1-4 weighting factor is set to 0.5 and you have a linear molecule
+with 5 atoms and bonds as follows: 1-2-3-4-5.  If your data file
+defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
+dihedral, then the pairwise interaction between atoms 1 and 4 will
+always be weighted by 0.5, but different force fields use different
+rules for weighting the pairwise interaction between atoms 2 and 5.
+If the *dihedral* keyword is specified as *yes*\ , then the pairwise
+interaction between atoms 2 and 5 will be unaffected (full weighting
+of 1.0).  If the *dihedral* keyword is specified as *no* which is the
+default, then the 2,5 interaction will also be weighted by 0.5.
+
+
+----------
+
+
+.. note::
+
+   LAMMPS stores and maintains a data structure with a list of the
+   1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
+   the system).  If new bonds are created (or molecules added containing
+   atoms with more special neighbors), the size of this list needs to
+   grow.  Note that adding a single bond always adds a new 1st neighbor
+   but may also induce \*many\* new 2nd and 3rd neighbors, depending on the
+   molecular topology of your system.  Using the *extra/special/per/atom*
+   keyword to either :doc:`read\_data <read_data>` or :doc:`create\_box <create_box>`
+   reserves empty space in the list for this N additional 1st, 2nd, or 3rd
+   neighbors to be added.  If you do not do this, you may get an error
+   when bonds (or molecules) are added.
+
+
+----------
+
+
+.. note::
+
+   If you reuse this command in an input script, you should set all
+   the options you need each time.  This command cannot be used a 2nd
+   time incrementally.  E.g. these two commands:
+
+
+.. parsed-literal::
+
+   special_bonds lj 0.0 1.0 1.0
+   special_bonds coul 0.0 0.0 1.0
+
+are not the same as
+
+
+.. parsed-literal::
+
+   special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0
+
+In the first case you end up with (after the 2nd command):
+
+
+.. parsed-literal::
+
+   LJ: 0.0 0.0 0.0
+   Coul: 0.0 0.0 1.0
+
+while only in the second case, you get the desired settings of:
+
+
+.. parsed-literal::
+
+   LJ: 0.0 1.0 1.0
+   Coul: 0.0 0.0 1.0
+
+This happens because the LJ (and Coul) settings are reset to
+their default values before modifying them, each time the
+*special\_bonds* command is issued.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`delete\_bonds <delete_bonds>`, :doc:`fix bond/create <fix_bond_create>`
+
+Default
+"""""""
+
+All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
+angle = no, dihedral = no.
+
+
+----------
+
+
+.. _Cornell:
+
+
+
+**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+
+.. _Kremer:
+
+
+
+**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
+
+.. _MacKerell:
+
+
+
+**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
+.. _Mayo:
+
+
+
+**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst
new file mode 100644
index 0000000000..263b83187c
--- /dev/null
+++ b/doc/src/suffix.rst
@@ -0,0 +1,117 @@
+.. index:: suffix
+
+suffix command
+==============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   suffix style args
+
+* style = *off* or *on* or *gpu* or *intel* or *kk* or *omp* or *opt* or *hybrid*
+* args = for hybrid style, default suffix to be used and alternative suffix
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   suffix off
+   suffix on
+   suffix gpu
+   suffix intel
+   suffix hybrid intel omp
+   suffix kk
+
+Description
+"""""""""""
+
+This command allows you to use variants of various styles if they
+exist.  In that respect it operates the same as the :doc:`-suffix command-line switch <Run_options>`.  It also has options to turn
+off or back on any suffix setting made via the command line.
+
+The specified style can be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt* or
+*hybrid*\ . These refer to optional packages that LAMMPS can be built
+with, as described on the :doc:`Build package <Build_package>` doc page.
+The "gpu" style corresponds to the GPU package, the "intel" style to
+the USER-INTEL package, the "kk" style to the KOKKOS package, the
+"omp" style to the USER-OMP package, and the "opt" style to the OPT
+package.
+
+These are the variants these packages provide:
+
+* GPU = a handful of pair styles and the PPPM kspace\_style, optimized to
+  run on one or more GPUs or multicore CPU/GPU nodes
+* USER-INTEL = a collection of pair styles and neighbor routines
+  optimized to run in single, mixed, or double precision on CPUs and
+  Intel(R) Xeon Phi(TM) co-processors.
+* KOKKOS = a collection of atom, pair, and fix styles optimized to run
+  using the Kokkos library on various kinds of hardware, including GPUs
+  via CUDA and many-core chips via OpenMP or threading.
+* USER-OMP = a collection of pair, bond, angle, dihedral, improper,
+  kspace, compute, and fix styles with support for OpenMP
+  multi-threading
+* OPT = a handful of pair styles, cache-optimized for faster CPU
+  performance
+* HYBRID = a combination of two packages can be specified (see below)
+
+
+As an example, all of the packages provide a :doc:`pair\_style lj/cut <pair_lj>` variant, with style names lj/cut/opt, lj/cut/omp,
+lj/cut/gpu, lj/cut/intel, or lj/cut/kk.  A variant styles
+can be specified explicitly in your input script, e.g. pair\_style
+lj/cut/gpu. If the suffix command is used with the appropriate style,
+you do not need to modify your input script.  The specified suffix
+(opt,omp,gpu,intel,kk) is automatically appended whenever your
+input script command creates a new :doc:`atom <atom_style>`,
+:doc:`pair <pair_style>`, :doc:`bond <bond_style>`,
+:doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`,
+:doc:`improper <improper_style>`, :doc:`kspace <kspace_style>`,
+:doc:`fix <fix>`, :doc:`compute <compute>`, or :doc:`run <run_style>` style.
+If the variant version does not exist, the standard version is
+created.
+
+For "hybrid", two packages are specified. The first is used whenever
+available. If a style with the first suffix is not available, the style
+with the suffix for the second package will be used if available. For
+example, "hybrid intel omp" will use styles from the USER-INTEL package
+as a first choice and styles from the USER-OMP package as a second choice
+if no USER-INTEL variant is available.
+
+If the specified style is *off*\ , then any previously specified suffix
+is temporarily disabled, whether it was specified by a command-line
+switch or a previous suffix command.  If the specified style is *on*\ ,
+a disabled suffix is turned back on.  The use of these 2 commands lets
+your input script use a standard LAMMPS style (i.e. a non-accelerated
+variant), which can be useful for testing or benchmarking purposes.
+Of course this is also possible by not using any suffix commands, and
+explicitly appending or not appending the suffix to the relevant
+commands in your input script.
+
+.. note::
+
+   The default :doc:`run\_style <run_style>` verlet is invoked prior to
+   reading the input script and is therefore not affected by a suffix command
+   in the input script. The KOKKOS package requires "run\_style verlet/kk",
+   so when using the KOKKOS package it is necessary to either use the command
+   line "-sf kk" command or add an explicit "run\_style verlet" command to the
+   input script.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`-suffix command-line switch <Run_options>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/tad.rst b/doc/src/tad.rst
new file mode 100644
index 0000000000..5322251ed5
--- /dev/null
+++ b/doc/src/tad.rst
@@ -0,0 +1,339 @@
+.. index:: tad
+
+tad command
+===========
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
+
+* N = # of timesteps to run (not including dephasing/quenching)
+* t\_event = timestep interval between event checks
+* T\_lo = temperature at which event times are desired
+* T\_hi = temperature at which MD simulation is performed
+* delta = desired confidence level for stopping criterion
+* tmax = reciprocal of lowest expected pre-exponential factor (time units)
+* compute-ID = ID of the compute used for event detection
+* zero or more keyword/value pairs may be appended
+* keyword = *min* or *neb* or *min\_style* or *neb\_style* or *neb\_log*
+  
+  .. parsed-literal::
+  
+       *min* values = etol ftol maxiter maxeval
+         etol = stopping tolerance for energy (energy units)
+         ftol = stopping tolerance for force (force units)
+         maxiter = max iterations of minimize
+         maxeval = max number of force/energy evaluations
+       *neb* values = ftol N1 N2 Nevery
+         etol = stopping tolerance for energy (energy units)
+         ftol = stopping tolerance for force (force units)
+         N1 = max # of iterations (timesteps) to run initial NEB
+         N2 = max # of iterations (timesteps) to run barrier-climbing NEB
+         Nevery = print NEB statistics every this many timesteps
+       *neb_style* value = *quickmin* or *fire*
+       *neb_step* value = dtneb
+         dtneb = timestep for NEB damped dynamics minimization
+       *neb_log* value = file where NEB statistics are printed
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   tad 2000 50 1800 2300 0.01 0.01 event
+   tad 2000 50 1800 2300 0.01 0.01 event &
+       min 1e-05 1e-05 100 100 &
+       neb 0.0 0.01 200 200 20 &
+       min_style cg &
+       neb_style fire &
+       neb_log log.neb
+
+Description
+"""""""""""
+
+Run a temperature accelerated dynamics (TAD) simulation. This method
+requires two or more partitions to perform NEB transition state
+searches.
+
+TAD is described in :ref:`this paper <Voter2000>` by Art Voter.  It is a method
+that uses accelerated dynamics at an elevated temperature to generate
+results at a specified lower temperature.  A good overview of
+accelerated dynamics methods for such systems is given in :ref:`this review paper <Voter2002>` from the same group. In general, these methods assume
+that the long-time dynamics is dominated by infrequent events i.e. the
+system is confined to low energy basins for long periods,
+punctuated by brief, randomly-occurring transitions to adjacent
+basins.  TAD is suitable for infrequent-event systems, where in
+addition, the transition kinetics are well-approximated by harmonic
+transition state theory (hTST). In hTST, the temperature dependence of
+transition rates follows the Arrhenius relation.  As a consequence a
+set of event times generated in a high-temperature simulation can be
+mapped to a set of much longer estimated times in the low-temperature
+system. However, because this mapping involves the energy barrier of
+the transition event, which is different for each event, the first
+event at the high temperature may not be the earliest event at the low
+temperature. TAD handles this by first generating a set of possible
+events from the current basin. After each event, the simulation is
+reflected backwards into the current basin.  This is repeated until
+the stopping criterion is satisfied, at which point the event with the
+earliest low-temperature occurrence time is selected.  The stopping
+criterion is that the confidence measure be greater than
+1-\ *delta*\ . The confidence measure is the probability that no earlier
+low-temperature event will occur at some later time in the
+high-temperature simulation.  hTST provides an lower bound for this
+probability, based on the user-specified minimum pre-exponential
+factor (reciprocal of *tmax*\ ).
+
+In order to estimate the energy barrier for each event, the TAD method
+invokes the :doc:`NEB <neb>` method. Each NEB replica runs on a
+partition of processors. The current NEB implementation in LAMMPS
+restricts you to having exactly one processor per replica. For more
+information, see the documentation for the :doc:`neb <neb>` command.  In
+the current LAMMPS implementation of TAD, all the non-NEB TAD
+operations are performed on the first partition, while the other
+partitions remain idle. See the :doc:`Howto replica <Howto_replica>` doc
+page for further discussion of multi-replica simulations.
+
+A TAD run has several stages, which are repeated each time an event is
+performed.  The logic for a TAD run is as follows:
+
+
+.. parsed-literal::
+
+   while (time remains):
+     while (time < tstop):
+       until (event occurs):
+         run dynamics for t_event steps
+         quench
+       run neb calculation using all replicas
+       compute tlo from energy barrier
+       update earliest event
+       update tstop
+       reflect back into current basin
+     execute earliest event
+
+Before this outer loop begins, the initial potential energy basin is
+identified by quenching (an energy minimization, see below) the
+initial state and storing the resulting coordinates for reference.
+
+Inside the inner loop, dynamics is run continuously according to
+whatever integrator has been specified by the user, stopping every
+*t\_event* steps to check if a transition event has occurred.  This
+check is performed by quenching the system and comparing the resulting
+atom coordinates to the coordinates from the previous basin.
+
+A quench is an energy minimization and is performed by whichever
+algorithm has been defined by the :doc:`min\_style <min_style>` command;
+its default is the CG minimizer.  The tolerances and limits for each
+quench can be set by the *min* keyword.  Note that typically, you do
+not need to perform a highly-converged minimization to detect a
+transition event.
+
+The event check is performed by a compute with the specified
+*compute-ID*\ .  Currently there is only one compute that works with the
+TAD command, which is the :doc:`compute event/displace <compute_event_displace>` command.  Other
+event-checking computes may be added.  :doc:`Compute event/displace <compute_event_displace>` checks whether any atom in
+the compute group has moved further than a specified threshold
+distance.  If so, an "event" has occurred.
+
+The NEB calculation is similar to that invoked by the :doc:`neb <neb>`
+command, except that the final state is generated internally, instead
+of being read in from a file.  The style of minimization performed by
+NEB is determined by the *neb\_style* keyword and must be a damped
+dynamics minimizer.  The tolerances and limits for each NEB
+calculation can be set by the *neb* keyword.  As discussed on the
+:doc:`neb <neb>`, it is often advantageous to use a larger timestep for
+NEB than for normal dynamics.  Since the size of the timestep set by
+the :doc:`timestep <timestep>` command is used by TAD for performing
+dynamics, there is a *neb\_step* keyword which can be used to set a
+larger timestep for each NEB calculation if desired.
+
+
+----------
+
+
+A key aspect of the TAD method is setting the stopping criterion
+appropriately.  If this criterion is too conservative, then many
+events must be generated before one is finally executed.  Conversely,
+if this criterion is too aggressive, high-entropy high-barrier events
+will be over-sampled, while low-entropy low-barrier events will be
+under-sampled. If the lowest pre-exponential factor is known fairly
+accurately, then it can be used to estimate *tmax*\ , and the value of
+*delta* can be set to the desired confidence level e.g. *delta* = 0.05
+corresponds to 95% confidence. However, for systems where the dynamics
+are not well characterized (the most common case), it will be
+necessary to experiment with the values of *delta* and *tmax* to get a
+good trade-off between accuracy and performance.
+
+A second key aspect is the choice of *t\_hi*. A larger value greatly
+increases the rate at which new events are generated.  However, too
+large a value introduces errors due to anharmonicity (not accounted
+for within hTST). Once again, for any given system, experimentation is
+necessary to determine the best value of *t\_hi*.
+
+
+----------
+
+
+Five kinds of output can be generated during a TAD run: event
+statistics, NEB statistics, thermodynamic output by each replica, dump
+files, and restart files.
+
+Event statistics are printed to the screen and master log.lammps file
+each time an event is executed. The quantities are the timestep, CPU
+time, global event number *N*\ , local event number *M*\ , event status,
+energy barrier, time margin, *t\_lo* and *delt\_lo*.  The timestep is
+the usual LAMMPS timestep, which corresponds to the high-temperature
+time at which the event was detected, in units of timestep.  The CPU
+time is the total processor time since the start of the TAD run.  The
+global event number *N* is a counter that increments with each
+executed event. The local event number *M* is a counter that resets to
+zero upon entering each new basin.  The event status is *E* when an
+event is executed, and is *D* for an event that is detected, while
+*DF* is for a detected event that is also the earliest (first) event
+at the low temperature.
+
+The time margin is the ratio of the high temperature time in the
+current basin to the stopping time. This last number can be used to
+judge whether the stopping time is too short or too long (see above).
+
+*t\_lo* is the low-temperature event time when the current basin was
+entered, in units of timestep.  del*t\_lo* is the time of each detected
+event, measured relative to *t\_lo*.  *delt\_lo* is equal to the
+high-temperature time since entering the current basin, scaled by an
+exponential factor that depends on the hi/lo temperature ratio and the
+energy barrier for that event.
+
+On lines for executed events, with status *E*\ , the global event number
+is incremented by one,
+the local event number and time margin are reset to zero,
+while the global event number, energy barrier, and
+*delt\_lo* match the last event with status *DF*
+in the immediately preceding block of detected events.
+The low-temperature event time *t\_lo* is incremented by *delt\_lo*.
+
+NEB statistics are written to the file specified by the *neb\_log*
+keyword. If the keyword value is "none", then no NEB statistics are
+printed out. The statistics are written every *Nevery* timesteps.  See
+the :doc:`neb <neb>` command for a full description of the NEB
+statistics. When invoked from TAD, NEB statistics are never printed to
+the screen.
+
+Because the NEB calculation must run on multiple partitions, LAMMPS
+produces additional screen and log files for each partition,
+e.g. log.lammps.0, log.lammps.1, etc. For the TAD command, these
+contain the thermodynamic output of each NEB replica. In addition, the
+log file for the first partition, log.lammps.0, will contain
+thermodynamic output from short runs and minimizations corresponding
+to the dynamics and quench operations, as well as a line for each new
+detected event, as described above.
+
+After the TAD command completes, timing statistics for the TAD run are
+printed in each replica's log file, giving a breakdown of how much CPU
+time was spent in each stage (NEB, dynamics, quenching, etc).
+
+Any :doc:`dump files <dump>` defined in the input script will be written
+to during a TAD run at timesteps when an event is executed.  This
+means the requested dump frequency in the :doc:`dump <dump>` command
+is ignored.  There will be one dump file (per dump command) created
+for all partitions.  The atom coordinates of the dump snapshot are
+those of the minimum energy configuration resulting from quenching
+following the executed event.  The timesteps written into the dump
+files correspond to the timestep at which the event occurred and NOT
+the clock.  A dump snapshot corresponding to the initial minimum state
+used for event detection is written to the dump file at the beginning
+of each TAD run.
+
+If the :doc:`restart <restart>` command is used, a single restart file
+for all the partitions is generated, which allows a TAD run to be
+continued by a new input script in the usual manner.  The restart file
+is generated after an event is executed. The restart file contains a
+snapshot of the system in the new quenched state, including the event
+number and the low-temperature time.  The restart frequency specified
+in the :doc:`restart <restart>` command is interpreted differently when
+performing a TAD run.  It does not mean the timestep interval between
+restart files.  Instead it means an event interval for executed
+events.  Thus a frequency of 1 means write a restart file every time
+an event is executed.  A frequency of 10 means write a restart file
+every 10th executed event.  When an input script reads a restart file
+from a previous TAD run, the new script can be run on a different
+number of replicas or processors.
+
+Note that within a single state, the dynamics will typically
+temporarily continue beyond the event that is ultimately chosen, until
+the stopping criterion is satisfied.  When the event is eventually
+executed, the timestep counter is reset to the value when the event
+was detected. Similarly, after each quench and NEB minimization, the
+timestep counter is reset to the value at the start of the
+minimization. This means that the timesteps listed in the replica log
+files do not always increase monotonically. However, the timestep
+values printed to the master log file, dump files, and restart files
+are always monotonically increasing.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+*N* setting must be integer multiple of *t\_event*.
+
+Runs restarted from restart files written during a TAD run will only
+produce identical results if the user-specified integrator supports
+exact restarts. So :doc:`fix nvt <fix_nh>` will produce an exact
+restart, but :doc:`fix langevin <fix_langevin>` will not.
+
+This command cannot be used when any fixes are defined that keep track
+of elapsed time to perform time-dependent operations.  Examples
+include the "ave" fixes such as :doc:`fix ave/chunk <fix_ave_chunk>`.
+Also :doc:`fix dt/reset <fix_dt_reset>` and :doc:`fix deposit <fix_deposit>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute event/displace <compute_event_displace>`,
+:doc:`min\_modify <min_modify>`, :doc:`min\_style <min_style>`,
+:doc:`run\_style <run_style>`, :doc:`minimize <minimize>`,
+:doc:`temper <temper>`, :doc:`neb <neb>`,
+:doc:`prd <prd>`
+
+Default
+"""""""
+
+The option defaults are *min* = 0.1 0.1 40 50, *neb* = 0.01 100 100
+10, *neb\_style* = *quickmin*\ , *neb\_step* = the same timestep set by
+the :doc:`timestep <timestep>` command, and *neb\_log* = "none".
+
+
+----------
+
+
+.. _Voter2000:
+
+
+
+**(Voter2000)** Sorensen and Voter, J Chem Phys, 112, 9599 (2000)
+
+.. _Voter2002:
+
+
+
+**(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials
+Research 32, 321 (2002).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/temper.rst b/doc/src/temper.rst
new file mode 100644
index 0000000000..ef73ef4094
--- /dev/null
+++ b/doc/src/temper.rst
@@ -0,0 +1,182 @@
+.. index:: temper
+
+temper command
+==============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   temper N M temp fix-ID seed1 seed2 index
+
+* N = total # of timesteps to run
+* M = attempt a tempering swap every this many steps
+* temp = initial temperature for this ensemble
+* fix-ID = ID of the fix that will control temperature during the run
+* seed1 = random # seed used to decide on adjacent temperature to partner with
+* seed2 = random # seed for Boltzmann factor in Metropolis swap
+* index = which temperature (0 to N-1) I am simulating (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   temper 100000 100 $t tempfix 0 58728
+   temper 40000 100 $t tempfix 0 32285 $w
+
+Description
+"""""""""""
+
+Run a parallel tempering or replica exchange simulation using multiple
+replicas (ensembles) of a system.  Two or more replicas must be used.
+
+Each replica runs on a partition of one or more processors.  Processor
+partitions are defined at run-time using the :doc:`-partition command-line switch <Run_options>`.  Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on one or two processors.  You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica.  See the :doc:`Howto replica <Howto_replica>`
+doc page for further discussion.
+
+Each replica's temperature is controlled at a different value by a fix
+with *fix-ID* that controls temperature. Most thermostat fix styles
+(with and without included time integration) are supported. The command
+will print an error message and abort, if the chosen fix is unsupported.
+The desired temperature is specified by *temp*\ , which is typically a
+variable previously set in the input script, so that each partition is
+assigned a different temperature.  See the :doc:`variable <variable>`
+command for more details.  For example:
+
+
+.. parsed-literal::
+
+   variable t world 300.0 310.0 320.0 330.0
+   fix myfix all nvt temp $t $t 100.0
+   temper 100000 100 $t myfix 3847 58382
+
+would define 4 temperatures, and assign one of them to the thermostat
+used by each replica, and to the temper command.
+
+As the tempering simulation runs for *N* timesteps, a temperature swap
+between adjacent ensembles will be attempted every *M* timesteps.  If
+*seed1* is 0, then the swap attempts will alternate between odd and
+even pairings.  If *seed1* is non-zero then it is used as a seed in a
+random number generator to randomly choose an odd or even pairing each
+time.  Each attempted swap of temperatures is either accepted or
+rejected based on a Boltzmann-weighted Metropolis criterion which uses
+*seed2* in the random number generator.
+
+As a tempering run proceeds, multiple log files and screen output
+files are created, one per replica.  By default these files are named
+log.lammps.M and screen.M where M is the replica number from 0 to N-1,
+with N = # of replicas.  See the :doc:`-log and -screen command-line swiches <Run_options>` for info on how to change these names.
+
+The main screen and log file (log.lammps) will list information about
+which temperature is assigned to each replica at each thermodynamic
+output timestep.  E.g. for a simulation with 16 replicas:
+
+
+.. parsed-literal::
+
+   Running on 16 partitions of processors
+   Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
+   0    0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+   500  1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
+   1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
+   1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
+   2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
+   2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
+   ...
+
+The column headings T0 to TN-1 mean which temperature is currently
+assigned to the replica 0 to N-1.  Thus the columns represent replicas
+and the value in each column is its temperature (also numbered 0 to
+N-1).  For example, a 0 in the 4th column (column T3, step 2500) means
+that the 4th replica is assigned temperature 0, i.e. the lowest
+temperature.  You can verify this time sequence of temperature
+assignments for the Nth replica by comparing the Nth column of screen
+output to the thermodynamic data in the corresponding log.lammps.N or
+screen.N files as time proceeds.
+
+You can have each replica create its own dump file in the following
+manner:
+
+
+.. parsed-literal::
+
+   variable rep world 0 1 2 3 4 5 6 7
+   dump 1 all atom 1000 dump.temper.$\ *rep*
+
+.. note::
+
+   Each replica's dump file will contain a continuous trajectory
+   for its atoms where the temperature varies over time as swaps take
+   place involving that replica.  If you want a series of dump files,
+   each with snapshots (from all replicas) that are all at a single
+   temperature, then you will need to post-process the dump files using
+   the information from the log.lammps file.  E.g. you could produce one
+   dump file with snapshots at 300K (from all replicas), another with
+   snapshots at 310K, etc.  Note that these new dump files will not
+   contain "continuous trajectories" for individual atoms, because two
+   successive snapshots (in time) may be from different replicas. The 
+   reorder\_remd\_traj python script can do the reordering for you 
+   (and additionally also calculated configurational log-weights of 
+   trajectory snapshots in the canonical ensemble). The script can be found
+   in the tools/replica directory while instructions on how to use it is
+   available in doc/Tools (in brief) and as a README file in tools/replica
+   (in detail).
+
+The last argument *index* in the temper command is optional and is
+used when restarting a tempering run from a set of restart files (one
+for each replica) which had previously swapped to new temperatures.
+The *index* value (from 0 to N-1, where N is the # of replicas)
+identifies which temperature the replica was simulating on the
+timestep the restart files were written.  Obviously, this argument
+must be a variable so that each partition has the correct value.  Set
+the variable to the *N* values listed in the log file for the previous
+run for the replica temperatures at that timestep.  For example if the
+log file listed the following for a simulation with 5 replicas:
+
+
+.. parsed-literal::
+
+   500000 2 4 0 1 3
+
+then a setting of
+
+
+.. parsed-literal::
+
+   variable w world 2 4 0 1 3
+
+would be used to restart the run with a tempering command like the
+example above with $w as the last argument.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`variable <variable>`, :doc:`prd <prd>`, :doc:`neb <neb>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/temper_grem.rst b/doc/src/temper_grem.rst
new file mode 100644
index 0000000000..e686ef23a4
--- /dev/null
+++ b/doc/src/temper_grem.rst
@@ -0,0 +1,133 @@
+.. index:: temper/grem
+
+temper/grem command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   temper/grem N M lambda fix-ID thermostat-ID seed1 seed2 index
+
+* N = total # of timesteps to run
+* M = attempt a tempering swap every this many steps
+* lambda = initial lambda for this ensemble
+* fix-ID = ID of fix\_grem
+* thermostat-ID = ID of the thermostat that controls kinetic temperature
+* seed1 = random # seed used to decide on adjacent temperature to partner with
+* seed2 = random # seed for Boltzmann factor in Metropolis swap
+* index = which temperature (0 to N-1) I am simulating (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   temper/grem 100000 1000 $\ *lambda* fxgREM fxnvt 0 58728
+   temper/grem 40000 100 $\ *lambda* fxgREM fxnpt 0 32285 $\ *walkers*
+
+Description
+"""""""""""
+
+Run a parallel tempering or replica exchange simulation in LAMMPS
+partition mode using multiple generalized replicas (ensembles) of a
+system defined by :doc:`fix grem <fix_grem>`, which stands for the
+generalized replica exchange method (gREM) originally developed by
+:ref:`(Kim) <KimStraub>`.  It uses non-Boltzmann ensembles to sample over first
+order phase transitions. The is done by defining replicas with an
+enthalpy dependent effective temperature
+
+Two or more replicas must be used.  See the :doc:`temper <temper>`
+command for an explanation of how to run replicas on multiple
+partitions of one or more processors.
+
+This command is a modification of the :doc:`temper <temper>` command and
+has the same dependencies, restraints, and input variables which are
+discussed there in greater detail.
+
+Instead of temperature, this command performs replica exchanges in
+lambda as per the generalized ensemble enforced by :doc:`fix grem <fix_grem>`.  The desired lambda is specified by *lambda*\ ,
+which is typically a variable previously set in the input script, so
+that each partition is assigned a different temperature.  See the
+:doc:`variable <variable>` command for more details.  For example:
+
+
+.. parsed-literal::
+
+   variable lambda world 400 420 440 460
+   fix fxnvt all nvt temp 300.0 300.0 100.0
+   fix fxgREM all grem $\ *lambda* -0.05 -50000 fxnvt
+   temper 100000 100 $\ *lambda* fxgREM fxnvt 3847 58382
+
+would define 4 lambdas with constant kinetic temperature but unique
+generalized temperature, and assign one of them to :doc:`fix grem <fix_grem>` used by each replica, and to the grem command.
+
+As the gREM simulation runs for *N* timesteps, a swap between adjacent
+ensembles will be attempted every *M* timesteps.  If *seed1* is 0,
+then the swap attempts will alternate between odd and even pairings.
+If *seed1* is non-zero then it is used as a seed in a random number
+generator to randomly choose an odd or even pairing each time.  Each
+attempted swap of temperatures is either accepted or rejected based on
+a Metropolis criterion, derived for gREM by :ref:`(Kim) <Kim>`, which uses
+*seed2* in the random number generator.
+
+File management works identical to the :doc:`temper <temper>` command.
+Dump files created by this fix contain continuous trajectories and
+require post-processing to obtain per-replica information.
+
+The last argument *index* in the grem command is optional and is used
+when restarting a run from a set of restart files (one for each
+replica) which had previously swapped to new lambda.  This is done
+using a variable. For example if the log file listed the following for
+a simulation with 5 replicas:
+
+
+.. parsed-literal::
+
+   500000 2 4 0 1 3
+
+then a setting of
+
+
+.. parsed-literal::
+
+   variable walkers world 2 4 0 1 3
+
+would be used to restart the run with a grem command like the example
+above with $\ *walkers* as the last argument. This functionality is
+identical to :doc:`temper <temper>`.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the USER-MISC
+package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+This command must be used with :doc:`fix grem <fix_grem>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix grem <fix_grem>`, :doc:`temper <temper>`, :doc:`variable <variable>`
+
+**Default:** none
+
+.. _KimStraub:
+
+
+
+**(Kim)** Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst
new file mode 100644
index 0000000000..8140989189
--- /dev/null
+++ b/doc/src/temper_npt.rst
@@ -0,0 +1,88 @@
+.. index:: temper/npt
+
+temper/npt command
+==================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   temper/npt  N M temp fix-ID seed1 seed2 pressure index
+
+* N = total # of timesteps to run
+* M = attempt a tempering swap every this many steps
+* temp = initial temperature for this ensemble
+* fix-ID = ID of the fix that will control temperature and pressure during the run
+* seed1 = random # seed used to decide on adjacent temperature to partner with
+* seed2 = random # seed for Boltzmann factor in Metropolis swap
+* pressure = setpoint pressure for the ensemble
+* index = which temperature (0 to N-1) I am simulating (optional)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   temper/npt 100000 100 $t nptfix 0 58728 1
+   temper/npt 2500000 1000 300 nptfix  0 32285 $p
+   temper/npt 5000000 2000 $t nptfix 0 12523 1 $w
+
+Description
+"""""""""""
+
+Run a parallel tempering or replica exchange simulation using multiple
+replicas (ensembles) of a system in the isothermal-isobaric (NPT)
+ensemble.  The command temper/npt works like :doc:`temper <temper>` but
+requires running replicas in the NPT ensemble instead of the canonical
+(NVT) ensemble and allows for pressure to be set in the ensembles.
+These multiple ensembles can run in parallel at different temperatures
+or different pressures.  The acceptance criteria for temper/npt is
+specific to the NPT ensemble and can be found in references
+:ref:`(Okabe) <Okabe2>` and :ref:`(Mori) <Mori2>`.
+
+Apart from the difference in acceptance criteria and the specification
+of pressure, this command works much like the :doc:`temper <temper>`
+command. See the documentation on :doc:`temper <temper>` for information
+on how the parallel tempering is handled in general.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command can only be used if LAMMPS was built with the USER-MISC
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
+
+This command should be used with a fix that maintains the
+isothermal-isobaric (NPT) ensemble.
+
+Related commands
+""""""""""""""""
+
+:doc:`temper <temper>`, :doc:`variable <variable>`, :doc:`fix\_npt <fix_nh>`
+
+**Default:** none
+
+.. _Okabe2:
+
+
+
+**(Okabe)** T. Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).
+
+.. _Mori2:
+
+
+
+**(Mori)** Y. Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst
new file mode 100644
index 0000000000..8b11ff9078
--- /dev/null
+++ b/doc/src/thermo.rst
@@ -0,0 +1,76 @@
+.. index:: thermo
+
+thermo command
+==============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   thermo N
+
+* N = output thermodynamics every N timesteps
+* N can be a variable (see below)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   thermo 100
+
+Description
+"""""""""""
+
+Compute and print thermodynamic info (e.g. temperature, energy,
+pressure) on timesteps that are a multiple of N and at the beginning
+and end of a simulation.  A value of 0 will only print thermodynamics
+at the beginning and end.
+
+The content and format of what is printed is controlled by the
+:doc:`thermo\_style <thermo_style>` and
+:doc:`thermo\_modify <thermo_modify>` commands.
+
+Instead of a numeric value, N can be specified as an :doc:`equal-style variable <variable>`, which should be specified as v\_name, where
+name is the variable name.  In this case, the variable is evaluated at
+the beginning of a run to determine the next timestep at which
+thermodynamic info will be written out.  On that timestep, the
+variable will be evaluated again to determine the next timestep, etc.
+Thus the variable should return timestep values.  See the stagger()
+and logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
+this context.  Other similar math functions could easily be added as
+options for :doc:`equal-style variables <variable>`.
+
+For example, the following commands will output thermodynamic info at
+timesteps 0,10,20,30,100,200,300,1000,2000,etc:
+
+
+.. parsed-literal::
+
+   variable        s equal logfreq(10,3,10)
+   thermo          v_s
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`thermo\_style <thermo_style>`, :doc:`thermo\_modify <thermo_modify>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   thermo 0
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst
new file mode 100644
index 0000000000..f0b27d2bc6
--- /dev/null
+++ b/doc/src/thermo_modify.rst
@@ -0,0 +1,200 @@
+.. index:: thermo\_modify
+
+thermo\_modify command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   thermo_modify keyword value ...
+
+* one or more keyword/value pairs may be listed
+  
+  .. parsed-literal::
+  
+     keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press*\ :l
+       *lost* value = *error* or *warn* or *ignore*
+       *lost/bond* value = *error* or *warn* or *ignore*
+       *norm* value = *yes* or *no*
+       *flush* value = *yes* or *no*
+       *line* value = *one* or *multi*
+       *format* values = *line* string, *int* string, *float* string, M string, or *none*
+         string = C-style format string
+         M = integer from 1 to N, where N = # of quantities being output
+       *temp* value = compute ID that calculates a temperature
+       *press* value = compute ID that calculates a pressure
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   thermo_modify lost ignore flush yes
+   thermo_modify temp myTemp format 3 %15.8g
+   thermo_modify temp myTemp format line "%ld %g %g %15.8g"
+   thermo_modify line multi format float %g
+
+Description
+"""""""""""
+
+Set options for how thermodynamic information is computed and printed
+by LAMMPS.
+
+.. note::
+
+   These options apply to the currently defined thermo style.  When
+   you specify a :doc:`thermo\_style <thermo_style>` command, all
+   thermodynamic settings are restored to their default values, including
+   those previously reset by a thermo\_modify command.  Thus if your input
+   script specifies a thermo\_style command, you should use the
+   thermo\_modify command after it.
+
+The *lost* keyword determines whether LAMMPS checks for lost atoms
+each time it computes thermodynamics and what it does if atoms are
+lost.  An atom can be "lost" if it moves across a non-periodic
+simulation box :doc:`boundary <boundary>` or if it moves more than a box
+length outside the simulation domain (or more than a processor
+sub-domain length) before reneighboring occurs.  The latter case is
+typically due to bad dynamics, e.g. too large a timestep or huge
+forces and velocities.  If the value is *ignore*\ , LAMMPS does not
+check for lost atoms.  If the value is *error* or *warn*\ , LAMMPS
+checks and either issues an error or warning.  The code will exit with
+an error and continue with a warning.  A warning will only be issued
+once, the first time an atom is lost.  This can be a useful debugging
+option.
+
+The *lost/bond* keyword determines whether LAMMPS throws an error or
+not if an atom in a bonded interaction (bond, angle, etc) cannot be
+found when it creates bonded neighbor lists.  By default this is a
+fatal error.  However in some scenarios it may be desirable to only
+issue a warning or ignore it and skip the computation of the missing
+bond, angle, etc.  An example would be when gas molecules in a vapor
+are drifting out of the box through a fixed boundary condition (see
+the :doc:`boundary <boundary>` command).  In this case one atom may be
+deleted before the rest of the molecule is, on a later timestep.
+
+The *norm* keyword determines whether various thermodynamic output
+values are normalized by the number of atoms or not, depending on
+whether it is set to *yes* or *no*\ .  Different unit styles have
+different defaults for this setting (see below).  Even if *norm* is
+set to *yes*\ , a value is only normalized if it is an "extensive"
+quantity, meaning that it scales with the number of atoms in the
+system.  For the thermo keywords described by the doc page for the
+:doc:`thermo\_style <thermo_style>` command, all energy-related keywords
+are extensive, such as *pe* or *ebond* or *enthalpy*\ .  Other keywords
+such as *temp* or *press* are "intensive" meaning their value is
+independent (in a statistical sense) of the number of atoms in the
+system and thus are never normalized.  For thermodynamic output values
+extracted from fixes and computes in a :doc:`thermo\_style custom <thermo_style>` command, the doc page for the individual
+:doc:`fix <fix>` or :doc:`compute <compute>` lists whether the value is
+"extensive" or "intensive" and thus whether it is normalized.
+Thermodynamic output values calculated by a variable formula are
+assumed to be "intensive" and thus are never normalized.  You can
+always include a divide by the number of atoms in the variable formula
+if this is not the case.
+
+The *flush* keyword invokes a flush operation after thermodynamic info
+is written to the log file.  This insures the output in that file is
+current (no buffering by the OS), even if LAMMPS halts before the
+simulation completes.
+
+The *line* keyword determines whether thermodynamics will be output as
+a series of numeric values on one line or in a multi-line format with
+3 quantities with text strings per line and a dashed-line header
+containing the timestep and CPU time.  This modify option overrides
+the *one* and *multi* thermo\_style settings.
+
+The *format* keyword can be used to change the default numeric format
+of any of quantities the :doc:`thermo\_style <thermo_style>` command
+outputs.  All the specified format strings are C-style formats,
+e.g. as used by the C/C++ printf() command.  The *line* keyword takes
+a single argument which is the format string for the entire line of
+thermo output, with N fields, which you must enclose in quotes if it
+is more than one field.  The *int* and *float* keywords take a single
+format argument and are applied to all integer or floating-point
+quantities output.  The setting for *M string* also takes a single
+format argument which is used for the Mth value output in each line,
+e.g. the 5th column is output in high precision for "format 5
+%20.15g".
+
+The *format* keyword can be used multiple times.  The precedence is
+that for each value in a line of output, the *M* format (if specified)
+is used, else the *int* or *float* setting (if specified) is used,
+else the *line* setting (if specified) for that value is used, else
+the default setting is used.  A setting of *none* clears all previous
+settings, reverting all values to their default format.
+
+.. note::
+
+   The thermo output values *step* and *atoms* are stored
+   internally as 8-byte signed integers, rather than the usual 4-byte
+   signed integers.  When specifying the *format int* option you can use
+   a "%d"-style format identifier in the format string and LAMMPS will
+   convert this to the corresponding 8-byte form when it is applied to
+   those keywords.  However, when specifying the *line* option or *format
+   M string* option for *step* and *natoms*\ , you should specify a format
+   string appropriate for an 8-byte signed integer, e.g. one with "%ld".
+
+The *temp* keyword is used to determine how thermodynamic temperature
+is calculated, which is used by all thermo quantities that require a
+temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc).
+The specified compute ID must have been previously defined by the user
+via the :doc:`compute <compute>` command and it must be a style of
+compute that calculates a temperature.  As described in the
+:doc:`thermo\_style <thermo_style>` command, thermo output uses a default
+compute for temperature with ID = *thermo\_temp*.  This option allows
+the user to override the default.
+
+The *press* keyword is used to determine how thermodynamic pressure is
+calculated, which is used by all thermo quantities that require a
+pressure ("press", "enthalpy", "pxx", etc).  The specified compute ID
+must have been previously defined by the user via the
+:doc:`compute <compute>` command and it must be a style of compute that
+calculates a pressure.  As described in the
+:doc:`thermo\_style <thermo_style>` command, thermo output uses a default
+compute for pressure with ID = *thermo\_press*.  This option allows the
+user to override the default.
+
+.. note::
+
+   If both the *temp* and *press* keywords are used in a single
+   thermo\_modify command (or in two separate commands), then the order in
+   which the keywords are specified is important.  Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
+   an argument when it is specified.  The *temp* keyword will override
+   this (for the pressure compute being used by thermodynamics), but only
+   if the *temp* keyword comes after the *press* keyword.  If the *temp*
+   keyword comes before the *press* keyword, then the new pressure
+   compute specified by the *press* keyword will be unaffected by the
+   *temp* setting.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`thermo <thermo>`, :doc:`thermo\_style <thermo_style>`
+
+Default
+"""""""
+
+The option defaults are lost = error, norm = yes for unit style of
+*lj*\ , norm = no for unit style of *real* and *metal*\ , flush = no,
+and temp/press = compute IDs defined by thermo\_style.
+
+The defaults for the line and format options depend on the thermo
+style.  For styles "one" and "custom", the line and format defaults
+are "one", "%8d", and "%12.8g".  For style "multi", the line and
+format defaults are "multi", "%8d", and "%14.4f".
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst
new file mode 100644
index 0000000000..480b14ae63
--- /dev/null
+++ b/doc/src/thermo_style.rst
@@ -0,0 +1,451 @@
+.. index:: thermo\_style
+
+thermo\_style command
+=====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   thermo_style style args
+
+* style = *one* or *multi* or *custom*
+* args = list of arguments for a particular style
+  
+  .. parsed-literal::
+  
+       *one* args = none
+       *multi* args = none
+       *custom* args = list of keywords
+         possible keywords = step, elapsed, elaplong, dt, time,
+                             cpu, tpcpu, spcpu, cpuremain, part, timeremain,
+                             atoms, temp, press, pe, ke, etotal, enthalpy,
+                             evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
+                             emol, elong, etail,
+                             vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
+                             xy, xz, yz, xlat, ylat, zlat,
+                             bonds, angles, dihedrals, impropers,
+                             pxx, pyy, pzz, pxy, pxz, pyz,
+                             fmax, fnorm, nbuild, ndanger,
+                             cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
+                             c_ID, c_ID[I], c_ID[I][J],
+                             f_ID, f_ID[I], f_ID[I][J],
+                             v_name, v_name[I]
+           step = timestep
+           elapsed = timesteps since start of this run
+           elaplong = timesteps since start of initial run in a series of runs
+           dt = timestep size
+           time = simulation time
+           cpu = elapsed CPU time in seconds since start of this run
+           tpcpu = time per CPU second
+           spcpu = timesteps per CPU second
+           cpuremain = estimated CPU time remaining in run
+           part = which partition (0 to Npartition-1) this is
+           timeremain = remaining time in seconds on timer timeout.
+           atoms = # of atoms
+           temp = temperature
+           press = pressure
+           pe = total potential energy
+           ke = kinetic energy
+           etotal = total energy (pe + ke)
+           enthalpy = enthalpy (etotal + press\*vol)
+           evdwl = VanderWaal pairwise energy (includes etail)
+           ecoul = Coulombic pairwise energy
+           epair = pairwise energy (evdwl + ecoul + elong)
+           ebond = bond energy
+           eangle = angle energy
+           edihed = dihedral energy
+           eimp = improper energy
+           emol = molecular energy (ebond + eangle + edihed + eimp)
+           elong = long-range kspace energy
+           etail = VanderWaal energy long-range tail correction
+           vol = volume
+           density = mass density of system
+           lx,ly,lz = box lengths in x,y,z
+           xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
+           xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
+           xlat,ylat,zlat = lattice spacings as calculated by :doc:`lattice <lattice>` command
+           bonds,angles,dihedrals,impropers = # of these interactions defined
+           pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
+           fmax = max component of force on any atom in any dimension
+           fnorm = length of force vector for all atoms
+           nbuild = # of neighbor list builds
+           ndanger = # of dangerous neighbor list builds
+           cella,cellb,cellc = periodic cell lattice constants a,b,c
+           cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
+           c_ID = global scalar value calculated by a compute with ID
+           c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
+           c_ID[I][J] = I,J component of global array calculated by a compute with ID
+           f_ID = global scalar value calculated by a fix with ID
+           f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
+           f_ID[I][J] = I,J component of global array calculated by a fix with ID
+           v_name = value calculated by an equal-style variable with name
+           v_name[I] = value calculated by a vector-style variable with name
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   thermo_style multi
+   thermo_style custom step temp pe etotal press vol
+   thermo_style custom step temp etotal c_myTemp v_abc
+   thermo_style custom step temp etotal c_myTemp[\*] v_abc
+
+Description
+"""""""""""
+
+Set the style and content for printing thermodynamic data to the
+screen and log file.
+
+Style *one* prints a one-line summary of thermodynamic info that is
+the equivalent of "thermo\_style custom step temp epair emol etotal
+press".  The line contains only numeric values.
+
+Style *multi* prints a multiple-line listing of thermodynamic info
+that is the equivalent of "thermo\_style custom etotal ke temp pe ebond
+eangle edihed eimp evdwl ecoul elong press".  The listing contains
+numeric values and a string ID for each quantity.
+
+Style *custom* is the most general setting and allows you to specify
+which of the keywords listed above you want printed on each
+thermodynamic timestep.  Note that the keywords c\_ID, f\_ID, v\_name are
+references to :doc:`computes <compute>`, :doc:`fixes <fix>`, and
+equal-style :doc:`variables <variable>` that have been defined elsewhere
+in the input script or can even be new styles which users have added
+to LAMMPS.  See the :doc:`Modify <Modify>` doc page for details on the
+latter.  Thus the *custom* style provides a flexible means of
+outputting essentially any desired quantity as a simulation proceeds.
+
+All styles except *custom* have *vol* appended to their list of
+outputs if the simulation box volume changes during the simulation.
+
+The values printed by the various keywords are instantaneous values,
+calculated on the current timestep.  Time-averaged quantities, which
+include values from previous timesteps, can be output by using the
+f\_ID keyword and accessing a fix that does time-averaging such as the
+:doc:`fix ave/time <fix_ave_time>` command.
+
+Options invoked by the :doc:`thermo\_modify <thermo_modify>` command can
+be used to set the one- or multi-line format of the print-out, the
+normalization of thermodynamic output (total values versus per-atom
+values for extensive quantities (ones which scale with the number of
+atoms in the system), and the numeric precision of each printed value.
+
+.. note::
+
+   When you use a "thermo\_style" command, all thermodynamic
+   settings are restored to their default values, including those
+   previously set by a :doc:`thermo\_modify <thermo_modify>` command.  Thus
+   if your input script specifies a thermo\_style command, you should use
+   the thermo\_modify command after it.
+
+
+----------
+
+
+Several of the thermodynamic quantities require a temperature to be
+computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc.  By
+default this is done by using a *temperature* compute which is created
+when LAMMPS starts up, as if this command had been issued:
+
+
+.. parsed-literal::
+
+   compute thermo_temp all temp
+
+See the :doc:`compute temp <compute_temp>` command for details.  Note
+that the ID of this compute is *thermo\_temp* and the group is *all*\ .
+You can change the attributes of this temperature (e.g. its
+degrees-of-freedom) via the :doc:`compute\_modify <compute_modify>`
+command.  Alternatively, you can directly assign a new compute (that
+calculates temperature) which you have defined, to be used for
+calculating any thermodynamic quantity that requires a temperature.
+This is done via the :doc:`thermo\_modify <thermo_modify>` command.
+
+Several of the thermodynamic quantities require a pressure to be
+computed: "press", "enthalpy", "pxx", etc.  By default this is done by
+using a *pressure* compute which is created when LAMMPS starts up, as
+if this command had been issued:
+
+
+.. parsed-literal::
+
+   compute thermo_press all pressure thermo_temp
+
+See the :doc:`compute pressure <compute_pressure>` command for details.
+Note that the ID of this compute is *thermo\_press* and the group is
+*all*\ .  You can change the attributes of this pressure via the
+:doc:`compute\_modify <compute_modify>` command.  Alternatively, you can
+directly assign a new compute (that calculates pressure) which you
+have defined, to be used for calculating any thermodynamic quantity
+that requires a pressure.  This is done via the
+:doc:`thermo\_modify <thermo_modify>` command.
+
+Several of the thermodynamic quantities require a potential energy to
+be computed: "pe", "etotal", "ebond", etc.  This is done by using a
+*pe* compute which is created when LAMMPS starts up, as if this
+command had been issued:
+
+
+.. parsed-literal::
+
+   compute thermo_pe all pe
+
+See the :doc:`compute pe <compute_pe>` command for details.  Note that
+the ID of this compute is *thermo\_pe* and the group is *all*\ .  You can
+change the attributes of this potential energy via the
+:doc:`compute\_modify <compute_modify>` command.
+
+
+----------
+
+
+The kinetic energy of the system *ke* is inferred from the temperature
+of the system with 1/2 Kb T of energy for each degree of freedom.
+Thus, using different :doc:`compute commands <compute>` for calculating
+temperature, via the :doc:`thermo\_modify temp <thermo_modify>` command,
+may yield different kinetic energies, since different computes that
+calculate temperature can subtract out different non-thermal
+components of velocity and/or include different degrees of freedom
+(translational, rotational, etc).
+
+The potential energy of the system *pe* will include contributions
+from fixes if the :doc:`fix\_modify thermo <fix_modify>` option is set
+for a fix that calculates such a contribution.  For example, the :doc:`fix wall/lj93 <fix_wall>` fix calculates the energy of atoms
+interacting with the wall.  See the doc pages for "individual fixes"
+to see which ones contribute.
+
+A long-range tail correction *etail* for the VanderWaal pairwise
+energy will be non-zero only if the :doc:`pair\_modify tail <pair_modify>` option is turned on.  The *etail* contribution
+is included in *evdwl*\ , *epair*\ , *pe*\ , and *etotal*\ , and the
+corresponding tail correction to the pressure is included in *press*
+and *pxx*\ , *pyy*\ , etc.
+
+
+----------
+
+
+The *step*\ , *elapsed*\ , and *elaplong* keywords refer to timestep
+count.  *Step* is the current timestep, or iteration count when a
+:doc:`minimization <minimize>` is being performed.  *Elapsed* is the
+number of timesteps elapsed since the beginning of this run.
+*Elaplong* is the number of timesteps elapsed since the beginning of
+an initial run in a series of runs.  See the *start* and *stop*
+keywords for the :doc:`run <run>` for info on how to invoke a series of
+runs that keep track of an initial starting time.  If these keywords
+are not used, then *elapsed* and *elaplong* are the same value.
+
+The *dt* keyword is the current timestep size in time
+:doc:`units <units>`.  The *time* keyword is the current elapsed
+simulation time, also in time :doc:`units <units>`, which is simply
+(step\*dt) if the timestep size has not changed and the timestep has
+not been reset.  If the timestep has changed (e.g. via :doc:`fix dt/reset <fix_dt_reset>`) or the timestep has been reset (e.g. via
+the "reset\_timestep" command), then the simulation time is effectively
+a cumulative value up to the current point.
+
+The *cpu* keyword is elapsed CPU seconds since the beginning of this
+run.  The *tpcpu* and *spcpu* keywords are measures of how fast your
+simulation is currently running.  The *tpcpu* keyword is simulation
+time per CPU second, where simulation time is in time
+:doc:`units <units>`.  E.g. for metal units, the *tpcpu* value would be
+picoseconds per CPU second.  The *spcpu* keyword is the number of
+timesteps per CPU second.  Both quantities are on-the-fly metrics,
+measured relative to the last time they were invoked.  Thus if you are
+printing out thermodynamic output every 100 timesteps, the two keywords
+will continually output the time and timestep rate for the last 100
+steps.  The *tpcpu* keyword does not attempt to track any changes in
+timestep size, e.g. due to using the :doc:`fix dt/reset <fix_dt_reset>`
+command.
+
+The *cpuremain* keyword estimates the CPU time remaining in the
+current run, based on the time elapsed thus far.  It will only be a
+good estimate if the CPU time/timestep for the rest of the run is
+similar to the preceding timesteps.  On the initial timestep the value
+will be 0.0 since there is no history to estimate from.  For a
+minimization run performed by the "minimize" command, the estimate is
+based on the *maxiter* parameter, assuming the minimization will
+proceed for the maximum number of allowed iterations.
+
+The *part* keyword is useful for multi-replica or multi-partition
+simulations to indicate which partition this output and this file
+corresponds to, or for use in a :doc:`variable <variable>` to append to
+a filename for output specific to this partition.  See discussion of
+the :doc:`-partition command-line switch <Run_options>` for details on
+running in multi-partition mode.
+
+The *timeremain* keyword returns the remaining seconds when a
+timeout has been configured via the :doc:`timer timeout <timer>` command.
+If the timeout timer is inactive, the value of this keyword is 0.0 and
+if the timer is expired, it is negative. This allows for example to exit
+loops cleanly, if the timeout is expired with:
+
+
+.. parsed-literal::
+
+   if "$(timeremain) < 0.0" then "quit 0"
+
+The *fmax* and *fnorm* keywords are useful for monitoring the progress
+of an :doc:`energy minimization <minimize>`.  The *fmax* keyword
+calculates the maximum force in any dimension on any atom in the
+system, or the infinity-norm of the force vector for the system.  The
+*fnorm* keyword calculates the 2-norm or length of the force vector.
+
+The *nbuild* and *ndanger* keywords are useful for monitoring neighbor
+list builds during a run.  Note that both these values are also
+printed with the end-of-run statistics.  The *nbuild* keyword is the
+number of re-builds during the current run.  The *ndanger* keyword is
+the number of re-builds that LAMMPS considered potentially
+"dangerous".  If atom movement triggered neighbor list rebuilding (see
+the :doc:`neigh\_modify <neigh_modify>` command), then dangerous
+reneighborings are those that were triggered on the first timestep
+atom movement was checked for.  If this count is non-zero you may wish
+to reduce the delay factor to insure no force interactions are missed
+by atoms moving beyond the neighbor skin distance before a rebuild
+takes place.
+
+The keywords *cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ ,
+*cellgamma*\ , correspond to the usual crystallographic quantities that
+define the periodic unit cell of a crystal.  See the :doc:`Howto triclinic <Howto_triclinic>` doc page for a geometric description
+of triclinic periodic cells, including a precise definition of these
+quantities in terms of the internal LAMMPS cell dimensions *lx*\ , *ly*\ ,
+*lz*\ , *yz*\ , *xz*\ , *xy*\ .
+
+
+----------
+
+
+For output values from a compute or fix, the bracketed index I used to
+index a vector, as in *c\_ID[I]* or *f\_ID[I]*, can be specified
+using a wildcard asterisk with the index to effectively specify
+multiple values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".
+If N = the size of the vector (for *mode* = scalar) or the number of
+columns in the array (for *mode* = vector), then an asterisk with no
+numeric values means all indices from 1 to N.  A leading asterisk
+means all indices from 1 to n (inclusive).  A trailing asterisk means
+all indices from n to N (inclusive).  A middle asterisk means all
+indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual elements of the
+vector had been listed one by one.  E.g. these 2 thermo\_style commands
+are equivalent, since the :doc:`compute temp <compute_temp>` command
+creates a global vector with 6 values.
+
+
+.. parsed-literal::
+
+   compute myTemp all temp
+   thermo_style custom step temp etotal c_myTemp[\*]
+   thermo_style custom step temp etotal &
+                c_myTemp[1] c_myTemp[2] c_myTemp[3] &
+                c_myTemp[4] c_myTemp[5] c_myTemp[6]
+
+
+----------
+
+
+The *c\_ID* and *c\_ID[I]* and *c\_ID[I][J]* keywords allow global
+values calculated by a compute to be output.  As discussed on the
+:doc:`compute <compute>` doc page, computes can calculate global,
+per-atom, or local values.  Only global values can be referenced by
+this command.  However, per-atom compute values for an individual atom
+can be referenced in a :doc:`variable <variable>` and the variable
+referenced by thermo\_style custom, as discussed below.  See the
+discussion above for how the I in *c\_ID[I]* can be specified with a
+wildcard asterisk to effectively specify multiple values from a global
+compute vector.
+
+The ID in the keyword should be replaced by the actual ID of a compute
+that has been defined elsewhere in the input script.  See the
+:doc:`compute <compute>` command for details.  If the compute calculates
+a global scalar, vector, or array, then the keyword formats with 0, 1,
+or 2 brackets will reference a scalar value from the compute.
+
+Note that some computes calculate "intensive" global quantities like
+temperature; others calculate "extensive" global quantities like
+kinetic energy that are summed over all atoms in the compute group.
+Intensive quantities are printed directly without normalization by
+thermo\_style custom.  Extensive quantities may be normalized by the
+total number of atoms in the simulation (NOT the number of atoms in
+the compute group) when output, depending on the :doc:`thermo\_modify norm <thermo_modify>` option being used.
+
+The *f\_ID* and *f\_ID[I]* and *f\_ID[I][J]* keywords allow global
+values calculated by a fix to be output.  As discussed on the
+:doc:`fix <fix>` doc page, fixes can calculate global, per-atom, or
+local values.  Only global values can be referenced by this command.
+However, per-atom fix values can be referenced for an individual atom
+in a :doc:`variable <variable>` and the variable referenced by
+thermo\_style custom, as discussed below.  See the discussion above for
+how the I in *f\_ID[I]* can be specified with a wildcard asterisk to
+effectively specify multiple values from a global fix vector.
+
+The ID in the keyword should be replaced by the actual ID of a fix
+that has been defined elsewhere in the input script.  See the
+:doc:`fix <fix>` command for details.  If the fix calculates a global
+scalar, vector, or array, then the keyword formats with 0, 1, or 2
+brackets will reference a scalar value from the fix.
+
+Note that some fixes calculate "intensive" global quantities like
+timestep size; others calculate "extensive" global quantities like
+energy that are summed over all atoms in the fix group.  Intensive
+quantities are printed directly without normalization by thermo\_style
+custom.  Extensive quantities may be normalized by the total number of
+atoms in the simulation (NOT the number of atoms in the fix group)
+when output, depending on the :doc:`thermo\_modify norm <thermo_modify>`
+option being used.
+
+The *v\_name* keyword allow the current value of a variable to be
+output.  The name in the keyword should be replaced by the variable
+name that has been defined elsewhere in the input script.  Only
+equal-style and vector-style variables can be referenced; the latter
+requires a bracketed term to specify the Ith element of the vector
+calculated by the variable.  However, an atom-style variable can be
+referenced for an individual atom by an equal-style variable and that
+variable referenced.  See the :doc:`variable <variable>` command for
+details.  Variables of style *equal* and *vector* and *atom* define a
+formula which can reference per-atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+evaluated, so this is a very general means of creating thermodynamic
+output.
+
+Note that equal-style and vector-style variables are assumed to
+produce "intensive" global quantities, which are thus printed as-is,
+without normalization by thermo\_style custom.  You can include a
+division by "natoms" in the variable formula if this is not the case.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command must come after the simulation box is defined by a
+:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
+:doc:`create\_box <create_box>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`thermo <thermo>`, :doc:`thermo\_modify <thermo_modify>`,
+:doc:`fix\_modify <fix_modify>`, :doc:`compute temp <compute_temp>`,
+:doc:`compute pressure <compute_pressure>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   thermo_style one
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst
new file mode 100644
index 0000000000..13a230d511
--- /dev/null
+++ b/doc/src/third_order.rst
@@ -0,0 +1,79 @@
+.. index:: third\_order
+
+third\_order command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   third_order group-ID style delta args keyword value ...
+
+* group-ID = ID of group of atoms to displace
+* style = *regular* or *eskm*
+* delta = finite different displacement length (distance units)
+* one or more keyword/arg pairs may be appended
+  
+  .. parsed-literal::
+  
+       keyword = *file* or *binary*
+         *file* name = name of output file for the third order tensor
+         *binary* arg = *yes* or *no* or *gzip*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   third_order 1 regular 0.000001
+   third_order 1 eskm 0.000001
+   third_order 3 regular 0.00004 file third_order.dat
+   third_order 5 eskm 0.00000001 file third_order.dat binary yes
+
+Description
+"""""""""""
+
+Calculate the third order force constant tensor by finite difference of the selected group,
+
+.. image:: JPG/third_order_force_constant.png
+   :align: center
+
+where Phi is the third order force constant tensor.
+
+The output of the command is the tensor, three elements at a time. The
+three elements correspond to the three gamma elements for a specific i/alpha/j/beta/k.
+The initial five numbers are i, alpha, j, beta, and k respectively.
+
+If the style eskm is selected, the tensor will be using energy units of 10 J/mol.
+These units conform to eskm style from the dynamical\_matrix command, which
+will simplify operations using dynamical matrices with third order tensors.
+
+Restrictions
+""""""""""""
+
+
+The command collects a 9 times the number of atoms in the group on every single MPI rank,
+so the memory requirements can be very significant for large systems.
+
+This command is part of the USER-PHONON package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix phonon <fix_phonon>` :doc:`dynamical\_matrix <dynamical_matrix>`
+
+Default
+"""""""
+
+The default settings are file = "third\_order.dat", binary = no
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/timer.rst b/doc/src/timer.rst
new file mode 100644
index 0000000000..c36b436b06
--- /dev/null
+++ b/doc/src/timer.rst
@@ -0,0 +1,140 @@
+.. index:: timer
+
+timer command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   timer args
+
+* *args* = one or more of *off* or *loop* or *normal* or *full* or *sync* or *nosync* or *timeout* or *every*
+
+.. parsed-literal::
+
+     *off* = do not collect or print any timing information
+     *loop* = collect only the total time for the simulation loop
+     *normal* = collect timer information broken down by sections (default)
+     *full* = like *normal* but also include CPU and thread utilization
+     *sync* = explicitly synchronize MPI tasks between sections
+     *nosync* = do not synchronize MPI tasks between sections (default)
+     *timeout* elapse = set wall time limit to *elapse*
+     *every* Ncheck = perform timeout check every *Ncheck* steps
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   timer full sync
+   timer timeout 2:00:00 every 100
+   timer loop
+
+Description
+"""""""""""
+
+Select the level of detail at which LAMMPS performs its CPU timings.
+Multiple keywords can be specified with the *timer* command.  For
+keywords that are mutually exclusive, the last one specified takes
+precedence.
+
+During a simulation run LAMMPS collects information about how much
+time is spent in different sections of the code and thus can provide
+information for determining performance and load imbalance problems.
+This can be done at different levels of detail and accuracy.  For more
+information about the timing output, see the :doc:`Run output <Run_output>` doc page.
+
+The *off* setting will turn all time measurements off. The *loop*
+setting will only measure the total time for a run and not collect any
+detailed per section information.  With the *normal* setting, timing
+information for portions of the timestep (pairwise calculations,
+neighbor list construction, output, etc) are collected as well as
+information about load imbalances for those sections across
+processors.  The *full* setting adds information about CPU
+utilization and thread utilization, when multi-threading is enabled.
+
+With the *sync* setting, all MPI tasks are synchronized at each timer
+call which measures load imbalance for each section more accurately,
+though it can also slow down the simulation by prohibiting overlapping
+independent computations on different MPI ranks  Using the *nosync*
+setting (which is the default) turns this synchronization off.
+
+With the *timeout* keyword a wall time limit can be imposed, that
+affects the :doc:`run <run>` and :doc:`minimize <minimize>` commands.
+This can be convenient when calculations have to comply with execution
+time limits, e.g. when running under a batch system when you want to
+maximize the utilization of the batch time slot, especially for runs
+where the time per timestep varies much and thus it becomes difficult
+to predict how many steps a simulation can perform for a given wall time
+limit. This also applies for difficult to converge minimizations.
+The timeout *elapse* value should be somewhat smaller than the maximum
+wall time requested from the batch system, as there is usually
+some overhead to launch jobs, and it is advisable to write
+out a restart after terminating a run due to a timeout.
+
+The timeout timer starts when the command is issued. When the time
+limit is reached, the run or energy minimization will exit on the
+next step or iteration that is a multiple of the *Ncheck* value
+which can be set with the *every* keyword. Default is checking
+every 10 steps. After the timer timeout has expired all subsequent
+run or minimize commands in the input script will be skipped.
+The remaining time or timer status can be accessed with the
+:doc:`thermo <thermo_style>` variable *timeremain*\ , which will be
+zero, if the timeout is inactive (default setting), it will be
+negative, if the timeout time is expired and positive if there
+is time remaining and in this case the value of the variable are
+the number of seconds remaining.
+
+When the *timeout* key word is used a second time, the timer is
+restarted with a new time limit. The timeout *elapse* value can
+be specified as *off* or *unlimited* to impose a no timeout condition
+(which is the default).  The *elapse* setting can be specified as
+a single number for seconds, two numbers separated by a colon (MM:SS)
+for minutes and seconds, or as three numbers separated by colons for
+hours, minutes, and seconds (H:MM:SS).
+
+The *every* keyword sets how frequently during a run or energy
+minimization the wall clock will be checked.  This check count applies
+to the outer iterations or time steps during minimizations or :doc:`r-RESPA runs <run_style>`, respectively.  Checking for timeout too often,
+can slow a calculation down.  Checking too infrequently can make the
+timeout measurement less accurate, with the run being stopped later
+than desired.
+
+.. note::
+
+   Using the *full* and *sync* options provides the most detailed
+   and accurate timing information, but can also have a negative
+   performance impact due to the overhead of the many required system
+   calls. It is thus recommended to use these settings only when testing
+   tests to identify performance bottlenecks. For calculations with few
+   atoms or a very large number of processors, even the *normal* setting
+   can have a measurable negative performance impact. In those cases you
+   can just use the *loop* or *off* setting.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`run post no <run>`, :doc:`kspace\_modify fftbench <kspace_modify>`
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   timer normal nosync
+   timer timeout off
+   timer every 10
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst
new file mode 100644
index 0000000000..da1a132a32
--- /dev/null
+++ b/doc/src/timestep.rst
@@ -0,0 +1,74 @@
+.. index:: timestep
+
+timestep command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   timestep dt
+
+* dt = timestep size (time units)
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   timestep 2.0
+   timestep 0.003
+
+Description
+"""""""""""
+
+Set the timestep size for subsequent molecular dynamics simulations.
+See the :doc:`units <units>` command for the time units associated with
+each choice of units that LAMMPS supports.
+
+The default value for the timestep size also depends on the choice of
+units for the simulation; see the default values below.
+
+When the :doc:`run style <run_style>` is *respa*\ , dt is the timestep for
+the outer loop (largest) timestep.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix dt/reset <fix_dt_reset>`, :doc:`run <run>`,
+:doc:`run\_style <run_style>` respa, :doc:`units <units>`
+
+Default
+"""""""
+
++--------------------------------+------------+-----------------------+
+| choice of :doc:`units <units>` | time units | default timestep size |
++--------------------------------+------------+-----------------------+
+| lj                             | tau        | 0.005 tau             |
++--------------------------------+------------+-----------------------+
+| real                           | fmsec      | 1.0 fmsec             |
++--------------------------------+------------+-----------------------+
+| metal                          | psec       | 0.001 psec            |
++--------------------------------+------------+-----------------------+
+| si                             | sec        | 1.0e-8 sec (10 nsec)  |
++--------------------------------+------------+-----------------------+
+| cgs                            | sec        | 1.0e-8 sec (10 nsec)  |
++--------------------------------+------------+-----------------------+
+| electron                       | fmsec      | 0.001 fmsec           |
++--------------------------------+------------+-----------------------+
+| micro                          | usec       | 2.0 usec              |
++--------------------------------+------------+-----------------------+
+| nano                           | nsec       | 0.00045 nsec          |
++--------------------------------+------------+-----------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/uncompute.rst b/doc/src/uncompute.rst
new file mode 100644
index 0000000000..e27a5fcc34
--- /dev/null
+++ b/doc/src/uncompute.rst
@@ -0,0 +1,46 @@
+.. index:: uncompute
+
+uncompute command
+=================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   uncompute compute-ID
+
+* compute-ID = ID of a previously defined compute
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   uncompute 2
+   uncompute lower-boundary
+
+Description
+"""""""""""
+
+Delete a compute that was previously defined with a :doc:`compute <compute>`
+command.  This also wipes out any additional changes made to the compute
+via the :doc:`compute\_modify <compute_modify>` command.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute <compute>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/undump.rst b/doc/src/undump.rst
new file mode 100644
index 0000000000..e79269e8dd
--- /dev/null
+++ b/doc/src/undump.rst
@@ -0,0 +1,45 @@
+.. index:: undump
+
+undump command
+==============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   undump dump-ID
+
+* dump-ID = ID of previously defined dump
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   undump mine
+   undump 2
+
+Description
+"""""""""""
+
+Turn off a previously defined dump so that it is no longer active.
+This closes the file associated with the dump.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/unfix.rst b/doc/src/unfix.rst
new file mode 100644
index 0000000000..dcd4e58c3d
--- /dev/null
+++ b/doc/src/unfix.rst
@@ -0,0 +1,46 @@
+.. index:: unfix
+
+unfix command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   unfix fix-ID
+
+* fix-ID = ID of a previously defined fix
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   unfix 2
+   unfix lower-boundary
+
+Description
+"""""""""""
+
+Delete a fix that was previously defined with a :doc:`fix <fix>`
+command.  This also wipes out any additional changes made to the fix
+via the :doc:`fix\_modify <fix_modify>` command.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix <fix>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/units.rst b/doc/src/units.rst
new file mode 100644
index 0000000000..6c0815f302
--- /dev/null
+++ b/doc/src/units.rst
@@ -0,0 +1,238 @@
+.. index:: units
+
+units command
+=============
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   units style
+
+* style = *lj* or *real* or *metal* or *si* or *cgs* or *electron* or *micro* or *nano*
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   units metal
+   units lj
+
+Description
+"""""""""""
+
+This command sets the style of units used for a simulation.  It
+determines the units of all quantities specified in the input script
+and data file, as well as quantities output to the screen, log file,
+and dump files.  Typically, this command is used at the very beginning
+of an input script.
+
+For all units except *lj*\ , LAMMPS uses physical constants from
+www.physics.nist.gov.  For the definition of Kcal in real units,
+LAMMPS uses the thermochemical calorie = 4.184 J.
+
+The choice you make for units simply sets some internal conversion
+factors within LAMMPS.  This means that any simulation you perform for
+one choice of units can be duplicated with any other unit setting
+LAMMPS supports.  In this context "duplicate" means the particles will
+have identical trajectories and all output generated by the simulation
+will be identical.  This will be the case for some number of timesteps
+until round-off effects accumulate, since the conversion factors for
+two different unit systems are not identical to infinite precision.
+
+To perform the same simulation in a different set of units you must
+change all the unit-based input parameters in your input script and
+other input files (data file, potential files, etc) correctly to the
+new units.  And you must correctly convert all output from the new
+units to the old units when comparing to the original results.  That
+is often not simple to do.
+
+
+----------
+
+
+For style *lj*\ , all quantities are unitless.  Without loss of
+generality, LAMMPS sets the fundamental quantities mass, sigma,
+epsilon, and the Boltzmann constant = 1.  The masses, distances,
+energies you specify are multiples of these fundamental values.  The
+formulas relating the reduced or unitless quantity (with an asterisk)
+to the same quantity with units is also given.  Thus you can use the
+mass & sigma & epsilon values for a specific material and convert the
+results from a unitless LJ simulation into physical quantities.
+
+* mass = mass or m
+* distance = sigma, where x\* = x / sigma
+* time = tau, where t\* = t (epsilon / m / sigma\^2)\^1/2
+* energy = epsilon, where E\* = E / epsilon
+* velocity = sigma/tau, where v\* = v tau / sigma
+* force = epsilon/sigma, where f\* = f sigma / epsilon
+* torque = epsilon, where t\* = t / epsilon
+* temperature = reduced LJ temperature, where T\* = T Kb / epsilon
+* pressure = reduced LJ pressure, where P\* = P sigma\^3 / epsilon
+* dynamic viscosity = reduced LJ viscosity, where eta\* = eta sigma\^3 / epsilon / tau
+* charge = reduced LJ charge, where q\* = q / (4 pi perm0 sigma epsilon)\^1/2
+* dipole = reduced LJ dipole, moment where \*mu = mu / (4 pi perm0 sigma\^3 epsilon)\^1/2
+* electric field = force/charge, where E\* = E (4 pi perm0 sigma epsilon)\^1/2 sigma / epsilon
+* density = mass/volume, where rho\* = rho sigma\^dim
+
+Note that for LJ units, the default mode of thermodynamic output via
+the :doc:`thermo\_style <thermo_style>` command is to normalize all
+extensive quantities by the number of atoms.  E.g. potential energy is
+extensive because it is summed over atoms, so it is output as
+energy/atom.  Temperature is intensive since it is already normalized
+by the number of atoms, so it is output as-is.  This behavior can be
+changed via the :doc:`thermo\_modify norm <thermo_modify>` command.
+
+For style *real*\ , these are the units:
+
+* mass = grams/mole
+* distance = Angstroms
+* time = femtoseconds
+* energy = Kcal/mole
+* velocity = Angstroms/femtosecond
+* force = Kcal/mole-Angstrom
+* torque = Kcal/mole
+* temperature = Kelvin
+* pressure = atmospheres
+* dynamic viscosity = Poise
+* charge = multiple of electron charge (1.0 is a proton)
+* dipole = charge\*Angstroms
+* electric field = volts/Angstrom
+* density = gram/cm\^dim
+
+For style *metal*\ , these are the units:
+
+* mass = grams/mole
+* distance = Angstroms
+* time = picoseconds
+* energy = eV
+* velocity = Angstroms/picosecond
+* force = eV/Angstrom
+* torque = eV
+* temperature = Kelvin
+* pressure = bars
+* dynamic viscosity = Poise
+* charge = multiple of electron charge (1.0 is a proton)
+* dipole = charge\*Angstroms
+* electric field = volts/Angstrom
+* density = gram/cm\^dim
+
+For style *si*\ , these are the units:
+
+* mass = kilograms
+* distance = meters
+* time = seconds
+* energy = Joules
+* velocity = meters/second
+* force = Newtons
+* torque = Newton-meters
+* temperature = Kelvin
+* pressure = Pascals
+* dynamic viscosity = Pascal\*second
+* charge = Coulombs (1.6021765e-19 is a proton)
+* dipole = Coulombs\*meters
+* electric field = volts/meter
+* density = kilograms/meter\^dim
+
+For style *cgs*\ , these are the units:
+
+* mass = grams
+* distance = centimeters
+* time = seconds
+* energy = ergs
+* velocity = centimeters/second
+* force = dynes
+* torque = dyne-centimeters
+* temperature = Kelvin
+* pressure = dyne/cm\^2 or barye = 1.0e-6 bars
+* dynamic viscosity = Poise
+* charge = statcoulombs or esu (4.8032044e-10 is a proton)
+* dipole = statcoul-cm = 10\^18 debye
+* electric field = statvolt/cm or dyne/esu
+* density = grams/cm\^dim
+
+For style *electron*\ , these are the units:
+
+* mass = atomic mass units
+* distance = Bohr
+* time = femtoseconds
+* energy = Hartrees
+* velocity = Bohr/atomic time units [1.03275e-15 seconds]
+* force = Hartrees/Bohr
+* temperature = Kelvin
+* pressure = Pascals
+* charge = multiple of electron charge (1.0 is a proton)
+* dipole moment = Debye
+* electric field = volts/cm
+
+For style *micro*\ , these are the units:
+
+* mass = picograms
+* distance = micrometers
+* time = microseconds
+* energy = picogram-micrometer\^2/microsecond\^2
+* velocity = micrometers/microsecond
+* force = picogram-micrometer/microsecond\^2
+* torque = picogram-micrometer\^2/microsecond\^2
+* temperature = Kelvin
+* pressure = picogram/(micrometer-microsecond\^2)
+* dynamic viscosity = picogram/(micrometer-microsecond)
+* charge = picocoulombs (1.6021765e-7 is a proton)
+* dipole = picocoulomb-micrometer
+* electric field = volt/micrometer
+* density = picograms/micrometer\^dim
+
+For style *nano*\ , these are the units:
+
+* mass = attograms
+* distance = nanometers
+* time = nanoseconds
+* energy = attogram-nanometer\^2/nanosecond\^2
+* velocity = nanometers/nanosecond
+* force = attogram-nanometer/nanosecond\^2
+* torque = attogram-nanometer\^2/nanosecond\^2
+* temperature = Kelvin
+* pressure = attogram/(nanometer-nanosecond\^2)
+* dynamic viscosity = attogram/(nanometer-nanosecond)
+* charge = multiple of electron charge (1.0 is a proton)
+* dipole = charge-nanometer
+* electric field = volt/nanometer
+* density = attograms/nanometer\^dim
+
+The units command also sets the timestep size and neighbor skin
+distance to default values for each style:
+
+* For style *lj* these are dt = 0.005 tau and skin = 0.3 sigma.
+* For style *real* these are dt = 1.0 femtoseconds and skin = 2.0 Angstroms.
+* For style *metal* these are dt = 0.001 picoseconds and skin = 2.0 Angstroms.
+* For style *si* these are dt = 1.0e-8 seconds and skin = 0.001 meters.
+* For style *cgs* these are dt = 1.0e-8 seconds and skin = 0.1 centimeters.
+* For style *electron* these are dt = 0.001 femtoseconds and skin = 2.0 Bohr.
+* For style *micro* these are dt = 2.0 microseconds and skin = 0.1 micrometers.
+* For style *nano* these are dt = 0.00045 nanoseconds and skin = 0.1 nanometers.
+
+Restrictions
+""""""""""""
+
+
+This command cannot be used after the simulation box is defined by a
+:doc:`read\_data <read_data>` or :doc:`create\_box <create_box>` command.
+
+**Related commands:** none
+
+Default
+"""""""
+
+
+.. parsed-literal::
+
+   units lj
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/variable.rst b/doc/src/variable.rst
new file mode 100644
index 0000000000..99413ce96c
--- /dev/null
+++ b/doc/src/variable.rst
@@ -0,0 +1,1481 @@
+.. index:: variable
+
+variable command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   variable name style args ...
+
+* name = name of variable to define
+* style = *delete* or *index* or *loop* or *world* or *universe* or *uloop* or *string* or *format* or *getenv* or *file* or *atomfile* or *python* or *internal* or *equal* or *vector* or *atom*
+  
+  .. parsed-literal::
+  
+       *delete* = no args
+       *index* args = one or more strings
+       *loop* args = N
+         N = integer size of loop, loop from 1 to N inclusive
+       *loop* args = N pad
+         N = integer size of loop, loop from 1 to N inclusive
+         pad = all values will be same length, e.g. 001, 002, ..., 100
+       *loop* args = N1 N2
+         N1,N2 = loop from N1 to N2 inclusive
+       *loop* args = N1 N2 pad
+         N1,N2 = loop from N1 to N2 inclusive
+         pad = all values will be same length, e.g. 050, 051, ..., 100
+       *world* args = one string for each partition of processors
+       *universe* args = one or more strings
+       *uloop* args = N
+         N = integer size of loop
+       *uloop* args = N pad
+         N = integer size of loop
+         pad = all values will be same length, e.g. 001, 002, ..., 100
+       *string* arg = one string
+       *format* args = vname fstr
+         vname = name of equal-style variable to evaluate
+         fstr = C-style format string
+       *getenv* arg = one string
+       *file* arg = filename
+       *atomfile* arg = filename
+       *python* arg = function
+       *internal* arg = numeric value
+       *equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
+         numbers = 0.0, 100, -5.4, 2.8e-4, etc
+         constants = PI, version, on, off, true, false, yes, no
+         thermo keywords = vol, ke, press, etc from :doc:`thermo_style <thermo_style>`
+         math operators = (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y,
+                          x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x
+         math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
+                          sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
+                          random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
+                          ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
+                          logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
+                          vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
+         group functions = count(group), mass(group), charge(group),
+                           xcm(group,dim), vcm(group,dim), fcm(group,dim),
+                           bound(group,dir), gyration(group), ke(group),
+                           angmom(group,dim), torque(group,dim),
+                           inertia(group,dimdim), omega(group,dim)
+         region functions = count(group,region), mass(group,region), charge(group,region),
+                           xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
+                           bound(group,dir,region), gyration(group,region), ke(group,reigon),
+                           angmom(group,dim,region), torque(group,dim,region),
+                           inertia(group,dimdim,region), omega(group,dim,region)
+         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
+         feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
+         atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
+         atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
+         compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
+         fix references = f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]
+         variable references = v_name, v_name[i]
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   variable x index run1 run2 run3 run4 run5 run6 run7 run8
+   variable LoopVar loop $n
+   variable beta equal temp/3.0
+   variable b1 equal x[234]+0.5\*vol
+   variable b1 equal "x[234] + 0.5\*vol"
+   variable b equal xcm(mol1,x)/2.0
+   variable b equal c_myTemp
+   variable b atom x\*y/vol
+   variable foo string myfile
+   variable foo internal 3.5
+   variable myPy python increase
+   variable f file values.txt
+   variable temp world 300.0 310.0 320.0 ${Tfinal}
+   variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+   variable x uloop 15 pad
+   variable str format x %.6g
+   variable x delete
+
+Description
+"""""""""""
+
+This command assigns one or more strings to a variable name for
+evaluation later in the input script or during a simulation.
+
+Variables can thus be useful in several contexts.  A variable can be
+defined and then referenced elsewhere in an input script to become
+part of a new input command.  For variable styles that store multiple
+strings, the :doc:`next <next>` command can be used to increment which
+string is assigned to the variable.  Variables of style *equal* store
+a formula which when evaluated produces a single numeric value which
+can be output either directly (see the :doc:`print <print>`, :doc:`fix print <fix_print>`, and :doc:`run every <run>` commands) or as part
+of thermodynamic output (see the :doc:`thermo\_style <thermo_style>`
+command), or used as input to an averaging fix (see the :doc:`fix ave/time <fix_ave_time>` command).  Variables of style *vector*
+store a formula which produces a vector of such values which can be
+used as input to various averaging fixes, or elements of which can be
+part of thermodynamic output.  Variables of style *atom* store a
+formula which when evaluated produces one numeric value per atom which
+can be output to a dump file (see the :doc:`dump custom <dump>` command)
+or used as input to an averaging fix (see the :doc:`fix ave/chunk <fix_ave_chunk>` and :doc:`fix ave/atom <fix_ave_atom>`
+commands).  Variables of style *atomfile* can be used anywhere in an
+input script that atom-style variables are used; they get their
+per-atom values from a file rather than from a formula.  Variables of
+style *python* can be hooked to Python functions using code you
+provide, so that the variable gets its value from the evaluation of
+the Python code.  Variables of style *internal* are used by a few
+commands which set their value directly.
+
+.. note::
+
+   As discussed on the :doc:`Commands parse <Commands_parse>` doc
+   page, an input script can use "immediate" variables, specified as
+   $(formula) with parenthesis, where the formula has the same syntax as
+   equal-style variables described on this page.  This is a convenient
+   way to evaluate a formula immediately without using the variable
+   command to define a named variable and then evaluate that
+   variable. See below for a more detailed discussion of this feature.
+
+In the discussion that follows, the "name" of the variable is the
+arbitrary string that is the 1st argument in the variable command.
+This name can only contain alphanumeric characters and underscores.
+The "string" is one or more of the subsequent arguments.  The "string"
+can be simple text as in the 1st example above, it can contain other
+variables as in the 2nd example, or it can be a formula as in the 3rd
+example.  The "value" is the numeric quantity resulting from
+evaluation of the string.  Note that the same string can generate
+different values when it is evaluated at different times during a
+simulation.
+
+.. note::
+
+   When an input script line is encountered that defines a variable
+   of style *equal* or *vector* or *atom* or *python* that contains a
+   formula or Python code, the formula is NOT immediately evaluated.  It
+   will be evaluated every time when the variable is **used** instead.  If
+   you simply want to evaluate a formula in place you can use as
+   so-called. See the section below about "Immediate Evaluation of
+   Variables" for more details on the topic.  This is also true of a
+   *format* style variable since it evaluates another variable when it is
+   invoked.
+
+Variables of style *equal* and *vector* and *atom* can be used as
+inputs to various other commands which evaluate their formulas as
+needed, e.g. at different timesteps during a :doc:`run <run>`.
+
+Variables of style *internal* can be used in place of an equal-style
+variable, except by commands that set the value stored by the
+internal-style variable.  Thus any command that states it can use an
+equal-style variable as an argument, can also use an internal-style
+variable.  This means that when the command evaluates the variable, it
+will use the value set (internally) by another command.
+
+Variables of style *python* can be used in place of an equal-style
+variable so long as the associated Python function, as defined by the
+:doc:`python <python>` command, returns a numeric value.  Thus any
+command that states it can use an equal-style variable as an argument,
+can also use such a python-style variable.  This means that when the
+LAMMPS command evaluates the variable, the Python function will be
+executed.
+
+.. note::
+
+   When a variable command is encountered in the input script and
+   the variable name has already been specified, the command is ignored.
+   This means variables can NOT be re-defined in an input script (with
+   two exceptions, read further).  This is to allow an input script to be
+   processed multiple times without resetting the variables; see the
+   :doc:`jump <jump>` or :doc:`include <include>` commands.  It also means
+   that using the :doc:`command-line switch <Run_options>` -var will
+   override a corresponding index variable setting in the input script.
+
+There are two exceptions to this rule.  First, variables of style
+*string*\ , *getenv*\ , *internal*\ , *equal*\ , *vector*\ , *atom*\ , and
+*python* ARE redefined each time the command is encountered.  This
+allows these style of variables to be redefined multiple times in an
+input script.  In a loop, this means the formula associated with an
+*equal* or *atom* style variable can change if it contains a
+substitution for another variable, e.g. $x or v\_x.
+
+Second, as described below, if a variable is iterated on to the end of
+its list of strings via the :doc:`next <next>` command, it is removed
+from the list of active variables, and is thus available to be
+re-defined in a subsequent variable command.  The *delete* style does
+the same thing.
+
+
+----------
+
+
+The :doc:`Commands parse <Commands_parse>` doc page explains how
+occurrences of a variable name in an input script line are replaced by
+the variable's string.  The variable name can be referenced as $x if
+the name "x" is a single character, or as ${LoopVar} if the name
+"LoopVar" is one or more characters.
+
+As described below, for variable styles *index*\ , *loop*\ , *file*\ ,
+*universe*\ , and *uloop*\ , which string is assigned to a variable can be
+incremented via the :doc:`next <next>` command.  When there are no more
+strings to assign, the variable is exhausted and a flag is set that
+causes the next :doc:`jump <jump>` command encountered in the input
+script to be skipped.  This enables the construction of simple loops
+in the input script that are iterated over and then exited from.
+
+As explained above, an exhausted variable can be re-used in an input
+script.  The *delete* style also removes the variable, the same as if
+it were exhausted, allowing it to be redefined later in the input
+script or when the input script is looped over.  This can be useful
+when breaking out of a loop via the :doc:`if <if>` and :doc:`jump <jump>`
+commands before the variable would become exhausted.  For example,
+
+
+.. parsed-literal::
+
+   label       loop
+   variable    a loop 5
+   print       "A = $a"
+   if          "$a > 2" then "jump in.script break"
+   next        a
+   jump        in.script loop
+   label       break
+   variable    a delete
+
+
+----------
+
+
+This section describes how all the various variable styles are defined
+and what they store.  Except for the *equal* and *vector* and *atom*
+styles, which are explained in the next section.
+
+Many of the styles store one or more strings.  Note that a single
+string can contain spaces (multiple words), if it is enclosed in
+quotes in the variable command.  When the variable is substituted for
+in another input script command, its returned string will then be
+interpreted as multiple arguments in the expanded command.
+
+For the *index* style, one or more strings are specified.  Initially,
+the 1st string is assigned to the variable.  Each time a
+:doc:`next <next>` command is used with the variable name, the next
+string is assigned.  All processors assign the same string to the
+variable.
+
+*Index* style variables with a single string value can also be set by
+using the :doc:`command-line switch -var <Run_options>`.
+
+The *loop* style is identical to the *index* style except that the
+strings are the integers from 1 to N inclusive, if only one argument N
+is specified.  This allows generation of a long list of runs
+(e.g. 1000) without having to list N strings in the input script.
+Initially, the string "1" is assigned to the variable.  Each time a
+:doc:`next <next>` command is used with the variable name, the next
+string ("2", "3", etc) is assigned.  All processors assign the same
+string to the variable.  The *loop* style can also be specified with
+two arguments N1 and N2.  In this case the loop runs from N1 to N2
+inclusive, and the string N1 is initially assigned to the variable.
+N1 <= N2 and N2 >= 0 is required.
+
+For the *world* style, one or more strings are specified.  There must
+be one string for each processor partition or "world".  LAMMPS can be
+run with multiple partitions via the :doc:`-partition command-line switch <Run_options>`.  This variable command assigns one string to
+each world.  All processors in the world are assigned the same string.
+The next command cannot be used with *equal* style variables, since
+there is only one value per world.  This style of variable is useful
+when you wish to run different simulations on different partitions, or
+when performing a parallel tempering simulation (see the
+:doc:`temper <temper>` command), to assign different temperatures to
+different partitions.
+
+For the *universe* style, one or more strings are specified.  There
+must be at least as many strings as there are processor partitions or
+"worlds".  LAMMPS can be run with multiple partitions via the
+:doc:`-partition command-line switch <Run_options>`.  This variable
+command initially assigns one string to each world.  When a
+:doc:`next <next>` command is encountered using this variable, the first
+processor partition to encounter it, is assigned the next available
+string.  This continues until all the variable strings are consumed.
+Thus, this command can be used to run 50 simulations on 8 processor
+partitions.  The simulations will be run one after the other on
+whatever partition becomes available, until they are all finished.
+*Universe* style variables are incremented using the files
+"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
+see in your directory during such a LAMMPS run.
+
+The *uloop* style is identical to the *universe* style except that the
+strings are the integers from 1 to N.  This allows generation of long
+list of runs (e.g. 1000) without having to list N strings in the input
+script.
+
+For the *string* style, a single string is assigned to the variable.
+Two differences between this style and using the *index* style exist:
+a variable with *string* style can be redefined, e.g. by another command later
+in the input script, or if the script is read again in a loop. The other
+difference is that *string* performs variable substitution even if the
+string parameter is quoted.
+
+For the *format* style, an equal-style variable is specified along
+with a C-style format string, e.g. "%f" or "%.10g", which must be
+appropriate for formatting a double-precision floating-point value.
+The default format is "%.15g".  This variable style allows an
+equal-style variable to be formatted precisely when it is evaluated.
+
+If you simply wish to print a variable value with desired precision to
+the screen or logfile via the :doc:`print <print>` or :doc:`fix print <fix_print>` commands, you can also do this by specifying an
+"immediate" variable with a trailing colon and format string, as part
+of the string argument of those commands.  This is explained on the
+:doc:`Commands parse <Commands_parse>` doc page.
+
+For the *getenv* style, a single string is assigned to the variable
+which should be the name of an environment variable.  When the
+variable is evaluated, it returns the value of the environment
+variable, or an empty string if it not defined.  This style of
+variable can be used to adapt the behavior of LAMMPS input scripts via
+environment variable settings, or to retrieve information that has
+been previously stored with the :doc:`shell putenv <shell>` command.
+Note that because environment variable settings are stored by the
+operating systems, they persist beyond a :doc:`clear <clear>` command.
+
+For the *file* style, a filename is provided which contains a list of
+strings to assign to the variable, one per line.  The strings can be
+numeric values if desired.  See the discussion of the next() function
+below for equal-style variables, which will convert the string of a
+file-style variable into a numeric value in a formula.
+
+When a file-style variable is defined, the file is opened and the
+string on the first line is read and stored with the variable.  This
+means the variable can then be evaluated as many times as desired and
+will return that string.  There are two ways to cause the next string
+from the file to be read: use the :doc:`next <next>` command or the
+next() function in an equal- or atom-style variable, as discussed
+below.
+
+The rules for formatting the file are as follows.  A comment character
+"#" can be used anywhere on a line; text starting with the comment
+character is stripped.  Blank lines are skipped.  The first "word" of
+a non-blank line, delimited by white-space, is the "string" assigned
+to the variable.
+
+For the *atomfile* style, a filename is provided which contains one or
+more sets of values, to assign on a per-atom basis to the variable.
+The format of the file is described below.
+
+When an atomfile-style variable is defined, the file is opened and the
+first set of per-atom values are read and stored with the variable.
+This means the variable can then be evaluated as many times as desired
+and will return those values.  There are two ways to cause the next
+set of per-atom values from the file to be read: use the
+:doc:`next <next>` command or the next() function in an atom-style
+variable, as discussed below.
+
+The rules for formatting the file are as follows.  Each time a set of
+per-atom values is read, a non-blank line is searched for in the file.
+A comment character "#" can be used anywhere on a line; text starting
+with the comment character is stripped.  Blank lines are skipped.  The
+first "word" of a non-blank line, delimited by white-space, is read as
+the count N of per-atom lines to immediately follow.  N can be the
+total number of atoms in the system, or only a subset.  The next N
+lines have the following format
+
+
+.. parsed-literal::
+
+   ID value
+
+where ID is an atom ID and value is the per-atom numeric value that
+will be assigned to that atom.  IDs can be listed in any order.
+
+.. note::
+
+   Every time a set of per-atom lines is read, the value for all
+   atoms is first set to 0.0.  Thus values for atoms whose ID does not
+   appear in the set, will remain 0.0.
+
+For the *python* style a Python function name is provided.  This needs
+to match a function name specified in a :doc:`python <python>` command
+which returns a value to this variable as defined by its *return*
+keyword.  For example these two commands would be self-consistent:
+
+
+.. parsed-literal::
+
+   variable foo python myMultiply
+   python myMultiply return v_foo format f file funcs.py
+
+The two commands can appear in either order so long as both are
+specified before the Python function is invoked for the first time.
+
+Each time the variable is evaluated, the associated Python function is
+invoked, and the value it returns is also returned by the variable.
+Since the Python function can use other LAMMPS variables as input, or
+query interal LAMMPS quantities to perform its computation, this means
+the variable can return a different value each time it is evaluated.
+
+The type of value stored in the variable is determined by the *format*
+keyword of the :doc:`python <python>` command.  It can be an integer
+(i), floating point (f), or string (s) value.  As mentioned above, if
+it is a numeric value (integer or floating point), then the
+python-style variable can be used in place of an equal-style variable
+anywhere in an input script, e.g. as an argument to another command
+that allows for equal-style variables.
+
+For the *internal* style a numeric value is provided.  This value will
+be assigned to the variable until a LAMMPS command sets it to a new
+value.  There are currently only two LAMMPS commands that require
+*internal* variables as inputs, because they reset them:
+:doc:`create\_atoms <create_atoms>` and :doc:`fix controller <fix_controller>`.  As mentioned above, an
+internal-style variable can be used in place of an equal-style
+variable anywhere else in an input script, e.g. as an argument to
+another command that allows for equal-style variables.
+
+
+----------
+
+
+For the *equal* and *vector* and *atom* styles, a single string is
+specified which represents a formula that will be evaluated afresh
+each time the variable is used.  If you want spaces in the string,
+enclose it in double quotes so the parser will treat it as a single
+argument.  For *equal*\ -style variables the formula computes a scalar
+quantity, which becomes the value of the variable whenever it is
+evaluated.  For *vector*\ -style variables the formula must compute a
+vector of quantities, which becomes the value of the variable whenever
+it is evaluated.  The calculated vector can be on length one, but it
+cannot be a simple scalar value like that produced by an equal-style
+compute.  I.e. the formula for a vector-style variable must have at
+least one quantity in it that refers to a global vector produced by a
+compute, fix, or other vector-style variable.  For *atom*\ -style
+variables the formula computes one quantity for each atom whenever it
+is evaluated.
+
+Note that *equal*\ , *vector*\ , and *atom* variables can produce
+different values at different stages of the input script or at
+different times during a run.  For example, if an *equal* variable is
+used in a :doc:`fix print <fix_print>` command, different values could
+be printed each timestep it was invoked.  If you want a variable to be
+evaluated immediately, so that the result is stored by the variable
+instead of the string, see the section below on "Immediate Evaluation
+of Variables".
+
+The next command cannot be used with *equal* or *vector* or *atom*
+style variables, since there is only one string.
+
+The formula for an *equal*\ , *vector*\ , or *atom* variable can contain a
+variety of quantities.  The syntax for each kind of quantity is
+simple, but multiple quantities can be nested and combined in various
+ways to build up formulas of arbitrary complexity.  For example, this
+is a valid (though strange) variable formula:
+
+
+.. parsed-literal::
+
+   variable x equal "pe + c_MyTemp / vol\^(1/3)"
+
+Specifically, a formula can contain numbers, constants, thermo
+keywords, math operators, math functions, group functions, region
+functions, atom values, atom vectors, compute references, fix
+references, and references to other variables.
+
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Number             | 0.2, 100, 1.0e20, -15.4, etc                                                                                                                                                                                                                                                                                                                              |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Constant           | PI, version, on, off, true, false, yes, no                                                                                                                                                                                                                                                                                                                |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Thermo keywords    | vol, pe, ebond, etc                                                                                                                                                                                                                                                                                                                                       |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Math operators     | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y,      x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x                                                                                                                                                                                                                                 |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Math functions     | sqrt(x), exp(x), ln(x), log(x), abs(x),      sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),      random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x),      ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),      logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),      vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Group functions    | count(ID), mass(ID), charge(ID), xcm(ID,dim),      vcm(ID,dim), fcm(ID,dim), bound(ID,dir),      gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim),      inertia(ID,dimdim), omega(ID,dim)                                                                                                                                                             |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Region functions   | count(ID,IDR), mass(ID,IDR), charge(ID,IDR),      xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR),      bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR),      angmom(ID,dim,IDR), torque(ID,dim,IDR),      inertia(ID,dimdim,IDR), omega(ID,dim,IDR)                                                                                                    |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Special functions  | sum(x), min(x), max(x), ave(x), trap(x),      slope(x), gmask(x), rmask(x), grmask(x,y), next(x)                                                                                                                                                                                                                                                          |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Atom values        | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i],              vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]                                                                                                                                                                                                                                            |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Atom vectors       | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q                                                                                                                                                                                                                                                                                                   |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Compute references | c\_ID, c\_ID[i], c\_ID[i][j], C\_ID, C\_ID[i]                                                                                                                                                                                                                                                                                                             |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Fix references     | f\_ID, f\_ID[i], f\_ID[i][j], F\_ID, F\_ID[i]                                                                                                                                                                                                                                                                                                             |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Other variables    | v\_name, v\_name[i]                                                                                                                                                                                                                                                                                                                                       |
++--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+
+Most of the formula elements produce a scalar value.  Some produce a
+global or per-atom vector of values.  Global vectors can be produced
+by computes or fixes or by other vector-style variables.  Per-atom
+vectors are produced by atom vectors, compute references that
+represent a per-atom vector, fix references that represent a per-atom
+vector, and variables that are atom-style variables.  Math functions
+that operate on scalar values produce a scalar value; math function
+that operate on global or per-atom vectors do so element-by-element
+and produce a global or per-atom vector.
+
+A formula for equal-style variables cannot use any formula element
+that produces a global or per-atom vector.  A formula for a
+vector-style variable can use formula elements that produce either a
+scalar value or a global vector value, but cannot use a formula
+element that produces a per-atom vector.  A formula for an atom-style
+variable can use formula elements that produce either a scalar value
+or a per-atom vector, but not one that produces a global vector.
+Atom-style variables are evaluated by other commands that define a
+:doc:`group <group>` on which they operate, e.g. a :doc:`dump <dump>` or
+:doc:`compute <compute>` or :doc:`fix <fix>` command.  When they invoke
+the atom-style variable, only atoms in the group are included in the
+formula evaluation.  The variable evaluates to 0.0 for atoms not in
+the group.
+
+
+----------
+
+
+Numbers, constants, and thermo keywords
+---------------------------------------
+
+Numbers can contain digits, scientific notation
+(3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs.
+
+Constants are set at compile time and cannot be changed. *PI* will
+return the number 3.14159265358979323846; *on*\ , *true* or *yes* will
+return 1.0; *off*\ , *false* or *no* will return 0.0; *version* will
+return a numeric version code of the current LAMMPS version (e.g.
+version 2 Sep 2015 will return the number 20150902). The corresponding
+value for newer versions of LAMMPS will be larger, for older versions
+of LAMMPS will be smaller. This can be used to have input scripts
+adapt automatically to LAMMPS versions, when non-backwards compatible
+syntax changes are introduced. Here is an illustrative example (which
+will not work, since the *version* has been introduced more recently):
+
+
+.. parsed-literal::
+
+   if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"
+
+The thermo keywords allowed in a formula are those defined by the
+:doc:`thermo\_style custom <thermo_style>` command.  Thermo keywords that
+require a :doc:`compute <compute>` to calculate their values such as
+"temp" or "press", use computes stored and invoked by the
+:doc:`thermo\_style <thermo_style>` command.  This means that you can
+only use those keywords in a variable if the style you are using with
+the thermo\_style command (and the thermo keywords associated with that
+style) also define and use the needed compute.  Note that some thermo
+keywords use a compute indirectly to calculate their value (e.g. the
+enthalpy keyword uses temp, pe, and pressure).  If a variable is
+evaluated directly in an input script (not during a run), then the
+values accessed by the thermo keyword must be current.  See the
+discussion below about "Variable Accuracy".
+
+
+----------
+
+
+Math Operators
+--------------
+
+Math operators are written in the usual way, where the "x" and "y" in
+the examples can themselves be arbitrarily complex formulas, as in the
+examples above.  In this syntax, "x" and "y" can be scalar values or
+per-atom vectors.  For example, "ke/natoms" is the division of two
+scalars, where "vy+vz" is the element-by-element sum of two per-atom
+vectors of y and z velocities.
+
+Operators are evaluated left to right and have the usual C-style
+precedence: unary minus and unary logical NOT operator "!" have the
+highest precedence, exponentiation "\^" is next; multiplication and
+division and the modulo operator "%" are next; addition and
+subtraction are next; the 4 relational operators "<", "<=", ">", and
+">=" are next; the two remaining relational operators "==" and "!="
+are next; then the logical AND operator "&&"; and finally the logical
+OR operator "\|\|" and logical XOR (exclusive or) operator "\|\^" have the
+lowest precedence.  Parenthesis can be used to group one or more
+portions of a formula and/or enforce a different order of evaluation
+than what would occur with the default precedence.
+
+.. note::
+
+   Because a unary minus is higher precedence than exponentiation,
+   the formula "-2\^2" will evaluate to 4, not -4.  This convention is
+   compatible with some programming languages, but not others.  As
+   mentioned, this behavior can be easily overridden with parenthesis;
+   the formula "-(2\^2)" will evaluate to -4.
+
+The 6 relational operators return either a 1.0 or 0.0 depending on
+whether the relationship between x and y is TRUE or FALSE.  For
+example the expression x<10.0 in an atom-style variable formula will
+return 1.0 for all atoms whose x-coordinate is less than 10.0, and 0.0
+for the others.  The logical AND operator will return 1.0 if both its
+arguments are non-zero, else it returns 0.0.  The logical OR operator
+will return 1.0 if either of its arguments is non-zero, else it
+returns 0.0.  The logical XOR operator will return 1.0 if one of its
+arguments is zero and the other non-zero, else it returns 0.0.  The
+logical NOT operator returns 1.0 if its argument is 0.0, else it
+returns 0.0.
+
+These relational and logical operators can be used as a masking or
+selection operation in a formula.  For example, the number of atoms
+whose properties satisfy one or more criteria could be calculated by
+taking the returned per-atom vector of ones and zeroes and passing it
+to the :doc:`compute reduce <compute_reduce>` command.
+
+
+----------
+
+
+Math Functions
+--------------
+
+Math functions are specified as keywords followed by one or more
+parenthesized arguments "x", "y", "z", each of which can themselves be
+arbitrarily complex formulas.  In this syntax, the arguments can
+represent scalar values or global vectors or per-atom vectors.  In the
+latter case, the math operation is performed on each element of the
+vector.  For example, "sqrt(natoms)" is the sqrt() of a scalar, where
+"sqrt(y\*z)" yields a per-atom vector with each element being the
+sqrt() of the product of one atom's y and z coordinates.
+
+Most of the math functions perform obvious operations.  The ln() is
+the natural log; log() is the base 10 log.
+
+The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z =
+seed.  It generates a uniform random number between lo and hi.  The
+normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and
+z = seed.  It generates a Gaussian variate centered on mu with
+variance sigma\^2.  In both cases the seed is used the first time the
+internal random number generator is invoked, to initialize it.  For
+equal-style and vector-style variables, every processor uses the same
+seed so that they each generate the same sequence of random numbers.
+For atom-style variables, a unique seed is created for each processor,
+based on the specified seed.  This effectively generates a different
+random number for each atom being looped over in the atom-style
+variable.
+
+.. note::
+
+   Internally, there is just one random number generator for all
+   equal-style and vector-style variables and another one for all
+   atom-style variables.  If you define multiple variables (of each
+   style) which use the random() or normal() math functions, then the
+   internal random number generators will only be initialized once, which
+   means only one of the specified seeds will determine the sequence of
+   generated random numbers.
+
+The ceil(), floor(), and round() functions are those in the C math
+library.  Ceil() is the smallest integer not less than its argument.
+Floor() if the largest integer not greater than its argument.  Round()
+is the nearest integer to its argument.
+
+The ramp(x,y) function uses the current timestep to generate a value
+linearly interpolated between the specified x,y values over the course
+of a run, according to this formula:
+
+
+.. parsed-literal::
+
+   value = x + (y-x) \* (timestep-startstep) / (stopstep-startstep)
+
+The run begins on startstep and ends on stopstep.  Startstep and
+stopstep can span multiple runs, using the *start* and *stop* keywords
+of the :doc:`run <run>` command.  See the :doc:`run <run>` command for
+details of how to do this.
+
+The stagger(x,y) function uses the current timestep to generate a new
+timestep.  X,y > 0 and x > y are required.  The generated timesteps
+increase in a staggered fashion, as the sequence
+x,x+y,2x,2x+y,3x,3x+y,etc.  For any current timestep, the next
+timestep in the sequence is returned.  Thus if stagger(1000,100) is
+used in a variable by the :doc:`dump\_modify every <dump_modify>`
+command, it will generate the sequence of output timesteps:
+
+
+.. parsed-literal::
+
+   100,1000,1100,2000,2100,3000,etc
+
+The logfreq(x,y,z) function uses the current timestep to generate a
+new timestep.  X,y,z > 0 and y < z are required.  The generated
+timesteps are on a base-z logarithmic scale, starting with x, and the
+y value is how many of the z-1 possible timesteps within one
+logarithmic interval are generated.  I.e. the timesteps follow the
+sequence x,2x,3x,...y\*x,x\*z,2x\*z,3x\*z,...y\*x\*z,x\*z\^2,2x\*z\^2,etc.  For
+any current timestep, the next timestep in the sequence is returned.
+Thus if logfreq(100,4,10) is used in a variable by the :doc:`dump\_modify every <dump_modify>` command, it will generate this sequence of
+output timesteps:
+
+
+.. parsed-literal::
+
+   100,200,300,400,1000,2000,3000,4000,10000,20000,etc
+
+The logfreq2(x,y,z) function is similar to logfreq, except a single
+logarithmic interval is divided into y equally-spaced timesteps and
+all of them are output.  Y < z is not required.  Thus, if
+logfreq2(100,18,10) is used in a variable by the :doc:`dump\_modify every <dump_modify>` command, then the interval between 100 and
+1000 is divided as 900/18 = 50 steps, and it will generate the
+sequence of output timesteps:
+
+
+.. parsed-literal::
+
+   100,150,200,...950,1000,1500,2000,...9500,10000,15000,etc
+
+The logfreq3(x,y,z) function generates y points between x and z (inclusive),
+that are separated by a multiplicative ratio: (z/x)\^(1/(y-1)). Constraints
+are: x,z > 0, y > 1, z-x >= y-1. For eg., if logfreq3(10,25,1000) is used in
+a variable by the :doc:`fix print <fix_print>` command, then the interval
+between 10 and 1000 is divided into 24 parts with a multiplicative
+separation of ~1.21, and it will generate the following sequence of output
+timesteps:
+
+
+.. parsed-literal::
+
+   10, 13, 15, 18, 22, 27, 32,...384, 465, 563, 682, 826, 1000
+
+The stride(x,y,z) function uses the current timestep to generate a new
+timestep.  X,y >= 0 and z > 0 and x <= y are required.  The generated
+timesteps increase in increments of z, from x to y, i.e. it generates
+the sequence x,x+z,x+2z,...,y.  If y-x is not a multiple of z, then
+similar to the way a for loop operates, the last value will be one
+that does not exceed y.  For any current timestep, the next timestep
+in the sequence is returned.  Thus if stride(1000,2000,100) is used
+in a variable by the :doc:`dump\_modify every <dump_modify>` command, it
+will generate the sequence of output timesteps:
+
+
+.. parsed-literal::
+
+   1000,1100,1200, ... ,1900,2000
+
+The stride2(x,y,z,a,b,c) function is similar to the stride() function
+except it generates two sets of strided timesteps, one at a coarser
+level and one at a finer level.  Thus it is useful for debugging,
+e.g. to produce output every timestep at the point in simulation when
+a problem occurs.  X,y >= 0 and z > 0 and x <= y are required, as are
+a,b >= 0 and c > 0 and a < b.  Also, a >= x and b <= y are required so
+that the second stride is inside the first.  The generated timesteps
+increase in increments of z, starting at x, until a is reached.  At
+that point the timestep increases in increments of c, from a to b,
+then after b, increments by z are resumed until y is reached.  For any
+current timestep, the next timestep in the sequence is returned.  Thus
+if stride2(1000,2000,100,1350,1360,1) is used in a variable by the
+:doc:`dump\_modify every <dump_modify>` command, it will generate the
+sequence of output timesteps:
+
+
+.. parsed-literal::
+
+   1000,1100,1200,1300,1350,1351,1352, ... 1359,1360,1400,1500, ... ,2000
+
+The vdisplace(x,y) function takes 2 arguments: x = value0 and y =
+velocity, and uses the elapsed time to change the value by a linear
+displacement due to the applied velocity over the course of a run,
+according to this formula:
+
+
+.. parsed-literal::
+
+   value = value0 + velocity\*(timestep-startstep)\*dt
+
+where dt = the timestep size.
+
+The run begins on startstep.  Startstep can span multiple runs, using
+the *start* keyword of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.  Note that the
+:doc:`thermo\_style <thermo_style>` keyword elaplong =
+timestep-startstep.
+
+The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments:
+x = value0, y = amplitude, z = period.  They use the elapsed time to
+oscillate the value by a sin() or cos() function over the course of a
+run, according to one of these formulas, where omega = 2 PI / period:
+
+
+.. parsed-literal::
+
+   value = value0 + Amplitude \* sin(omega\*(timestep-startstep)\*dt)
+   value = value0 + Amplitude \* (1 - cos(omega\*(timestep-startstep)\*dt))
+
+where dt = the timestep size.
+
+The run begins on startstep.  Startstep can span multiple runs, using
+the *start* keyword of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.  Note that the
+:doc:`thermo\_style <thermo_style>` keyword elaplong =
+timestep-startstep.
+
+
+----------
+
+
+Group and Region Functions
+--------------------------
+
+Group functions are specified as keywords followed by one or two
+parenthesized arguments.  The first argument *ID* is the group-ID.
+The *dim* argument, if it exists, is *x* or *y* or *z*\ .  The *dir*
+argument, if it exists, is *xmin*\ , *xmax*\ , *ymin*\ , *ymax*\ , *zmin*\ , or
+*zmax*\ .  The *dimdim* argument, if it exists, is *xx* or *yy* or *zz*
+or *xy* or *yz* or *xz*\ .
+
+The group function count() is the number of atoms in the group.  The
+group functions mass() and charge() are the total mass and charge of
+the group.  Xcm() and vcm() return components of the position and
+velocity of the center of mass of the group.  Fcm() returns a
+component of the total force on the group of atoms.  Bound() returns
+the min/max of a particular coordinate for all atoms in the group.
+Gyration() computes the radius-of-gyration of the group of atoms.  See
+the :doc:`compute gyration <compute_gyration>` command for a definition
+of the formula.  Angmom() returns components of the angular momentum
+of the group of atoms around its center of mass.  Torque() returns
+components of the torque on the group of atoms around its center of
+mass, based on current forces on the atoms.  Inertia() returns one of
+6 components of the symmetric inertia tensor of the group of atoms
+around its center of mass, ordered as Ixx,Iyy,Izz,Ixy,Iyz,Ixz.
+Omega() returns components of the angular velocity of the group of
+atoms around its center of mass.
+
+Region functions are specified exactly the same way as group functions
+except they take an extra final argument *IDR* which is the region ID.
+The function is computed for all atoms that are in both the group and
+the region.  If the group is "all", then the only criteria for atom
+inclusion is that it be in the region.
+
+
+----------
+
+
+Special Functions
+-----------------
+
+Special functions take specific kinds of arguments, meaning their
+arguments cannot be formulas themselves.
+
+The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
+each take 1 argument which is of the form "c\_ID" or "c\_ID[N]" or
+"f\_ID" or "f\_ID[N]" or "v\_name".  The first two are computes and the
+second two are fixes; the ID in the reference should be replaced by
+the ID of a compute or fix defined elsewhere in the input script.  The
+compute or fix must produce either a global vector or array.  If it
+produces a global vector, then the notation without "[N]" should be
+used.  If it produces a global array, then the notation with "[N]"
+should be used, when N is an integer, to specify which column of the
+global array is being referenced.  The last form of argument "v\_name"
+is for a vector-style variable where "name" is replaced by the name of
+the variable.
+
+These functions operate on a global vector of inputs and reduce it to
+a single scalar value.  This is analogous to the operation of the
+:doc:`compute reduce <compute_reduce>` command, which performs similar
+operations on per-atom and local vectors.
+
+The sum() function calculates the sum of all the vector elements.  The
+min() and max() functions find the minimum and maximum element
+respectively.  The ave() function is the same as sum() except that it
+divides the result by the length of the vector.
+
+The trap() function is the same as sum() except the first and last
+elements are multiplied by a weighting factor of 1/2 when performing
+the sum.  This effectively implements an integration via the
+trapezoidal rule on the global vector of data.  I.e. consider a set of
+points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2),
+..., (N,VN), where the Vi are the values in the global vector of
+length N.  The integral from 1 to N of these points is trap().  When
+appropriately normalized by the timestep size, this function is useful
+for calculating integrals of time-series data, like that generated by
+the :doc:`fix ave/correlate <fix_ave_correlate>` command.
+
+The slope() function uses linear regression to fit a line to the set
+of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2),
+..., (N,VN), where the Vi are the values in the global vector of
+length N.  The returned value is the slope of the line.  If the line
+has a single point or is vertical, it returns 1.0e20.
+
+The gmask(x) function takes 1 argument which is a group ID.  It
+can only be used in atom-style variables.  It returns a 1 for
+atoms that are in the group, and a 0 for atoms that are not.
+
+The rmask(x) function takes 1 argument which is a region ID.  It can
+only be used in atom-style variables.  It returns a 1 for atoms that
+are in the geometric region, and a 0 for atoms that are not.
+
+The grmask(x,y) function takes 2 arguments.  The first is a group ID,
+and the second is a region ID.  It can only be used in atom-style
+variables.  It returns a 1 for atoms that are in both the group and
+region, and a 0 for atoms that are not in both.
+
+The next(x) function takes 1 argument which is a variable ID (not
+"v\_foo", just "foo").  It must be for a file-style or atomfile-style
+variable.  Each time the next() function is invoked (i.e. each time
+the equal-style or atom-style variable is evaluated), the following
+steps occur.
+
+For file-style variables, the current string value stored by the
+file-style variable is converted to a numeric value and returned by
+the function.  And the next string value in the file is read and
+stored.  Note that if the line previously read from the file was not a
+numeric string, then it will typically evaluate to 0.0, which is
+likely not what you want.
+
+For atomfile-style variables, the current per-atom values stored by
+the atomfile-style variable are returned by the function.  And the
+next set of per-atom values in the file is read and stored.
+
+Since file-style and atomfile-style variables read and store the first
+line of the file or first set of per-atoms values when they are
+defined in the input script, these are the value(s) that will be
+returned the first time the next() function is invoked.  If next() is
+invoked more times than there are lines or sets of lines in the file,
+the variable is deleted, similar to how the :doc:`next <next>` command
+operates.
+
+
+----------
+
+
+Feature Functions
+-----------------
+
+Feature functions allow to probe the running LAMMPS executable for
+whether specific features are either active, defined, or available.
+The functions take two arguments, a *category* and a corresponding
+*argument*\ . The arguments are strings thus cannot be formulas
+themselves (only $-style immediate variable expansion is possible).
+Return value is either 1.0 or 0.0 depending on whether the function
+evaluates to true or false, respectively.
+
+The *is\_active()* function allows to query for active settings which
+are grouped by categories. Currently supported categories and
+arguments are:
+
+* *package* (argument = *gpu* or *intel* or *kokkos* or *omp*\ )
+* *newton* (argument = *pair* or *bond* or *any*\ )
+* *pair* (argument = *single* or *respa* or *manybody* or *tail* or *shift*\ )
+* *comm\_style* (argument = *brick* or *tiled*\ )
+* *min\_style* (argument = any of the compiled in minimizer styles)
+* *run\_style* (argument = any of the compiled in run styles)
+* *atom\_style* (argument = any of the compiled in atom styles)
+* *pair\_style* (argument = any of the compiled in pair styles)
+* *bond\_style* (argument = any of the compiled in bond styles)
+* *angle\_style* (argument = any of the compiled in angle styles)
+* *dihedral\_style* (argument = any of the compiled in dihedral styles)
+* *improper\_style* (argument = any of the compiled in improper styles)
+* *kspace\_style* (argument = any of the compiled in kspace styles)
+
+Most of the settings are self-explanatory, the *single* argument in the
+*pair* category allows to check whether a pair style supports a
+Pair::single() function as needed by compute group/group and others
+features or LAMMPS, *respa* allows to check whether the inner/middle/outer
+mode of r-RESPA is supported. In the various style categories,
+the checking is also done using suffix flags, if available and enabled.
+
+Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP).
+
+
+.. parsed-literal::
+
+   pair_style lj/cut/coul/long 14.0
+   if $(is_active(package,gpu)) then "suffix off"
+   kspace_style pppm
+
+Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step
+
+
+.. parsed-literal::
+
+   timestep $(2.0\*(1.0+2.0\*is_active(pair,respa))
+   if $(is_active(pair,respa)) then "run_style respa 4 3 2 2  improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2  improper 1 pair 2 kspace 3"
+
+The *is\_defined()* function allows to query categories like *compute*\ ,
+*dump*\ , *fix*\ , *group*\ , *region*\ , and *variable* whether an entry
+with the provided name or id is defined.
+
+The *is\_available(category,name)* function allows to query whether
+a specific optional feature is available, i.e. compiled in.
+This currently works for the following categories: *command*\ ,
+*compute*\ , *fix*\ , *pair\_style* and *feature*\ . For all categories
+except *command* and *feature* also appending active suffixes is
+tried before reporting failure.
+
+The *feature* category is used to check the availability of compiled in
+features such as GZIP support, PNG support, JPEG support, FFMPEG support,
+and C++ exceptions for error handling. Corresponding values for name are
+*gzip*\ , *png*\ , *jpeg*\ , *ffmpeg* and *exceptions*\ .
+
+This enables writing input scripts which only dump using a given format if
+the compiled binary supports it.
+
+
+.. parsed-literal::
+
+   if "$(is_available(feature,png))" then "print 'PNG supported'" else "print 'PNG not supported'"
+
+   if "$(is_available(feature,ffmpeg)" then "dump 3 all movie 25 movie.mp4 type type zoom 1.6 adiam 1.0"
+
+
+----------
+
+
+Atom Values and Vectors
+-----------------------
+
+Atom values take an integer argument I from 1 to N, where I is the
+atom-ID, e.g. x[243], which means use the x coordinate of the atom
+with ID = 243.  Or they can take a variable name, specified as v\_name,
+where name is the name of the variable, like x[v\_myIndex].  The
+variable can be of any style except *vector* or *atom* or *atomfile*
+variables.  The variable is evaluated and the result is expected to be
+numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an
+index, which must be a value from 1 to N.  Note that a "formula"
+cannot be used as the argument between the brackets, e.g. x[243+10]
+or x[v\_myIndex+1] are not allowed.  To do this a single variable can
+be defined that contains the needed formula.
+
+Note that the 0 < atom-ID <= N, where N is the largest atom ID
+in the system.  If an ID is specified for an atom that does not
+currently exist, then the generated value is 0.0.
+
+Atom vectors generate one value per atom, so that a reference like
+"vx" means the x-component of each atom's velocity will be used when
+evaluating the variable.
+
+The meaning of the different atom values and vectors is mostly
+self-explanatory.  *Mol* refers to the molecule ID of an atom, and is
+only defined if an :doc:`atom\_style <atom_style>` is being used that
+defines molecule IDs.
+
+Note that many other atom attributes can be used as inputs to a
+variable by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+a quantity from that compute.
+
+
+----------
+
+
+Compute References
+------------------
+
+Compute references access quantities calculated by a
+:doc:`compute <compute>`.  The ID in the reference should be replaced by
+the ID of a compute defined elsewhere in the input script.  As
+discussed in the doc page for the :doc:`compute <compute>` command,
+computes can produce global, per-atom, or local values.  Only global
+and per-atom values can be used in a variable.  Computes can also
+produce a scalar, vector, or array.
+
+An equal-style variable can only use scalar values, which means a
+global scalar, or an element of a global or per-atom vector or array.
+A vector-style variable can use scalar values or a global vector of
+values, or a column of a global array of values.  Atom-style variables
+can use global scalar values.  They can also use per-atom vector
+values, or a column of a per-atom array.  See the doc pages for
+individual computes to see what kind of values they produce.
+
+Examples of different kinds of compute references are as follows.
+There is typically no ambiguity (see exception below) as to what a
+reference means, since computes only produce either global or per-atom
+quantities, never both.
+
++-------------+-------------------------------------------------------------------------------------------------------+
+| c\_ID       | global scalar, or per-atom vector                                                                     |
++-------------+-------------------------------------------------------------------------------------------------------+
+| c\_ID[I]    | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array |
++-------------+-------------------------------------------------------------------------------------------------------+
+| c\_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array                                  |
++-------------+-------------------------------------------------------------------------------------------------------+
+
+For I and J indices, integers can be specified or a variable name,
+specified as v\_name, where name is the name of the variable.  The
+rules for this syntax are the same as for the "Atom Values and
+Vectors" discussion above.
+
+One source of ambiguity for compute references is when a vector-style
+variable refers to a compute that produces both a global scalar and a
+global vector.  Consider a compute with ID "foo" that does this,
+referenced as follows by variable "a", where "myVec" is another
+vector-style variable:
+
+
+.. parsed-literal::
+
+   variable a vector c_foo\*v_myVec
+
+The reference "c\_foo" could refer to either the global scalar or
+global vector produced by compute "foo".  In this case, "c\_foo" will
+always refer to the global scalar, and "C\_foo" can be used to
+reference the global vector.  Similarly if the compute produces both a
+global vector and global array, then "c\_foo[I]" will always refer to
+an element of the global vector, and "C\_foo[I]" can be used to
+reference the Ith column of the global array.
+
+Note that if a variable containing a compute is evaluated directly in
+an input script (not during a run), then the values accessed by the
+compute must be current.  See the discussion below about "Variable
+Accuracy".
+
+
+----------
+
+
+Fix References
+--------------
+
+Fix references access quantities calculated by a :doc:`fix <compute>`.
+The ID in the reference should be replaced by the ID of a fix defined
+elsewhere in the input script.  As discussed in the doc page for the
+:doc:`fix <fix>` command, fixes can produce global, per-atom, or local
+values.  Only global and per-atom values can be used in a variable.
+Fixes can also produce a scalar, vector, or array.  An equal-style
+variable can only use scalar values, which means a global scalar, or
+an element of a global or per-atom vector or array.  Atom-style
+variables can use the same scalar values.  They can also use per-atom
+vector values.  A vector value can be a per-atom vector itself, or a
+column of an per-atom array.  See the doc pages for individual fixes
+to see what kind of values they produce.
+
+The different kinds of fix references are exactly the same as the
+compute references listed in the above table, where "c\_" is replaced
+by "f\_".  Again, there is typically no ambiguity (see exception below)
+as to what a reference means, since fixes only produce either global
+or per-atom quantities, never both.
+
++-------------+-------------------------------------------------------------------------------------------------------+
+| f\_ID       | global scalar, or per-atom vector                                                                     |
++-------------+-------------------------------------------------------------------------------------------------------+
+| f\_ID[I]    | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array |
++-------------+-------------------------------------------------------------------------------------------------------+
+| f\_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array                                  |
++-------------+-------------------------------------------------------------------------------------------------------+
+
+For I and J indices, integers can be specified or a variable name,
+specified as v\_name, where name is the name of the variable.  The
+rules for this syntax are the same as for the "Atom Values and
+Vectors" discussion above.
+
+One source of ambiguity for fix references is the same ambiguity
+discussed for compute references above.  Namely when a vector-style
+variable refers to a fix that produces both a global scalar and a
+global vector.  The solution is the same as for compute references.
+For a fix with ID "foo", "f\_foo" will always refer to the global
+scalar, and "F\_foo" can be used to reference the global vector.  And
+similarly for distinguishing between a fix's global vector versus
+global array with "f\_foo[I]" versus "F\_foo[I]".
+
+Note that if a variable containing a fix is evaluated directly in an
+input script (not during a run), then the values accessed by the fix
+should be current.  See the discussion below about "Variable
+Accuracy".
+
+Note that some fixes only generate quantities on certain timesteps.
+If a variable attempts to access the fix on non-allowed timesteps, an
+error is generated.  For example, the :doc:`fix ave/time <fix_ave_time>`
+command may only generate averaged quantities every 100 steps.  See
+the doc pages for individual fix commands for details.
+
+
+----------
+
+
+Variable References
+-------------------
+
+Variable references access quantities stored or calculated by other
+variables, which will cause those variables to be evaluated.  The name
+in the reference should be replaced by the name of a variable defined
+elsewhere in the input script.
+
+As discussed on this doc page, equal-style variables generate a single
+global numeric value, vector-style variables generate a vector of
+global numeric values, and atom-style and atomfile-style variables
+generate a per-atom vector of numeric values.  All other variables
+store one or more strings.
+
+The formula for an equal-style variable can use any style of variable
+including a vector\_style or atom-style or atomfile-style.  For these
+3 styles, a subscript must be used to access a single value from
+the vector-, atom-, or atomfile-style variable.  If a string-storing
+variable is used, the string is converted to a numeric value.  Note
+that this will typically produce a 0.0 if the string is not a numeric
+string, which is likely not what you want.
+
+The formula for a vector-style variable can use any style of variable,
+including atom-style or atomfile-style variables.  For these 2 styles,
+a subscript must be used to access a single value from the atom-, or
+atomfile-style variable.
+
+The formula for an atom-style variable can use any style of variable,
+including other atom-style or atomfile-style variables.  If it uses a
+vector-style variable, a subscript must be used to access a single
+value from the vector-style variable.
+
+Examples of different kinds of variable references are as follows.
+There is no ambiguity as to what a reference means, since variables
+produce only a global scalar or global vector or per-atom vector.
+
++------------+----------------------------------------------------------------------+
+| v\_name    | global scalar from equal-style variable                              |
++------------+----------------------------------------------------------------------+
+| v\_name    | global vector from vector-style variable                             |
++------------+----------------------------------------------------------------------+
+| v\_name    | per-atom vector from atom-style or atomfile-style variable           |
++------------+----------------------------------------------------------------------+
+| v\_name[I] | Ith element of a global vector from vector-style variable            |
++------------+----------------------------------------------------------------------+
+| v\_name[I] | value of atom with ID = I from atom-style or atomfile-style variable |
++------------+----------------------------------------------------------------------+
+
+For the I index, an integer can be specified or a variable name,
+specified as v\_name, where name is the name of the variable.  The
+rules for this syntax are the same as for the "Atom Values and
+Vectors" discussion above.
+
+
+----------
+
+
+**Immediate Evaluation of Variables:**
+
+If you want an equal-style variable to be evaluated immediately, it
+may be the case that you do not need to define a variable at all.  See
+the :doc:`Commands parse <Commands_parse>` doc page for info on how to
+use "immediate" variables in an input script, specified as $(formula)
+with parenthesis, where the formula has the same syntax as equal-style
+variables described on this page.  This effectively evaluates a
+formula immediately without using the variable command to define a
+named variable.
+
+More generally, there is a difference between referencing a variable
+with a leading $ sign (e.g. $x or ${abc}) versus with a leading "v\_"
+(e.g. v\_x or v\_abc).  The former can be used in any input script
+command, including a variable command.  The input script parser
+evaluates the reference variable immediately and substitutes its value
+into the command.  As explained on the :doc:`Commands parse <Commands_parse>` doc page, you can also use un-named
+"immediate" variables for this purpose.  For example, a string like
+this $((xlo+xhi)/2+sqrt(v\_area)) in an input script command evaluates
+the string between the parenthesis as an equal-style variable formula.
+
+Referencing a variable with a leading "v\_" is an optional or required
+kind of argument for some commands (e.g. the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` or
+:doc:`thermo\_style <thermo_style>` commands) if you wish it to evaluate
+a variable periodically during a run.  It can also be used in a
+variable formula if you wish to reference a second variable.  The
+second variable will be evaluated whenever the first variable is
+evaluated.
+
+As an example, suppose you use this command in your input script to
+define the variable "v" as
+
+
+.. parsed-literal::
+
+   variable v equal vol
+
+before a run where the simulation box size changes.  You might think
+this will assign the initial volume to the variable "v".  That is not
+the case.  Rather it assigns a formula which evaluates the volume
+(using the thermo\_style keyword "vol") to the variable "v".  If you
+use the variable "v" in some other command like :doc:`fix ave/time <fix_ave_time>` then the current volume of the box will be
+evaluated continuously during the run.
+
+If you want to store the initial volume of the system, you can do it
+this way:
+
+
+.. parsed-literal::
+
+   variable v equal vol
+   variable v0 equal $v
+
+The second command will force "v" to be evaluated (yielding the
+initial volume) and assign that value to the variable "v0".  Thus the
+command
+
+
+.. parsed-literal::
+
+   thermo_style custom step v_v v_v0
+
+would print out both the current and initial volume periodically
+during the run.
+
+Note that it is a mistake to enclose a variable formula in double
+quotes if it contains variables preceded by $ signs.  For example,
+
+
+.. parsed-literal::
+
+   variable vratio equal "${vfinal}/${v0}"
+
+This is because the quotes prevent variable substitution (explained on
+the :doc:`Commands parse <Commands_parse>` doc page), and thus an error
+will occur when the formula for "vratio" is evaluated later.
+
+
+----------
+
+
+**Variable Accuracy:**
+
+Obviously, LAMMPS attempts to evaluate variables containing formulas
+(\ *equal* and *atom* style variables) accurately whenever the
+evaluation is performed.  Depending on what is included in the
+formula, this may require invoking a :doc:`compute <compute>`, either
+directly or indirectly via a thermo keyword, or accessing a value
+previously calculated by a compute, or accessing a value calculated
+and stored by a :doc:`fix <fix>`.  If the compute is one that calculates
+the pressure or energy of the system, then these quantities need to be
+tallied during the evaluation of the interatomic potentials (pair,
+bond, etc) on timesteps that the variable will need the values.
+
+LAMMPS keeps track of all of this during a :doc:`run <run>` or :doc:`energy minimization <minimize>`.  An error will be generated if you
+attempt to evaluate a variable on timesteps when it cannot produce
+accurate values.  For example, if a :doc:`thermo\_style custom <thermo_style>` command prints a variable which accesses
+values stored by a :doc:`fix ave/time <fix_ave_time>` command and the
+timesteps on which thermo output is generated are not multiples of the
+averaging frequency used in the fix command, then an error will occur.
+
+An input script can also request variables be evaluated before or
+after or in between runs, e.g. by including them in a
+:doc:`print <print>` command.  In this case, if a compute is needed to
+evaluate a variable (either directly or indirectly), LAMMPS will not
+invoke the compute, but it will use a value previously calculated by
+the compute, and can do this only if it was invoked on the current
+timestep.  Fixes will always provide a quantity needed by a variable,
+but the quantity may or may not be current.  This leads to one of
+three kinds of behavior:
+
+(1) The variable may be evaluated accurately.  If it contains
+references to a compute or fix, and these values were calculated on
+the last timestep of a preceding run, then they will be accessed and
+used by the variable and the result will be accurate.
+
+(2) LAMMPS may not be able to evaluate the variable and will generate
+an error message stating so.  For example, if the variable requires a
+quantity from a :doc:`compute <compute>` that has not been invoked on
+the current timestep, LAMMPS will generate an error.  This means, for
+example, that such a variable cannot be evaluated before the first run
+has occurred.  Likewise, in between runs, a variable containing a
+compute cannot be evaluated unless the compute was invoked on the last
+timestep of the preceding run, e.g. by thermodynamic output.
+
+One way to get around this problem is to perform a 0-timestep run
+before using the variable.  For example, these commands
+
+
+.. parsed-literal::
+
+   variable t equal temp
+   print "Initial temperature = $t"
+   run 1000
+
+will generate an error if the run is the first run specified in the
+input script, because generating a value for the "t" variable requires
+a compute for calculating the temperature to be invoked.
+
+However, this sequence of commands would be fine:
+
+
+.. parsed-literal::
+
+   run 0
+   variable t equal temp
+   print "Initial temperature = $t"
+   run 1000
+
+The 0-timestep run initializes and invokes various computes, including
+the one for temperature, so that the value it stores is current and
+can be accessed by the variable "t" after the run has completed.  Note
+that a 0-timestep run does not alter the state of the system, so it
+does not change the input state for the 1000-timestep run that
+follows.  Also note that the 0-timestep run must actually use and
+invoke the compute in question (e.g. via :doc:`thermo <thermo_style>` or
+:doc:`dump <dump>` output) in order for it to enable the compute to be
+used in a variable after the run.  Thus if you are trying to print a
+variable that uses a compute you have defined, you can insure it is
+invoked on the last timestep of the preceding run by including it in
+thermodynamic output.
+
+Unlike computes, :doc:`fixes <fix>` will never generate an error if
+their values are accessed by a variable in between runs.  They always
+return some value to the variable.  However, the value may not be what
+you expect if the fix has not yet calculated the quantity of interest
+or it is not current.  For example, the :doc:`fix indent <fix_indent>`
+command stores the force on the indenter.  But this is not computed
+until a run is performed.  Thus if a variable attempts to print this
+value before the first run, zeroes will be output.  Again, performing
+a 0-timestep run before printing the variable has the desired effect.
+
+(3) The variable may be evaluated incorrectly and LAMMPS may have no
+way to detect this has occurred.  Consider the following sequence of
+commands:
+
+
+.. parsed-literal::
+
+   pair_coeff 1 1 1.0 1.0
+   run 1000
+   pair_coeff 1 1 1.5 1.0
+   variable e equal pe
+   print "Final potential energy = $e"
+
+The first run is performed using one setting for the pairwise
+potential defined by the :doc:`pair\_style <pair_style>` and
+:doc:`pair\_coeff <pair_coeff>` commands.  The potential energy is
+evaluated on the final timestep and stored by the :doc:`compute pe <compute_pe>` compute (this is done by the
+:doc:`thermo\_style <thermo_style>` command).  Then a pair coefficient is
+changed, altering the potential energy of the system.  When the
+potential energy is printed via the "e" variable, LAMMPS will use the
+potential energy value stored by the :doc:`compute pe <compute_pe>`
+compute, thinking it is current.  There are many other commands which
+could alter the state of the system between runs, causing a variable
+to evaluate incorrectly.
+
+The solution to this issue is the same as for case (2) above, namely
+perform a 0-timestep run before the variable is evaluated to insure
+the system is up-to-date.  For example, this sequence of commands
+would print a potential energy that reflected the changed pairwise
+coefficient:
+
+
+.. parsed-literal::
+
+   pair_coeff 1 1 1.0 1.0
+   run 1000
+   pair_coeff 1 1 1.5 1.0
+   run 0
+   variable e equal pe
+   print "Final potential energy = $e"
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Indexing any formula element by global atom ID, such as an atom value,
+requires the :doc:`atom style <atom_style>` to use a global mapping in
+order to look up the vector indices.  By default, only atom styles
+with molecular information create global maps.  The :doc:`atom\_modify map <atom_modify>` command can override the default, e.g. for
+atomic-style atom styles.
+
+All *universe*\ - and *uloop*\ -style variables defined in an input script
+must have the same number of values.
+
+Related commands
+""""""""""""""""
+
+:doc:`next <next>`, :doc:`jump <jump>`, :doc:`include <include>`,
+:doc:`temper <temper>`, :doc:`fix print <fix_print>`, :doc:`print <print>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst
new file mode 100644
index 0000000000..5a4bb33d0c
--- /dev/null
+++ b/doc/src/velocity.rst
@@ -0,0 +1,288 @@
+.. index:: velocity
+
+velocity command
+================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   velocity group-ID style args keyword value ...
+
+* group-ID = ID of group of atoms whose velocity will be changed
+* style = *create* or *set* or *scale* or *ramp* or *zero*
+  
+  .. parsed-literal::
+  
+       *create* args = temp seed
+         temp = temperature value (temperature units)
+         seed = random # seed (positive integer)
+       *set* args = vx vy vz
+         vx,vy,vz = velocity value or NULL (velocity units)
+         any of vx,vy,vz van be a variable (see below)
+       *scale* arg = temp
+         temp = temperature value (temperature units)
+       *ramp* args = vdim vlo vhi dim clo chi
+         vdim = *vx* or *vy* or *vz*
+         vlo,vhi = lower and upper velocity value (velocity units)
+         dim = *x* or *y* or *z*
+         clo,chi = lower and upper coordinate bound (distance units)
+       *zero* arg = *linear* or *angular*
+         *linear* = zero the linear momentum
+         *angular* = zero the angular momentum
+
+* zero or more keyword/value pairs may be appended
+* keyword = *dist* or *sum* or *mom* or *rot* or *temp* or *bias* or *loop* or *units*
+  
+  .. parsed-literal::
+  
+       *dist* value = *uniform* or *gaussian*
+       *sum* value = *no* or *yes*
+       *mom* value = *no* or *yes*
+       *rot* value = *no* or *yes*
+       *temp* value = temperature compute ID
+       *bias* value = *no* or *yes*
+       *loop* value = *all* or *local* or *geom*
+       *rigid* value = fix-ID
+         fix-ID = ID of rigid body fix
+       *units* value = *box* or *lattice*
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   velocity all create 300.0 4928459 rot yes dist gaussian
+   velocity border set NULL 4.0 v_vz sum yes units box
+   velocity flow scale 300.0
+   velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
+   velocity all zero linear
+
+Description
+"""""""""""
+
+Set or change the velocities of a group of atoms in one of several
+styles.  For each style, there are required arguments and optional
+keyword/value parameters.  Not all options are used by each style.
+Each option has a default as listed below.
+
+The *create* style generates an ensemble of velocities using a random
+number generator with the specified seed at the specified temperature.
+
+The *set* style sets the velocities of all atoms in the group to the
+specified values.  If any component is specified as NULL, then it is
+not set.  Any of the vx,vy,vz velocity components can be specified as
+an equal-style or atom-style :doc:`variable <variable>`.  If the value
+is a variable, it should be specified as v\_name, where name is the
+variable name.  In this case, the variable will be evaluated, and its
+value used to determine the velocity component.  Note that if a
+variable is used, the velocity it calculates must be in box units, not
+lattice units; see the discussion of the *units* keyword below.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo\_style <thermo_style>` command
+keywords for the simulation box parameters or other parameters.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent
+velocity field.
+
+The *scale* style computes the current temperature of the group of
+atoms and then rescales the velocities to the specified temperature.
+
+The *ramp* style is similar to that used by the :doc:`compute temp/ramp <compute_temp_ramp>` command.  Velocities ramped
+uniformly from vlo to vhi are applied to dimension vx, or vy, or vz.
+The value assigned to a particular atom depends on its relative
+coordinate value (in dim) from clo to chi.  For the example above, an
+atom with y-coordinate of 10 (1/4 of the way from 5 to 25), would be
+assigned a x-velocity of 1.25 (1/4 of the way from 0.0 to 5.0).  Atoms
+outside the coordinate bounds (less than 5 or greater than 25 in this
+case), are assigned velocities equal to vlo or vhi (0.0 or 5.0 in this
+case).
+
+The *zero* style adjusts the velocities of the group of atoms so that
+the aggregate linear or angular momentum is zero.  No other changes
+are made to the velocities of the atoms.  If the *rigid* option is
+specified (see below), then the zeroing is performed on individual
+rigid bodies, as defined by the :doc:`fix rigid or fix rigid/small <fix_rigid>` commands.  In other words, zero linear
+will set the linear momentum of each rigid body to zero, and zero
+angular will set the angular momentum of each rigid body to zero.
+This is done by adjusting the velocities of the atoms in each rigid
+body.
+
+All temperatures specified in the velocity command are in temperature
+units; see the :doc:`units <units>` command.  The units of velocities and
+coordinates depend on whether the *units* keyword is set to *box* or
+*lattice*\ , as discussed below.
+
+For all styles, no atoms are assigned z-component velocities if the
+simulation is 2d; see the :doc:`dimension <dimension>` command.
+
+
+----------
+
+
+The keyword/value options are used in the following ways by the
+various styles.
+
+The *dist* keyword is used by *create*\ .  The ensemble of generated
+velocities can be a *uniform* distribution from some minimum to
+maximum value, scaled to produce the requested temperature.  Or it can
+be a *gaussian* distribution with a mean of 0.0 and a sigma scaled to
+produce the requested temperature.
+
+The *sum* keyword is used by all styles, except *zero*\ .  The new
+velocities will be added to the existing ones if sum = yes, or will
+replace them if sum = no.
+
+The *mom* and *rot* keywords are used by *create*\ .  If mom = yes, the
+linear momentum of the newly created ensemble of velocities is zeroed;
+if rot = yes, the angular momentum is zeroed.
+
+
+----------
+
+
+If specified, the *temp* keyword is used by *create* and *scale* to
+specify a :doc:`compute <compute>` that calculates temperature in a
+desired way, e.g. by first subtracting out a velocity bias, as
+discussed on the :doc:`Howto thermostat <Howto_thermostat>` doc page.
+If this keyword is not specified, *create* and *scale* calculate
+temperature using a compute that is defined internally as follows:
+
+
+.. parsed-literal::
+
+   compute velocity_temp group-ID temp
+
+where group-ID is the same ID used in the velocity command. i.e. the
+group of atoms whose velocity is being altered.  This compute is
+deleted when the velocity command is finished.  See the :doc:`compute temp <compute_temp>` command for details.  If the calculated
+temperature should have degrees-of-freedom removed due to fix
+constraints (e.g. SHAKE or rigid-body constraints), then the
+appropriate fix command must be specified before the velocity command
+is issued.
+
+The *bias* keyword with a *yes* setting is used by *create* and
+*scale*\ , but only if the *temp* keyword is also used to specify a
+:doc:`compute <compute>` that calculates temperature in a desired way.
+If the temperature compute also calculates a velocity bias, the
+bias is subtracted from atom velocities before the *create* and
+*scale* operations are performed.  After the operations, the bias is
+added back to the atom velocities.  See the :doc:`Howto thermostat <Howto_thermostat>` doc page for more discussion of
+temperature computes with biases.  Note that the velocity bias is only
+applied to atoms in the temperature compute specified with the *temp*
+keyword.
+
+As an example, assume atoms are currently streaming in a flow
+direction (which could be separately initialized with the *ramp*
+style), and you wish to initialize their thermal velocity to a desired
+temperature.  In this context thermal velocity means the per-particle
+velocity that remains when the streaming velocity is subtracted.  This
+can be done using the *create* style with the *temp* keyword
+specifying the ID of a :doc:`compute temp/ramp <compute_temp_ramp>` or
+:doc:`compute temp/profile <compute_temp_profile>` command, and the
+*bias* keyword set to a *yes* value.
+
+
+----------
+
+
+The *loop* keyword is used by *create* in the following ways.
+
+If loop = all, then each processor loops over all atoms in the
+simulation to create velocities, but only stores velocities for atoms
+it owns.  This can be a slow loop for a large simulation.  If atoms
+were read from a data file, the velocity assigned to a particular atom
+will be the same, independent of how many processors are being used.
+This will not be the case if atoms were created using the
+:doc:`create\_atoms <create_atoms>` command, since atom IDs will likely
+be assigned to atoms differently.
+
+If loop = local, then each processor loops over only its atoms to
+produce velocities.  The random number seed is adjusted to give a
+different set of velocities on each processor.  This is a fast loop,
+but the velocity assigned to a particular atom will depend on which
+processor owns it.  Thus the results will always be different when a
+simulation is run on a different number of processors.
+
+If loop = geom, then each processor loops over only its atoms.  For
+each atom a unique random number seed is created, based on the atom's
+xyz coordinates.  A velocity is generated using that seed.  This is a
+fast loop and the velocity assigned to a particular atom will be the
+same, independent of how many processors are used.  However, the set
+of generated velocities may be more correlated than if the *all* or
+*local* keywords are used.
+
+Note that the *loop geom* keyword will not necessarily assign
+identical velocities for two simulations run on different machines.
+This is because the computations based on xyz coordinates are
+sensitive to tiny differences in the double-precision value for a
+coordinate as stored on a particular machine.
+
+
+----------
+
+
+The *rigid* keyword only has meaning when used with the *zero* style.
+It allows specification of a fix-ID for one of the :doc:`rigid-body fix <fix_rigid>` variants which defines a set of rigid bodies.  The
+zeroing of linear or angular momentum is then performed for each rigid
+body defined by the fix, as described above.
+
+The *units* keyword is used by *set* and *ramp*\ .  If units = box,
+the velocities and coordinates specified in the velocity command are
+in the standard units described by the :doc:`units <units>` command
+(e.g. Angstroms/fmsec for real units).  If units = lattice, velocities
+are in units of lattice spacings per time (e.g. spacings/fmsec) and
+coordinates are in lattice spacings.  The :doc:`lattice <lattice>`
+command must have been previously used to define the lattice spacing.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+Assigning a temperature via the *create* style to a system with :doc:`rigid bodies <fix_rigid>` or :doc:`SHAKE constraints <fix_shake>` may not
+have the desired outcome for two reasons.  First, the velocity command
+can be invoked before all of the relevant fixes are created and
+initialized and the number of adjusted degrees of freedom (DOFs) is
+known.  Thus it is not possible to compute the target temperature
+correctly.  Second, the assigned velocities may be partially canceled
+when constraints are first enforced, leading to a different
+temperature than desired.  A workaround for this is to perform a :doc:`run 0 <run>` command, which insures all DOFs are accounted for
+properly, and then rescale the temperature to the desired value before
+performing a simulation.  For example:
+
+
+.. parsed-literal::
+
+   velocity all create 300.0 12345
+   run 0                             # temperature may not be 300K
+   velocity all scale 300.0          # now it should be
+
+Related commands
+""""""""""""""""
+
+:doc:`fix rigid <fix_rigid>`, :doc:`fix shake <fix_shake>`,
+:doc:`lattice <lattice>`
+
+Default
+"""""""
+
+The keyword defaults are dist = uniform, sum = no, mom = yes, rot =
+no, bias = no, loop = all, and units = lattice.  The temp and rigid
+keywords are not defined by default.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/write_coeff.rst b/doc/src/write_coeff.rst
new file mode 100644
index 0000000000..4b452d7928
--- /dev/null
+++ b/doc/src/write_coeff.rst
@@ -0,0 +1,58 @@
+.. index:: write\_coeff
+
+write\_coeff command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   write_coeff file
+
+   file = name of data file to write out
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   write_coeff polymer.coeff
+
+Description
+"""""""""""
+
+Write a text format file with the currently defined force field
+coefficients in a way, that it can be read by LAMMPS with the
+:doc:`include <include>` command. In combination with the nocoeff
+option of :doc:`write\_data <write_data>` this can be used to move
+the Coeffs sections from a data file into a separate file.
+
+.. note::
+
+   The write\_coeff command is not yet fully implemented as
+   some pair styles do not output their coefficient information.
+   This means you will need to add/copy this information manually.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+none
+
+Related commands
+""""""""""""""""
+
+:doc:`read\_data <read_data>`, :doc:`write\_restart <write_restart>`,
+:doc:`write\_data <write_data>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst
new file mode 100644
index 0000000000..63e15c45f3
--- /dev/null
+++ b/doc/src/write_data.rst
@@ -0,0 +1,152 @@
+.. index:: write\_data
+
+write\_data command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   write_data file keyword value ...
+
+* file = name of data file to write out
+* zero or more keyword/value pairs may be appended
+* keyword = *pair* or *nocoeff*
+  
+  .. parsed-literal::
+  
+       *nocoeff* = do not write out force field info
+       *nofix* = do not write out extra sections read by fixes
+       *pair* value = *ii* or *ij*
+         *ii* = write one line of pair coefficient info per atom type
+         *ij* = write one line of pair coefficient info per IJ atom type pair
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   write_data data.polymer
+   write_data data.\*
+
+Description
+"""""""""""
+
+Write a data file in text format of the current state of the
+simulation.  Data files can be read by the :doc:`read data <read_data>`
+command to begin a simulation.  The :doc:`read\_data <read_data>` command
+also describes their format.
+
+Similar to :doc:`dump <dump>` files, the data filename can contain a "\*"
+wild-card character.  The "\*" is replaced with the current timestep
+value.
+
+.. note::
+
+   The write-data command is not yet fully implemented in two
+   respects.  First, most pair styles do not yet write their coefficient
+   information into the data file.  This means you will need to specify
+   that information in your input script that reads the data file, via
+   the :doc:`pair\_coeff <pair_coeff>` command.  Second, a few of the :doc:`atom styles <atom_style>` (body, ellipsoid, line, tri) that store
+   auxiliary "bonus" information about aspherical particles, do not yet
+   write the bonus info into the data file.  Both these functionalities
+   will be added to the write\_data command later.
+
+Because a data file is in text format, if you use a data file written
+out by this command to restart a simulation, the initial state of the
+new run will be slightly different than the final state of the old run
+(when the file was written) which was represented internally by LAMMPS
+in binary format.  A new simulation which reads the data file will
+thus typically diverge from a simulation that continued in the
+original input script.
+
+If you want to do more exact restarts, using binary files, see the
+:doc:`restart <restart>`, :doc:`write\_restart <write_restart>`, and
+:doc:`read\_restart <read_restart>` commands.  You can also convert
+binary restart files to text data files, after a simulation has run,
+using the :doc:`-r command-line switch <Run_options>`.
+
+.. note::
+
+   Only limited information about a simulation is stored in a data
+   file.  For example, no information about atom :doc:`groups <group>` and
+   :doc:`fixes <fix>` are stored.  :doc:`Binary restart files <read_restart>`
+   store more information.
+
+Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete\_bonds <delete_bonds>` command will
+be written to a data file as if they are turned on.  This means they
+will need to be turned off again in a new run after the data file is
+read.
+
+Bonds that are broken (e.g. by a bond-breaking potential) are not
+written to the data file.  Thus these bonds will not exist when the
+data file is read.
+
+
+----------
+
+
+The *nocoeff* keyword requests that no force field parameters should
+be written to the data file. This can be very helpful, if one wants
+to make significant changes to the force field or if the parameters
+are read in separately anyway, e.g. from an include file.
+
+The *nofix* keyword requests that no extra sections read by fixes
+should be written to the data file (see the *fix* option of the
+:doc:`read\_data <read_data>` command for details). For example, this
+option excludes sections for user-created per-atom properties
+from :doc:`fix property/atom <fix_property_atom>`.
+
+The *pair* keyword lets you specify in what format the pair
+coefficient information is written into the data file.  If the value
+is specified as *ii*\ , then one line per atom type is written, to
+specify the coefficients for each of the I=J interactions.  This means
+that no cross-interactions for I != J will be specified in the data
+file and the pair style will apply its mixing rule, as documented on
+individual :doc:`pair\_style <pair_style>` doc pages.  Of course this
+behavior can be overridden in the input script after reading the data
+file, by specifying additional :doc:`pair\_coeff <pair_coeff>` commands
+for any desired I,J pairs.
+
+If the value is specified as *ij*\ , then one line of coefficients is
+written for all I,J pairs where I <= J.  These coefficients will
+include any specific settings made in the input script up to that
+point.  The presence of these I != J coefficients in the data file
+will effectively turn off the default mixing rule for the pair style.
+Again, the coefficient values in the data file can be overridden
+in the input script after reading the data file, by specifying
+additional :doc:`pair\_coeff <pair_coeff>` commands for any desired I,J
+pairs.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command requires inter-processor communication to migrate atoms
+before the data file is written.  This means that your system must be
+ready to perform a simulation before using this command (force fields
+setup, atom masses initialized, etc).
+
+Related commands
+""""""""""""""""
+
+:doc:`read\_data <read_data>`, :doc:`write\_restart <write_restart>`
+
+Default
+"""""""
+
+The option defaults are pair = ii.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/write_dump.rst b/doc/src/write_dump.rst
new file mode 100644
index 0000000000..e894406a22
--- /dev/null
+++ b/doc/src/write_dump.rst
@@ -0,0 +1,105 @@
+.. index:: write\_dump
+
+write\_dump command
+===================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   write_dump group-ID style file dump-args modify dump_modify-args
+
+* group-ID = ID of the group of atoms to be dumped
+* style = any of the supported :doc:`dump styles <dump>`
+* file = name of file to write dump info to
+* dump-args = any additional args needed for a particular :doc:`dump style <dump>`
+* modify = all args after this keyword are passed to :doc:`dump\_modify <dump_modify>` (optional)
+* dump-modify-args = args for :doc:`dump\_modify <dump_modify>` (optional)
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   write_dump all atom dump.atom
+   write_dump subgroup atom dump.run.bin
+   write_dump all custom dump.myforce.\* id type x y vx fx
+   write_dump flow custom dump.%.myforce id type c_myF[3] v_ke modify sort id
+   write_dump all xyz system.xyz modify sort id element O H
+   write_dump all image snap\*.jpg type type size 960 960 modify backcolor white
+   write_dump all image snap\*.jpg element element &
+      bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &
+      modify backcolor white element C C O H N C C C O H H S O H
+
+Description
+"""""""""""
+
+Dump a single snapshot of atom quantities to one or more files for the
+current state of the system.  This is a one-time immediate operation,
+in contrast to the :doc:`dump <dump>` command which will will set up a
+dump style to write out snapshots periodically during a running
+simulation.
+
+The syntax for this command is mostly identical to that of the
+:doc:`dump <dump>` and :doc:`dump\_modify <dump_modify>` commands as if
+they were concatenated together, with the following exceptions: There
+is no need for a dump ID or dump frequency and the keyword *modify* is
+added.  The latter is so that the full range of
+:doc:`dump\_modify <dump_modify>` options can be specified for the single
+snapshot, just as they can be for multiple snapshots.  The *modify*
+keyword separates the arguments that would normally be passed to the
+*dump* command from those that would be given the *dump\_modify*.  Both
+support optional arguments and thus LAMMPS needs to be able to cleanly
+separate the two sets of args.
+
+Note that if the specified filename uses wildcard characters "\*" or
+"%", as supported by the :doc:`dump <dump>` command, they will operate
+in the same fashion to create the new filename(s).  Normally, :doc:`dump image <dump_image>` files require a filename with a "\*" character
+for the timestep.  That is not the case for the write\_dump command; no
+wildcard "\*" character is necessary.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+All restrictions for the :doc:`dump <dump>` and
+:doc:`dump\_modify <dump_modify>` commands apply to this command as well,
+with the exception of the :doc:`dump image <dump_image>` filename not
+requiring a wildcard "\*" character, as noted above.
+
+Since dumps are normally written during a :doc:`run <run>` or :doc:`energy minimization <minimize>`, the simulation has to be ready to run
+before this command can be used.  Similarly, if the dump requires
+information from a compute, fix, or variable, the information needs to
+have been calculated for the current timestep (e.g. by a prior run),
+else LAMMPS will generate an error message.
+
+For example, it is not possible to dump per-atom energy with this
+command before a run has been performed, since no energies and forces
+have yet been calculated.  See the :doc:`variable <variable>` doc page
+section on Variable Accuracy for more information on this topic.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump image <dump_image>`,
+:doc:`dump\_modify <dump_modify>`
+
+Default
+"""""""
+
+The defaults are listed on the doc pages for the :doc:`dump <dump>` and
+:doc:`dump image <dump_image>` and :doc:`dump\_modify <dump_modify>`
+commands.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst
new file mode 100644
index 0000000000..853a046ed9
--- /dev/null
+++ b/doc/src/write_restart.rst
@@ -0,0 +1,144 @@
+.. index:: write\_restart
+
+write\_restart command
+======================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   write_restart file keyword value ...
+
+* file = name of file to write restart information to
+* zero or more keyword/value pairs may be appended
+* keyword = *fileper* or *nfile*
+  
+  .. parsed-literal::
+  
+       *fileper* arg = Np
+         Np = write one file for every this many processors
+       *nfile* arg = Nf
+         Nf = write this many files, one from each of Nf processors
+
+
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   write_restart restart.equil
+   write_restart restart.equil.mpiio
+   write_restart poly.%.\* nfile 10
+
+Description
+"""""""""""
+
+Write a binary restart file of the current state of the simulation.
+
+During a long simulation, the :doc:`restart <restart>` command is
+typically used to output restart files periodically.  The
+write\_restart command is useful after a minimization or whenever you
+wish to write out a single current restart file.
+
+Similar to :doc:`dump <dump>` files, the restart filename can contain
+two wild-card characters.  If a "\*" appears in the filename, it is
+replaced with the current timestep value.  If a "%" character appears
+in the filename, then one file is written by each processor and the
+"%" character is replaced with the processor ID from 0 to P-1.  An
+additional file with the "%" replaced by "base" is also written, which
+contains global information.  For example, the files written for
+filename restart.% would be restart.base, restart.0, restart.1, ...
+restart.P-1.  This creates smaller files and can be a fast mode of
+output and subsequent input on parallel machines that support parallel
+I/O.  The optional *fileper* and *nfile* keywords discussed below can
+alter the number of files written.
+
+The restart file can also be written in parallel as one large binary
+file via the MPI-IO library, which is part of the MPI standard for
+versions 2.0 and above.  Using MPI-IO requires two steps.  First,
+build LAMMPS with its MPIIO package installed, e.g.
+
+
+.. parsed-literal::
+
+   make yes-mpiio    # installs the MPIIO package
+   make mpi          # build LAMMPS for your platform
+
+Second, use a restart filename which contains ".mpiio".  Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO dump files, a particular restart file must be both
+written and read using MPI-IO.
+
+Restart files can be read by a :doc:`read\_restart <read_restart>`
+command to restart a simulation from a particular state.  Because the
+file is binary (to enable exact restarts), it may not be readable on
+another machine.  In this case, you can use the :doc:`-r command-line switch <Run_options>` to convert a restart file to a data file.
+
+.. note::
+
+   Although the purpose of restart files is to enable restarting a
+   simulation from where it left off, not all information about a
+   simulation is stored in the file.  For example, the list of fixes that
+   were specified during the initial run is not stored, which means the
+   new input script must specify any fixes you want to use.  Even when
+   restart information is stored in the file, as it is for some fixes,
+   commands may need to be re-specified in the new input script, in order
+   to re-use that information. Details are usually given in the
+   documentation of the respective command. Also, see the
+   :doc:`read\_restart <read_restart>` command for general information about
+   what is stored in a restart file.
+
+
+----------
+
+
+The optional *nfile* or *fileper* keywords can be used in conjunction
+with the "%" wildcard character in the specified restart file name.
+As explained above, the "%" character causes the restart file to be
+written in pieces, one piece for each of P processors.  By default P =
+the number of processors the simulation is running on.  The *nfile* or
+*fileper* keyword can be used to set P to a smaller value, which can
+be more efficient when running on a large number of processors.
+
+The *nfile* keyword sets P to the specified Nf value.  For example, if
+Nf = 4, and the simulation is running on 100 processors, 4 files will
+be written, by processors 0,25,50,75.  Each will collect information
+from itself and the next 24 processors and write it to a restart file.
+
+For the *fileper* keyword, the specified value of Np means write one
+file for every Np processors.  For example, if Np = 4, every 4th
+processor (0,4,8,12,etc) will collect information from itself and the
+next 3 processors and write it to a restart file.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This command requires inter-processor communication to migrate atoms
+before the restart file is written.  This means that your system must
+be ready to perform a simulation before using this command (force
+fields setup, atom masses initialized, etc).
+
+To write and read restart files in parallel with MPI-IO, the MPIIO
+package must be installed.
+
+Related commands
+""""""""""""""""
+
+:doc:`restart <restart>`, :doc:`read\_restart <read_restart>`,
+:doc:`write\_data <write_data>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html
diff --git a/doc/src/Build.txt b/doc/txt/Build.txt
similarity index 100%
rename from doc/src/Build.txt
rename to doc/txt/Build.txt
diff --git a/doc/src/Build_basics.txt b/doc/txt/Build_basics.txt
similarity index 100%
rename from doc/src/Build_basics.txt
rename to doc/txt/Build_basics.txt
diff --git a/doc/src/Build_cmake.txt b/doc/txt/Build_cmake.txt
similarity index 100%
rename from doc/src/Build_cmake.txt
rename to doc/txt/Build_cmake.txt
diff --git a/doc/src/Build_development.txt b/doc/txt/Build_development.txt
similarity index 98%
rename from doc/src/Build_development.txt
rename to doc/txt/Build_development.txt
index 16a3d3d20e..bd3897fba6 100644
--- a/doc/src/Build_development.txt
+++ b/doc/txt/Build_development.txt
@@ -50,7 +50,7 @@ Code Coverage and Testing :h4,link(testing)
 
 We do extensive regression testing of the LAMMPS code base on a continuous
 basis. Some of the logic to do this has been added to the CMake build so
-developers can run the tests directly on their workstation. 
+developers can run the tests directly on their workstation.
 
 NOTE: this is incomplete and only represents a small subset of tests that we run
 
diff --git a/doc/src/Build_extras.txt b/doc/txt/Build_extras.txt
similarity index 92%
rename from doc/src/Build_extras.txt
rename to doc/txt/Build_extras.txt
index 0a25a344ca..4cf40bbee4 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/txt/Build_extras.txt
@@ -186,13 +186,34 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
 [CMake build]:
 
--D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes :pre
+-D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes
+-D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on
+-D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes
+:pre
 
 If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
 environment variable so that libkim-api can be found.
 
+For using OpenKIM web queries in LAMMPS.
+
+If LMP_DEBUG_CURL is set, the libcurl verbose mode will be on, and any
+libcurl calls within the KIM web query display a lot of information about
+libcurl operations. You hardly ever want this set in production use, you will
+almost always want this when you debug/report problems.
+
+The libcurl performs peer SSL certificate verification by default. This
+verification is done using a CA certificate store that the SSL library can
+use to make sure the peer's server certificate is valid. If SSL reports an
+error ("certificate verify failed") during the handshake and thus refuses
+further communication with that server, you can set LMP_NO_SSL_CHECK.
+If LMP_NO_SSL_CHECK is set, libcurl does not verify the peer and connection
+succeeds regardless of the names in the certificate. This option is insecure.
+As an alternative, you can specify your own CA cert path by setting the
+environment variable CURL_CA_BUNDLE to the path of your choice. A call to the
+KIM web query would get this value from the environmental variable.
+
 [Traditional make]:
 
 You can download and build the KIM library manually if you prefer;
@@ -642,30 +663,61 @@ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 USER-COLVARS package :h4,link(user-colvars)
 
+This package includes into the LAMMPS distribution the Colvars library, which
+can be built for the most part with all major versions of the C++ language.
+
+A few of the most recent features require C++11 support.  In particular, the
+library is optionally built together with the
+"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also
+included in the LAMMPS distribution.  Lepton implements the
+"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction
+feature, and requires C++11 support.
+
+See "here"_https://colvars.github.io/README-c++11.html for a detailed list of
+C++11-only features.
+
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-COLVARS=yes".
+This is the recommended build recipe: no additional settings are normally
+needed besides "-D PKG_USER-COLVARS=yes".
+
+Building and linking of Lepton (or other C++11-only features) is enabled
+automatically when compilation is carried out with C++11 support, and disabled
+otherwise.  Optionally, Lepton build may be manually controlled with the flag
+"-D COLVARS_LEPTON=yes|no".
 
 [Traditional make]:
 
-Before building LAMMPS, you must build the COLVARS library in
-lib/colvars.  You can do this manually if you prefer; follow the
-instructions in lib/colvars/README.  You can also do it in one step
-from the lammps/src dir, using a command like these, which simply
-invoke the lib/colvars/Install.py script with the specified args:
+Before building LAMMPS, one must build the Colvars library in lib/colvars.
+
+This can be done manually in the same folder by using or adapting one of the
+provided Makefiles: for example, Makefile.g++ for the GNU compiler.
+
+In general, it is safer to use build setting consistent with the rest of
+LAMMPS.  This is best carried out from the LAMMPS src directory using a
+command like these, which simply invoke the lib/colvars/Install.py script with
+the specified args:
 
 make lib-colvars                      # print help message
 make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
 make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
 make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre
 
-The build should produce two files: lib/colvars/libcolvars.a and
-lib/colvars/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-COLVARS library (though typically the settings are just blank).  If
-necessary, you can edit/create a new lib/colvars/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
+The "machine" argument of the "-m" flag is used to find a Makefile.machine to
+use as build recipe.  If it does not already exist in lib/colvars, it will be
+auto-generated by using compiler flags consistent with those parsed from the
+core LAMMPS makefiles.
+
+Optional flags may be specified as environment variables:
+
+COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+
+The build should produce two files: the library lib/colvars/libcolvars.a
+(which also includes Lepton objects if enabled) and the specification file
+lib/colvars/Makefile.lammps.  The latter is auto-generated, and normally does
+not need to be edited.
+
 
 :line
 
@@ -1003,11 +1055,11 @@ lib/quip/README file for details on how to do this.
 
 [CMake build]:
 
--D QUIP_LIBRARIES=path     # path to libquip.a (only needed if a custom location) :pre
+-D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location) :pre
 
 CMake will not download and build the QUIP library.  But once you have
 done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should
-work.  Set QUIP_LIBRARIES if CMake cannot find the QUIP library.
+work.  Set QUIP_LIBRARY if CMake cannot find the QUIP library.
 
 [Traditional make]:
 
diff --git a/doc/src/Build_link.txt b/doc/txt/Build_link.txt
similarity index 100%
rename from doc/src/Build_link.txt
rename to doc/txt/Build_link.txt
diff --git a/doc/src/Build_make.txt b/doc/txt/Build_make.txt
similarity index 100%
rename from doc/src/Build_make.txt
rename to doc/txt/Build_make.txt
diff --git a/doc/src/Build_package.txt b/doc/txt/Build_package.txt
similarity index 100%
rename from doc/src/Build_package.txt
rename to doc/txt/Build_package.txt
diff --git a/doc/src/Build_settings.txt b/doc/txt/Build_settings.txt
similarity index 92%
rename from doc/src/Build_settings.txt
rename to doc/txt/Build_settings.txt
index 287cd39ff6..730d779d63 100644
--- a/doc/src/Build_settings.txt
+++ b/doc/txt/Build_settings.txt
@@ -12,6 +12,7 @@ Optional build settings :h3
 LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
+"C++11 standard compliance test"_#cxx11 when building all of LAMMPS
 "FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
 "Size of LAMMPS data types"_#size
 "Read or write compressed files"_#gzip
@@ -23,6 +24,33 @@ explain how to do this for building both with CMake and make.
 
 :line
 
+C++11 standard compliance test :h4,link(cxx11)
+
+The LAMMPS developers plan to transition to make the C++11 standard the
+minimum requirement for compiling LAMMPS.  Currently this only applies to
+some packages like KOKKOS while the rest aims to be compatible with the C++98
+standard.  Most currently used compilers are compatible with C++11; some need
+to set extra flags to switch.  To determine the impact of requiring C++11,
+we have added a simple compliance test to the source code, that will cause
+the compilation to abort, if C++11 compliance is not available or enabled.
+To bypass this check, you need to change a setting in the makefile or
+when calling CMake.
+
+[CMake variable]:
+
+-D DISABLE_CXX11_REQUIREMENT=yes :pre
+
+You can set additional C++ compiler flags (beyond those selected by CMake)
+through the CMAKE_CXX_FLAGS variable. Example for CentOS 7:
+
+-D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11" :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_CXX98 :pre
+
+:line
+
 FFT library :h4,link(fft)
 
 When the KSPACE package is included in a LAMMPS build, the
diff --git a/doc/src/Build_windows.txt b/doc/txt/Build_windows.txt
similarity index 100%
rename from doc/src/Build_windows.txt
rename to doc/txt/Build_windows.txt
diff --git a/doc/src/Errors.txt b/doc/txt/Errors.txt
similarity index 100%
rename from doc/src/Errors.txt
rename to doc/txt/Errors.txt
diff --git a/doc/src/Errors_bugs.txt b/doc/txt/Errors_bugs.txt
similarity index 100%
rename from doc/src/Errors_bugs.txt
rename to doc/txt/Errors_bugs.txt
diff --git a/doc/src/Errors_common.txt b/doc/txt/Errors_common.txt
similarity index 100%
rename from doc/src/Errors_common.txt
rename to doc/txt/Errors_common.txt
diff --git a/doc/src/Errors_messages.txt b/doc/txt/Errors_messages.txt
similarity index 99%
rename from doc/src/Errors_messages.txt
rename to doc/txt/Errors_messages.txt
index c131b10ec6..33593d4d53 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/txt/Errors_messages.txt
@@ -4791,6 +4791,22 @@ Self-explanatory. :dd
 
 This fix option cannot be used with point particles. :dd
 
+{Fix langevin gjf and respa are not compatible} :dt
+
+Self-explanatory. :dd
+
+{Fix langevin gjf cannot have period equal to dt/2} :dt
+
+If the period is equal to dt/2 then division by zero will happen. :dd
+
+{Fix langevin gjf should come before fix nve} :dt
+
+Self-explanatory. :dd
+
+{Fix langevin gjf with tbias is not yet implemented with kokkos} :dt
+
+This option is not yet available. :dd
+
 {Fix langevin omega is not yet implemented with kokkos} :dt
 
 This option is not yet available. :dd
diff --git a/doc/src/Errors_warnings.txt b/doc/txt/Errors_warnings.txt
similarity index 92%
rename from doc/src/Errors_warnings.txt
rename to doc/txt/Errors_warnings.txt
index 9f346ba8c1..cb22b7ad0c 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/txt/Errors_warnings.txt
@@ -47,6 +47,11 @@ too far away. :dd
 
 Self-explanatory. :dd
 
+{Angles are defined but no angle style is set} :dt
+
+The topology contains angles, but there are no angle forces computed
+since there was no angle_style command. :dd
+
 {Atom style in data file differs from currently defined atom style} :dt
 
 Self-explanatory. :dd
@@ -73,6 +78,11 @@ short or the bond has blown apart and an atom is too far away. :dd
 
 Self-explanatory. :dd
 
+{Bonds are defined but no bond style is set} :dt
+
+The topology contains bonds, but there are no bond forces computed
+since there was no bond_style command. :dd
+
 {Bond/angle/dihedral extent > half of periodic box length} :dt
 
 This is a restriction because LAMMPS can be confused about which image
@@ -186,6 +196,11 @@ to check your simulation geometry. :dd
 
 Self-explanatory. :dd
 
+{Dihedrals are defined but no dihedral style is set} :dt
+
+The topology contains dihedrals, but there are no dihedral forces computed
+since there was no dihedral_style command. :dd
+
 {Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt
 
 If the fix changes the timestep, the dump dcd file will not
@@ -224,6 +239,13 @@ will be truncated to attempt to prevent the bond from blowing up. :dd
 
 You likely want to set this in your input script. :dd
 
+{ Fix bond/create is used multiple times or with fix bond/break - may not work as expected} :dt
+
+When using fix bond/create multiple times or in combination with
+fix bond/break, the individual fix instances do not share information
+about changes they made at the same time step and thus it may result
+in unexpected behavior. :dd
+
 {Fix bond/swap will ignore defined angles} :dt
 
 See the doc page for fix bond/swap for more info on this
@@ -248,6 +270,10 @@ included one or more of the following: kspace, triclinic, a hybrid
 pair style, an eam pair style, or no "single" function for the pair
 style. :dd
 
+{Fix langevin gjf using random gaussians is not implemented with kokkos} :dt
+
+This will most likely cause errors in kinetic fluctuations.
+
 {Fix property/atom mol or charge w/out ghost communication} :dt
 
 A model typically needs these properties defined for ghost atoms. :dd
@@ -348,6 +374,11 @@ to check your simulation geometry. :dd
 
 Self-explanatory. :dd
 
+{Impropers are defined but no improper style is set} :dt
+
+The topology contains impropers, but there are no improper forces computed
+since there was no improper_style command. :dd
+
 {Inconsistent image flags} :dt
 
 The image flags for a pair on bonded atoms appear to be inconsistent.
@@ -366,6 +397,11 @@ have fully consistent image flags, since some bonds will cross
 periodic boundaries and connect two atoms with the same image
 flag. :dd
 
+{Increasing communication cutoff for GPU style} :dt
+
+The pair style has increased the communication cutoff to be consistent with
+the communication cutoff requirements for this pair style when run on the GPU. :dd
+
 {KIM Model does not provide 'energy'; Potential energy will be zero} :dt
 
 Self-explanatory. :dd
@@ -403,6 +439,30 @@ This library function cannot be used if atom IDs are not defined or
 are not consecutively numbered, or if no atom map is defined.  See the
 atom_modify command for details about atom maps. :dd
 
+{Likewise 1-2 special neighbor interactions != 1.0} :dt
+
+The topology contains bonds, but there is no bond style defined
+and a 1-2 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the bond style. :dd
+
+{Likewise 1-3 special neighbor interactions != 1.0} :dt
+
+The topology contains angles, but there is no angle style defined
+and a 1-3 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the angle style. :dd
+
+{Likewise 1-4 special neighbor interactions != 1.0} :dt
+
+The topology contains dihedrals, but there is no dihedral style defined
+and a 1-4 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the dihedral style. :dd
+
 {Lost atoms via change_box: original %ld current %ld} :dt
 
 The command options you have used caused atoms to be lost. :dd
diff --git a/doc/src/Examples.txt b/doc/txt/Examples.txt
similarity index 98%
rename from doc/src/Examples.txt
rename to doc/txt/Examples.txt
index 36d0ac86f9..04c211cb1d 100644
--- a/doc/src/Examples.txt
+++ b/doc/txt/Examples.txt
@@ -94,6 +94,7 @@ python:   using embedded Python in a LAMMPS input script
 qeq:      use of the QEQ package for charge equilibration
 rdf-adf:  computing radial and angle distribution functions for water
 reax:     RDX and TATB models using the ReaxFF
+rerun:    use of rerun and read_dump commands
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
 snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
@@ -141,6 +142,7 @@ HEAT: compute thermal conductivity for LJ and water via fix ehex
 KAPPA: compute thermal conductivity via several methods
 MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
 SPIN: examples for features of the SPIN package
+UNITS: examples that run the same simulation in lj, real, metal units
 USER: examples for USER packages and USER-contributed commands
 VISCOSITY: compute viscosity via several methods :tb(s=:)
 
diff --git a/doc/src/Howto.txt b/doc/txt/Howto.txt
similarity index 100%
rename from doc/src/Howto.txt
rename to doc/txt/Howto.txt
diff --git a/doc/src/Howto_2d.txt b/doc/txt/Howto_2d.txt
similarity index 100%
rename from doc/src/Howto_2d.txt
rename to doc/txt/Howto_2d.txt
diff --git a/doc/src/Howto_barostat.txt b/doc/txt/Howto_barostat.txt
similarity index 100%
rename from doc/src/Howto_barostat.txt
rename to doc/txt/Howto_barostat.txt
diff --git a/doc/src/Howto_bash.txt b/doc/txt/Howto_bash.txt
similarity index 100%
rename from doc/src/Howto_bash.txt
rename to doc/txt/Howto_bash.txt
diff --git a/doc/src/Howto_bioFF.txt b/doc/txt/Howto_bioFF.txt
similarity index 100%
rename from doc/src/Howto_bioFF.txt
rename to doc/txt/Howto_bioFF.txt
diff --git a/doc/src/Howto_body.txt b/doc/txt/Howto_body.txt
similarity index 100%
rename from doc/src/Howto_body.txt
rename to doc/txt/Howto_body.txt
diff --git a/doc/src/Howto_chunk.txt b/doc/txt/Howto_chunk.txt
similarity index 100%
rename from doc/src/Howto_chunk.txt
rename to doc/txt/Howto_chunk.txt
diff --git a/doc/src/Howto_client_server.txt b/doc/txt/Howto_client_server.txt
similarity index 100%
rename from doc/src/Howto_client_server.txt
rename to doc/txt/Howto_client_server.txt
diff --git a/doc/src/Howto_coreshell.txt b/doc/txt/Howto_coreshell.txt
similarity index 100%
rename from doc/src/Howto_coreshell.txt
rename to doc/txt/Howto_coreshell.txt
diff --git a/doc/src/Howto_couple.txt b/doc/txt/Howto_couple.txt
similarity index 100%
rename from doc/src/Howto_couple.txt
rename to doc/txt/Howto_couple.txt
diff --git a/doc/src/Howto_diffusion.txt b/doc/txt/Howto_diffusion.txt
similarity index 100%
rename from doc/src/Howto_diffusion.txt
rename to doc/txt/Howto_diffusion.txt
diff --git a/doc/src/Howto_dispersion.txt b/doc/txt/Howto_dispersion.txt
similarity index 100%
rename from doc/src/Howto_dispersion.txt
rename to doc/txt/Howto_dispersion.txt
diff --git a/doc/src/Howto_drude.txt b/doc/txt/Howto_drude.txt
similarity index 100%
rename from doc/src/Howto_drude.txt
rename to doc/txt/Howto_drude.txt
diff --git a/doc/src/Howto_drude2.txt b/doc/txt/Howto_drude2.txt
similarity index 100%
rename from doc/src/Howto_drude2.txt
rename to doc/txt/Howto_drude2.txt
diff --git a/doc/src/Howto_elastic.txt b/doc/txt/Howto_elastic.txt
similarity index 100%
rename from doc/src/Howto_elastic.txt
rename to doc/txt/Howto_elastic.txt
diff --git a/doc/src/Howto_github.txt b/doc/txt/Howto_github.txt
similarity index 100%
rename from doc/src/Howto_github.txt
rename to doc/txt/Howto_github.txt
diff --git a/doc/src/Howto_granular.txt b/doc/txt/Howto_granular.txt
similarity index 100%
rename from doc/src/Howto_granular.txt
rename to doc/txt/Howto_granular.txt
diff --git a/doc/src/Howto_kappa.txt b/doc/txt/Howto_kappa.txt
similarity index 100%
rename from doc/src/Howto_kappa.txt
rename to doc/txt/Howto_kappa.txt
diff --git a/doc/src/Howto_library.txt b/doc/txt/Howto_library.txt
similarity index 100%
rename from doc/src/Howto_library.txt
rename to doc/txt/Howto_library.txt
diff --git a/doc/src/Howto_manifold.txt b/doc/txt/Howto_manifold.txt
similarity index 100%
rename from doc/src/Howto_manifold.txt
rename to doc/txt/Howto_manifold.txt
diff --git a/doc/src/Howto_multiple.txt b/doc/txt/Howto_multiple.txt
similarity index 100%
rename from doc/src/Howto_multiple.txt
rename to doc/txt/Howto_multiple.txt
diff --git a/doc/src/Howto_nemd.txt b/doc/txt/Howto_nemd.txt
similarity index 100%
rename from doc/src/Howto_nemd.txt
rename to doc/txt/Howto_nemd.txt
diff --git a/doc/src/Howto_output.txt b/doc/txt/Howto_output.txt
similarity index 100%
rename from doc/src/Howto_output.txt
rename to doc/txt/Howto_output.txt
diff --git a/doc/src/Howto_polarizable.txt b/doc/txt/Howto_polarizable.txt
similarity index 100%
rename from doc/src/Howto_polarizable.txt
rename to doc/txt/Howto_polarizable.txt
diff --git a/doc/src/Howto_replica.txt b/doc/txt/Howto_replica.txt
similarity index 100%
rename from doc/src/Howto_replica.txt
rename to doc/txt/Howto_replica.txt
diff --git a/doc/src/Howto_restart.txt b/doc/txt/Howto_restart.txt
similarity index 100%
rename from doc/src/Howto_restart.txt
rename to doc/txt/Howto_restart.txt
diff --git a/doc/src/Howto_spc.txt b/doc/txt/Howto_spc.txt
similarity index 100%
rename from doc/src/Howto_spc.txt
rename to doc/txt/Howto_spc.txt
diff --git a/doc/src/Howto_spherical.txt b/doc/txt/Howto_spherical.txt
similarity index 100%
rename from doc/src/Howto_spherical.txt
rename to doc/txt/Howto_spherical.txt
diff --git a/doc/src/Howto_spins.txt b/doc/txt/Howto_spins.txt
similarity index 97%
rename from doc/src/Howto_spins.txt
rename to doc/txt/Howto_spins.txt
index 80b2a54fe4..c4bdc502ce 100644
--- a/doc/src/Howto_spins.txt
+++ b/doc/txt/Howto_spins.txt
@@ -43,19 +43,19 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
 the thermal energy of the Langevin thermostat, or to perform a
 relaxation of the magnetic configuration toward an equilibrium state.
 
-The command "fix setforce/spin"_fix_setforce.html allows to set the 
-components of the magnetic precession vectors (while erasing and 
-replacing the previously computed magnetic precession vectors on 
-the atom). 
-This command can be used to freeze the magnetic moment of certain 
-atoms in the simulation by zeroing their precession vector. 
+The command "fix setforce/spin"_fix_setforce.html allows to set the
+components of the magnetic precession vectors (while erasing and
+replacing the previously computed magnetic precession vectors on
+the atom).
+This command can be used to freeze the magnetic moment of certain
+atoms in the simulation by zeroing their precession vector.
 
 The command "fix nve/spin"_fix_nve_spin.html can be used to
-perform a symplectic integration of the combined dynamics of spins 
+perform a symplectic integration of the combined dynamics of spins
 and atomic motions.
 
 The minimization style "min/spin"_min_spin.html can be applied
-to the spins to perform a minimization of the spin configuration. 
+to the spins to perform a minimization of the spin configuration.
 
 
 All the computed magnetic properties can be output by two main
diff --git a/doc/src/Howto_temperature.txt b/doc/txt/Howto_temperature.txt
similarity index 100%
rename from doc/src/Howto_temperature.txt
rename to doc/txt/Howto_temperature.txt
diff --git a/doc/src/Howto_thermostat.txt b/doc/txt/Howto_thermostat.txt
similarity index 100%
rename from doc/src/Howto_thermostat.txt
rename to doc/txt/Howto_thermostat.txt
diff --git a/doc/src/Howto_tip3p.txt b/doc/txt/Howto_tip3p.txt
similarity index 100%
rename from doc/src/Howto_tip3p.txt
rename to doc/txt/Howto_tip3p.txt
diff --git a/doc/src/Howto_tip4p.txt b/doc/txt/Howto_tip4p.txt
similarity index 100%
rename from doc/src/Howto_tip4p.txt
rename to doc/txt/Howto_tip4p.txt
diff --git a/doc/src/Howto_triclinic.txt b/doc/txt/Howto_triclinic.txt
similarity index 100%
rename from doc/src/Howto_triclinic.txt
rename to doc/txt/Howto_triclinic.txt
diff --git a/doc/src/Howto_viscosity.txt b/doc/txt/Howto_viscosity.txt
similarity index 99%
rename from doc/src/Howto_viscosity.txt
rename to doc/txt/Howto_viscosity.txt
index ee070eba58..c87c8a3b84 100644
--- a/doc/src/Howto_viscosity.txt
+++ b/doc/txt/Howto_viscosity.txt
@@ -83,7 +83,7 @@ variable    d equal $p*$s   # dump interval :pre
 
 # convert from LAMMPS real units to SI :pre
 
-variable    kB equal 1.3806504e-23    # \[J/K/] Boltzmann
+variable    kB equal 1.3806504e-23    # \[J/K\] Boltzmann
 variable    atm2Pa equal 101325.0
 variable    A2m equal 1.0e-10
 variable    fs2s equal 1.0e-15
diff --git a/doc/src/Howto_viz.txt b/doc/txt/Howto_viz.txt
similarity index 100%
rename from doc/src/Howto_viz.txt
rename to doc/txt/Howto_viz.txt
diff --git a/doc/src/Howto_walls.txt b/doc/txt/Howto_walls.txt
similarity index 100%
rename from doc/src/Howto_walls.txt
rename to doc/txt/Howto_walls.txt
diff --git a/doc/src/Install_git.txt b/doc/txt/Install_git.txt
similarity index 100%
rename from doc/src/Install_git.txt
rename to doc/txt/Install_git.txt
diff --git a/doc/src/Install_linux.txt b/doc/txt/Install_linux.txt
similarity index 100%
rename from doc/src/Install_linux.txt
rename to doc/txt/Install_linux.txt
diff --git a/doc/src/Install_patch.txt b/doc/txt/Install_patch.txt
similarity index 100%
rename from doc/src/Install_patch.txt
rename to doc/txt/Install_patch.txt
diff --git a/doc/src/Install_svn.txt b/doc/txt/Install_svn.txt
similarity index 100%
rename from doc/src/Install_svn.txt
rename to doc/txt/Install_svn.txt
diff --git a/doc/src/Install_tarball.txt b/doc/txt/Install_tarball.txt
similarity index 100%
rename from doc/src/Install_tarball.txt
rename to doc/txt/Install_tarball.txt
diff --git a/doc/src/Install_windows.txt b/doc/txt/Install_windows.txt
similarity index 100%
rename from doc/src/Install_windows.txt
rename to doc/txt/Install_windows.txt
diff --git a/doc/src/Intro.txt b/doc/txt/Intro.txt
similarity index 100%
rename from doc/src/Intro.txt
rename to doc/txt/Intro.txt
diff --git a/doc/src/Intro_authors.txt b/doc/txt/Intro_authors.txt
similarity index 100%
rename from doc/src/Intro_authors.txt
rename to doc/txt/Intro_authors.txt
diff --git a/doc/src/Intro_features.txt b/doc/txt/Intro_features.txt
similarity index 100%
rename from doc/src/Intro_features.txt
rename to doc/txt/Intro_features.txt
diff --git a/doc/src/Intro_nonfeatures.txt b/doc/txt/Intro_nonfeatures.txt
similarity index 100%
rename from doc/src/Intro_nonfeatures.txt
rename to doc/txt/Intro_nonfeatures.txt
diff --git a/doc/src/Intro_opensource.txt b/doc/txt/Intro_opensource.txt
similarity index 100%
rename from doc/src/Intro_opensource.txt
rename to doc/txt/Intro_opensource.txt
diff --git a/doc/src/Intro_overview.txt b/doc/txt/Intro_overview.txt
similarity index 100%
rename from doc/src/Intro_overview.txt
rename to doc/txt/Intro_overview.txt
diff --git a/doc/src/Intro_website.txt b/doc/txt/Intro_website.txt
similarity index 100%
rename from doc/src/Intro_website.txt
rename to doc/txt/Intro_website.txt
diff --git a/doc/src/Manual_version.txt b/doc/txt/Manual_version.txt
similarity index 100%
rename from doc/src/Manual_version.txt
rename to doc/txt/Manual_version.txt
diff --git a/doc/src/Modify.txt b/doc/txt/Modify.txt
similarity index 100%
rename from doc/src/Modify.txt
rename to doc/txt/Modify.txt
diff --git a/doc/src/Modify_atom.txt b/doc/txt/Modify_atom.txt
similarity index 100%
rename from doc/src/Modify_atom.txt
rename to doc/txt/Modify_atom.txt
diff --git a/doc/src/Modify_body.txt b/doc/txt/Modify_body.txt
similarity index 100%
rename from doc/src/Modify_body.txt
rename to doc/txt/Modify_body.txt
diff --git a/doc/src/Modify_bond.txt b/doc/txt/Modify_bond.txt
similarity index 100%
rename from doc/src/Modify_bond.txt
rename to doc/txt/Modify_bond.txt
diff --git a/doc/src/Modify_command.txt b/doc/txt/Modify_command.txt
similarity index 100%
rename from doc/src/Modify_command.txt
rename to doc/txt/Modify_command.txt
diff --git a/doc/src/Modify_compute.txt b/doc/txt/Modify_compute.txt
similarity index 100%
rename from doc/src/Modify_compute.txt
rename to doc/txt/Modify_compute.txt
diff --git a/doc/src/Modify_contribute.txt b/doc/txt/Modify_contribute.txt
similarity index 100%
rename from doc/src/Modify_contribute.txt
rename to doc/txt/Modify_contribute.txt
diff --git a/doc/src/Modify_dump.txt b/doc/txt/Modify_dump.txt
similarity index 100%
rename from doc/src/Modify_dump.txt
rename to doc/txt/Modify_dump.txt
diff --git a/doc/src/Modify_fix.txt b/doc/txt/Modify_fix.txt
similarity index 100%
rename from doc/src/Modify_fix.txt
rename to doc/txt/Modify_fix.txt
diff --git a/doc/src/Modify_kspace.txt b/doc/txt/Modify_kspace.txt
similarity index 100%
rename from doc/src/Modify_kspace.txt
rename to doc/txt/Modify_kspace.txt
diff --git a/doc/src/Modify_min.txt b/doc/txt/Modify_min.txt
similarity index 100%
rename from doc/src/Modify_min.txt
rename to doc/txt/Modify_min.txt
diff --git a/doc/src/Modify_overview.txt b/doc/txt/Modify_overview.txt
similarity index 100%
rename from doc/src/Modify_overview.txt
rename to doc/txt/Modify_overview.txt
diff --git a/doc/src/Modify_pair.txt b/doc/txt/Modify_pair.txt
similarity index 100%
rename from doc/src/Modify_pair.txt
rename to doc/txt/Modify_pair.txt
diff --git a/doc/src/Modify_region.txt b/doc/txt/Modify_region.txt
similarity index 100%
rename from doc/src/Modify_region.txt
rename to doc/txt/Modify_region.txt
diff --git a/doc/src/Modify_thermo.txt b/doc/txt/Modify_thermo.txt
similarity index 100%
rename from doc/src/Modify_thermo.txt
rename to doc/txt/Modify_thermo.txt
diff --git a/doc/src/Modify_variable.txt b/doc/txt/Modify_variable.txt
similarity index 100%
rename from doc/src/Modify_variable.txt
rename to doc/txt/Modify_variable.txt
diff --git a/doc/src/Packages.txt b/doc/txt/Packages.txt
similarity index 100%
rename from doc/src/Packages.txt
rename to doc/txt/Packages.txt
diff --git a/doc/src/Packages_details.txt b/doc/txt/Packages_details.txt
similarity index 99%
rename from doc/src/Packages_details.txt
rename to doc/txt/Packages_details.txt
index eead133add..fc30c045cf 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/txt/Packages_details.txt
@@ -1746,11 +1746,12 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
 A "fix phonon"_fix_phonon.html command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.
-And a "dynamical_matrix" command to compute the dynamical matrix
-from finite differences.
+And a "dynamical_matrix"_dynamical_matrix.html as well as a
+"third_order"_third_order.html command to compute the dynamical matrix
+and third order tensor from finite differences.
 
 [Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
-and Charlie Sievers (UC Davis) for "dynamical_matrix"
+and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
 
 
 [Supporting info:]
@@ -1759,6 +1760,7 @@ src/USER-PHONON: filenames -> commands
 src/USER-PHONON/README
 "fix phonon"_fix_phonon.html
 "dynamical_matrix"_dynamical_matrix.html
+"third_order"_third_order.html
 examples/USER/phonon :ul
 
 :line
diff --git a/doc/src/Packages_standard.txt b/doc/txt/Packages_standard.txt
similarity index 100%
rename from doc/src/Packages_standard.txt
rename to doc/txt/Packages_standard.txt
diff --git a/doc/src/Packages_user.txt b/doc/txt/Packages_user.txt
similarity index 100%
rename from doc/src/Packages_user.txt
rename to doc/txt/Packages_user.txt
diff --git a/doc/src/Python_call.txt b/doc/txt/Python_call.txt
similarity index 100%
rename from doc/src/Python_call.txt
rename to doc/txt/Python_call.txt
diff --git a/doc/src/Python_examples.txt b/doc/txt/Python_examples.txt
similarity index 100%
rename from doc/src/Python_examples.txt
rename to doc/txt/Python_examples.txt
diff --git a/doc/src/Python_head.txt b/doc/txt/Python_head.txt
similarity index 100%
rename from doc/src/Python_head.txt
rename to doc/txt/Python_head.txt
diff --git a/doc/src/Python_install.txt b/doc/txt/Python_install.txt
similarity index 100%
rename from doc/src/Python_install.txt
rename to doc/txt/Python_install.txt
diff --git a/doc/src/Python_mpi.txt b/doc/txt/Python_mpi.txt
similarity index 100%
rename from doc/src/Python_mpi.txt
rename to doc/txt/Python_mpi.txt
diff --git a/doc/src/Python_overview.txt b/doc/txt/Python_overview.txt
similarity index 100%
rename from doc/src/Python_overview.txt
rename to doc/txt/Python_overview.txt
diff --git a/doc/src/Python_pylammps.txt b/doc/txt/Python_pylammps.txt
similarity index 100%
rename from doc/src/Python_pylammps.txt
rename to doc/txt/Python_pylammps.txt
diff --git a/doc/src/Python_run.txt b/doc/txt/Python_run.txt
similarity index 100%
rename from doc/src/Python_run.txt
rename to doc/txt/Python_run.txt
diff --git a/doc/src/Python_shlib.txt b/doc/txt/Python_shlib.txt
similarity index 100%
rename from doc/src/Python_shlib.txt
rename to doc/txt/Python_shlib.txt
diff --git a/doc/src/Python_test.txt b/doc/txt/Python_test.txt
similarity index 100%
rename from doc/src/Python_test.txt
rename to doc/txt/Python_test.txt
diff --git a/doc/src/Run_basics.txt b/doc/txt/Run_basics.txt
similarity index 100%
rename from doc/src/Run_basics.txt
rename to doc/txt/Run_basics.txt
diff --git a/doc/src/Run_head.txt b/doc/txt/Run_head.txt
similarity index 100%
rename from doc/src/Run_head.txt
rename to doc/txt/Run_head.txt
diff --git a/doc/src/Run_options.txt b/doc/txt/Run_options.txt
similarity index 100%
rename from doc/src/Run_options.txt
rename to doc/txt/Run_options.txt
diff --git a/doc/src/Run_output.txt b/doc/txt/Run_output.txt
similarity index 100%
rename from doc/src/Run_output.txt
rename to doc/txt/Run_output.txt
diff --git a/doc/src/Run_windows.txt b/doc/txt/Run_windows.txt
similarity index 100%
rename from doc/src/Run_windows.txt
rename to doc/txt/Run_windows.txt
diff --git a/doc/src/Speed.txt b/doc/txt/Speed.txt
similarity index 100%
rename from doc/src/Speed.txt
rename to doc/txt/Speed.txt
diff --git a/doc/src/Speed_bench.txt b/doc/txt/Speed_bench.txt
similarity index 100%
rename from doc/src/Speed_bench.txt
rename to doc/txt/Speed_bench.txt
diff --git a/doc/src/Speed_compare.txt b/doc/txt/Speed_compare.txt
similarity index 100%
rename from doc/src/Speed_compare.txt
rename to doc/txt/Speed_compare.txt
diff --git a/doc/src/Speed_gpu.txt b/doc/txt/Speed_gpu.txt
similarity index 100%
rename from doc/src/Speed_gpu.txt
rename to doc/txt/Speed_gpu.txt
diff --git a/doc/src/Speed_intel.txt b/doc/txt/Speed_intel.txt
similarity index 100%
rename from doc/src/Speed_intel.txt
rename to doc/txt/Speed_intel.txt
diff --git a/doc/src/Speed_kokkos.txt b/doc/txt/Speed_kokkos.txt
similarity index 97%
rename from doc/src/Speed_kokkos.txt
rename to doc/txt/Speed_kokkos.txt
index 99d29864dc..66f8fab8d9 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/txt/Speed_kokkos.txt
@@ -46,14 +46,14 @@ software version 7.5 or later must be installed on your system. See
 the discussion for the "GPU package"_Speed_gpu.html for details of how
 to check and do this.
 
-NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library 
-is CUDA-aware. This is not always the case, especially when using 
-pre-compiled MPI libraries provided by a Linux distribution. This is not 
-a problem when using only a single GPU with a single MPI rank. When 
-running with multiple MPI ranks, you may see segmentation faults without 
-CUDA-aware MPI support. These can be avoided by adding the flags "-pk 
-kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by 
-using the command "package kokkos cuda/aware off"_package.html in the 
+NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library
+is CUDA-aware. This is not always the case, especially when using
+pre-compiled MPI libraries provided by a Linux distribution. This is not
+a problem when using only a single GPU with a single MPI rank. When
+running with multiple MPI ranks, you may see segmentation faults without
+CUDA-aware MPI support. These can be avoided by adding the flags "-pk
+kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by
+using the command "package kokkos cuda/aware off"_package.html in the
 input file.
 
 [Building LAMMPS with the KOKKOS package:]
@@ -110,10 +110,10 @@ Makefile.kokkos_mpi_only) will give better performance than the OpenMP
 back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
 the code thread-safe is removed.
 
-NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to 
-change the default "package kokkos"_package.html options. See its doc 
-page for details and default settings. Experimenting with its options 
-can provide a speed-up for specific calculations. For example: 
+NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to
+change the default "package kokkos"_package.html options. See its doc
+page for details and default settings. Experimenting with its options
+can provide a speed-up for specific calculations. For example:
 
 mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm :pre
 
@@ -183,15 +183,15 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
 threads/task as Nt. The product of these two values should be N, i.e.
 256 or 264.
 
-NOTE: The default for the "package kokkos"_package.html command when 
-running on KNL is to use "half" neighbor lists and set the Newton flag 
-to "on" for both pairwise and bonded interactions. This will typically 
-be best for many-body potentials. For simpler pair-wise potentials, it 
-may be faster to use a "full" neighbor list with Newton flag to "off". 
-Use the "-pk kokkos" "command-line switch"_Run_options.html to change 
-the default "package kokkos"_package.html options. See its doc page for 
-details and default settings. Experimenting with its options can provide 
-a speed-up for specific calculations. For example: 
+NOTE: The default for the "package kokkos"_package.html command when
+running on KNL is to use "half" neighbor lists and set the Newton flag
+to "on" for both pairwise and bonded interactions. This will typically
+be best for many-body potentials. For simpler pair-wise potentials, it
+may be faster to use a "full" neighbor list with Newton flag to "off".
+Use the "-pk kokkos" "command-line switch"_Run_options.html to change
+the default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can provide
+a speed-up for specific calculations. For example:
 
 mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax      #  Newton on, half neighbor list, threaded comm
 mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm :pre
@@ -206,19 +206,19 @@ supports.
 
 [Running on GPUs:]
 
-Use the "-k" "command-line switch"_Run_options.html to specify the 
-number of GPUs per node. Typically the -np setting of the mpirun command 
-should set the number of MPI tasks/node to be equal to the number of 
-physical GPUs on the node. You can assign multiple MPI tasks to the same 
-GPU with the KOKKOS package, but this is usually only faster if some 
-portions of the input script have not been ported to use Kokkos. In this 
-case, also packing/unpacking communication buffers on the host may give 
-speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS 
+Use the "-k" "command-line switch"_Run_options.html to specify the
+number of GPUs per node. Typically the -np setting of the mpirun command
+should set the number of MPI tasks/node to be equal to the number of
+physical GPUs on the node. You can assign multiple MPI tasks to the same
+GPU with the KOKKOS package, but this is usually only faster if some
+portions of the input script have not been ported to use Kokkos. In this
+case, also packing/unpacking communication buffers on the host may give
+speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS
 is recommended in this scenario.
 
-Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be 
-avoided by using "-pk kokkos cuda/aware no"_package.html. As above for 
-multi-core CPUs (and no GPU), if N is the number of physical cores/node, 
+Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
+avoided by using "-pk kokkos cuda/aware no"_package.html. As above for
+multi-core CPUs (and no GPU), if N is the number of physical cores/node,
 then the number of MPI tasks/node should not exceed N.
 
 -k on g Ng :pre
@@ -229,18 +229,18 @@ one or more nodes, each with two GPUs:
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
 mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
 
-NOTE: The default for the "package kokkos"_package.html command when 
-running on GPUs is to use "full" neighbor lists and set the Newton flag 
-to "off" for both pairwise and bonded interactions, along with threaded 
-communication. When running on Maxwell or Kepler GPUs, this will 
-typically be best. For Pascal GPUs, using "half" neighbor lists and 
-setting the Newton flag to "on" may be faster. For many pair styles, 
-setting the neighbor binsize equal to twice the CPU default value will 
-give speedup, which is the default when running on GPUs. Use the "-pk 
-kokkos" "command-line switch"_Run_options.html to change the default 
-"package kokkos"_package.html options. See its doc page for details and 
-default settings. Experimenting with its options can provide a speed-up 
-for specific calculations. For example: 
+NOTE: The default for the "package kokkos"_package.html command when
+running on GPUs is to use "full" neighbor lists and set the Newton flag
+to "off" for both pairwise and bonded interactions, along with threaded
+communication. When running on Maxwell or Kepler GPUs, this will
+typically be best. For Pascal GPUs, using "half" neighbor lists and
+setting the Newton flag to "on" may be faster. For many pair styles,
+setting the neighbor binsize equal to twice the CPU default value will
+give speedup, which is the default when running on GPUs. Use the "-pk
+kokkos" "command-line switch"_Run_options.html to change the default
+"package kokkos"_package.html options. See its doc page for details and
+default settings. Experimenting with its options can provide a speed-up
+for specific calculations. For example:
 
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
 
diff --git a/doc/src/Speed_measure.txt b/doc/txt/Speed_measure.txt
similarity index 100%
rename from doc/src/Speed_measure.txt
rename to doc/txt/Speed_measure.txt
diff --git a/doc/src/Speed_omp.txt b/doc/txt/Speed_omp.txt
similarity index 100%
rename from doc/src/Speed_omp.txt
rename to doc/txt/Speed_omp.txt
diff --git a/doc/src/Speed_opt.txt b/doc/txt/Speed_opt.txt
similarity index 100%
rename from doc/src/Speed_opt.txt
rename to doc/txt/Speed_opt.txt
diff --git a/doc/src/Speed_packages.txt b/doc/txt/Speed_packages.txt
similarity index 100%
rename from doc/src/Speed_packages.txt
rename to doc/txt/Speed_packages.txt
diff --git a/doc/src/Speed_tips.txt b/doc/txt/Speed_tips.txt
similarity index 100%
rename from doc/src/Speed_tips.txt
rename to doc/txt/Speed_tips.txt
diff --git a/doc/src/Tools.txt b/doc/txt/Tools.txt
similarity index 98%
rename from doc/src/Tools.txt
rename to doc/txt/Tools.txt
index 90f598890f..dccdf77dee 100644
--- a/doc/src/Tools.txt
+++ b/doc/txt/Tools.txt
@@ -87,6 +87,7 @@ Miscellaneous tools :h3
 "emacs"_#emacs,
 "i-pi"_#ipi,
 "kate"_#kate,
+"singularity"_#singularity_tool,
 "vim"_#vim :tb(c=5,ea=c,a=l)
 
 :line
@@ -531,17 +532,26 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
 spin tool :h4,link(spin)
 
 The spin sub-directory contains a C file interpolate.c which can
-be compiled and used to perform a cubic polynomial interpolation of 
+be compiled and used to perform a cubic polynomial interpolation of
 the MEP following a GNEB calculation.
 
 See the README file in tools/spin/interpolate_gneb for more details.
 
 This tool was written by the SPIN package author, Julien
-Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei 
+Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
 Ivanov, at University of Iceland (ali5 at hi.is).
 
 :line
 
+singularity tool :h4,link(singularity_tool)
+
+The singularity sub-directory contains container definitions files
+that can be used to build container images for building and testing
+LAMMPS on specific OS variants using the "Singularity"_https://sylabs.io
+container software. Contributions for additional variants are welcome.
+
+:line
+
 vim tool :h4,link(vim)
 
 The files in the tools/vim directory are add-ons to the VIM editor
diff --git a/doc/src/balance.txt b/doc/txt/balance.txt
similarity index 100%
rename from doc/src/balance.txt
rename to doc/txt/balance.txt
diff --git a/doc/src/boundary.txt b/doc/txt/boundary.txt
similarity index 100%
rename from doc/src/boundary.txt
rename to doc/txt/boundary.txt
diff --git a/doc/src/box.txt b/doc/txt/box.txt
similarity index 100%
rename from doc/src/box.txt
rename to doc/txt/box.txt
diff --git a/doc/src/change_box.txt b/doc/txt/change_box.txt
similarity index 100%
rename from doc/src/change_box.txt
rename to doc/txt/change_box.txt
diff --git a/doc/src/clear.txt b/doc/txt/clear.txt
similarity index 100%
rename from doc/src/clear.txt
rename to doc/txt/clear.txt
diff --git a/doc/src/comm_modify.txt b/doc/txt/comm_modify.txt
similarity index 100%
rename from doc/src/comm_modify.txt
rename to doc/txt/comm_modify.txt
diff --git a/doc/src/comm_style.txt b/doc/txt/comm_style.txt
similarity index 100%
rename from doc/src/comm_style.txt
rename to doc/txt/comm_style.txt
diff --git a/doc/src/commands_list.txt b/doc/txt/commands_list.txt
similarity index 99%
rename from doc/src/commands_list.txt
rename to doc/txt/commands_list.txt
index a5c9b568ed..714aedefed 100644
--- a/doc/src/commands_list.txt
+++ b/doc/txt/commands_list.txt
@@ -108,6 +108,7 @@ Commands :h1
    thermo
    thermo_modify
    thermo_style
+   third_order
    timer
    timestep
    uncompute
diff --git a/doc/src/compute.txt b/doc/txt/compute.txt
similarity index 96%
rename from doc/src/compute.txt
rename to doc/txt/compute.txt
index 214fbdefc4..7b6274d21a 100644
--- a/doc/src/compute.txt
+++ b/doc/txt/compute.txt
@@ -182,6 +182,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "bond"_compute_bond.html - energy of each bond sub-style
 "bond/local"_compute_bond_local.html - distance and energy of each bond
 "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
+"centroid/stress/atom"_compute_stress_atom.html - centroid based stress tensor for each atom
 "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
 "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
 "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
@@ -213,7 +214,8 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "group/group"_compute_group_group.html - energy/force between two groups of atoms
 "gyration"_compute_gyration.html - radius of gyration of group of atoms
 "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
-"gyration/shape"_compute_gyration_shape.html - compute shape parameters from radius of gyration tensor
+"gyration/shape"_compute_gyration_shape.html - shape parameters from gyration tensor
+"gyration/shape/chunk"_compute_gyration_shape_chunk.html - shape parameters from gyration tensor for each chunk
 "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
 "heat/flux/tally"_compute_tally.html -
 "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
@@ -244,7 +246,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
 "pressure"_compute_pressure.html - total pressure and pressure tensor
 "pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates
-"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field 
+"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
 "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
 "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
 "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
@@ -276,15 +278,16 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
 "smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
 "smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
-"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
-"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
-"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
+"snap"_compute_sna_atom.html - bispectrum components and related quantities for a group of atoms
+"sna/atom"_compute_sna_atom.html - bispectrum components for each atom
+"snad/atom"_compute_sna_atom.html - derivative of bispectrum components for each atom
+"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum components for each atom
 "spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
 "stress/atom"_compute_stress_atom.html - stress tensor for each atom
 "stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
 "stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes
 "stress/tally"_compute_tally.html -
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle 
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
 "temp"_compute_temp.html - temperature of group of atoms
 "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
 "temp/body"_compute_temp_body.html - temperature of body particles
diff --git a/doc/src/compute_ackland_atom.txt b/doc/txt/compute_ackland_atom.txt
similarity index 100%
rename from doc/src/compute_ackland_atom.txt
rename to doc/txt/compute_ackland_atom.txt
diff --git a/doc/src/compute_adf.txt b/doc/txt/compute_adf.txt
similarity index 100%
rename from doc/src/compute_adf.txt
rename to doc/txt/compute_adf.txt
diff --git a/doc/src/compute_angle.txt b/doc/txt/compute_angle.txt
similarity index 100%
rename from doc/src/compute_angle.txt
rename to doc/txt/compute_angle.txt
diff --git a/doc/src/compute_angle_local.txt b/doc/txt/compute_angle_local.txt
similarity index 100%
rename from doc/src/compute_angle_local.txt
rename to doc/txt/compute_angle_local.txt
diff --git a/doc/src/compute_angmom_chunk.txt b/doc/txt/compute_angmom_chunk.txt
similarity index 100%
rename from doc/src/compute_angmom_chunk.txt
rename to doc/txt/compute_angmom_chunk.txt
diff --git a/doc/src/compute_basal_atom.txt b/doc/txt/compute_basal_atom.txt
similarity index 100%
rename from doc/src/compute_basal_atom.txt
rename to doc/txt/compute_basal_atom.txt
diff --git a/doc/src/compute_body_local.txt b/doc/txt/compute_body_local.txt
similarity index 100%
rename from doc/src/compute_body_local.txt
rename to doc/txt/compute_body_local.txt
diff --git a/doc/src/compute_bond.txt b/doc/txt/compute_bond.txt
similarity index 100%
rename from doc/src/compute_bond.txt
rename to doc/txt/compute_bond.txt
diff --git a/doc/src/compute_bond_local.txt b/doc/txt/compute_bond_local.txt
similarity index 100%
rename from doc/src/compute_bond_local.txt
rename to doc/txt/compute_bond_local.txt
diff --git a/doc/src/compute_centro_atom.txt b/doc/txt/compute_centro_atom.txt
similarity index 100%
rename from doc/src/compute_centro_atom.txt
rename to doc/txt/compute_centro_atom.txt
diff --git a/doc/src/compute_chunk_atom.txt b/doc/txt/compute_chunk_atom.txt
similarity index 100%
rename from doc/src/compute_chunk_atom.txt
rename to doc/txt/compute_chunk_atom.txt
diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/txt/compute_chunk_spread_atom.txt
similarity index 100%
rename from doc/src/compute_chunk_spread_atom.txt
rename to doc/txt/compute_chunk_spread_atom.txt
diff --git a/doc/src/compute_cluster_atom.txt b/doc/txt/compute_cluster_atom.txt
similarity index 100%
rename from doc/src/compute_cluster_atom.txt
rename to doc/txt/compute_cluster_atom.txt
diff --git a/doc/src/compute_cna_atom.txt b/doc/txt/compute_cna_atom.txt
similarity index 100%
rename from doc/src/compute_cna_atom.txt
rename to doc/txt/compute_cna_atom.txt
diff --git a/doc/src/compute_cnp_atom.txt b/doc/txt/compute_cnp_atom.txt
similarity index 100%
rename from doc/src/compute_cnp_atom.txt
rename to doc/txt/compute_cnp_atom.txt
diff --git a/doc/src/compute_com.txt b/doc/txt/compute_com.txt
similarity index 100%
rename from doc/src/compute_com.txt
rename to doc/txt/compute_com.txt
diff --git a/doc/src/compute_com_chunk.txt b/doc/txt/compute_com_chunk.txt
similarity index 100%
rename from doc/src/compute_com_chunk.txt
rename to doc/txt/compute_com_chunk.txt
diff --git a/doc/src/compute_contact_atom.txt b/doc/txt/compute_contact_atom.txt
similarity index 100%
rename from doc/src/compute_contact_atom.txt
rename to doc/txt/compute_contact_atom.txt
diff --git a/doc/src/compute_coord_atom.txt b/doc/txt/compute_coord_atom.txt
similarity index 99%
rename from doc/src/compute_coord_atom.txt
rename to doc/txt/compute_coord_atom.txt
index af0be4be56..e4d57a5dc5 100644
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/txt/compute_coord_atom.txt
@@ -47,7 +47,7 @@ neighboring atoms, unless selected by type, type range, or group option,
 are included in the coordination number tally.
 
 The optional {group} keyword allows to specify from which group atoms
-contribute to the coordination number. Default setting is group 'all'. 
+contribute to the coordination number. Default setting is group 'all'.
 
 The {typeN} keywords allow specification of which atom types
 contribute to each coordination number.  One coordination number is
diff --git a/doc/src/compute_damage_atom.txt b/doc/txt/compute_damage_atom.txt
similarity index 100%
rename from doc/src/compute_damage_atom.txt
rename to doc/txt/compute_damage_atom.txt
diff --git a/doc/src/compute_dihedral.txt b/doc/txt/compute_dihedral.txt
similarity index 100%
rename from doc/src/compute_dihedral.txt
rename to doc/txt/compute_dihedral.txt
diff --git a/doc/src/compute_dihedral_local.txt b/doc/txt/compute_dihedral_local.txt
similarity index 100%
rename from doc/src/compute_dihedral_local.txt
rename to doc/txt/compute_dihedral_local.txt
diff --git a/doc/src/compute_dilatation_atom.txt b/doc/txt/compute_dilatation_atom.txt
similarity index 100%
rename from doc/src/compute_dilatation_atom.txt
rename to doc/txt/compute_dilatation_atom.txt
diff --git a/doc/src/compute_dipole_chunk.txt b/doc/txt/compute_dipole_chunk.txt
similarity index 100%
rename from doc/src/compute_dipole_chunk.txt
rename to doc/txt/compute_dipole_chunk.txt
diff --git a/doc/src/compute_displace_atom.txt b/doc/txt/compute_displace_atom.txt
similarity index 100%
rename from doc/src/compute_displace_atom.txt
rename to doc/txt/compute_displace_atom.txt
diff --git a/doc/src/compute_dpd.txt b/doc/txt/compute_dpd.txt
similarity index 100%
rename from doc/src/compute_dpd.txt
rename to doc/txt/compute_dpd.txt
diff --git a/doc/src/compute_dpd_atom.txt b/doc/txt/compute_dpd_atom.txt
similarity index 100%
rename from doc/src/compute_dpd_atom.txt
rename to doc/txt/compute_dpd_atom.txt
diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/txt/compute_edpd_temp_atom.txt
similarity index 100%
rename from doc/src/compute_edpd_temp_atom.txt
rename to doc/txt/compute_edpd_temp_atom.txt
diff --git a/doc/src/compute_entropy_atom.txt b/doc/txt/compute_entropy_atom.txt
similarity index 100%
rename from doc/src/compute_entropy_atom.txt
rename to doc/txt/compute_entropy_atom.txt
diff --git a/doc/src/compute_erotate_asphere.txt b/doc/txt/compute_erotate_asphere.txt
similarity index 100%
rename from doc/src/compute_erotate_asphere.txt
rename to doc/txt/compute_erotate_asphere.txt
diff --git a/doc/src/compute_erotate_rigid.txt b/doc/txt/compute_erotate_rigid.txt
similarity index 100%
rename from doc/src/compute_erotate_rigid.txt
rename to doc/txt/compute_erotate_rigid.txt
diff --git a/doc/src/compute_erotate_sphere.txt b/doc/txt/compute_erotate_sphere.txt
similarity index 100%
rename from doc/src/compute_erotate_sphere.txt
rename to doc/txt/compute_erotate_sphere.txt
diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/txt/compute_erotate_sphere_atom.txt
similarity index 100%
rename from doc/src/compute_erotate_sphere_atom.txt
rename to doc/txt/compute_erotate_sphere_atom.txt
diff --git a/doc/src/compute_event_displace.txt b/doc/txt/compute_event_displace.txt
similarity index 100%
rename from doc/src/compute_event_displace.txt
rename to doc/txt/compute_event_displace.txt
diff --git a/doc/src/compute_fep.txt b/doc/txt/compute_fep.txt
similarity index 100%
rename from doc/src/compute_fep.txt
rename to doc/txt/compute_fep.txt
diff --git a/doc/src/compute_global_atom.txt b/doc/txt/compute_global_atom.txt
similarity index 100%
rename from doc/src/compute_global_atom.txt
rename to doc/txt/compute_global_atom.txt
diff --git a/doc/src/compute_group_group.txt b/doc/txt/compute_group_group.txt
similarity index 100%
rename from doc/src/compute_group_group.txt
rename to doc/txt/compute_group_group.txt
diff --git a/doc/src/compute_gyration.txt b/doc/txt/compute_gyration.txt
similarity index 100%
rename from doc/src/compute_gyration.txt
rename to doc/txt/compute_gyration.txt
diff --git a/doc/src/compute_gyration_chunk.txt b/doc/txt/compute_gyration_chunk.txt
similarity index 100%
rename from doc/src/compute_gyration_chunk.txt
rename to doc/txt/compute_gyration_chunk.txt
diff --git a/doc/src/compute_gyration_shape.txt b/doc/txt/compute_gyration_shape.txt
similarity index 89%
rename from doc/src/compute_gyration_shape.txt
rename to doc/txt/compute_gyration_shape.txt
index 7c428aea8a..5d97772544 100644
--- a/doc/src/compute_gyration_shape.txt
+++ b/doc/txt/compute_gyration_shape.txt
@@ -10,7 +10,7 @@ compute gyration/shape command :h3
 
 [Syntax:]
 
-compute ID group-ID gyration compute-ID :pre
+compute ID group-ID gyration/shape compute-ID :pre
 
 ID, group-ID are documented in "compute"_compute.html command
 gyration/shape = style name of this compute command
@@ -24,14 +24,16 @@ compute 1 molecule gyration/shape pe :pre
 
 Define a computation that calculates the eigenvalues of the gyration tensor of a
 group of atoms and three shape parameters. The computation includes all effects
-due to atoms passing thru periodic boundaries.
+due to atoms passing through periodic boundaries.
 
 The three computed shape parameters are the asphericity, b, the acylindricity, c,
 and the relative shape anisotropy, k:
 
 :c,image(Eqs/compute_shape_parameters.jpg)
 
-where lx <= ly <= lz are the three eigenvalues of the gyration tensor.
+where lx <= ly <= lz are the three eigenvalues of the gyration tensor. A general description 
+of these parameters is provided in "(Mattice)"_#Mattice1 while an application to polymer systems 
+can be found in "(Theodorou)"_#Theodorou1.
 The asphericity  is always non-negative and zero only when the three principal
 moments are equal. This zero condition is met when the distribution of particles
 is spherically symmetric (hence the name asphericity) but also whenever the particle
@@ -81,6 +83,9 @@ package"_Build_package.html doc page for more info.
 
 :line
 
-:link(Theodorou)
+:link(Mattice1)
+[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. 
+
+:link(Theodorou1)
 [(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).
 
diff --git a/doc/src/compute_hexorder_atom.txt b/doc/txt/compute_hexorder_atom.txt
similarity index 100%
rename from doc/src/compute_hexorder_atom.txt
rename to doc/txt/compute_hexorder_atom.txt
diff --git a/doc/src/compute_hma.txt b/doc/txt/compute_hma.txt
similarity index 93%
rename from doc/src/compute_hma.txt
rename to doc/txt/compute_hma.txt
index 4ab355abd7..289138eaa8 100644
--- a/doc/src/compute_hma.txt
+++ b/doc/txt/compute_hma.txt
@@ -34,7 +34,7 @@ compute 2 all hma 1 u cv :pre
 
 Define a computation that calculates the properties of a solid (potential
 energy, pressure or heat capacity), using the harmonically-mapped averaging
-(HMA) method. 
+(HMA) method.
 This command yields much higher precision than the equivalent compute commands
 ("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.)
 commands during a canonical simulation of an atomic crystal. Specifically,
@@ -52,7 +52,7 @@ restricted to simulations in the NVT ensemble.  While this compute may be
 used with any potential in LAMMPS, it will provide inaccurate results
 for potentials that do not go to 0 at the truncation distance;
 "pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should
-work fine, while "pair_lj"_pair_lj.html will perform poorly unless 
+work fine, while "pair_lj"_pair_lj.html will perform poorly unless
 the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large.  Furthermore, computation of the heat capacity with
 this compute is restricted to those that implement the single_hessian method
 in Pair.  Implementing single_hessian in additional pair styles is simple.
@@ -64,8 +64,8 @@ the list of pair styles that currently implement pair_hessian:
 :ule
 
 In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble
-averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination 
-by noise produced by the already-known harmonic behavior. 
+averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination
+by noise produced by the already-known harmonic behavior.
 A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula:
 
 \begin\{equation\}
@@ -74,9 +74,9 @@ A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa)
 
 where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's
 constant, \(T\) is the temperature, \(d\) is the
-dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the 
-atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of 
-pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies. 
+dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the
+atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of
+pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies.
 
 The pressure is computed by the formula:
 
@@ -118,30 +118,30 @@ When using this keyword, the compute must be first active (it must be included
 via a "thermo_style custom"_thermo_style.html command) while the atoms are
 still at their lattice sites (before equilibration).
 
-The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or 
-Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat 
-("fix langevin"_fix_langevin.html) 
-should be avoided as its extra forces interfere with the HMA implementation. 
+The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or
+Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat
+("fix langevin"_fix_langevin.html)
+should be avoided as its extra forces interfere with the HMA implementation.
 
- 
 
-NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites. 
+
+NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites.
 The simulation should not be started before this command has been used in the input script.
 
 
 The following example illustrates the placement of this command in the input script:
 
 
-min_style cg 
-minimize 1e-35 1e-15 50000 500000 
+min_style cg
+minimize 1e-35 1e-15 50000 500000
 compute 1 all hma thermostatid u
-fix thermostatid all nvt temp 600.0 600.0 100.0 :pre  
+fix thermostatid all nvt temp 600.0 600.0 100.0 :pre
 
 
 
 NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation.
 
- 
+
 NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command.
 
 An example input script that uses this compute is included in
@@ -180,5 +180,5 @@ this compute.
 :line
 
 :link(hma-Moustafa)
-[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation}, 
+[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation},
 "Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303
diff --git a/doc/src/compute_improper.txt b/doc/txt/compute_improper.txt
similarity index 100%
rename from doc/src/compute_improper.txt
rename to doc/txt/compute_improper.txt
diff --git a/doc/src/compute_improper_local.txt b/doc/txt/compute_improper_local.txt
similarity index 100%
rename from doc/src/compute_improper_local.txt
rename to doc/txt/compute_improper_local.txt
diff --git a/doc/src/compute_inertia_chunk.txt b/doc/txt/compute_inertia_chunk.txt
similarity index 100%
rename from doc/src/compute_inertia_chunk.txt
rename to doc/txt/compute_inertia_chunk.txt
diff --git a/doc/src/compute_ke.txt b/doc/txt/compute_ke.txt
similarity index 100%
rename from doc/src/compute_ke.txt
rename to doc/txt/compute_ke.txt
diff --git a/doc/src/compute_ke_atom.txt b/doc/txt/compute_ke_atom.txt
similarity index 100%
rename from doc/src/compute_ke_atom.txt
rename to doc/txt/compute_ke_atom.txt
diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/txt/compute_ke_atom_eff.txt
similarity index 100%
rename from doc/src/compute_ke_atom_eff.txt
rename to doc/txt/compute_ke_atom_eff.txt
diff --git a/doc/src/compute_ke_eff.txt b/doc/txt/compute_ke_eff.txt
similarity index 100%
rename from doc/src/compute_ke_eff.txt
rename to doc/txt/compute_ke_eff.txt
diff --git a/doc/src/compute_ke_rigid.txt b/doc/txt/compute_ke_rigid.txt
similarity index 100%
rename from doc/src/compute_ke_rigid.txt
rename to doc/txt/compute_ke_rigid.txt
diff --git a/doc/src/compute_meso_e_atom.txt b/doc/txt/compute_meso_e_atom.txt
similarity index 100%
rename from doc/src/compute_meso_e_atom.txt
rename to doc/txt/compute_meso_e_atom.txt
diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/txt/compute_meso_rho_atom.txt
similarity index 100%
rename from doc/src/compute_meso_rho_atom.txt
rename to doc/txt/compute_meso_rho_atom.txt
diff --git a/doc/src/compute_meso_t_atom.txt b/doc/txt/compute_meso_t_atom.txt
similarity index 100%
rename from doc/src/compute_meso_t_atom.txt
rename to doc/txt/compute_meso_t_atom.txt
diff --git a/doc/src/compute_modify.txt b/doc/txt/compute_modify.txt
similarity index 100%
rename from doc/src/compute_modify.txt
rename to doc/txt/compute_modify.txt
diff --git a/doc/src/compute_momentum.txt b/doc/txt/compute_momentum.txt
similarity index 100%
rename from doc/src/compute_momentum.txt
rename to doc/txt/compute_momentum.txt
diff --git a/doc/src/compute_msd.txt b/doc/txt/compute_msd.txt
similarity index 100%
rename from doc/src/compute_msd.txt
rename to doc/txt/compute_msd.txt
diff --git a/doc/src/compute_msd_chunk.txt b/doc/txt/compute_msd_chunk.txt
similarity index 100%
rename from doc/src/compute_msd_chunk.txt
rename to doc/txt/compute_msd_chunk.txt
diff --git a/doc/src/compute_msd_nongauss.txt b/doc/txt/compute_msd_nongauss.txt
similarity index 100%
rename from doc/src/compute_msd_nongauss.txt
rename to doc/txt/compute_msd_nongauss.txt
diff --git a/doc/src/compute_omega_chunk.txt b/doc/txt/compute_omega_chunk.txt
similarity index 100%
rename from doc/src/compute_omega_chunk.txt
rename to doc/txt/compute_omega_chunk.txt
diff --git a/doc/src/compute_orientorder_atom.txt b/doc/txt/compute_orientorder_atom.txt
similarity index 97%
rename from doc/src/compute_orientorder_atom.txt
rename to doc/txt/compute_orientorder_atom.txt
index da14c866bd..d59033f179 100644
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/txt/compute_orientorder_atom.txt
@@ -76,14 +76,14 @@ parameters up to {Q}12 for a range of commonly encountered
 high-symmetry structures are given in Table I of "Mickel et
 al."_#Mickel, and these can be reproduced with this compute
 
-The optional keyword {wl} will output the third-order invariants {Wl} 
+The optional keyword {wl} will output the third-order invariants {Wl}
 (see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as
 for the {Ql} parameters. For the FCC crystal with {nnn} =12,
 {W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136...
 
-The optional keyword {wl/hat} will output the normalized third-order 
-invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt) 
-for the same degrees as for the {Ql} parameters. For the FCC crystal 
+The optional keyword {wl/hat} will output the normalized third-order
+invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt)
+for the same degrees as for the {Ql} parameters. For the FCC crystal
 with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical
 values of {Wlhat} for a range of commonly encountered high-symmetry
 structures are given in Table I of "Steinhardt"_#Steinhardt, and these
@@ -127,9 +127,9 @@ range 0 <= {Ql} <= 1.
 If the keyword {wl} is set to yes, then the {Wl} values for each
 atom will be added to the output array, which are real numbers.
 
-If the keyword {wl/hat} is set to yes, then the {Wl_hat} 
+If the keyword {wl/hat} is set to yes, then the {Wl_hat}
 values for each atom will be added to the output array, which are real numbers.
- 
+
 If the keyword {components} is set, then the real and imaginary parts
 of each component of (normalized) {Ybar_lm} will be added to the
 output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
diff --git a/doc/src/compute_pair.txt b/doc/txt/compute_pair.txt
similarity index 100%
rename from doc/src/compute_pair.txt
rename to doc/txt/compute_pair.txt
diff --git a/doc/src/compute_pair_local.txt b/doc/txt/compute_pair_local.txt
similarity index 100%
rename from doc/src/compute_pair_local.txt
rename to doc/txt/compute_pair_local.txt
diff --git a/doc/src/compute_pe.txt b/doc/txt/compute_pe.txt
similarity index 100%
rename from doc/src/compute_pe.txt
rename to doc/txt/compute_pe.txt
diff --git a/doc/src/compute_pe_atom.txt b/doc/txt/compute_pe_atom.txt
similarity index 100%
rename from doc/src/compute_pe_atom.txt
rename to doc/txt/compute_pe_atom.txt
diff --git a/doc/src/compute_plasticity_atom.txt b/doc/txt/compute_plasticity_atom.txt
similarity index 100%
rename from doc/src/compute_plasticity_atom.txt
rename to doc/txt/compute_plasticity_atom.txt
diff --git a/doc/src/compute_pressure.txt b/doc/txt/compute_pressure.txt
similarity index 100%
rename from doc/src/compute_pressure.txt
rename to doc/txt/compute_pressure.txt
diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/txt/compute_pressure_cylinder.txt
similarity index 100%
rename from doc/src/compute_pressure_cylinder.txt
rename to doc/txt/compute_pressure_cylinder.txt
diff --git a/doc/src/compute_pressure_uef.txt b/doc/txt/compute_pressure_uef.txt
similarity index 100%
rename from doc/src/compute_pressure_uef.txt
rename to doc/txt/compute_pressure_uef.txt
diff --git a/doc/src/compute_property_atom.txt b/doc/txt/compute_property_atom.txt
similarity index 100%
rename from doc/src/compute_property_atom.txt
rename to doc/txt/compute_property_atom.txt
diff --git a/doc/src/compute_property_chunk.txt b/doc/txt/compute_property_chunk.txt
similarity index 100%
rename from doc/src/compute_property_chunk.txt
rename to doc/txt/compute_property_chunk.txt
diff --git a/doc/src/compute_property_local.txt b/doc/txt/compute_property_local.txt
similarity index 100%
rename from doc/src/compute_property_local.txt
rename to doc/txt/compute_property_local.txt
diff --git a/doc/src/compute_ptm_atom.txt b/doc/txt/compute_ptm_atom.txt
similarity index 100%
rename from doc/src/compute_ptm_atom.txt
rename to doc/txt/compute_ptm_atom.txt
diff --git a/doc/src/compute_rdf.txt b/doc/txt/compute_rdf.txt
similarity index 100%
rename from doc/src/compute_rdf.txt
rename to doc/txt/compute_rdf.txt
diff --git a/doc/src/compute_reduce.txt b/doc/txt/compute_reduce.txt
similarity index 100%
rename from doc/src/compute_reduce.txt
rename to doc/txt/compute_reduce.txt
diff --git a/doc/src/compute_reduce_chunk.txt b/doc/txt/compute_reduce_chunk.txt
similarity index 100%
rename from doc/src/compute_reduce_chunk.txt
rename to doc/txt/compute_reduce_chunk.txt
diff --git a/doc/src/compute_rigid_local.txt b/doc/txt/compute_rigid_local.txt
similarity index 100%
rename from doc/src/compute_rigid_local.txt
rename to doc/txt/compute_rigid_local.txt
diff --git a/doc/src/compute_saed.txt b/doc/txt/compute_saed.txt
similarity index 100%
rename from doc/src/compute_saed.txt
rename to doc/txt/compute_saed.txt
diff --git a/doc/src/compute_slice.txt b/doc/txt/compute_slice.txt
similarity index 100%
rename from doc/src/compute_slice.txt
rename to doc/txt/compute_slice.txt
diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/txt/compute_smd_contact_radius.txt
similarity index 100%
rename from doc/src/compute_smd_contact_radius.txt
rename to doc/txt/compute_smd_contact_radius.txt
diff --git a/doc/src/compute_smd_damage.txt b/doc/txt/compute_smd_damage.txt
similarity index 100%
rename from doc/src/compute_smd_damage.txt
rename to doc/txt/compute_smd_damage.txt
diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/txt/compute_smd_hourglass_error.txt
similarity index 100%
rename from doc/src/compute_smd_hourglass_error.txt
rename to doc/txt/compute_smd_hourglass_error.txt
diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/txt/compute_smd_internal_energy.txt
similarity index 100%
rename from doc/src/compute_smd_internal_energy.txt
rename to doc/txt/compute_smd_internal_energy.txt
diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/txt/compute_smd_plastic_strain.txt
similarity index 100%
rename from doc/src/compute_smd_plastic_strain.txt
rename to doc/txt/compute_smd_plastic_strain.txt
diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/txt/compute_smd_plastic_strain_rate.txt
similarity index 100%
rename from doc/src/compute_smd_plastic_strain_rate.txt
rename to doc/txt/compute_smd_plastic_strain_rate.txt
diff --git a/doc/src/compute_smd_rho.txt b/doc/txt/compute_smd_rho.txt
similarity index 100%
rename from doc/src/compute_smd_rho.txt
rename to doc/txt/compute_smd_rho.txt
diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/txt/compute_smd_tlsph_defgrad.txt
similarity index 100%
rename from doc/src/compute_smd_tlsph_defgrad.txt
rename to doc/txt/compute_smd_tlsph_defgrad.txt
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/txt/compute_smd_tlsph_dt.txt
similarity index 100%
rename from doc/src/compute_smd_tlsph_dt.txt
rename to doc/txt/compute_smd_tlsph_dt.txt
diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/txt/compute_smd_tlsph_num_neighs.txt
similarity index 100%
rename from doc/src/compute_smd_tlsph_num_neighs.txt
rename to doc/txt/compute_smd_tlsph_num_neighs.txt
diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/txt/compute_smd_tlsph_shape.txt
similarity index 100%
rename from doc/src/compute_smd_tlsph_shape.txt
rename to doc/txt/compute_smd_tlsph_shape.txt
diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/txt/compute_smd_tlsph_strain.txt
similarity index 100%
rename from doc/src/compute_smd_tlsph_strain.txt
rename to doc/txt/compute_smd_tlsph_strain.txt
diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/txt/compute_smd_tlsph_strain_rate.txt
similarity index 100%
rename from doc/src/compute_smd_tlsph_strain_rate.txt
rename to doc/txt/compute_smd_tlsph_strain_rate.txt
diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/txt/compute_smd_tlsph_stress.txt
similarity index 100%
rename from doc/src/compute_smd_tlsph_stress.txt
rename to doc/txt/compute_smd_tlsph_stress.txt
diff --git a/doc/src/compute_smd_triangle_vertices.txt b/doc/txt/compute_smd_triangle_vertices.txt
similarity index 100%
rename from doc/src/compute_smd_triangle_vertices.txt
rename to doc/txt/compute_smd_triangle_vertices.txt
diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/txt/compute_smd_ulsph_num_neighs.txt
similarity index 100%
rename from doc/src/compute_smd_ulsph_num_neighs.txt
rename to doc/txt/compute_smd_ulsph_num_neighs.txt
diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/txt/compute_smd_ulsph_strain.txt
similarity index 100%
rename from doc/src/compute_smd_ulsph_strain.txt
rename to doc/txt/compute_smd_ulsph_strain.txt
diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/txt/compute_smd_ulsph_strain_rate.txt
similarity index 100%
rename from doc/src/compute_smd_ulsph_strain_rate.txt
rename to doc/txt/compute_smd_ulsph_strain_rate.txt
diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/txt/compute_smd_ulsph_stress.txt
similarity index 100%
rename from doc/src/compute_smd_ulsph_stress.txt
rename to doc/txt/compute_smd_ulsph_stress.txt
diff --git a/doc/src/compute_smd_vol.txt b/doc/txt/compute_smd_vol.txt
similarity index 100%
rename from doc/src/compute_smd_vol.txt
rename to doc/txt/compute_smd_vol.txt
diff --git a/doc/src/compute_sna_atom.txt b/doc/txt/compute_sna_atom.txt
similarity index 80%
rename from doc/src/compute_sna_atom.txt
rename to doc/txt/compute_sna_atom.txt
index 518d28aec9..0bf63019f9 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/txt/compute_sna_atom.txt
@@ -9,12 +9,14 @@
 compute sna/atom command :h3
 compute snad/atom command :h3
 compute snav/atom command :h3
+compute snap command :h3
 
 [Syntax:]
 
 compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
 compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
+compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... 
+compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
 
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 sna/atom = style name of this compute command :l
@@ -41,12 +43,17 @@ keyword = {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
 
 compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
 compute db all sna/atom 1.4 0.95 6 2.0 1.0
-compute vb all sna/atom 1.4 0.95 6 2.0 1.0 :pre
+compute vb all sna/atom 1.4 0.95 6 2.0 1.0
+compute snap all snap 1.4 0.95 6 2.0 1.0 :pre
 
 [Description:]
 
-Define a computation that calculates a set of bispectrum components
-for each atom in a group.
+Define a computation that calculates a set of quantities related to the
+bispectrum components of the atoms in a group. These computes are
+used primarily for calculating the dependence of energy, force, and
+stress components on the linear coefficients in the 
+"snap pair_style"_pair_snap.html, which is useful when training a
+SNAP potential to match target data.
 
 Bispectrum components of an atom are order parameters characterizing
 the radial and angular distribution of neighbor atoms. The detailed
@@ -130,6 +137,27 @@ Again, the sum is over all atoms {i'} of atom type {I}.  For each atom
 virial components, each atom type, and each bispectrum component.  See
 section below on output for a detailed explanation.
 
+Compute {snap} calculates a global array contains information related
+to all three of the above per-atom computes {sna/atom}, {snad/atom},
+and {snav/atom}. The first row of the array contains the summation of 
+{sna/atom} over all atoms, but broken out by type. The last six rows
+of the array contain the summation of {snav/atom} over all atoms, broken
+out by type. In between these are 3*{N} rows containing the same values
+computed by {snad/atom} (these are already summed over all atoms and
+broken out by type). The element in the last column of each row contains
+the potential energy, force, or stress, according to the row.
+These quantities correspond to the user-specified reference potential
+that must be subtracted from the target data when fitting SNAP.
+The potential energy calculation uses the built in compute {thermo_pe}.
+The stress calculation uses a compute called {snap_press} that is
+automatically created behind the scenes, according to the following
+command:
+
+compute snap_press all pressure NULL virial :pre
+
+See section below on output for a detailed explanation of the data
+layout in the global array.
+
 The value of all bispectrum components will be zero for atoms not in
 the group. Neighbor atoms not in the group do not contribute to the
 bispectrum of atoms in the group.
@@ -196,7 +224,7 @@ for j1 in range(0,twojmax+1):
             if (j>=j1): print j1/2.,j2/2.,j/2. :pre
 
 NOTE: the {diagonal} keyword allowing other possible choices
-for the number of bispectrum components was removed in 2019, 
+for the number of bispectrum components was removed in 2019,
 since all potentials use the value of 3, corresponding to the
 above set of bispectrum components.
 
@@ -214,10 +242,25 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
 notation.  Each of these sub-blocks contains one column for each
 bispectrum component, the same as for compute {sna/atom}
 
+Compute {snap} evaluates a global array. 
+The columns are arranged into
+{ntypes} blocks, listed in order of atom type {I}. Each block
+contains one column for each bispectrum component, the same as for compute
+{sna/atom}. A final column contains the corresponding energy, force component
+on an atom, or virial stress component. The rows of the array appear 
+in the following order:
+
+   1 row: {sna/atom} quantities summed for all atoms of type {I}
+   3*{N} rows: {snad/atom} quantities, with derivatives w.r.t. x, y, and z coordinate of atom {i} appearing in consecutive rows. The atoms are sorted based on atom ID.
+   6 rows: {snav/atom} quantities summed for all atoms of type {I} :ul
+
 For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
 arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
 are 30, 90, and 180, respectively. With {quadratic} value=1,
 the numbers of columns are 930, 2790, and 5580, respectively.
+The number of columns in the global array generated by {snap}
+are 31, and 931, respectively, while the number of rows is
+1+3*{N}+6, where {N} is the total number of atoms.
 
 If the {quadratic} keyword value is set to 1, then additional
 columns are generated, corresponding to
diff --git a/doc/src/compute_stress_mop.txt b/doc/txt/compute_stress_mop.txt
similarity index 100%
rename from doc/src/compute_stress_mop.txt
rename to doc/txt/compute_stress_mop.txt
diff --git a/doc/src/compute_tally.txt b/doc/txt/compute_tally.txt
similarity index 100%
rename from doc/src/compute_tally.txt
rename to doc/txt/compute_tally.txt
diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/txt/compute_tdpd_cc_atom.txt
similarity index 100%
rename from doc/src/compute_tdpd_cc_atom.txt
rename to doc/txt/compute_tdpd_cc_atom.txt
diff --git a/doc/src/compute_temp.txt b/doc/txt/compute_temp.txt
similarity index 100%
rename from doc/src/compute_temp.txt
rename to doc/txt/compute_temp.txt
diff --git a/doc/src/compute_temp_asphere.txt b/doc/txt/compute_temp_asphere.txt
similarity index 100%
rename from doc/src/compute_temp_asphere.txt
rename to doc/txt/compute_temp_asphere.txt
diff --git a/doc/src/compute_temp_body.txt b/doc/txt/compute_temp_body.txt
similarity index 100%
rename from doc/src/compute_temp_body.txt
rename to doc/txt/compute_temp_body.txt
diff --git a/doc/src/compute_temp_chunk.txt b/doc/txt/compute_temp_chunk.txt
similarity index 100%
rename from doc/src/compute_temp_chunk.txt
rename to doc/txt/compute_temp_chunk.txt
diff --git a/doc/src/compute_temp_com.txt b/doc/txt/compute_temp_com.txt
similarity index 100%
rename from doc/src/compute_temp_com.txt
rename to doc/txt/compute_temp_com.txt
diff --git a/doc/src/compute_temp_cs.txt b/doc/txt/compute_temp_cs.txt
similarity index 100%
rename from doc/src/compute_temp_cs.txt
rename to doc/txt/compute_temp_cs.txt
diff --git a/doc/src/compute_temp_deform.txt b/doc/txt/compute_temp_deform.txt
similarity index 100%
rename from doc/src/compute_temp_deform.txt
rename to doc/txt/compute_temp_deform.txt
diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/txt/compute_temp_deform_eff.txt
similarity index 100%
rename from doc/src/compute_temp_deform_eff.txt
rename to doc/txt/compute_temp_deform_eff.txt
diff --git a/doc/src/compute_temp_drude.txt b/doc/txt/compute_temp_drude.txt
similarity index 100%
rename from doc/src/compute_temp_drude.txt
rename to doc/txt/compute_temp_drude.txt
diff --git a/doc/src/compute_temp_eff.txt b/doc/txt/compute_temp_eff.txt
similarity index 100%
rename from doc/src/compute_temp_eff.txt
rename to doc/txt/compute_temp_eff.txt
diff --git a/doc/src/compute_temp_partial.txt b/doc/txt/compute_temp_partial.txt
similarity index 100%
rename from doc/src/compute_temp_partial.txt
rename to doc/txt/compute_temp_partial.txt
diff --git a/doc/src/compute_temp_profile.txt b/doc/txt/compute_temp_profile.txt
similarity index 100%
rename from doc/src/compute_temp_profile.txt
rename to doc/txt/compute_temp_profile.txt
diff --git a/doc/src/compute_temp_ramp.txt b/doc/txt/compute_temp_ramp.txt
similarity index 100%
rename from doc/src/compute_temp_ramp.txt
rename to doc/txt/compute_temp_ramp.txt
diff --git a/doc/src/compute_temp_region.txt b/doc/txt/compute_temp_region.txt
similarity index 100%
rename from doc/src/compute_temp_region.txt
rename to doc/txt/compute_temp_region.txt
diff --git a/doc/src/compute_temp_region_eff.txt b/doc/txt/compute_temp_region_eff.txt
similarity index 100%
rename from doc/src/compute_temp_region_eff.txt
rename to doc/txt/compute_temp_region_eff.txt
diff --git a/doc/src/compute_temp_rotate.txt b/doc/txt/compute_temp_rotate.txt
similarity index 100%
rename from doc/src/compute_temp_rotate.txt
rename to doc/txt/compute_temp_rotate.txt
diff --git a/doc/src/compute_temp_sphere.txt b/doc/txt/compute_temp_sphere.txt
similarity index 100%
rename from doc/src/compute_temp_sphere.txt
rename to doc/txt/compute_temp_sphere.txt
diff --git a/doc/src/compute_temp_uef.txt b/doc/txt/compute_temp_uef.txt
similarity index 100%
rename from doc/src/compute_temp_uef.txt
rename to doc/txt/compute_temp_uef.txt
diff --git a/doc/src/compute_ti.txt b/doc/txt/compute_ti.txt
similarity index 100%
rename from doc/src/compute_ti.txt
rename to doc/txt/compute_ti.txt
diff --git a/doc/src/compute_torque_chunk.txt b/doc/txt/compute_torque_chunk.txt
similarity index 100%
rename from doc/src/compute_torque_chunk.txt
rename to doc/txt/compute_torque_chunk.txt
diff --git a/doc/src/compute_vacf.txt b/doc/txt/compute_vacf.txt
similarity index 100%
rename from doc/src/compute_vacf.txt
rename to doc/txt/compute_vacf.txt
diff --git a/doc/src/compute_vcm_chunk.txt b/doc/txt/compute_vcm_chunk.txt
similarity index 100%
rename from doc/src/compute_vcm_chunk.txt
rename to doc/txt/compute_vcm_chunk.txt
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/txt/compute_voronoi_atom.txt
similarity index 100%
rename from doc/src/compute_voronoi_atom.txt
rename to doc/txt/compute_voronoi_atom.txt
diff --git a/doc/src/compute_xrd.txt b/doc/txt/compute_xrd.txt
similarity index 100%
rename from doc/src/compute_xrd.txt
rename to doc/txt/compute_xrd.txt
diff --git a/doc/src/create_atoms.txt b/doc/txt/create_atoms.txt
similarity index 100%
rename from doc/src/create_atoms.txt
rename to doc/txt/create_atoms.txt
diff --git a/doc/src/create_bonds.txt b/doc/txt/create_bonds.txt
similarity index 70%
rename from doc/src/create_bonds.txt
rename to doc/txt/create_bonds.txt
index abd1959e81..9c073b6c55 100644
--- a/doc/src/create_bonds.txt
+++ b/doc/txt/create_bonds.txt
@@ -23,11 +23,14 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
     btype = bond type of new bond
     batom1,batom2 = atom IDs for two atoms in bond
   {single/angle} args = atype aatom1 aatom2 aatom3
-    atype = bond type of new angle
+    atype = angle type of new angle
     aatom1,aatom2,aatom3 = atom IDs for three atoms in angle
   {single/dihedral} args = dtype datom1 datom2 datom3 datom4
-    dtype = bond type of new dihedral
-    datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral :pre
+    dtype = dihedral type of new dihedral
+    datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral
+  {single/improper} args = itype iatom1 iatom2 iatom3 iatom4
+    itype = improper type of new improper
+    iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {special} :l
   {special} value = {yes} or {no} :pre
@@ -38,51 +41,54 @@ keyword = {special} :l
 create_bonds many all all 1 1.0 1.2
 create_bonds many surf solvent 3 2.0 2.4
 create_bonds single/bond 1 1 2
-create_bonds single/angle 5 52 98 107 special no :pre
+create_bonds single/angle 5 52 98 107 special no
+create_bonds single/dihedral 2 4 19 27 101
+create_bonds single/improper 3 23 26 31 57 :pre
 
 [Description:]
 
 Create bonds between pairs of atoms that meet a specified distance
-criteria.  Or create a single bond, angle, or dihedral between 2, 3,
+criteria.  Or create a single bond, angle, dihedral or improper between 2, 3,
 or 4 specified atoms.
 
-The new bond (angle, dihedral) interactions will then be computed
-during a simulation by the bond (angle, dihedral) potential defined by
+The new bond (angle, dihedral, improper) interactions will then be computed
+during a simulation by the bond (angle, dihedral, improper) potential defined by
 the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html,
 "angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html,
 "dihedral_style"_dihedral_style.html,
-"dihedral_coeff"_dihedral_coeff.html commands.
+"dihedral_coeff"_dihedral_coeff.html, "improper_style"_improper_style.html,
+"improper_coeff"_improper_coeff.html commands.
 
 The {many} style is useful for adding bonds to a system, e.g. between
 nearest neighbors in a lattice of atoms, without having to enumerate
 all the bonds in the data file read by the "read_data"_read_data.html
 command.
 
-The {single} styles are useful for adding bonds, angles, dihedrals
+The {single} styles are useful for adding bonds, angles, dihedrals, impropers
 to a system incrementally, then continuing a simulation.
 
-Note that this command does not auto-create any angle or dihedral
+Note that this command does not auto-create any angle, dihedral or improper
 interactions when a bond is added.  Nor does it auto-create any bonds
-when an angle or dihedral is added.  Or auto-create any angles when a
-dihedral is added.  Thus the flexibility of this command is limited.
+when an angle, dihedral or improper is added.  Or auto-create any angles when a
+dihedral or improper is added.  Thus the flexibility of this command is limited.
 It can be used several times to create different types of bond at
 different distances.  But it cannot typically auto-create all the
-bonds or angles or dihedral that would normally be defined in a data
-file for a complex system of molecules.
+bonds or angles or dihedrals or impropers that would normally be defined in a
+data file for a complex system of molecules.
 
-NOTE: If the system has no bonds (angles, dihedrals) to begin with, or
-if more bonds per atom are being added than currently exist, then you
+NOTE: If the system has no bonds (angles, dihedrals, impropers) to begin with,
+or if more bonds per atom are being added than currently exist, then you
 must insure that the number of bond types and the maximum number of
 bonds per atom are set to large enough values.  And similarly for
-angles and dihedrals.  Otherwise an error may occur when too many
-bonds (angles, dihedrals) are added to an atom.  If the
+angles, dihedrals and impropers.  Otherwise an error may occur when too many
+bonds (angles, dihedrals, impropers) are added to an atom.  If the
 "read_data"_read_data.html command is used to define the system, these
 parameters can be set via the "bond types" and "extra bond per atom"
 fields in the header section of the data file.  If the
 "create_box"_create_box.html command is used to define the system,
 these 2 parameters can be set via its optional "bond/types" and
-"extra/bond/per/atom" arguments.  And similarly for angles and
-dihedrals.  See the doc pages for these 2 commands for details.
+"extra/bond/per/atom" arguments.  And similarly for angles, dihedrals and
+impropers.  See the doc pages for these 2 commands for details.
 
 :line
 
@@ -137,18 +143,25 @@ ordered linearly within the angle; the central atom is {aatom2}.
 {Atype} must be a value between 1 and the number of angle types
 defined.
 
-The {single/dihedral} style creates a single dihedral of type {btype}
-between two atoms with IDs {batom1} and {batom2}.  The ordering of the
-atoms is the same as in the {Dihedrals} section of a data file read by
-the "read_data"_read_data.html command.  I.e. the 4 atoms are ordered
-linearly within the dihedral.  {Dtype} must be a value between 1 and
+The {single/dihedral} style creates a single dihedral of type {dtype}
+between four atoms with IDs {datom1}, {datom2}, {datom3}, and {datom4}.  The
+ordering of the atoms is the same as in the {Dihedrals} section of a data file
+read by the "read_data"_read_data.html command.  I.e. the 4 atoms are ordered
+linearly within the dihedral.  {dtype} must be a value between 1 and
 the number of dihedral types defined.
 
+The {single/improper} style creates a single improper of type {itype}
+between four atoms with IDs {iatom1}, {iatom2}, {iatom3}, and {iatom4}.  The
+ordering of the atoms is the same as in the {Impropers} section of a data file
+read by the "read_data"_read_data.html command.  I.e. the 4 atoms are ordered
+linearly within the improper.  {itype} must be a value between 1 and
+the number of improper types defined.
+
 :line
 
 The keyword {special} controls whether an internal list of special
-bonds is created after one or more bonds, or a single angle or
-dihedral is added to the system.
+bonds is created after one or more bonds, or a single angle, dihedral or
+improper is added to the system.
 
 The default value is {yes}.  A value of {no} cannot be used
 with the {many} style.
@@ -161,16 +174,16 @@ see the "special_bonds"_special_bonds.html command for details.
 Thus if you are adding a few bonds or a large list of angles all at
 the same time, by using this command repeatedly, it is more efficient
 to only trigger the internal list to be created once, after the last
-bond (or angle, or dihedral) is added:
+bond (or angle, or dihedral, or improper) is added:
 
 create_bonds single/bond 5 52 98 special no
-create_bonds single/bond  5 73 74 special no
+create_bonds single/bond 5 73 74 special no
 ...
 create_bonds single/bond 5 17 386 special no
 create_bonds single/bond 4 112 183 special yes :pre
 
 Note that you MUST insure the internal list is re-built after the last
-bond (angle, dihedral) is added, before performing a simulation.
+bond (angle, dihedral, improper) is added, before performing a simulation.
 Otherwise pairwise interactions will not be properly excluded or
 weighted.  LAMMPS does NOT check that you have done this correctly.
 
diff --git a/doc/src/create_box.txt b/doc/txt/create_box.txt
similarity index 100%
rename from doc/src/create_box.txt
rename to doc/txt/create_box.txt
diff --git a/doc/src/delete_atoms.txt b/doc/txt/delete_atoms.txt
similarity index 100%
rename from doc/src/delete_atoms.txt
rename to doc/txt/delete_atoms.txt
diff --git a/doc/src/delete_bonds.txt b/doc/txt/delete_bonds.txt
similarity index 100%
rename from doc/src/delete_bonds.txt
rename to doc/txt/delete_bonds.txt
diff --git a/doc/src/dielectric.txt b/doc/txt/dielectric.txt
similarity index 100%
rename from doc/src/dielectric.txt
rename to doc/txt/dielectric.txt
diff --git a/doc/src/dihedral_charmm.txt b/doc/txt/dihedral_charmm.txt
similarity index 100%
rename from doc/src/dihedral_charmm.txt
rename to doc/txt/dihedral_charmm.txt
diff --git a/doc/src/dihedral_class2.txt b/doc/txt/dihedral_class2.txt
similarity index 100%
rename from doc/src/dihedral_class2.txt
rename to doc/txt/dihedral_class2.txt
diff --git a/doc/src/dihedral_coeff.txt b/doc/txt/dihedral_coeff.txt
similarity index 100%
rename from doc/src/dihedral_coeff.txt
rename to doc/txt/dihedral_coeff.txt
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/txt/dihedral_cosine_shift_exp.txt
similarity index 100%
rename from doc/src/dihedral_cosine_shift_exp.txt
rename to doc/txt/dihedral_cosine_shift_exp.txt
diff --git a/doc/src/dihedral_fourier.txt b/doc/txt/dihedral_fourier.txt
similarity index 100%
rename from doc/src/dihedral_fourier.txt
rename to doc/txt/dihedral_fourier.txt
diff --git a/doc/src/dihedral_harmonic.txt b/doc/txt/dihedral_harmonic.txt
similarity index 100%
rename from doc/src/dihedral_harmonic.txt
rename to doc/txt/dihedral_harmonic.txt
diff --git a/doc/src/dihedral_helix.txt b/doc/txt/dihedral_helix.txt
similarity index 100%
rename from doc/src/dihedral_helix.txt
rename to doc/txt/dihedral_helix.txt
diff --git a/doc/src/dihedral_hybrid.txt b/doc/txt/dihedral_hybrid.txt
similarity index 100%
rename from doc/src/dihedral_hybrid.txt
rename to doc/txt/dihedral_hybrid.txt
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/txt/dihedral_multi_harmonic.txt
similarity index 100%
rename from doc/src/dihedral_multi_harmonic.txt
rename to doc/txt/dihedral_multi_harmonic.txt
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/txt/dihedral_nharmonic.txt
similarity index 100%
rename from doc/src/dihedral_nharmonic.txt
rename to doc/txt/dihedral_nharmonic.txt
diff --git a/doc/src/dihedral_none.txt b/doc/txt/dihedral_none.txt
similarity index 100%
rename from doc/src/dihedral_none.txt
rename to doc/txt/dihedral_none.txt
diff --git a/doc/src/dihedral_opls.txt b/doc/txt/dihedral_opls.txt
similarity index 100%
rename from doc/src/dihedral_opls.txt
rename to doc/txt/dihedral_opls.txt
diff --git a/doc/src/dihedral_quadratic.txt b/doc/txt/dihedral_quadratic.txt
similarity index 100%
rename from doc/src/dihedral_quadratic.txt
rename to doc/txt/dihedral_quadratic.txt
diff --git a/doc/src/dihedral_spherical.txt b/doc/txt/dihedral_spherical.txt
similarity index 100%
rename from doc/src/dihedral_spherical.txt
rename to doc/txt/dihedral_spherical.txt
diff --git a/doc/src/dihedral_style.txt b/doc/txt/dihedral_style.txt
similarity index 100%
rename from doc/src/dihedral_style.txt
rename to doc/txt/dihedral_style.txt
diff --git a/doc/src/dihedral_table.txt b/doc/txt/dihedral_table.txt
similarity index 100%
rename from doc/src/dihedral_table.txt
rename to doc/txt/dihedral_table.txt
diff --git a/doc/src/dihedral_table_cut.txt b/doc/txt/dihedral_table_cut.txt
similarity index 100%
rename from doc/src/dihedral_table_cut.txt
rename to doc/txt/dihedral_table_cut.txt
diff --git a/doc/src/dihedral_zero.txt b/doc/txt/dihedral_zero.txt
similarity index 100%
rename from doc/src/dihedral_zero.txt
rename to doc/txt/dihedral_zero.txt
diff --git a/doc/src/dimension.txt b/doc/txt/dimension.txt
similarity index 100%
rename from doc/src/dimension.txt
rename to doc/txt/dimension.txt
diff --git a/doc/src/displace_atoms.txt b/doc/txt/displace_atoms.txt
similarity index 100%
rename from doc/src/displace_atoms.txt
rename to doc/txt/displace_atoms.txt
diff --git a/doc/src/dump.txt b/doc/txt/dump.txt
similarity index 99%
rename from doc/src/dump.txt
rename to doc/txt/dump.txt
index ff1b2dc3a6..0d08fdf471 100644
--- a/doc/src/dump.txt
+++ b/doc/txt/dump.txt
@@ -21,7 +21,8 @@ dump ID group-ID style N file args :pre
 
 ID = user-assigned name for the dump :ulb,l
 group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or
+{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
 N = dump every this many timesteps :l
 file = name of file to write dump info to :l
 args = list of arguments for a particular style :l
diff --git a/doc/src/dump_adios.txt b/doc/txt/dump_adios.txt
similarity index 100%
rename from doc/src/dump_adios.txt
rename to doc/txt/dump_adios.txt
diff --git a/doc/src/dump_cfg_uef.txt b/doc/txt/dump_cfg_uef.txt
similarity index 100%
rename from doc/src/dump_cfg_uef.txt
rename to doc/txt/dump_cfg_uef.txt
diff --git a/doc/src/dump_h5md.txt b/doc/txt/dump_h5md.txt
similarity index 100%
rename from doc/src/dump_h5md.txt
rename to doc/txt/dump_h5md.txt
diff --git a/doc/src/dump_image.txt b/doc/txt/dump_image.txt
similarity index 100%
rename from doc/src/dump_image.txt
rename to doc/txt/dump_image.txt
diff --git a/doc/src/dump_modify.txt b/doc/txt/dump_modify.txt
similarity index 97%
rename from doc/src/dump_modify.txt
rename to doc/txt/dump_modify.txt
index 6be0d26463..63a3476d30 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/txt/dump_modify.txt
@@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {pbc} or {precision} or {region} or {refresh} or {scale} or {sfactor} or {sort} or {tfactor} or {thermo} or {thresh} or {time} or {units} or {unwrap} :l
   {append} arg = {yes} or {no}
   {at} arg = N
     N = index of frame written upon first dump
@@ -30,10 +30,10 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {fileper} arg = Np
     Np = write one file for every this many processors
   {first} arg = {yes} or {no}
+  {flush} arg = {yes} or {no}
   {format} args = {line} string, {int} string, {float} string, M string, or {none}
     string = C-style format string
     M = integer from 1 to N, where N = # of per-atom quantities being output
-  {flush} arg = {yes} or {no}
   {image} arg = {yes} or {no}
   {label} arg = string
     string = character string (e.g. BONDS) to use in header of dump local file
@@ -48,18 +48,20 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {refresh} arg = c_ID = compute ID that supports a refresh operation
   {scale} arg = {yes} or {no}
   {sfactor} arg = coordinate scaling factor (> 0.0)
-  {thermo} arg = {yes} or {no}
-  {tfactor} arg = time scaling factor (> 0.0)
   {sort} arg = {off} or {id} or N or -N
      off = no sorting of per-atom lines within a snapshot
      id = sort per-atom lines by atom ID
      N = sort per-atom lines in ascending order by the Nth column
      -N = sort per-atom lines in descending order by the Nth column
+  {tfactor} arg = time scaling factor (> 0.0)
+  {thermo} arg = {yes} or {no}
+  {time} arg = {yes} or {no}
   {thresh} args = attribute operator value
     attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
     operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
     value = numeric value to compare to, or LAST
     these 3 args can be replaced by the word "none" to turn off thresholding
+  {units} arg = {yes} or {no}
   {unwrap} arg = {yes} or {no} :pre
 these keywords apply only to the {image} and {movie} "styles"_dump_image.html :l
 keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l
@@ -620,6 +622,37 @@ threshold criterion is met.  Otherwise it is not met.
 
 :line
 
+The {time} keyword only applies to the dump {atom}, {custom}, and
+{local} styles (and their COMPRESS package versions {atom/gz},
+{custom/gz} and {local/gz}). If set to {yes}, each frame will will
+contain two extra lines before the "ITEM: TIMESTEP" entry:
+
+ITEM: TIME
+\<elapsed time\> :pre
+
+This will output the current elapsed simulation time in current
+time units equivalent to the "thermo keyword"_thermo_style.html {time}.
+This is to simplify post-processing of trajectories using a variable time
+step, e.g. when using "fix dt/reset"_fix_dt_reset.html.
+The default setting is {no}.
+
+:line
+
+The {units} keyword only applies to the dump {atom}, {custom}, and
+{local} styles (and their COMPRESS package versions {atom/gz},
+{custom/gz} and {local/gz}). If set to {yes}, each individual dump
+file will contain two extra lines at the very beginning with:
+
+ITEM: UNITS
+\<units style\> :pre
+
+This will output the current selected "units"_units.html style
+to the dump file and thus allows visualization and post-processing
+tools to determine the choice of units of the data in the dump file.
+The default setting is {no}.
+
+:line
+
 The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
 If set to {yes}, coordinates will be written "unwrapped" by the image
 flags for each atom.  Unwrapped means that if the atom has passed through
@@ -924,6 +957,7 @@ scale = yes
 sort = off for dump styles {atom}, {custom}, {cfg}, and {local}
 sort = id for dump styles {dcd}, {xtc}, and {xyz}
 thresh = none
+units = no
 unwrap = no :ul
 
 acolor = * red/green/blue/yellow/aqua/cyan
diff --git a/doc/src/dump_molfile.txt b/doc/txt/dump_molfile.txt
similarity index 100%
rename from doc/src/dump_molfile.txt
rename to doc/txt/dump_molfile.txt
diff --git a/doc/src/dump_netcdf.txt b/doc/txt/dump_netcdf.txt
similarity index 100%
rename from doc/src/dump_netcdf.txt
rename to doc/txt/dump_netcdf.txt
diff --git a/doc/src/dump_vtk.txt b/doc/txt/dump_vtk.txt
similarity index 100%
rename from doc/src/dump_vtk.txt
rename to doc/txt/dump_vtk.txt
diff --git a/doc/src/dynamical_matrix.txt b/doc/txt/dynamical_matrix.txt
similarity index 55%
rename from doc/src/dynamical_matrix.txt
rename to doc/txt/dynamical_matrix.txt
index 6291bdec52..2d9b256694 100644
--- a/doc/src/dynamical_matrix.txt
+++ b/doc/txt/dynamical_matrix.txt
@@ -30,14 +30,29 @@ dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre
 
 [Description:]
 
-Calculate the dynamical matrix of the selected group.
+Calculate the dynamical matrix by finite difference of the selected group,
+
+:c,image(JPG/dynamical_matrix_dynmat.jpg)
+
+where D is the dynamical matrix and Phi is the force constant matrix defined by
+
+:c,image(JPG/dynamical_matrix_force_constant.jpg).
+
+The output for the dynamical matrix is printed three elements at a time. The
+three elements are the three beta elements for a respective i/alpha/j combination. 
+Each line is printed in order of j increasing first, alpha second, and i last.
+
+If the style eskm is selected, the dynamical matrix will be in units of inverse squared
+femtoseconds. These units will then conveniently leave frequencies in THz, where
+frequencies, represented as omega, can be calculated from
+
+:c, image(Eqs/dynamical_matrix_phonons.jpg)
 
 [Restrictions:]
 
-The command collects the entire dynamical matrix a single MPI rank,
-so the memory requirements can be very significant for large systems.
-
-This command assumes a periodic system.
+The command collects an array of nine times the number of atoms in a group
+on every single MPI rank, so the memory requirements can be very significant
+for large systems.
 
 This command is part of the USER-PHONON package.  It is only enabled if
 LAMMPS was built with that package.  See the "Build
@@ -52,4 +67,4 @@ provided by Pair's single_hessian.
 
 [Default:]
 
-The default settings are file = "dynmat.dyn", binary = no  
+The default settings are file = "dynmat.dyn", binary = no
diff --git a/doc/src/echo.txt b/doc/txt/echo.txt
similarity index 100%
rename from doc/src/echo.txt
rename to doc/txt/echo.txt
diff --git a/doc/src/fix.txt b/doc/txt/fix.txt
similarity index 99%
rename from doc/src/fix.txt
rename to doc/txt/fix.txt
index 1dd9cc9f1b..fd281bce83 100644
--- a/doc/src/fix.txt
+++ b/doc/txt/fix.txt
@@ -188,7 +188,7 @@ accelerated styles exist.
 "box/relax"_fix_box_relax.html - relax box size during energy minimization
 "client/md"_fix_client_md.html - MD client for client/server simulations
 "cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
-"colvars"_fix_colvars.html - interface to the collective variables “Colvars� library
+"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library
 "controller"_fix_controller.html - apply control loop feedback mechanism
 "deform"_fix_deform.html - change the simulation box size/shape
 "deposit"_fix_deposit.html - add new atoms above a surface
@@ -221,7 +221,7 @@ accelerated styles exist.
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "hyper/global"_fix_hyper_global.html - global hyperdynamics
 "hyper/local"_fix_hyper_local.html - local hyperdynamics
-"imd"_fix_imd.html - implements the “Interactive MD� (IMD) protocol 
+"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol
 "indent"_fix_indent.html - impose force due to an indenter
 "ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
 "langevin"_fix_langevin.html - Langevin temperature control
@@ -327,7 +327,7 @@ accelerated styles exist.
 "rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
 "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
 "rx"_fix_rx.html -
-"saed/vtk"_fix_saed_vtk.html - 
+"saed/vtk"_fix_saed_vtk.html -
 "setforce"_fix_setforce.html - set the force on each atom
 "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
 "shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
diff --git a/doc/src/fix_adapt.txt b/doc/txt/fix_adapt.txt
similarity index 100%
rename from doc/src/fix_adapt.txt
rename to doc/txt/fix_adapt.txt
diff --git a/doc/src/fix_adapt_fep.txt b/doc/txt/fix_adapt_fep.txt
similarity index 100%
rename from doc/src/fix_adapt_fep.txt
rename to doc/txt/fix_adapt_fep.txt
diff --git a/doc/src/fix_addforce.txt b/doc/txt/fix_addforce.txt
similarity index 100%
rename from doc/src/fix_addforce.txt
rename to doc/txt/fix_addforce.txt
diff --git a/doc/src/fix_addtorque.txt b/doc/txt/fix_addtorque.txt
similarity index 100%
rename from doc/src/fix_addtorque.txt
rename to doc/txt/fix_addtorque.txt
diff --git a/doc/src/fix_append_atoms.txt b/doc/txt/fix_append_atoms.txt
similarity index 100%
rename from doc/src/fix_append_atoms.txt
rename to doc/txt/fix_append_atoms.txt
diff --git a/doc/src/fix_atc.txt b/doc/txt/fix_atc.txt
similarity index 100%
rename from doc/src/fix_atc.txt
rename to doc/txt/fix_atc.txt
diff --git a/doc/src/fix_atom_swap.txt b/doc/txt/fix_atom_swap.txt
similarity index 100%
rename from doc/src/fix_atom_swap.txt
rename to doc/txt/fix_atom_swap.txt
diff --git a/doc/src/fix_ave_atom.txt b/doc/txt/fix_ave_atom.txt
similarity index 99%
rename from doc/src/fix_ave_atom.txt
rename to doc/txt/fix_ave_atom.txt
index 10deaf64cd..596f9ee46c 100644
--- a/doc/src/fix_ave_atom.txt
+++ b/doc/txt/fix_ave_atom.txt
@@ -80,7 +80,7 @@ command creates a per-atom array with 6 columns:
 
 compute my_stress all stress/atom NULL
 fix 1 all ave/atom 10 20 1000 c_my_stress\[*\]
-fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[1\] &
+fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[2\] &
                               c_my_stress\[3\] c_my_stress\[4\] &
                               c_my_stress\[5\] c_my_stress\[6\] :pre
 
diff --git a/doc/src/fix_ave_chunk.txt b/doc/txt/fix_ave_chunk.txt
similarity index 100%
rename from doc/src/fix_ave_chunk.txt
rename to doc/txt/fix_ave_chunk.txt
diff --git a/doc/src/fix_ave_correlate.txt b/doc/txt/fix_ave_correlate.txt
similarity index 100%
rename from doc/src/fix_ave_correlate.txt
rename to doc/txt/fix_ave_correlate.txt
diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/txt/fix_ave_correlate_long.txt
similarity index 100%
rename from doc/src/fix_ave_correlate_long.txt
rename to doc/txt/fix_ave_correlate_long.txt
diff --git a/doc/src/fix_ave_histo.txt b/doc/txt/fix_ave_histo.txt
similarity index 100%
rename from doc/src/fix_ave_histo.txt
rename to doc/txt/fix_ave_histo.txt
diff --git a/doc/src/fix_ave_time.txt b/doc/txt/fix_ave_time.txt
similarity index 100%
rename from doc/src/fix_ave_time.txt
rename to doc/txt/fix_ave_time.txt
diff --git a/doc/src/fix_aveforce.txt b/doc/txt/fix_aveforce.txt
similarity index 100%
rename from doc/src/fix_aveforce.txt
rename to doc/txt/fix_aveforce.txt
diff --git a/doc/src/fix_balance.txt b/doc/txt/fix_balance.txt
similarity index 100%
rename from doc/src/fix_balance.txt
rename to doc/txt/fix_balance.txt
diff --git a/doc/src/fix_bocs.txt b/doc/txt/fix_bocs.txt
similarity index 100%
rename from doc/src/fix_bocs.txt
rename to doc/txt/fix_bocs.txt
diff --git a/doc/src/fix_bond_break.txt b/doc/txt/fix_bond_break.txt
similarity index 100%
rename from doc/src/fix_bond_break.txt
rename to doc/txt/fix_bond_break.txt
diff --git a/doc/src/fix_bond_create.txt b/doc/txt/fix_bond_create.txt
similarity index 100%
rename from doc/src/fix_bond_create.txt
rename to doc/txt/fix_bond_create.txt
diff --git a/doc/src/fix_bond_react.txt b/doc/txt/fix_bond_react.txt
similarity index 85%
rename from doc/src/fix_bond_react.txt
rename to doc/txt/fix_bond_react.txt
index 3f428e2103..d729f09b54 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/txt/fix_bond_react.txt
@@ -186,20 +186,25 @@ reacting atoms.
 
 Some atoms in the pre-reacted template that are not reacting may have
 missing topology with respect to the simulation. For example, the
-pre-reacted template may contain an atom that would connect to the
-rest of a long polymer chain. These are referred to as edge atoms, and
-are also specified in the map file. When the pre-reaction template
-contains edge atoms, not all atoms, bonds, charges, etc. specified in
-the reaction templates will be updated. Specifically, topology that
-involves only atoms that are 'too near' to template edges will not be
-updated. The definition of 'too near the edge' depends on which
-interactions are defined in the simulation. If the simulation has
-defined dihedrals, atoms within two bonds of edge atoms are considered
-'too near the edge.' If the simulation defines angles, but not
-dihedrals, atoms within one bond of edge atoms are considered 'too
-near the edge.' If just bonds are defined, only edge atoms are
+pre-reacted template may contain an atom that, in the simulation, is
+currently connected to the rest of a long polymer chain. These are
+referred to as edge atoms, and are also specified in the map file. All
+pre-reaction template atoms should be linked to a bonding atom, via at
+least one path that does not involve edge atoms. When the pre-reaction
+template contains edge atoms, not all atoms, bonds, charges, etc.
+specified in the reaction templates will be updated. Specifically,
+topology that involves only atoms that are 'too near' to template
+edges will not be updated. The definition of 'too near the edge'
+depends on which interactions are defined in the simulation. If the
+simulation has defined dihedrals, atoms within two bonds of edge atoms
+are considered 'too near the edge.' If the simulation defines angles,
+but not dihedrals, atoms within one bond of edge atoms are considered
+'too near the edge.' If just bonds are defined, only edge atoms are
 considered 'too near the edge.'
 
+NOTE: Small molecules, i.e. ones that have all their atoms contained
+within the reaction templates, never have edge atoms.
+
 Note that some care must be taken when a building a molecule template
 for a given simulation. All atom types in the pre-reacted template
 must be the same as those of a potential reaction site in the
@@ -261,7 +266,7 @@ either 'none' or 'charges.' Further details are provided in the
 discussion of the 'update_edges' keyword. The fourth optional section
 begins with the keyword 'Constraints' and lists additional criteria
 that must be satisfied in order for the reaction to occur. Currently,
-there is one type of constraint available, as discussed below.
+there are three types of constraints available, as discussed below.
 
 A sample map file is given below:
 
@@ -295,17 +300,47 @@ Equivalences :pre
 :line
 
 Any number of additional constraints may be specified in the
-Constraints section of the map file. Currently there is one type of
-additional constraint, of type 'distance', whose syntax is as follows:
+Constraints section of the map file. The constraint of type 'distance'
+has syntax as follows:
 
 distance {ID1} {ID2} {rmin} {rmax} :pre
 
 where 'distance' is the required keyword, {ID1} and {ID2} are
 pre-reaction atom IDs, and these two atoms must be separated by a
-distance between {rmin} and {rmax} for the reaction to occur. This
+distance between {rmin} and {rmax} for the reaction to occur.
+
+The constraint of type 'angle' has the following syntax:
+
+angle {ID1} {ID2} {ID3} {amin} {amax} :pre
+
+where 'angle' is the required keyword, {ID1}, {ID2} and {ID3} are
+pre-reaction atom IDs, and these three atoms must form an angle
+between {amin} and {amax} for the reaction to occur (where {ID2} is
+the central atom). Angles must be specified in degrees. This
 constraint can be used to enforce a certain orientation between
 reacting molecules.
 
+The constraint of type 'arrhenius' imposes an additional reaction
+probability according to the temperature-dependent Arrhenius equation:
+
+:c,image(Eqs/fix_bond_react.jpg)
+
+The Arrhenius constraint has the following syntax:
+
+arrhenius {A} {n} {E_a} {seed} :pre
+
+where 'arrhenius' is the required keyword, {A} is the pre-exponential
+factor, {n} is the exponent of the temperature dependence, {E_a} is
+the activation energy ("units"_units.html of energy), and {seed} is a
+random number seed. The temperature is defined as the instantaneous
+temperature averaged over all atoms in the reaction site, and is
+calculated in the same manner as for example
+"compute_temp_chunk"_compute_temp_chunk.html. Currently, there are no
+options for additional temperature averaging or velocity-biased
+temperature calculations. A uniform random number between 0 and 1 is
+generated using {seed}; if this number is less than the result of the
+Arrhenius equation above, the reaction is permitted to occur.
+
 Once a reaction site has been successfully identified, data structures
 within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
@@ -381,7 +416,7 @@ will apply to all reactions.
 Computationally, each timestep this fix operates, it loops over
 neighbor lists (for bond-forming reactions) and computes distances
 between pairs of atoms in the list. It also communicates between
-neighboring processors to coordinate which bonds  are created and/or
+neighboring processors to coordinate which bonds are created and/or
 removed. All of these operations increase the cost of a timestep. Thus
 you should be cautious about invoking this fix too frequently.
 
@@ -392,10 +427,11 @@ local command.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-No information about this fix is written to "binary restart
-files"_restart.html, aside from internally-created per-atom
-properties. None of the "fix_modify"_fix_modify.html options are
-relevant to this fix.
+Cumulative reaction counts for each reaction are written to "binary
+restart files"_restart.html. These values are associated with the
+reaction name (react-ID). Additionally, internally-created per-atom
+properties are stored to allow for smooth restarts. None of the
+"fix_modify"_fix_modify.html options are relevant to this fix.
 
 This fix computes one statistic for each {react} argument that it
 stores in a global vector, of length 'number of react arguments', that
@@ -406,8 +442,8 @@ These is 1 quantity for each react argument:
 
 (1) cumulative # of reactions occurred :ul
 
-No parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command.  This fix is not invoked during "energy
+No parameter of this fix can be used with the {start/stop} keywords
+of the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
 
 When fix bond/react is 'unfixed,' all internally-created groups are
@@ -417,18 +453,20 @@ all other fixes that use any group created by fix bond/react.
 [Restrictions:]
 
 This fix is part of the USER-MISC package.  It is only enabled if
-LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
+LAMMPS was built with that package.  See the
+"Build package"_Build_package.html doc page for more info.
 
 [Related commands:]
 
-"fix bond/create"_fix_bond_create.html, "fix
-bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
+"fix bond/create"_fix_bond_create.html,
+"fix bond/break"_fix_bond_break.html,
+"fix bond/swap"_fix_bond_swap.html,
 "dump local"_dump.html, "special_bonds"_special_bonds.html
 
 [Default:]
 
-The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
+update_edges = none
 
 :line
 
diff --git a/doc/src/fix_bond_swap.txt b/doc/txt/fix_bond_swap.txt
similarity index 100%
rename from doc/src/fix_bond_swap.txt
rename to doc/txt/fix_bond_swap.txt
diff --git a/doc/src/fix_box_relax.txt b/doc/txt/fix_box_relax.txt
similarity index 100%
rename from doc/src/fix_box_relax.txt
rename to doc/txt/fix_box_relax.txt
diff --git a/doc/src/fix_client_md.txt b/doc/txt/fix_client_md.txt
similarity index 100%
rename from doc/src/fix_client_md.txt
rename to doc/txt/fix_client_md.txt
diff --git a/doc/src/fix_cmap.txt b/doc/txt/fix_cmap.txt
similarity index 100%
rename from doc/src/fix_cmap.txt
rename to doc/txt/fix_cmap.txt
diff --git a/doc/src/fix_colvars.txt b/doc/txt/fix_colvars.txt
similarity index 100%
rename from doc/src/fix_colvars.txt
rename to doc/txt/fix_colvars.txt
diff --git a/doc/src/fix_controller.txt b/doc/txt/fix_controller.txt
similarity index 99%
rename from doc/src/fix_controller.txt
rename to doc/txt/fix_controller.txt
index 7458f1bcfa..45eb646b8e 100644
--- a/doc/src/fix_controller.txt
+++ b/doc/txt/fix_controller.txt
@@ -31,7 +31,6 @@ cvar = name of control variable :l
 
 [Examples:]
 
-		
 fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
 fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
 fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre
diff --git a/doc/src/fix_deform.txt b/doc/txt/fix_deform.txt
similarity index 100%
rename from doc/src/fix_deform.txt
rename to doc/txt/fix_deform.txt
diff --git a/doc/src/fix_deposit.txt b/doc/txt/fix_deposit.txt
similarity index 100%
rename from doc/src/fix_deposit.txt
rename to doc/txt/fix_deposit.txt
diff --git a/doc/src/fix_dpd_energy.txt b/doc/txt/fix_dpd_energy.txt
similarity index 100%
rename from doc/src/fix_dpd_energy.txt
rename to doc/txt/fix_dpd_energy.txt
diff --git a/doc/src/fix_dpd_source.txt b/doc/txt/fix_dpd_source.txt
similarity index 100%
rename from doc/src/fix_dpd_source.txt
rename to doc/txt/fix_dpd_source.txt
diff --git a/doc/src/fix_drag.txt b/doc/txt/fix_drag.txt
similarity index 100%
rename from doc/src/fix_drag.txt
rename to doc/txt/fix_drag.txt
diff --git a/doc/src/fix_drude.txt b/doc/txt/fix_drude.txt
similarity index 100%
rename from doc/src/fix_drude.txt
rename to doc/txt/fix_drude.txt
diff --git a/doc/src/fix_drude_transform.txt b/doc/txt/fix_drude_transform.txt
similarity index 100%
rename from doc/src/fix_drude_transform.txt
rename to doc/txt/fix_drude_transform.txt
diff --git a/doc/src/fix_dt_reset.txt b/doc/txt/fix_dt_reset.txt
similarity index 100%
rename from doc/src/fix_dt_reset.txt
rename to doc/txt/fix_dt_reset.txt
diff --git a/doc/src/fix_efield.txt b/doc/txt/fix_efield.txt
similarity index 100%
rename from doc/src/fix_efield.txt
rename to doc/txt/fix_efield.txt
diff --git a/doc/src/fix_ehex.txt b/doc/txt/fix_ehex.txt
similarity index 100%
rename from doc/src/fix_ehex.txt
rename to doc/txt/fix_ehex.txt
diff --git a/doc/src/fix_electron_stopping.txt b/doc/txt/fix_electron_stopping.txt
similarity index 100%
rename from doc/src/fix_electron_stopping.txt
rename to doc/txt/fix_electron_stopping.txt
diff --git a/doc/src/fix_enforce2d.txt b/doc/txt/fix_enforce2d.txt
similarity index 100%
rename from doc/src/fix_enforce2d.txt
rename to doc/txt/fix_enforce2d.txt
diff --git a/doc/src/fix_eos_cv.txt b/doc/txt/fix_eos_cv.txt
similarity index 100%
rename from doc/src/fix_eos_cv.txt
rename to doc/txt/fix_eos_cv.txt
diff --git a/doc/src/fix_eos_table.txt b/doc/txt/fix_eos_table.txt
similarity index 100%
rename from doc/src/fix_eos_table.txt
rename to doc/txt/fix_eos_table.txt
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/txt/fix_eos_table_rx.txt
similarity index 100%
rename from doc/src/fix_eos_table_rx.txt
rename to doc/txt/fix_eos_table_rx.txt
diff --git a/doc/src/fix_evaporate.txt b/doc/txt/fix_evaporate.txt
similarity index 100%
rename from doc/src/fix_evaporate.txt
rename to doc/txt/fix_evaporate.txt
diff --git a/doc/src/fix_external.txt b/doc/txt/fix_external.txt
similarity index 100%
rename from doc/src/fix_external.txt
rename to doc/txt/fix_external.txt
diff --git a/doc/src/fix_ffl.txt b/doc/txt/fix_ffl.txt
similarity index 100%
rename from doc/src/fix_ffl.txt
rename to doc/txt/fix_ffl.txt
diff --git a/doc/src/fix_filter_corotate.txt b/doc/txt/fix_filter_corotate.txt
similarity index 100%
rename from doc/src/fix_filter_corotate.txt
rename to doc/txt/fix_filter_corotate.txt
diff --git a/doc/src/fix_flow_gauss.txt b/doc/txt/fix_flow_gauss.txt
similarity index 100%
rename from doc/src/fix_flow_gauss.txt
rename to doc/txt/fix_flow_gauss.txt
diff --git a/doc/src/fix_freeze.txt b/doc/txt/fix_freeze.txt
similarity index 100%
rename from doc/src/fix_freeze.txt
rename to doc/txt/fix_freeze.txt
diff --git a/doc/src/fix_gcmc.txt b/doc/txt/fix_gcmc.txt
similarity index 97%
rename from doc/src/fix_gcmc.txt
rename to doc/txt/fix_gcmc.txt
index 3c0f2c2f17..f28cb5771f 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/txt/fix_gcmc.txt
@@ -48,7 +48,9 @@ keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energ
     group-ID = group-ID for inserted atoms (string)
   {intra_energy} value = intramolecular energy (energy units)
   {tfac_insert} value = scale up/down temperature of inserted atoms (unitless)
-  {overlap_cutoff} value = maximum pair distance for overlap rejection (distance units) :pre
+  {overlap_cutoff} value = maximum pair distance for overlap rejection (distance units)
+  {max} value = Maximum number of molecules allowed in the system
+  {min} value = Minimum number of molecules allowed in the system :pre
 :ule
 
 [Examples:]
@@ -364,6 +366,12 @@ assigning an infinite positive energy to all new configurations that
 place any pair of atoms closer than the specified overlap cutoff
 distance.
 
+The {max} and {min} keywords allow for the restriction of the number
+of atoms in the simulation. They automatically reject all insertion 
+or deletion moves that would take the system beyond the set boundaries.
+Should the system already be beyond the boundary, only moves that bring 
+the system closer to the bounds may be accepted.
+
 The {group} keyword adds all inserted atoms to the
 "group"_group.html of the group-ID value. The {grouptype} keyword
 adds all inserted atoms of the specified type to the
diff --git a/doc/src/fix_gld.txt b/doc/txt/fix_gld.txt
similarity index 100%
rename from doc/src/fix_gld.txt
rename to doc/txt/fix_gld.txt
diff --git a/doc/src/fix_gle.txt b/doc/txt/fix_gle.txt
similarity index 100%
rename from doc/src/fix_gle.txt
rename to doc/txt/fix_gle.txt
diff --git a/doc/src/fix_gravity.txt b/doc/txt/fix_gravity.txt
similarity index 100%
rename from doc/src/fix_gravity.txt
rename to doc/txt/fix_gravity.txt
diff --git a/doc/src/fix_grem.txt b/doc/txt/fix_grem.txt
similarity index 100%
rename from doc/src/fix_grem.txt
rename to doc/txt/fix_grem.txt
diff --git a/doc/src/fix_halt.txt b/doc/txt/fix_halt.txt
similarity index 100%
rename from doc/src/fix_halt.txt
rename to doc/txt/fix_halt.txt
diff --git a/doc/src/fix_heat.txt b/doc/txt/fix_heat.txt
similarity index 100%
rename from doc/src/fix_heat.txt
rename to doc/txt/fix_heat.txt
diff --git a/doc/src/fix_hyper_global.txt b/doc/txt/fix_hyper_global.txt
similarity index 100%
rename from doc/src/fix_hyper_global.txt
rename to doc/txt/fix_hyper_global.txt
diff --git a/doc/src/fix_hyper_local.txt b/doc/txt/fix_hyper_local.txt
similarity index 100%
rename from doc/src/fix_hyper_local.txt
rename to doc/txt/fix_hyper_local.txt
diff --git a/doc/src/fix_imd.txt b/doc/txt/fix_imd.txt
similarity index 100%
rename from doc/src/fix_imd.txt
rename to doc/txt/fix_imd.txt
diff --git a/doc/src/fix_indent.txt b/doc/txt/fix_indent.txt
similarity index 100%
rename from doc/src/fix_indent.txt
rename to doc/txt/fix_indent.txt
diff --git a/doc/src/fix_ipi.txt b/doc/txt/fix_ipi.txt
similarity index 100%
rename from doc/src/fix_ipi.txt
rename to doc/txt/fix_ipi.txt
diff --git a/doc/src/fix_langevin.txt b/doc/txt/fix_langevin.txt
similarity index 89%
rename from doc/src/fix_langevin.txt
rename to doc/txt/fix_langevin.txt
index 861eed4a6f..49ecf96ff6 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/txt/fix_langevin.txt
@@ -24,9 +24,10 @@ keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l
   {angmom} value = {no} or factor
     {no} = do not thermostat rotational degrees of freedom via the angular momentum
     factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
-  {gjf} value = {no} or {yes}
+  {gjf} value = {no} or {vfull} or {vhalf}
     {no} = use standard formulation
-    {yes} = use Gronbech-Jensen/Farago formulation
+    {vfull} = use Gronbech-Jensen/Farago formulation
+    {vhalf} = use 2GJ formulation
   {omega} value = {no} or {yes}
     {no} = do not thermostat rotational degrees of freedom via the angular velocity
     {yes} = do thermostat rotational degrees of freedom via the angular velocity
@@ -217,6 +218,10 @@ the particles.  As described below, this energy can then be printed
 out or added to the potential energy of the system to monitor energy
 conservation.
 
+NOTE: this accumulated energy does NOT include kinetic energy removed
+by the {zero} flag. LAMMPS will print a warning when both options are
+active.
+
 The keyword {zero} can be used to eliminate drift due to the
 thermostat. Because the random forces on different atoms are
 independent, they do not sum exactly to zero.  As a result, this fix
@@ -232,29 +237,24 @@ The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago
 described in the papers cited below, the purpose of this method is to
 enable longer timesteps to be used (up to the numerical stability
 limit of the integrator), while still producing the correct Boltzmann
-distribution of atom positions.  It is implemented within LAMMPS, by
-changing how the random force is applied so that it is composed of
-the average of two random forces representing half-contributions from
-the previous and current time intervals.
+distribution of atom positions.
 
-In common with all methods based on Verlet integration, the
-discretized velocities generated by this method in conjunction with
-velocity-Verlet time integration are not exactly conjugate to the
-positions.  As a result the temperature (computed from the discretized
-velocities) will be systematically lower than the target temperature,
-by a small amount which grows with the timestep.  Nonetheless, the
-distribution of atom positions will still be consistent with the
+The current implementation provides the user with the option to output
+the velocity in one of two forms: {vfull} or {vhalf}, which replaces
+the outdated option {yes}. The {gjf} option {vfull} outputs the on-site
+velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity
+is shown to be systematically lower than the target temperature by a small
+amount, which grows quadratically with the timestep.
+The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in
+"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; for linear systems,
+this velocity is shown to not have any statistical errors for any stable time step.
+An overview of statistically correct Boltzmann and Maxwell-Boltzmann
+sampling of true on-site and true half-step velocities is given in
+"Gronbech-Jensen"_#1Gronbech-Jensen.
+Regardless of the choice of output velocity, the sampling of the configurational
+distribution of atom positions is the same, and linearly consistent with the
 target temperature.
 
-As an example of using the {gjf} keyword, for molecules containing C-H
-bonds, configurational properties generated with dt = 2.5 fs and tdamp
-= 100 fs are indistinguishable from dt = 0.5 fs.  Because the velocity
-distribution systematically decreases with increasing timestep, the
-method should not be used to generate properties that depend on the
-velocity distribution, such as the velocity auto-correlation function
-(VACF). In this example, the velocity distribution at dt = 2.5fs
-generates an average temperature of 220 K, instead of 300 K.
-
 :line
 
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
@@ -312,7 +312,10 @@ This fix can ramp its target temperature over multiple runs, using the
 
 This fix is not invoked during "energy minimization"_minimize.html.
 
-[Restrictions:] none
+[Restrictions:]
+
+For {gjf} do not choose damp=dt/2. {gjf} is not compatible
+with run_style respa. 
 
 [Related commands:]
 
@@ -335,5 +338,10 @@ types, tally = no, zero = no, gjf = no.
 
 :link(Gronbech-Jensen)
 [(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983
-(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
-185, 524 (2014)
+(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
+
+:link(2Gronbech-Jensen)
+[(Gronbech-Jensen)] Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019)
+
+:link(1Gronbech-Jensen)
+[(Gronbech-Jensen)] Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506
diff --git a/doc/src/fix_langevin_drude.txt b/doc/txt/fix_langevin_drude.txt
similarity index 100%
rename from doc/src/fix_langevin_drude.txt
rename to doc/txt/fix_langevin_drude.txt
diff --git a/doc/src/fix_langevin_eff.txt b/doc/txt/fix_langevin_eff.txt
similarity index 100%
rename from doc/src/fix_langevin_eff.txt
rename to doc/txt/fix_langevin_eff.txt
diff --git a/doc/src/fix_langevin_spin.txt b/doc/txt/fix_langevin_spin.txt
similarity index 98%
rename from doc/src/fix_langevin_spin.txt
rename to doc/txt/fix_langevin_spin.txt
index e4065adad5..e5dccc5e57 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/txt/fix_langevin_spin.txt
@@ -50,7 +50,7 @@ As an example:
 
 fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
 fix 2 all langevin/spin 300.0 0.01 21
-fix 3 all nve/spin lattice yes :pre
+fix 3 all nve/spin lattice moving :pre
 
 is correct, but defining a force/spin command after the langevin/spin command
 would give an error message.
diff --git a/doc/src/fix_latte.txt b/doc/txt/fix_latte.txt
similarity index 100%
rename from doc/src/fix_latte.txt
rename to doc/txt/fix_latte.txt
diff --git a/doc/src/fix_lb_fluid.txt b/doc/txt/fix_lb_fluid.txt
similarity index 100%
rename from doc/src/fix_lb_fluid.txt
rename to doc/txt/fix_lb_fluid.txt
diff --git a/doc/src/fix_lb_momentum.txt b/doc/txt/fix_lb_momentum.txt
similarity index 100%
rename from doc/src/fix_lb_momentum.txt
rename to doc/txt/fix_lb_momentum.txt
diff --git a/doc/src/fix_lb_pc.txt b/doc/txt/fix_lb_pc.txt
similarity index 100%
rename from doc/src/fix_lb_pc.txt
rename to doc/txt/fix_lb_pc.txt
diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/txt/fix_lb_rigid_pc_sphere.txt
similarity index 100%
rename from doc/src/fix_lb_rigid_pc_sphere.txt
rename to doc/txt/fix_lb_rigid_pc_sphere.txt
diff --git a/doc/src/fix_lb_viscous.txt b/doc/txt/fix_lb_viscous.txt
similarity index 100%
rename from doc/src/fix_lb_viscous.txt
rename to doc/txt/fix_lb_viscous.txt
diff --git a/doc/src/fix_lineforce.txt b/doc/txt/fix_lineforce.txt
similarity index 100%
rename from doc/src/fix_lineforce.txt
rename to doc/txt/fix_lineforce.txt
diff --git a/doc/src/fix_manifoldforce.txt b/doc/txt/fix_manifoldforce.txt
similarity index 100%
rename from doc/src/fix_manifoldforce.txt
rename to doc/txt/fix_manifoldforce.txt
diff --git a/doc/src/fix_meso.txt b/doc/txt/fix_meso.txt
similarity index 100%
rename from doc/src/fix_meso.txt
rename to doc/txt/fix_meso.txt
diff --git a/doc/src/fix_meso_move.txt b/doc/txt/fix_meso_move.txt
similarity index 100%
rename from doc/src/fix_meso_move.txt
rename to doc/txt/fix_meso_move.txt
diff --git a/doc/src/fix_meso_stationary.txt b/doc/txt/fix_meso_stationary.txt
similarity index 100%
rename from doc/src/fix_meso_stationary.txt
rename to doc/txt/fix_meso_stationary.txt
diff --git a/doc/src/fix_modify.txt b/doc/txt/fix_modify.txt
similarity index 100%
rename from doc/src/fix_modify.txt
rename to doc/txt/fix_modify.txt
diff --git a/doc/src/fix_momentum.txt b/doc/txt/fix_momentum.txt
similarity index 100%
rename from doc/src/fix_momentum.txt
rename to doc/txt/fix_momentum.txt
diff --git a/doc/src/fix_move.txt b/doc/txt/fix_move.txt
similarity index 100%
rename from doc/src/fix_move.txt
rename to doc/txt/fix_move.txt
diff --git a/doc/src/fix_mscg.txt b/doc/txt/fix_mscg.txt
similarity index 100%
rename from doc/src/fix_mscg.txt
rename to doc/txt/fix_mscg.txt
diff --git a/doc/src/fix_msst.txt b/doc/txt/fix_msst.txt
similarity index 100%
rename from doc/src/fix_msst.txt
rename to doc/txt/fix_msst.txt
diff --git a/doc/src/fix_mvv_dpd.txt b/doc/txt/fix_mvv_dpd.txt
similarity index 100%
rename from doc/src/fix_mvv_dpd.txt
rename to doc/txt/fix_mvv_dpd.txt
diff --git a/doc/src/fix_neb.txt b/doc/txt/fix_neb.txt
similarity index 100%
rename from doc/src/fix_neb.txt
rename to doc/txt/fix_neb.txt
diff --git a/doc/src/fix_neb_spin.txt b/doc/txt/fix_neb_spin.txt
similarity index 87%
rename from doc/src/fix_neb_spin.txt
rename to doc/txt/fix_neb_spin.txt
index 89420f451c..e62d297270 100644
--- a/doc/src/fix_neb_spin.txt
+++ b/doc/txt/fix_neb_spin.txt
@@ -24,18 +24,18 @@ fix 1 active neb/spin 1.0
 [Description:]
 
 Add nudging forces to spins in the group for a multi-replica
-simulation run via the "neb/spin"_neb_spin.html command to perform a 
-geodesic nudged elastic band (GNEB) calculation for finding the 
+simulation run via the "neb/spin"_neb_spin.html command to perform a
+geodesic nudged elastic band (GNEB) calculation for finding the
 transition state.
-Hi-level explanations of GNEB are given with the 
-"neb/spin"_neb_spin.html command and on the 
-"Howto replica"_Howto_replica.html doc page.  
-The fix neb/spin command must be used with the "neb/spin" command and 
-defines how inter-replica nudging forces are computed.  A GNEB 
-calculation is divided in two stages. In the first stage n replicas 
-are relaxed toward a MEP until convergence.  In the second stage, the 
-climbing image scheme is enabled, so that the replica having the highest 
-energy relaxes toward the saddle point (i.e. the point of highest energy 
+Hi-level explanations of GNEB are given with the
+"neb/spin"_neb_spin.html command and on the
+"Howto replica"_Howto_replica.html doc page.
+The fix neb/spin command must be used with the "neb/spin" command and
+defines how inter-replica nudging forces are computed.  A GNEB
+calculation is divided in two stages. In the first stage n replicas
+are relaxed toward a MEP until convergence.  In the second stage, the
+climbing image scheme is enabled, so that the replica having the highest
+energy relaxes toward the saddle point (i.e. the point of highest energy
 along the MEP), and a second relaxation is performed.
 
 The nudging forces are calculated as explained in
diff --git a/doc/src/fix_nh.txt b/doc/txt/fix_nh.txt
similarity index 100%
rename from doc/src/fix_nh.txt
rename to doc/txt/fix_nh.txt
diff --git a/doc/src/fix_nh_eff.txt b/doc/txt/fix_nh_eff.txt
similarity index 100%
rename from doc/src/fix_nh_eff.txt
rename to doc/txt/fix_nh_eff.txt
diff --git a/doc/src/fix_nh_uef.txt b/doc/txt/fix_nh_uef.txt
similarity index 100%
rename from doc/src/fix_nh_uef.txt
rename to doc/txt/fix_nh_uef.txt
diff --git a/doc/src/fix_nph_asphere.txt b/doc/txt/fix_nph_asphere.txt
similarity index 100%
rename from doc/src/fix_nph_asphere.txt
rename to doc/txt/fix_nph_asphere.txt
diff --git a/doc/src/fix_nph_body.txt b/doc/txt/fix_nph_body.txt
similarity index 100%
rename from doc/src/fix_nph_body.txt
rename to doc/txt/fix_nph_body.txt
diff --git a/doc/src/fix_nph_sphere.txt b/doc/txt/fix_nph_sphere.txt
similarity index 100%
rename from doc/src/fix_nph_sphere.txt
rename to doc/txt/fix_nph_sphere.txt
diff --git a/doc/src/fix_nphug.txt b/doc/txt/fix_nphug.txt
similarity index 100%
rename from doc/src/fix_nphug.txt
rename to doc/txt/fix_nphug.txt
diff --git a/doc/src/fix_npt_asphere.txt b/doc/txt/fix_npt_asphere.txt
similarity index 100%
rename from doc/src/fix_npt_asphere.txt
rename to doc/txt/fix_npt_asphere.txt
diff --git a/doc/src/fix_npt_body.txt b/doc/txt/fix_npt_body.txt
similarity index 100%
rename from doc/src/fix_npt_body.txt
rename to doc/txt/fix_npt_body.txt
diff --git a/doc/src/fix_npt_sphere.txt b/doc/txt/fix_npt_sphere.txt
similarity index 100%
rename from doc/src/fix_npt_sphere.txt
rename to doc/txt/fix_npt_sphere.txt
diff --git a/doc/src/fix_nve.txt b/doc/txt/fix_nve.txt
similarity index 100%
rename from doc/src/fix_nve.txt
rename to doc/txt/fix_nve.txt
diff --git a/doc/src/fix_nve_asphere.txt b/doc/txt/fix_nve_asphere.txt
similarity index 100%
rename from doc/src/fix_nve_asphere.txt
rename to doc/txt/fix_nve_asphere.txt
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/txt/fix_nve_asphere_noforce.txt
similarity index 100%
rename from doc/src/fix_nve_asphere_noforce.txt
rename to doc/txt/fix_nve_asphere_noforce.txt
diff --git a/doc/src/fix_nve_awpmd.txt b/doc/txt/fix_nve_awpmd.txt
similarity index 100%
rename from doc/src/fix_nve_awpmd.txt
rename to doc/txt/fix_nve_awpmd.txt
diff --git a/doc/src/fix_nve_body.txt b/doc/txt/fix_nve_body.txt
similarity index 100%
rename from doc/src/fix_nve_body.txt
rename to doc/txt/fix_nve_body.txt
diff --git a/doc/src/fix_nve_eff.txt b/doc/txt/fix_nve_eff.txt
similarity index 100%
rename from doc/src/fix_nve_eff.txt
rename to doc/txt/fix_nve_eff.txt
diff --git a/doc/src/fix_nve_limit.txt b/doc/txt/fix_nve_limit.txt
similarity index 100%
rename from doc/src/fix_nve_limit.txt
rename to doc/txt/fix_nve_limit.txt
diff --git a/doc/src/fix_nve_line.txt b/doc/txt/fix_nve_line.txt
similarity index 100%
rename from doc/src/fix_nve_line.txt
rename to doc/txt/fix_nve_line.txt
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/txt/fix_nve_manifold_rattle.txt
similarity index 100%
rename from doc/src/fix_nve_manifold_rattle.txt
rename to doc/txt/fix_nve_manifold_rattle.txt
diff --git a/doc/src/fix_nve_noforce.txt b/doc/txt/fix_nve_noforce.txt
similarity index 100%
rename from doc/src/fix_nve_noforce.txt
rename to doc/txt/fix_nve_noforce.txt
diff --git a/doc/src/fix_nve_sphere.txt b/doc/txt/fix_nve_sphere.txt
similarity index 100%
rename from doc/src/fix_nve_sphere.txt
rename to doc/txt/fix_nve_sphere.txt
diff --git a/doc/src/fix_nve_spin.txt b/doc/txt/fix_nve_spin.txt
similarity index 76%
rename from doc/src/fix_nve_spin.txt
rename to doc/txt/fix_nve_spin.txt
index 7b382bb6ad..8e6284639b 100644
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/txt/fix_nve_spin.txt
@@ -15,22 +15,26 @@ fix ID group-ID nve/spin keyword values :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 nve/spin = style name of this fix command :l
 keyword = {lattice} :l
-  {lattice} value = {no} or {yes} :pre
+  {lattice} value = {moving} or {frozen}
+    moving = integrate both spin and atomic degress of freedom
+    frozen = integrate spins on a fixed lattice :pre
 :ule
 
 [Examples:]
 
-fix 3 all nve/spin lattice yes
-fix 1 all nve/spin lattice no :pre
+fix 3 all nve/spin lattice moving
+fix 1 all nve/spin lattice frozen :pre
 
 [Description:]
 
 Perform a symplectic integration for the spin or spin-lattice system.
 
 The {lattice} keyword defines if the spins are integrated on a lattice
-of fixed atoms (lattice = no), or if atoms are moving (lattice = yes).
-
-By default (lattice = yes), a spin-lattice integration is performed.
+of fixed atoms (lattice = frozen), or if atoms are moving
+(lattice = moving).
+The first case corresponds to a spin dynamics calculation, and
+the second to a spin-lattice calculation.
+By default a spin-lattice integration is performed (lattice = moving).
 
 The {nve/spin} fix applies a Suzuki-Trotter decomposition to
 the equations of motion of the spin lattice system, following the scheme:
@@ -63,7 +67,9 @@ instead of "array" is also valid.
 
 "atom_style spin"_atom_style.html, "fix nve"_fix_nve.html
 
-[Default:] none
+[Default:] 
+
+The option default is lattice = moving.
 
 :line
 
diff --git a/doc/src/fix_nve_tri.txt b/doc/txt/fix_nve_tri.txt
similarity index 100%
rename from doc/src/fix_nve_tri.txt
rename to doc/txt/fix_nve_tri.txt
diff --git a/doc/src/fix_nvk.txt b/doc/txt/fix_nvk.txt
similarity index 100%
rename from doc/src/fix_nvk.txt
rename to doc/txt/fix_nvk.txt
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/txt/fix_nvt_asphere.txt
similarity index 100%
rename from doc/src/fix_nvt_asphere.txt
rename to doc/txt/fix_nvt_asphere.txt
diff --git a/doc/src/fix_nvt_body.txt b/doc/txt/fix_nvt_body.txt
similarity index 100%
rename from doc/src/fix_nvt_body.txt
rename to doc/txt/fix_nvt_body.txt
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/txt/fix_nvt_manifold_rattle.txt
similarity index 100%
rename from doc/src/fix_nvt_manifold_rattle.txt
rename to doc/txt/fix_nvt_manifold_rattle.txt
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/txt/fix_nvt_sllod.txt
similarity index 100%
rename from doc/src/fix_nvt_sllod.txt
rename to doc/txt/fix_nvt_sllod.txt
diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/txt/fix_nvt_sllod_eff.txt
similarity index 100%
rename from doc/src/fix_nvt_sllod_eff.txt
rename to doc/txt/fix_nvt_sllod_eff.txt
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/txt/fix_nvt_sphere.txt
similarity index 100%
rename from doc/src/fix_nvt_sphere.txt
rename to doc/txt/fix_nvt_sphere.txt
diff --git a/doc/src/fix_oneway.txt b/doc/txt/fix_oneway.txt
similarity index 100%
rename from doc/src/fix_oneway.txt
rename to doc/txt/fix_oneway.txt
diff --git a/doc/src/fix_orient.txt b/doc/txt/fix_orient.txt
similarity index 100%
rename from doc/src/fix_orient.txt
rename to doc/txt/fix_orient.txt
diff --git a/doc/src/fix_phonon.txt b/doc/txt/fix_phonon.txt
similarity index 100%
rename from doc/src/fix_phonon.txt
rename to doc/txt/fix_phonon.txt
diff --git a/doc/src/fix_pimd.txt b/doc/txt/fix_pimd.txt
similarity index 100%
rename from doc/src/fix_pimd.txt
rename to doc/txt/fix_pimd.txt
diff --git a/doc/src/fix_planeforce.txt b/doc/txt/fix_planeforce.txt
similarity index 100%
rename from doc/src/fix_planeforce.txt
rename to doc/txt/fix_planeforce.txt
diff --git a/doc/src/fix_plumed.txt b/doc/txt/fix_plumed.txt
similarity index 100%
rename from doc/src/fix_plumed.txt
rename to doc/txt/fix_plumed.txt
diff --git a/doc/src/fix_poems.txt b/doc/txt/fix_poems.txt
similarity index 100%
rename from doc/src/fix_poems.txt
rename to doc/txt/fix_poems.txt
diff --git a/doc/src/fix_pour.txt b/doc/txt/fix_pour.txt
similarity index 100%
rename from doc/src/fix_pour.txt
rename to doc/txt/fix_pour.txt
diff --git a/doc/src/fix_press_berendsen.txt b/doc/txt/fix_press_berendsen.txt
similarity index 100%
rename from doc/src/fix_press_berendsen.txt
rename to doc/txt/fix_press_berendsen.txt
diff --git a/doc/src/fix_print.txt b/doc/txt/fix_print.txt
similarity index 100%
rename from doc/src/fix_print.txt
rename to doc/txt/fix_print.txt
diff --git a/doc/src/fix_property_atom.txt b/doc/txt/fix_property_atom.txt
similarity index 100%
rename from doc/src/fix_property_atom.txt
rename to doc/txt/fix_property_atom.txt
diff --git a/doc/src/fix_python_invoke.txt b/doc/txt/fix_python_invoke.txt
similarity index 100%
rename from doc/src/fix_python_invoke.txt
rename to doc/txt/fix_python_invoke.txt
diff --git a/doc/src/fix_python_move.txt b/doc/txt/fix_python_move.txt
similarity index 100%
rename from doc/src/fix_python_move.txt
rename to doc/txt/fix_python_move.txt
diff --git a/doc/src/fix_qbmsst.txt b/doc/txt/fix_qbmsst.txt
similarity index 100%
rename from doc/src/fix_qbmsst.txt
rename to doc/txt/fix_qbmsst.txt
diff --git a/doc/src/fix_qeq.txt b/doc/txt/fix_qeq.txt
similarity index 100%
rename from doc/src/fix_qeq.txt
rename to doc/txt/fix_qeq.txt
diff --git a/doc/src/fix_qeq_comb.txt b/doc/txt/fix_qeq_comb.txt
similarity index 100%
rename from doc/src/fix_qeq_comb.txt
rename to doc/txt/fix_qeq_comb.txt
diff --git a/doc/src/fix_qeq_reax.txt b/doc/txt/fix_qeq_reax.txt
similarity index 100%
rename from doc/src/fix_qeq_reax.txt
rename to doc/txt/fix_qeq_reax.txt
diff --git a/doc/src/fix_qmmm.txt b/doc/txt/fix_qmmm.txt
similarity index 100%
rename from doc/src/fix_qmmm.txt
rename to doc/txt/fix_qmmm.txt
diff --git a/doc/src/fix_qtb.txt b/doc/txt/fix_qtb.txt
similarity index 100%
rename from doc/src/fix_qtb.txt
rename to doc/txt/fix_qtb.txt
diff --git a/doc/src/fix_reaxc_bonds.txt b/doc/txt/fix_reaxc_bonds.txt
similarity index 100%
rename from doc/src/fix_reaxc_bonds.txt
rename to doc/txt/fix_reaxc_bonds.txt
diff --git a/doc/src/fix_reaxc_species.txt b/doc/txt/fix_reaxc_species.txt
similarity index 100%
rename from doc/src/fix_reaxc_species.txt
rename to doc/txt/fix_reaxc_species.txt
diff --git a/doc/src/fix_recenter.txt b/doc/txt/fix_recenter.txt
similarity index 100%
rename from doc/src/fix_recenter.txt
rename to doc/txt/fix_recenter.txt
diff --git a/doc/src/fix_rhok.txt b/doc/txt/fix_rhok.txt
similarity index 100%
rename from doc/src/fix_rhok.txt
rename to doc/txt/fix_rhok.txt
diff --git a/doc/src/fix_rigid.txt b/doc/txt/fix_rigid.txt
similarity index 100%
rename from doc/src/fix_rigid.txt
rename to doc/txt/fix_rigid.txt
diff --git a/doc/src/fix_rigid_meso.txt b/doc/txt/fix_rigid_meso.txt
similarity index 99%
rename from doc/src/fix_rigid_meso.txt
rename to doc/txt/fix_rigid_meso.txt
index 0819fdb2fb..a9c68b2c04 100644
--- a/doc/src/fix_rigid_meso.txt
+++ b/doc/txt/fix_rigid_meso.txt
@@ -44,7 +44,7 @@ fix 1 rods      rigid/meso molecule
 fix 1 spheres   rigid/meso single force 1 off off on
 fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on
 fix 2 spheres   rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off  :pre
-	
+
 [Description:]
 
 Treat one or more sets of mesoscopic SPH/SDPD particles as independent
diff --git a/doc/src/fix_rx.txt b/doc/txt/fix_rx.txt
similarity index 100%
rename from doc/src/fix_rx.txt
rename to doc/txt/fix_rx.txt
diff --git a/doc/src/fix_saed_vtk.txt b/doc/txt/fix_saed_vtk.txt
similarity index 100%
rename from doc/src/fix_saed_vtk.txt
rename to doc/txt/fix_saed_vtk.txt
diff --git a/doc/src/fix_setforce.txt b/doc/txt/fix_setforce.txt
similarity index 97%
rename from doc/src/fix_setforce.txt
rename to doc/txt/fix_setforce.txt
index 63713d87c2..5ee289ec5c 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/txt/fix_setforce.txt
@@ -67,15 +67,15 @@ to it.
 
 :line
 
-Style {spin} suffix sets the components of the magnetic precession 
-vectors instead of the mechanical forces. This also erases all 
-previously computed magnetic precession vectors on the atom, though 
+Style {spin} suffix sets the components of the magnetic precession
+vectors instead of the mechanical forces. This also erases all
+previously computed magnetic precession vectors on the atom, though
 additional magnetic fixes could add new forces.
 
-This command can be used to freeze the magnetic moment of certain 
-atoms in the simulation by zeroing their precession vector. 
+This command can be used to freeze the magnetic moment of certain
+atoms in the simulation by zeroing their precession vector.
 
-All options defined above remain valid, they just apply to the magnetic 
+All options defined above remain valid, they just apply to the magnetic
 precession vectors instead of the forces.
 
 :line
@@ -132,7 +132,7 @@ forces to any value besides zero when performing a minimization.  Use
 the "fix addforce"_fix_addforce.html command if you want to apply a
 non-zero force to atoms during a minimization.
 
-[Restrictions:] 
+[Restrictions:]
 
 The fix {setforce/spin} only makes sense when LAMMPS was built with the
 SPIN package.
diff --git a/doc/src/fix_shake.txt b/doc/txt/fix_shake.txt
similarity index 100%
rename from doc/src/fix_shake.txt
rename to doc/txt/fix_shake.txt
diff --git a/doc/src/fix_shardlow.txt b/doc/txt/fix_shardlow.txt
similarity index 100%
rename from doc/src/fix_shardlow.txt
rename to doc/txt/fix_shardlow.txt
diff --git a/doc/src/fix_smd.txt b/doc/txt/fix_smd.txt
similarity index 100%
rename from doc/src/fix_smd.txt
rename to doc/txt/fix_smd.txt
diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/txt/fix_smd_adjust_dt.txt
similarity index 100%
rename from doc/src/fix_smd_adjust_dt.txt
rename to doc/txt/fix_smd_adjust_dt.txt
diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/txt/fix_smd_integrate_tlsph.txt
similarity index 100%
rename from doc/src/fix_smd_integrate_tlsph.txt
rename to doc/txt/fix_smd_integrate_tlsph.txt
diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/txt/fix_smd_integrate_ulsph.txt
similarity index 100%
rename from doc/src/fix_smd_integrate_ulsph.txt
rename to doc/txt/fix_smd_integrate_ulsph.txt
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/txt/fix_smd_move_triangulated_surface.txt
similarity index 100%
rename from doc/src/fix_smd_move_triangulated_surface.txt
rename to doc/txt/fix_smd_move_triangulated_surface.txt
diff --git a/doc/src/fix_smd_setvel.txt b/doc/txt/fix_smd_setvel.txt
similarity index 100%
rename from doc/src/fix_smd_setvel.txt
rename to doc/txt/fix_smd_setvel.txt
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/txt/fix_smd_wall_surface.txt
similarity index 100%
rename from doc/src/fix_smd_wall_surface.txt
rename to doc/txt/fix_smd_wall_surface.txt
diff --git a/doc/src/fix_spring.txt b/doc/txt/fix_spring.txt
similarity index 100%
rename from doc/src/fix_spring.txt
rename to doc/txt/fix_spring.txt
diff --git a/doc/src/fix_spring_chunk.txt b/doc/txt/fix_spring_chunk.txt
similarity index 100%
rename from doc/src/fix_spring_chunk.txt
rename to doc/txt/fix_spring_chunk.txt
diff --git a/doc/src/fix_spring_rg.txt b/doc/txt/fix_spring_rg.txt
similarity index 100%
rename from doc/src/fix_spring_rg.txt
rename to doc/txt/fix_spring_rg.txt
diff --git a/doc/src/fix_spring_self.txt b/doc/txt/fix_spring_self.txt
similarity index 100%
rename from doc/src/fix_spring_self.txt
rename to doc/txt/fix_spring_self.txt
diff --git a/doc/src/fix_srd.txt b/doc/txt/fix_srd.txt
similarity index 100%
rename from doc/src/fix_srd.txt
rename to doc/txt/fix_srd.txt
diff --git a/doc/src/fix_store_force.txt b/doc/txt/fix_store_force.txt
similarity index 100%
rename from doc/src/fix_store_force.txt
rename to doc/txt/fix_store_force.txt
diff --git a/doc/src/fix_store_state.txt b/doc/txt/fix_store_state.txt
similarity index 100%
rename from doc/src/fix_store_state.txt
rename to doc/txt/fix_store_state.txt
diff --git a/doc/src/fix_temp_berendsen.txt b/doc/txt/fix_temp_berendsen.txt
similarity index 100%
rename from doc/src/fix_temp_berendsen.txt
rename to doc/txt/fix_temp_berendsen.txt
diff --git a/doc/src/fix_temp_csvr.txt b/doc/txt/fix_temp_csvr.txt
similarity index 100%
rename from doc/src/fix_temp_csvr.txt
rename to doc/txt/fix_temp_csvr.txt
diff --git a/doc/src/fix_temp_rescale.txt b/doc/txt/fix_temp_rescale.txt
similarity index 100%
rename from doc/src/fix_temp_rescale.txt
rename to doc/txt/fix_temp_rescale.txt
diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/txt/fix_temp_rescale_eff.txt
similarity index 100%
rename from doc/src/fix_temp_rescale_eff.txt
rename to doc/txt/fix_temp_rescale_eff.txt
diff --git a/doc/src/fix_tfmc.txt b/doc/txt/fix_tfmc.txt
similarity index 100%
rename from doc/src/fix_tfmc.txt
rename to doc/txt/fix_tfmc.txt
diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/txt/fix_thermal_conductivity.txt
similarity index 100%
rename from doc/src/fix_thermal_conductivity.txt
rename to doc/txt/fix_thermal_conductivity.txt
diff --git a/doc/src/fix_ti_spring.txt b/doc/txt/fix_ti_spring.txt
similarity index 100%
rename from doc/src/fix_ti_spring.txt
rename to doc/txt/fix_ti_spring.txt
diff --git a/doc/src/fix_tmd.txt b/doc/txt/fix_tmd.txt
similarity index 100%
rename from doc/src/fix_tmd.txt
rename to doc/txt/fix_tmd.txt
diff --git a/doc/src/fix_ttm.txt b/doc/txt/fix_ttm.txt
similarity index 100%
rename from doc/src/fix_ttm.txt
rename to doc/txt/fix_ttm.txt
diff --git a/doc/src/fix_tune_kspace.txt b/doc/txt/fix_tune_kspace.txt
similarity index 100%
rename from doc/src/fix_tune_kspace.txt
rename to doc/txt/fix_tune_kspace.txt
diff --git a/doc/src/fix_vector.txt b/doc/txt/fix_vector.txt
similarity index 100%
rename from doc/src/fix_vector.txt
rename to doc/txt/fix_vector.txt
diff --git a/doc/src/fix_viscosity.txt b/doc/txt/fix_viscosity.txt
similarity index 100%
rename from doc/src/fix_viscosity.txt
rename to doc/txt/fix_viscosity.txt
diff --git a/doc/src/fix_viscous.txt b/doc/txt/fix_viscous.txt
similarity index 100%
rename from doc/src/fix_viscous.txt
rename to doc/txt/fix_viscous.txt
diff --git a/doc/src/fix_wall.txt b/doc/txt/fix_wall.txt
similarity index 100%
rename from doc/src/fix_wall.txt
rename to doc/txt/fix_wall.txt
diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/txt/fix_wall_body_polygon.txt
similarity index 100%
rename from doc/src/fix_wall_body_polygon.txt
rename to doc/txt/fix_wall_body_polygon.txt
diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/txt/fix_wall_body_polyhedron.txt
similarity index 100%
rename from doc/src/fix_wall_body_polyhedron.txt
rename to doc/txt/fix_wall_body_polyhedron.txt
diff --git a/doc/src/fix_wall_ees.txt b/doc/txt/fix_wall_ees.txt
similarity index 100%
rename from doc/src/fix_wall_ees.txt
rename to doc/txt/fix_wall_ees.txt
diff --git a/doc/src/fix_wall_gran.txt b/doc/txt/fix_wall_gran.txt
similarity index 100%
rename from doc/src/fix_wall_gran.txt
rename to doc/txt/fix_wall_gran.txt
diff --git a/doc/src/fix_wall_gran_region.txt b/doc/txt/fix_wall_gran_region.txt
similarity index 100%
rename from doc/src/fix_wall_gran_region.txt
rename to doc/txt/fix_wall_gran_region.txt
diff --git a/doc/src/fix_wall_piston.txt b/doc/txt/fix_wall_piston.txt
similarity index 100%
rename from doc/src/fix_wall_piston.txt
rename to doc/txt/fix_wall_piston.txt
diff --git a/doc/src/fix_wall_reflect.txt b/doc/txt/fix_wall_reflect.txt
similarity index 100%
rename from doc/src/fix_wall_reflect.txt
rename to doc/txt/fix_wall_reflect.txt
diff --git a/doc/src/fix_wall_region.txt b/doc/txt/fix_wall_region.txt
similarity index 100%
rename from doc/src/fix_wall_region.txt
rename to doc/txt/fix_wall_region.txt
diff --git a/doc/src/fix_wall_srd.txt b/doc/txt/fix_wall_srd.txt
similarity index 100%
rename from doc/src/fix_wall_srd.txt
rename to doc/txt/fix_wall_srd.txt
diff --git a/doc/src/group.txt b/doc/txt/group.txt
similarity index 100%
rename from doc/src/group.txt
rename to doc/txt/group.txt
diff --git a/doc/src/group2ndx.txt b/doc/txt/group2ndx.txt
similarity index 100%
rename from doc/src/group2ndx.txt
rename to doc/txt/group2ndx.txt
diff --git a/doc/src/hyper.txt b/doc/txt/hyper.txt
similarity index 100%
rename from doc/src/hyper.txt
rename to doc/txt/hyper.txt
diff --git a/doc/src/if.txt b/doc/txt/if.txt
similarity index 100%
rename from doc/src/if.txt
rename to doc/txt/if.txt
diff --git a/doc/src/improper_class2.txt b/doc/txt/improper_class2.txt
similarity index 100%
rename from doc/src/improper_class2.txt
rename to doc/txt/improper_class2.txt
diff --git a/doc/src/improper_coeff.txt b/doc/txt/improper_coeff.txt
similarity index 100%
rename from doc/src/improper_coeff.txt
rename to doc/txt/improper_coeff.txt
diff --git a/doc/src/improper_cossq.txt b/doc/txt/improper_cossq.txt
similarity index 100%
rename from doc/src/improper_cossq.txt
rename to doc/txt/improper_cossq.txt
diff --git a/doc/src/improper_cvff.txt b/doc/txt/improper_cvff.txt
similarity index 100%
rename from doc/src/improper_cvff.txt
rename to doc/txt/improper_cvff.txt
diff --git a/doc/src/improper_distance.txt b/doc/txt/improper_distance.txt
similarity index 100%
rename from doc/src/improper_distance.txt
rename to doc/txt/improper_distance.txt
diff --git a/doc/src/improper_distharm.txt b/doc/txt/improper_distharm.txt
similarity index 100%
rename from doc/src/improper_distharm.txt
rename to doc/txt/improper_distharm.txt
diff --git a/doc/src/improper_fourier.txt b/doc/txt/improper_fourier.txt
similarity index 85%
rename from doc/src/improper_fourier.txt
rename to doc/txt/improper_fourier.txt
index 1b569b3894..f4f59ed636 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/txt/improper_fourier.txt
@@ -16,7 +16,7 @@ improper_style fourier :pre
 [Examples:]
 
 improper_style fourier
-improper_coeff 1 100.0 180.0 :pre
+improper_coeff 1 100.0 0.0 1.0 0.5 1 :pre
 
 [Description:]
 
@@ -24,12 +24,12 @@ The {fourier} improper style uses the following potential:
 
 :c,image(Eqs/improper_fourier.jpg)
 
-where K is the force constant and omega is the angle between the IL
-axis and the IJK plane:
+where K is the force constant, C0, C1, C2 are dimensionless coefficients,
+and omega is the angle between the IL axis and the IJK plane:
 
 :c,image(JPG/umbrella.jpg)
 
-If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.
+If all parameter (see below) is not zero, the all the three possible angles will taken in account.
 
 The following coefficients must be defined for each improper type via
 the "improper_coeff"_improper_coeff.html command as in the example
@@ -38,10 +38,10 @@ above, or in the data file or restart files read by the
 commands:
 
 K (energy)
-C0 (real)
-C1 (real)
-C2 (real)
-all  (integer >= 0) :ul
+C0 (unitless)
+C1 (unitless)
+C2 (unitless)
+all  (0 or 1, optional) :ul
 
 :line
 
diff --git a/doc/src/improper_harmonic.txt b/doc/txt/improper_harmonic.txt
similarity index 100%
rename from doc/src/improper_harmonic.txt
rename to doc/txt/improper_harmonic.txt
diff --git a/doc/src/improper_hybrid.txt b/doc/txt/improper_hybrid.txt
similarity index 100%
rename from doc/src/improper_hybrid.txt
rename to doc/txt/improper_hybrid.txt
diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/txt/improper_inversion_harmonic.txt
similarity index 100%
rename from doc/src/improper_inversion_harmonic.txt
rename to doc/txt/improper_inversion_harmonic.txt
diff --git a/doc/src/improper_none.txt b/doc/txt/improper_none.txt
similarity index 100%
rename from doc/src/improper_none.txt
rename to doc/txt/improper_none.txt
diff --git a/doc/src/improper_ring.txt b/doc/txt/improper_ring.txt
similarity index 100%
rename from doc/src/improper_ring.txt
rename to doc/txt/improper_ring.txt
diff --git a/doc/src/improper_sqdistharm.txt b/doc/txt/improper_sqdistharm.txt
similarity index 100%
rename from doc/src/improper_sqdistharm.txt
rename to doc/txt/improper_sqdistharm.txt
diff --git a/doc/src/improper_style.txt b/doc/txt/improper_style.txt
similarity index 100%
rename from doc/src/improper_style.txt
rename to doc/txt/improper_style.txt
diff --git a/doc/src/improper_umbrella.txt b/doc/txt/improper_umbrella.txt
similarity index 100%
rename from doc/src/improper_umbrella.txt
rename to doc/txt/improper_umbrella.txt
diff --git a/doc/src/improper_zero.txt b/doc/txt/improper_zero.txt
similarity index 100%
rename from doc/src/improper_zero.txt
rename to doc/txt/improper_zero.txt
diff --git a/doc/src/include.txt b/doc/txt/include.txt
similarity index 100%
rename from doc/src/include.txt
rename to doc/txt/include.txt
diff --git a/doc/src/info.txt b/doc/txt/info.txt
similarity index 100%
rename from doc/src/info.txt
rename to doc/txt/info.txt
diff --git a/doc/src/jump.txt b/doc/txt/jump.txt
similarity index 100%
rename from doc/src/jump.txt
rename to doc/txt/jump.txt
diff --git a/doc/src/kim_commands.txt b/doc/txt/kim_commands.txt
similarity index 65%
rename from doc/src/kim_commands.txt
rename to doc/txt/kim_commands.txt
index 47beb776a1..e50950eae7 100644
--- a/doc/src/kim_commands.txt
+++ b/doc/txt/kim_commands.txt
@@ -9,21 +9,37 @@
 kim_init command :h3
 kim_interactions command :h3
 kim_query command :h3
+kim_param command :h3
 
 [Syntax:]
 
 kim_init model user_units unitarg
 kim_interactions typeargs
-kim_query variable formatarg query_function queryargs :pre
+kim_query variable formatarg query_function queryargs
+kim_param get param_name index_range variables formatarg
+kim_param set param_name index_range values
+:pre
 
-model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM)
-user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script
-unitarg = {unit_conversion_mode} (optional)
-typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping
-variable = name of a (string style) variable where the result of the query is stored
-formatarg = {split} (optional)
-query_function = name of the OpenKIM web API query function to be used
-queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :ul
+:link(formatarg_options)
+model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) :ulb,l
+user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script :l
+unitarg = {unit_conversion_mode} (optional) :l
+typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping :l
+variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command. :l
+formatarg = {list, split, or explicit} (optional): :l
+{list} = returns a single string with a list of space separated values
+       (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as
+       defined by the {variable} argument. \[default for {kim_query}\]
+{split} = returns the values separately in new variables with names based
+       on the prefix specified in {variable} and a number appended to
+       indicate which element in the list of values is in the variable.
+{explicit} = returns the values separately in one more more variable names
+       provided as arguments that preceed {formatarg}. \[default for {kim_param}\] :pre
+query_function = name of the OpenKIM web API query function to be used :l
+queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :l
+param_name = name of a KIM portable model parameter :l
+index_range = KIM portable model parameter index range (an integer for a single element, or pair of integers separated by a colon for a range of elements) :l
+values = new value(s) to replace the current value(s) of a KIM portable model parameter :l,ule
 
 
 [Examples:]
@@ -33,9 +49,12 @@ kim_interactions Si
 kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
 kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode
 kim_interactions C H O
-Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_039297821658_000 real
+kim_init Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolventsPolymers__SM_039297821658_000 real
 kim_interactions fixed_types
-kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre
+kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]
+kim_param get gamma 1 varGamma
+kim_param set gamma 1 3.0
+:pre
 
 [Description:]
 
@@ -75,6 +94,7 @@ Types of IMs in OpenKIM :h4
 
 There are two types of IMs archived in OpenKIM:
 
+:link(PM_type)
 The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/).
 The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol
 
@@ -106,7 +126,7 @@ The URL for the Model Page is constructed from the
 https://openkim.org/id/extended_KIM_ID
 :pre
 
-For example for the Stillinger-Weber potential
+For example, for the Stillinger--Weber potential
 listed above the Model Page is located at:
 
 "https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005
@@ -196,7 +216,8 @@ print            "Cohesive Energy = $\{EcJ\} eV"
 
 The above script will end with an error in the {kim_init} line if the
 IM is changed to another potential for Al that does not work with {metal}
-units. To address this {kim_init} offers the {unit_conversion_mode}.
+units. To address this {kim_init} offers the {unit_conversion_mode}
+as shown below.
 If unit conversion mode {is} active, then {kim_init} calls the LAMMPS
 "units"_units.html command to set the units to the IM's required or
 preferred units. Conversion factors between the IM's units and the {user_units}
@@ -250,7 +271,7 @@ will work correctly for any IM for Al (KIM PM or SM) selected by the
 {kim_init} command.
 
 Care must be taken to apply unit conversion to dimensional variables read in
-from a file. For example if a configuration of atoms is read in from a
+from a file. For example, if a configuration of atoms is read in from a
 dump file using the "read_dump"_read_dump.html command, the following can
 be done to convert the box and all atomic positions to the correct units:
 
@@ -349,14 +370,34 @@ not appear in the input script.
 Using OpenKIM Web Queries in LAMMPS ({kim_query}) :h5
 
 The {kim_query} command performs a web query to retrieve the predictions
-of the IM set by {kim_init} for material properties archived in
-"OpenKIM"_https://openkim.org.  The {kim_query} command must be preceded
-by a {kim_init} command. The result of the query is stored in a
-"string style variable"_variable.html, the name of which is given as the first
-argument of the {kim_query command}.  (For the case of multiple
-return values, the optional {split} keyword can be used after the
-variable name to separate the results into multiple variables; see
-the "example"_#split_example below.)
+of an IM set by {kim_init} for material properties archived in
+"OpenKIM"_https://openkim.org.
+
+NOTE: The {kim_query} command must be preceded by a {kim_init} command.
+
+The syntax for the {kim_query} command is as follows:
+
+kim_query variable formatarg query_function queryargs
+:pre
+
+The result of the query is stored in one or more
+"string style variables"_variable.html as determined by the
+optional {formatarg} argument "documented above"_#formatarg_options.
+For the "list" setting of {formatarg} (or if {formatarg} is not
+specified), the result is returned as a space-separated list of
+values in {variable}.
+The {formatarg} keyword "split" separates the result values into
+individual variables of the form {prefix_I}, where {prefix} is set to the
+{kim_query} {variable} argument and {I} ranges from 1 to the number of
+returned values. The number and order of the returned values is determined
+by the type of query performed.  (Note that the "explicit" setting of
+{formatarg} is not supported by {kim_query}.)
+
+NOTE: {kim_query} only supports queries that return a single result or
+an array of values. More complex queries that return a JSON structure
+are not currently supported. An attempt to use {kim_query} in such
+cases will generate an error.
+
 The second required argument {query_function} is the name of the
 query function to be called (e.g. {get_lattice_constant_cubic}).
 All following "arguments"_Commands_parse.html are parameters handed over to
@@ -380,7 +421,7 @@ be provided to select the method of choice.  See the
 "query documentation"_https://openkim.org/doc/repository/kim-query
 to see which methods are available for a given {query function}.
 
-{kim_query} Usage Examples and Further Clarifications: :h6
+{kim_query} Usage Examples and Further Clarifications :h5
 
 The data obtained by {kim_query} commands can be used as part of the setup
 or analysis phases of LAMMPS simulations. Some examples are given below.
@@ -406,7 +447,6 @@ Note that in {unit_conversion_mode} the results obtained from a
 For example, in the above script, the lattice command would need to be
 changed to: "lattice fcc $\{a0\}*$\{_u_distance\}".
 
-:link(split_example)
 [Define an equilibrium hcp crystal]
 
 kim_init         EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal
@@ -421,12 +461,11 @@ lattice          custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c
 
 In this case the {kim_query} returns two arguments (since the hexagonal
 close packed (hcp) structure has two independent lattice constants).
-The default behavior of {kim_query} returns the result as a string
-with the values separated by commas. The optional keyword {split}
-separates the result values into individual variables of the form
-{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument
-and {I} ranges from 1 to the number of returned values. The number and order of
-the returned values is determined by the type of query performed.
+The {formatarg} keyword "split" places the two values into
+the variables {latconst_1} and {latconst_2}. (These variables are
+created if they do not already exist.) For convenience the variables
+{a0} and {c0} are created in order to make the remainder of the
+input script more readable.
 
 [Define a crystal at finite temperature accounting for thermal expansion]
 
@@ -477,6 +516,225 @@ In order to give credit to Test developers, the number of times results
 from these programs are queried is tracked. No other information about
 the nature of the query or its source is recorded.
 
+Accessing KIM Model Parameters from LAMMPS ({kim_param}) :h5
+
+All IMs are functional forms containing a set of
+parameters.  The values of these parameters are typically
+selected to best reproduce a training set of quantum mechanical
+calculations or available experimental data.  For example, a
+Lennard-Jones potential intended to model argon might have the values of
+its two parameters, epsilon and sigma, fit to the
+dimer dissociation energy or thermodynamic properties at a critical point
+of the phase diagram.
+
+Normally a user employing an IM should not modify its parameters since,
+as noted above, these are selected to reproduce material properties.
+However, there are cases where accessing and modifying IM parameters
+is desired, such as for assessing uncertainty, fitting an IM,
+or working with an ensemble of IMs. As explained "above"_#IM_types,
+IMs archived in OpenKIM are either Portable Models (PMs) or
+Simulator Models (SMs). KIM PMs are complete independent implementations
+of an IM, whereas KIM SMs are wrappers to an IM implemented within LAMMPS.
+Two different mechanisms are provided for accessing IM parameters in these
+two cases:
+
+For a KIM PM, the {kim_param} command can be used to {get} and {set} the values of the PM's parameters as explained below.
+For a KIM SM, the user should consult the documentation page for the specific IM and follow instructions there for how to modify its parameters (if possible). :ul
+
+The {kim_param get} and {kim_param set} commands provide an interface
+to access and change the parameters of a KIM PM that "publishes" its
+parameters and makes them publicly available (see the
+"KIM API documentation"_https://kim-api.readthedocs.io/en/devel/features.html
+for details).
+
+NOTE: The {kim_param get/set} commands must be preceded by {kim_init}.
+The {kim_param set} command must additionally be preceded by a
+{kim_interactions} command (or alternatively by a {pair_style kim}
+and {pair_coeff} commands).  The {kim_param set} command may be used wherever a {pair_coeff} command may occur.
+
+The syntax for the {kim_param} command is as follows:
+
+kim_param get param_name index_range variable formatarg
+kim_param set param_name index_range values
+:pre
+
+Here, {param_name} is the name of a KIM PM parameter (which is published
+by the PM and available for access). The specific string used to identify
+a parameter is defined by the PM. For example, for the
+"Stillinger--Weber (SW) potential in OpenKIM"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005,
+the parameter names are {A, B, p, q, sigma, gamma, cutoff, lambda, costheta0}.
+
+NOTE: The list of all the parameters that a PM exposes for access/mutation are
+automatically written to the lammps log file when {kim_init} is called.
+
+Each published parameter of a KIM PM takes the form of an array of
+numerical values. The array can contain one element for a single-valued
+parameter, or a set of values. For example, the
+"multispecies SW potential for the Zn-Cd-Hg-S-Se-Te system"_https://openkim.org/id/SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002
+has the same parameter names as the
+"single-species SW potential"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005,
+but each parameter array contains 21 entries that correspond to the parameter
+values used for each pairwise combination of the model's six supported species
+(this model does not have parameters specific to individual ternary
+combinations of its supported species).
+
+The {index_range} argument may either be an integer referring to
+a specific element within the array associated with the parameter
+specified by {param_name}, or a pair of integers separated by a colon
+that refer to a slice of this array.  In both cases, one-based indexing is
+used to refer to the entries of the array.
+
+The result of a {get} operation for a specific {index_range} is stored in
+one or more "LAMMPS string style variables"_variable.html as determined
+by the optional {formatarg} argument "documented above."_#formatarg_options
+If not specified, the default for {formatarg} is "explicit" for the
+{kim_param} command.
+
+For the case where the result is an array with multiple values
+(i.e. {index_range} contains a range), the optional "split" or "explicit"
+{formatarg} keywords can be used to separate the results into multiple
+variables; see the examples below.
+Multiple parameters can be retrieved with a single call to {kim_param get}
+by repeating the argument list following {get}.
+
+For a {set} operation, the {values} argument contains the new value(s)
+for the element(s) of the parameter specified by {index_range}. For the case
+where multiple values are being set, {values} contains a set of values
+separated by spaces. Multiple parameters can be set with a single call to
+{kim_param set} by repeating the argument list following {set}.
+
+{kim_param} Usage Examples and Further Clarifications :h5
+
+Examples of getting and setting KIM PM parameters with further
+clarifications are provided below.
+
+[Getting a scalar parameter]
+
+kim_init         SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+...
+kim_param        get A 1 VARA
+:pre
+
+In this case, the value of the SW {A} parameter is retrieved and placed
+in the LAMMPS variable {VARA}. The variable {VARA} can be used
+in the remainder of the input script in the same manner as any other
+LAMMPS variable.
+
+[Getting multiple scalar parameters with a single call]
+
+kim_init         SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+...
+kim_param        get A 1 VARA B 1 VARB
+:pre
+
+This retrieves the {A} and {B} parameters of the SW potential and stores
+them in the LAMMPS variables {VARA} and {VARB}.
+
+[Getting a range of values from a parameter]
+
+There are several options when getting a range of values from a parameter
+determined by the {formatarg} argument.
+
+kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+...
+kim_param        get lambda 7:9 LAM_TeTe LAM_TeZn LAM_TeSe
+:pre
+
+In this case, {formatarg} is not specified and therefore the default
+"explicit" mode is used. (The behavior would be the same if the word
+{explicit} were added after {LAM_TeSe}.) Elements 7, 8 and 9 of parameter
+lambda retrieved by the {get} operation are placed in the LAMMPS variables
+{LAM_TeTe}, {LAM_TeZn} and {LAM_TeSe}, respectively.
+
+NOTE: In the above example, elements 7--9 of the lambda parameter correspond
+to Te-Te, Te-Zm and Te-Se interactions. This can be determined by visiting
+the "model page for the specified potential"_https://openkim.org/id/SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002
+and looking at its parameter file linked to at the bottom of the page
+(file with .param ending) and consulting the README documentation
+provided with the driver for the PM being used. A link to the driver
+is provided at the top of the model page.
+
+kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+...
+kim_param        get lambda 15:17 LAMS list
+variable         LAM_VALUE index $\{LAMS\}
+label            loop_on_lambda
+...
+... do something with current value of lambda
+...
+next             LAM_VALUE
+jump             SELF loop_on_lambda
+:pre
+
+In this case, the "list" mode of {formatarg} is used.
+The result of the {get} operation is stored in the LAMMPS variable
+{LAMS} as a string containing the three retrieved values separated
+by spaces, e.g "1.0 2.0 3.0". This can be used in LAMMPS with an
+{index} variable to access the values one at a time within a loop
+as shown in the example. At each iteration of the loop {LAM_VALUE}
+contains the current value of lambda.
+
+kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+...
+kim_param        get lambda 15:17 LAM split
+:pre
+
+In this case, the "split" mode of {formatarg} is used.
+The three values retrieved by the {get} operation are stored in
+the three LAMMPS variables {LAM_15}, {LAM_16} and {LAM_17}.
+The provided name "LAM" is used as prefix and the location in
+the lambda array is appended to create the variable names.
+
+[Setting a scalar parameter]
+
+kim_init         SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+...
+kim_interactions Si
+kim_param        set gamma 1 2.6
+:pre
+
+Here, the SW potential's gamma parameter is set to 2.6.  Note that the {get}
+and {set} commands work together, so that a {get} following a {set}
+operation will return the new value that was set. For example:
+
+...
+kim_interactions Si
+kim_param        get gamma 1 ORIG_GAMMA
+kim_param        set gamma 1 2.6
+kim_param        get gamma 1 NEW_GAMMA
+...
+print            "original gamma = $\{ORIG_GAMMA\}, new gamma = $\{NEW_GAMMA\}"
+:pre
+
+Here, {ORIG_GAMMA} will contain the original gamma value for the SW
+potential, while {NEW_GAMMA} will contain the value 2.6.
+
+[Setting multiple scalar parameters with a single call]
+
+kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+...
+kim_interactions Cd Te
+variable        VARG equal 2.6
+variable        VARS equal 2.0951
+kim_param       set gamma 1 $\{VARG\} sigma 3 $\{VARS\}
+:pre
+
+In this case, the first element of the {gamma} parameter and
+third element of the {sigma} parameter are set to 2.6 and 2.0951,
+respectively. This example also shows how LAMMPS variables can
+be used when setting parameters.
+
+[Setting a range of values of a parameter]
+
+kim_init         SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
+...
+kim_interactions Cd Te Zn Se Hg S
+kim_param        set sigma 2:6 2.35214 2.23869 2.04516 2.43269 1.80415
+:pre
+
+In this case, elements 2 through 6 of the parameter {sigma}
+are set to the values 2.35214, 2.23869, 2.04516, 2.43269 and 1.80415 in
+order.
 
 Citation of OpenKIM IMs :h4
 
diff --git a/doc/src/kspace_modify.txt b/doc/txt/kspace_modify.txt
similarity index 100%
rename from doc/src/kspace_modify.txt
rename to doc/txt/kspace_modify.txt
diff --git a/doc/src/label.txt b/doc/txt/label.txt
similarity index 100%
rename from doc/src/label.txt
rename to doc/txt/label.txt
diff --git a/doc/src/lammps.book b/doc/txt/lammps.book
similarity index 99%
rename from doc/src/lammps.book
rename to doc/txt/lammps.book
index 3c856bde19..b2326c7218 100644
--- a/doc/src/lammps.book
+++ b/doc/txt/lammps.book
@@ -217,6 +217,7 @@ temper_npt.html
 thermo.html
 thermo_modify.html
 thermo_style.html
+third_order.html
 timer.html
 timestep.html
 uncompute.html
@@ -457,6 +458,7 @@ compute_group_group.html
 compute_gyration.html
 compute_gyration_chunk.html
 compute_gyration_shape.html
+compute_gyration_shape_chunk.html
 compute_heat_flux.html
 compute_hexorder_atom.html
 compute_improper.html
@@ -611,6 +613,7 @@ pair_lj_smooth.html
 pair_lj_smooth_linear.html
 pair_fep_soft.html
 pair_lj_switch3_coulgauss.html
+pair_local_density.html
 pair_lubricate.html
 pair_lubricateU.html
 pair_mdf.html
diff --git a/doc/src/lammps_commands.txt b/doc/txt/lammps_commands.txt
similarity index 100%
rename from doc/src/lammps_commands.txt
rename to doc/txt/lammps_commands.txt
diff --git a/doc/src/lammps_commands_angle.txt b/doc/txt/lammps_commands_angle.txt
similarity index 100%
rename from doc/src/lammps_commands_angle.txt
rename to doc/txt/lammps_commands_angle.txt
diff --git a/doc/src/lammps_commands_atc.txt b/doc/txt/lammps_commands_atc.txt
similarity index 100%
rename from doc/src/lammps_commands_atc.txt
rename to doc/txt/lammps_commands_atc.txt
diff --git a/doc/src/lammps_commands_bond.txt b/doc/txt/lammps_commands_bond.txt
similarity index 100%
rename from doc/src/lammps_commands_bond.txt
rename to doc/txt/lammps_commands_bond.txt
diff --git a/doc/src/lammps_commands_compute.txt b/doc/txt/lammps_commands_compute.txt
similarity index 100%
rename from doc/src/lammps_commands_compute.txt
rename to doc/txt/lammps_commands_compute.txt
diff --git a/doc/src/lammps_commands_dihedral.txt b/doc/txt/lammps_commands_dihedral.txt
similarity index 100%
rename from doc/src/lammps_commands_dihedral.txt
rename to doc/txt/lammps_commands_dihedral.txt
diff --git a/doc/src/lammps_commands_fix.txt b/doc/txt/lammps_commands_fix.txt
similarity index 100%
rename from doc/src/lammps_commands_fix.txt
rename to doc/txt/lammps_commands_fix.txt
diff --git a/doc/src/lammps_commands_improper.txt b/doc/txt/lammps_commands_improper.txt
similarity index 100%
rename from doc/src/lammps_commands_improper.txt
rename to doc/txt/lammps_commands_improper.txt
diff --git a/doc/src/lammps_commands_kspace.txt b/doc/txt/lammps_commands_kspace.txt
similarity index 100%
rename from doc/src/lammps_commands_kspace.txt
rename to doc/txt/lammps_commands_kspace.txt
diff --git a/doc/src/lammps_commands_pair.txt b/doc/txt/lammps_commands_pair.txt
similarity index 100%
rename from doc/src/lammps_commands_pair.txt
rename to doc/txt/lammps_commands_pair.txt
diff --git a/doc/src/lattice.txt b/doc/txt/lattice.txt
similarity index 100%
rename from doc/src/lattice.txt
rename to doc/txt/lattice.txt
diff --git a/doc/src/log.txt b/doc/txt/log.txt
similarity index 100%
rename from doc/src/log.txt
rename to doc/txt/log.txt
diff --git a/doc/src/mass.txt b/doc/txt/mass.txt
similarity index 100%
rename from doc/src/mass.txt
rename to doc/txt/mass.txt
diff --git a/doc/src/message.txt b/doc/txt/message.txt
similarity index 100%
rename from doc/src/message.txt
rename to doc/txt/message.txt
diff --git a/doc/src/min_modify.txt b/doc/txt/min_modify.txt
similarity index 59%
rename from doc/src/min_modify.txt
rename to doc/txt/min_modify.txt
index d342e8bf01..c23ca67852 100644
--- a/doc/src/min_modify.txt
+++ b/doc/txt/min_modify.txt
@@ -13,11 +13,15 @@ min_modify command :h3
 min_modify keyword values ... :pre
 
 one or more keyword/value pairs may be listed :ulb,l
-keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor}
+keyword = {dmax} or {line} or {norm} or {alpha_damp} or {discrete_factor}
   {dmax} value = max
     max = maximum distance for line search to move (distance units)
-  {line} value = {backtrack} or {quadratic} or {forcezero}
-    backtrack,quadratic,forcezero = style of linesearch to use 
+  {line} value = {backtrack} or {quadratic} or {forcezero} or {spin_cubic} or {spin_none}
+    backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use 
+  {norm} value = {two} or {max}
+    two = Euclidean two-norm (length of 3N vector)
+    inf = max force component across all 3-vectors
+    max = max force norm across all 3-vectors
   {alpha_damp} value = damping
     damping = fictitious Gilbert damping for spin minimization (adim)
   {discrete_factor} value = factor
@@ -69,18 +73,54 @@ difference of two large values (energy before and energy after) and
 that difference may be smaller than machine epsilon even if atoms
 could move in the gradient direction to reduce forces further.
 
+The choice of a norm can be modified for the min styles {cg}, {sd}, 
+{quickmin}, {fire}, {spin}, {spin/cg} and {spin/lbfgs} using 
+the {norm} keyword.
+The default {two} norm computes the 2-norm (Euclidean length) of the
+global force vector:
+
+:c,image(Eqs/norm_two.jpg) 
+
+The {max} norm computes the length of the 3-vector force 
+for each atom  (2-norm), and takes the maximum value of those across 
+all atoms
+
+:c,image(Eqs/norm_max.jpg) 
+
+The {inf} norm takes the maximum component across the forces of
+all atoms in the system: 
+
+:c,image(Eqs/norm_inf.jpg) 
+
+For the min styles {spin}, {spin/cg} and {spin/lbfgs}, the force
+norm is replaced by the spin-torque norm.
+
 Keywords {alpha_damp} and {discrete_factor} only make sense when
-a "min_spin"_min_spin.html command is declared. 
+a "min_spin"_min_spin.html command is declared.
 Keyword {alpha_damp} defines an analog of a magnetic Gilbert
 damping. It defines a relaxation rate toward an equilibrium for
-a given magnetic system. 
+a given magnetic system.
 Keyword {discrete_factor} defines a discretization factor for the
-adaptive timestep used in the {spin} minimization. 
+adaptive timestep used in the {spin} minimization.
 See "min_spin"_min_spin.html for more information about those
 quantities. 
-Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
 
-[Restrictions:] none
+The choice of a line search algorithm for the {spin/cg} and
+{spin/lbfgs} styles can be specified via the {line} keyword.
+The {spin_cubic} and  {spin_none} only make sense when one of those 
+two minimization styles is declared.
+The {spin_cubic} performs the line search based on a cubic interpolation
+of the energy along the search direction. The {spin_none} keyword
+deactivates the line search procedure.
+The {spin_none} is a default value for {line} keyword for both {spin/lbfgs}
+and {spin/cg}. Convergence of {spin/lbfgs} can be more robust if
+{spin_cubic} line search is used.
+
+[Restrictions:] 
+
+For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used
+when styles {spin/cg} and {spin/lbfgs} are employed.
+See "neb/spin"_neb_spin.html for more explanation.
 
 [Related commands:]
 
@@ -88,4 +128,8 @@ Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
 
 [Default:]
 
-The option defaults are dmax = 0.1 and line = quadratic.
+The option defaults are dmax = 0.1, line = quadratic and norm = two.
+
+For the {spin}, {spin/cg} and {spin/lbfgs} styles, the
+option defaults are alpha_damp = 1.0, discrete_factor = 10.0,
+line = spin_none, and norm = euclidean.
diff --git a/doc/txt/min_spin.txt b/doc/txt/min_spin.txt
new file mode 100644
index 0000000000..89766891c8
--- /dev/null
+++ b/doc/txt/min_spin.txt
@@ -0,0 +1,104 @@
+"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+:line
+
+min_style spin command :h3
+min_style spin/cg command :h3
+min_style spin/lbfgs command :h3
+
+[Syntax:]
+
+min_style spin 
+min_style spin/cg 
+min_style spin/lbfgs :pre
+
+[Examples:]
+
+min_style  spin/lbfgs
+min_modify line spin_cubic discrete_factor 10.0 :pre
+
+[Description:]
+
+Apply a minimization algorithm to use when a "minimize"_minimize.html
+command is performed.
+
+Style {spin} defines a damped spin dynamics with an adaptive
+timestep, according to:
+
+:c,image(Eqs/min_spin_damping.jpg)
+
+with lambda a damping coefficient (similar to a Gilbert
+damping).
+Lambda can be defined by setting the {alpha_damp} keyword with the
+"min_modify"_min_modify.html command.
+
+The minimization procedure solves this equation using an
+adaptive timestep. The value of this timestep is defined
+by the largest precession frequency that has to be solved in the
+system:
+
+:c,image(Eqs/min_spin_timestep.jpg)
+
+with {|omega|_{max}} the norm of the largest precession frequency
+in the system (across all processes, and across all replicas if a
+spin/neb calculation is performed).
+
+Kappa defines a discretization factor {discrete_factor} for the
+definition of this timestep.
+{discrete_factor} can be defined with the "min_modify"_min_modify.html
+command.
+
+Style {spin/cg} defines an orthogonal spin optimization
+(OSO) combined to a conjugate gradient (CG) algorithm. 
+The "min_modify"_min_modify.html command can be used to
+couple the {spin/cg} to a line search procedure, and to modify the 
+discretization factor {discrete_factor}.
+By default, style {spin/cg} does not employ the line search procedure 
+and uses the adaptive time-step technique in the same way as style {spin}.
+
+Style {spin/lbfgs} defines an orthogonal spin optimization
+(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno 
+(L-BFGS) algorithm.
+By default, style {spin/lbfgs} does not employ line search procedure.
+If the line search procedure is not used then the discrete factor defines
+the maximum root mean squared rotation angle of spins by equation {pi/(5*Kappa)}.
+The default value for Kappa is 10.
+The {spin_cubic} line search can improve the convergence of the 
+{spin/lbfgs} algorithm.
+
+The "min_modify"_min_modify.html command can be used to
+activate the line search procedure, and to modify the
+discretization factor {discrete_factor}. 
+
+For more information about styles {spin/cg} and {spin/lbfgs}, 
+see their implementation reported in "(Ivanov)"_#Ivanov1.
+
+NOTE: All the {spin} styles replace the force tolerance by a torque
+tolerance. See "minimize"_minimize.html for more explanation. 
+
+NOTE: The {spin/cg} and {spin/lbfgs} styles can be used
+for magnetic NEB calculations only if the line search procedure
+is deactivated. See "neb/spin"_neb_spin.html for more explanation. 
+
+[Restrictions:] 
+
+This minimization procedure is only applied to spin degrees of
+freedom for a frozen lattice configuration.
+
+[Related commands:]
+
+"min_style"_min_style.html, "minimize"_minimize.html,
+"min_modify"_min_modify.html
+
+[Default:]
+
+The option defaults are {alpha_damp} = 1.0, {discrete_factor} =
+10.0, {line} = spin_none and {norm} = euclidean.
+
+:line
+
+:link(Ivanov1)
+[(Ivanov)] Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019).
diff --git a/doc/src/min_style.txt b/doc/txt/min_style.txt
similarity index 85%
rename from doc/src/min_style.txt
rename to doc/txt/min_style.txt
index e27682cf97..8816d62ffa 100644
--- a/doc/src/min_style.txt
+++ b/doc/txt/min_style.txt
@@ -11,7 +11,7 @@ min_style command :h3
 
 min_style style :pre
 
-style = {cg} or {cg/kk} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
+style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} or {spin/cg} or {spin/lbfgs} :ul
 
 [Examples:]
 
@@ -62,22 +62,36 @@ the velocity non-parallel to the current force vector.  The velocity
 of each atom is initialized to 0.0 by this style, at the beginning of
 a minimization.
 
-Style {spin} is a damped spin dynamics with an adaptive 
+Style {spin} is a damped spin dynamics with an adaptive
 timestep.
-See the "min/spin"_min_spin.html doc page for more information.
+
+Style {spin/cg} uses an orthogonal spin optimization (OSO)
+combined to a conjugate gradient (CG) approach to minimize spin
+configurations. 
+
+Style {spin/lbfgs} uses an orthogonal spin optimization (OSO)
+combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
+(LBFGS) approach to minimize spin configurations. 
+
+See the "min/spin"_min_spin.html doc page for more information
+about the {spin}, {spin/cg} and {spin/lbfgs} styles.
 
 Either the {quickmin} and {fire} styles are useful in the context of
 nudged elastic band (NEB) calculations via the "neb"_neb.html command.
 
+Either the {spin}, {spin/cg} and {spin/lbfgs} styles are useful 
+in the context of magnetic geodesic nudged elastic band (GNEB) calculations 
+via the "neb/spin"_neb_spin.html command.
+
 NOTE: The damped dynamic minimizers use whatever timestep you have
 defined via the "timestep"_timestep.html command.  Often they will
 converge more quickly if you use a timestep about 10x larger than you
 would normally use for dynamics simulations.
 
-NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet 
-support the use of the "fix box/relax"_fix_box_relax.html command or 
-minimizations involving the electron radius in "eFF"_pair_eff.html 
-models. 
+NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet
+support the use of the "fix box/relax"_fix_box_relax.html command or
+minimizations involving the electron radius in "eFF"_pair_eff.html
+models.
 
 :line
 
diff --git a/doc/src/minimize.txt b/doc/txt/minimize.txt
similarity index 97%
rename from doc/src/minimize.txt
rename to doc/txt/minimize.txt
index 42315705e5..da203c7d2d 100644
--- a/doc/src/minimize.txt
+++ b/doc/txt/minimize.txt
@@ -104,12 +104,13 @@ the line search fails because the step distance backtracks to 0.0
 the number of outer iterations or timesteps exceeds {maxiter}
 the number of total force evaluations exceeds {maxeval} :ul
 
-NOTE: the "minimization style"_min_style.html {spin} replaces
+NOTE: the "minimization style"_min_style.html {spin},
+{spin/cg}, and {spin/lbfgs} replace
 the force tolerance {ftol} by a torque tolerance.
-The minimization procedure stops if the 2-norm (length) of the 
-global torque vector (defined as the cross product between the 
-spins and their precession vectors omega) is less than {ftol}, 
-or if any of the other criteria are met.
+The minimization procedure stops if the 2-norm (length) of the torque vector on atom
+(defined as the cross product between the
+atomic spin and its precession vectors omega) is less than {ftol},
+or if any of the other criteria are met. Torque have the same units as the energy.
 
 NOTE: You can also use the "fix halt"_fix_halt.html command to specify
 a general criterion for exiting a minimization, that is a calculation
diff --git a/doc/src/molecule.txt b/doc/txt/molecule.txt
similarity index 100%
rename from doc/src/molecule.txt
rename to doc/txt/molecule.txt
diff --git a/doc/src/neb.txt b/doc/txt/neb.txt
similarity index 100%
rename from doc/src/neb.txt
rename to doc/txt/neb.txt
diff --git a/doc/src/neb_spin.txt b/doc/txt/neb_spin.txt
similarity index 89%
rename from doc/src/neb_spin.txt
rename to doc/txt/neb_spin.txt
index 7dbd924cd2..217606289f 100644
--- a/doc/src/neb_spin.txt
+++ b/doc/txt/neb_spin.txt
@@ -45,7 +45,7 @@ and last are the end points of the transition path.
 GNEB is a method for finding both the spin configurations and height
 of the energy barrier associated with a transition state, e.g.
 spins to perform a collective rotation from one energy basin to
-another. 
+another.
 The implementation in LAMMPS follows the discussion in the
 following paper: "(BessarabA)"_#BessarabA.
 
@@ -59,35 +59,35 @@ performance speed-up you would see with one or more physical
 processors per replica.  See the "Howto replica"_Howto_replica.html
 doc page for further discussion.
 
-NOTE: As explained below, a GNEB calculation performs a damped dynamics
-minimization across all the replicas.  The "spin"_min_spin.html
-style minimizer has to be defined in your input script. 
+NOTE: As explained below, a GNEB calculation performs a
+minimization across all the replicas. One of the "spin"_min_spin.html
+style minimizers has to be defined in your input script. 
 
 When a GNEB calculation is performed, it is assumed that each replica
 is running the same system, though LAMMPS does not check for this.
-I.e. the simulation domain, the number of magnetic atoms, the 
-interaction potentials, and the starting configuration when the neb 
+I.e. the simulation domain, the number of magnetic atoms, the
+interaction potentials, and the starting configuration when the neb
 command is issued should be the same for every replica.
 
 In a GNEB calculation each replica is connected to other replicas by
 inter-replica nudging forces.  These forces are imposed by the "fix
-neb/spin"_fix_neb_spin.html command, which must be used in conjunction 
-with the neb command.  
+neb/spin"_fix_neb_spin.html command, which must be used in conjunction
+with the neb command.
 The group used to define the fix neb/spin command defines the
-GNEB magnetic atoms which are the only ones that inter-replica springs 
-are applied to.  
+GNEB magnetic atoms which are the only ones that inter-replica springs
+are applied to.
 If the group does not include all magnetic atoms, then non-GNEB
-magnetic atoms have no inter-replica springs and the torques they feel 
-and their precession motion is computed in the usual way due only 
-to other magnetic atoms within their replica.  
-Conceptually, the non-GNEB atoms provide a background force field for 
-the GNEB atoms.  
-Their magnetic spins can be allowed to evolve during the GNEB 
+magnetic atoms have no inter-replica springs and the torques they feel
+and their precession motion is computed in the usual way due only
+to other magnetic atoms within their replica.
+Conceptually, the non-GNEB atoms provide a background force field for
+the GNEB atoms.
+Their magnetic spins can be allowed to evolve during the GNEB
 minimization procedure.
 
 The initial spin configuration for each of the replicas can be
 specified in different manners via the {file-style} setting, as
-discussed below.  Only atomic spins whose initial coordinates should 
+discussed below.  Only atomic spins whose initial coordinates should
 differ from the current configuration need to be specified.
 
 Conceptually, the initial and final configurations for the first
@@ -106,21 +106,21 @@ closer to the MEP and read them in.
 :line
 
 For a {file-style} setting of {final}, a filename is specified which
-contains atomic and spin coordinates for zero or more atoms, in the 
-format described below.  
-For each atom that appears in the file, the new coordinates are 
-assigned to that atom in the final replica.  Each intermediate replica 
-also assigns a new spin to that atom in an interpolated manner.  
-This is done by using the current direction of the spin at the starting 
-point and the read-in direction as the final point.  
-The "angular distance" between them is calculated, and the new direction 
+contains atomic and spin coordinates for zero or more atoms, in the
+format described below.
+For each atom that appears in the file, the new coordinates are
+assigned to that atom in the final replica.  Each intermediate replica
+also assigns a new spin to that atom in an interpolated manner.
+This is done by using the current direction of the spin at the starting
+point and the read-in direction as the final point.
+The "angular distance" between them is calculated, and the new direction
 is assigned to be a fraction of the angular distance.
 
-NOTE: The "angular distance" between the starting and final point is 
-evaluated in the geodesic sense, as described in 
-"(BessarabA)"_#BessarabA. 
+NOTE: The "angular distance" between the starting and final point is
+evaluated in the geodesic sense, as described in
+"(BessarabA)"_#BessarabA.
 
-NOTE: The angular interpolation between the starting and final point 
+NOTE: The angular interpolation between the starting and final point
 is achieved using Rodrigues formula:
 
 :c,image(Eqs/neb_spin_rodrigues_formula.jpg)
@@ -130,7 +130,7 @@ omega_i^nu is a rotation angle defined as:
 
 :c,image(Eqs/neb_spin_angle.jpg)
 
-with nu the image number, Q the total number of images, and 
+with nu the image number, Q the total number of images, and
 omega_i the total rotation between the initial and final spins.
 k_i defines a rotation axis such as:
 
@@ -139,16 +139,16 @@ k_i defines a rotation axis such as:
 if the initial and final spins are not aligned.
 If the initial and final spins are aligned, then their cross
 product is null, and the expression above does not apply.
-If they point toward the same direction, the intermediate images 
+If they point toward the same direction, the intermediate images
 conserve the same orientation.
 If the initial and final spins are aligned, but point toward
 opposite directions, an arbitrary rotation vector belonging to
-the plane perpendicular to initial and final spins is chosen. 
+the plane perpendicular to initial and final spins is chosen.
 In this case, a warning message is displayed.
 
 For a {file-style} setting of {each}, a filename is specified which is
-assumed to be unique to each replica. 
-See the "neb"_neb.html documentation page for more information about this 
+assumed to be unique to each replica.
+See the "neb"_neb.html documentation page for more information about this
 option.
 
 For a {file-style} setting of {none}, no filename is specified.  Each
@@ -170,9 +170,10 @@ command is issued.
 :line
 
 A NEB calculation proceeds in two stages, each of which is a
-minimization procedure, performed via damped dynamics.  To enable
-this, you must first define a damped spin dynamics
-"min_style"_min_style.html, using the {spin} style (see
+minimization procedure.  To enable
+this, you must first define a
+"min_style"_min_style.html, using either the {spin},
+{spin/cg}, or {spin/lbfgs} style (see
 "min_spin"_min_spin.html for more information).  
 The other styles cannot be used, since they relax the lattice
 degrees of freedom instead of the spins.
@@ -195,9 +196,9 @@ damped dynamics is like a single timestep in a dynamics
 replica and its normalized distance along the reaction path (reaction
 coordinate RD) will be printed to the screen and log file every
 {Nevery} timesteps.  The RD is 0 and 1 for the first and last replica.
-For intermediate replicas, it is the cumulative angular distance 
-(normalized by the total cumulative angular distance) between adjacent 
-replicas, where "distance" is defined as the length of the 3N-vector of 
+For intermediate replicas, it is the cumulative angular distance
+(normalized by the total cumulative angular distance) between adjacent
+replicas, where "distance" is defined as the length of the 3N-vector of
 the geodesic distances in spin coordinates, with N the number of
 GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA).
 These outputs allow you to monitor NEB's progress in
@@ -207,11 +208,11 @@ of {Nevery}.
 In the first stage of GNEB, the set of replicas should converge toward
 a minimum energy path (MEP) of conformational states that transition
 over a barrier.  The MEP for a transition is defined as a sequence of
-3N-dimensional spin states, each of which has a potential energy 
-gradient parallel to the MEP itself.  
-The configuration of highest energy along a MEP corresponds to a saddle 
-point.  The replica states will also be roughly equally spaced along 
-the MEP due to the inter-replica nudging force added by the 
+3N-dimensional spin states, each of which has a potential energy
+gradient parallel to the MEP itself.
+The configuration of highest energy along a MEP corresponds to a saddle
+point.  The replica states will also be roughly equally spaced along
+the MEP due to the inter-replica nudging force added by the
 "fix neb"_fix_neb.html command.
 
 In the second stage of GNEB, the replica with the highest energy is
@@ -234,12 +235,12 @@ An atom map must be defined which it is not by default for "atom_style
 atomic"_atom_style.html problems.  The "atom_modify
 map"_atom_modify.html command can be used to do this.
 
-An initial value can be defined for the timestep. Although, the {spin} 
-minimization algorithm is an adaptive timestep methodology, so that 
-this timestep is likely to evolve during the calculation.  
+An initial value can be defined for the timestep. Although, the {spin}
+minimization algorithm is an adaptive timestep methodology, so that
+this timestep is likely to evolve during the calculation.
 
 The minimizers in LAMMPS operate on all spins in your system, even
-non-GNEB atoms, as defined above.  
+non-GNEB atoms, as defined above.
 
 :line
 
@@ -257,7 +258,7 @@ ID2 g2 x2 y2 z2 sx2 sy2 sz2
 ...
 IDN gN yN zN sxN syN szN :pre
 
-The fields are the atom ID, the norm of the associated magnetic spin, 
+The fields are the atom ID, the norm of the associated magnetic spin,
 followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates.
 The lines can be listed in any order.  Additional trailing information on
 the line is OK, such as a comment.
@@ -290,22 +291,22 @@ reaction coordinate and potential energy of each replica.
 
 The "maximum torque per replica" is the two-norm of the
 3N-length vector given by the cross product of a spin by its
-precession vector omega, in each replica, maximized across replicas, 
+precession vector omega, in each replica, maximized across replicas,
 which is what the {ttol} setting is checking against.  In this case, N is
 all the atoms in each replica.  The "maximum torque per atom" is the
 maximum torque component of any atom in any replica.  The potential
-gradients are the two-norm of the 3N-length magnetic precession vector 
-solely due to the interaction potential i.e. without adding in 
-inter-replica forces, and projected along the path tangent (as detailed 
+gradients are the two-norm of the 3N-length magnetic precession vector
+solely due to the interaction potential i.e. without adding in
+inter-replica forces, and projected along the path tangent (as detailed
 in Appendix D of "(BessarabA)"_#BessarabA).
 
 The "reaction coordinate" (RD) for each replica is the two-norm of the
 3N-length vector of geodesic distances between its spins and the preceding
-replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to 
-the RD of the preceding replica. The RD of the first replica RD1 = 0.0; 
-the RD of the final replica RDN = RDT, the total reaction coordinate.  
-The normalized RDs are divided by RDT, so that they form a monotonically 
-increasing sequence from zero to one. When computing RD, N only includes 
+replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to
+the RD of the preceding replica. The RD of the first replica RD1 = 0.0;
+the RD of the final replica RDN = RDT, the total reaction coordinate.
+The normalized RDs are divided by RDT, so that they form a monotonically
+increasing sequence from zero to one. When computing RD, N only includes
 the spins being operated on by the fix neb/spin command.
 
 The forward (reverse) energy barrier is the potential energy of the
@@ -313,17 +314,17 @@ highest replica minus the energy of the first (last) replica.
 
 Supplementary information for all replicas can be printed out to the
 screen and master log.lammps file by adding the verbose keyword. This
-information include the following. 
-The "GradVidottan" are the projections of the potential gradient for 
-the replica i on its tangent vector (as detailed in Appendix D of 
+information include the following.
+The "GradVidottan" are the projections of the potential gradient for
+the replica i on its tangent vector (as detailed in Appendix D of
 "(BessarabA)"_#BessarabA).
-The "DNi" are the non normalized geodesic distances (see equation (13) 
-of "(BessarabA)"_#BessarabA), between a replica i and the next replica 
+The "DNi" are the non normalized geodesic distances (see equation (13)
+of "(BessarabA)"_#BessarabA), between a replica i and the next replica
 i+1. For the last replica, this distance is not defined and a "NAN"
-value is the corresponding output. 
+value is the corresponding output.
 
 When a NEB calculation does not converge properly, the supplementary
-information can help understanding what is going wrong. 
+information can help understanding what is going wrong.
 
 When running on multiple partitions, LAMMPS produces additional log
 files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
@@ -346,9 +347,9 @@ restart the calculation from an intermediate point with altered
 parameters.
 
 A c file script in provided in the tool/spin/interpolate_gneb
-directory, that interpolates the MEP given the information provided 
+directory, that interpolates the MEP given the information provided
 by the verbose output option (as detailed in Appendix D of
-"(BessarabA)"_#BessarabA). 
+"(BessarabA)"_#BessarabA).
 
 :line
 
@@ -358,6 +359,9 @@ This command can only be used if LAMMPS was built with the SPIN
 package.  See the "Build package"_Build_package.html doc
 page for more info.
 
+For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used
+when styles {spin/cg} and {spin/lbfgs} are employed.
+
 :line
 
 [Related commands:]
diff --git a/doc/src/neigh_modify.txt b/doc/txt/neigh_modify.txt
similarity index 100%
rename from doc/src/neigh_modify.txt
rename to doc/txt/neigh_modify.txt
diff --git a/doc/src/neighbor.txt b/doc/txt/neighbor.txt
similarity index 100%
rename from doc/src/neighbor.txt
rename to doc/txt/neighbor.txt
diff --git a/doc/src/newton.txt b/doc/txt/newton.txt
similarity index 100%
rename from doc/src/newton.txt
rename to doc/txt/newton.txt
diff --git a/doc/src/next.txt b/doc/txt/next.txt
similarity index 100%
rename from doc/src/next.txt
rename to doc/txt/next.txt
diff --git a/doc/src/pair_adp.txt b/doc/txt/pair_adp.txt
similarity index 100%
rename from doc/src/pair_adp.txt
rename to doc/txt/pair_adp.txt
diff --git a/doc/src/pair_agni.txt b/doc/txt/pair_agni.txt
similarity index 93%
rename from doc/src/pair_agni.txt
rename to doc/txt/pair_agni.txt
index 8cb1bf34e4..aae9c161ca 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/txt/pair_agni.txt
@@ -97,8 +97,11 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]
 
 Currently, only elemental systems are implemented. Also, the method
-only provides access to the forces and not energies or
-stresses. However, one can access the energy via thermodynamic
+only provides access to the forces and not energies or stresses.
+The lack of potential energy data makes this pair style incompatible with
+several of the "minimizer algorthms"_min_style.html like {cg} or {sd}.
+It should work with damped dynamics based minimizers like {fire} or
+{quickmin}.  However, one can access the energy via thermodynamic
 integration of the forces as discussed in
 "(Botu3)"_#Botu2016construct.  This pair style is part of the
 USER-MISC package. It is only enabled if LAMMPS was built with that
diff --git a/doc/src/pair_airebo.txt b/doc/txt/pair_airebo.txt
similarity index 100%
rename from doc/src/pair_airebo.txt
rename to doc/txt/pair_airebo.txt
diff --git a/doc/src/pair_atm.txt b/doc/txt/pair_atm.txt
similarity index 100%
rename from doc/src/pair_atm.txt
rename to doc/txt/pair_atm.txt
diff --git a/doc/src/pair_awpmd.txt b/doc/txt/pair_awpmd.txt
similarity index 100%
rename from doc/src/pair_awpmd.txt
rename to doc/txt/pair_awpmd.txt
diff --git a/doc/src/pair_beck.txt b/doc/txt/pair_beck.txt
similarity index 100%
rename from doc/src/pair_beck.txt
rename to doc/txt/pair_beck.txt
diff --git a/doc/src/pair_body_nparticle.txt b/doc/txt/pair_body_nparticle.txt
similarity index 100%
rename from doc/src/pair_body_nparticle.txt
rename to doc/txt/pair_body_nparticle.txt
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/txt/pair_body_rounded_polygon.txt
similarity index 100%
rename from doc/src/pair_body_rounded_polygon.txt
rename to doc/txt/pair_body_rounded_polygon.txt
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/txt/pair_body_rounded_polyhedron.txt
similarity index 100%
rename from doc/src/pair_body_rounded_polyhedron.txt
rename to doc/txt/pair_body_rounded_polyhedron.txt
diff --git a/doc/src/pair_bop.txt b/doc/txt/pair_bop.txt
similarity index 100%
rename from doc/src/pair_bop.txt
rename to doc/txt/pair_bop.txt
diff --git a/doc/src/pair_born.txt b/doc/txt/pair_born.txt
similarity index 100%
rename from doc/src/pair_born.txt
rename to doc/txt/pair_born.txt
diff --git a/doc/src/pair_brownian.txt b/doc/txt/pair_brownian.txt
similarity index 100%
rename from doc/src/pair_brownian.txt
rename to doc/txt/pair_brownian.txt
diff --git a/doc/src/pair_buck.txt b/doc/txt/pair_buck.txt
similarity index 100%
rename from doc/src/pair_buck.txt
rename to doc/txt/pair_buck.txt
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/txt/pair_buck6d_coul_gauss.txt
similarity index 100%
rename from doc/src/pair_buck6d_coul_gauss.txt
rename to doc/txt/pair_buck6d_coul_gauss.txt
diff --git a/doc/src/pair_buck_long.txt b/doc/txt/pair_buck_long.txt
similarity index 100%
rename from doc/src/pair_buck_long.txt
rename to doc/txt/pair_buck_long.txt
diff --git a/doc/src/pair_charmm.txt b/doc/txt/pair_charmm.txt
similarity index 100%
rename from doc/src/pair_charmm.txt
rename to doc/txt/pair_charmm.txt
diff --git a/doc/src/pair_class2.txt b/doc/txt/pair_class2.txt
similarity index 100%
rename from doc/src/pair_class2.txt
rename to doc/txt/pair_class2.txt
diff --git a/doc/src/pair_coeff.txt b/doc/txt/pair_coeff.txt
similarity index 100%
rename from doc/src/pair_coeff.txt
rename to doc/txt/pair_coeff.txt
diff --git a/doc/src/pair_colloid.txt b/doc/txt/pair_colloid.txt
similarity index 100%
rename from doc/src/pair_colloid.txt
rename to doc/txt/pair_colloid.txt
diff --git a/doc/src/pair_comb.txt b/doc/txt/pair_comb.txt
similarity index 100%
rename from doc/src/pair_comb.txt
rename to doc/txt/pair_comb.txt
diff --git a/doc/src/pair_cosine_squared.txt b/doc/txt/pair_cosine_squared.txt
similarity index 100%
rename from doc/src/pair_cosine_squared.txt
rename to doc/txt/pair_cosine_squared.txt
diff --git a/doc/src/pair_coul.txt b/doc/txt/pair_coul.txt
similarity index 100%
rename from doc/src/pair_coul.txt
rename to doc/txt/pair_coul.txt
diff --git a/doc/src/pair_coul_diel.txt b/doc/txt/pair_coul_diel.txt
similarity index 100%
rename from doc/src/pair_coul_diel.txt
rename to doc/txt/pair_coul_diel.txt
diff --git a/doc/src/pair_coul_shield.txt b/doc/txt/pair_coul_shield.txt
similarity index 100%
rename from doc/src/pair_coul_shield.txt
rename to doc/txt/pair_coul_shield.txt
diff --git a/doc/src/pair_cs.txt b/doc/txt/pair_cs.txt
similarity index 100%
rename from doc/src/pair_cs.txt
rename to doc/txt/pair_cs.txt
diff --git a/doc/src/pair_dipole.txt b/doc/txt/pair_dipole.txt
similarity index 100%
rename from doc/src/pair_dipole.txt
rename to doc/txt/pair_dipole.txt
diff --git a/doc/src/pair_dpd.txt b/doc/txt/pair_dpd.txt
similarity index 100%
rename from doc/src/pair_dpd.txt
rename to doc/txt/pair_dpd.txt
diff --git a/doc/src/pair_dpd_fdt.txt b/doc/txt/pair_dpd_fdt.txt
similarity index 100%
rename from doc/src/pair_dpd_fdt.txt
rename to doc/txt/pair_dpd_fdt.txt
diff --git a/doc/src/pair_drip.txt b/doc/txt/pair_drip.txt
similarity index 100%
rename from doc/src/pair_drip.txt
rename to doc/txt/pair_drip.txt
diff --git a/doc/src/pair_dsmc.txt b/doc/txt/pair_dsmc.txt
similarity index 100%
rename from doc/src/pair_dsmc.txt
rename to doc/txt/pair_dsmc.txt
diff --git a/doc/src/pair_e3b.txt b/doc/txt/pair_e3b.txt
similarity index 97%
rename from doc/src/pair_e3b.txt
rename to doc/txt/pair_e3b.txt
index 6d1f992ca1..832b4719c3 100644
--- a/doc/src/pair_e3b.txt
+++ b/doc/txt/pair_e3b.txt
@@ -20,8 +20,8 @@ If the {preset} keyword is given, no others are needed.
 Otherwise, all are mandatory except for {neigh}.
 The {neigh} keyword is always optional. :l
   {preset} arg = {2011} or {2015} = which set of predefined parameters to use
-  	   2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011
-  	   2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015
+           2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011
+           2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015
   {Ea} arg = three-body energy for type A hydrogen bonding interactions (energy units)
   {Eb} arg = three-body energy for type B hydrogen bonding interactions (energy units)
   {Ec} arg = three-body energy for type C hydrogen bonding interactions (energy units)
diff --git a/doc/src/pair_eam.txt b/doc/txt/pair_eam.txt
similarity index 100%
rename from doc/src/pair_eam.txt
rename to doc/txt/pair_eam.txt
diff --git a/doc/src/pair_edip.txt b/doc/txt/pair_edip.txt
similarity index 100%
rename from doc/src/pair_edip.txt
rename to doc/txt/pair_edip.txt
diff --git a/doc/src/pair_eff.txt b/doc/txt/pair_eff.txt
similarity index 100%
rename from doc/src/pair_eff.txt
rename to doc/txt/pair_eff.txt
diff --git a/doc/src/pair_eim.txt b/doc/txt/pair_eim.txt
similarity index 100%
rename from doc/src/pair_eim.txt
rename to doc/txt/pair_eim.txt
diff --git a/doc/src/pair_exp6_rx.txt b/doc/txt/pair_exp6_rx.txt
similarity index 100%
rename from doc/src/pair_exp6_rx.txt
rename to doc/txt/pair_exp6_rx.txt
diff --git a/doc/src/pair_extep.txt b/doc/txt/pair_extep.txt
similarity index 100%
rename from doc/src/pair_extep.txt
rename to doc/txt/pair_extep.txt
diff --git a/doc/src/pair_fep_soft.txt b/doc/txt/pair_fep_soft.txt
similarity index 100%
rename from doc/src/pair_fep_soft.txt
rename to doc/txt/pair_fep_soft.txt
diff --git a/doc/src/pair_gauss.txt b/doc/txt/pair_gauss.txt
similarity index 100%
rename from doc/src/pair_gauss.txt
rename to doc/txt/pair_gauss.txt
diff --git a/doc/src/pair_gayberne.txt b/doc/txt/pair_gayberne.txt
similarity index 100%
rename from doc/src/pair_gayberne.txt
rename to doc/txt/pair_gayberne.txt
diff --git a/doc/src/pair_gran.txt b/doc/txt/pair_gran.txt
similarity index 100%
rename from doc/src/pair_gran.txt
rename to doc/txt/pair_gran.txt
diff --git a/doc/src/pair_granular.txt b/doc/txt/pair_granular.txt
similarity index 97%
rename from doc/src/pair_granular.txt
rename to doc/txt/pair_granular.txt
index f16cd9fe0b..2091163e91 100644
--- a/doc/src/pair_granular.txt
+++ b/doc/txt/pair_granular.txt
@@ -100,7 +100,7 @@ on particle {i} due to contact with particle {j} is given by:
 \mathbf\{F\}_\{ne, Hooke\} = k_N \delta_\{ij\} \mathbf\{n\}
 \end\{equation\}
 
-Where \(\delta = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle
+Where \(\delta_\{ij\} = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle
 overlap, \(R_i, R_j\) are the particle radii, \(\mathbf\{r\}_\{ij\} =
 \mathbf\{r\}_i - \mathbf\{r\}_j\) is the vector separating the two
 particle centers (note the i-j ordering so that \(F_\{ne\}\) is
@@ -177,7 +177,7 @@ following general form:
 \end\{equation\}
 
 Here, \(\mathbf\{v\}_\{n,rel\} = (\mathbf\{v\}_j - \mathbf\{v\}_i)
-\cdot \mathbf\{n\}\) is the component of relative velocity along
+\cdot \mathbf\{n\} \mathbf\{n\}\) is the component of relative velocity along
 \(\mathbf\{n\}\).
 
 The optional {damping} keyword to the {pair_coeff} command followed by
@@ -299,8 +299,8 @@ the normal damping \(\eta_n\) (see above):
 \eta_t = -x_\{\gamma,t\} \eta_n
 \end\{equation\}
 
-The normal damping prefactor \(\eta_n\) is determined by the choice of
-the {damping} keyword, as discussed above.  Thus, the {damping}
+The normal damping prefactor \(\eta_n\) is determined by the choice
+of the {damping} keyword, as discussed above.  Thus, the {damping}
 keyword also affects the tangential damping.  The parameter
 \(x_\{\gamma,t\}\) is a scaling coefficient. Several works in the
 literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009,
@@ -308,10 +308,10 @@ literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009,
 tangential velocity at the point of contact is given by
 \(\mathbf\{v\}_\{t, rel\} = \mathbf\{v\}_\{t\} - (R_i\Omega_i +
 R_j\Omega_j) \times \mathbf\{n\}\), where \(\mathbf\{v\}_\{t\} =
-\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\), \(\mathbf\{v\}_r =
-\mathbf\{v\}_j - \mathbf\{v\}_i\). The direction of the applied force
-is \(\mathbf\{t\} =
-\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\).
+\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\{n\}\),
+\(\mathbf\{v\}_r = \mathbf\{v\}_j - \mathbf\{v\}_i\).
+The direction of the applied force is \(\mathbf\{t\} =
+\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\) .
 
 The normal force value \(F_\{n0\}\) used to compute the critical force
 depends on the form of the contact model. For non-cohesive models
@@ -411,8 +411,8 @@ option by an additional factor of {a}, the radius of the contact region. The tan
 \mathbf\{F\}_t =  -min(\mu_t F_\{n0\}, \|-k_t a \mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
 \end\{equation\}
 
-Here, {a} is the radius of the contact region, given by \(a = \delta
-R\) for all normal contact models, except for {jkr}, where it is given
+Here, {a} is the radius of the contact region, given by \(a =\sqrt\{R\delta\}\)
+for all normal contact models, except for {jkr}, where it is given
 implicitly by \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\), see
 discussion above. To match the Mindlin solution, one should set \(k_t
 = 8G\), where \(G\) is the shear modulus, related to Young's modulus
@@ -680,7 +680,7 @@ The single() function of these pair styles returns 0.0 for the energy
 of a pairwise interaction, since energy is not conserved in these
 dissipative potentials.  It also returns only the normal component of
 the pairwise interaction force.  However, the single() function also
-calculates 10 extra pairwise quantities.  The first 3 are the
+calculates 12 extra pairwise quantities.  The first 3 are the
 components of the tangential force between particles I and J, acting
 on particle I.  The 4th is the magnitude of this tangential force.
 The next 3 (5-7) are the components of the rolling torque acting on
@@ -790,4 +790,4 @@ alternative contact force models during inelastic collisions. Powder
 Technology, 233, 30-46.
 
 :link(WaltonPC)
-[(Otis R. Walton)] Walton, O.R., Personal Communication	
+[(Otis R. Walton)] Walton, O.R., Personal Communication
diff --git a/doc/src/pair_gromacs.txt b/doc/txt/pair_gromacs.txt
similarity index 100%
rename from doc/src/pair_gromacs.txt
rename to doc/txt/pair_gromacs.txt
diff --git a/doc/src/pair_gw.txt b/doc/txt/pair_gw.txt
similarity index 100%
rename from doc/src/pair_gw.txt
rename to doc/txt/pair_gw.txt
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/txt/pair_hbond_dreiding.txt
similarity index 100%
rename from doc/src/pair_hbond_dreiding.txt
rename to doc/txt/pair_hbond_dreiding.txt
diff --git a/doc/src/pair_hybrid.txt b/doc/txt/pair_hybrid.txt
similarity index 100%
rename from doc/src/pair_hybrid.txt
rename to doc/txt/pair_hybrid.txt
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/txt/pair_ilp_graphene_hbn.txt
similarity index 100%
rename from doc/src/pair_ilp_graphene_hbn.txt
rename to doc/txt/pair_ilp_graphene_hbn.txt
diff --git a/doc/src/pair_kim.txt b/doc/txt/pair_kim.txt
similarity index 100%
rename from doc/src/pair_kim.txt
rename to doc/txt/pair_kim.txt
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/txt/pair_kolmogorov_crespi_full.txt
similarity index 98%
rename from doc/src/pair_kolmogorov_crespi_full.txt
rename to doc/txt/pair_kolmogorov_crespi_full.txt
index 5a2623ed89..b42027aada 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/txt/pair_kolmogorov_crespi_full.txt
@@ -43,8 +43,8 @@ when the tapper function is turned off. The formula of taper function
 can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
 
 NOTE: This potential (ILP) is intended for interlayer interactions between two
-different layers of graphene. To perform a realistic simulation, this potential 
-must be used in combination with intralayer potential, such as 
+different layers of graphene. To perform a realistic simulation, this potential
+must be used in combination with intralayer potential, such as
 "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
 To keep the intralayer properties unaffected, the interlayer interaction
 within the same layers should be avoided. Hence, each atom has to have a layer
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/txt/pair_kolmogorov_crespi_z.txt
similarity index 100%
rename from doc/src/pair_kolmogorov_crespi_z.txt
rename to doc/txt/pair_kolmogorov_crespi_z.txt
diff --git a/doc/src/pair_lcbop.txt b/doc/txt/pair_lcbop.txt
similarity index 100%
rename from doc/src/pair_lcbop.txt
rename to doc/txt/pair_lcbop.txt
diff --git a/doc/src/pair_lebedeva_z.txt b/doc/txt/pair_lebedeva_z.txt
similarity index 100%
rename from doc/src/pair_lebedeva_z.txt
rename to doc/txt/pair_lebedeva_z.txt
diff --git a/doc/src/pair_line_lj.txt b/doc/txt/pair_line_lj.txt
similarity index 100%
rename from doc/src/pair_line_lj.txt
rename to doc/txt/pair_line_lj.txt
diff --git a/doc/src/pair_lj.txt b/doc/txt/pair_lj.txt
similarity index 100%
rename from doc/src/pair_lj.txt
rename to doc/txt/pair_lj.txt
diff --git a/doc/src/pair_lj96.txt b/doc/txt/pair_lj96.txt
similarity index 100%
rename from doc/src/pair_lj96.txt
rename to doc/txt/pair_lj96.txt
diff --git a/doc/src/pair_lj_cubic.txt b/doc/txt/pair_lj_cubic.txt
similarity index 100%
rename from doc/src/pair_lj_cubic.txt
rename to doc/txt/pair_lj_cubic.txt
diff --git a/doc/src/pair_lj_expand.txt b/doc/txt/pair_lj_expand.txt
similarity index 100%
rename from doc/src/pair_lj_expand.txt
rename to doc/txt/pair_lj_expand.txt
diff --git a/doc/src/pair_lj_long.txt b/doc/txt/pair_lj_long.txt
similarity index 100%
rename from doc/src/pair_lj_long.txt
rename to doc/txt/pair_lj_long.txt
diff --git a/doc/src/pair_lj_smooth.txt b/doc/txt/pair_lj_smooth.txt
similarity index 100%
rename from doc/src/pair_lj_smooth.txt
rename to doc/txt/pair_lj_smooth.txt
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/txt/pair_lj_smooth_linear.txt
similarity index 100%
rename from doc/src/pair_lj_smooth_linear.txt
rename to doc/txt/pair_lj_smooth_linear.txt
diff --git a/doc/src/pair_lj_switch3_coulgauss.txt b/doc/txt/pair_lj_switch3_coulgauss.txt
similarity index 100%
rename from doc/src/pair_lj_switch3_coulgauss.txt
rename to doc/txt/pair_lj_switch3_coulgauss.txt
diff --git a/doc/txt/pair_local_density.txt b/doc/txt/pair_local_density.txt
new file mode 100644
index 0000000000..4def63c5fc
--- /dev/null
+++ b/doc/txt/pair_local_density.txt
@@ -0,0 +1,207 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+pair_style local/density command :h3
+
+[Syntax:]
+
+pair_style style arg :pre
+
+style = {local/density}
+arg = name of file containing tabulated values of local density and the potential :ul
+
+[Examples:]
+
+pair_style local/density benzene_water.localdensity.table :pre
+
+pair_style hybrid/overlay table spline 500 local/density 
+pair_coeff * * local/density  benzene_water.localdensity.table :pre
+
+[Description:]
+
+The local density (LD) potential is a mean-field manybody potential, and, in some 
+sense,a generalization of embedded atom models (EAM). The name "local density 
+potential" arises from the fact that it assigns an energy to an atom depending 
+on the number of neighboring atoms of given type around it within a predefined 
+spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
+literature suggests that such potentials can be widely useful  in capturing 
+effective multibody forces in a computationally efficient manner so as to 
+improve the quality of CG models of implicit solvation"(Sanyal1)"_#Sanyal1 and 
+phase-segregation in liquid mixtures"(Sanyal2)"_#Sanyal2, and provide guidelines 
+to determine the extent of manybody correlations present in a CG 
+model."(Rosenberger)"_#Rosenberger The LD potential in LAMMPS is primarily 
+intended to be used as a corrective potential over traditional pair potentials 
+in bottom-up CG models, i.e., as a hybrid pair style with 
+other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.). 
+Because the LD potential is not a pair potential per se,  it is implemented 
+simply as a single auxiliary file with all specifications that will be read 
+upon initialization.
+
+NOTE: Thus when used as the only interaction in the system, there is no 
+corresponding pair_coeff command and when used with other pair styles using the 
+hybrid/overlay option, the corresponding pair_coeff command must be supplied
+*  * as placeholders for the atom types.
+
+:line
+
+[System with a single CG atom type:]
+
+A system of a single atom type (e.g., LJ argon) with a single local density (LD)
+potential would have an energy given by:
+
+:c,image(Eqs/pair_local_density_energy.jpg)
+
+where rho_i is the LD at atom i and F(rho) is similar in spirit to the 
+embedding function used in EAM potentials. The LD at atom i is given by the sum
+
+:c,image(Eqs/pair_local_density_ld.jpg)
+
+where phi is an indicator function that is one at r=0 and zero beyond a cutoff 
+distance R2. The choice of the functional form of phi is somewhat arbitrary, 
+but the following piecewise cubic function has proven sufficiently general: 
+"(Sanyal1)"_#Sanyal1, "(Sanyal2)"_#Sanyal2 "(Rosenberger)"_#Rosenberger
+
+:c,image(Eqs/pair_local_density_indicator_func.jpg)
+
+The constants {c} are chosen so that the indicator function smoothly 
+interpolates between 1 and 0 between the distances R1 and R2, which are 
+called the inner and outer cutoffs, respectively. Thus phi satisfies 
+phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) =  dphi/dr @ (r=R2) = 0. The embedding 
+function F(rho) may or may not have a closed-form expression. To maintain 
+generality, it is practically represented with a spline-interpolated table 
+over a predetermined range of rho. Outside of that range it simply adopts zero 
+values at the endpoints.
+
+It can be shown that the total force between two atoms due to the LD potential 
+takes the form of a pair force, which motivates its designation as a LAMMPS 
+pair style. Please see "(Sanyal1)"_#Sanyal1 for details of the derivation. 
+
+:line
+
+[Systems with arbitrary numbers of atom types:]
+
+The potential is easily generalized to systems involving multiple atom types:
+
+:c,image(Eqs/pair_local_density_energy_multi.jpg)
+
+with the LD expressed as
+
+:c,image(Eqs/pair_local_density_ld_multi.jpg)
+
+where alpha gives the type of atom i, beta the type of atom j, and the 
+coefficients a and b filter for atom types as specified by the user. a is 
+called the central atom filter as it determines to which atoms the 
+potential applies; a_alpha = 1 if the LD potential applies to atom type alpha 
+else zero. On the other hand, b is called the neighbor atom filter because it 
+specifies which atom types to use in the calculation of the LD; b_beta = 1 if 
+atom type beta contributes to the LD and zero otherwise.
+
+NOTE: Note that the potentials need not be symmetric with respect to atom types, 
+which is the reason for two distinct sets of coefficients a and b. An atom type 
+may contribute to the LD but not the potential, or to the potential but not the 
+LD. Such decisions are made by the user and should (ideally) be motivated on 
+physical grounds for the problem at hand.
+
+:line
+
+[General form for implementation in LAMMPS:]
+
+Of course, a system with many atom types may have many different possible LD 
+potentials, each with their own atom type filters, cutoffs, and embedding 
+functions. The most general form of this potential as implemented in the 
+pair_style local/density is:
+
+:c,image(Eqs/pair_local_density_energy_implement.jpg)
+
+where, k is an index that spans the (arbitrary) number of applied LD potentials 
+N_LD. Each LD is calculated as before with:
+
+:c,image(Eqs/pair_local_density_ld_implement.jpg)
+
+The superscript on the indicator function phi simply indicates that it is 
+associated with specific values of the cutoff distances R1(k) and R2(k). In 
+summary, there may be N_LD distinct LD potentials. With each potential type (k), 
+one must specify:
+
+the inner and outer cutoffs as R1 and R2
+the central type filter a(k), where k = 1,2,...N_LD
+the neighbor type filter b(k), where k = 1,2,...N_LD
+the LD potential function F(k)(rho), typically as a table that is later spline-interpolated :ul
+
+:line
+
+[Tabulated input file format:]
+
+Line 1:             comment or blank (ignored)
+Line 2:             comment or blank (ignored)
+Line 3:             N_LD N_rho (# of LD potentials and # of tabulated values, single space separated)
+Line 4:             blank (ignored)
+Line 5:             R1(k) R2(k) (lower and upper cutoffs, single space separated)
+Line 6:             central-types (central atom types, single space separated)
+Line 7:             neighbor-types (neighbor atom types single space separated)
+Line 8:             rho_min rho_max drho (min, max and diff. in tabulated rho values, single space separated)
+Line 9:             F(k)(rho_min + 0.drho)
+Line 10:            F(k)(rho_min + 1.drho)
+Line 11:            F(k)(rho_min + 2.drho)
+...
+Line 9+N_rho:       F(k)(rho_min + N_rho . drho)
+Line 10+N_rho:      blank (ignored) :pre
+
+Block 2 :pre
+
+Block 3 :pre
+
+Block N_LD :pre
+
+Lines 5 to 9+N_rho constitute the first block. Thus the input file is separated 
+(by blank lines) into N_LD blocks each representing a separate LD potential and 
+each specifying its own upper and lower cutoffs, central and neighbor atoms, 
+and potential.  In general, blank lines anywhere are ignored. 
+
+:line
+
+[Mixing, shift, table, tail correction, restart, info]:
+This pair style does not support automatic mixing. For atom type pairs alpha,
+beta and alpha != beta, even if LD potentials of type (alpha, alpha) and 
+(beta, beta) are provided, you will need to explicitly provide LD potential 
+types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha,
+beta) means that alpha is the central atom to which the LD potential is applied
+and beta is the neighbor atom which contributes to the LD potential on alpha).
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+The local/density pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in tabulated potential files.
+Thus, you need to re-specify the pair_style and pair_coeff commands in
+an input script that reads a restart file.
+
+:line
+
+[Restrictions:]
+
+The local/density pair style is a part of the USER-MISC package. It is only
+enabled if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+
+:link(Sanyal1)
+[(Sanyal1)] Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109.
+:link(Sanyal2)
+[(Sanyal2)] Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
+
+:link(Rosenberger)
+[(Rosenberger)] Rosenberger, Sanyal, Shell and van der Vegt,  Journal of Chemical Physics, 2019, 151 (4), 044111.
diff --git a/doc/src/pair_lubricate.txt b/doc/txt/pair_lubricate.txt
similarity index 100%
rename from doc/src/pair_lubricate.txt
rename to doc/txt/pair_lubricate.txt
diff --git a/doc/src/pair_lubricateU.txt b/doc/txt/pair_lubricateU.txt
similarity index 100%
rename from doc/src/pair_lubricateU.txt
rename to doc/txt/pair_lubricateU.txt
diff --git a/doc/src/pair_mdf.txt b/doc/txt/pair_mdf.txt
similarity index 100%
rename from doc/src/pair_mdf.txt
rename to doc/txt/pair_mdf.txt
diff --git a/doc/src/pair_meam_spline.txt b/doc/txt/pair_meam_spline.txt
similarity index 100%
rename from doc/src/pair_meam_spline.txt
rename to doc/txt/pair_meam_spline.txt
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/txt/pair_meam_sw_spline.txt
similarity index 100%
rename from doc/src/pair_meam_sw_spline.txt
rename to doc/txt/pair_meam_sw_spline.txt
diff --git a/doc/src/pair_meso.txt b/doc/txt/pair_meso.txt
similarity index 100%
rename from doc/src/pair_meso.txt
rename to doc/txt/pair_meso.txt
diff --git a/doc/src/pair_mgpt.txt b/doc/txt/pair_mgpt.txt
similarity index 100%
rename from doc/src/pair_mgpt.txt
rename to doc/txt/pair_mgpt.txt
diff --git a/doc/src/pair_mie.txt b/doc/txt/pair_mie.txt
similarity index 100%
rename from doc/src/pair_mie.txt
rename to doc/txt/pair_mie.txt
diff --git a/doc/src/pair_momb.txt b/doc/txt/pair_momb.txt
similarity index 100%
rename from doc/src/pair_momb.txt
rename to doc/txt/pair_momb.txt
diff --git a/doc/src/pair_morse.txt b/doc/txt/pair_morse.txt
similarity index 100%
rename from doc/src/pair_morse.txt
rename to doc/txt/pair_morse.txt
diff --git a/doc/src/pair_multi_lucy.txt b/doc/txt/pair_multi_lucy.txt
similarity index 100%
rename from doc/src/pair_multi_lucy.txt
rename to doc/txt/pair_multi_lucy.txt
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/txt/pair_multi_lucy_rx.txt
similarity index 100%
rename from doc/src/pair_multi_lucy_rx.txt
rename to doc/txt/pair_multi_lucy_rx.txt
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/txt/pair_nb3b_harmonic.txt
similarity index 100%
rename from doc/src/pair_nb3b_harmonic.txt
rename to doc/txt/pair_nb3b_harmonic.txt
diff --git a/doc/src/pair_nm.txt b/doc/txt/pair_nm.txt
similarity index 100%
rename from doc/src/pair_nm.txt
rename to doc/txt/pair_nm.txt
diff --git a/doc/src/pair_none.txt b/doc/txt/pair_none.txt
similarity index 100%
rename from doc/src/pair_none.txt
rename to doc/txt/pair_none.txt
diff --git a/doc/src/pair_peri.txt b/doc/txt/pair_peri.txt
similarity index 100%
rename from doc/src/pair_peri.txt
rename to doc/txt/pair_peri.txt
diff --git a/doc/src/pair_polymorphic.txt b/doc/txt/pair_polymorphic.txt
similarity index 100%
rename from doc/src/pair_polymorphic.txt
rename to doc/txt/pair_polymorphic.txt
diff --git a/doc/src/pair_python.txt b/doc/txt/pair_python.txt
similarity index 100%
rename from doc/src/pair_python.txt
rename to doc/txt/pair_python.txt
diff --git a/doc/src/pair_quip.txt b/doc/txt/pair_quip.txt
similarity index 100%
rename from doc/src/pair_quip.txt
rename to doc/txt/pair_quip.txt
diff --git a/doc/src/pair_reaxc.txt b/doc/txt/pair_reaxc.txt
similarity index 100%
rename from doc/src/pair_reaxc.txt
rename to doc/txt/pair_reaxc.txt
diff --git a/doc/src/pair_resquared.txt b/doc/txt/pair_resquared.txt
similarity index 100%
rename from doc/src/pair_resquared.txt
rename to doc/txt/pair_resquared.txt
diff --git a/doc/src/pair_sdk.txt b/doc/txt/pair_sdk.txt
similarity index 100%
rename from doc/src/pair_sdk.txt
rename to doc/txt/pair_sdk.txt
diff --git a/doc/src/pair_sdpd_taitwater_isothermal.txt b/doc/txt/pair_sdpd_taitwater_isothermal.txt
similarity index 100%
rename from doc/src/pair_sdpd_taitwater_isothermal.txt
rename to doc/txt/pair_sdpd_taitwater_isothermal.txt
diff --git a/doc/src/pair_smd_hertz.txt b/doc/txt/pair_smd_hertz.txt
similarity index 100%
rename from doc/src/pair_smd_hertz.txt
rename to doc/txt/pair_smd_hertz.txt
diff --git a/doc/src/pair_smd_tlsph.txt b/doc/txt/pair_smd_tlsph.txt
similarity index 100%
rename from doc/src/pair_smd_tlsph.txt
rename to doc/txt/pair_smd_tlsph.txt
diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/txt/pair_smd_triangulated_surface.txt
similarity index 100%
rename from doc/src/pair_smd_triangulated_surface.txt
rename to doc/txt/pair_smd_triangulated_surface.txt
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/txt/pair_smd_ulsph.txt
similarity index 100%
rename from doc/src/pair_smd_ulsph.txt
rename to doc/txt/pair_smd_ulsph.txt
diff --git a/doc/src/pair_smtbq.txt b/doc/txt/pair_smtbq.txt
similarity index 100%
rename from doc/src/pair_smtbq.txt
rename to doc/txt/pair_smtbq.txt
diff --git a/doc/src/pair_snap.txt b/doc/txt/pair_snap.txt
similarity index 99%
rename from doc/src/pair_snap.txt
rename to doc/txt/pair_snap.txt
index 1fba74a188..37d1a1ed18 100644
--- a/doc/src/pair_snap.txt
+++ b/doc/txt/pair_snap.txt
@@ -50,7 +50,7 @@ the SNAP potential files themselves.
 Only a single pair_coeff command is used with the {snap} style which
 specifies a SNAP coefficient file followed by a SNAP parameter file
 and then N additional arguments specifying the mapping of SNAP
-elements to LAMMPS atom types, where N is the number of 
+elements to LAMMPS atom types, where N is the number of
 LAMMPS atom types:
 
 SNAP coefficient file
@@ -79,7 +79,7 @@ The name of the SNAP coefficient file usually ends in the
 ".snapcoeff" extension. It may contain coefficients
 for many SNAP elements. The only requirement is that it
 contain at least those element names appearing in the
-LAMMPS mapping list. 
+LAMMPS mapping list.
 The name of the SNAP parameter file usually ends in the ".snapparam"
 extension. It contains a small number
 of parameters that define the overall form of the SNAP potential.
diff --git a/doc/src/pair_soft.txt b/doc/txt/pair_soft.txt
similarity index 100%
rename from doc/src/pair_soft.txt
rename to doc/txt/pair_soft.txt
diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/txt/pair_sph_heatconduction.txt
similarity index 100%
rename from doc/src/pair_sph_heatconduction.txt
rename to doc/txt/pair_sph_heatconduction.txt
diff --git a/doc/src/pair_sph_idealgas.txt b/doc/txt/pair_sph_idealgas.txt
similarity index 100%
rename from doc/src/pair_sph_idealgas.txt
rename to doc/txt/pair_sph_idealgas.txt
diff --git a/doc/src/pair_sph_lj.txt b/doc/txt/pair_sph_lj.txt
similarity index 100%
rename from doc/src/pair_sph_lj.txt
rename to doc/txt/pair_sph_lj.txt
diff --git a/doc/src/pair_sph_rhosum.txt b/doc/txt/pair_sph_rhosum.txt
similarity index 100%
rename from doc/src/pair_sph_rhosum.txt
rename to doc/txt/pair_sph_rhosum.txt
diff --git a/doc/src/pair_sph_taitwater.txt b/doc/txt/pair_sph_taitwater.txt
similarity index 100%
rename from doc/src/pair_sph_taitwater.txt
rename to doc/txt/pair_sph_taitwater.txt
diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/txt/pair_sph_taitwater_morris.txt
similarity index 100%
rename from doc/src/pair_sph_taitwater_morris.txt
rename to doc/txt/pair_sph_taitwater_morris.txt
diff --git a/doc/src/pair_spin_dipole.txt b/doc/txt/pair_spin_dipole.txt
similarity index 77%
rename from doc/src/pair_spin_dipole.txt
rename to doc/txt/pair_spin_dipole.txt
index 0d6471e07f..36bcd25d5e 100644
--- a/doc/src/pair_spin_dipole.txt
+++ b/doc/txt/pair_spin_dipole.txt
@@ -11,7 +11,7 @@ pair_style spin/dipole/long command :h3
 
 [Syntax:]
 
-pair_style spin/dipole/cut cutoff 
+pair_style spin/dipole/cut cutoff
 pair_style spin/dipole/long cutoff :pre
 
 cutoff = global cutoff for magnetic dipole energy and forces
@@ -21,35 +21,34 @@ cutoff = global cutoff for magnetic dipole energy and forces
 [Examples:]
 
 pair_style spin/dipole/cut 10.0
-pair_coeff * * 10.0 
+pair_coeff * * 10.0
 pair_coeff 2 3 8.0 :pre
 
 pair_style spin/dipole/long 9.0
-pair_coeff * * 1.0 1.0
-pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
-pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
+pair_coeff * * 10.0
+pair_coeff 2 3 6.0 :pre
 
 [Description:]
 
 Style {spin/dipole/cut} computes a short-range dipole-dipole
-interaction between pairs of magnetic particles that each 
-have a magnetic spin. 
+interaction between pairs of magnetic particles that each
+have a magnetic spin.
 The magnetic dipole-dipole interactions are computed by the
-following formulas for the magnetic energy, magnetic precession 
+following formulas for the magnetic energy, magnetic precession
 vector omega and mechanical force between particles I and J.
 
 :c,image(Eqs/pair_spin_dipole.jpg)
 
-where si and sj are the spin on two magnetic particles, 
-r is their separation distance, and the vector e = (Ri - Rj)/|Ri - Rj| 
-is the direction vector between the two particles.  
+where si and sj are the spin on two magnetic particles,
+r is their separation distance, and the vector e = (Ri - Rj)/|Ri - Rj|
+is the direction vector between the two particles.
 
 Style {spin/dipole/long} computes long-range magnetic dipole-dipole
 interaction.
 A "kspace_style"_kspace_style.html must be defined to
-use this pair style.  Currently, "kspace_style 
+use this pair style.  Currently, "kspace_style
 ewald/dipole/spin"_kspace_style.html and "kspace_style
-pppm/dipole/spin"_kspace_style.html support long-range magnetic 
+pppm/dipole/spin"_kspace_style.html support long-range magnetic
 dipole-dipole interactions.
 
 :line
@@ -68,8 +67,8 @@ to be specified in an input script that reads a restart file.
 [Restrictions:]
 
 The {spin/dipole/cut} and {spin/dipole/long} styles are part of
-the SPIN package.  They are only enabled if LAMMPS was built with that 
-package.  See the "Build package"_Build_package.html doc page for more 
+the SPIN package.  They are only enabled if LAMMPS was built with that
+package.  See the "Build package"_Build_package.html doc page for more
 info.
 
 Using dipole/spin pair styles with {electron} "units"_units.html is not
diff --git a/doc/src/pair_spin_dmi.txt b/doc/txt/pair_spin_dmi.txt
similarity index 98%
rename from doc/src/pair_spin_dmi.txt
rename to doc/txt/pair_spin_dmi.txt
index 9ddff8a8dc..cca20d1136 100644
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/txt/pair_spin_dmi.txt
@@ -15,11 +15,11 @@ pair_style spin/dmi cutoff :pre
 cutoff = global cutoff pair (distance in metal units) :ulb,l
 
 :ule
-	
+
 [Examples:]
 
 pair_style spin/dmi 4.0
-pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0	
+pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0
 pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre
 
 [Description:]
diff --git a/doc/src/pair_spin_magelec.txt b/doc/txt/pair_spin_magelec.txt
similarity index 100%
rename from doc/src/pair_spin_magelec.txt
rename to doc/txt/pair_spin_magelec.txt
diff --git a/doc/src/pair_srp.txt b/doc/txt/pair_srp.txt
similarity index 100%
rename from doc/src/pair_srp.txt
rename to doc/txt/pair_srp.txt
diff --git a/doc/src/pair_sw.txt b/doc/txt/pair_sw.txt
similarity index 100%
rename from doc/src/pair_sw.txt
rename to doc/txt/pair_sw.txt
diff --git a/doc/src/pair_table.txt b/doc/txt/pair_table.txt
similarity index 100%
rename from doc/src/pair_table.txt
rename to doc/txt/pair_table.txt
diff --git a/doc/src/pair_table_rx.txt b/doc/txt/pair_table_rx.txt
similarity index 100%
rename from doc/src/pair_table_rx.txt
rename to doc/txt/pair_table_rx.txt
diff --git a/doc/src/pair_tersoff.txt b/doc/txt/pair_tersoff.txt
similarity index 100%
rename from doc/src/pair_tersoff.txt
rename to doc/txt/pair_tersoff.txt
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/txt/pair_tersoff_mod.txt
similarity index 100%
rename from doc/src/pair_tersoff_mod.txt
rename to doc/txt/pair_tersoff_mod.txt
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/txt/pair_tersoff_zbl.txt
similarity index 100%
rename from doc/src/pair_tersoff_zbl.txt
rename to doc/txt/pair_tersoff_zbl.txt
diff --git a/doc/src/pair_thole.txt b/doc/txt/pair_thole.txt
similarity index 100%
rename from doc/src/pair_thole.txt
rename to doc/txt/pair_thole.txt
diff --git a/doc/src/pair_tri_lj.txt b/doc/txt/pair_tri_lj.txt
similarity index 100%
rename from doc/src/pair_tri_lj.txt
rename to doc/txt/pair_tri_lj.txt
diff --git a/doc/src/pair_ufm.txt b/doc/txt/pair_ufm.txt
similarity index 100%
rename from doc/src/pair_ufm.txt
rename to doc/txt/pair_ufm.txt
diff --git a/doc/src/pair_vashishta.txt b/doc/txt/pair_vashishta.txt
similarity index 100%
rename from doc/src/pair_vashishta.txt
rename to doc/txt/pair_vashishta.txt
diff --git a/doc/src/pair_write.txt b/doc/txt/pair_write.txt
similarity index 100%
rename from doc/src/pair_write.txt
rename to doc/txt/pair_write.txt
diff --git a/doc/src/pair_yukawa.txt b/doc/txt/pair_yukawa.txt
similarity index 100%
rename from doc/src/pair_yukawa.txt
rename to doc/txt/pair_yukawa.txt
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/txt/pair_yukawa_colloid.txt
similarity index 100%
rename from doc/src/pair_yukawa_colloid.txt
rename to doc/txt/pair_yukawa_colloid.txt
diff --git a/doc/src/pair_zbl.txt b/doc/txt/pair_zbl.txt
similarity index 100%
rename from doc/src/pair_zbl.txt
rename to doc/txt/pair_zbl.txt
diff --git a/doc/src/pair_zero.txt b/doc/txt/pair_zero.txt
similarity index 93%
rename from doc/src/pair_zero.txt
rename to doc/txt/pair_zero.txt
index b324003bd1..def28b6856 100644
--- a/doc/src/pair_zero.txt
+++ b/doc/txt/pair_zero.txt
@@ -71,9 +71,8 @@ This pair style writes its information to "binary restart
 files"_restart.html, so pair_style and pair_coeff commands do not need
 to be specified in an input script that reads a restart file.
 
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
+This pair style supports the use of the {inner}, {middle},
+and {outer} keywords of the "run_style respa"_run_style.html command.
 
 :line
 
diff --git a/doc/src/partition.txt b/doc/txt/partition.txt
similarity index 100%
rename from doc/src/partition.txt
rename to doc/txt/partition.txt
diff --git a/doc/src/prd.txt b/doc/txt/prd.txt
similarity index 100%
rename from doc/src/prd.txt
rename to doc/txt/prd.txt
diff --git a/doc/src/print.txt b/doc/txt/print.txt
similarity index 100%
rename from doc/src/print.txt
rename to doc/txt/print.txt
diff --git a/doc/src/processors.txt b/doc/txt/processors.txt
similarity index 100%
rename from doc/src/processors.txt
rename to doc/txt/processors.txt
diff --git a/doc/src/python.txt b/doc/txt/python.txt
similarity index 100%
rename from doc/src/python.txt
rename to doc/txt/python.txt
diff --git a/doc/src/quit.txt b/doc/txt/quit.txt
similarity index 100%
rename from doc/src/quit.txt
rename to doc/txt/quit.txt
diff --git a/doc/src/read_data.txt b/doc/txt/read_data.txt
similarity index 100%
rename from doc/src/read_data.txt
rename to doc/txt/read_data.txt
diff --git a/doc/src/read_dump.txt b/doc/txt/read_dump.txt
similarity index 100%
rename from doc/src/read_dump.txt
rename to doc/txt/read_dump.txt
diff --git a/doc/src/read_restart.txt b/doc/txt/read_restart.txt
similarity index 100%
rename from doc/src/read_restart.txt
rename to doc/txt/read_restart.txt
diff --git a/doc/src/region.txt b/doc/txt/region.txt
similarity index 100%
rename from doc/src/region.txt
rename to doc/txt/region.txt
diff --git a/doc/src/replicate.txt b/doc/txt/replicate.txt
similarity index 100%
rename from doc/src/replicate.txt
rename to doc/txt/replicate.txt
diff --git a/doc/src/rerun.txt b/doc/txt/rerun.txt
similarity index 100%
rename from doc/src/rerun.txt
rename to doc/txt/rerun.txt
diff --git a/doc/src/reset_ids.txt b/doc/txt/reset_ids.txt
similarity index 100%
rename from doc/src/reset_ids.txt
rename to doc/txt/reset_ids.txt
diff --git a/doc/src/reset_timestep.txt b/doc/txt/reset_timestep.txt
similarity index 100%
rename from doc/src/reset_timestep.txt
rename to doc/txt/reset_timestep.txt
diff --git a/doc/src/restart.txt b/doc/txt/restart.txt
similarity index 100%
rename from doc/src/restart.txt
rename to doc/txt/restart.txt
diff --git a/doc/src/run.txt b/doc/txt/run.txt
similarity index 100%
rename from doc/src/run.txt
rename to doc/txt/run.txt
diff --git a/doc/src/run_style.txt b/doc/txt/run_style.txt
similarity index 100%
rename from doc/src/run_style.txt
rename to doc/txt/run_style.txt
diff --git a/doc/src/server.txt b/doc/txt/server.txt
similarity index 100%
rename from doc/src/server.txt
rename to doc/txt/server.txt
diff --git a/doc/src/server_mc.txt b/doc/txt/server_mc.txt
similarity index 100%
rename from doc/src/server_mc.txt
rename to doc/txt/server_mc.txt
diff --git a/doc/src/server_md.txt b/doc/txt/server_md.txt
similarity index 100%
rename from doc/src/server_md.txt
rename to doc/txt/server_md.txt
diff --git a/doc/src/set.txt b/doc/txt/set.txt
similarity index 100%
rename from doc/src/set.txt
rename to doc/txt/set.txt
diff --git a/doc/src/shell.txt b/doc/txt/shell.txt
similarity index 100%
rename from doc/src/shell.txt
rename to doc/txt/shell.txt
diff --git a/doc/src/special_bonds.txt b/doc/txt/special_bonds.txt
similarity index 100%
rename from doc/src/special_bonds.txt
rename to doc/txt/special_bonds.txt
diff --git a/doc/src/suffix.txt b/doc/txt/suffix.txt
similarity index 100%
rename from doc/src/suffix.txt
rename to doc/txt/suffix.txt
diff --git a/doc/src/tad.txt b/doc/txt/tad.txt
similarity index 100%
rename from doc/src/tad.txt
rename to doc/txt/tad.txt
diff --git a/doc/src/temper.txt b/doc/txt/temper.txt
similarity index 100%
rename from doc/src/temper.txt
rename to doc/txt/temper.txt
diff --git a/doc/src/temper_grem.txt b/doc/txt/temper_grem.txt
similarity index 100%
rename from doc/src/temper_grem.txt
rename to doc/txt/temper_grem.txt
diff --git a/doc/src/temper_npt.txt b/doc/txt/temper_npt.txt
similarity index 100%
rename from doc/src/temper_npt.txt
rename to doc/txt/temper_npt.txt
diff --git a/doc/src/thermo.txt b/doc/txt/thermo.txt
similarity index 100%
rename from doc/src/thermo.txt
rename to doc/txt/thermo.txt
diff --git a/doc/src/thermo_modify.txt b/doc/txt/thermo_modify.txt
similarity index 100%
rename from doc/src/thermo_modify.txt
rename to doc/txt/thermo_modify.txt
diff --git a/doc/src/thermo_style.txt b/doc/txt/thermo_style.txt
similarity index 100%
rename from doc/src/thermo_style.txt
rename to doc/txt/thermo_style.txt
diff --git a/doc/txt/third_order.txt b/doc/txt/third_order.txt
new file mode 100644
index 0000000000..9636ec830e
--- /dev/null
+++ b/doc/txt/third_order.txt
@@ -0,0 +1,62 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+third_order command :h3
+
+[Syntax:]
+
+third_order group-ID style delta args keyword value ... :pre
+
+group-ID = ID of group of atoms to displace :ulb,l
+style = {regular} or {eskm} :l
+delta = finite different displacement length (distance units) :l
+one or more keyword/arg pairs may be appended :l
+  keyword = {file} or {binary}
+    {file} name = name of output file for the third order tensor
+    {binary} arg = {yes} or {no} or {gzip} :pre
+:ule
+
+[Examples:]
+
+third_order 1 regular 0.000001
+third_order 1 eskm 0.000001
+third_order 3 regular 0.00004 file third_order.dat
+third_order 5 eskm 0.00000001 file third_order.dat binary yes :pre
+
+[Description:]
+
+Calculate the third order force constant tensor by finite difference of the selected group,
+
+:c,image(JPG/third_order_force_constant.png))
+
+where Phi is the third order force constant tensor.
+
+The output of the command is the tensor, three elements at a time. The
+three elements correspond to the three gamma elements for a specific i/alpha/j/beta/k.
+The initial five numbers are i, alpha, j, beta, and k respectively.
+
+If the style eskm is selected, the tensor will be using energy units of 10 J/mol.
+These units conform to eskm style from the dynamical_matrix command, which
+will simplify operations using dynamical matrices with third order tensors.
+
+[Restrictions:]
+
+The command collects a 9 times the number of atoms in the group on every single MPI rank,
+so the memory requirements can be very significant for large systems.
+
+This command is part of the USER-PHONON package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"fix phonon"_fix_phonon.html "dynamical_matrix"_dynamical_matrix.html
+
+[Default:]
+
+The default settings are file = "third_order.dat", binary = no
diff --git a/doc/src/timer.txt b/doc/txt/timer.txt
similarity index 100%
rename from doc/src/timer.txt
rename to doc/txt/timer.txt
diff --git a/doc/src/timestep.txt b/doc/txt/timestep.txt
similarity index 100%
rename from doc/src/timestep.txt
rename to doc/txt/timestep.txt
diff --git a/doc/src/uncompute.txt b/doc/txt/uncompute.txt
similarity index 100%
rename from doc/src/uncompute.txt
rename to doc/txt/uncompute.txt
diff --git a/doc/src/undump.txt b/doc/txt/undump.txt
similarity index 100%
rename from doc/src/undump.txt
rename to doc/txt/undump.txt
diff --git a/doc/src/unfix.txt b/doc/txt/unfix.txt
similarity index 100%
rename from doc/src/unfix.txt
rename to doc/txt/unfix.txt
diff --git a/doc/src/units.txt b/doc/txt/units.txt
similarity index 100%
rename from doc/src/units.txt
rename to doc/txt/units.txt
diff --git a/doc/src/variable.txt b/doc/txt/variable.txt
similarity index 100%
rename from doc/src/variable.txt
rename to doc/txt/variable.txt
diff --git a/doc/src/velocity.txt b/doc/txt/velocity.txt
similarity index 100%
rename from doc/src/velocity.txt
rename to doc/txt/velocity.txt
diff --git a/doc/src/write_coeff.txt b/doc/txt/write_coeff.txt
similarity index 100%
rename from doc/src/write_coeff.txt
rename to doc/txt/write_coeff.txt
diff --git a/doc/src/write_data.txt b/doc/txt/write_data.txt
similarity index 100%
rename from doc/src/write_data.txt
rename to doc/txt/write_data.txt
diff --git a/doc/src/write_dump.txt b/doc/txt/write_dump.txt
similarity index 100%
rename from doc/src/write_dump.txt
rename to doc/txt/write_dump.txt
diff --git a/doc/src/write_restart.txt b/doc/txt/write_restart.txt
similarity index 100%
rename from doc/src/write_restart.txt
rename to doc/txt/write_restart.txt
diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
new file mode 100755
index 0000000000..a5bf31801c
--- /dev/null
+++ b/doc/utils/check-styles.py
@@ -0,0 +1,244 @@
+#!/usr/bin/env python3
+
+from __future__ import print_function
+from glob import glob
+from argparse import ArgumentParser
+import os, re, sys
+
+parser = ArgumentParser(prog='check-styles.py',
+                        description="Check style table completeness")
+
+parser.add_argument("-v", "--verbose",
+                    action='store_const',
+                    const=True, default=False,
+                    help="Enable verbose output")
+
+parser.add_argument("-d", "--doc",
+                    help="Path to LAMMPS documentation sources")
+parser.add_argument("-s", "--src",
+                    help="Path to LAMMPS sources")
+
+args = parser.parse_args()
+verbose = args.verbose
+src = args.src
+doc = args.doc
+
+if not args.src or not args.doc:
+  parser.print_help()
+  sys.exit(1)
+
+if not os.path.isdir(src):
+    sys.exit("LAMMPS source path %s does not exist" % src)
+
+if not os.path.isdir(doc):
+    sys.exit("LAMMPS documentation source path %s does not exist" % doc)
+
+headers = glob(os.path.join(src, '*', '*.h'))
+headers += glob(os.path.join(src, '*.h'))
+
+angle = {}
+atom = {}
+body = {}
+bond = {}
+command = {}
+compute = {}
+dihedral = {}
+dump = {}
+fix = {}
+improper = {}
+integrate = {}
+kspace = {}
+minimize = {}
+pair = {}
+reader = {}
+region = {}
+
+upper = re.compile("[A-Z]+")
+gpu = re.compile("(.+)/gpu$")
+intel = re.compile("(.+)/intel$")
+kokkos = re.compile("(.+)/kk$")
+kokkos_skip = re.compile("(.+)/kk/(host|device)$")
+omp = re.compile("(.+)/omp$")
+opt = re.compile("(.+)/opt$")
+removed = re.compile("(.+)Deprecated$")
+
+def register_style(list,style,info):
+    if style in list.keys():
+        list[style]['gpu'] += info['gpu']
+        list[style]['intel'] += info['intel']
+        list[style]['kokkos'] += info['kokkos']
+        list[style]['omp'] += info['omp']
+        list[style]['opt'] += info['opt']
+        list[style]['removed'] += info['removed']
+    else:
+        list[style] = info
+
+def add_suffix(list,style):
+    suffix = ""
+    if list[style]['gpu']:
+        suffix += 'g'
+    if list[style]['intel']:
+        suffix += 'i'
+    if list[style]['kokkos']:
+        suffix += 'k'
+    if list[style]['omp']:
+        suffix += 'o'
+    if list[style]['opt']:
+        suffix += 't'
+    if suffix:
+        return style + ' (' + suffix + ')'
+    else:
+        return style
+
+def check_style(file,dir,pattern,list,name,suffix=False,skip=()):
+    f = os.path.join(dir, file)
+    fp = open(f)
+    text = fp.read()
+    fp.close()
+    matches = re.findall(pattern,text,re.MULTILINE)
+    counter = 0
+    for c in list.keys():
+        # known undocumented aliases we need to skip
+        if c in skip: continue
+        s = c
+        if suffix: s = add_suffix(list,c)
+        if not s in matches:
+            if not list[c]['removed']:
+                print("%s style entry %s" % (name,s),
+                      "is missing or incomplete in %s" % file)
+                counter += 1
+    return counter
+
+for h in headers:
+    if verbose: print("Checking ", h)
+    fp = open(h)
+    text = fp.read()
+    fp.close()
+    matches = re.findall("(.+)Style\((.+),(.+)\)",text,re.MULTILINE)
+    for m in matches:
+
+        # skip over internal styles w/o explicit documentation
+        style = m[1]
+        if upper.match(style):
+            continue
+
+        # detect, process, and flag suffix styles:
+        info = { 'kokkos':  0, 'gpu':     0, 'intel':   0, \
+                 'omp':     0, 'opt':     0, 'removed': 0 }
+        suffix = kokkos_skip.match(style)
+        if suffix:
+            continue
+        suffix = gpu.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['gpu'] = 1
+        suffix = intel.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['intel'] = 1
+        suffix = kokkos.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['kokkos'] = 1
+        suffix = omp.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['omp'] = 1
+        suffix = opt.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['opt'] = 1
+        deprecated = removed.match(m[2])
+        if deprecated:
+            info['removed'] = 1
+
+        # register style and suffix flags
+        if m[0] == 'Angle':
+            register_style(angle,style,info)
+        elif m[0] == 'Atom':
+            register_style(atom,style,info)
+        elif m[0] == 'Body':
+            register_style(body,style,info)
+        elif m[0] == 'Bond':
+            register_style(bond,style,info)
+        elif m[0] == 'Command':
+            register_style(command,style,info)
+        elif m[0] == 'Compute':
+            register_style(compute,style,info)
+        elif m[0] == 'Dihedral':
+            register_style(dihedral,style,info)
+        elif m[0] == 'Dump':
+            register_style(dump,style,info)
+        elif m[0] == 'Fix':
+            register_style(fix,style,info)
+        elif m[0] == 'Improper':
+            register_style(improper,style,info)
+        elif m[0] == 'Integrate':
+            register_style(integrate,style,info)
+        elif m[0] == 'KSpace':
+            register_style(kspace,style,info)
+        elif m[0] == 'Minimize':
+            register_style(minimize,style,info)
+        elif m[0] == 'Pair':
+            register_style(pair,style,info)
+        elif m[0] == 'Reader':
+            register_style(reader,style,info)
+        elif m[0] == 'Region':
+            register_style(region,style,info)
+        else:
+            print("Skipping over: ",m)
+
+
+print("""Parsed style names w/o suffixes from C++ tree in %s:
+   Angle styles:     %3d    Atom styles:      %3d
+   Body styles:      %3d    Bond styles:      %3d
+   Command styles:   %3d    Compute styles:   %3d
+   Dihedral styles:  %3d    Dump styles:      %3d
+   Fix styles:       %3d    Improper styles:  %3d
+   Integrate styles: %3d    Kspace styles:    %3d
+   Minimize styles:  %3d    Pair styles:      %3d
+   Reader styles:    %3d    Region styles:    %3d""" \
+      % (src, len(angle), len(atom), len(body), len(bond),   \
+       len(command), len(compute), len(dihedral), len(dump), \
+       len(fix), len(improper), len(integrate), len(kspace), \
+       len(minimize), len(pair), len(reader), len(region)))
+
+
+counter = 0
+
+counter += check_style('Commands_all.rst',doc,":doc:`(.+) <.+>`",
+                       command,'Command',suffix=False)
+counter += check_style('Commands_compute.rst',doc,":doc:`(.+) <compute.+>`",
+                       compute,'Compute',suffix=True)
+counter += check_style('compute.rst',doc,":doc:`(.+) <compute.+>` -",
+                       compute,'Compute',suffix=False)
+counter += check_style('Commands_fix.rst',doc,":doc:`(.+) <fix.+>`",
+                       fix,'Fix',skip=('python'),suffix=True)
+counter += check_style('fix.rst',doc,":doc:`(.+) <fix.+>` -",
+                       fix,'Fix',skip=('python'),suffix=False)
+counter += check_style('Commands_pair.rst',doc,":doc:`(.+) <pair.+>`",
+                       pair,'Pair',skip=('meam','lj/sf'),suffix=True)
+counter += check_style('pair_style.rst',doc,":doc:`(.+) <pair.+>` -",
+                       pair,'Pair',skip=('meam','lj/sf'),suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <bond.+>`",
+                       bond,'Bond',suffix=True)
+counter += check_style('bond_style.rst',doc,":doc:`(.+) <bond.+>` -",
+                       bond,'Bond',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <angle.+>`",
+                       angle,'Angle',suffix=True)
+counter += check_style('angle_style.rst',doc,":doc:`(.+) <angle.+>` -",
+                       angle,'Angle',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <dihedral.+>`",
+                       dihedral,'Dihedral',suffix=True)
+counter += check_style('dihedral_style.rst',doc,":doc:`(.+) <dihedral.+>` -",
+                       dihedral,'Dihedral',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <improper.+>`",
+                       improper,'Improper',suffix=True)
+counter += check_style('improper_style.rst',doc,":doc:`(.+) <improper.+>` -",
+                       improper,'Improper',suffix=False)
+counter += check_style('Commands_kspace.rst',doc,":doc:`(.+) <kspace_style>`",
+                       kspace,'KSpace',suffix=True)
+
+if counter:
+    print("Found %d issue(s) with style lists" % counter)
+
diff --git a/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py
new file mode 100644
index 0000000000..353eed8b6e
--- /dev/null
+++ b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py
@@ -0,0 +1,255 @@
+#! /usr/bin/env python3
+# LAMMPS Documentation Utilities
+#
+# Scan for duplicate anchor labels in documentation files
+#
+# Copyright (C) 2019 E. Anne Gunn
+# Based largely on doc_anchor_check.py by Richard Berger
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+import argparse
+import os
+import re
+import shutil
+import sys
+
+
+# We only want to replace image lines where image is
+# pulled from Eqs subfolder
+image_pattern = re.compile(r'.*image:: Eqs/(.*)\.jpg')
+tex_eq_pattern = re.compile(r'\$\$')
+latex_begin_eq_pattern = re.compile(r'\\begin{equation}')
+latex_end_eq_pattern = re.compile(r'\\end{equation}')
+latex_begin_eqArray_pattern = re.compile(r'\\begin{eqnarray\*}')
+latex_end_eqArray_pattern = re.compile(r'\\end{eqnarray\*}')
+
+imageMarker = ">>>image was here"
+image_marker_pattern = re.compile(r'>>>image was here')
+align_pattern = re.compile(r'.*:align: center')
+
+modifiedRstFolder = "src/modifiedRst/"
+safeRstFolder = "src/safeRst/"
+# Since this is a proof of concept implementation,
+# skip any rst files that are known to cause problems
+skipFileList = ["pair_tersoff_zbl.rst"]
+
+runReport = {
+}
+
+
+def checkForEquationStart(texLine):
+    eqType = None
+    texMatch = tex_eq_pattern.match(texLine)
+    if texMatch:
+        eqType = "texMatch"
+    else:
+        eqMatch = latex_begin_eq_pattern.match(texLine)
+        if eqMatch:
+            eqType = "eqMatch"
+        else:
+            eqArrayMatch = latex_begin_eqArray_pattern.match(texLine)
+            if eqArrayMatch:
+                eqType = "eqArrayMatch"
+    return eqType
+
+
+def checkForEquationEnd(texLine, eqType):
+    endPattern = tex_eq_pattern
+    if eqType == "texMatch":
+        endPattern = tex_eq_pattern
+    elif eqType == "eqMatch":
+        endPattern = latex_end_eq_pattern
+    elif eqType == "eqArrayMatch":
+        endPattern = latex_end_eqArray_pattern
+    else:
+        print("***error: unexpected eqType %s, will look for tex delimiter" % eqType)
+
+    endMatch = endPattern.match(texLine)
+    endFound = endMatch is not None
+    if endFound:
+        print("found pattern end, line: %s" % texLine)
+    return endFound
+
+
+def startMathjax():
+    mathjaxLines = []
+    mathjaxLines.append(".. math::\n\n")
+    return mathjaxLines
+
+
+def endMathjax(mathjaxLines):
+    mathjaxLines.append("\n")
+    mathjaxLines.append("%s\n" % imageMarker)
+    return mathjaxLines
+
+
+def processFile(filename):
+    print("in processFile for filename: %s" % filename)
+    imageCount = 0
+
+    modifiedFileLines = []
+    doWriteModifiedFile = False
+    with open(filename, 'rt') as f:
+        for line_number, line in enumerate(f):
+            m = image_pattern.match(line)
+            if m:
+                fileroot = m.group(1)
+                print("fileroot: {0}".format(fileroot))
+                imageCount += 1
+                texFilename = "src/Eqs/{0}.tex".format(fileroot)
+                print("will try to open %s" % texFilename)
+                eqType = None
+                eqLines = []
+                try:
+                    with open(texFilename, 'rt', encoding='utf-8') as t:
+                        print("%s file opened ok" % texFilename)
+                        eqLines = startMathjax()
+                        try:
+                            for dummy, texLine in enumerate(t):
+                                #print(texLine)
+                                if eqType == None:
+                                    eqType = checkForEquationStart(texLine)
+                                    if eqType != None:
+                                        print("equation type: {0}".format(eqType))
+                                else:
+                                    endFound = checkForEquationEnd(texLine, eqType)
+                                    if endFound != True:
+                                        eqLines.append(texLine)
+                                    else:
+                                        eqType = None
+                                        eqLines = endMathjax(eqLines)
+                                        print("Equation lines will be:")
+                                        print("-----------------------------")
+                                        print(*eqLines, sep="\n")
+                                        print("-----------------------------")
+                        except UnicodeDecodeError:
+                            print("UnicodeDecodeError reading file file %s, image markup will be left in place" % texFilename)
+                            break
+                except EnvironmentError:
+                    error = "could not open source tex file {0}, line: {1}".format(texFilename, line)
+                    print(error)
+                    print("image markup will be left in place")
+                    if filename not in runReport:
+                        runReport[filename] = []
+                    runReport[filename].append(error)
+                    # put the image line we could not replace back into the output
+                    eqLines.append(line)
+                if len(eqLines) > 0:
+                    modifiedFileLines.extend(eqLines)
+                    doWriteModifiedFile = True
+                    eqLines = []
+            else:
+                # not an equation line, so simply queue it up for output as is
+                modifiedFileLines.append(line)
+    if doWriteModifiedFile:
+        # We're going to write out a modified file, so first copy the original rst
+        # file into the original file folder.
+        nameParts = filename.split("/")
+        filenamePos = len(nameParts) - 1
+        safeFilePath = "{0}{1}".format(safeRstFolder, nameParts[filenamePos])
+        shutil.copyfile(filename, safeFilePath)
+
+        print("modifiedFileLines has %d lines before align center cleanup" % len(modifiedFileLines))
+        # First, go through the file and pull out the lines where there is
+        # now an image file marker followed by an align center directive
+        deleteLines = []
+        for lineNumber, line in enumerate(modifiedFileLines):
+            m = image_marker_pattern.match(line)
+            if m:
+                print("found image marker in line %d" % lineNumber)
+                n = align_pattern.match(modifiedFileLines[lineNumber+1])
+                if n:
+                    print("found align center")
+                    deleteLines.append(lineNumber)
+                    deleteLines.append(lineNumber+1)
+        #When deleting, always work from the back of the list to the front
+        for lineNumber in reversed(deleteLines):
+            print(lineNumber)
+            del modifiedFileLines[lineNumber]
+        print("modifiedFileLines has %d lines after align center cleanup" % len(modifiedFileLines))
+        # Now we can actually write out the new contents
+        try:
+            modFilePath = "{0}{1}".format(modifiedRstFolder, nameParts[filenamePos])
+            modRst = open(modFilePath, "w")
+            for rstLine in modifiedFileLines:
+                modRst.write(rstLine)
+            modRst.close()
+        except OSError:
+            print('Error: Creating directory. ' + modifiedRstFolder)
+    return imageCount
+
+
+def main():
+    fileCount = 0
+    totalImageCount = 0
+
+    parser = argparse.ArgumentParser(description='replace image markup in rst files with inline mathjax markup from .txt source of images')
+    parser.add_argument('files',  metavar='file', nargs='+', help='one or more files to scan')
+    parsed_args = parser.parse_args()
+    print(parsed_args)
+
+    if not os.path.exists(safeRstFolder):
+        os.makedirs(safeRstFolder)
+    if not os.path.exists(modifiedRstFolder):
+        os.makedirs(modifiedRstFolder)
+
+    # Because we may decide to add files to the skip list between runs,
+    # if we have more than one file to process,
+    # files from both original and modified folders
+    # zombie modifications
+    if len(parsed_args.files) > 1:
+        for outputFile in os.listdir(modifiedRstFolder):
+            filePath = os.path.join(modifiedRstFolder, outputFile)
+            try:
+                if os.path.isfile(filePath):
+                    os.unlink(filePath)
+            except Exception as e:
+                print(e)
+                sys.exit(1)
+        for safeFile in os.listdir(safeRstFolder):
+            filePath = os.path.join(safeRstFolder, safeFile)
+            try:
+                if os.path.isfile(filePath):
+                    os.unlink(filePath)
+            except Exception as e:
+                print(e)
+                sys.exit(1)
+
+    for filename in parsed_args.files:
+        print("filename: %s" % filename)
+        doSkip = False
+        for skipName in skipFileList:
+            if filename.find(skipName) != -1:
+                print("skipping file: %s" % filename)
+                doSkip = True
+                runReport[filename] = ["skipped based on skipFileList"]
+                break
+        if not doSkip:
+            fileCount += 1
+            ic = processFile(filename)
+            totalImageCount += ic
+
+    print("============================================")
+    print("Processed %d rst files." % fileCount)
+    print("Found %d image lines." % totalImageCount)
+
+    for fileKey in runReport:
+        print("--------------------------------------------")
+        print("run report for %s:" % fileKey)
+        print(*runReport[fileKey], sep="\n")
+
+    print("============================================")
+
+if __name__ == "__main__":
+    main()
diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py
new file mode 100644
index 0000000000..64a1308601
--- /dev/null
+++ b/doc/utils/converters/lammpsdoc/rst_anchor_check.py
@@ -0,0 +1,64 @@
+#! /usr/bin/env python3
+# LAMMPS Documentation Utilities
+#
+# Scan for duplicate anchor labels in documentation files
+#
+# Copyright (C) 2017 Richard Berger
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+import re
+import sys
+import argparse
+
+def main():
+    parser = argparse.ArgumentParser(description='scan for duplicate anchor labels in documentation files')
+    parser.add_argument('files',  metavar='file', nargs='+', help='one or more files to scan')
+    parsed_args = parser.parse_args()
+
+    anchor_pattern = re.compile(r'^\.\. _(.*):$')
+    anchors = {}
+
+    for filename in parsed_args.files:
+        #print("filename: %s" % filename)
+        with open(filename, 'rt') as f:
+            for line_number, line in enumerate(f):
+                m = anchor_pattern.match(line)
+                if m:
+                    label = m.group(1)
+                    #print("found label: %s" % label)
+                    if label in anchors:
+                        anchors[label].append((filename, line_number+1))
+                    else:
+                        anchors[label] = [(filename, line_number+1)]
+
+    print("Found %d anchor labels" % len(anchors))
+
+    count = 0
+
+    for label in sorted(anchors.keys()):
+        if len(anchors[label]) > 1:
+            print(label)
+            count += 1
+            for filename, line_number in anchors[label]:
+                print(" - %s:%d" % (filename, line_number))
+
+
+    if count > 0:
+        print("Found %d anchor label errors." % count)
+        sys.exit(1)
+    else:
+        print("No anchor label errors.")
+
+if __name__ == "__main__":
+    main()
diff --git a/doc/utils/converters/setup.py b/doc/utils/converters/setup.py
index f4656a7f69..d85669bcc1 100644
--- a/doc/utils/converters/setup.py
+++ b/doc/utils/converters/setup.py
@@ -13,6 +13,6 @@ setup(name='LAMMPS Documentation Utilities',
       entry_points = {
           "console_scripts": ['txt2html = lammpsdoc.txt2html:main',
                               'txt2rst  = lammpsdoc.txt2rst:main',
-                              'doc_anchor_check = lammpsdoc.doc_anchor_check:main ']
+                              'rst_anchor_check = lammpsdoc.rst_anchor_check:main ']
       },
 )
diff --git a/doc/utils/sha1sum.py b/doc/utils/sha1sum.py
deleted file mode 100755
index d4842ecf1a..0000000000
--- a/doc/utils/sha1sum.py
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/env python
-# simple utility which reimplements sha1sum using Python
-import hashlib
-import sys
-s = hashlib.sha1()
-s.update(sys.stdin.read().encode())
-print(s.hexdigest())
diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py
new file mode 100644
index 0000000000..6436be410d
--- /dev/null
+++ b/doc/utils/sphinx-config/LAMMPSLexer.py
@@ -0,0 +1,57 @@
+from pygments.lexer import RegexLexer, words
+from pygments.token import *
+
+LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
+"balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box",
+"change_box", "clear", "comm_modify", "comm_style", "compute",
+"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms",
+"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
+"displace_atoms", "dump", "dump_modify", "dynamical_matrix", "echo", "fix",
+"fix_modify", "group", "group2ndx", "hyper", "if", "improper_coeff",
+"improper_style", "include", "info", "jump", "kim_init", "kim_interactions",
+"kim_param", "kim_query", "kspace_modify", "kspace_style", "label", "lattice",
+"log", "mass", "message", "minimize", "min_modify", "min_style", "molecule",
+"ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next",
+"package", "pair_coeff", "pair_modify", "pair_style", "pair_write",
+"partition", "prd", "print", "processors", "python", "quit", "read_data",
+"read_dump", "read_restart", "region", "replicate", "rerun", "reset_ids",
+"reset_timestep", "restart", "run", "run_style", "server", "set", "shell",
+"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt",
+"thermo", "thermo_modify", "thermo_style", "then", "third_order", "timer", "timestep",
+"uncompute", "undump", "unfix", "units", "variable", "velocity", "write_coeff",
+"write_data", "write_dump", "write_restart")
+
+class LAMMPSLexer(RegexLexer):
+    name = 'LAMMPS'
+    tokens = {
+        'root': [
+            (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword),
+            (r'#.*?\n', Comment),
+            ('"', String, 'string'),
+            ('\'', String, 'single_quote_string'),
+            (r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
+            ('\$?\(', Name.Variable, 'expression'),
+            ('\$\{', Name.Variable, 'variable'),
+            (r'[\w_\.\[\]]+', Name),
+            (r'\$[\w_]+', Name.Variable),
+            (r'\s+', Whitespace),
+            (r'[\+\-\*\/&=<>]', Operator),
+        ],
+        'variable' : [
+            ('[^\}]+', Name.Variable),
+            ('\}', Name.Variable, '#pop'),
+        ],
+        'string' : [
+            ('[^"]+', String),
+            ('"', String, '#pop'),
+        ],
+        'single_quote_string' : [
+            ('[^\']+', String),
+            ('\'', String, '#pop'),
+        ],
+        'expression' : [
+            ('[^\(\)]+', Name.Variable),
+            ('\(', Name.Variable, 'expression'),
+            ('\)', Name.Variable, '#pop'),
+        ]
+    }
diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py
index 29de3af156..3e16963f01 100644
--- a/doc/utils/sphinx-config/conf.py
+++ b/doc/utils/sphinx-config/conf.py
@@ -20,6 +20,7 @@ import os
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #sys.path.insert(0, os.path.abspath('.'))
+sys.path.append(os.path.join(os.path.dirname(__file__), '../../src/_ext'))
 
 # -- General configuration ------------------------------------------------
 
@@ -31,6 +32,9 @@ import os
 # ones.
 extensions = [
     'sphinx.ext.mathjax',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.autodoc',
+    'table_from_list',
 ]
 # 2017-12-07: commented out, since this package is broken with Sphinx 16.x
 #             yet we can no longer use Sphinx 15.x, since that breaks with
@@ -201,6 +205,11 @@ htmlhelp_basename = 'LAMMPSdoc'
 
 html_add_permalinks = ''
 
+if 'epub' in sys.argv:
+  html_math_renderer = 'imgmath'
+else:
+  html_math_renderer = 'mathjax'
+
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
@@ -312,3 +321,11 @@ if spelling_spec:
 
     spelling_lang='en_US'
     spelling_word_list_filename='false_positives.txt'
+
+sys.path.append(os.path.join(os.path.dirname(__file__), '.'))
+import LAMMPSLexer
+from sphinx.highlighting import lexers
+
+lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
+
+sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python'))
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 4c7dc756cc..3182c8605e 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -71,6 +71,7 @@ AlO
 Alonso
 amap
 Amatrix
+AMD
 amino
 Amirjalayer
 Amit
@@ -108,6 +109,7 @@ Archlinux
 arcsin
 arg
 args
+arrhenius
 Arun
 arXiv
 asin
@@ -162,6 +164,7 @@ azimuthal
 Azuri
 ba
 Babadi
+Babaei
 backcolor
 Baczewski
 Bagi
@@ -210,6 +213,7 @@ Berne
 Bertotti
 Bessarab
 Beutler
+Bext
 bgq
 Bh
 Biersack
@@ -275,10 +279,12 @@ Broadwell
 Broglie
 brownian
 brownw
+Broyden
 Bryantsev
 Btarget
 btype
 buckPlusAttr
+builtin
 Bulatov
 Bureekaew
 burlywood
@@ -305,6 +311,7 @@ Cavium
 Cawkwell
 cbecker
 ccache
+ccachepiecewise
 ccmake
 ccNspecies
 CCu
@@ -408,6 +415,8 @@ computable
 compute
 concat
 cond
+conda
+Conda
 Condens
 conf
 config
@@ -516,6 +525,7 @@ Dasgupta
 dashpot
 dat
 datafile
+datatype
 datums
 Davidchack
 Daw
@@ -622,6 +632,7 @@ Doye
 dpd
 DPD
 dpdTheta
+dphi
 DPhil
 dr
 dR
@@ -705,6 +716,7 @@ Eike
 eim
 eimp
 Eindhoven
+Eisenforschung
 Ejtehadi
 El
 elaplong
@@ -778,6 +790,7 @@ erotate
 Ertas
 ervel
 Espanol
+eskm
 esu
 esub
 esw
@@ -922,6 +935,7 @@ funcs
 functionalities
 functionals
 funroll
+fuer
 fx
 fy
 fz
@@ -986,6 +1000,7 @@ gmask
 Gmask
 gneb
 GNEB
+Goldfarb
 googlemail
 Gordan
 GPa
@@ -1028,6 +1043,7 @@ Gunsteren
 Gunzenmuller
 Guo
 gw
+gyromagnetic
 gz
 gzipped
 Haak
@@ -1047,6 +1063,7 @@ Haswell
 Haugk
 Hayoun
 Hayre
+hbar
 hbcut
 hbn
 hbnewflag
@@ -1166,6 +1183,7 @@ initio
 initializations
 InP
 inregion
+Institut
 integrators
 Integrators
 intel
@@ -1242,6 +1260,7 @@ Jacobsen
 jagreat
 Jalalvand
 james
+Janssen
 Janssens
 Jaramillo
 Jarzynski
@@ -1325,6 +1344,7 @@ Khersonskii
 Khrapak
 Khvostov
 Ki
+Kikugawa
 kim
 kJ
 kk
@@ -1386,6 +1406,7 @@ Lammps
 LAMMPS
 lammpsplot
 Lamoureux
+Lande
 Landron
 langevin
 Langevin
@@ -1403,6 +1424,7 @@ Laupretre
 lavenderblush
 lawngreen
 lB
+lbfgs
 lbl
 LBtype
 lcbop
@@ -1503,6 +1525,7 @@ logfreq
 logicals
 Lomdahl
 Lond
+lookup
 lookups
 Lookups
 LoopVar
@@ -1532,6 +1555,7 @@ Mackay
 Mackrodt
 Macromolecules
 macroparticle
+macOS
 Madura
 Magda
 Magdeburg
@@ -1576,6 +1600,8 @@ Materias
 mathbf
 matlab
 matplotlib
+Matsubara
+Mattice
 Mattox
 Mattson
 maxangle
@@ -1753,6 +1779,7 @@ mtk
 Mtotal
 muB
 Muccioli
+mui
 Mukherjee
 Mulders
 multi
@@ -1998,6 +2025,7 @@ Nz
 ocl
 octahedral
 octants
+Ohara
 ohenrich
 ok
 Okabe
@@ -2028,6 +2056,7 @@ openmp
 openmpi
 opls
 Oppelstrup
+optimizations
 orangered
 organometallic
 orientational
@@ -2039,6 +2068,7 @@ Orsi
 ortho
 orthonormal
 orthorhombic
+oso
 ot
 Otype
 Ouldridge
@@ -2049,7 +2079,9 @@ Ouyang
 overlayed
 Ovito
 oxdna
+oxrna
 oxDNA
+oxRNA
 padua
 Padua
 palegoldenrod
@@ -2123,6 +2155,7 @@ ph
 Phillpot
 phiphi
 phonon
+phonons
 phophorous
 phosphide
 Phs
@@ -2136,6 +2169,7 @@ picograms
 picosecond
 picoseconds
 pid
+piecewise
 Pieniazek
 Pieter
 pimd
@@ -2269,6 +2303,7 @@ qoffload
 qopenmp
 qoverride
 qtb
+quadratically
 quadrupolar
 Quant
 quartic
@@ -2418,6 +2453,7 @@ Rodrigues
 Rohart
 Ronchetti
 Rosati
+Rosenberger
 Rossky
 rosybrown
 rotationally
@@ -2478,10 +2514,12 @@ Schulten
 Schunk
 Schuring
 Schwen
+screenshots
 Scripta
 sdk
 sdpd
 SDPD
+se
 seagreen
 Secor
 sectoring
@@ -2508,6 +2546,7 @@ setvel
 sfftw
 Sg
 Shan
+Shanno
 shapex
 shapey
 shapez
@@ -2575,6 +2614,7 @@ Snodin
 Sodani
 Soderlind
 solvated
+solvation
 Sorensen
 soundspeed
 Souza
@@ -2659,6 +2699,7 @@ Sunderland
 superset
 supersphere
 Supinski
+Surblys
 surfactants
 Suter
 Sutmann
@@ -2935,6 +2976,7 @@ vectorial
 vectorization
 Vectorization
 vectorized
+Vegt
 vel
 Verlag
 verlet
@@ -3134,3 +3176,4 @@ zx
 zy
 Zybin
 zz
+Zm
diff --git a/doc/utils/txt2html/README.html b/doc/utils/txt2html/README.html
deleted file mode 100644
index b92214425e..0000000000
--- a/doc/utils/txt2html/README.html
+++ /dev/null
@@ -1,237 +0,0 @@
-<HTML>
-<H3>txt2html - a text to HTML conversion tool 
-</H3>
-<P><B>txt2html</B> is a simple tool for converting text files into HTML files.
-Text files can contain simple formatting and mark-up commands that
-<B>txt2html</B> converts into HTML.
-</P>
-<P><B>txt2html</B> was written by <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>.  I use it for
-<A HREF = "http://www.cs.sandia.gov/~sjplimp/lammps.html">documentation</A> and <A HREF = "http://www.cs.sandia.gov/~sjplimp">WWW pages</A>.  Anna Reese added the table
-formatting options.
-</P>
-<P>See the <A HREF = "example.txt">example.txt</A> and <A HREF = "example.html">example.html</A>
-files in the <B>txt2html</B> directory for examples of what all the
-formatting commands and mark-up syntax end up looking like in HTML.
-</P>
-
-
-
-
-
-
-<HR>
-
-<P><B>Syntax:</B>
-</P>
-<DL><DT>txt2html file
-<DD>  read from text file, write HTML to standard output
-<DT>txt2html file1 file2 file3 ...
-<DD>  read each argument as text file, write one HTML file per argument 
-</DL>
-<P>Input files are first opened with the specified name.  If that fails,
-a ".txt" suffix is added.  Output files are created with an ".html"
-suffix, which is either added or replaces the ".txt" suffix.
-</P>
-<HR>
-
-<P><B>Compiling:</B>
-</P>
-<P>The source for <B>txt2html</B> is a single C++ file.  Compile it by typing:
-</P>
-<PRE>g++ -o txt2html txt2html.cpp 
-</PRE>
-<HR>
-
-<P><B>How the tool works:</B>
-</P>
-<P><B>txt2html</B> reads a text file, one <I>paragraph</I> at a time.  A paragraph
-ends with:
-</P>
-<UL><LI>  a blank line
-<LI>  a line whose final word starts with ":" (a format string)
-<LI>  the end of the file 
-</UL>
-<P>Any line in the paragraph which ends with "\" is concatenated to the
-following line by removing the "\" character and following newline.
-This can be useful for some of the formatting commands described below
-that operate on individual lines in the paragraph.
-</P>
-<P>If a paragraph starts with a "&lt;" character and ends with a "&gt;"
-character, it is treated as raw HTML and is written directly into the
-output file.
-</P>
-<P>If a paragraph does not end with a format string, then it is
-surrounded with HTML paragraph markers (&lt;P&gt; and &lt;/P&gt;),
-<A HREF = "#markup">mark-up</A> is performed, and the paragraph is written to the
-output file.
-</P>
-<P>If the paragraph ends with a format string, then <A HREF = "#format">formatting</A>
-is performed, <A HREF = "#markup">mark-up</A> is performed, and the paragraph is
-written to the output file.
-</P>
-<HR>
-
-<A NAME = "format"></A><B>Formatting:</B> 
-
-<P>A format string is the last word of a paragraph if it starts with a
-":" character.  A format string contains one or more comma-separated
-commands, like ":ulb,l" or ":c,h3".  Note that a format string cannot
-contain spaces, else it would not be the last word.  An individual
-command can have 0 or more arguments:
-</P>
-<UL><LI>  <I>b</I> or <I>line()</I> = 0 arguments
-<LI>  <I>image(file)</I> = 1 argument
-<LI>  <I>link(alias,value)</I> = 2 or more comma-separated arguments 
-</UL>
-<P>Format commands add HTML markers at the beginning or end of the
-paragraph and individual lines.  Commands are processed in the order
-they appear in the format string.  Thus if two commands add HTML
-markers to the beginning of the paragraph, the 2nd command's marker
-will appear 2nd.  The reverse is true at the end of the paragraph; the
-2nd command's marker will appear 1st.  Some comands, like <I>line</I> or
-<I>image</I> make most sense if used as stand-alone commands without an
-accompanying paragraph.
-</P>
-<P>Commands that format the entire paragraph:
-</P>
-<UL><LI>  p --&gt; surround the paragraph with &lt;P&gt; &lt;/P&gt;
-<LI>  b --&gt; put &lt;BR&gt; at the end of the paragraph
-<LI>  pre --&gt; surround the paragraph with &lt;PRE&gt; &lt;/PRE&gt;
-<LI>  c --&gt; surround the paragraph with &lt;CENTER&gt; &lt;/CENTER&gt;
-<LI>  h1,h2,h3,h4,h5,h6 --&gt; surround the paragraph with                            &lt;H1&gt; &lt;/H1&gt;, etc 
-</UL>
-<P>Commands that format the lines of the paragraph as a list:
-</P>
-<UL><LI>  ul --&gt; surround the paragraph with &lt;UL&gt; &lt;/UL&gt;,     put &lt;LI&gt; at start of every line
-<LI>  ol --&gt; surround the paragraph with &lt;OL&gt; &lt;/OL&gt;,     put &lt;LI&gt; at start of every line
-<LI>  dl --&gt; surround the paragraph with &lt;DL&gt; &lt;/DL&gt;,     alternate &lt;DT&gt; and &lt;DD&gt; at start of every line 
-</UL>
-<P>Commands that treat the paragraph as one entry in a list:
-</P>
-<UL><LI>  l --&gt; put &lt;LI&gt; at the beginning of the paragraph
-<LI>  dt --&gt; put &lt;DT&gt; at the beginning of the paragraph
-<LI>  dd --&gt; put &lt;DD&gt; at the beginning of the paragraph
-<LI>  ulb --&gt; put &lt;UL&gt; at the beginning of the paragraph
-<LI>  ule --&gt; put &lt;/UL&gt; at the end of the paragraph
-<LI>  olb --&gt; put &lt;OL&gt; at the beginning of the paragraph
-<LI>  ole --&gt; put &lt;/OL&gt; at the end of the paragraph
-<LI>  dlb --&gt; put &lt;DL&gt; at the beginning of the paragraph
-<LI>  dle --&gt; put &lt;/DL&gt; at the end of the paragraph 
-</UL>
-<P>Commands applied to each line of the paragraph:
-</P>
-<UL><LI>  all(p) --&gt; surround each line with &lt;P&gt; &lt;/P&gt;
-<LI>  all(c) --&gt; surround each line with &lt;CENTER&gt; &lt;/CENTER&gt;
-<LI>  all(b) --&gt; append a &lt;BR&gt; to each line
-<LI>  all(l) --&gt; prepend a &lt;LI&gt; to each line 
-</UL>
-<P>Special commands (all HTML is inserted at beginning of paragraph):
-</P>
-<UL><LI>  line --&gt; insert a horizontal line = &lt;HR&gt;
-<LI>  image(file) --&gt; insert an image = &lt;IMG SRC = "file"&gt;
-<LI>  image(file,link) --&gt; insert an image that when clicked on goes to link
-<LI>  link(name) --&gt; insert a named link that can be referred to     elsewhere (see <A HREF = "#markup">mark-up</A>) = &lt;A NAME = "name"&gt;&lt;/A&gt;
-<LI>  link(alias,value) --&gt; define a link alias that can be used     elsewhere in this file (see <A HREF = "#markup">mark-up</A>) 
-</UL>
-<P>Table command:
-</P>
-<UL><LI>  tb(c=3,b=5,w=100%,a=c) --&gt; format the paragraph as a table 
-</UL>
-<P>Arguments within tb() can appear in any order and are all optional,
-since they each have default values.
-</P>
-<UL><LI>  c=N --&gt; Make an N-column table.  Treat the paragraph as one
-  long list of entries (separated by the separator character) and put
-  them into N columns one after the other.  If N = 0, treat each line
-  of the paragraph as one row of the table with as many columns as
-  there are maximum entries in any line.  Default is c=0. 
-
-<LI>  s=: --&gt; Use the character string following the equal sign as
-  the separator between entries.  Default separator is a comma "," which
-  you cannot specify directly since the comma delimits the tb() arguments 
-
-<LI>  b=N --&gt; Create a border N pixels wide.  If N is 0, there is no
-  border between or outside the cells.  If N is 1, there is a minimal
-  border between and outside all cells.  For N > 1, the border between
-  cells does not change but the outside border gets wider.  Default is
-  b=1. 
-
-<LI>  w=N or w=N% --&gt The first form makes each cell of the table at
-  least N pixels wide.  The second form makes the entire table take up
-  N% of the width of the browser window.  Default is w=0 which means
-  each cell will be just as wide as the text it contains.  
-
-<LI>  a=X --&gt Align the entire table at the left, center, or right of the
-  browser window, for X = "l", "c", or "r".  Default is a=c. 
-
-<LI>  ea=X --&gt Align the text in each entry at the left, center, or
-  right of its cell, for X = "l", "c", or "r".  Default is browser's 
-  default (typically left). 
-
-<LI>  eva=X --&gt Vertically align the text in each entry at the
-  top, middle, baseline, or bottom of its cell, for X = "t", "m", "ba", 
-  or "bo".  Default is browser's default (typically middle). 
-
-<LI>  cwM=N or cwM=N% --&gt The first form makes column M be at least
-  N pixels wide.  The second form makes column M take up N% of the
-  width of the browser window.  This setting overrides the "w"
-  argument for column M.  Only one column per table can be tweaked
-  with this argument.  Default is no settings for any column. 
-
-<LI>  caM=X --&gt Align the text in each entry of column M at the left,
-  center, or right of its cell, for X = "l", "c", or "r".  This
-  setting overrides the "ea" argument for column M.  Only one column
-  per table can be tweaked with this argument.  Default is no settings
-  for any column. 
-
-<LI>  cvaM=X --&gt Vertically align the text in each entry of column m
-  at the top, middle, baseline, or bottom of its cell, for X = "t",
-  "m", "ba", or "bo".  This setting overrides the "eva" argument for
-  column M.  Only one column per table can be tweaked with this
-  argument.  Default is no settings for any column. 
-</UL>
-<HR>
-
-<A NAME = "markup"></A><B>Mark-up:</B> 
-
-<P>The text of the paragraph is scanned for special mark-up characters
-which are converted into HTML.
-</P>
-<P>Bold and italic characters:
-</P>
-  <UL> <LI> "[" (left brace) --&gt; turn-on bold by inserting a &lt;B&gt;
-  <LI> "]" (right brace) --&gt; turn-off bold by inserting a &lt;/B&gt;
-  <LI> "{" (left bracket) --&gt; turn-on italics by inserting a &lt;I&gt;
-  <LI> "}" (right bracket) --&gt; turn-off italics by 
-    inserting a &lt;/I&gt; </UL>
-
-<P>If a backspace '\' precedes any of the bold/italic mark-up characters,
-then mark-up is not performed; the mark-up character is simply left in
-the text.
-</P>
-<P>Links are inserted by enclosing a section of text in double quotes,
-and appending an underscore to the ending quote, followed by the link.
-The link ends when whitespace is found, except that trailing
-punctuation characters (comma, period, semi-colon, colon, question
-mark, exclamation point, parenthesis) are not considered part of the
-link.
-</P>
-<P> A link of the form "text"_link becomes &lt;A HREF =
-"link"&gt;text&lt;/A&gt; in the HTML output.  The only exception is if
-"link" is defined elsewhere in the file as an alias (see the link
-command above).  In that case, the value is used instead of the alias
-name. </P>
-
-<P>With these rules, links can take several forms.
-</P>
-<UL> <LI> "This links"_#abc to another part of this file which is
-labeled with a :link(abc) command. <BR>
-<LI> "This links"_other.html to another file named other.html. <BR>
-<LI> "This links"_other.html#abc to another file which has an "abc"
-location defined internally. <BR>
-<LI> "This links"_http://www.google.com to a WWW site. <BR>
-<LI> "This"_M12 could be used in place of any of the above forms.  It
-requires an alias like :link(M12,http://www.google.com) to be defined
-elsewhere in the file. </UL>
-
-</HTML>
diff --git a/doc/utils/txt2html/txt2html b/doc/utils/txt2html/txt2html
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diff --git a/doc/utils/txt2html/txt2html.cpp b/doc/utils/txt2html/txt2html.cpp
deleted file mode 100644
index ff71c262c8..0000000000
--- a/doc/utils/txt2html/txt2html.cpp
+++ /dev/null
@@ -1,940 +0,0 @@
-// txt2html - written by Steve Plimpton, May 2004
-// table formatting by Anna Reese, Jul 2004
-// Sandia National Labs, www.cs.sandia.gov/~sjplimp
-//
-// txt2html converts a text file with simple formatting & markup into HTML
-// formatting & markup specification is given in README
-//
-// Syntax: txt2html options file                read one file, write to stdout
-//         txt2html optoins file1 file2 ...     read files, write files.html
-//
-// options:
-//   -b = add a page-break comment to end of each HTML file
-//     useful when set of HTML files will be converted to PDF
-//   -x file = skip a file even if it appears in file list
-//     specify full file name of input file
-// input files are first opened as-is
-//   if that fails a .txt suffix is added
-// output files have an .html suffix added or replaced
-//   (unless written to stdout)
-
-#include <string>
-#include <vector>
-#include <iostream>
-
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-
-using namespace std;
-
-#define MAXLINE 1024
-
-// function prototypes
-
-static int next_paragraph(FILE *fp, string &paragraph);
-static int index_of_first_char_of_last_word(string &paragraph);
-static void process_commands(int flag, string &s, string &pre, string &post);
-static void substitute(string &s);
-static string td_tag(int currentc);
-static long find_n(string &s, int nend, int &n1);
-static void file_open(int npair, string &infile, FILE **in, FILE **out);
-
-// global variables for links, tables, lists, all command
-
-vector<string> alias1;
-vector<string> alias2;
-int nlink;
-
-int tableflag;       // makes a table if tb command specified
-int rowquit;         // number of cols per row if c=N specified (default = 0)
-string dwidth;       // width for all of the columns
-string tabledelim;   // speciallized separator
-string tablealign;   // alignment for the table as an image
-string dataalign;    // alignment for data in table
-string rowvalign;    // vertical alignment for table
-
-int ncnum;             // # of columns with specified width
-vector<int> cnum;      // column IDs
-vector<string> cwidth; // column widths
-
-int ncalign;              // # of columns with specified alignment
-vector<int> acolnum;      // column IDs
-vector<string> colalign ; // column alignment
-
-int ncvalign;              // # of columns with specified vertical alignment
-vector<int> vacolnum;      // column IDs
-vector<string> colvalign ; // column vertical alignment
-
-string listflag;
-string allflag;
-
-// main program
-
-int main(int narg, char **arg)
-{
-  int npair;
-  size_t n;
-  string *infile;
-  FILE *in,*out;
-  int style,ifirst,ilast;
-  string raw,pre,post,body,commands,final;
-
-  // parse command-line options and args
-  // setup list of files to process
-  // npair = # of files to process
-  // infile = input file names
-
-  if (narg == 1) {
-    fprintf(stderr,"Syntax: txt2html options file\n");
-    fprintf(stderr,"        txt2html options file1 file2 ...\n");
-    exit(1);
-  }
-
-  int breakflag = 0;
-  int nskip = 0;
-  char **skipfiles = NULL;
-
-  int iarg = 1;
-  while (arg[iarg][0] == '-') {
-    if (strcmp(arg[iarg],"-b") == 0) breakflag = 1;
-    else if (strcmp(arg[iarg],"-x") == 0) {
-      skipfiles = (char **) realloc(skipfiles,(nskip+1)*sizeof(char *));
-      n = strlen(arg[iarg+1]) + 1;
-      skipfiles[nskip] = new char[n];
-      strcpy(skipfiles[nskip],arg[iarg+1]);
-      nskip++;
-      iarg++;
-    } else {
-      fprintf(stderr,"Syntax: txt2html options file\n");
-      fprintf(stderr,"        txt2html options file1 file2 ...\n");
-      exit(1);
-    }
-    iarg++;
-  }
-
-  if (narg-iarg == 1) {
-    npair = 1;
-    infile = new string[npair];
-    infile[0] = arg[narg-1];
-  } else {
-    npair = narg-iarg;
-    infile = new string[npair];
-    for (int i = 0; i < npair; i++) infile[i] = arg[i+iarg];
-  }
-
-  // loop over files
-
-  for (int ipair = 0; ipair < npair; ipair++) {
-
-    // skip file if matches -x switch
-
-    int flag = 0;
-    for (int i = 0; i < nskip; i++)
-      if (strcmp(infile[ipair].c_str(),skipfiles[i]) == 0) flag = 1;
-    if (flag) continue;
-
-    // clear global variables before processing file
-
-    alias1.clear();
-    alias2.clear();
-    nlink = 0;
-    tableflag = 0;
-    listflag = "";
-    allflag = "";
-
-    // open files & message to screen
-
-    file_open(0,infile[ipair],&in,&out);
-    fprintf(stderr,"Converting %s ...\n",infile[ipair].c_str());
-
-    // scan file for link definitions
-    // read file one paragraph at a time
-    // process commands, looking only for link definitions
-
-    while ((style = next_paragraph(in,raw))) {
-
-      if (style == 2) {
-        int n = index_of_first_char_of_last_word(raw);
-        commands = raw.substr(n+1);
-        process_commands(0,commands,pre,post);
-      }
-
-      raw.erase();
-    }
-
-    // close & reopen files
-
-    fclose(in);
-    file_open(npair,infile[ipair],&in,&out);
-
-    // write leading <HTML>
-
-    fprintf(out,"<HTML>\n");
-
-    // process entire file
-    // read file one paragraph at a time
-    // delete newlines when line-continuation char at end-of-line
-    // process commands for each paragraph
-    // substitute text for each paragraph
-    // write HTML to output file
-
-    int rstflag = 0;
-
-    while ((style = next_paragraph(in,raw))) {
-      
-      if (rstflag && raw.find("END_RST -->") != string::npos) {
-        rstflag = 0;
-        raw.erase();
-        continue;
-      } else if (rstflag == 0 && raw.find("<!-- RST") != string::npos) {
-        rstflag = 1;
-        raw.erase();
-        continue;
-      } else if (rstflag) {
-        raw.erase();
-        continue;
-      }
-
-      n = raw.find("\\\n");
-      while (n < string::npos) {
-        raw.erase(n,2);
-        n = raw.find("\\\n");
-      }
-
-      ifirst = raw.find_first_not_of(" \t\n");
-      ilast = raw.find_last_not_of(" \t\n");
-
-      pre.erase();
-      post.erase();
-
-      if (raw[ifirst] == '<' && raw[ilast] == '>') {
-        body = raw;
-      } else if (style == 1) {
-        body = raw;
-        commands = "p\n";
-        process_commands(1,commands,pre,post);
-        substitute(body);
-      } else {
-        int n = index_of_first_char_of_last_word(raw);
-        body = raw.substr(0,n) + "\n";
-        commands = raw.substr(n+1);
-        process_commands(1,commands,pre,post);
-        substitute(body);
-      }
-
-      final = pre + body + post;
-      fprintf(out,"%s\n",final.c_str());
-
-      raw.erase();
-    }
-
-    // write trailing </HTML>
-
-    if (breakflag) fprintf(out,"<!-- PAGE BREAK -->\n");
-    fprintf(out,"</HTML>\n");
-
-    // close files
-
-    fclose(in);
-    if (out != stdout) fclose(out);
-  }
-
-  // clean up memory
-  
-  for (int i = 0; i < nskip; i++) delete [] skipfiles[i];
-  if (skipfiles) free(skipfiles);
-  delete [] infile;
-}
-
-// return next paragraph as string
-// discard leading blank lines
-// paragraph is terminated by:
-//   EOF or blank line or line ending with command that starts with ":"
-// return 0 if EOF and no paragraph
-// return 1 if no trailing command
-// return 2 if trailing command
-
-int next_paragraph(FILE *fp, string &paragraph)
-{
-  char *ptr;
-  char str[MAXLINE];
-  int first = 1;
-  int len = 0;
-
-  while (1) {
-    ptr = fgets(str,MAXLINE,fp);
-    if (ptr == NULL && first) return 0;
-    if (ptr == NULL) return 1;
-    len = strlen(str);
-    if (len == MAXLINE-1) {
-      fprintf(stderr,"ERROR: File has too-long a string - increase MAXLINE\n");
-      exit(1);
-    }
-
-    // check for valid 7-bit ascii characters
-    bool nonascii = false;
-    for (int i=0; i < len; ++i) {
-      char c = str[i];
-      if (c != '\n' && c != '\t' && (c < ' ' || c > '~'))
-        nonascii = true;
-    }
-    if (nonascii)
-      fprintf(stderr,"WARNING: Non-portable characters in line: %s",ptr);
-
-    if (strspn(str," \t\n") == strlen(str) && first) continue;
-    if (strspn(str," \t\n") == strlen(str)) return 1;
-    first = 0;
-
-    paragraph += str;
-    if (paragraph[index_of_first_char_of_last_word(paragraph)] == ':')
-      return 2;
-  }
-}
-
-// return index of first char in last word of paragraph string
-
-int index_of_first_char_of_last_word(string &paragraph)
-{
-  size_t n = paragraph.find_last_not_of(" \t\n");
-  size_t m = paragraph.find_last_of(" \t\n",n);
-  if (m == string::npos) return 0;
-  else return m+1;
-}
-
-// apply commands one after the other to the paragraph
-
-void process_commands(int flag, string &s, string &pre, string &post)
-{
-  size_t start,stop,last;
-  int narg;
-  string command;
-  vector<string> arg;
-
-  start = 0;
-  last = s.find_last_not_of(" \t\n");
-  if (last == string::npos) return;
-
-  while (start <= last) {
-
-    // grab a single command with optional arguments
-    // command = name of command
-    // narg = # of args
-    // arg = list of argument strings
-
-    stop = s.find_first_of(",( \t\n",start);
-    if (s[stop] == '(') {
-      command = s.substr(start,stop-start);
-      start = stop+1;
-      narg = 0;
-      while (1) {
-        stop = s.find_first_of(",)",start);
-        if (stop == string::npos) {
-          fprintf(stderr,"ERROR: No trailing parenthesis in %s\n",s.c_str());
-          exit(1);
-        }
-        arg.resize(narg+1);
-        arg[narg] = s.substr(start,stop-start);
-        narg++;
-        start = stop+1;
-        if (s[stop] == ')') {
-          start++;
-          break;
-        }
-      }
-    } else {
-      command = s.substr(start,stop-start);
-      start = stop+1;
-      narg = 0;
-    }
-
-    // if only in scan mode, just operate on link command
-
-    if (flag == 0) {
-      if (command == "link" && narg == 2) {
-        //      s.erase(s.length()-1,1);
-        for (int i = 0; i < nlink; i++)
-          if (alias1[i] == arg[0]) {
-            fprintf(stderr,"ERROR: Link %s appears more than once\n",
-                    arg[0].c_str());
-            exit(1);
-          }
-        alias1.resize(nlink+1);
-        alias2.resize(nlink+1);
-        alias1[nlink] = arg[0];
-        alias2[nlink] = arg[1];
-        nlink++;
-      } else continue;
-    }
-
-    // process the command
-
-    if (command == "line") {
-      pre.append("<HR>");
-    } else if (command == "p") {
-      pre.append("<P>");
-      post.insert(0,"</P>");
-    } else if (command == "pre") {
-      pre.append("<PRE>");
-      post.insert(0,"</PRE>");
-    } else if (command == "c") {
-      pre.append("<CENTER>");
-      post.insert(0,"</CENTER>");
-    } else if (command == "h1") {
-      pre.append("<H1>");
-      post.insert(0,"</H1>");
-    } else if (command == "h2") {
-      pre.append("<H2>");
-      post.insert(0,"</H2>");
-    } else if (command == "h3") {
-      pre.append("<H3>");
-      post.insert(0,"</H3>");
-    } else if (command == "h4") {
-      pre.append("<H4>");
-      post.insert(0,"</H4>");
-    } else if (command == "h5") {
-      pre.append("<H5>");
-      post.insert(0,"</H5>");
-    } else if (command == "h6") {
-      pre.append("<H6>");
-      post.insert(0,"</H6>");
-    } else if (command == "b") {
-      post.insert(0,"<BR>");
-    } else if (command == "ulb") {
-      pre.append("<UL>");
-    } else if (command == "ule") {
-      post.insert(0,"</UL>");
-    } else if (command == "olb") {
-      pre.append("<OL>");
-    } else if (command == "ole") {
-      post.insert(0,"</OL>");
-    } else if (command == "dlb") {
-      pre.append("<DL>");
-    } else if (command == "dle") {
-      post.insert(0,"</DL>");
-    } else if (command == "l") {
-      pre.append("<LI>");
-    } else if (command == "dt") {
-      pre.append("<DT>");
-    } else if (command == "dd") {
-      pre.append("<DD>");
-    } else if (command == "ul") {
-      listflag = command;
-      pre.append("<UL>");
-      post.insert(0,"</UL>");
-    } else if (command == "ol") {
-      listflag = command;
-      pre.append("<OL>");
-      post.insert(0,"</OL>");
-    } else if (command == "dl") {
-      listflag = command;
-      pre.append("<DL>");
-      post.insert(0,"</DL>");
-    } else if (command == "link") {
-      if (narg == 1) {
-        string aname = "<A NAME = \"" + arg[0] + "\"></A>";
-        pre.append(aname);
-      }
-    } else if (command == "image") {
-      if (narg == 1) {
-        string img = "<IMG SRC = \"" + arg[0] + "\">";
-        pre.append(img);
-      } else if (narg == 2) {
-        string img = "<A HREF = \"" + arg[1] + "\">" +
-          "<IMG SRC = \"" + arg[0] + "\">" + "</A>";
-        pre.append(img);
-      }
-    } else if (command == "tb") {   // read the table command and set settings
-      tableflag = 1;
-
-      string tableborder = "1";    // these are the table defaults
-      rowquit = 0;
-      tablealign = "c";
-      dataalign = "0";
-      rowvalign = "0";
-
-      ncnum = 0;
-      ncalign = 0;
-      ncvalign = 0;
-
-      cnum.clear();
-      acolnum.clear();
-      vacolnum.clear();
-
-      cwidth.clear();
-      colalign.clear();
-      colvalign.clear();
-
-      tabledelim = ",";
-      string tw = "";
-      dwidth = "0";
-
-      for (int i = 0; i < narg; i++) {     // loop through each tb() arg
-        int tbstop;
-        string tbcommand;
-        tbstop = 0;
-        tbstop = arg[i].find("=");
-        tbcommand = arg[i].substr(0,tbstop);
-        int n = arg[i].length();
-        if (tbstop == -1) {
-          continue;
-        } else if (tbcommand == "c") {
-          string collumn= arg[i].substr (tbstop+1,n-(tbstop+1));
-          rowquit = atoi(collumn.c_str());
-        } else if (tbcommand == "s") {
-          tabledelim= arg[i].substr (tbstop+1,n-(tbstop+1));
-        } else if (tbcommand == "b") {
-          tableborder= arg[i].substr (tbstop+1,n-(tbstop+1));
-        } else if (tbcommand == "w") {
-          string width = "0";       
-          if (arg[i].substr (n-1,1) == "%") {
-            string width = arg[i].substr (tbstop+1,n-(tbstop+1));
-            tw = " WIDTH=\"" + width + "\"";
-          } else
-            dwidth = arg[i].substr (tbstop+1,n-(tbstop+1));
-        } else if (tbcommand == "ea") {
-          dataalign= arg[i].substr (tbstop+1,n-(tbstop+1));
-        } else if (tbcommand == "eva") {
-          rowvalign= arg[i].substr (tbstop+1,n-(tbstop+1));
-        } else if (tbcommand == "a") {
-          tablealign= arg[i].substr (tbstop+1,n-(tbstop+1));
-        } else if (tbcommand.substr(0,2) == "cw") {
-          string cwnum= tbcommand.substr(2,tbstop-1);
-          cnum.resize(ncnum+1);
-          cnum[ncnum] = atoi(cwnum.c_str());
-          cwidth.resize(ncnum+1);
-          cwidth[ncnum]= arg[i].substr(tbstop+1,n-(tbstop+1));
-          ncnum++;
-        } else if (tbcommand.substr(0,2) ==  "ca") {
-          string canum= tbcommand.substr(2,tbstop-1);
-          acolnum.resize(ncalign+1);
-          acolnum[ncalign] = atoi(canum.c_str());
-          colalign.resize(ncalign+1);
-          colalign[ncalign]= arg[i].substr(tbstop+1,n-(tbstop+1));
-          ncalign++;
-        } else if (tbcommand.substr(0,3) ==  "cva") {
-          string cvanum= tbcommand.substr(2,tbstop-1);
-          vacolnum.resize(ncvalign+1);
-          vacolnum[ncvalign] = atoi(cvanum.c_str());
-          colvalign.resize(ncvalign+1);
-          colvalign[ncvalign]= arg[i].substr(tbstop+1,n-(tbstop+1));
-          ncvalign++;
-        } else {
-          fprintf(stderr,
-                  "ERROR: Unrecognized table command %s\n",tbcommand.c_str());
-          exit(1);
-        }
-        
-        tbstop = s.find("=");
-      }
-      
-      string align;
-      if (tablealign=="c") align="center";
-      else if (tablealign=="r") align="right ";
-      else if (tablealign=="l") align="left  ";
-      else align="center";
-      string tablea = "<DIV ALIGN=" + align + ">" ;
-      pre.append(tablea);
-      pre.append("<TABLE ");
-      pre.append(tw);
-      string border=" BORDER=" + tableborder + " >\n";
-      pre.append(border);
-      post.insert(0,"</TD></TR></TABLE></DIV>\n"); 
-      
-    } else if (command == "all") {
-      if (narg == 1) allflag = arg[0];
-      
-    } else {
-      fprintf(stderr,"ERROR: Unrecognized command %s\n",command.c_str());
-      exit(1);
-    }
-  }
-}
-  
-// perform substitutions within text of paragraph
-
-void substitute(string &s)
-{
-  size_t n,m,p;
-  char c;
-  string text,link,href;
-  string punctuation = ".,?!;:()";
-
-  // substitute for bold & italic markers
-  // if preceded by \ char, then leave markers in text
-
-  n = s.find_first_of("[]{}");
-  while (n != string::npos) {
-    c = s[n];
-    if (n > 0 && s[n-1] == '\\') s.erase(n-1,1);
-    else {
-      s.erase(n,1);
-      if (c == '[') s.insert(n,"<B>");
-      else if (c == ']') s.insert(n,"</B>");
-      else if (c == '{') s.insert(n,"<I>");
-      else if (c == '}') s.insert(n,"</I>");
-    }
-    n = s.find_first_of("[]{}",n);
-  }
-
-  // substitute for links
-
-  n = s.find("\"_");
-  while (n != string::npos) {
-    m = s.rfind("\"",n-1);
-    if (m == string::npos) {
-      fprintf(stderr,"ERROR: Could not find matching \" for \"_ in %s\n",
-              s.c_str());
-      exit(1);
-    }
-
-    p = s.find_first_of(" \t\n",n) - 1;
-    if (p == string::npos) {
-      fprintf(stderr,"ERROR: Could not find end-of-link in %s\n",s.c_str());
-      exit(1);
-    }
-    while (s.find_first_of(".,?!;:()",p) == p) p--;
-
-    text = s.substr(m+1,n-m-1);
-    link = s.substr(n+2,p-n-1);
-    for (int i = 0; i < nlink; i++)
-      if (alias1[i] == link) {
-        link = alias2[i];
-        break;
-      }
-
-    s.erase(m,p-m+1);
-    href = "<A HREF = \"" + link + "\">" + text + "</A>";
-    s.insert(m,href);
-    n = s.find("\"_");
-  }
-
-  // format the paragraph as a table
-  
-  if (tableflag) {
-    tableflag = 0;
-
-    string DT;
-
-    // set up <TR> tag
-    // alignment for data in rows
-
-    string tbalign;
-    if (dataalign != "0"){
-      string align;                                
-      if (dataalign=="c") align="\"center\"";
-      else if (dataalign=="r") align="\"right\"";
-      else if (dataalign=="l") align="\"left\"";
-      else {
-        fprintf(stderr,
-                "ERROR: Unrecognized table alignment argument %s for ea=X\n",
-                dataalign.c_str());
-        exit(1);
-      }
-      tbalign = " ALIGN=" + align;
-    } else tbalign="";
-    
-    // set up vertical  alignment for particular columns
-
-    string va;
-    if (rowvalign != "0"){
-      string valign;
-      if (rowvalign == "t") valign= "top";
-      else if (rowvalign == "m") valign= "middle";
-      else if (rowvalign == "ba") valign= "baseline";
-      else if (rowvalign == "bo") valign= "bottom";
-      else {
-        fprintf(stderr,
-                "ERROR: Unrecognized table alignment argument %s for eva=X\n",
-                rowvalign.c_str());
-        exit(1);
-      }
-      va = " VALIGN =\"" + valign + "\"";
-    } else va="";
-
-    //tr_tag is keyword for data in rows
-
-    string tr_tag= "<TR" + tbalign + va + ">";
-
-    //declare integers to help with counting and finding position
-    
-    int currentc=0; // current column
-    int nend = 0;
-    int n1=0;
-    long n = find_n(s,nend,n1);    
-    
-    // if there are no separators, go to the end of the string
-
-    if (n < 0) n = s.length();
-
-    // while n exists:
-
-    while (n != static_cast<long>(string::npos)) {
-
-      // ignore = 0 when pass by \n because looking for delimiters only
-      // when ignore==0 do not put in a <tr>
-      int ignore=1;
-
-      // For each loop starts nend at n
-      nend=n;
-      
-      // current column is 0, (very first loop), insert first <TR>
-      if (currentc == 0){    
-        currentc++;
-        DT=td_tag(currentc);
-        s.insert(0,tr_tag);
-        s.insert(tr_tag.length(),DT);
-        nend=nend+tr_tag.length()+DT.length();
-        n = find_n(s,nend,n1);
-        if (n==n1) currentc++;  
-        else { 
-          // currentc will remain one if rowquit==0
-          if (rowquit>0){
-            s.erase(n,1);
-            n = find_n(s,nend,n1);
-            currentc++;
-          }
-        }
-      } else {
-      
-        // if n is separator
-        if (n == n1){
-          s.erase(n,tabledelim.length());
-          if(currentc==(rowquit+1)&& rowquit!=0){
-            s.insert(nend,"</TD></TR>\n");
-            nend=nend+11;
-            // set current column back to one to start new line
-            currentc=1;
-          }else{
-            DT= td_tag(currentc);
-            s.insert (nend,"</TD>");
-            nend=nend+5;
-            s.insert (nend,DT);
-            nend=nend+DT.length();
-            // add one so current column is updated
-            currentc++;   
-            n = find_n(s,nend,n1);
-          }
-
-        }
-        //if n is newline character
-        else{
-          s.erase(n,1);
-          // if columns == 0 means ARE searching for newlines
-          // else erase and ignore insert <tr> later and
-          // search for next separator
-
-          if (rowquit==0){
-            s.insert(nend,"</TD></TR>\n");
-            nend=nend+11;
-            // set current column back to one to start new line
-            currentc=1;
-          }else{
-            ignore=0;
-            n = find_n(s,nend,n1);
-          }
-        }
-
-        // if we are at the beginning of the row then insert <TR>
-
-        if (currentc==1&&ignore) {
-          DT = td_tag(currentc); // find DT for currentc=1
-          s.insert(nend,tr_tag);
-          nend=nend+tr_tag.length();
-          s.insert(nend,DT);
-          n = find_n(s,nend,n1); // search for next separator
-          currentc++;
-        }
-      } // end to else statement
-    } // end to while loop
-  } // end to if tableflag
-
-  // if listflag is set, put list marker at beginning of every line
-
-  if (listflag != "") {
-    string marker;
-    int toggle = 0;
-
-    n = s.find('\n');
-    while (n != string::npos) {
-      m = s.rfind('\n',n-1);
-      if (listflag == "dl" && toggle == 0) marker = "<DT>";
-      else if (listflag == "dl" && toggle == 1) marker = "<DD>";
-      else marker = "<LI>";
-      if (m == string::npos) s.insert(0,marker);
-      else s.insert(m+1,marker);
-      n = s.find('\n',m+1);
-      n = s.find('\n',n+1);
-      if (toggle) toggle = 0;
-      else toggle = 1;
-    }
-
-    listflag = "";
-  }
-
-  // if allflag is set, add markers to every line
-
-  if (allflag != "") {
-    string marker1,marker2;
-    if (allflag == "p") {
-      marker1 = "<P>";
-      marker2 = "</P>";
-    } else if (allflag == "c") {
-      marker1 = "<CENTER>";
-      marker2 = "</CENTER>";
-    } else if (allflag == "b") {
-      marker1 = "";
-      marker2 = "<BR>";
-    } else if (allflag == "l") {
-      marker1 = "<LI>";
-      marker2 = "";
-    } else marker1 = marker2 = "";
-
-    n = s.find('\n');
-    while (n != string::npos) {
-      m = s.rfind('\n',n-1);
-      if (m == string::npos) s.insert(0,marker1);
-      else s.insert(m+1,marker1);
-      n = s.find('\n',m+1);
-      s.insert(n,marker2);
-      n = s.find('\n',n);
-      n = s.find('\n',n+1);
-    }
-
-    allflag = "";
-  }
-}
-
-// open input file as-is or as file.txt
-// if npair = 0, don't open output file (is just initial pass thru input)
-// if npair = 1, open output file as stdout
-// if npair > 1, open output file with .html suffix
-//   either replace .txt in input file, or append .html
-
-void file_open(int npair, string &infile, FILE **in, FILE **out)
-{
-  *in = fopen(infile.c_str(),"r");
-  if (*in == NULL) {
-    string root = infile;
-    infile = infile + ".txt";
-    *in = fopen(infile.c_str(),"r");
-    if (*in == NULL) {
-      fprintf(stderr,"ERROR: Could not open %s or %s\n",
-              root.c_str(),infile.c_str());
-      exit(1);
-    }
-  }
-
-  if (npair == 0) return;
-  else if (npair == 1) *out = stdout;
-  else {
-    string outfile;
-    size_t pos = infile.rfind(".txt");
-    if (pos == infile.length()-4) outfile = infile.substr(0,pos) + ".html";
-    else outfile = infile + ".html";
-    *out = fopen(outfile.c_str(),"w");
-    if (*out == NULL) {
-      fprintf(stderr,"ERROR: Could not open %s\n",outfile.c_str());
-      exit(1);
-    }
-  }
-}
-
-// for tables:
-// build <TD> string (DT) based on current column
-
-string td_tag(int currentc) {
-
-  // eacolumn gives the alignment printout of a specific column
-  string eacolumn;
-  // va gives vertical alignment to a specific column
-  string va;
-  // DT is the complete <td> tag, with width and align
-  string DT; 
-  // dw is the width for tables.  It is also the <dt> tag beginning
-  string dw;
-  
-  // set up alignment for particular columns
-
-  for (int counter=0; counter < ncalign; counter++){
-    if (ncalign != 0 && acolnum[counter] == currentc){
-      string align;
-      if (colalign[counter] == "l") align= "left";
-      else if (colalign[counter] == "r") align= "right";
-      else if (colalign[counter] == "c") align= "center";
-      else {
-        fprintf(stderr,
-                "ERROR: Unrecognized table alignment argument %s for caM=X\n",
-                colalign[counter].c_str());
-        exit(1);
-      }
-      eacolumn= " ALIGN =\"" + align +"\"";
-    }else eacolumn= "";
-  }
-
-  // set up vertical  alignment for particular columns
-
-  for (int counter=0; counter < ncvalign; counter++){
-    if (ncvalign != 0 && vacolnum[counter] == currentc){
-      string valign;
-      if (colvalign[counter] == "t") valign= "top";
-      else if (colvalign[counter] == "m") valign= "middle";
-      else if (colvalign[counter] == "ba") valign= "baseline";
-      else if (colvalign[counter] == "bo") valign= "bottom";
-      else {
-        fprintf(stderr,
-                "ERROR: Unrecognized table alignment argument %s for cvaM=X\n",
-                colvalign[counter].c_str());
-        exit(1);
-      }
-      va = " VALIGN =\"" + valign + "\"";
-    } else va = " ";
-  }
-
-  // put in special width if specified
-  // new code
-  // if dwidth has not been set, dw is blank
-  // if dwidth has been set, dw has that... unless
-
-  if (dwidth=="0") dw = " ";       
-  else dw =" WIDTH=\""+ dwidth + "\"";
-
-  for (int counter = 0; counter < ncnum; counter++){ 
-    // if it is the right column, dw = cwidth property
-    if (cnum[counter] == currentc) dw= " WIDTH=\"" + cwidth[counter] + "\"";
-  }
-  
-  // DT is set for all of this particular separator : reset next separator
-
-  DT = "<TD" + dw + eacolumn + va + ">"; 
-  
-  return DT;
-}
-
-// for tables:
-// find the next separator starting at nend(the end of the last .insert)
-// if there is either a delim or newline 
-// decide which is first
-// set n = to that position
-// nsep is position of the next separator. changes in here.
-
-long find_n(string &s, int nend, int &nsep)
-  // nsep is position of the next separator. changes in here.
-{
-  long n;
-  nsep = s.find(tabledelim,nend);
-  long n2 = s.find('\n',nend);
-  long m = s.length() - 1;
-  if (nsep >= 0 && n2 >= 0) {
-    if (nsep <= n2) n = nsep;
-    else n = n2;
-  } else {
-    if (nsep >= 0) n = nsep;
-    else{
-      if (n2 < m) n = n2;
-      else n = string::npos;
-    }
-  }
-      
-  return n;
-}
diff --git a/examples/README b/examples/README
index 46148aea8b..a0f27e2c05 100644
--- a/examples/README
+++ b/examples/README
@@ -76,6 +76,7 @@ ellipse:  ellipsoidal particles in spherical solvent, 2d system
 flow:     Couette and Poiseuille flow in a 2d channel
 friction: frictional contact of spherical asperities between 2d surfaces
 gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
+gjf:      use of fix langevin Gronbech-Jensen/Farago option
 granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 hyper:    global and local hyperdynamics of diffusion on Pt surface
@@ -99,12 +100,12 @@ pour:     pouring of granular particles into a 3d box, then chute flow
 prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   use of PYTHON package to invoke Python code from input script
 qeq:      use of QEQ package for charge equilibration
-reax:     RDX and TATB models using the ReaxFF
+reax:     RDX and TATB and several other models using ReaxFF
+rerun:    use of rerun and read_dump commands
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
-snap:     use of SNAP potential for Ta
+snap:     examples for using several bundled SNAP potentials
 srd:      stochastic rotation dynamics (SRD) particles as solvent
-snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
 steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
 streitz:  Streitz-Mintmire potential for Al2O3
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
@@ -164,6 +165,15 @@ The MC directory has an example script for using LAMMPS as an
 energy-evaluation engine in a iterative Monte Carlo energy-relaxation
 loop.
 
+The TIP4P directory has an example for testing forces computed on a
+GPU.
+
+The UNITS directory contains examples of input scripts modeling the
+same Lennard-Jones liquid model, written in 3 different unit systems:
+lj, real, and metal.  So that you can see how to scale/unscale input
+and output values read/written by LAMMPS to verify you are performing
+the same simulation in different unit systems.
+
 The USER directory contains subdirectories of user-provided example
 scripts for ser packages.  See the README files in those directories
 for more info.  See the doc/Section_start.html file for more info
diff --git a/examples/SPIN/README b/examples/SPIN/README
index 5ad252e7f2..affb1237f8 100644
--- a/examples/SPIN/README
+++ b/examples/SPIN/README
@@ -1,20 +1,24 @@
 This directory contains examples and applications of the SPIN package
 =====================================================================
 
+- the benchmark directory provides comparison between LAMMPS
+  results and a series of simple test problems (coded as python
+  scripts).
+
 - the iron, cobalt_hcp, cobalt_fcc and nickel directories provide 
-examples of spin-lattice calculations.
+  examples of spin-lattice calculations.
 
 - the bfo repository provides an example of spin dynamics calculation
-performed on a fixed lattice, and applied to the multiferroic 
-material bismuth-oxide. 
+  performed on a fixed lattice, and applied to the multiferroic 
+  material bismuth-oxide. 
 
 - the read_restart directory provides examples allowing to write or 
-read data files, and restart magneto-mechanical simulations.  
+  read data files, and restart magneto-mechanical simulations.  
 
 - vizualization of the dump files can be achieved using Ovito or 
-VMD. See the vmd repository for help vizualizing results with VMD. 
+  VMD. See the vmd repository for help vizualizing results with VMD. 
 
 ** Note, the aim of this repository is mainly to provide users with
 examples. Better values and tuning of the magnetic and mechanical 
-interactions can be achieved for more accurate materials 
+interactions can (have to...) be achieved for more accurate materials 
 simulations. **
diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo
index e3c88b0f06..b97f7e2d61 100644
--- a/examples/SPIN/bfo/in.spin.bfo
+++ b/examples/SPIN/bfo/in.spin.bfo
@@ -1,9 +1,7 @@
 # layer sc iron atoms (in the [001] plane) in bismuth oxide 
 
-clear 
 units 		metal
 atom_style 	spin
-
 dimension 	3
 boundary 	p p f
 
@@ -18,7 +16,6 @@ create_atoms 	1 box
 # setting mass, mag. moments, and interactions for bfo
 
 mass		1 1.0
-
 set 		group all spin/random 11 2.50
 
 #pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
@@ -32,7 +29,7 @@ neigh_modify 	every 10 check yes delay 20
 
 fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
 fix 		2 all langevin/spin 0.0 0.1 21
-fix 		3 all nve/spin lattice no
+fix 		3 all nve/spin lattice frozen
 
 timestep	0.0002
 
@@ -51,6 +48,6 @@ thermo_style    custom step time v_magnorm pe ke v_emag temp etotal
 thermo          10
 
 compute outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		500
diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1
deleted file mode 100644
index 8e9eb82d1f..0000000000
--- a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1
+++ /dev/null
@@ -1,212 +0,0 @@
-LAMMPS (11 May 2018)
-# layer sc iron atoms (in the [001] plane) in bismuth oxide
-
-clear
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p f
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	sc 3.96
-Lattice spacing in x,y,z = 3.96 3.96 3.96
-region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 5780 atoms
-  Time spent = 0.0013566 secs
-
-# setting mass, mag. moments, and interactions for bfo
-
-mass		1 1.0
-
-set 		group all spin/random 11 2.50
-  5780 settings made for spin/random
-
-pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
-pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
-pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.1 21
-fix 		3 all nve/spin lattice no
-
-timestep	0.0002
-
-compute 	out_mag	 all compute/spin
-compute 	out_pe	 all pe
-compute 	out_ke	 all ke
-compute 	out_temp all temp
-
-variable 	magz	 equal c_out_mag[3]
-variable 	magnorm	 equal c_out_mag[4]
-variable 	emag	 equal c_out_mag[5]
-variable 	tmag	 equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          50
-
-compute outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		5000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.1
-  ghost atom cutoff = 6.1
-  binsize = 3.05, bins = 45 45 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair spin/magelec, perpetual, copy from (1)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes
-Step Time v_magnorm v_emag Temp TotEng 
-       0            0  0.010071723  -0.13298298            0  -0.12034311 
-      50         0.01 0.0098643821   -1.3898985            0   -1.3772103 
-     100         0.02 0.0096526211   -2.6381677            0   -2.6254222 
-     150         0.03 0.0094342235   -3.8784006            0   -3.8656019 
-     200         0.04 0.0092074832    -5.111441            0   -5.0986001 
-     250         0.05 0.0089713115   -6.3380611            0   -6.3251904 
-     300         0.06 0.0087256081   -7.5587787            0   -7.5458894 
-     350         0.07 0.0084715548   -8.7738491            0   -8.7609521 
-     400         0.08  0.008211486   -9.9833855            0   -9.9704932 
-     450         0.09 0.0079483243    -11.18751            0   -11.174637 
-     500          0.1 0.0076849713   -12.386462            0    -12.37362 
-     550         0.11  0.007424064   -13.580633            0   -13.567832 
-     600         0.12 0.0071680699   -14.770519            0   -14.757759 
-     650         0.13 0.0069192726   -15.956579            0   -15.943853 
-     700         0.14 0.0066793495   -17.139049            0   -17.126343 
-     750         0.15 0.0064488038   -18.317803            0   -18.305099 
-     800         0.16 0.0062267571   -19.492336            0   -19.479616 
-     850         0.17 0.0060112235   -20.661925            0   -20.649176 
-     900         0.18 0.0057995251   -21.825931            0   -21.813141 
-     950         0.19 0.0055886511    -22.98413            0   -22.971297 
-    1000          0.2 0.0053757923   -24.136967            0   -24.124095 
-    1050         0.21 0.0051592263   -25.285621            0   -25.272717 
-    1100         0.22 0.0049391661   -26.431928            0   -26.419004 
-    1150         0.23 0.0047179149   -27.578212            0   -27.565281 
-    1200         0.24 0.0044991004   -28.727051            0   -28.714128 
-    1250         0.25 0.0042864034   -29.880967            0   -29.868062 
-    1300         0.26 0.0040824475   -31.042054            0   -31.029173 
-    1350         0.27 0.0038883007    -32.21165            0   -32.198795 
-    1400         0.28 0.0037036595   -33.390159            0   -33.377326 
-    1450         0.29 0.0035274815   -34.577121            0   -34.564302 
-    1500          0.3 0.0033587207   -35.771483            0   -35.758672 
-    1550         0.31 0.0031969501   -36.971996            0    -36.95919 
-    1600         0.32 0.0030429081   -38.177601            0   -38.164801 
-    1650         0.33 0.0028989804   -39.387757            0   -39.374962 
-    1700         0.34 0.0027692024   -40.602665            0   -40.589873 
-    1750         0.35 0.0026581403   -41.823341            0    -41.81054 
-    1800         0.36 0.0025686991    -43.05145            0   -43.038628 
-    1850         0.37  0.002500124   -44.288966            0   -44.276111 
-    1900         0.38 0.0024477804   -45.537752            0    -45.52486 
-    1950         0.39 0.0024050049   -46.799255            0   -46.786336 
-    2000          0.4 0.0023657031   -48.074388            0   -48.061466 
-    2050         0.41 0.0023260844   -49.363587            0   -49.350695 
-    2100         0.42 0.0022848329   -50.666866            0   -50.654039 
-    2150         0.43 0.0022419759   -51.983781            0   -51.971055 
-    2200         0.44 0.0021972506    -53.31336            0   -53.300764 
-    2250         0.45 0.0021488322   -54.654121            0   -54.641676 
-    2300         0.46 0.0020929483   -56.004207            0   -55.991918 
-    2350         0.47 0.0020244601   -57.361586            0   -57.349442 
-    2400         0.48  0.001938225    -58.72428            0   -58.712247 
-    2450         0.49 0.0018309419    -60.09064            0   -60.078671 
-    2500          0.5 0.0017030436   -61.459658            0   -61.447705 
-    2550         0.51 0.0015599449   -62.831213            0   -62.819237 
-    2600         0.52 0.0014117554   -64.206088            0   -64.194074 
-    2650         0.53 0.0012709942   -65.585701            0   -65.573657 
-    2700         0.54 0.0011490452   -66.971565            0   -66.959515 
-    2750         0.55  0.001053009   -68.364663            0   -68.352635 
-    2800         0.56 0.00098415327   -69.765002            0   -69.753017 
-    2850         0.57 0.00093809306   -71.171532            0   -71.159598 
-    2900         0.58 0.00090656933    -72.58234            0   -72.570459 
-    2950         0.59 0.00088069677   -73.994931            0   -73.983099 
-    3000          0.6 0.00085472643   -75.406507            0    -75.39472 
-    3050         0.61 0.00082842902   -76.814319            0   -76.802575 
-    3100         0.62 0.00080642618   -78.216074            0   -78.204373 
-    3150         0.63 0.00079463972   -79.610246            0   -79.598589 
-    3200         0.64 0.0007962304   -80.996103            0   -80.984494 
-    3250         0.65 0.00080980411    -82.37346            0   -82.361903 
-    3300         0.66 0.00083070982   -83.742356            0   -83.730855 
-    3350         0.67 0.00085389185   -85.102808            0   -85.091374 
-    3400         0.68 0.00087624091   -86.454619            0   -86.443259 
-    3450         0.69 0.00089741986   -87.797089            0   -87.785814 
-    3500          0.7 0.00091910796    -89.12875            0   -89.117567 
-    3550         0.71 0.00094318459   -90.447312            0   -90.436232 
-    3600         0.72 0.00096989367   -91.750008            0   -91.739046 
-    3650         0.73 0.00099713096   -93.034224            0   -93.023402 
-    3700         0.74 0.0010212995   -94.298186            0   -94.287529 
-    3750         0.75 0.0010391164     -95.5414            0   -95.530926 
-    3800         0.76 0.0010491462   -96.764626            0   -96.754338 
-    3850         0.77 0.0010521238   -97.969346            0    -97.95923 
-    3900         0.78 0.0010500324   -99.156875            0   -99.146899 
-    3950         0.79 0.0010447043   -100.32743            0   -100.31756 
-    4000          0.8 0.0010368986    -101.4796            0   -101.46978 
-    4050         0.81 0.0010263632   -102.61044            0   -102.60064 
-    4100         0.82 0.0010126933   -103.71619            0   -103.70639 
-    4150         0.83 0.00099631895   -104.79338            0   -104.78358 
-    4200         0.84 0.0009789075    -105.8398            0   -105.82998 
-    4250         0.85 0.00096287608   -106.85496            0   -106.84515 
-    4300         0.86 0.00095034023   -107.84011            0   -107.83029 
-    4350         0.87 0.00094219078    -108.7976            0   -108.78778 
-    4400         0.88 0.00093779428   -109.73016            0   -109.72031 
-    4450         0.89 0.0009354459   -110.63996            0   -110.63008 
-    4500          0.9 0.00093342614   -111.52805            0   -111.51812 
-    4550         0.91 0.0009311077   -112.39417            0   -112.38416 
-    4600         0.92 0.00092926689   -113.23706            0   -113.22697 
-    4650         0.93 0.00092921566   -114.05512            0   -114.04495 
-    4700         0.94 0.00093142598   -114.84701            0   -114.83675 
-    4750         0.95 0.00093479851   -115.61197            0   -115.60164 
-    4800         0.96 0.0009369799    -116.3499            0   -116.33951 
-    4850         0.97 0.00093516768   -117.06128            0   -117.05084 
-    4900         0.98 0.00092684411   -117.74695            0   -117.73645 
-    4950         0.99 0.00091046222   -118.40798            0   -118.39742 
-    5000            1 0.00088619957   -119.04554            0   -119.03492 
-Loop time of 128.304 on 1 procs for 5000 steps with 5780 atoms
-
-Performance: 0.673 ns/day, 35.640 hours/ns, 38.970 timesteps/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 24.227     | 24.227     | 24.227     |   0.0 | 18.88
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.081048   | 0.081048   | 0.081048   |   0.0 |  0.06
-Output  | 39.796     | 39.796     | 39.796     |   0.0 | 31.02
-Modify  | 64.112     | 64.112     | 64.112     |   0.0 | 49.97
-Other   |            | 0.08788    |            |       |  0.07
-
-Nlocal:    5780 ave 5780 max 5780 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1065 ave 1065 max 1065 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  92480 ave 92480 max 92480 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 92480
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:02:08
diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4
deleted file mode 100644
index c0f96b8195..0000000000
--- a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4
+++ /dev/null
@@ -1,212 +0,0 @@
-LAMMPS (11 May 2018)
-# layer sc iron atoms (in the [001] plane) in bismuth oxide
-
-clear
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p f
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	sc 3.96
-Lattice spacing in x,y,z = 3.96 3.96 3.96
-region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
-  2 by 2 by 1 MPI processor grid
-create_atoms 	1 box
-Created 5780 atoms
-  Time spent = 0.000355959 secs
-
-# setting mass, mag. moments, and interactions for bfo
-
-mass		1 1.0
-
-set 		group all spin/random 11 2.50
-  5780 settings made for spin/random
-
-pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
-pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
-pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.1 21
-fix 		3 all nve/spin lattice no
-
-timestep	0.0002
-
-compute 	out_mag	 all compute/spin
-compute 	out_pe	 all pe
-compute 	out_ke	 all ke
-compute 	out_temp all temp
-
-variable 	magz	 equal c_out_mag[3]
-variable 	magnorm	 equal c_out_mag[4]
-variable 	emag	 equal c_out_mag[5]
-variable 	tmag	 equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          50
-
-compute outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		5000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.1
-  ghost atom cutoff = 6.1
-  binsize = 3.05, bins = 45 45 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair spin/magelec, perpetual, copy from (1)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 6.862 | 6.862 | 6.862 Mbytes
-Step Time v_magnorm v_emag Temp TotEng 
-       0            0  0.010071723  -0.13298298            0  -0.12034311 
-      50         0.01 0.0098643821   -1.3898985            0   -1.3772103 
-     100         0.02  0.009652621   -2.6381677            0   -2.6254222 
-     150         0.03 0.0094342234   -3.8784007            0   -3.8656019 
-     200         0.04  0.009207483   -5.1114411            0   -5.0986001 
-     250         0.05 0.0089713114   -6.3380611            0   -6.3251904 
-     300         0.06 0.0087256079   -7.5587787            0   -7.5458894 
-     350         0.07 0.0084715546   -8.7738491            0   -8.7609521 
-     400         0.08 0.0082114858   -9.9833855            0   -9.9704932 
-     450         0.09 0.0079483242    -11.18751            0   -11.174637 
-     500          0.1 0.0076849711   -12.386462            0    -12.37362 
-     550         0.11 0.0074240638   -13.580633            0   -13.567832 
-     600         0.12 0.0071680697   -14.770519            0   -14.757759 
-     650         0.13 0.0069192724   -15.956579            0   -15.943853 
-     700         0.14 0.0066793493   -17.139049            0   -17.126343 
-     750         0.15 0.0064488035   -18.317803            0   -18.305099 
-     800         0.16 0.0062267569   -19.492336            0   -19.479616 
-     850         0.17 0.0060112233   -20.661925            0   -20.649176 
-     900         0.18  0.005799525   -21.825931            0   -21.813141 
-     950         0.19 0.0055886511    -22.98413            0   -22.971297 
-    1000          0.2 0.0053757923   -24.136967            0   -24.124095 
-    1050         0.21 0.0051592265   -25.285621            0   -25.272717 
-    1100         0.22 0.0049391664   -26.431928            0   -26.419004 
-    1150         0.23 0.0047179153   -27.578212            0   -27.565281 
-    1200         0.24 0.0044991009   -28.727051            0   -28.714128 
-    1250         0.25 0.0042864039   -29.880967            0   -29.868062 
-    1300         0.26  0.004082448   -31.042054            0   -31.029174 
-    1350         0.27 0.0038883012    -32.21165            0   -32.198795 
-    1400         0.28 0.0037036599   -33.390159            0   -33.377326 
-    1450         0.29 0.0035274817   -34.577121            0   -34.564302 
-    1500          0.3 0.0033587208   -35.771483            0   -35.758672 
-    1550         0.31 0.0031969501   -36.971996            0    -36.95919 
-    1600         0.32 0.0030429079   -38.177601            0   -38.164801 
-    1650         0.33 0.0028989801   -39.387757            0   -39.374962 
-    1700         0.34 0.0027692022   -40.602666            0   -40.589873 
-    1750         0.35 0.0026581401   -41.823341            0    -41.81054 
-    1800         0.36  0.002568699    -43.05145            0   -43.038628 
-    1850         0.37 0.0025001242   -44.288966            0   -44.276111 
-    1900         0.38 0.0024477808   -45.537752            0    -45.52486 
-    1950         0.39 0.0024050056   -46.799255            0   -46.786336 
-    2000          0.4  0.002365704   -48.074388            0   -48.061466 
-    2050         0.41 0.0023260854   -49.363587            0   -49.350695 
-    2100         0.42  0.002284834   -50.666866            0   -50.654039 
-    2150         0.43 0.0022419771   -51.983781            0   -51.971055 
-    2200         0.44 0.0021972518    -53.31336            0   -53.300764 
-    2250         0.45 0.0021488333   -54.654121            0   -54.641676 
-    2300         0.46 0.0020929494   -56.004207            0   -55.991918 
-    2350         0.47 0.0020244612   -57.361586            0   -57.349441 
-    2400         0.48 0.0019382262    -58.72428            0   -58.712247 
-    2450         0.49  0.001830943   -60.090639            0   -60.078671 
-    2500          0.5 0.0017030446   -61.459658            0   -61.447704 
-    2550         0.51 0.0015599459   -62.831213            0   -62.819237 
-    2600         0.52 0.0014117562   -64.206088            0   -64.194074 
-    2650         0.53  0.001270995     -65.5857            0   -65.573657 
-    2700         0.54  0.001149046   -66.971565            0   -66.959515 
-    2750         0.55 0.0010530098   -68.364663            0   -68.352635 
-    2800         0.56 0.00098415418   -69.765002            0   -69.753017 
-    2850         0.57 0.00093809402   -71.171532            0   -71.159598 
-    2900         0.58 0.00090657031    -72.58234            0   -72.570459 
-    2950         0.59 0.00088069773   -73.994931            0   -73.983099 
-    3000          0.6 0.00085472731   -75.406507            0    -75.39472 
-    3050         0.61 0.00082842975   -76.814319            0   -76.802575 
-    3100         0.62 0.00080642669   -78.216074            0   -78.204373 
-    3150         0.63   0.00079464   -79.610246            0    -79.59859 
-    3200         0.64 0.00079623049   -80.996103            0   -80.984494 
-    3250         0.65 0.00080980416   -82.373461            0   -82.361903 
-    3300         0.66 0.00083070997   -83.742356            0   -83.730856 
-    3350         0.67 0.00085389223   -85.102809            0   -85.091374 
-    3400         0.68 0.00087624159   -86.454619            0    -86.44326 
-    3450         0.69 0.00089742086    -87.79709            0   -87.785815 
-    3500          0.7 0.00091910931    -89.12875            0   -89.117568 
-    3550         0.71 0.00094318635   -90.447312            0   -90.436233 
-    3600         0.72 0.00096989594   -91.750008            0   -91.739047 
-    3650         0.73 0.00099713386   -93.034224            0   -93.023403 
-    3700         0.74 0.0010213031   -94.298186            0   -94.287529 
-    3750         0.75 0.0010391209   -95.541401            0   -95.530926 
-    3800         0.76 0.0010491514   -96.764626            0   -96.754339 
-    3850         0.77 0.0010521296   -97.969347            0   -97.959231 
-    3900         0.78 0.0010500386   -99.156876            0   -99.146899 
-    3950         0.79 0.0010447106   -100.32743            0   -100.31756 
-    4000          0.8 0.0010369046    -101.4796            0   -101.46978 
-    4050         0.81 0.0010263688   -102.61044            0   -102.60064 
-    4100         0.82 0.0010126985   -103.71619            0   -103.70639 
-    4150         0.83 0.00099632366   -104.79338            0   -104.78358 
-    4200         0.84 0.00097891183    -105.8398            0   -105.82998 
-    4250         0.85 0.00096288003   -106.85496            0   -106.84515 
-    4300         0.86 0.00095034371   -107.84011            0   -107.83029 
-    4350         0.87 0.00094219371    -108.7976            0   -108.78778 
-    4400         0.88 0.00093779663   -109.73016            0   -109.72031 
-    4450         0.89 0.00093544766   -110.63996            0   -110.63008 
-    4500          0.9 0.00093342739   -111.52805            0   -111.51812 
-    4550         0.91 0.00093110855   -112.39417            0   -112.38416 
-    4600         0.92 0.00092926746   -113.23706            0   -113.22697 
-    4650         0.93 0.00092921608   -114.05512            0   -114.04495 
-    4700         0.94 0.0009314263   -114.84701            0   -114.83675 
-    4750         0.95 0.0009347987   -115.61197            0   -115.60164 
-    4800         0.96 0.00093697985    -116.3499            0   -116.33951 
-    4850         0.97 0.00093516726   -117.06128            0   -117.05084 
-    4900         0.98 0.00092684316   -117.74695            0   -117.73645 
-    4950         0.99 0.00091046061   -118.40798            0   -118.39742 
-    5000            1 0.00088619727   -119.04554            0   -119.03492 
-Loop time of 37.142 on 4 procs for 5000 steps with 5780 atoms
-
-Performance: 2.326 ns/day, 10.317 hours/ns, 134.619 timesteps/s
-98.7% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 6.2804     | 6.3487     | 6.4569     |   2.7 | 17.09
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.15385    | 0.27957    | 0.36215    |  14.6 |  0.75
-Output  | 10.573     | 10.784     | 10.994     |   4.8 | 29.03
-Modify  | 19.48      | 19.707     | 19.925     |   3.7 | 53.06
-Other   |            | 0.02255    |            |       |  0.06
-
-Nlocal:    1445 ave 1445 max 1445 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    555 ave 555 max 555 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  23120 ave 23120 max 23120 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 92480
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:37
diff --git a/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1 b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1
new file mode 100644
index 0000000000..b14210e9d0
--- /dev/null
+++ b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.1
@@ -0,0 +1,167 @@
+LAMMPS (30 Oct 2019)
+# layer sc iron atoms (in the [001] plane) in bismuth oxide
+
+units 		metal
+atom_style 	spin
+dimension 	3
+boundary 	p p f
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00226784 secs
+
+# setting mass, mag. moments, and interactions for bfo
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+#pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice frozen
+
+timestep	0.0002
+
+compute 	out_mag	 all spin
+compute 	out_pe	 all pe
+compute 	out_ke	 all ke
+compute 	out_temp all temp
+
+variable 	magz	 equal c_out_mag[3]
+variable 	magnorm	 equal c_out_mag[4]
+variable 	emag	 equal c_out_mag[5]
+variable 	tmag	 equal c_out_mag[6]
+
+#thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo_style    custom step time v_magnorm pe ke v_emag temp etotal
+thermo          10
+
+compute outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		500
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.154 | 8.154 | 8.154 Mbytes
+Step Time v_magnorm PotEng KinEng v_emag Temp TotEng 
+       0            0  0.010071723 -0.059343109            0  -0.13132609            0 -0.059343109 
+      10        0.002   0.01003044  -0.18537022            0  -0.38338861            0  -0.18537022 
+      20        0.004 0.0099890716  -0.31121926            0  -0.63509581            0  -0.31121926 
+      30        0.006 0.0099475919  -0.43689013            0  -0.88644739            0  -0.43689013 
+      40        0.008 0.0099059782   -0.5623833            0   -1.1374442            0   -0.5623833 
+      50         0.01 0.0098642085  -0.68769978            0    -1.388088            0  -0.68769978 
+      60        0.012 0.0098222618  -0.81284106            0   -1.6383818            0  -0.81284106 
+      70        0.014 0.0097801186  -0.93780907            0   -1.8883294            0  -0.93780907 
+      80        0.016 0.0097377603   -1.0626062            0   -2.1379352            0   -1.0626062 
+      90        0.018 0.0096951693    -1.187235            0   -2.3872045            0    -1.187235 
+     100         0.02 0.0096523288   -1.3116986            0   -2.6361432            0   -1.3116986 
+     110        0.022 0.0096092227   -1.4360002            0   -2.8847577            0   -1.4360002 
+     120        0.024  0.009565836   -1.5601431            0   -3.1330547            0   -1.5601431 
+     130        0.026 0.0095221542   -1.6841309            0   -3.3810411            0   -1.6841309 
+     140        0.028 0.0094781635   -1.8079673            0   -3.6287241            0   -1.8079673 
+     150         0.03 0.0094338509   -1.9316557            0   -3.8761109            0   -1.9316557 
+     160        0.032 0.0093892044   -2.0551997            0   -4.1232085            0   -2.0551997 
+     170        0.034 0.0093442126    -2.178603            0    -4.370024            0    -2.178603 
+     180        0.036 0.0092988654   -2.3018687            0   -4.6165639            0   -2.3018687 
+     190        0.038 0.0092531537   -2.4250002            0   -4.8628348            0   -2.4250002 
+     200         0.04 0.0092070698   -2.5480003            0   -5.1088426            0   -2.5480003 
+     210        0.042 0.0091606073    -2.670872            0   -5.3545929            0    -2.670872 
+     220        0.044 0.0091137617   -2.7936178            0   -5.6000909            0   -2.7936178 
+     230        0.046 0.0090665298   -2.9162399            0   -5.8453412            0   -2.9162399 
+     240        0.048 0.0090189108   -3.0387405            0   -6.0903478            0   -3.0387405 
+     250         0.05 0.0089709056   -3.1611214            0   -6.3351146            0   -3.1611214 
+     260        0.052 0.0089225173   -3.2833841            0   -6.5796445            0   -3.2833841 
+     270        0.054 0.0088737511   -3.4055299            0   -6.8239403            0   -3.4055299 
+     280        0.056 0.0088246147     -3.52756            0   -7.0680043            0     -3.52756 
+     290        0.058 0.0087751176   -3.6494754            0   -7.3118383            0   -3.6494754 
+     300         0.06  0.008725272   -3.7712768            0   -7.5554438            0   -3.7712768 
+     310        0.062 0.0086750916   -3.8929648            0   -7.7988222            0   -3.8929648 
+     320        0.064 0.0086245927   -4.0145399            0   -8.0419744            0   -4.0145399 
+     330        0.066 0.0085737928   -4.1360026            0   -8.2849013            0   -4.1360026 
+     340        0.068 0.0085227116   -4.2573532            0   -8.5276035            0   -4.2573532 
+     350         0.07 0.0084713698    -4.378592            0   -8.7700818            0    -4.378592 
+     360        0.072 0.0084197895   -4.4997194            0   -9.0123367            0   -4.4997194 
+     370        0.074 0.0083679936   -4.6207358            0   -9.2543688            0   -4.6207358 
+     380        0.076 0.0083160058   -4.7416414            0    -9.496179            0   -4.7416414 
+     390        0.078 0.0082638503   -4.8624367            0   -9.7377681            0   -4.8624367 
+     400         0.08 0.0082115512   -4.9831222            0   -9.9791371            0   -4.9831222 
+     410        0.082 0.0081591329   -5.1036986            0   -10.220287            0   -5.1036986 
+     420        0.084 0.0081066195   -5.2241665            0    -10.46122            0   -5.2241665 
+     430        0.086 0.0080540347   -5.3445267            0   -10.701936            0   -5.3445267 
+     440        0.088  0.008001402   -5.4647802            0   -10.942439            0   -5.4647802 
+     450         0.09 0.0079487439   -5.5849281            0    -11.18273            0   -5.5849281 
+     460        0.092 0.0078960829   -5.7049716            0   -11.422811            0   -5.7049716 
+     470        0.094 0.0078434404    -5.824912            0   -11.662686            0    -5.824912 
+     480        0.096 0.0077908378   -5.9447508            0   -11.902357            0   -5.9447508 
+     490        0.098 0.0077382955   -6.0644896            0   -12.141828            0   -6.0644896 
+     500          0.1 0.0076858338   -6.1841301            0   -12.381101            0   -6.1841301 
+Loop time of 13.543 on 1 procs for 500 steps with 5780 atoms
+
+Performance: 0.638 ns/day, 37.619 hours/ns, 36.919 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.8138     | 3.8138     | 3.8138     |   0.0 | 28.16
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.011875   | 0.011875   | 0.011875   |   0.0 |  0.09
+Output  | 0.049726   | 0.049726   | 0.049726   |   0.0 |  0.37
+Modify  | 9.655      | 9.655      | 9.655      |   0.0 | 71.29
+Other   |            | 0.01262    |            |       |  0.09
+
+Nlocal:    5780 ave 5780 max 5780 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1065 ave 1065 max 1065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  92480 ave 92480 max 92480 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:13
diff --git a/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4 b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4
new file mode 100644
index 0000000000..8c701c93c1
--- /dev/null
+++ b/examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4
@@ -0,0 +1,167 @@
+LAMMPS (30 Oct 2019)
+# layer sc iron atoms (in the [001] plane) in bismuth oxide
+
+units 		metal
+atom_style 	spin
+dimension 	3
+boundary 	p p f
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00149798 secs
+
+# setting mass, mag. moments, and interactions for bfo
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+#pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice frozen
+
+timestep	0.0002
+
+compute 	out_mag	 all spin
+compute 	out_pe	 all pe
+compute 	out_ke	 all ke
+compute 	out_temp all temp
+
+variable 	magz	 equal c_out_mag[3]
+variable 	magnorm	 equal c_out_mag[4]
+variable 	emag	 equal c_out_mag[5]
+variable 	tmag	 equal c_out_mag[6]
+
+#thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo_style    custom step time v_magnorm pe ke v_emag temp etotal
+thermo          10
+
+compute outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		500
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.744 | 7.744 | 7.744 Mbytes
+Step Time v_magnorm PotEng KinEng v_emag Temp TotEng 
+       0            0  0.010071723  -0.11868622            0  -0.12966919            0  -0.11868622 
+      10        0.002  0.010030399  -0.37068593            0  -0.38171598            0  -0.37068593 
+      20        0.004 0.0099889925   -0.6223216            0   -0.6334048            0   -0.6223216 
+      30        0.006 0.0099474775  -0.87359359            0   -0.8847354            0  -0.87359359 
+      40        0.008 0.0099058307   -1.1245034            0   -1.1357086            0   -1.1245034 
+      50         0.01 0.0098640297   -1.3750538            0   -1.3863265            0   -1.3750538 
+      60        0.012 0.0098220535   -1.6252482            0   -1.6365919            0   -1.6252482 
+      70        0.014 0.0097798823   -1.8750914            0   -1.8865086            0   -1.8750914 
+      80        0.016 0.0097374973   -2.1245886            0   -2.1360814            0   -2.1245886 
+      90        0.018 0.0096948808   -2.3737458            0   -2.3853155            0   -2.3737458 
+     100         0.02 0.0096520159   -2.6225698            0   -2.6342168            0   -2.6225698 
+     110        0.022 0.0096088866   -2.8710677            0   -2.8827919            0   -2.8710677 
+     120        0.024 0.0095654776   -3.1192469            0   -3.1310475            0   -3.1192469 
+     130        0.026 0.0095217746    -3.367115            0   -3.3789906            0    -3.367115 
+     140        0.028 0.0094777638     -3.61468            0   -3.6266285            0     -3.61468 
+     150         0.03 0.0094334323   -3.8619496            0   -3.8739683            0   -3.8619496 
+     160        0.032 0.0093887679   -4.1089316            0   -4.1210173            0   -4.1089316 
+     170        0.034 0.0093437596   -4.3556335            0   -4.3677824            0   -4.3556335 
+     180        0.036 0.0092983972   -4.6020625            0   -4.6142704            0   -4.6020625 
+     190        0.038 0.0092526717   -4.8482255            0   -4.8604877            0   -4.8482255 
+     200         0.04 0.0092065755   -5.0941291            0   -5.1064403            0   -5.0941291 
+     210        0.042 0.0091601024   -5.3397792            0   -5.3521339            0   -5.3397792 
+     220        0.044 0.0091132478   -5.5851813            0   -5.5975736            0   -5.5851813 
+     230        0.046 0.0090660089   -5.8303404            0    -5.842764            0   -5.8303404 
+     240        0.048 0.0090183847   -6.0752609            0   -6.0877092            0   -6.0752609 
+     250         0.05 0.0089703764   -6.3199467            0   -6.3324129            0   -6.3199467 
+     260        0.052 0.0089219873   -6.5644011            0   -6.5768782            0   -6.5644011 
+     270        0.054 0.0088732228    -6.808627            0   -6.8211078            0    -6.808627 
+     280        0.056 0.0088240906   -7.0526266            0   -7.0651038            0   -7.0526266 
+     290        0.058 0.0087746006    -7.296402            0   -7.3088682            0    -7.296402 
+     300         0.06 0.0087247648   -7.5399545            0   -7.5524024            0   -7.5399545 
+     310        0.062 0.0086745976   -7.7832854            0   -7.7957077            0   -7.7832854 
+     320        0.064 0.0086241149   -8.0263956            0    -8.038785            0   -8.0263956 
+     330        0.066  0.008573335   -8.2692858            0    -8.281635            0   -8.2692858 
+     340        0.068 0.0085222772   -8.5119564            0   -8.5242586            0   -8.5119564 
+     350         0.07 0.0084709627   -8.7544078            0   -8.7666562            0   -8.7544078 
+     360        0.072 0.0084194136   -8.9966403            0   -9.0088285            0   -8.9966403 
+     370        0.074  0.008367653   -9.2386543            0   -9.2507761            0   -9.2386543 
+     380        0.076 0.0083157046   -9.4804501            0   -9.4924997            0   -9.4804501 
+     390        0.078 0.0082635925   -9.7220281            0   -9.7340001            0   -9.7220281 
+     400         0.08 0.0082113412   -9.9633888            0   -9.9752784            0   -9.9633888 
+     410        0.082 0.0081589747   -10.204533            0   -10.216336            0   -10.204533 
+     420        0.084 0.0081065173   -10.445462            0   -10.457173            0   -10.445462 
+     430        0.086 0.0080539925   -10.686176            0   -10.697793            0   -10.686176 
+     440        0.088 0.0080014235   -10.926676            0   -10.938197            0   -10.926676 
+     450         0.09 0.0079488329   -11.166966            0   -11.178387            0   -11.166966 
+     460        0.092 0.0078962427   -11.407045            0   -11.418366            0   -11.407045 
+     470        0.094 0.0078436743   -11.646917            0   -11.658136            0   -11.646917 
+     480        0.096 0.0077911486   -11.886583            0     -11.8977            0   -11.886583 
+     490        0.098  0.007738686   -12.126047            0   -12.137063            0   -12.126047 
+     500          0.1 0.0076863062   -12.365311            0   -12.376226            0   -12.365311 
+Loop time of 3.94852 on 4 procs for 500 steps with 5780 atoms
+
+Performance: 2.188 ns/day, 10.968 hours/ns, 126.630 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.97416    | 0.98668    | 1.0022     |   1.0 | 24.99
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.032618   | 0.04948    | 0.062614   |   5.0 |  1.25
+Output  | 0.014166   | 0.014229   | 0.014374   |   0.1 |  0.36
+Modify  | 2.8947     | 2.8957     | 2.8965     |   0.0 | 73.34
+Other   |            | 0.002385   |            |       |  0.06
+
+Nlocal:    1445 ave 1445 max 1445 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    555 ave 555 max 555 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  23120 ave 23120 max 23120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
index ea98eeba94..dd9ed890ee 100644
--- a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
+++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
@@ -35,7 +35,7 @@ fix_modify 	1 energy yes
 
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -57,7 +57,7 @@ variable 	tmag      equal c_out_mag[6]
 thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
 thermo          50
 
-#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+# compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+# dump 		1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
 run 		1000
diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1
deleted file mode 100644
index d832b0001a..0000000000
--- a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1
+++ /dev/null
@@ -1,142 +0,0 @@
-LAMMPS (11 May 2018)
-# fcc cobalt in a 3d periodic box
-
-clear
-units		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice fcc 	3.54
-Lattice spacing in x,y,z = 3.54 3.54 3.54
-region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  Time spent = 0.000651121 secs
-
-# setting mass, mag. moments, and interactions for fcc cobalt
-
-mass		1 58.93
-
-#set 		group all spin/random 31 1.72
-set 		group all spin 1.72 0.0 0.0 1.0
-  500 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix_modify 	1 energy yes
-
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-thermo_style	custom f_1
-
-variable 	magx      equal c_out_mag[1]
-variable 	magy      equal c_out_mag[2]
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
-thermo          50
-
-#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		1000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.59954
-  ghost atom cutoff = 6.59954
-  binsize = 3.29977, bins = 6 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes
-Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
-       0            0  0.049785486            0            0            1   -187.94116    100.00543   -2372.4636 
-      50        0.005  0.049785486            0            0            1   -187.94112    95.094679   -2372.4636 
-     100         0.01  0.049785486            0            0            1   -187.94071    81.578321   -2372.4636 
-     150        0.015  0.049785486            0            0            1   -187.93912    62.802727   -2372.4636 
-     200         0.02  0.049785486            0            0            1   -187.93551     43.35108   -2372.4636 
-     250        0.025  0.049785486            0            0            1   -187.92942    27.749821   -2372.4636 
-     300         0.03  0.049785486            0            0            1   -187.92118    19.149389   -2372.4636 
-     350        0.035  0.049785486            0            0            1   -187.91199    18.453387   -2372.4636 
-     400         0.04  0.049785486            0            0            1   -187.90364    24.249423   -2372.4636 
-     450        0.045  0.049785486            0            0            1   -187.89806    33.548008   -2372.4636 
-     500         0.05  0.049785486            0            0            1   -187.89668    42.973172   -2372.4636 
-     550        0.055  0.049785486            0            0            1       -187.9    49.902539   -2372.4636 
-     600         0.06  0.049785486            0            0            1   -187.90735    53.166772   -2372.4636 
-     650        0.065  0.049785486            0            0            1   -187.91706    53.153416   -2372.4636 
-     700         0.07  0.049785486            0            0            1   -187.92692    51.377187   -2372.4636 
-     750        0.075  0.049785486            0            0            1    -187.9348    49.725449   -2372.4636 
-     800         0.08  0.049785486            0            0            1   -187.93921    49.663576   -2372.4636 
-     850        0.085  0.049785486            0            0            1   -187.93974    51.681567   -2372.4636 
-     900         0.09  0.049785486            0            0            1     -187.937    55.166554   -2372.4636 
-     950        0.095  0.049785486            0            0            1   -187.93239    58.718232   -2372.4636 
-    1000          0.1  0.049785486            0            0            1   -187.92755     60.75567   -2372.4636 
-Loop time of 4.1303 on 1 procs for 1000 steps with 500 atoms
-
-Performance: 2.092 ns/day, 11.473 hours/ns, 242.113 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.142      | 2.142      | 2.142      |   0.0 | 51.86
-Neigh   | 0.0094573  | 0.0094573  | 0.0094573  |   0.0 |  0.23
-Comm    | 0.023293   | 0.023293   | 0.023293   |   0.0 |  0.56
-Output  | 0.00031972 | 0.00031972 | 0.00031972 |   0.0 |  0.01
-Modify  | 1.9488     | 1.9488     | 1.9488     |   0.0 | 47.18
-Other   |            | 0.006488   |            |       |  0.16
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1956 ave 1956 max 1956 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    24065 ave 24065 max 24065 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  48130 ave 48130 max 48130 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 48130
-Ave neighs/atom = 96.26
-Neighbor list builds = 6
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:04
diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4
deleted file mode 100644
index 358d7cfc7a..0000000000
--- a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4
+++ /dev/null
@@ -1,142 +0,0 @@
-LAMMPS (11 May 2018)
-# fcc cobalt in a 3d periodic box
-
-clear
-units		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice fcc 	3.54
-Lattice spacing in x,y,z = 3.54 3.54 3.54
-region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  Time spent = 0.000240088 secs
-
-# setting mass, mag. moments, and interactions for fcc cobalt
-
-mass		1 58.93
-
-#set 		group all spin/random 31 1.72
-set 		group all spin 1.72 0.0 0.0 1.0
-  500 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix_modify 	1 energy yes
-
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-thermo_style	custom f_1
-
-variable 	magx      equal c_out_mag[1]
-variable 	magy      equal c_out_mag[2]
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
-thermo          50
-
-#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		1000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.59954
-  ghost atom cutoff = 6.59954
-  binsize = 3.29977, bins = 6 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.163 | 5.163 | 5.163 Mbytes
-Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
-       0            0  0.049785486            0            0            1   -187.94116    100.00543   -2372.4636 
-      50        0.005  0.049785486            0            0            1   -187.94101    95.174807   -2372.4636 
-     100         0.01  0.049785486            0            0            1   -187.94029    81.854304   -2372.4636 
-     150        0.015  0.049785486            0            0            1   -187.93834    63.270938   -2372.4636 
-     200         0.02  0.049785486            0            0            1   -187.93446    43.867262   -2372.4636 
-     250        0.025  0.049785486            0            0            1   -187.92831    28.075261   -2372.4636 
-     300         0.03  0.049785486            0            0            1   -187.92031    19.046222   -2372.4636 
-     350        0.035  0.049785486            0            0            1   -187.91161     17.79071   -2372.4636 
-     400         0.04  0.049785486            0            0            1    -187.9039    23.079994   -2372.4636 
-     450        0.045  0.049785486            0            0            1   -187.89895    32.127316   -2372.4636 
-     500         0.05  0.049785486            0            0            1   -187.89801    41.709644   -2372.4636 
-     550        0.055  0.049785486            0            0            1   -187.90146    49.246292   -2372.4636 
-     600         0.06  0.049785486            0            0            1   -187.90859    53.465535   -2372.4636 
-     650        0.065  0.049785486            0            0            1   -187.91778    54.522857   -2372.4636 
-     700         0.07  0.049785486            0            0            1    -187.9269    53.635521   -2372.4636 
-     750        0.075  0.049785486            0            0            1   -187.93396    52.419678   -2372.4636 
-     800         0.08  0.049785486            0            0            1    -187.9376    52.176558   -2372.4636 
-     850        0.085  0.049785486            0            0            1   -187.93744    53.380592   -2372.4636 
-     900         0.09  0.049785486            0            0            1   -187.93412    55.551378   -2372.4636 
-     950        0.095  0.049785486            0            0            1   -187.92902    57.540047   -2372.4636 
-    1000          0.1  0.049785486            0            0            1   -187.92378    58.088674   -2372.4636 
-Loop time of 1.71411 on 4 procs for 1000 steps with 500 atoms
-
-Performance: 5.041 ns/day, 4.761 hours/ns, 583.392 timesteps/s
-97.7% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.54717    | 0.57392    | 0.58784    |   2.1 | 33.48
-Neigh   | 0.0023484  | 0.0025793  | 0.0026793  |   0.3 |  0.15
-Comm    | 0.058548   | 0.073335   | 0.10006    |   5.9 |  4.28
-Output  | 0.00042272 | 0.00079203 | 0.0018559  |   0.0 |  0.05
-Modify  | 1.0577     | 1.0611     | 1.0625     |   0.2 | 61.90
-Other   |            | 0.00239    |            |       |  0.14
-
-Nlocal:    125 ave 133 max 116 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Nghost:    1099 ave 1108 max 1091 min
-Histogram: 1 0 0 0 2 0 0 0 0 1
-Neighs:    6032.5 ave 6417 max 5489 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-FullNghs:  12065 ave 13062 max 10970 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-
-Total # of neighbors = 48260
-Ave neighs/atom = 96.52
-Neighbor list builds = 6
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01
diff --git a/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1 b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1
new file mode 100644
index 0000000000..06774d0858
--- /dev/null
+++ b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1
@@ -0,0 +1,142 @@
+LAMMPS (30 Oct 2019)
+# fcc cobalt in a 3d periodic box
+
+clear
+units		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice fcc 	3.54
+Lattice spacing in x,y,z = 3.54 3.54 3.54
+region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000470161 secs
+
+# setting mass, mag. moments, and interactions for fcc cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+  500 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+thermo_style	custom f_1
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
+thermo          50
+
+# compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+# dump 		1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.718 | 5.718 | 5.718 Mbytes
+Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
+       0            0 -0.099570972            0            0            1   -188.09051    100.00543   -2278.6175 
+      50        0.005 -0.099570972            0            0            1   -188.09048    95.094679   -2278.6175 
+     100         0.01 -0.099570972            0            0            1   -188.09007    81.578321   -2278.6177 
+     150        0.015 -0.099570972            0            0            1   -188.08848    62.802727   -2278.6185 
+     200         0.02 -0.099570972            0            0            1   -188.08487     43.35108   -2278.6203 
+     250        0.025 -0.099570972            0            0            1   -188.07877    27.749821   -2278.6233 
+     300         0.03 -0.099570972            0            0            1   -188.07054    19.149389   -2278.6274 
+     350        0.035 -0.099570972            0            0            1   -188.06135    18.453387    -2278.632 
+     400         0.04 -0.099570972            0            0            1     -188.053    24.249423   -2278.6362 
+     450        0.045 -0.099570972            0            0            1   -188.04742    33.548008    -2278.639 
+     500         0.05 -0.099570972            0            0            1   -188.04604    42.973172   -2278.6397 
+     550        0.055 -0.099570972            0            0            1   -188.04935    49.902539    -2278.638 
+     600         0.06 -0.099570972            0            0            1    -188.0567    53.166772   -2278.6344 
+     650        0.065 -0.099570972            0            0            1   -188.06642    53.153416   -2278.6295 
+     700         0.07 -0.099570972            0            0            1   -188.07628    51.377187   -2278.6246 
+     750        0.075 -0.099570972            0            0            1   -188.08415    49.725449   -2278.6206 
+     800         0.08 -0.099570972            0            0            1   -188.08857    49.663576   -2278.6184 
+     850        0.085 -0.099570972            0            0            1    -188.0891    51.681567   -2278.6182 
+     900         0.09 -0.099570972            0            0            1   -188.08636    55.166554   -2278.6195 
+     950        0.095 -0.099570972            0            0            1   -188.08174    58.718232   -2278.6218 
+    1000          0.1 -0.099570972            0            0            1    -188.0769     60.75567   -2278.6243 
+Loop time of 4.6196 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 1.870 ns/day, 12.832 hours/ns, 216.469 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.3116     | 2.3116     | 2.3116     |   0.0 | 50.04
+Neigh   | 0.011227   | 0.011227   | 0.011227   |   0.0 |  0.24
+Comm    | 0.032837   | 0.032837   | 0.032837   |   0.0 |  0.71
+Output  | 0.00039411 | 0.00039411 | 0.00039411 |   0.0 |  0.01
+Modify  | 2.2584     | 2.2584     | 2.2584     |   0.0 | 48.89
+Other   |            | 0.005152   |            |       |  0.11
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    24065 ave 24065 max 24065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  48130 ave 48130 max 48130 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 48130
+Ave neighs/atom = 96.26
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4 b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4
new file mode 100644
index 0000000000..331ed60315
--- /dev/null
+++ b/examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4
@@ -0,0 +1,142 @@
+LAMMPS (30 Oct 2019)
+# fcc cobalt in a 3d periodic box
+
+clear
+units		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice fcc 	3.54
+Lattice spacing in x,y,z = 3.54 3.54 3.54
+region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000808001 secs
+
+# setting mass, mag. moments, and interactions for fcc cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+  500 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+thermo_style	custom f_1
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
+thermo          50
+
+# compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+# dump 		1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.664 | 5.664 | 5.664 Mbytes
+Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
+       0            0 -0.099570972            0            0            1   -188.09051    100.00543   -2372.6129 
+      50        0.005 -0.099570972            0            0            1   -188.09036    95.174807   -2372.6129 
+     100         0.01 -0.099570972            0            0            1   -188.08965    81.854304   -2372.6129 
+     150        0.015 -0.099570972            0            0            1    -188.0877    63.270938   -2372.6129 
+     200         0.02 -0.099570972            0            0            1   -188.08381    43.867262   -2372.6129 
+     250        0.025 -0.099570972            0            0            1   -188.07767    28.075261   -2372.6129 
+     300         0.03 -0.099570972            0            0            1   -188.06966    19.046222   -2372.6129 
+     350        0.035 -0.099570972            0            0            1   -188.06096     17.79071   -2372.6129 
+     400         0.04 -0.099570972            0            0            1   -188.05326    23.079994   -2372.6129 
+     450        0.045 -0.099570972            0            0            1   -188.04831    32.127316   -2372.6129 
+     500         0.05 -0.099570972            0            0            1   -188.04737    41.709644   -2372.6129 
+     550        0.055 -0.099570972            0            0            1   -188.05082    49.246292   -2372.6129 
+     600         0.06 -0.099570972            0            0            1   -188.05795    53.465535   -2372.6129 
+     650        0.065 -0.099570972            0            0            1   -188.06713    54.522857   -2372.6129 
+     700         0.07 -0.099570972            0            0            1   -188.07626    53.635521   -2372.6129 
+     750        0.075 -0.099570972            0            0            1   -188.08332    52.419678   -2372.6129 
+     800         0.08 -0.099570972            0            0            1   -188.08696    52.176558   -2372.6129 
+     850        0.085 -0.099570972            0            0            1    -188.0868    53.380592   -2372.6129 
+     900         0.09 -0.099570972            0            0            1   -188.08348    55.551378   -2372.6129 
+     950        0.095 -0.099570972            0            0            1   -188.07838    57.540047   -2372.6129 
+    1000          0.1 -0.099570972            0            0            1   -188.07314    58.088674   -2372.6129 
+Loop time of 2.54753 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 3.392 ns/day, 7.076 hours/ns, 392.538 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.62017    | 0.6485     | 0.66275    |   2.1 | 25.46
+Neigh   | 0.0027115  | 0.0029724  | 0.0030868  |   0.3 |  0.12
+Comm    | 0.095047   | 0.1102     | 0.13819    |   5.0 |  4.33
+Output  | 0.00039029 | 0.00042999 | 0.00049996 |   0.0 |  0.02
+Modify  | 1.7801     | 1.7834     | 1.7852     |   0.1 | 70.01
+Other   |            | 0.002028   |            |       |  0.08
+
+Nlocal:    125 ave 133 max 116 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:    1099 ave 1108 max 1091 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Neighs:    6032.5 ave 6417 max 5489 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+FullNghs:  12065 ave 13062 max 10970 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+
+Total # of neighbors = 48260
+Ave neighs/atom = 96.52
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
index 3f34838553..dd114202cb 100644
--- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
+++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
@@ -25,8 +25,7 @@ velocity 	all create 100 4928459 rot yes dist gaussian
 
 #pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
 pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy ../examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy Co
-#pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
 pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
 #pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652  
 
@@ -37,7 +36,7 @@ neigh_modify 	every 10 check yes delay 20
 fix 		1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
 #fix 		2 all langevin/spin 0.0 0.0 21
 fix 		2 all langevin/spin 0.0 0.1 21
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 
 timestep	0.0001
 
@@ -52,10 +51,10 @@ variable 	magnorm   equal c_out_mag[4]
 variable 	emag      equal c_out_mag[5]
 variable 	tmag      equal c_out_mag[6]
 
-thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo_style    custom step time v_magnorm v_emag temp press etotal
 thermo          10
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		20000
+run 		1000
diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1
deleted file mode 100644
index 4bb513de18..0000000000
--- a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1
+++ /dev/null
@@ -1,318 +0,0 @@
-LAMMPS (11 May 2018)
-# hcp cobalt in a 3d periodic box
-
-clear
-units	 	metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	hcp 2.5071
-Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  Time spent = 0.000801802 secs
-
-# setting mass, mag. moments, and interactions for hcp cobalt
-
-mass		1 58.93
-
-#set 		group all spin/random 31 1.72
-set 		group all spin 1.72 0.0 0.0 1.0
-  500 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
-
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-fix 		3 all nve/spin lattice yes
-
-timestep	0.0001
-
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          10
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.59954
-  ghost atom cutoff = 6.59954
-  binsize = 3.29977, bins = 4 7 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes
-Step Time v_magnorm v_emag Temp TotEng 
-       0            0            1   -187.29499    100.00543   -2375.8943 
-      10        0.001            1   -187.29714    99.845593   -2375.8943 
-      20        0.002            1   -187.30356    99.367234   -2375.8943 
-      30        0.003            1   -187.31419    98.573996   -2375.8943 
-      40        0.004            1   -187.32896    97.472027   -2375.8943 
-      50        0.005            1   -187.34772    96.069944   -2375.8943 
-      60        0.006            1   -187.37032    94.378764   -2375.8943 
-      70        0.007            1   -187.39656    92.411827   -2375.8943 
-      80        0.008            1    -187.4262    90.184697   -2375.8943 
-      90        0.009            1     -187.459    87.715037   -2375.8943 
-     100         0.01            1   -187.49466    85.022479   -2375.8943 
-     110        0.011            1   -187.53289    82.128462   -2375.8943 
-     120        0.012            1   -187.57334     79.05606   -2375.8943 
-     130        0.013            1   -187.61568     75.82979   -2375.8943 
-     140        0.014            1   -187.65953    72.475403   -2375.8943 
-     150        0.015            1   -187.70453    69.019658   -2375.8943 
-     160        0.016            1   -187.75028    65.490086   -2375.8943 
-     170        0.017            1   -187.79642    61.914735   -2375.8943 
-     180        0.018            1   -187.84254    58.321911   -2375.8943 
-     190        0.019            1   -187.88828    54.739907   -2375.8943 
-     200         0.02            1   -187.93324    51.196728   -2375.8943 
-     210        0.021            1   -187.97708    47.719812   -2375.8943 
-     220        0.022            1   -188.01947    44.335762   -2375.8943 
-     230        0.023            1   -188.06003     41.07007   -2375.8943 
-     240        0.024            1   -188.09853    37.946852   -2375.8944 
-     250        0.025            1   -188.13457    34.988599   -2375.8944 
-     260        0.026            1   -188.16795    32.215943   -2375.8944 
-     270        0.027            1   -188.19851    29.647465   -2375.8944 
-     280        0.028            1   -188.22593    27.299481   -2375.8944 
-     290        0.029            1   -188.25011    25.185896   -2375.8944 
-     300         0.03            1   -188.27095    23.318075   -2375.8945 
-     310        0.031            1    -188.2883     21.70475   -2375.8945 
-     320        0.032            1   -188.30213     20.35194   -2375.8945 
-     330        0.033            1   -188.31251    19.262946   -2375.8945 
-     340        0.034            1   -188.31928    18.438347   -2375.8945 
-     350        0.035            1   -188.32258    17.876036   -2375.8945 
-     360        0.036            1   -188.32249    17.571322   -2375.8945 
-     370        0.037            1   -188.31913    17.517032   -2375.8945 
-     380        0.038            1   -188.31264    17.703653   -2375.8945 
-     390        0.039            1   -188.30321    18.119513   -2375.8945 
-     400         0.04            1   -188.29102    18.750969   -2375.8945 
-     410        0.041            1    -188.2763    19.582631   -2375.8945 
-     420        0.042            1   -188.25929    20.597597   -2375.8945 
-     430        0.043            1   -188.24025    21.777699   -2375.8945 
-     440        0.044            1   -188.21945    23.103765   -2375.8945 
-     450        0.045            1   -188.19719    24.555878   -2375.8946 
-     460        0.046            1   -188.17368    26.113643   -2375.8946 
-     470        0.047            1    -188.1493    27.756439   -2375.8946 
-     480        0.048            1   -188.12429    29.463677   -2375.8946 
-     490        0.049            1   -188.09895     31.21504   -2375.8946 
-     500         0.05            1   -188.07354    32.990713   -2375.8946 
-     510        0.051            1   -188.04832    34.771601   -2375.8945 
-     520        0.052            1   -188.02358    36.539517   -2375.8945 
-     530        0.053            1   -187.99951     38.27736   -2375.8945 
-     540        0.054            1   -187.97636    39.969275   -2375.8945 
-     550        0.055            1   -187.95437    41.600775   -2375.8945 
-     560        0.056            1   -187.93364    43.158863   -2375.8944 
-     570        0.057            1    -187.9144    44.632119   -2375.8944 
-     580        0.058            1   -187.89669    46.010765   -2375.8944 
-     590        0.059            1   -187.88074    47.286714   -2375.8944 
-     600         0.06            1   -187.86658    48.453573   -2375.8944 
-     610        0.061            1   -187.85422    49.506668   -2375.8943 
-     620        0.062            1   -187.84377    50.443021   -2375.8943 
-     630        0.063            1    -187.8352    51.261297   -2375.8943 
-     640        0.064            1    -187.8285    51.961764   -2375.8943 
-     650        0.065            1    -187.8236     52.54622   -2375.8943 
-     660        0.066            1    -187.8205    53.017899   -2375.8943 
-     670        0.067            1   -187.81909    53.381374   -2375.8943 
-     680        0.068            1   -187.81926     53.64244   -2375.8943 
-     690        0.069            1   -187.82092    53.807997   -2375.8943 
-     700         0.07            1   -187.82391    53.885909   -2375.8943 
-     710        0.071            1   -187.82814    53.884865   -2375.8943 
-     720        0.072            1   -187.83339    53.814238   -2375.8943 
-     730        0.073            1   -187.83952     53.68392   -2375.8943 
-     740        0.074            1   -187.84635    53.504185   -2375.8943 
-     750        0.075            1   -187.85375    53.285525   -2375.8943 
-     760        0.076            1   -187.86153    53.038494   -2375.8943 
-     770        0.077            1   -187.86952    52.773567   -2375.8943 
-     780        0.078            1   -187.87758    52.500994   -2375.8943 
-     790        0.079            1   -187.88549    52.230655   -2375.8943 
-     800         0.08            1   -187.89313    51.971933   -2375.8943 
-     810        0.081            1   -187.90035    51.733593   -2375.8943 
-     820        0.082            1   -187.90702    51.523671   -2375.8943 
-     830        0.083            1   -187.91302    51.349376   -2375.8943 
-     840        0.084            1   -187.91824    51.217006   -2375.8943 
-     850        0.085            1    -187.9226    51.131875   -2375.8943 
-     860        0.086            1   -187.92602    51.098259   -2375.8943 
-     870        0.087            1   -187.92844    51.119356   -2375.8943 
-     880        0.088            1   -187.92979    51.197261   -2375.8943 
-     890        0.089            1   -187.93011    51.332955   -2375.8943 
-     900         0.09            1   -187.92937    51.526314   -2375.8943 
-     910        0.091            1   -187.92757     51.77613   -2375.8943 
-     920        0.092            1   -187.92475    52.080145   -2375.8943 
-     930        0.093            1   -187.92096    52.435106   -2375.8943 
-     940        0.094            1   -187.91624    52.836825   -2375.8943 
-     950        0.095            1   -187.91068    53.280251   -2375.8943 
-     960        0.096            1   -187.90435    53.759559   -2375.8943 
-     970        0.097            1   -187.89734    54.268246   -2375.8943 
-     980        0.098            1   -187.88981    54.799223   -2375.8943 
-     990        0.099            1   -187.88185    55.344928   -2375.8943 
-    1000          0.1            1   -187.87357    55.897438   -2375.8943 
-    1010        0.101            1   -187.86511    56.448585   -2375.8943 
-    1020        0.102            1    -187.8566    56.990069   -2375.8943 
-    1030        0.103            1   -187.84817    57.513575   -2375.8943 
-    1040        0.104            1   -187.83995    58.010887   -2375.8943 
-    1050        0.105            1   -187.83208    58.474004   -2375.8943 
-    1060        0.106            1    -187.8247     58.89524   -2375.8943 
-    1070        0.107            1   -187.81789    59.267328   -2375.8943 
-    1080        0.108            1   -187.81177    59.583518   -2375.8943 
-    1090        0.109            1   -187.80646    59.837665   -2375.8943 
-    1100         0.11            1   -187.80204    60.024306   -2375.8943 
-    1110        0.111            1   -187.79861    60.138734   -2375.8943 
-    1120        0.112            1   -187.79625    60.177056   -2375.8943 
-    1130        0.113            1   -187.79497    60.136244   -2375.8943 
-    1140        0.114            1   -187.79485    60.014176   -2375.8943 
-    1150        0.115            1    -187.7959    59.809665   -2375.8943 
-    1160        0.116            1   -187.79811     59.52248   -2375.8943 
-    1170        0.117            1   -187.80157    59.153353   -2375.8943 
-    1180        0.118            1   -187.80618    58.703971   -2375.8943 
-    1190        0.119            1   -187.81193    58.176956   -2375.8943 
-    1200         0.12            1   -187.81879    57.575849   -2375.8943 
-    1210        0.121            1   -187.82668    56.905072   -2375.8943 
-    1220        0.122            1   -187.83554    56.169878   -2375.8943 
-    1230        0.123            1   -187.84528    55.376297   -2375.8943 
-    1240        0.124            1   -187.85581     54.53107   -2375.8943 
-    1250        0.125            1   -187.86702    53.641573   -2375.8943 
-    1260        0.126            1    -187.8788    52.715739   -2375.8943 
-    1270        0.127            1   -187.89103    51.761969   -2375.8943 
-    1280        0.128            1   -187.90358    50.789036   -2375.8943 
-    1290        0.129            1   -187.91632    49.805988   -2375.8943 
-    1300         0.13            1   -187.92911    48.822045   -2375.8943 
-    1310        0.131            1   -187.94182    47.846491   -2375.8943 
-    1320        0.132            1   -187.95428    46.888574   -2375.8943 
-    1330        0.133            1   -187.96643    45.957394   -2375.8943 
-    1340        0.134            1    -187.9781    45.061794   -2375.8943 
-    1350        0.135            1    -187.9892    44.210263   -2375.8943 
-    1360        0.136            1   -187.99955    43.410832   -2375.8943 
-    1370        0.137            1   -188.00907    42.670979   -2375.8943 
-    1380        0.138            1   -188.01767    41.997547   -2375.8943 
-    1390        0.139            1   -188.02525    41.396655   -2375.8943 
-    1400         0.14            1   -188.03177    40.873631   -2375.8944 
-    1410        0.141            1   -188.03711    40.432952   -2375.8944 
-    1420        0.142            1   -188.04124    40.078172   -2375.8944 
-    1430        0.143            1   -188.04413    39.811902   -2375.8944 
-    1440        0.144            1   -188.04575    39.635775   -2375.8944 
-    1450        0.145            1   -188.04607    39.550435   -2375.8943 
-    1460        0.146            1   -188.04515    39.555512   -2375.8943 
-    1470        0.147            1   -188.04298    39.649651   -2375.8943 
-    1480        0.148            1   -188.03961    39.830523   -2375.8943 
-    1490        0.149            1   -188.03508    40.094865   -2375.8943 
-    1500         0.15            1   -188.02944    40.438519   -2375.8943 
-    1510        0.151            1   -188.02275    40.856491   -2375.8943 
-    1520        0.152            1   -188.01515    41.343019   -2375.8943 
-    1530        0.153            1   -188.00671    41.891643   -2375.8943 
-    1540        0.154            1   -187.99753    42.495295   -2375.8943 
-    1550        0.155            1   -187.98772     43.14639   -2375.8943 
-    1560        0.156            1    -187.9774    43.836918   -2375.8943 
-    1570        0.157            1    -187.9667    44.558553   -2375.8943 
-    1580        0.158            1   -187.95576    45.302751   -2375.8943 
-    1590        0.159            1   -187.94466    46.060862   -2375.8943 
-    1600         0.16            1   -187.93356    46.824226   -2375.8943 
-    1610        0.161            1   -187.92257    47.584289   -2375.8943 
-    1620        0.162            1   -187.91183    48.332703   -2375.8943 
-    1630        0.163            1   -187.90145    49.061422   -2375.8943 
-    1640        0.164            1   -187.89155    49.762798   -2375.8943 
-    1650        0.165            1   -187.88222    50.429671   -2375.8943 
-    1660        0.166            1   -187.87357    51.055445   -2375.8943 
-    1670        0.167            1   -187.86569    51.634167   -2375.8943 
-    1680        0.168            1   -187.85864    52.160588   -2375.8943 
-    1690        0.169            1   -187.85249    52.630219   -2375.8943 
-    1700         0.17            1    -187.8473    53.039377   -2375.8943 
-    1710        0.171            1   -187.84311    53.385221   -2375.8943 
-    1720        0.172            1   -187.83994    53.665778   -2375.8943 
-    1730        0.173            1   -187.83781    53.879954   -2375.8943 
-    1740        0.174            1   -187.83671    54.027539   -2375.8943 
-    1750        0.175            1   -187.83663    54.109201   -2375.8943 
-    1760        0.176            1   -187.83753    54.126472   -2375.8943 
-    1770        0.177            1   -187.83941    54.081708   -2375.8943 
-    1780        0.178            1    -187.8422     53.97806   -2375.8943 
-    1790        0.179            1   -187.84584    53.819424   -2375.8943 
-    1800         0.18            1   -187.85025    53.610389   -2375.8943 
-    1810        0.181            1   -187.85535    53.356163   -2375.8943 
-    1820        0.182            1   -187.86105     53.06251   -2375.8943 
-    1830        0.183            1   -187.86723    52.735671   -2375.8943 
-    1840        0.184            1   -187.87384    52.382262   -2375.8943 
-    1850        0.185            1   -187.88075    52.009201   -2375.8943 
-    1860        0.186            1   -187.88784    51.623613   -2375.8943 
-    1870        0.187            1   -187.89501    51.232726   -2375.8943 
-    1880        0.188            1   -187.90214    50.843782   -2375.8943 
-    1890        0.189            1   -187.90912    50.463929   -2375.8943 
-    1900         0.19            1   -187.91585    50.100133   -2375.8943 
-    1910        0.191            1   -187.92222    49.759075   -2375.8943 
-    1920        0.192            1   -187.92814    49.447064   -2375.8943 
-    1930        0.193            1   -187.93351    49.169949   -2375.8943 
-    1940        0.194            1   -187.93826    48.933036   -2375.8943 
-    1950        0.195            1   -187.94232    48.741013   -2375.8943 
-    1960        0.196            1   -187.94561    48.597888   -2375.8943 
-    1970        0.197            1   -187.94809    48.506926   -2375.8943 
-    1980        0.198            1   -187.94972    48.470605   -2375.8943 
-    1990        0.199            1   -187.95047    48.490576   -2375.8943 
-    2000          0.2            1   -187.95033    48.567643   -2375.8943 
-Loop time of 10.5391 on 1 procs for 2000 steps with 500 atoms
-
-Performance: 1.640 ns/day, 14.638 hours/ns, 189.770 timesteps/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 4.9958     | 4.9958     | 4.9958     |   0.0 | 47.40
-Neigh   | 0.020741   | 0.020741   | 0.020741   |   0.0 |  0.20
-Comm    | 0.05899    | 0.05899    | 0.05899    |   0.0 |  0.56
-Output  | 1.1598     | 1.1598     | 1.1598     |   0.0 | 11.00
-Modify  | 4.2885     | 4.2885     | 4.2885     |   0.0 | 40.69
-Other   |            | 0.01522    |            |       |  0.14
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2444 ave 2444 max 2444 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    27041 ave 27041 max 27041 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  54082 ave 54082 max 54082 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 54082
-Ave neighs/atom = 108.164
-Neighbor list builds = 12
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:10
diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4
deleted file mode 100644
index 4e7e6b1b97..0000000000
--- a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4
+++ /dev/null
@@ -1,318 +0,0 @@
-LAMMPS (11 May 2018)
-# hcp cobalt in a 3d periodic box
-
-clear
-units	 	metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	hcp 2.5071
-Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  Time spent = 0.000241518 secs
-
-# setting mass, mag. moments, and interactions for hcp cobalt
-
-mass		1 58.93
-
-#set 		group all spin/random 31 1.72
-set 		group all spin 1.72 0.0 0.0 1.0
-  500 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
-
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-fix 		3 all nve/spin lattice yes
-
-timestep	0.0001
-
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          10
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.59954
-  ghost atom cutoff = 6.59954
-  binsize = 3.29977, bins = 4 7 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.314 | 7.314 Mbytes
-Step Time v_magnorm v_emag Temp TotEng 
-       0            0            1   -187.29499    100.00543   -2375.8943 
-      10        0.001            1   -187.29721    99.841045   -2375.8943 
-      20        0.002            1   -187.30385    99.349208   -2375.8943 
-      30        0.003            1   -187.31485    98.533905   -2375.8943 
-      40        0.004            1   -187.33011    97.401749   -2375.8943 
-      50        0.005            1   -187.34949    95.961938   -2375.8943 
-      60        0.006            1   -187.37283     94.22618   -2375.8943 
-      70        0.007            1   -187.39992    92.208606   -2375.8943 
-      80        0.008            1   -187.43051     89.92566   -2375.8943 
-      90        0.009            1   -187.46434     87.39597   -2375.8943 
-     100         0.01            1    -187.5011    84.640195   -2375.8943 
-     110        0.011            1   -187.54047    81.680862   -2375.8943 
-     120        0.012            1    -187.5821    78.542172   -2375.8943 
-     130        0.013            1   -187.62564    75.249797   -2375.8943 
-     140        0.014            1   -187.67069    71.830656   -2375.8943 
-     150        0.015            1   -187.71686    68.312673   -2375.8943 
-     160        0.016            1   -187.76377    64.724523   -2375.8943 
-     170        0.017            1   -187.81099    61.095365   -2375.8943 
-     180        0.018            1   -187.85814    57.454566   -2375.8943 
-     190        0.019            1   -187.90481    53.831412   -2375.8943 
-     200         0.02            1   -187.95061    50.254822   -2375.8943 
-     210        0.021            1   -187.99517    46.753056   -2375.8943 
-     220        0.022            1   -188.03812    43.353428   -2375.8943 
-     230        0.023            1   -188.07913    40.082023   -2375.8943 
-     240        0.024            1   -188.11787    36.963429   -2375.8943 
-     250        0.025            1   -188.15409    34.020481   -2375.8943 
-     260        0.026            1    -188.1875     31.27403   -2375.8943 
-     270        0.027            1   -188.21782     28.74271   -2375.8943 
-     280        0.028            1    -188.2449     26.44276   -2375.8943 
-     290        0.029            1   -188.26857    24.387875   -2375.8943 
-     300         0.03            1   -188.28877    22.589076   -2375.8944 
-     310        0.031            1   -188.30529    21.054615   -2375.8944 
-     320        0.032            1   -188.31814    19.789913   -2375.8944 
-     330        0.033            1    -188.3273    18.797563   -2375.8944 
-     340        0.034            1   -188.33284    18.077336   -2375.8944 
-     350        0.035            1   -188.33478    17.626237   -2375.8945 
-     360        0.036            1   -188.33319    17.438611   -2375.8945 
-     370        0.037            1   -188.32824    17.506247   -2375.8945 
-     380        0.038            1   -188.32007    17.818564   -2375.8945 
-     390        0.039            1   -188.30888    18.362769   -2375.8945 
-     400         0.04            1    -188.2949    19.124086   -2375.8945 
-     410        0.041            1   -188.27837    20.085983   -2375.8945 
-     420        0.042            1   -188.25957    21.230423   -2375.8945 
-     430        0.043            1   -188.23868    22.538112   -2375.8945 
-     440        0.044            1   -188.21604    23.988778   -2375.8945 
-     450        0.045            1   -188.19195    25.561447   -2375.8945 
-     460        0.046            1   -188.16672    27.234703   -2375.8945 
-     470        0.047            1   -188.14064    28.986964   -2375.8946 
-     480        0.048            1   -188.11402    30.796738   -2375.8946 
-     490        0.049            1   -188.08713    32.642869   -2375.8945 
-     500         0.05            1   -188.06032    34.504776   -2375.8945 
-     510        0.051            1   -188.03383    36.362662   -2375.8945 
-     520        0.052            1   -188.00793    38.197721   -2375.8945 
-     530        0.053            1   -187.98284    39.992314   -2375.8945 
-     540        0.054            1   -187.95884    41.730127   -2375.8945 
-     550        0.055            1   -187.93612    43.396298   -2375.8945 
-     560        0.056            1   -187.91489     44.97754   -2375.8945 
-     570        0.057            1   -187.89524    46.462224   -2375.8945 
-     580        0.058            1   -187.87735    47.840443   -2375.8945 
-     590        0.059            1    -187.8613    49.104064   -2375.8945 
-     600         0.06            1   -187.84719    50.246744   -2375.8945 
-     610        0.061            1   -187.83509     51.26393   -2375.8944 
-     620        0.062            1   -187.82506    52.152839   -2375.8944 
-     630        0.063            1   -187.81706    52.912413   -2375.8944 
-     640        0.064            1   -187.81109    53.543272   -2375.8944 
-     650        0.065            1   -187.80708    54.047636   -2375.8944 
-     660        0.066            1   -187.80499    54.429234   -2375.8944 
-     670        0.067            1    -187.8047    54.693202   -2375.8944 
-     680        0.068            1   -187.80613    54.845965   -2375.8944 
-     690        0.069            1   -187.80914    54.895106   -2375.8944 
-     700         0.07            1   -187.81356    54.849238   -2375.8944 
-     710        0.071            1   -187.81923     54.71786   -2375.8943 
-     720        0.072            1   -187.82608    54.511181   -2375.8943 
-     730        0.073            1   -187.83388    54.239987   -2375.8943 
-     740        0.074            1   -187.84244     53.91548   -2375.8943 
-     750        0.075            1   -187.85158    53.549112   -2375.8943 
-     760        0.076            1   -187.86112    53.152433   -2375.8943 
-     770        0.077            1   -187.87086    52.736925   -2375.8943 
-     780        0.078            1   -187.88063    52.313858   -2375.8943 
-     790        0.079            1   -187.89026    51.894138   -2375.8943 
-     800         0.08            1   -187.89958    51.488169   -2375.8943 
-     810        0.081            1   -187.90842    51.105725   -2375.8943 
-     820        0.082            1   -187.91663    50.755829   -2375.8943 
-     830        0.083            1   -187.92411    50.446651   -2375.8943 
-     840        0.084            1   -187.93071    50.185404   -2375.8943 
-     850        0.085            1   -187.93637    49.978262   -2375.8943 
-     860        0.086            1   -187.94099    49.830307   -2375.8943 
-     870        0.087            1    -187.9445    49.745473   -2375.8943 
-     880        0.088            1   -187.94685    49.726517   -2375.8943 
-     890        0.089            1   -187.94802    49.774999   -2375.8943 
-     900         0.09            1   -187.94799    49.891282   -2375.8943 
-     910        0.091            1   -187.94678    50.074549   -2375.8943 
-     920        0.092            1   -187.94441    50.322833   -2375.8943 
-     930        0.093            1   -187.94093    50.633063   -2375.8943 
-     940        0.094            1   -187.93639    51.001126   -2375.8943 
-     950        0.095            1   -187.93089    51.421938   -2375.8943 
-     960        0.096            1    -187.9245    51.889531   -2375.8943 
-     970        0.097            1   -187.91733    52.397148   -2375.8943 
-     980        0.098            1    -187.9095    52.937345   -2375.8943 
-     990        0.099            1   -187.90113    53.502108   -2375.8943 
-    1000          0.1            1   -187.89236    54.082966   -2375.8943 
-    1010        0.101            1   -187.88332    54.671115   -2375.8943 
-    1020        0.102            1   -187.87415    55.257545   -2375.8943 
-    1030        0.103            1   -187.86501    55.833162   -2375.8943 
-    1040        0.104            1   -187.85602    56.388915   -2375.8943 
-    1050        0.105            1   -187.84734    56.915918   -2375.8943 
-    1060        0.106            1   -187.83909    57.405575   -2375.8943 
-    1070        0.107            1   -187.83143    57.849686   -2375.8943 
-    1080        0.108            1   -187.82446    58.240564   -2375.8943 
-    1090        0.109            1    -187.8183    58.571132   -2375.8943 
-    1100         0.11            1   -187.81306    58.835016   -2375.8943 
-    1110        0.111            1   -187.80883    59.026633   -2375.8943 
-    1120        0.112            1    -187.8057    59.141258   -2375.8943 
-    1130        0.113            1   -187.80372     59.17509   -2375.8943 
-    1140        0.114            1   -187.80295    59.125305   -2375.8943 
-    1150        0.115            1   -187.80341    58.990092   -2375.8943 
-    1160        0.116            1   -187.80515     58.76868   -2375.8943 
-    1170        0.117            1   -187.80814    58.461352   -2375.8943 
-    1180        0.118            1   -187.81244    58.069457   -2375.8943 
-    1190        0.119            1   -187.81794    57.595377   -2375.8944 
-    1200         0.12            1   -187.82458    57.042514   -2375.8944 
-    1210        0.121            1   -187.83233    56.415256   -2375.8944 
-    1220        0.122            1   -187.84112    55.718931   -2375.8944 
-    1230        0.123            1   -187.85086    54.959744   -2375.8944 
-    1240        0.124            1   -187.86145    54.144707   -2375.8944 
-    1250        0.125            1   -187.87277    53.281562   -2375.8944 
-    1260        0.126            1   -187.88471    52.378686   -2375.8944 
-    1270        0.127            1   -187.89713       51.445   -2375.8944 
-    1280        0.128            1    -187.9099    50.489858   -2375.8944 
-    1290        0.129            1   -187.92288    49.522943   -2375.8944 
-    1300         0.13            1   -187.93591    48.554147   -2375.8944 
-    1310        0.131            1   -187.94886    47.593456   -2375.8944 
-    1320        0.132            1   -187.96157    46.650829   -2375.8944 
-    1330        0.133            1   -187.97391    45.736073   -2375.8944 
-    1340        0.134            1   -187.98573    44.858733   -2375.8944 
-    1350        0.135            1   -187.99691    44.027964   -2375.8944 
-    1360        0.136            1   -188.00731    43.252426   -2375.8944 
-    1370        0.137            1   -188.01678    42.540178   -2375.8943 
-    1380        0.138            1   -188.02529    41.898568   -2375.8943 
-    1390        0.139            1    -188.0327    41.334152   -2375.8943 
-    1400         0.14            1   -188.03894    40.852606   -2375.8943 
-    1410        0.141            1   -188.04396     40.45866   -2375.8944 
-    1420        0.142            1   -188.04768    40.156041   -2375.8944 
-    1430        0.143            1   -188.05007    39.947416   -2375.8944 
-    1440        0.144            1   -188.05107    39.834367   -2375.8944 
-    1450        0.145            1    -188.0507    39.817378   -2375.8944 
-    1460        0.146            1   -188.04898    39.895828   -2375.8944 
-    1470        0.147            1   -188.04595    40.068005   -2375.8945 
-    1480        0.148            1   -188.04164    40.331129   -2375.8945 
-    1490        0.149            1   -188.03603    40.681394   -2375.8945 
-    1500         0.15            1   -188.02929    41.114003   -2375.8945 
-    1510        0.151            1   -188.02148    41.623259   -2375.8945 
-    1520        0.152            1    -188.0127     42.20263   -2375.8945 
-    1530        0.153            1   -188.00302    42.844846   -2375.8945 
-    1540        0.154            1   -187.99255    43.541977   -2375.8945 
-    1550        0.155            1   -187.98148    44.285554   -2375.8945 
-    1560        0.156            1   -187.96989    45.066666   -2375.8945 
-    1570        0.157            1   -187.95793    45.876084   -2375.8945 
-    1580        0.158            1   -187.94574    46.704378   -2375.8945 
-    1590        0.159            1   -187.93346    47.542032   -2375.8945 
-    1600         0.16            1   -187.92122    48.379564   -2375.8945 
-    1610        0.161            1   -187.90916    49.207642   -2375.8945 
-    1620        0.162            1   -187.89742      50.0172   -2375.8945 
-    1630        0.163            1   -187.88613    50.799541   -2375.8945 
-    1640        0.164            1   -187.87536    51.546446   -2375.8944 
-    1650        0.165            1   -187.86531    52.250265   -2375.8944 
-    1660        0.166            1   -187.85604    52.904001   -2375.8944 
-    1670        0.167            1   -187.84765    53.501394   -2375.8944 
-    1680        0.168            1   -187.84021    54.036987   -2375.8944 
-    1690        0.169            1   -187.83379    54.506178   -2375.8944 
-    1700         0.17            1   -187.82846    54.905273   -2375.8944 
-    1710        0.171            1   -187.82424    55.231514   -2375.8944 
-    1720        0.172            1   -187.82117    55.483104   -2375.8944 
-    1730        0.173            1   -187.81922    55.659221   -2375.8944 
-    1740        0.174            1   -187.81843    55.760007   -2375.8944 
-    1750        0.175            1   -187.81881    55.786556   -2375.8944 
-    1760        0.176            1   -187.82029    55.740888   -2375.8944 
-    1770        0.177            1   -187.82284    55.625916   -2375.8944 
-    1780        0.178            1   -187.82639    55.445397   -2375.8944 
-    1790        0.179            1   -187.83088    55.203871   -2375.8944 
-    1800         0.18            1   -187.83623    54.906597   -2375.8944 
-    1810        0.181            1   -187.84235    54.559471   -2375.8944 
-    1820        0.182            1   -187.84913    54.168949   -2375.8944 
-    1830        0.183            1   -187.85646    53.741952   -2375.8943 
-    1840        0.184            1   -187.86424     53.28578   -2375.8943 
-    1850        0.185            1   -187.87239    52.807988   -2375.8943 
-    1860        0.186            1   -187.88077      52.3163   -2375.8943 
-    1870        0.187            1   -187.88925     51.81851   -2375.8943 
-    1880        0.188            1   -187.89772    51.322368   -2375.8943 
-    1890        0.189            1   -187.90605    50.835483   -2375.8943 
-    1900         0.19            1   -187.91415    50.365218   -2375.8943 
-    1910        0.191            1   -187.92189      49.9186   -2375.8943 
-    1920        0.192            1   -187.92917    49.502222   -2375.8943 
-    1930        0.193            1   -187.93591    49.122167   -2375.8943 
-    1940        0.194            1   -187.94198    48.783928   -2375.8943 
-    1950        0.195            1   -187.94737    48.492348   -2375.8943 
-    1960        0.196            1   -187.95199     48.25154   -2375.8943 
-    1970        0.197            1   -187.95576    48.064862   -2375.8943 
-    1980        0.198            1   -187.95866    47.934875   -2375.8943 
-    1990        0.199            1   -187.96065    47.863314   -2375.8943 
-    2000          0.2            1   -187.96171    47.851079   -2375.8943 
-Loop time of 4.40076 on 4 procs for 2000 steps with 500 atoms
-
-Performance: 3.927 ns/day, 6.112 hours/ns, 454.467 timesteps/s
-96.2% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.2934     | 1.3683     | 1.432      |   4.2 | 31.09
-Neigh   | 0.005039   | 0.0053418  | 0.0054908  |   0.2 |  0.12
-Comm    | 0.12642    | 0.1922     | 0.26891    |  11.6 |  4.37
-Output  | 0.39256    | 0.40875    | 0.43431    |   2.5 |  9.29
-Modify  | 2.395      | 2.4202     | 2.4352     |   1.0 | 54.99
-Other   |            | 0.006007   |            |       |  0.14
-
-Nlocal:    125 ave 130 max 122 min
-Histogram: 1 1 0 1 0 0 0 0 0 1
-Nghost:    1324 ave 1330 max 1316 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Neighs:    6747 ave 6959 max 6652 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-FullNghs:  13494 ave 14060 max 13186 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-
-Total # of neighbors = 53976
-Ave neighs/atom = 107.952
-Neighbor list builds = 12
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:04
diff --git a/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1 b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1
new file mode 100644
index 0000000000..781e2264a7
--- /dev/null
+++ b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1
@@ -0,0 +1,219 @@
+LAMMPS (30 Oct 2019)
+# hcp cobalt in a 3d periodic box
+
+clear
+units	 	metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  create_atoms CPU = 0.00105 secs
+
+# setting mass, mag. moments, and interactions for hcp cobalt
+
+mass		1 58.93
+
+set 		group all spin/random 31 1.72
+  500 settings made for spin/random
+#set 		group all spin 1.72 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
+#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 		1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
+#fix 		2 all langevin/spin 0.0 0.0 21
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice moving
+
+timestep	0.0001
+
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp press etotal
+thermo          10
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 4 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.902 | 7.902 | 7.902 Mbytes
+Step Time v_magnorm v_emag Temp Press TotEng 
+       0            0  0.076558814   -5.1073764    100.00543   -552.75983   -2189.4486 
+      10        0.001  0.074494403   -6.2746901    100.01038   -1571.7966   -2190.0317 
+      20        0.002  0.072366265   -7.4280779    99.885587   -2535.9845   -2190.5874 
+      30        0.003  0.070127018   -8.5667999    99.611653   -3445.9872   -2191.1169 
+      40        0.004  0.067755946   -9.6899272    99.164813   -4302.5715   -2191.6215 
+      50        0.005  0.065261592    -10.79648    98.520535   -5107.2841    -2192.103 
+      60        0.006  0.062676613   -11.885341    97.657148   -5862.7198   -2192.5638 
+      70        0.007  0.060046709   -12.955115    96.558718   -6572.0571   -2193.0064 
+      80        0.008  0.057417313   -14.004096    95.216748   -7238.1396   -2193.4327 
+      90        0.009  0.054822275   -15.030416    93.630634   -7862.5226   -2193.8437 
+     100         0.01  0.052277835   -16.032345     91.80711   -8445.2646   -2194.2391 
+     110        0.011  0.049783153   -17.008652    89.759163   -8985.5937   -2194.6181 
+     120        0.012  0.047326373   -17.958895    87.504922   -9483.1141     -2194.98 
+     130        0.013  0.044893289   -18.883574    85.066818   -9938.8838   -2195.3247 
+     140        0.014  0.042474822   -19.784052    82.471014   -10355.911   -2195.6533 
+     150        0.015  0.040070404   -20.662271    79.746901   -10739.081   -2195.9677 
+     160        0.016  0.037686856   -21.520294    76.926428   -11094.793   -2196.2709 
+     170        0.017  0.035334961   -22.359822    74.043181   -11430.247   -2196.5659 
+     180        0.018  0.033026799   -23.181822    71.131269   -11752.268   -2196.8556 
+     190        0.019  0.030775544   -23.986406    68.224204   -12065.774   -2197.1412 
+     200         0.02  0.028597121   -24.773013    65.353995   -12372.712   -2197.4226 
+     210        0.021  0.026511775   -25.540835     62.55053   -12672.055   -2197.6975 
+     220        0.022   0.02454383   -26.289327    59.841288   -12961.112   -2197.9631 
+     230        0.023   0.02271918   -27.018625    57.251361   -13237.544   -2198.2165 
+     240        0.024  0.021061271   -27.729714     54.80373   -13501.028   -2198.4564 
+     250        0.025  0.019587072    -28.42449    52.519717   -13754.325   -2198.6833 
+     260        0.026  0.018304494   -29.105398    50.419388   -14002.718   -2198.8994 
+     270        0.027  0.017211977   -29.775134    48.521812   -14253.089   -2199.1079 
+     280        0.028  0.016300002   -30.436204    46.845075   -14512.437   -2199.3119 
+     290        0.029  0.015553519   -31.090499    45.405985    -14786.53   -2199.5143 
+     300         0.03  0.014954102   -31.739026    44.219544   -15079.165   -2199.7168 
+     310        0.031  0.014481189   -32.381585    43.298175   -15391.531   -2199.9198 
+     320        0.032  0.014112494   -33.016984    42.650874   -15722.828   -2200.1226 
+     330        0.033  0.013824206   -33.643289    42.282535   -16070.874    -2200.324 
+     340        0.034  0.013591568   -34.258323     42.19365   -16433.065   -2200.5226 
+     350        0.035  0.013390035   -34.860184    42.380506   -16807.186   -2200.7174 
+     360        0.036   0.01319679   -35.447655    42.835832   -17191.816   -2200.9077 
+     370        0.037  0.012992271   -36.020512    43.549656   -17586.676   -2201.0935 
+     380        0.038  0.012761486   -36.579332    44.510078   -17991.857   -2201.2754 
+     390        0.039  0.012494918   -37.125414    45.703757   -18407.738   -2201.4538 
+     400         0.04    0.0121888   -37.660321    47.115967   -18834.276   -2201.6292 
+     410        0.041  0.011844474   -38.185489    48.730291   -19270.674   -2201.8019 
+     420        0.042  0.011466715    -38.70192    50.528119   -19715.276   -2201.9716 
+     430        0.043  0.011061388    -39.21005    52.488204    -20165.66   -2202.1377 
+     440        0.044  0.010633241   -39.709778    54.586528   -20618.997   -2202.2998 
+     450        0.045  0.010184696   -40.200724     56.79654   -21072.538   -2202.4571 
+     460        0.046 0.0097161044   -40.682449    59.089699   -21523.873   -2202.6094 
+     470        0.047 0.0092271788   -41.154614    61.436133   -21970.922   -2202.7565 
+     480        0.048 0.0087187266   -41.617256    63.805414    -22412.32   -2202.8989 
+     490        0.049 0.0081937768   -42.070708    66.167399   -22847.061    -2203.037 
+     500         0.05 0.0076576327    -42.51563    68.493235   -23274.619    -2203.172 
+     510        0.051 0.0071170477   -42.952841    70.756444   -23694.559   -2203.3046 
+     520        0.052  0.006579078   -43.383338    72.933996   -24106.717   -2203.4358 
+     530        0.053  0.006050144   -43.807962    75.007131   -24510.338   -2203.5662 
+     540        0.054 0.0055354475   -44.227552    76.961803   -24904.495   -2203.6957 
+     550        0.055 0.0050386503    -44.64268    78.788647   -25287.341   -2203.8241 
+     560        0.056 0.0045617699   -45.053996      80.4825    -25657.11   -2203.9504 
+     570        0.057 0.0041054334   -45.461923    82.041527   -26011.443   -2204.0737 
+     580        0.058  0.003669689   -45.866895    83.466142   -26348.265   -2204.1931 
+     590        0.059 0.0032553824   -46.269219    84.757926   -26665.834   -2204.3077 
+     600         0.06 0.0028655752   -46.669125    85.918711    -26963.24   -2204.4173 
+     610        0.061 0.0025060765   -47.066641        86.95   -27240.331   -2204.5218 
+     620        0.062 0.0021839971   -47.461566    87.852838   -27497.728   -2204.6218 
+     630        0.063 0.0019039581   -47.853462    88.628142   -27736.503   -2204.7177 
+     640        0.064 0.0016633855   -48.241747    89.277364    -27957.91     -2204.81 
+     650        0.065 0.0014502904   -48.625803    89.803307    -28163.11    -2204.899 
+     660        0.066 0.0012463786   -49.005026    90.210807   -28352.881   -2204.9847 
+     670        0.067 0.0010345087   -49.378935    90.507107   -28527.721   -2205.0668 
+     680        0.068 0.00080788134   -49.747325    90.701795   -28688.395   -2205.1453 
+     690        0.069  0.000586442   -50.110227     90.80636   -28836.094     -2205.22 
+     700         0.07 0.00046855102   -50.467799    90.833539   -28972.361   -2205.2911 
+     710        0.071 0.00061091693    -50.82044    90.796649    -29099.44   -2205.3592 
+     720        0.072 0.00094960177   -51.168606    90.709122   -29219.676   -2205.4249 
+     730        0.073 0.0013742455   -51.512913    90.584346   -29335.643   -2205.4887 
+     740        0.074 0.0018397629   -51.853957    90.435783   -29449.521   -2205.5511 
+     750        0.075 0.0023216474   -52.192407    90.277231   -29563.316   -2205.6124 
+     760        0.076 0.0028000512   -52.528883    90.123061   -29678.726   -2205.6729 
+     770        0.077 0.0032569295   -52.863859     89.98824   -29797.079   -2205.7329 
+     780        0.078 0.0036765431   -53.197843    89.888047   -29919.964   -2205.7925 
+     790        0.079 0.0040467094   -53.530921    89.837568   -30048.271   -2205.8521 
+     800         0.08 0.0043597837   -53.862938    89.850978   -30182.622   -2205.9119 
+     810        0.081 0.0046129296   -54.193489    89.940884   -30323.293   -2205.9718 
+     820        0.082 0.0048076151   -54.522077    90.117797   -30470.468   -2206.0321 
+     830        0.083  0.004948533    -54.84813    90.389814   -30624.056   -2206.0926 
+     840        0.084 0.0050423324   -55.171024    90.762454   -30783.658   -2206.1532 
+     850        0.085 0.0050965581   -55.490357    91.238681   -30949.141   -2206.2139 
+     860        0.086 0.0051190641   -55.805904    91.818973     -31120.5   -2206.2745 
+     870        0.087 0.0051180301   -56.117429    92.501449   -31297.412   -2206.3349 
+     880        0.088 0.0051024116   -56.424751    93.281992   -31479.436   -2206.3949 
+     890        0.089  0.005082454   -56.727832    94.154367   -31666.293   -2206.4544 
+     900         0.09 0.0050697645   -57.026442    95.110386   -31857.043    -2206.513 
+     910        0.091 0.0050765431   -57.320291    96.140056   -32050.436   -2206.5703 
+     920        0.092 0.0051139309   -57.609075    97.231838   -32245.079   -2206.6257 
+     930        0.093 0.0051899535    -57.89236    98.372982   -32439.141   -2206.6788 
+     940        0.094 0.0053078572   -58.169742     99.54995   -32630.727   -2206.7288 
+     950        0.095 0.0054654923    -58.44083    100.74893   -32817.882   -2206.7752 
+     960        0.096 0.0056558757   -58.705483    101.95638   -32999.116   -2206.8176 
+     970        0.097 0.0058685513   -58.963698    103.15953   -33173.159   -2206.8557 
+     980        0.098 0.0060912487   -59.215624    104.34681   -33338.961   -2206.8893 
+     990        0.099 0.0063114886   -59.461806    105.50819   -33496.345   -2206.9188 
+    1000          0.1 0.0065179843   -59.702883    106.63524   -33645.259   -2206.9444 
+Loop time of 5.20295 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 1.661 ns/day, 14.453 hours/ns, 192.199 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.6241     | 2.6241     | 2.6241     |   0.0 | 50.43
+Neigh   | 0.01424    | 0.01424    | 0.01424    |   0.0 |  0.27
+Comm    | 0.041207   | 0.041207   | 0.041207   |   0.0 |  0.79
+Output  | 0.0090086  | 0.0090086  | 0.0090086  |   0.0 |  0.17
+Modify  | 2.5084     | 2.5084     | 2.5084     |   0.0 | 48.21
+Other   |            | 0.006008   |            |       |  0.12
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2442 ave 2442 max 2442 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    27581 ave 27581 max 27581 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  55162 ave 55162 max 55162 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 55162
+Ave neighs/atom = 110.324
+Neighbor list builds = 7
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:05
diff --git a/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4 b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4
new file mode 100644
index 0000000000..de00d5be32
--- /dev/null
+++ b/examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4
@@ -0,0 +1,219 @@
+LAMMPS (30 Oct 2019)
+# hcp cobalt in a 3d periodic box
+
+clear
+units	 	metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  create_atoms CPU = 0.00101995 secs
+
+# setting mass, mag. moments, and interactions for hcp cobalt
+
+mass		1 58.93
+
+set 		group all spin/random 31 1.72
+  500 settings made for spin/random
+#set 		group all spin 1.72 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
+#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 		1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
+#fix 		2 all langevin/spin 0.0 0.0 21
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice moving
+
+timestep	0.0001
+
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp press etotal
+thermo          10
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 4 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.814 | 7.814 | 7.815 Mbytes
+Step Time v_magnorm v_emag Temp Press TotEng 
+       0            0  0.076558814   -5.1073764    100.00543   -552.75983   -2190.3478 
+      10        0.001  0.074494512   -6.2728301    99.980769   -1570.0726   -2191.5261 
+      20        0.002  0.072367013   -7.4259977    99.847801   -2531.5119   -2192.6655 
+      30        0.003  0.070129365    -8.566306    99.586282   -3438.1309   -2193.7672 
+      40        0.004  0.067761178   -9.6929189    99.171132    -4291.017   -2194.8323 
+      50        0.005  0.065270916     -10.8048    98.575397   -5091.9111   -2195.8628 
+      60        0.006  0.062690557   -11.900573    97.773618   -5843.4528   -2196.8612 
+      70        0.007  0.060064592   -12.978381    96.745047    -6548.726   -2197.8306 
+      80        0.008   0.05743694   -14.035923    95.476292   -7210.2954    -2198.773 
+      90        0.009  0.054839883    -15.07074    93.963026   -7829.4252    -2199.689 
+     100         0.01  0.052288504    -16.08066    92.210482   -8405.9983   -2200.5773 
+     110        0.011  0.049782155   -17.064251    90.232741   -8939.3051   -2201.4357 
+     120        0.012  0.047311759   -18.021135    88.051042   -9429.1353   -2202.2626 
+     130        0.013  0.044869196   -18.952065    85.691573   -9876.5628   -2203.0575 
+     140        0.014  0.042453961   -19.858739     83.18315   -10284.249   -2203.8215 
+     150        0.015  0.040074171   -20.743348    80.555177   -10656.417   -2204.5569 
+     160        0.016  0.037742459      -21.608    77.836156   -10998.818   -2205.2677 
+     170        0.017  0.035470168   -22.454209    75.052994   -11318.525   -2205.9587 
+     180        0.018  0.033263447   -23.282658    72.231211   -11623.118   -2206.6354 
+     190        0.019  0.031122821   -24.093311    69.395936   -11919.248   -2207.3023 
+     200         0.02  0.029045634    -24.88579    66.573223   -12211.306   -2207.9613 
+     210        0.021  0.027029857   -25.659817    63.791041   -12500.812   -2208.6115 
+     220        0.022  0.025077742   -26.415541    61.079413   -12787.018   -2209.2498 
+     230        0.023  0.023198048   -27.153652    58.469604   -13068.277   -2209.8722 
+     240        0.024   0.02140599   -27.875313    55.992687   -13343.621   -2210.4756 
+     250        0.025  0.019720922   -28.581973    53.678031    -13613.86   -2211.0588 
+     260        0.026  0.018162738   -29.275283    51.552191    -13882.15   -2211.6232 
+     270        0.027  0.016748514   -29.956802    49.638467   -14153.137   -2212.1718 
+     280        0.028   0.01549075   -30.628043    47.957071   -14432.246   -2212.7087 
+     290        0.029  0.014397611   -31.290177    46.525552   -14724.005   -2213.2371 
+     300         0.03  0.013474315   -31.943984    45.359085   -15031.315    -2213.759 
+     310        0.031  0.012723957   -32.589853     44.47023   -15355.595    -2214.275 
+     320        0.032  0.012146358   -33.227585    43.868153   -15696.845   -2214.7851 
+     330        0.033  0.011734827   -33.856656    43.557623   -16054.887    -2215.289 
+     340        0.034  0.011472508   -34.476313    43.538346    -16429.77   -2215.7871 
+     350        0.035  0.011330772   -35.085716    43.805034   -16821.627   -2216.2802 
+     360        0.036  0.011271169   -35.684147    44.348312    -17230.21   -2216.7687 
+     370        0.037   0.01125027   -36.271215    45.156046   -17654.485   -2217.2524 
+     380        0.038  0.011225354   -36.847053    46.214576   -18092.623   -2217.7301 
+     390        0.039  0.011159026   -37.412284    47.509345   -18542.156   -2218.2003 
+     400         0.04  0.011022073   -37.967916    49.024843   -19000.554   -2218.6614 
+     410        0.041   0.01079477   -38.515123    50.744046   -19465.713   -2219.1128 
+     420        0.042  0.010467095   -39.054921    52.647653   -19935.873   -2219.5544 
+     430        0.043  0.010038219   -39.588034    54.713405   -20409.666   -2219.9869 
+     440        0.044 0.0095155267   -40.114703    56.915658   -20885.556   -2220.4109 
+     450        0.045 0.0089134996   -40.634722    59.225397   -21361.621   -2220.8268 
+     460        0.046 0.0082528918   -41.147681    61.610799   -21835.762   -2221.2347 
+     470        0.047 0.0075606723   -41.653088    64.038349   -22305.687   -2221.6343 
+     480        0.048 0.0068707613   -42.150486    66.474377   -22768.948   -2222.0253 
+     490        0.049 0.0062249854   -42.639704    68.886721   -23223.418   -2222.4076 
+     500         0.05 0.0056723593   -43.120772     71.24617   -23667.077   -2222.7814 
+     510        0.051   0.00526312    -43.59404    73.527392   -24098.459    -2223.147 
+     520        0.052 0.0050342241   -44.059917    75.709206   -24516.163   -2223.5051 
+     530        0.053 0.0049906301   -44.518898    77.774314   -24919.192   -2223.8564 
+     540        0.054 0.0050976586   -44.971364    79.708763   -25306.611   -2224.2014 
+     550        0.055 0.0052941974   -45.417577    81.501347    -25677.67   -2224.5405 
+     560        0.056 0.0055157717   -45.857628    83.143173   -26031.673   -2224.8736 
+     570        0.057 0.0057113414   -46.291426    84.627457   -26367.904   -2225.2003 
+     580        0.058 0.0058493207   -46.718709    85.949497     -26685.6     -2225.52 
+     590        0.059 0.0059162201   -47.139052     87.10679   -26984.124   -2225.8316 
+     600         0.06 0.0059118584   -47.551892    88.099176   -27263.145   -2226.1347 
+     610        0.061  0.005843747   -47.956571    88.928929   -27522.773   -2226.4287 
+     620        0.062 0.0057222223   -48.352422    89.600763   -27763.549   -2226.7139 
+     630        0.063 0.0055570967   -48.738876     90.12173   -27986.321   -2226.9905 
+     640        0.064 0.0053558993   -49.115723    90.501081   -28192.238   -2227.2593 
+     650        0.065 0.0051233209   -49.483122    90.750056     -28382.3   -2227.5205 
+     660        0.066 0.0048614512   -49.841791    90.881635   -28557.623   -2227.7746 
+     670        0.067 0.0045706003   -50.192974    90.910245   -28719.422   -2228.0219 
+     680        0.068 0.0042506564   -50.538196    90.851397   -28868.809   -2228.2627 
+     690        0.069 0.0039028575   -50.879364    90.721317   -29007.619   -2228.4973 
+     700         0.07 0.0035319814   -51.218193    90.536521   -29137.623   -2228.7265 
+     710        0.071 0.0031491486   -51.556251    90.313501   -29261.193   -2228.9511 
+     720        0.072 0.0027758205   -51.894643    90.068503   -29380.924   -2229.1724 
+     730        0.073  0.002449449   -52.233987    89.817462   -29499.606   -2229.3917 
+     740        0.074 0.0022276613   -52.574465     89.57612   -29620.196   -2229.6103 
+     750        0.075 0.0021767124   -52.915641    89.360246   -29744.882    -2229.829 
+     760        0.076 0.0023310362   -53.256843    89.185838   -29875.573   -2230.0485 
+     770        0.077 0.0026637349   -53.597197    89.069228   -30013.477   -2230.2685 
+     780        0.078 0.0031129938    -53.93565    89.026943   -30158.812   -2230.4882 
+     790        0.079 0.0036204667   -54.271339    89.075322   -30311.602   -2230.7066 
+     800         0.08 0.0041448552   -54.603455    89.229912   -30471.244   -2230.9226 
+     810        0.081 0.0046613106   -54.931421    89.504766   -30636.938   -2231.1352 
+     820        0.082 0.0051580947   -55.255056    89.911726   -30808.087   -2231.3434 
+     830        0.083 0.0056329652   -55.574491    90.459766   -30984.153   -2231.5469 
+     840        0.084 0.0060893356   -55.890024    91.154456   -31164.372   -2231.7452 
+     850        0.085 0.0065324419   -56.202052    91.997528   -31347.792   -2231.9379 
+     860        0.086 0.0069661977   -56.511206    92.986622   -31533.977   -2232.1249 
+     870        0.087 0.0073913051   -56.817814    94.115192    -31721.92    -2232.306 
+     880        0.088 0.0078048547   -57.122061    95.372548   -31910.795   -2232.4809 
+     890        0.089  0.008201165   -57.423984    96.744135   -32100.108     -2232.65 
+     900         0.09 0.0085732702   -57.723377    98.212046   -32289.532   -2232.8136 
+     910        0.091 0.0089144724   -58.019938    99.755667   -32479.154   -2232.9728 
+     920        0.092 0.0092194916   -58.313266    101.35254   -32669.227   -2233.1285 
+     930        0.093 0.0094849872   -58.602956    102.97932   -32860.091   -2233.2822 
+     940        0.094 0.0097093572   -58.888668    104.61271   -33051.981   -2233.4348 
+     950        0.095 0.0098920175   -59.169925    106.23045   -33244.279   -2233.5871 
+     960        0.096   0.01003244    -59.44662    107.81212   -33436.562   -2233.7396 
+     970        0.097  0.010129313   -59.718668    109.33976   -33627.714   -2233.8925 
+     980        0.098  0.010180127   -59.986126    110.79823   -33816.218   -2234.0455 
+     990        0.099  0.010181304    -60.24929    112.17528   -34000.522   -2234.1984 
+    1000          0.1   0.01012881   -60.508632    113.46137   -34179.052   -2234.3508 
+Loop time of 2.93788 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 2.941 ns/day, 8.161 hours/ns, 340.381 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.72349    | 0.73783    | 0.7554     |   1.3 | 25.11
+Neigh   | 0.00353    | 0.0036981  | 0.0038559  |   0.2 |  0.13
+Comm    | 0.12285    | 0.14476    | 0.16041    |   3.6 |  4.93
+Output  | 0.0046515  | 0.0047909  | 0.0050418  |   0.2 |  0.16
+Modify  | 2.0407     | 2.0439     | 2.0482     |   0.2 | 69.57
+Other   |            | 0.00288    |            |       |  0.10
+
+Nlocal:    125 ave 136 max 119 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+Nghost:    1324 ave 1331 max 1310 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Neighs:    6897.25 ave 7552 max 6604 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+FullNghs:  13794.5 ave 15117 max 13164 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 55178
+Ave neighs/atom = 110.356
+Neighbor list builds = 7
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut b/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut
index a409fe0563..9c256338a2 100644
--- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut
+++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut
@@ -11,7 +11,7 @@ boundary 	p p p
 atom_modify 	map array 
 
 lattice 	bcc 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -33,7 +33,7 @@ fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -56,4 +56,4 @@ thermo          50
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		100
diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald b/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald
index 58b44b55fe..560fcbb650 100644
--- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald
+++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald
@@ -11,7 +11,7 @@ boundary 	p p p
 atom_modify 	map array 
 
 lattice 	bcc 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -35,7 +35,7 @@ fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -58,4 +58,4 @@ thermo          50
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		100
diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm b/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm
index 28d7e4a4bc..28d79e3d3e 100644
--- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm
+++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm
@@ -11,7 +11,7 @@ boundary 	p p p
 atom_modify 	map array 
 
 lattice 	bcc 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -36,7 +36,7 @@ fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -59,4 +59,4 @@ thermo          50
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		100
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1
new file mode 100644
index 0000000000..c2af23d167
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.1
@@ -0,0 +1,125 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.000741005 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/cut 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff      * * spin/dipole/cut 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/cut, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 13.4 | 13.4 | 13.4 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 1.0737264e-35   -768.37511   -15175.868   -15131.207 
+      50        0.005           -1 -2.7722752e-10 -2.1828666e-10            1 6.8846921e-09   -768.35793   -15174.244   -15131.215 
+     100         0.01           -1 -2.0983066e-09 -1.7330951e-09            1 1.0038885e-08   -768.30868   -15169.656    -15131.24 
+Loop time of 7.86359 on 1 procs for 100 steps with 3456 atoms
+
+Performance: 0.110 ns/day, 218.433 hours/ns, 12.717 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.6134     | 3.6134     | 3.6134     |   0.0 | 45.95
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.014062   | 0.014062   | 0.014062   |   0.0 |  0.18
+Output  | 0.006057   | 0.006057   | 0.006057   |   0.0 |  0.08
+Modify  | 4.226      | 4.226      | 4.226      |   0.0 | 53.74
+Other   |            | 0.004064   |            |       |  0.05
+
+Nlocal:    3456 ave 3456 max 3456 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7289 ave 7289 max 7289 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    290304 ave 290304 max 290304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  580608 ave 580608 max 580608 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:07
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4
new file mode 100644
index 0000000000..1f8157bb29
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_cut.g++.4
@@ -0,0 +1,125 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00090003 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/cut 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff      * * spin/dipole/cut 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/cut, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.217 | 9.217 | 9.217 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 1.0737264e-35   -768.37511   -15560.055   -15515.394 
+      50        0.005           -1 9.6204015e-11 -3.3767807e-10            1 6.6905249e-09   -768.35767   -15558.438   -15515.394 
+     100         0.01           -1 7.8881609e-10 -2.7017321e-09            1 9.8111281e-09   -768.30769   -15553.868   -15515.394 
+Loop time of 2.29116 on 4 procs for 100 steps with 3456 atoms
+
+Performance: 0.377 ns/day, 63.643 hours/ns, 43.646 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.92259    | 0.92963    | 0.93393    |   0.4 | 40.57
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.02284    | 0.027597   | 0.035185   |   2.8 |  1.20
+Output  | 0.0018489  | 0.0018544  | 0.0018642  |   0.0 |  0.08
+Modify  | 1.3296     | 1.3303     | 1.3308     |   0.0 | 58.06
+Other   |            | 0.001818   |            |       |  0.08
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    3785 ave 3785 max 3785 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    72576 ave 72576 max 72576 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  145152 ave 145152 max 145152 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1
new file mode 100644
index 0000000000..9a38445af5
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.1
@@ -0,0 +1,135 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00166988 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/long 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff	* * spin/dipole/long 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+kspace_style 	ewald/dipole/spin 1.0e-4
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+EwaldDipoleSpin initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.324623
+  estimated absolute RMS force accuracy = 9.55526e-84
+  estimated relative force accuracy = 6.63576e-85
+  KSpace vectors: actual max1d max3d = 2084 10 4630
+                  kxmax kymax kzmax  = 10 10 10
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/long, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 30.07 | 30.07 | 30.07 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 2.5872886e-37   -767.88567    -15175.39   -15130.729 
+      50        0.005           -1 4.3660916e-09 -2.1918692e-09            1 5.3480999e-10   -767.86847   -15173.766   -15130.738 
+     100         0.01           -1 9.9854966e-09 -4.2823677e-09            1 2.3267629e-09   -767.81917   -15169.178   -15130.762 
+Loop time of 24.9345 on 1 procs for 100 steps with 3456 atoms
+
+Performance: 0.035 ns/day, 692.624 hours/ns, 4.011 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.8022     | 4.8022     | 4.8022     |   0.0 | 19.26
+Kspace  | 10.337     | 10.337     | 10.337     |   0.0 | 41.46
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.013856   | 0.013856   | 0.013856   |   0.0 |  0.06
+Output  | 0.007138   | 0.007138   | 0.007138   |   0.0 |  0.03
+Modify  | 9.7705     | 9.7705     | 9.7705     |   0.0 | 39.18
+Other   |            | 0.004077   |            |       |  0.02
+
+Nlocal:    3456 ave 3456 max 3456 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7289 ave 7289 max 7289 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    290304 ave 290304 max 290304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  580608 ave 580608 max 580608 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:25
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4
new file mode 100644
index 0000000000..306799f576
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_ewald.g++.4
@@ -0,0 +1,135 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00088191 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/long 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff	* * spin/dipole/long 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+kspace_style 	ewald/dipole/spin 1.0e-4
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+EwaldDipoleSpin initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.324623
+  estimated absolute RMS force accuracy = 9.29828e-84
+  estimated relative force accuracy = 6.4573e-85
+  KSpace vectors: actual max1d max3d = 2084 10 4630
+                  kxmax kymax kzmax  = 10 10 10
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/long, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 25.89 | 25.89 | 25.89 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 3.5107565e-37   -767.88567   -15559.577   -15514.916 
+      50        0.005           -1 4.3196063e-09 -2.1966927e-09            1 5.1719577e-10   -767.86822    -15557.96   -15514.916 
+     100         0.01           -1 9.7636593e-09 -4.3236953e-09            1 2.2443181e-09   -767.81819    -15553.39   -15514.916 
+Loop time of 6.80139 on 4 procs for 100 steps with 3456 atoms
+
+Performance: 0.127 ns/day, 188.927 hours/ns, 14.703 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.248      | 1.2649     | 1.2816     |   1.1 | 18.60
+Kspace  | 2.523      | 2.5743     | 2.6505     |   3.0 | 37.85
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.029461   | 0.087268   | 0.13754    |  13.0 |  1.28
+Output  | 0.0018618  | 0.001869   | 0.0018811  |   0.0 |  0.03
+Modify  | 2.8692     | 2.8709     | 2.8741     |   0.1 | 42.21
+Other   |            | 0.002119   |            |       |  0.03
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    3785 ave 3785 max 3785 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    72576 ave 72576 max 72576 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  145152 ave 145152 max 145152 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:06
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1
new file mode 100644
index 0000000000..b0e87d786d
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.1
@@ -0,0 +1,137 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00166583 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/long 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff	* * spin/dipole/long 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+kspace_style 	pppm/dipole/spin 1.0e-4
+kspace_modify 	compute yes
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+PPPMDipoleSpin initialization ...
+  G vector (1/distance) = 0.329367
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00175808
+  estimated relative force accuracy = 0.000122092
+  using double precision FFTs
+  3d grid and FFT values/proc = 15625 8000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/long, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 16.27 | 16.27 | 16.27 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 3.7996771e-37   -767.89759   -15175.402   -15130.741 
+      50        0.005           -1 3.6585337e-09 -1.9445403e-09            1 5.1405121e-10   -767.88039   -15173.779    -15130.75 
+     100         0.01           -1 7.3585728e-09 -3.8640878e-09            1 2.0194927e-09   -767.83109   -15169.191   -15130.774 
+Loop time of 15.3615 on 1 procs for 100 steps with 3456 atoms
+
+Performance: 0.056 ns/day, 426.709 hours/ns, 6.510 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.8418     | 4.8418     | 4.8418     |   0.0 | 31.52
+Kspace  | 0.66626    | 0.66626    | 0.66626    |   0.0 |  4.34
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.014248   | 0.014248   | 0.014248   |   0.0 |  0.09
+Output  | 0.0064788  | 0.0064788  | 0.0064788  |   0.0 |  0.04
+Modify  | 9.8279     | 9.8279     | 9.8279     |   0.0 | 63.98
+Other   |            | 0.00478    |            |       |  0.03
+
+Nlocal:    3456 ave 3456 max 3456 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7289 ave 7289 max 7289 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    290304 ave 290304 max 290304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  580608 ave 580608 max 580608 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:16
diff --git a/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4 b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4
new file mode 100644
index 0000000000..4fbd0eb52b
--- /dev/null
+++ b/examples/SPIN/dipole_spin/log.19Nov19.spin.iron_dipole_pppm.g++.4
@@ -0,0 +1,137 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 12.0 0.0 12.0 0.0 12.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (34.398 34.398 34.398)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 3456 atoms
+  create_atoms CPU = 0.00123286 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  3456 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5 spin/dipole/long 8.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff	* * spin/dipole/long 8.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+kspace_style 	pppm/dipole/spin 1.0e-4
+kspace_modify 	compute yes
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		100
+PPPMDipoleSpin initialization ...
+  G vector (1/distance) = 0.329367
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00175808
+  estimated relative force accuracy = 0.000122092
+  using double precision FFTs
+  3d grid and FFT values/proc = 5625 2000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.1
+  ghost atom cutoff = 8.1
+  binsize = 4.05, bins = 9 9 9
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/dipole/long, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 10.42 | 10.42 | 10.42 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1 2.3173191e-37   -767.89759    -15559.59   -15514.929 
+      50        0.005           -1 3.6593054e-09 -1.9379563e-09            1 4.9747018e-10   -767.88014   -15557.972   -15514.929 
+     100         0.01           -1 7.3731919e-09 -3.8151563e-09            1 1.9544299e-09    -767.8301   -15553.402   -15514.929 
+Loop time of 4.4084 on 4 procs for 100 steps with 3456 atoms
+
+Performance: 0.196 ns/day, 122.455 hours/ns, 22.684 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.2326     | 1.2513     | 1.2693     |   1.3 | 28.38
+Kspace  | 0.22823    | 0.24585    | 0.26385    |   2.8 |  5.58
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.025352   | 0.028409   | 0.032299   |   1.6 |  0.64
+Output  | 0.001868   | 0.0018761  | 0.0018861  |   0.0 |  0.04
+Modify  | 2.8753     | 2.8788     | 2.8818     |   0.1 | 65.30
+Other   |            | 0.002175   |            |       |  0.05
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    3785 ave 3785 max 3785 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    72576 ave 72576 max 72576 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  145152 ave 145152 max 145152 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 580608
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron
index bb1b0e1b4d..d60e6b86f5 100644
--- a/examples/SPIN/iron/in.spin.iron
+++ b/examples/SPIN/iron/in.spin.iron
@@ -19,8 +19,8 @@ create_atoms 	1 box
 
 mass		1 55.845
 
-#set 		group all spin/random 31 2.2
-set 		group all spin 2.2 0.0 0.0 1.0
+set 		group all spin/random 31 2.2
+# set 		group all spin 2.2 0.0 0.0 1.0
 velocity 	all create 100 4928459 rot yes dist gaussian
 
 pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
@@ -33,7 +33,7 @@ neigh_modify 	every 10 check yes delay 20
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -48,10 +48,10 @@ variable 	magnorm   equal c_out_mag[4]
 variable 	emag      equal c_out_mag[5]
 variable 	tmag      equal c_out_mag[6]
 
-thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe etotal
+thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe press etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		50000
+run 		1000
diff --git a/examples/SPIN/iron/in.spin.iron_cubic b/examples/SPIN/iron/in.spin.iron_cubic
index d4703a2959..30a3e0e97c 100644
--- a/examples/SPIN/iron/in.spin.iron_cubic
+++ b/examples/SPIN/iron/in.spin.iron_cubic
@@ -31,7 +31,7 @@ fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -52,9 +52,9 @@ thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		1000
 # min_style 	spin
 # min_modify	alpha_damp 1.0 discrete_factor 10
 # minimize 	1.0e-16 1.0e-16 10000 10000
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1 b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1
new file mode 100644
index 0000000000..cbc749a1f7
--- /dev/null
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.1
@@ -0,0 +1,136 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.000422955 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+
+set 		group all spin/random 31 2.2
+  250 settings made for spin/random
+# set 		group all spin 2.2 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe press etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.77337
+  ghost atom cutoff = 5.77337
+  binsize = 2.88668, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.82 | 7.82 | 7.82 Mbytes
+Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng Press TotEng 
+       0            0  0.076456975    4554.5462    100.00358  -0.85791269    3.2186929    -1070.429    394.43342   -1067.2103 
+      50        0.005  0.076456974     4658.383    96.663685  -0.86504718    3.1111957   -1070.3179    709.50826   -1067.2067 
+     100         0.01  0.076456983    4744.1872    86.965803  -0.88035771    2.7990619   -1069.9981    1466.6938   -1067.1991 
+     150        0.015  0.076456973    4794.5283    72.421197   -0.8996913    2.3309324   -1069.5203    2534.3867   -1067.1894 
+     200         0.02  0.076456944    4707.6548    55.633188    -0.921682    1.7905973    -1068.969     3732.183   -1067.1784 
+     250        0.025  0.076456953    4439.4697    39.802206  -0.94649004    1.2810649    -1068.447    4831.5559    -1067.166 
+     300         0.03  0.076457027    4101.6694    27.882295  -0.97253854    0.8974133   -1068.0504    5612.0928    -1067.153 
+     350        0.035  0.076457103    3860.1545    21.776538  -0.99708692   0.70089477   -1067.8416    5906.3057   -1067.1407 
+     400         0.04  0.076457117    3765.5341    21.857102   -1.0190244   0.70348778   -1067.8332    5682.0053   -1067.1297 
+     450        0.045  0.076457072    3739.9037    26.959407   -1.0389343   0.86770942   -1067.9875    5066.5077   -1067.1198 
+     500         0.05  0.076457001    3730.8342     34.92521   -1.0582008     1.124095   -1068.2342    4279.2424   -1067.1101 
+     550        0.055  0.076456962    3698.0556    43.405912   -1.0785156     1.397053    -1068.497    3533.4153      -1067.1 
+     600         0.06  0.076456997     3560.947    50.544844    -1.102048     1.626825    -1068.715    2975.8479   -1067.0882 
+     650        0.065  0.076457079    3341.7402    55.261218   -1.1296588    1.7786252    -1068.853    2683.3023   -1067.0744 
+     700         0.07  0.076457136    3156.8448     57.25083   -1.1595102    1.8426624   -1068.9021    2640.5967   -1067.0595 
+     750        0.075  0.076457132    3099.5181    56.934336   -1.1893875    1.8324758    -1068.877    2778.3261   -1067.0445 
+     800         0.08  0.076457116    3132.9985    55.266343   -1.2181223    1.7787901    -1068.809    3020.1175   -1067.0302 
+     850        0.085  0.076457116    3163.2943    53.376453   -1.2443326    1.7179626    -1068.735    3287.9042   -1067.0171 
+     900         0.09  0.076457121     3168.063    52.279557   -1.2676425    1.6826581   -1068.6881    3504.7334   -1067.0054 
+     950        0.095  0.076457122    3144.2102    52.667743   -1.2902335    1.6951522   -1068.6893    3622.1382   -1066.9941 
+    1000          0.1  0.076457135    3061.0811    54.684094    -1.314147      1.76005   -1068.7422    3625.2935   -1066.9822 
+Loop time of 1.6779 on 1 procs for 1000 steps with 250 atoms
+
+Performance: 5.149 ns/day, 4.661 hours/ns, 595.982 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.78285    | 0.78285    | 0.78285    |   0.0 | 46.66
+Neigh   | 0.004487   | 0.004487   | 0.004487   |   0.0 |  0.27
+Comm    | 0.022926   | 0.022926   | 0.022926   |   0.0 |  1.37
+Output  | 0.003927   | 0.003927   | 0.003927   |   0.0 |  0.23
+Modify  | 0.86033    | 0.86033    | 0.86033    |   0.0 | 51.27
+Other   |            | 0.003381   |            |       |  0.20
+
+Nlocal:    250 ave 250 max 250 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1399 ave 1399 max 1399 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    7855 ave 7855 max 7855 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  15710 ave 15710 max 15710 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15710
+Ave neighs/atom = 62.84
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4 b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4
new file mode 100644
index 0000000000..a5cc9d7f0b
--- /dev/null
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron.g++.4
@@ -0,0 +1,136 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.000705957 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+
+set 		group all spin/random 31 2.2
+  250 settings made for spin/random
+# set 		group all spin 2.2 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe press etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.77337
+  ghost atom cutoff = 5.77337
+  binsize = 2.88668, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.766 | 7.766 | 7.766 Mbytes
+Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng Press TotEng 
+       0            0  0.076456975    4554.5462    100.00358  -0.85791269    3.2186929   -1070.8579    394.43342   -1067.6392 
+      50        0.005  0.076456995    4701.2004    96.298333  -0.85659448    3.0994366   -1070.7387    714.37866   -1067.6392 
+     100         0.01  0.076457028    4794.5923    86.330828  -0.87003341    2.7786247   -1070.4179    1484.2951   -1067.6392 
+     150        0.015  0.076457074    4836.9634    71.603402  -0.89006992    2.3046111   -1069.9438    2551.9258   -1067.6392 
+     200         0.02  0.076457106    4754.5574    54.648817  -0.91124541    1.7589146   -1069.3981    3731.1494   -1067.6392 
+     250        0.025  0.076457128     4502.135    38.599515  -0.93187522    1.2423553   -1068.8816     4804.619   -1067.6392 
+     300         0.03  0.076457157    4176.7186    26.383018  -0.95082226    0.8491579   -1068.4884    5563.3287   -1067.6392 
+     350        0.035  0.076457207    3955.5658     20.01039  -0.96826468   0.64404992   -1068.2833    5839.6479   -1067.6392 
+     400         0.04  0.076457243    3887.9746    20.097682  -0.98706373   0.64685949   -1068.2861    5601.1255   -1067.6392 
+     450        0.045  0.076457231    3868.5613    25.687511   -1.0095684   0.82677249    -1068.466    4974.0031   -1067.6392 
+     500         0.05  0.076457204    3838.4905    34.604697   -1.0349855     1.113779    -1068.753    4157.1837   -1067.6392 
+     550        0.055  0.076457196    3775.1404    44.251809   -1.0609123    1.4242788   -1069.0635       3357.1   -1067.6392 
+     600         0.06  0.076457188    3604.8828    52.475202   -1.0880854    1.6889551   -1069.3282    2752.0424   -1067.6392 
+     650        0.065   0.07645718    3345.5894    57.926479   -1.1179657    1.8644087   -1069.5036    2467.7403   -1067.6392 
+     700         0.07  0.076457185    3138.2001    60.030548   -1.1469999    1.9321298   -1069.5714    2510.1752   -1067.6392 
+     750        0.075   0.07645719    3074.9626    59.122504   -1.1721939    1.9029037   -1069.5421    2788.7489   -1067.6392 
+     800         0.08  0.076457195    3103.5294    56.349146   -1.1949365     1.813641   -1069.4529    3192.5158   -1067.6392 
+     850        0.085  0.076457199    3164.2317    53.154464   -1.2164642    1.7108177     -1069.35     3602.931   -1067.6392 
+     900         0.09  0.076457199    3228.1358    50.837416   -1.2366018    1.6362417   -1069.2755    3917.0758   -1067.6392 
+     950        0.095  0.076457222    3247.5532    50.234549   -1.2539657    1.6168379   -1069.2561    4059.9275   -1067.6392 
+    1000          0.1  0.076457266    3208.3875    51.592727   -1.2671834    1.6605519   -1069.2998    4001.4995   -1067.6392 
+Loop time of 1.47769 on 4 procs for 1000 steps with 250 atoms
+
+Performance: 5.847 ns/day, 4.105 hours/ns, 676.731 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.21791    | 0.22724    | 0.23568    |   1.4 | 15.38
+Neigh   | 0.001137   | 0.0011771  | 0.0012221  |   0.1 |  0.08
+Comm    | 0.066727   | 0.074288   | 0.083826   |   2.3 |  5.03
+Output  | 0.0017431  | 0.0017657  | 0.0018256  |   0.1 |  0.12
+Modify  | 1.1707     | 1.1718     | 1.1725     |   0.1 | 79.30
+Other   |            | 0.001427   |            |       |  0.10
+
+Nlocal:    62.5 ave 66 max 60 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost:    844 ave 857 max 829 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs:    1962.5 ave 2096 max 1855 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+FullNghs:  3925 ave 4139 max 3766 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 15700
+Ave neighs/atom = 62.8
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
diff --git a/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1 b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1
new file mode 100644
index 0000000000..22957c8498
--- /dev/null
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.1
@@ -0,0 +1,139 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.00101709 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 -1.0 0.0 0.0
+  250 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.77337
+  ghost atom cutoff = 5.77337
+  binsize = 2.88668, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.82 | 7.82 | 7.82 Mbytes
+Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
+       0            0           -1            0            0            1            0    -55.58269   -1097.7914   -1094.5727 
+      50        0.005           -1            0            0            1            0   -55.581417   -1097.6764   -1094.5733 
+     100         0.01           -1            0            0            1            0   -55.577759     -1097.35   -1094.5751 
+     150        0.015           -1            0            0            1            0    -55.57219   -1096.8677   -1094.5779 
+     200         0.02           -1            0            0            1            0   -55.565438   -1096.3163   -1094.5813 
+     250        0.025           -1            0            0            1            0   -55.558379   -1095.7987   -1094.5848 
+     300         0.03           -1            0            0            1            0   -55.551886   -1095.4103   -1094.5881 
+     350        0.035           -1            0            0            1            0   -55.546675   -1095.2124   -1094.5907 
+     400         0.04           -1            0            0            1            0   -55.543187   -1095.2153   -1094.5924 
+     450        0.045           -1            0            0            1            0    -55.54154    -1095.379   -1094.5932 
+     500         0.05           -1            0            0            1            0   -55.541574    -1095.633   -1094.5932 
+     550        0.055           -1            0            0            1            0   -55.542941   -1095.9006   -1094.5925 
+     600         0.06           -1            0            0            1            0   -55.545209   -1096.1205   -1094.5914 
+     650        0.065           -1            0            0            1            0   -55.547951   -1096.2575     -1094.59 
+     700         0.07           -1            0            0            1            0   -55.550801   -1096.3044   -1094.5886 
+     750        0.075           -1            0            0            1            0   -55.553483   -1096.2778   -1094.5873 
+     800         0.08           -1            0            0            1            0   -55.555816   -1096.2098   -1094.5861 
+     850        0.085           -1            0            0            1            0   -55.557706   -1096.1372   -1094.5852 
+     900         0.09           -1            0            0            1            0    -55.55913   -1096.0919   -1094.5844 
+     950        0.095           -1            0            0            1            0   -55.560111   -1096.0925    -1094.584 
+    1000          0.1           -1            0            0            1            0   -55.560705   -1096.1411   -1094.5837 
+Loop time of 1.74825 on 1 procs for 1000 steps with 250 atoms
+
+Performance: 4.942 ns/day, 4.856 hours/ns, 571.999 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.80384    | 0.80384    | 0.80384    |   0.0 | 45.98
+Neigh   | 0.004528   | 0.004528   | 0.004528   |   0.0 |  0.26
+Comm    | 0.022954   | 0.022954   | 0.022954   |   0.0 |  1.31
+Output  | 0.0034568  | 0.0034568  | 0.0034568  |   0.0 |  0.20
+Modify  | 0.91007    | 0.91007    | 0.91007    |   0.0 | 52.06
+Other   |            | 0.003404   |            |       |  0.19
+
+Nlocal:    250 ave 250 max 250 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1415 ave 1415 max 1415 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    7873 ave 7873 max 7873 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  15746 ave 15746 max 15746 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15746
+Ave neighs/atom = 62.984
+Neighbor list builds = 6
+Dangerous builds = 0
+# min_style 	spin
+# min_modify	alpha_damp 1.0 discrete_factor 10
+# minimize 	1.0e-16 1.0e-16 10000 10000
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4 b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
similarity index 58%
rename from examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4
rename to examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
index 677805d26a..60db1064e0 100644
--- a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.4
+++ b/examples/SPIN/iron/log.19Nov19.spin.iron_cubic.g++.4
@@ -1,9 +1,7 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
+LAMMPS (30 Oct 2019)
 # bcc iron in a 3d periodic box
 
 clear
-  using 1 OpenMP thread(s) per MPI task
 units 		metal
 atom_style 	spin
 
@@ -21,7 +19,7 @@ Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 250 atoms
-  create_atoms CPU = 0.000627756 secs
+  create_atoms CPU = 0.000651121 secs
 
 # setting mass, mag. moments, and interactions for bcc iron
 
@@ -40,7 +38,7 @@ fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -61,9 +59,9 @@ thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+dump 		1 all custom 100 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		2000
+run 		1000
 Neighbor list info ...
   update every 10 steps, delay 20 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -81,7 +79,7 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.766 | 7.766 | 7.766 Mbytes
 Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
        0            0           -1            0            0            1            0    -55.58269   -1125.5827    -1122.364 
       50        0.005           -1            0            0            1            0   -55.581457   -1125.4635    -1122.364 
@@ -104,53 +102,33 @@ Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng
      900         0.09           -1            0            0            1            0   -55.560147   -1123.8404    -1122.364 
      950        0.095           -1            0            0            1            0   -55.560992   -1123.8312    -1122.364 
     1000          0.1           -1            0            0            1            0   -55.561635   -1123.8853    -1122.364 
-    1050        0.105           -1            0            0            1            0   -55.562156   -1123.9898    -1122.364 
-    1100         0.11           -1            0            0            1            0   -55.562594   -1124.1174    -1122.364 
-    1150        0.115           -1            0            0            1            0   -55.562944   -1124.2349    -1122.364 
-    1200         0.12           -1            0            0            1            0   -55.563163   -1124.3115    -1122.364 
-    1250        0.125           -1            0            0            1            0   -55.563193   -1124.3273    -1122.364 
-    1300         0.13           -1            0            0            1            0   -55.562982   -1124.2776    -1122.364 
-    1350        0.135           -1            0            0            1            0   -55.562513   -1124.1744    -1122.364 
-    1400         0.14           -1            0            0            1            0   -55.561812   -1124.0433    -1122.364 
-    1450        0.145           -1            0            0            1            0   -55.560956   -1123.9169    -1122.364 
-    1500         0.15           -1            0            0            1            0   -55.560057   -1123.8268    -1122.364 
-    1550        0.155           -1            0            0            1            0   -55.559235   -1123.7951    -1122.364 
-    1600         0.16           -1            0            0            1            0    -55.55859   -1123.8282    -1122.364 
-    1650        0.165           -1            0            0            1            0   -55.558174   -1123.9155    -1122.364 
-    1700         0.17           -1            0            0            1            0   -55.557974   -1124.0311    -1122.364 
-    1750        0.175           -1            0            0            1            0   -55.557913   -1124.1409    -1122.364 
-    1800         0.18           -1            0            0            1            0    -55.55788    -1124.212    -1122.364 
-    1850        0.185           -1            0            0            1            0   -55.557753   -1124.2208    -1122.364 
-    1900         0.19           -1            0            0            1            0   -55.557448   -1124.1596    -1122.364 
-    1950        0.195           -1            0            0            1            0   -55.556942   -1124.0384    -1122.364 
-    2000          0.2           -1            0            0            1            0   -55.556288    -1123.883    -1122.364 
-Loop time of 4.39485 on 4 procs for 2000 steps with 250 atoms
+Loop time of 1.5074 on 4 procs for 1000 steps with 250 atoms
 
-Performance: 3.932 ns/day, 6.104 hours/ns, 455.078 timesteps/s
-98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 5.732 ns/day, 4.187 hours/ns, 663.393 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.64527    | 0.6695     | 0.71114    |   3.3 | 15.23
-Neigh   | 0.0032711  | 0.0034365  | 0.0036387  |   0.3 |  0.08
-Comm    | 0.14872    | 0.19108    | 0.21485    |   6.1 |  4.35
-Output  | 0.40622    | 0.43119    | 0.45149    |   2.5 |  9.81
-Modify  | 3.0688     | 3.0921     | 3.1179     |   1.0 | 70.36
-Other   |            | 0.007548   |            |       |  0.17
+Pair    | 0.22156    | 0.23223    | 0.24219    |   1.5 | 15.41
+Neigh   | 0.0011292  | 0.0011852  | 0.0012362  |   0.1 |  0.08
+Comm    | 0.067507   | 0.076341   | 0.087237   |   2.6 |  5.06
+Output  | 0.0015073  | 0.0015442  | 0.0015914  |   0.1 |  0.10
+Modify  | 1.1934     | 1.1947     | 1.1955     |   0.1 | 79.25
+Other   |            | 0.001434   |            |       |  0.10
 
-Nlocal:    62.5 ave 67 max 57 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost:    850.5 ave 856 max 847 min
-Histogram: 1 0 1 1 0 0 0 0 0 1
-Neighs:    1968.75 ave 2101 max 1792 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-FullNghs:  3937.5 ave 4217 max 3583 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
+Nlocal:    62.5 ave 66 max 60 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost:    848.25 ave 861 max 834 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    1962.75 ave 2087 max 1870 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+FullNghs:  3925.5 ave 4138 max 3776 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
 
-Total # of neighbors = 15750
-Ave neighs/atom = 63
-Neighbor list builds = 12
+Total # of neighbors = 15702
+Ave neighs/atom = 62.808
+Neighbor list builds = 6
 Dangerous builds = 0
 # min_style 	spin
 # min_modify	alpha_damp 1.0 discrete_factor 10
@@ -158,4 +136,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:04
+Total wall time: 0:00:01
diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1 b/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1
deleted file mode 100644
index f02c43e28c..0000000000
--- a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.1
+++ /dev/null
@@ -1,1117 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# bcc iron in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	bcc 2.8665
-Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 250 atoms
-  create_atoms CPU = 0.00074935 secs
-
-# setting mass, mag. moments, and interactions for bcc iron
-
-mass		1 55.845
-
-set 		group all spin/random 31 2.2
-  250 settings made for spin/random
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
-pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
-pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		50000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.77337
-  ghost atom cutoff = 5.77337
-  binsize = 2.88668, bins = 5 5 5
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes
-Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng 
-       0            0  0.076456975    9109.0924    100.00358  -0.85791269    3.2186929   -1070.8579   -1067.6392 
-      50        0.005  0.076456974    9316.7659    96.663685  -0.86504718    3.1111957   -1070.7504   -1067.6392 
-     100         0.01  0.076456983    9488.3743    86.965803  -0.88035771    2.7990619   -1070.4383   -1067.6392 
-     150        0.015  0.076456973    9589.0566    72.421197   -0.8996913    2.3309324   -1069.9702   -1067.6392 
-     200         0.02  0.076456944    9415.3095    55.633188    -0.921682    1.7905973   -1069.4298   -1067.6392 
-     250        0.025  0.076456953    8878.9394    39.802206  -0.94649004    1.2810649   -1068.9203   -1067.6392 
-     300         0.03  0.076457027    8203.3388    27.882295  -0.97253854    0.8974133   -1068.5366   -1067.6392 
-     350        0.035  0.076457103     7720.309    21.776538  -0.99708692   0.70089477   -1068.3401   -1067.6392 
-     400         0.04  0.076457117    7531.0683    21.857102   -1.0190244   0.70348778   -1068.3427   -1067.6392 
-     450        0.045  0.076457072    7479.8073    26.959407   -1.0389343   0.86770942   -1068.5069   -1067.6392 
-     500         0.05  0.076457001    7461.6683     34.92521   -1.0582008     1.124095   -1068.7633   -1067.6392 
-     550        0.055  0.076456962    7396.1112    43.405912   -1.0785156     1.397053   -1069.0363   -1067.6392 
-     600         0.06  0.076456997     7121.894    50.544844    -1.102048     1.626825   -1069.2661   -1067.6392 
-     650        0.065  0.076457079    6683.4805    55.261218   -1.1296588    1.7786252   -1069.4179   -1067.6392 
-     700         0.07  0.076457136    6313.6896     57.25083   -1.1595102    1.8426624   -1069.4819   -1067.6392 
-     750        0.075  0.076457132    6199.0363    56.934336   -1.1893875    1.8324758   -1069.4717   -1067.6392 
-     800         0.08  0.076457116     6265.997    55.266343   -1.2181223    1.7787901    -1069.418   -1067.6392 
-     850        0.085  0.076457116    6326.5886    53.376453   -1.2443326    1.7179626   -1069.3572   -1067.6392 
-     900         0.09  0.076457121    6336.1261    52.279557   -1.2676425    1.6826581   -1069.3219   -1067.6392 
-     950        0.095  0.076457122    6288.4204    52.667743   -1.2902335    1.6951522   -1069.3344   -1067.6392 
-    1000          0.1  0.076457135    6122.1622    54.684094    -1.314147      1.76005   -1069.3993   -1067.6392 
-    1050        0.105  0.076457155    5830.2219    57.880399   -1.3392396    1.8629256   -1069.5022   -1067.6392 
-    1100         0.11  0.076457162    5477.4214    61.505616   -1.3662331     1.979606   -1069.6188   -1067.6392 
-    1150        0.115  0.076457195    5194.1423    64.810972   -1.3984474    2.0859914   -1069.7252   -1067.6392 
-    1200         0.12  0.076457219    5096.2484    67.147472    -1.438326    2.1611935   -1069.8004   -1067.6392 
-    1250        0.125  0.076457214    5180.7444    67.957533   -1.4822383    2.1872659   -1069.8265   -1067.6392 
-    1300         0.13  0.076457208    5332.4483     66.96652   -1.5226303    2.1553694   -1069.7946   -1067.6392 
-    1350        0.135  0.076457225    5441.1287    64.471602   -1.5553539    2.0750686   -1069.7143   -1067.6392 
-    1400         0.14  0.076457244    5466.8622    61.292592   -1.5804721    1.9727496    -1069.612   -1067.6392 
-    1450        0.145   0.07645724     5403.309    58.518161   -1.6006864    1.8834524   -1069.5227   -1067.6392 
-    1500         0.15  0.076457224    5275.2171      57.1713   -1.6196756    1.8401027   -1069.4793   -1067.6392 
-    1550        0.155  0.076457217    5122.7481    57.878063   -1.6407322    1.8628504   -1069.5021   -1067.6392 
-    1600         0.16  0.076457217    4968.5049    60.639452   -1.6657935    1.9517278    -1069.591   -1067.6392 
-    1650        0.165  0.076457208    4850.1861    64.668839    -1.690847    2.0814168   -1069.7206   -1067.6392 
-    1700         0.17  0.076457217    4809.0194    68.693586   -1.7087416    2.2109564   -1069.8502   -1067.6392 
-    1750        0.175  0.076457274    4835.8611    71.611033   -1.7188587    2.3048567   -1069.9441   -1067.6392 
-    1800         0.18  0.076457318    4929.7428    72.815077   -1.7280248    2.3436098   -1069.9828   -1067.6392 
-    1850        0.185  0.076457279    5036.6365    72.102335   -1.7426092    2.3206696   -1069.9599   -1067.6392 
-    1900         0.19  0.076457222    5116.2436    69.579977   -1.7638235    2.2394856   -1069.8787   -1067.6392 
-    1950        0.195  0.076457228    5207.2334    65.715745   -1.7895824    2.1151122   -1069.7543   -1067.6392 
-    2000          0.2  0.076457288    5216.0413    61.340972   -1.8174915    1.9743068   -1069.6135   -1067.6392 
-    2050        0.205  0.076457267    5023.1601    57.468628   -1.8456914    1.8496724   -1069.4889   -1067.6392 
-    2100         0.21  0.076457198    4748.7818    55.033266   -1.8742291    1.7712884   -1069.4105   -1067.6392 
-    2150        0.215  0.076457199    4558.1302    54.573806   -1.9035225    1.7565003   -1069.3957   -1067.6392 
-    2200         0.22  0.076457185    4483.1644    56.074241   -1.9322669     1.804793    -1069.444   -1067.6392 
-    2250        0.225  0.076457114    4430.1583      59.0552   -1.9577399    1.9007374     -1069.54   -1067.6392 
-    2300         0.23  0.076457092    4353.7973    62.874849   -1.9801275    2.0236758   -1069.6629   -1067.6392 
-    2350        0.235  0.076457145    4303.5275    66.892738   -2.0022129    2.1529947   -1069.7922   -1067.6392 
-    2400         0.24  0.076457171    4258.6889    70.426826   -2.0233072    2.2667421    -1069.906   -1067.6392 
-    2450        0.245  0.076457169    4178.5775    72.910422   -2.0405304    2.3466785   -1069.9859   -1067.6392 
-    2500         0.25   0.07645717     4114.786    74.106367   -2.0531755    2.3851709   -1070.0244   -1067.6392 
-    2550        0.255  0.076457136    4067.5017    74.169349   -2.0634674    2.3871981   -1070.0264   -1067.6392 
-    2600         0.26  0.076457099    4045.3324    73.586199   -2.0755814    2.3684289   -1070.0077   -1067.6392 
-    2650        0.265  0.076457099     4137.898    72.914235   -2.0913646    2.3468012    -1069.986   -1067.6392 
-    2700         0.27  0.076457106     4332.063    72.583192   -2.1091075    2.3361464   -1069.9754   -1067.6392 
-    2750        0.275   0.07645709    4465.1953    72.814559    -2.125099    2.3435931   -1069.9828   -1067.6392 
-    2800         0.28  0.076457051    4516.5192    73.652154   -2.1371914    2.3705517   -1070.0098   -1067.6392 
-    2850        0.285  0.076457019    4555.5962    75.060211   -2.1489378    2.4158711   -1070.0551   -1067.6392 
-    2900         0.29  0.076457069    4544.2734    76.844795   -2.1667679    2.4733094   -1070.1125   -1067.6392 
-    2950        0.295  0.076457172    4460.2109     78.48171   -2.1924421    2.5259948   -1070.1652   -1067.6392 
-    3000          0.3  0.076457219    4323.2746     79.20682   -2.2209955     2.549333   -1070.1886   -1067.6392 
-    3050        0.305  0.076457213     4155.688    78.543529   -2.2505299    2.5279844   -1070.1672   -1067.6392 
-    3100         0.31  0.076457203    3969.6188    76.554785   -2.2858382    2.4639752   -1070.1032   -1067.6392 
-    3150        0.315  0.076457187     3761.432    73.396149   -2.3245055     2.362312   -1070.0015   -1067.6392 
-    3200         0.32  0.076457142    3602.8035    69.313196   -2.3577056     2.230899   -1069.8701   -1067.6392 
-    3250        0.325  0.076457116     3505.707    65.032482   -2.3836874    2.0931209   -1069.7324   -1067.6392 
-    3300         0.33   0.07645716    3424.8795    61.551539   -2.4057167    1.9810841   -1069.6203   -1067.6392 
-    3350        0.335  0.076457236    3335.9672    59.709703   -2.4251844    1.9218031    -1069.561   -1067.6392 
-    3400         0.34  0.076457298    3238.0186    60.026953   -2.4425501    1.9320141   -1069.5712   -1067.6392 
-    3450        0.345  0.076457297    3185.0674    62.613739   -2.4593531    2.0152718   -1069.6545   -1067.6392 
-    3500         0.35   0.07645723    3197.4087    67.011871   -2.4756907    2.1568291   -1069.7961   -1067.6392 
-    3550        0.355  0.076457177    3216.1428    72.316209   -2.4911379    2.3275533   -1069.9668   -1067.6392 
-    3600         0.36  0.076457165    3241.0326    77.550071   -2.5083858    2.4960092   -1070.1352   -1067.6392 
-    3650        0.365  0.076457168    3309.6874    81.877688   -2.5306273    2.6352969   -1070.2745   -1067.6392 
-    3700         0.37   0.07645718     3350.748    84.764646   -2.5595247    2.7282159   -1070.3674   -1067.6392 
-    3750        0.375   0.07645721     3368.085    86.031781   -2.5938559    2.7689996   -1070.4082   -1067.6392 
-    3800         0.38  0.076457208    3425.3173    85.733048   -2.6266899    2.7593847   -1070.3986   -1067.6392 
-    3850        0.385  0.076457165    3420.4429    84.240647   -2.6514805    2.7113506   -1070.3506   -1067.6392 
-    3900         0.39  0.076457146    3323.0403    82.320886   -2.6700966    2.6495616   -1070.2888   -1067.6392 
-    3950        0.395  0.076457179    3273.2625    80.780607   -2.6892405    2.5999865   -1070.2392   -1067.6392 
-    4000          0.4  0.076457229    3313.2671     79.92769    -2.709641    2.5725347   -1070.2118   -1067.6392 
-    4050        0.405  0.076457272    3381.1117    79.663389   -2.7291493     2.564028   -1070.2033   -1067.6392 
-    4100         0.41   0.07645731    3373.3005    79.895158   -2.7514856    2.5714877   -1070.2107   -1067.6392 
-    4150        0.415  0.076457296    3279.6989    80.402828   -2.7788004    2.5878274   -1070.2271   -1067.6392 
-    4200         0.42  0.076457251    3197.0478    80.770336   -2.8064773     2.599656   -1070.2389   -1067.6392 
-    4250        0.425  0.076457243    3160.9065    80.756747   -2.8307967    2.5992186   -1070.2385   -1067.6392 
-    4300         0.43  0.076457282    3173.9599    80.446488    -2.852192    2.5892326   -1070.2285   -1067.6392 
-    4350        0.435  0.076457289    3185.8003    80.110494   -2.8726607    2.5784184   -1070.2177   -1067.6392 
-    4400         0.44  0.076457262    3166.3054    80.045036   -2.8936787    2.5763116   -1070.2155   -1067.6392 
-    4450        0.445  0.076457226    3177.4332    80.500194   -2.9171408    2.5909612   -1070.2302   -1067.6392 
-    4500         0.45  0.076457174    3238.8362    81.573722   -2.9447352    2.6255135   -1070.2647   -1067.6392 
-    4550        0.455   0.07645714    3277.7104    83.104228    -2.975052    2.6747741    -1070.314   -1067.6392 
-    4600         0.46  0.076457157    3224.8571    84.845474   -3.0065552    2.7308174     -1070.37   -1067.6392 
-    4650        0.465  0.076457215    3112.9952    86.608217     -3.03972    2.7875527   -1070.4268   -1067.6392 
-    4700         0.47  0.076457254     3001.141     88.18732    -3.074928    2.8383773   -1070.4776   -1067.6392 
-    4750        0.475  0.076457235    2904.0735    89.204263   -3.1082127    2.8711084   -1070.5103   -1067.6392 
-    4800         0.48  0.076457195    2832.0276     89.24571    -3.134302    2.8724424   -1070.5117   -1067.6392 
-    4850        0.485  0.076457172    2833.7453    88.206351   -3.1541802    2.8389899   -1070.4782   -1067.6392 
-    4900         0.49  0.076457184     2941.993    86.310712   -3.1725372    2.7779773   -1070.4172   -1067.6392 
-    4950        0.495  0.076457228    3082.4825    84.029047   -3.1931038    2.7045401   -1070.3438   -1067.6392 
-    5000          0.5   0.07645727    3155.7096     81.99875   -3.2175967    2.6391934   -1070.2784   -1067.6392 
-    5050        0.505  0.076457297    3162.1875     80.72053   -3.2420202    2.5980529   -1070.2373   -1067.6392 
-    5100         0.51  0.076457279    3133.3889    80.483768   -3.2606472    2.5904325   -1070.2297   -1067.6392 
-    5150        0.515  0.076457223    3144.6361    81.566513   -3.2759117    2.6252815   -1070.2645   -1067.6392 
-    5200         0.52  0.076457166    3156.8183    84.062018   -3.2944729    2.7056013   -1070.3448   -1067.6392 
-    5250        0.525  0.076457128    3059.9886    87.694328   -3.3209415      2.82251   -1070.4617   -1067.6392 
-    5300         0.53  0.076457126    2891.6506    91.782947   -3.3547324    2.9541054   -1070.5933   -1067.6392 
-    5350        0.535  0.076457151    2751.9452    95.417928   -3.3914125    3.0711001   -1070.7103   -1067.6392 
-    5400         0.54   0.07645725    2681.0266    97.845096    -3.427665    3.1492204   -1070.7885   -1067.6392 
-    5450        0.545  0.076457325    2657.0872    98.736021   -3.4632111    3.1778955   -1070.8171   -1067.6392 
-    5500         0.55  0.076457263    2653.1919    98.075728   -3.4957627    3.1566434   -1070.7959   -1067.6392 
-    5550        0.555  0.076457185    2644.2052    96.114965   -3.5208827    3.0935347   -1070.7328   -1067.6392 
-    5600         0.56  0.076457195    2622.4173     93.52581   -3.5389264    3.0102008   -1070.6494   -1067.6392 
-    5650        0.565   0.07645725     2616.385    91.264371   -3.5558734    2.9374146   -1070.5766   -1067.6392 
-    5700         0.57  0.076457256     2608.245    90.135398   -3.5771375    2.9010777   -1070.5403   -1067.6392 
-    5750        0.575  0.076457193    2573.2163    90.456889   -3.6030063    2.9114252   -1070.5507   -1067.6392 
-    5800         0.58  0.076457145    2565.3319    92.099497   -3.6318266    2.9642938   -1070.6035   -1067.6392 
-    5850        0.585  0.076457161    2566.2757    94.625315   -3.6627042    3.0455892   -1070.6848   -1067.6392 
-    5900         0.59  0.076457186    2564.6803    97.321385   -3.6927592    3.1323643   -1070.7716   -1067.6392 
-    5950        0.595  0.076457195    2570.6302    99.384974   -3.7170024    3.1987825    -1070.838   -1067.6392 
-    6000          0.6  0.076457206    2556.8451     100.3814   -3.7363623    3.2308531   -1070.8701   -1067.6392 
-    6050        0.605  0.076457195    2521.7968    100.35236   -3.7587516    3.2299187   -1070.8692   -1067.6392 
-    6100         0.61  0.076457175    2476.1834    99.370379   -3.7869326    3.1983128   -1070.8375   -1067.6392 
-    6150        0.615  0.076457178    2397.2793     97.46598   -3.8168635    3.1370182   -1070.7763   -1067.6392 
-    6200         0.62   0.07645713    2286.8537    94.931722   -3.8450244    3.0554511   -1070.6947   -1067.6392 
-    6250        0.625  0.076457116    2250.5276    92.438472   -3.8722444    2.9752039   -1070.6144   -1067.6392 
-    6300         0.63  0.076457156    2338.5273    90.714367   -3.9006127    2.9197123   -1070.5589   -1067.6392 
-    6350        0.635   0.07645717    2433.0191    90.142302   -3.9291161       2.9013   -1070.5405   -1067.6392 
-    6400         0.64  0.076457159    2467.5427    90.771124   -3.9562695    2.9215391   -1070.5608   -1067.6392 
-    6450        0.645  0.076457107    2475.8649    92.488037   -3.9828137    2.9767993    -1070.616   -1067.6392 
-    6500         0.65    0.0764571    2489.7445    95.127495   -4.0122155    3.0617523    -1070.701   -1067.6392 
-    6550        0.655  0.076457169    2500.4772    98.171784   -4.0419204    3.1597351    -1070.799   -1067.6392 
-    6600         0.66  0.076457208    2530.8002    100.74954   -4.0632043    3.2427022   -1070.8819   -1067.6392 
-    6650        0.665  0.076457205    2539.1451     102.2625   -4.0743218    3.2913979   -1070.9306   -1067.6392 
-    6700         0.67  0.076457193    2456.6604    102.74354   -4.0834224    3.3068807   -1070.9461   -1067.6392 
-    6750        0.675  0.076457138    2387.6116    102.56283   -4.0973681    3.3010644   -1070.9403   -1067.6392 
-    6800         0.68  0.076457109     2401.109    102.04322   -4.1140004    3.2843402   -1070.9236   -1067.6392 
-    6850        0.685  0.076457149     2426.903    101.49411   -4.1282038    3.2666667   -1070.9059   -1067.6392 
-    6900         0.69  0.076457185    2389.4414    101.35418   -4.1401788    3.2621629   -1070.9014   -1067.6392 
-    6950        0.695  0.076457175    2323.8548    101.97407   -4.1517576    3.2821145   -1070.9213   -1067.6392 
-    7000          0.7  0.076457145    2273.8774    103.46341   -4.1630759    3.3300502   -1070.9693   -1067.6392 
-    7050        0.705  0.076457126     2231.652      105.807   -4.1769876    3.4054803   -1071.0447   -1067.6392 
-    7100         0.71  0.076457114    2185.0532    108.81826   -4.1989101    3.5024002   -1071.1416   -1067.6392 
-    7150        0.715  0.076457137    2139.1143    111.85634   -4.2283255    3.6001832   -1071.2394   -1067.6392 
-    7200         0.72  0.076457149    2101.4939    113.84909   -4.2559584    3.6643212   -1071.3036   -1067.6392 
-    7250        0.725   0.07645712    2118.2862    113.94356   -4.2760809    3.6673619   -1071.3066   -1067.6392 
-    7300         0.73  0.076457121    2191.9037    111.95148   -4.2925005    3.6032452   -1071.2425   -1067.6392 
-    7350        0.735  0.076457137    2227.2391     108.2126   -4.3103519    3.4829066   -1071.1221   -1067.6392 
-    7400         0.74  0.076457111     2182.826     103.4321   -4.3300063    3.3290426   -1070.9683   -1067.6392 
-    7450        0.745  0.076457109    2101.7168    98.840049   -4.3541992    3.1812437   -1070.8205   -1067.6392 
-    7500         0.75  0.076457149    2036.3108    95.828239    -4.386682    3.0843062   -1070.7235   -1067.6392 
-    7550        0.755  0.076457161    1994.4837    95.142177   -4.4221587    3.0622248   -1070.7015   -1067.6392 
-    7600         0.76  0.076457127    1970.6785    96.747859   -4.4522387    3.1139049   -1070.7531   -1067.6392 
-    7650        0.765  0.076457086    1993.9417    100.15534   -4.4763203    3.2235774   -1070.8628   -1067.6392 
-    7700         0.77  0.076457048    2073.7836    104.50424   -4.4979798    3.3635502   -1071.0028   -1067.6392 
-    7750        0.775  0.076457026    2168.4033    108.65953   -4.5168753    3.4972912   -1071.1365   -1067.6392 
-    7800         0.78   0.07645702    2217.6427    111.71942   -4.5326251    3.5957762    -1071.235   -1067.6392 
-    7850        0.785  0.076457017    2202.5357    113.33023   -4.5487958    3.6476215   -1071.2869   -1067.6392 
-    7900         0.79  0.076457015     2164.601    113.51362   -4.5690254     3.653524   -1071.2928   -1067.6392 
-    7950        0.795  0.076457037    2131.6906    112.46493   -4.5932729    3.6197711    -1071.259   -1067.6392 
-    8000          0.8  0.076457042    2076.7626    110.60384   -4.6198371    3.5598705   -1071.1991   -1067.6392 
-    8050        0.805   0.07645706    2008.3681    108.69863   -4.6506123    3.4985496   -1071.1378   -1067.6392 
-    8100         0.81  0.076457078    1991.1056    107.59889   -4.6874954    3.4631539   -1071.1024   -1067.6392 
-    8150        0.815  0.076457081     2030.108    107.96066   -4.7301631    3.4747976    -1071.114   -1067.6392 
-    8200         0.82   0.07645709    2053.0781    110.00158   -4.7752612    3.5404861   -1071.1797   -1067.6392 
-    8250        0.825  0.076457092    2080.7633    113.42163   -4.8192627     3.650563   -1071.2898   -1067.6392 
-    8300         0.83  0.076457092    2136.3278      117.426   -4.8602394    3.7794468   -1071.4187   -1067.6392 
-    8350        0.835  0.076457128    2143.1741    120.76905   -4.8928022    3.8870456   -1071.5263   -1067.6392 
-    8400         0.84  0.076457182    2096.2614    122.36127   -4.9132303    3.9382923   -1071.5775   -1067.6392 
-    8450        0.845  0.076457199    2045.0508    121.81432   -4.9242986    3.9206885   -1071.5599   -1067.6392 
-    8500         0.85  0.076457148      1988.55    119.39197   -4.9305717    3.8427231    -1071.482   -1067.6392 
-    8550        0.855  0.076457089    1927.6698    115.82938   -4.9366606    3.7280586   -1071.3673   -1067.6392 
-    8600         0.86    0.0764571    1904.9377    112.15467   -4.9485473    3.6097852    -1071.249   -1067.6392 
-    8650        0.865  0.076457183    1942.1657    109.35829   -4.9712735    3.5197814    -1071.159   -1067.6392 
-    8700         0.87  0.076457275    1995.7079    107.97044   -5.0032067    3.4751123   -1071.1143   -1067.6392 
-    8750        0.875  0.076457274    2021.2979    107.91844   -5.0351272    3.4734386   -1071.1127   -1067.6392 
-    8800         0.88  0.076457159    2019.7716    108.89001   -5.0595657    3.5047095   -1071.1439   -1067.6392 
-    8850        0.885  0.076457056    1997.5026    110.65412   -5.0764543    3.5614886   -1071.2007   -1067.6392 
-    8900         0.89  0.076457086    1958.2352    113.01816   -5.0898539    3.6375771   -1071.2768   -1067.6392 
-    8950        0.895  0.076457184    1948.1688    115.69887   -5.1049282     3.723858   -1071.3631   -1067.6392 
-    9000          0.9  0.076457251    1946.4034     118.2422    -5.125187    3.8057169   -1071.4449   -1067.6392 
-    9050        0.905  0.076457271    1929.5103    120.07623   -5.1485984    3.8647467    -1071.504   -1067.6392 
-    9100         0.91  0.076457223    1920.5823    120.83551   -5.1696144    3.8891848   -1071.5284   -1067.6392 
-    9150        0.915   0.07645719    1947.9739    120.53164   -5.1820234    3.8794043   -1071.5186   -1067.6392 
-    9200         0.92  0.076457191    2021.9322     119.4904   -5.1820769    3.8458913   -1071.4851   -1067.6392 
-    9250        0.925  0.076457189    2120.5676    118.28073   -5.1733083    3.8069571   -1071.4462   -1067.6392 
-    9300         0.93  0.076457202    2218.9759    117.51293   -5.1649043    3.7822448   -1071.4215   -1067.6392 
-    9350        0.935   0.07645722    2256.6996    117.52636    -5.163384    3.7826772   -1071.4219   -1067.6392 
-    9400         0.94  0.076457192    2219.8074    118.22843   -5.1666597    3.8052737   -1071.4445   -1067.6392 
-    9450        0.945  0.076457133    2130.6686    119.30164   -5.1680994    3.8398158    -1071.479   -1067.6392 
-    9500         0.95  0.076457125    2013.4271    120.65247   -5.1678977    3.8832933   -1071.5225   -1067.6392 
-    9550        0.955  0.076457169    1923.3398    122.44923   -5.1747845    3.9411236   -1071.5804   -1067.6392 
-    9600         0.96  0.076457205    1913.1904    124.48108   -5.1900088    4.0065202   -1071.6458   -1067.6392 
-    9650        0.965  0.076457203    1960.3017    126.09586   -5.2054982    4.0584932   -1071.6977   -1067.6392 
-    9700         0.97    0.0764572    1993.4886    126.91655   -5.2204458    4.0849076   -1071.7241   -1067.6392 
-    9750        0.975  0.076457237    2016.3395    126.88895   -5.2391789    4.0840193   -1071.7233   -1067.6392 
-    9800         0.98  0.076457278    2059.2841     125.9798   -5.2613642    4.0547577    -1071.694   -1067.6392 
-    9850        0.985  0.076457268    2076.0892    124.30551   -5.2849423    4.0008692   -1071.6401   -1067.6392 
-    9900         0.99  0.076457232    2054.9566    122.26397   -5.3097299    3.9351607   -1071.5744   -1067.6392 
-    9950        0.995  0.076457211    2050.2277    120.49535   -5.3384666    3.8782362   -1071.5175   -1067.6392 
-   10000            1  0.076457247    2069.6559    119.63397    -5.374562    3.8505122   -1071.4897   -1067.6392 
-   10050        1.005  0.076457306    2079.8366    119.92165   -5.4169176    3.8597712    -1071.499   -1067.6392 
-   10100         1.01  0.076457317    2051.4213     121.0737   -5.4602428     3.896851   -1071.5361   -1067.6392 
-   10150        1.015  0.076457329    2026.2947    122.36851   -5.4975255    3.9385254   -1071.5778   -1067.6392 
-   10200         1.02  0.076457353    2042.1162    122.97997   -5.5239278    3.9582059   -1071.5974   -1067.6392 
-   10250        1.025  0.076457364    2059.2177    122.42397   -5.5402625    3.9403105   -1071.5795   -1067.6392 
-   10300         1.03  0.076457332    2037.1418    120.82131   -5.5531843    3.8887277    -1071.528   -1067.6392 
-   10350        1.035  0.076457305    1953.9125    118.75093   -5.5690263    3.8220908   -1071.4613   -1067.6392 
-   10400         1.04  0.076457265    1845.8999    116.97821   -5.5872522    3.7650343   -1071.4043   -1067.6392 
-   10450        1.045  0.076457218    1789.9704    116.44416   -5.6054265    3.7478455   -1071.3871   -1067.6392 
-   10500         1.05  0.076457227    1790.1722    117.85441   -5.6201726    3.7932355   -1071.4325   -1067.6392 
-   10550        1.055  0.076457265    1792.8951    121.26237   -5.6302348    3.9029234   -1071.5422   -1067.6392 
-   10600         1.06  0.076457285    1801.2253    126.08926   -5.6408443    4.0582808   -1071.6975   -1067.6392 
-   10650        1.065  0.076457276     1848.312    131.30844   -5.6585268    4.2262642   -1071.8655   -1067.6392 
-   10700         1.07  0.076457228     1899.189    135.63605      -5.6833    4.3655515   -1072.0048   -1067.6392 
-   10750        1.075  0.076457196    1933.4466    137.94816   -5.7116789    4.4399687   -1072.0792   -1067.6392 
-   10800         1.08  0.076457209    1952.1407    137.53149   -5.7380474    4.4265577   -1072.0658   -1067.6392 
-   10850        1.085  0.076457232    1956.2467    134.36784   -5.7597709    4.3247333    -1071.964   -1067.6392 
-   10900         1.09  0.076457254    1935.3183    129.23046   -5.7778262    4.1593827   -1071.7986   -1067.6392 
-   10950        1.095   0.07645725    1894.1382    123.56602   -5.7940915    3.9770683   -1071.6163   -1067.6392 
-   11000          1.1  0.076457202    1869.9315    119.13104   -5.8115801    3.8343249   -1071.4736   -1067.6392 
-   11050        1.105  0.076457157    1872.2105     117.1706   -5.8302554    3.7712266   -1071.4105   -1067.6392 
-   11100         1.11  0.076457121    1910.0087    117.93509   -5.8479403    3.7958325   -1071.4351   -1067.6392 
-   11150        1.115  0.076457111    1974.5822     120.8604   -5.8628947    3.8899857   -1071.5292   -1067.6392 
-   11200         1.12  0.076457152    2017.5386    125.16424   -5.8764671    4.0285084   -1071.6677   -1067.6392 
-   11250        1.125  0.076457215    2006.1464    130.14791   -5.8926588    4.1889116   -1071.8281   -1067.6392 
-   11300         1.13  0.076457208    1981.6806    134.97307   -5.9111129     4.344213   -1071.9834   -1067.6392 
-   11350        1.135  0.076457154    1955.8911    138.78712   -5.9293384    4.4669713   -1072.1062   -1067.6392 
-   11400         1.14  0.076457103     1903.025    141.01634   -5.9477992    4.5387205    -1072.178   -1067.6392 
-   11450        1.145  0.076457082    1861.8231    141.41934   -5.9709229    4.5516912   -1072.1909   -1067.6392 
-   11500         1.15  0.076457105       1864.1    139.85754    -5.999873    4.5014233   -1072.1407   -1067.6392 
-   11550        1.155  0.076457135     1864.553    136.29668   -6.0269465    4.3868144    -1072.026   -1067.6392 
-   11600         1.16  0.076457167    1838.5238    131.42789   -6.0482365    4.2301086   -1071.8693   -1067.6392 
-   11650        1.165  0.076457207    1805.0176    126.80497   -6.0718009    4.0813163   -1071.7205   -1067.6392 
-   11700         1.17  0.076457247    1735.2577    124.00212   -6.1059505    3.9911044   -1071.6303   -1067.6392 
-   11750        1.175  0.076457255    1641.4793    123.80317   -6.1481291     3.984701   -1071.6239   -1067.6392 
-   11800         1.18  0.076457236    1596.2043      126.199   -6.1904504    4.0618126    -1071.701   -1067.6392 
-   11850        1.185  0.076457229    1622.0725    130.64719   -6.2272702    4.2049812   -1071.8442   -1067.6392 
-   11900         1.19  0.076457283    1669.7039    136.11282   -6.2551373    4.3808969   -1072.0201   -1067.6392 
-   11950        1.195  0.076457361    1687.4469    141.27818   -6.2753897    4.5471478   -1072.1864   -1067.6392 
-   12000          1.2  0.076457336     1685.355     144.8526    -6.294312    4.6621933   -1072.3014   -1067.6392 
-   12050        1.205  0.076457364    1684.0235    145.75585   -6.3137437     4.691265   -1072.3305   -1067.6392 
-   12100         1.21  0.076457364    1695.7222    143.63233   -6.3312278    4.6229181   -1072.2622   -1067.6392 
-   12150        1.215  0.076457301    1744.0573    139.27223   -6.3471908    4.4825848   -1072.1218   -1067.6392 
-   12200         1.22  0.076457264    1815.5391    134.28007   -6.3640171    4.3219083   -1071.9611   -1067.6392 
-   12250        1.225  0.076457306    1839.4868     130.2409    -6.378914    4.1919044   -1071.8311   -1067.6392 
-   12300         1.23  0.076457381    1791.3388    128.29684   -6.3893167    4.1293333   -1071.7686   -1067.6392 
-   12350        1.235  0.076457382     1713.284    129.07652   -6.4002273     4.154428   -1071.7937   -1067.6392 
-   12400         1.24  0.076457352    1639.3792    132.52697   -6.4176635    4.2654835   -1071.9047   -1067.6392 
-   12450        1.245  0.076457344    1579.8725    137.81757   -6.4424211    4.4357656    -1072.075   -1067.6392 
-   12500         1.25  0.076457303    1557.3644    143.52235   -6.4729454    4.6193783   -1072.2586   -1067.6392 
-   12550        1.255  0.076457277    1618.5087    148.11444   -6.5082137    4.7671782   -1072.4064   -1067.6392 
-   12600         1.26  0.076457326    1720.3013     150.5465   -6.5476118     4.845456   -1072.4847   -1067.6392 
-   12650        1.265  0.076457391    1778.5404    150.56002   -6.5906298    4.8458912   -1072.4851   -1067.6392 
-   12700         1.27  0.076457351    1788.5951    148.56554   -6.6347601    4.7816972   -1072.4209   -1067.6392 
-   12750        1.275  0.076457269    1779.1884    145.24576   -6.6730452    4.6748475   -1072.3141   -1067.6392 
-   12800         1.28   0.07645728    1758.2949    141.40165    -6.701303    4.5511219   -1072.1904   -1067.6392 
-   12850        1.285  0.076457312    1712.5641     137.9123   -6.7240908    4.4388145    -1072.078   -1067.6392 
-   12900         1.29  0.076457327    1668.6646    135.42155   -6.7444763    4.3586478   -1071.9979   -1067.6392 
-   12950        1.295  0.076457332    1653.7008    134.40911   -6.7622343    4.3260615   -1071.9653   -1067.6392 
-   13000          1.3  0.076457334    1678.1215     135.3964   -6.7808215    4.3578383   -1071.9971   -1067.6392 
-   13050        1.305  0.076457316    1709.6866    138.43433   -6.7994699    4.4556163   -1072.0948   -1067.6392 
-   13100         1.31  0.076457256    1719.9198    142.81982   -6.8124215    4.5967668    -1072.236   -1067.6392 
-   13150        1.315  0.076457227    1716.5741    147.42301   -6.8192217     4.744924   -1072.3842   -1067.6392 
-   13200         1.32  0.076457238    1743.2587    150.89049   -6.8222296    4.8565276   -1072.4958   -1067.6392 
-   13250        1.325  0.076457261    1793.7636    151.98662   -6.8200794    4.8918073    -1072.531   -1067.6392 
-   13300         1.33   0.07645729    1825.2569    150.42643   -6.8140605    4.8415915   -1072.4808   -1067.6392 
-   13350        1.335  0.076457252     1838.476    147.28172   -6.8146446    4.7403765   -1072.3796   -1067.6392 
-   13400         1.34  0.076457169    1838.3398    144.11825   -6.8303357    4.6385577   -1072.2778   -1067.6392 
-   13450        1.345  0.076457222    1801.0039    141.93725   -6.8583491    4.5683605   -1072.2076   -1067.6392 
-   13500         1.35  0.076457347     1755.582    140.99498     -6.89022    4.5380327   -1072.1773   -1067.6392 
-   13550        1.355  0.076457427    1733.1918    141.21311   -6.9214427    4.5450535   -1072.1843   -1067.6392 
-   13600         1.36  0.076457431    1712.5682    142.19629   -6.9465697    4.5766981   -1072.2159   -1067.6392 
-   13650        1.365  0.076457399     1717.694     143.5117   -6.9629204    4.6190353   -1072.2583   -1067.6392 
-   13700         1.37  0.076457334    1770.8346    145.13001   -6.9802142     4.671122   -1072.3104   -1067.6392 
-   13750        1.375  0.076457247    1825.1073    146.95312   -7.0064861    4.7298002    -1072.369   -1067.6392 
-   13800         1.38  0.076457256    1824.3539    148.48573   -7.0381068    4.7791285   -1072.4184   -1067.6392 
-   13850        1.385  0.076457313    1782.7326    149.20301   -7.0651441    4.8022147   -1072.4414   -1067.6392 
-   13900         1.39  0.076457295    1750.9167    149.18894   -7.0840385    4.8017618    -1072.441   -1067.6392 
-   13950        1.395  0.076457288    1760.1963    149.12388   -7.1020342    4.7996679   -1072.4389   -1067.6392 
-   14000          1.4  0.076457265    1776.4309    149.46795   -7.1245024    4.8107421     -1072.45   -1067.6392 
-   14050        1.405  0.076457201    1795.0829    150.25585   -7.1514213    4.8361011   -1072.4753   -1067.6392 
-   14100         1.41  0.076457229    1812.6337    151.48841   -7.1831839    4.8757722    -1072.515   -1067.6392 
-   14150        1.415  0.076457297    1801.8728    153.13675   -7.2174201     4.928825   -1072.5681   -1067.6392 
-   14200         1.42  0.076457305    1773.4672    155.06508   -7.2481606    4.9908901   -1072.6301   -1067.6392 
-   14250        1.425  0.076457282    1738.9317    157.04135   -7.2698182    5.0544977   -1072.6937   -1067.6392 
-   14300         1.43  0.076457306    1716.5389    158.77479   -7.2837833    5.1102898   -1072.7495   -1067.6392 
-   14350        1.435   0.07645735    1720.7949     159.7069   -7.2945528    5.1402904   -1072.7795   -1067.6392 
-   14400         1.44  0.076457333    1748.7885    159.02986   -7.3011362    5.1184995   -1072.7577   -1067.6392 
-   14450        1.445  0.076457295    1742.8885    156.42679   -7.3047662    5.0347176    -1072.674   -1067.6392 
-   14500         1.45  0.076457256    1670.5068    152.24569   -7.3102428    4.9001455   -1072.5394   -1067.6392 
-   14550        1.455  0.076457265    1584.5241    147.05373    -7.318176    4.7330384   -1072.3723   -1067.6392 
-   14600         1.46  0.076457287    1529.9826    141.71242   -7.3290619    4.5611241   -1072.2004   -1067.6392 
-   14650        1.465  0.076457308    1510.2873    137.60969   -7.3489824    4.4290747   -1072.0683   -1067.6392 
-   14700         1.47  0.076457333    1517.9737    136.06432   -7.3778607    4.3793359   -1072.0186   -1067.6392 
-   14750        1.475  0.076457349    1536.5785     137.7444   -7.4074887    4.4334105   -1072.0726   -1067.6392 
-   14800         1.48  0.076457332     1570.427    142.60265    -7.435251     4.589777    -1072.229   -1067.6392 
-   14850        1.485  0.076457277    1605.5273    149.55383   -7.4584362     4.813506   -1072.4527   -1067.6392 
-   14900         1.49  0.076457286    1619.5816    156.68247   -7.4687128     5.042947   -1072.6822   -1067.6392 
-   14950        1.495  0.076457352    1628.8798    162.48759   -7.4692532    5.2297891    -1072.869   -1067.6392 
-   15000          1.5  0.076457367    1645.2779    166.28468   -7.4710214    5.3520015   -1072.9912   -1067.6392 
-   15050        1.505  0.076457354    1659.3085    168.01268   -7.4835147    5.4076185   -1073.0469   -1067.6392 
-   15100         1.51  0.076457322    1657.5151     167.8691   -7.5090057    5.4029973   -1073.0422   -1067.6392 
-   15150        1.515  0.076457334    1619.1825    165.90116   -7.5343027    5.3396576   -1072.9789   -1067.6392 
-   15200         1.52  0.076457345     1564.833    162.54809   -7.5475534    5.2317363    -1072.871   -1067.6392 
-   15250        1.525  0.076457333    1526.2301     158.9992   -7.5544031    5.1175126   -1072.7567   -1067.6392 
-   15300         1.53  0.076457299    1516.6129    156.42636   -7.5677145    5.0347037   -1072.6739   -1067.6392 
-   15350        1.535   0.07645727    1514.4631    155.10745   -7.5910984    4.9922537   -1072.6315   -1067.6392 
-   15400         1.54  0.076457295    1489.0219    154.49939   -7.6168589    4.9726826   -1072.6119   -1067.6392 
-   15450        1.545  0.076457307      1454.98    154.09722   -7.6374985    4.9597386    -1072.599   -1067.6392 
-   15500         1.55  0.076457289    1465.2041    153.94567   -7.6532363    4.9548609   -1072.5941   -1067.6392 
-   15550        1.555  0.076457258    1507.1468     154.2404   -7.6663203     4.964347   -1072.6036   -1067.6392 
-   15600         1.56  0.076457196    1529.3808    154.91397   -7.6776911    4.9860264   -1072.6253   -1067.6392 
-   15650        1.565  0.076457177    1523.9817     156.0119    -7.695343     5.021364   -1072.6606   -1067.6392 
-   15700         1.57  0.076457193    1522.7643    157.82491   -7.7296805    5.0797172   -1072.7189   -1067.6392 
-   15750        1.575  0.076457243    1494.5697      160.297   -7.7768073    5.1592832   -1072.7985   -1067.6392 
-   15800         1.58  0.076457287    1432.4424    162.81609   -7.8203339    5.2403621   -1072.8796   -1067.6392 
-   15850        1.585   0.07645733    1402.4977    164.59576   -7.8451116    5.2976423   -1072.9369   -1067.6392 
-   15900         1.59  0.076457402     1416.812    165.26647   -7.8504137    5.3192297   -1072.9585   -1067.6392 
-   15950        1.595  0.076457391    1434.0052    165.00555   -7.8513437    5.3108318   -1072.9501   -1067.6392 
-   16000          1.6   0.07645732     1448.028     163.9183   -7.8607479    5.2758378   -1072.9151   -1067.6392 
-   16050        1.605  0.076457324    1476.1802    161.67871   -7.8741051    5.2037547    -1072.843   -1067.6392 
-   16100         1.61  0.076457365    1517.1195      158.257   -7.8821118    5.0936245   -1072.7329   -1067.6392 
-   16150        1.615   0.07645732    1551.8013    154.48554   -7.8845021    4.9722371   -1072.6115   -1067.6392 
-   16200         1.62  0.076457224    1563.4592    151.61692   -7.8867696    4.8799081   -1072.5191   -1067.6392 
-   16250        1.625  0.076457231    1568.8982    150.52413   -7.8928325    4.8447358    -1072.484   -1067.6392 
-   16300         1.63  0.076457315    1587.8208    151.31592   -7.9028799    4.8702203   -1072.5095   -1067.6392 
-   16350        1.635  0.076457401    1587.1658    153.58503   -7.9155357    4.9432533   -1072.5825   -1067.6392 
-   16400         1.64    0.0764574    1564.8466    156.97281   -7.9329671    5.0522917   -1072.6915   -1067.6392 
-   16450        1.645  0.076457324    1559.9515    161.25392   -7.9569659    5.1900827   -1072.8293   -1067.6392 
-   16500         1.65   0.07645729    1572.1491    166.16033   -7.9871415    5.3479991   -1072.9872   -1067.6392 
-   16550        1.655  0.076457319    1587.1041    171.09675   -8.0223182    5.5068818   -1073.1461   -1067.6392 
-   16600         1.66  0.076457367    1611.2738    175.10798   -8.0612322    5.6359861   -1073.2752   -1067.6392 
-   16650        1.665  0.076457363     1645.197    177.28144    -8.100579    5.7059409   -1073.3452   -1067.6392 
-   16700         1.67  0.076457373     1687.596    177.10275   -8.1330656    5.7001896   -1073.3394   -1067.6392 
-   16750        1.675  0.076457406    1741.0657    174.63626   -8.1549243    5.6208035     -1073.26   -1067.6392 
-   16800         1.68  0.076457428    1770.5295     170.6939   -8.1775588    5.4939157   -1073.1331   -1067.6392 
-   16850        1.685  0.076457412    1764.9164    166.35555   -8.2116214    5.3542824   -1072.9935   -1067.6392 
-   16900         1.69  0.076457377    1753.4555    162.46345     -8.24703    5.2290123   -1072.8682   -1067.6392 
-   16950        1.695  0.076457382    1737.3044    159.85392   -8.2679658    5.1450224   -1072.7843   -1067.6392 
-   17000          1.7  0.076457397    1698.4267    159.38372   -8.2771546    5.1298887   -1072.7691   -1067.6392 
-   17050        1.705  0.076457398    1648.5432    161.02257   -8.2829365    5.1826363   -1072.8219   -1067.6392 
-   17100         1.71  0.076457362    1597.8104    163.90303   -8.2883924    5.2753461   -1072.9146   -1067.6392 
-   17150        1.715  0.076457407    1581.3305    167.13768   -8.2982879    5.3794559   -1073.0187   -1067.6392 
-   17200         1.72  0.076457416    1615.3538    169.91691   -8.3147181    5.4689075   -1073.1081   -1067.6392 
-   17250        1.725  0.076457317     1640.517    171.76528   -8.3382653    5.5283989   -1073.1676   -1067.6392 
-   17300         1.73  0.076457279    1642.0824    172.72393   -8.3672834    5.5592538   -1073.1985   -1067.6392 
-   17350        1.735  0.076457358    1654.7782    173.20812   -8.3956352    5.5748377   -1073.2141   -1067.6392 
-   17400         1.74  0.076457387    1690.9444    174.02756   -8.4250034    5.6012122   -1073.2404   -1067.6392 
-   17450        1.745  0.076457318    1700.9667    175.61591   -8.4582001    5.6523344   -1073.2916   -1067.6392 
-   17500         1.75  0.076457288    1647.3737    177.46686   -8.4919066    5.7119087   -1073.3511   -1067.6392 
-   17550        1.755  0.076457298    1540.9506    178.64086   -8.5244634    5.7496947   -1073.3889   -1067.6392 
-   17600         1.76  0.076457329    1446.6813    178.43003    -8.554886    5.7429089   -1073.3821   -1067.6392 
-   17650        1.765  0.076457379    1412.0895    176.95558   -8.5854884    5.6954528   -1073.3347   -1067.6392 
-   17700         1.77  0.076457349     1414.559     175.0213   -8.6219735    5.6331963   -1073.2724   -1067.6392 
-   17750        1.775  0.076457246    1413.6264    173.04798   -8.6573217    5.5696835   -1073.2089   -1067.6392 
-   17800         1.78  0.076457222     1399.031    170.80066    -8.673405    5.4973518   -1073.1366   -1067.6392 
-   17850        1.785  0.076457257    1402.9589    168.32364   -8.6692442     5.417627   -1073.0569   -1067.6392 
-   17900         1.79  0.076457292    1421.4914    166.26754    -8.667908    5.3514498   -1072.9907   -1067.6392 
-   17950        1.795   0.07645729    1459.6161    165.06532   -8.6883597    5.3127556    -1072.952   -1067.6392 
-   18000          1.8   0.07645728    1526.0272     164.4467    -8.724083    5.2928448   -1072.9321   -1067.6392 
-   18050        1.805  0.076457285     1579.053    164.14599   -8.7580049     5.283166   -1072.9224   -1067.6392 
-   18100         1.81  0.076457295    1585.8299    164.68311   -8.7876471    5.3004537   -1072.9397   -1067.6392 
-   18150        1.815  0.076457311    1571.4213    167.11719     -8.82749    5.3787965    -1073.018   -1067.6392 
-   18200         1.82  0.076457253    1566.7735    171.84493   -8.8828984    5.5309623   -1073.1702   -1067.6392 
-   18250        1.825  0.076457211    1565.9409    178.03402   -8.9379169    5.7301632   -1073.3694   -1067.6392 
-   18300         1.83  0.076457261    1564.3982    184.19934    -8.977693    5.9285986   -1073.5678   -1067.6392 
-   18350        1.835   0.07645725    1565.4674    188.93147   -9.0068361    6.0809061   -1073.7201   -1067.6392 
-   18400         1.84  0.076457214    1575.9469    191.19229   -9.0319747    6.1536724   -1073.7929   -1067.6392 
-   18450        1.845  0.076457289    1591.7212    190.75232   -9.0530056    6.1395115   -1073.7787   -1067.6392 
-   18500         1.85  0.076457356    1602.2968    188.42238   -9.0750081    6.0645207   -1073.7038   -1067.6392 
-   18550        1.855  0.076457289     1601.939    185.22419   -9.1006094    5.9615844   -1073.6008   -1067.6392 
-   18600         1.86  0.076457199    1571.9204    181.88092   -9.1245655    5.8539786   -1073.4932   -1067.6392 
-   18650        1.865  0.076457174    1547.9534    179.20735   -9.1468721    5.7679277   -1073.4072   -1067.6392 
-   18700         1.87  0.076457165    1552.3316    177.96057   -9.1713552    5.7277992    -1073.367   -1067.6392 
-   18750        1.875  0.076457197    1553.5318     178.2992   -9.1953424    5.7386981   -1073.3779   -1067.6392 
-   18800         1.88  0.076457184    1502.7768    179.82752   -9.2133625    5.7878883   -1073.4271   -1067.6392 
-   18850        1.885  0.076457121     1411.167    181.98955    -9.226772     5.857475   -1073.4967   -1067.6392 
-   18900         1.89   0.07645718    1331.5599    184.25555    -9.244306    5.9304078   -1073.5696   -1067.6392 
-   18950        1.895  0.076457306    1300.8838    185.96704    -9.269864    5.9854936   -1073.6247   -1067.6392 
-   19000          1.9  0.076457332    1341.3268    186.45142   -9.2968684    6.0010837   -1073.6403   -1067.6392 
-   19050        1.905  0.076457294    1418.9495    185.73025   -9.3201217    5.9778722   -1073.6171   -1067.6392 
-   19100         1.91  0.076457261    1469.3348    184.71078   -9.3405594    5.9450597   -1073.5843   -1067.6392 
-   19150        1.915   0.07645726    1494.8858    184.40838   -9.3593456    5.9353267   -1073.5746   -1067.6392 
-   19200         1.92  0.076457302    1535.9214    185.12696   -9.3754395     5.958455   -1073.5977   -1067.6392 
-   19250        1.925  0.076457322    1578.5937     186.7022   -9.3955891    6.0091552   -1073.6484   -1067.6392 
-   19300         1.93   0.07645736    1578.7452    188.80101   -9.4323472     6.076707   -1073.7159   -1067.6392 
-   19350        1.935  0.076457464    1549.5413    190.55677   -9.4860328    6.1332175   -1073.7725   -1067.6392 
-   19400         1.94  0.076457401    1518.0105     190.8838    -9.545051    6.1437434    -1073.783   -1067.6392 
-   19450        1.945  0.076457226    1476.9524    189.41845   -9.6005799    6.0965799   -1073.7358   -1067.6392 
-   19500         1.95  0.076457236    1453.8032     186.8834   -9.6531215    6.0149872   -1073.6542   -1067.6392 
-   19550        1.955  0.076457309    1436.5876    184.62159   -9.7075641     5.942189   -1073.5814   -1067.6392 
-   19600         1.96  0.076457314    1395.5458    183.83049   -9.7642712    5.9167271    -1073.556   -1067.6392 
-   19650        1.965  0.076457309     1342.194    185.07394   -9.8173107    5.9567485    -1073.596   -1067.6392 
-   19700         1.97  0.076457382    1296.9221    188.42121    -9.866389    6.0644829   -1073.7037   -1067.6392 
-   19750        1.975  0.076457367    1284.6809    193.29911   -9.9107399    6.2214817   -1073.8607   -1067.6392 
-   19800         1.98  0.076457239    1277.2922    198.66316    -9.946204    6.3941279   -1074.0334   -1067.6392 
-   19850        1.985  0.076457182    1240.7957    203.40147   -9.9754722    6.5466343   -1074.1859   -1067.6392 
-   19900         1.99   0.07645726    1203.1195    206.12078   -10.001353    6.6341571   -1074.2734   -1067.6392 
-   19950        1.995  0.076457363    1202.7274    205.68644   -10.025039    6.6201776   -1074.2594   -1067.6392 
-   20000            2  0.076457341     1220.191    202.20273   -10.047292    6.5080517   -1074.1473   -1067.6392 
-   20050        2.005  0.076457241    1219.9293    197.12841   -10.066398    6.3447308    -1073.984   -1067.6392 
-   20100         2.01  0.076457168    1194.4117    192.23758   -10.079101    6.1873157   -1073.8265   -1067.6392 
-   20150        2.015  0.076457198    1169.6328    188.78101   -10.085348    6.0760632   -1073.7153   -1067.6392 
-   20200         2.02  0.076457237    1170.2112    187.39597   -10.084836    6.0314848   -1073.6707   -1067.6392 
-   20250        2.025  0.076457263    1178.3781    188.35798   -10.080252    6.0624476   -1073.7017   -1067.6392 
-   20300         2.03  0.076457263    1193.5136    191.43468   -10.076517    6.1614738   -1073.8007   -1067.6392 
-   20350        2.035  0.076457217     1217.151    195.69411   -10.073155    6.2985667   -1073.9378   -1067.6392 
-   20400         2.04  0.076457203    1235.3327     200.1109   -10.073615    6.4407245     -1074.08   -1067.6392 
-   20450        2.045  0.076457254    1242.9155    203.63993   -10.081258    6.5543091   -1074.1935   -1067.6392 
-   20500         2.05  0.076457271    1241.9055     205.2779   -10.095394    6.6070286   -1074.2463   -1067.6392 
-   20550        2.055  0.076457271    1221.6949    204.56884   -10.116586    6.5842068   -1074.2234   -1067.6392 
-   20600         2.06  0.076457294    1226.6359    201.68982   -10.144389    6.4915433   -1074.1308   -1067.6392 
-   20650        2.065   0.07645732    1283.4482    197.23304   -10.174916    6.3480985   -1073.9873   -1067.6392 
-   20700         2.07  0.076457316      1329.13    192.42022   -10.208859    6.1931942   -1073.8324   -1067.6392 
-   20750        2.075  0.076457251    1326.0056    189.01786   -10.251588    6.0836867   -1073.7229   -1067.6392 
-   20800         2.08  0.076457224    1289.0675    188.31447   -10.298492    6.0610474   -1073.7003   -1067.6392 
-   20850        2.085  0.076457272    1261.4039    190.77218   -10.344257    6.1401507   -1073.7794   -1067.6392 
-   20900         2.09  0.076457341    1274.4048    195.96512   -10.390177    6.3072895   -1073.9465   -1067.6392 
-   20950        2.095  0.076457382    1294.6179    202.31796    -10.42989    6.5117606    -1074.151   -1067.6392 
-   21000          2.1  0.076457336    1271.5204    207.81694   -10.451365    6.6887496    -1074.328   -1067.6392 
-   21050        2.105  0.076457218    1224.8924    211.49094   -10.462946    6.8070002   -1074.4462   -1067.6392 
-   21100         2.11  0.076457179    1197.0124    213.27369   -10.482662    6.8643792   -1074.5036   -1067.6392 
-   21150        2.115  0.076457232    1200.2169    213.01628   -10.509071    6.8560942   -1074.4953   -1067.6392 
-   21200         2.12  0.076457334    1233.3373    211.01674   -10.539776    6.7917377    -1074.431   -1067.6392 
-   21250        2.125  0.076457324    1292.2293    208.23361   -10.582784    6.7021603   -1074.3414   -1067.6392 
-   21300         2.13  0.076457234    1353.0348    205.33718   -10.632972    6.6089366   -1074.2482   -1067.6392 
-   21350        2.135  0.076457274    1390.9107    202.43255   -10.667402    6.5154488   -1074.1547   -1067.6392 
-   21400         2.14  0.076457309    1398.7408    199.69704   -10.670157    6.4274041   -1074.0666   -1067.6392 
-   21450        2.145  0.076457306    1400.5231    197.71241   -10.646924    6.3635274   -1074.0028   -1067.6392 
-   21500         2.15  0.076457319    1422.7259    197.36253   -10.618311    6.3522661   -1073.9915   -1067.6392 
-   21550        2.155  0.076457297    1434.7766    199.14128   -10.598724    6.4095165   -1074.0487   -1067.6392 
-   21600         2.16  0.076457278    1429.5442    202.52793   -10.589548    6.5185185   -1074.1577   -1067.6392 
-   21650        2.165  0.076457295     1420.497     206.1935   -10.591701     6.636498   -1074.2757   -1067.6392 
-   21700         2.17  0.076457276    1378.0825    208.36958   -10.599065    6.7065365   -1074.3458   -1067.6392 
-   21750        2.175  0.076457297    1325.5891    208.06821   -10.604715    6.6968368   -1074.3361   -1067.6392 
-   21800         2.18  0.076457341    1286.1379    205.87017   -10.612217    6.6260911   -1074.2653   -1067.6392 
-   21850        2.185  0.076457343    1249.4394    203.00417   -10.618963    6.5338467   -1074.1731   -1067.6392 
-   21900         2.19  0.076457342    1219.6068    200.92404   -10.618829    6.4668963   -1074.1061   -1067.6392 
-   21950        2.195  0.076457255    1203.2091    201.06239   -10.615316    6.4713491   -1074.1106   -1067.6392 
-   22000          2.2  0.076457157    1207.2707    203.83245   -10.616122    6.5605055   -1074.1997   -1067.6392 
-   22050        2.205  0.076457174    1213.7955    208.32753   -10.627885    6.7051832   -1074.3444   -1067.6392 
-   22100         2.21  0.076457305    1217.4318    212.84143   -10.652913    6.8504667   -1074.4897   -1067.6392 
-   22150        2.215  0.076457345    1210.5327     215.5321   -10.688094    6.9370678   -1074.5763   -1067.6392 
-   22200         2.22  0.076457215    1195.2458    215.20969    -10.73343    6.9266909   -1074.5659   -1067.6392 
-   22250        2.225  0.076457077    1182.8507    211.73156   -10.788326    6.8147447    -1074.454   -1067.6392 
-   22300         2.23  0.076457075    1161.1546    206.13732   -10.841515    6.6346895   -1074.2739   -1067.6392 
-   22350        2.235  0.076457134    1136.2879    200.67718   -10.880177    6.4589508   -1074.0982   -1067.6392 
-   22400         2.24   0.07645722    1141.1588    197.90394   -10.902196     6.369692   -1074.0089   -1067.6392 
-   22450        2.245   0.07645725    1183.4596    199.22083   -10.913175     6.412077   -1074.0513   -1067.6392 
-   22500         2.25  0.076457199    1229.4238    204.41082   -10.921755    6.5791208   -1074.2184   -1067.6392 
-   22550        2.255  0.076457171     1264.902    212.14836   -10.939819    6.8281595   -1074.4674   -1067.6392 
-   22600         2.26  0.076457158    1287.9026    220.33991   -10.971089     7.091811    -1074.731   -1067.6392 
-   22650        2.265  0.076457207    1311.4828     226.7258   -11.007167    7.2973458   -1074.9366   -1067.6392 
-   22700         2.27  0.076457319    1353.9253    229.84218   -11.040634    7.3976489   -1075.0369   -1067.6392 
-   22750        2.275  0.076457274    1390.1174    229.24441   -11.068644    7.3784091   -1075.0176   -1067.6392 
-   22800         2.28  0.076457156    1387.0664    225.36499   -11.095325    7.2535471   -1074.8928   -1067.6392 
-   22850        2.285  0.076457176    1360.9519    219.18675   -11.130488    7.0546956   -1074.6939   -1067.6392 
-   22900         2.29  0.076457316     1344.359    211.76274   -11.174978    6.8157482    -1074.455   -1067.6392 
-   22950        2.295   0.07645732    1299.3984    204.35647   -11.214963    6.5773717   -1074.2166   -1067.6392 
-   23000          2.3  0.076457162    1231.7571    198.93484     -11.2383    6.4028722   -1074.0421   -1067.6392 
-   23050        2.305   0.07645712    1199.0791    197.45133   -11.245595    6.3551243   -1073.9944   -1067.6392 
-   23100         2.31  0.076457206    1194.5403    200.36018   -11.246069    6.4487479    -1074.088   -1067.6392 
-   23150        2.315   0.07645717    1213.0855    206.27572   -11.249945    6.6391441   -1074.2784   -1067.6392 
-   23200         2.32  0.076457149    1247.0389    212.62317    -11.25317    6.8434419   -1074.4827   -1067.6392 
-   23250        2.325  0.076457232    1252.9771    217.14066   -11.243809    6.9888406   -1074.6281   -1067.6392 
-   23300         2.33  0.076457298    1246.3963     219.5467   -11.230203    7.0662811   -1074.7055   -1067.6392 
-   23350        2.335  0.076457347    1263.8532    220.90621   -11.226826    7.1100378   -1074.7493   -1067.6392 
-   23400         2.34  0.076457343    1278.9193    222.02245   -11.231757    7.1459649   -1074.7852   -1067.6392 
-   23450        2.345  0.076457298    1271.4615    223.28544   -11.242585    7.1866153   -1074.8258   -1067.6392 
-   23500         2.35  0.076457216    1263.4764    224.76526   -11.261772    7.2342444   -1074.8735   -1067.6392 
-   23550        2.355  0.076457156    1269.5953    225.95356   -11.284145    7.2724905   -1074.9117   -1067.6392 
-   23600         2.36  0.076457239     1268.359    226.26773   -11.305282    7.2826025   -1074.9218   -1067.6392 
-   23650        2.365  0.076457257    1265.5906    225.69913     -11.3327    7.2643016   -1074.9035   -1067.6392 
-   23700         2.37  0.076457123    1275.7614    224.53597   -11.374051    7.2268646   -1074.8661   -1067.6392 
-   23750        2.375  0.076457085    1287.3169    222.75095   -11.424079    7.1694122   -1074.8086   -1067.6392 
-   23800         2.38  0.076457174    1303.4659    219.83945   -11.467156    7.0757035   -1074.7149   -1067.6392 
-   23850        2.385  0.076457349    1312.2776     215.4104   -11.491657    6.9331509   -1074.5724   -1067.6392 
-   23900         2.39  0.076457447    1300.2196    210.22181   -11.505842     6.766152   -1074.4054   -1067.6392 
-   23950        2.395  0.076457318    1285.3883    205.91466   -11.523034    6.6275231   -1074.2668   -1067.6392 
-   24000          2.4  0.076457215    1271.3069    203.89116   -11.544141    6.5623954   -1074.2016   -1067.6392 
-   24050        2.405   0.07645717    1275.6297    204.82158   -11.568504    6.5923414   -1074.2316   -1067.6392 
-   24100         2.41  0.076457155    1308.5278    208.28691   -11.593169     6.703876   -1074.3431   -1067.6392 
-   24150        2.415  0.076457173    1320.3939    213.14435   -11.610405    6.8602164   -1074.4994   -1067.6392 
-   24200         2.42  0.076457286    1290.2677    218.34701   -11.616172    7.0276681   -1074.6669   -1067.6392 
-   24250        2.425   0.07645742    1266.5534    223.16759   -11.612622     7.182822   -1074.8221   -1067.6392 
-   24300         2.43  0.076457424    1263.1458    227.14553   -11.607449     7.310855   -1074.9501   -1067.6392 
-   24350        2.435  0.076457322    1278.3394    229.88879   -11.606753    7.3991491   -1075.0384   -1067.6392 
-   24400         2.44  0.076457217    1299.8856    231.18375    -11.60862    7.4408286   -1075.0801   -1067.6392 
-   24450        2.445  0.076457261    1314.6037    231.51695   -11.609751    7.4515526   -1075.0908   -1067.6392 
-   24500         2.45  0.076457395    1306.5195    231.80528   -11.609243    7.4608328   -1075.1001   -1067.6392 
-   24550        2.455  0.076457379    1284.1202    232.64324    -11.61431    7.4878034    -1075.127   -1067.6392 
-   24600         2.46  0.076457237    1266.9925    233.34522   -11.628582     7.510397   -1075.1496   -1067.6392 
-   24650        2.465  0.076457198    1282.9995    232.39636   -11.648257    7.4798573   -1075.1191   -1067.6392 
-   24700         2.47   0.07645726     1305.414    229.20359   -11.674265    7.3770956   -1075.0163   -1067.6392 
-   24750        2.475   0.07645732    1301.6393    224.60137   -11.703977    7.2289695   -1074.8682   -1067.6392 
-   24800         2.48  0.076457337    1286.6037    220.28411   -11.728511     7.090015   -1074.7292   -1067.6392 
-   24850        2.485  0.076457248    1285.2636    217.75575   -11.741746    7.0086378   -1074.6479   -1067.6392 
-   24900         2.49  0.076457211    1273.3347    217.15842   -11.738866    6.9894122   -1074.6286   -1067.6392 
-   24950        2.495  0.076457314    1254.4627    217.67065   -11.724117    7.0058988   -1074.6451   -1067.6392 
-   25000          2.5   0.07645736    1252.7349     218.6929   -11.717307    7.0388007    -1074.678   -1067.6392 
-   25050        2.505  0.076457303    1253.3725     220.1096   -11.733758    7.0843985   -1074.7236   -1067.6392 
-   25100         2.51  0.076457303    1226.6085    221.88399   -11.763112    7.1415083   -1074.7807   -1067.6392 
-   25150        2.515  0.076457323    1179.7816    224.12648   -11.787319    7.2136847   -1074.8529   -1067.6392 
-   25200         2.52  0.076457341    1147.9357    227.17475   -11.806595    7.3117955    -1074.951   -1067.6392 
-   25250        2.525  0.076457289    1122.8538    230.61744   -11.827081    7.4226013   -1075.0618   -1067.6392 
-   25300         2.53  0.076457275    1123.0584    232.62891   -11.840179     7.487342   -1075.1266   -1067.6392 
-   25350        2.535  0.076457325    1135.7283    231.67931   -11.840266    7.4567784    -1075.096   -1067.6392 
-   25400         2.54  0.076457369    1132.9884    228.34818   -11.841402    7.3495632   -1074.9888   -1067.6392 
-   25450        2.545  0.076457373    1126.8396    224.33046   -11.849704    7.2202499   -1074.8595   -1067.6392 
-   25500         2.55  0.076457345    1138.9754    220.94924   -11.854541    7.1114227   -1074.7507   -1067.6392 
-   25550        2.555  0.076457293    1161.4091    218.97947    -11.85351    7.0480242   -1074.6873   -1067.6392 
-   25600         2.56  0.076457314    1174.3492    218.77523   -11.860158    7.0414507   -1074.6807   -1067.6392 
-   25650        2.565   0.07645744    1168.4635    220.04213   -11.881157    7.0822266   -1074.7215   -1067.6392 
-   25700         2.57  0.076457455    1176.9925    222.26325   -11.910611     7.153715   -1074.7929   -1067.6392 
-   25750        2.575  0.076457341    1184.7961    225.03857   -11.939316    7.2430409   -1074.8823   -1067.6392 
-   25800         2.58  0.076457304    1154.7511    227.79451   -11.960291    7.3317431    -1074.971   -1067.6392 
-   25850        2.585  0.076457382    1114.3611    229.90007    -11.97576    7.3995122   -1075.0387   -1067.6392 
-   25900         2.59  0.076457443    1085.8869    230.83015   -11.989347    7.4294476   -1075.0687   -1067.6392 
-   25950        2.595  0.076457402    1078.3201    230.19636   -12.002061    7.4090485   -1075.0483   -1067.6392 
-   26000          2.6  0.076457319    1095.9541    227.61221   -12.008597    7.3258755   -1074.9651   -1067.6392 
-   26050        2.605  0.076457291    1140.9903    223.50282   -12.008527    7.1936117   -1074.8328   -1067.6392 
-   26100         2.61  0.076457385     1178.622    219.76032   -12.018995    7.0731563   -1074.7124   -1067.6392 
-   26150        2.615  0.076457448    1173.4374    218.06955   -12.044671    7.0187377    -1074.658   -1067.6392 
-   26200         2.62  0.076457408    1151.1453    218.96082   -12.075861    7.0474238   -1074.6867   -1067.6392 
-   26250        2.625  0.076457383    1155.4138    222.06391   -12.101821    7.1472992   -1074.7865   -1067.6392 
-   26300         2.63  0.076457372    1194.7964    226.66949   -12.116261    7.2955333   -1074.9348   -1067.6392 
-   26350        2.635  0.076457363    1223.2766    232.21329   -12.127208    7.4739649   -1075.1132   -1067.6392 
-   26400         2.64  0.076457354    1223.9805    237.61275   -12.140513    7.6477507    -1075.287   -1067.6392 
-   26450        2.645  0.076457281     1218.086    241.25999    -12.14955    7.7651401   -1075.4044   -1067.6392 
-   26500         2.65   0.07645724    1226.9905    242.22464   -12.151248    7.7961882   -1075.4354   -1067.6392 
-   26550        2.655  0.076457293    1247.8203     240.6035   -12.151475    7.7440104   -1075.3832   -1067.6392 
-   26600         2.66  0.076457269    1242.9798    237.04434   -12.161376    7.6294559   -1075.2687   -1067.6392 
-   26650        2.665  0.076457162    1205.6877    232.19203   -12.183196    7.4732806   -1075.1125   -1067.6392 
-   26700         2.67   0.07645716    1172.6996    227.25303   -12.214748    7.3143152   -1074.9535   -1067.6392 
-   26750        2.675  0.076457262    1153.9255    224.05517   -12.256042    7.2113895   -1074.8506   -1067.6392 
-   26800         2.68  0.076457311    1136.0414    223.48738   -12.295525    7.1931146   -1074.8323   -1067.6392 
-   26850        2.685  0.076457307    1118.9445    225.12955   -12.319088    7.2459693   -1074.8852   -1067.6392 
-   26900         2.69  0.076457308    1108.0624     228.2382   -12.325255    7.3460238   -1074.9853   -1067.6392 
-   26950        2.695  0.076457378    1116.2269    232.45212   -12.323702    7.4816518   -1075.1209   -1067.6392 
-   27000          2.7   0.07645739    1134.9488    237.58432   -12.328662    7.6468358   -1075.2861   -1067.6392 
-   27050        2.705   0.07645735    1138.9878    242.69968   -12.344967    7.8114775   -1075.4507   -1067.6392 
-   27100         2.71   0.07645736    1129.3313    246.18245   -12.366079    7.9235733   -1075.5628   -1067.6392 
-   27150        2.715  0.076457354    1124.2775    246.92127   -12.384885    7.9473528   -1075.5866   -1067.6392 
-   27200         2.72  0.076457305     1108.739    245.14655   -12.403913    7.8902318   -1075.5295   -1067.6392 
-   27250        2.725  0.076457306    1108.6304    241.74994   -12.427874    7.7809096   -1075.4201   -1067.6392 
-   27300         2.73  0.076457366    1145.8269    237.40384   -12.453673     7.641027   -1075.2803   -1067.6392 
-   27350        2.735  0.076457346    1182.0337    232.72259   -12.475581    7.4903572   -1075.1296   -1067.6392 
-   27400         2.74  0.076457288    1197.1644    228.48145   -12.490327    7.3538529   -1074.9931   -1067.6392 
-   27450        2.745  0.076457272    1211.3793    225.74198    -12.50044    7.2656808   -1074.9049   -1067.6392 
-   27500         2.75  0.076457331    1258.8799    225.52316   -12.511305    7.2586379   -1074.8979   -1067.6392 
-   27550        2.755  0.076457388    1308.0524    227.54337   -12.522462    7.3236601   -1074.9629   -1067.6392 
-   27600         2.76  0.076457348     1328.121    230.14115   -12.523762    7.4072716   -1075.0465   -1067.6392 
-   27650        2.765  0.076457243    1340.2612    232.32442   -12.510293    7.4775417   -1075.1168   -1067.6392 
-   27700         2.77  0.076457161    1351.5963     234.3197   -12.488706    7.5417616    -1075.181   -1067.6392 
-   27750        2.775  0.076457282    1357.7982    236.12334   -12.460757    7.5998128    -1075.239   -1067.6392 
-   27800         2.78  0.076457422    1361.4651    237.29306   -12.430447    7.6374614   -1075.2767   -1067.6392 
-   27850        2.785  0.076457378    1361.9438    237.41071   -12.408369    7.6412479   -1075.2805   -1067.6392 
-   27900         2.79  0.076457207    1354.0021    236.45794   -12.402868    7.6105824   -1075.2498   -1067.6392 
-   27950        2.795  0.076457167    1330.2965    235.02473   -12.414971    7.5644534   -1075.2037   -1067.6392 
-   28000          2.8  0.076457251    1299.3048     233.7726    -12.43317    7.5241524   -1075.1634   -1067.6392 
-   28050        2.805  0.076457269    1277.0133    233.28243   -12.448406    7.5083761   -1075.1476   -1067.6392 
-   28100         2.81  0.076457225    1251.8497     234.0353   -12.464212    7.5326077   -1075.1718   -1067.6392 
-   28150        2.815  0.076457297    1208.4966    235.64084   -12.477803    7.5842833   -1075.2235   -1067.6392 
-   28200         2.82  0.076457399    1198.6158    237.16084   -12.484054    7.6332057   -1075.2724   -1067.6392 
-   28250        2.825  0.076457406    1239.4401     237.9696   -12.486107    7.6592361   -1075.2985   -1067.6392 
-   28300         2.83  0.076457357    1293.9124     237.8743   -12.489779    7.6561691   -1075.2954   -1067.6392 
-   28350        2.835  0.076457319    1312.3301    237.34832    -12.50409      7.63924   -1075.2785   -1067.6392 
-   28400         2.84  0.076457322    1285.5505    237.14016   -12.527163    7.6325402   -1075.2718   -1067.6392 
-   28450        2.845  0.076457378    1245.9557    237.75445   -12.548289    7.6523114   -1075.2915   -1067.6392 
-   28500         2.85  0.076457388    1235.3861    238.91062   -12.557157    7.6895238   -1075.3288   -1067.6392 
-   28550        2.855  0.076457337    1268.9513    240.25184   -12.560084    7.7326918   -1075.3719   -1067.6392 
-   28600         2.86  0.076457363    1304.4221    241.87684   -12.576878    7.7849937   -1075.4242   -1067.6392 
-   28650        2.865  0.076457362    1297.8936    243.05258    -12.60596    7.8228358   -1075.4621   -1067.6392 
-   28700         2.87  0.076457347    1249.8912    242.36176   -12.630048    7.8006014   -1075.4398   -1067.6392 
-   28750        2.875  0.076457391    1211.5737    239.53884   -12.648513    7.7097434    -1075.349   -1067.6392 
-   28800         2.88  0.076457383    1202.6703    235.69511   -12.669768      7.58603   -1075.2253   -1067.6392 
-   28850        2.885   0.07645729    1216.8735    232.20584   -12.686867    7.4737252    -1075.113   -1067.6392 
-   28900         2.89  0.076457246    1241.5924    230.54911   -12.693862    7.4204019   -1075.0596   -1067.6392 
-   28950        2.895  0.076457286     1240.767    231.97347   -12.701097    7.4662461   -1075.1055   -1067.6392 
-   29000          2.9  0.076457358    1217.5962    236.18629   -12.716277    7.6018392   -1075.2411   -1067.6392 
-   29050        2.905  0.076457432    1196.6203    241.17448    -12.73636    7.7623879   -1075.4016   -1067.6392 
-   29100         2.91  0.076457522    1195.7297     244.6264   -12.752906    7.8734904   -1075.5127   -1067.6392 
-   29150        2.915  0.076457557    1231.0931    245.54928   -12.765411    7.9031941   -1075.5424   -1067.6392 
-   29200         2.92   0.07645753    1267.4904    244.15127   -12.781472    7.8581982   -1075.4974   -1067.6392 
-   29250        2.925  0.076457521    1284.1755     240.9389   -12.800258    7.7548054    -1075.394   -1067.6392 
-   29300         2.93  0.076457564    1286.0387    237.25035   -12.821281    7.6360866   -1075.2753   -1067.6392 
-   29350        2.935  0.076457553    1256.2955    235.11519   -12.847909    7.5673647   -1075.2066   -1067.6392 
-   29400         2.94  0.076457534    1204.4184     235.8746   -12.878902     7.591807    -1075.231   -1067.6392 
-   29450        2.945  0.076457502    1156.6997    239.23804   -12.906804     7.700062   -1075.3393   -1067.6392 
-   29500         2.95  0.076457485    1116.1408    243.69565   -12.924534    7.8435336   -1075.4828   -1067.6392 
-   29550        2.955  0.076457504    1105.9977    247.90665   -12.938831     7.979068   -1075.6183   -1067.6392 
-   29600         2.96  0.076457547    1114.6315    250.84823   -12.956708    8.0737448    -1075.713   -1067.6392 
-   29650        2.965   0.07645753    1139.9431    251.55972   -12.974842    8.0966448   -1075.7359   -1067.6392 
-   29700         2.97  0.076457492    1194.9224    249.83103   -12.990073    8.0410056   -1075.6802   -1067.6392 
-   29750        2.975  0.076457443     1239.364     246.6967   -13.001472    7.9401246   -1075.5794   -1067.6392 
-   29800         2.98  0.076457457    1252.6783    243.80542   -13.010513    7.8470666   -1075.4863   -1067.6392 
-   29850        2.985  0.076457512    1240.1645    241.74022   -13.018373    7.7805965   -1075.4198   -1067.6392 
-   29900         2.99  0.076457565    1223.7615    239.43409   -13.020593    7.7063721   -1075.3456   -1067.6392 
-   29950        2.995  0.076457595    1204.1487    235.75951   -13.015055    7.5881027   -1075.2273   -1067.6392 
-   30000            3  0.076457625    1186.3894     230.7717   -13.002308    7.4275663   -1075.0668   -1067.6392 
-   30050        3.005  0.076457551    1196.5894    226.06185   -12.988551     7.275976   -1074.9152   -1067.6392 
-   30100         3.01  0.076457433    1233.2652    224.05561    -12.98272    7.2114038   -1074.8506   -1067.6392 
-   30150        3.015  0.076457506    1263.4065     226.5763   -12.989178    7.2925339   -1074.9318   -1067.6392 
-   30200         3.02  0.076457597    1273.2272    233.82971   -13.003426    7.5259905   -1075.1652   -1067.6392 
-   30250        3.025  0.076457526    1276.9473    244.40258   -13.018097    7.8662868   -1075.5055   -1067.6392 
-   30300         3.03  0.076457432    1275.5446    255.93782   -13.034602    8.2375574   -1075.8768   -1067.6392 
-   30350        3.035  0.076457464    1250.8783    265.87839   -13.057824    8.5575024   -1076.1967   -1067.6392 
-   30400         3.04  0.076457427    1235.9551    272.00442   -13.083661    8.7546732   -1076.3939   -1067.6392 
-   30450        3.045  0.076457316    1235.5042    273.37792   -13.111283    8.7988804   -1076.4381   -1067.6392 
-   30500         3.05   0.07645726    1230.6233    270.64686   -13.146707    8.7109792   -1076.3502   -1067.6392 
-   30550        3.055  0.076457233    1224.1115     265.0222   -13.182314    8.5299452   -1076.1692   -1067.6392 
-   30600         3.06  0.076457361    1212.3027    257.68391   -13.202367    8.2937568    -1075.933   -1067.6392 
-   30650        3.065  0.076457487    1190.0178    249.77024   -13.201564    8.0390489   -1075.6783   -1067.6392 
-   30700         3.07  0.076457394    1161.8109    242.31657   -13.191293    7.7991468   -1075.4384   -1067.6392 
-   30750        3.075  0.076457252    1158.6855    236.08427    -13.18911    7.5985553   -1075.2378   -1067.6392 
-   30800         3.08  0.076457183    1168.5206    231.60347   -13.197075    7.4543374   -1075.0936   -1067.6392 
-   30850        3.085  0.076457279    1158.9328    229.71585   -13.209643    7.3935831   -1075.0328   -1067.6392 
-   30900         3.09  0.076457454    1136.1168    231.05928   -13.230895    7.4368221   -1075.0761   -1067.6392 
-   30950        3.095  0.076457365    1140.4629    234.79871   -13.261019    7.5571786   -1075.1964   -1067.6392 
-   31000          3.1  0.076457233    1151.4718    238.95885     -13.2835     7.691076   -1075.3303   -1067.6392 
-   31050        3.105  0.076457249    1136.0165    241.99628   -13.285479    7.7888381   -1075.4281   -1067.6392 
-   31100         3.11  0.076457312    1095.4919     243.6173   -13.274528     7.841012   -1075.4802   -1067.6392 
-   31150        3.115  0.076457361    1043.3403    244.60685   -13.261288    7.8728613   -1075.5121   -1067.6392 
-   31200         3.12  0.076457255    1000.1386    246.53553   -13.250369    7.9349374   -1075.5742   -1067.6392 
-   31250        3.125  0.076457166    991.81643    250.55835    -13.24872    8.0644151   -1075.7036   -1067.6392 
-   31300         3.13  0.076457166    1022.1079     256.4075   -13.267835    8.2526743   -1075.8919   -1067.6392 
-   31350        3.135  0.076457189    1054.9092    262.76827   -13.305663    8.4574006   -1076.0966   -1067.6392 
-   31400         3.14   0.07645724    1060.5815    267.85735   -13.342713    8.6211968   -1076.2604   -1067.6392 
-   31450        3.145  0.076457287    1049.3579    269.97994    -13.36678    8.6895138   -1076.3287   -1067.6392 
-   31500         3.15  0.076457292    1020.7582     268.2573   -13.386937    8.6340694   -1076.2733   -1067.6392 
-   31550        3.155  0.076457309    996.86817    262.55532   -13.414409    8.4505467   -1076.0898   -1067.6392 
-   31600         3.16  0.076457265     988.4472    253.14804    -13.44617    8.1477662    -1075.787   -1067.6392 
-   31650        3.165   0.07645717    975.20678     241.3533   -13.472839    7.7681433   -1075.4074   -1067.6392 
-   31700         3.17  0.076457122    978.08946    230.12225   -13.489241    7.4066632   -1075.0459   -1067.6392 
-   31750        3.175  0.076457159     994.1906    223.24272     -13.4961    7.1852402   -1074.8245   -1067.6392 
-   31800         3.18  0.076457198    1011.9808    223.61603   -13.502125    7.1972556   -1074.8365   -1067.6392 
-   31850        3.185  0.076457197    1043.2929    231.32793   -13.514524    7.4454691   -1075.0847   -1067.6392 
-   31900         3.19  0.076457211    1073.2125    243.48614   -13.529663    7.8367904    -1075.476   -1067.6392 
-   31950        3.195  0.076457283     1089.512    255.96547   -13.531619    8.2384474   -1075.8777   -1067.6392 
-   32000          3.2  0.076457346    1091.1766    265.64481   -13.515072    8.5499844   -1076.1892   -1067.6392 
-   32050        3.205  0.076457238    1107.4466    271.60773   -13.502747    8.7419056   -1076.3811   -1067.6392 
-   32100         3.21  0.076457153    1117.8805    274.08365    -13.50656    8.8215948   -1076.4608   -1067.6392 
-   32150        3.215  0.076457122    1123.2092    273.86962   -13.522054    8.8147064   -1076.4539   -1067.6392 
-   32200         3.22  0.076457105    1152.6197    271.95614   -13.543888    8.7531194   -1076.3924   -1067.6392 
-   32250        3.225  0.076457164    1168.3769    268.86435   -13.563301    8.6536078   -1076.2928   -1067.6392 
-   32300         3.23  0.076457237    1158.6589    265.10575   -13.580865    8.5326342   -1076.1719   -1067.6392 
-   32350        3.235  0.076457159    1152.9881    261.29815   -13.605255    8.4100836   -1076.0493   -1067.6392 
-   32400         3.24   0.07645703    1164.2634    257.27542   -13.625646     8.280609   -1075.9198   -1067.6392 
-   32450        3.245  0.076457057    1173.0337    252.87376   -13.637472    8.1389381   -1075.7782   -1067.6392 
-   32500         3.25  0.076457171    1170.4615    248.34575   -13.651248    7.9932007   -1075.6324   -1067.6392 
-   32550        3.255  0.076457164    1172.6715    244.01198   -13.667945    7.8537149   -1075.4929   -1067.6392 
-   32600         3.26  0.076457072    1178.0602    240.61161   -13.683594    7.7442715   -1075.3835   -1067.6392 
-   32650        3.265  0.076457132    1164.2276    239.08635   -13.693266    7.6951799   -1075.3344   -1067.6392 
-   32700         3.27   0.07645721    1135.6536      239.997   -13.697188    7.7244896   -1075.3637   -1067.6392 
-   32750        3.275   0.07645717    1122.6725    242.77278   -13.697307    7.8138302   -1075.4531   -1067.6392 
-   32800         3.28  0.076457087    1124.7984    246.08264   -13.698507    7.9203608   -1075.5596   -1067.6392 
-   32850        3.285  0.076457071    1132.9874     248.8912    -13.71026    8.0107565     -1075.65   -1067.6392 
-   32900         3.29  0.076457146    1144.7957    250.92712   -13.736297    8.0762841   -1075.7155   -1067.6392 
-   32950        3.295   0.07645721    1152.7642    252.46291   -13.764351    8.1257148   -1075.7649   -1067.6392 
-   33000          3.3  0.076457168    1146.2857    254.10358   -13.779597    8.1785209   -1075.8178   -1067.6392 
-   33050        3.305  0.076457077    1145.5084     256.8303   -13.789612    8.2662826   -1075.9055   -1067.6392 
-   33100         3.31  0.076457096    1154.4041    261.13865   -13.808552      8.40495   -1076.0442   -1067.6392 
-   33150        3.315   0.07645715    1125.5641     266.3904   -13.833889    8.5739819   -1076.2132   -1067.6392 
-   33200         3.32   0.07645715    1093.2946     271.0557   -13.855364     8.724138   -1076.3634   -1067.6392 
-   33250        3.325  0.076457145    1095.5775    273.48025   -13.872191    8.8021741   -1076.4414   -1067.6392 
-   33300         3.33  0.076457162    1100.9708    272.81497   -13.884719    8.7807615     -1076.42   -1067.6392 
-   33350        3.335   0.07645717     1097.446    269.39464   -13.884534    8.6706755   -1076.3099   -1067.6392 
-   33400         3.34  0.076457107    1081.3925    264.90836   -13.877973    8.5262812   -1076.1655   -1067.6392 
-   33450        3.345  0.076457118    1078.1638    261.34438   -13.882973    8.4115716   -1076.0508   -1067.6392 
-   33500         3.35  0.076457263    1098.4302    259.43885   -13.901235    8.3502409   -1075.9895   -1067.6392 
-   33550        3.355    0.0764573     1113.653    258.79858   -13.925503    8.3296331   -1075.9689   -1067.6392 
-   33600         3.36  0.076457139    1102.1918    258.64576   -13.952352    8.3247147   -1075.9639   -1067.6392 
-   33650        3.365  0.076457044    1079.3943    258.32267   -13.984128    8.3143157   -1075.9535   -1067.6392 
-   33700         3.37  0.076457092    1080.4816     257.3355   -14.022263    8.2825429   -1075.9218   -1067.6392 
-   33750        3.375  0.076457159    1091.9482    255.16753   -14.058006    8.2127649    -1075.852   -1067.6392 
-   33800         3.38  0.076457132    1093.3842     251.7622   -14.081909    8.1031619   -1075.7424   -1067.6392 
-   33850        3.385  0.076457194    1089.6902     248.0965   -14.095869    7.9851785   -1075.6244   -1067.6392 
-   33900         3.39   0.07645727    1096.6474    246.01593   -14.105391    7.9182138   -1075.5574   -1067.6392 
-   33950        3.395  0.076457209     1126.664    247.11823   -14.104952    7.9536921   -1075.5929   -1067.6392 
-   34000          3.4  0.076457164    1147.9196    251.93896   -14.093155    8.1088509   -1075.7481   -1067.6392 
-   34050        3.405  0.076457179    1139.0305    259.69551   -14.085668    8.3585014   -1075.9977   -1067.6392 
-   34100         3.41  0.076457311    1111.5824    268.28371   -14.096523    8.6349193   -1076.2742   -1067.6392 
-   34150        3.415  0.076457318    1093.8889    274.76774   -14.115851    8.8436128   -1076.4828   -1067.6392 
-   34200         3.42  0.076457165     1080.138    277.06119   -14.126901    8.9174293   -1076.5567   -1067.6392 
-   34250        3.425  0.076457126    1068.8702    275.51584   -14.137497     8.867691   -1076.5069   -1067.6392 
-   34300         3.43  0.076457173    1079.0654    272.17988   -14.166544    8.7603208   -1076.3996   -1067.6392 
-   34350        3.435  0.076457237    1097.2929    268.53315   -14.204534    8.6429479   -1076.2822   -1067.6392 
-   34400         3.44  0.076457306    1090.4064    265.24166   -14.230854    8.5370086   -1076.1762   -1067.6392 
-   34450        3.445  0.076457334    1094.1532    263.10158    -14.24558    8.4681285   -1076.1074   -1067.6392 
-   34500         3.45  0.076457326    1091.6462    262.74486   -14.260327    8.4566473   -1076.0959   -1067.6392 
-   34550        3.455  0.076457285    1048.9417    263.68384   -14.279645     8.486869   -1076.1261   -1067.6392 
-   34600         3.46  0.076457322    1035.8659    264.38837   -14.298673     8.509545   -1076.1488   -1067.6392 
-   34650        3.465  0.076457348    1072.1468    263.89728   -14.317443    8.4937389    -1076.133   -1067.6392 
-   34700         3.47  0.076457257    1099.9068     262.7456   -14.336515    8.4566712   -1076.0959   -1067.6392 
-   34750        3.475   0.07645724    1086.8308    262.31079   -14.346872    8.4426763   -1076.0819   -1067.6392 
-   34800         3.48  0.076457278    1063.2908     263.8317   -14.348034     8.491628   -1076.1309   -1067.6392 
-   34850        3.485  0.076457253    1055.3547    267.54832   -14.355638    8.6112503   -1076.2505   -1067.6392 
-   34900         3.49  0.076457295    1035.2728    272.01532   -14.373099    8.7550243   -1076.3943   -1067.6392 
-   34950        3.495  0.076457375     1040.634    275.06802   -14.390413    8.8532777   -1076.4925   -1067.6392 
-   35000          3.5  0.076457344    1063.0087     275.5042   -14.407745    8.8673167   -1076.5065   -1067.6392 
-   35050        3.505  0.076457312    1058.6708    273.65876   -14.433515    8.8079196   -1076.4472   -1067.6392 
-   35100         3.51  0.076457257    1060.8523    271.14098   -14.474773    8.7268829   -1076.3661   -1067.6392 
-   35150        3.515  0.076457289    1067.0827    269.23085   -14.526301    8.6654039   -1076.3046   -1067.6392 
-   35200         3.52   0.07645742    1062.2236    268.14335   -14.573177    8.6304019   -1076.2696   -1067.6392 
-   35250        3.525  0.076457337    1070.5812    267.81607    -14.60424    8.6198681   -1076.2591   -1067.6392 
-   35300         3.53  0.076457217    1072.5143    267.83883   -14.617097    8.6206007   -1076.2598   -1067.6392 
-   35350        3.535  0.076457254    1028.3355    267.52283   -14.622569    8.6104298   -1076.2497   -1067.6392 
-   35400         3.54  0.076457305    1002.1085    266.59937   -14.633762    8.5807077   -1076.2199   -1067.6392 
-   35450        3.545  0.076457409     1029.413    265.25698   -14.649797    8.5375018   -1076.1767   -1067.6392 
-   35500         3.55  0.076457478    1063.6674    263.65567   -14.671113    8.4859625   -1076.1252   -1067.6392 
-   35550        3.555  0.076457385    1064.2389    261.55993   -14.712306    8.4185094   -1076.0577   -1067.6392 
-   35600         3.56  0.076457248     1043.973    258.13746   -14.765767    8.3083544   -1075.9476   -1067.6392 
-   35650        3.565  0.076457197    1018.5052    253.81996   -14.810087    8.1693925   -1075.8086   -1067.6392 
-   35700         3.57  0.076457358    1000.6206    251.22894   -14.843694    8.0859983   -1075.7252   -1067.6392 
-   35750        3.575  0.076457447    1017.4159    252.90054   -14.876657       8.1398    -1075.779   -1067.6392 
-   35800         3.58  0.076457294    1047.8317    258.96411   -14.909538    8.3349608   -1075.9742   -1067.6392 
-   35850        3.585  0.076457191    1082.9886    267.72357   -14.939208    8.6168909   -1076.2561   -1067.6392 
-   35900         3.59  0.076457278    1100.5702    277.23543   -14.962644    8.9230375   -1076.5623   -1067.6392 
-   35950        3.595  0.076457309     1086.933    285.96591   -14.977753    9.2040346   -1076.8433   -1067.6392 
-   36000          3.6  0.076457255    1074.2647     292.9362   -14.987968     9.428379   -1077.0676   -1067.6392 
-   36050        3.605   0.07645718    1055.2238    298.01121   -14.998446    9.5917221    -1077.231   -1067.6392 
-   36100         3.61  0.076457233    1047.2166    302.00821   -15.020568    9.7203687   -1077.3596   -1067.6392 
-   36150        3.615  0.076457349    1052.6407    305.28298   -15.059957    9.8257696    -1077.465   -1067.6392 
-   36200         3.62  0.076457311    1060.7211    306.93482    -15.10603    9.8789354   -1077.5182   -1067.6392 
-   36250        3.625  0.076457193    1068.8892    305.84803   -15.141949    9.8439561   -1077.4832   -1067.6392 
-   36300         3.63  0.076457194    1061.6868    301.87989    -15.16629    9.7162384   -1077.3555   -1067.6392 
-   36350        3.635  0.076457258    1057.9527     295.4431   -15.185933    9.5090656   -1077.1483   -1067.6392 
-   36400         3.64  0.076457264    1064.3799    287.24818   -15.203507    9.2453055   -1076.8845   -1067.6392 
-   36450        3.645  0.076457194    1063.7064    278.74515   -15.224498    8.9716288   -1076.6109   -1067.6392 
-   36500         3.65  0.076457136    1061.3588    271.32268     -15.2455     8.732731    -1076.372   -1067.6392 
-   36550        3.655  0.076457182    1067.1517    265.76761   -15.260325    8.5539369   -1076.1932   -1067.6392 
-   36600         3.66   0.07645727    1089.9772    261.85411   -15.267562    8.4279778   -1076.0672   -1067.6392 
-   36650        3.665  0.076457221     1104.789     258.4444   -15.265264    8.3182336   -1075.9575   -1067.6392 
-   36700         3.67   0.07645716    1092.8435    255.00082    -15.25529    8.2073992   -1075.8466   -1067.6392 
-   36750        3.675  0.076457168    1061.6595     252.8329   -15.247428    8.1376232   -1075.7769   -1067.6392 
-   36800         3.68  0.076457215    1035.3281    254.03876   -15.243457    8.1764346   -1075.8157   -1067.6392 
-   36850        3.685  0.076457264    1012.6747    259.66792   -15.232713    8.3576136   -1075.9968   -1067.6392 
-   36900         3.69   0.07645721    1000.1165    269.04132   -15.219475    8.6593036   -1076.2985   -1067.6392 
-   36950        3.695  0.076457158    1004.3738     279.5229   -15.222136    8.9966614   -1076.6359   -1067.6392 
-   37000          3.7  0.076457194    1015.0789    287.52665   -15.242557    9.2542684   -1076.8935   -1067.6392 
-   37050        3.705  0.076457209    1006.6001    291.33936   -15.269368    9.3769835   -1077.0162   -1067.6392 
-   37100         3.71  0.076457215    1009.5254    292.25598   -15.292099    9.4064856   -1077.0457   -1067.6392 
-   37150        3.715  0.076457221    1035.7983     292.7155   -15.306557    9.4212757   -1077.0605   -1067.6392 
-   37200         3.72  0.076457114    1030.9374    293.77202   -15.308274    9.4552805   -1077.0945   -1067.6392 
-   37250        3.725  0.076457028    982.50822     295.2423   -15.305932    9.5026027   -1077.1418   -1067.6392 
-   37300         3.73  0.076457035    948.55083    296.17303   -15.311999    9.5325589   -1077.1718   -1067.6392 
-   37350        3.735  0.076457098    937.47027    295.49824   -15.335364    9.5108401   -1077.1501   -1067.6392 
-   37400         3.74  0.076457181    936.77662    292.98591   -15.385092     9.429979   -1077.0692   -1067.6392 
-   37450        3.745  0.076457164    937.43311    288.88554    -15.44922    9.2980054   -1076.9372   -1067.6392 
-   37500         3.75  0.076457095    942.75677     284.1287   -15.497475    9.1449027   -1076.7841   -1067.6392 
-   37550        3.755  0.076457051    973.14442    280.71281   -15.516447    9.0349597   -1076.6742   -1067.6392 
-   37600         3.76  0.076457064    1023.9535    280.23051   -15.517936    9.0194364   -1076.6587   -1067.6392 
-   37650        3.765  0.076457028    1061.1038    282.66393   -15.519455    9.0977579    -1076.737   -1067.6392 
-   37700         3.77  0.076457072    1070.7829    287.04664   -15.525411    9.2388189   -1076.8781   -1067.6392 
-   37750        3.775  0.076457124    1066.3938    291.68394   -15.520525     9.388074   -1077.0273   -1067.6392 
-   37800         3.78  0.076457071    1048.9796    294.14399   -15.497921    9.4672528   -1077.1065   -1067.6392 
-   37850        3.785  0.076457038    1038.2533    292.47043   -15.480179    9.4133879   -1077.0526   -1067.6392 
-   37900         3.79  0.076457018     1045.648    286.41439   -15.491193    9.2184695   -1076.8577   -1067.6392 
-   37950        3.795  0.076457122    1065.9631    277.89366   -15.523881    8.9442232   -1076.5835   -1067.6392 
-   38000          3.8   0.07645714    1090.5261    270.72264   -15.554861    8.7134183   -1076.3526   -1067.6392 
-   38050        3.805  0.076457032    1113.2307    268.45698   -15.575531    8.6404964   -1076.2797   -1067.6392 
-   38100         3.81  0.076457024    1116.2952    271.45106   -15.582548    8.7368631   -1076.3761   -1067.6392 
-   38150        3.815   0.07645699    1093.8664    277.51108   -15.573712    8.9319094   -1076.5711   -1067.6392 
-   38200         3.82  0.076456911     1051.845    284.62475    -15.56289    9.1608685   -1076.8001   -1067.6392 
-   38250        3.825  0.076456883    1005.6732    291.31425   -15.566443    9.3761751   -1077.0154   -1067.6392 
-   38300         3.83  0.076456909    998.58464    295.80008   -15.577737    9.5205551   -1077.1598   -1067.6392 
-   38350        3.835  0.076456917    1023.8255    296.91935    -15.58617    9.5565797   -1077.1958   -1067.6392 
-   38400         3.84  0.076457007    1038.0022     294.9054   -15.596528    9.4917592    -1077.131   -1067.6392 
-   38450        3.845  0.076457031    1037.6121    290.96422   -15.616202    9.3649092   -1077.0041   -1067.6392 
-   38500         3.85  0.076456984    1040.5904    286.88024   -15.646786    9.2334631   -1076.8727   -1067.6392 
-   38550        3.855  0.076456918    1043.2321    284.56473   -15.689543    9.1589367   -1076.7982   -1067.6392 
-   38600         3.86  0.076456877    1038.0862    284.74376   -15.739663    9.1646989   -1076.8039   -1067.6392 
-   38650        3.865  0.076456988    1038.4376    285.95011   -15.776018    9.2035262   -1076.8428   -1067.6392 
-   38700         3.87  0.076457066    1046.7517    286.45113   -15.793545    9.2196518   -1076.8589   -1067.6392 
-   38750        3.875  0.076457085    1069.8363     286.1605   -15.809275    9.2102978   -1076.8495   -1067.6392 
-   38800         3.88  0.076457103    1099.7649    286.35508   -15.838882    9.2165605   -1076.8558   -1067.6392 
-   38850        3.885  0.076457029    1113.9425    288.09011   -15.885059    9.2724039   -1076.9116   -1067.6392 
-   38900         3.89  0.076457017    1105.7043    290.97132   -15.928294    9.3651376   -1077.0044   -1067.6392 
-   38950        3.895  0.076456995    1093.6515    294.07778   -15.945379    9.4651215   -1077.1044   -1067.6392 
-   39000          3.9   0.07645694    1103.4477     297.5125   -15.943567    9.5756706   -1077.2149   -1067.6392 
-   39050        3.905  0.076457006    1109.1277    301.82187   -15.951259    9.7143712   -1077.3536   -1067.6392 
-   39100         3.91  0.076456969    1114.3237    306.51524   -15.985628     9.865431   -1077.5047   -1067.6392 
-   39150        3.915  0.076456912    1114.4623    309.57518   -16.034747    9.9639174   -1077.6032   -1067.6392 
-   39200         3.92   0.07645697    1087.5299    308.28093   -16.061177    9.9222609   -1077.5615   -1067.6392 
-   39250        3.925  0.076457004    1085.9492    302.29555   -16.058242    9.7296168   -1077.3688   -1067.6392 
-   39300         3.93  0.076456952    1107.8421    294.53188   -16.053056    9.4797371    -1077.119   -1067.6392 
-   39350        3.935  0.076456973    1124.1513    288.15688   -16.067119    9.2745528   -1076.9138   -1067.6392 
-   39400         3.94  0.076457054    1137.2475    283.95115   -16.101525    9.1391882   -1076.7784   -1067.6392 
-   39450        3.945   0.07645698    1135.1662    281.54817   -16.141252    9.0618462   -1076.7011   -1067.6392 
-   39500         3.95  0.076456838    1099.0721    281.13694   -16.174509    9.0486105   -1076.6878   -1067.6392 
-   39550        3.955  0.076456882    1049.5257    282.67803   -16.205325    9.0982117   -1076.7374   -1067.6392 
-   39600         3.96  0.076457011    1027.3757    284.94192   -16.234406    9.1710768   -1076.8103   -1067.6392 
-   39650        3.965  0.076456971     1017.794    286.75472   -16.252188    9.2294233   -1076.8687   -1067.6392 
-   39700         3.97  0.076456888    1007.7805    288.56666    -16.25612    9.2877419    -1076.927   -1067.6392 
-   39750        3.975  0.076456865    1012.8541    292.07722   -16.261884    9.4007319     -1077.04   -1067.6392 
-   39800         3.98  0.076456816    1043.1577    297.78139   -16.277698     9.584325   -1077.2236   -1067.6392 
-   39850        3.985  0.076456836    1077.8248    304.26971   -16.297835    9.7931567   -1077.4324   -1067.6392 
-   39900         3.99   0.07645687    1094.0855    309.71669   -16.325371    9.9684719   -1077.6077   -1067.6392 
-   39950        3.995  0.076456883    1064.1015    312.41437   -16.358615    10.055299   -1077.6945   -1067.6392 
-   40000            4  0.076456877    1022.9431    310.99163   -16.375546    10.009507   -1077.6487   -1067.6392 
-   40050        4.005  0.076456756    1013.7056    306.64402   -16.373477    9.8695757   -1077.5088   -1067.6392 
-   40100         4.01  0.076456759    1007.6913    303.35311   -16.376022    9.7636554   -1077.4029   -1067.6392 
-   40150        4.015  0.076456864     1004.252    303.81576   -16.385329    9.7785462   -1077.4178   -1067.6392 
-   40200         4.02  0.076456912    1013.1412    307.22942   -16.384285    9.8884172   -1077.5276   -1067.6392 
-   40250        4.025  0.076456867    1030.3871    310.68562   -16.369477    9.9996578   -1077.6389   -1067.6392 
-   40300         4.03  0.076456789    1034.7373    311.09098   -16.352628    10.012705   -1077.6519   -1067.6392 
-   40350        4.035  0.076456729    1033.1387    307.52717   -16.345575    9.8980007   -1077.5372   -1067.6392 
-   40400         4.04   0.07645669    1062.9045    301.64635   -16.348471     9.708722    -1077.348   -1067.6392 
-   40450        4.045  0.076456729    1073.8352    295.54356   -16.354824    9.5122988   -1077.1515   -1067.6392 
-   40500         4.05  0.076456875    1045.0985    290.52511    -16.36464    9.3507761     -1076.99   -1067.6392 
-   40550        4.055  0.076456839    1027.9258    287.44019   -16.379541    9.2514857   -1076.8907   -1067.6392 
-   40600         4.06  0.076456646    1031.5216    286.57721   -16.388491      9.22371   -1076.8629   -1067.6392 
-   40650        4.065  0.076456606    1055.0251    287.81611   -16.386366    9.2635847   -1076.9028   -1067.6392 
-   40700         4.07  0.076456834    1081.6077    290.98909   -16.384202    9.3657097   -1077.0049   -1067.6392 
-   40750        4.075  0.076457031    1095.8624    295.35171   -16.381535    9.5061241   -1077.1454   -1067.6392 
-   40800         4.08  0.076456927    1091.1884    299.74612   -16.369379    9.6475614   -1077.2868   -1067.6392 
-   40850        4.085  0.076456677    1072.8108    303.12714   -16.353468    9.7563823   -1077.3956   -1067.6392 
-   40900         4.09  0.076456612    1071.4265    304.47082   -16.345218    9.7996295   -1077.4389   -1067.6392 
-   40950        4.095  0.076456759    1087.5691    303.62065   -16.343756    9.7722663   -1077.4115   -1067.6392 
-   41000          4.1   0.07645689    1093.1572    302.41466   -16.342931    9.7334506   -1077.3727   -1067.6392 
-   41050        4.105  0.076456787    1077.0283    303.03079   -16.350207    9.7532811   -1077.3925   -1067.6392 
-   41100         4.11    0.0764566    1063.8174    304.59541     -16.3659    9.8036396   -1077.4429   -1067.6392 
-   41150        4.115  0.076456666    1067.2044    305.05378   -16.383874    9.8183927   -1077.4576   -1067.6392 
-   41200         4.12  0.076456794    1067.5418    304.12177   -16.408325    9.7883952   -1077.4276   -1067.6392 
-   41250        4.125  0.076456816    1047.1076    301.87307   -16.437615     9.716019   -1077.3553   -1067.6392 
-   41300         4.13  0.076456766    1000.8676    298.01778   -16.464716    9.5919337   -1077.2312   -1067.6392 
-   41350        4.135  0.076456687    958.82868    293.49143   -16.485682    9.4462495   -1077.0855   -1067.6392 
-   41400         4.14  0.076456739    951.84883    290.80384   -16.499012    9.3597472    -1076.999   -1067.6392 
-   41450        4.145  0.076456812    963.65591    292.08601   -16.507392    9.4010149   -1077.0402   -1067.6392 
-   41500         4.15  0.076456843    975.72148    297.16323   -16.520849    9.5644292   -1077.2037   -1067.6392 
-   41550        4.155  0.076456845    984.53332    303.16542    -16.53794    9.7576142   -1077.3968   -1067.6392 
-   41600         4.16  0.076456751    985.80319    307.28815   -16.557303    9.8903077   -1077.5295   -1067.6392 
-   41650        4.165  0.076456683    1002.2286    308.88612   -16.587168    9.9417395    -1077.581   -1067.6392 
-   41700         4.17  0.076456643    1030.6323    308.39988   -16.625508    9.9260895   -1077.5653   -1067.6392 
-   41750        4.175   0.07645661    1034.2586    306.29955   -16.665355    9.8584887   -1077.4977   -1067.6392 
-   41800         4.18  0.076456559    1020.0175    303.06426   -16.703335    9.7543583   -1077.3936   -1067.6392 
-   41850        4.185  0.076456676    991.59829    299.14498   -16.725328    9.6282135   -1077.2674   -1067.6392 
-   41900         4.19  0.076456761    967.85853    296.19757   -16.730689    9.5333487   -1077.1726   -1067.6392 
-   41950        4.195  0.076456701    975.82892    296.71617   -16.740926    9.5500402   -1077.1893   -1067.6392 
-   42000          4.2  0.076456713    1002.2491    300.92024   -16.770609    9.6853516   -1077.3246   -1067.6392 
-   42050        4.205  0.076456664    1009.6687    305.97966   -16.813995    9.8481928   -1077.4874   -1067.6392 
-   42100         4.21  0.076456626    1003.7314    309.08496   -16.851376    9.9481394   -1077.5874   -1067.6392 
-   42150        4.215  0.076456675    1009.5258     310.0374   -16.864204    9.9787942    -1077.618   -1067.6392 
-   42200         4.22  0.076456733    1016.8827     310.8272    -16.85494    10.004215   -1077.6434   -1067.6392 
-   42250        4.225  0.076456828      1023.91    312.80966   -16.842511    10.068022   -1077.7073   -1067.6392 
-   42300         4.23  0.076456807    1019.5709    315.15173   -16.836523    10.143403   -1077.7826   -1067.6392 
-   42350        4.235  0.076456685    1017.6755    316.23931   -16.830978    10.178408   -1077.8176   -1067.6392 
-   42400         4.24  0.076456572    1035.9763    314.95382   -16.817532    10.137033   -1077.7763   -1067.6392 
-   42450        4.245  0.076456544     1057.572    310.93678   -16.799682    10.007741    -1077.647   -1067.6392 
-   42500         4.25  0.076456618    1077.1806    305.03796   -16.792574    9.8178834   -1077.4571   -1067.6392 
-   42550        4.255  0.076456744    1090.5444     299.3483   -16.809848    9.6347572    -1077.274   -1067.6392 
-   42600         4.26  0.076456726     1096.922    295.41747   -16.837401    9.5082406   -1077.1475   -1067.6392 
-   42650        4.265  0.076456617    1103.2531    293.46673   -16.859813    9.4454545   -1077.0847   -1067.6392 
-   42700         4.27  0.076456587    1104.4238    293.26317   -16.892288    9.4389029   -1077.0781   -1067.6392 
-   42750        4.275  0.076456665    1083.3823    294.65311   -16.933936    9.4836391   -1077.1229   -1067.6392 
-   42800         4.28  0.076456664    1042.3438    298.70068   -16.959665    9.6139133   -1077.2531   -1067.6392 
-   42850        4.285  0.076456687    1013.4416    306.95616   -16.966168    9.8796223   -1077.5189   -1067.6392 
-   42900         4.29  0.076456725    1011.1467    318.14544    -16.97008    10.239758    -1077.879   -1067.6392 
-   42950        4.295  0.076456665    1017.4449    328.03985   -16.982627    10.558217   -1078.1975   -1067.6392 
-   43000          4.3  0.076456617    1019.3575    333.03871   -17.008768    10.719109   -1078.3583   -1067.6392 
-   43050        4.305  0.076456693     999.2679    332.30906   -17.055549    10.695625   -1078.3349   -1067.6392 
-   43100         4.31  0.076456762     967.7236    326.28709   -17.109853    10.501803    -1078.141   -1067.6392 
-   43150        4.315  0.076456687    976.16726    316.29296   -17.144504    10.180134   -1077.8194   -1067.6392 
-   43200         4.32  0.076456692    1009.9146    306.30886   -17.155114    9.8587883    -1077.498   -1067.6392 
-   43250        4.325  0.076456822    1011.5832    301.46146   -17.160687    9.7027711    -1077.342   -1067.6392 
-   43300         4.33  0.076456891    993.25245    303.09136   -17.173125    9.7552307   -1077.3945   -1067.6392 
-   43350        4.335  0.076456691     978.1423    307.90834   -17.186565     9.910269   -1077.5495   -1067.6392 
-   43400         4.34   0.07645663     966.7299    311.62095   -17.191657    10.029762    -1077.669   -1067.6392 
-   43450        4.345  0.076456883    971.37208    311.68351   -17.189726    10.031776    -1077.671   -1067.6392 
-   43500         4.35  0.076456994    978.85437    307.94316   -17.193481    9.9113896   -1077.5506   -1067.6392 
-   43550        4.355  0.076456767    996.27549    302.13712   -17.211228    9.7245177   -1077.3637   -1067.6392 
-   43600         4.36  0.076456685    1016.7792     297.0799   -17.235609    9.5617472    -1077.201   -1067.6392 
-   43650        4.365  0.076456862    1020.5319    294.98379   -17.245695    9.4942822   -1077.1335   -1067.6392 
-   43700         4.37  0.076456832    1016.3483    296.10415   -17.238216     9.530342   -1077.1696   -1067.6392 
-   43750        4.375  0.076456643    1012.7306    299.25575   -17.241809    9.6317786    -1077.271   -1067.6392 
-   43800         4.38  0.076456789    1005.3285    303.54214   -17.262691    9.7697394    -1077.409   -1067.6392 
-   43850        4.385  0.076456982    1003.3326    310.06269   -17.281251    9.9796085   -1077.6188   -1067.6392 
-   43900         4.39  0.076456965    987.54044    320.52249   -17.299417    10.316265   -1077.9555   -1067.6392 
-   43950        4.395  0.076456761     963.2584    333.20523   -17.330466    10.724469   -1078.3637   -1067.6392 
-   44000          4.4  0.076456706    963.73639    342.88698   -17.367857    11.036084   -1078.6753   -1067.6392 
-   44050        4.405  0.076456821    986.80537    345.16932   -17.395458    11.109542   -1078.7488   -1067.6392 
-   44100         4.41  0.076456831    1009.8445    339.67355    -17.41311    10.932657   -1078.5719   -1067.6392 
-   44150        4.415  0.076456785    1014.6601    330.05625   -17.436389    10.623116   -1078.2623   -1067.6392 
-   44200         4.42  0.076456797    984.52199     321.8216    -17.48274    10.358078   -1077.9973   -1067.6392 
-   44250        4.425  0.076456753    957.80787    317.33913    -17.54731    10.213806    -1077.853   -1067.6392 
-   44300         4.43  0.076456643    940.00066    314.53772   -17.596853    10.123641   -1077.7629   -1067.6392 
-   44350        4.435  0.076456628     918.4875    312.37225   -17.612235    10.053943   -1077.6932   -1067.6392 
-   44400         4.44   0.07645672    913.57846     310.8786   -17.595301    10.005869   -1077.6451   -1067.6392 
-   44450        4.445  0.076456761     919.4865    309.82858   -17.561225    9.9720734   -1077.6113   -1067.6392 
-   44500         4.45   0.07645674     926.5393    309.78037   -17.534259    9.9705218   -1077.6097   -1067.6392 
-   44550        4.455  0.076456708    929.10063    311.77335   -17.538056    10.034667   -1077.6739   -1067.6392 
-   44600         4.46  0.076456694    933.10594    315.21765   -17.566473    10.145525   -1077.7848   -1067.6392 
-   44650        4.465  0.076456702    926.71966    318.06782   -17.591174     10.23726   -1077.8765   -1067.6392 
-   44700         4.47  0.076456707    911.59951    319.12218   -17.602472    10.271195   -1077.9104   -1067.6392 
-   44750        4.475  0.076456688    910.70606     318.9204   -17.609049    10.264701   -1077.9039   -1067.6392 
-   44800         4.48    0.0764567    905.05917    318.54255   -17.616129    10.252539   -1077.8918   -1067.6392 
-   44850        4.485  0.076456621    894.49408    318.42782   -17.623448    10.248847   -1077.8881   -1067.6392 
-   44900         4.49  0.076456517     906.7452    318.55777   -17.630547    10.253029   -1077.8923   -1067.6392 
-   44950        4.495  0.076456564     912.1438    318.94548   -17.639597    10.265508   -1077.9047   -1067.6392 
-   45000          4.5  0.076456621    904.16689     319.6676   -17.650569     10.28875    -1077.928   -1067.6392 
-   45050        4.505  0.076456591    906.29138    321.41748   -17.664978    10.345071   -1077.9843   -1067.6392 
-   45100         4.51  0.076456544    905.96789    325.06187   -17.678666    10.462369   -1078.1016   -1067.6392 
-   45150        4.515  0.076456576    898.50939    330.26103   -17.687185    10.629708   -1078.2689   -1067.6392 
-   45200         4.52  0.076456663    905.35412    334.94433   -17.701241    10.780443   -1078.4197   -1067.6392 
-   45250        4.525   0.07645673    930.80225    336.07069    -17.72859    10.816696   -1078.4559   -1067.6392 
-   45300         4.53  0.076456595     959.3922     331.6008   -17.765016    10.672829   -1078.3121   -1067.6392 
-   45350        4.535  0.076456568    984.36318    321.62814   -17.802524    10.351851   -1077.9911   -1067.6392 
-   45400         4.54   0.07645668    990.20053     308.8639   -17.836056    9.9410245   -1077.5803   -1067.6392 
-   45450        4.545  0.076456648    947.25396    298.78614   -17.865782    9.6166638   -1077.2559   -1067.6392 
-   45500         4.55  0.076456577    910.56022    297.55292   -17.905424    9.5769716   -1077.2162   -1067.6392 
-   45550        4.555  0.076456563    888.63811    306.74089   -17.960609    9.8726936   -1077.5119   -1067.6392 
-   45600         4.56  0.076456599    859.98987    321.07118   -18.005145    10.333925   -1077.9732   -1067.6392 
-   45650        4.565  0.076456612    856.19145    333.40125   -18.019594    10.730778     -1078.37   -1067.6392 
-   45700         4.57  0.076456557    878.62104    340.06144   -18.020894    10.945141   -1078.5844   -1067.6392 
-   45750        4.575  0.076456566    897.45139    340.97037   -18.029395    10.974396   -1078.6136   -1067.6392 
-   45800         4.58  0.076456592    900.06632    337.73275   -18.042178    10.870191   -1078.5094   -1067.6392 
-   45850        4.585  0.076456653    905.65224    333.13083   -18.060834    10.722074   -1078.3613   -1067.6392 
-   45900         4.59  0.076456731    911.50958    329.86483    -18.10231    10.616955   -1078.2562   -1067.6392 
-   45950        4.595  0.076456674    934.98117    327.78934   -18.158233    10.550154   -1078.1894   -1067.6392 
-   46000          4.6  0.076456573    960.91441    324.26975   -18.195778    10.436874   -1078.0761   -1067.6392 
-   46050        4.605  0.076456596    962.59058     317.8452   -18.203481    10.230095   -1077.8693   -1067.6392 
-   46100         4.61  0.076456671    960.19967    310.62901   -18.213042    9.9978359   -1077.6371   -1067.6392 
-   46150        4.615  0.076456686    958.71855    305.95972   -18.235837    9.8475511   -1077.4868   -1067.6392 
-   46200         4.62  0.076456612    966.32277     305.9278    -18.25351    9.8465235   -1077.4858   -1067.6392 
-   46250        4.625  0.076456484    976.33095    310.79103   -18.261143     10.00305   -1077.6423   -1067.6392 
-   46300         4.63  0.076456455     971.1525    319.21516   -18.262509    10.274188   -1077.9134   -1067.6392 
-   46350        4.635  0.076456555    942.98388      329.128   -18.258965     10.59324   -1078.2325   -1067.6392 
-   46400         4.64   0.07645659    931.95574    338.94782   -18.258301    10.909299   -1078.5485   -1067.6392 
-   46450        4.645  0.076456634    952.04764    347.69672   -18.270432    11.190889   -1078.8301   -1067.6392 
-   46500         4.65  0.076456695    954.27972    354.28335   -18.291901    11.402884   -1079.0421   -1067.6392 
-   46550        4.655  0.076456718    932.47699    357.80024   -18.314064    11.516078   -1079.1553   -1067.6392 
-   46600         4.66  0.076456571    917.15783      358.255    -18.33944    11.530715   -1079.1699   -1067.6392 
-   46650        4.665  0.076456487    914.53778    356.10608   -18.373204     11.46155   -1079.1008   -1067.6392 
-   46700         4.67   0.07645664    926.29271    351.32545   -18.410415    11.307682   -1078.9469   -1067.6392 
-   46750        4.675  0.076456722    955.90982    343.62423   -18.443075    11.059813    -1078.699   -1067.6392 
-   46800         4.68  0.076456662    968.52074    333.76849   -18.472665    10.742598   -1078.3818   -1067.6392 
-   46850        4.685  0.076456611    960.55547    323.74847   -18.502955    10.420096   -1078.0593   -1067.6392 
-   46900         4.69   0.07645658    969.48482    315.29249   -18.530555    10.147933   -1077.7872   -1067.6392 
-   46950        4.695  0.076456538    970.41435    309.50703   -18.552649    9.9617239    -1077.601   -1067.6392 
-   47000          4.7  0.076456607     973.5826    307.27705   -18.562429    9.8899503   -1077.5292   -1067.6392 
-   47050        4.705  0.076456741    971.31274    309.44374   -18.561975    9.9596868   -1077.5989   -1067.6392 
-   47100         4.71  0.076456567    974.56171    315.87966   -18.571858    10.166832   -1077.8061   -1067.6392 
-   47150        4.715  0.076456487      989.886     324.3948    -18.59552    10.440899   -1078.0801   -1067.6392 
-   47200         4.72  0.076456752    991.34022    333.02825   -18.624859    10.718773    -1078.358   -1067.6392 
-   47250        4.725  0.076456811    982.33055    341.27988   -18.652892    10.984358   -1078.6236   -1067.6392 
-   47300         4.73  0.076456654    969.07699    348.54206   -18.671538    11.218097   -1078.8573   -1067.6392 
-   47350        4.735  0.076456603    950.49208    353.80509   -18.681778    11.387491   -1079.0267   -1067.6392 
-   47400         4.74  0.076456655    932.53448    356.59027   -18.691148    11.477134   -1079.1164   -1067.6392 
-   47450        4.745   0.07645674    914.98082    356.88075   -18.707177    11.486484   -1079.1257   -1067.6392 
-   47500         4.75  0.076456846    910.29391    354.25323   -18.733572    11.401915   -1079.0411   -1067.6392 
-   47550        4.755  0.076456842    911.79249    348.56319   -18.768858    11.218777    -1078.858   -1067.6392 
-   47600         4.76  0.076456764    896.25715    341.13087   -18.817172    10.979562   -1078.6188   -1067.6392 
-   47650        4.765  0.076456752    893.56376    333.65355   -18.869281    10.738898   -1078.3781   -1067.6392 
-   47700         4.77  0.076456851    923.22366    328.05385   -18.908457    10.558668   -1078.1979   -1067.6392 
-   47750        4.775  0.076456872    942.84866    326.28411   -18.929889    10.501707   -1078.1409   -1067.6392 
-   47800         4.78  0.076456844    930.32583    328.44034   -18.932985    10.571107   -1078.2103   -1067.6392 
-   47850        4.785  0.076456902    912.36756    332.89004   -18.922464    10.714324   -1078.3536   -1067.6392 
-   47900         4.79  0.076456964    916.62133    338.11673   -18.919206    10.882549   -1078.5218   -1067.6392 
-   47950        4.795  0.076457014    930.75246    342.30195   -18.922007    11.017254   -1078.6565   -1067.6392 
-   48000          4.8  0.076457014    936.01421    343.78811   -18.908628    11.065087   -1078.7043   -1067.6392 
-   48050        4.805  0.076456953    944.54584    342.44511   -18.878537    11.021862   -1078.6611   -1067.6392 
-   48100         4.81  0.076456972    941.98405    339.08691   -18.851545    10.913775    -1078.553   -1067.6392 
-   48150        4.815  0.076456898    920.11331    334.61456   -18.839033    10.769829   -1078.4091   -1067.6392 
-   48200         4.82  0.076456871    907.83719    330.10701   -18.832157     10.62475    -1078.264   -1067.6392 
-   48250        4.825  0.076456918    912.20647    327.58291   -18.826744     10.54351   -1078.1827   -1067.6392 
-   48300         4.83   0.07645699    932.39917    329.24117   -18.830768    10.596882   -1078.2361   -1067.6392 
-   48350        4.835   0.07645701     945.1163     335.0398   -18.840255    10.783516   -1078.4227   -1067.6392 
-   48400         4.84  0.076456836    950.22061    342.35702   -18.841461    11.019026   -1078.6583   -1067.6392 
-   48450        4.845    0.0764567    952.16965    348.50659   -18.834984    11.216955   -1078.8562   -1067.6392 
-   48500         4.85  0.076456712    955.36854    352.21576   -18.825983    11.336338   -1078.9756   -1067.6392 
-   48550        4.855  0.076456801    959.48836    353.76389   -18.820533    11.386165   -1079.0254   -1067.6392 
-   48600         4.86  0.076456823    964.22846    354.04554   -18.822337    11.395231   -1079.0345   -1067.6392 
-   48650        4.865  0.076456815    974.22885    352.93972   -18.818132    11.359639   -1078.9989   -1067.6392 
-   48700         4.87  0.076456877    987.44079    349.70581   -18.807017    11.255553   -1078.8948   -1067.6392 
-   48750        4.875  0.076456856    980.80712    344.37973   -18.808379    11.084129   -1078.7234   -1067.6392 
-   48800         4.88  0.076456847    965.79638    337.63651    -18.81979    10.867093   -1078.5063   -1067.6392 
-   48850        4.885  0.076457001    966.05115     330.7499   -18.830692    10.645442   -1078.2847   -1067.6392 
-   48900         4.89  0.076457069    965.02834    325.77373   -18.849924     10.48528   -1078.1245   -1067.6392 
-   48950        4.895  0.076456805    951.50135    324.61657   -18.890071    10.448036   -1078.0873   -1067.6392 
-   49000          4.9  0.076456678    947.91103    327.27966   -18.934537     10.53375    -1078.173   -1067.6392 
-   49050        4.905  0.076456661    958.11234    332.39046   -18.962498    10.698245   -1078.3375   -1067.6392 
-   49100         4.91  0.076456829    970.05161    338.47836   -18.976168    10.894189   -1078.5334   -1067.6392 
-   49150        4.915   0.07645699    968.15446    343.93729    -18.98603    11.069889   -1078.7091   -1067.6392 
-   49200         4.92  0.076456985    960.59968    346.43043   -18.994109    11.150132   -1078.7894   -1067.6392 
-   49250        4.925  0.076456928    945.53084     343.0733   -18.986613    11.042081   -1078.6813   -1067.6392 
-   49300         4.93  0.076456888    920.51419    333.13647   -18.959986    10.722256   -1078.3615   -1067.6392 
-   49350        4.935  0.076456851    907.35436    320.38291   -18.938752    10.311773    -1077.951   -1067.6392 
-   49400         4.94   0.07645685    893.81547    310.99739   -18.938412    10.009692   -1077.6489   -1067.6392 
-   49450        4.945  0.076456896    870.23823    309.67527    -18.95594    9.9671388   -1077.6064   -1067.6392 
-   49500         4.95  0.076456955    872.77052    317.13999   -18.978605    10.207397   -1077.8466   -1067.6392 
-   49550        4.955  0.076456967    894.83445    330.73629    -18.98876    10.645004   -1078.2842   -1067.6392 
-   49600         4.96  0.076456979     912.1661    346.73247   -18.984428    11.159854   -1078.7991   -1067.6392 
-   49650        4.965  0.076456993    915.70238    361.26297   -18.978545    11.627529   -1079.2668   -1067.6392 
-   49700         4.97  0.076456983    924.58803    370.71298   -18.984487    11.931685   -1079.5709   -1067.6392 
-   49750        4.975  0.076456922    944.17323    372.65166   -18.998747    11.994083   -1079.6333   -1067.6392 
-   49800         4.98  0.076456923    948.92864    367.69228     -19.0113    11.834461   -1079.4737   -1067.6392 
-   49850        4.985  0.076456921    953.93531    359.51215   -19.018592    11.571177   -1079.2104   -1067.6392 
-   49900         4.99  0.076456974    963.60708    351.14054   -19.013112    11.301731    -1078.941   -1067.6392 
-   49950        4.995  0.076456997      970.081    343.67798   -19.003119    11.061543   -1078.7008   -1067.6392 
-   50000            5  0.076457012    1001.2522    337.57276   -19.005327    10.865041   -1078.5043   -1067.6392 
-Loop time of 149.65 on 1 procs for 50000 steps with 250 atoms
-
-Performance: 2.887 ns/day, 8.314 hours/ns, 334.113 timesteps/s
-98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 56.939     | 56.939     | 56.939     |   0.0 | 38.05
-Neigh   | 0.65017    | 0.65017    | 0.65017    |   0.0 |  0.43
-Comm    | 1.4958     | 1.4958     | 1.4958     |   0.0 |  1.00
-Output  | 37.503     | 37.503     | 37.503     |   0.0 | 25.06
-Modify  | 52.788     | 52.788     | 52.788     |   0.0 | 35.27
-Other   |            | 0.2742     |            |       |  0.18
-
-Nlocal:    250 ave 250 max 250 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1335 ave 1335 max 1335 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    7746 ave 7746 max 7746 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  15492 ave 15492 max 15492 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 15492
-Ave neighs/atom = 61.968
-Neighbor list builds = 608
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:02:29
diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4 b/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4
deleted file mode 100644
index 6fc3e307f0..0000000000
--- a/examples/SPIN/iron/log.30Apr19.spin.iron.g++.4
+++ /dev/null
@@ -1,1117 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# bcc iron in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	bcc 2.8665
-Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 250 atoms
-  create_atoms CPU = 0.00056982 secs
-
-# setting mass, mag. moments, and interactions for bcc iron
-
-mass		1 55.845
-
-set 		group all spin/random 31 2.2
-  250 settings made for spin/random
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
-pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
-pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		50000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.77337
-  ghost atom cutoff = 5.77337
-  binsize = 2.88668, bins = 5 5 5
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes
-Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng 
-       0            0  0.076456975    9109.0924    100.00358  -0.85791269    3.2186929   -1070.8579   -1067.6392 
-      50        0.005  0.076456995    9402.4007    96.298333  -0.85659448    3.0994366   -1070.7387   -1067.6392 
-     100         0.01  0.076457028    9589.1846    86.330828  -0.87003341    2.7786247   -1070.4179   -1067.6392 
-     150        0.015  0.076457074    9673.9268    71.603402  -0.89006992    2.3046111   -1069.9438   -1067.6392 
-     200         0.02  0.076457106    9509.1148    54.648817  -0.91124541    1.7589146   -1069.3981   -1067.6392 
-     250        0.025  0.076457128      9004.27    38.599515  -0.93187522    1.2423553   -1068.8816   -1067.6392 
-     300         0.03  0.076457157    8353.4371    26.383018  -0.95082226    0.8491579   -1068.4884   -1067.6392 
-     350        0.035  0.076457207    7911.1316     20.01039  -0.96826468   0.64404992   -1068.2833   -1067.6392 
-     400         0.04  0.076457243    7775.9492    20.097682  -0.98706373   0.64685949   -1068.2861   -1067.6392 
-     450        0.045  0.076457231    7737.1225    25.687511   -1.0095684   0.82677249    -1068.466   -1067.6392 
-     500         0.05  0.076457204    7676.9809    34.604697   -1.0349855     1.113779    -1068.753   -1067.6392 
-     550        0.055  0.076457196    7550.2809    44.251809   -1.0609123    1.4242788   -1069.0635   -1067.6392 
-     600         0.06  0.076457188    7209.7657    52.475202   -1.0880854    1.6889551   -1069.3282   -1067.6392 
-     650        0.065   0.07645718    6691.1787    57.926479   -1.1179657    1.8644087   -1069.5036   -1067.6392 
-     700         0.07  0.076457185    6276.4003    60.030548   -1.1469999    1.9321298   -1069.5714   -1067.6392 
-     750        0.075   0.07645719    6149.9253    59.122504   -1.1721939    1.9029037   -1069.5421   -1067.6392 
-     800         0.08  0.076457195    6207.0587    56.349146   -1.1949365     1.813641   -1069.4529   -1067.6392 
-     850        0.085  0.076457199    6328.4635    53.154464   -1.2164642    1.7108177     -1069.35   -1067.6392 
-     900         0.09  0.076457199    6456.2716    50.837416   -1.2366018    1.6362417   -1069.2755   -1067.6392 
-     950        0.095  0.076457222    6495.1064    50.234549   -1.2539657    1.6168379   -1069.2561   -1067.6392 
-    1000          0.1  0.076457266     6416.775    51.592727   -1.2671834    1.6605519   -1069.2998   -1067.6392 
-    1050        0.105  0.076457256    6305.9015    54.719414   -1.2794824    1.7611868   -1069.4004   -1067.6392 
-    1100         0.11  0.076457222     6165.987     59.01343   -1.2960617    1.8993931   -1069.5386   -1067.6392 
-    1150        0.115  0.076457194    5941.7807    63.475298    -1.317859    2.0430017   -1069.6822   -1067.6392 
-    1200         0.12  0.076457182    5692.0982    67.036713   -1.3432854    2.1576286   -1069.7969   -1067.6392 
-    1250        0.125  0.076457217    5543.1736    68.917405   -1.3719994    2.2181602   -1069.8574   -1067.6392 
-    1300         0.13  0.076457263    5507.9968    68.753418   -1.4042339    2.2128821   -1069.8521   -1067.6392 
-    1350        0.135  0.076457286    5500.7848    66.608286   -1.4385667    2.1438394   -1069.7831   -1067.6392 
-    1400         0.14  0.076457254     5523.456    62.967429   -1.4712143    2.0266556   -1069.6659   -1067.6392 
-    1450        0.145  0.076457188    5501.5777     58.75732   -1.4990458      1.89115   -1069.5304   -1067.6392 
-    1500         0.15  0.076457175    5324.4931    55.246308   -1.5236774    1.7781453   -1069.4174   -1067.6392 
-    1550        0.155  0.076457234    5025.5908    53.607297   -1.5492947    1.7253925   -1069.3646   -1067.6392 
-    1600         0.16  0.076457297    4742.9546    54.443418   -1.5785798    1.7523036   -1069.3915   -1067.6392 
-    1650        0.165  0.076457321     4558.083    57.572305   -1.6113848    1.8530093   -1069.4922   -1067.6392 
-    1700         0.17  0.076457304    4479.4352    62.073307   -1.6443595    1.9978776   -1069.6371   -1067.6392 
-    1750        0.175  0.076457272    4520.5577    66.677964   -1.6742729     2.146082   -1069.7853   -1067.6392 
-    1800         0.18  0.076457253    4659.9114    70.277293   -1.7021557    2.2619292   -1069.9012   -1067.6392 
-    1850        0.185  0.076457257    4734.1597    72.135028   -1.7307798    2.3217219    -1069.961   -1067.6392 
-    1900         0.19  0.076457279    4632.2637    71.873382   -1.7598165    2.3133006   -1069.9525   -1067.6392 
-    1950        0.195  0.076457276    4496.6621     69.52131   -1.7866398    2.2375973   -1069.8768   -1067.6392 
-    2000          0.2  0.076457276    4507.4594     65.61098   -1.8106776    2.1117403    -1069.751   -1067.6392 
-    2050        0.205  0.076457288    4652.9279    61.016261   -1.8317479    1.9638557   -1069.6031   -1067.6392 
-    2100         0.21  0.076457307    4738.4188    56.745795   -1.8489776    1.8264074   -1069.4656   -1067.6392 
-    2150        0.215  0.076457279     4643.423    53.837376   -1.8647516    1.7327977    -1069.372   -1067.6392 
-    2200         0.22  0.076457215    4517.9871    53.044053   -1.8828305     1.707264   -1069.3465   -1067.6392 
-    2250        0.225   0.07645717    4436.4399    54.521839   -1.9038753    1.7548277   -1069.3941   -1067.6392 
-    2300         0.23  0.076457132    4318.8261    57.895634   -1.9276454    1.8634159   -1069.5026   -1067.6392 
-    2350        0.235  0.076457114    4148.8616    62.484473   -1.9559372    2.0111113   -1069.6503   -1067.6392 
-    2400         0.24  0.076457144    4014.8498    67.404243   -1.9902034    2.1694579   -1069.8087   -1067.6392 
-    2450        0.245  0.076457189     4004.017    71.654167   -2.0278558     2.306245   -1069.9455   -1067.6392 
-    2500         0.25  0.076457202    4109.5497    74.379393   -2.0629968    2.3939585   -1070.0332   -1067.6392 
-    2550        0.255  0.076457205    4251.6933    75.255112   -2.0918484    2.4221442   -1070.0614   -1067.6392 
-    2600         0.26  0.076457208    4320.6876    74.700611   -2.1169691    2.4042972   -1070.0435   -1067.6392 
-    2650        0.265  0.076457197    4297.5527    73.627823       -2.143    2.3697686    -1070.009   -1067.6392 
-    2700         0.27  0.076457213    4198.4852    72.957211   -2.1702374    2.3481845   -1069.9874   -1067.6392 
-    2750        0.275  0.076457256    4019.2384    73.353574   -2.1967187    2.3609417   -1070.0002   -1067.6392 
-    2800         0.28  0.076457288    3867.2492    75.083781   -2.2227117    2.4166298   -1070.0559   -1067.6392 
-    2850        0.285  0.076457302    3879.8471     77.82546   -2.2488766    2.5048728   -1070.1441   -1067.6392 
-    2900         0.29  0.076457321    4003.8986    80.741745   -2.2742584    2.5987357    -1070.238   -1067.6392 
-    2950        0.295  0.076457347    4026.6754    82.934399   -2.3001834     2.669308   -1070.3085   -1067.6392 
-    3000          0.3  0.076457334    3857.2183    83.701738   -2.3291113    2.6940054   -1070.3332   -1067.6392 
-    3050        0.305  0.076457295    3640.7581    82.615991   -2.3614721    2.6590598   -1070.2983   -1067.6392 
-    3100         0.31   0.07645725     3489.102    79.573679   -2.3943974    2.5611406   -1070.2004   -1067.6392 
-    3150        0.315  0.076457232    3396.4301    74.896125   -2.4236621    2.4105899   -1070.0498   -1067.6392 
-    3200         0.32  0.076457259      3378.11    69.450128   -2.4483292    2.2353063   -1069.8745   -1067.6392 
-    3250        0.325  0.076457289    3463.7734    64.542714   -2.4729224    2.0773573   -1069.7166   -1067.6392 
-    3300         0.33  0.076457318    3637.4971    61.346221    -2.500303    1.9744757   -1069.6137   -1067.6392 
-    3350        0.335  0.076457361    3833.5389    60.346704   -2.5252732    1.9423055   -1069.5815   -1067.6392 
-    3400         0.34  0.076457387    3965.2081    61.464125   -2.5426842    1.9782706   -1069.6175   -1067.6392 
-    3450        0.345  0.076457375    3976.7956     64.41797   -2.5565409    2.0733424   -1069.7126   -1067.6392 
-    3500         0.35  0.076457371    3862.8334    68.714547   -2.5743062     2.211631   -1069.8509   -1067.6392 
-    3550        0.355  0.076457375     3697.284    73.534942   -2.5974674    2.3667792    -1070.006   -1067.6392 
-    3600         0.36  0.076457362    3575.9012    77.902682   -2.6209385    2.5073583   -1070.1466   -1067.6392 
-    3650        0.365  0.076457345    3550.0667    81.043684   -2.6394846    2.6084539   -1070.2477   -1067.6392 
-    3700         0.37  0.076457309    3535.0981    82.730976     -2.65464    2.6627607    -1070.302   -1067.6392 
-    3750        0.375  0.076457309    3444.1795    83.322515   -2.6736085    2.6817998    -1070.321   -1067.6392 
-    3800         0.38  0.076457348    3323.7191    83.436143   -2.7008525     2.685457   -1070.3247   -1067.6392 
-    3850        0.385  0.076457368    3252.5404     83.62535   -2.7353937    2.6915468   -1070.3308   -1067.6392 
-    3900         0.39  0.076457344    3219.5349    84.088597   -2.7722909    2.7064568   -1070.3457   -1067.6392 
-    3950        0.395  0.076457316    3210.4164    84.636475   -2.8060651    2.7240906   -1070.3633   -1067.6392 
-    4000          0.4  0.076457319    3223.9708    85.042888   -2.8352998    2.7371713   -1070.3764   -1067.6392 
-    4050        0.405  0.076457335    3232.7108    85.266853   -2.8607963    2.7443798   -1070.3836   -1067.6392 
-    4100         0.41  0.076457314    3206.1428    85.444074   -2.8837721    2.7500838   -1070.3893   -1067.6392 
-    4150        0.415  0.076457325    3146.4589    85.771643   -2.9074131    2.7606269   -1070.3999   -1067.6392 
-    4200         0.42  0.076457395    3092.6283     86.24875   -2.9341331     2.775983   -1070.4152   -1067.6392 
-    4250        0.425   0.07645742    3103.0319    86.563557   -2.9622203    2.7861153   -1070.4253   -1067.6392 
-    4300         0.43  0.076457425    3116.9053    86.320099   -2.9880208    2.7782794   -1070.4175   -1067.6392 
-    4350        0.435  0.076457427    3061.2259    85.306966   -3.0085539    2.7456709   -1070.3849   -1067.6392 
-    4400         0.44  0.076457432    3033.5229    83.703441   -3.0243431    2.6940602   -1070.3333   -1067.6392 
-    4450        0.445  0.076457411    3042.5167    82.058057   -3.0397518    2.6411023   -1070.2803   -1067.6392 
-    4500         0.45  0.076457387    2994.5161    81.002427   -3.0597817     2.607126   -1070.2464   -1067.6392 
-    4550        0.455  0.076457413     2868.381    80.936403    -3.086593     2.605001   -1070.2442   -1067.6392 
-    4600         0.46  0.076457454    2716.5128    81.904984   -3.1192161    2.6361755   -1070.2754   -1067.6392 
-    4650        0.465  0.076457402     2628.691    83.537981   -3.1529675    2.6887347    -1070.328   -1067.6392 
-    4700         0.47  0.076457327    2609.7253    85.196185   -3.1819342    2.7421053   -1070.3813   -1067.6392 
-    4750        0.475  0.076457328    2604.4797    86.479192   -3.2088497    2.7833999   -1070.4226   -1067.6392 
-    4800         0.48  0.076457385    2610.7583    87.294321    -3.242028    2.8096355   -1070.4489   -1067.6392 
-    4850        0.485  0.076457398    2649.7853    87.477655   -3.2810534    2.8155362   -1070.4548   -1067.6392 
-    4900         0.49  0.076457371    2678.8351    86.820207   -3.3154833    2.7943757   -1070.4336   -1067.6392 
-    4950        0.495  0.076457344     2687.924    85.543066   -3.3381845      2.75327   -1070.3925   -1067.6392 
-    5000          0.5  0.076457351    2720.6587    84.363474   -3.3508261    2.7153039   -1070.3545   -1067.6392 
-    5050        0.505  0.076457408    2755.8292    84.030245   -3.3582878    2.7045787   -1070.3438   -1067.6392 
-    5100         0.51  0.076457454    2753.2313    84.932962   -3.3648805    2.7336333   -1070.3729   -1067.6392 
-    5150        0.515  0.076457453    2706.7195    86.928397   -3.3711152    2.7978579   -1070.4371   -1067.6392 
-    5200         0.52  0.076457474     2678.177    89.583728   -3.3768576    2.8833218   -1070.5226   -1067.6392 
-    5250        0.525  0.076457519    2699.6154     92.51484   -3.3860255    2.9776619   -1070.6169   -1067.6392 
-    5300         0.53  0.076457531     2703.409    95.385751   -3.4040809    3.0700644   -1070.7093   -1067.6392 
-    5350        0.535  0.076457501    2642.6927    97.779641   -3.4335521    3.1471136   -1070.7863   -1067.6392 
-    5400         0.54  0.076457502    2536.3506     99.09318   -3.4686216    3.1893909   -1070.8286   -1067.6392 
-    5450        0.545  0.076457526     2496.939    98.768917   -3.4975315    3.1789543   -1070.8182   -1067.6392 
-    5500         0.55   0.07645752    2590.2956    96.816601   -3.5146308    3.1161175   -1070.7554   -1067.6392 
-    5550        0.555   0.07645751     2736.468    93.934193   -3.5252273    3.0233449   -1070.6626   -1067.6392 
-    5600         0.56  0.076457511    2852.5253    91.119522   -3.5395987    2.9327525    -1070.572   -1067.6392 
-    5650        0.565   0.07645752    2911.6956    89.034641   -3.5601373     2.865649   -1070.5049   -1067.6392 
-    5700         0.57  0.076457504    2872.1071    87.822315   -3.5786029    2.8266294   -1070.4659   -1067.6392 
-    5750        0.575  0.076457514    2742.4368    87.594068   -3.5903293    2.8192831   -1070.4585   -1067.6392 
-    5800         0.58  0.076457541    2620.8059     88.56771   -3.5997031    2.8506205   -1070.4899   -1067.6392 
-    5850        0.585  0.076457558    2577.6659    90.685494   -3.6121768     2.918783    -1070.558   -1067.6392 
-    5900         0.59  0.076457556    2603.2365    93.377823   -3.6265073    3.0054377   -1070.6447   -1067.6392 
-    5950        0.595  0.076457545    2622.1463    95.785547   -3.6355062    3.0829322   -1070.7222   -1067.6392 
-    6000          0.6  0.076457592    2584.5093    97.370119   -3.6379265    3.1339328   -1070.7732   -1067.6392 
-    6050        0.605  0.076457628    2511.2983    98.197844   -3.6436108    3.1605738   -1070.7998   -1067.6392 
-    6100         0.61  0.076457605    2460.1937    98.607325   -3.6641337    3.1737533    -1070.813   -1067.6392 
-    6150        0.615  0.076457552    2425.1581    98.777199   -3.7023507    3.1792208   -1070.8185   -1067.6392 
-    6200         0.62  0.076457529     2378.858    98.671036   -3.7529167    3.1758039    -1070.815   -1067.6392 
-    6250        0.625  0.076457536    2373.6174    98.176109   -3.8075652    3.1598743   -1070.7991   -1067.6392 
-    6300         0.63  0.076457584    2457.9895    97.287993   -3.8600038    3.1312896   -1070.7705   -1067.6392 
-    6350        0.635  0.076457603    2571.5862    96.270876   -3.9092349    3.0985529   -1070.7378   -1067.6392 
-    6400         0.64  0.076457558    2610.0136    95.435972   -3.9541069    3.0716808   -1070.7109   -1067.6392 
-    6450        0.645  0.076457543    2587.7608    94.898692   -3.9898247    3.0543881   -1070.6936   -1067.6392 
-    6500         0.65  0.076457571    2592.7016    94.731712   -4.0156706    3.0490137   -1070.6882   -1067.6392 
-    6550        0.655  0.076457601    2601.6484     95.02635   -4.0381241    3.0584968   -1070.6977   -1067.6392 
-    6600         0.66  0.076457634    2566.7083    95.637112   -4.0616073    3.0781547   -1070.7174   -1067.6392 
-    6650        0.665  0.076457648    2514.9403    96.272248   -4.0866876     3.098597   -1070.7378   -1067.6392 
-    6700         0.67  0.076457667    2469.8797    96.811623   -4.1148391    3.1159572   -1070.7552   -1067.6392 
-    6750        0.675  0.076457679    2455.7631    97.232703   -4.1435988      3.12951   -1070.7687   -1067.6392 
-    6800         0.68  0.076457673    2468.7416    97.598183   -4.1658052    3.1412733   -1070.7805   -1067.6392 
-    6850        0.685  0.076457641      2449.95    98.364331   -4.1815152    3.1659323   -1070.8052   -1067.6392 
-    6900         0.69  0.076457591    2353.8808    100.13602   -4.1974936    3.2229556   -1070.8622   -1067.6392 
-    6950        0.695  0.076457574     2209.815    103.01374   -4.2144943    3.3155771   -1070.9548   -1067.6392 
-    7000          0.7   0.07645757    2076.4955    106.68046   -4.2313525    3.4335935   -1071.0728   -1067.6392 
-    7050        0.705  0.076457532    2018.5608    110.71726   -4.2520006    3.5635208   -1071.2028   -1067.6392 
-    7100         0.71  0.076457492    2066.0289    114.55462   -4.2812097    3.6870294   -1071.3263   -1067.6392 
-    7150        0.715   0.07645748    2155.5953    117.31153   -4.3158511    3.7757627    -1071.415   -1067.6392 
-    7200         0.72  0.076457494     2209.404    118.11478   -4.3476294    3.8016159   -1071.4408   -1067.6392 
-    7250        0.725  0.076457549     2217.455    116.73546   -4.3751645    3.7572213   -1071.3965   -1067.6392 
-    7300         0.73  0.076457599    2194.7896    113.55484   -4.4007803    3.6548507   -1071.2941   -1067.6392 
-    7350        0.735   0.07645757    2162.9678    109.25541   -4.4240013    3.5164702   -1071.1557   -1067.6392 
-    7400         0.74  0.076457504    2179.1755     104.7762   -4.4454261    3.3723033   -1071.0115   -1067.6392 
-    7450        0.745  0.076457518    2259.3755    101.07852   -4.4663804    3.2532905   -1070.8925   -1067.6392 
-    7500         0.75  0.076457572    2343.5728    98.882923   -4.4874367    3.1826236   -1070.8219   -1067.6392 
-    7550        0.755  0.076457589    2398.3228    98.458717   -4.5060637    3.1689702   -1070.8082   -1067.6392 
-    7600         0.76  0.076457555    2420.6576    99.703599   -4.5200762    3.2090377   -1070.8483   -1067.6392 
-    7650        0.765  0.076457552    2412.3104    102.42619   -4.5351178    3.2966665   -1070.9359   -1067.6392 
-    7700         0.77  0.076457571     2388.742    106.24497   -4.5597331    3.4195769   -1071.0588   -1067.6392 
-    7750        0.775  0.076457574    2379.8392    110.33126   -4.5953993    3.5510971   -1071.1903   -1067.6392 
-    7800         0.78  0.076457547    2387.9692    113.47154   -4.6333122    3.6521696   -1071.2914   -1067.6392 
-    7850        0.785  0.076457584    2375.3173    114.64931   -4.6633154    3.6900771   -1071.3293   -1067.6392 
-    7900         0.79  0.076457607    2347.9452    113.52456   -4.6810365    3.6538759   -1071.2931   -1067.6392 
-    7950        0.795  0.076457576    2325.3437    110.51925   -4.6879165    3.5571478   -1071.1964   -1067.6392 
-    8000          0.8  0.076457576    2298.9574    106.80135   -4.6933853    3.4374844   -1071.0767   -1067.6392 
-    8050        0.805  0.076457591    2279.7296     103.7714   -4.7072185     3.339963   -1070.9792   -1067.6392 
-    8100         0.81  0.076457594    2277.4281    102.48909   -4.7324485     3.298691   -1070.9379   -1067.6392 
-    8150        0.815  0.076457634    2249.9673    103.46477   -4.7678493    3.3300941   -1070.9693   -1067.6392 
-    8200         0.82  0.076457642    2192.5499    106.44615   -4.8061066    3.4260518   -1071.0653   -1067.6392 
-    8250        0.825  0.076457605    2153.4317    110.64954   -4.8384076    3.5613412   -1071.2006   -1067.6392 
-    8300         0.83   0.07645754    2141.4131    115.25212   -4.8632501     3.709479   -1071.3487   -1067.6392 
-    8350        0.835  0.076457494    2140.5445    119.40588   -4.8830278    3.8431708   -1071.4824   -1067.6392 
-    8400         0.84  0.076457514     2137.788     122.1619   -4.8981204    3.9318754   -1071.5711   -1067.6392 
-    8450        0.845  0.076457574    2137.0667    122.97752   -4.9139635     3.958127   -1071.5974   -1067.6392 
-    8500         0.85  0.076457574    2145.0503    121.91147   -4.9379125    3.9238154    -1071.563   -1067.6392 
-    8550        0.855  0.076457593    2147.0889    119.37696   -4.9688875      3.84224   -1071.4815   -1067.6392 
-    8600         0.86   0.07645763    2081.6527    116.07646   -5.0006593     3.736011   -1071.3752   -1067.6392 
-    8650        0.865  0.076457595    1962.5911    112.96131   -5.0308687    3.6357476    -1071.275   -1067.6392 
-    8700         0.87  0.076457564    1869.6563    110.95387   -5.0615711    3.5711363   -1071.2104   -1067.6392 
-    8750        0.875  0.076457589    1834.0748    110.57729   -5.0928561    3.5590158   -1071.1982   -1067.6392 
-    8800         0.88  0.076457596      1854.43    111.81118   -5.1197787    3.5987297    -1071.238   -1067.6392 
-    8850        0.885  0.076457575    1865.6826    114.38971   -5.1401001    3.6817215    -1071.321   -1067.6392 
-    8900         0.89  0.076457601    1833.0206    117.96559   -5.1581048     3.796814    -1071.436   -1067.6392 
-    8950        0.895  0.076457671    1792.8832    121.88891   -5.1778019    3.9230893   -1071.5623   -1067.6392 
-    9000          0.9  0.076457726    1758.5023    125.25302   -5.2006688    4.0313657   -1071.6706   -1067.6392 
-    9050        0.905  0.076457731    1735.1309    127.17393   -5.2254334    4.0931918   -1071.7324   -1067.6392 
-    9100         0.91  0.076457741     1762.187    127.10436   -5.2491072    4.0909526   -1071.7302   -1067.6392 
-    9150        0.915  0.076457708    1843.8804    124.99484   -5.2685152    4.0230558   -1071.6623   -1067.6392 
-    9200         0.92  0.076457667    1957.8234    121.30407   -5.2827478    3.9042658   -1071.5435   -1067.6392 
-    9250        0.925  0.076457686    2062.5914    117.02709   -5.2984278    3.7666077   -1071.4058   -1067.6392 
-    9300         0.93  0.076457701    2105.5399    113.37476   -5.3254121    3.6490547   -1071.2883   -1067.6392 
-    9350        0.935  0.076457698    2097.1011    111.14541   -5.3634987    3.5773012   -1071.2165   -1067.6392 
-    9400         0.94  0.076457691    2074.0275    110.80542   -5.4086147    3.5663585   -1071.2056   -1067.6392 
-    9450        0.945  0.076457741    2084.2231    112.48714   -5.4565921    3.6204859   -1071.2597   -1067.6392 
-    9500         0.95  0.076457742    2098.9606    115.74433   -5.4989221     3.725321   -1071.3646   -1067.6392 
-    9550        0.955   0.07645769    2076.1518    119.81614   -5.5288469    3.8563755   -1071.4956   -1067.6392 
-    9600         0.96  0.076457671    2028.8268    123.94506   -5.5445735     3.989268   -1071.6285   -1067.6392 
-    9650        0.965    0.0764577    2001.4552     127.5336    -5.548578     4.104768    -1071.744   -1067.6392 
-    9700         0.97  0.076457704    1998.3789    130.13306   -5.5456805    4.1884336   -1071.8277   -1067.6392 
-    9750        0.975  0.076457717     1975.232     131.4781   -5.5424564    4.2317247    -1071.871   -1067.6392 
-    9800         0.98  0.076457754    1943.5946    131.52534    -5.543939    4.2332452   -1071.8725   -1067.6392 
-    9850        0.985  0.076457767    1925.7258    130.61182   -5.5541538    4.2038429   -1071.8431   -1067.6392 
-    9900         0.99  0.076457768    1912.4426    129.30485   -5.5732953    4.1617771    -1071.801   -1067.6392 
-    9950        0.995   0.07645781    1906.7982    128.04744   -5.5944645    4.1213064   -1071.7605   -1067.6392 
-   10000            1  0.076457853    1902.6667    127.24846   -5.6139316    4.0955905   -1071.7348   -1067.6392 
-   10050        1.005  0.076457894    1903.6495    127.22624   -5.6350055    4.0948754   -1071.7341   -1067.6392 
-   10100         1.01  0.076457899    1913.5279    127.69735   -5.6543581    4.1100384   -1071.7493   -1067.6392 
-   10150        1.015  0.076457799    1907.6348    128.06173   -5.6658197    4.1217662    -1071.761   -1067.6392 
-   10200         1.02  0.076457733    1899.2476    128.11218   -5.6733688      4.12339   -1071.7626   -1067.6392 
-   10250        1.025  0.076457747    1895.8986    127.94169   -5.6840919    4.1179026   -1071.7571   -1067.6392 
-   10300         1.03  0.076457816    1877.4598     127.6041   -5.7004798     4.107037   -1071.7463   -1067.6392 
-   10350        1.035  0.076457876    1829.2074    127.11751   -5.7241722    4.0913757   -1071.7306   -1067.6392 
-   10400         1.04  0.076457884    1806.0757    126.48167    -5.756364    4.0709108   -1071.7101   -1067.6392 
-   10450        1.045  0.076457869    1822.1953     125.5947   -5.7930905     4.042363   -1071.6816   -1067.6392 
-   10500         1.05  0.076457879    1827.9173    124.33858   -5.8252681    4.0019336   -1071.6412   -1067.6392 
-   10550        1.055  0.076457858    1812.1963    122.79649   -5.8435788    3.9523004   -1071.5915   -1067.6392 
-   10600         1.06  0.076457791    1797.2949    121.53225   -5.8488847    3.9116096   -1071.5508   -1067.6392 
-   10650        1.065  0.076457757      1775.25    121.32451   -5.8518555    3.9049236   -1071.5442   -1067.6392 
-   10700         1.07  0.076457792    1740.3273    122.44046   -5.8607258    3.9408413   -1071.5801   -1067.6392 
-   10750        1.075  0.076457855    1729.7945    124.41086   -5.8780857    4.0042601   -1071.6435   -1067.6392 
-   10800         1.08  0.076457901    1741.2893    126.28784   -5.9016509    4.0646721   -1071.7039   -1067.6392 
-   10850        1.085  0.076457859    1751.6811    127.09185   -5.9236888    4.0905498   -1071.7298   -1067.6392 
-   10900         1.09  0.076457795     1764.679    126.41883    -5.937278    4.0688881   -1071.7081   -1067.6392 
-   10950        1.095   0.07645779    1769.3986    124.77704   -5.9433211    4.0160458   -1071.6553   -1067.6392 
-   11000          1.1  0.076457827    1761.3552    123.29516   -5.9478426    3.9683506   -1071.6076   -1067.6392 
-   11050        1.105  0.076457857    1751.4218    123.17488   -5.9566275    3.9644792   -1071.6037   -1067.6392 
-   11100         1.11  0.076457863    1726.8666    125.22443   -5.9741936    4.0304456   -1071.6697   -1067.6392 
-   11150        1.115  0.076457878    1735.2828    129.42028   -6.0014992    4.1654923   -1071.8047   -1067.6392 
-   11200         1.12  0.076457903    1805.6904    134.81633   -6.0340926    4.3391683   -1071.9784   -1067.6392 
-   11250        1.125  0.076457923    1847.8249    139.98198   -6.0631111    4.5054288   -1072.1447   -1067.6392 
-   11300         1.13  0.076457865    1818.7912    143.90555   -6.0856034    4.6317119   -1072.2709   -1067.6392 
-   11350        1.135  0.076457825    1798.9525    146.44555   -6.1101917    4.7134638   -1072.3527   -1067.6392 
-   11400         1.14  0.076457815    1837.1775    147.67989   -6.1418356    4.7531917   -1072.3924   -1067.6392 
-   11450        1.145  0.076457893    1909.6101    147.41836   -6.1737085    4.7447744    -1072.384   -1067.6392 
-   11500         1.15  0.076457962    1946.7114    145.59364   -6.1998495    4.6860443   -1072.3253   -1067.6392 
-   11550        1.155  0.076457957     1967.998    142.69304   -6.2256371    4.5926863   -1072.2319   -1067.6392 
-   11600         1.16  0.076457903     2034.228    139.43936   -6.2585164    4.4879639   -1072.1272   -1067.6392 
-   11650        1.165  0.076457847    2063.6908     136.1161   -6.2925345    4.3810023   -1072.0202   -1067.6392 
-   11700         1.17  0.076457857    1990.1311    132.80435   -6.3184969    4.2744111   -1071.9136   -1067.6392 
-   11750        1.175  0.076457901      1933.95    129.89649   -6.3394362    4.1808193   -1071.8201   -1067.6392 
-   11800         1.18  0.076457953    1947.2099    127.68121   -6.3585167    4.1095189   -1071.7488   -1067.6392 
-   11850        1.185  0.076457986    1940.4995    126.35451   -6.3779087    4.0668179    -1071.706   -1067.6392 
-   11900         1.19  0.076457947    1896.3696    126.25109   -6.4040311    4.0634894   -1071.7027   -1067.6392 
-   11950        1.195  0.076457956    1843.5682     127.5666   -6.4410172    4.1058301   -1071.7451   -1067.6392 
-   12000          1.2  0.076457964    1811.4472    130.04643   -6.4846233    4.1856452   -1071.8249   -1067.6392 
-   12050        1.205  0.076457972    1814.5828    133.04634   -6.5254215    4.2821996   -1071.9214   -1067.6392 
-   12100         1.21  0.076457967    1813.6628    135.85077   -6.5555239    4.3724623   -1072.0117   -1067.6392 
-   12150        1.215  0.076457935    1806.3763    138.19822   -6.5770911     4.448017   -1072.0872   -1067.6392 
-   12200         1.22  0.076457946    1794.9644    140.31834   -6.5982636    4.5162546   -1072.1555   -1067.6392 
-   12250        1.225  0.076457982    1772.5404    142.42677   -6.6192794    4.5841162   -1072.2233   -1067.6392 
-   12300         1.23  0.076457963    1753.3843    144.61375   -6.6346864    4.6545058   -1072.2937   -1067.6392 
-   12350        1.235  0.076457949    1737.1545    146.94235   -6.6429412    4.7294536   -1072.3687   -1067.6392 
-   12400         1.24  0.076457977     1726.207    149.46271   -6.6518876    4.8105732   -1072.4498   -1067.6392 
-   12450        1.245  0.076457983    1731.0662    151.80715   -6.6670425    4.8860309   -1072.5253   -1067.6392 
-   12500         1.25  0.076457915    1760.4467    153.07641   -6.6813282    4.9268832   -1072.5661   -1067.6392 
-   12550        1.255  0.076457879    1799.0622    152.72464   -6.6918933    4.9155611   -1072.5548   -1067.6392 
-   12600         1.26  0.076457914    1822.2254    151.04918    -6.710248     4.861635   -1072.5009   -1067.6392 
-   12650        1.265   0.07645795    1816.7324    148.37072   -6.7389019    4.7754268   -1072.4147   -1067.6392 
-   12700         1.27  0.076457955    1812.8602    144.86733   -6.7666889    4.6626674   -1072.3019   -1067.6392 
-   12750        1.275  0.076457984    1810.7634    141.22215    -6.788381    4.5453446   -1072.1846   -1067.6392 
-   12800         1.28  0.076458017    1784.5198    138.39541   -6.8065328    4.4543636   -1072.0936   -1067.6392 
-   12850        1.285  0.076458007    1723.1734    136.86317   -6.8200203    4.4050473   -1072.0443   -1067.6392 
-   12900         1.29  0.076457981    1676.1889    136.77495   -6.8278227    4.4022078   -1072.0414   -1067.6392 
-   12950        1.295   0.07645799     1686.883    138.26769   -6.8341741    4.4502528   -1072.0895   -1067.6392 
-   13000          1.3     0.076458    1750.0412    141.08411    -6.841283    4.5409017   -1072.1801   -1067.6392 
-   13050        1.305  0.076457933     1814.788    144.61706   -6.8510949    4.6546122   -1072.2938   -1067.6392 
-   13100         1.31  0.076457918    1840.2708    148.22464   -6.8662706     4.770725     -1072.41   -1067.6392 
-   13150        1.315   0.07645799    1855.2415     151.3832   -6.8883549    4.8723856   -1072.5116   -1067.6392 
-   13200         1.32  0.076458049    1867.3248    153.53322   -6.9142169    4.9415857   -1072.5808   -1067.6392 
-   13250        1.325  0.076458096    1847.9049    154.02873   -6.9377296    4.9575343   -1072.5968   -1067.6392 
-   13300         1.33  0.076458112     1840.483    152.42018   -6.9562822    4.9057618    -1072.545   -1067.6392 
-   13350        1.335  0.076458098    1855.9464    148.69839    -6.970188    4.7859732   -1072.4252   -1067.6392 
-   13400         1.34   0.07645806    1820.6867     143.5401   -6.9830712    4.6199497   -1072.2592   -1067.6392 
-   13450        1.345  0.076457976    1745.2435    138.19145   -6.9989611    4.4477992    -1072.087   -1067.6392 
-   13500         1.35  0.076457963    1697.5473    133.92117   -7.0152512     4.310357   -1071.9496   -1067.6392 
-   13550        1.355  0.076458016    1684.8882    131.80734   -7.0311044    4.2423215   -1071.8816   -1067.6392 
-   13600         1.36  0.076458061    1708.2521     132.4772    -7.051885    4.2638815   -1071.9031   -1067.6392 
-   13650        1.365   0.07645807    1723.4416    135.53906   -7.0750853      4.36243   -1072.0017   -1067.6392 
-   13700         1.37   0.07645806     1706.999    139.94405   -7.0945976    4.5042079   -1072.1434   -1067.6392 
-   13750        1.375  0.076458036    1712.8033    144.85597   -7.1159258    4.6623018   -1072.3015   -1067.6392 
-   13800         1.38  0.076457971    1751.0123    149.63395   -7.1458169    4.8160849   -1072.4553   -1067.6392 
-   13850        1.385  0.076458021    1772.9962    153.59227   -7.1786728    4.9434865   -1072.5827   -1067.6392 
-   13900         1.39  0.076458106    1773.7385    156.28506   -7.2050465     5.030156   -1072.6694   -1067.6392 
-   13950        1.395  0.076458102    1748.7335    157.81358   -7.2259294    5.0793525   -1072.7186   -1067.6392 
-   14000          1.4  0.076458031    1718.5394    158.78508   -7.2557377     5.110621   -1072.7499   -1067.6392 
-   14050        1.405  0.076457985    1759.6811     159.6226   -7.3026227    5.1375772   -1072.7768   -1067.6392 
-   14100         1.41  0.076457949     1848.058    160.13835    -7.353886     5.154177   -1072.7934   -1067.6392 
-   14150        1.415   0.07645791    1902.6843    160.00219    -7.387799    5.1497946    -1072.789   -1067.6392 
-   14200         1.42  0.076457928    1921.0383    159.34446   -7.3946089    5.1286251   -1072.7679   -1067.6392 
-   14250        1.425  0.076458016    1906.9383    158.81344   -7.3863965     5.111534   -1072.7508   -1067.6392 
-   14300         1.43  0.076458065    1861.3283      158.866   -7.3810737    5.1132253   -1072.7525   -1067.6392 
-   14350        1.435  0.076458033    1831.4331    159.34444   -7.3867848    5.1286245   -1072.7679   -1067.6392 
-   14400         1.44  0.076457975    1816.0391     159.7047   -7.4029452    5.1402197   -1072.7795   -1067.6392 
-   14450        1.445  0.076457983    1762.1574    159.29777   -7.4235285    5.1271223   -1072.7664   -1067.6392 
-   14500         1.45  0.076458063    1709.2993    157.82112   -7.4454745    5.0795953   -1072.7188   -1067.6392 
-   14550        1.455  0.076458051    1677.4867    155.54554   -7.4726077    5.0063538   -1072.6456   -1067.6392 
-   14600         1.46  0.076457997    1654.1484    152.98432    -7.507262    4.9239192   -1072.5632   -1067.6392 
-   14650        1.465  0.076457952    1662.1842    150.42233   -7.5432446    4.8414594   -1072.4807   -1067.6392 
-   14700         1.47  0.076457903    1676.4959    147.93139   -7.5725021    4.7612867   -1072.4005   -1067.6392 
-   14750        1.475  0.076457859    1647.8468    145.84289   -7.5959112    4.6940666   -1072.3333   -1067.6392 
-   14800         1.48  0.076457877    1565.6357     144.8914   -7.6195017    4.6634423   -1072.3027   -1067.6392 
-   14850        1.485  0.076457947    1482.0818    145.74233   -7.6439027      4.69083   -1072.3301   -1067.6392 
-   14900         1.49  0.076457952    1458.8328    148.56937   -7.6680645    4.7818206   -1072.4211   -1067.6392 
-   14950        1.495  0.076457894    1499.3699    152.90243   -7.6925072    4.9212832   -1072.5605   -1067.6392 
-   15000          1.5  0.076457943    1551.7726    157.93125   -7.7198204    5.0831399   -1072.7224   -1067.6392 
-   15050        1.505  0.076457986    1571.2434     162.8654   -7.7546524    5.2419492   -1072.8812   -1067.6392 
-   15100         1.51  0.076457935    1575.6395    166.87268   -7.7966882    5.3709267   -1073.0102   -1067.6392 
-   15150        1.515  0.076457852    1577.2167    169.36633   -7.8445178    5.4511868   -1073.0904   -1067.6392 
-   15200         1.52  0.076457871    1551.3549    170.15934   -7.8947687    5.4767104   -1073.1159   -1067.6392 
-   15250        1.525  0.076457931    1540.7825    169.38479   -7.9379114    5.4517809    -1073.091   -1067.6392 
-   15300         1.53  0.076457872    1542.7519      167.721   -7.9689255    5.3982305   -1073.0375   -1067.6392 
-   15350        1.535  0.076457794    1515.2436    166.07279   -7.9891151    5.3451817   -1072.9844   -1067.6392 
-   15400         1.54  0.076457791    1471.3138    164.91456   -8.0001719    5.3079031   -1072.9471   -1067.6392 
-   15450        1.545  0.076457806    1446.0781    164.17878    -8.005266    5.2842213   -1072.9235   -1067.6392 
-   15500         1.55  0.076457866    1437.1273    163.51385    -8.007144    5.2628202   -1072.9021   -1067.6392 
-   15550        1.555  0.076457955    1429.6394     162.9507   -8.0109974    5.2446946   -1072.8839   -1067.6392 
-   15600         1.56  0.076457952    1428.0365    163.16031   -8.0290067    5.2514413   -1072.8907   -1067.6392 
-   15650        1.565  0.076457861    1443.4131    164.39868   -8.0647449     5.291299   -1072.9305   -1067.6392 
-   15700         1.57  0.076457793    1455.1522    165.85145    -8.105615    5.3380576   -1072.9773   -1067.6392 
-   15750        1.575  0.076457798    1463.0529    166.37099   -8.1380795    5.3547794    -1072.994   -1067.6392 
-   15800         1.58    0.0764579    1465.1315    165.43643   -8.1598171    5.3246998   -1072.9639   -1067.6392 
-   15850        1.585  0.076457964    1481.9518    163.30816   -8.1737913    5.2561998   -1072.8954   -1067.6392 
-   15900         1.59  0.076457915    1527.4564    160.78551   -8.1825869    5.1750065   -1072.8142   -1067.6392 
-   15950        1.595  0.076457836    1575.6511    158.77652   -8.1876334    5.1103456   -1072.7496   -1067.6392 
-   16000          1.6   0.07645778    1614.7527    157.95908   -8.1929355    5.0840356   -1072.7233   -1067.6392 
-   16050        1.605  0.076457779    1617.7108     158.3895   -8.1978312    5.0978888   -1072.7371   -1067.6392 
-   16100         1.61  0.076457748     1603.592     159.6981   -8.1974276    5.1400074   -1072.7792   -1067.6392 
-   16150        1.615  0.076457683    1621.7853    161.62591   -8.1934309    5.2020553   -1072.8413   -1067.6392 
-   16200         1.62  0.076457713    1666.2189    163.90851   -8.1904572    5.2755226   -1072.9148   -1067.6392 
-   16250        1.625  0.076457784    1699.4521    166.19825   -8.1928336    5.3492197   -1072.9885   -1067.6392 
-   16300         1.63  0.076457822    1732.0779     168.1831   -8.2032476    5.4131037   -1073.0523   -1067.6392 
-   16350        1.635  0.076457792    1749.3266    169.69701   -8.2214781    5.4618299   -1073.1011   -1067.6392 
-   16400         1.64  0.076457743    1727.9265    170.72169   -8.2470147    5.4948102    -1073.134   -1067.6392 
-   16450        1.645  0.076457802    1695.7397    171.03962   -8.2748768    5.5050428   -1073.1443   -1067.6392 
-   16500         1.65  0.076457865    1654.9001     170.1718   -8.2900487    5.4771114   -1073.1163   -1067.6392 
-   16550        1.655  0.076457864    1599.4818    168.42964   -8.2855859    5.4210388   -1073.0603   -1067.6392 
-   16600         1.66  0.076457829    1549.0403    167.32713   -8.2743004    5.3855536   -1073.0248   -1067.6392 
-   16650        1.665  0.076457816    1552.8738    168.16653   -8.2712688    5.4125703   -1073.0518   -1067.6392 
-   16700         1.67  0.076457855    1613.3994    170.72875    -8.278589    5.4950374   -1073.1343   -1067.6392 
-   16750        1.675  0.076457923    1657.1911    173.60042    -8.287191    5.5874642   -1073.2267   -1067.6392 
-   16800         1.68  0.076457913     1642.492    175.54043    -8.290541    5.6499049   -1073.2891   -1067.6392 
-   16850        1.685  0.076457804    1591.5457    176.27819   -8.2944475    5.6736502   -1073.3129   -1067.6392 
-   16900         1.69  0.076457721    1535.2384    176.07329   -8.3085794    5.6670554   -1073.3063   -1067.6392 
-   16950        1.695  0.076457718     1505.622    175.05532   -8.3334071    5.6342912   -1073.2735   -1067.6392 
-   17000          1.7  0.076457759    1497.9484    173.29107   -8.3636107    5.5775077   -1073.2167   -1067.6392 
-   17050        1.705  0.076457839    1497.0049    170.93476   -8.3927083    5.5016678   -1073.1409   -1067.6392 
-   17100         1.71  0.076457875    1511.4053    168.29935   -8.4139231    5.4168451   -1073.0561   -1067.6392 
-   17150        1.715  0.076457846    1513.6863    166.13296   -8.4263326    5.3471182   -1072.9863   -1067.6392 
-   17200         1.72  0.076457792    1500.5415    165.41134   -8.4331329    5.3238925   -1072.9631   -1067.6392 
-   17250        1.725  0.076457779    1516.4257    166.86136   -8.4395441    5.3705623   -1073.0098   -1067.6392 
-   17300         1.73  0.076457719    1560.1678    170.36031   -8.4473104    5.4831788   -1073.1224   -1067.6392 
-   17350        1.735  0.076457713    1589.7681    174.76749   -8.4563024    5.6250272   -1073.2643   -1067.6392 
-   17400         1.74  0.076457713    1591.6237    178.46853   -8.4713912    5.7441481   -1073.3834   -1067.6392 
-   17450        1.745  0.076457675    1596.2649    179.85013   -8.4922285    5.7886159   -1073.4279   -1067.6392 
-   17500         1.75  0.076457641    1584.0194    177.91175   -8.5124955    5.7262277   -1073.3655   -1067.6392 
-   17550        1.755  0.076457729    1561.3047     172.8566   -8.5331849    5.5635239   -1073.2028   -1067.6392 
-   17600         1.76  0.076457773    1572.5958    165.81832   -8.5554415    5.3369913   -1072.9762   -1067.6392 
-   17650        1.765  0.076457741    1605.3403    158.62222   -8.5744278    5.1053792   -1072.7446   -1067.6392 
-   17700         1.77  0.076457777    1625.9857    153.83663   -8.5928174    4.9513512   -1072.5906   -1067.6392 
-   17750        1.775  0.076457794    1624.2493    153.59935   -8.6164551    4.9437143   -1072.5829   -1067.6392 
-   17800         1.78  0.076457697    1600.4975    158.02997    -8.639484    5.0863173   -1072.7255   -1067.6392 
-   17850        1.785  0.076457635    1572.3161    165.46312   -8.6573098    5.3255589   -1072.9648   -1067.6392 
-   17900         1.79  0.076457609    1561.9769    173.49259   -8.6712589    5.5839937   -1073.2232   -1067.6392 
-   17950        1.795  0.076457688    1562.7517    180.08491   -8.6850112    5.7961727   -1073.4354   -1067.6392 
-   18000          1.8  0.076457774    1534.5231    184.30185   -8.7046968    5.9318979   -1073.5711   -1067.6392 
-   18050        1.805  0.076457734    1514.7751    185.91513   -8.7282196    5.9838228   -1073.6231   -1067.6392 
-   18100         1.81  0.076457673    1529.4218     185.3585   -8.7536862    5.9659073   -1073.6051   -1067.6392 
-   18150        1.815  0.076457707    1528.0858    183.58143   -8.7834393    5.9087109   -1073.5479   -1067.6392 
-   18200         1.82    0.0764577     1527.873    181.50762   -8.8147286    5.8419635   -1073.4812   -1067.6392 
-   18250        1.825  0.076457665    1548.9614    179.99555   -8.8428647    5.7932965   -1073.4325   -1067.6392 
-   18300         1.83  0.076457588    1549.3007    179.95539   -8.8681457    5.7920039   -1073.4312   -1067.6392 
-   18350        1.835  0.076457533     1526.091    181.95841   -8.8948825    5.8564725   -1073.4957   -1067.6392 
-   18400         1.84  0.076457629    1493.8372    185.43374   -8.9193239     5.968329   -1073.6076   -1067.6392 
-   18450        1.845  0.076457747    1466.0305    188.93806   -8.9346392    6.0811179   -1073.7204   -1067.6392 
-   18500         1.85  0.076457732    1463.6299    191.18823   -8.9432273    6.1535417   -1073.7928   -1067.6392 
-   18550        1.855  0.076457611    1470.3581    191.71361   -8.9569487    6.1704514   -1073.8097   -1067.6392 
-   18600         1.86  0.076457576    1465.3642    190.61383   -8.9856472     6.135054   -1073.7743   -1067.6392 
-   18650        1.865  0.076457589    1435.5034     187.7372   -9.0216033    6.0424676   -1073.6817   -1067.6392 
-   18700         1.87  0.076457602    1387.1168    182.94758   -9.0538168    5.8883099   -1073.5275   -1067.6392 
-   18750        1.875  0.076457646    1370.2898     176.6874   -9.0814451     5.686821   -1073.3261   -1067.6392 
-   18800         1.88  0.076457607    1396.5471    169.73777   -9.1008384    5.4631417   -1073.1024   -1067.6392 
-   18850        1.885  0.076457617    1424.9718     163.2588    -9.109503    5.2546111   -1072.8938   -1067.6392 
-   18900         1.89  0.076457679    1428.3173    158.69622   -9.1168953     5.107761    -1072.747   -1067.6392 
-   18950        1.895  0.076457649    1439.2765    156.82172   -9.1272053    5.0474288   -1072.6867   -1067.6392 
-   19000          1.9  0.076457629    1459.8802    157.73056   -9.1321959    5.0766804   -1072.7159   -1067.6392 
-   19050        1.905  0.076457635     1504.363    162.01011   -9.1350256    5.2144212   -1072.8536   -1067.6392 
-   19100         1.91   0.07645765    1534.7588    170.14098   -9.1510965    5.4761196   -1073.1153   -1067.6392 
-   19150        1.915  0.076457653    1508.0173    180.71726   -9.1848155    5.8165254   -1073.4558   -1067.6392 
-   19200         1.92  0.076457613     1467.829    190.69721   -9.2245704    6.1377378    -1073.777   -1067.6392 
-   19250        1.925  0.076457631    1432.4759    197.48699   -9.2604662    6.3562721   -1073.9955   -1067.6392 
-   19300         1.93   0.07645763    1411.3494    200.09216   -9.2919631    6.4401214   -1074.0794   -1067.6392 
-   19350        1.935  0.076457594    1414.8241    198.83025   -9.3208023     6.399506   -1074.0387   -1067.6392 
-   19400         1.94  0.076457607     1435.692    194.74665   -9.3453509    6.2680721   -1073.9073   -1067.6392 
-   19450        1.945  0.076457654    1457.6905     189.4249   -9.3649457    6.0967875    -1073.736   -1067.6392 
-   19500         1.95  0.076457645    1449.0474     184.9571   -9.3864711    5.9529879   -1073.5922   -1067.6392 
-   19550        1.955  0.076457606    1409.8482    183.36678   -9.4200425     5.901802    -1073.541   -1067.6392 
-   19600         1.96  0.076457637    1376.8581     185.3704   -9.4660084    5.9662902   -1073.6055   -1067.6392 
-   19650        1.965  0.076457676    1394.1961    189.79341    -9.512099    6.1086483   -1073.7479   -1067.6392 
-   19700         1.97  0.076457666    1444.3533    194.43969   -9.5410671    6.2581922   -1073.8974   -1067.6392 
-   19750        1.975  0.076457652    1456.9001    197.74076   -9.5468975    6.3644397   -1074.0037   -1067.6392 
-   19800         1.98  0.076457697    1416.4247    199.50327   -9.5434518    6.4211677   -1074.0604   -1067.6392 
-   19850        1.985   0.07645765    1363.4589    200.03465   -9.5469461    6.4382705   -1074.0775   -1067.6392 
-   19900         1.99  0.076457547    1331.9006    199.31164   -9.5615968    6.4149999   -1074.0542   -1067.6392 
-   19950        1.995  0.076457526    1324.5585    197.29584   -9.5885975    6.3501197   -1073.9894   -1067.6392 
-   20000            2  0.076457553     1337.069    194.04585   -9.6231448    6.2455162   -1073.8847   -1067.6392 
-   20050        2.005  0.076457648    1351.0753    189.93086   -9.6575947     6.113072   -1073.7523   -1067.6392 
-   20100         2.01  0.076457655    1339.7133     185.8145   -9.6913164     5.980584   -1073.6198   -1067.6392 
-   20150        2.015  0.076457614    1318.0742    182.57664   -9.7225895    5.8763709   -1073.5156   -1067.6392 
-   20200         2.02  0.076457601    1288.6368    180.87905   -9.7460096    5.8217325    -1073.461   -1067.6392 
-   20250        2.025  0.076457595    1270.6138    181.09203   -9.7599966    5.8285875   -1073.4678   -1067.6392 
-   20300         2.03   0.07645759    1297.0333    183.14558    -9.771863    5.8946825   -1073.5339   -1067.6392 
-   20350        2.035  0.076457544     1322.481    186.19746   -9.7878745    5.9929098   -1073.6321   -1067.6392 
-   20400         2.04  0.076457529    1321.8589    188.69758   -9.8051647    6.0733781   -1073.7126   -1067.6392 
-   20450        2.045  0.076457552    1334.9839    189.43488   -9.8222144    6.0971087   -1073.7363   -1067.6392 
-   20500         2.05  0.076457581    1383.7092    188.25801   -9.8390497      6.05923   -1073.6985   -1067.6392 
-   20550        2.055  0.076457593    1422.9993     186.0328   -9.8547027    5.9876099   -1073.6268   -1067.6392 
-   20600         2.06   0.07645748    1399.9508    184.16392   -9.8728024    5.9274586   -1073.5667   -1067.6392 
-   20650        2.065  0.076457422    1335.1662    183.59411   -9.8931369    5.9091189   -1073.5483   -1067.6392 
-   20700         2.07  0.076457465     1306.751    184.55079   -9.9118543    5.9399103   -1073.5791   -1067.6392 
-   20750        2.075  0.076457483    1305.5888    187.07424   -9.9311695    6.0211296   -1073.6604   -1067.6392 
-   20800         2.08  0.076457441    1294.1667    191.05858   -9.9508151    6.1493686   -1073.7886   -1067.6392 
-   20850        2.085  0.076457401    1282.0253    196.07833   -9.9647464    6.3109334   -1073.9502   -1067.6392 
-   20900         2.09  0.076457455    1292.0201    201.33144   -9.9711707    6.4800088   -1074.1192   -1067.6392 
-   20950        2.095  0.076457576    1320.8835     205.6673   -9.9717153    6.6195616   -1074.2588   -1067.6392 
-   21000          2.1  0.076457569    1327.4497    207.97171   -9.9627916    6.6937308    -1074.333   -1067.6392 
-   21050        2.105  0.076457524    1302.0315    208.01339   -9.9425688    6.6950725   -1074.3343   -1067.6392 
-   21100         2.11  0.076457555    1283.4817    206.79741   -9.9230585    6.6559351   -1074.2952   -1067.6392 
-   21150        2.115  0.076457542    1295.1909     205.4375    -9.914788    6.6121654   -1074.2514   -1067.6392 
-   21200         2.12  0.076457479    1321.5201     204.1527    -9.909418    6.5708132     -1074.21   -1067.6392 
-   21250        2.125  0.076457453    1325.0561    202.79152   -9.8961399    6.5270024   -1074.1662   -1067.6392 
-   21300         2.13  0.076457519    1301.9167    201.35361   -9.8787376    6.4807223     -1074.12   -1067.6392 
-   21350        2.135  0.076457579    1274.9532    199.72664    -9.868175     6.428357   -1074.0676   -1067.6392 
-   21400         2.14  0.076457544    1261.6495     197.3916   -9.8684802    6.3532018   -1073.9924   -1067.6392 
-   21450        2.145  0.076457471    1267.8867    193.48031   -9.8693012    6.2273138   -1073.8665   -1067.6392 
-   21500         2.15  0.076457431    1293.2863    187.70474   -9.8616374    6.0414226   -1073.6807   -1067.6392 
-   21550        2.155   0.07645745    1323.0989    181.26349   -9.8574218    5.8341061   -1073.4733   -1067.6392 
-   21600         2.16  0.076457464    1324.9095    175.93101   -9.8707078     5.662476   -1073.3017   -1067.6392 
-   21650        2.165  0.076457483    1337.2372    172.83131   -9.9003355      5.56271   -1073.2019   -1067.6392 
-   21700         2.17  0.076457536    1353.6476    172.28199   -9.9335024    5.5450296   -1073.1843   -1067.6392 
-   21750        2.175  0.076457522    1337.4658    174.63693   -9.9656126    5.6208252   -1073.2601   -1067.6392 
-   21800         2.18  0.076457492    1319.6144    180.27032   -10.002014    5.8021402   -1073.4414   -1067.6392 
-   21850        2.185  0.076457468    1325.9534     188.6868   -10.042097     6.073031   -1073.7123   -1067.6392 
-   21900         2.19    0.0764574     1351.519    198.20437   -10.076426    6.3793615   -1074.0186   -1067.6392 
-   21950        2.195  0.076457412    1373.8526    206.68615   -10.099592    6.6523543   -1074.2916   -1067.6392 
-   22000          2.2  0.076457518     1392.659    212.65494    -10.12001    6.8444642   -1074.4837   -1067.6392 
-   22050        2.205  0.076457606    1390.3967    215.42094   -10.145572      6.93349   -1074.5727   -1067.6392 
-   22100         2.21  0.076457602    1347.4452    214.94045   -10.173725    6.9180253   -1074.5573   -1067.6392 
-   22150        2.215  0.076457513    1283.3202    211.98537   -10.199933    6.8229137   -1074.4621   -1067.6392 
-   22200         2.22  0.076457494    1222.5665    207.95995   -10.224493    6.6933523   -1074.3326   -1067.6392 
-   22250        2.225  0.076457542    1202.5195    204.45409   -10.254994    6.5805135   -1074.2197   -1067.6392 
-   22300         2.23  0.076457582    1210.7113    202.41627   -10.292456    6.5149247   -1074.1542   -1067.6392 
-   22350        2.235  0.076457593    1220.7645    201.90137   -10.329195    6.4983524   -1074.1376   -1067.6392 
-   22400         2.24  0.076457607    1234.7446    202.62559    -10.36471     6.521662   -1074.1609   -1067.6392 
-   22450        2.245  0.076457614    1256.0665    204.20591   -10.403554    6.5725258   -1074.2118   -1067.6392 
-   22500         2.25  0.076457647    1289.6179    206.08787    -10.44356    6.6330979   -1074.2723   -1067.6392 
-   22550        2.255  0.076457648    1318.2401    207.71118   -10.483186    6.6853454   -1074.3246   -1067.6392 
-   22600         2.26  0.076457621    1319.5232    208.34289   -10.522979    6.7056776   -1074.3449   -1067.6392 
-   22650        2.265  0.076457589    1316.8506    207.24251   -10.561044     6.670261   -1074.3095   -1067.6392 
-   22700         2.27  0.076457617     1331.642    204.29832   -10.595084    6.5755001   -1074.2147   -1067.6392 
-   22750        2.275  0.076457638    1346.6949    200.13918   -10.622417    6.4416347   -1074.0809   -1067.6392 
-   22800         2.28  0.076457572     1347.787      196.067   -10.645862    6.3105686   -1073.9498   -1067.6392 
-   22850        2.285  0.076457478    1357.3814    193.71126   -10.672581    6.2347474    -1073.874   -1067.6392 
-   22900         2.29  0.076457506    1359.0604    194.23136   -10.704942    6.2514872   -1073.8907   -1067.6392 
-   22950        2.295   0.07645755    1347.1653    197.67464   -10.741957    6.3623116   -1074.0015   -1067.6392 
-   23000          2.3  0.076457564    1321.3672    202.79941   -10.780161    6.5272563   -1074.1665   -1067.6392 
-   23050        2.305  0.076457626    1300.8493     207.8112   -10.812965    6.6885649   -1074.3278   -1067.6392 
-   23100         2.31  0.076457662    1289.7113     211.5894   -10.839288    6.8101691   -1074.4494   -1067.6392 
-   23150        2.315  0.076457654    1266.9494    213.84528    -10.86234    6.8827763    -1074.522   -1067.6392 
-   23200         2.32  0.076457651    1237.4556    214.46793   -10.878861    6.9028167    -1074.542   -1067.6392 
-   23250        2.325  0.076457588    1216.4817    213.53906    -10.88737    6.8729203   -1074.5122   -1067.6392 
-   23300         2.33  0.076457561    1198.6768     211.4015   -10.892244    6.8041213   -1074.4434   -1067.6392 
-   23350        2.335  0.076457617      1218.46    208.62206   -10.896503     6.714663   -1074.3539   -1067.6392 
-   23400         2.34  0.076457697    1274.0141    206.18082   -10.898818    6.6360899   -1074.2753   -1067.6392 
-   23450        2.345  0.076457697    1310.0462    205.39475   -10.899188    6.6107893     -1074.25   -1067.6392 
-   23500         2.35  0.076457625    1309.8688    206.85671   -10.898274    6.6578437   -1074.2971   -1067.6392 
-   23550        2.355  0.076457607    1294.4375    210.05998   -10.904793    6.7609436   -1074.4002   -1067.6392 
-   23600         2.36  0.076457638    1272.3829    213.64213   -10.924411    6.8762376   -1074.5155   -1067.6392 
-   23650        2.365   0.07645764    1263.3834    215.89726   -10.943246    6.9488208   -1074.5881   -1067.6392 
-   23700         2.37    0.0764576    1265.3339    216.28708    -10.95133    6.9613674   -1074.6006   -1067.6392 
-   23750        2.375  0.076457533    1265.7883    215.64775   -10.954658    6.9407901     -1074.58   -1067.6392 
-   23800         2.38  0.076457509     1270.324    215.14847   -10.964811    6.9247203    -1074.564   -1067.6392 
-   23850        2.385  0.076457647    1295.1389    215.59482   -10.992719    6.9390865   -1074.5783   -1067.6392 
-   23900         2.39   0.07645774    1317.1304    216.50299   -11.032267    6.9683166   -1074.6075   -1067.6392 
-   23950        2.395  0.076457678    1323.3993    216.86149    -11.06922    6.9798554   -1074.6191   -1067.6392 
-   24000          2.4  0.076457616    1327.0079    216.51416   -11.098994    6.9686763   -1074.6079   -1067.6392 
-   24050        2.405  0.076457602    1347.1187    215.98329   -11.123989    6.9515898   -1074.5908   -1067.6392 
-   24100         2.41  0.076457633    1373.0058     215.6582   -11.147405    6.9411267   -1074.5804   -1067.6392 
-   24150        2.415  0.076457606    1357.3622    215.33306   -11.168833    6.9306616   -1074.5699   -1067.6392 
-   24200         2.42  0.076457558    1293.9783     214.6673   -11.190176    6.9092338   -1074.5485   -1067.6392 
-   24250        2.425  0.076457575    1262.6983    213.59841   -11.211793    6.8748305   -1074.5141   -1067.6392 
-   24300         2.43  0.076457586    1296.1082    212.60059   -11.234851    6.8427151   -1074.4819   -1067.6392 
-   24350        2.435   0.07645758    1338.5152    212.36533   -11.263922    6.8351428   -1074.4744   -1067.6392 
-   24400         2.44   0.07645762    1359.7328    212.76414   -11.288804     6.847979   -1074.4872   -1067.6392 
-   24450        2.445  0.076457613    1354.6032    213.05104   -11.296422    6.8572131   -1074.4964   -1067.6392 
-   24500         2.45   0.07645752    1340.1858    212.64499   -11.294481    6.8441441   -1074.4834   -1067.6392 
-   24550        2.455   0.07645749    1331.5151    211.50434   -11.306624    6.8074314   -1074.4467   -1067.6392 
-   24600         2.46  0.076457509    1316.1319    209.75998   -11.338874    6.7512878   -1074.3905   -1067.6392 
-   24650        2.465  0.076457501    1303.2352    208.01652   -11.382268    6.6951732   -1074.3344   -1067.6392 
-   24700         2.47  0.076457554    1316.5042    207.54508   -11.432653    6.6799995   -1074.3192   -1067.6392 
-   24750        2.475  0.076457644    1323.4729    209.08952   -11.480943    6.7297085   -1074.3689   -1067.6392 
-   24800         2.48  0.076457563    1316.2449    212.60405   -11.521223    6.8428264   -1074.4821   -1067.6392 
-   24850        2.485  0.076457464     1303.023    217.39017   -11.549403    6.9968714   -1074.6361   -1067.6392 
-   24900         2.49  0.076457476    1306.7431    222.37347   -11.558822    7.1572628   -1074.7965   -1067.6392 
-   24950        2.495   0.07645745    1300.9383    226.66891     -11.5504    7.2955148   -1074.9347   -1067.6392 
-   25000          2.5  0.076457461    1270.8966    229.83334   -11.536542    7.3973644   -1075.0366   -1067.6392 
-   25050        2.505  0.076457456    1266.2646    231.90105   -11.533642    7.4639151   -1075.1031   -1067.6392 
-   25100         2.51  0.076457446    1270.2017    233.06025   -11.547509     7.501225   -1075.1405   -1067.6392 
-   25150        2.515   0.07645757    1231.6171    233.15738    -11.56954    7.5043513   -1075.1436   -1067.6392 
-   25200         2.52  0.076457709    1191.0767    231.73714   -11.589225    7.4586397   -1075.0979   -1067.6392 
-   25250        2.525  0.076457772    1193.1019    228.87762   -11.611584     7.366604   -1075.0058   -1067.6392 
-   25300         2.53  0.076457705    1202.8442    225.48075   -11.647482     7.257273   -1074.8965   -1067.6392 
-   25350        2.535  0.076457601    1201.3602    222.49225   -11.687125    7.1610856   -1074.8003   -1067.6392 
-   25400         2.54  0.076457625    1191.7307    220.47028   -11.711225    7.0960072   -1074.7352   -1067.6392 
-   25450        2.545  0.076457676     1184.558     219.7896    -11.72244     7.074099   -1074.7133   -1067.6392 
-   25500         2.55   0.07645769    1209.0131    220.21101   -11.729634    7.0876623   -1074.7269   -1067.6392 
-   25550        2.555  0.076457694    1252.4527    221.39919   -11.740381    7.1259047   -1074.7651   -1067.6392 
-   25600         2.56  0.076457651    1266.8561    223.37443   -11.758317    7.1894793   -1074.8287   -1067.6392 
-   25650        2.565  0.076457702    1260.0162    226.18443   -11.779767    7.2799214   -1074.9192   -1067.6392 
-   25700         2.57  0.076457766    1258.0807    229.46946   -11.803244    7.3856527   -1075.0249   -1067.6392 
-   25750        2.575    0.0764577    1260.0577    231.96891   -11.827028    7.4660992   -1075.1053   -1067.6392 
-   25800         2.58   0.07645766    1263.5682    232.00397   -11.843175    7.4672278   -1075.1065   -1067.6392 
-   25850        2.585  0.076457679    1267.6331    229.22367   -11.852724    7.3777416    -1075.017   -1067.6392 
-   25900         2.59  0.076457667    1273.4873    224.95936   -11.864844    7.2404915   -1074.8797   -1067.6392 
-   25950        2.595  0.076457638    1259.3238    220.69283   -11.875369    7.1031702   -1074.7424   -1067.6392 
-   26000          2.6   0.07645756    1234.4517    217.53504    -11.87838    7.0015342   -1074.6408   -1067.6392 
-   26050        2.605  0.076457531    1223.5843    216.47883   -11.885283     6.967539   -1074.6068   -1067.6392 
-   26100         2.61  0.076457579    1239.4383     217.6799   -11.906525    7.0061965   -1074.6454   -1067.6392 
-   26150        2.615  0.076457676    1254.9755    220.14626     -11.9364    7.0855781   -1074.7248   -1067.6392 
-   26200         2.62  0.076457691    1263.4276    222.78599    -11.96794      7.17054   -1074.8098   -1067.6392 
-   26250        2.625  0.076457661    1290.9982    225.11879   -12.002676    7.2456229   -1074.8849   -1067.6392 
-   26300         2.63  0.076457625    1320.5003    226.53955   -12.032325    7.2913511   -1074.9306   -1067.6392 
-   26350        2.635  0.076457604    1325.6925    226.42099   -12.045972    7.2875353   -1074.9268   -1067.6392 
-   26400         2.64  0.076457635    1323.8314    225.04813   -12.050265    7.2433489   -1074.8826   -1067.6392 
-   26450        2.645  0.076457683    1337.7763    223.39584   -12.056562    7.1901684   -1074.8294   -1067.6392 
-   26500         2.65  0.076457646      1356.26    222.47285   -12.072437    7.1604612   -1074.7997   -1067.6392 
-   26550        2.655  0.076457593    1368.7452    222.81131   -12.102517    7.1713548   -1074.8106   -1067.6392 
-   26600         2.66  0.076457577    1372.4772     224.2612   -12.136283    7.2180208   -1074.8573   -1067.6392 
-   26650        2.665  0.076457669    1353.1116    226.93203    -12.15666    7.3039835   -1074.9432   -1067.6392 
-   26700         2.67   0.07645782    1296.4345    231.54488   -12.162395    7.4524517   -1075.0917   -1067.6392 
-   26750        2.675   0.07645786     1233.171    238.00107    -12.16795    7.6602491   -1075.2995   -1067.6392 
-   26800         2.68    0.0764578    1205.1226    244.60391    -12.18481    7.8727668    -1075.512   -1067.6392 
-   26850        2.685  0.076457751    1203.9449    249.24116   -12.214765    8.0220202   -1075.6613   -1067.6392 
-   26900         2.69  0.076457871     1220.793    250.32595   -12.247789    8.0569351   -1075.6962   -1067.6392 
-   26950        2.695   0.07645797     1250.922    247.65941   -12.281839    7.9711102   -1075.6103   -1067.6392 
-   27000          2.7  0.076457916    1272.2527    242.25891   -12.319204    7.7972911   -1075.4365   -1067.6392 
-   27050        2.705  0.076457909    1260.7801     235.6016    -12.35094    7.5830204   -1075.2223   -1067.6392 
-   27100         2.71  0.076457849    1229.7859    229.49227   -12.367756    7.3863867   -1075.0256   -1067.6392 
-   27150        2.715  0.076457776    1230.1984    225.87326    -12.37385    7.2699062   -1074.9091   -1067.6392 
-   27200         2.72  0.076457788    1256.5205    226.01981   -12.383103    7.2746231   -1074.9139   -1067.6392 
-   27250        2.725  0.076457742     1269.109    229.57592   -12.401772    7.3890791   -1075.0283   -1067.6392 
-   27300         2.73  0.076457757    1278.2216    234.37745    -12.41951    7.5436201   -1075.1829   -1067.6392 
-   27350        2.735  0.076457815    1281.9146    237.72622   -12.426299     7.651403   -1075.2906   -1067.6392 
-   27400         2.74  0.076457895    1266.5327    238.04161   -12.428658    7.6615539   -1075.3008   -1067.6392 
-   27450        2.745  0.076457976    1238.9201    235.37217   -12.441314    7.5756359   -1075.2149   -1067.6392 
-   27500         2.75  0.076457843    1230.4481    230.70667   -12.466737    7.4254733   -1075.0647   -1067.6392 
-   27550        2.755  0.076457656    1236.7255    225.51713   -12.497899    7.2584439   -1074.8977   -1067.6392 
-   27600         2.76   0.07645776      1238.11    221.28548    -12.52521    7.1222449   -1074.7615   -1067.6392 
-   27650        2.765  0.076457889    1218.4037    219.08795   -12.543581    7.0515156   -1074.6907   -1067.6392 
-   27700         2.77  0.076457882    1198.4777    219.33613   -12.554891    7.0595037   -1074.6987   -1067.6392 
-   27750        2.775  0.076457863     1183.089    221.96976   -12.561518     7.144269   -1074.7835   -1067.6392 
-   27800         2.78  0.076457885      1169.37    227.37353   -12.573341    7.3181935   -1074.9574   -1067.6392 
-   27850        2.785  0.076457897    1169.7411    235.91312   -12.602269    7.5930469   -1075.2323   -1067.6392 
-   27900         2.79  0.076457851    1151.3464    246.28711   -12.644365    7.9269419   -1075.5662   -1067.6392 
-   27950        2.795  0.076457843    1106.9771    255.46726   -12.682364    8.2224121   -1075.8616   -1067.6392 
-   28000          2.8  0.076457826    1068.9543    260.54346    -12.70329    8.3857935    -1076.025   -1067.6392 
-   28050        2.805  0.076457783    1046.8631    260.38287   -12.707616    8.3806246   -1076.0199   -1067.6392 
-   28100         2.81  0.076457851    1035.4028    255.75262   -12.701329    8.2315965   -1075.8708   -1067.6392 
-   28150        2.815  0.076457914    1039.8478    248.80323   -12.698053    8.0079252   -1075.6472   -1067.6392 
-   28200         2.82  0.076457945    1077.5288    241.99763   -12.714207    7.7888815   -1075.4281   -1067.6392 
-   28250        2.825  0.076457907    1106.7726     236.8129   -12.748192    7.6220071   -1075.2612   -1067.6392 
-   28300         2.83  0.076457858    1088.3383    233.07492   -12.770565     7.501697   -1075.1409   -1067.6392 
-   28350        2.835  0.076457962    1067.6408     230.2341   -12.762291    7.4102632   -1075.0495   -1067.6392 
-   28400         2.84  0.076458053    1085.7765    228.74782   -12.741859     7.362426   -1075.0017   -1067.6392 
-   28450        2.845  0.076458069    1116.0156    229.35012   -12.732966    7.3818115    -1075.021   -1067.6392 
-   28500         2.85   0.07645799    1140.0561    231.95241   -12.737452    7.4655684   -1075.1048   -1067.6392 
-   28550        2.855  0.076457881    1175.3679    235.63809   -12.744967    7.5841948   -1075.2234   -1067.6392 
-   28600         2.86  0.076457945    1191.5122    239.06582   -12.744692    7.6945191   -1075.3338   -1067.6392 
-   28650        2.865  0.076458033    1165.8181     241.0619   -12.730571    7.7587645    -1075.398   -1067.6392 
-   28700         2.87  0.076458003    1144.2872    241.42924   -12.708938    7.7705875   -1075.4098   -1067.6392 
-   28750        2.875  0.076457916    1156.9296    241.00794    -12.69273    7.7570275   -1075.3963   -1067.6392 
-   28800         2.88  0.076457978    1169.6062    241.01439   -12.691343    7.7572351   -1075.3965   -1067.6392 
-   28850        2.885  0.076458067    1153.2461    242.11608   -12.703125    7.7926941   -1075.4319   -1067.6392 
-   28900         2.89  0.076458128    1137.1648    244.24646   -12.730476    7.8612619   -1075.5005   -1067.6392 
-   28950        2.895  0.076458132    1144.0676    245.87591   -12.765806    7.9137071   -1075.5529   -1067.6392 
-   29000          2.9  0.076458055    1166.7003    244.81325   -12.786467    7.8795045   -1075.5187   -1067.6392 
-   29050        2.905  0.076458115     1201.626    240.80417   -12.786117    7.7504692   -1075.3897   -1067.6392 
-   29100         2.91  0.076458234    1227.2794    235.81398   -12.775018    7.5898561   -1075.2291   -1067.6392 
-   29150        2.915  0.076458217    1233.5955    232.10337   -12.761015     7.470427   -1075.1097   -1067.6392 
-   29200         2.92  0.076458111    1222.4273    231.10647   -12.757278    7.4383412   -1075.0776   -1067.6392 
-   29250        2.925  0.076458074    1212.9521    232.98759   -12.778062    7.4988864   -1075.1381   -1067.6392 
-   29300         2.93  0.076458082    1220.2844    236.56821   -12.814589    7.6141315   -1075.2534   -1067.6392 
-   29350        2.935  0.076458085    1197.6267    240.71244   -12.847172    7.7475166   -1075.3867   -1067.6392 
-   29400         2.94  0.076458174    1166.2296     245.3581   -12.871897    7.8970407   -1075.5363   -1067.6392 
-   29450        2.945    0.0764582    1162.6548    250.15917   -12.892997    8.0515671   -1075.6908   -1067.6392 
-   29500         2.95  0.076458192    1166.7685    253.39653   -12.905195    8.1557639    -1075.795   -1067.6392 
-   29550        2.955  0.076458187    1155.8258    253.69254   -12.906863    8.1652912   -1075.8045   -1067.6392 
-   29600         2.96  0.076458159    1155.2633    251.58259   -12.911192    8.0973809   -1075.7366   -1067.6392 
-   29650        2.965  0.076458142    1187.0841      248.958    -12.92707    8.0129065   -1075.6521   -1067.6392 
-   29700         2.97  0.076458107    1216.9951    247.40312   -12.945328    7.9628616   -1075.6021   -1067.6392 
-   29750        2.975  0.076458054    1194.8857    246.85295   -12.955382    7.9451538   -1075.5844   -1067.6392 
-   29800         2.98  0.076458024    1170.1087    246.10026   -12.960888    7.9209279   -1075.5602   -1067.6392 
-   29850        2.985  0.076458073    1169.1596    244.20885   -12.971119    7.8600515   -1075.4993   -1067.6392 
-   29900         2.99  0.076458181    1160.4286    240.86241   -12.984094    7.7523436   -1075.3916   -1067.6392 
-   29950        2.995  0.076458232    1131.8843    236.46352   -12.994209    7.6107619     -1075.25   -1067.6392 
-   30000            3  0.076458157    1094.5416    232.18947     -13.0017    7.4731984   -1075.1124   -1067.6392 
-   30050        3.005  0.076458011    1065.8494    229.55114   -13.006404    7.3882816   -1075.0275   -1067.6392 
-   30100         3.01  0.076458026    1061.4657    229.77899   -13.012924    7.3956153   -1075.0348   -1067.6392 
-   30150        3.015  0.076458159    1064.4309    232.81858   -13.028261    7.4934467   -1075.1327   -1067.6392 
-   30200         3.02  0.076458266    1064.5403    237.18963   -13.051358    7.6341323   -1075.2734   -1067.6392 
-   30250        3.025  0.076458254     1077.435     241.1768    -13.07564    7.7624624   -1075.4017   -1067.6392 
-   30300         3.03  0.076458129    1120.7955    244.00429   -13.099282    7.8534675   -1075.4927   -1067.6392 
-   30350        3.035  0.076458123    1166.6115    245.76237   -13.120127    7.9100525   -1075.5493   -1067.6392 
-   30400         3.04  0.076458222    1186.7887    246.73143    -13.12997    7.9412425   -1075.5805   -1067.6392 
-   30450        3.045  0.076458192    1210.3729     247.3058   -13.131142    7.9597292    -1075.599   -1067.6392 
-   30500         3.05  0.076458205    1226.7005    247.41892   -13.129466    7.9633701   -1075.6026   -1067.6392 
-   30550        3.055  0.076458239    1218.1054    246.53578   -13.123602    7.9349454   -1075.5742   -1067.6392 
-   30600         3.06  0.076458222    1213.5049    244.89144   -13.119076     7.882021   -1075.5213   -1067.6392 
-   30650        3.065  0.076458209     1197.742    243.51998   -13.124172    7.8378794   -1075.4771   -1067.6392 
-   30700         3.07  0.076458217    1173.0375    243.32265   -13.142559    7.8315283   -1075.4708   -1067.6392 
-   30750        3.075  0.076458232    1174.7744     244.4044   -13.175375    7.8663454   -1075.5056   -1067.6392 
-   30800         3.08  0.076458215    1182.8312    245.99614   -13.218442    7.9175767   -1075.5568   -1067.6392 
-   30850        3.085  0.076458183      1183.66    247.03526   -13.258527    7.9510216   -1075.5903   -1067.6392 
-   30900         3.09  0.076458319     1177.992     247.2078   -13.284596    7.9565748   -1075.5958   -1067.6392 
-   30950        3.095  0.076458373    1176.7211    247.34132   -13.301899    7.9608722   -1075.6001   -1067.6392 
-   31000          3.1  0.076458253    1164.7417    248.53603   -13.327025    7.9993251   -1075.6386   -1067.6392 
-   31050        3.105  0.076458217    1128.9001    250.94808   -13.365858    8.0769586   -1075.7162   -1067.6392 
-   31100         3.11  0.076458294    1092.9077    253.74162   -13.407353    8.1668708   -1075.8061   -1067.6392 
-   31150        3.115  0.076458358    1079.4871    256.46396   -13.445278    8.2544917   -1075.8937   -1067.6392 
-   31200         3.12  0.076458421    1088.7747    259.60213   -13.488098    8.3554961   -1075.9947   -1067.6392 
-   31250        3.125   0.07645843    1133.6001      263.188   -13.540135      8.47091   -1076.1101   -1067.6392 
-   31300         3.13  0.076458393    1192.6693    265.96082   -13.591815    8.5601553   -1076.1994   -1067.6392 
-   31350        3.135  0.076458398    1206.7015    266.41337   -13.631689    8.5747211    -1076.214   -1067.6392 
-   31400         3.14   0.07645845    1184.8303    264.21376   -13.660682    8.5039248   -1076.1432   -1067.6392 
-   31450        3.145   0.07645848    1183.6347    260.39213   -13.689676     8.380923   -1076.0202   -1067.6392 
-   31500         3.15  0.076458598    1199.1745    256.21199   -13.723387    8.2463816   -1075.8856   -1067.6392 
-   31550        3.155  0.076458602    1226.3861    252.38445   -13.753029    8.1231895   -1075.7624   -1067.6392 
-   31600         3.16  0.076458505    1232.7936    249.62393   -13.772372    8.0343401   -1075.6736   -1067.6392 
-   31650        3.165  0.076458472    1194.1646    248.63142    -13.78451    8.0023952   -1075.6416   -1067.6392 
-   31700         3.17  0.076458402    1135.0204    248.67712   -13.784757    8.0038662   -1075.6431   -1067.6392 
-   31750        3.175  0.076458444    1088.5207     248.0804   -13.772118    7.9846602   -1075.6239   -1067.6392 
-   31800         3.18  0.076458483    1079.5555    246.27927   -13.761932    7.9266895   -1075.5659   -1067.6392 
-   31850        3.185  0.076458412    1103.2185     244.3339   -13.766697    7.8640762   -1075.5033   -1067.6392 
-   31900         3.19   0.07645842    1120.0872     243.8787   -13.782801    7.8494252   -1075.4887   -1067.6392 
-   31950        3.195  0.076458479    1119.4512    245.95725   -13.799444    7.9163248   -1075.5556   -1067.6392 
-   32000          3.2   0.07645851    1092.4855    250.30658   -13.803665    8.0563117   -1075.6955   -1067.6392 
-   32050        3.205  0.076458415     1067.424    255.82203   -13.785579    8.2338307   -1075.8731   -1067.6392 
-   32100         3.21  0.076458345    1068.4429    261.44517   -13.748535    8.4148156    -1076.054   -1067.6392 
-   32150        3.215   0.07645841    1080.7046    266.36957   -13.713453    8.5733114   -1076.2125   -1067.6392 
-   32200         3.22  0.076458507    1092.5849    269.83978   -13.708135    8.6850028   -1076.3242   -1067.6392 
-   32250        3.225  0.076458535    1099.8414     270.7057    -13.73358    8.7128731   -1076.3521   -1067.6392 
-   32300         3.23  0.076458534    1114.7135    268.29144   -13.763677    8.6351683   -1076.2744   -1067.6392 
-   32350        3.235  0.076458458    1109.1702    263.87403   -13.783235    8.4929906   -1076.1322   -1067.6392 
-   32400         3.24   0.07645842    1084.0276    259.90176   -13.803644      8.36514   -1076.0044   -1067.6392 
-   32450        3.245  0.076458464    1083.1937    257.32785   -13.835634    8.2822966   -1075.9215   -1067.6392 
-   32500         3.25   0.07645845    1114.4646    255.14878   -13.870961    8.2121616   -1075.8514   -1067.6392 
-   32550        3.255  0.076458381    1152.8289     252.6422   -13.897547    8.1314852   -1075.7707   -1067.6392 
-   32600         3.26  0.076458468     1177.486    250.67802   -13.912211    8.0682668   -1075.7075   -1067.6392 
-   32650        3.265  0.076458565    1185.3078    250.60277   -13.918256    8.0658447   -1075.7051   -1067.6392 
-   32700         3.27  0.076458542    1191.2786     252.7908   -13.926328     8.136268   -1075.7755   -1067.6392 
-   32750        3.275  0.076458529    1180.3288     256.6616   -13.948559    8.2608527   -1075.9001   -1067.6392 
-   32800         3.28  0.076458451    1153.7783    261.08347   -13.985264    8.4031741   -1076.0424   -1067.6392 
-   32850        3.285  0.076458392    1133.2496    264.84942   -14.024763    8.5243841   -1076.1636   -1067.6392 
-   32900         3.29  0.076458438    1115.3658    267.38276   -14.053439    8.6059217   -1076.2452   -1067.6392 
-   32950        3.295  0.076458471     1127.683    269.00733   -14.070131    8.6582097   -1076.2974   -1067.6392 
-   33000          3.3  0.076458479    1149.7773    269.98003   -14.072925    8.6895169   -1076.3287   -1067.6392 
-   33050        3.305  0.076458432    1151.5261    270.25086   -14.062159    8.6982337   -1076.3375   -1067.6392 
-   33100         3.31  0.076458345     1155.116    269.80119   -14.049957    8.6837609    -1076.323   -1067.6392 
-   33150        3.315  0.076458436      1135.61    268.22847   -14.036071    8.6331415   -1076.2724   -1067.6392 
-   33200         3.32  0.076458577     1111.738    265.73519   -14.027508    8.5528932   -1076.1921   -1067.6392 
-   33250        3.325  0.076458535    1116.9245    263.26799   -14.038682    8.4734846   -1076.1127   -1067.6392 
-   33300         3.33  0.076458501    1131.8225    261.47169   -14.068281    8.4156693   -1076.0549   -1067.6392 
-   33350        3.335  0.076458475    1120.8199    260.14815   -14.108099    8.3730701   -1076.0123   -1067.6392 
-   33400         3.34  0.076458435    1094.4035    258.29932   -14.149771    8.3135641   -1075.9528   -1067.6392 
-   33450        3.345  0.076458459    1082.1878    255.19265   -14.184258    8.2135735   -1075.8528   -1067.6392 
-   33500         3.35  0.076458528    1083.2242    251.14433   -14.202792    8.0832751   -1075.7225   -1067.6392 
-   33550        3.355  0.076458529    1103.4532    247.60346   -14.210592    7.9693094   -1075.6085   -1067.6392 
-   33600         3.36  0.076458486    1137.7183    246.24059   -14.222506    7.9254445   -1075.5647   -1067.6392 
-   33650        3.365  0.076458516    1150.4421    247.37214   -14.233399    7.9618644   -1075.6011   -1067.6392 
-   33700         3.37  0.076458507    1143.7496    250.70305   -14.237383    8.0690723   -1075.7083   -1067.6392 
-   33750        3.375  0.076458425    1135.9529    256.43973    -14.24743    8.2537116   -1075.8929   -1067.6392 
-   33800         3.38  0.076458392    1126.2288    264.31662   -14.271937    8.5072354   -1076.1465   -1067.6392 
-   33850        3.385   0.07645848    1105.1309    272.68103   -14.305504    8.7764506   -1076.4157   -1067.6392 
-   33900         3.39  0.076458564    1085.1215     279.2817   -14.345574    8.9888984   -1076.6281   -1067.6392 
-   33950        3.395  0.076458555    1076.9206    282.71636   -14.394902    9.0994454   -1076.7387   -1067.6392 
-   34000          3.4  0.076458512    1086.4333    282.84295   -14.446959      9.10352   -1076.7428   -1067.6392 
-   34050        3.405   0.07645848    1099.4638    280.63434   -14.486843    9.0324339   -1076.6717   -1067.6392 
-   34100         3.41  0.076458382     1093.368    278.40903   -14.515246    8.9608108      -1076.6   -1067.6392 
-   34150        3.415  0.076458423    1088.8094    278.43798   -14.545814    8.9617425    -1076.601   -1067.6392 
-   34200         3.42  0.076458529    1070.3036    280.46333   -14.587151    9.0269298   -1076.6662   -1067.6392 
-   34250        3.425  0.076458454    1052.8089    281.70843   -14.639127    9.0670046   -1076.7062   -1067.6392 
-   34300         3.43  0.076458324    1067.0859    279.60749   -14.693017    8.9993839   -1076.6386   -1067.6392 
-   34350        3.435   0.07645844    1078.4994    274.06548   -14.735218    8.8210102   -1076.4602   -1067.6392 
-   34400         3.44  0.076458576     1065.194    267.45347     -14.7594    8.6081974   -1076.2474   -1067.6392 
-   34450        3.445  0.076458493    1044.6764     262.6287   -14.769981    8.4529085   -1076.0921   -1067.6392 
-   34500         3.45  0.076458493    1031.1327    261.22703   -14.778334    8.4077947    -1076.047   -1067.6392 
-   34550        3.455  0.076458662    1001.3241     263.2628   -14.787349    8.4733177   -1076.1125   -1067.6392 
-   34600         3.46  0.076458744    972.94591    267.72772   -14.797072    8.6170244   -1076.2563   -1067.6392 
-   34650        3.465  0.076458639    990.70544    272.38909   -14.802726    8.7670542   -1076.4063   -1067.6392 
-   34700         3.47    0.0764585    1025.1974    274.74718   -14.798109    8.8429511   -1076.4822   -1067.6392 
-   34750        3.475  0.076458513    1061.0651    274.45565   -14.798547    8.8335681   -1076.4728   -1067.6392 
-   34800         3.48  0.076458471     1123.989    273.19344   -14.824615    8.7929427   -1076.4322   -1067.6392 
-   34850        3.485   0.07645842    1192.2777    272.33238   -14.868829    8.7652289   -1076.4045   -1067.6392 
-   34900         3.49  0.076458595    1219.3889     271.4554    -14.89476    8.7370026   -1076.3762   -1067.6392 
-   34950        3.495  0.076458742    1206.5159    270.21752   -14.898336    8.6971606   -1076.3364   -1067.6392 
-   35000          3.5  0.076458628    1197.9968    269.40678   -14.907691    8.6710664   -1076.3103   -1067.6392 
-   35050        3.505  0.076458539    1199.2614    270.09068   -14.937895    8.6930781   -1076.3323   -1067.6392 
-   35100         3.51  0.076458542    1195.6006    272.66182   -14.979789    8.7758322   -1076.4151   -1067.6392 
-   35150        3.515  0.076458532    1184.1758    276.31503   -15.015192    8.8934136   -1076.5326   -1067.6392 
-   35200         3.52  0.076458506    1177.2232    279.44786    -15.03426    8.9942462   -1076.6335   -1067.6392 
-   35250        3.525  0.076458498     1165.906    281.04835   -15.043888    9.0457593    -1076.685   -1067.6392 
-   35300         3.53  0.076458547    1122.7378    281.23471    -15.05217    9.0517575    -1076.691   -1067.6392 
-   35350        3.535   0.07645859    1089.1258    281.40192   -15.068688    9.0571393   -1076.6964   -1067.6392 
-   35400         3.54  0.076458581    1071.6628    283.20912   -15.098467    9.1153054   -1076.7545   -1067.6392 
-   35450        3.545  0.076458561    1061.0287     286.5938   -15.126471     9.224244   -1076.8635   -1067.6392 
-   35500         3.55  0.076458577    1073.4644    290.07888   -15.144262     9.336414   -1076.9756   -1067.6392 
-   35550        3.555  0.076458498    1108.9235    291.84501   -15.154818    9.3932582   -1077.0325   -1067.6392 
-   35600         3.56  0.076458531    1144.2606    290.86582   -15.170369    9.3617421    -1077.001   -1067.6392 
-   35650        3.565  0.076458588    1167.6046    287.19918   -15.196185    9.2437284    -1076.883   -1067.6392 
-   35700         3.57   0.07645856    1179.6333    282.11602   -15.229568    9.0801229   -1076.7194   -1067.6392 
-   35750        3.575  0.076458589    1168.0753    277.29692   -15.269679    8.9250164   -1076.5642   -1067.6392 
-   35800         3.58  0.076458495    1150.8477    273.36789   -15.307138    8.7985576   -1076.4378   -1067.6392 
-   35850        3.585  0.076458358    1134.8391    270.61841   -15.336424    8.7100634   -1076.3493   -1067.6392 
-   35900         3.59  0.076458438    1131.4083    269.61936   -15.365921    8.6779085   -1076.3171   -1067.6392 
-   35950        3.595  0.076458656    1156.3165    270.44071   -15.401487     8.704344   -1076.3436   -1067.6392 
-   36000          3.6  0.076458662    1183.5929    272.83276   -15.446386    8.7813341   -1076.4206   -1067.6392 
-   36050        3.605  0.076458511    1175.8081    276.36312   -15.497044    8.8949617   -1076.5342   -1067.6392 
-   36100         3.61  0.076458487    1137.1434    280.08603   -15.537522    9.0147862    -1076.654   -1067.6392 
-   36150        3.615  0.076458492    1123.4073     282.9067   -15.557122    9.1055719   -1076.7448   -1067.6392 
-   36200         3.62  0.076458546    1127.9754    284.11149   -15.565186    9.1443489   -1076.7836   -1067.6392 
-   36250        3.625  0.076458599    1122.4255    283.84703   -15.578297    9.1358371   -1076.7751   -1067.6392 
-   36300         3.63   0.07645858     1122.041    283.02913   -15.596263    9.1095122   -1076.7487   -1067.6392 
-   36350        3.635  0.076458589    1127.0768     282.3869   -15.600033    9.0888416   -1076.7281   -1067.6392 
-   36400         3.64   0.07645861    1130.6907    282.23737   -15.584507    9.0840287   -1076.7233   -1067.6392 
-   36450        3.645  0.076458646    1150.3415    282.27709   -15.560741    9.0853074   -1076.7245   -1067.6392 
-   36500         3.65  0.076458621    1161.8202    282.18974   -15.546059    9.0824956   -1076.7217   -1067.6392 
-   36550        3.655  0.076458506     1140.503    282.57893     -15.5606    9.0950221   -1076.7343   -1067.6392 
-   36600         3.66   0.07645853    1126.9511    283.97898   -15.602756    9.1400839   -1076.7793   -1067.6392 
-   36650        3.665  0.076458682    1117.8456    286.05487   -15.646548    9.2068979   -1076.8461   -1067.6392 
-   36700         3.67  0.076458755    1118.3433    288.56573   -15.675811    9.2877121   -1076.9269   -1067.6392 
-   36750        3.675  0.076458745    1135.4181    291.29108   -15.685173    9.3754294   -1077.0147   -1067.6392 
-   36800         3.68  0.076458756    1121.3092     293.8519   -15.677476    9.4578516   -1077.0971   -1067.6392 
-   36850        3.685  0.076458796    1089.7128    296.34944   -15.680319    9.5382369   -1077.1775   -1067.6392 
-   36900         3.69  0.076458813    1078.8527    298.59269   -15.709588    9.6104374   -1077.2497   -1067.6392 
-   36950        3.695  0.076458823    1068.4725    300.08588   -15.752456    9.6584969   -1077.2977   -1067.6392 
-   37000          3.7   0.07645894    1065.6302    300.97074   -15.794642    9.6869768   -1077.3262   -1067.6392 
-   37050        3.705  0.076458928    1060.1083    301.92719   -15.834491    9.7177609    -1077.357   -1067.6392 
-   37100         3.71  0.076458812    1062.0442    303.02051   -15.872538    9.7529504   -1077.3922   -1067.6392 
-   37150        3.715  0.076458776    1077.0906    303.12539   -15.902945     9.756326   -1077.3956   -1067.6392 
-   37200         3.72  0.076458783    1094.3589    300.82035   -15.918455    9.6821365   -1077.3214   -1067.6392 
-   37250        3.725  0.076458796     1106.983    295.78025   -15.917907     9.519917   -1077.1592   -1067.6392 
-   37300         3.73    0.0764587    1117.8928    288.74175   -15.902363    9.2933774   -1076.9326   -1067.6392 
-   37350        3.735  0.076458595     1115.003    281.03285   -15.877976    9.0452603   -1076.6845   -1067.6392 
-   37400         3.74  0.076458589    1067.6392    274.76086   -15.863011    8.8433914   -1076.4826   -1067.6392 
-   37450        3.745  0.076458768    1025.0964    271.80953    -15.86958    8.7484006   -1076.3876   -1067.6392 
-   37500         3.75  0.076458888    1008.1779    272.35831   -15.896126    8.7660636   -1076.4053   -1067.6392 
-   37550        3.755  0.076458753    1006.7337    275.07578   -15.933997    8.8535276   -1076.4928   -1067.6392 
-   37600         3.76   0.07645857    1015.7845    279.29514   -15.983502    8.9893309   -1076.6286   -1067.6392 
-   37650        3.765  0.076458646    1037.2238    285.21821   -16.044625    9.1799695   -1076.8192   -1067.6392 
-   37700         3.77  0.076458804     1064.362    291.89353   -16.093253    9.3948198   -1077.0341   -1067.6392 
-   37750        3.775  0.076458938    1093.2339    297.54927   -16.113154    9.5768541   -1077.2161   -1067.6392 
-   37800         3.78  0.076459003    1111.3525    301.09404   -16.115824    9.6909453   -1077.3302   -1067.6392 
-   37850        3.785  0.076458993    1106.8732    302.49314   -16.121107    9.7359763   -1077.3752   -1067.6392 
-   37900         3.79  0.076458927    1063.9114    302.20192   -16.138918    9.7266034   -1077.3658   -1067.6392 
-   37950        3.795  0.076458914    1026.1339    300.74509   -16.166089     9.679714   -1077.3189   -1067.6392 
-   38000          3.8  0.076458899    1031.7602    298.64261    -16.19177    9.6120443   -1077.2513   -1067.6392 
-   38050        3.805  0.076458867    1069.7247    296.45336   -16.206246    9.5415814   -1077.1808   -1067.6392 
-   38100         3.81  0.076458911    1107.4666     295.0445   -16.217521    9.4962363   -1077.1355   -1067.6392 
-   38150        3.815  0.076458901    1131.7783    294.91865   -16.235949    9.4921858   -1077.1314   -1067.6392 
-   38200         3.82  0.076458864    1148.5656    295.74562   -16.253565    9.5188023    -1077.158   -1067.6392 
-   38250        3.825  0.076458822    1148.7391    297.07753   -16.259815    9.5616709   -1077.2009   -1067.6392 
-   38300         3.83  0.076458755    1156.7033    299.00407   -16.260728     9.623678   -1077.2629   -1067.6392 
-   38350        3.835  0.076458804    1159.1829    301.28024   -16.263754    9.6969383   -1077.3362   -1067.6392 
-   38400         3.84  0.076458983    1147.0294    302.84565   -16.273506    9.7473221   -1077.3866   -1067.6392 
-   38450        3.845  0.076458991    1136.4112    302.27164   -16.282019    9.7288474   -1077.3681   -1067.6392 
-   38500         3.85   0.07645888    1113.9868    298.97061   -16.274402    9.6226012   -1077.2618   -1067.6392 
-   38550        3.855  0.076458691     1101.738    294.06527   -16.251341     9.464719    -1077.104   -1067.6392 
-   38600         3.86  0.076458665    1085.4951    289.46444   -16.218831    9.3166378   -1076.9559   -1067.6392 
-   38650        3.865   0.07645876    1061.2109    287.27235   -16.190308    9.2460835   -1076.8853   -1067.6392 
-   38700         3.87  0.076458765     1055.773    288.81749   -16.176864    9.2958149    -1076.935   -1067.6392 
-   38750        3.875  0.076458766     1051.082    293.80099   -16.177139    9.4562127   -1077.0954   -1067.6392 
-   38800         3.88  0.076458791    1034.9231    300.50343   -16.186889    9.6719362   -1077.3112   -1067.6392 
-   38850        3.885  0.076458765    1027.5343    306.11666   -16.197928    9.8526023   -1077.4918   -1067.6392 
-   38900         3.89  0.076458838    1018.2888    308.22875   -16.207065    9.9205815   -1077.5598   -1067.6392 
-   38950        3.895  0.076458884    1014.4073    306.63445   -16.226798    9.8692679   -1077.5085   -1067.6392 
-   39000          3.9  0.076458788    1003.5264    302.69876   -16.256287    9.7425945   -1077.3818   -1067.6392 
-   39050        3.905  0.076458731    996.07885     298.3808   -16.280659    9.6036175   -1077.2428   -1067.6392 
-   39100         3.91  0.076458769    1027.0513    295.40443   -16.293344    9.5078209   -1077.1471   -1067.6392 
-   39150        3.915  0.076458854    1072.3569    294.24208   -16.298011    9.4704097   -1077.1096   -1067.6392 
-   39200         3.92   0.07645888    1080.7481    294.38216   -16.312666    9.4749184   -1077.1142   -1067.6392 
-   39250        3.925  0.076458798    1074.2137    294.25738    -16.34058    9.4709023   -1077.1101   -1067.6392 
-   39300         3.93  0.076458746    1072.9308    292.45791   -16.371754    9.4129849   -1077.0522   -1067.6392 
-   39350        3.935  0.076458686     1052.258    289.46155    -16.40727    9.3165447   -1076.9558   -1067.6392 
-   39400         3.94  0.076458677    1011.4712    286.99005   -16.441308    9.2369974   -1076.8762   -1067.6392 
-   39450        3.945  0.076458657    968.89107    287.00247    -16.46678    9.2373973   -1076.8766   -1067.6392 
-   39500         3.95  0.076458611    967.37752    290.38424    -16.48508     9.346242   -1076.9855   -1067.6392 
-   39550        3.955  0.076458569    982.34862    295.78407   -16.492955    9.5200397   -1077.1593   -1067.6392 
-   39600         3.96  0.076458595     978.6948    301.01012   -16.490336    9.6882442   -1077.3275   -1067.6392 
-   39650        3.965  0.076458753    981.93177    304.90328   -16.481839    9.8135487   -1077.4528   -1067.6392 
-   39700         3.97  0.076458768     1019.382    308.08081   -16.477585    9.9158201   -1077.5551   -1067.6392 
-   39750        3.975  0.076458612    1051.8152    311.88767   -16.490813    10.038347   -1077.6776   -1067.6392 
-   39800         3.98  0.076458521    1042.8378    316.19618   -16.511509    10.177019   -1077.8163   -1067.6392 
-   39850        3.985  0.076458483     1001.149    319.35878   -16.519321     10.27881    -1077.918   -1067.6392 
-   39900         3.99  0.076458542     973.4915     319.4656   -16.514459    10.282248   -1077.9215   -1067.6392 
-   39950        3.995  0.076458719    972.67572    315.26025    -16.50944    10.146896   -1077.7861   -1067.6392 
-   40000            4  0.076458687    994.49843    307.54177   -16.514066    9.8984707   -1077.5377   -1067.6392 
-   40050        4.005  0.076458609    1020.1483    299.32861   -16.525567    9.6341236   -1077.2734   -1067.6392 
-   40100         4.01  0.076458534    1028.6046    293.95707   -16.536961    9.4612366   -1077.1005   -1067.6392 
-   40150        4.015  0.076458539     1021.124    292.82994    -16.54357     9.424959   -1077.0642   -1067.6392 
-   40200         4.02  0.076458617    1003.8564    295.01881   -16.539479    9.4954094   -1077.1346   -1067.6392 
-   40250        4.025  0.076458708    1006.3834    298.32236   -16.525081    9.6017365    -1077.241   -1067.6392 
-   40300         4.03  0.076458753    1049.8514    300.72691   -16.515775    9.6791289   -1077.3184   -1067.6392 
-   40350        4.035  0.076458712    1095.1887    301.23959   -16.528202    9.6956299   -1077.3349   -1067.6392 
-   40400         4.04   0.07645859    1095.7277    299.27704   -16.553461    9.6324637   -1077.2717   -1067.6392 
-   40450        4.045  0.076458512    1074.8132     294.7824   -16.567973    9.4878003    -1077.127   -1067.6392 
-   40500         4.05  0.076458607    1054.9582    288.94001   -16.563212    9.2997586    -1076.939   -1067.6392 
-   40550        4.055  0.076458679    1033.1657    283.78395   -16.555924    9.1338066    -1076.773   -1067.6392 
-   40600         4.06   0.07645866    1029.0046    281.14635   -16.566778    9.0489136   -1076.6881   -1067.6392 
-   40650        4.065  0.076458604    1026.6036     282.2669   -16.593805    9.0849793   -1076.7242   -1067.6392 
-   40700         4.07  0.076458581    1024.2464    287.64133   -16.619273    9.2579595   -1076.8972   -1067.6392 
-   40750        4.075  0.076458663    1014.2573    296.48178   -16.635414    9.5424961   -1077.1817   -1067.6392 
-   40800         4.08  0.076458634    1003.9119    306.29768   -16.644226    9.8584286   -1077.4977   -1067.6392 
-   40850        4.085  0.076458596    997.14687     313.7758   -16.644922    10.099118   -1077.7384   -1067.6392 
-   40900         4.09  0.076458698    1003.6464    316.62645   -16.638874    10.190868   -1077.8301   -1067.6392 
-   40950        4.095  0.076458737    1009.5074    314.15339   -16.626746    10.111271   -1077.7505   -1067.6392 
-   41000          4.1  0.076458626    990.49508    306.88333   -16.607056     9.877278   -1077.5165   -1067.6392 
-   41050        4.105  0.076458539    1003.9156    296.82556   -16.581033    9.5535609   -1077.1928   -1067.6392 
-   41100         4.11  0.076458624    1025.7889    287.94279   -16.555411    9.2676623   -1076.9069   -1067.6392 
-   41150        4.115  0.076458727    1019.8472    284.75687   -16.545411    9.1651209   -1076.8043   -1067.6392 
-   41200         4.12  0.076458658    1009.1747     288.8934   -16.556045    9.2982584   -1076.9375   -1067.6392 
-   41250        4.125  0.076458476    986.14702    297.74613   -16.573101    9.5831902   -1077.2224   -1067.6392 
-   41300         4.13  0.076458533    970.56183    307.17123   -16.586828    9.8865443   -1077.5258   -1067.6392 
-   41350        4.135  0.076458666    982.32883    313.98696   -16.593184    10.105914   -1077.7451   -1067.6392 
-   41400         4.14  0.076458558    998.00634    316.68471   -16.585096    10.192743    -1077.832   -1067.6392 
-   41450        4.145  0.076458375    988.08432    315.93321   -16.578349    10.168555   -1077.8078   -1067.6392 
-   41500         4.15  0.076458387    968.13272    312.86745   -16.587207    10.069882   -1077.7091   -1067.6392 
-   41550        4.155   0.07645851    962.22331    308.01319    -16.60083    9.9136436   -1077.5529   -1067.6392 
-   41600         4.16  0.076458592    977.28521      302.567    -16.60995    9.7383536   -1077.3776   -1067.6392 
-   41650        4.165  0.076458508    989.72477    297.98726   -16.609001    9.5909514   -1077.2302   -1067.6392 
-   41700         4.17  0.076458343    1002.0807    295.07216   -16.600686    9.4971264   -1077.1364   -1067.6392 
-   41750        4.175  0.076458382    1016.3945    293.91041   -16.584772    9.4597347    -1077.099   -1067.6392 
-   41800         4.18  0.076458495    1009.6321    295.39416   -16.566658    9.5074902   -1077.1467   -1067.6392 
-   41850        4.185  0.076458517    981.99051    300.65179   -16.561637    9.6767113   -1077.3159   -1067.6392 
-   41900         4.19  0.076458508    963.70095    308.76413   -16.575186    9.9378133    -1077.577   -1067.6392 
-   41950        4.195   0.07645848    934.77452    316.95219   -16.596303    10.201352   -1077.8406   -1067.6392 
-   42000          4.2  0.076458508    904.42332    322.22055   -16.611182    10.370919   -1078.0102   -1067.6392 
-   42050        4.205   0.07645857    902.29913    322.33865   -16.615342     10.37472    -1078.014   -1067.6392 
-   42100         4.21  0.076458573    919.95355    316.51673   -16.615481    10.187337   -1077.8266   -1067.6392 
-   42150        4.215  0.076458639    929.08587    305.64828   -16.617453    9.8375273   -1077.4768   -1067.6392 
-   42200         4.22  0.076458638    921.14374    292.41301   -16.622157    9.4115396   -1077.0508   -1067.6392 
-   42250        4.225  0.076458624    918.70221     281.1294   -16.634159    9.0483679   -1076.6876   -1067.6392 
-   42300         4.23  0.076458699    936.43193    275.83201     -16.6517    8.8778674   -1076.5171   -1067.6392 
-   42350        4.235   0.07645883    969.33399    278.31739   -16.669195    8.9578611   -1076.5971   -1067.6392 
-   42400         4.24  0.076458843    1009.9309    287.35916   -16.679204    9.2488775   -1076.8881   -1067.6392 
-   42450        4.245   0.07645864    1036.0019    299.66752   -16.672063    9.6450318   -1077.2843   -1067.6392 
-   42500         4.25  0.076458571    1027.6855    312.04895   -16.657188    10.043538   -1077.6828   -1067.6392 
-   42550        4.255  0.076458623    1015.0072    322.01276   -16.654314    10.364231   -1078.0035   -1067.6392 
-   42600         4.26  0.076458688    1013.2933    327.27486   -16.660339    10.533595   -1078.1728   -1067.6392 
-   42650        4.265  0.076458817    1018.1646    326.73267   -16.660439    10.516145   -1078.1554   -1067.6392 
-   42700         4.27  0.076458894    1010.1919    321.82992    -16.65551    10.358346   -1077.9976   -1067.6392 
-   42750        4.275  0.076458864    1005.0687    315.35709   -16.653726    10.150013   -1077.7892   -1067.6392 
-   42800         4.28  0.076458884    1010.6833     308.9802   -16.655199    9.9447675    -1077.584   -1067.6392 
-   42850        4.285  0.076458814    1016.6151    303.05879   -16.657304    9.7541825   -1077.3934   -1067.6392 
-   42900         4.29  0.076458713    1017.0053    298.08717   -16.662548    9.5941669   -1077.2334   -1067.6392 
-   42950        4.295  0.076458716    1044.7957    294.65223   -16.669187    9.4836106   -1077.1228   -1067.6392 
-   43000          4.3  0.076458705    1100.4358    292.80033   -16.665407    9.4240058   -1077.0632   -1067.6392 
-   43050        4.305  0.076458683    1131.0739    293.34724   -16.656462    9.4416087   -1077.0808   -1067.6392 
-   43100         4.31  0.076458605    1142.3657    296.86691   -16.653769     9.554892   -1077.1941   -1067.6392 
-   43150        4.315  0.076458599    1142.8044    301.19681   -16.655832     9.694253   -1077.3335   -1067.6392 
-   43200         4.32  0.076458671    1131.7209    302.63924   -16.652234    9.7406789   -1077.3799   -1067.6392 
-   43250        4.325   0.07645862     1107.868    299.38237   -16.640553    9.6358538   -1077.2751   -1067.6392 
-   43300         4.33  0.076458564    1086.9877     293.0869   -16.632969    9.4332293   -1077.0725   -1067.6392 
-   43350        4.335  0.076458694    1085.9393    287.23945   -16.637169    9.2450247   -1076.8843   -1067.6392 
-   43400         4.34  0.076458728    1084.4536    284.62782   -16.651022    9.1609673   -1076.8002   -1067.6392 
-   43450        4.345  0.076458737    1071.0304    286.42024   -16.664054    9.2186576   -1076.8579   -1067.6392 
-   43500         4.35   0.07645867    1071.4218    292.14965   -16.663945    9.4030633   -1077.0423   -1067.6392 
-   43550        4.355  0.076458545    1058.5175     299.7894   -16.651551    9.6489546   -1077.2882   -1067.6392 
-   43600         4.36  0.076458522    1017.0691    307.34199   -16.653799    9.8920404   -1077.5313   -1067.6392 
-   43650        4.365   0.07645853    984.06733    313.34684   -16.684092    10.085311   -1077.7245   -1067.6392 
-   43700         4.37  0.076458526    972.47105    317.13488   -16.726591    10.207232   -1077.8465   -1067.6392 
-   43750        4.375  0.076458563    982.95807    319.12477   -16.764918    10.271278   -1077.9105   -1067.6392 
-   43800         4.38  0.076458569    1000.5706    319.98217   -16.791105    10.298874   -1077.9381   -1067.6392 
-   43850        4.385  0.076458604    1012.6091    319.95908   -16.796106    10.298131   -1077.9374   -1067.6392 
-   43900         4.39  0.076458647    1016.6021    319.07693   -16.782232    10.269739    -1077.909   -1067.6392 
-   43950        4.395  0.076458717    1039.7933    317.11992   -16.765953    10.206751    -1077.846   -1067.6392 
-   44000          4.4   0.07645855    1076.1914    313.94493    -16.75837    10.104561   -1077.7438   -1067.6392 
-   44050        4.405  0.076458354    1103.7125    309.85364   -16.755308    9.9728798   -1077.6121   -1067.6392 
-   44100         4.41  0.076458497    1123.4426    305.92806   -16.754699    9.8465319   -1077.4858   -1067.6392 
-   44150        4.415  0.076458707     1128.503    303.80427   -16.759223    9.7781762   -1077.4174   -1067.6392 
-   44200         4.42   0.07645872    1109.8757    305.14407   -16.773282    9.8212987   -1077.4605   -1067.6392 
-   44250        4.425  0.076458604    1077.7556    310.10841   -16.799981    9.9810798   -1077.6203   -1067.6392 
-   44300         4.43  0.076458461    1058.8761    316.28846   -16.829881     10.17999   -1077.8192   -1067.6392 
-   44350        4.435  0.076458508    1050.5707    320.51508   -16.852668    10.316027   -1077.9553   -1067.6392 
-   44400         4.44  0.076458673    1056.8449    320.97804   -16.866357    10.330927   -1077.9702   -1067.6392 
-   44450        4.445  0.076458651    1050.8827    318.14487   -16.875492    10.239739    -1077.879   -1067.6392 
-   44500         4.45  0.076458481     1013.764    314.16723   -16.897045    10.111716   -1077.7509   -1067.6392 
-   44550        4.455  0.076458392     980.5404    310.15036   -16.935928    9.9824299   -1077.6217   -1067.6392 
-   44600         4.46  0.076458504    982.46196    305.57929   -16.974614    9.8353065   -1077.4745   -1067.6392 
-   44650        4.465  0.076458584     999.3409    300.38563   -17.000466    9.6681446   -1077.3074   -1067.6392 
-   44700         4.47  0.076458532    1009.2469    295.28724      -17.008    9.5040491   -1077.1433   -1067.6392 
-   44750        4.475  0.076458496    1041.4242    291.50055   -17.008549    9.3821713   -1077.0214   -1067.6392 
-   44800         4.48  0.076458487     1086.602    289.52839   -17.016148    9.3186959   -1076.9579   -1067.6392 
-   44850        4.485  0.076458613    1103.5806    288.55396   -17.029368     9.287333   -1076.9266   -1067.6392 
-   44900         4.49   0.07645858    1102.8142    287.89912   -17.042093    9.2662566   -1076.9055   -1067.6392 
-   44950        4.495   0.07645852    1106.0548    288.11976   -17.050281     9.273358   -1076.9126   -1067.6392 
-   45000          4.5  0.076458412    1109.2471    290.73864   -17.064227    9.3576488   -1076.9969   -1067.6392 
-   45050        4.505  0.076458467    1081.3367    296.40828   -17.091233    9.5401305   -1077.1794   -1067.6392 
-   45100         4.51  0.076458612    1061.7915     304.1106   -17.120168    9.7880355   -1077.4273   -1067.6392 
-   45150        4.515  0.076458508    1075.8664    312.21278   -17.139278    10.048811    -1077.688   -1067.6392 
-   45200         4.52  0.076458381    1086.9758     319.4826   -17.149932    10.282795    -1077.922   -1067.6392 
-   45250        4.525  0.076458463    1081.4821    325.45586   -17.161699     10.47505   -1078.1143   -1067.6392 
-   45300         4.53  0.076458584     1102.657    330.33928   -17.184503    10.632226   -1078.2715   -1067.6392 
-   45350        4.535  0.076458507    1115.9422    333.72518   -17.208225    10.741204   -1078.3804   -1067.6392 
-   45400         4.54  0.076458398    1094.6076    334.77591   -17.228637    10.775023   -1078.4143   -1067.6392 
-   45450        4.545  0.076458455    1089.9234    332.91387   -17.252893    10.715091   -1078.3543   -1067.6392 
-   45500         4.55  0.076458651    1088.2901    328.25855   -17.279739    10.565256   -1078.2045   -1067.6392 
-   45550        4.555  0.076458679    1067.4543    322.55465   -17.319717    10.381672   -1078.0209   -1067.6392 
-   45600         4.56  0.076458491    1051.2478     317.7723   -17.374362    10.227748    -1077.867   -1067.6392 
-   45650        4.565  0.076458315    1034.4257    314.73532   -17.430482    10.130001   -1077.7692   -1067.6392 
-   45700         4.57  0.076458379     1013.128    312.65325   -17.476583    10.062987   -1077.7022   -1067.6392 
-   45750        4.575  0.076458582    1006.4499    309.50085   -17.496142    9.9615252   -1077.6008   -1067.6392 
-   45800         4.58   0.07645865    1024.4651    304.73909    -17.49261    9.8082641   -1077.4475   -1067.6392 
-   45850        4.585  0.076458631    1046.9622    300.08416   -17.492695    9.6584417   -1077.2977   -1067.6392 
-   45900         4.59  0.076458586    1042.5796    296.72782    -17.49113    9.5504152   -1077.1896   -1067.6392 
-   45950        4.595  0.076458607    1008.0854    295.42286    -17.47404     9.508414   -1077.1476   -1067.6392 
-   46000          4.6   0.07645866    1008.1817     297.6509   -17.457674    9.5801252   -1077.2194   -1067.6392 
-   46050        4.605  0.076458648    1055.0177    303.82712   -17.454258    9.7789116   -1077.4181   -1067.6392 
-   46100         4.61  0.076458681    1067.8096    312.06106   -17.459314    10.043927   -1077.6832   -1067.6392 
-   46150        4.615  0.076458697    1032.3327    319.35809   -17.472054    10.278788    -1077.918   -1067.6392 
-   46200         4.62  0.076458669    1011.4049    323.68987   -17.497176     10.41821   -1078.0574   -1067.6392 
-   46250        4.625  0.076458694    1013.1694    324.55935   -17.524643    10.446195   -1078.0854   -1067.6392 
-   46300         4.63  0.076458699    1019.9594    322.92316   -17.537516    10.393533   -1078.0328   -1067.6392 
-   46350        4.635  0.076458638     1019.574    321.37933    -17.53535    10.343843   -1077.9831   -1067.6392 
-   46400         4.64  0.076458549    1012.1208     322.2852   -17.529784    10.372999   -1078.0122   -1067.6392 
-   46450        4.645  0.076458548    1009.7285    324.98438    -17.51749    10.459874   -1078.0991   -1067.6392 
-   46500         4.65  0.076458739    1028.6359    327.73895   -17.495382    10.548533   -1078.1878   -1067.6392 
-   46550        4.655  0.076458848    1054.5382    329.99374   -17.486615    10.621105   -1078.2603   -1067.6392 
-   46600         4.66  0.076458871    1059.0432    330.41234   -17.496838    10.634578   -1078.2738   -1067.6392 
-   46650        4.665  0.076458903    1042.6963    327.41225   -17.503279    10.538018   -1078.1773   -1067.6392 
-   46700         4.67  0.076458964    1022.4908    322.64011    -17.50695    10.384422   -1078.0237   -1067.6392 
-   46750        4.675  0.076458954    994.76603    319.77739    -17.52877    10.292284   -1077.9315   -1067.6392 
-   46800         4.68  0.076458851    984.77354    320.04823   -17.564766    10.301001   -1077.9402   -1067.6392 
-   46850        4.685  0.076458817    982.80807    322.12061    -17.59199    10.367702   -1078.0069   -1067.6392 
-   46900         4.69  0.076458814    979.08705    324.60632   -17.607769    10.447706   -1078.0869   -1067.6392 
-   46950        4.695  0.076458855    991.35981    325.87675   -17.625638    10.488596   -1078.1278   -1067.6392 
-   47000          4.7  0.076459013    990.03823    324.25249   -17.644352    10.436318   -1078.0756   -1067.6392 
-   47050        4.705  0.076459109    971.57257    320.13246   -17.664176    10.303712   -1077.9429   -1067.6392 
-   47100         4.71  0.076459008    942.51677    315.82868   -17.695488    10.165191   -1077.8044   -1067.6392 
-   47150        4.715  0.076458834    914.38458    312.92259   -17.729828    10.071656   -1077.7109   -1067.6392 
-   47200         4.72  0.076458733    915.09427    311.73756   -17.757168    10.033515   -1077.6727   -1067.6392 
-   47250        4.725  0.076458745    929.51292    311.72739   -17.778102    10.033188   -1077.6724   -1067.6392 
-   47300         4.73  0.076458807    924.69906     311.5334   -17.787073    10.026944   -1077.6662   -1067.6392 
-   47350        4.735  0.076458753    911.78727    310.21898   -17.784392    9.9846387   -1077.6239   -1067.6392 
-   47400         4.74  0.076458811    927.84413    308.28881   -17.783399    9.9225147   -1077.5617   -1067.6392 
-   47450        4.745  0.076458948    980.47197    307.41202   -17.799967    9.8942944   -1077.5335   -1067.6392 
-   47500         4.75  0.076458921    1017.4095    308.92974   -17.837931    9.9431434   -1077.5824   -1067.6392 
-   47550        4.755  0.076458813    1013.2842    313.10487   -17.889197    10.077523   -1077.7168   -1067.6392 
-   47600         4.76  0.076458768    999.59926    319.59121    -17.94301    10.286291   -1077.9255   -1067.6392 
-   47650        4.765   0.07645894    987.28899    327.28821   -17.990152    10.534025   -1078.1733   -1067.6392 
-   47700         4.77  0.076459039     970.5822    333.98868   -18.025704    10.749685   -1078.3889   -1067.6392 
-   47750        4.775  0.076458976    960.77569     337.1295   -18.039516    10.850774     -1078.49   -1067.6392 
-   47800         4.78  0.076458945    970.90315    335.79522   -18.031317     10.80783   -1078.4471   -1067.6392 
-   47850        4.785   0.07645907    982.20263    331.08028   -18.021902    10.656076   -1078.2953   -1067.6392 
-   47900         4.79  0.076459119    990.67784    324.66683   -18.027289    10.449654   -1078.0889   -1067.6392 
-   47950        4.795  0.076459083    998.43821    318.73987    -18.04994     10.25889   -1077.8981   -1067.6392 
-   48000          4.8  0.076459069    1008.9151    315.53792   -18.077243    10.155833   -1077.7951   -1067.6392 
-   48050        4.805  0.076458972    1028.1309    316.51509   -18.096678    10.187284   -1077.8265   -1067.6392 
-   48100         4.81  0.076458972    1046.4248     321.4715    -18.10541     10.34681    -1077.986   -1067.6392 
-   48150        4.815  0.076458847    1072.5091     328.3071   -18.108273    10.566819   -1078.2061   -1067.6392 
-   48200         4.82  0.076458729    1115.3266    334.27433   -18.108253    10.758879   -1078.3981   -1067.6392 
-   48250        4.825  0.076458863    1132.7705     338.0335   -18.108395    10.879871   -1078.5191   -1067.6392 
-   48300         4.83  0.076458983    1104.4857    340.31669   -18.122648    10.953357   -1078.5926   -1067.6392 
-   48350        4.835  0.076458942    1068.6895    341.52058   -18.147861    10.992105   -1078.6313   -1067.6392 
-   48400         4.84  0.076458895    1050.2826    340.59905   -18.165876    10.962445   -1078.6017   -1067.6392 
-   48450        4.845  0.076458979     1048.172    336.60118   -18.175839     10.83377    -1078.473   -1067.6392 
-   48500         4.85  0.076458957    1026.5586    330.00847   -18.186406    10.621579   -1078.2608   -1067.6392 
-   48550        4.855  0.076458886    999.91162    322.83938   -18.201023    10.390836   -1078.0301   -1067.6392 
-   48600         4.86  0.076458961    989.90718    317.46387   -18.226455    10.217821   -1077.8571   -1067.6392 
-   48650        4.865  0.076459015    982.96635    315.18649   -18.260376    10.144522   -1077.7838   -1067.6392 
-   48700         4.87  0.076458922    987.30339    316.51586   -18.291398    10.187309   -1077.8265   -1067.6392 
-   48750        4.875  0.076458754    1001.7173    321.20925   -18.314994    10.338369   -1077.9776   -1067.6392 
-   48800         4.88   0.07645878    1018.8788    327.87563   -18.327226    10.552932   -1078.1922   -1067.6392 
-   48850        4.885  0.076458771    1034.4957    334.62729   -18.332453    10.770239   -1078.4095   -1067.6392 
-   48900         4.89  0.076458899    1028.6393    339.07218   -18.341739    10.913301   -1078.5525   -1067.6392 
-   48950        4.895  0.076459103    1007.6856    338.61189   -18.356096    10.898487   -1078.5377   -1067.6392 
-   49000          4.9  0.076459192    999.24745    332.23323   -18.365334    10.693184   -1078.3324   -1067.6392 
-   49050        4.905  0.076459086    996.76706    322.52584   -18.367263    10.380744     -1078.02   -1067.6392 
-   49100         4.91  0.076459029    995.85019    315.08451   -18.370824     10.14124   -1077.7805   -1067.6392 
-   49150        4.915  0.076459032    983.16555    314.29119   -18.382926    10.115706   -1077.7549   -1067.6392 
-   49200         4.92  0.076459075     965.8709    319.65382   -18.396231    10.288306   -1077.9275   -1067.6392 
-   49250        4.925  0.076459124    962.09918    328.07092   -18.405747    10.559217   -1078.1984   -1067.6392 
-   49300         4.93  0.076459019      986.327    337.01122   -18.409264    10.846968   -1078.4862   -1067.6392 
-   49350        4.935  0.076458927      1004.57    345.36436   -18.407413     11.11582   -1078.7551   -1067.6392 
-   49400         4.94  0.076458977    993.98483    352.63606    -18.40944    11.349865   -1078.9891   -1067.6392 
-   49450        4.945  0.076459082    991.26185    357.60801   -18.416364    11.509891   -1079.1491   -1067.6392 
-   49500         4.95  0.076459093    1024.0819    359.05103   -18.425791    11.556336   -1079.1956   -1067.6392 
-   49550        4.955  0.076458927    1033.8368    356.67554   -18.441932    11.479879   -1079.1191   -1067.6392 
-   49600         4.96  0.076458838    1019.5756    350.49667   -18.455292    11.281007   -1078.9202   -1067.6392 
-   49650        4.965  0.076458925    1015.2811     341.2581    -18.44834    10.983657   -1078.6229   -1067.6392 
-   49700         4.97  0.076458904    1000.5326    331.64361   -18.423481    10.674207   -1078.3134   -1067.6392 
-   49750        4.975  0.076458763    997.47426    325.30523   -18.400499    10.470201   -1078.1094   -1067.6392 
-   49800         4.98  0.076458774    1001.6165     323.8013   -18.387438    10.421796    -1078.061   -1067.6392 
-   49850        4.985  0.076458923    1003.6919    325.43465   -18.371483    10.474367   -1078.1136   -1067.6392 
-   49900         4.99  0.076458997    1014.0371    327.90126   -18.352198    10.553757    -1078.193   -1067.6392 
-   49950        4.995  0.076458983    1024.0345    329.92754   -18.340929    10.618974   -1078.2582   -1067.6392 
-   50000            5  0.076458894    1024.5951    330.62163   -18.327421    10.641314   -1078.2805   -1067.6392 
-Loop time of 104.807 on 4 procs for 50000 steps with 250 atoms
-
-Performance: 4.122 ns/day, 5.823 hours/ns, 477.068 timesteps/s
-98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 16.436     | 16.633     | 16.862     |   4.5 | 15.87
-Neigh   | 0.16699    | 0.17008    | 0.17166    |   0.4 |  0.16
-Comm    | 4.1416     | 4.3331     | 4.5047     |   7.9 |  4.13
-Output  | 10.767     | 11.845     | 12.706     |  20.7 | 11.30
-Modify  | 70.815     | 71.648     | 72.683     |   8.2 | 68.36
-Other   |            | 0.1775     |            |       |  0.17
-
-Nlocal:    62.5 ave 65 max 60 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Nghost:    757.75 ave 776 max 743 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-Neighs:    1932.75 ave 2015 max 1844 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-FullNghs:  3865.5 ave 4024 max 3710 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 15462
-Ave neighs/atom = 61.848
-Neighbor list builds = 612
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:01:45
diff --git a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1 b/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1
deleted file mode 100644
index ee1e71131e..0000000000
--- a/examples/SPIN/iron/log.30Apr19.spin.iron_cubic.g++.1
+++ /dev/null
@@ -1,161 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# bcc iron in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	bcc 2.8665
-Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 250 atoms
-  create_atoms CPU = 0.0527296 secs
-
-# setting mass, mag. moments, and interactions for bcc iron
-
-mass		1 55.845
-set 		group all spin 2.2 -1.0 0.0 0.0
-  250 settings made for spin
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
-pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
-pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
-fix_modify 	1 energy yes
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magx      equal c_out_mag[1]
-variable 	magy      equal c_out_mag[2]
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.77337
-  ghost atom cutoff = 5.77337
-  binsize = 2.88668, bins = 5 5 5
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes
-Step Time v_magx v_magy v_magz v_magnorm v_tmag v_emag PotEng TotEng 
-       0            0           -1            0            0            1            0    -55.58269   -1125.5827    -1122.364 
-      50        0.005           -1            0            0            1            0   -55.581417   -1125.4672    -1122.364 
-     100         0.01           -1            0            0            1            0   -55.577759   -1125.1389    -1122.364 
-     150        0.015           -1            0            0            1            0    -55.57219   -1124.6538    -1122.364 
-     200         0.02           -1            0            0            1            0   -55.565438    -1124.099    -1122.364 
-     250        0.025           -1            0            0            1            0   -55.558379   -1123.5779    -1122.364 
-     300         0.03           -1            0            0            1            0   -55.551886   -1123.1862    -1122.364 
-     350        0.035           -1            0            0            1            0   -55.546675   -1122.9858    -1122.364 
-     400         0.04           -1            0            0            1            0   -55.543187   -1122.9869    -1122.364 
-     450        0.045           -1            0            0            1            0    -55.54154   -1123.1498    -1122.364 
-     500         0.05           -1            0            0            1            0   -55.541574   -1123.4037    -1122.364 
-     550        0.055           -1            0            0            1            0   -55.542941    -1123.672    -1122.364 
-     600         0.06           -1            0            0            1            0   -55.545209   -1123.8931    -1122.364 
-     650        0.065           -1            0            0            1            0   -55.547951   -1124.0315    -1122.364 
-     700         0.07           -1            0            0            1            0   -55.550801   -1124.0798    -1122.364 
-     750        0.075           -1            0            0            1            0   -55.553483   -1124.0546    -1122.364 
-     800         0.08           -1            0            0            1            0   -55.555816   -1123.9877    -1122.364 
-     850        0.085           -1            0            0            1            0   -55.557706    -1123.916    -1122.364 
-     900         0.09           -1            0            0            1            0    -55.55913   -1123.8714    -1122.364 
-     950        0.095           -1            0            0            1            0   -55.560111   -1123.8726    -1122.364 
-    1000          0.1           -1            0            0            1            0   -55.560705   -1123.9215    -1122.364 
-    1050        0.105           -1            0            0            1            0   -55.560979   -1124.0049    -1122.364 
-    1100         0.11           -1            0            0            1            0   -55.561005   -1124.0998    -1122.364 
-    1150        0.115           -1            0            0            1            0   -55.560847   -1124.1802    -1122.364 
-    1200         0.12           -1            0            0            1            0   -55.560562   -1124.2247    -1122.364 
-    1250        0.125           -1            0            0            1            0   -55.560199   -1124.2224    -1122.364 
-    1300         0.13           -1            0            0            1            0   -55.559804   -1124.1752    -1122.364 
-    1350        0.135           -1            0            0            1            0   -55.559416   -1124.0977    -1122.364 
-    1400         0.14           -1            0            0            1            0   -55.559073   -1124.0124    -1122.364 
-    1450        0.145           -1            0            0            1            0   -55.558803   -1123.9437    -1122.364 
-    1500         0.15           -1            0            0            1            0   -55.558617   -1123.9107    -1122.364 
-    1550        0.155           -1            0            0            1            0   -55.558503   -1123.9224    -1122.364 
-    1600         0.16           -1            0            0            1            0   -55.558425   -1123.9749    -1122.364 
-    1650        0.165           -1            0            0            1            0   -55.558323   -1124.0529    -1122.364 
-    1700         0.17           -1            0            0            1            0   -55.558122   -1124.1331    -1122.364 
-    1750        0.175           -1            0            0            1            0   -55.557751   -1124.1899    -1122.364 
-    1800         0.18           -1            0            0            1            0   -55.557157   -1124.2023    -1122.364 
-    1850        0.185           -1            0            0            1            0   -55.556326   -1124.1592    -1122.364 
-    1900         0.19           -1            0            0            1            0   -55.555301   -1124.0633    -1122.364 
-    1950        0.195           -1            0            0            1            0   -55.554178   -1123.9313    -1122.364 
-    2000          0.2           -1            0            0            1            0   -55.553099   -1123.7904    -1122.364 
-Loop time of 254.052 on 1 procs for 2000 steps with 250 atoms
-
-Performance: 0.068 ns/day, 352.850 hours/ns, 7.872 timesteps/s
-99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 60.584     | 60.584     | 60.584     |   0.0 | 23.85
-Neigh   | 0.34793    | 0.34793    | 0.34793    |   0.0 |  0.14
-Comm    | 1.9994     | 1.9994     | 1.9994     |   0.0 |  0.79
-Output  | 126.24     | 126.24     | 126.24     |   0.0 | 49.69
-Modify  | 64.475     | 64.475     | 64.475     |   0.0 | 25.38
-Other   |            | 0.4024     |            |       |  0.16
-
-Nlocal:    250 ave 250 max 250 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1419 ave 1419 max 1419 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    7878 ave 7878 max 7878 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  15756 ave 15756 max 15756 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 15756
-Ave neighs/atom = 63.024
-Neighbor list builds = 12
-Dangerous builds = 0
-# min_style 	spin
-# min_modify	alpha_damp 1.0 discrete_factor 10
-# minimize 	1.0e-16 1.0e-16 10000 10000
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:04:16
diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel
index 0ed2fac410..1d62188d8f 100644
--- a/examples/SPIN/nickel/in.spin.nickel
+++ b/examples/SPIN/nickel/in.spin.nickel
@@ -1,58 +1,57 @@
 # fcc nickel in a 3d periodic box
 
 clear 
-units 		metal
-atom_style 	spin
+units           metal
+atom_style      spin
 
-dimension 	3
-boundary 	p p p
+dimension       3
+boundary        p p p
 
 # necessary for the serial algorithm (sametag)
-atom_modify 	map array 
+atom_modify     map array 
 
-lattice 	fcc 3.524
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-create_atoms 	1 box
+lattice         fcc 3.524
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+create_atoms    1 box
 
 # setting mass, mag. moments, and interactions for cobalt
 
-mass		1 58.69
+mass            1 58.69
 
-set 		group all spin/random 31 0.63
-#set 		group all spin 0.63 0.0 0.0 1.0 
-velocity 	all create 100 4928459 rot yes dist gaussian
+set             group all spin/random 31 0.63
+#set            group all spin 0.63 0.0 0.0 1.0 
+velocity        all create 100 4928459 rot yes dist gaussian
 
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
-pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Ni99.eam.alloy Ni
+pair_coeff      * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
 
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
 
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
+fix             3 all nve/spin lattice moving
+timestep        0.0001
 
 # compute and output options
 
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
 
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
 
 thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		2000
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
+run             1000
diff --git a/examples/SPIN/nickel/in.spin.nickel_cubic b/examples/SPIN/nickel/in.spin.nickel_cubic
index 3c97b284ae..1ae069a64f 100644
--- a/examples/SPIN/nickel/in.spin.nickel_cubic
+++ b/examples/SPIN/nickel/in.spin.nickel_cubic
@@ -35,7 +35,7 @@ fix 		1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -54,7 +54,7 @@ thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
-run 		2000
+run 		1000
 
diff --git a/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1 b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1
new file mode 100644
index 0000000000..7871d82ae9
--- /dev/null
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.1
@@ -0,0 +1,136 @@
+LAMMPS (30 Oct 2019)
+# fcc nickel in a 3d periodic box
+
+clear
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+lattice         fcc 3.524
+Lattice spacing in x,y,z = 3.524 3.524 3.524
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  create_atoms CPU = 0.000484943 secs
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass            1 58.69
+
+set             group all spin/random 31 0.63
+  500 settings made for spin/random
+#set            group all spin 0.63 0.0 0.0 1.0
+velocity        all create 100 4928459 rot yes dist gaussian
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Ni99.eam.alloy Ni
+pair_coeff      * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# compute and output options
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
+thermo          50
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run             1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.90375
+  ghost atom cutoff = 5.90375
+  binsize = 2.95187, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.885 | 7.885 | 7.885 Mbytes
+Step Time v_magnorm v_emag Temp v_tmag TotEng 
+       0            0  0.028733803   0.40997576    100.03408   -4775.0671   -2218.3068 
+      50        0.005  0.028733807  0.070491717    101.47879   -28153.519   -2218.1371 
+     100         0.01  0.028733815  -0.70937134     101.7311    2925.8177   -2217.7471 
+     150        0.015  0.028733823    -1.853981     99.63039    1197.9339   -2217.1748 
+     200         0.02  0.028733828   -3.2679239    94.850105    741.17431   -2216.4678 
+     250        0.025  0.028733824    -4.863967    88.444584    550.36979   -2215.6698 
+     300         0.03  0.028733807   -6.5763457    82.689581    449.78321   -2214.8136 
+     350        0.035  0.028733783   -8.3489158    80.108798    384.32228   -2213.9273 
+     400         0.04  0.028733763   -10.120216    82.374947    335.01545   -2213.0417 
+     450        0.045  0.028733755   -11.828932    89.814597    296.88965   -2212.1873 
+     500         0.05  0.028733762   -13.423712    101.39613    267.51686     -2211.39 
+     550        0.055  0.028733783   -14.866724    115.07399    244.96012   -2210.6684 
+     600         0.06  0.028733801   -16.135279    128.57849    229.33327   -2210.0342 
+     650        0.065  0.028733804   -17.222838    140.22402    220.05718   -2209.4904 
+     700         0.07  0.028733795   -18.154813    149.61295    212.95678   -2209.0244 
+     750        0.075  0.028733781   -18.996903     157.5814    206.41327   -2208.6034 
+     800         0.08  0.028733768   -19.804249    164.92075    203.88977   -2208.1997 
+     850        0.085  0.028733752   -20.579151    171.67278    203.42363   -2207.8122 
+     900         0.09  0.028733728   -21.294277    177.67238    199.84817   -2207.4547 
+     950        0.095  0.028733715   -21.943945     183.2621     194.9614   -2207.1298 
+    1000          0.1   0.02873374   -22.551277    188.99284    191.59796   -2206.8262 
+Loop time of 4.30614 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 2.006 ns/day, 11.961 hours/ns, 232.227 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.038      | 2.038      | 2.038      |   0.0 | 47.33
+Neigh   | 0.01566    | 0.01566    | 0.01566    |   0.0 |  0.36
+Comm    | 0.032802   | 0.032802   | 0.032802   |   0.0 |  0.76
+Output  | 0.014146   | 0.014146   | 0.014146   |   0.0 |  0.33
+Modify  | 2.2003     | 2.2003     | 2.2003     |   0.0 | 51.10
+Other   |            | 0.005288   |            |       |  0.12
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    19504 ave 19504 max 19504 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  39008 ave 39008 max 39008 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 39008
+Ave neighs/atom = 78.016
+Neighbor list builds = 9
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4 b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4
new file mode 100644
index 0000000000..638ab5e635
--- /dev/null
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel.g++.4
@@ -0,0 +1,136 @@
+LAMMPS (30 Oct 2019)
+# fcc nickel in a 3d periodic box
+
+clear
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+lattice         fcc 3.524
+Lattice spacing in x,y,z = 3.524 3.524 3.524
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  create_atoms CPU = 0.000733852 secs
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass            1 58.69
+
+set             group all spin/random 31 0.63
+  500 settings made for spin/random
+#set            group all spin 0.63 0.0 0.0 1.0
+velocity        all create 100 4928459 rot yes dist gaussian
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Ni99.eam.alloy Ni
+pair_coeff      * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# compute and output options
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
+thermo          50
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run             1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.90375
+  ghost atom cutoff = 5.90375
+  binsize = 2.95187, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.799 | 7.799 | 7.799 Mbytes
+Step Time v_magnorm v_emag Temp v_tmag TotEng 
+       0            0  0.028733803   0.40997576    100.03408   -4775.0671   -2218.1018 
+      50        0.005  0.028733805   0.25324083    98.741633   -7863.8744   -2218.1018 
+     100         0.01  0.028733812  -0.37320751    97.073875    5622.1863   -2218.1018 
+     150        0.015  0.028733819   -1.3971549    94.073447    1625.0258   -2218.1018 
+     200         0.02  0.028733825   -2.7238372    89.419944    919.37601   -2218.1018 
+     250        0.025  0.028733829   -4.2684428     84.07494    652.18375   -2218.1018 
+     300         0.03  0.028733824   -5.9636712     80.06368    512.89077   -2218.1018 
+     350        0.035   0.02873381   -7.7386326    79.366702    422.24864   -2218.1018 
+     400         0.04  0.028733802   -9.5148059    83.052751    357.60379   -2218.1018 
+     450        0.045  0.028733806   -11.234935    91.282747    310.87776   -2218.1018 
+     500         0.05   0.02873381   -12.875184    103.49836     275.0224   -2218.1018 
+     550        0.055  0.028733808   -14.413473    118.16526    247.85208   -2218.1018 
+     600         0.06  0.028733803   -15.812466    132.83837    230.67903   -2218.1018 
+     650        0.065  0.028733808   -17.061311    145.41049    222.19476   -2218.1018 
+     700         0.07  0.028733818   -18.181903    154.83414    219.42933   -2218.1018 
+     750        0.075  0.028733823   -19.176259    160.58645    218.45231   -2218.1018 
+     800         0.08  0.028733825   -20.035157    163.02829    214.86596   -2218.1018 
+     850        0.085  0.028733825   -20.806548     164.4197    209.86881   -2218.1018 
+     900         0.09  0.028733829   -21.571419     167.8571    205.79849   -2218.1018 
+     950        0.095  0.028733825   -22.365879    175.00875    201.33088   -2218.1018 
+    1000          0.1  0.028733821   -23.133464    184.68305    195.52912   -2218.1018 
+Loop time of 2.47211 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 3.495 ns/day, 6.867 hours/ns, 404.513 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.5549     | 0.56708    | 0.58627    |   1.6 | 22.94
+Neigh   | 0.0039728  | 0.0041007  | 0.0042598  |   0.2 |  0.17
+Comm    | 0.087296   | 0.10802    | 0.11917    |   3.8 |  4.37
+Output  | 0.0046923  | 0.0047188  | 0.0047917  |   0.1 |  0.19
+Modify  | 1.7832     | 1.7862     | 1.7879     |   0.1 | 72.25
+Other   |            | 0.002016   |            |       |  0.08
+
+Nlocal:    125 ave 139 max 112 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:    1099 ave 1112 max 1085 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:    4876 ave 5386 max 4426 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs:  9752 ave 10845 max 8737 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 39008
+Ave neighs/atom = 78.016
+Neighbor list builds = 9
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1 b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
similarity index 54%
rename from examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1
rename to examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
index 425572dedf..4f3b94df53 100644
--- a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.1
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.1
@@ -1,9 +1,7 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
+LAMMPS (30 Oct 2019)
 # fcc nickel in a 3d periodic box
 
 clear
-  using 1 OpenMP thread(s) per MPI task
 units 		metal
 atom_style 	spin
 
@@ -21,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.00068903 secs
+  create_atoms CPU = 0.00109196 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -43,7 +41,7 @@ fix 		1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -62,9 +60,9 @@ thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
-run 		2000
+run 		1000
 Neighbor list info ...
   update every 10 steps, delay 20 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -82,79 +80,59 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.885 | 7.885 | 7.885 Mbytes
 Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803     0.455085    100.03408    -8603.706   -2218.0905 
-      50        0.005  0.028732021   0.11535308    101.47887   -34407.888   -2218.0904 
-     100         0.01    0.0287304    -0.665283    101.73105    6238.4535     -2218.09 
-     150        0.015  0.028729403   -1.8105707    99.629794    2452.7607   -2218.0896 
-     200         0.02  0.028731067    -3.224763    94.849715    1501.8625   -2218.0895 
-     250        0.025  0.028732765   -4.8207784    88.447019    1110.3291   -2218.0895 
-     300         0.03  0.028728169   -6.5331538    82.697813     905.2202   -2218.0896 
-     350        0.035   0.02871707   -8.3059526    80.122838    772.40218   -2218.0896 
-     400         0.04  0.028706605   -10.077613    82.389555    672.72236   -2218.0895 
-     450        0.045  0.028701727    -11.78634    89.823176    595.82956   -2218.0894 
-     500         0.05  0.028706691   -13.380919    101.39804    536.65866   -2218.0894 
-     550        0.055  0.028714065   -14.824128    115.07511    491.25787   -2218.0893 
-     600         0.06  0.028713691   -16.093505    128.58093    459.82107    -2218.089 
-     650        0.065  0.028713232   -17.181217    140.22137    441.15183    -2218.089 
-     700         0.07   0.02871245   -18.113035    149.60156    426.80154   -2218.0889 
-     750        0.075  0.028712431   -18.954952    157.56849    413.61924   -2218.0891 
-     800         0.08   0.02872489   -19.762756    164.91833    408.49483   -2218.0892 
-     850        0.085  0.028733709   -20.538757    171.69348    407.47868   -2218.0894 
-     900         0.09  0.028737031   -21.256095    177.71981    400.24086   -2218.0894 
-     950        0.095  0.028743446   -21.908156    183.31613    390.46773    -2218.089 
-    1000          0.1  0.028751809   -22.516179    189.01672    383.80802   -2218.0888 
-    1050        0.105  0.028761625   -23.084057    194.48882    376.54433    -2218.089 
-    1100         0.11  0.028768138   -23.565036    198.12295    366.13309   -2218.0891 
-    1150        0.115  0.028770301   -23.937136    198.95102    354.82763    -2218.089 
-    1200         0.12  0.028771334   -24.273509    198.31348    347.20512   -2218.0891 
-    1250        0.125  0.028769662   -24.672789    198.26173    344.02095   -2218.0889 
-    1300         0.13  0.028774175    -25.13917    199.48259    337.81596   -2218.0889 
-    1350        0.135  0.028795936   -25.594094    201.33509      329.891   -2218.0889 
-    1400         0.14  0.028824328   -25.978285     203.4984    328.81092   -2218.0886 
-    1450        0.145  0.028846467   -26.299501    206.52931    328.61151   -2218.0886 
-    1500         0.15  0.028858261   -26.605847    211.09044    324.29045   -2218.0888 
-    1550        0.155  0.028852825    -26.92321    216.70656    317.24339   -2218.0888 
-    1600         0.16   0.02885238   -27.232535    221.73117    312.50182   -2218.0888 
-    1650        0.165  0.028857985   -27.513725    224.82466    312.32346   -2218.0887 
-    1700         0.17  0.028863985   -27.764471    225.85697    312.80779   -2218.0887 
-    1750        0.175  0.028868714   -27.983273    225.71411    315.37238   -2218.0888 
-    1800         0.18  0.028871144   -28.187572    225.78979    319.44034   -2218.0888 
-    1850        0.185  0.028865191   -28.395615     226.7477    321.25107   -2218.0889 
-    1900         0.19  0.028855316   -28.597095    227.90237    319.98739   -2218.0889 
-    1950        0.195  0.028853072    -28.79277    228.54008    313.04557   -2218.0886 
-    2000          0.2  0.028855814   -29.015073     228.8643    300.40018   -2218.0885 
-Loop time of 16.5858 on 1 procs for 2000 steps with 500 atoms
+       0            0  0.028733803     0.455085    100.03408    -4301.853   -2218.2955 
+      50        0.005  0.028732021   0.11535308    101.47887   -17203.944   -2218.1258 
+     100         0.01    0.0287304    -0.665283    101.73105    3119.2267   -2217.7358 
+     150        0.015  0.028729403   -1.8105707    99.629794    1226.3803   -2217.1636 
+     200         0.02  0.028731067    -3.224763    94.849715    750.93124   -2216.4566 
+     250        0.025  0.028732765   -4.8207784    88.447019    555.16456   -2215.6585 
+     300         0.03  0.028728169   -6.5331538    82.697813     452.6101   -2214.8022 
+     350        0.035   0.02871707   -8.3059526    80.122838    386.20109   -2213.9158 
+     400         0.04  0.028706605   -10.077613    82.389555    336.36118     -2213.03 
+     450        0.045  0.028701727    -11.78634    89.823176    297.91478   -2212.1758 
+     500         0.05  0.028706691   -13.380919    101.39804    268.32933   -2211.3785 
+     550        0.055  0.028714065   -14.824128    115.07511    245.62893   -2210.6569 
+     600         0.06  0.028713691   -16.093505    128.58093    229.91054   -2210.0225 
+     650        0.065  0.028713232   -17.181217    140.22137    220.57591   -2209.4787 
+     700         0.07   0.02871245   -18.113035    149.60156    213.40077   -2209.0127 
+     750        0.075  0.028712431   -18.954952    157.56849    206.80962   -2208.5916 
+     800         0.08   0.02872489   -19.762756    164.91833    204.24742   -2208.1876 
+     850        0.085  0.028733709   -20.538757    171.69348    203.73934   -2207.7993 
+     900         0.09  0.028737031   -21.256095    177.71981    200.12043   -2207.4406 
+     950        0.095  0.028743446   -21.908156    183.31613    195.23386   -2207.1149 
+    1000          0.1  0.028751809   -22.516179    189.01672    191.90401   -2206.8111 
+Loop time of 4.3661 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 1.042 ns/day, 23.036 hours/ns, 120.585 timesteps/s
-99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 1.979 ns/day, 12.128 hours/ns, 229.037 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.8835     | 5.8835     | 5.8835     |   0.0 | 35.47
-Neigh   | 0.05244    | 0.05244    | 0.05244    |   0.0 |  0.32
-Comm    | 0.092997   | 0.092997   | 0.092997   |   0.0 |  0.56
-Output  | 5.213      | 5.213      | 5.213      |   0.0 | 31.43
-Modify  | 5.3275     | 5.3275     | 5.3275     |   0.0 | 32.12
-Other   |            | 0.01636    |            |       |  0.10
+Pair    | 2.0467     | 2.0467     | 2.0467     |   0.0 | 46.88
+Neigh   | 0.015636   | 0.015636   | 0.015636   |   0.0 |  0.36
+Comm    | 0.032918   | 0.032918   | 0.032918   |   0.0 |  0.75
+Output  | 0.027737   | 0.027737   | 0.027737   |   0.0 |  0.64
+Modify  | 2.2379     | 2.2379     | 2.2379     |   0.0 | 51.26
+Other   |            | 0.005233   |            |       |  0.12
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 Nghost:    1956 ave 1956 max 1956 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    19507 ave 19507 max 19507 min
+Neighs:    19504 ave 19504 max 19504 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  39014 ave 39014 max 39014 min
+FullNghs:  39008 ave 39008 max 39008 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 39014
-Ave neighs/atom = 78.028
-Neighbor list builds = 21
+Total # of neighbors = 39008
+Ave neighs/atom = 78.016
+Neighbor list builds = 9
 Dangerous builds = 0
 
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:16
+Total wall time: 0:00:04
diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4 b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
similarity index 52%
rename from examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4
rename to examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
index fd9ce80533..1724ef9df8 100644
--- a/examples/SPIN/nickel/log.30Apr19.spin.nickel_cubic.g++.4
+++ b/examples/SPIN/nickel/log.19Nov19.spin.nickel_cubic.g++.4
@@ -1,9 +1,7 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
+LAMMPS (30 Oct 2019)
 # fcc nickel in a 3d periodic box
 
 clear
-  using 1 OpenMP thread(s) per MPI task
 units 		metal
 atom_style 	spin
 
@@ -21,7 +19,7 @@ Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  create_atoms CPU = 0.000639439 secs
+  create_atoms CPU = 0.000827074 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -43,7 +41,7 @@ fix 		1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.
 fix_modify 	1 energy yes
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # compute and output options
@@ -62,9 +60,9 @@ thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
 thermo          50
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
-run 		2000
+run 		1000
 Neighbor list info ...
   update every 10 steps, delay 20 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -82,79 +80,59 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.799 | 7.799 | 7.799 Mbytes
 Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803     0.455085    100.03408    -8603.706   -2218.0905 
-      50        0.005  0.028732088    0.2980989     98.74184   -13360.862   -2218.0904 
-     100         0.01   0.02873076  -0.32911738    97.074246    12749.405     -2218.09 
-     150        0.015  0.028730298   -1.3537059    94.073558    3353.8731   -2218.0897 
-     200         0.02  0.028733079   -2.6807428    89.419616    1868.0661   -2218.0895 
-     250        0.025  0.028735725   -4.2256641    84.074249    1317.4563   -2218.0893 
-     300         0.03  0.028728939   -5.9209085    80.063263    1033.1632   -2218.0893 
-     350        0.035  0.028716731   -7.6957087     79.36782     849.1925   -2218.0893 
-     400         0.04   0.02871114   -9.4720832    83.055773    718.36408   -2218.0893 
-     450        0.045   0.02870879    -11.19254     91.28713    624.04151   -2218.0891 
-     500         0.05  0.028708873   -12.832707    103.50343    551.85983   -2218.0892 
-     550        0.055  0.028710315   -14.370603    118.16778    497.19527   -2218.0893 
-     600         0.06  0.028707016   -15.769641    132.83264    462.57721    -2218.089 
-     650        0.065  0.028706727   -17.018362    145.39247    445.40608   -2218.0888 
-     700         0.07  0.028710482   -18.137792    154.80131    439.71677   -2218.0889 
-     750        0.075  0.028705169   -19.130471    160.53663    437.67621   -2218.0892 
-     800         0.08  0.028695336   -19.988452    162.95918    430.42912    -2218.089 
-     850        0.085  0.028688393   -20.758389    164.33238    420.42991   -2218.0889 
-     900         0.09  0.028684101   -21.521505    167.76167    412.29955    -2218.089 
-     950        0.095  0.028684705   -22.314351      174.918    403.31757   -2218.0891 
-    1000          0.1  0.028691284   -23.080026    184.60192      391.677   -2218.0893 
-    1050        0.105  0.028687846   -23.714845    193.76312    379.81345   -2218.0893 
-    1100         0.11  0.028682371   -24.191738    200.43041    372.65414   -2218.0893 
-    1150        0.115  0.028684765   -24.569816    204.39323    368.53291   -2218.0891 
-    1200         0.12  0.028678139   -24.892093      205.879    364.46365   -2218.0892 
-    1250        0.125  0.028669738   -25.160227    205.09197    361.98015   -2218.0893 
-    1300         0.13  0.028666626   -25.367813    202.69136    360.10649   -2218.0891 
-    1350        0.135  0.028665511   -25.520784    199.79027    359.68033   -2218.0892 
-    1400         0.14   0.02866749   -25.655936    197.91217      361.218   -2218.0892 
-    1450        0.145  0.028666916    -25.80086     198.1933     361.5167   -2218.0889 
-    1500         0.15  0.028660248   -25.953194     200.8243     356.0167    -2218.089 
-    1550        0.155  0.028641778   -26.137444    205.80307    349.94961   -2218.0887 
-    1600         0.16  0.028626894   -26.393372     212.6879    347.30341   -2218.0888 
-    1650        0.165  0.028619835   -26.707923    219.63834    340.80511   -2218.0885 
-    1700         0.17  0.028615681   -27.023214    224.25635    329.60947   -2218.0882 
-    1750        0.175   0.02861597   -27.301445    225.47908    321.35253   -2218.0884 
-    1800         0.18  0.028614544    -27.53764    224.03527    320.92639   -2218.0884 
-    1850        0.185   0.02860894   -27.741581    221.74286    323.07034   -2218.0884 
-    1900         0.19  0.028604135   -27.943034      220.659    322.60989   -2218.0884 
-    1950        0.195  0.028602672   -28.160901    221.85908     318.8957   -2218.0885 
-    2000          0.2  0.028597155   -28.365986    224.55298    311.53587   -2218.0886 
-Loop time of 7.21663 on 4 procs for 2000 steps with 500 atoms
+       0            0  0.028733803     0.455085    100.03408    -4301.853   -2218.0905 
+      50        0.005  0.028732088    0.2980989     98.74184   -6680.4308   -2218.0904 
+     100         0.01   0.02873076  -0.32911738    97.074246    6374.7026     -2218.09 
+     150        0.015  0.028730298   -1.3537059    94.073558    1676.9365   -2218.0897 
+     200         0.02  0.028733079   -2.6807428    89.419616    934.03305   -2218.0895 
+     250        0.025  0.028735725   -4.2256641    84.074249    658.72816   -2218.0893 
+     300         0.03  0.028728939   -5.9209085    80.063263    516.58161   -2218.0893 
+     350        0.035  0.028716731   -7.6957087     79.36782    424.59625   -2218.0893 
+     400         0.04   0.02871114   -9.4720832    83.055773    359.18204   -2218.0893 
+     450        0.045   0.02870879    -11.19254     91.28713    312.02076   -2218.0891 
+     500         0.05  0.028708873   -12.832707    103.50343    275.92991   -2218.0892 
+     550        0.055  0.028710315   -14.370603    118.16778    248.59763   -2218.0893 
+     600         0.06  0.028707016   -15.769641    132.83264     231.2886    -2218.089 
+     650        0.065  0.028706727   -17.018362    145.39247    222.70304   -2218.0888 
+     700         0.07  0.028710482   -18.137792    154.80131    219.85838   -2218.0889 
+     750        0.075  0.028705169   -19.130471    160.53663    218.83811   -2218.0892 
+     800         0.08  0.028695336   -19.988452    162.95918    215.21456    -2218.089 
+     850        0.085  0.028688393   -20.758389    164.33238    210.21496   -2218.0889 
+     900         0.09  0.028684101   -21.521505    167.76167    206.14977    -2218.089 
+     950        0.095  0.028684705   -22.314351      174.918    201.65878   -2218.0891 
+    1000          0.1  0.028691284   -23.080026    184.60192     195.8385   -2218.0893 
+Loop time of 2.5947 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 2.394 ns/day, 10.023 hours/ns, 277.138 timesteps/s
-98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 3.330 ns/day, 7.207 hours/ns, 385.402 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.6337     | 1.6726     | 1.7259     |   2.7 | 23.18
-Neigh   | 0.013023   | 0.01361    | 0.014188   |   0.4 |  0.19
-Comm    | 0.19005    | 0.24933    | 0.2905     |   7.5 |  3.45
-Output  | 1.4595     | 1.5171     | 1.5725     |   3.4 | 21.02
-Modify  | 3.6943     | 3.7537     | 3.8093     |   2.3 | 52.01
-Other   |            | 0.01025    |            |       |  0.14
+Pair    | 0.56409    | 0.58139    | 0.605      |   2.0 | 22.41
+Neigh   | 0.0039618  | 0.0041058  | 0.0042889  |   0.2 |  0.16
+Comm    | 0.095324   | 0.12147    | 0.13892    |   4.8 |  4.68
+Output  | 0.008945   | 0.0089793  | 0.0090477  |   0.0 |  0.35
+Modify  | 1.8745     | 1.8765     | 1.8795     |   0.1 | 72.32
+Other   |            | 0.002217   |            |       |  0.09
 
-Nlocal:    125 ave 132 max 121 min
-Histogram: 2 0 0 0 1 0 0 0 0 1
-Nghost:    1099 ave 1103 max 1092 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Neighs:    4877 ave 5097 max 4747 min
-Histogram: 2 0 0 0 1 0 0 0 0 1
-FullNghs:  9754 ave 10298 max 9440 min
-Histogram: 2 0 0 0 1 0 0 0 0 1
+Nlocal:    125 ave 139 max 112 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:    1099 ave 1112 max 1085 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:    4876 ave 5385 max 4427 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs:  9752 ave 10845 max 8737 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
 
-Total # of neighbors = 39016
-Ave neighs/atom = 78.032
-Neighbor list builds = 21
+Total # of neighbors = 39008
+Ave neighs/atom = 78.016
+Neighbor list builds = 9
 Dangerous builds = 0
 
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:07
+Total wall time: 0:00:02
diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1 b/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1
deleted file mode 100644
index 8d7284f5e2..0000000000
--- a/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.1
+++ /dev/null
@@ -1,159 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# fcc nickel in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	fcc 3.524
-Lattice spacing in x,y,z = 3.524 3.524 3.524
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  create_atoms CPU = 0.000835896 secs
-
-# setting mass, mag. moments, and interactions for cobalt
-
-mass		1 58.69
-
-set 		group all spin/random 31 0.63
-  500 settings made for spin/random
-#set 		group all spin 0.63 0.0 0.0 1.0
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
-pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.90375
-  ghost atom cutoff = 5.90375
-  binsize = 2.95187, bins = 6 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes
-Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803   0.40997576    100.03408   -9550.1342   -2218.1018 
-      50        0.005  0.028733807  0.070491717    101.47879   -56307.038   -2218.1018 
-     100         0.01  0.028733815  -0.70937134     101.7311    5851.6355   -2218.1018 
-     150        0.015  0.028733823    -1.853981     99.63039    2395.8677   -2218.1018 
-     200         0.02  0.028733828   -3.2679239    94.850105    1482.3486   -2218.1018 
-     250        0.025  0.028733824    -4.863967    88.444584    1100.7396   -2218.1018 
-     300         0.03  0.028733807   -6.5763457    82.689581    899.56642   -2218.1018 
-     350        0.035  0.028733783   -8.3489158    80.108798    768.64457   -2218.1018 
-     400         0.04  0.028733763   -10.120216    82.374947    670.03091   -2218.1018 
-     450        0.045  0.028733755   -11.828932    89.814597    593.77931   -2218.1018 
-     500         0.05  0.028733762   -13.423712    101.39613    535.03371   -2218.1018 
-     550        0.055  0.028733783   -14.866724    115.07399    489.92024   -2218.1018 
-     600         0.06  0.028733801   -16.135279    128.57849    458.66654   -2218.1018 
-     650        0.065  0.028733804   -17.222838    140.22402    440.11437   -2218.1018 
-     700         0.07  0.028733795   -18.154813    149.61295    425.91356   -2218.1018 
-     750        0.075  0.028733781   -18.996903     157.5814    412.82654   -2218.1018 
-     800         0.08  0.028733768   -19.804249    164.92075    407.77954   -2218.1018 
-     850        0.085  0.028733752   -20.579151    171.67278    406.84726   -2218.1018 
-     900         0.09  0.028733728   -21.294277    177.67238    399.69633   -2218.1018 
-     950        0.095  0.028733715   -21.943945     183.2621    389.92281   -2218.1018 
-    1000          0.1   0.02873374   -22.551277    188.99284    383.19592   -2218.1018 
-    1050        0.105  0.028733783   -23.120147    194.51391    375.87245   -2218.1018 
-    1100         0.11  0.028733792   -23.602325    198.18631    365.37753   -2218.1018 
-    1150        0.115  0.028733774   -23.976048    199.04022    354.04863   -2218.1018 
-    1200         0.12   0.02873376    -24.31575    198.41999    346.40397   -2218.1018 
-    1250        0.125  0.028733759   -24.718347     198.3669     343.1701   -2218.1018 
-    1300         0.13  0.028733765   -25.189073    199.57949    336.90052   -2218.1018 
-    1350        0.135  0.028733774   -25.650252    201.45897    329.07023   -2218.1018 
-    1400         0.14  0.028733785   -26.042702     203.6926    327.97373   -2218.1018 
-    1450        0.145  0.028733791   -26.373965    206.80469    327.38747   -2218.1018 
-    1500         0.15  0.028733791   -26.691802    211.43923    322.75885   -2218.1018 
-    1550        0.155  0.028733794   -27.021573    217.10969    315.55781   -2218.1018 
-    1600         0.16  0.028733792   -27.344066    222.16052     310.6743   -2218.1018 
-    1650        0.165  0.028733788   -27.640017    225.28449    310.49671   -2218.1018 
-    1700         0.17  0.028733803   -27.907241    226.37676     310.9389   -2218.1018 
-    1750        0.175  0.028733828   -28.143477    226.31095    313.28034   -2218.1018 
-    1800         0.18  0.028733833   -28.363397    226.43633    317.31668   -2218.1018 
-    1850        0.185  0.028733811    -28.58153    227.36287    318.98645   -2218.1018 
-    1900         0.19  0.028733796   -28.785208    228.39889     316.9972   -2218.1018 
-    1950        0.195  0.028733826     -28.9724    228.84666     309.8027   -2218.1018 
-    2000          0.2   0.02873386   -29.175039      228.918    297.88519   -2218.1018 
-Loop time of 15.9256 on 1 procs for 2000 steps with 500 atoms
-
-Performance: 1.085 ns/day, 22.119 hours/ns, 125.584 timesteps/s
-99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 5.8677     | 5.8677     | 5.8677     |   0.0 | 36.84
-Neigh   | 0.051965   | 0.051965   | 0.051965   |   0.0 |  0.33
-Comm    | 0.088829   | 0.088829   | 0.088829   |   0.0 |  0.56
-Output  | 4.7019     | 4.7019     | 4.7019     |   0.0 | 29.52
-Modify  | 5.199      | 5.199      | 5.199      |   0.0 | 32.65
-Other   |            | 0.01632    |            |       |  0.10
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1956 ave 1956 max 1956 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    19508 ave 19508 max 19508 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  39016 ave 39016 max 39016 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 39016
-Ave neighs/atom = 78.032
-Neighbor list builds = 21
-Dangerous builds = 0
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:16
diff --git a/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4 b/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4
deleted file mode 100644
index a186253db3..0000000000
--- a/examples/SPIN/nickel/log.30Apr19.spin.nickel.g++.4
+++ /dev/null
@@ -1,159 +0,0 @@
-LAMMPS (30 Apr 2019)
-  using 1 OpenMP thread(s) per MPI task
-# fcc nickel in a 3d periodic box
-
-clear
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	fcc 3.524
-Lattice spacing in x,y,z = 3.524 3.524 3.524
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  create_atoms CPU = 0.000492096 secs
-
-# setting mass, mag. moments, and interactions for cobalt
-
-mass		1 58.69
-
-set 		group all spin/random 31 0.63
-  500 settings made for spin/random
-#set 		group all spin 0.63 0.0 0.0 1.0
-velocity 	all create 100 4928459 rot yes dist gaussian
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
-pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
-thermo          50
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		2000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.90375
-  ghost atom cutoff = 5.90375
-  binsize = 2.95187, bins = 6 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes
-Step Time v_magnorm v_emag Temp v_tmag TotEng 
-       0            0  0.028733803   0.40997576    100.03408   -9550.1342   -2218.1018 
-      50        0.005  0.028733805   0.25324083    98.741633   -15727.749   -2218.1018 
-     100         0.01  0.028733812  -0.37320751    97.073875    11244.373   -2218.1018 
-     150        0.015  0.028733819   -1.3971549    94.073447    3250.0517   -2218.1018 
-     200         0.02  0.028733825   -2.7238372    89.419944     1838.752   -2218.1018 
-     250        0.025  0.028733829   -4.2684428     84.07494    1304.3675   -2218.1018 
-     300         0.03  0.028733824   -5.9636712     80.06368    1025.7815   -2218.1018 
-     350        0.035   0.02873381   -7.7386326    79.366702    844.49729   -2218.1018 
-     400         0.04  0.028733802   -9.5148059    83.052751    715.20758   -2218.1018 
-     450        0.045  0.028733806   -11.234935    91.282747    621.75552   -2218.1018 
-     500         0.05   0.02873381   -12.875184    103.49836    550.04479   -2218.1018 
-     550        0.055  0.028733808   -14.413473    118.16526    495.70417   -2218.1018 
-     600         0.06  0.028733803   -15.812466    132.83837    461.35805   -2218.1018 
-     650        0.065  0.028733808   -17.061311    145.41049    444.38951   -2218.1018 
-     700         0.07  0.028733818   -18.181903    154.83414    438.85866   -2218.1018 
-     750        0.075  0.028733823   -19.176259    160.58645    436.90462   -2218.1018 
-     800         0.08  0.028733825   -20.035157    163.02829    429.73193   -2218.1018 
-     850        0.085  0.028733825   -20.806548     164.4197    419.73763   -2218.1018 
-     900         0.09  0.028733829   -21.571419     167.8571    411.59699   -2218.1018 
-     950        0.095  0.028733825   -22.365879    175.00875    402.66175   -2218.1018 
-    1000          0.1  0.028733821   -23.133464    184.68305    391.05824   -2218.1018 
-    1050        0.105  0.028733833   -23.770507    193.83795    379.23354   -2218.1018 
-    1100         0.11   0.02873385   -24.249882     200.5039    372.08521   -2218.1018 
-    1150        0.115  0.028733864   -24.630489    204.46984    367.92135   -2218.1018 
-    1200         0.12  0.028733877   -24.956281    205.96624    363.72367   -2218.1018 
-    1250        0.125  0.028733884   -25.227332    205.18503    361.09236   -2218.1018 
-    1300         0.13  0.028733877    -25.43568    202.76969    359.10924   -2218.1018 
-    1350        0.135  0.028733868   -25.588748    199.85462    358.69556   -2218.1018 
-    1400         0.14  0.028733866   -25.723582    197.99165    360.27856   -2218.1018 
-    1450        0.145  0.028733851   -25.866283    198.30283    360.46623   -2218.1018 
-    1500         0.15  0.028733812   -26.014569    200.95517    354.66722   -2218.1018 
-    1550        0.155   0.02873379   -26.192673    205.95485    348.37935   -2218.1018 
-    1600         0.16  0.028733795   -26.444059    212.87557    345.53576   -2218.1018 
-    1650        0.165  0.028733838    -26.75551    219.86449     338.9224   -2218.1018 
-    1700         0.17  0.028733868   -27.068513    224.47868    327.81241   -2218.1018 
-    1750        0.175  0.028733862   -27.344118    225.62318    319.85486   -2218.1018 
-    1800         0.18  0.028733849    -27.57563    224.07463    320.07064   -2218.1018 
-    1850        0.185  0.028733852   -27.774274    221.70618    323.12599   -2218.1018 
-    1900         0.19  0.028733864   -27.967999    220.53947     322.9504   -2218.1018 
-    1950        0.195  0.028733863   -28.173041    221.61407    318.63401   -2218.1018 
-    2000          0.2  0.028733853   -28.362177    224.22281    310.55185   -2218.1018 
-Loop time of 7.69012 on 4 procs for 2000 steps with 500 atoms
-
-Performance: 2.247 ns/day, 10.681 hours/ns, 260.074 timesteps/s
-98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.5623     | 1.5999     | 1.6541     |   2.7 | 20.80
-Neigh   | 0.012559   | 0.013043   | 0.013682   |   0.4 |  0.17
-Comm    | 0.1843     | 0.24254    | 0.27935    |   7.2 |  3.15
-Output  | 1.4749     | 1.5228     | 1.5694     |   2.9 | 19.80
-Modify  | 4.2492     | 4.3019     | 4.3507     |   1.8 | 55.94
-Other   |            | 0.009925   |            |       |  0.13
-
-Nlocal:    125 ave 132 max 120 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-Nghost:    1099 ave 1104 max 1092 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Neighs:    4876.5 ave 5100 max 4721 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-FullNghs:  9753 ave 10296 max 9362 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-
-Total # of neighbors = 39012
-Ave neighs/atom = 78.024
-Neighbor list builds = 21
-Dangerous builds = 0
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:07
diff --git a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
deleted file mode 120000
index 6a47c9eebe..0000000000
--- a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
+++ /dev/null
@@ -1 +0,0 @@
-../cobalt_fcc/Co_PurjaPun_2012.eam.alloy
\ No newline at end of file
diff --git a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
new file mode 100644
index 0000000000..3af058baf7
--- /dev/null
+++ b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
@@ -0,0 +1,6006 @@
+Cobalt EAM potential: G. P. Purja Pun and Y. Mishin, Phys. Rev. B xx, 004100 (2012) (in press)
+Data below r = 1.5 A is extrapolated. F(Rho) data not extrapolated.
+Created on Wed Sep 26 17:29:54 2012
+1 Co
+10000 4.788742913000000e-04 10000 6.499539000000001e-04 6.499539000000000e+00
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+ 8.309518568825200e-05 8.182033994906239e-05 8.056004718218619e-05 7.931419998170841e-05 7.808269064296404e-05
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+ 4.955424365336747e-06 4.799901525655197e-06 4.648049820836300e-06 4.499811793985402e-06 4.355130438087899e-06
+ 4.213949069835453e-06 4.076211399540344e-06 3.941861865039729e-06 3.810845196499976e-06 3.683106361660463e-06
+ 3.558590910585118e-06 3.437244835818923e-06 3.319014541070219e-06 3.203846795533912e-06 3.091688852089737e-06
+ 2.982488579295818e-06 2.876194109656037e-06 2.772753925582794e-06 2.672117063800105e-06 2.574233014808049e-06
+ 2.479051643033932e-06 2.386523210361943e-06 2.296598552297165e-06 2.209228971591383e-06 2.124366069775506e-06
+ 2.041961906232304e-06 1.961969019732135e-06 1.884340423438541e-06 1.809029507182080e-06 1.735990071613592e-06
+ 1.665176534356502e-06 1.596543687803830e-06 1.530046658503296e-06 1.465641105678908e-06 1.403283128309336e-06
+ 1.342929271825179e-06 1.284536503035511e-06 1.228062233226246e-06 1.173464436795038e-06 1.120701460082181e-06
+ 1.069732028902882e-06 1.020515399241352e-06 9.730112822753146e-07 9.271798002921477e-07 8.829815278752155e-07
+ 8.403775374680640e-07 7.993293716485992e-07 7.597989809176624e-07 7.217487560416926e-07 6.851415619710593e-07
+ 6.499407524191172e-07 6.161100929136179e-07 5.836137918783888e-07 5.524166028233452e-07 5.224836968385216e-07
+ 4.937806609639881e-07 4.662735849361845e-07 4.399289991547822e-07 4.147139110260500e-07 3.905957813609555e-07
+ 3.675425084859321e-07 3.455225231396512e-07 3.245046871736890e-07 3.044582778536548e-07 2.853530928283095e-07
+ 2.671593859185241e-07 2.498478511400059e-07 2.333896726605378e-07 2.177564985206194e-07 2.029204500538344e-07
+ 1.888541210793108e-07 1.755305458522738e-07 1.629232393506973e-07 1.510062144201093e-07 1.397539174372155e-07
+ 1.291412703741045e-07 1.191437050672961e-07 1.097370923617762e-07 1.008977778162274e-07 9.260259669902208e-08
+ 8.482883141984319e-08 7.755426670738778e-08 7.075715683240311e-08 6.441620467100832e-08 5.851063608240125e-08
+ 5.302013495440350e-08 4.792483459927075e-08 4.320538955913144e-08 3.884291294265582e-08 3.481898425658018e-08
+ 3.111569527451850e-08 2.771559342817648e-08 2.460171067137196e-08 2.175758348333717e-08 1.916719757773861e-08
+ 1.681503457183268e-08 1.468607978947252e-08 1.276576812429566e-08 1.104003874048358e-08 9.495328649625366e-09
+ 8.118528715645258e-09 6.897042498203040e-09 5.818760232281117e-09 4.872032311209139e-09 4.045732447740840e-09
+ 3.329210679517489e-09 2.712284881132093e-09 2.185301687016959e-09 1.739076161987666e-09 1.364901589086205e-09
+ 1.054599065845252e-09 8.004535320102697e-10 5.952414597054672e-10 4.322622496028902e-10 3.052766304104823e-10
+ 2.085502003918036e-10 1.368642901349301e-10 8.546164059834664e-11 5.010215808832263e-11 2.705311520847365e-11
+ 1.304599438344934e-11 5.339090781311160e-12 1.692041320615927e-12 3.321208355096226e-13 6.781366937015517e-15
diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data
index a450421699..e788ecf67e 100644
--- a/examples/SPIN/read_restart/in.spin.read_data
+++ b/examples/SPIN/read_restart/in.spin.read_data
@@ -20,7 +20,7 @@ neigh_modify 	every 1 check no delay 0
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # define outputs and computes
diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart
index 39157fdac4..ccce25b254 100644
--- a/examples/SPIN/read_restart/in.spin.restart
+++ b/examples/SPIN/read_restart/in.spin.restart
@@ -24,7 +24,7 @@ neigh_modify 	every 1 check no delay 0
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # define outputs
diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart
index 42f07fd316..c127101093 100644
--- a/examples/SPIN/read_restart/in.spin.write_restart
+++ b/examples/SPIN/read_restart/in.spin.write_restart
@@ -29,7 +29,7 @@ neigh_modify 	every 10 check yes delay 20
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 100.0 0.01 21
 
-fix 		3 all nve/spin lattice no
+fix 		3 all nve/spin lattice frozen
 timestep	0.0001
 
 # compute and output options
diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4
deleted file mode 100644
index 56fed35307..0000000000
--- a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4
+++ /dev/null
@@ -1,112 +0,0 @@
-LAMMPS (11 May 2018)
-units 		metal
-dimension 	3
-boundary 	p p p
-
-atom_style 	spin
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-read_data 	Norm_randXY_8x8x32.data
-  orthogonal box = (0 0 0) to (28.32 28.32 113.28)
-  1 by 1 by 4 MPI processor grid
-  reading atoms ...
-  8192 atoms
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# define outputs and computes
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          10
-thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 8 8 31
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.994 | 8.25 Mbytes
-Step Time v_magnorm v_emag v_tmag Temp TotEng 
-       0                    0    0.980832325249103     -2984.9466433509     51.7121203365411                    0    -38881.8459242507 
-      10                0.001    0.980832325329477    -2984.94800197307     52.2550778515409  0.00128259391683994    -38881.8459243698 
-      20                0.002    0.980832324654401    -2984.95196908569     53.4253110612179  0.00502068532291255    -38881.8459246487 
-      30                0.003     0.98083232312993    -2984.95826683995      55.148898005011   0.0109316232931419      -38881.84592505 
-      40                0.004    0.980832320808156     -2984.9664981035     57.3218040934977   0.0186091337978305    -38881.8459255198 
-      50                0.005    0.980832317596783    -2984.97619813016      59.827198436387   0.0275752665472358    -38881.8459260035 
-      60                0.006    0.980832313514709    -2984.98688847322     62.5519331668858    0.037334879488755      -38881.84592645 
-      70                0.007    0.980832309220414    -2984.99812399537     65.3979760533737   0.0474235360022736    -38881.8459268243 
-      80                0.008    0.980832304490479    -2985.00952678209     68.2863250613635   0.0574425728014485    -38881.8459271068 
-      90                0.009    0.980832299379824    -2985.02080456789     71.1540940309591   0.0670788096168283    -38881.8459272917 
-     100                 0.01    0.980832294622694    -2985.03175503971     73.9487734241296   0.0761100584457276    -38881.8459273851 
-Loop time of 3.6612 on 4 procs for 100 steps with 8192 atoms
-
-Performance: 0.236 ns/day, 101.700 hours/ns, 27.313 timesteps/s
-98.8% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0622     | 1.076      | 1.0936     |   1.1 | 29.39
-Neigh   | 0.77462    | 0.79542    | 0.81798    |   1.9 | 21.73
-Comm    | 0.024701   | 0.066122   | 0.10261    |  11.1 |  1.81
-Output  | 0.50304    | 0.51253    | 0.52111    |   0.9 | 14.00
-Modify  | 1.2006     | 1.2082     | 1.2205     |   0.7 | 33.00
-Other   |            | 0.002962   |            |       |  0.08
-
-Nlocal:    2048 ave 2095 max 1981 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Nghost:    5765 ave 5832 max 5718 min
-Histogram: 1 0 0 2 0 0 0 0 0 1
-Neighs:    143360 ave 146361 max 139058 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-FullNghs:  286720 ave 293300 max 277340 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-
-Total # of neighbors = 1146880
-Ave neighs/atom = 140
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4
deleted file mode 100644
index f93605a10a..0000000000
--- a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4
+++ /dev/null
@@ -1,118 +0,0 @@
-LAMMPS (11 May 2018)
-# start a spin-lattice simulation from a data file
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-read_restart	restart_hcp_cobalt.equil
-WARNING: Restart file used different # of processors (../read_restart.cpp:723)
-  restoring atom style spin from restart
-  orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 2 by 2 MPI processor grid
-  restoring pair style spin/exchange from restart
-  500 atoms
-
-# setting mass, mag. moments, and interactions
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice yes
-timestep	0.0001
-
-# define outputs
-
-compute 	out_mag    all compute/spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          10
-thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 4 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.203 | 6.203 | 6.203 Mbytes
-Step Time v_magnorm v_emag v_tmag Temp TotEng 
-    1000                    0    0.106120063678768    -11.8110267448939     5244.87332482316                    0    -2206.81097898003 
-    1010                0.001    0.106120030254187    -11.8198467883806     5263.87550015043    0.136650306637598    -2206.81097929055 
-    1020                0.002    0.106119996655714    -11.8460960476455       5267.299198699    0.542282344092749    -2206.81098022997 
-    1030                0.003    0.106119967407682    -11.8891433919665     5252.95473019843     1.20401809237154    -2206.81098172552 
-    1040                0.004    0.106119960016585    -11.9479778326021     5220.88686874944     2.10120827278397    -2206.81098371049 
-    1050                0.005    0.106119961252471    -12.0212426191481     5172.58712301374     3.20622343988728    -2206.81098610703 
-    1060                0.006    0.106119967598995    -12.1072712483404     5110.57504803718     4.48535830705751    -2206.81098879724 
-    1070                0.007    0.106119967669058    -12.2041566468564     5038.48927079832     5.90031039867811    -2206.81099161179 
-    1080                0.008    0.106119969263395    -12.3098693905406     4961.03212459716     7.41044810751949     -2206.8109943465 
-    1090                0.009    0.106119960964075    -12.4224156966204     4883.31968289062     8.97568865379831    -2206.81099680112 
-    1100                 0.01    0.106119945605273    -12.5400036591612     4809.87930844463     10.5594596175303    -2206.81099883101 
-Loop time of 0.304678 on 4 procs for 100 steps with 500 atoms
-
-Performance: 2.836 ns/day, 8.463 hours/ns, 328.215 timesteps/s
-98.0% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.071445   | 0.073018   | 0.074151   |   0.4 | 23.97
-Neigh   | 0.054448   | 0.055709   | 0.057528   |   0.5 | 18.28
-Comm    | 0.0061178  | 0.0074609  | 0.0090766  |   1.2 |  2.45
-Output  | 0.037489   | 0.038586   | 0.039952   |   0.5 | 12.66
-Modify  | 0.12826    | 0.12954    | 0.13065    |   0.3 | 42.52
-Other   |            | 0.0003686  |            |       |  0.12
-
-Nlocal:    125 ave 129 max 120 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-Nghost:    1387 ave 1392 max 1383 min
-Histogram: 1 0 1 0 0 1 0 0 0 1
-Neighs:    9125 ave 9428 max 8740 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-FullNghs:  18250 ave 18834 max 17520 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-
-Total # of neighbors = 73000
-Ave neighs/atom = 146
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:00
diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
similarity index 51%
rename from examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1
rename to examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
index 405be50bd9..d5c38a9967 100644
--- a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (11 May 2018)
+LAMMPS (30 Oct 2019)
 units 		metal
 dimension 	3
 boundary 	p p p
@@ -12,6 +12,7 @@ read_data 	Norm_randXY_8x8x32.data
   1 by 1 by 1 MPI processor grid
   reading atoms ...
   8192 atoms
+  read_data CPU = 0.0127251 secs
 
 mass		1 58.93
 
@@ -25,12 +26,12 @@ neigh_modify 	every 1 check no delay 0
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # define outputs and computes
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp
@@ -45,7 +46,7 @@ thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
 thermo_modify   format float %20.15g
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
 run 		100
 Neighbor list info ...
@@ -65,33 +66,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 19.68 | 19.68 | 19.68 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-       0                    0    0.980832325249102     -2984.9466433509     51.7121203365409                    0    -38881.8459242429 
-      10                0.001    0.980832325038224    -2984.94800197308     52.2550760237226  0.00128259392155095    -38881.8459243688 
-      20                0.002    0.980832322622779    -2984.95196908579     53.4253029071033   0.0050206854169363    -38881.8459246487 
-      30                0.003    0.980832317889283    -2984.95826684048     55.1488791221993   0.0109316238061975    -38881.8459250502 
-      40                0.004    0.980832310888481    -2984.96649810512     57.3217709603901   0.0186091353316915    -38881.8459255204 
-      50                0.005    0.980832301939686    -2984.97619813381     59.8271487572311   0.0275752699737783    -38881.8459260027 
-      60                0.006    0.980832291654664    -2984.98688847988     62.5518654049861   0.0373348857300743    -38881.8459264498 
-      70                0.007    0.980832280861627    -2984.99812400566     65.3978892661935   0.0474235455824994     -38881.845926824 
-      80                0.008    0.980832270462785    -2985.00952679611      68.286219599829   0.0574425858114516    -38881.8459271072 
-      90                0.009    0.980832261284587    -2985.02080458573     71.1539714621652   0.0670788260497413    -38881.8459272915 
-     100                 0.01    0.980832253960703    -2985.03175506188     73.9486358176052   0.0761100787140068    -38881.8459273845 
-Loop time of 12.4286 on 1 procs for 100 steps with 8192 atoms
+       0                    0   0.0177864461018737    -1323.65841279979       1274.398774669                    0    -36558.7284872918 
+      10                0.001   0.0177864363786085    -1323.66900862123     1270.76616762926   0.0100007025152235    -36558.7231900452 
+      20                0.002   0.0177864377251544    -1323.70032173151     1259.90270462032   0.0394803272360477    -36558.7075350597 
+      30                0.003   0.0177864511986563    -1323.75117991179     1243.50772254923   0.0871132837928349    -36558.6821082609 
+      40                0.004   0.0177864729727686    -1323.81992477224     1223.91535595806    0.150986538096776    -36558.6477386289 
+      50                0.005    0.017786495620418    -1323.90456907402     1203.45497846157     0.22877054554493    -36558.6054195788 
+      60                0.006   0.0177865119365897    -1324.00293472823     1183.95496070422    0.317876389336898     -36558.556239967 
+      70                0.007   0.0177865186121948    -1324.11277680481     1166.52445270059    0.415601818818485    -36558.5013220755 
+      80                0.008   0.0177865171615599    -1324.23190710734     1151.59958937508    0.519276751090729    -36558.4417598279 
+      90                0.009   0.0177865117923882    -1324.35831839963     1139.14485136813    0.626407059487507    -36558.3785566998 
+     100                 0.01   0.0177865063215865    -1324.49029089774     1128.88117273962    0.734797362055872    -36558.3125725035 
+Loop time of 14.8985 on 1 procs for 100 steps with 8192 atoms
 
-Performance: 0.070 ns/day, 345.239 hours/ns, 8.046 timesteps/s
+Performance: 0.058 ns/day, 413.847 hours/ns, 6.712 timesteps/s
 99.6% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 4.0123     | 4.0123     | 4.0123     |   0.0 | 32.28
-Neigh   | 3.005      | 3.005      | 3.005      |   0.0 | 24.18
-Comm    | 0.041798   | 0.041798   | 0.041798   |   0.0 |  0.34
-Output  | 1.8465     | 1.8465     | 1.8465     |   0.0 | 14.86
-Modify  | 3.5157     | 3.5157     | 3.5157     |   0.0 | 28.29
-Other   |            | 0.007261   |            |       |  0.06
+Pair    | 4.5996     | 4.5996     | 4.5996     |   0.0 | 30.87
+Neigh   | 3.6        | 3.6        | 3.6        |   0.0 | 24.16
+Comm    | 0.057512   | 0.057512   | 0.057512   |   0.0 |  0.39
+Output  | 2.4463     | 2.4463     | 2.4463     |   0.0 | 16.42
+Modify  | 4.1766     | 4.1766     | 4.1766     |   0.0 | 28.03
+Other   |            | 0.01854    |            |       |  0.12
 
 Nlocal:    8192 ave 8192 max 8192 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -109,4 +110,4 @@ Dangerous builds not checked
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:12
+Total wall time: 0:00:15
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4
new file mode 100644
index 0000000000..decd7f66de
--- /dev/null
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.read_data.g++.4
@@ -0,0 +1,113 @@
+LAMMPS (30 Oct 2019)
+units 		metal
+dimension 	3
+boundary 	p p p
+
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+read_data 	Norm_randXY_8x8x32.data
+  orthogonal box = (0 0 0) to (28.32 28.32 113.28)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  8192 atoms
+  read_data CPU = 0.0103889 secs
+
+mass		1 58.93
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor 	1.0 bin
+neigh_modify 	every 1 check no delay 0
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# define outputs and computes
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          10
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.49954
+  ghost atom cutoff = 7.49954
+  binsize = 3.74977, bins = 8 8 31
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.422 | 8.508 | 8.751 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0177864461018739    -1323.65841279979       1274.398774669                    0    -37220.5576936996 
+      10                0.001   0.0177864050983603    -1323.66900862096     1270.76618998865   0.0100007022583634    -37220.5576943555 
+      20                0.002   0.0177863936833753    -1323.70032172864     1259.90276925185   0.0394803245313843    -37220.5576959254 
+      30                0.003   0.0177864120892274    -1323.75117990111     1243.50783331745    0.087113273744231    -37220.5576982173 
+      40                0.004   0.0177864533855652     -1323.8199247464     1223.91551103958    0.150986513868405     -37220.557701015 
+      50                0.005   0.0177865078997919    -1323.90456902433     1203.45516787752    0.228770499151177    -37220.5577041159 
+      60                0.006   0.0177865576955448     -1324.0029346455     1183.95517338662    0.317876312538184    -37220.5577073314 
+      70                0.007   0.0177865860816348    -1324.11277667948     1166.52467969539    0.415601703342581    -37220.5577104775 
+      80                0.008   0.0177865881669081    -1324.23190693081     1151.59982868413    0.519276589926842     -37220.557713381 
+      90                0.009   0.0177865780982769    -1324.35831816525     1139.14509878533    0.626406847905203     -37220.557715901 
+     100                 0.01    0.017786564605084    -1324.49029060173     1128.88143013641    0.734797098519806     -37220.557717952 
+Loop time of 4.32342 on 4 procs for 100 steps with 8192 atoms
+
+Performance: 0.200 ns/day, 120.095 hours/ns, 23.130 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.185      | 1.1925     | 1.1991     |   0.5 | 27.58
+Neigh   | 0.93459    | 0.93934    | 0.94983    |   0.6 | 21.73
+Comm    | 0.042462   | 0.059373   | 0.069249   |   4.1 |  1.37
+Output  | 0.61823    | 0.63273    | 0.64528    |   1.3 | 14.63
+Modify  | 1.4827     | 1.4955     | 1.5099     |   0.8 | 34.59
+Other   |            | 0.003968   |            |       |  0.09
+
+Nlocal:    2048 ave 2061 max 2035 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    5765 ave 5778 max 5752 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:    143360 ave 144262 max 142469 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+FullNghs:  286720 ave 288540 max 284900 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 1146880
+Ave neighs/atom = 140
+Neighbor list builds = 100
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
similarity index 52%
rename from examples/SPIN/read_restart/log.11May18.spin.restart.g++.1
rename to examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
index 16eb7c3f5e..c7544dedfa 100644
--- a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (11 May 2018)
+LAMMPS (30 Oct 2019)
 # start a spin-lattice simulation from a data file
 units 		metal
 atom_style 	spin
@@ -10,11 +10,13 @@ boundary 	p p p
 atom_modify 	map array
 
 read_restart	restart_hcp_cobalt.equil
+WARNING: Restart file used different # of processors: 4 vs. 1 (../read_restart.cpp:742)
   restoring atom style spin from restart
   orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 1 by 1 MPI processor grid
   restoring pair style spin/exchange from restart
   500 atoms
+  read_restart CPU = 0.000396967 secs
 
 # setting mass, mag. moments, and interactions
 
@@ -30,12 +32,12 @@ neigh_modify 	every 1 check no delay 0
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice yes
+fix 		3 all nve/spin lattice moving
 timestep	0.0001
 
 # define outputs
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp
@@ -70,33 +72,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.315 | 6.315 | 6.315 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 6.816 | 6.816 | 6.816 Mbytes
 Step Time v_magnorm v_emag v_tmag Temp TotEng 
-    1000                    0    0.106120063678768    -11.8110267448938     5244.87332482316                    0    -2206.81097898043 
-    1010                0.001    0.106120047478105    -11.8198467887534     5263.87502105137    0.136650312456579    -2206.81097929055 
-    1020                0.002    0.106120026430373    -11.8460960518731     5267.29822866382    0.542282409605327    -2206.81098022997 
-    1030                0.003    0.106120005015917    -11.8891434078861     5252.95323564256       1.204018338139    -2206.81098172551 
-    1040                0.004    0.106119988532653    -11.9479778701641     5220.88508622311     2.10120884995911    -2206.81098371047 
-    1050                0.005     0.10611998133687     -12.021242685853     5172.58549378915     3.20622445795757    -2206.81098610701 
-    1060                0.006     0.10611998489458     -12.107271344148     5110.57395203849     4.48535975411235    -2206.81098879725 
-    1070                0.007    0.106119996964771     -12.204156761765     5038.48903231346      5.9003121044977    -2206.81099161183 
-    1080                0.008    0.106120013042521    -12.3098695046152      4961.0327167967      7.4104497466856    -2206.81099434653 
-    1090                0.009    0.106120029236234    -12.4224157835754      4883.3210922213     8.97568980540163    -2206.81099680117 
-    1100                 0.01    0.106120044071404    -12.5400036896932     4809.88136080052      10.559459821976    -2206.81099883104 
-Loop time of 0.833234 on 1 procs for 100 steps with 500 atoms
+    1000                    0    0.108317262557656    -10.7649197733649      2538.4247868621                    0    -2200.38241212222 
+    1010                0.001    0.108317281393701    -10.7743543303502     2527.22692799144    0.146167392153018     -2200.3776953858 
+    1020                0.002    0.108317318482233    -10.8022550516195     2509.47863584151    0.577304300153637    -2200.36374625815 
+    1030                0.003    0.108317366763426    -10.8476659807571      2487.5614649682     1.27529086243277    -2200.34104256596 
+    1040                0.004    0.108317415532953    -10.9092708333549     2463.97963921611     2.21443906326453    -2200.31024227618 
+    1050                0.005    0.108317453851058      -10.98553406179     2440.70473642157     3.36396898978859    -2200.27211302201 
+    1060                0.006    0.108317473584086    -11.0748008072977     2418.66477599297     4.68991434259399    -2200.22748216359 
+    1070                0.007    0.108317471632913     -11.175325501803     2397.59274785581     6.15596240129541    -2200.17722244953 
+    1080                0.008    0.108317450667394    -11.2852665400894     2376.32871275528      7.7237909750654    -2200.12225459883 
+    1090                0.009    0.108317417687893    -11.4027246787047     2353.52646917989     9.35409156720424    -2200.06352807392 
+    1100                 0.01    0.108317381194814      -11.52585602487     2328.41541723561     11.0087303030003     -2200.0019646458 
+Loop time of 0.964681 on 1 procs for 100 steps with 500 atoms
 
-Performance: 1.037 ns/day, 23.145 hours/ns, 120.014 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.896 ns/day, 26.797 hours/ns, 103.661 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.26558    | 0.26558    | 0.26558    |   0.0 | 31.87
-Neigh   | 0.21352    | 0.21352    | 0.21352    |   0.0 | 25.62
-Comm    | 0.0057988  | 0.0057988  | 0.0057988  |   0.0 |  0.70
-Output  | 0.12463    | 0.12463    | 0.12463    |   0.0 | 14.96
-Modify  | 0.22275    | 0.22275    | 0.22275    |   0.0 | 26.73
-Other   |            | 0.0009537  |            |       |  0.11
+Pair    | 0.29842    | 0.29842    | 0.29842    |   0.0 | 30.93
+Neigh   | 0.25359    | 0.25359    | 0.25359    |   0.0 | 26.29
+Comm    | 0.0069926  | 0.0069926  | 0.0069926  |   0.0 |  0.72
+Output  | 0.14398    | 0.14398    | 0.14398    |   0.0 | 14.93
+Modify  | 0.26045    | 0.26045    | 0.26045    |   0.0 | 27.00
+Other   |            | 0.001249   |            |       |  0.13
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -114,4 +116,4 @@ Dangerous builds not checked
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:00
+Total wall time: 0:00:01
diff --git a/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4
new file mode 100644
index 0000000000..6443d341cd
--- /dev/null
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.restart.g++.4
@@ -0,0 +1,118 @@
+LAMMPS (30 Oct 2019)
+# start a spin-lattice simulation from a data file
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+read_restart	restart_hcp_cobalt.equil
+  restoring atom style spin from restart
+  orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
+  1 by 2 by 2 MPI processor grid
+  restoring pair style spin/exchange from restart
+  500 atoms
+  read_restart CPU = 0.000922918 secs
+
+# setting mass, mag. moments, and interactions
+
+mass		1 58.93
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor 	1.0 bin
+neigh_modify 	every 1 check no delay 0
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# define outputs
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          10
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.49954
+  ghost atom cutoff = 7.49954
+  binsize = 3.74977, bins = 4 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.704 | 6.704 | 6.704 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+    1000                    0    0.108317262557656    -10.7649197733649      2538.4247868621                    0     -2205.7648720085 
+    1010                0.001    0.108317290362529    -10.7743543303489     2527.22680531097    0.146167392137698    -2205.76487255096 
+    1020                0.002    0.108317316207642    -10.8022550521284     2509.47840782645    0.577304308061779    -2205.76487378396 
+    1030                0.003    0.108317335980455    -10.8476659832667     2487.56119588937     1.27529090130452    -2205.76487555634 
+    1040                0.004    0.108317347902639    -10.9092708400684     2463.97936529674     2.21443916694928    -2205.76487769286 
+    1050                0.005    0.108317349786635    -10.9855340757384      2440.7044253165     3.36396920446814    -2205.76488005291 
+    1060                0.006    0.108317342445881    -11.0748008315013     2418.66438763214     4.68991471343994    -2205.76488256723 
+    1070                0.007     0.10831733355314    -11.1753255362286     2397.59228728929     6.15596292529133    -2205.76488520046 
+    1080                0.008    0.108317320750099    -11.2852665775656     2376.32820919279      7.7237915384778    -2205.76488786888 
+    1090                0.009    0.108317304079233     -11.402724701646     2353.52588586648     9.35409189724323     -2205.7648904133 
+    1100                 0.01    0.108317284409678    -11.5258560062539     2328.41472376239     11.0087299868288    -2205.76489265829 
+Loop time of 0.410707 on 4 procs for 100 steps with 500 atoms
+
+Performance: 2.104 ns/day, 11.409 hours/ns, 243.483 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.083043   | 0.083714   | 0.084202   |   0.1 | 20.38
+Neigh   | 0.063158   | 0.064429   | 0.065314   |   0.3 | 15.69
+Comm    | 0.012237   | 0.013588   | 0.014798   |   0.8 |  3.31
+Output  | 0.039088   | 0.040653   | 0.042176   |   0.6 |  9.90
+Modify  | 0.20645    | 0.20795    | 0.20945    |   0.2 | 50.63
+Other   |            | 0.0003724  |            |       |  0.09
+
+Nlocal:    125 ave 127 max 122 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost:    1387 ave 1390 max 1385 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs:    9125 ave 9272 max 8945 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+FullNghs:  18250 ave 18542 max 17812 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 73000
+Ave neighs/atom = 146
+Neighbor list builds = 100
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
similarity index 62%
rename from examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1
rename to examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
index c3be90cb50..9dbe1a3548 100644
--- a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (11 May 2018)
+LAMMPS (30 Oct 2019)
 # fcc cobalt in a 3d periodic box
 
 units 		metal
@@ -18,7 +18,7 @@ Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 1 by 1 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  Time spent = 0.00027585 secs
+  create_atoms CPU = 0.000552893 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -36,12 +36,12 @@ neigh_modify 	every 10 check yes delay 20
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 100.0 0.01 21
 
-fix 		3 all nve/spin lattice no
+fix 		3 all nve/spin lattice frozen
 timestep	0.0001
 
 # compute and output options
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp
@@ -70,33 +70,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.446 | 6.446 | 6.446 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 6.947 | 6.947 | 6.947 Mbytes
 Step Time v_magnorm v_emag Temp TotEng 
-       0            0  0.076558814    1.7982359            0    1.7982359 
-     100         0.01  0.079107243   0.56368447            0   0.56368447 
-     200         0.02   0.08225862  -0.42421042            0  -0.42421042 
-     300         0.03   0.08397714   -1.4964948            0   -1.4964948 
-     400         0.04  0.084704989   -2.6740652            0   -2.6740652 
-     500         0.05  0.087486342   -4.2043382            0   -4.2043382 
-     600         0.06   0.09187261   -5.6687169            0   -5.6687169 
-     700         0.07  0.096925249    -6.937499            0    -6.937499 
-     800         0.08  0.098988236   -8.2456715            0   -8.2456715 
-     900         0.09   0.10434092   -10.111953            0   -10.111953 
-    1000          0.1   0.10612006   -11.811027            0   -11.811027 
-Loop time of 2.60215 on 1 procs for 1000 steps with 500 atoms
+       0            0  0.076558814    1.7982359            0   0.89911794 
+     100         0.01  0.077628154   0.73387834            0   0.36693917 
+     200         0.02  0.076678996   -0.4048463            0  -0.20242315 
+     300         0.03  0.079174837   -1.3519103            0  -0.67595514 
+     400         0.04  0.085031632   -3.0345702            0   -1.5172851 
+     500         0.05   0.08702747   -4.0853256            0   -2.0426628 
+     600         0.06  0.087066482    -5.259549            0   -2.6297745 
+     700         0.07  0.089788894    -6.629076            0    -3.314538 
+     800         0.08  0.091699611   -8.0574087            0   -4.0287043 
+     900         0.09  0.090038899   -9.2012019            0    -4.600601 
+    1000          0.1  0.093257309   -10.470452            0   -5.2352261 
+Loop time of 3.37852 on 1 procs for 1000 steps with 500 atoms
 
-Performance: 3.320 ns/day, 7.228 hours/ns, 384.297 timesteps/s
-99.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 2.557 ns/day, 9.385 hours/ns, 295.987 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.35178    | 0.35178    | 0.35178    |   0.0 | 13.52
+Pair    | 0.45808    | 0.45808    | 0.45808    |   0.0 | 13.56
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.014421   | 0.014421   | 0.014421   |   0.0 |  0.55
-Output  | 1.2046     | 1.2046     | 1.2046     |   0.0 | 46.29
-Modify  | 1.0274     | 1.0274     | 1.0274     |   0.0 | 39.48
-Other   |            | 0.004006   |            |       |  0.15
+Comm    | 0.019707   | 0.019707   | 0.019707   |   0.0 |  0.58
+Output  | 1.3865     | 1.3865     | 1.3865     |   0.0 | 41.04
+Modify  | 1.5106     | 1.5106     | 1.5106     |   0.0 | 44.71
+Other   |            | 0.003624   |            |       |  0.11
 
 Nlocal:    500 ave 500 max 500 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -116,4 +116,4 @@ write_restart 	restart_hcp_cobalt.equil
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:02
+Total wall time: 0:00:03
diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
similarity index 64%
rename from examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4
rename to examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
index e54299b9dd..cb98274603 100644
--- a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4
+++ b/examples/SPIN/read_restart/log.19Nov19.spin.write_restart.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (11 May 2018)
+LAMMPS (30 Oct 2019)
 # fcc cobalt in a 3d periodic box
 
 units 		metal
@@ -18,7 +18,7 @@ Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
   1 by 2 by 2 MPI processor grid
 create_atoms 	1 box
 Created 500 atoms
-  Time spent = 0.000257969 secs
+  create_atoms CPU = 0.000751972 secs
 
 # setting mass, mag. moments, and interactions for cobalt
 
@@ -36,12 +36,12 @@ neigh_modify 	every 10 check yes delay 20
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
 fix 		2 all langevin/spin 100.0 0.01 21
 
-fix 		3 all nve/spin lattice no
+fix 		3 all nve/spin lattice frozen
 timestep	0.0001
 
 # compute and output options
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp
@@ -70,33 +70,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.367 | 6.367 | 6.367 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 6.868 | 6.868 | 6.868 Mbytes
 Step Time v_magnorm v_emag Temp TotEng 
        0            0  0.076558814    1.7982359            0    1.7982359 
-     100         0.01  0.081414414   0.70545723            0   0.70545723 
-     200         0.02  0.084519539  -0.33171078            0  -0.33171078 
-     300         0.03  0.089334139   -1.3988283            0   -1.3988283 
-     400         0.04  0.092873722   -2.8519371            0   -2.8519371 
-     500         0.05    0.0970839   -4.1531164            0   -4.1531164 
-     600         0.06  0.099626132   -5.7993765            0   -5.7993765 
-     700         0.07   0.10467169   -7.3011333            0   -7.3011333 
-     800         0.08   0.10893493   -8.6918141            0   -8.6918141 
-     900         0.09   0.11389657   -10.236174            0   -10.236174 
-    1000          0.1    0.1180057   -11.896933            0   -11.896933 
-Loop time of 1.05012 on 4 procs for 1000 steps with 500 atoms
+     100         0.01  0.078299981   0.88259584            0   0.88259584 
+     200         0.02  0.081260508  -0.43484722            0  -0.43484722 
+     300         0.03  0.081195603   -1.7408209            0   -1.7408209 
+     400         0.04  0.087298495   -3.4139038            0   -3.4139038 
+     500         0.05  0.087663924   -4.3766089            0   -4.3766089 
+     600         0.06  0.091713683   -5.8534921            0   -5.8534921 
+     700         0.07  0.093779119    -6.706628            0    -6.706628 
+     800         0.08  0.097960611   -7.8688568            0   -7.8688568 
+     900         0.09   0.10193463   -9.5888008            0   -9.5888008 
+    1000          0.1   0.10831726    -10.76492            0    -10.76492 
+Loop time of 1.70473 on 4 procs for 1000 steps with 500 atoms
 
-Performance: 8.228 ns/day, 2.917 hours/ns, 952.272 timesteps/s
-98.1% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5.068 ns/day, 4.735 hours/ns, 586.602 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.08972    | 0.090456   | 0.091872   |   0.3 |  8.61
+Pair    | 0.11636    | 0.11927    | 0.12069    |   0.5 |  7.00
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.016958   | 0.018047   | 0.019791   |   0.8 |  1.72
-Output  | 0.36286    | 0.37483    | 0.38975    |   1.6 | 35.69
-Modify  | 0.55131    | 0.56541    | 0.57702    |   1.3 | 53.84
-Other   |            | 0.001374   |            |       |  0.13
+Comm    | 0.049208   | 0.052445   | 0.057424   |   1.4 |  3.08
+Output  | 0.38579    | 0.40345    | 0.4199     |   2.0 | 23.67
+Modify  | 1.1138     | 1.1282     | 1.1436     |   1.1 | 66.18
+Other   |            | 0.001322   |            |       |  0.08
 
 Nlocal:    125 ave 125 max 125 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
diff --git a/examples/SPIN/run_spin_examples.sh b/examples/SPIN/run_spin_examples.sh
new file mode 100755
index 0000000000..a71da82a04
--- /dev/null
+++ b/examples/SPIN/run_spin_examples.sh
@@ -0,0 +1,120 @@
+#!/bin/bash
+
+DATE=19Nov19
+
+# bfo
+cd bfo/
+../../../src/lmp_serial -in in.spin.bfo
+cp log.lammps log.${DATE}.spin.bfo.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo
+cp log.lammps log.${DATE}.spin.bfo.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# fcc cobalt
+cd cobalt_fcc/
+../../../src/lmp_serial -in in.spin.cobalt_fcc
+cp log.lammps log.${DATE}.spin.cobalt_fcc.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.cobalt_fcc
+cp log.lammps log.${DATE}.spin.cobalt_fcc.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# hcp cobalt
+cd cobalt_hcp/
+../../../src/lmp_serial -in in.spin.cobalt_hcp
+cp log.lammps log.${DATE}.spin.cobalt_hcp.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.cobalt_hcp
+cp log.lammps log.${DATE}.spin.cobalt_hcp.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# dipole spin
+cd dipole_spin/
+../../../src/lmp_serial -in in.spin.iron_dipole_cut
+cp log.lammps log.${DATE}.spin.iron_dipole_cut.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_dipole_cut
+cp log.lammps log.${DATE}.spin.iron_dipole_cut.g++.4
+../../../src/lmp_serial -in in.spin.iron_dipole_ewald
+cp log.lammps log.${DATE}.spin.iron_dipole_ewald.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_dipole_ewald
+cp log.lammps log.${DATE}.spin.iron_dipole_ewald.g++.4
+../../../src/lmp_serial -in in.spin.iron_dipole_pppm
+cp log.lammps log.${DATE}.spin.iron_dipole_pppm.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_dipole_pppm
+cp log.lammps log.${DATE}.spin.iron_dipole_pppm.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# bcc iron
+cd iron/
+../../../src/lmp_serial -in in.spin.iron
+cp log.lammps log.${DATE}.spin.iron.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron
+cp log.lammps log.${DATE}.spin.iron.g++.4
+../../../src/lmp_serial -in in.spin.iron_cubic
+cp log.lammps log.${DATE}.spin.iron_cubic.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_cubic
+cp log.lammps log.${DATE}.spin.iron_cubic.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# fcc nickel
+cd nickel/
+../../../src/lmp_serial -in in.spin.nickel
+cp log.lammps log.${DATE}.spin.nickel.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.nickel
+cp log.lammps log.${DATE}.spin.nickel.g++.4
+../../../src/lmp_serial -in in.spin.nickel_cubic
+cp log.lammps log.${DATE}.spin.nickel_cubic.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.nickel_cubic
+cp log.lammps log.${DATE}.spin.nickel_cubic.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# read restart
+cd read_restart/
+../../../src/lmp_serial -in in.spin.write_restart
+cp log.lammps log.${DATE}.spin.write_restart.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.write_restart
+cp log.lammps log.${DATE}.spin.write_restart.g++.4
+../../../src/lmp_serial -in in.spin.restart
+cp log.lammps log.${DATE}.spin.restart.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.restart
+cp log.lammps log.${DATE}.spin.restart.g++.4
+../../../src/lmp_serial -in in.spin.read_data
+cp log.lammps log.${DATE}.spin.read_data.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.read_data
+cp log.lammps log.${DATE}.spin.read_data.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# setforce
+cd setforce_spin/
+../../../src/lmp_serial -in in.spin.setforce
+cp log.lammps log.${DATE}.spin.setforce.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.setforce
+cp log.lammps log.${DATE}.spin.setforce.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
+
+# spin minimizers
+cd spinmin/
+../../../src/lmp_serial -in in.spin.bfo_min
+cp log.lammps log.${DATE}.spin.bfo_min.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo_min
+cp log.lammps log.${DATE}.spin.bfo_min.g++.4
+../../../src/lmp_serial -in in.spin.bfo_min_cg
+cp log.lammps log.${DATE}.spin.bfo_min_cg.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo_min_cg
+cp log.lammps log.${DATE}.spin.bfo_min_cg.g++.4
+../../../src/lmp_serial -in in.spin.bfo_min_lbfgs
+cp log.lammps log.${DATE}.spin.bfo_min_lbfgs.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo_min_lbfgs
+cp log.lammps log.${DATE}.spin.bfo_min_lbfgs.g++.4
+../../../src/lmp_serial -in in.spin.iron_min
+cp log.lammps log.${DATE}.spin.iron_min.g++.1
+mpirun -np 4 ../../../src/lmp_mpi -in in.spin.iron_min
+cp log.lammps log.${DATE}.spin.iron_min.g++.4
+rm log.lammps log.cite dump*.lammpstrj
+cd ..
diff --git a/examples/SPIN/setforce_spin/in.spinmin.setforce b/examples/SPIN/setforce_spin/in.spin.setforce
similarity index 85%
rename from examples/SPIN/setforce_spin/in.spinmin.setforce
rename to examples/SPIN/setforce_spin/in.spin.setforce
index 10d4df66ed..0d65955a29 100644
--- a/examples/SPIN/setforce_spin/in.spinmin.setforce
+++ b/examples/SPIN/setforce_spin/in.spin.setforce
@@ -8,7 +8,7 @@ atom_style 	spin
 atom_modify 	map array 
 
 lattice 	sc 3.0
-region 		box block 0.0 10.0 0.0 10.0 0.0 1.0
+region 		box block 0.0 10.0 0.0 10.0 0.0 4.0
 create_box 	2 box
 region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
 region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
@@ -35,7 +35,7 @@ fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
 fix_modify	1 energy yes
 fix 		2 fixed_spin setforce/spin 0.0 0.0 0.0
 fix 		3 all langevin/spin 0.0 0.1 21
-fix		4 all nve/spin lattice no 
+fix		4 all nve/spin lattice frozen 
 
 timestep	0.0001
 
@@ -47,13 +47,13 @@ variable 	magnorm   equal c_out_mag[4]
 variable 	emag      equal c_out_mag[5]
 variable 	tmag      equal c_out_mag[6]
 
-thermo          1000
+thermo          100
 thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
 thermo_modify   format float %20.15g
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 1000 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
 
 min_style	spin
 min_modify 	alpha_damp 1.0 discrete_factor 20.0
-minimize        1.0e-16 1.0e-16 50000 1000
+minimize        1.0e-16 1.0e-16 1000 100
diff --git a/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1 b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1
new file mode 100644
index 0000000000..ed5c037feb
--- /dev/null
+++ b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.1
@@ -0,0 +1,141 @@
+LAMMPS (30 Oct 2019)
+
+units 		metal
+dimension 	3
+boundary 	f f f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.0
+Lattice spacing in x,y,z = 3 3 3
+region 		box block 0.0 10.0 0.0 10.0 0.0 4.0
+create_box 	2 box
+Created orthogonal box = (0 0 0) to (30 30 12)
+  1 by 1 by 1 MPI processor grid
+region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
+region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
+create_atoms 	1 region reg1
+Created 120 atoms
+  create_atoms CPU = 0.000998974 secs
+create_atoms 	2 region reg2
+Created 80 atoms
+  create_atoms CPU = 4.1008e-05 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+mass		2 55.845
+set 		region reg1 spin 2.2 0.0 0.0 1.0
+  120 settings made for spin
+set 		region reg2 spin/random 31 2.2
+  80 settings made for spin/random
+
+group 		fixed_spin region reg1
+120 atoms in group fixed_spin
+
+pair_style 	hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
+pair_coeff 	* * spin/exchange exchange 3.1 -0.01593 0.06626915552 1.211
+pair_coeff	* * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
+fix_modify	1 energy yes
+fix 		2 fixed_spin setforce/spin 0.0 0.0 0.0
+fix 		3 all langevin/spin 0.0 0.1 21
+fix		4 all nve/spin lattice frozen
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 20.0
+minimize        1.0e-16 1.0e-16 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.2
+  ghost atom cutoff = 3.2
+  binsize = 1.6, bins = 19 19 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.215 | 7.215 | 7.215 Mbytes
+Step Time v_magx v_magz v_magnorm v_tmag TotEng 
+       0                    0 0.000143282585570239    0.615515043943419    0.615726279597251     24.9364200982478    0.121881906963737 
+     100                 0.01 0.000616167502203097    0.594467364025194    0.594498630048783  0.00188964439583802   0.0371335982020527 
+     200                 0.02 0.000498981016106215    0.595175581059792    0.595218717456538 0.000158614984300385    0.036877233648055 
+     300                 0.03 0.000211899815837572    0.595357874794342    0.595402442288391 1.44454891242177e-05   0.0368548794182375 
+     400                 0.04 7.98967577397158e-05    0.595395828381057    0.595440657806237 1.50721782707597e-06   0.0368527556548781 
+     500                 0.05  2.9121648914103e-05    0.595403174462525    0.595448064489507 1.74330474543395e-07   0.0368525254239539 
+     600                 0.06 1.04772320898497e-05    0.595404457003426    0.595449362424563 2.12204214498221e-08   0.0368524982492743 
+     700                 0.07 3.74634771616422e-06    0.595404627382825    0.595449536940641 2.63852407890463e-09    0.036852494912626 
+     800                 0.08 1.33525617457914e-06    0.595404626884198    0.595449537611055 3.30772506699851e-10   0.0368524944963445 
+     900                 0.09 4.75054785504803e-07    0.595404613763238    0.595449524836571 4.15940445257144e-11   0.0368524944440918 
+    1000                  0.1 1.68843135202601e-07     0.59540460640039    0.595449517580793 5.23632581178917e-12    0.036852494437518 
+Loop time of 0.0966749 on 1 procs for 1000 steps with 200 atoms
+
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        0.121881906964    0.0368524944375    0.0368524944375
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.08679    | 0.08679    | 0.08679    |   0.0 | 89.77
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 7.2956e-05 | 7.2956e-05 | 7.2956e-05 |   0.0 |  0.08
+Output  | 0.0033231  | 0.0033231  | 0.0033231  |   0.0 |  3.44
+Modify  | 0.0022919  | 0.0022919  | 0.0022919  |   0.0 |  2.37
+Other   |            | 0.004197   |            |       |  4.34
+
+Nlocal:    200 ave 200 max 200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  920 ave 920 max 920 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 920
+Ave neighs/atom = 4.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4 b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4
new file mode 100644
index 0000000000..4ce1497957
--- /dev/null
+++ b/examples/SPIN/setforce_spin/log.19Nov19.spin.setforce.g++.4
@@ -0,0 +1,141 @@
+LAMMPS (30 Oct 2019)
+
+units 		metal
+dimension 	3
+boundary 	f f f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.0
+Lattice spacing in x,y,z = 3 3 3
+region 		box block 0.0 10.0 0.0 10.0 0.0 4.0
+create_box 	2 box
+Created orthogonal box = (0 0 0) to (30 30 12)
+  2 by 2 by 1 MPI processor grid
+region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
+region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
+create_atoms 	1 region reg1
+Created 120 atoms
+  create_atoms CPU = 0.000770092 secs
+create_atoms 	2 region reg2
+Created 80 atoms
+  create_atoms CPU = 7.9155e-05 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+mass		2 55.845
+set 		region reg1 spin 2.2 0.0 0.0 1.0
+  120 settings made for spin
+set 		region reg2 spin/random 31 2.2
+  80 settings made for spin/random
+
+group 		fixed_spin region reg1
+120 atoms in group fixed_spin
+
+pair_style 	hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
+pair_coeff 	* * spin/exchange exchange 3.1 -0.01593 0.06626915552 1.211
+pair_coeff	* * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
+fix_modify	1 energy yes
+fix 		2 fixed_spin setforce/spin 0.0 0.0 0.0
+fix 		3 all langevin/spin 0.0 0.1 21
+fix		4 all nve/spin lattice frozen
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 20.0
+minimize        1.0e-16 1.0e-16 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.2
+  ghost atom cutoff = 3.2
+  binsize = 1.6, bins = 19 19 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.2 | 7.2 | 7.2 Mbytes
+Step Time v_magx v_magz v_magnorm v_tmag TotEng 
+       0                    0 0.000143282585570239    0.615515043943419    0.615726279597251      21.735436446264    0.251043691626527 
+     100                 0.01 -0.00116085697754605    0.590264559350799    0.590315072966953  0.00283413081085227   0.0846048989956832 
+     200                 0.02 -0.000147570523236238      0.5896197627388    0.589686497206689 0.000451051163122381   0.0839054390713705 
+     300                 0.03 2.64982966536902e-05     0.59002969475615    0.590102003120244 5.22539631503911e-05   0.0838351677819014 
+     400                 0.04 1.77805448780033e-05    0.590195117338991    0.590268726215095 4.46490059775722e-06   0.0838382933245032 
+     500                 0.05 6.71566571038784e-06    0.590243842081075    0.590317756995865 3.63227563542099e-07   0.0838411433937997 
+     600                 0.06  2.2410340743112e-06    0.590257551861528    0.590331542128336 2.99360370345601e-08   0.0838420708305252 
+     700                 0.07 7.12179152897591e-07      0.5902614042958    0.590335413637884 2.51559188415894e-09   0.0838423375091767 
+     800                 0.08 2.20574733079126e-07    0.590262494529884    0.590336508799302 2.14455748236281e-10   0.0838424126463497 
+     900                 0.09 6.72564339365689e-08    0.590262805532644    0.590336821097688 1.84495767133404e-11   0.0838424338620728 
+    1000                  0.1 2.03001940390912e-08    0.590262894882646    0.590336910794094  1.5958531383517e-12   0.0838424398944951 
+Loop time of 0.0617704 on 4 procs for 1000 steps with 200 atoms
+
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        0.251043691627    0.0838424398641    0.0838424398945
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.023753   | 0.029762   | 0.035936   |   3.3 | 48.18
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.011783   | 0.019131   | 0.025404   |   4.3 | 30.97
+Output  | 0.0019517  | 0.0019774  | 0.0020368  |   0.1 |  3.20
+Modify  | 0.0006361  | 0.00087249 | 0.0011525  |   0.0 |  1.41
+Other   |            | 0.01003    |            |       | 16.23
+
+Nlocal:    50 ave 50 max 50 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    34.5 ave 48 max 22 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  230 ave 230 max 230 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 920
+Ave neighs/atom = 4.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/spinmin/in.spinmin.bfo b/examples/SPIN/spinmin/in.spin.bfo_min
similarity index 97%
rename from examples/SPIN/spinmin/in.spinmin.bfo
rename to examples/SPIN/spinmin/in.spin.bfo_min
index 5ebc9e0afe..701e049de3 100644
--- a/examples/SPIN/spinmin/in.spinmin.bfo
+++ b/examples/SPIN/spinmin/in.spin.bfo_min
@@ -9,7 +9,7 @@ atom_style 	spin
 atom_modify 	map array 
 
 lattice 	sc 3.96
-region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
 create_box 	1 box
 create_atoms 	1 box
 
diff --git a/examples/SPIN/spinmin/in.spin.bfo_min_cg b/examples/SPIN/spinmin/in.spin.bfo_min_cg
new file mode 100644
index 0000000000..7ce29b35ab
--- /dev/null
+++ b/examples/SPIN/spinmin/in.spin.bfo_min_cg
@@ -0,0 +1,54 @@
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	sc 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+# pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/cg
+# min_modify 	line spin_none discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
diff --git a/examples/SPIN/spinmin/in.spin.bfo_min_lbfgs b/examples/SPIN/spinmin/in.spin.bfo_min_lbfgs
new file mode 100644
index 0000000000..055903ab04
--- /dev/null
+++ b/examples/SPIN/spinmin/in.spin.bfo_min_lbfgs
@@ -0,0 +1,55 @@
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	sc 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/lbfgs
+# min_modify 	line spin_cubic discrete_factor 10.0
+min_modify	norm max
+minimize        1.0e-15 1.0e-10 1000 100
diff --git a/examples/SPIN/spinmin/in.spinmin.iron b/examples/SPIN/spinmin/in.spin.iron_min
similarity index 94%
rename from examples/SPIN/spinmin/in.spinmin.iron
rename to examples/SPIN/spinmin/in.spin.iron_min
index ebbd229b89..9ed07eccc7 100644
--- a/examples/SPIN/spinmin/in.spinmin.iron
+++ b/examples/SPIN/spinmin/in.spin.iron_min
@@ -9,7 +9,7 @@ atom_style 	spin
 atom_modify 	map array 
 
 lattice 	bcc 2.8665
-region 		box block 0.0 4.0 0.0 4.0 0.0 4.0
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
 create_box 	1 box
 create_atoms 	1 box
 
@@ -52,4 +52,4 @@ dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[
 
 min_style	spin
 min_modify 	alpha_damp 1.0 discrete_factor 10.0
-minimize        1.0e-10 1.0e-10 100000 1000
+minimize        1.0e-10 1.0e-10 1000 100
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1
new file mode 100644
index 0000000000..61b6ad8700
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.1
@@ -0,0 +1,148 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00107217 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 0.0 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.331 | 8.331 | 8.331 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0100717228668283   -0.163834417271778     14831.3069413956                    0  -0.0819172086358848 
+      50                0.005 0.000106105812337003    -128.307447484203    0.104264818055985                    0    -64.1537237421011 
+     100                 0.01 7.95347901119144e-06    -131.449389798071   0.0221943604064967                    0    -65.7246948990356 
+     150                0.015 5.63006161138875e-07    -132.296453030419   0.0085472877724348                    0    -66.1482265152089 
+     200                 0.02 5.07390677383517e-07    -132.622857703805  0.00361380451198708                    0    -66.3114288519012 
+     250                0.025 3.28458336892231e-07    -132.774411992703  0.00187753161968493                    0    -66.3872059963511 
+     300                 0.03 1.93294839202864e-07    -132.861283726084  0.00121374398924599                    0    -66.4306418630428 
+     350                0.035 1.13872157437693e-07    -132.923137019136 0.000954736871701507                    0    -66.4615685095675 
+     400                 0.04 6.42075545620808e-08    -132.975239148591 0.000854064736183609                    0    -66.4876195742954 
+     450                0.045 3.44210513403008e-08    -133.023523287306 0.000812909459005007                    0    -66.5117616436536 
+     500                 0.05 1.80394981485933e-08    -133.070071976252 0.000789742875305133                    0    -66.5350359881254 
+     550                0.055 9.54697157105863e-09     -133.11541233939 0.000769860218895372                    0    -66.5577061696963 
+     600                 0.06 5.22455110720346e-09    -133.159676447906 0.000752941158466282                    0    -66.5798382239526 
+     650                0.065 2.95172977724016e-09    -133.203196195612 0.000745065216626277                    0    -66.6015980978057 
+     700                 0.07  1.6727567441294e-09    -133.246696814329 0.000752898926000619                    0    -66.6233484071653 
+     750                0.075 9.17127001723567e-10    -133.291227007554 0.000780491405791262                    0    -66.6456135037769 
+     800                 0.08 4.72669535949609e-10    -133.337962593396 0.000827942834401386                    0    -66.6689812966976 
+     850                0.085 2.25696738407094e-10    -133.387945245851 0.000890246383931885                    0    -66.6939726229243 
+     900                 0.09  1.0030717061716e-10    -133.441737087546 0.000955403731484674                    0     -66.720868543773 
+     950                0.095 4.19867626359036e-11    -133.498969798312  0.00100352240545389                    0    -66.7494848991554 
+    1000                  0.1 1.64283478182092e-11    -133.557979904763  0.00101162410316333                    0    -66.7789899523816 
+Loop time of 9.23057 on 1 procs for 1000 steps with 5780 atoms
+
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+      -0.0819172086359      -66.778399627     -66.7789899524
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.7576     | 8.7576     | 8.7576     |   0.0 | 94.88
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.023815   | 0.023815   | 0.023815   |   0.0 |  0.26
+Output  | 0.31665    | 0.31665    | 0.31665    |   0.0 |  3.43
+Modify  | 0.029446   | 0.029446   | 0.029446   |   0.0 |  0.32
+Other   |            | 0.1031     |            |       |  1.12
+
+Nlocal:    5780 ave 5780 max 5780 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1065 ave 1065 max 1065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  92480 ave 92480 max 92480 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:09
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4
new file mode 100644
index 0000000000..efc4628b9e
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min.g++.4
@@ -0,0 +1,148 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00102711 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 0.0 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0100717228668283   -0.162177519662199      14970.709092345                    0   -0.157514482753586 
+      50                0.005 0.000134061770654521    -128.226118665465    0.102634444037434                    0    -128.286182424672 
+     100                 0.01 7.67769618983817e-06    -131.374599259781   0.0222596977749883                    0    -131.428418504308 
+     150                0.015 6.02904602224806e-07    -132.224372015825  0.00974271828169071                    0    -132.273190134602 
+     200                 0.02 6.50197247050491e-07    -132.573383315469  0.00374227079785921                    0    -132.617565541034 
+     250                0.025  4.4053438575152e-07    -132.729743470508   0.0019334097282578                    0    -132.770567114743 
+     300                 0.03 2.78356316513274e-07    -132.819255077939  0.00124938353773497                    0    -132.857574876413 
+     350                0.035 1.79684785125388e-07    -132.882714312877 0.000973166792896165                    0    -132.919261229742 
+     400                 0.04 1.10949878459078e-07    -132.935357748213 0.000852955460997588                    0    -132.970786605995 
+     450                0.045 6.49064465617817e-08    -132.982991683198 0.000790741148426224                    0    -133.017887798927 
+     500                 0.05 3.70514666559952e-08    -133.027689959766  0.00074794913288275                    0     -133.06256199189 
+     550                0.055 2.12433814830885e-08    -133.070148920145  0.00071263732127117                    0    -133.105417593745 
+     600                 0.06 1.24676590171361e-08    -133.110772798503 0.000685051841817325                    0     -133.14676746928 
+     650                0.065 7.53611859129351e-09    -133.150126417754 0.000669443562813208                    0    -133.187094895708 
+     700                 0.07 4.63539338651321e-09    -133.189024073453 0.000669619853917953                    0    -133.227152349439 
+     750                0.075 2.82145833974835e-09     -133.22844627026 0.000687338035086961                    0    -133.267881315198 
+     800                 0.08 1.64378151566173e-09    -133.269413776733 0.000722197692175127                    0    -133.310284062463 
+     850                0.085   8.883310104497e-10    -133.312863108454 0.000771645398804486                    0    -133.355293578462 
+     900                 0.09 4.33874801863461e-10    -133.359507749172 0.000830255722998156                    0    -133.403626236688 
+     950                0.095  1.8812784924272e-10    -133.409630495316 0.000888348219681112                    0    -133.455560507802 
+    1000                  0.1 7.17748875671948e-11    -133.462806227865 0.000931427722404681                    0    -133.510640942679 
+Loop time of 2.53419 on 4 procs for 1000 steps with 5780 atoms
+
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.157514482754     -133.509516066     -133.510640943
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.2697     | 2.2995     | 2.3564     |   2.2 | 90.74
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.05711    | 0.11414    | 0.14368    |  10.1 |  4.50
+Output  | 0.084883   | 0.084915   | 0.084985   |   0.0 |  3.35
+Modify  | 0.0071826  | 0.0072024  | 0.0072234  |   0.0 |  0.28
+Other   |            | 0.02847    |            |       |  1.12
+
+Nlocal:    1445 ave 1445 max 1445 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    555 ave 555 max 555 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  23120 ave 23120 max 23120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1
new file mode 100644
index 0000000000..ffd244b146
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.1
@@ -0,0 +1,141 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00135589 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+# pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/cg
+# min_modify 	line spin_none discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Line search incompatible gneb (../min_spin_cg.cpp:105)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.331 | 8.331 | 8.331 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0100717228668283   -0.163834417271778     14831.3069413956                    0  -0.0819172086358848 
+     100                 0.01 8.80197005314557e-06     -132.80634639767  0.00226660536216922                    0    -66.4031731988347 
+     200                 0.02 6.70903250218956e-06    -133.127078243354  0.00103783628361662                    0     -66.563539121677 
+     300                 0.03  4.5381603452565e-06    -133.471076972345  0.00144833375067451                    0    -66.7355384861738 
+     400                 0.04 9.04820921016732e-07    -133.767843456662 0.000682239601485924                    0    -66.8839217283314 
+     500                 0.05  1.6866160174916e-06    -133.893922160731  0.00032462625992713                    0     -66.946961080365 
+     600                 0.06 1.78038217785001e-06    -133.957222680701 0.000160730704849448                    0    -66.9786113403509 
+     700                 0.07 1.49199057723078e-06    -133.987255887786 7.39864656758093e-05                    0    -66.9936279438931 
+     800                 0.08 1.15173756711067e-06    -134.000921126053 3.33959465206462e-05                    0    -67.0004605630278 
+     900                 0.09 8.48526364752965e-07    -134.007049858868 1.49345737358251e-05                    0    -67.0035249294347 
+    1000                  0.1 6.10346492876059e-07    -134.009791515671 6.71648807105468e-06                    0    -67.0048957578347 
+Loop time of 9.4449 on 1 procs for 1000 steps with 5780 atoms
+
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+      -0.0819172086359     -67.0048809251     -67.0048957578
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 2.122e-314 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.7686     | 8.7686     | 8.7686     |   0.0 | 92.84
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.02386    | 0.02386    | 0.02386    |   0.0 |  0.25
+Output  | 0.31808    | 0.31808    | 0.31808    |   0.0 |  3.37
+Modify  | 0.029416   | 0.029416   | 0.029416   |   0.0 |  0.31
+Other   |            | 0.305      |            |       |  3.23
+
+Nlocal:    5780 ave 5780 max 5780 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1065 ave 1065 max 1065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  92480 ave 92480 max 92480 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:09
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4
new file mode 100644
index 0000000000..730bf477d4
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_cg.g++.4
@@ -0,0 +1,141 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  create_atoms CPU = 0.00138712 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+# pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/cg
+# min_modify 	line spin_none discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Line search incompatible gneb (../min_spin_cg.cpp:105)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0100717228668283   -0.162177519662199      14970.709092345                    0   -0.157514482753586 
+     100                 0.01 8.97646420936397e-06    -132.756468673032  0.00226858475243123                    0     -132.79881239587 
+     200                 0.02  5.7049674439631e-06    -133.065966570145 0.000924384747875186                    0    -133.105411060402 
+     300                 0.03 7.08166486348038e-06    -133.359072681024  0.00128114254070688                    0    -133.406669528642 
+     400                 0.04 4.60224970353229e-06    -133.668643035703 0.000822334798448062                    0    -133.725353643022 
+     500                 0.05 3.13737045264193e-06    -133.819548711647 0.000369678417461456                    0    -133.878037514585 
+     600                 0.06 2.55239214469856e-06    -133.889302880669   0.0001696142482835                    0    -133.948327309746 
+     700                 0.07 1.92236411979341e-06    -133.920147501261 7.31985644003847e-05                    0    -133.979597440788 
+     800                 0.08 1.40879742055238e-06    -133.933445418833 3.19349095035109e-05                    0    -133.993344750158 
+     900                 0.09 1.02629246257047e-06    -133.939321574068 1.44399877051467e-05                    0    -133.999611147322 
+    1000                  0.1 7.52253147824893e-07    -133.942032102451 6.85789018963965e-06                    0    -134.002604512509 
+Loop time of 2.49676 on 4 procs for 1000 steps with 5780 atoms
+
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.157514482754      -134.00257032     -134.002604513
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.2509     | 2.2589     | 2.2629     |   0.3 | 90.47
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.06036    | 0.064254   | 0.072356   |   1.9 |  2.57
+Output  | 0.084002   | 0.085009   | 0.085985   |   0.3 |  3.40
+Modify  | 0.0072496  | 0.0072694  | 0.0073116  |   0.0 |  0.29
+Other   |            | 0.08134    |            |       |  3.26
+
+Nlocal:    1445 ave 1445 max 1445 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    555 ave 555 max 555 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  23120 ave 23120 max 23120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1
new file mode 100644
index 0000000000..a8685eb2cf
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.1
@@ -0,0 +1,139 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 3.96)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 1156 atoms
+  create_atoms CPU = 0.00136805 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  1156 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/lbfgs
+# min_modify 	line spin_cubic discrete_factor 10.0
+min_modify	norm max
+minimize        1.0e-15 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Line search incompatible gneb (../min_spin_lbfgs.cpp:109)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 2
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.748 | 7.748 | 7.748 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0205636053306396   -0.218504643888467     1537.40479337332                    0   -0.109252321944233 
+      50                0.005 0.000800557938107919    -19.2937186217138    0.293526226015746                    0    -9.65918446070018 
+     100                 0.01 0.000434178067296136    -19.6225314972776    0.136842093090897                    0    -9.81803976806459 
+     150                0.015 9.48307628510239e-06    -19.7062424007137 0.000835148627123792                    0    -9.85315267460932 
+     200                 0.02 9.40072944704056e-06    -19.7072931204571 7.72334770010361e-06                    0    -9.85364693487844 
+     250                0.025 5.05117500164935e-07    -19.7072952885901 5.72437821949831e-08                    0    -9.85364764712939 
+     300                 0.03 2.15063977474981e-09     -19.707295295749 2.09970244523395e-12                    0     -9.8536476478746 
+     303               0.0303 1.43831710574092e-09    -19.7072952957498 1.70336397715489e-13                    0    -9.85364764787493 
+Loop time of 0.335897 on 1 procs for 303 steps with 1156 atoms
+
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+       -0.109252321944     -9.85364764787     -9.85364764787
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 303 303
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.28129    | 0.28129    | 0.28129    |   0.0 | 83.74
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0010796  | 0.0010796  | 0.0010796  |   0.0 |  0.32
+Output  | 0.017942   | 0.017942   | 0.017942   |   0.0 |  5.34
+Modify  | 0.001771   | 0.001771   | 0.001771   |   0.0 |  0.53
+Other   |            | 0.03382    |            |       | 10.07
+
+Nlocal:    1156 ave 1156 max 1156 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    213 ave 213 max 213 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  9248 ave 9248 max 9248 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9248
+Ave neighs/atom = 8
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4
new file mode 100644
index 0000000000..f2756d0f5e
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.bfo_min_lbfgs.g++.4
@@ -0,0 +1,139 @@
+LAMMPS (30 Oct 2019)
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 3.96)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 1156 atoms
+  create_atoms CPU = 0.000981808 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+  1156 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin/lbfgs
+# min_modify 	line spin_cubic discrete_factor 10.0
+min_modify	norm max
+minimize        1.0e-15 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Line search incompatible gneb (../min_spin_lbfgs.cpp:109)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 2
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair spin/dmi, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.619 | 7.619 | 7.619 Mbytes
+Step Time v_magnorm v_emag v_tmag Temp TotEng 
+       0                    0   0.0205636053306396   -0.217760509274282     1541.29975585882                    0   -0.217230771393012 
+      50                0.005 0.000966655616837406    -19.2878369426356    0.312860071233841                    0    -19.3229939390148 
+     100                 0.01  0.00154452800191107    -19.5948898197917    0.365367666925029                    0    -19.6389064900413 
+     150                0.015 4.89955946750017e-05    -19.6962580067431 0.000385536538802408                    0    -19.7047140195852 
+     200                 0.02 5.66300530875654e-05    -19.6975252647309  9.8679922880911e-05                    0    -19.7059140354146 
+     250                0.025 5.21141123128679e-08    -19.6975359469038 2.52554968535685e-09                    0    -19.7059189333986 
+     300                 0.03  2.9845103782958e-09    -19.6975359475094 2.31782597655471e-11                    0    -19.7059191124033 
+     342               0.0342  1.0526549233076e-10    -19.6975359475123 3.65641352240487e-16                    0    -19.7059191178145 
+Loop time of 0.117672 on 4 procs for 342 steps with 1156 atoms
+
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = force tolerance
+  Energy initial, next-to-last, final = 
+       -0.217230771393     -19.7059191178     -19.7059191178
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 342 342
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.084558   | 0.086668   | 0.091471   |   1.0 | 73.65
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0052197  | 0.010042   | 0.012191   |   2.8 |  8.53
+Output  | 0.0050647  | 0.0050726  | 0.0050921  |   0.0 |  4.31
+Modify  | 0.00052595 | 0.00053537 | 0.00055242 |   0.0 |  0.45
+Other   |            | 0.01535    |            |       | 13.05
+
+Nlocal:    289 ave 289 max 289 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    111 ave 111 max 111 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  2312 ave 2312 max 2312 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9248
+Ave neighs/atom = 8
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1 b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1
new file mode 100644
index 0000000000..6df5959c0b
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.1
@@ -0,0 +1,126 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.000965834 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin/random 31 2.2
+  250 settings made for spin/random
+#set 		group all spin 2.2 1.0 1.0 -1.0
+
+pair_style 	spin/exchange 3.5
+pair_coeff 	* * exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
+fix 		1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.6
+  ghost atom cutoff = 3.6
+  binsize = 1.8, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.848 | 6.848 | 6.848 Mbytes
+Step Time v_magx v_magz v_magnorm v_tmag TotEng 
+       0                    0  -0.0285071136621457 -0.00948990815281275   0.0764569750905723     5048.56076237679   -0.354774619362398 
+     100                 0.01   -0.584953861980204  -0.0517163256267969    0.999992350892306 6.25556948778472e-05    -25.2894057771132 
+     200                 0.02   -0.584864756506845  -0.0547143484057153    0.999999990495506 3.49782260454062e-06     -25.289435991418 
+     300                 0.03     -0.5847600493607  -0.0578846348986585    0.999999999988174 3.83095226805016e-06    -25.2894449433165 
+     400                 0.04   -0.584642875238893  -0.0612373075362701    0.999999999999986 4.28575832708226e-06    -25.2894549277735 
+     500                 0.05   -0.584511765589529  -0.0647826190376231                    1 4.79421486949086e-06    -25.2894660972709 
+     600                 0.06   -0.584365074206159  -0.0685313536438759                    1 5.36242072641834e-06    -25.2894785912384 
+     700                 0.07   -0.584200963215273   -0.072494846958872                    1 5.99725249459222e-06    -25.2894925651485 
+     800                 0.08   -0.584017381477007  -0.0766850043611195    0.999999999999999 6.70634191991825e-06     -25.289508192325 
+     900                 0.09   -0.583812040722351  -0.0811143180675364    0.999999999999999 7.49814943594148e-06    -25.2895256658925 
+    1000                  0.1   -0.583582389243979  -0.0857958823565731    0.999999999999998 8.38204259112222e-06    -25.2895452009133 
+Loop time of 0.195254 on 1 procs for 1000 steps with 250 atoms
+
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.354774619362     -25.2895449946     -25.2895452009
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.17668    | 0.17668    | 0.17668    |   0.0 | 90.49
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0052176  | 0.0052176  | 0.0052176  |   0.0 |  2.67
+Output  | 0.0067751  | 0.0067751  | 0.0067751  |   0.0 |  3.47
+Modify  | 0.0013788  | 0.0013788  | 0.0013788  |   0.0 |  0.71
+Other   |            | 0.005203   |            |       |  2.66
+
+Nlocal:    250 ave 250 max 250 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    315 ave 315 max 315 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  3200 ave 3200 max 3200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3200
+Ave neighs/atom = 12.8
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4 b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4
new file mode 100644
index 0000000000..b0cdd4f94a
--- /dev/null
+++ b/examples/SPIN/spinmin/log.19Nov19.spin.iron_min.g++.4
@@ -0,0 +1,126 @@
+LAMMPS (30 Oct 2019)
+# bcc iron in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 250 atoms
+  create_atoms CPU = 0.000759125 secs
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin/random 31 2.2
+  250 settings made for spin/random
+#set 		group all spin 2.2 1.0 1.0 -1.0
+
+pair_style 	spin/exchange 3.5
+pair_coeff 	* * exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
+fix 		1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 1000 100
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:177)
+WARNING: Using spin pair style without nve/spin or neb/spin (../pair_spin.cpp:87)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.6
+  ghost atom cutoff = 3.6
+  binsize = 1.8, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.828 | 6.829 | 6.829 Mbytes
+Step Time v_magx v_magz v_magnorm v_tmag TotEng 
+       0                    0  -0.0285071136621457 -0.00948990815281275   0.0764569750905723      5048.5607623768   -0.701465876910695 
+     100                 0.01   -0.584953861980204  -0.0517163256267969    0.999992350892306 6.25556948778489e-05    -50.5787443620229 
+     200                 0.02   -0.584864756506845  -0.0547143484057154    0.999999990495506 3.49782260454051e-06    -50.5787971409246 
+     300                 0.03     -0.5847600493607  -0.0578846348986585    0.999999999988173 3.83095226804998e-06    -50.5788061208592 
+     400                 0.04   -0.584642875238891    -0.06123730753627    0.999999999999984 4.28575832708228e-06    -50.5788161053499 
+     500                 0.05   -0.584511765589526  -0.0647826190376232    0.999999999999999 4.79421486949061e-06    -50.5788272748473 
+     600                 0.06   -0.584365074206158  -0.0685313536438759    0.999999999999999 5.36242072641826e-06    -50.5788397688148 
+     700                 0.07   -0.584200963215272  -0.0724948469588718                    1 5.99725249459218e-06    -50.5788537427249 
+     800                 0.08   -0.584017381477007  -0.0766850043611196                    1  6.7063419199184e-06    -50.5788693699014 
+     900                 0.09   -0.583812040722352  -0.0811143180675365    0.999999999999998 7.49814943594153e-06    -50.5788868434688 
+    1000                  0.1   -0.583582389243979  -0.0857958823565732    0.999999999999999 8.38204259112203e-06    -50.5789063784897 
+Loop time of 0.0845464 on 4 procs for 1000 steps with 250 atoms
+
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+       -0.701465876911     -50.5789061722     -50.5789063785
+  Force two-norm initial, final = 0 0
+  Force max component initial, final = 0 0
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 1000 1000
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.043007   | 0.045307   | 0.04776    |   0.8 | 53.59
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.026827   | 0.029139   | 0.031438   |   1.0 | 34.47
+Output  | 0.0023198  | 0.0023302  | 0.0023572  |   0.0 |  2.76
+Modify  | 0.00041103 | 0.0004673  | 0.00054026 |   0.0 |  0.55
+Other   |            | 0.007303   |            |       |  8.64
+
+Nlocal:    62.5 ave 65 max 60 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    217.5 ave 240 max 195 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  800 ave 825 max 775 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3200
+Ave neighs/atom = 12.8
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/SPIN/test_problems/README b/examples/SPIN/test_problems/README
new file mode 100644
index 0000000000..5557e3d42b
--- /dev/null
+++ b/examples/SPIN/test_problems/README
@@ -0,0 +1,47 @@
+** The objective of the benchmark examples in this directory 
+   is the following twofold: 
+- verify the implementation of the LAMMPS' SPIN package by 
+  comparing its results to well-known analytic results, or 
+  to simple test problems,
+- provide users with simple comparisons, allowing them to 
+  better understand what is implemented in the code.
+
+The LAMMPS input file (bench-*) can be modified, as well as the
+associated python script, in order to try different comparisons.
+
+All scripts can be run by executing the shell script from its
+directory. Example:
+./run-bench-exchange.sh from the benchmarck_damped_exchange/
+directory. 
+
+** Below a brief description of the different benchmark 
+   problems:
+
+- benchmarck_damped_precession:
+  simulates the damped precession of a single spin in a magnetic
+  field. 
+  Run as: ./run-bench-prec.sh
+  Output: x, y and z components of the magnetization, and
+  magnetic energy.
+
+- benchmarck_damped_exchange:
+  simulates two spins interacting through the exchange
+  interaction. The parameters in the LAMMPS input script
+  (bench-spin-precession.in) are calibrated to match the
+  exchange definition in the python script (llg_exchange.py). 
+  Run as: ./run-bench-exchange.sh
+  Output: average magnetization resulting from the damped 
+  precession of the two interacting spins. Also plots the 
+  evolution of the magnetic energy.
+  
+- benchmarck_langevin_precession:
+  simulates a single spin in a magnetic field and in contact
+  with a thermal bath, and compares the statistical averages of 
+  the output to the analytical result of the Langevin function. 
+  Run as: ./run-bench-prec.sh
+  Output: statistical average of the z-component of the
+  magnetization (along the applied field) and of the magnetic
+  energy versus temperature. Comparison to the Langevin function
+  results (computed by the python script).
+  Note: This example is a reworked version of a test problem 
+  provided by Martin Kroger (ETHZ).  
diff --git a/examples/SPIN/test_problems/validation_damped_exchange/bench-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/bench-spin-precession.in
new file mode 100644
index 0000000000..0ca49364d2
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_damped_exchange/bench-spin-precession.in
@@ -0,0 +1,39 @@
+#LAMMPS in.run 
+ 
+units           metal
+atom_style      spin
+atom_modify     map array
+boundary        f f f 
+
+read_data	two_spins.data
+
+pair_style      spin/exchange 3.1
+pair_coeff	* * exchange 3.1 11.254 0.0 1.0
+
+group bead      type 1  
+ 
+variable        H equal 0.0
+variable        Kan equal 0.0
+variable        Temperature equal 0.0 
+variable        RUN equal 30000
+
+fix             1 all nve/spin lattice no
+fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
+fix_modify      2 energy yes
+fix             3 all langevin/spin ${Temperature} 0.01 12345
+
+compute		out_mag    all spin
+compute		out_pe     all pe
+
+variable	magx      equal c_out_mag[1]
+variable	magy      equal c_out_mag[2]
+variable	magz      equal c_out_mag[3]
+variable	magnorm   equal c_out_mag[4]
+variable	emag      equal c_out_mag[5]
+
+thermo_style    custom step time v_magx v_magy v_magz v_emag pe etotal
+thermo          10
+
+timestep	0.0001
+
+run             ${RUN}
diff --git a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
new file mode 100755
index 0000000000..dd1c543bb3
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+
+import numpy as np , pylab, tkinter
+import math
+import matplotlib.pyplot as plt
+import mpmath as mp
+
+hbar=0.658212           # Planck's constant (eV.fs/rad)
+J0=0.05                 # per-neighbor exchange interaction (eV)
+S1 = np.array([1.0, 0.0, 0.0])
+S2 = np.array([0.0, 1.0, 0.0])
+alpha=0.01              # damping coefficient
+pi=math.pi
+
+N=30000                 # number of timesteps
+dt=0.1                  # timestep (fs)
+
+# Rodrigues rotation formula
+def rotation_matrix(axis, theta):
+  """
+  Return the rotation matrix associated with counterclockwise
+  rotation about the given axis by theta radians
+  """
+  axis = np.asarray(axis)
+  a = math.cos(theta / 2.0)
+  b, c, d = -axis * math.sin(theta / 2.0)
+  aa, bb, cc, dd = a * a, b * b, c * c, d * d
+  bc, ad, ac, ab, bd, cd = b * c, a * d, a * c, a * b, b * d, c * d
+  return np.array([[aa + bb - cc - dd, 2 * (bc + ad), 2 * (bd - ac)],
+      [2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
+      [2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
+
+# calculating precession field of spin Sr
+def calc_rot_vector(Sr,Sf):
+  rot = (J0/hbar)*(Sf-alpha*np.cross(Sf,Sr))/(1.0+alpha**2)
+  return rot
+  
+# second-order ST decomposition as implemented in LAMMPS 
+for t in range (0,N):
+  # advance s1 by dt/4
+  wf1 = calc_rot_vector(S1,S2)
+  theta=dt*np.linalg.norm(wf1)*0.25
+  axis=wf1/np.linalg.norm(wf1)
+  S1 = np.dot(rotation_matrix(axis, theta), S1)
+  # advance s2 by dt/2
+  wf2 = calc_rot_vector(S2,S1)
+  theta=dt*np.linalg.norm(wf2)*0.5
+  axis=wf2/np.linalg.norm(wf2)
+  S2 = np.dot(rotation_matrix(axis, theta), S2)
+  # advance s1 by dt/2
+  wf1 = calc_rot_vector(S1,S2)
+  theta=dt*np.linalg.norm(wf1)*0.5
+  axis=wf1/np.linalg.norm(wf1)
+  S1 = np.dot(rotation_matrix(axis, theta), S1)
+  # advance s2 by dt/2
+  wf2 = calc_rot_vector(S2,S1)
+  theta=dt*np.linalg.norm(wf2)*0.5
+  axis=wf2/np.linalg.norm(wf2)
+  S2 = np.dot(rotation_matrix(axis, theta), S2)
+  # advance s1 by dt/4
+  wf1 = calc_rot_vector(S1,S2)
+  theta=dt*np.linalg.norm(wf1)*0.25
+  axis=wf1/np.linalg.norm(wf1)
+  S1 = np.dot(rotation_matrix(axis, theta), S1)
+  # calc. average magnetization
+  Sm = (S1+S2)*0.5
+  # calc. energy
+  en = -J0*(np.dot(S1,S2))
+  # print res. in ps for comparison with LAMMPS
+  print(t*dt/1000.0,Sm[0],Sm[1],Sm[2],en)
diff --git a/examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py b/examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py
new file mode 100755
index 0000000000..bbc7c8f54e
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_damped_exchange/plot_precession.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+import sys, string, os
+
+
+argv = sys.argv
+if len(argv) != 3:
+  print("Syntax: ./plot_precession.py res_lammps.dat res_llg.dat")
+  sys.exit()
+
+lammps_file = sys.argv[1]
+llg_file = sys.argv[2]
+
+t_lmp,Sx_lmp,Sy_lmp,Sz_lmp,e_lmp = np.loadtxt(lammps_file,skiprows=0, usecols=(1,2,3,4,7),unpack=True)
+t_llg,Sx_llg,Sy_llg,Sz_llg,e_llg = np.loadtxt(llg_file,skiprows=0, usecols=(0,1,2,3,4),unpack=True)
+
+plt.figure()
+plt.subplot(411)
+plt.ylabel('Sx')
+plt.plot(t_lmp, Sx_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sx_llg, 'r--', label='LLG')
+
+plt.subplot(412)
+plt.ylabel('Sy')
+plt.plot(t_lmp, Sy_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sy_llg, 'r--', label='LLG')
+
+plt.subplot(413)
+plt.ylabel('Sz')
+plt.plot(t_lmp, Sz_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sz_llg, 'r--', label='LLG')
+
+plt.subplot(414)
+plt.ylabel('E (eV)')
+plt.plot(t_lmp, e_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, e_llg, 'r--', label='LLG')
+
+plt.xlabel('time (in ps)')
+plt.legend()
+plt.show()
diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh
new file mode 100755
index 0000000000..15de8d350e
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# clean old res
+rm res_*.dat
+
+# compute Lammps 
+./../../../../src/lmp_serial \
+  -in bench-spin-precession.in 
+in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
+en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
+in="$(echo "$in+1" | bc -l)"
+en="$(echo "$en-$in" | bc -l)"
+tail -n +$in log.lammps | head -n $en > res_lammps.dat
+
+# compute Langevin
+python3 -m llg_exchange.py > res_llg.dat
+
+# plot results
+python3 -m plot_precession.py res_lammps.dat res_llg.dat
diff --git a/examples/SPIN/test_problems/validation_damped_precession/bench-spin-precession.in b/examples/SPIN/test_problems/validation_damped_precession/bench-spin-precession.in
new file mode 100644
index 0000000000..ed8a5caeaf
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_damped_precession/bench-spin-precession.in
@@ -0,0 +1,47 @@
+#LAMMPS in.run 
+ 
+units           metal
+atom_style      spin
+atom_modify     map array
+boundary        p p p
+
+# read_data     singlespin.data
+
+lattice         sc 3.0
+region          box block 0.0 1.0 0.0 1.0 0.0 1.0
+create_box      1 box
+create_atoms    1 box
+
+mass            1 1.0
+set             type 1 spin 2.0 1.0 0.0 0.0
+
+pair_style      spin/exchange 4.0
+pair_coeff      * * exchange 1.0 0.0 0.0 1.0
+
+group bead      type 1  
+ 
+variable        H equal 10.0
+variable        Kan equal 0.0
+variable        Temperature equal 0.0 
+variable        Nsteps equal 500000
+
+fix             1 all nve/spin lattice no
+fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
+fix_modify      2 energy yes
+fix             3 all langevin/spin ${Temperature} 0.01 12345
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+
+thermo_style    custom step time v_magx v_magy v_magz v_emag pe etotal
+thermo          100
+
+timestep	0.0001
+
+run             ${Nsteps}
diff --git a/examples/SPIN/test_problems/validation_damped_precession/llg_precession.py b/examples/SPIN/test_problems/validation_damped_precession/llg_precession.py
new file mode 100755
index 0000000000..e8a46f389a
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_damped_precession/llg_precession.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python3
+
+import numpy as np , pylab, tkinter
+import math
+import matplotlib.pyplot as plt
+import mpmath as mp
+
+mub=5.78901e-5          # Bohr magneton (eV/T)
+hbar=0.658212           # Planck's constant (eV.fs/rad)
+g=2.0                   # Lande factor (adim)
+gyro=g*mub/hbar         # gyromag ratio (rad/fs/T)
+alpha=0.01              # damping coefficient
+pi=math.pi
+
+Bnrm=10.0               # mag. field (T)
+Bext = np.array([0.0, 0.0, 1.0])
+Sn = 2.0                # spin norm (in # of muB)
+S = np.array([1.0, 0.0, 0.0])
+
+N=500000                # number of timesteps
+dt=0.1                  # timestep (fs)
+
+# Rodrigues rotation formula
+def rotation_matrix(axis, theta):
+  """
+  Return the rotation matrix associated with counterclockwise
+  rotation about the given axis by theta radians
+  """
+  axis = np.asarray(axis)
+  a = math.cos(theta / 2.0)
+  b, c, d = -axis * math.sin(theta / 2.0)
+  aa, bb, cc, dd = a * a, b * b, c * c, d * d
+  bc, ad, ac, ab, bd, cd = b * c, a * d, a * c, a * b, b * d, c * d
+  return np.array([[aa + bb - cc - dd, 2 * (bc + ad), 2 * (bd - ac)],
+      [2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
+      [2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
+
+# calc. precession field
+def calc_rot_vector(Fi,Sp):
+  rot = gyro*Sn*Bnrm*(Fi-alpha*np.cross(Fi,Sp))
+  return rot
+  
+# np.set_printoptions(precision=4)
+for t in range (0,N):
+  wf = calc_rot_vector(Bext,S)
+  theta=dt*np.linalg.norm(wf)
+  axis=wf/np.linalg.norm(wf)
+  S = np.dot(rotation_matrix(axis, theta), S)
+  en = -hbar*gyro*Sn*Bnrm*np.dot(S,Bext)
+  # print res. in ps for comparison with LAMMPS
+  print(t*dt/1000.0,S[0],S[1],S[2],en)
+
diff --git a/examples/SPIN/test_problems/validation_damped_precession/plot_precession.py b/examples/SPIN/test_problems/validation_damped_precession/plot_precession.py
new file mode 100755
index 0000000000..9c07f1cefa
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_damped_precession/plot_precession.py
@@ -0,0 +1,45 @@
+#!/usr/bin/env python3
+
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+import sys, string, os
+
+
+argv = sys.argv
+if len(argv) != 3:
+  print("Syntax: ./plot_precession.py res_lammps.dat res_llg.dat")
+  sys.exit()
+
+lammps_file = sys.argv[1]
+llg_file = sys.argv[2]
+
+t_lmp,Sx_lmp,Sy_lmp,Sz_lmp,en_lmp = np.loadtxt(lammps_file,
+        skiprows=0, usecols=(1,2,3,4,5),unpack=True)
+t_llg,Sx_llg,Sy_llg,Sz_llg,en_llg = np.loadtxt(llg_file, skiprows=0, usecols=(0,1,2,3,4),unpack=True)
+
+plt.figure()
+plt.subplot(411)
+plt.ylabel('Sx')
+plt.plot(t_lmp, Sx_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sx_llg, 'r--', label='LLG')
+
+plt.subplot(412)
+plt.ylabel('Sy')
+plt.plot(t_lmp, Sy_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sy_llg, 'r--', label='LLG')
+
+plt.subplot(413)
+plt.ylabel('Sz')
+plt.plot(t_lmp, Sz_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, Sz_llg, 'r--', label='LLG')
+
+plt.subplot(414)
+plt.ylabel('En (eV)')
+plt.plot(t_lmp, en_lmp, 'b-', label='LAMMPS')
+plt.plot(t_llg, en_llg, 'r--', label='LLG')
+
+plt.xlabel('time (in ps)')
+plt.legend()
+plt.show()
diff --git a/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh
new file mode 100755
index 0000000000..49ebc2ac4e
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# clean old res
+rm res_*.dat
+
+# compute Lammps 
+./../../../../src/lmp_serial \
+  -in bench-spin-precession.in 
+in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
+en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
+in="$(echo "$in+1" | bc -l)"
+en="$(echo "$en-$in" | bc -l)"
+tail -n +$in log.lammps | head -n $en > res_lammps.dat
+
+# compute Langevin
+python3 -m llg_precession.py > res_llg.dat
+
+# plot results
+python3 -m plot_precession.py res_lammps.dat res_llg.dat
diff --git a/examples/SPIN/test_problems/validation_langevin_precession/bench-prec-spin.template b/examples/SPIN/test_problems/validation_langevin_precession/bench-prec-spin.template
new file mode 100644
index 0000000000..52f6a105ea
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_langevin_precession/bench-prec-spin.template
@@ -0,0 +1,46 @@
+#LAMMPS in.run 
+ 
+units           metal
+atom_style      spin
+atom_modify     map array
+boundary        p p p
+
+# read_data     singlespin.data
+
+lattice         sc 3.0
+region          box block 0.0 1.0 0.0 1.0 0.0 1.0
+create_box      1 box
+create_atoms    1 box
+
+mass            1 1.0
+set             type 1 spin 1.0 0.0 0.0 1.0
+
+# defines a pair/style for neighbor list, but do not use it
+pair_style      spin/exchange 4.0
+pair_coeff      * * exchange 1.0 0.0 0.0 1.0
+
+group bead      type 1  
+ 
+variable        H equal 10.0
+variable        Kan equal 0.0
+variable        Temperature equal temperature
+variable        RUN equal 1000000
+
+fix             1 all nve/spin lattice no
+fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
+fix_modify      2 energy yes
+fix             3 all langevin/spin ${Temperature} 0.01 12345
+
+compute         compute_spin all spin
+compute         outsp all property/atom spx spy spz sp
+compute         magsz all reduce ave c_outsp[3]
+
+thermo          50000
+thermo_style    custom step time temp vol pe c_compute_spin[5] etotal  
+
+variable        magnetic_energy equal c_compute_spin[5]
+
+fix             avespin all ave/time 1 ${RUN} ${RUN} v_Temperature v_H v_Kan c_magsz v_magnetic_energy file average_spin
+
+timestep        0.1
+run             ${RUN}
diff --git a/examples/SPIN/test_problems/validation_langevin_precession/langevin.py b/examples/SPIN/test_problems/validation_langevin_precession/langevin.py
new file mode 100755
index 0000000000..7acb780143
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_langevin_precession/langevin.py
@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+
+#Program fitting the exchange interaction
+#Model curve: Bethe-Slater function
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+import mpmath as mp
+# from scipy.optimize import curve_fit
+# from decimal import *
+
+mub=5.78901e-5          # Bohr magneton (eV/T)
+kb=8.617333262145e-5    # Boltzman constant (eV/K)
+g=2.0                   # Lande factor (adim)
+
+Hz=10.0                # mag. field (T)
+
+#Definition of the Langevin function
+def func(t):
+    return mp.coth(g*mub*Hz/(kb*t))-1.0/(g*mub*Hz/(kb*t))
+
+npoints=200
+ti=0.01
+tf=20.0
+for i in range (0,npoints): 
+    temp=ti+i*(tf-ti)/npoints
+    print('%lf %lf %lf' % (temp,func(temp),-g*mub*Hz*func(temp)))
+
diff --git a/examples/SPIN/test_problems/validation_langevin_precession/plot_precession.py b/examples/SPIN/test_problems/validation_langevin_precession/plot_precession.py
new file mode 100755
index 0000000000..0141af56a0
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_langevin_precession/plot_precession.py
@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+
+#Program fitting the exchange interaction
+#Model curve: Bethe-Slater function
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+import sys, string, os
+
+
+argv = sys.argv
+if len(argv) != 3:
+  print("Syntax: ./plot_precession.py res_lammps.dat res_langevin.dat")
+  sys.exit()
+
+lammps_file = sys.argv[1]
+langevin_file = sys.argv[2]
+
+T_lmp,S_lmp,E_lmp = np.loadtxt(lammps_file, skiprows=0, usecols=(0,2,3),unpack=True)
+T_lan,S_lan,E_lan = np.loadtxt(langevin_file, skiprows=0, usecols=(0,1,2),unpack=True)
+
+plt.figure()
+plt.subplot(211)
+plt.ylabel('<Sz>')
+plt.plot(T_lmp, S_lmp, 'b-', label='LAMMPS')
+plt.plot(T_lan, S_lan, 'r--', label='Langevin')
+
+plt.subplot(212)
+plt.ylabel('E (in eV)')
+plt.plot(T_lmp, E_lmp, 'b-', label='LAMMPS')
+plt.plot(T_lan, E_lan, 'r--', label='Langevin')
+
+plt.xlabel('T (in K)')
+pylab.xlim([0,20.0])
+plt.legend()
+plt.show()
diff --git a/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh
new file mode 100755
index 0000000000..98fceeca95
--- /dev/null
+++ b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+tempi=0.0
+tempf=20.0
+
+rm res_*.dat
+
+# compute Lammps 
+N=20
+for (( i=0; i<$N; i++ ))
+do
+  temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)"
+  sed s/temperature/${temp}/g bench-prec-spin.template > \
+    bench-prec-spin.in
+  ./../../../../src/lmp_serial \
+    -in bench-prec-spin.in 
+  Hz="$(tail -n 1 average_spin | awk -F " " '{print $3}')"
+  sz="$(tail -n 1 average_spin | awk -F " " '{print $5}')"
+  en="$(tail -n 1 average_spin | awk -F " " '{print $6}')"
+  echo $temp $Hz $sz $en >> res_lammps.dat
+done
+
+# compute Langevin
+python3 -m langevin.py > res_langevin.dat
+
+# plot results
+python3 -m plot_precession.py res_lammps.dat res_langevin.dat
diff --git a/examples/TIP4P/gpu_dump/data.spce b/examples/TIP4P/gpu_dump/data.spce
new file mode 120000
index 0000000000..4c8051fdff
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/data.spce
@@ -0,0 +1 @@
+../../rdf-adf/data.spce
\ No newline at end of file
diff --git a/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1 b/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1
new file mode 100644
index 0000000000..faa6d3c117
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1
@@ -0,0 +1,9018 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+4500
+ITEM: BOX BOUNDS pp pp pp
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6409999999999999e-02 3.5473599999999998e+01
+ITEM: ATOMS id type x y z fx fy fz 
+1 1 12.1247 28.092 22.2745 44.3296 17.0725 48.5356 
+2 2 12.4974 28.7565 22.854 -24.598 -41.7029 -32.885 
+3 2 11.5314 28.5784 21.7021 -26.0334 10.24 -23.1056 
+4 1 1.17081 29.3781 23.7307 -74.0189 -7.00332 56.5394 
+5 2 1.86259 29.4619 23.0745 28.6874 -4.77355 -53.1747 
+6 2 0.455888 28.9379 23.2709 28.8474 14.4006 -7.70694 
+7 1 29.6824 14.7369 21.6275 -6.84135 -10.4682 -14.9806 
+8 2 30.5192 14.9459 21.2125 -6.0991 2.52794 20.3786 
+9 2 29.7669 15.072 22.5202 13.979 5.65532 2.32707 
+10 1 10.8733 7.00191 35.1099 71.1535 29.5945 64.996 
+11 2 11.0641 6.25389 34.5439 -29.2143 -6.46229 -20.2952 
+12 2 9.99418 7.27965 34.8524 -52.7015 -16.0671 -37.9354 
+13 1 9.46552 6.437 19.7997 85.2674 -39.8413 10.9994 
+14 2 9.09748 6.31006 18.9252 -72.8621 17.4338 -56.4264 
+15 2 10.2738 5.92429 19.7966 -6.89627 25.8832 52.2923 
+16 1 3.17887 29.6978 22.1201 11.0669 36.9603 2.15921 
+17 2 3.20092 30.5775 21.7434 1.96842 -53.5324 1.10468 
+18 2 3.38088 29.1173 21.3863 -1.13041 18.9593 -2.63733 
+19 1 23.3853 11.3001 30.7823 -23.52 11.4998 -1.78141 
+20 2 23.7233 10.5129 31.2094 -10.6549 -69.8744 42.1205 
+21 2 24.1635 11.7415 30.442 31.685 49.5553 -38.1127 
+22 1 11.0372 10.4605 30.1467 -38.6093 -16.0236 -66.6776 
+23 2 10.974 11.4059 30.2831 -19.3275 67.6485 -7.84838 
+24 2 11.5859 10.1503 30.8671 54.5017 -54.8943 68.1861 
+25 1 26.2405 25.4087 21.068 -56.1074 83.4996 53.8252 
+26 2 25.6867 26.079 21.4683 35.5039 -49.8834 28.2082 
+27 2 26.1991 25.5923 20.1295 25.5629 -23.0759 -81.8338 
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diff --git a/examples/TIP4P/gpu_dump/dump.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp b/examples/TIP4P/gpu_dump/dump.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp
new file mode 100644
index 0000000000..faa6d3c117
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/dump.force_gpu.19Dec19.tip4p.g++.1.gtx1070.dp
@@ -0,0 +1,9018 @@
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+ITEM: TIMESTEP
+1
+ITEM: NUMBER OF ATOMS
+4500
+ITEM: BOX BOUNDS pp pp pp
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6450000000000001e-02 3.5532800000000002e+01
+2.6409999999999999e-02 3.5473599999999998e+01
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+4380 2 21.3181 25.1281 16.9343 1.91105 0.442844 0.0444748 
+4381 1 30.9762 0.893719 8.90624 6.84658 4.89315 4.34164 
+4382 2 31.2866 0.970928 8.00407 -1.30872 -1.28953 0.0387564 
+4383 2 30.0457 1.11331 8.85952 1.85147 1.23716 1.21913 
+4384 1 25.4566 22.8733 21.0012 8.46941 -6.2365 -4.41175 
+4385 2 26.2934 22.4661 21.2251 -0.0869085 0.997113 -0.522472 
+4386 2 25.6712 23.793 20.8454 -2.04348 -0.380031 3.58637 
+4387 1 24.8743 30.4839 12.6069 5.18592 -5.90954 -3.66721 
+4388 2 25.6363 30.6355 12.0478 -2.47753 -1.31299 -1.73489 
+4389 2 25.0041 29.602 12.9557 1.098 0.771613 1.03075 
+4390 1 13.8113 7.99004 5.29125 -6.25539 2.54191 5.22156 
+4391 2 13.7892 8.73645 4.69241 1.40451 -0.877124 -0.322734 
+4392 2 14.7345 7.89861 5.52688 -0.824712 -3.60413 -2.23204 
+4393 1 33.9717 12.8445 16.8206 -5.08834 3.24579 2.32558 
+4394 2 34.7638 12.3611 17.0557 -0.912544 -1.123 -1.64622 
+4395 2 33.6042 13.1252 17.6586 -0.0818337 -2.83827 1.19082 
+4396 1 26.5929 21.8369 5.4998 15.2188 -12.8758 -3.5611 
+4397 2 27.193 22.4961 5.15108 1.54123 -0.472239 4.36294 
+4398 2 27.1503 21.0829 5.69232 0.775207 0.532331 0.731822 
+4399 1 5.16966 25.9262 12.3542 3.63388 -10.9707 -4.2268 
+4400 2 4.39065 25.3778 12.4469 0.868663 0.512582 0.49162 
+4401 2 5.73068 25.672 13.0869 1.15015 -1.40555 -2.02342 
+4402 1 26.7931 35.4254 5.15069 -2.58439 4.8653 0.22666 
+4403 2 26.5925 34.8211 5.86542 2.47532 -0.574882 -0.655596 
+4404 2 27.2131 0.665389 5.57819 2.08955 -0.944702 -1.56575 
+4405 1 1.20884 3.82973 0.244724 1.66138 -1.50883 -2.97877 
+4406 2 2.01641 3.42102 0.556221 -0.565104 -0.453085 -0.98583 
+4407 2 0.510904 3.36319 0.704569 -0.652139 1.89174 -3.14661 
+4408 1 26.4335 3.26352 13.8621 2.94116 4.56618 2.38726 
+4409 2 26.7833 4.04332 14.2931 1.33818 -0.0840263 -3.07679 
+4410 2 25.7332 3.59406 13.2994 -3.10068 -2.3533 4.10846 
+4411 1 33.2055 12.6395 8.23391 5.45516 1.9919 5.8193 
+4412 2 32.6787 12.8131 9.01402 -0.345731 -1.59928 -1.24485 
+4413 2 34.1053 12.8183 8.50726 -0.805487 1.53365 1.78742 
+4414 1 29.9023 24.5626 20.7116 3.42295 -6.98403 -0.952027 
+4415 2 29.4679 25.4132 20.6473 -0.48284 -2.69496 0.222901 
+4416 2 30.2739 24.4166 19.8417 -0.244826 -2.35878 0.7128 
+4417 1 15.2998 4.02453 16.4417 -2.15742 4.79241 6.05563 
+4418 2 15.7057 4.6226 17.0692 0.191126 1.42105 -2.21766 
+4419 2 14.9946 3.28953 16.9736 -0.120429 1.69431 2.26192 
+4420 1 31.2753 25.1783 0.424078 -3.05861 -1.08728 17.9787 
+4421 2 31.0586 24.4517 35.287 4.05906 -1.40755 1.82856 
+4422 2 30.7422 25.0259 1.20438 -1.38424 0.164027 -0.204301 
+4423 1 12.1221 3.02324 0.180171 5.54245 -1.23026 6.11818 
+4424 2 11.8464 2.17458 35.281 1.14317 0.150516 -0.180026 
+4425 2 11.3607 3.34415 0.66332 2.03454 -2.74467 1.9593 
+4426 1 32.8431 11.557 14.38 0.147749 2.67556 -1.98289 
+4427 2 31.9068 11.5678 14.1811 0.291943 -1.00905 2.75821 
+4428 2 32.9664 12.2812 14.9936 1.19966 -2.12497 2.082 
+4429 1 20.5645 17.4424 12.4515 6.55406 0.156517 0.559841 
+4430 2 19.8459 16.8903 12.1433 -1.42603 2.83887 0.952488 
+4431 2 20.6495 17.2292 13.3808 1.56555 -1.24922 -0.696423 
+4432 1 15.2816 11.6269 18.8168 5.55975 3.4447 3.66971 
+4433 2 14.386 11.8473 19.0727 -0.646747 -2.40537 -4.21442 
+4434 2 15.3862 10.7109 19.0741 1.74861 1.0941 -0.195148 
+4435 1 29.7377 20.372 3.36652 0.797329 -7.98301 -8.63454 
+4436 2 30.4736 19.7997 3.5836 -1.83703 -0.890419 1.54523 
+4437 2 29.86 20.5792 2.44008 0.781849 -1.5009 -0.273719 
+4438 1 10.4638 28.1009 15.3794 8.14468 4.22684 -0.814723 
+4439 2 9.53379 28.2306 15.5652 0.0260372 -2.67835 -1.69305 
+4440 2 10.6322 28.642 14.608 -0.570693 -1.3859 -1.11001 
+4441 1 16.7704 6.13101 17.944 -0.211983 -1.47772 3.31 
+4442 2 17.2683 6.32159 18.7389 1.86764 1.15901 -3.46209 
+4443 2 16.6681 6.98075 17.5153 -2.39931 -1.61441 -0.74807 
+4444 1 21.5135 0.327334 25.1409 8.66564 11.1895 -11.7105 
+4445 2 22.2279 0.15114 25.7531 -4.2921 0.404201 4.61487 
+4446 2 21.4118 35.0184 24.6498 0.519456 -0.928846 2.19863 
+4447 1 8.71062 23.6629 10.1362 3.05079 1.60887 0.77512 
+4448 2 9.03714 24.1011 10.9221 0.259856 1.17771 -1.23482 
+4449 2 9.41576 23.0672 9.88307 -1.85123 -1.62472 0.915088 
+4450 1 20.2468 3.67222 10.3704 0.4777 5.10365 7.10224 
+4451 2 20.359 3.07898 11.1132 -0.765711 0.100413 -2.14552 
+4452 2 19.4836 3.33128 9.90403 2.85534 1.08452 -0.754728 
+4453 1 5.99164 17.0864 14.8678 -5.37574 3.84131 -0.459775 
+4454 2 6.63127 17.7689 14.6646 3.22934 -2.98012 2.44679 
+4455 2 5.554 17.396 15.6608 -0.457156 0.512177 -0.289605 
+4456 1 9.83882 21.0265 7.18035 5.95081 -1.40299 -8.14061 
+4457 2 9.12061 21.5838 6.88056 -2.6067 -3.24929 2.7288 
+4458 2 9.85976 21.1517 8.1291 3.24078 0.788148 -1.58199 
+4459 1 14.2806 22.3479 30.4744 -5.28704 8.01428 14.3895 
+4460 2 13.8253 23.128 30.1575 2.20354 -0.167513 -4.00018 
+4461 2 14.4934 21.8556 29.6816 1.73645 -3.40489 3.93134 
+4462 1 9.99574 22.3649 18.625 -1.24662 -2.70761 -10.6994 
+4463 2 10.4595 21.9481 17.8987 0.183494 1.6516 0.642745 
+4464 2 10.6595 22.4657 19.3072 -3.1201 -0.222712 1.57266 
+4465 1 13.5444 23.3091 25.3305 6.03923 1.55312 0.42896 
+4466 2 13.2633 22.9728 26.1815 -0.932337 -1.00851 -1.27722 
+4467 2 14.4265 22.9566 25.2126 -1.02044 -2.61951 -0.48294 
+4468 1 20.38 18.6937 28.3968 7.14119 -6.8925 -2.09374 
+4469 2 20.0167 18.9886 27.5617 0.316244 -5.43562 -1.75257 
+4470 2 21.3206 18.6184 28.2361 0.666353 0.344779 0.815735 
+4471 1 31.9689 7.20731 11.1996 7.34708 3.16447 9.75319 
+4472 2 31.6099 7.15114 12.0852 0.998483 0.911771 -1.0382 
+4473 2 32.8409 6.81882 11.269 -0.906482 -0.425175 -2.58612 
+4474 1 3.59826 34.1759 15.1126 -11.7123 -5.68349 5.97393 
+4475 2 3.21043 33.454 14.6179 1.39026 0.0576551 1.52481 
+4476 2 3.54331 33.8972 16.0267 0.654449 -1.39662 -0.127074 
+4477 1 16.7556 18.4081 28.9987 8.31009 -1.52636 -3.73736 
+4478 2 17.6307 18.6606 29.2931 -1.43242 0.172472 0.00350369 
+4479 2 16.5433 17.6311 29.5158 -4.3853 4.025 1.85791 
+4480 1 4.3102 29.9995 27.41 12.3163 -5.69934 9.04024 
+4481 2 5.14895 30.4141 27.2079 -1.45489 3.42303 0.773461 
+4482 2 3.71946 30.3049 26.7216 -0.489848 -3.13791 0.780952 
+4483 1 6.15571 15.7166 24.0745 -10.4675 14.0348 8.09529 
+4484 2 5.31022 15.8535 24.5019 -1.15491 -4.01696 -1.7966 
+4485 2 6.50126 14.9194 24.4761 0.366863 0.626035 -2.42182 
+4486 1 1.16849 28.775 19.8427 0.210476 14.8941 -2.95759 
+4487 2 0.55835 28.0645 19.6452 -0.37833 1.16517 1.01041 
+4488 2 2.02094 28.3459 19.9163 -1.22217 1.3797 3.29741 
+4489 1 23.2346 29.7445 8.55319 -3.19073 0.0591217 -1.71373 
+4490 2 24.177 29.8703 8.66448 -1.37464 0.315561 0.0894517 
+4491 2 22.981 30.3965 7.89984 0.244518 -1.23007 0.476314 
+4492 1 19.4825 19.1594 6.42054 2.91673 9.05689 -8.3853 
+4493 2 19.0036 18.5381 5.87205 1.04646 3.76482 -1.27192 
+4494 2 18.8796 19.8942 6.5334 2.07477 2.20963 -2.23813 
+4495 1 33.0425 24.822 13.641 6.63183 6.2187 -2.78039 
+4496 2 33.7809 24.3577 13.2468 -0.641414 -1.92179 0.68381 
+4497 2 32.2751 24.3054 13.3949 -0.245517 -1.04267 4.99319 
+4498 1 26.0476 6.03912 17.2588 1.74441 -5.97008 8.24573 
+4499 2 26.4147 5.4419 17.9106 -0.885223 -2.61028 -1.33276 
+4500 2 26.4184 5.74408 16.4271 1.8916 3.73175 0.920143 
diff --git a/examples/TIP4P/gpu_dump/in.tip4p b/examples/TIP4P/gpu_dump/in.tip4p
new file mode 100644
index 0000000000..b31960d203
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/in.tip4p
@@ -0,0 +1,49 @@
+# sample script to compare and debug GPU accelerated tip4p water
+# use '-sf gpu' to enables the GPU accelerated pair style
+# without it the original lj/cut/tip4p/long from module KSPACE will be used
+
+units         real
+boundary      p p p
+
+atom_style    full
+bond_style    harmonic
+angle_style   harmonic
+atom_modify   map array
+
+pair_style    lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
+pair_modify   table 0
+
+#long-range solver for TIP4P from module KSPACE works on CPU
+suffix off
+newton on
+kspace_style  pppm/tip4p 1.0e-5
+suffix on
+
+read_data     data.spce
+
+pair_coeff    * * 0.0 0.0
+pair_coeff    1 1 0.1852 3.1589
+
+bond_coeff    1 0.0 0.9572
+angle_coeff   1 0.0 104.52
+
+group water type 1 2
+
+#maintain the water molecule rigid
+fix           1 water shake 1.0e-4 200 0 b 1 a 1
+fix           2 water nve
+
+thermo        100
+thermo_style  custom step etotal ke pe temp  evdwl ecoul elong press
+thermo_modify format float "%.15g"
+
+velocity      water create 300 123
+
+if $(is_active(package,gpu)) &
+ then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz"&
+ else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+dump_modify 11 sort id
+
+timestep      1
+
+run           1
diff --git a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1 b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1
new file mode 100644
index 0000000000..57b0db597c
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1
@@ -0,0 +1,127 @@
+LAMMPS (30 Oct 2019)
+#
+
+units         real
+boundary      p p p
+
+atom_style    full
+bond_style    harmonic
+angle_style   harmonic
+atom_modify   map array
+
+pair_style    lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
+pair_modify   table 0
+
+#long-range solver for TIP4P from module KSPACE works on CPU
+suffix off
+newton on
+kspace_style  pppm/tip4p 1.0e-5
+suffix on
+
+read_data     data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.00143709 secs
+  read_data CPU = 0.0185545 secs
+
+pair_coeff    * * 0.0 0.0
+pair_coeff    1 1 0.1852 3.1589
+
+bond_coeff    1 0.0 0.9572
+angle_coeff   1 0.0 104.52
+
+group water type 1 2
+4500 atoms in group water
+
+#maintain the water molecule rigid
+fix           1 water shake 1.0e-4 200 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  1500 = # of frozen angles
+fix           2 water nve
+
+thermo        100
+thermo_style  custom step etotal ke pe temp  evdwl ecoul elong press
+thermo_modify format float "%.15g"
+
+velocity      water create 300 123
+
+if $(is_active(package,gpu))  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+if 0  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz
+dump_modify 11 sort id
+
+timestep      1
+
+run           1
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using polynomial approximation for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.342797
+  grid = 36 36 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00261362
+  estimated relative force accuracy = 7.87083e-06
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 79507 46656
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.3092
+  ghost atom cutoff = 11.3092
+  binsize = 5.6546, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/tip4p/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 30.18 | 30.18 | 30.18 Mbytes
+Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press 
+       0 -6581.1098053463 2681.834801985 -9262.9446073313 300 3652.16918734499 90723.8782743546 -103638.992069031 20828.2770003273 
+       1 -6293.09711304554 1787.55263217222 -8080.64974521776 199.96227554909 3652.66537554581 91910.2042281151 -103643.519348879 20986.2037813061 
+Loop time of 0.0943946 on 1 procs for 1 steps with 4500 atoms
+
+Performance: 0.915 ns/day, 26.221 hours/ns, 10.594 timesteps/s
+101.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.071838   | 0.071838   | 0.071838   |   0.0 | 76.10
+Bond    | 1.974e-06  | 1.974e-06  | 1.974e-06  |   0.0 |  0.00
+Kspace  | 0.012686   | 0.012686   | 0.012686   |   0.0 | 13.44
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00012462 | 0.00012462 | 0.00012462 |   0.0 |  0.13
+Output  | 0.0093175  | 0.0093175  | 0.0093175  |   0.0 |  9.87
+Modify  | 0.00038138 | 0.00038138 | 0.00038138 |   0.0 |  0.40
+Other   |            | 4.484e-05  |            |       |  0.05
+
+Nlocal:    4500 ave 4500 max 4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    15219 ave 15219 max 15219 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.37151e+06 ave 1.37151e+06 max 1.37151e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1371514
+Ave neighs/atom = 304.781
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp
new file mode 100644
index 0000000000..4441a448da
--- /dev/null
+++ b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp
@@ -0,0 +1,120 @@
+LAMMPS (30 Oct 2019)
+package gpu 1
+#
+
+units         real
+boundary      p p p
+
+atom_style    full
+bond_style    harmonic
+angle_style   harmonic
+atom_modify   map array
+
+pair_style    lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
+pair_modify   table 0
+
+#long-range solver for TIP4P from module KSPACE works on CPU
+suffix off
+newton on
+kspace_style  pppm/tip4p 1.0e-5
+suffix on
+
+read_data     data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.000921346 secs
+  read_data CPU = 0.0115216 secs
+
+pair_coeff    * * 0.0 0.0
+pair_coeff    1 1 0.1852 3.1589
+
+bond_coeff    1 0.0 0.9572
+angle_coeff   1 0.0 104.52
+
+group water type 1 2
+4500 atoms in group water
+
+#maintain the water molecule rigid
+fix           1 water shake 1.0e-4 200 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  1500 = # of frozen angles
+fix           2 water nve
+
+thermo        100
+thermo_style  custom step etotal ke pe temp  evdwl ecoul elong press
+thermo_modify format float "%.15g"
+
+velocity      water create 300 123
+
+if $(is_active(package,gpu))  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+if 1  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"
+dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz
+dump_modify 11 sort id
+
+timestep      1
+
+run           1
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using polynomial approximation for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.342797
+  grid = 36 36 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00261362
+  estimated relative force accuracy = 7.87083e-06
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 79507 46656
+WARNING: Increasing communication cutoff for TIP4P GPU style (../pair_lj_cut_tip4p_long_gpu.cpp:220)
+Per MPI rank memory allocation (min/avg/max) = 25.12 | 25.12 | 25.12 Mbytes
+Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press 
+       0 -6581.10980534572 2681.834801985 -9262.94460733072 300 3652.169187345 90723.8782743551 -103638.992069031 20828.2770003278 
+       1 -6293.09711304691 1787.55263217221 -8080.64974521913 199.96227554909 3652.6653755458 91910.2042281137 -103643.519348879 20986.203781307 
+Loop time of 0.0230916 on 1 procs for 1 steps with 4500 atoms
+
+Performance: 3.742 ns/day, 6.414 hours/ns, 43.306 timesteps/s
+103.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.000606   | 0.000606   | 0.000606   |   0.0 |  2.62
+Bond    | 1.682e-06  | 1.682e-06  | 1.682e-06  |   0.0 |  0.01
+Kspace  | 0.012588   | 0.012588   | 0.012588   |   0.0 | 54.51
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00015025 | 0.00015025 | 0.00015025 |   0.0 |  0.65
+Output  | 0.0093124  | 0.0093124  | 0.0093124  |   0.0 | 40.33
+Modify  | 0.00039674 | 0.00039674 | 0.00039674 |   0.0 |  1.72
+Other   |            | 3.623e-05  |            |       |  0.16
+
+Nlocal:    4500 ave 4500 max 4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    16834 ave 16834 max 16834 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/UNITS/README b/examples/UNITS/README
new file mode 100644
index 0000000000..3980b38688
--- /dev/null
+++ b/examples/UNITS/README
@@ -0,0 +1,54 @@
+This directory has 3 scripts which show how to run the same problem
+using the 3 most common units system used in LAMMPS: lj, real, and
+metal units.  As stated on the units command doc page:
+
+"Any simulation you perform for one choice of units can be duplicated
+with any other unit setting LAMMPS supports. ...  To perform the same
+simulation in a different set of units you must change all the
+unit-based input parameters in your input script and other input files
+(data file, potential files, etc) correctly to the new units.  And you
+must correctly convert all output from the new units to the old units
+when comparing to the original results.  That is often not simple to
+do."
+
+These examples are meant to illustrate how to do this for a simple
+Lennard-Jones liquid (argon).  All of the scripts have a set of
+variables defined at the top which can be changed as command line
+arguments (e.g. -v cutoff 3.0).  All 3 scripts give identical output,
+modulo round-offs due to the finite precision of the conversion
+factors used, either internally in LAMMPS or in the scripts.  If there
+were run for a long time, the trajectories would diverge, but they
+would still give statistically identical results.
+
+The LJ script is the simplest; it is similar to the bench/in.lj
+script.
+
+The real and metal scripts each have a set of variables at the top
+which define scale factors for converting quantities like distance,
+energy, pressure from reduced LJ units to real or metal units.  Once
+these are defined the rest of the input script is very similar to the
+LJ script.  The approprate scale factor is applied to every input.
+Output quantities are printed in both the native real/metal units and
+unscaled back to LJ units.  So that you can see the outputs are the
+same if you examine the log files.  Comments about this comparison
+are at the bottom of the real and metal scripts.
+
+These 3 scripts are provided, because converting from lj reduced units
+to physical units (e.g. real or metal) or vice versa is the trickiest
+case.  Converting input scripts between 2 sets of physical units
+(e.g. reak <--> metal) is much easier.  But you can use the same ideas
+as in these scripts; just define a set of scale/unscale factors.
+
+See Allen & Tildesley's Computer Simulation of Liquids, Appendix B for
+a nice discussion of reduced units.  It will explain the conversion
+formulas used in the real and metal scripts.
+
+Hopefully, if you study these scripts, you should be able to convert
+an input script of your own, written in one set of units, to an
+identical input script in an alternate set of units.  Where
+"identical" means it runs the same simulation in a statistical sense.
+
+You can find the full set of scale factors LAMMPS uses internally for
+different unit systems it supports, at the top of the src/udpate.cpp
+file.  A couple of those values are used in the real and metal
+scripts.
diff --git a/examples/UNITS/in.ar.lj b/examples/UNITS/in.ar.lj
new file mode 100644
index 0000000000..264ead8ab8
--- /dev/null
+++ b/examples/UNITS/in.ar.lj
@@ -0,0 +1,43 @@
+# Ar in lj units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon = sigma = mass = 1.0
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# script
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rhostar}
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create ${tinitial} 12345
+
+pair_style	lj/cut ${cutoff}
+pair_coeff	1 1 1.0 1.0
+
+neighbor	${skin} bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	${dt}
+
+thermo		10
+
+run		100
diff --git a/examples/UNITS/in.ar.metal b/examples/UNITS/in.ar.metal
new file mode 100644
index 0000000000..50f105530e
--- /dev/null
+++ b/examples/UNITS/in.ar.metal
@@ -0,0 +1,98 @@
+# Ar in metal units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon, sigma, mass set below
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# physical constants from update.cpp
+
+variable        kb index 8.617343e-5          # kB in eV/K
+variable        avogadro index 6.02214129e23  # Avogadro's number
+
+# Ar properties in metal units
+
+variable        epskb index 117.7             # LJ epsilon/kB in degrees K
+variable        sigma index 3.504             # LJ sigma in Angstroms
+variable        epsilon equal ${epskb}*${kb}  # LJ epsilon in eV
+variable        mass index 39.95              # mass in g/mole
+
+# scale factors
+
+# sigma = scale factor on distance, converts reduced distance to Angs
+# epsilon = scale factor on energy, converts reduced energy to eV
+# tmpscale = scale factor on temperature, converts reduced temp to degrees K
+# tscale = scale factor on time, converts reduced time to ps
+#   formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
+#   use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds
+# pscale = scale factor on pressure, converts reduced pressure to bars
+#   formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
+#   use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars
+
+variable        eVtoJoule index 1.602e-19     # convert eV to Joules
+variable        NtMtoAtm equal 1.0e-5         # convert Nt/meter^2 to bars
+
+variable        tmpscale equal ${epskb}
+variable        epsilonJ equal ${epsilon}*${eVtoJoule}
+variable        massKgAtom equal ${mass}/1000.0/${avogadro}
+variable        sigmaM equal ${sigma}/1.0e10
+variable        sigmaMsq equal ${sigmaM}*${sigmaM}
+variable        tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq})
+variable        sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
+variable        pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ}))
+
+# variables
+# alat = lattice constant in Angs (at reduced density rhostar)
+# temp = reduced temperature for output
+# epair,emol,etotal = reduced epair,emol,etotal energies for output
+# press = reduced pressure for output
+
+variable        alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        temp equal temp/${tmpscale}
+variable        epair equal epair/${epsilon}
+variable        emol equal emol/${epsilon}
+variable        etotal equal etotal/${epsilon}
+variable        press equal press/${pscale}
+
+# same script as in.ar.lj
+
+units		metal
+atom_style	atomic
+
+lattice		fcc ${alat}
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 ${mass}
+
+velocity	all create $(v_tinitial*v_epskb) 12345
+
+pair_style	lj/cut $(v_cutoff*v_sigma)
+pair_coeff	1 1 ${epsilon} ${sigma}
+
+neighbor	$(v_skin*v_sigma) bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	$(v_dt*v_tscale)
+
+# columns 2,3,4 = temp,pe,press in metal units
+# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
+# need to include metal unit output to enable use of reduced variables
+
+thermo_style    custom step temp pe press v_temp v_epair v_emol v_etotal v_press
+thermo_modify	norm yes
+thermo		${nthermo}
+
+run		${nsteps}
diff --git a/examples/UNITS/in.ar.real b/examples/UNITS/in.ar.real
new file mode 100644
index 0000000000..ea9670e599
--- /dev/null
+++ b/examples/UNITS/in.ar.real
@@ -0,0 +1,98 @@
+# Ar in real units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon, sigma, mass set below
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# physical constants from update.cpp
+
+variable        kb index 0.0019872067         # kB in Kcal/mole/K
+variable        avogadro index 6.02214129e23  # Avogadro's number
+
+# Ar properties in real units
+
+variable        epskb index 117.7             # LJ epsilon/kB in degrees K
+variable        sigma index 3.504             # LJ sigma in Angstroms
+variable        epsilon equal ${epskb}*${kb}  # LJ epsilon in Kcal/mole
+variable        mass index 39.95              # mass in g/mole
+
+# scale factors
+
+# sigma = scale factor on distance, converts reduced distance to Angs
+# epsilon = scale factor on energy, converts reduced energy to Kcal/mole
+# tmpscale = scale factor on temperature, converts reduced temp to degrees K
+# tscale = scale factor on time, converts reduced time to fs
+#   formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
+#   use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds
+# pscale = scale factor on pressure, converts reduced pressure to atmospheres
+#   formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
+#   use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms
+
+variable        KcaltoJoule index 4.1868e3    # convert Kcals to Joules
+variable        NtMtoAtm equal 1.0/1.0135e5   # convert Nt/meter^2 to Atmospheres
+
+variable        tmpscale equal ${epskb}
+variable        epsJmole equal ${epsilon}*${KcaltoJoule}
+variable        massKgmole equal ${mass}/1000.0
+variable        sigmaM equal ${sigma}/1.0e10
+variable        sigmaMsq equal ${sigmaM}*${sigmaM}
+variable        tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
+variable        sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
+variable        pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
+
+# variables
+# alat = lattice constant in Angs (at reduced density rhostar)
+# temp = reduced temperature for output
+# epair,emol,etotal = reduced epair,emol,etotal energies for output
+# press = reduced pressure for output
+
+variable        alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        temp equal temp/${tmpscale}
+variable        epair equal epair/${epsilon}
+variable        emol equal emol/${epsilon}
+variable        etotal equal etotal/${epsilon}
+variable        press equal press/${pscale}
+
+# same script as in.ar.lj
+
+units		real
+atom_style	atomic
+
+lattice		fcc ${alat}
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 ${mass}
+
+velocity	all create $(v_tinitial*v_epskb) 12345
+
+pair_style	lj/cut $(v_cutoff*v_sigma)
+pair_coeff	1 1 ${epsilon} ${sigma}
+
+neighbor	$(v_skin*v_sigma) bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	$(v_dt*v_tscale)
+
+# columns 2,3,4 = temp,pe,press in real units
+# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
+# need to include real unit output to enable use of reduced variables
+
+thermo_style    custom step temp pe press v_temp v_epair v_emol v_etotal v_press
+thermo_modify	norm yes
+thermo		${nthermo}
+
+run		${nsteps}
diff --git a/examples/UNITS/log.ar.lj.8Oct19.g++.1 b/examples/UNITS/log.ar.lj.8Oct19.g++.1
new file mode 100644
index 0000000000..39c3143cf5
--- /dev/null
+++ b/examples/UNITS/log.ar.lj.8Oct19.g++.1
@@ -0,0 +1,109 @@
+LAMMPS (19 Sep 2019)
+# Ar in lj units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon = sigma = mass = 1.0
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# script
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rhostar}
+lattice		fcc 0.8842
+Lattice spacing in x,y,z = 1.65388 1.65388 1.65388
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.26938 8.26938 8.26938)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000547171 secs
+mass		1 1.0
+
+velocity	all create ${tinitial} 12345
+velocity	all create 1.0 12345
+
+pair_style	lj/cut ${cutoff}
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	${skin} bin
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	${dt}
+timestep	0.005
+
+thermo		10
+
+run		100
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1   -7.1026383            0   -5.6056383   -5.1224757 
+      10   0.74213042   -6.7245488            0   -5.6135795   -3.1363153 
+      20   0.36167746   -6.1681704            0   -5.6267393  -0.40461854 
+      30    0.4684512   -6.3315744            0    -5.630303   -1.0390065 
+      40   0.46774191   -6.3308002            0   -5.6305906    -1.077533 
+      50   0.48323399   -6.3533122            0   -5.6299109   -1.1506287 
+      60   0.49569105   -6.3711644            0   -5.6291149   -1.2296104 
+      70    0.5208333   -6.4096336            0   -5.6299462   -1.4483636 
+      80   0.53708431   -6.4345933            0   -5.6305781   -1.5945708 
+      90   0.52618946   -6.4185937            0   -5.6308881   -1.5264055 
+     100   0.52862701   -6.4231724            0   -5.6318178   -1.5714077 
+Loop time of 0.065218 on 1 procs for 100 steps with 500 atoms
+
+Performance: 662394.104 tau/day, 1533.320 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.053584   | 0.053584   | 0.053584   |   0.0 | 82.16
+Neigh   | 0.0075939  | 0.0075939  | 0.0075939  |   0.0 | 11.64
+Comm    | 0.0022638  | 0.0022638  | 0.0022638  |   0.0 |  3.47
+Output  | 0.00021172 | 0.00021172 | 0.00021172 |   0.0 |  0.32
+Modify  | 0.0011077  | 0.0011077  | 0.0011077  |   0.0 |  1.70
+Other   |            | 0.0004568  |            |       |  0.70
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1946 ave 1946 max 1946 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    19572 ave 19572 max 19572 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19572
+Ave neighs/atom = 39.144
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/UNITS/log.ar.lj.8Oct19.g++.4 b/examples/UNITS/log.ar.lj.8Oct19.g++.4
new file mode 100644
index 0000000000..dba5ffb66a
--- /dev/null
+++ b/examples/UNITS/log.ar.lj.8Oct19.g++.4
@@ -0,0 +1,109 @@
+LAMMPS (19 Sep 2019)
+# Ar in lj units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon = sigma = mass = 1.0
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# script
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rhostar}
+lattice		fcc 0.8842
+Lattice spacing in x,y,z = 1.65388 1.65388 1.65388
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (8.26938 8.26938 8.26938)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000570774 secs
+mass		1 1.0
+
+velocity	all create ${tinitial} 12345
+velocity	all create 1.0 12345
+
+pair_style	lj/cut ${cutoff}
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	${skin} bin
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	${dt}
+timestep	0.005
+
+thermo		10
+
+run		100
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1   -7.1026383            0   -5.6056383   -5.1224757 
+      10   0.73621446   -6.7154544            0   -5.6133413    -3.089257 
+      20   0.35775263   -6.1618707            0    -5.626315  -0.37875949 
+      30   0.47139877   -6.3359656            0   -5.6302816   -1.1018761 
+      40   0.46337135   -6.3247084            0   -5.6310415   -1.0985336 
+      50   0.48738877    -6.360393            0    -5.630772   -1.2274707 
+      60   0.50832261   -6.3913892            0   -5.6304302    -1.374293 
+      70   0.50988271   -6.3936997            0   -5.6304053   -1.4112286 
+      80   0.53931444   -6.4367444            0   -5.6293906   -1.6484686 
+      90   0.55277272   -6.4563334            0   -5.6288326    -1.760598 
+     100   0.54916776   -6.4507537            0   -5.6286495    -1.728837 
+Loop time of 0.0237499 on 4 procs for 100 steps with 500 atoms
+
+Performance: 1818955.951 tau/day, 4210.546 timesteps/s
+97.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0098808  | 0.011585   | 0.015043   |   1.9 | 48.78
+Neigh   | 0.0015168  | 0.0017335  | 0.001997   |   0.4 |  7.30
+Comm    | 0.005949   | 0.0097297  | 0.011739   |   2.3 | 40.97
+Output  | 0.00019789 | 0.0002324  | 0.00032282 |   0.0 |  0.98
+Modify  | 0.00021482 | 0.00025994 | 0.00031853 |   0.0 |  1.09
+Other   |            | 0.0002095  |            |       |  0.88
+
+Nlocal:    125 ave 133 max 117 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    1099 ave 1107 max 1091 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:    4909 ave 5493 max 4644 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 19636
+Ave neighs/atom = 39.272
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/UNITS/log.ar.metal.8Oct19.g++.1 b/examples/UNITS/log.ar.metal.8Oct19.g++.1
new file mode 100644
index 0000000000..8bcf54f6ed
--- /dev/null
+++ b/examples/UNITS/log.ar.metal.8Oct19.g++.1
@@ -0,0 +1,197 @@
+LAMMPS (19 Sep 2019)
+# Ar in metal units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon, sigma, mass set below
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# physical constants from update.cpp
+
+variable        kb index 8.617343e-5          # kB in eV/K
+variable        avogadro index 6.02214129e23  # Avogadro's number
+
+# Ar properties in metal units
+
+variable        epskb index 117.7             # LJ epsilon/kB in degrees K
+variable        sigma index 3.504             # LJ sigma in Angstroms
+variable        epsilon equal ${epskb}*${kb}  # LJ epsilon in eV
+variable        epsilon equal 117.7*${kb}  
+variable        epsilon equal 117.7*8.617343e-5  
+variable        mass index 39.95              # mass in g/mole
+
+# scale factors
+
+# sigma = scale factor on distance, converts reduced distance to Angs
+# epsilon = scale factor on energy, converts reduced energy to eV
+# tmpscale = scale factor on temperature, converts reduced temp to degrees K
+# tscale = scale factor on time, converts reduced time to ps
+#   formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
+#   use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds
+# pscale = scale factor on pressure, converts reduced pressure to bars
+#   formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
+#   use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars
+
+variable        eVtoJoule index 1.602e-19     # convert eV to Joules
+variable        NtMtoAtm equal 1.0e-5         # convert Nt/meter^2 to bars
+
+variable        tmpscale equal ${epskb}
+variable        tmpscale equal 117.7
+variable        epsilonJ equal ${epsilon}*${eVtoJoule}
+variable        epsilonJ equal 0.010142612711*${eVtoJoule}
+variable        epsilonJ equal 0.010142612711*1.602e-19
+variable        massKgAtom equal ${mass}/1000.0/${avogadro}
+variable        massKgAtom equal 39.95/1000.0/${avogadro}
+variable        massKgAtom equal 39.95/1000.0/6.02214129e23
+variable        sigmaM equal ${sigma}/1.0e10
+variable        sigmaM equal 3.504/1.0e10
+variable        sigmaMsq equal ${sigmaM}*${sigmaM}
+variable        sigmaMsq equal 3.504e-10*${sigmaM}
+variable        sigmaMsq equal 3.504e-10*3.504e-10
+variable        tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq})
+variable        tscale equal 1.0e12/sqrt(1.6248465563022e-21/${massKgAtom}/${sigmaMsq})
+variable        tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/${sigmaMsq})
+variable        tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/1.2278016e-19)
+variable        sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
+variable        pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ}))
+variable        pscale equal 1e-05/(${sigmaM3}/(${epsilonJ}))
+variable        pscale equal 1e-05/(4.3022168064e-29/(${epsilonJ}))
+variable        pscale equal 1e-05/(4.3022168064e-29/(1.6248465563022e-21))
+
+# variables
+# alat = lattice constant in Angs (at reduced density rhostar)
+# temp = reduced temperature for output
+# epair,emol,etotal = reduced epair,emol,etotal energies for output
+# press = reduced pressure for output
+
+variable        alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
+variable        temp equal temp/${tmpscale}
+variable        temp equal temp/117.7
+variable        epair equal epair/${epsilon}
+variable        epair equal epair/0.010142612711
+variable        emol equal emol/${epsilon}
+variable        emol equal emol/0.010142612711
+variable        etotal equal etotal/${epsilon}
+variable        etotal equal etotal/0.010142612711
+variable        press equal press/${pscale}
+variable        press equal press/377.676586146256
+
+# same script as in.ar.lj
+
+units		metal
+atom_style	atomic
+
+lattice		fcc ${alat}
+lattice		fcc 5.79518437579763
+Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000549078 secs
+mass		1 ${mass}
+mass		1 39.95
+
+velocity	all create $(v_tinitial*v_epskb) 12345
+velocity	all create 117.70000000000000284 12345
+
+pair_style	lj/cut $(v_cutoff*v_sigma)
+pair_style	lj/cut 8.7599999999999997868
+pair_coeff	1 1 ${epsilon} ${sigma}
+pair_coeff	1 1 0.010142612711 ${sigma}
+pair_coeff	1 1 0.010142612711 3.504
+
+neighbor	$(v_skin*v_sigma) bin
+neighbor	1.0511999999999999122 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	$(v_dt*v_tscale)
+timestep	0.011194658410003900315
+
+# columns 2,3,4 = temp,pe,press in metal units
+# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
+# need to include metal unit output to enable use of reduced variables
+
+thermo_style    custom step temp pe press v_temp v_epair v_emol v_etotal v_press
+thermo_modify	norm yes
+thermo		${nthermo}
+thermo		10
+
+run		${nsteps}
+run		100
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9.8112
+  ghost atom cutoff = 9.8112
+  binsize = 4.9056, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes
+Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press 
+       0        117.7  -0.07203931   -1934.8523            1   -7.1026383            0   -5.6056383     -5.12304 
+      10    87.345225  -0.06820404   -1184.5618   0.74210047    -6.724504            0   -5.6135796   -3.1364449 
+      20    42.569809 -0.062561408   -152.82812   0.36168062   -6.1681748            0   -5.6267389  -0.40465341 
+      30    55.137637 -0.064219154   -392.49645   0.46845911   -6.3316185            0   -5.6303352   -1.0392396 
+      40    55.053014 -0.064210828   -406.99941   0.46774014   -6.3307976            0   -5.6305906     -1.07764 
+      50     56.87723 -0.064439241   -434.61958     0.483239   -6.3533177            0   -5.6299089   -1.1507718 
+      60    58.344019 -0.064620383    -464.4684    0.4957011   -6.3711772            0   -5.6291126   -1.2298046 
+      70     61.30301 -0.065010529   -547.09852    0.5208412   -6.4096433            0    -5.629944     -1.44859 
+      80    63.214836 -0.065263563   -602.29599   0.53708442   -6.4345909            0   -5.6305755   -1.5947401 
+      90    61.931826 -0.065101194    -576.5342   0.52618374   -6.4185823            0   -5.6308852   -1.5265288 
+     100    62.221816 -0.065148028   -593.59878   0.52864755   -6.4231998            0   -5.6318144   -1.5717119 
+Loop time of 0.04864 on 1 procs for 100 steps with 500 atoms
+
+Performance: 1988.524 ns/day, 0.012 hours/ns, 2055.921 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.039802   | 0.039802   | 0.039802   |   0.0 | 81.83
+Neigh   | 0.0057771  | 0.0057771  | 0.0057771  |   0.0 | 11.88
+Comm    | 0.0015905  | 0.0015905  | 0.0015905  |   0.0 |  3.27
+Output  | 0.00033736 | 0.00033736 | 0.00033736 |   0.0 |  0.69
+Modify  | 0.00077343 | 0.00077343 | 0.00077343 |   0.0 |  1.59
+Other   |            | 0.0003595  |            |       |  0.74
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1946 ave 1946 max 1946 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    19572 ave 19572 max 19572 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19572
+Ave neighs/atom = 39.144
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/UNITS/log.ar.metal.8Oct19.g++.4 b/examples/UNITS/log.ar.metal.8Oct19.g++.4
new file mode 100644
index 0000000000..5a88231128
--- /dev/null
+++ b/examples/UNITS/log.ar.metal.8Oct19.g++.4
@@ -0,0 +1,197 @@
+LAMMPS (19 Sep 2019)
+# Ar in metal units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon, sigma, mass set below
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# physical constants from update.cpp
+
+variable        kb index 8.617343e-5          # kB in eV/K
+variable        avogadro index 6.02214129e23  # Avogadro's number
+
+# Ar properties in metal units
+
+variable        epskb index 117.7             # LJ epsilon/kB in degrees K
+variable        sigma index 3.504             # LJ sigma in Angstroms
+variable        epsilon equal ${epskb}*${kb}  # LJ epsilon in eV
+variable        epsilon equal 117.7*${kb}  
+variable        epsilon equal 117.7*8.617343e-5  
+variable        mass index 39.95              # mass in g/mole
+
+# scale factors
+
+# sigma = scale factor on distance, converts reduced distance to Angs
+# epsilon = scale factor on energy, converts reduced energy to eV
+# tmpscale = scale factor on temperature, converts reduced temp to degrees K
+# tscale = scale factor on time, converts reduced time to ps
+#   formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
+#   use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds
+# pscale = scale factor on pressure, converts reduced pressure to bars
+#   formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
+#   use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars
+
+variable        eVtoJoule index 1.602e-19     # convert eV to Joules
+variable        NtMtoAtm equal 1.0e-5         # convert Nt/meter^2 to bars
+
+variable        tmpscale equal ${epskb}
+variable        tmpscale equal 117.7
+variable        epsilonJ equal ${epsilon}*${eVtoJoule}
+variable        epsilonJ equal 0.010142612711*${eVtoJoule}
+variable        epsilonJ equal 0.010142612711*1.602e-19
+variable        massKgAtom equal ${mass}/1000.0/${avogadro}
+variable        massKgAtom equal 39.95/1000.0/${avogadro}
+variable        massKgAtom equal 39.95/1000.0/6.02214129e23
+variable        sigmaM equal ${sigma}/1.0e10
+variable        sigmaM equal 3.504/1.0e10
+variable        sigmaMsq equal ${sigmaM}*${sigmaM}
+variable        sigmaMsq equal 3.504e-10*${sigmaM}
+variable        sigmaMsq equal 3.504e-10*3.504e-10
+variable        tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq})
+variable        tscale equal 1.0e12/sqrt(1.6248465563022e-21/${massKgAtom}/${sigmaMsq})
+variable        tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/${sigmaMsq})
+variable        tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/1.2278016e-19)
+variable        sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
+variable        pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ}))
+variable        pscale equal 1e-05/(${sigmaM3}/(${epsilonJ}))
+variable        pscale equal 1e-05/(4.3022168064e-29/(${epsilonJ}))
+variable        pscale equal 1e-05/(4.3022168064e-29/(1.6248465563022e-21))
+
+# variables
+# alat = lattice constant in Angs (at reduced density rhostar)
+# temp = reduced temperature for output
+# epair,emol,etotal = reduced epair,emol,etotal energies for output
+# press = reduced pressure for output
+
+variable        alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
+variable        temp equal temp/${tmpscale}
+variable        temp equal temp/117.7
+variable        epair equal epair/${epsilon}
+variable        epair equal epair/0.010142612711
+variable        emol equal emol/${epsilon}
+variable        emol equal emol/0.010142612711
+variable        etotal equal etotal/${epsilon}
+variable        etotal equal etotal/0.010142612711
+variable        press equal press/${pscale}
+variable        press equal press/377.676586146256
+
+# same script as in.ar.lj
+
+units		metal
+atom_style	atomic
+
+lattice		fcc ${alat}
+lattice		fcc 5.79518437579763
+Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000674009 secs
+mass		1 ${mass}
+mass		1 39.95
+
+velocity	all create $(v_tinitial*v_epskb) 12345
+velocity	all create 117.70000000000000284 12345
+
+pair_style	lj/cut $(v_cutoff*v_sigma)
+pair_style	lj/cut 8.7599999999999997868
+pair_coeff	1 1 ${epsilon} ${sigma}
+pair_coeff	1 1 0.010142612711 ${sigma}
+pair_coeff	1 1 0.010142612711 3.504
+
+neighbor	$(v_skin*v_sigma) bin
+neighbor	1.0511999999999999122 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	$(v_dt*v_tscale)
+timestep	0.011194658410003900315
+
+# columns 2,3,4 = temp,pe,press in metal units
+# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
+# need to include metal unit output to enable use of reduced variables
+
+thermo_style    custom step temp pe press v_temp v_epair v_emol v_etotal v_press
+thermo_modify	norm yes
+thermo		${nthermo}
+thermo		10
+
+run		${nsteps}
+run		100
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9.8112
+  ghost atom cutoff = 9.8112
+  binsize = 4.9056, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
+Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press 
+       0        117.7  -0.07203931   -1934.8523            1   -7.1026383            0   -5.6056383     -5.12304 
+      10    86.648851  -0.06811179   -1166.7855   0.73618395   -6.7154088            0   -5.6133414   -3.0893774 
+      20    42.107954 -0.062497536   -143.06615   0.35775662   -6.1618774            0   -5.6263157  -0.37880598 
+      30    55.484504 -0.064263032   -416.20245   0.47140615   -6.3359445            0   -5.6302495   -1.1020075 
+      40    54.538222 -0.064148334   -414.88071   0.46336637   -6.3246361            0   -5.6309766   -1.0985079 
+      50    57.367693 -0.064511259   -463.67683   0.48740606   -6.3604182            0   -5.6307714   -1.2277087 
+      60    59.828794 -0.064824938   -519.05997   0.50831601   -6.3913451            0    -5.630396   -1.3743504 
+      70    60.014616 -0.064848979   -533.07604   0.50989478   -6.3937154            0   -5.6304029   -1.4114617 
+      80     63.47861 -0.065285885   -622.71073   0.53932549   -6.4367917            0   -5.6294215   -1.6487936 
+      90    65.060881 -0.065484011   -664.99883   0.55276874   -6.4563257            0   -5.6288309   -1.7607627 
+     100    64.637033 -0.065427467   -653.00765   0.54916765   -6.4507508            0   -5.6286468   -1.7290128 
+Loop time of 0.0258265 on 4 procs for 100 steps with 500 atoms
+
+Performance: 3745.060 ns/day, 0.006 hours/ns, 3871.990 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0090213  | 0.012419   | 0.015494   |   2.1 | 48.09
+Neigh   | 0.0013709  | 0.0018765  | 0.0022483  |   0.7 |  7.27
+Comm    | 0.0071132  | 0.010597   | 0.014538   |   2.6 | 41.03
+Output  | 0.00039983 | 0.00042897 | 0.00049567 |   0.0 |  1.66
+Modify  | 0.00024104 | 0.00028801 | 0.00031543 |   0.0 |  1.12
+Other   |            | 0.0002173  |            |       |  0.84
+
+Nlocal:    125 ave 133 max 117 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    1099 ave 1107 max 1091 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:    4908.75 ave 5492 max 4644 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 19635
+Ave neighs/atom = 39.27
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/UNITS/log.ar.real.8Oct19.g++.1 b/examples/UNITS/log.ar.real.8Oct19.g++.1
new file mode 100644
index 0000000000..7c046ab965
--- /dev/null
+++ b/examples/UNITS/log.ar.real.8Oct19.g++.1
@@ -0,0 +1,197 @@
+LAMMPS (19 Sep 2019)
+# Ar in real units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon, sigma, mass set below
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# physical constants from update.cpp
+
+variable        kb index 0.0019872067         # kB in Kcal/mole/K
+variable        avogadro index 6.02214129e23  # Avogadro's number
+
+# Ar properties in real units
+
+variable        epskb index 117.7             # LJ epsilon/kB in degrees K
+variable        sigma index 3.504             # LJ sigma in Angstroms
+variable        epsilon equal ${epskb}*${kb}  # LJ epsilon in Kcal/mole
+variable        epsilon equal 117.7*${kb}  
+variable        epsilon equal 117.7*0.0019872067  
+variable        mass index 39.95              # mass in g/mole
+
+# scale factors
+
+# sigma = scale factor on distance, converts reduced distance to Angs
+# epsilon = scale factor on energy, converts reduced energy to Kcal/mole
+# tmpscale = scale factor on temperature, converts reduced temp to degrees K
+# tscale = scale factor on time, converts reduced time to fs
+#   formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
+#   use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds
+# pscale = scale factor on pressure, converts reduced pressure to atmospheres
+#   formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
+#   use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms
+
+variable        KcaltoJoule index 4.1868e3    # convert Kcals to Joules
+variable        NtMtoAtm equal 1.0/1.0135e5   # convert Nt/meter^2 to Atmospheres
+
+variable        tmpscale equal ${epskb}
+variable        tmpscale equal 117.7
+variable        epsJmole equal ${epsilon}*${KcaltoJoule}
+variable        epsJmole equal 0.23389422859*${KcaltoJoule}
+variable        epsJmole equal 0.23389422859*4.1868e3
+variable        massKgmole equal ${mass}/1000.0
+variable        massKgmole equal 39.95/1000.0
+variable        sigmaM equal ${sigma}/1.0e10
+variable        sigmaM equal 3.504/1.0e10
+variable        sigmaMsq equal ${sigmaM}*${sigmaM}
+variable        sigmaMsq equal 3.504e-10*${sigmaM}
+variable        sigmaMsq equal 3.504e-10*3.504e-10
+variable        tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
+variable        tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq})
+variable        tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq})
+variable        tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-19)
+variable        sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
+variable        pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
+variable        pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro}))
+variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro}))
+variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro}))
+variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23))
+
+# variables
+# alat = lattice constant in Angs (at reduced density rhostar)
+# temp = reduced temperature for output
+# epair,emol,etotal = reduced epair,emol,etotal energies for output
+# press = reduced pressure for output
+
+variable        alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
+variable        temp equal temp/${tmpscale}
+variable        temp equal temp/117.7
+variable        epair equal epair/${epsilon}
+variable        epair equal epair/0.23389422859
+variable        emol equal emol/${epsilon}
+variable        emol equal emol/0.23389422859
+variable        etotal equal etotal/${epsilon}
+variable        etotal equal etotal/0.23389422859
+variable        press equal press/${pscale}
+variable        press equal press/372.936366301003
+
+# same script as in.ar.lj
+
+units		real
+atom_style	atomic
+
+lattice		fcc ${alat}
+lattice		fcc 5.79518437579763
+Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000550985 secs
+mass		1 ${mass}
+mass		1 39.95
+
+velocity	all create $(v_tinitial*v_epskb) 12345
+velocity	all create 117.70000000000000284 12345
+
+pair_style	lj/cut $(v_cutoff*v_sigma)
+pair_style	lj/cut 8.7599999999999997868
+pair_coeff	1 1 ${epsilon} ${sigma}
+pair_coeff	1 1 0.23389422859 ${sigma}
+pair_coeff	1 1 0.23389422859 3.504
+
+neighbor	$(v_skin*v_sigma) bin
+neighbor	1.0511999999999999122 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	$(v_dt*v_tscale)
+timestep	11.190297512378050371
+
+# columns 2,3,4 = temp,pe,press in real units
+# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
+# need to include real unit output to enable use of reduced variables
+
+thermo_style    custom step temp pe press v_temp v_epair v_emol v_etotal v_press
+thermo_modify	norm yes
+thermo		${nthermo}
+thermo		10
+
+run		${nsteps}
+run		100
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9.8112
+  ghost atom cutoff = 9.8112
+  binsize = 4.9056, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes
+Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press 
+       0        117.7   -1.6612661   -1909.5509            1   -7.1026383            0   -5.6056383   -5.1203128 
+      10    87.369977   -1.5728967   -1169.6414   0.74231077   -6.7248204            0   -5.6135812   -3.1363029 
+      20    42.567295   -1.4427006   -150.87379   0.36165926   -6.1681752            0   -5.6267713  -0.40455638 
+      30    55.130978    -1.480902   -387.17817   0.46840253   -6.3315028            0   -5.6303042   -1.0381883 
+      40    55.054202   -1.4807485   -401.72653   0.46775023   -6.3308469            0   -5.6306248   -1.0771986 
+      50    56.873955   -1.4860029    -428.9126   0.48321117   -6.3533113            0   -5.6299442   -1.1500959 
+      60     58.33701    -1.490161   -458.23636   0.49564154   -6.3710892            0   -5.6291138   -1.2287253 
+      70     61.29671   -1.4991528   -539.72484   0.52078768   -6.4095331            0    -5.629914   -1.4472304 
+      80    63.214984    -1.504992   -594.34987   0.53708567   -6.4344983            0    -5.630481   -1.5937032 
+      90    61.936907   -1.5013008   -569.13985    0.5262269   -6.4187169            0   -5.6309552   -1.5261045 
+     100     62.20662   -1.5023046   -585.49121   0.52851844   -6.4230083            0   -5.6318162   -1.5699494 
+Loop time of 0.047307 on 1 procs for 100 steps with 500 atoms
+
+Performance: 2043.760 ns/day, 0.012 hours/ns, 2113.851 timesteps/s
+98.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.038646   | 0.038646   | 0.038646   |   0.0 | 81.69
+Neigh   | 0.0056832  | 0.0056832  | 0.0056832  |   0.0 | 12.01
+Comm    | 0.0015347  | 0.0015347  | 0.0015347  |   0.0 |  3.24
+Output  | 0.0003581  | 0.0003581  | 0.0003581  |   0.0 |  0.76
+Modify  | 0.00075364 | 0.00075364 | 0.00075364 |   0.0 |  1.59
+Other   |            | 0.0003314  |            |       |  0.70
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1946 ave 1946 max 1946 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    19572 ave 19572 max 19572 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19572
+Ave neighs/atom = 39.144
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/UNITS/log.ar.real.8Oct19.g++.4 b/examples/UNITS/log.ar.real.8Oct19.g++.4
new file mode 100644
index 0000000000..d5c01eb22d
--- /dev/null
+++ b/examples/UNITS/log.ar.real.8Oct19.g++.4
@@ -0,0 +1,197 @@
+LAMMPS (19 Sep 2019)
+# Ar in real units
+
+# simulation params in reduced units
+# settable from command line
+# epsilon, sigma, mass set below
+
+variable	x index 5
+variable	y index 5
+variable	z index 5
+variable        rhostar index 0.8842
+variable        dt index 0.005
+variable        cutoff index 2.5
+variable        skin index 0.3
+variable        tinitial index 1.0
+variable        nthermo index 10
+variable        nsteps index 100
+
+# physical constants from update.cpp
+
+variable        kb index 0.0019872067         # kB in Kcal/mole/K
+variable        avogadro index 6.02214129e23  # Avogadro's number
+
+# Ar properties in real units
+
+variable        epskb index 117.7             # LJ epsilon/kB in degrees K
+variable        sigma index 3.504             # LJ sigma in Angstroms
+variable        epsilon equal ${epskb}*${kb}  # LJ epsilon in Kcal/mole
+variable        epsilon equal 117.7*${kb}  
+variable        epsilon equal 117.7*0.0019872067  
+variable        mass index 39.95              # mass in g/mole
+
+# scale factors
+
+# sigma = scale factor on distance, converts reduced distance to Angs
+# epsilon = scale factor on energy, converts reduced energy to Kcal/mole
+# tmpscale = scale factor on temperature, converts reduced temp to degrees K
+# tscale = scale factor on time, converts reduced time to fs
+#   formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
+#   use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds
+# pscale = scale factor on pressure, converts reduced pressure to atmospheres
+#   formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
+#   use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms
+
+variable        KcaltoJoule index 4.1868e3    # convert Kcals to Joules
+variable        NtMtoAtm equal 1.0/1.0135e5   # convert Nt/meter^2 to Atmospheres
+
+variable        tmpscale equal ${epskb}
+variable        tmpscale equal 117.7
+variable        epsJmole equal ${epsilon}*${KcaltoJoule}
+variable        epsJmole equal 0.23389422859*${KcaltoJoule}
+variable        epsJmole equal 0.23389422859*4.1868e3
+variable        massKgmole equal ${mass}/1000.0
+variable        massKgmole equal 39.95/1000.0
+variable        sigmaM equal ${sigma}/1.0e10
+variable        sigmaM equal 3.504/1.0e10
+variable        sigmaMsq equal ${sigmaM}*${sigmaM}
+variable        sigmaMsq equal 3.504e-10*${sigmaM}
+variable        sigmaMsq equal 3.504e-10*3.504e-10
+variable        tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
+variable        tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq})
+variable        tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq})
+variable        tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-19)
+variable        sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
+variable        sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
+variable        pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
+variable        pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro}))
+variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro}))
+variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro}))
+variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23))
+
+# variables
+# alat = lattice constant in Angs (at reduced density rhostar)
+# temp = reduced temperature for output
+# epair,emol,etotal = reduced epair,emol,etotal energies for output
+# press = reduced pressure for output
+
+variable        alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
+variable        alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
+variable        temp equal temp/${tmpscale}
+variable        temp equal temp/117.7
+variable        epair equal epair/${epsilon}
+variable        epair equal epair/0.23389422859
+variable        emol equal emol/${epsilon}
+variable        emol equal emol/0.23389422859
+variable        etotal equal etotal/${epsilon}
+variable        etotal equal etotal/0.23389422859
+variable        press equal press/${pscale}
+variable        press equal press/372.936366301003
+
+# same script as in.ar.lj
+
+units		real
+atom_style	atomic
+
+lattice		fcc ${alat}
+lattice		fcc 5.79518437579763
+Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
+region		box block 0 $x 0 $y 0 $z
+region		box block 0 5 0 $y 0 $z
+region		box block 0 5 0 5 0 $z
+region		box block 0 5 0 5 0 5
+create_box	1 box
+Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+  create_atoms CPU = 0.000664949 secs
+mass		1 ${mass}
+mass		1 39.95
+
+velocity	all create $(v_tinitial*v_epskb) 12345
+velocity	all create 117.70000000000000284 12345
+
+pair_style	lj/cut $(v_cutoff*v_sigma)
+pair_style	lj/cut 8.7599999999999997868
+pair_coeff	1 1 ${epsilon} ${sigma}
+pair_coeff	1 1 0.23389422859 ${sigma}
+pair_coeff	1 1 0.23389422859 3.504
+
+neighbor	$(v_skin*v_sigma) bin
+neighbor	1.0511999999999999122 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+timestep	$(v_dt*v_tscale)
+timestep	11.190297512378050371
+
+# columns 2,3,4 = temp,pe,press in real units
+# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
+# need to include real unit output to enable use of reduced variables
+
+thermo_style    custom step temp pe press v_temp v_epair v_emol v_etotal v_press
+thermo_modify	norm yes
+thermo		${nthermo}
+thermo		10
+
+run		${nsteps}
+run		100
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9.8112
+  ghost atom cutoff = 9.8112
+  binsize = 4.9056, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
+Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press 
+       0        117.7   -1.6612661   -1909.5509            1   -7.1026383            0   -5.6056383   -5.1203128 
+      10    86.674156   -1.5707707   -1152.1077   0.73639895    -6.715731            0   -5.6133417   -3.0892877 
+      20    42.104452   -1.4412091   -141.16344   0.35772687   -6.1617986            0   -5.6262815  -0.37851883 
+      30    55.478223   -1.4819221   -410.58592   0.47135278   -6.3358644            0   -5.6302493   -1.1009544 
+      40     54.54231   -1.4793231   -409.58446    0.4634011   -6.3247524            0    -5.631041    -1.098269 
+      50    57.354168   -1.4876242   -457.34719   0.48729115   -6.3602431            0   -5.6307682   -1.2263411 
+      60    59.835295   -1.4949249   -512.38519   0.50837124    -6.391457            0   -5.6304252   -1.3739212 
+      70    60.005554   -1.4954174     -525.858   0.50981779   -6.3935625            0   -5.6303653   -1.4100475 
+      80    63.469566    -1.505493   -614.29111   0.53924865   -6.4366403            0   -5.6293851   -1.6471741 
+      90    65.064012   -1.5100983   -656.32951   0.55279535   -6.4563301            0   -5.6287955   -1.7598968 
+     100     64.63774   -1.5088033   -644.51211   0.54917366   -6.4507932            0   -5.6286803   -1.7282093 
+Loop time of 0.0285767 on 4 procs for 100 steps with 500 atoms
+
+Performance: 3383.318 ns/day, 0.007 hours/ns, 3499.350 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.012398   | 0.014826   | 0.016774   |   1.6 | 51.88
+Neigh   | 0.001797   | 0.0021547  | 0.0025899  |   0.6 |  7.54
+Comm    | 0.0079622  | 0.010444   | 0.013427   |   2.3 | 36.55
+Output  | 0.00042987 | 0.00047708 | 0.00059676 |   0.0 |  1.67
+Modify  | 0.00028896 | 0.00038844 | 0.00049448 |   0.0 |  1.36
+Other   |            | 0.0002864  |            |       |  1.00
+
+Nlocal:    125 ave 133 max 117 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    1099 ave 1107 max 1091 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:    4908.75 ave 5493 max 4644 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 19635
+Ave neighs/atom = 39.27
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README
index 8a9dc44359..49b7cd1f84 100644
--- a/examples/USER/cgdna/README
+++ b/examples/USER/cgdna/README
@@ -1,8 +1,12 @@
 This directory contains example data and input files 
-and utility scripts for the oxDNA coarse-grained model 
-for DNA.
+as well as utility scripts for the oxDNA/oxDNA2/oxRNA2 
+coarse-grained model of DNA and RNA.
+
+/******************************************************************************/
+
+/examples/oxDNA/duplex1:
+/examples/oxDNA2/duplex1:
 
-/examples/duplex1:
 Input, data and log files for a DNA duplex (double-stranded DNA) 
 consisiting of 5 base pairs. The duplex contains two strands with 
 complementary base pairs. The topology is
@@ -11,7 +15,14 @@ A - C - G - T - A
 |   |   |   |   |
 T - G - C - A - T     
 
-/examples/duplex2:
+Note that in this example the stacking and hydrogen-bonding interactions 
+are sequence-averaged (cf. keyword 'seqav' in according pair styles).
+
+/******************************************************************************/
+
+/examples/oxDNA/duplex2:
+/examples/oxDNA2/duplex2:
+
 Input, data and log files for a nicked DNA duplex (double-stranded DNA) 
 consisiting of 8 base pairs. The duplex contains strands with 
 complementary base pairs, but the backbone on one side is not continuous: 
@@ -22,16 +33,52 @@ A - C - G - T - A - C - G - T
 |   |   |   |   |   |   |   |
 T - G - C - A   T - G - C - A
 
-/examples/duplex3:
-This is basically the duplex1 run with sequence-dependent stacking
-and hydrogen-bonding strengths enabled and both nucleotide mass and 
-moment of inertia set to the value of the standalone implementation 
-of oxDNA (M = I = 1). To achieve this, the masses can be set directly 
-in the input and data file, whereas the moment of inertia is set via 
-the diameter of the ellipsoid in the data file and has a value of 3.16227766.
+Note that in this example the stacking and hydrogen-bonding interactions 
+are sequence-averaged (cf. keyword 'seqav' in according pair styles).
+
+/******************************************************************************/
+
+/examples/oxDNA2/duplex3:
+
+This example uses the duplex1 with sequence-dependent stacking and
+hydrogen-bonding interactions and both nucleotide mass and 
+moment of inertia set to the value used in the standalone implementation 
+of oxDNA (M = I = 1). The masses can be set directly in the input and 
+data file, whereas the moment of inertia is set via the diameter of the 
+ellipsoid in the data file and has a value of 3.16227766.
 The change of mass and moment of inertia allows direct comparision of 
-e.g. trajectory data, energies or time-dependent observables on a per-timestep 
-basis until numerical noise causes deviations at later simulation times. 
+trajectory data or time-dependent observables on a per-timestep basis. 
+
+As mentioned above, the stacking and hydrogen-bonding interactions 
+are sequence-dependent (cf. keyword 'seqdep' in according pair styles).
+
+/******************************************************************************/
+
+/examples/oxDNA2/unique_bp:
+
+This example uses atom types 1-8 to model a 13 base pair duplex.
+The nucleotide types are assigned as follows:
+A = 1,5; C = 2,6; G = 3,7; T = 4,8
+
+The topology is
+A   C   G   T   A   C   G   T   A   C   G   T   A
+1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 1 - 2 - 7 - 8 - 1
+|   |   |   |   |   |   |   |   |   |   |   |   |
+4 - 3 - 2 - 1 - 8 - 7 - 6 - 5 - 4 - 3 - 6 - 5 - 4
+T   G   C   A   T   G   C   A   T   G   C   A   T
+
+With a large (32 or 64) number of atom types quasi-unique base pairing 
+between two individual nucleotides can be established.
+
+/******************************************************************************/
+
+/examples/oxRNA2/duplex4
+
+This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or 
+oxDNA2 force field. Sequence-dependent stacking and hydrogen-bonding 
+strengths enabled (cf. keyword 'seqdep' in according pair styles).
+
+/******************************************************************************/
 
 /util:
 This directory contains a simple python setup tool which creates 
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 b/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
index 34e17380af..254c551f4e 100644
--- a/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
+++ b/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
@@ -31,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1
new file mode 100644
index 0000000000..3a4b84bffd
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1
@@ -0,0 +1,1166 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  10 atoms
+  reading velocities ...
+  10 velocities
+  10 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  8 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+  special bonds CPU = 9.5e-05 secs
+  read_data CPU = 0.001865 secs
+
+set atom * mass 3.1575
+  10 settings made for mass
+
+group all type 1 4
+10 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+fix 1 all nve/dot
+#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 1000000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.956
+  ghost atom cutoff = 1.956
+  binsize = 0.978, bins = 41 41 41
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
+Per MPI rank memory allocation (min/avg/max) = 2.836 | 2.836 | 2.836 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.4711818 0.0069384985   -1.4642433 2.5836586e-06 
+1000  ekin = 0.00113448721737003 |  erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
+2000  ekin = 0.00449927223902336 |  erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
+3000  ekin = 0.00997964450841065 |  erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
+4000  ekin = 0.0173888111295073 |  erot = 0.0643039804300224 | epot = -14.7241260365031 | etot = -14.6424332449436
+5000  ekin = 0.0264744514136619 |  erot = 0.0987844033142069 | epot = -14.7676920997383 | etot = -14.6424332450104
+6000  ekin = 0.0369277948556079 |  erot = 0.139336571052566 | epot = -14.8186976109956 | etot = -14.6424332450875
+7000  ekin = 0.04839505571915 |  erot = 0.185086295692081 | epot = -14.8759145965832 | etot = -14.642433245172
+8000  ekin = 0.0604909336920643 |  erot = 0.235071307523532 | epot = -14.9379954864767 | etot = -14.6424332452611
+9000  ekin = 0.0728137406440561 |  erot = 0.288273694501538 | epot = -15.003520680497 | etot = -14.6424332453514
+10000  ekin = 0.0849615563085878 |  erot = 0.343654369293473 | epot = -15.0710491710418 | etot = -14.6424332454398
+11000  ekin = 0.0965486715045649 |  erot = 0.400187932108223 | epot = -15.1391698491357 | etot = -14.6424332455229
+12000  ekin = 0.10722146628289 |  erot = 0.456896095459165 | epot = -15.20655080734 | etot = -14.642433245598
+13000  ekin = 0.116672809719548 |  erot = 0.512877765427643 | epot = -15.2719838208099 | etot = -14.6424332456627
+14000  ekin = 0.12465407373104 |  erot = 0.567333962045116 | epot = -15.3344212814913 | etot = -14.6424332457151
+15000  ekin = 0.13098393968427 |  erot = 0.619586028256667 | epot = -15.3930032136954 | etot = -14.6424332457544
+16000  ekin = 0.135553354544872 |  erot = 0.669086028489761 | epot = -15.447072628815 | etot = -14.6424332457804
+17000  ekin = 0.138326263958247 |  erot = 0.715418858085449 | epot = -15.4961783678372 | etot = -14.6424332457935
+18000  ekin = 0.139336096664052 |  erot = 0.758296324627745 | epot = -15.5400656670872 | etot = -14.6424332457954
+19000  ekin = 0.138678360045177 |  erot = 0.797544234275864 | epot = -15.5786558401088 | etot = -14.6424332457878
+20000  ekin = 0.136500074655373 |  erot = 0.83308420441103 | epot = -15.6120175248394 | etot = -14.642433245773
+21000  ekin = 0.132987065285671 |  erot = 0.864912408452581 | epot = -15.6403327194916 | etot = -14.6424332457533
+22000  ekin = 0.128350288213556 |  erot = 0.893077649557994 | epot = -15.6638611835027 | etot = -14.6424332457311
+23000  ekin = 0.122812385135508 |  erot = 0.917661024683965 | epot = -15.6829066555277 | etot = -14.6424332457083
+24000  ekin = 0.116595521408284 |  erot = 0.938759014332098 | epot = -15.6977877814267 | etot = -14.6424332456863
+25000  ekin = 0.109911323474816 |  erot = 0.956471207347239 | epot = -15.7088157764882 | etot = -14.6424332456662
+26000  ekin = 0.102953426207644 |  erot = 0.970893163953205 | epot = -15.7162798358091 | etot = -14.6424332456483
+27000  ekin = 0.0958928250746637 |  erot = 0.982114250194058 | epot = -15.7204403209013 | etot = -14.6424332456325
+28000  ekin = 0.0888759410950343 |  erot = 0.990219731539854 | epot = -15.7215289182535 | etot = -14.6424332456186
+29000  ekin = 0.0820250748773376 |  erot = 0.995296041202929 | epot = -15.719754361686 | etot = -14.6424332456058
+30000  ekin = 0.0754407616839748 |  erot = 0.997437949320997 | epot = -15.7153119565981 | etot = -14.6424332455932
+31000  ekin = 0.0692054432610605 |  erot = 0.996756332762286 | epot = -15.7083950216035 | etot = -14.6424332455802
+32000  ekin = 0.0633878377978472 |  erot = 0.993385345349225 | epot = -15.699206428713 | etot = -14.6424332455659
+33000  ekin = 0.0580474070871663 |  erot = 0.987487973309971 | epot = -15.6879686259471 | etot = -14.64243324555
+34000  ekin = 0.0532383791888181 |  erot = 0.979259192921751 | epot = -15.6749308176426 | etot = -14.642433245532
+35000  ekin = 0.0490128758307997 |  erot = 0.968926197407229 | epot = -15.66037231875 | etot = -14.642433245512
+36000  ekin = 0.0454228081410748 |  erot = 0.956745409625975 | epot = -15.6446014632576 | etot = -14.6424332454906
+37000  ekin = 0.0425203357176439 |  erot = 0.942996238000726 | epot = -15.6279498191869 | etot = -14.6424332454685
+38000  ekin = 0.0403568280949571 |  erot = 0.927971766616668 | epot = -15.6107618401582 | etot = -14.6424332454465
+39000  ekin = 0.0389804214212713 |  erot = 0.911966804110017 | epot = -15.5933804709572 | etot = -14.642433245426
+40000  ekin = 0.0384324238856427 |  erot = 0.895263959562923 | epot = -15.5761296288567 | etot = -14.6424332454081
+41000  ekin = 0.0387429860408528 |  erot = 0.878118672838279 | epot = -15.5592949042733 | etot = -14.6424332453942
+42000  ekin = 0.0399266053637511 |  erot = 0.860744395135508 | epot = -15.5431042458848 | etot = -14.6424332453855
+43000  ekin = 0.0419781561011213 |  erot = 0.843299365355989 | epot = -15.52771076684 | etot = -14.6424332453829
+44000  ekin = 0.0448701894086714 |  erot = 0.82587660331255 | epot = -15.5131800381078 | etot = -14.6424332453866
+45000  ekin = 0.0485521857411517 |  erot = 0.808498758184885 | epot = -15.4994841893228 | etot = -14.6424332453968
+46000  ekin = 0.0529522094031971 |  erot = 0.791119212186815 | epot = -15.4865046670025 | etot = -14.6424332454125
+47000  ekin = 0.0579809824236746 |  erot = 0.773630265882156 | epot = -15.4740444937379 | etot = -14.6424332454321
+48000  ekin = 0.0635377846493077 |  erot = 0.755878310836116 | epot = -15.4618493409392 | etot = -14.6424332454537
+49000  ekin = 0.069516912445729 |  erot = 0.737684732482671 | epot = -15.4496348904037 | etot = -14.6424332454753
+50000  ekin = 0.0758129058454751 |  erot = 0.718870126218106 | epot = -15.4371162775587 | etot = -14.6424332454952
+51000  ekin = 0.0823226638641914 |  erot = 0.699278599518873 | epot = -15.4240345088949 | etot = -14.6424332455118
+52000  ekin = 0.0889431481334987 |  erot = 0.678798807098492 | epot = -15.4101752007567 | etot = -14.6424332455248
+53000  ekin = 0.0955646689255783 |  erot = 0.657379086770007 | epot = -15.3953770012299 | etot = -14.6424332455343
+54000  ekin = 0.102061477509349 |  erot = 0.635035489168657 | epot = -15.3795302122191 | etot = -14.6424332455411
+55000  ekin = 0.108282960174 |  erot = 0.611853171347175 | epot = -15.362569377067 | etot = -14.6424332455459
+56000  ekin = 0.114049426281782 |  erot = 0.587982945924791 | epot = -15.344465617755 | etot = -14.6424332455484
+57000  ekin = 0.119155806186855 |  erot = 0.56363525592402 | epot = -15.3252243076595 | etot = -14.6424332455486
+58000  ekin = 0.123384552305435 |  erot = 0.539073355224031 | epot = -15.3048911530747 | etot = -14.6424332455452
+59000  ekin = 0.126526300954941 |  erot = 0.514606324860987 | epot = -15.2835658713528 | etot = -14.6424332455369
+60000  ekin = 0.128404399836503 |  erot = 0.490581338842511 | epot = -15.2614189842015 | etot = -14.6424332455224
+61000  ekin = 0.128898142362337 |  erot = 0.467373892403714 | epot = -15.2387052802675 | etot = -14.6424332455015
+62000  ekin = 0.127959880290302 |  erot = 0.445374820089113 | epot = -15.2157679458544 | etot = -14.6424332454749
+63000  ekin = 0.125622870624954 |  erot = 0.424973765390048 | epot = -15.1930298814588 | etot = -14.6424332454438
+64000  ekin = 0.121999044843202 |  erot = 0.406539918574853 | epot = -15.1709722088285 | etot = -14.6424332454104
+65000  ekin = 0.117268056619303 |  erot = 0.390401831022836 | epot = -15.1501031330193 | etot = -14.6424332453771
+66000  ekin = 0.111660385257243 |  erot = 0.376828594081003 | epot = -15.1309222246847 | etot = -14.6424332453465
+67000  ekin = 0.105437746905135 |  erot = 0.366014539812687 | epot = -15.1138855320383 | etot = -14.6424332453205
+68000  ekin = 0.0988737375607857 |  erot = 0.358069014156216 | epot = -15.0993759970176 | etot = -14.6424332453006
+69000  ekin = 0.0922368286502244 |  erot = 0.353011948772493 | epot = -15.0876820227105 | etot = -14.6424332452877
+70000  ekin = 0.0857769015274457 |  erot = 0.350775174164874 | epot = -15.0789853209744 | etot = -14.6424332452821
+71000  ekin = 0.0797156921642124 |  erot = 0.35120884424483 | epot = -15.0733577816925 | etot = -14.6424332452834
+72000  ekin = 0.0742409440406404 |  erot = 0.354092037745959 | epot = -15.0707662270775 | etot = -14.6424332452909
+73000  ekin = 0.069503749870144 |  erot = 0.359146526959529 | epot = -15.0710835221333 | etot = -14.6424332453037
+74000  ekin = 0.0656184497423043 |  erot = 0.36605276987658 | epot = -15.0741044649392 | etot = -14.6424332453203
+75000  ekin = 0.0626644690389273 |  erot = 0.37446729003154 | epot = -15.07956500441 | etot = -14.6424332453395
+76000  ekin = 0.0606895535086071 |  erot = 0.384040683400773 | epot = -15.0871634822692 | etot = -14.6424332453599
+77000  ekin = 0.0597139401235039 |  erot = 0.394435495890113 | epot = -15.0965826813933 | etot = -14.6424332453797
+78000  ekin = 0.0597350629869167 |  erot = 0.405343151479122 | epot = -15.1075114598641 | etot = -14.6424332453981
+79000  ekin = 0.0607324264355599 |  erot = 0.416499017639979 | epot = -15.1196646894891 | etot = -14.6424332454136
+80000  ekin = 0.0626722904949853 |  erot = 0.427694630236173 | epot = -15.1328001661567 | etot = -14.6424332454256
+81000  ekin = 0.0655118235328824 |  erot = 0.438786127846776 | epot = -15.1467311968131 | etot = -14.6424332454334
+82000  ekin = 0.0692024020835959 |  erot = 0.449698113828529 | epot = -15.1613337613492 | etot = -14.6424332454371
+83000  ekin = 0.0736917936906687 |  erot = 0.460422490739007 | epot = -15.1765475298665 | etot = -14.6424332454368
+84000  ekin = 0.0789250526546792 |  erot = 0.471012272293637 | epot = -15.1923705703818 | etot = -14.6424332454335
+85000  ekin = 0.0848440878750104 |  erot = 0.481570908649218 | epot = -15.2088482419521 | etot = -14.6424332454279
+86000  ekin = 0.0913860133254689 |  erot = 0.492238169205271 | epot = -15.226057427952 | etot = -14.6424332454213
+87000  ekin = 0.0984805441200107 |  erot = 0.503174014616583 | epot = -15.2440878041518 | etot = -14.6424332454152
+88000  ekin = 0.106046830304303 |  erot = 0.514542076496116 | epot = -15.2630221522109 | etot = -14.6424332454105
+89000  ekin = 0.113990204127989 |  erot = 0.526494309539271 | epot = -15.2829177590758 | etot = -14.6424332454086
+90000  ekin = 0.122199339151899 |  erot = 0.539158097285764 | epot = -15.3037906818476 | etot = -14.64243324541
+91000  ekin = 0.130544275971407 |  erot = 0.552626637865788 | epot = -15.3256041592523 | etot = -14.6424332454151
+92000  ekin = 0.138875666148818 |  erot = 0.566952900962214 | epot = -15.3482618125354 | etot = -14.6424332454244
+93000  ekin = 0.147025440614644 |  erot = 0.58214693373749 | epot = -15.3716056197896 | etot = -14.6424332454375
+94000  ekin = 0.154808946847823 |  erot = 0.598175891801268 | epot = -15.3954180841032 | etot = -14.6424332454541
+95000  ekin = 0.162028449602152 |  erot = 0.6149659424539 | epot = -15.4194276375298 | etot = -14.6424332454737
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+816000  ekin = 0.20100275104127 |  erot = 0.678586569749112 | epot = -15.5220225661217 | etot = -14.6424332453314
+817000  ekin = 0.182521261074943 |  erot = 0.639675603866084 | epot = -15.4646301101505 | etot = -14.6424332452094
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+819000  ekin = 0.150503789775692 |  erot = 0.563608719249991 | epot = -15.3565457540359 | etot = -14.6424332450102
+820000  ekin = 0.138078032174242 |  erot = 0.528474068972577 | epot = -15.308985346087 | etot = -14.6424332449401
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+822000  ekin = 0.122284066133886 |  erot = 0.467617125514411 | epot = -15.2323344365174 | etot = -14.6424332448691
+823000  ekin = 0.119278020922195 |  erot = 0.44266622847641 | epot = -15.2043774942678 | etot = -14.6424332448692
+824000  ekin = 0.119546158602377 |  erot = 0.42149068273525 | epot = -15.1834700862294 | etot = -14.6424332448917
+825000  ekin = 0.122931110514134 |  erot = 0.403904342219283 | epot = -15.1692686976682 | etot = -14.6424332449348
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+852000  ekin = 0.258829686440298 |  erot = 0.290257858698357 | epot = -15.1915207904045 | etot = -14.6424332452658
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+893000  ekin = 0.341522004916641 |  erot = 0.569344767729577 | epot = -15.55330001812 | etot = -14.6424332454737
+894000  ekin = 0.34011793412299 |  erot = 0.54258751991292 | epot = -15.5251386995396 | etot = -14.6424332455037
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+908000  ekin = 0.0775759855948257 |  erot = 0.0805066337401618 | epot = -14.800515863918 | etot = -14.642433244583
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+957000  ekin = 0.240343066496815 |  erot = 0.460233438090351 | epot = -15.3430097496926 | etot = -14.6424332451055
+958000  ekin = 0.253600493836713 |  erot = 0.428032849889673 | epot = -15.3240665888504 | etot = -14.642433245124
+959000  ekin = 0.26508043374484 |  erot = 0.400452005453744 | epot = -15.3079656843521 | etot = -14.6424332451535
+960000  ekin = 0.274268068126469 |  erot = 0.3776065494438 | epot = -15.2943078627599 | etot = -14.6424332451896
+961000  ekin = 0.280767177999005 |  erot = 0.359393861243336 | epot = -15.2825942844696 | etot = -14.6424332452273
+962000  ekin = 0.284346484058609 |  erot = 0.345524198810109 | epot = -15.2723039281299 | etot = -14.6424332452611
+963000  ekin = 0.284976816085041 |  erot = 0.335562232322697 | epot = -15.2629722936944 | etot = -14.6424332452867
+964000  ekin = 0.282852494243525 |  erot = 0.32897598649065 | epot = -15.2542617260345 | etot = -14.6424332453003
+965000  ekin = 0.278391086611735 |  erot = 0.325189577593081 | epot = -15.2460139095051 | etot = -14.6424332453002
+966000  ekin = 0.272207924676681 |  erot = 0.32363564014577 | epot = -15.2382768101091 | etot = -14.6424332452866
+967000  ekin = 0.265065367869008 |  erot = 0.323803079983236 | epot = -15.2313016931137 | etot = -14.6424332452614
+968000  ekin = 0.25780129371369 |  erot = 0.325275872287489 | epot = -15.2255104112296 | etot = -14.6424332452284
+969000  ekin = 0.251245661475409 |  erot = 0.327759142573897 | epot = -15.2214380492417 | etot = -14.6424332451924
+970000  ekin = 0.246137008995692 |  erot = 0.331089781179722 | epot = -15.2196600353337 | etot = -14.6424332451582
+971000  ekin = 0.243051319619915 |  erot = 0.335230325664632 | epot = -15.2207148904151 | etot = -14.6424332451306
+972000  ekin = 0.242353409643559 |  erot = 0.340246678804852 | epot = -15.2250333335614 | etot = -14.642433245113
+973000  ekin = 0.244176338167963 |  erot = 0.346272190711359 | epot = -15.2328817739871 | etot = -14.6424332451077
+974000  ekin = 0.248428661663719 |  erot = 0.353462430362792 | epot = -15.2443243371426 | etot = -14.6424332451161
+975000  ekin = 0.254824314808527 |  erot = 0.361946299431624 | epot = -15.2592038593783 | etot = -14.6424332451381
+976000  ekin = 0.262926848825399 |  erot = 0.371779749930863 | epot = -15.2771398439293 | etot = -14.6424332451731
+977000  ekin = 0.272199235334822 |  erot = 0.382908123264924 | epot = -15.2975406038191 | etot = -14.6424332452194
+978000  ekin = 0.282052066854486 |  erot = 0.395142048097982 | epot = -15.3196273602273 | etot = -14.6424332452748
+979000  ekin = 0.291885751915432 |  erot = 0.408150081471576 | epot = -15.3424690787237 | etot = -14.6424332453367
+980000  ekin = 0.301125083790032 |  erot = 0.421469125222411 | epot = -15.365027454414 | etot = -14.6424332454016
+981000  ekin = 0.309246535916151 |  erot = 0.434531423655712 | epot = -15.3862112050375 | etot = -14.6424332454657
+982000  ekin = 0.315799497488435 |  erot = 0.446704965615556 | epot = -15.4049377086287 | etot = -14.6424332455247
+983000  ekin = 0.320422573217695 |  erot = 0.457342632742344 | epot = -15.4201984515349 | etot = -14.6424332455749
+984000  ekin = 0.322855465254384 |  erot = 0.465834622597573 | epot = -15.4311233334643 | etot = -14.6424332456124
+985000  ekin = 0.322946302470594 |  erot = 0.471658590972097 | epot = -15.4370381390772 | etot = -14.6424332456345
+986000  ekin = 0.32065391780096 |  erot = 0.47442255658858 | epot = -15.437509720029 | etot = -14.6424332456394
+987000  ekin = 0.316044627357463 |  erot = 0.473896755513782 | epot = -15.432374628498 | etot = -14.6424332456268
+988000  ekin = 0.309283477264372 |  erot = 0.470032116943487 | epot = -15.421748839805 | etot = -14.6424332455972
+989000  ekin = 0.300620522165357 |  erot = 0.462964620620384 | epot = -15.4060183883382 | etot = -14.6424332455525
+990000  ekin = 0.290373280688083 |  erot = 0.453006262993474 | epot = -15.3858127891769 | etot = -14.6424332454953
+991000  ekin = 0.27890691570339 |  erot = 0.440624526217875 | epot = -15.3619646873503 | etot = -14.642433245429
+992000  ekin = 0.266613826413786 |  erot = 0.426413006889876 | epot = -15.3354600786606 | etot = -14.642433245357
+993000  ekin = 0.253894212446129 |  erot = 0.411056197523116 | epot = -15.3073836552521 | etot = -14.6424332452828
+994000  ekin = 0.241138837000641 |  erot = 0.3952913723868 | epot = -15.2788634545973 | etot = -14.6424332452098
+995000  ekin = 0.228714768908433 |  erot = 0.379870207853254 | epot = -15.2510182219026 | etot = -14.6424332451409
+996000  ekin = 0.216954417472708 |  erot = 0.365522282704992 | epot = -15.2249099452563 | etot = -14.6424332450786
+997000  ekin = 0.206147766459094 |  erot = 0.352922066135596 | epot = -15.2015030776196 | etot = -14.6424332450249
+998000  ekin = 0.196537413161582 |  erot = 0.342660495987547 | epot = -15.1816311541306 | etot = -14.6424332449815
+999000  ekin = 0.188315843917336 |  erot = 0.335221830001114 | epot = -15.1659709188676 | etot = -14.6424332449491
+1000000  ekin = 0.1816243230724 |  erot = 0.33096613964385 | epot = -15.155023707645 | etot = -14.6424332449287
+ 1000000  0.013453654   -1.5270261  0.011523695   -1.4973399 -8.4815516e-05 
+Loop time of 17.1797 on 1 procs for 1000000 steps with 10 atoms
+
+Performance: 50291.944 tau/day, 58208.268 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 13.871     | 13.871     | 13.871     |   0.0 | 80.74
+Bond    | 0.52454    | 0.52454    | 0.52454    |   0.0 |  3.05
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.14987    | 0.14987    | 0.14987    |   0.0 |  0.87
+Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
+Modify  | 2.4075     | 2.4075     | 2.4075     |   0.0 | 14.01
+Other   |            | 0.227      |            |       |  1.32
+
+Nlocal:    10 ave 10 max 10 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    45 ave 45 max 45 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 45
+Ave neighs/atom = 4.5
+Ave special neighs/atom = 3.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:17
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4
new file mode 100644
index 0000000000..4616a7453a
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4
@@ -0,0 +1,1166 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  10 atoms
+  reading velocities ...
+  10 velocities
+  10 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  8 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+  special bonds CPU = 0.000216 secs
+  read_data CPU = 0.003061 secs
+
+set atom * mass 3.1575
+  10 settings made for mass
+
+group all type 1 4
+10 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+fix 1 all nve/dot
+#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 1000000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.956
+  ghost atom cutoff = 1.956
+  binsize = 0.978, bins = 41 41 41
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
+Per MPI rank memory allocation (min/avg/max) = 7.33 | 7.512 | 7.694 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.4711818 0.0069384985   -1.4642433 2.5836586e-06 
+1000  ekin = 0.00113448721737009 |  erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
+2000  ekin = 0.00449927223902292 |  erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
+3000  ekin = 0.00997964450840756 |  erot = 0.0366523356056466 | epot = -14.6890652250033 | etot = -14.6424332448892
+4000  ekin = 0.017388811129498 |  erot = 0.0643039804300251 | epot = -14.7241260365031 | etot = -14.6424332449436
+5000  ekin = 0.0264744514136422 |  erot = 0.0987844033142134 | epot = -14.7676920997383 | etot = -14.6424332450104
+6000  ekin = 0.0369277948555727 |  erot = 0.13933657105258 | epot = -14.8186976109956 | etot = -14.6424332450875
+7000  ekin = 0.0483950557190949 |  erot = 0.185086295692109 | epot = -14.8759145965832 | etot = -14.642433245172
+8000  ekin = 0.0604909336919856 |  erot = 0.235071307523581 | epot = -14.9379954864767 | etot = -14.6424332452611
+9000  ekin = 0.0728137406439518 |  erot = 0.288273694501615 | epot = -15.003520680497 | etot = -14.6424332453514
+10000  ekin = 0.0849615563084574 |  erot = 0.343654369293589 | epot = -15.0710491710418 | etot = -14.6424332454398
+11000  ekin = 0.0965486715044103 |  erot = 0.400187932108393 | epot = -15.1391698491357 | etot = -14.6424332455229
+12000  ekin = 0.107221466282716 |  erot = 0.456896095459393 | epot = -15.2065508073401 | etot = -14.642433245598
+13000  ekin = 0.116672809719361 |  erot = 0.512877765427945 | epot = -15.27198382081 | etot = -14.6424332456627
+14000  ekin = 0.124654073730849 |  erot = 0.567333962045501 | epot = -15.3344212814915 | etot = -14.6424332457151
+15000  ekin = 0.130983939684084 |  erot = 0.619586028257145 | epot = -15.3930032136957 | etot = -14.6424332457544
+16000  ekin = 0.135553354544703 |  erot = 0.66908602849033 | epot = -15.4470726288154 | etot = -14.6424332457804
+17000  ekin = 0.138326263958104 |  erot = 0.715418858086098 | epot = -15.4961783678378 | etot = -14.6424332457936
+18000  ekin = 0.139336096663942 |  erot = 0.758296324628463 | epot = -15.5400656670878 | etot = -14.6424332457954
+19000  ekin = 0.138678360045107 |  erot = 0.797544234276633 | epot = -15.5786558401095 | etot = -14.6424332457878
+20000  ekin = 0.136500074655344 |  erot = 0.833084204411832 | epot = -15.6120175248401 | etot = -14.642433245773
+21000  ekin = 0.13298706528568 |  erot = 0.864912408453387 | epot = -15.6403327194924 | etot = -14.6424332457533
+22000  ekin = 0.128350288213599 |  erot = 0.893077649558743 | epot = -15.6638611835035 | etot = -14.6424332457311
+23000  ekin = 0.122812385135574 |  erot = 0.917661024684626 | epot = -15.6829066555285 | etot = -14.6424332457083
+24000  ekin = 0.116595521408358 |  erot = 0.938759014332623 | epot = -15.6977877814273 | etot = -14.6424332456863
+25000  ekin = 0.109911323474882 |  erot = 0.956471207347589 | epot = -15.7088157764886 | etot = -14.6424332456661
+26000  ekin = 0.102953426207684 |  erot = 0.970893163953319 | epot = -15.7162798358093 | etot = -14.6424332456483
+27000  ekin = 0.0958928250746599 |  erot = 0.982114250193934 | epot = -15.7204403209012 | etot = -14.6424332456326
+28000  ekin = 0.0888759410949697 |  erot = 0.990219731539457 | epot = -15.721528918253 | etot = -14.6424332456186
+29000  ekin = 0.0820250748771988 |  erot = 0.995296041202221 | epot = -15.7197543616852 | etot = -14.6424332456058
+30000  ekin = 0.0754407616837521 |  erot = 0.997437949319969 | epot = -15.7153119565969 | etot = -14.6424332455932
+31000  ekin = 0.0692054432607507 |  erot = 0.996756332760959 | epot = -15.708395021602 | etot = -14.6424332455803
+32000  ekin = 0.0633878377974527 |  erot = 0.993385345347641 | epot = -15.6992064287111 | etot = -14.642433245566
+33000  ekin = 0.0580474070866972 |  erot = 0.987487973308198 | epot = -15.6879686259451 | etot = -14.6424332455502
+34000  ekin = 0.0532383791882911 |  erot = 0.979259192919845 | epot = -15.6749308176403 | etot = -14.6424332455322
+35000  ekin = 0.0490128758302368 |  erot = 0.968926197405304 | epot = -15.6603723187477 | etot = -14.6424332455122
+36000  ekin = 0.0454228081405029 |  erot = 0.9567454096241 | epot = -15.6446014632554 | etot = -14.6424332454908
+37000  ekin = 0.0425203357170925 |  erot = 0.942996237999004 | epot = -15.6279498191848 | etot = -14.6424332454687
+38000  ekin = 0.0403568280944576 |  erot = 0.927971766615168 | epot = -15.6107618401563 | etot = -14.6424332454467
+39000  ekin = 0.0389804214208548 |  erot = 0.911966804108811 | epot = -15.5933804709558 | etot = -14.6424332454262
+40000  ekin = 0.0384324238853382 |  erot = 0.89526395956208 | epot = -15.5761296288558 | etot = -14.6424332454084
+41000  ekin = 0.038742986040685 |  erot = 0.878118672837852 | epot = -15.559294904273 | etot = -14.6424332453944
+42000  ekin = 0.0399266053637394 |  erot = 0.860744395135542 | epot = -15.543104245885 | etot = -14.6424332453857
+43000  ekin = 0.0419781561012778 |  erot = 0.843299365356476 | epot = -15.5277107668409 | etot = -14.6424332453831
+44000  ekin = 0.044870189409001 |  erot = 0.825876603313475 | epot = -15.5131800381094 | etot = -14.6424332453869
+45000  ekin = 0.0485521857416515 |  erot = 0.808498758186206 | epot = -15.4994841893249 | etot = -14.642433245397
+46000  ekin = 0.0529522094038557 |  erot = 0.791119212188469 | epot = -15.486504667005 | etot = -14.6424332454127
+47000  ekin = 0.0579809824244727 |  erot = 0.773630265884061 | epot = -15.4740444937409 | etot = -14.6424332454323
+48000  ekin = 0.063537784650219 |  erot = 0.755878310838164 | epot = -15.4618493409424 | etot = -14.642433245454
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+52000  ekin = 0.0889431481345008 |  erot = 0.678798807099979 | epot = -15.4101752007595 | etot = -14.642433245525
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+911000  ekin = 0.0501789452889314 |  erot = 0.0600446989611976 | epot = -14.7526568886895 | etot = -14.6424332444394
+912000  ekin = 0.0567846925720761 |  erot = 0.0657906450222932 | epot = -14.7650085820985 | etot = -14.6424332445042
+913000  ekin = 0.0706603747930264 |  erot = 0.0774445361866898 | epot = -14.7905381555969 | etot = -14.6424332446172
+914000  ekin = 0.0905398584091763 |  erot = 0.0944735694303653 | epot = -14.8274466726047 | etot = -14.6424332447652
+915000  ekin = 0.114756144628428 |  erot = 0.116178630207615 | epot = -14.8733680197682 | etot = -14.6424332449321
+916000  ekin = 0.141447043402292 |  erot = 0.141736093139118 | epot = -14.9256163816431 | etot = -14.6424332451017
+917000  ekin = 0.168758535419861 |  erot = 0.170247440488538 | epot = -14.9814392211683 | etot = -14.6424332452599
+918000  ekin = 0.195014913439662 |  erot = 0.200793639368136 | epot = -15.0382417982035 | etot = -14.6424332453957
+919000  ekin = 0.218837422083706 |  erot = 0.232490666335444 | epot = -15.0937613339213 | etot = -14.6424332455022
+920000  ekin = 0.239206641023781 |  erot = 0.264542267091206 | epot = -15.1461821536913 | etot = -14.6424332455763
+921000  ekin = 0.255474577148722 |  erot = 0.29628605080145 | epot = -15.1941938735681 | etot = -14.6424332456179
+922000  ekin = 0.26733863121584 |  erot = 0.327229363204498 | epot = -15.2370012400495 | etot = -14.6424332456292
+923000  ekin = 0.274791412214288 |  erot = 0.357072039936907 | epot = -15.2742966977651 | etot = -14.6424332456139
+924000  ekin = 0.278059017516471 |  erot = 0.385714059432095 | epot = -15.3062063225254 | etot = -14.6424332455768
+925000  ekin = 0.277537405168489 |  erot = 0.413247220094928 | epot = -15.3332178707869 | etot = -14.6424332455235
+926000  ekin = 0.273733135238468 |  erot = 0.439931173660914 | epot = -15.3560975543588 | etot = -14.6424332454594
+927000  ekin = 0.26721185964169 |  erot = 0.466155363881716 | epot = -15.3758004689138 | etot = -14.6424332453904
+928000  ekin = 0.258555847536273 |  erot = 0.492389553502083 | epot = -15.3933786463605 | etot = -14.6424332453221
+929000  ekin = 0.248330567892114 |  erot = 0.519126582981251 | epot = -15.4098903961332 | etot = -14.6424332452599
+930000  ekin = 0.237059747166417 |  erot = 0.546821711631313 | epot = -15.4263147040061 | etot = -14.6424332452084
+931000  ekin = 0.225208144806099 |  erot = 0.575833282923054 | epot = -15.4434746729006 | etot = -14.6424332451714
+932000  ekin = 0.213171319366128 |  erot = 0.606369490851291 | epot = -15.4619740553693 | etot = -14.6424332451519
+933000  ekin = 0.201271722996209 |  erot = 0.638445690378466 | epot = -15.482150658526 | etot = -14.6424332451513
+934000  ekin = 0.189760460110485 |  erot = 0.671856006698808 | epot = -15.5040497119792 | etot = -14.6424332451699
+935000  ekin = 0.178823941838717 |  erot = 0.706161996587126 | epot = -15.5274191836321 | etot = -14.6424332452063
+936000  ekin = 0.168594479115294 |  erot = 0.740699865837039 | epot = -15.5517275902103 | etot = -14.6424332452579
+937000  ekin = 0.159163635635195 |  erot = 0.774606336205919 | epot = -15.5762032171622 | etot = -14.6424332453211
+938000  ekin = 0.150596971915171 |  erot = 0.806861786796075 | epot = -15.5998920041023 | etot = -14.6424332453911
+939000  ekin = 0.142948711632666 |  erot = 0.836347883526529 | epot = -15.6217298406219 | etot = -14.6424332454627
+940000  ekin = 0.136274889171384 |  erot = 0.861915676028721 | epot = -15.6406238107305 | etot = -14.6424332455304
+941000  ekin = 0.130643703199134 |  erot = 0.882459199120404 | epot = -15.6555361479088 | etot = -14.6424332455893
+942000  ekin = 0.126142088160929 |  erot = 0.896989065172066 | epot = -15.6655643989677 | etot = -14.6424332456347
+943000  ekin = 0.122877886110378 |  erot = 0.904700444358843 | epot = -15.6700115761325 | etot = -14.6424332456633
+944000  ekin = 0.12097740741224 |  erot = 0.905030230236918 | epot = -15.6684408833219 | etot = -14.6424332456728
+945000  ekin = 0.120578563690818 |  erot = 0.897699054745715 | epot = -15.660710864099 | etot = -14.6424332456625
+946000  ekin = 0.121820103593603 |  erot = 0.882735070928584 | epot = -15.6469884201552 | etot = -14.642433245633
+947000  ekin = 0.124827761129181 |  erot = 0.860477935596529 | epot = -15.6277389423121 | etot = -14.6424332455864
+948000  ekin = 0.129698334168747 |  erot = 0.831563037038142 | epot = -15.6036946167331 | etot = -14.6424332455262
+949000  ekin = 0.136482857558223 |  erot = 0.796887554722467 | epot = -15.5758036577371 | etot = -14.6424332454564
+950000  ekin = 0.145170138931244 |  erot = 0.757561255988665 | epot = -15.545164640302 | etot = -14.6424332453821
+951000  ekin = 0.155672002995198 |  erot = 0.714845916094193 | epot = -15.5129511643977 | etot = -14.6424332453083
+952000  ekin = 0.167811650836288 |  erot = 0.670087833250747 | epot = -15.4803327293271 | etot = -14.64243324524
+953000  ekin = 0.181316579471282 |  erot = 0.62464809521251 | epot = -15.4483979198655 | etot = -14.6424332451817
+954000  ekin = 0.195817500701168 |  erot = 0.579835080696309 | epot = -15.4180858265343 | etot = -14.6424332451368
+955000  ekin = 0.210854606876659 |  erot = 0.536843219769282 | epot = -15.3901310717537 | etot = -14.6424332451077
+956000  ekin = 0.225892299837258 |  erot = 0.49670137679197 | epot = -15.3650269217247 | etot = -14.6424332450955
+957000  ekin = 0.240343066498473 |  erot = 0.460233438094331 | epot = -15.3430097496925 | etot = -14.6424332450997
+958000  ekin = 0.253600493839208 |  erot = 0.428032849894538 | epot = -15.324066588852 | etot = -14.6424332451182
+959000  ekin = 0.26508043374811 |  erot = 0.400452005459373 | epot = -15.3079656843552 | etot = -14.6424332451478
+960000  ekin = 0.274268068130398 |  erot = 0.377606549450015 | epot = -15.2943078627643 | etot = -14.6424332451839
+961000  ekin = 0.280767178003419 |  erot = 0.359393861249926 | epot = -15.2825942844748 | etot = -14.6424332452215
+962000  ekin = 0.284346484063279 |  erot = 0.345524198816832 | epot = -15.2723039281355 | etot = -14.6424332452554
+963000  ekin = 0.284976816089691 |  erot = 0.3355622323293 | epot = -15.2629722936999 | etot = -14.6424332452809
+964000  ekin = 0.282852494247854 |  erot = 0.328975986496892 | epot = -15.2542617260392 | etot = -14.6424332452945
+965000  ekin = 0.278391086615428 |  erot = 0.325189577598743 | epot = -15.2460139095086 | etot = -14.6424332452944
+966000  ekin = 0.272207924679439 |  erot = 0.323635640150665 | epot = -15.2382768101109 | etot = -14.6424332452808
+967000  ekin = 0.265065367870575 |  erot = 0.323803079987219 | epot = -15.2313016931133 | etot = -14.6424332452555
+968000  ekin = 0.257801293713888 |  erot = 0.325275872290492 | epot = -15.2255104112269 | etot = -14.6424332452225
+969000  ekin = 0.251245661474162 |  erot = 0.327759142575902 | epot = -15.2214380492365 | etot = -14.6424332451864
+970000  ekin = 0.24613700899304 |  erot = 0.331089781180773 | epot = -15.2196600353261 | etot = -14.6424332451523
+971000  ekin = 0.243051319616021 |  erot = 0.335230325664833 | epot = -15.2207148904054 | etot = -14.6424332451246
+972000  ekin = 0.242353409638695 |  erot = 0.340246678804358 | epot = -15.22503333355 | etot = -14.6424332451069
+973000  ekin = 0.244176338162489 |  erot = 0.346272190710356 | epot = -15.2328817739745 | etot = -14.6424332451017
+974000  ekin = 0.248428661658042 |  erot = 0.353462430361478 | epot = -15.2443243371296 | etot = -14.6424332451101
+975000  ekin = 0.254824314803068 |  erot = 0.361946299430202 | epot = -15.2592038593654 | etot = -14.6424332451321
+976000  ekin = 0.262926848820545 |  erot = 0.371779749929518 | epot = -15.2771398439171 | etot = -14.642433245167
+977000  ekin = 0.27219923533091 |  erot = 0.382908123263806 | epot = -15.297540603808 | etot = -14.6424332452133
+978000  ekin = 0.282052066851764 |  erot = 0.395142048097211 | epot = -15.3196273602177 | etot = -14.6424332452688
+979000  ekin = 0.291885751914043 |  erot = 0.408150081471225 | epot = -15.3424690787159 | etot = -14.6424332453306
+980000  ekin = 0.301125083790016 |  erot = 0.421469125222495 | epot = -15.365027454408 | etot = -14.6424332453955
+981000  ekin = 0.309246535917451 |  erot = 0.434531423656212 | epot = -15.3862112050333 | etot = -14.6424332454596
+982000  ekin = 0.315799497490911 |  erot = 0.446704965616411 | epot = -15.404937708626 | etot = -14.6424332455187
+983000  ekin = 0.32042257322114 |  erot = 0.457342632743475 | epot = -15.4201984515335 | etot = -14.6424332455688
+984000  ekin = 0.322855465258551 |  erot = 0.465834622598882 | epot = -15.4311233334638 | etot = -14.6424332456063
+985000  ekin = 0.322946302475207 |  erot = 0.47165859097348 | epot = -15.4370381390771 | etot = -14.6424332456284
+986000  ekin = 0.320653917805744 |  erot = 0.474422556589946 | epot = -15.4375097200291 | etot = -14.6424332456334
+987000  ekin = 0.316044627362153 |  erot = 0.473896755515053 | epot = -15.4323746284979 | etot = -14.6424332456207
+988000  ekin = 0.309283477268727 |  erot = 0.470032116944613 | epot = -15.4217488398044 | etot = -14.6424332455911
+989000  ekin = 0.300620522169168 |  erot = 0.462964620621354 | epot = -15.4060183883369 | etot = -14.6424332455464
+990000  ekin = 0.290373280691188 |  erot = 0.453006262994313 | epot = -15.3858127891748 | etot = -14.6424332454893
+991000  ekin = 0.278906915705663 |  erot = 0.440624526218637 | epot = -15.3619646873472 | etot = -14.6424332454229
+992000  ekin = 0.266613826415146 |  erot = 0.426413006890641 | epot = -15.3354600786566 | etot = -14.6424332453509
+993000  ekin = 0.253894212446534 |  erot = 0.411056197524004 | epot = -15.3073836552473 | etot = -14.6424332452767
+994000  ekin = 0.24113883700009 |  erot = 0.395291372387941 | epot = -15.2788634545917 | etot = -14.6424332452037
+995000  ekin = 0.22871476890696 |  erot = 0.379870207854789 | epot = -15.2510182218965 | etot = -14.6424332451348
+996000  ekin = 0.216954417470376 |  erot = 0.365522282707067 | epot = -15.2249099452499 | etot = -14.6424332450725
+997000  ekin = 0.206147766455999 |  erot = 0.352922066138332 | epot = -15.2015030776131 | etot = -14.6424332450188
+998000  ekin = 0.196537413157836 |  erot = 0.342660495991062 | epot = -15.1816311541242 | etot = -14.6424332449753
+999000  ekin = 0.18831584391307 |  erot = 0.335221830005501 | epot = -15.1659709188615 | etot = -14.642433244943
+1000000  ekin = 0.181624323067755 |  erot = 0.330966139649165 | epot = -15.1550237076395 | etot = -14.6424332449226
+ 1000000  0.013453654   -1.5270261  0.011523695   -1.4973399 -8.4815516e-05 
+Loop time of 18.6281 on 4 procs for 1000000 steps with 10 atoms
+
+Performance: 46381.610 tau/day, 53682.419 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.50691    | 7.0285     | 12.641     | 197.6 | 37.73
+Bond    | 0.081876   | 0.27627    | 0.44175    |  28.5 |  1.48
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.7692     | 2.0629     | 2.3468     |  17.0 | 11.07
+Output  | 1.8e-05    | 2.625e-05  | 3e-05      |   0.0 |  0.00
+Modify  | 0.17309    | 0.88362    | 1.5352     |  58.4 |  4.74
+Other   |            | 8.377      |            |       | 44.97
+
+Nlocal:    2.5 ave 5 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    7.5 ave 10 max 5 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs:    18.5 ave 35 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+
+Total # of neighbors = 74
+Ave neighs/atom = 7.4
+Ave special neighs/atom = 3.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:18
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1
deleted file mode 100644
index 8b1c5c3807..0000000000
--- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1
+++ /dev/null
@@ -1,1165 +0,0 @@
-LAMMPS (18 Jun 2019)
-variable number	equal 1
-variable ofreq	equal 1000
-variable efreq	equal 1000
-variable T      equal 0.1
-
-units lj
-
-dimension 3
-
-newton off
-
-boundary  p p p
-
-atom_style hybrid bond ellipsoid
-atom_modify sort 0 1.0
-
-# Pair interactions require lists of neighbours to be calculated
-neighbor 1.0 bin
-neigh_modify every 1 delay 0 check yes
-
-read_data data.duplex1
-  orthogonal box = (-20 -20 -20) to (20 20 20)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  10 atoms
-  reading velocities ...
-  10 velocities
-  10 ellipsoids
-  scanning bonds ...
-  2 = max bonds/atom
-  reading bonds ...
-  8 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of 1-3 neighbors
-  2 = max # of 1-4 neighbors
-  4 = max # of special neighbors
-  special bonds CPU = 5e-05 secs
-  read_data CPU = 0.001522 secs
-
-set atom * mass 3.1575
-  10 settings made for mass
-
-group all type 1 4
-10 atoms in group all
-
-# oxDNA bond interactions - FENE backbone
-bond_style oxdna/fene
-bond_coeff * 2.0 0.25 0.7525
-
-# oxDNA pair interactions
-pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
-pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
-
-# NVE ensemble
-fix 1 all nve/dot
-#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
-#fix 1 all nve/asphere
-#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
-
-timestep 1e-5
-
-#comm_style tiled
-#fix 3 all balance 10000 1.1 rcb
-
-#compute mol all chunk/atom molecule
-#compute mychunk all vcm/chunk mol
-#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
-
-#dump pos all xyz ${ofreq} traj.${number}.xyz
-
-#compute quat all property/atom quatw quati quatj quatk
-#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
-#dump_modify quat sort id
-#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
-
-compute erot all erotate/asphere
-compute ekin all ke
-compute epot all pe
-variable erot equal c_erot
-variable ekin equal c_ekin
-variable epot equal c_epot
-variable etot equal c_erot+c_ekin+c_epot
-fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-
-#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
-#dump_modify out sort id
-#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
-
-run 1000000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.92828
-  ghost atom cutoff = 1.92828
-  binsize = 0.964142, bins = 42 42 42
-  5 neighbor lists, perpetual/occasional/extra = 5 0 0
-  (1) pair oxdna/excv, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-  (2) pair oxdna/stk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (3) pair oxdna/hbond, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (4) pair oxdna/xstk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) pair oxdna/coaxstk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -1.4711818 0.0069384985   -1.4642433 2.5836586e-06 
-1000  ekin = 0.00113448721737003 |  erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
-2000  ekin = 0.00449927223902336 |  erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
-3000  ekin = 0.00997964450841065 |  erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
-4000  ekin = 0.0173888111295073 |  erot = 0.0643039804300224 | epot = -14.7241260365031 | etot = -14.6424332449436
-5000  ekin = 0.0264744514136619 |  erot = 0.0987844033142069 | epot = -14.7676920997383 | etot = -14.6424332450104
-6000  ekin = 0.0369277948556079 |  erot = 0.139336571052566 | epot = -14.8186976109956 | etot = -14.6424332450875
-7000  ekin = 0.04839505571915 |  erot = 0.185086295692081 | epot = -14.8759145965832 | etot = -14.642433245172
-8000  ekin = 0.0604909336920643 |  erot = 0.235071307523532 | epot = -14.9379954864767 | etot = -14.6424332452611
-9000  ekin = 0.0728137406440561 |  erot = 0.288273694501538 | epot = -15.003520680497 | etot = -14.6424332453514
-10000  ekin = 0.0849615563085878 |  erot = 0.343654369293473 | epot = -15.0710491710418 | etot = -14.6424332454398
-11000  ekin = 0.0965486715045649 |  erot = 0.400187932108223 | epot = -15.1391698491357 | etot = -14.6424332455229
-12000  ekin = 0.10722146628289 |  erot = 0.456896095459165 | epot = -15.20655080734 | etot = -14.642433245598
-13000  ekin = 0.116672809719548 |  erot = 0.512877765427643 | epot = -15.2719838208099 | etot = -14.6424332456627
-14000  ekin = 0.12465407373104 |  erot = 0.567333962045116 | epot = -15.3344212814913 | etot = -14.6424332457151
-15000  ekin = 0.13098393968427 |  erot = 0.619586028256667 | epot = -15.3930032136954 | etot = -14.6424332457544
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-17000  ekin = 0.138326263958247 |  erot = 0.715418858085449 | epot = -15.4961783678372 | etot = -14.6424332457935
-18000  ekin = 0.139336096664052 |  erot = 0.758296324627745 | epot = -15.5400656670872 | etot = -14.6424332457954
-19000  ekin = 0.138678360045177 |  erot = 0.797544234275864 | epot = -15.5786558401088 | etot = -14.6424332457878
-20000  ekin = 0.136500074655373 |  erot = 0.83308420441103 | epot = -15.6120175248394 | etot = -14.642433245773
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-22000  ekin = 0.128350288213556 |  erot = 0.893077649557994 | epot = -15.6638611835027 | etot = -14.6424332457311
-23000  ekin = 0.122812385135508 |  erot = 0.917661024683964 | epot = -15.6829066555277 | etot = -14.6424332457083
-24000  ekin = 0.116595521408284 |  erot = 0.938759014332096 | epot = -15.6977877814267 | etot = -14.6424332456863
-25000  ekin = 0.109911323474816 |  erot = 0.956471207347236 | epot = -15.7088157764882 | etot = -14.6424332456662
-26000  ekin = 0.102953426207644 |  erot = 0.970893163953198 | epot = -15.7162798358091 | etot = -14.6424332456483
-27000  ekin = 0.0958928250746637 |  erot = 0.982114250194049 | epot = -15.7204403209013 | etot = -14.6424332456326
-28000  ekin = 0.0888759410950343 |  erot = 0.990219731539835 | epot = -15.7215289182535 | etot = -14.6424332456186
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-39000  ekin = 0.0389804214212708 |  erot = 0.911966804110001 | epot = -15.5933804709572 | etot = -14.642433245426
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-100000  ekin = 0.182480533643598 |  erot = 0.705250413407778 | epot = -15.5301641926495 | etot = -14.6424332455981
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-725000  ekin = 0.295155116710332 |  erot = 0.659377522493187 | epot = -15.5969658852808 | etot = -14.6424332460772
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-744000  ekin = 0.225100508722008 |  erot = 0.557126762307225 | epot = -15.4246605168831 | etot = -14.6424332458539
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-746000  ekin = 0.23707991346408 |  erot = 0.558614810498058 | epot = -15.4381279697723 | etot = -14.6424332458102
-747000  ekin = 0.236308652983949 |  erot = 0.556125790081372 | epot = -15.4348676888016 | etot = -14.6424332457363
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-750000  ekin = 0.215574369391403 |  erot = 0.540486233484167 | epot = -15.3984938482956 | etot = -14.64243324542
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-752000  ekin = 0.196313335741561 |  erot = 0.52919581521731 | epot = -15.3679423961964 | etot = -14.6424332452375
-753000  ekin = 0.187866475787076 |  erot = 0.524881252730185 | epot = -15.3551809736995 | etot = -14.6424332451822
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-757000  ekin = 0.173693190270073 |  erot = 0.518265706177119 | epot = -15.3343921417132 | etot = -14.642433245266
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-794000  ekin = 0.152510350035351 |  erot = 0.545660777312736 | epot = -15.3406043723442 | etot = -14.6424332449961
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-829000  ekin = 0.160453205764727 |  erot = 0.359651737503703 | epot = -15.1625381885089 | etot = -14.6424332452404
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-864000  ekin = 0.239677655585439 |  erot = 0.530065823506495 | epot = -15.412176724455 | etot = -14.642433245363
-865000  ekin = 0.23132088944446 |  erot = 0.541610953536998 | epot = -15.4153650882816 | etot = -14.6424332453002
-866000  ekin = 0.223481813673878 |  erot = 0.552927233334005 | epot = -15.41884229225 | etot = -14.6424332452421
-867000  ekin = 0.216679174488124 |  erot = 0.564346499433549 | epot = -15.4234589191144 | etot = -14.6424332451927
-868000  ekin = 0.211369750013082 |  erot = 0.576136138939065 | epot = -15.4299391341069 | etot = -14.6424332451547
-869000  ekin = 0.207923502302006 |  erot = 0.588478941150607 | epot = -15.4388356885827 | etot = -14.64243324513
-870000  ekin = 0.206606152993159 |  erot = 0.601459626888393 | epot = -15.4504990250012 | etot = -14.6424332451197
-871000  ekin = 0.207568796750574 |  erot = 0.615058451102447 | epot = -15.4650604929769 | etot = -14.6424332451239
-872000  ekin = 0.210843969893514 |  erot = 0.629151875755212 | epot = -15.4824290907906 | etot = -14.6424332451419
-873000  ekin = 0.216347593110671 |  erot = 0.643519970828197 | epot = -15.5023008091114 | etot = -14.6424332451726
-874000  ekin = 0.223886305134761 |  erot = 0.65785990972427 | epot = -15.5241794600729 | etot = -14.6424332452139
-875000  ekin = 0.233169807544781 |  erot = 0.671804662203727 | epot = -15.5474077150118 | etot = -14.6424332452633
-876000  ekin = 0.243827877955837 |  erot = 0.684945735792129 | epot = -15.5712068590658 | etot = -14.6424332453179
-877000  ekin = 0.255431632539029 |  erot = 0.69685856734628 | epot = -15.5947234452596 | etot = -14.6424332453743
-878000  ekin = 0.267518408507424 |  erot = 0.707128927380235 | epot = -15.6170805813169 | etot = -14.6424332454292
-879000  ekin = 0.279619300254511 |  erot = 0.715378495712557 | epot = -15.6374310414462 | etot = -14.6424332454792
-880000  ekin = 0.291287955017456 |  erot = 0.721287639190631 | epot = -15.6550088397293 | etot = -14.6424332455213
-881000  ekin = 0.302128778463176 |  erot = 0.724613422802369 | epot = -15.6691754468184 | etot = -14.6424332455529
-882000  ekin = 0.311822304069024 |  erot = 0.725201068168812 | epot = -15.6794566178103 | etot = -14.6424332455725
-883000  ekin = 0.320145243789556 |  erot = 0.722987481096488 | epot = -15.6855659704653 | etot = -14.6424332455793
-884000  ekin = 0.326982762202337 |  erot = 0.717996120151906 | epot = -15.6874121279283 | etot = -14.642433245574
-885000  ekin = 0.332330882217347 |  erot = 0.710323349665211 | epot = -15.6850874774409 | etot = -14.6424332455584
-886000  ekin = 0.336287673337102 |  erot = 0.700117442969765 | epot = -15.6788383618422 | etot = -14.6424332455353
-887000  ekin = 0.33903296415872 |  erot = 0.687552454430858 | epot = -15.6690186640981 | etot = -14.6424332455086
-888000  ekin = 0.340797654552155 |  erot = 0.67280010093964 | epot = -15.6560310009741 | etot = -14.6424332454823
-889000  ekin = 0.341825106167166 |  erot = 0.656003407096678 | epot = -15.6402617587246 | etot = -14.6424332454608
-890000  ekin = 0.342328347583419 |  erot = 0.637256013160556 | epot = -15.6220176061914 | etot = -14.6424332454474
-891000  ekin = 0.342447730500021 |  erot = 0.616590618565289 | epot = -15.6014715945102 | etot = -14.6424332454449
-892000  ekin = 0.342214057419104 |  erot = 0.593979026501831 | epot = -15.5786263293753 | etot = -14.6424332454543
-893000  ekin = 0.34152200491664 |  erot = 0.569344767729407 | epot = -15.5533000181212 | etot = -14.6424332454752
-894000  ekin = 0.340117934122997 |  erot = 0.542587519912816 | epot = -15.525138699541 | etot = -14.6424332455052
-895000  ekin = 0.337605044786637 |  erot = 0.513616778977938 | epot = -15.4936550693051 | etot = -14.6424332455405
-896000  ekin = 0.333467462875054 |  erot = 0.48239077517223 | epot = -15.4582914836235 | etot = -14.6424332455762
-897000  ekin = 0.327113397523327 |  erot = 0.448955709001807 | epot = -15.4185023521314 | etot = -14.6424332456062
-898000  ekin = 0.317936017621265 |  erot = 0.413480165458539 | epot = -15.3738494287041 | etot = -14.6424332456243
-899000  ekin = 0.305389123795979 |  erot = 0.376280077469313 | epot = -15.3241024468894 | etot = -14.6424332456241
-900000  ekin = 0.289072881395148 |  erot = 0.337830752319287 | epot = -15.2693368793143 | etot = -14.6424332455999
-901000  ekin = 0.268822686259622 |  erot = 0.298764046957452 | epot = -15.2100199787646 | etot = -14.6424332455475
-902000  ekin = 0.244791653968919 |  erot = 0.259850521118035 | epot = -15.1470754205513 | etot = -14.6424332454644
-903000  ekin = 0.217514571462472 |  erot = 0.221968047210473 | epot = -15.0819158640236 | etot = -14.6424332453507
-904000  ekin = 0.187939204411346 |  erot = 0.186059692012592 | epot = -15.0164321416341 | etot = -14.6424332452102
-905000  ekin = 0.157410847731204 |  erot = 0.153084564883822 | epot = -14.9529286576653 | etot = -14.6424332450503
-906000  ekin = 0.127599356271268 |  erot = 0.123965703545286 | epot = -14.8939983046991 | etot = -14.6424332448825
-907000  ekin = 0.100365589130667 |  erot = 0.0995389863896931 | epot = -14.8423378202422 | etot = -14.6424332447218
-908000  ekin = 0.0775759855945855 |  erot = 0.0805066337401435 | epot = -14.800515863919 | etot = -14.6424332445842
-909000  ekin = 0.0608876950034 |  erot = 0.0673982354567511 | epot = -14.7707191749454 | etot = -14.6424332444853
-910000  ekin = 0.0515382922989042 |  erot = 0.0605415547706379 | epot = -14.7545130915067 | etot = -14.6424332444371
-911000  ekin = 0.0501789452911252 |  erot = 0.0600446989620123 | epot = -14.7526568886991 | etot = -14.642433244446
-912000  ekin = 0.0567846925755769 |  erot = 0.0657906450221707 | epot = -14.7650085821085 | etot = -14.6424332445108
-913000  ekin = 0.0706603747975489 |  erot = 0.0774445361855688 | epot = -14.790538155607 | etot = -14.6424332446239
-914000  ekin = 0.0905398584143666 |  erot = 0.0944735694282315 | epot = -14.8274466726145 | etot = -14.6424332447719
-915000  ekin = 0.114756144633904 |  erot = 0.116178630204502 | epot = -14.8733680197774 | etot = -14.642433244939
-916000  ekin = 0.141447043407684 |  erot = 0.141736093135102 | epot = -14.9256163816514 | etot = -14.6424332451087
-917000  ekin = 0.168758535424836 |  erot = 0.170247440483737 | epot = -14.9814392211754 | etot = -14.6424332452668
-918000  ekin = 0.195014913443954 |  erot = 0.200793639362701 | epot = -15.0382417982093 | etot = -14.6424332454026
-919000  ekin = 0.218837422087121 |  erot = 0.232490666329554 | epot = -15.0937613339258 | etot = -14.6424332455091
-920000  ekin = 0.239206641026195 |  erot = 0.264542267085039 | epot = -15.1461821536945 | etot = -14.6424332455832
-921000  ekin = 0.25547457715008 |  erot = 0.296286050795184 | epot = -15.1941938735701 | etot = -14.6424332456248
-922000  ekin = 0.267338631216139 |  erot = 0.327229363198297 | epot = -15.2370012400506 | etot = -14.6424332456361
-923000  ekin = 0.274791412213564 |  erot = 0.357072039930916 | epot = -15.2742966977653 | etot = -14.6424332456208
-924000  ekin = 0.278059017514789 |  erot = 0.385714059426418 | epot = -15.306206322525 | etot = -14.6424332455838
-925000  ekin = 0.277537405165931 |  erot = 0.413247220089643 | epot = -15.333217870786 | etot = -14.6424332455304
-926000  ekin = 0.273733135235124 |  erot = 0.439931173656047 | epot = -15.3560975543575 | etot = -14.6424332454664
-927000  ekin = 0.267211859637652 |  erot = 0.466155363877246 | epot = -15.3758004689123 | etot = -14.6424332453974
-928000  ekin = 0.258555847531632 |  erot = 0.492389553497958 | epot = -15.3933786463587 | etot = -14.6424332453291
-929000  ekin = 0.248330567886967 |  erot = 0.519126582977394 | epot = -15.4098903961312 | etot = -14.6424332452668
-930000  ekin = 0.23705974716086 |  erot = 0.546821711627624 | epot = -15.4263147040038 | etot = -14.6424332452153
-931000  ekin = 0.225208144800234 |  erot = 0.575833282919438 | epot = -15.4434746728981 | etot = -14.6424332451784
-932000  ekin = 0.213171319360063 |  erot = 0.606369490847652 | epot = -15.4619740553666 | etot = -14.6424332451589
-933000  ekin = 0.201271722990057 |  erot = 0.638445690374705 | epot = -15.4821506585231 | etot = -14.6424332451583
-934000  ekin = 0.189760460104366 |  erot = 0.67185600669489 | epot = -15.5040497119762 | etot = -14.6424332451769
-935000  ekin = 0.178823941832753 |  erot = 0.706161996583042 | epot = -15.5274191836291 | etot = -14.6424332452133
-936000  ekin = 0.168594479109611 |  erot = 0.74069986583281 | epot = -15.5517275902074 | etot = -14.642433245265
-937000  ekin = 0.159163635629916 |  erot = 0.774606336201627 | epot = -15.5762032171597 | etot = -14.6424332453281
-938000  ekin = 0.150596971910416 |  erot = 0.806861786791798 | epot = -15.5998920041003 | etot = -14.6424332453981
-939000  ekin = 0.142948711628538 |  erot = 0.83634788352242 | epot = -15.6217298406206 | etot = -14.6424332454696
-940000  ekin = 0.136274889167971 |  erot = 0.861915676024924 | epot = -15.6406238107303 | etot = -14.6424332455374
-941000  ekin = 0.130643703196498 |  erot = 0.882459199117052 | epot = -15.6555361479098 | etot = -14.6424332455962
-942000  ekin = 0.126142088159105 |  erot = 0.896989065169274 | epot = -15.66556439897 | etot = -14.6424332456417
-943000  ekin = 0.122877886109369 |  erot = 0.904700444356692 | epot = -15.6700115761362 | etot = -14.6424332456702
-944000  ekin = 0.120977407412015 |  erot = 0.905030230235472 | epot = -15.6684408833271 | etot = -14.6424332456797
-945000  ekin = 0.120578563691314 |  erot = 0.897699054744981 | epot = -15.6607108641056 | etot = -14.6424332456693
-946000  ekin = 0.121820103594724 |  erot = 0.882735070928503 | epot = -15.646988420163 | etot = -14.6424332456398
-947000  ekin = 0.124827761130805 |  erot = 0.860477935596992 | epot = -15.6277389423211 | etot = -14.6424332455933
-948000  ekin = 0.129698334170726 |  erot = 0.831563037038998 | epot = -15.6036946167428 | etot = -14.642433245533
-949000  ekin = 0.136482857560392 |  erot = 0.796887554723542 | epot = -15.5758036577472 | etot = -14.6424332454633
-950000  ekin = 0.145170138933426 |  erot = 0.757561255989732 | epot = -15.5451646403121 | etot = -14.642433245389
-951000  ekin = 0.155672002997215 |  erot = 0.714845916095059 | epot = -15.5129511644075 | etot = -14.6424332453152
-952000  ekin = 0.167811650837965 |  erot = 0.67008783325118 | epot = -15.480332729336 | etot = -14.6424332452469
-953000  ekin = 0.181316579472455 |  erot = 0.624648095212333 | epot = -15.4483979198734 | etot = -14.6424332451886
-954000  ekin = 0.195817500701693 |  erot = 0.579835080695355 | epot = -15.4180858265408 | etot = -14.6424332451437
-955000  ekin = 0.210854606876419 |  erot = 0.536843219767442 | epot = -15.3901310717585 | etot = -14.6424332451147
-956000  ekin = 0.22589229983617 |  erot = 0.496701376789191 | epot = -15.3650269217278 | etot = -14.6424332451025
-957000  ekin = 0.240343066496498 |  erot = 0.460233438090612 | epot = -15.3430097496938 | etot = -14.6424332451067
-958000  ekin = 0.253600493836355 |  erot = 0.428032849889929 | epot = -15.3240665888515 | etot = -14.6424332451252
-959000  ekin = 0.265080433744447 |  erot = 0.400452005453988 | epot = -15.3079656843532 | etot = -14.6424332451548
-960000  ekin = 0.274268068126047 |  erot = 0.37760654944402 | epot = -15.294307862761 | etot = -14.6424332451909
-961000  ekin = 0.280767177998564 |  erot = 0.359393861243516 | epot = -15.2825942844706 | etot = -14.6424332452285
-962000  ekin = 0.284346484058158 |  erot = 0.34552419881024 | epot = -15.2723039281308 | etot = -14.6424332452624
-963000  ekin = 0.284976816084592 |  erot = 0.335562232322765 | epot = -15.2629722936953 | etot = -14.6424332452879
-964000  ekin = 0.282852494243092 |  erot = 0.328975986490651 | epot = -15.2542617260353 | etot = -14.6424332453015
-965000  ekin = 0.278391086611333 |  erot = 0.325189577593016 | epot = -15.2460139095058 | etot = -14.6424332453015
-966000  ekin = 0.272207924676324 |  erot = 0.323635640145639 | epot = -15.2382768101098 | etot = -14.6424332452879
-967000  ekin = 0.265065367868708 |  erot = 0.323803079983033 | epot = -15.2313016931144 | etot = -14.6424332452627
-968000  ekin = 0.257801293713459 |  erot = 0.325275872287221 | epot = -15.2255104112304 | etot = -14.6424332452297
-969000  ekin = 0.251245661475255 |  erot = 0.327759142573571 | epot = -15.2214380492424 | etot = -14.6424332451936
-970000  ekin = 0.246137008995617 |  erot = 0.331089781179348 | epot = -15.2196600353345 | etot = -14.6424332451595
-971000  ekin = 0.243051319619918 |  erot = 0.335230325664218 | epot = -15.220714890416 | etot = -14.6424332451318
-972000  ekin = 0.242353409643632 |  erot = 0.340246678804405 | epot = -15.2250333335622 | etot = -14.6424332451142
-973000  ekin = 0.2441763381681 |  erot = 0.346272190710886 | epot = -15.2328817739879 | etot = -14.642433245109
-974000  ekin = 0.248428661663904 |  erot = 0.353462430362299 | epot = -15.2443243371435 | etot = -14.6424332451173
-975000  ekin = 0.254824314808745 |  erot = 0.361946299431111 | epot = -15.2592038593792 | etot = -14.6424332451394
-976000  ekin = 0.26292684882563 |  erot = 0.371779749930331 | epot = -15.2771398439303 | etot = -14.6424332451743
-977000  ekin = 0.27219923533505 |  erot = 0.382908123264369 | epot = -15.29754060382 | etot = -14.6424332452206
-978000  ekin = 0.282052066854694 |  erot = 0.395142048097406 | epot = -15.3196273602282 | etot = -14.6424332452761
-979000  ekin = 0.291885751915604 |  erot = 0.408150081470976 | epot = -15.3424690787245 | etot = -14.6424332453379
-980000  ekin = 0.301125083790157 |  erot = 0.421469125221772 | epot = -15.3650274544147 | etot = -14.6424332454028
-981000  ekin = 0.309246535916217 |  erot = 0.434531423655031 | epot = -15.3862112050381 | etot = -14.6424332454669
-982000  ekin = 0.315799497488439 |  erot = 0.446704965614828 | epot = -15.4049377086292 | etot = -14.642433245526
-983000  ekin = 0.320422573217629 |  erot = 0.457342632741568 | epot = -15.4201984515353 | etot = -14.6424332455761
-984000  ekin = 0.322855465254252 |  erot = 0.465834622596749 | epot = -15.4311233334646 | etot = -14.6424332456136
-985000  ekin = 0.322946302470394 |  erot = 0.47165859097122 | epot = -15.4370381390773 | etot = -14.6424332456357
-986000  ekin = 0.320653917800696 |  erot = 0.474422556587648 | epot = -15.437509720029 | etot = -14.6424332456406
-987000  ekin = 0.31604462735714 |  erot = 0.473896755512796 | epot = -15.4323746284979 | etot = -14.642433245628
-988000  ekin = 0.309283477263999 |  erot = 0.470032116942454 | epot = -15.4217488398048 | etot = -14.6424332455984
-989000  ekin = 0.300620522164939 |  erot = 0.462964620619315 | epot = -15.406018388338 | etot = -14.6424332455537
-990000  ekin = 0.290373280687637 |  erot = 0.453006262992374 | epot = -15.3858127891766 | etot = -14.6424332454965
-991000  ekin = 0.278906915702925 |  erot = 0.440624526216757 | epot = -15.3619646873499 | etot = -14.6424332454302
-992000  ekin = 0.266613826413316 |  erot = 0.42641300688875 | epot = -15.3354600786602 | etot = -14.6424332453582
-993000  ekin = 0.253894212445666 |  erot = 0.411056197521998 | epot = -15.3073836552517 | etot = -14.6424332452841
-994000  ekin = 0.241138837000196 |  erot = 0.395291372385701 | epot = -15.2788634545969 | etot = -14.642433245211
-995000  ekin = 0.228714768908018 |  erot = 0.379870207852185 | epot = -15.2510182219023 | etot = -14.6424332451421
-996000  ekin = 0.216954417472331 |  erot = 0.365522282703969 | epot = -15.2249099452561 | etot = -14.6424332450798
-997000  ekin = 0.206147766458768 |  erot = 0.352922066134627 | epot = -15.2015030776195 | etot = -14.6424332450261
-998000  ekin = 0.196537413161314 |  erot = 0.34266049598664 | epot = -15.1816311541306 | etot = -14.6424332449827
-999000  ekin = 0.188315843917132 |  erot = 0.335221830000276 | epot = -15.1659709188677 | etot = -14.6424332449503
-1000000  ekin = 0.181624323072266 |  erot = 0.330966139643081 | epot = -15.1550237076453 | etot = -14.6424332449299
- 1000000  0.013453654   -1.5270261  0.011523695   -1.4973399 -8.4815516e-05 
-Loop time of 18.9591 on 1 procs for 1000000 steps with 10 atoms
-
-Performance: 45571.887 tau/day, 52745.239 timesteps/s
-98.5% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 15.272     | 15.272     | 15.272     |   0.0 | 80.55
-Bond    | 0.58511    | 0.58511    | 0.58511    |   0.0 |  3.09
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.19027    | 0.19027    | 0.19027    |   0.0 |  1.00
-Output  | 8e-06      | 8e-06      | 8e-06      |   0.0 |  0.00
-Modify  | 2.6225     | 2.6225     | 2.6225     |   0.0 | 13.83
-Other   |            | 0.2893     |            |       |  1.53
-
-Nlocal:    10 ave 10 max 10 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    43 ave 43 max 43 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 43
-Ave neighs/atom = 4.3
-Ave special neighs/atom = 3.6
-Neighbor list builds = 0
-Dangerous builds = 0
-
-#write_restart config.${number}.*
-Total wall time: 0:00:18
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4
deleted file mode 100644
index 59800043d3..0000000000
--- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4
+++ /dev/null
@@ -1,1165 +0,0 @@
-LAMMPS (18 Jun 2019)
-variable number	equal 1
-variable ofreq	equal 1000
-variable efreq	equal 1000
-variable T      equal 0.1
-
-units lj
-
-dimension 3
-
-newton off
-
-boundary  p p p
-
-atom_style hybrid bond ellipsoid
-atom_modify sort 0 1.0
-
-# Pair interactions require lists of neighbours to be calculated
-neighbor 1.0 bin
-neigh_modify every 1 delay 0 check yes
-
-read_data data.duplex1
-  orthogonal box = (-20 -20 -20) to (20 20 20)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  10 atoms
-  reading velocities ...
-  10 velocities
-  10 ellipsoids
-  scanning bonds ...
-  2 = max bonds/atom
-  reading bonds ...
-  8 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of 1-3 neighbors
-  2 = max # of 1-4 neighbors
-  4 = max # of special neighbors
-  special bonds CPU = 0.000462 secs
-  read_data CPU = 0.004857 secs
-
-set atom * mass 3.1575
-  10 settings made for mass
-
-group all type 1 4
-10 atoms in group all
-
-# oxDNA bond interactions - FENE backbone
-bond_style oxdna/fene
-bond_coeff * 2.0 0.25 0.7525
-
-# oxDNA pair interactions
-pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
-pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
-
-# NVE ensemble
-fix 1 all nve/dot
-#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
-#fix 1 all nve/asphere
-#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
-
-timestep 1e-5
-
-#comm_style tiled
-#fix 3 all balance 10000 1.1 rcb
-
-#compute mol all chunk/atom molecule
-#compute mychunk all vcm/chunk mol
-#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
-
-#dump pos all xyz ${ofreq} traj.${number}.xyz
-
-#compute quat all property/atom quatw quati quatj quatk
-#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
-#dump_modify quat sort id
-#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
-
-compute erot all erotate/asphere
-compute ekin all ke
-compute epot all pe
-variable erot equal c_erot
-variable ekin equal c_ekin
-variable epot equal c_epot
-variable etot equal c_erot+c_ekin+c_epot
-fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-
-#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
-#dump_modify out sort id
-#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
-
-run 1000000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.92828
-  ghost atom cutoff = 1.92828
-  binsize = 0.964142, bins = 42 42 42
-  5 neighbor lists, perpetual/occasional/extra = 5 0 0
-  (1) pair oxdna/excv, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-  (2) pair oxdna/stk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (3) pair oxdna/hbond, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (4) pair oxdna/xstk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) pair oxdna/coaxstk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -1.4711818 0.0069384985   -1.4642433 2.5836586e-06 
-1000  ekin = 0.00113448721737009 |  erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
-2000  ekin = 0.00449927223902292 |  erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
-3000  ekin = 0.00997964450840756 |  erot = 0.0366523356056466 | epot = -14.6890652250033 | etot = -14.6424332448892
-4000  ekin = 0.017388811129498 |  erot = 0.0643039804300251 | epot = -14.7241260365031 | etot = -14.6424332449436
-5000  ekin = 0.0264744514136422 |  erot = 0.0987844033142134 | epot = -14.7676920997383 | etot = -14.6424332450104
-6000  ekin = 0.0369277948555727 |  erot = 0.13933657105258 | epot = -14.8186976109956 | etot = -14.6424332450875
-7000  ekin = 0.0483950557190949 |  erot = 0.18508629569211 | epot = -14.8759145965832 | etot = -14.642433245172
-8000  ekin = 0.0604909336919856 |  erot = 0.235071307523581 | epot = -14.9379954864767 | etot = -14.6424332452611
-9000  ekin = 0.0728137406439518 |  erot = 0.288273694501614 | epot = -15.003520680497 | etot = -14.6424332453514
-10000  ekin = 0.0849615563084574 |  erot = 0.343654369293588 | epot = -15.0710491710418 | etot = -14.6424332454398
-11000  ekin = 0.0965486715044103 |  erot = 0.400187932108392 | epot = -15.1391698491357 | etot = -14.6424332455229
-12000  ekin = 0.107221466282716 |  erot = 0.456896095459393 | epot = -15.2065508073401 | etot = -14.642433245598
-13000  ekin = 0.116672809719361 |  erot = 0.512877765427946 | epot = -15.27198382081 | etot = -14.6424332456627
-14000  ekin = 0.124654073730849 |  erot = 0.567333962045503 | epot = -15.3344212814915 | etot = -14.6424332457151
-15000  ekin = 0.130983939684084 |  erot = 0.619586028257146 | epot = -15.3930032136957 | etot = -14.6424332457544
-16000  ekin = 0.135553354544703 |  erot = 0.66908602849033 | epot = -15.4470726288154 | etot = -14.6424332457804
-17000  ekin = 0.138326263958104 |  erot = 0.715418858086103 | epot = -15.4961783678378 | etot = -14.6424332457936
-18000  ekin = 0.139336096663942 |  erot = 0.758296324628468 | epot = -15.5400656670878 | etot = -14.6424332457954
-19000  ekin = 0.138678360045107 |  erot = 0.797544234276629 | epot = -15.5786558401095 | etot = -14.6424332457878
-20000  ekin = 0.136500074655344 |  erot = 0.83308420441182 | epot = -15.6120175248401 | etot = -14.642433245773
-21000  ekin = 0.13298706528568 |  erot = 0.864912408453368 | epot = -15.6403327194924 | etot = -14.6424332457533
-22000  ekin = 0.128350288213599 |  erot = 0.893077649558725 | epot = -15.6638611835035 | etot = -14.6424332457311
-23000  ekin = 0.122812385135574 |  erot = 0.917661024684598 | epot = -15.6829066555285 | etot = -14.6424332457083
-24000  ekin = 0.116595521408358 |  erot = 0.938759014332585 | epot = -15.6977877814273 | etot = -14.6424332456863
-25000  ekin = 0.109911323474882 |  erot = 0.95647120734756 | epot = -15.7088157764886 | etot = -14.6424332456662
-26000  ekin = 0.102953426207684 |  erot = 0.970893163953299 | epot = -15.7162798358093 | etot = -14.6424332456483
-27000  ekin = 0.0958928250746602 |  erot = 0.982114250193902 | epot = -15.7204403209011 | etot = -14.6424332456326
-28000  ekin = 0.08887594109497 |  erot = 0.990219731539409 | epot = -15.721528918253 | etot = -14.6424332456186
-29000  ekin = 0.0820250748771992 |  erot = 0.995296041202176 | epot = -15.7197543616852 | etot = -14.6424332456058
-30000  ekin = 0.0754407616837525 |  erot = 0.997437949319921 | epot = -15.7153119565969 | etot = -14.6424332455933
-31000  ekin = 0.0692054432607511 |  erot = 0.996756332760935 | epot = -15.708395021602 | etot = -14.6424332455803
-32000  ekin = 0.0633878377974532 |  erot = 0.993385345347625 | epot = -15.6992064287111 | etot = -14.6424332455661
-33000  ekin = 0.0580474070866977 |  erot = 0.987487973308193 | epot = -15.6879686259451 | etot = -14.6424332455502
-34000  ekin = 0.0532383791882916 |  erot = 0.979259192919847 | epot = -15.6749308176403 | etot = -14.6424332455322
-35000  ekin = 0.0490128758302373 |  erot = 0.96892619740531 | epot = -15.6603723187477 | etot = -14.6424332455122
-36000  ekin = 0.0454228081405034 |  erot = 0.956745409624112 | epot = -15.6446014632554 | etot = -14.6424332454908
-37000  ekin = 0.0425203357170931 |  erot = 0.942996237999014 | epot = -15.6279498191848 | etot = -14.6424332454687
-38000  ekin = 0.0403568280944582 |  erot = 0.927971766615185 | epot = -15.6107618401563 | etot = -14.6424332454467
-39000  ekin = 0.0389804214208553 |  erot = 0.911966804108842 | epot = -15.5933804709559 | etot = -14.6424332454262
-40000  ekin = 0.0384324238853386 |  erot = 0.89526395956212 | epot = -15.5761296288558 | etot = -14.6424332454083
-41000  ekin = 0.0387429860406854 |  erot = 0.878118672837898 | epot = -15.559294904273 | etot = -14.6424332453944
-42000  ekin = 0.0399266053637397 |  erot = 0.860744395135588 | epot = -15.543104245885 | etot = -14.6424332453857
-43000  ekin = 0.041978156101278 |  erot = 0.84329936535652 | epot = -15.5277107668409 | etot = -14.6424332453831
-44000  ekin = 0.044870189409001 |  erot = 0.825876603313516 | epot = -15.5131800381094 | etot = -14.6424332453868
-45000  ekin = 0.0485521857416513 |  erot = 0.808498758186241 | epot = -15.4994841893249 | etot = -14.642433245397
-46000  ekin = 0.0529522094038552 |  erot = 0.791119212188506 | epot = -15.486504667005 | etot = -14.6424332454127
-47000  ekin = 0.0579809824244721 |  erot = 0.773630265884098 | epot = -15.4740444937409 | etot = -14.6424332454323
-48000  ekin = 0.0635377846502182 |  erot = 0.755878310838203 | epot = -15.4618493409424 | etot = -14.6424332454539
-49000  ekin = 0.0695169124467202 |  erot = 0.737684732484798 | epot = -15.4496348904071 | etot = -14.6424332454756
-50000  ekin = 0.0758129058465097 |  erot = 0.718870126220151 | epot = -15.437116277562 | etot = -14.6424332454953
-51000  ekin = 0.0823226638652294 |  erot = 0.699278599520714 | epot = -15.424034508898 | etot = -14.642433245512
-52000  ekin = 0.0889431481344998 |  erot = 0.67879880710002 | epot = -15.4101752007595 | etot = -14.642433245525
-53000  ekin = 0.0955646689265025 |  erot = 0.657379086771117 | epot = -15.3953770012321 | etot = -14.6424332455345
-54000  ekin = 0.10206147751016 |  erot = 0.635035489169276 | epot = -15.3795302122208 | etot = -14.6424332455414
-55000  ekin = 0.108282960174665 |  erot = 0.611853171347244 | epot = -15.362569377068 | etot = -14.6424332455461
-56000  ekin = 0.114049426282277 |  erot = 0.587982945924297 | epot = -15.3444656177552 | etot = -14.6424332455486
-57000  ekin = 0.119155806187163 |  erot = 0.563635255922951 | epot = -15.3252243076589 | etot = -14.6424332455488
-58000  ekin = 0.123384552305545 |  erot = 0.539073355222428 | epot = -15.3048911530734 | etot = -14.6424332455454
-59000  ekin = 0.126526300954853 |  erot = 0.514606324858911 | epot = -15.2835658713509 | etot = -14.6424332455371
-60000  ekin = 0.128404399836229 |  erot = 0.490581338840044 | epot = -15.261418984199 | etot = -14.6424332455227
-61000  ekin = 0.128898142361897 |  erot = 0.467373892400972 | epot = -15.2387052802646 | etot = -14.6424332455018
-62000  ekin = 0.127959880289726 |  erot = 0.445374820086222 | epot = -15.2157679458511 | etot = -14.6424332454752
-63000  ekin = 0.125622870624277 |  erot = 0.424973765387148 | epot = -15.1930298814554 | etot = -14.642433245444
-64000  ekin = 0.121999044842466 |  erot = 0.406539918572074 | epot = -15.1709722088251 | etot = -14.6424332454105
-65000  ekin = 0.117268056618551 |  erot = 0.390401831020312 | epot = -15.1501031330161 | etot = -14.6424332453772
-66000  ekin = 0.11166038525652 |  erot = 0.376828594078856 | epot = -15.1309222246818 | etot = -14.6424332453464
-67000  ekin = 0.105437746904482 |  erot = 0.366014539811009 | epot = -15.1138855320359 | etot = -14.6424332453204
-68000  ekin = 0.0988737375602389 |  erot = 0.358069014155077 | epot = -15.0993759970158 | etot = -14.6424332453005
-69000  ekin = 0.0922368286498126 |  erot = 0.353011948771943 | epot = -15.0876820227093 | etot = -14.6424332452876
-70000  ekin = 0.0857769015271899 |  erot = 0.350775174164931 | epot = -15.078985320974 | etot = -14.6424332452819
-71000  ekin = 0.0797156921641249 |  erot = 0.351208844245481 | epot = -15.0733577816927 | etot = -14.6424332452831
-72000  ekin = 0.0742409440407228 |  erot = 0.354092037747166 | epot = -15.0707662270784 | etot = -14.6424332452906
-73000  ekin = 0.069503749870388 |  erot = 0.359146526961232 | epot = -15.0710835221349 | etot = -14.6424332453033
-74000  ekin = 0.065618449742691 |  erot = 0.366052769878692 | epot = -15.0741044649412 | etot = -14.6424332453199
-75000  ekin = 0.0626644690394284 |  erot = 0.374467290033975 | epot = -15.0795650044124 | etot = -14.642433245339
-76000  ekin = 0.0606895535091863 |  erot = 0.384040683403432 | epot = -15.087163482272 | etot = -14.6424332453594
-77000  ekin = 0.0597139401241188 |  erot = 0.394435495892894 | epot = -15.0965826813962 | etot = -14.6424332453792
-78000  ekin = 0.0597350629875199 |  erot = 0.405343151481916 | epot = -15.107511459867 | etot = -14.6424332453975
-79000  ekin = 0.0607324264361021 |  erot = 0.4164990176427 | epot = -15.1196646894919 | etot = -14.6424332454131
-80000  ekin = 0.0626722904954161 |  erot = 0.427694630238743 | epot = -15.1328001661592 | etot = -14.6424332454251
-81000  ekin = 0.0655118235331528 |  erot = 0.438786127849131 | epot = -15.1467311968152 | etot = -14.6424332454329
-82000  ekin = 0.0692024020836604 |  erot = 0.449698113830624 | epot = -15.1613337613509 | etot = -14.6424332454366
-83000  ekin = 0.0736917936904884 |  erot = 0.460422490740831 | epot = -15.1765475298676 | etot = -14.6424332454363
-84000  ekin = 0.0789250526542207 |  erot = 0.471012272295187 | epot = -15.1923705703823 | etot = -14.6424332454329
-85000  ekin = 0.0848440878742484 |  erot = 0.481570908650517 | epot = -15.2088482419521 | etot = -14.6424332454273
-86000  ekin = 0.0913860133243867 |  erot = 0.492238169206351 | epot = -15.2260574279515 | etot = -14.6424332454207
-87000  ekin = 0.0984805441186007 |  erot = 0.503174014617495 | epot = -15.2440878041506 | etot = -14.6424332454146
-88000  ekin = 0.106046830302566 |  erot = 0.514542076496893 | epot = -15.2630221522094 | etot = -14.6424332454099
-89000  ekin = 0.113990204125935 |  erot = 0.526494309539958 | epot = -15.2829177590739 | etot = -14.642433245408
-90000  ekin = 0.122199339149549 |  erot = 0.539158097286396 | epot = -15.3037906818453 | etot = -14.6424332454094
-91000  ekin = 0.130544275968789 |  erot = 0.552626637866402 | epot = -15.3256041592497 | etot = -14.6424332454146
-92000  ekin = 0.138875666145969 |  erot = 0.566952900962838 | epot = -15.3482618125326 | etot = -14.6424332454238
-93000  ekin = 0.14702544061161 |  erot = 0.582146933738122 | epot = -15.3716056197866 | etot = -14.6424332454369
-94000  ekin = 0.154808946844654 |  erot = 0.598175891801918 | epot = -15.3954180841001 | etot = -14.6424332454535
-95000  ekin = 0.162028449598908 |  erot = 0.614965942454569 | epot = -15.4194276375267 | etot = -14.6424332454732
-96000  ekin = 0.168477779664562 |  erot = 0.632405154082769 | epot = -15.4433161792427 | etot = -14.6424332454953
-97000  ekin = 0.173947863023519 |  erot = 0.650346631629065 | epot = -15.466727740172 | etot = -14.6424332455194
-98000  ekin = 0.178232875001165 |  erot = 0.668611435746703 | epot = -15.4892775562927 | etot = -14.6424332455449
-99000  ekin = 0.181136831923469 |  erot = 0.686991165056991 | epot = -15.5105612425515 | etot = -14.6424332455711
-100000  ekin = 0.182480533640974 |  erot = 0.705250413408614 | epot = -15.530164192647 | etot = -14.6424332455974
-101000  ekin = 0.182108871449632 |  erot = 0.723129571004103 | epot = -15.5476716880769 | etot = -14.6424332456232
-102000  ekin = 0.179898581168339 |  erot = 0.740348571091352 | epot = -15.5626803979071 | etot = -14.6424332456474
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-104000  ekin = 0.169678431534372 |  erot = 0.771617166852996 | epot = -15.5837288440748 | etot = -14.6424332456874
-105000  ekin = 0.161658036036246 |  erot = 0.785061742963598 | epot = -15.5891530247003 | etot = -14.6424332457005
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-112000  ekin = 0.0687764915886182 |  erot = 0.815804215096852 | epot = -15.5270139522588 | etot = -14.6424332455734
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-119000  ekin = 0.0171359296540399 |  erot = 0.72993256457469 | epot = -15.3895017395652 | etot = -14.6424332453364
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-121000  ekin = 0.0269649552324778 |  erot = 0.692336677371657 | epot = -15.3617348779503 | etot = -14.6424332453462
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-124000  ekin = 0.0572521324300892 |  erot = 0.632399068063538 | epot = -15.3320844459047 | etot = -14.6424332454111
-125000  ekin = 0.0692913736007693 |  erot = 0.612390156183436 | epot = -15.3241147752204 | etot = -14.6424332454362
-126000  ekin = 0.0812564128179015 |  erot = 0.592751635107163 | epot = -15.3164412933838 | etot = -14.6424332454587
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-128000  ekin = 0.102594692019405 |  erot = 0.555565138942023 | epot = -15.3005930764495 | etot = -14.6424332454881
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-132000  ekin = 0.123095155540088 |  erot = 0.496904390905875 | epot = -15.2624327918998 | etot = -14.6424332454539
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-682000  ekin = 0.13645246152461 |  erot = 0.419938865037855 | epot = -15.1988245718826 | etot = -14.6424332453201
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-717000  ekin = 0.216355400176877 |  erot = 0.621454592037058 | epot = -15.4802432376869 | etot = -14.6424332454729
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-819000  ekin = 0.15050378978042 |  erot = 0.563608719249299 | epot = -15.3565457540354 | etot = -14.6424332450057
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-821000  ekin = 0.128588386730135 |  erot = 0.496309093117806 | epot = -15.2673307247362 | etot = -14.6424332448883
-822000  ekin = 0.122284066136812 |  erot = 0.467617125515789 | epot = -15.2323344365172 | etot = -14.6424332448646
-823000  ekin = 0.119278020924339 |  erot = 0.44266622847877 | epot = -15.2043774942677 | etot = -14.6424332448646
-824000  ekin = 0.119546158603677 |  erot = 0.421490682738665 | epot = -15.1834700862295 | etot = -14.6424332448872
-825000  ekin = 0.122931110514549 |  erot = 0.403904342223771 | epot = -15.1692686976685 | etot = -14.6424332449302
-826000  ekin = 0.129150803764327 |  erot = 0.389525075000029 | epot = -15.161109123755 | etot = -14.6424332449907
-827000  ekin = 0.137812176399179 |  erot = 0.377809252270532 | epot = -15.1580546737345 | etot = -14.6424332450648
-828000  ekin = 0.148430331608382 |  erot = 0.368094906962796 | epot = -15.1589584837191 | etot = -14.6424332451479
-829000  ekin = 0.160453205761696 |  erot = 0.359651737511967 | epot = -15.1625381885082 | etot = -14.6424332452346
-830000  ekin = 0.17329138289678 |  erot = 0.351735589545236 | epot = -15.1674602177611 | etot = -14.6424332453191
-831000  ekin = 0.186352012962992 |  erot = 0.343644456329796 | epot = -15.1724297146884 | etot = -14.6424332453957
-832000  ekin = 0.19907492460549 |  erot = 0.334772487920949 | epot = -15.1762806579855 | etot = -14.642433245459
-833000  ekin = 0.21096808488054 |  erot = 0.324658115188717 | epot = -15.1780594455737 | etot = -14.6424332455044
-834000  ekin = 0.22163875725698 |  erot = 0.313022323442326 | epot = -15.1770943262282 | etot = -14.6424332455289
-835000  ekin = 0.230816330001966 |  erot = 0.299793483326653 | epot = -15.1730430588596 | etot = -14.642433245531
-836000  ekin = 0.238363132174234 |  erot = 0.28511603996084 | epot = -15.1659124176466 | etot = -14.6424332455115
-837000  ekin = 0.244270841530998 |  erot = 0.269341751259632 | epot = -15.1560458382641 | etot = -14.6424332454734
-838000  ekin = 0.248642320235733 |  erot = 0.25300390410384 | epot = -15.1440794697607 | etot = -14.6424332454212
-839000  ekin = 0.251661569327697 |  erot = 0.23677675898714 | epot = -15.1308715736755 | etot = -14.6424332453607
-840000  ekin = 0.253557306828274 |  erot = 0.221424057161473 | epot = -15.1174146092878 | etot = -14.642433245298
-841000  ekin = 0.254567562696821 |  erot = 0.207741475743574 | epot = -15.104742283679 | etot = -14.6424332452386
-842000  ekin = 0.254912814683751 |  erot = 0.196498262354278 | epot = -15.0938443222248 | etot = -14.6424332451868
-843000  ekin = 0.254783130765828 |  erot = 0.188382921787058 | epot = -15.085599297698 | etot = -14.6424332451451
-844000  ekin = 0.254340789697888 |  erot = 0.183956927272106 | epot = -15.0807309620847 | etot = -14.6424332451147
-845000  ekin = 0.253734932891713 |  erot = 0.183619247980611 | epot = -15.0797874259676 | etot = -14.6424332450953
-846000  ekin = 0.253120504196155 |  erot = 0.187583282239862 | epot = -15.0831370315226 | etot = -14.6424332450866
-847000  ekin = 0.252671650088266 |  erot = 0.195866742639111 | epot = -15.0909716378154 | etot = -14.642433245088
-848000  ekin = 0.25258091531028 |  erot = 0.20829422246314 | epot = -15.1033083828732 | etot = -14.6424332450998
-849000  ekin = 0.253039966848252 |  erot = 0.224511555531826 | epot = -15.1199847675027 | etot = -14.6424332451227
-850000  ekin = 0.254204001798515 |  erot = 0.244010590097797 | epot = -15.1406478370536 | etot = -14.6424332451573
-851000  ekin = 0.256148339026787 |  erot = 0.26616256360263 | epot = -15.1647441478333 | etot = -14.6424332452039
-852000  ekin = 0.258829686440588 |  erot = 0.290257858698213 | epot = -15.1915207904 | etot = -14.6424332452612
-853000  ekin = 0.262064657828587 |  erot = 0.315549558167727 | epot = -15.2200474613225 | etot = -14.6424332453262
-854000  ekin = 0.265534116122648 |  erot = 0.341297947736379 | epot = -15.2492653092531 | etot = -14.6424332453941
-855000  ekin = 0.26881517465358 |  erot = 0.366813004430893 | epot = -15.2780614245436 | etot = -14.6424332454591
-856000  ekin = 0.271435486954603 |  erot = 0.391492007901445 | epot = -15.305360740371 | etot = -14.642433245515
-857000  ekin = 0.272939108063008 |  erot = 0.414849750473414 | epot = -15.3302221040928 | etot = -14.6424332455564
-858000  ekin = 0.272951155039785 |  erot = 0.436539390688027 | epot = -15.3519237913071 | etot = -14.6424332455793
-859000  ekin = 0.271229880676472 |  erot = 0.456362750059341 | epot = -15.3700258763176 | etot = -14.6424332455817
-860000  ekin = 0.267698633833911 |  erot = 0.474269718460682 | epot = -15.3844015978589 | etot = -14.6424332455643
-861000  ekin = 0.262455001752904 |  erot = 0.490347316007815 | epot = -15.3952355632896 | etot = -14.6424332455289
-862000  ekin = 0.255758797176706 |  erot = 0.504799761298941 | epot = -15.402991803955 | etot = -14.6424332454794
-863000  ekin = 0.248003564341433 |  erot = 0.517921532812514 | epot = -15.4083583425743 | etot = -14.6424332454204
-864000  ekin = 0.23967765558487 |  erot = 0.5300658235034 | epot = -15.4121767244453 | etot = -14.642433245357
-865000  ekin = 0.23132088944539 |  erot = 0.541610953534341 | epot = -15.4153650882739 | etot = -14.6424332452941
-866000  ekin = 0.223481813676297 |  erot = 0.552927233331988 | epot = -15.4188422922445 | etot = -14.6424332452362
-867000  ekin = 0.216679174491969 |  erot = 0.564346499432351 | epot = -15.4234589191111 | etot = -14.6424332451867
-868000  ekin = 0.211369750018244 |  erot = 0.57613613893885 | epot = -15.4299391341058 | etot = -14.6424332451487
-869000  ekin = 0.207923502308331 |  erot = 0.588478941151472 | epot = -15.4388356885839 | etot = -14.6424332451241
-870000  ekin = 0.206606153000455 |  erot = 0.601459626890416 | epot = -15.4504990250046 | etot = -14.6424332451137
-871000  ekin = 0.207568796758621 |  erot = 0.615058451105655 | epot = -15.4650604929822 | etot = -14.6424332451179
-872000  ekin = 0.210843969902065 |  erot = 0.62915187575959 | epot = -15.4824290907976 | etot = -14.642433245136
-873000  ekin = 0.216347593119461 |  erot = 0.643519970833663 | epot = -15.5023008091198 | etot = -14.6424332451666
-874000  ekin = 0.223886305143511 |  erot = 0.65785990973072 | epot = -15.5241794600822 | etot = -14.6424332452079
-875000  ekin = 0.233169807553207 |  erot = 0.67180466221101 | epot = -15.5474077150216 | etot = -14.6424332452574
-876000  ekin = 0.243827877963662 |  erot = 0.684945735800061 | epot = -15.5712068590757 | etot = -14.642433245312
-877000  ekin = 0.255431632545988 |  erot = 0.696858567354671 | epot = -15.5947234452691 | etot = -14.6424332453684
-878000  ekin = 0.267518408513276 |  erot = 0.707128927388885 | epot = -15.6170805813255 | etot = -14.6424332454234
-879000  ekin = 0.279619300259048 |  erot = 0.71537849572129 | epot = -15.6374310414537 | etot = -14.6424332454734
-880000  ekin = 0.291287955020511 |  erot = 0.721287639199272 | epot = -15.6550088397353 | etot = -14.6424332455155
-881000  ekin = 0.30212877846463 |  erot = 0.724613422810775 | epot = -15.6691754468226 | etot = -14.6424332455472
-882000  ekin = 0.311822304068824 |  erot = 0.725201068176889 | epot = -15.6794566178125 | etot = -14.6424332455668
-883000  ekin = 0.320145243787706 |  erot = 0.722987481104172 | epot = -15.6855659704655 | etot = -14.6424332455736
-884000  ekin = 0.326982762198909 |  erot = 0.717996120159159 | epot = -15.6874121279265 | etot = -14.6424332455684
-885000  ekin = 0.332330882212481 |  erot = 0.710323349672059 | epot = -15.6850874774374 | etot = -14.6424332455528
-886000  ekin = 0.33628767333099 |  erot = 0.700117442976239 | epot = -15.678838361837 | etot = -14.6424332455298
-887000  ekin = 0.339032964151614 |  erot = 0.687552454437006 | epot = -15.6690186640916 | etot = -14.642433245503
-888000  ekin = 0.340797654544347 |  erot = 0.67280010094551 | epot = -15.6560310009666 | etot = -14.6424332454768
-889000  ekin = 0.341825106158976 |  erot = 0.656003407102339 | epot = -15.6402617587166 | etot = -14.6424332454552
-890000  ekin = 0.342328347575176 |  erot = 0.63725601316603 | epot = -15.6220176061831 | etot = -14.6424332454419
-891000  ekin = 0.342447730492056 |  erot = 0.616590618570594 | epot = -15.601471594502 | etot = -14.6424332454393
-892000  ekin = 0.342214057411724 |  erot = 0.593979026506924 | epot = -15.5786263293674 | etot = -14.6424332454488
-893000  ekin = 0.341522004910123 |  erot = 0.569344767734232 | epot = -15.5533000181139 | etot = -14.6424332454695
-894000  ekin = 0.340117934117577 |  erot = 0.542587519917294 | epot = -15.5251386995343 | etot = -14.6424332454994
-895000  ekin = 0.337605044782497 |  erot = 0.51361677898196 | epot = -15.4936550692992 | etot = -14.6424332455348
-896000  ekin = 0.333467462872322 |  erot = 0.482390775175684 | epot = -15.4582914836184 | etot = -14.6424332455704
-897000  ekin = 0.327113397522066 |  erot = 0.448955709004578 | epot = -15.418502352127 | etot = -14.6424332456003
-898000  ekin = 0.317936017621476 |  erot = 0.413480165460528 | epot = -15.3738494287003 | etot = -14.6424332456182
-899000  ekin = 0.305389123797598 |  erot = 0.376280077470489 | epot = -15.3241024468861 | etot = -14.642433245618
-900000  ekin = 0.289072881398049 |  erot = 0.337830752319602 | epot = -15.2693368793114 | etot = -14.6424332455938
-901000  ekin = 0.268822686263612 |  erot = 0.298764046956934 | epot = -15.2100199787618 | etot = -14.6424332455413
-902000  ekin = 0.244791653973738 |  erot = 0.259850521116738 | epot = -15.1470754205486 | etot = -14.6424332454581
-903000  ekin = 0.217514571467803 |  erot = 0.221968047208507 | epot = -15.0819158640206 | etot = -14.6424332453443
-904000  ekin = 0.187939204416829 |  erot = 0.186059692010109 | epot = -15.0164321416307 | etot = -14.6424332452037
-905000  ekin = 0.157410847736455 |  erot = 0.153084564881008 | epot = -14.9529286576612 | etot = -14.6424332450437
-906000  ekin = 0.127599356275899 |  erot = 0.123965703542346 | epot = -14.8939983046941 | etot = -14.6424332448759
-907000  ekin = 0.100365589134322 |  erot = 0.0995389863868474 | epot = -14.8423378202363 | etot = -14.6424332447151
-908000  ekin = 0.077575985596966 |  erot = 0.0805066337376087 | epot = -14.800515863912 | etot = -14.6424332445775
-909000  ekin = 0.0608876950043041 |  erot = 0.0673982354547353 | epot = -14.7707191749375 | etot = -14.6424332444784
-910000  ekin = 0.0515382922982525 |  erot = 0.0605415547693243 | epot = -14.7545130914978 | etot = -14.6424332444302
-911000  ekin = 0.0501789452889699 |  erot = 0.0600446989615507 | epot = -14.7526568886895 | etot = -14.642433244439
-912000  ekin = 0.0567846925720978 |  erot = 0.065790645022677 | epot = -14.7650085820984 | etot = -14.6424332445036
-913000  ekin = 0.0706603747930292 |  erot = 0.0774445361871137 | epot = -14.7905381555968 | etot = -14.6424332446166
-914000  ekin = 0.0905398584091615 |  erot = 0.0944735694308371 | epot = -14.8274466726047 | etot = -14.6424332447647
-915000  ekin = 0.114756144628398 |  erot = 0.116178630208142 | epot = -14.8733680197681 | etot = -14.6424332449316
-916000  ekin = 0.141447043402251 |  erot = 0.141736093139704 | epot = -14.9256163816432 | etot = -14.6424332451012
-917000  ekin = 0.168758535419812 |  erot = 0.170247440489189 | epot = -14.9814392211683 | etot = -14.6424332452593
-918000  ekin = 0.195014913439607 |  erot = 0.200793639368855 | epot = -15.0382417982036 | etot = -14.6424332453951
-919000  ekin = 0.218837422083647 |  erot = 0.232490666336242 | epot = -15.0937613339215 | etot = -14.6424332455016
-920000  ekin = 0.239206641023718 |  erot = 0.264542267092076 | epot = -15.1461821536915 | etot = -14.6424332455757
-921000  ekin = 0.255474577148654 |  erot = 0.296286050802385 | epot = -15.1941938735684 | etot = -14.6424332456174
-922000  ekin = 0.267338631215765 |  erot = 0.327229363205489 | epot = -15.2370012400499 | etot = -14.6424332456286
-923000  ekin = 0.274791412214202 |  erot = 0.357072039937939 | epot = -15.2742966977655 | etot = -14.6424332456134
-924000  ekin = 0.278059017516371 |  erot = 0.385714059433155 | epot = -15.3062063225259 | etot = -14.6424332455763
-925000  ekin = 0.277537405168372 |  erot = 0.41324722009601 | epot = -15.3332178707874 | etot = -14.642433245523
-926000  ekin = 0.273733135238329 |  erot = 0.439931173662005 | epot = -15.3560975543592 | etot = -14.6424332454589
-927000  ekin = 0.267211859641524 |  erot = 0.466155363882809 | epot = -15.3758004689143 | etot = -14.6424332453899
-928000  ekin = 0.258555847536078 |  erot = 0.492389553503158 | epot = -15.3933786463609 | etot = -14.6424332453217
-929000  ekin = 0.248330567891891 |  erot = 0.519126582982283 | epot = -15.4098903961336 | etot = -14.6424332452594
-930000  ekin = 0.237059747166165 |  erot = 0.546821711632301 | epot = -15.4263147040064 | etot = -14.6424332452079
-931000  ekin = 0.22520814480582 |  erot = 0.575833282923993 | epot = -15.4434746729008 | etot = -14.6424332451709
-932000  ekin = 0.213171319365827 |  erot = 0.606369490852174 | epot = -15.4619740553694 | etot = -14.6424332451514
-933000  ekin = 0.201271722995889 |  erot = 0.63844569037927 | epot = -15.482150658526 | etot = -14.6424332451508
-934000  ekin = 0.189760460110152 |  erot = 0.671856006699522 | epot = -15.5040497119791 | etot = -14.6424332451694
-935000  ekin = 0.178823941838377 |  erot = 0.706161996587761 | epot = -15.527419183632 | etot = -14.6424332452058
-936000  ekin = 0.168594479114955 |  erot = 0.740699865837585 | epot = -15.55172759021 | etot = -14.6424332452575
-937000  ekin = 0.159163635634861 |  erot = 0.774606336206385 | epot = -15.5762032171619 | etot = -14.6424332453207
-938000  ekin = 0.150596971914849 |  erot = 0.806861786796458 | epot = -15.5998920041019 | etot = -14.6424332453906
-939000  ekin = 0.142948711632359 |  erot = 0.836347883526831 | epot = -15.6217298406214 | etot = -14.6424332454622
-940000  ekin = 0.136274889171099 |  erot = 0.861915676028948 | epot = -15.64062381073 | etot = -14.6424332455299
-941000  ekin = 0.130643703198872 |  erot = 0.882459199120565 | epot = -15.6555361479082 | etot = -14.6424332455888
-942000  ekin = 0.126142088160694 |  erot = 0.896989065172162 | epot = -15.6655643989671 | etot = -14.6424332456342
-943000  ekin = 0.122877886110172 |  erot = 0.904700444358873 | epot = -15.6700115761318 | etot = -14.6424332456628
-944000  ekin = 0.120977407412063 |  erot = 0.905030230236876 | epot = -15.6684408833212 | etot = -14.6424332456723
-945000  ekin = 0.120578563690669 |  erot = 0.897699054745604 | epot = -15.6607108640983 | etot = -14.642433245662
-946000  ekin = 0.12182010359348 |  erot = 0.882735070928404 | epot = -15.6469884201544 | etot = -14.6424332456325
-947000  ekin = 0.124827761129084 |  erot = 0.86047793559626 | epot = -15.6277389423113 | etot = -14.642433245586
-948000  ekin = 0.129698334168674 |  erot = 0.831563037037796 | epot = -15.6036946167321 | etot = -14.6424332455257
-949000  ekin = 0.13648285755817 |  erot = 0.796887554722047 | epot = -15.5758036577362 | etot = -14.6424332454559
-950000  ekin = 0.14517013893121 |  erot = 0.757561255988166 | epot = -15.545164640301 | etot = -14.6424332453816
-951000  ekin = 0.155672002995183 |  erot = 0.71484591609363 | epot = -15.5129511643966 | etot = -14.6424332453078
-952000  ekin = 0.167811650836291 |  erot = 0.670087833250127 | epot = -15.480332729326 | etot = -14.6424332452396
-953000  ekin = 0.181316579471303 |  erot = 0.624648095211848 | epot = -15.4483979198644 | etot = -14.6424332451812
-954000  ekin = 0.195817500701208 |  erot = 0.579835080695611 | epot = -15.4180858265331 | etot = -14.6424332451363
-955000  ekin = 0.21085460687672 |  erot = 0.536843219768569 | epot = -15.3901310717525 | etot = -14.6424332451072
-956000  ekin = 0.225892299837344 |  erot = 0.496701376791255 | epot = -15.3650269217236 | etot = -14.642433245095
-957000  ekin = 0.240343066498587 |  erot = 0.460233438093626 | epot = -15.3430097496914 | etot = -14.6424332450992
-958000  ekin = 0.253600493839353 |  erot = 0.428032849893872 | epot = -15.324066588851 | etot = -14.6424332451178
-959000  ekin = 0.265080433748287 |  erot = 0.400452005458765 | epot = -15.3079656843544 | etot = -14.6424332451473
-960000  ekin = 0.274268068130606 |  erot = 0.377606549449485 | epot = -15.2943078627635 | etot = -14.6424332451834
-961000  ekin = 0.280767178003658 |  erot = 0.359393861249483 | epot = -15.2825942844742 | etot = -14.642433245221
-962000  ekin = 0.284346484063545 |  erot = 0.345524198816493 | epot = -15.2723039281349 | etot = -14.6424332452549
-963000  ekin = 0.28497681608998 |  erot = 0.33556223232907 | epot = -15.2629722936994 | etot = -14.6424332452804
-964000  ekin = 0.282852494248157 |  erot = 0.328975986496775 | epot = -15.2542617260389 | etot = -14.642433245294
-965000  ekin = 0.278391086615737 |  erot = 0.325189577598745 | epot = -15.2460139095084 | etot = -14.6424332452939
-966000  ekin = 0.272207924679743 |  erot = 0.323635640150781 | epot = -15.2382768101107 | etot = -14.6424332452802
-967000  ekin = 0.265065367870864 |  erot = 0.323803079987444 | epot = -15.2313016931133 | etot = -14.642433245255
-968000  ekin = 0.25780129371415 |  erot = 0.325275872290811 | epot = -15.2255104112269 | etot = -14.6424332452219
-969000  ekin = 0.251245661474385 |  erot = 0.327759142576306 | epot = -15.2214380492365 | etot = -14.6424332451859
-970000  ekin = 0.246137008993216 |  erot = 0.331089781181249 | epot = -15.2196600353262 | etot = -14.6424332451517
-971000  ekin = 0.243051319616145 |  erot = 0.33523032566537 | epot = -15.2207148904055 | etot = -14.642433245124
-972000  ekin = 0.242353409638764 |  erot = 0.340246678804933 | epot = -15.2250333335501 | etot = -14.6424332451064
-973000  ekin = 0.244176338162503 |  erot = 0.346272190710957 | epot = -15.2328817739746 | etot = -14.6424332451011
-974000  ekin = 0.248428661658007 |  erot = 0.353462430362089 | epot = -15.2443243371296 | etot = -14.6424332451095
-975000  ekin = 0.254824314802991 |  erot = 0.361946299430811 | epot = -15.2592038593653 | etot = -14.6424332451315
-976000  ekin = 0.262926848820441 |  erot = 0.371779749930123 | epot = -15.277139843917 | etot = -14.6424332451665
-977000  ekin = 0.272199235330791 |  erot = 0.382908123264411 | epot = -15.2975406038079 | etot = -14.6424332452127
-978000  ekin = 0.282052066851645 |  erot = 0.395142048097818 | epot = -15.3196273602177 | etot = -14.6424332452682
-979000  ekin = 0.291885751913936 |  erot = 0.408150081471835 | epot = -15.3424690787158 | etot = -14.6424332453301
-980000  ekin = 0.301125083789936 |  erot = 0.421469125223117 | epot = -15.365027454408 | etot = -14.642433245395
-981000  ekin = 0.309246535917406 |  erot = 0.434531423656849 | epot = -15.3862112050333 | etot = -14.642433245459
-982000  ekin = 0.315799497490907 |  erot = 0.446704965617073 | epot = -15.4049377086261 | etot = -14.6424332455181
-983000  ekin = 0.320422573221183 |  erot = 0.457342632744156 | epot = -15.4201984515336 | etot = -14.6424332455683
-984000  ekin = 0.322855465258642 |  erot = 0.465834622599602 | epot = -15.431123333464 | etot = -14.6424332456058
-985000  ekin = 0.322946302475343 |  erot = 0.471658590974231 | epot = -15.4370381390774 | etot = -14.6424332456279
-986000  ekin = 0.320653917805922 |  erot = 0.474422556590712 | epot = -15.4375097200295 | etot = -14.6424332456328
-987000  ekin = 0.316044627362369 |  erot = 0.473896755515841 | epot = -15.4323746284984 | etot = -14.6424332456202
-988000  ekin = 0.309283477268975 |  erot = 0.470032116945433 | epot = -15.421748839805 | etot = -14.6424332455906
-989000  ekin = 0.300620522169441 |  erot = 0.462964620622199 | epot = -15.4060183883375 | etot = -14.6424332455459
-990000  ekin = 0.290373280691476 |  erot = 0.45300626299518 | epot = -15.3858127891754 | etot = -14.6424332454887
-991000  ekin = 0.278906915705959 |  erot = 0.440624526219509 | epot = -15.3619646873478 | etot = -14.6424332454224
-992000  ekin = 0.266613826415441 |  erot = 0.426413006891514 | epot = -15.3354600786573 | etot = -14.6424332453503
-993000  ekin = 0.253894212446822 |  erot = 0.411056197524864 | epot = -15.3073836552479 | etot = -14.6424332452762
-994000  ekin = 0.241138837000364 |  erot = 0.395291372388786 | epot = -15.2788634545923 | etot = -14.6424332452032
-995000  ekin = 0.228714768907212 |  erot = 0.379870207855612 | epot = -15.2510182218971 | etot = -14.6424332451343
-996000  ekin = 0.2169544174706 |  erot = 0.365522282707863 | epot = -15.2249099452504 | etot = -14.642433245072
-997000  ekin = 0.206147766456188 |  erot = 0.352922066139109 | epot = -15.2015030776136 | etot = -14.6424332450183
-998000  ekin = 0.196537413157987 |  erot = 0.342660495991805 | epot = -15.1816311541246 | etot = -14.6424332449748
-999000  ekin = 0.188315843913178 |  erot = 0.335221830006205 | epot = -15.1659709188618 | etot = -14.6424332449424
-1000000  ekin = 0.181624323067817 |  erot = 0.330966139649826 | epot = -15.1550237076397 | etot = -14.642433244922
- 1000000  0.013453654   -1.5270261  0.011523695   -1.4973399 -8.4815516e-05 
-Loop time of 29.1595 on 4 procs for 1000000 steps with 10 atoms
-
-Performance: 29630.171 tau/day, 34294.179 timesteps/s
-96.5% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.8549     | 9.7585     | 17.369     | 226.0 | 33.47
-Bond    | 0.12382    | 0.38401    | 0.60938    |  32.9 |  1.32
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 2.9104     | 3.7862     | 4.6404     |  31.7 | 12.98
-Output  | 2e-05      | 2.775e-05  | 3.1e-05    |   0.0 |  0.00
-Modify  | 0.27411    | 1.1629     | 1.994      |  64.7 |  3.99
-Other   |            | 14.07      |            |       | 48.24
-
-Nlocal:    2.5 ave 5 max 0 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost:    7.5 ave 10 max 5 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Neighs:    17.5 ave 33 max 0 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-
-Total # of neighbors = 70
-Ave neighs/atom = 7
-Ave special neighs/atom = 3.6
-Neighbor list builds = 0
-Dangerous builds = 0
-
-#write_restart config.${number}.*
-Total wall time: 0:00:29
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 b/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2
index d80e7bbc0e..143e20c70b 100644
--- a/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2
+++ b/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2
@@ -31,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1
new file mode 100644
index 0000000000..be12914ad6
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1
@@ -0,0 +1,1168 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.0001 secs
+  read_data CPU = 0.001436 secs
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+#fix 1 all nve/dot
+fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
+fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10
+fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 1000000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.956
+  ghost atom cutoff = 1.956
+  binsize = 0.978, bins = 41 41 41
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
+Per MPI rank memory allocation (min/avg/max) = 2.838 | 2.838 | 2.838 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.5402493 0.0070469125   -1.5332024 6.0760034e-06 
+1000  ekin = 1.54234964773389 |  erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
+2000  ekin = 1.85988866919215 |  erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
+3000  ekin = 2.68354339452998 |  erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
+4000  ekin = 2.04461800191989 |  erot = 1.49015219763161 | epot = -24.2959428773347 | etot = -20.7611726777832
+5000  ekin = 1.76794859210155 |  erot = 2.54289684465819 | epot = -24.2337587736863 | etot = -19.9229133369266
+6000  ekin = 3.1106424806079 |  erot = 2.04409805200893 | epot = -24.1585729744133 | etot = -19.0038324417964
+7000  ekin = 3.21360097519306 |  erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
+8000  ekin = 2.82489935901743 |  erot = 2.66790555575695 | epot = -24.0194805097633 | etot = -18.526675594989
+9000  ekin = 2.69381302856378 |  erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
+10000  ekin = 2.65765007662471 |  erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
+11000  ekin = 2.33860420545645 |  erot = 2.06778039137701 | epot = -23.6589739475584 | etot = -19.2525893507249
+12000  ekin = 2.71377849618258 |  erot = 2.08757199120023 | epot = -23.5483571834756 | etot = -18.7470066960928
+13000  ekin = 2.62930153930326 |  erot = 2.36926332727578 | epot = -23.4509629615768 | etot = -18.4523980949977
+14000  ekin = 3.08200416316113 |  erot = 2.52340746291245 | epot = -23.3378147651053 | etot = -17.7324031390317
+15000  ekin = 2.98008664779269 |  erot = 1.871644860882 | epot = -23.1940665570191 | etot = -18.3423350483444
+16000  ekin = 2.18422481774796 |  erot = 2.13029325858585 | epot = -23.0709946755646 | etot = -18.7564765992308
+17000  ekin = 1.86029951221073 |  erot = 2.30856215831156 | epot = -22.9148241979648 | etot = -18.7459625274425
+18000  ekin = 2.26757205264074 |  erot = 1.23282183419698 | epot = -22.7667657090377 | etot = -19.2663718222
+19000  ekin = 2.39717301992408 |  erot = 2.43814713185076 | epot = -22.6249045514987 | etot = -17.7895843997239
+20000  ekin = 2.4972090427325 |  erot = 2.14695469209109 | epot = -22.4687873897505 | etot = -17.8246236549269
+21000  ekin = 2.97591775854817 |  erot = 2.40996811711196 | epot = -22.580475447988 | etot = -17.1945895723278
+22000  ekin = 3.04727168578733 |  erot = 1.83825256427931 | epot = -22.6695853833015 | etot = -17.7840611332348
+23000  ekin = 2.64835731773193 |  erot = 2.22162785501705 | epot = -22.6565689169972 | etot = -17.7865837442483
+24000  ekin = 2.64866576787001 |  erot = 2.80157082833923 | epot = -22.6222797420052 | etot = -17.172043145796
+25000  ekin = 2.29527970143855 |  erot = 2.22049811939068 | epot = -22.6228421013006 | etot = -18.1070642804714
+26000  ekin = 1.6242512251805 |  erot = 2.52390475262917 | epot = -22.6746055892862 | etot = -18.5264496114765
+27000  ekin = 1.74746467550781 |  erot = 3.7138606202505 | epot = -22.7150312690974 | etot = -17.253705973339
+28000  ekin = 2.26500128280479 |  erot = 2.34791343563182 | epot = -22.7926648585827 | etot = -18.1797501401461
+29000  ekin = 2.04774074424512 |  erot = 1.86347261547111 | epot = -22.8081204933408 | etot = -18.8969071336246
+30000  ekin = 2.41140146125466 |  erot = 1.8629691542147 | epot = -22.7764612164305 | etot = -18.5020906009611
+31000  ekin = 2.76447800297261 |  erot = 2.73932534046809 | epot = -22.7808698156252 | etot = -17.2770664721845
+32000  ekin = 2.08103539953574 |  erot = 2.81216171106145 | epot = -22.8081908465747 | etot = -17.9149937359775
+33000  ekin = 2.08672340074227 |  erot = 3.65510023442519 | epot = -22.7575363468642 | etot = -17.0157127116967
+34000  ekin = 2.34180742039869 |  erot = 3.10027175201876 | epot = -22.6657421559553 | etot = -17.2236629835378
+35000  ekin = 2.32430602395272 |  erot = 2.01607522370048 | epot = -22.5813705492547 | etot = -18.2409893016015
+36000  ekin = 1.91917507775106 |  erot = 1.97289747304336 | epot = -22.481118994336 | etot = -18.5890464435415
+37000  ekin = 1.57560528527468 |  erot = 2.63029511887644 | epot = -22.4456699464305 | etot = -18.2397695422794
+38000  ekin = 2.20652731867584 |  erot = 2.89671984141264 | epot = -22.3965902387972 | etot = -17.2933430787087
+39000  ekin = 2.54765822667969 |  erot = 2.47352619735436 | epot = -22.3525131983352 | etot = -17.3313287743011
+40000  ekin = 2.24172560748699 |  erot = 1.87314319107769 | epot = -22.3791956830638 | etot = -18.2643268844991
+41000  ekin = 2.45176361826215 |  erot = 2.49992612251746 | epot = -22.4441192111886 | etot = -17.492429470409
+42000  ekin = 2.68254780786499 |  erot = 2.0438213169699 | epot = -22.4352265851614 | etot = -17.7088574603265
+43000  ekin = 2.39383336858508 |  erot = 1.66587291396323 | epot = -22.4337243898147 | etot = -18.3740181072664
+44000  ekin = 2.30758870966957 |  erot = 2.39381816537747 | epot = -22.4636201484765 | etot = -17.7622132734295
+45000  ekin = 1.84308929771583 |  erot = 2.25880380151545 | epot = -22.5697712917434 | etot = -18.4678781925121
+46000  ekin = 1.98608215049724 |  erot = 3.02136983211364 | epot = -22.5606085774834 | etot = -17.5531565948725
+47000  ekin = 1.31457586857023 |  erot = 1.99780932836914 | epot = -22.5522289127255 | etot = -19.2398437157861
+48000  ekin = 2.59855199680394 |  erot = 1.90772345027383 | epot = -22.5972680906755 | etot = -18.0909926435977
+49000  ekin = 2.32140483916261 |  erot = 2.72932938830521 | epot = -22.6070371995253 | etot = -17.5563029720575
+50000  ekin = 2.48248035385828 |  erot = 3.42713570109106 | epot = -22.5294064222472 | etot = -16.6197903672978
+51000  ekin = 2.73677705777971 |  erot = 1.43285265191039 | epot = -22.4272695862992 | etot = -18.2576398766091
+52000  ekin = 3.03746109762767 |  erot = 1.97878223690382 | epot = -22.4105817052323 | etot = -17.3943383707008
+53000  ekin = 2.4689045601064 |  erot = 4.26434186327669 | epot = -22.4059567857723 | etot = -15.6727103623892
+54000  ekin = 2.48025904071626 |  erot = 2.36957879662633 | epot = -22.4049729842648 | etot = -17.5551351469222
+55000  ekin = 2.28269445417385 |  erot = 1.92149293107792 | epot = -22.4643082993723 | etot = -18.2601209141205
+56000  ekin = 2.36225428889468 |  erot = 2.21818002425494 | epot = -22.5516502452858 | etot = -17.9712159321362
+57000  ekin = 2.5222034650231 |  erot = 2.87044520913644 | epot = -22.6517599833464 | etot = -17.2591113091869
+58000  ekin = 2.50677816066749 |  erot = 2.80087142998997 | epot = -22.7046490897181 | etot = -17.3969994990606
+59000  ekin = 2.7442153349817 |  erot = 2.17375311266844 | epot = -22.7630968852436 | etot = -17.8451284375935
+60000  ekin = 3.28881699963203 |  erot = 1.98491245229836 | epot = -22.7493813857703 | etot = -17.47565193384
+61000  ekin = 2.42749732003947 |  erot = 1.80500042748844 | epot = -22.6954080097403 | etot = -18.4629102622124
+62000  ekin = 2.82051548232979 |  erot = 1.69220614985812 | epot = -22.5840860651656 | etot = -18.0713644329777
+63000  ekin = 3.66818847100114 |  erot = 1.91510536540652 | epot = -22.4235299160084 | etot = -16.8402360796007
+64000  ekin = 3.60192162647095 |  erot = 3.02302140162941 | epot = -22.4028966408393 | etot = -15.777953612739
+65000  ekin = 3.37797300912953 |  erot = 3.90646944425566 | epot = -22.3508227873684 | etot = -15.0663803339832
+66000  ekin = 2.90796062513305 |  erot = 2.46538835419996 | epot = -22.2656130116827 | etot = -16.8922640323497
+67000  ekin = 2.57641483706472 |  erot = 2.10639257083139 | epot = -22.1586423836372 | etot = -17.4758349757411
+68000  ekin = 2.55169027274651 |  erot = 2.46870040285814 | epot = -22.1454741588101 | etot = -17.1250834832055
+69000  ekin = 2.42897294997603 |  erot = 2.86774435615082 | epot = -22.1788582092805 | etot = -16.8821409031537
+70000  ekin = 3.08406596014674 |  erot = 2.51171720098585 | epot = -22.2680651617951 | etot = -16.6722820006625
+71000  ekin = 2.55052721315253 |  erot = 2.49486492124422 | epot = -22.3940848075588 | etot = -17.3486926731621
+72000  ekin = 1.77666138705941 |  erot = 2.52301579845698 | epot = -22.4956655989823 | etot = -18.195988413466
+73000  ekin = 1.86857924146303 |  erot = 2.33110810852355 | epot = -22.5401005215028 | etot = -18.3404131715162
+74000  ekin = 3.14875320805145 |  erot = 2.120028079616 | epot = -22.5354282257997 | etot = -17.2666469381323
+75000  ekin = 2.60566180511119 |  erot = 2.16421143606062 | epot = -22.5109742574449 | etot = -17.7411010162731
+76000  ekin = 1.94500512300058 |  erot = 1.94681992806367 | epot = -22.513456138446 | etot = -18.6216310873818
+77000  ekin = 2.09005510206219 |  erot = 2.13354294429721 | epot = -22.5157248384152 | etot = -18.2921267920558
+78000  ekin = 2.48381695181472 |  erot = 2.49598603867483 | epot = -22.449809286019 | etot = -17.4700062955294
+79000  ekin = 3.09582217320064 |  erot = 2.46630074007713 | epot = -22.3464652405845 | etot = -16.7843423273067
+80000  ekin = 2.51380629427529 |  erot = 1.89207626467031 | epot = -22.2775752521274 | etot = -17.8716926931818
+81000  ekin = 2.32322780911516 |  erot = 2.24954513249786 | epot = -22.2655235360185 | etot = -17.6927505944055
+82000  ekin = 1.54779729878415 |  erot = 2.01487148845306 | epot = -22.2126473128098 | etot = -18.6499785255726
+83000  ekin = 2.24267653112482 |  erot = 3.34721522119021 | epot = -22.2063282117648 | etot = -16.6164364594498
+84000  ekin = 2.86948852339533 |  erot = 2.11915315181828 | epot = -22.2055386975617 | etot = -17.2168970223481
+85000  ekin = 3.13802387827786 |  erot = 2.93900498543376 | epot = -22.2240733080823 | etot = -16.1470444443707
+86000  ekin = 3.46160079449537 |  erot = 2.80798287444336 | epot = -22.2732645073154 | etot = -16.0036808383767
+87000  ekin = 3.63139446909085 |  erot = 2.3166794204513 | epot = -22.2567856660101 | etot = -16.3087117764679
+88000  ekin = 3.15348314879937 |  erot = 2.27857637090329 | epot = -22.2154422326698 | etot = -16.7833827129672
+89000  ekin = 3.30271147105659 |  erot = 1.80791256125565 | epot = -22.1564153597822 | etot = -17.04579132747
+90000  ekin = 2.42655906518195 |  erot = 2.24507038389519 | epot = -21.9481188512568 | etot = -17.2764894021797
+91000  ekin = 1.89051217909395 |  erot = 2.51049066719492 | epot = -21.7877769537305 | etot = -17.3867741074417
+92000  ekin = 2.0783366846668 |  erot = 2.218324246302 | epot = -21.6997103074281 | etot = -17.4030493764594
+93000  ekin = 1.94321435585196 |  erot = 2.99473985773913 | epot = -21.6748650469777 | etot = -16.7369108333866
+94000  ekin = 2.07878576812463 |  erot = 3.37631892101902 | epot = -21.7659932416399 | etot = -16.3108885524962
+95000  ekin = 2.1051772140777 |  erot = 2.08345895044788 | epot = -21.8951718799354 | etot = -17.7065357154098
+96000  ekin = 2.68821593238919 |  erot = 1.86988637992411 | epot = -21.9622848400866 | etot = -17.4041825277733
+97000  ekin = 1.95061152706206 |  erot = 2.81054215683074 | epot = -22.0229813258884 | etot = -17.2618276419956
+98000  ekin = 1.98463063611221 |  erot = 2.05732763357978 | epot = -22.0930102039111 | etot = -18.0510519342191
+99000  ekin = 2.51292852217217 |  erot = 3.54194472638844 | epot = -22.1990887572979 | etot = -16.1442155087373
+100000  ekin = 1.8757570387949 |  erot = 2.36907855808758 | epot = -22.3484095874379 | etot = -18.1035739905555
+101000  ekin = 1.66160772204006 |  erot = 3.59766032223856 | epot = -22.3604908173889 | etot = -17.1012227731103
+102000  ekin = 1.62075182718473 |  erot = 3.34420068488168 | epot = -22.3063629504086 | etot = -17.3414104383422
+103000  ekin = 2.00871148652538 |  erot = 2.33677124900284 | epot = -22.2755578526919 | etot = -17.9300751171637
+104000  ekin = 2.04513709976292 |  erot = 2.74664593650968 | epot = -22.2818713634636 | etot = -17.490088327191
+105000  ekin = 1.87027868596139 |  erot = 1.9892238921824 | epot = -22.2235039092989 | etot = -18.3640013311551
+106000  ekin = 1.71540784443942 |  erot = 1.91779531106878 | epot = -22.2562839843324 | etot = -18.6230808288242
+107000  ekin = 2.61024905591622 |  erot = 1.57446439985465 | epot = -22.3171357124015 | etot = -18.1324222566306
+108000  ekin = 2.13751756724178 |  erot = 2.18822458113097 | epot = -22.2268794585968 | etot = -17.9011373102241
+109000  ekin = 2.24408198608307 |  erot = 2.11438299352725 | epot = -22.076564108576 | etot = -17.7180991289656
+110000  ekin = 1.66706562020821 |  erot = 2.50986066169371 | epot = -22.0833343008135 | etot = -17.9064080189116
+111000  ekin = 2.30463895640873 |  erot = 2.2498256085699 | epot = -22.0940837732695 | etot = -17.5396192082909
+112000  ekin = 2.63019524472748 |  erot = 2.43696110420533 | epot = -22.0953344558745 | etot = -17.0281781069417
+113000  ekin = 2.42282638113981 |  erot = 3.06190927482914 | epot = -22.1061661458172 | etot = -16.6214304898483
+114000  ekin = 2.34214572325658 |  erot = 2.31899235523686 | epot = -22.0941430549287 | etot = -17.4330049764353
+115000  ekin = 1.70336449422736 |  erot = 3.10166879044198 | epot = -22.1252095896431 | etot = -17.3201763049738
+116000  ekin = 1.51705870113214 |  erot = 2.21425252709697 | epot = -22.1823772627204 | etot = -18.4510660344913
+117000  ekin = 1.70129809180508 |  erot = 2.34142425076373 | epot = -22.2067668262467 | etot = -18.1640444836778
+118000  ekin = 2.20482827236051 |  erot = 2.31797148095037 | epot = -22.1855414590756 | etot = -17.6627417057647
+119000  ekin = 2.54272629601484 |  erot = 2.46528921750297 | epot = -22.2113175246519 | etot = -17.2033020111341
+120000  ekin = 1.76640390552554 |  erot = 2.16116304616033 | epot = -22.1536331723645 | etot = -18.2260662206786
+121000  ekin = 2.81281157959689 |  erot = 2.31761005518346 | epot = -22.1492969323238 | etot = -17.0188752975435
+122000  ekin = 3.25156823587966 |  erot = 3.31679050874321 | epot = -22.2050361016165 | etot = -15.6366773569937
+123000  ekin = 2.87462309654082 |  erot = 3.25604816714397 | epot = -22.1785374359393 | etot = -16.0478661722545
+124000  ekin = 2.18213410260632 |  erot = 2.77182209342783 | epot = -22.0161464482697 | etot = -17.0621902522356
+125000  ekin = 1.85317252616068 |  erot = 1.36623599567638 | epot = -21.8721650279343 | etot = -18.6527565060973
+126000  ekin = 2.47747071965844 |  erot = 3.09909384826332 | epot = -21.8840309142636 | etot = -16.3074663463419
+127000  ekin = 2.42177426273027 |  erot = 2.35209644429657 | epot = -21.8861939604609 | etot = -17.112323253434
+128000  ekin = 2.76000040231248 |  erot = 1.82316788372391 | epot = -21.8538456680959 | etot = -17.2706773820595
+129000  ekin = 2.78355536315488 |  erot = 2.888519816215 | epot = -21.9251039267855 | etot = -16.2530287474156
+130000  ekin = 3.26834278926798 |  erot = 2.56228354573333 | epot = -22.0546105678548 | etot = -16.2239842328535
+131000  ekin = 2.64714688907849 |  erot = 2.51107513446137 | epot = -22.096116019268 | etot = -16.9378939957281
+132000  ekin = 2.61847248883525 |  erot = 3.3889916433416 | epot = -22.1218916777657 | etot = -16.1144275455889
+133000  ekin = 2.03408861514006 |  erot = 2.87401070790187 | epot = -22.0785989417619 | etot = -17.17049961872
+134000  ekin = 1.64140897264888 |  erot = 1.66986416585675 | epot = -22.0323643102284 | etot = -18.7210911717227
+135000  ekin = 2.46650096367446 |  erot = 2.11112061110699 | epot = -21.9976572593398 | etot = -17.4200356845584
+136000  ekin = 2.32880805911731 |  erot = 3.05940125193233 | epot = -21.8983392007846 | etot = -16.510129889735
+137000  ekin = 2.7601019905106 |  erot = 2.47443779429795 | epot = -21.7521252642038 | etot = -16.5175854793953
+138000  ekin = 3.30162084678948 |  erot = 1.73084735415552 | epot = -21.7423849642074 | etot = -16.7099167632624
+139000  ekin = 2.76669064053124 |  erot = 1.72642745910432 | epot = -21.8898577306653 | etot = -17.3967396310297
+140000  ekin = 2.73595287215366 |  erot = 2.46891829250481 | epot = -21.9884857831832 | etot = -16.7836146185247
+141000  ekin = 2.79316289615843 |  erot = 2.46753088695596 | epot = -22.0064855648442 | etot = -16.7457917817298
+142000  ekin = 3.51694745558128 |  erot = 3.49862438784826 | epot = -21.962319333545 | etot = -14.9467474901155
+143000  ekin = 2.58689934548697 |  erot = 2.04008576044028 | epot = -21.9563338194556 | etot = -17.3293487135283
+144000  ekin = 3.72611917000993 |  erot = 3.04855733322794 | epot = -21.9536376487795 | etot = -15.1789611455416
+145000  ekin = 3.61191106831146 |  erot = 2.71915407989906 | epot = -21.8705426653329 | etot = -15.5394775171224
+146000  ekin = 3.85060594912678 |  erot = 2.47210219931339 | epot = -21.828585815392 | etot = -15.5058776669519
+147000  ekin = 3.26481933196161 |  erot = 2.06864347299802 | epot = -21.6752809049182 | etot = -16.3418180999586
+148000  ekin = 2.47977997895053 |  erot = 1.65169267241013 | epot = -21.4172781734275 | etot = -17.2858055220668
+149000  ekin = 2.70771685463074 |  erot = 2.28028425953226 | epot = -21.2324293178538 | etot = -16.2444282036908
+150000  ekin = 2.60726181496431 |  erot = 2.88955230103661 | epot = -21.1265494068529 | etot = -15.629735290852
+151000  ekin = 2.06865005733849 |  erot = 2.13537039813292 | epot = -21.0304193709382 | etot = -16.8263989154668
+152000  ekin = 2.41210154812788 |  erot = 2.60104053370076 | epot = -20.8967777045301 | etot = -15.8836356227015
+153000  ekin = 2.12406231442824 |  erot = 2.25444655142795 | epot = -20.9199278716093 | etot = -16.5414190057531
+154000  ekin = 2.34622678455546 |  erot = 2.58439374093404 | epot = -21.0040588663532 | etot = -16.0734383408637
+155000  ekin = 2.08240965570453 |  erot = 3.02621505767145 | epot = -21.0204738431415 | etot = -15.9118491297655
+156000  ekin = 2.04576145796301 |  erot = 3.17151405834468 | epot = -20.8558463949478 | etot = -15.6385708786401
+157000  ekin = 2.36459548410747 |  erot = 1.89207417055427 | epot = -20.8025485082276 | etot = -16.5458788535658
+158000  ekin = 2.16996178916575 |  erot = 2.46547727482115 | epot = -20.8673070433023 | etot = -16.2318679793154
+159000  ekin = 2.86272730849306 |  erot = 2.27590841865057 | epot = -20.9710387207244 | etot = -15.8324029935808
+160000  ekin = 2.19288173853783 |  erot = 2.36312829884112 | epot = -21.0403123366074 | etot = -16.4843022992285
+161000  ekin = 2.14059248149909 |  erot = 2.42872837990481 | epot = -21.1333683100402 | etot = -16.5640474486363
+162000  ekin = 1.76077466564934 |  erot = 2.66561836368342 | epot = -21.1782130850258 | etot = -16.751820055693
+163000  ekin = 2.23068698955416 |  erot = 2.02664945757243 | epot = -21.3281780197228 | etot = -17.0708415725962
+164000  ekin = 2.75358320318999 |  erot = 1.43717365990088 | epot = -21.4675480212853 | etot = -17.2767911581944
+165000  ekin = 2.65171600986478 |  erot = 2.29632253260763 | epot = -21.493178025826 | etot = -16.5451394833535
+166000  ekin = 3.27298673277591 |  erot = 2.41252396730594 | epot = -21.4477711984926 | etot = -15.7622604984108
+167000  ekin = 3.02574105268454 |  erot = 2.02770436019795 | epot = -21.5236773217565 | etot = -16.470231908874
+168000  ekin = 3.14659813654157 |  erot = 1.83746079413209 | epot = -21.5547269116735 | etot = -16.5706679809999
+169000  ekin = 2.22493755697303 |  erot = 2.67175500860651 | epot = -21.466220607731 | etot = -16.5695280421515
+170000  ekin = 2.41921977325642 |  erot = 2.49142716001799 | epot = -21.3123035293872 | etot = -16.4016565961128
+171000  ekin = 1.89798915040775 |  erot = 2.39492100285877 | epot = -21.2153991969518 | etot = -16.9224890436852
+172000  ekin = 2.86894215563085 |  erot = 3.22914449693157 | epot = -21.182735220644 | etot = -15.0846485680816
+173000  ekin = 2.74888252418688 |  erot = 2.13556434483052 | epot = -21.2166792789417 | etot = -16.3322324099243
+174000  ekin = 2.45887587066864 |  erot = 2.23682521338054 | epot = -21.263305665856 | etot = -16.5676045818068
+175000  ekin = 2.84703517745998 |  erot = 2.3938125491638 | epot = -21.2430876358358 | etot = -16.002239909212
+176000  ekin = 2.14025231000119 |  erot = 1.89894722702465 | epot = -21.3238321496633 | etot = -17.2846326126374
+177000  ekin = 2.5795061901144 |  erot = 2.75365074391217 | epot = -21.3022195274207 | etot = -15.9690625933941
+178000  ekin = 1.83122028490792 |  erot = 2.59468068841507 | epot = -21.2483113201278 | etot = -16.8224103468048
+179000  ekin = 2.50706581632049 |  erot = 2.39180466236872 | epot = -21.3152464598323 | etot = -16.4163759811431
+180000  ekin = 1.88211034410738 |  erot = 2.47063835849691 | epot = -21.4741119346399 | etot = -17.1213632320356
+181000  ekin = 1.74209654097779 |  erot = 3.05723824722444 | epot = -21.4808621715441 | etot = -16.6815273833419
+182000  ekin = 1.55789914013104 |  erot = 2.05767448814763 | epot = -21.423526482018 | etot = -17.8079528537393
+183000  ekin = 2.00937540548924 |  erot = 2.80898978674436 | epot = -21.491360735728 | etot = -16.6729955434944
+184000  ekin = 2.69285960778353 |  erot = 2.42969439668745 | epot = -21.6024209898207 | etot = -16.4798669853497
+185000  ekin = 3.01326925127938 |  erot = 3.19083239326424 | epot = -21.673025896793 | etot = -15.4689242522494
+186000  ekin = 3.20830671536381 |  erot = 2.428990168692 | epot = -21.7143665695974 | etot = -16.0770696855416
+187000  ekin = 2.67290610091901 |  erot = 3.415604047156 | epot = -21.6726605039612 | etot = -15.5841503558862
+188000  ekin = 2.89349337388583 |  erot = 3.06258669113778 | epot = -21.6216664732831 | etot = -15.6655864082595
+189000  ekin = 2.65435973176119 |  erot = 1.82043381700643 | epot = -21.5604872976484 | etot = -17.0856937488808
+190000  ekin = 2.21855159698309 |  erot = 1.84826944038784 | epot = -21.5263477340277 | etot = -17.4595266966568
+191000  ekin = 2.26980616064111 |  erot = 2.05944589507645 | epot = -21.4543005141096 | etot = -17.1250484583921
+192000  ekin = 2.27219103053707 |  erot = 3.11210788791053 | epot = -21.4899273087561 | etot = -16.1056283903085
+193000  ekin = 1.95008147026928 |  erot = 1.8964892153402 | epot = -21.4843079374127 | etot = -17.6377372518032
+194000  ekin = 2.45477671526092 |  erot = 2.02723042426762 | epot = -21.3709228769336 | etot = -16.8889157374051
+195000  ekin = 3.09567411006595 |  erot = 2.10081767143638 | epot = -21.3012041149762 | etot = -16.1047123334738
+196000  ekin = 2.67423122149492 |  erot = 2.5073818975552 | epot = -21.2164124023052 | etot = -16.0347992832551
+197000  ekin = 2.50338730962556 |  erot = 2.07349764616723 | epot = -21.0418674869219 | etot = -16.4649825311292
+198000  ekin = 2.66945928982615 |  erot = 1.79012921820211 | epot = -21.0169215356765 | etot = -16.5573330276482
+199000  ekin = 2.53947964790256 |  erot = 2.33176467953654 | epot = -21.0171165577067 | etot = -16.1458722302676
+200000  ekin = 2.90451062704866 |  erot = 1.42170066957003 | epot = -21.0113804229742 | etot = -16.6851691263555
+201000  ekin = 2.68927776239674 |  erot = 1.56650335894555 | epot = -21.024591639958 | etot = -16.7688105186157
+202000  ekin = 2.2601329351618 |  erot = 2.25401443373178 | epot = -20.9769308007641 | etot = -16.4627834318705
+203000  ekin = 2.12073487355488 |  erot = 2.03553028991747 | epot = -20.9190359464919 | etot = -16.7627707830196
+204000  ekin = 2.11829086582789 |  erot = 1.89731962488618 | epot = -20.9376264283537 | etot = -16.9220159376396
+205000  ekin = 1.30964171332167 |  erot = 2.12770406224884 | epot = -20.9991335630718 | etot = -17.5617877875013
+206000  ekin = 1.39940057572523 |  erot = 2.24496791209125 | epot = -20.9639192190619 | etot = -17.3195507312454
+207000  ekin = 1.8871608804017 |  erot = 1.79849326266381 | epot = -21.0552898160204 | etot = -17.3696356729549
+208000  ekin = 1.81558541079754 |  erot = 3.24210836817276 | epot = -21.3060144768833 | etot = -16.248320697913
+209000  ekin = 2.79588064252181 |  erot = 2.34671491738324 | epot = -21.4301997554494 | etot = -16.2876041955444
+210000  ekin = 3.17544887511568 |  erot = 3.12704516116656 | epot = -21.5100449360931 | etot = -15.2075508998109
+211000  ekin = 2.47442327377227 |  erot = 2.0990867711376 | epot = -21.6455723047062 | etot = -17.0720622597963
+212000  ekin = 2.36672302145397 |  erot = 1.93445871446417 | epot = -21.7283038297487 | etot = -17.4271220938306
+213000  ekin = 1.91045426241161 |  erot = 2.52535628540463 | epot = -21.8158508544504 | etot = -17.3800403066341
+214000  ekin = 1.99794025866062 |  erot = 2.49896939492129 | epot = -21.8606548137084 | etot = -17.3637451601265
+215000  ekin = 1.97741561009525 |  erot = 3.17667494473256 | epot = -21.8701701582032 | etot = -16.7160796033754
+216000  ekin = 1.88829990821377 |  erot = 1.87402623825167 | epot = -21.8343889393413 | etot = -18.0720627928758
+217000  ekin = 2.10000293878933 |  erot = 1.95052404495888 | epot = -21.8965404786646 | etot = -17.8460134949164
+218000  ekin = 2.34753598782339 |  erot = 1.696950195044 | epot = -21.8560027679963 | etot = -17.8115165851289
+219000  ekin = 2.497223564463 |  erot = 2.20999914485703 | epot = -21.8797649478059 | etot = -17.1725422384859
+220000  ekin = 1.75274593087922 |  erot = 3.03992746556403 | epot = -21.8491595252171 | etot = -17.0564861287739
+221000  ekin = 1.78874686645809 |  erot = 2.79359542964648 | epot = -21.869798634642 | etot = -17.2874563385374
+222000  ekin = 2.63608430516661 |  erot = 2.86817933637385 | epot = -21.8351218383832 | etot = -16.3308581968427
+223000  ekin = 3.02706758581511 |  erot = 1.93888641555348 | epot = -21.8582453001765 | etot = -16.8922912988079
+224000  ekin = 2.71704451339112 |  erot = 2.42079327531438 | epot = -21.8188420875657 | etot = -16.6810042988602
+225000  ekin = 2.04245190508396 |  erot = 3.38216222891908 | epot = -21.8232190868647 | etot = -16.3986049528616
+226000  ekin = 2.37968015829255 |  erot = 2.38384696857064 | epot = -21.8913549487127 | etot = -17.1278278218495
+227000  ekin = 2.73883397024414 |  erot = 2.62491632372019 | epot = -21.9496900700866 | etot = -16.5859397761223
+228000  ekin = 2.06833362780412 |  erot = 2.25049628751226 | epot = -21.9946760345141 | etot = -17.6758461191977
+229000  ekin = 1.78618617304217 |  erot = 1.8050959150033 | epot = -22.0671964085329 | etot = -18.4759143204874
+230000  ekin = 2.76967283780387 |  erot = 2.22492545317995 | epot = -22.0913590121729 | etot = -17.096760721189
+231000  ekin = 3.15653922952316 |  erot = 2.77099247609324 | epot = -22.0635255129442 | etot = -16.1359938073278
+232000  ekin = 1.86633326635991 |  erot = 1.70672288688982 | epot = -22.0959715052868 | etot = -18.5229153520371
+233000  ekin = 1.75856846080021 |  erot = 1.55694263125625 | epot = -22.0729289884755 | etot = -18.757417896419
+234000  ekin = 2.32322575892498 |  erot = 2.05793864740336 | epot = -21.9849429433607 | etot = -17.6037785370324
+235000  ekin = 1.95327191686568 |  erot = 2.5251933888586 | epot = -21.9357201856671 | etot = -17.4572548799429
+236000  ekin = 2.25952484966859 |  erot = 1.90005304846995 | epot = -21.942247136874 | etot = -17.7826692387355
+237000  ekin = 2.49082301609303 |  erot = 2.65327564887437 | epot = -22.0049130762793 | etot = -16.8608144113119
+238000  ekin = 2.21076048871751 |  erot = 2.74154862479022 | epot = -22.0553236426831 | etot = -17.1030145291753
+239000  ekin = 2.71464884454142 |  erot = 2.48739530580561 | epot = -22.0661894571024 | etot = -16.8641453067553
+240000  ekin = 3.08961933821573 |  erot = 2.17857064931928 | epot = -21.9596599475175 | etot = -16.6914699599825
+241000  ekin = 3.04172562407922 |  erot = 2.64442433974962 | epot = -21.8729500648239 | etot = -16.186800100995
+242000  ekin = 2.21355627539455 |  erot = 2.33429157450905 | epot = -21.7850463200937 | etot = -17.2371984701901
+243000  ekin = 1.52065138183895 |  erot = 2.81375224845252 | epot = -21.7246720043569 | etot = -17.3902683740654
+244000  ekin = 1.9035257658383 |  erot = 2.43821138840077 | epot = -21.6320468184553 | etot = -17.2903096642163
+245000  ekin = 1.96342069667741 |  erot = 2.61760141174562 | epot = -21.5097899449579 | etot = -16.9287678365349
+246000  ekin = 2.05478829283867 |  erot = 2.42643933263095 | epot = -21.4781109635141 | etot = -16.9968833380445
+247000  ekin = 1.54618395739204 |  erot = 2.28537401295508 | epot = -21.4411828355571 | etot = -17.60962486521
+248000  ekin = 1.83924983769608 |  erot = 2.55904554412921 | epot = -21.4587985205917 | etot = -17.0605031387664
+249000  ekin = 1.78703007063825 |  erot = 2.0341134947543 | epot = -21.5166075601389 | etot = -17.6954639947463
+250000  ekin = 1.69317901626952 |  erot = 3.38262002358101 | epot = -21.5380480709887 | etot = -16.4622490311382
+251000  ekin = 2.13799462687096 |  erot = 3.25868442484789 | epot = -21.5254595658407 | etot = -16.1287805141218
+252000  ekin = 2.04357045453397 |  erot = 2.53079336098229 | epot = -21.5456931883613 | etot = -16.9713293728451
+253000  ekin = 1.63287738205388 |  erot = 3.20992823373495 | epot = -21.5622010587546 | etot = -16.7193954429658
+254000  ekin = 2.31269246359595 |  erot = 3.10766702207072 | epot = -21.5505863172023 | etot = -16.1302268315356
+255000  ekin = 2.50767926641465 |  erot = 2.76631276495167 | epot = -21.5288449153182 | etot = -16.2548528839519
+256000  ekin = 1.97163698305487 |  erot = 2.61682132599932 | epot = -21.5273539828766 | etot = -16.9388956738224
+257000  ekin = 2.21091422886156 |  erot = 3.2624387389365 | epot = -21.5385504601778 | etot = -16.0651974923797
+258000  ekin = 2.0351730783025 |  erot = 1.8469346151236 | epot = -21.6544556001777 | etot = -17.7723479067517
+259000  ekin = 2.85718947138203 |  erot = 2.78701165242274 | epot = -21.7587237542941 | etot = -16.1145226304893
+260000  ekin = 2.90387286634677 |  erot = 2.18817434737476 | epot = -21.8080383126912 | etot = -16.7159910989697
+261000  ekin = 2.76190440948559 |  erot = 2.33968169215534 | epot = -21.8592909726424 | etot = -16.7577048710014
+262000  ekin = 3.50919242681177 |  erot = 1.76925994550144 | epot = -21.8779228441576 | etot = -16.5994704718444
+263000  ekin = 3.07696270254057 |  erot = 2.41477320555762 | epot = -21.807856600428 | etot = -16.3161206923298
+264000  ekin = 2.26633389925754 |  erot = 2.04161743361597 | epot = -21.837292812857 | etot = -17.5293414799835
+265000  ekin = 1.95747124461578 |  erot = 2.50813008798838 | epot = -21.8490876266416 | etot = -17.3834862940374
+266000  ekin = 2.34517905801099 |  erot = 3.31486209922485 | epot = -21.8287737874741 | etot = -16.1687326302383
+267000  ekin = 1.7403019336191 |  erot = 2.23366459528058 | epot = -21.699850097441 | etot = -17.7258835685413
+268000  ekin = 2.04858677018809 |  erot = 3.28744422098426 | epot = -21.6459408923622 | etot = -16.3099099011899
+269000  ekin = 1.93146929709292 |  erot = 2.79280735598121 | epot = -21.5497738027119 | etot = -16.8254971496378
+270000  ekin = 2.19788894271021 |  erot = 2.64563279687103 | epot = -21.4165389672397 | etot = -16.5730172276584
+271000  ekin = 2.21923220579694 |  erot = 3.10768708967445 | epot = -21.2197121954352 | etot = -15.8927928999638
+272000  ekin = 2.54992061853164 |  erot = 2.29721880581853 | epot = -21.0816515756818 | etot = -16.2345121513317
+273000  ekin = 1.91461840783801 |  erot = 2.01420401968474 | epot = -21.0503637141725 | etot = -17.1215412866498
+274000  ekin = 1.89671513770877 |  erot = 2.24334386161734 | epot = -21.09671034383 | etot = -16.9566513445039
+275000  ekin = 1.78930707116537 |  erot = 3.0975468786599 | epot = -21.1385700371941 | etot = -16.2517160873688
+276000  ekin = 3.37110328153969 |  erot = 2.4195732425753 | epot = -21.0908388312032 | etot = -15.3001623070883
+277000  ekin = 2.38921825148496 |  erot = 1.50604988822735 | epot = -21.0346208839969 | etot = -17.1393527442846
+278000  ekin = 2.51997301930637 |  erot = 2.14026171776895 | epot = -21.0117379332913 | etot = -16.351503196216
+279000  ekin = 1.88315206280857 |  erot = 2.37342905263992 | epot = -20.9993757709145 | etot = -16.742794655466
+280000  ekin = 2.33534713190787 |  erot = 3.5862646828722 | epot = -20.8573252930133 | etot = -14.9357134782333
+281000  ekin = 1.75252641954511 |  erot = 1.7907930540809 | epot = -20.9036528826791 | etot = -17.3603334090531
+282000  ekin = 2.26373977259215 |  erot = 3.04032073608634 | epot = -20.8497513702237 | etot = -15.5456908615452
+283000  ekin = 2.17833871394429 |  erot = 2.20833158301337 | epot = -20.8002776734785 | etot = -16.4136073765208
+284000  ekin = 1.9148667268656 |  erot = 2.21521993135969 | epot = -20.8277491648056 | etot = -16.6976625065803
+285000  ekin = 3.15634443167765 |  erot = 1.8003323160485 | epot = -21.0046435881196 | etot = -16.0479668403934
+286000  ekin = 3.8487757495733 |  erot = 1.82969969667575 | epot = -21.1628555811447 | etot = -15.4843801348956
+287000  ekin = 3.60615742824732 |  erot = 2.91608688151216 | epot = -21.2126952882302 | etot = -14.6904509784707
+288000  ekin = 3.19613259393802 |  erot = 1.67736393077136 | epot = -21.1713552834963 | etot = -16.297858758787
+289000  ekin = 2.45584885114799 |  erot = 2.77781979747334 | epot = -21.1669115721543 | etot = -15.9332429235329
+290000  ekin = 2.74570408981358 |  erot = 2.40443247852242 | epot = -21.1874427766533 | etot = -16.0373062083173
+291000  ekin = 2.10295274468233 |  erot = 2.37092484671536 | epot = -21.2419107014543 | etot = -16.7680331100566
+292000  ekin = 2.36118713930733 |  erot = 2.05558127949018 | epot = -21.3137361602548 | etot = -16.8969677414573
+293000  ekin = 2.27861963088251 |  erot = 2.35874555054765 | epot = -21.4302415460532 | etot = -16.7928763646231
+294000  ekin = 2.9331598281302 |  erot = 2.90313008187785 | epot = -21.5210917917479 | etot = -15.6848018817398
+295000  ekin = 2.66360761710435 |  erot = 2.28100565751945 | epot = -21.6885021477336 | etot = -16.7438888731098
+296000  ekin = 2.1876782716447 |  erot = 2.90589885547355 | epot = -21.7355037190159 | etot = -16.6419265918976
+297000  ekin = 2.15987738107364 |  erot = 3.29819575592636 | epot = -21.7177655658755 | etot = -16.2596924288755
+298000  ekin = 2.92956976611296 |  erot = 2.36377210613469 | epot = -21.6748271071565 | etot = -16.3814852349089
+299000  ekin = 3.19167138064488 |  erot = 2.23480811780852 | epot = -21.8042612344918 | etot = -16.3777817360384
+300000  ekin = 3.31335728469821 |  erot = 1.38932157247169 | epot = -21.8799906137234 | etot = -17.1773117565535
+301000  ekin = 2.39061971962409 |  erot = 3.30110260608967 | epot = -21.8919200817915 | etot = -16.2001977560777
+302000  ekin = 2.95446070602901 |  erot = 3.2304815881765 | epot = -21.8557645140423 | etot = -15.6708222198368
+303000  ekin = 2.44700205353934 |  erot = 2.60676303242281 | epot = -21.8414046718167 | etot = -16.7876395858546
+304000  ekin = 2.23578509140698 |  erot = 2.68770420047941 | epot = -21.7680601199659 | etot = -16.8445708280795
+305000  ekin = 2.35505207220215 |  erot = 2.38230031155849 | epot = -21.7344089784493 | etot = -16.9970565946886
+306000  ekin = 1.91790567526689 |  erot = 2.9010749400323 | epot = -21.717000482235 | etot = -16.8980198669359
+307000  ekin = 2.48241777758708 |  erot = 2.0836708009946 | epot = -21.6510481218459 | etot = -17.0849595432642
+308000  ekin = 2.77531620706104 |  erot = 2.63103510715158 | epot = -21.6349123878085 | etot = -16.2285610735959
+309000  ekin = 2.30440955942791 |  erot = 2.1249829765834 | epot = -21.5927938975113 | etot = -17.1634013615
+310000  ekin = 2.50879527040005 |  erot = 3.21338829421538 | epot = -21.6043932917724 | etot = -15.882209727157
+311000  ekin = 2.31939145866558 |  erot = 3.03649241514155 | epot = -21.6247503351754 | etot = -16.2688664613682
+312000  ekin = 1.78383134659847 |  erot = 3.26262247889992 | epot = -21.4948144284683 | etot = -16.4483606029699
+313000  ekin = 1.6465994694839 |  erot = 2.08133087588837 | epot = -21.4920309735611 | etot = -17.7641006281888
+314000  ekin = 2.2552391830868 |  erot = 2.55077633299238 | epot = -21.5103692936943 | etot = -16.7043537776152
+315000  ekin = 2.53527343915149 |  erot = 2.13089997124612 | epot = -21.5923709217299 | etot = -16.9261975113323
+316000  ekin = 1.99944427781285 |  erot = 1.80072924409704 | epot = -21.6039893771529 | etot = -17.803815855243
+317000  ekin = 2.11848744585804 |  erot = 2.01459693810074 | epot = -21.5948976630665 | etot = -17.4618132791077
+318000  ekin = 2.29013024301854 |  erot = 1.92405818620914 | epot = -21.564369594692 | etot = -17.3501811654644
+319000  ekin = 1.97314693278018 |  erot = 1.67996578959134 | epot = -21.455480840084 | etot = -17.8023681177125
+320000  ekin = 2.45681719546632 |  erot = 3.0783514449974 | epot = -21.39241255381 | etot = -15.8572439133463
+321000  ekin = 1.85729238455499 |  erot = 2.67083565671244 | epot = -21.4338188292509 | etot = -16.9056907879835
+322000  ekin = 1.96132292396412 |  erot = 3.36792274118282 | epot = -21.3663490830084 | etot = -16.0371034178615
+323000  ekin = 1.94437285233568 |  erot = 2.09558156605688 | epot = -21.4151250968679 | etot = -17.3751706784753
+324000  ekin = 2.229181524904 |  erot = 2.4674418745061 | epot = -21.5323859085629 | etot = -16.8357625091528
+325000  ekin = 2.74582842770392 |  erot = 2.36717454305098 | epot = -21.6443544237971 | etot = -16.5313514530422
+326000  ekin = 1.91124551133375 |  erot = 1.93084217743114 | epot = -21.7077957426601 | etot = -17.8657080538952
+327000  ekin = 3.05627483509655 |  erot = 1.67325209460962 | epot = -21.7948818019127 | etot = -17.0653548722066
+328000  ekin = 2.73933273476856 |  erot = 1.92380912803776 | epot = -21.8364014823585 | etot = -17.1732596195522
+329000  ekin = 2.95907896099514 |  erot = 3.1565416835668 | epot = -21.898199971646 | etot = -15.782579327084
+330000  ekin = 2.90795110595274 |  erot = 2.01765890034967 | epot = -21.9037795505257 | etot = -16.9781695442233
+331000  ekin = 2.27446048340228 |  erot = 2.03754878634057 | epot = -21.8760842049291 | etot = -17.5640749351862
+332000  ekin = 2.43262938612094 |  erot = 3.19219171897212 | epot = -21.9305186945661 | etot = -16.3056975894731
+333000  ekin = 2.47357651298171 |  erot = 2.700610458147 | epot = -22.0416691323271 | etot = -16.8674821611983
+334000  ekin = 2.38171387374892 |  erot = 3.00424927873367 | epot = -22.0746318522987 | etot = -16.6886686998161
+335000  ekin = 2.10465470910016 |  erot = 3.57382014016835 | epot = -22.1175420615631 | etot = -16.4390672122946
+336000  ekin = 2.61374577374184 |  erot = 2.133869272813 | epot = -22.0898825119599 | etot = -17.3422674654051
+337000  ekin = 2.72124526751511 |  erot = 2.748004804814 | epot = -22.076853713162 | etot = -16.6076036408329
+338000  ekin = 1.83524121485422 |  erot = 2.24338894827196 | epot = -22.1591955034455 | etot = -18.0805653403193
+339000  ekin = 1.54928432997333 |  erot = 2.49812246084902 | epot = -22.2022398834669 | etot = -18.1548330926446
+340000  ekin = 1.44405714940631 |  erot = 4.0451327092417 | epot = -22.1149458734012 | etot = -16.6257560147532
+341000  ekin = 1.67447392575554 |  erot = 2.77749751745985 | epot = -22.0760831546714 | etot = -17.624111711456
+342000  ekin = 1.9825676117275 |  erot = 2.71655566521085 | epot = -22.1563522566983 | etot = -17.4572289797599
+343000  ekin = 2.68213676683887 |  erot = 3.16686462846914 | epot = -22.2498477633288 | etot = -16.4008463680208
+344000  ekin = 1.77905771753907 |  erot = 2.19153667254072 | epot = -22.2907212723871 | etot = -18.3201268823073
+345000  ekin = 1.5460499615042 |  erot = 1.85960255696713 | epot = -22.3447003428976 | etot = -18.9390478244263
+346000  ekin = 1.71554664484034 |  erot = 1.79880968736712 | epot = -22.3117022609054 | etot = -18.7973459286979
+347000  ekin = 1.38672912049481 |  erot = 2.61484473767932 | epot = -22.3325032395119 | etot = -18.3309293813378
+348000  ekin = 2.15015924850684 |  erot = 2.86300326453563 | epot = -22.3337312775956 | etot = -17.3205687645531
+349000  ekin = 1.83066085453602 |  erot = 1.98441326494869 | epot = -22.3967822584584 | etot = -18.5817081389737
+350000  ekin = 1.83318738252649 |  erot = 2.56907029661255 | epot = -22.4577827539416 | etot = -18.0555250748025
+351000  ekin = 1.72790505260219 |  erot = 2.87456274671835 | epot = -22.5159555107051 | etot = -17.9134877113846
+352000  ekin = 2.80786740016944 |  erot = 2.0875044812577 | epot = -22.6549834386892 | etot = -17.759611557262
+353000  ekin = 3.5492801472091 |  erot = 1.42584537334882 | epot = -22.6849212734238 | etot = -17.7097957528659
+354000  ekin = 3.49129244374804 |  erot = 2.25156548638802 | epot = -22.6041826206929 | etot = -16.8613246905569
+355000  ekin = 2.06248783371663 |  erot = 2.92733565233051 | epot = -22.5494488364626 | etot = -17.5596253504155
+356000  ekin = 2.13415426306311 |  erot = 3.32668319049642 | epot = -22.6122425286522 | etot = -17.1514050750926
+357000  ekin = 2.75897049849731 |  erot = 2.51843165594441 | epot = -22.6042888591884 | etot = -17.3268867047467
+358000  ekin = 2.51778220496547 |  erot = 2.28374144764325 | epot = -22.5654155469983 | etot = -17.7638918943896
+359000  ekin = 3.2037278512604 |  erot = 2.5552016027623 | epot = -22.6749569097325 | etot = -16.9160274557098
+360000  ekin = 2.52669169359922 |  erot = 1.97563796824026 | epot = -22.7314557612253 | etot = -18.2291260993859
+361000  ekin = 2.60424632123629 |  erot = 2.51068088850828 | epot = -22.771502374375 | etot = -17.6565751646305
+362000  ekin = 2.43350156723209 |  erot = 3.84566788758402 | epot = -22.7352151098033 | etot = -16.4560456549872
+363000  ekin = 2.91069717970493 |  erot = 1.99710098714123 | epot = -22.6302259934473 | etot = -17.7224278266012
+364000  ekin = 2.25538328683251 |  erot = 1.87832387363457 | epot = -22.508362529619 | etot = -18.3746553691519
+365000  ekin = 2.04575884197224 |  erot = 2.79774206841199 | epot = -22.3322627384259 | etot = -17.4887618280416
+366000  ekin = 2.26894187965217 |  erot = 1.94379382552235 | epot = -22.2788727984905 | etot = -18.066137093316
+367000  ekin = 2.82509630766736 |  erot = 2.50361468767087 | epot = -22.3209381619451 | etot = -16.9922271666069
+368000  ekin = 2.81542036602321 |  erot = 2.1873362764449 | epot = -22.4297259451244 | etot = -17.4269693026563
+369000  ekin = 2.30426035796381 |  erot = 2.85653411706989 | epot = -22.4923286665587 | etot = -17.331534191525
+370000  ekin = 2.67871033327546 |  erot = 2.11464921695178 | epot = -22.5780698607969 | etot = -17.7847103105697
+371000  ekin = 2.19281044135006 |  erot = 3.6016596066429 | epot = -22.6424730832336 | etot = -16.8480030352406
+372000  ekin = 1.77481259468411 |  erot = 3.40654744438101 | epot = -22.7147683829007 | etot = -17.5334083438356
+373000  ekin = 2.15551547517191 |  erot = 2.78778252361832 | epot = -22.755949721432 | etot = -17.8126517226417
+374000  ekin = 2.71938368055485 |  erot = 3.58127823243844 | epot = -22.9084433694728 | etot = -16.6077814564795
+375000  ekin = 2.42759321485977 |  erot = 2.97421271787163 | epot = -22.9740378563777 | etot = -17.5722319236463
+376000  ekin = 3.39126830110572 |  erot = 3.24733797625005 | epot = -22.9874015798134 | etot = -16.3487953024577
+377000  ekin = 3.20966733323473 |  erot = 2.6593406036448 | epot = -22.9452111216364 | etot = -17.0762031847569
+378000  ekin = 1.56095946168132 |  erot = 2.6615903394499 | epot = -22.9575870308252 | etot = -18.735037229694
+379000  ekin = 1.94985687485381 |  erot = 2.5408521625583 | epot = -22.9834751642938 | etot = -18.4927661268817
+380000  ekin = 2.65820438237073 |  erot = 2.88045867212572 | epot = -22.9984703542082 | etot = -17.4598072997117
+381000  ekin = 2.97084599252829 |  erot = 2.18892549461573 | epot = -23.0341895570111 | etot = -17.8744180698671
+382000  ekin = 2.61355176942653 |  erot = 2.02938704043227 | epot = -23.0084119715099 | etot = -18.3654731616511
+383000  ekin = 2.03830671072154 |  erot = 2.50516194855526 | epot = -23.0393965606452 | etot = -18.4959279013684
+384000  ekin = 2.1060608733416 |  erot = 2.21840250458949 | epot = -23.0602182522592 | etot = -18.7357548743281
+385000  ekin = 1.89114918519107 |  erot = 1.63701051320101 | epot = -23.0834434146805 | etot = -19.5552837162885
+386000  ekin = 1.55124380123707 |  erot = 1.36147797265396 | epot = -23.1300518396948 | etot = -20.2173300658038
+387000  ekin = 2.19627825752355 |  erot = 1.75751396098972 | epot = -23.1280875332419 | etot = -19.1742953147286
+388000  ekin = 1.96387084539616 |  erot = 1.95852585326806 | epot = -23.0327752892414 | etot = -19.1103785905772
+389000  ekin = 2.50801560941705 |  erot = 2.32519825784834 | epot = -23.0011464671234 | etot = -18.167932599858
+390000  ekin = 2.03596866068489 |  erot = 1.88295618907178 | epot = -22.8810338311574 | etot = -18.9621089814008
+391000  ekin = 1.8098591016452 |  erot = 2.39622167162876 | epot = -22.8195566463199 | etot = -18.613475873046
+392000  ekin = 2.17725370142732 |  erot = 2.87094426544089 | epot = -22.7839731045438 | etot = -17.7357751376756
+393000  ekin = 2.14224634181996 |  erot = 3.1724297430366 | epot = -22.8435025538356 | etot = -17.5288264689791
+394000  ekin = 1.97769550804366 |  erot = 2.16375300420729 | epot = -22.8342667825711 | etot = -18.6928182703201
+395000  ekin = 2.03687268736298 |  erot = 2.49567469731649 | epot = -22.8892034986303 | etot = -18.3566561139508
+396000  ekin = 2.16189109047463 |  erot = 1.95308746486161 | epot = -22.9781386034885 | etot = -18.8631600481523
+397000  ekin = 2.41744222422408 |  erot = 1.65310699287474 | epot = -23.0900453292844 | etot = -19.0194961121856
+398000  ekin = 3.58905654436294 |  erot = 2.5193025650333 | epot = -23.2070733343384 | etot = -17.0987142249422
+399000  ekin = 2.65051654249497 |  erot = 1.78138450529863 | epot = -23.3040478764214 | etot = -18.8721468286278
+400000  ekin = 2.49402752614129 |  erot = 2.10290777432181 | epot = -23.3608759462318 | etot = -18.7639406457687
+401000  ekin = 2.04176177605463 |  erot = 2.154995213856 | epot = -23.403960339401 | etot = -19.2072033494904
+402000  ekin = 2.4450587586146 |  erot = 2.11318097973378 | epot = -23.3975262709887 | etot = -18.8392865326403
+403000  ekin = 2.54858079745147 |  erot = 2.81138206601918 | epot = -23.4760646986769 | etot = -18.1161018352062
+404000  ekin = 2.21063952462117 |  erot = 2.64710865829565 | epot = -23.574696037266 | etot = -18.7169478543492
+405000  ekin = 2.47328118101333 |  erot = 2.40933750599425 | epot = -23.5927917139468 | etot = -18.7101730269392
+406000  ekin = 2.24891173527799 |  erot = 2.23777884116048 | epot = -23.6086191890416 | etot = -19.1219286126031
+407000  ekin = 2.0107940045037 |  erot = 2.78642832526901 | epot = -23.5246032469977 | etot = -18.727380917225
+408000  ekin = 2.59464051790823 |  erot = 2.59123578102095 | epot = -23.4198302602655 | etot = -18.2339539613363
+409000  ekin = 2.37170880608735 |  erot = 2.26136902851216 | epot = -23.3172581937239 | etot = -18.6841803591244
+410000  ekin = 1.99754661347186 |  erot = 1.95523998485755 | epot = -23.2950402043272 | etot = -19.3422536059978
+411000  ekin = 1.8693657058423 |  erot = 2.63899492681176 | epot = -23.249036763304 | etot = -18.7406761306499
+412000  ekin = 1.98214047746227 |  erot = 2.68315820775203 | epot = -23.198735748328 | etot = -18.5334370631137
+413000  ekin = 2.39078873487372 |  erot = 2.65589562872907 | epot = -23.1435198518626 | etot = -18.0968354882598
+414000  ekin = 2.40821090859774 |  erot = 1.75574324408226 | epot = -23.0725048141376 | etot = -18.9085506614576
+415000  ekin = 2.74601981183014 |  erot = 2.43675176686817 | epot = -23.1211711904485 | etot = -17.9383996117502
+416000  ekin = 2.08828454200993 |  erot = 2.7678350652622 | epot = -23.1383119239964 | etot = -18.2821923167243
+417000  ekin = 2.01455344430628 |  erot = 1.95306265456051 | epot = -23.1433633505286 | etot = -19.1757472516618
+418000  ekin = 2.42716528853986 |  erot = 2.57642821145487 | epot = -23.1275317971309 | etot = -18.1239382971362
+419000  ekin = 3.04095103685797 |  erot = 2.58427576972737 | epot = -23.0602279332616 | etot = -17.4350011266763
+420000  ekin = 2.6360746280152 |  erot = 2.44478111019392 | epot = -22.9820923151719 | etot = -17.9012365769628
+421000  ekin = 2.53019765722915 |  erot = 1.78389585255477 | epot = -22.9707435541328 | etot = -18.6566500443489
+422000  ekin = 2.72457425772367 |  erot = 1.6776863488635 | epot = -22.9542997027494 | etot = -18.5520390961622
+423000  ekin = 2.11402997037893 |  erot = 2.55034580375606 | epot = -22.8263851956496 | etot = -18.1620094215146
+424000  ekin = 1.8895880210325 |  erot = 2.31332431343562 | epot = -22.7726668881719 | etot = -18.5697545537038
+425000  ekin = 2.3595116370971 |  erot = 1.95762380637299 | epot = -22.7752082759345 | etot = -18.4580728324644
+426000  ekin = 2.23706657164627 |  erot = 2.60016134755149 | epot = -22.7844114251539 | etot = -17.9471835059561
+427000  ekin = 1.88801598248841 |  erot = 2.12415782350884 | epot = -22.9416586386638 | etot = -18.9294848326665
+428000  ekin = 1.92849031333042 |  erot = 2.44097902588718 | epot = -23.0611368174398 | etot = -18.6916674782222
+429000  ekin = 1.70536802258415 |  erot = 2.14916257389791 | epot = -23.0556586745392 | etot = -19.2011280780571
+430000  ekin = 2.30226095973205 |  erot = 2.14689932813605 | epot = -23.0606502516207 | etot = -18.6114899637526
+431000  ekin = 2.45988288454318 |  erot = 2.42278380298656 | epot = -23.072977722388 | etot = -18.1903110348583
+432000  ekin = 2.80869332724974 |  erot = 2.19954129490929 | epot = -23.0939746542043 | etot = -18.0857400320453
+433000  ekin = 2.21130556188281 |  erot = 1.62882156110629 | epot = -23.1534080352157 | etot = -19.3132809122266
+434000  ekin = 2.60574953870751 |  erot = 2.36088790768805 | epot = -23.1901717047878 | etot = -18.2235342583922
+435000  ekin = 2.30377529593091 |  erot = 2.53917715731258 | epot = -23.1716983948431 | etot = -18.3287459415996
+436000  ekin = 2.42707603554826 |  erot = 2.75234181061923 | epot = -23.2197996577196 | etot = -18.0403818115521
+437000  ekin = 1.65090540276075 |  erot = 3.25345231298367 | epot = -23.2216366145387 | etot = -18.3172788987943
+438000  ekin = 1.56145302974407 |  erot = 2.60950810563797 | epot = -23.1303770792278 | etot = -18.9594159438457
+439000  ekin = 2.30955439722235 |  erot = 1.94011743371101 | epot = -23.1353170794496 | etot = -18.8856452485163
+440000  ekin = 2.53037674867674 |  erot = 3.06527042861028 | epot = -23.1968589452919 | etot = -17.6012117680049
+441000  ekin = 2.80107707952535 |  erot = 2.53664155736543 | epot = -23.1712373428918 | etot = -17.833518706001
+442000  ekin = 2.92536323090713 |  erot = 2.88384500930019 | epot = -23.1123001627208 | etot = -17.3030919225134
+443000  ekin = 1.96543935969483 |  erot = 1.75344963155201 | epot = -23.0380529084377 | etot = -19.3191639171909
+444000  ekin = 2.00309477401364 |  erot = 2.23897509587737 | epot = -22.9472103119533 | etot = -18.7051404420622
+445000  ekin = 2.20302071819723 |  erot = 2.06928381371827 | epot = -22.7775434364172 | etot = -18.5052389045017
+446000  ekin = 2.43487889302299 |  erot = 2.377515560078 | epot = -22.6838190597697 | etot = -17.8714246066687
+447000  ekin = 2.2620819636031 |  erot = 2.41400188145195 | epot = -22.7082516636545 | etot = -18.0321678185995
+448000  ekin = 2.16184472791984 |  erot = 1.93539407204276 | epot = -22.8144859493263 | etot = -18.7172471493637
+449000  ekin = 2.21107967973114 |  erot = 2.3465968297874 | epot = -22.9059503054159 | etot = -18.3482737958973
+450000  ekin = 2.74677740004439 |  erot = 1.97222921372039 | epot = -22.860755926716 | etot = -18.1417493129512
+451000  ekin = 2.2050889378155 |  erot = 2.13042736119388 | epot = -22.8862608894795 | etot = -18.5507445904702
+452000  ekin = 2.52760608607095 |  erot = 2.34006815636601 | epot = -22.9138111972132 | etot = -18.0461369547763
+453000  ekin = 2.23448825172916 |  erot = 1.77834418215733 | epot = -22.887923830179 | etot = -18.8750913962925
+454000  ekin = 2.4343851915949 |  erot = 2.59700848533281 | epot = -22.8184361849035 | etot = -17.7870425079758
+455000  ekin = 2.04195793930991 |  erot = 2.79639043747678 | epot = -22.6032980500353 | etot = -17.7649496732486
+456000  ekin = 2.00799933710202 |  erot = 2.53653815407518 | epot = -22.4355596266521 | etot = -17.8910221354749
+457000  ekin = 2.60426208759882 |  erot = 2.4660961287619 | epot = -22.3409120082077 | etot = -17.270553791847
+458000  ekin = 2.01368468059036 |  erot = 1.99613816245311 | epot = -22.2549400327204 | etot = -18.245117189677
+459000  ekin = 1.73688781588864 |  erot = 2.48572034306896 | epot = -22.2282088298766 | etot = -18.005600670919
+460000  ekin = 1.91682575775988 |  erot = 2.08308677023945 | epot = -22.2211874714415 | etot = -18.2212749434422
+461000  ekin = 1.54933673126937 |  erot = 1.29454502815254 | epot = -22.1945151049366 | etot = -19.3506333455147
+462000  ekin = 2.44160489340629 |  erot = 1.34721473707676 | epot = -22.2846713076969 | etot = -18.4958516772139
+463000  ekin = 2.63165365707666 |  erot = 2.0814376012804 | epot = -22.4004513395624 | etot = -17.6873600812053
+464000  ekin = 2.67929276186416 |  erot = 3.72563793061089 | epot = -22.5200042545287 | etot = -16.1150735620537
+465000  ekin = 1.94880111369478 |  erot = 2.23148844819347 | epot = -22.6855542963289 | etot = -18.5052647344406
+466000  ekin = 2.1385304963889 |  erot = 2.95056624305954 | epot = -22.7822881705531 | etot = -17.6931914311046
+467000  ekin = 2.46452767169614 |  erot = 2.10778480770081 | epot = -22.9485753844865 | etot = -18.3762629050896
+468000  ekin = 1.98589158006998 |  erot = 1.62816092182055 | epot = -23.0180008829523 | etot = -19.4039483810618
+469000  ekin = 2.498810820967 |  erot = 2.63615462725918 | epot = -23.054783396884 | etot = -17.9198179486578
+470000  ekin = 2.91491361681312 |  erot = 3.19115611298995 | epot = -23.0448741101698 | etot = -16.9388043803668
+471000  ekin = 2.37554627514204 |  erot = 1.71739792236247 | epot = -22.9932329645512 | etot = -18.9002887670467
+472000  ekin = 2.18486807923518 |  erot = 2.00687069908099 | epot = -22.9563182572701 | etot = -18.7645794789539
+473000  ekin = 2.36185345820898 |  erot = 2.86259041401026 | epot = -22.9161024426124 | etot = -17.6916585703932
+474000  ekin = 2.17077693495272 |  erot = 2.59376596740917 | epot = -22.7894018760352 | etot = -18.0248589736733
+475000  ekin = 2.37844153079293 |  erot = 2.01112751381906 | epot = -22.6793191497968 | etot = -18.2897501051848
+476000  ekin = 2.08763676439641 |  erot = 2.5964762445522 | epot = -22.6700039875051 | etot = -17.9858909785565
+477000  ekin = 2.52249432714936 |  erot = 3.55251934739866 | epot = -22.6424099194916 | etot = -16.5673962449435
+478000  ekin = 2.40424947791157 |  erot = 2.73239117258612 | epot = -22.5447763252279 | etot = -17.4081356747302
+479000  ekin = 1.27637524434413 |  erot = 2.99749792697948 | epot = -22.4994949498981 | etot = -18.2256217785744
+480000  ekin = 1.81374950293816 |  erot = 2.1438931713594 | epot = -22.4678405170784 | etot = -18.5101978427808
+481000  ekin = 2.39496774186199 |  erot = 3.18299441824516 | epot = -22.4930736763177 | etot = -16.9151115162106
+482000  ekin = 3.21051763720184 |  erot = 2.40962326270832 | epot = -22.4479376181303 | etot = -16.8277967182201
+483000  ekin = 3.06081116762376 |  erot = 2.49856996934408 | epot = -22.4288948733282 | etot = -16.8695137363604
+484000  ekin = 2.7452293328759 |  erot = 2.53012629993102 | epot = -22.483756332919 | etot = -17.2084007001121
+485000  ekin = 3.3310309518052 |  erot = 2.42091818181916 | epot = -22.4922555047181 | etot = -16.7403063710937
+486000  ekin = 1.99323479363108 |  erot = 1.76127718142274 | epot = -22.5432098594131 | etot = -18.7886978843592
+487000  ekin = 2.64825718911654 |  erot = 2.50204426232018 | epot = -22.6407366935241 | etot = -17.4904352420874
+488000  ekin = 1.76385891719471 |  erot = 2.64266555173499 | epot = -22.6990728058785 | etot = -18.2925483369488
+489000  ekin = 2.10357630534276 |  erot = 2.95613916443126 | epot = -22.7877124402072 | etot = -17.7279969704332
+490000  ekin = 2.33515649128315 |  erot = 2.32995416999058 | epot = -22.7920703811402 | etot = -18.1269597198665
+491000  ekin = 2.48752587426648 |  erot = 2.58310949760556 | epot = -22.7834811495388 | etot = -17.7128457776667
+492000  ekin = 3.2982066520449 |  erot = 2.18682924183924 | epot = -22.7674519489923 | etot = -17.2824160551081
+493000  ekin = 3.40238156707507 |  erot = 2.35717041222451 | epot = -22.7149408840448 | etot = -16.9553889047452
+494000  ekin = 3.59348050162499 |  erot = 2.23182460532056 | epot = -22.708168229549 | etot = -16.8828631226035
+495000  ekin = 2.52030309238563 |  erot = 2.16229430067424 | epot = -22.6973031832711 | etot = -18.0147057902112
+496000  ekin = 1.96100991422337 |  erot = 3.58581695215167 | epot = -22.7342002900882 | etot = -17.1873734237132
+497000  ekin = 2.22286479259681 |  erot = 2.49495319949133 | epot = -22.752706201593 | etot = -18.0348882095048
+498000  ekin = 1.71033952564695 |  erot = 2.41331591511583 | epot = -22.7131621100867 | etot = -18.5895066693239
+499000  ekin = 2.4191986430073 |  erot = 2.8234951953182 | epot = -22.7304918052926 | etot = -17.4877979669671
+500000  ekin = 2.76271068346558 |  erot = 2.22796445937143 | epot = -22.810945568044 | etot = -17.820270425207
+501000  ekin = 2.97642553987186 |  erot = 1.97769778889399 | epot = -22.8306304048615 | etot = -17.8765070760957
+502000  ekin = 2.96175345860855 |  erot = 1.80859086419486 | epot = -22.8525538190094 | etot = -18.082209496206
+503000  ekin = 2.51126831088416 |  erot = 2.88572311841927 | epot = -22.8673362278445 | etot = -17.4703447985411
+504000  ekin = 2.84611165351303 |  erot = 2.67626783872459 | epot = -22.784891957601 | etot = -17.2625124653634
+505000  ekin = 2.96124584448914 |  erot = 2.59100575301931 | epot = -22.8251284225259 | etot = -17.2728768250174
+506000  ekin = 2.19858217910528 |  erot = 1.97142936872076 | epot = -22.8530995461461 | etot = -18.6830879983201
+507000  ekin = 2.27398115142402 |  erot = 2.68837996151519 | epot = -22.8141163798141 | etot = -17.8517552668749
+508000  ekin = 2.64439339973838 |  erot = 2.0475646786945 | epot = -22.8146247157345 | etot = -18.1226666373017
+509000  ekin = 2.96023637315629 |  erot = 2.90549934754533 | epot = -22.8719625385966 | etot = -17.006226817895
+510000  ekin = 2.26067558634545 |  erot = 2.8086491851952 | epot = -22.9774448292235 | etot = -17.9081200576829
+511000  ekin = 2.88512738978599 |  erot = 2.15263877534437 | epot = -23.0866728482479 | etot = -18.0489066831176
+512000  ekin = 2.17783748155516 |  erot = 2.31389139764185 | epot = -23.1520181882638 | etot = -18.6602893090668
+513000  ekin = 1.69717952556151 |  erot = 2.88265468656803 | epot = -23.1640284548406 | etot = -18.5841942427111
+514000  ekin = 1.72432024724117 |  erot = 2.32742209152174 | epot = -23.1602225830814 | etot = -19.1084802443185
+515000  ekin = 2.00525337522086 |  erot = 1.80102864435032 | epot = -23.1548763180746 | etot = -19.3485942985034
+516000  ekin = 3.04706172157038 |  erot = 1.54171785431327 | epot = -23.1202751246552 | etot = -18.5314955487715
+517000  ekin = 2.47323892251936 |  erot = 2.10799615007356 | epot = -23.0942246440307 | etot = -18.5129895714378
+518000  ekin = 2.03556879740597 |  erot = 2.51531294708502 | epot = -23.01998934344 | etot = -18.469107598949
+519000  ekin = 1.59255614728459 |  erot = 1.63520468579906 | epot = -22.9787913166931 | etot = -19.7510304836094
+520000  ekin = 2.17210761761844 |  erot = 1.89753667353918 | epot = -22.9877149955356 | etot = -18.918070704378
+521000  ekin = 1.98466680078867 |  erot = 2.09219045542652 | epot = -23.0348541858322 | etot = -18.957996929617
+522000  ekin = 2.72098469914433 |  erot = 2.1956565861946 | epot = -23.1001210576501 | etot = -18.1834797723112
+523000  ekin = 2.26033454380754 |  erot = 1.67112114369622 | epot = -23.1475509854344 | etot = -19.2160952979307
+524000  ekin = 2.34603831546138 |  erot = 2.10546610119491 | epot = -23.1746761633772 | etot = -18.7231717467209
+525000  ekin = 2.13671314300235 |  erot = 2.07172081705865 | epot = -23.241177743004 | etot = -19.032743782943
+526000  ekin = 2.50849953901566 |  erot = 2.27662230434507 | epot = -23.3179050583979 | etot = -18.5327832150372
+527000  ekin = 3.04322527932213 |  erot = 1.8128057083239 | epot = -23.3977373118239 | etot = -18.5417063241779
+528000  ekin = 2.57230318237901 |  erot = 2.54386055260816 | epot = -23.4208428708382 | etot = -18.3046791358511
+529000  ekin = 2.39361269633634 |  erot = 1.91637577362227 | epot = -23.3966015599491 | etot = -19.0866130899905
+530000  ekin = 3.35629379074241 |  erot = 3.41683815876465 | epot = -23.2977853851851 | etot = -16.5246534356781
+531000  ekin = 2.52741741752382 |  erot = 2.3407534240764 | epot = -23.1721175623278 | etot = -18.3039467207275
+532000  ekin = 2.78397051305127 |  erot = 1.78575123294092 | epot = -23.2171711834401 | etot = -18.6474494374479
+533000  ekin = 2.27408274334042 |  erot = 2.01427501035043 | epot = -23.2885684059726 | etot = -19.0002106522818
+534000  ekin = 2.54998010491124 |  erot = 2.01645453645071 | epot = -23.340767920006 | etot = -18.7743332786441
+535000  ekin = 2.49595662250557 |  erot = 2.09586427439367 | epot = -23.3878755759449 | etot = -18.7960546790457
+536000  ekin = 2.47717157546008 |  erot = 1.92116873587366 | epot = -23.3847675210095 | etot = -18.9864272096758
+537000  ekin = 1.75235621440223 |  erot = 2.11852052216088 | epot = -23.4590860280326 | etot = -19.5882092914695
+538000  ekin = 2.19317209186636 |  erot = 2.75191518419655 | epot = -23.5517834707225 | etot = -18.6066961946596
+539000  ekin = 2.16135327665118 |  erot = 2.25935011393787 | epot = -23.5718250119028 | etot = -19.1511216213138
+540000  ekin = 2.35701554620647 |  erot = 1.64495290573329 | epot = -23.5490867129451 | etot = -19.5471182610053
+541000  ekin = 2.61451212811978 |  erot = 2.52550284426681 | epot = -23.5334576350384 | etot = -18.3934426626519
+542000  ekin = 2.78909215024064 |  erot = 2.09346850400964 | epot = -23.5754619290989 | etot = -18.6929012748486
+543000  ekin = 2.77024528778679 |  erot = 1.84116991183092 | epot = -23.4849560716084 | etot = -18.8735408719907
+544000  ekin = 2.1580752918837 |  erot = 1.50139575300258 | epot = -23.4530822422947 | etot = -19.7936111974084
+545000  ekin = 1.7286020488633 |  erot = 2.56468335549414 | epot = -23.4524953434144 | etot = -19.159209939057
+546000  ekin = 2.38494138419347 |  erot = 1.87772638427252 | epot = -23.4950389557033 | etot = -19.2323711872373
+547000  ekin = 2.44871634556834 |  erot = 2.44464466893215 | epot = -23.544915775382 | etot = -18.6515547608815
+548000  ekin = 2.36962922994878 |  erot = 2.40235228488721 | epot = -23.5548428056052 | etot = -18.7828612907692
+549000  ekin = 2.57958168249613 |  erot = 2.04930779813672 | epot = -23.5565149978683 | etot = -18.9276255172355
+550000  ekin = 1.97931366474269 |  erot = 1.85207468704395 | epot = -23.5614067919063 | etot = -19.7300184401196
+551000  ekin = 2.4121774327081 |  erot = 2.03489368862991 | epot = -23.5115216908382 | etot = -19.0644505695002
+552000  ekin = 2.6621149390197 |  erot = 1.41279265378133 | epot = -23.3450678435402 | etot = -19.2701602507391
+553000  ekin = 1.76359346131444 |  erot = 2.63019210822712 | epot = -23.1435570943958 | etot = -18.7497715248542
+554000  ekin = 2.29840754300074 |  erot = 2.34424452982823 | epot = -23.1114395278817 | etot = -18.4687874550527
+555000  ekin = 3.29672420152567 |  erot = 1.64146930698358 | epot = -23.0891292168917 | etot = -18.1509357083825
+556000  ekin = 2.92076699655597 |  erot = 2.59602967895814 | epot = -23.0268314200472 | etot = -17.5100347445331
+557000  ekin = 2.90322014804996 |  erot = 3.1605266889492 | epot = -23.0146480567181 | etot = -16.950901219719
+558000  ekin = 2.78018761002223 |  erot = 2.5982694700676 | epot = -22.7877399275349 | etot = -17.4092828474451
+559000  ekin = 2.48661596771862 |  erot = 3.22596665511857 | epot = -22.8226574327834 | etot = -17.1100748099462
+560000  ekin = 2.34942852601697 |  erot = 2.327731628774 | epot = -22.8255608134696 | etot = -18.1484006586786
+561000  ekin = 2.0520192544917 |  erot = 2.90306975046936 | epot = -22.8488516051139 | etot = -17.8937626001529
+562000  ekin = 2.18821919117372 |  erot = 3.66499439159822 | epot = -22.7618817506902 | etot = -16.9086681679183
+563000  ekin = 3.11505518852414 |  erot = 2.28057725990563 | epot = -22.791430640287 | etot = -17.3957981918573
+564000  ekin = 2.45343120006931 |  erot = 2.36321638506707 | epot = -22.75807077839 | etot = -17.9414231932536
+565000  ekin = 2.7783583550222 |  erot = 2.07073547186411 | epot = -22.7486053888412 | etot = -17.8995115619549
+566000  ekin = 2.43655641927934 |  erot = 2.19832280178868 | epot = -22.7227654505166 | etot = -18.0878862294486
+567000  ekin = 2.71233133108495 |  erot = 2.01281091173406 | epot = -22.8839744455115 | etot = -18.1588322026925
+568000  ekin = 3.12450796157709 |  erot = 1.93520150351062 | epot = -22.9625972279254 | etot = -17.9028877628377
+569000  ekin = 3.72714267701978 |  erot = 2.06562452789051 | epot = -22.9814174117752 | etot = -17.1886502068649
+570000  ekin = 2.68808623045676 |  erot = 2.36042122391806 | epot = -22.9989590266921 | etot = -17.9504515723172
+571000  ekin = 1.97223467321356 |  erot = 2.85558181274648 | epot = -22.9369001315648 | etot = -18.1090836456047
+572000  ekin = 2.41820497321229 |  erot = 2.40910077907643 | epot = -22.934930836907 | etot = -18.1076250846182
+573000  ekin = 1.76702714285011 |  erot = 2.31739567602696 | epot = -22.9768902017483 | etot = -18.8924673828712
+574000  ekin = 2.0874025921411 |  erot = 2.59288012722137 | epot = -23.0518321557917 | etot = -18.3715494364292
+575000  ekin = 2.34020490338785 |  erot = 2.78500973557001 | epot = -23.106579446946 | etot = -17.9813648079881
+576000  ekin = 2.15506609467458 |  erot = 3.30452875380292 | epot = -23.1521162771299 | etot = -17.6925214286524
+577000  ekin = 2.45698150895878 |  erot = 2.31876672704205 | epot = -23.1781917242716 | etot = -18.4024434882707
+578000  ekin = 2.59353106592521 |  erot = 2.33790294336519 | epot = -23.2101395643706 | etot = -18.2787055550802
+579000  ekin = 2.58102015460711 |  erot = 1.71748063175117 | epot = -23.1865014452815 | etot = -18.8880006589232
+580000  ekin = 2.30361750578347 |  erot = 2.8741056437962 | epot = -23.2045008793077 | etot = -18.026777729728
+581000  ekin = 2.45915247103345 |  erot = 2.59640238490727 | epot = -23.1882783600354 | etot = -18.1327235040947
+582000  ekin = 2.33801590725495 |  erot = 3.19256035650618 | epot = -23.2501410058056 | etot = -17.7195647420445
+583000  ekin = 1.95982078382854 |  erot = 2.81944051586209 | epot = -23.4085593869414 | etot = -18.6292980872508
+584000  ekin = 2.00358327245437 |  erot = 1.71267270263011 | epot = -23.4960310960901 | etot = -19.7797751210056
+585000  ekin = 2.28859150562676 |  erot = 2.0630904691126 | epot = -23.5306230166998 | etot = -19.1789410419605
+586000  ekin = 2.21858454582015 |  erot = 1.97776854350182 | epot = -23.4873397268816 | etot = -19.2909866375597
+587000  ekin = 3.70065233550663 |  erot = 1.82187748311298 | epot = -23.4652388428898 | etot = -17.9427090242702
+588000  ekin = 3.49447328534893 |  erot = 2.31981981591505 | epot = -23.3985567739262 | etot = -17.5842636726622
+589000  ekin = 2.66144502802388 |  erot = 3.02756546370718 | epot = -23.2783756079917 | etot = -17.5893651162606
+590000  ekin = 1.52141257336427 |  erot = 2.09874614600564 | epot = -23.1290158071881 | etot = -19.5088570878182
+591000  ekin = 1.82897193042274 |  erot = 1.75592223095375 | epot = -23.0622736076073 | etot = -19.4773794462309
+592000  ekin = 2.49491276892189 |  erot = 2.54829881978519 | epot = -23.054885494985 | etot = -18.0116739062779
+593000  ekin = 2.36845716276157 |  erot = 1.78503341410574 | epot = -23.005264310194 | etot = -18.8517737333267
+594000  ekin = 2.07907010887473 |  erot = 2.14563658430187 | epot = -22.9611396232755 | etot = -18.7364329300989
+595000  ekin = 2.62736231723873 |  erot = 2.03975825744529 | epot = -22.9495489717352 | etot = -18.2824283970512
+596000  ekin = 2.58985967531624 |  erot = 2.12449830164847 | epot = -22.9908505579802 | etot = -18.2764925810155
+597000  ekin = 3.02540042664856 |  erot = 3.14256707367046 | epot = -22.9740991012936 | etot = -16.8061316009745
+598000  ekin = 3.44397104083287 |  erot = 2.86057908398569 | epot = -23.0035411551227 | etot = -16.6989910303041
+599000  ekin = 2.13932500926498 |  erot = 3.49187029024977 | epot = -22.9657391359987 | etot = -17.334543836484
+600000  ekin = 2.19758597945325 |  erot = 2.49610822362373 | epot = -22.9452235009931 | etot = -18.2515292979161
+601000  ekin = 2.80918982916751 |  erot = 2.81768433603374 | epot = -22.8970508934525 | etot = -17.2701767282512
+602000  ekin = 2.30031523379462 |  erot = 2.40907304500536 | epot = -22.8523950981498 | etot = -18.1430068193498
+603000  ekin = 1.91335501396421 |  erot = 1.99518053980753 | epot = -22.7884152302357 | etot = -18.879879676464
+604000  ekin = 2.5976715095492 |  erot = 3.14351403383687 | epot = -22.7430641975848 | etot = -17.0018786541988
+605000  ekin = 2.63203298717973 |  erot = 2.07906613894389 | epot = -22.7307949909782 | etot = -18.0196958648546
+606000  ekin = 2.9467839928978 |  erot = 2.03982213630798 | epot = -22.6555302524726 | etot = -17.6689241232668
+607000  ekin = 2.85272606479019 |  erot = 2.36693467257681 | epot = -22.6318548820143 | etot = -17.4121941446473
+608000  ekin = 3.6642968125636 |  erot = 2.46706737589237 | epot = -22.5724662590777 | etot = -16.4411020706218
+609000  ekin = 2.69343886620625 |  erot = 2.25873504143679 | epot = -22.6007364465804 | etot = -17.6485625389374
+610000  ekin = 2.99904616523659 |  erot = 2.13621966615345 | epot = -22.5973658485054 | etot = -17.4621000171154
+611000  ekin = 3.86832985948945 |  erot = 2.12096644577641 | epot = -22.5702925425382 | etot = -16.5809962372723
+612000  ekin = 2.88515301824619 |  erot = 2.45910554524357 | epot = -22.4848584522585 | etot = -17.1405998887687
+613000  ekin = 2.9367425327116 |  erot = 2.14436169371535 | epot = -22.465526703267 | etot = -17.38442247684
+614000  ekin = 2.791164628763 |  erot = 2.02440953964802 | epot = -22.5207406301148 | etot = -17.7051664617038
+615000  ekin = 2.29338048298908 |  erot = 2.3882887247098 | epot = -22.6082782403584 | etot = -17.9266090326595
+616000  ekin = 1.78195169789474 |  erot = 2.45334803626969 | epot = -22.6887534547644 | etot = -18.4534537206
+617000  ekin = 2.57505808534158 |  erot = 2.55345758187858 | epot = -22.7014638394959 | etot = -17.5729481722758
+618000  ekin = 2.29561379442387 |  erot = 2.680432593555 | epot = -22.629958627306 | etot = -17.6539122393271
+619000  ekin = 1.94323313590202 |  erot = 2.009649111577 | epot = -22.5681911047399 | etot = -18.6153088572609
+620000  ekin = 2.92263589097657 |  erot = 2.15657756066215 | epot = -22.6264664894927 | etot = -17.547253037854
+621000  ekin = 2.90437881656455 |  erot = 1.70649555848316 | epot = -22.6654194475729 | etot = -18.0545450725252
+622000  ekin = 2.03426149564846 |  erot = 2.51826459248401 | epot = -22.6086250578043 | etot = -18.0560989696718
+623000  ekin = 1.98348786592096 |  erot = 3.08484972830227 | epot = -22.6234743341759 | etot = -17.5551367399526
+624000  ekin = 2.08463083558977 |  erot = 2.64004606903046 | epot = -22.6266529328942 | etot = -17.901976028274
+625000  ekin = 2.52963490334088 |  erot = 2.37033264022621 | epot = -22.6750436783155 | etot = -17.7750761347484
+626000  ekin = 2.73147680333726 |  erot = 2.07051651598001 | epot = -22.7272383647964 | etot = -17.9252450454791
+627000  ekin = 2.23447399123207 |  erot = 2.35288557052268 | epot = -22.7136740507756 | etot = -18.1263144890208
+628000  ekin = 2.28933754695897 |  erot = 2.29676268895052 | epot = -22.6176528573237 | etot = -18.0315526214142
+629000  ekin = 2.5355466362136 |  erot = 1.92082543033527 | epot = -22.5693331526923 | etot = -18.1129610861434
+630000  ekin = 3.11700824717167 |  erot = 2.51611049765935 | epot = -22.5144695759914 | etot = -16.8813508311604
+631000  ekin = 2.38844807455605 |  erot = 3.31601650504459 | epot = -22.5190998334877 | etot = -16.8146352538871
+632000  ekin = 2.59939587493747 |  erot = 2.51496212358956 | epot = -22.4711049664696 | etot = -17.3567469679426
+633000  ekin = 2.45338619933598 |  erot = 1.89874016257144 | epot = -22.4394257686937 | etot = -18.0872994067863
+634000  ekin = 2.23819111967046 |  erot = 1.98305652730464 | epot = -22.3433365860708 | etot = -18.1220889390957
+635000  ekin = 2.22438000857701 |  erot = 1.95893208021227 | epot = -22.2877959440852 | etot = -18.1044838552959
+636000  ekin = 2.26938644192168 |  erot = 2.77816773779857 | epot = -22.304696935737 | etot = -17.2571427560167
+637000  ekin = 1.97799147515645 |  erot = 2.59610837639353 | epot = -22.3353238115757 | etot = -17.7612239600257
+638000  ekin = 2.54901279963356 |  erot = 3.14232301833367 | epot = -22.3113570318406 | etot = -16.6200212138734
+639000  ekin = 2.38194254982011 |  erot = 2.49468098011845 | epot = -22.2696251856513 | etot = -17.3930016557128
+640000  ekin = 2.07438054408915 |  erot = 2.20336226777043 | epot = -22.1673693230787 | etot = -17.8896265112191
+641000  ekin = 2.49150296422893 |  erot = 3.53882164550033 | epot = -22.0473233874349 | etot = -16.0169987777057
+642000  ekin = 3.37964058409635 |  erot = 2.18458831029802 | epot = -21.9324522713975 | etot = -16.3682233770031
+643000  ekin = 2.80862431007863 |  erot = 2.40815089193716 | epot = -21.8726014240441 | etot = -16.6558262220283
+644000  ekin = 2.952235016065 |  erot = 1.92776262379328 | epot = -21.826057423183 | etot = -16.9460597833247
+645000  ekin = 4.10488984334312 |  erot = 1.89062109330212 | epot = -21.7981661301139 | etot = -15.8026551934687
+646000  ekin = 2.50234872105284 |  erot = 2.00205075040523 | epot = -21.7221642434957 | etot = -17.2177647720376
+647000  ekin = 2.52267281239588 |  erot = 2.19481558810104 | epot = -21.7438885460027 | etot = -17.0264001455058
+648000  ekin = 2.99344241657583 |  erot = 2.11139263207284 | epot = -21.7373240000025 | etot = -16.6324889513538
+649000  ekin = 2.55027365085816 |  erot = 3.20350991793738 | epot = -21.7192481424448 | etot = -15.9654645736493
+650000  ekin = 3.75163896052813 |  erot = 2.4418921228228 | epot = -21.6756681314987 | etot = -15.4821370481477
+651000  ekin = 3.29740056237165 |  erot = 2.36780448747274 | epot = -21.5372361691658 | etot = -15.8720311193214
+652000  ekin = 2.54645886055824 |  erot = 2.99097829596978 | epot = -21.4549655298412 | etot = -15.9175283733132
+653000  ekin = 2.88682688109756 |  erot = 2.53633970608341 | epot = -21.4696471597398 | etot = -16.0464805725588
+654000  ekin = 2.28614085804932 |  erot = 2.12026601708472 | epot = -21.5642684321318 | etot = -17.1578615569977
+655000  ekin = 2.20709609517087 |  erot = 2.10729950549553 | epot = -21.5349466292622 | etot = -17.2205510285958
+656000  ekin = 2.40310876229413 |  erot = 2.09663823500904 | epot = -21.5631924595209 | etot = -17.0634454622177
+657000  ekin = 2.7886551346751 |  erot = 2.19608839827218 | epot = -21.794507747247 | etot = -16.8097642142997
+658000  ekin = 3.1025713807162 |  erot = 2.59154293692775 | epot = -21.9667559942099 | etot = -16.272641676566
+659000  ekin = 2.88891106020276 |  erot = 3.47010878893494 | epot = -22.0542552611187 | etot = -15.695235411981
+660000  ekin = 2.90074521854052 |  erot = 1.62850743298555 | epot = -22.1003034196589 | etot = -17.5710507681328
+661000  ekin = 3.26666543815737 |  erot = 1.86223225384177 | epot = -22.202664217118 | etot = -17.0737665251188
+662000  ekin = 3.1558491019044 |  erot = 2.16868634291727 | epot = -22.3049478747804 | etot = -16.9804124299587
+663000  ekin = 1.94349853674084 |  erot = 2.45687952722592 | epot = -22.3908978754177 | etot = -17.990519811451
+664000  ekin = 1.454458209604 |  erot = 1.37641815749115 | epot = -22.5088813854797 | etot = -19.6780050183846
+665000  ekin = 1.57568561901953 |  erot = 2.30379312359824 | epot = -22.5957949572926 | etot = -18.7163162146748
+666000  ekin = 2.46162449261636 |  erot = 1.76978614573264 | epot = -22.7431602236663 | etot = -18.5117495853173
+667000  ekin = 2.82410423268351 |  erot = 2.33836663659489 | epot = -22.9350563238977 | etot = -17.7725854546193
+668000  ekin = 2.7371768611619 |  erot = 3.18779777915036 | epot = -23.0188768131826 | etot = -17.0939021728703
+669000  ekin = 3.41035672635338 |  erot = 2.45479601777613 | epot = -23.0718232403885 | etot = -17.206670496259
+670000  ekin = 2.54649164859505 |  erot = 1.99520979169172 | epot = -23.0246775830825 | etot = -18.4829761427958
+671000  ekin = 2.3802025684166 |  erot = 3.0074273699854 | epot = -23.0023479116087 | etot = -17.6147179732067
+672000  ekin = 3.0126952152146 |  erot = 2.55297219144564 | epot = -22.9947723733501 | etot = -17.4291049666899
+673000  ekin = 3.39486270740071 |  erot = 2.38087002620332 | epot = -22.9033457919094 | etot = -17.1276130583054
+674000  ekin = 3.13698489626099 |  erot = 2.10609113054063 | epot = -22.8089270617647 | etot = -17.5658510349631
+675000  ekin = 2.32294130821675 |  erot = 1.5285851482073 | epot = -22.6840603385672 | etot = -18.8325338821431
+676000  ekin = 2.43564726401376 |  erot = 2.26860623636407 | epot = -22.6133446272027 | etot = -17.9090911268249
+677000  ekin = 2.75162757613842 |  erot = 1.94219014743456 | epot = -22.7039380847022 | etot = -18.0101203611292
+678000  ekin = 2.86321973687601 |  erot = 1.66387788364135 | epot = -22.7223510604726 | etot = -18.1952534399552
+679000  ekin = 2.35079208772869 |  erot = 2.70386328048643 | epot = -22.7977445343494 | etot = -17.7430891661343
+680000  ekin = 2.48449675729004 |  erot = 2.90645575582477 | epot = -22.8559375688936 | etot = -17.4649850557788
+681000  ekin = 1.91581136662334 |  erot = 2.58179603882022 | epot = -22.7891325966099 | etot = -18.2915251911663
+682000  ekin = 2.10466427353706 |  erot = 2.69470735868806 | epot = -22.6959043279181 | etot = -17.896532695693
+683000  ekin = 2.34504535409022 |  erot = 2.11592035700792 | epot = -22.5718670441909 | etot = -18.1109013330928
+684000  ekin = 2.87198876498959 |  erot = 2.65732173958707 | epot = -22.4986977268024 | etot = -16.9693872222258
+685000  ekin = 3.03375238110976 |  erot = 2.18190577381517 | epot = -22.4634189289575 | etot = -17.2477607740326
+686000  ekin = 2.46248931777657 |  erot = 2.43025710170916 | epot = -22.4079029677659 | etot = -17.5151565482801
+687000  ekin = 2.74662486817896 |  erot = 1.7960915256241 | epot = -22.3360381567114 | etot = -17.7933217629083
+688000  ekin = 1.81703718003043 |  erot = 2.06511603415636 | epot = -22.3083758541198 | etot = -18.426222639933
+689000  ekin = 2.84202633430564 |  erot = 1.92033962884778 | epot = -22.3752571185822 | etot = -17.6128911554288
+690000  ekin = 2.07525448405017 |  erot = 2.46342632176819 | epot = -22.4633535431152 | etot = -17.9246727372969
+691000  ekin = 2.12558517800138 |  erot = 2.52961097164003 | epot = -22.483426266766 | etot = -17.8282301171246
+692000  ekin = 2.86720433292881 |  erot = 2.65102150657024 | epot = -22.4003374064863 | etot = -16.8821115669873
+693000  ekin = 2.30143055084864 |  erot = 2.5229094638336 | epot = -22.2859681228792 | etot = -17.461628108197
+694000  ekin = 2.88400701080874 |  erot = 2.34320802755438 | epot = -22.206318584282 | etot = -16.9791035459188
+695000  ekin = 2.93184722112895 |  erot = 2.22933507376833 | epot = -22.2348177906806 | etot = -17.0736354957833
+696000  ekin = 2.63173546326796 |  erot = 2.3427536957083 | epot = -22.274597219839 | etot = -17.3001080608628
+697000  ekin = 1.87084079501972 |  erot = 1.78050094908735 | epot = -22.2730387150936 | etot = -18.6216969709865
+698000  ekin = 2.19791428580687 |  erot = 2.8288358175635 | epot = -22.2819378523405 | etot = -17.2551877489701
+699000  ekin = 2.34279295545267 |  erot = 2.07514436344562 | epot = -22.2061425261575 | etot = -17.7882052072592
+700000  ekin = 2.576803119019 |  erot = 2.32167543064961 | epot = -22.1658685747825 | etot = -17.2673900251139
+701000  ekin = 2.9943865807539 |  erot = 1.89982533986206 | epot = -22.2191193266439 | etot = -17.324907406028
+702000  ekin = 2.68548464757459 |  erot = 2.65050744453208 | epot = -22.2547415922757 | etot = -16.918749500169
+703000  ekin = 2.01996957402024 |  erot = 2.04032822241737 | epot = -22.3253693056515 | etot = -18.2650715092139
+704000  ekin = 1.58871069317829 |  erot = 1.64014270467762 | epot = -22.3617232281452 | etot = -19.1328698302893
+705000  ekin = 2.30894157549819 |  erot = 1.90252913035992 | epot = -22.4307958564623 | etot = -18.2193251506042
+706000  ekin = 2.61729186445574 |  erot = 3.218798680391 | epot = -22.5603358780911 | etot = -16.7242453332444
+707000  ekin = 2.60797107906866 |  erot = 2.31455039977395 | epot = -22.7102471053997 | etot = -17.7877256265571
+708000  ekin = 1.81633850341999 |  erot = 2.34822575669415 | epot = -22.841408787855 | etot = -18.6768445277409
+709000  ekin = 1.83541322105378 |  erot = 2.51792380003795 | epot = -23.0137235815795 | etot = -18.6603865604878
+710000  ekin = 2.2142058326246 |  erot = 1.92378721690473 | epot = -23.1433453130909 | etot = -19.0053522635615
+711000  ekin = 2.06744054454475 |  erot = 2.39811709353191 | epot = -23.1532717948857 | etot = -18.687714156809
+712000  ekin = 2.17279472706359 |  erot = 1.75362175342097 | epot = -23.0479262273957 | etot = -19.1215097469111
+713000  ekin = 2.87118830138478 |  erot = 1.54943993787552 | epot = -22.8430575230907 | etot = -18.4224292838304
+714000  ekin = 2.01079466743967 |  erot = 1.87510988392748 | epot = -22.9212969433221 | etot = -19.035392391955
+715000  ekin = 2.49921829589267 |  erot = 1.91934008289236 | epot = -22.9679126658062 | etot = -18.5493542870212
+716000  ekin = 2.94666510633352 |  erot = 2.18714442405523 | epot = -23.0339970974289 | etot = -17.9001875670402
+717000  ekin = 3.07404079722086 |  erot = 2.46628262765132 | epot = -23.1869721551174 | etot = -17.6466487302453
+718000  ekin = 3.4706007837111 |  erot = 2.28206620506092 | epot = -23.2524492340769 | etot = -17.4997822453048
+719000  ekin = 4.08343792096554 |  erot = 3.10429377075216 | epot = -23.2448292181926 | etot = -16.0570975264749
+720000  ekin = 2.52774819763972 |  erot = 1.92867508904583 | epot = -23.1435084559682 | etot = -18.6870851692827
+721000  ekin = 2.58294244811584 |  erot = 2.03830531780331 | epot = -23.0601633758883 | etot = -18.4389156099692
+722000  ekin = 1.94458885450861 |  erot = 2.32008660802526 | epot = -22.9811929404573 | etot = -18.7165174779234
+723000  ekin = 2.41998340576259 |  erot = 2.1236972897937 | epot = -23.0570939793877 | etot = -18.5134132838314
+724000  ekin = 1.90406371300861 |  erot = 1.97533505769878 | epot = -23.1267629042384 | etot = -19.247364133531
+725000  ekin = 2.14287056473421 |  erot = 2.79289687450021 | epot = -23.1695632046138 | etot = -18.2337957653794
+726000  ekin = 2.2642331709972 |  erot = 2.55343019202652 | epot = -23.243290908371 | etot = -18.4256275453472
+727000  ekin = 1.69816397656715 |  erot = 2.64011919415554 | epot = -23.298837689321 | etot = -18.9605545185983
+728000  ekin = 2.23000862561933 |  erot = 3.58521470578671 | epot = -23.3528245832468 | etot = -17.5376012518407
+729000  ekin = 2.70076566380344 |  erot = 1.73367306410749 | epot = -23.3971276122796 | etot = -18.9626888843687
+730000  ekin = 2.5481867380276 |  erot = 2.77394958410254 | epot = -23.3988686964745 | etot = -18.0767323743443
+731000  ekin = 2.69782550956094 |  erot = 2.04855826523076 | epot = -23.4310969813891 | etot = -18.6847132065974
+732000  ekin = 2.79613002753752 |  erot = 1.87867430486715 | epot = -23.4885161441653 | etot = -18.8137118117607
+733000  ekin = 2.20346728125046 |  erot = 2.64365594749975 | epot = -23.5261309431819 | etot = -18.6790077144317
+734000  ekin = 1.69780111261444 |  erot = 2.3091790956079 | epot = -23.5188046470475 | etot = -19.5118244388251
+735000  ekin = 2.18402736165936 |  erot = 2.7205162023087 | epot = -23.4712689506938 | etot = -18.5667253867257
+736000  ekin = 2.26138696009404 |  erot = 1.17083930058802 | epot = -23.4348107178754 | etot = -20.0025844571934
+737000  ekin = 2.22219419044795 |  erot = 3.14114682990361 | epot = -23.3869288757725 | etot = -18.023587855421
+738000  ekin = 1.75464981631084 |  erot = 2.28485941478057 | epot = -23.2709893028053 | etot = -19.2314800717139
+739000  ekin = 1.41806378584361 |  erot = 2.1671403411282 | epot = -23.2213775300889 | etot = -19.6361734031171
+740000  ekin = 1.90901017596351 |  erot = 2.27102763422489 | epot = -23.1829198366047 | etot = -19.0028820264163
+741000  ekin = 1.9930994487751 |  erot = 2.73523269523397 | epot = -23.1169670577824 | etot = -18.3886349137733
+742000  ekin = 1.99876411117686 |  erot = 1.89882876917754 | epot = -23.0300825800851 | etot = -19.1324896997307
+743000  ekin = 1.96472814667687 |  erot = 2.79504722629174 | epot = -22.8990488521609 | etot = -18.1392734791923
+744000  ekin = 2.02442646092311 |  erot = 2.35044838626027 | epot = -22.8186526150799 | etot = -18.4437777678966
+745000  ekin = 1.65344231988822 |  erot = 1.87919095141021 | epot = -22.7624827109091 | etot = -19.2298494396107
+746000  ekin = 2.1034668185472 |  erot = 2.03078530569665 | epot = -22.743454277698 | etot = -18.6092021534542
+747000  ekin = 3.06690414848489 |  erot = 1.67540297869492 | epot = -22.7625979159322 | etot = -18.0202907887524
+748000  ekin = 3.069654144834 |  erot = 1.86014593098644 | epot = -22.8118567150739 | etot = -17.8820566392535
+749000  ekin = 2.53718696167217 |  erot = 2.02710579059033 | epot = -22.8431046011969 | etot = -18.2788118489344
+750000  ekin = 2.75657354808099 |  erot = 2.34953156046291 | epot = -22.9548205390759 | etot = -17.848715430532
+751000  ekin = 2.52290020835147 |  erot = 2.3487376359998 | epot = -23.0238691402084 | etot = -18.1522312958571
+752000  ekin = 2.47222247869325 |  erot = 1.68679846444686 | epot = -22.9958559112492 | etot = -18.836834968109
+753000  ekin = 2.48263277172424 |  erot = 1.54669382815741 | epot = -23.0858212396418 | etot = -19.0564946397602
+754000  ekin = 2.54806257410879 |  erot = 2.26636466676165 | epot = -23.1896472696843 | etot = -18.3752200288138
+755000  ekin = 1.53168409517921 |  erot = 2.22665478278015 | epot = -23.2059118234918 | etot = -19.4475729455324
+756000  ekin = 2.10751715527953 |  erot = 2.4052577432668 | epot = -23.114150245375 | etot = -18.6013753468287
+757000  ekin = 2.93395895491028 |  erot = 2.05821177584909 | epot = -23.0783355599275 | etot = -18.0861648291681
+758000  ekin = 2.38307945406232 |  erot = 2.50598165375058 | epot = -22.9691152621287 | etot = -18.0800541543158
+759000  ekin = 2.60292884338835 |  erot = 2.36916677072546 | epot = -22.7987274767846 | etot = -17.8266318626708
+760000  ekin = 3.2284318196987 |  erot = 2.73822716520638 | epot = -22.6756147646272 | etot = -16.7089557797221
+761000  ekin = 3.41868727786494 |  erot = 1.68975765213406 | epot = -22.5638952547581 | etot = -17.4554503247591
+762000  ekin = 3.43033946346107 |  erot = 2.5283975140253 | epot = -22.3549032489322 | etot = -16.3961662714458
+763000  ekin = 2.65773094814485 |  erot = 1.83975133975561 | epot = -22.234833339183 | etot = -17.7373510512825
+764000  ekin = 2.3815484472129 |  erot = 2.70684992442147 | epot = -22.0890752688231 | etot = -17.0006768971887
+765000  ekin = 2.23212803588897 |  erot = 1.94868597739427 | epot = -21.9918715237933 | etot = -17.81105751051
+766000  ekin = 2.49097891886065 |  erot = 1.96764603993156 | epot = -21.8443436680801 | etot = -17.3857187092879
+767000  ekin = 2.3457921497675 |  erot = 2.64636009163513 | epot = -21.7634962034013 | etot = -16.7713439619986
+768000  ekin = 1.87671147825106 |  erot = 2.05549869178485 | epot = -21.7324638416528 | etot = -17.8002536716169
+769000  ekin = 3.05058687860239 |  erot = 2.66104171022372 | epot = -21.66792195987 | etot = -15.9562933710439
+770000  ekin = 2.44115683640633 |  erot = 1.97554932479749 | epot = -21.644882066475 | etot = -17.2281759052712
+771000  ekin = 2.2368746400443 |  erot = 2.55040970708786 | epot = -21.5811924169692 | etot = -16.793908069837
+772000  ekin = 2.76529680592008 |  erot = 1.97873499811185 | epot = -21.6543448952384 | etot = -16.9103130912064
+773000  ekin = 2.14632888240093 |  erot = 2.41330587525514 | epot = -21.7728828090227 | etot = -17.2132480513667
+774000  ekin = 2.19848545803079 |  erot = 1.9765131024719 | epot = -21.8398858604883 | etot = -17.6648872999856
+775000  ekin = 2.52300137989083 |  erot = 2.80935365273515 | epot = -22.0219985274259 | etot = -16.6896434947999
+776000  ekin = 3.15842485269273 |  erot = 2.47066157093647 | epot = -22.183029096161 | etot = -16.5539426725318
+777000  ekin = 1.91784338934576 |  erot = 1.76045300517084 | epot = -22.2259652888115 | etot = -18.5476688942949
+778000  ekin = 2.93738066043324 |  erot = 2.2945784249029 | epot = -22.2339481852394 | etot = -17.0019890999032
+779000  ekin = 3.09847206114319 |  erot = 2.04557717006051 | epot = -22.240438366259 | etot = -17.0963891350553
+780000  ekin = 2.86127568397807 |  erot = 3.12055135138658 | epot = -22.1865692766137 | etot = -16.204742241249
+781000  ekin = 2.36069914420785 |  erot = 3.53186431088486 | epot = -22.1210563364352 | etot = -16.2284928813425
+782000  ekin = 2.31592690319261 |  erot = 2.85730598644038 | epot = -22.0302855151548 | etot = -16.8570526255218
+783000  ekin = 1.86647729944746 |  erot = 3.03450246093098 | epot = -21.8860143679489 | etot = -16.9850346075704
+784000  ekin = 2.04055627573201 |  erot = 2.26047908607292 | epot = -21.7534271639392 | etot = -17.4523918021343
+785000  ekin = 2.02248469828703 |  erot = 2.13950421850547 | epot = -21.6318967501917 | etot = -17.4699078333992
+786000  ekin = 2.34211746551601 |  erot = 2.34838133643265 | epot = -21.5890308210084 | etot = -16.8985320190597
+787000  ekin = 2.74971447554938 |  erot = 2.24123553296042 | epot = -21.5192132515562 | etot = -16.5282632430464
+788000  ekin = 2.14142056672038 |  erot = 2.27008574684965 | epot = -21.4982362621713 | etot = -17.0867299486013
+789000  ekin = 1.98580913341303 |  erot = 2.00702444041792 | epot = -21.5235331659838 | etot = -17.5306995921528
+790000  ekin = 1.68578263083924 |  erot = 1.43485602862151 | epot = -21.64400815936 | etot = -18.5233694998993
+791000  ekin = 2.13583938840528 |  erot = 2.53730095458943 | epot = -21.7916440698418 | etot = -17.1185037268471
+792000  ekin = 1.71937483898028 |  erot = 2.19563804216009 | epot = -21.8794946709408 | etot = -17.9644817898004
+793000  ekin = 3.15868943755339 |  erot = 1.94575875708421 | epot = -22.0398145404618 | etot = -16.9353663458242
+794000  ekin = 2.45478602538954 |  erot = 3.00825554959563 | epot = -22.0843165283013 | etot = -16.6212749533161
+795000  ekin = 2.87760320917195 |  erot = 3.06920266633563 | epot = -22.1595628991904 | etot = -16.2127570236828
+796000  ekin = 2.29816690595059 |  erot = 1.61510864654315 | epot = -22.1869705548184 | etot = -18.2736950023247
+797000  ekin = 2.19015256067211 |  erot = 3.65734446008355 | epot = -22.1432608090644 | etot = -16.2957637883088
+798000  ekin = 2.12018787925579 |  erot = 2.92822258455554 | epot = -22.1311312789224 | etot = -17.0827208151111
+799000  ekin = 2.49416140154829 |  erot = 2.73328283280218 | epot = -22.0825726051882 | etot = -16.8551283708377
+800000  ekin = 2.18932007838552 |  erot = 2.97640731559392 | epot = -21.979362152191 | etot = -16.8136347582115
+801000  ekin = 2.58827112124839 |  erot = 2.74404424837261 | epot = -21.9108490336924 | etot = -16.5785336640714
+802000  ekin = 3.07870342348167 |  erot = 2.87961505564287 | epot = -21.822560433681 | etot = -15.8642419545565
+803000  ekin = 2.23986243680641 |  erot = 2.50525058807596 | epot = -21.7275940818101 | etot = -16.9824810569277
+804000  ekin = 2.91885860068427 |  erot = 1.5788904045143 | epot = -21.6896376725624 | etot = -17.1918886673638
+805000  ekin = 2.68277363980194 |  erot = 3.05527868915739 | epot = -21.6710764398127 | etot = -15.9330241108534
+806000  ekin = 2.77769607049014 |  erot = 2.18887276909082 | epot = -21.6314833902337 | etot = -16.6649145506527
+807000  ekin = 2.12673239079667 |  erot = 2.86003407600808 | epot = -21.7295924017744 | etot = -16.7428259349697
+808000  ekin = 1.89599614774678 |  erot = 2.29237053227661 | epot = -21.7511361510417 | etot = -17.5627694710183
+809000  ekin = 1.96405066221971 |  erot = 1.92110393348365 | epot = -21.7075506883706 | etot = -17.8223960926673
+810000  ekin = 2.01518137594274 |  erot = 2.60119247286599 | epot = -21.678838587473 | etot = -17.0624647386642
+811000  ekin = 2.31084800889289 |  erot = 1.75270367309064 | epot = -21.6837819033719 | etot = -17.6202302213883
+812000  ekin = 2.57701031002089 |  erot = 2.34932304073588 | epot = -21.7246716033188 | etot = -16.7983382525621
+813000  ekin = 2.87706904926075 |  erot = 2.35686610624155 | epot = -21.837592223605 | etot = -16.6036570681027
+814000  ekin = 2.89908405023865 |  erot = 2.31423299883228 | epot = -21.8379261473902 | etot = -16.6246090983192
+815000  ekin = 2.54050064212256 |  erot = 2.82732568868833 | epot = -21.6068952707049 | etot = -16.2390689398941
+816000  ekin = 2.17040404256386 |  erot = 2.53711088209172 | epot = -21.5560322071983 | etot = -16.8485172825427
+817000  ekin = 1.7842696071831 |  erot = 2.67810959410574 | epot = -21.8738878035325 | etot = -17.4115086022437
+818000  ekin = 2.29659398017838 |  erot = 2.63718862373663 | epot = -22.164277271391 | etot = -17.230494667476
+819000  ekin = 2.15801167884062 |  erot = 2.62095572928875 | epot = -22.1816109590115 | etot = -17.4026435508822
+820000  ekin = 1.94384548213955 |  erot = 2.28597987799276 | epot = -22.0986187375022 | etot = -17.8687933773699
+821000  ekin = 2.10513194007576 |  erot = 2.38698175569218 | epot = -22.1146754444785 | etot = -17.6225617487105
+822000  ekin = 2.24819716786441 |  erot = 2.15258805680875 | epot = -22.0539472940486 | etot = -17.6531620693754
+823000  ekin = 2.26584952085582 |  erot = 2.60619852526611 | epot = -22.0924201800579 | etot = -17.220372133936
+824000  ekin = 1.65187935478513 |  erot = 1.4870311903723 | epot = -22.1682955997986 | etot = -19.0293850546411
+825000  ekin = 1.60213094818648 |  erot = 1.98592524368395 | epot = -22.1687104063708 | etot = -18.5806542145004
+826000  ekin = 1.97430720107255 |  erot = 2.19175014677162 | epot = -22.1061881978655 | etot = -17.9401308500213
+827000  ekin = 2.1793755983405 |  erot = 2.44975419075934 | epot = -21.9704586607304 | etot = -17.3413288716306
+828000  ekin = 1.90399088418587 |  erot = 2.72532994798818 | epot = -21.9585923270583 | etot = -17.3292714948842
+829000  ekin = 2.06478103068883 |  erot = 2.96583035402588 | epot = -21.9849402038682 | etot = -16.9543288191535
+830000  ekin = 1.98920675238979 |  erot = 2.15331250444996 | epot = -22.0339146439702 | etot = -17.8913953871305
+831000  ekin = 2.33567462674689 |  erot = 2.36888807413496 | epot = -22.1271573756461 | etot = -17.4225946747643
+832000  ekin = 2.0119470999192 |  erot = 1.94769143293625 | epot = -22.2038482709588 | etot = -18.2442097381034
+833000  ekin = 2.26025933495881 |  erot = 2.16012558191463 | epot = -22.2882501045414 | etot = -17.867865187668
+834000  ekin = 2.11529426445865 |  erot = 1.52405523315359 | epot = -22.3075608649826 | etot = -18.6682113673703
+835000  ekin = 2.89920750905511 |  erot = 2.7380108175103 | epot = -22.3942491248321 | etot = -16.7570307982667
+836000  ekin = 3.33069528982658 |  erot = 2.42771267807861 | epot = -22.4321737300744 | etot = -16.6737657621692
+837000  ekin = 2.74831774333782 |  erot = 2.31991750378627 | epot = -22.4290234552873 | etot = -17.3607882081632
+838000  ekin = 3.13714871682187 |  erot = 3.21601751721778 | epot = -22.4642383906451 | etot = -16.1110721566054
+839000  ekin = 2.73358272751807 |  erot = 2.60144488190506 | epot = -22.4062682687368 | etot = -17.0712406593137
+840000  ekin = 2.96121930874636 |  erot = 1.42725942278118 | epot = -22.3293755621294 | etot = -17.9408968306019
+841000  ekin = 2.95134811170867 |  erot = 2.67666861874609 | epot = -22.2936348151224 | etot = -16.6656180846677
+842000  ekin = 2.15783928636402 |  erot = 2.30287195796693 | epot = -22.2978011147172 | etot = -17.8370898703863
+843000  ekin = 2.84565152669617 |  erot = 2.05108014775141 | epot = -22.3162908719779 | etot = -17.4195591975303
+844000  ekin = 2.99645803669157 |  erot = 1.50433298006521 | epot = -22.3768320579304 | etot = -17.8760410411737
+845000  ekin = 3.20248025697125 |  erot = 2.27246140825563 | epot = -22.3985708422076 | etot = -16.9236291769807
+846000  ekin = 3.35773945734322 |  erot = 2.54074745551552 | epot = -22.4144833015876 | etot = -16.5159963887289
+847000  ekin = 2.17779203733109 |  erot = 2.7381758118846 | epot = -22.3524825149514 | etot = -17.4365146657357
+848000  ekin = 2.51627348417144 |  erot = 2.81170686694718 | epot = -22.2066307862469 | etot = -16.8786504351283
+849000  ekin = 1.99679455190556 |  erot = 2.56855846773091 | epot = -22.0763062134929 | etot = -17.5109531938564
+850000  ekin = 2.05799123916876 |  erot = 1.80888056240784 | epot = -22.0665032506706 | etot = -18.1996314490939
+851000  ekin = 2.08889793767921 |  erot = 1.8617218179029 | epot = -22.0629711763889 | etot = -18.1123514208068
+852000  ekin = 1.68990805178902 |  erot = 1.42763535981883 | epot = -22.002100112701 | etot = -18.8845567010931
+853000  ekin = 1.99310886654811 |  erot = 3.05226969048295 | epot = -22.0306903552278 | etot = -16.9853117981967
+854000  ekin = 2.98378700534986 |  erot = 2.23102745240541 | epot = -22.1115820238811 | etot = -16.8967675661258
+855000  ekin = 2.17087415585277 |  erot = 2.83781472268789 | epot = -22.1115106395971 | etot = -17.1028217610564
+856000  ekin = 2.42228475387308 |  erot = 1.53328604594478 | epot = -22.0841888628209 | etot = -18.128618063003
+857000  ekin = 2.50431566526893 |  erot = 2.80498769176515 | epot = -21.9881235267534 | etot = -16.6788201697193
+858000  ekin = 2.17333686672378 |  erot = 2.82591115507169 | epot = -21.9093201368614 | etot = -16.910072115066
+859000  ekin = 2.29930070497242 |  erot = 2.3241736893906 | epot = -21.8849849636104 | etot = -17.2615105692473
+860000  ekin = 1.99153024057672 |  erot = 1.9467463860015 | epot = -21.8998709373217 | etot = -17.9615943107435
+861000  ekin = 2.69177523559624 |  erot = 2.23997750036372 | epot = -21.8915522194994 | etot = -16.9597994835394
+862000  ekin = 2.86117050047984 |  erot = 2.41530060322762 | epot = -21.876687883023 | etot = -16.6002167793155
+863000  ekin = 2.59841547044275 |  erot = 3.3501705008543 | epot = -21.8162649771436 | etot = -15.8676790058466
+864000  ekin = 2.92496272611018 |  erot = 2.30350236144452 | epot = -21.7820358973268 | etot = -16.5535708097721
+865000  ekin = 1.94718216128952 |  erot = 2.16572180916631 | epot = -21.7000823492195 | etot = -17.5871783787637
+866000  ekin = 1.99006127871689 |  erot = 1.65011901234954 | epot = -21.6190182409268 | etot = -17.9788379498603
+867000  ekin = 1.76250718110787 |  erot = 3.37958608370305 | epot = -21.5401486584561 | etot = -16.3980553936452
+868000  ekin = 1.845623450314 |  erot = 2.78812196028612 | epot = -21.5771917352235 | etot = -16.9434463246233
+869000  ekin = 2.39300849969204 |  erot = 2.38301618173174 | epot = -21.6710790825578 | etot = -16.8950544011341
+870000  ekin = 1.91899243212541 |  erot = 3.2222244071739 | epot = -21.6734733803871 | etot = -16.5322565410878
+871000  ekin = 3.10255827845531 |  erot = 2.95454268850896 | epot = -21.5913249106744 | etot = -15.5342239437101
+872000  ekin = 2.94582883077842 |  erot = 1.38261935263093 | epot = -21.4597055547832 | etot = -17.1312573713739
+873000  ekin = 2.72830997927424 |  erot = 2.23223699637274 | epot = -21.3657566950046 | etot = -16.4052097193576
+874000  ekin = 2.41464704842015 |  erot = 2.10351476791495 | epot = -21.2635161734954 | etot = -16.7453543571603
+875000  ekin = 2.99468455803482 |  erot = 2.72761242382526 | epot = -21.2488881289381 | etot = -15.526591147078
+876000  ekin = 2.13382009818493 |  erot = 2.23152059294678 | epot = -21.2388603913311 | etot = -16.8735197001994
+877000  ekin = 1.839391763993 |  erot = 1.60727997722601 | epot = -21.2015948102408 | etot = -17.7549230690218
+878000  ekin = 2.01267175782179 |  erot = 2.73109796378377 | epot = -21.2125253160263 | etot = -16.4687555944207
+879000  ekin = 1.42911941081343 |  erot = 2.17371661448624 | epot = -21.1345316334464 | etot = -17.5316956081467
+880000  ekin = 2.10605339224632 |  erot = 2.58847517789128 | epot = -21.0787246891645 | etot = -16.3841961190269
+881000  ekin = 1.54924791070118 |  erot = 2.0068513915418 | epot = -21.1356465207066 | etot = -17.5795472184636
+882000  ekin = 2.19964315713499 |  erot = 2.65509097106008 | epot = -21.2389026935677 | etot = -16.3841685653726
+883000  ekin = 2.20850404171077 |  erot = 2.22833605977578 | epot = -21.3067394383395 | etot = -16.8698993368529
+884000  ekin = 2.76978562647275 |  erot = 2.10395845939756 | epot = -21.3429618615585 | etot = -16.4692177756882
+885000  ekin = 1.93339807672781 |  erot = 1.77156241344967 | epot = -21.3858074096933 | etot = -17.6808469195158
+886000  ekin = 2.00408769971894 |  erot = 3.10736267931441 | epot = -21.3935346347812 | etot = -16.2820842557478
+887000  ekin = 1.96987943750801 |  erot = 2.82035886899743 | epot = -21.3967073105592 | etot = -16.6064690040538
+888000  ekin = 1.91464371566411 |  erot = 2.33371232948867 | epot = -21.4767119016419 | etot = -17.2283558564891
+889000  ekin = 1.88227414130202 |  erot = 2.45915914930409 | epot = -21.5790392436829 | etot = -17.2376059530768
+890000  ekin = 1.84515176532447 |  erot = 2.24992378831494 | epot = -21.6747594004542 | etot = -17.5796838468148
+891000  ekin = 2.6016566869706 |  erot = 2.34500453305754 | epot = -21.8016735536793 | etot = -16.8550123336512
+892000  ekin = 2.7128775188686 |  erot = 2.69544224573133 | epot = -21.9063749565584 | etot = -16.4980551919585
+893000  ekin = 2.17862714611329 |  erot = 2.98452123742224 | epot = -21.9155556335137 | etot = -16.7524072499782
+894000  ekin = 2.52079948361477 |  erot = 2.46355933674926 | epot = -21.915110079455 | etot = -16.930751259091
+895000  ekin = 2.53566097944338 |  erot = 2.45130454442941 | epot = -21.9477860878339 | etot = -16.9608205639611
+896000  ekin = 1.84455393639214 |  erot = 2.77499090684944 | epot = -21.9167554809878 | etot = -17.2972106377462
+897000  ekin = 2.38519326880695 |  erot = 2.01980287317302 | epot = -21.8644918203992 | etot = -17.4594956784193
+898000  ekin = 2.14354914407572 |  erot = 1.89196669459414 | epot = -21.7953104274974 | etot = -17.7597945888275
+899000  ekin = 2.65485657727374 |  erot = 2.32374560038192 | epot = -21.6964754705568 | etot = -16.7178732929012
+900000  ekin = 2.1437154528087 |  erot = 2.28119066740276 | epot = -21.6934954112434 | etot = -17.268589291032
+901000  ekin = 1.93965814946881 |  erot = 1.81495571440911 | epot = -21.7369092433376 | etot = -17.9822953794597
+902000  ekin = 2.60993957981555 |  erot = 2.50321386623392 | epot = -21.6842517568354 | etot = -16.5710983107859
+903000  ekin = 1.87484955546756 |  erot = 2.17008893987963 | epot = -21.6383913984978 | etot = -17.5934529031506
+904000  ekin = 1.87454064845764 |  erot = 2.32484081519397 | epot = -21.5866637125315 | etot = -17.3872822488799
+905000  ekin = 2.31407473814843 |  erot = 2.1509486854239 | epot = -21.5154415841816 | etot = -17.0504181606093
+906000  ekin = 2.49583383758853 |  erot = 2.25091096848465 | epot = -21.5170853902294 | etot = -16.7703405841563
+907000  ekin = 4.19798796104344 |  erot = 2.50305323228071 | epot = -21.5976736513859 | etot = -14.8966324580618
+908000  ekin = 3.26730891548756 |  erot = 2.11222217905481 | epot = -21.7526644402476 | etot = -16.3731333457052
+909000  ekin = 2.64106561110374 |  erot = 1.92197432194202 | epot = -21.8748043207924 | etot = -17.3117643877466
+910000  ekin = 2.61805562731904 |  erot = 2.90737422678701 | epot = -21.9709470207745 | etot = -16.4455171666684
+911000  ekin = 2.62012718860141 |  erot = 4.35318528241846 | epot = -22.0282478750366 | etot = -15.0549354040167
+912000  ekin = 3.07628909273118 |  erot = 3.69371809788395 | epot = -22.0511180009901 | etot = -15.281110810375
+913000  ekin = 2.82956898268831 |  erot = 2.17078429141199 | epot = -22.0149543706266 | etot = -17.0146010965263
+914000  ekin = 2.16386655780066 |  erot = 1.22303673036133 | epot = -21.9243495493209 | etot = -18.5374462611589
+915000  ekin = 1.59447095066509 |  erot = 2.95966391292002 | epot = -21.8264580452026 | etot = -17.2723231816175
+916000  ekin = 2.58365539107523 |  erot = 3.75147270955031 | epot = -21.8922962938608 | etot = -15.5571681932352
+917000  ekin = 3.01643029206974 |  erot = 2.88035639021002 | epot = -21.9150526568514 | etot = -16.0182659745717
+918000  ekin = 2.89929776900147 |  erot = 2.64137394041292 | epot = -21.9078998623094 | etot = -16.367228152895
+919000  ekin = 3.20476671865013 |  erot = 2.76036957969156 | epot = -21.8878055443404 | etot = -15.9226692459988
+920000  ekin = 2.28949350558684 |  erot = 2.38558870046818 | epot = -21.8659406759968 | etot = -17.1908584699418
+921000  ekin = 2.39158312157105 |  erot = 2.44959700788173 | epot = -21.8638974869224 | etot = -17.0227173574697
+922000  ekin = 2.30678787768012 |  erot = 2.42145678067296 | epot = -21.8218369909645 | etot = -17.0935923326115
+923000  ekin = 2.49697778842282 |  erot = 2.66565493744117 | epot = -21.8078634464733 | etot = -16.6452307206093
+924000  ekin = 1.55676047489502 |  erot = 2.97115254541004 | epot = -21.7829722234117 | etot = -17.2550592031067
+925000  ekin = 1.86603413909289 |  erot = 1.96274861601778 | epot = -21.7288604040749 | etot = -17.9000776489642
+926000  ekin = 1.36993364395821 |  erot = 2.11749584641398 | epot = -21.7083442855148 | etot = -18.2209147951426
+927000  ekin = 2.55718977538496 |  erot = 2.0810909504888 | epot = -21.7242353526193 | etot = -17.0859546267455
+928000  ekin = 2.0974272910786 |  erot = 2.73922911267238 | epot = -21.7673808868819 | etot = -16.9307244831309
+929000  ekin = 1.85550591174834 |  erot = 1.84990976935038 | epot = -21.8639426090857 | etot = -18.158526927987
+930000  ekin = 1.99594723517185 |  erot = 2.09151231016389 | epot = -21.8461015073053 | etot = -17.7586419619695
+931000  ekin = 2.45331651079282 |  erot = 1.86703658018613 | epot = -21.7382799817762 | etot = -17.4179268907972
+932000  ekin = 2.76909250526758 |  erot = 2.34990175754268 | epot = -21.7639792890093 | etot = -16.6449850261991
+933000  ekin = 3.0474736633548 |  erot = 2.52740756503519 | epot = -21.6783727845496 | etot = -16.1034915561596
+934000  ekin = 2.93463275640818 |  erot = 2.48893095891024 | epot = -21.5784996926914 | etot = -16.154935977373
+935000  ekin = 2.77799347567548 |  erot = 2.13929358412249 | epot = -21.5334239467005 | etot = -16.6161368869026
+936000  ekin = 2.96529953690397 |  erot = 2.07095365726716 | epot = -21.5249249864244 | etot = -16.4886717922532
+937000  ekin = 3.04850537701749 |  erot = 2.32432162998051 | epot = -21.4386642161072 | etot = -16.0658372091092
+938000  ekin = 2.99262628505359 |  erot = 2.35224559307843 | epot = -21.3457080466207 | etot = -16.0008361684887
+939000  ekin = 2.61238181353702 |  erot = 2.26780356837291 | epot = -21.3079422537804 | etot = -16.4277568718705
+940000  ekin = 2.65930112044941 |  erot = 2.75497479722395 | epot = -21.2170493356503 | etot = -15.802773417977
+941000  ekin = 2.27574261339217 |  erot = 2.61419196501688 | epot = -21.1297657597673 | etot = -16.2398311813582
+942000  ekin = 1.89172011891054 |  erot = 2.82029488513786 | epot = -21.0410099256113 | etot = -16.3289949215629
+943000  ekin = 2.47643464476757 |  erot = 2.34737109151876 | epot = -21.0466687727979 | etot = -16.2228630365116
+944000  ekin = 2.13883995897326 |  erot = 1.92577316206138 | epot = -21.0114219746513 | etot = -16.9468088536167
+945000  ekin = 2.57768697869113 |  erot = 2.2147013612407 | epot = -21.0634624131725 | etot = -16.2710740732407
+946000  ekin = 2.36420709243625 |  erot = 2.89647330776423 | epot = -21.088814693033 | etot = -15.8281342928325
+947000  ekin = 2.07104171538468 |  erot = 1.86575631327234 | epot = -21.1004860950452 | etot = -17.1636880663882
+948000  ekin = 1.85532958802996 |  erot = 1.3695283408655 | epot = -21.1364231315616 | etot = -17.9115652026661
+949000  ekin = 1.76206591178366 |  erot = 2.3173732855863 | epot = -21.1463744779337 | etot = -17.0669352805638
+950000  ekin = 1.72021033353108 |  erot = 2.24191394295308 | epot = -21.1376324866856 | etot = -17.1755082102014
+951000  ekin = 1.96140007830504 |  erot = 2.32248863487759 | epot = -21.1955927656813 | etot = -16.9117040524987
+952000  ekin = 2.93256201500608 |  erot = 2.74550490827502 | epot = -21.2347810245411 | etot = -15.55671410126
+953000  ekin = 2.95031285986317 |  erot = 2.39822873263993 | epot = -21.2526091831331 | etot = -15.90406759063
+954000  ekin = 3.09579074538114 |  erot = 1.98159252445736 | epot = -21.1641538136742 | etot = -16.0867705438357
+955000  ekin = 3.59360323486037 |  erot = 2.06789679071822 | epot = -21.0522880782498 | etot = -15.3907880526712
+956000  ekin = 2.97416074498496 |  erot = 3.66953591785752 | epot = -20.9097603766373 | etot = -14.2660637137949
+957000  ekin = 3.03140562067951 |  erot = 2.66078083760708 | epot = -20.7419058677841 | etot = -15.0497194094975
+958000  ekin = 2.68913434704071 |  erot = 2.94057112873836 | epot = -20.5488384129042 | etot = -14.9191329371251
+959000  ekin = 1.93264217407773 |  erot = 2.45198406257093 | epot = -20.468781161493 | etot = -16.0841549248444
+960000  ekin = 1.49632279167951 |  erot = 3.13346348599985 | epot = -20.4844974178569 | etot = -15.8547111401775
+961000  ekin = 1.96353429663481 |  erot = 2.07553358516995 | epot = -20.4805590123498 | etot = -16.441491130545
+962000  ekin = 2.02830196392006 |  erot = 1.88908496389352 | epot = -20.5374211599972 | etot = -16.6200342321836
+963000  ekin = 1.80829526034561 |  erot = 2.46258345726263 | epot = -20.5841835730968 | etot = -16.3133048554886
+964000  ekin = 2.79449124937197 |  erot = 2.42527551362849 | epot = -20.6238805444481 | etot = -15.4041137814476
+965000  ekin = 2.53493670506136 |  erot = 2.27804362684504 | epot = -20.6549300812152 | etot = -15.8419497493088
+966000  ekin = 2.0920817650402 |  erot = 2.27478990703182 | epot = -20.7044739042411 | etot = -16.3376022321691
+967000  ekin = 1.55562260797661 |  erot = 3.55543363172459 | epot = -20.739375276301 | etot = -15.6283190365998
+968000  ekin = 1.93439891222236 |  erot = 2.37295903815892 | epot = -20.7189229543385 | etot = -16.4115650039573
+969000  ekin = 2.16199728898304 |  erot = 2.46012052524939 | epot = -20.6747113173024 | etot = -16.05259350307
+970000  ekin = 1.84926216722517 |  erot = 2.96951777569265 | epot = -20.6011599981509 | etot = -15.7823800552331
+971000  ekin = 1.93656411083027 |  erot = 3.08724923997924 | epot = -20.5835250734812 | etot = -15.5597117226717
+972000  ekin = 1.90452783927712 |  erot = 2.58230766783158 | epot = -20.578290598021 | etot = -16.0914550909123
+973000  ekin = 2.1922712122506 |  erot = 2.92686386394502 | epot = -20.5868173702649 | etot = -15.4676822940693
+974000  ekin = 2.53094641465528 |  erot = 2.69271305556796 | epot = -20.5382547781502 | etot = -15.314595307927
+975000  ekin = 3.41187201669924 |  erot = 2.32917219553093 | epot = -20.5109803919918 | etot = -14.7699361797616
+976000  ekin = 2.88156114272554 |  erot = 3.10474521611247 | epot = -20.5158119249461 | etot = -14.5295055661081
+977000  ekin = 2.73962881168093 |  erot = 2.50884169958545 | epot = -20.4964590298 | etot = -15.2479885185336
+978000  ekin = 1.79682802545478 |  erot = 2.06924041504343 | epot = -20.4730821934977 | etot = -16.6070137529995
+979000  ekin = 1.86521389998383 |  erot = 2.22151626929009 | epot = -20.4069392895634 | etot = -16.3202091202895
+980000  ekin = 1.92383169177415 |  erot = 1.56425965548878 | epot = -20.3533353734708 | etot = -16.8652440262079
+981000  ekin = 1.5511019928294 |  erot = 2.05381225133935 | epot = -20.3970890782076 | etot = -16.7921748340389
+982000  ekin = 1.85559395816059 |  erot = 1.96991369841494 | epot = -20.499354149896 | etot = -16.6738464933205
+983000  ekin = 2.75061857015335 |  erot = 1.7944840218308 | epot = -20.5241519929378 | etot = -15.9790494009537
+984000  ekin = 3.65069712553538 |  erot = 2.64237329124736 | epot = -20.6374699142712 | etot = -14.3443994974885
+985000  ekin = 2.95637321931061 |  erot = 2.18846412126772 | epot = -20.8122975273334 | etot = -15.6674601867551
+986000  ekin = 2.87072902054599 |  erot = 2.18810434250118 | epot = -20.9390290724606 | etot = -15.8801957094134
+987000  ekin = 3.37463328642758 |  erot = 2.53713666674669 | epot = -21.0098323012659 | etot = -15.0980623480916
+988000  ekin = 3.45107854450337 |  erot = 3.23625536313168 | epot = -21.0554260480417 | etot = -14.3680921404067
+989000  ekin = 2.83591404363755 |  erot = 2.20564156324815 | epot = -21.19499265416 | etot = -16.1534370472743
+990000  ekin = 2.79864389348437 |  erot = 1.8317842666354 | epot = -21.1880268304373 | etot = -16.5575986703175
+991000  ekin = 3.14781925181036 |  erot = 3.20782471808911 | epot = -21.1115234865128 | etot = -14.7558795166133
+992000  ekin = 3.30033725309946 |  erot = 2.62749912694386 | epot = -21.0030296251662 | etot = -15.0751932451229
+993000  ekin = 3.07374297249948 |  erot = 2.22697230616356 | epot = -20.9385586572609 | etot = -15.6378433785979
+994000  ekin = 3.21461776403449 |  erot = 2.80599707993707 | epot = -20.8790524582442 | etot = -14.8584376142726
+995000  ekin = 3.25071478747345 |  erot = 1.73415439498321 | epot = -20.8037804714002 | etot = -15.8189112889435
+996000  ekin = 3.07999632962569 |  erot = 3.18107550500823 | epot = -20.7805295335828 | etot = -14.5194576989488
+997000  ekin = 2.97118118001025 |  erot = 3.14046656474894 | epot = -20.7334885248755 | etot = -14.6218407801163
+998000  ekin = 3.09169861594907 |  erot = 1.99060706981745 | epot = -20.6553134096535 | etot = -15.573007723887
+999000  ekin = 2.07498130576584 |  erot = 2.75045972766921 | epot = -20.616091526295 | etot = -15.7906504928599
+1000000  ekin = 2.07851119592057 |  erot = 2.11869313853035 | epot = -20.4539417072875 | etot = -16.2567373728365
+ 1000000  0.092378275   -1.3359709  0.057599499   -1.1484644 2.8477973e-05 
+Loop time of 36.5086 on 1 procs for 1000000 steps with 16 atoms
+
+Performance: 23665.686 tau/day, 27390.840 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 26.481     | 26.481     | 26.481     |   0.0 | 72.53
+Bond    | 0.7951     | 0.7951     | 0.7951     |   0.0 |  2.18
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.16717    | 0.16717    | 0.16717    |   0.0 |  0.46
+Output  | 1.1e-05    | 1.1e-05    | 1.1e-05    |   0.0 |  0.00
+Modify  | 8.7926     | 8.7926     | 8.7926     |   0.0 | 24.08
+Other   |            | 0.273      |            |       |  0.75
+
+Nlocal:    16 ave 16 max 16 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    102 ave 102 max 102 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 102
+Ave neighs/atom = 6.375
+Ave special neighs/atom = 3.75
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:36
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4
new file mode 100644
index 0000000000..730853a0da
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4
@@ -0,0 +1,1168 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000184 secs
+  read_data CPU = 0.003429 secs
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+#fix 1 all nve/dot
+fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
+fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10
+fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 1000000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.956
+  ghost atom cutoff = 1.956
+  binsize = 0.978, bins = 41 41 41
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
+Per MPI rank memory allocation (min/avg/max) = 7.455 | 7.637 | 7.819 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.5402493 0.0070469125   -1.5332024 6.0760034e-06 
+1000  ekin = 1.34565986428024 |  erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
+2000  ekin = 2.15911766687235 |  erot = 2.16031365874706 | epot = -24.4723177103698 | etot = -20.1528863847504
+3000  ekin = 3.26561948796015 |  erot = 2.75651822936605 | epot = -24.412573068346 | etot = -18.3904353510198
+4000  ekin = 1.92438809241066 |  erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038505
+5000  ekin = 1.35986357015476 |  erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
+6000  ekin = 2.19432475124593 |  erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
+7000  ekin = 2.65619274477635 |  erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
+8000  ekin = 2.51333548501169 |  erot = 2.34649854571052 | epot = -24.0812769481836 | etot = -19.2214429174614
+9000  ekin = 2.24506493169711 |  erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
+10000  ekin = 2.36632635249862 |  erot = 1.79592471761529 | epot = -23.9002627850602 | etot = -19.7380117149463
+11000  ekin = 2.03296432220126 |  erot = 1.687070009478 | epot = -23.8527188138995 | etot = -20.1326844822202
+12000  ekin = 2.65352743446956 |  erot = 2.50226345616878 | epot = -23.8480805937578 | etot = -18.6922897031194
+13000  ekin = 1.89067421214403 |  erot = 2.35043092595414 | epot = -23.7714712440931 | etot = -19.5303661059949
+14000  ekin = 1.90680463918722 |  erot = 2.12745987027399 | epot = -23.7545354032947 | etot = -19.7202708938335
+15000  ekin = 2.40428667481004 |  erot = 2.06172433796653 | epot = -23.6726347642127 | etot = -19.2066237514361
+16000  ekin = 2.7510166356243 |  erot = 1.18896277635344 | epot = -23.5745121257654 | etot = -19.6345327137876
+17000  ekin = 2.44090826892662 |  erot = 2.38166706806441 | epot = -23.5888433865641 | etot = -18.766268049573
+18000  ekin = 2.16977970545217 |  erot = 2.46915729098831 | epot = -23.6023194416344 | etot = -18.9633824451939
+19000  ekin = 2.19378610033861 |  erot = 2.45183819484609 | epot = -23.5449084745393 | etot = -18.8992841793546
+20000  ekin = 2.07734013817241 |  erot = 1.81448496219961 | epot = -23.5782673056893 | etot = -19.6864422053173
+21000  ekin = 2.27781532351243 |  erot = 2.76369118136086 | epot = -23.5986545956161 | etot = -18.5571480907428
+22000  ekin = 2.69375785791379 |  erot = 1.86436952967315 | epot = -23.5521083325077 | etot = -18.9939809449207
+23000  ekin = 1.99952884103097 |  erot = 2.28032953163857 | epot = -23.4448504933921 | etot = -19.1649921207226
+24000  ekin = 2.19993258930349 |  erot = 2.97916455146848 | epot = -23.365299008021 | etot = -18.1862018672491
+25000  ekin = 2.28089469652686 |  erot = 2.97627567077201 | epot = -23.2873526827526 | etot = -18.0301823154537
+26000  ekin = 1.99390998801617 |  erot = 2.79250495479074 | epot = -23.1859723519608 | etot = -18.3995574091539
+27000  ekin = 2.00992865272585 |  erot = 2.66533768693446 | epot = -23.0781687640813 | etot = -18.402902424421
+28000  ekin = 2.00322172723407 |  erot = 2.36418499091004 | epot = -23.0032647032354 | etot = -18.6358579850913
+29000  ekin = 2.52361436071784 |  erot = 2.06140753694879 | epot = -22.9685706338047 | etot = -18.383548736138
+30000  ekin = 1.94969919616482 |  erot = 2.13601590002587 | epot = -22.8657664932105 | etot = -18.7800513970198
+31000  ekin = 1.81286761012387 |  erot = 2.31717861791922 | epot = -22.8372197907213 | etot = -18.7071735626782
+32000  ekin = 1.88389491638451 |  erot = 2.00512246825909 | epot = -22.9321024454487 | etot = -19.0430850608051
+33000  ekin = 1.78524470387102 |  erot = 1.83154598239148 | epot = -22.9538943248059 | etot = -19.3371036385434
+34000  ekin = 2.28023843988047 |  erot = 3.11357086039974 | epot = -23.0617618407572 | etot = -17.667952540477
+35000  ekin = 2.88795920533174 |  erot = 1.81662227096289 | epot = -23.1342233361349 | etot = -18.4296418598403
+36000  ekin = 2.40018487148211 |  erot = 2.59182059399979 | epot = -23.2153198761915 | etot = -18.2233144107096
+37000  ekin = 2.22699211630433 |  erot = 1.73889017332475 | epot = -23.2291614908027 | etot = -19.2632792011737
+38000  ekin = 2.13593461964592 |  erot = 3.07590136326315 | epot = -23.1607724763685 | etot = -17.9489364934594
+39000  ekin = 2.08839393640823 |  erot = 2.80471150509566 | epot = -23.1352878747759 | etot = -18.242182433272
+40000  ekin = 2.94982054413846 |  erot = 2.19484102372241 | epot = -23.1842229043853 | etot = -18.0395613365244
+41000  ekin = 2.47855373480179 |  erot = 3.46795094832272 | epot = -23.1698888629099 | etot = -17.2233841797854
+42000  ekin = 2.57225931171306 |  erot = 3.11160980977123 | epot = -23.0914425999525 | etot = -17.4075734784682
+43000  ekin = 2.16695829201326 |  erot = 2.67063324875935 | epot = -22.9841690345739 | etot = -18.1465774938013
+44000  ekin = 2.3251045436594 |  erot = 3.31069456451415 | epot = -22.9099977707014 | etot = -17.2741986625279
+45000  ekin = 1.8593572517472 |  erot = 3.48256913429864 | epot = -22.7853293556222 | etot = -17.4434029695763
+46000  ekin = 2.59906260222481 |  erot = 2.2320785378511 | epot = -22.67184319375 | etot = -17.8407020536741
+47000  ekin = 1.90419350976819 |  erot = 3.39352467596445 | epot = -22.5624536061979 | etot = -17.2647354204652
+48000  ekin = 2.46191536162942 |  erot = 2.50024189038397 | epot = -22.5888330081063 | etot = -17.6266757560929
+49000  ekin = 3.18008619674969 |  erot = 2.18329398142911 | epot = -22.6110647388652 | etot = -17.2476845606864
+50000  ekin = 2.92380640638812 |  erot = 1.5483538313346 | epot = -22.6682279672282 | etot = -18.1960677295054
+51000  ekin = 2.8672950322524 |  erot = 2.67529217516736 | epot = -22.6748886664557 | etot = -17.132301459036
+52000  ekin = 2.30283827457733 |  erot = 1.82645474029551 | epot = -22.6607030819086 | etot = -18.5314100670358
+53000  ekin = 3.18697616339314 |  erot = 1.6721126504968 | epot = -22.7158951183044 | etot = -17.8568063044145
+54000  ekin = 2.63274995193147 |  erot = 1.96664130685842 | epot = -22.7877787224364 | etot = -18.1883874636465
+55000  ekin = 3.18311630681889 |  erot = 2.85127254864952 | epot = -22.8390589862477 | etot = -16.8046701307793
+56000  ekin = 2.55275960671528 |  erot = 3.05720384772626 | epot = -22.8187750450683 | etot = -17.2088115906267
+57000  ekin = 2.43682051944964 |  erot = 3.45782031837858 | epot = -22.7770565571277 | etot = -16.8824157192995
+58000  ekin = 1.93888380963701 |  erot = 2.51321017005837 | epot = -22.7135987564736 | etot = -18.2615047767782
+59000  ekin = 2.5584899615086 |  erot = 3.52166542523796 | epot = -22.6623202639297 | etot = -16.5821648771831
+60000  ekin = 2.80661395039301 |  erot = 2.89055248290058 | epot = -22.5801959967487 | etot = -16.8830295634551
+61000  ekin = 2.68598657973729 |  erot = 2.54741083070049 | epot = -22.4806361765055 | etot = -17.2472387660677
+62000  ekin = 2.74493324548126 |  erot = 2.23648307303268 | epot = -22.4129547813458 | etot = -17.4315384628319
+63000  ekin = 2.65627195091607 |  erot = 2.46107949280746 | epot = -22.3986334001314 | etot = -17.2812819564079
+64000  ekin = 2.12379240032878 |  erot = 2.79203441675509 | epot = -22.3495990435982 | etot = -17.4337722265143
+65000  ekin = 1.86782238979936 |  erot = 2.70277079938777 | epot = -22.3710220966341 | etot = -17.8004289074469
+66000  ekin = 2.74983103317414 |  erot = 1.93532287297332 | epot = -22.3642892005434 | etot = -17.679135294396
+67000  ekin = 2.51092055125345 |  erot = 2.46618624666166 | epot = -22.3997780561407 | etot = -17.4226712582256
+68000  ekin = 2.95469759114171 |  erot = 1.97026833535318 | epot = -22.465077041847 | etot = -17.5401111153521
+69000  ekin = 2.60179538487172 |  erot = 2.27022574694886 | epot = -22.4013876082185 | etot = -17.529366476398
+70000  ekin = 2.38624525335422 |  erot = 2.82124637267727 | epot = -22.3329612644328 | etot = -17.1254696384013
+71000  ekin = 2.6264191985346 |  erot = 2.8933242992384 | epot = -22.3324946257813 | etot = -16.8127511280083
+72000  ekin = 2.93199679301318 |  erot = 2.83600213853039 | epot = -22.4418753486332 | etot = -16.6738764170896
+73000  ekin = 2.20521324648382 |  erot = 3.05063841714452 | epot = -22.5078076718832 | etot = -17.2519560082549
+74000  ekin = 2.16594519672766 |  erot = 2.82993872672919 | epot = -22.5187768617569 | etot = -17.5228929383001
+75000  ekin = 1.52753824412461 |  erot = 1.91758574309004 | epot = -22.6434864113427 | etot = -19.198362424128
+76000  ekin = 1.89477517532867 |  erot = 2.83145375092216 | epot = -22.7507099037207 | etot = -18.0244809774698
+77000  ekin = 2.84722966394523 |  erot = 3.20523918524772 | epot = -22.8263123696514 | etot = -16.7738435204584
+78000  ekin = 2.44900478430451 |  erot = 2.80964787966681 | epot = -22.811923730311 | etot = -17.5532710663397
+79000  ekin = 2.16549328835507 |  erot = 1.67531288307153 | epot = -22.8278994273521 | etot = -18.9870932559255
+80000  ekin = 2.38929173610466 |  erot = 2.5835599737549 | epot = -22.7453472674482 | etot = -17.7724955575887
+81000  ekin = 2.74182188149 |  erot = 1.92580771183152 | epot = -22.6872721828912 | etot = -18.0196425895697
+82000  ekin = 1.90254633515813 |  erot = 1.70958501101744 | epot = -22.5904815431895 | etot = -18.9783501970139
+83000  ekin = 1.63862423461032 |  erot = 1.87668722448406 | epot = -22.5030898166236 | etot = -18.9877783575292
+84000  ekin = 1.65768128899531 |  erot = 2.10186039233844 | epot = -22.4199436013011 | etot = -18.6604019199674
+85000  ekin = 2.40787065796921 |  erot = 2.04965431830703 | epot = -22.3401854879212 | etot = -17.882660511645
+86000  ekin = 2.51073542405177 |  erot = 1.79768841940749 | epot = -22.3948638623201 | etot = -18.0864400188608
+87000  ekin = 2.13729284484532 |  erot = 1.97886338867606 | epot = -22.4457225556766 | etot = -18.3295663221553
+88000  ekin = 1.7511616822056 |  erot = 2.36434608342923 | epot = -22.4232555875235 | etot = -18.3077478218887
+89000  ekin = 1.85498863251071 |  erot = 3.29466014836524 | epot = -22.4615925106509 | etot = -17.3119437297749
+90000  ekin = 2.22730928223451 |  erot = 2.36761183779185 | epot = -22.5498488806969 | etot = -17.9549277606706
+91000  ekin = 2.40026068010467 |  erot = 3.13124542611032 | epot = -22.5445138059197 | etot = -17.0130076997047
+92000  ekin = 2.69184894487886 |  erot = 3.01111638487596 | epot = -22.5488335054242 | etot = -16.8458681756694
+93000  ekin = 3.04452081584098 |  erot = 3.02893158250343 | epot = -22.4857514998612 | etot = -16.4122991015168
+94000  ekin = 3.21054020599498 |  erot = 1.87554208928456 | epot = -22.58235617796 | etot = -17.4962738826805
+95000  ekin = 3.49164555041805 |  erot = 2.891072597541 | epot = -22.651746211573 | etot = -16.269028063614
+96000  ekin = 2.89611459837769 |  erot = 2.3840369162805 | epot = -22.6376886129393 | etot = -17.3575370982811
+97000  ekin = 1.94001816357314 |  erot = 2.09603205774619 | epot = -22.6212143095229 | etot = -18.5851640882036
+98000  ekin = 2.21812472183551 |  erot = 3.66512951907027 | epot = -22.540020786367 | etot = -16.6567665454612
+99000  ekin = 1.96304801418099 |  erot = 2.78092002528642 | epot = -22.4500077741119 | etot = -17.7060397346445
+100000  ekin = 1.78146596589238 |  erot = 2.66087063973067 | epot = -22.380628502186 | etot = -17.9382918965629
+101000  ekin = 2.13576431486591 |  erot = 2.39189697670581 | epot = -22.3671198416411 | etot = -17.8394585500694
+102000  ekin = 1.54265458925823 |  erot = 2.31301627489862 | epot = -22.3596033820569 | etot = -18.5039325179
+103000  ekin = 1.6493299781162 |  erot = 2.8270014677761 | epot = -22.4044472055819 | etot = -17.9281157596896
+104000  ekin = 1.88425130865015 |  erot = 3.36695629589131 | epot = -22.4614117565727 | etot = -17.2102041520312
+105000  ekin = 2.0873628063424 |  erot = 1.99902589912496 | epot = -22.4857870795246 | etot = -18.3993983740573
+106000  ekin = 2.85192200005482 |  erot = 1.96124421177816 | epot = -22.4885148263279 | etot = -17.6753486144949
+107000  ekin = 2.27699301124082 |  erot = 1.54572940373457 | epot = -22.4328687856414 | etot = -18.610146370666
+108000  ekin = 2.43341212242249 |  erot = 1.71014523953267 | epot = -22.4750159709764 | etot = -18.3314586090212
+109000  ekin = 2.3240302459673 |  erot = 2.92730273400666 | epot = -22.454444740465 | etot = -17.203111760491
+110000  ekin = 2.75939007795593 |  erot = 2.37261248457831 | epot = -22.4066316113364 | etot = -17.2746290488021
+111000  ekin = 2.30202775259985 |  erot = 2.09098171366695 | epot = -22.340628179725 | etot = -17.9476187134582
+112000  ekin = 2.89672803093986 |  erot = 1.84536318388285 | epot = -22.189229344937 | etot = -17.4471381301143
+113000  ekin = 2.80286812020301 |  erot = 1.68317583122193 | epot = -22.1739192926258 | etot = -17.6878753412008
+114000  ekin = 3.41134331362354 |  erot = 2.66279011393035 | epot = -22.2993892060878 | etot = -16.225255778534
+115000  ekin = 3.04096848543599 |  erot = 1.72164164793761 | epot = -22.3101669297006 | etot = -17.547556796327
+116000  ekin = 3.18249263106367 |  erot = 3.2187278057963 | epot = -22.376612031037 | etot = -15.975391594177
+117000  ekin = 3.04033644338919 |  erot = 2.41632774149289 | epot = -22.3406101341932 | etot = -16.8839459493112
+118000  ekin = 3.22976632794611 |  erot = 1.46870208555872 | epot = -22.262910646297 | etot = -17.5644422327922
+119000  ekin = 2.35815331598994 |  erot = 3.0746467591689 | epot = -22.21629705762 | etot = -16.7834969824611
+120000  ekin = 1.93901604028919 |  erot = 2.21087803685819 | epot = -22.1596747789505 | etot = -18.0097807018031
+121000  ekin = 1.9479198834689 |  erot = 3.06697908719323 | epot = -22.1473490758083 | etot = -17.1324501051462
+122000  ekin = 1.69642311218451 |  erot = 1.71065948591523 | epot = -22.235021693017 | etot = -18.8279390949172
+123000  ekin = 1.74537927001903 |  erot = 2.31042772730644 | epot = -22.3250546948603 | etot = -18.2692476975348
+124000  ekin = 2.74229806685693 |  erot = 1.94346011848798 | epot = -22.3376426377462 | etot = -17.6518844524013
+125000  ekin = 2.7762803161376 |  erot = 1.95737420539166 | epot = -22.3561899601979 | etot = -17.6225354386687
+126000  ekin = 2.05898577806786 |  erot = 1.47493157618748 | epot = -22.3918669376121 | etot = -18.8579495833568
+127000  ekin = 1.88620727578863 |  erot = 1.58698481884328 | epot = -22.3753405588623 | etot = -18.9021484642304
+128000  ekin = 1.65027256647601 |  erot = 1.87589048163674 | epot = -22.3576574967822 | etot = -18.8314944486694
+129000  ekin = 2.51771860981078 |  erot = 2.38745668871878 | epot = -22.3622404512641 | etot = -17.4570651527345
+130000  ekin = 1.60778116741171 |  erot = 2.81983062254804 | epot = -22.3043401463427 | etot = -17.8767283563829
+131000  ekin = 2.27966529707091 |  erot = 2.29465997580787 | epot = -22.1860056729234 | etot = -17.6116804000446
+132000  ekin = 2.94605151024306 |  erot = 2.34727265039698 | epot = -22.1004107829513 | etot = -16.8070866223112
+133000  ekin = 2.00184520718143 |  erot = 2.13597622566091 | epot = -22.0860804435183 | etot = -17.948259010676
+134000  ekin = 1.54536260297594 |  erot = 2.86019181856985 | epot = -22.0324797134652 | etot = -17.6269252919194
+135000  ekin = 1.7899169229158 |  erot = 2.40585579784187 | epot = -22.0564792277569 | etot = -17.8607065069993
+136000  ekin = 1.63315069688348 |  erot = 2.13968964990471 | epot = -22.0645410751456 | etot = -18.2917007283574
+137000  ekin = 2.36475220491125 |  erot = 1.9307510547685 | epot = -22.101884847306 | etot = -17.8063815876263
+138000  ekin = 2.9554682114977 |  erot = 1.58329215843879 | epot = -22.1589207193491 | etot = -17.6201603494126
+139000  ekin = 3.18559985564368 |  erot = 2.24978247982886 | epot = -22.2766713145626 | etot = -16.84128897909
+140000  ekin = 2.25331500051846 |  erot = 3.04264261269698 | epot = -22.4413209794808 | etot = -17.1453633662654
+141000  ekin = 1.8939664036255 |  erot = 3.12730191483889 | epot = -22.6943708703896 | etot = -17.6731025519252
+142000  ekin = 2.48698722341786 |  erot = 2.50204475841096 | epot = -22.8022645411413 | etot = -17.8132325593125
+143000  ekin = 2.39031114354902 |  erot = 2.72027514737476 | epot = -22.7789363640122 | etot = -17.6683500730884
+144000  ekin = 1.93009742932804 |  erot = 2.68112648713777 | epot = -22.6600942975093 | etot = -18.0488703810435
+145000  ekin = 1.81543048110687 |  erot = 1.73927524532866 | epot = -22.6290694904769 | etot = -19.0743637640414
+146000  ekin = 2.4125202126428 |  erot = 2.08569022934172 | epot = -22.5607640770181 | etot = -18.0625536350336
+147000  ekin = 1.44642974398304 |  erot = 1.86921415702346 | epot = -22.4437745695726 | etot = -19.1281306685661
+148000  ekin = 1.94224767107088 |  erot = 2.57935525538891 | epot = -22.4110987100047 | etot = -17.8894957835449
+149000  ekin = 2.03195649040454 |  erot = 3.31786202502785 | epot = -22.312227106758 | etot = -16.9624085913257
+150000  ekin = 2.47792894576432 |  erot = 2.68612874200304 | epot = -22.1392843642773 | etot = -16.97522667651
+151000  ekin = 2.75692645092955 |  erot = 1.8812256584813 | epot = -21.9329416416723 | etot = -17.2947895322614
+152000  ekin = 2.7753834344323 |  erot = 1.78115734250796 | epot = -21.7450724909841 | etot = -17.1885317140438
+153000  ekin = 3.09316888168833 |  erot = 1.80744228044955 | epot = -21.6451473427313 | etot = -16.7445361805934
+154000  ekin = 2.31433640945477 |  erot = 2.19304386678895 | epot = -21.5946356595637 | etot = -17.08725538332
+155000  ekin = 1.94169881401553 |  erot = 2.67959698479411 | epot = -21.6941053409437 | etot = -17.072809542134
+156000  ekin = 2.69151609119638 |  erot = 2.25048211983204 | epot = -21.7610571974251 | etot = -16.8190589863967
+157000  ekin = 3.89507004263776 |  erot = 2.74501587672577 | epot = -21.8157728797743 | etot = -15.1756869604107
+158000  ekin = 2.88173407476086 |  erot = 2.69702262693025 | epot = -21.8854957137509 | etot = -16.3067390120598
+159000  ekin = 3.15173323195918 |  erot = 2.6174347371013 | epot = -21.8245251626835 | etot = -16.055357193623
+160000  ekin = 2.54983562435716 |  erot = 3.26037467643909 | epot = -21.8527884226329 | etot = -16.0425781218367
+161000  ekin = 2.47569624391789 |  erot = 2.4441841652721 | epot = -21.7973550812187 | etot = -16.8774746720287
+162000  ekin = 2.94228722137381 |  erot = 2.59784970938384 | epot = -21.7813251561029 | etot = -16.2411882253452
+163000  ekin = 3.25812805712344 |  erot = 2.25239331007842 | epot = -21.8200893075211 | etot = -16.3095679403192
+164000  ekin = 3.52786799143084 |  erot = 2.22392713421412 | epot = -21.7646946348872 | etot = -16.0128995092423
+165000  ekin = 2.47839548873418 |  erot = 2.58744140761169 | epot = -21.6790952945041 | etot = -16.6132583981583
+166000  ekin = 2.14435847552792 |  erot = 3.04732688845808 | epot = -21.6219995979977 | etot = -16.4303142340117
+167000  ekin = 2.77664659649902 |  erot = 2.89037999868329 | epot = -21.5339928834654 | etot = -15.8669662882831
+168000  ekin = 1.74464407802389 |  erot = 2.78052653338966 | epot = -21.4288999288375 | etot = -16.903729317424
+169000  ekin = 1.8068912909333 |  erot = 2.46391033708928 | epot = -21.4128285618694 | etot = -17.1420269338468
+170000  ekin = 1.69498145941511 |  erot = 2.88911238881156 | epot = -21.4319269866204 | etot = -16.8478331383937
+171000  ekin = 2.15326316196646 |  erot = 1.6134654780187 | epot = -21.2861470779284 | etot = -17.5194184379432
+172000  ekin = 1.67904916339532 |  erot = 2.36509147316374 | epot = -21.1250864759441 | etot = -17.080945839385
+173000  ekin = 2.05349972960735 |  erot = 2.18864665107749 | epot = -21.0744450592631 | etot = -16.8322986785783
+174000  ekin = 2.49402795941962 |  erot = 3.1039231700088 | epot = -20.9332609664625 | etot = -15.335309837034
+175000  ekin = 2.60611029063986 |  erot = 2.90993176119179 | epot = -20.8533230180669 | etot = -15.3372809662352
+176000  ekin = 2.14535974511638 |  erot = 2.6771051102154 | epot = -20.8508037764829 | etot = -16.0283389211512
+177000  ekin = 2.82654664242577 |  erot = 2.8064781965732 | epot = -20.9303681620826 | etot = -15.2973433230837
+178000  ekin = 3.17006270723388 |  erot = 1.88204403688962 | epot = -21.0665744865168 | etot = -16.0144677423933
+179000  ekin = 2.33834827123179 |  erot = 2.84870047825868 | epot = -21.1082901606944 | etot = -15.9212414112039
+180000  ekin = 2.39362550925046 |  erot = 2.94575326168225 | epot = -21.1089731290028 | etot = -15.7695943580701
+181000  ekin = 2.78703231260152 |  erot = 3.29998898392533 | epot = -21.0761138110654 | etot = -14.9890925145385
+182000  ekin = 3.023383912392 |  erot = 2.3253310746288 | epot = -21.0444377426861 | etot = -15.6957227556653
+183000  ekin = 2.44126401356994 |  erot = 2.19853056632819 | epot = -20.8846280234405 | etot = -16.2448334435424
+184000  ekin = 2.56448211253962 |  erot = 2.77267067014069 | epot = -20.6657911214549 | etot = -15.3286383387746
+185000  ekin = 2.16427057092672 |  erot = 1.95880146934287 | epot = -20.5647658775173 | etot = -16.4416938372477
+186000  ekin = 2.06536030915311 |  erot = 3.1459346313777 | epot = -20.4537584304771 | etot = -15.2424634899463
+187000  ekin = 2.43846121057803 |  erot = 1.93593042270706 | epot = -20.4775765627296 | etot = -16.1031849294445
+188000  ekin = 2.28827356508696 |  erot = 2.89699235589217 | epot = -20.6028880527163 | etot = -15.4176221317372
+189000  ekin = 1.67206333515897 |  erot = 3.05807378739725 | epot = -20.6184572736204 | etot = -15.8883201510642
+190000  ekin = 1.96995062226967 |  erot = 2.943019674394 | epot = -20.6150380630742 | etot = -15.7020677664105
+191000  ekin = 2.31558303301195 |  erot = 2.65062200614568 | epot = -20.5845049099943 | etot = -15.6182998708366
+192000  ekin = 3.58105122568799 |  erot = 2.89866835149673 | epot = -20.5550364560059 | etot = -14.0753168788212
+193000  ekin = 2.69738971383614 |  erot = 3.08390984677749 | epot = -20.5718609412494 | etot = -14.7905613806358
+194000  ekin = 2.65963556416735 |  erot = 2.28486501061266 | epot = -20.4488832942326 | etot = -15.5043827194525
+195000  ekin = 1.85289053427901 |  erot = 2.65318671222086 | epot = -20.3816844231207 | etot = -15.8756071766209
+196000  ekin = 2.28257181147918 |  erot = 2.31175601065464 | epot = -20.4051132325268 | etot = -15.810785410393
+197000  ekin = 2.49770460330585 |  erot = 2.55587879440512 | epot = -20.4716020539923 | etot = -15.4180186562813
+198000  ekin = 2.01700960777428 |  erot = 1.51922008609382 | epot = -20.4907970823155 | etot = -16.9545673884474
+199000  ekin = 1.50027537520987 |  erot = 2.19604462463445 | epot = -20.5138434458212 | etot = -16.8175234459769
+200000  ekin = 1.64850512926723 |  erot = 2.45966335482571 | epot = -20.4934420686449 | etot = -16.385273584552
+201000  ekin = 2.62997533994907 |  erot = 2.61637339049483 | epot = -20.5569645618355 | etot = -15.3106158313916
+202000  ekin = 2.30895175475241 |  erot = 2.55653293887659 | epot = -20.6262537118088 | etot = -15.7607690181798
+203000  ekin = 1.64768887888552 |  erot = 2.11556417528284 | epot = -20.6617888215465 | etot = -16.8985357673782
+204000  ekin = 2.01924097320136 |  erot = 1.97748949636931 | epot = -20.7002685556681 | etot = -16.7035380860975
+205000  ekin = 2.97656554045711 |  erot = 3.25408007971553 | epot = -20.9425038008424 | etot = -14.7118581806697
+206000  ekin = 2.56613069661945 |  erot = 2.2162424422446 | epot = -21.0621833598182 | etot = -16.2798102209542
+207000  ekin = 3.44850636848559 |  erot = 2.48816050856267 | epot = -21.2038849430866 | etot = -15.2672180660384
+208000  ekin = 2.54208934028226 |  erot = 2.22605232144503 | epot = -21.3476404533667 | etot = -16.5794987916394
+209000  ekin = 3.84151461096732 |  erot = 2.16534559513904 | epot = -21.4932373455843 | etot = -15.486377139478
+210000  ekin = 3.06873591712904 |  erot = 2.24760815652572 | epot = -21.6427793540355 | etot = -16.3264352803807
+211000  ekin = 1.64176280869923 |  erot = 2.17721976802013 | epot = -21.8130439048271 | etot = -17.9940613281078
+212000  ekin = 2.5985934050661 |  erot = 2.41520703335867 | epot = -21.9964648294562 | etot = -16.9826643910315
+213000  ekin = 2.51136104390039 |  erot = 1.99503544560739 | epot = -22.161492842604 | etot = -17.6550963530962
+214000  ekin = 2.77089845962619 |  erot = 3.17247228684199 | epot = -22.208715104286 | etot = -16.2653443578179
+215000  ekin = 2.53408528186206 |  erot = 1.84963848601796 | epot = -22.1148567901871 | etot = -17.7311330223071
+216000  ekin = 2.52671619876928 |  erot = 2.77873014449688 | epot = -22.1370884570131 | etot = -16.8316421137469
+217000  ekin = 2.50171921508545 |  erot = 1.89238935467003 | epot = -22.226079201001 | etot = -17.8319706312455
+218000  ekin = 2.43936294263937 |  erot = 2.41974828067302 | epot = -22.2447049583244 | etot = -17.385593735012
+219000  ekin = 2.30221269367205 |  erot = 2.65120674162377 | epot = -22.2807164841742 | etot = -17.3272970488784
+220000  ekin = 1.70065256620687 |  erot = 2.34758543213917 | epot = -22.2809933538228 | etot = -18.2327553554767
+221000  ekin = 2.09298237125575 |  erot = 2.4788648159591 | epot = -22.267957001012 | etot = -17.6961098137972
+222000  ekin = 1.58469709510937 |  erot = 2.14490786301286 | epot = -22.1867412404881 | etot = -18.4571362823659
+223000  ekin = 1.83926923346352 |  erot = 1.89456034969536 | epot = -22.131893392038 | etot = -18.3980638088791
+224000  ekin = 2.59583657132575 |  erot = 2.93869915115498 | epot = -22.1425986650605 | etot = -16.6080629425798
+225000  ekin = 3.29351563254165 |  erot = 2.84339535814139 | epot = -22.12757310355 | etot = -15.990662112867
+226000  ekin = 3.03135339447922 |  erot = 2.08293143143603 | epot = -22.15283624886 | etot = -17.0385514229448
+227000  ekin = 2.50176282992082 |  erot = 3.15084128846394 | epot = -22.2250438959745 | etot = -16.5724397775897
+228000  ekin = 2.32013498351673 |  erot = 2.67554406359434 | epot = -22.3177515383564 | etot = -17.3220724912453
+229000  ekin = 2.89545450975318 |  erot = 2.90735055857064 | epot = -22.4361496683347 | etot = -16.6333446000109
+230000  ekin = 2.28321229485933 |  erot = 3.48420465632866 | epot = -22.548785995051 | etot = -16.781369043863
+231000  ekin = 2.0778632375453 |  erot = 3.1067397369644 | epot = -22.5896609633152 | etot = -17.4050579888055
+232000  ekin = 2.1202374109541 |  erot = 1.98747810033065 | epot = -22.5738924334392 | etot = -18.4661769221544
+233000  ekin = 2.33571877855589 |  erot = 2.83585090202734 | epot = -22.5402065195541 | etot = -17.3686368389708
+234000  ekin = 2.10578223747154 |  erot = 2.07381218733635 | epot = -22.5507693150832 | etot = -18.3711748902754
+235000  ekin = 2.44321041214394 |  erot = 2.80846352304316 | epot = -22.5606929563186 | etot = -17.3090190211315
+236000  ekin = 2.93630791731799 |  erot = 3.06315918531728 | epot = -22.4860653874721 | etot = -16.4865982848368
+237000  ekin = 3.21264879506079 |  erot = 3.26866508478298 | epot = -22.3683553437861 | etot = -15.8870414639423
+238000  ekin = 2.46595539123277 |  erot = 2.32502019506662 | epot = -22.3144456769666 | etot = -17.5234700906672
+239000  ekin = 2.10325864915823 |  erot = 2.47631139904042 | epot = -22.301139292181 | etot = -17.7215692439824
+240000  ekin = 1.77270999777839 |  erot = 2.60141429112663 | epot = -22.2344206081543 | etot = -17.8602963192493
+241000  ekin = 1.94952922244078 |  erot = 1.39715216866763 | epot = -22.2207225048761 | etot = -18.8740411137677
+242000  ekin = 3.05687991591411 |  erot = 2.00862394928705 | epot = -22.2213200390943 | etot = -17.1558161738932
+243000  ekin = 2.86735711945299 |  erot = 1.7994811867468 | epot = -22.2697610280427 | etot = -17.6029227218429
+244000  ekin = 2.00525854269389 |  erot = 2.36445341214556 | epot = -22.2726788994494 | etot = -17.90296694461
+245000  ekin = 2.28011102404838 |  erot = 2.787005205328 | epot = -22.2995433574618 | etot = -17.2324271280854
+246000  ekin = 2.06819738789813 |  erot = 2.24624952782284 | epot = -22.2551680110137 | etot = -17.9407210952928
+247000  ekin = 1.69964711256213 |  erot = 3.22260619239826 | epot = -22.1916408256116 | etot = -17.2693875206512
+248000  ekin = 1.92997585194759 |  erot = 3.61155944514366 | epot = -22.0096484177852 | etot = -16.468113120694
+249000  ekin = 2.16278530892653 |  erot = 3.27771891456707 | epot = -21.8856058980726 | etot = -16.445101674579
+250000  ekin = 2.32204054211025 |  erot = 2.46317574116849 | epot = -21.8028762710591 | etot = -17.0176599877804
+251000  ekin = 1.23768964067255 |  erot = 2.241505337621 | epot = -21.7630657074039 | etot = -18.2838707291104
+252000  ekin = 1.79818833522214 |  erot = 2.12556386664128 | epot = -21.7586349357284 | etot = -17.834882733865
+253000  ekin = 2.12809689846393 |  erot = 2.59685639208403 | epot = -21.7226495687757 | etot = -16.9976962782278
+254000  ekin = 2.46813261968533 |  erot = 2.00391812662871 | epot = -21.7113918037362 | etot = -17.2393410574221
+255000  ekin = 2.31566729087291 |  erot = 2.03619058028117 | epot = -21.7265453183256 | etot = -17.3746874471715
+256000  ekin = 2.87223929491326 |  erot = 2.61790933826622 | epot = -21.659332511914 | etot = -16.1691838787345
+257000  ekin = 2.85756762932926 |  erot = 2.08174673916199 | epot = -21.6161821054731 | etot = -16.6768677369818
+258000  ekin = 2.06111021157734 |  erot = 2.32748664972428 | epot = -21.5132485706726 | etot = -17.124651709371
+259000  ekin = 2.23305784057759 |  erot = 2.88843859953736 | epot = -21.5040039667854 | etot = -16.3825075266705
+260000  ekin = 2.49862397932476 |  erot = 2.3833688584839 | epot = -21.488210637319 | etot = -16.6062177995103
+261000  ekin = 2.09280296934734 |  erot = 2.39632540029206 | epot = -21.4325331777953 | etot = -16.9434048081559
+262000  ekin = 2.33576913564289 |  erot = 2.67273419354396 | epot = -21.3832241450035 | etot = -16.3747208158166
+263000  ekin = 2.20536189489354 |  erot = 2.71530627040564 | epot = -21.4329409070981 | etot = -16.5122727417989
+264000  ekin = 2.2858247573423 |  erot = 2.76839346219662 | epot = -21.3931084431599 | etot = -16.338890223621
+265000  ekin = 1.70928536820409 |  erot = 1.79395423442895 | epot = -21.2682341921474 | etot = -17.7649945895143
+266000  ekin = 2.48721735474525 |  erot = 2.08745460533225 | epot = -21.1746995817337 | etot = -16.6000276216562
+267000  ekin = 2.69283567987773 |  erot = 2.10301910407212 | epot = -21.1705161290062 | etot = -16.3746613450563
+268000  ekin = 3.00000233743719 |  erot = 2.80954585635721 | epot = -21.1647521126509 | etot = -15.3552039188565
+269000  ekin = 3.50713810468527 |  erot = 2.35763817348002 | epot = -21.1537110688983 | etot = -15.288934790733
+270000  ekin = 3.50686942248863 |  erot = 1.86462765875889 | epot = -21.1925508822801 | etot = -15.8210538010326
+271000  ekin = 3.57026082273992 |  erot = 2.08172467795388 | epot = -21.277581718294 | etot = -15.6255962176003
+272000  ekin = 2.4484752533773 |  erot = 3.08466485039763 | epot = -21.3619851902072 | etot = -15.8288450864322
+273000  ekin = 2.39748176307242 |  erot = 3.1335505044672 | epot = -21.4386234252579 | etot = -15.9075911577183
+274000  ekin = 2.48208144431864 |  erot = 2.00552494041966 | epot = -21.4476232953882 | etot = -16.9600169106499
+275000  ekin = 2.4872108114937 |  erot = 3.05413598233607 | epot = -21.4713984309062 | etot = -15.9300516370765
+276000  ekin = 2.82709589676966 |  erot = 2.88384306577857 | epot = -21.443459011816 | etot = -15.7325200492678
+277000  ekin = 2.23479555963312 |  erot = 2.20310851955639 | epot = -21.3883073251199 | etot = -16.9504032459304
+278000  ekin = 2.81418916407429 |  erot = 3.24537052192614 | epot = -21.3155364074003 | etot = -15.2559767213999
+279000  ekin = 2.57366525203698 |  erot = 1.81705578305929 | epot = -21.2862101233851 | etot = -16.8954890882888
+280000  ekin = 2.41063464320149 |  erot = 1.76282693004732 | epot = -21.254962528096 | etot = -17.0815009548472
+281000  ekin = 2.58126226070487 |  erot = 2.29258221702168 | epot = -21.306394928225 | etot = -16.4325504504985
+282000  ekin = 3.02016903398222 |  erot = 2.4309452389034 | epot = -21.4340900724633 | etot = -15.9829757995777
+283000  ekin = 2.5926914979033 |  erot = 2.11330689541034 | epot = -21.6296517079942 | etot = -16.9236533146805
+284000  ekin = 2.51704243107537 |  erot = 3.13156683036759 | epot = -21.7452694753527 | etot = -16.0966602139097
+285000  ekin = 2.4236537221525 |  erot = 1.77228258125505 | epot = -21.8557019037769 | etot = -17.6597656003694
+286000  ekin = 1.94467195521662 |  erot = 2.03660974116722 | epot = -21.901435736722 | etot = -17.9201540403382
+287000  ekin = 2.56319670376176 |  erot = 2.60867050510154 | epot = -21.9067509934901 | etot = -16.7348837846268
+288000  ekin = 2.19574207425736 |  erot = 1.69805542160022 | epot = -21.8143855675961 | etot = -17.9205880717385
+289000  ekin = 2.35326278833023 |  erot = 1.65840109676148 | epot = -21.6976038565285 | etot = -17.6859399714368
+290000  ekin = 2.35194561775041 |  erot = 1.99444238353745 | epot = -21.6551012116075 | etot = -17.3087132103196
+291000  ekin = 1.48585281531713 |  erot = 2.66475825861556 | epot = -21.56036793472 | etot = -17.4097568607873
+292000  ekin = 2.1073994475645 |  erot = 2.42809824662638 | epot = -21.4451596117638 | etot = -16.9096619175729
+293000  ekin = 2.11618090223715 |  erot = 1.86694554151196 | epot = -21.3593625692768 | etot = -17.3762361255277
+294000  ekin = 2.06078090566327 |  erot = 2.13941873359473 | epot = -21.232623310094 | etot = -17.032423670836
+295000  ekin = 2.11467178034796 |  erot = 2.32673436675183 | epot = -21.1123588667461 | etot = -16.6709527196463
+296000  ekin = 1.53087058859334 |  erot = 2.94008409149154 | epot = -21.2112197533848 | etot = -16.7402650732999
+297000  ekin = 2.52732986791201 |  erot = 2.18380855337859 | epot = -21.1955190508786 | etot = -16.484380629588
+298000  ekin = 1.89033945823201 |  erot = 2.02521913176003 | epot = -21.2593750718295 | etot = -17.3438164818375
+299000  ekin = 1.87142873048437 |  erot = 1.6640456322155 | epot = -21.2919162310488 | etot = -17.7564418683489
+300000  ekin = 2.23872615546785 |  erot = 1.50807257618898 | epot = -21.3339204593826 | etot = -17.5871217277257
+301000  ekin = 1.99965506724556 |  erot = 2.00145094516845 | epot = -21.4707589194324 | etot = -17.4696529070184
+302000  ekin = 1.76370349732521 |  erot = 2.2378770890149 | epot = -21.5675275978257 | etot = -17.5659470114856
+303000  ekin = 2.69610887251788 |  erot = 1.69957221429742 | epot = -21.5563765448091 | etot = -17.1606954579938
+304000  ekin = 2.55447143501921 |  erot = 2.02060813090351 | epot = -21.5692327321341 | etot = -16.9941531662114
+305000  ekin = 2.38230604232715 |  erot = 2.31489374428117 | epot = -21.5335950166329 | etot = -16.8363952300246
+306000  ekin = 2.07785475765117 |  erot = 2.45230660685968 | epot = -21.4550895345846 | etot = -16.9249281700738
+307000  ekin = 3.17130424567277 |  erot = 3.29574614566804 | epot = -21.4151535289883 | etot = -14.9481031376475
+308000  ekin = 3.40959217051674 |  erot = 2.68389483402971 | epot = -21.4778643688409 | etot = -15.3843773642944
+309000  ekin = 2.36068264180093 |  erot = 2.91715332823343 | epot = -21.5794336507741 | etot = -16.3015976807397
+310000  ekin = 2.49952357229221 |  erot = 2.3602895089614 | epot = -21.5982142524176 | etot = -16.738401171164
+311000  ekin = 2.53288726180907 |  erot = 2.29596940545853 | epot = -21.6418553661547 | etot = -16.8129986988871
+312000  ekin = 2.05123272208704 |  erot = 2.92023923411836 | epot = -21.7377547517075 | etot = -16.7662827955021
+313000  ekin = 1.80834719374889 |  erot = 2.29357283142128 | epot = -21.7993116362532 | etot = -17.697391611083
+314000  ekin = 2.30684015099018 |  erot = 2.20859462712275 | epot = -21.8029398081388 | etot = -17.2875050300258
+315000  ekin = 1.86413924486173 |  erot = 2.14748794238473 | epot = -21.8550418960799 | etot = -17.8434147088335
+316000  ekin = 2.20558056533516 |  erot = 3.03447287931581 | epot = -21.8868412075708 | etot = -16.6467877629199
+317000  ekin = 2.4782093112548 |  erot = 3.56870099099487 | epot = -21.9902146748518 | etot = -15.9433043726022
+318000  ekin = 2.36582343801679 |  erot = 3.01887804681551 | epot = -22.1178732891163 | etot = -16.7331718042839
+319000  ekin = 2.40464629760758 |  erot = 3.15910789488741 | epot = -22.2289401281564 | etot = -16.6651859356615
+320000  ekin = 1.80206494109346 |  erot = 2.83527990295433 | epot = -22.3120263401861 | etot = -17.6746814961383
+321000  ekin = 2.91146951948762 |  erot = 2.25772268449837 | epot = -22.3029455835946 | etot = -17.1337533796087
+322000  ekin = 2.8226351296685 |  erot = 2.67950826833979 | epot = -22.3041650189947 | etot = -16.8020216209864
+323000  ekin = 2.067323568424 |  erot = 2.31975284775299 | epot = -22.3338840353559 | etot = -17.9468076191789
+324000  ekin = 2.6012747278288 |  erot = 2.58351861537749 | epot = -22.3215168526943 | etot = -17.1367235094881
+325000  ekin = 3.45560055552842 |  erot = 2.50162515355503 | epot = -22.1825527777624 | etot = -16.2253270686789
+326000  ekin = 3.51422890604519 |  erot = 2.8442606101801 | epot = -22.0201095272524 | etot = -15.6616200110271
+327000  ekin = 2.63551490316294 |  erot = 2.20570805472232 | epot = -21.9384479867006 | etot = -17.0972250288154
+328000  ekin = 1.8043914440792 |  erot = 2.37599512200969 | epot = -21.8619803976419 | etot = -17.681593831553
+329000  ekin = 2.15766181563134 |  erot = 2.45286496267961 | epot = -21.8518523862111 | etot = -17.2413256079002
+330000  ekin = 1.8483425992464 |  erot = 2.03367429366602 | epot = -21.7684095252419 | etot = -17.8863926323295
+331000  ekin = 2.3531484336258 |  erot = 1.80165819621477 | epot = -21.7197009414848 | etot = -17.5648943116442
+332000  ekin = 1.67855936307207 |  erot = 2.53341219651311 | epot = -21.733643435588 | etot = -17.5216718760028
+333000  ekin = 1.60376334688456 |  erot = 2.14058675025446 | epot = -21.835637958395 | etot = -18.091287861256
+334000  ekin = 2.2655199008178 |  erot = 2.62486254825417 | epot = -21.879497107847 | etot = -16.989114658775
+335000  ekin = 2.91208137486082 |  erot = 3.11052870452009 | epot = -21.9161692767171 | etot = -15.8935591973362
+336000  ekin = 2.73132973682385 |  erot = 2.56213100489405 | epot = -21.8312488568505 | etot = -16.5377881151326
+337000  ekin = 3.15411918141902 |  erot = 3.875128198312 | epot = -21.9061152574783 | etot = -14.8768678777473
+338000  ekin = 2.33141760424507 |  erot = 2.13211945089679 | epot = -21.913746111238 | etot = -17.4502090560961
+339000  ekin = 1.71915361945718 |  erot = 2.31270220754042 | epot = -21.9042074773719 | etot = -17.8723516503743
+340000  ekin = 1.62199393011805 |  erot = 3.16990972384469 | epot = -21.8898233676231 | etot = -17.0979197136604
+341000  ekin = 1.71588704296646 |  erot = 3.17642860992462 | epot = -21.8345558128149 | etot = -16.9422401599238
+342000  ekin = 1.82178091247658 |  erot = 2.58875985611025 | epot = -21.7161502950572 | etot = -17.3056095264704
+343000  ekin = 3.08559255942693 |  erot = 2.94813449265469 | epot = -21.7030445300996 | etot = -15.669317478018
+344000  ekin = 2.95985387154984 |  erot = 3.11547515850352 | epot = -21.681548329552 | etot = -15.6062192994986
+345000  ekin = 2.33428072266864 |  erot = 2.8804443128302 | epot = -21.6567075042343 | etot = -16.4419824687354
+346000  ekin = 2.02077664062698 |  erot = 3.45936833964706 | epot = -21.5877268821218 | etot = -16.1075819018477
+347000  ekin = 2.34924784800441 |  erot = 1.93056350805623 | epot = -21.4896151766054 | etot = -17.2098038205448
+348000  ekin = 2.79839267202794 |  erot = 2.79408776517961 | epot = -21.4682057474677 | etot = -15.8757253102602
+349000  ekin = 2.33820470114615 |  erot = 3.12966318670512 | epot = -21.5603039389198 | etot = -16.0924360510685
+350000  ekin = 2.22383234890832 |  erot = 2.3888687038801 | epot = -21.5375784703117 | etot = -16.9248774175232
+351000  ekin = 2.33329735253339 |  erot = 2.84447430695177 | epot = -21.5078106306152 | etot = -16.33003897113
+352000  ekin = 2.74923373919409 |  erot = 2.76796181793622 | epot = -21.5537134920816 | etot = -16.0365179349513
+353000  ekin = 1.76111836153718 |  erot = 2.12255592617517 | epot = -21.5037017999955 | etot = -17.6200275122832
+354000  ekin = 2.29967358188085 |  erot = 2.37615363620183 | epot = -21.559257977819 | etot = -16.8834307597363
+355000  ekin = 2.32956787601564 |  erot = 2.41406261152025 | epot = -21.5311925684016 | etot = -16.7875620808657
+356000  ekin = 2.99536507165416 |  erot = 3.01337867890171 | epot = -21.461213826164 | etot = -15.4524700756081
+357000  ekin = 1.79487551861702 |  erot = 2.1478177575683 | epot = -21.4425100027869 | etot = -17.4998167266015
+358000  ekin = 2.06856992699964 |  erot = 1.91585051553708 | epot = -21.4597512525557 | etot = -17.475330810019
+359000  ekin = 2.03457633089973 |  erot = 2.13725650388116 | epot = -21.4345843672419 | etot = -17.2627515324611
+360000  ekin = 2.64289898809605 |  erot = 2.45722294398596 | epot = -21.3798303659972 | etot = -16.2797084339152
+361000  ekin = 2.44681633772951 |  erot = 2.40323525392196 | epot = -21.4535746870957 | etot = -16.6035230954443
+362000  ekin = 2.27284400709389 |  erot = 2.04866562998477 | epot = -21.4444048899961 | etot = -17.1228952529174
+363000  ekin = 3.23945885057604 |  erot = 1.79247859381385 | epot = -21.4992698914106 | etot = -16.4673324470207
+364000  ekin = 3.01124200487832 |  erot = 2.16495867321709 | epot = -21.5330648567406 | etot = -16.3568641786452
+365000  ekin = 2.51472285580871 |  erot = 2.29864111879032 | epot = -21.6252096459668 | etot = -16.8118456713678
+366000  ekin = 2.59356655410024 |  erot = 2.21031948632571 | epot = -21.6397726115723 | etot = -16.8358865711463
+367000  ekin = 2.23422490605625 |  erot = 1.85375489374337 | epot = -21.7036464131406 | etot = -17.615666613341
+368000  ekin = 2.4774770785368 |  erot = 2.36511710555107 | epot = -21.7442459693683 | etot = -16.9016517852804
+369000  ekin = 2.03854183495617 |  erot = 2.80790943599038 | epot = -21.8295461127419 | etot = -16.9830948417954
+370000  ekin = 2.08495509326203 |  erot = 2.15717784784086 | epot = -21.8579547558588 | etot = -17.6158218147559
+371000  ekin = 2.1649158804987 |  erot = 2.10731342711639 | epot = -21.7507302872469 | etot = -17.4785009796318
+372000  ekin = 1.83416420958724 |  erot = 1.90082367490456 | epot = -21.6784224725519 | etot = -17.9434345880601
+373000  ekin = 1.97176482573297 |  erot = 1.7779600789095 | epot = -21.6393712386778 | etot = -17.8896463340353
+374000  ekin = 2.89940710658305 |  erot = 1.91194262525378 | epot = -21.5337545453635 | etot = -16.7224048135267
+375000  ekin = 2.32339676163341 |  erot = 1.92362318361284 | epot = -21.421709102519 | etot = -17.1746891572728
+376000  ekin = 2.59047552311153 |  erot = 2.32394149083979 | epot = -21.4139727856534 | etot = -16.4995557717021
+377000  ekin = 2.24598863840517 |  erot = 1.65770205797294 | epot = -21.3405339068232 | etot = -17.4368432104451
+378000  ekin = 2.38351514056703 |  erot = 2.54156262207208 | epot = -21.3122380587448 | etot = -16.3871602961057
+379000  ekin = 2.08457212928957 |  erot = 2.11819645676891 | epot = -21.2663127721437 | etot = -17.0635441860852
+380000  ekin = 2.62168026009058 |  erot = 2.36576073073355 | epot = -21.2469701231191 | etot = -16.259529132295
+381000  ekin = 2.42554871977307 |  erot = 2.21588725182519 | epot = -21.2594018196931 | etot = -16.6179658480948
+382000  ekin = 2.04454090532122 |  erot = 3.35199327879854 | epot = -21.3507561156203 | etot = -15.9542219315006
+383000  ekin = 2.5775676978984 |  erot = 1.58356833947096 | epot = -21.4206473136967 | etot = -17.2595112763273
+384000  ekin = 2.32411392435712 |  erot = 2.07034159075991 | epot = -21.4254017003271 | etot = -17.0309461852101
+385000  ekin = 1.93815279071873 |  erot = 3.2997037447625 | epot = -21.4993838182002 | etot = -16.2615272827189
+386000  ekin = 2.10645704249442 |  erot = 2.94380940917573 | epot = -21.5050572923383 | etot = -16.4547908406681
+387000  ekin = 2.28625118399722 |  erot = 2.40488022694899 | epot = -21.4350466670762 | etot = -16.74391525613
+388000  ekin = 2.84183807689895 |  erot = 2.72440789072404 | epot = -21.448767296848 | etot = -15.882521329225
+389000  ekin = 3.39750799106376 |  erot = 3.08194517695383 | epot = -21.6559630447603 | etot = -15.1765098767427
+390000  ekin = 2.82211920760118 |  erot = 2.04880343622588 | epot = -21.7229608878358 | etot = -16.8520382440088
+391000  ekin = 2.25113345866118 |  erot = 2.45876014532077 | epot = -21.7793475672487 | etot = -17.0694539632668
+392000  ekin = 2.6777973992177 |  erot = 2.7527860471579 | epot = -21.9200377033298 | etot = -16.4894542569542
+393000  ekin = 2.07336639249412 |  erot = 1.66102921524042 | epot = -22.0500496423093 | etot = -18.3156540345748
+394000  ekin = 2.1138614951422 |  erot = 2.4065490584156 | epot = -22.0647062581752 | etot = -17.5442957046174
+395000  ekin = 2.46967791557608 |  erot = 2.46187607744979 | epot = -22.0113006362931 | etot = -17.0797466432672
+396000  ekin = 3.17858061422169 |  erot = 1.60030928107608 | epot = -21.9570022338792 | etot = -17.1781123385814
+397000  ekin = 2.37483507726777 |  erot = 2.17387816921976 | epot = -21.8769234701934 | etot = -17.3282102237059
+398000  ekin = 2.29815779154461 |  erot = 2.20148627030488 | epot = -21.8293641014529 | etot = -17.3297200396034
+399000  ekin = 2.66620669497936 |  erot = 2.78316441348841 | epot = -21.7420307764657 | etot = -16.2926596679979
+400000  ekin = 1.8196142363994 |  erot = 2.77573291920481 | epot = -21.7225828560707 | etot = -17.1272357004665
+401000  ekin = 2.39347596566752 |  erot = 3.11237720134103 | epot = -21.763219812775 | etot = -16.2573666457665
+402000  ekin = 4.0137909252526 |  erot = 3.58756310879366 | epot = -21.6952307126455 | etot = -14.0938766785993
+403000  ekin = 3.6423872335827 |  erot = 3.44210139074532 | epot = -21.6932224157202 | etot = -14.6087337913922
+404000  ekin = 2.52116102522202 |  erot = 2.99286839639892 | epot = -21.7395466120138 | etot = -16.2255171903929
+405000  ekin = 2.80514548558626 |  erot = 3.09807228440151 | epot = -21.809681120553 | etot = -15.9064633505652
+406000  ekin = 2.32696376764902 |  erot = 2.03572639782902 | epot = -21.9111381639248 | etot = -17.5484479984467
+407000  ekin = 2.33504128016394 |  erot = 1.91320949168965 | epot = -21.9359478399847 | etot = -17.6876970681311
+408000  ekin = 1.90942025822264 |  erot = 2.20375631379572 | epot = -21.9849314014527 | etot = -17.8717548294343
+409000  ekin = 1.98818542800297 |  erot = 1.95540808206522 | epot = -22.03783497597 | etot = -18.0942414659018
+410000  ekin = 1.59823476401333 |  erot = 1.9127296785249 | epot = -22.0830507565095 | etot = -18.5720863139713
+411000  ekin = 1.87320182179615 |  erot = 2.46575148951074 | epot = -22.1911106440467 | etot = -17.8521573327398
+412000  ekin = 2.51909186028136 |  erot = 2.65534868642726 | epot = -22.281680067606 | etot = -17.1072395208973
+413000  ekin = 2.80929435327118 |  erot = 3.19888285052217 | epot = -22.190767996874 | etot = -16.1825907930807
+414000  ekin = 2.79014519733558 |  erot = 2.72515195410933 | epot = -22.1448630242429 | etot = -16.629565872798
+415000  ekin = 2.4678901908732 |  erot = 2.24891720770208 | epot = -22.1977268949424 | etot = -17.4809194963671
+416000  ekin = 3.30766536008867 |  erot = 1.55878918639504 | epot = -22.1694878213559 | etot = -17.3030332748721
+417000  ekin = 3.95074944679109 |  erot = 2.44780201516574 | epot = -22.1018895242094 | etot = -15.7033380622526
+418000  ekin = 2.77340936693416 |  erot = 2.68993840817536 | epot = -21.977327562767 | etot = -16.5139797876575
+419000  ekin = 2.38275203991917 |  erot = 2.97769109273479 | epot = -21.9010102007428 | etot = -16.5405670680889
+420000  ekin = 1.80397709765343 |  erot = 1.82715488758969 | epot = -21.8849019003165 | etot = -18.2537699150733
+421000  ekin = 1.35294173647286 |  erot = 1.7746327595132 | epot = -21.8324727162454 | etot = -18.7048982202594
+422000  ekin = 1.39101035408782 |  erot = 2.74626781088315 | epot = -21.892204423852 | etot = -17.7549262588811
+423000  ekin = 1.58313118355037 |  erot = 3.07988587276088 | epot = -21.9303489156375 | etot = -17.2673318593263
+424000  ekin = 2.38308976422853 |  erot = 2.02905632834229 | epot = -22.0003513420111 | etot = -17.5882052494403
+425000  ekin = 2.32292982636641 |  erot = 2.54472792699358 | epot = -22.0461884305752 | etot = -17.1785306772153
+426000  ekin = 2.07274921207621 |  erot = 3.12068562025983 | epot = -21.9899604929779 | etot = -16.7965256606418
+427000  ekin = 2.16499158921496 |  erot = 2.43609860560844 | epot = -21.8837565028179 | etot = -17.2826663079945
+428000  ekin = 1.81001230881453 |  erot = 1.65184910311941 | epot = -21.8651168729133 | etot = -18.4032554609794
+429000  ekin = 1.67080799563552 |  erot = 2.55829004033941 | epot = -21.823203822061 | etot = -17.5941057860861
+430000  ekin = 2.68658781224627 |  erot = 2.85919253371561 | epot = -21.8545360487503 | etot = -16.3087557027884
+431000  ekin = 2.77334901985549 |  erot = 1.57746917070685 | epot = -21.8360353910943 | etot = -17.485217200532
+432000  ekin = 2.50244674166437 |  erot = 1.60779258881598 | epot = -21.7381087453319 | etot = -17.6278694148515
+433000  ekin = 1.85649371322474 |  erot = 2.4917335891794 | epot = -21.7919912827364 | etot = -17.4437639803322
+434000  ekin = 2.89302367450635 |  erot = 2.79890045602688 | epot = -21.923157505168 | etot = -16.2312333746347
+435000  ekin = 3.67647442700572 |  erot = 1.38588132381275 | epot = -22.1019777057281 | etot = -17.0396219549096
+436000  ekin = 3.05510329104703 |  erot = 2.00142902882896 | epot = -22.1034257027065 | etot = -17.0468933828305
+437000  ekin = 3.23341172893811 |  erot = 1.78346855436478 | epot = -22.113702088725 | etot = -17.0968218054221
+438000  ekin = 2.86378458795303 |  erot = 1.84588842157477 | epot = -22.072414124752 | etot = -17.3627411152242
+439000  ekin = 2.41407153953135 |  erot = 2.70066632790347 | epot = -22.0535011599235 | etot = -16.9387632924887
+440000  ekin = 2.22110309163133 |  erot = 3.01674685818988 | epot = -22.0773629228071 | etot = -16.8395129729859
+441000  ekin = 2.89520033479411 |  erot = 2.87911130379517 | epot = -22.209849236351 | etot = -16.4355375977617
+442000  ekin = 2.05598301233623 |  erot = 1.73562369066664 | epot = -22.2689079268811 | etot = -18.4773012238783
+443000  ekin = 1.86650631344268 |  erot = 2.00816178040311 | epot = -22.3072964279924 | etot = -18.4326283341466
+444000  ekin = 2.06088560705619 |  erot = 2.15265011198711 | epot = -22.3186686701218 | etot = -18.1051329510785
+445000  ekin = 2.10029110633058 |  erot = 2.2800331405132 | epot = -22.3739249314238 | etot = -17.99360068458
+446000  ekin = 2.42121462246176 |  erot = 2.8536509710476 | epot = -22.4030820729313 | etot = -17.128216479422
+447000  ekin = 2.19905370994783 |  erot = 2.98216231903378 | epot = -22.4760062523441 | etot = -17.2947902233625
+448000  ekin = 2.35344530580996 |  erot = 2.94496431571717 | epot = -22.4927466941726 | etot = -17.1943370726455
+449000  ekin = 2.39032460069844 |  erot = 2.92889137252357 | epot = -22.5027878081879 | etot = -17.1835718349658
+450000  ekin = 1.87543018481826 |  erot = 1.69603328668915 | epot = -22.4562462785527 | etot = -18.8847828070453
+451000  ekin = 2.01850498861611 |  erot = 1.92812989993404 | epot = -22.4817672986218 | etot = -18.5351324100716
+452000  ekin = 1.36652609658347 |  erot = 1.87105620810406 | epot = -22.4501755877893 | etot = -19.2125932831017
+453000  ekin = 2.0599225820261 |  erot = 2.56027964608567 | epot = -22.2765869721545 | etot = -17.6563847440427
+454000  ekin = 1.47421749728914 |  erot = 2.19120144206329 | epot = -22.1381671023588 | etot = -18.4727481630063
+455000  ekin = 1.65550022307771 |  erot = 2.72165814308167 | epot = -21.9904394751434 | etot = -17.613281108984
+456000  ekin = 2.34827062603187 |  erot = 2.00722438151078 | epot = -21.9105114729144 | etot = -17.5550164653718
+457000  ekin = 2.01338249991754 |  erot = 2.37170378033693 | epot = -21.8819790372449 | etot = -17.4968927569904
+458000  ekin = 1.72815421955305 |  erot = 2.26329746701055 | epot = -21.911604405066 | etot = -17.9201527185024
+459000  ekin = 2.48347398227002 |  erot = 2.3237619692994 | epot = -21.9949404038568 | etot = -17.1877044522873
+460000  ekin = 2.18770854699574 |  erot = 2.00081662918321 | epot = -21.9585322440375 | etot = -17.7700070678585
+461000  ekin = 2.27716435663743 |  erot = 2.90195656269068 | epot = -21.8877682177659 | etot = -16.7086472984378
+462000  ekin = 2.61244889701714 |  erot = 1.79757533309512 | epot = -21.9143949779912 | etot = -17.5043707478789
+463000  ekin = 2.55684814656523 |  erot = 3.31200610027655 | epot = -21.8497749242033 | etot = -15.9809206773615
+464000  ekin = 2.15312235839157 |  erot = 2.38947690136822 | epot = -21.7825241097983 | etot = -17.2399248500385
+465000  ekin = 2.5257577253008 |  erot = 3.61331808321474 | epot = -21.7072705251899 | etot = -15.5681947166744
+466000  ekin = 1.97943618964771 |  erot = 2.8868852833762 | epot = -21.7222514097774 | etot = -16.8559299367534
+467000  ekin = 1.62882257493983 |  erot = 2.60892282315519 | epot = -21.8080861041927 | etot = -17.5703407060977
+468000  ekin = 1.09823854644375 |  erot = 3.35073251937298 | epot = -21.8523811012329 | etot = -17.4034100354162
+469000  ekin = 1.70229597385131 |  erot = 2.75889840726388 | epot = -21.8665756757502 | etot = -17.405381294635
+470000  ekin = 1.85844768422772 |  erot = 2.8706546217625 | epot = -21.9036130079376 | etot = -17.1745107019474
+471000  ekin = 2.74399539924327 |  erot = 2.34943354955081 | epot = -21.9543989717239 | etot = -16.8609700229298
+472000  ekin = 2.7182617922689 |  erot = 2.13581917182001 | epot = -22.0449294707038 | etot = -17.1908485066148
+473000  ekin = 2.29380642077304 |  erot = 2.07595163501546 | epot = -22.0706135180041 | etot = -17.7008554622156
+474000  ekin = 2.22690782122655 |  erot = 2.16470599013948 | epot = -22.0704871162386 | etot = -17.6788733048726
+475000  ekin = 2.4978679533329 |  erot = 2.09510196885224 | epot = -22.0509742163569 | etot = -17.4580042941717
+476000  ekin = 2.20264299239668 |  erot = 1.76757923556402 | epot = -21.9427521555982 | etot = -17.9725299276375
+477000  ekin = 2.45872237399503 |  erot = 2.38426997478537 | epot = -21.9051474088982 | etot = -17.0621550601178
+478000  ekin = 1.8990596403089 |  erot = 2.04864356713722 | epot = -21.9114508304737 | etot = -17.9637476230276
+479000  ekin = 2.2713390213749 |  erot = 3.08755197682257 | epot = -21.8872829373265 | etot = -16.5283919391291
+480000  ekin = 1.67015605151468 |  erot = 2.76560365045838 | epot = -21.8968158425889 | etot = -17.4610561406158
+481000  ekin = 1.81882995680353 |  erot = 2.94136105971067 | epot = -21.8571304925408 | etot = -17.0969394760266
+482000  ekin = 2.15305069632652 |  erot = 2.07327897823918 | epot = -21.8152992914385 | etot = -17.5889696168728
+483000  ekin = 1.50004535981758 |  erot = 1.99364343935403 | epot = -21.7843644990947 | etot = -18.2906756999231
+484000  ekin = 1.85234844255529 |  erot = 2.3400023120278 | epot = -21.8614293841666 | etot = -17.6690786295835
+485000  ekin = 1.64682178328831 |  erot = 2.50437862576678 | epot = -21.8969405008956 | etot = -17.7457400918405
+486000  ekin = 1.86104257115938 |  erot = 2.15995925522771 | epot = -21.8879397421696 | etot = -17.8669379157825
+487000  ekin = 2.34639026339217 |  erot = 3.11622773972824 | epot = -21.9707194220382 | etot = -16.5081014189178
+488000  ekin = 2.27484994031488 |  erot = 3.28147617368228 | epot = -21.9426475486812 | etot = -16.3863214346841
+489000  ekin = 2.38811933287365 |  erot = 2.56070014238266 | epot = -21.8600861168089 | etot = -16.9112666415526
+490000  ekin = 2.12976254880773 |  erot = 3.54525746010286 | epot = -21.7617637919249 | etot = -16.0867437830143
+491000  ekin = 2.20850764560418 |  erot = 2.48919239454319 | epot = -21.6468680069132 | etot = -16.9491679667658
+492000  ekin = 2.43957739853024 |  erot = 2.7632318669038 | epot = -21.6230951653168 | etot = -16.4202858998828
+493000  ekin = 1.79391622496105 |  erot = 2.2905251847004 | epot = -21.6945975278841 | etot = -17.6101561182226
+494000  ekin = 2.11542949642227 |  erot = 3.01313865872483 | epot = -21.7637004472039 | etot = -16.6351322920568
+495000  ekin = 2.1568591957283 |  erot = 2.49005677705245 | epot = -21.8783556810053 | etot = -17.2314397082246
+496000  ekin = 2.0603755282602 |  erot = 2.606986291047 | epot = -21.9276220332962 | etot = -17.260260213989
+497000  ekin = 2.52228141248763 |  erot = 1.71013019276801 | epot = -21.8769629373864 | etot = -17.6445513321307
+498000  ekin = 2.1539450080541 |  erot = 1.78777085700022 | epot = -21.8243748366057 | etot = -17.8826589715514
+499000  ekin = 3.01296343053108 |  erot = 1.73934813146709 | epot = -21.839263268044 | etot = -17.0869517060458
+500000  ekin = 2.7664211971855 |  erot = 2.50182215373005 | epot = -21.830671988603 | etot = -16.5624286376875
+501000  ekin = 2.69367571720338 |  erot = 2.99042817784737 | epot = -21.7039103667138 | etot = -16.0198064716631
+502000  ekin = 1.91666556639459 |  erot = 3.89815239299715 | epot = -21.5845300715443 | etot = -15.7697121121525
+503000  ekin = 1.80513448090424 |  erot = 2.94463129244922 | epot = -21.408846856306 | etot = -16.6590810829525
+504000  ekin = 1.70082883689618 |  erot = 3.04312463877849 | epot = -21.3315058298563 | etot = -16.5875523541817
+505000  ekin = 2.75953000022913 |  erot = 2.14635942194521 | epot = -21.3525103549444 | etot = -16.4466209327701
+506000  ekin = 2.29728093923375 |  erot = 2.04403144683578 | epot = -21.3794572010067 | etot = -17.0381448149372
+507000  ekin = 3.17636857959624 |  erot = 2.42164349794529 | epot = -21.4731108320935 | etot = -15.8750987545519
+508000  ekin = 2.53590109429522 |  erot = 2.52790695399208 | epot = -21.6300410847596 | etot = -16.5662330364723
+509000  ekin = 2.12748393236721 |  erot = 2.83071060777934 | epot = -21.7781347526393 | etot = -16.8199402124928
+510000  ekin = 2.16138023827908 |  erot = 1.44739524871433 | epot = -21.8661383228762 | etot = -18.2573628358828
+511000  ekin = 2.5432337386743 |  erot = 2.7710867437818 | epot = -21.9670096484362 | etot = -16.65268916598
+512000  ekin = 2.32820226144234 |  erot = 2.80424931634042 | epot = -22.0177071813426 | etot = -16.8852556035598
+513000  ekin = 2.47700215188742 |  erot = 2.17127792631492 | epot = -22.0110285387343 | etot = -17.362748460532
+514000  ekin = 2.76651136580706 |  erot = 2.55680467976049 | epot = -22.0909970005814 | etot = -16.7676809550139
+515000  ekin = 2.5202331965388 |  erot = 1.82499891391154 | epot = -22.1712715169566 | etot = -17.8260394065062
+516000  ekin = 2.81741012640848 |  erot = 2.22255273815335 | epot = -22.2621950124766 | etot = -17.2222321479148
+517000  ekin = 2.03287831599843 |  erot = 2.04932227860397 | epot = -22.2794486174447 | etot = -18.1972480228423
+518000  ekin = 2.18753527424292 |  erot = 2.76011341951324 | epot = -22.2667176836094 | etot = -17.3190689898532
+519000  ekin = 2.23127004412532 |  erot = 2.23036422155453 | epot = -22.3641437250361 | etot = -17.9025094593563
+520000  ekin = 1.88835704965194 |  erot = 2.20137678015023 | epot = -22.4547788180202 | etot = -18.365044988218
+521000  ekin = 2.57911594310158 |  erot = 1.87216207270883 | epot = -22.6071563154982 | etot = -18.1558782996878
+522000  ekin = 3.47551915105824 |  erot = 1.7762374523623 | epot = -22.6852629490162 | etot = -17.4335063455957
+523000  ekin = 2.84545293485785 |  erot = 2.47507537559666 | epot = -22.727728352182 | etot = -17.4072000417275
+524000  ekin = 2.40278895519472 |  erot = 2.37529684497553 | epot = -22.6643160930411 | etot = -17.8862302928709
+525000  ekin = 1.5950703357501 |  erot = 2.61508341973266 | epot = -22.5633164974796 | etot = -18.3531627419968
+526000  ekin = 1.67007684014044 |  erot = 1.59545284095806 | epot = -22.511319978416 | etot = -19.2457902973175
+527000  ekin = 2.19667533945247 |  erot = 1.9333023124675 | epot = -22.4181345854017 | etot = -18.2881569334817
+528000  ekin = 2.6386695788743 |  erot = 2.84200507572112 | epot = -22.4271496272375 | etot = -16.9464749726421
+529000  ekin = 2.71685924097597 |  erot = 3.01195511036351 | epot = -22.4607209136928 | etot = -16.7319065623533
+530000  ekin = 2.59646038482582 |  erot = 2.1317692819235 | epot = -22.3209630404852 | etot = -17.5927333737359
+531000  ekin = 2.96818211550215 |  erot = 2.35836906019033 | epot = -22.2240561584028 | etot = -16.8975049827104
+532000  ekin = 2.54400448114086 |  erot = 2.32266423688291 | epot = -22.2383323718679 | etot = -17.3716636538441
+533000  ekin = 2.47235456553947 |  erot = 2.96337386592411 | epot = -22.2434312615742 | etot = -16.8077028301106
+534000  ekin = 2.104894788263 |  erot = 2.03894640697442 | epot = -22.2624131617689 | etot = -18.1185719665315
+535000  ekin = 3.76811893478762 |  erot = 2.64694643296526 | epot = -22.2342741399369 | etot = -15.819208772184
+536000  ekin = 2.78932048770647 |  erot = 1.95046774407586 | epot = -22.1710588414062 | etot = -17.4312706096239
+537000  ekin = 2.84547413963847 |  erot = 2.62354406512568 | epot = -22.0792539675812 | etot = -16.610235762817
+538000  ekin = 2.67615418297318 |  erot = 2.08962546790894 | epot = -21.9560559397441 | etot = -17.190276288862
+539000  ekin = 2.73041224389435 |  erot = 2.35761678189142 | epot = -22.0360310245606 | etot = -16.9480019987748
+540000  ekin = 2.45513520817504 |  erot = 2.49807124796169 | epot = -22.1997448500024 | etot = -17.2465383938656
+541000  ekin = 3.48268229748521 |  erot = 2.77797330372247 | epot = -22.2939060084684 | etot = -16.0332504072607
+542000  ekin = 2.48960436886327 |  erot = 2.8733247922981 | epot = -22.3004887690915 | etot = -16.9375596079301
+543000  ekin = 2.34699181381529 |  erot = 2.86167842257192 | epot = -22.3027783678197 | etot = -17.0941081314325
+544000  ekin = 2.22918134297116 |  erot = 1.46827924617159 | epot = -22.2757921511234 | etot = -18.5783315619807
+545000  ekin = 2.45393652663684 |  erot = 2.14178562937395 | epot = -22.2696521197313 | etot = -17.6739299637206
+546000  ekin = 1.98434977645849 |  erot = 2.24144093113159 | epot = -22.232171992891 | etot = -18.0063812853009
+547000  ekin = 2.56230350196472 |  erot = 1.89574625912019 | epot = -22.2013923967025 | etot = -17.7433426356176
+548000  ekin = 1.72907614338158 |  erot = 1.64127030305736 | epot = -22.1897325934373 | etot = -18.8193861469984
+549000  ekin = 1.95696682165777 |  erot = 2.64539988943053 | epot = -22.3281210018679 | etot = -17.7257542907796
+550000  ekin = 1.80672944936439 |  erot = 1.58554489058936 | epot = -22.4379557312283 | etot = -19.0456813912745
+551000  ekin = 2.19785864069661 |  erot = 2.26344341600384 | epot = -22.4944444264338 | etot = -18.0331423697333
+552000  ekin = 2.074442528674 |  erot = 2.49246441473271 | epot = -22.5313734934249 | etot = -17.9644665500182
+553000  ekin = 2.94841939583913 |  erot = 2.12309786300742 | epot = -22.5870982488507 | etot = -17.5155809900042
+554000  ekin = 2.86687820100223 |  erot = 1.94287298381726 | epot = -22.755332978123 | etot = -17.9455817933035
+555000  ekin = 2.43102414091851 |  erot = 2.28708167460999 | epot = -22.8409516497234 | etot = -18.1228458341949
+556000  ekin = 2.31020008885682 |  erot = 2.55815314755914 | epot = -22.8777743355339 | etot = -18.0094210991179
+557000  ekin = 2.81359485404959 |  erot = 1.42586137655668 | epot = -22.93912738 | etot = -18.6996711493938
+558000  ekin = 2.79709708533547 |  erot = 1.99545051650402 | epot = -22.9823826800612 | etot = -18.1898350782217
+559000  ekin = 3.34842854089641 |  erot = 2.30939572175805 | epot = -23.0558646505447 | etot = -17.3980403878902
+560000  ekin = 3.12583165184862 |  erot = 2.33613566970364 | epot = -23.0537007225862 | etot = -17.591733401034
+561000  ekin = 2.91276096736789 |  erot = 2.07459481236915 | epot = -22.9822607654341 | etot = -17.994904985697
+562000  ekin = 3.33017095598494 |  erot = 2.52215992853225 | epot = -22.8889363116258 | etot = -17.0366054271086
+563000  ekin = 2.70200701416855 |  erot = 1.647701133792 | epot = -22.8712722594835 | etot = -18.521564111523
+564000  ekin = 2.82953631474814 |  erot = 2.52900560163797 | epot = -22.8387855460795 | etot = -17.4802436296934
+565000  ekin = 2.67999888917709 |  erot = 2.05091800967451 | epot = -22.7937507048715 | etot = -18.0628338060199
+566000  ekin = 2.32986557500305 |  erot = 2.16379904557212 | epot = -22.8028233873669 | etot = -18.3091587667917
+567000  ekin = 1.92319601586312 |  erot = 2.83258522428555 | epot = -22.7588270107033 | etot = -18.0030457705546
+568000  ekin = 2.1767237164987 |  erot = 2.23391201707387 | epot = -22.7857243432792 | etot = -18.3750886097066
+569000  ekin = 2.44197408396629 |  erot = 2.65159536305571 | epot = -22.7197314796374 | etot = -17.6261620326154
+570000  ekin = 2.4317740620905 |  erot = 1.89764945519459 | epot = -22.6963472615905 | etot = -18.3669237443054
+571000  ekin = 2.86160521289846 |  erot = 2.96804382024776 | epot = -22.6961835038032 | etot = -16.8665344706569
+572000  ekin = 1.92662919536387 |  erot = 3.79135909534693 | epot = -22.6587081618988 | etot = -16.940719871188
+573000  ekin = 2.40137439242945 |  erot = 2.2998261335634 | epot = -22.6365074046859 | etot = -17.935306878693
+574000  ekin = 1.68882589350908 |  erot = 2.3209740449249 | epot = -22.6783832960445 | etot = -18.6685833576106
+575000  ekin = 1.85490665091732 |  erot = 1.85640808911422 | epot = -22.7444448136904 | etot = -19.0331300736588
+576000  ekin = 3.24775679594035 |  erot = 2.9556926821431 | epot = -22.6991990620438 | etot = -16.4957495839603
+577000  ekin = 2.89423151645282 |  erot = 2.87486712706734 | epot = -22.6284365608021 | etot = -16.8593379172819
+578000  ekin = 2.40460916677569 |  erot = 2.78216711024701 | epot = -22.4348874817265 | etot = -17.2481112047038
+579000  ekin = 2.40580528046575 |  erot = 1.99557814482532 | epot = -22.2889136736671 | etot = -17.887530248376
+580000  ekin = 2.69817090358906 |  erot = 1.94741864170503 | epot = -22.1754486864787 | etot = -17.5298591411846
+581000  ekin = 2.06309668646281 |  erot = 2.97621367011722 | epot = -22.0670098600828 | etot = -17.0276995035027
+582000  ekin = 2.33869527454826 |  erot = 3.07898324506956 | epot = -21.9478320300714 | etot = -16.5301535104536
+583000  ekin = 2.23428959741494 |  erot = 2.68476693088862 | epot = -21.837983720672 | etot = -16.9189271923684
+584000  ekin = 2.94321016295283 |  erot = 2.59995039730548 | epot = -21.7517635625831 | etot = -16.2086030023248
+585000  ekin = 2.36063475490837 |  erot = 2.49112677628939 | epot = -21.7173359488816 | etot = -16.8655744176838
+586000  ekin = 3.56583702163526 |  erot = 2.02487858259688 | epot = -21.7707868137138 | etot = -16.1800712094817
+587000  ekin = 3.53727585853245 |  erot = 1.97258932652022 | epot = -21.7665121756112 | etot = -16.2566469905585
+588000  ekin = 2.82339556293758 |  erot = 1.59340504807044 | epot = -21.7545319340973 | etot = -17.3377313230892
+589000  ekin = 2.31627310139818 |  erot = 2.20582604523298 | epot = -21.8199173705564 | etot = -17.2978182239252
+590000  ekin = 2.57616671531331 |  erot = 1.72768273328208 | epot = -21.8427138199642 | etot = -17.5388643713688
+591000  ekin = 1.91473306171853 |  erot = 3.80604384238377 | epot = -21.9351393124188 | etot = -16.2143624083165
+592000  ekin = 2.11222958764659 |  erot = 2.84208333850203 | epot = -21.9639458839076 | etot = -17.0096329577589
+593000  ekin = 1.66462149590471 |  erot = 2.46217253451012 | epot = -21.9921445323971 | etot = -17.8653505019823
+594000  ekin = 1.86314045588477 |  erot = 2.37275936142268 | epot = -22.1149191228505 | etot = -17.879019305543
+595000  ekin = 1.6397125755004 |  erot = 2.14970246798561 | epot = -22.2960530768755 | etot = -18.5066380333895
+596000  ekin = 1.86247376576132 |  erot = 1.56938095427869 | epot = -22.4014957466218 | etot = -18.9696410265818
+597000  ekin = 2.21073901406701 |  erot = 2.3087175693751 | epot = -22.4599242604732 | etot = -17.9404676770311
+598000  ekin = 1.8660134932493 |  erot = 3.02311727399813 | epot = -22.5165298316334 | etot = -17.6273990643859
+599000  ekin = 2.86271635930755 |  erot = 2.19928854437227 | epot = -22.536599708025 | etot = -17.4745948043452
+600000  ekin = 2.65062163067179 |  erot = 2.14533898812782 | epot = -22.4620537969304 | etot = -17.6660931781308
+601000  ekin = 2.97018864875202 |  erot = 3.19824090103878 | epot = -22.3271949752462 | etot = -16.1587654254554
+602000  ekin = 2.93416893709001 |  erot = 2.68627449040958 | epot = -22.2245183728174 | etot = -16.6040749453178
+603000  ekin = 2.5987545006459 |  erot = 2.71301833029978 | epot = -22.1705323477201 | etot = -16.8587595167745
+604000  ekin = 1.79059859762797 |  erot = 2.11515305424794 | epot = -22.1931056020217 | etot = -18.2873539501458
+605000  ekin = 1.82914051863722 |  erot = 2.27656979248766 | epot = -22.2183915784731 | etot = -18.1126812673482
+606000  ekin = 2.33864125390345 |  erot = 2.204164937778 | epot = -22.1617656383863 | etot = -17.6189594467048
+607000  ekin = 2.72666217259876 |  erot = 2.97710334336218 | epot = -22.1572786906588 | etot = -16.4535131746978
+608000  ekin = 2.45226937954678 |  erot = 2.41232790919961 | epot = -22.1263051367364 | etot = -17.2617078479901
+609000  ekin = 1.91032127854288 |  erot = 2.62712516529566 | epot = -22.0127581830193 | etot = -17.4753117391807
+610000  ekin = 3.01319055031108 |  erot = 2.17098104720964 | epot = -21.930499629869 | etot = -16.7463280323483
+611000  ekin = 2.44410994437292 |  erot = 2.75159061185421 | epot = -21.9258193850468 | etot = -16.7301188288197
+612000  ekin = 2.50271115837173 |  erot = 2.16817640692168 | epot = -21.9676183236645 | etot = -17.2967307583711
+613000  ekin = 3.01842230632867 |  erot = 2.12784419676567 | epot = -22.0277467117808 | etot = -16.8814802086864
+614000  ekin = 2.25331711369829 |  erot = 2.99334048390157 | epot = -22.0701464667307 | etot = -16.8234888691309
+615000  ekin = 1.66376443031995 |  erot = 2.63613776051569 | epot = -21.9985978951916 | etot = -17.698695704356
+616000  ekin = 1.89454248699046 |  erot = 2.87318355169532 | epot = -22.0041678369047 | etot = -17.2364417982189
+617000  ekin = 2.14789714287838 |  erot = 2.51249074123956 | epot = -22.0251474680604 | etot = -17.3647595839425
+618000  ekin = 3.11174934178843 |  erot = 2.74374306269141 | epot = -21.980284295602 | etot = -16.1247918911221
+619000  ekin = 3.4103621396818 |  erot = 2.10616794159728 | epot = -21.9557959924961 | etot = -16.4392659112171
+620000  ekin = 4.28430989238205 |  erot = 2.19572475327593 | epot = -21.9033881020935 | etot = -15.4233534564355
+621000  ekin = 3.095687767491 |  erot = 2.55794040804605 | epot = -21.8286763731363 | etot = -16.1750481975993
+622000  ekin = 2.76030419206697 |  erot = 2.60754397958254 | epot = -21.7459002641757 | etot = -16.3780520925262
+623000  ekin = 2.87269212022169 |  erot = 2.90401311950188 | epot = -21.5853226709314 | etot = -15.8086174312079
+624000  ekin = 2.01889500087931 |  erot = 3.41825755609794 | epot = -21.4095311686242 | etot = -15.972378611647
+625000  ekin = 2.87966631754696 |  erot = 2.69115421564282 | epot = -21.2859406043045 | etot = -15.7151200711147
+626000  ekin = 2.56087279949319 |  erot = 2.15801254335178 | epot = -21.2329175358055 | etot = -16.5140321929605
+627000  ekin = 2.30197939613517 |  erot = 2.40176668957968 | epot = -21.2932794652838 | etot = -16.589533379569
+628000  ekin = 2.23988628353727 |  erot = 2.75332535542196 | epot = -21.4558642198861 | etot = -16.4626525809268
+629000  ekin = 2.20891060851904 |  erot = 1.97036896055008 | epot = -21.6109313731644 | etot = -17.4316518040953
+630000  ekin = 2.48711004105954 |  erot = 2.14055508379569 | epot = -21.6286281269544 | etot = -17.0009630020992
+631000  ekin = 2.05035510102044 |  erot = 1.78519131042562 | epot = -21.633635046353 | etot = -17.7980886349069
+632000  ekin = 1.65439924450982 |  erot = 3.28310987077494 | epot = -21.6999899301469 | etot = -16.7624808148621
+633000  ekin = 2.34657988531209 |  erot = 2.34109631044866 | epot = -21.8317647703271 | etot = -17.1440885745664
+634000  ekin = 2.31570267703931 |  erot = 2.471293173825 | epot = -21.8814211467029 | etot = -17.0944252958386
+635000  ekin = 1.99068848818426 |  erot = 3.35493927676211 | epot = -21.9111632351734 | etot = -16.565535470227
+636000  ekin = 2.50156763858621 |  erot = 2.48847742334418 | epot = -21.8752689055209 | etot = -16.8852238435905
+637000  ekin = 2.76558055064046 |  erot = 2.80410341825293 | epot = -21.7874464522771 | etot = -16.2177624833837
+638000  ekin = 2.45488734924466 |  erot = 2.8151636333562 | epot = -21.8973623385979 | etot = -16.627311355997
+639000  ekin = 1.89221088715375 |  erot = 2.13319565970052 | epot = -21.932098303477 | etot = -17.9066917566227
+640000  ekin = 2.12173400886946 |  erot = 3.32302167857403 | epot = -21.8808288554835 | etot = -16.43607316804
+641000  ekin = 2.09554541112561 |  erot = 2.23098450754965 | epot = -21.9203390995501 | etot = -17.5938091808749
+642000  ekin = 2.28696138506763 |  erot = 2.67378976619351 | epot = -21.9723604262127 | etot = -17.0116092749516
+643000  ekin = 2.74450005384908 |  erot = 2.20403941809547 | epot = -21.9235240791533 | etot = -16.9749846072087
+644000  ekin = 2.87909523138453 |  erot = 3.40688779630215 | epot = -21.9417833997401 | etot = -15.6558003720534
+645000  ekin = 2.38284095628022 |  erot = 2.10846397463902 | epot = -21.8306349073152 | etot = -17.3393299763959
+646000  ekin = 2.68568471833193 |  erot = 1.80852105367058 | epot = -21.6853054888873 | etot = -17.1910997168848
+647000  ekin = 2.44462012552757 |  erot = 2.00446720103468 | epot = -21.4974635292911 | etot = -17.0483762027288
+648000  ekin = 2.22150753159448 |  erot = 1.69679185313771 | epot = -21.5947311257684 | etot = -17.6764317410362
+649000  ekin = 2.55943952639506 |  erot = 1.77203724563614 | epot = -22.016770390185 | etot = -17.6852936181538
+650000  ekin = 2.72347255721059 |  erot = 2.20418229003755 | epot = -22.1594214535889 | etot = -17.2317666063407
+651000  ekin = 2.25383373914402 |  erot = 3.26326768595795 | epot = -22.2274805933885 | etot = -16.7103791682865
+652000  ekin = 2.35810253390822 |  erot = 2.29591208392312 | epot = -22.2332195197311 | etot = -17.5792049018997
+653000  ekin = 2.06421004499471 |  erot = 2.14171845474571 | epot = -22.2265612208312 | etot = -18.0206327210908
+654000  ekin = 2.30460304373657 |  erot = 1.85567946278894 | epot = -22.2521914868227 | etot = -18.0919089802972
+655000  ekin = 2.1118882401511 |  erot = 1.79072614414008 | epot = -22.2262193909715 | etot = -18.3236050066803
+656000  ekin = 2.44561836830366 |  erot = 2.32567811025774 | epot = -22.187237628634 | etot = -17.4159411500726
+657000  ekin = 2.45751083141108 |  erot = 2.86439216413737 | epot = -22.1805503246548 | etot = -16.8586473291064
+658000  ekin = 2.49955432693124 |  erot = 2.85472680235229 | epot = -22.1390040132353 | etot = -16.7847228839518
+659000  ekin = 3.37980090980362 |  erot = 2.77552992994233 | epot = -21.9898923341708 | etot = -15.8345614944248
+660000  ekin = 2.6941462621918 |  erot = 1.99094454704572 | epot = -21.839770569098 | etot = -17.1546797598605
+661000  ekin = 2.21049176877593 |  erot = 2.52393650500611 | epot = -21.6857326790217 | etot = -16.9513044052396
+662000  ekin = 2.06962867519899 |  erot = 2.53976085175022 | epot = -21.6239147287108 | etot = -17.0145252017615
+663000  ekin = 2.27770295544224 |  erot = 2.30124717941155 | epot = -21.5870186127932 | etot = -17.0080684779394
+664000  ekin = 2.39061717453214 |  erot = 1.87616423363736 | epot = -21.4930500427881 | etot = -17.2262686346186
+665000  ekin = 2.6692440512318 |  erot = 2.29240983153227 | epot = -21.4402310096657 | etot = -16.4785771269017
+666000  ekin = 1.66318176263893 |  erot = 2.30827907651666 | epot = -21.3477804932103 | etot = -17.3763196540547
+667000  ekin = 1.65573830146343 |  erot = 2.8261361193353 | epot = -21.2651811028886 | etot = -16.7833066820899
+668000  ekin = 2.50126196238916 |  erot = 3.29062396521941 | epot = -21.1310768281354 | etot = -15.3391909005268
+669000  ekin = 1.61008562219097 |  erot = 2.65727107854378 | epot = -21.0513800034041 | etot = -16.7840233026694
+670000  ekin = 2.21851826153844 |  erot = 2.60770568109396 | epot = -20.9727942140714 | etot = -16.146570271439
+671000  ekin = 2.25905318343359 |  erot = 2.1596549557503 | epot = -20.920836534986 | etot = -16.5021283958021
+672000  ekin = 1.93426342346647 |  erot = 1.65365047668441 | epot = -20.8333028169839 | etot = -17.245388916833
+673000  ekin = 1.880896686753 |  erot = 2.07483128120029 | epot = -20.79952620348 | etot = -16.8437982355267
+674000  ekin = 2.067834680573 |  erot = 2.16234064938725 | epot = -20.8176950919606 | etot = -16.5875197620003
+675000  ekin = 2.03952283590142 |  erot = 2.48129689359269 | epot = -20.8297865902612 | etot = -16.3089668607671
+676000  ekin = 2.44687523374789 |  erot = 2.77932995735253 | epot = -20.8513819036484 | etot = -15.625176712548
+677000  ekin = 2.18851088067448 |  erot = 2.61928925664188 | epot = -20.8589021998565 | etot = -16.0511020625401
+678000  ekin = 2.13451298865477 |  erot = 2.78742961560771 | epot = -20.7380850837789 | etot = -15.8161424795164
+679000  ekin = 2.15556981522704 |  erot = 2.17593910434841 | epot = -20.629255081746 | etot = -16.2977461621705
+680000  ekin = 2.07717451414439 |  erot = 2.68436897198808 | epot = -20.6512705044544 | etot = -15.889727018322
+681000  ekin = 2.16836766753576 |  erot = 1.8266629484308 | epot = -20.7392652191905 | etot = -16.744234603224
+682000  ekin = 3.01810965188601 |  erot = 2.39774897550359 | epot = -20.7185667085479 | etot = -15.3027080811583
+683000  ekin = 2.84169666492797 |  erot = 2.09885122074905 | epot = -20.7261705834807 | etot = -15.7856226978037
+684000  ekin = 1.96250352869369 |  erot = 2.99543980855395 | epot = -20.769704567373 | etot = -15.8117612301254
+685000  ekin = 1.50086016290166 |  erot = 2.04478648729578 | epot = -20.778895252848 | etot = -17.2332486026506
+686000  ekin = 2.30092983530379 |  erot = 2.55442118756322 | epot = -20.7673358731011 | etot = -15.9119848502341
+687000  ekin = 1.86053862979304 |  erot = 2.84846934037477 | epot = -20.7009117540898 | etot = -15.9919037839219
+688000  ekin = 2.56859020075851 |  erot = 2.23263295871679 | epot = -20.6563366249256 | etot = -15.8551134654503
+689000  ekin = 2.74930141700632 |  erot = 2.68327386026121 | epot = -20.8092642099637 | etot = -15.3766889326962
+690000  ekin = 2.67477310841299 |  erot = 2.52397256899157 | epot = -21.0730303416649 | etot = -15.8742846642604
+691000  ekin = 2.28465281003007 |  erot = 2.52273866559284 | epot = -21.2401157605126 | etot = -16.4327242848897
+692000  ekin = 2.42087744380445 |  erot = 3.24812320332686 | epot = -21.2665776826931 | etot = -15.5975770355618
+693000  ekin = 2.37642605279042 |  erot = 2.99546830568892 | epot = -21.3330277418611 | etot = -15.9611333833818
+694000  ekin = 2.69750178365984 |  erot = 2.53085866970816 | epot = -21.521485598392 | etot = -16.293125145024
+695000  ekin = 2.49230316198816 |  erot = 1.18105864485318 | epot = -21.6959912399269 | etot = -18.0226294330856
+696000  ekin = 1.86075498586631 |  erot = 1.46501529683133 | epot = -21.6808441671222 | etot = -18.3550738844245
+697000  ekin = 2.40460770445908 |  erot = 2.10461647488795 | epot = -21.7143559347048 | etot = -17.2051317553578
+698000  ekin = 2.32098148261586 |  erot = 1.91506962097517 | epot = -21.7787361369849 | etot = -17.5426850333939
+699000  ekin = 2.44943497732062 |  erot = 2.56143482106644 | epot = -21.7638026578475 | etot = -16.7529328594605
+700000  ekin = 2.13119890669415 |  erot = 2.28802336161955 | epot = -21.6714710604343 | etot = -17.2522487921206
+701000  ekin = 2.1501316931424 |  erot = 2.18565847708908 | epot = -21.5488216255628 | etot = -17.2130314553313
+702000  ekin = 1.57482438035703 |  erot = 1.99931097090509 | epot = -21.5047640382371 | etot = -17.930628686975
+703000  ekin = 2.08829522236785 |  erot = 2.17557396869524 | epot = -21.5242713758433 | etot = -17.2604021847802
+704000  ekin = 2.82144699483839 |  erot = 1.94479401958833 | epot = -21.5462466947694 | etot = -16.7800056803427
+705000  ekin = 2.81019786745821 |  erot = 2.16662483548889 | epot = -21.497690476826 | etot = -16.5208677738789
+706000  ekin = 1.97639068263159 |  erot = 2.31468002405233 | epot = -21.494117475981 | etot = -17.2030467692971
+707000  ekin = 1.90740387464487 |  erot = 2.04436544372038 | epot = -21.5505486138141 | etot = -17.5987792954489
+708000  ekin = 2.4927128838246 |  erot = 2.15829540621564 | epot = -21.5728746117359 | etot = -16.9218663216957
+709000  ekin = 2.89296518644075 |  erot = 2.58120965850486 | epot = -21.6152997801578 | etot = -16.1411249352122
+710000  ekin = 2.18515172086139 |  erot = 2.27924743097099 | epot = -21.5865916502444 | etot = -17.122192498412
+711000  ekin = 2.31589231212299 |  erot = 1.401439259779 | epot = -21.6089597508522 | etot = -17.8916281789502
+712000  ekin = 2.55835611026778 |  erot = 2.27281573655803 | epot = -21.7227687229585 | etot = -16.8915968761327
+713000  ekin = 1.95615391137192 |  erot = 2.31806852238961 | epot = -21.8059432402922 | etot = -17.5317208065307
+714000  ekin = 2.56238583099812 |  erot = 2.10850361056243 | epot = -21.8681675013086 | etot = -17.1972780597481
+715000  ekin = 2.4232111465345 |  erot = 3.74023135295618 | epot = -21.8498336266088 | etot = -15.6863911271181
+716000  ekin = 2.83316600532177 |  erot = 2.84850242081139 | epot = -21.7640231598546 | etot = -16.0823547337214
+717000  ekin = 3.45113934412559 |  erot = 3.205984621772 | epot = -21.667790662391 | etot = -15.0106666964934
+718000  ekin = 3.10736232683018 |  erot = 3.94031338601798 | epot = -21.5629179727886 | etot = -14.5152422599405
+719000  ekin = 2.38564322644681 |  erot = 2.9508981175584 | epot = -21.5481188237003 | etot = -16.211577479695
+720000  ekin = 2.22543420991222 |  erot = 3.14305432696275 | epot = -21.5381615962024 | etot = -16.1696730593274
+721000  ekin = 1.71709109813907 |  erot = 2.2393943036399 | epot = -21.4645851946691 | etot = -17.5080997928901
+722000  ekin = 1.93213958129582 |  erot = 2.81573218276728 | epot = -21.4896847080113 | etot = -16.7418129439482
+723000  ekin = 2.3814534534689 |  erot = 2.55666957995949 | epot = -21.4374887927968 | etot = -16.4993657593684
+724000  ekin = 1.74740284448188 |  erot = 2.45556175689041 | epot = -21.4125175551609 | etot = -17.2095529537886
+725000  ekin = 2.29233638352032 |  erot = 2.9526701477774 | epot = -21.4751392844086 | etot = -16.2301327531109
+726000  ekin = 1.63503646092183 |  erot = 2.30649262262118 | epot = -21.5156851039583 | etot = -17.5741560204153
+727000  ekin = 2.46705454176008 |  erot = 3.19802987014479 | epot = -21.5382715508197 | etot = -15.8731871389148
+728000  ekin = 2.21709576272191 |  erot = 2.16616227421247 | epot = -21.5244744557248 | etot = -17.1412164187904
+729000  ekin = 1.89396537247993 |  erot = 1.66596987620968 | epot = -21.5644109232526 | etot = -18.004475674563
+730000  ekin = 1.78155182892059 |  erot = 2.15399661961712 | epot = -21.5594738957829 | etot = -17.6239254472452
+731000  ekin = 2.16713092512296 |  erot = 2.96875570154115 | epot = -21.4952326145865 | etot = -16.3593459879224
+732000  ekin = 2.40927355189018 |  erot = 2.27189990077001 | epot = -21.3831563581627 | etot = -16.7019829055025
+733000  ekin = 3.04824198143783 |  erot = 2.57289903054808 | epot = -21.429005165309 | etot = -15.8078641533231
+734000  ekin = 2.36703883022854 |  erot = 2.04468815017472 | epot = -21.4926214065432 | etot = -17.0808944261399
+735000  ekin = 2.13292788677937 |  erot = 1.55097035487249 | epot = -21.5455592190822 | etot = -17.8616609774303
+736000  ekin = 2.13562110082196 |  erot = 3.45795834862289 | epot = -21.6515763333194 | etot = -16.0579968838746
+737000  ekin = 1.73550703692746 |  erot = 3.58781244645386 | epot = -21.6785680654269 | etot = -16.3552485820456
+738000  ekin = 2.0113668076702 |  erot = 2.50533140705365 | epot = -21.7068415263434 | etot = -17.1901433116196
+739000  ekin = 1.85122466968334 |  erot = 2.19323904324284 | epot = -21.7211705032463 | etot = -17.6767067903201
+740000  ekin = 2.84677298867338 |  erot = 2.79086338446698 | epot = -21.7460997683893 | etot = -16.108463395249
+741000  ekin = 2.47281769013275 |  erot = 2.90867674862121 | epot = -21.8038806031312 | etot = -16.4223861643773
+742000  ekin = 2.74212748781964 |  erot = 3.26601844940294 | epot = -21.9417105639309 | etot = -15.9335646267083
+743000  ekin = 2.23337436613032 |  erot = 3.2075209993525 | epot = -22.0769938861091 | etot = -16.6360985206263
+744000  ekin = 2.0100758296396 |  erot = 3.7920839882707 | epot = -22.1581491314472 | etot = -16.3559893135369
+745000  ekin = 3.14168435406401 |  erot = 2.32756039064278 | epot = -22.155279170971 | etot = -16.6860344262642
+746000  ekin = 2.96147960587595 |  erot = 2.6491977864153 | epot = -22.131657657659 | etot = -16.5209802653678
+747000  ekin = 2.31713973406909 |  erot = 2.05388385027237 | epot = -22.1362115743712 | etot = -17.7651879900298
+748000  ekin = 2.36228107661837 |  erot = 2.41530550223612 | epot = -22.1703943251347 | etot = -17.3928077462802
+749000  ekin = 2.07006713072585 |  erot = 2.7743291960411 | epot = -22.1708421357978 | etot = -17.3264458090308
+750000  ekin = 1.65834656870048 |  erot = 2.38415657369843 | epot = -22.2465520170919 | etot = -18.204048874693
+751000  ekin = 1.79302728344389 |  erot = 2.82710216006102 | epot = -22.3488339479635 | etot = -17.7287045044586
+752000  ekin = 1.35555517803007 |  erot = 1.4601978358921 | epot = -22.4342877547318 | etot = -19.6185347408097
+753000  ekin = 1.88586262445723 |  erot = 2.44014879801272 | epot = -22.3837690917336 | etot = -18.0577576692637
+754000  ekin = 1.74745498380874 |  erot = 2.73612011854202 | epot = -22.2852965474799 | etot = -17.8017214451291
+755000  ekin = 2.39590781949903 |  erot = 2.41019902787153 | epot = -22.2066358684386 | etot = -17.400529021068
+756000  ekin = 1.83745653598817 |  erot = 2.79024351605602 | epot = -22.133592240187 | etot = -17.5058921881428
+757000  ekin = 1.97281200687049 |  erot = 2.57792722235947 | epot = -22.0604464398181 | etot = -17.5097072105881
+758000  ekin = 1.18945619136922 |  erot = 2.72372183682493 | epot = -21.9899494795137 | etot = -18.0767714513196
+759000  ekin = 2.16230453116658 |  erot = 1.39722896511083 | epot = -22.0003304659983 | etot = -18.4407969697209
+760000  ekin = 2.57253050230033 |  erot = 2.33269711137816 | epot = -22.0357457302398 | etot = -17.1305181165613
+761000  ekin = 2.08545216810508 |  erot = 2.24940559703297 | epot = -22.1132097744114 | etot = -17.7783520092733
+762000  ekin = 2.13509249172208 |  erot = 1.66078369856518 | epot = -22.1380840935026 | etot = -18.3422079032154
+763000  ekin = 2.42851727622126 |  erot = 3.36016749294485 | epot = -22.2079173436288 | etot = -16.4192325744626
+764000  ekin = 2.84703530894743 |  erot = 2.79172375883346 | epot = -22.2143624032421 | etot = -16.5756033354612
+765000  ekin = 1.81325658345262 |  erot = 2.77448180912351 | epot = -22.1194010453623 | etot = -17.5316626527862
+766000  ekin = 2.64831101430988 |  erot = 2.31381649708591 | epot = -21.9919179324216 | etot = -17.0297904210258
+767000  ekin = 2.58949745571041 |  erot = 2.86718473216887 | epot = -21.9087370669524 | etot = -16.4520548790732
+768000  ekin = 1.86313167956692 |  erot = 2.78552244417216 | epot = -21.9381577980074 | etot = -17.2895036742683
+769000  ekin = 2.40162376419982 |  erot = 2.31402374045874 | epot = -22.0373843590673 | etot = -17.3217368544087
+770000  ekin = 2.49146487205159 |  erot = 3.23101926076329 | epot = -22.1439576198693 | etot = -16.4214734870544
+771000  ekin = 2.3322633774286 |  erot = 2.27787220200643 | epot = -22.1812213688414 | etot = -17.5710857894063
+772000  ekin = 2.28990016215835 |  erot = 2.99389364569334 | epot = -22.2765115340955 | etot = -16.9927177262438
+773000  ekin = 2.23002457595115 |  erot = 1.82240115552767 | epot = -22.3379686916384 | etot = -18.2855429601596
+774000  ekin = 2.82350297312971 |  erot = 2.21054815770296 | epot = -22.331524297742 | etot = -17.2974731669094
+775000  ekin = 1.82305982105504 |  erot = 1.8710033654222 | epot = -22.2729891281483 | etot = -18.5789259416711
+776000  ekin = 1.39169167990076 |  erot = 3.16027505319294 | epot = -22.2459295451277 | etot = -17.6939628120339
+777000  ekin = 1.6265637770548 |  erot = 2.80881827044758 | epot = -22.1611617112313 | etot = -17.7257796637289
+778000  ekin = 1.49436478903863 |  erot = 2.24161236856228 | epot = -22.1732646444852 | etot = -18.4372874868843
+779000  ekin = 1.88107404119766 |  erot = 1.90732846459751 | epot = -22.2125828989309 | etot = -18.4241803931357
+780000  ekin = 1.70209634464212 |  erot = 2.30515299210351 | epot = -22.2800747799125 | etot = -18.2728254431668
+781000  ekin = 2.12615575710868 |  erot = 2.56065358398065 | epot = -22.3657963731658 | etot = -17.6789870320765
+782000  ekin = 2.60319344794517 |  erot = 1.95716880667361 | epot = -22.278889588664 | etot = -17.7185273340452
+783000  ekin = 2.19489638548848 |  erot = 2.9003350616753 | epot = -22.2004563501245 | etot = -17.1052249029607
+784000  ekin = 2.84914111009349 |  erot = 2.24051018422877 | epot = -22.2093010900996 | etot = -17.1196497957773
+785000  ekin = 3.14240765153577 |  erot = 2.92860772919915 | epot = -22.2500274240077 | etot = -16.1790120432728
+786000  ekin = 2.83372300736036 |  erot = 3.44593690351847 | epot = -22.2923595270368 | etot = -16.0126996161579
+787000  ekin = 2.41074903520556 |  erot = 3.01381650302091 | epot = -22.2329745868673 | etot = -16.8084090486409
+788000  ekin = 1.99557665602945 |  erot = 2.01600225895996 | epot = -22.1996915458458 | etot = -18.1881126308564
+789000  ekin = 2.46258971641134 |  erot = 2.27406771625315 | epot = -22.1314921413931 | etot = -17.3948347087286
+790000  ekin = 3.5794195002921 |  erot = 2.82440864812442 | epot = -22.0691321886934 | etot = -15.6653040402769
+791000  ekin = 3.1240271028451 |  erot = 2.42401718962738 | epot = -22.0808685046086 | etot = -16.5328242121361
+792000  ekin = 3.95429056548242 |  erot = 1.97241939137156 | epot = -22.0156932891881 | etot = -16.0889833323341
+793000  ekin = 2.26828416500901 |  erot = 2.58677202552917 | epot = -21.9219598803777 | etot = -17.0669036898395
+794000  ekin = 2.16106559150924 |  erot = 2.4431093127412 | epot = -21.7619518452423 | etot = -17.1577769409919
+795000  ekin = 1.62519700428841 |  erot = 2.41826691867446 | epot = -21.6012749849542 | etot = -17.5578110619913
+796000  ekin = 2.18377144801669 |  erot = 2.13093440679002 | epot = -21.4820337714693 | etot = -17.1673279166626
+797000  ekin = 1.81427862345352 |  erot = 1.99534051513422 | epot = -21.473919591557 | etot = -17.6643004529692
+798000  ekin = 2.22012195132989 |  erot = 2.51363796316556 | epot = -21.5008270155092 | etot = -16.7670671010137
+799000  ekin = 1.88984581553594 |  erot = 2.87047971528298 | epot = -21.4708608053325 | etot = -16.7105352745136
+800000  ekin = 2.14235800297793 |  erot = 2.35196377273804 | epot = -21.3792596865245 | etot = -16.8849379108086
+801000  ekin = 1.84302686949433 |  erot = 1.65480855802627 | epot = -21.2211741734437 | etot = -17.7233387459231
+802000  ekin = 2.20305615004887 |  erot = 2.22355768328246 | epot = -21.1073599995259 | etot = -16.6807461661946
+803000  ekin = 2.64836814873033 |  erot = 1.90761871804861 | epot = -21.0752041885471 | etot = -16.5192173217681
+804000  ekin = 2.34495845479317 |  erot = 2.89112045330492 | epot = -21.0176734836814 | etot = -15.7815945755833
+805000  ekin = 1.79915640284781 |  erot = 2.71685844764874 | epot = -20.8858433761952 | etot = -16.3698285256987
+806000  ekin = 1.74992507845556 |  erot = 2.08517047523252 | epot = -20.8503301901419 | etot = -17.0152346364538
+807000  ekin = 1.57172452594495 |  erot = 1.70422569898767 | epot = -20.9092333967052 | etot = -17.6332831717726
+808000  ekin = 2.08106901002531 |  erot = 2.40367065218829 | epot = -20.9858691795981 | etot = -16.5011295173845
+809000  ekin = 2.61736488835992 |  erot = 1.51251405170843 | epot = -20.9790910298502 | etot = -16.8492120897818
+810000  ekin = 3.07344763503492 |  erot = 2.65428122600393 | epot = -20.896297890317 | etot = -15.1685690292781
+811000  ekin = 3.02889983101699 |  erot = 3.61686315729188 | epot = -20.939661602879 | etot = -14.2938986145701
+812000  ekin = 2.13832655324419 |  erot = 2.7919099294265 | epot = -21.0260005012597 | etot = -16.095764018589
+813000  ekin = 2.19077235410927 |  erot = 3.16158040032407 | epot = -21.2169108164964 | etot = -15.864558062063
+814000  ekin = 1.70775111413747 |  erot = 2.98436840501864 | epot = -21.308951189013 | etot = -16.6168316698569
+815000  ekin = 2.14630779714624 |  erot = 2.27335416843265 | epot = -21.3099230783926 | etot = -16.8902611128137
+816000  ekin = 2.70331501775258 |  erot = 1.53093796189123 | epot = -21.3384418834226 | etot = -17.1041889037787
+817000  ekin = 2.55738086811903 |  erot = 2.58558173150041 | epot = -21.4691891608916 | etot = -16.3262265612721
+818000  ekin = 2.27829786328906 |  erot = 2.260897256821 | epot = -21.5162183667694 | etot = -16.9770232466593
+819000  ekin = 2.10478260130361 |  erot = 3.02380855832958 | epot = -21.5292309310153 | etot = -16.4006397713821
+820000  ekin = 2.50608188233135 |  erot = 2.71783485224717 | epot = -21.5036816055507 | etot = -16.2797648709722
+821000  ekin = 2.62609848062628 |  erot = 2.55164634943843 | epot = -21.4787661851639 | etot = -16.3010213550992
+822000  ekin = 3.63941681915299 |  erot = 2.2024689491713 | epot = -21.4688230156577 | etot = -15.6269372473334
+823000  ekin = 3.58953515450024 |  erot = 2.73556206545622 | epot = -21.4650227341942 | etot = -15.1399255142377
+824000  ekin = 4.11304720722591 |  erot = 3.29174595135478 | epot = -21.4062011377905 | etot = -14.0014079792098
+825000  ekin = 2.90620097853795 |  erot = 3.46409084826251 | epot = -21.2436944546109 | etot = -14.8734026278104
+826000  ekin = 1.7218843819517 |  erot = 1.97028277378147 | epot = -21.0473904580338 | etot = -17.3552233023006
+827000  ekin = 1.9124069409458 |  erot = 2.55760488338654 | epot = -20.9206700763424 | etot = -16.45065825201
+828000  ekin = 2.38145056979363 |  erot = 2.55544957149179 | epot = -20.8204865756542 | etot = -15.8835864343688
+829000  ekin = 2.24733826946605 |  erot = 1.78474837345225 | epot = -20.7084449579387 | etot = -16.6763583150204
+830000  ekin = 2.52795893691036 |  erot = 2.3414672428271 | epot = -20.5883731027638 | etot = -15.7189469230263
+831000  ekin = 2.68310001004753 |  erot = 2.07407005901147 | epot = -20.4364451382899 | etot = -15.6792750692309
+832000  ekin = 2.67323424264011 |  erot = 2.02167788192501 | epot = -20.3691783993746 | etot = -15.6742662748095
+833000  ekin = 2.55071664949192 |  erot = 2.59972899624768 | epot = -20.3036213925319 | etot = -15.1531757467923
+834000  ekin = 2.87089088359563 |  erot = 2.32463192225235 | epot = -20.2984653371648 | etot = -15.1029425313168
+835000  ekin = 2.77558903596269 |  erot = 2.73757154391998 | epot = -20.4022293845422 | etot = -14.8890688046595
+836000  ekin = 2.57713146919654 |  erot = 2.85322310545494 | epot = -20.5403137141641 | etot = -15.1099591395126
+837000  ekin = 1.78075406754283 |  erot = 1.97503243561096 | epot = -20.5889142070484 | etot = -16.8331277038946
+838000  ekin = 1.98032617531701 |  erot = 2.79829467073938 | epot = -20.6049667376349 | etot = -15.8263458915785
+839000  ekin = 2.0003179521848 |  erot = 2.70198331564816 | epot = -20.5921495833285 | etot = -15.8898483154956
+840000  ekin = 1.70031236242703 |  erot = 2.95685689490569 | epot = -20.6678372916037 | etot = -16.010668034271
+841000  ekin = 2.77705100359314 |  erot = 2.84742847205068 | epot = -20.7929304121764 | etot = -15.1684509365326
+842000  ekin = 2.54393458307436 |  erot = 2.87172695192628 | epot = -20.8173418291016 | etot = -15.401680294101
+843000  ekin = 2.00273625390939 |  erot = 2.63437491598434 | epot = -20.8053999188197 | etot = -16.168288748926
+844000  ekin = 1.52900749569349 |  erot = 1.92882434140972 | epot = -20.8427655387949 | etot = -17.3849337016917
+845000  ekin = 2.27176799938834 |  erot = 2.308436365406 | epot = -20.9384881501646 | etot = -16.3582837853702
+846000  ekin = 2.06718804989496 |  erot = 2.33108662324979 | epot = -21.0085032159671 | etot = -16.6102285428223
+847000  ekin = 2.457310325364 |  erot = 2.64112097293887 | epot = -20.9624761048838 | etot = -15.8640448065809
+848000  ekin = 2.13894899278459 |  erot = 1.46487099434192 | epot = -20.9909626022984 | etot = -17.3871426151719
+849000  ekin = 2.0007946308419 |  erot = 2.48568109050423 | epot = -20.9995492646628 | etot = -16.5130735433167
+850000  ekin = 2.54186297995285 |  erot = 2.66929613872207 | epot = -20.9906717645298 | etot = -15.7795126458549
+851000  ekin = 2.16443404123472 |  erot = 2.92830981454153 | epot = -20.9932718794597 | etot = -15.9005280236835
+852000  ekin = 2.48255398040851 |  erot = 2.46238001266594 | epot = -21.018749118108 | etot = -16.0738151250335
+853000  ekin = 2.4154146701692 |  erot = 2.97520224443384 | epot = -20.9598722543997 | etot = -15.5692553397967
+854000  ekin = 2.35150751079562 |  erot = 2.85453387569364 | epot = -20.8693696367608 | etot = -15.6633282502715
+855000  ekin = 2.36749640703667 |  erot = 2.06753408358231 | epot = -20.8980197782033 | etot = -16.4629892875844
+856000  ekin = 2.52164598863741 |  erot = 2.75265020302048 | epot = -20.800830948998 | etot = -15.5265347573401
+857000  ekin = 2.55862872070476 |  erot = 3.03030828592915 | epot = -20.6910887919773 | etot = -15.1021517853434
+858000  ekin = 3.12628251408762 |  erot = 2.14554604261068 | epot = -20.6394579492303 | etot = -15.367629392532
+859000  ekin = 2.91259413572112 |  erot = 2.23773675238282 | epot = -20.6611486479508 | etot = -15.5108177598468
+860000  ekin = 2.88318377110752 |  erot = 1.51972062646443 | epot = -20.6828066069552 | etot = -16.2799022093832
+861000  ekin = 2.33529167415754 |  erot = 2.8511661779126 | epot = -20.6796212139896 | etot = -15.4931633619195
+862000  ekin = 3.06091745354043 |  erot = 1.86960550588563 | epot = -20.7257485328209 | etot = -15.7952255733948
+863000  ekin = 2.88295223464283 |  erot = 1.77743902656173 | epot = -20.8340328987095 | etot = -16.1736416375049
+864000  ekin = 2.95602292127632 |  erot = 2.65056410715308 | epot = -21.0162954561449 | etot = -15.4097084277155
+865000  ekin = 3.3172549369506 |  erot = 2.24347319046513 | epot = -21.1441095096618 | etot = -15.583381382246
+866000  ekin = 2.8446879555804 |  erot = 3.16802464112884 | epot = -21.2275167371631 | etot = -15.2148041404539
+867000  ekin = 2.74149808612436 |  erot = 3.09628634794253 | epot = -21.2140642048228 | etot = -15.3762797707559
+868000  ekin = 2.1914148486481 |  erot = 2.23765996064103 | epot = -21.1661691183493 | etot = -16.7370943090602
+869000  ekin = 2.92726848075923 |  erot = 2.49663936074754 | epot = -21.1109612585255 | etot = -15.6870534170188
+870000  ekin = 2.47986538741064 |  erot = 2.11907230969516 | epot = -21.0900293946684 | etot = -16.4910916975626
+871000  ekin = 2.18342640526418 |  erot = 2.37474045896627 | epot = -20.9804914418025 | etot = -16.422324577572
+872000  ekin = 1.52873571215978 |  erot = 2.08908078804673 | epot = -20.9343176993391 | etot = -17.3165011991326
+873000  ekin = 1.39281578471524 |  erot = 2.29034780878958 | epot = -21.0007866828842 | etot = -17.3176230893794
+874000  ekin = 1.40786554880768 |  erot = 2.7700797003235 | epot = -21.1600842742429 | etot = -16.9821390251117
+875000  ekin = 1.18320018517441 |  erot = 2.73058842883511 | epot = -21.2959059488291 | etot = -17.3821173348196
+876000  ekin = 1.8300189393038 |  erot = 2.99586941144886 | epot = -21.3298635968752 | etot = -16.5039752461226
+877000  ekin = 2.38032906471076 |  erot = 2.03722695211226 | epot = -21.415279075283 | etot = -16.99772305846
+878000  ekin = 2.12938516841269 |  erot = 1.75666654131942 | epot = -21.412657760354 | etot = -17.5266060506219
+879000  ekin = 2.23837299177367 |  erot = 2.71307243504656 | epot = -21.4006541150457 | etot = -16.4492086882254
+880000  ekin = 2.68032631557358 |  erot = 2.78439945590096 | epot = -21.4462782448912 | etot = -15.9815524734167
+881000  ekin = 2.86810525851389 |  erot = 2.35959915589953 | epot = -21.4314549447334 | etot = -16.20375053032
+882000  ekin = 2.33172283615115 |  erot = 2.17176020371465 | epot = -21.369535469283 | etot = -16.8660524294172
+883000  ekin = 2.36331150998289 |  erot = 1.97634374053965 | epot = -21.1748990104138 | etot = -16.8352437598913
+884000  ekin = 2.53782271833829 |  erot = 2.25243670168426 | epot = -21.0795767771653 | etot = -16.2893173571427
+885000  ekin = 2.86057103069744 |  erot = 2.27462544190307 | epot = -21.0782171958266 | etot = -15.9430207232261
+886000  ekin = 3.17034195996096 |  erot = 1.74832646729411 | epot = -21.1280719510453 | etot = -16.2094035237903
+887000  ekin = 2.66023408534638 |  erot = 2.49426802108018 | epot = -21.1909579488462 | etot = -16.0364558424197
+888000  ekin = 2.14156056158803 |  erot = 2.83065920295554 | epot = -21.2749898508176 | etot = -16.302770086274
+889000  ekin = 2.13776380125426 |  erot = 2.19994227158627 | epot = -21.1902576201104 | etot = -16.8525515472698
+890000  ekin = 1.76446650263826 |  erot = 2.97354753014624 | epot = -21.2518724314555 | etot = -16.513858398671
+891000  ekin = 1.64433607192947 |  erot = 2.28044235221046 | epot = -21.375947191058 | etot = -17.4511687669181
+892000  ekin = 1.97381907006142 |  erot = 2.35969977765342 | epot = -21.5200869372681 | etot = -17.1865680895533
+893000  ekin = 1.77998159671209 |  erot = 1.83959134574388 | epot = -21.5960425863495 | etot = -17.9764696438935
+894000  ekin = 2.8098996128374 |  erot = 2.80337844303784 | epot = -21.6896955865519 | etot = -16.0764175306767
+895000  ekin = 2.03570642281182 |  erot = 2.73641442629083 | epot = -21.77632807541 | etot = -17.0042072263074
+896000  ekin = 1.6670401968188 |  erot = 2.55842313387756 | epot = -21.9079691828366 | etot = -17.6825058521402
+897000  ekin = 1.79364820755772 |  erot = 2.35937074837062 | epot = -22.0466195733302 | etot = -17.8936006174018
+898000  ekin = 1.8410334890959 |  erot = 2.41596980112091 | epot = -22.0792153246985 | etot = -17.8222120344817
+899000  ekin = 1.6644807831865 |  erot = 3.06295573986189 | epot = -22.0050930291629 | etot = -17.2776565061145
+900000  ekin = 2.15301263014261 |  erot = 2.62503812958041 | epot = -21.9769631774149 | etot = -17.1989124176919
+901000  ekin = 2.4332352507602 |  erot = 2.69661561775584 | epot = -22.0455467285607 | etot = -16.9156958600446
+902000  ekin = 2.57983518470479 |  erot = 2.40634661051273 | epot = -22.0504126836938 | etot = -17.0642308884763
+903000  ekin = 2.38804084084237 |  erot = 2.40369143268286 | epot = -22.0548572254259 | etot = -17.2631249519006
+904000  ekin = 1.9975679938241 |  erot = 3.15736733739655 | epot = -22.0783783499621 | etot = -16.9234430187414
+905000  ekin = 2.28042135995783 |  erot = 2.20746001153526 | epot = -22.092475444409 | etot = -17.6045940729159
+906000  ekin = 2.49914497220397 |  erot = 1.67106173041058 | epot = -22.064929274197 | etot = -17.8947225715825
+907000  ekin = 2.34170753461351 |  erot = 2.16830189815579 | epot = -21.9182395193391 | etot = -17.4082300865698
+908000  ekin = 2.83101675354561 |  erot = 2.39226452568029 | epot = -21.9393923471478 | etot = -16.7161110679219
+909000  ekin = 3.13519044247879 |  erot = 2.07053636961477 | epot = -22.044039894957 | etot = -16.8383130828635
+910000  ekin = 2.91492350277448 |  erot = 3.54269221448406 | epot = -22.1774209001616 | etot = -15.7198051829031
+911000  ekin = 1.86299522014884 |  erot = 2.75425299355676 | epot = -22.2318842654016 | etot = -17.614636051696
+912000  ekin = 2.64270620869814 |  erot = 1.86916034984856 | epot = -22.2816929482531 | etot = -17.7698263897064
+913000  ekin = 2.45835259040075 |  erot = 2.03343540339216 | epot = -22.4051980318983 | etot = -17.9134100381054
+914000  ekin = 2.01630257583654 |  erot = 3.01931541129968 | epot = -22.505580829989 | etot = -17.4699628428528
+915000  ekin = 2.73550820750709 |  erot = 2.14051989379167 | epot = -22.5067223019054 | etot = -17.6306942006067
+916000  ekin = 2.38833694849903 |  erot = 3.26236542376324 | epot = -22.5299732656691 | etot = -16.8792708934068
+917000  ekin = 2.21211072529668 |  erot = 2.24425221182157 | epot = -22.5175498112378 | etot = -18.0611868741195
+918000  ekin = 2.11721632678553 |  erot = 2.05681940825278 | epot = -22.4485798442658 | etot = -18.2745441092275
+919000  ekin = 2.6606540164524 |  erot = 2.41853759346261 | epot = -22.4819256778216 | etot = -17.4027340679066
+920000  ekin = 3.26471044916532 |  erot = 2.75531911342507 | epot = -22.5858600689149 | etot = -16.5658305063245
+921000  ekin = 2.72028388628926 |  erot = 1.96960596371279 | epot = -22.639440275186 | etot = -17.949550425184
+922000  ekin = 1.43428549123066 |  erot = 1.52428475569853 | epot = -22.6914991306332 | etot = -19.732928883704
+923000  ekin = 1.67603986848274 |  erot = 1.86522020655461 | epot = -22.7510571233686 | etot = -19.2097970483312
+924000  ekin = 2.15000311118185 |  erot = 1.53327070095754 | epot = -22.722341324193 | etot = -19.0390675120536
+925000  ekin = 2.27769316315993 |  erot = 1.35582914777291 | epot = -22.6317669747038 | etot = -18.9982446637709
+926000  ekin = 2.00370753803371 |  erot = 2.07123237010035 | epot = -22.5811533157097 | etot = -18.5062134075756
+927000  ekin = 2.51631428248841 |  erot = 1.98711239136866 | epot = -22.6957752134474 | etot = -18.1923485395903
+928000  ekin = 2.57502157703452 |  erot = 2.51449316644154 | epot = -22.8486668477058 | etot = -17.7591521042298
+929000  ekin = 2.66015175923782 |  erot = 1.82991995656989 | epot = -22.8894816710891 | etot = -18.3994099552814
+930000  ekin = 2.41758548277495 |  erot = 2.00977019739401 | epot = -22.9023129289068 | etot = -18.4749572487379
+931000  ekin = 3.01936517399357 |  erot = 2.11115283295648 | epot = -22.8598478032752 | etot = -17.7293297963251
+932000  ekin = 2.34904883629147 |  erot = 1.8713492953404 | epot = -22.900230384769 | etot = -18.6798322531371
+933000  ekin = 2.16775611540091 |  erot = 2.8379626481367 | epot = -22.9075292968864 | etot = -17.9018105333488
+934000  ekin = 2.17428610858913 |  erot = 2.118912762995 | epot = -22.9275911153101 | etot = -18.634392243726
+935000  ekin = 2.35380058127246 |  erot = 2.22719757040087 | epot = -22.9178791070039 | etot = -18.3368809553305
+936000  ekin = 2.29398857252167 |  erot = 2.52122883801966 | epot = -23.0254587453495 | etot = -18.2102413348082
+937000  ekin = 2.32405492839276 |  erot = 2.82571975062451 | epot = -23.1134869099966 | etot = -17.9637122309793
+938000  ekin = 2.46190818228192 |  erot = 1.99586541720566 | epot = -23.1690855883853 | etot = -18.7113119888977
+939000  ekin = 2.99494633358445 |  erot = 2.11200579979089 | epot = -23.1621265982256 | etot = -18.0551744648502
+940000  ekin = 3.76773061527755 |  erot = 2.67954167018355 | epot = -23.1020260319689 | etot = -16.6547537465078
+941000  ekin = 3.15108874053801 |  erot = 2.26610050109567 | epot = -23.0042404655516 | etot = -17.587051223918
+942000  ekin = 3.50311245643908 |  erot = 1.88373602143018 | epot = -22.9671180112669 | etot = -17.5802695333976
+943000  ekin = 3.82043792465856 |  erot = 2.71285823250349 | epot = -22.9404059827705 | etot = -16.4071098256084
+944000  ekin = 2.68278476017665 |  erot = 2.75585489458162 | epot = -22.919058077481 | etot = -17.4804184227228
+945000  ekin = 2.55880828345199 |  erot = 2.02741981318915 | epot = -22.8232630911494 | etot = -18.2370349945083
+946000  ekin = 2.47548691870273 |  erot = 1.66864059361738 | epot = -22.6586979544826 | etot = -18.5145704421625
+947000  ekin = 2.41867478100658 |  erot = 1.99274780926995 | epot = -22.5542133657 | etot = -18.1427907754235
+948000  ekin = 3.54970439277898 |  erot = 2.57756240201335 | epot = -22.4104376157296 | etot = -16.2831708209373
+949000  ekin = 2.9858997616607 |  erot = 2.44208964275301 | epot = -22.197141123001 | etot = -16.7691517185873
+950000  ekin = 1.82147308870195 |  erot = 3.0508389937934 | epot = -22.0435130221227 | etot = -17.1712009396273
+951000  ekin = 2.20031505253436 |  erot = 2.38004890424645 | epot = -22.0174402075992 | etot = -17.4370762508184
+952000  ekin = 2.14165422682636 |  erot = 1.67045420750587 | epot = -21.9875031647927 | etot = -18.1753947304605
+953000  ekin = 2.29833469428311 |  erot = 1.97349532600851 | epot = -21.9532851584681 | etot = -17.6814551381765
+954000  ekin = 1.48835290094507 |  erot = 3.35692451991829 | epot = -21.8812774176255 | etot = -17.0359999967621
+955000  ekin = 1.87513794155826 |  erot = 2.65898918540887 | epot = -21.7919528937349 | etot = -17.2578257667677
+956000  ekin = 1.6947359470094 |  erot = 2.15427252360414 | epot = -21.7268035908356 | etot = -17.8777951202221
+957000  ekin = 1.75579814865835 |  erot = 1.63901039608815 | epot = -21.7007270322021 | etot = -18.3059184874556
+958000  ekin = 1.59869777656518 |  erot = 2.20104985114388 | epot = -21.7023937250484 | etot = -17.9026460973393
+959000  ekin = 2.58438881562724 |  erot = 2.4897790743314 | epot = -21.7153511733982 | etot = -16.6411832834396
+960000  ekin = 2.53916903929276 |  erot = 2.05995138561216 | epot = -21.7134163297425 | etot = -17.1142959048376
+961000  ekin = 2.28282707786747 |  erot = 2.18347157951505 | epot = -21.7152390799839 | etot = -17.2489404226014
+962000  ekin = 1.65520100959905 |  erot = 3.51416445242779 | epot = -21.7329558565077 | etot = -16.5635903944808
+963000  ekin = 1.99568689924178 |  erot = 1.50126173817714 | epot = -21.6847527677603 | etot = -18.1878041303414
+964000  ekin = 2.18616111169191 |  erot = 2.27601428306194 | epot = -21.6212716735791 | etot = -17.1590962788252
+965000  ekin = 2.12688674785305 |  erot = 2.31141713690626 | epot = -21.6018715374843 | etot = -17.163567652725
+966000  ekin = 3.18043989665769 |  erot = 3.42455452205087 | epot = -21.638305203769 | etot = -15.0333107850605
+967000  ekin = 3.07300409154253 |  erot = 2.17511749698305 | epot = -21.5951488445701 | etot = -16.3470272560445
+968000  ekin = 2.0866315065553 |  erot = 2.13997027735021 | epot = -21.5232721871232 | etot = -17.2966704032177
+969000  ekin = 2.26951411936363 |  erot = 2.21822796004343 | epot = -21.4611553284776 | etot = -16.9734132490706
+970000  ekin = 2.49167396599781 |  erot = 2.62083774678041 | epot = -21.4077353682587 | etot = -16.2952236554805
+971000  ekin = 2.497450596106 |  erot = 2.64553775005008 | epot = -21.3712924820093 | etot = -16.2283041358532
+972000  ekin = 3.2069302084461 |  erot = 2.47011294488449 | epot = -21.3144344371103 | etot = -15.6373912837797
+973000  ekin = 3.3593544808794 |  erot = 2.62917582888826 | epot = -21.2433830591838 | etot = -15.2548527494161
+974000  ekin = 2.71069552226069 |  erot = 2.13944446989065 | epot = -21.140426885518 | etot = -16.2902868933666
+975000  ekin = 1.81165819781674 |  erot = 2.10218924092724 | epot = -21.0499905566304 | etot = -17.1361431178865
+976000  ekin = 2.36984742020937 |  erot = 1.38488988265326 | epot = -20.9803229653516 | etot = -17.225585662489
+977000  ekin = 2.83728662155799 |  erot = 3.02976542728587 | epot = -21.086860961914 | etot = -15.2198089130702
+978000  ekin = 3.14169266917129 |  erot = 3.02799812032624 | epot = -21.1408187166748 | etot = -14.9711279271773
+979000  ekin = 3.63725915757345 |  erot = 2.47075910077981 | epot = -21.0348329782418 | etot = -14.9268147198886
+980000  ekin = 3.42622785415584 |  erot = 3.24164435781271 | epot = -20.9604411583363 | etot = -14.2925689463678
+981000  ekin = 2.9282364939793 |  erot = 2.44516658563951 | epot = -20.9993890158381 | etot = -15.6259859362193
+982000  ekin = 2.04558911070081 |  erot = 2.21302288881361 | epot = -21.0172581853275 | etot = -16.7586461858131
+983000  ekin = 2.56053983213182 |  erot = 1.98406283304106 | epot = -21.0054554868711 | etot = -16.4608528216982
+984000  ekin = 2.31455025377678 |  erot = 2.58584391470351 | epot = -21.05287489473 | etot = -16.1524807262497
+985000  ekin = 2.31703817263369 |  erot = 2.99965025262552 | epot = -21.1270579315131 | etot = -15.8103695062539
+986000  ekin = 2.05103854432386 |  erot = 2.1535155091137 | epot = -21.2182405597612 | etot = -17.0136865063237
+987000  ekin = 2.41899263793244 |  erot = 1.58416150281502 | epot = -21.1906087726859 | etot = -17.1874546319385
+988000  ekin = 2.75135283132847 |  erot = 2.70498731016256 | epot = -21.0902697836801 | etot = -15.633929642189
+989000  ekin = 2.29408577956131 |  erot = 2.85656205344492 | epot = -21.0178170251466 | etot = -15.8671691921404
+990000  ekin = 2.23414139649767 |  erot = 2.58987928207188 | epot = -20.9412338597722 | etot = -16.1172131812026
+991000  ekin = 2.20140095465642 |  erot = 2.53421928109186 | epot = -20.8284298905317 | etot = -16.0928096547835
+992000  ekin = 1.73516341340694 |  erot = 2.49726908126816 | epot = -20.8981414535471 | etot = -16.665708958872
+993000  ekin = 1.38883779880923 |  erot = 1.96818984395136 | epot = -20.9939445972527 | etot = -17.6369169544921
+994000  ekin = 1.48978908674571 |  erot = 2.95636513336702 | epot = -21.0608370227912 | etot = -16.6146828026784
+995000  ekin = 2.31404204513712 |  erot = 1.67482961392506 | epot = -21.1264761824826 | etot = -17.1376045234204
+996000  ekin = 2.8977650484701 |  erot = 2.85063328331353 | epot = -21.0879631716189 | etot = -15.3395648398353
+997000  ekin = 3.12980664910276 |  erot = 2.14994147346884 | epot = -21.0789162715404 | etot = -15.7991681489688
+998000  ekin = 2.21592279552962 |  erot = 3.03017611615785 | epot = -20.9989402817529 | etot = -15.7528413700655
+999000  ekin = 2.60947995309596 |  erot = 1.73829419308786 | epot = -20.9136108602424 | etot = -16.5658367140585
+1000000  ekin = 2.32269547490306 |  erot = 2.87794942105205 | epot = -20.9071852604882 | etot = -15.7065403645331
+ 1000000   0.10323091    -1.356822  0.050122912   -1.1615306 0.00013791576 
+Loop time of 36.2166 on 4 procs for 1000000 steps with 16 atoms
+
+Performance: 23856.477 tau/day, 27611.663 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.54933    | 13.254     | 25.208     | 308.0 | 36.60
+Bond    | 0.08723    | 0.416      | 0.70003    |  44.1 |  1.15
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 2.659      | 2.7239     | 2.7669     |   2.4 |  7.52
+Output  | 1.4e-05    | 2.25e-05   | 2.6e-05    |   0.0 |  0.00
+Modify  | 0.22084    | 2.7927     | 5.3062     | 134.0 |  7.71
+Other   |            | 17.03      |            |       | 47.02
+
+Nlocal:    4 ave 8 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    10 ave 12 max 8 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:    39.75 ave 77 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 159
+Ave neighs/atom = 9.9375
+Ave special neighs/atom = 3.75
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:36
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1
deleted file mode 100644
index 29eaec2dab..0000000000
--- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1
+++ /dev/null
@@ -1,1167 +0,0 @@
-LAMMPS (18 Jun 2019)
-variable number	equal 2
-variable ofreq	equal 1000
-variable efreq	equal 1000
-variable T      equal 0.1
-
-units lj
-
-dimension 3
-
-newton off
-
-boundary  p p p
-
-atom_style hybrid bond ellipsoid
-atom_modify sort 0 1.0
-
-# Pair interactions require lists of neighbours to be calculated
-neighbor 1.0 bin
-neigh_modify every 1 delay 0 check yes
-
-read_data data.duplex2
-  orthogonal box = (-20 -20 -20) to (20 20 20)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  16 atoms
-  reading velocities ...
-  16 velocities
-  16 ellipsoids
-  scanning bonds ...
-  2 = max bonds/atom
-  reading bonds ...
-  13 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of 1-3 neighbors
-  4 = max # of 1-4 neighbors
-  6 = max # of special neighbors
-  special bonds CPU = 0.000135 secs
-  read_data CPU = 0.002118 secs
-
-set atom * mass 3.1575
-  16 settings made for mass
-
-group all type 1 4
-16 atoms in group all
-
-# oxDNA bond interactions - FENE backbone
-bond_style oxdna/fene
-bond_coeff * 2.0 0.25 0.7525
-
-# oxDNA pair interactions
-pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
-pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
-
-# NVE ensemble
-#fix 1 all nve/dot
-fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
-fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10
-fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
-#fix 1 all nve/asphere
-#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
-
-timestep 1e-5
-
-#comm_style tiled
-#fix 3 all balance 10000 1.1 rcb
-
-#compute mol all chunk/atom molecule
-#compute mychunk all vcm/chunk mol
-#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
-
-#dump pos all xyz ${ofreq} traj.${number}.xyz
-
-#compute quat all property/atom quatw quati quatj quatk
-#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
-#dump_modify quat sort id
-#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
-
-compute erot all erotate/asphere
-compute ekin all ke
-compute epot all pe
-variable erot equal c_erot
-variable ekin equal c_ekin
-variable epot equal c_epot
-variable etot equal c_erot+c_ekin+c_epot
-fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-
-#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
-#dump_modify out sort id
-#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
-
-run 1000000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.92828
-  ghost atom cutoff = 1.92828
-  binsize = 0.964142, bins = 42 42 42
-  5 neighbor lists, perpetual/occasional/extra = 5 0 0
-  (1) pair oxdna/excv, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-  (2) pair oxdna/stk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (3) pair oxdna/hbond, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (4) pair oxdna/xstk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) pair oxdna/coaxstk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -1.5402493 0.0070469125   -1.5332024 6.0760034e-06 
-1000  ekin = 1.54234964773389 |  erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
-2000  ekin = 1.85988866919215 |  erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
-3000  ekin = 2.68354339452998 |  erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
-4000  ekin = 2.04461800191989 |  erot = 1.49015219763161 | epot = -24.2959428773347 | etot = -20.7611726777832
-5000  ekin = 1.76794859210155 |  erot = 2.54289684465819 | epot = -24.2337587736863 | etot = -19.9229133369266
-6000  ekin = 3.1106424806079 |  erot = 2.04409805200893 | epot = -24.1585729744133 | etot = -19.0038324417964
-7000  ekin = 3.21360097519306 |  erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
-8000  ekin = 2.82489935901743 |  erot = 2.66790555575695 | epot = -24.0194805097633 | etot = -18.526675594989
-9000  ekin = 2.69381302856378 |  erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
-10000  ekin = 2.65765007662471 |  erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
-11000  ekin = 2.33860420545645 |  erot = 2.067780391377 | epot = -23.6589739475584 | etot = -19.2525893507249
-12000  ekin = 2.71377849618258 |  erot = 2.08757199120023 | epot = -23.5483571834756 | etot = -18.7470066960928
-13000  ekin = 2.62930153930326 |  erot = 2.36926332727578 | epot = -23.4509629615768 | etot = -18.4523980949977
-14000  ekin = 3.08200416316113 |  erot = 2.52340746291244 | epot = -23.3378147651053 | etot = -17.7324031390317
-15000  ekin = 2.98008664779269 |  erot = 1.871644860882 | epot = -23.1940665570191 | etot = -18.3423350483444
-16000  ekin = 2.18422481774796 |  erot = 2.13029325858584 | epot = -23.0709946755646 | etot = -18.7564765992308
-17000  ekin = 1.86029951221073 |  erot = 2.30856215831156 | epot = -22.9148241979648 | etot = -18.7459625274425
-18000  ekin = 2.26757205264074 |  erot = 1.23282183419698 | epot = -22.7667657090377 | etot = -19.2663718222
-19000  ekin = 2.39717301992408 |  erot = 2.43814713185077 | epot = -22.6249045514987 | etot = -17.7895843997239
-20000  ekin = 2.4972090427325 |  erot = 2.14695469209109 | epot = -22.4687873897505 | etot = -17.824623654927
-21000  ekin = 2.97591775854817 |  erot = 2.40996811711195 | epot = -22.580475447988 | etot = -17.1945895723278
-22000  ekin = 3.04727168578733 |  erot = 1.83825256427932 | epot = -22.6695853833015 | etot = -17.7840611332348
-23000  ekin = 2.64835731773193 |  erot = 2.22162785501705 | epot = -22.6565689169972 | etot = -17.7865837442483
-24000  ekin = 2.64866576787001 |  erot = 2.80157082833922 | epot = -22.6222797420052 | etot = -17.172043145796
-25000  ekin = 2.29527970143855 |  erot = 2.22049811939069 | epot = -22.6228421013006 | etot = -18.1070642804714
-26000  ekin = 1.6242512251805 |  erot = 2.52390475262917 | epot = -22.6746055892862 | etot = -18.5264496114765
-27000  ekin = 1.74746467550781 |  erot = 3.7138606202505 | epot = -22.7150312690973 | etot = -17.253705973339
-28000  ekin = 2.26500128280479 |  erot = 2.34791343563183 | epot = -22.7926648585827 | etot = -18.179750140146
-29000  ekin = 2.04774074424512 |  erot = 1.86347261547111 | epot = -22.8081204933408 | etot = -18.8969071336246
-30000  ekin = 2.41140146125466 |  erot = 1.86296915421469 | epot = -22.7764612164305 | etot = -18.5020906009612
-31000  ekin = 2.76447800297261 |  erot = 2.7393253404681 | epot = -22.7808698156252 | etot = -17.2770664721845
-32000  ekin = 2.08103539953574 |  erot = 2.81216171106146 | epot = -22.8081908465747 | etot = -17.9149937359775
-33000  ekin = 2.08672340074227 |  erot = 3.65510023442519 | epot = -22.7575363468642 | etot = -17.0157127116967
-34000  ekin = 2.34180742039869 |  erot = 3.10027175201874 | epot = -22.6657421559553 | etot = -17.2236629835378
-35000  ekin = 2.32430602395272 |  erot = 2.01607522370048 | epot = -22.5813705492547 | etot = -18.2409893016015
-36000  ekin = 1.91917507775106 |  erot = 1.97289747304336 | epot = -22.481118994336 | etot = -18.5890464435416
-37000  ekin = 1.57560528527468 |  erot = 2.63029511887642 | epot = -22.4456699464305 | etot = -18.2397695422794
-38000  ekin = 2.20652731867584 |  erot = 2.89671984141264 | epot = -22.3965902387972 | etot = -17.2933430787087
-39000  ekin = 2.54765822667968 |  erot = 2.47352619735437 | epot = -22.3525131983352 | etot = -17.3313287743012
-40000  ekin = 2.24172560748699 |  erot = 1.87314319107769 | epot = -22.3791956830638 | etot = -18.2643268844991
-41000  ekin = 2.45176361826215 |  erot = 2.49992612251747 | epot = -22.4441192111887 | etot = -17.492429470409
-42000  ekin = 2.68254780786499 |  erot = 2.04382131696989 | epot = -22.4352265851614 | etot = -17.7088574603266
-43000  ekin = 2.39383336858508 |  erot = 1.66587291396325 | epot = -22.4337243898148 | etot = -18.3740181072664
-44000  ekin = 2.30758870966958 |  erot = 2.39381816537748 | epot = -22.4636201484766 | etot = -17.7622132734295
-45000  ekin = 1.84308929771583 |  erot = 2.25880380151546 | epot = -22.5697712917435 | etot = -18.4678781925122
-46000  ekin = 1.98608215049724 |  erot = 3.02136983211363 | epot = -22.5606085774834 | etot = -17.5531565948725
-47000  ekin = 1.31457586857024 |  erot = 1.99780932836913 | epot = -22.5522289127255 | etot = -19.2398437157862
-48000  ekin = 2.59855199680394 |  erot = 1.90772345027383 | epot = -22.5972680906756 | etot = -18.0909926435978
-49000  ekin = 2.32140483916261 |  erot = 2.72932938830521 | epot = -22.6070371995253 | etot = -17.5563029720575
-50000  ekin = 2.48248035385828 |  erot = 3.42713570109107 | epot = -22.5294064222472 | etot = -16.6197903672979
-51000  ekin = 2.73677705777971 |  erot = 1.43285265191038 | epot = -22.4272695862992 | etot = -18.2576398766091
-52000  ekin = 3.03746109762767 |  erot = 1.97878223690383 | epot = -22.4105817052324 | etot = -17.3943383707009
-53000  ekin = 2.4689045601064 |  erot = 4.26434186327668 | epot = -22.4059567857723 | etot = -15.6727103623892
-54000  ekin = 2.48025904071626 |  erot = 2.36957879662632 | epot = -22.4049729842648 | etot = -17.5551351469222
-55000  ekin = 2.28269445417385 |  erot = 1.92149293107792 | epot = -22.4643082993723 | etot = -18.2601209141205
-56000  ekin = 2.36225428889468 |  erot = 2.21818002425493 | epot = -22.5516502452859 | etot = -17.9712159321363
-57000  ekin = 2.5222034650231 |  erot = 2.87044520913643 | epot = -22.6517599833465 | etot = -17.259111309187
-58000  ekin = 2.50677816066749 |  erot = 2.80087142998998 | epot = -22.7046490897181 | etot = -17.3969994990606
-59000  ekin = 2.7442153349817 |  erot = 2.17375311266844 | epot = -22.7630968852437 | etot = -17.8451284375935
-60000  ekin = 3.28881699963202 |  erot = 1.98491245229834 | epot = -22.7493813857704 | etot = -17.47565193384
-61000  ekin = 2.42749732003947 |  erot = 1.80500042748845 | epot = -22.6954080097403 | etot = -18.4629102622124
-62000  ekin = 2.82051548232979 |  erot = 1.69220614985812 | epot = -22.5840860651657 | etot = -18.0713644329778
-63000  ekin = 3.66818847100113 |  erot = 1.91510536540651 | epot = -22.4235299160084 | etot = -16.8402360796008
-64000  ekin = 3.60192162647095 |  erot = 3.02302140162941 | epot = -22.4028966408394 | etot = -15.777953612739
-65000  ekin = 3.37797300912952 |  erot = 3.90646944425564 | epot = -22.3508227873685 | etot = -15.0663803339833
-66000  ekin = 2.90796062513305 |  erot = 2.46538835419998 | epot = -22.2656130116827 | etot = -16.8922640323497
-67000  ekin = 2.57641483706472 |  erot = 2.1063925708314 | epot = -22.1586423836372 | etot = -17.4758349757411
-68000  ekin = 2.5516902727465 |  erot = 2.46870040285813 | epot = -22.1454741588102 | etot = -17.1250834832056
-69000  ekin = 2.42897294997603 |  erot = 2.86774435615082 | epot = -22.1788582092806 | etot = -16.8821409031537
-70000  ekin = 3.08406596014674 |  erot = 2.51171720098584 | epot = -22.2680651617951 | etot = -16.6722820006626
-71000  ekin = 2.55052721315253 |  erot = 2.49486492124423 | epot = -22.3940848075589 | etot = -17.3486926731621
-72000  ekin = 1.77666138705941 |  erot = 2.52301579845699 | epot = -22.4956655989824 | etot = -18.195988413466
-73000  ekin = 1.86857924146303 |  erot = 2.33110810852355 | epot = -22.5401005215029 | etot = -18.3404131715163
-74000  ekin = 3.14875320805144 |  erot = 2.12002807961601 | epot = -22.5354282257998 | etot = -17.2666469381323
-75000  ekin = 2.60566180511119 |  erot = 2.16421143606062 | epot = -22.5109742574449 | etot = -17.7411010162731
-76000  ekin = 1.94500512300058 |  erot = 1.94681992806367 | epot = -22.5134561384461 | etot = -18.6216310873819
-77000  ekin = 2.09005510206219 |  erot = 2.13354294429721 | epot = -22.5157248384152 | etot = -18.2921267920558
-78000  ekin = 2.48381695181472 |  erot = 2.49598603867482 | epot = -22.449809286019 | etot = -17.4700062955295
-79000  ekin = 3.09582217320064 |  erot = 2.46630074007712 | epot = -22.3464652405845 | etot = -16.7843423273068
-80000  ekin = 2.51380629427529 |  erot = 1.89207626467031 | epot = -22.2775752521275 | etot = -17.8716926931819
-81000  ekin = 2.32322780911516 |  erot = 2.24954513249787 | epot = -22.2655235360186 | etot = -17.6927505944055
-82000  ekin = 1.54779729878415 |  erot = 2.01487148845307 | epot = -22.2126473128098 | etot = -18.6499785255726
-83000  ekin = 2.24267653112482 |  erot = 3.34721522119025 | epot = -22.2063282117648 | etot = -16.6164364594498
-84000  ekin = 2.86948852339533 |  erot = 2.11915315181827 | epot = -22.2055386975617 | etot = -17.2168970223481
-85000  ekin = 3.13802387827786 |  erot = 2.93900498543376 | epot = -22.2240733080824 | etot = -16.1470444443708
-86000  ekin = 3.46160079449538 |  erot = 2.80798287444336 | epot = -22.2732645073155 | etot = -16.0036808383767
-87000  ekin = 3.63139446909085 |  erot = 2.3166794204513 | epot = -22.2567856660101 | etot = -16.308711776468
-88000  ekin = 3.15348314879937 |  erot = 2.2785763709033 | epot = -22.2154422326699 | etot = -16.7833827129672
-89000  ekin = 3.30271147105659 |  erot = 1.80791256125564 | epot = -22.1564153597823 | etot = -17.04579132747
-90000  ekin = 2.42655906518194 |  erot = 2.24507038389518 | epot = -21.9481188512569 | etot = -17.2764894021798
-91000  ekin = 1.89051217909395 |  erot = 2.51049066719493 | epot = -21.7877769537306 | etot = -17.3867741074417
-92000  ekin = 2.07833668466679 |  erot = 2.218324246302 | epot = -21.6997103074282 | etot = -17.4030493764594
-93000  ekin = 1.94321435585196 |  erot = 2.99473985773914 | epot = -21.6748650469777 | etot = -16.7369108333866
-94000  ekin = 2.07878576812463 |  erot = 3.37631892101902 | epot = -21.7659932416399 | etot = -16.3108885524963
-95000  ekin = 2.10517721407769 |  erot = 2.08345895044788 | epot = -21.8951718799354 | etot = -17.7065357154098
-96000  ekin = 2.68821593238919 |  erot = 1.86988637992409 | epot = -21.9622848400866 | etot = -17.4041825277733
-97000  ekin = 1.95061152706206 |  erot = 2.81054215683073 | epot = -22.0229813258884 | etot = -17.2618276419957
-98000  ekin = 1.98463063611221 |  erot = 2.05732763357977 | epot = -22.0930102039112 | etot = -18.0510519342192
-99000  ekin = 2.51292852217217 |  erot = 3.54194472638845 | epot = -22.199088757298 | etot = -16.1442155087374
-100000  ekin = 1.8757570387949 |  erot = 2.3690785580876 | epot = -22.348409587438 | etot = -18.1035739905555
-101000  ekin = 1.66160772204006 |  erot = 3.59766032223856 | epot = -22.3604908173889 | etot = -17.1012227731103
-102000  ekin = 1.62075182718474 |  erot = 3.3442006848817 | epot = -22.3063629504087 | etot = -17.3414104383422
-103000  ekin = 2.00871148652538 |  erot = 2.33677124900284 | epot = -22.275557852692 | etot = -17.9300751171637
-104000  ekin = 2.04513709976292 |  erot = 2.74664593650967 | epot = -22.2818713634637 | etot = -17.4900883271911
-105000  ekin = 1.87027868596139 |  erot = 1.98922389218239 | epot = -22.223503909299 | etot = -18.3640013311552
-106000  ekin = 1.71540784443942 |  erot = 1.9177953110688 | epot = -22.2562839843324 | etot = -18.6230808288242
-107000  ekin = 2.61024905591622 |  erot = 1.57446439985464 | epot = -22.3171357124015 | etot = -18.1324222566306
-108000  ekin = 2.13751756724178 |  erot = 2.18822458113098 | epot = -22.2268794585969 | etot = -17.9011373102241
-109000  ekin = 2.24408198608307 |  erot = 2.11438299352724 | epot = -22.076564108576 | etot = -17.7180991289657
-110000  ekin = 1.66706562020821 |  erot = 2.50986066169373 | epot = -22.0833343008135 | etot = -17.9064080189116
-111000  ekin = 2.30463895640872 |  erot = 2.24982560856989 | epot = -22.0940837732696 | etot = -17.539619208291
-112000  ekin = 2.63019524472749 |  erot = 2.43696110420532 | epot = -22.0953344558745 | etot = -17.0281781069417
-113000  ekin = 2.42282638113981 |  erot = 3.06190927482913 | epot = -22.1061661458173 | etot = -16.6214304898484
-114000  ekin = 2.34214572325658 |  erot = 2.31899235523686 | epot = -22.0941430549288 | etot = -17.4330049764353
-115000  ekin = 1.70336449422736 |  erot = 3.10166879044198 | epot = -22.1252095896431 | etot = -17.3201763049738
-116000  ekin = 1.51705870113214 |  erot = 2.21425252709695 | epot = -22.1823772627204 | etot = -18.4510660344913
-117000  ekin = 1.70129809180508 |  erot = 2.34142425076372 | epot = -22.2067668262467 | etot = -18.1640444836779
-118000  ekin = 2.20482827236051 |  erot = 2.3179714809504 | epot = -22.1855414590757 | etot = -17.6627417057647
-119000  ekin = 2.54272629601484 |  erot = 2.46528921750297 | epot = -22.2113175246519 | etot = -17.2033020111341
-120000  ekin = 1.76640390552554 |  erot = 2.16116304616032 | epot = -22.1536331723646 | etot = -18.2260662206787
-121000  ekin = 2.81281157959688 |  erot = 2.31761005518346 | epot = -22.1492969323239 | etot = -17.0188752975435
-122000  ekin = 3.25156823587966 |  erot = 3.31679050874322 | epot = -22.2050361016166 | etot = -15.6366773569938
-123000  ekin = 2.87462309654081 |  erot = 3.25604816714397 | epot = -22.1785374359393 | etot = -16.0478661722546
-124000  ekin = 2.18213410260632 |  erot = 2.77182209342785 | epot = -22.0161464482698 | etot = -17.0621902522356
-125000  ekin = 1.85317252616068 |  erot = 1.36623599567638 | epot = -21.8721650279344 | etot = -18.6527565060973
-126000  ekin = 2.47747071965844 |  erot = 3.09909384826334 | epot = -21.8840309142636 | etot = -16.3074663463419
-127000  ekin = 2.42177426273027 |  erot = 2.35209644429656 | epot = -21.8861939604609 | etot = -17.1123232534341
-128000  ekin = 2.76000040231245 |  erot = 1.8231678837239 | epot = -21.8538456680958 | etot = -17.2706773820595
-129000  ekin = 2.78355536315491 |  erot = 2.88851981621501 | epot = -21.9251039267855 | etot = -16.2530287474156
-130000  ekin = 3.26834278926799 |  erot = 2.56228354573336 | epot = -22.0546105678549 | etot = -16.2239842328536
-131000  ekin = 2.64714688907849 |  erot = 2.51107513446137 | epot = -22.0961160192681 | etot = -16.9378939957282
-132000  ekin = 2.61847248883524 |  erot = 3.38899164334156 | epot = -22.1218916777659 | etot = -16.1144275455891
-133000  ekin = 2.03408861514006 |  erot = 2.87401070790187 | epot = -22.0785989417621 | etot = -17.1704996187202
-134000  ekin = 1.64140897264888 |  erot = 1.66986416585675 | epot = -22.0323643102285 | etot = -18.7210911717228
-135000  ekin = 2.46650096367446 |  erot = 2.111120611107 | epot = -21.9976572593399 | etot = -17.4200356845585
-136000  ekin = 2.32880805911731 |  erot = 3.05940125193231 | epot = -21.8983392007847 | etot = -16.5101298897351
-137000  ekin = 2.7601019905106 |  erot = 2.47443779429795 | epot = -21.752125264204 | etot = -16.5175854793954
-138000  ekin = 3.30162084678948 |  erot = 1.73084735415554 | epot = -21.7423849642075 | etot = -16.7099167632625
-139000  ekin = 2.76669064053124 |  erot = 1.72642745910431 | epot = -21.8898577306654 | etot = -17.3967396310298
-140000  ekin = 2.73595287215366 |  erot = 2.46891829250481 | epot = -21.9884857831833 | etot = -16.7836146185249
-141000  ekin = 2.79316289615844 |  erot = 2.46753088695597 | epot = -22.0064855648443 | etot = -16.7457917817299
-142000  ekin = 3.51694745558129 |  erot = 3.49862438784827 | epot = -21.9623193335451 | etot = -14.9467474901156
-143000  ekin = 2.58689934548697 |  erot = 2.04008576044027 | epot = -21.9563338194557 | etot = -17.3293487135285
-144000  ekin = 3.72611917000993 |  erot = 3.04855733322793 | epot = -21.9536376487796 | etot = -15.1789611455417
-145000  ekin = 3.61191106831147 |  erot = 2.71915407989904 | epot = -21.870542665333 | etot = -15.5394775171225
-146000  ekin = 3.85060594912677 |  erot = 2.47210219931339 | epot = -21.8285858153921 | etot = -15.505877666952
-147000  ekin = 3.26481933196161 |  erot = 2.06864347299802 | epot = -21.6752809049183 | etot = -16.3418180999587
-148000  ekin = 2.47977997895053 |  erot = 1.65169267241014 | epot = -21.4172781734276 | etot = -17.2858055220669
-149000  ekin = 2.70771685463074 |  erot = 2.28028425953227 | epot = -21.2324293178539 | etot = -16.2444282036909
-150000  ekin = 2.60726181496431 |  erot = 2.88955230103659 | epot = -21.126549406853 | etot = -15.6297352908521
-151000  ekin = 2.06865005733849 |  erot = 2.13537039813292 | epot = -21.0304193709383 | etot = -16.8263989154669
-152000  ekin = 2.41210154812787 |  erot = 2.60104053370075 | epot = -20.8967777045302 | etot = -15.8836356227016
-153000  ekin = 2.12406231442824 |  erot = 2.25444655142795 | epot = -20.9199278716094 | etot = -16.5414190057532
-154000  ekin = 2.34622678455546 |  erot = 2.58439374093403 | epot = -21.0040588663533 | etot = -16.0734383408638
-155000  ekin = 2.08240965570452 |  erot = 3.02621505767145 | epot = -21.0204738431416 | etot = -15.9118491297656
-156000  ekin = 2.04576145796301 |  erot = 3.17151405834467 | epot = -20.8558463949479 | etot = -15.6385708786402
-157000  ekin = 2.36459548410747 |  erot = 1.89207417055424 | epot = -20.8025485082277 | etot = -16.545878853566
-158000  ekin = 2.16996178916575 |  erot = 2.46547727482113 | epot = -20.8673070433024 | etot = -16.2318679793155
-159000  ekin = 2.86272730849306 |  erot = 2.27590841865057 | epot = -20.9710387207245 | etot = -15.8324029935809
-160000  ekin = 2.19288173853782 |  erot = 2.36312829884111 | epot = -21.0403123366075 | etot = -16.4843022992286
-161000  ekin = 2.14059248149909 |  erot = 2.4287283799048 | epot = -21.1333683100403 | etot = -16.5640474486365
-162000  ekin = 1.76077466564934 |  erot = 2.66561836368342 | epot = -21.1782130850259 | etot = -16.7518200556931
-163000  ekin = 2.23068698955417 |  erot = 2.02664945757243 | epot = -21.3281780197228 | etot = -17.0708415725963
-164000  ekin = 2.75358320318999 |  erot = 1.43717365990088 | epot = -21.4675480212853 | etot = -17.2767911581945
-165000  ekin = 2.65171600986478 |  erot = 2.29632253260765 | epot = -21.493178025826 | etot = -16.5451394833536
-166000  ekin = 3.27298673277591 |  erot = 2.41252396730596 | epot = -21.4477711984927 | etot = -15.7622604984108
-167000  ekin = 3.02574105268454 |  erot = 2.02770436019795 | epot = -21.5236773217566 | etot = -16.4702319088741
-168000  ekin = 3.14659813654158 |  erot = 1.8374607941321 | epot = -21.5547269116736 | etot = -16.5706679809999
-169000  ekin = 2.22493755697302 |  erot = 2.67175500860652 | epot = -21.4662206077311 | etot = -16.5695280421515
-170000  ekin = 2.41921977325643 |  erot = 2.49142716001801 | epot = -21.3123035293873 | etot = -16.4016565961128
-171000  ekin = 1.89798915040775 |  erot = 2.39492100285877 | epot = -21.2153991969519 | etot = -16.9224890436853
-172000  ekin = 2.86894215563086 |  erot = 3.22914449693158 | epot = -21.1827352206441 | etot = -15.0846485680816
-173000  ekin = 2.74888252418688 |  erot = 2.13556434483052 | epot = -21.2166792789418 | etot = -16.3322324099244
-174000  ekin = 2.45887587066864 |  erot = 2.23682521338056 | epot = -21.2633056658561 | etot = -16.5676045818069
-175000  ekin = 2.84703517745999 |  erot = 2.39381254916381 | epot = -21.2430876358358 | etot = -16.002239909212
-176000  ekin = 2.14025231000119 |  erot = 1.89894722702466 | epot = -21.3238321496633 | etot = -17.2846326126375
-177000  ekin = 2.5795061901144 |  erot = 2.75365074391219 | epot = -21.3022195274207 | etot = -15.9690625933941
-178000  ekin = 1.83122028490793 |  erot = 2.59468068841507 | epot = -21.2483113201278 | etot = -16.8224103468048
-179000  ekin = 2.50706581632049 |  erot = 2.3918046623687 | epot = -21.3152464598324 | etot = -16.4163759811432
-180000  ekin = 1.88211034410738 |  erot = 2.47063835849692 | epot = -21.4741119346399 | etot = -17.1213632320356
-181000  ekin = 1.74209654097779 |  erot = 3.05723824722444 | epot = -21.4808621715442 | etot = -16.681527383342
-182000  ekin = 1.55789914013104 |  erot = 2.05767448814763 | epot = -21.423526482018 | etot = -17.8079528537394
-183000  ekin = 2.00937540548925 |  erot = 2.80898978674436 | epot = -21.491360735728 | etot = -16.6729955434944
-184000  ekin = 2.69285960778353 |  erot = 2.42969439668747 | epot = -21.6024209898208 | etot = -16.4798669853498
-185000  ekin = 3.01326925127938 |  erot = 3.19083239326424 | epot = -21.6730258967931 | etot = -15.4689242522495
-186000  ekin = 3.2083067153638 |  erot = 2.42899016869201 | epot = -21.7143665695974 | etot = -16.0770696855416
-187000  ekin = 2.672906100919 |  erot = 3.41560404715603 | epot = -21.6726605039613 | etot = -15.5841503558862
-188000  ekin = 2.89349337388582 |  erot = 3.06258669113775 | epot = -21.6216664732832 | etot = -15.6655864082597
-189000  ekin = 2.65435973176118 |  erot = 1.82043381700644 | epot = -21.5604872976485 | etot = -17.0856937488809
-190000  ekin = 2.21855159698309 |  erot = 1.84826944038784 | epot = -21.5263477340278 | etot = -17.4595266966569
-191000  ekin = 2.26980616064111 |  erot = 2.05944589507645 | epot = -21.4543005141097 | etot = -17.1250484583921
-192000  ekin = 2.27219103053707 |  erot = 3.11210788791052 | epot = -21.4899273087562 | etot = -16.1056283903086
-193000  ekin = 1.95008147026928 |  erot = 1.89648921534019 | epot = -21.4843079374128 | etot = -17.6377372518033
-194000  ekin = 2.45477671526091 |  erot = 2.0272304242676 | epot = -21.3709228769337 | etot = -16.8889157374052
-195000  ekin = 3.09567411006595 |  erot = 2.10081767143638 | epot = -21.3012041149762 | etot = -16.1047123334739
-196000  ekin = 2.67423122149492 |  erot = 2.50738189755519 | epot = -21.2164124023053 | etot = -16.0347992832552
-197000  ekin = 2.50338730962556 |  erot = 2.07349764616723 | epot = -21.041867486922 | etot = -16.4649825311292
-198000  ekin = 2.66945928982616 |  erot = 1.79012921820209 | epot = -21.0169215356766 | etot = -16.5573330276483
-199000  ekin = 2.53947964790256 |  erot = 2.33176467953655 | epot = -21.0171165577067 | etot = -16.1458722302676
-200000  ekin = 2.90451062704866 |  erot = 1.42170066957004 | epot = -21.0113804229743 | etot = -16.6851691263556
-201000  ekin = 2.68927776239674 |  erot = 1.56650335894554 | epot = -21.0245916399581 | etot = -16.7688105186158
-202000  ekin = 2.2601329351618 |  erot = 2.25401443373177 | epot = -20.9769308007641 | etot = -16.4627834318706
-203000  ekin = 2.12073487355488 |  erot = 2.03553028991747 | epot = -20.919035946492 | etot = -16.7627707830197
-204000  ekin = 2.11829086582788 |  erot = 1.89731962488617 | epot = -20.9376264283538 | etot = -16.9220159376397
-205000  ekin = 1.30964171332167 |  erot = 2.12770406224885 | epot = -20.9991335630718 | etot = -17.5617877875013
-206000  ekin = 1.39940057572522 |  erot = 2.24496791209126 | epot = -20.963919219062 | etot = -17.3195507312455
-207000  ekin = 1.8871608804017 |  erot = 1.79849326266382 | epot = -21.0552898160204 | etot = -17.3696356729549
-208000  ekin = 1.81558541079753 |  erot = 3.24210836817276 | epot = -21.3060144768834 | etot = -16.2483206979131
-209000  ekin = 2.79588064252181 |  erot = 2.3467149173832 | epot = -21.4301997554495 | etot = -16.2876041955445
-210000  ekin = 3.17544887511567 |  erot = 3.12704516116654 | epot = -21.5100449360932 | etot = -15.2075508998109
-211000  ekin = 2.47442327377226 |  erot = 2.0990867711376 | epot = -21.6455723047062 | etot = -17.0720622597963
-212000  ekin = 2.36672302145397 |  erot = 1.93445871446419 | epot = -21.7283038297487 | etot = -17.4271220938306
-213000  ekin = 1.91045426241161 |  erot = 2.52535628540462 | epot = -21.8158508544504 | etot = -17.3800403066341
-214000  ekin = 1.99794025866061 |  erot = 2.49896939492127 | epot = -21.8606548137084 | etot = -17.3637451601266
-215000  ekin = 1.97741561009525 |  erot = 3.17667494473254 | epot = -21.8701701582032 | etot = -16.7160796033754
-216000  ekin = 1.88829990821377 |  erot = 1.87402623825167 | epot = -21.8343889393413 | etot = -18.0720627928759
-217000  ekin = 2.10000293878932 |  erot = 1.95052404495887 | epot = -21.8965404786646 | etot = -17.8460134949164
-218000  ekin = 2.34753598782339 |  erot = 1.69695019504401 | epot = -21.8560027679962 | etot = -17.8115165851288
-219000  ekin = 2.497223564463 |  erot = 2.20999914485705 | epot = -21.8797649478059 | etot = -17.1725422384859
-220000  ekin = 1.75274593087921 |  erot = 3.03992746556406 | epot = -21.8491595252171 | etot = -17.0564861287739
-221000  ekin = 1.78874686645809 |  erot = 2.79359542964647 | epot = -21.869798634642 | etot = -17.2874563385375
-222000  ekin = 2.63608430516661 |  erot = 2.86817933637385 | epot = -21.8351218383832 | etot = -16.3308581968427
-223000  ekin = 3.02706758581511 |  erot = 1.93888641555348 | epot = -21.8582453001765 | etot = -16.8922912988079
-224000  ekin = 2.71704451339112 |  erot = 2.42079327531441 | epot = -21.8188420875657 | etot = -16.6810042988601
-225000  ekin = 2.04245190508395 |  erot = 3.38216222891907 | epot = -21.8232190868647 | etot = -16.3986049528616
-226000  ekin = 2.37968015829255 |  erot = 2.38384696857065 | epot = -21.8913549487127 | etot = -17.1278278218495
-227000  ekin = 2.73883397024414 |  erot = 2.62491632372019 | epot = -21.9496900700867 | etot = -16.5859397761223
-228000  ekin = 2.06833362780412 |  erot = 2.25049628751225 | epot = -21.9946760345141 | etot = -17.6758461191977
-229000  ekin = 1.78618617304217 |  erot = 1.80509591500329 | epot = -22.0671964085329 | etot = -18.4759143204874
-230000  ekin = 2.76967283780387 |  erot = 2.22492545317995 | epot = -22.0913590121729 | etot = -17.0967607211891
-231000  ekin = 3.15653922952316 |  erot = 2.77099247609325 | epot = -22.0635255129442 | etot = -16.1359938073278
-232000  ekin = 1.86633326635991 |  erot = 1.70672288688982 | epot = -22.0959715052869 | etot = -18.5229153520371
-233000  ekin = 1.75856846080021 |  erot = 1.55694263125625 | epot = -22.0729289884755 | etot = -18.7574178964191
-234000  ekin = 2.32322575892498 |  erot = 2.05793864740336 | epot = -21.9849429433607 | etot = -17.6037785370324
-235000  ekin = 1.95327191686568 |  erot = 2.52519338885861 | epot = -21.9357201856672 | etot = -17.4572548799429
-236000  ekin = 2.25952484966859 |  erot = 1.90005304846995 | epot = -21.9422471368741 | etot = -17.7826692387355
-237000  ekin = 2.49082301609303 |  erot = 2.65327564887437 | epot = -22.0049130762794 | etot = -16.860814411312
-238000  ekin = 2.21076048871751 |  erot = 2.74154862479023 | epot = -22.0553236426831 | etot = -17.1030145291754
-239000  ekin = 2.71464884454142 |  erot = 2.48739530580561 | epot = -22.0661894571024 | etot = -16.8641453067554
-240000  ekin = 3.08961933821573 |  erot = 2.17857064931927 | epot = -21.9596599475175 | etot = -16.6914699599825
-241000  ekin = 3.04172562407922 |  erot = 2.64442433974962 | epot = -21.872950064824 | etot = -16.1868001009951
-242000  ekin = 2.21355627539455 |  erot = 2.33429157450905 | epot = -21.7850463200938 | etot = -17.2371984701902
-243000  ekin = 1.52065138183895 |  erot = 2.81375224845254 | epot = -21.724672004357 | etot = -17.3902683740655
-244000  ekin = 1.90352576583831 |  erot = 2.43821138840079 | epot = -21.6320468184555 | etot = -17.2903096642164
-245000  ekin = 1.96342069667742 |  erot = 2.61760141174562 | epot = -21.509789944958 | etot = -16.928767836535
-246000  ekin = 2.05478829283868 |  erot = 2.42643933263093 | epot = -21.4781109635143 | etot = -16.9968833380447
-247000  ekin = 1.54618395739204 |  erot = 2.28537401295509 | epot = -21.4411828355572 | etot = -17.6096248652101
-248000  ekin = 1.83924983769609 |  erot = 2.55904554412921 | epot = -21.4587985205918 | etot = -17.0605031387665
-249000  ekin = 1.78703007063825 |  erot = 2.03411349475431 | epot = -21.516607560139 | etot = -17.6954639947464
-250000  ekin = 1.69317901626952 |  erot = 3.382620023581 | epot = -21.5380480709889 | etot = -16.4622490311384
-251000  ekin = 2.13799462687096 |  erot = 3.25868442484789 | epot = -21.5254595658408 | etot = -16.1287805141219
-252000  ekin = 2.04357045453396 |  erot = 2.53079336098227 | epot = -21.5456931883614 | etot = -16.9713293728452
-253000  ekin = 1.63287738205387 |  erot = 3.20992823373492 | epot = -21.5622010587548 | etot = -16.719395442966
-254000  ekin = 2.31269246359595 |  erot = 3.10766702207071 | epot = -21.5505863172024 | etot = -16.1302268315358
-255000  ekin = 2.50767926641465 |  erot = 2.76631276495167 | epot = -21.5288449153183 | etot = -16.254852883952
-256000  ekin = 1.97163698305487 |  erot = 2.61682132599931 | epot = -21.5273539828767 | etot = -16.9388956738225
-257000  ekin = 2.21091422886157 |  erot = 3.2624387389365 | epot = -21.5385504601779 | etot = -16.0651974923798
-258000  ekin = 2.0351730783025 |  erot = 1.84693461512361 | epot = -21.6544556001779 | etot = -17.7723479067518
-259000  ekin = 2.85718947138204 |  erot = 2.78701165242275 | epot = -21.7587237542941 | etot = -16.1145226304893
-260000  ekin = 2.90387286634678 |  erot = 2.18817434737477 | epot = -21.8080383126913 | etot = -16.7159910989698
-261000  ekin = 2.76190440948559 |  erot = 2.33968169215532 | epot = -21.8592909726424 | etot = -16.7577048710015
-262000  ekin = 3.50919242681178 |  erot = 1.76925994550144 | epot = -21.8779228441577 | etot = -16.5994704718445
-263000  ekin = 3.07696270254058 |  erot = 2.41477320555763 | epot = -21.8078566004281 | etot = -16.3161206923299
-264000  ekin = 2.26633389925754 |  erot = 2.04161743361595 | epot = -21.8372928128571 | etot = -17.5293414799836
-265000  ekin = 1.95747124461577 |  erot = 2.5081300879884 | epot = -21.8490876266416 | etot = -17.3834862940375
-266000  ekin = 2.34517905801099 |  erot = 3.31486209922478 | epot = -21.8287737874741 | etot = -16.1687326302383
-267000  ekin = 1.74030193361906 |  erot = 2.23366459528059 | epot = -21.699850097441 | etot = -17.7258835685413
-268000  ekin = 2.04858677018814 |  erot = 3.28744422098426 | epot = -21.6459408923623 | etot = -16.3099099011899
-269000  ekin = 1.93146929709294 |  erot = 2.79280735598121 | epot = -21.549773802712 | etot = -16.8254971496378
-270000  ekin = 2.19788894271016 |  erot = 2.64563279687103 | epot = -21.4165389672397 | etot = -16.5730172276585
-271000  ekin = 2.21923220579694 |  erot = 3.10768708967444 | epot = -21.2197121954353 | etot = -15.8927928999639
-272000  ekin = 2.54992061853163 |  erot = 2.29721880581853 | epot = -21.0816515756819 | etot = -16.2345121513317
-273000  ekin = 1.914618407838 |  erot = 2.01420401968473 | epot = -21.0503637141725 | etot = -17.1215412866498
-274000  ekin = 1.89671513770876 |  erot = 2.24334386161735 | epot = -21.0967103438301 | etot = -16.9566513445039
-275000  ekin = 1.78930707116537 |  erot = 3.09754687865994 | epot = -21.1385700371941 | etot = -16.2517160873688
-276000  ekin = 3.37110328153971 |  erot = 2.41957324257529 | epot = -21.0908388312033 | etot = -15.3001623070883
-277000  ekin = 2.38921825148496 |  erot = 1.50604988822737 | epot = -21.034620883997 | etot = -17.1393527442847
-278000  ekin = 2.51997301930638 |  erot = 2.14026171776896 | epot = -21.0117379332914 | etot = -16.351503196216
-279000  ekin = 1.88315206280857 |  erot = 2.37342905263994 | epot = -20.9993757709145 | etot = -16.742794655466
-280000  ekin = 2.33534713190787 |  erot = 3.58626468287222 | epot = -20.8573252930133 | etot = -14.9357134782332
-281000  ekin = 1.75252641954511 |  erot = 1.7907930540809 | epot = -20.9036528826792 | etot = -17.3603334090531
-282000  ekin = 2.26373977259215 |  erot = 3.04032073608633 | epot = -20.8497513702237 | etot = -15.5456908615452
-283000  ekin = 2.1783387139443 |  erot = 2.20833158301333 | epot = -20.8002776734785 | etot = -16.4136073765209
-284000  ekin = 1.9148667268656 |  erot = 2.21521993135969 | epot = -20.8277491648056 | etot = -16.6976625065804
-285000  ekin = 3.15634443167765 |  erot = 1.80033231604849 | epot = -21.0046435881196 | etot = -16.0479668403934
-286000  ekin = 3.84877574957331 |  erot = 1.82969969667577 | epot = -21.1628555811447 | etot = -15.4843801348956
-287000  ekin = 3.60615742824732 |  erot = 2.91608688151215 | epot = -21.2126952882302 | etot = -14.6904509784708
-288000  ekin = 3.19613259393802 |  erot = 1.67736393077137 | epot = -21.1713552834963 | etot = -16.297858758787
-289000  ekin = 2.45584885114799 |  erot = 2.77781979747336 | epot = -21.1669115721543 | etot = -15.9332429235329
-290000  ekin = 2.74570408981357 |  erot = 2.40443247852242 | epot = -21.1874427766533 | etot = -16.0373062083173
-291000  ekin = 2.10295274468233 |  erot = 2.37092484671539 | epot = -21.2419107014544 | etot = -16.7680331100567
-292000  ekin = 2.36118713930732 |  erot = 2.05558127949017 | epot = -21.3137361602548 | etot = -16.8969677414573
-293000  ekin = 2.2786196308825 |  erot = 2.35874555054765 | epot = -21.4302415460533 | etot = -16.7928763646231
-294000  ekin = 2.93315982813019 |  erot = 2.90313008187785 | epot = -21.5210917917479 | etot = -15.6848018817399
-295000  ekin = 2.66360761710434 |  erot = 2.28100565751945 | epot = -21.6885021477336 | etot = -16.7438888731098
-296000  ekin = 2.18767827164471 |  erot = 2.90589885547353 | epot = -21.7355037190159 | etot = -16.6419265918977
-297000  ekin = 2.15987738107365 |  erot = 3.29819575592636 | epot = -21.7177655658756 | etot = -16.2596924288756
-298000  ekin = 2.92956976611296 |  erot = 2.36377210613469 | epot = -21.6748271071566 | etot = -16.3814852349089
-299000  ekin = 3.19167138064488 |  erot = 2.23480811780853 | epot = -21.8042612344918 | etot = -16.3777817360384
-300000  ekin = 3.3133572846982 |  erot = 1.38932157247169 | epot = -21.8799906137235 | etot = -17.1773117565536
-301000  ekin = 2.39061971962408 |  erot = 3.30110260608963 | epot = -21.8919200817915 | etot = -16.2001977560778
-302000  ekin = 2.954460706029 |  erot = 3.2304815881765 | epot = -21.8557645140423 | etot = -15.6708222198368
-303000  ekin = 2.44700205353933 |  erot = 2.60676303242282 | epot = -21.8414046718167 | etot = -16.7876395858546
-304000  ekin = 2.23578509140697 |  erot = 2.68770420047938 | epot = -21.7680601199659 | etot = -16.8445708280796
-305000  ekin = 2.35505207220215 |  erot = 2.3823003115585 | epot = -21.7344089784493 | etot = -16.9970565946887
-306000  ekin = 1.91790567526689 |  erot = 2.90107494003232 | epot = -21.7170004822351 | etot = -16.8980198669359
-307000  ekin = 2.48241777758708 |  erot = 2.0836708009946 | epot = -21.6510481218459 | etot = -17.0849595432642
-308000  ekin = 2.77531620706104 |  erot = 2.63103510715158 | epot = -21.6349123878086 | etot = -16.2285610735959
-309000  ekin = 2.30440955942791 |  erot = 2.1249829765834 | epot = -21.5927938975113 | etot = -17.1634013615
-310000  ekin = 2.50879527040005 |  erot = 3.21338829421535 | epot = -21.6043932917725 | etot = -15.8822097271571
-311000  ekin = 2.31939145866558 |  erot = 3.03649241514151 | epot = -21.6247503351754 | etot = -16.2688664613683
-312000  ekin = 1.78383134659847 |  erot = 3.26262247889992 | epot = -21.4948144284683 | etot = -16.4483606029699
-313000  ekin = 1.6465994694839 |  erot = 2.08133087588833 | epot = -21.4920309735611 | etot = -17.7641006281889
-314000  ekin = 2.2552391830868 |  erot = 2.55077633299239 | epot = -21.5103692936944 | etot = -16.7043537776152
-315000  ekin = 2.5352734391515 |  erot = 2.13089997124613 | epot = -21.5923709217299 | etot = -16.9261975113323
-316000  ekin = 1.99944427781285 |  erot = 1.80072924409704 | epot = -21.6039893771529 | etot = -17.803815855243
-317000  ekin = 2.11848744585804 |  erot = 2.01459693810075 | epot = -21.5948976630665 | etot = -17.4618132791077
-318000  ekin = 2.29013024301854 |  erot = 1.92405818620914 | epot = -21.5643695946921 | etot = -17.3501811654644
-319000  ekin = 1.97314693278018 |  erot = 1.67996578959134 | epot = -21.4554808400841 | etot = -17.8023681177126
-320000  ekin = 2.45681719546631 |  erot = 3.07835144499744 | epot = -21.3924125538101 | etot = -15.8572439133463
-321000  ekin = 1.85729238455498 |  erot = 2.67083565671245 | epot = -21.433818829251 | etot = -16.9056907879836
-322000  ekin = 1.96132292396412 |  erot = 3.36792274118279 | epot = -21.3663490830085 | etot = -16.0371034178616
-323000  ekin = 1.94437285233567 |  erot = 2.09558156605687 | epot = -21.4151250968679 | etot = -17.3751706784754
-324000  ekin = 2.229181524904 |  erot = 2.4674418745061 | epot = -21.532385908563 | etot = -16.8357625091529
-325000  ekin = 2.74582842770392 |  erot = 2.36717454305098 | epot = -21.6443544237971 | etot = -16.5313514530422
-326000  ekin = 1.91124551133375 |  erot = 1.93084217743114 | epot = -21.7077957426602 | etot = -17.8657080538953
-327000  ekin = 3.05627483509655 |  erot = 1.67325209460963 | epot = -21.7948818019128 | etot = -17.0653548722066
-328000  ekin = 2.73933273476856 |  erot = 1.92380912803777 | epot = -21.8364014823586 | etot = -17.1732596195523
-329000  ekin = 2.95907896099514 |  erot = 3.15654168356681 | epot = -21.898199971646 | etot = -15.7825793270841
-330000  ekin = 2.90795110595274 |  erot = 2.01765890034968 | epot = -21.9037795505258 | etot = -16.9781695442234
-331000  ekin = 2.27446048340228 |  erot = 2.03754878634056 | epot = -21.8760842049291 | etot = -17.5640749351863
-332000  ekin = 2.43262938612094 |  erot = 3.19219171897213 | epot = -21.9305186945662 | etot = -16.3056975894732
-333000  ekin = 2.47357651298171 |  erot = 2.70061045814697 | epot = -22.0416691323271 | etot = -16.8674821611985
-334000  ekin = 2.38171387374892 |  erot = 3.00424927873366 | epot = -22.0746318522988 | etot = -16.6886686998162
-335000  ekin = 2.10465470910016 |  erot = 3.57382014016833 | epot = -22.1175420615632 | etot = -16.4390672122947
-336000  ekin = 2.61374577374183 |  erot = 2.13386927281299 | epot = -22.08988251196 | etot = -17.3422674654052
-337000  ekin = 2.72124526751511 |  erot = 2.74800480481403 | epot = -22.0768537131621 | etot = -16.607603640833
-338000  ekin = 1.83524121485421 |  erot = 2.24338894827196 | epot = -22.1591955034455 | etot = -18.0805653403194
-339000  ekin = 1.54928432997334 |  erot = 2.49812246084905 | epot = -22.202239883467 | etot = -18.1548330926446
-340000  ekin = 1.44405714940632 |  erot = 4.0451327092417 | epot = -22.1149458734013 | etot = -16.6257560147533
-341000  ekin = 1.67447392575555 |  erot = 2.77749751745982 | epot = -22.0760831546714 | etot = -17.624111711456
-342000  ekin = 1.9825676117275 |  erot = 2.71655566521084 | epot = -22.1563522566984 | etot = -17.45722897976
-343000  ekin = 2.68213676683887 |  erot = 3.16686462846914 | epot = -22.2498477633288 | etot = -16.4008463680208
-344000  ekin = 1.77905771753907 |  erot = 2.19153667254074 | epot = -22.2907212723871 | etot = -18.3201268823073
-345000  ekin = 1.5460499615042 |  erot = 1.85960255696712 | epot = -22.3447003428977 | etot = -18.9390478244264
-346000  ekin = 1.71554664484034 |  erot = 1.79880968736714 | epot = -22.3117022609055 | etot = -18.797345928698
-347000  ekin = 1.38672912049481 |  erot = 2.61484473767931 | epot = -22.332503239512 | etot = -18.3309293813379
-348000  ekin = 2.15015924850684 |  erot = 2.86300326453563 | epot = -22.3337312775957 | etot = -17.3205687645532
-349000  ekin = 1.83066085453602 |  erot = 1.9844132649487 | epot = -22.3967822584585 | etot = -18.5817081389738
-350000  ekin = 1.83318738252649 |  erot = 2.56907029661254 | epot = -22.4577827539416 | etot = -18.0555250748026
-351000  ekin = 1.72790505260219 |  erot = 2.87456274671834 | epot = -22.5159555107051 | etot = -17.9134877113846
-352000  ekin = 2.80786740016944 |  erot = 2.08750448125769 | epot = -22.6549834386892 | etot = -17.7596115572621
-353000  ekin = 3.5492801472091 |  erot = 1.42584537334883 | epot = -22.6849212734238 | etot = -17.7097957528659
-354000  ekin = 3.49129244374804 |  erot = 2.25156548638802 | epot = -22.604182620693 | etot = -16.861324690557
-355000  ekin = 2.06248783371663 |  erot = 2.92733565233054 | epot = -22.5494488364627 | etot = -17.5596253504155
-356000  ekin = 2.13415426306312 |  erot = 3.32668319049641 | epot = -22.6122425286523 | etot = -17.1514050750927
-357000  ekin = 2.75897049849731 |  erot = 2.51843165594436 | epot = -22.6042888591885 | etot = -17.3268867047468
-358000  ekin = 2.51778220496547 |  erot = 2.28374144764325 | epot = -22.5654155469984 | etot = -17.7638918943897
-359000  ekin = 3.2037278512604 |  erot = 2.5552016027623 | epot = -22.6749569097326 | etot = -16.91602745571
-360000  ekin = 2.52669169359923 |  erot = 1.97563796824025 | epot = -22.7314557612254 | etot = -18.229126099386
-361000  ekin = 2.60424632123629 |  erot = 2.51068088850826 | epot = -22.7715023743751 | etot = -17.6565751646306
-362000  ekin = 2.43350156723209 |  erot = 3.84566788758402 | epot = -22.7352151098034 | etot = -16.4560456549873
-363000  ekin = 2.91069717970492 |  erot = 1.99710098714122 | epot = -22.6302259934474 | etot = -17.7224278266013
-364000  ekin = 2.2553832868325 |  erot = 1.87832387363455 | epot = -22.5083625296191 | etot = -18.374655369152
-365000  ekin = 2.04575884197224 |  erot = 2.797742068412 | epot = -22.332262738426 | etot = -17.4887618280417
-366000  ekin = 2.26894187965217 |  erot = 1.94379382552235 | epot = -22.2788727984906 | etot = -18.0661370933161
-367000  ekin = 2.82509630766737 |  erot = 2.50361468767084 | epot = -22.3209381619452 | etot = -16.992227166607
-368000  ekin = 2.81542036602322 |  erot = 2.18733627644489 | epot = -22.4297259451244 | etot = -17.4269693026563
-369000  ekin = 2.30426035796382 |  erot = 2.85653411706989 | epot = -22.4923286665588 | etot = -17.3315341915251
-370000  ekin = 2.67871033327547 |  erot = 2.11464921695177 | epot = -22.578069860797 | etot = -17.7847103105697
-371000  ekin = 2.19281044135007 |  erot = 3.60165960664287 | epot = -22.6424730832337 | etot = -16.8480030352407
-372000  ekin = 1.77481259468411 |  erot = 3.406547444381 | epot = -22.7147683829008 | etot = -17.5334083438357
-373000  ekin = 2.15551547517191 |  erot = 2.7877825236183 | epot = -22.7559497214321 | etot = -17.8126517226419
-374000  ekin = 2.71938368055486 |  erot = 3.58127823243842 | epot = -22.9084433694729 | etot = -16.6077814564796
-375000  ekin = 2.42759321485976 |  erot = 2.9742127178716 | epot = -22.9740378563778 | etot = -17.5722319236464
-376000  ekin = 3.39126830110572 |  erot = 3.24733797625004 | epot = -22.9874015798135 | etot = -16.3487953024578
-377000  ekin = 3.20966733323472 |  erot = 2.65934060364476 | epot = -22.9452111216365 | etot = -17.076203184757
-378000  ekin = 1.56095946168131 |  erot = 2.66159033944991 | epot = -22.9575870308253 | etot = -18.7350372296941
-379000  ekin = 1.9498568748538 |  erot = 2.54085216255828 | epot = -22.9834751642939 | etot = -18.4927661268818
-380000  ekin = 2.65820438237073 |  erot = 2.88045867212573 | epot = -22.9984703542083 | etot = -17.4598072997118
-381000  ekin = 2.97084599252829 |  erot = 2.18892549461574 | epot = -23.0341895570111 | etot = -17.8744180698671
-382000  ekin = 2.61355176942653 |  erot = 2.02938704043227 | epot = -23.00841197151 | etot = -18.3654731616512
-383000  ekin = 2.03830671072154 |  erot = 2.50516194855525 | epot = -23.0393965606452 | etot = -18.4959279013684
-384000  ekin = 2.1060608733416 |  erot = 2.2184025045895 | epot = -23.0602182522593 | etot = -18.7357548743282
-385000  ekin = 1.89114918519107 |  erot = 1.63701051320103 | epot = -23.0834434146806 | etot = -19.5552837162885
-386000  ekin = 1.55124380123707 |  erot = 1.36147797265396 | epot = -23.1300518396949 | etot = -20.2173300658039
-387000  ekin = 2.19627825752355 |  erot = 1.75751396098972 | epot = -23.1280875332419 | etot = -19.1742953147287
-388000  ekin = 1.96387084539616 |  erot = 1.95852585326804 | epot = -23.0327752892415 | etot = -19.1103785905773
-389000  ekin = 2.50801560941705 |  erot = 2.32519825784836 | epot = -23.0011464671235 | etot = -18.1679325998581
-390000  ekin = 2.03596866068489 |  erot = 1.88295618907177 | epot = -22.8810338311575 | etot = -18.9621089814009
-391000  ekin = 1.8098591016452 |  erot = 2.39622167162874 | epot = -22.81955664632 | etot = -18.613475873046
-392000  ekin = 2.17725370142733 |  erot = 2.87094426544089 | epot = -22.7839731045438 | etot = -17.7357751376756
-393000  ekin = 2.14224634181997 |  erot = 3.17242974303658 | epot = -22.8435025538357 | etot = -17.5288264689792
-394000  ekin = 1.97769550804367 |  erot = 2.16375300420729 | epot = -22.8342667825711 | etot = -18.6928182703201
-395000  ekin = 2.03687268736298 |  erot = 2.49567469731651 | epot = -22.8892034986303 | etot = -18.3566561139508
-396000  ekin = 2.16189109047463 |  erot = 1.95308746486161 | epot = -22.9781386034885 | etot = -18.8631600481523
-397000  ekin = 2.41744222422408 |  erot = 1.65310699287476 | epot = -23.0900453292844 | etot = -19.0194961121856
-398000  ekin = 3.58905654436294 |  erot = 2.51930256503331 | epot = -23.2070733343384 | etot = -17.0987142249422
-399000  ekin = 2.65051654249497 |  erot = 1.78138450529865 | epot = -23.3040478764215 | etot = -18.8721468286279
-400000  ekin = 2.49402752614129 |  erot = 2.10290777432183 | epot = -23.3608759462318 | etot = -18.7639406457687
-401000  ekin = 2.04176177605462 |  erot = 2.154995213856 | epot = -23.4039603394011 | etot = -19.2072033494905
-402000  ekin = 2.44505875861459 |  erot = 2.11318097973378 | epot = -23.3975262709888 | etot = -18.8392865326404
-403000  ekin = 2.54858079745147 |  erot = 2.81138206601919 | epot = -23.476064698677 | etot = -18.1161018352063
-404000  ekin = 2.21063952462117 |  erot = 2.64710865829565 | epot = -23.574696037266 | etot = -18.7169478543492
-405000  ekin = 2.47328118101332 |  erot = 2.40933750599425 | epot = -23.5927917139469 | etot = -18.7101730269393
-406000  ekin = 2.24891173527799 |  erot = 2.23777884116047 | epot = -23.6086191890417 | etot = -19.1219286126032
-407000  ekin = 2.0107940045037 |  erot = 2.78642832526904 | epot = -23.5246032469978 | etot = -18.727380917225
-408000  ekin = 2.59464051790823 |  erot = 2.59123578102097 | epot = -23.4198302602656 | etot = -18.2339539613364
-409000  ekin = 2.37170880608734 |  erot = 2.26136902851213 | epot = -23.317258193724 | etot = -18.6841803591245
-410000  ekin = 1.99754661347185 |  erot = 1.95523998485755 | epot = -23.2950402043273 | etot = -19.3422536059979
-411000  ekin = 1.8693657058423 |  erot = 2.63899492681176 | epot = -23.2490367633041 | etot = -18.74067613065
-412000  ekin = 1.98214047746227 |  erot = 2.68315820775202 | epot = -23.1987357483281 | etot = -18.5334370631139
-413000  ekin = 2.39078873487373 |  erot = 2.65589562872907 | epot = -23.1435198518627 | etot = -18.0968354882599
-414000  ekin = 2.40821090859775 |  erot = 1.75574324408225 | epot = -23.0725048141377 | etot = -18.9085506614577
-415000  ekin = 2.74601981183015 |  erot = 2.43675176686816 | epot = -23.1211711904486 | etot = -17.9383996117503
-416000  ekin = 2.08828454200993 |  erot = 2.76783506526218 | epot = -23.1383119239965 | etot = -18.2821923167244
-417000  ekin = 2.01455344430628 |  erot = 1.95306265456051 | epot = -23.1433633505287 | etot = -19.1757472516619
-418000  ekin = 2.42716528853985 |  erot = 2.57642821145486 | epot = -23.127531797131 | etot = -18.1239382971363
-419000  ekin = 3.04095103685797 |  erot = 2.58427576972734 | epot = -23.0602279332617 | etot = -17.4350011266764
-420000  ekin = 2.6360746280152 |  erot = 2.44478111019393 | epot = -22.982092315172 | etot = -17.9012365769629
-421000  ekin = 2.53019765722915 |  erot = 1.78389585255477 | epot = -22.9707435541329 | etot = -18.6566500443489
-422000  ekin = 2.72457425772367 |  erot = 1.67768634886349 | epot = -22.9542997027495 | etot = -18.5520390961623
-423000  ekin = 2.11402997037893 |  erot = 2.55034580375608 | epot = -22.8263851956497 | etot = -18.1620094215147
-424000  ekin = 1.8895880210325 |  erot = 2.31332431343561 | epot = -22.772666888172 | etot = -18.5697545537039
-425000  ekin = 2.3595116370971 |  erot = 1.95762380637298 | epot = -22.7752082759346 | etot = -18.4580728324645
-426000  ekin = 2.23706657164627 |  erot = 2.60016134755148 | epot = -22.7844114251539 | etot = -17.9471835059562
-427000  ekin = 1.88801598248841 |  erot = 2.12415782350886 | epot = -22.9416586386639 | etot = -18.9294848326666
-428000  ekin = 1.92849031333042 |  erot = 2.44097902588716 | epot = -23.0611368174399 | etot = -18.6916674782223
-429000  ekin = 1.70536802258415 |  erot = 2.14916257389792 | epot = -23.0556586745393 | etot = -19.2011280780572
-430000  ekin = 2.30226095973205 |  erot = 2.14689932813604 | epot = -23.0606502516208 | etot = -18.6114899637527
-431000  ekin = 2.45988288454318 |  erot = 2.42278380298657 | epot = -23.0729777223881 | etot = -18.1903110348583
-432000  ekin = 2.80869332724974 |  erot = 2.19954129490925 | epot = -23.0939746542044 | etot = -18.0857400320454
-433000  ekin = 2.21130556188282 |  erot = 1.62882156110628 | epot = -23.1534080352157 | etot = -19.3132809122266
-434000  ekin = 2.60574953870752 |  erot = 2.36088790768803 | epot = -23.1901717047879 | etot = -18.2235342583923
-435000  ekin = 2.30377529593091 |  erot = 2.53917715731259 | epot = -23.1716983948432 | etot = -18.3287459415997
-436000  ekin = 2.42707603554825 |  erot = 2.75234181061924 | epot = -23.2197996577197 | etot = -18.0403818115522
-437000  ekin = 1.65090540276074 |  erot = 3.25345231298367 | epot = -23.2216366145388 | etot = -18.3172788987944
-438000  ekin = 1.56145302974407 |  erot = 2.60950810563796 | epot = -23.1303770792278 | etot = -18.9594159438458
-439000  ekin = 2.30955439722234 |  erot = 1.94011743371103 | epot = -23.1353170794497 | etot = -18.8856452485163
-440000  ekin = 2.53037674867674 |  erot = 3.0652704286103 | epot = -23.196858945292 | etot = -17.601211768005
-441000  ekin = 2.80107707952534 |  erot = 2.53664155736544 | epot = -23.1712373428919 | etot = -17.8335187060011
-442000  ekin = 2.92536323090713 |  erot = 2.88384500930017 | epot = -23.1123001627208 | etot = -17.3030919225135
-443000  ekin = 1.96543935969482 |  erot = 1.753449631552 | epot = -23.0380529084377 | etot = -19.3191639171909
-444000  ekin = 2.00309477401363 |  erot = 2.23897509587739 | epot = -22.9472103119533 | etot = -18.7051404420623
-445000  ekin = 2.20302071819722 |  erot = 2.06928381371828 | epot = -22.7775434364172 | etot = -18.5052389045017
-446000  ekin = 2.43487889302299 |  erot = 2.37751556007798 | epot = -22.6838190597697 | etot = -17.8714246066687
-447000  ekin = 2.2620819636031 |  erot = 2.41400188145197 | epot = -22.7082516636546 | etot = -18.0321678185995
-448000  ekin = 2.16184472791984 |  erot = 1.93539407204278 | epot = -22.8144859493263 | etot = -18.7172471493637
-449000  ekin = 2.21107967973114 |  erot = 2.34659682978741 | epot = -22.9059503054159 | etot = -18.3482737958974
-450000  ekin = 2.74677740004439 |  erot = 1.97222921372039 | epot = -22.860755926716 | etot = -18.1417493129513
-451000  ekin = 2.2050889378155 |  erot = 2.13042736119389 | epot = -22.8862608894796 | etot = -18.5507445904702
-452000  ekin = 2.52760608607095 |  erot = 2.34006815636601 | epot = -22.9138111972133 | etot = -18.0461369547763
-453000  ekin = 2.23448825172916 |  erot = 1.77834418215733 | epot = -22.8879238301791 | etot = -18.8750913962926
-454000  ekin = 2.4343851915949 |  erot = 2.59700848533281 | epot = -22.8184361849036 | etot = -17.7870425079759
-455000  ekin = 2.04195793930991 |  erot = 2.79639043747681 | epot = -22.6032980500354 | etot = -17.7649496732487
-456000  ekin = 2.00799933710202 |  erot = 2.53653815407518 | epot = -22.4355596266522 | etot = -17.891022135475
-457000  ekin = 2.60426208759883 |  erot = 2.46609612876191 | epot = -22.3409120082078 | etot = -17.270553791847
-458000  ekin = 2.01368468059037 |  erot = 1.9961381624531 | epot = -22.2549400327205 | etot = -18.2451171896771
-459000  ekin = 1.73688781588865 |  erot = 2.48572034306896 | epot = -22.2282088298767 | etot = -18.0056006709191
-460000  ekin = 1.91682575775988 |  erot = 2.08308677023944 | epot = -22.2211874714416 | etot = -18.2212749434423
-461000  ekin = 1.54933673126938 |  erot = 1.29454502815255 | epot = -22.1945151049368 | etot = -19.3506333455148
-462000  ekin = 2.44160489340629 |  erot = 1.34721473707676 | epot = -22.284671307697 | etot = -18.495851677214
-463000  ekin = 2.63165365707667 |  erot = 2.08143760128039 | epot = -22.4004513395625 | etot = -17.6873600812055
-464000  ekin = 2.67929276186416 |  erot = 3.72563793061087 | epot = -22.5200042545289 | etot = -16.1150735620538
-465000  ekin = 1.94880111369479 |  erot = 2.23148844819348 | epot = -22.685554296329 | etot = -18.5052647344407
-466000  ekin = 2.13853049638891 |  erot = 2.95056624305957 | epot = -22.7822881705531 | etot = -17.6931914311046
-467000  ekin = 2.46452767169615 |  erot = 2.1077848077008 | epot = -22.9485753844866 | etot = -18.3762629050896
-468000  ekin = 1.98589158006998 |  erot = 1.62816092182055 | epot = -23.0180008829524 | etot = -19.4039483810618
-469000  ekin = 2.498810820967 |  erot = 2.6361546272592 | epot = -23.0547833968841 | etot = -17.9198179486579
-470000  ekin = 2.91491361681313 |  erot = 3.19115611298998 | epot = -23.0448741101699 | etot = -16.9388043803668
-471000  ekin = 2.37554627514204 |  erot = 1.71739792236247 | epot = -22.9932329645513 | etot = -18.9002887670468
-472000  ekin = 2.18486807923518 |  erot = 2.00687069908099 | epot = -22.9563182572702 | etot = -18.764579478954
-473000  ekin = 2.36185345820899 |  erot = 2.86259041401023 | epot = -22.9161024426125 | etot = -17.6916585703933
-474000  ekin = 2.17077693495272 |  erot = 2.59376596740919 | epot = -22.7894018760352 | etot = -18.0248589736733
-475000  ekin = 2.37844153079293 |  erot = 2.01112751381907 | epot = -22.6793191497969 | etot = -18.2897501051849
-476000  ekin = 2.0876367643964 |  erot = 2.59647624455221 | epot = -22.6700039875052 | etot = -17.9858909785566
-477000  ekin = 2.52249432714936 |  erot = 3.55251934739867 | epot = -22.6424099194916 | etot = -16.5673962449436
-478000  ekin = 2.40424947791157 |  erot = 2.7323911725861 | epot = -22.544776325228 | etot = -17.4081356747303
-479000  ekin = 1.27637524434413 |  erot = 2.99749792697945 | epot = -22.4994949498981 | etot = -18.2256217785745
-480000  ekin = 1.81374950293817 |  erot = 2.14389317135939 | epot = -22.4678405170784 | etot = -18.5101978427809
-481000  ekin = 2.39496774186199 |  erot = 3.18299441824521 | epot = -22.4930736763177 | etot = -16.9151115162105
-482000  ekin = 3.21051763720184 |  erot = 2.40962326270833 | epot = -22.4479376181304 | etot = -16.8277967182202
-483000  ekin = 3.06081116762377 |  erot = 2.49856996934407 | epot = -22.4288948733283 | etot = -16.8695137363604
-484000  ekin = 2.7452293328759 |  erot = 2.53012629993099 | epot = -22.483756332919 | etot = -17.2084007001121
-485000  ekin = 3.33103095180521 |  erot = 2.42091818181918 | epot = -22.4922555047182 | etot = -16.7403063710938
-486000  ekin = 1.99323479363108 |  erot = 1.76127718142275 | epot = -22.5432098594131 | etot = -18.7886978843593
-487000  ekin = 2.64825718911654 |  erot = 2.50204426232017 | epot = -22.6407366935241 | etot = -17.4904352420874
-488000  ekin = 1.76385891719471 |  erot = 2.64266555173498 | epot = -22.6990728058786 | etot = -18.2925483369489
-489000  ekin = 2.10357630534276 |  erot = 2.95613916443127 | epot = -22.7877124402073 | etot = -17.7279969704332
-490000  ekin = 2.33515649128314 |  erot = 2.32995416999058 | epot = -22.7920703811403 | etot = -18.1269597198666
-491000  ekin = 2.48752587426647 |  erot = 2.58310949760555 | epot = -22.7834811495388 | etot = -17.7128457776668
-492000  ekin = 3.29820665204489 |  erot = 2.18682924183924 | epot = -22.7674519489923 | etot = -17.2824160551082
-493000  ekin = 3.40238156707506 |  erot = 2.35717041222451 | epot = -22.7149408840448 | etot = -16.9553889047452
-494000  ekin = 3.59348050162499 |  erot = 2.23182460532058 | epot = -22.7081682295491 | etot = -16.8828631226035
-495000  ekin = 2.52030309238562 |  erot = 2.16229430067423 | epot = -22.6973031832711 | etot = -18.0147057902113
-496000  ekin = 1.96100991422337 |  erot = 3.58581695215166 | epot = -22.7342002900882 | etot = -17.1873734237132
-497000  ekin = 2.2228647925968 |  erot = 2.49495319949133 | epot = -22.752706201593 | etot = -18.0348882095048
-498000  ekin = 1.71033952564695 |  erot = 2.41331591511584 | epot = -22.7131621100867 | etot = -18.589506669324
-499000  ekin = 2.41919864300729 |  erot = 2.82349519531821 | epot = -22.7304918052927 | etot = -17.4877979669672
-500000  ekin = 2.76271068346558 |  erot = 2.22796445937143 | epot = -22.810945568044 | etot = -17.820270425207
-501000  ekin = 2.97642553987186 |  erot = 1.97769778889399 | epot = -22.8306304048616 | etot = -17.8765070760957
-502000  ekin = 2.96175345860856 |  erot = 1.80859086419487 | epot = -22.8525538190094 | etot = -18.082209496206
-503000  ekin = 2.51126831088417 |  erot = 2.88572311841927 | epot = -22.8673362278446 | etot = -17.4703447985412
-504000  ekin = 2.84611165351303 |  erot = 2.67626783872459 | epot = -22.784891957601 | etot = -17.2625124653634
-505000  ekin = 2.96124584448914 |  erot = 2.59100575301934 | epot = -22.8251284225258 | etot = -17.2728768250174
-506000  ekin = 2.19858217910528 |  erot = 1.97142936872076 | epot = -22.8530995461462 | etot = -18.6830879983201
-507000  ekin = 2.27398115142402 |  erot = 2.68837996151517 | epot = -22.8141163798141 | etot = -17.8517552668749
-508000  ekin = 2.64439339973837 |  erot = 2.04756467869449 | epot = -22.8146247157345 | etot = -18.1226666373017
-509000  ekin = 2.96023637315629 |  erot = 2.90549934754532 | epot = -22.8719625385967 | etot = -17.0062268178951
-510000  ekin = 2.26067558634546 |  erot = 2.80864918519521 | epot = -22.9774448292236 | etot = -17.9081200576829
-511000  ekin = 2.88512738978599 |  erot = 2.15263877534437 | epot = -23.086672848248 | etot = -18.0489066831176
-512000  ekin = 2.17783748155516 |  erot = 2.31389139764186 | epot = -23.1520181882638 | etot = -18.6602893090668
-513000  ekin = 1.69717952556151 |  erot = 2.88265468656805 | epot = -23.1640284548407 | etot = -18.5841942427111
-514000  ekin = 1.72432024724117 |  erot = 2.32742209152174 | epot = -23.1602225830814 | etot = -19.1084802443185
-515000  ekin = 2.00525337522086 |  erot = 1.80102864435032 | epot = -23.1548763180746 | etot = -19.3485942985034
-516000  ekin = 3.04706172157038 |  erot = 1.54171785431326 | epot = -23.1202751246552 | etot = -18.5314955487716
-517000  ekin = 2.47323892251936 |  erot = 2.10799615007355 | epot = -23.0942246440307 | etot = -18.5129895714378
-518000  ekin = 2.03556879740597 |  erot = 2.51531294708502 | epot = -23.01998934344 | etot = -18.4691075989491
-519000  ekin = 1.59255614728459 |  erot = 1.63520468579907 | epot = -22.9787913166931 | etot = -19.7510304836094
-520000  ekin = 2.17210761761845 |  erot = 1.8975366735392 | epot = -22.9877149955356 | etot = -18.918070704378
-521000  ekin = 1.98466680078867 |  erot = 2.09219045542651 | epot = -23.0348541858322 | etot = -18.9579969296171
-522000  ekin = 2.72098469914434 |  erot = 2.19565658619456 | epot = -23.1001210576502 | etot = -18.1834797723113
-523000  ekin = 2.26033454380754 |  erot = 1.67112114369622 | epot = -23.1475509854345 | etot = -19.2160952979307
-524000  ekin = 2.34603831546138 |  erot = 2.1054661011949 | epot = -23.1746761633773 | etot = -18.723171746721
-525000  ekin = 2.13671314300235 |  erot = 2.07172081705863 | epot = -23.241177743004 | etot = -19.032743782943
-526000  ekin = 2.50849953901566 |  erot = 2.27662230434506 | epot = -23.3179050583979 | etot = -18.5327832150372
-527000  ekin = 3.04322527932213 |  erot = 1.8128057083239 | epot = -23.3977373118239 | etot = -18.5417063241779
-528000  ekin = 2.572303182379 |  erot = 2.54386055260816 | epot = -23.4208428708383 | etot = -18.3046791358511
-529000  ekin = 2.39361269633634 |  erot = 1.91637577362227 | epot = -23.3966015599491 | etot = -19.0866130899905
-530000  ekin = 3.3562937907424 |  erot = 3.41683815876463 | epot = -23.2977853851852 | etot = -16.5246534356781
-531000  ekin = 2.52741741752381 |  erot = 2.34075342407645 | epot = -23.1721175623278 | etot = -18.3039467207275
-532000  ekin = 2.78397051305127 |  erot = 1.78575123294094 | epot = -23.2171711834401 | etot = -18.6474494374479
-533000  ekin = 2.27408274334042 |  erot = 2.01427501035043 | epot = -23.2885684059727 | etot = -19.0002106522818
-534000  ekin = 2.54998010491125 |  erot = 2.0164545364507 | epot = -23.340767920006 | etot = -18.7743332786441
-535000  ekin = 2.49595662250557 |  erot = 2.09586427439366 | epot = -23.3878755759449 | etot = -18.7960546790457
-536000  ekin = 2.47717157546008 |  erot = 1.92116873587364 | epot = -23.3847675210095 | etot = -18.9864272096758
-537000  ekin = 1.75235621440219 |  erot = 2.11852052216092 | epot = -23.4590860280326 | etot = -19.5882092914695
-538000  ekin = 2.19317209186629 |  erot = 2.75191518419657 | epot = -23.5517834707225 | etot = -18.6066961946597
-539000  ekin = 2.16135327665114 |  erot = 2.25935011393788 | epot = -23.5718250119029 | etot = -19.1511216213139
-540000  ekin = 2.35701554620647 |  erot = 1.6449529057333 | epot = -23.5490867129451 | etot = -19.5471182610054
-541000  ekin = 2.61451212811978 |  erot = 2.52550284426682 | epot = -23.5334576350385 | etot = -18.3934426626519
-542000  ekin = 2.78909215024063 |  erot = 2.09346850400965 | epot = -23.5754619290989 | etot = -18.6929012748486
-543000  ekin = 2.77024528778678 |  erot = 1.84116991183092 | epot = -23.4849560716084 | etot = -18.8735408719907
-544000  ekin = 2.15807529188369 |  erot = 1.50139575300257 | epot = -23.4530822422947 | etot = -19.7936111974084
-545000  ekin = 1.72860204886329 |  erot = 2.56468335549414 | epot = -23.4524953434144 | etot = -19.159209939057
-546000  ekin = 2.38494138419348 |  erot = 1.87772638427254 | epot = -23.4950389557033 | etot = -19.2323711872372
-547000  ekin = 2.44871634556835 |  erot = 2.44464466893214 | epot = -23.544915775382 | etot = -18.6515547608815
-548000  ekin = 2.36962922994878 |  erot = 2.40235228488721 | epot = -23.5548428056052 | etot = -18.7828612907692
-549000  ekin = 2.57958168249614 |  erot = 2.04930779813674 | epot = -23.5565149978683 | etot = -18.9276255172355
-550000  ekin = 1.9793136647427 |  erot = 1.85207468704394 | epot = -23.5614067919063 | etot = -19.7300184401196
-551000  ekin = 2.4121774327081 |  erot = 2.0348936886299 | epot = -23.5115216908382 | etot = -19.0644505695002
-552000  ekin = 2.6621149390197 |  erot = 1.41279265378133 | epot = -23.3450678435402 | etot = -19.2701602507391
-553000  ekin = 1.76359346131444 |  erot = 2.63019210822711 | epot = -23.1435570943958 | etot = -18.7497715248542
-554000  ekin = 2.29840754300073 |  erot = 2.34424452982823 | epot = -23.1114395278817 | etot = -18.4687874550527
-555000  ekin = 3.29672420152566 |  erot = 1.64146930698359 | epot = -23.0891292168918 | etot = -18.1509357083825
-556000  ekin = 2.92076699655596 |  erot = 2.59602967895818 | epot = -23.0268314200472 | etot = -17.5100347445331
-557000  ekin = 2.90322014804994 |  erot = 3.16052668894921 | epot = -23.0146480567181 | etot = -16.950901219719
-558000  ekin = 2.78018761002222 |  erot = 2.59826947006759 | epot = -22.7877399275349 | etot = -17.4092828474451
-559000  ekin = 2.48661596771862 |  erot = 3.22596665511856 | epot = -22.8226574327834 | etot = -17.1100748099462
-560000  ekin = 2.34942852601698 |  erot = 2.32773162877396 | epot = -22.8255608134696 | etot = -18.1484006586786
-561000  ekin = 2.0520192544917 |  erot = 2.90306975046936 | epot = -22.8488516051139 | etot = -17.8937626001529
-562000  ekin = 2.18821919117372 |  erot = 3.66499439159819 | epot = -22.7618817506902 | etot = -16.9086681679183
-563000  ekin = 3.11505518852414 |  erot = 2.28057725990564 | epot = -22.791430640287 | etot = -17.3957981918572
-564000  ekin = 2.45343120006931 |  erot = 2.36321638506708 | epot = -22.75807077839 | etot = -17.9414231932536
-565000  ekin = 2.77835835502221 |  erot = 2.07073547186409 | epot = -22.7486053888412 | etot = -17.8995115619549
-566000  ekin = 2.43655641927934 |  erot = 2.19832280178868 | epot = -22.7227654505166 | etot = -18.0878862294486
-567000  ekin = 2.71233133108494 |  erot = 2.01281091173405 | epot = -22.8839744455115 | etot = -18.1588322026925
-568000  ekin = 3.12450796157708 |  erot = 1.93520150351061 | epot = -22.9625972279254 | etot = -17.9028877628377
-569000  ekin = 3.72714267701977 |  erot = 2.06562452789051 | epot = -22.9814174117752 | etot = -17.1886502068649
-570000  ekin = 2.68808623045676 |  erot = 2.36042122391805 | epot = -22.998959026692 | etot = -17.9504515723172
-571000  ekin = 1.97223467321356 |  erot = 2.85558181274648 | epot = -22.9369001315648 | etot = -18.1090836456047
-572000  ekin = 2.4182049732123 |  erot = 2.40910077907643 | epot = -22.934930836907 | etot = -18.1076250846182
-573000  ekin = 1.76702714285012 |  erot = 2.31739567602694 | epot = -22.9768902017483 | etot = -18.8924673828712
-574000  ekin = 2.08740259214111 |  erot = 2.59288012722136 | epot = -23.0518321557917 | etot = -18.3715494364293
-575000  ekin = 2.34020490338786 |  erot = 2.78500973557001 | epot = -23.106579446946 | etot = -17.9813648079881
-576000  ekin = 2.15506609467459 |  erot = 3.3045287538029 | epot = -23.1521162771299 | etot = -17.6925214286524
-577000  ekin = 2.45698150895878 |  erot = 2.31876672704204 | epot = -23.1781917242715 | etot = -18.4024434882707
-578000  ekin = 2.59353106592521 |  erot = 2.33790294336519 | epot = -23.2101395643707 | etot = -18.2787055550803
-579000  ekin = 2.58102015460712 |  erot = 1.71748063175117 | epot = -23.1865014452815 | etot = -18.8880006589232
-580000  ekin = 2.30361750578347 |  erot = 2.87410564379621 | epot = -23.2045008793077 | etot = -18.026777729728
-581000  ekin = 2.45915247103344 |  erot = 2.59640238490727 | epot = -23.1882783600354 | etot = -18.1327235040947
-582000  ekin = 2.33801590725494 |  erot = 3.19256035650617 | epot = -23.2501410058056 | etot = -17.7195647420445
-583000  ekin = 1.95982078382855 |  erot = 2.81944051586213 | epot = -23.4085593869414 | etot = -18.6292980872508
-584000  ekin = 2.00358327245437 |  erot = 1.7126727026301 | epot = -23.4960310960901 | etot = -19.7797751210056
-585000  ekin = 2.28859150562676 |  erot = 2.06309046911262 | epot = -23.5306230166998 | etot = -19.1789410419604
-586000  ekin = 2.21858454582016 |  erot = 1.97776854350186 | epot = -23.4873397268816 | etot = -19.2909866375596
-587000  ekin = 3.70065233550663 |  erot = 1.82187748311298 | epot = -23.4652388428899 | etot = -17.9427090242702
-588000  ekin = 3.49447328534893 |  erot = 2.31981981591506 | epot = -23.3985567739262 | etot = -17.5842636726622
-589000  ekin = 2.66144502802388 |  erot = 3.02756546370717 | epot = -23.2783756079917 | etot = -17.5893651162607
-590000  ekin = 1.52141257336428 |  erot = 2.09874614600563 | epot = -23.1290158071881 | etot = -19.5088570878182
-591000  ekin = 1.82897193042274 |  erot = 1.75592223095374 | epot = -23.0622736076073 | etot = -19.4773794462309
-592000  ekin = 2.49491276892191 |  erot = 2.5482988197852 | epot = -23.054885494985 | etot = -18.0116739062779
-593000  ekin = 2.36845716276159 |  erot = 1.78503341410575 | epot = -23.005264310194 | etot = -18.8517737333267
-594000  ekin = 2.07907010887474 |  erot = 2.14563658430187 | epot = -22.9611396232755 | etot = -18.7364329300989
-595000  ekin = 2.62736231723874 |  erot = 2.0397582574453 | epot = -22.9495489717352 | etot = -18.2824283970512
-596000  ekin = 2.58985967531625 |  erot = 2.12449830164849 | epot = -22.9908505579803 | etot = -18.2764925810155
-597000  ekin = 3.02540042664856 |  erot = 3.14256707367048 | epot = -22.9740991012936 | etot = -16.8061316009746
-598000  ekin = 3.44397104083287 |  erot = 2.8605790839857 | epot = -23.0035411551228 | etot = -16.6989910303042
-599000  ekin = 2.13932500926498 |  erot = 3.49187029024979 | epot = -22.9657391359988 | etot = -17.334543836484
-600000  ekin = 2.19758597945326 |  erot = 2.49610822362376 | epot = -22.9452235009931 | etot = -18.2515292979161
-601000  ekin = 2.80918982916752 |  erot = 2.81768433603376 | epot = -22.8970508934525 | etot = -17.2701767282513
-602000  ekin = 2.30031523379463 |  erot = 2.40907304500534 | epot = -22.8523950981499 | etot = -18.1430068193499
-603000  ekin = 1.91335501396421 |  erot = 1.99518053980753 | epot = -22.7884152302358 | etot = -18.879879676464
-604000  ekin = 2.5976715095492 |  erot = 3.14351403383687 | epot = -22.7430641975849 | etot = -17.0018786541988
-605000  ekin = 2.63203298717972 |  erot = 2.07906613894389 | epot = -22.7307949909783 | etot = -18.0196958648547
-606000  ekin = 2.94678399289781 |  erot = 2.03982213630799 | epot = -22.6555302524726 | etot = -17.6689241232668
-607000  ekin = 2.85272606479019 |  erot = 2.36693467257681 | epot = -22.6318548820144 | etot = -17.4121941446474
-608000  ekin = 3.6642968125636 |  erot = 2.46706737589234 | epot = -22.5724662590778 | etot = -16.4411020706219
-609000  ekin = 2.69343886620625 |  erot = 2.25873504143679 | epot = -22.6007364465805 | etot = -17.6485625389374
-610000  ekin = 2.99904616523658 |  erot = 2.13621966615343 | epot = -22.5973658485054 | etot = -17.4621000171154
-611000  ekin = 3.86832985948944 |  erot = 2.12096644577641 | epot = -22.5702925425382 | etot = -16.5809962372724
-612000  ekin = 2.88515301824618 |  erot = 2.45910554524357 | epot = -22.4848584522585 | etot = -17.1405998887688
-613000  ekin = 2.9367425327116 |  erot = 2.14436169371533 | epot = -22.465526703267 | etot = -17.3844224768401
-614000  ekin = 2.79116462876301 |  erot = 2.024409539648 | epot = -22.5207406301148 | etot = -17.7051664617038
-615000  ekin = 2.29338048298908 |  erot = 2.38828872470982 | epot = -22.6082782403584 | etot = -17.9266090326595
-616000  ekin = 1.78195169789474 |  erot = 2.45334803626968 | epot = -22.6887534547644 | etot = -18.4534537206
-617000  ekin = 2.57505808534158 |  erot = 2.55345758187858 | epot = -22.701463839496 | etot = -17.5729481722758
-618000  ekin = 2.29561379442387 |  erot = 2.68043259355499 | epot = -22.629958627306 | etot = -17.6539122393272
-619000  ekin = 1.94323313590202 |  erot = 2.00964911157699 | epot = -22.56819110474 | etot = -18.6153088572609
-620000  ekin = 2.92263589097657 |  erot = 2.15657756066215 | epot = -22.6264664894927 | etot = -17.547253037854
-621000  ekin = 2.90437881656455 |  erot = 1.70649555848315 | epot = -22.665419447573 | etot = -18.0545450725253
-622000  ekin = 2.03426149564846 |  erot = 2.51826459248401 | epot = -22.6086250578043 | etot = -18.0560989696718
-623000  ekin = 1.98348786592096 |  erot = 3.08484972830227 | epot = -22.6234743341759 | etot = -17.5551367399527
-624000  ekin = 2.08463083558977 |  erot = 2.64004606903047 | epot = -22.6266529328942 | etot = -17.901976028274
-625000  ekin = 2.52963490334089 |  erot = 2.37033264022622 | epot = -22.6750436783156 | etot = -17.7750761347485
-626000  ekin = 2.73147680333726 |  erot = 2.07051651598004 | epot = -22.7272383647964 | etot = -17.9252450454791
-627000  ekin = 2.23447399123207 |  erot = 2.35288557052269 | epot = -22.7136740507756 | etot = -18.1263144890208
-628000  ekin = 2.28933754695897 |  erot = 2.29676268895054 | epot = -22.6176528573237 | etot = -18.0315526214142
-629000  ekin = 2.5355466362136 |  erot = 1.92082543033528 | epot = -22.5693331526924 | etot = -18.1129610861435
-630000  ekin = 3.11700824717166 |  erot = 2.51611049765935 | epot = -22.5144695759915 | etot = -16.8813508311605
-631000  ekin = 2.38844807455604 |  erot = 3.31601650504458 | epot = -22.5190998334878 | etot = -16.8146352538871
-632000  ekin = 2.59939587493746 |  erot = 2.51496212358955 | epot = -22.4711049664696 | etot = -17.3567469679426
-633000  ekin = 2.45338619933597 |  erot = 1.89874016257143 | epot = -22.4394257686937 | etot = -18.0872994067863
-634000  ekin = 2.23819111967047 |  erot = 1.98305652730466 | epot = -22.3433365860708 | etot = -18.1220889390957
-635000  ekin = 2.22438000857702 |  erot = 1.95893208021227 | epot = -22.2877959440852 | etot = -18.1044838552959
-636000  ekin = 2.26938644192167 |  erot = 2.77816773779856 | epot = -22.304696935737 | etot = -17.2571427560168
-637000  ekin = 1.97799147515645 |  erot = 2.59610837639352 | epot = -22.3353238115758 | etot = -17.7612239600258
-638000  ekin = 2.54901279963355 |  erot = 3.14232301833368 | epot = -22.3113570318407 | etot = -16.6200212138734
-639000  ekin = 2.38194254982011 |  erot = 2.49468098011844 | epot = -22.2696251856514 | etot = -17.3930016557128
-640000  ekin = 2.07438054408915 |  erot = 2.20336226777045 | epot = -22.1673693230788 | etot = -17.8896265112192
-641000  ekin = 2.49150296422893 |  erot = 3.53882164550033 | epot = -22.047323387435 | etot = -16.0169987777057
-642000  ekin = 3.37964058409635 |  erot = 2.18458831029801 | epot = -21.9324522713976 | etot = -16.3682233770032
-643000  ekin = 2.80862431007863 |  erot = 2.40815089193716 | epot = -21.8726014240441 | etot = -16.6558262220283
-644000  ekin = 2.952235016065 |  erot = 1.92776262379328 | epot = -21.826057423183 | etot = -16.9460597833247
-645000  ekin = 4.10488984334312 |  erot = 1.89062109330214 | epot = -21.7981661301139 | etot = -15.8026551934687
-646000  ekin = 2.50234872105284 |  erot = 2.00205075040523 | epot = -21.7221642434957 | etot = -17.2177647720377
-647000  ekin = 2.52267281239589 |  erot = 2.19481558810105 | epot = -21.7438885460027 | etot = -17.0264001455058
-648000  ekin = 2.99344241657584 |  erot = 2.11139263207284 | epot = -21.7373240000025 | etot = -16.6324889513538
-649000  ekin = 2.55027365085816 |  erot = 3.20350991793738 | epot = -21.7192481424448 | etot = -15.9654645736493
-650000  ekin = 3.75163896052813 |  erot = 2.44189212282279 | epot = -21.6756681314987 | etot = -15.4821370481478
-651000  ekin = 3.29740056237165 |  erot = 2.36780448747275 | epot = -21.5372361691658 | etot = -15.8720311193214
-652000  ekin = 2.54645886055823 |  erot = 2.99097829596978 | epot = -21.4549655298412 | etot = -15.9175283733132
-653000  ekin = 2.88682688109756 |  erot = 2.53633970608342 | epot = -21.4696471597398 | etot = -16.0464805725588
-654000  ekin = 2.28614085804932 |  erot = 2.12026601708473 | epot = -21.5642684321318 | etot = -17.1578615569978
-655000  ekin = 2.20709609517087 |  erot = 2.10729950549551 | epot = -21.5349466292622 | etot = -17.2205510285959
-656000  ekin = 2.40310876229413 |  erot = 2.09663823500903 | epot = -21.5631924595209 | etot = -17.0634454622178
-657000  ekin = 2.7886551346751 |  erot = 2.19608839827219 | epot = -21.794507747247 | etot = -16.8097642142998
-658000  ekin = 3.1025713807162 |  erot = 2.59154293692773 | epot = -21.96675599421 | etot = -16.2726416765661
-659000  ekin = 2.88891106020275 |  erot = 3.47010878893494 | epot = -22.0542552611187 | etot = -15.695235411981
-660000  ekin = 2.90074521854052 |  erot = 1.62850743298554 | epot = -22.1003034196589 | etot = -17.5710507681328
-661000  ekin = 3.26666543815737 |  erot = 1.86223225384175 | epot = -22.202664217118 | etot = -17.0737665251189
-662000  ekin = 3.1558491019044 |  erot = 2.16868634291728 | epot = -22.3049478747805 | etot = -16.9804124299588
-663000  ekin = 1.94349853674083 |  erot = 2.45687952722591 | epot = -22.3908978754178 | etot = -17.990519811451
-664000  ekin = 1.45445820960401 |  erot = 1.37641815749115 | epot = -22.5088813854798 | etot = -19.6780050183846
-665000  ekin = 1.57568561901953 |  erot = 2.30379312359823 | epot = -22.5957949572927 | etot = -18.7163162146749
-666000  ekin = 2.46162449261636 |  erot = 1.76978614573263 | epot = -22.7431602236664 | etot = -18.5117495853174
-667000  ekin = 2.82410423268351 |  erot = 2.3383666365949 | epot = -22.9350563238978 | etot = -17.7725854546194
-668000  ekin = 2.73717686116191 |  erot = 3.18779777915035 | epot = -23.0188768131827 | etot = -17.0939021728704
-669000  ekin = 3.41035672635339 |  erot = 2.45479601777612 | epot = -23.0718232403886 | etot = -17.2066704962591
-670000  ekin = 2.54649164859505 |  erot = 1.99520979169172 | epot = -23.0246775830826 | etot = -18.4829761427959
-671000  ekin = 2.3802025684166 |  erot = 3.00742736998541 | epot = -23.0023479116088 | etot = -17.6147179732068
-672000  ekin = 3.0126952152146 |  erot = 2.55297219144565 | epot = -22.9947723733502 | etot = -17.4291049666899
-673000  ekin = 3.39486270740071 |  erot = 2.3808700262033 | epot = -22.9033457919095 | etot = -17.1276130583054
-674000  ekin = 3.13698489626099 |  erot = 2.10609113054063 | epot = -22.8089270617647 | etot = -17.5658510349631
-675000  ekin = 2.32294130821675 |  erot = 1.5285851482073 | epot = -22.6840603385672 | etot = -18.8325338821432
-676000  ekin = 2.43564726401376 |  erot = 2.26860623636408 | epot = -22.6133446272028 | etot = -17.909091126825
-677000  ekin = 2.75162757613842 |  erot = 1.94219014743457 | epot = -22.7039380847023 | etot = -18.0101203611293
-678000  ekin = 2.86321973687601 |  erot = 1.66387788364136 | epot = -22.7223510604726 | etot = -18.1952534399553
-679000  ekin = 2.35079208772869 |  erot = 2.70386328048641 | epot = -22.7977445343495 | etot = -17.7430891661344
-680000  ekin = 2.48449675729004 |  erot = 2.90645575582477 | epot = -22.8559375688936 | etot = -17.4649850557788
-681000  ekin = 1.91581136662333 |  erot = 2.58179603882022 | epot = -22.7891325966099 | etot = -18.2915251911664
-682000  ekin = 2.10466427353705 |  erot = 2.69470735868807 | epot = -22.6959043279182 | etot = -17.896532695693
-683000  ekin = 2.34504535409021 |  erot = 2.11592035700791 | epot = -22.5718670441909 | etot = -18.1109013330928
-684000  ekin = 2.87198876498958 |  erot = 2.65732173958706 | epot = -22.4986977268025 | etot = -16.9693872222258
-685000  ekin = 3.03375238110975 |  erot = 2.18190577381518 | epot = -22.4634189289575 | etot = -17.2477607740326
-686000  ekin = 2.46248931777656 |  erot = 2.43025710170918 | epot = -22.4079029677658 | etot = -17.5151565482801
-687000  ekin = 2.74662486817896 |  erot = 1.79609152562411 | epot = -22.3360381567114 | etot = -17.7933217629083
-688000  ekin = 1.81703718003042 |  erot = 2.06511603415635 | epot = -22.3083758541198 | etot = -18.426222639933
-689000  ekin = 2.84202633430564 |  erot = 1.92033962884777 | epot = -22.3752571185822 | etot = -17.6128911554288
-690000  ekin = 2.07525448405017 |  erot = 2.46342632176817 | epot = -22.4633535431152 | etot = -17.9246727372969
-691000  ekin = 2.12558517800138 |  erot = 2.52961097164 | epot = -22.483426266766 | etot = -17.8282301171246
-692000  ekin = 2.86720433292881 |  erot = 2.65102150657025 | epot = -22.4003374064863 | etot = -16.8821115669873
-693000  ekin = 2.30143055084864 |  erot = 2.52290946383361 | epot = -22.2859681228792 | etot = -17.4616281081969
-694000  ekin = 2.88400701080875 |  erot = 2.34320802755437 | epot = -22.206318584282 | etot = -16.9791035459189
-695000  ekin = 2.93184722112895 |  erot = 2.22933507376834 | epot = -22.2348177906806 | etot = -17.0736354957833
-696000  ekin = 2.63173546326796 |  erot = 2.34275369570833 | epot = -22.274597219839 | etot = -17.3001080608627
-697000  ekin = 1.87084079501972 |  erot = 1.78050094908734 | epot = -22.2730387150935 | etot = -18.6216969709865
-698000  ekin = 2.19791428580687 |  erot = 2.82883581756349 | epot = -22.2819378523405 | etot = -17.2551877489701
-699000  ekin = 2.34279295545267 |  erot = 2.07514436344563 | epot = -22.2061425261575 | etot = -17.7882052072592
-700000  ekin = 2.576803119019 |  erot = 2.32167543064962 | epot = -22.1658685747825 | etot = -17.2673900251139
-701000  ekin = 2.9943865807539 |  erot = 1.89982533986206 | epot = -22.2191193266439 | etot = -17.324907406028
-702000  ekin = 2.68548464757459 |  erot = 2.65050744453208 | epot = -22.2547415922757 | etot = -16.918749500169
-703000  ekin = 2.01996957402024 |  erot = 2.04032822241737 | epot = -22.3253693056515 | etot = -18.2650715092139
-704000  ekin = 1.58871069317829 |  erot = 1.64014270467762 | epot = -22.3617232281452 | etot = -19.1328698302893
-705000  ekin = 2.3089415754982 |  erot = 1.90252913035993 | epot = -22.4307958564623 | etot = -18.2193251506042
-706000  ekin = 2.61729186445574 |  erot = 3.21879868039103 | epot = -22.5603358780911 | etot = -16.7242453332443
-707000  ekin = 2.60797107906866 |  erot = 2.31455039977396 | epot = -22.7102471053997 | etot = -17.7877256265571
-708000  ekin = 1.81633850341999 |  erot = 2.3482257566942 | epot = -22.841408787855 | etot = -18.6768445277408
-709000  ekin = 1.83541322105378 |  erot = 2.51792380003796 | epot = -23.0137235815795 | etot = -18.6603865604878
-710000  ekin = 2.2142058326246 |  erot = 1.92378721690473 | epot = -23.1433453130909 | etot = -19.0053522635615
-711000  ekin = 2.06744054454467 |  erot = 2.3981170935319 | epot = -23.1532717948855 | etot = -18.687714156809
-712000  ekin = 2.1727947270635 |  erot = 1.75362175342097 | epot = -23.0479262273955 | etot = -19.121509746911
-713000  ekin = 2.87118830138474 |  erot = 1.54943993787555 | epot = -22.8430575230906 | etot = -18.4224292838303
-714000  ekin = 2.0107946674397 |  erot = 1.87510988392751 | epot = -22.9212969433221 | etot = -19.0353923919549
-715000  ekin = 2.4992182958927 |  erot = 1.91934008289236 | epot = -22.9679126658062 | etot = -18.5493542870211
-716000  ekin = 2.94666510633353 |  erot = 2.18714442405523 | epot = -23.033997097429 | etot = -17.9001875670402
-717000  ekin = 3.07404079722085 |  erot = 2.46628262765133 | epot = -23.1869721551174 | etot = -17.6466487302452
-718000  ekin = 3.47060078371109 |  erot = 2.28206620506093 | epot = -23.2524492340768 | etot = -17.4997822453048
-719000  ekin = 4.08343792096552 |  erot = 3.10429377075217 | epot = -23.2448292181926 | etot = -16.0570975264749
-720000  ekin = 2.52774819763971 |  erot = 1.92867508904585 | epot = -23.1435084559682 | etot = -18.6870851692826
-721000  ekin = 2.58294244811584 |  erot = 2.0383053178033 | epot = -23.0601633758883 | etot = -18.4389156099691
-722000  ekin = 1.9445888545086 |  erot = 2.32008660802523 | epot = -22.9811929404572 | etot = -18.7165174779234
-723000  ekin = 2.41998340576259 |  erot = 2.12369728979369 | epot = -23.0570939793876 | etot = -18.5134132838314
-724000  ekin = 1.90406371300861 |  erot = 1.97533505769876 | epot = -23.1267629042383 | etot = -19.247364133531
-725000  ekin = 2.14287056473422 |  erot = 2.79289687450022 | epot = -23.1695632046138 | etot = -18.2337957653794
-726000  ekin = 2.26423317099721 |  erot = 2.55343019202652 | epot = -23.2432909083709 | etot = -18.4256275453472
-727000  ekin = 1.69816397656716 |  erot = 2.64011919415556 | epot = -23.298837689321 | etot = -18.9605545185982
-728000  ekin = 2.23000862561934 |  erot = 3.58521470578671 | epot = -23.3528245832467 | etot = -17.5376012518407
-729000  ekin = 2.70076566380343 |  erot = 1.73367306410751 | epot = -23.3971276122796 | etot = -18.9626888843686
-730000  ekin = 2.54818673802759 |  erot = 2.77394958410256 | epot = -23.3988686964744 | etot = -18.0767323743443
-731000  ekin = 2.69782550956093 |  erot = 2.04855826523075 | epot = -23.4310969813891 | etot = -18.6847132065974
-732000  ekin = 2.79613002753752 |  erot = 1.87867430486715 | epot = -23.4885161441653 | etot = -18.8137118117607
-733000  ekin = 2.20346728125046 |  erot = 2.64365594749975 | epot = -23.5261309431819 | etot = -18.6790077144317
-734000  ekin = 1.69780111261443 |  erot = 2.30917909560787 | epot = -23.5188046470475 | etot = -19.5118244388252
-735000  ekin = 2.18402736165936 |  erot = 2.72051620230871 | epot = -23.4712689506938 | etot = -18.5667253867257
-736000  ekin = 2.26138696009404 |  erot = 1.17083930058803 | epot = -23.4348107178754 | etot = -20.0025844571934
-737000  ekin = 2.22219419044796 |  erot = 3.14114682990362 | epot = -23.3869288757725 | etot = -18.0235878554209
-738000  ekin = 1.75464981631084 |  erot = 2.28485941478058 | epot = -23.2709893028052 | etot = -19.2314800717138
-739000  ekin = 1.41806378584362 |  erot = 2.16714034112821 | epot = -23.2213775300889 | etot = -19.636173403117
-740000  ekin = 1.90901017596351 |  erot = 2.27102763422491 | epot = -23.1829198366046 | etot = -19.0028820264162
-741000  ekin = 1.9930994487751 |  erot = 2.73523269523399 | epot = -23.1169670577824 | etot = -18.3886349137733
-742000  ekin = 1.99876411117685 |  erot = 1.89882876917754 | epot = -23.0300825800851 | etot = -19.1324896997307
-743000  ekin = 1.96472814667687 |  erot = 2.79504722629174 | epot = -22.8990488521609 | etot = -18.1392734791923
-744000  ekin = 2.02442646092311 |  erot = 2.35044838626024 | epot = -22.8186526150799 | etot = -18.4437777678966
-745000  ekin = 1.65344231988822 |  erot = 1.87919095141018 | epot = -22.7624827109091 | etot = -19.2298494396107
-746000  ekin = 2.1034668185472 |  erot = 2.03078530569663 | epot = -22.743454277698 | etot = -18.6092021534542
-747000  ekin = 3.06690414848489 |  erot = 1.6754029786949 | epot = -22.7625979159322 | etot = -18.0202907887524
-748000  ekin = 3.06965414483401 |  erot = 1.86014593098643 | epot = -22.8118567150739 | etot = -17.8820566392535
-749000  ekin = 2.53718696167217 |  erot = 2.02710579059033 | epot = -22.8431046011969 | etot = -18.2788118489344
-750000  ekin = 2.75657354808099 |  erot = 2.34953156046291 | epot = -22.9548205390759 | etot = -17.848715430532
-751000  ekin = 2.52290020835147 |  erot = 2.34873763599977 | epot = -23.0238691402084 | etot = -18.1522312958572
-752000  ekin = 2.47222247869325 |  erot = 1.68679846444683 | epot = -22.9958559112491 | etot = -18.8368349681091
-753000  ekin = 2.48263277172423 |  erot = 1.54669382815742 | epot = -23.0858212396418 | etot = -19.0564946397602
-754000  ekin = 2.54806257410878 |  erot = 2.26636466676163 | epot = -23.1896472696842 | etot = -18.3752200288138
-755000  ekin = 1.53168409517921 |  erot = 2.22665478278013 | epot = -23.2059118234918 | etot = -19.4475729455324
-756000  ekin = 2.10751715527953 |  erot = 2.40525774326678 | epot = -23.114150245375 | etot = -18.6013753468287
-757000  ekin = 2.93395895491028 |  erot = 2.05821177584909 | epot = -23.0783355599275 | etot = -18.0861648291682
-758000  ekin = 2.38307945406232 |  erot = 2.50598165375058 | epot = -22.9691152621287 | etot = -18.0800541543158
-759000  ekin = 2.60292884338835 |  erot = 2.36916677072548 | epot = -22.7987274767845 | etot = -17.8266318626707
-760000  ekin = 3.2284318196987 |  erot = 2.73822716520638 | epot = -22.6756147646272 | etot = -16.7089557797221
-761000  ekin = 3.41868727786494 |  erot = 1.68975765213408 | epot = -22.5638952547581 | etot = -17.4554503247591
-762000  ekin = 3.43033946346107 |  erot = 2.5283975140253 | epot = -22.3549032489322 | etot = -16.3961662714458
-763000  ekin = 2.65773094814485 |  erot = 1.83975133975562 | epot = -22.234833339183 | etot = -17.7373510512825
-764000  ekin = 2.3815484472129 |  erot = 2.70684992442147 | epot = -22.0890752688231 | etot = -17.0006768971887
-765000  ekin = 2.23212803588897 |  erot = 1.94868597739427 | epot = -21.9918715237933 | etot = -17.81105751051
-766000  ekin = 2.49097891886066 |  erot = 1.96764603993156 | epot = -21.8443436680801 | etot = -17.3857187092879
-767000  ekin = 2.3457921497675 |  erot = 2.64636009163513 | epot = -21.7634962034012 | etot = -16.7713439619986
-768000  ekin = 1.87671147825106 |  erot = 2.05549869178485 | epot = -21.7324638416528 | etot = -17.8002536716169
-769000  ekin = 3.05058687860239 |  erot = 2.66104171022372 | epot = -21.66792195987 | etot = -15.9562933710439
-770000  ekin = 2.44115683640633 |  erot = 1.97554932479751 | epot = -21.6448820664751 | etot = -17.2281759052712
-771000  ekin = 2.23687464004429 |  erot = 2.55040970708789 | epot = -21.5811924169692 | etot = -16.793908069837
-772000  ekin = 2.76529680592008 |  erot = 1.97873499811185 | epot = -21.6543448952384 | etot = -16.9103130912064
-773000  ekin = 2.14632888240094 |  erot = 2.41330587525514 | epot = -21.7728828090228 | etot = -17.2132480513667
-774000  ekin = 2.19848545803079 |  erot = 1.9765131024719 | epot = -21.8398858604883 | etot = -17.6648872999856
-775000  ekin = 2.52300137989083 |  erot = 2.80935365273515 | epot = -22.0219985274259 | etot = -16.6896434947999
-776000  ekin = 3.15842485269274 |  erot = 2.47066157093645 | epot = -22.183029096161 | etot = -16.5539426725319
-777000  ekin = 1.91784338934576 |  erot = 1.76045300517081 | epot = -22.2259652888115 | etot = -18.547668894295
-778000  ekin = 2.93738066043324 |  erot = 2.29457842490289 | epot = -22.2339481852394 | etot = -17.0019890999032
-779000  ekin = 3.09847206114319 |  erot = 2.0455771700605 | epot = -22.240438366259 | etot = -17.0963891350553
-780000  ekin = 2.86127568397807 |  erot = 3.12055135138658 | epot = -22.1865692766137 | etot = -16.204742241249
-781000  ekin = 2.36069914420785 |  erot = 3.53186431088487 | epot = -22.1210563364352 | etot = -16.2284928813425
-782000  ekin = 2.31592690319261 |  erot = 2.85730598644035 | epot = -22.0302855151548 | etot = -16.8570526255218
-783000  ekin = 1.86647729944746 |  erot = 3.03450246093099 | epot = -21.886014367949 | etot = -16.9850346075705
-784000  ekin = 2.04055627573201 |  erot = 2.26047908607293 | epot = -21.7534271639393 | etot = -17.4523918021343
-785000  ekin = 2.02248469828703 |  erot = 2.13950421850547 | epot = -21.6318967501918 | etot = -17.4699078333993
-786000  ekin = 2.34211746551602 |  erot = 2.34838133643265 | epot = -21.5890308210084 | etot = -16.8985320190598
-787000  ekin = 2.74971447554938 |  erot = 2.24123553296042 | epot = -21.5192132515563 | etot = -16.5282632430465
-788000  ekin = 2.14142056672039 |  erot = 2.27008574684965 | epot = -21.4982362621714 | etot = -17.0867299486013
-789000  ekin = 1.98580913341303 |  erot = 2.00702444041791 | epot = -21.5235331659838 | etot = -17.5306995921529
-790000  ekin = 1.68578263083924 |  erot = 1.43485602862151 | epot = -21.6440081593601 | etot = -18.5233694998993
-791000  ekin = 2.13583938840528 |  erot = 2.5373009545894 | epot = -21.7916440698418 | etot = -17.1185037268471
-792000  ekin = 1.71937483898028 |  erot = 2.19563804216011 | epot = -21.8794946709408 | etot = -17.9644817898004
-793000  ekin = 3.15868943755338 |  erot = 1.94575875708421 | epot = -22.0398145404617 | etot = -16.9353663458242
-794000  ekin = 2.45478602538954 |  erot = 3.00825554959563 | epot = -22.0843165283013 | etot = -16.6212749533161
-795000  ekin = 2.87760320917193 |  erot = 3.06920266633565 | epot = -22.1595628991904 | etot = -16.2127570236829
-796000  ekin = 2.29816690595058 |  erot = 1.61510864654315 | epot = -22.1869705548184 | etot = -18.2736950023247
-797000  ekin = 2.1901525606721 |  erot = 3.65734446008353 | epot = -22.1432608090644 | etot = -16.2957637883088
-798000  ekin = 2.12018787925578 |  erot = 2.92822258455555 | epot = -22.1311312789224 | etot = -17.0827208151111
-799000  ekin = 2.49416140154829 |  erot = 2.73328283280216 | epot = -22.0825726051882 | etot = -16.8551283708378
-800000  ekin = 2.18932007838552 |  erot = 2.97640731559393 | epot = -21.979362152191 | etot = -16.8136347582115
-801000  ekin = 2.58827112124838 |  erot = 2.7440442483726 | epot = -21.9108490336924 | etot = -16.5785336640714
-802000  ekin = 3.07870342348167 |  erot = 2.87961505564287 | epot = -21.822560433681 | etot = -15.8642419545565
-803000  ekin = 2.2398624368064 |  erot = 2.50525058807596 | epot = -21.72759408181 | etot = -16.9824810569277
-804000  ekin = 2.91885860068426 |  erot = 1.57889040451428 | epot = -21.6896376725624 | etot = -17.1918886673638
-805000  ekin = 2.68277363980193 |  erot = 3.05527868915738 | epot = -21.6710764398127 | etot = -15.9330241108534
-806000  ekin = 2.77769607049014 |  erot = 2.1888727690908 | epot = -21.6314833902337 | etot = -16.6649145506527
-807000  ekin = 2.12673239079668 |  erot = 2.86003407600806 | epot = -21.7295924017744 | etot = -16.7428259349697
-808000  ekin = 1.89599614774678 |  erot = 2.29237053227662 | epot = -21.7511361510417 | etot = -17.5627694710183
-809000  ekin = 1.96405066221971 |  erot = 1.92110393348368 | epot = -21.7075506883706 | etot = -17.8223960926672
-810000  ekin = 2.01518137594275 |  erot = 2.60119247286596 | epot = -21.6788385874729 | etot = -17.0624647386642
-811000  ekin = 2.31084800889289 |  erot = 1.75270367309064 | epot = -21.6837819033719 | etot = -17.6202302213883
-812000  ekin = 2.5770103100209 |  erot = 2.34932304073588 | epot = -21.7246716033188 | etot = -16.798338252562
-813000  ekin = 2.87706904926076 |  erot = 2.35686610624154 | epot = -21.8375922236049 | etot = -16.6036570681026
-814000  ekin = 2.89908405023866 |  erot = 2.31423299883226 | epot = -21.8379261473901 | etot = -16.6246090983192
-815000  ekin = 2.54050064212256 |  erot = 2.82732568868829 | epot = -21.6068952707049 | etot = -16.2390689398941
-816000  ekin = 2.17040404256387 |  erot = 2.53711088209172 | epot = -21.5560322071983 | etot = -16.8485172825427
-817000  ekin = 1.7842696071831 |  erot = 2.67810959410576 | epot = -21.8738878035325 | etot = -17.4115086022437
-818000  ekin = 2.29659398017838 |  erot = 2.63718862373664 | epot = -22.164277271391 | etot = -17.230494667476
-819000  ekin = 2.15801167884062 |  erot = 2.62095572928877 | epot = -22.1816109590116 | etot = -17.4026435508822
-820000  ekin = 1.94384548213955 |  erot = 2.28597987799275 | epot = -22.0986187375022 | etot = -17.8687933773699
-821000  ekin = 2.10513194007576 |  erot = 2.38698175569219 | epot = -22.1146754444785 | etot = -17.6225617487105
-822000  ekin = 2.24819716786441 |  erot = 2.15258805680875 | epot = -22.0539472940486 | etot = -17.6531620693754
-823000  ekin = 2.26584952085583 |  erot = 2.60619852526611 | epot = -22.0924201800579 | etot = -17.220372133936
-824000  ekin = 1.65187935478514 |  erot = 1.48703119037228 | epot = -22.1682955997986 | etot = -19.0293850546412
-825000  ekin = 1.60213094818648 |  erot = 1.98592524368393 | epot = -22.1687104063708 | etot = -18.5806542145004
-826000  ekin = 1.97430720107255 |  erot = 2.19175014677159 | epot = -22.1061881978655 | etot = -17.9401308500213
-827000  ekin = 2.1793755983405 |  erot = 2.44975419075935 | epot = -21.9704586607304 | etot = -17.3413288716305
-828000  ekin = 1.90399088418588 |  erot = 2.72532994798816 | epot = -21.9585923270583 | etot = -17.3292714948842
-829000  ekin = 2.06478103068884 |  erot = 2.9658303540259 | epot = -21.9849402038682 | etot = -16.9543288191534
-830000  ekin = 1.98920675238979 |  erot = 2.15331250444996 | epot = -22.0339146439702 | etot = -17.8913953871305
-831000  ekin = 2.33567462674689 |  erot = 2.36888807413497 | epot = -22.1271573756461 | etot = -17.4225946747643
-832000  ekin = 2.0119470999192 |  erot = 1.94769143293625 | epot = -22.2038482709588 | etot = -18.2442097381034
-833000  ekin = 2.26025933495881 |  erot = 2.16012558191462 | epot = -22.2882501045414 | etot = -17.867865187668
-834000  ekin = 2.11529426445865 |  erot = 1.52405523315358 | epot = -22.3075608649826 | etot = -18.6682113673703
-835000  ekin = 2.8992075090551 |  erot = 2.73801081751029 | epot = -22.3942491248321 | etot = -16.7570307982667
-836000  ekin = 3.33069528982658 |  erot = 2.4277126780786 | epot = -22.4321737300744 | etot = -16.6737657621692
-837000  ekin = 2.74831774333782 |  erot = 2.31991750378628 | epot = -22.4290234552872 | etot = -17.3607882081631
-838000  ekin = 3.13714871682188 |  erot = 3.21601751721777 | epot = -22.4642383906451 | etot = -16.1110721566054
-839000  ekin = 2.73358272751807 |  erot = 2.60144488190506 | epot = -22.4062682687368 | etot = -17.0712406593137
-840000  ekin = 2.96121930874637 |  erot = 1.42725942278118 | epot = -22.3293755621294 | etot = -17.9408968306018
-841000  ekin = 2.95134811170866 |  erot = 2.67666861874608 | epot = -22.2936348151224 | etot = -16.6656180846677
-842000  ekin = 2.15783928636401 |  erot = 2.30287195796693 | epot = -22.2978011147172 | etot = -17.8370898703863
-843000  ekin = 2.84565152669617 |  erot = 2.0510801477514 | epot = -22.3162908719779 | etot = -17.4195591975303
-844000  ekin = 2.99645803669157 |  erot = 1.50433298006521 | epot = -22.3768320579304 | etot = -17.8760410411736
-845000  ekin = 3.20248025697125 |  erot = 2.27246140825564 | epot = -22.3985708422076 | etot = -16.9236291769807
-846000  ekin = 3.35773945734322 |  erot = 2.54074745551552 | epot = -22.4144833015876 | etot = -16.5159963887289
-847000  ekin = 2.17779203733109 |  erot = 2.73817581188461 | epot = -22.3524825149514 | etot = -17.4365146657357
-848000  ekin = 2.51627348417144 |  erot = 2.81170686694717 | epot = -22.2066307862469 | etot = -16.8786504351283
-849000  ekin = 1.99679455190557 |  erot = 2.56855846773092 | epot = -22.0763062134929 | etot = -17.5109531938564
-850000  ekin = 2.05799123916876 |  erot = 1.80888056240785 | epot = -22.0665032506706 | etot = -18.1996314490939
-851000  ekin = 2.0888979376792 |  erot = 1.86172181790289 | epot = -22.0629711763889 | etot = -18.1123514208068
-852000  ekin = 1.68990805178902 |  erot = 1.42763535981882 | epot = -22.002100112701 | etot = -18.8845567010931
-853000  ekin = 1.99310886654811 |  erot = 3.05226969048292 | epot = -22.0306903552278 | etot = -16.9853117981968
-854000  ekin = 2.98378700534986 |  erot = 2.2310274524054 | epot = -22.1115820238811 | etot = -16.8967675661258
-855000  ekin = 2.17087415585277 |  erot = 2.8378147226879 | epot = -22.1115106395971 | etot = -17.1028217610564
-856000  ekin = 2.42228475387308 |  erot = 1.53328604594478 | epot = -22.0841888628209 | etot = -18.128618063003
-857000  ekin = 2.50431566526894 |  erot = 2.80498769176516 | epot = -21.9881235267534 | etot = -16.6788201697193
-858000  ekin = 2.17333686672378 |  erot = 2.8259111550717 | epot = -21.9093201368614 | etot = -16.9100721150659
-859000  ekin = 2.29930070497243 |  erot = 2.32417368939061 | epot = -21.8849849636104 | etot = -17.2615105692473
-860000  ekin = 1.99153024057672 |  erot = 1.94674638600151 | epot = -21.8998709373217 | etot = -17.9615943107434
-861000  ekin = 2.69177523559624 |  erot = 2.23997750036373 | epot = -21.8915522194994 | etot = -16.9597994835394
-862000  ekin = 2.86117050047984 |  erot = 2.41530060322761 | epot = -21.876687883023 | etot = -16.6002167793156
-863000  ekin = 2.59841547044276 |  erot = 3.3501705008543 | epot = -21.8162649771437 | etot = -15.8676790058467
-864000  ekin = 2.92496272611018 |  erot = 2.30350236144453 | epot = -21.7820358973268 | etot = -16.5535708097721
-865000  ekin = 1.94718216128952 |  erot = 2.16572180916633 | epot = -21.7000823492195 | etot = -17.5871783787636
-866000  ekin = 1.99006127871689 |  erot = 1.65011901234952 | epot = -21.6190182409268 | etot = -17.9788379498604
-867000  ekin = 1.76250718110787 |  erot = 3.37958608370307 | epot = -21.5401486584561 | etot = -16.3980553936452
-868000  ekin = 1.845623450314 |  erot = 2.78812196028616 | epot = -21.5771917352235 | etot = -16.9434463246234
-869000  ekin = 2.39300849969205 |  erot = 2.38301618173176 | epot = -21.6710790825578 | etot = -16.895054401134
-870000  ekin = 1.91899243212541 |  erot = 3.22222440717393 | epot = -21.6734733803871 | etot = -16.5322565410878
-871000  ekin = 3.10255827845531 |  erot = 2.95454268850896 | epot = -21.5913249106744 | etot = -15.5342239437101
-872000  ekin = 2.94582883077842 |  erot = 1.38261935263093 | epot = -21.4597055547833 | etot = -17.1312573713739
-873000  ekin = 2.72830997927423 |  erot = 2.23223699637274 | epot = -21.3657566950046 | etot = -16.4052097193577
-874000  ekin = 2.41464704842015 |  erot = 2.10351476791496 | epot = -21.2635161734954 | etot = -16.7453543571603
-875000  ekin = 2.99468455803482 |  erot = 2.72761242382524 | epot = -21.2488881289381 | etot = -15.526591147078
-876000  ekin = 2.13382009818493 |  erot = 2.23152059294678 | epot = -21.2388603913311 | etot = -16.8735197001994
-877000  ekin = 1.839391763993 |  erot = 1.607279977226 | epot = -21.2015948102408 | etot = -17.7549230690218
-878000  ekin = 2.01267175782178 |  erot = 2.73109796378376 | epot = -21.2125253160263 | etot = -16.4687555944208
-879000  ekin = 1.42911941081343 |  erot = 2.17371661448622 | epot = -21.1345316334464 | etot = -17.5316956081468
-880000  ekin = 2.10605339224633 |  erot = 2.5884751778913 | epot = -21.0787246891645 | etot = -16.3841961190269
-881000  ekin = 1.54924791070118 |  erot = 2.0068513915418 | epot = -21.1356465207066 | etot = -17.5795472184637
-882000  ekin = 2.199643157135 |  erot = 2.65509097106007 | epot = -21.2389026935677 | etot = -16.3841685653726
-883000  ekin = 2.20850404171077 |  erot = 2.22833605977577 | epot = -21.3067394383395 | etot = -16.869899336853
-884000  ekin = 2.76978562647275 |  erot = 2.10395845939756 | epot = -21.3429618615585 | etot = -16.4692177756882
-885000  ekin = 1.93339807672781 |  erot = 1.77156241344967 | epot = -21.3858074096933 | etot = -17.6808469195158
-886000  ekin = 2.00408769971894 |  erot = 3.10736267931439 | epot = -21.3935346347812 | etot = -16.2820842557479
-887000  ekin = 1.96987943750801 |  erot = 2.82035886899744 | epot = -21.3967073105593 | etot = -16.6064690040538
-888000  ekin = 1.91464371566411 |  erot = 2.33371232948867 | epot = -21.4767119016419 | etot = -17.2283558564891
-889000  ekin = 1.88227414130201 |  erot = 2.45915914930408 | epot = -21.5790392436829 | etot = -17.2376059530768
-890000  ekin = 1.84515176532447 |  erot = 2.24992378831499 | epot = -21.6747594004542 | etot = -17.5796838468148
-891000  ekin = 2.6016566869706 |  erot = 2.34500453305753 | epot = -21.8016735536793 | etot = -16.8550123336512
-892000  ekin = 2.71287751886859 |  erot = 2.69544224573131 | epot = -21.9063749565585 | etot = -16.4980551919586
-893000  ekin = 2.17862714611329 |  erot = 2.98452123742221 | epot = -21.9155556335137 | etot = -16.7524072499782
-894000  ekin = 2.52079948361477 |  erot = 2.46355933674925 | epot = -21.915110079455 | etot = -16.930751259091
-895000  ekin = 2.53566097944338 |  erot = 2.4513045444294 | epot = -21.947786087834 | etot = -16.9608205639612
-896000  ekin = 1.84455393639213 |  erot = 2.77499090684945 | epot = -21.9167554809878 | etot = -17.2972106377463
-897000  ekin = 2.38519326880694 |  erot = 2.019802873173 | epot = -21.8644918203993 | etot = -17.4594956784193
-898000  ekin = 2.14354914407572 |  erot = 1.89196669459414 | epot = -21.7953104274974 | etot = -17.7597945888276
-899000  ekin = 2.65485657727374 |  erot = 2.3237456003819 | epot = -21.6964754705568 | etot = -16.7178732929012
-900000  ekin = 2.1437154528087 |  erot = 2.28119066740275 | epot = -21.6934954112434 | etot = -17.2685892910319
-901000  ekin = 1.93965814946881 |  erot = 1.81495571440908 | epot = -21.7369092433376 | etot = -17.9822953794597
-902000  ekin = 2.60993957981555 |  erot = 2.50321386623391 | epot = -21.6842517568354 | etot = -16.571098310786
-903000  ekin = 1.87484955546757 |  erot = 2.17008893987962 | epot = -21.6383913984978 | etot = -17.5934529031506
-904000  ekin = 1.87454064845764 |  erot = 2.32484081519398 | epot = -21.5866637125315 | etot = -17.3872822488799
-905000  ekin = 2.31407473814844 |  erot = 2.15094868542391 | epot = -21.5154415841816 | etot = -17.0504181606093
-906000  ekin = 2.49583383758853 |  erot = 2.25091096848461 | epot = -21.5170853902294 | etot = -16.7703405841563
-907000  ekin = 4.19798796104344 |  erot = 2.5030532322807 | epot = -21.5976736513859 | etot = -14.8966324580618
-908000  ekin = 3.26730891548756 |  erot = 2.11222217905481 | epot = -21.7526644402476 | etot = -16.3731333457052
-909000  ekin = 2.64106561110374 |  erot = 1.92197432194202 | epot = -21.8748043207924 | etot = -17.3117643877467
-910000  ekin = 2.61805562731904 |  erot = 2.90737422678703 | epot = -21.9709470207745 | etot = -16.4455171666685
-911000  ekin = 2.62012718860141 |  erot = 4.35318528241844 | epot = -22.0282478750366 | etot = -15.0549354040167
-912000  ekin = 3.07628909273118 |  erot = 3.69371809788395 | epot = -22.0511180009901 | etot = -15.281110810375
-913000  ekin = 2.82956898268831 |  erot = 2.17078429141201 | epot = -22.0149543706266 | etot = -17.0146010965263
-914000  ekin = 2.16386655780066 |  erot = 1.22303673036133 | epot = -21.9243495493208 | etot = -18.5374462611589
-915000  ekin = 1.59447095066509 |  erot = 2.95966391292002 | epot = -21.8264580452026 | etot = -17.2723231816175
-916000  ekin = 2.58365539107523 |  erot = 3.75147270955029 | epot = -21.8922962938608 | etot = -15.5571681932352
-917000  ekin = 3.01643029206973 |  erot = 2.88035639021004 | epot = -21.9150526568514 | etot = -16.0182659745717
-918000  ekin = 2.89929776900147 |  erot = 2.64137394041291 | epot = -21.9078998623094 | etot = -16.367228152895
-919000  ekin = 3.20476671865012 |  erot = 2.76036957969153 | epot = -21.8878055443404 | etot = -15.9226692459988
-920000  ekin = 2.28949350558683 |  erot = 2.38558870046816 | epot = -21.8659406759967 | etot = -17.1908584699418
-921000  ekin = 2.39158312157105 |  erot = 2.44959700788167 | epot = -21.8638974869225 | etot = -17.0227173574697
-922000  ekin = 2.30678787768012 |  erot = 2.42145678067298 | epot = -21.8218369909645 | etot = -17.0935923326114
-923000  ekin = 2.49697778842282 |  erot = 2.66565493744118 | epot = -21.8078634464733 | etot = -16.6452307206093
-924000  ekin = 1.55676047489501 |  erot = 2.97115254541007 | epot = -21.7829722234117 | etot = -17.2550592031067
-925000  ekin = 1.86603413909288 |  erot = 1.96274861601779 | epot = -21.7288604040749 | etot = -17.9000776489642
-926000  ekin = 1.36993364395821 |  erot = 2.11749584641399 | epot = -21.7083442855147 | etot = -18.2209147951426
-927000  ekin = 2.55718977538496 |  erot = 2.08109095048881 | epot = -21.7242353526192 | etot = -17.0859546267455
-928000  ekin = 2.0974272910786 |  erot = 2.73922911267236 | epot = -21.7673808868819 | etot = -16.9307244831309
-929000  ekin = 1.85550591174834 |  erot = 1.84990976935039 | epot = -21.8639426090857 | etot = -18.158526927987
-930000  ekin = 1.99594723517184 |  erot = 2.09151231016387 | epot = -21.8461015073053 | etot = -17.7586419619696
-931000  ekin = 2.45331651079283 |  erot = 1.86703658018613 | epot = -21.7382799817762 | etot = -17.4179268907972
-932000  ekin = 2.76909250526759 |  erot = 2.34990175754269 | epot = -21.7639792890094 | etot = -16.6449850261991
-933000  ekin = 3.04747366335481 |  erot = 2.52740756503515 | epot = -21.6783727845496 | etot = -16.1034915561597
-934000  ekin = 2.93463275640818 |  erot = 2.48893095891026 | epot = -21.5784996926914 | etot = -16.1549359773729
-935000  ekin = 2.77799347567549 |  erot = 2.1392935841225 | epot = -21.5334239467005 | etot = -16.6161368869025
-936000  ekin = 2.96529953690398 |  erot = 2.07095365726714 | epot = -21.5249249864244 | etot = -16.4886717922533
-937000  ekin = 3.0485053770175 |  erot = 2.32432162998051 | epot = -21.4386642161072 | etot = -16.0658372091092
-938000  ekin = 2.9926262850536 |  erot = 2.35224559307843 | epot = -21.3457080466208 | etot = -16.0008361684887
-939000  ekin = 2.61238181353703 |  erot = 2.26780356837292 | epot = -21.3079422537804 | etot = -16.4277568718705
-940000  ekin = 2.65930112044942 |  erot = 2.75497479722395 | epot = -21.2170493356504 | etot = -15.802773417977
-941000  ekin = 2.27574261339217 |  erot = 2.61419196501686 | epot = -21.1297657597673 | etot = -16.2398311813583
-942000  ekin = 1.89172011891055 |  erot = 2.82029488513784 | epot = -21.0410099256114 | etot = -16.328994921563
-943000  ekin = 2.47643464476757 |  erot = 2.34737109151876 | epot = -21.046668772798 | etot = -16.2228630365117
-944000  ekin = 2.13883995897326 |  erot = 1.92577316206138 | epot = -21.0114219746514 | etot = -16.9468088536167
-945000  ekin = 2.57768697869113 |  erot = 2.21470136124069 | epot = -21.0634624131725 | etot = -16.2710740732407
-946000  ekin = 2.36420709243625 |  erot = 2.89647330776424 | epot = -21.088814693033 | etot = -15.8281342928325
-947000  ekin = 2.07104171538467 |  erot = 1.86575631327232 | epot = -21.1004860950452 | etot = -17.1636880663882
-948000  ekin = 1.85532958802997 |  erot = 1.36952834086551 | epot = -21.1364231315616 | etot = -17.9115652026661
-949000  ekin = 1.76206591178366 |  erot = 2.31737328558629 | epot = -21.1463744779337 | etot = -17.0669352805638
-950000  ekin = 1.72021033353108 |  erot = 2.24191394295309 | epot = -21.1376324866856 | etot = -17.1755082102014
-951000  ekin = 1.96140007830504 |  erot = 2.32248863487758 | epot = -21.1955927656813 | etot = -16.9117040524987
-952000  ekin = 2.93256201500608 |  erot = 2.74550490827503 | epot = -21.234781024541 | etot = -15.5567141012599
-953000  ekin = 2.95031285986317 |  erot = 2.39822873263993 | epot = -21.252609183133 | etot = -15.9040675906299
-954000  ekin = 3.09579074538114 |  erot = 1.98159252445734 | epot = -21.1641538136742 | etot = -16.0867705438357
-955000  ekin = 3.59360323486038 |  erot = 2.06789679071821 | epot = -21.0522880782498 | etot = -15.3907880526712
-956000  ekin = 2.97416074498497 |  erot = 3.66953591785751 | epot = -20.9097603766373 | etot = -14.2660637137948
-957000  ekin = 3.03140562067951 |  erot = 2.66078083760708 | epot = -20.741905867784 | etot = -15.0497194094974
-958000  ekin = 2.68913434704072 |  erot = 2.94057112873834 | epot = -20.5488384129041 | etot = -14.9191329371251
-959000  ekin = 1.93264217407773 |  erot = 2.45198406257092 | epot = -20.468781161493 | etot = -16.0841549248444
-960000  ekin = 1.49632279167952 |  erot = 3.13346348599987 | epot = -20.4844974178568 | etot = -15.8547111401774
-961000  ekin = 1.96353429663481 |  erot = 2.07553358516994 | epot = -20.4805590123497 | etot = -16.441491130545
-962000  ekin = 2.02830196392007 |  erot = 1.88908496389356 | epot = -20.5374211599971 | etot = -16.6200342321835
-963000  ekin = 1.80829526034561 |  erot = 2.46258345726267 | epot = -20.5841835730967 | etot = -16.3133048554884
-964000  ekin = 2.79449124937198 |  erot = 2.42527551362846 | epot = -20.623880544448 | etot = -15.4041137814476
-965000  ekin = 2.53493670506137 |  erot = 2.27804362684503 | epot = -20.6549300812151 | etot = -15.8419497493087
-966000  ekin = 2.0920817650402 |  erot = 2.27478990703181 | epot = -20.704473904241 | etot = -16.337602232169
-967000  ekin = 1.55562260797661 |  erot = 3.55543363172458 | epot = -20.739375276301 | etot = -15.6283190365998
-968000  ekin = 1.93439891222236 |  erot = 2.37295903815892 | epot = -20.7189229543385 | etot = -16.4115650039572
-969000  ekin = 2.16199728898303 |  erot = 2.4601205252494 | epot = -20.6747113173023 | etot = -16.0525935030699
-970000  ekin = 1.84926216722517 |  erot = 2.96951777569267 | epot = -20.6011599981509 | etot = -15.7823800552331
-971000  ekin = 1.93656411083027 |  erot = 3.08724923997924 | epot = -20.5835250734812 | etot = -15.5597117226717
-972000  ekin = 1.90452783927713 |  erot = 2.5823076678316 | epot = -20.5782905980209 | etot = -16.0914550909122
-973000  ekin = 2.1922712122506 |  erot = 2.92686386394502 | epot = -20.5868173702649 | etot = -15.4676822940693
-974000  ekin = 2.53094641465528 |  erot = 2.69271305556795 | epot = -20.5382547781502 | etot = -15.314595307927
-975000  ekin = 3.41187201669925 |  erot = 2.32917219553093 | epot = -20.5109803919917 | etot = -14.7699361797616
-976000  ekin = 2.88156114272554 |  erot = 3.10474521611246 | epot = -20.5158119249461 | etot = -14.5295055661081
-977000  ekin = 2.73962881168093 |  erot = 2.50884169958543 | epot = -20.4964590297999 | etot = -15.2479885185336
-978000  ekin = 1.79682802545478 |  erot = 2.06924041504343 | epot = -20.4730821934977 | etot = -16.6070137529995
-979000  ekin = 1.86521389998383 |  erot = 2.22151626929011 | epot = -20.4069392895634 | etot = -16.3202091202894
-980000  ekin = 1.92383169177414 |  erot = 1.56425965548877 | epot = -20.3533353734708 | etot = -16.8652440262079
-981000  ekin = 1.55110199282939 |  erot = 2.05381225133935 | epot = -20.3970890782076 | etot = -16.7921748340389
-982000  ekin = 1.85559395816058 |  erot = 1.96991369841493 | epot = -20.499354149896 | etot = -16.6738464933205
-983000  ekin = 2.75061857015333 |  erot = 1.7944840218308 | epot = -20.5241519929378 | etot = -15.9790494009537
-984000  ekin = 3.65069712553537 |  erot = 2.64237329124733 | epot = -20.6374699142712 | etot = -14.3443994974885
-985000  ekin = 2.9563732193106 |  erot = 2.18846412126773 | epot = -20.8122975273334 | etot = -15.6674601867551
-986000  ekin = 2.87072902054599 |  erot = 2.18810434250119 | epot = -20.9390290724605 | etot = -15.8801957094134
-987000  ekin = 3.37463328642758 |  erot = 2.5371366667467 | epot = -21.0098323012658 | etot = -15.0980623480916
-988000  ekin = 3.45107854450338 |  erot = 3.23625536313169 | epot = -21.0554260480417 | etot = -14.3680921404067
-989000  ekin = 2.83591404363756 |  erot = 2.20564156324817 | epot = -21.19499265416 | etot = -16.1534370472743
-990000  ekin = 2.79864389348437 |  erot = 1.83178426663539 | epot = -21.1880268304373 | etot = -16.5575986703175
-991000  ekin = 3.14781925181036 |  erot = 3.2078247180891 | epot = -21.1115234865128 | etot = -14.7558795166133
-992000  ekin = 3.30033725309946 |  erot = 2.62749912694387 | epot = -21.0030296251662 | etot = -15.0751932451229
-993000  ekin = 3.07374297249949 |  erot = 2.22697230616356 | epot = -20.9385586572609 | etot = -15.6378433785979
-994000  ekin = 3.21461776403449 |  erot = 2.80599707993708 | epot = -20.8790524582442 | etot = -14.8584376142727
-995000  ekin = 3.25071478747345 |  erot = 1.73415439498321 | epot = -20.8037804714002 | etot = -15.8189112889436
-996000  ekin = 3.07999632962569 |  erot = 3.18107550500824 | epot = -20.7805295335828 | etot = -14.5194576989488
-997000  ekin = 2.97118118001025 |  erot = 3.14046656474894 | epot = -20.7334885248756 | etot = -14.6218407801164
-998000  ekin = 3.09169861594907 |  erot = 1.99060706981745 | epot = -20.6553134096535 | etot = -15.573007723887
-999000  ekin = 2.07498130576584 |  erot = 2.75045972766921 | epot = -20.616091526295 | etot = -15.79065049286
-1000000  ekin = 2.07851119592057 |  erot = 2.11869313853035 | epot = -20.4539417072875 | etot = -16.2567373728366
- 1000000  0.092378275   -1.3359709  0.057599499   -1.1484644 2.8477973e-05 
-Loop time of 38.201 on 1 procs for 1000000 steps with 16 atoms
-
-Performance: 22617.237 tau/day, 26177.358 timesteps/s
-98.6% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 27.344     | 27.344     | 27.344     |   0.0 | 71.58
-Bond    | 0.88043    | 0.88043    | 0.88043    |   0.0 |  2.30
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.2073     | 0.2073     | 0.2073     |   0.0 |  0.54
-Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
-Modify  | 9.4379     | 9.4379     | 9.4379     |   0.0 | 24.71
-Other   |            | 0.331      |            |       |  0.87
-
-Nlocal:    16 ave 16 max 16 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    88 ave 88 max 88 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 88
-Ave neighs/atom = 5.5
-Ave special neighs/atom = 3.75
-Neighbor list builds = 0
-Dangerous builds = 0
-
-#write_restart config.${number}.*
-Total wall time: 0:00:38
diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4
deleted file mode 100644
index 3010570379..0000000000
--- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4
+++ /dev/null
@@ -1,1167 +0,0 @@
-LAMMPS (18 Jun 2019)
-variable number	equal 2
-variable ofreq	equal 1000
-variable efreq	equal 1000
-variable T      equal 0.1
-
-units lj
-
-dimension 3
-
-newton off
-
-boundary  p p p
-
-atom_style hybrid bond ellipsoid
-atom_modify sort 0 1.0
-
-# Pair interactions require lists of neighbours to be calculated
-neighbor 1.0 bin
-neigh_modify every 1 delay 0 check yes
-
-read_data data.duplex2
-  orthogonal box = (-20 -20 -20) to (20 20 20)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  16 atoms
-  reading velocities ...
-  16 velocities
-  16 ellipsoids
-  scanning bonds ...
-  2 = max bonds/atom
-  reading bonds ...
-  13 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of 1-3 neighbors
-  4 = max # of 1-4 neighbors
-  6 = max # of special neighbors
-  special bonds CPU = 0.000189 secs
-  read_data CPU = 0.003505 secs
-
-set atom * mass 3.1575
-  16 settings made for mass
-
-group all type 1 4
-16 atoms in group all
-
-# oxDNA bond interactions - FENE backbone
-bond_style oxdna/fene
-bond_coeff * 2.0 0.25 0.7525
-
-# oxDNA pair interactions
-pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
-pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
-
-# NVE ensemble
-#fix 1 all nve/dot
-fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
-fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10
-fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
-#fix 1 all nve/asphere
-#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
-
-timestep 1e-5
-
-#comm_style tiled
-#fix 3 all balance 10000 1.1 rcb
-
-#compute mol all chunk/atom molecule
-#compute mychunk all vcm/chunk mol
-#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
-
-#dump pos all xyz ${ofreq} traj.${number}.xyz
-
-#compute quat all property/atom quatw quati quatj quatk
-#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
-#dump_modify quat sort id
-#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
-
-compute erot all erotate/asphere
-compute ekin all ke
-compute epot all pe
-variable erot equal c_erot
-variable ekin equal c_ekin
-variable epot equal c_epot
-variable etot equal c_erot+c_ekin+c_epot
-fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-
-#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
-#dump_modify out sort id
-#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
-
-run 1000000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.92828
-  ghost atom cutoff = 1.92828
-  binsize = 0.964142, bins = 42 42 42
-  5 neighbor lists, perpetual/occasional/extra = 5 0 0
-  (1) pair oxdna/excv, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-  (2) pair oxdna/stk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (3) pair oxdna/hbond, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (4) pair oxdna/xstk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) pair oxdna/coaxstk, perpetual, copy from (1)
-      attributes: half, newton off
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -1.5402493 0.0070469125   -1.5332024 6.0760034e-06 
-1000  ekin = 1.34565986428024 |  erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
-2000  ekin = 2.15911766687235 |  erot = 2.16031365874706 | epot = -24.4723177103698 | etot = -20.1528863847504
-3000  ekin = 3.26561948796015 |  erot = 2.75651822936605 | epot = -24.412573068346 | etot = -18.3904353510198
-4000  ekin = 1.92438809241066 |  erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038505
-5000  ekin = 1.35986357015476 |  erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
-6000  ekin = 2.19432475124593 |  erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
-7000  ekin = 2.65619274477635 |  erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
-8000  ekin = 2.51333548501169 |  erot = 2.34649854571052 | epot = -24.0812769481836 | etot = -19.2214429174614
-9000  ekin = 2.24506493169711 |  erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
-10000  ekin = 2.36632635249862 |  erot = 1.79592471761529 | epot = -23.9002627850602 | etot = -19.7380117149463
-11000  ekin = 2.03296432220126 |  erot = 1.687070009478 | epot = -23.8527188138995 | etot = -20.1326844822202
-12000  ekin = 2.65352743446956 |  erot = 2.50226345616878 | epot = -23.8480805937578 | etot = -18.6922897031194
-13000  ekin = 1.89067421214403 |  erot = 2.35043092595414 | epot = -23.7714712440931 | etot = -19.5303661059949
-14000  ekin = 1.90680463918722 |  erot = 2.127459870274 | epot = -23.7545354032947 | etot = -19.7202708938335
-15000  ekin = 2.40428667481004 |  erot = 2.06172433796653 | epot = -23.6726347642127 | etot = -19.2066237514361
-16000  ekin = 2.7510166356243 |  erot = 1.18896277635345 | epot = -23.5745121257654 | etot = -19.6345327137876
-17000  ekin = 2.44090826892662 |  erot = 2.38166706806442 | epot = -23.5888433865641 | etot = -18.766268049573
-18000  ekin = 2.16977970545217 |  erot = 2.46915729098831 | epot = -23.6023194416344 | etot = -18.9633824451939
-19000  ekin = 2.19378610033861 |  erot = 2.45183819484608 | epot = -23.5449084745393 | etot = -18.8992841793546
-20000  ekin = 2.07734013817241 |  erot = 1.81448496219961 | epot = -23.5782673056894 | etot = -19.6864422053173
-21000  ekin = 2.27781532351243 |  erot = 2.76369118136087 | epot = -23.5986545956161 | etot = -18.5571480907428
-22000  ekin = 2.69375785791379 |  erot = 1.86436952967315 | epot = -23.5521083325077 | etot = -18.9939809449208
-23000  ekin = 1.99952884103097 |  erot = 2.28032953163858 | epot = -23.4448504933921 | etot = -19.1649921207226
-24000  ekin = 2.19993258930349 |  erot = 2.97916455146846 | epot = -23.365299008021 | etot = -18.1862018672491
-25000  ekin = 2.28089469652686 |  erot = 2.97627567077201 | epot = -23.2873526827526 | etot = -18.0301823154537
-26000  ekin = 1.99390998801618 |  erot = 2.79250495479073 | epot = -23.1859723519608 | etot = -18.3995574091539
-27000  ekin = 2.00992865272585 |  erot = 2.66533768693446 | epot = -23.0781687640813 | etot = -18.402902424421
-28000  ekin = 2.00322172723407 |  erot = 2.36418499091004 | epot = -23.0032647032354 | etot = -18.6358579850913
-29000  ekin = 2.52361436071784 |  erot = 2.06140753694879 | epot = -22.9685706338047 | etot = -18.383548736138
-30000  ekin = 1.94969919616482 |  erot = 2.13601590002587 | epot = -22.8657664932105 | etot = -18.7800513970198
-31000  ekin = 1.81286761012387 |  erot = 2.31717861791922 | epot = -22.8372197907213 | etot = -18.7071735626782
-32000  ekin = 1.88389491638451 |  erot = 2.00512246825909 | epot = -22.9321024454487 | etot = -19.0430850608051
-33000  ekin = 1.78524470387102 |  erot = 1.83154598239148 | epot = -22.9538943248059 | etot = -19.3371036385434
-34000  ekin = 2.28023843988047 |  erot = 3.11357086039976 | epot = -23.0617618407572 | etot = -17.6679525404769
-35000  ekin = 2.88795920533174 |  erot = 1.81662227096288 | epot = -23.1342233361349 | etot = -18.4296418598403
-36000  ekin = 2.40018487148211 |  erot = 2.59182059399979 | epot = -23.2153198761915 | etot = -18.2233144107096
-37000  ekin = 2.22699211630433 |  erot = 1.73889017332476 | epot = -23.2291614908027 | etot = -19.2632792011736
-38000  ekin = 2.13593461964592 |  erot = 3.07590136326317 | epot = -23.1607724763685 | etot = -17.9489364934594
-39000  ekin = 2.08839393640823 |  erot = 2.80471150509565 | epot = -23.1352878747759 | etot = -18.242182433272
-40000  ekin = 2.94982054413846 |  erot = 2.19484102372242 | epot = -23.1842229043853 | etot = -18.0395613365244
-41000  ekin = 2.47855373480178 |  erot = 3.46795094832273 | epot = -23.1698888629099 | etot = -17.2233841797854
-42000  ekin = 2.57225931171306 |  erot = 3.11160980977123 | epot = -23.0914425999525 | etot = -17.4075734784682
-43000  ekin = 2.16695829201326 |  erot = 2.67063324875933 | epot = -22.9841690345739 | etot = -18.1465774938013
-44000  ekin = 2.3251045436594 |  erot = 3.31069456451417 | epot = -22.9099977707014 | etot = -17.2741986625278
-45000  ekin = 1.8593572517472 |  erot = 3.48256913429863 | epot = -22.7853293556222 | etot = -17.4434029695763
-46000  ekin = 2.59906260222482 |  erot = 2.2320785378511 | epot = -22.67184319375 | etot = -17.8407020536741
-47000  ekin = 1.9041935097682 |  erot = 3.39352467596442 | epot = -22.5624536061979 | etot = -17.2647354204653
-48000  ekin = 2.46191536162938 |  erot = 2.50024189038396 | epot = -22.5888330081063 | etot = -17.626675756093
-49000  ekin = 3.18008619674965 |  erot = 2.18329398142911 | epot = -22.6110647388653 | etot = -17.2476845606865
-50000  ekin = 2.92380640638808 |  erot = 1.5483538313346 | epot = -22.6682279672282 | etot = -18.1960677295055
-51000  ekin = 2.86729503225236 |  erot = 2.67529217516738 | epot = -22.6748886664557 | etot = -17.132301459036
-52000  ekin = 2.30283827457731 |  erot = 1.82645474029553 | epot = -22.6607030819086 | etot = -18.5314100670358
-53000  ekin = 3.18697616339313 |  erot = 1.67211265049679 | epot = -22.7158951183044 | etot = -17.8568063044145
-54000  ekin = 2.63274995193146 |  erot = 1.96664130685844 | epot = -22.7877787224364 | etot = -18.1883874636465
-55000  ekin = 3.18311630681888 |  erot = 2.85127254864952 | epot = -22.8390589862477 | etot = -16.8046701307793
-56000  ekin = 2.55275960671527 |  erot = 3.05720384772627 | epot = -22.8187750450683 | etot = -17.2088115906267
-57000  ekin = 2.43682051944963 |  erot = 3.45782031837861 | epot = -22.7770565571277 | etot = -16.8824157192995
-58000  ekin = 1.93888380963701 |  erot = 2.51321017005842 | epot = -22.7135987564736 | etot = -18.2615047767781
-59000  ekin = 2.5584899615086 |  erot = 3.52166542523796 | epot = -22.6623202639297 | etot = -16.5821648771831
-60000  ekin = 2.80661395039301 |  erot = 2.89055248290059 | epot = -22.5801959967487 | etot = -16.8830295634551
-61000  ekin = 2.68598657973729 |  erot = 2.54741083070049 | epot = -22.4806361765055 | etot = -17.2472387660677
-62000  ekin = 2.74493324548126 |  erot = 2.23648307303268 | epot = -22.4129547813458 | etot = -17.4315384628319
-63000  ekin = 2.65627195091608 |  erot = 2.46107949280746 | epot = -22.3986334001314 | etot = -17.2812819564079
-64000  ekin = 2.12379240032878 |  erot = 2.79203441675508 | epot = -22.3495990435982 | etot = -17.4337722265143
-65000  ekin = 1.86782238979936 |  erot = 2.70277079938775 | epot = -22.3710220966341 | etot = -17.800428907447
-66000  ekin = 2.74983103317414 |  erot = 1.93532287297328 | epot = -22.3642892005435 | etot = -17.6791352943961
-67000  ekin = 2.51092055125345 |  erot = 2.46618624666164 | epot = -22.3997780561407 | etot = -17.4226712582257
-68000  ekin = 2.95469759114172 |  erot = 1.97026833535316 | epot = -22.465077041847 | etot = -17.5401111153521
-69000  ekin = 2.60179538487173 |  erot = 2.27022574694886 | epot = -22.4013876082186 | etot = -17.529366476398
-70000  ekin = 2.38624525335423 |  erot = 2.82124637267728 | epot = -22.3329612644329 | etot = -17.1254696384013
-71000  ekin = 2.62641919853461 |  erot = 2.89332429923839 | epot = -22.3324946257813 | etot = -16.8127511280083
-72000  ekin = 2.93199679301318 |  erot = 2.83600213853038 | epot = -22.4418753486332 | etot = -16.6738764170897
-73000  ekin = 2.20521324648382 |  erot = 3.0506384171445 | epot = -22.5078076718832 | etot = -17.2519560082549
-74000  ekin = 2.16594519672766 |  erot = 2.82993872672918 | epot = -22.5187768617569 | etot = -17.5228929383001
-75000  ekin = 1.52753824412461 |  erot = 1.91758574309003 | epot = -22.6434864113427 | etot = -19.198362424128
-76000  ekin = 1.89477517532868 |  erot = 2.83145375092217 | epot = -22.7507099037207 | etot = -18.0244809774699
-77000  ekin = 2.84722966394523 |  erot = 3.20523918524771 | epot = -22.8263123696514 | etot = -16.7738435204585
-78000  ekin = 2.44900478430451 |  erot = 2.80964787966682 | epot = -22.8119237303111 | etot = -17.5532710663397
-79000  ekin = 2.16549328835506 |  erot = 1.67531288307153 | epot = -22.8278994273521 | etot = -18.9870932559255
-80000  ekin = 2.38929173610466 |  erot = 2.58355997375491 | epot = -22.7453472674483 | etot = -17.7724955575887
-81000  ekin = 2.74182188148999 |  erot = 1.92580771183151 | epot = -22.6872721828913 | etot = -18.0196425895698
-82000  ekin = 1.90254633515813 |  erot = 1.70958501101745 | epot = -22.5904815431895 | etot = -18.9783501970139
-83000  ekin = 1.63862423461032 |  erot = 1.87668722448406 | epot = -22.5030898166236 | etot = -18.9877783575292
-84000  ekin = 1.65768128899531 |  erot = 2.10186039233844 | epot = -22.4199436013011 | etot = -18.6604019199674
-85000  ekin = 2.40787065796921 |  erot = 2.04965431830703 | epot = -22.3401854879212 | etot = -17.882660511645
-86000  ekin = 2.51073542405177 |  erot = 1.79768841940749 | epot = -22.3948638623201 | etot = -18.0864400188608
-87000  ekin = 2.13729284484532 |  erot = 1.97886338867606 | epot = -22.4457225556767 | etot = -18.3295663221553
-88000  ekin = 1.7511616822056 |  erot = 2.36434608342924 | epot = -22.4232555875236 | etot = -18.3077478218887
-89000  ekin = 1.85498863251071 |  erot = 3.29466014836527 | epot = -22.4615925106509 | etot = -17.3119437297749
-90000  ekin = 2.22730928223451 |  erot = 2.36761183779185 | epot = -22.5498488806969 | etot = -17.9549277606706
-91000  ekin = 2.40026068010467 |  erot = 3.1312454261103 | epot = -22.5445138059197 | etot = -17.0130076997047
-92000  ekin = 2.69184894487886 |  erot = 3.01111638487596 | epot = -22.5488335054242 | etot = -16.8458681756693
-93000  ekin = 3.04452081584098 |  erot = 3.0289315825034 | epot = -22.4857514998612 | etot = -16.4122991015169
-94000  ekin = 3.21054020599498 |  erot = 1.87554208928457 | epot = -22.58235617796 | etot = -17.4962738826805
-95000  ekin = 3.49164555041805 |  erot = 2.89107259754101 | epot = -22.651746211573 | etot = -16.2690280636139
-96000  ekin = 2.8961145983777 |  erot = 2.38403691628048 | epot = -22.6376886129393 | etot = -17.3575370982811
-97000  ekin = 1.94001816357315 |  erot = 2.09603205774619 | epot = -22.6212143095229 | etot = -18.5851640882036
-98000  ekin = 2.21812472183551 |  erot = 3.66512951907029 | epot = -22.5400207863669 | etot = -16.6567665454611
-99000  ekin = 1.96304801418099 |  erot = 2.78092002528644 | epot = -22.4500077741119 | etot = -17.7060397346444
-100000  ekin = 1.78146596589238 |  erot = 2.66087063973067 | epot = -22.3806285021859 | etot = -17.9382918965629
-101000  ekin = 2.13576431486591 |  erot = 2.39189697670582 | epot = -22.3671198416411 | etot = -17.8394585500694
-102000  ekin = 1.54265458925823 |  erot = 2.31301627489861 | epot = -22.3596033820568 | etot = -18.5039325179
-103000  ekin = 1.6493299781162 |  erot = 2.82700146777614 | epot = -22.4044472055819 | etot = -17.9281157596895
-104000  ekin = 1.88425130865015 |  erot = 3.36695629589132 | epot = -22.4614117565727 | etot = -17.2102041520312
-105000  ekin = 2.0873628063424 |  erot = 1.99902589912497 | epot = -22.4857870795246 | etot = -18.3993983740572
-106000  ekin = 2.85192200005481 |  erot = 1.96124421177818 | epot = -22.4885148263279 | etot = -17.6753486144949
-107000  ekin = 2.27699301124082 |  erot = 1.54572940373457 | epot = -22.4328687856414 | etot = -18.610146370666
-108000  ekin = 2.43341212242248 |  erot = 1.7101452395327 | epot = -22.4750159709763 | etot = -18.3314586090212
-109000  ekin = 2.3240302459673 |  erot = 2.92730273400661 | epot = -22.4544447404649 | etot = -17.203111760491
-110000  ekin = 2.75939007795593 |  erot = 2.3726124845783 | epot = -22.4066316113363 | etot = -17.2746290488021
-111000  ekin = 2.30202775259985 |  erot = 2.09098171366697 | epot = -22.340628179725 | etot = -17.9476187134581
-112000  ekin = 2.89672803093986 |  erot = 1.84536318388285 | epot = -22.189229344937 | etot = -17.4471381301143
-113000  ekin = 2.802868120203 |  erot = 1.68317583122193 | epot = -22.1739192926257 | etot = -17.6878753412008
-114000  ekin = 3.41134331362353 |  erot = 2.66279011393036 | epot = -22.2993892060878 | etot = -16.2252557785339
-115000  ekin = 3.04096848543598 |  erot = 1.72164164793761 | epot = -22.3101669297006 | etot = -17.547556796327
-116000  ekin = 3.18249263106367 |  erot = 3.21872780579631 | epot = -22.3766120310369 | etot = -15.975391594177
-117000  ekin = 3.04033644338918 |  erot = 2.4163277414929 | epot = -22.3406101341932 | etot = -16.8839459493111
-118000  ekin = 3.2297663279461 |  erot = 1.46870208555873 | epot = -22.262910646297 | etot = -17.5644422327922
-119000  ekin = 2.35815331598994 |  erot = 3.07464675916892 | epot = -22.21629705762 | etot = -16.7834969824611
-120000  ekin = 1.93901604028919 |  erot = 2.21087803685818 | epot = -22.1596747789505 | etot = -18.0097807018031
-121000  ekin = 1.94791988346889 |  erot = 3.06697908719322 | epot = -22.1473490758084 | etot = -17.1324501051462
-122000  ekin = 1.69642311218451 |  erot = 1.71065948591522 | epot = -22.235021693017 | etot = -18.8279390949172
-123000  ekin = 1.74537927001903 |  erot = 2.31042772730644 | epot = -22.3250546948603 | etot = -18.2692476975348
-124000  ekin = 2.74229806685692 |  erot = 1.94346011848795 | epot = -22.3376426377462 | etot = -17.6518844524013
-125000  ekin = 2.77628031613761 |  erot = 1.95737420539167 | epot = -22.3561899601979 | etot = -17.6225354386686
-126000  ekin = 2.05898577806786 |  erot = 1.47493157618749 | epot = -22.3918669376121 | etot = -18.8579495833568
-127000  ekin = 1.88620727578863 |  erot = 1.58698481884328 | epot = -22.3753405588623 | etot = -18.9021484642304
-128000  ekin = 1.65027256647601 |  erot = 1.87589048163674 | epot = -22.3576574967822 | etot = -18.8314944486694
-129000  ekin = 2.51771860981078 |  erot = 2.38745668871875 | epot = -22.3622404512641 | etot = -17.4570651527346
-130000  ekin = 1.60778116741171 |  erot = 2.81983062254802 | epot = -22.3043401463426 | etot = -17.8767283563829
-131000  ekin = 2.27966529707091 |  erot = 2.29465997580789 | epot = -22.1860056729234 | etot = -17.6116804000446
-132000  ekin = 2.94605151024306 |  erot = 2.34727265039698 | epot = -22.1004107829512 | etot = -16.8070866223112
-133000  ekin = 2.00184520718143 |  erot = 2.13597622566089 | epot = -22.0860804435183 | etot = -17.948259010676
-134000  ekin = 1.54536260297594 |  erot = 2.86019181856985 | epot = -22.0324797134652 | etot = -17.6269252919194
-135000  ekin = 1.7899169229158 |  erot = 2.40585579784188 | epot = -22.0564792277569 | etot = -17.8607065069992
-136000  ekin = 1.63315069688348 |  erot = 2.13968964990471 | epot = -22.0645410751455 | etot = -18.2917007283573
-137000  ekin = 2.36475220491125 |  erot = 1.93075105476848 | epot = -22.101884847306 | etot = -17.8063815876262
-138000  ekin = 2.9554682114977 |  erot = 1.58329215843879 | epot = -22.158920719349 | etot = -17.6201603494125
-139000  ekin = 3.18559985564368 |  erot = 2.24978247982886 | epot = -22.2766713145625 | etot = -16.84128897909
-140000  ekin = 2.25331500051846 |  erot = 3.04264261269698 | epot = -22.4413209794807 | etot = -17.1453633662653
-141000  ekin = 1.8939664036255 |  erot = 3.12730191483887 | epot = -22.6943708703895 | etot = -17.6731025519251
-142000  ekin = 2.48698722341786 |  erot = 2.50204475841097 | epot = -22.8022645411412 | etot = -17.8132325593124
-143000  ekin = 2.39031114354901 |  erot = 2.72027514737474 | epot = -22.7789363640121 | etot = -17.6683500730884
-144000  ekin = 1.93009742932803 |  erot = 2.68112648713777 | epot = -22.6600942975092 | etot = -18.0488703810434
-145000  ekin = 1.81543048110687 |  erot = 1.73927524532866 | epot = -22.6290694904769 | etot = -19.0743637640413
-146000  ekin = 2.4125202126428 |  erot = 2.0856902293417 | epot = -22.560764077018 | etot = -18.0625536350335
-147000  ekin = 1.44642974398304 |  erot = 1.86921415702345 | epot = -22.4437745695725 | etot = -19.128130668566
-148000  ekin = 1.94224767107089 |  erot = 2.57935525538892 | epot = -22.4110987100046 | etot = -17.8894957835448
-149000  ekin = 2.03195649040454 |  erot = 3.31786202502786 | epot = -22.312227106758 | etot = -16.9624085913256
-150000  ekin = 2.47792894576431 |  erot = 2.68612874200302 | epot = -22.1392843642772 | etot = -16.9752266765099
-151000  ekin = 2.75692645092955 |  erot = 1.88122565848133 | epot = -21.9329416416722 | etot = -17.2947895322613
-152000  ekin = 2.7753834344323 |  erot = 1.78115734250796 | epot = -21.745072490984 | etot = -17.1885317140438
-153000  ekin = 3.09316888168833 |  erot = 1.80744228044955 | epot = -21.6451473427313 | etot = -16.7445361805934
-154000  ekin = 2.31433640945477 |  erot = 2.19304386678896 | epot = -21.5946356595636 | etot = -17.0872553833199
-155000  ekin = 1.94169881401553 |  erot = 2.67959698479411 | epot = -21.6941053409436 | etot = -17.0728095421339
-156000  ekin = 2.69151609119638 |  erot = 2.25048211983205 | epot = -21.7610571974251 | etot = -16.8190589863966
-157000  ekin = 3.89507004263776 |  erot = 2.74501587672577 | epot = -21.8157728797742 | etot = -15.1756869604107
-158000  ekin = 2.88173407476086 |  erot = 2.69702262693026 | epot = -21.8854957137509 | etot = -16.3067390120597
-159000  ekin = 3.15173323195919 |  erot = 2.61743473710129 | epot = -21.8245251626835 | etot = -16.055357193623
-160000  ekin = 2.54983562435716 |  erot = 3.26037467643908 | epot = -21.8527884226329 | etot = -16.0425781218366
-161000  ekin = 2.47569624391789 |  erot = 2.44418416527208 | epot = -21.7973550812186 | etot = -16.8774746720287
-162000  ekin = 2.9422872213738 |  erot = 2.59784970938383 | epot = -21.7813251561028 | etot = -16.2411882253452
-163000  ekin = 3.25812805712343 |  erot = 2.2523933100784 | epot = -21.820089307521 | etot = -16.3095679403192
-164000  ekin = 3.52786799143084 |  erot = 2.22392713421413 | epot = -21.7646946348872 | etot = -16.0128995092422
-165000  ekin = 2.47839548873417 |  erot = 2.58744140761171 | epot = -21.679095294504 | etot = -16.6132583981582
-166000  ekin = 2.14435847552791 |  erot = 3.04732688845808 | epot = -21.6219995979976 | etot = -16.4303142340116
-167000  ekin = 2.77664659649902 |  erot = 2.89037999868329 | epot = -21.5339928834654 | etot = -15.8669662882831
-168000  ekin = 1.74464407802389 |  erot = 2.78052653338967 | epot = -21.4288999288374 | etot = -16.9037293174239
-169000  ekin = 1.80689129093329 |  erot = 2.46391033708927 | epot = -21.4128285618694 | etot = -17.1420269338468
-170000  ekin = 1.6949814594151 |  erot = 2.88911238881154 | epot = -21.4319269866203 | etot = -16.8478331383937
-171000  ekin = 2.15326316196645 |  erot = 1.61346547801869 | epot = -21.2861470779283 | etot = -17.5194184379432
-172000  ekin = 1.67904916339532 |  erot = 2.36509147316375 | epot = -21.1250864759441 | etot = -17.080945839385
-173000  ekin = 2.05349972960735 |  erot = 2.1886466510775 | epot = -21.0744450592631 | etot = -16.8322986785782
-174000  ekin = 2.49402795941962 |  erot = 3.10392317000879 | epot = -20.9332609664624 | etot = -15.335309837034
-175000  ekin = 2.60611029063986 |  erot = 2.90993176119182 | epot = -20.8533230180668 | etot = -15.3372809662352
-176000  ekin = 2.14535974511637 |  erot = 2.67710511021539 | epot = -20.8508037764829 | etot = -16.0283389211511
-177000  ekin = 2.82654664242577 |  erot = 2.80647819657321 | epot = -20.9303681620826 | etot = -15.2973433230836
-178000  ekin = 3.17006270723388 |  erot = 1.88204403688962 | epot = -21.0665744865168 | etot = -16.0144677423933
-179000  ekin = 2.33834827123178 |  erot = 2.84870047825869 | epot = -21.1082901606943 | etot = -15.9212414112039
-180000  ekin = 2.39362550925045 |  erot = 2.94575326168227 | epot = -21.1089731290028 | etot = -15.7695943580701
-181000  ekin = 2.78703231260152 |  erot = 3.29998898392537 | epot = -21.0761138110654 | etot = -14.9890925145385
-182000  ekin = 3.02338391239199 |  erot = 2.32533107462881 | epot = -21.0444377426861 | etot = -15.6957227556653
-183000  ekin = 2.44126401356994 |  erot = 2.19853056632819 | epot = -20.8846280234405 | etot = -16.2448334435424
-184000  ekin = 2.56448211253962 |  erot = 2.77267067014066 | epot = -20.6657911214549 | etot = -15.3286383387746
-185000  ekin = 2.16427057092672 |  erot = 1.95880146934286 | epot = -20.5647658775173 | etot = -16.4416938372477
-186000  ekin = 2.06536030915311 |  erot = 3.14593463137772 | epot = -20.4537584304771 | etot = -15.2424634899463
-187000  ekin = 2.43846121057803 |  erot = 1.93593042270703 | epot = -20.4775765627296 | etot = -16.1031849294445
-188000  ekin = 2.28827356508696 |  erot = 2.89699235589217 | epot = -20.6028880527163 | etot = -15.4176221317372
-189000  ekin = 1.67206333515898 |  erot = 3.05807378739729 | epot = -20.6184572736204 | etot = -15.8883201510642
-190000  ekin = 1.96995062226968 |  erot = 2.94301967439401 | epot = -20.6150380630742 | etot = -15.7020677664105
-191000  ekin = 2.31558303301195 |  erot = 2.65062200614568 | epot = -20.5845049099943 | etot = -15.6182998708367
-192000  ekin = 3.58105122568799 |  erot = 2.89866835149675 | epot = -20.555036456006 | etot = -14.0753168788213
-193000  ekin = 2.69738971383614 |  erot = 3.08390984677749 | epot = -20.5718609412494 | etot = -14.7905613806358
-194000  ekin = 2.65963556416735 |  erot = 2.28486501061268 | epot = -20.4488832942326 | etot = -15.5043827194526
-195000  ekin = 1.85289053427901 |  erot = 2.65318671222087 | epot = -20.3816844231208 | etot = -15.8756071766209
-196000  ekin = 2.28257181147918 |  erot = 2.31175601065462 | epot = -20.4051132325268 | etot = -15.810785410393
-197000  ekin = 2.49770460330585 |  erot = 2.55587879440511 | epot = -20.4716020539923 | etot = -15.4180186562814
-198000  ekin = 2.01700960777427 |  erot = 1.51922008609382 | epot = -20.4907970823156 | etot = -16.9545673884475
-199000  ekin = 1.50027537520987 |  erot = 2.19604462463446 | epot = -20.5138434458212 | etot = -16.8175234459769
-200000  ekin = 1.64850512926723 |  erot = 2.4596633548257 | epot = -20.4934420686449 | etot = -16.385273584552
-201000  ekin = 2.62997533994907 |  erot = 2.61637339049483 | epot = -20.5569645618355 | etot = -15.3106158313916
-202000  ekin = 2.3089517547524 |  erot = 2.5565329388766 | epot = -20.6262537118088 | etot = -15.7607690181798
-203000  ekin = 1.64768887888551 |  erot = 2.11556417528285 | epot = -20.6617888215465 | etot = -16.8985357673782
-204000  ekin = 2.01924097320136 |  erot = 1.97748949636931 | epot = -20.7002685556682 | etot = -16.7035380860975
-205000  ekin = 2.97656554045711 |  erot = 3.25408007971553 | epot = -20.9425038008424 | etot = -14.7118581806698
-206000  ekin = 2.56613069661945 |  erot = 2.21624244224461 | epot = -21.0621833598182 | etot = -16.2798102209542
-207000  ekin = 3.44850636848559 |  erot = 2.48816050856267 | epot = -21.2038849430867 | etot = -15.2672180660384
-208000  ekin = 2.54208934028226 |  erot = 2.22605232144502 | epot = -21.3476404533667 | etot = -16.5794987916394
-209000  ekin = 3.84151461096732 |  erot = 2.16534559513903 | epot = -21.4932373455843 | etot = -15.486377139478
-210000  ekin = 3.06873591712904 |  erot = 2.24760815652574 | epot = -21.6427793540355 | etot = -16.3264352803807
-211000  ekin = 1.64176280869923 |  erot = 2.17721976802011 | epot = -21.8130439048272 | etot = -17.9940613281078
-212000  ekin = 2.5985934050661 |  erot = 2.41520703335869 | epot = -21.9964648294563 | etot = -16.9826643910315
-213000  ekin = 2.51136104390039 |  erot = 1.99503544560738 | epot = -22.161492842604 | etot = -17.6550963530962
-214000  ekin = 2.77089845962619 |  erot = 3.17247228684199 | epot = -22.208715104286 | etot = -16.2653443578179
-215000  ekin = 2.53408528186206 |  erot = 1.84963848601798 | epot = -22.1148567901871 | etot = -17.7311330223071
-216000  ekin = 2.52671619876928 |  erot = 2.77873014449688 | epot = -22.1370884570131 | etot = -16.8316421137469
-217000  ekin = 2.50171921508545 |  erot = 1.89238935467003 | epot = -22.226079201001 | etot = -17.8319706312455
-218000  ekin = 2.43936294263937 |  erot = 2.41974828067303 | epot = -22.2447049583244 | etot = -17.385593735012
-219000  ekin = 2.30221269367205 |  erot = 2.65120674162376 | epot = -22.2807164841742 | etot = -17.3272970488784
-220000  ekin = 1.70065256620687 |  erot = 2.34758543213915 | epot = -22.2809933538228 | etot = -18.2327553554768
-221000  ekin = 2.09298237125575 |  erot = 2.47886481595909 | epot = -22.267957001012 | etot = -17.6961098137972
-222000  ekin = 1.58469709510937 |  erot = 2.14490786301286 | epot = -22.1867412404881 | etot = -18.4571362823659
-223000  ekin = 1.83926923346352 |  erot = 1.89456034969536 | epot = -22.131893392038 | etot = -18.3980638088791
-224000  ekin = 2.59583657132575 |  erot = 2.93869915115497 | epot = -22.1425986650605 | etot = -16.6080629425798
-225000  ekin = 3.29351563254165 |  erot = 2.8433953581414 | epot = -22.12757310355 | etot = -15.9906621128669
-226000  ekin = 3.03135339447922 |  erot = 2.08293143143602 | epot = -22.15283624886 | etot = -17.0385514229448
-227000  ekin = 2.50176282992082 |  erot = 3.15084128846394 | epot = -22.2250438959744 | etot = -16.5724397775897
-228000  ekin = 2.32013498351673 |  erot = 2.67554406359439 | epot = -22.3177515383563 | etot = -17.3220724912452
-229000  ekin = 2.89545450975319 |  erot = 2.90735055857068 | epot = -22.4361496683348 | etot = -16.6333446000109
-230000  ekin = 2.28321229485933 |  erot = 3.48420465632866 | epot = -22.548785995051 | etot = -16.781369043863
-231000  ekin = 2.0778632375453 |  erot = 3.10673973696436 | epot = -22.5896609633152 | etot = -17.4050579888055
-232000  ekin = 2.1202374109541 |  erot = 1.98747810033065 | epot = -22.5738924334392 | etot = -18.4661769221544
-233000  ekin = 2.33571877855589 |  erot = 2.83585090202738 | epot = -22.5402065195541 | etot = -17.3686368389708
-234000  ekin = 2.10578223747154 |  erot = 2.07381218733635 | epot = -22.5507693150833 | etot = -18.3711748902754
-235000  ekin = 2.44321041214394 |  erot = 2.80846352304318 | epot = -22.5606929563186 | etot = -17.3090190211315
-236000  ekin = 2.93630791731799 |  erot = 3.0631591853173 | epot = -22.4860653874722 | etot = -16.4865982848369
-237000  ekin = 3.21264879506079 |  erot = 3.26866508478298 | epot = -22.3683553437862 | etot = -15.8870414639424
-238000  ekin = 2.46595539123277 |  erot = 2.32502019506664 | epot = -22.3144456769666 | etot = -17.5234700906672
-239000  ekin = 2.10325864915823 |  erot = 2.47631139904042 | epot = -22.3011392921811 | etot = -17.7215692439825
-240000  ekin = 1.77270999777839 |  erot = 2.60141429112664 | epot = -22.2344206081543 | etot = -17.8602963192493
-241000  ekin = 1.94952922244078 |  erot = 1.39715216866764 | epot = -22.2207225048761 | etot = -18.8740411137677
-242000  ekin = 3.05687991591411 |  erot = 2.00862394928705 | epot = -22.2213200390944 | etot = -17.1558161738932
-243000  ekin = 2.86735711945299 |  erot = 1.79948118674678 | epot = -22.2697610280427 | etot = -17.6029227218429
-244000  ekin = 2.00525854269389 |  erot = 2.36445341214555 | epot = -22.2726788994494 | etot = -17.90296694461
-245000  ekin = 2.28011102404838 |  erot = 2.787005205328 | epot = -22.2995433574618 | etot = -17.2324271280854
-246000  ekin = 2.06819738789813 |  erot = 2.24624952782285 | epot = -22.2551680110138 | etot = -17.9407210952928
-247000  ekin = 1.69964711256213 |  erot = 3.22260619239827 | epot = -22.1916408256116 | etot = -17.2693875206512
-248000  ekin = 1.92997585194759 |  erot = 3.61155944514373 | epot = -22.0096484177853 | etot = -16.4681131206939
-249000  ekin = 2.16278530892653 |  erot = 3.27771891456709 | epot = -21.8856058980727 | etot = -16.4451016745791
-250000  ekin = 2.32204054211024 |  erot = 2.46317574116847 | epot = -21.8028762710592 | etot = -17.0176599877804
-251000  ekin = 1.23768964067254 |  erot = 2.24150533762101 | epot = -21.763065707404 | etot = -18.2838707291104
-252000  ekin = 1.79818833522214 |  erot = 2.12556386664128 | epot = -21.7586349357285 | etot = -17.8348827338651
-253000  ekin = 2.12809689846393 |  erot = 2.59685639208402 | epot = -21.7226495687758 | etot = -16.9976962782278
-254000  ekin = 2.46813261968532 |  erot = 2.00391812662869 | epot = -21.7113918037362 | etot = -17.2393410574222
-255000  ekin = 2.3156672908729 |  erot = 2.03619058028117 | epot = -21.7265453183257 | etot = -17.3746874471716
-256000  ekin = 2.87223929491326 |  erot = 2.61790933826624 | epot = -21.659332511914 | etot = -16.1691838787345
-257000  ekin = 2.85756762932927 |  erot = 2.081746739162 | epot = -21.6161821054731 | etot = -16.6768677369819
-258000  ekin = 2.06111021157734 |  erot = 2.32748664972428 | epot = -21.5132485706727 | etot = -17.124651709371
-259000  ekin = 2.23305784057759 |  erot = 2.88843859953735 | epot = -21.5040039667855 | etot = -16.3825075266705
-260000  ekin = 2.49862397932476 |  erot = 2.38336885848389 | epot = -21.488210637319 | etot = -16.6062177995103
-261000  ekin = 2.09280296934734 |  erot = 2.39632540029205 | epot = -21.4325331777953 | etot = -16.9434048081559
-262000  ekin = 2.33576913564289 |  erot = 2.67273419354397 | epot = -21.3832241450035 | etot = -16.3747208158166
-263000  ekin = 2.20536189489354 |  erot = 2.71530627040565 | epot = -21.4329409070981 | etot = -16.5122727417989
-264000  ekin = 2.2858247573423 |  erot = 2.76839346219664 | epot = -21.39310844316 | etot = -16.338890223621
-265000  ekin = 1.70928536820409 |  erot = 1.79395423442894 | epot = -21.2682341921474 | etot = -17.7649945895144
-266000  ekin = 2.48721735474525 |  erot = 2.08745460533224 | epot = -21.1746995817337 | etot = -16.6000276216562
-267000  ekin = 2.69283567987773 |  erot = 2.10301910407211 | epot = -21.1705161290062 | etot = -16.3746613450564
-268000  ekin = 3.00000233743719 |  erot = 2.80954585635721 | epot = -21.164752112651 | etot = -15.3552039188566
-269000  ekin = 3.50713810468527 |  erot = 2.35763817348003 | epot = -21.1537110688984 | etot = -15.2889347907331
-270000  ekin = 3.50686942248863 |  erot = 1.86462765875888 | epot = -21.1925508822801 | etot = -15.8210538010326
-271000  ekin = 3.57026082273992 |  erot = 2.08172467795384 | epot = -21.2775817182941 | etot = -15.6255962176003
-272000  ekin = 2.4484752533773 |  erot = 3.08466485039761 | epot = -21.3619851902072 | etot = -15.8288450864322
-273000  ekin = 2.39748176307241 |  erot = 3.13355050446718 | epot = -21.4386234252579 | etot = -15.9075911577183
-274000  ekin = 2.48208144431863 |  erot = 2.00552494041967 | epot = -21.4476232953882 | etot = -16.9600169106499
-275000  ekin = 2.48721081149369 |  erot = 3.05413598233603 | epot = -21.4713984309062 | etot = -15.9300516370765
-276000  ekin = 2.82709589676966 |  erot = 2.88384306577856 | epot = -21.4434590118161 | etot = -15.7325200492679
-277000  ekin = 2.23479555963313 |  erot = 2.20310851955638 | epot = -21.3883073251199 | etot = -16.9504032459304
-278000  ekin = 2.81418916407429 |  erot = 3.24537052192613 | epot = -21.3155364074003 | etot = -15.2559767213999
-279000  ekin = 2.57366525203699 |  erot = 1.81705578305929 | epot = -21.2862101233851 | etot = -16.8954890882888
-280000  ekin = 2.41063464320149 |  erot = 1.76282693004731 | epot = -21.2549625280961 | etot = -17.0815009548473
-281000  ekin = 2.58126226070487 |  erot = 2.29258221702166 | epot = -21.306394928225 | etot = -16.4325504504985
-282000  ekin = 3.02016903398222 |  erot = 2.43094523890341 | epot = -21.4340900724633 | etot = -15.9829757995777
-283000  ekin = 2.59269149790331 |  erot = 2.11330689541033 | epot = -21.6296517079942 | etot = -16.9236533146806
-284000  ekin = 2.51704243107537 |  erot = 3.13156683036761 | epot = -21.7452694753527 | etot = -16.0966602139097
-285000  ekin = 2.4236537221525 |  erot = 1.77228258125507 | epot = -21.8557019037769 | etot = -17.6597656003693
-286000  ekin = 1.9446719552166 |  erot = 2.0366097411672 | epot = -21.901435736722 | etot = -17.9201540403382
-287000  ekin = 2.56319670376172 |  erot = 2.60867050510166 | epot = -21.90675099349 | etot = -16.7348837846266
-288000  ekin = 2.19574207425738 |  erot = 1.69805542160023 | epot = -21.8143855675961 | etot = -17.9205880717385
-289000  ekin = 2.35326278833027 |  erot = 1.65840109676146 | epot = -21.6976038565284 | etot = -17.6859399714367
-290000  ekin = 2.3519456177505 |  erot = 1.99444238353744 | epot = -21.6551012116075 | etot = -17.3087132103195
-291000  ekin = 1.48585281531715 |  erot = 2.66475825861554 | epot = -21.56036793472 | etot = -17.4097568607873
-292000  ekin = 2.10739944756451 |  erot = 2.42809824662638 | epot = -21.4451596117638 | etot = -16.9096619175729
-293000  ekin = 2.11618090223716 |  erot = 1.86694554151198 | epot = -21.3593625692767 | etot = -17.3762361255276
-294000  ekin = 2.06078090566332 |  erot = 2.13941873359476 | epot = -21.2326233100941 | etot = -17.032423670836
-295000  ekin = 2.11467178034793 |  erot = 2.3267343667518 | epot = -21.1123588667461 | etot = -16.6709527196464
-296000  ekin = 1.53087058859331 |  erot = 2.94008409149153 | epot = -21.2112197533848 | etot = -16.7402650732999
-297000  ekin = 2.52732986791196 |  erot = 2.18380855337858 | epot = -21.1955190508786 | etot = -16.4843806295881
-298000  ekin = 1.89033945823196 |  erot = 2.02521913176001 | epot = -21.2593750718296 | etot = -17.3438164818376
-299000  ekin = 1.87142873048436 |  erot = 1.66404563221549 | epot = -21.2919162310488 | etot = -17.7564418683489
-300000  ekin = 2.23872615546788 |  erot = 1.50807257618897 | epot = -21.3339204593826 | etot = -17.5871217277258
-301000  ekin = 1.99965506724558 |  erot = 2.00145094516844 | epot = -21.4707589194325 | etot = -17.4696529070184
-302000  ekin = 1.76370349732521 |  erot = 2.23787708901487 | epot = -21.5675275978257 | etot = -17.5659470114856
-303000  ekin = 2.69610887251788 |  erot = 1.6995722142974 | epot = -21.5563765448092 | etot = -17.1606954579939
-304000  ekin = 2.55447143501921 |  erot = 2.02060813090349 | epot = -21.5692327321341 | etot = -16.9941531662114
-305000  ekin = 2.38230604232717 |  erot = 2.31489374428114 | epot = -21.5335950166329 | etot = -16.8363952300246
-306000  ekin = 2.07785475765118 |  erot = 2.4523066068597 | epot = -21.4550895345847 | etot = -16.9249281700738
-307000  ekin = 3.17130424567278 |  erot = 3.29574614566806 | epot = -21.4151535289883 | etot = -14.9481031376474
-308000  ekin = 3.40959217051674 |  erot = 2.68389483402973 | epot = -21.4778643688409 | etot = -15.3843773642944
-309000  ekin = 2.36068264180093 |  erot = 2.91715332823342 | epot = -21.5794336507741 | etot = -16.3015976807398
-310000  ekin = 2.4995235722922 |  erot = 2.36028950896138 | epot = -21.5982142524176 | etot = -16.738401171164
-311000  ekin = 2.53288726180906 |  erot = 2.29596940545851 | epot = -21.6418553661547 | etot = -16.8129986988871
-312000  ekin = 2.05123272208704 |  erot = 2.92023923411834 | epot = -21.7377547517075 | etot = -16.7662827955022
-313000  ekin = 1.80834719374888 |  erot = 2.29357283142125 | epot = -21.7993116362532 | etot = -17.6973916110831
-314000  ekin = 2.30684015099018 |  erot = 2.20859462712272 | epot = -21.8029398081388 | etot = -17.2875050300259
-315000  ekin = 1.86413924486173 |  erot = 2.14748794238475 | epot = -21.8550418960799 | etot = -17.8434147088335
-316000  ekin = 2.20558056533516 |  erot = 3.03447287931582 | epot = -21.8868412075709 | etot = -16.6467877629199
-317000  ekin = 2.47820931125479 |  erot = 3.56870099099487 | epot = -21.9902146748519 | etot = -15.9433043726022
-318000  ekin = 2.36582343801679 |  erot = 3.01887804681552 | epot = -22.1178732891163 | etot = -16.733171804284
-319000  ekin = 2.40464629760758 |  erot = 3.15910789488741 | epot = -22.2289401281565 | etot = -16.6651859356615
-320000  ekin = 1.80206494109346 |  erot = 2.83527990295434 | epot = -22.3120263401861 | etot = -17.6746814961383
-321000  ekin = 2.91146951948762 |  erot = 2.25772268449837 | epot = -22.3029455835947 | etot = -17.1337533796087
-322000  ekin = 2.8226351296685 |  erot = 2.67950826833977 | epot = -22.3041650189947 | etot = -16.8020216209865
-323000  ekin = 2.067323568424 |  erot = 2.319752847753 | epot = -22.3338840353559 | etot = -17.9468076191789
-324000  ekin = 2.6012747278288 |  erot = 2.58351861537749 | epot = -22.3215168526944 | etot = -17.1367235094881
-325000  ekin = 3.45560055552843 |  erot = 2.50162515355505 | epot = -22.1825527777624 | etot = -16.2253270686789
-326000  ekin = 3.51422890604519 |  erot = 2.84426061018012 | epot = -22.0201095272525 | etot = -15.6616200110272
-327000  ekin = 2.63551490316295 |  erot = 2.20570805472231 | epot = -21.9384479867007 | etot = -17.0972250288154
-328000  ekin = 1.8043914440792 |  erot = 2.37599512200968 | epot = -21.861980397642 | etot = -17.6815938315531
-329000  ekin = 2.15766181563134 |  erot = 2.45286496267961 | epot = -21.8518523862112 | etot = -17.2413256079002
-330000  ekin = 1.8483425992464 |  erot = 2.03367429366601 | epot = -21.768409525242 | etot = -17.8863926323296
-331000  ekin = 2.3531484336258 |  erot = 1.80165819621476 | epot = -21.7197009414848 | etot = -17.5648943116443
-332000  ekin = 1.67855936307207 |  erot = 2.5334121965131 | epot = -21.7336434355881 | etot = -17.5216718760029
-333000  ekin = 1.60376334688456 |  erot = 2.14058675025446 | epot = -21.835637958395 | etot = -18.091287861256
-334000  ekin = 2.26551990081779 |  erot = 2.62486254825415 | epot = -21.8794971078471 | etot = -16.9891146587751
-335000  ekin = 2.91208137486081 |  erot = 3.11052870452009 | epot = -21.9161692767172 | etot = -15.8935591973363
-336000  ekin = 2.73132973682385 |  erot = 2.56213100489412 | epot = -21.8312488568505 | etot = -16.5377881151325
-337000  ekin = 3.15411918141902 |  erot = 3.87512819831194 | epot = -21.9061152574783 | etot = -14.8768678777473
-338000  ekin = 2.33141760424507 |  erot = 2.13211945089677 | epot = -21.913746111238 | etot = -17.4502090560962
-339000  ekin = 1.71915361945719 |  erot = 2.31270220754042 | epot = -21.904207477372 | etot = -17.8723516503744
-340000  ekin = 1.62199393011804 |  erot = 3.16990972384471 | epot = -21.8898233676232 | etot = -17.0979197136604
-341000  ekin = 1.71588704296646 |  erot = 3.17642860992459 | epot = -21.8345558128149 | etot = -16.9422401599239
-342000  ekin = 1.82178091247658 |  erot = 2.58875985611024 | epot = -21.7161502950573 | etot = -17.3056095264705
-343000  ekin = 3.08559255942693 |  erot = 2.94813449265471 | epot = -21.7030445300997 | etot = -15.669317478018
-344000  ekin = 2.95985387154984 |  erot = 3.1154751585035 | epot = -21.6815483295521 | etot = -15.6062192994987
-345000  ekin = 2.33428072266864 |  erot = 2.88044431283017 | epot = -21.6567075042343 | etot = -16.4419824687355
-346000  ekin = 2.02077664062698 |  erot = 3.45936833964707 | epot = -21.5877268821218 | etot = -16.1075819018478
-347000  ekin = 2.34924784800441 |  erot = 1.93056350805623 | epot = -21.4896151766055 | etot = -17.2098038205448
-348000  ekin = 2.79839267202794 |  erot = 2.79408776517963 | epot = -21.4682057474678 | etot = -15.8757253102602
-349000  ekin = 2.33820470114614 |  erot = 3.12966318670513 | epot = -21.5603039389198 | etot = -16.0924360510685
-350000  ekin = 2.22383234890832 |  erot = 2.38886870388011 | epot = -21.5375784703117 | etot = -16.9248774175233
-351000  ekin = 2.33329735253339 |  erot = 2.84447430695179 | epot = -21.5078106306152 | etot = -16.33003897113
-352000  ekin = 2.74923373919408 |  erot = 2.76796181793625 | epot = -21.5537134920816 | etot = -16.0365179349512
-353000  ekin = 1.76111836153717 |  erot = 2.12255592617518 | epot = -21.5037017999955 | etot = -17.6200275122832
-354000  ekin = 2.29967358188085 |  erot = 2.37615363620183 | epot = -21.559257977819 | etot = -16.8834307597364
-355000  ekin = 2.32956787601564 |  erot = 2.41406261152025 | epot = -21.5311925684016 | etot = -16.7875620808657
-356000  ekin = 2.99536507165417 |  erot = 3.0133786789017 | epot = -21.461213826164 | etot = -15.4524700756081
-357000  ekin = 1.79487551861702 |  erot = 2.14781775756832 | epot = -21.4425100027869 | etot = -17.4998167266016
-358000  ekin = 2.06856992699964 |  erot = 1.9158505155371 | epot = -21.4597512525557 | etot = -17.475330810019
-359000  ekin = 2.03457633089973 |  erot = 2.13725650388114 | epot = -21.434584367242 | etot = -17.2627515324611
-360000  ekin = 2.64289898809605 |  erot = 2.45722294398598 | epot = -21.3798303659973 | etot = -16.2797084339152
-361000  ekin = 2.44681633772951 |  erot = 2.40323525392197 | epot = -21.4535746870958 | etot = -16.6035230954443
-362000  ekin = 2.27284400709389 |  erot = 2.04866562998477 | epot = -21.4444048899961 | etot = -17.1228952529175
-363000  ekin = 3.23945885057604 |  erot = 1.79247859381387 | epot = -21.4992698914106 | etot = -16.4673324470207
-364000  ekin = 3.01124200487831 |  erot = 2.16495867321708 | epot = -21.5330648567406 | etot = -16.3568641786452
-365000  ekin = 2.51472285580867 |  erot = 2.29864111879035 | epot = -21.6252096459669 | etot = -16.8118456713679
-366000  ekin = 2.59356655410022 |  erot = 2.21031948632573 | epot = -21.6397726115723 | etot = -16.8358865711464
-367000  ekin = 2.23422490605626 |  erot = 1.85375489374336 | epot = -21.7036464131406 | etot = -17.615666613341
-368000  ekin = 2.47747707853682 |  erot = 2.36511710555106 | epot = -21.7442459693683 | etot = -16.9016517852804
-369000  ekin = 2.03854183495619 |  erot = 2.80790943599038 | epot = -21.829546112742 | etot = -16.9830948417954
-370000  ekin = 2.08495509326204 |  erot = 2.15717784784087 | epot = -21.8579547558588 | etot = -17.6158218147559
-371000  ekin = 2.1649158804987 |  erot = 2.10731342711637 | epot = -21.750730287247 | etot = -17.4785009796319
-372000  ekin = 1.83416420958724 |  erot = 1.90082367490453 | epot = -21.6784224725519 | etot = -17.9434345880602
-373000  ekin = 1.97176482573297 |  erot = 1.77796007890949 | epot = -21.6393712386778 | etot = -17.8896463340354
-374000  ekin = 2.89940710658305 |  erot = 1.91194262525378 | epot = -21.5337545453636 | etot = -16.7224048135267
-375000  ekin = 2.32339676163341 |  erot = 1.92362318361284 | epot = -21.4217091025191 | etot = -17.1746891572728
-376000  ekin = 2.59047552311153 |  erot = 2.32394149083979 | epot = -21.4139727856534 | etot = -16.4995557717021
-377000  ekin = 2.24598863840517 |  erot = 1.65770205797294 | epot = -21.3405339068232 | etot = -17.4368432104451
-378000  ekin = 2.38351514056703 |  erot = 2.54156262207207 | epot = -21.3122380587448 | etot = -16.3871602961057
-379000  ekin = 2.08457212928958 |  erot = 2.11819645676889 | epot = -21.2663127721437 | etot = -17.0635441860853
-380000  ekin = 2.62168026009058 |  erot = 2.36576073073357 | epot = -21.2469701231192 | etot = -16.259529132295
-381000  ekin = 2.42554871977308 |  erot = 2.21588725182519 | epot = -21.2594018196931 | etot = -16.6179658480948
-382000  ekin = 2.04454090532126 |  erot = 3.35199327879852 | epot = -21.3507561156204 | etot = -15.9542219315006
-383000  ekin = 2.57756769789846 |  erot = 1.58356833947095 | epot = -21.4206473136967 | etot = -17.2595112763272
-384000  ekin = 2.32411392435712 |  erot = 2.07034159075996 | epot = -21.425401700327 | etot = -17.03094618521
-385000  ekin = 1.93815279071873 |  erot = 3.29970374476252 | epot = -21.4993838182002 | etot = -16.2615272827189
-386000  ekin = 2.10645704249442 |  erot = 2.94380940917572 | epot = -21.5050572923383 | etot = -16.4547908406681
-387000  ekin = 2.28625118399721 |  erot = 2.404880226949 | epot = -21.4350466670762 | etot = -16.74391525613
-388000  ekin = 2.84183807689895 |  erot = 2.72440789072405 | epot = -21.448767296848 | etot = -15.882521329225
-389000  ekin = 3.39750799106372 |  erot = 3.08194517695386 | epot = -21.6559630447603 | etot = -15.1765098767427
-390000  ekin = 2.82211920760115 |  erot = 2.04880343622589 | epot = -21.7229608878358 | etot = -16.8520382440088
-391000  ekin = 2.25113345866117 |  erot = 2.45876014532077 | epot = -21.7793475672488 | etot = -17.0694539632668
-392000  ekin = 2.6777973992177 |  erot = 2.75278604715789 | epot = -21.9200377033298 | etot = -16.4894542569542
-393000  ekin = 2.07336639249413 |  erot = 1.66102921524042 | epot = -22.0500496423094 | etot = -18.3156540345748
-394000  ekin = 2.1138614951422 |  erot = 2.4065490584156 | epot = -22.0647062581752 | etot = -17.5442957046174
-395000  ekin = 2.46967791557607 |  erot = 2.46187607744978 | epot = -22.0113006362931 | etot = -17.0797466432672
-396000  ekin = 3.17858061422168 |  erot = 1.60030928107608 | epot = -21.9570022338792 | etot = -17.1781123385814
-397000  ekin = 2.37483507726776 |  erot = 2.17387816921976 | epot = -21.8769234701935 | etot = -17.3282102237059
-398000  ekin = 2.29815779154461 |  erot = 2.2014862703049 | epot = -21.8293641014529 | etot = -17.3297200396034
-399000  ekin = 2.66620669497936 |  erot = 2.78316441348845 | epot = -21.7420307764657 | etot = -16.2926596679979
-400000  ekin = 1.8196142363994 |  erot = 2.77573291920477 | epot = -21.7225828560707 | etot = -17.1272357004666
-401000  ekin = 2.39347596566753 |  erot = 3.11237720134102 | epot = -21.7632198127751 | etot = -16.2573666457665
-402000  ekin = 4.01379092525261 |  erot = 3.58756310879361 | epot = -21.6952307126456 | etot = -14.0938766785994
-403000  ekin = 3.64238723358271 |  erot = 3.44210139074533 | epot = -21.6932224157202 | etot = -14.6087337913922
-404000  ekin = 2.52116102522202 |  erot = 2.99286839639893 | epot = -21.7395466120138 | etot = -16.2255171903929
-405000  ekin = 2.80514548558626 |  erot = 3.09807228440149 | epot = -21.809681120553 | etot = -15.9064633505653
-406000  ekin = 2.32696376764902 |  erot = 2.03572639782902 | epot = -21.9111381639248 | etot = -17.5484479984468
-407000  ekin = 2.33504128016395 |  erot = 1.91320949168965 | epot = -21.9359478399848 | etot = -17.6876970681312
-408000  ekin = 1.90942025822265 |  erot = 2.20375631379574 | epot = -21.9849314014528 | etot = -17.8717548294344
-409000  ekin = 1.98818542800297 |  erot = 1.95540808206523 | epot = -22.0378349759701 | etot = -18.0942414659019
-410000  ekin = 1.59823476401333 |  erot = 1.91272967852491 | epot = -22.0830507565096 | etot = -18.5720863139714
-411000  ekin = 1.87320182179615 |  erot = 2.46575148951076 | epot = -22.1911106440468 | etot = -17.8521573327399
-412000  ekin = 2.51909186028136 |  erot = 2.65534868642724 | epot = -22.281680067606 | etot = -17.1072395208974
-413000  ekin = 2.80929435327118 |  erot = 3.19888285052217 | epot = -22.1907679968741 | etot = -16.1825907930808
-414000  ekin = 2.79014519733558 |  erot = 2.7251519541093 | epot = -22.144863024243 | etot = -16.6295658727981
-415000  ekin = 2.46789019087319 |  erot = 2.24891720770208 | epot = -22.1977268949425 | etot = -17.4809194963672
-416000  ekin = 3.30766536008866 |  erot = 1.55878918639505 | epot = -22.1694878213559 | etot = -17.3030332748722
-417000  ekin = 3.95074944679108 |  erot = 2.44780201516577 | epot = -22.1018895242095 | etot = -15.7033380622526
-418000  ekin = 2.77340936693415 |  erot = 2.68993840817536 | epot = -21.977327562767 | etot = -16.5139797876575
-419000  ekin = 2.38275203991917 |  erot = 2.97769109273478 | epot = -21.9010102007429 | etot = -16.5405670680889
-420000  ekin = 1.80397709765343 |  erot = 1.82715488758969 | epot = -21.8849019003165 | etot = -18.2537699150734
-421000  ekin = 1.35294173647286 |  erot = 1.7746327595132 | epot = -21.8324727162455 | etot = -18.7048982202595
-422000  ekin = 1.39101035408781 |  erot = 2.74626781088313 | epot = -21.8922044238521 | etot = -17.7549262588811
-423000  ekin = 1.58313118355036 |  erot = 3.0798858727609 | epot = -21.9303489156376 | etot = -17.2673318593263
-424000  ekin = 2.38308976422853 |  erot = 2.0290563283423 | epot = -22.0003513420112 | etot = -17.5882052494403
-425000  ekin = 2.32292982636642 |  erot = 2.54472792699355 | epot = -22.0461884305753 | etot = -17.1785306772154
-426000  ekin = 2.07274921207622 |  erot = 3.12068562025985 | epot = -21.9899604929779 | etot = -16.7965256606419
-427000  ekin = 2.16499158921497 |  erot = 2.43609860560844 | epot = -21.883756502818 | etot = -17.2826663079946
-428000  ekin = 1.81001230881454 |  erot = 1.6518491031194 | epot = -21.8651168729134 | etot = -18.4032554609795
-429000  ekin = 1.67080799563552 |  erot = 2.55829004033943 | epot = -21.823203822061 | etot = -17.5941057860861
-430000  ekin = 2.68658781224627 |  erot = 2.8591925337156 | epot = -21.8545360487503 | etot = -16.3087557027885
-431000  ekin = 2.77334901985549 |  erot = 1.57746917070686 | epot = -21.8360353910944 | etot = -17.485217200532
-432000  ekin = 2.50244674166436 |  erot = 1.60779258881598 | epot = -21.7381087453319 | etot = -17.6278694148516
-433000  ekin = 1.85649371322473 |  erot = 2.4917335891794 | epot = -21.7919912827364 | etot = -17.4437639803323
-434000  ekin = 2.89302367450635 |  erot = 2.7989004560269 | epot = -21.923157505168 | etot = -16.2312333746348
-435000  ekin = 3.67647442700572 |  erot = 1.38588132381276 | epot = -22.1019777057281 | etot = -17.0396219549097
-436000  ekin = 3.05510329104703 |  erot = 2.00142902882896 | epot = -22.1034257027066 | etot = -17.0468933828306
-437000  ekin = 3.2334117289381 |  erot = 1.78346855436481 | epot = -22.1137020887251 | etot = -17.0968218054222
-438000  ekin = 2.86378458795303 |  erot = 1.84588842157479 | epot = -22.072414124752 | etot = -17.3627411152242
-439000  ekin = 2.41407153953135 |  erot = 2.70066632790346 | epot = -22.0535011599236 | etot = -16.9387632924888
-440000  ekin = 2.22110309163132 |  erot = 3.0167468581899 | epot = -22.0773629228072 | etot = -16.839512972986
-441000  ekin = 2.8952003347941 |  erot = 2.87911130379518 | epot = -22.2098492363511 | etot = -16.4355375977618
-442000  ekin = 2.05598301233622 |  erot = 1.73562369066667 | epot = -22.2689079268812 | etot = -18.4773012238783
-443000  ekin = 1.86650631344267 |  erot = 2.00816178040311 | epot = -22.3072964279925 | etot = -18.4326283341467
-444000  ekin = 2.06088560705618 |  erot = 2.15265011198712 | epot = -22.3186686701219 | etot = -18.1051329510786
-445000  ekin = 2.10029110633057 |  erot = 2.2800331405132 | epot = -22.3739249314238 | etot = -17.9936006845801
-446000  ekin = 2.42121462246176 |  erot = 2.85365097104764 | epot = -22.4030820729314 | etot = -17.128216479422
-447000  ekin = 2.19905370994782 |  erot = 2.98216231903379 | epot = -22.4760062523442 | etot = -17.2947902233625
-448000  ekin = 2.35344530580996 |  erot = 2.94496431571713 | epot = -22.4927466941727 | etot = -17.1943370726456
-449000  ekin = 2.39032460069844 |  erot = 2.92889137252356 | epot = -22.5027878081879 | etot = -17.1835718349659
-450000  ekin = 1.87543018481826 |  erot = 1.69603328668916 | epot = -22.4562462785528 | etot = -18.8847828070454
-451000  ekin = 2.01850498861611 |  erot = 1.92812989993404 | epot = -22.4817672986218 | etot = -18.5351324100716
-452000  ekin = 1.36652609658347 |  erot = 1.87105620810406 | epot = -22.4501755877893 | etot = -19.2125932831018
-453000  ekin = 2.0599225820261 |  erot = 2.56027964608567 | epot = -22.2765869721545 | etot = -17.6563847440428
-454000  ekin = 1.47421749728914 |  erot = 2.19120144206327 | epot = -22.1381671023588 | etot = -18.4727481630064
-455000  ekin = 1.65550022307771 |  erot = 2.72165814308168 | epot = -21.9904394751434 | etot = -17.613281108984
-456000  ekin = 2.34827062603187 |  erot = 2.00722438151074 | epot = -21.9105114729144 | etot = -17.5550164653718
-457000  ekin = 2.01338249991754 |  erot = 2.37170378033695 | epot = -21.8819790372449 | etot = -17.4968927569904
-458000  ekin = 1.72815421955305 |  erot = 2.26329746701056 | epot = -21.9116044050661 | etot = -17.9201527185024
-459000  ekin = 2.48347398227002 |  erot = 2.32376196929941 | epot = -21.9949404038568 | etot = -17.1877044522874
-460000  ekin = 2.18770854699575 |  erot = 2.00081662918322 | epot = -21.9585322440375 | etot = -17.7700070678586
-461000  ekin = 2.27716435663744 |  erot = 2.9019565626907 | epot = -21.8877682177659 | etot = -16.7086472984378
-462000  ekin = 2.61244889701715 |  erot = 1.79757533309513 | epot = -21.9143949779912 | etot = -17.5043707478789
-463000  ekin = 2.55684814656524 |  erot = 3.31200610027657 | epot = -21.8497749242034 | etot = -15.9809206773616
-464000  ekin = 2.15312235839157 |  erot = 2.38947690136822 | epot = -21.7825241097983 | etot = -17.2399248500385
-465000  ekin = 2.5257577253008 |  erot = 3.61331808321477 | epot = -21.70727052519 | etot = -15.5681947166744
-466000  ekin = 1.97943618964772 |  erot = 2.88688528337621 | epot = -21.7222514097774 | etot = -16.8559299367535
-467000  ekin = 1.62882257493983 |  erot = 2.60892282315519 | epot = -21.8080861041928 | etot = -17.5703407060978
-468000  ekin = 1.09823854644375 |  erot = 3.35073251937299 | epot = -21.8523811012329 | etot = -17.4034100354162
-469000  ekin = 1.70229597385131 |  erot = 2.7588984072639 | epot = -21.8665756757502 | etot = -17.405381294635
-470000  ekin = 1.85844768422772 |  erot = 2.8706546217625 | epot = -21.9036130079376 | etot = -17.1745107019474
-471000  ekin = 2.74399539924327 |  erot = 2.34943354955083 | epot = -21.9543989717239 | etot = -16.8609700229298
-472000  ekin = 2.7182617922689 |  erot = 2.13581917182001 | epot = -22.0449294707038 | etot = -17.1908485066149
-473000  ekin = 2.29380642077304 |  erot = 2.07595163501546 | epot = -22.0706135180041 | etot = -17.7008554622156
-474000  ekin = 2.22690782122656 |  erot = 2.1647059901395 | epot = -22.0704871162386 | etot = -17.6788733048726
-475000  ekin = 2.4978679533329 |  erot = 2.09510196885223 | epot = -22.0509742163569 | etot = -17.4580042941718
-476000  ekin = 2.20264299239668 |  erot = 1.76757923556403 | epot = -21.9427521555982 | etot = -17.9725299276375
-477000  ekin = 2.45872237399503 |  erot = 2.38426997478539 | epot = -21.9051474088983 | etot = -17.0621550601178
-478000  ekin = 1.89905964030889 |  erot = 2.04864356713722 | epot = -21.9114508304737 | etot = -17.9637476230276
-479000  ekin = 2.27133902137491 |  erot = 3.08755197682257 | epot = -21.8872829373266 | etot = -16.5283919391291
-480000  ekin = 1.67015605151468 |  erot = 2.76560365045837 | epot = -21.8968158425889 | etot = -17.4610561406158
-481000  ekin = 1.81882995680354 |  erot = 2.94136105971067 | epot = -21.8571304925407 | etot = -17.0969394760265
-482000  ekin = 2.15305069632653 |  erot = 2.07327897823918 | epot = -21.8152992914385 | etot = -17.5889696168728
-483000  ekin = 1.50004535981758 |  erot = 1.99364343935404 | epot = -21.7843644990947 | etot = -18.2906756999231
-484000  ekin = 1.85234844255529 |  erot = 2.34000231202781 | epot = -21.8614293841666 | etot = -17.6690786295835
-485000  ekin = 1.64682178328831 |  erot = 2.50437862576679 | epot = -21.8969405008956 | etot = -17.7457400918405
-486000  ekin = 1.86104257115938 |  erot = 2.15995925522771 | epot = -21.8879397421696 | etot = -17.8669379157825
-487000  ekin = 2.34639026339217 |  erot = 3.11622773972825 | epot = -21.9707194220382 | etot = -16.5081014189178
-488000  ekin = 2.27484994031488 |  erot = 3.28147617368226 | epot = -21.9426475486812 | etot = -16.3863214346841
-489000  ekin = 2.38811933287365 |  erot = 2.56070014238266 | epot = -21.8600861168089 | etot = -16.9112666415526
-490000  ekin = 2.12976254880773 |  erot = 3.54525746010289 | epot = -21.7617637919249 | etot = -16.0867437830143
-491000  ekin = 2.20850764560417 |  erot = 2.48919239454317 | epot = -21.6468680069132 | etot = -16.9491679667658
-492000  ekin = 2.43957739853024 |  erot = 2.76323186690378 | epot = -21.6230951653168 | etot = -16.4202858998828
-493000  ekin = 1.79391622496105 |  erot = 2.29052518470042 | epot = -21.6945975278841 | etot = -17.6101561182226
-494000  ekin = 2.11542949642227 |  erot = 3.01313865872481 | epot = -21.7637004472039 | etot = -16.6351322920568
-495000  ekin = 2.1568591957283 |  erot = 2.49005677705245 | epot = -21.8783556810053 | etot = -17.2314397082246
-496000  ekin = 2.06037552826019 |  erot = 2.60698629104699 | epot = -21.9276220332962 | etot = -17.260260213989
-497000  ekin = 2.52228141248763 |  erot = 1.710130192768 | epot = -21.8769629373864 | etot = -17.6445513321307
-498000  ekin = 2.15394500805411 |  erot = 1.78777085700022 | epot = -21.8243748366056 | etot = -17.8826589715513
-499000  ekin = 3.01296343053108 |  erot = 1.73934813146708 | epot = -21.8392632680439 | etot = -17.0869517060458
-500000  ekin = 2.76642119718551 |  erot = 2.50182215373002 | epot = -21.830671988603 | etot = -16.5624286376875
-501000  ekin = 2.69367571720338 |  erot = 2.99042817784739 | epot = -21.7039103667138 | etot = -16.0198064716631
-502000  ekin = 1.91666556639459 |  erot = 3.89815239299714 | epot = -21.5845300715443 | etot = -15.7697121121525
-503000  ekin = 1.80513448090424 |  erot = 2.94463129244922 | epot = -21.408846856306 | etot = -16.6590810829525
-504000  ekin = 1.70082883689617 |  erot = 3.04312463877848 | epot = -21.3315058298563 | etot = -16.5875523541817
-505000  ekin = 2.75953000022913 |  erot = 2.14635942194519 | epot = -21.3525103549444 | etot = -16.4466209327701
-506000  ekin = 2.29728093923375 |  erot = 2.04403144683579 | epot = -21.3794572010067 | etot = -17.0381448149372
-507000  ekin = 3.17636857959624 |  erot = 2.42164349794529 | epot = -21.4731108320934 | etot = -15.8750987545519
-508000  ekin = 2.53590109429522 |  erot = 2.52790695399208 | epot = -21.6300410847596 | etot = -16.5662330364723
-509000  ekin = 2.12748393236722 |  erot = 2.83071060777933 | epot = -21.7781347526393 | etot = -16.8199402124927
-510000  ekin = 2.16138023827908 |  erot = 1.44739524871434 | epot = -21.8661383228762 | etot = -18.2573628358828
-511000  ekin = 2.5432337386743 |  erot = 2.77108674378182 | epot = -21.9670096484361 | etot = -16.65268916598
-512000  ekin = 2.32820226144235 |  erot = 2.8042493163404 | epot = -22.0177071813425 | etot = -16.8852556035598
-513000  ekin = 2.47700215188743 |  erot = 2.17127792631492 | epot = -22.0110285387343 | etot = -17.3627484605319
-514000  ekin = 2.76651136580707 |  erot = 2.55680467976047 | epot = -22.0909970005814 | etot = -16.7676809550138
-515000  ekin = 2.5202331965388 |  erot = 1.82499891391154 | epot = -22.1712715169565 | etot = -17.8260394065062
-516000  ekin = 2.81741012640848 |  erot = 2.22255273815334 | epot = -22.2621950124766 | etot = -17.2222321479148
-517000  ekin = 2.03287831599844 |  erot = 2.04932227860395 | epot = -22.2794486174447 | etot = -18.1972480228423
-518000  ekin = 2.18753527424292 |  erot = 2.76011341951323 | epot = -22.2667176836093 | etot = -17.3190689898532
-519000  ekin = 2.23127004412533 |  erot = 2.23036422155453 | epot = -22.3641437250361 | etot = -17.9025094593562
-520000  ekin = 1.88835704965194 |  erot = 2.20137678015021 | epot = -22.4547788180201 | etot = -18.365044988218
-521000  ekin = 2.57911594310157 |  erot = 1.87216207270883 | epot = -22.6071563154982 | etot = -18.1558782996878
-522000  ekin = 3.47551915105823 |  erot = 1.7762374523623 | epot = -22.6852629490162 | etot = -17.4335063455956
-523000  ekin = 2.84545293485784 |  erot = 2.47507537559667 | epot = -22.727728352182 | etot = -17.4072000417275
-524000  ekin = 2.40278895519472 |  erot = 2.37529684497552 | epot = -22.6643160930411 | etot = -17.8862302928709
-525000  ekin = 1.59507033575009 |  erot = 2.61508341973268 | epot = -22.5633164974795 | etot = -18.3531627419968
-526000  ekin = 1.67007684014044 |  erot = 1.59545284095808 | epot = -22.511319978416 | etot = -19.2457902973175
-527000  ekin = 2.19667533945247 |  erot = 1.93330231246752 | epot = -22.4181345854017 | etot = -18.2881569334817
-528000  ekin = 2.6386695788743 |  erot = 2.84200507572115 | epot = -22.4271496272375 | etot = -16.946474972642
-529000  ekin = 2.71685924097597 |  erot = 3.01195511036354 | epot = -22.4607209136928 | etot = -16.7319065623533
-530000  ekin = 2.59646038482582 |  erot = 2.1317692819235 | epot = -22.3209630404852 | etot = -17.5927333737358
-531000  ekin = 2.96818211550215 |  erot = 2.35836906019033 | epot = -22.2240561584028 | etot = -16.8975049827103
-532000  ekin = 2.54400448114086 |  erot = 2.32266423688292 | epot = -22.2383323718678 | etot = -17.3716636538441
-533000  ekin = 2.47235456553948 |  erot = 2.96337386592411 | epot = -22.2434312615742 | etot = -16.8077028301106
-534000  ekin = 2.104894788263 |  erot = 2.03894640697441 | epot = -22.2624131617689 | etot = -18.1185719665315
-535000  ekin = 3.76811893478762 |  erot = 2.64694643296526 | epot = -22.2342741399369 | etot = -15.819208772184
-536000  ekin = 2.78932048770646 |  erot = 1.95046774407585 | epot = -22.1710588414062 | etot = -17.4312706096239
-537000  ekin = 2.84547413963846 |  erot = 2.6235440651257 | epot = -22.0792539675812 | etot = -16.610235762817
-538000  ekin = 2.67615418297317 |  erot = 2.08962546790895 | epot = -21.9560559397441 | etot = -17.190276288862
-539000  ekin = 2.73041224389434 |  erot = 2.35761678189143 | epot = -22.0360310245606 | etot = -16.9480019987748
-540000  ekin = 2.45513520817505 |  erot = 2.4980712479617 | epot = -22.1997448500024 | etot = -17.2465383938656
-541000  ekin = 3.48268229748523 |  erot = 2.77797330372245 | epot = -22.2939060084685 | etot = -16.0332504072608
-542000  ekin = 2.48960436886327 |  erot = 2.87332479229809 | epot = -22.3004887690915 | etot = -16.9375596079301
-543000  ekin = 2.34699181381528 |  erot = 2.86167842257193 | epot = -22.3027783678197 | etot = -17.0941081314325
-544000  ekin = 2.22918134297116 |  erot = 1.4682792461716 | epot = -22.2757921511235 | etot = -18.5783315619807
-545000  ekin = 2.45393652663684 |  erot = 2.14178562937392 | epot = -22.2696521197313 | etot = -17.6739299637206
-546000  ekin = 1.98434977645849 |  erot = 2.24144093113159 | epot = -22.232171992891 | etot = -18.0063812853009
-547000  ekin = 2.56230350196472 |  erot = 1.8957462591202 | epot = -22.2013923967025 | etot = -17.7433426356176
-548000  ekin = 1.72907614338158 |  erot = 1.64127030305735 | epot = -22.1897325934373 | etot = -18.8193861469984
-549000  ekin = 1.95696682165776 |  erot = 2.64539988943055 | epot = -22.3281210018679 | etot = -17.7257542907796
-550000  ekin = 1.80672944936439 |  erot = 1.58554489058937 | epot = -22.4379557312283 | etot = -19.0456813912745
-551000  ekin = 2.19785864069661 |  erot = 2.26344341600386 | epot = -22.4944444264338 | etot = -18.0331423697333
-552000  ekin = 2.074442528674 |  erot = 2.49246441473273 | epot = -22.5313734934249 | etot = -17.9644665500182
-553000  ekin = 2.94841939583913 |  erot = 2.1230978630074 | epot = -22.5870982488507 | etot = -17.5155809900042
-554000  ekin = 2.86687820100223 |  erot = 1.9428729838172 | epot = -22.755332978123 | etot = -17.9455817933036
-555000  ekin = 2.43102414091851 |  erot = 2.28708167460996 | epot = -22.8409516497233 | etot = -18.1228458341949
-556000  ekin = 2.31020008885682 |  erot = 2.55815314755913 | epot = -22.8777743355338 | etot = -18.0094210991179
-557000  ekin = 2.81359485404958 |  erot = 1.42586137655665 | epot = -22.93912738 | etot = -18.6996711493938
-558000  ekin = 2.7970970853355 |  erot = 1.99545051650404 | epot = -22.9823826800611 | etot = -18.1898350782216
-559000  ekin = 3.34842854089643 |  erot = 2.30939572175805 | epot = -23.0558646505447 | etot = -17.3980403878902
-560000  ekin = 3.12583165184862 |  erot = 2.33613566970363 | epot = -23.0537007225862 | etot = -17.591733401034
-561000  ekin = 2.9127609673679 |  erot = 2.07459481236913 | epot = -22.982260765434 | etot = -17.994904985697
-562000  ekin = 3.33017095598494 |  erot = 2.52215992853225 | epot = -22.8889363116257 | etot = -17.0366054271086
-563000  ekin = 2.70200701416854 |  erot = 1.64770113379199 | epot = -22.8712722594835 | etot = -18.521564111523
-564000  ekin = 2.82953631474813 |  erot = 2.52900560163798 | epot = -22.8387855460795 | etot = -17.4802436296934
-565000  ekin = 2.67999888917708 |  erot = 2.05091800967453 | epot = -22.7937507048715 | etot = -18.0628338060199
-566000  ekin = 2.32986557500305 |  erot = 2.16379904557213 | epot = -22.8028233873669 | etot = -18.3091587667917
-567000  ekin = 1.92319601586312 |  erot = 2.83258522428556 | epot = -22.7588270107033 | etot = -18.0030457705546
-568000  ekin = 2.1767237164987 |  erot = 2.23391201707386 | epot = -22.7857243432792 | etot = -18.3750886097066
-569000  ekin = 2.44197408396629 |  erot = 2.6515953630557 | epot = -22.7197314796374 | etot = -17.6261620326154
-570000  ekin = 2.43177406209051 |  erot = 1.89764945519458 | epot = -22.6963472615904 | etot = -18.3669237443054
-571000  ekin = 2.86160521289847 |  erot = 2.96804382024775 | epot = -22.6961835038031 | etot = -16.8665344706569
-572000  ekin = 1.92662919536387 |  erot = 3.79135909534691 | epot = -22.6587081618987 | etot = -16.940719871188
-573000  ekin = 2.40137439242946 |  erot = 2.29982613356341 | epot = -22.6365074046858 | etot = -17.935306878693
-574000  ekin = 1.68882589350908 |  erot = 2.3209740449249 | epot = -22.6783832960445 | etot = -18.6685833576105
-575000  ekin = 1.85490665091732 |  erot = 1.8564080891142 | epot = -22.7444448136904 | etot = -19.0331300736588
-576000  ekin = 3.24775679594035 |  erot = 2.9556926821431 | epot = -22.6991990620437 | etot = -16.4957495839603
-577000  ekin = 2.89423151645282 |  erot = 2.87486712706735 | epot = -22.628436560802 | etot = -16.8593379172818
-578000  ekin = 2.4046091667757 |  erot = 2.78216711024699 | epot = -22.4348874817265 | etot = -17.2481112047039
-579000  ekin = 2.40580528046576 |  erot = 1.9955781448253 | epot = -22.288913673667 | etot = -17.887530248376
-580000  ekin = 2.69817090358906 |  erot = 1.94741864170502 | epot = -22.1754486864787 | etot = -17.5298591411846
-581000  ekin = 2.06309668646281 |  erot = 2.97621367011722 | epot = -22.0670098600828 | etot = -17.0276995035027
-582000  ekin = 2.33869527454826 |  erot = 3.07898324506955 | epot = -21.9478320300713 | etot = -16.5301535104535
-583000  ekin = 2.23428959741495 |  erot = 2.68476693088864 | epot = -21.837983720672 | etot = -16.9189271923684
-584000  ekin = 2.94321016295282 |  erot = 2.59995039730549 | epot = -21.7517635625832 | etot = -16.2086030023248
-585000  ekin = 2.36063475490835 |  erot = 2.49112677628938 | epot = -21.7173359488816 | etot = -16.8655744176839
-586000  ekin = 3.56583702163525 |  erot = 2.02487858259688 | epot = -21.7707868137138 | etot = -16.1800712094817
-587000  ekin = 3.53727585853243 |  erot = 1.9725893265202 | epot = -21.7665121756112 | etot = -16.2566469905585
-588000  ekin = 2.82339556293757 |  erot = 1.59340504807046 | epot = -21.7545319340972 | etot = -17.3377313230892
-589000  ekin = 2.31627310139818 |  erot = 2.20582604523299 | epot = -21.8199173705563 | etot = -17.2978182239252
-590000  ekin = 2.57616671531331 |  erot = 1.72768273328208 | epot = -21.8427138199642 | etot = -17.5388643713688
-591000  ekin = 1.91473306171853 |  erot = 3.80604384238379 | epot = -21.9351393124187 | etot = -16.2143624083164
-592000  ekin = 2.11222958764659 |  erot = 2.84208333850205 | epot = -21.9639458839076 | etot = -17.0096329577589
-593000  ekin = 1.66462149590471 |  erot = 2.46217253451014 | epot = -21.9921445323971 | etot = -17.8653505019822
-594000  ekin = 1.86314045588476 |  erot = 2.37275936142268 | epot = -22.1149191228505 | etot = -17.879019305543
-595000  ekin = 1.6397125755004 |  erot = 2.1497024679856 | epot = -22.2960530768755 | etot = -18.5066380333895
-596000  ekin = 1.86247376576131 |  erot = 1.5693809542787 | epot = -22.4014957466218 | etot = -18.9696410265818
-597000  ekin = 2.210739014067 |  erot = 2.3087175693751 | epot = -22.4599242604733 | etot = -17.9404676770312
-598000  ekin = 1.8660134932493 |  erot = 3.02311727399809 | epot = -22.5165298316334 | etot = -17.627399064386
-599000  ekin = 2.86271635930755 |  erot = 2.19928854437227 | epot = -22.536599708025 | etot = -17.4745948043452
-600000  ekin = 2.65062163067179 |  erot = 2.14533898812782 | epot = -22.4620537969303 | etot = -17.6660931781307
-601000  ekin = 2.97018864875202 |  erot = 3.19824090103877 | epot = -22.3271949752462 | etot = -16.1587654254554
-602000  ekin = 2.93416893709001 |  erot = 2.68627449040958 | epot = -22.2245183728173 | etot = -16.6040749453177
-603000  ekin = 2.5987545006459 |  erot = 2.71301833029982 | epot = -22.1705323477201 | etot = -16.8587595167744
-604000  ekin = 1.79059859762797 |  erot = 2.11515305424796 | epot = -22.1931056020217 | etot = -18.2873539501458
-605000  ekin = 1.82914051863723 |  erot = 2.27656979248766 | epot = -22.2183915784731 | etot = -18.1126812673482
-606000  ekin = 2.33864125390345 |  erot = 2.204164937778 | epot = -22.1617656383863 | etot = -17.6189594467048
-607000  ekin = 2.72666217259876 |  erot = 2.97710334336218 | epot = -22.1572786906588 | etot = -16.4535131746978
-608000  ekin = 2.45226937954678 |  erot = 2.41232790919959 | epot = -22.1263051367364 | etot = -17.2617078479901
-609000  ekin = 1.91032127854288 |  erot = 2.62712516529567 | epot = -22.0127581830193 | etot = -17.4753117391807
-610000  ekin = 3.01319055031108 |  erot = 2.17098104720965 | epot = -21.930499629869 | etot = -16.7463280323483
-611000  ekin = 2.44410994437293 |  erot = 2.75159061185424 | epot = -21.9258193850468 | etot = -16.7301188288197
-612000  ekin = 2.50271115837174 |  erot = 2.16817640692169 | epot = -21.9676183236645 | etot = -17.2967307583711
-613000  ekin = 3.01842230632868 |  erot = 2.12784419676567 | epot = -22.0277467117807 | etot = -16.8814802086864
-614000  ekin = 2.25331711369829 |  erot = 2.99334048390158 | epot = -22.0701464667307 | etot = -16.8234888691309
-615000  ekin = 1.66376443031995 |  erot = 2.63613776051569 | epot = -21.9985978951916 | etot = -17.698695704356
-616000  ekin = 1.89454248699046 |  erot = 2.87318355169532 | epot = -22.0041678369046 | etot = -17.2364417982189
-617000  ekin = 2.14789714287838 |  erot = 2.51249074123957 | epot = -22.0251474680604 | etot = -17.3647595839425
-618000  ekin = 3.11174934178844 |  erot = 2.74374306269141 | epot = -21.980284295602 | etot = -16.1247918911221
-619000  ekin = 3.41036213968179 |  erot = 2.10616794159728 | epot = -21.9557959924962 | etot = -16.4392659112171
-620000  ekin = 4.28430989238205 |  erot = 2.19572475327593 | epot = -21.9033881020935 | etot = -15.4233534564355
-621000  ekin = 3.095687767491 |  erot = 2.55794040804605 | epot = -21.8286763731363 | etot = -16.1750481975993
-622000  ekin = 2.76030419206697 |  erot = 2.60754397958254 | epot = -21.7459002641757 | etot = -16.3780520925262
-623000  ekin = 2.87269212022169 |  erot = 2.90401311950186 | epot = -21.5853226709315 | etot = -15.8086174312079
-624000  ekin = 2.01889500087932 |  erot = 3.41825755609791 | epot = -21.4095311686242 | etot = -15.972378611647
-625000  ekin = 2.87966631754697 |  erot = 2.69115421564283 | epot = -21.2859406043045 | etot = -15.7151200711147
-626000  ekin = 2.56087279949319 |  erot = 2.15801254335177 | epot = -21.2329175358055 | etot = -16.5140321929606
-627000  ekin = 2.30197939613517 |  erot = 2.40176668957967 | epot = -21.2932794652839 | etot = -16.589533379569
-628000  ekin = 2.23988628353727 |  erot = 2.75332535542195 | epot = -21.4558642198861 | etot = -16.4626525809268
-629000  ekin = 2.20891060851904 |  erot = 1.97036896055006 | epot = -21.6109313731644 | etot = -17.4316518040953
-630000  ekin = 2.48711004105954 |  erot = 2.14055508379566 | epot = -21.6286281269545 | etot = -17.0009630020993
-631000  ekin = 2.05035510102044 |  erot = 1.78519131042561 | epot = -21.633635046353 | etot = -17.798088634907
-632000  ekin = 1.65439924450982 |  erot = 3.28310987077496 | epot = -21.6999899301469 | etot = -16.7624808148621
-633000  ekin = 2.34657988531209 |  erot = 2.34109631044869 | epot = -21.8317647703271 | etot = -17.1440885745664
-634000  ekin = 2.31570267703931 |  erot = 2.471293173825 | epot = -21.8814211467029 | etot = -17.0944252958386
-635000  ekin = 1.99068848818427 |  erot = 3.35493927676214 | epot = -21.9111632351734 | etot = -16.565535470227
-636000  ekin = 2.5015676385862 |  erot = 2.48847742334419 | epot = -21.8752689055209 | etot = -16.8852238435905
-637000  ekin = 2.76558055064046 |  erot = 2.80410341825293 | epot = -21.7874464522772 | etot = -16.2177624833838
-638000  ekin = 2.45488734924466 |  erot = 2.81516363335622 | epot = -21.897362338598 | etot = -16.6273113559971
-639000  ekin = 1.89221088715375 |  erot = 2.13319565970052 | epot = -21.932098303477 | etot = -17.9066917566227
-640000  ekin = 2.12173400886946 |  erot = 3.32302167857403 | epot = -21.8808288554836 | etot = -16.4360731680401
-641000  ekin = 2.09554541112562 |  erot = 2.23098450754968 | epot = -21.9203390995502 | etot = -17.5938091808749
-642000  ekin = 2.28696138506763 |  erot = 2.67378976619349 | epot = -21.9723604262128 | etot = -17.0116092749517
-643000  ekin = 2.74450005384908 |  erot = 2.20403941809548 | epot = -21.9235240791533 | etot = -16.9749846072088
-644000  ekin = 2.87909523138453 |  erot = 3.40688779630214 | epot = -21.9417833997402 | etot = -15.6558003720535
-645000  ekin = 2.38284095628021 |  erot = 2.10846397463902 | epot = -21.8306349073152 | etot = -17.339329976396
-646000  ekin = 2.68568471833193 |  erot = 1.8085210536706 | epot = -21.6853054888873 | etot = -17.1910997168848
-647000  ekin = 2.44462012552757 |  erot = 2.00446720103467 | epot = -21.4974635292911 | etot = -17.0483762027288
-648000  ekin = 2.22150753159449 |  erot = 1.69679185313772 | epot = -21.5947311257684 | etot = -17.6764317410362
-649000  ekin = 2.55943952639507 |  erot = 1.77203724563615 | epot = -22.016770390185 | etot = -17.6852936181538
-650000  ekin = 2.7234725572106 |  erot = 2.20418229003755 | epot = -22.1594214535889 | etot = -17.2317666063407
-651000  ekin = 2.25383373914402 |  erot = 3.26326768595798 | epot = -22.2274805933885 | etot = -16.7103791682865
-652000  ekin = 2.35810253390822 |  erot = 2.29591208392313 | epot = -22.2332195197311 | etot = -17.5792049018997
-653000  ekin = 2.06421004499471 |  erot = 2.1417184547457 | epot = -22.2265612208312 | etot = -18.0206327210908
-654000  ekin = 2.30460304373657 |  erot = 1.85567946278894 | epot = -22.2521914868228 | etot = -18.0919089802973
-655000  ekin = 2.11188824015111 |  erot = 1.79072614414006 | epot = -22.2262193909715 | etot = -18.3236050066803
-656000  ekin = 2.44561836830367 |  erot = 2.32567811025775 | epot = -22.1872376286341 | etot = -17.4159411500727
-657000  ekin = 2.45751083141108 |  erot = 2.86439216413734 | epot = -22.1805503246548 | etot = -16.8586473291064
-658000  ekin = 2.49955432693124 |  erot = 2.85472680235227 | epot = -22.1390040132353 | etot = -16.7847228839518
-659000  ekin = 3.37980090980363 |  erot = 2.77552992994233 | epot = -21.9898923341708 | etot = -15.8345614944249
-660000  ekin = 2.6941462621918 |  erot = 1.99094454704574 | epot = -21.839770569098 | etot = -17.1546797598605
-661000  ekin = 2.21049176877594 |  erot = 2.52393650500608 | epot = -21.6857326790217 | etot = -16.9513044052397
-662000  ekin = 2.06962867519899 |  erot = 2.53976085175021 | epot = -21.6239147287108 | etot = -17.0145252017616
-663000  ekin = 2.27770295544224 |  erot = 2.30124717941155 | epot = -21.5870186127932 | etot = -17.0080684779394
-664000  ekin = 2.39061717453214 |  erot = 1.87616423363735 | epot = -21.4930500427881 | etot = -17.2262686346187
-665000  ekin = 2.66924405123179 |  erot = 2.29240983153227 | epot = -21.4402310096658 | etot = -16.4785771269017
-666000  ekin = 1.66318176263893 |  erot = 2.30827907651666 | epot = -21.3477804932103 | etot = -17.3763196540548
-667000  ekin = 1.65573830146343 |  erot = 2.8261361193353 | epot = -21.2651811028886 | etot = -16.7833066820899
-668000  ekin = 2.50126196238916 |  erot = 3.29062396521939 | epot = -21.1310768281354 | etot = -15.3391909005269
-669000  ekin = 1.61008562219097 |  erot = 2.65727107854378 | epot = -21.0513800034042 | etot = -16.7840233026694
-670000  ekin = 2.21851826153844 |  erot = 2.60770568109394 | epot = -20.9727942140714 | etot = -16.146570271439
-671000  ekin = 2.25905318343359 |  erot = 2.15965495575029 | epot = -20.920836534986 | etot = -16.5021283958021
-672000  ekin = 1.93426342346647 |  erot = 1.65365047668441 | epot = -20.8333028169839 | etot = -17.245388916833
-673000  ekin = 1.880896686753 |  erot = 2.07483128120029 | epot = -20.79952620348 | etot = -16.8437982355267
-674000  ekin = 2.06783468057301 |  erot = 2.16234064938726 | epot = -20.8176950919606 | etot = -16.5875197620003
-675000  ekin = 2.03952283590142 |  erot = 2.48129689359269 | epot = -20.8297865902612 | etot = -16.3089668607671
-676000  ekin = 2.44687523374789 |  erot = 2.77932995735251 | epot = -20.8513819036485 | etot = -15.6251767125481
-677000  ekin = 2.18851088067448 |  erot = 2.6192892566419 | epot = -20.8589021998565 | etot = -16.0511020625401
-678000  ekin = 2.13451298865477 |  erot = 2.78742961560772 | epot = -20.7380850837789 | etot = -15.8161424795164
-679000  ekin = 2.15556981522704 |  erot = 2.17593910434841 | epot = -20.629255081746 | etot = -16.2977461621706
-680000  ekin = 2.0771745141444 |  erot = 2.68436897198806 | epot = -20.6512705044545 | etot = -15.889727018322
-681000  ekin = 2.16836766753576 |  erot = 1.82666294843077 | epot = -20.7392652191906 | etot = -16.744234603224
-682000  ekin = 3.01810965188601 |  erot = 2.39774897550361 | epot = -20.7185667085479 | etot = -15.3027080811583
-683000  ekin = 2.84169666492797 |  erot = 2.09885122074905 | epot = -20.7261705834808 | etot = -15.7856226978037
-684000  ekin = 1.9625035286937 |  erot = 2.99543980855394 | epot = -20.7697045673731 | etot = -15.8117612301254
-685000  ekin = 1.50086016290167 |  erot = 2.04478648729578 | epot = -20.7788952528481 | etot = -17.2332486026506
-686000  ekin = 2.3009298353038 |  erot = 2.55442118756325 | epot = -20.7673358731011 | etot = -15.9119848502341
-687000  ekin = 1.86053862979306 |  erot = 2.84846934037481 | epot = -20.7009117540898 | etot = -15.9919037839219
-688000  ekin = 2.56859020075852 |  erot = 2.23263295871676 | epot = -20.6563366249257 | etot = -15.8551134654504
-689000  ekin = 2.7493014170063 |  erot = 2.68327386026116 | epot = -20.8092642099637 | etot = -15.3766889326963
-690000  ekin = 2.67477310841297 |  erot = 2.52397256899153 | epot = -21.0730303416649 | etot = -15.8742846642604
-691000  ekin = 2.28465281003006 |  erot = 2.52273866559282 | epot = -21.2401157605126 | etot = -16.4327242848897
-692000  ekin = 2.42087744380444 |  erot = 3.24812320332686 | epot = -21.2665776826931 | etot = -15.5975770355618
-693000  ekin = 2.37642605279041 |  erot = 2.99546830568891 | epot = -21.3330277418611 | etot = -15.9611333833818
-694000  ekin = 2.69750178365984 |  erot = 2.53085866970816 | epot = -21.521485598392 | etot = -16.293125145024
-695000  ekin = 2.49230316198816 |  erot = 1.18105864485318 | epot = -21.6959912399269 | etot = -18.0226294330856
-696000  ekin = 1.86075498586631 |  erot = 1.46501529683133 | epot = -21.6808441671222 | etot = -18.3550738844245
-697000  ekin = 2.40460770445908 |  erot = 2.10461647488794 | epot = -21.7143559347048 | etot = -17.2051317553578
-698000  ekin = 2.32098148261586 |  erot = 1.91506962097515 | epot = -21.7787361369849 | etot = -17.5426850333939
-699000  ekin = 2.44943497732062 |  erot = 2.56143482106644 | epot = -21.7638026578475 | etot = -16.7529328594605
-700000  ekin = 2.13119890669415 |  erot = 2.28802336161954 | epot = -21.6714710604343 | etot = -17.2522487921206
-701000  ekin = 2.15013169314239 |  erot = 2.18565847708907 | epot = -21.5488216255628 | etot = -17.2130314553313
-702000  ekin = 1.57482438035702 |  erot = 1.99931097090508 | epot = -21.5047640382371 | etot = -17.930628686975
-703000  ekin = 2.08829522236785 |  erot = 2.17557396869524 | epot = -21.5242713758434 | etot = -17.2604021847803
-704000  ekin = 2.82144699483839 |  erot = 1.94479401958833 | epot = -21.5462466947694 | etot = -16.7800056803427
-705000  ekin = 2.81019786745821 |  erot = 2.16662483548889 | epot = -21.497690476826 | etot = -16.5208677738789
-706000  ekin = 1.97639068263159 |  erot = 2.31468002405233 | epot = -21.494117475981 | etot = -17.2030467692971
-707000  ekin = 1.90740387464487 |  erot = 2.04436544372037 | epot = -21.5505486138142 | etot = -17.5987792954489
-708000  ekin = 2.4927128838246 |  erot = 2.15829540621563 | epot = -21.5728746117359 | etot = -16.9218663216957
-709000  ekin = 2.89296518644075 |  erot = 2.58120965850485 | epot = -21.6152997801578 | etot = -16.1411249352122
-710000  ekin = 2.18515172086139 |  erot = 2.27924743097097 | epot = -21.5865916502444 | etot = -17.122192498412
-711000  ekin = 2.31589231212299 |  erot = 1.40143925977899 | epot = -21.6089597508522 | etot = -17.8916281789502
-712000  ekin = 2.55835611026778 |  erot = 2.27281573655802 | epot = -21.7227687229586 | etot = -16.8915968761328
-713000  ekin = 1.95615391137192 |  erot = 2.3180685223896 | epot = -21.8059432402922 | etot = -17.5317208065307
-714000  ekin = 2.56238583099812 |  erot = 2.10850361056242 | epot = -21.8681675013087 | etot = -17.1972780597481
-715000  ekin = 2.42321114653449 |  erot = 3.74023135295615 | epot = -21.8498336266088 | etot = -15.6863911271181
-716000  ekin = 2.83316600532177 |  erot = 2.84850242081136 | epot = -21.7640231598546 | etot = -16.0823547337214
-717000  ekin = 3.45113934412558 |  erot = 3.20598462177201 | epot = -21.667790662391 | etot = -15.0106666964934
-718000  ekin = 3.10736232683018 |  erot = 3.94031338601797 | epot = -21.5629179727886 | etot = -14.5152422599405
-719000  ekin = 2.38564322644681 |  erot = 2.95089811755838 | epot = -21.5481188237003 | etot = -16.2115774796951
-720000  ekin = 2.22543420991222 |  erot = 3.14305432696276 | epot = -21.5381615962024 | etot = -16.1696730593274
-721000  ekin = 1.71709109813907 |  erot = 2.23939430363989 | epot = -21.4645851946691 | etot = -17.5080997928902
-722000  ekin = 1.93213958129581 |  erot = 2.81573218276728 | epot = -21.4896847080113 | etot = -16.7418129439482
-723000  ekin = 2.3814534534689 |  erot = 2.55666957995948 | epot = -21.4374887927968 | etot = -16.4993657593684
-724000  ekin = 1.74740284448188 |  erot = 2.4555617568904 | epot = -21.4125175551609 | etot = -17.2095529537886
-725000  ekin = 2.29233638352032 |  erot = 2.9526701477774 | epot = -21.4751392844086 | etot = -16.2301327531109
-726000  ekin = 1.63503646092182 |  erot = 2.30649262262117 | epot = -21.5156851039584 | etot = -17.5741560204154
-727000  ekin = 2.46705454176008 |  erot = 3.19802987014479 | epot = -21.5382715508196 | etot = -15.8731871389148
-728000  ekin = 2.21709576272191 |  erot = 2.16616227421244 | epot = -21.5244744557248 | etot = -17.1412164187904
-729000  ekin = 1.89396537247993 |  erot = 1.66596987620967 | epot = -21.5644109232526 | etot = -18.004475674563
-730000  ekin = 1.78155182892059 |  erot = 2.15399661961713 | epot = -21.5594738957829 | etot = -17.6239254472452
-731000  ekin = 2.16713092512296 |  erot = 2.96875570154118 | epot = -21.4952326145865 | etot = -16.3593459879223
-732000  ekin = 2.40927355189018 |  erot = 2.27189990077002 | epot = -21.3831563581627 | etot = -16.7019829055024
-733000  ekin = 3.04824198143784 |  erot = 2.57289903054807 | epot = -21.429005165309 | etot = -15.8078641533231
-734000  ekin = 2.36703883022855 |  erot = 2.04468815017469 | epot = -21.4926214065432 | etot = -17.0808944261399
-735000  ekin = 2.13292788677937 |  erot = 1.55097035487251 | epot = -21.5455592190822 | etot = -17.8616609774303
-736000  ekin = 2.13562110082196 |  erot = 3.45795834862287 | epot = -21.6515763333194 | etot = -16.0579968838746
-737000  ekin = 1.73550703692746 |  erot = 3.58781244645382 | epot = -21.6785680654269 | etot = -16.3552485820456
-738000  ekin = 2.01136680767019 |  erot = 2.50533140705366 | epot = -21.7068415263434 | etot = -17.1901433116196
-739000  ekin = 1.85122466968333 |  erot = 2.19323904324285 | epot = -21.7211705032462 | etot = -17.6767067903201
-740000  ekin = 2.84677298867337 |  erot = 2.79086338446698 | epot = -21.7460997683893 | etot = -16.108463395249
-741000  ekin = 2.47281769013274 |  erot = 2.90867674862121 | epot = -21.8038806031312 | etot = -16.4223861643772
-742000  ekin = 2.74212748781964 |  erot = 3.26601844940295 | epot = -21.9417105639309 | etot = -15.9335646267083
-743000  ekin = 2.23337436613032 |  erot = 3.20752099935254 | epot = -22.0769938861091 | etot = -16.6360985206262
-744000  ekin = 2.01007582963959 |  erot = 3.79208398827071 | epot = -22.1581491314472 | etot = -16.3559893135369
-745000  ekin = 3.14168435406402 |  erot = 2.32756039064277 | epot = -22.1552791709709 | etot = -16.6860344262642
-746000  ekin = 2.96147960587595 |  erot = 2.64919778641529 | epot = -22.131657657659 | etot = -16.5209802653678
-747000  ekin = 2.31713973406909 |  erot = 2.0538838502724 | epot = -22.1362115743712 | etot = -17.7651879900297
-748000  ekin = 2.36228107661837 |  erot = 2.41530550223615 | epot = -22.1703943251347 | etot = -17.3928077462802
-749000  ekin = 2.07006713072585 |  erot = 2.7743291960411 | epot = -22.1708421357978 | etot = -17.3264458090308
-750000  ekin = 1.65834656870048 |  erot = 2.38415657369843 | epot = -22.2465520170919 | etot = -18.204048874693
-751000  ekin = 1.79302728344389 |  erot = 2.827102160061 | epot = -22.3488339479635 | etot = -17.7287045044586
-752000  ekin = 1.35555517803007 |  erot = 1.46019783589209 | epot = -22.4342877547318 | etot = -19.6185347408096
-753000  ekin = 1.88586262445723 |  erot = 2.44014879801272 | epot = -22.3837690917336 | etot = -18.0577576692636
-754000  ekin = 1.74745498380874 |  erot = 2.73612011854199 | epot = -22.2852965474798 | etot = -17.8017214451291
-755000  ekin = 2.39590781949902 |  erot = 2.41019902787154 | epot = -22.2066358684386 | etot = -17.400529021068
-756000  ekin = 1.83745653598818 |  erot = 2.79024351605605 | epot = -22.133592240187 | etot = -17.5058921881428
-757000  ekin = 1.97281200687049 |  erot = 2.57792722235948 | epot = -22.0604464398181 | etot = -17.5097072105881
-758000  ekin = 1.18945619136922 |  erot = 2.72372183682492 | epot = -21.9899494795137 | etot = -18.0767714513196
-759000  ekin = 2.16230453116658 |  erot = 1.39722896511084 | epot = -22.0003304659983 | etot = -18.4407969697208
-760000  ekin = 2.57253050230035 |  erot = 2.33269711137819 | epot = -22.0357457302398 | etot = -17.1305181165612
-761000  ekin = 2.08545216810511 |  erot = 2.24940559703297 | epot = -22.1132097744113 | etot = -17.7783520092733
-762000  ekin = 2.13509249172209 |  erot = 1.66078369856518 | epot = -22.1380840935026 | etot = -18.3422079032154
-763000  ekin = 2.42851727622128 |  erot = 3.36016749294484 | epot = -22.2079173436287 | etot = -16.4192325744626
-764000  ekin = 2.84703530894743 |  erot = 2.79172375883345 | epot = -22.2143624032421 | etot = -16.5756033354612
-765000  ekin = 1.81325658345262 |  erot = 2.77448180912351 | epot = -22.1194010453623 | etot = -17.5316626527862
-766000  ekin = 2.64831101430988 |  erot = 2.3138164970859 | epot = -21.9919179324216 | etot = -17.0297904210258
-767000  ekin = 2.58949745571041 |  erot = 2.86718473216884 | epot = -21.9087370669524 | etot = -16.4520548790732
-768000  ekin = 1.86313167956692 |  erot = 2.78552244417217 | epot = -21.9381577980074 | etot = -17.2895036742683
-769000  ekin = 2.40162376419982 |  erot = 2.31402374045875 | epot = -22.0373843590672 | etot = -17.3217368544087
-770000  ekin = 2.49146487205159 |  erot = 3.23101926076328 | epot = -22.1439576198693 | etot = -16.4214734870544
-771000  ekin = 2.33226337742861 |  erot = 2.27787220200643 | epot = -22.1812213688414 | etot = -17.5710857894063
-772000  ekin = 2.28990016215835 |  erot = 2.99389364569332 | epot = -22.2765115340955 | etot = -16.9927177262439
-773000  ekin = 2.23002457595115 |  erot = 1.82240115552767 | epot = -22.3379686916384 | etot = -18.2855429601596
-774000  ekin = 2.82350297312971 |  erot = 2.21054815770298 | epot = -22.331524297742 | etot = -17.2974731669093
-775000  ekin = 1.82305982105504 |  erot = 1.87100336542221 | epot = -22.2729891281483 | etot = -18.578925941671
-776000  ekin = 1.39169167990077 |  erot = 3.16027505319296 | epot = -22.2459295451276 | etot = -17.6939628120339
-777000  ekin = 1.6265637770548 |  erot = 2.80881827044756 | epot = -22.1611617112313 | etot = -17.7257796637289
-778000  ekin = 1.49436478903862 |  erot = 2.24161236856226 | epot = -22.1732646444852 | etot = -18.4372874868843
-779000  ekin = 1.88107404119766 |  erot = 1.90732846459751 | epot = -22.2125828989308 | etot = -18.4241803931357
-780000  ekin = 1.70209634464211 |  erot = 2.30515299210351 | epot = -22.2800747799124 | etot = -18.2728254431668
-781000  ekin = 2.12615575710868 |  erot = 2.5606535839807 | epot = -22.3657963731658 | etot = -17.6789870320765
-782000  ekin = 2.60319344794517 |  erot = 1.9571688066736 | epot = -22.278889588664 | etot = -17.7185273340452
-783000  ekin = 2.19489638548848 |  erot = 2.9003350616753 | epot = -22.2004563501245 | etot = -17.1052249029607
-784000  ekin = 2.84914111009349 |  erot = 2.24051018422878 | epot = -22.2093010900996 | etot = -17.1196497957773
-785000  ekin = 3.14240765153577 |  erot = 2.92860772919915 | epot = -22.2500274240077 | etot = -16.1790120432728
-786000  ekin = 2.83372300736036 |  erot = 3.44593690351849 | epot = -22.2923595270367 | etot = -16.0126996161579
-787000  ekin = 2.41074903520556 |  erot = 3.01381650302092 | epot = -22.2329745868673 | etot = -16.8084090486408
-788000  ekin = 1.99557665602945 |  erot = 2.01600225895996 | epot = -22.1996915458458 | etot = -18.1881126308564
-789000  ekin = 2.46258971641133 |  erot = 2.27406771625316 | epot = -22.1314921413931 | etot = -17.3948347087286
-790000  ekin = 3.5794195002921 |  erot = 2.82440864812442 | epot = -22.0691321886934 | etot = -15.6653040402769
-791000  ekin = 3.1240271028451 |  erot = 2.42401718962737 | epot = -22.0808685046086 | etot = -16.5328242121361
-792000  ekin = 3.95429056548242 |  erot = 1.97241939137157 | epot = -22.0156932891881 | etot = -16.0889833323341
-793000  ekin = 2.26828416500901 |  erot = 2.58677202552917 | epot = -21.9219598803777 | etot = -17.0669036898395
-794000  ekin = 2.16106559150924 |  erot = 2.44310931274122 | epot = -21.7619518452423 | etot = -17.1577769409919
-795000  ekin = 1.62519700428841 |  erot = 2.41826691867446 | epot = -21.6012749849542 | etot = -17.5578110619913
-796000  ekin = 2.18377144801669 |  erot = 2.13093440679001 | epot = -21.4820337714693 | etot = -17.1673279166626
-797000  ekin = 1.81427862345353 |  erot = 1.99534051513419 | epot = -21.4739195915569 | etot = -17.6643004529692
-798000  ekin = 2.2201219513299 |  erot = 2.51363796316553 | epot = -21.5008270155092 | etot = -16.7670671010138
-799000  ekin = 1.88984581553595 |  erot = 2.87047971528298 | epot = -21.4708608053325 | etot = -16.7105352745136
-800000  ekin = 2.14235800297794 |  erot = 2.35196377273805 | epot = -21.3792596865246 | etot = -16.8849379108086
-801000  ekin = 1.84302686949433 |  erot = 1.65480855802629 | epot = -21.2211741734437 | etot = -17.7233387459231
-802000  ekin = 2.20305615004888 |  erot = 2.22355768328245 | epot = -21.1073599995259 | etot = -16.6807461661946
-803000  ekin = 2.64836814873033 |  erot = 1.90761871804858 | epot = -21.0752041885471 | etot = -16.5192173217682
-804000  ekin = 2.34495845479317 |  erot = 2.89112045330492 | epot = -21.0176734836814 | etot = -15.7815945755833
-805000  ekin = 1.79915640284781 |  erot = 2.71685844764875 | epot = -20.8858433761952 | etot = -16.3698285256987
-806000  ekin = 1.74992507845556 |  erot = 2.08517047523252 | epot = -20.8503301901419 | etot = -17.0152346364538
-807000  ekin = 1.57172452594494 |  erot = 1.70422569898767 | epot = -20.9092333967053 | etot = -17.6332831717727
-808000  ekin = 2.08106901002531 |  erot = 2.4036706521883 | epot = -20.9858691795981 | etot = -16.5011295173845
-809000  ekin = 2.61736488835992 |  erot = 1.51251405170843 | epot = -20.9790910298502 | etot = -16.8492120897819
-810000  ekin = 3.07344763503492 |  erot = 2.65428122600395 | epot = -20.896297890317 | etot = -15.1685690292781
-811000  ekin = 3.028899831017 |  erot = 3.61686315729187 | epot = -20.939661602879 | etot = -14.2938986145701
-812000  ekin = 2.13832655324419 |  erot = 2.7919099294265 | epot = -21.0260005012597 | etot = -16.095764018589
-813000  ekin = 2.19077235410927 |  erot = 3.16158040032406 | epot = -21.2169108164964 | etot = -15.8645580620631
-814000  ekin = 1.70775111413747 |  erot = 2.98436840501864 | epot = -21.3089511890131 | etot = -16.6168316698569
-815000  ekin = 2.14630779714624 |  erot = 2.27335416843263 | epot = -21.3099230783927 | etot = -16.8902611128138
-816000  ekin = 2.70331501775258 |  erot = 1.53093796189124 | epot = -21.3384418834226 | etot = -17.1041889037788
-817000  ekin = 2.55738086811903 |  erot = 2.58558173150041 | epot = -21.4691891608916 | etot = -16.3262265612722
-818000  ekin = 2.27829786328906 |  erot = 2.26089725682103 | epot = -21.5162183667694 | etot = -16.9770232466593
-819000  ekin = 2.10478260130361 |  erot = 3.02380855832961 | epot = -21.5292309310153 | etot = -16.4006397713821
-820000  ekin = 2.50608188233135 |  erot = 2.71783485224719 | epot = -21.5036816055507 | etot = -16.2797648709722
-821000  ekin = 2.62609848062629 |  erot = 2.55164634943844 | epot = -21.478766185164 | etot = -16.3010213550993
-822000  ekin = 3.63941681915299 |  erot = 2.20246894917129 | epot = -21.4688230156577 | etot = -15.6269372473334
-823000  ekin = 3.58953515450024 |  erot = 2.73556206545619 | epot = -21.4650227341943 | etot = -15.1399255142378
-824000  ekin = 4.11304720722591 |  erot = 3.2917459513548 | epot = -21.4062011377905 | etot = -14.0014079792098
-825000  ekin = 2.90620097853796 |  erot = 3.46409084826251 | epot = -21.2436944546109 | etot = -14.8734026278105
-826000  ekin = 1.72188438195169 |  erot = 1.97028277378148 | epot = -21.0473904580338 | etot = -17.3552233023007
-827000  ekin = 1.9124069409458 |  erot = 2.55760488338657 | epot = -20.9206700763425 | etot = -16.4506582520101
-828000  ekin = 2.38145056979363 |  erot = 2.55544957149182 | epot = -20.8204865756543 | etot = -15.8835864343689
-829000  ekin = 2.24733826946605 |  erot = 1.78474837345228 | epot = -20.7084449579388 | etot = -16.6763583150204
-830000  ekin = 2.52795893691035 |  erot = 2.34146724282711 | epot = -20.5883731027638 | etot = -15.7189469230264
-831000  ekin = 2.68310001004752 |  erot = 2.07407005901145 | epot = -20.4364451382899 | etot = -15.679275069231
-832000  ekin = 2.6732342426401 |  erot = 2.02167788192499 | epot = -20.3691783993746 | etot = -15.6742662748095
-833000  ekin = 2.55071664949192 |  erot = 2.59972899624767 | epot = -20.3036213925319 | etot = -15.1531757467923
-834000  ekin = 2.87089088359563 |  erot = 2.32463192225235 | epot = -20.2984653371648 | etot = -15.1029425313168
-835000  ekin = 2.77558903596269 |  erot = 2.73757154391999 | epot = -20.4022293845421 | etot = -14.8890688046595
-836000  ekin = 2.57713146919653 |  erot = 2.85322310545496 | epot = -20.5403137141641 | etot = -15.1099591395126
-837000  ekin = 1.78075406754283 |  erot = 1.97503243561096 | epot = -20.5889142070484 | etot = -16.8331277038946
-838000  ekin = 1.98032617531701 |  erot = 2.7982946707394 | epot = -20.6049667376349 | etot = -15.8263458915785
-839000  ekin = 2.0003179521848 |  erot = 2.70198331564815 | epot = -20.5921495833285 | etot = -15.8898483154955
-840000  ekin = 1.70031236242703 |  erot = 2.95685689490568 | epot = -20.6678372916037 | etot = -16.010668034271
-841000  ekin = 2.77705100359315 |  erot = 2.84742847205069 | epot = -20.7929304121763 | etot = -15.1684509365325
-842000  ekin = 2.54393458307436 |  erot = 2.87172695192627 | epot = -20.8173418291016 | etot = -15.401680294101
-843000  ekin = 2.00273625390939 |  erot = 2.63437491598434 | epot = -20.8053999188197 | etot = -16.1682887489259
-844000  ekin = 1.52900749569349 |  erot = 1.92882434140971 | epot = -20.8427655387949 | etot = -17.3849337016917
-845000  ekin = 2.27176799938834 |  erot = 2.308436365406 | epot = -20.9384881501645 | etot = -16.3582837853702
-846000  ekin = 2.06718804989496 |  erot = 2.33108662324981 | epot = -21.008503215967 | etot = -16.6102285428222
-847000  ekin = 2.457310325364 |  erot = 2.64112097293887 | epot = -20.9624761048838 | etot = -15.8640448065809
-848000  ekin = 2.13894899278459 |  erot = 1.46487099434192 | epot = -20.9909626022984 | etot = -17.3871426151719
-849000  ekin = 2.0007946308419 |  erot = 2.48568109050424 | epot = -20.9995492646628 | etot = -16.5130735433167
-850000  ekin = 2.54186297995285 |  erot = 2.66929613872204 | epot = -20.9906717645298 | etot = -15.7795126458549
-851000  ekin = 2.16443404123472 |  erot = 2.92830981454153 | epot = -20.9932718794597 | etot = -15.9005280236835
-852000  ekin = 2.48255398040851 |  erot = 2.46238001266592 | epot = -21.018749118108 | etot = -16.0738151250336
-853000  ekin = 2.41541467016921 |  erot = 2.97520224443385 | epot = -20.9598722543997 | etot = -15.5692553397966
-854000  ekin = 2.35150751079563 |  erot = 2.85453387569363 | epot = -20.8693696367608 | etot = -15.6633282502715
-855000  ekin = 2.36749640703667 |  erot = 2.0675340835823 | epot = -20.8980197782034 | etot = -16.4629892875844
-856000  ekin = 2.52164598863741 |  erot = 2.75265020302047 | epot = -20.800830948998 | etot = -15.5265347573401
-857000  ekin = 2.55862872070476 |  erot = 3.03030828592914 | epot = -20.6910887919773 | etot = -15.1021517853434
-858000  ekin = 3.12628251408762 |  erot = 2.1455460426107 | epot = -20.6394579492303 | etot = -15.367629392532
-859000  ekin = 2.91259413572113 |  erot = 2.23773675238284 | epot = -20.6611486479508 | etot = -15.5108177598468
-860000  ekin = 2.88318377110752 |  erot = 1.51972062646443 | epot = -20.6828066069552 | etot = -16.2799022093833
-861000  ekin = 2.33529167415754 |  erot = 2.85116617791259 | epot = -20.6796212139896 | etot = -15.4931633619195
-862000  ekin = 3.06091745354043 |  erot = 1.86960550588563 | epot = -20.7257485328209 | etot = -15.7952255733949
-863000  ekin = 2.88295223464283 |  erot = 1.77743902656171 | epot = -20.8340328987095 | etot = -16.173641637505
-864000  ekin = 2.95602292127633 |  erot = 2.6505641071531 | epot = -21.016295456145 | etot = -15.4097084277156
-865000  ekin = 3.3172549369506 |  erot = 2.24347319046513 | epot = -21.1441095096619 | etot = -15.5833813822461
-866000  ekin = 2.8446879555804 |  erot = 3.16802464112883 | epot = -21.2275167371632 | etot = -15.214804140454
-867000  ekin = 2.74149808612435 |  erot = 3.09628634794253 | epot = -21.2140642048229 | etot = -15.376279770756
-868000  ekin = 2.19141484864809 |  erot = 2.23765996064101 | epot = -21.1661691183494 | etot = -16.7370943090603
-869000  ekin = 2.92726848075923 |  erot = 2.49663936074752 | epot = -21.1109612585256 | etot = -15.6870534170189
-870000  ekin = 2.47986538741064 |  erot = 2.11907230969515 | epot = -21.0900293946685 | etot = -16.4910916975627
-871000  ekin = 2.18342640526418 |  erot = 2.37474045896628 | epot = -20.9804914418025 | etot = -16.422324577572
-872000  ekin = 1.52873571215978 |  erot = 2.08908078804674 | epot = -20.9343176993392 | etot = -17.3165011991327
-873000  ekin = 1.39281578471524 |  erot = 2.29034780878957 | epot = -21.0007866828842 | etot = -17.3176230893794
-874000  ekin = 1.40786554880768 |  erot = 2.77007970032348 | epot = -21.160084274243 | etot = -16.9821390251118
-875000  ekin = 1.18320018517441 |  erot = 2.7305884288351 | epot = -21.2959059488291 | etot = -17.3821173348196
-876000  ekin = 1.8300189393038 |  erot = 2.99586941144887 | epot = -21.3298635968753 | etot = -16.5039752461226
-877000  ekin = 2.38032906471076 |  erot = 2.03722695211227 | epot = -21.4152790752831 | etot = -16.99772305846
-878000  ekin = 2.1293851684127 |  erot = 1.75666654131943 | epot = -21.412657760354 | etot = -17.5266060506219
-879000  ekin = 2.23837299177368 |  erot = 2.71307243504657 | epot = -21.4006541150457 | etot = -16.4492086882254
-880000  ekin = 2.68032631557358 |  erot = 2.78439945590096 | epot = -21.4462782448912 | etot = -15.9815524734167
-881000  ekin = 2.86810525851389 |  erot = 2.35959915589952 | epot = -21.4314549447334 | etot = -16.20375053032
-882000  ekin = 2.33172283615115 |  erot = 2.17176020371467 | epot = -21.369535469283 | etot = -16.8660524294172
-883000  ekin = 2.36331150998289 |  erot = 1.97634374053966 | epot = -21.1748990104138 | etot = -16.8352437598913
-884000  ekin = 2.53782271833829 |  erot = 2.25243670168427 | epot = -21.0795767771653 | etot = -16.2893173571427
-885000  ekin = 2.86057103069745 |  erot = 2.27462544190307 | epot = -21.0782171958267 | etot = -15.9430207232262
-886000  ekin = 3.17034195996096 |  erot = 1.74832646729409 | epot = -21.1280719510453 | etot = -16.2094035237903
-887000  ekin = 2.66023408534638 |  erot = 2.49426802108016 | epot = -21.1909579488462 | etot = -16.0364558424197
-888000  ekin = 2.14156056158802 |  erot = 2.83065920295552 | epot = -21.2749898508176 | etot = -16.302770086274
-889000  ekin = 2.13776380125426 |  erot = 2.19994227158624 | epot = -21.1902576201104 | etot = -16.8525515472699
-890000  ekin = 1.76446650263826 |  erot = 2.97354753014624 | epot = -21.2518724314555 | etot = -16.513858398671
-891000  ekin = 1.64433607192947 |  erot = 2.28044235221045 | epot = -21.3759471910581 | etot = -17.4511687669181
-892000  ekin = 1.97381907006142 |  erot = 2.35969977765342 | epot = -21.5200869372681 | etot = -17.1865680895533
-893000  ekin = 1.77998159671209 |  erot = 1.83959134574388 | epot = -21.5960425863495 | etot = -17.9764696438935
-894000  ekin = 2.8098996128374 |  erot = 2.80337844303785 | epot = -21.6896955865519 | etot = -16.0764175306767
-895000  ekin = 2.03570642281182 |  erot = 2.73641442629084 | epot = -21.77632807541 | etot = -17.0042072263074
-896000  ekin = 1.6670401968188 |  erot = 2.55842313387756 | epot = -21.9079691828366 | etot = -17.6825058521403
-897000  ekin = 1.79364820755772 |  erot = 2.35937074837063 | epot = -22.0466195733302 | etot = -17.8936006174018
-898000  ekin = 1.84103348909591 |  erot = 2.4159698011209 | epot = -22.0792153246985 | etot = -17.8222120344817
-899000  ekin = 1.6644807831865 |  erot = 3.06295573986192 | epot = -22.0050930291629 | etot = -17.2776565061145
-900000  ekin = 2.15301263014261 |  erot = 2.62503812958044 | epot = -21.9769631774149 | etot = -17.1989124176918
-901000  ekin = 2.43323525076021 |  erot = 2.69661561775585 | epot = -22.0455467285607 | etot = -16.9156958600446
-902000  ekin = 2.57983518470479 |  erot = 2.40634661051271 | epot = -22.0504126836938 | etot = -17.0642308884763
-903000  ekin = 2.38804084084236 |  erot = 2.40369143268286 | epot = -22.0548572254258 | etot = -17.2631249519006
-904000  ekin = 1.9975679938241 |  erot = 3.15736733739655 | epot = -22.0783783499621 | etot = -16.9234430187414
-905000  ekin = 2.28042135995781 |  erot = 2.20746001153526 | epot = -22.092475444409 | etot = -17.604594072916
-906000  ekin = 2.49914497220395 |  erot = 1.67106173041057 | epot = -22.0649292741971 | etot = -17.8947225715826
-907000  ekin = 2.34170753461351 |  erot = 2.16830189815579 | epot = -21.9182395193391 | etot = -17.4082300865698
-908000  ekin = 2.83101675354561 |  erot = 2.39226452568031 | epot = -21.9393923471479 | etot = -16.7161110679219
-909000  ekin = 3.13519044247878 |  erot = 2.07053636961478 | epot = -22.044039894957 | etot = -16.8383130828634
-910000  ekin = 2.91492350277448 |  erot = 3.54269221448408 | epot = -22.1774209001616 | etot = -15.719805182903
-911000  ekin = 1.86299522014884 |  erot = 2.75425299355676 | epot = -22.2318842654016 | etot = -17.614636051696
-912000  ekin = 2.64270620869814 |  erot = 1.86916034984858 | epot = -22.2816929482531 | etot = -17.7698263897064
-913000  ekin = 2.45835259040075 |  erot = 2.03343540339216 | epot = -22.4051980318983 | etot = -17.9134100381054
-914000  ekin = 2.01630257583653 |  erot = 3.01931541129968 | epot = -22.505580829989 | etot = -17.4699628428528
-915000  ekin = 2.73550820750709 |  erot = 2.14051989379169 | epot = -22.5067223019054 | etot = -17.6306942006067
-916000  ekin = 2.38833694849903 |  erot = 3.26236542376325 | epot = -22.5299732656691 | etot = -16.8792708934068
-917000  ekin = 2.21211072529667 |  erot = 2.24425221182159 | epot = -22.5175498112378 | etot = -18.0611868741195
-918000  ekin = 2.11721632678553 |  erot = 2.05681940825278 | epot = -22.4485798442659 | etot = -18.2745441092275
-919000  ekin = 2.6606540164524 |  erot = 2.41853759346262 | epot = -22.4819256778217 | etot = -17.4027340679066
-920000  ekin = 3.26471044916532 |  erot = 2.75531911342505 | epot = -22.5858600689149 | etot = -16.5658305063245
-921000  ekin = 2.72028388628927 |  erot = 1.9696059637128 | epot = -22.639440275186 | etot = -17.949550425184
-922000  ekin = 1.43428549123066 |  erot = 1.52428475569853 | epot = -22.6914991306332 | etot = -19.732928883704
-923000  ekin = 1.67603986848274 |  erot = 1.86522020655464 | epot = -22.7510571233686 | etot = -19.2097970483313
-924000  ekin = 2.15000311118185 |  erot = 1.53327070095755 | epot = -22.722341324193 | etot = -19.0390675120536
-925000  ekin = 2.27769316315993 |  erot = 1.3558291477729 | epot = -22.6317669747038 | etot = -18.9982446637709
-926000  ekin = 2.0037075380337 |  erot = 2.07123237010034 | epot = -22.5811533157097 | etot = -18.5062134075756
-927000  ekin = 2.5163142824884 |  erot = 1.98711239136866 | epot = -22.6957752134474 | etot = -18.1923485395904
-928000  ekin = 2.57502157703452 |  erot = 2.51449316644151 | epot = -22.8486668477058 | etot = -17.7591521042298
-929000  ekin = 2.66015175923782 |  erot = 1.82991995656989 | epot = -22.8894816710891 | etot = -18.3994099552814
-930000  ekin = 2.41758548277495 |  erot = 2.00977019739402 | epot = -22.9023129289068 | etot = -18.4749572487378
-931000  ekin = 3.01936517399357 |  erot = 2.11115283295647 | epot = -22.8598478032752 | etot = -17.7293297963252
-932000  ekin = 2.34904883629147 |  erot = 1.87134929534042 | epot = -22.900230384769 | etot = -18.6798322531371
-933000  ekin = 2.16775611540091 |  erot = 2.83796264813669 | epot = -22.9075292968864 | etot = -17.9018105333488
-934000  ekin = 2.17428610858913 |  erot = 2.11891276299501 | epot = -22.9275911153101 | etot = -18.634392243726
-935000  ekin = 2.35380058127247 |  erot = 2.22719757040085 | epot = -22.9178791070039 | etot = -18.3368809553306
-936000  ekin = 2.29398857252167 |  erot = 2.52122883801967 | epot = -23.0254587453496 | etot = -18.2102413348082
-937000  ekin = 2.32405492839276 |  erot = 2.82571975062453 | epot = -23.1134869099967 | etot = -17.9637122309794
-938000  ekin = 2.46190818228192 |  erot = 1.99586541720566 | epot = -23.1690855883853 | etot = -18.7113119888978
-939000  ekin = 2.99494633358444 |  erot = 2.1120057997909 | epot = -23.1621265982256 | etot = -18.0551744648503
-940000  ekin = 3.76773061527755 |  erot = 2.67954167018356 | epot = -23.1020260319689 | etot = -16.6547537465078
-941000  ekin = 3.15108874053801 |  erot = 2.26610050109568 | epot = -23.0042404655517 | etot = -17.587051223918
-942000  ekin = 3.50311245643907 |  erot = 1.88373602143018 | epot = -22.9671180112669 | etot = -17.5802695333976
-943000  ekin = 3.82043792465856 |  erot = 2.71285823250348 | epot = -22.9404059827705 | etot = -16.4071098256085
-944000  ekin = 2.68278476017665 |  erot = 2.75585489458161 | epot = -22.919058077481 | etot = -17.4804184227228
-945000  ekin = 2.55880828345198 |  erot = 2.02741981318914 | epot = -22.8232630911495 | etot = -18.2370349945083
-946000  ekin = 2.47548691870273 |  erot = 1.66864059361738 | epot = -22.6586979544826 | etot = -18.5145704421625
-947000  ekin = 2.41867478100658 |  erot = 1.99274780926995 | epot = -22.5542133657 | etot = -18.1427907754235
-948000  ekin = 3.54970439277899 |  erot = 2.57756240201333 | epot = -22.4104376157296 | etot = -16.2831708209373
-949000  ekin = 2.98589976166071 |  erot = 2.44208964275302 | epot = -22.1971411230011 | etot = -16.7691517185873
-950000  ekin = 1.82147308870195 |  erot = 3.05083899379338 | epot = -22.0435130221227 | etot = -17.1712009396274
-951000  ekin = 2.20031505253436 |  erot = 2.38004890424644 | epot = -22.0174402075992 | etot = -17.4370762508184
-952000  ekin = 2.14165422682636 |  erot = 1.67045420750585 | epot = -21.9875031647927 | etot = -18.1753947304605
-953000  ekin = 2.2983346942831 |  erot = 1.97349532600851 | epot = -21.9532851584681 | etot = -17.6814551381765
-954000  ekin = 1.48835290094507 |  erot = 3.35692451991831 | epot = -21.8812774176255 | etot = -17.0359999967621
-955000  ekin = 1.87513794155827 |  erot = 2.65898918540887 | epot = -21.7919528937348 | etot = -17.2578257667677
-956000  ekin = 1.6947359470094 |  erot = 2.15427252360414 | epot = -21.7268035908356 | etot = -17.877795120222
-957000  ekin = 1.75579814865835 |  erot = 1.63901039608816 | epot = -21.700727032202 | etot = -18.3059184874555
-958000  ekin = 1.59869777656518 |  erot = 2.20104985114387 | epot = -21.7023937250484 | etot = -17.9026460973393
-959000  ekin = 2.58438881562724 |  erot = 2.4897790743314 | epot = -21.7153511733982 | etot = -16.6411832834396
-960000  ekin = 2.53916903929276 |  erot = 2.05995138561213 | epot = -21.7134163297425 | etot = -17.1142959048376
-961000  ekin = 2.28282707786747 |  erot = 2.18347157951504 | epot = -21.7152390799838 | etot = -17.2489404226013
-962000  ekin = 1.65520100959905 |  erot = 3.51416445242775 | epot = -21.7329558565076 | etot = -16.5635903944808
-963000  ekin = 1.99568689924178 |  erot = 1.50126173817713 | epot = -21.6847527677603 | etot = -18.1878041303413
-964000  ekin = 2.18616111169191 |  erot = 2.27601428306196 | epot = -21.621271673579 | etot = -17.1590962788252
-965000  ekin = 2.12688674785305 |  erot = 2.31141713690626 | epot = -21.6018715374842 | etot = -17.1635676527249
-966000  ekin = 3.18043989665769 |  erot = 3.42455452205085 | epot = -21.638305203769 | etot = -15.0333107850605
-967000  ekin = 3.07300409154252 |  erot = 2.17511749698304 | epot = -21.5951488445701 | etot = -16.3470272560445
-968000  ekin = 2.08663150655529 |  erot = 2.13997027735021 | epot = -21.5232721871232 | etot = -17.2966704032177
-969000  ekin = 2.26951411936363 |  erot = 2.21822796004341 | epot = -21.4611553284775 | etot = -16.9734132490705
-970000  ekin = 2.49167396599781 |  erot = 2.62083774678039 | epot = -21.4077353682587 | etot = -16.2952236554805
-971000  ekin = 2.497450596106 |  erot = 2.64553775005007 | epot = -21.3712924820092 | etot = -16.2283041358532
-972000  ekin = 3.2069302084461 |  erot = 2.4701129448845 | epot = -21.3144344371103 | etot = -15.6373912837797
-973000  ekin = 3.35935448087941 |  erot = 2.62917582888825 | epot = -21.2433830591837 | etot = -15.254852749416
-974000  ekin = 2.71069552226069 |  erot = 2.13944446989067 | epot = -21.1404268855179 | etot = -16.2902868933666
-975000  ekin = 1.81165819781674 |  erot = 2.10218924092727 | epot = -21.0499905566304 | etot = -17.1361431178864
-976000  ekin = 2.36984742020937 |  erot = 1.38488988265325 | epot = -20.9803229653515 | etot = -17.2255856624889
-977000  ekin = 2.83728662155799 |  erot = 3.02976542728586 | epot = -21.086860961914 | etot = -15.2198089130701
-978000  ekin = 3.14169266917128 |  erot = 3.0279981203262 | epot = -21.1408187166748 | etot = -14.9711279271773
-979000  ekin = 3.63725915757345 |  erot = 2.47075910077982 | epot = -21.0348329782418 | etot = -14.9268147198885
-980000  ekin = 3.42622785415583 |  erot = 3.24164435781272 | epot = -20.9604411583362 | etot = -14.2925689463677
-981000  ekin = 2.9282364939793 |  erot = 2.44516658563954 | epot = -20.999389015838 | etot = -15.6259859362192
-982000  ekin = 2.0455891107008 |  erot = 2.21302288881361 | epot = -21.0172581853275 | etot = -16.7586461858131
-983000  ekin = 2.56053983213181 |  erot = 1.98406283304104 | epot = -21.0054554868711 | etot = -16.4608528216982
-984000  ekin = 2.31455025377678 |  erot = 2.58584391470351 | epot = -21.0528748947299 | etot = -16.1524807262496
-985000  ekin = 2.31703817263368 |  erot = 2.99965025262552 | epot = -21.1270579315131 | etot = -15.8103695062539
-986000  ekin = 2.05103854432386 |  erot = 2.1535155091137 | epot = -21.2182405597612 | etot = -17.0136865063236
-987000  ekin = 2.41899263793244 |  erot = 1.58416150281503 | epot = -21.1906087726859 | etot = -17.1874546319384
-988000  ekin = 2.75135283132848 |  erot = 2.70498731016258 | epot = -21.09026978368 | etot = -15.633929642189
-989000  ekin = 2.29408577956131 |  erot = 2.85656205344493 | epot = -21.0178170251465 | etot = -15.8671691921403
-990000  ekin = 2.23414139649767 |  erot = 2.58987928207187 | epot = -20.9412338597721 | etot = -16.1172131812026
-991000  ekin = 2.20140095465642 |  erot = 2.53421928109187 | epot = -20.8284298905317 | etot = -16.0928096547834
-992000  ekin = 1.73516341340694 |  erot = 2.49726908126814 | epot = -20.8981414535471 | etot = -16.665708958872
-993000  ekin = 1.38883779880922 |  erot = 1.96818984395137 | epot = -20.9939445972527 | etot = -17.6369169544921
-994000  ekin = 1.48978908674571 |  erot = 2.95636513336706 | epot = -21.0608370227912 | etot = -16.6146828026784
-995000  ekin = 2.31404204513712 |  erot = 1.67482961392509 | epot = -21.1264761824825 | etot = -17.1376045234203
-996000  ekin = 2.89776504847011 |  erot = 2.85063328331353 | epot = -21.0879631716189 | etot = -15.3395648398353
-997000  ekin = 3.12980664910277 |  erot = 2.14994147346883 | epot = -21.0789162715404 | etot = -15.7991681489688
-998000  ekin = 2.21592279552962 |  erot = 3.03017611615784 | epot = -20.9989402817529 | etot = -15.7528413700654
-999000  ekin = 2.60947995309596 |  erot = 1.73829419308785 | epot = -20.9136108602423 | etot = -16.5658367140585
-1000000  ekin = 2.32269547490306 |  erot = 2.87794942105203 | epot = -20.9071852604882 | etot = -15.7065403645331
- 1000000   0.10323091    -1.356822  0.050122912   -1.1615306 0.00013791576 
-Loop time of 52.0267 on 4 procs for 1000000 steps with 16 atoms
-
-Performance: 16606.850 tau/day, 19220.892 timesteps/s
-96.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.92946    | 16.932     | 31.787     | 338.2 | 32.55
-Bond    | 0.12904    | 0.54878    | 0.89134    |  46.8 |  1.05
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 4.2008     | 5.1678     | 6.1197     |  36.6 |  9.93
-Output  | 2.1e-05    | 3.15e-05   | 3.6e-05    |   0.0 |  0.00
-Modify  | 0.32128    | 3.4221     | 6.4024     | 143.6 |  6.58
-Other   |            | 25.96      |            |       | 49.89
-
-Nlocal:    4 ave 8 max 0 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Nghost:    9 ave 10 max 8 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:    34.5 ave 67 max 0 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 138
-Ave neighs/atom = 8.625
-Ave special neighs/atom = 3.75
-Neighbor list builds = 0
-Dangerous builds = 0
-
-#write_restart config.${number}.*
-Total wall time: 0:00:52
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1
index 9ff9d3c4db..0f7fd1c0db 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1
@@ -24,14 +24,14 @@ set atom * mass 3.1575
 
 group all type 1 4
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.1
similarity index 99%
rename from examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1
rename to examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.1
index a699d8726d..5a8d156ec4 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (18 Jun 2019)
+LAMMPS (7 Aug 2019)
 variable number	equal 1
 variable ofreq	equal 1000
 variable efreq	equal 1000
@@ -35,8 +35,8 @@ read_data data.duplex1
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000102 secs
-  read_data CPU = 0.002436 secs
+  special bonds CPU = 0.000116 secs
+  read_data CPU = 0.002026 secs
 
 set atom * mass 3.1575
   10 settings made for mass
@@ -44,15 +44,15 @@ set atom * mass 3.1575
 group all type 1 4
 10 atoms in group all
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/stk     seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -135,7 +135,7 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4712768  0.009525411   -1.4617514 4.663076e-06 
 1000  ekin = 0.00113086229080528 |  erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
@@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.190992053959174 |  erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562
 1000000  ekin = 0.179708146665509 |  erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937
  1000000  0.013311715   -1.5443684  0.033490821   -1.4929067 -3.7544839e-05 
-Loop time of 20.4903 on 1 procs for 1000000 steps with 10 atoms
+Loop time of 18.4193 on 1 procs for 1000000 steps with 10 atoms
 
-Performance: 42166.322 tau/day, 48803.614 timesteps/s
-98.3% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 46907.305 tau/day, 54290.862 timesteps/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 16.542     | 16.542     | 16.542     |   0.0 | 80.73
-Bond    | 0.62224    | 0.62224    | 0.62224    |   0.0 |  3.04
+Pair    | 14.935     | 14.935     | 14.935     |   0.0 | 81.08
+Bond    | 0.55556    | 0.55556    | 0.55556    |   0.0 |  3.02
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.21974    | 0.21974    | 0.21974    |   0.0 |  1.07
+Comm    | 0.16028    | 0.16028    | 0.16028    |   0.0 |  0.87
 Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
-Modify  | 2.7798     | 2.7798     | 2.7798     |   0.0 | 13.57
-Other   |            | 0.3269     |            |       |  1.60
+Modify  | 2.5402     | 2.5402     | 2.5402     |   0.0 | 13.79
+Other   |            | 0.2285     |            |       |  1.24
 
 Nlocal:    10 ave 10 max 10 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -1169,4 +1169,4 @@ Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:20
+Total wall time: 0:00:18
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.4
similarity index 99%
rename from examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4
rename to examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.4
index 9856a9c95b..329e720074 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (18 Jun 2019)
+LAMMPS (7 Aug 2019)
 variable number	equal 1
 variable ofreq	equal 1000
 variable efreq	equal 1000
@@ -35,8 +35,8 @@ read_data data.duplex1
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000196 secs
-  read_data CPU = 0.003266 secs
+  special bonds CPU = 0.000198 secs
+  read_data CPU = 0.004522 secs
 
 set atom * mass 3.1575
   10 settings made for mass
@@ -44,15 +44,15 @@ set atom * mass 3.1575
 group all type 1 4
 10 atoms in group all
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/stk     seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -135,7 +135,7 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4712768  0.009525411   -1.4617514 4.663076e-06 
 1000  ekin = 0.00113086229080478 |  erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
@@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.190992053959209 |  erot = 0.320462575794744 | epot = -15.1289686644103 | etot = -14.6175140346563
 1000000  ekin = 0.179708146665587 |  erot = 0.311553394428757 | epot = -15.1087755756882 | etot = -14.6175140345938
  1000000  0.013311715   -1.5443684  0.033490821   -1.4929067 -3.7544839e-05 
-Loop time of 28.9854 on 4 procs for 1000000 steps with 10 atoms
+Loop time of 20.7945 on 4 procs for 1000000 steps with 10 atoms
 
-Performance: 29808.075 tau/day, 34500.086 timesteps/s
-96.6% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 41549.361 tau/day, 48089.538 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.85571    | 9.8341     | 18.111     | 228.8 | 33.93
-Bond    | 0.12393    | 0.38078    | 0.62324    |  32.7 |  1.31
+Pair    | 0.66725    | 7.9254     | 14.304     | 209.9 | 38.11
+Bond    | 0.095496   | 0.30973    | 0.49863    |  30.5 |  1.49
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 2.795      | 3.6269     | 4.4228     |  30.4 | 12.51
-Output  | 1.8e-05    | 2.575e-05  | 2.9e-05    |   0.0 |  0.00
-Modify  | 0.24721    | 1.1083     | 1.9206     |  64.1 |  3.82
-Other   |            | 14.04      |            |       | 48.42
+Comm    | 1.8943     | 2.1825     | 2.4604     |  15.6 | 10.50
+Output  | 2e-05      | 2.9e-05    | 3.2e-05    |   0.0 |  0.00
+Modify  | 0.18231    | 0.95644    | 1.673      |  62.4 |  4.60
+Other   |            | 9.421      |            |       | 45.30
 
 Nlocal:    2.5 ave 5 max 0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
@@ -1169,4 +1169,4 @@ Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:28
+Total wall time: 0:00:20
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 b/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2
index 3850dfcedf..5f2fde4b12 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2
@@ -2,6 +2,7 @@ variable number	equal 2
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
+
 units lj
 
 dimension 3
@@ -23,14 +24,14 @@ set atom * mass 3.1575
 
 group all type 1 4
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.1
similarity index 99%
rename from examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1
rename to examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.1
index e4478a8942..c934279c1a 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.1
@@ -1,8 +1,9 @@
-LAMMPS (18 Jun 2019)
+LAMMPS (7 Aug 2019)
 variable number	equal 2
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
+
 units lj
 
 dimension 3
@@ -34,8 +35,8 @@ read_data data.duplex2
   2 = max # of 1-3 neighbors
   4 = max # of 1-4 neighbors
   6 = max # of special neighbors
-  special bonds CPU = 0.000103 secs
-  read_data CPU = 0.00215 secs
+  special bonds CPU = 0.000127 secs
+  read_data CPU = 0.001506 secs
 
 set atom * mass 3.1575
   16 settings made for mass
@@ -43,15 +44,15 @@ set atom * mass 3.1575
 group all type 1 4
 16 atoms in group all
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/stk     seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -136,7 +137,7 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.026 | 3.026 | 3.026 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.5358787 0.0096742456   -1.5262045 1.0127369e-05 
 1000  ekin = 1.54282272464468 |  erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
@@ -1140,21 +1141,21 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 2.08919327368179 |  erot = 2.76364485800616 | epot = -20.9705413117635 | etot = -16.1177031800756
 1000000  ekin = 2.11761701334905 |  erot = 2.1409630347026 | epot = -20.9096627221725 | etot = -16.6510826741208
  1000000  0.094116312   -1.3659956  0.059141691   -1.1745029 -3.0654283e-05 
-Loop time of 43.6978 on 1 procs for 1000000 steps with 16 atoms
+Loop time of 39.73 on 1 procs for 1000000 steps with 16 atoms
 
-Performance: 19772.150 tau/day, 22884.433 timesteps/s
-98.6% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 21746.777 tau/day, 25169.881 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 32.769     | 32.769     | 32.769     |   0.0 | 74.99
-Bond    | 0.93071    | 0.93071    | 0.93071    |   0.0 |  2.13
+Pair    | 29.698     | 29.698     | 29.698     |   0.0 | 74.75
+Bond    | 0.84677    | 0.84677    | 0.84677    |   0.0 |  2.13
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.19584    | 0.19584    | 0.19584    |   0.0 |  0.45
-Output  | 1e-05      | 1e-05      | 1e-05      |   0.0 |  0.00
-Modify  | 9.4507     | 9.4507     | 9.4507     |   0.0 | 21.63
-Other   |            | 0.3515     |            |       |  0.80
+Comm    | 0.15576    | 0.15576    | 0.15576    |   0.0 |  0.39
+Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
+Modify  | 8.7714     | 8.7714     | 8.7714     |   0.0 | 22.08
+Other   |            | 0.2585     |            |       |  0.65
 
 Nlocal:    16 ave 16 max 16 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -1170,4 +1171,4 @@ Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:43
+Total wall time: 0:00:39
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.4
similarity index 99%
rename from examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4
rename to examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.4
index 8989bce5ef..ba8fd4a657 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.4
@@ -1,8 +1,9 @@
-LAMMPS (18 Jun 2019)
+LAMMPS (7 Aug 2019)
 variable number	equal 2
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
+
 units lj
 
 dimension 3
@@ -34,8 +35,8 @@ read_data data.duplex2
   2 = max # of 1-3 neighbors
   4 = max # of 1-4 neighbors
   6 = max # of special neighbors
-  special bonds CPU = 0.000162 secs
-  read_data CPU = 0.002971 secs
+  special bonds CPU = 0.000188 secs
+  read_data CPU = 0.002335 secs
 
 set atom * mass 3.1575
   16 settings made for mass
@@ -43,15 +44,15 @@ set atom * mass 3.1575
 group all type 1 4
 16 atoms in group all
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/stk     seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -136,7 +137,7 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.778 | 7.96 | 8.143 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.5358787 0.0096742456   -1.5262045 1.0127369e-05 
 1000  ekin = 1.34554291364716 |  erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
@@ -1140,21 +1141,21 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 2.61553981530106 |  erot = 1.7387289184571 | epot = -21.0217257279766 | etot = -16.6674569942185
 1000000  ekin = 2.34012577497833 |  erot = 2.86436388995813 | epot = -21.0201566044041 | etot = -15.8156669394676
  1000000   0.10400559   -1.3746133  0.060853481   -1.1675019 0.00013752759 
-Loop time of 59.4195 on 4 procs for 1000000 steps with 16 atoms
+Loop time of 44.9291 on 4 procs for 1000000 steps with 16 atoms
 
-Performance: 14540.686 tau/day, 16829.497 timesteps/s
-96.3% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 19230.287 tau/day, 22257.276 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.0304     | 20.212     | 37.839     | 369.5 | 34.02
-Bond    | 0.12844    | 0.57006    | 0.95643    |  49.6 |  0.96
+Pair    | 0.75183    | 16.839     | 31.47      | 339.4 | 37.48
+Bond    | 0.10416    | 0.48181    | 0.82289    |  46.2 |  1.07
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 4.3935     | 5.5635     | 6.7052     |  44.2 |  9.36
-Output  | 2.3e-05    | 3.575e-05  | 4.1e-05    |   0.0 |  0.00
-Modify  | 0.3513     | 3.4695     | 6.4366     | 144.3 |  5.84
-Other   |            | 29.6       |            |       | 49.82
+Comm    | 3.0032     | 3.0414     | 3.0759     |   1.7 |  6.77
+Output  | 1.6e-05    | 2.2e-05    | 2.4e-05    |   0.0 |  0.00
+Modify  | 0.25426    | 2.929      | 5.4956     | 134.9 |  6.52
+Other   |            | 21.64      |            |       | 48.16
 
 Nlocal:    4 ave 8 max 0 min
 Histogram: 1 1 0 0 0 0 0 0 1 1
@@ -1170,4 +1171,4 @@ Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:59
+Total wall time: 0:00:44
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
index 51d6334f55..033783dc15 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3
@@ -1,4 +1,4 @@
-variable number	equal 1
+variable number	equal 3
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
@@ -24,14 +24,14 @@ set atom * mass 1.0
 
 group all type 1 4
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1
similarity index 99%
rename from examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1
rename to examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1
index 6b8b7161d5..9172c99492 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1
@@ -1,5 +1,5 @@
-LAMMPS (18 Jun 2019)
-variable number	equal 1
+LAMMPS (7 Aug 2019)
+variable number	equal 3
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
@@ -35,8 +35,8 @@ read_data data.duplex3
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000113 secs
-  read_data CPU = 0.00275 secs
+  special bonds CPU = 0.000145 secs
+  read_data CPU = 0.001965 secs
 
 set atom * mass 1.0
   10 settings made for mass
@@ -44,15 +44,15 @@ set atom * mass 1.0
 group all type 1 4
 10 atoms in group all
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -135,7 +135,7 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4720158  0.009525411   -1.4624904 3.1370518e-06 
 1000  ekin = 0.00366431201929618 |  erot = 0.00193726360267488 | epot = -14.630505317301 | etot = -14.624903741679
@@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.330110494517114 |  erot = 0.658973630822449 | epot = -15.6139878677246 | etot = -14.624903742385
 1000000  ekin = 0.345190458650495 |  erot = 0.661138339466907 | epot = -15.6312325406154 | etot = -14.624903742498
  1000000  0.025569664   -1.5839232  0.020799898   -1.5286042 -3.5789082e-06 
-Loop time of 20.5464 on 1 procs for 1000000 steps with 10 atoms
+Loop time of 25.9663 on 1 procs for 1000000 steps with 10 atoms
 
-Performance: 42051.215 tau/day, 48670.388 timesteps/s
-98.3% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 33273.840 tau/day, 38511.388 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 16.716     | 16.716     | 16.716     |   0.0 | 81.36
-Bond    | 0.6285     | 0.6285     | 0.6285     |   0.0 |  3.06
+Pair    | 21.428     | 21.428     | 21.428     |   0.0 | 82.52
+Bond    | 0.76981    | 0.76981    | 0.76981    |   0.0 |  2.96
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.187      | 0.187      | 0.187      |   0.0 |  0.91
-Output  | 6e-06      | 6e-06      | 6e-06      |   0.0 |  0.00
-Modify  | 2.7186     | 2.7186     | 2.7186     |   0.0 | 13.23
-Other   |            | 0.2965     |            |       |  1.44
+Comm    | 0.25709    | 0.25709    | 0.25709    |   0.0 |  0.99
+Output  | 9e-06      | 9e-06      | 9e-06      |   0.0 |  0.00
+Modify  | 3.1584     | 3.1584     | 3.1584     |   0.0 | 12.16
+Other   |            | 0.3534     |            |       |  1.36
 
 Nlocal:    10 ave 10 max 10 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -1169,4 +1169,4 @@ Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:20
+Total wall time: 0:00:25
diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4
similarity index 99%
rename from examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4
rename to examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4
index 60722d1063..491f91e671 100644
--- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4
@@ -1,5 +1,5 @@
-LAMMPS (18 Jun 2019)
-variable number	equal 1
+LAMMPS (7 Aug 2019)
+variable number	equal 3
 variable ofreq	equal 1000
 variable efreq	equal 1000
 variable T      equal 0.1
@@ -35,8 +35,8 @@ read_data data.duplex3
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000189 secs
-  read_data CPU = 0.003302 secs
+  special bonds CPU = 0.000188 secs
+  read_data CPU = 0.002791 secs
 
 set atom * mass 1.0
   10 settings made for mass
@@ -44,15 +44,15 @@ set atom * mass 1.0
 group all type 1 4
 10 atoms in group all
 
-# oxDNA bond interactions - FENE backbone
+# oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
 
-# oxDNA pair interactions
+# oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -135,7 +135,7 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4720158  0.009525411   -1.4624904 3.1370518e-06 
 1000  ekin = 0.00366431201929595 |  erot = 0.00193726360268106 | epot = -14.630505317301 | etot = -14.624903741679
@@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.330110494517446 |  erot = 0.658973630822486 | epot = -15.613987867725 | etot = -14.6249037423851
 1000000  ekin = 0.345190458651126 |  erot = 0.66113833946702 | epot = -15.6312325406162 | etot = -14.624903742498
  1000000  0.025569664   -1.5839232  0.020799898   -1.5286042 -3.5789082e-06 
-Loop time of 30.1999 on 4 procs for 1000000 steps with 10 atoms
+Loop time of 20.0167 on 4 procs for 1000000 steps with 10 atoms
 
-Performance: 28609.339 tau/day, 33112.661 timesteps/s
-96.4% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 43164.007 tau/day, 49958.342 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.90762    | 10.291     | 18.476     | 234.3 | 34.08
-Bond    | 0.11783    | 0.39332    | 0.61914    |  34.0 |  1.30
+Pair    | 0.59089    | 7.5652     | 13.908     | 205.5 | 37.79
+Bond    | 0.090803   | 0.29363    | 0.47758    |  29.6 |  1.47
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 2.8711     | 3.8042     | 4.7159     |  34.0 | 12.60
-Output  | 2e-05      | 3.15e-05   | 3.6e-05    |   0.0 |  0.00
-Modify  | 0.27052    | 1.1583     | 1.9428     |  63.9 |  3.84
-Other   |            | 14.55      |            |       | 48.19
+Comm    | 1.7298     | 2.0312     | 2.2983     |  16.6 | 10.15
+Output  | 1.4e-05    | 2.075e-05  | 2.3e-05    |   0.0 |  0.00
+Modify  | 0.17638    | 0.90613    | 1.5893     |  60.1 |  4.53
+Other   |            | 9.22       |            |       | 46.06
 
 Nlocal:    2.5 ave 5 max 0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
@@ -1169,4 +1169,4 @@ Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:30
+Total wall time: 0:00:20
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type
new file mode 100644
index 0000000000..a8412eef07
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type
@@ -0,0 +1,130 @@
+# LAMMPS data file
+26 atoms
+26 ellipsoids
+24 bonds
+
+4 atom types
+1 bond types
+
+# System size
+-20.000000 20.000000 xlo xhi
+-20.000000 20.000000 ylo yhi
+-20.000000 20.000000 zlo zhi
+
+# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
+Atoms
+
+1 1 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.957432645895970e-01 -3.379920348381733e-01  3.897628551303122e-01 1 1 1
+3 3 -2.192046146198370e-01 -5.585242491865227e-01  7.795257102606244e-01 1 1 1
+4 4  1.335125603737887e-01 -5.849567473090943e-01  1.169288565390937e+00 1 1 1
+5 1  4.398311230978960e-01 -4.081036426625517e-01  1.559051420521249e+00 1 1 1
+6 2  5.932984957350773e-01 -8.942535970570469e-02  1.948814275651561e+00 1 1 1
+7 3  5.405813207414517e-01  2.603302434705350e-01  2.338577130781873e+00 1 1 1
+8 4  3.000000000000002e-01  5.196152422706634e-01  2.728339985912185e+00 1 1 1
+9 1 -4.483805615185452e-02  5.983222783087083e-01  3.118102841042497e+00 1 1 1
+10 2 -3.740938811152403e-01  4.690988894808181e-01  3.507865696172809e+00 1 1 1
+11 3 -5.733436834716847e-01  1.768531046465427e-01  3.897628551303121e+00 1 1 1
+12 4 -5.733436834716849e-01 -1.768531046465427e-01  4.287391406433434e+00 1 1 1
+13 1 -3.740938811152403e-01 -4.690988894808182e-01  4.677154261563746e+00 1 1 1
+14 4  3.740938811152403e-01  4.690988894808182e-01  4.677154261563746e+00 2 1 1
+15 1  5.733436834716849e-01  1.768531046465427e-01  4.287391406433434e+00 2 1 1
+16 2  5.733436834716849e-01 -1.768531046465426e-01  3.897628551303122e+00 2 1 1
+17 3  3.740938811152403e-01 -4.690988894808181e-01  3.507865696172810e+00 2 1 1
+18 4  4.483805615185462e-02 -5.983222783087085e-01  3.118102841042498e+00 2 1 1
+19 1 -3.000000000000003e-01 -5.196152422706636e-01  2.728339985912186e+00 2 1 1
+20 2 -5.405813207414519e-01 -2.603302434705351e-01  2.338577130781874e+00 2 1 1
+21 3 -5.932984957350776e-01  8.942535970570474e-02  1.948814275651561e+00 2 1 1
+22 4 -4.398311230978962e-01  4.081036426625520e-01  1.559051420521249e+00 2 1 1
+23 1 -1.335125603737888e-01  5.849567473090947e-01  1.169288565390937e+00 2 1 1
+24 2  2.192046146198373e-01  5.585242491865231e-01  7.795257102606246e-01 2 1 1
+25 3  4.957432645895974e-01  3.379920348381736e-01  3.897628551303123e-01 2 1 1
+26 4  6.000000000000006e-01  0.000000000000000e+00  1.110223024625157e-16 2 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+11  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+12  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+13  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+14  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+15  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+16  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+17  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+18  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+19  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+20  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+21  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+22  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+23  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+24  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+25  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+26  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.555728057861408e-01  0.000000000000000e+00  0.000000000000000e+00  2.947551744109042e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.262387743159949e-01  0.000000000000000e+00  0.000000000000000e+00  5.633200580636221e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  6.234898018587335e-01  0.000000000000000e+00  0.000000000000000e+00  7.818314824680299e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.653410243663950e-01  0.000000000000000e+00  0.000000000000000e+00  9.308737486442042e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  7.473009358642424e-02  0.000000000000000e+00  0.000000000000000e+00  9.972037971811802e-01
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -2.225209339563144e-01  0.000000000000000e+00  0.000000000000000e+00  9.749279121818237e-01
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -5.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00  8.660254037844387e-01
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  7.330518718298263e-01 -0.000000000000000e+00  0.000000000000000e+00 -6.801727377709196e-01
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.009688679024190e-01 -0.000000000000000e+00  0.000000000000000e+00 -4.338837391175581e-01
+11  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.888308262251286e-01 -0.000000000000000e+00  0.000000000000000e+00 -1.490422661761745e-01
+12  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.888308262251286e-01  0.000000000000000e+00  0.000000000000000e+00  1.490422661761745e-01
+13  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.009688679024190e-01  0.000000000000000e+00  0.000000000000000e+00  4.338837391175582e-01
+14  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00 -4.338837391175582e-01  9.009688679024190e-01  0.000000000000000e+00
+15  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01  9.888308262251286e-01  0.000000000000000e+00
+16  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  1.490422661761745e-01  9.888308262251286e-01 -0.000000000000000e+00
+17  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  4.338837391175581e-01  9.009688679024190e-01 -0.000000000000000e+00
+18  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  6.801727377709192e-01  7.330518718298267e-01  0.000000000000000e+00
+19  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.660254037844386e-01  5.000000000000001e-01  0.000000000000000e+00
+20  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.749279121818235e-01  2.225209339563145e-01  0.000000000000000e+00
+21  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.972037971811801e-01 -7.473009358642428e-02  0.000000000000000e+00
+22  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.308737486442041e-01 -3.653410243663952e-01  0.000000000000000e+00
+23  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  7.818314824680296e-01 -6.234898018587339e-01  0.000000000000000e+00
+24  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.633200580636215e-01 -8.262387743159952e-01  0.000000000000000e+00
+25  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01  9.555728057861407e-01  0.000000000000000e+00
+26  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  0.000000000000000e+00  1.000000000000000e+00 -0.000000000000000e+00
+
+# Bond topology
+Bonds
+
+1  1  1  2
+2  1  2  3
+3  1  3  4
+4  1  4  5
+5  1  5  6
+6  1  6  7
+7  1  7  8
+8  1  8  9
+9  1  9  10
+10  1  10  11
+11  1  11  12
+12  1  12  13
+13  1  14  15
+14  1  15  16
+15  1  16  17
+16  1  17  18
+17  1  18  19
+18  1  19  20
+19  1  20  21
+20  1  21  22
+21  1  22  23
+22  1  23  24
+23  1  24  25
+24  1  25  26
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type
new file mode 100644
index 0000000000..b4d622ac46
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type
@@ -0,0 +1,130 @@
+# LAMMPS data file
+26 atoms
+26 ellipsoids
+24 bonds
+
+8 atom types
+1 bond types
+
+# System size
+-20.000000 20.000000 xlo xhi
+-20.000000 20.000000 ylo yhi
+-20.000000 20.000000 zlo zhi
+
+# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
+Atoms
+
+1 1 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.957432645895970e-01 -3.379920348381733e-01  3.897628551303122e-01 1 1 1
+3 3 -2.192046146198370e-01 -5.585242491865227e-01  7.795257102606244e-01 1 1 1
+4 4  1.335125603737887e-01 -5.849567473090943e-01  1.169288565390937e+00 1 1 1
+5 5  4.398311230978960e-01 -4.081036426625517e-01  1.559051420521249e+00 1 1 1
+6 6  5.932984957350773e-01 -8.942535970570469e-02  1.948814275651561e+00 1 1 1
+7 7  5.405813207414517e-01  2.603302434705350e-01  2.338577130781873e+00 1 1 1
+8 8  3.000000000000002e-01  5.196152422706634e-01  2.728339985912185e+00 1 1 1
+9 1 -4.483805615185452e-02  5.983222783087083e-01  3.118102841042497e+00 1 1 1
+10 2 -3.740938811152403e-01  4.690988894808181e-01  3.507865696172809e+00 1 1 1
+11 7 -5.733436834716847e-01  1.768531046465427e-01  3.897628551303121e+00 1 1 1
+12 8 -5.733436834716849e-01 -1.768531046465427e-01  4.287391406433434e+00 1 1 1
+13 1 -3.740938811152403e-01 -4.690988894808182e-01  4.677154261563746e+00 1 1 1
+14 4  3.740938811152403e-01  4.690988894808182e-01  4.677154261563746e+00 2 1 1
+15 5  5.733436834716849e-01  1.768531046465427e-01  4.287391406433434e+00 2 1 1
+16 6  5.733436834716849e-01 -1.768531046465426e-01  3.897628551303122e+00 2 1 1
+17 3  3.740938811152403e-01 -4.690988894808181e-01  3.507865696172810e+00 2 1 1
+18 4  4.483805615185462e-02 -5.983222783087085e-01  3.118102841042498e+00 2 1 1
+19 5 -3.000000000000003e-01 -5.196152422706636e-01  2.728339985912186e+00 2 1 1
+20 6 -5.405813207414519e-01 -2.603302434705351e-01  2.338577130781874e+00 2 1 1
+21 7 -5.932984957350776e-01  8.942535970570474e-02  1.948814275651561e+00 2 1 1
+22 8 -4.398311230978962e-01  4.081036426625520e-01  1.559051420521249e+00 2 1 1
+23 1 -1.335125603737888e-01  5.849567473090947e-01  1.169288565390937e+00 2 1 1
+24 2  2.192046146198373e-01  5.585242491865231e-01  7.795257102606246e-01 2 1 1
+25 3  4.957432645895974e-01  3.379920348381736e-01  3.897628551303123e-01 2 1 1
+26 4  6.000000000000006e-01  0.000000000000000e+00  1.110223024625157e-16 2 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+11  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+12  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+13  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+14  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+15  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+16  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+17  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+18  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+19  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+20  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+21  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+22  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+23  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+24  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+25  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+26  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.555728057861408e-01  0.000000000000000e+00  0.000000000000000e+00  2.947551744109042e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.262387743159949e-01  0.000000000000000e+00  0.000000000000000e+00  5.633200580636221e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  6.234898018587335e-01  0.000000000000000e+00  0.000000000000000e+00  7.818314824680299e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.653410243663950e-01  0.000000000000000e+00  0.000000000000000e+00  9.308737486442042e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  7.473009358642424e-02  0.000000000000000e+00  0.000000000000000e+00  9.972037971811802e-01
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -2.225209339563144e-01  0.000000000000000e+00  0.000000000000000e+00  9.749279121818237e-01
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -5.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00  8.660254037844387e-01
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  7.330518718298263e-01 -0.000000000000000e+00  0.000000000000000e+00 -6.801727377709196e-01
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.009688679024190e-01 -0.000000000000000e+00  0.000000000000000e+00 -4.338837391175581e-01
+11  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.888308262251286e-01 -0.000000000000000e+00  0.000000000000000e+00 -1.490422661761745e-01
+12  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.888308262251286e-01  0.000000000000000e+00  0.000000000000000e+00  1.490422661761745e-01
+13  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.009688679024190e-01  0.000000000000000e+00  0.000000000000000e+00  4.338837391175582e-01
+14  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00 -4.338837391175582e-01  9.009688679024190e-01  0.000000000000000e+00
+15  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01  9.888308262251286e-01  0.000000000000000e+00
+16  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  1.490422661761745e-01  9.888308262251286e-01 -0.000000000000000e+00
+17  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  4.338837391175581e-01  9.009688679024190e-01 -0.000000000000000e+00
+18  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  6.801727377709192e-01  7.330518718298267e-01  0.000000000000000e+00
+19  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.660254037844386e-01  5.000000000000001e-01  0.000000000000000e+00
+20  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.749279121818235e-01  2.225209339563145e-01  0.000000000000000e+00
+21  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.972037971811801e-01 -7.473009358642428e-02  0.000000000000000e+00
+22  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.308737486442041e-01 -3.653410243663952e-01  0.000000000000000e+00
+23  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  7.818314824680296e-01 -6.234898018587339e-01  0.000000000000000e+00
+24  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.633200580636215e-01 -8.262387743159952e-01  0.000000000000000e+00
+25  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01  9.555728057861407e-01  0.000000000000000e+00
+26  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  0.000000000000000e+00  1.000000000000000e+00 -0.000000000000000e+00
+
+# Bond topology
+Bonds
+
+1  1  1  2
+2  1  2  3
+3  1  3  4
+4  1  4  5
+5  1  5  6
+6  1  6  7
+7  1  7  8
+8  1  8  9
+9  1  9  10
+10  1  10  11
+11  1  11  12
+12  1  12  13
+13  1  14  15
+14  1  15  16
+15  1  16  17
+16  1  17  18
+17  1  18  19
+18  1  19  20
+19  1  20  21
+20  1  21  22
+21  1  22  23
+22  1  23  24
+23  1  24  25
+24  1  25  26
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
new file mode 100644
index 0000000000..e5141bc47a
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
@@ -0,0 +1,828 @@
+#!/usr/bin/env python
+"""
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+"""
+"""
+Creates unique base-pairings to avoid asymmetrical H-bonds.  
+
+Modified to create the bead wall setup.
+N_BEADS is the number of beads along one direction, the final system will have N_BEADS^2 beads in the wall. N_BEADS should be set to be odd number.
+"""
+
+
+#Define number of base-pairs per turn for B-form DNA
+N = 10.5
+#Define distance between the big bead and the centre of mass of the last base-pair
+BEAD_OFFSET = 2.0
+WALL_PARTICLE_SIZE = 2.0
+N_BEADS = 11
+
+#Number of unique base type groups (1-4) ACGT counts as one group
+N_BASE_TYPES = 20
+
+
+"""
+Import basic modules
+"""
+import sys, os, timeit
+
+from timeit import default_timer as timer
+start_time = timer()
+"""
+Try to import numpy; if failed, import a local version mynumpy 
+which needs to be provided
+"""
+try:
+    import numpy as np
+except:
+    print("numpy not found. Exiting.", file=sys.stderr)
+    sys.exit(1)
+
+"""
+Check that the required arguments (box offset and size in simulation units 
+and the sequence file were provided
+"""
+try:
+    box_offset = float(sys.argv[1])
+    box_length = float(sys.argv[2])
+    infile = sys.argv[3]
+    if len(sys.argv) == 4:
+        topo = 'strand'
+        lk = 0
+    elif len(sys.argv) == 5:
+        topo = 'strand'
+        lk = int(sys.argv[4])
+           
+except:
+    print("Usage: %s <%s> <%s> <%s> <%s> " % (sys.argv[0], \
+	"box offset", "box length", "file with sequences", "[Lk]"), file=sys.stderr)
+    sys.exit(1)
+box = np.array ([box_length, box_length, box_length])
+
+"""
+Try to open the file and fail gracefully if file cannot be opened
+"""
+try:
+    inp = open (infile, 'r')
+    inp.close()
+except:
+    print("Could not open file '%s' for reading. \
+					      Aborting." % infile, file=sys.stderr)
+    sys.exit(2)
+
+# return parts of a string
+def partition(s, d):
+    if d in s:
+        sp = s.split(d, 1)
+        return sp[0], d, sp[1]
+    else:
+        return s, "", ""
+
+"""
+Define the model constants
+"""
+# set model constants
+PI = np.pi
+POS_BASE =  0.4
+POS_BACK = -0.4
+EXCL_RC1 =  0.711879214356
+EXCL_RC2 =  0.335388426126
+EXCL_RC3 =  0.52329943261
+
+"""
+Define auxillary variables for the construction of a helix
+"""
+# center of the double strand
+COM_CENTRE_DS = POS_BASE + 0.2
+
+# ideal rise between two consecutive nucleotides on the
+# same strand which are to be base paired in a duplex
+BASE_BASE = 0.3897628551303122
+
+# cutoff distance for overlap check
+RC2 = 16
+
+# squares of the excluded volume distances for overlap check
+RC2_BACK = EXCL_RC1**2
+RC2_BASE = EXCL_RC2**2
+RC2_BACK_BASE = EXCL_RC3**2
+
+# enumeration to translate from letters to numbers and vice versa
+number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
+base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
+                  'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
+
+# auxillary arrays
+positions = []
+a1s = []
+a3s = []
+quaternions = []
+
+newpositions = []
+newa1s = []
+newa3s = []
+
+basetype  = []
+strandnum = []
+
+bonds = []
+
+""" 
+Convert local body frame to quaternion DOF
+"""
+def exyz_to_quat (mya1, mya3):
+
+    mya2 = np.cross(mya3, mya1)
+    myquat = [1,0,0,0]
+
+    q0sq = 0.25 * (mya1[0] + mya2[1] + mya3[2] + 1.0)
+    q1sq = q0sq - 0.5 * (mya2[1] + mya3[2])
+    q2sq = q0sq - 0.5 * (mya1[0] + mya3[2])
+    q3sq = q0sq - 0.5 * (mya1[0] + mya2[1])
+
+    # some component must be greater than 1/4 since they sum to 1
+    # compute other components from it
+
+    if q0sq >= 0.25:
+        myquat[0] = np.sqrt(q0sq)
+        myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
+        myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
+        myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
+    elif q1sq >= 0.25:
+        myquat[1] = np.sqrt(q1sq)
+        myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
+        myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
+        myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
+    elif q2sq >= 0.25:
+        myquat[2] = np.sqrt(q2sq)
+        myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
+        myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
+        myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
+    elif q3sq >= 0.25:
+        myquat[3] = np.sqrt(q3sq)
+        myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
+        myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
+        myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
+
+    norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
+			  myquat[2]*myquat[2] + myquat[3]*myquat[3])
+    myquat[0] *= norm
+    myquat[1] *= norm
+    myquat[2] *= norm
+    myquat[3] *= norm
+
+    return np.array([myquat[0],myquat[1],myquat[2],myquat[3]])
+
+"""
+Adds a strand to the system by appending it to the array of previous strands
+"""
+def add_strands (mynewpositions, mynewa1s, mynewa3s):
+    overlap = False
+	
+    # This is a simple check for each of the particles where for previously 
+    # placed particles i we check whether it overlaps with any of the 
+    # newly created particles j
+
+    print("## Checking for overlaps", file=sys.stdout)
+
+    for i in range(len(positions)):
+
+        p = positions[i]
+        pa1 = a1s[i]
+
+        for j in range (len(mynewpositions)):
+
+            q = mynewpositions[j]
+            qa1 = mynewa1s[j]
+
+            # skip particles that are anyway too far away
+            dr = p - q
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) > RC2:
+                continue
+
+            # base site and backbone site of the two particles
+            p_pos_back = p + pa1 * POS_BACK
+            p_pos_base = p + pa1 * POS_BASE
+            q_pos_back = q + qa1 * POS_BACK
+            q_pos_base = q + qa1 * POS_BASE
+
+            # check for no overlap between the two backbone sites
+            dr = p_pos_back - q_pos_back
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK:
+                overlap = True
+
+            # check for no overlap between the two base sites
+            dr = p_pos_base -  q_pos_base
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BASE:
+                overlap = True
+
+            # check for no overlap between backbone site of particle p 
+            # with base site of particle q
+            dr = p_pos_back - q_pos_base
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK_BASE:
+                overlap = True
+
+            # check for no overlap between base site of particle p and 
+            # backbone site of particle q
+            dr = p_pos_base - q_pos_back
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK_BASE:
+                overlap = True
+
+            # exit if there is an overlap
+            if overlap:
+                return False
+
+    # append to the existing list if no overlap is found
+    if not overlap:
+
+        for p in mynewpositions:
+            positions.append(p)
+        for p in mynewa1s:
+            a1s.append (p)
+        for p in mynewa3s:
+            a3s.append (p)
+	# calculate quaternion from local body frame and append
+        for ia in range(len(mynewpositions)):
+            mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
+            quaternions.append(mynewquaternions)
+
+    return True
+
+"""
+Calculate angle of rotation site to site
+"""
+def get_angle(bp):
+   #n, minimal number of bases per turn
+   n = 10.5
+   found = False
+   while found == False:
+       turns = bp/n
+       diff = abs( turns - round(turns))
+       if diff < 0.03:
+           found = True
+           turns = round(turns)+lk
+           angle = (360*turns)/bp
+           angle = round (angle,2)
+           #angle =round( 360/n,2)
+       elif n > 11.5:
+           angle = 35.9
+           found = True
+       else:
+           n += 0.02
+   return angle
+
+
+def get_angle2(bp):
+    turns = bp/N + lk
+    angle = (360*turns)/bp
+    
+    return angle
+
+    
+
+"""
+Returns the rotation matrix defined by an axis and angle
+"""
+def get_rotation_matrix(axis, anglest, nbp=0):
+    # The argument anglest can be either an angle in radiants
+    # (accepted types are float, int or np.float64 or np.float64)
+    # or a tuple [angle, units] where angle is a number and
+    # units is a string. It tells the routine whether to use degrees,
+    # radiants (the default) or base pairs turns.
+    if not isinstance (anglest, (np.float64, np.float32, float, int)):
+        if len(anglest) > 1:
+            if anglest[1] in ["degrees", "deg", "o"]:
+                angle = (np.pi / 180.) * (anglest[0])
+            elif anglest[1] in ["bp"]:
+                if nbp == 0:
+                    angle = int(anglest[0]) * (np.pi / 180.) * (35.9)
+                else:    
+                    ang = get_angle2(nbp)
+                    angle = int(anglest[0]) * (np.pi / 180.) * (ang)
+            else:
+                angle = float(anglest[0])
+        else:
+            angle = float(anglest[0])
+    else:
+        angle = float(anglest) # in degrees (?)
+
+    axis = np.array(axis)
+    axis /= np.sqrt(np.dot(axis, axis))
+
+    ct = np.cos(angle)
+    st = np.sin(angle)
+    olc = 1. - ct
+    x, y, z = axis
+
+    return np.array([[olc*x*x+ct, olc*x*y-st*z, olc*x*z+st*y],
+                    [olc*x*y+st*z, olc*y*y+ct, olc*y*z-st*x],
+                    [olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
+
+"""
+Generates the position and orientation vectors of a 
+(single or double) strand from a sequence string
+"""
+def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
+	  dir=np.array([0, 0, 1]), perp=False, double=True, rot=0.):
+    # generate empty arrays
+    mynewpositions, mynewa1s, mynewa3s = [], [], []
+
+    # cast the provided start_pos array into a numpy array
+    start_pos = np.array(start_pos, dtype=float)
+
+    # overall direction of the helix
+    dir = np.array(dir, dtype=float)
+    #if sequence == None:
+    #    sequence = np.random.randint(1, 5, bp)
+
+    # the elseif here is most likely redundant 
+    #elif len(sequence) != bp:
+    #    n = bp - len(sequence)
+    #    sequence += np.random.randint(1, 5, n)
+    #    print("sequence is too short, adding %d random bases" % n, file=sys.stderr)
+
+    # normalize direction
+    dir_norm = np.sqrt(np.dot(dir,dir))
+    if dir_norm < 1e-10:
+        print("direction must be a valid vector,\
+                defaulting to (0, 0, 1)", file=sys.stderr)
+        dir = np.array([0, 0, 1])
+    else: dir /= dir_norm
+
+    # find a vector orthogonal to dir to act as helix direction,
+    # if not provided switch off random orientation
+    if perp is None or perp is False:
+        v1 = np.random.random_sample(3)
+        # comment in to suppress randomised base vector
+        v1 = [1,0,0]
+        v1 -= dir * (np.dot(dir, v1))
+        v1 /= np.sqrt(sum(v1*v1))
+    else:
+        v1 = perp;
+
+    # generate rotational matrix representing the overall rotation of the helix
+    R0 = get_rotation_matrix(dir, rot)
+	    
+    # rotation matrix corresponding to one step along the helix
+    R = get_rotation_matrix(dir, [1, "bp"],bp)
+
+    # set the vector a1 (backbone to base) to v1 
+    a1 = v1
+    
+    # apply the global rotation to a1 
+    a1 = np.dot(R0, a1)
+    
+    # set the position of the fist backbone site to start_pos
+    rb = np.array(start_pos)
+	    
+    # set a3 to the direction of the helix
+    a3 = dir
+
+    for i in range(bp):
+    # work out the position of the centre of mass of the nucleotide
+        rcom = rb - COM_CENTRE_DS * a1
+
+        # append to newpositions
+        mynewpositions.append(rcom)
+        mynewa1s.append(a1)
+        mynewa3s.append(a3)
+
+        # if we are not at the end of the helix, we work out a1 and rb for the 
+        # next nucleotide along the helix
+        if i != bp - 1:
+            a1 = np.dot(R, a1)
+            rb += a3 * BASE_BASE
+
+    # if we are working on a double strand, we do a cycle similar 
+    # to the previous one but backwards
+    if double == True:
+        a1 = -a1
+        a3 = -dir
+        R = R.transpose()
+        for i in range(bp):
+            rcom = rb - COM_CENTRE_DS * a1
+            mynewpositions.append (rcom)
+            mynewa1s.append (a1)
+            mynewa3s.append (a3)
+            a1 = np.dot(R, a1)
+            rb += a3 * BASE_BASE
+    
+  
+    #Calculate the positions of the bead wall
+    
+    last_base1 = mynewpositions[int( len(mynewpositions)/2 - 1) ]
+    last_base2 = mynewpositions[int( len(mynewpositions)/2) ]
+    mid_point =  (last_base1 + last_base2) / 2 
+    
+    NN = N_BEADS**2
+    p1 = [mid_point[0] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[1] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[2] + BEAD_OFFSET ]
+    for i in range(N_BEADS):
+        for j in range(N_BEADS):
+            position = [ p1[0] + 2*i*WALL_PARTICLE_SIZE, p1[1] + 2*j*WALL_PARTICLE_SIZE, p1[2]]
+            mynewa1s.append([1,0,0])
+            mynewa3s.append([1,0,0])
+            mynewpositions.append(position)
+
+    assert (len (mynewpositions) > 0)
+
+    return [mynewpositions, mynewa1s, mynewa3s]
+
+
+
+"""
+Main function for this script.
+Reads a text file with the following format:
+- Each line contains the sequence for a single strand (A,C,G,T)
+- Lines beginning with the keyword 'DOUBLE' produce double-stranded DNA
+
+Ex: Two ssDNA (single stranded DNA)
+ATATATA
+GCGCGCG
+
+Ex: Two strands, one double stranded, the other single stranded.
+DOUBLE AGGGCT
+CCTGTA
+
+"""
+
+def read_strands(filename):
+    try:
+        infile = open (filename)
+    except:
+        print("Could not open file '%s'. Aborting." % filename, file=sys.stderr)
+        sys.exit(2)
+
+    # This block works out the number of nucleotides and strands by reading 
+    # the number of non-empty lines in the input file and the number of letters,
+    # taking the possible DOUBLE keyword into account.
+    nstrands, nnucl, nbonds = 0, 0, 0
+    lines = infile.readlines()
+    for line in lines:
+        line = line.upper().strip()
+        if len(line) == 0:
+            continue
+        if line[:6] == 'DOUBLE':
+            line = line.split()[1]
+            length = len(line)
+            print("## Found duplex of %i base pairs" % length, file=sys.stdout)
+            nnucl += 2*length
+            nstrands += 2
+            nbonds+= 2*length
+            
+        else:
+            line = line.split()[0]
+            length = len(line)
+            print("## Found single strand of %i bases" % length, file=sys.stdout)
+            nnucl += length
+            nstrands += 1
+            if topo == 'ring':
+                nbonds =+ length
+            else:
+                nbonds += length+1
+    # rewind the sequence input file
+    infile.seek(0)
+
+    print("## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
+
+    # generate the data file in LAMMPS format
+    try:
+        out = open ("data.oxdna", "w")
+    except:
+        print("Could not open data file for writing. Aborting.", file=sys.stderr)
+        sys.exit(2)
+	
+    lines = infile.readlines()
+    nlines = len(lines)
+    i = 1
+    myns = 0
+    noffset = 1
+
+    for line in lines:
+        line = line.upper().strip()
+
+        # skip empty lines
+        if len(line) == 0: 
+            i += 1
+            continue
+
+	# block for duplexes: last argument of the generate function 
+	# is set to 'True'
+        if line[:6] == 'DOUBLE':
+            line = line.split()[1]
+            length = len(line)
+            seq = [(base_to_number[x]) for x in line]
+            seq = np.array(seq,dtype=int)
+            n_a, n_c, n_g, n_t = 0, 0, 0, 0
+            for s in range(seq.size):
+                if seq[s] == 1:
+                    n_a += 1
+                elif seq[s] == 2:
+                    n_c += 1
+                elif seq[s] ==3:
+                    n_g += 1
+                elif seq[s] == 4:
+                    n_t += 1
+            smallest_n_bases = n_c
+            if n_a < n_c:
+                smallest_n_bases = n_a
+            if smallest_n_bases > n_t:
+                smallest_n_bases = n_t
+            if smallest_n_bases > n_g:
+                smallest_n_bases = n_g
+             
+            if smallest_n_bases < N_BASE_TYPES:
+                print('## Not enough occurances of base types in the sequence for ' + str(N_BASE_TYPES))
+                print('## unique base types, switching to ' + str(smallest_n_bases) + ' unique types')
+            else:
+                smallest_n_bases = N_BASE_TYPES
+           
+            a, c, g, t = -3, -2, -1, 0
+            for s in range(seq.size):
+                if seq[s] == 1: 
+                    if a < (smallest_n_bases*4-3):
+                        a += 4
+                    else:
+                        a = 1
+                    seq[s] = a
+                
+                elif seq[s] == 2: 
+                    if c < (smallest_n_bases*4-2):
+                        c += 4
+                    else:
+                        c = 2
+                    seq[s] = c
+
+                elif seq[s] == 3:
+                    if g < (smallest_n_bases*4-1):
+                        g += 4
+                    else:
+                        g = 3
+                    seq[s] = g
+                elif seq[s] == 4:
+                    if t < (smallest_n_bases*4):
+                        t += 4
+                    else:
+                        t = 4
+                    seq[s] = t
+                
+
+
+            myns += 1
+
+            for b in range(length):
+                basetype.append(seq[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+     
+            
+            noffset += length 
+
+            # create the sequence of the second strand as made of 
+            # complementary bases
+            #seq2 = [5-s for s in seq]
+            seq2 = seq
+            for s in range(seq2.size):
+                if seq2[s]%4 == 1:
+                    seq2[s] += 3
+                elif seq2[s]%4 == 2:
+                    seq2[s] += 1
+                elif seq2[s]%4 == 3:
+                    seq2[s] -= 1
+                elif seq2[s]%4 == 0:
+                    seq2[s] -= 3    
+
+            #seq2.reverse()
+
+            myns += 1
+
+            for b in range(length):
+                basetype.append(seq2[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+
+                     
+            #create wall bead types
+            bead_type = 4*smallest_n_bases + 1
+            for i in range(N_BEADS**2):
+                
+                basetype.append(bead_type)
+                basetype.append(bead_type)
+                strandnum.append(bead_type)
+                strandnum.append(bead_type)
+            #bonds.append([length, noffset + length])
+            #bonds.append([length+1, noffset + length])
+
+            noffset += length
+
+            print("## Created duplex of %i bases" % (2*length), file=sys.stdout)
+
+            # generate random position of the first nucleotide
+            com = box_offset + np.random.random_sample(3) * box
+            # comment out to randomise
+            com = [0,0,0]
+
+            # generate the random direction of the helix 
+            axis = np.random.random_sample(3)
+            # comment out to randomise
+            axis = [0,0,1]
+            axis /= np.sqrt(np.dot(axis, axis))
+
+            # use the generate function defined above to create 
+            # the position and orientation vector of the strand
+            if topo == 'ring':
+                newpositions, newa1s, newa3s = generate_ring(len(line), \
+                      sequence=seq, dir=axis, start_pos=com, double=True)
+            else:
+                newpositions, newa1s, newa3s = generate_strand(len(line), \
+                    sequence=seq, dir=axis, start_pos=com, double=True)
+
+            # generate a new position for the strand until it does not overlap
+            # with anything already present
+            start = timer()
+            while not add_strands(newpositions, newa1s, newa3s):
+                com = box_offset + np.random.random_sample(3) * box
+                axis = np.random.random_sample(3)
+                axis /= np.sqrt(np.dot(axis, axis))
+                if topo == 'ring':
+                    newpositions, newa1s, newa3s = generate_ring(len(line), \
+                        sequence=seq, dir=axis, start_pos=com, double=True)
+                else:
+                    newpositions, newa1s, newa3s = generate_strand(len(line), \
+                        sequence=seq, dir=axis, start_pos=com, double=True)
+                print("## Trying %i" % i, file=sys.stdout)
+            end = timer()
+            print("## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
+                          (2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
+
+	# block for single strands: last argument of the generate function 
+	# is set to 'False'
+        else:
+            length = len(line)
+            seq = [(base_to_number[x]) for x in line]
+
+            myns += 1
+            for b in range(length):
+                basetype.append(seq[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+            if topo == 'ring':    
+                bondpair = [noffset, noffset + length-1]
+                bonds.append(bondpair)
+            noffset += length
+            
+
+	    # generate random position of the first nucleotide
+            com = box_offset + np.random.random_sample(3) * box
+            # comment out to randomise
+            com = [-30,0,0]
+
+            # generate the random direction of the helix 
+            axis = np.random.random_sample(3)
+            # comment out to randomise
+            axis = [0,0,1]
+            axis /= np.sqrt(np.dot(axis, axis))
+
+            print("## Created single strand of %i bases" % length, file=sys.stdout)
+            if topo == 'ring':    
+                newpositions, newa1s, newa3s = generate_ring(length, \
+		              sequence=seq, dir=axis, start_pos=com, double=False)
+            else:
+                newpositions, newa1s, newa3s = generate_strand(length, \
+		               sequence=seq, dir=axis, start_pos=com, double=False)
+            start = timer()
+            while not add_strands(newpositions, newa1s, newa3s):
+                com = box_offset + np.random.random_sample(3) * box
+                axis = np.random.random_sample(3)
+                axis /= np.sqrt(np.dot(axis, axis))
+                if topo == 'ring':
+                    newpositions, newa1s, newa3s = generate_ring(length, \
+                          sequence=seq, dir=axis, start_pos=com, double=False)
+
+                else:    
+                    newpositions, newa1s, newa3s = generate_strand(length, \
+                          sequence=seq, dir=axis, start_pos=com, double=False)
+                print("## Trying  %i" % (i), file=sys.stdout)
+            end = timer()
+            print("## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
+				      (length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
+
+        i += 1
+
+    # sanity check
+    #if not len(positions) == nnucl:
+    #    print(len(positions), nnucl)
+    #    raise AssertionError
+    nnucl = nnucl + (N_BEADS**2)
+    nbonds -= 4
+	
+    out.write('# LAMMPS data file\n')
+    out.write('%d atoms\n' % nnucl)
+    out.write('%d ellipsoids\n' % nnucl)
+    out.write('%d bonds\n' % nbonds)
+    out.write('\n')
+    out.write('%d atom types\n' %bead_type )
+    out.write('1 bond types\n')
+    out.write('\n')
+    out.write('# System size\n')
+    out.write('%f %f xlo xhi\n' % (box_offset,box_offset+box_length))
+    out.write('%f %f ylo yhi\n' % (box_offset,box_offset+box_length))
+    out.write('%f %f zlo zhi\n' % (0,box_length))
+
+    #out.write('\n')
+    #out.write('Masses\n')
+    #out.write('\n')
+    #out.write('1 3.1575\n')
+    #out.write('2 3.1575\n')
+    #out.write('3 3.1575\n')
+    #out.write('4 3.1575\n')
+    #out.write('5 3.1575\n')
+
+    # for each nucleotide print a line under the headers
+    # Atoms, Velocities, Ellipsoids and Bonds
+    out.write('\n')
+    out.write(\
+      '# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
+    out.write('Atoms\n')
+    out.write('\n')
+    
+    for i in range(nnucl):
+        out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
+                  % (i+1, basetype[i], \
+                     positions[i][0], positions[i][1], positions[i][2], \
+                     strandnum[i]))
+
+    out.write('\n')
+    out.write('# Atom-ID, translational, rotational velocity\n')
+    out.write('Velocities\n')
+    out.write('\n')
+
+    for i in range(nnucl):
+        out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
+                  % (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
+
+    out.write('\n')
+    out.write('# Atom-ID, shape, quaternion\n')
+    out.write('Ellipsoids\n')
+    out.write('\n')
+
+    for i in range(nnucl):
+        out.write(\
+    "%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n"  \
+      % (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
+	quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
+ 
+    out.write('\n')
+    out.write('# Bond topology\n')
+    out.write('Bonds\n')
+    out.write('\n')
+
+    for i in range(nbonds):
+        if i < nbonds-2:
+             out.write("%d  %d  %d  %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
+        #else:
+        
+        #out.write("%d  %d  %d  %d\n" % (i+1,2,bonds[i][0],bonds[i][1]))
+
+    out.close()
+
+    print("## Wrote data to 'data.oxdna'", file=sys.stdout)
+    print("## DONE", file=sys.stdout)
+
+# call the above main() function, which executes the program
+read_strands (infile)
+
+end_time=timer()
+runtime = end_time-start_time
+hours = runtime/3600
+minutes = (runtime-np.rint(hours)*3600)/60
+seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
+print("## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type
new file mode 100644
index 0000000000..0570cf042d
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type
@@ -0,0 +1,94 @@
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 4
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin 
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.4type
+mass * 3.1575
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene 
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype} 
+  variable basemod equal ${base}%4
+  if "${basemod} == 1" then &
+    "variable comp equal ${base}+3" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then &
+    "variable comp equal ${base}+1" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz 
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+
+#write_restart config.${number}.*
+
+
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type
new file mode 100644
index 0000000000..dae853a113
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type
@@ -0,0 +1,94 @@
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 8
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin 
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.8type
+mass * 3.1575
+
+group all type 1 8
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene 
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype} 
+  variable basemod equal ${base}%4
+  if "${basemod} == 1" then &
+    "variable comp equal ${base}+3" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then &
+    "variable comp equal ${base}+1" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz 
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+
+#write_restart config.${number}.*
+
+
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1
new file mode 100644
index 0000000000..d0195dd8e8
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1
@@ -0,0 +1,232 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 4
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.4type
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  26 atoms
+  reading velocities ...
+  26 velocities
+  26 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  24 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 6.2e-05 secs
+  read_data CPU = 0.001124 secs
+mass * 3.1575
+
+group all type 1 4
+26 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 1%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 1+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 2%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 2+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 3%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 4%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 10000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.63899
+  ghost atom cutoff = 5.63899
+  binsize = 2.81949, bins = 15 15 15
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.89 | 3.89 | 3.89 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
+10000  ekin = 1.01296379553452 |  erot = 1.38476360245491 | epot = -41.9785360036035 | etot = -39.5808086056141
+20000  ekin = 1.75607695499755 |  erot = 1.86620102096623 | epot = -41.9558496477913 | etot = -38.3335716718275
+30000  ekin = 2.25878673688255 |  erot = 2.60035907744906 | epot = -41.2869827431736 | etot = -36.427836928842
+40000  ekin = 2.11105717434601 |  erot = 3.16611217122795 | epot = -40.2762731426449 | etot = -34.999103797071
+50000  ekin = 3.05379083545185 |  erot = 2.45050275456902 | epot = -40.3032957287999 | etot = -34.799002138779
+60000  ekin = 3.05154113920288 |  erot = 2.52539576708931 | epot = -39.6800099891302 | etot = -34.103073082838
+70000  ekin = 3.23212209366503 |  erot = 3.28914763888578 | epot = -40.1240667487288 | etot = -33.602797016178
+80000  ekin = 2.82623224207568 |  erot = 2.91292948677805 | epot = -39.0983962904507 | etot = -33.3592345615969
+90000  ekin = 3.05995314905566 |  erot = 3.5429982411034 | epot = -39.1646070343971 | etot = -32.561655644238
+100000  ekin = 3.46139546969836 |  erot = 4.11704803295073 | epot = -38.5124679837256 | etot = -30.9340244810765
+  100000  0.092303879   -1.5243833  0.043134544   -1.3481182 6.862374e-06 
+Loop time of 7.99505 on 1 procs for 100000 steps with 26 atoms
+
+Performance: 108066.893 tau/day, 12507.742 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.2072     | 7.2072     | 7.2072     |   0.0 | 90.15
+Bond    | 0.14292    | 0.14292    | 0.14292    |   0.0 |  1.79
+Neigh   | 1.9e-05    | 1.9e-05    | 1.9e-05    |   0.0 |  0.00
+Comm    | 0.015676   | 0.015676   | 0.015676   |   0.0 |  0.20
+Output  | 0.001372   | 0.001372   | 0.001372   |   0.0 |  0.02
+Modify  | 0.61071    | 0.61071    | 0.61071    |   0.0 |  7.64
+Other   |            | 0.01714    |            |       |  0.21
+
+Nlocal:    26 ave 26 max 26 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    325 ave 325 max 325 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 325
+Ave neighs/atom = 12.5
+Ave special neighs/atom = 5.07692
+Neighbor list builds = 1
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+
+
+Total wall time: 0:00:07
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4
new file mode 100644
index 0000000000..a5647ccd77
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4
@@ -0,0 +1,232 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 4
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.4type
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  26 atoms
+  reading velocities ...
+  26 velocities
+  26 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  24 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000173 secs
+  read_data CPU = 0.00242 secs
+mass * 3.1575
+
+group all type 1 4
+26 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 1%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 1+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 2%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 2+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 3%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+variable base loop ${ntype}
+variable base loop 4
+  variable basemod equal ${base}%4
+  variable basemod equal 4%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.4type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 10000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.63899
+  ghost atom cutoff = 5.63899
+  binsize = 2.81949, bins = 15 15 15
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.499 | 9.682 | 9.864 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
+10000  ekin = 1.20524984175817 |  erot = 1.2679122962101 | epot = -41.9183873815797 | etot = -39.4452252436114
+20000  ekin = 1.60856540355485 |  erot = 2.64140880508964 | epot = -41.0106168994545 | etot = -36.76064269081
+30000  ekin = 2.821101638199 |  erot = 3.06373823252434 | epot = -40.9348041675027 | etot = -35.0499642967793
+40000  ekin = 2.36296917392486 |  erot = 3.53353555114673 | epot = -39.5591676362755 | etot = -33.6626629112039
+50000  ekin = 2.93383938780818 |  erot = 3.39920211088179 | epot = -40.3602175538497 | etot = -34.0271760551597
+60000  ekin = 2.42811021532829 |  erot = 2.75130045540831 | epot = -39.3178531324554 | etot = -34.1384424617188
+70000  ekin = 2.7282200818863 |  erot = 3.76502037022117 | epot = -40.5673105068195 | etot = -34.074070054712
+80000  ekin = 2.90877851656705 |  erot = 2.43617899356904 | epot = -38.4099618426175 | etot = -33.0650043324814
+90000  ekin = 3.89203816080263 |  erot = 2.67194811393274 | epot = -39.1880466354802 | etot = -32.6240603607448
+100000  ekin = 3.98445325397832 |  erot = 2.77079124049636 | epot = -39.2805505658488 | etot = -32.5253060713741
+  100000   0.10625209   -1.5603519  0.049561514   -1.3575422 -1.7755557e-05 
+Loop time of 7.14827 on 4 procs for 100000 steps with 26 atoms
+
+Performance: 120868.376 tau/day, 13989.395 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.047776   | 3.0726     | 6.3143     | 172.8 | 42.98
+Bond    | 0.00736    | 0.056846   | 0.10864    |  20.7 |  0.80
+Neigh   | 1.9e-05    | 1.9e-05    | 1.9e-05    |   0.0 |  0.00
+Comm    | 0.30925    | 3.451      | 6.3739     | 157.5 | 48.28
+Output  | 0.000896   | 0.0010197  | 0.001301   |   0.5 |  0.01
+Modify  | 0.015512   | 0.18417    | 0.37845    |  39.4 |  2.58
+Other   |            | 0.3826     |            |       |  5.35
+
+Nlocal:    6.5 ave 13 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    19.5 ave 26 max 13 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    123.5 ave 247 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 494
+Ave neighs/atom = 19
+Ave special neighs/atom = 5.07692
+Neighbor list builds = 1
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+
+
+Total wall time: 0:00:07
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1
new file mode 100644
index 0000000000..c93943a4c7
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1
@@ -0,0 +1,274 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 8
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.8type
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  26 atoms
+  reading velocities ...
+  26 velocities
+  26 ellipsoids
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  24 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 6.5e-05 secs
+  read_data CPU = 0.001139 secs
+mass * 3.1575
+
+group all type 1 8
+26 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 1%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 1+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 2%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 2+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 3%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 4%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 5%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 5+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 5 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 5 8 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 6%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 6+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 6 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 6 7 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 7%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 8%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 10000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.63899
+  ghost atom cutoff = 4.63899
+  binsize = 2.31949, bins = 18 18 18
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.905 | 3.905 | 3.905 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
+10000  ekin = 1.0129637955345 |  erot = 1.38476360245492 | epot = -41.9785360036034 | etot = -39.580808605614
+20000  ekin = 1.75607695499755 |  erot = 1.86620102096618 | epot = -41.9558496477911 | etot = -38.3335716718274
+30000  ekin = 2.25878673688259 |  erot = 2.60035907744898 | epot = -41.2869827431736 | etot = -36.427836928842
+40000  ekin = 2.11105717434584 |  erot = 3.16611217122799 | epot = -40.2762731426449 | etot = -34.9991037970711
+50000  ekin = 3.05379083545187 |  erot = 2.45050275456888 | epot = -40.3032957287998 | etot = -34.7990021387791
+60000  ekin = 3.05154113920291 |  erot = 2.5253957670889 | epot = -39.6800099891299 | etot = -34.1030730828381
+70000  ekin = 3.23212209366464 |  erot = 3.28914763888543 | epot = -40.1240667487278 | etot = -33.6027970161777
+80000  ekin = 2.82623224207591 |  erot = 2.91292948677732 | epot = -39.0983962904496 | etot = -33.3592345615963
+90000  ekin = 3.05995314905694 |  erot = 3.54299824110274 | epot = -39.164607034397 | etot = -32.5616556442373
+100000  ekin = 3.46139546969892 |  erot = 4.11704803295143 | epot = -38.512467983727 | etot = -30.9340244810767
+  100000  0.092303879   -1.5243833  0.043134544   -1.3481182 6.862374e-06 
+Loop time of 7.94086 on 1 procs for 100000 steps with 26 atoms
+
+Performance: 108804.336 tau/day, 12593.094 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.1507     | 7.1507     | 7.1507     |   0.0 | 90.05
+Bond    | 0.14487    | 0.14487    | 0.14487    |   0.0 |  1.82
+Neigh   | 6.4e-05    | 6.4e-05    | 6.4e-05    |   0.0 |  0.00
+Comm    | 0.032259   | 0.032259   | 0.032259   |   0.0 |  0.41
+Output  | 0.003484   | 0.003484   | 0.003484   |   0.0 |  0.04
+Modify  | 0.59013    | 0.59013    | 0.59013    |   0.0 |  7.43
+Other   |            | 0.01934    |            |       |  0.24
+
+Nlocal:    26 ave 26 max 26 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    323 ave 323 max 323 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 323
+Ave neighs/atom = 12.4231
+Ave special neighs/atom = 5.07692
+Neighbor list builds = 4
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+
+
+Total wall time: 0:00:07
diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4
new file mode 100644
index 0000000000..5cda079e9c
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4
@@ -0,0 +1,274 @@
+LAMMPS (7 Aug 2019)
+variable number	equal 1
+variable ofreq	equal 10000
+variable efreq	equal 10000
+
+variable ntype equal 8
+
+variable T equal 0.1
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.8type
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  26 atoms
+  reading velocities ...
+  26 velocities
+  26 ellipsoids
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  24 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000232 secs
+  read_data CPU = 0.002447 secs
+mass * 3.1575
+
+group all type 1 8
+26 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+
+label loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 1%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 1+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 2%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 2+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 3%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 4%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 5%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+3
+variable comp equal 5+3
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 5 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 5 8 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 6%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+variable comp equal ${base}+1
+variable comp equal 6+1
+pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 6 ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 6 7 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 7%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+variable base loop ${ntype}
+variable base loop 8
+  variable basemod equal ${base}%4
+  variable basemod equal 8%4
+  if "${basemod} == 1" then     "variable comp equal ${base}+3"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+  if "${basemod} == 2" then     "variable comp equal ${base}+1"     "pair_coeff ${base} ${comp} oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
+next base
+jump in.duplex4.8type loop
+
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} 0.2 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
+fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
+
+timestep 1e-4
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 10000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4]  vx vy vz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %13.6le %13.6le %13.6le %d %d %d  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le "
+
+#restart 10000 config0_restart config1_restart
+
+run 100000
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.63899
+  ghost atom cutoff = 4.63899
+  binsize = 2.31949, bins = 18 18 18
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.381 | 9.563 | 9.746 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
+10000  ekin = 1.20524984175816 |  erot = 1.26791229621008 | epot = -41.9183873815797 | etot = -39.4452252436115
+20000  ekin = 1.6085654035548 |  erot = 2.6414088050897 | epot = -41.0106168994546 | etot = -36.7606426908101
+30000  ekin = 2.82110163819891 |  erot = 3.06373823252419 | epot = -40.9348041675026 | etot = -35.0499642967795
+40000  ekin = 2.35553603700794 |  erot = 3.60405945883761 | epot = -39.5418687902286 | etot = -33.5822732943831
+50000  ekin = 3.06061403125833 |  erot = 3.35548669087246 | epot = -40.3236585928169 | etot = -33.9075578706861
+60000  ekin = 2.7347216991605 |  erot = 4.23926242244084 | epot = -39.5379959923263 | etot = -32.564011870725
+70000  ekin = 3.46562604991873 |  erot = 2.8521307045909 | epot = -38.7237000550356 | etot = -32.4059433005259
+80000  ekin = 3.17815543267806 |  erot = 3.11078099027451 | epot = -39.7525036398366 | etot = -33.463567216884
+90000  ekin = 3.51635117668857 |  erot = 2.58384069017333 | epot = -39.4762533092413 | etot = -33.3760614423795
+100000  ekin = 3.64218174280962 |  erot = 2.88607181210736 | epot = -37.6002449519119 | etot = -31.0719913969949
+  100000  0.097124846   -1.5164679  0.070304678   -1.3060794 -2.9111933e-05 
+Loop time of 5.64462 on 4 procs for 100000 steps with 26 atoms
+
+Performance: 153066.031 tau/day, 17715.976 timesteps/s
+99.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.069668   | 2.1601     | 4.2189     | 138.7 | 38.27
+Bond    | 0.008542   | 0.052544   | 0.095929   |  18.7 |  0.93
+Neigh   | 4.8e-05    | 5.6e-05    | 6.4e-05    |   0.0 |  0.00
+Comm    | 0.90402    | 3.1443     | 5.4155     | 124.9 | 55.70
+Output  | 0.001003   | 0.0011317  | 0.001468   |   0.6 |  0.02
+Modify  | 0.021098   | 0.20024    | 0.38154    |  39.2 |  3.55
+Other   |            | 0.0863     |            |       |  1.53
+
+Nlocal:    6.5 ave 13 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    17.5 ave 22 max 13 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    80.25 ave 167 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 321
+Ave neighs/atom = 12.3462
+Ave special neighs/atom = 5.07692
+Neighbor list builds = 3
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+
+
+Total wall time: 0:00:05
diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4
new file mode 100644
index 0000000000..72872d431a
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4
@@ -0,0 +1,96 @@
+# LAMMPS data file
+16 atoms
+16 ellipsoids
+13 bonds
+
+4 atom types
+1 bond types
+
+# System size
+-20.000000 20.000000 xlo xhi
+-20.000000 20.000000 ylo yhi
+-20.000000 20.000000 zlo zhi
+
+Masses
+
+1 3.1575
+2 3.1575
+3 3.1575
+4 3.1575
+
+# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
+Atoms
+
+1 1 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.860249842674776e-01 -3.518234140414736e-01  3.897628551303122e-01 1 1 1
+3 3 -1.874009511073395e-01 -5.699832309147915e-01  7.795257102606244e-01 1 1 1
+4 4  1.824198365552941e-01 -5.715968887521518e-01  1.169288565390937e+00 1 1 1
+5 1  4.829362784135484e-01 -3.560513319622209e-01  1.559051420521249e+00 1 1 1
+6 2  5.999771538385027e-01 -5.235921299024461e-03  1.948814275651561e+00 1 1 1
+7 3  4.890766774371325e-01  3.475687034056071e-01  2.338577130781873e+00 1 1 1
+8 4  1.923677943514057e-01  5.683261666476170e-01  2.728339985912185e+00 1 1 1
+9 1 -1.923677943514057e-01 -5.683261666476170e-01  2.728339985912185e+00 2 1 1
+10 2 -4.890766774371324e-01 -3.475687034056071e-01  2.338577130781873e+00 2 1 1
+11 3 -5.999771538385025e-01  5.235921299024461e-03  1.948814275651561e+00 2 1 1
+12 4 -4.829362784135481e-01  3.560513319622207e-01  1.559051420521249e+00 2 1 1
+13 1 -1.824198365552940e-01  5.715968887521514e-01  1.169288565390936e+00 2 1 1
+14 2  1.874009511073395e-01  5.699832309147912e-01  7.795257102606241e-01 2 1 1
+15 3  4.860249842674773e-01  3.518234140414733e-01  3.897628551303119e-01 2 1 1
+16 4  5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
+
+# Atom-ID, translational velocity, angular momentum
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+11  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+12  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+13  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+14  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+15  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+16  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.513258223252946e-01  0.000000000000000e+00  0.000000000000000e+00  3.081869234362515e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.100416404457962e-01  0.000000000000000e+00  0.000000000000000e+00  5.863723567357894e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.899012371043606e-01  0.000000000000000e+00  0.000000000000000e+00  8.074754054847398e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.123349185122326e-01  0.000000000000000e+00  0.000000000000000e+00  9.499720515246527e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  4.363309284746654e-03  0.000000000000000e+00  0.000000000000000e+00  9.999904807207346e-01
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -3.040330609254902e-01  0.000000000000000e+00  0.000000000000000e+00  9.526614812535865e-01
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.828323126827837e-01  0.000000000000000e+00  0.000000000000000e+00 -8.125924533816677e-01
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.125924533816681e-01  5.828323126827832e-01 -0.000000000000000e+00
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.526614812535864e-01  3.040330609254902e-01  0.000000000000000e+00
+11  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.999904807207346e-01 -4.363309284746654e-03  0.000000000000000e+00
+12  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.499720515246526e-01 -3.123349185122325e-01  0.000000000000000e+00
+13  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.074754054847402e-01 -5.899012371043603e-01  0.000000000000000e+00
+14  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.863723567357898e-01 -8.100416404457959e-01  0.000000000000000e+00
+15  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01  9.513258223252948e-01  0.000000000000000e+00
+16  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  2.775557561562893e-17  1.000000000000000e+00 -0.000000000000000e+00
+
+# Bond topology
+Bonds
+
+1  1  1  2
+2  1  2  3
+3  1  3  4
+4  1  4  5
+5  1  5  6
+6  1  6  7
+7  1  7  8
+8  1  9  10
+9  1  10  11
+10  1  11  12
+11  1  13  14
+12  1  14  15
+13  1  15  16
diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4
new file mode 100644
index 0000000000..ed2fafbe8b
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4
@@ -0,0 +1,80 @@
+variable number	equal 4
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex4
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxRNA2 bond interactions - FENE backbone
+bond_style oxrna2/fene
+bond_coeff * 2.0 0.25 0.761070781051
+
+# oxRNA2 pair interactions
+pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+
+pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxrna2/stk     seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 3 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 
+pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+pair_coeff * * oxrna2/dh      ${T} 0.5 1.02455
+
+# NVE ensemble
+#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all   nve/dot
+fix 1 all nve/asphere
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f"
+
+run 1000000
+
+#write_restart config.${number}.*
diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1 b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1
new file mode 100644
index 0000000000..d4c9fa3fcc
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1
@@ -0,0 +1,1174 @@
+LAMMPS (30 Oct 2019)
+variable number	equal 4
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex4
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 5.9e-05 secs
+  read_data CPU = 0.038375 secs
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxRNA2 bond interactions - FENE backbone
+bond_style oxrna2/fene
+bond_coeff * 2.0 0.25 0.761070781051
+
+# oxRNA2 pair interactions
+pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+
+pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxrna2/stk     seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/stk     seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 3 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
+pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+pair_coeff * * oxrna2/dh      ${T} 0.5 1.02455
+pair_coeff * * oxrna2/dh      0.1 0.5 1.02455
+
+# NVE ensemble
+#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all   nve/dot
+fix 1 all nve/asphere
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f"
+
+run 1000000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3015
+  ghost atom cutoff = 3.3015
+  binsize = 1.65075, bins = 25 25 25
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxrna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxrna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxrna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxrna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxrna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxrna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+0  ekin = 0 |  erot = 0 | epot = -13.282537590974 | etot = -13.282537590974
+Per MPI rank memory allocation (min/avg/max) = 2.951 | 2.951 | 2.951 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0  -0.84341458  0.013255977   -0.8301586 -2.0169485e-05 
+1000  ekin = 0.00448503054656468 |  erot = 0.00825381229611384 | epot = -13.2952764343122 | etot = -13.2825375914695
+2000  ekin = 0.0179027901180511 |  erot = 0.0327684151335467 | epot = -13.3332087967732 | etot = -13.2825375915216
+3000  ekin = 0.0401478317723584 |  erot = 0.0728240143066062 | epot = -13.3955094376815 | etot = -13.2825375916026
+4000  ekin = 0.0710654348932282 |  erot = 0.127292706283096 | epot = -13.4808957328808 | etot = -13.2825375917044
+5000  ekin = 0.110480309743662 |  erot = 0.194739074279834 | epot = -13.5877569758405 | etot = -13.282537591817
+6000  ekin = 0.158231230694432 |  erot = 0.273546913858903 | epot = -13.7143157364827 | etot = -13.2825375919294
+7000  ekin = 0.214206450831754 |  erot = 0.362058396901232 | epot = -13.8588024397642 | etot = -13.2825375920312
+8000  ekin = 0.278374111850069 |  erot = 0.458709556672181 | epot = -14.0196212606361 | etot = -13.2825375921138
+9000  ekin = 0.35080209403022 |  erot = 0.562145629088178 | epot = -14.1954853152903 | etot = -13.2825375921719
+10000  ekin = 0.431663021447766 |  erot = 0.671302139462136 | epot = -14.385502753114 | etot = -13.2825375922041
+11000  ekin = 0.521222365620265 |  erot = 0.78544264622411 | epot = -14.5892026040572 | etot = -13.2825375922128
+12000  ekin = 0.61981039873542 |  erot = 0.904150888366026 | epot = -14.8064988793055 | etot = -13.2825375922041
+13000  ekin = 0.72778153179885 |  erot = 1.02728222251243 | epot = -15.0376013464974 | etot = -13.2825375921861
+14000  ekin = 0.845466747659446 |  erot = 1.154885201864 | epot = -15.2828895416915 | etot = -13.2825375921681
+15000  ekin = 0.973515286429446 |  erot = 1.28640002432487 | epot = -15.5424529041413 | etot = -13.2825375933869
+16000  ekin = 1.12323013751098 |  erot = 1.40387495398598 | epot = -15.8096426839256 | etot = -13.2825375924286
+17000  ekin = 1.2976927283263 |  erot = 1.51347784068661 | epot = -16.0937081607397 | etot = -13.2825375917268
+18000  ekin = 1.48565191084531 |  erot = 1.63592970999661 | epot = -16.4041192134347 | etot = -13.2825375925928
+19000  ekin = 1.66750911163348 |  erot = 1.77940241938721 | epot = -16.7294491246368 | etot = -13.2825375936161
+20000  ekin = 1.84148924290423 |  erot = 1.93695511183687 | epot = -17.0609819484057 | etot = -13.2825375936646
+21000  ekin = 2.02307741366163 |  erot = 2.09844265792961 | epot = -17.4040576653939 | etot = -13.2825375938027
+22000  ekin = 2.21183606977224 |  erot = 2.26260708947302 | epot = -17.7569807531587 | etot = -13.2825375939134
+23000  ekin = 2.40735468792977 |  erot = 2.42817202047308 | epot = -18.1180643024997 | etot = -13.2825375940968
+24000  ekin = 2.60896890448861 |  erot = 2.59357882573853 | epot = -18.485085324508 | etot = -13.2825375942809
+25000  ekin = 2.81580135477345 |  erot = 2.75706655667055 | epot = -18.855405505957 | etot = -13.282537594513
+26000  ekin = 3.02680083558485 |  erot = 2.91667946897257 | epot = -19.2260178993271 | etot = -13.2825375947697
+27000  ekin = 3.24067707260308 |  erot = 3.07027299756498 | epot = -19.5934876652175 | etot = -13.2825375950495
+28000  ekin = 3.45601412953572 |  erot = 3.21560615188039 | epot = -19.9541578767293 | etot = -13.2825375953132
+29000  ekin = 3.6713683081319 |  erot = 3.35037905822946 | epot = -20.304284961999 | etot = -13.2825375956376
+30000  ekin = 3.88476027224393 |  erot = 3.47208481891837 | epot = -20.639382687185 | etot = -13.2825375960227
+31000  ekin = 4.09387957878895 |  erot = 3.57821385032035 | epot = -20.9546310254509 | etot = -13.2825375963416
+32000  ekin = 4.29662185345806 |  erot = 3.66648606531138 | epot = -21.2456455154186 | etot = -13.2825375966492
+33000  ekin = 4.49089153394062 |  erot = 3.73482555362569 | epot = -21.5082546845018 | etot = -13.2825375969355
+34000  ekin = 4.67464118182276 |  erot = 3.78142516888995 | epot = -21.738603947901 | etot = -13.2825375971883
+35000  ekin = 4.84586411782047 |  erot = 3.80480460777895 | epot = -21.9332063229962 | etot = -13.2825375973967
+36000  ekin = 5.00270940487365 |  erot = 3.8039453503275 | epot = -22.0891923527593 | etot = -13.2825375975582
+37000  ekin = 5.14355281474259 |  erot = 3.7783370953036 | epot = -22.204427507712 | etot = -13.2825375976658
+38000  ekin = 5.26699752588855 |  erot = 3.72801268545693 | epot = -22.2775478090594 | etot = -13.2825375977139
+39000  ekin = 5.37191151713863 |  erot = 3.65359747923659 | epot = -22.3080465940736 | etot = -13.2825375976984
+40000  ekin = 5.45746010972423 |  erot = 3.55633701588595 | epot = -22.2963347232305 | etot = -13.2825375976203
+41000  ekin = 5.52312188621308 |  erot = 3.43809872369854 | epot = -22.2437582073842 | etot = -13.2825375974726
+42000  ekin = 5.56872044211992 |  erot = 3.30135279333163 | epot = -22.1526108327155 | etot = -13.2825375972639
+43000  ekin = 5.59443660082917 |  erot = 3.14910305123731 | epot = -22.0260772490691 | etot = -13.2825375970026
+44000  ekin = 5.60078634437692 |  erot = 2.98477133565124 | epot = -21.8680952767294 | etot = -13.2825375967012
+45000  ekin = 5.58859564323333 |  erot = 2.81204277265316 | epot = -21.6831760122617 | etot = -13.2825375963752
+46000  ekin = 5.55896198288794 |  erot = 2.63469562167501 | epot = -21.4761952006007 | etot = -13.2825375960378
+47000  ekin = 5.51320424221946 |  erot = 2.45646420183046 | epot = -21.2522060397483 | etot = -13.2825375956984
+48000  ekin = 5.45280176988517 |  erot = 2.28095947573118 | epot = -21.0162988409769 | etot = -13.2825375953605
+49000  ekin = 5.37933239946638 |  erot = 2.11161440403257 | epot = -20.7734843985446 | etot = -13.2825375950457
+50000  ekin = 5.29440598595185 |  erot = 1.95156309993188 | epot = -20.5285066806346 | etot = -13.2825375947508
+51000  ekin = 5.19960275040233 |  erot = 1.8036634398305 | epot = -20.2858037847152 | etot = -13.2825375944824
+52000  ekin = 5.09244091535756 |  erot = 1.66034071449473 | epot = -20.0353192196127 | etot = -13.2825375897604
+53000  ekin = 5.00219098599272 |  erot = 1.54003539006211 | epot = -19.8247639698981 | etot = -13.2825375938433
+54000  ekin = 4.90058329526777 |  erot = 1.45132465506075 | epot = -19.6344455614683 | etot = -13.2825376111398
+55000  ekin = 4.70838087935139 |  erot = 1.38368494594893 | epot = -19.3746034336678 | etot = -13.2825376083675
+56000  ekin = 4.44064498303545 |  erot = 1.42525549496303 | epot = -19.1484380668508 | etot = -13.2825375888523
+57000  ekin = 4.28012764787285 |  erot = 1.59067222265512 | epot = -19.1533374833604 | etot = -13.2825376128325
+58000  ekin = 4.17606446205098 |  erot = 1.6926959141941 | epot = -19.1512979674148 | etot = -13.2825375911697
+59000  ekin = 4.0674801293444 |  erot = 1.75788112721294 | epot = -19.1078988477137 | etot = -13.2825375911564
+60000  ekin = 3.9544882347638 |  erot = 1.84391663061768 | epot = -19.0809424565336 | etot = -13.2825375911521
+61000  ekin = 3.83840387031284 |  erot = 1.95003019237208 | epot = -19.0709716537088 | etot = -13.2825375910239
+62000  ekin = 3.72130809963045 |  erot = 2.07501703895377 | epot = -19.0788627296237 | etot = -13.2825375910394
+63000  ekin = 3.60440089032981 |  erot = 2.21773397929798 | epot = -19.1046724606768 | etot = -13.282537591049
+64000  ekin = 3.48898621429844 |  erot = 2.37695650761985 | epot = -19.1484803129713 | etot = -13.282537591053
+65000  ekin = 3.37647880025293 |  erot = 2.55140907448467 | epot = -19.2104254657961 | etot = -13.2825375910585
+66000  ekin = 3.26833067403372 |  erot = 2.73974236805088 | epot = -19.2906106331593 | etot = -13.2825375910747
+67000  ekin = 3.16594788215578 |  erot = 2.94047174698236 | epot = -19.3889572202528 | etot = -13.2825375911146
+68000  ekin = 3.07060531612276 |  erot = 3.15188029478627 | epot = -19.5050232021015 | etot = -13.2825375911924
+69000  ekin = 2.98334905059819 |  erot = 3.37190853325577 | epot = -19.6377951751758 | etot = -13.2825375913219
+70000  ekin = 2.90492955397884 |  erot = 3.59802295152975 | epot = -19.7854900970223 | etot = -13.2825375915137
+71000  ekin = 2.83572376329218 |  erot = 3.8271560839742 | epot = -19.9454174390314 | etot = -13.282537591765
+72000  ekin = 2.77568510798997 |  erot = 4.05569348668259 | epot = -20.1139161867768 | etot = -13.2825375921043
+73000  ekin = 2.72437405649527 |  erot = 4.27929863267978 | epot = -20.2862102816556 | etot = -13.2825375924805
+74000  ekin = 2.6809894320095 |  erot = 4.4934031024691 | epot = -20.4569301273605 | etot = -13.2825375928819
+75000  ekin = 2.6444530940616 |  erot = 4.69339307186043 | epot = -20.6203837591939 | etot = -13.2825375932719
+76000  ekin = 2.61355415206022 |  erot = 4.87501053156087 | epot = -20.7711022772329 | etot = -13.2825375936118
+77000  ekin = 2.58710084062323 |  erot = 5.03478939172066 | epot = -20.9044278262183 | etot = -13.2825375938744
+78000  ekin = 2.56403853914049 |  erot = 5.17029283961051 | epot = -21.0168689727798 | etot = -13.2825375940288
+79000  ekin = 2.54361120788211 |  erot = 5.28037161018751 | epot = -21.1065204121487 | etot = -13.2825375940791
+80000  ekin = 2.52540527324247 |  erot = 5.36512720853065 | epot = -21.173070075803 | etot = -13.2825375940298
+81000  ekin = 2.50929384303298 |  erot = 5.42576598242971 | epot = -21.2175974194025 | etot = -13.2825375939398
+82000  ekin = 2.49524917644589 |  erot = 5.46414530531067 | epot = -21.2419320755728 | etot = -13.2825375938163
+83000  ekin = 2.4833426959312 |  erot = 5.48242032921998 | epot = -21.248300618845 | etot = -13.2825375936939
+84000  ekin = 2.47365997802594 |  erot = 5.48271691205541 | epot = -21.2389144836696 | etot = -13.2825375935882
+85000  ekin = 2.46626808184772 |  erot = 5.46691083838924 | epot = -21.2157165137399 | etot = -13.2825375935029
+86000  ekin = 2.46123154184243 |  erot = 5.43653398177485 | epot = -21.1803031170841 | etot = -13.2825375934668
+87000  ekin = 2.45852093879055 |  erot = 5.39265692383446 | epot = -21.1337154560121 | etot = -13.2825375933871
+88000  ekin = 2.45840646060175 |  erot = 5.33627030736198 | epot = -21.0772143612561 | etot = -13.2825375932924
+89000  ekin = 2.46146480126887 |  erot = 5.26838646846783 | epot = -21.0123888631742 | etot = -13.2825375934375
+90000  ekin = 2.4677317783594 |  erot = 5.18930366181446 | epot = -20.9395730335193 | etot = -13.2825375933455
+91000  ekin = 2.47726011905719 |  erot = 5.09951749277777 | epot = -20.8593152050595 | etot = -13.2825375932246
+92000  ekin = 2.49074261962909 |  erot = 5.00022791911595 | epot = -20.7735081318254 | etot = -13.2825375930803
+93000  ekin = 2.50902833057362 |  erot = 4.89281259013106 | epot = -20.6843785136292 | etot = -13.2825375929245
+94000  ekin = 2.53301288183075 |  erot = 4.77876912035546 | epot = -20.5943195949544 | etot = -13.2825375927682
+95000  ekin = 2.56354598704907 |  erot = 4.6596420581626 | epot = -20.5057256378352 | etot = -13.2825375926235
+96000  ekin = 2.60133194738611 |  erot = 4.53693642149354 | epot = -20.4208059613806 | etot = -13.2825375925009
+97000  ekin = 2.64684712537105 |  erot = 4.41204173729005 | epot = -20.3414264550665 | etot = -13.2825375924053
+98000  ekin = 2.70029551800324 |  erot = 4.28619503995162 | epot = -20.2690281502928 | etot = -13.2825375923379
+99000  ekin = 2.76159183076381 |  erot = 4.16048163754163 | epot = -20.2046110606006 | etot = -13.2825375922951
+100000  ekin = 2.83036874776579 |  erot = 4.03587523010376 | epot = -20.1487815701408 | etot = -13.2825375922712
+101000  ekin = 2.90599845693996 |  erot = 3.91330077540588 | epot = -20.1018368246064 | etot = -13.2825375922606
+102000  ekin = 2.98761606367604 |  erot = 3.79369343963812 | epot = -20.0638470955752 | etot = -13.2825375922611
+103000  ekin = 3.07413620026802 |  erot = 3.67802597580043 | epot = -20.0346997683418 | etot = -13.2825375922734
+104000  ekin = 3.16426099663645 |  erot = 3.56728973636564 | epot = -20.0140883253047 | etot = -13.2825375923026
+105000  ekin = 3.25648344622793 |  erot = 3.46242766269272 | epot = -20.0014487012763 | etot = -13.2825375923557
+106000  ekin = 3.34909407537355 |  erot = 3.36423261094161 | epot = -19.9958642787542 | etot = -13.282537592439
+107000  ekin = 3.4401993069765 |  erot = 3.27323316283015 | epot = -19.9959700623645 | etot = -13.2825375925578
+108000  ekin = 3.52775814523602 |  erot = 3.18959025645786 | epot = -19.999885994407 | etot = -13.2825375927131
+109000  ekin = 3.60964009104214 |  erot = 3.11302339299888 | epot = -20.0052010769433 | etot = -13.2825375929023
+110000  ekin = 3.68370388524509 |  erot = 3.04277828887564 | epot = -20.0090197672386 | etot = -13.2825375931179
+111000  ekin = 3.74789440567183 |  erot = 2.97764201100029 | epot = -20.0080740100205 | etot = -13.2825375933484
+112000  ekin = 3.80035415830428 |  erot = 2.91600823448521 | epot = -19.9988999863676 | etot = -13.2825375935781
+113000  ekin = 3.839544891464 |  erot = 2.8559933088984 | epot = -19.9780757941506 | etot = -13.2825375937882
+114000  ekin = 3.86437452036816 |  erot = 2.79560177874327 | epot = -19.9425138930678 | etot = -13.2825375939563
+115000  ekin = 3.87432139555448 |  erot = 2.7329343736024 | epot = -19.8897933632161 | etot = -13.2825375940592
+116000  ekin = 3.86954570193439 |  erot = 2.66642221950682 | epot = -19.8185055155168 | etot = -13.2825375940755
+117000  ekin = 3.85097050791378 |  erot = 2.59505981730843 | epot = -19.7285679191997 | etot = -13.2825375939775
+118000  ekin = 3.82031843896371 |  erot = 2.51866416069826 | epot = -19.6215201934448 | etot = -13.2825375937828
+119000  ekin = 3.78008379969918 |  erot = 2.43788144963878 | epot = -19.5005028428254 | etot = -13.2825375934874
+120000  ekin = 3.73339325084433 |  erot = 2.35417060362233 | epot = -19.3701014475786 | etot = -13.282537593112
+121000  ekin = 3.68379362023519 |  erot = 2.26974086129527 | epot = -19.23607207422 | etot = -13.2825375926895
+122000  ekin = 3.63497633455468 |  erot = 2.18733107351197 | epot = -19.1048450003258 | etot = -13.2825375922591
+123000  ekin = 3.59047168903067 |  erot = 2.10992442969337 | epot = -18.9829337105841 | etot = -13.2825375918601
+124000  ekin = 3.55336069064742 |  erot = 2.040449477976 | epot = -18.8763477601487 | etot = -13.2825375915253
+125000  ekin = 3.526052756485 |  erot = 1.98151529341996 | epot = -18.7901056411805 | etot = -13.2825375912756
+126000  ekin = 3.51088386083626 |  erot = 1.93492307727824 | epot = -18.728344529054 | etot = -13.2825375909395
+127000  ekin = 3.51016542665131 |  erot = 1.90135594382336 | epot = -18.6940589614221 | etot = -13.2825375909474
+128000  ekin = 3.52366007691459 |  erot = 1.88146923500262 | epot = -18.6876669021183 | etot = -13.2825375902011
+129000  ekin = 3.52804447871109 |  erot = 1.87939379818812 | epot = -18.6899759099344 | etot = -13.2825376330352
+130000  ekin = 3.39121727536937 |  erot = 1.95375354402963 | epot = -18.6275084102343 | etot = -13.2825375908353
+131000  ekin = 3.51597185423296 |  erot = 2.06600773707502 | epot = -18.8645172230933 | etot = -13.2825376317853
+132000  ekin = 3.65680948155273 |  erot = 2.09675964820427 | epot = -19.0361067214651 | etot = -13.2825375917081
+133000  ekin = 3.78260898444153 |  erot = 2.11778864665409 | epot = -19.1829352240667 | etot = -13.2825375929711
+134000  ekin = 3.90291219401782 |  erot = 2.13993246768634 | epot = -19.3253822549312 | etot = -13.282537593227
+135000  ekin = 4.0130725329214 |  erot = 2.16317596346888 | epot = -19.4587860898102 | etot = -13.2825375934199
+136000  ekin = 4.10942813981085 |  erot = 2.18779054238602 | epot = -19.579756275755 | etot = -13.2825375935581
+137000  ekin = 4.18918244084739 |  erot = 2.21413018926373 | epot = -19.6858502237401 | etot = -13.282537593629
+138000  ekin = 4.25055180725538 |  erot = 2.24252417705096 | epot = -19.7756135779486 | etot = -13.2825375936422
+139000  ekin = 4.29264193993076 |  erot = 2.27334414892611 | epot = -19.8485236824514 | etot = -13.2825375935945
+140000  ekin = 4.31542981069473 |  erot = 2.30704736065647 | epot = -19.9050147648392 | etot = -13.282537593488
+141000  ekin = 4.31969657449582 |  erot = 2.34420108979785 | epot = -19.9464352576258 | etot = -13.2825375933322
+142000  ekin = 4.30689625825181 |  erot = 2.38546661972145 | epot = -19.9749004711164 | etot = -13.2825375931432
+143000  ekin = 4.27897643633865 |  erot = 2.43154322469962 | epot = -19.9930572539778 | etot = -13.2825375929395
+144000  ekin = 4.23817759048809 |  erot = 2.4830525431645 | epot = -20.0037677263996 | etot = -13.282537592747
+145000  ekin = 4.18683687366757 |  erot = 2.54040585524226 | epot = -20.0097803214924 | etot = -13.2825375925826
+146000  ekin = 4.1272243777605 |  erot = 2.60369949546902 | epot = -20.0134614656897 | etot = -13.2825375924601
+147000  ekin = 4.06142641942193 |  erot = 2.67262771534946 | epot = -20.0165917271588 | etot = -13.2825375923874
+148000  ekin = 3.9912803569092 |  erot = 2.74643868481959 | epot = -20.0202566340943 | etot = -13.2825375923655
+149000  ekin = 3.91835859675027 |  erot = 2.82393987441759 | epot = -20.0248360635575 | etot = -13.2825375923896
+150000  ekin = 3.84399502540854 |  erot = 2.90355368904202 | epot = -20.0300863068999 | etot = -13.2825375924493
+151000  ekin = 3.76934462696646 |  erot = 2.98342057410476 | epot = -20.0353027936018 | etot = -13.2825375925305
+152000  ekin = 3.69546503896298 |  erot = 3.06154297168136 | epot = -20.0395456032602 | etot = -13.2825375926159
+153000  ekin = 3.62340677772839 |  erot = 3.13595781467703 | epot = -20.0419021850935 | etot = -13.2825375926881
+154000  ekin = 3.55429442921676 |  erot = 3.20491770297265 | epot = -20.0417497249216 | etot = -13.2825375927321
+155000  ekin = 3.48935808553585 |  erot = 3.26703376494699 | epot = -20.0389294432276 | etot = -13.2825375927448
+156000  ekin = 3.42995719397496 |  erot = 3.32146386703849 | epot = -20.0339586537003 | etot = -13.2825375926868
+157000  ekin = 3.37758377439356 |  erot = 3.36807693572793 | epot = -20.0281983027502 | etot = -13.2825375926288
+158000  ekin = 3.32977839475207 |  erot = 3.40502394976504 | epot = -20.0173399361875 | etot = -13.2825375916704
+159000  ekin = 3.28790229188226 |  erot = 3.43232801110884 | epot = -20.0027678906268 | etot = -13.2825375876357
+160000  ekin = 3.2827995172835 |  erot = 3.46457454882488 | epot = -20.0299116571487 | etot = -13.2825375910404
+161000  ekin = 3.29006841785848 |  erot = 3.48756894666501 | epot = -20.0601749524886 | etot = -13.2825375879651
+162000  ekin = 3.30320279765029 |  erot = 3.50064541816097 | epot = -20.0863858038423 | etot = -13.282537588031
+163000  ekin = 3.32680445360257 |  erot = 3.50703979240478 | epot = -20.1163818341648 | etot = -13.2825375881575
+164000  ekin = 3.35978204864574 |  erot = 3.50639799900046 | epot = -20.1487176359768 | etot = -13.2825375883306
+165000  ekin = 3.40052448161995 |  erot = 3.49807859199014 | epot = -20.1811406621343 | etot = -13.2825375885243
+166000  ekin = 3.44710440323596 |  erot = 3.48135096319306 | epot = -20.2109929551315 | etot = -13.2825375887025
+167000  ekin = 3.4975648313672 |  erot = 3.45565303648312 | epot = -20.2357554566791 | etot = -13.2825375888288
+168000  ekin = 3.55023572858497 |  erot = 3.42084325030349 | epot = -20.2536165677605 | etot = -13.282537588872
+169000  ekin = 3.60406985696843 |  erot = 3.37750569995077 | epot = -20.2641131456975 | etot = -13.2825375887783
+170000  ekin = 3.41798406778448 |  erot = 3.07782048145476 | epot = -19.7783420668553 | etot = -13.282537517616
+171000  ekin = 3.24552871157827 |  erot = 2.73637390316214 | epot = -19.2644400103087 | etot = -13.2825373955683
+172000  ekin = 3.78367855051371 |  erot = 3.0727453748938 | epot = -20.1389614956922 | etot = -13.2825375702847
+173000  ekin = 4.03457273059443 |  erot = 3.1833646910841 | epot = -20.5004749222031 | etot = -13.2825375005245
+174000  ekin = 4.14002439986023 |  erot = 3.16763893899922 | epot = -20.5902008391762 | etot = -13.2825375003167
+175000  ekin = 4.24061478727573 |  erot = 3.15086312051219 | epot = -20.6740154078953 | etot = -13.2825375001074
+176000  ekin = 4.33750550891641 |  erot = 3.1355261006119 | epot = -20.7555691095056 | etot = -13.2825374999773
+177000  ekin = 4.43118634626255 |  erot = 3.12342668205083 | epot = -20.8371505282964 | etot = -13.282537499983
+178000  ekin = 4.52112038535911 |  erot = 3.11516996838714 | epot = -20.9188278538863 | etot = -13.28253750014
+179000  ekin = 4.60569122910559 |  erot = 3.10997891303161 | epot = -20.9982076425525 | etot = -13.2825375004153
+180000  ekin = 4.68248742105205 |  erot = 3.10587534040976 | epot = -21.0709002621995 | etot = -13.2825375007377
+181000  ekin = 4.74885008880769 |  erot = 3.10016969122633 | epot = -21.1315572810546 | etot = -13.2825375010206
+182000  ekin = 4.80252004240904 |  erot = 3.09010778323153 | epot = -21.1751653268271 | etot = -13.2825375011865
+183000  ekin = 4.84185836209392 |  erot = 3.07355401450656 | epot = -21.1979498780501 | etot = -13.2825375014496
+184000  ekin = 4.86305938218274 |  erot = 3.04972947015758 | epot = -21.1953263537857 | etot = -13.2825375014454
+185000  ekin = 4.86484048379853 |  erot = 3.01830532387125 | epot = -21.165683308955 | etot = -13.2825375012852
+186000  ekin = 4.84781115921877 |  erot = 2.97987576045986 | epot = -21.1102244206817 | etot = -13.2825375010031
+187000  ekin = 4.8135776433552 |  erot = 2.93597501879465 | epot = -21.032090162799 | etot = -13.2825375006491
+188000  ekin = 4.76439584097176 |  erot = 2.8887503176203 | epot = -20.9356836588659 | etot = -13.2825375002739
+189000  ekin = 4.7028202134345 |  erot = 2.84056846871295 | epot = -20.8259261820664 | etot = -13.282537499919
+190000  ekin = 4.63141632940872 |  erot = 2.79367442377689 | epot = -20.7076282527969 | etot = -13.2825374996113
+191000  ekin = 4.55257205219687 |  erot = 2.74995133907398 | epot = -20.5850608906317 | etot = -13.2825374993609
+192000  ekin = 4.46841445137449 |  erot = 2.7108083514329 | epot = -20.4617603019722 | etot = -13.2825374991648
+193000  ekin = 4.38080987485702 |  erot = 2.67717312167301 | epot = -20.3405204955445 | etot = -13.2825374990145
+194000  ekin = 4.29140314493158 |  erot = 2.64952891334607 | epot = -20.2234695571822 | etot = -13.2825374989045
+195000  ekin = 4.20164846020147 |  erot = 2.62793199519283 | epot = -20.1121179542319 | etot = -13.2825374988376
+196000  ekin = 4.112799736886 |  erot = 2.6119729730638 | epot = -20.0073102087726 | etot = -13.2825374988228
+197000  ekin = 4.0258589719236 |  erot = 2.60069607327732 | epot = -19.9090925440707 | etot = -13.2825374988698
+198000  ekin = 3.94151021740635 |  erot = 2.59254113732139 | epot = -19.8165888537063 | etot = -13.2825374989786
+199000  ekin = 3.86008920571504 |  erot = 2.58539978552083 | epot = -19.728026490366 | etot = -13.2825374991301
+200000  ekin = 3.78163650515412 |  erot = 2.57685633277384 | epot = -19.6410303372136 | etot = -13.2825374992857
+201000  ekin = 3.70604145366868 |  erot = 2.56461316993842 | epot = -19.5531921230031 | etot = -13.282537499396
+202000  ekin = 3.63323784111708 |  erot = 2.54700321074533 | epot = -19.4627785512819 | etot = -13.2825374994195
+203000  ekin = 3.56337600429933 |  erot = 2.52342549129417 | epot = -19.3693389949301 | etot = -13.2825374993366
+204000  ekin = 3.49690618989364 |  erot = 2.49455276327499 | epot = -19.2739964523245 | etot = -13.2825374991559
+205000  ekin = 3.43455338767261 |  erot = 2.46224574346265 | epot = -19.1793366300441 | etot = -13.2825374989088
+206000  ekin = 3.37721205721374 |  erot = 2.42921548153353 | epot = -19.0889650373857 | etot = -13.2825374986384
+207000  ekin = 3.32580575275754 |  erot = 2.39854397251178 | epot = -19.0068872236571 | etot = -13.2825374983878
+208000  ekin = 3.28114891016496 |  erot = 2.37318814654829 | epot = -18.9368745549054 | etot = -13.2825374981921
+209000  ekin = 3.24383236356932 |  erot = 2.35556506548921 | epot = -18.8819349271337 | etot = -13.2825374980752
+210000  ekin = 3.21413821976281 |  erot = 2.34727297364745 | epot = -18.8439486914582 | etot = -13.282537498048
+211000  ekin = 3.19199204395966 |  erot = 2.34895966766644 | epot = -18.823489209736 | etot = -13.2825374981099
+212000  ekin = 3.17695628121177 |  erot = 2.360321472034 | epot = -18.819815251497 | etot = -13.2825374982512
+213000  ekin = 3.16826455951518 |  erot = 2.38020171954861 | epot = -18.8310037775187 | etot = -13.2825374984549
+214000  ekin = 3.16489343854634 |  erot = 2.4067605217501 | epot = -18.8541914589957 | etot = -13.2825374986993
+215000  ekin = 3.16566474352153 |  erot = 2.4376973804056 | epot = -18.8858996228856 | etot = -13.2825374989585
+216000  ekin = 3.16936807503256 |  erot = 2.47051711068081 | epot = -18.9224226849174 | etot = -13.282537499204
+217000  ekin = 3.16266988026838 |  erot = 2.47868467134127 | epot = -18.9238920507831 | etot = -13.2825374991734
+218000  ekin = 3.17835235865319 |  erot = 2.45704329444878 | epot = -18.9179331413792 | etot = -13.2825374882772
+219000  ekin = 3.26524817202019 |  erot = 2.48120766962855 | epot = -19.0289933444494 | etot = -13.2825375028007
+220000  ekin = 3.31083663795614 |  erot = 2.50602061547625 | epot = -19.0993947418608 | etot = -13.2825374884285
+221000  ekin = 3.33748530919716 |  erot = 2.52276996124467 | epot = -19.1427927588607 | etot = -13.2825374884189
+222000  ekin = 3.36243211589499 |  erot = 2.53668587910066 | epot = -19.181655483376 | etot = -13.2825374883803
+223000  ekin = 3.38541896904217 |  erot = 2.54888617169842 | epot = -19.2168426290796 | etot = -13.282537488339
+224000  ekin = 3.40625812507986 |  erot = 2.56049920868626 | epot = -19.2492948220809 | etot = -13.2825374883148
+225000  ekin = 3.42484722909618 |  erot = 2.57234499865719 | epot = -19.2797297160695 | etot = -13.2825374883162
+226000  ekin = 3.44121067431411 |  erot = 2.58472036633686 | epot = -19.3084685289968 | etot = -13.2825374883458
+227000  ekin = 3.45552721377379 |  erot = 2.59730386680743 | epot = -19.3353685689834 | etot = -13.2825374884022
+228000  ekin = 3.46810974282139 |  erot = 2.6091693120744 | epot = -19.3598165433777 | etot = -13.2825374884819
+229000  ekin = 3.4793267631311 |  erot = 2.61888809507087 | epot = -19.3807523467836 | etot = -13.2825374885816
+230000  ekin = 3.48948003513645 |  erot = 2.62469570471749 | epot = -19.3967132285507 | etot = -13.2825374886968
+231000  ekin = 3.49867242979377 |  erot = 2.62469374220078 | epot = -19.4059036608153 | etot = -13.2825374888207
+232000  ekin = 3.50671171842654 |  erot = 2.6170613032781 | epot = -19.4063105106474 | etot = -13.2825374889427
+233000  ekin = 3.51309701132125 |  erot = 2.60026316425572 | epot = -19.395897664621 | etot = -13.2825374890441
+234000  ekin = 3.51712117494327 |  erot = 2.5732608561 | epot = -19.3729195201406 | etot = -13.2825374890973
+235000  ekin = 3.51809173982137 |  erot = 2.53573892922866 | epot = -19.3363681581185 | etot = -13.2825374890685
+236000  ekin = 3.51562949139304 |  erot = 2.48833922691111 | epot = -19.2865062072295 | etot = -13.2825374889254
+237000  ekin = 3.50996386129235 |  erot = 2.43285732073676 | epot = -19.2253586706787 | etot = -13.2825374886496
+238000  ekin = 3.50212794781253 |  erot = 2.37232394343562 | epot = -19.1569893794952 | etot = -13.2825374882471
+239000  ekin = 3.49397580570111 |  erot = 2.31089750062538 | epot = -19.0874107940787 | etot = -13.2825374877522
+240000  ekin = 3.48799489984455 |  erot = 2.2535377170645 | epot = -19.0240701041318 | etot = -13.2825374872227
+241000  ekin = 3.4869474415209 |  erot = 2.2054938684223 | epot = -18.9749787966723 | etot = -13.2825374867291
+242000  ekin = 3.49341769740518 |  erot = 2.1716922310321 | epot = -18.9476474147781 | etot = -13.2825374863409
+243000  ekin = 3.50935803683834 |  erot = 2.15612557817114 | epot = -18.9480211011257 | etot = -13.2825374861162
+244000  ekin = 3.53571412218956 |  erot = 2.16133426987289 | epot = -18.979585878157 | etot = -13.2825374860946
+245000  ekin = 3.57218201231806 |  erot = 2.18803987534361 | epot = -19.0427593739549 | etot = -13.2825374862933
+246000  ekin = 3.61712090977309 |  erot = 2.23496626996945 | epot = -19.134624666449 | etot = -13.2825374867064
+247000  ekin = 3.66762313707197 |  erot = 2.29886938892499 | epot = -19.2490300133012 | etot = -13.2825374873042
+248000  ekin = 3.7197330409766 |  erot = 2.3747925366233 | epot = -19.377063065633 | etot = -13.2825374880331
+249000  ekin = 3.7687988475912 |  erot = 2.45655776432188 | epot = -19.5078941007305 | etot = -13.2825374888175
+250000  ekin = 3.80993596354031 |  erot = 2.53748030029899 | epot = -19.6299537534039 | etot = -13.2825374895646
+251000  ekin = 3.83856187827056 |  erot = 2.61124537605178 | epot = -19.7323447445001 | etot = -13.2825374901778
+252000  ekin = 3.85094160348732 |  erot = 2.67282602420842 | epot = -19.8063051182675 | etot = -13.2825374905717
+253000  ekin = 3.84466267221376 |  erot = 2.71927370140095 | epot = -19.8464738643054 | etot = -13.2825374906907
+254000  ekin = 3.81895334833665 |  erot = 2.75020964906229 | epot = -19.8517004879202 | etot = -13.2825374905212
+255000  ekin = 3.77477712370614 |  erot = 2.76789565653814 | epot = -19.8252102703408 | etot = -13.2825374900966
+256000  ekin = 3.71467746908406 |  erot = 2.77685421459328 | epot = -19.7740691731677 | etot = -13.2825374894904
+257000  ekin = 3.64239785971379 |  erot = 2.78310854270386 | epot = -19.7080438912194 | etot = -13.2825374888018
+258000  ekin = 3.56234912666851 |  erot = 2.79319020432263 | epot = -19.6380768191282 | etot = -13.2825374881371
+259000  ekin = 3.47902170398396 |  erot = 2.81309489223268 | epot = -19.5746540838083 | etot = -13.2825374875917
+260000  ekin = 3.39644765746004 |  erot = 2.84735592157315 | epot = -19.5263410662695 | etot = -13.2825374872363
+261000  ekin = 3.31779785755485 |  erot = 2.89836390677654 | epot = -19.4986992514401 | etot = -13.2825374871087
+262000  ekin = 3.24516405277549 |  erot = 2.96601202360082 | epot = -19.493713563585 | etot = -13.2825374872087
+263000  ekin = 3.17954694530476 |  erot = 3.04771661067519 | epot = -19.509801043485 | etot = -13.2825374875051
+264000  ekin = 3.12100159498054 |  erot = 3.13875568824872 | epot = -19.5422947711677 | etot = -13.2825374879384
+265000  ekin = 3.068909969511 |  erot = 3.23291804297596 | epot = -19.5843655009193 | etot = -13.2825374884324
+266000  ekin = 3.02230555156861 |  erot = 3.32335252530508 | epot = -19.6281955657834 | etot = -13.2825374889098
+267000  ekin = 2.98016989218859 |  erot = 3.40345614747457 | epot = -19.6661635289715 | etot = -13.2825374893083
+268000  ekin = 2.94163501488609 |  erot = 3.46763177350625 | epot = -19.6918042779853 | etot = -13.282537489593
+269000  ekin = 2.90604069318514 |  erot = 3.51175626238839 | epot = -19.7003344453578 | etot = -13.2825374897842
+270000  ekin = 2.87284037255906 |  erot = 3.53329819601916 | epot = -19.6886760584274 | etot = -13.2825374898492
+271000  ekin = 2.84156688817829 |  erot = 3.53141495904851 | epot = -19.6555193370576 | etot = -13.2825374898308
+272000  ekin = 2.81169493920539 |  erot = 3.50673144119823 | epot = -19.6009638701441 | etot = -13.2825374897405
+273000  ekin = 2.78262532285011 |  erot = 3.46115906465197 | epot = -19.5263218770821 | etot = -13.28253748958
+274000  ekin = 2.7538098130557 |  erot = 3.39781487150794 | epot = -19.4341621738894 | etot = -13.2825374893258
+275000  ekin = 2.72497357924299 |  erot = 3.32097131772016 | epot = -19.3284823859418 | etot = -13.2825374889787
+276000  ekin = 2.69631002934824 |  erot = 3.23585259467473 | epot = -19.2147001125792 | etot = -13.2825374885562
+277000  ekin = 2.66855210196767 |  erot = 3.14826501869249 | epot = -19.0993546087625 | etot = -13.2825374881024
+278000  ekin = 2.64286719085242 |  erot = 3.06403640806158 | epot = -18.9894410865919 | etot = -13.2825374876779
+279000  ekin = 2.6206102822317 |  erot = 2.98836162249344 | epot = -18.8915093920683 | etot = -13.2825374873432
+280000  ekin = 2.60303022005365 |  erot = 2.92520891289703 | epot = -18.810776620091 | etot = -13.2825374871403
+281000  ekin = 2.59103448458094 |  erot = 2.87693253510625 | epot = -18.7505045067693 | etot = -13.2825374870821
+282000  ekin = 2.58508390620569 |  erot = 2.84417540765416 | epot = -18.7117968010114 | etot = -13.2825374871516
+283000  ekin = 2.58523135936705 |  erot = 2.82606103956356 | epot = -18.6938298862415 | etot = -13.2825374873109
+284000  ekin = 2.59126091870015 |  erot = 2.82059473157549 | epot = -18.6943931377914 | etot = -13.2825374875157
+285000  ekin = 2.6028463107778 |  erot = 2.82514472713204 | epot = -18.7105285256397 | etot = -13.2825374877299
+286000  ekin = 2.61964775973889 |  erot = 2.83687342635821 | epot = -18.7390586740322 | etot = -13.2825374879351
+287000  ekin = 2.64167894317198 |  erot = 2.8528506609398 | epot = -18.777067092287 | etot = -13.2825374881753
+288000  ekin = 2.6687167813722 |  erot = 2.87022930110005 | epot = -18.8214835708729 | etot = -13.2825374884007
+289000  ekin = 2.69931643718217 |  erot = 2.88698660758031 | epot = -18.8688405333603 | etot = -13.2825374885979
+290000  ekin = 2.73194963658564 |  erot = 2.90163654912848 | epot = -18.91612367448 | etot = -13.2825374887658
+291000  ekin = 2.76502957907501 |  erot = 2.91324911168725 | epot = -18.9608161796579 | etot = -13.2825374888956
+292000  ekin = 2.79700561900648 |  erot = 2.92149576190988 | epot = -19.0010388698883 | etot = -13.282537488972
+293000  ekin = 2.82654239554718 |  erot = 2.92669002283955 | epot = -19.0357699073658 | etot = -13.2825374889791
+294000  ekin = 2.85272969462388 |  erot = 2.92951972788893 | epot = -19.0647869114596 | etot = -13.2825374889468
+295000  ekin = 2.87508597590098 |  erot = 2.9311082644765 | epot = -19.0887317291891 | etot = -13.2825374888116
+296000  ekin = 2.89378047526675 |  erot = 2.93349300132876 | epot = -19.1098109651873 | etot = -13.2825374885917
+297000  ekin = 2.90976516784938 |  erot = 2.93912517174385 | epot = -19.1314278279134 | etot = -13.2825374883201
+298000  ekin = 2.92469477926692 |  erot = 2.95047845944716 | epot = -19.1577107267524 | etot = -13.2825374880383
+299000  ekin = 2.94065805823336 |  erot = 2.96967690612592 | epot = -19.1928724521541 | etot = -13.2825374877948
+300000  ekin = 2.95980003469262 |  erot = 2.99812642992008 | epot = -19.2404639522493 | etot = -13.2825374876367
+301000  ekin = 2.98391272977048 |  erot = 3.03621252497702 | epot = -19.302662742346 | etot = -13.2825374875985
+302000  ekin = 3.01408971368422 |  erot = 3.08312901018064 | epot = -19.3797562115572 | etot = -13.2825374876923
+303000  ekin = 3.05053302665408 |  erot = 3.13689255668996 | epot = -19.4699630712472 | etot = -13.2825374879032
+304000  ekin = 3.08584972584671 |  erot = 3.19556015974062 | epot = -19.5639473752475 | etot = -13.2825374896602
+305000  ekin = 3.11890909070302 |  erot = 3.26281224727061 | epot = -19.6642588266132 | etot = -13.2825374886396
+306000  ekin = 3.16699270587545 |  erot = 3.33070506272287 | epot = -19.7802352601681 | etot = -13.2825374915697
+307000  ekin = 3.22023032257278 |  erot = 3.3799777181515 | epot = -19.8827455298064 | etot = -13.2825374890821
+308000  ekin = 3.27268739663165 |  erot = 3.41969099128438 | epot = -19.9749158771467 | etot = -13.2825374892307
+309000  ekin = 3.32280425481028 |  erot = 3.44976402097079 | epot = -20.0551057651176 | etot = -13.2825374893365
+310000  ekin = 3.36903652740728 |  erot = 3.46970323071463 | epot = -20.1212772475588 | etot = -13.2825374894369
+311000  ekin = 3.40972253534196 |  erot = 3.47940229944893 | epot = -20.1716623243582 | etot = -13.2825374895673
+312000  ekin = 3.44308129108907 |  erot = 3.47898447382754 | epot = -20.204603254423 | etot = -13.2825374895064
+313000  ekin = 3.46879202758663 |  erot = 3.47087869840748 | epot = -20.2222082156487 | etot = -13.2825374896546
+314000  ekin = 3.48565385463278 |  erot = 3.45582059749242 | epot = -20.2240119419355 | etot = -13.2825374898103
+315000  ekin = 3.4921631329082 |  erot = 3.43373104094955 | epot = -20.2084316637809 | etot = -13.2825374899231
+316000  ekin = 3.48736213303232 |  erot = 3.40482567255629 | epot = -20.1747252955269 | etot = -13.2825374899383
+317000  ekin = 3.46994132507374 |  erot = 3.36841330847356 | epot = -20.1208921250387 | etot = -13.2825374914914
+318000  ekin = 3.43614022048189 |  erot = 3.32066657788102 | epot = -20.0393442896713 | etot = -13.2825374913084
+319000  ekin = 3.38694293952315 |  erot = 3.2636491069797 | epot = -19.9331295374394 | etot = -13.2825374909366
+320000  ekin = 3.32506744212965 |  erot = 3.20113650606275 | epot = -19.8087414386365 | etot = -13.2825374904441
+321000  ekin = 3.25415482891539 |  erot = 3.13766117542953 | epot = -19.6743534942655 | etot = -13.2825374899206
+322000  ekin = 3.17813669787398 |  erot = 3.07780020747378 | epot = -19.5384743947986 | etot = -13.2825374894508
+323000  ekin = 3.10066688252112 |  erot = 3.02549088180775 | epot = -19.4086952534164 | etot = -13.2825374890875
+324000  ekin = 3.02479637479555 |  erot = 2.9835512249436 | epot = -19.2908850885836 | etot = -13.2825374888444
+325000  ekin = 2.95294332411579 |  erot = 2.95347420684863 | epot = -19.1889550196703 | etot = -13.2825374887059
+326000  ekin = 2.88706743998012 |  erot = 2.93544936652532 | epot = -19.1050542951527 | etot = -13.2825374886473
+327000  ekin = 2.82887581625042 |  erot = 2.92851219862423 | epot = -19.0399255035249 | etot = -13.2825374886502
+328000  ekin = 2.7799083006856 |  erot = 2.93074772300673 | epot = -18.9931935123989 | etot = -13.2825374887065
+329000  ekin = 2.74145002280429 |  erot = 2.93954016638564 | epot = -18.9635276780016 | etot = -13.2825374888116
+330000  ekin = 2.71432845550724 |  erot = 2.95189909643594 | epot = -18.9487650408976 | etot = -13.2825374889545
+331000  ekin = 2.69870867088015 |  erot = 2.96486608415783 | epot = -18.9461122441539 | etot = -13.2825374891159
+332000  ekin = 2.69398517733071 |  erot = 2.9759351218084 | epot = -18.9524577884139 | etot = -13.2825374892748
+333000  ekin = 2.69881348537833 |  erot = 2.98337443171614 | epot = -18.9647254065077 | etot = -13.2825374894133
+334000  ekin = 2.71127609678656 |  erot = 2.98637176000363 | epot = -18.9801853463082 | etot = -13.282537489518
+335000  ekin = 2.72916096430101 |  erot = 2.98501165510017 | epot = -18.9967101089767 | etot = -13.2825374895756
+336000  ekin = 2.75032164400955 |  erot = 2.98016551096549 | epot = -19.0130246445444 | etot = -13.2825374895694
+337000  ekin = 2.77304615866171 |  erot = 2.97336445321275 | epot = -19.0289481013653 | etot = -13.2825374894909
+338000  ekin = 2.79631213711555 |  erot = 2.96664518651948 | epot = -19.0454948129873 | etot = -13.2825374893522
+339000  ekin = 2.8198251309544 |  erot = 2.96230352229863 | epot = -19.0646661424453 | etot = -13.2825374891923
+340000  ekin = 2.84381599358249 |  erot = 2.96250923740561 | epot = -19.0888627200583 | etot = -13.2825374890702
+341000  ekin = 2.86861716322249 |  erot = 2.96879944354184 | epot = -19.1199540958278 | etot = -13.2825374890635
+342000  ekin = 2.8942330530754 |  erot = 2.98159830919509 | epot = -19.1583688514537 | etot = -13.2825374891832
+343000  ekin = 2.92230469127443 |  erot = 3.00151195978065 | epot = -19.2063541396099 | etot = -13.2825374885548
+344000  ekin = 2.95328542678957 |  erot = 3.02739469587516 | epot = -19.2632176118817 | etot = -13.282537489217
+345000  ekin = 2.98288076792584 |  erot = 3.05397730230856 | epot = -19.3193955601209 | etot = -13.2825374898865
+346000  ekin = 3.0068362280629 |  erot = 3.07579634903275 | epot = -19.3651700675335 | etot = -13.2825374904379
+347000  ekin = 3.021682039197 |  erot = 3.0883226978178 | epot = -19.3925422277954 | etot = -13.2825374907806
+348000  ekin = 3.02528371459214 |  erot = 3.08873432783574 | epot = -19.3965555333152 | etot = -13.2825374908873
+349000  ekin = 3.01708434471769 |  erot = 3.07610751269362 | epot = -19.3757293482008 | etot = -13.2825374907895
+350000  ekin = 2.99803087494402 |  erot = 3.05108999688533 | epot = -19.3316583623752 | etot = -13.2825374905459
+351000  ekin = 2.97033325354314 |  erot = 3.01539362128504 | epot = -19.268264365027 | etot = -13.2825374901988
+352000  ekin = 2.93755453890544 |  erot = 2.97175102427381 | epot = -19.1918430529999 | etot = -13.2825374898207
+353000  ekin = 2.90330530001813 |  erot = 2.92291261114237 | epot = -19.1087554005693 | etot = -13.2825374894088
+354000  ekin = 2.87126755833568 |  erot = 2.87170321125813 | epot = -19.0255082585641 | etot = -13.2825374889703
+355000  ekin = 2.84520639660643 |  erot = 2.82119115452776 | epot = -18.948935039652 | etot = -13.2825374885178
+356000  ekin = 2.8287863971603 |  erot = 2.7746321329023 | epot = -18.8859560181437 | etot = -13.2825374880811
+357000  ekin = 2.82589501110754 |  erot = 2.73507904234615 | epot = -18.8435115424282 | etot = -13.2825374889745
+358000  ekin = 2.83567543256197 |  erot = 2.6999034357179 | epot = -18.8181163574566 | etot = -13.2825374891768
+359000  ekin = 2.85413863003174 |  erot = 2.66477535390921 | epot = -18.8014514734662 | etot = -13.2825374895252
+360000  ekin = 2.87797108635824 |  erot = 2.62716069413401 | epot = -18.7876692705271 | etot = -13.2825374900349
+361000  ekin = 2.90295419334403 |  erot = 2.58324525246715 | epot = -18.7687369364404 | etot = -13.2825374906292
+362000  ekin = 2.92446718933308 |  erot = 2.52862237257544 | epot = -18.7356270530351 | etot = -13.2825374911266
+363000  ekin = 2.93848759933348 |  erot = 2.45989164640849 | epot = -18.680916737042 | etot = -13.2825374913
+364000  ekin = 2.94271150164586 |  erot = 2.37661313123214 | epot = -18.6018621239955 | etot = -13.2825374911175
+365000  ekin = 2.93600170081438 |  erot = 2.28250131433965 | epot = -18.5010405056253 | etot = -13.2825374904713
+366000  ekin = 2.91934189957478 |  erot = 2.18525996401368 | epot = -18.3871393531652 | etot = -13.2825374895768
+367000  ekin = 2.89548895825519 |  erot = 2.0946888564492 | epot = -18.2727153033882 | etot = -13.2825374886839
+368000  ekin = 2.86763306547926 |  erot = 2.02026878405327 | epot = -18.1704393375192 | etot = -13.2825374879867
+369000  ekin = 2.83845106986046 |  erot = 1.96931673436804 | epot = -18.0903052917965 | etot = -13.282537487568
+370000  ekin = 2.80963551309284 |  erot = 1.94618455936313 | epot = -18.0383575598705 | etot = -13.2825374874145
+371000  ekin = 2.78188668089849 |  erot = 1.95235490032645 | epot = -18.0167790686888 | etot = -13.2825374874639
+372000  ekin = 2.75518266190993 |  erot = 1.98699478725745 | epot = -18.0247149368147 | etot = -13.2825374876473
+373000  ekin = 2.7291288052834 |  erot = 2.04757125854604 | epot = -18.0592375517431 | etot = -13.2825374879136
+374000  ekin = 2.7032481730965 |  erot = 2.13030562163268 | epot = -18.1160912829679 | etot = -13.2825374882387
+375000  ekin = 2.67714701016873 |  erot = 2.23039820126271 | epot = -18.1900827000525 | etot = -13.282537488621
+376000  ekin = 2.65054772278943 |  erot = 2.34206662745006 | epot = -18.2751518393106 | etot = -13.2825374890711
+377000  ekin = 2.62322866602789 |  erot = 2.45852983339147 | epot = -18.3642959890092 | etot = -13.2825374895898
+378000  ekin = 2.59495135704074 |  erot = 2.57214449993232 | epot = -18.4496333471184 | etot = -13.2825374901453
+379000  ekin = 2.56546707826881 |  erot = 2.67491697597423 | epot = -18.522921544903 | etot = -13.2825374906599
+380000  ekin = 2.53466143096452 |  erot = 2.75950320018323 | epot = -18.5767021221686 | etot = -13.2825374910209
+381000  ekin = 2.50280930121905 |  erot = 2.82054519918234 | epot = -18.605891991525 | etot = -13.2825374911236
+382000  ekin = 2.47081272773286 |  erot = 2.85587907290837 | epot = -18.6092292915673 | etot = -13.2825374909261
+383000  ekin = 2.44026108011578 |  erot = 2.86702983653801 | epot = -18.5898284071325 | etot = -13.2825374904788
+384000  ekin = 2.41324034479873 |  erot = 2.85867137365971 | epot = -18.5544492083626 | etot = -13.2825374899041
+385000  ekin = 2.3919736779495 |  erot = 2.83724859058569 | epot = -18.5117597578745 | etot = -13.2825374893393
+386000  ekin = 2.37848037079693 |  erot = 2.80936838549168 | epot = -18.4703862451677 | etot = -13.2825374888791
+387000  ekin = 2.37440773877138 |  erot = 2.78057799551461 | epot = -18.4375232228406 | etot = -13.2825374885547
+388000  ekin = 2.38106033998944 |  erot = 2.75482980994152 | epot = -18.4184276382777 | etot = -13.2825374883468
+389000  ekin = 2.3995269472836 |  erot = 2.73455852133737 | epot = -18.4166229568386 | etot = -13.2825374882176
+390000  ekin = 2.43075796801538 |  erot = 2.72108399953604 | epot = -18.4343794556925 | etot = -13.2825374881411
+391000  ekin = 2.47547758104125 |  erot = 2.71503282252802 | epot = -18.4730478916894 | etot = -13.2825374881201
+392000  ekin = 2.53389941336301 |  erot = 2.71657607916961 | epot = -18.5330129807166 | etot = -13.282537488184
+393000  ekin = 2.60531467139514 |  erot = 2.72543162367145 | epot = -18.6132837834377 | etot = -13.2825374883712
+394000  ekin = 2.68770614221053 |  erot = 2.74072420161599 | epot = -18.710967832529 | etot = -13.2825374887024
+395000  ekin = 2.77757589910946 |  erot = 2.76089277951269 | epot = -18.821006167779 | etot = -13.2825374891568
+396000  ekin = 2.87012638573289 |  erot = 2.78383015196004 | epot = -18.9364940273591 | etot = -13.2825374896661
+397000  ekin = 2.95979968456986 |  erot = 2.80730760068458 | epot = -19.0496447753932 | etot = -13.2825374901387
+398000  ekin = 3.04101675292502 |  erot = 2.82953067572591 | epot = -19.1530849191498 | etot = -13.2825374904989
+399000  ekin = 3.10335323687934 |  erot = 2.84223393462917 | epot = -19.2281247208206 | etot = -13.2825375493121
+400000  ekin = 3.10435999781796 |  erot = 2.68059016642954 | epot = -19.0674876235022 | etot = -13.2825374592547
+401000  ekin = 3.39309095570315 |  erot = 2.63997900103007 | epot = -19.3156074940371 | etot = -13.2825375373039
+402000  ekin = 3.44106634979645 |  erot = 2.659790716706 | epot = -19.3833945765517 | etot = -13.2825375100493
+403000  ekin = 3.43207406397009 |  erot = 2.67998452069831 | epot = -19.394596094653 | etot = -13.2825375099846
+404000  ekin = 3.40426891789311 |  erot = 2.70237957195789 | epot = -19.3891859997632 | etot = -13.2825375099122
+405000  ekin = 3.3593347341666 |  erot = 2.72607645467142 | epot = -19.367948698657 | etot = -13.282537509819
+406000  ekin = 3.29966540905146 |  erot = 2.74995079993995 | epot = -19.3321537186901 | etot = -13.2825375096987
+407000  ekin = 3.2282311798008 |  erot = 2.77286165525633 | epot = -19.2836303446157 | etot = -13.2825375095586
+408000  ekin = 3.1483591073718 |  erot = 2.79373949027867 | epot = -19.2246361070933 | etot = -13.2825375094428
+409000  ekin = 3.06351542881959 |  erot = 2.81131469884056 | epot = -19.1573676369638 | etot = -13.2825375093037
+410000  ekin = 2.97699949579686 |  erot = 2.82462679197841 | epot = -19.0841637969767 | etot = -13.2825375092014
+411000  ekin = 2.89165449989684 |  erot = 2.83289882075493 | epot = -19.0070908297837 | etot = -13.2825375091319
+412000  ekin = 2.80978906687504 |  erot = 2.83549592230531 | epot = -18.9278224982521 | etot = -13.2825375090718
+413000  ekin = 2.73325536965585 |  erot = 2.83215388787228 | epot = -18.8479467665131 | etot = -13.282537508985
+414000  ekin = 2.66364879696115 |  erot = 2.82325639291671 | epot = -18.7694426987162 | etot = -13.2825375088383
+415000  ekin = 2.60253860597198 |  erot = 2.81004531899789 | epot = -18.6951214335864 | etot = -13.2825375086165
+416000  ekin = 2.55161661471215 |  erot = 2.7946463118532 | epot = -18.6288004349012 | etot = -13.2825375083358
+417000  ekin = 2.51265407611577 |  erot = 2.77984605489432 | epot = -18.5750376413434 | etot = -13.2825375103333
+418000  ekin = 2.47334604007925 |  erot = 2.77799997552572 | epot = -18.5338835235875 | etot = -13.2825375079825
+419000  ekin = 2.44559608969893 |  erot = 2.79655231012718 | epot = -18.5246859081463 | etot = -13.2825375083202
+420000  ekin = 2.44884495813904 |  erot = 2.81276776866598 | epot = -18.5441502345702 | etot = -13.2825375077651
+421000  ekin = 2.47134322854002 |  erot = 2.82756585669941 | epot = -18.5814465933144 | etot = -13.2825375080749
+422000  ekin = 2.50522487694504 |  erot = 2.84806830842347 | epot = -18.6358306938984 | etot = -13.2825375085299
+423000  ekin = 2.54673540365736 |  erot = 2.87162843047175 | epot = -18.7009013431671 | etot = -13.282537509038
+424000  ekin = 2.5915545267989 |  erot = 2.89540834353031 | epot = -18.7695003798181 | etot = -13.2825375094888
+425000  ekin = 2.63549518712503 |  erot = 2.9172494646209 | epot = -18.8352821615391 | etot = -13.2825375097932
+426000  ekin = 2.67515430284032 |  erot = 2.93632167691171 | epot = -18.8940134896611 | etot = -13.2825375099091
+427000  ekin = 2.70835356711895 |  erot = 2.95332774897864 | epot = -18.9442188259411 | etot = -13.2825375098435
+428000  ekin = 2.73429370857904 |  erot = 2.97029523905205 | epot = -18.9871264572657 | etot = -13.2825375096346
+429000  ekin = 2.75344687778548 |  erot = 2.99015713231241 | epot = -19.026141519429 | etot = -13.2825375093311
+430000  ekin = 2.76726512076715 |  erot = 3.01631311484004 | epot = -19.0661157445923 | etot = -13.2825375089851
+431000  ekin = 2.77776520584482 |  erot = 3.05220345439827 | epot = -19.1125061689064 | etot = -13.2825375086633
+432000  ekin = 2.78700254672782 |  erot = 3.10077153004471 | epot = -19.1703115852294 | etot = -13.2825375084569
+433000  ekin = 2.79644099946406 |  erot = 3.16368547122764 | epot = -19.2426639791689 | etot = -13.2825375084772
+434000  ekin = 2.8062952810192 |  erot = 3.24036053939458 | epot = -19.3291933292362 | etot = -13.2825375088224
+435000  ekin = 2.81503854863169 |  erot = 3.32707633256549 | epot = -19.4246523907207 | etot = -13.2825375095236
+436000  ekin = 2.81936003428183 |  erot = 3.41666372807462 | epot = -19.5185612728498 | etot = -13.2825375104934
+437000  ekin = 2.81480689571151 |  erot = 3.49920681099962 | epot = -19.5965512182294 | etot = -13.2825375115182
+438000  ekin = 2.79709037800121 |  erot = 3.56380823492809 | epot = -19.643436125261 | etot = -13.2825375123317
+439000  ekin = 2.76357573484572 |  erot = 3.60097663047473 | epot = -19.6470898780363 | etot = -13.2825375127159
+440000  ekin = 2.71419714341371 |  erot = 3.6047593537822 | epot = -19.6014940098261 | etot = -13.2825375126302
+441000  ekin = 2.65147586146338 |  erot = 3.57350682801194 | epot = -19.5075202016436 | etot = -13.2825375121683
+442000  ekin = 2.57978868207942 |  erot = 3.50949061111828 | epot = -19.3718168046656 | etot = -13.2825375114679
+443000  ekin = 2.50456558754104 |  erot = 3.4178674196423 | epot = -19.2049705178168 | etot = -13.2825375106335
+444000  ekin = 2.43185299049922 |  erot = 3.30558723792078 | epot = -19.0199777381447 | etot = -13.2825375097247
+445000  ekin = 2.36817510309063 |  erot = 3.18052048207573 | epot = -18.8312330939526 | etot = -13.2825375087862
+446000  ekin = 2.32036350430527 |  erot = 3.05081891044131 | epot = -18.6537199226123 | etot = -13.2825375078657
+447000  ekin = 2.29507009387958 |  erot = 2.92434156859069 | epot = -18.5019491695481 | etot = -13.2825375070778
+448000  ekin = 2.29792306265903 |  erot = 2.80795199471116 | epot = -18.3884125638822 | etot = -13.282537506512
+449000  ekin = 2.33256968728525 |  erot = 2.7069587718453 | epot = -18.3220659653954 | etot = -13.2825375062648
+450000  ekin = 2.39980570006764 |  erot = 2.6245346844449 | epot = -18.3068778909135 | etot = -13.282537506401
+451000  ekin = 2.49706752601175 |  erot = 2.56128240620743 | epot = -18.3408874391531 | etot = -13.2825375069339
+452000  ekin = 2.61842576959501 |  erot = 2.51510244034445 | epot = -18.4160657177213 | etot = -13.2825375077819
+453000  ekin = 2.75505822099958 |  erot = 2.48156991528656 | epot = -18.5191656452411 | etot = -13.2825375089549
+454000  ekin = 2.89583245290297 |  erot = 2.45420794646339 | epot = -18.6325779096657 | etot = -13.2825375102994
+455000  ekin = 3.02803920576056 |  erot = 2.42568753016163 | epot = -18.736264247583 | etot = -13.2825375116608
+456000  ekin = 3.13847091959985 |  erot = 2.38932191986942 | epot = -18.8103303522404 | etot = -13.2825375127711
+457000  ekin = 3.21547363215232 |  erot = 2.34093725374963 | epot = -18.83894839917 | etot = -13.2825375132681
+458000  ekin = 3.2519255085167 |  erot = 2.28077893487382 | epot = -18.8152419562951 | etot = -13.2825375129046
+459000  ekin = 3.24761130320326 |  erot = 2.21429904484092 | epot = -18.744447859815 | etot = -13.2825375117708
+460000  ekin = 3.20922400634736 |  erot = 2.15086461860742 | epot = -18.6426261352081 | etot = -13.2825375102533
+461000  ekin = 3.14796311215653 |  erot = 2.10092694607039 | epot = -18.5314275670048 | etot = -13.2825375087779
+462000  ekin = 3.07634336775073 |  erot = 2.07329933806439 | epot = -18.4321802134279 | etot = -13.2825375076128
+463000  ekin = 3.00570913413418 |  erot = 2.07367404520667 | epot = -18.3619206861977 | etot = -13.2825375068568
+464000  ekin = 2.9448582997097 |  erot = 2.10431183996111 | epot = -18.331707646191 | etot = -13.2825375065202
+465000  ekin = 2.89946798284609 |  erot = 2.16425406354561 | epot = -18.3462595529816 | etot = -13.2825375065899
+466000  ekin = 2.87195252749972 |  erot = 2.24955307487499 | epot = -18.4040431094255 | etot = -13.2825375070508
+467000  ekin = 2.86158324930207 |  erot = 2.3533892427293 | epot = -18.4975099999046 | etot = -13.2825375078732
+468000  ekin = 2.86493243611993 |  erot = 2.46640127706619 | epot = -18.6138712219846 | etot = -13.2825375087985
+469000  ekin = 2.87700241085747 |  erot = 2.57824581694139 | epot = -18.7377857379035 | etot = -13.2825375101046
+470000  ekin = 2.89115454215414 |  erot = 2.67606199010798 | epot = -18.8497540435902 | etot = -13.2825375113281
+471000  ekin = 2.90087699699085 |  erot = 2.74765202467846 | epot = -18.9310665338721 | etot = -13.2825375122028
+472000  ekin = 2.90129360656583 |  erot = 2.7844228810356 | epot = -18.9682540001117 | etot = -13.2825375125102
+473000  ekin = 2.89014262487726 |  erot = 2.78350866545128 | epot = -18.9561888025163 | etot = -13.2825375121877
+474000  ekin = 2.8679845551896 |  erot = 2.74843722225596 | epot = -18.8989592888163 | etot = -13.2825375113708
+475000  ekin = 2.83751222123126 |  erot = 2.68789202057427 | epot = -18.8079417521389 | etot = -13.2825375103333
+476000  ekin = 2.80225697256743 |  erot = 2.61311305367502 | epot = -18.6979075356038 | etot = -13.2825375093613
+477000  ekin = 2.76525060538535 |  erot = 2.53510543119006 | epot = -18.5828935452222 | etot = -13.2825375086468
+478000  ekin = 2.72814283271883 |  erot = 2.46266477167839 | epot = -18.4733451126463 | etot = -13.282537508249
+479000  ekin = 2.69099471858041 |  erot = 2.40160392945098 | epot = -18.375136156148 | etot = -13.2825375081166
+480000  ekin = 2.6526681049776 |  erot = 2.35496214915731 | epot = -18.2901677623243 | etot = -13.2825375081894
+481000  ekin = 2.611442355162 |  erot = 2.32364519373677 | epot = -18.2176250571627 | etot = -13.282537508264
+482000  ekin = 2.565776730153 |  erot = 2.30767778316155 | epot = -18.1559920216392 | etot = -13.2825375083247
+483000  ekin = 2.51481850308162 |  erot = 2.30660853349362 | epot = -18.1039645449013 | etot = -13.2825375083261
+484000  ekin = 2.45838132863017 |  erot = 2.3198450068296 | epot = -18.0607638434524 | etot = -13.2825375079926
+485000  ekin = 2.37536403481855 |  erot = 2.30798475223331 | epot = -17.9658863029946 | etot = -13.2825375159427
+486000  ekin = 2.31029787369058 |  erot = 2.27486987654653 | epot = -17.8677052455649 | etot = -13.2825374953278
+487000  ekin = 2.35903895728042 |  erot = 2.35840823831765 | epot = -17.9999847156837 | etot = -13.2825375200856
+488000  ekin = 2.35207405535098 |  erot = 2.45495770508831 | epot = -18.0895692764695 | etot = -13.2825375160302
+489000  ekin = 2.32025825397052 |  erot = 2.54616767539779 | epot = -18.1489634454364 | etot = -13.2825375160681
+490000  ekin = 2.29515153869984 |  erot = 2.64227715696153 | epot = -18.2199662119964 | etot = -13.282537516335
+491000  ekin = 2.27724499850078 |  erot = 2.73950547060331 | epot = -18.2992879857125 | etot = -13.2825375166084
+492000  ekin = 2.26670396937252 |  erot = 2.83351832936053 | epot = -18.3827598156682 | etot = -13.2825375169351
+493000  ekin = 2.26314468317306 |  erot = 2.91977614251813 | epot = -18.4654583429642 | etot = -13.282537517273
+494000  ekin = 2.26577113863215 |  erot = 2.99399214332928 | epot = -18.5423007995401 | etot = -13.2825375175787
+495000  ekin = 2.27355094493377 |  erot = 3.05259857144223 | epot = -18.6086870341908 | etot = -13.2825375178148
+496000  ekin = 2.28538641733465 |  erot = 3.09313022185941 | epot = -18.661054157153 | etot = -13.282537517959
+497000  ekin = 2.3002347482521 |  erot = 3.11444072103781 | epot = -18.6972129872905 | etot = -13.2825375180006
+498000  ekin = 2.31719365941364 |  erot = 3.11678508297333 | epot = -18.7165162603266 | etot = -13.2825375179397
+499000  ekin = 2.33554254163157 |  erot = 3.10178716717433 | epot = -18.7198672265901 | etot = -13.2825375177842
+500000  ekin = 2.31317350075609 |  erot = 3.05449093052383 | epot = -18.6502019679387 | etot = -13.2825375366588
+501000  ekin = 2.31231722963358 |  erot = 3.00810318070389 | epot = -18.6029579370661 | etot = -13.2825375267286
+502000  ekin = 2.38999638954889 |  erot = 2.98467042895374 | epot = -18.657204342138 | etot = -13.2825375236353
+503000  ekin = 2.41312387634462 |  erot = 2.93091691360098 | epot = -18.6265783132937 | etot = -13.2825375233481
+504000  ekin = 2.43600229238282 |  erot = 2.88130858484448 | epot = -18.5998484003617 | etot = -13.2825375231344
+505000  ekin = 2.45757791197103 |  erot = 2.84011866669662 | epot = -18.5802341017161 | etot = -13.2825375230484
+506000  ekin = 2.47627134224707 |  erot = 2.81025901810999 | epot = -18.5690678834978 | etot = -13.2825375231408
+507000  ekin = 2.48985246050729 |  erot = 2.79268587937519 | epot = -18.5650758633262 | etot = -13.2825375234437
+508000  ekin = 2.49542483825231 |  erot = 2.78597986942009 | epot = -18.5639422316207 | etot = -13.2825375239483
+509000  ekin = 2.48963204749862 |  erot = 2.78630577999958 | epot = -18.5584753520799 | etot = -13.2825375245818
+510000  ekin = 2.46917438876006 |  erot = 2.78796571286371 | epot = -18.5396776268285 | etot = -13.2825375252047
+511000  ekin = 2.43159454916956 |  erot = 2.78459744700141 | epot = -18.4987295218192 | etot = -13.2825375256482
+512000  ekin = 2.37609227914812 |  erot = 2.7707369794783 | epot = -18.4293667844085 | etot = -13.2825375257821
+513000  ekin = 2.30402039320529 |  erot = 2.74317280239451 | epot = -18.3297307211707 | etot = -13.2825375255709
+514000  ekin = 2.21884081240883 |  erot = 2.70155414867794 | epot = -18.2029324861636 | etot = -13.2825375250768
+515000  ekin = 2.12561338169144 |  erot = 2.64810551844221 | epot = -18.0562564245494 | etot = -13.2825375244158
+516000  ekin = 2.0302995856451 |  erot = 2.5867398599196 | epot = -17.8995769692659 | etot = -13.2825375237012
+517000  ekin = 1.93914577194817 |  erot = 2.52206054313542 | epot = -17.7437438380945 | etot = -13.2825375230109
+518000  ekin = 1.85826662411615 |  erot = 2.45858700715108 | epot = -17.5993911536592 | etot = -13.2825375223919
+519000  ekin = 1.79333215324367 |  erot = 2.40035341708211 | epot = -17.4762230921876 | etot = -13.2825375218619
+520000  ekin = 1.74929005168975 |  erot = 2.35078235676691 | epot = -17.3826099298929 | etot = -13.2825375214363
+521000  ekin = 1.73007209345073 |  erot = 2.31266171840817 | epot = -17.3252713329969 | etot = -13.282537521138
+522000  ekin = 1.73822781682595 |  erot = 2.2881155718937 | epot = -17.3088809097143 | etot = -13.2825375209947
+523000  ekin = 1.77456624772603 |  erot = 2.2785083458307 | epot = -17.3356121145903 | etot = -13.2825375210336
+524000  ekin = 1.83790458514344 |  erot = 2.28429322274723 | epot = -17.4047353291616 | etot = -13.2825375212709
+525000  ekin = 1.92500868748296 |  erot = 2.30484700359195 | epot = -17.5123932127819 | etot = -13.282537521707
+526000  ekin = 2.0307578025818 |  erot = 2.33833465322601 | epot = -17.651629978134 | etot = -13.2825375223262
+527000  ekin = 2.14850843905356 |  erot = 2.38164040104833 | epot = -17.8126863631983 | etot = -13.2825375230964
+528000  ekin = 2.27060096649051 |  erot = 2.43041424715665 | epot = -17.9835527376135 | etot = -13.2825375239663
+529000  ekin = 2.38896012863249 |  erot = 2.4793138751117 | epot = -18.1508115286032 | etot = -13.282537524859
+530000  ekin = 2.49576940535655 |  erot = 2.52254117021849 | epot = -18.3008481012414 | etot = -13.2825375256663
+531000  ekin = 2.58420744220974 |  erot = 2.55472238426385 | epot = -18.4214673527334 | etot = -13.2825375262598
+532000  ekin = 2.64918587017627 |  erot = 2.57201883162556 | epot = -18.5037422283274 | etot = -13.2825375265255
+533000  ekin = 2.68793333155572 |  erot = 2.57313230810709 | epot = -18.5436031660763 | etot = -13.2825375264134
+534000  ekin = 2.70021208216117 |  erot = 2.55975253147949 | epot = -18.542502139612 | etot = -13.2825375259714
+535000  ekin = 2.68802701634936 |  erot = 2.53615014862128 | epot = -18.5067146903044 | etot = -13.2825375253337
+536000  ekin = 2.65489019113449 |  erot = 2.50801671125187 | epot = -18.445444427055 | etot = -13.2825375246686
+537000  ekin = 2.60490332065097 |  erot = 2.48102333788784 | epot = -18.3684641826523 | etot = -13.2825375241135
+538000  ekin = 2.54198784537002 |  erot = 2.45965628961172 | epot = -18.2841816579271 | etot = -13.2825375229454
+539000  ekin = 2.47150013366557 |  erot = 2.44756195583901 | epot = -18.2015996124771 | etot = -13.2825375229725
+540000  ekin = 2.39647534126896 |  erot = 2.4452543590462 | epot = -18.1242672233716 | etot = -13.2825375230564
+541000  ekin = 2.31786635168338 |  erot = 2.45130088253407 | epot = -18.0517047573377 | etot = -13.2825375231202
+542000  ekin = 2.23702678132889 |  erot = 2.4642388816219 | epot = -17.983803186044 | etot = -13.2825375230932
+543000  ekin = 2.15612181951174 |  erot = 2.483136674149 | epot = -17.9217960165952 | etot = -13.2825375229345
+544000  ekin = 2.07836492819822 |  erot = 2.50789688708103 | epot = -17.8687993379301 | etot = -13.2825375226508
+545000  ekin = 2.00794258372951 |  erot = 2.53918840886296 | epot = -17.8296685148941 | etot = -13.2825375223016
+546000  ekin = 1.94957099412975 |  erot = 2.578008196098 | epot = -17.8101167122069 | etot = -13.2825375219791
+547000  ekin = 1.9077624243153 |  erot = 2.62501532097517 | epot = -17.8153152670783 | etot = -13.2825375217878
+548000  ekin = 1.88600984710573 |  erot = 2.67988146408135 | epot = -17.8484288329841 | etot = -13.282537521797
+549000  ekin = 1.88615242689691 |  erot = 2.74090375620349 | epot = -17.909593705124 | etot = -13.2825375220236
+550000  ekin = 1.90811801080135 |  erot = 2.80501593005898 | epot = -17.9956714632894 | etot = -13.282537522429
+551000  ekin = 1.95008337623402 |  erot = 2.86816804419082 | epot = -18.1007889433658 | etot = -13.2825375229409
+552000  ekin = 2.00893649351174 |  erot = 2.92590890426342 | epot = -18.2173829212562 | etot = -13.282537523481
+553000  ekin = 2.08084803911103 |  erot = 2.97396311008449 | epot = -18.3373486731828 | etot = -13.2825375239872
+554000  ekin = 2.16178844742615 |  erot = 3.00865361313796 | epot = -18.4529795849852 | etot = -13.2825375244211
+555000  ekin = 2.24792031030894 |  erot = 3.02713377648476 | epot = -18.5575916115531 | etot = -13.2825375247594
+556000  ekin = 2.3358895304738 |  erot = 3.02749801445229 | epot = -18.6459250699077 | etot = -13.2825375249816
+557000  ekin = 2.42273135018697 |  erot = 3.00799378133903 | epot = -18.7132626568713 | etot = -13.2825375253453
+558000  ekin = 2.50467530619079 |  erot = 2.96457109807151 | epot = -18.7517839296409 | etot = -13.2825375253786
+559000  ekin = 2.57989829547792 |  erot = 2.89795083547094 | epot = -18.7603866561117 | etot = -13.2825375251628
+560000  ekin = 2.64819333040997 |  erot = 2.8115011418383 | epot = -18.7422319969952 | etot = -13.282537524747
+561000  ekin = 2.71041014716014 |  erot = 2.71050571090859 | epot = -18.7034533823107 | etot = -13.282537524242
+562000  ekin = 2.76764108184349 |  erot = 2.60142670481719 | epot = -18.6516053104339 | etot = -13.2825375237732
+563000  ekin = 2.82041332178183 |  erot = 2.49094539995269 | epot = -18.5938962451522 | etot = -13.2825375234177
+564000  ekin = 2.86835957176528 |  erot = 2.38512022706598 | epot = -18.5360173220094 | etot = -13.2825375231781
+565000  ekin = 2.9105055625117 |  erot = 2.2888699309895 | epot = -18.4819130165188 | etot = -13.2825375230176
+566000  ekin = 2.9458361953691 |  erot = 2.20572382108587 | epot = -18.4340975393717 | etot = -13.2825375229167
+567000  ekin = 2.97364576057443 |  erot = 2.13764971279795 | epot = -18.3938329962642 | etot = -13.2825375228919
+568000  ekin = 2.99348659092395 |  erot = 2.08490808290625 | epot = -18.3609321968044 | etot = -13.2825375229742
+569000  ekin = 3.00487691648673 |  erot = 2.04604350391468 | epot = -18.3334579435673 | etot = -13.2825375231659
+570000  ekin = 3.00710556183365 |  erot = 2.01819764938775 | epot = -18.3078407346463 | etot = -13.2825375234249
+571000  ekin = 2.99930468668979 |  erot = 1.99774357915448 | epot = -18.2795857895248 | etot = -13.2825375236806
+572000  ekin = 2.98076231240025 |  erot = 1.98107714031761 | epot = -18.2443769765725 | etot = -13.2825375238547
+573000  ekin = 2.95134611356941 |  erot = 1.96535938854021 | epot = -18.1992430259928 | etot = -13.2825375238832
+574000  ekin = 2.91190615159568 |  erot = 1.94906161388935 | epot = -18.1435052892122 | etot = -13.2825375237272
+575000  ekin = 2.86455063786228 |  erot = 1.93223482555562 | epot = -18.0793229868005 | etot = -13.2825375233826
+576000  ekin = 2.81270724058511 |  erot = 1.91646454101314 | epot = -18.0117093044836 | etot = -13.2825375228853
+577000  ekin = 2.76090536133269 |  erot = 1.90450382048591 | epot = -17.9479467041287 | etot = -13.2825375223101
+578000  ekin = 2.71428886863997 |  erot = 1.89991544414445 | epot = -17.8967418344493 | etot = -13.2825375216648
+579000  ekin = 2.67747364116322 |  erot = 1.90598531717311 | epot = -17.8659964796474 | etot = -13.2825375213111
+580000  ekin = 2.65399321105106 |  erot = 1.92422800253716 | epot = -17.8607587347071 | etot = -13.2825375211188
+581000  ekin = 2.64614770794032 |  erot = 1.95489680825185 | epot = -17.8835820373323 | etot = -13.2825375211401
+582000  ekin = 2.65445309241879 |  erot = 1.99685469221747 | epot = -17.9338453060313 | etot = -13.2825375213951
+583000  ekin = 2.67733631615637 |  erot = 2.04763712314961 | epot = -18.0075109611623 | etot = -13.2825375218563
+584000  ekin = 2.71054840612045 |  erot = 2.10372916962355 | epot = -18.096815098413 | etot = -13.282537522669
+585000  ekin = 2.7473776369314 |  erot = 2.16073411837509 | epot = -18.1906492786902 | etot = -13.2825375233837
+586000  ekin = 2.78137869995175 |  erot = 2.21419390101714 | epot = -18.2781101249393 | etot = -13.2825375239704
+587000  ekin = 2.80697388616102 |  erot = 2.26053952383221 | epot = -18.3500509343302 | etot = -13.282537524337
+588000  ekin = 2.82026432882546 |  erot = 2.29760845660692 | epot = -18.4004103098989 | etot = -13.2825375244665
+589000  ekin = 2.81926713949848 |  erot = 2.32471340247678 | epot = -18.4265180663829 | etot = -13.2825375244076
+590000  ekin = 2.80363912226355 |  erot = 2.34232144628702 | epot = -18.4284980927864 | etot = -13.2825375242358
+591000  ekin = 2.77414618261205 |  erot = 2.35158565793045 | epot = -18.4082693645578 | etot = -13.2825375240153
+592000  ekin = 2.7321416208566 |  erot = 2.3539767270547 | epot = -18.3686558716927 | etot = -13.2825375237814
+593000  ekin = 2.67919893320834 |  erot = 2.35111989743036 | epot = -18.3128563541844 | etot = -13.2825375235457
+594000  ekin = 2.61691997595324 |  erot = 2.34478637080631 | epot = -18.2442438700672 | etot = -13.2825375233077
+595000  ekin = 2.54687226720393 |  erot = 2.33692048101831 | epot = -18.1663302712882 | etot = -13.282537523066
+596000  ekin = 2.47060065869688 |  erot = 2.32961421032747 | epot = -18.0827523918473 | etot = -13.2825375228229
+597000  ekin = 2.38967001339545 |  erot = 2.32500896596326 | epot = -17.9972165019425 | etot = -13.2825375225838
+598000  ekin = 2.30571268105541 |  erot = 2.32515834060355 | epot = -17.913408544013 | etot = -13.2825375223541
+599000  ekin = 2.22046028573514 |  erot = 2.33189649117281 | epot = -17.8348942990478 | etot = -13.2825375221398
+600000  ekin = 2.13574370513921 |  erot = 2.34673734055139 | epot = -17.7650185676378 | etot = -13.2825375219472
+601000  ekin = 2.05345123960456 |  erot = 2.37080533027377 | epot = -17.7067940916633 | etot = -13.282537521785
+602000  ekin = 1.97544542075628 |  erot = 2.40478648027266 | epot = -17.6627694226918 | etot = -13.2825375216629
+603000  ekin = 1.90345105222632 |  erot = 2.44889273151597 | epot = -17.6348813053331 | etot = -13.2825375215908
+604000  ekin = 1.83893895965995 |  erot = 2.50284547564257 | epot = -17.6243219568744 | etot = -13.2825375215719
+605000  ekin = 1.78304137675034 |  erot = 2.56590806862715 | epot = -17.6314869669817 | etot = -13.2825375216042
+606000  ekin = 1.73651700581096 |  erot = 2.63697396076247 | epot = -17.6560284882492 | etot = -13.2825375216757
+607000  ekin = 1.69978182244358 |  erot = 2.71471645477294 | epot = -17.6970357989852 | etot = -13.2825375217686
+608000  ekin = 1.67299629761026 |  erot = 2.79777529949349 | epot = -17.7533091189676 | etot = -13.2825375218638
+609000  ekin = 1.65617951207475 |  erot = 2.88492902620219 | epot = -17.8236460602245 | etot = -13.2825375219476
+610000  ekin = 1.64931072757095 |  erot = 2.97519911997342 | epot = -17.9070473695603 | etot = -13.282537522016
+611000  ekin = 1.65238727041245 |  erot = 3.06785620888426 | epot = -18.0027810013707 | etot = -13.282537522074
+612000  ekin = 1.66542824850629 |  erot = 3.16233835683711 | epot = -18.1103041274766 | etot = -13.2825375221332
+613000  ekin = 1.68843555876185 |  erot = 3.25812385015835 | epot = -18.229096931125 | etot = -13.2825375222048
+614000  ekin = 1.72133601897789 |  erot = 3.35460405549752 | epot = -18.3584775967737 | etot = -13.2825375222983
+615000  ekin = 1.7639238606995 |  erot = 3.45098117154084 | epot = -18.4974425546615 | etot = -13.2825375224212
+616000  ekin = 1.81580855367603 |  erot = 3.54618284196742 | epot = -18.6445289182257 | etot = -13.2825375225823
+617000  ekin = 1.87635766459386 |  erot = 3.63876572276478 | epot = -18.7976609101535 | etot = -13.2825375227949
+618000  ekin = 1.94461656677602 |  erot = 3.72678561689433 | epot = -18.9539397067471 | etot = -13.2825375230768
+619000  ekin = 2.01919440960516 |  erot = 3.80764382999315 | epot = -19.1093757630453 | etot = -13.282537523447
+620000  ekin = 2.09812821746402 |  erot = 3.87796751070656 | epot = -19.2586332520846 | etot = -13.282537523914
+621000  ekin = 2.17876896466308 |  erot = 3.93362434682925 | epot = -19.3949308359561 | etot = -13.2825375244638
+622000  ekin = 2.25776112958401 |  erot = 3.96997899351304 | epot = -19.5102776481477 | etot = -13.2825375250507
+623000  ekin = 2.33118920334088 |  erot = 3.98244070292824 | epot = -19.5961674318684 | etot = -13.2825375255993
+624000  ekin = 2.39492361725441 |  erot = 3.96722578250777 | epot = -19.6446869257843 | etot = -13.2825375260221
+625000  ekin = 2.44512221108716 |  erot = 3.9221202536408 | epot = -19.6497799909757 | etot = -13.2825375262478
+626000  ekin = 2.47876984854015 |  erot = 3.84697362699248 | epot = -19.6082810017757 | etot = -13.282537526243
+627000  ekin = 2.49411681806274 |  erot = 3.74375083232696 | epot = -19.5204051764073 | etot = -13.2825375260176
+628000  ekin = 2.49092177732992 |  erot = 3.61617309028914 | epot = -19.3896323932286 | etot = -13.2825375256095
+629000  ekin = 2.47048208798929 |  erot = 3.46915451618023 | epot = -19.2221741292344 | etot = -13.2825375250648
+630000  ekin = 2.43548970076025 |  erot = 3.30827690339842 | epot = -19.0263041285834 | etot = -13.2825375244248
+631000  ekin = 2.38975949010187 |  erot = 3.13944249310663 | epot = -18.8117395069329 | etot = -13.2825375237244
+632000  ekin = 2.33785618710456 |  erot = 2.96869689900809 | epot = -18.5890906091134 | etot = -13.2825375230008
+633000  ekin = 2.28462964554081 |  erot = 2.80211551079199 | epot = -18.3692826786328 | etot = -13.2825375223
+634000  ekin = 2.2346774623099 |  erot = 2.64563252181923 | epot = -18.1628475058086 | etot = -13.2825375216794
+635000  ekin = 2.15322765553028 |  erot = 2.4783509433522 | epot = -17.9141161496004 | etot = -13.2825375507179
+636000  ekin = 2.045499081381 |  erot = 2.31412508402215 | epot = -17.6421616868316 | etot = -13.2825375214284
+637000  ekin = 2.11104805172142 |  erot = 2.29419960724925 | epot = -17.6877852051452 | etot = -13.2825375461745
+638000  ekin = 2.16990019918255 |  erot = 2.26795673930499 | epot = -17.720394476478 | etot = -13.2825375379904
+639000  ekin = 2.15825321743049 |  erot = 2.17815663921299 | epot = -17.618947382429 | etot = -13.2825375257855
+640000  ekin = 2.18911467639275 |  erot = 2.15600946820072 | epot = -17.627661668601 | etot = -13.2825375240076
+641000  ekin = 2.26653815117271 |  erot = 2.22106973659358 | epot = -17.7701454239566 | etot = -13.2825375361904
+642000  ekin = 2.31444694707114 |  erot = 2.28426426133692 | epot = -17.881248736019 | etot = -13.282537527611
+643000  ekin = 2.32966846048322 |  erot = 2.3262511385741 | epot = -17.9384571271816 | etot = -13.2825375281243
+644000  ekin = 2.33971908597949 |  erot = 2.36941556707019 | epot = -17.9916721815437 | etot = -13.2825375284941
+645000  ekin = 2.34497836829283 |  erot = 2.40804261243074 | epot = -18.0355585093822 | etot = -13.2825375286587
+646000  ekin = 2.34716147904814 |  erot = 2.43809135035135 | epot = -18.0677903580053 | etot = -13.2825375286058
+647000  ekin = 2.3490135196742 |  erot = 2.45765540462488 | epot = -18.0892064526769 | etot = -13.2825375283778
+648000  ekin = 2.35429037946817 |  erot = 2.46814608860667 | epot = -18.1049739961949 | etot = -13.28253752812
+649000  ekin = 2.36637490458858 |  erot = 2.47306901786727 | epot = -18.1219814504981 | etot = -13.2825375280423
+650000  ekin = 2.38594651005796 |  erot = 2.47280388226564 | epot = -18.1412879203047 | etot = -13.2825375279811
+651000  ekin = 2.4129073237406 |  erot = 2.4679750054794 | epot = -18.163419857161 | etot = -13.282537527941
+652000  ekin = 2.44657292389676 |  erot = 2.45942209560756 | epot = -18.1885325474125 | etot = -13.2825375279081
+653000  ekin = 2.48591189111066 |  erot = 2.44818643115487 | epot = -18.2166358501265 | etot = -13.282537527861
+654000  ekin = 2.52980786333011 |  erot = 2.43558904341108 | epot = -18.2479344345246 | etot = -13.2825375277834
+655000  ekin = 2.57725720727345 |  erot = 2.42329690324718 | epot = -18.2830916381947 | etot = -13.2825375276741
+656000  ekin = 2.62745567851939 |  erot = 2.41329334478414 | epot = -18.3232865508506 | etot = -13.2825375275471
+657000  ekin = 2.67977157718863 |  erot = 2.40771681171411 | epot = -18.3700259163334 | etot = -13.2825375274306
+658000  ekin = 2.73363379212944 |  erot = 2.40858022047282 | epot = -18.4247515399622 | etot = -13.2825375273599
+659000  ekin = 2.78837854445156 |  erot = 2.41741767313059 | epot = -18.4883337449508 | etot = -13.2825375273687
+660000  ekin = 2.8431453631021 |  erot = 2.43497153575953 | epot = -18.5606544262937 | etot = -13.282537527432
+661000  ekin = 2.89550751705154 |  erot = 2.46002725134826 | epot = -18.6380722964866 | etot = -13.2825375280868
+662000  ekin = 2.93874528639294 |  erot = 2.48685588449209 | epot = -18.708138699583 | etot = -13.282537528698
+663000  ekin = 2.96871719420213 |  erot = 2.51022783061785 | epot = -18.7614825540622 | etot = -13.2825375292422
+664000  ekin = 2.98246138426592 |  erot = 2.52516926728115 | epot = -18.7901681811315 | etot = -13.2825375295844
+665000  ekin = 2.97884445496409 |  erot = 2.52787955702933 | epot = -18.7892615416111 | etot = -13.2825375296177
+666000  ekin = 2.95920183358837 |  erot = 2.5166150843606 | epot = -18.7583544472577 | etot = -13.2825375293087
+667000  ekin = 2.92742550364064 |  erot = 2.49210329863614 | epot = -18.7020663309941 | etot = -13.2825375287173
+668000  ekin = 2.88934250727334 |  erot = 2.45736670758744 | epot = -18.6292467428357 | etot = -13.2825375279749
+669000  ekin = 2.85155010055246 |  erot = 2.41708074188009 | epot = -18.5511683696627 | etot = -13.2825375272301
+670000  ekin = 2.82014314483841 |  erot = 2.37673699564913 | epot = -18.4794176670842 | etot = -13.2825375265966
+671000  ekin = 2.79977472973266 |  erot = 2.34183940288387 | epot = -18.4241516588856 | etot = -13.2825375262691
+672000  ekin = 2.7929325264564 |  erot = 2.3169522602719 | epot = -18.3924223127253 | etot = -13.282537525997
+673000  ekin = 2.80034442418812 |  erot = 2.30554472221923 | epot = -18.3884266723436 | etot = -13.2825375259362
+674000  ekin = 2.82129825266147 |  erot = 2.30955451996833 | epot = -18.4133902987243 | etot = -13.2825375260945
+675000  ekin = 2.85361934154458 |  erot = 2.32878748983352 | epot = -18.4649443578395 | etot = -13.2825375264614
+676000  ekin = 2.89394925003076 |  erot = 2.36084337721496 | epot = -18.5373301542345 | etot = -13.2825375269888
+677000  ekin = 2.93819888444081 |  erot = 2.40146056818827 | epot = -18.6221969802158 | etot = -13.2825375275867
+678000  ekin = 2.98219881053812 |  erot = 2.44527797803552 | epot = -18.7100143167158 | etot = -13.2825375281422
+679000  ekin = 3.02242735526952 |  erot = 2.48684948039664 | epot = -18.7918143642177 | etot = -13.2825375285515
+680000  ekin = 3.05660821688331 |  erot = 2.52163649392475 | epot = -18.860782239561 | etot = -13.282537528753
+681000  ekin = 3.08399348193173 |  erot = 2.54671087872184 | epot = -18.913241889389 | etot = -13.2825375287354
+682000  ekin = 3.10527370313695 |  erot = 2.56103519422108 | epot = -18.9488464258989 | etot = -13.2825375285409
+683000  ekin = 3.12217420792303 |  erot = 2.5653012869435 | epot = -18.9700130231063 | etot = -13.2825375282397
+684000  ekin = 3.13689854385765 |  erot = 2.56147023269689 | epot = -18.9809063044635 | etot = -13.282537527909
+685000  ekin = 3.15161752084921 |  erot = 2.55220833209368 | epot = -18.9863633805374 | etot = -13.2825375275945
+686000  ekin = 3.16825656296352 |  erot = 2.54047141966045 | epot = -18.9912655100342 | etot = -13.2825375274102
+687000  ekin = 3.18756268905896 |  erot = 2.5286150857463 | epot = -18.9987153021306 | etot = -13.2825375273253
+688000  ekin = 3.20935294731744 |  erot = 2.51834078650268 | epot = -19.010231261173 | etot = -13.2825375273529
+689000  ekin = 3.23260385768977 |  erot = 2.51058529366538 | epot = -19.0257266788501 | etot = -13.2825375274949
+690000  ekin = 3.25550449418191 |  erot = 2.50541094761942 | epot = -19.0434529695448 | etot = -13.2825375277435
+691000  ekin = 3.27559454465419 |  erot = 2.50196131508042 | epot = -19.0600933878108 | etot = -13.2825375280762
+692000  ekin = 3.29000453531072 |  erot = 2.49851988080605 | epot = -19.0710619445671 | etot = -13.2825375284504
+693000  ekin = 3.29579865375948 |  erot = 2.4927397485969 | epot = -19.0710759311631 | etot = -13.2825375288067
+694000  ekin = 3.290367420064 |  erot = 2.48207188558618 | epot = -19.0549768347317 | etot = -13.2825375290815
+695000  ekin = 3.27176421099226 |  erot = 2.46431581834491 | epot = -19.0186175585658 | etot = -13.2825375292286
+696000  ekin = 3.23887890264527 |  erot = 2.43812365839389 | epot = -18.9595400902738 | etot = -13.2825375292346
+697000  ekin = 3.19141377365438 |  erot = 2.40329594557291 | epot = -18.8772472483422 | etot = -13.2825375291149
+698000  ekin = 3.12971664160265 |  erot = 2.3607993405226 | epot = -18.7730535110309 | etot = -13.2825375289056
+699000  ekin = 3.05458980607575 |  erot = 2.31258576051436 | epot = -18.6497130952223 | etot = -13.2825375286322
+700000  ekin = 2.96718102277338 |  erot = 2.26139197222678 | epot = -18.5111105233092 | etot = -13.282537528309
+701000  ekin = 2.86896613270987 |  erot = 2.21057215475942 | epot = -18.3620758154114 | etot = -13.2825375279421
+702000  ekin = 2.76178671310755 |  erot = 2.16397434370647 | epot = -18.2082985843512 | etot = -13.2825375275372
+703000  ekin = 2.64787120281757 |  erot = 2.12574771765488 | epot = -18.0561564514672 | etot = -13.2825375309947
+704000  ekin = 2.52933762816201 |  erot = 2.08674637167894 | epot = -17.8986215285157 | etot = -13.2825375286748
+705000  ekin = 2.41679696488455 |  erot = 2.0566401236899 | epot = -17.7559746148443 | etot = -13.2825375262699
+706000  ekin = 2.30501007301267 |  erot = 2.06115876579317 | epot = -17.6487063632602 | etot = -13.2825375244543
+707000  ekin = 2.19269241312063 |  erot = 2.11375046401179 | epot = -17.5889804017709 | etot = -13.2825375246385
+708000  ekin = 2.09960598295589 |  erot = 2.19681319913428 | epot = -17.5789567090833 | etot = -13.2825375269932
+709000  ekin = 2.01320280572636 |  erot = 2.28016876669421 | epot = -17.5759090978068 | etot = -13.2825375253862
+710000  ekin = 1.93302644378252 |  erot = 2.3747322880584 | epot = -17.5902962577935 | etot = -13.2825375259526
+711000  ekin = 1.85957279021245 |  erot = 2.47358324949964 | epot = -17.6156935663468 | etot = -13.2825375266347
+712000  ekin = 1.79282630225992 |  erot = 2.56690430163368 | epot = -17.6422681311821 | etot = -13.2825375272885
+713000  ekin = 1.73341814837551 |  erot = 2.64462400363359 | epot = -17.660579679756 | etot = -13.2825375277469
+714000  ekin = 1.68328438218602 |  erot = 2.6981736471422 | epot = -17.6639955572078 | etot = -13.2825375278795
+715000  ekin = 1.64594117620278 |  erot = 2.72207244137003 | epot = -17.6505511452259 | etot = -13.2825375276531
+716000  ekin = 1.62610172677928 |  erot = 2.71479815184846 | epot = -17.6234374057783 | etot = -13.2825375271506
+717000  ekin = 1.62864489608611 |  erot = 2.67867233654835 | epot = -17.5898547591674 | etot = -13.2825375265329
+718000  ekin = 1.65730138294327 |  erot = 2.6189183930066 | epot = -17.5587573019149 | etot = -13.282537525965
+719000  ekin = 1.71360335043978 |  erot = 2.54235654261391 | epot = -17.5384974186061 | etot = -13.2825375255524
+720000  ekin = 1.79650653895858 |  erot = 2.45621436721656 | epot = -17.5352584314959 | etot = -13.2825375253208
+721000  ekin = 1.90273489837533 |  erot = 2.36731439674759 | epot = -17.5525868203611 | etot = -13.2825375252382
+722000  ekin = 2.02756635859999 |  erot = 2.28163864623686 | epot = -17.5917425300939 | etot = -13.2825375252571
+723000  ekin = 2.16566245404416 |  erot = 2.20411346317412 | epot = -17.6523134425647 | etot = -13.2825375253464
+724000  ekin = 2.31164907954197 |  erot = 2.13844446421075 | epot = -17.7326310692571 | etot = -13.2825375255043
+725000  ekin = 2.46036017261476 |  erot = 2.0869120442021 | epot = -17.8298097425667 | etot = -13.2825375257498
+726000  ekin = 2.6068349632846 |  erot = 2.05013619410202 | epot = -17.9395086834918 | etot = -13.2825375261052
+727000  ekin = 2.74622028370769 |  erot = 2.02690424048558 | epot = -18.0556620507673 | etot = -13.2825375265741
+728000  ekin = 2.87374866232265 |  erot = 2.01419303060157 | epot = -18.1704792200511 | etot = -13.2825375271269
+729000  ekin = 2.98490085153144 |  erot = 2.00751009684072 | epot = -18.2749484760646 | etot = -13.2825375276924
+730000  ekin = 3.07576690645469 |  erot = 2.00160558057494 | epot = -18.3599100152017 | etot = -13.2825375281721
+731000  ekin = 3.14351022556136 |  erot = 1.99146923005515 | epot = -18.4175169840844 | etot = -13.2825375284679
+732000  ekin = 3.18676307270908 |  erot = 1.9733775068131 | epot = -18.4426781080378 | etot = -13.2825375285156
+733000  ekin = 3.20579220143817 |  erot = 1.94568706577985 | epot = -18.4340167955229 | etot = -13.2825375283049
+734000  ekin = 3.20238921808403 |  erot = 1.9091725140226 | epot = -18.3940992599778 | etot = -13.2825375278711
+735000  ekin = 3.17951096478395 |  erot = 1.86680153214189 | epot = -18.3288500242332 | etot = -13.2825375273073
+736000  ekin = 3.1407386539016 |  erot = 1.82300587571906 | epot = -18.2462820563141 | etot = -13.2825375266935
+737000  ekin = 3.08984658439833 |  erot = 1.78292392999538 | epot = -18.1553080405002 | etot = -13.2825375261065
+738000  ekin = 3.03043228105068 |  erot = 1.7516193492114 | epot = -18.0645891558627 | etot = -13.2825375256006
+739000  ekin = 2.96566842761532 |  erot = 1.73346651074128 | epot = -17.9816724635652 | etot = -13.2825375252086
+740000  ekin = 2.89817088990248 |  erot = 1.73175552827542 | epot = -17.9124639431193 | etot = -13.2825375249414
+741000  ekin = 2.82995232215527 |  erot = 1.74850528578322 | epot = -17.8609951327411 | etot = -13.2825375248026
+742000  ekin = 2.76247533975977 |  erot = 1.78434362324901 | epot = -17.8293564878077 | etot = -13.2825375247989
+743000  ekin = 2.69668176522496 |  erot = 1.83847103615502 | epot = -17.8176903262763 | etot = -13.2825375248963
+744000  ekin = 2.63311444617166 |  erot = 1.90875045497562 | epot = -17.8244024262527 | etot = -13.2825375251054
+745000  ekin = 2.57196493518836 |  erot = 1.99171779916653 | epot = -17.8462202597747 | etot = -13.2825375254198
+746000  ekin = 2.5131159615418 |  erot = 2.08264215541026 | epot = -17.8782956427778 | etot = -13.2825375258257
+747000  ekin = 2.4562102402775 |  erot = 2.17571767167211 | epot = -17.9144654382424 | etot = -13.2825375262928
+748000  ekin = 2.4007641204688 |  erot = 2.2644524277425 | epot = -17.9477540749797 | etot = -13.2825375267684
+749000  ekin = 2.34635697391007 |  erot = 2.34231237519854 | epot = -17.9712068762851 | etot = -13.2825375271765
+750000  ekin = 2.29290375451717 |  erot = 2.40359513791455 | epot = -17.979036419863 | etot = -13.2825375274312
+751000  ekin = 2.24097207238015 |  erot = 2.44437862762129 | epot = -17.9678882274625 | etot = -13.2825375274611
+752000  ekin = 2.19206377657606 |  erot = 2.46328788077229 | epot = -17.937889184575 | etot = -13.2825375272267
+753000  ekin = 2.0191073671841 |  erot = 2.37844688220293 | epot = -17.6800917192494 | etot = -13.2825374698623
+754000  ekin = 2.03397419691681 |  erot = 2.38379927449377 | epot = -17.7003109683856 | etot = -13.282537496975
+755000  ekin = 2.10287082567493 |  erot = 2.42269050483285 | epot = -17.8080987746467 | etot = -13.2825374441389
+756000  ekin = 2.09556625439565 |  erot = 2.405750962181 | epot = -17.7838546600866 | etot = -13.2825374435099
+757000  ekin = 2.11013463581362 |  erot = 2.39174642164209 | epot = -17.7844185004694 | etot = -13.2825374430137
+758000  ekin = 2.14991880579705 |  erot = 2.38537981437436 | epot = -17.8178360628955 | etot = -13.2825374427241
+759000  ekin = 2.21691275063063 |  erot = 2.38948785825167 | epot = -17.8889380515667 | etot = -13.2825374426844
+760000  ekin = 2.31141054860375 |  erot = 2.40468264900161 | epot = -17.9986306405271 | etot = -13.2825374429218
+761000  ekin = 2.4317547235321 |  erot = 2.42917556854271 | epot = -18.14346773552 | etot = -13.2825374434452
+762000  ekin = 2.57423243233675 |  erot = 2.45878794777349 | epot = -18.3155578243444 | etot = -13.2825374442342
+763000  ekin = 2.73317609318437 |  erot = 2.48721280711223 | epot = -18.5029263455259 | etot = -13.2825374452293
+764000  ekin = 2.90131643265847 |  erot = 2.50663479921391 | epot = -18.6904886781953 | etot = -13.2825374463229
+765000  ekin = 3.07040159501002 |  erot = 2.50879317398454 | epot = -18.8617322163581 | etot = -13.2825374473636
+766000  ekin = 3.23203070978082 |  erot = 2.48644536574614 | epot = -19.0010135237083 | etot = -13.2825374481813
+767000  ekin = 3.37856609433327 |  erot = 2.43498274045147 | epot = -19.096086283418 | etot = -13.2825374486333
+768000  ekin = 3.50392633253189 |  erot = 2.35374465438907 | epot = -19.14020843557 | etot = -13.282537448649
+769000  ekin = 3.60408079934929 |  erot = 2.2465665844398 | epot = -19.1331848320412 | etot = -13.2825374482521
+770000  ekin = 3.67731902040089 |  erot = 2.12129310034524 | epot = -19.0811495682864 | etot = -13.2825374475402
+771000  ekin = 3.7250046645363 |  erot = 1.98803923032005 | epot = -18.9955813415612 | etot = -13.2825374467049
+772000  ekin = 3.73784328843035 |  erot = 1.84847100678562 | epot = -18.8688517433746 | etot = -13.2825374481586
+773000  ekin = 3.73518377757204 |  erot = 1.74399251359463 | epot = -18.7617137365844 | etot = -13.2825374454177
+774000  ekin = 3.73326270308357 |  erot = 1.69319142531066 | epot = -18.7089915825401 | etot = -13.2825374541459
+775000  ekin = 3.70600760956875 |  erot = 1.65662399761182 | epot = -18.6451690552018 | etot = -13.2825374480212
+776000  ekin = 3.66620955944038 |  erot = 1.65229490513874 | epot = -18.6010419124108 | etot = -13.2825374478317
+777000  ekin = 3.6164959066655 |  erot = 1.68124406400525 | epot = -18.5802774185067 | etot = -13.2825374478359
+778000  ekin = 3.5589217195722 |  erot = 1.74156460645431 | epot = -18.5830237740648 | etot = -13.2825374480383
+779000  ekin = 3.49505249793887 |  erot = 1.82861083484593 | epot = -18.6062007816394 | etot = -13.2825374488546
+780000  ekin = 3.4260605289351 |  erot = 1.93200454544541 | epot = -18.6406025240164 | etot = -13.2825374496359
+781000  ekin = 3.35141348649702 |  erot = 2.04005284529073 | epot = -18.6740037822594 | etot = -13.2825374504716
+782000  ekin = 3.27002343600189 |  erot = 2.14152553689654 | epot = -18.6940864240875 | etot = -13.2825374511891
+783000  ekin = 3.18141085606315 |  erot = 2.22636120778713 | epot = -18.6903095154617 | etot = -13.2825374516114
+784000  ekin = 3.08656488448361 |  erot = 2.28735807323151 | epot = -18.6564604093344 | etot = -13.2825374516193
+785000  ekin = 2.98843913984933 |  erot = 2.32136711553602 | epot = -18.592343706592 | etot = -13.2825374512067
+786000  ekin = 2.89178850735618 |  erot = 2.32954149828313 | epot = -18.5038674561269 | etot = -13.2825374504876
+787000  ekin = 2.80233070714568 |  erot = 2.31656731743012 | epot = -18.4014354742217 | etot = -13.2825374496459
+788000  ekin = 2.72556137455006 |  erot = 2.28924565768276 | epot = -18.2973444810906 | etot = -13.2825374488578
+789000  ekin = 2.66569850120894 |  erot = 2.25498711353627 | epot = -18.2032230629877 | etot = -13.2825374482425
+790000  ekin = 2.62507547495403 |  erot = 2.22062577794997 | epot = -18.1282387007584 | etot = -13.2825374478544
+791000  ekin = 2.60400664845757 |  erot = 2.19166523695208 | epot = -18.0782093331145 | etot = -13.2825374477048
+792000  ekin = 2.60095165826993 |  erot = 2.17186849883267 | epot = -18.0553576048892 | etot = -13.2825374477866
+793000  ekin = 2.61278727136947 |  erot = 2.1630579475058 | epot = -18.0583826669628 | etot = -13.2825374480875
+794000  ekin = 2.63509078750899 |  erot = 2.16503786010594 | epot = -18.0826660962031 | etot = -13.2825374485882
+795000  ekin = 2.66245645496094 |  erot = 2.17562900151097 | epot = -18.1206229057215 | etot = -13.2825374492496
+796000  ekin = 2.68895951797515 |  erot = 2.19088748039119 | epot = -18.1623844483558 | etot = -13.2825374499895
+797000  ekin = 2.70892452636473 |  erot = 2.20564060882902 | epot = -18.197102585859 | etot = -13.2825374506652
+798000  ekin = 2.7187387406754 |  erot = 2.21455364300775 | epot = -18.2158298332747 | etot = -13.2825374495916
+799000  ekin = 2.70000300099405 |  erot = 2.21050545408876 | epot = -18.193045904985 | etot = -13.2825374499022
+800000  ekin = 2.65392049001821 |  erot = 2.17300546938151 | epot = -18.109463378289 | etot = -13.2825374188892
+801000  ekin = 2.82505345096871 |  erot = 2.13616134701489 | epot = -18.2437522525054 | etot = -13.2825374545218
+802000  ekin = 2.90470228802172 |  erot = 2.10953657449614 | epot = -18.2967762799053 | etot = -13.2825374173874
+803000  ekin = 2.9677525986453 |  erot = 2.08137573444383 | epot = -18.3316657512964 | etot = -13.2825374182072
+804000  ekin = 3.01419864036155 |  erot = 2.05336319939514 | epot = -18.3500992581057 | etot = -13.282537418349
+805000  ekin = 3.03950260682403 |  erot = 2.02738087474037 | epot = -18.3494208999164 | etot = -13.282537418352
+806000  ekin = 3.04147612212525 |  erot = 2.00524180108709 | epot = -18.3292553414124 | etot = -13.2825374182001
+807000  ekin = 3.02009152418646 |  erot = 1.98876425940777 | epot = -18.2913932015099 | etot = -13.2825374179157
+808000  ekin = 2.97716861905469 |  erot = 1.9797928070483 | epot = -18.2394988436566 | etot = -13.2825374175536
+809000  ekin = 2.91576405317411 |  erot = 1.98007542202132 | epot = -18.1783768923745 | etot = -13.282537417179
+810000  ekin = 2.83951999241211 |  erot = 1.9910201414007 | epot = -18.1130775506578 | etot = -13.282537416845
+811000  ekin = 2.75216924413256 |  erot = 2.01344070631007 | epot = -18.0481473670229 | etot = -13.2825374165802
+812000  ekin = 2.65727213949033 |  erot = 2.04739495870437 | epot = -17.9872045145838 | etot = -13.2825374163891
+813000  ekin = 2.55815480063288 |  erot = 2.0921579466292 | epot = -17.9328501635216 | etot = -13.2825374162596
+814000  ekin = 2.45796623947603 |  erot = 2.14630993528002 | epot = -17.8868135909302 | etot = -13.2825374161741
+815000  ekin = 2.35976627429823 |  erot = 2.20788718833984 | epot = -17.8501908787554 | etot = -13.2825374161174
+816000  ekin = 2.26657575180629 |  erot = 2.27454135561794 | epot = -17.8236545235058 | etot = -13.2825374160815
+817000  ekin = 2.18134946662811 |  erot = 2.34367133400565 | epot = -17.807558216702 | etot = -13.2825374160682
+818000  ekin = 2.10686415591836 |  erot = 2.41251844102779 | epot = -17.8019200130316 | etot = -13.2825374160855
+819000  ekin = 2.04554497258418 |  erot = 2.47824070162555 | epot = -17.806323090351 | etot = -13.2825374161413
+820000  ekin = 1.99927680295696 |  erot = 2.53799486378974 | epot = -17.8198090829855 | etot = -13.2825374162388
+821000  ekin = 1.9692530805303 |  erot = 2.58905270210877 | epot = -17.8408431990125 | etot = -13.2825374163734
+822000  ekin = 1.95590272174924 |  erot = 2.62895986938386 | epot = -17.8674000076635 | etot = -13.2825374165304
+823000  ekin = 1.95890926788755 |  erot = 2.6557286058008 | epot = -17.8971752903778 | etot = -13.2825374166894
+824000  ekin = 1.97731046162633 |  erot = 2.66804286128345 | epot = -17.9278907397372 | etot = -13.2825374168275
+825000  ekin = 2.00964945342457 |  erot = 2.66544750451175 | epot = -17.9576343748594 | etot = -13.2825374169231
+826000  ekin = 2.05414423139186 |  erot = 2.64849047550104 | epot = -17.985172123854 | etot = -13.2825374169611
+827000  ekin = 2.10884212199665 |  erot = 2.61877894485958 | epot = -18.0101584837945 | etot = -13.2825374169382
+828000  ekin = 2.1717293569375 |  erot = 2.57890618314315 | epot = -18.0331729569469 | etot = -13.2825374168662
+829000  ekin = 2.24077304847179 |  erot = 2.53221651091816 | epot = -18.0555269761626 | etot = -13.2825374167726
+830000  ekin = 2.31389012743404 |  erot = 2.4824115756111 | epot = -18.0788391197418 | etot = -13.2825374166967
+831000  ekin = 2.38886546542343 |  erot = 2.43305573494131 | epot = -18.1044586170416 | etot = -13.2825374166768
+832000  ekin = 2.4632691578231 |  erot = 2.3870870487244 | epot = -18.1328936232866 | etot = -13.2825374167391
+833000  ekin = 2.5344365632194 |  erot = 2.34645691813147 | epot = -18.1634308982373 | etot = -13.2825374168864
+834000  ekin = 2.59956439019907 |  erot = 2.31199374777391 | epot = -18.1940955550686 | etot = -13.2825374170956
+835000  ekin = 2.65594315943653 |  erot = 2.28352232821168 | epot = -18.2220029049695 | etot = -13.2825374173213
+836000  ekin = 2.70130042683167 |  erot = 2.26019210697788 | epot = -18.244029951319 | etot = -13.2825374175095
+837000  ekin = 2.73418787962871 |  erot = 2.24090836893314 | epot = -18.2576336661722 | etot = -13.2825374176104
+838000  ekin = 2.75431729342696 |  erot = 2.22474076288568 | epot = -18.2615954739057 | etot = -13.2825374175931
+839000  ekin = 2.76274241629131 |  erot = 2.21121141093012 | epot = -18.256491244675 | etot = -13.2825374174536
+840000  ekin = 2.76179432989972 |  erot = 2.20041723303662 | epot = -18.2447489801545 | etot = -13.2825374172182
+841000  ekin = 2.75470877518085 |  erot = 2.19297958495076 | epot = -18.2302257770756 | etot = -13.2825374169439
+842000  ekin = 2.74495192528053 |  erot = 2.18982916449433 | epot = -18.2173185064846 | etot = -13.2825374167098
+843000  ekin = 2.73536701846579 |  erot = 2.19185320024881 | epot = -18.2097576353086 | etot = -13.282537416594
+844000  ekin = 2.72739699349177 |  erot = 2.1994851694244 | epot = -18.2094195795621 | etot = -13.2825374166459
+845000  ekin = 2.7206968024524 |  erot = 2.21238342751528 | epot = -18.2156176468218 | etot = -13.2825374168541
+846000  ekin = 2.71335246036253 |  erot = 2.22935500856137 | epot = -18.2252448860709 | etot = -13.282537417147
+847000  ekin = 2.70267547916117 |  erot = 2.24859000373239 | epot = -18.2338029003123 | etot = -13.2825374174188
+848000  ekin = 2.68627675195779 |  erot = 2.26812231144288 | epot = -18.236936480973 | etot = -13.2825374175723
+849000  ekin = 2.66300406671244 |  erot = 2.2863229263121 | epot = -18.2318644105805 | etot = -13.282537417556
+850000  ekin = 2.63341305523148 |  erot = 2.30223029747857 | epot = -18.2181807700874 | etot = -13.2825374173774
+851000  ekin = 2.59966043365591 |  erot = 2.3156167587262 | epot = -18.1978146094748 | etot = -13.2825374170927
+852000  ekin = 2.56493307993571 |  erot = 2.32681510713484 | epot = -18.1742856038479 | etot = -13.2825374167774
+853000  ekin = 2.53268459155754 |  erot = 2.33642702138572 | epot = -18.1516490294471 | etot = -13.2825374165038
+854000  ekin = 2.50591352797944 |  erot = 2.34503055123976 | epot = -18.1334814955374 | etot = -13.2825374163182
+855000  ekin = 2.4866740476675 |  erot = 2.35297873120409 | epot = -18.1221901951049 | etot = -13.2825374162333
+856000  ekin = 2.47592780860343 |  erot = 2.36034202539965 | epot = -18.1188072502362 | etot = -13.2825374162331
+857000  ekin = 2.47367803510516 |  erot = 2.36697109794411 | epot = -18.1231865493438 | etot = -13.2825374162946
+858000  ekin = 2.47922391681366 |  erot = 2.37260088210265 | epot = -18.1343622152926 | etot = -13.2825374163763
+859000  ekin = 2.49150776870147 |  erot = 2.37701215984104 | epot = -18.1510573449986 | etot = -13.282537416456
+860000  ekin = 2.50937686784747 |  erot = 2.38013993594023 | epot = -18.1720542203101 | etot = -13.2825374165224
+861000  ekin = 2.53170635996116 |  erot = 2.38211817150425 | epot = -18.1963619480387 | etot = -13.2825374165732
+862000  ekin = 2.55742566626407 |  erot = 2.38328933264109 | epot = -18.2232524155165 | etot = -13.2825374166114
+863000  ekin = 2.58549483187838 |  erot = 2.38419488482973 | epot = -18.252227133347 | etot = -13.2825374166389
+864000  ekin = 2.61488041066499 |  erot = 2.38555368834993 | epot = -18.2829715156728 | etot = -13.2825374166579
+865000  ekin = 2.64455846347095 |  erot = 2.38821849192421 | epot = -18.3153143720654 | etot = -13.2825374166702
+866000  ekin = 2.67354800424437 |  erot = 2.39309523344314 | epot = -18.3491806543665 | etot = -13.282537416679
+867000  ekin = 2.70096216988177 |  erot = 2.40101926554071 | epot = -18.3845188521138 | etot = -13.2825374166913
+868000  ekin = 2.72584498338572 |  erot = 2.41260829074957 | epot = -18.420990690944 | etot = -13.2825374168087
+869000  ekin = 2.74685098606623 |  erot = 2.42808376653873 | epot = -18.4574721694777 | etot = -13.2825374168728
+870000  ekin = 2.76334516398283 |  erot = 2.44707202879413 | epot = -18.4929546097441 | etot = -13.2825374169672
+871000  ekin = 2.77488977710316 |  erot = 2.46856883163597 | epot = -18.5259960258323 | etot = -13.2825374170932
+872000  ekin = 2.7811573123189 |  erot = 2.49101078851438 | epot = -18.5547055180778 | etot = -13.2825374172445
+873000  ekin = 2.78190152502928 |  erot = 2.51241399879738 | epot = -18.5768529412309 | etot = -13.2825374174043
+874000  ekin = 2.77696693725528 |  erot = 2.53063897161364 | epot = -18.5901433264131 | etot = -13.2825374175441
+875000  ekin = 2.76636320213146 |  erot = 2.54374754436265 | epot = -18.5926481641224 | etot = -13.2825374176283
+876000  ekin = 2.7504069828229 |  erot = 2.55039472310231 | epot = -18.5833391235459 | etot = -13.2825374176207
+877000  ekin = 2.72989722810813 |  erot = 2.55017286557422 | epot = -18.5626075111784 | etot = -13.2825374174961
+878000  ekin = 2.70625700294355 |  erot = 2.54382115071376 | epot = -18.5326155709077 | etot = -13.2825374172503
+879000  ekin = 2.68156506653427 |  erot = 2.5332421351554 | epot = -18.4973446185932 | etot = -13.2825374169036
+880000  ekin = 2.65843100554442 |  erot = 2.52132216836891 | epot = -18.4622905904093 | etot = -13.282537416496
+881000  ekin = 2.63972432922979 |  erot = 2.51160592366972 | epot = -18.4338676689779 | etot = -13.2825374160784
+882000  ekin = 2.62822235403347 |  erot = 2.50790034454678 | epot = -18.4186601142802 | etot = -13.2825374157
+883000  ekin = 2.62626662137136 |  erot = 2.51387422299541 | epot = -18.4226782597687 | etot = -13.2825374154019
+884000  ekin = 2.63550251772652 |  erot = 2.53269090787765 | epot = -18.4507308408175 | etot = -13.2825374152133
+885000  ekin = 2.65673814855014 |  erot = 2.56668643457077 | epot = -18.5059619982733 | etot = -13.2825374151524
+886000  ekin = 2.68991717237218 |  erot = 2.61709354768266 | epot = -18.5895481352837 | etot = -13.2825374152289
+887000  ekin = 2.734175532827 |  erot = 2.68381522130244 | epot = -18.700528169575 | etot = -13.2825374154455
+888000  ekin = 2.78795008719356 |  erot = 2.76526591136903 | epot = -18.8357534143588 | etot = -13.2825374157962
+889000  ekin = 2.8491201813508 |  erot = 2.85831710930318 | epot = -18.989974706918 | etot = -13.282537416264
+890000  ekin = 2.91517691868807 |  erot = 2.95839462643955 | epot = -19.1561089619448 | etot = -13.2825374168172
+891000  ekin = 2.98341767192295 |  erot = 3.0597676506775 | epot = -19.3257227400102 | etot = -13.2825374174098
+892000  ekin = 3.05115351644501 |  erot = 3.15603968258129 | epot = -19.4897306170114 | etot = -13.2825374179851
+893000  ekin = 3.11590367361418 |  erot = 3.24080526805507 | epot = -19.6392463601538 | etot = -13.2825374184846
+894000  ekin = 3.17554453075818 |  erot = 3.30838805788589 | epot = -19.7664700075009 | etot = -13.2825374188568
+895000  ekin = 3.22839008561766 |  erot = 3.35454380060236 | epot = -19.8654713052867 | etot = -13.2825374190666
+896000  ekin = 3.27319975165836 |  erot = 3.37700709394957 | epot = -19.9327442647079 | etot = -13.2825374191
+897000  ekin = 3.30912548499472 |  erot = 3.37578332995761 | epot = -19.9674462339186 | etot = -13.2825374189663
+898000  ekin = 3.33561719415195 |  erot = 3.35313099566656 | epot = -19.9712856085154 | etot = -13.2825374186968
+899000  ekin = 3.3523031028265 |  erot = 3.31323476596136 | epot = -19.9480752871285 | etot = -13.2825374183407
+900000  ekin = 3.35886034531518 |  erot = 3.26162723064569 | epot = -19.9030249939161 | etot = -13.2825374179552
+901000  ekin = 3.35489762759567 |  erot = 3.2044644832284 | epot = -19.8418995284194 | etot = -13.2825374175953
+902000  ekin = 3.33988398839342 |  erot = 3.14778460407791 | epot = -19.7702060097741 | etot = -13.2825374173028
+903000  ekin = 3.31316641909532 |  erot = 3.09687096103035 | epot = -19.6925747972223 | etot = -13.2825374170966
+904000  ekin = 3.27411465419852 |  erot = 3.05580881217869 | epot = -19.6124608833472 | etot = -13.2825374169699
+905000  ekin = 3.22240761869358 |  erot = 3.02727711490202 | epot = -19.5322221504879 | etot = -13.2825374168923
+906000  ekin = 3.15843123363071 |  erot = 3.01257047164431 | epot = -19.4535391220934 | etot = -13.2825374168184
+907000  ekin = 3.08369713046712 |  erot = 3.01180553644323 | epot = -19.3780400836148 | etot = -13.2825374167044
+908000  ekin = 3.00113487352882 |  erot = 3.02423547646297 | epot = -19.3079077665171 | etot = -13.2825374165253
+909000  ekin = 2.91509126964 |  erot = 3.04858097597399 | epot = -19.246209661904 | etot = -13.28253741629
+910000  ekin = 2.83091809249006 |  erot = 3.08328866196603 | epot = -19.1967441705011 | etot = -13.282537416045
+911000  ekin = 2.75416042802549 |  erot = 3.12665661766781 | epot = -19.1633544615573 | etot = -13.282537415864
+912000  ekin = 2.68982240197673 |  erot = 3.17670303509253 | epot = -19.1490628528293 | etot = -13.2825374157601
+913000  ekin = 2.64026279480142 |  erot = 3.23106967171228 | epot = -19.1538698824696 | etot = -13.2825374159559
+914000  ekin = 2.60494541586834 |  erot = 3.28757760350067 | epot = -19.1750604355173 | etot = -13.2825374161483
+915000  ekin = 2.58331294380949 |  erot = 3.34356245576663 | epot = -19.2094128163232 | etot = -13.282537416747
+916000  ekin = 2.572225278094 |  erot = 3.39542630003117 | epot = -19.250188995406 | etot = -13.2825374172809
+917000  ekin = 2.56717380000648 |  erot = 3.43991413165374 | epot = -19.2896253494389 | etot = -13.2825374177786
+918000  ekin = 2.56366862414259 |  erot = 3.47431911369141 | epot = -19.3205251559853 | etot = -13.2825374181513
+919000  ekin = 2.55808580528835 |  erot = 3.4968825160616 | epot = -19.337505739687 | etot = -13.2825374183371
+920000  ekin = 2.54828083604877 |  erot = 3.50706786620944 | epot = -19.3378861205732 | etot = -13.2825374183149
+921000  ekin = 2.5338583783986 |  erot = 3.5055796155901 | epot = -19.3219754120972 | etot = -13.2825374181085
+922000  ekin = 2.516060534879 |  erot = 3.49409623125511 | epot = -19.2926941839177 | etot = -13.2825374177836
+923000  ekin = 2.49728909023619 |  erot = 3.47476611514256 | epot = -19.2545926228132 | etot = -13.2825374174344
+924000  ekin = 2.48035717414061 |  erot = 3.44958564359935 | epot = -19.2124802348989 | etot = -13.282537417159
+925000  ekin = 2.46765713433988 |  erot = 3.41982437245358 | epot = -19.1700189238237 | etot = -13.2825374170303
+926000  ekin = 2.46048446299621 |  erot = 3.38566546870185 | epot = -19.1286873487718 | etot = -13.2825374170737
+927000  ekin = 2.45872404418899 |  erot = 3.34617863044022 | epot = -19.0874400918875 | etot = -13.2825374172583
+928000  ekin = 2.46097855235184 |  erot = 3.29964380866974 | epot = -19.043159778532 | etot = -13.2825374175104
+929000  ekin = 2.46505358100394 |  erot = 3.24413140303551 | epot = -18.99172240178 | etot = -13.2825374177406
+930000  ekin = 2.46859437790869 |  erot = 3.17816487222183 | epot = -18.9292966680023 | etot = -13.2825374178718
+931000  ekin = 2.46965047248253 |  erot = 3.10127887163483 | epot = -18.8534667619775 | etot = -13.2825374178601
+932000  ekin = 2.46701732520898 |  erot = 3.01434779059203 | epot = -18.7639025334928 | etot = -13.2825374176918
+933000  ekin = 2.46031519086868 |  erot = 2.91973998893973 | epot = -18.662592597222 | etot = -13.2825374174136
+934000  ekin = 2.44985996507097 |  erot = 2.82081794907183 | epot = -18.5532153312021 | etot = -13.2825374170593
+935000  ekin = 2.43642057973712 |  erot = 2.72162862891861 | epot = -18.4405866253331 | etot = -13.2825374166773
+936000  ekin = 2.42095423648383 |  erot = 2.62651830339036 | epot = -18.3300099561839 | etot = -13.2825374163097
+937000  ekin = 2.40438434874151 |  erot = 2.53973621394318 | epot = -18.2266579786711 | etot = -13.2825374159864
+938000  ekin = 2.38744919883856 |  erot = 2.46512923461683 | epot = -18.1351158491807 | etot = -13.2825374157253
+939000  ekin = 2.37062067030574 |  erot = 2.40593643917341 | epot = -18.0590945250148 | etot = -13.2825374155357
+940000  ekin = 2.35407564413747 |  erot = 2.36465978775718 | epot = -18.0012728473171 | etot = -13.2825374154225
+941000  ekin = 2.33770002379755 |  erot = 2.34297759096208 | epot = -17.9632150301481 | etot = -13.2825374153884
+942000  ekin = 2.32111004775224 |  erot = 2.34167204163274 | epot = -17.9453195048215 | etot = -13.2825374154365
+943000  ekin = 2.30368578996793 |  erot = 2.36056240830405 | epot = -17.9467856138391 | etot = -13.2825374155671
+944000  ekin = 2.28462216232314 |  erot = 2.39846175787113 | epot = -17.9656213359689 | etot = -13.2825374157746
+945000  ekin = 2.26300913007938 |  erot = 2.45319770726134 | epot = -17.9987442533843 | etot = -13.2825374160436
+946000  ekin = 2.23795189170117 |  erot = 2.52174524353285 | epot = -18.0422345515794 | etot = -13.2825374163454
+947000  ekin = 2.20873145116087 |  erot = 2.60050188059525 | epot = -18.091770748396 | etot = -13.2825374166398
+948000  ekin = 2.17498954714479 |  erot = 2.685690959925 | epot = -18.1432179239527 | etot = -13.2825374168829
+949000  ekin = 2.13690579554511 |  erot = 2.77382147697832 | epot = -18.1932646895605 | etot = -13.2825374170371
+950000  ekin = 2.09532426593736 |  erot = 2.86208909954954 | epot = -18.23995078257 | etot = -13.2825374170831
+951000  ekin = 2.05179335117992 |  erot = 2.94860198603871 | epot = -18.2829327542442 | etot = -13.2825374170256
+952000  ekin = 2.00850116862718 |  erot = 3.03236285097458 | epot = -18.3234014364934 | etot = -13.2825374168917
+953000  ekin = 1.96811370669122 |  erot = 3.11301524857533 | epot = -18.3636663719922 | etot = -13.2825374167257
+954000  ekin = 1.93354422355624 |  erot = 3.19043207917699 | epot = -18.4065137193093 | etot = -13.2825374165761
+955000  ekin = 1.907692996046 |  erot = 3.26426019428037 | epot = -18.4544906068132 | etot = -13.2825374164868
+956000  ekin = 1.89319483896647 |  erot = 3.33353105128001 | epot = -18.5092633067365 | etot = -13.28253741649
+957000  ekin = 1.89220136882553 |  erot = 3.39641763089531 | epot = -18.5711564163223 | etot = -13.2825374166015
+958000  ekin = 1.90621184477869 |  erot = 3.45018116396587 | epot = -18.6389304255644 | etot = -13.2825374168199
+959000  ekin = 1.93595602669004 |  erot = 3.49131884076761 | epot = -18.7098122845856 | etot = -13.2825374171279
+960000  ekin = 1.98132739841468 |  erot = 3.51589596637559 | epot = -18.7797607822856 | etot = -13.2825374174953
+961000  ekin = 2.04135467368814 |  erot = 3.5202262282781 | epot = -18.8441183198727 | etot = -13.2825374179065
+962000  ekin = 2.11395441204344 |  erot = 3.50134462359753 | epot = -18.8978364539492 | etot = -13.2825374183082
+963000  ekin = 2.19624676723989 |  erot = 3.45688460115197 | epot = -18.9356687870206 | etot = -13.2825374186287
+964000  ekin = 2.28502253674575 |  erot = 3.38607259828084 | epot = -18.9536325538576 | etot = -13.282537418831
+965000  ekin = 2.37703902148585 |  erot = 3.29004867798671 | epot = -18.9496251180009 | etot = -13.2825374185283
+966000  ekin = 2.47063968385215 |  erot = 3.17235139654337 | epot = -18.9255284988459 | etot = -13.2825374184504
+967000  ekin = 2.56372995555254 |  erot = 3.03797961239301 | epot = -18.8842469861485 | etot = -13.2825374182029
+968000  ekin = 2.65424152965125 |  erot = 2.89333165879526 | epot = -18.83011060625 | etot = -13.2825374178035
+969000  ekin = 2.74102205813625 |  erot = 2.74597895036798 | epot = -18.769538425812 | etot = -13.2825374173078
+970000  ekin = 2.82317857011101 |  erot = 2.60419008501349 | epot = -18.7099060720296 | etot = -13.2825374169051
+971000  ekin = 2.89946896083441 |  erot = 2.47604958426315 | epot = -18.658055961612 | etot = -13.2825374165144
+972000  ekin = 2.96927883277251 |  erot = 2.36783972346085 | epot = -18.6196559725141 | etot = -13.2825374162807
+973000  ekin = 3.03160430380023 |  erot = 2.28373901071249 | epot = -18.5978807307479 | etot = -13.2825374162352
+974000  ekin = 3.08487810119919 |  erot = 2.22552920056088 | epot = -18.5929447181232 | etot = -13.2825374163631
+975000  ekin = 3.12708218363217 |  erot = 2.1927093869337 | epot = -18.6023289871792 | etot = -13.2825374166133
+976000  ekin = 3.15606698430949 |  erot = 2.18294126831253 | epot = -18.6215456695412 | etot = -13.2825374169192
+977000  ekin = 3.16994500357178 |  erot = 2.19267118206454 | epot = -18.6451536028545 | etot = -13.2825374172182
+978000  ekin = 3.16742946522118 |  erot = 2.21776877494467 | epot = -18.6677356576302 | etot = -13.2825374174643
+979000  ekin = 3.14804045998247 |  erot = 2.25406876588806 | epot = -18.6846466435015 | etot = -13.282537417631
+980000  ekin = 3.11216367723466 |  erot = 2.29776911466814 | epot = -18.6924702096109 | etot = -13.2825374177081
+981000  ekin = 3.06099215360332 |  erot = 2.34569300138965 | epot = -18.6892225726894 | etot = -13.2825374176964
+982000  ekin = 2.99639965214887 |  erot = 2.39544433518914 | epot = -18.6743814049394 | etot = -13.2825374176014
+983000  ekin = 2.92078844513084 |  erot = 2.44547840887849 | epot = -18.6488042714436 | etot = -13.2825374174343
+984000  ekin = 2.83693459670618 |  erot = 2.4950891273926 | epot = -18.6145611413098 | etot = -13.282537417211
+985000  ekin = 2.74783420133486 |  erot = 2.54430433679905 | epot = -18.5746759550876 | etot = -13.2825374169537
+986000  ekin = 2.65654532109889 |  erot = 2.59369131660279 | epot = -18.5327740543913 | etot = -13.2825374166896
+987000  ekin = 2.56602544086508 |  erot = 2.64409904101799 | epot = -18.4926618983298 | etot = -13.2825374164468
+988000  ekin = 2.47897321649663 |  erot = 2.69638105882724 | epot = -18.4578916915741 | etot = -13.2825374162503
+989000  ekin = 2.39763961716918 |  erot = 2.75059396137744 | epot = -18.4307709947858 | etot = -13.2825374162392
+990000  ekin = 2.32368779821633 |  erot = 2.80603342998527 | epot = -18.4122586443938 | etot = -13.2825374161922
+991000  ekin = 2.2582530149192 |  erot = 2.86226671787586 | epot = -18.4030571490211 | etot = -13.282537416226
+992000  ekin = 2.20187988997662 |  erot = 2.91825634939035 | epot = -18.4026736557096 | etot = -13.2825374163427
+993000  ekin = 2.15452775947043 |  erot = 2.97231721293149 | epot = -18.4093823889398 | etot = -13.2825374165378
+994000  ekin = 2.11561176914432 |  erot = 3.02214023523714 | epot = -18.4202894211813 | etot = -13.2825374167998
+995000  ekin = 2.08408161375424 |  erot = 3.06489403643897 | epot = -18.4315130673008 | etot = -13.2825374171076
+996000  ekin = 2.05854312749319 |  erot = 3.09743221500535 | epot = -18.4385127599264 | etot = -13.2825374174279
+997000  ekin = 2.03742523569505 |  erot = 3.11662356420229 | epot = -18.4365862176148 | etot = -13.2825374177175
+998000  ekin = 2.01918449064732 |  erot = 3.11978989603429 | epot = -18.42151180461 | etot = -13.2825374179284
+999000  ekin = 2.00252382621622 |  erot = 3.10518925481745 | epot = -18.390250499052 | etot = -13.2825374180184
+1000000  ekin = 1.98658902577819 |  erot = 3.07244217845672 | epot = -18.3415686221954 | etot = -13.2825374179605
+ 1000000  0.088292846   -1.1874188  0.041070751   -1.0221862 -7.1515284e-05 
+Loop time of 31.7925 on 1 procs for 1000000 steps with 16 atoms
+
+Performance: 27176.198 tau/day, 31453.933 timesteps/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 28.401     | 28.401     | 28.401     |   0.0 | 89.33
+Bond    | 0.86019    | 0.86019    | 0.86019    |   0.0 |  2.71
+Neigh   | 0.00018    | 0.00018    | 0.00018    |   0.0 |  0.00
+Comm    | 0.16311    | 0.16311    | 0.16311    |   0.0 |  0.51
+Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
+Modify  | 2.1003     | 2.1003     | 2.1003     |   0.0 |  6.61
+Other   |            | 0.2673     |            |       |  0.84
+
+Nlocal:    16 ave 16 max 16 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    93 ave 93 max 93 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 93
+Ave neighs/atom = 5.8125
+Ave special neighs/atom = 3.75
+Neighbor list builds = 6
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:31
diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4
new file mode 100644
index 0000000000..8a3a723a1e
--- /dev/null
+++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4
@@ -0,0 +1,1174 @@
+LAMMPS (30 Oct 2019)
+variable number	equal 4
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex4
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000281 secs
+  read_data CPU = 0.003043 secs
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxRNA2 bond interactions - FENE backbone
+bond_style oxrna2/fene
+bond_coeff * 2.0 0.25 0.761070781051
+
+# oxRNA2 pair interactions
+pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+
+pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxrna2/stk     seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/stk     seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 3 4 oxrna2/hbond   seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
+pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+pair_coeff * * oxrna2/dh      ${T} 0.5 1.02455
+pair_coeff * * oxrna2/dh      0.1 0.5 1.02455
+
+# NVE ensemble
+#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all   nve/dot
+fix 1 all nve/asphere
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f  %13.9f %13.9f %13.9f"
+
+run 1000000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3015
+  ghost atom cutoff = 3.3015
+  binsize = 1.65075, bins = 25 25 25
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxrna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxrna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxrna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxrna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxrna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxrna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+0  ekin = 0 |  erot = 0 | epot = -13.282537590974 | etot = -13.282537590974
+Per MPI rank memory allocation (min/avg/max) = 7.755 | 7.937 | 8.119 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0  -0.84341458  0.013255977   -0.8301586 -2.0169485e-05 
+1000  ekin = 0.00448503054655829 |  erot = 0.00825381229599554 | epot = -13.2952764343121 | etot = -13.2825375914696
+2000  ekin = 0.0179027901180383 |  erot = 0.0327684151333158 | epot = -13.333208796773 | etot = -13.2825375915216
+3000  ekin = 0.0401478317723388 |  erot = 0.0728240143062734 | epot = -13.3955094376812 | etot = -13.2825375916026
+4000  ekin = 0.0710654348932012 |  erot = 0.127292706282676 | epot = -13.4808957328803 | etot = -13.2825375917044
+5000  ekin = 0.110480309743627 |  erot = 0.194739074279345 | epot = -13.58775697584 | etot = -13.282537591817
+6000  ekin = 0.158231230694386 |  erot = 0.273546913858364 | epot = -13.7143157364821 | etot = -13.2825375919294
+7000  ekin = 0.214206450831694 |  erot = 0.362058396900661 | epot = -13.8588024397635 | etot = -13.2825375920312
+8000  ekin = 0.27837411184999 |  erot = 0.458709556671591 | epot = -14.0196212606354 | etot = -13.2825375921138
+9000  ekin = 0.350802094030117 |  erot = 0.562145629087582 | epot = -14.1954853152897 | etot = -13.282537592172
+10000  ekin = 0.431663021447632 |  erot = 0.671302139461542 | epot = -14.3855027531133 | etot = -13.2825375922041
+11000  ekin = 0.521222365620092 |  erot = 0.785442646223518 | epot = -14.5892026040564 | etot = -13.2825375922128
+12000  ekin = 0.619810398735201 |  erot = 0.90415088836544 | epot = -14.8064988793047 | etot = -13.2825375922041
+13000  ekin = 0.727781531798581 |  erot = 1.02728222251184 | epot = -15.0376013464965 | etot = -13.2825375921861
+14000  ekin = 0.845466747659119 |  erot = 1.15488520186341 | epot = -15.2828895416906 | etot = -13.2825375921681
+15000  ekin = 0.973515286429056 |  erot = 1.28640002432427 | epot = -15.5424529041403 | etot = -13.282537593387
+16000  ekin = 1.12323013751051 |  erot = 1.4038749539854 | epot = -15.8096426839246 | etot = -13.2825375924286
+17000  ekin = 1.29769272832575 |  erot = 1.51347784068601 | epot = -16.0937081607386 | etot = -13.2825375917268
+18000  ekin = 1.48565191084472 |  erot = 1.63592970999597 | epot = -16.4041192134335 | etot = -13.2825375925929
+19000  ekin = 1.66750911163292 |  erot = 1.77940241938649 | epot = -16.7294491246356 | etot = -13.2825375936162
+20000  ekin = 1.84148924290367 |  erot = 1.93695511183614 | epot = -17.0609819484045 | etot = -13.2825375936647
+21000  ekin = 2.02307741366106 |  erot = 2.09844265792887 | epot = -17.4040576653927 | etot = -13.2825375938028
+22000  ekin = 2.21183606977167 |  erot = 2.26260708947227 | epot = -17.7569807531574 | etot = -13.2825375939135
+23000  ekin = 2.40735468792923 |  erot = 2.42817202047232 | epot = -18.1180643024984 | etot = -13.2825375940969
+24000  ekin = 2.60896890448811 |  erot = 2.59357882573777 | epot = -18.4850853245068 | etot = -13.2825375942809
+25000  ekin = 2.815801354773 |  erot = 2.75706655666979 | epot = -18.8554055059558 | etot = -13.282537594513
+26000  ekin = 3.02680083558447 |  erot = 2.91667946897181 | epot = -19.2260178993261 | etot = -13.2825375947698
+27000  ekin = 3.24067707260278 |  erot = 3.07027299756425 | epot = -19.5934876652165 | etot = -13.2825375950495
+28000  ekin = 3.45601412953551 |  erot = 3.21560615187967 | epot = -19.9541578767284 | etot = -13.2825375953133
+29000  ekin = 3.67136830813179 |  erot = 3.35037905822876 | epot = -20.3042849619982 | etot = -13.2825375956377
+30000  ekin = 3.88476027224393 |  erot = 3.47208481891771 | epot = -20.6393826871844 | etot = -13.2825375960227
+31000  ekin = 4.09387957878907 |  erot = 3.57821385031972 | epot = -20.9546310254505 | etot = -13.2825375963417
+32000  ekin = 4.2966218534583 |  erot = 3.6664860653108 | epot = -21.2456455154184 | etot = -13.2825375966493
+33000  ekin = 4.49089153394099 |  erot = 3.73482555362516 | epot = -21.5082546845017 | etot = -13.2825375969356
+34000  ekin = 4.67464118182325 |  erot = 3.78142516888949 | epot = -21.7386039479011 | etot = -13.2825375971883
+35000  ekin = 4.84586411782109 |  erot = 3.80480460777856 | epot = -21.9332063229965 | etot = -13.2825375973968
+36000  ekin = 5.0027094048744 |  erot = 3.80394535032719 | epot = -22.0891923527598 | etot = -13.2825375975582
+37000  ekin = 5.14355281474345 |  erot = 3.77833709530338 | epot = -22.2044275077127 | etot = -13.2825375976659
+38000  ekin = 5.26699752588952 |  erot = 3.72801268545681 | epot = -22.2775478090603 | etot = -13.282537597714
+39000  ekin = 5.37191151713971 |  erot = 3.65359747923658 | epot = -22.3080465940747 | etot = -13.2825375976984
+40000  ekin = 5.45746010972539 |  erot = 3.55633701588603 | epot = -22.2963347232318 | etot = -13.2825375976204
+41000  ekin = 5.52312188621432 |  erot = 3.43809872369872 | epot = -22.2437582073857 | etot = -13.2825375974727
+42000  ekin = 5.56872044212123 |  erot = 3.3013527933319 | epot = -22.1526108327172 | etot = -13.2825375972641
+43000  ekin = 5.59443660083054 |  erot = 3.14910305123766 | epot = -22.0260772490709 | etot = -13.2825375970027
+44000  ekin = 5.60078634437832 |  erot = 2.98477133565166 | epot = -21.8680952767313 | etot = -13.2825375967014
+45000  ekin = 5.58859564323475 |  erot = 2.81204277265363 | epot = -21.6831760122637 | etot = -13.2825375963753
+46000  ekin = 5.55896198288938 |  erot = 2.6346956216755 | epot = -21.4761952006028 | etot = -13.2825375960379
+47000  ekin = 5.51320424222089 |  erot = 2.45646420183095 | epot = -21.2522060397504 | etot = -13.2825375956985
+48000  ekin = 5.45280176988658 |  erot = 2.28095947573165 | epot = -21.0162988409789 | etot = -13.2825375953606
+49000  ekin = 5.37933239946777 |  erot = 2.11161440403301 | epot = -20.7734843985466 | etot = -13.2825375950459
+50000  ekin = 5.29440598595322 |  erot = 1.95156309993227 | epot = -20.5285066806364 | etot = -13.2825375947509
+51000  ekin = 5.19960275040365 |  erot = 1.80366343983081 | epot = -20.2858037847169 | etot = -13.2825375944825
+52000  ekin = 5.09244091535893 |  erot = 1.66034071449528 | epot = -20.0353192196147 | etot = -13.2825375897605
+53000  ekin = 5.00219098599359 |  erot = 1.54003539006203 | epot = -19.8247639698989 | etot = -13.2825375938433
+54000  ekin = 4.9005832952689 |  erot = 1.45132465506065 | epot = -19.6344455614694 | etot = -13.2825376111398
+55000  ekin = 4.70838087935279 |  erot = 1.38368494594859 | epot = -19.374603433669 | etot = -13.2825376083676
+56000  ekin = 4.44064498303654 |  erot = 1.42525549496225 | epot = -19.1484380668512 | etot = -13.2825375888524
+57000  ekin = 4.28012764787381 |  erot = 1.59067222265449 | epot = -19.1533374833608 | etot = -13.2825376128325
+58000  ekin = 4.17606446205197 |  erot = 1.69269591419354 | epot = -19.1512979674153 | etot = -13.2825375911698
+59000  ekin = 4.06748012934537 |  erot = 1.75788112721229 | epot = -19.107898847714 | etot = -13.2825375911564
+60000  ekin = 3.95448823476477 |  erot = 1.84391663061692 | epot = -19.0809424565338 | etot = -13.2825375911521
+61000  ekin = 3.83840387031379 |  erot = 1.95003019237122 | epot = -19.0709716537089 | etot = -13.2825375910239
+62000  ekin = 3.72130809963139 |  erot = 2.0750170389528 | epot = -19.0788627296236 | etot = -13.2825375910394
+63000  ekin = 3.60440089033071 |  erot = 2.21773397929691 | epot = -19.1046724606766 | etot = -13.282537591049
+64000  ekin = 3.4889862142993 |  erot = 2.37695650761868 | epot = -19.148480312971 | etot = -13.282537591053
+65000  ekin = 3.37647880025376 |  erot = 2.55140907448341 | epot = -19.2104254657956 | etot = -13.2825375910584
+66000  ekin = 3.26833067403449 |  erot = 2.73974236804954 | epot = -19.2906106331586 | etot = -13.2825375910746
+67000  ekin = 3.16594788215649 |  erot = 2.94047174698095 | epot = -19.388957220252 | etot = -13.2825375911146
+68000  ekin = 3.0706053161234 |  erot = 3.15188029478479 | epot = -19.5050232021006 | etot = -13.2825375911924
+69000  ekin = 2.98334905059876 |  erot = 3.37190853325425 | epot = -19.6377951751748 | etot = -13.2825375913218
+70000  ekin = 2.90492955397934 |  erot = 3.59802295152821 | epot = -19.7854900970212 | etot = -13.2825375915136
+71000  ekin = 2.8357237632926 |  erot = 3.82715608397267 | epot = -19.9454174390302 | etot = -13.282537591765
+72000  ekin = 2.77568510799032 |  erot = 4.05569348668108 | epot = -20.1139161867756 | etot = -13.2825375921042
+73000  ekin = 2.72437405649554 |  erot = 4.27929863267833 | epot = -20.2862102816544 | etot = -13.2825375924805
+74000  ekin = 2.68098943200971 |  erot = 4.49340310246777 | epot = -20.4569301273593 | etot = -13.2825375928818
+75000  ekin = 2.64445309406174 |  erot = 4.69339307185924 | epot = -20.6203837591928 | etot = -13.2825375932718
+76000  ekin = 2.6135541520603 |  erot = 4.87501053155987 | epot = -20.7711022772319 | etot = -13.2825375936117
+77000  ekin = 2.58710084062325 |  erot = 5.03478939171986 | epot = -20.9044278262174 | etot = -13.2825375938743
+78000  ekin = 2.56403853914047 |  erot = 5.17029283960992 | epot = -21.0168689727791 | etot = -13.2825375940288
+79000  ekin = 2.54361120788205 |  erot = 5.28037161018718 | epot = -21.1065204121483 | etot = -13.2825375940791
+80000  ekin = 2.52540527324235 |  erot = 5.36512720853055 | epot = -21.1730700758027 | etot = -13.2825375940298
+81000  ekin = 2.50929384303282 |  erot = 5.42576598242984 | epot = -21.2175974194024 | etot = -13.2825375939398
+82000  ekin = 2.49524917644569 |  erot = 5.46414530531101 | epot = -21.2419320755729 | etot = -13.2825375938162
+83000  ekin = 2.48334269593095 |  erot = 5.4824203292205 | epot = -21.2483006188452 | etot = -13.2825375936938
+84000  ekin = 2.47365997802566 |  erot = 5.48271691205612 | epot = -21.2389144836699 | etot = -13.2825375935881
+85000  ekin = 2.46626808184741 |  erot = 5.46691083839012 | epot = -21.2157165137403 | etot = -13.2825375935028
+86000  ekin = 2.46123154184209 |  erot = 5.43653398177587 | epot = -21.1803031170847 | etot = -13.2825375934667
+87000  ekin = 2.45852093879021 |  erot = 5.39265692383558 | epot = -21.1337154560128 | etot = -13.282537593387
+88000  ekin = 2.45840646060141 |  erot = 5.33627030736318 | epot = -21.0772143612568 | etot = -13.2825375932922
+89000  ekin = 2.46146480126854 |  erot = 5.26838646846911 | epot = -21.012388863175 | etot = -13.2825375934373
+90000  ekin = 2.46773177835907 |  erot = 5.18930366181577 | epot = -20.9395730335201 | etot = -13.2825375933453
+91000  ekin = 2.47726011905689 |  erot = 5.09951749277907 | epot = -20.8593152050603 | etot = -13.2825375932243
+92000  ekin = 2.4907426196288 |  erot = 5.00022791911722 | epot = -20.7735081318261 | etot = -13.2825375930801
+93000  ekin = 2.50902833057334 |  erot = 4.89281259013229 | epot = -20.6843785136299 | etot = -13.2825375929243
+94000  ekin = 2.53301288183049 |  erot = 4.77876912035663 | epot = -20.5943195949551 | etot = -13.282537592768
+95000  ekin = 2.56354598704884 |  erot = 4.6596420581637 | epot = -20.5057256378358 | etot = -13.2825375926232
+96000  ekin = 2.60133194738592 |  erot = 4.53693642149458 | epot = -20.4208059613811 | etot = -13.2825375925006
+97000  ekin = 2.6468471253709 |  erot = 4.41204173729102 | epot = -20.341426455067 | etot = -13.2825375924051
+98000  ekin = 2.70029551800313 |  erot = 4.28619503995253 | epot = -20.2690281502933 | etot = -13.2825375923376
+99000  ekin = 2.76159183076374 |  erot = 4.1604816375425 | epot = -20.2046110606011 | etot = -13.2825375922949
+100000  ekin = 2.83036874776577 |  erot = 4.0358752301046 | epot = -20.1487815701413 | etot = -13.2825375922709
+101000  ekin = 2.90599845693998 |  erot = 3.9133007754067 | epot = -20.101836824607 | etot = -13.2825375922603
+102000  ekin = 2.98761606367611 |  erot = 3.79369343963891 | epot = -20.0638470955759 | etot = -13.2825375922608
+103000  ekin = 3.07413620026815 |  erot = 3.67802597580122 | epot = -20.0346997683425 | etot = -13.2825375922731
+104000  ekin = 3.16426099663664 |  erot = 3.5672897363664 | epot = -20.0140883253055 | etot = -13.2825375923024
+105000  ekin = 3.25648344622817 |  erot = 3.46242766269347 | epot = -20.0014487012771 | etot = -13.2825375923554
+106000  ekin = 3.34909407537385 |  erot = 3.36423261094233 | epot = -19.995864278755 | etot = -13.2825375924388
+107000  ekin = 3.44019930697686 |  erot = 3.27323316283083 | epot = -19.9959700623653 | etot = -13.2825375925576
+108000  ekin = 3.52775814523643 |  erot = 3.18959025645848 | epot = -19.9998859944077 | etot = -13.2825375927128
+109000  ekin = 3.6096400910426 |  erot = 3.11302339299944 | epot = -20.005201076944 | etot = -13.282537592902
+110000  ekin = 3.6837038852456 |  erot = 3.04277828887611 | epot = -20.0090197672392 | etot = -13.2825375931175
+111000  ekin = 3.74789440567239 |  erot = 2.97764201100065 | epot = -20.008074010021 | etot = -13.2825375933479
+112000  ekin = 3.80035415830488 |  erot = 2.91600823448545 | epot = -19.998899986368 | etot = -13.2825375935777
+113000  ekin = 3.83954489146462 |  erot = 2.8559933088985 | epot = -19.9780757941509 | etot = -13.2825375937878
+114000  ekin = 3.86437452036879 |  erot = 2.79560177874322 | epot = -19.9425138930679 | etot = -13.2825375939559
+115000  ekin = 3.87432139555512 |  erot = 2.7329343736022 | epot = -19.8897933632162 | etot = -13.2825375940589
+116000  ekin = 3.86954570193501 |  erot = 2.66642221950647 | epot = -19.8185055155167 | etot = -13.2825375940752
+117000  ekin = 3.85097050791437 |  erot = 2.59505981730791 | epot = -19.7285679191994 | etot = -13.2825375939772
+118000  ekin = 3.82031843896425 |  erot = 2.5186641606976 | epot = -19.6215201934443 | etot = -13.2825375937824
+119000  ekin = 3.78008379969966 |  erot = 2.43788144963801 | epot = -19.5005028428247 | etot = -13.282537593487
+120000  ekin = 3.73339325084474 |  erot = 2.35417060362146 | epot = -19.3701014475778 | etot = -13.2825375931116
+121000  ekin = 3.68379362023552 |  erot = 2.26974086129434 | epot = -19.2360720742189 | etot = -13.282537592689
+122000  ekin = 3.63497633455493 |  erot = 2.187331073511 | epot = -19.1048450003246 | etot = -13.2825375922586
+123000  ekin = 3.59047168903083 |  erot = 2.10992442969239 | epot = -18.9829337105828 | etot = -13.2825375918596
+124000  ekin = 3.55336069064751 |  erot = 2.04044947797503 | epot = -18.8763477601473 | etot = -13.2825375915248
+125000  ekin = 3.52605275648501 |  erot = 1.98151529341901 | epot = -18.7901056411792 | etot = -13.2825375912752
+126000  ekin = 3.51088386083619 |  erot = 1.93492307727733 | epot = -18.7283445290526 | etot = -13.2825375909391
+127000  ekin = 3.51016542665117 |  erot = 1.90135594382251 | epot = -18.6940589614207 | etot = -13.282537590947
+128000  ekin = 3.52366007691443 |  erot = 1.88146923500183 | epot = -18.6876669021169 | etot = -13.2825375902006
+129000  ekin = 3.52804447870926 |  erot = 1.87939379818771 | epot = -18.6899759099317 | etot = -13.2825376330347
+130000  ekin = 3.3912172753683 |  erot = 1.9537535440301 | epot = -18.6275084102333 | etot = -13.2825375908349
+131000  ekin = 3.51597185423426 |  erot = 2.06600773707507 | epot = -18.8645172230942 | etot = -13.2825376317848
+132000  ekin = 3.65680948155317 |  erot = 2.09675964820366 | epot = -19.0361067214645 | etot = -13.2825375917077
+133000  ekin = 3.7826089844419 |  erot = 2.11778864665351 | epot = -19.1829352240661 | etot = -13.2825375929707
+134000  ekin = 3.90291219401812 |  erot = 2.13993246768579 | epot = -19.3253822549305 | etot = -13.2825375932266
+135000  ekin = 4.01307253292161 |  erot = 2.16317596346837 | epot = -19.4587860898094 | etot = -13.2825375934194
+136000  ekin = 4.10942813981098 |  erot = 2.18779054238556 | epot = -19.5797562757542 | etot = -13.2825375935576
+137000  ekin = 4.18918244084745 |  erot = 2.21413018926333 | epot = -19.6858502237394 | etot = -13.2825375936286
+138000  ekin = 4.2505518072554 |  erot = 2.24252417705063 | epot = -19.7756135779478 | etot = -13.2825375936417
+139000  ekin = 4.29264193993074 |  erot = 2.27334414892585 | epot = -19.8485236824507 | etot = -13.2825375935941
+140000  ekin = 4.3154298106947 |  erot = 2.30704736065629 | epot = -19.9050147648385 | etot = -13.2825375934876
+141000  ekin = 4.31969657449578 |  erot = 2.34420108979774 | epot = -19.9464352576252 | etot = -13.2825375933317
+142000  ekin = 4.30689625825177 |  erot = 2.38546661972142 | epot = -19.9749004711159 | etot = -13.2825375931427
+143000  ekin = 4.27897643633862 |  erot = 2.43154322469966 | epot = -19.9930572539773 | etot = -13.282537592939
+144000  ekin = 4.23817759048806 |  erot = 2.48305254316461 | epot = -20.0037677263992 | etot = -13.2825375927466
+145000  ekin = 4.18683687366753 |  erot = 2.54040585524244 | epot = -20.009780321492 | etot = -13.2825375925821
+146000  ekin = 4.12722437776044 |  erot = 2.60369949546926 | epot = -20.0134614656893 | etot = -13.2825375924596
+147000  ekin = 4.06142641942185 |  erot = 2.67262771534978 | epot = -20.0165917271585 | etot = -13.2825375923869
+148000  ekin = 3.99128035690908 |  erot = 2.74643868481997 | epot = -20.020256634094 | etot = -13.282537592365
+149000  ekin = 3.91835859675011 |  erot = 2.82393987441806 | epot = -20.0248360635573 | etot = -13.2825375923891
+150000  ekin = 3.84399502540833 |  erot = 2.90355368904256 | epot = -20.0300863068997 | etot = -13.2825375924488
+151000  ekin = 3.76934462696621 |  erot = 2.98342057410539 | epot = -20.0353027936016 | etot = -13.28253759253
+152000  ekin = 3.69546503896268 |  erot = 3.06154297168208 | epot = -20.0395456032601 | etot = -13.2825375926153
+153000  ekin = 3.62340677772804 |  erot = 3.13595781467784 | epot = -20.0419021850934 | etot = -13.2825375926875
+154000  ekin = 3.55429442921638 |  erot = 3.20491770297356 | epot = -20.0417497249215 | etot = -13.2825375927316
+155000  ekin = 3.48935808553542 |  erot = 3.267033764948 | epot = -20.0389294432276 | etot = -13.2825375927442
+156000  ekin = 3.42995719397451 |  erot = 3.32146386703958 | epot = -20.0339586537004 | etot = -13.2825375926863
+157000  ekin = 3.37758377439308 |  erot = 3.3680769357291 | epot = -20.0281983027503 | etot = -13.2825375926282
+158000  ekin = 3.32977839475207 |  erot = 3.40502394976649 | epot = -20.0173399361884 | etot = -13.2825375916698
+159000  ekin = 3.28790229188182 |  erot = 3.43232801111001 | epot = -20.0027678906269 | etot = -13.2825375876351
+160000  ekin = 3.28279951728226 |  erot = 3.4645745488256 | epot = -20.0299116571476 | etot = -13.2825375910398
+161000  ekin = 3.29006841785755 |  erot = 3.48756894666592 | epot = -20.060174952488 | etot = -13.2825375879645
+162000  ekin = 3.30320279764929 |  erot = 3.5006454181618 | epot = -20.0863858038415 | etot = -13.2825375880305
+163000  ekin = 3.3268044536015 |  erot = 3.5070397924055 | epot = -20.1163818341639 | etot = -13.2825375881569
+164000  ekin = 3.35978204864461 |  erot = 3.50639799900104 | epot = -20.1487176359757 | etot = -13.2825375883301
+165000  ekin = 3.40052448161875 |  erot = 3.49807859199056 | epot = -20.181140662133 | etot = -13.2825375885237
+166000  ekin = 3.44710440323471 |  erot = 3.48135096319333 | epot = -20.2109929551299 | etot = -13.2825375887019
+167000  ekin = 3.49756483136592 |  erot = 3.45565303648324 | epot = -20.2357554566773 | etot = -13.2825375888282
+168000  ekin = 3.55023572858368 |  erot = 3.42084325030349 | epot = -20.2536165677586 | etot = -13.2825375888714
+169000  ekin = 3.60406985696714 |  erot = 3.37750569995069 | epot = -20.2641131456955 | etot = -13.2825375887777
+170000  ekin = 3.41798406778751 |  erot = 3.07782048145922 | epot = -19.778342066862 | etot = -13.2825375176153
+171000  ekin = 3.24552871157498 |  erot = 2.73637390316101 | epot = -19.2644400103033 | etot = -13.2825373955674
+172000  ekin = 3.78367855050775 |  erot = 3.07274537488996 | epot = -20.1389614956815 | etot = -13.2825375702838
+173000  ekin = 4.03457273059295 |  erot = 3.18336469108423 | epot = -20.5004749222008 | etot = -13.2825375005236
+174000  ekin = 4.14002439985893 |  erot = 3.16763893899956 | epot = -20.5902008391742 | etot = -13.2825375003158
+175000  ekin = 4.24061478727453 |  erot = 3.15086312051272 | epot = -20.6740154078936 | etot = -13.2825375001064
+176000  ekin = 4.33750550891526 |  erot = 3.13552610061259 | epot = -20.7555691095042 | etot = -13.2825374999763
+177000  ekin = 4.43118634626137 |  erot = 3.12342668205163 | epot = -20.8371505282951 | etot = -13.2825374999821
+178000  ekin = 4.52112038535783 |  erot = 3.11516996838801 | epot = -20.9188278538849 | etot = -13.282537500139
+179000  ekin = 4.60569122910417 |  erot = 3.10997891303252 | epot = -20.998207642551 | etot = -13.2825375004143
+180000  ekin = 4.68248742105047 |  erot = 3.1058753404107 | epot = -21.0709002621979 | etot = -13.2825375007368
+181000  ekin = 4.74885008880596 |  erot = 3.10016969122731 | epot = -21.1315572810529 | etot = -13.2825375010196
+182000  ekin = 4.8025200424072 |  erot = 3.09010778323257 | epot = -21.1751653268254 | etot = -13.2825375011856
+183000  ekin = 4.84185836209202 |  erot = 3.07355401450771 | epot = -21.1979498780484 | etot = -13.2825375014487
+184000  ekin = 4.86305938218088 |  erot = 3.04972947015888 | epot = -21.1953263537842 | etot = -13.2825375014444
+185000  ekin = 4.86484048379678 |  erot = 3.01830532387275 | epot = -21.1656833089538 | etot = -13.2825375012843
+186000  ekin = 4.84781115921716 |  erot = 2.97987576046156 | epot = -21.1102244206809 | etot = -13.2825375010021
+187000  ekin = 4.81357764335378 |  erot = 2.93597501879657 | epot = -21.0320901627985 | etot = -13.2825375006482
+188000  ekin = 4.76439584097053 |  erot = 2.8887503176224 | epot = -20.9356836588659 | etot = -13.282537500273
+189000  ekin = 4.70282021343345 |  erot = 2.84056846871519 | epot = -20.8259261820667 | etot = -13.282537499918
+190000  ekin = 4.63141632940784 |  erot = 2.79367442377921 | epot = -20.7076282527974 | etot = -13.2825374996104
+191000  ekin = 4.55257205219614 |  erot = 2.74995133907631 | epot = -20.5850608906324 | etot = -13.28253749936
+192000  ekin = 4.4684144513739 |  erot = 2.71080835143519 | epot = -20.461760301973 | etot = -13.2825374991639
+193000  ekin = 4.38080987485654 |  erot = 2.67717312167521 | epot = -20.3405204955454 | etot = -13.2825374990136
+194000  ekin = 4.29140314493119 |  erot = 2.64952891334815 | epot = -20.223469557183 | etot = -13.2825374989037
+195000  ekin = 4.20164846020117 |  erot = 2.62793199519477 | epot = -20.1121179542326 | etot = -13.2825374988367
+196000  ekin = 4.11279973688578 |  erot = 2.61197297306555 | epot = -20.0073102087732 | etot = -13.2825374988219
+197000  ekin = 4.02585897192346 |  erot = 2.6006960732789 | epot = -19.9090925440713 | etot = -13.2825374988689
+198000  ekin = 3.94151021740631 |  erot = 2.59254113732279 | epot = -19.8165888537068 | etot = -13.2825374989777
+199000  ekin = 3.8600892057151 |  erot = 2.58539978552207 | epot = -19.7280264903664 | etot = -13.2825374991292
+200000  ekin = 3.78163650515432 |  erot = 2.57685633277492 | epot = -19.641030337214 | etot = -13.2825374992847
+201000  ekin = 3.70604145366902 |  erot = 2.56461316993936 | epot = -19.5531921230034 | etot = -13.2825374993951
+202000  ekin = 3.63323784111755 |  erot = 2.54700321074615 | epot = -19.4627785512822 | etot = -13.2825374994185
+203000  ekin = 3.56337600429993 |  erot = 2.52342549129483 | epot = -19.3693389949304 | etot = -13.2825374993357
+204000  ekin = 3.49690618989434 |  erot = 2.49455276327548 | epot = -19.2739964523247 | etot = -13.2825374991549
+205000  ekin = 3.4345533876734 |  erot = 2.46224574346295 | epot = -19.1793366300441 | etot = -13.2825374989078
+206000  ekin = 3.37721205721461 |  erot = 2.42921548153362 | epot = -19.0889650373856 | etot = -13.2825374986374
+207000  ekin = 3.32580575275846 |  erot = 2.39854397251164 | epot = -19.0068872236569 | etot = -13.2825374983868
+208000  ekin = 3.28114891016592 |  erot = 2.3731881465479 | epot = -18.9368745549049 | etot = -13.2825374981911
+209000  ekin = 3.24383236357031 |  erot = 2.35556506548857 | epot = -18.881934927133 | etot = -13.2825374980741
+210000  ekin = 3.21413821976384 |  erot = 2.34727297364657 | epot = -18.8439486914573 | etot = -13.2825374980469
+211000  ekin = 3.1919920439607 |  erot = 2.34895966766535 | epot = -18.8234892097349 | etot = -13.2825374981088
+212000  ekin = 3.17695628121283 |  erot = 2.36032147203272 | epot = -18.8198152514957 | etot = -13.2825374982501
+213000  ekin = 3.16826455951627 |  erot = 2.3802017195472 | epot = -18.8310037775173 | etot = -13.2825374984538
+214000  ekin = 3.16489343854745 |  erot = 2.40676052174862 | epot = -18.8541914589943 | etot = -13.2825374986982
+215000  ekin = 3.16566474352266 |  erot = 2.43769738040411 | epot = -18.8858996228842 | etot = -13.2825374989574
+216000  ekin = 3.16936807503371 |  erot = 2.47051711067938 | epot = -18.922422684916 | etot = -13.2825374992029
+217000  ekin = 3.16266988026928 |  erot = 2.47868467133945 | epot = -18.9238920507811 | etot = -13.2825374991723
+218000  ekin = 3.17835235865462 |  erot = 2.45704329444748 | epot = -18.9179331413782 | etot = -13.2825374882761
+219000  ekin = 3.26524817202182 |  erot = 2.48120766962804 | epot = -19.0289933444494 | etot = -13.2825375027995
+220000  ekin = 3.3108366379572 |  erot = 2.50602061547593 | epot = -19.0993947418604 | etot = -13.2825374884273
+221000  ekin = 3.33748530919814 |  erot = 2.52276996124463 | epot = -19.1427927588605 | etot = -13.2825374884177
+222000  ekin = 3.36243211589585 |  erot = 2.53668587910087 | epot = -19.1816554833759 | etot = -13.2825374883791
+223000  ekin = 3.38541896904289 |  erot = 2.54888617169885 | epot = -19.2168426290795 | etot = -13.2825374883378
+224000  ekin = 3.40625812508042 |  erot = 2.56049920868685 | epot = -19.2492948220808 | etot = -13.2825374883136
+225000  ekin = 3.42484722909655 |  erot = 2.57234499865789 | epot = -19.2797297160694 | etot = -13.2825374883149
+226000  ekin = 3.44121067431426 |  erot = 2.5847203663376 | epot = -19.3084685289965 | etot = -13.2825374883446
+227000  ekin = 3.45552721377372 |  erot = 2.59730386680816 | epot = -19.3353685689828 | etot = -13.2825374884009
+228000  ekin = 3.46810974282108 |  erot = 2.60916931207508 | epot = -19.3598165433769 | etot = -13.2825374884807
+229000  ekin = 3.47932676313057 |  erot = 2.61888809507148 | epot = -19.3807523467825 | etot = -13.2825374885804
+230000  ekin = 3.48948003513572 |  erot = 2.62469570471801 | epot = -19.3967132285493 | etot = -13.2825374886956
+231000  ekin = 3.49867242979287 |  erot = 2.62469374220123 | epot = -19.4059036608136 | etot = -13.2825374888195
+232000  ekin = 3.50671171842553 |  erot = 2.61706130327851 | epot = -19.4063105106456 | etot = -13.2825374889415
+233000  ekin = 3.51309701132019 |  erot = 2.60026316425614 | epot = -19.3958976646192 | etot = -13.2825374890429
+234000  ekin = 3.51712117494225 |  erot = 2.57326085610047 | epot = -19.3729195201389 | etot = -13.2825374890961
+235000  ekin = 3.51809173982046 |  erot = 2.53573892922922 | epot = -19.336368158117 | etot = -13.2825374890673
+236000  ekin = 3.51562949139228 |  erot = 2.48833922691179 | epot = -19.2865062072283 | etot = -13.2825374889242
+237000  ekin = 3.50996386129181 |  erot = 2.43285732073755 | epot = -19.2253586706778 | etot = -13.2825374886484
+238000  ekin = 3.50212794781223 |  erot = 2.37232394343651 | epot = -19.1569893794947 | etot = -13.2825374882459
+239000  ekin = 3.49397580570105 |  erot = 2.3108975006263 | epot = -19.0874107940784 | etot = -13.282537487751
+240000  ekin = 3.48799489984471 |  erot = 2.25353771706539 | epot = -19.0240701041317 | etot = -13.2825374872216
+241000  ekin = 3.48694744152127 |  erot = 2.20549386842306 | epot = -18.9749787966723 | etot = -13.2825374867279
+242000  ekin = 3.4934176974057 |  erot = 2.17169223103266 | epot = -18.947647414778 | etot = -13.2825374863397
+243000  ekin = 3.50935803683896 |  erot = 2.15612557817141 | epot = -18.9480211011254 | etot = -13.282537486115
+244000  ekin = 3.53571412219025 |  erot = 2.16133426987283 | epot = -18.9795858781565 | etot = -13.2825374860934
+245000  ekin = 3.57218201231882 |  erot = 2.18803987534321 | epot = -19.0427593739541 | etot = -13.2825374862921
+246000  ekin = 3.61712090977394 |  erot = 2.23496626996872 | epot = -19.1346246664479 | etot = -13.2825374867053
+247000  ekin = 3.66762313707291 |  erot = 2.29886938892395 | epot = -19.2490300132999 | etot = -13.282537487303
+248000  ekin = 3.71973304097767 |  erot = 2.37479253662205 | epot = -19.3770630656317 | etot = -13.282537488032
+249000  ekin = 3.76879884759244 |  erot = 2.45655776432051 | epot = -19.5078941007293 | etot = -13.2825374888163
+250000  ekin = 3.80993596354176 |  erot = 2.5374803002976 | epot = -19.6299537534029 | etot = -13.2825374895636
+251000  ekin = 3.83856187827227 |  erot = 2.6112453760505 | epot = -19.7323447444996 | etot = -13.2825374901768
+252000  ekin = 3.85094160348931 |  erot = 2.67282602420732 | epot = -19.8063051182674 | etot = -13.2825374905708
+253000  ekin = 3.84466267221602 |  erot = 2.71927370140011 | epot = -19.8464738643058 | etot = -13.2825374906897
+254000  ekin = 3.81895334833917 |  erot = 2.75020964906172 | epot = -19.8517004879211 | etot = -13.2825374905202
+255000  ekin = 3.77477712370886 |  erot = 2.76789565653784 | epot = -19.8252102703423 | etot = -13.2825374900956
+256000  ekin = 3.71467746908689 |  erot = 2.7768542145932 | epot = -19.7740691731695 | etot = -13.2825374894894
+257000  ekin = 3.64239785971663 |  erot = 2.78310854270393 | epot = -19.7080438912214 | etot = -13.2825374888008
+258000  ekin = 3.56234912667125 |  erot = 2.79319020432275 | epot = -19.6380768191301 | etot = -13.2825374881361
+259000  ekin = 3.47902170398649 |  erot = 2.81309489223277 | epot = -19.5746540838101 | etot = -13.2825374875908
+260000  ekin = 3.39644765746229 |  erot = 2.84735592157313 | epot = -19.5263410662708 | etot = -13.2825374872354
+261000  ekin = 3.31779785755677 |  erot = 2.89836390677638 | epot = -19.4986992514409 | etot = -13.2825374871077
+262000  ekin = 3.24516405277705 |  erot = 2.96601202360051 | epot = -19.4937135635853 | etot = -13.2825374872077
+263000  ekin = 3.179546945306 |  erot = 3.04771661067476 | epot = -19.5098010434848 | etot = -13.2825374875041
+264000  ekin = 3.12100159498149 |  erot = 3.13875568824824 | epot = -19.5422947711671 | etot = -13.2825374879374
+265000  ekin = 3.06890996951173 |  erot = 3.23291804297549 | epot = -19.5843655009186 | etot = -13.2825374884314
+266000  ekin = 3.02230555156918 |  erot = 3.3233525253047 | epot = -19.6281955657826 | etot = -13.2825374889087
+267000  ekin = 2.98016989218907 |  erot = 3.40345614747432 | epot = -19.6661635289706 | etot = -13.2825374893072
+268000  ekin = 2.94163501488653 |  erot = 3.46763177350614 | epot = -19.6918042779846 | etot = -13.2825374895919
+269000  ekin = 2.90604069318559 |  erot = 3.5117562623884 | epot = -19.7003344453572 | etot = -13.2825374897832
+270000  ekin = 2.87284037255953 |  erot = 3.53329819601925 | epot = -19.688676058427 | etot = -13.2825374898482
+271000  ekin = 2.8415668881788 |  erot = 3.53141495904858 | epot = -19.6555193370572 | etot = -13.2825374898299
+272000  ekin = 2.81169493920591 |  erot = 3.50673144119824 | epot = -19.6009638701438 | etot = -13.2825374897396
+273000  ekin = 2.78262532285067 |  erot = 3.46115906465187 | epot = -19.5263218770816 | etot = -13.282537489579
+274000  ekin = 2.75380981305629 |  erot = 3.39781487150763 | epot = -19.4341621738888 | etot = -13.2825374893249
+275000  ekin = 2.7249735792436 |  erot = 3.32097131771962 | epot = -19.3284823859411 | etot = -13.2825374889778
+276000  ekin = 2.6963100293489 |  erot = 3.23585259467393 | epot = -19.2147001125781 | etot = -13.2825374885553
+277000  ekin = 2.66855210196835 |  erot = 3.14826501869141 | epot = -19.0993546087612 | etot = -13.2825374881014
+278000  ekin = 2.64286719085315 |  erot = 3.06403640806022 | epot = -18.9894410865903 | etot = -13.282537487677
+279000  ekin = 2.62061028223249 |  erot = 2.98836162249181 | epot = -18.8915093920665 | etot = -13.2825374873422
+280000  ekin = 2.60303022005452 |  erot = 2.92520891289514 | epot = -18.810776620089 | etot = -13.2825374871393
+281000  ekin = 2.59103448458187 |  erot = 2.87693253510413 | epot = -18.7505045067671 | etot = -13.2825374870811
+282000  ekin = 2.58508390620669 |  erot = 2.84417540765184 | epot = -18.7117968010092 | etot = -13.2825374871506
+283000  ekin = 2.58523135936813 |  erot = 2.82606103956109 | epot = -18.6938298862392 | etot = -13.2825374873099
+284000  ekin = 2.59126091870129 |  erot = 2.82059473157291 | epot = -18.6943931377889 | etot = -13.2825374875147
+285000  ekin = 2.60284631077899 |  erot = 2.82514472712939 | epot = -18.7105285256372 | etot = -13.2825374877289
+286000  ekin = 2.61964775974011 |  erot = 2.83687342635554 | epot = -18.7390586740297 | etot = -13.2825374879341
+287000  ekin = 2.6416789431732 |  erot = 2.85285066093716 | epot = -18.7770670922847 | etot = -13.2825374881743
+288000  ekin = 2.6687167813734 |  erot = 2.8702293010975 | epot = -18.8214835708707 | etot = -13.2825374883998
+289000  ekin = 2.69931643718338 |  erot = 2.88698660757789 | epot = -18.8688405333582 | etot = -13.282537488597
+290000  ekin = 2.73194963658688 |  erot = 2.90163654912622 | epot = -18.9161236744781 | etot = -13.282537488765
+291000  ekin = 2.76502957907631 |  erot = 2.91324911168519 | epot = -18.9608161796562 | etot = -13.2825374888947
+292000  ekin = 2.79700561900786 |  erot = 2.92149576190804 | epot = -19.0010388698871 | etot = -13.2825374889712
+293000  ekin = 2.82654239554868 |  erot = 2.92669002283791 | epot = -19.0357699073648 | etot = -13.2825374889783
+294000  ekin = 2.85272969462551 |  erot = 2.92951972788748 | epot = -19.064786911459 | etot = -13.282537488946
+295000  ekin = 2.87508597590273 |  erot = 2.9311082644752 | epot = -19.0887317291887 | etot = -13.2825374888108
+296000  ekin = 2.8937804752686 |  erot = 2.93349300132756 | epot = -19.1098109651871 | etot = -13.2825374885909
+297000  ekin = 2.90976516785128 |  erot = 2.93912517174271 | epot = -19.1314278279134 | etot = -13.2825374883194
+298000  ekin = 2.92469477926885 |  erot = 2.95047845944604 | epot = -19.1577107267523 | etot = -13.2825374880374
+299000  ekin = 2.94065805823525 |  erot = 2.96967690612477 | epot = -19.192872452154 | etot = -13.282537487794
+300000  ekin = 2.95980003469444 |  erot = 2.99812642991887 | epot = -19.2404639522491 | etot = -13.2825374876358
+301000  ekin = 2.9839127297722 |  erot = 3.03621252497576 | epot = -19.3026627423455 | etot = -13.2825374875976
+302000  ekin = 3.01408971368584 |  erot = 3.08312901017938 | epot = -19.3797562115566 | etot = -13.2825374876914
+303000  ekin = 3.05053302665562 |  erot = 3.13689255668877 | epot = -19.4699630712467 | etot = -13.2825374879023
+304000  ekin = 3.08584972584791 |  erot = 3.19556015973973 | epot = -19.563947375247 | etot = -13.2825374896594
+305000  ekin = 3.11890909070429 |  erot = 3.26281224727038 | epot = -19.6642588266134 | etot = -13.2825374886387
+306000  ekin = 3.16699270587699 |  erot = 3.33070506272307 | epot = -19.7802352601689 | etot = -13.2825374915688
+307000  ekin = 3.22023032257454 |  erot = 3.3799777181521 | epot = -19.8827455298078 | etot = -13.2825374890812
+308000  ekin = 3.2726873966337 |  erot = 3.41969099128558 | epot = -19.974915877149 | etot = -13.2825374892298
+309000  ekin = 3.32280425481262 |  erot = 3.44976402097258 | epot = -20.0551057651207 | etot = -13.2825374893356
+310000  ekin = 3.36903652740989 |  erot = 3.46970323071698 | epot = -20.1212772475628 | etot = -13.282537489436
+311000  ekin = 3.40972253534481 |  erot = 3.47940229945176 | epot = -20.1716623243629 | etot = -13.2825374895663
+312000  ekin = 3.44308129109209 |  erot = 3.47898447383071 | epot = -20.2046032544282 | etot = -13.2825374895054
+313000  ekin = 3.46879202758971 |  erot = 3.47087869841085 | epot = -20.2222082156542 | etot = -13.2825374896536
+314000  ekin = 3.48565385463582 |  erot = 3.45582059749585 | epot = -20.2240119419411 | etot = -13.2825374898094
+315000  ekin = 3.49216313291107 |  erot = 3.43373104095289 | epot = -20.2084316637861 | etot = -13.2825374899221
+316000  ekin = 3.4873621330349 |  erot = 3.4048256725594 | epot = -20.1747252955317 | etot = -13.2825374899373
+317000  ekin = 3.4699413250759 |  erot = 3.36841330847627 | epot = -20.1208921250426 | etot = -13.2825374914904
+318000  ekin = 3.43614022048349 |  erot = 3.32066657788322 | epot = -20.0393442896741 | etot = -13.2825374913073
+319000  ekin = 3.38694293952412 |  erot = 3.26364910698136 | epot = -19.933129537441 | etot = -13.2825374909355
+320000  ekin = 3.32506744212997 |  erot = 3.20113650606391 | epot = -19.8087414386369 | etot = -13.282537490443
+321000  ekin = 3.25415482891508 |  erot = 3.13766117543029 | epot = -19.6743534942649 | etot = -13.2825374899195
+322000  ekin = 3.17813669787313 |  erot = 3.07780020747427 | epot = -19.5384743947971 | etot = -13.2825374894497
+323000  ekin = 3.10066688251982 |  erot = 3.0254908818081 | epot = -19.4086952534143 | etot = -13.2825374890864
+324000  ekin = 3.02479637479388 |  erot = 2.98355122494391 | epot = -19.2908850885811 | etot = -13.2825374888433
+325000  ekin = 2.95294332411383 |  erot = 2.95347420684896 | epot = -19.1889550196676 | etot = -13.2825374887048
+326000  ekin = 2.88706743997792 |  erot = 2.93544936652566 | epot = -19.1050542951497 | etot = -13.2825374886462
+327000  ekin = 2.82887581624799 |  erot = 2.92851219862454 | epot = -19.0399255035216 | etot = -13.2825374886491
+328000  ekin = 2.77990830068301 |  erot = 2.93074772300687 | epot = -18.9931935123953 | etot = -13.2825374887054
+329000  ekin = 2.74145002280153 |  erot = 2.9395401663855 | epot = -18.9635276779975 | etot = -13.2825374888105
+330000  ekin = 2.71432845550434 |  erot = 2.95189909643542 | epot = -18.948765040893 | etot = -13.2825374889532
+331000  ekin = 2.69870867087714 |  erot = 2.96486608415688 | epot = -18.9461122441487 | etot = -13.2825374891147
+332000  ekin = 2.69398517732769 |  erot = 2.97593512180702 | epot = -18.9524577884083 | etot = -13.2825374892736
+333000  ekin = 2.69881348537541 |  erot = 2.98337443171444 | epot = -18.9647254065019 | etot = -13.282537489412
+334000  ekin = 2.71127609678388 |  erot = 2.98637176000176 | epot = -18.9801853463025 | etot = -13.2825374895168
+335000  ekin = 2.72916096429869 |  erot = 2.9850116550983 | epot = -18.9967101089713 | etot = -13.2825374895743
+336000  ekin = 2.75032164400772 |  erot = 2.98016551096382 | epot = -19.0130246445397 | etot = -13.2825374895682
+337000  ekin = 2.77304615866046 |  erot = 2.97336445321142 | epot = -19.0289481013616 | etot = -13.2825374894897
+338000  ekin = 2.79631213711493 |  erot = 2.96664518651861 | epot = -19.0454948129846 | etot = -13.2825374893511
+339000  ekin = 2.81982513095444 |  erot = 2.96230352229829 | epot = -19.0646661424439 | etot = -13.2825374891912
+340000  ekin = 2.84381599358321 |  erot = 2.96250923740585 | epot = -19.0888627200581 | etot = -13.282537489069
+341000  ekin = 2.86861716322387 |  erot = 2.96879944354266 | epot = -19.1199540958289 | etot = -13.2825374890623
+342000  ekin = 2.8942330530774 |  erot = 2.9815983091965 | epot = -19.1583688514559 | etot = -13.282537489182
+343000  ekin = 2.92230469127694 |  erot = 3.00151195978259 | epot = -19.2063541396131 | etot = -13.2825374885536
+344000  ekin = 2.95328542679254 |  erot = 3.02739469587761 | epot = -19.263217611886 | etot = -13.2825374892158
+345000  ekin = 2.98288076792924 |  erot = 3.0539773023115 | epot = -19.319395560126 | etot = -13.2825374898853
+346000  ekin = 3.00683622806662 |  erot = 3.07579634903604 | epot = -19.3651700675394 | etot = -13.2825374904367
+347000  ekin = 3.02168203920098 |  erot = 3.08832269782129 | epot = -19.3925422278017 | etot = -13.2825374907794
+348000  ekin = 3.02528371459624 |  erot = 3.08873432783917 | epot = -19.3965555333216 | etot = -13.2825374908862
+349000  ekin = 3.01708434472178 |  erot = 3.07610751269672 | epot = -19.3757293482069 | etot = -13.2825374907884
+350000  ekin = 2.99803087494797 |  erot = 3.05108999688778 | epot = -19.3316583623806 | etot = -13.2825374905448
+351000  ekin = 2.97033325354683 |  erot = 3.0153936212866 | epot = -19.2682643650312 | etot = -13.2825374901978
+352000  ekin = 2.9375545389088 |  erot = 2.97175102427437 | epot = -19.1918430530028 | etot = -13.2825374898196
+353000  ekin = 2.90330530002109 |  erot = 2.9229126111419 | epot = -19.1087554005707 | etot = -13.2825374894077
+354000  ekin = 2.87126755833817 |  erot = 2.8717032112567 | epot = -19.0255082585642 | etot = -13.2825374889693
+355000  ekin = 2.8452063966084 |  erot = 2.82119115452554 | epot = -18.9489350396508 | etot = -13.2825374885168
+356000  ekin = 2.8287863971617 |  erot = 2.77463213289955 | epot = -18.8859560181414 | etot = -13.2825374880802
+357000  ekin = 2.82589501110838 |  erot = 2.73507904234315 | epot = -18.8435115424251 | etot = -13.2825374889736
+358000  ekin = 2.83567543256236 |  erot = 2.69990343571512 | epot = -18.8181163574533 | etot = -13.2825374891758
+359000  ekin = 2.85413863003171 |  erot = 2.66477535390693 | epot = -18.8014514734629 | etot = -13.2825374895243
+360000  ekin = 2.87797108635789 |  erot = 2.62716069413247 | epot = -18.7876692705243 | etot = -13.2825374900339
+361000  ekin = 2.90295419334349 |  erot = 2.58324525246655 | epot = -18.7687369364383 | etot = -13.2825374906282
+362000  ekin = 2.92446718933245 |  erot = 2.52862237257584 | epot = -18.7356270530339 | etot = -13.2825374911256
+363000  ekin = 2.93848759933288 |  erot = 2.4598916464099 | epot = -18.6809167370418 | etot = -13.282537491299
+364000  ekin = 2.94271150164537 |  erot = 2.37661313123448 | epot = -18.6018621239963 | etot = -13.2825374911165
+365000  ekin = 2.93600170081407 |  erot = 2.28250131434272 | epot = -18.5010405056271 | etot = -13.2825374904703
+366000  ekin = 2.91934189957468 |  erot = 2.18525996401723 | epot = -18.3871393531676 | etot = -13.2825374895757
+367000  ekin = 2.89548895825523 |  erot = 2.09468885645295 | epot = -18.272715303391 | etot = -13.2825374886828
+368000  ekin = 2.86763306547941 |  erot = 2.02026878405696 | epot = -18.170439337522 | etot = -13.2825374879856
+369000  ekin = 2.83845106986062 |  erot = 1.96931673437145 | epot = -18.0903052917991 | etot = -13.282537487567
+370000  ekin = 2.80963551309293 |  erot = 1.9461845593661 | epot = -18.0383575598726 | etot = -13.2825374874135
+371000  ekin = 2.78188668089845 |  erot = 1.95235490032886 | epot = -18.0167790686903 | etot = -13.282537487463
+372000  ekin = 2.75518266190969 |  erot = 1.98699478725925 | epot = -18.0247149368153 | etot = -13.2825374876464
+373000  ekin = 2.72912880528294 |  erot = 2.04757125854723 | epot = -18.059237551743 | etot = -13.2825374879128
+374000  ekin = 2.7032481730958 |  erot = 2.13030562163336 | epot = -18.116091282967 | etot = -13.2825374882379
+375000  ekin = 2.67714701016783 |  erot = 2.230398201263 | epot = -18.190082700051 | etot = -13.2825374886202
+376000  ekin = 2.65054772278835 |  erot = 2.34206662745015 | epot = -18.2751518393088 | etot = -13.2825374890703
+377000  ekin = 2.6232286660267 |  erot = 2.4585298333916 | epot = -18.3642959890073 | etot = -13.282537489589
+378000  ekin = 2.59495135703951 |  erot = 2.57214449993273 | epot = -18.4496333471167 | etot = -13.2825374901445
+379000  ekin = 2.56546707826761 |  erot = 2.67491697597518 | epot = -18.5229215449019 | etot = -13.2825374906591
+380000  ekin = 2.5346614309634 |  erot = 2.75950320018496 | epot = -18.5767021221684 | etot = -13.28253749102
+381000  ekin = 2.50280930121805 |  erot = 2.820545199185 | epot = -18.6058919915259 | etot = -13.2825374911229
+382000  ekin = 2.470812727732 |  erot = 2.85587907291203 | epot = -18.6092292915694 | etot = -13.2825374909253
+383000  ekin = 2.44026108011508 |  erot = 2.86702983654261 | epot = -18.5898284071357 | etot = -13.282537490478
+384000  ekin = 2.41324034479816 |  erot = 2.85867137366513 | epot = -18.5544492083667 | etot = -13.2825374899034
+385000  ekin = 2.39197367794907 |  erot = 2.83724859059171 | epot = -18.5117597578793 | etot = -13.2825374893386
+386000  ekin = 2.37848037079664 |  erot = 2.80936838549805 | epot = -18.4703862451731 | etot = -13.2825374888784
+387000  ekin = 2.37440773877127 |  erot = 2.78057799552109 | epot = -18.4375232228463 | etot = -13.282537488554
+388000  ekin = 2.38106033998957 |  erot = 2.75482980994791 | epot = -18.4184276382837 | etot = -13.2825374883462
+389000  ekin = 2.39952694728403 |  erot = 2.73455852134344 | epot = -18.4166229568446 | etot = -13.2825374882171
+390000  ekin = 2.43075796801616 |  erot = 2.72108399954165 | epot = -18.4343794556986 | etot = -13.2825374881408
+391000  ekin = 2.47547758104241 |  erot = 2.71503282253302 | epot = -18.4730478916951 | etot = -13.2825374881197
+392000  ekin = 2.53389941336453 |  erot = 2.7165760791739 | epot = -18.5330129807221 | etot = -13.2825374881837
+393000  ekin = 2.60531467139695 |  erot = 2.72543162367493 | epot = -18.6132837834427 | etot = -13.2825374883708
+394000  ekin = 2.68770614221252 |  erot = 2.74072420161865 | epot = -18.7109678325333 | etot = -13.2825374887021
+395000  ekin = 2.77757589911151 |  erot = 2.76089277951452 | epot = -18.8210061677825 | etot = -13.2825374891565
+396000  ekin = 2.87012638573488 |  erot = 2.78383015196109 | epot = -18.9364940273617 | etot = -13.2825374896658
+397000  ekin = 2.95979968457167 |  erot = 2.80730760068494 | epot = -19.049644775395 | etot = -13.2825374901384
+398000  ekin = 3.04101675292653 |  erot = 2.82953067572568 | epot = -19.1530849191508 | etot = -13.2825374904986
+399000  ekin = 3.10335323688597 |  erot = 2.84223393463616 | epot = -19.228124720834 | etot = -13.2825375493118
+400000  ekin = 3.10435999780448 |  erot = 2.68059016645162 | epot = -19.0674876235106 | etot = -13.2825374592545
+401000  ekin = 3.39309095567053 |  erot = 2.6399790010433 | epot = -19.3156074940173 | etot = -13.2825375373034
+402000  ekin = 3.44106634978254 |  erot = 2.65979071672222 | epot = -19.3833945765536 | etot = -13.2825375100489
+403000  ekin = 3.43207406395648 |  erot = 2.67998452071647 | epot = -19.3945960946571 | etot = -13.2825375099842
+404000  ekin = 3.40426891788004 |  erot = 2.70237957197844 | epot = -19.3891859997704 | etot = -13.2825375099119
+405000  ekin = 3.35933473415418 |  erot = 2.72607645469475 | epot = -19.3679486986676 | etot = -13.2825375098187
+406000  ekin = 3.29966540903968 |  erot = 2.74995079996642 | epot = -19.3321537187046 | etot = -13.2825375096985
+407000  ekin = 3.22823117978945 |  erot = 2.77286165528619 | epot = -19.2836303446341 | etot = -13.2825375095584
+408000  ekin = 3.1483591073605 |  erot = 2.79373949031154 | epot = -19.2246361071148 | etot = -13.2825375094427
+409000  ekin = 3.06351542880808 |  erot = 2.81131469887469 | epot = -19.1573676369864 | etot = -13.2825375093037
+410000  ekin = 2.97699949578463 |  erot = 2.8246267920136 | epot = -19.0841637969997 | etot = -13.2825375092014
+411000  ekin = 2.89165449988321 |  erot = 2.83289882079081 | epot = -19.007090829806 | etot = -13.282537509132
+412000  ekin = 2.80978906685915 |  erot = 2.83549592234132 | epot = -18.9278224982724 | etot = -13.2825375090719
+413000  ekin = 2.73325536963672 |  erot = 2.83215388790773 | epot = -18.8479467665295 | etot = -13.2825375089851
+414000  ekin = 2.66364879693787 |  erot = 2.82325639295092 | epot = -18.7694426987271 | etot = -13.2825375088383
+415000  ekin = 2.60253860594386 |  erot = 2.81004531903034 | epot = -18.6951214335909 | etot = -13.2825375086167
+416000  ekin = 2.55161661467894 |  erot = 2.79464631188373 | epot = -18.6288004348987 | etot = -13.2825375083361
+417000  ekin = 2.51265407607916 |  erot = 2.77984605492258 | epot = -18.5750376413351 | etot = -13.2825375103333
+418000  ekin = 2.4733460400696 |  erot = 2.77799997552928 | epot = -18.5338835235814 | etot = -13.2825375079825
+419000  ekin = 2.44559608968299 |  erot = 2.79655231011318 | epot = -18.5246859081161 | etot = -13.2825375083199
+420000  ekin = 2.44884495810883 |  erot = 2.8127677686639 | epot = -18.5441502345376 | etot = -13.2825375077648
+421000  ekin = 2.47134322850907 |  erot = 2.8275658566971 | epot = -18.581446593281 | etot = -13.2825375080748
+422000  ekin = 2.50522487691509 |  erot = 2.84806830842189 | epot = -18.6358306938666 | etot = -13.2825375085297
+423000  ekin = 2.54673540362963 |  erot = 2.87162843047139 | epot = -18.7009013431387 | etot = -13.2825375090377
+424000  ekin = 2.59155452677409 |  erot = 2.89540834353099 | epot = -18.7695003797936 | etot = -13.2825375094885
+425000  ekin = 2.63549518710331 |  erot = 2.91724946462186 | epot = -18.8352821615182 | etot = -13.282537509793
+426000  ekin = 2.67515430282142 |  erot = 2.9363216769118 | epot = -18.8940134896421 | etot = -13.2825375099089
+427000  ekin = 2.70835356710237 |  erot = 2.95332774897657 | epot = -18.9442188259222 | etot = -13.2825375098433
+428000  ekin = 2.73429370856415 |  erot = 2.97029523904671 | epot = -18.9871264572452 | etot = -13.2825375096344
+429000  ekin = 2.75344687777166 |  erot = 2.99015713230311 | epot = -19.0261415194056 | etot = -13.2825375093308
+430000  ekin = 2.76726512075389 |  erot = 3.01631311482664 | epot = -19.0661157445654 | etot = -13.2825375089849
+431000  ekin = 2.77776520583174 |  erot = 3.05220345438128 | epot = -19.1125061688761 | etot = -13.282537508663
+432000  ekin = 2.78700254671475 |  erot = 3.10077153002521 | epot = -19.1703115851965 | etot = -13.2825375084566
+433000  ekin = 2.79644099945107 |  erot = 3.16368547120708 | epot = -19.2426639791351 | etot = -13.2825375084769
+434000  ekin = 2.80629528100655 |  erot = 3.24036053937453 | epot = -19.3291933292032 | etot = -13.2825375088222
+435000  ekin = 2.81503854861979 |  erot = 3.32707633254736 | epot = -19.4246523906905 | etot = -13.2825375095233
+436000  ekin = 2.81936003427121 |  erot = 3.41666372805949 | epot = -19.5185612728238 | etot = -13.2825375104931
+437000  ekin = 2.81480689570261 |  erot = 3.4992068109881 | epot = -19.5965512182087 | etot = -13.282537511518
+438000  ekin = 2.79709037799446 |  erot = 3.56380823491998 | epot = -19.6434361252458 | etot = -13.2825375123314
+439000  ekin = 2.76357573484127 |  erot = 3.60097663046949 | epot = -19.6470898780263 | etot = -13.2825375127155
+440000  ekin = 2.71419714341147 |  erot = 3.60475935377896 | epot = -19.6014940098203 | etot = -13.2825375126299
+441000  ekin = 2.65147586146302 |  erot = 3.5735068280095 | epot = -19.5075202016404 | etot = -13.2825375121679
+442000  ekin = 2.57978868208042 |  erot = 3.50949061111538 | epot = -19.3718168046633 | etot = -13.2825375114675
+443000  ekin = 2.5045655875428 |  erot = 3.41786741963772 | epot = -19.2049705178136 | etot = -13.2825375106331
+444000  ekin = 2.4318529905012 |  erot = 3.30558723791353 | epot = -19.0199777381389 | etot = -13.2825375097241
+445000  ekin = 2.36817510309247 |  erot = 3.18052048206526 | epot = -18.8312330939434 | etot = -13.2825375087857
+446000  ekin = 2.32036350430697 |  erot = 3.05081891042797 | epot = -18.6537199226 | etot = -13.2825375078651
+447000  ekin = 2.29507009388122 |  erot = 2.92434156857507 | epot = -18.5019491695335 | etot = -13.2825375070773
+448000  ekin = 2.29792306266074 |  erot = 2.80795199469404 | epot = -18.3884125638663 | etot = -13.2825375065115
+449000  ekin = 2.33256968728711 |  erot = 2.7069587718276 | epot = -18.3220659653791 | etot = -13.2825375062644
+450000  ekin = 2.39980570006952 |  erot = 2.62453468442755 | epot = -18.3068778908976 | etot = -13.2825375064006
+451000  ekin = 2.49706752601316 |  erot = 2.56128240619122 | epot = -18.340887439138 | etot = -13.2825375069336
+452000  ekin = 2.61842576959522 |  erot = 2.51510244033024 | epot = -18.4160657177069 | etot = -13.2825375077814
+453000  ekin = 2.75505822099767 |  erot = 2.4815699152751 | epot = -18.5191656452272 | etot = -13.2825375089544
+454000  ekin = 2.89583245289786 |  erot = 2.45420794645489 | epot = -18.6325779096516 | etot = -13.2825375102988
+455000  ekin = 3.02803920575135 |  erot = 2.42568753015633 | epot = -18.7362642475679 | etot = -13.2825375116602
+456000  ekin = 3.13847091958599 |  erot = 2.38932191986764 | epot = -18.8103303522241 | etot = -13.2825375127704
+457000  ekin = 3.21547363213364 |  erot = 2.34093725375183 | epot = -18.838948399153 | etot = -13.2825375132675
+458000  ekin = 3.2519255084935 |  erot = 2.28077893488055 | epot = -18.8152419562781 | etot = -13.282537512904
+459000  ekin = 3.24761130317629 |  erot = 2.2142990448528 | epot = -18.7444478597993 | etot = -13.2825375117702
+460000  ekin = 3.20922400631774 |  erot = 2.15086461862506 | epot = -18.6426261351955 | etot = -13.2825375102527
+461000  ekin = 3.14796311212567 |  erot = 2.10092694609436 | epot = -18.5314275669974 | etot = -13.2825375087774
+462000  ekin = 3.07634336772018 |  erot = 2.07329933809505 | epot = -18.4321802134275 | etot = -13.2825375076122
+463000  ekin = 3.00570913410551 |  erot = 2.0736740452441 | epot = -18.3619206862057 | etot = -13.2825375068561
+464000  ekin = 2.94485829968431 |  erot = 2.104311840005 | epot = -18.3317076462087 | etot = -13.2825375065194
+465000  ekin = 2.89946798282509 |  erot = 2.16425406359513 | epot = -18.3462595530094 | etot = -13.2825375065892
+466000  ekin = 2.87195252748384 |  erot = 2.24955307492882 | epot = -18.4040431094629 | etot = -13.2825375070502
+467000  ekin = 2.86158324929155 |  erot = 2.35338924278566 | epot = -18.4975099999498 | etot = -13.2825375078726
+468000  ekin = 2.86493243611462 |  erot = 2.46640127712313 | epot = -18.6138712220354 | etot = -13.2825375087976
+469000  ekin = 2.87700241085683 |  erot = 2.57824581699685 | epot = -18.7377857379574 | etot = -13.2825375101037
+470000  ekin = 2.89115454215717 |  erot = 2.6760619901597 | epot = -18.8497540436439 | etot = -13.2825375113271
+471000  ekin = 2.90087699699639 |  erot = 2.74765202472445 | epot = -18.9310665339225 | etot = -13.2825375122017
+472000  ekin = 2.90129360657261 |  erot = 2.78442288107442 | epot = -18.968254000156 | etot = -13.282537512509
+473000  ekin = 2.89014262488401 |  erot = 2.78350866548211 | epot = -18.9561888025525 | etot = -13.2825375121863
+474000  ekin = 2.86798455519513 |  erot = 2.74843722227868 | epot = -18.8989592888434 | etot = -13.2825375113696
+475000  ekin = 2.83751222123448 |  erot = 2.68789202058937 | epot = -18.8079417521561 | etot = -13.2825375103323
+476000  ekin = 2.80225697256735 |  erot = 2.6131130536835 | epot = -18.6979075356112 | etot = -13.2825375093603
+477000  ekin = 2.76525060538104 |  erot = 2.5351054311932 | epot = -18.5828935452201 | etot = -13.2825375086459
+478000  ekin = 2.72814283270942 |  erot = 2.46266477167759 | epot = -18.4733451126352 | etot = -13.2825375082482
+479000  ekin = 2.69099471856512 |  erot = 2.40160392944764 | epot = -18.3751361561287 | etot = -13.282537508116
+480000  ekin = 2.65266810495577 |  erot = 2.35496214915267 | epot = -18.2901677622972 | etot = -13.2825375081888
+481000  ekin = 2.61144235513308 |  erot = 2.32364519373199 | epot = -18.2176250571285 | etot = -13.2825375082635
+482000  ekin = 2.56577673011677 |  erot = 2.30767778315765 | epot = -18.1559920215987 | etot = -13.2825375083243
+483000  ekin = 2.51481850303814 |  erot = 2.3066085334913 | epot = -18.1039645448551 | etot = -13.2825375083257
+484000  ekin = 2.4583813285785 |  erot = 2.31984500682984 | epot = -18.0607638434006 | etot = -13.2825375079923
+485000  ekin = 2.37536403472682 |  erot = 2.30798475217265 | epot = -17.9658863028417 | etot = -13.2825375159423
+486000  ekin = 2.31029787366189 |  erot = 2.2748698765298 | epot = -17.8677052455195 | etot = -13.2825374953278
+487000  ekin = 2.35903895729104 |  erot = 2.35840823836807 | epot = -17.999984715744 | etot = -13.2825375200849
+488000  ekin = 2.35207405530543 |  erot = 2.45495770512307 | epot = -18.0895692764582 | etot = -13.2825375160297
+489000  ekin = 2.32025825392693 |  erot = 2.54616767543756 | epot = -18.1489634454321 | etot = -13.2825375160676
+490000  ekin = 2.29515153865843 |  erot = 2.64227715700559 | epot = -18.2199662119985 | etot = -13.2825375163345
+491000  ekin = 2.2772449984618 |  erot = 2.73950547065074 | epot = -18.2992879857204 | etot = -13.2825375166078
+492000  ekin = 2.26670396933619 |  erot = 2.83351832941017 | epot = -18.3827598156809 | etot = -13.2825375169346
+493000  ekin = 2.26314468313945 |  erot = 2.91977614256862 | epot = -18.4654583429805 | etot = -13.2825375172724
+494000  ekin = 2.26577113860128 |  erot = 2.99399214337922 | epot = -18.5423007995586 | etot = -13.2825375175781
+495000  ekin = 2.27355094490557 |  erot = 3.05259857148999 | epot = -18.6086870342097 | etot = -13.2825375178141
+496000  ekin = 2.28538641730899 |  erot = 3.09313022190335 | epot = -18.6610541571706 | etot = -13.2825375179582
+497000  ekin = 2.3002347482288 |  erot = 3.1144407210763 | epot = -18.6972129873049 | etot = -13.2825375179998
+498000  ekin = 2.3171936593925 |  erot = 3.11678508300488 | epot = -18.7165162603363 | etot = -13.2825375179389
+499000  ekin = 2.33554254161235 |  erot = 3.10178716719771 | epot = -18.7198672265934 | etot = -13.2825375177834
+500000  ekin = 2.31317350059265 |  erot = 3.05449093047628 | epot = -18.6502019677268 | etot = -13.2825375366579
+501000  ekin = 2.31231722972123 |  erot = 3.00810318076113 | epot = -18.6029579372101 | etot = -13.2825375267278
+502000  ekin = 2.3899963895355 |  erot = 2.98467042894116 | epot = -18.657204342111 | etot = -13.2825375236343
+503000  ekin = 2.41312387633379 |  erot = 2.93091691357846 | epot = -18.6265783132594 | etot = -13.2825375233471
+504000  ekin = 2.43600229237452 |  erot = 2.88130858481333 | epot = -18.5998484003212 | etot = -13.2825375231333
+505000  ekin = 2.45757791196529 |  erot = 2.8401186666586 | epot = -18.5802341016713 | etot = -13.2825375230474
+506000  ekin = 2.47627134224398 |  erot = 2.81025901806717 | epot = -18.5690678834509 | etot = -13.2825375231397
+507000  ekin = 2.48985246050699 |  erot = 2.79268587932984 | epot = -18.5650758632795 | etot = -13.2825375234427
+508000  ekin = 2.49542483825493 |  erot = 2.78597986937444 | epot = -18.5639422315766 | etot = -13.2825375239472
+509000  ekin = 2.48963204750428 |  erot = 2.78630577995571 | epot = -18.5584753520407 | etot = -13.2825375245807
+510000  ekin = 2.4691743887688 |  erot = 2.78796571282341 | epot = -18.5396776267959 | etot = -13.2825375252037
+511000  ekin = 2.43159454918128 |  erot = 2.78459744696608 | epot = -18.4987295217946 | etot = -13.2825375256472
+512000  ekin = 2.37609227916261 |  erot = 2.77073697944887 | epot = -18.4293667843926 | etot = -13.2825375257811
+513000  ekin = 2.30402039322225 |  erot = 2.74317280237148 | epot = -18.3297307211636 | etot = -13.2825375255699
+514000  ekin = 2.21884081242786 |  erot = 2.7015541486614 | epot = -18.2029324861651 | etot = -13.2825375250758
+515000  ekin = 2.12561338171218 |  erot = 2.64810551843191 | epot = -18.056256424559 | etot = -13.2825375244149
+516000  ekin = 2.03029958566718 |  erot = 2.58673985991495 | epot = -17.8995769692823 | etot = -13.2825375237002
+517000  ekin = 1.93914577197132 |  erot = 2.5220605431355 | epot = -17.7437438381168 | etot = -13.28253752301
+518000  ekin = 1.85826662413893 |  erot = 2.45858700715527 | epot = -17.5993911536849 | etot = -13.2825375223908
+519000  ekin = 1.79333215326611 |  erot = 2.40035341708905 | epot = -17.476223092216 | etot = -13.2825375218608
+520000  ekin = 1.74929005171215 |  erot = 2.35078235677519 | epot = -17.3826099299227 | etot = -13.2825375214353
+521000  ekin = 1.73007209347361 |  erot = 2.31266171841647 | epot = -17.3252713330271 | etot = -13.282537521137
+522000  ekin = 1.73822781685003 |  erot = 2.28811557190088 | epot = -17.3088809097447 | etot = -13.2825375209937
+523000  ekin = 1.77456624775216 |  erot = 2.27850834583591 | epot = -17.3356121146208 | etot = -13.2825375210327
+524000  ekin = 1.8379045851724 |  erot = 2.28429322274985 | epot = -17.4047353291923 | etot = -13.28253752127
+525000  ekin = 1.92500868751529 |  erot = 2.30484700359158 | epot = -17.5123932128129 | etot = -13.282537521706
+526000  ekin = 2.03075780261764 |  erot = 2.33833465322237 | epot = -17.6516299781653 | etot = -13.2825375223253
+527000  ekin = 2.14850843909257 |  erot = 2.38164040104111 | epot = -17.8126863632292 | etot = -13.2825375230955
+528000  ekin = 2.2706009665318 |  erot = 2.43041424714547 | epot = -17.9835527376429 | etot = -13.2825375239656
+529000  ekin = 2.38896012867467 |  erot = 2.47931387509597 | epot = -18.150811528629 | etot = -13.2825375248584
+530000  ekin = 2.4957694053979 |  erot = 2.52254117019752 | epot = -18.3008481012612 | etot = -13.2825375256658
+531000  ekin = 2.58420744224834 |  erot = 2.55472238423688 | epot = -18.4214673527446 | etot = -13.2825375262593
+532000  ekin = 2.64918587021021 |  erot = 2.57201883159204 | epot = -18.5037422283274 | etot = -13.2825375265252
+533000  ekin = 2.68793333158334 |  erot = 2.57313230806675 | epot = -18.5436031660632 | etot = -13.2825375264131
+534000  ekin = 2.7002120821811 |  erot = 2.55975253143246 | epot = -18.5425021395846 | etot = -13.2825375259711
+535000  ekin = 2.68802701636055 |  erot = 2.5361501485681 | epot = -18.5067146902622 | etot = -13.2825375253335
+536000  ekin = 2.65489019113613 |  erot = 2.50801671119336 | epot = -18.4454444269979 | etot = -13.2825375246684
+537000  ekin = 2.60490332064252 |  erot = 2.481023337825 | epot = -18.3684641825809 | etot = -13.2825375241133
+538000  ekin = 2.54198784535114 |  erot = 2.45965628954573 | epot = -18.2841816578421 | etot = -13.2825375229452
+539000  ekin = 2.47150013363699 |  erot = 2.44756195577151 | epot = -18.2015996123808 | etot = -13.2825375229723
+540000  ekin = 2.39647534123056 |  erot = 2.44525435897827 | epot = -18.124267223265 | etot = -13.2825375230561
+541000  ekin = 2.31786635163547 |  erot = 2.45130088246703 | epot = -18.0517047572224 | etot = -13.2825375231199
+542000  ekin = 2.23702678127242 |  erot = 2.46423888155736 | epot = -17.9838031859226 | etot = -13.2825375230928
+543000  ekin = 2.15612181944835 |  erot = 2.4831366740889 | epot = -17.9217960164714 | etot = -13.2825375229342
+544000  ekin = 2.07836492813028 |  erot = 2.50789688702757 | epot = -17.8687993378082 | etot = -13.2825375226504
+545000  ekin = 2.0079425836599 |  erot = 2.5391884088184 | epot = -17.8296685147796 | etot = -13.2825375223013
+546000  ekin = 1.94957099406152 |  erot = 2.57800819606447 | epot = -17.8101167121046 | etot = -13.2825375219786
+547000  ekin = 1.90776242425117 |  erot = 2.62501532095444 | epot = -17.8153152669927 | etot = -13.2825375217871
+548000  ekin = 1.88600984704774 |  erot = 2.67988146407457 | epot = -17.8484288329186 | etot = -13.2825375217963
+549000  ekin = 1.88615242684612 |  erot = 2.7409037562111 | epot = -17.90959370508 | etot = -13.2825375220228
+550000  ekin = 1.90811801075785 |  erot = 2.80501593008068 | epot = -17.9956714632668 | etot = -13.2825375224283
+551000  ekin = 1.95008337619707 |  erot = 2.8681680442257 | epot = -18.1007889433631 | etot = -13.2825375229403
+552000  ekin = 2.00893649348012 |  erot = 2.92590890431006 | epot = -18.2173829212704 | etot = -13.2825375234803
+553000  ekin = 2.08084803908336 |  erot = 2.97396311014114 | epot = -18.3373486732109 | etot = -13.2825375239864
+554000  ekin = 2.16178844740114 |  erot = 3.00865361320263 | epot = -18.452979585024 | etot = -13.2825375244202
+555000  ekin = 2.24792031028555 |  erot = 3.02713377655537 | epot = -18.5575916115995 | etot = -13.2825375247586
+556000  ekin = 2.3358895304513 |  erot = 3.02749801452678 | epot = -18.6459250699588 | etot = -13.2825375249808
+557000  ekin = 2.42273135016537 |  erot = 3.0079937814166 | epot = -18.7132626569264 | etot = -13.2825375253445
+558000  ekin = 2.50467530617043 |  erot = 2.96457109815147 | epot = -18.7517839296998 | etot = -13.2825375253779
+559000  ekin = 2.57989829545908 |  erot = 2.89795083555213 | epot = -18.7603866561733 | etot = -13.2825375251621
+560000  ekin = 2.64819333039288 |  erot = 2.81150114191978 | epot = -18.742231997059 | etot = -13.2825375247463
+561000  ekin = 2.7104101471449 |  erot = 2.71050571098959 | epot = -18.7034533823758 | etot = -13.2825375242413
+562000  ekin = 2.76764108182985 |  erot = 2.60142670489701 | epot = -18.6516053104994 | etot = -13.2825375237726
+563000  ekin = 2.8204133217691 |  erot = 2.4909454000306 | epot = -18.5938962452166 | etot = -13.2825375234169
+564000  ekin = 2.86835957175242 |  erot = 2.38512022714126 | epot = -18.536017322071 | etot = -13.2825375231773
+565000  ekin = 2.91050556249757 |  erot = 2.28886993106156 | epot = -18.481913016576 | etot = -13.2825375230169
+566000  ekin = 2.94583619535282 |  erot = 2.20572382115438 | epot = -18.4340975394231 | etot = -13.2825375229159
+567000  ekin = 2.97364576055568 |  erot = 2.13764971286302 | epot = -18.3938329963098 | etot = -13.2825375228911
+568000  ekin = 2.99348659090309 |  erot = 2.08490808296841 | epot = -18.360932196845 | etot = -13.2825375229735
+569000  ekin = 3.00487691646457 |  erot = 2.04604350397463 | epot = -18.3334579436043 | etot = -13.2825375231651
+570000  ekin = 3.00710556181106 |  erot = 2.01819764944608 | epot = -18.3078407346813 | etot = -13.2825375234241
+571000  ekin = 2.99930468666728 |  erot = 1.99774357921139 | epot = -18.2795857895585 | etot = -13.2825375236798
+572000  ekin = 2.98076231237764 |  erot = 1.98107714037278 | epot = -18.2443769766043 | etot = -13.2825375238539
+573000  ekin = 2.95134611354571 |  erot = 1.96535938859269 | epot = -18.1992430260208 | etot = -13.2825375238824
+574000  ekin = 2.91190615156914 |  erot = 1.94906161393782 | epot = -18.1435052892334 | etot = -13.2825375237264
+575000  ekin = 2.86455063783071 |  erot = 1.93223482559859 | epot = -18.079322986811 | etot = -13.2825375233817
+576000  ekin = 2.81270724054619 |  erot = 1.91646454104923 | epot = -18.0117093044799 | etot = -13.2825375228844
+577000  ekin = 2.76090536128439 |  erot = 1.9045038205141 | epot = -17.9479467041077 | etot = -13.2825375223092
+578000  ekin = 2.71428886858076 |  erot = 1.89991544416371 | epot = -17.8967418344083 | etot = -13.2825375216638
+579000  ekin = 2.67747364109253 |  erot = 1.90598531718256 | epot = -17.8659964795852 | etot = -13.2825375213101
+580000  ekin = 2.65399321096934 |  erot = 1.92422800253644 | epot = -17.8607587346238 | etot = -13.282537521118
+581000  ekin = 2.64614770784911 |  erot = 1.95489680824256 | epot = -17.883582037231 | etot = -13.2825375211393
+582000  ekin = 2.65445309232027 |  erot = 1.99685469220196 | epot = -17.9338453059165 | etot = -13.2825375213943
+583000  ekin = 2.67733631605306 |  erot = 2.04763712313085 | epot = -18.0075109610395 | etot = -13.2825375218556
+584000  ekin = 2.71054840601244 |  erot = 2.10372916960457 | epot = -18.0968150982853 | etot = -13.2825375226683
+585000  ekin = 2.74737763681928 |  erot = 2.16073411835811 | epot = -18.1906492785603 | etot = -13.282537523383
+586000  ekin = 2.7813786998355 |  erot = 2.21419390100359 | epot = -18.2781101248089 | etot = -13.2825375239698
+587000  ekin = 2.80697388603962 |  erot = 2.26053952382245 | epot = -18.3500509341984 | etot = -13.2825375243363
+588000  ekin = 2.82026432869703 |  erot = 2.29760845660022 | epot = -18.4004103097634 | etot = -13.2825375244661
+589000  ekin = 2.81926713936076 |  erot = 2.32471340247167 | epot = -18.4265180662398 | etot = -13.2825375244073
+590000  ekin = 2.80363912211435 |  erot = 2.34232144628174 | epot = -18.4284980926317 | etot = -13.2825375242356
+591000  ekin = 2.77414618244973 |  erot = 2.35158565792353 | epot = -18.4082693643883 | etot = -13.282537524015
+592000  ekin = 2.73214162068033 |  erot = 2.35397672704535 | epot = -18.3686558715069 | etot = -13.2825375237812
+593000  ekin = 2.67919893301821 |  erot = 2.35111989741865 | epot = -18.3128563539823 | etot = -13.2825375235455
+594000  ekin = 2.61691997575019 |  erot = 2.34478637079319 | epot = -18.2442438698508 | etot = -13.2825375233074
+595000  ekin = 2.54687226698967 |  erot = 2.33692048100541 | epot = -18.1663302710608 | etot = -13.2825375230657
+596000  ekin = 2.47060065847364 |  erot = 2.32961421031687 | epot = -18.0827523916134 | etot = -13.2825375228228
+597000  ekin = 2.38967001316585 |  erot = 2.32500896595718 | epot = -17.9972165017067 | etot = -13.2825375225837
+598000  ekin = 2.30571268082223 |  erot = 2.32515834060408 | epot = -17.9134085437803 | etot = -13.282537522354
+599000  ekin = 2.22046028550116 |  erot = 2.33189649118178 | epot = -17.8348942988225 | etot = -13.2825375221395
+600000  ekin = 2.13574370490705 |  erot = 2.34673734057022 | epot = -17.7650185674242 | etot = -13.2825375219469
+601000  ekin = 2.05345123937653 |  erot = 2.37080533030337 | epot = -17.7067940914646 | etot = -13.2825375217847
+602000  ekin = 1.97544542053429 |  erot = 2.40478648031343 | epot = -17.6627694225103 | etot = -13.2825375216626
+603000  ekin = 1.9034510520118 |  erot = 2.44889273156788 | epot = -17.6348813051703 | etot = -13.2825375215906
+604000  ekin = 1.83893895945378 |  erot = 2.50284547570514 | epot = -17.6243219567308 | etot = -13.2825375215719
+605000  ekin = 1.78304137655287 |  erot = 2.56590806869957 | epot = -17.6314869668566 | etot = -13.2825375216041
+606000  ekin = 1.736517005622 |  erot = 2.63697396084372 | epot = -17.6560284881414 | etot = -13.2825375216757
+607000  ekin = 1.69978182226254 |  erot = 2.71471645486191 | epot = -17.6970357988931 | etot = -13.2825375217686
+608000  ekin = 1.67299629743623 |  erot = 2.79777529958915 | epot = -17.7533091188892 | etot = -13.2825375218638
+609000  ekin = 1.65617951190665 |  erot = 2.88492902630375 | epot = -17.8236460601579 | etot = -13.2825375219475
+610000  ekin = 1.64931072740771 |  erot = 2.97519912008037 | epot = -17.9070473695038 | etot = -13.2825375220157
+611000  ekin = 1.65238727025306 |  erot = 3.06785620899647 | epot = -18.0027810013235 | etot = -13.2825375220739
+612000  ekin = 1.66542824834998 |  erot = 3.16233835695483 | epot = -18.1103041274379 | etot = -13.2825375221331
+613000  ekin = 1.68843555860806 |  erot = 3.25812385028217 | epot = -18.229096931095 | etot = -13.2825375222048
+614000  ekin = 1.72133601882631 |  erot = 3.35460405562833 | epot = -18.3584775967531 | etot = -13.2825375222984
+615000  ekin = 1.76392386055006 |  erot = 3.45098117167973 | epot = -18.4974425546512 | etot = -13.2825375224214
+616000  ekin = 1.81580855352879 |  erot = 3.54618284211553 | epot = -18.6445289182269 | etot = -13.2825375225826
+617000  ekin = 1.87635766444892 |  erot = 3.63876572292309 | epot = -18.7976609101672 | etot = -13.2825375227952
+618000  ekin = 1.94461656663335 |  erot = 3.72678561706335 | epot = -18.9539397067739 | etot = -13.2825375230772
+619000  ekin = 2.01919440946448 |  erot = 3.80764383017264 | epot = -19.1093757630845 | etot = -13.2825375234473
+620000  ekin = 2.09812821732459 |  erot = 3.87796751089518 | epot = -19.258633252134 | etot = -13.2825375239142
+621000  ekin = 2.17876896452369 |  erot = 3.9336243470245 | epot = -19.3949308360123 | etot = -13.2825375244641
+622000  ekin = 2.25776112944306 |  erot = 3.96997899371136 | epot = -19.5102776482054 | etot = -13.282537525051
+623000  ekin = 2.33118920319666 |  erot = 3.98244070312544 | epot = -19.5961674319216 | etot = -13.2825375255995
+624000  ekin = 2.39492361710553 |  erot = 3.96722578269959 | epot = -19.6446869258275 | etot = -13.2825375260223
+625000  ekin = 2.445122210933 |  erot = 3.92212025382369 | epot = -19.6497799910047 | etot = -13.282537526248
+626000  ekin = 2.47876984838125 |  erot = 3.84697362716387 | epot = -19.6082810017884 | etot = -13.2825375262432
+627000  ekin = 2.49411681790099 |  erot = 3.74375083248538 | epot = -19.5204051764041 | etot = -13.2825375260178
+628000  ekin = 2.49092177716844 |  erot = 3.61617309043397 | epot = -19.3896323932121 | etot = -13.2825375256096
+629000  ekin = 2.47048208783205 |  erot = 3.46915451631132 | epot = -19.2221741292085 | etot = -13.2825375250651
+630000  ekin = 2.43548970061162 |  erot = 3.30827690351569 | epot = -19.0263041285523 | etot = -13.282537524425
+631000  ekin = 2.38975948996613 |  erot = 3.13944249320995 | epot = -18.8117395069008 | etot = -13.2825375237248
+632000  ekin = 2.33785618698542 |  erot = 2.96869689909723 | epot = -18.5890906090837 | etot = -13.2825375230011
+633000  ekin = 2.28462964544115 |  erot = 2.80211551086663 | epot = -18.3692826786082 | etot = -13.2825375223005
+634000  ekin = 2.23467746223165 |  erot = 2.64563252187923 | epot = -18.1628475057907 | etot = -13.2825375216799
+635000  ekin = 2.15322765543132 |  erot = 2.47835094336846 | epot = -17.9141161495184 | etot = -13.2825375507186
+636000  ekin = 2.04549908133069 |  erot = 2.31412508405115 | epot = -17.6421616868109 | etot = -13.2825375214291
+637000  ekin = 2.11104805175097 |  erot = 2.29419960731515 | epot = -17.6877852052413 | etot = -13.2825375461752
+638000  ekin = 2.16990019917156 |  erot = 2.2679567393031 | epot = -17.7203944764658 | etot = -13.2825375379911
+639000  ekin = 2.15825321743296 |  erot = 2.17815663923705 | epot = -17.618947382456 | etot = -13.282537525786
+640000  ekin = 2.18911467644369 |  erot = 2.15600946831685 | epot = -17.627661668769 | etot = -13.2825375240084
+641000  ekin = 2.26653815123457 |  erot = 2.22106973674797 | epot = -17.7701454241734 | etot = -13.2825375361909
+642000  ekin = 2.3144469471055 |  erot = 2.28426426145084 | epot = -17.8812487361676 | etot = -13.2825375276113
+643000  ekin = 2.32966846054207 |  erot = 2.32625113868682 | epot = -17.9384571273534 | etot = -13.2825375281245
+644000  ekin = 2.33971908606118 |  erot = 2.36941556717976 | epot = -17.9916721817351 | etot = -13.2825375284942
+645000  ekin = 2.34497836839587 |  erot = 2.40804261253567 | epot = -18.0355585095904 | etot = -13.2825375286589
+646000  ekin = 2.34716147917123 |  erot = 2.43809135045114 | epot = -18.0677903582286 | etot = -13.2825375286062
+647000  ekin = 2.34901351981608 |  erot = 2.45765540472021 | epot = -18.0892064529145 | etot = -13.2825375283782
+648000  ekin = 2.35429037962735 |  erot = 2.46814608869922 | epot = -18.104973996447 | etot = -13.2825375281204
+649000  ekin = 2.36637490476275 |  erot = 2.47306901795835 | epot = -18.1219814507637 | etot = -13.2825375280426
+650000  ekin = 2.38594651024424 |  erot = 2.47280388235694 | epot = -18.1412879205825 | etot = -13.2825375279813
+651000  ekin = 2.41290732393566 |  erot = 2.46797500557286 | epot = -18.1634198574497 | etot = -13.2825375279412
+652000  ekin = 2.44657292409709 |  erot = 2.45942209570518 | epot = -18.1885325477104 | etot = -13.2825375279081
+653000  ekin = 2.48591189131261 |  erot = 2.44818643125859 | epot = -18.216635850432 | etot = -13.2825375278608
+654000  ekin = 2.52980786353021 |  erot = 2.43558904352257 | epot = -18.2479344348361 | etot = -13.2825375277833
+655000  ekin = 2.57725720746836 |  erot = 2.42329690336763 | epot = -18.2830916385098 | etot = -13.2825375276738
+656000  ekin = 2.62745567870598 |  erot = 2.41329334491405 | epot = -18.3232865511668 | etot = -13.2825375275468
+657000  ekin = 2.67977157736399 |  erot = 2.40771681185305 | epot = -18.3700259166474 | etot = -13.2825375274304
+658000  ekin = 2.73363379229086 |  erot = 2.40858022061921 | epot = -18.4247515402698 | etot = -13.2825375273597
+659000  ekin = 2.78837854459658 |  erot = 2.41741767328155 | epot = -18.4883337452466 | etot = -13.2825375273685
+660000  ekin = 2.84314536322858 |  erot = 2.43497153591091 | epot = -18.5606544265713 | etot = -13.2825375274319
+661000  ekin = 2.89550751715279 |  erot = 2.46002725149102 | epot = -18.6380722967303 | etot = -13.2825375280865
+662000  ekin = 2.93874528646413 |  erot = 2.48685588461621 | epot = -18.708138699778 | etot = -13.2825375286977
+663000  ekin = 2.9687171942415 |  erot = 2.51022783071497 | epot = -18.7614825541983 | etot = -13.2825375292419
+664000  ekin = 2.98246138427311 |  erot = 2.52516926734448 | epot = -18.7901681812018 | etot = -13.2825375295842
+665000  ekin = 2.97884445494023 |  erot = 2.52787955705445 | epot = -18.7892615416123 | etot = -13.2825375296177
+666000  ekin = 2.95920183353605 |  erot = 2.51661508434599 | epot = -18.7583544471906 | etot = -13.2825375293085
+667000  ekin = 2.92742550356365 |  erot = 2.49210329858316 | epot = -18.702066330864 | etot = -13.2825375287172
+668000  ekin = 2.88934250717656 |  erot = 2.45736670750009 | epot = -18.6292467426517 | etot = -13.282537527975
+669000  ekin = 2.85155010044156 |  erot = 2.41708074176435 | epot = -18.5511683694359 | etot = -13.28253752723
+670000  ekin = 2.82014314471955 |  erot = 2.37673699551223 | epot = -18.4794176668284 | etot = -13.2825375265966
+671000  ekin = 2.79977472961205 |  erot = 2.34183940273354 | epot = -18.4241516586146 | etot = -13.282537526269
+672000  ekin = 2.79293252634008 |  erot = 2.31695226011576 | epot = -18.3924223124527 | etot = -13.2825375259969
+673000  ekin = 2.80034442408037 |  erot = 2.30554472206325 | epot = -18.3884266720798 | etot = -13.2825375259361
+674000  ekin = 2.82129825256449 |  erot = 2.30955451981648 | epot = -18.4133902984753 | etot = -13.2825375260944
+675000  ekin = 2.85361934145821 |  erot = 2.32878748968739 | epot = -18.4649443576069 | etot = -13.2825375264613
+676000  ekin = 2.89394924995267 |  erot = 2.36084337707399 | epot = -18.5373301540152 | etot = -13.2825375269885
+677000  ekin = 2.93819888436731 |  erot = 2.40146056805032 | epot = -18.622196980004 | etot = -13.2825375275863
+678000  ekin = 2.98219881046511 |  erot = 2.44527797789796 | epot = -18.7100143165049 | etot = -13.2825375281419
+679000  ekin = 3.0224273551935 |  erot = 2.48684948025749 | epot = -18.7918143640021 | etot = -13.2825375285511
+680000  ekin = 3.05660821680256 |  erot = 2.52163649378434 | epot = -18.8607822393395 | etot = -13.2825375287526
+681000  ekin = 3.08399348184627 |  erot = 2.54671087858252 | epot = -18.913241889164 | etot = -13.2825375287352
+682000  ekin = 3.10527370304788 |  erot = 2.56103519408599 | epot = -18.9488464256748 | etot = -13.2825375285409
+683000  ekin = 3.12217420783238 |  erot = 2.56530128681684 | epot = -18.970013022889 | etot = -13.2825375282398
+684000  ekin = 3.13689854376774 |  erot = 2.56147023258304 | epot = -18.9809063042598 | etot = -13.282537527909
+685000  ekin = 3.1516175207619 |  erot = 2.55220833199615 | epot = -18.9863633803528 | etot = -13.2825375275947
+686000  ekin = 3.16825656288024 |  erot = 2.5404714195813 | epot = -18.9912655098718 | etot = -13.2825375274103
+687000  ekin = 3.18756268898112 |  erot = 2.52861508568613 | epot = -18.9987153019925 | etot = -13.2825375273252
+688000  ekin = 3.20935294724633 |  erot = 2.51834078646032 | epot = -19.0102312610592 | etot = -13.2825375273526
+689000  ekin = 3.232603857627 |  erot = 2.51058529363817 | epot = -19.0257266787599 | etot = -13.2825375274947
+690000  ekin = 3.25550449412986 |  erot = 2.50541094760363 | epot = -19.0434529694767 | etot = -13.2825375277432
+691000  ekin = 3.27559454461619 |  erot = 2.50196131507165 | epot = -19.0600933877637 | etot = -13.2825375280759
+692000  ekin = 3.29000453529088 |  erot = 2.49851988079962 | epot = -19.0710619445408 | etot = -13.2825375284503
+693000  ekin = 3.29579865376218 |  erot = 2.49273974858803 | epot = -19.0710759311567 | etot = -13.2825375288065
+694000  ekin = 3.29036742009323 |  erot = 2.48207188557003 | epot = -19.0549768347445 | etot = -13.2825375290813
+695000  ekin = 3.27176421105106 |  erot = 2.46431581831664 | epot = -19.018617558596 | etot = -13.2825375292283
+696000  ekin = 3.23887890273548 |  erot = 2.43812365834886 | epot = -18.9595400903186 | etot = -13.2825375292342
+697000  ekin = 3.19141377377666 |  erot = 2.40329594550704 | epot = -18.8772472483983 | etot = -13.2825375291146
+698000  ekin = 3.12971664175668 |  erot = 2.36079934043281 | epot = -18.7730535110947 | etot = -13.2825375289052
+699000  ekin = 3.05458980626054 |  erot = 2.31258576039904 | epot = -18.6497130952911 | etot = -13.2825375286315
+700000  ekin = 2.96718102298747 |  erot = 2.26139197208619 | epot = -18.511110523382 | etot = -13.2825375283083
+701000  ekin = 2.86896613295136 |  erot = 2.21057215459575 | epot = -18.3620758154883 | etot = -13.2825375279412
+702000  ekin = 2.76178671337415 |  erot = 2.16397434352371 | epot = -18.2082985844344 | etot = -13.2825375275365
+703000  ekin = 2.6478712031048 |  erot = 2.12574771744291 | epot = -18.0561564515416 | etot = -13.2825375309939
+704000  ekin = 2.52933762848166 |  erot = 2.08674637122766 | epot = -17.8986215283831 | etot = -13.2825375286737
+705000  ekin = 2.41679696536635 |  erot = 2.05664012325241 | epot = -17.7559746148874 | etot = -13.2825375262686
+706000  ekin = 2.30501007356423 |  erot = 2.0611587655127 | epot = -17.6487063635301 | etot = -13.2825375244532
+707000  ekin = 2.19269241365679 |  erot = 2.113750463821 | epot = -17.5889804021149 | etot = -13.2825375246371
+708000  ekin = 2.09960598348176 |  erot = 2.19681319891601 | epot = -17.57895670939 | etot = -13.2825375269922
+709000  ekin = 2.01320280623464 |  erot = 2.28016876647 | epot = -17.5759090980898 | etot = -13.2825375253852
+710000  ekin = 1.93302644427356 |  erot = 2.37473228784994 | epot = -17.5902962580752 | etot = -13.2825375259517
+711000  ekin = 1.85957279067715 |  erot = 2.47358324929754 | epot = -17.6156935666084 | etot = -13.2825375266337
+712000  ekin = 1.79282630268912 |  erot = 2.56690430142539 | epot = -17.642268131402 | etot = -13.2825375272875
+713000  ekin = 1.73341814876089 |  erot = 2.64462400340569 | epot = -17.6605796799123 | etot = -13.2825375277457
+714000  ekin = 1.68328438252143 |  erot = 2.69817364688335 | epot = -17.6639955572831 | etot = -13.2825375278783
+715000  ekin = 1.64594117648568 |  erot = 2.72207244107394 | epot = -17.6505511452113 | etot = -13.2825375276517
+716000  ekin = 1.62610172701181 |  erot = 2.71479815151566 | epot = -17.6234374056764 | etot = -13.282537527149
+717000  ekin = 1.62864489627545 |  erot = 2.67867233618631 | epot = -17.589854758993 | etot = -13.2825375265313
+718000  ekin = 1.65730138310094 |  erot = 2.6189183926284 | epot = -17.5587573016927 | etot = -13.2825375259634
+719000  ekin = 1.71360335058015 |  erot = 2.54235654223589 | epot = -17.5384974183669 | etot = -13.2825375255509
+720000  ekin = 1.79650653909672 |  erot = 2.45621436685583 | epot = -17.5352584312718 | etot = -13.2825375253192
+721000  ekin = 1.90273489852489 |  erot = 2.36731439641998 | epot = -17.5525868201814 | etot = -13.2825375252366
+722000  ekin = 2.02756635877135 |  erot = 2.28163864595547 | epot = -17.5917425299821 | etot = -13.2825375252553
+723000  ekin = 2.16566245424335 |  erot = 2.20411346294851 | epot = -17.6523134425365 | etot = -13.2825375253446
+724000  ekin = 2.31164907977026 |  erot = 2.13844446404667 | epot = -17.7326310693194 | etot = -13.2825375255025
+725000  ekin = 2.46036017286876 |  erot = 2.0869120441014 | epot = -17.8298097427178 | etot = -13.2825375257477
+726000  ekin = 2.60683496355671 |  erot = 2.05013619406281 | epot = -17.9395086837224 | etot = -13.2825375261029
+727000  ekin = 2.74622028398704 |  erot = 2.02690424050256 | epot = -18.0556620510616 | etot = -13.282537526572
+728000  ekin = 2.87374866259628 |  erot = 2.01419303066656 | epot = -18.1704792203877 | etot = -13.2825375271249
+729000  ekin = 2.98490085178579 |  erot = 2.00751009694371 | epot = -18.27494847642 | etot = -13.2825375276905
+730000  ekin = 3.07576690667731 |  erot = 2.00160558070566 | epot = -18.359910015553 | etot = -13.28253752817
+731000  ekin = 3.14351022574244 |  erot = 1.99146923020489 | epot = -18.4175169844133 | etot = -13.282537528466
+732000  ekin = 3.18676307284264 |  erot = 1.97337750697634 | epot = -18.4426781083327 | etot = -13.2825375285137
+733000  ekin = 3.20579220152253 |  erot = 1.9456870659553 | epot = -18.4340167957808 | etot = -13.282537528303
+734000  ekin = 3.20238921812918 |  erot = 1.90917251422492 | epot = -18.3940992602234 | etot = -13.2825375278693
+735000  ekin = 3.17951096479738 |  erot = 1.86680153237891 | epot = -18.3288500244819 | etot = -13.2825375273056
+736000  ekin = 3.14073865389039 |  erot = 1.8230058759971 | epot = -18.2462820565793 | etot = -13.2825375266918
+737000  ekin = 3.08984658437012 |  erot = 1.78292393032115 | epot = -18.1553080407961 | etot = -13.2825375261048
+738000  ekin = 3.03043228101277 |  erot = 1.75161934959083 | epot = -18.0645891562027 | etot = -13.2825375255991
+739000  ekin = 2.96566842757407 |  erot = 1.73346651117868 | epot = -17.9816724639599 | etot = -13.2825375252071
+740000  ekin = 2.89817088986259 |  erot = 1.73175552877345 | epot = -17.912463943576 | etot = -13.28253752494
+741000  ekin = 2.82995232211993 |  erot = 1.74850528634245 | epot = -17.8609951332633 | etot = -13.282537524801
+742000  ekin = 2.76247533972923 |  erot = 1.78434362386512 | epot = -17.8293564883915 | etot = -13.2825375247972
+743000  ekin = 2.69668176519633 |  erot = 1.83847103681881 | epot = -17.8176903269097 | etot = -13.2825375248946
+744000  ekin = 2.6331144461464 |  erot = 1.90875045568272 | epot = -17.8244024269328 | etot = -13.2825375251037
+745000  ekin = 2.5719649351672 |  erot = 1.99171779991018 | epot = -17.8462202604955 | etot = -13.2825375254181
+746000  ekin = 2.51311596152491 |  erot = 2.0826421561814 | epot = -17.8782956435303 | etot = -13.282537525824
+747000  ekin = 2.45621024026481 |  erot = 2.17571767245968 | epot = -17.9144654390156 | etot = -13.2825375262911
+748000  ekin = 2.4007641204603 |  erot = 2.26445242853415 | epot = -17.9477540757611 | etot = -13.2825375267666
+749000  ekin = 2.34635697390621 |  erot = 2.34231237598165 | epot = -17.9712068770626 | etot = -13.2825375271748
+750000  ekin = 2.29290375451926 |  erot = 2.40359513867759 | epot = -17.9790364206262 | etot = -13.2825375274293
+751000  ekin = 2.24097207239074 |  erot = 2.44437862835496 | epot = -17.9678882282051 | etot = -13.2825375274594
+752000  ekin = 2.19206377659927 |  erot = 2.46328788147024 | epot = -17.9378891852944 | etot = -13.2825375272249
+753000  ekin = 2.01910736680425 |  erot = 2.37844688257153 | epot = -17.6800917192355 | etot = -13.2825374698597
+754000  ekin = 2.03397419758721 |  erot = 2.38379927539831 | epot = -17.7003109699574 | etot = -13.2825374969719
+755000  ekin = 2.10287082583243 |  erot = 2.42269050537392 | epot = -17.808098775342 | etot = -13.2825374441357
+756000  ekin = 2.09556625459035 |  erot = 2.40575096267731 | epot = -17.7838546607744 | etot = -13.2825374435067
+757000  ekin = 2.11013463605079 |  erot = 2.39174642208689 | epot = -17.7844185011481 | etot = -13.2825374430104
+758000  ekin = 2.14991880608121 |  erot = 2.38537981475823 | epot = -17.8178360635602 | etot = -13.2825374427207
+759000  ekin = 2.21691275096553 |  erot = 2.38948785856312 | epot = -17.8889380522097 | etot = -13.2825374426811
+760000  ekin = 2.31141054899228 |  erot = 2.40468264922822 | epot = -17.9986306411391 | etot = -13.2825374429186
+761000  ekin = 2.43175472397619 |  erot = 2.42917556867249 | epot = -18.1434677360907 | etot = -13.282537443442
+762000  ekin = 2.57423243283704 |  erot = 2.45878794779634 | epot = -18.3155578248644 | etot = -13.2825374442311
+763000  ekin = 2.73317609373997 |  erot = 2.48721280702134 | epot = -18.5029263459876 | etot = -13.2825374452263
+764000  ekin = 2.90131643326679 |  erot = 2.50663479900723 | epot = -18.690488678594 | etot = -13.28253744632
+765000  ekin = 3.07040159566699 |  erot = 2.50879317366612 | epot = -18.8617322166939 | etot = -13.2825374473608
+766000  ekin = 3.23203071048149 |  erot = 2.48644536532744 | epot = -19.0010135239876 | etot = -13.2825374481786
+767000  ekin = 3.37856609507255 |  erot = 2.43498273995184 | epot = -19.0960862836549 | etot = -13.2825374486305
+768000  ekin = 3.50392633330507 |  erot = 2.35374465383522 | epot = -19.1402084357865 | etot = -13.2825374486462
+769000  ekin = 3.60408080015212 |  erot = 2.24656658386371 | epot = -19.1331848322651 | etot = -13.2825374482493
+770000  ekin = 3.67731902122504 |  erot = 2.12129309978206 | epot = -19.0811495685446 | etot = -13.2825374475374
+771000  ekin = 3.72500466537174 |  erot = 1.98803922980452 | epot = -18.9955813418785 | etot = -13.2825374467023
+772000  ekin = 3.73784328897891 |  erot = 1.84847100615872 | epot = -18.8688517432933 | etot = -13.2825374481557
+773000  ekin = 3.73518377850858 |  erot = 1.74399251375944 | epot = -18.761713737683 | etot = -13.2825374454149
+774000  ekin = 3.73326270400355 |  erot = 1.69319142559955 | epot = -18.7089915837464 | etot = -13.2825374541433
+775000  ekin = 3.70600761043796 |  erot = 1.6566239979388 | epot = -18.6451690563952 | etot = -13.2825374480184
+776000  ekin = 3.66620956029523 |  erot = 1.65229490555453 | epot = -18.6010419136787 | etot = -13.282537447829
+777000  ekin = 3.61649590749819 |  erot = 1.68124406448108 | epot = -18.5802774198126 | etot = -13.2825374478333
+778000  ekin = 3.55892172037955 |  erot = 1.74156460696009 | epot = -18.5830237753754 | etot = -13.2825374480357
+779000  ekin = 3.49505249872284 |  erot = 1.82861083535278 | epot = -18.6062007829277 | etot = -13.2825374488521
+780000  ekin = 3.42606052970244 |  erot = 1.93200454593087 | epot = -18.6406025252668 | etot = -13.2825374496335
+781000  ekin = 3.35141348725842 |  erot = 2.04005284573706 | epot = -18.6740037834645 | etot = -13.2825374504691
+782000  ekin = 3.2700234367696 |  erot = 2.14152553729048 | epot = -18.6940864252466 | etot = -13.2825374511865
+783000  ekin = 3.18141085684875 |  erot = 2.22636120811957 | epot = -18.690309516577 | etot = -13.2825374516087
+784000  ekin = 3.08656488529642 |  erot = 2.28735807349748 | epot = -18.6564604104105 | etot = -13.2825374516166
+785000  ekin = 2.98843914069599 |  erot = 2.32136711573499 | epot = -18.592343707635 | etot = -13.282537451204
+786000  ekin = 2.89178850824096 |  erot = 2.3295414984193 | epot = -18.5038674571453 | etot = -13.2825374504851
+787000  ekin = 2.8023307080712 |  erot = 2.31656731751225 | epot = -18.4014354752266 | etot = -13.2825374496432
+788000  ekin = 2.72556137551752 |  erot = 2.28924565772307 | epot = -18.2973444820957 | etot = -13.2825374488551
+789000  ekin = 2.6656985022175 |  erot = 2.25498711354848 | epot = -18.2032230640058 | etot = -13.2825374482399
+790000  ekin = 2.62507547599935 |  erot = 2.22062577794683 | epot = -18.1282387017979 | etot = -13.2825374478518
+791000  ekin = 2.60400664952963 |  erot = 2.19166523694291 | epot = -18.0782093341748 | etot = -13.2825374477022
+792000  ekin = 2.60095165935059 |  erot = 2.17186849882108 | epot = -18.0553576059557 | etot = -13.282537447784
+793000  ekin = 2.61278727243034 |  erot = 2.1630579474879 | epot = -18.0583826680031 | etot = -13.2825374480849
+794000  ekin = 2.63509078851047 |  erot = 2.16503786006958 | epot = -18.0826660971656 | etot = -13.2825374485855
+795000  ekin = 2.66245645585368 |  erot = 2.1756290014367 | epot = -18.1206229065374 | etot = -13.282537449247
+796000  ekin = 2.68895951870523 |  erot = 2.19088748025581 | epot = -18.1623844489478 | etot = -13.2825374499868
+797000  ekin = 2.70892452688332 |  erot = 2.2056406086122 | epot = -18.197102586158 | etot = -13.2825374506625
+798000  ekin = 2.71873874100197 |  erot = 2.21455364270924 | epot = -18.2158298332998 | etot = -13.2825374495886
+799000  ekin = 2.70000299973817 |  erot = 2.2105054534633 | epot = -18.1930459030985 | etot = -13.282537449897
+800000  ekin = 2.65392049094459 |  erot = 2.17300546859124 | epot = -18.1094633784201 | etot = -13.2825374188843
+801000  ekin = 2.82505345316557 |  erot = 2.13616134654269 | epot = -18.2437522542245 | etot = -13.2825374545162
+802000  ekin = 2.90470228885208 |  erot = 2.10953657420558 | epot = -18.2967762804394 | etot = -13.2825374173817
+803000  ekin = 2.96775259915972 |  erot = 2.08137573430732 | epot = -18.3316657516683 | etot = -13.2825374182013
+804000  ekin = 3.01419864043949 |  erot = 2.05336319944923 | epot = -18.3500992582319 | etot = -13.2825374183431
+805000  ekin = 3.03950260644552 |  erot = 2.02738087501351 | epot = -18.3494208998051 | etot = -13.2825374183461
+806000  ekin = 3.04147612131243 |  erot = 2.00524180159513 | epot = -18.3292553411016 | etot = -13.2825374181941
+807000  ekin = 3.02009152298814 |  erot = 1.98876426014739 | epot = -18.2913932010452 | etot = -13.2825374179097
+808000  ekin = 2.97716861753119 |  erot = 1.97979280799342 | epot = -18.2394988430722 | etot = -13.2825374175476
+809000  ekin = 2.91576405138726 |  erot = 1.98007542312432 | epot = -18.1783768916846 | etot = -13.282537417173
+810000  ekin = 2.83951999042134 |  erot = 1.99102014259852 | epot = -18.1130775498589 | etot = -13.282537416839
+811000  ekin = 2.75216924199515 |  erot = 2.01344070753323 | epot = -18.0481473661025 | etot = -13.2825374165741
+812000  ekin = 2.65727213726343 |  erot = 2.04739495988655 | epot = -17.987204513533 | etot = -13.282537416383
+813000  ekin = 2.55815479837528 |  erot = 2.09215794771562 | epot = -17.9328501623443 | etot = -13.2825374162534
+814000  ekin = 2.4579662372483 |  erot = 2.14630993623329 | epot = -17.8868135896497 | etot = -13.2825374161681
+815000  ekin = 2.35976627216073 |  erot = 2.20788718914275 | epot = -17.8501908774147 | etot = -13.2825374161112
+816000  ekin = 2.26657574981526 |  erot = 2.27454135627298 | epot = -17.8236545221636 | etot = -13.2825374160753
+817000  ekin = 2.18134946483051 |  erot = 2.3436713345316 | epot = -17.8075582154243 | etot = -13.2825374160622
+818000  ekin = 2.10686415434699 |  erot = 2.41251844145424 | epot = -17.8019200118806 | etot = -13.2825374160794
+819000  ekin = 2.04554497125477 |  erot = 2.47824070198672 | epot = -17.8063230893767 | etot = -13.2825374161352
+820000  ekin = 1.99927680186843 |  erot = 2.53799486411919 | epot = -17.8198090822204 | etot = -13.2825374162328
+821000  ekin = 1.96925307966866 |  erot = 2.58905270243613 | epot = -17.840843198472 | etot = -13.2825374163673
+822000  ekin = 1.95590272109404 |  erot = 2.62895986973405 | epot = -17.8674000073523 | etot = -13.2825374165242
+823000  ekin = 1.95890926741904 |  erot = 2.65572860619527 | epot = -17.8971752902976 | etot = -13.2825374166833
+824000  ekin = 1.977310461331 |  erot = 2.66804286174235 | epot = -17.9278907398948 | etot = -13.2825374168215
+825000  ekin = 2.00964945329754 |  erot = 2.66544750505568 | epot = -17.9576343752703 | etot = -13.2825374169171
+826000  ekin = 2.0541442314356 |  erot = 2.64849047615147 | epot = -17.9851721245422 | etot = -13.2825374169552
+827000  ekin = 2.10884212221679 |  erot = 2.61877894563757 | epot = -18.0101584847866 | etot = -13.2825374169322
+828000  ekin = 2.17172935733676 |  erot = 2.57890618406652 | epot = -18.0331729582634 | etot = -13.2825374168601
+829000  ekin = 2.24077304904372 |  erot = 2.5322165119978 | epot = -18.0555269778081 | etot = -13.2825374167666
+830000  ekin = 2.31389012815757 |  erot = 2.48241157684725 | epot = -18.0788391216955 | etot = -13.2825374166907
+831000  ekin = 2.38886546625953 |  erot = 2.43305573632076 | epot = -18.104458619251 | etot = -13.2825374166707
+832000  ekin = 2.46326915871406 |  erot = 2.38708705021977 | epot = -18.1328936256668 | etot = -13.282537416733
+833000  ekin = 2.53443656409172 |  erot = 2.34645691970375 | epot = -18.1634309006758 | etot = -13.2825374168804
+834000  ekin = 2.59956439097001 |  erot = 2.31199374937919 | epot = -18.1940955574388 | etot = -13.2825374170896
+835000  ekin = 2.65594316002407 |  erot = 2.28352232981187 | epot = -18.2220029071513 | etot = -13.2825374173153
+836000  ekin = 2.70130042716651 |  erot = 2.26019210855364 | epot = -18.2440299532235 | etot = -13.2825374175034
+837000  ekin = 2.73418787966583 |  erot = 2.24090837049561 | epot = -18.2576336677656 | etot = -13.2825374176041
+838000  ekin = 2.75431729315362 |  erot = 2.22474076448287 | epot = -18.2615954752233 | etot = -13.2825374175868
+839000  ekin = 2.76274241572831 |  erot = 2.21121141264461 | epot = -18.2564912458202 | etot = -13.2825374174473
+840000  ekin = 2.76179432909388 |  erot = 2.20041723497348 | epot = -18.2447489812793 | etot = -13.282537417212
+841000  ekin = 2.75470877418902 |  erot = 2.1929795872171 | epot = -18.2302257783439 | etot = -13.2825374169378
+842000  ekin = 2.74495192414829 |  erot = 2.18982916717498 | epot = -18.2173185080269 | etot = -13.2825374167036
+843000  ekin = 2.73536701720752 |  erot = 2.19185320338424 | epot = -18.2097576371796 | etot = -13.2825374165879
+844000  ekin = 2.72739699207957 |  erot = 2.19948517299773 | epot = -18.2094195817172 | etot = -13.2825374166399
+845000  ekin = 2.72069680081942 |  erot = 2.2123834314525 | epot = -18.2156176491199 | etot = -13.282537416848
+846000  ekin = 2.71335245842044 |  erot = 2.22935501274494 | epot = -18.2252448883063 | etot = -13.2825374171409
+847000  ekin = 2.70267547682563 |  erot = 2.24859000802352 | epot = -18.2338029022618 | etot = -13.2825374174127
+848000  ekin = 2.68627674917249 |  erot = 2.26812231570546 | epot = -18.2369364824441 | etot = -13.2825374175662
+849000  ekin = 2.66300406346419 |  erot = 2.28632293043157 | epot = -18.2318644114456 | etot = -13.2825374175499
+850000  ekin = 2.63341305155328 |  erot = 2.30223030137244 | epot = -18.218180770297 | etot = -13.2825374173713
+851000  ekin = 2.59966042962012 |  erot = 2.31561676234611 | epot = -18.1978146090528 | etot = -13.2825374170866
+852000  ekin = 2.5649330756416 |  erot = 2.32681511046273 | epot = -18.1742856028756 | etot = -13.2825374167712
+853000  ekin = 2.53268458711828 |  erot = 2.33642702442706 | epot = -18.1516490280431 | etot = -13.2825374164977
+854000  ekin = 2.50591352350999 |  erot = 2.34503055401556 | epot = -18.1334814938378 | etot = -13.2825374163123
+855000  ekin = 2.48667404327569 |  erot = 2.3529787337437 | epot = -18.1221901932468 | etot = -13.2825374162274
+856000  ekin = 2.47592780438371 |  erot = 2.3603420277346 | epot = -18.1188072483454 | etot = -13.2825374162271
+857000  ekin = 2.47367803113421 |  erot = 2.36697110010333 | epot = -18.1231865475261 | etot = -13.2825374162886
+858000  ekin = 2.47922391314762 |  erot = 2.37260088410896 | epot = -18.1343622136269 | etot = -13.2825374163703
+859000  ekin = 2.49150776537562 |  erot = 2.37701216170971 | epot = -18.1510573435355 | etot = -13.2825374164502
+860000  ekin = 2.50937686487663 |  erot = 2.38013993767848 | epot = -18.1720542190715 | etot = -13.2825374165164
+861000  ekin = 2.53170635734158 |  erot = 2.382118173112 | epot = -18.1963619470209 | etot = -13.2825374165673
+862000  ekin = 2.55742566397641 |  erot = 2.38328933411273 | epot = -18.2232524146946 | etot = -13.2825374166054
+863000  ekin = 2.58549482989182 |  erot = 2.38419488615669 | epot = -18.2522271326816 | etot = -13.2825374166331
+864000  ekin = 2.61488040894193 |  erot = 2.38555368952377 | epot = -18.2829715151176 | etot = -13.2825374166519
+865000  ekin = 2.64455846197211 |  erot = 2.38821849293994 | epot = -18.3153143715761 | etot = -13.282537416664
+866000  ekin = 2.67354800293375 |  erot = 2.39309523430222 | epot = -18.3491806539087 | etot = -13.2825374166727
+867000  ekin = 2.70096216873101 |  erot = 2.40101926625376 | epot = -18.3845188516697 | etot = -13.282537416685
+868000  ekin = 2.72584498237102 |  erot = 2.41260829133849 | epot = -18.4209906905118 | etot = -13.2825374168023
+869000  ekin = 2.74685098517846 |  erot = 2.42808376703703 | epot = -18.4574721690819 | etot = -13.2825374168664
+870000  ekin = 2.7633451632292 |  erot = 2.44707202924713 | epot = -18.492954609437 | etot = -13.2825374169607
+871000  ekin = 2.77488977650291 |  erot = 2.46856883210016 | epot = -18.52599602569 | etot = -13.2825374170869
+872000  ekin = 2.78115731189941 |  erot = 2.49101078905502 | epot = -18.5547055181929 | etot = -13.2825374172384
+873000  ekin = 2.78190152481948 |  erot = 2.51241399948397 | epot = -18.5768529417016 | etot = -13.2825374173982
+874000  ekin = 2.77696693727655 |  erot = 2.53063897251365 | epot = -18.5901433273283 | etot = -13.2825374175381
+875000  ekin = 2.76636320238677 |  erot = 2.54374754553387 | epot = -18.5926481655429 | etot = -13.2825374176222
+876000  ekin = 2.75040698328634 |  erot = 2.55039472458546 | epot = -18.5833391254864 | etot = -13.2825374176146
+877000  ekin = 2.72989722871737 |  erot = 2.55017286738757 | epot = -18.5626075135949 | etot = -13.28253741749
+878000  ekin = 2.70625700359845 |  erot = 2.54382115285145 | epot = -18.5326155736941 | etot = -13.2825374172442
+879000  ekin = 2.68156506710304 |  erot = 2.5332421375899 | epot = -18.4973446215902 | etot = -13.2825374168973
+880000  ekin = 2.65843100587721 |  erot = 2.52132217105652 | epot = -18.4622905934235 | etot = -13.2825374164897
+881000  ekin = 2.63972432917675 |  erot = 2.51160592655705 | epot = -18.4338676718058 | etot = -13.282537416072
+882000  ekin = 2.62822235346356 |  erot = 2.50790034757638 | epot = -18.4186601167335 | etot = -13.2825374156936
+883000  ekin = 2.62626662018779 |  erot = 2.51387422610971 | epot = -18.4226782616929 | etot = -13.2825374153954
+884000  ekin = 2.63550251587674 |  erot = 2.53269091102144 | epot = -18.4507308421049 | etot = -13.2825374152068
+885000  ekin = 2.65673814602945 |  erot = 2.56668643769325 | epot = -18.5059619988685 | etot = -13.2825374151458
+886000  ekin = 2.68991716922188 |  erot = 2.61709355073984 | epot = -18.5895481351839 | etot = -13.2825374152222
+887000  ekin = 2.73417552912835 |  erot = 2.6838152242605 | epot = -18.7005281688277 | etot = -13.2825374154388
+888000  ekin = 2.78795008305904 |  erot = 2.76526591420808 | epot = -18.8357534130565 | etot = -13.2825374157894
+889000  ekin = 2.84912017691373 |  erot = 2.85831711202064 | epot = -18.9899747051915 | etot = -13.2825374162572
+890000  ekin = 2.91517691409144 |  erot = 2.95839462905156 | epot = -19.1561089599533 | etot = -13.2825374168103
+891000  ekin = 2.98341766730812 |  erot = 3.05976765321724 | epot = -19.325722737928 | etot = -13.2825374174026
+892000  ekin = 3.05115351194122 |  erot = 3.15603968509377 | epot = -19.4897306150129 | etot = -13.2825374179779
+893000  ekin = 3.11590366932995 |  erot = 3.24080527058909 | epot = -19.6392463583964 | etot = -13.2825374184774
+894000  ekin = 3.17554452677574 |  erot = 3.30838806048503 | epot = -19.7664700061104 | etot = -13.2825374188496
+895000  ekin = 3.22839008199059 |  erot = 3.35454380329715 | epot = -19.8654713043472 | etot = -13.2825374190595
+896000  ekin = 3.27319974841242 |  erot = 3.37700709675264 | epot = -19.9327442642579 | etot = -13.2825374190928
+897000  ekin = 3.30912548213112 |  erot = 3.37578333286277 | epot = -19.967446233953 | etot = -13.2825374189591
+898000  ekin = 3.33561719165196 |  erot = 3.3531309986516 | epot = -19.9712856089931 | etot = -13.2825374186895
+899000  ekin = 3.35230310065721 |  erot = 3.31323476899373 | epot = -19.9480752879843 | etot = -13.2825374183334
+900000  ekin = 3.35886034343544 |  erot = 3.26162723368974 | epot = -19.9030249950731 | etot = -13.2825374179479
+901000  ekin = 3.35489762596209 |  erot = 3.20446448625264 | epot = -19.8418995298029 | etot = -13.2825374175882
+902000  ekin = 3.33988398696538 |  erot = 3.14778460706124 | epot = -19.7702060113224 | etot = -13.2825374172958
+903000  ekin = 3.31316641783821 |  erot = 3.09687096396604 | epot = -19.6925747988938 | etot = -13.2825374170895
+904000  ekin = 3.27411465308455 |  erot = 3.05580881507587 | epot = -19.6124608851232 | etot = -13.2825374169628
+905000  ekin = 3.22240761769978 |  erot = 3.02727711778411 | epot = -19.5322221523689 | etot = -13.282537416885
+906000  ekin = 3.15843123273498 |  erot = 3.01257047454492 | epot = -19.4535391240911 | etot = -13.2825374168112
+907000  ekin = 3.08369712964382 |  erot = 3.01180553940022 | epot = -19.3780400857413 | etot = -13.2825374166972
+908000  ekin = 3.00113487274611 |  erot = 3.02423547951158 | epot = -19.3079077687759 | etot = -13.2825374165182
+909000  ekin = 2.91509126886064 |  erot = 3.0485809791401 | epot = -19.2462096642835 | etot = -13.2825374162828
+910000  ekin = 2.83091809167562 |  erot = 3.08328866526031 | epot = -19.1967441729738 | etot = -13.2825374160379
+911000  ekin = 2.7541604271422 |  erot = 3.1266566210814 | epot = -19.1633544640806 | etot = -13.282537415857
+912000  ekin = 2.68982240100996 |  erot = 3.1767030385921 | epot = -19.1490628553551 | etot = -13.2825374157531
+913000  ekin = 2.64026279373643 |  erot = 3.23106967523778 | epot = -19.1538698849232 | etot = -13.282537415949
+914000  ekin = 2.60494541465082 |  erot = 3.28757760697213 | epot = -19.1750604377642 | etot = -13.2825374161413
+915000  ekin = 2.58331294239456 |  erot = 3.34356245911015 | epot = -19.2094128182448 | etot = -13.2825374167401
+916000  ekin = 2.57222527647779 |  erot = 3.39542630316431 | epot = -19.2501889969159 | etot = -13.2825374172738
+917000  ekin = 2.56717379817942 |  erot = 3.43991413449175 | epot = -19.2896253504428 | etot = -13.2825374177716
+918000  ekin = 2.56366862210109 |  erot = 3.47431911616615 | epot = -19.3205251564115 | etot = -13.2825374181443
+919000  ekin = 2.55808580304574 |  erot = 3.49688251813148 | epot = -19.3375057395072 | etot = -13.28253741833
+920000  ekin = 2.54828083364558 |  erot = 3.5070678678649 | epot = -19.3378861198184 | etot = -13.2825374183079
+921000  ekin = 2.53385837590705 |  erot = 3.50557961685233 | epot = -19.3219754108608 | etot = -13.2825374181014
+922000  ekin = 2.51606053239869 |  erot = 3.49409623216883 | epot = -19.2926941823441 | etot = -13.2825374177766
+923000  ekin = 2.49728908788132 |  erot = 3.47476611576438 | epot = -19.2545926210732 | etot = -13.2825374174275
+924000  ekin = 2.48035717202194 |  erot = 3.44958564398511 | epot = -19.2124802331591 | etot = -13.2825374171521
+925000  ekin = 2.46765713254659 |  erot = 3.41982437264767 | epot = -19.1700189222178 | etot = -13.2825374170235
+926000  ekin = 2.46048446158288 |  erot = 3.38566546873097 | epot = -19.1286873473806 | etot = -13.2825374170668
+927000  ekin = 2.45872404317125 |  erot = 3.34617863031278 | epot = -19.0874400907354 | etot = -13.2825374172514
+928000  ekin = 2.46097855171065 |  erot = 3.29964380838023 | epot = -19.0431597775946 | etot = -13.2825374175038
+929000  ekin = 2.46505358069594 |  erot = 3.24413140257229 | epot = -18.991722401002 | etot = -13.2825374177338
+930000  ekin = 2.46859437787823 |  erot = 3.17816487157566 | epot = -18.9292966673187 | etot = -13.2825374178649
+931000  ekin = 2.46965047267191 |  erot = 3.10127887080617 | epot = -18.8534667613313 | etot = -13.2825374178532
+932000  ekin = 2.4670173255647 |  erot = 3.01434778959557 | epot = -18.7639025328451 | etot = -13.2825374176848
+933000  ekin = 2.46031519134382 |  erot = 2.9197399878057 | epot = -18.6625925965562 | etot = -13.2825374174067
+934000  ekin = 2.44985996562476 |  erot = 2.82081794784481 | epot = -18.5532153305218 | etot = -13.2825374170523
+935000  ekin = 2.436420580333 |  erot = 2.72162862765433 | epot = -18.4405866246576 | etot = -13.2825374166703
+936000  ekin = 2.42095423708767 |  erot = 2.62651830215161 | epot = -18.3300099555418 | etot = -13.2825374163026
+937000  ekin = 2.40438434932027 |  erot = 2.53973621279557 | epot = -18.226657978095 | etot = -13.2825374159791
+938000  ekin = 2.38744919935998 |  erot = 2.4651292336249 | epot = -18.135115848703 | etot = -13.2825374157181
+939000  ekin = 2.37062067073867 |  erot = 2.40593643839711 | epot = -18.0590945246642 | etot = -13.2825374155285
+940000  ekin = 2.35407564445261 |  erot = 2.36465978724872 | epot = -18.0012728471164 | etot = -13.2825374154151
+941000  ekin = 2.33770002396805 |  erot = 2.3429775907629 | epot = -17.9632150301122 | etot = -13.2825374153812
+942000  ekin = 2.3211100477539 |  erot = 2.34167204177044 | epot = -17.9453195049536 | etot = -13.2825374154293
+943000  ekin = 2.30368578977883 |  erot = 2.36056240878928 | epot = -17.9467856141281 | etot = -13.28253741556
+944000  ekin = 2.28462216192276 |  erot = 2.39846175869457 | epot = -17.965621336385 | etot = -13.2825374157677
+945000  ekin = 2.2630091294477 |  erot = 2.45319770839139 | epot = -17.9987442538757 | etot = -13.2825374160366
+946000  ekin = 2.23795189081835 |  erot = 2.52174524491464 | epot = -18.0422345520714 | etot = -13.2825374163384
+947000  ekin = 2.20873145000821 |  erot = 2.60050188215201 | epot = -18.0917707487932 | etot = -13.282537416633
+948000  ekin = 2.17498954570766 |  erot = 2.68569096156255 | epot = -18.1432179241464 | etot = -13.2825374168762
+949000  ekin = 2.13690579381781 |  erot = 2.77382147859291 | epot = -18.1932646894412 | etot = -13.2825374170305
+950000  ekin = 2.09532426392926 |  erot = 2.86208910103834 | epot = -18.2399507820441 | etot = -13.2825374170765
+951000  ekin = 2.05179334892108 |  erot = 2.94860198731117 | epot = -18.2829327532513 | etot = -13.282537417019
+952000  ekin = 2.00850116617196 |  erot = 3.03236285196215 | epot = -18.3234014350193 | etot = -13.2825374168852
+953000  ekin = 1.96811370411823 |  erot = 3.11301524923778 | epot = -18.3636663700751 | etot = -13.2825374167191
+954000  ekin = 1.93354422096465 |  erot = 3.19043207950452 | epot = -18.4065137170385 | etot = -13.2825374165694
+955000  ekin = 1.90769299354898 |  erot = 3.26426019429227 | epot = -18.4544906043215 | etot = -13.2825374164802
+956000  ekin = 1.89319483668346 |  erot = 3.3335310510213 | epot = -18.5092633041882 | etot = -13.2825374164834
+957000  ekin = 1.89220136687493 |  erot = 3.39641763043281 | epot = -18.5711564139026 | etot = -13.2825374165948
+958000  ekin = 1.90621184327196 |  erot = 3.45018116338437 | epot = -18.6389304234696 | etot = -13.2825374168133
+959000  ekin = 1.93595602572738 |  erot = 3.49131884016615 | epot = -18.7098122830149 | etot = -13.2825374171214
+960000  ekin = 1.98132739808155 |  erot = 3.51589596586286 | epot = -18.7797607814332 | etot = -13.2825374174888
+961000  ekin = 2.04135467404736 |  erot = 3.52022622800403 | epot = -18.8441183199515 | etot = -13.2825374179001
+962000  ekin = 2.11395441310799 |  erot = 3.50134462367084 | epot = -18.8978364550807 | etot = -13.2825374183019
+963000  ekin = 2.19624676899701 |  erot = 3.45688460164827 | epot = -18.9356687892675 | etot = -13.2825374186222
+964000  ekin = 2.28502253915305 |  erot = 3.38607259923977 | epot = -18.9536325572173 | etot = -13.2825374188245
+965000  ekin = 2.37703902445876 |  erot = 3.290048679397 | epot = -18.9496251223776 | etot = -13.2825374185219
+966000  ekin = 2.47063968725093 |  erot = 3.1723513983338 | epot = -18.9255285040288 | etot = -13.2825374184441
+967000  ekin = 2.56372995923146 |  erot = 3.03797961445187 | epot = -18.8842469918799 | etot = -13.2825374181965
+968000  ekin = 2.65424153344269 |  erot = 2.89333166097639 | epot = -18.8301106122161 | etot = -13.282537417797
+969000  ekin = 2.74102206186552 |  erot = 2.74597895251273 | epot = -18.7695384316796 | etot = -13.2825374173014
+970000  ekin = 2.82317857356224 |  erot = 2.604190086995 | epot = -18.7099060774559 | etot = -13.2825374168987
+971000  ekin = 2.8994689638118 |  erot = 2.4760495859706 | epot = -18.6580559662902 | etot = -13.2825374165078
+972000  ekin = 2.9692788351105 |  erot = 2.36783972481189 | epot = -18.6196559761964 | etot = -13.282537416274
+973000  ekin = 3.03160430536472 |  erot = 2.2837390116559 | epot = -18.5978807332491 | etot = -13.2825374162285
+974000  ekin = 3.08487810189262 |  erot = 2.22552920107224 | epot = -18.5929447193212 | etot = -13.2825374163564
+975000  ekin = 3.12708218339791 |  erot = 2.19270938701088 | epot = -18.6023289870154 | etot = -13.2825374166067
+976000  ekin = 3.15606698313496 |  erot = 2.18294126797245 | epot = -18.6215456680199 | etot = -13.2825374169125
+977000  ekin = 3.16994500148915 |  erot = 2.19267118134068 | epot = -18.6451536000414 | etot = -13.2825374172116
+978000  ekin = 3.16742946230438 |  erot = 2.21776877388408 | epot = -18.6677356536463 | etot = -13.2825374174579
+979000  ekin = 3.14804045634032 |  erot = 2.25406876454721 | epot = -18.6846466385122 | etot = -13.2825374176247
+980000  ekin = 3.11216367300116 |  erot = 2.29776911310777 | epot = -18.6924702038109 | etot = -13.282537417702
+981000  ekin = 3.06099214892659 |  erot = 2.3456929996696 | epot = -18.6892225662862 | etot = -13.28253741769
+982000  ekin = 2.99639964718071 |  erot = 2.39544433336442 | epot = -18.6743813981403 | etot = -13.2825374175951
+983000  ekin = 2.92078844001815 |  erot = 2.44547840699747 | epot = -18.6488042644435 | etot = -13.2825374174279
+984000  ekin = 2.83693459158518 |  erot = 2.49508912549767 | epot = -18.6145611342876 | etot = -13.2825374172048
+985000  ekin = 2.74783419632812 |  erot = 2.5443043349293 | epot = -18.574675948205 | etot = -13.2825374169476
+986000  ekin = 2.65654531631453 |  erot = 2.59369131479764 | epot = -18.5327740477957 | etot = -13.2825374166835
+987000  ekin = 2.56602543639744 |  erot = 2.64409903932047 | epot = -18.4926618921587 | etot = -13.2825374164408
+988000  ekin = 2.47897321242724 |  erot = 2.69638105728562 | epot = -18.4578916859573 | etot = -13.2825374162445
+989000  ekin = 2.39763961356463 |  erot = 2.75059396001095 | epot = -18.4307709898088 | etot = -13.2825374162332
+990000  ekin = 2.32368779513216 |  erot = 2.8060334288419 | epot = -18.4122586401602 | etot = -13.2825374161862
+991000  ekin = 2.25825301239778 |  erot = 2.86226671700632 | epot = -18.403057145624 | etot = -13.2825374162199
+992000  ekin = 2.20187988804497 |  erot = 2.91825634883864 | epot = -18.40267365322 | etot = -13.2825374163364
+993000  ekin = 2.15452775813786 |  erot = 2.97231721272995 | epot = -18.4093823873994 | etot = -13.2825374165316
+994000  ekin = 2.1156117684003 |  erot = 3.02214023540268 | epot = -18.4202894205965 | etot = -13.2825374167935
+995000  ekin = 2.0840816135671 |  erot = 3.0648940369717 | epot = -18.4315130676401 | etot = -13.2825374171013
+996000  ekin = 2.05854312781033 |  erot = 3.09743221589021 | epot = -18.4385127611221 | etot = -13.2825374174216
+997000  ekin = 2.03742523644506 |  erot = 3.11662356541409 | epot = -18.4365862195703 | etot = -13.2825374177112
+998000  ekin = 2.0191844917443 |  erot = 3.11978989754515 | epot = -18.4215118072117 | etot = -13.2825374179223
+999000  ekin = 2.00252382756565 |  erot = 3.10518925660486 | epot = -18.3902505021827 | etot = -13.2825374180121
+1000000  ekin = 1.98658902728357 |  erot = 3.07244218051013 | epot = -18.341568625748 | etot = -13.2825374179543
+ 1000000  0.088292846   -1.1874188  0.041070751   -1.0221862 -7.1515284e-05 
+Loop time of 31.8631 on 4 procs for 1000000 steps with 16 atoms
+
+Performance: 27116.007 tau/day, 31384.268 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.7557     | 14.198     | 24.52      | 210.8 | 44.56
+Bond    | 0.22678    | 0.45105    | 0.74273    |  29.9 |  1.42
+Neigh   | 0.00012    | 0.00012675 | 0.00013    |   0.0 |  0.00
+Comm    | 2.6837     | 2.8338     | 3.0258     |   7.8 |  8.89
+Output  | 2e-05      | 2.75e-05   | 3e-05      |   0.0 |  0.00
+Modify  | 0.43472    | 0.8763     | 1.3871     |  38.7 |  2.75
+Other   |            | 13.5       |            |       | 42.38
+
+Nlocal:    4 ave 7 max 1 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:    10.5 ave 12 max 9 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    38.75 ave 63 max 11 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 155
+Ave neighs/atom = 9.6875
+Ave special neighs/atom = 3.75
+Neighbor list builds = 6
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:31
diff --git a/examples/USER/drude/toluene/data.toluene b/examples/USER/drude/toluene/data.toluene
index 48d44016d7..d67af7c311 100644
--- a/examples/USER/drude/toluene/data.toluene
+++ b/examples/USER/drude/toluene/data.toluene
@@ -79,10 +79,10 @@ Dihedral Coeffs
 
 Improper Coeffs
 
-   1    0.0000    2.1999    0.0000    0.0000 # CAO-CAO-CAT-CTT
-   2    0.0000    2.1999    0.0000    0.0000 # CAT-CAM-CAO-HAT
-   3    0.0000    2.1999    0.0000    0.0000 # CAO-CAP-CAM-HAT
-   4    0.0000    2.1999    0.0000    0.0000 # CAM-CAM-CAP-HAT
+   1    2.1999    0.0000    0.0000   -1.0000 0 # CAO-CAO-CAT-CTT
+   2    2.1999    0.0000    0.0000   -1.0000 0 # CAT-CAM-CAO-HAT
+   3    2.1999    0.0000    0.0000   -1.0000 0 # CAO-CAP-CAM-HAT
+   4    2.1999    0.0000    0.0000   -1.0000 0 # CAM-CAM-CAP-HAT
 
 Atoms
 
diff --git a/examples/USER/drude/toluene/in.toluene.lang b/examples/USER/drude/toluene/in.toluene.lang
index 8f00c24a4b..ba40a3bcde 100644
--- a/examples/USER/drude/toluene/in.toluene.lang
+++ b/examples/USER/drude/toluene/in.toluene.lang
@@ -7,7 +7,7 @@ atom_style full
 bond_style harmonic
 angle_style harmonic
 dihedral_style opls
-improper_style opls
+improper_style fourier
 special_bonds lj/coul 0.0 0.0 0.5
 
 pair_style lj/cut/thole/long 2.600 8.0 8.0
@@ -109,7 +109,7 @@ fix fNPH all nve
 
 compute cTEMP all temp/drude
 
-thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
 thermo 50
 
 timestep 0.5
diff --git a/examples/USER/drude/toluene/in.toluene.nh b/examples/USER/drude/toluene/in.toluene.nh
index 05b35ca919..7a5aecc579 100644
--- a/examples/USER/drude/toluene/in.toluene.nh
+++ b/examples/USER/drude/toluene/in.toluene.nh
@@ -7,7 +7,7 @@ atom_style full
 bond_style harmonic
 angle_style harmonic
 dihedral_style opls
-improper_style opls
+improper_style fourier
 special_bonds lj/coul 0.0 0.0 0.5
 
 pair_style lj/cut/thole/long 2.600 8.0 8.0
@@ -115,7 +115,7 @@ fix fINVERSE all drude/transform/inverse
 
 fix fMOMENTUM all momentum 100 linear 1 1 1
 
-thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
 thermo 50
 
 timestep 0.5
diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1
deleted file mode 100644
index 08cc2f0f5c..0000000000
--- a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1
+++ /dev/null
@@ -1,14 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 250 toluene system for drude polarizability example (Langevin)
-
-units real
-boundary p p p
-
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style opls
-improper_style opls
-ERROR: Unknown improper style opls (src/force.cpp:634)
-Last command: improper_style opls
diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4
deleted file mode 100644
index 08cc2f0f5c..0000000000
--- a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4
+++ /dev/null
@@ -1,14 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 250 toluene system for drude polarizability example (Langevin)
-
-units real
-boundary p p p
-
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style opls
-improper_style opls
-ERROR: Unknown improper style opls (src/force.cpp:634)
-Last command: improper_style opls
diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1
deleted file mode 100644
index a6807f8ee1..0000000000
--- a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1
+++ /dev/null
@@ -1,14 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 250 toluene system for drude polarizability example (Nose-Hoover)
-
-units real
-boundary p p p
-
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style opls
-improper_style opls
-ERROR: Unknown improper style opls (src/force.cpp:634)
-Last command: improper_style opls
diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4
deleted file mode 100644
index a6807f8ee1..0000000000
--- a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4
+++ /dev/null
@@ -1,14 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 250 toluene system for drude polarizability example (Nose-Hoover)
-
-units real
-boundary p p p
-
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style opls
-improper_style opls
-ERROR: Unknown improper style opls (src/force.cpp:634)
-Last command: improper_style opls
diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1 b/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1
new file mode 100644
index 0000000000..71ffdb0c8c
--- /dev/null
+++ b/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1
@@ -0,0 +1,254 @@
+LAMMPS (7 Aug 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style fourier
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+  special bonds CPU = 0.00199628 secs
+  read_data CPU = 0.0169649 secs
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+  find clusters CPU = 0.000807762 secs
+
+fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
+fix fNPH all nve
+
+compute cTEMP all temp/drude
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 103823 64000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50    4782.1702    4728.7435    328.28767    53.426722    1812.2203    685.37824    683.70917   -3277.1645    797.34329    1305983.2   -1306631.2    16874.358    48631.318    448.52419    116.25477 
+     100    2906.0879    3699.8031    256.85465    -793.7152    978.15364    778.36908    862.30899   -3270.1722    468.44888    1306096.8   -1306707.6    15631.384    48631.318    382.26408    35.748403 
+     150    2089.0918    3593.0499    249.44342   -1503.9581    751.32283    803.47802     668.4757   -3277.5983    128.17444    1306138.5   -1306716.3     15193.04    48631.318    384.75632    10.892446 
+     200    1547.3302     3248.639    225.53309   -1701.3089    699.65977    814.31164    692.83227   -3276.3957   -66.671816    1306160.9   -1306725.9    13787.676    48631.318    351.28242    3.8458668 
+     250    1177.9323     3095.949    214.93276   -1918.0167    688.87262    842.44531    615.89218   -3278.4465   -210.06178    1306154.3     -1306731    8808.5835    48631.318     335.8115    1.8330994 
+     300    895.90313    2870.3451    199.27046    -1974.442    734.95873    858.58147    624.00862   -3278.6022   -342.01951    1306163.6     -1306735    3388.4841    48631.318    311.56815    1.2987715 
+     350    669.25785    2764.9587    191.95413   -2095.7009    662.44028    860.79714    602.69567    -3278.776   -376.37081    1306172.3   -1306738.8    8494.9184    48631.318    300.19414    1.1358594 
+     400    531.21609    2722.6775    189.01881   -2191.4614    684.34049    868.77818    576.86096   -3280.1649   -459.66591      1306160   -1306741.6    6726.3087    48631.318    295.59622    1.1315427 
+     450    427.05425    2611.7588     181.3184   -2184.7046     719.2042    891.88178     591.2282    -3279.339   -534.65069    1306172.2   -1306745.2    2398.5394    48631.318    283.56126    1.0726045 
+     500    310.44891    2556.0967    177.45412   -2245.6477    720.86526    841.50195     586.3417   -3279.3029   -539.81715    1306169.5   -1306744.8     3028.595    48631.318    277.52314    1.0406334 
+     550    207.83114    2531.3051    175.73299   -2323.4739    674.71188     855.2132    555.53227   -3280.0378   -553.93222    1306171.9   -1306746.9    4609.4408    48631.318    274.80629    1.0748601 
+     600     88.81557    2459.9059    170.77619   -2371.0903     692.4485    834.47484    550.85905   -3280.9086   -595.31802    1306171.4     -1306744    2107.9995    48631.318    267.06312    1.0301965 
+     650    75.616307    2416.9747    167.79573   -2341.3584    703.57186    869.98959    564.81201   -3280.7522    -619.8016      1306168   -1306747.2    1236.4829    48631.318     262.3542    1.0968447 
+     700    49.832719    2415.7344    167.70963   -2365.9017    683.61663    882.67915    555.23571   -3280.7778   -615.06862    1306159.9   -1306751.4    2985.7048    48631.318    262.23095    1.0762424 
+     750    41.513638     2427.218    168.50687   -2385.7044    698.87619     863.2938    564.58197   -3280.0156   -637.29964    1306160.1   -1306755.3     1653.117    48631.318    263.49803    1.0451977 
+     800    109.53032    2481.9041    172.30339   -2372.3738    697.22709    897.36555    561.28745   -3280.6784   -651.29564      1306155   -1306751.3    1219.8761    48631.318    269.43698    1.0647792 
+     850    98.142203    2502.3132    173.72026    -2404.171     696.5382    878.83293    566.44302   -3280.2837   -663.94587    1306155.6   -1306757.4    1122.7487    48631.318    271.67716     1.030267 
+     900    62.992675    2409.7324    167.29295   -2346.7397    722.00541    896.64662    560.66083   -3279.4915   -644.05458    1306153.6   -1306756.1     1604.295    48631.318    261.58656    1.0609836 
+     950    5.6677468    2403.5067    166.86073    -2397.839    725.07222    891.00249    556.81977   -3279.7848   -672.66389      1306141   -1306759.2    1019.1694    48631.318    260.91187    1.0562387 
+    1000    38.526968      2444.97    169.73928   -2406.4431    704.72993    920.68493    534.59035   -3281.2673   -667.78091    1306141.1   -1306758.5    486.79846    48631.318    265.39928     1.098473 
+    1050    21.698026    2388.6306    165.82798   -2366.9326    712.15539    934.39244    546.92027   -3281.1469    -654.7449    1306137.4   -1306761.9    1556.1256    48631.318    259.28203    1.0760765 
+    1100   -26.971225    2433.8428    168.96678    -2460.814    710.11081    881.19212    524.51547   -3281.7925   -667.53202    1306137.1   -1306764.4    1203.8971    48631.318    264.20441    1.0706085 
+    1150   -49.171269    2375.9688    164.94895     -2425.14    729.78127    918.79575    518.21967   -3281.6542    -675.7239    1306130.4     -1306765    229.44016    48631.318    257.89845     1.086519 
+    1200   -53.421342    2422.0091    168.14524   -2475.4304    710.67274     884.2589    523.32524   -3282.2275   -674.49333    1306130.9   -1306767.9   -131.09655    48631.318    262.91124    1.0804821 
+    1250   -58.534776    2394.4031    166.22873   -2452.9378    680.27486    909.58096    532.81959   -3281.5551   -653.13731      1306127   -1306767.9    546.96357    48631.318    259.92916    1.0424914 
+    1300   -24.151217    2431.9902    168.83817   -2456.1414    681.27127    919.39245    536.41899   -3281.3717   -661.90875    1306121.6   -1306771.5    1455.7512    48631.318    264.00712    1.0630558 
+    1350   -38.973062    2438.6194     169.2984   -2477.5925    707.96118    912.62518    519.44533   -3281.6739   -687.67183    1306126.1   -1306774.4   -1470.4442    48631.318    264.70225    1.1091537 
+    1400    11.896539    2384.5407    165.54404   -2372.6442    719.03374    950.93261     550.5639   -3280.4581    -663.4921      1306122   -1306771.3    465.12854    48631.318    258.83564    1.0785364 
+    1450   -13.118691    2436.6246    169.15991   -2449.7433    661.04397    933.07103    561.29537   -3280.6997   -672.68495    1306123.9   -1306775.7   -108.46564    48631.318    264.50636    1.0718787 
+    1500   -38.151755    2417.4849    167.83116   -2455.6367    688.81484    892.35701    565.29013   -3279.6716    -662.1817    1306116.9   -1306777.2    517.89634    48631.318    262.44549    1.0338083 
+    1550   -71.663334    2405.7016    167.01311   -2477.3649    681.78925    876.31247      559.003    -3280.451   -649.16641    1306112.8   -1306777.7    925.49349    48631.318      261.148    1.0609731 
+    1600   -13.900431     2419.481    167.96973   -2433.3814    718.46559    909.67964    559.06779   -3280.8163    -667.6092      1306108   -1306780.2     13.95808    48631.318    262.63632     1.080229 
+    1650   -16.403222     2431.075    168.77464   -2447.4783    710.99509    907.65662    551.60307   -3279.8852   -661.52624    1306104.5   -1306780.8    726.89923    48631.318    263.91553    1.0489963 
+    1700   -18.555086    2438.2062    169.26971   -2456.7613    665.90475    943.02217    542.86579   -3280.9017   -657.99229      1306108   -1306777.7    801.41078    48631.318    264.67663    1.0750708 
+    1750   -6.9249446    2443.9707     169.6699   -2450.8956    733.23573    890.06857    560.83229    -3280.362   -670.93883    1306098.3   -1306782.1    47.037748    48631.318    265.30892    1.0661143 
+    1800   -21.686222    2434.3375    169.00113   -2456.0237    729.35297     899.9733    561.59516   -3280.4727   -680.98901    1306096.5     -1306782    495.63617    48631.318    264.25723    1.0723683 
+    1850   -72.916947    2408.8254    167.22998   -2481.7423    683.24984    904.13282    549.97726   -3279.6699   -652.63212    1306099.2     -1306786   -120.61674    48631.318    261.48504    1.0659808 
+    1900     -55.4099     2415.455    167.69023   -2470.8649     700.4473    904.72264     565.5266   -3280.4533   -673.23082    1306099.6   -1306787.4    202.15936    48631.318    262.20353    1.0709756 
+    1950   -79.877997    2409.2307    167.25812   -2489.1087     695.9536     894.4541     564.7034   -3279.3581   -680.33472    1306100.8   -1306785.3    213.72828    48631.318    261.52921    1.0658433 
+    2000   -102.20457    2399.4263    166.57746   -2501.6309    689.67819    894.58596    565.53233   -3280.7595   -680.39032    1306096.4   -1306786.6    1113.7499    48631.318    260.46311    1.0647045 
+Loop time of 68.4185 on 1 procs for 2000 steps with 5500 atoms
+
+Performance: 1.263 ns/day, 19.005 hours/ns, 29.232 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 48.825     | 48.825     | 48.825     |   0.0 | 71.36
+Bond    | 2.8852     | 2.8852     | 2.8852     |   0.0 |  4.22
+Kspace  | 13.795     | 13.795     | 13.795     |   0.0 | 20.16
+Neigh   | 1.0731     | 1.0731     | 1.0731     |   0.0 |  1.57
+Comm    | 0.27067    | 0.27067    | 0.27067    |   0.0 |  0.40
+Output  | 0.0031168  | 0.0031168  | 0.0031168  |   0.0 |  0.00
+Modify  | 1.5207     | 1.5207     | 1.5207     |   0.0 |  2.22
+Other   |            | 0.04541    |            |       |  0.07
+
+Nlocal:    5500 ave 5500 max 5500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    13157 ave 13157 max 13157 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.33822e+06 ave 1.33822e+06 max 1.33822e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1338215
+Ave neighs/atom = 243.312
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:01:08
diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4 b/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4
new file mode 100644
index 0000000000..df7d58ac88
--- /dev/null
+++ b/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4
@@ -0,0 +1,254 @@
+LAMMPS (7 Aug 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style fourier
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+  special bonds CPU = 0.000747919 secs
+  read_data CPU = 0.0168228 secs
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+  find clusters CPU = 0.000355244 secs
+
+fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
+fix fNPH all nve
+
+compute cTEMP all temp/drude
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 34263 16000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50    4712.9507    4669.1606    324.15119    43.790082     1798.561    670.61319    690.16967   -3276.9493      811.643    1305983.2   -1306633.5    17164.771    48631.318    442.24313    116.13094 
+     100    2865.9139    3726.4166    258.70226   -860.50272    968.87546    749.70761    860.70151   -3270.7784    427.14745    1306104.7   -1306700.9    15017.273    48631.318    385.10628    35.845353 
+     150    1982.6673     3535.974      245.481   -1553.3068    764.86116    768.15837    658.70182   -3278.7906    108.49859    1306136.5   -1306711.2    16495.352    48631.318    378.64023    10.723986 
+     200    1440.0277    3240.5932    224.97452   -1800.5656    687.71813    791.29356    643.82915   -3276.9293   -99.549986    1306172.9   -1306719.8    13234.476    48631.318    350.46321    3.7468464 
+     250    1103.2915     3018.496    209.55567   -1915.2045    677.97905    825.32748    642.78891   -3278.0801    -226.1853    1306168.5   -1306725.5    8774.9103    48631.318    327.36313    1.8722119 
+     300    789.07159    2827.1716    196.27319      -2038.1    735.96101    852.72545    589.14167   -3280.0357   -374.66018      1306169   -1306730.2    2259.1028    48631.318    306.85585    1.3262598 
+     350    599.10023    2732.3739    189.69197   -2133.2737    677.67006    863.22888    565.41674   -3280.5231   -403.28794    1306177.4   -1306733.2     7989.222    48631.318    296.64126    1.1534418 
+     400    428.26436    2591.2884    179.89727   -2163.0241    676.18745    849.24505    612.34065   -3277.4703   -457.85799    1306173.6   -1306739.1    7282.1438    48631.318    281.34719    1.0502762 
+     450    307.26859    2534.2468    175.93722   -2226.9782    712.17636    853.98862    578.01327   -3279.7731   -533.87422    1306179.7   -1306737.2    1897.9643    48631.318    275.11317    1.0980929 
+     500    234.60959    2495.1082    173.22007   -2260.4987    707.43541    878.25753    547.08402   -3281.2756   -549.04991    1306176.5   -1306739.5    2683.0639    48631.318    270.85452    1.0984718 
+     550    203.34751    2445.6535    169.78673    -2242.306    669.03724    892.85034    599.20664   -3279.0757   -559.81157    1306175.9   -1306740.4    4512.9992    48631.318    265.49465    1.0628812 
+     600    205.63573    2526.5892     175.4056   -2320.9535    685.64073    887.97693    557.42296   -3280.0332   -597.34755    1306167.8   -1306742.5    2999.5823    48631.318    274.29935     1.064682 
+     650    176.23031    2526.3124    175.38638   -2350.0821    714.15285    895.42115    540.39191   -3280.8567   -636.27783    1306165.7   -1306748.6    871.68316    48631.318     274.2807    1.0442089 
+     700    106.97524    2441.1059    169.47101   -2334.1306    697.16018    905.51407    564.71847   -3279.6208   -631.62324    1306159.4   -1306749.6    1953.8241    48631.318    264.98935    1.0771037 
+     750    76.695104    2435.6635    169.09318   -2358.9684    672.01039    934.63351    545.64024   -3281.1075   -629.89722    1306152.4   -1306752.6    3044.0155    48631.318    264.39002    1.0932471 
+     800    57.614075     2456.928    170.56945   -2399.3139    720.76364    898.68013    534.10051   -3281.5897   -659.64354    1306145.5   -1306757.1    1691.9503    48631.318    266.72089    1.0622697 
+     850   -44.931126    2390.0608    165.92727   -2434.9919    708.70192    888.26851    537.13087    -3281.355   -665.17283    1306137.8   -1306760.3    123.07165    48631.318    259.45151    1.0516426 
+     900   -96.878205     2358.862    163.76133   -2455.7403    672.98976    868.41571    546.69492   -3280.6939   -636.80102    1306134.5   -1306760.9    1955.7005    48631.318    256.05598      1.05337 
+     950   -80.012575    2374.4497    164.84349   -2454.4623    679.59722    880.35157    548.35372   -3280.6061   -643.44517    1306125.8   -1306764.5    1510.9809    48631.318    257.72442    1.1017392 
+    1000   -21.440874    2440.6729    169.44096   -2462.1138    718.56593    868.65109    555.54643   -3279.8516   -686.71673    1306126.6     -1306765   -1148.6212    48631.318    264.92977    1.1019339 
+    1050     16.46903    2382.6961    165.41598   -2366.2271    712.51245    913.35848    579.81678   -3280.0559   -657.12122    1306129.3     -1306764    1004.5778    48631.318    258.64076    1.0684155 
+    1100    35.847247    2483.1985    172.39325   -2447.3513    685.05704    889.42278    553.73166   -3280.0177   -663.67201    1306134.3   -1306766.2     699.1824    48631.318    269.56773    1.0838094 
+    1150   -4.9817843    2431.4725    168.80223   -2436.4543    720.51056    868.17547    569.09902   -3280.5829   -677.99865    1306133.1   -1306768.7    435.19118    48631.318    263.96966    1.0303202 
+    1200   -23.907197    2443.6035    169.64441   -2467.5107    684.96437    887.58483    549.43666   -3280.3144   -679.46182    1306137.2   -1306766.9    367.11148    48631.318    265.28645    1.0344036 
+    1250   -16.904671    2389.9447    165.91921   -2406.8494    722.06959    902.90076    568.35616   -3280.6829   -683.32029    1306132.9   -1306769.1    76.759445    48631.318    259.41697    1.0908431 
+    1300   -1.7822102    2410.2768    167.33074   -2412.0591    706.98675    904.31941    551.23506   -3280.7552   -651.51211    1306127.3   -1306769.6    1659.1113    48631.318    261.64093    1.0701648 
+    1350    -3.569473    2446.3901    169.83786   -2449.9595    686.13971    894.85839    558.36242   -3279.9941   -664.59508      1306129   -1306773.7    783.32881    48631.318     265.5696    1.0709072 
+    1400   -33.385576     2400.262    166.63547   -2433.6476     709.5808    890.68408    571.13105   -3280.1428   -674.51247    1306123.4   -1306773.8   -751.38571    48631.318    260.54522     1.080234 
+    1450   -11.215152    2405.5409    167.00196    -2416.756    703.72038    913.21131    552.64196   -3280.9831   -649.19774    1306120.3   -1306776.4    1817.2174    48631.318    261.14741     1.031193 
+    1500   -25.974102    2435.8375    169.10527   -2461.8116    689.93174    900.70619    552.63711   -3280.1497   -671.17989      1306124   -1306777.8   -98.941796    48631.318    264.45069    1.0190784 
+    1550   -76.496407    2394.8126    166.25716    -2471.309    706.96953    886.06919     549.9101   -3280.8434   -659.57745    1306105.9   -1306779.7   -7.0989994    48631.318    259.95403    1.0772144 
+    1600   -79.549932    2395.1114     166.2779   -2474.6614    684.11692    888.93332    562.94522   -3280.1665   -665.21744    1306114.4   -1306779.6    320.58515    48631.318    260.00641    1.0425978 
+    1650   -99.702003    2360.5652    163.87957   -2460.2672    706.21244     900.9253    540.36599   -3280.2308   -655.96077    1306109.7   -1306781.3    307.35487    48631.318    256.23383    1.0666637 
+    1700   -69.422658    2372.1727    164.68541   -2441.5954    676.79347    913.90473    581.60658    -3279.997   -670.33218    1306115.7   -1306779.3   -204.22848    48631.318    257.50963    1.0434075 
+    1750   -80.889897    2425.3592    168.37782   -2506.2491    672.88937    911.52373    523.74733   -3280.4796   -673.90027      1306122     -1306782    965.12568    48631.318    263.26491    1.1001595 
+    1800   -82.419368     2361.798    163.96515   -2444.2173    716.51571     882.9729    577.92505   -3278.9279   -671.67438    1306111.6   -1306782.6   -44.954517    48631.318    256.36957    1.0636692 
+    1850   -93.715705    2373.3359    164.76616   -2467.0516    713.02466    907.03621    563.38626   -3280.2576   -693.30963    1306104.6   -1306781.5   -979.95945    48631.318    257.62543    1.0628288 
+    1900    -73.60945    2449.5873    170.05983   -2523.1967    683.65116    893.94251    539.90847   -3281.4318   -680.16358      1306108   -1306787.1    598.18213    48631.318    265.91405    1.0766352 
+    1950   -66.068291    2437.3691    169.21159   -2503.4374     672.5168    877.42934    573.56499    -3279.885   -668.54185    1306109.2   -1306787.7    733.05074    48631.318    264.61409    1.0224258 
+    2000   -91.043979    2374.4077    164.84057   -2465.4516    692.13299    909.46192    574.60109    -3279.837   -672.33599    1306102.4   -1306791.8   -665.61581    48631.318    257.76275    1.0263294 
+Loop time of 23.7656 on 4 procs for 2000 steps with 5500 atoms
+
+Performance: 3.636 ns/day, 6.602 hours/ns, 84.155 timesteps/s
+94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.918     | 13.096     | 14.137     |  27.0 | 55.10
+Bond    | 0.74012    | 0.76511    | 0.79225    |   2.9 |  3.22
+Kspace  | 6.7821     | 7.8285     | 9.0172     |  35.4 | 32.94
+Neigh   | 0.37249    | 0.37262    | 0.37278    |   0.0 |  1.57
+Comm    | 0.70503    | 0.7188     | 0.72807    |   1.1 |  3.02
+Output  | 0.0018752  | 0.0047592  | 0.013386   |   7.2 |  0.02
+Modify  | 0.91164    | 0.91644    | 0.92123    |   0.5 |  3.86
+Other   |            | 0.06335    |            |       |  0.27
+
+Nlocal:    1375 ave 1381 max 1368 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost:    7803.75 ave 7856 max 7755 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:    334465 ave 349504 max 315867 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 1337859
+Ave neighs/atom = 243.247
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:00:23
diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1 b/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1
new file mode 100644
index 0000000000..be5d856d1e
--- /dev/null
+++ b/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1
@@ -0,0 +1,262 @@
+LAMMPS (7 Aug 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Nose-Hoover)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style fourier
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+  special bonds CPU = 0.0019815 secs
+  read_data CPU = 0.0168803 secs
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+  find clusters CPU = 0.000715256 secs
+
+compute cTEMP_CORE gCORES temp/com
+compute cTEMP all temp/drude
+
+fix fDIRECT all drude/transform/direct
+fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 260 100.0
+fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 1 20.0
+fix fINVERSE all drude/transform/inverse
+
+fix fMOMENTUM all momentum 100 linear 1 1 1
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 103823 64000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50    3563.3755    4630.6343    321.47655   -1067.2588    735.72049    604.78665    689.14827    -3277.411    815.58183    1306088.7   -1306723.8    17813.424    48631.318      503.827 0.0087118192 
+     100    3327.4724    4395.1107    305.12559   -1067.6382    597.93176    651.62645     945.4151   -3267.2851    584.58833    1306135.9   -1306715.8    17407.337    48631.318    478.20171 0.0075985539 
+     150    3036.9065    4740.2304    329.08513   -1703.3239    558.64983    619.91284    658.80687   -3278.7837    285.12462      1306173     -1306720    18448.248    48631.318    515.75286 0.0063215188 
+     200     2697.958    4559.3445    316.52733   -1861.3864    522.09334    593.89129    754.61446     -3273.49    87.660461    1306183.9     -1306730    17888.936    48631.318    496.07143 0.0068706164 
+     250    2348.7568     4410.585    306.19988   -2061.8283    506.05007    575.35171    715.55054   -3276.3261   -18.364473    1306177.3   -1306741.4     11592.05    48631.318    479.88562 0.0071741032 
+     300    2019.8258    4040.1415    280.48226   -2020.3157     604.3077    641.66689    693.93801   -3278.5312   -115.73641    1306183.2   -1306749.1    3631.3628    48631.318    439.57995 0.0069886387 
+     350    1699.5166    3944.9851    273.87613   -2245.4685    452.07416     638.0653    658.79117   -3279.6053   -157.07584    1306196.9   -1306754.6    13544.368    48631.318    429.22694 0.0062868111 
+     400    1399.2929     3726.098    258.68014   -2326.8051    457.91943    621.44726    639.39903   -3279.2395   -188.85914    1306185.4   -1306762.8    10792.274    48631.318    405.41134 0.0059340078 
+     450    1120.5249     3518.345    244.25712   -2397.8201    519.48856    584.65789    646.36689   -3278.6685   -289.59913    1306184.1   -1306764.2    2755.5598    48631.318    382.80716 0.0055707485 
+     500     868.0166    3359.8794    233.25583   -2491.8628     460.7393    581.49563    581.01731   -3281.5544   -252.20169    1306184.3   -1306765.7    6120.3639    48631.318    365.56528 0.0058756154 
+     550    637.01567    3214.9521    223.19441   -2577.9364    431.81483    578.87411    540.94047   -3281.5337   -266.36075    1306182.8   -1306764.5    8622.4334    48631.318    349.79661 0.0058589653 
+     600    418.04086    3113.4064    216.14472   -2695.3655    430.45935    538.68157    522.24598    -3283.456   -311.87901    1306174.3   -1306765.8    7068.9273    48631.318    338.74797 0.0059567598 
+     650     218.5966    2930.8439    203.47052   -2712.2473    514.47294    514.28379    551.52551   -3282.0904   -405.37401    1306164.5   -1306769.5   -13.553736    48631.318    318.88482 0.0052667842 
+     700     45.22721    2830.1443    196.47956    -2784.917    451.11156    498.26423    541.18835   -3282.1427   -375.95313    1306157.1   -1306774.4    3947.6276    48631.318    307.92741 0.0068019029 
+     750   -114.28621    2798.3153    194.26988   -2912.6016      412.753     503.2878    481.32173   -3284.3411   -393.53984      1306147   -1306779.1    7143.3414    48631.318    304.46466 0.0061596717 
+     800   -263.63817    2694.8084    187.08403   -2958.4466    455.67914    487.49754     476.8659   -3284.3133    -451.9578      1306145   -1306787.2    1185.9502    48631.318    293.20288 0.0058203332 
+     850   -397.71592    2559.1921    177.66902   -2956.9081    458.83317     481.2262    478.31241    -3284.068   -437.26503    1306138.6   -1306792.6    346.80209    48631.318    278.44745 0.0054921692 
+     900    -515.1823    2544.8753    176.67509   -3060.0576    395.00163    457.58988    446.68352    -3285.485   -423.56221      1306145   -1306795.3    3712.8598    48631.318    276.88864 0.0074054008 
+     950   -617.28259    2451.1723    170.16987   -3068.4549    383.64277    446.59877     434.4624   -3285.1348   -391.59344    1306142.3   -1306798.7    5429.2488    48631.318    266.69431 0.0057487316 
+    1000   -703.15534     2334.837    162.09342   -3037.9923    424.34948    462.21112    451.80809   -3284.3803   -426.53369    1306133.9   -1306799.3    1137.6145    48631.318    254.03675 0.0053914731 
+    1050    -771.1763     2303.837    159.94128   -3075.0133    426.21409    436.50718    435.09987   -3285.1939   -411.14054    1306125.6   -1306802.1    1636.9383    48631.318    250.66295 0.0069342505 
+    1100   -822.72236    2283.4196    158.52382    -3106.142    376.67684    447.77729    418.45768   -3286.5919   -377.48204    1306118.9   -1306803.8    4760.5163    48631.318    248.44119 0.0074025012 
+    1150   -857.06075    2259.0717     156.8335   -3116.1324    400.31523    431.65981    457.68066   -3285.1977   -430.47723    1306115.8   -1306805.9    3194.5161    48631.318    245.79223  0.007063589 
+    1200   -875.50848    2238.2637    155.38893   -3113.7722    445.38524    460.97125    432.10511   -3285.4238   -472.46606    1306114.7     -1306809   -653.49784    48631.318    243.52819 0.0071448738 
+    1250   -880.37572    2294.6889    159.30618   -3175.0646    411.35427    444.73793    420.06468   -3286.0366   -458.05371    1306104.4   -1306811.5    945.80793    48631.318    249.66481  0.011853487 
+    1300   -871.31064    2284.2298    158.58007   -3155.5405    404.97412    441.75285    426.34477   -3285.4859   -424.79609    1306094.9   -1306813.2    4406.6196    48631.318    248.48563  0.084424118 
+    1350   -816.70005    2325.9264    161.47481   -3142.6265    696.80296    442.50053    431.19923   -3285.7859    -450.2699    1305836.2   -1306813.3     593.8098    48631.318    251.40749    2.9297319 
+    1400   -794.25335    2263.5101    157.14163   -3057.7635    645.65165    466.22086    446.22268   -3285.1821   -420.65317    1305903.7   -1306813.8    1386.3633    48631.318    245.20554    1.8916154 
+    1450   -776.10866    2287.6575    158.81803   -3063.7661    427.03477    479.10627    439.67495   -3285.9537   -395.13186    1306087.6   -1306816.1    2936.7806    48631.318    248.87167  0.061343245 
+    1500   -725.48181     2371.413    164.63266   -3096.8948    390.03204    464.30903    446.91959   -3284.7809   -393.16613    1306095.4   -1306815.6      3544.25    48631.318    258.01286  0.011586563 
+    1550    -671.4904    2315.9297     160.7808   -2987.4201    457.04935    500.25282    464.76203   -3284.9311   -400.98103    1306091.7   -1306815.3    2052.6339    48631.318    251.97726 0.0094517862 
+    1600   -618.83633    2449.0918    170.02543   -3067.9281    425.47487    474.65876    471.99171   -3284.3677   -430.32107    1306091.3   -1306816.6    441.15682    48631.318    266.46311  0.014260935 
+    1650   -567.82245    2425.2238    168.36842   -2993.0462    421.01953    511.27133    463.22065    -3285.038   -377.24066    1306088.4   -1306814.7    5198.8565    48631.318    263.83185  0.074738268 
+    1700    -502.4486    2441.8554    169.52305    -2944.304    642.39962    512.90234    490.38297   -3283.9751   -417.39288    1305929.1   -1306817.7    1141.4411    48631.318    264.52393     2.043674 
+    1750   -459.52196    2499.0746    173.49543   -2958.5966    679.38259    505.31787    484.77659   -3284.6272   -384.27736    1305861.6   -1306820.8    1527.2046    48631.318    270.10074    3.1869342 
+    1800   -471.14403    2476.2266    171.90923   -2947.3706    442.47741    530.45656    474.03057   -3284.0954   -371.95117    1306084.3   -1306822.6    3392.2533    48631.318    269.36446   0.10416401 
+    1850   -462.80763    2536.7112    176.10831   -2999.5188    437.08241    525.07462     474.0838   -3283.7906   -422.23719    1306091.6   -1306821.3    1629.8629    48631.318    275.99502  0.016806806 
+    1900   -469.89289    2468.9765     171.4059   -2938.8694    446.77624    531.61059    496.01046   -3284.2338   -395.15325    1306085.7   -1306819.6    3119.5402    48631.318    268.62645  0.014601992 
+    1950   -491.08007    2445.5966    169.78278   -2936.6767    457.80452    527.23373    470.18125   -3283.9608   -391.86377    1306101.9     -1306818    1122.5275    48631.318    266.08018  0.018911601 
+    2000   -518.40811    2418.7208    167.91696   -2937.1289    415.93135     536.5973    480.44651   -3283.7881   -363.72783    1306096.2   -1306818.7    4475.7317    48631.318    263.09007   0.13504326 
+Loop time of 70.696 on 1 procs for 2000 steps with 5500 atoms
+
+Performance: 1.222 ns/day, 19.638 hours/ns, 28.290 timesteps/s
+97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 48.367     | 48.367     | 48.367     |   0.0 | 68.42
+Bond    | 2.9191     | 2.9191     | 2.9191     |   0.0 |  4.13
+Kspace  | 14.266     | 14.266     | 14.266     |   0.0 | 20.18
+Neigh   | 1.5262     | 1.5262     | 1.5262     |   0.0 |  2.16
+Comm    | 0.27841    | 0.27841    | 0.27841    |   0.0 |  0.39
+Output  | 0.0035572  | 0.0035572  | 0.0035572  |   0.0 |  0.01
+Modify  | 3.2856     | 3.2856     | 3.2856     |   0.0 |  4.65
+Other   |            | 0.05018    |            |       |  0.07
+
+Nlocal:    5500 ave 5500 max 5500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    15317 ave 15317 max 15317 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.30285e+06 ave 1.30285e+06 max 1.30285e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1302849
+Ave neighs/atom = 236.882
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 44
+Dangerous builds = 0
+Total wall time: 0:01:10
diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4 b/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4
new file mode 100644
index 0000000000..8d58260754
--- /dev/null
+++ b/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4
@@ -0,0 +1,262 @@
+LAMMPS (7 Aug 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Nose-Hoover)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style fourier
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+  special bonds CPU = 0.000718355 secs
+  read_data CPU = 0.0167146 secs
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+  find clusters CPU = 0.000344038 secs
+
+compute cTEMP_CORE gCORES temp/com
+compute cTEMP all temp/drude
+
+fix fDIRECT all drude/transform/direct
+fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 260 100.0
+fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 1 20.0
+fix fINVERSE all drude/transform/inverse
+
+fix fMOMENTUM all momentum 100 linear 1 1 1
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 34263 16000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50     3563.376    4630.6343    321.47655   -1067.2583    735.72048    604.78665    689.14826    -3277.411    815.58183    1306088.7   -1306723.8    17813.425    48631.318      503.827 0.0087118179 
+     100    3327.4722    4395.1107    305.12559   -1067.6385    597.93175    651.62645     945.4151   -3267.2851    584.58833    1306135.9   -1306715.8    17407.335    48631.318     478.2017 0.0075985638 
+     150    3036.9065    4740.2304    329.08513   -1703.3238    558.64983    619.91284    658.80686   -3278.7837    285.12462      1306173     -1306720    18448.248    48631.318    515.75286 0.0063215227 
+     200    2697.9581    4559.3445    316.52734   -1861.3864    522.09335     593.8913    754.61446     -3273.49    87.660464    1306183.9     -1306730    17888.937    48631.318    496.07143  0.006870622 
+     250    2348.7563     4410.585    306.19988   -2061.8288    506.05006    575.35172    715.55055   -3276.3261   -18.364482    1306177.3   -1306741.4    11592.049    48631.318    479.88562 0.0071741023 
+     300    2019.8256    4040.1415    280.48225   -2020.3159    604.30771    641.66688    693.93802   -3278.5312   -115.73639    1306183.2   -1306749.1    3631.3625    48631.318    439.57995 0.0069886424 
+     350    1699.5169    3944.9851    273.87613   -2245.4682    452.07416    638.06529    658.79116   -3279.6053   -157.07584    1306196.9   -1306754.6    13544.368    48631.318    429.22695 0.0062868216 
+     400    1399.2927     3726.098    258.68014   -2326.8053    457.91943    621.44727    639.39905   -3279.2395   -188.85912    1306185.4   -1306762.8    10792.273    48631.318    405.41133 0.0059340084 
+     450    1120.5246     3518.345    244.25712   -2397.8204    519.48859     584.6579    646.36688   -3278.6685   -289.59912    1306184.1   -1306764.2    2755.5597    48631.318    382.80717  0.005570751 
+     500    868.01643    3359.8794    233.25583    -2491.863    460.73928    581.49568    581.01732   -3281.5544   -252.20168    1306184.3   -1306765.7     6120.364    48631.318    365.56528 0.0058756204 
+     550    637.01646    3214.9521    223.19441   -2577.9356    431.81484    578.87415    540.94046   -3281.5337   -266.36074    1306182.8   -1306764.5    8622.4353    48631.318    349.79661 0.0058589476 
+     600    418.04028    3113.4063    216.14471   -2695.3661    430.45936    538.68158    522.24597    -3283.456   -311.87897    1306174.3   -1306765.8    7068.9275    48631.318    338.74796 0.0059567639 
+     650    218.59562    2930.8439    203.47052   -2712.2482    514.47296     514.2838    551.52551   -3282.0904   -405.37401    1306164.5   -1306769.5   -13.554086    48631.318    318.88481 0.0052667849 
+     700    45.227739    2830.1443    196.47957   -2784.9165    451.11157    498.26426    541.18833   -3282.1427   -375.95321    1306157.1   -1306774.4    3947.6268    48631.318    307.92741 0.0068018884 
+     750   -114.28676    2798.3154    194.26988   -2912.6022    412.75298    503.28782    481.32167   -3284.3411   -393.53987      1306147   -1306779.1    7143.3424    48631.318    304.46466 0.0061596613 
+     800   -263.63827    2694.8085    187.08403   -2958.4468    455.67916    487.49754    476.86576   -3284.3133   -451.95784      1306145   -1306787.2    1185.9474    48631.318    293.20289 0.0058203323 
+     850   -397.71592    2559.1922    177.66903   -2956.9082    458.83313    481.22619    478.31233    -3284.068   -437.26509    1306138.6   -1306792.6    346.80221    48631.318    278.44747 0.0054921238 
+     900   -515.18134    2544.8753    176.67509   -3060.0567     395.0016     457.5898    446.68361    -3285.485   -423.56234    1306145.1   -1306795.3    3712.8594    48631.318    276.88864 0.0074054726 
+     950   -617.28607    2451.1721    170.16985   -3068.4582     383.6428    446.59872    434.46241   -3285.1348   -391.59326    1306142.3   -1306798.7    5429.2191    48631.318    266.69429 0.0057487961 
+    1000   -703.15541    2334.8366    162.09339    -3037.992    424.34957    462.21115    451.80811   -3284.3803   -426.53346    1306133.9   -1306799.3    1137.6144    48631.318    254.03671 0.0053915025 
+    1050   -771.17572    2303.8364    159.94123   -3075.0121    426.21406    436.50744    435.10013   -3285.1938   -411.13999    1306125.6   -1306802.1    1636.9467    48631.318    250.66288 0.0069341736 
+    1100   -822.72317     2283.421    158.52392   -3106.1442    376.67703    447.77728    418.45763   -3286.5919   -377.48075    1306118.9   -1306803.8    4760.4718    48631.318    248.44134 0.0074024122 
+    1150   -857.06061    2259.0725    156.83355   -3116.1331    400.31517    431.65949    457.68078   -3285.1977   -430.47775    1306115.8   -1306805.9    3194.5159    48631.318    245.79231  0.007063706 
+    1200   -875.50971    2238.2632    155.38889   -3113.7729    445.38534    460.97161    432.10511   -3285.4238   -472.46582    1306114.7     -1306809   -653.49627    48631.318    243.52813 0.0071446561 
+    1250   -880.37609     2294.689    159.30619   -3175.0651    411.35498    444.73774    420.06429   -3286.0366   -458.05353    1306104.4   -1306811.5    945.79687    48631.318    249.66483  0.011854196 
+    1300   -871.31122    2284.2295    158.58005   -3155.5407    404.97869    441.75305    426.34479   -3285.4859   -424.79602    1306094.8   -1306813.2    4406.6128    48631.318     248.4856  0.084411062 
+    1350   -816.69657    2325.9211    161.47444   -3142.6176    696.85542    442.50059    431.19981   -3285.7859   -450.27129    1305836.1   -1306813.3    593.86622    48631.318    251.40736    2.9289249 
+    1400   -794.25213    2263.5122    157.14177   -3057.7643     645.6531     466.2204    446.22253   -3285.1821   -420.65316    1305903.7   -1306813.8    1386.3481    48631.318    245.20568    1.8917548 
+    1450    -776.1076    2287.6591    158.81814   -3063.7667     427.0331    479.10417    439.67675   -3285.9536   -395.13308    1306087.6   -1306816.1    2936.7117    48631.318    248.87185  0.061341392 
+    1500   -725.48032    2371.4108    164.63251   -3096.8911    390.03135    464.30817    446.91941   -3284.7808   -393.16302    1306095.4   -1306815.6    3544.3635    48631.318    258.01262  0.011585228 
+    1550   -671.48696    2315.9233    160.78035   -2987.4102    457.04771    500.26018     464.7623    -3284.931   -400.98142    1306091.7   -1306815.3    2052.6204    48631.318    251.97656 0.0094518433 
+    1600   -618.82679    2449.0893    170.02525   -3067.9161    425.47171    474.66369    471.99137   -3284.3677    -430.3224    1306091.3   -1306816.6    441.31257    48631.318    266.46283  0.014263201 
+    1650   -567.82233    2425.2281    168.36872   -2993.0504    421.02008    511.26686    463.22202   -3285.0378   -377.24205    1306088.4   -1306814.7    5198.6214    48631.318    263.83232  0.074728934 
+    1700   -502.46013    2441.8437    169.52224   -2944.3039    642.39863    512.90005    490.39655    -3283.975   -417.39351    1305929.1   -1306817.7    1141.2401    48631.318    264.52268    2.0436397 
+    1750   -459.52135    2499.0847    173.49613    -2958.606    679.34078    505.30943    484.78276   -3284.6269   -384.28217    1305861.7   -1306820.8    1527.0852    48631.318    270.10144    3.1876179 
+    1800   -471.14322    2476.2445    171.91047   -2947.3877    442.48278     530.4566     474.0343   -3284.0957   -371.97492    1306084.3   -1306822.6    3392.0306    48631.318    269.36641    0.1041603 
+    1850   -462.80151    2536.7173    176.10873   -2999.5188    437.07855    525.05914    474.07725   -3283.7908   -422.22641    1306091.6   -1306821.3    1630.1204    48631.318    275.99568  0.016808725 
+    1900    -469.8785    2468.9596    171.40473   -2938.8381     446.7879     531.6128    496.02681   -3284.2335   -395.17163    1306085.7   -1306819.6    3119.2384    48631.318    268.62462  0.014603394 
+    1950   -491.07182    2445.6794    169.78853   -2936.7512    457.80204    527.21208     470.1608   -3283.9622   -391.90163    1306101.9     -1306818    1122.0978    48631.318    266.08919  0.018903661 
+    2000   -518.41243     2418.604    167.90885   -2937.0165    415.92605    536.62844    480.48912   -3283.7876   -363.72641    1306096.2   -1306818.7    4474.8778    48631.318    263.07743   0.13492637 
+Loop time of 22.3198 on 4 procs for 2000 steps with 5500 atoms
+
+Performance: 3.871 ns/day, 6.200 hours/ns, 89.606 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.452     | 12.249     | 12.556     |  13.2 | 54.88
+Bond    | 0.71352    | 0.72923    | 0.74557    |   1.3 |  3.27
+Kspace  | 5.7189     | 6.0293     | 6.8195     |  18.6 | 27.01
+Neigh   | 0.44028    | 0.44044    | 0.44065    |   0.0 |  1.97
+Comm    | 0.39667    | 0.40817    | 0.41558    |   1.1 |  1.83
+Output  | 0.0019479  | 0.0032187  | 0.0068657  |   3.7 |  0.01
+Modify  | 2.413      | 2.4256     | 2.4347     |   0.5 | 10.87
+Other   |            | 0.0349     |            |       |  0.16
+
+Nlocal:    1375 ave 1407 max 1349 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Nghost:    8082.5 ave 8114 max 8047 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    325715 ave 343636 max 314954 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 1302860
+Ave neighs/atom = 236.884
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 44
+Dangerous builds = 0
+Total wall time: 0:00:22
diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.data b/examples/USER/misc/local_density/benzene_water/benzene_water.data
new file mode 100644
index 0000000000..96a969670e
--- /dev/null
+++ b/examples/USER/misc/local_density/benzene_water/benzene_water.data
@@ -0,0 +1,1406 @@
+LAMMPS data file for 380 CG benzene, 1000 CG water particles
+
+        1380  atoms
+           0  bonds
+           0  angles
+           0  dihedrals
+           0  impropers
+
+           2  atom types
+           0  bond types
+           0  angle types
+           0  dihedral types
+           0  improper types
+       
+-1.2865e+01  1.2865e+01 xlo xhi
+-1.2865e+01  1.2865e+01 ylo yhi
+-6.4829e+01  6.4829e+01 zlo zhi
+
+Masses
+
+  1     78.1100
+  2     18.0100
+
+Atoms
+
+         1     1     1  1.13167e+01  1.36833e+00  3.59100e+01
+         2     2     1 -2.54005e+00 -6.77848e+00  6.31800e+01
+         3     3     1  3.45833e+00  2.99833e+00  1.77200e+01
+         4     4     1 -5.29338e+00 -3.98015e+00  1.79183e+01
+         5     5     1  3.53500e+00  1.13833e+01  4.63833e+01
+         6     6     1  7.65167e+00 -6.10150e-01  6.08133e+01
+         7     7     1 -3.04172e+00 -1.08435e+01  1.49817e+01
+         8     8     1  9.06000e+00 -6.93348e+00  4.72967e+01
+         9     9     1  1.24400e+01  1.15750e+01  2.26183e+01
+        10    10     1  1.03467e+01  1.12017e+01  5.86533e+01
+        11    11     1 -4.09672e+00  1.20333e+01  2.08300e+01
+        12    12     1 -3.49338e+00 -6.45682e+00  3.52333e+00
+        13    13     1 -3.49672e+00 -7.83515e+00  1.11433e+01
+        14    14     1  3.23833e+00  1.86500e+00 -5.10695e+01
+        15    15     1 -7.12672e+00 -1.15385e+01  9.44333e+00
+        16    16     1  1.28000e+00  1.09700e+01 -1.65118e+00
+        17    17     1  1.55667e+00  5.65000e-01  3.40117e+01
+        18    18     1  1.18500e+01  7.30667e+00  1.88083e+01
+        19    19     1 -4.35005e+00  7.33833e+00  3.27417e+01
+        20    20     1 -1.12884e+01  1.08583e+01  2.75500e+00
+        21    21     1  3.66167e+00  2.29500e+00 -5.68778e+01
+        22    22     1  5.64667e+00  6.78000e+00  4.53733e+01
+        23    23     1 -9.83384e-01  1.08800e+01  5.10883e+01
+        24    24     1 -1.24467e+01  5.65500e+00 -6.30578e+01
+        25    25     1 -4.58384e-01 -5.32848e+00  1.37250e+01
+        26    26     1 -1.17084e+01 -8.37515e+00  3.66933e+01
+        27    27     1 -1.12351e+01  7.00000e-01  4.80717e+01
+        28    28     1  1.93833e+00  1.73333e+00  1.49667e+00
+        29    29     1  1.50000e-02  5.44000e+00  3.67267e+01
+        30    30     1  8.41000e+00  8.69833e+00  3.12633e+01
+        31    31     1  8.89667e+00  2.18167e+00 -5.41712e+01
+        32    32     1 -1.19317e+01 -1.04301e+01  5.96933e+01
+        33    33     1 -7.92838e+00  6.11000e+00  5.62183e+01
+        34    34     1  2.62500e+00  8.58833e+00  2.83100e+01
+        35    35     1  9.49333e+00 -6.19682e+00 -5.17362e+01
+        36    36     1  5.28833e+00 -1.16185e+01 -4.91667e-01
+        37    37     1 -1.21617e+01  7.89333e+00  5.02417e+01
+        38    38     1 -6.30505e+00  9.31333e+00 -5.45045e+01
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+      1244  1244     2  4.66000e+00 -7.22015e+00 -1.56878e+01
+      1245  1245     2  5.32000e+00 -4.00150e-01 -5.00785e+00
+      1246  1246     2 -8.10051e-01 -2.62015e+00 -2.98778e+01
+      1247  1247     2 -1.08101e+01  7.68000e+00 -6.23785e+00
+      1248  1248     2  7.19000e+00 -7.80015e+00 -3.14078e+01
+      1249  1249     2  9.90000e+00  3.92000e+00 -8.91785e+00
+      1250  1250     2 -1.01005e+00  1.27600e+01 -2.62278e+01
+      1251  1251     2 -1.79005e+00 -5.91015e+00 -1.03678e+01
+      1252  1252     2 -1.61005e+00 -1.14201e+01 -2.87878e+01
+      1253  1253     2 -8.35005e+00 -1.69015e+00 -3.05978e+01
+      1254  1254     2 -1.01001e+01 -7.20015e+00 -1.16878e+01
+      1255  1255     2  1.12300e+01 -8.67015e+00 -1.58878e+01
+      1256  1256     2  7.40000e+00 -1.76015e+00 -1.65678e+01
+      1257  1257     2 -5.20005e+00 -1.09802e+01 -2.84278e+01
+      1258  1258     2  1.08800e+01  7.74000e+00 -2.96078e+01
+      1259  1259     2  4.80000e+00 -7.70015e+00 -3.99778e+01
+      1260  1260     2  1.49000e+00 -1.30150e-01 -3.65178e+01
+      1261  1261     2 -5.56005e+00 -9.87015e+00 -3.67178e+01
+      1262  1262     2 -9.83005e+00 -1.10602e+01 -3.49778e+01
+      1263  1263     2 -1.12001e+01  2.48000e+00 -1.58478e+01
+      1264  1264     2 -3.41005e+00  7.12000e+00 -1.40078e+01
+      1265  1265     2  1.17200e+01  4.81000e+00 -1.86578e+01
+      1266  1266     2 -1.22001e+01  2.82000e+00 -3.06378e+01
+      1267  1267     2 -9.60005e+00  1.10100e+01 -4.71878e+01
+      1268  1268     2 -9.04005e+00  5.10000e-01 -2.50878e+01
+      1269  1269     2 -5.96005e+00 -2.01500e-02 -3.72478e+01
+      1270  1270     2  1.27800e+01 -4.50015e+00 -1.37178e+01
+      1271  1271     2  9.00000e-02  7.49000e+00 -3.86678e+01
+      1272  1272     2  5.99000e+00 -8.09015e+00 -1.35178e+01
+      1273  1273     2  1.13100e+01 -5.61015e+00 -1.87778e+01
+      1274  1274     2  1.18700e+01 -1.06102e+01 -3.84478e+01
+      1275  1275     2  3.53000e+00 -6.05015e+00 -3.39678e+01
+      1276  1276     2 -6.20005e+00  3.51000e+00 -1.48878e+01
+      1277  1277     2  1.16400e+01  3.59000e+00 -3.85778e+01
+      1278  1278     2  1.14000e+01 -1.27701e+01 -3.58478e+01
+      1279  1279     2 -2.54005e+00  1.25300e+01 -4.23378e+01
+      1280  1280     2 -7.68005e+00 -6.93015e+00 -1.92678e+01
+      1281  1281     2  7.61000e+00 -1.63015e+00 -3.97078e+01
+      1282  1282     2 -3.45005e+00  3.35000e+00 -1.30978e+01
+      1283  1283     2 -4.44005e+00 -1.16402e+01 -4.82978e+01
+      1284  1284     2 -1.70000e-01  8.37000e+00 -2.26178e+01
+      1285  1285     2  9.78000e+00  6.78000e+00 -4.03278e+01
+      1286  1286     2 -6.58005e+00  3.79000e+00 -3.93778e+01
+      1287  1287     2  3.43000e+00 -1.06901e+01 -4.47078e+01
+      1288  1288     2  1.14100e+01 -1.26901e+01 -3.53785e+00
+      1289  1289     2 -2.10005e+00 -1.11701e+01 -2.25678e+01
+      1290  1290     2 -7.97005e+00  1.01400e+01 -3.68178e+01
+      1291  1291     2 -2.11005e+00  1.94000e+00 -3.94678e+01
+      1292  1292     2  4.75000e+00  1.07900e+01 -2.96878e+01
+      1293  1293     2  6.04000e+00 -1.28401e+01 -3.54278e+01
+      1294  1294     2  9.83000e+00  8.26000e+00 -3.22478e+01
+      1295  1295     2  9.44000e+00 -7.93015e+00 -2.88678e+01
+      1296  1296     2  1.16000e+01 -2.78015e+00 -7.80785e+00
+      1297  1297     2  1.06900e+01 -1.21402e+01 -5.94785e+00
+      1298  1298     2  3.51000e+00  9.25000e+00 -1.65078e+01
+      1299  1299     2 -8.50005e+00  4.88000e+00 -2.61678e+01
+      1300  1300     2  3.34000e+00 -1.03902e+01 -3.07978e+01
+      1301  1301     2  5.18000e+00  6.88000e+00 -2.16178e+01
+      1302  1302     2 -1.24001e+01  6.40000e+00 -1.09778e+01
+      1303  1303     2 -7.55005e+00 -6.93015e+00 -1.49378e+01
+      1304  1304     2 -1.18301e+01  8.58000e+00 -2.16785e+00
+      1305  1305     2 -1.11601e+01  4.20000e+00 -6.70785e+00
+      1306  1306     2 -7.07005e+00  8.69000e+00 -9.76785e+00
+      1307  1307     2  1.06600e+01  4.55000e+00 -1.20878e+01
+      1308  1308     2  2.64000e+00 -1.64015e+00 -1.54978e+01
+      1309  1309     2  2.99000e+00  2.74000e+00 -4.49278e+01
+      1310  1310     2  9.29000e+00 -7.03015e+00 -4.50078e+01
+      1311  1311     2  4.29000e+00  7.97000e+00 -4.54078e+01
+      1312  1312     2 -1.12701e+01 -8.00015e+00 -2.14078e+01
+      1313  1313     2 -8.40005e+00 -5.54015e+00 -2.24478e+01
+      1314  1314     2 -6.09005e+00  4.48000e+00 -3.67478e+01
+      1315  1315     2  9.15000e+00  5.23000e+00 -3.37778e+01
+      1316  1316     2 -4.68005e+00 -4.82015e+00 -4.66478e+01
+      1317  1317     2  7.52000e+00  1.57000e+00 -1.43878e+01
+      1318  1318     2 -2.77005e+00  1.19000e+00 -1.69778e+01
+      1319  1319     2  9.14000e+00 -1.53015e+00 -8.01785e+00
+      1320  1320     2  6.97000e+00 -3.24015e+00 -2.83078e+01
+      1321  1321     2  1.91000e+00  7.59000e+00 -9.15785e+00
+      1322  1322     2  6.85000e+00  4.06000e+00 -3.62578e+01
+      1323  1323     2  1.27000e+00 -3.27015e+00 -3.15078e+01
+      1324  1324     2  4.35000e+00  9.50000e+00 -5.44785e+00
+      1325  1325     2 -7.14005e+00 -6.48015e+00 -4.66478e+01
+      1326  1326     2  8.30000e-01 -1.06015e+00 -4.33785e+00
+      1327  1327     2  2.71000e+00 -1.11202e+01 -2.20978e+01
+      1328  1328     2 -9.59005e+00 -3.70015e+00 -1.81878e+01
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+      1330  1330     2 -9.11005e+00  9.59000e+00 -4.33878e+01
+      1331  1331     2  1.62000e+00  5.40000e+00 -1.84785e+00
+      1332  1332     2 -4.00051e-01 -3.22015e+00 -2.13578e+01
+      1333  1333     2  8.34000e+00 -3.06015e+00 -1.43378e+01
+      1334  1334     2 -8.45005e+00  7.58000e+00 -2.39178e+01
+      1335  1335     2  8.81000e+00  9.65000e+00 -4.30678e+01
+      1336  1336     2  2.17000e+00 -9.83015e+00 -1.26478e+01
+      1337  1337     2 -4.31005e+00  7.43000e+00 -2.58078e+01
+      1338  1338     2  8.92000e+00  8.37000e+00 -7.99785e+00
+      1339  1339     2  6.05000e+00 -3.75015e+00 -1.30278e+01
+      1340  1340     2  5.74000e+00  1.21100e+01 -4.43785e+00
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+      1344  1344     2 -1.15001e+01 -3.89015e+00 -8.07785e+00
+      1345  1345     2 -2.06005e+00 -5.76015e+00 -1.73478e+01
+      1346  1346     2 -1.24001e+01  1.08600e+01 -4.71578e+01
+      1347  1347     2 -3.59005e+00  5.39000e+00 -9.73785e+00
+      1348  1348     2  6.91000e+00 -4.28015e+00 -5.88785e+00
+      1349  1349     2 -9.64005e+00  6.56000e+00 -2.14178e+01
+      1350  1350     2  9.69000e+00  1.12200e+01 -1.51878e+01
+      1351  1351     2  1.14500e+01 -1.74015e+00  5.60000e-01
+      1352  1352     2 -6.61005e+00  1.20500e+01 -4.26078e+01
+      1353  1353     2  6.52000e+00  1.06600e+01 -1.45078e+01
+      1354  1354     2  1.03600e+01 -2.89015e+00 -4.28278e+01
+      1355  1355     2  9.30000e-01 -7.60015e+00 -2.89778e+01
+      1356  1356     2  7.04000e+00 -1.12002e+01 -4.48378e+01
+      1357  1357     2  7.40000e-01  4.14000e+00 -1.25878e+01
+      1358  1358     2  8.00000e-02 -4.35015e+00 -3.89678e+01
+      1359  1359     2  7.31000e+00  6.91000e+00 -2.43078e+01
+      1360  1360     2 -1.00401e+01 -3.51015e+00 -4.29978e+01
+      1361  1361     2 -1.75005e+00 -2.26015e+00 -1.81178e+01
+      1362  1362     2  1.12700e+01 -1.67015e+00 -1.57278e+01
+      1363  1363     2  1.01500e+01  2.95000e+00 -3.49478e+01
+      1364  1364     2 -1.22001e+01  9.13000e+00 -1.48778e+01
+      1365  1365     2 -9.12005e+00  2.42000e+00 -3.46778e+01
+      1366  1366     2  2.96000e+00  6.12000e+00 -2.66378e+01
+      1367  1367     2 -5.30005e+00  9.71000e+00 -1.68678e+01
+      1368  1368     2  9.84000e+00 -3.46015e+00 -1.09178e+01
+      1369  1369     2  3.99000e+00  4.59000e+00 -2.89778e+01
+      1370  1370     2  9.78000e+00  1.10400e+01 -3.14178e+01
+      1371  1371     2  1.03500e+01 -5.34015e+00 -1.44278e+01
+      1372  1372     2 -3.43005e+00 -9.17015e+00 -2.84178e+01
+      1373  1373     2  4.45000e+00 -3.71015e+00 -1.52778e+01
+      1374  1374     2  1.57000e+00 -7.99015e+00 -2.61278e+01
+      1375  1375     2  5.46000e+00 -2.57015e+00 -4.72978e+01
+      1376  1376     2 -1.14501e+01  1.47000e+00 -6.54785e+00
+      1377  1377     2  6.75000e+00 -5.59015e+00 -4.47678e+01
+      1378  1378     2 -5.04005e+00 -1.10502e+01 -2.49178e+01
+      1379  1379     2 -1.02401e+01 -9.00150e-01 -2.25278e+01
+      1380  1380     2  4.23000e+00 -7.94015e+00 -2.07378e+01
+
diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.in b/examples/USER/misc/local_density/benzene_water/benzene_water.in
new file mode 100644
index 0000000000..01fb3f27e5
--- /dev/null
+++ b/examples/USER/misc/local_density/benzene_water/benzene_water.in
@@ -0,0 +1,62 @@
+# LAMMPS input file for 26.5% benzene mole fraction solution
+# with 380 benzene and 1000 water molecules,
+# using all possible local density potentials
+# between benzene and water
+#
+# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
+#
+# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
+
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p 
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       benzene_water.data
+velocity        all create  3.0000e+02 16611 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1    table          benzene_water.pair.table      PairBB
+pair_coeff          1     2    table          benzene_water.pair.table      PairWW
+pair_coeff          2     2    table          benzene_water.pair.table      PairBW
+pair_coeff          *     *    local/density  benzene_water.localdensity.table
+
+# Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+# Thermostat & time integration
+timestep        2.0 
+thermo          100
+thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
+
+# Minimization
+minimize        1.e-4 0.0 10000 10000
+
+# Set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
+
+# Equilibration (for realistic results, run for 5000000 steps)
+reset_timestep  0
+run             5000
+
+# Turn off recentering during production phase
+unfix recentering
+
+# Setup trajectory output
+dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element B W
+dump_modify     myDump sort id
+
+# Production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+run             1000             
+
+
diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.localdensity.table b/examples/USER/misc/local_density/benzene_water/benzene_water.localdensity.table
new file mode 100644
index 0000000000..b0d63dbbbf
--- /dev/null
+++ b/examples/USER/misc/local_density/benzene_water/benzene_water.localdensity.table
@@ -0,0 +1,2024 @@
+# local density potentials: (B,B), (W,W), (B,W), (W,B)
+
+4 500
+
+ 6.5000000e+00  7.5000000e+00
+1
+1
+ 0.0000000e+00  2.0000000e+01  4.0080160e-02
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
+ 1.5200000e+00
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diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.pair.table b/examples/USER/misc/local_density/benzene_water/benzene_water.pair.table
new file mode 100644
index 0000000000..348bccfa0e
--- /dev/null
+++ b/examples/USER/misc/local_density/benzene_water/benzene_water.pair.table
@@ -0,0 +1,2024 @@
+
+PairBB
+N 500 R  2.00000e-02  1.32500e+01
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+427 8.5371e+00  0.0000e+00  0.0000e+00 
+428 8.5571e+00  0.0000e+00  0.0000e+00 
+429 8.5772e+00  0.0000e+00  0.0000e+00 
+430 8.5972e+00  0.0000e+00  0.0000e+00 
+431 8.6172e+00  0.0000e+00  0.0000e+00 
+432 8.6373e+00  0.0000e+00  0.0000e+00 
+433 8.6573e+00  0.0000e+00  0.0000e+00 
+434 8.6774e+00  0.0000e+00  0.0000e+00 
+435 8.6974e+00  0.0000e+00  0.0000e+00 
+436 8.7174e+00  0.0000e+00  0.0000e+00 
+437 8.7375e+00  0.0000e+00  0.0000e+00 
+438 8.7575e+00  0.0000e+00  0.0000e+00 
+439 8.7776e+00  0.0000e+00  0.0000e+00 
+440 8.7976e+00  0.0000e+00  0.0000e+00 
+441 8.8176e+00  0.0000e+00  0.0000e+00 
+442 8.8377e+00  0.0000e+00  0.0000e+00 
+443 8.8577e+00  0.0000e+00  0.0000e+00 
+444 8.8778e+00  0.0000e+00  0.0000e+00 
+445 8.8978e+00  0.0000e+00  0.0000e+00 
+446 8.9178e+00  0.0000e+00  0.0000e+00 
+447 8.9379e+00  0.0000e+00  0.0000e+00 
+448 8.9579e+00  0.0000e+00  0.0000e+00 
+449 8.9780e+00  0.0000e+00  0.0000e+00 
+450 8.9980e+00  0.0000e+00  0.0000e+00 
+451 9.0180e+00  0.0000e+00  0.0000e+00 
+452 9.0381e+00  0.0000e+00  0.0000e+00 
+453 9.0581e+00  0.0000e+00  0.0000e+00 
+454 9.0782e+00  0.0000e+00  0.0000e+00 
+455 9.0982e+00  0.0000e+00  0.0000e+00 
+456 9.1182e+00  0.0000e+00  0.0000e+00 
+457 9.1383e+00  0.0000e+00  0.0000e+00 
+458 9.1583e+00  0.0000e+00  0.0000e+00 
+459 9.1784e+00  0.0000e+00  0.0000e+00 
+460 9.1984e+00  0.0000e+00  0.0000e+00 
+461 9.2184e+00  0.0000e+00  0.0000e+00 
+462 9.2385e+00  0.0000e+00  0.0000e+00 
+463 9.2585e+00  0.0000e+00  0.0000e+00 
+464 9.2786e+00  0.0000e+00  0.0000e+00 
+465 9.2986e+00  0.0000e+00  0.0000e+00 
+466 9.3186e+00  0.0000e+00  0.0000e+00 
+467 9.3387e+00  0.0000e+00  0.0000e+00 
+468 9.3587e+00  0.0000e+00  0.0000e+00 
+469 9.3788e+00  0.0000e+00  0.0000e+00 
+470 9.3988e+00  0.0000e+00  0.0000e+00 
+471 9.4188e+00  0.0000e+00  0.0000e+00 
+472 9.4389e+00  0.0000e+00  0.0000e+00 
+473 9.4589e+00  0.0000e+00  0.0000e+00 
+474 9.4790e+00  0.0000e+00  0.0000e+00 
+475 9.4990e+00  0.0000e+00  0.0000e+00 
+476 9.5190e+00  0.0000e+00  0.0000e+00 
+477 9.5391e+00  0.0000e+00  0.0000e+00 
+478 9.5591e+00  0.0000e+00  0.0000e+00 
+479 9.5792e+00  0.0000e+00  0.0000e+00 
+480 9.5992e+00  0.0000e+00  0.0000e+00 
+481 9.6192e+00  0.0000e+00  0.0000e+00 
+482 9.6393e+00  0.0000e+00  0.0000e+00 
+483 9.6593e+00  0.0000e+00  0.0000e+00 
+484 9.6794e+00  0.0000e+00  0.0000e+00 
+485 9.6994e+00  0.0000e+00  0.0000e+00 
+486 9.7194e+00  0.0000e+00  0.0000e+00 
+487 9.7395e+00  0.0000e+00  0.0000e+00 
+488 9.7595e+00  0.0000e+00  0.0000e+00 
+489 9.7796e+00  0.0000e+00  0.0000e+00 
+490 9.7996e+00  0.0000e+00  0.0000e+00 
+491 9.8196e+00  0.0000e+00  0.0000e+00 
+492 9.8397e+00  0.0000e+00  0.0000e+00 
+493 9.8597e+00  0.0000e+00  0.0000e+00 
+494 9.8798e+00  0.0000e+00  0.0000e+00 
+495 9.8998e+00  0.0000e+00  0.0000e+00 
+496 9.9198e+00  0.0000e+00  0.0000e+00 
+497 9.9399e+00  0.0000e+00  0.0000e+00 
+498 9.9599e+00  0.0000e+00  0.0000e+00 
+499 9.9800e+00  0.0000e+00  0.0000e+00 
+500 1.0000e+01  0.0000e+00  0.0000e+00 
+
+
diff --git a/examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1 b/examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1
new file mode 100644
index 0000000000..928906edbd
--- /dev/null
+++ b/examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1
@@ -0,0 +1,267 @@
+LAMMPS (7 Aug 2019)
+# LAMMPS input file for 26.5% benzene mole fraction solution
+# with 380 benzene and 1000 water molecules,
+# using all possible local density potentials
+# between benzene and water
+#
+# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
+#
+# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
+
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       benzene_water.data
+  orthogonal box = (-12.865 -12.865 -64.829) to (12.865 12.865 64.829)
+  1 by 1 by 8 MPI processor grid
+  reading atoms ...
+  1380 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000566959 secs
+  read_data CPU = 0.00661397 secs
+velocity        all create  3.0000e+02 16611 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1    table          benzene_water.pair.table      PairBB
+WARNING: 33 of 500 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:483)
+WARNING: 150 of 500 distance values in table with relative error
+  over 1e-06 to re-computed values (../pair_table.cpp:492)
+pair_coeff          1     2    table          benzene_water.pair.table      PairWW
+WARNING: 61 of 500 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:483)
+WARNING: 90 of 500 distance values in table with relative error
+  over 1e-06 to re-computed values (../pair_table.cpp:492)
+pair_coeff          2     2    table          benzene_water.pair.table      PairBW
+WARNING: 108 of 500 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:483)
+WARNING: 135 of 500 distance values in table with relative error
+  over 1e-06 to re-computed values (../pair_table.cpp:492)
+pair_coeff          *     *    local/density  benzene_water.localdensity.table
+
+# Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+# Thermostat & time integration
+timestep        2.0
+thermo          100
+thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
+
+# Minimization
+minimize        1.e-4 0.0 10000 10000
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 15.25
+  ghost atom cutoff = 15.25
+  binsize = 7.625, bins = 4 4 18
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.061 | 8.32 | 8.674 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    4162.3053    5395.4665            0            0            0    4162.3053 
+         300    1233.1611     2275.526    3508.6871            0            0            0     2275.526 
+Loop time of 0.352822 on 8 procs for 40 steps with 1380 atoms
+
+71.3% CPU use with 8 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = linesearch alpha is zero
+  Energy initial, next-to-last, final = 
+         4162.30533361      2208.86525108      2275.52597861
+  Force two-norm initial, final = 259.364 69.3915
+  Force max component initial, final = 22.2077 8.31436
+  Final line search alpha, max atom move = 2.90022e-12 2.41135e-11
+  Iterations, force evaluations = 40 110
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.053192   | 0.23903    | 0.32779    |  17.2 | 67.75
+Bond    | 9.0599e-06 | 1.6302e-05 | 2.5272e-05 |   0.0 |  0.00
+Neigh   | 0.00044513 | 0.0023614  | 0.0063851  |   5.1 |  0.67
+Comm    | 0.015469   | 0.090432   | 0.20295    |  20.0 | 25.63
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.02098    |            |       |  5.95
+
+Nlocal:    172.5 ave 348 max 72 min
+Histogram: 5 0 0 0 0 0 0 0 1 2
+Nghost:    2193.62 ave 4352 max 932 min
+Histogram: 3 0 0 2 0 0 2 0 0 1
+Neighs:    9700.5 ave 20535 max 3685 min
+Histogram: 5 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 77604
+Ave neighs/atom = 56.2348
+Ave special neighs/atom = 0
+Neighbor list builds = 2
+Dangerous builds = 0
+
+# Set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
+
+# Equilibration (for realistic results, run for 5000000 steps)
+reset_timestep  0
+run             5000
+WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
+Per MPI rank memory allocation (min/avg/max) = 6.936 | 7.195 | 7.552 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    2866.9109    4100.0721            0            0            0    2866.9109 
+   273.33541    1123.5553    3983.2007     5106.756            0            0            0    3983.2007 
+   293.68078    1207.1857    3319.6601    4526.8458            0            0            0    3319.6601 
+   314.21462    1291.5908    3389.2178    4680.8086            0            0            0    3389.2178 
+   323.77563    1330.8917    3332.9828    4663.8745            0            0            0    3332.9828 
+    302.5902    1243.8082    3461.7692    4705.5774            0            0            0    3461.7692 
+   295.39324    1214.2249    3411.5727    4625.7976            0            0            0    3411.5727 
+   320.52341    1317.5234    3453.1931    4770.7164            0            0            0    3453.1931 
+   312.00777    1282.5195    3403.3443    4685.8638            0            0            0    3403.3443 
+   307.96774    1265.9128    3429.7809    4695.6937            0            0            0    3429.7809 
+   294.75922    1211.6187    3388.8404    4600.4591            0            0            0    3388.8404 
+   311.24567    1279.3869    3514.9603    4794.3472            0            0            0    3514.9603 
+    306.6152    1260.3531    3447.2011    4707.5542            0            0            0    3447.2011 
+   305.23306    1254.6718    3375.5092     4630.181            0            0            0    3375.5092 
+   321.62889    1322.0675    3460.2581    4782.3256            0            0            0    3460.2581 
+   316.37725    1300.4804    3437.0312    4737.5116            0            0            0    3437.0312 
+   322.90522    1327.3139    3389.1262      4716.44            0            0            0    3389.1262 
+   307.57893    1264.3146    3359.8491    4624.1637            0            0            0    3359.8491 
+   302.22607    1242.3115    3406.1711    4648.4826            0            0            0    3406.1711 
+   302.73997    1244.4239    3220.2582    4464.6821            0            0            0    3220.2582 
+   303.66194    1248.2137    3318.4629    4566.6765            0            0            0    3318.4629 
+   308.73862    1269.0815    3369.5894     4638.671            0            0            0    3369.5894 
+   315.60294    1297.2976    3411.2405    4708.5381            0            0            0    3411.2405 
+    310.0113    1274.3129    3360.1054    4634.4183            0            0            0    3360.1054 
+   302.36229    1242.8714    3326.9845    4569.8559            0            0            0    3326.9845 
+   317.78659    1306.2735    3355.4976    4661.7711            0            0            0    3355.4976 
+   302.50479    1243.4571    3317.6846    4561.1417            0            0            0    3317.6846 
+   304.29249    1250.8056    3423.5068    4674.3124            0            0            0    3423.5068 
+   305.99948    1257.8222    3432.9395    4690.7617            0            0            0    3432.9395 
+   309.93363    1273.9937     3393.657    4667.6506            0            0            0     3393.657 
+   316.14884    1299.5415    3463.0636    4762.6051            0            0            0    3463.0636 
+   300.38817    1234.7567    3309.2495    4544.0062            0            0            0    3309.2495 
+   311.05735    1278.6128    3304.4418    4583.0546            0            0            0    3304.4418 
+   311.11872     1278.865    3291.1891    4570.0542            0            0            0    3291.1891 
+   315.74338    1297.8749    3341.3063    4639.1812            0            0            0    3341.3063 
+    297.5658    1223.1552    3316.3862    4539.5414            0            0            0    3316.3862 
+   311.79033    1281.6257    3357.4556    4639.0813            0            0            0    3357.4556 
+   310.93666    1278.1167    3414.7694    4692.8861            0            0            0    3414.7694 
+   307.37298     1263.468    3337.3889    4600.8569            0            0            0    3337.3889 
+   298.84185    1228.4005    3329.6173    4558.0178            0            0            0    3329.6173 
+   310.54684    1276.5143    3351.0852    4627.5995            0            0            0    3351.0852 
+    300.0871    1233.5191    3302.2315    4535.7506            0            0            0    3302.2315 
+   304.69078    1252.4427    3324.2508    4576.6935            0            0            0    3324.2508 
+   313.50714    1288.6827    3330.4088    4619.0915            0            0            0    3330.4088 
+   329.80018    1355.6559      3301.86    4657.5159            0            0            0      3301.86 
+   304.57609    1251.9713    3365.2938    4617.2652            0            0            0    3365.2938 
+   308.73584    1269.0701    3344.4155    4613.4856            0            0            0    3344.4155 
+   306.90951    1261.5629    3304.4698    4566.0327            0            0            0    3304.4698 
+   308.85761    1269.5707    3392.1511    4661.7218            0            0            0    3392.1511 
+   302.78788    1244.6208    3317.0849    4561.7057            0            0            0    3317.0849 
+   321.68092    1322.2813    3321.5755    4643.8568            0            0            0    3321.5755 
+Loop time of 16.3061 on 8 procs for 5000 steps with 1380 atoms
+
+Performance: 52.986 ns/day, 0.453 hours/ns, 306.634 timesteps/s
+69.6% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.1872     | 10.542     | 14.607     | 116.7 | 64.65
+Bond    | 0.00044084 | 0.00069669 | 0.00095081 |   0.0 |  0.00
+Neigh   | 0.026948   | 0.15225    | 0.44344    |  42.0 |  0.93
+Comm    | 0.63452    | 4.2953     | 9.49       | 133.9 | 26.34
+Output  | 0.0016391  | 0.012378   | 0.050919   |  13.9 |  0.08
+Modify  | 0.45894    | 1.2107     | 4.4629     | 116.4 |  7.42
+Other   |            | 0.09292    |            |       |  0.57
+
+Nlocal:    172.5 ave 380 max 70 min
+Histogram: 5 0 0 0 0 0 0 1 1 1
+Nghost:    2213 ave 4440 max 903 min
+Histogram: 3 0 0 2 0 0 2 0 0 1
+Neighs:    10042.5 ave 24051 max 3500 min
+Histogram: 5 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 80340
+Ave neighs/atom = 58.2174
+Ave special neighs/atom = 0
+Neighbor list builds = 123
+Dangerous builds = 1
+
+# Turn off recentering during production phase
+unfix recentering
+
+# Setup trajectory output
+dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element B W
+dump_modify     myDump sort id
+
+# Production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+run             1000
+Per MPI rank memory allocation (min/avg/max) = 8.232 | 8.492 | 8.851 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+   321.68092    1322.2813    3784.0834    5106.3647            0            0            0    3784.0834 
+   310.59763    1276.7231    3318.3283    4595.0513            0            0            0    3318.3283 
+   303.39445    1247.1141    3324.1191    4571.2332            0            0            0    3324.1191 
+   311.37275    1279.9092    3305.0901    4584.9993            0            0            0    3305.0901 
+   311.29071     1279.572     3248.216     4527.788            0            0            0     3248.216 
+   314.53456     1292.906    3283.4563    4576.3623            0            0            0    3283.4563 
+   316.52595    1301.0916    3258.9171    4560.0087            0            0            0    3258.9171 
+   318.92447    1310.9509    3235.6256    4546.5765            0            0            0    3235.6256 
+   311.79212    1281.6331     3308.099    4589.7321            0            0            0     3308.099 
+   305.52477    1255.8709    3267.6907    4523.5616            0            0            0    3267.6907 
+   301.07457    1237.5782    3206.3997    4443.9779            0            0            0    3206.3997 
+Loop time of 4.44139 on 8 procs for 1000 steps with 1380 atoms
+
+Performance: 38.907 ns/day, 0.617 hours/ns, 225.155 timesteps/s
+60.8% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.656      | 2.5078     | 3.5775     |  57.7 | 56.46
+Bond    | 0.00013375 | 0.0001854  | 0.0002377  |   0.0 |  0.00
+Neigh   | 0.0048757  | 0.029188   | 0.090432   |  18.9 |  0.66
+Comm    | 0.51836    | 1.4427     | 2.6285     |  56.9 | 32.48
+Output  | 0.083084   | 0.089199   | 0.10333    |   2.3 |  2.01
+Modify  | 0.0087376  | 0.019705   | 0.038437   |   8.4 |  0.44
+Other   |            | 0.3526     |            |       |  7.94
+
+Nlocal:    172.5 ave 388 max 69 min
+Histogram: 5 0 0 0 0 0 0 2 0 1
+Nghost:    2207.88 ave 4429 max 896 min
+Histogram: 3 0 0 2 0 0 2 0 0 1
+Neighs:    10094.1 ave 24847 max 3403 min
+Histogram: 5 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 80753
+Ave neighs/atom = 58.5167
+Ave special neighs/atom = 0
+Neighbor list builds = 23
+Dangerous builds = 0
+
+
+Total wall time: 0:00:21
diff --git a/examples/USER/misc/local_density/methanol_implicit_water/log.04Sep19.g++.1 b/examples/USER/misc/local_density/methanol_implicit_water/log.04Sep19.g++.1
new file mode 100644
index 0000000000..618e994946
--- /dev/null
+++ b/examples/USER/misc/local_density/methanol_implicit_water/log.04Sep19.g++.1
@@ -0,0 +1,226 @@
+LAMMPS (7 Aug 2019)
+# LAMMPS input file for 50.0% methanol mole fraction solution
+# with 2500 methanol molecules in implicit water.
+#
+#
+# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
+#
+# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       methanol_implicit_water.data
+  orthogonal box = (-31.123 -31.123 -31.123) to (31.123 31.123 31.123)
+  2 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2500 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.00063014 secs
+  read_data CPU = 0.00599909 secs
+velocity        all create  3.0000e+02 12142 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
+WARNING: 93 of 500 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:483)
+WARNING: 254 of 500 distance values in table with relative error
+  over 1e-06 to re-computed values (../pair_table.cpp:492)
+pair_coeff          *     * local/density methanol_implicit_water.localdensity.table
+
+
+
+
+#Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+#Thermostat & time integration
+timestep        1.0
+thermo          100
+thermo_style    custom etotal ke pe temp evdwl
+
+#minimization
+minimize        1.e-4 0.0 1000 1000
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 17
+  ghost atom cutoff = 17
+  binsize = 8.5, bins = 8 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.411 | 7.411 | 7.412 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1470.3564    2234.7133   -764.35689          300   -764.35689 
+   46.496766    2234.7133   -2188.2165          300   -2188.2165 
+   7.9030246    2234.7133   -2226.8103          300   -2226.8103 
+Loop time of 0.463996 on 8 procs for 121 steps with 2500 atoms
+
+91.4% CPU use with 8 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = linesearch alpha is zero
+  Energy initial, next-to-last, final = 
+        -764.356892369     -2227.85589084     -2226.81026984
+  Force two-norm initial, final = 134.911 3.83896
+  Force max component initial, final = 14.1117 1.07422
+  Final line search alpha, max atom move = 5.06747e-10 5.44356e-10
+  Iterations, force evaluations = 121 154
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.41442    | 0.41976    | 0.42434    |   0.5 | 90.47
+Bond    | 1.1683e-05 | 2.0713e-05 | 3.5048e-05 |   0.0 |  0.00
+Neigh   | 0.0084722  | 0.0090862  | 0.010038   |   0.5 |  1.96
+Comm    | 0.022712   | 0.028157   | 0.034072   |   1.9 |  6.07
+Output  | 3.1948e-05 | 3.6925e-05 | 6.6996e-05 |   0.0 |  0.01
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.006937   |            |       |  1.50
+
+Nlocal:    312.5 ave 333 max 299 min
+Histogram: 2 2 0 0 1 0 2 0 0 1
+Nghost:    2546 ave 2580 max 2517 min
+Histogram: 1 1 0 3 0 1 0 0 0 2
+Neighs:    33215.4 ave 37251 max 29183 min
+Histogram: 1 0 0 1 2 2 0 1 0 1
+
+Total # of neighbors = 265723
+Ave neighs/atom = 106.289
+Ave special neighs/atom = 0
+Neighbor list builds = 6
+Dangerous builds = 0
+
+#set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915
+
+#Equilibration (for realistic results, run for 2000000  steps)
+reset_timestep  0
+thermo          200
+thermo_style    custom etotal ke pe temp evdwl
+
+#run equilibration
+run             2000
+WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
+Per MPI rank memory allocation (min/avg/max) = 6.286 | 6.286 | 6.287 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   177.26822    2234.7133   -2057.4451          300   -2057.4451 
+   736.24287    2151.2608   -1415.0179    288.79688   -1415.0179 
+   963.07617    2090.6433   -1127.5671    280.65926   -1127.5671 
+   1148.9049    2173.1327   -1024.2279    291.73309   -1024.2279 
+   1303.6409    2279.8586   -976.21767    306.06055   -976.21767 
+     1355.42    2281.0383   -925.61826    306.21892   -925.61826 
+   1394.5206    2276.2093   -881.68863    305.57064   -881.68863 
+   1346.9764    2215.2973   -868.32091     297.3935   -868.32091 
+   1381.3654    2248.8061   -867.44063    301.89189   -867.44063 
+   1315.8059    2189.3193   -873.51332    293.90606   -873.51332 
+   1314.4456    2209.7431   -895.29752    296.64787   -895.29752 
+Loop time of 6.38989 on 8 procs for 2000 steps with 2500 atoms
+
+Performance: 27.043 ns/day, 0.887 hours/ns, 312.994 timesteps/s
+80.5% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.2693     | 5.3572     | 5.457      |   2.1 | 83.84
+Bond    | 0.00028825 | 0.00033835 | 0.00039148 |   0.0 |  0.01
+Neigh   | 0.0296     | 0.032337   | 0.035071   |   0.9 |  0.51
+Comm    | 0.64679    | 0.73397    | 0.80847    |   5.2 | 11.49
+Output  | 0.00033498 | 0.00051582 | 0.0015228  |   0.0 |  0.01
+Modify  | 0.16395    | 0.18919    | 0.21056    |   3.9 |  2.96
+Other   |            | 0.07636    |            |       |  1.19
+
+Nlocal:    312.5 ave 337 max 295 min
+Histogram: 2 2 0 1 0 0 0 1 1 1
+Nghost:    2551.62 ave 2582 max 2525 min
+Histogram: 2 1 0 0 1 1 1 0 1 1
+Neighs:    33241.8 ave 37659 max 29705 min
+Histogram: 2 0 0 2 2 0 0 0 1 1
+
+Total # of neighbors = 265934
+Ave neighs/atom = 106.374
+Ave special neighs/atom = 0
+Neighbor list builds = 21
+Dangerous builds = 0
+
+#turn off recentering during production run
+unfix recentering
+
+
+#setup trajectory output
+dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element M
+dump_modify     myDump sort id
+
+#run production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+thermo          1000
+thermo_style    custom etotal ke pe temp  evdwl
+run             10000
+Per MPI rank memory allocation (min/avg/max) = 7.588 | 7.589 | 7.589 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1442.5428    2209.7431   -767.20027    296.64787   -767.20027 
+   1391.8624    2262.6889   -870.82656     303.7556   -870.82656 
+    1375.914    2244.6176    -868.7036     301.3296    -868.7036 
+   1345.9064    2227.2324   -881.32599    298.99573   -881.32599 
+   1379.2334    2278.1156   -898.88222    305.82657   -898.88222 
+   1389.7928    2255.8062   -866.01341    302.83163   -866.01341 
+   1380.4549    2258.2108   -877.75582    303.15443   -877.75582 
+   1380.8489    2256.9432   -876.09428    302.98426   -876.09428 
+   1326.5151    2225.7408   -899.22577    298.79549   -899.22577 
+   1376.6025    2253.0128   -876.41028    302.45662   -876.41028 
+   1331.0008    2218.1033   -887.10258    297.77019   -887.10258 
+Loop time of 25.4591 on 8 procs for 10000 steps with 2500 atoms
+
+Performance: 33.937 ns/day, 0.707 hours/ns, 392.787 timesteps/s
+89.3% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 21.635     | 21.916     | 22.237     |   3.9 | 86.08
+Bond    | 0.0011308  | 0.0013149  | 0.0016932  |   0.5 |  0.01
+Neigh   | 0.14593    | 0.15675    | 0.16667    |   1.9 |  0.62
+Comm    | 1.3789     | 1.7502     | 1.9558     |  13.7 |  6.87
+Output  | 0.34664    | 0.82927    | 1.2013     |  32.8 |  3.26
+Modify  | 0.24904    | 0.25842    | 0.26907    |   1.2 |  1.02
+Other   |            | 0.5475     |            |       |  2.15
+
+Nlocal:    312.5 ave 327 max 298 min
+Histogram: 2 0 0 1 1 0 1 1 1 1
+Nghost:    2575 ave 2601 max 2559 min
+Histogram: 2 0 3 1 0 0 0 0 1 1
+Neighs:    33223.2 ave 35920 max 30303 min
+Histogram: 1 1 1 1 0 1 0 0 0 3
+
+Total # of neighbors = 265786
+Ave neighs/atom = 106.314
+Ave special neighs/atom = 0
+Neighbor list builds = 103
+Dangerous builds = 0
+
+
+Total wall time: 0:00:32
diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.data b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.data
new file mode 100644
index 0000000000..1dd9eccc7c
--- /dev/null
+++ b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.data
@@ -0,0 +1,2525 @@
+LAMMPS Description
+
+        2500  atoms
+           0  bonds
+           0  angles
+           0  dihedrals
+           0  impropers
+
+           1  atom types
+           0  bond types
+           0  angle types
+           0  dihedral types
+           0  improper types
+       
+-3.1123e+01  3.1123e+01 xlo xhi
+-3.1123e+01  3.1123e+01 ylo yhi
+-3.1123e+01  3.1123e+01 zlo zhi
+
+Masses
+
+  1     32.0000
+
+Atoms
+
+         1     1     1 -1.20055e+01  1.00800e+01  5.26000e+00
+         2     2     1 -5.60545e+00  2.34700e+01  3.10400e+01
+         3     3     1  1.33900e+01  1.50700e+01 -1.56654e+01
+         4     4     1 -3.57545e+00 -1.71754e+01 -7.17545e+00
+         5     5     1  1.09000e+01  1.67100e+01 -2.57554e+01
+         6     6     1  1.96400e+01 -6.07545e+00 -2.72454e+01
+         7     7     1 -7.56545e+00 -1.92354e+01 -2.37154e+01
+         8     8     1 -5.72545e+00 -2.45654e+01 -2.34154e+01
+         9     9     1 -1.71655e+01  2.46700e+01  1.76300e+01
+        10    10     1  8.06000e+00  4.73000e+00 -7.34545e+00
+        11    11     1  2.32300e+01 -2.01054e+01  1.78600e+01
+        12    12     1 -2.05955e+01  1.44500e+01 -6.35545e+00
+        13    13     1  1.80700e+01  2.19800e+01 -4.22545e+00
+        14    14     1 -1.26355e+01 -2.92545e+00 -2.09154e+01
+        15    15     1 -2.05255e+01 -2.12254e+01 -2.21454e+01
+        16    16     1  6.69000e+00  2.60700e+01  1.22700e+01
+        17    17     1  1.08600e+01 -2.00054e+01 -2.82854e+01
+        18    18     1 -1.89255e+01  3.30000e-01  1.15200e+01
+        19    19     1  1.85400e+01  1.31900e+01 -7.98545e+00
+        20    20     1 -1.49055e+01  1.45900e+01 -2.19354e+01
+        21    21     1  1.91400e+01 -2.43054e+01 -2.54454e+01
+        22    22     1  1.04200e+01 -2.94954e+01 -2.95654e+01
+        23    23     1 -7.37545e+00  2.08500e+01  2.58700e+01
+        24    24     1  1.25600e+01  2.80000e-01 -1.38054e+01
+        25    25     1 -2.11055e+01  1.01500e+01  3.10000e+01
+        26    26     1  2.78800e+01 -1.10254e+01  1.86300e+01
+        27    27     1  2.17000e+00 -3.01454e+01  1.67700e+01
+        28    28     1  2.76700e+01  1.44600e+01 -1.37954e+01
+        29    29     1  2.15200e+01 -3.45545e+00  4.45000e+00
+        30    30     1 -8.15545e+00  1.89500e+01 -2.73954e+01
+        31    31     1 -5.89545e+00 -1.45954e+01  2.62100e+01
+        32    32     1  2.29600e+01 -1.23154e+01  2.91800e+01
+        33    33     1  4.87000e+00 -2.65754e+01  8.54000e+00
+        34    34     1  1.93000e+00 -1.43554e+01  1.85200e+01
+        35    35     1 -2.78355e+01 -2.84754e+01 -2.38454e+01
+        36    36     1  3.08000e+00 -2.54354e+01  1.99500e+01
+        37    37     1  2.12700e+01 -6.71545e+00  1.28000e+00
+        38    38     1 -3.45545e+00 -2.41754e+01  1.49600e+01
+        39    39     1  2.54700e+01  1.63000e+01  6.99000e+00
+        40    40     1 -1.80855e+01  2.44800e+01  4.97000e+00
+        41    41     1  1.28400e+01 -1.15446e-01 -2.87954e+01
+        42    42     1 -7.86545e+00  2.17000e+00  1.67100e+01
+        43    43     1  2.42300e+01 -8.29545e+00  2.04200e+01
+        44    44     1 -4.35545e+00  4.68000e+00  2.66200e+01
+        45    45     1 -1.53655e+01 -1.15154e+01  1.35000e+00
+        46    46     1 -2.67255e+01 -2.33054e+01 -3.01254e+01
+        47    47     1  1.13800e+01 -3.05554e+01 -2.18054e+01
+        48    48     1  2.05100e+01  1.55100e+01 -6.31545e+00
+        49    49     1 -7.45545e+00  2.28000e+00 -2.04754e+01
+        50    50     1 -6.11545e+00  2.97900e+01 -2.21154e+01
+        51    51     1 -1.21355e+01  2.64200e+01  1.95100e+01
+        52    52     1  1.78800e+01  1.04000e+00  2.19500e+01
+        53    53     1 -1.64755e+01  1.01300e+01  1.40700e+01
+        54    54     1 -1.92955e+01 -2.53654e+01 -2.21754e+01
+        55    55     1  2.55800e+01 -2.55154e+01  3.60000e-01
+        56    56     1  1.79800e+01  1.51100e+01  2.99700e+01
+        57    57     1  2.65400e+01  2.17200e+01  2.76100e+01
+        58    58     1 -3.43545e+00  9.65000e+00  2.66700e+01
+        59    59     1 -1.77455e+01  3.02400e+01  1.95100e+01
+        60    60     1  2.93400e+01  3.01500e+01 -7.77545e+00
+        61    61     1  1.95600e+01 -1.14354e+01 -2.76154e+01
+        62    62     1  2.69600e+01 -1.91054e+01  1.92300e+01
+        63    63     1 -2.29855e+01  1.28800e+01  2.24600e+01
+        64    64     1  2.91000e+01 -9.55446e-01  1.35600e+01
+        65    65     1  2.06800e+01 -1.73545e+00 -1.27454e+01
+        66    66     1 -5.86545e+00 -1.14854e+01  1.16000e+01
+        67    67     1  2.67700e+01 -2.98654e+01 -1.12545e+00
+        68    68     1 -1.23655e+01 -2.27554e+01 -2.15654e+01
+        69    69     1 -4.60545e+00  2.12800e+01 -7.00000e-02
+        70    70     1 -5.55450e-01 -7.06545e+00  1.73000e+01
+        71    71     1 -5.79545e+00 -1.63354e+01 -2.29654e+01
+        72    72     1  4.00000e-02  1.56000e+00  1.93200e+01
+        73    73     1  3.02400e+01 -1.67854e+01 -2.48154e+01
+        74    74     1 -3.09355e+01  1.86700e+01 -1.22454e+01
+        75    75     1 -1.19955e+01 -8.34545e+00  2.04400e+01
+        76    76     1  3.89000e+00 -2.16854e+01  1.56300e+01
+        77    77     1  2.14900e+01 -1.14254e+01  8.10000e-01
+        78    78     1  2.74400e+01  1.13900e+01 -2.49545e+00
+        79    79     1 -2.99545e+00 -1.55154e+01 -1.94554e+01
+        80    80     1  2.07000e+00  9.21000e+00 -1.05154e+01
+        81    81     1  6.50000e-01  2.59100e+01 -2.39854e+01
+        82    82     1 -1.04255e+01  1.96100e+01  8.64000e+00
+        83    83     1  8.40000e+00 -1.56954e+01  8.10000e-01
+        84    84     1  7.39000e+00 -2.82254e+01 -4.90545e+00
+        85    85     1  1.14500e+01 -1.95054e+01 -7.24545e+00
+        86    86     1  2.47300e+01 -4.21545e+00 -1.81254e+01
+        87    87     1  1.06900e+01  1.46200e+01 -1.34754e+01
+        88    88     1  6.61000e+00  2.26100e+01 -1.62454e+01
+        89    89     1  1.64000e+01  2.74400e+01  8.31000e+00
+        90    90     1 -6.37545e+00 -4.54457e-02 -4.79545e+00
+        91    91     1  2.96500e+01 -2.74154e+01 -1.73854e+01
+        92    92     1  1.20600e+01  9.85000e+00 -6.06545e+00
+        93    93     1  2.11300e+01  4.90000e-01  9.35000e+00
+        94    94     1 -2.94255e+01 -2.17554e+01 -1.88354e+01
+        95    95     1  9.67000e+00 -1.47154e+01 -1.30854e+01
+        96    96     1 -1.04355e+01  1.95200e+01  3.58000e+00
+        97    97     1  1.39600e+01 -7.77545e+00  2.75700e+01
+        98    98     1  1.22700e+01  4.36000e+00 -7.43545e+00
+        99    99     1 -3.38545e+00  1.87500e+01  2.47000e+01
+       100   100     1 -1.34055e+01 -2.84054e+01 -2.52554e+01
+       101   101     1  1.13900e+01 -7.85545e+00  1.70300e+01
+       102   102     1 -4.00000e-01  2.16200e+01 -1.14954e+01
+       103   103     1  6.01000e+00 -5.74545e+00 -3.00854e+01
+       104   104     1 -1.96655e+01 -1.18854e+01 -2.29854e+01
+       105   105     1  2.12000e+00 -2.43654e+01  2.36400e+01
+       106   106     1 -2.53545e+00 -2.06554e+01  2.50000e+00
+       107   107     1 -3.06555e+01 -1.93654e+01  2.53600e+01
+       108   108     1  2.62600e+01  1.55000e+01 -3.03054e+01
+       109   109     1 -1.65055e+01 -5.86545e+00 -5.13545e+00
+       110   110     1 -1.66055e+01 -2.46754e+01 -1.04554e+01
+       111   111     1 -2.04545e+00  2.36200e+01  3.02600e+01
+       112   112     1  7.06000e+00  2.82900e+01 -2.83545e+00
+       113   113     1  2.48200e+01 -2.12545e+00 -2.29854e+01
+       114   114     1 -2.89655e+01  2.78300e+01  6.81000e+00
+       115   115     1  1.70900e+01  1.87200e+01  1.21000e+01
+       116   116     1 -1.67855e+01  4.83000e+00  1.19600e+01
+       117   117     1  2.31900e+01 -2.17554e+01 -2.28054e+01
+       118   118     1  1.88400e+01  1.95000e+01  2.83400e+01
+       119   119     1 -9.95545e+00  1.46300e+01 -3.17545e+00
+       120   120     1  1.72000e+01 -2.67354e+01 -2.82654e+01
+       121   121     1  2.95000e+00 -1.74354e+01  1.54900e+01
+       122   122     1  8.31000e+00 -3.22545e+00 -2.01254e+01
+       123   123     1  2.75400e+01  6.82000e+00  1.73800e+01
+       124   124     1  2.94000e+01  2.36900e+01  2.82500e+01
+       125   125     1  1.44600e+01 -4.81545e+00  5.55000e+00
+       126   126     1 -2.36545e+00  3.55000e+00 -1.71154e+01
+       127   127     1  1.93600e+01  1.67700e+01  2.56200e+01
+       128   128     1 -9.42545e+00  2.30900e+01 -1.49154e+01
+       129   129     1  3.28000e+00 -2.20454e+01 -7.81545e+00
+       130   130     1 -9.65545e+00  1.68700e+01 -8.51545e+00
+       131   131     1 -2.03155e+01  2.34000e+01 -1.09754e+01
+       132   132     1  2.63100e+01 -8.29545e+00 -4.80545e+00
+       133   133     1  1.92100e+01 -2.67954e+01  1.41700e+01
+       134   134     1  4.99000e+00  1.44600e+01  2.29400e+01
+       135   135     1  4.54000e+00  1.01600e+01  3.10900e+01
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+      2491  2491     1 -2.91855e+01 -8.43545e+00  2.32500e+01
+      2492  2492     1  2.81900e+01  3.17000e+00  2.42000e+01
+      2493  2493     1 -2.47355e+01  1.11400e+01 -2.31454e+01
+      2494  2494     1 -2.98455e+01  6.67000e+00  2.34500e+01
+      2495  2495     1  1.05700e+01  4.19000e+00  2.24900e+01
+      2496  2496     1  2.57900e+01  7.07000e+00 -2.83454e+01
+      2497  2497     1 -5.55545e+00  1.41600e+01  2.53600e+01
+      2498  2498     1 -1.19855e+01 -2.52754e+01 -2.81154e+01
+      2499  2499     1  2.19000e+00 -3.04154e+01  2.90800e+01
+      2500  2500     1  5.98000e+00 -2.65154e+01 -5.44540e-03
+
diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.in b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.in
new file mode 100644
index 0000000000..ef92fbe655
--- /dev/null
+++ b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.in
@@ -0,0 +1,68 @@
+# LAMMPS input file for 50.0% methanol mole fraction solution
+# with 2500 methanol molecules in implicit water.
+# 
+#
+# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
+#
+# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p 
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       methanol_implicit_water.data 
+velocity        all create  3.0000e+02 12142 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
+pair_coeff          *     * local/density methanol_implicit_water.localdensity.table
+
+
+
+
+#Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+#Thermostat & time integration
+timestep        1.0 
+thermo          100
+thermo_style    custom etotal ke pe temp evdwl
+
+#minimization
+minimize        1.e-4 0.0 1000 1000
+
+#set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915
+
+#Equilibration (for realistic results, run for 2000000  steps)
+reset_timestep  0
+thermo          200
+thermo_style    custom etotal ke pe temp evdwl
+
+#run equilibration
+run             2000
+
+#turn off recentering during production run
+unfix recentering
+
+
+#setup trajectory output
+dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element M
+dump_modify     myDump sort id
+
+#run production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+thermo          1000
+thermo_style    custom etotal ke pe temp  evdwl
+run             10000
+
+
diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table
new file mode 100644
index 0000000000..b9b4a082bc
--- /dev/null
+++ b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table
@@ -0,0 +1,509 @@
+#LOCAL DENSITY POTENTIALS
+
+1 500
+
+ 5.3000000e+00  6.3000000e+00
+1
+1
+ 0.0000000e+00  2.6000000e+01  5.2104208e-02
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
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+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
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+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4810000e-01
+ 1.4807157e-01
+ 1.4782582e-01
+ 1.4711763e-01
+ 1.4570179e-01
+ 1.4333312e-01
+ 1.3976643e-01
+ 1.3478059e-01
+ 1.2856173e-01
+ 1.2163552e-01
+ 1.1453802e-01
+ 1.0780525e-01
+ 1.0197328e-01
+ 9.7575837e-02
+ 9.4875548e-02
+ 9.3613063e-02
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+ 6.0072080e-02
+ 5.9621717e-02
+ 5.8765838e-02
+ 5.7388366e-02
+ 5.5373224e-02
+ 5.2623498e-02
+ 4.9261717e-02
+ 4.5550390e-02
+ 4.1754290e-02
+ 3.8138193e-02
+ 3.4966871e-02
+ 3.2501662e-02
+ 3.0825931e-02
+ 2.9762256e-02
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+ 2.4405000e-02
+ 2.4405000e-02
+
diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.pair.table b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.pair.table
new file mode 100644
index 0000000000..b74fe398e8
--- /dev/null
+++ b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.pair.table
@@ -0,0 +1,1012 @@
+
+PairMM
+N 500 R  2.00000e-02  1.50000e+01
+
+1    2.00000e-02  9.19945e+01   2.97871e+01
+2    5.00200e-02  9.11003e+01   2.97871e+01
+3    8.00401e-02  9.02061e+01   2.97871e+01
+4    1.10060e-01  8.93119e+01   2.97871e+01
+5    1.40080e-01  8.84177e+01   2.97871e+01
+6    1.70100e-01  8.75235e+01   2.97871e+01
+7    2.00120e-01  8.66293e+01   2.97871e+01
+8    2.30140e-01  8.57350e+01   2.97871e+01
+9    2.60160e-01  8.48408e+01   2.97871e+01
+10   2.90180e-01  8.39466e+01   2.97871e+01
+11   3.20200e-01  8.30524e+01   2.97871e+01
+12   3.50220e-01  8.21582e+01   2.97871e+01
+13   3.80240e-01  8.12640e+01   2.97871e+01
+14   4.10261e-01  8.03698e+01   2.97871e+01
+15   4.40281e-01  7.94756e+01   2.97871e+01
+16   4.70301e-01  7.85814e+01   2.97871e+01
+17   5.00321e-01  7.76872e+01   2.97871e+01
+18   5.30341e-01  7.67929e+01   2.97871e+01
+19   5.60361e-01  7.58987e+01   2.97871e+01
+20   5.90381e-01  7.50045e+01   2.97871e+01
+21   6.20401e-01  7.41103e+01   2.97871e+01
+22   6.50421e-01  7.32161e+01   2.97871e+01
+23   6.80441e-01  7.23219e+01   2.97871e+01
+24   7.10461e-01  7.14277e+01   2.97871e+01
+25   7.40481e-01  7.05335e+01   2.97871e+01
+26   7.70501e-01  6.96393e+01   2.97871e+01
+27   8.00521e-01  6.87450e+01   2.97871e+01
+28   8.30541e-01  6.78508e+01   2.97871e+01
+29   8.60561e-01  6.69566e+01   2.97871e+01
+30   8.90581e-01  6.60624e+01   2.97871e+01
+31   9.20601e-01  6.51682e+01   2.97871e+01
+32   9.50621e-01  6.42740e+01   2.97871e+01
+33   9.80641e-01  6.33798e+01   2.97871e+01
+34   1.01066e+00  6.24856e+01   2.97871e+01
+35   1.04068e+00  6.15914e+01   2.97871e+01
+36   1.07070e+00  6.06972e+01   2.97871e+01
+37   1.10072e+00  5.98029e+01   2.97871e+01
+38   1.13074e+00  5.89087e+01   2.97871e+01
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+441 8.8176e+00  0.0000e+00  0.0000e+00 
+442 8.8377e+00  0.0000e+00  0.0000e+00 
+443 8.8577e+00  0.0000e+00  0.0000e+00 
+444 8.8778e+00  0.0000e+00  0.0000e+00 
+445 8.8978e+00  0.0000e+00  0.0000e+00 
+446 8.9178e+00  0.0000e+00  0.0000e+00 
+447 8.9379e+00  0.0000e+00  0.0000e+00 
+448 8.9579e+00  0.0000e+00  0.0000e+00 
+449 8.9780e+00  0.0000e+00  0.0000e+00 
+450 8.9980e+00  0.0000e+00  0.0000e+00 
+451 9.0180e+00  0.0000e+00  0.0000e+00 
+452 9.0381e+00  0.0000e+00  0.0000e+00 
+453 9.0581e+00  0.0000e+00  0.0000e+00 
+454 9.0782e+00  0.0000e+00  0.0000e+00 
+455 9.0982e+00  0.0000e+00  0.0000e+00 
+456 9.1182e+00  0.0000e+00  0.0000e+00 
+457 9.1383e+00  0.0000e+00  0.0000e+00 
+458 9.1583e+00  0.0000e+00  0.0000e+00 
+459 9.1784e+00  0.0000e+00  0.0000e+00 
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+461 9.2184e+00  0.0000e+00  0.0000e+00 
+462 9.2385e+00  0.0000e+00  0.0000e+00 
+463 9.2585e+00  0.0000e+00  0.0000e+00 
+464 9.2786e+00  0.0000e+00  0.0000e+00 
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+499 9.9800e+00  0.0000e+00  0.0000e+00 
+500 1.0000e+01  0.0000e+00  0.0000e+00 
+
+
diff --git a/examples/USER/phonon/dynamical_matrix_command/python/README.md b/examples/USER/phonon/dynamical_matrix_command/python/README.md
new file mode 100755
index 0000000000..5b3c11febd
--- /dev/null
+++ b/examples/USER/phonon/dynamical_matrix_command/python/README.md
@@ -0,0 +1,12 @@
+# LAMMPS LATTICE DYNAMICS COMMANDS
+
+## DYNAMICAL MATRIX CALCULATOR
+
+This directory contains the ingredients to calculate a dynamical matrix with python.  
+
+Example:
+```
+python dynmat.py
+```
+
+## Requires: MANYBODY and MOLECULE packages and the Python Library Interface
diff --git a/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py b/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py
new file mode 100644
index 0000000000..2a3a0b5a2f
--- /dev/null
+++ b/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py
@@ -0,0 +1,42 @@
+"""Made by Charlie Sievers Ph.D. Candidate, UC Davis, Donadio Lab 2019"""
+# from mpi4py import MPI
+from lammps import lammps
+import numpy as np
+
+# comm = MPI.COMM_WORLD
+# rank = comm.Get_rank()
+
+""" LAMMPS  VARIABLES """
+
+# data files
+infile = "silicon_input_file.lmp"
+ff_file = "ff-silicon.lmp"
+
+# full output useful for testing
+lmp = lammps()
+
+# reduced output useful reducing IO for production runs
+# lmp = lammps(cmdargs=["-screen", "none", "-log", "none"])
+
+# lammps commands
+lmp.command("atom_style full")
+lmp.command("units metal")
+lmp.command("processors * * *")
+lmp.command("neighbor 1 bin")
+lmp.command("boundary p p p")
+
+# read data and force field file
+lmp.command("read_data {}".format(infile))
+lmp.file("{}".format(ff_file))
+
+lmp.command("dynamical_matrix all eskm 0.000001 file dynmat.dat")
+
+dynmat = np.loadtxt("dynmat.dat")
+dynlen = int(3*np.sqrt(len(dynmat)/3))
+dynmat = dynmat.reshape((dynlen, dynlen))
+
+eigvals, eigvecs = np.linalg.eig(dynmat)
+
+# frequencies in THz
+omegas = np.sqrt(np.abs(eigvals))
+print(omegas)
diff --git a/examples/gcmc/CO2.txt b/examples/gcmc/CO2.txt
index 72e593e3f2..c9fb8616c2 100644
--- a/examples/gcmc/CO2.txt
+++ b/examples/gcmc/CO2.txt
@@ -12,15 +12,15 @@ Coords
 
 Types
 
-1        1  
-2        2   
-3        2  
+1        1
+2        2
+3        2
 
-Charges 
+Charges
 
-1        0.7 
-2       -0.35   
-3       -0.35    
+1        0.7
+2       -0.35
+3       -0.35
 
 Bonds
 
diff --git a/examples/gcmc/H2O.txt b/examples/gcmc/H2O.txt
index b56f869693..e5a5e4fe93 100644
--- a/examples/gcmc/H2O.txt
+++ b/examples/gcmc/H2O.txt
@@ -1,4 +1,4 @@
-# CO2 molecule file. TraPPE model.
+# Water molecule. SPC/E model.
 
 3 atoms
 2 bonds
@@ -12,15 +12,15 @@ Coords
 
 Types
 
-1        1  
-2        2   
-3        2  
+1        1
+2        2
+3        2
 
-Charges 
+Charges
 
 1       -0.8472
-2        0.4236 
-3        0.4236  
+2        0.4236
+3        0.4236
 
 Bonds
 
diff --git a/examples/gjf/README.md b/examples/gjf/README.md
new file mode 100644
index 0000000000..e6886cb2dd
--- /dev/null
+++ b/examples/gjf/README.md
@@ -0,0 +1,13 @@
+# LAMMPS GJF-2GJ THERMOSTAT EXAMPLE
+
+## GJF-2GJ THERMOSTAT
+
+This directory contains the ingredients to run an NVT simulation using the GJF-2GJ thermostat.
+
+Example:
+```
+NP=4 #number of processors
+mpirun -np $NP lmp_mpi -in.gjf.vhalf
+```
+
+## Required LAMMPS packages: MOLECULE package
diff --git a/examples/gjf/argon.lmp b/examples/gjf/argon.lmp
new file mode 100644
index 0000000000..00214b4c54
--- /dev/null
+++ b/examples/gjf/argon.lmp
@@ -0,0 +1,886 @@
+LAMMPS description
+
+     864      atoms    
+       0      bonds    
+       0      angles   
+       0      dihedrals
+       0      impropers
+
+       1      atom types    
+       0      bond types    
+       0      angle types   
+       0      dihedral types
+       0      improper types
+
+
+  0.0000000      32.146000     xlo xhi
+  0.0000000      32.146000     ylo yhi
+  0.0000000      32.146000     zlo zhi
+
+ Atoms
+
+      1      1      1      0.0000000      0.0000000      2.6790000      2.6790000
+      2      2      1      0.0000000      0.0000000      2.6790000      8.0360000
+      3      3      1      0.0000000      0.0000000      2.6790000     13.3940000
+      4      4      1      0.0000000      0.0000000      2.6790000     18.7520000
+      5      5      1      0.0000000      0.0000000      2.6790000     24.1090000
+      6      6      1      0.0000000      0.0000000      2.6790000     29.4670000
+      7      7      1      0.0000000      0.0000000      8.0360000      2.6790000
+      8      8      1      0.0000000      0.0000000      8.0360000      8.0360000
+      9      9      1      0.0000000      0.0000000      8.0360000     13.3940000
+     10     10      1      0.0000000      0.0000000      8.0360000     18.7520000
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+    750    750      1      0.0000000     10.7150000     26.7880000     32.1460000
+    751    751      1      0.0000000     10.7150000     32.1460000      5.3580000
+    752    752      1      0.0000000     10.7150000     32.1460000     10.7150000
+    753    753      1      0.0000000     10.7150000     32.1460000     16.0730000
+    754    754      1      0.0000000     10.7150000     32.1460000     21.4310000
+    755    755      1      0.0000000     10.7150000     32.1460000     26.7880000
+    756    756      1      0.0000000     10.7150000     32.1460000     32.1460000
+    757    757      1      0.0000000     16.0730000      5.3580000      5.3580000
+    758    758      1      0.0000000     16.0730000      5.3580000     10.7150000
+    759    759      1      0.0000000     16.0730000      5.3580000     16.0730000
+    760    760      1      0.0000000     16.0730000      5.3580000     21.4310000
+    761    761      1      0.0000000     16.0730000      5.3580000     26.7880000
+    762    762      1      0.0000000     16.0730000      5.3580000     32.1460000
+    763    763      1      0.0000000     16.0730000     10.7150000      5.3580000
+    764    764      1      0.0000000     16.0730000     10.7150000     10.7150000
+    765    765      1      0.0000000     16.0730000     10.7150000     16.0730000
+    766    766      1      0.0000000     16.0730000     10.7150000     21.4310000
+    767    767      1      0.0000000     16.0730000     10.7150000     26.7880000
+    768    768      1      0.0000000     16.0730000     10.7150000     32.1460000
+    769    769      1      0.0000000     16.0730000     16.0730000      5.3580000
+    770    770      1      0.0000000     16.0730000     16.0730000     10.7150000
+    771    771      1      0.0000000     16.0730000     16.0730000     16.0730000
+    772    772      1      0.0000000     16.0730000     16.0730000     21.4310000
+    773    773      1      0.0000000     16.0730000     16.0730000     26.7880000
+    774    774      1      0.0000000     16.0730000     16.0730000     32.1460000
+    775    775      1      0.0000000     16.0730000     21.4310000      5.3580000
+    776    776      1      0.0000000     16.0730000     21.4310000     10.7150000
+    777    777      1      0.0000000     16.0730000     21.4310000     16.0730000
+    778    778      1      0.0000000     16.0730000     21.4310000     21.4310000
+    779    779      1      0.0000000     16.0730000     21.4310000     26.7880000
+    780    780      1      0.0000000     16.0730000     21.4310000     32.1460000
+    781    781      1      0.0000000     16.0730000     26.7880000      5.3580000
+    782    782      1      0.0000000     16.0730000     26.7880000     10.7150000
+    783    783      1      0.0000000     16.0730000     26.7880000     16.0730000
+    784    784      1      0.0000000     16.0730000     26.7880000     21.4310000
+    785    785      1      0.0000000     16.0730000     26.7880000     26.7880000
+    786    786      1      0.0000000     16.0730000     26.7880000     32.1460000
+    787    787      1      0.0000000     16.0730000     32.1460000      5.3580000
+    788    788      1      0.0000000     16.0730000     32.1460000     10.7150000
+    789    789      1      0.0000000     16.0730000     32.1460000     16.0730000
+    790    790      1      0.0000000     16.0730000     32.1460000     21.4310000
+    791    791      1      0.0000000     16.0730000     32.1460000     26.7880000
+    792    792      1      0.0000000     16.0730000     32.1460000     32.1460000
+    793    793      1      0.0000000     21.4310000      5.3580000      5.3580000
+    794    794      1      0.0000000     21.4310000      5.3580000     10.7150000
+    795    795      1      0.0000000     21.4310000      5.3580000     16.0730000
+    796    796      1      0.0000000     21.4310000      5.3580000     21.4310000
+    797    797      1      0.0000000     21.4310000      5.3580000     26.7880000
+    798    798      1      0.0000000     21.4310000      5.3580000     32.1460000
+    799    799      1      0.0000000     21.4310000     10.7150000      5.3580000
+    800    800      1      0.0000000     21.4310000     10.7150000     10.7150000
+    801    801      1      0.0000000     21.4310000     10.7150000     16.0730000
+    802    802      1      0.0000000     21.4310000     10.7150000     21.4310000
+    803    803      1      0.0000000     21.4310000     10.7150000     26.7880000
+    804    804      1      0.0000000     21.4310000     10.7150000     32.1460000
+    805    805      1      0.0000000     21.4310000     16.0730000      5.3580000
+    806    806      1      0.0000000     21.4310000     16.0730000     10.7150000
+    807    807      1      0.0000000     21.4310000     16.0730000     16.0730000
+    808    808      1      0.0000000     21.4310000     16.0730000     21.4310000
+    809    809      1      0.0000000     21.4310000     16.0730000     26.7880000
+    810    810      1      0.0000000     21.4310000     16.0730000     32.1460000
+    811    811      1      0.0000000     21.4310000     21.4310000      5.3580000
+    812    812      1      0.0000000     21.4310000     21.4310000     10.7150000
+    813    813      1      0.0000000     21.4310000     21.4310000     16.0730000
+    814    814      1      0.0000000     21.4310000     21.4310000     21.4310000
+    815    815      1      0.0000000     21.4310000     21.4310000     26.7880000
+    816    816      1      0.0000000     21.4310000     21.4310000     32.1460000
+    817    817      1      0.0000000     21.4310000     26.7880000      5.3580000
+    818    818      1      0.0000000     21.4310000     26.7880000     10.7150000
+    819    819      1      0.0000000     21.4310000     26.7880000     16.0730000
+    820    820      1      0.0000000     21.4310000     26.7880000     21.4310000
+    821    821      1      0.0000000     21.4310000     26.7880000     26.7880000
+    822    822      1      0.0000000     21.4310000     26.7880000     32.1460000
+    823    823      1      0.0000000     21.4310000     32.1460000      5.3580000
+    824    824      1      0.0000000     21.4310000     32.1460000     10.7150000
+    825    825      1      0.0000000     21.4310000     32.1460000     16.0730000
+    826    826      1      0.0000000     21.4310000     32.1460000     21.4310000
+    827    827      1      0.0000000     21.4310000     32.1460000     26.7880000
+    828    828      1      0.0000000     21.4310000     32.1460000     32.1460000
+    829    829      1      0.0000000     26.7880000      5.3580000      5.3580000
+    830    830      1      0.0000000     26.7880000      5.3580000     10.7150000
+    831    831      1      0.0000000     26.7880000      5.3580000     16.0730000
+    832    832      1      0.0000000     26.7880000      5.3580000     21.4310000
+    833    833      1      0.0000000     26.7880000      5.3580000     26.7880000
+    834    834      1      0.0000000     26.7880000      5.3580000     32.1460000
+    835    835      1      0.0000000     26.7880000     10.7150000      5.3580000
+    836    836      1      0.0000000     26.7880000     10.7150000     10.7150000
+    837    837      1      0.0000000     26.7880000     10.7150000     16.0730000
+    838    838      1      0.0000000     26.7880000     10.7150000     21.4310000
+    839    839      1      0.0000000     26.7880000     10.7150000     26.7880000
+    840    840      1      0.0000000     26.7880000     10.7150000     32.1460000
+    841    841      1      0.0000000     26.7880000     16.0730000      5.3580000
+    842    842      1      0.0000000     26.7880000     16.0730000     10.7150000
+    843    843      1      0.0000000     26.7880000     16.0730000     16.0730000
+    844    844      1      0.0000000     26.7880000     16.0730000     21.4310000
+    845    845      1      0.0000000     26.7880000     16.0730000     26.7880000
+    846    846      1      0.0000000     26.7880000     16.0730000     32.1460000
+    847    847      1      0.0000000     26.7880000     21.4310000      5.3580000
+    848    848      1      0.0000000     26.7880000     21.4310000     10.7150000
+    849    849      1      0.0000000     26.7880000     21.4310000     16.0730000
+    850    850      1      0.0000000     26.7880000     21.4310000     21.4310000
+    851    851      1      0.0000000     26.7880000     21.4310000     26.7880000
+    852    852      1      0.0000000     26.7880000     21.4310000     32.1460000
+    853    853      1      0.0000000     26.7880000     26.7880000      5.3580000
+    854    854      1      0.0000000     26.7880000     26.7880000     10.7150000
+    855    855      1      0.0000000     26.7880000     26.7880000     16.0730000
+    856    856      1      0.0000000     26.7880000     26.7880000     21.4310000
+    857    857      1      0.0000000     26.7880000     26.7880000     26.7880000
+    858    858      1      0.0000000     26.7880000     26.7880000     32.1460000
+    859    859      1      0.0000000     26.7880000     32.1460000      5.3580000
+    860    860      1      0.0000000     26.7880000     32.1460000     10.7150000
+    861    861      1      0.0000000     26.7880000     32.1460000     16.0730000
+    862    862      1      0.0000000     26.7880000     32.1460000     21.4310000
+    863    863      1      0.0000000     26.7880000     32.1460000     26.7880000
+    864    864      1      0.0000000     26.7880000     32.1460000     32.1460000
+
diff --git a/examples/gjf/ff-argon.lmp b/examples/gjf/ff-argon.lmp
new file mode 100644
index 0000000000..b6f7bc931a
--- /dev/null
+++ b/examples/gjf/ff-argon.lmp
@@ -0,0 +1,20 @@
+#############################
+#Atoms types - mass - charge#
+#############################
+#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
+
+variable Ar equal 1
+
+#############
+#Atom Masses#
+#############
+
+mass ${Ar}      39.903
+
+###########################
+#Pair Potentials - Tersoff#
+###########################
+
+pair_style      lj/cubic
+pair_coeff      * * 0.0102701 3.42
+
diff --git a/examples/gjf/in.gjf.vfull b/examples/gjf/in.gjf.vfull
new file mode 100644
index 0000000000..40512ac37a
--- /dev/null
+++ b/examples/gjf/in.gjf.vfull
@@ -0,0 +1,23 @@
+# GJF-2GJ thermostat
+
+units   	metal
+atom_style      full
+
+boundary 	p p p
+read_data argon.lmp
+
+include ff-argon.lmp
+
+velocity all create 10 2357 mom yes dist gaussian
+
+neighbor 1 bin
+
+timestep 0.1
+
+fix lang all langevin 10 10 1 26488 gjf vfull
+fix nve all nve
+
+thermo 200
+run 5000
+
+
diff --git a/examples/gjf/in.gjf.vhalf b/examples/gjf/in.gjf.vhalf
new file mode 100644
index 0000000000..63fb8bd467
--- /dev/null
+++ b/examples/gjf/in.gjf.vhalf
@@ -0,0 +1,23 @@
+# GJF-2GJ thermostat
+
+units   	metal
+atom_style      full
+
+boundary 	p p p
+read_data argon.lmp
+
+include ff-argon.lmp
+
+velocity all create 10 2357 mom yes dist gaussian
+
+neighbor 1 bin
+
+timestep 0.1
+
+fix lang all langevin 10 10 1 26488 gjf vhalf
+fix nve all nve
+
+thermo 200
+run 5000
+
+
diff --git a/examples/gjf/log.15Oct19.gjf.vfull.g++.1 b/examples/gjf/log.15Oct19.gjf.vfull.g++.1
new file mode 100644
index 0000000000..e3e9cce124
--- /dev/null
+++ b/examples/gjf/log.15Oct19.gjf.vfull.g++.1
@@ -0,0 +1,125 @@
+LAMMPS (19 Sep 2019)
+  using 1 OpenMP thread(s) per MPI task
+# GJF-2GJ thermostat
+
+units   	metal
+atom_style      full
+
+boundary 	p p p
+read_data argon.lmp
+  orthogonal box = (0 0 0) to (32.146 32.146 32.146)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  864 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000150019 secs
+  read_data CPU = 0.001946 secs
+
+include ff-argon.lmp
+#############################
+#Atoms types - mass - charge#
+#############################
+#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
+
+variable Ar equal 1
+
+#############
+#Atom Masses#
+#############
+
+mass ${Ar}      39.903
+mass 1      39.903
+
+###########################
+#Pair Potentials - Tersoff#
+###########################
+
+pair_style      lj/cubic
+pair_coeff      * * 0.0102701 3.42
+
+
+velocity all create 10 2357 mom yes dist gaussian
+
+neighbor 1 bin
+
+timestep 0.1
+
+fix lang all langevin 10 10 1 26488 gjf vfull
+fix nve all nve
+
+thermo 200
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.94072
+  ghost atom cutoff = 6.94072
+  binsize = 3.47036, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cubic, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.875 | 6.875 | 6.875 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    11.080223   -56.207655            0    -54.97164    37.215524 
+     200    8.2588471   -55.073602            0   -54.152316    339.80416 
+     400    8.1427292   -55.072244            0    -54.16391    338.91883 
+     600    8.7595618   -55.066739            0   -54.089596    344.25426 
+     800     8.550633   -55.148315            0   -54.194479     318.9385 
+    1000    8.5394337   -55.125709            0   -54.173122    326.59471 
+    1200     8.565973   -55.114892            0   -54.159345     328.5193 
+    1400    8.2092914   -55.109233            0   -54.193475    329.56161 
+    1600     8.209495   -55.138161            0    -54.22238    321.39971 
+    1800    8.4039924    -55.13355            0   -54.196072    322.64214 
+    2000    8.4548937   -55.062994            0   -54.119838    343.29888 
+    2200    8.3775139    -55.13364            0   -54.199116    323.63744 
+    2400     8.537332   -55.163702            0    -54.21135    315.62864 
+    2600     8.672488   -55.112054            0   -54.144625     330.1106 
+    2800    8.3000218   -55.147275            0   -54.221396    318.73112 
+    3000    8.3552421   -55.135164            0   -54.203124    323.53075 
+    3200    8.4126798   -55.135753            0   -54.197306    321.48817 
+    3400    8.4986413   -55.135408            0   -54.187372    323.42951 
+    3600      8.38431   -55.103932            0    -54.16865    330.68929 
+    3800    8.8262454   -55.103648            0   -54.119067    332.97779 
+    4000    7.9658136   -55.120402            0   -54.231803     324.9595 
+    4200    8.2265544   -55.129011            0   -54.211327    323.87069 
+    4400    8.1253738   -55.153089            0   -54.246691      316.304 
+    4600    8.2010823   -55.124053            0    -54.20921    325.98402 
+    4800    8.5512149   -55.075877            0   -54.121976    338.30137 
+    5000    8.4737659   -55.158604            0   -54.213343    316.22418 
+Loop time of 2.73236 on 1 procs for 5000 steps with 864 atoms
+
+Performance: 15810.507 ns/day, 0.002 hours/ns, 1829.920 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.4262     | 1.4262     | 1.4262     |   0.0 | 52.20
+Bond    | 0.00042836 | 0.00042836 | 0.00042836 |   0.0 |  0.02
+Neigh   | 0.12819    | 0.12819    | 0.12819    |   0.0 |  4.69
+Comm    | 0.058611   | 0.058611   | 0.058611   |   0.0 |  2.15
+Output  | 0.00047283 | 0.00047283 | 0.00047283 |   0.0 |  0.02
+Modify  | 1.0924     | 1.0924     | 1.0924     |   0.0 | 39.98
+Other   |            | 0.02605    |            |       |  0.95
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1593 ave 1593 max 1593 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    18143 ave 18143 max 18143 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18143
+Ave neighs/atom = 20.9988
+Ave special neighs/atom = 0
+Neighbor list builds = 158
+Dangerous builds = 5
+
+
+Total wall time: 0:00:02
diff --git a/examples/gjf/log.15Oct19.gjf.vfull.g++.4 b/examples/gjf/log.15Oct19.gjf.vfull.g++.4
new file mode 100644
index 0000000000..95caed5dc9
--- /dev/null
+++ b/examples/gjf/log.15Oct19.gjf.vfull.g++.4
@@ -0,0 +1,125 @@
+LAMMPS (19 Sep 2019)
+  using 1 OpenMP thread(s) per MPI task
+# GJF-2GJ thermostat
+
+units   	metal
+atom_style      full
+
+boundary 	p p p
+read_data argon.lmp
+  orthogonal box = (0 0 0) to (32.146 32.146 32.146)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  864 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000556268 secs
+  read_data CPU = 0.003817 secs
+
+include ff-argon.lmp
+#############################
+#Atoms types - mass - charge#
+#############################
+#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
+
+variable Ar equal 1
+
+#############
+#Atom Masses#
+#############
+
+mass ${Ar}      39.903
+mass 1      39.903
+
+###########################
+#Pair Potentials - Tersoff#
+###########################
+
+pair_style      lj/cubic
+pair_coeff      * * 0.0102701 3.42
+
+
+velocity all create 10 2357 mom yes dist gaussian
+
+neighbor 1 bin
+
+timestep 0.1
+
+fix lang all langevin 10 10 1 26488 gjf vfull
+fix nve all nve
+
+thermo 200
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.94072
+  ghost atom cutoff = 6.94072
+  binsize = 3.47036, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cubic, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.808 | 6.808 | 6.808 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    11.080228   -56.207655            0   -54.971639    37.215541 
+     200    8.4818184   -55.127334            0   -54.181174    324.96159 
+     400    8.5960916    -55.09236            0   -54.133453    334.83136 
+     600    8.1607556   -55.073136            0   -54.162791      339.035 
+     800    8.8350489   -55.133382            0   -54.147819    324.48149 
+    1000    8.5692704   -55.118463            0   -54.162548    327.26328 
+    1200    8.4174147   -55.126297            0   -54.187322     324.4248 
+    1400    8.6362603   -55.123075            0   -54.159688     326.7798 
+    1600     8.222512   -55.153799            0   -54.236565     317.8147 
+    1800     8.324523   -55.116698            0   -54.188085    327.35373 
+    2000    7.9615959   -55.155825            0   -54.267697    315.37215 
+    2200     8.495968   -55.083943            0   -54.136205    336.67775 
+    2400    7.7926986   -55.044816            0   -54.175529    344.87758 
+    2600    8.1551351   -55.069404            0   -54.159687    339.60901 
+    2800    8.2593599   -55.084151            0   -54.162807    336.54935 
+    3000    8.2860869   -55.110296            0   -54.185971    328.99074 
+    3200    8.4074534   -55.123576            0   -54.185712    326.06823 
+    3400    8.6694364   -55.128925            0   -54.161836    324.67512 
+    3600    8.5718984   -55.129861            0   -54.173653    325.20586 
+    3800     8.508102   -55.099093            0   -54.150001    333.91437 
+    4000    8.2966658   -55.117782            0   -54.192276    327.13516 
+    4200    8.7641728   -55.135792            0   -54.158136    324.00844 
+    4400    8.8827909   -55.096369            0    -54.10548    335.08467 
+    4600    8.7666577   -55.127213            0   -54.149279    326.15539 
+    4800    8.6670762   -55.163395            0    -54.19657    316.48383 
+    5000    8.1893094   -55.073756            0   -54.160226    337.95271 
+Loop time of 0.870594 on 4 procs for 5000 steps with 864 atoms
+
+Performance: 49621.267 ns/day, 0.000 hours/ns, 5743.202 timesteps/s
+96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.33582    | 0.35125    | 0.3724     |   2.3 | 40.35
+Bond    | 0.00030267 | 0.00031316 | 0.00033538 |   0.0 |  0.04
+Neigh   | 0.034246   | 0.03479    | 0.035904   |   0.4 |  4.00
+Comm    | 0.15068    | 0.17419    | 0.19191    |   3.6 | 20.01
+Output  | 0.00044776 | 0.00054703 | 0.00083177 |   0.0 |  0.06
+Modify  | 0.27679    | 0.28079    | 0.28849    |   0.9 | 32.25
+Other   |            | 0.02871    |            |       |  3.30
+
+Nlocal:    216 ave 216 max 216 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    888.75 ave 899 max 876 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:    4536 ave 4737 max 4335 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 18144
+Ave neighs/atom = 21
+Ave special neighs/atom = 0
+Neighbor list builds = 178
+Dangerous builds = 11
+
+
+Total wall time: 0:00:00
diff --git a/examples/gjf/log.15Oct19.gjf.vhalf.g++.1 b/examples/gjf/log.15Oct19.gjf.vhalf.g++.1
new file mode 100644
index 0000000000..a87b20a887
--- /dev/null
+++ b/examples/gjf/log.15Oct19.gjf.vhalf.g++.1
@@ -0,0 +1,125 @@
+LAMMPS (19 Sep 2019)
+  using 1 OpenMP thread(s) per MPI task
+# GJF-2GJ thermostat
+
+units   	metal
+atom_style      full
+
+boundary 	p p p
+read_data argon.lmp
+  orthogonal box = (0 0 0) to (32.146 32.146 32.146)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  864 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000147804 secs
+  read_data CPU = 0.00194898 secs
+
+include ff-argon.lmp
+#############################
+#Atoms types - mass - charge#
+#############################
+#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
+
+variable Ar equal 1
+
+#############
+#Atom Masses#
+#############
+
+mass ${Ar}      39.903
+mass 1      39.903
+
+###########################
+#Pair Potentials - Tersoff#
+###########################
+
+pair_style      lj/cubic
+pair_coeff      * * 0.0102701 3.42
+
+
+velocity all create 10 2357 mom yes dist gaussian
+
+neighbor 1 bin
+
+timestep 0.1
+
+fix lang all langevin 10 10 1 26488 gjf vhalf
+fix nve all nve
+
+thermo 200
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.94072
+  ghost atom cutoff = 6.94072
+  binsize = 3.47036, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cubic, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.5 | 6.5 | 6.5 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    11.080223   -56.207655            0    -54.97164    37.215524 
+     200    9.8808568   -55.073602            0   -53.971378    345.62207 
+     400    9.8712816   -55.072244            0   -53.971088    345.11889 
+     600    10.528988   -55.066739            0   -53.892214    350.60093 
+     800    10.167171   -55.148315            0   -54.014152    324.73679 
+    1000    10.029026   -55.125709            0   -54.006956    331.93766 
+    1200    10.194424   -55.114892            0   -53.977688    334.36032 
+    1400    9.3473846   -55.109233            0   -54.066518    333.64378 
+    1600    9.7774071   -55.138161            0   -54.047477    327.02358 
+    1800    9.9814275    -55.13355            0   -54.020107    328.30017 
+    2000      10.2515   -55.062994            0   -53.919424    349.74304 
+    2200    9.8126922    -55.13364            0   -54.039019    328.78521 
+    2400    10.044314   -55.163702            0   -54.043244    321.03397 
+    2600    10.543316   -55.112054            0   -53.935932    336.82099 
+    2800    9.7874375   -55.147275            0   -54.055472    324.06626 
+    3000    9.7703821   -55.135164            0   -54.045263    328.60665 
+    3200    10.141958   -55.135753            0   -54.004402    327.69084 
+    3400    10.160576   -55.135408            0    -54.00198    329.39063 
+    3600    10.044652   -55.103932            0   -53.983436    336.64469 
+    3800    10.662403   -55.103648            0   -53.914241    339.56382 
+    4000    9.2921047   -55.120402            0   -54.083853    329.71671 
+    4200    9.8744553   -55.129011            0   -54.027501    329.78147 
+    4400    9.4085964   -55.153089            0   -54.103546    320.90673 
+    4600    9.5463801   -55.124053            0    -54.05914    330.80941 
+    4800    10.223884   -55.075877            0   -53.935387    344.30099 
+    5000    9.6243338   -55.158604            0   -54.084996     320.3511 
+Loop time of 2.29551 on 1 procs for 5000 steps with 864 atoms
+
+Performance: 18819.358 ns/day, 0.001 hours/ns, 2178.166 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.4393     | 1.4393     | 1.4393     |   0.0 | 62.70
+Bond    | 0.0004441  | 0.0004441  | 0.0004441  |   0.0 |  0.02
+Neigh   | 0.12136    | 0.12136    | 0.12136    |   0.0 |  5.29
+Comm    | 0.059342   | 0.059342   | 0.059342   |   0.0 |  2.59
+Output  | 0.00046968 | 0.00046968 | 0.00046968 |   0.0 |  0.02
+Modify  | 0.64937    | 0.64937    | 0.64937    |   0.0 | 28.29
+Other   |            | 0.02522    |            |       |  1.10
+
+Nlocal:    864 ave 864 max 864 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1593 ave 1593 max 1593 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    18143 ave 18143 max 18143 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18143
+Ave neighs/atom = 20.9988
+Ave special neighs/atom = 0
+Neighbor list builds = 158
+Dangerous builds = 5
+
+
+Total wall time: 0:00:02
diff --git a/examples/gjf/log.15Oct19.gjf.vhalf.g++.4 b/examples/gjf/log.15Oct19.gjf.vhalf.g++.4
new file mode 100644
index 0000000000..a70a67a89c
--- /dev/null
+++ b/examples/gjf/log.15Oct19.gjf.vhalf.g++.4
@@ -0,0 +1,125 @@
+LAMMPS (19 Sep 2019)
+  using 1 OpenMP thread(s) per MPI task
+# GJF-2GJ thermostat
+
+units   	metal
+atom_style      full
+
+boundary 	p p p
+read_data argon.lmp
+  orthogonal box = (0 0 0) to (32.146 32.146 32.146)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  864 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000315903 secs
+  read_data CPU = 0.0653752 secs
+
+include ff-argon.lmp
+#############################
+#Atoms types - mass - charge#
+#############################
+#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
+
+variable Ar equal 1
+
+#############
+#Atom Masses#
+#############
+
+mass ${Ar}      39.903
+mass 1      39.903
+
+###########################
+#Pair Potentials - Tersoff#
+###########################
+
+pair_style      lj/cubic
+pair_coeff      * * 0.0102701 3.42
+
+
+velocity all create 10 2357 mom yes dist gaussian
+
+neighbor 1 bin
+
+timestep 0.1
+
+fix lang all langevin 10 10 1 26488 gjf vhalf
+fix nve all nve
+
+thermo 200
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.94072
+  ghost atom cutoff = 6.94072
+  binsize = 3.47036, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cubic, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.433 | 6.433 | 6.433 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    11.080228   -56.207655            0   -54.971639    37.215541 
+     200    9.8046716   -55.127334            0   -54.033608    329.70647 
+     400    10.174622    -55.09236            0   -53.957366    340.49331 
+     600    9.9812299   -55.073136            0   -53.959714    345.56477 
+     800    10.512874   -55.133382            0   -53.960655     330.4996 
+    1000    9.9587885   -55.118463            0   -54.007545    332.24728 
+    1200    10.236607   -55.126297            0   -53.984388    330.94998 
+    1400    10.134679   -55.123075            0   -53.992537    332.15441 
+    1600    9.8934078   -55.153799            0   -54.050174    323.80795 
+    1800    10.064966   -55.116698            0   -53.993936    333.59644 
+    2000    9.6736107   -55.155825            0   -54.076719     321.5129 
+    2200    10.264537   -55.083943            0   -53.938918    343.02135 
+    2400    9.5640032   -55.044816            0   -53.977937    351.23099 
+    2600    9.6581077   -55.069404            0   -53.992028    344.99996 
+    2800    9.9622575   -55.084151            0   -53.972846     342.6574 
+    3000    9.8724909   -55.110296            0   -54.009005    334.68094 
+    3200    10.032027   -55.123576            0   -54.004488    331.89534 
+    3400    10.221132   -55.128925            0   -53.988742    330.24082 
+    3600    10.085802   -55.129861            0   -54.004774    330.63601 
+    3800    10.098545   -55.099093            0   -53.972585    339.61905 
+    4000    10.000257   -55.117782            0   -54.002238    333.24569 
+    4200     10.20477   -55.135792            0   -53.997435    329.17565 
+    4400    10.545132   -55.096369            0   -53.920044    341.04725 
+    4600    10.376108   -55.127213            0   -53.969743    331.92825 
+    4800    10.247392   -55.163395            0   -54.020283    322.15219 
+    5000    9.7753102   -55.073756            0   -53.983305    343.64146 
+Loop time of 1.19785 on 4 procs for 5000 steps with 864 atoms
+
+Performance: 36064.674 ns/day, 0.001 hours/ns, 4174.152 timesteps/s
+88.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.36387    | 0.38652    | 0.44086    |   5.1 | 32.27
+Bond    | 0.00028847 | 0.00030833 | 0.000338   |   0.0 |  0.03
+Neigh   | 0.033934   | 0.034959   | 0.036917   |   0.6 |  2.92
+Comm    | 0.39292    | 0.47821    | 0.52198    |   7.3 | 39.92
+Output  | 0.00050343 | 0.0012343  | 0.0023338  |   1.9 |  0.10
+Modify  | 0.1605     | 0.17963    | 0.19457    |   2.9 | 15.00
+Other   |            | 0.117      |            |       |  9.77
+
+Nlocal:    216 ave 216 max 216 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    888.75 ave 899 max 876 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:    4536 ave 4737 max 4335 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 18144
+Ave neighs/atom = 21
+Ave special neighs/atom = 0
+Neighbor list builds = 178
+Dangerous builds = 11
+
+
+Total wall time: 0:00:01
diff --git a/examples/python/in.fix_python_invoke_neighlist b/examples/python/in.fix_python_invoke_neighlist
new file mode 100644
index 0000000000..50f1d52c33
--- /dev/null
+++ b/examples/python/in.fix_python_invoke_neighlist
@@ -0,0 +1,72 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 2 0 2 0 2
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.1 bin
+
+neigh_modify	every 20 delay 0 check no
+
+python         post_force_callback here """
+from __future__ import print_function
+from lammps import lammps
+
+def post_force_callback(lmp, v):
+  try:
+    import os
+    pid = os.getpid()
+    pid_prefix = "[{}] ".format(pid)
+
+    L = lammps(ptr=lmp)
+    t = L.extract_global("ntimestep", 0)
+    print(pid_prefix, "### POST_FORCE ###", t)
+
+    #mylist = L.get_neighlist(0)
+    mylist = L.find_pair_neighlist("lj/cut", request=0)
+    print(pid_prefix, mylist)
+    nlocal = L.extract_global("nlocal", 0)
+    nghost = L.extract_global("nghost", 0)
+    ntypes = L.extract_global("ntypes", 0)
+    mass = L.numpy.extract_atom_darray("mass", ntypes+1)
+    atype = L.numpy.extract_atom_iarray("type", nlocal+nghost)
+    x = L.numpy.extract_atom_darray("x", nlocal+nghost, dim=3)
+    v = L.numpy.extract_atom_darray("v", nlocal+nghost, dim=3)
+    f = L.numpy.extract_atom_darray("f", nlocal+nghost, dim=3)
+
+    for iatom, numneigh, neighs in mylist:
+      print(pid_prefix, "- {}".format(iatom), x[iatom], v[iatom], f[iatom], " : ",  numneigh, "Neighbors")
+      for jatom in neighs:
+        if jatom < nlocal:
+            print(pid_prefix, "    *  ", jatom, x[jatom], v[jatom], f[jatom])
+        else:
+            print(pid_prefix, "    * [GHOST]", jatom, x[jatom], v[jatom], f[jatom])
+  except Exception as e:
+    print(e)
+"""
+
+fix		1 all nve
+fix     3 all python/invoke 50 post_force post_force_callback
+
+#dump		id all atom 1 dump.melt
+
+#dump		2 all image 1 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+#dump		3 all movie 1 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3
+
+thermo		1
+run		100
diff --git a/examples/rerun/README b/examples/rerun/README
new file mode 100644
index 0000000000..66db685d92
--- /dev/null
+++ b/examples/rerun/README
@@ -0,0 +1,17 @@
+Examples of how to use the rerun and read_dump commands
+
+in.first - run on any number of procs for any size problem
+in.rerun - run on same or different proc count for same size problem
+in.read_dump - ditto to in.rerun
+
+The thermo output on the same timesteps should be identical
+to within round-off errors.
+
+in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma
+in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma
+
+In both bases the time averaged RDF is computed 10x times, every 100
+steps for 1000 total.  In the rerun, the pair style cutoff is changed
+so the RDF can be computed to a longer distance without re-running the
+simulation.  The RDF values in the 2 files should be the same (within
+round-off) for the first 50 bins.
diff --git a/examples/rerun/in.first b/examples/rerun/in.first
new file mode 100644
index 0000000000..2aa4c1974c
--- /dev/null
+++ b/examples/rerun/in.first
@@ -0,0 +1,33 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z vx vy vz
+
+thermo          100
+run		1000
diff --git a/examples/rerun/in.rdf.first b/examples/rerun/in.rdf.first
new file mode 100644
index 0000000000..f9d1ecf55e
--- /dev/null
+++ b/examples/rerun/in.rdf.first
@@ -0,0 +1,36 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z
+
+compute         myRDF all rdf 50 cutoff 2.5
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
+
+thermo          100
+run		1000
diff --git a/examples/rerun/in.rdf.rerun b/examples/rerun/in.rdf.rerun
new file mode 100644
index 0000000000..5562cac74d
--- /dev/null
+++ b/examples/rerun/in.rdf.rerun
@@ -0,0 +1,31 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 5.0
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+
+compute         myRDF all rdf 100 cutoff 5.0
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
+
+thermo          100
+
+rerun           lj.dump dump x y z
+
diff --git a/examples/rerun/in.read_dump b/examples/rerun/in.read_dump
new file mode 100644
index 0000000000..3c1310b305
--- /dev/null
+++ b/examples/rerun/in.read_dump
@@ -0,0 +1,37 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+read_dump       lj.dump 200 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 800 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 600 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 400 x y z vx vy vz
+run             0 post no
diff --git a/examples/rerun/in.rerun b/examples/rerun/in.rerun
new file mode 100644
index 0000000000..a695006f26
--- /dev/null
+++ b/examples/rerun/in.rerun
@@ -0,0 +1,29 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+rerun           lj.dump first 200 last 800 every 200 &
+                dump x y z vx vy vz
+
diff --git a/examples/rerun/log.09Jan20.first.g++.4 b/examples/rerun/log.09Jan20.first.g++.4
new file mode 100644
index 0000000000..cabc17c851
--- /dev/null
+++ b/examples/rerun/log.09Jan20.first.g++.4
@@ -0,0 +1,97 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00173283 secs
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z vx vy vz
+
+thermo          100
+run		1000
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.869 | 7.869 | 7.869 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+     200   0.75953175   -5.7618892            0   -4.6226272   0.20910575 
+     300   0.74624286    -5.741962            0   -4.6226327   0.32016436 
+     400   0.74155675   -5.7343359            0   -4.6220356    0.3777989 
+     500   0.73249345   -5.7206946            0   -4.6219887   0.44253023 
+     600   0.72087255   -5.7029314            0   -4.6216563   0.55730354 
+     700   0.71489947    -5.693532            0   -4.6212164   0.61322381 
+     800   0.70876958   -5.6840594            0   -4.6209382   0.66822293 
+     900   0.70799522   -5.6828388            0   -4.6208791   0.66961272 
+    1000   0.70325878   -5.6750833            0   -4.6202281    0.7112575 
+Loop time of 6.3349 on 4 procs for 1000 steps with 32000 atoms
+
+Performance: 68193.673 tau/day, 157.856 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.3538     | 4.6712     | 5.0021     |  12.8 | 73.74
+Neigh   | 0.59378    | 0.65229    | 0.75202    |   8.0 | 10.30
+Comm    | 0.28101    | 0.69839    | 1.0586     |  38.5 | 11.02
+Output  | 0.21601    | 0.21682    | 0.21718    |   0.1 |  3.42
+Modify  | 0.074002   | 0.074803   | 0.075779   |   0.2 |  1.18
+Other   |            | 0.0214     |            |       |  0.34
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    8632.5 ave 8685 max 8591 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs:    299934 ave 303105 max 295137 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 1199738
+Ave neighs/atom = 37.4918
+Neighbor list builds = 50
+Dangerous builds not checked
+Total wall time: 0:00:06
diff --git a/examples/rerun/log.09Jan20.rdf.first.g++.4 b/examples/rerun/log.09Jan20.rdf.first.g++.4
new file mode 100644
index 0000000000..7d029f23d4
--- /dev/null
+++ b/examples/rerun/log.09Jan20.rdf.first.g++.4
@@ -0,0 +1,105 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00100017 secs
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z
+
+compute         myRDF all rdf 50 cutoff 2.5
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
+
+thermo          100
+run		1000
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute rdf, occasional
+      attributes: half, newton on, cut 2.8
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.487 | 8.487 | 8.487 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+     200   0.75953175   -5.7618892            0   -4.6226272   0.20910575 
+     300   0.74624286    -5.741962            0   -4.6226327   0.32016436 
+     400   0.74155675   -5.7343359            0   -4.6220356    0.3777989 
+     500   0.73249345   -5.7206946            0   -4.6219887   0.44253023 
+     600   0.72087255   -5.7029314            0   -4.6216563   0.55730354 
+     700   0.71489947    -5.693532            0   -4.6212164   0.61322381 
+     800   0.70876958   -5.6840594            0   -4.6209382   0.66822293 
+     900   0.70799522   -5.6828388            0   -4.6208791   0.66961272 
+    1000   0.70325878   -5.6750833            0   -4.6202281    0.7112575 
+Loop time of 7.44016 on 4 procs for 1000 steps with 32000 atoms
+
+Performance: 58063.267 tau/day, 134.406 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.3881     | 5.5809     | 5.7111     |   5.4 | 75.01
+Neigh   | 0.80101    | 0.82776    | 0.85702    |   2.2 | 11.13
+Comm    | 0.31801    | 0.48426    | 0.72201    |  22.5 |  6.51
+Output  | 0.17801    | 0.17801    | 0.17801    |   0.0 |  2.39
+Modify  | 0.31201    | 0.33076    | 0.33701    |   1.9 |  4.45
+Other   |            | 0.0385     |            |       |  0.52
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    8632.5 ave 8685 max 8591 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs:    299934 ave 303105 max 295137 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 1199738
+Ave neighs/atom = 37.4918
+Neighbor list builds = 50
+Dangerous builds not checked
+Total wall time: 0:00:07
diff --git a/examples/rerun/log.09Jan20.rdf.rerun.g++.4 b/examples/rerun/log.09Jan20.rdf.rerun.g++.4
new file mode 100644
index 0000000000..7c5137bb08
--- /dev/null
+++ b/examples/rerun/log.09Jan20.rdf.rerun.g++.4
@@ -0,0 +1,100 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00183487 secs
+mass		1 1.0
+
+pair_style	lj/cut 5.0
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+
+compute         myRDF all rdf 100 cutoff 5.0
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
+
+thermo          100
+
+rerun           lj.dump dump x y z
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.3
+  ghost atom cutoff = 5.3
+  binsize = 2.65, bins = 13 13 13
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute rdf, occasional
+      attributes: half, newton on, cut 5.3
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -7.1616928            0   -7.1616928   -6.8899898 
+     100            0   -6.1442754            0   -6.1442754   -1.0825318 
+     200            0   -6.1472483            0   -6.1472483   -1.0817213 
+     300            0   -6.1274033            0   -6.1274033  -0.95961014 
+     400            0   -6.1202956            0   -6.1202956   -0.8988851 
+     500            0   -6.1067136            0   -6.1067136  -0.82660368 
+     600            0   -6.0893179            0   -6.0893179  -0.70264528 
+     700            0   -6.0803044            0   -6.0803044  -0.64232743 
+     800            0   -6.0710303            0   -6.0710303   -0.5824798 
+     900            0   -6.0698963            0   -6.0698963  -0.58057929 
+    1000            0   -6.0627642            0   -6.0627642  -0.53599799 
+Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms
+
+Performance: 1544.558 tau/day, 3.575 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 3.077      |            |       |100.00
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    20028 ave 20060 max 19988 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:    2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 8416685
+Ave neighs/atom = 263.021
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03
diff --git a/examples/rerun/log.09Jan20.read_dump.g++.4 b/examples/rerun/log.09Jan20.read_dump.g++.4
new file mode 100644
index 0000000000..874309aaa3
--- /dev/null
+++ b/examples/rerun/log.09Jan20.read_dump.g++.4
@@ -0,0 +1,118 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.001724 secs
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+read_dump       lj.dump 200 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     200   0.75953173   -5.7618854            0   -4.6226234   0.20912952 
+Loop time of 2.26498e-06 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 800 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     800   0.70876957   -5.6840545            0   -4.6209334   0.66823926 
+Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 600 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     600   0.72087256   -5.7029306            0   -4.6216556   0.55729873 
+Loop time of 7.7486e-07 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 400 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     400   0.74155677   -5.7343336            0   -4.6220332   0.37780193 
+Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
+
+Total wall time: 0:00:00
diff --git a/examples/rerun/log.09Jan20.rerun.g++.4 b/examples/rerun/log.09Jan20.rerun.g++.4
new file mode 100644
index 0000000000..f654e2c777
--- /dev/null
+++ b/examples/rerun/log.09Jan20.rerun.g++.4
@@ -0,0 +1,86 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00100017 secs
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+rerun           lj.dump first 200 last 800 every 200                 dump x y z vx vy vz
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.716 | 6.718 | 6.721 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     200   0.75953173   -5.7618854            0   -4.6226234   0.20912952 
+     400   0.74155677   -5.7343336            0   -4.6220332   0.37780193 
+     600   0.72087256   -5.7029306            0   -4.6216556   0.55729873 
+     800   0.70876957   -5.6840545            0   -4.6209334   0.66823926 
+Loop time of 0.375898 on 4 procs for 4 steps with 32000 atoms
+
+Performance: 4596.990 tau/day, 10.641 timesteps/s
+98.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.3759     |            |       |100.00
+
+Nlocal:    8000 ave 8073 max 7933 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:    8693.25 ave 8731 max 8658 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    299786 ave 302947 max 293888 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 1199142
+Ave neighs/atom = 37.4732
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00
diff --git a/examples/rerun/rdf.09Jan20.first.g++.4 b/examples/rerun/rdf.09Jan20.first.g++.4
new file mode 100644
index 0000000000..d78e0ce2c1
--- /dev/null
+++ b/examples/rerun/rdf.09Jan20.first.g++.4
@@ -0,0 +1,54 @@
+# Time-averaged data for fix 2
+# TimeStep Number-of-rows
+# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
+1000 50
+1 0.025 0 0
+2 0.075 0 0
+3 0.125 0 0
+4 0.175 0 0
+5 0.225 0 0
+6 0.275 0 0
+7 0.325 0 0
+8 0.375 0 0
+9 0.425 0 0
+10 0.475 0 0
+11 0.525 0 0
+12 0.575 0 0
+13 0.625 0 0
+14 0.675 0 0
+15 0.725 0 0
+16 0.775 0 0
+17 0.825 0 0
+18 0.875 1.53863e-05 6.25e-06
+19 0.925 0.0217263 0.00986875
+20 0.975 0.506735 0.265431
+21 1.025 1.92083 1.33605
+22 1.075 2.8749 3.09855
+23 1.125 2.7805 4.96541
+24 1.175 2.21879 6.59047
+25 1.225 1.67622 7.92484
+26 1.275 1.25407 9.00629
+27 1.325 0.963413 9.90353
+28 1.375 0.774441 10.6802
+29 1.425 0.656196 11.3871
+30 1.475 0.589364 12.0672
+31 1.525 0.560681 12.7589
+32 1.575 0.560195 13.4961
+33 1.625 0.587995 14.3197
+34 1.675 0.632155 15.2605
+35 1.725 0.706585 16.3758
+36 1.775 0.805303 17.7216
+37 1.825 0.925415 19.3565
+38 1.875 1.05672 21.3271
+39 1.925 1.17634 23.6394
+40 1.975 1.2557 26.2375
+41 2.025 1.30009 29.0653
+42 2.075 1.30889 32.0546
+43 2.125 1.27704 35.1135
+44 2.175 1.21808 38.17
+45 2.225 1.13622 41.1536
+46 2.275 1.05072 44.0382
+47 2.325 0.973786 46.8303
+48 2.375 0.910095 49.5533
+49 2.425 0.866474 52.256
+50 2.475 0.841724 54.991
diff --git a/examples/rerun/rdf.09Jan20.rerun.g++.4 b/examples/rerun/rdf.09Jan20.rerun.g++.4
new file mode 100644
index 0000000000..3fa6acc461
--- /dev/null
+++ b/examples/rerun/rdf.09Jan20.rerun.g++.4
@@ -0,0 +1,104 @@
+# Time-averaged data for fix 2
+# TimeStep Number-of-rows
+# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
+1000 100
+1 0.025 0 0
+2 0.075 0 0
+3 0.125 0 0
+4 0.175 0 0
+5 0.225 0 0
+6 0.275 0 0
+7 0.325 0 0
+8 0.375 0 0
+9 0.425 0 0
+10 0.475 0 0
+11 0.525 0 0
+12 0.575 0 0
+13 0.625 0 0
+14 0.675 0 0
+15 0.725 0 0
+16 0.775 0 0
+17 0.825 0 0
+18 0.875 1.53863e-05 6.25e-06
+19 0.925 0.021685 0.00985
+20 0.975 0.506834 0.265463
+21 1.025 1.92047 1.33588
+22 1.075 2.87514 3.09853
+23 1.125 2.78062 4.96547
+24 1.175 2.21869 6.59046
+25 1.225 1.67626 7.92486
+26 1.275 1.25409 9.00633
+27 1.325 0.963245 9.90341
+28 1.375 0.774535 10.6802
+29 1.425 0.65626 11.3871
+30 1.475 0.58925 12.0672
+31 1.525 0.560782 12.759
+32 1.575 0.560133 13.496
+33 1.625 0.588008 14.3197
+34 1.675 0.632185 15.2605
+35 1.725 0.706541 16.3757
+36 1.775 0.805341 17.7216
+37 1.825 0.925351 19.3565
+38 1.875 1.05677 21.3271
+39 1.925 1.17639 23.6395
+40 1.975 1.25571 26.2376
+41 2.025 1.30011 29.0655
+42 2.075 1.30883 32.0547
+43 2.125 1.27702 35.1134
+44 2.175 1.21813 38.17
+45 2.225 1.13617 41.1536
+46 2.275 1.05073 44.0382
+47 2.325 0.97376 46.8302
+48 2.375 0.91012 49.5533
+49 2.425 0.866556 52.2563
+50 2.475 0.841651 54.991
+51 2.525 0.839516 57.8301
+52 2.575 0.848795 60.8153
+53 2.625 0.868861 63.991
+54 2.675 0.896335 67.393
+55 2.725 0.925794 71.0395
+56 2.775 0.961909 74.9685
+57 2.825 0.999727 79.2005
+58 2.875 1.03745 83.749
+59 2.925 1.07355 88.6208
+60 2.975 1.10406 93.8039
+61 3.025 1.11993 99.2397
+62 3.075 1.12062 104.86
+63 3.125 1.10531 110.586
+64 3.175 1.07711 116.345
+65 3.225 1.04268 122.097
+66 3.275 1.00838 127.834
+67 3.325 0.974855 133.55
+68 3.375 0.949817 139.289
+69 3.425 0.936519 145.116
+70 3.475 0.92942 151.069
+71 3.525 0.930926 157.205
+72 3.575 0.940561 163.581
+73 3.625 0.94956 170.199
+74 3.675 0.964202 177.107
+75 3.725 0.97905 184.312
+76 3.775 0.991906 191.81
+77 3.825 1.00093 199.577
+78 3.875 1.01248 207.641
+79 3.925 1.02301 216.001
+80 3.975 1.03474 224.673
+81 4.025 1.04171 233.624
+82 4.075 1.04725 242.849
+83 4.125 1.04997 252.325
+84 4.175 1.04758 262.01
+85 4.225 1.03985 271.856
+86 4.275 1.02755 281.817
+87 4.325 1.00883 291.826
+88 4.375 0.99045 301.882
+89 4.425 0.97287 311.986
+90 4.475 0.958469 322.166
+91 4.525 0.952552 332.512
+92 4.575 0.948064 343.037
+93 4.625 0.952592 353.845
+94 4.675 0.958837 364.96
+95 4.725 0.970831 376.457
+96 4.775 0.985248 388.372
+97 4.825 0.998873 400.707
+98 4.875 1.0119 413.462
+99 4.925 1.02446 426.643
+100 4.975 1.03613 440.245
diff --git a/examples/rigid/in.rigid.gravity b/examples/rigid/in.rigid.gravity
new file mode 100644
index 0000000000..1094681f18
--- /dev/null
+++ b/examples/rigid/in.rigid.gravity
@@ -0,0 +1,63 @@
+#Pour composite granular particles on flat wall
+
+newton		on
+atom_style	sphere
+atom_modify	map array sort 0 0
+
+thermo_modify	flush yes
+units 		si  
+
+variable	minrad equal 0.5
+variable	maxrad equal 1.4
+
+variable 	skin equal 0.3*${maxrad}
+
+boundary	p p f
+region		reg block 0 20 0 20 0 200 units box
+create_box	1 reg
+
+fix             prop all property/atom mol ghost yes
+
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+pair_style	gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0
+pair_coeff	* *
+
+timestep 	0.0001
+
+group		particles type 1
+atom_modify     first particles
+
+neighbor        ${skin} bin
+group		rigid type 1
+neigh_modify	every 1 delay 0 check yes exclude molecule/intra all 
+
+thermo 		${logfreq}
+thermo_style	custom step cpu atoms ke
+thermo_modify	flush yes lost warn
+
+comm_modify	vel yes cutoff 3
+
+molecule	mymol molecule.data
+region		pourreg block 5 15 5 15 80 100 side in units box
+
+#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity
+# and the 'gravity' keyword to fix rigid/small were not available.
+# These settings produce undesirable behavior, where gravity can induce
+# torque on rigid bodies.
+#fix		gravfix all gravity 9.8 vector 0 0 -1 #disable
+#fix		rigidfix all rigid/small molecule mol mymol #gravity gravfix
+
+#The correct behavior is recovered with the following settings:
+fix		gravfix all gravity 9.8 vector 0 0 -1 disable
+fix		rigidfix all rigid/small molecule mol mymol gravity gravfix
+
+fix		pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix
+
+fix		zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL
+
+#dump		1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
+
+run		100000
+
diff --git a/examples/rigid/molecule.data b/examples/rigid/molecule.data
new file mode 100644
index 0000000000..e0677b0f63
--- /dev/null
+++ b/examples/rigid/molecule.data
@@ -0,0 +1,41 @@
+LAMMPS data file created for rigid body molecule template
+
+5 atoms
+
+2.3388800000000005 mass
+
+6.002239704473936 4.99 4.989999999999999 com
+
+116.79265620480001 144.26721336320003 144.26721336320006 -70.05220681600004 -70.05220681600002 -58.238345888000005 inertia
+
+Coords
+
+1 5 5 5
+2 5.1 5.0 5.0
+3 5.2 5.0 5.0
+4 6.2 5.0 5.0
+5 7.2 5.0 5.0
+
+Types
+
+1 1
+2 1
+3 1
+4 1
+5 1
+
+Diameters
+
+1 1.0
+2 0.9
+3 1.2
+4 1.2
+5 1.0
+
+Masses
+
+1 0.5235987755982988
+2 0.3817035074111599
+3 0.9047786842338602
+4 0.9047786842338602
+5 0.5235987755982988
diff --git a/examples/snap/WBe_Wood_PRB2019.snap b/examples/snap/WBe_Wood_PRB2019.snap
new file mode 120000
index 0000000000..35454e3eb8
--- /dev/null
+++ b/examples/snap/WBe_Wood_PRB2019.snap
@@ -0,0 +1 @@
+../../potentials/WBe_Wood_PRB2019.snap
\ No newline at end of file
diff --git a/examples/snap/WBe_Wood_PRB2019.snapcoeff b/examples/snap/WBe_Wood_PRB2019.snapcoeff
new file mode 120000
index 0000000000..b734e52610
--- /dev/null
+++ b/examples/snap/WBe_Wood_PRB2019.snapcoeff
@@ -0,0 +1 @@
+../../potentials/WBe_Wood_PRB2019.snapcoeff
\ No newline at end of file
diff --git a/examples/snap/WBe_Wood_PRB2019.snapparam b/examples/snap/WBe_Wood_PRB2019.snapparam
new file mode 120000
index 0000000000..8f3530ffd6
--- /dev/null
+++ b/examples/snap/WBe_Wood_PRB2019.snapparam
@@ -0,0 +1 @@
+../../potentials/WBe_Wood_PRB2019.snapparam
\ No newline at end of file
diff --git a/examples/snap/in.snap.Mo_Chen b/examples/snap/in.snap.Mo_Chen
index 007bce2462..bb9fb0900d 100644
--- a/examples/snap/in.snap.Mo_Chen
+++ b/examples/snap/in.snap.Mo_Chen
@@ -1,11 +1,11 @@
-# Demonstrate SNAP Ta potential
+# Demonstrate SNAP Mo potential
 
 # Initialize simulation
 
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.160
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -13,12 +13,12 @@ variable nx equal ${nrep}
 variable ny equal ${nrep}
 variable nz equal ${nrep}
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-create_box	1 box
-create_atoms	1 box
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
 
 mass 1 183.84
 
@@ -28,7 +28,7 @@ include Mo_Chen_PRM2017.snap
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
diff --git a/examples/snap/in.snap.Ta06A b/examples/snap/in.snap.Ta06A
index 38a24b8c06..0ca5275e97 100644
--- a/examples/snap/in.snap.Ta06A
+++ b/examples/snap/in.snap.Ta06A
@@ -5,7 +5,7 @@
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.316
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -13,12 +13,12 @@ variable nx equal ${nrep}
 variable ny equal ${nrep}
 variable nz equal ${nrep}
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-create_box	1 box
-create_atoms	1 box
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
 
 mass 1 180.88
 
@@ -28,7 +28,7 @@ include Ta06A.snap
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
diff --git a/examples/snap/in.snap.W.2940 b/examples/snap/in.snap.W.2940
index e1abf861e6..7e59b5198e 100644
--- a/examples/snap/in.snap.W.2940
+++ b/examples/snap/in.snap.W.2940
@@ -1,11 +1,11 @@
-# Demonstrate SNAP Ta potential
+# Demonstrate SNAP W potential
 
 # Initialize simulation
 
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.1803
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -13,12 +13,12 @@ variable nx equal ${nrep}
 variable ny equal ${nrep}
 variable nz equal ${nrep}
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-create_box	1 box
-create_atoms	1 box
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
 
 mass 1 183.84
 
@@ -28,7 +28,7 @@ include W_2940_2017_2.snap
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
diff --git a/examples/snap/in.snap.WBe.PRB2019 b/examples/snap/in.snap.WBe.PRB2019
new file mode 100644
index 0000000000..6b342ea56f
--- /dev/null
+++ b/examples/snap/in.snap.WBe.PRB2019
@@ -0,0 +1,48 @@
+# Demonstrate SNAP W-Be potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         bcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      2 box
+create_atoms    1 box
+mass 1 183.84
+mass 2 9.012182
+
+set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+group   tungsten         type 1
+group   beryllium        type 2
+# choose potential
+
+include WBe_Wood_PRB2019.snap
+
+# Setup output
+
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+
diff --git a/examples/snap/in.snap.compute b/examples/snap/in.snap.compute
new file mode 100644
index 0000000000..e698a134a6
--- /dev/null
+++ b/examples/snap/in.snap.compute
@@ -0,0 +1,100 @@
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	ny equal ${nrep}
+variable 	nz equal ${nrep}
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	2 box
+create_atoms	2 box
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 0
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string &
+"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_coeff 	* * ${zblz} ${zblz}
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	vb all snav/atom ${snap_options}
+compute 	db all snad/atom ${snap_options}
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+group 		snapgroup2 type 2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_30 equal c_db[2][30]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(B_{000}^i, all i of type 2) 
+#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom &
+		pe            pxy            c_bsum2[1]   c_vbsum[60]    v_db_2_30 &
+		c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10] 
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
diff --git a/examples/snap/in.snap.compute.quadratic b/examples/snap/in.snap.compute.quadratic
new file mode 100644
index 0000000000..00e46bd3a8
--- /dev/null
+++ b/examples/snap/in.snap.compute.quadratic
@@ -0,0 +1,100 @@
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	ny equal ${nrep}
+variable 	nz equal ${nrep}
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	2 box
+create_atoms	2 box
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 1
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string &
+"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_coeff 	* * ${zblz} ${zblz}
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	vb all snav/atom ${snap_options}
+compute 	db all snad/atom ${snap_options}
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+group 		snapgroup2 type 2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_120 equal c_db[2][120]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2) 
+#                4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j) 
+#                5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom &
+		pe            pxy            c_bsum2[20]   c_vbsum[240]   v_db_2_120 & 
+		c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
diff --git a/examples/snap/in.snap.hybrid.WSNAP.HePair b/examples/snap/in.snap.hybrid.WSNAP.HePair
index 1f16fa64a2..1092c28119 100644
--- a/examples/snap/in.snap.hybrid.WSNAP.HePair
+++ b/examples/snap/in.snap.hybrid.WSNAP.HePair
@@ -1,11 +1,11 @@
-# Demonstrate SNAP Ta potential
+# Demonstrate SNAP W with tabulated He-He and W-He using hybrid pair style
 
 # Initialize simulation
 
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.1803
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -13,25 +13,25 @@ variable nx equal ${nrep}
 variable ny equal ${nrep}
 variable nz equal ${nrep}
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-create_box	2 box
-create_atoms	1 box
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      2 box
+create_atoms    1 box
 mass 1 183.84
 mass 2 4.0026
 
-set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
-group	tungsten type 1
-group	helium	type 2
+set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+group   tungsten type 1
+group   helium  type 2
 # choose potential
 
 include W_2940_2017_2_He_JW2013.snap
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
diff --git a/examples/snap/log.18Sep19.snap.WBeSNAP.g++.1 b/examples/snap/log.18Sep19.snap.WBeSNAP.g++.1
new file mode 100644
index 0000000000..2b889e036b
--- /dev/null
+++ b/examples/snap/log.18Sep19.snap.WBeSNAP.g++.1
@@ -0,0 +1,154 @@
+LAMMPS (7 Aug 2019)
+# Demonstrate SNAP W-Be potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	2 box
+Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+  create_atoms CPU = 0.000234842 secs
+mass 1 183.84
+mass 2 9.012182
+
+set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fraction
+group	tungsten 	 type 1
+123 atoms in group tungsten
+group	beryllium	 type 2
+5 atoms in group beryllium
+# choose potential
+
+include WBe_Wood_PRB2019.snap
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz1 equal 74
+variable zblz2 equal 4
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 1 zbl 74 ${zblz1}
+pair_coeff 1 1 zbl 74 74
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 1 2 zbl 74 ${zblz2}
+pair_coeff 1 2 zbl 74 4
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff 2 2 zbl 4 ${zblz2}
+pair_coeff 2 2 zbl 4 4
+pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
+SNAP Element = W, Radius 0.5, Weight 1 
+SNAP Element = Be, Radius 0.417932, Weight 0.959049 
+SNAP keyword rcutfac 4.8123 
+SNAP keyword twojmax 8 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 1 
+SNAP keyword quadraticflag 0 
+
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8123
+  ghost atom cutoff = 5.8123
+  binsize = 2.90615, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -8.5980876            0   -8.5596125   -35284.855 
+      10    299.29029   -8.5979965            0   -8.5596125   -35299.259 
+      20    288.99334   -8.5966759            0   -8.5596124   -35004.093 
+      30    269.91027   -8.5942284            0   -8.5596123   -34447.077 
+      40    243.57361   -8.5908505            0   -8.5596121   -33687.105 
+      50    212.21385   -8.5868284            0   -8.5596119   -32821.864 
+      60    178.77144   -8.5825391            0   -8.5596116    -31971.17 
+      70    146.71854    -8.578428            0   -8.5596113    -31245.51 
+      80    119.50956   -8.5749383            0   -8.5596111   -30724.137 
+      90    99.872785   -8.5724197            0    -8.559611   -30440.244 
+     100    89.604584   -8.5711027            0   -8.5596109   -30392.805 
+Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms
+
+Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s
+199.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.1672     | 3.1672     | 3.1672     |   0.0 | 99.97
+Neigh   | 0.00030208 | 0.00030208 | 0.00030208 |   0.0 |  0.01
+Comm    | 0.00029612 | 0.00029612 | 0.00029612 |   0.0 |  0.01
+Output  | 0.00019813 | 0.00019813 | 0.00019813 |   0.0 |  0.01
+Modify  | 0.00014448 | 0.00014448 | 0.00014448 |   0.0 |  0.00
+Other   |            | 0.0001433  |            |       |  0.00
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3710 ave 3710 max 3710 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7420 ave 7420 max 7420 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7420
+Ave neighs/atom = 57.9688
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:03
diff --git a/examples/snap/log.18Sep19.snap.WBeSNAP.g++.4 b/examples/snap/log.18Sep19.snap.WBeSNAP.g++.4
new file mode 100644
index 0000000000..d8cdae6810
--- /dev/null
+++ b/examples/snap/log.18Sep19.snap.WBeSNAP.g++.4
@@ -0,0 +1,154 @@
+LAMMPS (7 Aug 2019)
+# Demonstrate SNAP W-Be potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	2 box
+Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+  create_atoms CPU = 0.000317097 secs
+mass 1 183.84
+mass 2 9.012182
+
+set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fraction
+group	tungsten 	 type 1
+123 atoms in group tungsten
+group	beryllium	 type 2
+5 atoms in group beryllium
+# choose potential
+
+include WBe_Wood_PRB2019.snap
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz1 equal 74
+variable zblz2 equal 4
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 1 zbl 74 ${zblz1}
+pair_coeff 1 1 zbl 74 74
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 1 2 zbl 74 ${zblz2}
+pair_coeff 1 2 zbl 74 4
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff 2 2 zbl 4 ${zblz2}
+pair_coeff 2 2 zbl 4 4
+pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
+SNAP Element = W, Radius 0.5, Weight 1 
+SNAP Element = Be, Radius 0.417932, Weight 0.959049 
+SNAP keyword rcutfac 4.8123 
+SNAP keyword twojmax 8 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 1 
+SNAP keyword quadraticflag 0 
+
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8123
+  ghost atom cutoff = 5.8123
+  binsize = 2.90615, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -8.5980876            0   -8.5596125   -35284.855 
+      10    296.24946   -8.5976065            0   -8.5596124    -35140.29 
+      20    282.27904   -8.5958147            0   -8.5596123     -34710.3 
+      30    259.54978   -8.5928995            0   -8.5596121    -34060.43 
+      40    230.41412   -8.5891626            0   -8.5596119   -33258.275 
+      50    197.85135   -8.5849861            0   -8.5596116   -32389.527 
+      60    165.21732   -8.5808005            0   -8.5596113   -31550.426 
+      70    135.94024   -8.5770455            0   -8.5596111   -30839.006 
+      80    113.06617   -8.5741117            0   -8.5596109   -30339.177 
+      90    98.542347    -8.572249            0   -8.5596109    -30094.29 
+     100    92.524343   -8.5714774            0   -8.5596111   -30091.988 
+Loop time of 0.813674 on 4 procs for 100 steps with 128 atoms
+
+Performance: 5.309 ns/day, 4.520 hours/ns, 122.899 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.79079    | 0.79788    | 0.80888    |   0.8 | 98.06
+Neigh   | 7.1049e-05 | 8.0049e-05 | 9.2983e-05 |   0.0 |  0.01
+Comm    | 0.0041246  | 0.01515    | 0.022235   |   5.5 |  1.86
+Output  | 0.000144   | 0.00017095 | 0.00024796 |   0.0 |  0.02
+Modify  | 4.4823e-05 | 5.8889e-05 | 7.2718e-05 |   0.0 |  0.01
+Other   |            | 0.000338   |            |       |  0.04
+
+Nlocal:    32 ave 37 max 28 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Nghost:    431 ave 435 max 426 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Neighs:    927 ave 1071 max 821 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+FullNghs:  1854 ave 2144 max 1624 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 7416
+Ave neighs/atom = 57.9375
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:00
diff --git a/examples/snap/log.27Nov18.snap.compute.g++.1 b/examples/snap/log.27Nov18.snap.compute.g++.1
new file mode 100644
index 0000000000..b189c552da
--- /dev/null
+++ b/examples/snap/log.27Nov18.snap.compute.g++.1
@@ -0,0 +1,198 @@
+LAMMPS (20 Nov 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	nx equal 1
+variable 	ny equal ${nrep}
+variable 	ny equal 1
+variable 	nz equal ${nrep}
+variable 	nz equal 1
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+lattice         bcc 2
+Lattice spacing in x,y,z = 2 2 2
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 1 0 ${ny} 0 ${nz}
+region		box block 0 1 0 1 0 ${nz}
+region		box block 0 1 0 1 0 1
+create_box	2 box
+Created orthogonal box = (0 0 0) to (2 2 2)
+  1 by 1 by 1 MPI processor grid
+create_atoms	2 box
+Created 2 atoms
+  create_atoms CPU = 0.000478029 secs
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 0
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_style 	zero 1
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_style 	zbl 4 ${zblcutouter}
+pair_style 	zbl 4 4.8
+pair_coeff 	* * ${zblz} ${zblz}
+pair_coeff 	* * 73 ${zblz}
+pair_coeff 	* * 73 73
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${snap_options}
+compute 	vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${snap_options}
+compute 	db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+0 atoms in group snapgroup1
+group 		snapgroup2 type 2
+2 atoms in group snapgroup2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_30 equal c_db[2][30]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+compute 	snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(B_{000}^i, all i of type 2)
+#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom 		pe            pxy            c_bsum2[1]   c_vbsum[60]    v_db_2_30 		c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
+run             0
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 1 1 1
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair zbl, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute sna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute snav/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute snad/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute snap, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.06 | 10.06 Mbytes
+PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10] 
+   322.86952    1505558.1    364182.88    381.32218   -855.04473    322.86952    1505558.1    364182.88    381.32218   -855.04473 
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 2 atoms
+
+104.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 9.537e-07  |            |       |100.00
+
+Nlocal:    2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    853 ave 853 max 853 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    330 ave 330 max 330 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  660 ave 660 max 660 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 660
+Ave neighs/atom = 330
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/snap/log.27Nov18.snap.compute.g++.4 b/examples/snap/log.27Nov18.snap.compute.g++.4
new file mode 100644
index 0000000000..f979123b2a
--- /dev/null
+++ b/examples/snap/log.27Nov18.snap.compute.g++.4
@@ -0,0 +1,199 @@
+LAMMPS (20 Nov 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	nx equal 1
+variable 	ny equal ${nrep}
+variable 	ny equal 1
+variable 	nz equal ${nrep}
+variable 	nz equal 1
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+lattice         bcc 2
+Lattice spacing in x,y,z = 2 2 2
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 1 0 ${ny} 0 ${nz}
+region		box block 0 1 0 1 0 ${nz}
+region		box block 0 1 0 1 0 1
+create_box	2 box
+Created orthogonal box = (0 0 0) to (2 2 2)
+  1 by 2 by 2 MPI processor grid
+create_atoms	2 box
+Created 2 atoms
+  create_atoms CPU = 0.000610113 secs
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 0
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_style 	zero 1
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_style 	zbl 4 ${zblcutouter}
+pair_style 	zbl 4 4.8
+pair_coeff 	* * ${zblz} ${zblz}
+pair_coeff 	* * 73 ${zblz}
+pair_coeff 	* * 73 73
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${snap_options}
+compute 	vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${snap_options}
+compute 	db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+0 atoms in group snapgroup1
+group 		snapgroup2 type 2
+2 atoms in group snapgroup2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_30 equal c_db[2][30]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+compute 	snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(B_{000}^i, all i of type 2)
+#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom 		pe            pxy            c_bsum2[1]   c_vbsum[60]    v_db_2_30 		c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
+run             0
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 1 1 1
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair zbl, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute sna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute snav/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute snad/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute snap, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:936)
+Per MPI rank memory allocation (min/avg/max) = 8.211 | 8.254 | 8.295 Mbytes
+PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10] 
+   322.86952    1505558.1    364182.88    381.32218   -855.04473    322.86952    1505558.1    364182.88    381.32218   -855.04473 
+Loop time of 2.38419e-06 on 4 procs for 0 steps with 2 atoms
+
+104.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 2.384e-06  |            |       |100.00
+
+Nlocal:    0.5 ave 1 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    734.5 ave 735 max 734 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    82.5 ave 177 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+FullNghs:  165 ave 330 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 660
+Ave neighs/atom = 330
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/snap/log.27Nov18.snap.compute.quadratic.g++.1 b/examples/snap/log.27Nov18.snap.compute.quadratic.g++.1
new file mode 100644
index 0000000000..c2054023ed
--- /dev/null
+++ b/examples/snap/log.27Nov18.snap.compute.quadratic.g++.1
@@ -0,0 +1,198 @@
+LAMMPS (20 Nov 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	nx equal 1
+variable 	ny equal ${nrep}
+variable 	ny equal 1
+variable 	nz equal ${nrep}
+variable 	nz equal 1
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+lattice         bcc 2
+Lattice spacing in x,y,z = 2 2 2
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 1 0 ${ny} 0 ${nz}
+region		box block 0 1 0 1 0 ${nz}
+region		box block 0 1 0 1 0 1
+create_box	2 box
+Created orthogonal box = (0 0 0) to (2 2 2)
+  1 by 1 by 1 MPI processor grid
+create_atoms	2 box
+Created 2 atoms
+  create_atoms CPU = 0.000473976 secs
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 1
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_style 	zero 1
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_style 	zbl 4 ${zblcutouter}
+pair_style 	zbl 4 4.8
+pair_coeff 	* * ${zblz} ${zblz}
+pair_coeff 	* * 73 ${zblz}
+pair_coeff 	* * 73 73
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${snap_options}
+compute 	vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${snap_options}
+compute 	db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+0 atoms in group snapgroup1
+group 		snapgroup2 type 2
+2 atoms in group snapgroup2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_120 equal c_db[2][120]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+compute 	snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
+#                4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom 		pe            pxy            c_bsum2[20]   c_vbsum[240]   v_db_2_120 		c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
+run             0
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 1 1 1
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair zbl, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute sna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute snav/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute snad/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute snap, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 21.78 | 21.78 | 21.78 Mbytes
+PotEng Pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40] 
+   322.86952    1505558.1 4.2492771e+08    7860489.6    -17625699    322.86952    1505558.1 4.2492771e+08    7860489.6    -17625699 
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 2 atoms
+
+93.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 2.146e-06  |            |       |100.00
+
+Nlocal:    2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    853 ave 853 max 853 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    330 ave 330 max 330 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  660 ave 660 max 660 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 660
+Ave neighs/atom = 330
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/snap/log.27Nov18.snap.compute.quadratic.g++.4 b/examples/snap/log.27Nov18.snap.compute.quadratic.g++.4
new file mode 100644
index 0000000000..819397f745
--- /dev/null
+++ b/examples/snap/log.27Nov18.snap.compute.quadratic.g++.4
@@ -0,0 +1,199 @@
+LAMMPS (20 Nov 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate bispectrum computes
+
+# initialize simulation
+
+variable 	nsteps index 0
+variable 	nrep equal 1
+variable 	a equal 2.0
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable 	nx equal ${nrep}
+variable 	nx equal 1
+variable 	ny equal ${nrep}
+variable 	ny equal 1
+variable 	nz equal ${nrep}
+variable 	nz equal 1
+
+boundary	p p p
+
+atom_modify	map hash
+lattice         bcc $a
+lattice         bcc 2
+Lattice spacing in x,y,z = 2 2 2
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 1 0 ${ny} 0 ${nz}
+region		box block 0 1 0 1 0 ${nz}
+region		box block 0 1 0 1 0 1
+create_box	2 box
+Created orthogonal box = (0 0 0) to (2 2 2)
+  1 by 2 by 2 MPI processor grid
+create_atoms	2 box
+Created 2 atoms
+  create_atoms CPU = 0.000118971 secs
+
+mass 		* 180.88
+
+displace_atoms 	all random 0.1 0.1 0.1 123456
+
+# choose SNA parameters
+
+variable 	twojmax equal 2
+variable 	rcutfac equal 1.0
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	radelem1 equal 2.3
+variable 	radelem2 equal 2.0
+variable	wj1 equal 1.0
+variable	wj2 equal 0.96
+variable	quadratic equal 1
+variable	bzero equal 0
+variable	switch equal 0
+variable 	snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
+1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+
+# set up dummy potential to satisfy cutoff
+
+pair_style 	zero ${rcutfac}
+pair_style 	zero 1
+pair_coeff 	* *
+
+# set up reference potential
+
+variable 	zblcutinner equal 4
+variable 	zblcutouter equal 4.8
+variable 	zblz equal 73
+pair_style 	zbl ${zblcutinner} ${zblcutouter}
+pair_style 	zbl 4 ${zblcutouter}
+pair_style 	zbl 4 4.8
+pair_coeff 	* * ${zblz} ${zblz}
+pair_coeff 	* * 73 ${zblz}
+pair_coeff 	* * 73 73
+
+# set up per-atom computes
+
+compute 	b all sna/atom ${snap_options}
+compute 	b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+compute 	vb all snav/atom ${snap_options}
+compute 	vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+compute 	db all snad/atom ${snap_options}
+compute 	db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+
+# perform sums over atoms
+
+group 		snapgroup1 type 1
+0 atoms in group snapgroup1
+group 		snapgroup2 type 2
+2 atoms in group snapgroup2
+compute         bsum1 snapgroup1 reduce sum c_b[*]
+compute         bsum2 snapgroup2 reduce sum c_b[*]
+# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
+# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
+compute		vbsum all reduce sum c_vb[*]
+# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
+variable	db_2_120 equal c_db[2][120]
+
+# set up compute snap generating global array
+
+compute 	snap all snap ${snap_options}
+compute 	snap all snap 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
+fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
+
+thermo 		100
+
+# test output:   1: total potential energy
+#                2: xy component of stress tensor
+#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
+#                4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
+#                5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
+#
+#                followed by 5 counterparts from compute snap
+
+thermo_style	custom 		pe            pxy            c_bsum2[20]   c_vbsum[240]   v_db_2_120 		c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
+thermo_modify 	norm no
+
+# dump 		mydump_db all custom 1000 dump_db id c_db[*]
+# dump_modify 	mydump_db sort id
+
+# Run MD
+
+run             ${nsteps}
+run             0
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 1 1 1
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair zbl, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute sna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute snav/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute snad/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute snap, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:936)
+Per MPI rank memory allocation (min/avg/max) = 19.7 | 19.74 | 19.78 Mbytes
+PotEng Pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40] 
+   322.86952    1505558.1 4.2492771e+08    7860489.6    -17625699    322.86952    1505558.1 4.2492771e+08    7860489.6    -17625699 
+Loop time of 2.80142e-06 on 4 procs for 0 steps with 2 atoms
+
+107.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 2.801e-06  |            |       |100.00
+
+Nlocal:    0.5 ave 1 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    734.5 ave 735 max 734 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    82.5 ave 177 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+FullNghs:  165 ave 330 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 660
+Ave neighs/atom = 330
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/lib/atc/ATC_Coupling.cpp b/lib/atc/ATC_Coupling.cpp
index b021584186..9468064f8d 100644
--- a/lib/atc/ATC_Coupling.cpp
+++ b/lib/atc/ATC_Coupling.cpp
@@ -1693,7 +1693,7 @@ namespace ATC {
     extrinsicModelManager_.construct_transfers();
   }
   //--------------------------------------------------
-  void ATC_Coupling::delete_mass_mat_time_filter(FieldName thisField)
+  void ATC_Coupling::delete_mass_mat_time_filter(FieldName /* thisField */)
   {
   }
   //--------------------------------------------------
diff --git a/lib/atc/ATC_Coupling.h b/lib/atc/ATC_Coupling.h
index 002041b536..3816a82798 100644
--- a/lib/atc/ATC_Coupling.h
+++ b/lib/atc/ATC_Coupling.h
@@ -131,7 +131,7 @@ namespace ATC {
     virtual void initialize_mesh_data(void);  
 
 // public for FieldIntegrator
-    bool source_atomic_quadrature(FieldName field)  
+    bool source_atomic_quadrature(FieldName /* field */)  
       { return (sourceIntegration_ == FULL_DOMAIN_ATOMIC_QUADRATURE_SOURCE); }
     ATC::IntegrationDomainType source_integration() 
       { return sourceIntegration_; }
diff --git a/lib/atc/ATC_CouplingMomentumEnergy.cpp b/lib/atc/ATC_CouplingMomentumEnergy.cpp
index c4f7829c60..bf0edc71fb 100644
--- a/lib/atc/ATC_CouplingMomentumEnergy.cpp
+++ b/lib/atc/ATC_CouplingMomentumEnergy.cpp
@@ -319,7 +319,7 @@ namespace ATC {
   //  modify
   //    parses inputs and modifies state of the filter
   //--------------------------------------------------------
-  bool ATC_CouplingMomentumEnergy::modify(int narg, char **arg)
+  bool ATC_CouplingMomentumEnergy::modify(int /* narg */, char ** /* arg */)
   {
     return false;
   }
diff --git a/lib/atc/ATC_Method.h b/lib/atc/ATC_Method.h
index aa8f238721..e356243e03 100644
--- a/lib/atc/ATC_Method.h
+++ b/lib/atc/ATC_Method.h
@@ -140,9 +140,9 @@ namespace ATC {
     /** compute scalar for output */
     virtual double compute_scalar() {return 0.;}
     /** compute vector for output */
-    virtual double compute_vector(int n) {return 0.;}
+    virtual double compute_vector(int /* n */) {return 0.;}
     /** compute vector for output */
-    virtual double compute_array(int irow, int icol) {return 0.;}; 
+    virtual double compute_array(int /* irow */, int /* icol */) {return 0.;}; 
     int scalar_flag() const {return scalarFlag_;}
     int vector_flag() const {return vectorFlag_;}
     int size_vector() const {return sizeVector_;}
@@ -398,8 +398,8 @@ namespace ATC {
 //    /** determine weighting method for atomic integration */
 //    void compute_consistent_md_mass_matrix(const SPAR_MAT & shapeFunctionMatrix,
  //                                          SPAR_MAT & mdMassMatrix);
-    virtual void compute_md_mass_matrix(FieldName thisField,
-                                        DIAG_MAT & massMat) {};
+    virtual void compute_md_mass_matrix(FieldName /* thisField */,
+                                        DIAG_MAT & /* massMat */) {};
 /** access to md mass matrices */
 
     DIAG_MAN &mass_mat_md_inv(FieldName thisField)
diff --git a/lib/atc/ATC_Transfer.cpp b/lib/atc/ATC_Transfer.cpp
index 968dcbbea7..c876f46634 100644
--- a/lib/atc/ATC_Transfer.cpp
+++ b/lib/atc/ATC_Transfer.cpp
@@ -1658,7 +1658,7 @@ namespace ATC {
   }
   //--------------------------------------------------------------------
   void ATC_Transfer::compute_vacancy_concentration(DENS_MAT & Cv,
-    const DENS_MAT & H, const DENS_MAT & rhoN)
+                                                   const DENS_MAT & H, const DENS_MAT & /* rhoN */)
   {
     int * type = lammpsInterface_->atom_type();
     DENS_MAT new_rho(nNodes_,1);
diff --git a/lib/atc/ATC_TransferPartitionOfUnity.cpp b/lib/atc/ATC_TransferPartitionOfUnity.cpp
index a847a8ee3b..5d83fd8fd7 100644
--- a/lib/atc/ATC_TransferPartitionOfUnity.cpp
+++ b/lib/atc/ATC_TransferPartitionOfUnity.cpp
@@ -54,7 +54,7 @@ namespace ATC {
 
   //-------------------------------------------------------------------
   void ATC_TransferPartitionOfUnity::compute_projection(
-    const DENS_MAT & atomData, DENS_MAT & nodeData)
+    const DENS_MAT & /* atomData */, DENS_MAT & /* nodeData */)
   {
     throw ATC_Error("unimplemented function");
   }
diff --git a/lib/atc/AtomicRegulator.cpp b/lib/atc/AtomicRegulator.cpp
index 9d329852af..9c7e758816 100644
--- a/lib/atc/AtomicRegulator.cpp
+++ b/lib/atc/AtomicRegulator.cpp
@@ -158,7 +158,7 @@ namespace ATC {
   //    parses and adjusts controller state based on
   //    user input, in the style of LAMMPS user input
   //--------------------------------------------------------
-  bool AtomicRegulator::modify(int narg, char **arg)
+  bool AtomicRegulator::modify(int /* narg */, char **arg)
   {
     bool foundMatch = false;
 
diff --git a/lib/atc/AtomicRegulator.h b/lib/atc/AtomicRegulator.h
index 454f54989d..8fb7de1006 100644
--- a/lib/atc/AtomicRegulator.h
+++ b/lib/atc/AtomicRegulator.h
@@ -90,7 +90,7 @@ namespace ATC {
         
     /** add output information */
     virtual void output(OUTPUT_LIST & outputData) const;
-    virtual double compute_vector(int n) const {return 0;}
+    virtual double compute_vector(int /* n */) const {return 0;}
     
     /** final work at the end of a run */
     virtual void finish();
@@ -123,14 +123,15 @@ namespace ATC {
     virtual void pack_fields(RESTART_LIST & data);
 
     /** thermo output */
-    virtual int size_vector(int s) const {return 0;};
+    virtual int size_vector(int /* s */) const {return 0;};
 
     // coupling to FE state
     /** FE state variable regulator is applied to */
     virtual RegulatorTargetType regulator_target() const {return regulatorTarget_;};
     /** type of boundary coupling */
     //TEMP_JAT field variable should be removed
-    virtual RegulatorCouplingType coupling_mode(const FieldName field=NUM_TOTAL_FIELDS) const {return couplingMode_;};
+    virtual RegulatorCouplingType coupling_mode(const FieldName /* field */) const {return couplingMode_;};
+    virtual RegulatorCouplingType coupling_mode() const {return couplingMode_;};
     /** compute the thermal boundary flux, must be consistent with regulator */
     virtual void compute_boundary_flux(FIELDS & fields);
     /** add contributions (if any) to the finite element right-hand side */
@@ -140,7 +141,7 @@ namespace ATC {
     /** returns a pointer to the DENS_MAN associated with the tag, creates a new data member if necessary */
     DENS_MAN * regulator_data(const std::string tag, int nCols);
     /** can externally set regulator dynamic contributions */
-    virtual void reset_lambda_contribution(const DENS_MAT & target, const FieldName field) {};
+    virtual void reset_lambda_contribution(const DENS_MAT & /* target */, const FieldName /* field */) {};
     virtual void reset_lambda_contribution(const DENS_MAT & target) { reset_lambda_contribution(target,NUM_TOTAL_FIELDS); }
     /** returns a const pointer to the DENS_MAN associated with the tag, or NULL */
     const DENS_MAN * regulator_data(const std::string tag) const;
@@ -291,29 +292,29 @@ namespace ATC {
     virtual void reset_nlocal(){};
 
     /** set up atom to material identification */
-    virtual void reset_atom_materials(const Array<int> & elementToMaterialMap,
-                                      const MatrixDependencyManager<DenseMatrix, int> * atomElement){};
+    virtual void reset_atom_materials(const Array<int> & /* elementToMaterialMap */,
+                                      const MatrixDependencyManager<DenseMatrix, int> * /* atomElement */){};
         
     /** applies regulator to atoms in the pre-predictor phase */
-    virtual void apply_pre_predictor(double dt){};
+    virtual void apply_pre_predictor(double /* dt */){};
 
     /** applies regulator to atoms in the mid-predictor phase */
-    virtual void apply_mid_predictor(double dt){};
+    virtual void apply_mid_predictor(double /* dt */){};
 
     /** applies regulator to atoms in the post-predictor phase */
-    virtual void apply_post_predictor(double dt){};
+    virtual void apply_post_predictor(double /* dt */){};
 
     /** applies regulator to atoms in the pre-corrector phase */
-    virtual void apply_pre_corrector(double dt){};
+    virtual void apply_pre_corrector(double /* dt */){};
 
     /** applies regulator to atoms in the post-corrector phase */
-    virtual void apply_post_corrector(double dt){};
+    virtual void apply_post_corrector(double /* dt */){};
 
     /** applies regulator to atoms in the pre-corrector phase */
-    virtual void apply_pre_force(double dt){};
+    virtual void apply_pre_force(double /* dt */){};
 
     /** applies regulator to atoms in the post-corrector phase */
-    virtual void apply_post_force(double dt){};
+    virtual void apply_post_force(double /* dt */){};
 
     /** applies regulator in pre-force phase */
     virtual void pre_force(){};
@@ -328,17 +329,17 @@ namespace ATC {
     virtual void compute_boundary_flux(FIELDS & fields);
 
     /** add contributions (if any) to the finite element right-hand side */
-    virtual void add_to_rhs(FIELDS & rhs){};
+    virtual void add_to_rhs(FIELDS & /* rhs */){};
 
     /** get data for output */
-    virtual void output(OUTPUT_LIST & outputData){};
-    virtual double compute_vector(int n) const {return 0;}
+    virtual void output(OUTPUT_LIST & /* outputData */){};
+    virtual double compute_vector(int /* n */) const {return 0;}
 
     /** final work at the end of a run */
     virtual void finish(){};
 
     /** pack fields for restart */
-    virtual void pack_fields(RESTART_LIST & data){};
+    virtual void pack_fields(RESTART_LIST & /* data */){};
         
   protected:
 
diff --git a/lib/atc/BodyForce.h b/lib/atc/BodyForce.h
index eef5df03be..10d7cf66c1 100644
--- a/lib/atc/BodyForce.h
+++ b/lib/atc/BodyForce.h
@@ -18,8 +18,8 @@ namespace ATC {
     public:
       BodyForce()   {};
       virtual ~BodyForce() {};
-      virtual bool body_force(const FIELD_MATS &fields,
-                                    DENS_MAT &flux) const { return false; };
+      virtual bool body_force(const FIELD_MATS & /* fields */,
+                              DENS_MAT & /* flux */) const { return false; };
   };
 
   /**
@@ -49,7 +49,7 @@ namespace ATC {
   class BodyForceElectricField : public BodyForce
   {
     public:
-      BodyForceElectricField(std::fstream &matfile,std::map<std::string,double> & parameters) 
+    BodyForceElectricField(std::fstream & /* matfile */,std::map<std::string,double> & /* parameters */) 
         { throw ATC_Error("unimplemented due to issues with accessing electric field"); }
       virtual ~BodyForceElectricField() {};
       virtual bool body_force(const FIELD_MATS &fields,
diff --git a/lib/atc/CbPotential.h b/lib/atc/CbPotential.h
index 44b9b7c1de..e218ae2254 100644
--- a/lib/atc/CbPotential.h
+++ b/lib/atc/CbPotential.h
@@ -40,7 +40,7 @@ namespace ATC
 
     //! @name Pairwise interaction term and derivatives.
     //@{
-    virtual double phi    (const double &r) const { return 0.0; }
+    virtual double phi    (const double & /* r */) const { return 0.0; }
     virtual double phi_r  (const double &r) const;
     virtual double phi_rr (const double &r) const;
     virtual double phi_rrr(const double &r) const;
@@ -48,11 +48,11 @@ namespace ATC
 
     //! @name Embedding terms. Electron cloud density and embedding functions
     //@{
-    virtual double rho   (const double &r) const { return 0.0; }
+    virtual double rho   (const double & /* r */) const { return 0.0; }
     virtual double rho_r (const double &r) const;
     virtual double rho_rr(const double &r) const;
     virtual double rho_rrr(const double &r) const;
-    virtual double F   (const double &p) const { return 0.0; }
+    virtual double F   (const double & /* p */) const { return 0.0; }
     virtual double F_p (const double &p) const;
     virtual double F_pp(const double &p) const;
     virtual double F_ppp(const double &p) const;
@@ -60,7 +60,7 @@ namespace ATC
 
     //! @name Three-body terms and derivatives
     //@{
-    virtual double phi3   (const double &q) const {return 0.0; }
+    virtual double phi3   (const double & /* q */) const {return 0.0; }
     virtual double phi3_q (const double &q) const;
     virtual double phi3_qq(const double &q) const;
     //@}
diff --git a/lib/atc/ChargeRegulator.cpp b/lib/atc/ChargeRegulator.cpp
index 2e899fcc8e..cbfda69480 100644
--- a/lib/atc/ChargeRegulator.cpp
+++ b/lib/atc/ChargeRegulator.cpp
@@ -53,7 +53,7 @@ namespace ATC {
   //    parses and adjusts charge regulator state based on
   //    user input, in the style of LAMMPS user input
   //--------------------------------------------------------
-  bool ChargeRegulator::modify(int narg, char **arg)
+  bool ChargeRegulator::modify(int /* narg */, char ** /* arg */)
   {
     bool foundMatch = false;
     return foundMatch;
@@ -241,7 +241,7 @@ namespace ATC {
   //--------------------------------------------------------
   //  output
   //--------------------------------------------------------
-  void ChargeRegulatorMethod::output(OUTPUT_LIST & outputData)
+  void ChargeRegulatorMethod::output(OUTPUT_LIST & /* outputData */)
   {
     //vector<double> localSum(sum_.size());
     //lammpsInteface_->allsum(localSum.pointer,sum_.pointer,sum_.size());
@@ -383,7 +383,7 @@ namespace ATC {
   //--------------------------------------------------------
   // change potential/charge pre-force calculation
   //--------------------------------------------------------
-  void ChargeRegulatorMethodFeedback::apply_pre_force(double dt)
+  void ChargeRegulatorMethodFeedback::apply_pre_force(double /* dt */)
   {
 
     sum_ = 0; 
@@ -455,7 +455,7 @@ namespace ATC {
   //--------------------------------------------------------
   // change potential/charge post-force calculation
   //--------------------------------------------------------
-  void ChargeRegulatorMethodImageCharge::apply_post_force(double dt)
+  void ChargeRegulatorMethodImageCharge::apply_post_force(double /* dt */)
   {
     sum_ = 0;
     apply_local_forces();
@@ -644,7 +644,7 @@ namespace ATC {
   //--------------------------------------------------------
   //  add effective forces post LAMMPS force call
   //--------------------------------------------------------
-  void ChargeRegulatorMethodEffectiveCharge::apply_post_force(double dt) 
+  void ChargeRegulatorMethodEffectiveCharge::apply_post_force(double /* dt */) 
   {
     apply_local_forces();
   }
diff --git a/lib/atc/ChargeRegulator.h b/lib/atc/ChargeRegulator.h
index b51707b9cd..f250a955e8 100644
--- a/lib/atc/ChargeRegulator.h
+++ b/lib/atc/ChargeRegulator.h
@@ -65,7 +65,7 @@ namespace ATC {
     virtual void apply_pre_force(double dt);
     virtual void apply_post_force(double dt);
     virtual void output(OUTPUT_LIST & outputData) const;
-    virtual double compute_vector(int n) const {return 0;} // TODO
+    virtual double compute_vector(int /* n */) const {return 0;} // TODO
 
     void assign_poisson_solver(PoissonSolver * solver) { poissonSolver_ = solver;}  
     PoissonSolver * poisson_solver(void) { return poissonSolver_;} 
@@ -97,8 +97,8 @@ namespace ATC {
     ~ChargeRegulatorMethod(){};
     virtual void initialize(void); 
     void set_greens_functions();
-    virtual void apply_pre_force(double dt){}; 
-    virtual void apply_post_force(double dt){}; 
+    virtual void apply_pre_force(double /* dt */){}; 
+    virtual void apply_post_force(double /* dt */){}; 
     virtual void set_weights() {};
     const DENS_VEC & total_influence() const { return sum_;}
     virtual void output(OUTPUT_LIST & outputData);
diff --git a/lib/atc/CloneVector.h b/lib/atc/CloneVector.h
index 0c3bef8c59..02db700f27 100644
--- a/lib/atc/CloneVector.h
+++ b/lib/atc/CloneVector.h
@@ -72,7 +72,7 @@ CloneVector<T>::CloneVector(const Matrix<T> &c, int dim, INDEX idx)
 // Construct from a DiagonalMatrix
 //-----------------------------------------------------------------------------
 template<typename T>
-CloneVector<T>::CloneVector(const DiagonalMatrix<T> &c, INDEX idx) 
+CloneVector<T>::CloneVector(const DiagonalMatrix<T> &c, INDEX /* idx */) 
  : Vector<T>(), _baseV(NULL), _baseM(const_cast<DiagonalMatrix<T>*>(&c))
  , _clone_type(CLONE_DIAG), _idx(0)
 {}
@@ -80,7 +80,7 @@ CloneVector<T>::CloneVector(const DiagonalMatrix<T> &c, INDEX idx)
 // value (const) indexing operator
 //-----------------------------------------------------------------------------
 template<typename T>
-T CloneVector<T>::operator()(INDEX i, INDEX j) const 
+  T CloneVector<T>::operator()(INDEX i, INDEX /* j */) const 
 {
   return (*this)[i];
 }
@@ -88,7 +88,7 @@ T CloneVector<T>::operator()(INDEX i, INDEX j) const
 // reference index operator
 //-----------------------------------------------------------------------------
 template<typename T>
-T& CloneVector<T>::operator()(INDEX i, INDEX j)
+T& CloneVector<T>::operator()(INDEX i, INDEX /* j */)
 {
   return (*this)[i];
 }
diff --git a/lib/atc/ConcentrationRegulator.cpp b/lib/atc/ConcentrationRegulator.cpp
index c734a5d98d..8055433f5d 100644
--- a/lib/atc/ConcentrationRegulator.cpp
+++ b/lib/atc/ConcentrationRegulator.cpp
@@ -47,7 +47,7 @@ const double kMinScale_ = 10000.;
   //    parses and adjusts charge regulator state based on
   //    user input, in the style of LAMMPS user input
   //--------------------------------------------------------
-  bool ConcentrationRegulator::modify(int narg, char **arg)
+  bool ConcentrationRegulator::modify(int /* narg */, char ** /* arg */)
   {
     bool foundMatch = false;
     return foundMatch;
@@ -166,7 +166,7 @@ const double kMinScale_ = 10000.;
   //--------------------------------------------------------
   //  size vector
   //--------------------------------------------------------
-  int ConcentrationRegulator::size_vector(int i) const
+  int ConcentrationRegulator::size_vector(int /* i */) const
   {
     int n = (regulators_.size())*5; 
     if (n==0) n = 20; 
@@ -319,7 +319,7 @@ const double kMinScale_ = 10000.;
   //--------------------------------------------------------
   //  accept
   //--------------------------------------------------------
-  bool ConcentrationRegulatorMethodTransition::accept(double energy, double T) const 
+  bool ConcentrationRegulatorMethodTransition::accept(double energy, double /* T */) const 
   { 
 #ifdef ATC_VERBOSE2
     if (energy < maxEnergy_) lammpsInterface_->print_msg(" energy "+to_string(energy)+" "+to_string(rngCounter_));
@@ -423,7 +423,7 @@ const double kMinScale_ = 10000.;
     int * tag = lammpsInterface_->atom_tag();
     for (itr = list.begin(); itr != list.end(); itr++) {
       int atag = tag[itr->second]; 
-      double d = abs(atag-r);
+      double d = fabs(atag-r);
       if (d < min) {
         min = d;
         idx = i;
diff --git a/lib/atc/ConcentrationRegulator.h b/lib/atc/ConcentrationRegulator.h
index 3645880cc5..952cf88339 100644
--- a/lib/atc/ConcentrationRegulator.h
+++ b/lib/atc/ConcentrationRegulator.h
@@ -60,19 +60,19 @@ namespace ATC {
     //WIP_JAT need a nicer way to consistently handle sets of regulators, not sure how yet
     // application steps
     /** apply the regulator in the pre-predictor phase */
-    virtual void apply_pre_predictor(double dt, int timeStep){};
+    virtual void apply_pre_predictor(double /* dt */, int /* timeStep */){};
     /** apply the regulator in the mid-predictor phase */
-    virtual void apply_mid_predictor(double dt, int timeStep){};
+    virtual void apply_mid_predictor(double /* dt */, int /* timeStep */){};
     /** apply the regulator in the post-predictor phase */
-    virtual void apply_post_predictor(double dt, int timeStep){};
+    virtual void apply_post_predictor(double /* dt */, int /* timeStep */){};
     /** apply the regulator in the pre-correction phase */
-    virtual void apply_pre_corrector(double dt, int timeStep){};
+    virtual void apply_pre_corrector(double /* dt */, int /* timeStep */){};
     /** apply the regulator in the post-correction phase */
-    virtual void apply_post_corrector(double dt, int timeStep){};
+    virtual void apply_post_corrector(double /* dt */, int /* timeStep */){};
     /** compute the thermal boundary flux, must be consistent with regulator */
-    virtual void compute_boundary_flux(FIELDS & fields){};
+    virtual void compute_boundary_flux(FIELDS & /* fields */){};
     /** add contributions (if any) to the finite element right-hand side */
-    virtual void add_to_rhs(FIELDS & rhs){};
+    virtual void add_to_rhs(FIELDS & /* rhs */){};
 
     /** prior to exchanges */
     virtual void pre_force();
@@ -113,8 +113,8 @@ namespace ATC {
     virtual void pre_exchange() {};  
     virtual void finish() {};  
     virtual void set_weights() {};
-    virtual double compute_vector(int n) const { return 0;}
-    virtual void output(OUTPUT_LIST & outputData){};
+    virtual double compute_vector(int /* n */) const { return 0;}
+    virtual void output(OUTPUT_LIST & /* outputData */){};
   private:
     ConcentrationRegulatorMethod(); // DO NOT define this
   };
@@ -144,7 +144,7 @@ namespace ATC {
     virtual double compute_vector(int n) const;
   protected:
     /** set transition state: epsilon and charge */
-    int mask(int type, int groupbit) {return 0;}
+    int mask(int /* type */, int /* groupbit */) {return 0;}
     int count(void) const;
     int excess(void) const;
     double energy(int id) const;
diff --git a/lib/atc/DenseVector.h b/lib/atc/DenseVector.h
index 70e223d988..38ed68f937 100644
--- a/lib/atc/DenseVector.h
+++ b/lib/atc/DenseVector.h
@@ -31,8 +31,10 @@ public:
   // overloaded inline virtual functions
   T  operator[](INDEX i) const { VICK(i) return _data[i]; }
   T& operator[](INDEX i)       { VICK(i) return _data[i]; }
-  T  operator()(INDEX i, INDEX j=0) const { VICK(i) return _data[i]; }
-  T& operator()(INDEX i, INDEX j=0)       { VICK(i) return _data[i]; }
+  T  operator()(INDEX i, INDEX /* j */) const { VICK(i) return _data[i]; }
+  T& operator()(INDEX i, INDEX /* j */)       { VICK(i) return _data[i]; }
+  T  operator()(INDEX i) const { VICK(i) return _data[i]; }
+  T& operator()(INDEX i)       { VICK(i) return _data[i]; }
   void set_all_elements_to(const T &v)    { 
                                             int sz = this->size();
                                             for (INDEX i = 0; i < sz; i++) _data[i] = v;
@@ -62,7 +64,7 @@ private:
 // resizes the matrix and optionally copies over what still fits, ignores cols
 //-----------------------------------------------------------------------------
 template <typename T>
-void DenseVector<T>::resize(INDEX rows, INDEX cols, bool copy)
+  void DenseVector<T>::resize(INDEX rows, INDEX /* cols */, bool copy)
 {
   if (_size==rows) return;  // if is correct size, done
   if (!copy)
diff --git a/lib/atc/DiagonalMatrix.h b/lib/atc/DiagonalMatrix.h
index 516fb47878..6c2fe23144 100644
--- a/lib/atc/DiagonalMatrix.h
+++ b/lib/atc/DiagonalMatrix.h
@@ -49,7 +49,8 @@ class DiagonalMatrix : public Matrix<T>
   void write_restart(FILE *f)     const;
 
   // Dump matrix contents to screen (not defined for all datatypes)
-  std::string to_string(int p=myPrecision) const { return _data->to_string(); }
+  std::string to_string(int /* p */) const { return _data->to_string(); }
+  std::string to_string() const { return _data->to_string(); }
 
   using Matrix<T>::matlab;
   void matlab(std::ostream &o, const std::string &s="D") const;
@@ -78,8 +79,8 @@ class DiagonalMatrix : public Matrix<T>
 
 protected:
   void _set_equal(const Matrix<T> &r);
-  DiagonalMatrix& operator=(const Vector<T> &c) {}
-  DiagonalMatrix& operator=(const Matrix<T> &c) {}
+  DiagonalMatrix& operator=(const Vector<T> & /* c */) {}
+  DiagonalMatrix& operator=(const Matrix<T> & /* c */) {}
 
 private: 
   void _delete();
@@ -246,7 +247,7 @@ void DiagonalMatrix<T>::_delete()
 // resizes the matrix, ignores nCols, optionally zeros 
 //-----------------------------------------------------------------------------
 template<typename T>
-void DiagonalMatrix<T>::reset(INDEX rows, INDEX cols, bool zero)
+void DiagonalMatrix<T>::reset(INDEX rows, INDEX /* cols */, bool zero)
 {
   _delete();
   _data = new DenseVector<T>(rows, zero);
@@ -255,7 +256,7 @@ void DiagonalMatrix<T>::reset(INDEX rows, INDEX cols, bool zero)
 // resizes the matrix, ignores nCols, optionally copies what fits
 //-----------------------------------------------------------------------------
 template<typename T>
-void DiagonalMatrix<T>::resize(INDEX rows, INDEX cols, bool copy)
+void DiagonalMatrix<T>::resize(INDEX rows, INDEX /* cols */, bool copy)
 {
   _data->resize(rows, copy);  
 }
@@ -327,7 +328,7 @@ void DiagonalMatrix<T>::shallowreset(const DenseMatrix<T> &c)
 // reference indexing operator - must throw an error if i!=j
 //-----------------------------------------------------------------------------
 template<typename T>
-T& DiagonalMatrix<T>::operator()(INDEX i, INDEX j)
+T& DiagonalMatrix<T>::operator()(INDEX i, INDEX /* j */)
 {
   GCK(*this,*this,i!=j,"DiagonalMatrix: tried to index off diagonal");
   return (*this)[i];
diff --git a/lib/atc/ElasticTimeIntegrator.cpp b/lib/atc/ElasticTimeIntegrator.cpp
index c2a592d46c..9793f6a58e 100644
--- a/lib/atc/ElasticTimeIntegrator.cpp
+++ b/lib/atc/ElasticTimeIntegrator.cpp
@@ -27,7 +27,7 @@ namespace ATC {
   //  modify
   //    parses inputs and modifies state of the integrator
   //--------------------------------------------------------
-  bool MomentumTimeIntegrator::modify(int narg, char **arg)
+  bool MomentumTimeIntegrator::modify(int /* narg */, char **arg)
   {
     bool foundMatch = false;
     int argIndex = 0;
@@ -611,7 +611,7 @@ namespace ATC {
   //  compute_velocity_delta
   //--------------------------------------------------------
   void ElasticTimeIntegratorFractionalStep::compute_velocity_delta(const DENS_MAT & atomicMomentumDelta,
-                                                                   double dt)
+                                                                   double /* dt */)
   {
     DENS_MAT & myAtomicVelocityDelta(atomicVelocityDelta_.set_quantity());
     myAtomicVelocityDelta = nodalAtomicMomentumOld_ + atomicMomentumDelta;
@@ -832,7 +832,7 @@ namespace ATC {
   //  compute_velocity_delta
   //--------------------------------------------------------
   void FluidsTimeIntegratorGear::compute_velocity_delta(const DENS_MAT & atomicMomentumDelta,
-                                                        double dt)
+                                                        double /* dt */)
   {
     DENS_MAT & myAtomicVelocityDelta(atomicVelocityDelta_.set_quantity());
     myAtomicVelocityDelta = nodalAtomicMomentumOld_ + atomicMomentumDelta;
diff --git a/lib/atc/ElectronChargeDensity.cpp b/lib/atc/ElectronChargeDensity.cpp
index 69127a9335..14c764e46e 100644
--- a/lib/atc/ElectronChargeDensity.cpp
+++ b/lib/atc/ElectronChargeDensity.cpp
@@ -14,7 +14,7 @@ using std::vector;
 
 namespace ATC {
 ElectronChargeDensityInterpolation::ElectronChargeDensityInterpolation(
-  fstream &fileId, map<string,double> & parameters) 
+  fstream &fileId, map<string,double> & /* parameters */) 
   : ElectronChargeDensity(), n_()
 {
   if (!fileId.is_open()) throw ATC_Error("cannot open material file");
diff --git a/lib/atc/ElectronChargeDensity.h b/lib/atc/ElectronChargeDensity.h
index a5288c0b19..ac6052a9ef 100644
--- a/lib/atc/ElectronChargeDensity.h
+++ b/lib/atc/ElectronChargeDensity.h
@@ -21,17 +21,17 @@ namespace ATC {
     public:
       ElectronChargeDensity()   {};
       virtual ~ElectronChargeDensity() {};
-      virtual bool electron_charge_density(const FIELD_MATS &fields,
-                                           DENS_MAT &flux) const { return false; };
+      virtual bool electron_charge_density(const FIELD_MATS & /* fields */,
+                                           DENS_MAT & /* flux */) const { return false; };
 
       
-      virtual void D_electron_charge_density(const FieldName fieldName, 
-                                             const FIELD_MATS &fields,
-                                             DENS_MAT &flux) const 
+      virtual void D_electron_charge_density(const FieldName /* fieldName */, 
+                                             const FIELD_MATS & /* fields */,
+                                             DENS_MAT & /* flux */) const 
         { throw ATC_Error("Charge density D_electron_charge_density unimplemented function");}
 
-      virtual void band_edge_potential(const FIELD_MATS &fields,
-                                       DENS_MAT &density) const
+      virtual void band_edge_potential(const FIELD_MATS & /* fields */,
+                                       DENS_MAT & /* density */) const
         { throw ATC_Error("Charge density band_edge_potential unimplemented function");}
   };
   //-----------------------------------------------------------------------
@@ -58,7 +58,7 @@ namespace ATC {
         flux *= -1.;
         return true;
       }; 
-      virtual void D_electron_charge_density(const FieldName field,
+      virtual void D_electron_charge_density(const FieldName /* field */,
                                              const FIELD_MATS &fields,
                                              DENS_MAT &coef) const
       {
@@ -94,7 +94,7 @@ namespace ATC {
         flux *= -C_;
         return true;
       }; 
-      virtual void D_electron_charge_density(const FieldName field,
+      virtual void D_electron_charge_density(const FieldName /* field */,
                                              const FIELD_MATS &fields,
                                              DENS_MAT &coef) const
       {
@@ -150,7 +150,7 @@ namespace ATC {
         density *= -1.;
         return true;
       }; 
-      virtual void D_electron_charge_density(const FieldName field,
+      virtual void D_electron_charge_density(const FieldName /* field */,
                                              const FIELD_MATS &fields,
                                              DENS_MAT &coef) const
       {
@@ -235,7 +235,7 @@ namespace ATC {
         }
         return true;
       }; 
-      virtual void D_electron_charge_density(const FieldName fieldName, 
+      virtual void D_electron_charge_density(const FieldName /* fieldName */, 
                                              const FIELD_MATS &fields,
                                              DENS_MAT &coef) const
       {
diff --git a/lib/atc/ElectronDragPower.cpp b/lib/atc/ElectronDragPower.cpp
index aff6be6106..7fe31f0120 100644
--- a/lib/atc/ElectronDragPower.cpp
+++ b/lib/atc/ElectronDragPower.cpp
@@ -39,7 +39,7 @@ ElectronDragPowerLinear::ElectronDragPowerLinear(fstream &fileId,
 }
 
   bool ElectronDragPowerLinear::electron_drag_power(const FIELD_MATS &fields,
-                                                    const GRAD_FIELD_MATS &gradFields,
+                                                    const GRAD_FIELD_MATS & /* gradFields */,
                                                     DENS_MAT & flux)
 {
   
diff --git a/lib/atc/ElectronDragPower.h b/lib/atc/ElectronDragPower.h
index 92103fe3e8..12c1472e37 100644
--- a/lib/atc/ElectronDragPower.h
+++ b/lib/atc/ElectronDragPower.h
@@ -21,9 +21,9 @@ namespace ATC {
     ElectronDragPower() {};
     virtual ~ElectronDragPower() {};
     /** computes drag power */
-    virtual bool electron_drag_power(const FIELD_MATS &fields,
-                                     const GRAD_FIELD_MATS &gradFields,
-                                           DENS_MAT & flux)
+    virtual bool electron_drag_power(const FIELD_MATS & /* fields */,
+                                     const GRAD_FIELD_MATS & /* gradFields */,
+                                     DENS_MAT & /* flux */)
     {
       return false;
     };
diff --git a/lib/atc/ElectronFlux.cpp b/lib/atc/ElectronFlux.cpp
index 8ae8503a31..4894a32dae 100644
--- a/lib/atc/ElectronFlux.cpp
+++ b/lib/atc/ElectronFlux.cpp
@@ -79,7 +79,7 @@ ElectronFluxThermopower::ElectronFluxThermopower(
 }
 
 ElectronFluxConvection::ElectronFluxConvection(
-  fstream &fileId, map<string,double> & parameters) 
+  fstream &fileId, map<string,double> & /* parameters */) 
   : ElectronFlux()
 {
   if (!fileId.is_open()) throw ATC_Error("cannot open material file");
diff --git a/lib/atc/ElectronFlux.h b/lib/atc/ElectronFlux.h
index 013f9aac42..b9cfd2305c 100644
--- a/lib/atc/ElectronFlux.h
+++ b/lib/atc/ElectronFlux.h
@@ -19,7 +19,7 @@ namespace ATC {
       virtual ~ElectronFlux() {};
       /** computes flux */
       virtual void electron_flux(const FIELD_MATS &fields,
-                                 const GRAD_FIELD_MATS &gradFields,
+                                 const GRAD_FIELD_MATS & /* gradFields */,
                                        DENS_MAT_VEC &flux) 
       {
          
@@ -211,7 +211,7 @@ namespace ATC {
       ElectronFluxConvection(std::fstream &matfile,std::map<std::string,double> & parameters);
       virtual ~ElectronFluxConvection() {};
       virtual void electron_flux(const FIELD_MATS &fields,
-                                 const GRAD_FIELD_MATS &gradFields,
+                                 const GRAD_FIELD_MATS & /* gradFields */,
                                        DENS_MAT_VEC &flux)
       {
         // flux = n v
diff --git a/lib/atc/ElectronHeatCapacity.h b/lib/atc/ElectronHeatCapacity.h
index aefc3d681c..f27d8193a0 100644
--- a/lib/atc/ElectronHeatCapacity.h
+++ b/lib/atc/ElectronHeatCapacity.h
@@ -51,7 +51,7 @@ namespace ATC {
         capacity = electronHeatCapacity_;
       };
       virtual void D_electron_heat_capacity(const FIELD_MATS &fields,
-                                            const GRAD_FIELD_MATS &gradFields,
+                                            const GRAD_FIELD_MATS & /* gradFields */,
                                                   DENS_MAT_VEC & Dcapacity)
       {
         FIELD_MATS::const_iterator etField = fields.find(ELECTRON_TEMPERATURE);
@@ -91,7 +91,7 @@ namespace ATC {
         const DENS_MAT & T = etField->second;
         capacity = electronHeatCapacity_*T;
       };
-      virtual void D_electron_heat_capacity(const FIELD_MATS &fields,
+      virtual void D_electron_heat_capacity(const FIELD_MATS & /* fields */,
                                             const GRAD_FIELD_MATS &gradFields,
                                                   DENS_MAT_VEC &Dcapacity)
       {
diff --git a/lib/atc/ElectronHeatFlux.h b/lib/atc/ElectronHeatFlux.h
index 12a68fed70..41c89d6c6d 100644
--- a/lib/atc/ElectronHeatFlux.h
+++ b/lib/atc/ElectronHeatFlux.h
@@ -21,7 +21,7 @@ namespace ATC {
       virtual ~ElectronHeatFlux() {};
       /** computes heat flux */
       virtual void electron_heat_flux(const FIELD_MATS &fields,
-                                      const GRAD_FIELD_MATS &gradFields,
+                                      const GRAD_FIELD_MATS & /* gradFields */,
                                             DENS_MAT_VEC &flux)
       {
          
@@ -70,7 +70,7 @@ namespace ATC {
     ElectronHeatFluxLinear(std::fstream &matfile,std::map<std::string,double> & parameters,
                            /*const*/ ElectronHeatCapacity * electronHeatCapacity = NULL);
       virtual ~ElectronHeatFluxLinear() {};
-      virtual void electron_heat_flux(const FIELD_MATS &fields,
+      virtual void electron_heat_flux(const FIELD_MATS & /* fields */,
                                       const GRAD_FIELD_MATS &gradFields,
                                             DENS_MAT_VEC &flux)
       {
diff --git a/lib/atc/ElectronPhononExchange.h b/lib/atc/ElectronPhononExchange.h
index 59cc61b4d2..3037451513 100644
--- a/lib/atc/ElectronPhononExchange.h
+++ b/lib/atc/ElectronPhononExchange.h
@@ -21,8 +21,8 @@ namespace ATC {
       ElectronPhononExchange()  {};
       virtual ~ElectronPhononExchange() {};
       /** computes heat capacity */
-      virtual bool electron_phonon_exchange(const FIELD_MATS &fields,
-                                                  DENS_MAT &flux) { return false; }
+      virtual bool electron_phonon_exchange(const FIELD_MATS & /* fields */,
+                                            DENS_MAT & /* flux */) { return false; }
   };
   //-------------------------------------------------------------------
 
diff --git a/lib/atc/ExtrinsicModel.cpp b/lib/atc/ExtrinsicModel.cpp
index cdf556f4c1..b20b2a26d1 100644
--- a/lib/atc/ExtrinsicModel.cpp
+++ b/lib/atc/ExtrinsicModel.cpp
@@ -114,7 +114,7 @@ namespace ATC {
       ATC::LammpsInterface::instance()->print_msg_once(ss.str());
       myModel = new ExtrinsicModelElectrostatic
         (this,modelType,matFileName);
-    }
+    } else myModel = NULL;
     extrinsicModels_.push_back(myModel);
 
      // add new fields to fields data
@@ -339,7 +339,7 @@ namespace ATC {
   //--------------------------------------------------------
   ExtrinsicModel::ExtrinsicModel(ExtrinsicModelManager * modelManager,
                                  ExtrinsicModelType modelType,
-                                 string matFileName) :
+                                 string /* matFileName */) :
     atc_(modelManager->atc()),
     modelManager_(modelManager),
     modelType_(modelType),
diff --git a/lib/atc/ExtrinsicModel.h b/lib/atc/ExtrinsicModel.h
index 99acf59ef2..66282fb505 100644
--- a/lib/atc/ExtrinsicModel.h
+++ b/lib/atc/ExtrinsicModel.h
@@ -221,7 +221,7 @@ namespace ATC {
     virtual ~ExtrinsicModel();
 
     /** parser/modifier */
-    virtual bool modify(int narg, char **arg) {return false;};
+    virtual bool modify(int /* narg */, char ** /* arg */) {return false;};
 
     /** construct transfers needed by the model */
     virtual void construct_transfers(){};
@@ -230,11 +230,11 @@ namespace ATC {
     virtual void initialize();
 
     /** set up LAMMPS display variables */
-    virtual int size_vector(int externalSize) {return 0;};
+    virtual int size_vector(int /* externalSize */) {return 0;};
 
     /** get LAMMPS display variables */
     virtual double compute_scalar(void) { return 0.0; }
-    virtual bool compute_vector(int n, double & value) {return false;};
+    virtual bool compute_vector(int /* n */, double & /* value */) {return false;};
 
     /** post integration run */
     // is this called at end of run or simulation
@@ -259,10 +259,10 @@ namespace ATC {
     virtual void post_final_integrate(){};
 
     /** Set sources to AtC equation */
-    virtual void set_sources(FIELDS & fields, FIELDS & sources){};
+    virtual void set_sources(FIELDS & /* fields */, FIELDS & /* sources */){};
 
     /** Add model-specific output data */
-    virtual void output(OUTPUT_LIST & outputData){};
+    virtual void output(OUTPUT_LIST & /* outputData */){};
 
     /** get the fields and their sizes */
     void num_fields(std::map<FieldName,int> & fieldSizes);
diff --git a/lib/atc/ExtrinsicModelElectrostatic.cpp b/lib/atc/ExtrinsicModelElectrostatic.cpp
index 03766920e3..b10e77a306 100644
--- a/lib/atc/ExtrinsicModelElectrostatic.cpp
+++ b/lib/atc/ExtrinsicModelElectrostatic.cpp
@@ -827,7 +827,7 @@ namespace ATC {
   //  apply_charged_surfaces
   //--------------------------------------------------------
   void ExtrinsicModelElectrostatic::apply_charged_surfaces
-    (MATRIX & potential)
+  (MATRIX & /* potential */)
   {
     //double qE2f = LammpsInterface::instance()->qe2f();
     double qV2e = LammpsInterface::instance()->qv2e();
diff --git a/lib/atc/FE_Engine.cpp b/lib/atc/FE_Engine.cpp
index efcde66d78..bef135a5f2 100644
--- a/lib/atc/FE_Engine.cpp
+++ b/lib/atc/FE_Engine.cpp
@@ -721,7 +721,7 @@ namespace ATC{
                             const SPAR_MAT      &N,
                             const SPAR_MAT_VEC  &dN,
                             SPAR_MAT &tangent,
-                            const DenseMatrix<bool> *elementMask ) const
+                                         const DenseMatrix<bool> * /* elementMask */ ) const
   {
     int nn = nNodesUnique_;
     FieldName rowField = row_col.first;
@@ -1298,7 +1298,7 @@ namespace ATC{
     const PhysicsModel * physicsModel,
     const Array<int>   & elementMaterials,
     FIELDS &rhs,
-    bool freeOnly,
+                                     bool /* freeOnly */,
     const DenseMatrix<bool> *elementMask) const
   {
     vector<FieldName> usedFields;
@@ -2503,7 +2503,7 @@ namespace ATC{
   // previously computed nodal sources
   //-----------------------------------------------------------------
   void FE_Engine::add_sources(const Array<bool> &fieldMask,
-    const double time,
+                              const double /* time */,
     const FIELDS &sources,
     FIELDS &nodalSources) const
   {
diff --git a/lib/atc/FE_Engine.h b/lib/atc/FE_Engine.h
index bc3fb0e4a5..18dae0e6b4 100644
--- a/lib/atc/FE_Engine.h
+++ b/lib/atc/FE_Engine.h
@@ -345,7 +345,7 @@ namespace ATC {
 
 
     /** integrate a nodal field over an face set */
-    DENS_VEC integrate(const DENS_MAT  &field, const FSET & fset) const
+    DENS_VEC integrate(const DENS_MAT  & /* field */, const FSET & /* fset */) const
     { throw ATC_Error(FILELINE,"unimplemented function"); }
 
     /*@}*/
@@ -496,7 +496,8 @@ namespace ATC {
     /** set kernel */
     
     void set_kernel(KernelFunction* ptr);
-    KernelFunction *kernel(int i=0) { return kernelFunction_; }
+    KernelFunction *kernel(int /* i */) { return kernelFunction_; }
+    KernelFunction *kernel() { return kernelFunction_; }
 
   private:
     //----------------------------------------------------------------
diff --git a/lib/atc/FE_Mesh.cpp b/lib/atc/FE_Mesh.cpp
index b090bf2881..4ea10a681a 100644
--- a/lib/atc/FE_Mesh.cpp
+++ b/lib/atc/FE_Mesh.cpp
@@ -797,7 +797,7 @@ namespace ATC {
         {
           int node = element_connectivity_unique(ielem, inode);
           nodeSet.insert(node);
-          inode++;
+          inode++; // XXX: is this correct?
         }
       }
     }
@@ -832,7 +832,7 @@ namespace ATC {
         {
           int node = element_connectivity_unique(ielem, inode);
           nodeSet.erase(node);
-          inode++;
+          inode++; // XXX: is this correct?
         }
       }
     }
@@ -1788,7 +1788,7 @@ namespace ATC {
   // -------------------------------------------------------------
   //  setup_periodicity
   // -------------------------------------------------------------
-  void FE_3DMesh::setup_periodicity(double tol)
+  void FE_3DMesh::setup_periodicity(double /* tol */)
   {
     // unique <-> global id maps
     globalToUniqueMap_.reset(nNodes_);
@@ -2119,10 +2119,9 @@ namespace ATC {
       // divide between all processors, we get the next-highest
       // power of 2.
     vector<vector<int> > procEltLists = tree_->getElemIDs(depth);
-    int numEltLists = procEltLists.size();
     
     // Make sure the KD tree is behaving as expected.
-    assert(numEltLists >= nProcs);
+    assert(procEltLists.size() >= nProcs);
  
     // If the KD-tree was not able to return enough divisions,
     // duplicate the largest list.
diff --git a/lib/atc/FE_Mesh.h b/lib/atc/FE_Mesh.h
index be40d7cb28..0b2df7b656 100644
--- a/lib/atc/FE_Mesh.h
+++ b/lib/atc/FE_Mesh.h
@@ -691,7 +691,7 @@ namespace ATC {
 
     void departition_mesh(void);
     
-    virtual void element_size(const int ielem, 
+    virtual void element_size(const int /* ielem */, 
                               double &hx, double &hy, double &hz)
     { hx = L_[0]/n_[0]; hy = L_[1]/n_[1]; hz = L_[2]/n_[2]; }
 
diff --git a/lib/atc/FieldEulerIntegrator.cpp b/lib/atc/FieldEulerIntegrator.cpp
index eeea0cd4eb..0abc71cbab 100644
--- a/lib/atc/FieldEulerIntegrator.cpp
+++ b/lib/atc/FieldEulerIntegrator.cpp
@@ -46,7 +46,7 @@ FieldExplicitEulerIntegrator::FieldExplicitEulerIntegrator(
 // --------------------------------------------------------------------
 // update 
 // --------------------------------------------------------------------
-void FieldExplicitEulerIntegrator::update(const double dt, double time,
+  void FieldExplicitEulerIntegrator::update(const double dt, double /* time */,
   FIELDS & fields, FIELDS & rhs)
 { 
   // write and add update mass matrix to handled time variation
@@ -81,7 +81,7 @@ FieldImplicitEulerIntegrator::FieldImplicitEulerIntegrator(
 // update 
 // --------------------------------------------------------------------
 void FieldImplicitEulerIntegrator::update(const double dt, double time,
-  FIELDS & fields, FIELDS & rhs) 
+                                          FIELDS & fields, FIELDS & /* rhs */) 
 { // solver handles bcs
   FieldImplicitSolveOperator solver(atc_, 
     fields, fieldName_, rhsMask_, physicsModel_,
@@ -127,8 +127,8 @@ FieldImplicitDirectEulerIntegrator::~FieldImplicitDirectEulerIntegrator()
 // --------------------------------------------------------------------
 // initialize 
 // --------------------------------------------------------------------
-void FieldImplicitDirectEulerIntegrator::initialize(const double dt, double time,
-  FIELDS & fields) 
+  void FieldImplicitDirectEulerIntegrator::initialize(const double dt, double /* time */,
+                                                      FIELDS & /* fields */) 
 { 
    std::pair<FieldName,FieldName> p(fieldName_,fieldName_);
    Array2D <bool>  rmask = atc_->rhs_mask();
@@ -140,7 +140,7 @@ void FieldImplicitDirectEulerIntegrator::initialize(const double dt, double time
 // --------------------------------------------------------------------
 // update 
 // --------------------------------------------------------------------
-void FieldImplicitDirectEulerIntegrator::update(const double dt, double time,
+  void FieldImplicitDirectEulerIntegrator::update(const double /* dt */, double /* time */,
   FIELDS & fields, FIELDS & rhs) 
 { 
   atc_->compute_rhs_vector(rhsMask_, fields, rhs,
diff --git a/lib/atc/FieldEulerIntegrator.h b/lib/atc/FieldEulerIntegrator.h
index f349ada5d4..c7b79f85d9 100644
--- a/lib/atc/FieldEulerIntegrator.h
+++ b/lib/atc/FieldEulerIntegrator.h
@@ -41,8 +41,8 @@ class FieldEulerIntegrator {
   virtual ~FieldEulerIntegrator() {};
 
   /** initialize */
-  virtual void initialize(const double dt, const double time,
-    FIELDS & fields) {};
+  virtual void initialize(const double /* dt */, const double /* time */,
+                          FIELDS & /* fields */) {};
 
   /** update */
   virtual void update(const double dt, const double time,
diff --git a/lib/atc/FieldManager.cpp b/lib/atc/FieldManager.cpp
index ce9f859533..338f06acad 100644
--- a/lib/atc/FieldManager.cpp
+++ b/lib/atc/FieldManager.cpp
@@ -298,7 +298,7 @@ typedef PerAtomQuantity<double> PAQ;
 //-----------------------------------------------------------------------------
 //* REFERENCE_POTENTIAL_ENERGY 
 //-----------------------------------------------------------------------------
-  DENS_MAN * FieldManager::reference_potential_energy(string name)
+  DENS_MAN * FieldManager::reference_potential_energy(string /* name */)
   {
     DENS_MAN * rpe = interscaleManager_.dense_matrix(field_to_string(REFERENCE_POTENTIAL_ENERGY));
     if (! rpe ) { 
diff --git a/lib/atc/FieldManager.h b/lib/atc/FieldManager.h
index d3db3f268a..9a98676417 100644
--- a/lib/atc/FieldManager.h
+++ b/lib/atc/FieldManager.h
@@ -123,7 +123,7 @@ namespace ATC {
     DENS_MAN * projected_atom_quantity(FieldName field,std::string name, PAQ * atomic,  DIAG_MAN * normalization = NULL);
     DENS_MAN * scaled_projected_atom_quantity(FieldName field,std::string name, PAQ * atomic, double scale, DIAG_MAN * normalization = NULL);
     DENS_MAN * referenced_projected_atom_quantity(FieldName field, std::string name, PAQ * atomic, DENS_MAN * reference, DIAG_MAN * normalization = NULL);
-    DENS_MAN * inferred_atom_quantity(FieldName field, std::string name, PAQ * atomic){return NULL;};
+    DENS_MAN * inferred_atom_quantity(FieldName /* field */, std::string /* name */, PAQ * /* atomic */){return NULL;};
     PAQ * prolonged_field(FieldName field);
   private:
     FieldManager(void);
diff --git a/lib/atc/Function.cpp b/lib/atc/Function.cpp
index 12396937bd..70f8bbfa41 100644
--- a/lib/atc/Function.cpp
+++ b/lib/atc/Function.cpp
@@ -16,7 +16,7 @@ namespace ATC {
   //====================================================================
   //  UXT_Function
   //===================================================================
-  UXT_Function::UXT_Function(int narg, double* args) { }
+  UXT_Function::UXT_Function(int /* narg */, double* /* args */) { }
   //====================================================================
   //  UXT_Function_Mgr
   //====================================================================
@@ -312,7 +312,7 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL;
     }
     ATC::LammpsInterface::instance()->print_msg_once(ss.str());
   }
-  double PiecewiseLinearFunction::f(double * x, double t)
+  double PiecewiseLinearFunction::f(double * x, double /* t */)
   {
 
     double s = mask[0]*(x[0]-x0[0])+mask[1]*(x[1]-x0[1])+mask[2]*(x[2]-x0[2]);
@@ -355,7 +355,7 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL;
     return slope[0]*(x[0]-x0[0])+slope[1]*(x[1]-x0[1])+slope[2]*(x[2]-x0[2]) + C0;
   }
 
-  double LinearTemporalRamp::dfdt(double* x, double t) {
+  double LinearTemporalRamp::dfdt(double* x, double /* t */) {
     return mask_slope[0]*(x[0]-x0[0])+mask_slope[1]*(x[1]-x0[1])+mask_slope[2]*(x[2]-x0[2]) + C0_slope;
   }
 
@@ -499,7 +499,7 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL;
        if      (i   == 0)     { dx = xs_(1)-xs_(0); }
        else if (i+1 == npts_) { dx = xs_(npts_-1)-xs_(npts_-2); }
        else { dx= 0.5*(xs_(i+1)-xs_(i-1)); }
-       if (abs(dx-dx0) > 1.e-8) throw ATC_Error("InterpolationFunction::initialize non-uniform data spacing not handled currently");
+       if (fabs(dx-dx0) > 1.e-8) throw ATC_Error("InterpolationFunction::initialize non-uniform data spacing not handled currently");
        fps_(i) *= dx;
      }
      // options: calculate / adjust tangents for monotonicity
diff --git a/lib/atc/Function.h b/lib/atc/Function.h
index 4572009f92..0c654fa47c 100644
--- a/lib/atc/Function.h
+++ b/lib/atc/Function.h
@@ -29,8 +29,8 @@ namespace ATC {
     virtual inline ARG_NAMES args(void) {ARG_NAMES names; return names;};
 
     /** (1st) derivative of function wrt to a field */
-    virtual inline double dfd(FieldName field, ARGS& args ) {return 0.0;};
-    virtual inline void   dfd(FieldName field, ARGS& args, DENS_MAT vals ) {};
+    virtual inline double dfd(FieldName /* field */, ARGS& /* args */) {return 0.0;};
+    virtual inline void   dfd(FieldName /* field */, ARGS& /* args */, DENS_MAT /* vals */ ) {};
 
     // addl: d2fd2(field1, field2, args), linearization(), grad_args
 
@@ -70,8 +70,8 @@ namespace ATC {
     LinearFieldFunction(int nargs, char** args);
     virtual ~LinearFieldFunction(void) {};
   
-    inline double f(double* u, double* x, double t) {return c1_*u[0]-c0_;}
-    inline double dfd(FieldName field, ARGS& args) {return c1_;}
+    inline double f(double* u, double* /* x */, double /* t */) {return c1_*u[0]-c0_;}
+    inline double dfd(FieldName /* field */, ARGS& /* args */) {return c1_;}
 
     private :
       double c0_,c1_;
@@ -90,9 +90,9 @@ namespace ATC {
     const std::string & tag() { return tag_;}
 
     /** function value */
-    virtual inline double f(double * u, double* x, double t) {return 0.0;};
+    virtual inline double f(double * /* u */, double* /* x */, double /* t */) {return 0.0;};
     /** derivative of function wrt to field */
-    virtual inline double dfdu(double * u, double* x, double t) {return 0.0;};
+    virtual inline double dfdu(double * /* u */, double* /* x */, double /* t */) {return 0.0;};
 
   protected:
     /** tag : name of function */
@@ -136,8 +136,8 @@ namespace ATC {
   
     //inline double f(double* u, double* x, double t) {return c1_*(u[0]-c0_);}
 
-    inline double f(double* u, double* x, double t) {return c1_*u[0]+c0_;}
-    inline double dfdu(double* u, double* x, double t) {return c1_;}
+    inline double f(double* u, double* /* x */, double /* t */) {return c1_*u[0]+c0_;}
+    inline double dfdu(double* /* u */, double* /* x */, double /* t */) {return c1_;}
 
     private :
       double c0_,c1_;
@@ -156,13 +156,13 @@ namespace ATC {
     const std::string & tag() { return tag_;}
 
     /** function value */
-    virtual inline double f(double* x, double t) {return 0.0;};
+    virtual inline double f(double* /* x */, double /* t */) {return 0.0;};
     /** time derivative of function */
-    virtual inline double dfdt(double* x, double t) {return 0.0;};
+    virtual inline double dfdt(double* /* x */, double /* t */) {return 0.0;};
     /** 2nd time derivative of function */
-    virtual inline double ddfdt(double* x, double t) {return 0.0;};
+    virtual inline double ddfdt(double* /* x */, double /* t */) {return 0.0;};
     /** 3rd time derivative of function */
-    virtual inline double dddfdt(double* x, double t) {return 0.0;};
+    virtual inline double dddfdt(double* /* x */, double /* t */) {return 0.0;};
 
   protected:
     /** mask : masks x,y,z dependence, x0 : origin */
@@ -210,7 +210,7 @@ namespace ATC {
     ConstantFunction(double arg);
     virtual ~ConstantFunction(void) {};
   
-    inline double f(double* x, double t) 
+    inline double f(double* /* x */, double /* t */) 
     {return C0;};
 
     private :
@@ -227,7 +227,7 @@ namespace ATC {
     LinearFunction(int nargs, double* args);
     virtual ~LinearFunction(void) {};
   
-    double f(double* x, double t) 
+    double f(double* x, double /* t */) 
       {return mask[0]*(x[0]-x0[0])+mask[1]*(x[1]-x0[1])+mask[2]*(x[2]-x0[2]) + C0;};
 
     private :
@@ -280,7 +280,7 @@ namespace ATC {
     QuadraticFunction(int nargs, double* args);
     virtual ~QuadraticFunction(void) {};
   
-    inline double f(double* x, double t) 
+    inline double f(double* x, double /* t */) 
       {return 
        C2[0]*(x[0]-x0[0])*(x[0]-x0[0])+
        C2[1]*(x[1]-x0[1])*(x[1]-x0[1])+
@@ -324,7 +324,7 @@ namespace ATC {
     virtual ~GaussianFunction(void){};
 
     // 1/(2 pi \sigma)^(n/2) exp(-1/2 x.x/\sigma^2 ) for n = dimension
-    inline double f(double* x, double t) 
+    inline double f(double* x, double /* t */) 
       {return  C*exp(-(mask[0]*(x[0]-x0[0])*(x[0]-x0[0])
                       +mask[1]*(x[1]-x0[1])*(x[1]-x0[1])
                       +mask[2]*(x[2]-x0[2])*(x[2]-x0[2]))/tau/tau) + C0;};
@@ -362,10 +362,10 @@ namespace ATC {
     TemporalRamp(int nargs, double* args);
     virtual ~TemporalRamp(void) {};
   
-    inline double f(double* x, double t) 
+    inline double f(double* /* x */, double t) 
     {return f_initial + slope*t;};
 
-    inline double dfdt(double* x, double t) 
+    inline double dfdt(double* /* x */, double /* t */) 
     {return slope;};
 
     private :
@@ -382,7 +382,7 @@ namespace ATC {
     RadialPower(int nargs, double* args);
     virtual ~RadialPower(void) {};
     
-    inline double f(double* x, double t) 
+    inline double f(double* x, double /* t */) 
     {
       double dx = x[0]-x0[0]; double dy = x[1]-x0[1]; double dz = x[2]-x0[2];
       double r = mask[0]*dx*dx+mask[1]*dy*dy+mask[2]*dz*dz; r = sqrt(r);
diff --git a/lib/atc/FundamentalAtomicQuantity.h b/lib/atc/FundamentalAtomicQuantity.h
index 63c4747552..6561b8112d 100644
--- a/lib/atc/FundamentalAtomicQuantity.h
+++ b/lib/atc/FundamentalAtomicQuantity.h
@@ -82,43 +82,43 @@ namespace ATC {
     virtual ~AtomMass() {};
 
     /** sets the quantity to a given value */
-    virtual void operator=(const DENS_MAT & target)
+    virtual void operator=(const DENS_MAT & /* target */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const double & target)
+    virtual void operator=(const double & /* target */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const DENS_MAT & addition)
+    virtual void operator+=(const DENS_MAT & /* addition */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(double addition)
+    virtual void operator+=(double /* addition */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const DENS_MAT & subtraction)
+    virtual void operator-=(const DENS_MAT & /* subtraction */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(double subtracts)
+    virtual void operator-=(double /* subtracts */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const DENS_MAT & multiplier)
+    virtual void operator*=(const DENS_MAT & /* multiplier */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(double multiplier)
+    virtual void operator*=(double /* multiplier */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const DENS_MAT & divisor)
+    virtual void operator/=(const DENS_MAT & /* divisor */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(double divisor)
+    virtual void operator/=(double /* divisor */)
       {throw ATC_Error("Cannot modify type-based atom mass");};
 
   protected:
@@ -182,39 +182,39 @@ namespace ATC {
       {throw ATC_Error("ComputedAtomQuantity::set_quantity - Cannot modify computed per atom quantities"); return quantity_;};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const DENS_MAT & target)
+    virtual void operator=(const DENS_MAT & /* target */)
       {throw ATC_Error("ComputedAtomQuantity::operator= - Cannot modify computed per atom quantities");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const DENS_MAT & addition)
+    virtual void operator+=(const DENS_MAT & /* addition */)
       {throw ATC_Error("ComputedAtomQuantity::operator+= - Cannot modify computed per atom quantities");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(double addition)
+    virtual void operator+=(double /* addition */)
       {throw ATC_Error("ComputedAtomQuantity::operator+= - Cannot modify computed per atom quantities");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const DENS_MAT & subtraction)
+    virtual void operator-=(const DENS_MAT & /* subtraction */)
       {throw ATC_Error("ComputedAtomQuantity::operator-= - Cannot modify computed per atom quantities");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(double subtraction)
+    virtual void operator-=(double /* subtraction */)
       {throw ATC_Error("ComputedAtomQuantity::operator-= - Cannot modify computed per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const DENS_MAT & multiplier)
+    virtual void operator*=(const DENS_MAT & /* multiplier */)
       {throw ATC_Error("ComputedAtomQuantity::operator*= - Cannot modify computed per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(double multiplier)
+    virtual void operator*=(double /* multiplier */)
       {throw ATC_Error("ComputedAtomQuantity::operator*= - Cannot modify computed per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const DENS_MAT & divisor)
+    virtual void operator/=(const DENS_MAT & /* divisor */)
       {throw ATC_Error("ComputedAtomQuantity::operator/= - Cannot modify computed per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(double divisor)
+    virtual void operator/=(double /* divisor */)
       {throw ATC_Error("ComputedAtomQuantity::operator/= - Cannot modify computed per atom quantities");};
 
   protected:
diff --git a/lib/atc/KernelFunction.cpp b/lib/atc/KernelFunction.cpp
index 80e41a1550..70a1616e01 100644
--- a/lib/atc/KernelFunction.cpp
+++ b/lib/atc/KernelFunction.cpp
@@ -123,7 +123,7 @@ namespace ATC {
   //  KernelFunction
   //------------------------------------------------------------------------
   // constructor
-  KernelFunction::KernelFunction(int nparameters, double* parameters):
+  KernelFunction::KernelFunction(int /* nparameters */, double* parameters):
     Rc_(0),invRc_(0),nsd_(3),
     lammpsInterface_(LammpsInterface::instance())
   { 
@@ -286,7 +286,7 @@ namespace ATC {
   }
   
   // function derivative value
-  void KernelFunctionStep::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const
+  void KernelFunctionStep::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const
   {
      deriv.reset(nsd_);
   }
@@ -378,7 +378,7 @@ namespace ATC {
   }
 
   // function derivative value
-  void KernelFunctionCell::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const
+  void KernelFunctionCell::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const
   {
      deriv.reset(nsd_);
   }
@@ -518,7 +518,7 @@ namespace ATC {
   } 
 
   // function derivative value
-  void KernelFunctionCubicSphere::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const
+  void KernelFunctionCubicSphere::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const
   {
      deriv.reset(nsd_);
   }
@@ -548,7 +548,7 @@ namespace ATC {
   } 
 
   // function derivative value
-  void KernelFunctionQuarticSphere::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const
+  void KernelFunctionQuarticSphere::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const
   {
      deriv.reset(nsd_);
   }
@@ -581,7 +581,7 @@ namespace ATC {
   } 
 
   // function derivative value
-  void KernelFunctionCubicCyl::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const
+  void KernelFunctionCubicCyl::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const
   {
      deriv.reset(nsd_);
   }
@@ -614,7 +614,7 @@ namespace ATC {
   } 
 
   // function derivative value
-  void KernelFunctionQuarticCyl::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const
+  void KernelFunctionQuarticCyl::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const
   {
      deriv.reset(nsd_);
   }
@@ -646,7 +646,7 @@ namespace ATC {
   } 
 
   // function derivative value
-  void KernelFunctionCubicBar::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const
+  void KernelFunctionCubicBar::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const
   {
      deriv.reset(nsd_);
   }
@@ -719,7 +719,7 @@ namespace ATC {
   } 
 
   // function derivative value
-  void KernelFunctionQuarticBar::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const
+  void KernelFunctionQuarticBar::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const
   {
      deriv.reset(nsd_);
   }
diff --git a/lib/atc/KernelFunction.h b/lib/atc/KernelFunction.h
index 9966852537..6922ed9a7b 100644
--- a/lib/atc/KernelFunction.h
+++ b/lib/atc/KernelFunction.h
@@ -83,7 +83,7 @@ namespace ATC {
     // function derivative 
     virtual void derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const;
     // bond function value
-    virtual double bond(DENS_VEC& xa, DENS_VEC&xb, double lam1, double lam2) const
+    virtual double bond(DENS_VEC& /* xa */, DENS_VEC& /* xb */, double lam1, double lam2) const
       { return lam2-lam1; }
   };
 
@@ -105,7 +105,7 @@ namespace ATC {
     // function derivative 
     virtual void derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const;     
     // bond function value
-    virtual double bond(DENS_VEC& xa, DENS_VEC&xb, double lam1, double lam2) const
+    virtual double bond(DENS_VEC& /* xa */, DENS_VEC& /* xb */, double lam1, double lam2) const
       {return lam2 -lam1;}
     // bond intercept values : origin is the node position
     void bond_intercepts(DENS_VEC& xa, DENS_VEC& xb, 
diff --git a/lib/atc/KinetoThermostat.cpp b/lib/atc/KinetoThermostat.cpp
index bdc11238ad..c10f7eb458 100644
--- a/lib/atc/KinetoThermostat.cpp
+++ b/lib/atc/KinetoThermostat.cpp
@@ -32,7 +32,7 @@ namespace ATC {
   //    parses and adjusts thermostat state based on
   //    user input, in the style of LAMMPS user input
   //--------------------------------------------------------
-  bool KinetoThermostat::modify(int narg, char **arg)
+  bool KinetoThermostat::modify(int /* narg */, char ** /* arg */)
   {
     bool foundMatch = false;
     return foundMatch;
@@ -171,7 +171,7 @@ namespace ATC {
   //            sets up the right-hand side of the
   //            kinetostat equations
   //--------------------------------------------------------
-  void VelocityRescaleCombined::set_kinetostat_rhs(DENS_MAT & rhs, double dt)
+  void VelocityRescaleCombined::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */)
   {
     rhs = ((atc_->mass_mat_md(VELOCITY)).quantity())*(velocity_.quantity());
     rhs -= thermostatCorrection_->quantity();
@@ -682,8 +682,8 @@ namespace ATC {
   //   sets up and solves linear system for lambda, if the
   //   bool is true it iterators to a non-linear solution
   //--------------------------------------------------------
-  void KinetoThermostatGlcFs::compute_lambda(double dt,
-                                       bool iterateSolution)
+  void KinetoThermostatGlcFs::compute_lambda(double /* dt */,
+                                             bool /* iterateSolution */)
   {
     // ITERATIVE SOLUTION
   }
@@ -692,7 +692,7 @@ namespace ATC {
   //  output:
   //    adds all relevant output to outputData
   //--------------------------------------------------------
-  void KinetoThermostatGlcFs::output(OUTPUT_LIST & outputData)
+  void KinetoThermostatGlcFs::output(OUTPUT_LIST & /* outputData */)
   {
     // DO NOT CALL INDIVIDUAL REGULATORS
     // OUTPUT TOTAL FORCE AND TOTAL POWER 
diff --git a/lib/atc/KinetoThermostat.h b/lib/atc/KinetoThermostat.h
index 465da6b49a..6f7d113734 100644
--- a/lib/atc/KinetoThermostat.h
+++ b/lib/atc/KinetoThermostat.h
@@ -75,8 +75,11 @@ namespace ATC {
   
     KinetoThermostatShapeFunction(AtomicRegulator * kinetoThermostat,
                                   int couplingMaxIterations,
-                                  const std::string & regulatorPrefix = "") : RegulatorMethod(kinetoThermostat),
+                                  const std::string & /* regulatorPrefix */) : RegulatorMethod(kinetoThermostat),
       couplingMaxIterations_(couplingMaxIterations) {};
+    KinetoThermostatShapeFunction(AtomicRegulator * kinetoThermostat,
+                                  int couplingMaxIterations)
+      : RegulatorMethod(kinetoThermostat), couplingMaxIterations_(couplingMaxIterations) {};
         
     virtual ~KinetoThermostatShapeFunction() {};
 
@@ -120,9 +123,9 @@ namespace ATC {
     virtual void initialize();
     
     /** applies kinetostat to atoms */
-    virtual void apply_mid_predictor(double dt){};
+    virtual void apply_mid_predictor(double /* dt */){};
     /** applies kinetostat to atoms */
-    virtual void apply_post_corrector(double dt){};
+    virtual void apply_post_corrector(double /* dt */){};
     
     /** local shape function matrices are incompatible with this mode */
     virtual bool use_local_shape_functions() const {return false;};
@@ -142,15 +145,17 @@ namespace ATC {
 
     // disable un-needed functionality
     /** does initial filtering operations before main computation */
-    virtual void apply_pre_filtering(double dt){};
+    virtual void apply_pre_filtering(double /* dt */){};
     /** applies kinetostat correction to atoms */
-    virtual void apply_kinetostat(double dt) {};
+    virtual void apply_kinetostat(double /* dt */) {};
     /** computes the nodal FE force applied by the kinetostat */
-    virtual void compute_nodal_lambda_force(double dt){};
+    virtual void compute_nodal_lambda_force(double /* dt */){};
     /** apply any required corrections for localized kinetostats */
-    virtual void apply_localization_correction(const DENS_MAT & source,
-                                               DENS_MAT & nodalField,
-                                               double weight = 1.){};
+    virtual void apply_localization_correction(const DENS_MAT & /* source */,
+                                               DENS_MAT & /* nodalField */,
+                                               double /* weight */){};
+    virtual void apply_localization_correction(const DENS_MAT & /* source */,
+                                               DENS_MAT & /* nodalField */){};
 
   private:
 
@@ -177,7 +182,7 @@ namespace ATC {
         
     // deactivate un-needed methods
     /** applies thermostat to atoms in the post-corrector phase */
-    virtual void apply_post_corrector(double dt){};
+    virtual void apply_post_corrector(double /* dt */){};
         
   protected:
 
@@ -187,7 +192,7 @@ namespace ATC {
 
     // deactivate un-needed methods
     /** apply solution to atomic quantities */
-    virtual void apply_to_atoms(PerAtomQuantity<double> * atomVelocities){};
+    virtual void apply_to_atoms(PerAtomQuantity<double> * /* atomVelocities */){};
 
     /** construct the RHS vector */
     virtual void set_rhs(DENS_MAT & rhs);
@@ -223,7 +228,7 @@ namespace ATC {
     virtual void apply_post_corrector(double dt);
 
     /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
-    virtual void compute_boundary_flux(FIELDS & fields)
+    virtual void compute_boundary_flux(FIELDS & /* fields */)
     {boundaryFlux_[TEMPERATURE] = 0.; boundaryFlux_[VELOCITY] = 0.;};
 
     /** get data for output */
@@ -291,7 +296,7 @@ namespace ATC {
         
     // deactivate un-needed methods
     /** applies thermostat to atoms in the post-corrector phase */
-    virtual void apply_post_corrector(double dt){};
+    virtual void apply_post_corrector(double /* dt */){};
         
   protected:
 
@@ -301,7 +306,7 @@ namespace ATC {
 
     // deactivate un-needed methods
     /** apply solution to atomic quantities */
-    virtual void apply_to_atoms(PerAtomQuantity<double> * atomVelocities){};
+    virtual void apply_to_atoms(PerAtomQuantity<double> * /* atomVelocities */){};
 
     /** construct the RHS vector */
     virtual void set_rhs(DENS_MAT & rhs);
diff --git a/lib/atc/Kinetostat.cpp b/lib/atc/Kinetostat.cpp
index 17c5b6caf7..8093d5925a 100644
--- a/lib/atc/Kinetostat.cpp
+++ b/lib/atc/Kinetostat.cpp
@@ -445,7 +445,7 @@ namespace ATC {
   //--------------------------------------------------------
   void GlcKinetostat::apply_to_atoms(PerAtomQuantity<double> * quantity,
                                      const DENS_MAT & lambdaAtom,
-                                     double dt)
+                                     double /* dt */)
   {
     *quantity -= lambdaAtom;
   }
@@ -576,7 +576,7 @@ namespace ATC {
   //            sets up the right-hand side of the
   //            kinetostat equations
   //--------------------------------------------------------
-  void DisplacementGlc::set_kinetostat_rhs(DENS_MAT & rhs, double dt)
+  void DisplacementGlc::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */)
   {
     // form rhs : sum_a (hatN_Ia * x_ai) - (Upsilon)_Ii
     rhs = nodalAtomicMassWeightedDisplacement_->quantity();
@@ -922,7 +922,7 @@ namespace ATC {
   //            sets up the right-hand side of the
   //            kinetostat equations
   //--------------------------------------------------------
-  void VelocityGlc::set_kinetostat_rhs(DENS_MAT & rhs, double dt)
+  void VelocityGlc::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */)
   {
     // form rhs : sum_a (hatN_Ia * x_ai) - (\dot{Upsilon})_Ii
     rhs = nodalAtomicMomentum_->quantity();
@@ -1252,7 +1252,7 @@ namespace ATC {
   //            sets up the RHS of the kinetostat equations
   //            for the coupling parameter lambda
   //--------------------------------------------------------
-  void StressFlux::set_kinetostat_rhs(DENS_MAT & rhs, double dt)
+  void StressFlux::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */)
   {
     // (a) for flux based : 
     // form rhs :  \int N_I r dV - \sum_g N_Ig^* f_g
@@ -1381,7 +1381,7 @@ namespace ATC {
   //    computes the boundary flux to be consistent with
   //    the controller
   //--------------------------------------------------------
-  void StressFluxGhost::compute_boundary_flux(FIELDS & fields)
+  void StressFluxGhost::compute_boundary_flux(FIELDS & /* fields */)
   {
     // This is only used in computation of atomic sources
     boundaryFlux_[VELOCITY] = 0.;
@@ -1407,7 +1407,7 @@ namespace ATC {
   //            sets up the RHS of the kinetostat equations
   //            for the coupling parameter lambda
   //--------------------------------------------------------
-  void StressFluxGhost::set_kinetostat_rhs(DENS_MAT & rhs, double dt)
+  void StressFluxGhost::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */)
   {
     // (a) for flux based : 
     // form rhs :  \int N_I r dV - \sum_g N_Ig^* f_g
@@ -1985,7 +1985,7 @@ namespace ATC {
   //            sets up the RHS of the kinetostat equations
   //            for the coupling parameter lambda
   //--------------------------------------------------------
-  void KinetostatFlux::set_kinetostat_rhs(DENS_MAT & rhs, double dt)
+  void KinetostatFlux::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */)
   {
     // (a) for flux based : 
     // form rhs :  \int N_I r dV - \sum_g N_Ig^* f_g
@@ -2056,7 +2056,7 @@ namespace ATC {
   //    computes the boundary flux to be consistent with
   //    the controller
   //--------------------------------------------------------
-  void KinetostatFluxGhost::compute_boundary_flux(FIELDS & fields)
+  void KinetostatFluxGhost::compute_boundary_flux(FIELDS & /* fields */)
   {
     // This is only used in computation of atomic sources
     boundaryFlux_[VELOCITY] = 0.;
@@ -2086,7 +2086,7 @@ namespace ATC {
   //            sets up the RHS of the kinetostat equations
   //            for the coupling parameter lambda
   //--------------------------------------------------------
-  void KinetostatFluxGhost::set_kinetostat_rhs(DENS_MAT & rhs, double dt)
+  void KinetostatFluxGhost::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */)
   {
     // (a) for flux based : 
     // form rhs :  \int N_I r dV - \sum_g N_Ig^* f_g
@@ -2348,7 +2348,7 @@ namespace ATC {
   //--------------------------------------------------------
   void KinetostatFixed::add_to_momentum(const DENS_MAT & nodalLambdaForce,
                                        DENS_MAT & deltaMomentum,
-                                       double dt)
+                                        double /* dt */)
   {
     deltaMomentum.resize(nNodes_,nsd_);
     const set<int> & regulatedNodes(regulatedNodes_->quantity());
diff --git a/lib/atc/Kinetostat.h b/lib/atc/Kinetostat.h
index 3d9b8cd5d2..691b929e9f 100644
--- a/lib/atc/Kinetostat.h
+++ b/lib/atc/Kinetostat.h
@@ -129,9 +129,11 @@ namespace ATC {
                                 double dt=0.);
 
     /** apply any required corrections for localized kinetostats */
-    virtual void apply_localization_correction(const DENS_MAT & source,
-                                               DENS_MAT & nodalField,
-                                               double weight = 1.){};
+    virtual void apply_localization_correction(const DENS_MAT & /* source */,
+                                               DENS_MAT & /* nodalField */,
+                                               double /* weight */){};
+    virtual void apply_localization_correction(const DENS_MAT & /* source */,
+                                               DENS_MAT & /* nodalField */){};
 
     // member data
     /** nodeset corresponding to Hoover coupling */
@@ -761,7 +763,7 @@ namespace ATC {
     virtual void apply_post_corrector(double dt);
 
     /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
-    virtual void compute_boundary_flux(FIELDS & fields)
+    virtual void compute_boundary_flux(FIELDS & /* fields */)
       {boundaryFlux_[VELOCITY] = 0.;};
 
     /** determine if local shape function matrices are needed */
diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp
index 2238d930f4..9c2223f555 100644
--- a/lib/atc/LammpsInterface.cpp
+++ b/lib/atc/LammpsInterface.cpp
@@ -902,7 +902,7 @@ int LammpsInterface::reset_ghosts(int deln) const
 
 //* energy for interactions within the shortrange cutoff
 double LammpsInterface::shortrange_energy(double *coord, 
-  int itype, int id, double max) const
+                                          int itype, int id, double /* max */) const
 {
   LAMMPS_NS::Atom * atom  = lammps_->atom;
   double **x = atom->x;
@@ -1293,7 +1293,7 @@ int LammpsInterface::nsteps() const    { return lammps_->update->nsteps; }
 
 int LammpsInterface::sbmask(int j) const {return j >> SBBITS & 3; }
 
-void LammpsInterface::set_list(int id, LAMMPS_NS::NeighList *ptr) { list_ = ptr; }
+void LammpsInterface::set_list(int /* id */, LAMMPS_NS::NeighList *ptr) { list_ = ptr; }
 
 int   LammpsInterface::neighbor_list_inum() const { return list_->inum; }
 
diff --git a/lib/atc/Material.cpp b/lib/atc/Material.cpp
index 22273de2ef..676a87524f 100644
--- a/lib/atc/Material.cpp
+++ b/lib/atc/Material.cpp
@@ -816,7 +816,7 @@ void Material::inv_effective_mass(
 };
 //---------------------------------------------------------------------
 void Material::heat_flux(
-  const FIELD_MATS & fields,
+  const FIELD_MATS & /* fields */,
   const GRAD_FIELD_MATS & gradFields,
   DENS_MAT_VEC & flux) const
 {
@@ -865,7 +865,7 @@ bool  Material::electron_drag_power(
 //---------------------------------------------------------------------
 bool Material::electron_recombination(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &gradFields,
+  const GRAD_FIELD_MATS & /* gradFields */,
   DENS_MAT & recombination) const
 {
   // 1/tau (n - n0)
@@ -937,7 +937,7 @@ void Material::electron_flux(
 }
 //---------------------------------------------------------------------
 void Material::electric_field(
-  const FIELD_MATS &fields,
+  const FIELD_MATS & /* fields */,
   const GRAD_FIELD_MATS &gradFields,
   DENS_MAT_VEC &flux) const
 {
@@ -950,7 +950,7 @@ void Material::electric_field(
 }
 //---------------------------------------------------------------------
 void Material::electric_displacement(
-  const FIELD_MATS &fields,
+  const FIELD_MATS & /* fields */,
   const GRAD_FIELD_MATS &gradFields,
   DENS_MAT_VEC &flux) const
 {
diff --git a/lib/atc/Matrix.h b/lib/atc/Matrix.h
index e806ebd016..6745ea96db 100644
--- a/lib/atc/Matrix.h
+++ b/lib/atc/Matrix.h
@@ -248,7 +248,7 @@ DenseMatrix<T> operator-(const Matrix<T> &A, const Matrix<T> &B)
 //* performs a matrix-matrix multiply with general type implementation
 template<typename T>
 void MultAB(const Matrix<T> &A, const Matrix<T> &B, DenseMatrix<T> &C, 
-            const bool At, const bool Bt, T a, T b)
+            const bool At, const bool Bt, T /* a */, T b)
 {
   const INDEX sA[2] = {A.nRows(), A.nCols()};  // m is sA[At] k is sA[!At]
   const INDEX sB[2] = {B.nRows(), B.nCols()};  // k is sB[Bt] n is sB[!Bt]
diff --git a/lib/atc/MeshReader.cpp b/lib/atc/MeshReader.cpp
index 14101f1297..c4896ec727 100644
--- a/lib/atc/MeshReader.cpp
+++ b/lib/atc/MeshReader.cpp
@@ -20,7 +20,7 @@ namespace ATC {
   /** constructor, takes a filename */
   MeshReader::MeshReader(string filename, 
                          Array<bool> periodicity, 
-                         double tol)
+                         double /* tol */)
     : meshfile_(filename),
       periodicity_(periodicity),
       nNodes_(0),
diff --git a/lib/atc/MoleculeSet.cpp b/lib/atc/MoleculeSet.cpp
index 618261f186..e3b1ed30d4 100644
--- a/lib/atc/MoleculeSet.cpp
+++ b/lib/atc/MoleculeSet.cpp
@@ -165,7 +165,7 @@ namespace ATC {
   //  Constructor
   //--------------------------------------------------------
   SmallMoleculeSet::SmallMoleculeSet(ATC_Method * atc, int groupBit,
-                                     PerAtomQuantity<int> * bondList, PerAtomQuantity<int> * numBond) :
+                                     PerAtomQuantity<int> * bondList, PerAtomQuantity<int> * /* numBond */) :
     MoleculeSet(atc,groupBit),
     bondList_(bondList)
   {
diff --git a/lib/atc/NonLinearSolver.h b/lib/atc/NonLinearSolver.h
index d3d906a39a..010e3ee72e 100644
--- a/lib/atc/NonLinearSolver.h
+++ b/lib/atc/NonLinearSolver.h
@@ -20,7 +20,7 @@ class TangentOperator {
  public:
   TangentOperator(){};
   virtual ~TangentOperator(){};
-  virtual void function(const VECTOR & x, DENS_VEC & f) {}; // =0;
+  virtual void function(const VECTOR & /* x */, DENS_VEC & /* f */) {}; // =0;
   virtual void tangent(const VECTOR & x, DENS_VEC & f, MATRIX & dfdx) =0;
   //virtual void function(const VECTOR & x, VECTOR & f) {}; // =0;
   //virtual void tangent(const VECTOR & x, VECTOR & f, MATRIX & dfdx) {}; // =0;
diff --git a/lib/atc/OutputManager.cpp b/lib/atc/OutputManager.cpp
index 4340c8b8b0..066c240cab 100644
--- a/lib/atc/OutputManager.cpp
+++ b/lib/atc/OutputManager.cpp
@@ -161,8 +161,8 @@ void OutputManager::read_restart_file(string fileName, RESTART_LIST *data)
     for (int i = 0; i < field_data->nRows(); ++i) {
       for (int j = 0; j < field_data->nCols(); ++j) {
         double myVal;
-        fread(&myVal,sizeof(double),1,fp);
-        (*field_data)(i,j) = myVal;  
+        if (fread(&myVal,sizeof(double),1,fp) == 1)
+          (*field_data)(i,j) = myVal;  
     
       }
     }
@@ -792,7 +792,7 @@ void OutputManager::write_data_vtk(OUTPUT_LIST *data)
 }
 
 /** write (ensight gold : ASCII "C" format) dictionary */
-void OutputManager::write_dictionary(double time, OUTPUT_LIST *data)
+void OutputManager::write_dictionary(double /* time */, OUTPUT_LIST *data)
 {
   // file names
   string dict_file_name = outputPrefix_ + ".case";
diff --git a/lib/atc/POEMSChain.h b/lib/atc/POEMSChain.h
deleted file mode 100644
index 7dc143a9d9..0000000000
--- a/lib/atc/POEMSChain.h
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- *_________________________________________________________________________*
- *      POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE     *
- *      DESCRIPTION: SEE READ-ME                                           *
- *      FILE NAME: PoemsChain.h                                            *
- *      AUTHORS: See Author List                                           * 
- *      GRANTS: See Grants List                                            *
- *      COPYRIGHT: (C) 2005 by Authors as listed in Author's List          *
- *      LICENSE: Please see License Agreement                              *
- *      DOWNLOAD: Free at www.rpi.edu/~anderk5                             *
- *      ADMINISTRATOR: Prof. Kurt Anderson                                 *
- *                     Computational Dynamics Lab                          *
- *                     Rensselaer Polytechnic Institute                    *
- *                     110 8th St. Troy NY 12180                           * 
- *      CONTACT:        anderk5@rpi.edu                                    *
- *_________________________________________________________________________*/
-
-#ifndef POEMSCHAIN_H_
-#define POEMSCHAIN_H_
-
-#include "poemslist.h"
-
-struct ChildRingData {
-	List<int> * childRing;
-	int entranceNodeId;
-};
-
-struct POEMSChain{
-	~POEMSChain(){
-		for(int i = 0; i < childChains.GetNumElements(); i++)
-		{
-			delete childChains(i);
-		}
-	}
-	//void printTreeStructure(int tabs);
-	//void getTreeAsList(List<int> * temp);
-	List<int> listOfNodes;
-	List<POEMSChain> childChains;
-	POEMSChain * parentChain;
-	List<ChildRingData> childRings;
-	
-	
-	void printTreeStructure(int tabs){
-		for(int i = 0; i < tabs; i++)
-		{
-			cout << "\t";
-		}
-		cout << "Chain: ";
-		for(int i = 0; i < listOfNodes.GetNumElements(); i++)
-		{
-			cout << *(listOfNodes(i)) << " ";
-		}
-		cout << endl;
-		for(int i = 0; i < childChains.GetNumElements(); i++)
-		{
-			childChains(i)->printTreeStructure(tabs + 1);
-		}
-	}
-	void getTreeAsList(List<int> * temp)
-	{
-		for(int i = 0; i < listOfNodes.GetNumElements(); i++)
-		{
-			int * integer = new int;
-			*integer = *(listOfNodes(i));
-			temp->Append(integer);
-		}
-		for(int i = 0; i < childChains.GetNumElements(); i++)
-		{
-			childChains(i)->getTreeAsList(temp);
-		}
-	}
-};
-#endif
diff --git a/lib/atc/PerAtomQuantity-inl.h b/lib/atc/PerAtomQuantity-inl.h
index 037c3adeda..f95e5d306d 100644
--- a/lib/atc/PerAtomQuantity-inl.h
+++ b/lib/atc/PerAtomQuantity-inl.h
@@ -177,7 +177,7 @@ namespace ATC {
   //-----------------------------------------------------------------
   template <typename T>
   int PerAtomQuantity<T>::pack_comm(int index, double *buf, 
-                                    int pbc_flag, int *pbc)
+                                    int /* pbc_flag */, int * /* pbc */)
   {
     if (this->need_reset()) this->reset();
     DenseMatrix<T> & myQuantity(this->quantity_);
@@ -256,7 +256,7 @@ namespace ATC {
   //-----------------------------------------------------------------
   template <typename T>
   int LammpsAtomQuantity<T>::pack_comm(int index, double *buf, 
-                                       int pbc_flag, int *pbc)
+                                       int /* pbc_flag */, int * /* pbc */)
   {
     if (this->need_reset()) this->reset();
     int bufIdx = 0;
@@ -550,7 +550,7 @@ namespace ATC {
   //-----------------------------------------------------------------
   template <typename T>
   int PerAtomDiagonalMatrix<T>::pack_comm(int index, double *buf, 
-                                          int pbc_flag, int *pbc)
+                                          int /* pbc_flag */, int * /* pbc */)
   {
     if (this->need_reset()) this->reset();
     DiagonalMatrix<T> & myQuantity(this->quantity_);
@@ -756,8 +756,8 @@ namespace ATC {
   // pack values in local atom-based arrays for passing to ghosts on another proc 
   //-----------------------------------------------------------------
   template <typename T>
-  int PerAtomSparseMatrix<T>::pack_comm(int index, double *buf, 
-                                        int pbc_flag, int *pbc)
+    int PerAtomSparseMatrix<T>::pack_comm(int /* index */, double * /* buf */, 
+                                          int /* pbc_flag */, int */* pbc */)
   {
     return 0;
   }
@@ -766,7 +766,7 @@ namespace ATC {
   // unpack values in local atom-based arrays for passing to ghosts on another proc
   //-----------------------------------------------------------------
   template <typename T>
-  int PerAtomSparseMatrix<T>::unpack_comm(int index, double *buf)
+    int PerAtomSparseMatrix<T>::unpack_comm(int /* index */, double * /* buf */)
   {
     return 0;
   }
diff --git a/lib/atc/PerAtomQuantity.h b/lib/atc/PerAtomQuantity.h
index 548918c9cc..e6cb19981a 100644
--- a/lib/atc/PerAtomQuantity.h
+++ b/lib/atc/PerAtomQuantity.h
@@ -274,26 +274,26 @@ namespace ATC {
     virtual int memory_usage() const {return 0;};
 
     /** packs up data for parallel transfer when atoms change processors */
-    virtual int pack_exchange(int i, double *buffer) {return 0;};
+    virtual int pack_exchange(int /* i */, double */* buffer */) {return 0;};
 
     /** unpacks data after parallel transfer when atoms change processors */
-    virtual int unpack_exchange(int i, double *buffer) {return 0;};
+    virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     /** packs up data for parallel transfer to ghost atoms on other processors */
-    virtual int pack_comm(int index, double *buf, 
-                          int pbc_flag, int *pbc) {return 0;};
+    virtual int pack_comm(int /* index */, double * /* buf */, 
+                          int /* pbc_flag */, int * /* pbc */) {return 0;};
 
     /** unpacks data after parallel transfer to ghost atoms on other processors */
-    virtual int unpack_comm(int index, double *buf) {return 0;};
+    virtual int unpack_comm(int /* index */, double * /* buf */) {return 0;};
 
     /** returns size of per-atom communication */
     virtual int size_comm() const {return 0;};
 
     /** changes size of temperary lammps storage data if transfer is being used */
-    virtual void grow_lammps_array(int nmax, const std::string & tag) {};
+    virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {};
 
     /** rearrange memory of temporary lammps storage data, called from copy_array */
-    virtual void copy_lammps_array(int i, int j) {};
+    virtual void copy_lammps_array(int /* i */, int /* j */) {};
 
   protected:
 
@@ -396,43 +396,43 @@ namespace ATC {
       {throw ATC_Error("ProtectedClonedAtomQuantity::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;};
 
     /** sets the quantity to a given value */
-    virtual void operator=(const DenseMatrix<T> & target)
+    virtual void operator=(const DenseMatrix<T> & /* target */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::set_quantity - Cannot modify protected per atom quantities");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const T & target)
+    virtual void operator=(const T & /* target */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator= - Cannot modify protected per atom quantities");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const DenseMatrix<T> & addition)
+    virtual void operator+=(const DenseMatrix<T> & /* addition */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator+= - Cannot modify protected per atom quantities");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(T addition)
+    virtual void operator+=(T /* addition */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator+= - Cannot modify protected per atom quantities");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const DenseMatrix<T> & subtraction)
+    virtual void operator-=(const DenseMatrix<T> & /* subtraction */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator-= - Cannot modify protected per atom quantities");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(T subtraction)
+    virtual void operator-=(T /* subtraction */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator-= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const DenseMatrix<T> & multiplier)
+    virtual void operator*=(const DenseMatrix<T> & /* multiplier */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(T multiplier)
+    virtual void operator*=(T /* multiplier */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const DenseMatrix<T> & divisor)
+    virtual void operator/=(const DenseMatrix<T> & /* divisor */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator/= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(T divisor)
+    virtual void operator/=(T /* divisor */)
       {throw ATC_Error("ProtectedClonedAtomQuantity::operator/= - Cannot modify protected per atom quantities");};
 
   protected:
@@ -517,43 +517,43 @@ namespace ATC {
       {throw ATC_Error("ProtectedAtomQuantity::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;};
 
     /** sets the quantity to a given value */
-    virtual void operator=(const DenseMatrix<T> & target)
+    virtual void operator=(const DenseMatrix<T> & /* target */)
       {throw ATC_Error("ProtectedAtomQuantity::set_quantity - Cannot modify protected per atom quantities");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const T & target)
+    virtual void operator=(const T & /* target */)
       {throw ATC_Error("ProtectedAtomQuantity::operator= - Cannot modify protected per atom quantities");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const DenseMatrix<T> & addition)
+    virtual void operator+=(const DenseMatrix<T> & /* addition */)
       {throw ATC_Error("ProtectedAtomQuantity::operator+= - Cannot modify protected per atom quantities");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(T addition)
+    virtual void operator+=(T /* addition */)
       {throw ATC_Error("ProtectedAtomQuantity::operator+= - Cannot modify protected per atom quantities");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const DenseMatrix<T> & subtraction)
+    virtual void operator-=(const DenseMatrix<T> & /* subtraction */)
       {throw ATC_Error("ProtectedAtomQuantity::operator-= - Cannot modify protected per atom quantities");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(T subtraction)
+    virtual void operator-=(T /* subtraction */)
       {throw ATC_Error("ProtectedAtomQuantity::operator-= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const DenseMatrix<T> & multiplier)
+    virtual void operator*=(const DenseMatrix<T> & /* multiplier */)
       {throw ATC_Error("ProtectedAtomQuantity::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(T multiplier)
+    virtual void operator*=(T /* multiplier */)
       {throw ATC_Error("ProtectedAtomQuantity::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const DenseMatrix<T> & divisor)
+    virtual void operator/=(const DenseMatrix<T> & /* divisor */)
       {throw ATC_Error("ProtectedAtomQuantity::operator/= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(T divisor)
+    virtual void operator/=(T /* divisor */)
       {throw ATC_Error("ProtectedAtomQuantity::operator/= - Cannot modify protected per atom quantities");};
 
   protected:
@@ -646,43 +646,43 @@ namespace ATC {
       {throw ATC_Error("ProtectedLammpsAtomQuantity::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;};
 
         /** sets the quantity to a given value */
-    virtual void operator=(const DenseMatrix<T> & target)
+    virtual void operator=(const DenseMatrix<T> & /* target */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::set_quantity - Cannot modify protected per atom quantities");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const T & target)
+    virtual void operator=(const T & /* target */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator= - Cannot modify protected per atom quantities");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const DenseMatrix<T> & addition)
+    virtual void operator+=(const DenseMatrix<T> & /* addition */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator+= - Cannot modify protected per atom quantities");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(T addition)
+    virtual void operator+=(T /* addition */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator+= - Cannot modify protected per atom quantities");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const DenseMatrix<T> & subtraction)
+    virtual void operator-=(const DenseMatrix<T> & /* subtraction */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator-= - Cannot modify protected per atom quantities");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(T subtraction)
+    virtual void operator-=(T /* subtraction */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator-= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const DenseMatrix<T> & multiplier)
+    virtual void operator*=(const DenseMatrix<T> & /* multiplier */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(T multiplier)
+    virtual void operator*=(T /* multiplier */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const DenseMatrix<T> & divisor)
+    virtual void operator/=(const DenseMatrix<T> & /* divisor */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator/= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(T divisor)
+    virtual void operator/=(T /* divisor */)
       {throw ATC_Error("ProtectedLammpsAtomQuantity::operator/= - Cannot modify protected per atom quantities");};
 
   protected:
@@ -734,16 +734,16 @@ namespace ATC {
     virtual int memory_usage() const {return 0;};
 
     /** packs up data for parallel transfer */
-    virtual int pack_exchange(int i, double *buffer) {return 0;};
+    virtual int pack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     /** unpacks data after parallel transfer */
-    virtual int unpack_exchange(int i, double *buffer) {return 0;};
+    virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     /** changes size of temperary lammps storage data if transfer is being used */
-    virtual void grow_lammps_array(int nmax, const std::string & tag) {};
+    virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {};
 
     /** rearrange memory of temporary lammps storage data, called from copy_array */
-    virtual void copy_lammps_array(int i, int j) {};
+    virtual void copy_lammps_array(int /* i */, int /* j */) {};
 
   protected:
 
@@ -791,16 +791,16 @@ namespace ATC {
     virtual int memory_usage() const {return 0;};
 
     /** packs up data for parallel transfer */
-    virtual int pack_exchange(int i, double *buffer) {return 0;};
+    virtual int pack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     /** unpacks data after parallel transfer */
-    virtual int unpack_exchange(int i, double *buffer) {return 0;};
+    virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     /** changes size of temperary lammps storage data if transfer is being used */
-    virtual void grow_lammps_array(int nmax, const std::string & tag) {};
+    virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {};
 
     /** rearrange memory of temporary lammps storage data, called from copy_array */
-    virtual void copy_lammps_array(int i, int j) {};
+    virtual void copy_lammps_array(int /* i */, int /* j */) {};
 
   protected:
 
@@ -1066,43 +1066,43 @@ namespace ATC {
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;};
 
     /** sets the quantity to a given value */
-    virtual void operator=(const DiagonalMatrix<T> & target)
+    virtual void operator=(const DiagonalMatrix<T> & /* target */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::set_quantity - Cannot modify protected per atom quantities");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const T & target)
+    virtual void operator=(const T & /* target */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator= - Cannot modify protected per atom quantities");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const DiagonalMatrix<T> & addition)
+    virtual void operator+=(const DiagonalMatrix<T> & /* addition */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator+= - Cannot modify protected per atom quantities");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(T addition)
+    virtual void operator+=(T /* addition */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator+= - Cannot modify protected per atom quantities");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const DiagonalMatrix<T> & subtraction)
+    virtual void operator-=(const DiagonalMatrix<T> & /* subtraction */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator-= - Cannot modify protected per atom quantities");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(T subtraction)
+    virtual void operator-=(T /* subtraction */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator-= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const DiagonalMatrix<T> & multiplier)
+    virtual void operator*=(const DiagonalMatrix<T> & /* multiplier */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(T multiplier)
+    virtual void operator*=(T /* multiplier */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const DiagonalMatrix<T> & divisor)
+    virtual void operator/=(const DiagonalMatrix<T> & /* divisor */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator/= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(T divisor)
+    virtual void operator/=(T /* divisor */)
       {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator/= - Cannot modify protected per atom quantities");};
 
   protected:
@@ -1331,43 +1331,43 @@ namespace ATC {
       {throw ATC_Error("ProtectedAtomSparseMatrix::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;};
 
     /** sets the quantity to a given value */
-    virtual void operator=(const SparseMatrix<T> & target)
+    virtual void operator=(const SparseMatrix<T> & /* target */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::set_quantity - Cannot modify protected per atom quantities");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const T & target)
+    virtual void operator=(const T & /* target */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator= - Cannot modify protected per atom quantities");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const SparseMatrix<T> & addition)
+    virtual void operator+=(const SparseMatrix<T> & /* addition */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator+= - Cannot modify protected per atom quantities");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(T addition)
+    virtual void operator+=(T /* addition */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator+= - Cannot modify protected per atom quantities");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const SparseMatrix<T> & subtraction)
+    virtual void operator-=(const SparseMatrix<T> & /* subtraction */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator-= - Cannot modify protected per atom quantities");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(T subtraction)
+    virtual void operator-=(T /* subtraction */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator-= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const SparseMatrix<T> & multiplier)
+    virtual void operator*=(const SparseMatrix<T> & /* multiplier */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(T multiplier)
+    virtual void operator*=(T /* multiplier */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator*= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const SparseMatrix<T> & divisor)
+    virtual void operator/=(const SparseMatrix<T> & /* divisor */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator/= - Cannot modify protected per atom quantities");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(T divisor)
+    virtual void operator/=(T /* divisor */)
       {throw ATC_Error("ProtectedAtomSparseMatrix::operator/= - Cannot modify protected per atom quantities");};
 
   protected:
@@ -1420,27 +1420,27 @@ namespace ATC {
     virtual int memory_usage() const {return 0;};
 
     /** packs up data for parallel transfer when atoms change processors */
-    virtual int pack_exchange(int i, double *buffer) {return 0;};
+    virtual int pack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     /** unpacks data after parallel transfer when atoms change processors */
-    virtual int unpack_exchange(int i, double *buffer) {return 0;};
+    virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     // pack/unpack_comm only valid if the quantity is over all real and processor ghost atoms
     /** packs up data for parallel transfer to ghost atoms on other processors */
-    virtual int pack_comm(int index, double *buf,
-                          int pbc_flag, int *pbc) {return 0;};
+    virtual int pack_comm(int /* index */, double * /* buf */,
+                          int /* pbc_flag */, int * /* pbc */) {return 0;};
 
     /** unpacks data after parallel transfer to ghost atoms on other processors */
-    virtual int unpack_comm(int index, double *buf) {return 0;};
+    virtual int unpack_comm(int /* index */, double * /* buf */) {return 0;};
 
     /** returns per-atom size of communicated data */
     virtual int size_comm() const {return 0;};
 
     /** changes size of temperary lammps storage data if transfer is being used */
-    virtual void grow_lammps_array(int nmax, const std::string & tag) {};
+    virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {};
 
     /** rearrange memory of temporary lammps storage data, called from copy_array */
-    virtual void copy_lammps_array(int i, int j) {};
+    virtual void copy_lammps_array(int /* i */, int /* j */) {};
 
   protected:
 
diff --git a/lib/atc/PerAtomQuantityLibrary.cpp b/lib/atc/PerAtomQuantityLibrary.cpp
index 36f9252451..7f8a9b879a 100644
--- a/lib/atc/PerAtomQuantityLibrary.cpp
+++ b/lib/atc/PerAtomQuantityLibrary.cpp
@@ -1129,7 +1129,7 @@ namespace ATC {
   FluctuatingKineticTensor::FluctuatingKineticTensor(ATC_Method * atc,
      PerAtomQuantity<double> * atomVelocities,
      PerAtomQuantity<double> * atomMasses,
-     PerAtomQuantity<double> * atomMeanVelocities,
+                                                     PerAtomQuantity<double> * /* atomMeanVelocities */,
      AtomType atomType) :
     ProtectedAtomQuantity<double>(atc,6,atomType),
     atomVelocities_(atomVelocities),
diff --git a/lib/atc/PerAtomQuantityLibrary.h b/lib/atc/PerAtomQuantityLibrary.h
index b3db140f82..0089df7855 100644
--- a/lib/atc/PerAtomQuantityLibrary.h
+++ b/lib/atc/PerAtomQuantityLibrary.h
@@ -1045,26 +1045,26 @@ namespace ATC {
     virtual int memory_usage() const {return 0;};
 
     /** packs up data for parallel transfer when atoms change processors */
-    virtual int pack_exchange(int i, double *buffer) {return 0;};
+    virtual int pack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     /** unpacks data after parallel transfer when atoms change processors */
-    virtual int unpack_exchange(int i, double *buffer) {return 0;};
+    virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;};
 
     /** packs up data for parallel transfer to ghost atoms on other processors */
-    virtual int pack_comm(int index, double *buf, 
-                          int pbc_flag, int *pbc) {return 0;};
+    virtual int pack_comm(int /* index */, double * /* buf */, 
+                          int /* pbc_flag */, int * /* pbc */) {return 0;};
 
     /** unpacks data after parallel transfer to ghost atoms on other processors */
-    virtual int unpack_comm(int index, double *buf) {return 0;};
+    virtual int unpack_comm(int /* index */, double * /* buf */) {return 0;};
 
     /** returns size of per-atom communication */
     virtual int size_comm() const {return 0;};
 
     /** changes size of temperary lammps storage data if transfer is being used */
-    virtual void grow_lammps_array(int nmax, const std::string & tag) {};
+    virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {};
 
     /** rearrange memory of temporary lammps storage data, called from copy_array */
-    virtual void copy_lammps_array(int i, int j) {};
+    virtual void copy_lammps_array(int /* i */, int /* j */) {};
 
   protected:
 
diff --git a/lib/atc/PerPairQuantity.cpp b/lib/atc/PerPairQuantity.cpp
index 86ad331eca..3632a87aa9 100644
--- a/lib/atc/PerPairQuantity.cpp
+++ b/lib/atc/PerPairQuantity.cpp
@@ -281,7 +281,6 @@ void BondMatrixKernel::reset(void) const
   int nNodes = feMesh_->num_nodes_unique(); 
   quantity_.reset(nNodes,nPairs);
   double lam1,lam2;
-  std::pair< int,int > pair_jk;
   int heartbeatFreq = (nNodes <= 10 ? 1 : (int) nNodes / 10);
   HeartBeat beat("computing bond matrix ",heartbeatFreq);
   beat.start();
@@ -337,7 +336,6 @@ void BondMatrixPartitionOfUnity::reset(void) const
   int nodes_per_element = feMesh_->num_nodes_per_element(); 
   Array<int> node_list(nodes_per_element); 
   DENS_VEC shp(nodes_per_element);
-  std::pair< int,int > pair_jk;
   int heartbeatFreq = (int) nPairs / 10;
   HeartBeat beat("computing bond matrix ",heartbeatFreq);
   beat.start();
diff --git a/lib/atc/PhysicsModel.h b/lib/atc/PhysicsModel.h
index ce25174d90..50b327ce0b 100644
--- a/lib/atc/PhysicsModel.h
+++ b/lib/atc/PhysicsModel.h
@@ -47,7 +47,7 @@ namespace ATC
     void initialize(void); 
 
     // set timescale parameters based on a given lengthscale
-    virtual void set_timescales(const double lengthscale) {};
+    virtual void set_timescales(const double /* lengthscale */) {};
 
     /** access number of materials */
     int nMaterials(void) const { return materials_.size(); }
diff --git a/lib/atc/PoissonSolver.cpp b/lib/atc/PoissonSolver.cpp
index b3c077b593..86670ae218 100644
--- a/lib/atc/PoissonSolver.cpp
+++ b/lib/atc/PoissonSolver.cpp
@@ -71,7 +71,7 @@ PoissonSolver::~PoissonSolver()
 //  Parser
 // --------------------------------------------------------------------
 
-bool PoissonSolver::modify(int narg, char **arg)
+  bool PoissonSolver::modify(int /* narg */, char **arg)
 {
   bool match = false;
   /*! \page man_poisson_solver fix_modify AtC poisson_solver 
diff --git a/lib/atc/PolynomialSolver.cpp b/lib/atc/PolynomialSolver.cpp
index 9088a7eaf3..b498b3b5bb 100644
--- a/lib/atc/PolynomialSolver.cpp
+++ b/lib/atc/PolynomialSolver.cpp
@@ -104,7 +104,7 @@ namespace ATC {
 
   // solve ode with polynomial source : y'n + a_n-1 y'n-1 + ... = b_n x^n +...
   void integrate_ode(double x, 
-    int na, double * a, double * y0, double * y, int nb, double *b )
+                     int na, double * a, double * y0, double * y, int nb, double * /* b */ )
   {
     if (na == 2) {
       // particular
diff --git a/lib/atc/SchrodingerSolver.cpp b/lib/atc/SchrodingerSolver.cpp
index 92eb1a7a62..d79fa85595 100644
--- a/lib/atc/SchrodingerSolver.cpp
+++ b/lib/atc/SchrodingerSolver.cpp
@@ -66,7 +66,7 @@ double fermi_dirac(const double E, const double T)
     M_ = sparseM.dense_copy();
   }
   //-----------------------------------------------------
-  bool SchrodingerSolver::solve(FIELDS & fields)
+  bool SchrodingerSolver::solve(FIELDS & /* fields */)
   {
 
 // typedef  struct{float real, imag;} COMPLEX;
@@ -132,7 +132,7 @@ double fermi_dirac(const double E, const double T)
   //--------------------------------------------------------
   // compute charge density per slice
   //--------------------------------------------------------
-  bool SliceSchrodingerSolver::solve(FIELDS & fields)
+  bool SliceSchrodingerSolver::solve(FIELDS & /* fields */)
   {
     // fields
     DENS_MAT & psi   = (atc_->field(ELECTRON_WAVEFUNCTION)).set_quantity();
@@ -250,7 +250,7 @@ double fermi_dirac(const double E, const double T)
   {
   }
   //----------------------------------------------------------
-  bool SchrodingerPoissonManager::modify(int narg, char **arg)
+  bool SchrodingerPoissonManager::modify(int /* narg */, char **arg)
   {
     bool match = false;
     int argIndx = 0;
@@ -350,7 +350,7 @@ double fermi_dirac(const double E, const double T)
   }
   //----------------------------------------------------------------------
 
-  void SchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & fluxes)
+  void SchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & /* fluxes */)
   {
     if ((atc_->prescribed_data_manager()->all_fixed(ELECTRON_WAVEFUNCTION))
      && (atc_->prescribed_data_manager()->all_fixed(ELECTRIC_POTENTIAL)))  {
@@ -739,7 +739,7 @@ double fermi_dirac(const double E, const double T)
     if (solver_) delete solver_;
   }
   //--------------------------------------------------------------------------
-  void GlobalSliceSchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & fluxes)
+  void GlobalSliceSchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & /* fluxes */)
   {
     const DENS_MAT & phi = (atc_->fields_[ELECTRIC_POTENTIAL]).quantity();
     const DENS_MAT & n   = (atc_->fields_[ELECTRON_DENSITY]  ).quantity();
diff --git a/lib/atc/SchrodingerSolver.h b/lib/atc/SchrodingerSolver.h
index 9b8616b458..e2addc48a3 100644
--- a/lib/atc/SchrodingerSolver.h
+++ b/lib/atc/SchrodingerSolver.h
@@ -41,7 +41,7 @@ class SchrodingerSolver {
   virtual ~SchrodingerSolver(){};
 
   /** parser */
-  bool modify(int narg, char **arg){ return false;}
+  bool modify(int /* narg */, char ** /* arg */){ return false;}
 
   /** initialize */
   void initialize(void);
@@ -103,7 +103,7 @@ class SliceSchrodingerSolver : public SchrodingerSolver {
   virtual ~SliceSchrodingerSolver(){};
 
   /** parser */
-  bool modify(int narg, char **arg){return false;}
+  bool modify(int /* narg */, char ** /* arg */){return false;}
 
   /** initialize */
   void initialize(void);
diff --git a/lib/atc/SparseMatrix-inl.h b/lib/atc/SparseMatrix-inl.h
index f70dd0361d..36867ad8de 100644
--- a/lib/atc/SparseMatrix-inl.h
+++ b/lib/atc/SparseMatrix-inl.h
@@ -498,7 +498,7 @@ TRIPLET<T> SparseMatrix<T>::triplet(INDEX i) const
 // full reset - completely wipes out all SparseMatrix data, zero is ignored
 //-----------------------------------------------------------------------------
 template<typename T>
-void SparseMatrix<T>::reset(INDEX rows, INDEX cols, bool zero)
+void SparseMatrix<T>::reset(INDEX rows, INDEX cols, bool /* zero */)
 {
   _delete();
   _nRows = rows;
@@ -545,7 +545,7 @@ void SparseMatrix<T>::reset(const DenseMatrix<T>& D, double TOL)
 // copy - dangerous: ignores rows & columns
 //-----------------------------------------------------------------------------
 template<typename T>
-void SparseMatrix<T>::copy(const T * ptr, INDEX rows, INDEX cols)
+void SparseMatrix<T>::copy(const T * /* ptr */, INDEX /* rows */, INDEX /* cols */)
 {
   std::cout << "SparseMatrix<T>::copy() has no effect.\n";
   throw;
diff --git a/lib/atc/SparseVector-inl.h b/lib/atc/SparseVector-inl.h
index 204c412d6d..760eb66f58 100644
--- a/lib/atc/SparseVector-inl.h
+++ b/lib/atc/SparseVector-inl.h
@@ -106,7 +106,7 @@ std::string SparseVector<T>::to_string() const
 
 // Indexes the ith component of the vector or returns zero if not found. 
 template<class T>
-T SparseVector<T>::operator()(INDEX i, INDEX j) const
+T SparseVector<T>::operator()(INDEX i, INDEX /* j */) const
 {
   STORE::const_iterator it = data_.find(i);
   if (it == data_.end()) return 0.0;
@@ -115,7 +115,7 @@ T SparseVector<T>::operator()(INDEX i, INDEX j) const
 
 // Indexes the ith component of the vector or returns zero if not found. 
 template<class T>
-T& SparseVector<T>::operator()(INDEX i, INDEX j)
+T& SparseVector<T>::operator()(INDEX i, INDEX /* j */)
 {
   return data_[i]; 
 }
@@ -129,7 +129,7 @@ template<class T> T SparseVector<T>::operator[](INDEX i) const
 // Indexes the ith component of the vector or returns zero if not found. 
 template<class T> T& SparseVector<T>::operator[](INDEX i)
 {
-  return (*this)[i];
+  return (*this)(i);
 }
 
 // Returns a pair (index, value) for a nonzero in the vector.
@@ -177,7 +177,7 @@ SparseVector<T>& SparseVector<T>::operator=(const SparseVector<T> &c)
 
 // Changes the size of the SparseVector
 template<class T>
-void SparseVector<T>::resize(INDEX nRows, INDEX nCols, bool copy)
+void SparseVector<T>::resize(INDEX nRows, INDEX /* nCols */, bool copy)
 {
   length_ = nRows;
   STORE::iterator it;
@@ -202,16 +202,14 @@ void SparseVector<T>::zero()
 
 
 template<class T>
-void SparseVector<T>::copy(const T* ptr, INDEX nRows, INDEX nCols)
+void SparseVector<T>::copy(const T* /* ptr */, INDEX /* nRows */, INDEX /* nCols */)
 {
-
 }
 
 
 template<class T>
-void SparseVector<T>::write_restart(FILE *F) const
+void SparseVector<T>::write_restart(FILE */* F */) const
 {
-
 }
 
 // writes a stream to a matlab script to recreate this variable 
diff --git a/lib/atc/SpeciesTimeIntegrator.cpp b/lib/atc/SpeciesTimeIntegrator.cpp
index bf9f1a8888..3a196e745a 100644
--- a/lib/atc/SpeciesTimeIntegrator.cpp
+++ b/lib/atc/SpeciesTimeIntegrator.cpp
@@ -37,7 +37,7 @@ namespace ATC {
   //  modify
   //    parses inputs and modifies state of the filter
   //--------------------------------------------------------
-  bool SpeciesTimeIntegrator::modify(int narg, char **arg)
+  bool SpeciesTimeIntegrator::modify(int /* narg */, char ** /* arg */)
   {
     bool match = false;
 
@@ -185,7 +185,7 @@ namespace ATC {
   //    first time integration computations 
   //    before FractionalStep step 2
   //--------------------------------------------------------
-  void SpeciesTimeIntegratorFractionalStep::pre_final_integrate1(double dt)
+  void SpeciesTimeIntegratorFractionalStep::pre_final_integrate1(double /* dt */)
   {
     // Compute MD contribution to FEM equation
     
@@ -244,7 +244,7 @@ namespace ATC {
   //--------------------------------------------------------
   //  pre_initial_integrate1
   //--------------------------------------------------------
-  void SpeciesTimeIntegratorFractionalStepFiltered::pre_final_integrate1(double dt)
+  void SpeciesTimeIntegratorFractionalStepFiltered::pre_final_integrate1(double /* dt */)
   {
   }
 
diff --git a/lib/atc/Stress.cpp b/lib/atc/Stress.cpp
index df329f9faf..906b15986e 100644
--- a/lib/atc/Stress.cpp
+++ b/lib/atc/Stress.cpp
@@ -62,7 +62,7 @@ void deformation_gradient(const DENS_MAT_VEC &du, INDEX q, MATRIX &F)
 
 // E = 1/2 stress*strain for linear elastic models
 //=============================================================================
-void Stress::elastic_energy(const FIELD_MATS &fields,
+  void Stress::elastic_energy(const FIELD_MATS & /* fields */,
                             const GRAD_FIELD_MATS &gradFields,
                             DENS_MAT &energy) const
 {
@@ -103,7 +103,7 @@ StressLinearElastic::StressLinearElastic(fstream &fileId)
 // compute the stress at N integration points from the displacement gradient
 // T_{ij} = 1/2*C_{ijkl}* (u_{k,l} + u_{l,k})
 //=============================================================================
-void StressLinearElastic::stress(const FIELD_MATS      &fields,
+  void StressLinearElastic::stress(const FIELD_MATS      & /* fields */,
                                  const GRAD_FIELD_MATS &gradFields,
                                  DENS_MAT_VEC &sigma)
 {
@@ -159,7 +159,7 @@ StressCubicElastic::StressCubicElastic(fstream &fileId)
 // compute the stress at N integration points from the displacement gradient
 // T_{ij} = 1/2*C_{ijkl}*(u_{k,l} + u_{l,k}) 
 //---------------------------------------------------------------------------
-void StressCubicElastic::stress(const FIELD_MATS      &fields,
+  void StressCubicElastic::stress(const FIELD_MATS      & /* fields */,
                                 const GRAD_FIELD_MATS &gradFields,
                                 DENS_MAT_VEC  &sigma)  
 {
@@ -200,7 +200,7 @@ void StressCubicElastic::stress(const FIELD_MATS      &fields,
 //   = 1/2 (4 c44 (u12^2 + u13^2 + u23^2) + 2 c12 (u11 u22 + u11 u33 + u22 u33) 
 //        + c11 (u11^2 + u22^2 + u33^2))
 //---------------------------------------------------------------------------
-void StressCubicElastic::elastic_energy(const FIELD_MATS      &fields,
+  void StressCubicElastic::elastic_energy(const FIELD_MATS      & /* fields */,
                                         const GRAD_FIELD_MATS &gradFields,
                                         DENS_MAT  &energy) const
 {
diff --git a/lib/atc/Stress.h b/lib/atc/Stress.h
index bf40655192..513cdb2d97 100644
--- a/lib/atc/Stress.h
+++ b/lib/atc/Stress.h
@@ -24,7 +24,7 @@ namespace ATC {
       virtual ~Stress() {};
       virtual void initialize(void){};
       //* Returns parameter values, (Nothing uses this).
-      virtual void parameters(std::map<std::string,double> &parameters) {}
+      virtual void parameters(std::map<std::string,double> & /* parameters */) {}
       //* Computes stress given a displacement gradient.
       //* Units: mvv/L^3 (i.e. for units Real: g/(mol ps^2 A^2) )
       virtual void stress(const FIELD_MATS &fields,
@@ -36,7 +36,7 @@ namespace ATC {
                                   const GRAD_FIELD_MATS &gradFields,
                                   DENS_MAT &energy) const;
       //* Returns the material tangent at a given deformation gradient.
-      virtual void tangent(const MATRIX &F, MATRIX &C) const 
+      virtual void tangent(const MATRIX & /* F */, MATRIX & /* C */) const 
         {throw ATC_Error("Stress::tangent: unimplemented function");}
   };
 
@@ -59,7 +59,7 @@ namespace ATC {
       virtual void elastic_energy(const FIELD_MATS &fields,
                           const GRAD_FIELD_MATS &gradFields,
                           DENS_MAT &energy) const;
-      virtual void tangent(const MATRIX &F, MATRIX &C) const {C=C_;}
+      virtual void tangent(const MATRIX & /* F */, MATRIX &C) const {C=C_;}
     protected:
       double c11_, c12_, c44_;
       DENS_MAT C_;
diff --git a/lib/atc/SystemProcessor.h b/lib/atc/SystemProcessor.h
deleted file mode 100644
index 9ef511f997..0000000000
--- a/lib/atc/SystemProcessor.h
+++ /dev/null
@@ -1,283 +0,0 @@
-/*
- *_________________________________________________________________________*
- *      POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE     *
- *      DESCRIPTION: SEE READ-ME                                           *
- *      FILE NAME: SystemProcessor.h                                       *
- *      AUTHORS: See Author List                                           * 
- *      GRANTS: See Grants List                                            *
- *      COPYRIGHT: (C) 2005 by Authors as listed in Author's List          *
- *      LICENSE: Please see License Agreement                              *
- *      DOWNLOAD: Free at www.rpi.edu/~anderk5                             *
- *      ADMINISTRATOR: Prof. Kurt Anderson                                 *
- *                     Computational Dynamics Lab                          *
- *                     Rensselaer Polytechnic Institute                    *
- *                     110 8th St. Troy NY 12180                           * 
- *      CONTACT:        anderk5@rpi.edu                                    *
- *_________________________________________________________________________*/
-
-#ifndef _SYS_PROCESSOR_H_
-#define _SYS_PROCESSOR_H_
-#include "poemslist.h"
-#include "poemstree.h"
-#include "POEMSChain.h"
-
-
-struct POEMSNode {
-	List<POEMSNode> links;
-	List<bool> taken;
-	int idNumber;
-	bool visited;
-	
-	~POEMSNode(){
-		for(int i = 0; i < taken.GetNumElements(); i++)
-		{
-			delete taken(i);
-		}
-	};	
-};
-
-
-class SystemProcessor{
-private:
-	Tree nodes;
-//	List<POEMSNode> forDeletion;
-	List<POEMSChain> headsOfSystems;
-	List<List<int> > ringsInSystem;
-	POEMSNode * findSingleLink(TreeNode * aNode);
-	POEMSChain * AddNewChain(POEMSNode * currentNode);
-	bool setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode);
-public:
-	SystemProcessor(void);
-	
-	~SystemProcessor(void)	{
-		headsOfSystems.DeleteValues();
-		for(int i = 0; i < ringsInSystem.GetNumElements(); i++)
-		{
-			for(int k = 0; k < ringsInSystem(i)->GetNumElements(); i++)
-			{
-				delete (*ringsInSystem(i))(k);
-			}
-		}
-	};
-	void processArray(int** links, int numLinks);
-	List<POEMSChain> * getSystemData();
-	int getNumberOfHeadChains();
-};
-
-SystemProcessor::SystemProcessor(void){
-}
-
-void SystemProcessor::processArray(int** links, int numLinks)
-{
-	bool * false_var;					//holds the value false; needed because a constant cannot be put into a list; the list requires a
-										//reference.
-	for(int i = 0; i < numLinks; i++)	//go through all the links in the input array
-	{
-		if(!nodes.Find(links[i][0]))	//if the first node in the pair is not found in the storage tree
-		{
-			POEMSNode * newNode = new POEMSNode;	//make a new node
-//			forDeletion.Append(newNode);
-			newNode->idNumber = links[i][0];		//set its ID to the value
-			newNode->visited = false;				//set it to be unvisited
-			nodes.Insert(links[i][0], links[i][0], (void *) newNode);	//and add it to the tree storage structure
-		}
-		if(!nodes.Find(links[i][1]))				//repeat process for the other half of each link
-		{
-			POEMSNode * newNode = new POEMSNode;
-//			forDeletion.Append(newNode);
-			newNode->idNumber = links[i][1];
-			newNode->visited = false;
-			nodes.Insert(links[i][1], links[i][1], (void *) newNode);
-		}
-		POEMSNode * firstNode = (POEMSNode *)nodes.Find(links[i][0]);	//now that we are sure both nodes exist,
-		POEMSNode * secondNode = (POEMSNode *)nodes.Find(links[i][1]);	//we can get both of them out of the tree
-		firstNode->links.Append(secondNode);							//and add the link from the first to the second...
-		false_var = new bool;
-		*false_var = false;												//make a new false boolean to note that the link between these two
-		firstNode->taken.Append(false_var);								//has not already been taken, and append it to the taken list
-		secondNode->links.Append(firstNode);							//repeat process for link from second node to first
-		false_var = new bool;
-		*false_var = false;
-		secondNode->taken.Append(false_var);
-	}	
-	
-	TreeNode * temp = nodes.GetRoot();							//get the root node of the node storage tree
-	POEMSNode * currentNode;
-	do
-	{
-		currentNode = findSingleLink(temp);						//find the start of the next available chain
-		if(currentNode != NULL)
-		{
-			headsOfSystems.Append(AddNewChain(currentNode));							//and add it to the headsOfSystems list of chains
-		}
-	} 
-	while(currentNode != NULL);									//repeat this until all chains have been added		
-}
-
-POEMSChain * SystemProcessor::AddNewChain(POEMSNode * currentNode){
-	if(currentNode == NULL)	//Termination condition; if the currentNode is null, then return null
-	{
-		return NULL;
-	}
-	int * tmp;
-	POEMSNode * nextNode = NULL;	//nextNode stores the proposed next node to add to the chain.  this will be checked to make sure no backtracking is occuring before being assigned as the current node.
-	POEMSChain * newChain = new POEMSChain;	//make a new POEMSChain object.  This will be the object returned
-
-	if(currentNode->links.GetNumElements() == 0)	//if we have no links from this node, then the whole chain is only one node.  Add this node to the chain and return it; mark node as visited for future reference
-	{
-		currentNode->visited = true;
-		tmp = new int;
-		*tmp = currentNode->idNumber;
-		newChain->listOfNodes.Append(tmp);
-		return newChain;
-	}
-	while(currentNode->links.GetNumElements() <= 2)	//we go until we get to a node that branches, or both branches have already been taken both branches can already be taken if a loop with no spurs is found in the input data
-	{
-		currentNode->visited = true;
-		tmp = new int;
-		*tmp = currentNode->idNumber;
-		newChain->listOfNodes.Append(tmp);	//append the current node to the chain & mark as visited
-		//cout << "Appending node " << currentNode->idNumber << " to chain" << endl;
-		nextNode = currentNode->links.GetHeadElement()->value;	//the next node is the first or second value stored in the links array
-																//of the current node.  We get the first value...
-		if(!setLinkVisited(currentNode, nextNode))					//...and see if it points back to where we came from. If it does...
-		{														//either way, we set this link as visited
-			if(currentNode->links.GetNumElements() == 1)		//if it does, then if that is the only link to this node, we're done with the chain, so append the chain to the list and return the newly created chain
-			{
-//				headsOfSystems.Append(newChain);
-				return newChain;
-			}
-			nextNode = currentNode->links.GetHeadElement()->next->value;//follow the other link if there is one, so we go down the chain
-			if(!setLinkVisited(currentNode, nextNode))				//mark link as followed, so we know not to backtrack			
-			{
-	//			headsOfSystems.Append(newChain);
-				return newChain;								//This condition, where no branches have occurred but both links have already
-																//been taken can only occur in a loop with no spurs; add this loop to the
-																//system (currently added as a chain for consistency), and return.
-			}
-		}
-		currentNode = nextNode;									//set the current node to be the next node in the chain
-	}
-	currentNode->visited = true;
-	tmp = new int;
-	*tmp = currentNode->idNumber;
-	newChain->listOfNodes.Append(tmp);		//append the last node before branch (node shared jointly with branch chains)
-																//re-mark as visited, just to make sure
-	ListElement<POEMSNode> * tempNode = currentNode->links.GetHeadElement();	//go through all of the links, one at a time that branch
-	POEMSChain * tempChain = NULL;								//temporary variable to hold data 
-	while(tempNode != NULL)										//when we have followed all links, stop
-	{
-		if(setLinkVisited(tempNode->value, currentNode))		//dont backtrack, or create closed loops
-		{
-			tempChain = AddNewChain(tempNode->value);			//Add a new chain created out of the next node down that link
-			tempChain->parentChain = newChain;					//set the parent to be this chain
-			newChain->childChains.Append(tempChain);			//append the chain to this chain's list of child chains
-		}
-		tempNode = tempNode->next;								//go to process the next chain
-	}
-	//headsOfSystems.Append(newChain);							//append this chain to the system list		
-	return newChain;	
-}
-
-POEMSNode * SystemProcessor::findSingleLink(TreeNode * aNode)
-//This function takes the root of a search tree containing POEMSNodes and returns a POEMSNode corresponding to the start of a chain in the
-//system.  It finds a node that has not been visited before, and only has one link; this node will be used as the head of the chain.
-{
-	if(aNode == NULL)	
-	{
-		return NULL;
-	}
-	POEMSNode * returnVal =  (POEMSNode *)aNode->GetAuxData();	//get the poemsnode data out of the treenode
-	POEMSNode * detectLoneLoops = NULL;							//is used to handle a loop that has no protruding chains
-	if(returnVal->visited == false)
-	{
-		detectLoneLoops = returnVal;							//if we find any node that has not been visited yet, save it
-	}
-	if(returnVal->links.GetNumElements() == 1 && returnVal->visited == false)	//see if it has one element and hasnt been visited already
-	{
-		return returnVal;														//return the node is it meets this criteria
-	}
-	returnVal = findSingleLink(aNode->Left());									//otherwise, check the left subtree
-	if(returnVal == NULL)														//and if we find nothing...
-	{
-		returnVal = findSingleLink(aNode->Right());								//check the right subtree
-	}
-	if(returnVal == NULL)														//if we could not find any chains
-	{
-		returnVal = detectLoneLoops;											//see if we found any nodes at all that havent been processed
-	}
-	return returnVal;															//return what we find (will be NULL if no new chains are 
-																				//found)
-}
-
-bool SystemProcessor::setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode)
-//setLinkVisited sets the links between these two nodes as visited. If they are already visited, it returns false.  Otherwise, it sets
-//them as visited and returns true.  This function is used to see whether a certain path has been taken already in the graph structure.
-//If it has been, then we need to know so we dont follow it again; this prevents infinite recursion when there is a loop, and prevents
-//backtracking up a chain that has already been made.  The list of booleans denoting if a link has been visited is called 'taken' and is
-//part of the POEMSNode struct.  The list is the same size as the list of pointers to other nodes, and stores the boolean visited/unvisited
-//value for that particular link.  Because each link is represented twice, (once at each node in the link), both of the boolean values need
-//to be set in the event that the link has to be set as visited.
-{
-	//cout << "Checking link between nodes " << firstNode->idNumber << " and " << secondNode->idNumber << "... ";
-	ListElement<POEMSNode> * tmp = firstNode->links.GetHeadElement();	//get the head element of the list of pointers for node 1
-	ListElement<bool> * tmp2 = firstNode->taken.GetHeadElement();		//get the head element of the list of bool isVisited flags for node 1
-	while(tmp->value != NULL || tmp2->value != NULL)					//go through untill we reach the end of the lists
-	{
-		if(tmp->value == secondNode)							//if we find the link to the other node
-		{
-			if(*(tmp2->value) == true)							//if the link has already been visited
-			{
-				 //cout << "visited already" << endl;
-				return false;									//return false to indicate that the link has been visited before this attempt
-			}
-			else												//otherwise, visit it
-			{
-				*tmp2->value = true;
-			}
-			break;
-		}
-		tmp = tmp->next;										//go check next link
-		tmp2 = tmp2->next;
-	}
-
-	tmp = secondNode->links.GetHeadElement();			//now, if the link was unvisited, we need to go set the other node's list such that
-														//it also knows this link is being visited
-	tmp2 = secondNode->taken.GetHeadElement();
-	while(tmp->value != NULL || tmp2->value != NULL)	//go through the list
-	{
-		if(tmp->value == firstNode)						//if we find the link
-		{
-			if(*(tmp2->value) == true)					//and it has already been visited, then signal an error; this shouldnt ever happen
-			{
-				cout << "Error in parsing structure! Should never reach this condition! \n" << 
-						"Record of visited links out of synch between two adjacent nodes.\n";
-				return false;
-			}
-			else
-			{
-				*tmp2->value = true;					//set the appropriate value to true to indicate this link has been visited
-			}
-			break;
-		}
-		tmp = tmp->next;
-		tmp2 = tmp2->next;
-	}
-	//cout << "not visited" << endl;
-	return true;										//return true to indicate that this is the first time the link has been visited
-}
-
-List<POEMSChain> * SystemProcessor::getSystemData(void)	//Gets the list of POEMSChains that comprise the system.  Might eventually only
-														//return chains linked to the reference plane, but currently returns every chain
-														//in the system.
-{
-	return &headsOfSystems;
-}
-
-int SystemProcessor::getNumberOfHeadChains(void) //This function isnt implemented yet, and might be taken out entirely; this was a holdover
-												//from when I intended to return an array of chain pointers, rather than a list of chains
-												//It will probably be deleted once I finish figuring out exactly what needs to be returned
-{
-	return 0;
-}
-#endif
diff --git a/lib/atc/ThermalTimeIntegrator.cpp b/lib/atc/ThermalTimeIntegrator.cpp
index 8186437bfa..f68f46b01f 100644
--- a/lib/atc/ThermalTimeIntegrator.cpp
+++ b/lib/atc/ThermalTimeIntegrator.cpp
@@ -28,7 +28,7 @@ namespace ATC {
   //  modify
   //    parses inputs and modifies state of the integrator
   //--------------------------------------------------------
-  bool ThermalTimeIntegrator::modify(int narg, char **arg)
+  bool ThermalTimeIntegrator::modify(int /* narg */, char **arg)
   {
     bool foundMatch = false;
     int argIndex = 0;
@@ -570,7 +570,7 @@ namespace ATC {
   //  compute_temperature_delta
   //--------------------------------------------------------
   void ThermalTimeIntegratorFractionalStep::compute_temperature_delta(const DENS_MAT & atomicEnergyDelta,
-                                                                      double dt)
+                                                                      double /* dt */)
   {
     DENS_MAT & myAtomicTemperatureDelta(atomicTemperatureDelta_.set_quantity());
     myAtomicTemperatureDelta = nodalAtomicEnergyOld_.quantity() + atomicEnergyDelta;
diff --git a/lib/atc/Thermostat.cpp b/lib/atc/Thermostat.cpp
index 41312bd851..0ede724371 100644
--- a/lib/atc/Thermostat.cpp
+++ b/lib/atc/Thermostat.cpp
@@ -483,7 +483,7 @@ namespace ATC {
   //            manages the solution of the
   //            thermostat equations and variables
   //--------------------------------------------------------
-  void ThermostatRescale::compute_thermostat(double dt)
+  void ThermostatRescale::compute_thermostat(double /* dt */)
   {
     // compute right-hand side
     this->set_rhs(_rhs_);
@@ -738,7 +738,7 @@ namespace ATC {
   //  Constructor
   //--------------------------------------------------------
   ThermostatGlcFs::ThermostatGlcFs(AtomicRegulator * thermostat,
-                                   int lambdaMaxIterations,
+                                   int /* lambdaMaxIterations */,
                                    const string & regulatorPrefix) :
     RegulatorMethod(thermostat,regulatorPrefix),
     lambdaSolver_(NULL),
@@ -1225,7 +1225,7 @@ namespace ATC {
   //    fixed (uncoupled) nodes
   //--------------------------------------------------------
   void ThermostatIntegratorFlux::set_thermostat_rhs(DENS_MAT & rhs,
-                                                    double dt)
+                                                    double /* dt */)
   {
     
     // only tested with flux != 0 + ess bc = 0
@@ -1586,7 +1586,7 @@ namespace ATC {
   //--------------------------------------------------------
   void ThermostatIntegratorFixed::add_to_energy(const DENS_MAT & nodalLambdaPower,
                                                 DENS_MAT & deltaEnergy,
-                                                double dt)
+                                                double /* dt */)
   {
     deltaEnergy.resize(nNodes_,1);
     
@@ -2387,7 +2387,7 @@ namespace ATC {
   //    determines the power exerted by the Hoover 
   //    thermostat at each FE node
   //--------------------------------------------------------
-  void ThermostatHooverVerlet::add_to_lambda_power(const DENS_MAT & myLambdaForce,
+  void ThermostatHooverVerlet::add_to_lambda_power(const DENS_MAT & /* myLambdaForce */,
                                                    double dt)
   {
     _myNodalLambdaPower_ = nodalAtomicHooverLambdaPower_->quantity();
@@ -2593,7 +2593,7 @@ namespace ATC {
   //    determines the power exerted by the Hoover 
   //    thermostat at each FE node
   //--------------------------------------------------------
-  void ThermostatHooverVerletFiltered::add_to_lambda_power(const DENS_MAT & myLambdaForce,
+  void ThermostatHooverVerletFiltered::add_to_lambda_power(const DENS_MAT & /* myLambdaForce */,
                                                            double dt)
   {
     _myNodalLambdaPower_ = nodalAtomicHooverLambdaPower_->quantity();
diff --git a/lib/atc/Thermostat.h b/lib/atc/Thermostat.h
index 65dbba7e15..95d2d1162d 100644
--- a/lib/atc/Thermostat.h
+++ b/lib/atc/Thermostat.h
@@ -128,7 +128,7 @@ namespace ATC {
     virtual void apply_post_corrector(double dt);
 
     /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
-    virtual void compute_boundary_flux(FIELDS & fields)
+    virtual void compute_boundary_flux(FIELDS & /* fields */)
       {boundaryFlux_[TEMPERATURE] = 0.;};
 
     /** get data for output */
@@ -540,7 +540,7 @@ namespace ATC {
     virtual void apply_post_corrector(double dt);
 
     /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
-    virtual void compute_boundary_flux(FIELDS & fields)
+    virtual void compute_boundary_flux(FIELDS & /* fields */)
       {boundaryFlux_[TEMPERATURE] = 0.;};
 
     /** determine if local shape function matrices are needed */
@@ -917,7 +917,7 @@ namespace ATC {
     virtual void finish() {};
 
     /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
-    virtual void compute_boundary_flux(FIELDS & fields)
+    virtual void compute_boundary_flux(FIELDS & /* fields */)
       {boundaryFlux_[TEMPERATURE] = 0.;};
 
   protected:
@@ -1022,7 +1022,7 @@ namespace ATC {
     virtual void finish() {};
     
     /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
-    virtual void compute_boundary_flux(FIELDS & fields)
+    virtual void compute_boundary_flux(FIELDS & /* fields */)
       {boundaryFlux_[TEMPERATURE] = 0.;};
 
   protected:
diff --git a/lib/atc/TimeFilter.cpp b/lib/atc/TimeFilter.cpp
index cb6aff9beb..08cb64c8fe 100644
--- a/lib/atc/TimeFilter.cpp
+++ b/lib/atc/TimeFilter.cpp
@@ -40,7 +40,7 @@ namespace ATC {
   //  modify
   //    parses input commands
   //--------------------------------------------------------
-  bool TimeFilterManager::modify(int narg, char ** arg)
+  bool TimeFilterManager::modify(int /* narg */, char ** arg)
   {
     bool foundMatch = false;
   
@@ -210,7 +210,7 @@ namespace ATC {
       }
       else if (filterType_ == STEP_FILTER) {
         newTimeFilter = new TimeFilterStep(*this); 
-      }
+      } else newTimeFilter = NULL;
     }
     else { // default to return base class
       newTimeFilter = new TimeFilter(*this); 
diff --git a/lib/atc/TimeFilter.h b/lib/atc/TimeFilter.h
index 6f7d65f366..321d9bb8e6 100644
--- a/lib/atc/TimeFilter.h
+++ b/lib/atc/TimeFilter.h
@@ -143,62 +143,62 @@ namespace ATC {
     virtual void initialize(){};
 
     /** pre time integration with a target for an initial condition */
-    virtual void initialize(const MATRIX & target){initialize();};
+    virtual void initialize(const MATRIX & /* target */){initialize();};
         
     /** Step 1:
         apply first step in a time filter update in the pre integration phase */
-    virtual void apply_pre_step1(MATRIX & filteredQuantity,
+    virtual void apply_pre_step1(MATRIX & /* filteredQuantity */,
                                  const MATRIX & unFilteredQuantity,
-                                 double dt)
+                                 double /* dt */)
       { TimeFilter::unFilteredQuantityOld_ = unFilteredQuantity;}
         
     /** Step 2:
          apply second step in a time filter update in pre integration phase */
-    virtual void apply_pre_step2(MATRIX & filteredQuantity,
-                                 const MATRIX & unFilteredQuantity,
-                                 double dt) {};
+    virtual void apply_pre_step2(MATRIX & /* filteredQuantity */,
+                                 const MATRIX & /* unFilteredQuantity */,
+                                 double /* dt */) {};
         
     /** Step 3:
         apply first step in a time filter update in post integration phase */
     virtual void apply_post_step1(MATRIX & filteredQuantity,
                                   const MATRIX & unFilteredQuantity,
-                                  double dt) 
+                                  double /* dt */) 
       { filteredQuantity = unFilteredQuantity;};
         
     /** Step 4:
         apply second step in a time filter update in post integration phase */
     virtual void apply_post_step2(MATRIX & filteredQuantity,
                                   const MATRIX & unFilteredQuantity,
-                                  double dt)
+                                  double /* dt */)
       { filteredQuantity = unFilteredQuantity;}
                                                   
     /** coefficient multipling unfiltered terms in apply_pre_step1 method */
-    virtual double unfiltered_coefficient_pre_s1(double dt){return 0.;};
+    virtual double unfiltered_coefficient_pre_s1(double /* dt */){return 0.;};
 
     /** coefficient multipling old filtered terms in apply_pre_step1 method */
-    virtual double filtered_coefficient_pre_s1(double dt){return 0.;};
+    virtual double filtered_coefficient_pre_s1(double /* dt */){return 0.;};
         
     /** coefficient multipling unfiltered terms in apply_post_step1 method */
-    virtual double unfiltered_coefficient_post_s1(double dt){return 0.;};
+    virtual double unfiltered_coefficient_post_s1(double /* dt */){return 0.;};
 
     /** coefficient multipling old filtered terms in apply_post_step1 method */
-    virtual double filtered_coefficient_post_s1(double dt){return 0.;};
+    virtual double filtered_coefficient_post_s1(double /* dt */){return 0.;};
         
     /** coefficient multipling unfiltered terms in apply_pre_step2 method */
-    virtual double unfiltered_coefficient_pre_s2(double dt){return 0.;};
+    virtual double unfiltered_coefficient_pre_s2(double /* dt */){return 0.;};
 
     /** coefficient multipling old filtered terms in apply_pre_step2 method */
-    virtual double filtered_coefficient_pre_s2(double dt){return 0.;};
+    virtual double filtered_coefficient_pre_s2(double /* dt */){return 0.;};
         
     /** coefficient multipling unfiltered terms in apply_post_step2 method */
-    virtual double unfiltered_coefficient_post_s2(double dt){return 0.;};
+    virtual double unfiltered_coefficient_post_s2(double /* dt */){return 0.;};
 
     /** coefficient multipling old filtered terms in apply_post_step2 method */
-    virtual double filtered_coefficient_post_s2(double dt){return 0.;};
+    virtual double filtered_coefficient_post_s2(double /* dt */){return 0.;};
   
     /** rate of filtered quantity to be called in post integration phase */
     virtual void rate(MATRIX & rate,
-                      const MATRIX & filteredQuantity,
+                      const MATRIX & /* filteredQuantity */,
                       const MATRIX & unFilteredQuantity,
                       double dt = 0.0)
       { rate = 1/dt*(unFilteredQuantity - TimeFilter::unFilteredQuantityOld_);}; 
@@ -243,30 +243,36 @@ namespace ATC {
     // destructor
     virtual ~TimeFilterExponential(){};
     /** apply first step in a time filter update in the pre integration phase */
-    virtual void apply_pre_step1(MATRIX & filteredQuantity,
-                                 const MATRIX & unFilteredQuantity,
-                                 double dt) {};
+    virtual void apply_pre_step1(MATRIX & /* filteredQuantity */,
+                                 const MATRIX & /* unFilteredQuantity */,
+                                 double /* dt */) {};
         
     /** apply second step in a time filter update in pre integration phase */
-    virtual void apply_pre_step2(MATRIX & filteredQuantity,
-                                 const MATRIX & unFilteredQuantity,
-                                 double dt) {};
+    virtual void apply_pre_step2(MATRIX & /* filteredQuantity */,
+                                 const MATRIX & /* unFilteredQuantity */,
+                                 double /* dt */) {};
         
     /** apply first step in a time filter update in post integration phase */
-    virtual void apply_post_step1(MATRIX & filteredQuantity,
-                                  const MATRIX & unFilteredQuantity,
-                                  double dt) {};
+    virtual void apply_post_step1(MATRIX & /* filteredQuantity */,
+                                  const MATRIX & /* unFilteredQuantity */,
+                                  double /* dt */) {};
         
     /** apply second step in a time filter update in post integration phase */
-    virtual void apply_post_step2(MATRIX & filteredQuantity,
-                                  const MATRIX & unFilteredQuantity,
-                                  double dt) {};
+    virtual void apply_post_step2(MATRIX & /* filteredQuantity */,
+                                  const MATRIX & /* unFilteredQuantity */,
+                                  double /* dt */) {};
 
     /** time rate of filtered quantity */
     virtual void rate(MATRIX & rate,
-        const MATRIX & filteredQuantity,
-                                const MATRIX & unfilteredQuantity,
-                                double dt = 0)
+                      const MATRIX & filteredQuantity,
+                      const MATRIX & unfilteredQuantity,
+                      double /* dt */)
+    { double tau = TimeFilter::filterScale_;
+      rate = 1/tau*(unfilteredQuantity - filteredQuantity); };
+
+    virtual void rate(MATRIX & rate,
+                      const MATRIX & filteredQuantity,
+                      const MATRIX & unfilteredQuantity)
     { double tau = TimeFilter::filterScale_;
       rate = 1/tau*(unfilteredQuantity - filteredQuantity); };
 
@@ -702,19 +708,19 @@ namespace ATC {
     virtual void initialize(const MATRIX & target);
 
     /** apply first step in a time filter update in the pre integration phase */
-    virtual void apply_pre_step1(MATRIX & filteredQuantity,
-                                 const MATRIX & unFilteredQuantity,
-                                 double dt) {};
+    virtual void apply_pre_step1(MATRIX & /* filteredQuantity */,
+                                 const MATRIX & /* unFilteredQuantity */,
+                                 double /* dt */) {};
         
     /** apply second step in a time filter update in pre integration phase */
-    virtual void apply_pre_step2(MATRIX & filteredQuantity,
-                                 const MATRIX & unFilteredQuantity,
-                                 double dt) {};
+    virtual void apply_pre_step2(MATRIX & /* filteredQuantity */,
+                                 const MATRIX & /* unFilteredQuantity */,
+                                 double /* dt */) {};
         
     /** apply first step in a time filter update in post integration phase */
-    virtual void apply_post_step1(MATRIX & filteredQuantity,
-                                  const MATRIX & unFilteredQuantity,
-                                  double dt) {};
+    virtual void apply_post_step1(MATRIX & /* filteredQuantity */,
+                                  const MATRIX & /* unFilteredQuantity */,
+                                  double /* dt */) {};
         
     /** apply second step in a time filter update in post integration phase */
     virtual void apply_post_step2(MATRIX & filteredQuantity,
@@ -726,9 +732,14 @@ namespace ATC {
 
     /** time rate of filtered quantity */
     virtual void rate(MATRIX & rate,
-        const MATRIX & filteredQuantity,
-                                const MATRIX & unfilteredQuantity,
-                                double dt = 0)
+                      const MATRIX & filteredQuantity,
+                      const MATRIX & unfilteredQuantity,
+                      double /* dt */)
+    { rate = 1/elapsedTime_*(unfilteredQuantity - filteredQuantity); }
+
+    virtual void rate(MATRIX & rate,
+                      const MATRIX & filteredQuantity,
+                      const MATRIX & unfilteredQuantity)
     { rate = 1/elapsedTime_*(unfilteredQuantity - filteredQuantity); }
 
   protected:
diff --git a/lib/atc/TimeIntegrator.h b/lib/atc/TimeIntegrator.h
index 2753386d06..ceeb7610fb 100644
--- a/lib/atc/TimeIntegrator.h
+++ b/lib/atc/TimeIntegrator.h
@@ -31,13 +31,13 @@ namespace ATC {
     virtual void construct_transfers(){};
         
    /** Predictor phase, Verlet first step for velocity */
-    virtual void init_integrate_velocity(double dt){};
+    virtual void init_integrate_velocity(double /* dt */){};
 
     /** Predictor phase, Verlet first step for position */
-    virtual void init_integrate_position(double dt){};
+    virtual void init_integrate_position(double /* dt */){};
 
     /** Corrector phase, Verlet second step for velocity */
-    virtual void final_integrate(double dt){};
+    virtual void final_integrate(double /* dt */){};
 
   };
 
@@ -128,7 +128,7 @@ namespace ATC {
     virtual ~TimeIntegrator();
         
     /** parser/modifier */
-    virtual bool modify(int narg, char **arg){return false;};
+    virtual bool modify(int /* narg */, char ** /* arg */){return false;};
 
     /** create objects to implement requested numerical method */
     virtual void construct_methods() = 0;
@@ -251,26 +251,26 @@ namespace ATC {
         
     // time step methods, corresponding to ATC_Coupling and TimeIntegrator
     /** first part of pre_initial_integrate */
-    virtual void pre_initial_integrate1(double dt){};
+    virtual void pre_initial_integrate1(double /* dt */){};
     /** second part of pre_initial_integrate */
-    virtual void pre_initial_integrate2(double dt){};
+    virtual void pre_initial_integrate2(double /* dt */){};
 
     /** first part of post_initial_integrate */
-    virtual void post_initial_integrate1(double dt){};
+    virtual void post_initial_integrate1(double /* dt */){};
     /** second part of post_initial_integrate */
-    virtual void post_initial_integrate2(double dt){};
+    virtual void post_initial_integrate2(double /* dt */){};
         
     /** first part of pre_final_integrate */
-    virtual void pre_final_integrate1(double dt){};
+    virtual void pre_final_integrate1(double /* dt */){};
     /** second part of pre_final_integrate */
-    virtual void pre_final_integrate2(double dt){};
+    virtual void pre_final_integrate2(double /* dt */){};
         
     /** first part of post_final_integrate */
-    virtual void post_final_integrate1(double dt){};
+    virtual void post_final_integrate1(double /* dt */){};
     /** second part of post_final_integrate */
-    virtual void post_final_integrate2(double dt){};
+    virtual void post_final_integrate2(double /* dt */){};
     /** third part of post_final_integrate */
-    virtual void post_final_integrate3(double dt){};
+    virtual void post_final_integrate3(double /* dt */){};
 
     /** checks to see if first RHS computation is needed */
     virtual bool has_final_predictor() {return false;};
@@ -282,9 +282,9 @@ namespace ATC {
     /** post processing step */
     virtual void post_process(){};
     /** add output data */
-    virtual void output(OUTPUT_LIST & outputData){};
+    virtual void output(OUTPUT_LIST & /* outputData */){};
     /** pack persistent fields */
-    virtual void pack_fields(RESTART_LIST & data){};
+    virtual void pack_fields(RESTART_LIST & /* data */){};
 
     /** finalize any states */
     virtual void finish(){};
diff --git a/lib/atc/TransferLibrary.cpp b/lib/atc/TransferLibrary.cpp
index a6bba5ca23..d0db0076d7 100644
--- a/lib/atc/TransferLibrary.cpp
+++ b/lib/atc/TransferLibrary.cpp
@@ -705,7 +705,7 @@ namespace ATC {
   //--------------------------------------------------------
   //  Constructor
   //--------------------------------------------------------
-  ReducedSparseMatrix::ReducedSparseMatrix(ATC_Method * atc,
+  ReducedSparseMatrix::ReducedSparseMatrix(ATC_Method * /* atc */,
                                            SPAR_MAN * source,
                                            LargeToSmallAtomMap * map) :
     SparseMatrixTransfer<double>(),
@@ -782,7 +782,7 @@ namespace ATC {
   //--------------------------------------------------------
   //  Constructor
   //--------------------------------------------------------
-  RowMappedSparseMatrixVector::RowMappedSparseMatrixVector(ATC_Method * atc,
+  RowMappedSparseMatrixVector::RowMappedSparseMatrixVector(ATC_Method * /* atc */,
                                                            VectorDependencyManager<SPAR_MAT * > * source,
                                                            LargeToSmallAtomMap * map) :
     VectorTransfer<SPAR_MAT * >(),
@@ -846,7 +846,7 @@ namespace ATC {
   //--------------------------------------------------------
   //  Constructor
   //--------------------------------------------------------
-  MappedDiagonalMatrix::MappedDiagonalMatrix(ATC_Method * atc,
+  MappedDiagonalMatrix::MappedDiagonalMatrix(ATC_Method * /* atc */,
                                              DIAG_MAN * source,
                                              LargeToSmallAtomMap * map) :
     DiagonalMatrixTransfer<double>(),
@@ -892,7 +892,7 @@ namespace ATC {
   //--------------------------------------------------------
   //  Constructor
   //--------------------------------------------------------
-  MappedQuantity::MappedQuantity(ATC_Method * atc,
+  MappedQuantity::MappedQuantity(ATC_Method * /* atc */,
                                  DENS_MAN * source,
                                  LargeToSmallMap * map) :
     DenseMatrixTransfer<double>(),
diff --git a/lib/atc/TransferOperator.cpp b/lib/atc/TransferOperator.cpp
index efa4bc1da2..ab91141c6a 100644
--- a/lib/atc/TransferOperator.cpp
+++ b/lib/atc/TransferOperator.cpp
@@ -868,7 +868,7 @@ namespace ATC {
   //--------------------------------------------------------
   // Constructor
   //--------------------------------------------------------
-  MatToGradBySparse::MatToGradBySparse(ATC_Method * atc,
+  MatToGradBySparse::MatToGradBySparse(ATC_Method * /* atc */,
                                        DENS_MAN * source,
                                        VectorDependencyManager<SPAR_MAT * > * gradientMatrices) :
     MatToMatTransfer<double>(source),
diff --git a/lib/atc/TransferOperator.h b/lib/atc/TransferOperator.h
index 333e8d2a69..0ab92805be 100644
--- a/lib/atc/TransferOperator.h
+++ b/lib/atc/TransferOperator.h
@@ -42,43 +42,43 @@ namespace ATC {
 
 
         /** sets the quantity to a given value */
-    virtual void operator=(const DenseMatrix<T> & target)
+    virtual void operator=(const DenseMatrix<T> & /* target */)
       {throw ATC_Error("DenseMatrixTransfer::set_quantity - Cannot modify transfer-based matrices");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const T & target)
+    virtual void operator=(const T & /* target */)
       {throw ATC_Error("DenseMatrixTransfer::operator= - Cannot modify transfer-based matrices");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const DenseMatrix<T> & addition)
+    virtual void operator+=(const DenseMatrix<T> & /* addition */)
       {throw ATC_Error("DenseMatrixTransfer::operator+= - Cannot modify transfer-based matrices");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(T addition)
+    virtual void operator+=(T /* addition */)
       {throw ATC_Error("DenseMatrixTransfer::operator+= - Cannot modify transfer-based matrices");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const DenseMatrix<T> & subtraction)
+    virtual void operator-=(const DenseMatrix<T> & /* subtraction */)
       {throw ATC_Error("DenseMatrixTransfer::operator-= - Cannot modify transfer-based matrices");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(T subtraction)
+    virtual void operator-=(T /* subtraction */)
       {throw ATC_Error("DenseMatrixTransfer::operator-= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const DenseMatrix<T> & multiplier)
+    virtual void operator*=(const DenseMatrix<T> & /* multiplier */)
       {throw ATC_Error("DenseMatrixTransfer::operator*= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(T multiplier)
+    virtual void operator*=(T /* multiplier */)
       {throw ATC_Error("DenseMatrixTransfer::operator*= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const DenseMatrix<T> & divisor)
+    virtual void operator/=(const DenseMatrix<T> & /* divisor */)
       {throw ATC_Error("DenseMatrixTransfer::operator/= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(T divisor)
+    virtual void operator/=(T /* divisor */)
       {throw ATC_Error("DenseMatrixTransfer::operator/= - Cannot modify transfer-based matrices");};
 
   protected:
@@ -113,43 +113,43 @@ namespace ATC {
 
 
         /** sets the quantity to a given value */
-    virtual void operator=(const SparseMatrix<T> & target)
+    virtual void operator=(const SparseMatrix<T> & /* target */)
       {throw ATC_Error("SparseMatrixTransfer::set_quantity - Cannot modify transfer-based matrices");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const T & target)
+    virtual void operator=(const T & /* target */)
       {throw ATC_Error("SparseMatrixTransfer::operator= - Cannot modify transfer-based matrices");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const SparseMatrix<T> & addition)
+    virtual void operator+=(const SparseMatrix<T> & /* addition */)
       {throw ATC_Error("SparseMatrixTransfer::operator+= - Cannot modify transfer-based matrices");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(T addition)
+    virtual void operator+=(T /* addition */)
       {throw ATC_Error("SparseMatrixTransfer::operator+= - Cannot modify transfer-based matrices");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const SparseMatrix<T> & subtraction)
+    virtual void operator-=(const SparseMatrix<T> & /* subtraction */)
       {throw ATC_Error("SparseMatrixTransfer::operator-= - Cannot modify transfer-based matrices");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(T subtraction)
+    virtual void operator-=(T /* subtraction */)
       {throw ATC_Error("SparseMatrixTransfer::operator-= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const SparseMatrix<T> & multiplier)
+    virtual void operator*=(const SparseMatrix<T> & /* multiplier */)
       {throw ATC_Error("SparseMatrixTransfer::operator*= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(T multiplier)
+    virtual void operator*=(T /* multiplier */)
       {throw ATC_Error("SparseMatrixTransfer::operator*= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const SparseMatrix<T> & divisor)
+    virtual void operator/=(const SparseMatrix<T> & /* divisor */)
       {throw ATC_Error("SparseMatrixTransfer::operator/= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(T divisor)
+    virtual void operator/=(T /* divisor */)
       {throw ATC_Error("SparseMatrixTransfer::operator/= - Cannot modify transfer-based matrices");};
 
   protected:
@@ -184,43 +184,43 @@ namespace ATC {
 
 
         /** sets the quantity to a given value */
-    virtual void operator=(const DiagonalMatrix<T> & target)
+    virtual void operator=(const DiagonalMatrix<T> & /* target */)
       {throw ATC_Error("DiagonalMatrixTransfer::set_quantity - Cannot modify transfer-based matrices");};
 
     /** sets the quantity to a given constant value */
-    virtual void operator=(const T & target)
+    virtual void operator=(const T & /* target */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator= - Cannot modify transfer-based matrices");};
 
     /** adds the given data to the Lammps quantity */
-    virtual void operator+=(const DiagonalMatrix<T> & addition)
+    virtual void operator+=(const DiagonalMatrix<T> & /* addition */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator+= - Cannot modify transfer-based matrices");};
 
     /** adds the scalar data to the Lammps quantity for AtC atoms */
-    virtual void operator+=(T addition)
+    virtual void operator+=(T /* addition */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator+= - Cannot modify transfer-based matrices");};
 
     /** subtracts the given data from the Lammps quantity */
-    virtual void operator-=(const DiagonalMatrix<T> & subtraction)
+    virtual void operator-=(const DiagonalMatrix<T> & /* subtraction */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator-= - Cannot modify transfer-based matrices");};
 
     /** subtracts the scalar data from the Lammps quantity for AtC atoms */
-    virtual void operator-=(T subtraction)
+    virtual void operator-=(T /* subtraction */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator-= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(const DiagonalMatrix<T> & multiplier)
+    virtual void operator*=(const DiagonalMatrix<T> & /* multiplier */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator*= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator*=(T multiplier)
+    virtual void operator*=(T /* multiplier */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator*= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(const DiagonalMatrix<T> & divisor)
+    virtual void operator/=(const DiagonalMatrix<T> & /* divisor */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator/= - Cannot modify transfer-based matrices");};
 
     /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */
-    virtual void operator/=(T divisor)
+    virtual void operator/=(T /* divisor */)
       {throw ATC_Error("DiagonalMatrixTransfer::operator/= - Cannot modify transfer-based matrices");};
 
   protected:
diff --git a/lib/atc/Utility.h b/lib/atc/Utility.h
index d975d4804a..2c0ea7270f 100644
--- a/lib/atc/Utility.h
+++ b/lib/atc/Utility.h
@@ -59,10 +59,10 @@ namespace ATC_Utility
     return ( (dblL >   dblR) ||
             ((dblL <= (dblR + \
                        std::numeric_limits<double>::epsilon() * \
-                       tolMult * std::max(abs(dblL), abs(dblR)))) && 
+                       tolMult * std::max(fabs(dblL), fabs(dblR)))) && 
              (dblR <= (dblL + \
                        std::numeric_limits<double>::epsilon() * \
-                       tolMult * std::max(abs(dblL), abs(dblR))))));
+                       tolMult * std::max(fabs(dblL), fabs(dblR))))));
   }
 
   inline double tolerance(double x, double tol = parsetol_) {
diff --git a/lib/atc/Vector.h b/lib/atc/Vector.h
index ff04b0720d..884a080d7d 100644
--- a/lib/atc/Vector.h
+++ b/lib/atc/Vector.h
@@ -61,7 +61,7 @@ public:
 //* performs a matrix-vector multiply with default naive implementation
 template<typename T>
 void MultMv(const Matrix<T> &A, const Vector<T> &v, DenseVector<T> &c, 
-            const bool At, T a, T b)
+            const bool At, T /* a */, T b)
 {
   const INDEX sA[2] = {A.nRows(), A.nCols()};  // m is sA[At] k is sA[!At]
   const INDEX M=sA[At], K=sA[!At];
diff --git a/lib/atc/ViscousStress.cpp b/lib/atc/ViscousStress.cpp
index 4053cf6cb7..305769af68 100644
--- a/lib/atc/ViscousStress.cpp
+++ b/lib/atc/ViscousStress.cpp
@@ -34,7 +34,7 @@ ViscousStressConstant::ViscousStressConstant(fstream &fileId)
 // compute the stress at N integration points from the velocity gradients
 // T_{ij} = viscosity * du_i/dx_j
 //=============================================================================
-void ViscousStressConstant::viscous_stress(const FIELD_MATS      &fields,
+  void ViscousStressConstant::viscous_stress(const FIELD_MATS      & /* fields */,
                                            const GRAD_FIELD_MATS &gradFields,
                                            DENS_MAT_VEC &sigma)
 {
diff --git a/lib/atc/ViscousStress.h b/lib/atc/ViscousStress.h
index d9da270452..1636aa5bc3 100644
--- a/lib/atc/ViscousStress.h
+++ b/lib/atc/ViscousStress.h
@@ -22,17 +22,17 @@ namespace ATC {
       virtual ~ViscousStress() {};
       virtual void initialize(void){};
       //* Returns parameter values, (Nothing uses this).
-      virtual void parameters(std::map<std::string,double> &parameters) {}
+      virtual void parameters(std::map<std::string,double> & /* parameters */) {}
       //* Computes viscous stress given a strain rate tensor.
       //* Units: mvv/L^3 (i.e. for units Real: g/(mol ps^2 A^2) )
       virtual void viscous_stress(const FIELD_MATS &fields,
                                   const GRAD_FIELD_MATS &gradFields,
                                   DENS_MAT_VEC &stress)=0; 
-      virtual void viscosity(const FIELD_MATS & fields,
-                             DENS_MAT & coefs) const
+      virtual void viscosity(const FIELD_MATS & /* fields */,
+                             DENS_MAT & /* coefs */) const
         {throw ATC_Error("ViscousStress::viscosity: unimplemented function");}
       //* Returns the derivative of the stress tensor for a given strain-rate tensor.
-      virtual void tangent(const MATRIX &F, MATRIX &C) const 
+      virtual void tangent(const MATRIX & /* F */, MATRIX & /* C */) const 
         {throw ATC_Error("ViscousStress::tangent: unimplemented function");}
   };
 
diff --git a/lib/atc/WeakEquation.h b/lib/atc/WeakEquation.h
index 84f2b5bb48..bf349a2a53 100644
--- a/lib/atc/WeakEquation.h
+++ b/lib/atc/WeakEquation.h
@@ -32,52 +32,52 @@ class WeakEquation {
   
   /** integrand  that used to form the energy */
   virtual bool has_E_integrand(void) const {return false;}
-  virtual void E_integrand(const FIELD_MATS &fields,
-                           const GRAD_FIELD_MATS &grad_fields,
-                           const Material * material,
-                           DENS_MAT &energy ) const {};
+  virtual void E_integrand(const FIELD_MATS & /* fields */,
+                           const GRAD_FIELD_MATS & /* grad_fields */,
+                           const Material * /* material */,
+                           DENS_MAT & /* energy */ ) const {};
 
   /** density that used to form the mass matrix */
   virtual bool has_M_integrand(void) const {return false;}
-  virtual void M_integrand(const FIELD_MATS &fields,
-                           const Material * material,
-                           DENS_MAT &density ) const {}; 
+  virtual void M_integrand(const FIELD_MATS & /* fields */,
+                           const Material * /* material */,
+                           DENS_MAT & /* density */ ) const {}; 
 
   /** flux that is integrated with B = Grad N as its weight */
   virtual bool has_B_integrand(void) const {return false;}
-  virtual void B_integrand(const FIELD_MATS &fields,
-                           const GRAD_FIELD_MATS &grad_fields,
-                           const Material * material,
-                           DENS_MAT_VEC &flux) const {};
+  virtual void B_integrand(const FIELD_MATS & /* fields */,
+                           const GRAD_FIELD_MATS & /* grad_fields */,
+                           const Material * /* material */,
+                           DENS_MAT_VEC & /* flux */) const {};
 
   /** flux that is integrated with N as its weight */
   virtual bool has_N_integrand(void) const {return false;}
   // N_integrand bool is for masking in FE_Engine
-  virtual bool N_integrand(const FIELD_MATS &fields, 
-                           const GRAD_FIELD_MATS &grad_fields,
-                           const Material * material,
-                           DENS_MAT &flux) const {return false;};
+  virtual bool N_integrand(const FIELD_MATS & /* fields */, 
+                           const GRAD_FIELD_MATS & /* grad_fields */,
+                           const Material * /* material */,
+                           DENS_MAT & /* flux */) const {return false;};
 
   /** stiffness matrix */ 
 
   // linear
-  virtual void BB_tangent_coefficients(const FieldName field,
-                                       const Material * material,
-                                       DENS_MAT &coefs) const {};
-  virtual void NN_tangent_coefficients(const FieldName field,
-                                       const Material * material,
-                                       DENS_MAT &coefs) const {};
+  virtual void BB_tangent_coefficients(const FieldName /* field */,
+                                       const Material * /* material */,
+                                       DENS_MAT & /* coefs */) const {};
+  virtual void NN_tangent_coefficients(const FieldName /* field */,
+                                       const Material * /* material */,
+                                       DENS_MAT & /* coefs */) const {};
   // non-linear
   virtual bool has_BB_tangent_coefficients(void) const {return false;}
-  virtual void BB_tangent_coefficients(const FieldName field,
-                                       const FIELD_MATS &fields, 
-                                       const Material * material,
-                                       DENS_MAT &coefs) const {};
+  virtual void BB_tangent_coefficients(const FieldName /* field */,
+                                       const FIELD_MATS & /* fields */, 
+                                       const Material * /* material */,
+                                       DENS_MAT & /* coefs */) const {};
   virtual bool has_NN_tangent_coefficients(void) const {return false;}
-  virtual void NN_tangent_coefficients(const FieldName field,
-                                       const FIELD_MATS &fields, 
-                                       const Material * material,
-                                       DENS_MAT &coefs) const {};
+  virtual void NN_tangent_coefficients(const FieldName /* field */,
+                                       const FIELD_MATS & /* fields */, 
+                                       const Material * /* material */,
+                                       DENS_MAT & /* coefs */) const {};
   
   /** type of equation */
   PDE_Type type(void) const {return type_;}
diff --git a/lib/atc/WeakEquationChargeDiffusion.cpp b/lib/atc/WeakEquationChargeDiffusion.cpp
index 05152579fc..6593e90622 100644
--- a/lib/atc/WeakEquationChargeDiffusion.cpp
+++ b/lib/atc/WeakEquationChargeDiffusion.cpp
@@ -26,7 +26,7 @@ WeakEquationChargeDiffusion::~WeakEquationChargeDiffusion(void)
 //---------------------------------------------------------------------
 void WeakEquationChargeDiffusion::M_integrand(
   const FIELD_MATS &fields,
-  const Material * material,
+  const Material * /* material */,
   DENS_MAT & capacity ) const
 {
   FIELD_MATS::const_iterator rhoField = fields.find(CHARGE_DENSITY);
diff --git a/lib/atc/WeakEquationDiffusion.cpp b/lib/atc/WeakEquationDiffusion.cpp
index 1af7d2f7f3..5470d30b1b 100644
--- a/lib/atc/WeakEquationDiffusion.cpp
+++ b/lib/atc/WeakEquationDiffusion.cpp
@@ -26,7 +26,7 @@ WeakEquationDiffusion::~WeakEquationDiffusion(void)
 //---------------------------------------------------------------------
 void WeakEquationDiffusion::M_integrand(
   const FIELD_MATS &fields,
-  const Material * material,
+  const Material * /* material */,
   DENS_MAT & capacity ) const
 {
   FIELD_MATS::const_iterator rhoField = fields.find(SPECIES_CONCENTRATION);
@@ -38,10 +38,10 @@ void WeakEquationDiffusion::M_integrand(
 //  compute flux
 //--------------------------------------------------------------
 void WeakEquationDiffusion::B_integrand(
-  const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
-  const Material * material,
-  DENS_MAT_VEC &flux) const
+  const FIELD_MATS & /* fields */,
+  const GRAD_FIELD_MATS & /* grad_fields */,
+  const Material * /* material */,
+  DENS_MAT_VEC & /* flux */) const
 {
 //  material->diffusion_flux(fields, grad_fields, flux[SPECIES_CONCENTRATION]);
 }
diff --git a/lib/atc/WeakEquationElectronContinuity.cpp b/lib/atc/WeakEquationElectronContinuity.cpp
index 3b2a18b0f2..193da6e2c7 100644
--- a/lib/atc/WeakEquationElectronContinuity.cpp
+++ b/lib/atc/WeakEquationElectronContinuity.cpp
@@ -24,7 +24,7 @@ WeakEquationElectronContinuity::~WeakEquationElectronContinuity(void)
 //---------------------------------------------------------------------
 void WeakEquationElectronContinuity::M_integrand(
   const FIELD_MATS &fields,
-  const Material * material,
+  const Material * /* material */,
   DENS_MAT & density ) const
 {
   FIELD_MATS::const_iterator nField = fields.find(ELECTRON_DENSITY);
@@ -72,7 +72,7 @@ WeakEquationElectronEquilibrium::~WeakEquationElectronEquilibrium(void)
 //---------------------------------------------------------------------
 void WeakEquationElectronEquilibrium::M_integrand(
   const FIELD_MATS &fields,
-  const Material * material,
+  const Material * /* material */,
   DENS_MAT & density ) const
 {
   FIELD_MATS::const_iterator nField = fields.find(ELECTRON_DENSITY);
@@ -85,7 +85,7 @@ void WeakEquationElectronEquilibrium::M_integrand(
 
 bool WeakEquationElectronEquilibrium::N_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
+  const GRAD_FIELD_MATS & /* grad_fields */,
   const Material * material,
   DENS_MAT &flux) const
 {
diff --git a/lib/atc/WeakEquationElectronMomentum.cpp b/lib/atc/WeakEquationElectronMomentum.cpp
index 37484f61d5..c4728c7bd5 100644
--- a/lib/atc/WeakEquationElectronMomentum.cpp
+++ b/lib/atc/WeakEquationElectronMomentum.cpp
@@ -79,7 +79,7 @@ void WeakEquationElectronMomentum::M_integrand(
 //--------------------------------------------------------------
 void WeakEquationElectronMomentum::B_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
+  const GRAD_FIELD_MATS & /* grad_fields */,
   const Material * material,
   DENS_MAT_VEC &flux) const
 {
diff --git a/lib/atc/WeakEquationElectronMomentum.h b/lib/atc/WeakEquationElectronMomentum.h
index a3bc62bef7..0010b012cd 100644
--- a/lib/atc/WeakEquationElectronMomentum.h
+++ b/lib/atc/WeakEquationElectronMomentum.h
@@ -78,10 +78,10 @@ namespace ATC{
     
     /** flux that is integrated with grad N as its weight */
     virtual bool has_B_integrand(void) const {return false;}
-    virtual void B_integrand(const FIELD_MATS &fields,
-                             const GRAD_FIELD_MATS &grad_fields,
-                             const Material * material,
-                             DENS_MAT_VEC &flux) const {};
+    virtual void B_integrand(const FIELD_MATS & /* fields */,
+                             const GRAD_FIELD_MATS & /* grad_fields */,
+                             const Material * /* material */,
+                             DENS_MAT_VEC &/* flux */) const {};
     
     /** flux that is integrated with N as its weight */
     virtual bool has_N_integrand(void) const {return true;}
diff --git a/lib/atc/WeakEquationElectronTemperature.cpp b/lib/atc/WeakEquationElectronTemperature.cpp
index 97a21628d8..72315dd1e6 100644
--- a/lib/atc/WeakEquationElectronTemperature.cpp
+++ b/lib/atc/WeakEquationElectronTemperature.cpp
@@ -26,7 +26,7 @@ WeakEquationElectronTemperature::~WeakEquationElectronTemperature(void)
 //---------------------------------------------------------------------
 void WeakEquationElectronTemperature::E_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
+  const GRAD_FIELD_MATS & /* grad_fields */,
   const Material * material,
   DENS_MAT & energy ) const
 {
@@ -61,7 +61,7 @@ void WeakEquationElectronTemperature::B_integrand(
 //---------------------------------------------------------------------
 bool WeakEquationElectronTemperature::N_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
+  const GRAD_FIELD_MATS & /* grad_fields */,
   const Material * material,
   DENS_MAT &flux) const
 {
diff --git a/lib/atc/WeakEquationMassDiffusion.cpp b/lib/atc/WeakEquationMassDiffusion.cpp
index 5e4445442b..47ca01bbe4 100644
--- a/lib/atc/WeakEquationMassDiffusion.cpp
+++ b/lib/atc/WeakEquationMassDiffusion.cpp
@@ -26,7 +26,7 @@ WeakEquationMassDiffusion::~WeakEquationMassDiffusion(void)
 //---------------------------------------------------------------------
 void WeakEquationMassDiffusion::M_integrand(
   const FIELD_MATS &fields,
-  const Material * material,
+  const Material * /* material */,
   DENS_MAT & capacity ) const
 {
   FIELD_MATS::const_iterator dField = fields.find(MASS_DENSITY);
@@ -38,10 +38,10 @@ void WeakEquationMassDiffusion::M_integrand(
 //  compute flux
 //--------------------------------------------------------------
 void WeakEquationMassDiffusion::B_integrand(
-  const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
-  const Material * material,
-  DENS_MAT_VEC &flux) const
+  const FIELD_MATS & /* fields */,
+  const GRAD_FIELD_MATS & /* grad_fields */,
+  const Material * /* material */,
+  DENS_MAT_VEC & /* flux */) const
 {
 //  material->mass_flux(fields, grad_fields, flux[MASS_DENSITY]);
 }
diff --git a/lib/atc/WeakEquationMomentum.cpp b/lib/atc/WeakEquationMomentum.cpp
index 04e52b6c9c..39400d3167 100644
--- a/lib/atc/WeakEquationMomentum.cpp
+++ b/lib/atc/WeakEquationMomentum.cpp
@@ -45,7 +45,7 @@ void WeakEquationMomentum::B_integrand(
 //--------------------------------------------------------------
 bool WeakEquationMomentum::N_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
+  const GRAD_FIELD_MATS & /* grad_fields */,
   const Material * material,
   DENS_MAT &flux) const
 {
@@ -137,7 +137,7 @@ void WeakEquationMomentumDiffusion::B_integrand(
 
 //---------------------------------------------------------------------
 void WeakEquationMomentumDiffusion::BB_tangent_coefficients(
-  const FieldName field,
+  const FieldName /* field */,
   const FIELD_MATS &fields,
   const Material* material,
   DENS_MAT &coefs) const
@@ -148,7 +148,7 @@ void WeakEquationMomentumDiffusion::BB_tangent_coefficients(
 //--------------------------------------------------------------
 bool WeakEquationMomentumDiffusion::N_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
+  const GRAD_FIELD_MATS & /* grad_fields */,
   const Material * material,
   DENS_MAT &flux) const
 {
diff --git a/lib/atc/WeakEquationPhononTemperature.cpp b/lib/atc/WeakEquationPhononTemperature.cpp
index aef1cd4c53..fe1ac894bd 100644
--- a/lib/atc/WeakEquationPhononTemperature.cpp
+++ b/lib/atc/WeakEquationPhononTemperature.cpp
@@ -26,7 +26,7 @@ WeakEquationPhononTemperature::~WeakEquationPhononTemperature(void)
 //---------------------------------------------------------------------
 void WeakEquationPhononTemperature::E_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &gradFields,
+  const GRAD_FIELD_MATS & /* gradFields */,
   const Material * material,
   DENS_MAT &energy) const
 {
diff --git a/lib/atc/WeakEquationPoisson.cpp b/lib/atc/WeakEquationPoisson.cpp
index 02e8655dc0..4440c02bd3 100644
--- a/lib/atc/WeakEquationPoisson.cpp
+++ b/lib/atc/WeakEquationPoisson.cpp
@@ -36,7 +36,7 @@ void WeakEquationPoisson::B_integrand(
 
 //---------------------------------------------------------------------
 void WeakEquationPoisson::BB_tangent_coefficients(
-  const FieldName field,
+  const FieldName /* field */,
   const FIELD_MATS &fields,
   const Material* material,
   DENS_MAT &coefs) const
@@ -47,7 +47,7 @@ void WeakEquationPoisson::BB_tangent_coefficients(
 //---------------------------------------------------------------------
 bool WeakEquationPoisson::N_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
+  const GRAD_FIELD_MATS & /* grad_fields */,
   const Material * material,
   DENS_MAT &flux) const
 {
@@ -56,7 +56,7 @@ bool WeakEquationPoisson::N_integrand(
 
 //---------------------------------------------------------------------
 void WeakEquationPoisson::NN_tangent_coefficients(
-  const FieldName field,
+  const FieldName /* field */,
   const FIELD_MATS &fields,
   const Material* material,
   DENS_MAT &coefs) const
@@ -78,8 +78,8 @@ WeakEquationPoissonConstantRHS::WeakEquationPoissonConstantRHS()
 //---------------------------------------------------------------------
 bool WeakEquationPoissonConstantRHS::N_integrand(
   const FIELD_MATS &fields,
-  const GRAD_FIELD_MATS &grad_fields,
-  const Material * material,
+  const GRAD_FIELD_MATS & /* grad_fields */,
+  const Material * /* material */,
   DENS_MAT &flux) const
 
 {
diff --git a/lib/atc/WeakEquationPoisson.h b/lib/atc/WeakEquationPoisson.h
index 667034525d..b004b350ce 100644
--- a/lib/atc/WeakEquationPoisson.h
+++ b/lib/atc/WeakEquationPoisson.h
@@ -98,10 +98,10 @@ class WeakEquationPoissonConstantRHS : public WeakEquationPoisson {
 
   /** rhs is constant */
   virtual bool has_NN_tangent_coefficients(void) const {return false;}
-  virtual void NN_tangent_coefficients(const FieldName field,
-                                       const FIELD_MATS &fields,
-                                       const Material * material,
-                                       DENS_MAT &coefs) const {};
+  virtual void NN_tangent_coefficients(const FieldName /* field */,
+                                       const FIELD_MATS & /* fields */,
+                                       const Material * /* material */,
+                                       DENS_MAT & /* coefs */) const {};
 
   virtual std::set<std::string> needs_material_functions(void) const
   {
diff --git a/lib/atc/WeakEquationSchrodinger.cpp b/lib/atc/WeakEquationSchrodinger.cpp
index 3663b8c806..07497b1fd5 100644
--- a/lib/atc/WeakEquationSchrodinger.cpp
+++ b/lib/atc/WeakEquationSchrodinger.cpp
@@ -23,7 +23,7 @@ WeakEquationSchrodinger::~WeakEquationSchrodinger(void)
 
 //---------------------------------------------------------------------
 void WeakEquationSchrodinger::BB_tangent_coefficients(
-  const FieldName field,
+  const FieldName /* field */,
   const FIELD_MATS & fields,
   const Material* material,
   DENS_MAT &coefs) const
@@ -33,7 +33,7 @@ void WeakEquationSchrodinger::BB_tangent_coefficients(
 //---------------------------------------------------------------------
 
 void WeakEquationSchrodinger::NN_tangent_coefficients(
-  const FieldName field,
+  const FieldName /* field */,
   const FIELD_MATS & fields,
   const Material* material,
   DENS_MAT & V) const
diff --git a/lib/awpmd/ivutils/include/logexc.h b/lib/awpmd/ivutils/include/logexc.h
index 400b3fb7d2..4c8364671a 100644
--- a/lib/awpmd/ivutils/include/logexc.h
+++ b/lib/awpmd/ivutils/include/logexc.h
@@ -43,12 +43,12 @@ enum vbLEVELS{
 template<class exc_t>
 struct log_exception_traits{
   /// exeption level according to the vbLEVELS
-  static int level(const exc_t &signal){ return vblFATAL; } 
+  static int level(const exc_t & /* signal */){ return vblFATAL; } 
   /// the string name of exception category
-  static string name(const exc_t &signal){ return typeid(exc_t).name();}
+  static string name(const exc_t & /* signal */){ return typeid(exc_t).name();}
   /// adds some more explanations to the description
   /// default behaviour: nothing done
-  static exc_t add_words(const exc_t &orig, const char *words){
+  static exc_t add_words(const exc_t &orig, const char * /* words */){
     return orig;
   }
 };
@@ -80,7 +80,7 @@ struct log_exception_traits<int>{
       return "integer exception";*/
   }
   /// default behaviour: nothing done
-  static int add_words(const int &orig, const char *words){
+  static int add_words(const int &orig, const char * /* words */){
     return orig;
   }
 };
@@ -90,14 +90,11 @@ template<>
 struct log_exception_traits<enum vbLEVELS>{
   static int level(const enum vbLEVELS &signal){ return log_exception_traits<int>::level(signal); } 
   static string name(const enum vbLEVELS &signal){ return log_exception_traits<int>::name(signal); } 
-  static enum vbLEVELS add_words(const enum vbLEVELS &orig, const char *words){
+  static enum vbLEVELS add_words(const enum vbLEVELS &orig, const char * /* words */){
     return orig;
   }
 };
 
-
-
-
 /// Logger class to control (computational) function behaviour when something requiring user attention has happened.
 /// message(signal,errcode, text) is used to either throw an exception or return errorcode
 /// At first, the the level of error is determined via log_exception_traits<>::level(signal)
@@ -205,7 +202,7 @@ public:
     return errcode;
   }
 
-  virtual void log_text(int level, const char *messtype, const char *messtext){
+  virtual void log_text(int /* level */, const char *messtype, const char *messtext){
     if(descriptor!="") // descriptor is used as header
       printf("%s:\n",descriptor.c_str());
     if(string(messtype)!=string(""))
diff --git a/lib/awpmd/ivutils/include/pairhash.h b/lib/awpmd/ivutils/include/pairhash.h
index a4eed54385..1fbc1b8b64 100644
--- a/lib/awpmd/ivutils/include/pairhash.h
+++ b/lib/awpmd/ivutils/include/pairhash.h
@@ -324,7 +324,7 @@ public:
   }
 
   //e initializes by unmanaged pointer
-  sqmatrix(size_t n, T *ptr):size(n){ 
+  sqmatrix(size_t n, T * /* ptr */):size(n){ 
     init(n);
   }
 
diff --git a/lib/awpmd/ivutils/include/wavepacket.h b/lib/awpmd/ivutils/include/wavepacket.h
index e24ac4e237..c4f3837022 100644
--- a/lib/awpmd/ivutils/include/wavepacket.h
+++ b/lib/awpmd/ivutils/include/wavepacket.h
@@ -24,7 +24,7 @@ class WavePacket;
 ///\en Template for v=der operation in \ref Wavepacket::int2phys_der()
 template<class Type>
 struct eq_second : public binary_function <Type, Type, Type> {
-  Type operator()(const Type& _Left, const Type& _Right) const{
+  Type operator()(const Type& /* _Left */, const Type& _Right) const{
     return _Right;
   }
 };
@@ -32,7 +32,7 @@ struct eq_second : public binary_function <Type, Type, Type> {
 ///\en Template for v=-der operation in \ref Wavepacket::int2phys_der()
 template<class Type>
 struct eq_minus_second : public binary_function <Type, Type, Type> {
-  Type operator()(const Type& _Left, const Type& _Right) const{
+  Type operator()(const Type& /* _Left */, const Type& _Right) const{
     return -_Right;
   }
 };
diff --git a/lib/awpmd/systems/interact/TCP/wpmd.h b/lib/awpmd/systems/interact/TCP/wpmd.h
index c0132bd6e3..bcb99e2092 100644
--- a/lib/awpmd/systems/interact/TCP/wpmd.h
+++ b/lib/awpmd/systems/interact/TCP/wpmd.h
@@ -425,7 +425,7 @@ public:
   ///    calculated only once based on particle tags)
   ///    If force multiplier is zero, then the term may be omitted (energy will also be zero).
   ///    NOW ASSIGNS BASED ON THE FIRST PAIR ONLY
-  pair<double, double> check_part1(int s1,int icj1,int ick2, int s2=-1,int icj3=-1,int ick4=-1){
+  pair<double, double> check_part1(int s1,int icj1,int ick2){
     int res=check_ee(s1,icj1,ick2);    
     if(res==1){ // my term
       //printf(" *\n");
diff --git a/lib/awpmd/systems/interact/TCP/wpmd_split.cpp b/lib/awpmd/systems/interact/TCP/wpmd_split.cpp
index 361fae1f34..691dbac91b 100644
--- a/lib/awpmd/systems/interact/TCP/wpmd_split.cpp
+++ b/lib/awpmd/systems/interact/TCP/wpmd_split.cpp
@@ -331,7 +331,7 @@ void AWPMD_split::get_el_forces(int flag, Vector_3P fe_x,
           fe_pw[ic1+k1]+=E_der[s1][indw1+8*k1+1]/(2*w*h_plank);
           for(int i=0;i<3;i++){
             fe_x[ic1+k1][i]+= -2*real(wk.a)*E_der[s1][indw1+8*k1+2+2*i]-2*imag(wk.a)*E_der[s1][indw1+8*k1+2+2*i+1];
-            fe_p[ic1+k1][i]+= (-E_der[s1][indw1+8*k1+2+2*i+1])*(m_electron/h_plank); //*(h_plank/m_electron);
+            fe_p[ic1+k1][i]+= (-E_der[s1][indw1+8*k1+2+2*i+1])*(m_electron/h_plank); // *(h_plank/m_electron);
             fe_pw[ic1+k1]+=(r[i]*E_der[s1][indw1+8*k1+2+2*i+1]/w)/h_plank;  
             fe_w[ic1+k1]+=2*r[i]*(t*E_der[s1][indw1+8*k1+2+2*i]+imag(wk.a)*E_der[s1][indw1+8*k1+2+2*i+1]/w);
           }*/
@@ -368,7 +368,6 @@ int  AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x,
     
     for(int c1=0;c1<ne[s1];c1++){
       // calculating single-electron quantities within block
-      double Ee1=0., Ew1=0., Eei1=0.;
       double pref=-h2_me/(2*wf_norm[s1][c1]); // ekin
       double pref_ei=coul_pref/wf_norm[s1][c1];
       
@@ -502,7 +501,6 @@ int  AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x,
                 continue;
 
               double pref_ee=coul_pref/(wf_norm[s1][c1]*wf_norm[s2][c2]);
-              double dE=0.;
               for(int j2=0;j2<nspl[s2][c2];j2++){
                 
                 cdouble cj2(split_c[s2][ic2+j2][0],split_c[s2][ic2+j2][1]);
@@ -513,9 +511,8 @@ int  AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x,
                   o2.set1(wj2);
 
                 for(int k2=j2;k2<nspl[s2][c2];k2++){
-                  int M2a=(j2==k2 ? 1: 2);
                   double M2e, M2f;
-                  _mytie(M2e,M2f)=check_part1(s1,ic1+j1,ic1+k1,s2,ic2+j2,ic2+k2);
+                  _mytie(M2e,M2f)=check_part1(s1,ic1+j1,ic1+k1);
 
                   cdouble ck2(split_c[s2][ic2+k2][0],split_c[s2][ic2+k2][1]);
 
@@ -1180,7 +1177,7 @@ int AWPMD_split::interaction(int flag, Vector_3P fi, Vector_3P fe_x,
                         M0= (c1==c2 && c3==c4 ? 1: 2); // will have exchange term for different pairs instead of M12*M34 factor
                       }
                       double Me, Mf;
-                      _mytie(Me,Mf)=check_part1(s1,ic1+j1,ic2+k2,s2,ic3+j3,ic4+k4)*M0;
+                      _mytie(Me,Mf)=check_part1(s1,ic1+j1,ic2+k2)*M0;
                       if(!Mf)
                         continue;
 
@@ -1322,4 +1319,4 @@ int AWPMD_split::interaction(int flag, Vector_3P fi, Vector_3P fe_x,
     interaction_ii(flag,fi);
 
   return 1;
-}
\ No newline at end of file
+}
diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py
index e481536768..0a6fecf5a4 100644
--- a/lib/colvars/Install.py
+++ b/lib/colvars/Install.py
@@ -57,7 +57,7 @@ suffix = args.extramake
 def get_lammps_machine_flags(machine):
   """Parse Makefile.machine from LAMMPS, return dictionary of compiler flags"""
   if not os.path.exists("../../src/MAKE/MACHINES/Makefile.%s" % machine):
-    sys.exit("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)
+    sys.exit("ERROR: Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)
   lines = open("../../src/MAKE/MACHINES/Makefile.%s" % machine,
                'r').readlines()
   machine_flags = {}
@@ -70,6 +70,8 @@ def get_lammps_machine_flags(machine):
           (words[0] == 'SHFLAGS') or (words[0] == 'ARCHIVE') or
           (words[0] == 'ARFLAGS') or (words[0] == 'SHELL')):
         machine_flags[words[0]] = ' '.join(words[2:])
+  if machine_flags:
+    print("Detected the following flags: ", machine_flags)
   return machine_flags
 
 def gen_colvars_makefile_machine(machine, machine_flags):
@@ -103,7 +105,7 @@ if not os.path.exists("Makefile.%s" % machine):
   machine_flags = get_lammps_machine_flags(machine)
   gen_colvars_makefile_machine(machine, machine_flags)
 if not os.path.exists("Makefile.%s" % machine):
-  sys.exit("lib/%s/Makefile.%s does not exist" % (lib,machine))
+  sys.exit("ERROR: lib/%s/Makefile.%s does not exist" % (lib,machine))
 
 # create Makefile.auto as copy of Makefile.machine
 # reset EXTRAMAKE if requested
@@ -123,15 +125,17 @@ fp.close()
 n_cpus = get_cpus()
 
 print("Building lib%s.a ..." % lib)
-cmd = ["make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus]
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
 try:
-  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True);
+  txt = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT);
   print(txt.decode('UTF-8'))
 except subprocess.CalledProcessError as e:
-  print("Make failed with:\n %s" % e.output.decode('UTF-8'))
-  sys.exit(1)
+  sys.exit("Make failed with:\n %s" % e.output.decode('UTF-8'))
+
+if os.path.exists("lib%s.a" % lib):
+  print("Build was successful")
+else:
+  sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib, lib))
 
-if os.path.exists("lib%s.a" % lib): print("Build was successful")
-else: sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
 if not os.path.exists("Makefile.lammps"):
-  print("lib/%s/Makefile.lammps was NOT created" % lib)
+  print("WARNING: lib/%s/Makefile.lammps was NOT created" % lib)
diff --git a/lib/colvars/Makefile.common b/lib/colvars/Makefile.common
index 5958765077..c555c534d8 100644
--- a/lib/colvars/Makefile.common
+++ b/lib/colvars/Makefile.common
@@ -52,25 +52,29 @@ LEPTON_SRCS = \
 	lepton/src/ParsedExpression.cpp lepton/src/ExpressionProgram.cpp    \
 	lepton/src/Operation.cpp lepton/src/Parser.cpp
 
-LEPTON_OBJS = \
-	lepton/src/CompiledExpression.o lepton/src/ExpressionTreeNode.o \
-	lepton/src/ParsedExpression.o lepton/src/ExpressionProgram.o    \
-	lepton/src/Operation.o lepton/src/Parser.o
 
-COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) $(LEPTON_OBJS)
+# Allow to selectively turn off Lepton
+ifeq ($(COLVARS_LEPTON),no)
+LEPTON_INCFLAGS = 
+COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o)
+else
+LEPTON_INCFLAGS = -Ilepton/include -DLEPTON
+COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) $(LEPTON_SRCS:.cpp=.o)
+endif
+
 
 %.o: %.cpp
-	$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) -Ilepton/include -DLEPTON -c -o $@ $<
+	$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) $(LEPTON_INCFLAGS) -c -o $@ $<
 
 $(COLVARS_LIB):	Makefile.deps $(COLVARS_OBJS)
-	$(AR) $(ARFLAGS) $(COLVARS_LIB) $(COLVARS_OBJS) $(LEPTON_OBJS)
+	$(AR) $(ARFLAGS) $(COLVARS_LIB) $(COLVARS_OBJS)
 
 
 Makefile.deps: $(COLVARS_SRCS)
 	@echo > $@
 	@for src in $^ ; do \
 	  obj=`basename $$src .cpp`.o ; \
-	  $(CXX) -MM $(COLVARS_INCFLAGS)  -Ilepton/include -DLEPTON \
+	  $(CXX) -MM $(COLVARS_INCFLAGS)  $(LEPTON_INCFLAGS) \
 	    -MT '$$(COLVARS_OBJ_DIR)'$$obj $$src >> $@ ; \
 	  done
 
diff --git a/lib/colvars/Makefile.g++ b/lib/colvars/Makefile.g++
index 556e39d070..6fa5131d6f 100644
--- a/lib/colvars/Makefile.g++
+++ b/lib/colvars/Makefile.g++
@@ -6,7 +6,7 @@ COLVARS_LIB = libcolvars.a
 COLVARS_OBJ_DIR =
 
 CXX =		g++
-CXXFLAGS =	-O2 -g -Wall -fPIC -funroll-loops
+CXXFLAGS =	-std=c++0x -O2 -g -Wall -fPIC -funroll-loops
 AR =		ar
 ARFLAGS =	-rscv
 SHELL =		/bin/sh
diff --git a/lib/colvars/Makefile.g++-debug b/lib/colvars/Makefile.g++-debug
index a6ca2f8124..89c650a0fe 100644
--- a/lib/colvars/Makefile.g++-debug
+++ b/lib/colvars/Makefile.g++-debug
@@ -1,5 +1,5 @@
 # -*- makefile -*- to build Colvars module with GNU compiler
 
-COLVARS_DEBUG = "YES"
+COLVARS_DEBUG = yes
 
 include Makefile.g++
diff --git a/lib/colvars/Makefile.g++-no-lepton b/lib/colvars/Makefile.g++-no-lepton
new file mode 100644
index 0000000000..19497272aa
--- /dev/null
+++ b/lib/colvars/Makefile.g++-no-lepton
@@ -0,0 +1,5 @@
+# -*- makefile -*- to build Colvars module with GNU compiler
+
+COLVARS_LEPTON = no
+
+include Makefile.g++
diff --git a/lib/colvars/README b/lib/colvars/README
index 087528748b..6be1b8dd58 100644
--- a/lib/colvars/README
+++ b/lib/colvars/README
@@ -8,79 +8,83 @@ The module itself implements a variety of functions and algorithms, including
 free-energy estimators based on thermodynamic forces, non-equilibrium work and
 probability distributions.
 
-For a brief description see:
-  http://colvars.github.io/
-  https://github.com/colvars/colvars/
-
-
-## How to build
-
-This directory has source files to build a library that LAMMPS
-links against when using the USER-COLVARS package.
-
-This library must be built with a C++ compiler, *before* LAMMPS is built and
-*after* packages are configured, so that LAMMPS can link against it.
-You can use the provided Makefile.* files or create your own, specific to your
-compiler and system.  For example:
-
-  cd src
-  make yes-user-colvars
-  cd ../lib/colvars
-  make -f Makefile.g++
-
-where Makefile.g++ uses the GNU C++ compiler and is a good template to start.
-
-**Optional**: if you use the Install.py script provided in this folder, you
-can give the machine name as the '-m' argument.  This can be the suffix of one
-of the files from either this folder, or from src/MAKE/MACHINES.
-*This is only supported by the Install.py within the lib/colvars folder*.
-
-When you are done building this library, two files should
-exist in this directory:
-
-libcolvars.a		the library LAMMPS will link against
-Makefile.lammps		settings the LAMMPS Makefile will import
-
-IMPORTANT: You must examine the final Makefile.lammps to insure it is
-correct for your system, else the LAMMPS build will likely fail.
-
-If you want to set a debug flag recognized by the library, the
-settings in Makefile.common should work.
-
-Note: some Colvars functions use the Lepton mathematical expression parser,
-which is here included (no additional steps required).  For more details, see:
-  https://simtk.org/projects/lepton
-
 
 ## Documentation
 
+For a brief description see:
+  https://colvars.github.io/
+  https://github.com/Colvars/colvars/
+
 For the reference manual see:
   http://colvars.github.io/colvars-refman-lammps
 
-A copy of the reference manual is also in:
+A PDF copy is also at:
   doc/PDF/colvars-refman-lammps.pdf
 
 Also available is a Doxygen-based developer documentation:
   http://colvars.github.io/doxygen/html/
 
 The reference article is:
-  G. Fiorin, M. L. Klein, and J. Henin,
+  G. Fiorin, M. L. Klein, and J. Hénin,
   Molecular Physics 111, 3345 (2013).
   http://dx.doi.org/10.1080/00268976.2013.813594
 
 
-## Updating to the latest version
+## Requirements
 
-To recompile LAMMPS with the most recent version of this module, the `master`
-branch of this repository from GitHub, or clone it via git:
+The Colvars library can be built for the most part with all major versions of
+the C++ language.
 
-  git clone https://github.com/colvars/colvars.git
+A few of the most recent features require C++11 support.  In particular, the
+library is optionally built together with the
+"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also
+included in the LAMMPS distribution.  Lepton implements the
+"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction
+feature, and requires C++11 support.
 
-and run the provided `update-colvars-code.sh` script against the unpacked
-LAMMPS source tree:
+See "here"_https://colvars.github.io/README-c++11.html for a detailed list of
+C++11-only features.
 
-  ./update-colvars-code.sh /path/to/lammps/folder
 
-Please report bugs and request new features at:
-https://github.com/colvars/colvars/issues
+## How to build (CMake)
 
+This is the recommended build recipe: no additional settings are normally
+needed besides "-D PKG_USER-COLVARS=yes".
+
+Building and linking of Lepton (or other C++11-only features) is enabled
+automatically when compilation is carried out with C++11 support, and disabled
+otherwise.  Optionally, Lepton build may be manually controlled with the flag
+"-D COLVARS_LEPTON=yes|no".
+
+
+## How to build (traditional make)
+
+Before building LAMMPS, one must build the Colvars library in lib/colvars.
+
+This can be done manually in the same folder by using or adapting one of the
+provided Makefiles: for example, Makefile.g++ for the GNU compiler.
+
+In general, it is safer to use build setting consistent with the rest of
+LAMMPS.  This is best carried out from the LAMMPS src directory using a
+command like these, which simply invoke the lib/colvars/Install.py script with
+the specified args:
+
+make lib-colvars                      # print help message
+make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre
+
+The "machine" argument of the "-m" flag is used to find a Makefile.machine to
+use as build recipe.  If it does not already exist in lib/colvars, it will be
+auto-generated by using compiler flags consistent with those parsed from the
+core LAMMPS makefiles.
+
+Optional flags may be specified as environment variables:
+
+COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+
+The build should produce two files: the library lib/colvars/libcolvars.a
+(which also includes Lepton objects if enabled) and the specification file
+lib/colvars/Makefile.lammps.  The latter is auto-generated, and normally does
+not need to be edited.
diff --git a/lib/colvars/lepton/include/lepton/CompiledExpression.h b/lib/colvars/lepton/include/lepton/CompiledExpression.h
index 67442e0cf5..c7e393e93b 100644
--- a/lib/colvars/lepton/include/lepton/CompiledExpression.h
+++ b/lib/colvars/lepton/include/lepton/CompiledExpression.h
@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -52,9 +52,9 @@ class ParsedExpression;
  * A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate
  * it many times as quickly as possible.  You should treat it as an opaque object; none of the internal representation
  * is visible.
- * 
+ *
  * A CompiledExpression is created by calling createCompiledExpression() on a ParsedExpression.
- * 
+ *
  * WARNING: CompiledExpression is NOT thread safe.  You should never access a CompiledExpression from two threads at
  * the same time.
  */
@@ -99,10 +99,11 @@ private:
     mutable std::vector<double> workspace;
     mutable std::vector<double> argValues;
     std::map<std::string, double> dummyVariables;
-    void* jitCode;
+    double (*jitCode)();
 #ifdef LEPTON_USE_JIT
     void generateJitCode();
-    void generateSingleArgCall(asmjit::X86Compiler& c, asmjit::X86XmmVar& dest, asmjit::X86XmmVar& arg, double (*function)(double));
+    void generateSingleArgCall(asmjit::X86Compiler& c, asmjit::X86Xmm& dest, asmjit::X86Xmm& arg, double (*function)(double));
+    void generateTwoArgCall(asmjit::X86Compiler& c, asmjit::X86Xmm& dest, asmjit::X86Xmm& arg1, asmjit::X86Xmm& arg2, double (*function)(double, double));
     std::vector<double> constants;
     asmjit::JitRuntime runtime;
 #endif
diff --git a/lib/colvars/lepton/include/lepton/CustomFunction.h b/lib/colvars/lepton/include/lepton/CustomFunction.h
index 5c5586105f..fbb0ddd52a 100644
--- a/lib/colvars/lepton/include/lepton/CustomFunction.h
+++ b/lib/colvars/lepton/include/lepton/CustomFunction.h
@@ -72,6 +72,38 @@ public:
     virtual CustomFunction* clone() const = 0;
 };
 
+/**
+ * This class is an implementation of CustomFunction that does no computation.  It just returns
+ * 0 for the value and derivatives.  This is useful when using the parser to analyze expressions
+ * rather than to evaluate them.  You can just create PlaceholderFunctions to represent any custom
+ * functions that may appear in expressions.
+ */
+
+class LEPTON_EXPORT PlaceholderFunction : public CustomFunction {
+public:
+    /**
+     * Create a Placeholder function.
+     *
+     * @param numArgs    the number of arguments the function expects
+     */
+    PlaceholderFunction(int numArgs) : numArgs(numArgs) {
+    }
+    int getNumArguments() const {
+        return numArgs;
+    }
+    double evaluate(const double* arguments) const {
+        return 0.0;
+    }
+    double evaluateDerivative(const double* arguments, const int* derivOrder) const {
+        return 0.0;
+    }
+    CustomFunction* clone() const {
+        return new PlaceholderFunction(numArgs);
+    };
+private:
+    int numArgs;
+};
+
 } // namespace Lepton
 
 #endif /*LEPTON_CUSTOM_FUNCTION_H_*/
diff --git a/lib/colvars/lepton/include/lepton/ExpressionProgram.h b/lib/colvars/lepton/include/lepton/ExpressionProgram.h
index 94d37f471d..a49a9094d0 100644
--- a/lib/colvars/lepton/include/lepton/ExpressionProgram.h
+++ b/lib/colvars/lepton/include/lepton/ExpressionProgram.h
@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Portions copyright (c) 2009-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -65,6 +65,14 @@ public:
      * Get an Operation in this program.
      */
     const Operation& getOperation(int index) const;
+    /**
+     * Change an Operation in this program.
+     *
+     * The Operation must have been allocated on the heap with the "new" operator.
+     * The ExpressionProgram assumes ownership of it and will delete it when it
+     * is no longer needed.
+     */
+    void setOperation(int index, Operation* operation);
     /**
      * Get the size of the stack needed to execute this program.  This is the largest number of elements present
      * on the stack at any point during evaluation.
diff --git a/lib/colvars/lepton/include/lepton/Operation.h b/lib/colvars/lepton/include/lepton/Operation.h
index f7a8b78163..1ddde0b8c0 100644
--- a/lib/colvars/lepton/include/lepton/Operation.h
+++ b/lib/colvars/lepton/include/lepton/Operation.h
@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -63,7 +63,7 @@ public:
      * can be used when processing or analyzing parsed expressions.
      */
     enum Id {CONSTANT, VARIABLE, CUSTOM, ADD, SUBTRACT, MULTIPLY, DIVIDE, POWER, NEGATE, SQRT, EXP, LOG,
-             SIN, COS, SEC, CSC, TAN, COT, ASIN, ACOS, ATAN, SINH, COSH, TANH, ERF, ERFC, STEP, DELTA, SQUARE, CUBE, RECIPROCAL,
+             SIN, COS, SEC, CSC, TAN, COT, ASIN, ACOS, ATAN, ATAN2, SINH, COSH, TANH, ERF, ERFC, STEP, DELTA, SQUARE, CUBE, RECIPROCAL,
              ADD_CONSTANT, MULTIPLY_CONSTANT, POWER_CONSTANT, MIN, MAX, ABS, FLOOR, CEIL, SELECT};
     /**
      * Get the name of this Operation.
@@ -137,6 +137,7 @@ public:
     class Asin;
     class Acos;
     class Atan;
+    class Atan2;
     class Sinh;
     class Cosh;
     class Tanh;
@@ -226,6 +227,11 @@ class LEPTON_EXPORT Operation::Custom : public Operation {
 public:
     Custom(const std::string& name, CustomFunction* function) : name(name), function(function), isDerivative(false), derivOrder(function->getNumArguments(), 0) {
     }
+    Custom(const std::string& name, CustomFunction* function, const std::vector<int>& derivOrder) : name(name), function(function), isDerivative(false), derivOrder(derivOrder) {
+        for (int order : derivOrder)
+            if (order != 0)
+                isDerivative = true;
+    }
     Custom(const Custom& base, int derivIndex) : name(base.name), function(base.function->clone()), isDerivative(true), derivOrder(base.derivOrder) {
         derivOrder[derivIndex]++;
     }
@@ -684,6 +690,28 @@ public:
     ExpressionTreeNode differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const;
 };
 
+class LEPTON_EXPORT Operation::Atan2 : public Operation {
+public:
+    Atan2() {
+    }
+    std::string getName() const {
+        return "atan2";
+    }
+    Id getId() const {
+        return ATAN2;
+    }
+    int getNumArguments() const {
+        return 2;
+    }
+    Operation* clone() const {
+        return new Atan2();
+    }
+    double evaluate(double* args, const std::map<std::string, double>& variables) const {
+        return std::atan2(args[0], args[1]);
+    }
+    ExpressionTreeNode differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const;
+};
+
 class LEPTON_EXPORT Operation::Sinh : public Operation {
 public:
     Sinh() {
@@ -989,7 +1017,7 @@ public:
     double evaluate(double* args, const std::map<std::string, double>& variables) const {
         if (isIntPower) {
             // Integer powers can be computed much more quickly by repeated multiplication.
-            
+
             int exponent = intValue;
             double base = args[0];
             if (exponent < 0) {
diff --git a/lib/colvars/lepton/src/CompiledExpression.cpp b/lib/colvars/lepton/src/CompiledExpression.cpp
index 302f294ee2..1ad348b47d 100644
--- a/lib/colvars/lepton/src/CompiledExpression.cpp
+++ b/lib/colvars/lepton/src/CompiledExpression.cpp
@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -84,17 +84,17 @@ CompiledExpression& CompiledExpression::operator=(const CompiledExpression& expr
 void CompiledExpression::compileExpression(const ExpressionTreeNode& node, vector<pair<ExpressionTreeNode, int> >& temps) {
     if (findTempIndex(node, temps) != -1)
         return; // We have already processed a node identical to this one.
-    
+
     // Process the child nodes.
-    
+
     vector<int> args;
     for (int i = 0; i < node.getChildren().size(); i++) {
         compileExpression(node.getChildren()[i], temps);
         args.push_back(findTempIndex(node.getChildren()[i], temps));
     }
-    
+
     // Process this node.
-    
+
     if (node.getOperation().getId() == Operation::VARIABLE) {
         variableIndices[node.getOperation().getName()] = (int) workspace.size();
         variableNames.insert(node.getOperation().getName());
@@ -108,7 +108,7 @@ void CompiledExpression::compileExpression(const ExpressionTreeNode& node, vecto
             arguments[stepIndex].push_back(0); // The value won't actually be used.  We just need something there.
         else {
             // If the arguments are sequential, we can just pass a pointer to the first one.
-            
+
             bool sequential = true;
             for (int i = 1; i < args.size(); i++)
                 if (args[i] != args[i-1]+1)
@@ -148,12 +148,12 @@ void CompiledExpression::setVariableLocations(map<string, double*>& variableLoca
     variablePointers = variableLocations;
 #ifdef LEPTON_USE_JIT
     // Rebuild the JIT code.
-    
+
     if (workspace.size() > 0)
         generateJitCode();
 #else
     // Make a list of all variables we will need to copy before evaluating the expression.
-    
+
     variablesToCopy.clear();
     for (map<string, int>::const_iterator iter = variableIndices.begin(); iter != variableIndices.end(); ++iter) {
         map<string, double*>::iterator pointer = variablePointers.find(iter->first);
@@ -165,13 +165,13 @@ void CompiledExpression::setVariableLocations(map<string, double*>& variableLoca
 
 double CompiledExpression::evaluate() const {
 #ifdef LEPTON_USE_JIT
-    return ((double (*)()) jitCode)();
+    return jitCode();
 #else
     for (int i = 0; i < variablesToCopy.size(); i++)
         *variablesToCopy[i].first = *variablesToCopy[i].second;
 
     // Loop over the operations and evaluate each one.
-    
+
     for (int step = 0; step < operation.size(); step++) {
         const vector<int>& args = arguments[step];
         if (args.size() == 1)
@@ -188,34 +188,36 @@ double CompiledExpression::evaluate() const {
 
 #ifdef LEPTON_USE_JIT
 static double evaluateOperation(Operation* op, double* args) {
-    map<string, double>* dummyVariables = NULL;
-    return op->evaluate(args, *dummyVariables);
+    static map<string, double> dummyVariables;
+    return op->evaluate(args, dummyVariables);
 }
 
 void CompiledExpression::generateJitCode() {
-    X86Compiler c(&runtime);
-    c.addFunc(kFuncConvHost, FuncBuilder0<double>());
-    vector<X86XmmVar> workspaceVar(workspace.size());
+    CodeHolder code;
+    code.init(runtime.getCodeInfo());
+    X86Compiler c(&code);
+    c.addFunc(FuncSignature0<double>());
+    vector<X86Xmm> workspaceVar(workspace.size());
     for (int i = 0; i < (int) workspaceVar.size(); i++)
-        workspaceVar[i] = c.newXmmVar(kX86VarTypeXmmSd);
-    X86GpVar argsPointer(c);
+        workspaceVar[i] = c.newXmmSd();
+    X86Gp argsPointer = c.newIntPtr();
     c.mov(argsPointer, imm_ptr(&argValues[0]));
-    
+
     // Load the arguments into variables.
-    
+
     for (set<string>::const_iterator iter = variableNames.begin(); iter != variableNames.end(); ++iter) {
         map<string, int>::iterator index = variableIndices.find(*iter);
-        X86GpVar variablePointer(c);
+        X86Gp variablePointer = c.newIntPtr();
         c.mov(variablePointer, imm_ptr(&getVariableReference(index->first)));
         c.movsd(workspaceVar[index->second], x86::ptr(variablePointer, 0, 0));
     }
 
     // Make a list of all constants that will be needed for evaluation.
-    
+
     vector<int> operationConstantIndex(operation.size(), -1);
     for (int step = 0; step < (int) operation.size(); step++) {
         // Find the constant value (if any) used by this operation.
-        
+
         Operation& op = *operation[step];
         double value;
         if (op.getId() == Operation::CONSTANT)
@@ -232,9 +234,9 @@ void CompiledExpression::generateJitCode() {
             value = 1.0;
         else
             continue;
-        
+
         // See if we already have a variable for this constant.
-        
+
         for (int i = 0; i < (int) constants.size(); i++)
             if (value == constants[i]) {
                 operationConstantIndex[step] = i;
@@ -245,33 +247,33 @@ void CompiledExpression::generateJitCode() {
             constants.push_back(value);
         }
     }
-    
+
     // Load constants into variables.
-    
-    vector<X86XmmVar> constantVar(constants.size());
+
+    vector<X86Xmm> constantVar(constants.size());
     if (constants.size() > 0) {
-        X86GpVar constantsPointer(c);
+        X86Gp constantsPointer = c.newIntPtr();
         c.mov(constantsPointer, imm_ptr(&constants[0]));
         for (int i = 0; i < (int) constants.size(); i++) {
-            constantVar[i] = c.newXmmVar(kX86VarTypeXmmSd);
+            constantVar[i] = c.newXmmSd();
             c.movsd(constantVar[i], x86::ptr(constantsPointer, 8*i, 0));
         }
     }
-    
+
     // Evaluate the operations.
-    
+
     for (int step = 0; step < (int) operation.size(); step++) {
         Operation& op = *operation[step];
         vector<int> args = arguments[step];
         if (args.size() == 1) {
             // One or more sequential arguments.  Fill out the list.
-            
+
             for (int i = 1; i < op.getNumArguments(); i++)
                 args.push_back(args[0]+i);
         }
-        
+
         // Generate instructions to execute this operation.
-        
+
         switch (op.getId()) {
             case Operation::CONSTANT:
                 c.movsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]);
@@ -292,6 +294,9 @@ void CompiledExpression::generateJitCode() {
                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);
                 c.divsd(workspaceVar[target[step]], workspaceVar[args[1]]);
                 break;
+            case Operation::POWER:
+                generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], pow);
+                break;
             case Operation::NEGATE:
                 c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]);
                 c.subsd(workspaceVar[target[step]], workspaceVar[args[0]]);
@@ -323,6 +328,9 @@ void CompiledExpression::generateJitCode() {
             case Operation::ATAN:
                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], atan);
                 break;
+            case Operation::ATAN2:
+                generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], atan2);
+                break;
             case Operation::SINH:
                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinh);
                 break;
@@ -374,12 +382,12 @@ void CompiledExpression::generateJitCode() {
                 break;
             default:
                 // Just invoke evaluateOperation().
-                
+
                 for (int i = 0; i < (int) args.size(); i++)
                     c.movsd(x86::ptr(argsPointer, 8*i, 0), workspaceVar[args[i]]);
-                X86GpVar fn(c, kVarTypeIntPtr);
+                X86Gp fn = c.newIntPtr();
                 c.mov(fn, imm_ptr((void*) evaluateOperation));
-                X86CallNode* call = c.call(fn, kFuncConvHost, FuncBuilder2<double, Operation*, double*>());
+                CCFuncCall* call = c.call(fn, FuncSignature2<double, Operation*, double*>());
                 call->setArg(0, imm_ptr(&op));
                 call->setArg(1, imm_ptr(&argValues[0]));
                 call->setRet(0, workspaceVar[target[step]]);
@@ -387,14 +395,24 @@ void CompiledExpression::generateJitCode() {
     }
     c.ret(workspaceVar[workspace.size()-1]);
     c.endFunc();
-    jitCode = c.make();
+    c.finalize();
+    runtime.add(&jitCode, &code);
 }
 
-void CompiledExpression::generateSingleArgCall(X86Compiler& c, X86XmmVar& dest, X86XmmVar& arg, double (*function)(double)) {
-    X86GpVar fn(c, kVarTypeIntPtr);
+void CompiledExpression::generateSingleArgCall(X86Compiler& c, X86Xmm& dest, X86Xmm& arg, double (*function)(double)) {
+    X86Gp fn = c.newIntPtr();
     c.mov(fn, imm_ptr((void*) function));
-    X86CallNode* call = c.call(fn, kFuncConvHost, FuncBuilder1<double, double>());
+    CCFuncCall* call = c.call(fn, FuncSignature1<double, double>());
     call->setArg(0, arg);
     call->setRet(0, dest);
 }
+
+void CompiledExpression::generateTwoArgCall(X86Compiler& c, X86Xmm& dest, X86Xmm& arg1, X86Xmm& arg2, double (*function)(double, double)) {
+    X86Gp fn = c.newIntPtr();
+    c.mov(fn, imm_ptr((void*) function));
+    CCFuncCall* call = c.call(fn, FuncSignature2<double, double, double>());
+    call->setArg(0, arg1);
+    call->setArg(1, arg2);
+    call->setRet(0, dest);
+}
 #endif
diff --git a/lib/colvars/lepton/src/ExpressionProgram.cpp b/lib/colvars/lepton/src/ExpressionProgram.cpp
index 65d3f0c79a..bbbae8533f 100644
--- a/lib/colvars/lepton/src/ExpressionProgram.cpp
+++ b/lib/colvars/lepton/src/ExpressionProgram.cpp
@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -84,6 +84,11 @@ const Operation& ExpressionProgram::getOperation(int index) const {
     return *operations[index];
 }
 
+void ExpressionProgram::setOperation(int index, Operation* operation) {
+    delete operations[index];
+    operations[index] = operation;
+}
+
 int ExpressionProgram::getStackSize() const {
     return stackSize;
 }
diff --git a/lib/colvars/lepton/src/MSVC_erfc.h b/lib/colvars/lepton/src/MSVC_erfc.h
index eadb20fdf8..c30a8ce542 100644
--- a/lib/colvars/lepton/src/MSVC_erfc.h
+++ b/lib/colvars/lepton/src/MSVC_erfc.h
@@ -3,15 +3,15 @@
 
 /*
  * Up to version 11 (VC++ 2012), Microsoft does not support the
- * standard C99 erf() and erfc() functions so we have to fake them here. 
+ * standard C99 erf() and erfc() functions so we have to fake them here.
  * These were added in version 12 (VC++ 2013), which sets _MSC_VER=1800
  * (VC11 has _MSC_VER=1700).
  */
 
-#if defined(_MSC_VER) 
+#if defined(_MSC_VER)
 #define M_PI 3.14159265358979323846264338327950288
 
-#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12 
+#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12
 /***************************
 *   erf.cpp
 *   author:  Steve Strand
diff --git a/lib/colvars/lepton/src/Operation.cpp b/lib/colvars/lepton/src/Operation.cpp
index 693dea2ede..78741c4814 100644
--- a/lib/colvars/lepton/src/Operation.cpp
+++ b/lib/colvars/lepton/src/Operation.cpp
@@ -7,7 +7,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -202,6 +202,16 @@ ExpressionTreeNode Operation::Atan::differentiate(const std::vector<ExpressionTr
                               childDerivs[0]);
 }
 
+ExpressionTreeNode Operation::Atan2::differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const {
+    return ExpressionTreeNode(new Operation::Divide(),
+                              ExpressionTreeNode(new Operation::Subtract(),
+                                                 ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]),
+                                                 ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1])),
+                              ExpressionTreeNode(new Operation::Add(),
+                                                 ExpressionTreeNode(new Operation::Square(), children[0]),
+                                                 ExpressionTreeNode(new Operation::Square(), children[1])));
+}
+
 ExpressionTreeNode Operation::Sinh::differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const {
     return ExpressionTreeNode(new Operation::Multiply(),
                               ExpressionTreeNode(new Operation::Cosh(),
diff --git a/lib/colvars/lepton/src/ParsedExpression.cpp b/lib/colvars/lepton/src/ParsedExpression.cpp
index 6effd06007..fd3b091d3c 100644
--- a/lib/colvars/lepton/src/ParsedExpression.cpp
+++ b/lib/colvars/lepton/src/ParsedExpression.cpp
@@ -271,6 +271,16 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
                 return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()), children[0].getChildren()[0]);
             break;
         }
+        case Operation::SQRT:
+        {
+            if (children[0].getOperation().getId() == Operation::SQUARE) // sqrt(square(x)) = abs(x)
+                return ExpressionTreeNode(new Operation::Abs(), children[0].getChildren()[0]);
+        }
+        case Operation::SQUARE:
+        {
+            if (children[0].getOperation().getId() == Operation::SQRT) // square(sqrt(x)) = x
+                return children[0].getChildren()[0];
+        }
         default:
         {
             // If operation ID is not one of the above,
diff --git a/lib/colvars/lepton/src/Parser.cpp b/lib/colvars/lepton/src/Parser.cpp
index 6b19d7370d..e284add258 100644
--- a/lib/colvars/lepton/src/Parser.cpp
+++ b/lib/colvars/lepton/src/Parser.cpp
@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -66,7 +66,7 @@ private:
 
 string Parser::trim(const string& expression) {
     // Remove leading and trailing spaces.
-    
+
     int start, end;
     for (start = 0; start < (int) expression.size() && isspace(expression[start]); start++)
         ;
@@ -313,6 +313,7 @@ Operation* Parser::getFunctionOperation(const std::string& name, const map<strin
         opMap["asin"] = Operation::ASIN;
         opMap["acos"] = Operation::ACOS;
         opMap["atan"] = Operation::ATAN;
+        opMap["atan2"] = Operation::ATAN2;
         opMap["sinh"] = Operation::SINH;
         opMap["cosh"] = Operation::COSH;
         opMap["tanh"] = Operation::TANH;
@@ -368,6 +369,8 @@ Operation* Parser::getFunctionOperation(const std::string& name, const map<strin
             return new Operation::Acos();
         case Operation::ATAN:
             return new Operation::Atan();
+        case Operation::ATAN2:
+            return new Operation::Atan2();
         case Operation::SINH:
             return new Operation::Sinh();
         case Operation::COSH:
diff --git a/lib/gpu/Makefile.lammps.standard b/lib/gpu/Makefile.lammps.standard
index 1ceb93b342..9526e8e373 100644
--- a/lib/gpu/Makefile.lammps.standard
+++ b/lib/gpu/Makefile.lammps.standard
@@ -7,5 +7,5 @@ endif
 
 gpu_SYSINC =
 gpu_SYSLIB =  -lcudart -lcuda
-gpu_SYSPATH = -L$(CUDA_HOME)/lib64
+gpu_SYSPATH = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 
diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux
index 7001c6d8b9..a26fbe114c 100644
--- a/lib/gpu/Makefile.linux
+++ b/lib/gpu/Makefile.linux
@@ -54,7 +54,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
 
 CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
diff --git a/lib/gpu/Makefile.linux.double b/lib/gpu/Makefile.linux.double
index e65647f160..05f083697d 100644
--- a/lib/gpu/Makefile.linux.double
+++ b/lib/gpu/Makefile.linux.double
@@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_DOUBLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Makefile.linux.mixed b/lib/gpu/Makefile.linux.mixed
index a036b84ee3..ca414f1fc1 100644
--- a/lib/gpu/Makefile.linux.mixed
+++ b/lib/gpu/Makefile.linux.mixed
@@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Makefile.linux.single b/lib/gpu/Makefile.linux.single
index 808647cea7..1b349faac2 100644
--- a/lib/gpu/Makefile.linux.single
+++ b/lib/gpu/Makefile.linux.single
@@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_SINGLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Makefile.linux_multi b/lib/gpu/Makefile.linux_multi
index 2f75ca0e2b..ba50170f39 100644
--- a/lib/gpu/Makefile.linux_multi
+++ b/lib/gpu/Makefile.linux_multi
@@ -40,7 +40,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98"
 
 CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
diff --git a/lib/gpu/Makefile.mac b/lib/gpu/Makefile.mac
index f9f8d5179a..b571e8d85a 100644
--- a/lib/gpu/Makefile.mac
+++ b/lib/gpu/Makefile.mac
@@ -14,7 +14,7 @@ NVCC = nvcc -m64
 CUDA_ARCH = -arch=sm_11
 CUDA_PRECISION = -D_SINGLE_SINGLE
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib
+CUDA_LIB = -L$(CUDA_HOME)/lib -L$(CUDA_HOME)/lib/stubs
 CUDA_OPTS = -DUNIX -DUCL_NO_EXIT -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -m64
diff --git a/lib/gpu/Makefile.serial b/lib/gpu/Makefile.serial
index 99153fc471..b0cfb3c86b 100644
--- a/lib/gpu/Makefile.serial
+++ b/lib/gpu/Makefile.serial
@@ -34,7 +34,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64 -L../../src/STUBS -lmpi_stubs
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs -L../../src/STUBS -lmpi_stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC)
 
 CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -fPIC -I../../src/STUBS
diff --git a/lib/gpu/Makefile.shannon b/lib/gpu/Makefile.shannon
index 22c2dc89d7..b14bd01ec2 100644
--- a/lib/gpu/Makefile.shannon
+++ b/lib/gpu/Makefile.shannon
@@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
 CUDA_PRECISION = -D_DOUBLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Makefile.xk7 b/lib/gpu/Makefile.xk7
index 0b9f029399..f3050575e1 100644
--- a/lib/gpu/Makefile.xk7
+++ b/lib/gpu/Makefile.xk7
@@ -14,7 +14,7 @@ CUDA_ARCH = -arch=sm_35
 
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
 CUDA_OPTS = -DUNIX -O3 --use_fast_math
 
 CUDR_CPP = CC -DCUDA_PROXY -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile
index 233f43380f..65dcae7bdb 100644
--- a/lib/gpu/Nvidia.makefile
+++ b/lib/gpu/Nvidia.makefile
@@ -82,7 +82,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
        $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
        $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
        $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
-       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o
+       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
+       $(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
 
 CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
        $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \
@@ -143,7 +144,8 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
        $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \
        $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \
        $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \
-       $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h
+       $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h \
+       $(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long_cubin.h
 
 all: $(OBJ_DIR) $(GPU_LIB) $(EXECS)
 
@@ -297,6 +299,18 @@ $(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp $(OBJ_DIR)/lj_cubin.h $(OBJ_DI
 $(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
 	$(CUDR) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
 
+$(OBJ_DIR)/lj_tip4p_long.cubin: lal_lj_tip4p_long.cu lal_precision.h lal_preprocessor.h
+	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_tip4p_long.cu
+
+$(OBJ_DIR)/lj_tip4p_long_cubin.h: $(OBJ_DIR)/lj_tip4p_long.cubin $(OBJ_DIR)/lj_tip4p_long.cubin
+	$(BIN2C)  -c -n lj_tip4p_long $(OBJ_DIR)/lj_tip4p_long.cubin > $(OBJ_DIR)/lj_tip4p_long_cubin.h
+
+$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp  $(OBJ_DIR)/lj_tip4p_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o
+	$(CUDR) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
+	$(CUDR) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
+
 $(OBJ_DIR)/lj_coul.cubin: lal_lj_coul.cu lal_precision.h lal_preprocessor.h
 	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_coul.cu
 
diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile
index 86991a1e98..1b1932858b 100644
--- a/lib/gpu/Opencl.makefile
+++ b/lib/gpu/Opencl.makefile
@@ -71,7 +71,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \
        $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
        $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
        $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
-       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o
+       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o \
+       $(OBJ_DIR)/lal_lj_tip4p_long.o $(OBJ_DIR)/lal_lj_tip4p_long_ext.o
 
 KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
        $(OBJ_DIR)/neighbor_cpu_cl.h $(OBJ_DIR)/pppm_cl.h \
@@ -102,7 +103,8 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
        $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h \
        $(OBJ_DIR)/ufm_cl.h  $(OBJ_DIR)/dipole_long_lj_cl.h \
        $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/coul_long_cs_cl.h \
-       $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h
+       $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h \
+       $(OBJ_DIR)/lj_tip4p_long_cl.h
 
 
 OCL_EXECS = $(BIN_DIR)/ocl_get_devices
@@ -202,6 +204,15 @@ $(OBJ_DIR)/lal_lj.o: $(ALL_H) lal_lj.h lal_lj.cpp  $(OBJ_DIR)/lj_cl.h $(OBJ_DIR)
 $(OBJ_DIR)/lal_lj_ext.o: $(ALL_H) lal_lj.h lal_lj_ext.cpp lal_base_atomic.h
 	$(OCL) -o $@ -c lal_lj_ext.cpp -I$(OBJ_DIR)
 
+$(OBJ_DIR)/lj_tip4p_long_cl.h: lal_lj_tip4p_long.cu $(PRE1_H)
+	$(BSH) ./geryon/file_to_cstr.sh lj_tip4p_long $(PRE1_H) lal_lj_tip4p_long.cu $(OBJ_DIR)/lj_tip4p_long_cl.h;
+
+$(OBJ_DIR)/lal_lj_tip4p_long.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long.cpp  $(OBJ_DIR)/lj_tip4p_long_cl.h $(OBJ_DIR)/lj_tip4p_long_cl.h $(OBJ_DIR)/lal_base_atomic.o
+	$(OCL) -o $@ -c lal_lj_tip4p_long.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_lj_tip4p_long_ext.o: $(ALL_H) lal_lj_tip4p_long.h lal_lj_tip4p_long_ext.cpp lal_base_atomic.h
+	$(OCL) -o $@ -c lal_lj_tip4p_long_ext.cpp -I$(OBJ_DIR)
+
 $(OBJ_DIR)/lj_coul_cl.h: lal_lj_coul.cu $(PRE1_H)
 	$(BSH) ./geryon/file_to_cstr.sh lj_coul $(PRE1_H) lal_lj_coul.cu $(OBJ_DIR)/lj_coul_cl.h;
 
diff --git a/lib/gpu/README b/lib/gpu/README
index 6cc386270d..2d98749a40 100644
--- a/lib/gpu/README
+++ b/lib/gpu/README
@@ -3,7 +3,7 @@
                   --------------------------------
                      
                        W. Michael Brown (ORNL)
-                        Trung Dac Nguyen (ORNL)
+                        Trung Dac Nguyen (ORNL/Northwestern)
                           Peng Wang (NVIDIA)
                        Axel Kohlmeyer (Temple)
                          Steve Plimpton (SNL)
@@ -129,7 +129,8 @@ that ships with the CUDA toolkit, but also with the CUDA driver library
 on the head node of a GPU cluster, this library may not be installed,
 so you may need to copy it over from one of the compute nodes (best into
 this directory). Recent CUDA toolkits starting from CUDA 9 provide a dummy
-libcuda.so library, that can be used for linking (but not for running).
+libcuda.so library (typically under $(CUDA_HOME)/lib64/stubs), that can be used for
+linking.
 
 The gpu library supports 3 precision modes as determined by 
 the CUDA_PRECISION variable:
diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h
index 14455e38a5..e414e7b69c 100644
--- a/lib/gpu/geryon/ocl_device.h
+++ b/lib/gpu/geryon/ocl_device.h
@@ -28,6 +28,14 @@
 #include <vector>
 #include <iostream>
 
+/* We default to OpenCL 1.2 as target version for now as
+ * there are known issues with OpenCL 2.0 and later.
+ * This is also to silence warnings from generic OpenCL headers */
+
+#if !defined(CL_TARGET_OPENCL_VERSION)
+#define CL_TARGET_OPENCL_VERSION 120
+#endif
+
 #ifdef __APPLE__
 #include <OpenCL/cl.h>
 #include <OpenCL/cl_platform.h>
diff --git a/lib/gpu/geryon/ocl_macros.h b/lib/gpu/geryon/ocl_macros.h
index 5fb7665817..aeff689859 100644
--- a/lib/gpu/geryon/ocl_macros.h
+++ b/lib/gpu/geryon/ocl_macros.h
@@ -4,6 +4,14 @@
 #include <cstdio>
 #include <cassert>
 
+/* We default to OpenCL 1.2 as target version for now as
+ * there are known issues with OpenCL 2.0 and later.
+ * This is also to silence warnings from generic OpenCL headers */
+
+#if !defined(CL_TARGET_OPENCL_VERSION)
+#define CL_TARGET_OPENCL_VERSION 120
+#endif
+
 #ifdef __APPLE__
 #include <OpenCL/cl.h>
 #else
diff --git a/lib/gpu/lal_base_atomic.cpp b/lib/gpu/lal_base_atomic.cpp
index 4aadd3754c..eb0eab87b6 100644
--- a/lib/gpu/lal_base_atomic.cpp
+++ b/lib/gpu/lal_base_atomic.cpp
@@ -25,12 +25,17 @@ BaseAtomicT::BaseAtomic() : _compiled(false), _max_bytes(0)  {
   device=&global_device;
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
+  pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseAtomicT::~BaseAtomic() {
   delete ans;
   delete nbor;
+  k_pair_fast.clear();
+  k_pair.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -74,6 +79,8 @@ int BaseAtomicT::init_atomic(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
@@ -109,19 +116,11 @@ void BaseAtomicT::clear_atomic() {
   device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
                        _gpu_overhead,_driver_overhead,_threads_per_atom,screen);
 
-  if (_compiled) {
-    k_pair_fast.clear();
-    k_pair.clear();
-    delete pair_program;
-    _compiled=false;
-  }
-
   time_pair.clear();
   hd_balancer.clear();
 
   nbor->clear();
   ans->clear();
-  device->clear();
 }
 
 // ---------------------------------------------------------------------------
@@ -276,6 +275,7 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str,
     return;
 
   std::string s_fast=std::string(kname)+"_fast";
+  if (pair_program) delete pair_program;
   pair_program=new UCL_Program(dev);
   pair_program->load_string(pair_str,device->compile_string().c_str());
   k_pair_fast.set_function(*pair_program,s_fast.c_str());
diff --git a/lib/gpu/lal_base_charge.cpp b/lib/gpu/lal_base_charge.cpp
index 760e759201..52e8ae2d89 100644
--- a/lib/gpu/lal_base_charge.cpp
+++ b/lib/gpu/lal_base_charge.cpp
@@ -25,12 +25,17 @@ BaseChargeT::BaseCharge() : _compiled(false), _max_bytes(0) {
   device=&global_device;
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
+  pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseChargeT::~BaseCharge() {
   delete ans;
   delete nbor;
+  k_pair_fast.clear();
+  k_pair.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -74,6 +79,8 @@ int BaseChargeT::init_atomic(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
@@ -111,19 +118,11 @@ void BaseChargeT::clear_atomic() {
   device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
                        _gpu_overhead,_driver_overhead,_threads_per_atom,screen);
 
-  if (_compiled) {
-    k_pair_fast.clear();
-    k_pair.clear();
-    delete pair_program;
-    _compiled=false;
-  }
-
   time_pair.clear();
   hd_balancer.clear();
 
   nbor->clear();
   ans->clear();
-  device->clear();
 }
 
 // ---------------------------------------------------------------------------
@@ -291,6 +290,7 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str,
     return;
 
   std::string s_fast=std::string(kname)+"_fast";
+  if (pair_program) delete pair_program;
   pair_program=new UCL_Program(dev);
   pair_program->load_string(pair_str,device->compile_string().c_str());
   k_pair_fast.set_function(*pair_program,s_fast.c_str());
diff --git a/lib/gpu/lal_base_dipole.cpp b/lib/gpu/lal_base_dipole.cpp
index 56dcaf8e12..ed71029e68 100644
--- a/lib/gpu/lal_base_dipole.cpp
+++ b/lib/gpu/lal_base_dipole.cpp
@@ -25,12 +25,17 @@ BaseDipoleT::BaseDipole() : _compiled(false), _max_bytes(0) {
   device=&global_device;
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
+  pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseDipoleT::~BaseDipole() {
   delete ans;
   delete nbor;
+  k_pair_fast.clear();
+  k_pair.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -75,6 +80,8 @@ int BaseDipoleT::init_atomic(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
@@ -113,19 +120,11 @@ void BaseDipoleT::clear_atomic() {
   device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
                        _gpu_overhead,_driver_overhead,_threads_per_atom,screen);
 
-  if (_compiled) {
-    k_pair_fast.clear();
-    k_pair.clear();
-    delete pair_program;
-    _compiled=false;
-  }
-
   time_pair.clear();
   hd_balancer.clear();
 
   nbor->clear();
   ans->clear();
-  device->clear();
 }
 
 // ---------------------------------------------------------------------------
@@ -299,6 +298,7 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str,
     return;
 
   std::string s_fast=std::string(kname)+"_fast";
+  if (pair_program) delete pair_program;
   pair_program=new UCL_Program(dev);
   pair_program->load_string(pair_str,device->compile_string().c_str());
   k_pair_fast.set_function(*pair_program,s_fast.c_str());
diff --git a/lib/gpu/lal_base_dpd.cpp b/lib/gpu/lal_base_dpd.cpp
index 66c8cf09e9..c0d7ad47bc 100644
--- a/lib/gpu/lal_base_dpd.cpp
+++ b/lib/gpu/lal_base_dpd.cpp
@@ -25,12 +25,17 @@ BaseDPDT::BaseDPD() : _compiled(false), _max_bytes(0) {
   device=&global_device;
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
+  pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseDPDT::~BaseDPD() {
   delete ans;
   delete nbor;
+  k_pair_fast.clear();
+  k_pair.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -75,6 +80,8 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
@@ -112,19 +119,11 @@ void BaseDPDT::clear_atomic() {
   device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
                        _gpu_overhead,_driver_overhead,_threads_per_atom,screen);
 
-  if (_compiled) {
-    k_pair_fast.clear();
-    k_pair.clear();
-    delete pair_program;
-    _compiled=false;
-  }
-
   time_pair.clear();
   hd_balancer.clear();
 
   nbor->clear();
   ans->clear();
-  device->clear();
 }
 
 // ---------------------------------------------------------------------------
@@ -297,6 +296,7 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str,
     return;
 
   std::string s_fast=std::string(kname)+"_fast";
+  if (pair_program) delete pair_program;
   pair_program=new UCL_Program(dev);
   pair_program->load_string(pair_str,device->compile_string().c_str());
   k_pair_fast.set_function(*pair_program,s_fast.c_str());
diff --git a/lib/gpu/lal_base_ellipsoid.cpp b/lib/gpu/lal_base_ellipsoid.cpp
index b8d0b7a666..abc8807a8b 100644
--- a/lib/gpu/lal_base_ellipsoid.cpp
+++ b/lib/gpu/lal_base_ellipsoid.cpp
@@ -33,12 +33,26 @@ BaseEllipsoidT::BaseEllipsoid() : _compiled(false), _max_bytes(0) {
   device=&global_device;
   ans=new Answer<numtyp,acctyp>();
   nbor=new Neighbor();
+  nbor_program=NULL;
+  ellipsoid_program=NULL;
+  lj_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
 BaseEllipsoidT::~BaseEllipsoid() {
   delete ans;
   delete nbor;
+  k_nbor_fast.clear();
+  k_nbor.clear();
+  k_ellipsoid.clear();
+  k_ellipsoid_sphere.clear();
+  k_sphere_ellipsoid.clear();
+  k_lj_fast.clear();
+  k_lj.clear();
+  if (nbor_program) delete nbor_program;
+  if (ellipsoid_program) delete ellipsoid_program;
+  if (lj_program) delete lj_program;
 }
 
 template <class numtyp, class acctyp>
@@ -79,7 +93,9 @@ int BaseEllipsoidT::init_base(const int nlocal, const int nall,
                   max_nbors,cell_size,true,1);
   if (success!=0)
     return success;
-  
+
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
@@ -146,20 +162,6 @@ void BaseEllipsoidT::clear_base() {
   output_times();
   host_olist.clear();
 
-  if (_compiled) {
-    k_nbor_fast.clear();
-    k_nbor.clear();
-    k_ellipsoid.clear();
-    k_ellipsoid_sphere.clear();
-    k_sphere_ellipsoid.clear();
-    k_lj_fast.clear();
-    k_lj.clear();
-    delete nbor_program;
-    delete ellipsoid_program;
-    delete lj_program;
-    _compiled=false;
-  }
-
   time_nbor1.clear();
   time_ellipsoid.clear();
   time_nbor2.clear();
@@ -171,7 +173,6 @@ void BaseEllipsoidT::clear_base() {
 
   nbor->clear();
   ans->clear();
-  device->clear();
 }
 
 template <class numtyp, class acctyp>
@@ -437,6 +438,7 @@ int** BaseEllipsoidT::compute(const int ago, const int inum_full, const int nall
   ans->copy_answers(eflag,vflag,eatom,vatom);
   device->add_ans_object(ans);
   hd_balancer.stop_timer();
+
   return nbor->host_jlist.begin()-host_start;
 }
 
@@ -462,18 +464,21 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev,
 
   std::string flags=device->compile_string();
 
+  if (nbor_program) delete nbor_program;
   nbor_program=new UCL_Program(dev);
   nbor_program->load_string(ellipsoid_nbor,flags.c_str());
   k_nbor_fast.set_function(*nbor_program,"kernel_nbor_fast");
   k_nbor.set_function(*nbor_program,"kernel_nbor");
   neigh_tex.get_texture(*nbor_program,"pos_tex");
 
+  if (ellipsoid_program) delete ellipsoid_program;
   ellipsoid_program=new UCL_Program(dev);
   ellipsoid_program->load_string(ellipsoid_string,flags.c_str());
   k_ellipsoid.set_function(*ellipsoid_program,kname);
   pos_tex.get_texture(*ellipsoid_program,"pos_tex");
   quat_tex.get_texture(*ellipsoid_program,"quat_tex");
 
+  if (lj_program) delete lj_program;
   lj_program=new UCL_Program(dev);
   lj_program->load_string(lj_string,flags.c_str());
   k_sphere_ellipsoid.set_function(*lj_program,s_sphere_ellipsoid.c_str());
diff --git a/lib/gpu/lal_base_three.cpp b/lib/gpu/lal_base_three.cpp
index dc5678dd24..0b4dbdc89a 100644
--- a/lib/gpu/lal_base_three.cpp
+++ b/lib/gpu/lal_base_three.cpp
@@ -27,6 +27,8 @@ BaseThreeT::BaseThree() : _compiled(false), _max_bytes(0) {
   #ifdef THREE_CONCURRENT
   ans2=new Answer<numtyp,acctyp>();
   #endif
+  pair_program=NULL;
+  ucl_device=NULL;
 }
 
 template <class numtyp, class acctyp>
@@ -36,6 +38,12 @@ BaseThreeT::~BaseThree() {
   #ifdef THREE_CONCURRENT
   delete ans2;
   #endif
+  k_three_center.clear();
+  k_three_end.clear();
+  k_three_end_vatom.clear();
+  k_pair.clear();
+  k_short_nbor.clear();
+  if (pair_program) delete pair_program;
 }
 
 template <class numtyp, class acctyp>
@@ -87,6 +95,8 @@ int BaseThreeT::init_three(const int nlocal, const int nall,
   if (success!=0)
     return success;
 
+  if (ucl_device!=device->gpu) _compiled=false;
+
   ucl_device=device->gpu;
   atom=&device->atom;
 
@@ -139,16 +149,6 @@ void BaseThreeT::clear_atomic() {
   device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
                        _gpu_overhead,_driver_overhead,_threads_per_atom,screen);
 
-  if (_compiled) {
-    k_three_center.clear();
-    k_three_end.clear();
-    k_three_end_vatom.clear();
-    k_pair.clear();
-    k_short_nbor.clear();
-    delete pair_program;
-    _compiled=false;
-  }
-
   time_pair.clear();
   hd_balancer.clear();
 
@@ -161,7 +161,6 @@ void BaseThreeT::clear_atomic() {
   // ucl_device will clean up the command queue in its destructor
 //  ucl_device->pop_command_queue();
   #endif
-  device->clear();
 }
 
 // ---------------------------------------------------------------------------
@@ -378,7 +377,7 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str,
     return;
 
   std::string vatom_name=std::string(three_end)+"_vatom";
-
+  if (pair_program) delete pair_program;
   pair_program=new UCL_Program(dev);
   pair_program->load_string(pair_str,device->compile_string().c_str());
   k_three_center.set_function(*pair_program,three_center);
diff --git a/lib/gpu/lal_gayberne.cu b/lib/gpu/lal_gayberne.cu
index dc6e00ec82..cd1ee59fc6 100644
--- a/lib/gpu/lal_gayberne.cu
+++ b/lib/gpu/lal_gayberne.cu
@@ -316,10 +316,9 @@ __kernel void k_gayberne(const __global numtyp4 *restrict x_,
         numtyp tempv[3];
         gpu_row_times3(iota,b1,tempv);
         gpu_cross3(tempv,iota,tchi);
-        temp1 = (numtyp)-4.0*ir*ir;
-        tchi[0] *= temp1;
-        tchi[1] *= temp1;
-        tchi[2] *= temp1;
+        tchi[0] *= temp2;
+        tchi[1] *= temp2;
+        tchi[2] *= temp2;
       }
 
       numtyp temp2 = factor_lj*eta*chi;
diff --git a/lib/gpu/lal_lj_tip4p_long.cpp b/lib/gpu/lal_lj_tip4p_long.cpp
new file mode 100644
index 0000000000..208d0ecbb0
--- /dev/null
+++ b/lib/gpu/lal_lj_tip4p_long.cpp
@@ -0,0 +1,372 @@
+/**************************************************************************
+                               lj_tip4p_long.cpp
+                             -------------------
+                              V. Nikolskiy (HSE)
+
+  Class for acceleration of the lj/tip4p/long pair style
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : thevsevak@gmail.com
+***************************************************************************/
+
+#if defined(USE_OPENCL)
+#include "lj_tip4p_long_cl.h"
+#elif defined(USE_CUDART)
+const char *lj_tip4p=0;
+#else
+#include "lj_tip4p_long_cubin.h"
+#endif
+
+#include "lal_lj_tip4p_long.h"
+#include <cassert>
+using namespace LAMMPS_AL;
+#define LJTIP4PLongT LJ_TIP4PLong<numtyp, acctyp>
+
+extern Device<PRECISION,ACC_PRECISION> device;
+
+template <class numtyp, class acctyp>
+LJTIP4PLongT::LJ_TIP4PLong(): BaseCharge<numtyp,acctyp>(), _allocated(false) {
+}
+
+template <class numtyp, class acctyp>
+LJTIP4PLongT::~LJ_TIP4PLong() {
+  clear();
+}
+
+template <class numtyp, class acctyp>
+int LJTIP4PLongT::bytes_per_atom(const int max_nbors) const {
+  return this->bytes_per_atom_atomic(max_nbors);
+}
+
+template <class numtyp, class acctyp>
+int LJTIP4PLongT::init(const int ntypes,
+    double **host_cutsq, double **host_lj1,
+    double **host_lj2, double **host_lj3,
+    double **host_lj4, double **host_offset,
+    double *host_special_lj, const int nlocal,
+    const int tH, const int tO,
+    const double a, const double qd,
+    const int nall, const int max_nbors,
+    const int maxspecial, const double cell_size,
+    const double gpu_split, FILE *_screen,
+    double **host_cut_ljsq,
+    const double host_cut_coulsq, const double host_cut_coulsqplus,
+    double *host_special_coul, const double qqrd2e,
+    const double g_ewald, int map_size, int max_same) {
+  int success;
+  success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
+                            _screen,lj_tip4p_long,"k_lj_tip4p_long");
+  if (success!=0)
+    return success;
+  k_pair_distrib.set_function(*this->pair_program,"k_lj_tip4p_long_distrib");
+  k_pair_reneigh.set_function(*this->pair_program,"k_lj_tip4p_reneigh");
+  k_pair_newsite.set_function(*this->pair_program,"k_lj_tip4p_newsite");
+
+  TypeH = tH;
+  TypeO = tO;
+  alpha = a;
+  qdist = qd;
+
+  // If atom type constants fit in shared memory use fast kernel
+  int lj_types=ntypes;
+  shared_types=false;
+//  int max_shared_types=this->device->max_shared_types();
+//  if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
+//    lj_types=max_shared_types;
+//    shared_types=true;
+//  }
+  _lj_types=lj_types;
+
+  // Allocate a host write buffer for data initialization
+  UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
+                               UCL_WRITE_ONLY);
+
+  for (int i=0; i<lj_types*lj_types; i++)
+    host_write[i]=0.0;
+
+  lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+  this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2,
+                         host_cut_ljsq);
+
+  lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+  this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4,
+                         host_offset);
+
+  cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+  this->atom->type_pack1(ntypes,lj_types,cutsq,host_write,host_cutsq);
+
+  sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY);
+  for (int i=0; i<4; i++) {
+    host_write[i]=host_special_lj[i];
+    host_write[i+4]=host_special_coul[i];
+  }
+  ucl_copy(sp_lj,host_write,8,false);
+
+  //force_comp.alloc(72*72, *(this->ucl_device), UCL_READ_WRITE);
+
+  _qqrd2e=qqrd2e;
+  _g_ewald=g_ewald;
+  cut_coulsq = host_cut_coulsq;
+  cut_coulsqplus = host_cut_coulsqplus;
+
+  hneight.alloc(nall*4,*(this->ucl_device), UCL_READ_WRITE);
+  m.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
+  ansO.alloc(nall,*(this->ucl_device), UCL_READ_WRITE);
+
+  this->tag.alloc(nall,*(this->ucl_device), UCL_READ_ONLY);
+  this->atom_sametag.alloc(max_same, *(this->ucl_device), UCL_READ_ONLY);
+  this->map_array.alloc(map_size,*(this->ucl_device), UCL_READ_ONLY);
+
+  _allocated=true;
+  this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+cutsq.row_bytes()+
+      sp_lj.row_bytes() + hneight.row_bytes()+m.row_bytes()+
+      this->tag.row_bytes()+this->atom_sametag.row_bytes() +
+      this->map_array.row_bytes();
+  return 0;
+}
+
+
+template <class numtyp, class acctyp>
+void LJTIP4PLongT::clear() {
+  if (!_allocated)
+    return;
+  _allocated=false;
+
+  lj1.clear();
+  lj3.clear();
+  sp_lj.clear();
+  cutsq.clear();
+  hneight.clear();
+  m.clear();
+  tag.clear();
+  atom_sametag.clear();
+  map_array.clear();
+  ansO.clear();
+  //force_comp.clear();
+
+  k_pair_distrib.clear();
+  k_pair_reneigh.clear();
+  k_pair_newsite.clear();
+
+  this->clear_atomic();
+}
+
+template <class numtyp, class acctyp>
+double LJTIP4PLongT::host_memory_usage() const {
+  return this->host_memory_usage_atomic()+sizeof(LJ_TIP4PLong<numtyp,acctyp>);
+}
+
+// ---------------------------------------------------------------------------
+// Calculate energies, forces, and torques
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+void LJTIP4PLongT::loop(const bool _eflag, const bool _vflag) {
+  // Compute the block size and grid size to keep all cores busy
+  const int BX=this->block_size();
+  int eflag, vflag;
+  if (_eflag)
+    eflag=1;
+  else
+    eflag=0;
+
+  if (_vflag)
+    vflag=1;
+  else
+    vflag=0;
+
+  int ainum=this->ans->inum();
+  const int nall = this->atom->nall();
+  int nbor_pitch=this->nbor->nbor_pitch();
+  this->time_pair.start();
+  int GX;
+  GX=static_cast<int>(ceil(static_cast<double>(nall)/BX));
+  if (t_ago == 0) {
+    this->k_pair_reneigh.set_size(GX,BX);
+    this->k_pair_reneigh.run(&this->atom->x,
+        &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+        &nall, &ainum,&nbor_pitch, &this->_threads_per_atom,
+        &hneight, &m, &TypeO, &TypeH,
+        &tag, &map_array, &atom_sametag);
+  }
+  this->k_pair_newsite.set_size(GX,BX);
+  this->k_pair_newsite.run(&this->atom->x,
+          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+          &nall, &ainum,
+          &nbor_pitch, &this->_threads_per_atom,
+          &hneight, &m, &TypeO, &TypeH, &alpha,
+          &this->atom->q, &tag, &map_array,
+          &atom_sametag);
+
+  GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
+                               (BX/this->_threads_per_atom)));
+  this->k_pair.set_size(GX,BX);
+  if (vflag) {
+          this->ansO.resize_ib(ainum*3);
+  } else {
+          this->ansO.resize_ib(ainum);
+  }
+  this->ansO.zero();
+  this->device->gpu->sync();
+  this->k_pair.run(&this->atom->x, &lj1, &lj3, &_lj_types, &sp_lj,
+          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+          &this->ans->force, &this->ans->engv, &eflag, &vflag,
+          &ainum, &nbor_pitch, &this->_threads_per_atom,
+          &hneight, &m, &TypeO, &TypeH, &alpha,
+          &this->atom->q, &cutsq, &_qqrd2e, &_g_ewald,
+          &cut_coulsq, &cut_coulsqplus, &tag, &map_array,
+          &atom_sametag, &this->ansO);
+  GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
+  this->k_pair_distrib.set_size(GX,BX);
+  this->k_pair_distrib.run(&this->atom->x, &this->ans->force, &this->ans->engv,
+      &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom,
+      &hneight, &m, &TypeO, &TypeH, &alpha,&this->atom->q,  &this->ansO);
+  this->time_pair.stop();
+}
+
+
+template <class numtyp, class acctyp>
+void LJTIP4PLongT::copy_relations_data(int n, tagint *tag, int *map_array,
+                      int map_size, int *sametag, int max_same, int ago) {
+  int nall = n;
+  const int hn_sz = n*4; // matrix size = col size * col number
+  hneight.resize_ib(hn_sz);
+  if (ago == 0)
+    hneight.zero();
+  m.resize_ib(n);
+  m.zero();
+
+  UCL_H_Vec<int> host_tag_write(nall,*(this->ucl_device),UCL_WRITE_ONLY);
+  this->tag.resize_ib(nall);
+  for(int i=0; i<nall; ++i) host_tag_write[i] = tag[i];
+  ucl_copy(this->tag, host_tag_write, nall, false);
+
+  host_tag_write.resize_ib(max_same);
+  this->atom_sametag.resize_ib(max_same);
+  for(int i=0; i<max_same; ++i) host_tag_write[i] = sametag[i];
+  ucl_copy(this->atom_sametag, host_tag_write, max_same, false);
+
+  host_tag_write.resize_ib(map_size);
+  this->map_array.resize_ib(map_size);
+  for(int i=0; i<map_size; ++i) host_tag_write[i] = map_array[i];
+  ucl_copy(this->map_array, host_tag_write, map_size, false);
+}
+
+
+
+
+// ---------------------------------------------------------------------------
+// Copy nbor list from host if necessary and then calculate forces, virials,..
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+void LJTIP4PLongT::compute(const int f_ago, const int inum_full,
+                               const int nall, double **host_x, int *host_type,
+                               int *ilist, int *numj, int **firstneigh,
+                               const bool eflag, const bool vflag,
+                               const bool eatom, const bool vatom,
+                               int &host_start, const double cpu_time,
+                               bool &success, double *host_q,
+                               const int nlocal, double *boxlo, double *prd) {
+  this->acc_timers();
+  if (inum_full==0) {
+    host_start=0;
+    // Make sure textures are correct if realloc by a different hybrid style
+    this->resize_atom(0,nall,success);
+    this->zero_timers();
+    return;
+  }
+
+  int ago=this->hd_balancer.ago_first(f_ago);
+  int inum=this->hd_balancer.balance(ago,inum_full,cpu_time);
+  this->ans->inum(inum);
+  host_start=inum;
+
+  if (ago==0) {
+    this->reset_nbors(nall, inum, ilist, numj, firstneigh, success);
+    if (!success)
+      return;
+  }
+
+  this->atom->cast_x_data(host_x,host_type);
+  this->atom->cast_q_data(host_q);
+  this->hd_balancer.start_timer();
+  this->atom->add_x_data(host_x,host_type);
+  this->atom->add_q_data();
+
+  this->device->precompute(f_ago,nlocal,nall,host_x,host_type,success,host_q,
+                     boxlo, prd);
+
+  t_ago = ago;
+  loop(eflag,vflag);
+  this->ans->copy_answers(eflag,vflag,eatom,vatom,ilist);
+  this->device->add_ans_object(this->ans);
+  this->hd_balancer.stop_timer();
+}
+
+// ---------------------------------------------------------------------------
+// Reneighbor on GPU if necessary and then compute forces, virials, energies
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+int** LJTIP4PLongT::compute(const int ago, const int inum_full,
+                                const int nall, double **host_x, int *host_type,
+                                double *sublo, double *subhi, tagint *tag,
+                                int *map_array, int map_size, int *sametag, int max_same,
+                                int **nspecial, tagint **special, const bool eflag,
+                                const bool vflag, const bool eatom,
+                                const bool vatom, int &host_start,
+                                int **ilist, int **jnum,
+                                const double cpu_time, bool &success,
+                                double *host_q, double *boxlo, double *prd) {
+  this->acc_timers();
+  if (inum_full==0) {
+    host_start=0;
+    // Make sure textures are correct if realloc by a different hybrid style
+    this->resize_atom(0,nall,success);
+    this->zero_timers();
+    return NULL;
+  }
+
+  this->hd_balancer.balance(cpu_time);
+  int inum=this->hd_balancer.get_gpu_count(ago,inum_full);
+  this->ans->inum(inum);
+  host_start=inum;
+
+  // Build neighbor list on GPU if necessary
+  if (ago==0) {
+    this->build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
+                    sublo, subhi, tag, nspecial, special, success);
+    if (!success)
+      return NULL;
+    this->atom->cast_q_data(host_q);
+    this->hd_balancer.start_timer();
+  } else {
+    this->atom->cast_x_data(host_x,host_type);
+    this->atom->cast_q_data(host_q);
+    this->hd_balancer.start_timer();
+    this->atom->add_x_data(host_x,host_type);
+  }
+  this->atom->add_q_data();
+  *ilist=this->nbor->host_ilist.begin();
+  *jnum=this->nbor->host_acc.begin();
+
+  copy_relations_data(nall, tag, map_array, map_size, sametag, max_same, ago);
+
+  this->device->precompute(ago,inum_full,nall,host_x,host_type,success,host_q,
+                     boxlo, prd);
+
+  t_ago = ago;
+  loop(eflag,vflag);
+  this->ans->copy_answers(eflag,vflag,eatom,vatom);
+  this->device->add_ans_object(this->ans);
+  this->hd_balancer.stop_timer();
+
+  return this->nbor->host_jlist.begin()-host_start;
+}
+
+
+
+
+template class LJ_TIP4PLong<PRECISION,ACC_PRECISION>;
diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu
new file mode 100644
index 0000000000..10ac5b8454
--- /dev/null
+++ b/lib/gpu/lal_lj_tip4p_long.cu
@@ -0,0 +1,568 @@
+// **************************************************************************
+//                               lj_tip4p_long.cu
+//                             -------------------
+//                              V. Nikolskiy (HSE)
+//
+//  Device code for acceleration of the lj/tip4p/long pair style
+//
+// __________________________________________________________________________
+//    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+//    begin                :
+//    email                : thevsevak@gmail.com
+// ***************************************************************************
+
+#ifdef NV_KERNEL
+
+#include "lal_aux_fun1.h"
+#ifndef _DOUBLE_DOUBLE
+texture<float4> pos_tex;
+texture<float> q_tex;
+#else
+texture<int4,1> pos_tex;
+texture<int2> q_tex;
+#endif
+
+#else
+#define pos_tex x_
+#define q_tex q_
+#endif
+
+ucl_inline int atom_mapping(const __global int *map, int glob) {
+  return map[glob];
+}
+
+ucl_inline int closest_image(int i, int j, const __global int* sametag,
+                             const __global numtyp4 *restrict x_)
+{
+  if (j < 0) return j;
+
+  numtyp4 xi; fetch4(xi,i,pos_tex); // = x[i];
+  numtyp4 xj; fetch4(xj,j,pos_tex);
+
+  int closest = j;
+  numtyp delx = xi.x - xj.x;
+  numtyp dely = xi.y - xj.y;
+  numtyp delz = xi.z - xj.z;
+  numtyp rsqmin = delx*delx + dely*dely + delz*delz;
+  numtyp rsq;
+
+  while (sametag[j] >= 0) {
+    j = sametag[j];
+    fetch4(xj,j,pos_tex);
+    delx = xi.x - xj.x;
+    dely = xi.y - xj.y;
+    delz = xi.z - xj.z;
+    rsq = delx*delx + dely*dely + delz*delz;
+    if (rsq < rsqmin) {
+      rsqmin = rsq;
+      closest = j;
+    }
+  }
+
+  return closest;
+}
+
+ucl_inline void compute_newsite(int iO, int  iH1, int  iH2,
+    __global numtyp4 *xM, numtyp q,
+    numtyp alpha, const __global numtyp4 *restrict x_) {
+  numtyp4 xO;  fetch4(xO,iO,pos_tex);
+  numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+  numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+  numtyp4 M;
+
+  numtyp delx1 = xH1.x - xO.x;
+  numtyp dely1 = xH1.y - xO.y;
+  numtyp delz1 = xH1.z - xO.z;
+
+  numtyp delx2 = xH2.x - xO.x;
+  numtyp dely2 = xH2.y - xO.y;
+  numtyp delz2 = xH2.z - xO.z;
+
+  numtyp ap = alpha * (numtyp)0.5;
+
+  M.x = xO.x + ap * (delx1 + delx2);
+  M.y = xO.y + ap * (dely1 + dely2);
+  M.z = xO.z + ap * (delz1 + delz2);
+  M.w = q;
+
+  *xM = M;
+}
+
+__kernel void k_lj_tip4p_long_distrib(const __global numtyp4 *restrict x_,
+    __global acctyp4 *restrict ans,
+    __global acctyp *restrict engv,
+    const int eflag, const int vflag, const int inum,
+    const int nbor_pitch, const int t_per_atom,
+    __global int *restrict hneigh,
+    __global numtyp4 *restrict m,
+    const int typeO, const int typeH,
+    const numtyp alpha,
+    const __global numtyp *restrict q_, const __global acctyp4 *restrict ansO) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+  int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
+
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+
+  if (i<inum) {
+    numtyp4 ix; fetch4(ix,i,pos_tex);// = x_[i];
+    int itype = ix.w;
+    acctyp4 fM, vM;
+    acctyp eM;
+    if (itype == typeH) {
+      int iO = hneigh[i*4];
+      if (iO < inum) {
+        fM = ansO[iO];
+        f.x += fM.x * (acctyp)0.5 * alpha;
+        f.y += fM.y * (acctyp)0.5 * alpha;
+        f.z += fM.z * (acctyp)0.5 * alpha;
+        if (vflag > 0) {
+          vM = ansO[inum  +iO];
+          engv[inum*2 + i] += vM.x * (acctyp)0.5 * alpha;
+          engv[inum*3 + i] += vM.y * (acctyp)0.5 * alpha;
+          engv[inum*4 + i] += vM.z * (acctyp)0.5 * alpha;
+          vM = ansO[inum*2+iO];
+          engv[inum*5 + i] += vM.x * (acctyp)0.5 * alpha;
+          engv[inum*6 + i] += vM.y * (acctyp)0.5 * alpha;
+          engv[inum*7 + i] += vM.z * (acctyp)0.5 * alpha;
+        }
+      }
+    } else {
+      fM = ansO[i];
+      int iH1 = hneigh[i*4  ];
+      int iH2 = hneigh[i*4+1];
+      f.x += fM.x * (acctyp)(1 - alpha);
+      f.y += fM.y * (acctyp)(1 - alpha);
+      f.z += fM.z * (acctyp)(1 - alpha);
+      if (eflag > 0) {
+        eM = engv[i+inum];
+        engv[inum+i] = eM*(acctyp)(1 - alpha);
+        if (iH1 < inum) engv[inum+iH1] += eM * (acctyp)0.5 * alpha;
+        if (iH2 < inum) engv[inum+iH2] += eM * (acctyp)0.5 * alpha;
+      }
+      if (vflag > 0) {
+        vM = ansO[inum   + i];
+        engv[inum*2 + i] += vM.x * (acctyp)(1 - alpha);
+        engv[inum*3 + i] += vM.y * (acctyp)(1 - alpha);
+        engv[inum*4 + i] += vM.z * (acctyp)(1 - alpha);
+        vM = ansO[inum*2 + i];
+        engv[inum*5 + i] += vM.x * (acctyp)(1 - alpha);
+        engv[inum*6 + i] += vM.y * (acctyp)(1 - alpha);
+        engv[inum*7 + i] += vM.z * (acctyp)(1 - alpha);
+      }
+    }
+    acctyp4 old=ans[i];
+    old.x+=f.x;
+    old.y+=f.y;
+    old.z+=f.z;
+    ans[i]=old;
+  } // if ii
+}
+
+__kernel void k_lj_tip4p_reneigh(const __global numtyp4 *restrict x_,
+    const __global int * dev_nbor,
+    const __global int * dev_packed,
+    const int nall, const int inum,
+    const int nbor_pitch, const int t_per_atom,
+    __global int *restrict hneigh,
+    __global numtyp4 *restrict m,
+    const int typeO, const int typeH,
+    const __global int *restrict tag, const __global int *restrict map,
+    const __global int *restrict sametag) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+  int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
+
+  if (i<nall) {
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+
+    int iH1, iH2, iO;
+    int itype = ix.w;
+    if(itype == typeO) {
+      iO  = i;
+      if (hneigh[i*4+2] != -1) {
+        iH1 = atom_mapping(map, tag[i] + 1);
+        iH2 = atom_mapping(map, tag[i] + 2);
+        // set iH1,iH2 to closest image to O
+        iH1 = closest_image(i, iH1, sametag, x_);
+        iH2 = closest_image(i, iH2, sametag, x_);
+        hneigh[i*4  ] = iH1;
+        hneigh[i*4+1] = iH2;
+        hneigh[i*4+2] = -1;
+      }
+    } else {
+      if (hneigh[i*4+2] != -1) {
+        int iI, iH;
+        iI = atom_mapping(map,tag[i] - 1);
+        numtyp4 iIx; fetch4(iIx,iI,pos_tex); //x_[iI];
+        if ((int)iIx.w == typeH) {
+          iO = atom_mapping(map,tag[i] - 2);
+          iO  = closest_image(i, iO, sametag, x_);
+          iH1 = closest_image(i, iI, sametag, x_);
+          iH2 = i;
+        } else { //if ((int)iIx.w == typeO)
+          iH = atom_mapping(map, tag[i] + 1);
+          iO  = closest_image(i,iI,sametag, x_);
+          iH1 = i;
+          iH2 = closest_image(i,iH,sametag, x_);
+        }
+        hneigh[i*4+0] = iO;
+        hneigh[i*4+1] += -1;
+        hneigh[i*4+2] = -1;
+      }
+    }
+  }
+}
+
+
+__kernel void k_lj_tip4p_newsite(const __global numtyp4 *restrict x_,
+    const __global int * dev_nbor,
+    const __global int * dev_packed,
+    const int nall, const int inum,
+    const int nbor_pitch, const int t_per_atom,
+    __global int *restrict hneigh,
+    __global numtyp4 *restrict m,
+    const int typeO, const int typeH,
+    const numtyp alpha, const __global numtyp *restrict q_,
+    const __global int *restrict tag, const __global int *restrict map,
+    const __global int *restrict sametag) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+  int i = BLOCK_ID_X*(BLOCK_SIZE_X)+tid;
+
+  if (i<nall) {
+    int iO, iH1, iH2;
+    iO  = i;
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype = ix.w;
+    if (itype == typeO) {
+      int iH1, iH2, iO;
+      iH1 = hneigh[i*4  ];
+      iH2 = hneigh[i*4+1];
+      iO  = i;
+      numtyp qO; fetch(qO,iO,q_tex);
+      compute_newsite(iO,iH1,iH2, &m[iO], qO, alpha, x_);
+    }
+  }
+}
+
+__kernel void k_lj_tip4p_long(const __global numtyp4 *restrict x_,
+    const __global numtyp4 *restrict lj1,
+    const __global numtyp4 *restrict lj3,
+    const int lj_types,
+    const __global numtyp *restrict sp_lj,
+    const __global int * dev_nbor,
+    const __global int * dev_packed,
+    __global acctyp4 *restrict ans,
+    __global acctyp *restrict engv,
+    const int eflag, const int vflag, const int inum,
+    const int nbor_pitch, const int t_per_atom,
+    __global int *restrict hneigh,
+    __global numtyp4 *restrict m,
+    const int typeO, const int typeH,
+    const numtyp alpha,
+    const __global numtyp *restrict q_,
+    const __global numtyp *restrict cutsq,
+    const numtyp qqrd2e, const numtyp g_ewald,
+    const numtyp cut_coulsq, const numtyp cut_coulsqplus,
+    const __global int *restrict tag, const __global int *restrict map,
+    const __global int *restrict sametag, __global acctyp4 *restrict ansO) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+
+  const numtyp eq_zero = 1e-6;
+
+  acctyp energy = (acctyp)0;
+  acctyp e_coul = (acctyp)0;
+  acctyp4 f, fO;
+  f.x=(acctyp)0;  f.y=(acctyp)0;  f.z=(acctyp)0;
+  fO.x=(acctyp)0; fO.y=(acctyp)0; fO.z=(acctyp)0;
+  acctyp virial[6],vO[6];
+  for (int i=0; i<6; i++) {
+    virial[i]=(acctyp)0;
+    vO[i]=(acctyp)0;
+  }
+
+  if (ii<inum) {
+    int i, numj, nbor, nbor_end;
+    __local int n_stride;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
+        n_stride,nbor_end,nbor);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    numtyp qtmp; fetch(qtmp,i,q_tex);
+    int itype = ix.w;
+    numtyp4 x1 = ix;
+
+    int non_local_oxy = 0;
+    int iH1, iH2, iO;
+
+    if(itype == typeO) {
+      iO  = i;
+      iH1 = hneigh[i*4  ];
+      iH2 = hneigh[i*4+1];
+      x1 = m[iO];
+    } else {
+      iO  = hneigh[i *4  ];
+      iH1 = hneigh[iO*4  ];
+      iH2 = hneigh[iO*4+1];
+      if (iO >= inum) {
+        non_local_oxy = 1;
+      }
+    }
+
+    for ( ; nbor<nbor_end; nbor+=n_stride) {
+      int j=dev_packed[nbor];
+
+      numtyp factor_lj,factor_coul;
+      factor_lj = sp_lj[sbmask(j)];
+      factor_coul = (numtyp)1.0-sp_lj[sbmask(j)+4];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype = jx.w;
+
+      // Compute r12
+      numtyp delx = ix.x-jx.x;
+      numtyp dely = ix.y-jx.y;
+      numtyp delz = ix.z-jx.z;
+      numtyp rsq = delx*delx+dely*dely+delz*delz;
+
+      int mtype = itype*lj_types+jtype;
+      if (rsq < lj1[mtype].z) { // cut_ljsq
+        numtyp r2inv = ucl_recip(rsq);
+        numtyp r6inv = r2inv*r2inv*r2inv;
+        numtyp forcelj = r6inv*(lj1[mtype].x*r6inv-lj1[mtype].y);
+        forcelj *= r2inv*factor_lj;
+
+        f.x += delx*forcelj;
+        f.y += dely*forcelj;
+        f.z += delz*forcelj;
+
+        if (eflag>0) {
+          numtyp e = r6inv * (lj3[mtype].x*r6inv-lj3[mtype].y);
+          energy += factor_lj * (e - lj3[mtype].z);
+        }
+        if (vflag>0) {
+          virial[0] += delx*delx*forcelj;
+          virial[1] += dely*dely*forcelj;
+          virial[2] += delz*delz*forcelj;
+          virial[3] += delx*dely*forcelj;
+          virial[4] += delx*delz*forcelj;
+          virial[5] += dely*delz*forcelj;
+        }
+      } // if LJ
+
+      if (rsq < cut_coulsqplus) { //cut_coulsqplus
+        int jH1, jH2, jO;
+        numtyp qj; fetch(qj,j,q_tex);
+        numtyp4 x2 = jx;
+        if(itype == typeO || jtype == typeO) {
+          if (jtype == typeO) {
+            jO = j;
+            jH1 = hneigh[j*4  ];
+            jH2 = hneigh[j*4+1];
+            x2 = m[j];
+          }
+          delx = x1.x-x2.x;
+          dely = x1.y-x2.y;
+          delz = x1.z-x2.z;
+          rsq = delx*delx+dely*dely+delz*delz;
+        }
+        if (rsq < cut_coulsq) {
+          numtyp r2inv = ucl_recip(rsq);
+          numtyp r = ucl_rsqrt(r2inv);
+          numtyp grij = g_ewald * r;
+          numtyp expm2 = ucl_exp(-grij*grij);
+          numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
+          numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+
+          numtyp prefactor = qj;
+          prefactor *= qqrd2e*qtmp/r;
+          numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
+
+          if (itype == typeH) {
+            f.x += delx * force_coul;
+            f.y += dely * force_coul;
+            f.z += delz * force_coul;
+            f.w += 0;
+          } else {
+            fO.x += delx * force_coul;
+            fO.y += dely * force_coul;
+            fO.z += delz * force_coul;
+            fO.w += 0;
+          }
+          if (eflag>0) {
+            e_coul += prefactor*(_erfc-factor_coul);
+          }
+          if (vflag>0) {
+            acctyp4 fd;
+            fd.x = delx*force_coul;
+            fd.y = dely*force_coul;
+            fd.z = delz*force_coul;
+            if (itype == typeH) {
+              if (jtype == typeH) {
+                virial[0] += delx*fd.x;
+                virial[1] += dely*fd.y;
+                virial[2] += delz*fd.z;
+                virial[3] += delx*fd.y;
+                virial[4] += delx*fd.z;
+                virial[5] += dely*fd.z;
+              } else {
+                numtyp cO = 1 - alpha, cH = 0.5*alpha;
+                numtyp4 vdj;
+                numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
+                numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
+                numtyp4 xjO; fetch4(xjO,jO,pos_tex);
+                vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
+                vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
+                vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
+                //vdj.w = vdj.w;
+                virial[0] += (ix.x - vdj.x)*fd.x;
+                virial[1] += (ix.y - vdj.y)*fd.y;
+                virial[2] += (ix.z - vdj.z)*fd.z;
+                virial[3] += (ix.x - vdj.x)*fd.y;
+                virial[4] += (ix.x - vdj.x)*fd.z;
+                virial[5] += (ix.y - vdj.y)*fd.z;
+              }
+            } else {
+              numtyp cO = 1 - alpha, cH = 0.5*alpha;
+              numtyp4 vdi, vdj;
+              numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+              numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+              numtyp4 xO; fetch4(xO,iO,pos_tex);
+              vdi.x = xO.x*cO + xH1.x*cH + xH2.x*cH;
+              vdi.y = xO.y*cO + xH1.y*cH + xH2.y*cH;
+              vdi.z = xO.z*cO + xH1.z*cH + xH2.z*cH;
+              //vdi.w = vdi.w;
+              if (jtype != typeH) {
+                numtyp4 xjH1; fetch4(xjH1,jH1,pos_tex);
+                numtyp4 xjH2; fetch4(xjH2,jH2,pos_tex);
+                numtyp4 xjO; fetch4(xjO,jO,pos_tex);
+                vdj.x = xjO.x*cO + xjH1.x*cH + xjH2.x*cH;
+                vdj.y = xjO.y*cO + xjH1.y*cH + xjH2.y*cH;
+                vdj.z = xjO.z*cO + xjH1.z*cH + xjH2.z*cH;
+                //vdj.w = vdj.w;
+              } else vdj = jx;
+              vO[0] += 0.5*(vdi.x - vdj.x)*fd.x;
+              vO[1] += 0.5*(vdi.y - vdj.y)*fd.y;
+              vO[2] += 0.5*(vdi.z - vdj.z)*fd.z;
+              vO[3] += 0.5*(vdi.x - vdj.x)*fd.y;
+              vO[4] += 0.5*(vdi.x - vdj.x)*fd.z;
+              vO[5] += 0.5*(vdi.y - vdj.y)*fd.z;
+            }
+          }
+        }
+        if (non_local_oxy == 1) {
+          if (iO == j) {
+            x2 = ix;
+            qj = qtmp;
+          }
+          numtyp4 x1m = m[iO];
+          delx = x1m.x-x2.x;
+          dely = x1m.y-x2.y;
+          delz = x1m.z-x2.z;
+          rsq = delx*delx+dely*dely+delz*delz;
+          if (rsq < cut_coulsq) {
+            numtyp r2inv = ucl_recip(rsq);
+            numtyp r = ucl_rsqrt(r2inv);
+            numtyp grij = g_ewald * r;
+            numtyp expm2 = ucl_exp(-grij*grij);
+            numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
+            numtyp _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+
+            numtyp prefactor = qj;
+            prefactor *= qqrd2e*x1m.w/r;
+            numtyp force_coul = r2inv*prefactor * (_erfc + EWALD_F*grij*expm2 - factor_coul);
+
+            numtyp cO = 1 - alpha, cH = 0.5*alpha;
+            numtyp4 fd;
+            fd.x = delx * force_coul * cH;
+            fd.y = dely * force_coul * cH;
+            fd.z = delz * force_coul * cH;
+
+            f.x += fd.x;
+            f.y += fd.y;
+            f.z += fd.z;
+
+            if (eflag>0) {
+              e_coul += prefactor*(_erfc-factor_coul) * (acctyp)0.5 * alpha;
+            }
+            if (vflag>0) {
+              numtyp4 xH1; fetch4(xH1,iH1,pos_tex);
+              numtyp4 xH2; fetch4(xH2,iH2,pos_tex);
+              numtyp4 xO;  fetch4(xO,iO,pos_tex);
+
+              virial[0] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.x;
+              virial[1] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.y;
+              virial[2] += ((xO.z*cO + xH1.z*cH + xH2.z*cH) - x2.z) * fd.z;
+              virial[3] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.y;
+              virial[4] += ((xO.x*cO + xH1.x*cH + xH2.x*cH) - x2.x) * fd.z;
+              virial[5] += ((xO.y*cO + xH1.y*cH + xH2.y*cH) - x2.y) * fd.z;
+            }
+          }
+        }
+      } // if cut_coulsqplus
+    } // for nbor
+    if (t_per_atom>1) {
+#if (ARCH < 300)
+      __local acctyp red_acc[6][BLOCK_PAIR];
+      red_acc[0][tid]=fO.x;
+      red_acc[1][tid]=fO.y;
+      red_acc[2][tid]=fO.z;
+      red_acc[3][tid]=fO.w;
+      for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+        if (offset < s) {
+          for (int r=0; r<4; r++)
+            red_acc[r][tid] += red_acc[r][tid+s];
+        }
+      }
+      fO.x=red_acc[0][tid];
+      fO.y=red_acc[1][tid];
+      fO.z=red_acc[2][tid];
+      fO.w=red_acc[3][tid];
+      if (vflag>0) {
+        for (int r=0; r<6; r++) red_acc[r][tid]=vO[r];
+        for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+          if (offset < s) {
+            for (int r=0; r<6; r++)
+              red_acc[r][tid] += red_acc[r][tid+s];
+          }
+        }
+        for (int r=0; r<6; r++) vO[r]=red_acc[r][tid];
+      }
+#else
+      for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+        fO.x += shfl_xor(fO.x, s, t_per_atom);
+        fO.y += shfl_xor(fO.y, s, t_per_atom);
+        fO.z += shfl_xor(fO.z, s, t_per_atom);
+        fO.w += shfl_xor(fO.w, s, t_per_atom);
+      }
+      if (vflag>0) {
+        for (unsigned int s=t_per_atom/2; s>0; s>>=1) {
+          for (int r=0; r<6; r++)
+            vO[r] += shfl_xor(vO[r], s, t_per_atom);
+        }
+      }
+#endif
+    }
+    if(offset == 0) {
+      ansO[i] = fO;
+      if (vflag>0) {
+        ansO[inum   + i].x = vO[0];
+        ansO[inum   + i].y = vO[1];
+        ansO[inum   + i].z = vO[2];
+        ansO[inum*2 + i].x = vO[3];
+        ansO[inum*2 + i].y = vO[4];
+        ansO[inum*2 + i].z = vO[5];
+      }
+    }
+    store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
+        vflag,ans,engv);
+  } // if ii
+}
+
+__kernel void k_lj_tip4p_long_fast() {}
diff --git a/lib/gpu/lal_lj_tip4p_long.h b/lib/gpu/lal_lj_tip4p_long.h
new file mode 100644
index 0000000000..584a53e22b
--- /dev/null
+++ b/lib/gpu/lal_lj_tip4p_long.h
@@ -0,0 +1,127 @@
+/**************************************************************************
+                               lj_tip4p_long.h
+                             -------------------
+                              V. Nikolskiy (HSE)
+
+  Class for acceleration of the lj/tip4p/long pair style
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : thevsevak@gmail.com
+***************************************************************************/
+
+#ifndef LAL_LJ_TIP4P_LONG_H
+#define LAL_LJ_TIP4P_LONG_H
+
+#include "lal_base_charge.h"
+
+namespace LAMMPS_AL {
+
+template <class numtyp, class acctyp>
+class LJ_TIP4PLong : public BaseCharge<numtyp, acctyp> {
+public:
+  LJ_TIP4PLong();
+  ~LJ_TIP4PLong();
+
+  /// Clear any previous data and set up for a new LAMMPS run
+  /** \param max_nbors initial number of rows in the neighbor matrix
+    * \param cell_size cutoff + skin
+    * \param gpu_split fraction of particles handled by device
+    *
+    * Returns:
+    * -  0 if successfull
+    * - -1 if fix gpu not found
+    * - -3 if there is an out of memory error
+    * - -4 if the GPU library was not compiled for GPU
+    * - -5 Double precision is not supported on card **/
+  int init(const int ntypes, double **host_cutsq,
+           double **host_lj1, double **host_lj2, double **host_lj3,
+           double **host_lj4, double **host_offset, double *host_special_lj,
+           const int nlocal, const int tH, const int tO,
+           const double alpha, const double qdist,
+           const int nall, const int max_nbors,
+           const int maxspecial, const double cell_size,
+           const double gpu_split, FILE *screen,
+           double **host_cut_ljsq,
+           const double host_cut_coulsq, const double host_cut_coulsqplus,
+           double *host_special_coul, const double qqrd2e,
+           const double g_ewald, int map_size,int max_same);
+
+  /// Clear all host and device data
+  /** \note This is called at the beginning of the init() routine **/
+  void clear();
+
+  /// Returns memory usage on device per atom
+  int bytes_per_atom(const int max_nbors) const;
+
+  /// Total host memory used by library for pair style
+  double host_memory_usage() const;
+
+  /// Copy data from LAMMPS_NS
+  void copy_relations_data(int n, tagint* tag, int *map_array, int map_size,
+                           int *sametag, int max_same, int ago);
+
+  /// Reimplement BaseCharge pair loop with host neighboring
+  void compute(const int f_ago, const int inum_full, const int nall,
+               double **host_x, int *host_type, int *ilist, int *numj,
+               int **firstneigh, const bool eflag, const bool vflag,
+               const bool eatom, const bool vatom, int &host_start,
+               const double cpu_time, bool &success, double *charge,
+               const int nlocal, double *boxlo, double *prd);
+
+  /// Reimplement BaseCharge pair loop with device neighboring
+  int** compute(const int ago, const int inum_full, const int nall,
+                double **host_x, int *host_type, double *sublo,
+                double *subhi, tagint *tag,int *map_array, int map_size, int *sametag, int max_same,
+                int **nspecial,
+                tagint **special, const bool eflag, const bool vflag,
+                const bool eatom, const bool vatom, int &host_start,
+                int **ilist, int **numj, const double cpu_time, bool &success,
+                double *charge, double *boxlo, double *prd);
+
+
+  // --------------------------- TYPE DATA --------------------------
+
+  /// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq_vdw
+  UCL_D_Vec<numtyp4> lj1;
+  /// lj3.x = lj3, lj3.y = lj4, lj3.z = offset
+  UCL_D_Vec<numtyp4> lj3;
+  /// cutsq
+  UCL_D_Vec<numtyp> cutsq;
+  /// Special LJ values [0-3] and Special Coul values [4-7]
+  UCL_D_Vec<numtyp> sp_lj;
+
+  bool shared_types;
+
+  /// Number of atom types
+  int _lj_types;
+
+  numtyp _qqrd2e, _g_ewald;
+  /// TIP4P water parameters
+  int TypeO, TypeH;
+  numtyp alpha, qdist;
+  numtyp cut_coulsq, cut_coulsqplus;
+
+  UCL_D_Vec<int> hneight;
+  UCL_D_Vec<numtyp4> m; // position and charge of virtual particle
+  UCL_D_Vec<acctyp4> ansO; // force applied to virtual particle
+  // UCL_D_Vec<acctyp4> force_comp;
+
+  UCL_D_Vec<int> tag;
+  UCL_D_Vec<int> map_array;
+  UCL_D_Vec<int> atom_sametag;
+
+  UCL_Kernel k_pair_distrib, k_pair_reneigh, k_pair_newsite;
+
+ private:
+  bool _allocated;
+  int t_ago;
+  void loop(const bool _eflag, const bool _vflag);
+};
+
+}
+
+#endif
diff --git a/lib/gpu/lal_lj_tip4p_long_ext.cpp b/lib/gpu/lal_lj_tip4p_long_ext.cpp
new file mode 100644
index 0000000000..d0d6c7a3d2
--- /dev/null
+++ b/lib/gpu/lal_lj_tip4p_long_ext.cpp
@@ -0,0 +1,147 @@
+/***************************************************************************
+                            lj_tip4p_long_ext.cpp
+                             -------------------
+                              V. Nikolskiy (HSE)
+
+  Functions for LAMMPS access to lj/tip4p/long acceleration functions
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : thevsevak@gmail.com
+ ***************************************************************************/
+
+#include <iostream>
+#include <cassert>
+#include <cmath>
+
+#include "lal_lj_tip4p_long.h"
+
+using namespace std;
+using namespace LAMMPS_AL;
+
+static LJ_TIP4PLong<PRECISION,ACC_PRECISION> LJTIP4PLMF;
+
+// ---------------------------------------------------------------------------
+// Allocate memory on host and device and copy constants to device
+// ---------------------------------------------------------------------------
+int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
+    double **host_lj2, double **host_lj3, double **host_lj4,
+    double **offset, double *special_lj, const int inum,
+    const int tH, const int tO,
+    const double alpha, const double qdist,
+    const int nall, const int max_nbors,  const int maxspecial,
+    const double cell_size, int &gpu_mode, FILE *screen,
+    double **host_cut_ljsq,
+    const double host_cut_coulsq, const double host_cut_coulsqplus,
+    double *host_special_coul, const double qqrd2e,
+    const double g_ewald, int map_size,int max_same) {
+  LJTIP4PLMF.clear();
+  gpu_mode=LJTIP4PLMF.device->gpu_mode();
+  double gpu_split=LJTIP4PLMF.device->particle_split();
+  int first_gpu=LJTIP4PLMF.device->first_device();
+  int last_gpu=LJTIP4PLMF.device->last_device();
+  int world_me=LJTIP4PLMF.device->world_me();
+  int gpu_rank=LJTIP4PLMF.device->gpu_rank();
+  int procs_per_gpu=LJTIP4PLMF.device->procs_per_gpu();
+
+  LJTIP4PLMF.device->init_message(screen,"lj/cut/tip4p/long/gpu",first_gpu,last_gpu);
+
+  bool message=false;
+  if (LJTIP4PLMF.device->replica_me()==0 && screen)
+    message=true;
+
+  if (message) {
+    fprintf(screen,"Initializing Device and compiling on process 0...");
+    fflush(screen);
+  }
+
+  int init_ok=0;
+  if (world_me==0)
+    init_ok=LJTIP4PLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3,
+        host_lj4, offset, special_lj, inum,
+        tH, tO, alpha, qdist, nall, 300,
+        maxspecial, cell_size, gpu_split, screen,
+        host_cut_ljsq, host_cut_coulsq, host_cut_coulsqplus,
+        host_special_coul, qqrd2e, g_ewald, map_size, max_same);
+
+  LJTIP4PLMF.device->world_barrier();
+  if (message)
+    fprintf(screen,"Done.\n");
+
+  for (int i=0; i<procs_per_gpu; i++) {
+    if (message) {
+      if (last_gpu-first_gpu==0)
+        fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
+      else
+        fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
+                last_gpu,i);
+      fflush(screen);
+    }
+    if (gpu_rank==i && world_me!=0)
+      init_ok=LJTIP4PLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
+          offset, special_lj, inum,
+          tH, tO, alpha, qdist, nall, 300, maxspecial,
+          cell_size, gpu_split, screen, host_cut_ljsq,
+          host_cut_coulsq, host_cut_coulsqplus,
+          host_special_coul, qqrd2e,
+          g_ewald, map_size, max_same);
+
+    LJTIP4PLMF.device->gpu_barrier();
+    if (message)
+      fprintf(screen,"Done.\n");
+  }
+  if (message)
+    fprintf(screen,"\n");
+
+  if (init_ok==0)
+    LJTIP4PLMF.estimate_gpu_overhead();
+  return init_ok;
+}
+
+void ljtip4p_long_gpu_clear() {
+  LJTIP4PLMF.clear();
+}
+
+int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum_full,
+                        const int nall, double **host_x, int *host_type,
+                        double *sublo, double *subhi,
+                        tagint *tag, int *map_array, int map_size,
+                        int *sametag, int max_same,
+                        int **nspecial,
+                        tagint **special, const bool eflag, const bool vflag,
+                        const bool eatom, const bool vatom, int &host_start,
+                        int **ilist, int **jnum, const double cpu_time,
+                        bool &success, double *host_q, double *boxlo,
+                        double *prd) {
+  return LJTIP4PLMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
+                       subhi, tag, map_array, map_size, sametag, max_same,
+                       nspecial, special, eflag, vflag, eatom,
+                       vatom, host_start, ilist, jnum, cpu_time, success,
+                       host_q,boxlo, prd);
+}
+
+void ljtip4p_long_gpu_compute(const int ago, const int inum_full, const int nall,
+                     double **host_x, int *host_type, int *ilist, int *numj,
+                     int **firstneigh, const bool eflag, const bool vflag,
+                     const bool eatom, const bool vatom, int &host_start,
+                     const double cpu_time, bool &success,double *host_q,
+                     const int nlocal, double *boxlo, double *prd) {
+  LJTIP4PLMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
+      firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,host_q,
+      nlocal,boxlo,prd);
+}
+
+double ljtip4p_long_gpu_bytes() {
+  return LJTIP4PLMF.host_memory_usage();
+}
+
+void ljtip4p_long_copy_molecule_data(int n, tagint* tag,
+                                     int *map_array, int map_size,
+                                     int *sametag, int max_same, int ago) {
+  LJTIP4PLMF.copy_relations_data(n, tag, map_array, map_size, sametag, max_same, ago);
+}
+
+
diff --git a/lib/gpu/lal_pppm.cpp b/lib/gpu/lal_pppm.cpp
index 8b5012f312..84d6c16e14 100644
--- a/lib/gpu/lal_pppm.cpp
+++ b/lib/gpu/lal_pppm.cpp
@@ -35,12 +35,17 @@ PPPMT::PPPM() : _allocated(false), _compiled(false),
                                   _max_bytes(0) {
   device=&global_device;
   ans=new Answer<numtyp,acctyp>();
+  pppm_program=NULL;
 }
 
 template <class numtyp, class acctyp, class grdtyp, class grdtyp4>
 PPPMT::~PPPM() {
   clear(0.0);
   delete ans;
+  k_particle_map.clear();
+  k_make_rho.clear();
+  k_interp.clear();
+  if (pppm_program) delete pppm_program;
 }
 
 template <class numtyp, class acctyp, class grdtyp, class grdtyp4>
@@ -192,14 +197,6 @@ void PPPMT::clear(const double cpu_time) {
                               *ans,_max_bytes+_max_an_bytes,cpu_time,
                               _cpu_idle_time,screen);
 
-  if (_compiled) {
-    k_particle_map.clear();
-    k_make_rho.clear();
-    k_interp.clear();
-    delete pppm_program;
-    _compiled=false;
-  }
-
   time_in.clear();
   time_out.clear();
   time_map.clear();
@@ -207,7 +204,6 @@ void PPPMT::clear(const double cpu_time) {
   time_interp.clear();
 
   ans->clear();
-  device->clear();
 }
 
 // ---------------------------------------------------------------------------
@@ -380,6 +376,7 @@ void PPPMT::compile_kernels(UCL_Device &dev) {
          ucl_template_name<grdtyp>()+"4";
   #endif
 
+  if (pppm_program) delete pppm_program;
   pppm_program=new UCL_Program(dev);
 
   #ifdef USE_OPENCL
diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp
index 336ba87588..7c75a39929 100644
--- a/lib/message/cslib/src/cslib.cpp
+++ b/lib/message/cslib/src/cslib.cpp
@@ -641,6 +641,7 @@ void CSlib::onefield(int ftype, int flen, int &nbytes, int &nbytesround)
   else if (ftype == 3) bigbytes = biglen * sizeof(float);
   else if (ftype == 4) bigbytes = biglen * sizeof(double);
   else if (ftype == 5) bigbytes = biglen * sizeof(char);
+  else bigbytes = 0;
   bigbytesround = roundup(bigbytes,8);
 
   if (nbuf + bigbytesround > INT_MAX)
diff --git a/lib/message/cslib/src/cslib.h b/lib/message/cslib/src/cslib.h
index b4da968026..f2bf006881 100644
--- a/lib/message/cslib/src/cslib.h
+++ b/lib/message/cslib/src/cslib.h
@@ -17,6 +17,10 @@
 
 #include <stdint.h>
 
+#if defined(LAMMPS_BIGBIG)
+#error CSlib is not compatible with -DLAMMPS_BIGBIG
+#endif
+
 namespace CSLIB_NS {
 
 class CSlib {
diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py
index d56b68b877..668e681b3c 100644
--- a/lib/plumed/Install.py
+++ b/lib/plumed/Install.py
@@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',
 
 # settings
 
-version = "2.5.2"
+version = "2.5.3"
 mode = "static"
 
 # help message
@@ -45,6 +45,7 @@ checksums = { \
         '2.5.0' : '6224cd089493661e19ceacccd35cf911', \
         '2.5.1' : 'c2a7b519e32197a120cdf47e0f194f81', \
         '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \
+        '2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \
         }
 
 # parse and process arguments
diff --git a/potentials/AlCu.bop.table b/potentials/AlCu.bop.table
index cc74dbb62a..8e19658c62 100644
--- a/potentials/AlCu.bop.table
+++ b/potentials/AlCu.bop.table
@@ -1,4 +1,4 @@
-# DATE: 2015-07-06 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, Don Ward, donward@sandia.gov, CITATION: Zhou, Ward, and Foster, Phys. Chem. Chem. Phys., under consideration
+# DATE: 2015-07-06 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, Don Ward, donward@sandia.gov, CITATION: Zhou, Ward, and Foster, J. Alloys Compd., 680, 752 (2016).
     2
    13  2.69800000e+01 Al
    29  6.35500000e+01 Cu
@@ -4835,7 +4835,7 @@
   0.00000000e+00
   0.00000000e+00
   0.00000000e+00
-  4.90000000e+00
+  0.00000000e+00
   0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
@@ -5681,4 +5681,359 @@
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
-  0.00000000e+00  0.00000000e+00  
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
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+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
+  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
diff --git a/potentials/WBe_Wood_PRB2019.snap b/potentials/WBe_Wood_PRB2019.snap
new file mode 100644
index 0000000000..6c32256a19
--- /dev/null
+++ b/potentials/WBe_Wood_PRB2019.snap
@@ -0,0 +1,15 @@
+# DATE: 2019-09-18 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) 
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz1 equal 74
+variable zblz2 equal 4
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
+
diff --git a/potentials/WBe_Wood_PRB2019.snapcoeff b/potentials/WBe_Wood_PRB2019.snapcoeff
new file mode 100644
index 0000000000..c72baabd74
--- /dev/null
+++ b/potentials/WBe_Wood_PRB2019.snapcoeff
@@ -0,0 +1,117 @@
+# LAMMPS SNAP coefficients for WBe
+
+2 56
+W 0.5 1
+ -0.000000000000 # B[0] 
+ -0.001487061994 # B[1, 0, 0, 0] 
+  0.075808306870 # B[2, 1, 0, 1] 
+  0.538735683870 # B[3, 1, 1, 2] 
+ -0.074148039366 # B[4, 2, 0, 2] 
+  0.602629813770 # B[5, 2, 1, 3] 
+ -0.147022424344 # B[6, 2, 2, 2] 
+  0.117756828488 # B[7, 2, 2, 4] 
+ -0.026490439049 # B[8, 3, 0, 3] 
+ -0.035162708767 # B[9, 3, 1, 4] 
+  0.064315385091 # B[10, 3, 2, 3] 
+ -0.131936948089 # B[11, 3, 2, 5] 
+ -0.021272860272 # B[12, 3, 3, 4] 
+ -0.091171134054 # B[13, 3, 3, 6] 
+ -0.024396224398 # B[14, 4, 0, 4] 
+ -0.059813132803 # B[15, 4, 1, 5] 
+  0.069585393203 # B[16, 4, 2, 4] 
+ -0.085344044181 # B[17, 4, 2, 6] 
+ -0.155425254597 # B[18, 4, 3, 5] 
+ -0.117031758367 # B[19, 4, 3, 7] 
+ -0.040956258020 # B[20, 4, 4, 4] 
+ -0.084465000389 # B[21, 4, 4, 6] 
+ -0.020367513630 # B[22, 4, 4, 8] 
+ -0.010730484318 # B[23, 5, 0, 5] 
+ -0.054777575658 # B[24, 5, 1, 6] 
+  0.050742893747 # B[25, 5, 2, 5] 
+ -0.004686334611 # B[26, 5, 2, 7] 
+ -0.116372907121 # B[27, 5, 3, 6] 
+  0.005542497708 # B[28, 5, 3, 8] 
+ -0.126526795635 # B[29, 5, 4, 5] 
+ -0.080163926221 # B[30, 5, 4, 7] 
+ -0.082426250179 # B[31, 5, 5, 6] 
+ -0.010558777281 # B[32, 5, 5, 8] 
+ -0.001939058038 # B[33, 6, 0, 6] 
+ -0.027907949962 # B[34, 6, 1, 7] 
+  0.049483908476 # B[35, 6, 2, 6] 
+  0.005103754385 # B[36, 6, 2, 8] 
+ -0.054751505141 # B[37, 6, 3, 7] 
+ -0.055556071011 # B[38, 6, 4, 6] 
+ -0.006026917619 # B[39, 6, 4, 8] 
+ -0.060889030109 # B[40, 6, 5, 7] 
+ -0.029977673973 # B[41, 6, 6, 6] 
+ -0.014987527280 # B[42, 6, 6, 8] 
+ -0.006697686658 # B[43, 7, 0, 7] 
+  0.017369624409 # B[44, 7, 1, 8] 
+  0.047864358817 # B[45, 7, 2, 7] 
+ -0.001989812679 # B[46, 7, 3, 8] 
+  0.000153530925 # B[47, 7, 4, 7] 
+ -0.003862356345 # B[48, 7, 5, 8] 
+ -0.009754314198 # B[49, 7, 6, 7] 
+  0.000777958970 # B[50, 7, 7, 8] 
+ -0.003031424287 # B[51, 8, 0, 8] 
+  0.015612715209 # B[52, 8, 2, 8] 
+  0.003210129646 # B[53, 8, 4, 8] 
+ -0.013088799947 # B[54, 8, 6, 8] 
+  0.001465970755 # B[55, 8, 8, 8] 
+Be 0.417932 0.959049
+  0.000000000000 # B[0] 
+ -0.000112143918 # B[1, 0, 0, 0] 
+  0.002449805180 # B[2, 1, 0, 1] 
+  0.189705916830 # B[3, 1, 1, 2] 
+ -0.019967429692 # B[4, 2, 0, 2] 
+  0.286015704682 # B[5, 2, 1, 3] 
+  0.072864063124 # B[6, 2, 2, 2] 
+  0.108748154196 # B[7, 2, 2, 4] 
+ -0.005203284351 # B[8, 3, 0, 3] 
+  0.043948598532 # B[9, 3, 1, 4] 
+  0.105425889093 # B[10, 3, 2, 3] 
+  0.060460134045 # B[11, 3, 2, 5] 
+ -0.003406205141 # B[12, 3, 3, 4] 
+  0.002306765306 # B[13, 3, 3, 6] 
+ -0.003845115174 # B[14, 4, 0, 4] 
+  0.029471162073 # B[15, 4, 1, 5] 
+  0.054901130330 # B[16, 4, 2, 4] 
+  0.010910192753 # B[17, 4, 2, 6] 
+  0.033885210622 # B[18, 4, 3, 5] 
+  0.008053439551 # B[19, 4, 3, 7] 
+ -0.001432298168 # B[20, 4, 4, 4] 
+  0.017478027729 # B[21, 4, 4, 6] 
+ -0.003402034990 # B[22, 4, 4, 8] 
+ -0.002655339820 # B[23, 5, 0, 5] 
+  0.012668749892 # B[24, 5, 1, 6] 
+  0.037521561888 # B[25, 5, 2, 5] 
+ -0.000682693314 # B[26, 5, 2, 7] 
+  0.008525913627 # B[27, 5, 3, 6] 
+  0.008977936348 # B[28, 5, 3, 8] 
+  0.006922732235 # B[29, 5, 4, 5] 
+  0.003031883044 # B[30, 5, 4, 7] 
+ -0.000345577975 # B[31, 5, 5, 6] 
+ -0.001041600679 # B[32, 5, 5, 8] 
+ -0.001407625493 # B[33, 6, 0, 6] 
+  0.004211558640 # B[34, 6, 1, 7] 
+  0.014450875461 # B[35, 6, 2, 6] 
+ -0.007033326252 # B[36, 6, 2, 8] 
+  0.004998742185 # B[37, 6, 3, 7] 
+ -0.002824617682 # B[38, 6, 4, 6] 
+  0.003831871934 # B[39, 6, 4, 8] 
+ -0.005700892700 # B[40, 6, 5, 7] 
+  0.000184422409 # B[41, 6, 6, 6] 
+  0.001592696824 # B[42, 6, 6, 8] 
+ -0.000804927645 # B[43, 7, 0, 7] 
+  0.008465358642 # B[44, 7, 1, 8] 
+  0.005460531160 # B[45, 7, 2, 7] 
+ -0.000639605094 # B[46, 7, 3, 8] 
+ -0.002403948393 # B[47, 7, 4, 7] 
+ -0.001267042453 # B[48, 7, 5, 8] 
+  0.003836940623 # B[49, 7, 6, 7] 
+  0.002333141437 # B[50, 7, 7, 8] 
+ -0.000665360637 # B[51, 8, 0, 8] 
+ -0.003460637865 # B[52, 8, 2, 8] 
+ -0.001598726043 # B[53, 8, 4, 8] 
+  0.001478744304 # B[54, 8, 6, 8] 
+  0.000806643203 # B[55, 8, 8, 8] 
diff --git a/potentials/WBe_Wood_PRB2019.snapparam b/potentials/WBe_Wood_PRB2019.snapparam
new file mode 100644
index 0000000000..e4fc4b4459
--- /dev/null
+++ b/potentials/WBe_Wood_PRB2019.snapparam
@@ -0,0 +1,11 @@
+# required
+rcutfac 4.8123
+twojmax 8
+
+# optional
+
+rfac0 0.99363
+rmin0 0
+bzeroflag 1
+quadraticflag 0 
+
diff --git a/python/lammps.py b/python/lammps.py
index 36cf2d2fdd..e8fc240c75 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -32,6 +32,11 @@ import select
 import re
 import sys
 
+LAMMPS_INT    = 0
+LAMMPS_DOUBLE = 1
+LAMMPS_BIGINT = 2
+LAMMPS_TAGINT = 3
+
 def get_ctypes_int(size):
   if size == 4:
     return c_int32
@@ -46,6 +51,57 @@ class MPIAbortException(Exception):
   def __str__(self):
     return repr(self.message)
 
+class NeighList:
+    """This is a wrapper class that exposes the contents of a neighbor list
+
+    It can be used like a regular Python list.
+
+    Internally it uses the lower-level LAMMPS C-library interface.
+
+    :param lmp: reference to instance of :class:`lammps`
+    :type  lmp: lammps
+    :param idx: neighbor list index
+    :type  idx: int
+    """
+    def __init__(self, lmp, idx):
+        self.lmp = lmp
+        self.idx = idx
+
+    def __str__(self):
+        return "Neighbor List ({} atoms)".format(self.size)
+
+    def __repr__(self):
+        return self.__str__()
+
+    @property
+    def size(self):
+        """
+        :return: number of elements in neighbor list
+        """
+        return self.lmp.get_neighlist_size(self.idx)
+
+    def get(self, element):
+        """
+        :return: tuple with atom local index, number of neighbors and array of neighbor local atom indices
+        :rtype:  (int, int, numpy.array)
+        """
+        iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)
+        return iatom, numneigh, neighbors
+
+    # the methods below implement the iterator interface, so NeighList can be used like a regular Python list
+
+    def __getitem__(self, element):
+        return self.get(element)
+
+    def __len__(self):
+        return self.size
+
+    def __iter__(self):
+        inum = self.size
+
+        for ii in range(inum):
+            yield self.get(ii)
+
 class lammps(object):
 
   # detect if Python is using version of mpi4py that can pass a communicator
@@ -68,6 +124,7 @@ class lammps(object):
 
     modpath = dirname(abspath(getsourcefile(lambda:0)))
     self.lib = None
+    self.lmp = None
 
     # if a pointer to a LAMMPS object is handed in,
     # all symbols should already be available
@@ -132,6 +189,21 @@ class lammps(object):
       [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
     self.lib.lammps_scatter_atoms_subset.restype = None
 
+    self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int]
+    self.lib.lammps_find_pair_neighlist.restype  = c_int
+
+    self.lib.lammps_find_fix_neighlist.argtypes = [c_void_p, c_char_p, c_int]
+    self.lib.lammps_find_fix_neighlist.restype  = c_int
+
+    self.lib.lammps_find_compute_neighlist.argtypes = [c_void_p, c_char_p, c_int]
+    self.lib.lammps_find_compute_neighlist.restype  = c_int
+
+    self.lib.lammps_neighlist_num_elements.argtypes = [c_void_p, c_int]
+    self.lib.lammps_neighlist_num_elements.restype  = c_int
+
+    self.lib.lammps_neighlist_element_neighbors.argtypes = [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
+    self.lib.lammps_neighlist_element_neighbors.restype  = None
+
     # if no ptr provided, create an instance of LAMMPS
     #   don't know how to pass an MPI communicator from PyPar
     #   but we can pass an MPI communicator from mpi4py v2.0.0 and later
@@ -221,8 +293,8 @@ class lammps(object):
 
     # add way to insert Python callback for fix external
     self.callback = {}
-    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, c_void_p, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
-    self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, c_void_p]
+    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
+    self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, py_object]
     self.lib.lammps_set_fix_external_callback.restype = None
 
   # shut-down LAMMPS instance
@@ -283,10 +355,14 @@ class lammps(object):
 
   def extract_global(self,name,type):
     if name: name = name.encode()
-    if type == 0:
+    if type == LAMMPS_INT:
       self.lib.lammps_extract_global.restype = POINTER(c_int)
-    elif type == 1:
+    elif type == LAMMPS_DOUBLE:
       self.lib.lammps_extract_global.restype = POINTER(c_double)
+    elif type == LAMMPS_BIGINT:
+      self.lib.lammps_extract_global.restype = POINTER(self.c_bigint)
+    elif type == LAMMPS_TAGINT:
+      self.lib.lammps_extract_global.restype = POINTER(self.c_tagint)
     else: return None
     ptr = self.lib.lammps_extract_global(self.lmp,name)
     return ptr[0]
@@ -357,26 +433,38 @@ class lammps(object):
           else:
             c_int_type = c_int
 
+          if dim == 1:
+            raw_ptr = self.lmp.extract_atom(name, 0)
+          else:
+            raw_ptr = self.lmp.extract_atom(name, 1)
+
+          return self.iarray(c_int_type, raw_ptr, nelem, dim)
+
+        def extract_atom_darray(self, name, nelem, dim=1):
+          if dim == 1:
+            raw_ptr = self.lmp.extract_atom(name, 2)
+          else:
+            raw_ptr = self.lmp.extract_atom(name, 3)
+
+          return self.darray(raw_ptr, nelem, dim)
+
+        def iarray(self, c_int_type, raw_ptr, nelem, dim=1):
           np_int_type = self._ctype_to_numpy_int(c_int_type)
 
           if dim == 1:
-            tmp = self.lmp.extract_atom(name, 0)
-            ptr = cast(tmp, POINTER(c_int_type * nelem))
+            ptr = cast(raw_ptr, POINTER(c_int_type * nelem))
           else:
-            tmp = self.lmp.extract_atom(name, 1)
-            ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
+            ptr = cast(raw_ptr[0], POINTER(c_int_type * nelem * dim))
 
           a = np.frombuffer(ptr.contents, dtype=np_int_type)
           a.shape = (nelem, dim)
           return a
 
-        def extract_atom_darray(self, name, nelem, dim=1):
+        def darray(self, raw_ptr, nelem, dim=1):
           if dim == 1:
-            tmp = self.lmp.extract_atom(name, 2)
-            ptr = cast(tmp, POINTER(c_double * nelem))
+            ptr = cast(raw_ptr, POINTER(c_double * nelem))
           else:
-            tmp = self.lmp.extract_atom(name, 3)
-            ptr = cast(tmp[0], POINTER(c_double * nelem * dim))
+            ptr = cast(raw_ptr[0], POINTER(c_double * nelem * dim))
 
           a = np.frombuffer(ptr.contents)
           a.shape = (nelem, dim)
@@ -390,23 +478,23 @@ class lammps(object):
   def extract_compute(self,id,style,type):
     if id: id = id.encode()
     if type == 0:
-      if style > 0: return None
-      self.lib.lammps_extract_compute.restype = POINTER(c_double)
-      ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
-      return ptr[0]
+      if style == 0:
+        self.lib.lammps_extract_compute.restype = POINTER(c_double)
+        ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
+        return ptr[0]
+      elif style == 1:
+        return None
+      elif style == 2:
+        self.lib.lammps_extract_compute.restype = POINTER(c_int)
+        return ptr[0]
     if type == 1:
       self.lib.lammps_extract_compute.restype = POINTER(c_double)
       ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
       return ptr
     if type == 2:
-      if style == 0:
-        self.lib.lammps_extract_compute.restype = POINTER(c_int)
-        ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
-        return ptr[0]
-      else:
-        self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
-        ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
-        return ptr
+      self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
+      ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
+      return ptr
     return None
 
   # extract fix info
@@ -617,33 +705,114 @@ class lammps(object):
             return np.int64
           return np.intc
 
-    def callback_wrapper(caller_ptr, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
-      if cast(caller_ptr,POINTER(py_object)).contents:
-        pyCallerObj = cast(caller_ptr,POINTER(py_object)).contents.value
-      else:
-        pyCallerObj = None
-
-      tptr = cast(tag_ptr, POINTER(self.c_tagint * nlocal))
-      tag = np.frombuffer(tptr.contents, dtype=_ctype_to_numpy_int(self.c_tagint))
-      tag.shape = (nlocal)
-
-      xptr = cast(x_ptr[0], POINTER(c_double * nlocal * 3))
-      x = np.frombuffer(xptr.contents)
-      x.shape = (nlocal, 3)
-
-      fptr = cast(fext_ptr[0], POINTER(c_double * nlocal * 3))
-      f = np.frombuffer(fptr.contents)
-      f.shape = (nlocal, 3)
-
-      callback(pyCallerObj, ntimestep, nlocal, tag, x, f)
+    def callback_wrapper(caller, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
+      tag = self.numpy.iarray(self.c_tagint, tag_ptr, nlocal, 1)
+      x   = self.numpy.darray(x_ptr, nlocal, 3)
+      f   = self.numpy.darray(fext_ptr, nlocal, 3)
+      callback(caller, ntimestep, nlocal, tag, x, f)
 
     cFunc   = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper)
-    cCaller = cast(pointer(py_object(caller)), c_void_p)
+    cCaller = caller
 
     self.callback[fix_name] = { 'function': cFunc, 'caller': caller }
 
     self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller)
 
+  def get_neighlist(self, idx):
+    """Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index
+
+    :param idx: index of neighbor list
+    :type  idx: int
+    :return: an instance of :class:`NeighList` wrapping access to neighbor list data
+    :rtype:  NeighList
+    """
+    if idx < 0:
+        return None
+    return NeighList(self, idx)
+
+  def find_pair_neighlist(self, style, exact=True, nsub=0, request=0):
+    """Find neighbor list index of pair style neighbor list
+
+    Try finding pair instance that matches style. If exact is set, the pair must
+    match style exactly. If exact is 0, style must only be contained. If pair is
+    of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style.
+
+    Once the pair instance has been identified, multiple neighbor list requests
+    may be found. Every neighbor list is uniquely identified by its request
+    index. Thus, providing this request index ensures that the correct neighbor
+    list index is returned.
+
+    :param style: name of pair style that should be searched for
+    :type  style: string
+    :param exact: controls whether style should match exactly or only must be contained in pair style name, defaults to True
+    :type  exact: bool, optional
+    :param nsub:  match nsub-th hybrid sub-style, defaults to 0
+    :type  nsub:  int, optional
+    :param request:   index of neighbor list request, in case there are more than one, defaults to 0
+    :type  request:   int, optional
+    :return: neighbor list index if found, otherwise -1
+    :rtype:  int
+     """
+    style = style.encode()
+    exact = int(exact)
+    idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, request)
+    return self.get_neighlist(idx)
+
+  def find_fix_neighlist(self, fixid, request=0):
+    """Find neighbor list index of fix neighbor list
+
+    :param fixid: name of fix
+    :type  fixid: string
+    :param request:   index of neighbor list request, in case there are more than one, defaults to 0
+    :type  request:   int, optional
+    :return: neighbor list index if found, otherwise -1
+    :rtype:  int
+     """
+    fixid = fixid.encode()
+    idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request)
+    return self.get_neighlist(idx)
+
+  def find_compute_neighlist(self, computeid, request=0):
+    """Find neighbor list index of compute neighbor list
+
+    :param computeid: name of compute
+    :type  computeid: string
+    :param request:   index of neighbor list request, in case there are more than one, defaults to 0
+    :type  request:   int, optional
+    :return: neighbor list index if found, otherwise -1
+    :rtype:  int
+     """
+    computeid = computeid.encode()
+    idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request)
+    return self.get_neighlist(idx)
+
+  def get_neighlist_size(self, idx):
+    """Return the number of elements in neighbor list with the given index
+
+    :param idx: neighbor list index
+    :type  idx: int
+    :return: number of elements in neighbor list with index idx
+    :rtype:  int
+     """
+    return self.lib.lammps_neighlist_num_elements(self.lmp, idx)
+
+  def get_neighlist_element_neighbors(self, idx, element):
+    """Return data of neighbor list entry
+
+    :param element: neighbor list index
+    :type  element: int
+    :param element: neighbor list element index
+    :type  element: int
+    :return: tuple with atom local index, number of neighbors and array of neighbor local atom indices
+    :rtype:  (int, int, numpy.array)
+    """
+    c_iatom = c_int()
+    c_numneigh = c_int()
+    c_neighbors = POINTER(c_int)()
+    self.lib.lammps_neighlist_element_neighbors(self.lmp, idx, element, byref(c_iatom), byref(c_numneigh), byref(c_neighbors))
+    neighbors = self.numpy.iarray(c_int, c_neighbors, c_numneigh.value, 1)
+    return c_iatom.value, c_numneigh.value, neighbors
+
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
diff --git a/src/.gitignore b/src/.gitignore
index 2d79018b28..1b7dc7e6b2 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -161,6 +161,10 @@
 /fix_setforce_spin.h
 /min_spin.cpp
 /min_spin.h
+/min_spin_cg.cpp
+/min_spin_cg.h
+/min_spin_lbfgs.cpp
+/min_spin_lbfgs.h
 /neb_spin.cpp
 /neb_spin.h
 /pair_spin.cpp
@@ -276,6 +280,8 @@
 /bond_oxdna_fene.h
 /bond_oxdna2_fene.cpp
 /bond_oxdna2_fene.h
+/bond_oxrna2_fene.cpp
+/bond_oxrna2_fene.h
 /bond_quartic.cpp
 /bond_quartic.h
 /bond_table.cpp
@@ -978,6 +984,8 @@
 /pair_oxdna_*.h
 /pair_oxdna2_*.cpp
 /pair_oxdna2_*.h
+/pair_oxrna2_*.cpp
+/pair_oxrna2_*.h
 /mf_oxdna.h
 /pair_peri_eps.cpp
 /pair_peri_eps.h
diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp
index 93b164c503..51896aab85 100644
--- a/src/ASPHERE/pair_gayberne.cpp
+++ b/src/ASPHERE/pair_gayberne.cpp
@@ -28,6 +28,7 @@
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -460,20 +461,20 @@ void PairGayBerne::read_restart(FILE *fp)
   int i,j;
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
-    if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
     if (setwell[i]) {
-      if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
+      if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error);
       MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
     }
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -505,12 +506,12 @@ void PairGayBerne::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&gamma,sizeof(double),1,fp);
-    fread(&upsilon,sizeof(double),1,fp);
-    fread(&mu,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&gamma,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&upsilon,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&gamma,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&upsilon,1,MPI_DOUBLE,0,world);
@@ -643,10 +644,10 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],
   dchi[2] = temp2*(iota[2]-temp1*r12hat[2]);
 
   temp1 = -eta*u_r;
-  temp2 = eta*chi;
-  fforce[0] = temp1*dchi[0]-temp2*dUr[0];
-  fforce[1] = temp1*dchi[1]-temp2*dUr[1];
-  fforce[2] = temp1*dchi[2]-temp2*dUr[2];
+  temp3 = eta*chi;
+  fforce[0] = temp1*dchi[0]-temp3*dUr[0];
+  fforce[1] = temp1*dchi[1]-temp3*dUr[1];
+  fforce[2] = temp1*dchi[2]-temp3*dUr[2];
 
   // torque for particle 1 and 2
   // compute dUr
@@ -667,18 +668,17 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],
 
   MathExtra::vecmat(iota,b1,tempv);
   MathExtra::cross3(tempv,iota,dchi);
-  temp1 = -4.0/rsq;
-  dchi[0] *= temp1;
-  dchi[1] *= temp1;
-  dchi[2] *= temp1;
+  dchi[0] *= temp2;
+  dchi[1] *= temp2;
+  dchi[2] *= temp2;
   double dchi2[3];
 
   if (newton_pair || j < nlocal) {
     MathExtra::vecmat(iota,b2,tempv);
     MathExtra::cross3(tempv,iota,dchi2);
-    dchi2[0] *= temp1;
-    dchi2[1] *= temp1;
-    dchi2[2] *= temp1;
+    dchi2[0] *= temp2;
+    dchi2[1] *= temp2;
+    dchi2[2] *= temp2;
   }
 
   // compute d_eta
diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp
index f139564320..dd4b11935e 100644
--- a/src/ASPHERE/pair_resquared.cpp
+++ b/src/ASPHERE/pair_resquared.cpp
@@ -27,6 +27,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -438,20 +439,20 @@ void PairRESquared::read_restart(FILE *fp)
   int i,j;
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
-    if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
     if (setwell[i]) {
-      if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
+      if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error);
       MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
     }
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -479,8 +480,8 @@ void PairRESquared::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp
index d60372781a..d855c5aea7 100644
--- a/src/BODY/body_rounded_polygon.cpp
+++ b/src/BODY/body_rounded_polygon.cpp
@@ -116,7 +116,7 @@ double BodyRoundedPolygon::enclosing_radius(struct AtomVecBody::Bonus *bonus)
 {
   int nvertices = bonus->ivalue[0];
   if (nvertices == 1 || nvertices == 2)
-	return *(bonus->dvalue+3*nsub(bonus)+2);
+        return *(bonus->dvalue+3*nsub(bonus)+2);
   return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus));
 }
 
@@ -126,7 +126,7 @@ double BodyRoundedPolygon::rounded_radius(struct AtomVecBody::Bonus *bonus)
 {
   int nvertices = bonus->ivalue[0];
   if (nvertices == 1 || nvertices == 2)
-	return *(bonus->dvalue+3*nsub(bonus)+2+1);
+        return *(bonus->dvalue+3*nsub(bonus)+2+1);
   return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus)+1);
 }
 
@@ -156,7 +156,7 @@ int BodyRoundedPolygon::unpack_border_body(AtomVecBody::Bonus *bonus,
 ------------------------------------------------------------------------- */
 
 void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble,
-				   int *ifile, double *dfile)
+                                   int *ifile, double *dfile)
 {
   AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
 
@@ -327,7 +327,7 @@ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble,
 ------------------------------------------------------------------------- */
 
 double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble,
-				       int *ifile, double *dfile)
+                                       int *ifile, double *dfile)
 {
   int nsub = ifile[0];
   if (nsub < 1)
diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp
index 49ec6f1d78..a82404ab15 100644
--- a/src/BODY/body_rounded_polyhedron.cpp
+++ b/src/BODY/body_rounded_polyhedron.cpp
@@ -134,7 +134,7 @@ double BodyRoundedPolyhedron::enclosing_radius(struct AtomVecBody::Bonus *bonus)
 {
   int nvertices = bonus->ivalue[0];
   if (nvertices == 1 || nvertices == 2)
-  	return *(bonus->dvalue+3*nsub(bonus)+2);
+        return *(bonus->dvalue+3*nsub(bonus)+2);
   return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) +
            MAX_FACE_SIZE*nfaces(bonus));
 }
@@ -385,7 +385,7 @@ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble,
 ------------------------------------------------------------------------- */
 
 double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble,
-				       int *ifile, double *dfile)
+                                       int *ifile, double *dfile)
 {
   int nsub = ifile[0];
   int ned = ifile[1];
diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index f5e18e9d89..8e51f3ac5f 100644
--- a/src/BODY/pair_body_rounded_polygon.cpp
+++ b/src/BODY/pair_body_rounded_polygon.cpp
@@ -105,7 +105,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
   int ni,nj,npi,npj,ifirst,jfirst;
   int nei,nej,iefirst,jefirst;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl;
-  double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij;
+  double rsq,r,radi,radj,k_nij,k_naij;
   double facc[3];
   int *ilist,*jlist,*numneigh,**firstneigh;
 
@@ -170,8 +170,6 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
       ifirst = dfirst[i];
       nei = ednum[i];
       iefirst = edfirst[i];
-      eradi = enclosing_radius[i];
-      rradi = rounded_radius[i];
     }
 
     for (jj = 0; jj < jnum; jj++) {
@@ -197,8 +195,6 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
       jfirst = dfirst[j];
       nej = ednum[j];
       jefirst = edfirst[j];
-      eradj = enclosing_radius[j];
-      rradj = rounded_radius[j];
 
       k_nij = k_n[itype][jtype];
       k_naij = k_na[itype][jtype];
@@ -207,7 +203,6 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
 
       r = sqrt(rsq);
       if (r > radi + radj + cut_inner) continue;
-      rsqinv = 1.0 / rsq;
 
       if (npi == 1 && npj == 1) {
         sphere_against_sphere(i, j, delx, dely, delz, rsq,
@@ -598,16 +593,13 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
                        double k_n, double k_na, double** /*x*/, double** v,
                        double** f, int evflag)
 {
-  double eradi,eradj,rradi,rradj;
+  double rradi,rradj;
   double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
-  double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy;
+  double rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
   int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
 
-  eradi = enclosing_radius[i];
   rradi = rounded_radius[i];
-
-  eradj = enclosing_radius[j];
   rradj = rounded_radius[j];
 
   rsqinv = 1.0/rsq;
@@ -649,19 +641,6 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
     vt1 = vr1 - vn1;
     vt2 = vr2 - vn2;
     vt3 = vr3 - vn3;
-
-    // normal friction term at contact
-
-    fn[0] = -c_n * vn1;
-    fn[1] = -c_n * vn2;
-    fn[2] = -c_n * vn3;
-
-    // tangential friction term at contact
-    // excluding the tangential deformation term
-
-    ft[0] = -c_t * vt1;
-    ft[1] = -c_t * vt2;
-    ft[2] = -c_t * vt3;
   }
 
   f[i][0] += fx;
@@ -703,20 +682,16 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j,
                                                 int &num_contacts,
                                                 double &evdwl, double* facc)
 {
-  int ni, npi, ifirst, nei, iefirst;
-  int nj, npj, jfirst, nej, jefirst;
-  double xpi[3], xpj[3], dist, eradi, eradj, rradi, rradj;
+  int ni, npi, ifirst;
+  int nj, jfirst, nej, jefirst;
+  double xpi[3], xpj[3], dist, eradj, rradi, rradj;
   double fx, fy, fz, energy;
   int interact;
 
   npi = dnum[i];
   ifirst = dfirst[i];
-  nei = ednum[i];
-  iefirst = edfirst[i];
-  eradi = enclosing_radius[i];
   rradi = rounded_radius[i];
 
-  npj = dnum[j];
   jfirst = dfirst[j];
   nej = ednum[j];
   jefirst = edfirst[j];
diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index 2df58d45cd..ff7e7fc25e 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -271,7 +271,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
         continue;
       }
 
-      int interact, num_contacts;
+      int num_contacts;
       Contact contact_list[MAX_CONTACTS];
 
       num_contacts = 0;
@@ -280,22 +280,22 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
       #ifdef _POLYHEDRON_DEBUG
       printf("INTERACTION between edges of %d vs. faces of %d:\n", i, j);
       #endif
-      interact = edge_against_face(i, j, itype, jtype, x, contact_list,
-                                   num_contacts, evdwl, facc);
+      edge_against_face(i, j, itype, jtype, x, contact_list,
+                        num_contacts, evdwl, facc);
 
       // check interaction between j's edges and i' faces
       #ifdef _POLYHEDRON_DEBUG
       printf("\nINTERACTION between edges of %d vs. faces of %d:\n", j, i);
       #endif
-      interact = edge_against_face(j, i, jtype, itype, x, contact_list,
-                                   num_contacts, evdwl, facc);
+      edge_against_face(j, i, jtype, itype, x, contact_list,
+                        num_contacts, evdwl, facc);
 
       // check interaction between i's edges and j' edges
       #ifdef _POLYHEDRON_DEBUG
       printf("INTERACTION between edges of %d vs. edges of %d:\n", i, j);
       #endif
-      interact = edge_against_edge(i, j, itype, jtype, x, contact_list,
-                                   num_contacts, evdwl, facc);
+      edge_against_edge(i, j, itype, jtype, x, contact_list,
+                        num_contacts, evdwl, facc);
 
       // estimate the contact area
       // also consider point contacts and line contacts
@@ -2341,13 +2341,11 @@ void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list,
 void PairBodyRoundedPolyhedron::sanity_check()
 {
 
-  double x1[3],x2[3],x3[3],x4[3],h_a[3],h_b[3],d_a,d_b;
+  double x1[3],x2[3],h_a[3],h_b[3],d_a,d_b;
   double a[3],b[3],t_a,t_b;
 
   x1[0] = 0; x1[1] = 3; x1[2] = 0;
   x2[0] = 3; x2[1] = 0; x2[2] = 0;
-  x3[0] = 4; x3[1] = 3; x3[2] = 0;
-  x4[0] = 5; x4[1] = 3; x4[2] = 0;
 
   a[0] = 0; a[1] = 0; a[2] = 0;
   b[0] = 4; b[1] = 0; b[2] = 0;
diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp
index 99e1b39c9d..fe567ead34 100644
--- a/src/CLASS2/angle_class2.cpp
+++ b/src/CLASS2/angle_class2.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -372,19 +373,19 @@ void AngleClass2::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k2[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k3[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k4[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,NULL,error);
 
-    fread(&bb_k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp);
-    fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&bb_k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&bb_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&bb_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
 
-    fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp);
-    fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp);
-    fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp);
-    fread(&ba_r2[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&ba_k1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&ba_k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&ba_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&ba_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
 
   MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp
index cfc1a93bde..0651db75fb 100644
--- a/src/CLASS2/bond_class2.cpp
+++ b/src/CLASS2/bond_class2.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -182,10 +183,10 @@ void BondClass2::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&k2[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&k3[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&k4[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&k2[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&k3[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&k4[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index 725228666e..6b43257908 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -181,6 +182,11 @@ void DihedralClass2::compute(int eflag, int vflag)
     costh13 = c0;
     costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
 
+    costh12 = MAX(MIN(costh12, 1.0), -1.0);
+    costh13 = MAX(MIN(costh13, 1.0), -1.0);
+    costh23 = MAX(MIN(costh23, 1.0), -1.0);
+    c0 = costh13;
+
     // cos and sin of 2 angles and final c
 
     sin2 = MAX(1.0 - costh12*costh12,0.0);
@@ -835,45 +841,45 @@ void DihedralClass2::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&k1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&k2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&k3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&phi1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&phi2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&phi3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
 
-    fread(&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
 
-    fread(&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
 
-    fread(&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
 
-    fread(&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
 
-    fread(&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
 
-    fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&aat_k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
 
-    fread(&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
   }
 
   MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index ca7ac95239..a3b8b4b672 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -604,15 +605,15 @@ void ImproperClass2::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k0[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&chi0[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&chi0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
 
-    fread(&aa_k1[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&aa_k2[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&aa_k3[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&aa_theta0_1[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&aa_theta0_2[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&aa_theta0_3[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&aa_k1[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&aa_k2[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&aa_k3[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&aa_theta0_1[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&aa_theta0_2[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&aa_theta0_3[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&chi0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp
index a0088e52b7..47b3185bbf 100644
--- a/src/CLASS2/pair_lj_class2.cpp
+++ b/src/CLASS2/pair_lj_class2.cpp
@@ -24,6 +24,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -34,6 +35,7 @@ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp)
 {
   respa_enable = 1;
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -187,8 +189,8 @@ void PairLJClass2::compute_inner()
 
       if (rsq < cut_out_off_sq) {
         r2inv = 1.0/rsq;
-		rinv = sqrt(r2inv);
-		r3inv = r2inv*rinv;
+                rinv = sqrt(r2inv);
+                r3inv = r2inv*rinv;
         r6inv = r3inv*r3inv;
         jtype = type[j];
         forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
@@ -267,8 +269,8 @@ void PairLJClass2::compute_middle()
 
       if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
         r2inv = 1.0/rsq;
-		rinv = sqrt(r2inv);
-		r3inv = r2inv*rinv;
+                rinv = sqrt(r2inv);
+                r3inv = r2inv*rinv;
         r6inv = r3inv*r3inv;
         jtype = type[j];
         forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
@@ -351,8 +353,8 @@ void PairLJClass2::compute_outer(int eflag, int vflag)
       if (rsq < cutsq[itype][jtype]) {
         if (rsq > cut_in_off_sq) {
           r2inv = 1.0/rsq;
-		  rinv = sqrt(r2inv);
-		  r3inv = r2inv*rinv;
+                  rinv = sqrt(r2inv);
+                  r3inv = r2inv*rinv;
           r6inv = r3inv*r3inv;
           forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
           fpair = factor_lj*forcelj*r2inv;
@@ -373,8 +375,8 @@ void PairLJClass2::compute_outer(int eflag, int vflag)
 
         if (eflag) {
           r2inv = 1.0/rsq;
-		  rinv = sqrt(r2inv);
-		  r3inv = r2inv*rinv;
+                  rinv = sqrt(r2inv);
+                  r3inv = r2inv*rinv;
           r6inv = r3inv*r3inv;
           evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
             offset[itype][jtype];
@@ -384,8 +386,8 @@ void PairLJClass2::compute_outer(int eflag, int vflag)
         if (vflag) {
           if (rsq <= cut_in_off_sq) {
             r2inv = 1.0/rsq;
-			rinv = sqrt(r2inv);
-			r3inv = r2inv*rinv;
+                        rinv = sqrt(r2inv);
+                        r3inv = r2inv*rinv;
             r6inv = r3inv*r3inv;
             forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
             fpair = factor_lj*forcelj*r2inv;
@@ -610,13 +612,13 @@ void PairLJClass2::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -645,10 +647,10 @@ void PairLJClass2::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp
index e999a3682e..3635c21c8c 100644
--- a/src/CLASS2/pair_lj_class2_coul_cut.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp
@@ -23,6 +23,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -32,6 +33,7 @@ using namespace MathConst;
 PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -362,14 +364,14 @@ void PairLJClass2CoulCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
-          fread(&cut_coul[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -399,11 +401,11 @@ void PairLJClass2CoulCut::write_restart_settings(FILE *fp)
 void PairLJClass2CoulCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp
index b56c076996..0bb802579c 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_long.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -47,6 +48,7 @@ PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp)
   respa_enable = 1;
   writedata = 1;
   ftable = NULL;
+  cut_respa = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -261,8 +263,8 @@ void PairLJClass2CoulLong::compute_inner()
 
         jtype = type[j];
         if (rsq < cut_ljsq[itype][jtype]) {
-		  rinv = sqrt(r2inv);
-		  r3inv = r2inv*rinv;
+                  rinv = sqrt(r2inv);
+                  r3inv = r2inv*rinv;
           r6inv = r3inv*r3inv;
           forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
         } else forcelj = 0.0;
@@ -353,8 +355,8 @@ void PairLJClass2CoulLong::compute_middle()
 
         jtype = type[j];
         if (rsq < cut_ljsq[itype][jtype]) {
-		  rinv = sqrt(r2inv);
-		  r3inv = r2inv*rinv;
+                  rinv = sqrt(r2inv);
+                  r3inv = r2inv*rinv;
           r6inv = r3inv*r3inv;
           forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
         } else forcelj = 0.0;
@@ -486,9 +488,9 @@ void PairLJClass2CoulLong::compute_outer(int eflag, int vflag)
         } else forcecoul = 0.0;
 
         if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) {
-		  rinv = sqrt(r2inv);
-		  r3inv = r2inv*rinv;
-		  r6inv = r3inv*r3inv;
+                  rinv = sqrt(r2inv);
+                  r3inv = r2inv*rinv;
+                  r6inv = r3inv*r3inv;
           forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
           if (rsq < cut_in_on_sq) {
             rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
@@ -524,9 +526,9 @@ void PairLJClass2CoulLong::compute_outer(int eflag, int vflag)
           } else ecoul = 0.0;
 
           if (rsq < cut_ljsq[itype][jtype]) {
-			rinv = sqrt(r2inv);
-			r3inv = r2inv*rinv;
-			r6inv = r3inv*r3inv;
+                        rinv = sqrt(r2inv);
+                        r3inv = r2inv*rinv;
+                        r6inv = r3inv*r3inv;
             evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
               offset[itype][jtype];
             evdwl *= factor_lj;
@@ -551,13 +553,13 @@ void PairLJClass2CoulLong::compute_outer(int eflag, int vflag)
 
           if (rsq <= cut_in_off_sq) {
             rinv = sqrt(r2inv);
-			r3inv = r2inv*rinv;
-			r6inv = r3inv*r3inv;
+                        r3inv = r2inv*rinv;
+                        r6inv = r3inv*r3inv;
             forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
           } else if (rsq <= cut_in_on_sq) {
-			rinv = sqrt(r2inv);
-			r3inv = r2inv*rinv;
-			r6inv = r3inv*r3inv;
+                        rinv = sqrt(r2inv);
+                        r3inv = r2inv*rinv;
+                        r6inv = r3inv*r3inv;
             forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
           }
           fpair = (forcecoul + factor_lj*forcelj) * r2inv;
@@ -663,33 +665,33 @@ void PairLJClass2CoulLong::init_style()
   if (!atom->q_flag)
     error->all(FLERR,
                "Pair style lj/class2/coul/long requires atom attribute q");
-  
+
   // request regular or rRESPA neighbor list
-  
+
   int irequest;
   int respa = 0;
-  
+
   if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
     if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
-	if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+        if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
   }
-  
+
   irequest = neighbor->request(this,instance_me);
-  
+
   if (respa >= 1) {
     neighbor->requests[irequest]->respaouter = 1;
-	neighbor->requests[irequest]->respainner = 1;
+        neighbor->requests[irequest]->respainner = 1;
   }
   if (respa == 2) neighbor->requests[irequest]->respamiddle = 1;
 
   cut_coulsq = cut_coul * cut_coul;
-  
+
   // set rRESPA cutoffs
-  
+
   if (strstr(update->integrate_style,"respa") &&
       ((Respa *) update->integrate)->level_inner >= 0)
     cut_respa = ((Respa *) update->integrate)->cutoff;
-  else cut_respa = NULL;	
+  else cut_respa = NULL;
 
   // insure use of KSpace long-range solver, set g_ewald
 
@@ -738,9 +740,9 @@ double PairLJClass2CoulLong::init_one(int i, int j)
   lj3[j][i] = lj3[i][j];
   lj4[j][i] = lj4[i][j];
   offset[j][i] = offset[i][j];
-  
+
   // check interior rRESPA cutoff
-  
+
   if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
     error->all(FLERR,"Pair cutoff < Respa interior cutoff");
 
@@ -805,13 +807,13 @@ void PairLJClass2CoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -842,13 +844,13 @@ void PairLJClass2CoulLong::write_restart_settings(FILE *fp)
 void PairLJClass2CoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/CLASS2/pair_lj_class2_coul_long.h b/src/CLASS2/pair_lj_class2_coul_long.h
index 50d7092541..7b68382295 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.h
+++ b/src/CLASS2/pair_lj_class2_coul_long.h
@@ -40,7 +40,7 @@ class PairLJClass2CoulLong : public Pair {
   void write_data(FILE *);
   void write_data_all(FILE *);
   double single(int, int, int, int, double, double, double, double &);
- 
+
   void compute_inner();
   void compute_middle();
   void compute_outer(int, int);
diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp
index 71a5f8c056..d73789d890 100644
--- a/src/COLLOID/pair_brownian.cpp
+++ b/src/COLLOID/pair_brownian.cpp
@@ -36,6 +36,7 @@
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -602,12 +603,12 @@ void PairBrownian::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -642,17 +643,17 @@ void PairBrownian::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&mu,sizeof(double),1,fp);
-    fread(&flaglog,sizeof(int),1,fp);
-    fread(&flagfld,sizeof(int),1,fp);
-    fread(&cut_inner_global,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&t_target, sizeof(double),1,fp);
-    fread(&seed, sizeof(int),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&flagHI,sizeof(int),1,fp);
-    fread(&flagVF,sizeof(int),1,fp);
+    utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&flagfld,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&t_target, sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed, sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&flaglog,1,MPI_INT,0,world);
diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp
index ad25184181..d1c6e4594f 100644
--- a/src/COLLOID/pair_colloid.cpp
+++ b/src/COLLOID/pair_colloid.cpp
@@ -25,6 +25,7 @@
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;
@@ -394,15 +395,15 @@ void PairColloid::read_restart(FILE *fp)
 
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (comm->me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (comm->me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (comm->me == 0) {
-          fread(&a12[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&d1[i][j],sizeof(double),1,fp);
-          fread(&d2[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a12[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&d1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&d2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a12[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -432,9 +433,9 @@ void PairColloid::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp
index b6288c34d2..a72eaef679 100644
--- a/src/COLLOID/pair_lubricate.cpp
+++ b/src/COLLOID/pair_lubricate.cpp
@@ -35,6 +35,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -682,12 +683,12 @@ void PairLubricate::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -720,15 +721,15 @@ void PairLubricate::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&mu,sizeof(double),1,fp);
-    fread(&flaglog,sizeof(int),1,fp);
-    fread(&flagfld,sizeof(int),1,fp);
-    fread(&cut_inner_global,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&flagHI,sizeof(int),1,fp);
-    fread(&flagVF,sizeof(int),1,fp);
+    utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&flagfld,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&flaglog,1,MPI_INT,0,world);
diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp
index 4f7e3917e8..e8715cec36 100644
--- a/src/COLLOID/pair_lubricateU.cpp
+++ b/src/COLLOID/pair_lubricateU.cpp
@@ -34,6 +34,7 @@
 #include "variable.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -1908,12 +1909,12 @@ void PairLubricateU::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -1945,14 +1946,14 @@ void PairLubricateU::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&mu,sizeof(double),1,fp);
-    fread(&flaglog,sizeof(int),1,fp);
-    fread(&cut_inner_global,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&flagHI,sizeof(int),1,fp);
-    fread(&flagVF,sizeof(int),1,fp);
+    utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&flaglog,1,MPI_INT,0,world);
diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp
index ef7e6583be..9be8d17b06 100644
--- a/src/COMPRESS/dump_atom_gz.cpp
+++ b/src/COMPRESS/dump_atom_gz.cpp
@@ -108,27 +108,28 @@ void DumpAtomGZ::openfile()
 void DumpAtomGZ::write_header(bigint ndump)
 {
   if ((multiproc) || (!multiproc && me == 0)) {
+    if (unit_flag && !unit_count) {
+      ++unit_count;
+      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+    }
+    if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time());
+
+    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
     if (domain->triclinic == 0) {
-      gzprintf(gzFp,"ITEM: TIMESTEP\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
-      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
       gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
       gzprintf(gzFp,"%g %g\n",boxxlo,boxxhi);
       gzprintf(gzFp,"%g %g\n",boxylo,boxyhi);
       gzprintf(gzFp,"%g %g\n",boxzlo,boxzhi);
-      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
     } else {
-      gzprintf(gzFp,"ITEM: TIMESTEP\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
-      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
       gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
       gzprintf(gzFp,"%g %g %g\n",boxxlo,boxxhi,boxxy);
       gzprintf(gzFp,"%g %g %g\n",boxylo,boxyhi,boxxz);
       gzprintf(gzFp,"%g %g %g\n",boxzlo,boxzhi,boxyz);
-      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
     }
+    gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
   }
 }
 
diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp
index 9c30f4742f..58ce98ad06 100644
--- a/src/COMPRESS/dump_custom_gz.cpp
+++ b/src/COMPRESS/dump_custom_gz.cpp
@@ -108,27 +108,28 @@ void DumpCustomGZ::openfile()
 void DumpCustomGZ::write_header(bigint ndump)
 {
   if ((multiproc) || (!multiproc && me == 0)) {
+    if (unit_flag && !unit_count) {
+      ++unit_count;
+      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+    }
+    if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time());
+
+    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
     if (domain->triclinic == 0) {
-      gzprintf(gzFp,"ITEM: TIMESTEP\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
-      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
       gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
       gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
       gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
       gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
-      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
     } else {
-      gzprintf(gzFp,"ITEM: TIMESTEP\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
-      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
       gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
       gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
       gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
       gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
-      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
     }
+    gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
   }
 }
 
diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp
new file mode 100644
index 0000000000..c27c795f75
--- /dev/null
+++ b/src/COMPRESS/dump_local_gz.cpp
@@ -0,0 +1,173 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "dump_local_gz.h"
+#include "domain.h"
+#include "error.h"
+#include "update.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
+  DumpLocal(lmp, narg, arg)
+{
+  gzFp = NULL;
+
+  if (!compressed)
+    error->all(FLERR,"Dump local/gz only writes compressed files");
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+DumpLocalGZ::~DumpLocalGZ()
+{
+  if (gzFp) gzclose(gzFp);
+  gzFp = NULL;
+  fp = NULL;
+}
+
+
+/* ----------------------------------------------------------------------
+   generic opening of a dump file
+   ASCII or binary or gzipped
+   some derived classes override this function
+------------------------------------------------------------------------- */
+
+void DumpLocalGZ::openfile()
+{
+  // single file, already opened, so just return
+
+  if (singlefile_opened) return;
+  if (multifile == 0) singlefile_opened = 1;
+
+  // if one file per timestep, replace '*' with current timestep
+
+  char *filecurrent = filename;
+  if (multiproc) filecurrent = multiname;
+
+  if (multifile) {
+    char *filestar = filecurrent;
+    filecurrent = new char[strlen(filestar) + 16];
+    char *ptr = strchr(filestar,'*');
+    *ptr = '\0';
+    if (padflag == 0)
+      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+              filestar,update->ntimestep,ptr+1);
+    else {
+      char bif[8],pad[16];
+      strcpy(bif,BIGINT_FORMAT);
+      sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
+      sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
+    }
+    *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
+  }
+
+  // each proc with filewriter = 1 opens a file
+
+  if (filewriter) {
+    if (append_flag) {
+      gzFp = gzopen(filecurrent,"ab9");
+    } else {
+      gzFp = gzopen(filecurrent,"wb9");
+    }
+
+    if (gzFp == NULL) error->one(FLERR,"Cannot open dump file");
+  } else gzFp = NULL;
+
+  // delete string with timestep replaced
+
+  if (multifile) delete [] filecurrent;
+}
+
+void DumpLocalGZ::write_header(bigint ndump)
+{
+  if ((multiproc) || (!multiproc && me == 0)) {
+    if (unit_flag && !unit_count) {
+      ++unit_count;
+      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+    }
+    if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time());
+
+    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
+    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
+    if (domain->triclinic == 0) {
+      gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
+      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
+      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
+      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
+    } else {
+      gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
+      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
+      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
+      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
+    }
+    gzprintf(gzFp,"ITEM: %s %s\n",label,columns);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpLocalGZ::write_data(int n, double *mybuf)
+{
+  if (buffer_flag == 1) {
+    gzwrite(gzFp,mybuf,sizeof(char)*n);
+
+  } else {
+    int i,j;
+    int m = 0;
+    for (i = 0; i < n; i++) {
+      for (j = 0; j < size_one; j++) {
+        if (vtype[j] == INT)
+          gzprintf(gzFp,vformat[j],static_cast<int> (mybuf[m]));
+        else gzprintf(gzFp,vformat[j],mybuf[m]);
+        m++;
+      }
+      gzprintf(gzFp,"\n");
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpLocalGZ::write()
+{
+  DumpLocal::write();
+  if (filewriter) {
+    if (multifile) {
+      gzclose(gzFp);
+      gzFp = NULL;
+    } else {
+      if (flush_flag)
+        gzflush(gzFp,Z_SYNC_FLUSH);
+    }
+  }
+}
+
diff --git a/src/COMPRESS/dump_local_gz.h b/src/COMPRESS/dump_local_gz.h
new file mode 100644
index 0000000000..cc788863de
--- /dev/null
+++ b/src/COMPRESS/dump_local_gz.h
@@ -0,0 +1,57 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef DUMP_CLASS
+
+DumpStyle(local/gz,DumpLocalGZ)
+
+#else
+
+#ifndef LMP_DUMP_LOCAL_GZ_H
+#define LMP_DUMP_LOCAL_GZ_H
+
+#include "dump_local.h"
+#include <zlib.h>
+
+namespace LAMMPS_NS {
+
+class DumpLocalGZ : public DumpLocal {
+ public:
+  DumpLocalGZ(class LAMMPS *, int, char **);
+  virtual ~DumpLocalGZ();
+
+ protected:
+  gzFile gzFp;  // file pointer for the compressed output stream
+
+  virtual void openfile();
+  virtual void write_header(bigint);
+  virtual void write_data(int, double *);
+  virtual void write();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Dump local/gz only writes compressed files
+
+The dump local/gz output file name must have a .gz suffix.
+
+E: Cannot open dump file
+
+Self-explanatory.
+
+*/
diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
index 14c511c100..9f9e897357 100644
--- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
@@ -23,6 +23,7 @@
 #include "memory.h"
 #include "error.h"
 #include "update.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -437,14 +438,14 @@ void PairLJCutDipoleCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
-          fread(&cut_coul[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -473,10 +474,10 @@ void PairLJCutDipoleCut::write_restart_settings(FILE *fp)
 void PairLJCutDipoleCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
index fe020ed2e6..7fc03005b5 100644
--- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
@@ -25,7 +25,7 @@
 #include "memory.h"
 #include "error.h"
 #include "update.h"
-
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -490,13 +490,13 @@ void PairLJCutDipoleLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -524,10 +524,10 @@ void PairLJCutDipoleLong::write_restart_settings(FILE *fp)
 void PairLJCutDipoleLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp
index 5e7819c2f4..481191534f 100644
--- a/src/DIPOLE/pair_lj_long_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp
@@ -30,6 +30,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -63,10 +64,10 @@ void PairLJLongDipoleLong::options(char **arg, int order)
   if (!*arg) error->all(FLERR,"Illegal pair_style lj/long/dipole/long command");
   for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
   switch (i) {
-    default: error->all(FLERR,"Illegal pair_style lj/long/dipole/long command");
     case 0: ewald_order |= 1<<order; break;             // set kspace r^-order
     case 2: ewald_off |= 1<<order;                      // turn r^-order off
     case 1: break;
+    default: error->all(FLERR,"Illegal pair_style lj/long/dipole/long command");
   }
 }
 
@@ -344,13 +345,13 @@ void PairLJLongDipoleLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon_read[i][j],sizeof(double),1,fp);
-          fread(&sigma_read[i][j],sizeof(double),1,fp);
-          fread(&cut_lj_read[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon_read[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma_read[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj_read[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world);
@@ -379,11 +380,11 @@ void PairLJLongDipoleLong::write_restart_settings(FILE *fp)
 void PairLJLongDipoleLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&ewald_order,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh
index 20429009db..f46c3b7fe0 100755
--- a/src/GPU/Install.sh
+++ b/src/GPU/Install.sh
@@ -143,6 +143,8 @@ action pair_ufm_gpu.cpp
 action pair_ufm_gpu.h
 action pair_lj_cut_dipole_long_gpu.cpp pair_lj_cut_dipole_long.cpp
 action pair_lj_cut_dipole_long_gpu.h pair_lj_cut_dipole_long.cpp
+action pair_lj_cut_tip4p_long_gpu.h
+action pair_lj_cut_tip4p_long_gpu.cpp
 
 # edit 2 Makefile.package files to include/exclude package info
 
diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp
index d4397503dc..cb2930a3ea 100644
--- a/src/GPU/fix_gpu.cpp
+++ b/src/GPU/fix_gpu.cpp
@@ -88,6 +88,12 @@ static const char cite_gpu_package[] =
   " year =    2017,\n"
   " volume =  212,\n"
   " pages =   {113--122}\n"
+  "}\n\n"
+  "@Article{Nikolskiy19,\n"
+  " author = {V. Nikolskiy, V. Stegailov},\n"
+  " title = {GPU acceleration of four-site water models in LAMMPS},\n"
+  " journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},\n"
+  " year =    2019\n"
   "}\n\n";
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h
index 111d13c563..115e1f0574 100644
--- a/src/GPU/gpu_extra.h
+++ b/src/GPU/gpu_extra.h
@@ -133,4 +133,9 @@ E: Unknown error in GPU library
 
 Self-explanatory.
 
+W: Increasing communication cutoff for GPU style
+
+The pair style has increased the communication cutoff to be consistent with
+the communication cutoff requirements for this pair style when run on the GPU.
+
 */
diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp
index d4d36a5837..f4b73ba5a6 100644
--- a/src/GPU/pair_beck_gpu.cpp
+++ b/src/GPU/pair_beck_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "gpu_extra.h"
 #include "math_special.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;
@@ -68,6 +69,7 @@ PairBeckGPU::PairBeckGPU(LAMMPS *lmp) : PairBeck(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp
index 7314024d71..bab66e0351 100644
--- a/src/GPU/pair_born_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -90,6 +91,7 @@ PairBornCoulLongCSGPU::PairBornCoulLongCSGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp
index 79c0d5f147..39d34420a8 100644
--- a/src/GPU/pair_born_coul_long_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -85,6 +86,7 @@ PairBornCoulLongGPU::PairBornCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
index 5f74d3fc7c..b00b5a0b56 100644
--- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -78,6 +79,7 @@ PairBornCoulWolfCSGPU::PairBornCoulWolfCSGPU(LAMMPS *lmp) : PairBornCoulWolfCS(l
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp
index 693c2abffb..c5243dc443 100644
--- a/src/GPU/pair_born_coul_wolf_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -76,6 +77,7 @@ PairBornCoulWolfGPU::PairBornCoulWolfGPU(LAMMPS *lmp) : PairBornCoulWolf(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp
index e9edc4f1c2..b71a296d66 100644
--- a/src/GPU/pair_born_gpu.cpp
+++ b/src/GPU/pair_born_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairBornGPU::PairBornGPU(LAMMPS *lmp) : PairBorn(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp
index 182673fb0d..5d27ee8c51 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.cpp
+++ b/src/GPU/pair_buck_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index 75e784fafa..e30230d5a0 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -81,6 +82,7 @@ PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp
index 1559c45b88..b4d5677d53 100644
--- a/src/GPU/pair_buck_gpu.cpp
+++ b/src/GPU/pair_buck_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairBuckGPU::PairBuckGPU(LAMMPS *lmp) : PairBuck(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp
index 4db18dbc52..230adb3db0 100644
--- a/src/GPU/pair_colloid_gpu.cpp
+++ b/src/GPU/pair_colloid_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairColloidGPU::PairColloidGPU(LAMMPS *lmp) : PairColloid(lmp), gpu_mode(GPU_FOR
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp
index 8a3eb12f8d..0242c98343 100644
--- a/src/GPU/pair_coul_cut_gpu.cpp
+++ b/src/GPU/pair_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairCoulCutGPU::PairCoulCutGPU(LAMMPS *lmp) : PairCoulCut(lmp), gpu_mode(GPU_FOR
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp
index 1fc07f8dac..198f7f5f67 100644
--- a/src/GPU/pair_coul_debye_gpu.cpp
+++ b/src/GPU/pair_coul_debye_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairCoulDebyeGPU::PairCoulDebyeGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp
index 408be036dd..67d025ff70 100644
--- a/src/GPU/pair_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_coul_dsf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
@@ -81,6 +82,7 @@ PairCoulDSFGPU::PairCoulDSFGPU(LAMMPS *lmp) : PairCoulDSF(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp
index c70424e472..afd0d6cf56 100644
--- a/src/GPU/pair_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_coul_long_cs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -83,6 +84,7 @@ PairCoulLongCSGPU::PairCoulLongCSGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index 9623c25f2f..485e45ddc6 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -78,6 +79,7 @@ PairCoulLongGPU::PairCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp
index 5fcad6a350..9e14164c57 100644
--- a/src/GPU/pair_dpd_gpu.cpp
+++ b/src/GPU/pair_dpd_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -209,6 +210,7 @@ PairDPDGPU::PairDPDGPU(LAMMPS *lmp) : PairDPD(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp
index 2d6798a12d..920eb8dd8a 100644
--- a/src/GPU/pair_dpd_tstat_gpu.cpp
+++ b/src/GPU/pair_dpd_tstat_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -212,6 +213,7 @@ PairDPDTstatGPU::PairDPDTstatGPU(LAMMPS *lmp) : PairDPDTstat(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index bc55c66676..e7503839f6 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -30,7 +30,7 @@
 #include "gpu_extra.h"
 #include "domain.h"
 #include "utils.h"
-
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +72,7 @@ PairEAMAlloyGPU::PairEAMAlloyGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index ac379a9ce6..6edfa69359 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -29,6 +29,7 @@
 #include "neigh_request.h"
 #include "gpu_extra.h"
 #include "domain.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairEAMFSGPU::PairEAMFSGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index 57106f48a4..fb851770f9 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -30,6 +30,7 @@
 #include "error.h"
 #include "neigh_request.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MAXLINE 1024
 
@@ -71,6 +72,7 @@ PairEAMGPU::PairEAMGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp
index 842b84acf2..17125f9875 100644
--- a/src/GPU/pair_gauss_gpu.cpp
+++ b/src/GPU/pair_gauss_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -66,6 +67,7 @@ PairGaussGPU::PairGaussGPU(LAMMPS *lmp) : PairGauss(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index f00accda15..445c74487f 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "update.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -74,6 +75,7 @@ PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
   quat_nmax = 0;
   reinitflag = 0;
   quat = NULL;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index 16b6b835c0..f6f9bd379b 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -66,6 +67,7 @@ PairLJ96CutGPU::PairLJ96CutGPU(LAMMPS *lmp) : PairLJ96Cut(lmp), gpu_mode(GPU_FOR
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index bacbb400b1..6eda677928 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index e34dbb0f99..4ee776b4ff 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -80,6 +81,7 @@ PairLJClass2CoulLongGPU::PairLJClass2CoulLongGPU(LAMMPS *lmp) :
 {
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp
index 68f27598f3..643e3ff090 100644
--- a/src/GPU/pair_lj_class2_gpu.cpp
+++ b/src/GPU/pair_lj_class2_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -65,6 +66,7 @@ PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_
 {
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp
index 542de37840..64fd6119c3 100644
--- a/src/GPU/pair_lj_cubic_gpu.cpp
+++ b/src/GPU/pair_lj_cubic_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace PairLJCubicConstants;
@@ -70,6 +71,7 @@ PairLJCubicGPU::PairLJCubicGPU(LAMMPS *lmp) : PairLJCubic(lmp),
   respa_enable = 0;
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index cf3dd711dc..e52a971786 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJCutCoulCutGPU::PairLJCutCoulCutGPU(LAMMPS *lmp) : PairLJCutCoulCut(lmp), g
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
index 20354e732c..4c8920450f 100644
--- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairLJCutCoulDebyeGPU::PairLJCutCoulDebyeGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
index ccaf86efa6..acfbcd847e 100644
--- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
@@ -82,6 +83,7 @@ PairLJCutCoulDSFGPU::PairLJCutCoulDSFGPU(LAMMPS *lmp) : PairLJCutCoulDSF(lmp), g
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index 36c72f1143..24ce118c6d 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJCutCoulLongGPU::PairLJCutCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
index 79ca90698a..0e700f6fb2 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairLJCutCoulMSMGPU::PairLJCutCoulMSMGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
index e2c8b8d686..6c53b02227 100644
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairLJCutDipoleCutGPU::PairLJCutDipoleCutGPU(LAMMPS *lmp) : PairLJCutDipoleCut(l
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
index fb76376d34..0535735820 100644
--- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
@@ -36,6 +36,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -84,6 +85,7 @@ PairLJCutDipoleLongGPU::PairLJCutDipoleLongGPU(LAMMPS *lmp) : PairLJCutDipoleLon
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index 809e5cf05e..c6f61a7e96 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairLJCutGPU::PairLJCutGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
new file mode 100644
index 0000000000..a7875f15c4
--- /dev/null
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -0,0 +1,252 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Vsevolod Nikolskiy (HSE)
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_lj_cut_tip4p_long_gpu.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "integrate.h"
+#include "memory.h"
+#include "error.h"
+#include "neigh_request.h"
+#include "universe.h"
+#include "update.h"
+#include "domain.h"
+#include "kspace.h"
+#include "angle.h"
+#include "bond.h"
+#include "gpu_extra.h"
+#include "suffix.h"
+
+#define EWALD_F   1.12837917
+#define EWALD_P   0.3275911
+#define A1        0.254829592
+#define A2       -0.284496736
+#define A3        1.421413741
+#define A4       -1.453152027
+#define A5        1.061405429
+
+using namespace LAMMPS_NS;
+
+// External functions from cuda library for atom decomposition
+
+int ljtip4p_long_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
+    double **host_lj2, double **host_lj3, double **host_lj4,
+    double **offset, double *special_lj, const int nlocal,
+    const int tH, const int tO, const double alpha, const double qdist,
+    const int nall, const int max_nbors, const int maxspecial,
+    const double cell_size, int &gpu_mode, FILE *screen,
+    double **host_cut_ljsq, const double host_cut_coulsq,
+    const double host_cut_coulsqplus, double *host_special_coul,
+    const double qqrd2e, const double g_ewald,
+    int map_size, int max_same);
+void ljtip4p_long_gpu_clear();
+int ** ljtip4p_long_gpu_compute_n(const int ago, const int inum,
+    const int nall, double **host_x, int *host_type,
+    double *sublo, double *subhi,
+    tagint *tag, int *map_array, int map_size,
+    int *sametag, int max_same,
+    int **nspecial,
+    tagint **special, const bool eflag, const bool vflag,
+    const bool eatom, const bool vatom, int &host_start,
+    int **ilist, int **jnum,
+    const double cpu_time, bool &success, double *host_q,
+    double *boxlo, double *prd);
+void ljtip4p_long_gpu_compute(const int ago, const int inum, const int nall,
+    double **host_x, int *host_type, int *ilist, int *numj,
+    int **firstneigh, const bool eflag, const bool vflag,
+    const bool eatom, const bool vatom, int &host_start,
+    const double cpu_time,
+    bool &success, double *host_q, const int nlocal,
+    double *boxlo, double *prd);
+double ljtip4p_long_gpu_bytes();
+void ljtip4p_long_copy_molecule_data(int, tagint *, int *,
+                                     int, int *, int, int);
+
+/* ---------------------------------------------------------------------- */
+
+PairLJCutTIP4PLongGPU::PairLJCutTIP4PLongGPU(LAMMPS *lmp)
+: PairLJCutTIP4PLong(lmp), gpu_mode(GPU_FORCE)
+{
+  respa_enable = 0;
+  reinitflag = 0;
+  cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
+  GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+}
+
+/* ----------------------------------------------------------------------
+   free all arrays
+------------------------------------------------------------------------- */
+
+PairLJCutTIP4PLongGPU::~PairLJCutTIP4PLongGPU()
+{
+  ljtip4p_long_gpu_clear();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJCutTIP4PLongGPU::compute(int eflag, int vflag)
+{
+
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  int nall = atom->nlocal + atom->nghost;
+  int inum, host_start;
+
+  bool success = true;
+  int *ilist, *numneigh, **firstneigh;
+  if (gpu_mode != GPU_FORCE) {
+    inum = atom->nlocal;
+    firstneigh = ljtip4p_long_gpu_compute_n(neighbor->ago, inum, nall,
+        atom->x, atom->type, domain->sublo,
+        domain->subhi,
+        atom->tag, atom->get_map_array(), atom->get_map_size(),
+        atom->sametag, atom->get_max_same(),
+        atom->nspecial,
+        atom->special, eflag, vflag, eflag_atom,
+        vflag_atom, host_start, &ilist, &numneigh,
+        cpu_time, success, atom->q, domain->boxlo,
+        domain->prd);
+  } else {
+    inum = list->inum;
+    ilist = list->ilist;
+    numneigh = list->numneigh;
+    firstneigh = list->firstneigh;
+    ljtip4p_long_copy_molecule_data(nall, atom->tag,
+        atom->get_map_array(), atom->get_map_size(),
+        atom->sametag, atom->get_max_same(), neighbor->ago);
+    ljtip4p_long_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
+        ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
+        vflag_atom, host_start, cpu_time, success, atom->q,
+        atom->nlocal, domain->boxlo, domain->prd);
+  }
+  if (!success)
+    error->one(FLERR,"Insufficient memory on accelerator");
+
+//  if (host_start<inum) {
+//    cpu_time = MPI_Wtime();
+//    cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
+//    cpu_time = MPI_Wtime() - cpu_time;
+//  }
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJCutTIP4PLongGPU::init_style()
+{
+
+  cut_respa = NULL;
+  if (atom->tag_enable == 0)
+    error->all(FLERR,"Pair style lj/cut/tip4p/long/gpu requires atom IDs");
+  if (!atom->q_flag)
+    error->all(FLERR,
+               "Pair style lj/cut/tip4p/long/gpu requires atom attribute q");
+  if (force->bond == NULL)
+    error->all(FLERR,"Must use a bond style with TIP4P potential");
+  if (force->angle == NULL)
+    error->all(FLERR,"Must use an angle style with TIP4P potential");
+
+  if (atom->map_style == 2)
+    error->all(FLERR,"GPU-accelerated lj/cut/tip4p/long currently"
+        " requires map style 'array' (atom_modify map array)");
+
+  //PairLJCutCoulLong::init_style();
+  // Repeat cutsq calculation because done after call to init_style
+  double maxcut = -1.0;
+  double cut;
+  for (int i = 1; i <= atom->ntypes; i++) {
+    for (int j = i; j <= atom->ntypes; j++) {
+      if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
+        cut = init_one(i,j);
+        cut *= cut;
+        if (cut > maxcut)
+          maxcut = cut;
+        cutsq[i][j] = cutsq[j][i] = cut;
+      } else
+        cutsq[i][j] = cutsq[j][i] = 0.0;
+    }
+  }
+  double cell_size = sqrt(maxcut) + neighbor->skin;
+
+  // insure use of KSpace long-range solver, set g_ewald
+  if (force->kspace == NULL)
+    error->all(FLERR,"Pair style requires a KSpace style");
+  g_ewald = force->kspace->g_ewald;
+
+  // setup force tables
+  if (ncoultablebits) init_tables(cut_coul,cut_respa);
+
+  int maxspecial=0;
+  if (atom->molecular)
+    maxspecial=atom->maxspecial;
+
+  // set alpha parameter
+  double theta = force->angle->equilibrium_angle(typeA);
+  double blen = force->bond->equilibrium_distance(typeB);
+  alpha = qdist / (cos(0.5*theta) * blen);
+
+  cut_coulsq = cut_coul * cut_coul;
+  double cut_coulsqplus = (cut_coul+qdist+blen) * (cut_coul+qdist+blen);
+  if (maxcut < cut_coulsqplus) {
+    cell_size = (cut_coul+qdist+blen) + neighbor->skin;
+  }
+  if (comm->cutghostuser < cell_size) {
+    comm->cutghostuser = cell_size;
+    if (comm->me == 0)
+      error->warning(FLERR,"Increasing communication cutoff for TIP4P GPU style");
+  }
+
+  int success = ljtip4p_long_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
+                             offset, force->special_lj, atom->nlocal,
+                             typeH, typeO, alpha, qdist,
+                             atom->nlocal+atom->nghost, 300, maxspecial,
+                             cell_size, gpu_mode, screen, cut_ljsq,
+                             cut_coulsq, cut_coulsqplus,
+                             force->special_coul, force->qqrd2e,
+                             g_ewald, atom->get_map_size(),
+                             atom->get_max_same());
+  GPU_EXTRA::check_flag(success,error,world);
+  if (gpu_mode == GPU_FORCE) {
+    int irequest = neighbor->request(this,instance_me);
+    neighbor->requests[irequest]->half = 0;
+    neighbor->requests[irequest]->full = 1;
+    neighbor->requests[irequest]->cut = 1;
+    neighbor->requests[irequest]->cutoff = cut_coul+qdist+blen + neighbor->skin;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairLJCutTIP4PLongGPU::memory_usage()
+{
+  double bytes = PairLJCutTIP4PLong::memory_usage();
+  return bytes + ljtip4p_long_gpu_bytes();
+}
+
+/* ---------------------------------------------------------------------- */
+
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.h b/src/GPU/pair_lj_cut_tip4p_long_gpu.h
new file mode 100644
index 0000000000..e7ba93afb2
--- /dev/null
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.h
@@ -0,0 +1,48 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Vsevolod Nikolskiy (HSE)
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(lj/cut/tip4p/long/gpu,PairLJCutTIP4PLongGPU)
+
+#else
+
+#ifndef LMP_PAIR_LJ_TIP4P_LONG_GPU_H
+#define LMP_PAIR_LJ_TIP4P_LONG_GPU_H
+
+#include "pair_lj_cut_tip4p_long.h"
+
+namespace LAMMPS_NS {
+
+class PairLJCutTIP4PLongGPU : public PairLJCutTIP4PLong {
+ public:
+  PairLJCutTIP4PLongGPU(LAMMPS *lmp);
+  ~PairLJCutTIP4PLongGPU();
+  void compute(int, int);
+  void init_style();
+  double memory_usage();
+
+ enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
+
+ private:
+  int gpu_mode;
+  double cpu_time;
+};
+
+}
+#endif
+#endif
diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
index a530f7ff9a..a906f57707 100644
--- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJExpandCoulLongGPU::PairLJExpandCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp
index 86f8a76b52..db88e8dae8 100644
--- a/src/GPU/pair_lj_expand_gpu.cpp
+++ b/src/GPU/pair_lj_expand_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairLJExpandGPU::PairLJExpandGPU(LAMMPS *lmp) : PairLJExpand(lmp), gpu_mode(GPU_
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp
index 78f8b8b461..6989d73d50 100644
--- a/src/GPU/pair_lj_gromacs_gpu.cpp
+++ b/src/GPU/pair_lj_gromacs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJGromacsGPU::PairLJGromacsGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
index 24ff8a4f28..3bcaa78d46 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -86,6 +87,7 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp
index 2621f49aeb..c0a3e8ec39 100644
--- a/src/GPU/pair_lj_sdk_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
index cf26cdf3b4..d001c282e2 100644
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairLJSFDipoleSFGPU::PairLJSFDipoleSFGPU(LAMMPS *lmp) : PairLJSFDipoleSF(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp
index f3a384113f..84cc903dee 100644
--- a/src/GPU/pair_mie_cut_gpu.cpp
+++ b/src/GPU/pair_mie_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -67,6 +68,7 @@ PairMIECutGPU::PairMIECutGPU(LAMMPS *lmp) : PairMIECut(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index dcad227045..5bcda54d85 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -65,6 +66,7 @@ PairMorseGPU::PairMorseGPU(LAMMPS *lmp) : PairMorse(lmp), gpu_mode(GPU_FORCE)
 {
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index b12a790c81..b03834d5d1 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "update.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -76,6 +77,7 @@ PairRESquaredGPU::PairRESquaredGPU(LAMMPS *lmp) : PairRESquared(lmp),
     error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
   quat_nmax = 0;
   quat = NULL;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp
index 0efcb20c8d..04efb1e96a 100644
--- a/src/GPU/pair_soft_gpu.cpp
+++ b/src/GPU/pair_soft_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "gpu_extra.h"
 #include "math_const.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairSoftGPU::PairSoftGPU(LAMMPS *lmp) : PairSoft(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp
index 8999cb6c47..8e75aff545 100644
--- a/src/GPU/pair_sw_gpu.cpp
+++ b/src/GPU/pair_sw_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairSWGPU::PairSWGPU(LAMMPS *lmp) : PairSW(lmp), gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
@@ -206,8 +208,11 @@ void PairSWGPU::init_style()
     neighbor->requests[irequest]->ghost = 1;
   }
 
-  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) )
+  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) {
     comm->cutghostuser=2.0*cutmax + neighbor->skin;
+    if (comm->me == 0)
+       error->warning(FLERR,"Increasing communication cutoff for GPU style");
+  }
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index 4432265874..563b070bda 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define LOOKUP 0
 #define LINEAR 1
@@ -73,6 +74,7 @@ PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp
index e0dc021b57..33bac49e5e 100644
--- a/src/GPU/pair_tersoff_gpu.cpp
+++ b/src/GPU/pair_tersoff_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -76,6 +77,7 @@ extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
 PairTersoffGPU::PairTersoffGPU(LAMMPS *lmp) : PairTersoff(lmp), gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
@@ -240,8 +242,11 @@ void PairTersoffGPU::init_style()
     neighbor->requests[irequest]->ghost = 1;
   }
 
-  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) )
+  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) {
     comm->cutghostuser = 2.0*cutmax + neighbor->skin;
+    if (comm->me == 0)
+       error->warning(FLERR,"Increasing communication cutoff for GPU style");
+  }
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp
index a17efb55e8..ebcdf0f7dd 100644
--- a/src/GPU/pair_tersoff_mod_gpu.cpp
+++ b/src/GPU/pair_tersoff_mod_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairTersoffMODGPU::PairTersoffMODGPU(LAMMPS *lmp) : PairTersoffMOD(lmp),
   gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
@@ -232,8 +234,11 @@ void PairTersoffMODGPU::init_style()
     neighbor->requests[irequest]->ghost = 1;
   }
 
-  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) )
+  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) {
     comm->cutghostuser = 2.0*cutmax + neighbor->skin;
+    if (comm->me == 0)
+       error->warning(FLERR,"Increasing communication cutoff for GPU style");
+  }
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp
index 765d25f8e6..09b5a7f838 100644
--- a/src/GPU/pair_tersoff_zbl_gpu.cpp
+++ b/src/GPU/pair_tersoff_zbl_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -77,6 +78,7 @@ PairTersoffZBLGPU::PairTersoffZBLGPU(LAMMPS *lmp) : PairTersoffZBL(lmp),
   gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
@@ -254,8 +256,11 @@ void PairTersoffZBLGPU::init_style()
     neighbor->requests[irequest]->ghost = 1;
   }
 
-  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) )
+  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) {
     comm->cutghostuser = 2.0*cutmax + neighbor->skin;
+    if (comm->me == 0)
+       error->warning(FLERR,"Increasing communication cutoff for GPU style");
+  }
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index 97c2eebf24..49ed6289e1 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -36,6 +36,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairUFMGPU::PairUFMGPU(LAMMPS *lmp) : PairUFM(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp
index 3b74e5685e..6f0d938440 100644
--- a/src/GPU/pair_vashishta_gpu.cpp
+++ b/src/GPU/pair_vashishta_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairVashishtaGPU::PairVashishtaGPU(LAMMPS *lmp) : PairVashishta(lmp), gpu_mode(G
   cpu_time = 0.0;
   reinitflag = 0;
   gpu_allocated = false;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
@@ -234,9 +236,11 @@ void PairVashishtaGPU::init_style()
     neighbor->requests[irequest]->ghost = 1;
   }
 
-  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) )
+  if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) {
     comm->cutghostuser=2.0*cutmax + neighbor->skin;
-
+    if (comm->me == 0)
+       error->warning(FLERR,"Increasing communication cutoff for GPU style");
+  }
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp
index 51c7e683db..7bbed7d89b 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.cpp
+++ b/src/GPU/pair_yukawa_colloid_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -68,6 +69,7 @@ PairYukawaColloidGPU::PairYukawaColloidGPU(LAMMPS *lmp) : PairYukawaColloid(lmp)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index 5dc13c7750..9d702daf20 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -67,6 +68,7 @@ PairYukawaGPU::PairYukawaGPU(LAMMPS *lmp) : PairYukawa(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp
index 5e24281145..23c3c077fa 100644
--- a/src/GPU/pair_zbl_gpu.cpp
+++ b/src/GPU/pair_zbl_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairZBLGPU::PairZBLGPU(LAMMPS *lmp) : PairZBL(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index b62b630be5..2255f64eb2 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -54,7 +54,8 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg < 6) error->all(FLERR,"Illegal fix pour command");
 
-  if (lmp->kokkos) error->all(FLERR,"Cannot yet use fix pour with the KOKKOS package");
+  if (lmp->kokkos)
+    error->all(FLERR,"Cannot yet use fix pour with the KOKKOS package");
 
   time_depend = 1;
 
@@ -167,8 +168,11 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
   if (idnext) find_maxid();
 
   // random number generator, same for all procs
+  // warm up the generator 30x to avoid correlations in first-particle
+  // positions if runs are repeated with consecutive seeds
 
   random = new RanPark(lmp,seed);
+  for (int ii=0; ii < 30; ii++) random->uniform();
 
   // allgather arrays
 
@@ -180,11 +184,8 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
   // grav = gravity in distance/time^2 units
   // assume grav = -magnitude at this point, enforce in init()
 
-  int ifix;
-  for (ifix = 0; ifix < modify->nfix; ifix++)
-    if (utils::strmatch(modify->fix[ifix]->style,"^gravity")) break;
-
-  if (ifix == modify->nfix)
+  int ifix = modify->find_fix_by_style("^gravity");
+  if (ifix == -1)
     error->all(FLERR,"No fix gravity defined for fix pour");
   grav = - ((FixGravity *) modify->fix[ifix])->magnitude * force->ftm2v;
 
@@ -309,17 +310,12 @@ void FixPour::init()
   if (domain->triclinic)
     error->all(FLERR,"Cannot use fix pour with triclinic box");
 
-  // insure gravity fix exists
+  // insure gravity fix (still) exists
   // for 3d must point in -z, for 2d must point in -y
   // else insertion cannot work
 
-  int ifix;
-  for (ifix = 0; ifix < modify->nfix; ifix++) {
-    if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break;
-    if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break;
-    if (strstr(modify->fix[ifix]->style,"gravity/kk") != NULL) break;
-  }
-  if (ifix == modify->nfix)
+  int ifix = modify->find_fix_by_style("^gravity");
+  if (ifix == -1)
     error->all(FLERR,"No fix gravity defined for fix pour");
 
   double xgrav = ((FixGravity *) modify->fix[ifix])->xgrav;
@@ -790,25 +786,34 @@ int FixPour::overlap(int i)
    return 1 if value is outside, 0 if inside
 ------------------------------------------------------------------------- */
 
-int FixPour::outside(int dim, double value, double lo, double hi)
+bool FixPour::outside(int dim, double value, double lo, double hi)
 {
   double boxlo = domain->boxlo[dim];
   double boxhi = domain->boxhi[dim];
 
-  if (domain->periodicity[dim]) {
-    if (lo < boxlo && hi > boxhi) {
-      return 0;
-    } else if (lo < boxlo) {
-      if (value > hi && value < lo + domain->prd[dim]) return 1;
-    } else if (hi > boxhi) {
-      if (value > hi - domain->prd[dim] && value < lo) return 1;
-    } else {
-      if (value < lo || value > hi) return 1;
-    }
+  // check for value inside/outside range, ignoring periodicity
+  // if inside or dim is non-periodic, only this test is needed
+
+  bool outside_range = (value < lo || value > hi);
+  if (!outside_range || !domain->periodicity[dim]) return outside_range;
+
+  // for periodic dimension:
+  // must perform additional tests if range wraps around the periodic box
+
+  bool outside_pbc_range = true;
+
+  if ((lo < boxlo && hi > boxhi) || (hi - lo) > domain->prd[dim]) {
+    // value is always inside
+    outside_pbc_range = false;
+  } else if (lo < boxlo) {
+    // lower boundary crosses periodic boundary
+    outside_pbc_range = (value > hi && value < lo + domain->prd[dim]);
+  } else if (hi > boxhi) {
+    // upper boundary crosses periodic boundary
+    outside_pbc_range = (value < lo && value > hi - domain->prd[dim]);
   }
 
-  if (value < lo || value > hi) return 1;
-  return 0;
+  return outside_pbc_range;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h
index 63d0d39152..933ce8e6b7 100644
--- a/src/GRANULAR/fix_pour.h
+++ b/src/GRANULAR/fix_pour.h
@@ -70,7 +70,7 @@ class FixPour : public Fix {
 
   void find_maxid();
   int overlap(int);
-  int outside(int, double, double, double);
+  bool outside(int, double, double, double);
   void xyz_random(double, double *);
   double radius_sample();
   void options(int, char **);
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index a6e67e06ff..c8eec53a1d 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -1143,8 +1143,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
     a2 = a*a;
     knfac = normal_coeffs[0]*a;
     Fne = knfac*a2/Reff - TWOPI*a2*sqrt(4*coh*E/(M_PI*a));
-  }
-  else{
+  } else {
     knfac = E; //Hooke
     a = sqrt(dR);
     Fne = knfac*delta;
@@ -1158,16 +1157,13 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
 
   if (damping_model == VELOCITY) {
     damp_normal = 1;
-  }
-  else if (damping_model == MASS_VELOCITY) {
+  } else if (damping_model == MASS_VELOCITY) {
     damp_normal = meff;
-  }
-  else if (damping_model == VISCOELASTIC) {
+  } else if (damping_model == VISCOELASTIC) {
     damp_normal = a*meff;
-  }
-  else if (damping_model == TSUJI) {
+  } else if (damping_model == TSUJI) {
     damp_normal = sqrt(meff*knfac);
-  }
+  } else damp_normal = 0.0;
 
   damp_normal_prefactor = normal_coeffs[1]*damp_normal;
   Fdamp = -damp_normal_prefactor*vnnr;
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index 771a5566df..de205dce91 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -31,6 +31,7 @@
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -540,7 +541,7 @@ void PairGranHookeHistory::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
     }
 }
@@ -566,12 +567,12 @@ void PairGranHookeHistory::write_restart_settings(FILE *fp)
 void PairGranHookeHistory::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&kn,sizeof(double),1,fp);
-    fread(&kt,sizeof(double),1,fp);
-    fread(&gamman,sizeof(double),1,fp);
-    fread(&gammat,sizeof(double),1,fp);
-    fread(&xmu,sizeof(double),1,fp);
-    fread(&dampflag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&kn,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&kt,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&gamman,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&gammat,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&xmu,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&dampflag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&kn,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&kt,1,MPI_DOUBLE,0,world);
diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp
index b87e64a456..85eab1fb9e 100644
--- a/src/GRANULAR/pair_granular.cpp
+++ b/src/GRANULAR/pair_granular.cpp
@@ -34,6 +34,7 @@ See the README file in the top-level LAMMPS directory.
 #include "error.h"
 #include "math_const.h"
 #include "math_special.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -139,7 +140,7 @@ void PairGranular::compute(int eflag, int vflag)
   double wr1,wr2,wr3;
   double vtr1,vtr2,vtr3,vrel;
 
-  double knfac, damp_normal, damp_normal_prefactor;
+  double knfac, damp_normal=0.0, damp_normal_prefactor;
   double k_tangential, damp_tangential;
   double Fne, Ft, Fdamp, Fntot, Fncrit, Fscrit, Frcrit;
   double fs, fs1, fs2, fs3, tor1, tor2, tor3;
@@ -305,6 +306,7 @@ void PairGranular::compute(int eflag, int vflag)
 
         delta = radsum - r;
         dR = delta*Reff;
+
         if (normal_model[itype][jtype] == JKR) {
           touch[jj] = 1;
           R2=Reff*Reff;
@@ -391,6 +393,7 @@ void PairGranular::compute(int eflag, int vflag)
         } else {
           Fncrit = fabs(Fntot);
         }
+        Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit;
 
         //------------------------------
         // tangential forces
@@ -446,7 +449,6 @@ void PairGranular::compute(int eflag, int vflag)
           fs3 = -k_tangential*history[2] - damp_tangential*vtr3;
 
           // rescale frictional displacements and forces if needed
-          Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit;
           fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
           if (fs > Fscrit) {
             shrmag = sqrt(history[0]*history[0] + history[1]*history[1] +
@@ -464,20 +466,20 @@ void PairGranular::compute(int eflag, int vflag)
             } else fs1 = fs2 = fs3 = 0.0;
           }
         } else { // classic pair gran/hooke (no history)
-          fs = meff*damp_tangential*vrel;
-          if (vrel != 0.0) Ft = MIN(Fne,fs) / vrel;
+          fs = damp_tangential*vrel;
+          if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel;
           else Ft = 0.0;
           fs1 = -Ft*vtr1;
           fs2 = -Ft*vtr2;
           fs3 = -Ft*vtr3;
         }
 
-	if (roll_model[itype][jtype] != ROLL_NONE ||
-	    twist_model[itype][jtype] != TWIST_NONE){
+        if (roll_model[itype][jtype] != ROLL_NONE ||
+            twist_model[itype][jtype] != TWIST_NONE){
           relrot1 = omega[i][0] - omega[j][0];
           relrot2 = omega[i][1] - omega[j][1];
           relrot3 = omega[i][2] - omega[j][2];
-	  // rolling velocity,
+          // rolling velocity,
           // see eq. 31 of Wang et al, Particuology v 23, p 49 (2015)
           // this is different from the Marshall papers,
           // which use the Bagi/Kuhn formulation
@@ -485,7 +487,7 @@ void PairGranular::compute(int eflag, int vflag)
           // - 0.5*((radj-radi)/radsum)*vtr1;
           // - 0.5*((radj-radi)/radsum)*vtr2;
           // - 0.5*((radj-radi)/radsum)*vtr3;
-	}
+        }
         //****************************************
         // rolling resistance
         //****************************************
@@ -635,7 +637,7 @@ void PairGranular::compute(int eflag, int vflag)
             torque[j][2] -= torroll3;
           }
         }
-        if (evflag) ev_tally_xyz(i,j,nlocal,0,
+        if (evflag) ev_tally_xyz(i,j,nlocal,force->newton_pair,
             0.0,0.0,fx,fy,fz,delx,dely,delz);
       }
     }
@@ -1114,7 +1116,7 @@ void PairGranular::init_style()
 
 double PairGranular::init_one(int i, int j)
 {
-  double cutoff;
+  double cutoff=0.0;
 
   if (setflag[i][j] == 0) {
     if ((normal_model[i][i] != normal_model[j][j]) ||
@@ -1250,20 +1252,20 @@ void PairGranular::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&normal_model[i][j],sizeof(int),1,fp);
-          fread(&damping_model[i][j],sizeof(int),1,fp);
-          fread(&tangential_model[i][j],sizeof(int),1,fp);
-          fread(&roll_model[i][j],sizeof(int),1,fp);
-          fread(&twist_model[i][j],sizeof(int),1,fp);
-          fread(normal_coeffs[i][j],sizeof(double),4,fp);
-          fread(tangential_coeffs[i][j],sizeof(double),3,fp);
-          fread(roll_coeffs[i][j],sizeof(double),3,fp);
-          fread(twist_coeffs[i][j],sizeof(double),3,fp);
-          fread(&cutoff_type[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&normal_model[i][j],sizeof(int),1,fp,NULL,error);
+          utils::sfread(FLERR,&damping_model[i][j],sizeof(int),1,fp,NULL,error);
+          utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,NULL,error);
+          utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,NULL,error);
+          utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,NULL,error);
+          utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,NULL,error);
+          utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,NULL,error);
+          utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,NULL,error);
+          utils::sfread(FLERR,twist_coeffs[i][j],sizeof(double),3,fp,NULL,error);
+          utils::sfread(FLERR,&cutoff_type[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&normal_model[i][j],1,MPI_INT,0,world);
         MPI_Bcast(&damping_model[i][j],1,MPI_INT,0,world);
@@ -1374,22 +1376,6 @@ double PairGranular::single(int i, int j, int itype, int jtype,
   vn2 = ny*vnnr;
   vn3 = nz*vnnr;
 
-  double *rmass = atom->rmass;
-  int *mask = atom->mask;
-  mi = rmass[i];
-  mj = rmass[j];
-  if (fix_rigid) {
-    if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
-    if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
-  }
-
-  meff = mi*mj / (mi+mj);
-  if (mask[i] & freeze_group_bit) meff = mj;
-  if (mask[j] & freeze_group_bit) meff = mi;
-
-  delta = radsum - r;
-  dR = delta*Reff;
-
   // tangential component
 
   vt1 = vr1 - vn1;
@@ -1407,6 +1393,9 @@ double PairGranular::single(int i, int j, int itype, int jtype,
   // if I or J part of rigid body, use body mass
   // if I or J is frozen, meff is other particle
 
+  double *rmass = atom->rmass;
+  int *mask = atom->mask;
+
   mi = rmass[i];
   mj = rmass[j];
   if (fix_rigid) {
@@ -1451,11 +1440,13 @@ double PairGranular::single(int i, int j, int itype, int jtype,
   }
 
   if (damping_model[itype][jtype] == VELOCITY) {
-    damp_normal = normal_coeffs[itype][jtype][1];
+    damp_normal = 1;
+  } else if (damping_model[itype][jtype] == MASS_VELOCITY) {
+    damp_normal = meff;
   } else if (damping_model[itype][jtype] == VISCOELASTIC) {
-    damp_normal = normal_coeffs[itype][jtype][1]*a*meff;
+    damp_normal = a*meff;
   } else if (damping_model[itype][jtype] == TSUJI) {
-    damp_normal = normal_coeffs[itype][jtype][1]*sqrt(meff*knfac);
+    damp_normal = sqrt(meff*knfac);
   }
 
   damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal;
@@ -1506,6 +1497,7 @@ double PairGranular::single(int i, int j, int itype, int jtype,
   } else {
     Fncrit = fabs(Fntot);
   }
+  Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit;
 
   //------------------------------
   // tangential forces
@@ -1518,13 +1510,6 @@ double PairGranular::single(int i, int j, int itype, int jtype,
       k_tangential *= a;
     } else if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE) {
       k_tangential *= a;
-      // on unloading, rescale the shear displacements
-      if (a < history[3]) {
-        double factor = a/history[3];
-        history[0] *= factor;
-        history[1] *= factor;
-        history[2] *= factor;
-      }
     }
 
     shrmag = sqrt(history[0]*history[0] + history[1]*history[1] +
@@ -1535,35 +1520,34 @@ double PairGranular::single(int i, int j, int itype, int jtype,
     fs2 = -k_tangential*history[1] - damp_tangential*vtr2;
     fs3 = -k_tangential*history[2] - damp_tangential*vtr3;
 
-    // rescale frictional displacements and forces if needed
-    Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit;
+    // rescale frictional forces if needed
     fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
     if (fs > Fscrit) {
       if (shrmag != 0.0) {
-        history[0] = -1.0/k_tangential*(Fscrit*fs1/fs + damp_tangential*vtr1);
-        history[1] = -1.0/k_tangential*(Fscrit*fs2/fs + damp_tangential*vtr2);
-        history[2] = -1.0/k_tangential*(Fscrit*fs3/fs + damp_tangential*vtr3);
         fs1 *= Fscrit/fs;
         fs2 *= Fscrit/fs;
         fs3 *= Fscrit/fs;
-      } else fs1 = fs2 = fs3 = 0.0;
+                fs *= Fscrit/fs;
+      } else fs1 = fs2 = fs3 = fs = 0.0;
     }
 
   // classic pair gran/hooke (no history)
   } else {
-    fs = meff*damp_tangential*vrel;
-    if (vrel != 0.0) Ft = MIN(Fne,fs) / vrel;
+    fs = damp_tangential*vrel;
+    if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel;
     else Ft = 0.0;
     fs1 = -Ft*vtr1;
     fs2 = -Ft*vtr2;
     fs3 = -Ft*vtr3;
+    fs = Ft*vrel;
   }
 
   //****************************************
   // rolling resistance
   //****************************************
 
-  if (roll_model[itype][jtype] != ROLL_NONE) {
+  if ((roll_model[itype][jtype] != ROLL_NONE)
+      || (twist_model[itype][jtype] != TWIST_NONE)) {
     relrot1 = omega[i][0] - omega[j][0];
     relrot2 = omega[i][1] - omega[j][1];
     relrot3 = omega[i][2] - omega[j][2];
@@ -1601,10 +1585,10 @@ double PairGranular::single(int i, int j, int itype, int jtype,
         fr1 *= Frcrit/fr;
         fr2 *= Frcrit/fr;
         fr3 *= Frcrit/fr;
-      } else fr1 = fr2 = fr3 = 0.0;
+                fr *= Frcrit/fr;
+      } else fr1 = fr2 = fr3 = fr = 0.0;
     }
-
-  }
+  } else fr1 = fr2 = fr3 = fr = 0.0;
 
   //****************************************
   // twisting torque, including history effects
@@ -1628,8 +1612,12 @@ double PairGranular::single(int i, int j, int itype, int jtype,
     Mtcrit = mu_twist*Fncrit; // critical torque (eq 44)
     if (fabs(magtortwist) > Mtcrit) {
       magtortwist = -Mtcrit * signtwist; // eq 34
-    }
-  }
+    } else magtortwist = 0.0;
+  } else magtortwist = 0.0;
+
+  // set force and return no energy
+
+  fforce = Fntot*rinv;
 
   // set single_extra quantities
 
diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp
index a4272caa01..1d3830c275 100644
--- a/src/KIM/kim_init.cpp
+++ b/src/KIM/kim_init.cpp
@@ -13,8 +13,9 @@
 
 /* ----------------------------------------------------------------------
    Contributing authors: Axel Kohlmeyer (Temple U),
-                         Ryan S. Elliott (UMN)
-                         Ellad B. Tadmor (UMN)
+                         Ryan S. Elliott (UMN),
+                         Ellad B. Tadmor (UMN),
+                         Yaser Afshar (UMN)
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
@@ -77,6 +78,14 @@ extern "C" {
 #include "KIM_SimulatorHeaders.h"
 }
 
+#ifdef SNUM
+#undef SNUM
+#endif
+
+#define SNUM(x)                                                \
+  static_cast<std::ostringstream const &>(std::ostringstream() \
+                                          << std::dec << x).str()
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
@@ -98,11 +107,13 @@ void KimInit::command(int narg, char **arg)
   } else unit_conversion_mode = false;
 
   char *model_units;
-  determine_model_type_and_units(model_name, user_units, &model_units);
+  KIM_Model *pkim = NULL;
+
+  determine_model_type_and_units(model_name, user_units, &model_units, pkim);
 
   write_log_cite(model_name);
 
-  do_init(model_name, user_units, model_units);
+  do_init(model_name, user_units, model_units, pkim);
 }
 
 
@@ -156,7 +167,8 @@ void get_kim_unit_names(
 }  // namespace
 void KimInit::determine_model_type_and_units(char * model_name,
                                              char * user_units,
-                                             char ** model_units)
+                                             char ** model_units,
+                                             KIM_Model *&pkim)
 {
   KIM_LengthUnit lengthUnit;
   KIM_EnergyUnit energyUnit;
@@ -183,7 +195,6 @@ void KimInit::determine_model_type_and_units(char * model_name,
   {
     get_kim_unit_names(user_units, lengthUnit, energyUnit,
                        chargeUnit, temperatureUnit, timeUnit, error);
-    KIM_Model * kim_MO;
     int kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased,
                                      lengthUnit,
                                      energyUnit,
@@ -192,19 +203,19 @@ void KimInit::determine_model_type_and_units(char * model_name,
                                      timeUnit,
                                      model_name,
                                      &units_accepted,
-                                     &kim_MO);
+                                     &pkim);
 
     if (kim_error)
       error->all(FLERR,"Unable to load KIM Simulator Model.");
 
     model_type = MO;
-    KIM_Model_Destroy(&kim_MO);
 
     if (units_accepted) {
       *model_units = new char[strlen(user_units)+1];
       strcpy(*model_units,user_units);
       return;
     } else if (unit_conversion_mode) {
+      KIM_Model_Destroy(&pkim);
       int const num_systems = 5;
       char const * const systems[num_systems]
           = {"metal", "real", "si", "cgs", "electron"};
@@ -219,15 +230,17 @@ void KimInit::determine_model_type_and_units(char * model_name,
                                      timeUnit,
                                      model_name,
                                      &units_accepted,
-                                     &kim_MO);
-        KIM_Model_Destroy(&kim_MO);
+                                     &pkim);
         if (units_accepted) {
           *model_units = new char[strlen(systems[i])+1];
           strcpy(*model_units,systems[i]);
           return;
         }
-      } error->all(FLERR,"KIM Model does not support any lammps unit system");
+        KIM_Model_Destroy(&pkim);
+      }
+      error->all(FLERR,"KIM Model does not support any lammps unit system");
     } else {
+      KIM_Model_Destroy(&pkim);
       error->all(FLERR,"KIM Model does not support the requested unit system");
     }
   }
@@ -270,7 +283,7 @@ void KimInit::determine_model_type_and_units(char * model_name,
 
 /* ---------------------------------------------------------------------- */
 
-void KimInit::do_init(char *model_name, char *user_units, char *model_units)
+void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM_Model *&pkim)
 {
   // create storage proxy fix. delete existing fix, if needed.
 
@@ -358,6 +371,68 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units)
     // reset template map.
     KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel);
   }
+  else if (model_type == MO)
+  {
+    int numberOfParameters;
+    KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters);
+
+    std::string mesg = "\nThis model has ";
+    if (numberOfParameters)
+    {
+      KIM_DataType kim_DataType;
+      int extent;
+      char const *str_name = NULL;
+      char const *str_desc = NULL;
+
+      mesg += SNUM(numberOfParameters);
+      mesg += " mutable parameters. \n";
+
+      int max_len(0);
+      for (int i = 0; i < numberOfParameters; ++i)
+      {
+        KIM_Model_GetParameterMetadata(pkim, i, &kim_DataType,
+        &extent, &str_name, &str_desc);
+        max_len = MAX(max_len, strlen(str_name));
+      }
+      ++max_len;
+      mesg += "No.     |  Parameter name  ";
+      for (int i = 18; i < max_len; ++i)
+        mesg += " ";
+      mesg += "|  data type  |  extent\n";
+      for (int i = 0; i < 8 + MAX(18, max_len); ++i)
+        mesg += "-";
+      mesg += "-----------------------\n";
+      for (int i = 0; i < numberOfParameters; ++i)
+      {
+        KIM_Model_GetParameterMetadata(pkim, i, &kim_DataType,
+        &extent, &str_name, &str_desc);
+        mesg += SNUM(i+1);
+        for (int j = SNUM(i+1).size(); j < 8; ++j)
+          mesg += " ";
+        mesg += "| ";
+        mesg += str_name;
+        for (int j = strlen(str_name) + 1; j < MAX(18, strlen(str_name) + 1); ++j)
+          mesg += " ";
+        mesg += "|  \"";
+        mesg += KIM_DataType_ToString(kim_DataType);
+        if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer))
+          mesg += "\"  | ";
+        else
+          mesg += "\"   | ";
+        mesg += SNUM(extent);
+        mesg += "\n";
+      }
+    }
+    else
+      mesg += "No mutable parameters. \n";
+
+    KIM_Model_Destroy(&pkim);
+
+    if (comm->me == 0)
+    {
+      input->write_echo(mesg.c_str());
+    }
+  }
 
   // End output to log file
   kim_init_log_delimiter("end");
@@ -366,7 +441,7 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units)
 
 /* ---------------------------------------------------------------------- */
 
-void KimInit::kim_init_log_delimiter(std::string const begin_end) const
+void KimInit::kim_init_log_delimiter(std::string const &begin_end) const
 {
   if (comm->me == 0) {
     std::string mesg;
@@ -506,3 +581,5 @@ void KimInit::write_log_cite(char * model_name)
 
   KIM_Collections_Destroy(&coll);
 }
+
+#undef SNUM
diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h
index 2b5dc520c7..62c404212b 100644
--- a/src/KIM/kim_init.h
+++ b/src/KIM/kim_init.h
@@ -13,8 +13,9 @@
 
 /* ----------------------------------------------------------------------
    Contributing authors: Axel Kohlmeyer (Temple U),
-                         Ryan S. Elliott (UMN)
-                         Ellad B. Tadmor (UMN)
+                         Ryan S. Elliott (UMN),
+                         Ellad B. Tadmor (UMN),
+                         Yaser Afshar (UMN)
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
@@ -67,6 +68,9 @@ CommandStyle(kim_init,KimInit)
 #include "pointers.h"
 #include <string>
 
+// Forward declaration.
+class KIM_Model;
+
 namespace LAMMPS_NS {
 
 class KimInit : protected Pointers {
@@ -78,11 +82,11 @@ class KimInit : protected Pointers {
   model_type_enum model_type;
   bool unit_conversion_mode;
 
-  void determine_model_type_and_units(char *, char *, char **);
+  void determine_model_type_and_units(char *, char *, char **, KIM_Model *&);
   void write_log_cite(char *);
-  void do_init(char *, char *, char *);
+  void do_init(char *, char *, char *, KIM_Model *&);
   void do_variables(char*, char*);
-  void kim_init_log_delimiter(std::string const begin_end) const;
+  void kim_init_log_delimiter(std::string const &begin_end) const;
 };
 
 }
diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp
new file mode 100644
index 0000000000..f5a154f2d9
--- /dev/null
+++ b/src/KIM/kim_param.cpp
@@ -0,0 +1,569 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Yaser Afshar (UMN),
+                         Ryan S. Elliott (UMN),
+                         Ellad B. Tadmor (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.1.0 (and newer) package
+------------------------------------------------------------------------- */
+
+#include "kim_param.h"
+#include <mpi.h>
+#include <cstring>
+#include <string>
+#include <sstream>
+#include "comm.h"
+#include "error.h"
+#include "input.h"
+#include "modify.h"
+#include "variable.h"
+#include "force.h"
+#include "fix_store_kim.h"
+#include "pair_kim.h"
+
+extern "C"
+{
+#include "KIM_SimulatorHeaders.h"
+}
+
+#ifdef SNUM
+#undef SNUM
+#endif
+
+#define SNUM(x)                                                \
+  static_cast<std::ostringstream const &>(std::ostringstream() \
+                                          << std::dec << x).str()
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+namespace
+{
+void get_kim_unit_names(
+    char const *const system,
+    KIM_LengthUnit &lengthUnit,
+    KIM_EnergyUnit &energyUnit,
+    KIM_ChargeUnit &chargeUnit,
+    KIM_TemperatureUnit &temperatureUnit,
+    KIM_TimeUnit &timeUnit,
+    Error *error)
+{
+  if ((strcmp(system, "real") == 0)) {
+    lengthUnit = KIM_LENGTH_UNIT_A;
+    energyUnit = KIM_ENERGY_UNIT_kcal_mol;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_fs;
+  } else if ((strcmp(system, "metal") == 0)) {
+    lengthUnit = KIM_LENGTH_UNIT_A;
+    energyUnit = KIM_ENERGY_UNIT_eV;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_ps;
+  } else if ((strcmp(system, "si") == 0)) {
+    lengthUnit = KIM_LENGTH_UNIT_m;
+    energyUnit = KIM_ENERGY_UNIT_J;
+    chargeUnit = KIM_CHARGE_UNIT_C;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_s;
+  } else if ((strcmp(system, "cgs") == 0)) {
+    lengthUnit = KIM_LENGTH_UNIT_cm;
+    energyUnit = KIM_ENERGY_UNIT_erg;
+    chargeUnit = KIM_CHARGE_UNIT_statC;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_s;
+  } else if ((strcmp(system, "electron") == 0)) {
+    lengthUnit = KIM_LENGTH_UNIT_Bohr;
+    energyUnit = KIM_ENERGY_UNIT_Hartree;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_fs;
+  } else if ((strcmp(system, "lj") == 0)) {
+    error->all(FLERR, "LAMMPS unit_style lj not supported by KIM models");
+  } else
+    error->all(FLERR, "Unknown unit_style");
+}
+} // namespace
+
+/* ---------------------------------------------------------------------- */
+
+KimParam::KimParam(LAMMPS *lmp) : Pointers(lmp) {}
+
+KimParam::~KimParam() {}
+
+void KimParam::command(int narg, char **arg)
+{
+  // kim_param is a command for
+  // getting/setting the value of a %KIM PM parameter
+  //
+  // kim_param get param_name index_range variables formatarg
+  // kim_param set param_name index_range values
+
+  // kim_param   get paramname 1 varname
+  // kim_param   get paramname index_range varname_1, ..., varname_N
+  // kim_param   get paramname index_range varname_base split
+  // kim_param   get paramname index_range varname_base list
+  // kim_param   set paramname index_range values
+
+  if (narg < 4)
+    error->all(FLERR, "Illegal kim_param command");
+
+  kim_param_get = (strcmp(arg[0], "get") == 0);
+  kim_param_set = (strcmp(arg[0], "set") == 0);
+
+  if (!kim_param_get && !kim_param_set) {
+    std::string msg("Incorrect arguments in kim_param command.\n");
+    msg += "'kim_param get/set' is mandatory.";
+    error->all(FLERR, msg.c_str());
+  }
+
+  // Check if we called a kim_init command
+  // by finding fix STORE/KIM
+  // retrieve model name and model units.
+
+  char *model_name;
+  char *model_units;
+
+  bool isPortableModel(false);
+
+  int const ifix = modify->find_fix("KIM_MODEL_STORE");
+  if (ifix >= 0) {
+    FixStoreKIM *fix_store = reinterpret_cast<FixStoreKIM *>(modify->fix[ifix]);
+
+    KIM_SimulatorModel *simulatorModel =
+        reinterpret_cast<KIM_SimulatorModel *>(
+            fix_store->getptr("simulator_model"));
+
+    isPortableModel = simulatorModel ? false : true;
+    if (!isPortableModel)
+      error->all(FLERR, "kim_param can only be used with a KIM Portable Model");
+
+    model_name = (char *)fix_store->getptr("model_name");
+    model_units = (char *)fix_store->getptr("model_units");
+  }
+  else
+    error->all(FLERR, "Must use 'kim_init' before 'kim_param'");
+
+  kim_param_log_delimiter("begin");
+
+  KIM_Model *pkim = NULL;
+
+  std::string atom_type_list;
+
+  int kim_error;
+
+  bool isPairStyleAssigned = force->pair ? true : false;
+  if (isPairStyleAssigned) {
+    Pair *pair = force->pair_match("kim", 1, 0);
+    if (pair) {
+      PairKIM *pairKIM = reinterpret_cast<PairKIM *>(pair);
+
+      pkim = pairKIM->get_KIM_Model();
+      if (!pkim)
+        error->all(FLERR, "Unable to get the KIM Portable Model.");
+
+      if (kim_param_set) {
+        atom_type_list = pairKIM->get_atom_type_list();
+        if (atom_type_list.empty())
+          error->all(FLERR, "The requested atom type list is empty.");
+      }
+    } else
+      error->all(FLERR, "Pair style is defined,"
+                        " but there is no match for kim style in lammps.");
+  } else {
+    if (kim_param_set) {
+      std::string msg("Wrong kim_param set command.\n");
+      msg += "To set the new parameter values, pair style must be assigned.\n";
+      msg += "Must use 'kim_interactions' or";
+      msg += "'pair_style kim ' before 'kim_param set'";
+      error->all(FLERR, msg.c_str());
+    } else {
+      KIM_LengthUnit lengthUnit;
+      KIM_EnergyUnit energyUnit;
+      KIM_ChargeUnit chargeUnit;
+      KIM_TemperatureUnit temperatureUnit;
+      KIM_TimeUnit timeUnit;
+
+      get_kim_unit_names(model_units, lengthUnit, energyUnit,
+                         chargeUnit, temperatureUnit, timeUnit,
+                         error);
+
+      int units_accepted;
+
+      kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased,
+                                   lengthUnit,
+                                   energyUnit,
+                                   chargeUnit,
+                                   temperatureUnit,
+                                   timeUnit,
+                                   model_name,
+                                   &units_accepted,
+                                   &pkim);
+      if (kim_error)
+        error->all(FLERR, "Unable to create KIM Portable Model.");
+    }
+  }
+
+  // Get the number of mutable parameters in the kim model
+  int numberOfParameters(0);
+
+  KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters);
+  if (numberOfParameters) {
+    // Get the parameters
+    if (kim_param_get) {
+      // Parameter name
+      char *paramname = NULL;
+      // Variable name
+      char *varname = NULL;
+
+      // Loop over all the arguments
+      for (int i = 1; i < narg;) {
+        // Parameter name
+        if (i < narg)
+          paramname = arg[i++];
+        else
+          break;
+
+        // Find the requested parameter within the model parameters
+        int param_index;
+        KIM_DataType kim_DataType;
+        int extent;
+        char const *str_name = NULL;
+        char const *str_desc = NULL;
+
+        for (param_index = 0; param_index < numberOfParameters; ++param_index) {
+          kim_error = KIM_Model_GetParameterMetadata(pkim, param_index,
+                                                     &kim_DataType, &extent,
+                                                     &str_name, &str_desc);
+          if (kim_error)
+            error->all(FLERR, "KIM GetParameterMetadata returned error.");
+
+          if (strcmp(paramname, str_name) == 0)
+            break;
+        }
+
+        if (param_index >= numberOfParameters) {
+          std::string msg("Wrong argument in kim_param get command.\n");
+          msg += "This Model does not have the requested '";
+          msg += paramname;
+          msg += "' parameter.";
+          error->all(FLERR, msg.c_str());
+        }
+
+        // Get the index_range for the requested parameter
+        int nlbound(0);
+        int nubound(0);
+
+        if (i < narg) {
+          std::string argtostr(arg[i++]);
+
+          // Check to see if the indices range contains
+          // only integer numbers and/or range :
+          if (argtostr.find_first_not_of("0123456789:") != std::string::npos) {
+            std::string msg("Illegal index_range.\n");
+            msg += "Expected integer parameter(s) instead of '";
+            msg += argtostr;
+            msg += "' in index_range.";
+            error->all(FLERR, msg.c_str());
+          }
+
+          std::string::size_type npos = argtostr.find(':');
+          if (npos != std::string::npos) {
+            argtostr[npos] = ' ';
+            std::stringstream str(argtostr);
+            str >> nlbound >> nubound;
+            if (nubound < 1 || nubound > extent ||
+                nlbound < 1 || nlbound > nubound) {
+              std::string msg("Illegal index_range '");
+              msg += SNUM(nlbound) + "-" + SNUM(nubound);
+              msg += "' for '";
+              msg += paramname;
+              msg += "' parameter with extent of '";
+              msg += SNUM(extent);
+              msg += "' .";
+              error->all(FLERR, msg.c_str());
+            }
+          } else {
+            std::stringstream str(argtostr);
+            str >> nlbound;
+            if (nlbound < 1 || nlbound > extent) {
+              std::string msg("Illegal index '");
+              msg += SNUM(nlbound) + "' for parameter '";
+              msg += paramname;
+              msg += "' with the extent of '";
+              msg += SNUM(extent);
+              msg += "' .";
+              error->all(FLERR, msg.c_str());
+            }
+            nubound = nlbound;
+          }
+        } else {
+          std::string msg("Wrong number of arguments in ");
+          msg += "kim_param get command.\n";
+          msg += "Index range after parameter name is mandatory.";
+          error->all(FLERR, msg.c_str());
+        }
+
+        int const nvars = nubound - nlbound + 1;
+        char **varsname = NULL;
+
+        if (i < narg) {
+          // Get the variable/variable_base name
+          varname = arg[i++];
+        } else {
+          std::string msg("Wrong number of arguments in ");
+          msg += "kim_param get command.\n";
+          msg += "The LAMMPS variable name is mandatory.";
+          error->all(FLERR, msg.c_str());
+        }
+
+        // indicator flag for list request
+        bool list_requested(false);
+
+        if (nvars > 1) {
+          if (i < narg) {
+            if (strcmp(arg[i], "split") == 0) {
+              varsname = new char *[nvars];
+              for (int j = 0, k = nlbound; j < nvars; ++j, ++k) {
+                std::stringstream str;
+                str << varname << "_" << k;
+                varsname[j] = const_cast<char *>(str.str().c_str());
+              }
+            } else if (strcmp(arg[i], "list") == 0) {
+              list_requested = true;
+              varsname = new char *[1];
+              varsname[0] = varname;
+            // Default explicit (optional) formatarg
+            } else if (i - 1 + nvars < narg) {
+              varsname = new char *[nvars];
+              --i;
+              for (int j = 0; j < nvars; ++j, ++i)
+                varsname[j] = arg[i];
+              if (i < narg) {
+                if (strcmp(arg[i], "explicit") == 0)
+                  ++i;
+              }
+            } else {
+              std::string msg("Wrong number of arguments in ");
+              msg += "kim_param get command.\n";
+              msg += "The LAMMPS '";
+              msg += SNUM(nvars);
+              msg += "' variable names or '";
+              msg += varname;
+              msg += " split' is mandatory.";
+              error->all(FLERR, msg.c_str());
+            }
+          } else {
+            std::string msg("Wrong number of arguments in ");
+            msg += "kim_param get command.\n";
+            msg += "The LAMMPS '";
+            msg += SNUM(nvars);
+            msg += "' variable names or '";
+            msg += varname;
+            msg += " split/list' is mandatory.";
+            error->all(FLERR, msg.c_str());
+          }
+        } else {
+          varsname = new char *[1];
+          if (i < narg)
+          {
+            if (strcmp(arg[i], "split") == 0)
+            {
+              std::stringstream str;
+              str << varname << "_" << nlbound;
+              varsname[0] = const_cast<char *>(str.str().c_str());
+              ++i;
+            } else {
+              if ((strcmp(arg[i], "list") == 0) ||
+                  (strcmp(arg[i], "explicit") == 0))
+                ++i;
+              varsname[0] = varname;
+            }
+          } else {
+            varsname[0] = varname;
+          }
+        }
+
+        char **varcmd = new char *[3];
+        varcmd[1] = const_cast<char *>("string");
+
+        if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Double)) {
+          if (list_requested) {
+            std::stringstream str;
+            double V;
+            {
+              kim_error = KIM_Model_GetParameterDouble(pkim, param_index,
+                                                       nlbound - 1, &V);
+              if (kim_error)
+                error->all(FLERR, "KIM GetParameterDouble returned error.");
+              str << V;
+            }
+            for (int j = 1; j < nvars; ++j) {
+              kim_error = KIM_Model_GetParameterDouble(pkim, param_index,
+                                                       nlbound - 1 + j, &V);
+              if (kim_error)
+                error->all(FLERR, "KIM GetParameterDouble returned error.");
+              str << " " << V;
+            }
+            varcmd[0] = varsname[0];
+            varcmd[2] = const_cast<char *>(str.str().c_str());
+            input->variable->set(3, varcmd);
+            echo_var_assign(varcmd[0], varcmd[2]);
+          } else {
+            for (int j = 0; j < nvars; ++j) {
+              varcmd[0] = varsname[j];
+              double V;
+              kim_error = KIM_Model_GetParameterDouble(pkim, param_index,
+                                                       nlbound - 1 + j, &V);
+              if (kim_error)
+                error->all(FLERR, "KIM GetParameterDouble returned error.");
+              std::stringstream str;
+              str << V;
+              varcmd[2] = const_cast<char *>(str.str().c_str());
+              input->variable->set(3, varcmd);
+              echo_var_assign(varcmd[0], varcmd[2]);
+            }
+          }
+        } else if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) {
+          if (list_requested) {
+            std::stringstream str;
+            int V;
+            {
+              kim_error = KIM_Model_GetParameterInteger(pkim, param_index,
+                                                        nlbound - 1, &V);
+              if (kim_error)
+                error->all(FLERR, "KIM GetParameterInteger returned error.");
+              str << V;
+            }
+            for (int j = 1; j < nvars; ++j) {
+              kim_error = KIM_Model_GetParameterInteger(pkim, param_index,
+                                                        nlbound - 1 + j, &V);
+              if (kim_error)
+                error->all(FLERR, "KIM GetParameterInteger returned error.");
+              str << " " << V;
+            }
+            varcmd[0] = varsname[0];
+            varcmd[2] = const_cast<char *>(str.str().c_str());
+            input->variable->set(3, varcmd);
+            echo_var_assign(varcmd[0], varcmd[2]);
+          } else {
+            for (int j = 0; j < nvars; ++j) {
+              varcmd[0] = varsname[j];
+              int V;
+              kim_error = KIM_Model_GetParameterInteger(pkim, param_index,
+                                                        nlbound - 1 + j, &V);
+              if (kim_error)
+                error->all(FLERR, "KIM GetParameterInteger returned error.");
+              std::stringstream str;
+              str << V;
+              varcmd[2] = const_cast<char *>(str.str().c_str());
+              input->variable->set(3, varcmd);
+              echo_var_assign(varcmd[0], varcmd[2]);
+            }
+          }
+        } else
+          error->all(FLERR, "Wrong parameter type.");
+
+        delete[] varcmd;
+        delete[] varsname;
+      } // End of loop over all the arguments
+    // Set the parameters
+    } else {
+      std::string set_cmd("pair_coeff * * ");
+      set_cmd += atom_type_list;
+      for (int i = 1; i < narg; ++i) {
+        set_cmd += " ";
+        set_cmd += arg[i];
+      }
+      input->one(set_cmd.c_str());
+    }
+  } else
+    error->all(FLERR, "This model has No mutable parameters.");
+
+  if (!isPairStyleAssigned)
+    KIM_Model_Destroy(&pkim);
+
+  kim_param_log_delimiter("end");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void KimParam::kim_param_log_delimiter(std::string const &begin_end) const
+{
+  if (comm->me == 0) {
+    std::string msg;
+    if (begin_end == "begin") {
+      msg = "#=== BEGIN kim-param ";
+      msg += kim_param_get ? "get " : "set ";
+      msg += "=====================================\n";
+    } else if (begin_end == "end") {
+      msg = "#=== END kim-param ";
+      msg += kim_param_get ? "get " : "set ";
+      msg += "=======================================\n\n";
+    }
+    input->write_echo(msg.c_str());
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void KimParam::echo_var_assign(std::string const &name,
+                               std::string const &value) const
+{
+  if (comm->me == 0) {
+    std::string msg;
+    msg += "variable " + name + " string " + value + "\n";
+    input->write_echo(msg.c_str());
+  }
+}
+
+#undef SNUM
diff --git a/src/KIM/kim_param.h b/src/KIM/kim_param.h
new file mode 100644
index 0000000000..5a9298628d
--- /dev/null
+++ b/src/KIM/kim_param.h
@@ -0,0 +1,100 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Yaser Afshar (UMN),
+                         Ryan S. Elliott (UMN),
+                         Ellad B. Tadmor (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.1.0 (and newer) package
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(kim_param, KimParam)
+
+#else
+
+#ifndef LMP_KIM_PARAM_H
+#define LMP_KIM_PARAM_H
+
+#include "pointers.h"
+#include <string>
+
+namespace LAMMPS_NS
+{
+
+class KimParam : protected Pointers
+{
+public:
+  KimParam(class LAMMPS *lmp);
+
+  ~KimParam();
+
+  void command(int, char **);
+
+private:
+  void kim_param_log_delimiter(std::string const &begin_end) const;
+
+  void echo_var_assign(std::string const &name, std::string const &value)
+      const;
+
+private:
+  bool kim_param_get;
+  bool kim_param_set;
+};
+
+} // namespace LAMMPS_NS
+
+#endif // LMP_KIM_PARAM_H
+#endif // COMMAND_CLASS
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp
index 8ceefeceaf..12c93c80c2 100644
--- a/src/KIM/kim_query.cpp
+++ b/src/KIM/kim_query.cpp
@@ -13,7 +13,8 @@
 
 /* ----------------------------------------------------------------------
    Contributing authors: Axel Kohlmeyer (Temple U),
-                         Ryan S. Elliott (UMN)
+                         Ryan S. Elliott (UMN),
+                         Yaser Afshar (UMN)
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
@@ -71,6 +72,7 @@
 #if defined(LMP_KIM_CURL)
 #include <sys/types.h>
 #include <curl/curl.h>
+#include <cstdlib>
 #endif
 
 using namespace LAMMPS_NS;
@@ -105,15 +107,25 @@ void KimQuery::command(int narg, char **arg)
     model_name = (char *)fix_store->getptr("model_name");
   } else error->all(FLERR,"Must use 'kim_init' before 'kim_query'");
 
-
   varname = arg[0];
   bool split = false;
   if (0 == strcmp("split",arg[1])) {
     if (narg == 2) error->all(FLERR,"Illegal kim_query command");
+    if (0 == strcmp("list",arg[2]))
+      error->all(FLERR,"Illegal kim_query command");
     split = true;
     arg++;
     narg--;
   }
+
+  // The “list� is the default setting
+  // the result is returned as a space-separated list of values in variable
+  if (0 == strcmp("list",arg[1])) {
+    if (narg == 2) error->all(FLERR,"Illegal kim_query command");
+    if (split) error->all(FLERR,"Illegal kim_query command");
+    arg++;
+    narg--;
+  }
   function = arg[1];
   for (int i = 2; i < narg; ++i)
   {
@@ -143,12 +155,13 @@ void KimQuery::command(int narg, char **arg)
 
   kim_query_log_delimiter("begin");
   char **varcmd = new char*[3];
+  varcmd[1] = (char *) "string";
+
+  std::stringstream ss(value);
+  std::string token;
+
   if (split) {
     int counter = 1;
-    std::stringstream ss(value);
-    std::string token;
-    varcmd[1] = (char *) "string";
-
     while(std::getline(ss, token, ',')) {
       token.erase(0,token.find_first_not_of(" \n\r\t"));  // ltrim
       token.erase(token.find_last_not_of(" \n\r\t") + 1);  // rtrim
@@ -161,11 +174,17 @@ void KimQuery::command(int narg, char **arg)
     }
   } else {
     varcmd[0] = varname;
-    varcmd[1] = (char *) "string";
-    varcmd[2] = value;
+    std::string value_string;
+    while(std::getline(ss, token, ',')) {
+      token.erase(0,token.find_first_not_of(" \n\r\t"));  // ltrim
+      token.erase(token.find_last_not_of(" \n\r\t") + 1);  // rtrim
+      if (value_string.size() && token.size())
+        value_string += " ";
+      value_string += token;
+    }
+    varcmd[2] = const_cast<char *>(value_string.c_str());;
     input->variable->set(3,varcmd);
-
-    echo_var_assign(varname, value);
+    echo_var_assign(varname, value_string);
   }
   kim_query_log_delimiter("end");
 
@@ -239,11 +258,25 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
       curl_easy_setopt(handle, CURLOPT_VERBOSE, 1L);
 #endif
 
-#if defined(LMP_NO_SSL_CHECK)
-      // disable verifying SSL certificate and host name
+#if LMP_NO_SSL_CHECK
+      // Certificate Verification
+      // by telling libcurl to not verify the peer.
+      // Disable verifying SSL certificate and host name. Insecure.
       curl_easy_setopt(handle, CURLOPT_SSL_VERIFYPEER, 0L);
       curl_easy_setopt(handle, CURLOPT_SSL_VERIFYHOST, 0L);
 #endif
+
+      {
+        char *env_c = std::getenv("CURL_CA_BUNDLE");
+        if (env_c)
+        {
+          // Certificate Verification
+          // by specifying your own CA cert path. Set the environment variable
+          // CURL_CA_BUNDLE to the path of your choice.
+          curl_easy_setopt(handle, CURLOPT_CAINFO, env_c);
+        }
+      }
+
       std::string user_agent = std::string("kim_query--LAMMPS/")
                                + LAMMPS_VERSION
                                + " (" + Info::get_os_info() + ")";
diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index d935d994bd..e54c76397f 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -14,6 +14,7 @@
 /* ----------------------------------------------------------------------
    Contributing authors: Ryan S. Elliott (UMinn)
                          Axel Kohlmeyer (Temple U)
+                         Yaser Afshar (UMN)
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
@@ -57,6 +58,7 @@
 #include <cstring>
 #include <cstdlib>
 #include <string>
+#include <sstream>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -66,6 +68,7 @@
 #include "update.h"
 #include "memory.h"
 #include "domain.h"
+#include "utils.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -330,6 +333,14 @@ void PairKIM::settings(int narg, char **arg)
    set coeffs for one or more type pairs
 ------------------------------------------------------------------------- */
 
+#ifdef SNUM
+#undef SNUM
+#endif
+
+#define SNUM(x)                                                \
+  static_cast<std::ostringstream const &>(std::ostringstream() \
+                                          << std::dec << x).str()
+
 void PairKIM::coeff(int narg, char **arg)
 {
   // This is called when "pair_coeff ..." is read from input
@@ -339,7 +350,7 @@ void PairKIM::coeff(int narg, char **arg)
 
   if (!allocated) allocate();
 
-  if (narg != 2 + atom->ntypes)
+  if (narg < 2 + atom->ntypes)
     error->all(FLERR,"Incorrect args for pair coefficients");
 
   // insure I,J args are * *
@@ -368,10 +379,10 @@ void PairKIM::coeff(int narg, char **arg)
 
   // Assume all species arguments are valid
   // errors will be detected by below
-  std::string atom_type_sym_list;
+  atom_type_list.clear();
   lmps_num_unique_elements = 0;
-  for (i = 2; i < narg; i++) {
-    atom_type_sym_list += std::string(" ") + arg[i];
+  for (i = 2; i < 2 + atom->ntypes; i++) {
+    atom_type_list += std::string(" ") + arg[i];
     for (j = 0; j < lmps_num_unique_elements; j++)
       if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break;
     lmps_map_species_to_unique[i-1] = j;
@@ -421,8 +432,147 @@ void PairKIM::coeff(int narg, char **arg)
       error->all(FLERR, msg.c_str());
     }
   }
+  // Set the new values for PM parameters
+  if (narg > 2 + atom->ntypes) {
+    // Get the number of mutable parameters in the kim model
+    int numberOfParameters(0);
+    KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters);
+
+    if (!numberOfParameters) {
+      std::string msg("Incorrect args for pair coefficients \n");
+      msg += "This model has No mutable parameters.";
+      error->all(FLERR, msg.c_str());
+    }
+
+    int kimerror;
+
+    // Parameter name
+    char *paramname = NULL;
+
+    for (int i = 2 + atom->ntypes; i < narg;) {
+      // Parameter name
+      if (i < narg)
+        paramname = arg[i++];
+      else
+        break;
+
+      // Find the requested parameter within the model parameters
+      int param_index;
+      KIM_DataType kim_DataType;
+      int extent;
+      char const *str_name = NULL;
+      char const *str_desc = NULL;
+
+      for (param_index = 0; param_index < numberOfParameters; ++param_index) {
+        kimerror = KIM_Model_GetParameterMetadata(pkim, param_index,
+                   &kim_DataType, &extent, &str_name, &str_desc);
+        if (kimerror)
+          error->all(FLERR,"KIM GetParameterMetadata returned error");
+
+        if (strcmp(paramname, str_name) == 0) break;
+      }
+
+      if (param_index >= numberOfParameters) {
+        std::string msg("Wrong argument for pair coefficients.\n");
+        msg += "This Model does not have the requested '";
+        msg += paramname;
+        msg += "' parameter.";
+        error->all(FLERR, msg.c_str());
+      }
+
+      // Get the index_range for the requested parameter
+      int nlbound(0);
+      int nubound(0);
+
+      if (i < narg) {
+        std::string argtostr(arg[i++]);
+
+        // Check to see if the indices range contains only integer numbers & :
+        if (argtostr.find_first_not_of("0123456789:") != std::string::npos) {
+          std::string msg("Illegal index_range.\n");
+          msg += "Expected integer parameter(s) instead of '";
+          msg += argtostr;
+          msg += "' in index_range.";
+          error->all(FLERR, msg.c_str());
+        }
+
+        std::string::size_type npos = argtostr.find(':');
+        if (npos != std::string::npos) {
+          argtostr[npos] = ' ';
+          std::stringstream str(argtostr);
+          str >> nlbound >> nubound;
+          if (nubound < 1 || nubound > extent ||
+              nlbound < 1 || nlbound > nubound) {
+            std::string msg("Illegal index_range '");
+            msg += SNUM(nlbound) + "-" + SNUM(nubound);
+            msg += "' for '";
+            msg += paramname;
+            msg += "' parameter with extent of '";
+            msg += SNUM(extent);
+            msg += "' .";
+            error->all(FLERR, msg.c_str());
+          }
+        } else {
+          std::stringstream str(argtostr);
+          str >> nlbound;
+          if (nlbound < 1 || nlbound > extent) {
+            std::string msg("Illegal index '");
+            msg += SNUM(nlbound) + "' for '";
+            msg += paramname;
+            msg += "' parameter with extent of '";
+            msg += SNUM(extent);
+            msg += "' .";
+            error->all(FLERR, msg.c_str());
+          }
+          nubound = nlbound;
+        }
+      } else {
+        std::string msg =
+        "Wrong number of arguments for pair coefficients.\n";
+        msg += "Index range after parameter name is mandatory.";
+        error->all(FLERR, msg.c_str());
+      }
+
+      // Parameter values
+      if (i + nubound - nlbound < narg) {
+        if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Double)) {
+          for (int j = 0; j < nubound - nlbound + 1; ++j) {
+            double const V = utils::numeric(FLERR, arg[i++], true, lmp);
+            kimerror = KIM_Model_SetParameterDouble(pkim, param_index,
+                       nlbound - 1 + j, V);
+            if (kimerror)
+              error->all(FLERR, "KIM SetParameterDouble returned error.");
+          }
+        } else if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) {
+          for (int j = 0; j < nubound - nlbound + 1; ++j) {
+            int const V = utils::inumeric(FLERR, arg[i++], true, lmp);
+            kimerror = KIM_Model_SetParameterInteger(pkim, param_index,
+                       nlbound - 1 + j, V);
+            if (kimerror)
+              error->all(FLERR, "KIM SetParameterInteger returned error.");
+          }
+        } else
+          error->all(FLERR, "Wrong parameter type to update");
+      } else {
+        std::string msg =
+        "Wrong number of variable values for pair coefficients.\n";
+        msg += "'";
+        msg += SNUM(nubound - nlbound + 1);
+        msg += "' values are requested for '";
+        msg += paramname;
+        msg += "' parameter.";
+        error->all(FLERR, msg.c_str());
+      }
+    }
+
+    kimerror = KIM_Model_ClearThenRefresh(pkim);
+    if (kimerror)
+      error->all(FLERR, "KIM KIM_Model_ClearThenRefresh returned error");
+  }
 }
 
+#undef SNUM
+
 /* ----------------------------------------------------------------------
    init specific to this pair style
 ------------------------------------------------------------------------- */
@@ -740,11 +890,7 @@ void PairKIM::kim_init()
   kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs,
     KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles,
     &lmps_local_tot_num_atoms);
-  if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy,
-                                 KIM_SUPPORT_STATUS_notSupported))
-    kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs,
-      KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,
-      &(eng_vdwl));
+  if (kimerror) error->all(FLERR,"Unable to set KIM argument pointer");
 
   kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs,
     KIM_COMPUTE_CALLBACK_NAME_GetNeighborList,
@@ -752,7 +898,7 @@ void PairKIM::kim_init()
     reinterpret_cast<KIM_Function *>(get_neigh),
     reinterpret_cast<void *>(this));
 
-  if (kimerror) error->all(FLERR,"Unable to register KIM pointers");
+  if (kimerror) error->all(FLERR,"Unable to set KIM call back pointer");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -763,6 +909,27 @@ void PairKIM::set_argument_pointers()
   kimerror = KIM_ComputeArguments_SetArgumentPointerDouble(
     pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0]));
 
+  // Set KIM pointer appropriately for Energy
+  if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy,
+                                 KIM_SUPPORT_STATUS_notSupported))
+  {
+      if (KIM_SupportStatus_Equal(kim_model_support_for_energy,
+                                  KIM_SUPPORT_STATUS_required)
+        || (eflag_global == 1))
+      {
+        kimerror = kimerror ||
+        KIM_ComputeArguments_SetArgumentPointerDouble(
+          pargs,KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,&(eng_vdwl));
+      }
+      else
+      {
+        kimerror = kimerror ||
+        KIM_ComputeArguments_SetArgumentPointerDouble(
+          pargs,KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,
+          reinterpret_cast<double * const>(NULL));
+      }
+  }
+
   // Set KIM pointer appropriately for particalEnergy
   if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy,
                               KIM_SUPPORT_STATUS_required)
@@ -994,3 +1161,7 @@ void PairKIM::set_kim_model_has_flags()
       error->all(FLERR,"KIM Model requires unsupported compute callback");
   }
 }
+
+KIM_Model *PairKIM::get_KIM_Model() { return pkim; }
+
+std::string PairKIM::get_atom_type_list() { return atom_type_list; }
diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h
index aa33b9b271..1f2c8c8599 100644
--- a/src/KIM/pair_kim.h
+++ b/src/KIM/pair_kim.h
@@ -65,6 +65,7 @@ PairStyle(kim,PairKIM)
 // includes from KIM & LAMMPS
 class KIM_API_model;
 #include "pair.h"
+#include <string>
 
 extern "C" {
 #include "KIM_SimulatorHeaders.h"
@@ -88,6 +89,11 @@ class PairKIM : public Pair {
   virtual void unpack_reverse_comm(int, int*, double*);
   virtual double memory_usage();
 
+  // Get the KIM_Model object
+  KIM_Model *get_KIM_Model();
+
+  // Get the atom type list
+  std::string get_atom_type_list();
  protected:
   // (nearly) all bool flags are not initialized in constructor, but set
   // explicitly in the indicated function.  All other data members are
@@ -98,6 +104,9 @@ class PairKIM : public Pair {
   // values set in settings()
   char* kim_modelname;
 
+  // list of args that map atom species to KIM elements
+  std::string atom_type_list;
+
   // values set in coeff()
 
   // values set in allocate(), called by coeff()
diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp
index 7e217df2a6..67aaa32c21 100644
--- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp
@@ -247,13 +247,13 @@ struct AtomVecSphereKokkos_PackComm {
       _buf(i,2) = _x(j,2);
     } else {
       if (TRICLINIC == 0) {
-	_buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
-	_buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
-	_buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+        _buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
+        _buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
+        _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
       } else {
-	_buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
-	_buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
-	_buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+        _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+        _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+        _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
       }
     }
     _buf(i,3) = _radius(j);
@@ -419,13 +419,13 @@ struct AtomVecSphereKokkos_PackCommVel {
       _buf(i,2) = _x(j,2);
     } else {
       if (TRICLINIC == 0) {
-	_buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
-	_buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
-	_buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+        _buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
+        _buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
+        _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
       } else {
-	_buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
-	_buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
-	_buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+        _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+        _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+        _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
       }
     }
     if (DEFORM_VREMAP == 0) {
@@ -772,13 +772,13 @@ struct AtomVecSphereKokkos_PackCommSelf {
       _xw(i+_nfirst,2) = _x(j,2);
     } else {
       if (TRICLINIC == 0) {
-	_xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
-	_xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
-	_xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+        _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
+        _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
+        _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
       } else {
-	_xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
-	_xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
-	_xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+        _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+        _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+        _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
       }
     }
     _radius(i+_nfirst) = _radius(j);
@@ -799,39 +799,39 @@ int AtomVecSphereKokkos::pack_comm_self(
     atomKK->modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK);
     if(pbc_flag) {
       if(domain->triclinic) {
-	struct AtomVecSphereKokkos_PackCommSelf<LMPHostType,1,1> f(
+        struct AtomVecSphereKokkos_PackCommSelf<LMPHostType,1,1> f(
           atomKK->k_x,
-	  atomKK->k_radius,atomKK->k_rmass,
-	  nfirst,list,iswap,
-	  domain->xprd,domain->yprd,domain->zprd,
-	  domain->xy,domain->xz,domain->yz,pbc);
-	Kokkos::parallel_for(n,f);
+          atomKK->k_radius,atomKK->k_rmass,
+          nfirst,list,iswap,
+          domain->xprd,domain->yprd,domain->zprd,
+          domain->xy,domain->xz,domain->yz,pbc);
+        Kokkos::parallel_for(n,f);
       } else {
-	struct AtomVecSphereKokkos_PackCommSelf<LMPHostType,1,0> f(
+        struct AtomVecSphereKokkos_PackCommSelf<LMPHostType,1,0> f(
           atomKK->k_x,
-	  atomKK->k_radius,atomKK->k_rmass,
-	  nfirst,list,iswap,
-	  domain->xprd,domain->yprd,domain->zprd,
-	  domain->xy,domain->xz,domain->yz,pbc);
-	Kokkos::parallel_for(n,f);
+          atomKK->k_radius,atomKK->k_rmass,
+          nfirst,list,iswap,
+          domain->xprd,domain->yprd,domain->zprd,
+          domain->xy,domain->xz,domain->yz,pbc);
+        Kokkos::parallel_for(n,f);
       }
     } else {
       if(domain->triclinic) {
-	struct AtomVecSphereKokkos_PackCommSelf<LMPHostType,0,1> f(
+        struct AtomVecSphereKokkos_PackCommSelf<LMPHostType,0,1> f(
           atomKK->k_x,
-	  atomKK->k_radius,atomKK->k_rmass,
-	  nfirst,list,iswap,
-	  domain->xprd,domain->yprd,domain->zprd,
-	  domain->xy,domain->xz,domain->yz,pbc);
-	Kokkos::parallel_for(n,f);
+          atomKK->k_radius,atomKK->k_rmass,
+          nfirst,list,iswap,
+          domain->xprd,domain->yprd,domain->zprd,
+          domain->xy,domain->xz,domain->yz,pbc);
+        Kokkos::parallel_for(n,f);
       } else {
-	struct AtomVecSphereKokkos_PackCommSelf<LMPHostType,0,0> f(
+        struct AtomVecSphereKokkos_PackCommSelf<LMPHostType,0,0> f(
           atomKK->k_x,
-	  atomKK->k_radius,atomKK->k_rmass,
-	  nfirst,list,iswap,
-	  domain->xprd,domain->yprd,domain->zprd,
-	  domain->xy,domain->xz,domain->yz,pbc);
-	Kokkos::parallel_for(n,f);
+          atomKK->k_radius,atomKK->k_rmass,
+          nfirst,list,iswap,
+          domain->xprd,domain->yprd,domain->zprd,
+          domain->xy,domain->xz,domain->yz,pbc);
+        Kokkos::parallel_for(n,f);
       }
     }
   } else {
@@ -839,39 +839,39 @@ int AtomVecSphereKokkos::pack_comm_self(
     atomKK->modified(Device,X_MASK|RADIUS_MASK|RMASS_MASK);
     if(pbc_flag) {
       if(domain->triclinic) {
-	struct AtomVecSphereKokkos_PackCommSelf<LMPDeviceType,1,1> f(
+        struct AtomVecSphereKokkos_PackCommSelf<LMPDeviceType,1,1> f(
           atomKK->k_x,
-	  atomKK->k_radius,atomKK->k_rmass,
-	  nfirst,list,iswap,
-	  domain->xprd,domain->yprd,domain->zprd,
-	  domain->xy,domain->xz,domain->yz,pbc);
-	Kokkos::parallel_for(n,f);
+          atomKK->k_radius,atomKK->k_rmass,
+          nfirst,list,iswap,
+          domain->xprd,domain->yprd,domain->zprd,
+          domain->xy,domain->xz,domain->yz,pbc);
+        Kokkos::parallel_for(n,f);
       } else {
-	struct AtomVecSphereKokkos_PackCommSelf<LMPDeviceType,1,0> f(
+        struct AtomVecSphereKokkos_PackCommSelf<LMPDeviceType,1,0> f(
           atomKK->k_x,
-	  atomKK->k_radius,atomKK->k_rmass,
-	  nfirst,list,iswap,
-	  domain->xprd,domain->yprd,domain->zprd,
-	  domain->xy,domain->xz,domain->yz,pbc);
-	Kokkos::parallel_for(n,f);
+          atomKK->k_radius,atomKK->k_rmass,
+          nfirst,list,iswap,
+          domain->xprd,domain->yprd,domain->zprd,
+          domain->xy,domain->xz,domain->yz,pbc);
+        Kokkos::parallel_for(n,f);
       }
     } else {
       if(domain->triclinic) {
-	struct AtomVecSphereKokkos_PackCommSelf<LMPDeviceType,0,1> f(
+        struct AtomVecSphereKokkos_PackCommSelf<LMPDeviceType,0,1> f(
           atomKK->k_x,
-	  atomKK->k_radius,atomKK->k_rmass,
-	  nfirst,list,iswap,
-	  domain->xprd,domain->yprd,domain->zprd,
-	  domain->xy,domain->xz,domain->yz,pbc);
-	Kokkos::parallel_for(n,f);
+          atomKK->k_radius,atomKK->k_rmass,
+          nfirst,list,iswap,
+          domain->xprd,domain->yprd,domain->zprd,
+          domain->xy,domain->xz,domain->yz,pbc);
+        Kokkos::parallel_for(n,f);
       } else {
-	struct AtomVecSphereKokkos_PackCommSelf<LMPDeviceType,0,0> f(
+        struct AtomVecSphereKokkos_PackCommSelf<LMPDeviceType,0,0> f(
           atomKK->k_x,
-	  atomKK->k_radius,atomKK->k_rmass,
-	  nfirst,list,iswap,
-	  domain->xprd,domain->yprd,domain->zprd,
-	  domain->xy,domain->xz,domain->yz,pbc);
-	Kokkos::parallel_for(n,f);
+          atomKK->k_radius,atomKK->k_rmass,
+          nfirst,list,iswap,
+          domain->xprd,domain->yprd,domain->zprd,
+          domain->xy,domain->xz,domain->yz,pbc);
+        Kokkos::parallel_for(n,f);
       }
     }
   }
@@ -1037,7 +1037,7 @@ void AtomVecSphereKokkos::unpack_comm_vel_kokkos(
 /* ---------------------------------------------------------------------- */
 
 int AtomVecSphereKokkos::pack_comm(int n, int *list, double *buf,
-			           int pbc_flag, int *pbc)
+                                   int pbc_flag, int *pbc)
 {
   int i,j,m;
   double dx,dy,dz;
@@ -1109,7 +1109,7 @@ int AtomVecSphereKokkos::pack_comm(int n, int *list, double *buf,
 /* ---------------------------------------------------------------------- */
 
 int AtomVecSphereKokkos::pack_comm_vel(int n, int *list, double *buf,
-				       int pbc_flag, int *pbc)
+                                       int pbc_flag, int *pbc)
 {
   int i,j,m;
   double dx,dy,dz,dvx,dvy,dvz;
@@ -1926,7 +1926,7 @@ struct AtomVecSphereKokkos_UnpackBorder {
 /* ---------------------------------------------------------------------- */
 
 void AtomVecSphereKokkos::unpack_border_kokkos(const int &n, const int &first,
-					       const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) {
+                                               const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) {
   while (first+n >= nmax) grow(0);
   if(space==Host) {
     struct AtomVecSphereKokkos_UnpackBorder<LMPHostType> f(buf.view<LMPHostType>(),
@@ -1943,7 +1943,7 @@ void AtomVecSphereKokkos::unpack_border_kokkos(const int &n, const int &first,
   }
 
   atomKK->modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|
-	         RADIUS_MASK|RMASS_MASK);
+                 RADIUS_MASK|RMASS_MASK);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -2053,7 +2053,7 @@ void AtomVecSphereKokkos::unpack_border_vel_kokkos(
   }
 
   atomKK->modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|
-	         RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK);
+                 RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -2496,7 +2496,7 @@ int AtomVecSphereKokkos::unpack_restart(double *buf)
 
   atomKK->modified(Host,X_MASK | TAG_MASK | TYPE_MASK |
                 MASK_MASK | IMAGE_MASK | V_MASK |
-	        RADIUS_MASK | RMASS_MASK | OMEGA_MASK);
+                RADIUS_MASK | RMASS_MASK | OMEGA_MASK);
 
   atom->nlocal++;
   return m;
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index d0bd978ae7..774d7040cc 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -210,7 +210,7 @@ void CommKokkos::forward_comm_device(int dummy)
             MPI_Send(k_buf_send.view<DeviceType>().data(),
                      n,MPI_DOUBLE,sendproc[iswap],0,world);
           }
-    
+
           if (size_forward_recv[iswap]) {
             MPI_Wait(&request,MPI_STATUS_IGNORE);
             atomKK->modified(ExecutionSpaceFromDevice<DeviceType>::
diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index 4b8d171f61..0310053b5e 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -243,15 +243,20 @@ void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTO
   const F_FLOAT sb3 = 1.0/r3mag2;
   const F_FLOAT rb3 = 1.0/r3;
 
-  const F_FLOAT c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
+  F_FLOAT c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
 
   // 1st and 2nd angle
 
   const F_FLOAT r12c1 = rb1*rb2;
   const F_FLOAT r12c2 = rb2*rb3;
-  const F_FLOAT costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
-  const F_FLOAT costh13 = c0;
-  const F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
+  F_FLOAT costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
+  F_FLOAT costh13 = c0;
+  F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
+
+  costh12 = MAX(MIN(costh12, 1.0), -1.0);
+  costh13 = MAX(MIN(costh13, 1.0), -1.0);
+  costh23 = MAX(MIN(costh23, 1.0), -1.0);
+  c0 = costh13;
 
   // cos and sin of 2 angles and final c
 
diff --git a/src/KOKKOS/domain_kokkos.cpp b/src/KOKKOS/domain_kokkos.cpp
index 4cf3e6ab52..cb4eaddfec 100644
--- a/src/KOKKOS/domain_kokkos.cpp
+++ b/src/KOKKOS/domain_kokkos.cpp
@@ -340,11 +340,11 @@ struct DomainPBCFunctor {
 
 void DomainKokkos::pbc()
 {
- 
+
   if (lmp->kokkos->exchange_comm_classic) {
- 
+
    // reduce GPU data movement
- 
+
     atomKK->sync(Host,X_MASK|V_MASK|MASK_MASK|IMAGE_MASK);
     Domain::pbc();
     atomKK->modified(Host,X_MASK|V_MASK|MASK_MASK|IMAGE_MASK);
diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp
index bf2a882539..205451d96f 100644
--- a/src/KOKKOS/fix_enforce2d_kokkos.cpp
+++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp
@@ -34,10 +34,10 @@ FixEnforce2DKokkos<DeviceType>::FixEnforce2DKokkos(LAMMPS *lmp, int narg, char *
   execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
 
   datamask_read   = V_MASK | F_MASK | OMEGA_MASK | MASK_MASK
-	  | TORQUE_MASK | ANGMOM_MASK;
+          | TORQUE_MASK | ANGMOM_MASK;
 
   datamask_modify = V_MASK | F_MASK | OMEGA_MASK
-	  | TORQUE_MASK | ANGMOM_MASK;
+          | TORQUE_MASK | ANGMOM_MASK;
 }
 
 
diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp
index 651f790a25..8818d60a11 100644
--- a/src/KOKKOS/fix_langevin_kokkos.cpp
+++ b/src/KOKKOS/fix_langevin_kokkos.cpp
@@ -61,7 +61,6 @@ FixLangevinKokkos<DeviceType>::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a
   k_ratio.template modify<LMPHostType>();
 
   if(gjfflag){
-    nvalues = 3;
     grow_arrays(atomKK->nmax);
     atom->add_callback(0);
     // initialize franprev to zero
@@ -69,8 +68,12 @@ FixLangevinKokkos<DeviceType>::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a
       franprev[i][0] = 0.0;
       franprev[i][1] = 0.0;
       franprev[i][2] = 0.0;
+      lv[i][0] = 0.0;
+      lv[i][1] = 0.0;
+      lv[i][2] = 0.0;
     }
     k_franprev.template modify<LMPHostType>();
+    k_lv.template modify<LMPHostType>();
   }
   if(zeroflag){
     k_fsumall = tdual_double_1d_3n("langevin:fsumall");
@@ -94,6 +97,7 @@ FixLangevinKokkos<DeviceType>::~FixLangevinKokkos()
   memoryKK->destroy_kokkos(k_ratio,ratio);
   memoryKK->destroy_kokkos(k_flangevin,flangevin);
   if(gjfflag) memoryKK->destroy_kokkos(k_franprev,franprev);
+  if(gjfflag) memoryKK->destroy_kokkos(k_lv,lv);
   memoryKK->destroy_kokkos(k_tforce,tforce);
 }
 
@@ -107,6 +111,10 @@ void FixLangevinKokkos<DeviceType>::init()
     error->all(FLERR,"Fix langevin omega is not yet implemented with kokkos");
   if(ascale)
     error->all(FLERR,"Fix langevin angmom is not yet implemented with kokkos");
+  if(gjfflag && tbiasflag)
+    error->all(FLERR,"Fix langevin gjf + tbias is not yet implemented with kokkos");
+  if(gjfflag && tbiasflag)
+    error->warning(FLERR,"Fix langevin gjf + kokkos is not implemented with random gaussians");
 
   // prefactors are modified in the init
   k_gfactor1.template modify<LMPHostType>();
@@ -121,6 +129,40 @@ void FixLangevinKokkos<DeviceType>::grow_arrays(int nmax)
   memoryKK->grow_kokkos(k_franprev,franprev,nmax,3,"langevin:franprev");
   d_franprev = k_franprev.template view<DeviceType>();
   h_franprev = k_franprev.template view<LMPHostType>();
+  memoryKK->grow_kokkos(k_lv,lv,nmax,3,"langevin:lv");
+  d_lv = k_lv.template view<DeviceType>();
+  h_lv = k_lv.template view<LMPHostType>();
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::initial_integrate(int vflag)
+{
+  atomKK->sync(execution_space,datamask_read);
+  atomKK->modified(execution_space,datamask_modify);
+
+  v = atomKK->k_v.view<DeviceType>();
+  f = atomKK->k_f.view<DeviceType>();
+  int nlocal = atomKK->nlocal;
+  if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst;
+
+  FixLangevinKokkosInitialIntegrateFunctor<DeviceType> functor(this);
+  Kokkos::parallel_for(nlocal,functor);
+}
+
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void FixLangevinKokkos<DeviceType>::initial_integrate_item(int i) const
+{
+  if (mask[i] & groupbit) {
+    f(i,0) /= gjfa;
+    f(i,1) /= gjfa;
+    f(i,2) /= gjfa;
+    v(i,0) = d_lv(i,0);
+    v(i,1) = d_lv(i,1);
+    v(i,2) = d_lv(i,2);
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -140,6 +182,7 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
   k_gfactor2.template sync<DeviceType>();
   k_ratio.template sync<DeviceType>();
   if(gjfflag) k_franprev.template sync<DeviceType>();
+  if(gjfflag) k_lv.template sync<DeviceType>();
 
   boltz = force->boltz;
   dt = update->dt;
@@ -162,7 +205,7 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
   }
 
   // reallocate flangevin if necessary
-  if (tallyflag) {
+  if (tallyflag || osflag) {
     if (nlocal > maxatom1) {
       memoryKK->destroy_kokkos(k_flangevin,flangevin);
       maxatom1 = atomKK->nmax;
@@ -177,7 +220,7 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
     atomKK->sync(temperature->execution_space,temperature->datamask_read);
     temperature->compute_scalar();
     temperature->remove_bias_all(); // modifies velocities
-    // if temeprature compute is kokkosized host-devcie comm won't be needed
+    // if temeprature compute is kokkosized host-device comm won't be needed
     atomKK->modified(temperature->execution_space,temperature->datamask_modify);
     atomKK->sync(execution_space,temperature->datamask_modify);
   }
@@ -186,7 +229,7 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
   FSUM s_fsum;
   if (tstyle == ATOM)
     if (gjfflag)
-      if (tallyflag)
+      if (tallyflag || osflag)
         if (tbiasflag == BIAS)
           if (rmass.data())
             if (zeroflag) {
@@ -257,7 +300,7 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
               Kokkos::parallel_for(nlocal,post_functor);
             }
     else
-      if (tallyflag)
+      if (tallyflag || osflag)
         if (tbiasflag == BIAS)
           if (rmass.data())
             if (zeroflag) {
@@ -329,7 +372,7 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
             }
   else
     if (gjfflag)
-      if (tallyflag)
+      if (tallyflag || osflag)
         if (tbiasflag == BIAS)
           if (rmass.data())
             if (zeroflag) {
@@ -400,7 +443,7 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
               Kokkos::parallel_for(nlocal,post_functor);
             }
     else
-      if (tallyflag)
+      if (tallyflag || osflag)
         if (tbiasflag == BIAS)
           if (rmass.data())
             if (zeroflag) {
@@ -481,7 +524,8 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
 
   // set modify flags for the views modified in post_force functor
   if (gjfflag) k_franprev.template modify<DeviceType>();
-  if (tallyflag) k_flangevin.template modify<DeviceType>();
+  if (gjfflag) k_lv.template modify<DeviceType>();
+  if (tallyflag || osflag) k_flangevin.template modify<DeviceType>();
 
   // set total force to zero
   if (zeroflag) {
@@ -550,6 +594,10 @@ FSUM FixLangevinKokkos<DeviceType>::post_force_item(int i) const
     }
 
     if (Tp_GJF) {
+      d_lv(i,0) = gjfsib*v(i,0);
+      d_lv(i,1) = gjfsib*v(i,1);
+      d_lv(i,2) = gjfsib*v(i,2);
+
       fswap = 0.5*(fran[0]+d_franprev(i,0));
       d_franprev(i,0) = fran[0];
       fran[0] = fswap;
@@ -560,15 +608,15 @@ FSUM FixLangevinKokkos<DeviceType>::post_force_item(int i) const
       d_franprev(i,2) = fran[2];
       fran[2] = fswap;
 
-      fdrag[0] *= gjffac;
-      fdrag[1] *= gjffac;
-      fdrag[2] *= gjffac;
-      fran[0] *= gjffac;
-      fran[1] *= gjffac;
-      fran[2] *= gjffac;
-      f(i,0) *= gjffac;
-      f(i,1) *= gjffac;
-      f(i,2) *= gjffac;
+      fdrag[0] *= gjfa;
+      fdrag[1] *= gjfa;
+      fdrag[2] *= gjfa;
+      fran[0] *= gjfa;
+      fran[1] *= gjfa;
+      fran[2] *= gjfa;
+      f(i,0) *= gjfa;
+      f(i,1) *= gjfa;
+      f(i,2) *= gjfa;
     }
 
     f(i,0) += fdrag[0] + fran[0];
@@ -576,6 +624,17 @@ FSUM FixLangevinKokkos<DeviceType>::post_force_item(int i) const
     f(i,2) += fdrag[2] + fran[2];
 
     if (Tp_TALLY) {
+      if (Tp_GJF){
+        fdrag[0] = gamma1*d_lv(i,0)/gjfsib/gjfsib;
+        fdrag[1] = gamma1*d_lv(i,1)/gjfsib/gjfsib;
+        fdrag[2] = gamma1*d_lv(i,2)/gjfsib/gjfsib;
+        fswap = (2*fran[0]/gjfa - d_franprev(i,0))/gjfsib;
+        fran[0] = fswap;
+        fswap = (2*fran[1]/gjfa - d_franprev(i,1))/gjfsib;
+        fran[1] = fswap;
+        fswap = (2*fran[2]/gjfa - d_franprev(i,2))/gjfsib;
+        fran[2] = fswap;
+      }
       d_flangevin(i,0) = fdrag[0] + fran[0];
       d_flangevin(i,1) = fdrag[1] + fran[1];
       d_flangevin(i,2) = fdrag[2] + fran[2];
@@ -719,9 +778,10 @@ double FixLangevinKokkos<DeviceType>::compute_energy_item(int i) const
 template<class DeviceType>
 void FixLangevinKokkos<DeviceType>::end_of_step()
 {
-  if (!tallyflag) return;
+  if (!tallyflag && !gjfflag) return;
 
   v = atomKK->k_v.template view<DeviceType>();
+  f = atomKK->k_f.template view<DeviceType>();
   mask = atomKK->k_mask.template view<DeviceType>();
 
   atomKK->sync(execution_space,V_MASK | MASK_MASK);
@@ -733,9 +793,81 @@ void FixLangevinKokkos<DeviceType>::end_of_step()
   FixLangevinKokkosTallyEnergyFunctor<DeviceType> tally_functor(this);
   Kokkos::parallel_reduce(nlocal,tally_functor,energy_onestep);
 
+  if (gjfflag){
+    if (rmass.data()) {
+      FixLangevinKokkosEndOfStepFunctor<DeviceType,1> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+    } else {
+      mass = atomKK->k_mass.view<DeviceType>();
+      FixLangevinKokkosEndOfStepFunctor<DeviceType,0> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+    }
+  }
+
   energy += energy_onestep*update->dt;
 }
 
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void FixLangevinKokkos<DeviceType>::end_of_step_item(int i) const {
+  double tmp[3];
+  if (mask[i] & groupbit) {
+    const double dtfm = force->ftm2v * 0.5 * dt / mass[type[i]];
+    tmp[0] = v(i,0);
+    tmp[1] = v(i,1);
+    tmp[2] = v(i,2);
+    if (!osflag){
+      v(i,0) = d_lv(i,0);
+      v(i,1) = d_lv(i,1);
+      v(i,2) = d_lv(i,2);
+    } else {
+      v(i,0) = 0.5 * gjfsib * gjfsib * (v(i,0) + dtfm * f(i,0) / gjfa) +
+                dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,0)) +
+                (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,0);
+      v(i,1) = 0.5 * gjfsib * gjfsib * (v(i,1) + dtfm * f(i,1) / gjfa) +
+                dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,1)) +
+                (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,1);
+      v(i,2) = 0.5 * gjfsib * gjfsib * (v(i,2) + dtfm * f(i,2) / gjfa) +
+                dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,2)) +
+                (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,2);
+    }
+    d_lv(i,0) = tmp[0];
+    d_lv(i,1) = tmp[1];
+    d_lv(i,2) = tmp[2];
+  }
+}
+
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void FixLangevinKokkos<DeviceType>::end_of_step_rmass_item(int i) const
+{
+  double tmp[3];
+  if (mask[i] & groupbit) {
+    const double dtfm = force->ftm2v * 0.5 * dt / rmass[i];
+    tmp[0] = v(i,0);
+    tmp[1] = v(i,1);
+    tmp[2] = v(i,2);
+    if (!osflag){
+      v(i,0) = d_lv(i,0);
+      v(i,1) = d_lv(i,1);
+      v(i,2) = d_lv(i,2);
+    } else {
+      v(i,0) = 0.5 * gjfsib * gjfsib * (v(i,0) + dtfm * f(i,0) / gjfa) +
+                dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,0)) +
+                (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,0);
+      v(i,1) = 0.5 * gjfsib * gjfsib * (v(i,1) + dtfm * f(i,1) / gjfa) +
+                dtfm * 0.5 * (gjfsib * d_flangevin(i,1) - d_franprev(i,1)) +
+                (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,1);
+      v(i,2) = 0.5 * gjfsib * gjfsib * (v(i,2) + dtfm * f(i,2) / gjfa) +
+                dtfm * 0.5 * (gjfsib * d_flangevin(i,2) - d_franprev(i,2)) +
+                (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,2);
+    }
+    d_lv(i,0) = tmp[0];
+    d_lv(i,1) = tmp[1];
+    d_lv(i,2) = tmp[2];
+  }
+}
+
 /* ----------------------------------------------------------------------
    copy values within local atom-based array
    ------------------------------------------------------------------------- */
@@ -743,10 +875,15 @@ void FixLangevinKokkos<DeviceType>::end_of_step()
 template<class DeviceType>
 void FixLangevinKokkos<DeviceType>::copy_arrays(int i, int j, int delflag)
 {
-  for (int m = 0; m < nvalues; m++)
-    h_franprev(j,m) = h_franprev(i,m);
+  h_franprev(j,0) = h_franprev(i,0);
+  h_franprev(j,1) = h_franprev(i,1);
+  h_franprev(j,2) = h_franprev(i,2);
+  h_lv(j,0) = h_lv(i,0);
+  h_lv(j,1) = h_lv(i,1);
+  h_lv(j,2) = h_lv(i,2);
 
   k_franprev.template modify<LMPHostType>();
+  k_lv.template modify<LMPHostType>();
 
 }
 
@@ -765,6 +902,7 @@ void FixLangevinKokkos<DeviceType>::cleanup_copy()
   tforce = NULL;
   gjfflag = 0;
   franprev = NULL;
+  lv = NULL;
   id = style = NULL;
   vatom = NULL;
 }
diff --git a/src/KOKKOS/fix_langevin_kokkos.h b/src/KOKKOS/fix_langevin_kokkos.h
index 140fea81d6..a6d467dfd7 100644
--- a/src/KOKKOS/fix_langevin_kokkos.h
+++ b/src/KOKKOS/fix_langevin_kokkos.h
@@ -56,6 +56,9 @@ namespace LAMMPS_NS {
   template<class DeviceType>
     class FixLangevinKokkos;
 
+  template <class DeviceType>
+  class FixLangevinKokkosInitialIntegrateFunctor;
+
   template<class DeviceType,int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
     int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
     class FixLangevinKokkosPostForceFunctor;
@@ -72,6 +75,7 @@ namespace LAMMPS_NS {
 
     void cleanup_copy();
     void init();
+    void initial_integrate(int);
     void post_force(int);
     void reset_dt();
     void grow_arrays(int);
@@ -79,6 +83,12 @@ namespace LAMMPS_NS {
     double compute_scalar();
     void end_of_step();
 
+    KOKKOS_INLINE_FUNCTION
+      void initial_integrate_item(int) const;
+
+    KOKKOS_INLINE_FUNCTION
+      void initial_integrate_rmass_item(int) const;
+
     template<int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
       int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
       KOKKOS_INLINE_FUNCTION
@@ -90,14 +100,25 @@ namespace LAMMPS_NS {
     KOKKOS_INLINE_FUNCTION
       double compute_energy_item(int) const;
 
+    KOKKOS_INLINE_FUNCTION
+      void end_of_step_item(int) const;
+
+    KOKKOS_INLINE_FUNCTION
+      void end_of_step_rmass_item(int) const;
+
   private:
     class CommKokkos *commKK;
 
     typename ArrayTypes<DeviceType>::t_float_1d rmass;
+    typename ArrayTypes<DeviceType>::t_float_1d mass;
     typename ArrayTypes<DeviceType>::tdual_double_2d k_franprev;
     typename ArrayTypes<DeviceType>::t_double_2d d_franprev;
     HAT::t_double_2d h_franprev;
 
+    typename ArrayTypes<DeviceType>::tdual_double_2d k_lv;
+    typename ArrayTypes<DeviceType>::t_double_2d d_lv;
+    HAT::t_double_2d h_lv;
+
     typename ArrayTypes<DeviceType>::tdual_double_2d k_flangevin;
     typename ArrayTypes<DeviceType>::t_double_2d d_flangevin;
     HAT::t_double_2d h_flangevin;
@@ -130,6 +151,21 @@ namespace LAMMPS_NS {
 
   };
 
+  template <class DeviceType>
+  struct FixLangevinKokkosInitialIntegrateFunctor  {
+    typedef DeviceType  device_type ;
+    FixLangevinKokkos<DeviceType> c;
+
+  FixLangevinKokkosInitialIntegrateFunctor(FixLangevinKokkos<DeviceType>* c_ptr):
+    c(*c_ptr) {c.cleanup_copy();};
+
+    KOKKOS_INLINE_FUNCTION
+    void operator()(const int i) const {
+      c.initial_integrate_item(i);
+    }
+  };
+
+
   template <class DeviceType,int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
     int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
     struct FixLangevinKokkosPostForceFunctor {
@@ -207,6 +243,21 @@ namespace LAMMPS_NS {
         update += source;
       }
     };
+
+  template <class DeviceType, int RMass>
+  struct FixLangevinKokkosEndOfStepFunctor {
+    typedef DeviceType  device_type ;
+    FixLangevinKokkos<DeviceType> c;
+
+    FixLangevinKokkosEndOfStepFunctor(FixLangevinKokkos<DeviceType>* c_ptr):
+      c(*c_ptr) {c.cleanup_copy();}
+
+    KOKKOS_INLINE_FUNCTION
+    void operator()(const int i) const {
+      if (RMass) c.end_of_step_rmass_item(i);
+      else c.end_of_step_item(i);
+    }
+  };
 }
 
 #endif
@@ -231,4 +282,12 @@ E: Fix langevin variable returned negative temperature
 
 Self-explanatory.
 
+E: Fix langevin gjf with tbias is not yet implemented with kokkos
+
+This option is not yet available.
+
+W: Fix langevin gjf using random gaussians is not implemented with kokkos
+
+This will most likely cause errors in kinetic fluctuations.
+
 */
diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp
index 8cfe7111dd..7906d37cc3 100644
--- a/src/KOKKOS/fix_neigh_history_kokkos.cpp
+++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp
@@ -122,21 +122,21 @@ void FixNeighHistoryKokkos<DeviceType>::pre_exchange_item(const int &ii) const
       j &= NEIGHMASK;
       int m = Kokkos::atomic_fetch_add(&d_npartner[i],1);
       if (m < maxpartner) {
-	d_partner(i,m) = tag[j];
-	for (int k = 0; k < dnum; k++)
-	  d_valuepartner(i,dnum*m+k) = d_firstvalue(i,dnum*jj+k);
+        d_partner(i,m) = tag[j];
+        for (int k = 0; k < dnum; k++)
+          d_valuepartner(i,dnum*m+k) = d_firstvalue(i,dnum*jj+k);
       } else {
-	d_resize() = 1;
+        d_resize() = 1;
       }
       if (j < nlocal_neigh) {
-	m = Kokkos::atomic_fetch_add(&d_npartner[j],1);
-	if (m < maxpartner) {
-	  d_partner(j,m) = tag[i];
-	  for (int k = 0; k < dnum; k++)
-	    d_valuepartner(j,dnum*m+k) = d_firstvalue(i,dnum*jj+k);
-	} else {
-	  d_resize() = 1;
-	}
+        m = Kokkos::atomic_fetch_add(&d_npartner[j],1);
+        if (m < maxpartner) {
+          d_partner(j,m) = tag[i];
+          for (int k = 0; k < dnum; k++)
+            d_valuepartner(j,dnum*m+k) = d_firstvalue(i,dnum*jj+k);
+        } else {
+          d_resize() = 1;
+        }
       }
     }
   }
@@ -205,22 +205,22 @@ void FixNeighHistoryKokkos<DeviceType>::post_neighbor_item(const int &ii) const
     if (rflag) {
       int jtag = tag(j);
       for (m = 0; m < np; m++)
-	if (d_partner(i, m) == jtag) break;
+        if (d_partner(i, m) == jtag) break;
       if (m < np) {
-	d_firstflag(i,jj) = 1;
-	for (int k = 0; k < dnum; k++) {
-	  d_firstvalue(i, dnum*jj+k) = d_valuepartner(i, dnum*m+k);
-	}
+        d_firstflag(i,jj) = 1;
+        for (int k = 0; k < dnum; k++) {
+          d_firstvalue(i, dnum*jj+k) = d_valuepartner(i, dnum*m+k);
+        }
       } else {
-	d_firstflag(i,jj) = 0;
-	for (int k = 0; k < dnum; k++) {
-	  d_firstvalue(i, dnum*jj+k) = 0;
-	}
+        d_firstflag(i,jj) = 0;
+        for (int k = 0; k < dnum; k++) {
+          d_firstvalue(i, dnum*jj+k) = 0;
+        }
       }
     } else {
       d_firstflag(i,jj) = 0;
       for (int k = 0; k < dnum; k++) {
-	d_firstvalue(i, dnum*jj+k) = 0;
+        d_firstvalue(i, dnum*jj+k) = 0;
       }
     }
   }
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index 18dff991b2..8f60f3526d 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -187,7 +187,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
 
   binsize = 0.0;
 #ifdef KOKKOS_ENABLE_CUDA
-  cuda_aware_flag = 1; 
+  cuda_aware_flag = 1;
 #else
   cuda_aware_flag = 0;
 #endif
@@ -220,7 +220,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
 
   int nmpi = 0;
   MPI_Comm_size(world,&nmpi);
-  if (nmpi > 0) {
+  if (nmpi > 1) {
 
 #if defined(MPI_VERSION) && (MPI_VERSION > 2)
     // Check for IBM Spectrum MPI
@@ -397,9 +397,14 @@ void KokkosLMP::accelerator(int narg, char **arg)
     } else error->all(FLERR,"Illegal package kokkos command");
   }
 
+#ifdef KOKKOS_ENABLE_CUDA
+
+  int nmpi = 0;
+  MPI_Comm_size(world,&nmpi);
+
   // if "cuda/aware off" and "comm device", change to "comm host"
 
-  if (!cuda_aware_flag) {
+  if (!cuda_aware_flag && nmpi > 1) {
     if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) {
       exchange_comm_on_host = 1;
       exchange_comm_changed = 1;
@@ -431,6 +436,8 @@ void KokkosLMP::accelerator(int narg, char **arg)
     }
   }
 
+#endif
+
   // set newton flags
   // set neighbor binsize, same as neigh_modify command
 
diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp
index 4daf4b84c5..dc0efbc193 100644
--- a/src/KOKKOS/npair_kokkos.cpp
+++ b/src/KOKKOS/npair_kokkos.cpp
@@ -101,7 +101,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_stencil_info()
     // copy stencil to device as it may have changed
 
     int maxstencil = ns->get_maxstencil();
-    
+
     if (maxstencil > k_stencil.extent(0))
       k_stencil = DAT::tdual_int_1d("neighlist:stencil",maxstencil);
     for (int k = 0; k < maxstencil; k++)
@@ -224,49 +224,49 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::build(NeighList *list_)
       Kokkos::parallel_for(nall, f);
     } else {
       if (newton_pair) {
-	if (SIZE) {
-	  NPairKokkosBuildFunctorSize<DeviceType,TRI?0:HALF_NEIGH,1,TRI> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
+        if (SIZE) {
+          NPairKokkosBuildFunctorSize<DeviceType,TRI?0:HALF_NEIGH,1,TRI> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
 #ifdef KOKKOS_ENABLE_CUDA
-	  if (ExecutionSpaceFromDevice<DeviceType>::space == Device)
-	    Kokkos::parallel_for(config, f);
-	  else
-	    Kokkos::parallel_for(nall, f);
+          if (ExecutionSpaceFromDevice<DeviceType>::space == Device)
+            Kokkos::parallel_for(config, f);
+          else
+            Kokkos::parallel_for(nall, f);
 #else
-	  Kokkos::parallel_for(nall, f);
+          Kokkos::parallel_for(nall, f);
 #endif
-	} else {
-	  NPairKokkosBuildFunctor<DeviceType,TRI?0:HALF_NEIGH,1,TRI> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
+        } else {
+          NPairKokkosBuildFunctor<DeviceType,TRI?0:HALF_NEIGH,1,TRI> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
 #ifdef KOKKOS_ENABLE_CUDA
-	  if (ExecutionSpaceFromDevice<DeviceType>::space == Device)
-	    Kokkos::parallel_for(config, f);
-	  else
-	    Kokkos::parallel_for(nall, f);
+          if (ExecutionSpaceFromDevice<DeviceType>::space == Device)
+            Kokkos::parallel_for(config, f);
+          else
+            Kokkos::parallel_for(nall, f);
 #else
-	  Kokkos::parallel_for(nall, f);
+          Kokkos::parallel_for(nall, f);
 #endif
-	}
+        }
       } else {
-	if (SIZE) {
-	  NPairKokkosBuildFunctorSize<DeviceType,HALF_NEIGH,0,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
+        if (SIZE) {
+          NPairKokkosBuildFunctorSize<DeviceType,HALF_NEIGH,0,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
 #ifdef KOKKOS_ENABLE_CUDA
-	  if (ExecutionSpaceFromDevice<DeviceType>::space == Device)
-	    Kokkos::parallel_for(config, f);
-	  else
-	    Kokkos::parallel_for(nall, f);
+          if (ExecutionSpaceFromDevice<DeviceType>::space == Device)
+            Kokkos::parallel_for(config, f);
+          else
+            Kokkos::parallel_for(nall, f);
 #else
-	  Kokkos::parallel_for(nall, f);
+          Kokkos::parallel_for(nall, f);
 #endif
-	} else {
-	  NPairKokkosBuildFunctor<DeviceType,HALF_NEIGH,0,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
+        } else {
+          NPairKokkosBuildFunctor<DeviceType,HALF_NEIGH,0,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
 #ifdef KOKKOS_ENABLE_CUDA
-	  if (ExecutionSpaceFromDevice<DeviceType>::space == Device)
-	    Kokkos::parallel_for(config, f);
-	  else
-	    Kokkos::parallel_for(nall, f);
+          if (ExecutionSpaceFromDevice<DeviceType>::space == Device)
+            Kokkos::parallel_for(config, f);
+          else
+            Kokkos::parallel_for(nall, f);
 #else
-	  Kokkos::parallel_for(nall, f);
+          Kokkos::parallel_for(nall, f);
 #endif
-	}
+        }
       }
     }
     Kokkos::deep_copy(h_scalars, d_scalars);
@@ -871,8 +871,8 @@ void NeighborKokkosExecute<DeviceType>::
 
     if(rsq <= cutsq) {
       if(n<neigh_list.maxneighs) {
-	if(neigh_list.history && rsq < radsum*radsum) neighbors_i(n++) = j ^ mask_history;
-	else neighbors_i(n++) = j;
+        if(neigh_list.history && rsq < radsum*radsum) neighbors_i(n++) = j ^ mask_history;
+        else neighbors_i(n++) = j;
       }
       else n++;
     }
@@ -892,14 +892,14 @@ void NeighborKokkosExecute<DeviceType>::
       if(HalfNeigh && !Newton && (j < i)) continue;
       if(!HalfNeigh && j==i) continue;
       if(Tri) {
-	if (x(j,2) < ztmp) continue;
-	if (x(j,2) == ztmp) {
-	  if (x(j,1) < ytmp) continue;
-	  if (x(j,1) == ytmp) {
-	    if (x(j,0) < xtmp) continue;
-	    if (x(j,0) == xtmp && j <= i) continue;
-	  }
-	}
+        if (x(j,2) < ztmp) continue;
+        if (x(j,2) == ztmp) {
+          if (x(j,1) < ytmp) continue;
+          if (x(j,1) == ytmp) {
+            if (x(j,0) < xtmp) continue;
+            if (x(j,0) == xtmp && j <= i) continue;
+          }
+        }
       }
       if(exclude && exclusion(i,j,itype,jtype)) continue;
 
@@ -911,11 +911,11 @@ void NeighborKokkosExecute<DeviceType>::
       const X_FLOAT cutsq = (radsum + skin) * (radsum + skin);
 
       if(rsq <= cutsq) {
-	if(n<neigh_list.maxneighs) {
-	  if(neigh_list.history && rsq < radsum*radsum) neighbors_i(n++) = j ^ mask_history;
-	  else neighbors_i(n++) = j;
-	}
-	else n++;
+        if(n<neigh_list.maxneighs) {
+          if(neigh_list.history && rsq < radsum*radsum) neighbors_i(n++) = j ^ mask_history;
+          else neighbors_i(n++) = j;
+        }
+        else n++;
       }
     }
   }
@@ -990,17 +990,17 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeCuda(typename Kokkos::Team
     if(i >= 0 && i < nlocal) {
       #pragma unroll 4
       for(int m = 0; m < bincount_current; m++) {
-	int j = other_id[m];
-	const int jtype = other_x[m + 3 * atoms_per_bin];
+        int j = other_id[m];
+        const int jtype = other_x[m + 3 * atoms_per_bin];
 
-	//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists
-	if((j == i) ||
-	   (HalfNeigh && !Newton && (j < i))  ||
-	   (HalfNeigh && Newton &&
+        //for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists
+        if((j == i) ||
+           (HalfNeigh && !Newton && (j < i))  ||
+           (HalfNeigh && Newton &&
             ((j < i) ||
-	     ((j >= nlocal) && ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) ||
-				(x(j, 2) == ztmp && x(j, 1)  == ytmp && x(j, 0) < xtmp)))))
-	   ) continue;
+             ((j >= nlocal) && ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) ||
+                                (x(j, 2) == ztmp && x(j, 1)  == ytmp && x(j, 0) < xtmp)))))
+           ) continue;
         if(Tri) {
           if (x(j,2) < ztmp) continue;
           if (x(j,2) == ztmp) {
@@ -1011,21 +1011,21 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeCuda(typename Kokkos::Team
             }
           }
         }
-	if(exclude && exclusion(i,j,itype,jtype)) continue;
-	const X_FLOAT delx = xtmp - other_x[m];
-	const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
-	const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
-	const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
-	const X_FLOAT radsum = radi + other_x[m + 4 * atoms_per_bin];
-	const X_FLOAT cutsq = (radsum + skin) * (radsum + skin);
+        if(exclude && exclusion(i,j,itype,jtype)) continue;
+        const X_FLOAT delx = xtmp - other_x[m];
+        const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
+        const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
+        const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
+        const X_FLOAT radsum = radi + other_x[m + 4 * atoms_per_bin];
+        const X_FLOAT cutsq = (radsum + skin) * (radsum + skin);
 
-	if(rsq <= cutsq) {
-	  if(n<neigh_list.maxneighs) {
-	    if (neigh_list.history && rsq < radsum*radsum) neighbors_i(n++) = j ^ mask_history;
-	    else neighbors_i(n++) = j;
-	  }
-	  else n++;
-	}
+        if(rsq <= cutsq) {
+          if(n<neigh_list.maxneighs) {
+            if (neigh_list.history && rsq < radsum*radsum) neighbors_i(n++) = j ^ mask_history;
+            else neighbors_i(n++) = j;
+          }
+          else n++;
+        }
       }
     }
     __syncthreads();
@@ -1041,11 +1041,11 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeCuda(typename Kokkos::Team
       int j = MY_II < bincount_current ? c_bins(jbin, MY_II) : -1;
 
       if(j >= 0) {
-	other_x[MY_II] = x(j, 0);
-	other_x[MY_II + atoms_per_bin] = x(j, 1);
-	other_x[MY_II + 2 * atoms_per_bin] = x(j, 2);
-	other_x[MY_II + 3 * atoms_per_bin] = type(j);
-	other_x[MY_II + 4 * atoms_per_bin] = radius(j);
+        other_x[MY_II] = x(j, 0);
+        other_x[MY_II + atoms_per_bin] = x(j, 1);
+        other_x[MY_II + 2 * atoms_per_bin] = x(j, 2);
+        other_x[MY_II + 3 * atoms_per_bin] = type(j);
+        other_x[MY_II + 4 * atoms_per_bin] = radius(j);
       }
 
       other_id[MY_II] = j;
@@ -1054,40 +1054,40 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeCuda(typename Kokkos::Team
 
       if(i >= 0 && i < nlocal) {
         #pragma unroll 8
-	for(int m = 0; m < bincount_current; m++) {
-	  const int j = other_id[m];
-	  const int jtype = other_x[m + 3 * atoms_per_bin];
+        for(int m = 0; m < bincount_current; m++) {
+          const int j = other_id[m];
+          const int jtype = other_x[m + 3 * atoms_per_bin];
 
-	  if(HalfNeigh && (j < i))  continue;
-	  if(HalfNeigh && !Newton && (j < i)) continue;
-	  if(!HalfNeigh && j==i) continue;
-	  if(Tri) {
-	    if (x(j,2) < ztmp) continue;
-	    if (x(j,2) == ztmp) {
-	      if (x(j,1) < ytmp) continue;
-	      if (x(j,1) == ytmp) {
-		if (x(j,0) < xtmp) continue;
-		if (x(j,0) == xtmp && j <= i) continue;
-	      }
-	    }
-	  }
-	  if(exclude && exclusion(i,j,itype,jtype)) continue;
+          if(HalfNeigh && (j < i))  continue;
+          if(HalfNeigh && !Newton && (j < i)) continue;
+          if(!HalfNeigh && j==i) continue;
+          if(Tri) {
+            if (x(j,2) < ztmp) continue;
+            if (x(j,2) == ztmp) {
+              if (x(j,1) < ytmp) continue;
+              if (x(j,1) == ytmp) {
+                if (x(j,0) < xtmp) continue;
+                if (x(j,0) == xtmp && j <= i) continue;
+              }
+            }
+          }
+          if(exclude && exclusion(i,j,itype,jtype)) continue;
 
-	  const X_FLOAT delx = xtmp - other_x[m];
-	  const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
-	  const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
-	  const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
-	  const X_FLOAT radsum = radi + other_x[m + 4 * atoms_per_bin];
-	  const X_FLOAT cutsq = (radsum + skin) * (radsum + skin);
+          const X_FLOAT delx = xtmp - other_x[m];
+          const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
+          const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
+          const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
+          const X_FLOAT radsum = radi + other_x[m + 4 * atoms_per_bin];
+          const X_FLOAT cutsq = (radsum + skin) * (radsum + skin);
 
-	  if(rsq <= cutsq) {
-	    if(n<neigh_list.maxneighs) {
-	      if (neigh_list.history && rsq < radsum*radsum) neighbors_i(n++) = j ^ mask_history;
-	      else neighbors_i(n++) = j;
-	    }
-	    else n++;
-	  }
-	}
+          if(rsq <= cutsq) {
+            if(n<neigh_list.maxneighs) {
+              if (neigh_list.history && rsq < radsum*radsum) neighbors_i(n++) = j ^ mask_history;
+              else neighbors_i(n++) = j;
+            }
+            else n++;
+          }
+        }
       }
       __syncthreads();
     }
diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h
index 2a3994f584..7650bf3350 100644
--- a/src/KOKKOS/npair_kokkos.h
+++ b/src/KOKKOS/npair_kokkos.h
@@ -443,7 +443,7 @@ struct NPairKokkosBuildFunctorSize {
   const size_t sharedsize;
 
   NPairKokkosBuildFunctorSize(const NeighborKokkosExecute<DeviceType> &_c,
-			      const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {};
+                              const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {};
 
   KOKKOS_INLINE_FUNCTION
   void operator() (const int & i) const {
@@ -467,7 +467,7 @@ struct NPairKokkosBuildFunctorSize<LMPHostType,HALF_NEIGH,GHOST_NEWTON,TRI> {
   const size_t sharedsize;
 
   NPairKokkosBuildFunctorSize(const NeighborKokkosExecute<LMPHostType> &_c,
-			      const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {};
+                              const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {};
 
   KOKKOS_INLINE_FUNCTION
   void operator() (const int & i) const {
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index f6eef5b53c..3358fe709c 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -37,6 +37,7 @@ template<class DeviceType>
 PairEAMKokkos<DeviceType>::PairEAMKokkos(LAMMPS *lmp) : PairEAM(lmp)
 {
   respa_enable = 0;
+  single_enable = 0;
 
   atomKK = (AtomKokkos *) atom;
   execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp
index 068580b525..5071bae32f 100644
--- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp
+++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp
@@ -174,85 +174,85 @@ void PairGranHookeHistoryKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   if (lmp->kokkos->neighflag == HALF) {
     if (force->newton_pair) {
       if (vflag_atom) {
-	if (shearupdate) {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,2,1>>(0,inum),*this);
-	} else {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,2,0>>(0,inum),*this);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,2,1>>(0,inum),*this);
+        } else {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,2,0>>(0,inum),*this);
+        }
       } else if (vflag_global) {
-	if (shearupdate) {
-	  Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,1,1>>(0,inum),*this, ev);
-	} else {
-	  Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,1,0>>(0,inum),*this, ev);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,1,1>>(0,inum),*this, ev);
+        } else {
+          Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,1,0>>(0,inum),*this, ev);
+        }
       } else {
-	if (shearupdate) {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,0,1>>(0,inum),*this);
-	} else {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,0,0>>(0,inum),*this);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,0,1>>(0,inum),*this);
+        } else {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,1,0,0>>(0,inum),*this);
+        }
       }
     } else {
       if (vflag_atom) {
-	if (shearupdate) {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,2,1>>(0,inum),*this);
-	} else {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,2,0>>(0,inum),*this);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,2,1>>(0,inum),*this);
+        } else {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,2,0>>(0,inum),*this);
+        }
       } else if (vflag_global) {
-	if (shearupdate) {
-	  Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,1,1>>(0,inum),*this, ev);
-	} else {
-	  Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,1,0>>(0,inum),*this, ev);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,1,1>>(0,inum),*this, ev);
+        } else {
+          Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,1,0>>(0,inum),*this, ev);
+        }
       } else {
-	if (shearupdate) {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,0,1>>(0,inum),*this);
-	} else {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,0,0>>(0,inum),*this);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,0,1>>(0,inum),*this);
+        } else {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALF,0,0,0>>(0,inum),*this);
+        }
       }
     }
   } else { // HALFTHREAD
     if (force->newton_pair) {
       if (vflag_atom) {
-	if (shearupdate) {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,2,1>>(0,inum),*this);
-	} else {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,2,0>>(0,inum),*this);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,2,1>>(0,inum),*this);
+        } else {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,2,0>>(0,inum),*this);
+        }
       } else if (vflag_global) {
-	if (shearupdate) {
-	  Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,1,1>>(0,inum),*this, ev);
-	} else {
-	  Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,1,0>>(0,inum),*this, ev);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,1,1>>(0,inum),*this, ev);
+        } else {
+          Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,1,0>>(0,inum),*this, ev);
+        }
       } else {
-	if (shearupdate) {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,0,1>>(0,inum),*this);
-	} else {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,0,0>>(0,inum),*this);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,0,1>>(0,inum),*this);
+        } else {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,1,0,0>>(0,inum),*this);
+        }
       }
     } else {
       if (vflag_atom) {
-	if (shearupdate) {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,2,1>>(0,inum),*this);
-	} else {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,2,0>>(0,inum),*this);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,2,1>>(0,inum),*this);
+        } else {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,2,0>>(0,inum),*this);
+        }
       } else if (vflag_global) {
-	if (shearupdate) {
-	  Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,1,1>>(0,inum),*this, ev);
-	} else {
-	  Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,1,0>>(0,inum),*this, ev);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,1,1>>(0,inum),*this, ev);
+        } else {
+          Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,1,0>>(0,inum),*this, ev);
+        }
       } else {
-	if (shearupdate) {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,0,1>>(0,inum),*this);
-	} else {
-	  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,0,0>>(0,inum),*this);
-	}
+        if (shearupdate) {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,0,1>>(0,inum),*this);
+        } else {
+          Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairGranHookeHistoryCompute<HALFTHREAD,0,0,0>>(0,inum),*this);
+        }
       }
     }
   }
@@ -408,7 +408,7 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
       shear3 += vtr3*dt;
     }
     X_FLOAT shrmag = sqrt(shear1*shear1 + shear2*shear2 +
-			  shear3*shear3);
+                          shear3*shear3);
 
     // rotate shear displacements
 
@@ -433,15 +433,15 @@ void PairGranHookeHistoryKokkos<DeviceType>::operator()(TagPairGranHookeHistoryC
 
     if (fs > fn) {
       if (shrmag != 0.0) {
-	shear1 = (fn/fs) * (shear1 + meff*gammat*vtr1/kt) -
-	  meff*gammat*vtr1/kt;
-	shear2 = (fn/fs) * (shear2 + meff*gammat*vtr2/kt) -
-	  meff*gammat*vtr2/kt;
-	shear3 = (fn/fs) * (shear3 + meff*gammat*vtr3/kt) -
-	  meff*gammat*vtr3/kt;
-	fs1 *= fn/fs;
-	fs2 *= fn/fs;
-	fs3 *= fn/fs;
+        shear1 = (fn/fs) * (shear1 + meff*gammat*vtr1/kt) -
+          meff*gammat*vtr1/kt;
+        shear2 = (fn/fs) * (shear2 + meff*gammat*vtr2/kt) -
+          meff*gammat*vtr2/kt;
+        shear3 = (fn/fs) * (shear3 + meff*gammat*vtr3/kt) -
+          meff*gammat*vtr3/kt;
+        fs1 *= fn/fs;
+        fs2 *= fn/fs;
+        fs3 *= fn/fs;
       } else fs1 = fs2 = fs3 = 0.0;
     }
 
@@ -503,8 +503,8 @@ template<class DeviceType>
 template<int NEWTON_PAIR>
 KOKKOS_INLINE_FUNCTION
 void PairGranHookeHistoryKokkos<DeviceType>::ev_tally_xyz(EV_FLOAT &ev, int i, int j,
-							  F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
-							  X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
+                                                          F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
+                                                          X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
 {
   F_FLOAT v[6];
 
@@ -546,8 +546,8 @@ template<class DeviceType>
 template<int NEIGHFLAG, int NEWTON_PAIR>
 KOKKOS_INLINE_FUNCTION
 void PairGranHookeHistoryKokkos<DeviceType>::ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j,
-							       F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
-							       X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
+                                                               F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
+                                                               X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const
 {
   Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
 
diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h
index 8d1778e091..e40353d970 100644
--- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h
+++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h
@@ -61,13 +61,13 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory {
   template<int NEWTON_PAIR>
   KOKKOS_INLINE_FUNCTION
   void ev_tally_xyz(EV_FLOAT &ev, int i, int j,
-		    F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
-		    X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const;
+                    F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
+                    X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const;
   template<int NEIGHFLAG, int NEWTON_PAIR>
   KOKKOS_INLINE_FUNCTION
   void ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j,
-			 F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
-			 X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const;
+                         F_FLOAT fx, F_FLOAT fy, F_FLOAT fz,
+                         X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const;
 
  protected:
   typename AT::t_x_array_randomread x;
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index 9ca5d9578d..52a05b3991 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -293,7 +293,7 @@ struct PairComputeFunctor  {
         const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
 
         if(rsq < (STACKPARAMS?c.m_cutsq[itype][jtype]:c.d_cutsq(itype,jtype))) {
-    
+
           const F_FLOAT fpair = factor_lj*c.template compute_fpair<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
 
           ftmp.x += delx*fpair;
@@ -412,7 +412,7 @@ struct PairComputeFunctor  {
         const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
 
         if(rsq < (STACKPARAMS?c.m_cutsq[itype][jtype]:c.d_cutsq(itype,jtype))) {
-    
+
           const F_FLOAT fpair = factor_lj*c.template compute_fpair<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
 
           fev_tmp.f[0] += delx*fpair;
diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h
index 2193e9ff24..8586c4bdab 100644
--- a/src/KOKKOS/pair_snap_kokkos.h
+++ b/src/KOKKOS/pair_snap_kokkos.h
@@ -39,6 +39,7 @@ struct TagPairSNAPPreUi{};
 struct TagPairSNAPComputeUi{};
 struct TagPairSNAPComputeZi{};
 struct TagPairSNAPComputeBi{};
+struct TagPairSNAPZeroYi{};
 struct TagPairSNAPComputeYi{};
 struct TagPairSNAPComputeDuidrj{};
 struct TagPairSNAPComputeDeidrj{};
@@ -73,19 +74,22 @@ public:
   void operator() (TagPairSNAPComputeNeigh,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeNeigh>::member_type& team) const;
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPPreUi>::member_type& team) const;
+  void operator() (TagPairSNAPPreUi,const int& ii) const;
 
   KOKKOS_INLINE_FUNCTION
   void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi>::member_type& team) const;
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (TagPairSNAPComputeZi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeZi>::member_type& team) const;
+  void operator() (TagPairSNAPComputeZi,const int& ii) const;
 
   KOKKOS_INLINE_FUNCTION
   void operator() (TagPairSNAPComputeBi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeBi>::member_type& team) const;
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (TagPairSNAPComputeYi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeYi>::member_type& team) const;
+  void operator() (TagPairSNAPZeroYi,const int& ii) const;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (TagPairSNAPComputeYi,const int& ii) const;
 
   KOKKOS_INLINE_FUNCTION
   void operator() (TagPairSNAPComputeDuidrj,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrj>::member_type& team) const;
diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h
index 95afcc5ec7..ef01ec5ea3 100644
--- a/src/KOKKOS/pair_snap_kokkos_impl.h
+++ b/src/KOKKOS/pair_snap_kokkos_impl.h
@@ -184,22 +184,12 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   Kokkos::parallel_reduce("PairSNAPKokkos::find_max_neighs",inum, FindMaxNumNeighs<DeviceType>(k_list), Kokkos::Experimental::Max<int>(max_neighs));
 
   int vector_length = 1;
-  int ui_vector_length = 1;
   int team_size = 1;
-  int yi_team_size = 1;
   int team_size_max = Kokkos::TeamPolicy<DeviceType>::team_size_max(*this);
 #ifdef KOKKOS_ENABLE_CUDA
   team_size = 32;//max_neighs;
   if (team_size*vector_length > team_size_max)
     team_size = team_size_max/vector_length;
-
-  yi_team_size = 256;
-  if (yi_team_size*vector_length > team_size_max)
-    yi_team_size = team_size_max/vector_length;
-
-  ui_vector_length = 8;
-  if (team_size*ui_vector_length > team_size_max)
-    team_size = team_size_max/ui_vector_length;
 #endif
 
   if (beta_max < inum) {
@@ -227,17 +217,21 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     Kokkos::parallel_for("ComputeNeigh",policy_neigh,*this);
 
     //PreUi
-    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPPreUi> policy_preui(chunk_size,team_size,vector_length);
+    typename Kokkos::RangePolicy<DeviceType, TagPairSNAPPreUi> policy_preui(0,chunk_size);
     Kokkos::parallel_for("PreUi",policy_preui,*this);
 
     //ComputeUi
-    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi> policy_ui(((inum+team_size-1)/team_size)*max_neighs,team_size,ui_vector_length);
+    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi> policy_ui(((inum+team_size-1)/team_size)*max_neighs,team_size,vector_length);
     Kokkos::parallel_for("ComputeUi",policy_ui,*this);
 
+    //Ulisttot transpose
+    snaKK.transpose_ulisttot();
+
     //Compute bispectrum
     if (quadraticflag || eflag) {
       //ComputeZi
-      typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeZi> policy_zi(chunk_size,team_size,vector_length);
+      int idxz_max = snaKK.idxz_max;
+      typename Kokkos::RangePolicy<DeviceType, TagPairSNAPComputeZi> policy_zi(0,chunk_size*idxz_max);
       Kokkos::parallel_for("ComputeZi",policy_zi,*this);
 
       //ComputeBi
@@ -250,7 +244,12 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     Kokkos::parallel_for("ComputeBeta",policy_beta,*this);
 
     //ComputeYi
-    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeYi> policy_yi(chunk_size,yi_team_size,vector_length);
+    typename Kokkos::RangePolicy<DeviceType, TagPairSNAPZeroYi> policy_zero_yi(0,chunk_size);
+    Kokkos::parallel_for("ZeroYi",policy_zero_yi,*this);
+
+    //ComputeYi
+    int idxz_max = snaKK.idxz_max;
+    typename Kokkos::RangePolicy<DeviceType, TagPairSNAPComputeYi> policy_yi(0,chunk_size*idxz_max);
     Kokkos::parallel_for("ComputeYi",policy_yi,*this);
 
     //ComputeDuidrj
@@ -504,10 +503,9 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeNeigh,const typen
 
 template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
-void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPPreUi>::member_type& team) const {
-  int ii = team.league_rank();
+void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPPreUi,const int& ii) const {
   SNAKokkos<DeviceType> my_sna = snaKK;
-  my_sna.pre_ui(team,ii);
+  my_sna.pre_ui(ii);
 }
 
 template<class DeviceType>
@@ -529,18 +527,23 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeUi,const typename
 
 template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
-void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeYi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeYi>::member_type& team) const {
-  int ii = team.league_rank();
+void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPZeroYi,const int& ii) const {
   SNAKokkos<DeviceType> my_sna = snaKK;
-  my_sna.compute_yi(team,ii,d_beta);
+  my_sna.zero_yi(ii);
 }
 
 template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
-void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeZi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeZi>::member_type& team) const {
-  int ii = team.league_rank();
+void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeYi,const int& ii) const {
   SNAKokkos<DeviceType> my_sna = snaKK;
-  my_sna.compute_zi(team,ii);
+  my_sna.compute_yi(ii,d_beta);
+}
+
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeZi,const int& ii) const {
+  SNAKokkos<DeviceType> my_sna = snaKK;
+  my_sna.compute_zi(ii);
 }
 
 template<class DeviceType>
@@ -581,7 +584,7 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeDeidrj,const type
   const int jj = team.league_rank() / ((inum+team.team_size()-1)/team.team_size());
   const int ninside = d_ninside(ii);
   if (jj >= ninside) return;
- 
+
   my_sna.compute_deidrj(team,ii,jj);
 }
 
@@ -616,9 +619,9 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeForce<NEIGHFLAG,E
       a_f(j,0) -= fij[0];
       a_f(j,1) -= fij[1];
       a_f(j,2) -= fij[2];
-      
+
       // tally global and per-atom virial contribution
-      
+
       if (EVFLAG) {
         if (vflag_either) {
           v_tally_xyz<NEIGHFLAG>(ev,i,j,
@@ -627,7 +630,7 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeForce<NEIGHFLAG,E
             -my_sna.rij(ii,jj,2));
         }
       }
-      
+
     });
   });
 
@@ -646,16 +649,16 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeForce<NEIGHFLAG,E
         // evdwl = energy of atom I, sum over coeffs_k * Bi_k
 
         double evdwl = d_coeffi[0];
-        
+
         // E = beta.B + 0.5*B^t.alpha.B
 
         // linear contributions
-        
+
         for (int icoeff = 0; icoeff < ncoeff; icoeff++)
           evdwl += d_coeffi[icoeff+1]*my_sna.blist(ii,icoeff);
-        
+
         // quadratic contributions
-        
+
         if (quadraticflag) {
           int k = ncoeff+1;
           for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h
index 2dbfdcb47c..775c8eead4 100644
--- a/src/KOKKOS/sna_kokkos.h
+++ b/src/KOKKOS/sna_kokkos.h
@@ -26,15 +26,28 @@
 namespace LAMMPS_NS {
 
 typedef double SNAreal;
-typedef struct { SNAreal re, im; } SNAcomplex;
 
-struct SNAKK_ZINDICES {
-  int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju;
+//typedef struct { SNAreal re, im; } SNAcomplex;
+struct alignas(2*sizeof(SNAreal)) SNAcomplex{
+  SNAreal re, im;
+
+  KOKKOS_INLINE_FUNCTION
+  SNAcomplex() : re(0),im(0)
+  {}
+
+  KOKKOS_INLINE_FUNCTION
+  SNAcomplex(SNAreal real_in, SNAreal imag_in)
+      :re(real_in),im(imag_in)
+  {}
 };
 
-struct SNAKK_BINDICES {
-  int j1, j2, j;
-};
+//struct SNAKK_ZINDICES {
+//  int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju;
+//};
+//
+//struct SNAKK_BINDICES {
+//  int j1, j2, j;
+//};
 
 template<class DeviceType>
 class SNAKokkos {
@@ -53,12 +66,32 @@ public:
   typedef Kokkos::View<SNAcomplex*, DeviceType> t_sna_1c;
   typedef Kokkos::View<SNAcomplex*, DeviceType, Kokkos::MemoryTraits<Kokkos::Atomic> > t_sna_1c_atomic;
   typedef Kokkos::View<SNAcomplex**, DeviceType> t_sna_2c;
-  typedef Kokkos::View<SNAcomplex**, Kokkos::LayoutRight, DeviceType> t_sna_2c_cpu;
+  typedef Kokkos::View<SNAcomplex**, Kokkos::LayoutRight, DeviceType> t_sna_2c_lr;
   typedef Kokkos::View<SNAcomplex***, DeviceType> t_sna_3c;
   typedef Kokkos::View<SNAcomplex***[3], DeviceType> t_sna_4c;
   typedef Kokkos::View<SNAcomplex**[3], DeviceType> t_sna_3c3;
   typedef Kokkos::View<SNAcomplex*****, DeviceType> t_sna_5c;
 
+// Helper class to get ulisttot_r
+
+template<typename DeviceLayout, typename T1, typename T2>
+class UlisttotHelper {
+public:
+  inline
+  static void transpose(T1 &ulisttot_lr, const T2 &ulisttot) {
+    Kokkos::deep_copy(ulisttot_lr,ulisttot);
+  }
+};
+
+template<typename T1, typename T2>
+class UlisttotHelper<Kokkos::LayoutRight,T1,T2> {
+public:
+  inline
+  static void transpose(T1 &ulisttot_lr, const T2 &ulisttot) {
+    ulisttot_lr = ulisttot;
+  }
+};
+
 inline
   SNAKokkos() {};
   KOKKOS_INLINE_FUNCTION
@@ -80,17 +113,22 @@ inline
 
   int ncoeff;
 
+inline
+  void transpose_ulisttot();
+
   // functions for bispectrum coefficients
   KOKKOS_INLINE_FUNCTION
-  void pre_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int); // ForceSNAP
+  void pre_ui(const int&); // ForceSNAP
   KOKKOS_INLINE_FUNCTION
   void compute_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); // ForceSNAP
   KOKKOS_INLINE_FUNCTION
   void compute_ui_orig(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); // ForceSNAP
   KOKKOS_INLINE_FUNCTION
-  void compute_zi(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int);    // ForceSNAP
+  void compute_zi(const int&);    // ForceSNAP
   KOKKOS_INLINE_FUNCTION
-  void compute_yi(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int,
+  void zero_yi(const int&);
+  KOKKOS_INLINE_FUNCTION
+  void compute_yi(int,
    const Kokkos::View<F_FLOAT**, DeviceType> &beta); // ForceSNAP
   KOKKOS_INLINE_FUNCTION
   void compute_bi(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int);    // ForceSNAP
@@ -127,25 +165,27 @@ inline
   void grow_rij(int, int);
 
   int twojmax, diagonalstyle;
-  
+
   t_sna_2d blist;
-  t_sna_2c_cpu ulisttot;
+  t_sna_2c ulisttot;
+  t_sna_2c_lr ulisttot_lr;
   t_sna_2c zlist;
 
   t_sna_3c ulist;
-  t_sna_2c ylist;
+  t_sna_2c_lr ylist;
 
   // derivatives of data
   t_sna_4c dulist;
 
+  int idxcg_max, idxu_max, idxz_max, idxb_max;
+
 private:
   double rmin0, rfac0;
 
   //use indexlist instead of loops, constructor generates these
   // Same across all SNAKokkos
-  Kokkos::View<SNAKK_ZINDICES*, DeviceType> idxz;
-  Kokkos::View<SNAKK_BINDICES*, DeviceType> idxb;
-  int idxcg_max, idxu_max, idxz_max, idxb_max;
+  Kokkos::View<int*[10], DeviceType> idxz;
+  Kokkos::View<int*[3], DeviceType> idxb;
   Kokkos::View<int***, DeviceType> idxcg_block;
   Kokkos::View<int*, DeviceType> idxu_block;
   Kokkos::View<int***, DeviceType> idxz_block;
@@ -173,9 +213,9 @@ inline
 inline
   void init_rootpqarray();    // init()
   KOKKOS_INLINE_FUNCTION
-  void zero_uarraytot(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int);      // compute_ui
+  void zero_uarraytot(const int&);      // compute_ui
   KOKKOS_INLINE_FUNCTION
-  void addself_uarraytot(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, double); // compute_ui
+  void addself_uarraytot(const int&, const double&); // compute_ui
   KOKKOS_INLINE_FUNCTION
   void add_uarraytot(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int, double, double, double); // compute_ui
 
diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h
index 36765e9cd6..8d5a4a21be 100644
--- a/src/KOKKOS/sna_kokkos_impl.h
+++ b/src/KOKKOS/sna_kokkos_impl.h
@@ -83,7 +83,7 @@ void SNAKokkos<DeviceType>::build_indexlist()
   for(int j1 = 0; j1 <= twojmax; j1++)
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) {
-        h_idxcg_block(j1,j2,j) = idxcg_count; 
+        h_idxcg_block(j1,j2,j) = idxcg_count;
         for (int m1 = 0; m1 <= j1; m1++)
           for (int m2 = 0; m2 <= j2; m2++)
             idxcg_count++;
@@ -98,9 +98,9 @@ void SNAKokkos<DeviceType>::build_indexlist()
   auto h_idxu_block = Kokkos::create_mirror_view(idxu_block);
 
   int idxu_count = 0;
-  
+
   for(int j = 0; j <= twojmax; j++) {
-    h_idxu_block[j] = idxu_count; 
+    h_idxu_block[j] = idxu_count;
     for(int mb = 0; mb <= j; mb++)
       for(int ma = 0; ma <= j; ma++)
         idxu_count++;
@@ -110,24 +110,24 @@ void SNAKokkos<DeviceType>::build_indexlist()
 
   // index list for beta and B
 
-  int idxb_count = 0;  
+  int idxb_count = 0;
   for(int j1 = 0; j1 <= twojmax; j1++)
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2)
         if (j >= j1) idxb_count++;
-  
+
   idxb_max = idxb_count;
-  idxb = Kokkos::View<SNAKK_BINDICES*, DeviceType>("SNAKokkos::idxb",idxb_max);
+  idxb = Kokkos::View<int*[3], DeviceType>("SNAKokkos::idxb",idxb_max);
   auto h_idxb = Kokkos::create_mirror_view(idxb);
-  
+
   idxb_count = 0;
   for(int j1 = 0; j1 <= twojmax; j1++)
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2)
         if (j >= j1) {
-          h_idxb[idxb_count].j1 = j1;
-          h_idxb[idxb_count].j2 = j2;
-          h_idxb[idxb_count].j = j;
+          h_idxb(idxb_count,0) = j1;
+          h_idxb(idxb_count,1) = j2;
+          h_idxb(idxb_count,2) = j;
           idxb_count++;
         }
   Kokkos::deep_copy(idxb,h_idxb);
@@ -142,7 +142,7 @@ void SNAKokkos<DeviceType>::build_indexlist()
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) {
         if (j >= j1) {
-          h_idxb_block(j1,j2,j) = idxb_count; 
+          h_idxb_block(j1,j2,j) = idxb_count;
           idxb_count++;
         }
       }
@@ -158,19 +158,19 @@ void SNAKokkos<DeviceType>::build_indexlist()
         for (int mb = 0; 2*mb <= j; mb++)
           for (int ma = 0; ma <= j; ma++)
             idxz_count++;
-  
+
   idxz_max = idxz_count;
-  idxz = Kokkos::View<SNAKK_ZINDICES*, DeviceType>("SNAKokkos::idxz",idxz_max);
+  idxz = Kokkos::View<int*[10], DeviceType>("SNAKokkos::idxz",idxz_max);
   auto h_idxz = Kokkos::create_mirror_view(idxz);
 
   idxz_block = Kokkos::View<int***, DeviceType>("SNAKokkos::idxz_block", jdim,jdim,jdim);
   auto h_idxz_block = Kokkos::create_mirror_view(idxz_block);
-  
+
   idxz_count = 0;
   for(int j1 = 0; j1 <= twojmax; j1++)
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) {
-        h_idxz_block(j1,j2,j) = idxz_count; 
+        h_idxz_block(j1,j2,j) = idxz_count;
 
         // find right beta(ii,jjb) entry
         // multiply and divide by j+1 factors
@@ -178,20 +178,20 @@ void SNAKokkos<DeviceType>::build_indexlist()
 
         for (int mb = 0; 2*mb <= j; mb++)
           for (int ma = 0; ma <= j; ma++) {
-            h_idxz[idxz_count].j1 = j1;
-            h_idxz[idxz_count].j2 = j2;
-            h_idxz[idxz_count].j = j;
-            h_idxz[idxz_count].ma1min = MAX(0, (2 * ma - j - j2 + j1) / 2);
-            h_idxz[idxz_count].ma2max = (2 * ma - j - (2 * h_idxz[idxz_count].ma1min - j1) + j2) / 2;
-            h_idxz[idxz_count].na = MIN(j1, (2 * ma - j + j2 + j1) / 2) - h_idxz[idxz_count].ma1min + 1;
-            h_idxz[idxz_count].mb1min = MAX(0, (2 * mb - j - j2 + j1) / 2);
-            h_idxz[idxz_count].mb2max = (2 * mb - j - (2 * h_idxz[idxz_count].mb1min - j1) + j2) / 2;
-            h_idxz[idxz_count].nb = MIN(j1, (2 * mb - j + j2 + j1) / 2) - h_idxz[idxz_count].mb1min + 1;
+            h_idxz(idxz_count,0) = j1;
+            h_idxz(idxz_count,1) = j2;
+            h_idxz(idxz_count,2) = j;
+            h_idxz(idxz_count,3) = MAX(0, (2 * ma - j - j2 + j1) / 2);
+            h_idxz(idxz_count,4) = (2 * ma - j - (2 * h_idxz(idxz_count,3) - j1) + j2) / 2;
+            h_idxz(idxz_count,5) = MAX(0, (2 * mb - j - j2 + j1) / 2);
+            h_idxz(idxz_count,6) = (2 * mb - j - (2 * h_idxz(idxz_count,5) - j1) + j2) / 2;
+            h_idxz(idxz_count,7) = MIN(j1, (2 * ma - j + j2 + j1) / 2) - h_idxz(idxz_count,3) + 1;
+            h_idxz(idxz_count,8) = MIN(j1, (2 * mb - j + j2 + j1) / 2) - h_idxz(idxz_count,5) + 1;
 
             // apply to z(j1,j2,j,ma,mb) to unique element of y(j)
 
             const int jju = h_idxu_block[j] + (j+1)*mb + ma;
-            h_idxz[idxz_count].jju = jju;
+            h_idxz(idxz_count,9) = jju;
 
             idxz_count++;
           }
@@ -225,11 +225,13 @@ void SNAKokkos<DeviceType>::grow_rij(int newnatom, int newnmax)
   dedr = t_sna_3d("sna:dedr",natom,nmax,3);
 
   blist = t_sna_2d("sna:blist",natom,idxb_max);
-  ulisttot = t_sna_2c_cpu("sna:ulisttot",natom,idxu_max);
+  ulisttot = t_sna_2c("sna:ulisttot",natom,idxu_max);
+  if (!Kokkos::Impl::is_same<typename DeviceType::array_layout,Kokkos::LayoutRight>::value)
+    ulisttot_lr = t_sna_2c_lr("sna:ulisttot_lr",natom,idxu_max);
   zlist = t_sna_2c("sna:zlist",natom,idxz_max);
 
   ulist = t_sna_3c("sna:ulist",natom,nmax,idxu_max);
-  ylist = t_sna_2c("sna:ylist",natom,idxu_max);
+  ylist = t_sna_2c_lr("sna:ylist",natom,idxu_max);
 
   dulist = t_sna_4c("sna:dulist",natom,nmax,idxu_max);
 }
@@ -240,15 +242,15 @@ void SNAKokkos<DeviceType>::grow_rij(int newnatom, int newnmax)
 
 template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
-void SNAKokkos<DeviceType>::pre_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom)
+void SNAKokkos<DeviceType>::pre_ui(const int& iatom)
 {
-  if(team.team_rank() == 0) {
-    zero_uarraytot(team,iatom);
+  //if(team.team_rank() == 0) {
+    zero_uarraytot(iatom);
     //Kokkos::single(Kokkos::PerThread(team), [&] (){
-    addself_uarraytot(team,iatom,wself);
+    addself_uarraytot(iatom,wself);
     //});
-  }
-  team.team_barrier();
+  //}
+  //team.team_barrier();
 }
 
 /* ----------------------------------------------------------------------
@@ -278,50 +280,7 @@ void SNAKokkos<DeviceType>::compute_ui(const typename Kokkos::TeamPolicy<DeviceT
   z0 = r / tan(theta0);
 
   compute_uarray(team, iatom, jnbor, x, y, z, z0, r);
-  //Kokkos::single(Kokkos::PerThread(team), [&] (){
   add_uarraytot(team, iatom, jnbor, r, wj(iatom,jnbor), rcutij(iatom,jnbor));
-  //});
-}
-
-template<class DeviceType>
-KOKKOS_INLINE_FUNCTION
-void SNAKokkos<DeviceType>::compute_ui_orig(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnum)
-{
-  double rsq, r, x, y, z, z0, theta0;
-
-  // utot(j,ma,mb) = 0 for all j,ma,ma
-  // utot(j,ma,ma) = 1 for all j,ma
-  // for j in neighbors of i:
-  //   compute r0 = (x,y,z,z0)
-  //   utot(j,ma,mb) += u(r0;j,ma,mb) for all j,ma,mb
-
-  if(team.team_rank() == 0) {
-    zero_uarraytot(team,iatom);
-    //Kokkos::single(Kokkos::PerThread(team), [&] (){
-    addself_uarraytot(team,iatom,wself);
-    //});
-  }
-  team.team_barrier();
-
-  Kokkos::parallel_for(Kokkos::TeamThreadRange(team,jnum),
-      [&] (const int& j) {
-  //for(int j = 0; j < jnum; j++) {
-    x = rij(iatom,j,0);
-    y = rij(iatom,j,1);
-    z = rij(iatom,j,2);
-    rsq = x * x + y * y + z * z;
-    r = sqrt(rsq);
-
-    theta0 = (r - rmin0) * rfac0 * MY_PI / (rcutij(iatom,j) - rmin0);
-    //    theta0 = (r - rmin0) * rscale0;
-    z0 = r / tan(theta0);
-
-    compute_uarray(team, iatom, j, x, y, z, z0, r);
-    //Kokkos::single(Kokkos::PerThread(team), [&] (){
-    add_uarraytot(team, iatom, j, r, wj(iatom,j), rcutij(iatom,j));
-    //});
-  });
-
 }
 
 /* ----------------------------------------------------------------------
@@ -330,54 +289,52 @@ void SNAKokkos<DeviceType>::compute_ui_orig(const typename Kokkos::TeamPolicy<De
 
 template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
-void SNAKokkos<DeviceType>::compute_zi(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom)
+void SNAKokkos<DeviceType>::compute_zi(const int& iter)
 {
-  Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxz_max),
-      [&] (const int& jjz) {
-  //for(int jjz = 0; jjz < idxz_max; jjz++) {
-    const int j1 = idxz[jjz].j1;
-    const int j2 = idxz[jjz].j2;
-    const int j = idxz[jjz].j;
-    const int ma1min = idxz[jjz].ma1min;
-    const int ma2max = idxz[jjz].ma2max;
-    const int na = idxz[jjz].na;
-    const int mb1min = idxz[jjz].mb1min;
-    const int mb2max = idxz[jjz].mb2max;
-    const int nb = idxz[jjz].nb;
+  const int iatom = iter / idxz_max;
+  const int jjz = iter % idxz_max;
 
-    const double* cgblock = cglist.data() + idxcg_block(j1,j2,j);
+  const int j1 = idxz(jjz,0);
+  const int j2 = idxz(jjz,1);
+  const int j = idxz(jjz,2);
+  const int ma1min = idxz(jjz,3);
+  const int ma2max = idxz(jjz,4);
+  const int mb1min = idxz(jjz,5);
+  const int mb2max = idxz(jjz,6);
+  const int na = idxz(jjz,7);
+  const int nb = idxz(jjz,8);
 
-    zlist(iatom,jjz).re = 0.0; 
-    zlist(iatom,jjz).im = 0.0;
+  const double* cgblock = cglist.data() + idxcg_block(j1,j2,j);
 
-    int jju1 = idxu_block[j1] + (j1+1)*mb1min;
-    int jju2 = idxu_block[j2] + (j2+1)*mb2max;
-    int icgb = mb1min*(j2+1) + mb2max;
-    for(int ib = 0; ib < nb; ib++) {
+  zlist(iatom,jjz).re = 0.0;
+  zlist(iatom,jjz).im = 0.0;
 
-      double suma1_r = 0.0;
-      double suma1_i = 0.0;
+  int jju1 = idxu_block[j1] + (j1+1)*mb1min;
+  int jju2 = idxu_block[j2] + (j2+1)*mb2max;
+  int icgb = mb1min*(j2+1) + mb2max;
+  for(int ib = 0; ib < nb; ib++) {
 
-      int ma1 = ma1min;
-      int ma2 = ma2max;
-      int icga = ma1min*(j2+1) + ma2max;
-      for(int ia = 0; ia < na; ia++) {
-        suma1_r += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).re - ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).im);
-        suma1_i += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).im + ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).re);
-        ma1++;
-        ma2--;
-        icga += j2;
-      } // end loop over ia
+    double suma1_r = 0.0;
+    double suma1_i = 0.0;
 
-      zlist(iatom,jjz).re += cgblock[icgb] * suma1_r;
-      zlist(iatom,jjz).im += cgblock[icgb] * suma1_i;
+    int ma1 = ma1min;
+    int ma2 = ma2max;
+    int icga = ma1min*(j2+1) + ma2max;
+    for(int ia = 0; ia < na; ia++) {
+      suma1_r += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).re - ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).im);
+      suma1_i += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).im + ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).re);
+      ma1++;
+      ma2--;
+      icga += j2;
+    } // end loop over ia
 
-      jju1 += j1+1;
-      jju2 -= j2+1;
-      icgb += j2;
-    } // end loop over ib
+    zlist(iatom,jjz).re += cgblock[icgb] * suma1_r;
+    zlist(iatom,jjz).im += cgblock[icgb] * suma1_i;
 
-  }); // end loop over jjz
+    jju1 += j1+1;
+    jju2 -= j2+1;
+    icgb += j2;
+  } // end loop over ib
 }
 
 /* ----------------------------------------------------------------------
@@ -386,102 +343,94 @@ void SNAKokkos<DeviceType>::compute_zi(const typename Kokkos::TeamPolicy<DeviceT
 
 template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
-void SNAKokkos<DeviceType>::compute_yi(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom,
+void SNAKokkos<DeviceType>::zero_yi(const int& iatom)
+{
+    for (int j = 0; j < idxu_max; j++)
+      ylist(iatom,j) = {0.0,0.0};
+}
+
+/* ----------------------------------------------------------------------
+   compute Yi from Ui without storing Zi, looping over zlist indices
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void SNAKokkos<DeviceType>::compute_yi(int iter,
  const Kokkos::View<F_FLOAT**, DeviceType> &beta)
 {
   double betaj;
-  const int ii = iatom;
+  const int iatom = iter / idxz_max;
+  const int jjz = iter % idxz_max;
 
-  {
-    Kokkos::parallel_for(Kokkos::TeamThreadRange(team,ylist.extent(1)),
-        [&] (const int& i) {
-      ylist(iatom,i).re = 0.0;
-      ylist(iatom,i).im = 0.0;
-    });
-  }
+  const int j1 = idxz(jjz,0);
+  const int j2 = idxz(jjz,1);
+  const int j = idxz(jjz,2);
+  const int ma1min = idxz(jjz,3);
+  const int ma2max = idxz(jjz,4);
+  const int mb1min = idxz(jjz,5);
+  const int mb2max = idxz(jjz,6);
+  const int na = idxz(jjz,7);
+  const int nb = idxz(jjz,8);
+  const int jju = idxz(jjz,9);
 
-  //int flopsum = 0;
+  const double* cgblock = cglist.data() + idxcg_block(j1,j2,j);
+  //int mb = (2 * (mb1min+mb2max) - j1 - j2 + j) / 2;
+  //int ma = (2 * (ma1min+ma2max) - j1 - j2 + j) / 2;
 
-  Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxz_max),
-      [&] (const int& jjz) {
-  //for(int jjz = 0; jjz < idxz_max; jjz++) {
-    const int j1 = idxz[jjz].j1;
-    const int j2 = idxz[jjz].j2;
-    const int j = idxz[jjz].j;
-    const int ma1min = idxz[jjz].ma1min;
-    const int ma2max = idxz[jjz].ma2max;
-    const int na = idxz[jjz].na;
-    const int mb1min = idxz[jjz].mb1min;
-    const int mb2max = idxz[jjz].mb2max;
-    const int nb = idxz[jjz].nb;
+  double ztmp_r = 0.0;
+  double ztmp_i = 0.0;
 
-    const double* cgblock = cglist.data() + idxcg_block(j1,j2,j);
-    //int mb = (2 * (mb1min+mb2max) - j1 - j2 + j) / 2;
-    //int ma = (2 * (ma1min+ma2max) - j1 - j2 + j) / 2;
+  int jju1 = idxu_block[j1] + (j1+1)*mb1min;
+  int jju2 = idxu_block[j2] + (j2+1)*mb2max;
+  int icgb = mb1min*(j2+1) + mb2max;
+  for(int ib = 0; ib < nb; ib++) {
 
-    double ztmp_r = 0.0;
-    double ztmp_i = 0.0;
+    double suma1_r = 0.0;
+    double suma1_i = 0.0;
 
-    int jju1 = idxu_block[j1] + (j1+1)*mb1min;
-    int jju2 = idxu_block[j2] + (j2+1)*mb2max;
-    int icgb = mb1min*(j2+1) + mb2max;
-    for(int ib = 0; ib < nb; ib++) {
+    int ma1 = ma1min;
+    int ma2 = ma2max;
+    int icga = ma1min*(j2+1) + ma2max;
 
-      double suma1_r = 0.0;
-      double suma1_i = 0.0;
+    for(int ia = 0; ia < na; ia++) {
+      suma1_r += cgblock[icga] * (ulisttot_lr(iatom,jju1+ma1).re * ulisttot_lr(iatom,jju2+ma2).re - ulisttot_lr(iatom,jju1+ma1).im * ulisttot_lr(iatom,jju2+ma2).im);
+      suma1_i += cgblock[icga] * (ulisttot_lr(iatom,jju1+ma1).re * ulisttot_lr(iatom,jju2+ma2).im + ulisttot_lr(iatom,jju1+ma1).im * ulisttot_lr(iatom,jju2+ma2).re);
+      ma1++;
+      ma2--;
+      icga += j2;
+    } // end loop over ia
 
-      int ma1 = ma1min;
-      int ma2 = ma2max;
-      int icga = ma1min*(j2+1) + ma2max;
+    ztmp_r += cgblock[icgb] * suma1_r;
+    ztmp_i += cgblock[icgb] * suma1_i;
+    jju1 += j1+1;
+    jju2 -= j2+1;
+    icgb += j2;
+  } // end loop over ib
 
-      for(int ia = 0; ia < na; ia++) {
-        suma1_r += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).re - ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).im);
-        suma1_i += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).im + ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).re);
-        //flopsum += 10;
-        ma1++;
-        ma2--;
-        icga += j2;
-      } // end loop over ia
-
-      ztmp_r += cgblock[icgb] * suma1_r;
-      ztmp_i += cgblock[icgb] * suma1_i;
-      jju1 += j1+1;
-      jju2 -= j2+1;
-      icgb += j2;
-    } // end loop over ib
-
-    // apply to z(j1,j2,j,ma,mb) to unique element of y(j)
-    // find right y_list[jju] and beta(ii,jjb) entries
-    // multiply and divide by j+1 factors
-    // account for multiplicity of 1, 2, or 3
-
-    const int jju = idxz[jjz].jju;
+  // apply to z(j1,j2,j,ma,mb) to unique element of y(j)
+  // find right y_list[jju] and beta(iatom,jjb) entries
+  // multiply and divide by j+1 factors
+  // account for multiplicity of 1, 2, or 3
 
   // pick out right beta value
 
-    if (j >= j1) {
-      const int jjb = idxb_block(j1,j2,j);
-      if (j1 == j) {
-        if (j2 == j) betaj = 3*beta(ii,jjb);
-        else betaj = 2*beta(ii,jjb);
-      } else betaj = beta(ii,jjb); 
-    } else if (j >= j2) {
-      const int jjb = idxb_block(j,j2,j1);
-      if (j2 == j) betaj = 2*beta(ii,jjb)*(j1+1)/(j+1.0);
-      else betaj = beta(ii,jjb)*(j1+1)/(j+1.0);
-    } else {
-      const int jjb = idxb_block(j2,j,j1);
-      betaj = beta(ii,jjb)*(j1+1)/(j+1.0);
-    }
+  if (j >= j1) {
+    const int jjb = idxb_block(j1,j2,j);
+    if (j1 == j) {
+      if (j2 == j) betaj = 3*beta(iatom,jjb);
+      else betaj = 2*beta(iatom,jjb);
+    } else betaj = beta(iatom,jjb);
+  } else if (j >= j2) {
+    const int jjb = idxb_block(j,j2,j1);
+    if (j2 == j) betaj = 2*beta(iatom,jjb)*(j1+1)/(j+1.0);
+    else betaj = beta(iatom,jjb)*(j1+1)/(j+1.0);
+  } else {
+    const int jjb = idxb_block(j2,j,j1);
+    betaj = beta(iatom,jjb)*(j1+1)/(j+1.0);
+  }
 
-  Kokkos::single(Kokkos::PerThread(team), [&] () {
-    Kokkos::atomic_add(&(ylist(iatom,jju).re), betaj*ztmp_r);
-    Kokkos::atomic_add(&(ylist(iatom,jju).im), betaj*ztmp_i);
-  });
-
-  }); // end loop over jjz
-
-  //printf("sum %i\n",flopsum);
+  Kokkos::atomic_add(&(ylist(iatom,jju).re), betaj*ztmp_r);
+  Kokkos::atomic_add(&(ylist(iatom,jju).im), betaj*ztmp_i);
 }
 
 /* ----------------------------------------------------------------------
@@ -556,9 +505,9 @@ void SNAKokkos<DeviceType>::compute_bi(const typename Kokkos::TeamPolicy<DeviceT
   Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxb_max),
       [&] (const int& jjb) {
   //for(int jjb = 0; jjb < idxb_max; jjb++) {
-    const int j1 = idxb[jjb].j1;
-    const int j2 = idxb[jjb].j2;
-    const int j = idxb[jjb].j;
+    const int j1 = idxb(jjb,0);
+    const int j2 = idxb(jjb,1);
+    const int j = idxb(jjb,2);
 
     int jjz = idxz_block(j1,j2,j);
     int jju = idxu_block[j];
@@ -648,14 +597,16 @@ void SNAKokkos<DeviceType>::compute_duidrj(const typename Kokkos::TeamPolicy<Dev
 
 template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
-void SNAKokkos<DeviceType>::zero_uarraytot(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom)
+void SNAKokkos<DeviceType>::zero_uarraytot(const int& iatom)
 {
   {
-    Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot.extent(1)),
-        [&] (const int& i) {
+    //Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot.extent(1)),
+    //    [&] (const int& i) {
+    for (int i = 0; i < ulisttot.extent(1); i++) {
       ulisttot(iatom,i).re = 0.0;
       ulisttot(iatom,i).im = 0.0;
-    });
+    }
+    //});
   }
 }
 
@@ -663,18 +614,18 @@ void SNAKokkos<DeviceType>::zero_uarraytot(const typename Kokkos::TeamPolicy<Dev
 
 template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
-void SNAKokkos<DeviceType>::addself_uarraytot(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, double wself_in)
+void SNAKokkos<DeviceType>::addself_uarraytot(const int& iatom, const double& wself_in)
 {
-  Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1),
-    [&] (const int& j) {
-  //for (int j = 0; j <= twojmax; j++)
+  //Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1),
+  //  [&] (const int& j) {
+  for (int j = 0; j <= twojmax; j++) {
     int jju = idxu_block[j];
     for (int ma = 0; ma <= j; ma++) {
       ulisttot(iatom,jju).re = wself_in;
       ulisttot(iatom,jju).im = 0.0;
       jju += j+2;
     }
-  });
+  }//});
 }
 
 /* ----------------------------------------------------------------------
@@ -786,6 +737,12 @@ void SNAKokkos<DeviceType>::compute_uarray(const typename Kokkos::TeamPolicy<Dev
   }
 }
 
+template<class DeviceType>
+void SNAKokkos<DeviceType>::transpose_ulisttot()
+{
+  UlisttotHelper<typename DeviceType::array_layout,decltype(ulisttot_lr),decltype(ulisttot)>::transpose(ulisttot_lr,ulisttot);
+}
+
 /* ----------------------------------------------------------------------
    compute derivatives of Wigner U-functions for one neighbor
    see comments in compute_uarray()
@@ -1219,7 +1176,7 @@ void SNAKokkos<DeviceType>::init_clebsch_gordan()
                           factorial((j  + cc2) / 2) *
                           factorial((j  - cc2) / 2) *
                           (j + 1));
-            
+
             h_cglist[idxcg_count] = sum * dcg * sfaccg;
             idxcg_count++;
           }
@@ -1318,8 +1275,10 @@ double SNAKokkos<DeviceType>::memory_usage()
 
   bytes += natom * idxu_max * sizeof(double) * 2;        // ulist
   bytes += natom * idxu_max * sizeof(double) * 2;        // ulisttot
+  if (!Kokkos::Impl::is_same<typename DeviceType::array_layout,Kokkos::LayoutRight>::value)
+    bytes += natom * idxu_max * sizeof(double) * 2;        // ulisttot_lr
   bytes += natom * idxu_max * 3 * sizeof(double) * 2;    // dulist
-                                                       
+
   bytes += natom * idxz_max * sizeof(double) * 2;        // zlist
   bytes += natom * idxb_max * sizeof(double);            // blist
   bytes += natom * idxu_max * sizeof(double) * 2;        // ylist
@@ -1329,8 +1288,8 @@ double SNAKokkos<DeviceType>::memory_usage()
   bytes += jdim * jdim * jdim * sizeof(int);             // idxz_block
   bytes += jdim * jdim * jdim * sizeof(int);             // idxb_block
 
-  bytes += idxz_max * sizeof(SNAKK_ZINDICES);            // idxz
-  bytes += idxb_max * sizeof(SNAKK_BINDICES);            // idxb
+  bytes += idxz_max * 10 * sizeof(int);                  // idxz
+  bytes += idxb_max * 3 * sizeof(int);                   // idxb
 
   bytes += jdim * sizeof(double);                        // bzero
 
diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp
index 23952b71d8..3367e97c6d 100644
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@@ -614,8 +614,8 @@ void VerletKokkos::force_clear()
       atomKK->modified(Device,F_MASK);
 
       if (torqueflag) {
-	Kokkos::parallel_for(range, Zero<typename ArrayTypes<LMPDeviceType>::t_f_array>(atomKK->k_torque.view<LMPDeviceType>()));
-	atomKK->modified(Device,TORQUE_MASK);
+        Kokkos::parallel_for(range, Zero<typename ArrayTypes<LMPDeviceType>::t_f_array>(atomKK->k_torque.view<LMPDeviceType>()));
+        atomKK->modified(Device,TORQUE_MASK);
       }
     }
   }
diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp
index c3442beef5..1939742bfc 100644
--- a/src/KSPACE/ewald_dipole.cpp
+++ b/src/KSPACE/ewald_dipole.cpp
@@ -69,7 +69,7 @@ void EwaldDipole::init()
   }
 
   // error check
-  
+
   dipoleflag = atom->mu?1:0;
   qsum_qsq(0); // q[i] might not be declared ?
 
@@ -77,13 +77,13 @@ void EwaldDipole::init()
     error->all(FLERR,"Cannot (yet) use charges with Kspace style EwaldDipole");
 
   triclinic_check();
-  
+
   // no triclinic ewald dipole (yet)
-  
+
   triclinic = domain->triclinic;
   if (triclinic)
     error->all(FLERR,"Cannot (yet) use EwaldDipole with triclinic box");
-  
+
   if (domain->dimension == 2)
     error->all(FLERR,"Cannot use EwaldDipole with 2d simulation");
 
@@ -91,7 +91,7 @@ void EwaldDipole::init()
 
   if (dipoleflag && strcmp(update->unit_style,"electron") == 0)
     error->all(FLERR,"Cannot (yet) use 'electron' units with dipoles");
-  
+
   if (slabflag == 0 && domain->nonperiodic > 0)
     error->all(FLERR,"Cannot use nonperiodic boundaries with EwaldDipole");
   if (slabflag) {
@@ -154,20 +154,20 @@ void EwaldDipole::init()
   if (!gewaldflag) {
     if (accuracy <= 0.0)
       error->all(FLERR,"KSpace accuracy must be > 0");
-    
+
     // initial guess with old method
-    
+
     g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*mu2);
     if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff;
     else g_ewald = sqrt(-log(g_ewald)) / cutoff;
-    
+
     // try Newton solver
 
     double g_ewald_new =
       NewtonSolve(g_ewald,cutoff,natoms,xprd*yprd*zprd,mu2);
     if (g_ewald_new > 0.0) g_ewald = g_ewald_new;
     else error->warning(FLERR,"Ewald/disp Newton solver failed, "
-                        "using old method to estimate g_ewald");  
+                        "using old method to estimate g_ewald");
   }
 
   // setup EwaldDipole coefficients so can print stats
@@ -246,7 +246,7 @@ void EwaldDipole::setup()
     double err;
     kxmax = 1;
     kymax = 1;
-    kzmax = 1;	
+    kzmax = 1;
 
     // set kmax in 3 directions to respect accuracy
 
@@ -340,7 +340,7 @@ double EwaldDipole::rms_dipole(int km, double prd, bigint natoms)
   if (natoms == 0) natoms = 1;   // avoid division by zero
 
   // error from eq.(46), Wang et al., JCP 115, 6351 (2001)
-  
+
   double value = 8*MY_PI*mu2*g_ewald/volume *
     sqrt(2*MY_PI*km*km*km/(15.0*natoms)) *
     exp(-MY_PI*MY_PI*km*km/(g_ewald*g_ewald*prd*prd));
@@ -410,7 +410,7 @@ void EwaldDipole::compute(int eflag, int vflag)
 
   int kx,ky,kz;
   double cypz,sypz,exprl,expim;
-  double partial,partial2,partial_peratom;
+  double partial,partial_peratom;
   double vcik[6];
   double mudotk;
 
@@ -428,7 +428,7 @@ void EwaldDipole::compute(int eflag, int vflag)
     for (i = 0; i < nlocal; i++) {
 
       for (j = 0; j<6; j++) vcik[j] = 0.0;
-      
+
       // re-evaluating mu dot k
       mudotk = mu[i][0]*kx*unitk[0] + mu[i][1]*ky*unitk[1] + mu[i][2]*kz*unitk[2];
 
@@ -461,15 +461,15 @@ void EwaldDipole::compute(int eflag, int vflag)
       vc[k][3] += vcik[3] = -(partial_peratom * mu[i][0] * eg[k][1]);
       vc[k][4] += vcik[4] = -(partial_peratom * mu[i][0] * eg[k][2]);
       vc[k][5] += vcik[5] = -(partial_peratom * mu[i][1] * eg[k][2]);
-      
-      // taking re-part of struct_fact x exp(i*k*ri) 
+
+      // taking re-part of struct_fact x exp(i*k*ri)
       // (for per-atom energy and virial calc.)
 
       if (evflag_atom) {
         if (eflag_atom) eatom[i] += mudotk*ug[k]*partial_peratom;
         if (vflag_atom)
           for (j = 0; j < 6; j++)
-	    vatom[i][j] += (ug[k]*mudotk*vg[k][j]*partial_peratom - vcik[j]);
+            vatom[i][j] += (ug[k]*mudotk*vg[k][j]*partial_peratom - vcik[j]);
       }
     }
   }
@@ -503,7 +503,7 @@ void EwaldDipole::compute(int eflag, int vflag)
   // global virial
 
   if (vflag_global) {
-    double uk, vk;
+    double uk;
     for (k = 0; k < kcount; k++) {
       uk = ug[k] * (sfacrl_all[k]*sfacrl_all[k] + sfacim_all[k]*sfacim_all[k]);
       for (j = 0; j < 6; j++) virial[j] += uk*vg[k][j] - vc[k][j];
@@ -518,7 +518,7 @@ void EwaldDipole::compute(int eflag, int vflag)
     if (eflag_atom) {
       for (i = 0; i < nlocal; i++) {
         eatom[i] -= (mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2])
-	  *2.0*g3/3.0/MY_PIS;
+          *2.0*g3/3.0/MY_PIS;
         eatom[i] *= muscale;
       }
     }
@@ -556,7 +556,7 @@ void EwaldDipole::eik_dot_r()
   // loop on n kpoints and nlocal atoms
 
   // (k,0,0), (0,l,0), (0,0,m)
-  
+
   // loop 1: k=1, l=1, m=1
   // define first val. of cos and sin
 
@@ -596,7 +596,7 @@ void EwaldDipole::eik_dot_r()
             cs[m-1][ic][i]*sn[1][ic][i];
           cs[-m][ic][i] = cs[m][ic][i];
           sn[-m][ic][i] = -sn[m][ic][i];
-	  mudotk = (mu[i][ic]*m*unitk[ic]);
+          mudotk = (mu[i][ic]*m*unitk[ic]);
           cstr1 += mudotk*cs[m][ic][i];
           sstr1 += mudotk*sn[m][ic][i];
         }
@@ -617,19 +617,19 @@ void EwaldDipole::eik_dot_r()
         cstr2 = 0.0;
         sstr2 = 0.0;
         for (i = 0; i < nlocal; i++) {
-	  mux = mu[i][0];
-	  muy = mu[i][1];
+          mux = mu[i][0];
+          muy = mu[i][1];
 
-	  // dir 1: (k,l,0)
-	  mudotk = (mux*k*unitk[0] + muy*l*unitk[1]);
+          // dir 1: (k,l,0)
+          mudotk = (mux*k*unitk[0] + muy*l*unitk[1]);
           cstr1 += mudotk*(cs[k][0][i]*cs[l][1][i]-sn[k][0][i]*sn[l][1][i]);
           sstr1 += mudotk*(sn[k][0][i]*cs[l][1][i]+cs[k][0][i]*sn[l][1][i]);
-	  
-	  // dir 2: (k,-l,0)
-	  mudotk = (mux*k*unitk[0] - muy*l*unitk[1]);
+
+          // dir 2: (k,-l,0)
+          mudotk = (mux*k*unitk[0] - muy*l*unitk[1]);
           cstr2 += mudotk*(cs[k][0][i]*cs[l][1][i]+sn[k][0][i]*sn[l][1][i]);
           sstr2 += mudotk*(sn[k][0][i]*cs[l][1][i]-cs[k][0][i]*sn[l][1][i]);
-	}
+        }
         sfacrl[n] = cstr1;
         sfacim[n++] = sstr1;
         sfacrl[n] = cstr2;
@@ -649,16 +649,16 @@ void EwaldDipole::eik_dot_r()
         cstr2 = 0.0;
         sstr2 = 0.0;
         for (i = 0; i < nlocal; i++) {
-	  muy = mu[i][1];
-	  muz = mu[i][2];
+          muy = mu[i][1];
+          muz = mu[i][2];
 
-	  // dir 1: (0,l,m)
-      	  mudotk = (muy*l*unitk[1] + muz*m*unitk[2]); 
+          // dir 1: (0,l,m)
+          mudotk = (muy*l*unitk[1] + muz*m*unitk[2]);
           cstr1 += mudotk*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]);
           sstr1 += mudotk*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]);
-	  
-	  // dir 2: (0,l,-m)
-	  mudotk = (muy*l*unitk[1] - muz*m*unitk[2]); 
+
+          // dir 2: (0,l,-m)
+          mudotk = (muy*l*unitk[1] - muz*m*unitk[2]);
           cstr2 += mudotk*(cs[l][1][i]*cs[m][2][i]+sn[l][1][i]*sn[m][2][i]);
           sstr2 += mudotk*(sn[l][1][i]*cs[m][2][i]-cs[l][1][i]*sn[m][2][i]);
         }
@@ -681,16 +681,16 @@ void EwaldDipole::eik_dot_r()
         cstr2 = 0.0;
         sstr2 = 0.0;
         for (i = 0; i < nlocal; i++) {
-      	  mux = mu[i][0];
-	  muz = mu[i][2];
+          mux = mu[i][0];
+          muz = mu[i][2];
 
-	  // dir 1: (k,0,m)
-	  mudotk = (mux*k*unitk[0] + muz*m*unitk[2]); 
+          // dir 1: (k,0,m)
+          mudotk = (mux*k*unitk[0] + muz*m*unitk[2]);
           cstr1 += mudotk*(cs[k][0][i]*cs[m][2][i]-sn[k][0][i]*sn[m][2][i]);
           sstr1 += mudotk*(sn[k][0][i]*cs[m][2][i]+cs[k][0][i]*sn[m][2][i]);
-	  
-	  // dir 2: (k,0,-m)
-	  mudotk = (mux*k*unitk[0] - muz*m*unitk[2]); 
+
+          // dir 2: (k,0,-m)
+          mudotk = (mux*k*unitk[0] - muz*m*unitk[2]);
           cstr2 += mudotk*(cs[k][0][i]*cs[m][2][i]+sn[k][0][i]*sn[m][2][i]);
           sstr2 += mudotk*(sn[k][0][i]*cs[m][2][i]-cs[k][0][i]*sn[m][2][i]);
         }
@@ -719,33 +719,33 @@ void EwaldDipole::eik_dot_r()
           cstr4 = 0.0;
           sstr4 = 0.0;
           for (i = 0; i < nlocal; i++) {
-      	    mux = mu[i][0];
-	    muy = mu[i][1];
-	    muz = mu[i][2];
+            mux = mu[i][0];
+            muy = mu[i][1];
+            muz = mu[i][2];
 
-	    // dir 1: (k,l,m)
-	    mudotk = (mux*k*unitk[0] + muy*l*unitk[1] + muz*m*unitk[2]); 
+            // dir 1: (k,l,m)
+            mudotk = (mux*k*unitk[0] + muy*l*unitk[1] + muz*m*unitk[2]);
             clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
             slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
             cstr1 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
             sstr1 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
 
-	    // dir 2: (k,-l,m)
-	    mudotk = (mux*k*unitk[0] - muy*l*unitk[1] + muz*m*unitk[2]); 
+            // dir 2: (k,-l,m)
+            mudotk = (mux*k*unitk[0] - muy*l*unitk[1] + muz*m*unitk[2]);
             clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
             slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
             cstr2 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
             sstr2 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
 
-	    // dir 3: (k,l,-m)
-	    mudotk = (mux*k*unitk[0] + muy*l*unitk[1] - muz*m*unitk[2]); 
+            // dir 3: (k,l,-m)
+            mudotk = (mux*k*unitk[0] + muy*l*unitk[1] - muz*m*unitk[2]);
             clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
             slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
             cstr3 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
             sstr3 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
 
-	    // dir 4: (k,-l,-m)
-	    mudotk = (mux*k*unitk[0] - muy*l*unitk[1] - muz*m*unitk[2]); 
+            // dir 4: (k,-l,-m)
+            mudotk = (mux*k*unitk[0] - muy*l*unitk[1] - muz*m*unitk[2]);
             clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
             slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
             cstr4 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
@@ -777,12 +777,10 @@ void EwaldDipole::slabcorr()
 {
   // compute local contribution to global dipole moment
 
-  double **x = atom->x;
-  double zprd = domain->zprd;
-  int nlocal = atom->nlocal;
-
   double dipole = 0.0;
   double **mu = atom->mu;
+  int nlocal = atom->nlocal;
+
   for (int i = 0; i < nlocal; i++) dipole += mu[i][2];
 
   // sum local contributions to get global dipole moment
diff --git a/src/KSPACE/ewald_dipole.h b/src/KSPACE/ewald_dipole.h
index 741756487b..c8dd18565c 100644
--- a/src/KSPACE/ewald_dipole.h
+++ b/src/KSPACE/ewald_dipole.h
@@ -34,10 +34,10 @@ class EwaldDipole : public Ewald {
 
  protected:
   double musum,musqsum,mu2;
-  double **tk;			// field for torque 
-  double **vc;			// virial per k
+  double **tk;                  // field for torque
+  double **vc;                  // virial per k
 
-  void musum_musq(); 
+  void musum_musq();
   double rms_dipole(int, double, bigint);
   virtual void eik_dot_r();
   void slabcorr();
diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp
index e7d67680a1..82832f6e4c 100644
--- a/src/KSPACE/ewald_dipole_spin.cpp
+++ b/src/KSPACE/ewald_dipole_spin.cpp
@@ -36,17 +36,17 @@ using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-EwaldDipoleSpin::EwaldDipoleSpin(LAMMPS *lmp) : 
+EwaldDipoleSpin::EwaldDipoleSpin(LAMMPS *lmp) :
   EwaldDipole(lmp)
 {
   dipoleflag = 0;
   spinflag = 1;
-  
-  hbar = force->hplanck/MY_2PI;         	// eV/(rad.THz)
-  mub = 9.274e-4;                     		// in A.Ang^2
-  mu_0 = 785.15;               			// in eV/Ang/A^2
-  mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);	// in eV.Ang^3
-  mub2mu0hbinv = mub2mu0 / hbar;        	// in rad.THz
+
+  hbar = force->hplanck/MY_2PI;                 // eV/(rad.THz)
+  mub = 9.274e-4;                               // in A.Ang^2
+  mu_0 = 785.15;                                // in eV/Ang/A^2
+  mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);     // in eV.Ang^3
+  mub2mu0hbinv = mub2mu0 / hbar;                // in rad.THz
 }
 
 /* ----------------------------------------------------------------------
@@ -67,17 +67,17 @@ void EwaldDipoleSpin::init()
   }
 
   // error check
-  
+
   spinflag = atom->sp?1:0;
 
   triclinic_check();
-  
+
   // no triclinic ewald spin (yet)
-  
+
   triclinic = domain->triclinic;
   if (triclinic)
     error->all(FLERR,"Cannot (yet) use EwaldDipoleSpin with triclinic box");
-  
+
   if (domain->dimension == 2)
     error->all(FLERR,"Cannot use EwaldDipoleSpin with 2d simulation");
 
@@ -85,7 +85,7 @@ void EwaldDipoleSpin::init()
 
   if ((spinflag && strcmp(update->unit_style,"metal")) != 0)
     error->all(FLERR,"'metal' units have to be used with spins");
-  
+
   if (slabflag == 0 && domain->nonperiodic > 0)
     error->all(FLERR,"Cannot use nonperiodic boundaries with EwaldDipoleSpin");
   if (slabflag) {
@@ -144,20 +144,20 @@ void EwaldDipoleSpin::init()
   if (!gewaldflag) {
     if (accuracy <= 0.0)
       error->all(FLERR,"KSpace accuracy must be > 0");
-    
+
     // initial guess with old method
-    
+
     g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*mu2);
     if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff;
     else g_ewald = sqrt(-log(g_ewald)) / cutoff;
-    
+
     // try Newton solver
 
     double g_ewald_new =
       NewtonSolve(g_ewald,cutoff,natoms,xprd*yprd*zprd,mu2);
     if (g_ewald_new > 0.0) g_ewald = g_ewald_new;
     else error->warning(FLERR,"Ewald/disp Newton solver failed, "
-                        "using old method to estimate g_ewald");  
+                        "using old method to estimate g_ewald");
   }
 
   // setup EwaldDipoleSpin coefficients so can print stats
@@ -236,7 +236,7 @@ void EwaldDipoleSpin::setup()
     double err;
     kxmax = 1;
     kymax = 1;
-    kzmax = 1;	
+    kzmax = 1;
 
     // set kmax in 3 directions to respect accuracy
 
@@ -384,7 +384,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag)
 
   int kx,ky,kz;
   double cypz,sypz,exprl,expim;
-  double partial,partial2,partial_peratom;
+  double partial,partial_peratom;
   double vcik[6];
   double mudotk;
 
@@ -404,7 +404,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag)
       for (j = 0; j<6; j++) vcik[j] = 0.0;
 
       // re-evaluating sp dot k
-      
+
       spx = sp[i][0]*sp[i][3];
       spy = sp[i][1]*sp[i][3];
       spz = sp[i][2]*sp[i][3];
@@ -427,33 +427,33 @@ void EwaldDipoleSpin::compute(int eflag, int vflag)
       // compute field for torque calculation
 
       partial_peratom = exprl*sfacrl_all[k] + expim*sfacim_all[k];
-      tk[i][0] += partial2*eg[k][0];
-      tk[i][1] += partial2*eg[k][1];
-      tk[i][2] += partial2*eg[k][2];
+      tk[i][0] += partial_peratom*eg[k][0];
+      tk[i][1] += partial_peratom*eg[k][1];
+      tk[i][2] += partial_peratom*eg[k][2];
 
       // total and per-atom virial correction
-      
+
       vc[k][0] += vcik[0] = -(partial_peratom * spx * eg[k][0]);
       vc[k][1] += vcik[1] = -(partial_peratom * spy * eg[k][1]);
       vc[k][2] += vcik[2] = -(partial_peratom * spz * eg[k][2]);
       vc[k][3] += vcik[3] = -(partial_peratom * spx * eg[k][1]);
       vc[k][4] += vcik[4] = -(partial_peratom * spx * eg[k][2]);
       vc[k][5] += vcik[5] = -(partial_peratom * spy * eg[k][2]);
-      
-      // taking re-part of struct_fact x exp(i*k*ri) 
+
+      // taking re-part of struct_fact x exp(i*k*ri)
       // (for per-atom energy and virial calc.)
 
       if (evflag_atom) {
         if (eflag_atom) eatom[i] += mudotk*ug[k]*partial_peratom;
         if (vflag_atom)
           for (j = 0; j < 6; j++)
-	    vatom[i][j] += (ug[k]*mudotk*vg[k][j]*partial_peratom - vcik[j]);
+            vatom[i][j] += (ug[k]*mudotk*vg[k][j]*partial_peratom - vcik[j]);
       }
     }
   }
 
   // force and mag. precession vectors calculation
-  
+
   const double spscale = mub2mu0 * scale;
   const double spscale2 = mub2mu0hbinv * scale;
 
@@ -465,7 +465,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag)
     fm_long[i][1] += spscale2 * tk[i][1];
     if (slabflag != 2) fm_long[i][2] += spscale2 * tk[i][3];
   }
-  
+
   // sum global energy across Kspace vevs and add in volume-dependent term
   // taking the re-part of struct_fact_i x struct_fact_j
   // substracting self energy and scaling
@@ -482,7 +482,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag)
   // global virial
 
   if (vflag_global) {
-    double uk, vk;
+    double uk;
     for (k = 0; k < kcount; k++) {
       uk = ug[k] * (sfacrl_all[k]*sfacrl_all[k] + sfacim_all[k]*sfacim_all[k]);
       for (j = 0; j < 6; j++) virial[j] += uk*vg[k][j] - vc[k][j];
@@ -496,11 +496,11 @@ void EwaldDipoleSpin::compute(int eflag, int vflag)
   if (evflag_atom) {
     if (eflag_atom) {
       for (i = 0; i < nlocal; i++) {
-	spx = sp[i][0]*sp[i][3];
-	spy = sp[i][1]*sp[i][3];
-	spz = sp[i][2]*sp[i][3];
+        spx = sp[i][0]*sp[i][3];
+        spy = sp[i][1]*sp[i][3];
+        spz = sp[i][2]*sp[i][3];
         eatom[i] -= (spx*spx + spy*spy + spz*spz)
-	  *2.0*g3/3.0/MY_PIS;
+          *2.0*g3/3.0/MY_PIS;
         eatom[i] *= spscale;
       }
     }
@@ -540,7 +540,7 @@ void EwaldDipoleSpin::eik_dot_r()
   // store n values of sum_j[ (mu_j dot k) exp(-k dot r_j) ]
 
   // (k,0,0), (0,l,0), (0,0,m)
-  
+
   // loop 1: k=1, l=1, m=1
   // define first val. of cos and sin
 
@@ -556,7 +556,7 @@ void EwaldDipoleSpin::eik_dot_r()
         sn[1][ic][i] = sin(unitk[ic]*x[i][ic]);
         cs[-1][ic][i] = cs[1][ic][i];
         sn[-1][ic][i] = -sn[1][ic][i];
-	spi = sp[i][ic]*sp[i][3];
+        spi = sp[i][ic]*sp[i][3];
         mudotk = (spi*unitk[ic]);
         cstr1 += mudotk*cs[1][ic][i];
         sstr1 += mudotk*sn[1][ic][i];
@@ -581,8 +581,8 @@ void EwaldDipoleSpin::eik_dot_r()
             cs[m-1][ic][i]*sn[1][ic][i];
           cs[-m][ic][i] = cs[m][ic][i];
           sn[-m][ic][i] = -sn[m][ic][i];
-	  spi = sp[i][ic]*sp[i][3];
-	  mudotk = (spi*m*unitk[ic]);
+          spi = sp[i][ic]*sp[i][3];
+          mudotk = (spi*m*unitk[ic]);
           cstr1 += mudotk*cs[m][ic][i];
           sstr1 += mudotk*sn[m][ic][i];
         }
@@ -603,19 +603,19 @@ void EwaldDipoleSpin::eik_dot_r()
         cstr2 = 0.0;
         sstr2 = 0.0;
         for (i = 0; i < nlocal; i++) {
-	  spx = sp[i][0]*sp[i][3];
-	  spy = sp[i][1]*sp[i][3];
+          spx = sp[i][0]*sp[i][3];
+          spy = sp[i][1]*sp[i][3];
 
-	  // dir 1: (k,l,0)
-	  mudotk = (spx*k*unitk[0] + spy*l*unitk[1]);
+          // dir 1: (k,l,0)
+          mudotk = (spx*k*unitk[0] + spy*l*unitk[1]);
           cstr1 += mudotk*(cs[k][0][i]*cs[l][1][i]-sn[k][0][i]*sn[l][1][i]);
           sstr1 += mudotk*(sn[k][0][i]*cs[l][1][i]+cs[k][0][i]*sn[l][1][i]);
-	  
-	  // dir 2: (k,-l,0)
-	  mudotk = (spx*k*unitk[0] - spy*l*unitk[1]);
+
+          // dir 2: (k,-l,0)
+          mudotk = (spx*k*unitk[0] - spy*l*unitk[1]);
           cstr2 += mudotk*(cs[k][0][i]*cs[l][1][i]+sn[k][0][i]*sn[l][1][i]);
           sstr2 += mudotk*(sn[k][0][i]*cs[l][1][i]-cs[k][0][i]*sn[l][1][i]);
-	}
+        }
         sfacrl[n] = cstr1;
         sfacim[n++] = sstr1;
         sfacrl[n] = cstr2;
@@ -635,16 +635,16 @@ void EwaldDipoleSpin::eik_dot_r()
         cstr2 = 0.0;
         sstr2 = 0.0;
         for (i = 0; i < nlocal; i++) {
-	  spy = sp[i][1]*sp[i][3];
-	  spz = sp[i][2]*sp[i][3];
+          spy = sp[i][1]*sp[i][3];
+          spz = sp[i][2]*sp[i][3];
 
-	  // dir 1: (0,l,m)
-      	  mudotk = (spy*l*unitk[1] + spz*m*unitk[2]); 
+          // dir 1: (0,l,m)
+          mudotk = (spy*l*unitk[1] + spz*m*unitk[2]);
           cstr1 += mudotk*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]);
           sstr1 += mudotk*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]);
-	  
-	  // dir 2: (0,l,-m)
-	  mudotk = (spy*l*unitk[1] - spz*m*unitk[2]); 
+
+          // dir 2: (0,l,-m)
+          mudotk = (spy*l*unitk[1] - spz*m*unitk[2]);
           cstr2 += mudotk*(cs[l][1][i]*cs[m][2][i]+sn[l][1][i]*sn[m][2][i]);
           sstr2 += mudotk*(sn[l][1][i]*cs[m][2][i]-cs[l][1][i]*sn[m][2][i]);
         }
@@ -667,16 +667,16 @@ void EwaldDipoleSpin::eik_dot_r()
         cstr2 = 0.0;
         sstr2 = 0.0;
         for (i = 0; i < nlocal; i++) {
-      	  spx = sp[i][0]*sp[i][3];
-	  spz = sp[i][2]*sp[i][3];
+          spx = sp[i][0]*sp[i][3];
+          spz = sp[i][2]*sp[i][3];
 
-	  // dir 1: (k,0,m)
-	  mudotk = (spx*k*unitk[0] + spz*m*unitk[2]); 
+          // dir 1: (k,0,m)
+          mudotk = (spx*k*unitk[0] + spz*m*unitk[2]);
           cstr1 += mudotk*(cs[k][0][i]*cs[m][2][i]-sn[k][0][i]*sn[m][2][i]);
           sstr1 += mudotk*(sn[k][0][i]*cs[m][2][i]+cs[k][0][i]*sn[m][2][i]);
-	  
-	  // dir 2: (k,0,-m)
-	  mudotk = (spx*k*unitk[0] - spz*m*unitk[2]); 
+
+          // dir 2: (k,0,-m)
+          mudotk = (spx*k*unitk[0] - spz*m*unitk[2]);
           cstr2 += mudotk*(cs[k][0][i]*cs[m][2][i]+sn[k][0][i]*sn[m][2][i]);
           sstr2 += mudotk*(sn[k][0][i]*cs[m][2][i]-cs[k][0][i]*sn[m][2][i]);
         }
@@ -705,33 +705,33 @@ void EwaldDipoleSpin::eik_dot_r()
           cstr4 = 0.0;
           sstr4 = 0.0;
           for (i = 0; i < nlocal; i++) {
-      	    spx = sp[i][0]*sp[i][3];
-	    spy = sp[i][1]*sp[i][3];
-	    spz = sp[i][2]*sp[i][3];
+            spx = sp[i][0]*sp[i][3];
+            spy = sp[i][1]*sp[i][3];
+            spz = sp[i][2]*sp[i][3];
 
-	    // dir 1: (k,l,m)
-	    mudotk = (spx*k*unitk[0] + spy*l*unitk[1] + spz*m*unitk[2]); 
+            // dir 1: (k,l,m)
+            mudotk = (spx*k*unitk[0] + spy*l*unitk[1] + spz*m*unitk[2]);
             clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
             slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
             cstr1 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
             sstr1 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
 
-	    // dir 2: (k,-l,m)
-	    mudotk = (spx*k*unitk[0] - spy*l*unitk[1] + spz*m*unitk[2]); 
+            // dir 2: (k,-l,m)
+            mudotk = (spx*k*unitk[0] - spy*l*unitk[1] + spz*m*unitk[2]);
             clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
             slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
             cstr2 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
             sstr2 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
 
-	    // dir 3: (k,l,-m)
-	    mudotk = (spx*k*unitk[0] + spy*l*unitk[1] - spz*m*unitk[2]); 
+            // dir 3: (k,l,-m)
+            mudotk = (spx*k*unitk[0] + spy*l*unitk[1] - spz*m*unitk[2]);
             clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
             slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
             cstr3 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
             sstr3 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
 
-	    // dir 4: (k,-l,-m)
-	    mudotk = (spx*k*unitk[0] - spy*l*unitk[1] - spz*m*unitk[2]); 
+            // dir 4: (k,-l,-m)
+            mudotk = (spx*k*unitk[0] - spy*l*unitk[1] - spz*m*unitk[2]);
             clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
             slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
             cstr4 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
@@ -763,14 +763,12 @@ void EwaldDipoleSpin::slabcorr()
 {
   // compute local contribution to global dipole/spin moment
 
-  double **x = atom->x;
-  double zprd = domain->zprd;
-  int nlocal = atom->nlocal;
-
   double spin = 0.0;
   double **sp = atom->sp;
-  double spx,spy,spz;
-  for (int i = 0; i < nlocal; i++) { 
+  double spz;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++) {
     spz = sp[i][2]*sp[i][3];
     spin += spz;
   }
diff --git a/src/KSPACE/ewald_dipole_spin.h b/src/KSPACE/ewald_dipole_spin.h
index 20852c08c1..32c7ddb5f1 100644
--- a/src/KSPACE/ewald_dipole_spin.h
+++ b/src/KSPACE/ewald_dipole_spin.h
@@ -33,13 +33,13 @@ class EwaldDipoleSpin : public EwaldDipole {
   void compute(int, int);
 
  protected:
-  double hbar;                  // reduced Planck's constant      
-  double mub;                   // Bohr's magneton                
+  double hbar;                  // reduced Planck's constant
+  double mub;                   // Bohr's magneton
   double mu_0;                  // vacuum permeability
   double mub2mu0;               // prefactor for mech force
   double mub2mu0hbinv;          // prefactor for mag force
 
-  void spsum_musq(); 
+  void spsum_musq();
   virtual void eik_dot_r();
   void slabcorr();
 
diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp
index a7ac66fdd3..a7f0698c0c 100644
--- a/src/KSPACE/ewald_disp.cpp
+++ b/src/KSPACE/ewald_disp.cpp
@@ -131,6 +131,7 @@ void EwaldDisp::init()
           else if (ewald_mix==Pair::ARITHMETIC) { k = 2; break; }
           error->all(FLERR,
                      "Unsupported mixing rule in kspace_style ewald/disp");
+          break;
         default:
           error->all(FLERR,"Unsupported order in kspace_style ewald/disp");
       }
diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp
index cfd88609b3..a3a4956214 100644
--- a/src/KSPACE/fix_tune_kspace.cpp
+++ b/src/KSPACE/fix_tune_kspace.cpp
@@ -29,6 +29,7 @@
 #include "neighbor.h"
 #include "modify.h"
 #include "compute.h"
+
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
 #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
 #define GOLD 1.618034
diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp
index e248a24ef7..b5b3eda64f 100644
--- a/src/KSPACE/pair_born_coul_long.cpp
+++ b/src/KSPACE/pair_born_coul_long.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -421,16 +422,16 @@ void PairBornCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&rho[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&d[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@@ -464,13 +465,13 @@ void PairBornCoulLong::write_restart_settings(FILE *fp)
 void PairBornCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp
index c97856fa3c..a46424baf7 100644
--- a/src/KSPACE/pair_buck_coul_long.cpp
+++ b/src/KSPACE/pair_buck_coul_long.cpp
@@ -24,6 +24,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -399,14 +400,14 @@ void PairBuckCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&rho[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@@ -438,13 +439,13 @@ void PairBuckCoulLong::write_restart_settings(FILE *fp)
 void PairBuckCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp
index 8127cbc127..7f369045c3 100644
--- a/src/KSPACE/pair_buck_long_coul_long.cpp
+++ b/src/KSPACE/pair_buck_long_coul_long.cpp
@@ -31,6 +31,7 @@
 #include "respa.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -65,10 +66,10 @@ void PairBuckLongCoulLong::options(char **arg, int order)
   if (!*arg) error->all(FLERR,"Illegal pair_style buck/long/coul/long command");
   for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
   switch (i) {
-    default: error->all(FLERR,"Illegal pair_style buck/long/coul/long command");
     case 0: ewald_order |= 1<<order; break;
-    case 2: ewald_off |= 1<<order;
+    case 2: ewald_off |= 1<<order; break;
     case 1: break;
+    default: error->all(FLERR,"Illegal pair_style buck/long/coul/long command");
   }
 }
 
@@ -355,14 +356,14 @@ void PairBuckLongCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&buck_a_read[i][j],sizeof(double),1,fp);
-          fread(&buck_rho_read[i][j],sizeof(double),1,fp);
-          fread(&buck_c_read[i][j],sizeof(double),1,fp);
-          fread(&cut_buck_read[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&buck_a_read[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&buck_rho_read[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&buck_c_read[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_buck_read[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&buck_a_read[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&buck_rho_read[i][j],1,MPI_DOUBLE,0,world);
@@ -394,13 +395,13 @@ void PairBuckLongCoulLong::write_restart_settings(FILE *fp)
 void PairBuckLongCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_buck_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
-    fread(&ewald_order,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_buck_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_buck_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp
index 7cedf3d003..004835007d 100644
--- a/src/KSPACE/pair_coul_long.cpp
+++ b/src/KSPACE/pair_coul_long.cpp
@@ -27,6 +27,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -289,10 +290,10 @@ void PairCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
-        if (me == 0) fread(&scale[i][j],sizeof(double),1,fp);
+        if (me == 0) utils::sfread(FLERR,&scale[i][j],sizeof(double),1,fp,NULL,error);
         MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world);
       }
     }
@@ -318,11 +319,11 @@ void PairCoulLong::write_restart_settings(FILE *fp)
 void PairCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp
index 751ee77388..22ed923b49 100644
--- a/src/KSPACE/pair_lj_charmm_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp
@@ -29,6 +29,7 @@
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -822,14 +823,14 @@ void PairLJCharmmCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&eps14[i][j],sizeof(double),1,fp);
-          fread(&sigma14[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -861,13 +862,13 @@ void PairLJCharmmCoulLong::write_restart_settings(FILE *fp)
 void PairLJCharmmCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_inner,sizeof(double),1,fp);
-    fread(&cut_lj,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);
diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
index 494a349768..ce7fda5f18 100644
--- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
@@ -33,6 +33,7 @@
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -889,14 +890,14 @@ void PairLJCharmmfswCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&eps14[i][j],sizeof(double),1,fp);
-          fread(&sigma14[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -928,13 +929,13 @@ void PairLJCharmmfswCoulLong::write_restart_settings(FILE *fp)
 void PairLJCharmmfswCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_inner,sizeof(double),1,fp);
-    fread(&cut_lj,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);
diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp
index fb79451b37..23e182435d 100644
--- a/src/KSPACE/pair_lj_cut_coul_long.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_long.cpp
@@ -31,6 +31,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -793,13 +794,13 @@ void PairLJCutCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -830,13 +831,13 @@ void PairLJCutCoulLong::write_restart_settings(FILE *fp)
 void PairLJCutCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
index c98092f19b..a4f115568f 100644
--- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
@@ -30,6 +30,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -528,19 +529,19 @@ void PairLJCutTIP4PLong::write_restart_settings(FILE *fp)
 void PairLJCutTIP4PLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&typeO,sizeof(int),1,fp);
-    fread(&typeH,sizeof(int),1,fp);
-    fread(&typeB,sizeof(int),1,fp);
-    fread(&typeA,sizeof(int),1,fp);
-    fread(&qdist,sizeof(double),1,fp);
+    utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
 
   MPI_Bcast(&typeO,1,MPI_INT,0,world);
diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp
index 610fc4e89b..4af3cdeecd 100644
--- a/src/KSPACE/pair_lj_long_coul_long.cpp
+++ b/src/KSPACE/pair_lj_long_coul_long.cpp
@@ -33,6 +33,7 @@
 #include "respa.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -68,10 +69,10 @@ void PairLJLongCoulLong::options(char **arg, int order)
   if (!*arg) error->all(FLERR,"Illegal pair_style lj/long/coul/long command");
   for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
   switch (i) {
-    default: error->all(FLERR,"Illegal pair_style lj/long/coul/long command");
     case 0: ewald_order |= 1<<order; break;
-    case 2: ewald_off |= 1<<order;
+    case 2: ewald_off |= 1<<order; break;
     case 1: break;
+    default: error->all(FLERR,"Illegal pair_style lj/long/coul/long command");
   }
 }
 
@@ -355,13 +356,13 @@ void PairLJLongCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon_read[i][j],sizeof(double),1,fp);
-          fread(&sigma_read[i][j],sizeof(double),1,fp);
-          fread(&cut_lj_read[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon_read[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma_read[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj_read[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world);
@@ -392,13 +393,13 @@ void PairLJLongCoulLong::write_restart_settings(FILE *fp)
 void PairLJLongCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
-    fread(&ewald_order,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp
index 08409dce72..b46fb64898 100644
--- a/src/KSPACE/pair_lj_long_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp
@@ -30,6 +30,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -1539,18 +1540,18 @@ void PairLJLongTIP4PLong::write_restart_settings(FILE *fp)
 void PairLJLongTIP4PLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&typeO,sizeof(int),1,fp);
-    fread(&typeH,sizeof(int),1,fp);
-    fread(&typeB,sizeof(int),1,fp);
-    fread(&typeA,sizeof(int),1,fp);
-    fread(&qdist,sizeof(double),1,fp);
+    utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
 
   MPI_Bcast(&typeO,1,MPI_INT,0,world);
diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp
index 2c47f42beb..c3ec44b7eb 100644
--- a/src/KSPACE/pair_tip4p_long.cpp
+++ b/src/KSPACE/pair_tip4p_long.cpp
@@ -30,6 +30,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -467,11 +468,11 @@ void PairTIP4PLong::read_restart_settings(FILE *fp)
   PairCoulLong::read_restart_settings(fp);
 
   if (comm->me == 0) {
-    fread(&typeO,sizeof(int),1,fp);
-    fread(&typeH,sizeof(int),1,fp);
-    fread(&typeB,sizeof(int),1,fp);
-    fread(&typeA,sizeof(int),1,fp);
-    fread(&qdist,sizeof(double),1,fp);
+    utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
   }
 
   MPI_Bcast(&typeO,1,MPI_INT,0,world);
diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp
index 0eb761d9be..40d0c1ac73 100644
--- a/src/KSPACE/pppm_dipole.cpp
+++ b/src/KSPACE/pppm_dipole.cpp
@@ -58,19 +58,19 @@ enum{FORWARD_MU,FORWARD_MU_PERATOM};
 /* ---------------------------------------------------------------------- */
 
 PPPMDipole::PPPMDipole(LAMMPS *lmp) : PPPM(lmp),
-  densityx_brick_dipole(NULL), densityy_brick_dipole(NULL), 
-  densityz_brick_dipole(NULL), ux_brick_dipole(NULL), 
-  uy_brick_dipole(NULL), uz_brick_dipole(NULL), vdxx_brick_dipole(NULL), 
-  vdxy_brick_dipole(NULL), vdyy_brick_dipole(NULL), 
-  vdxz_brick_dipole(NULL), vdyz_brick_dipole(NULL), 
-  vdzz_brick_dipole(NULL), v0x_brick_dipole(NULL), v1x_brick_dipole(NULL), 
-  v2x_brick_dipole(NULL), v3x_brick_dipole(NULL), v4x_brick_dipole(NULL), 
-  v5x_brick_dipole(NULL), v0y_brick_dipole(NULL), v1y_brick_dipole(NULL), 
-  v2y_brick_dipole(NULL), v3y_brick_dipole(NULL), v4y_brick_dipole(NULL), 
-  v5y_brick_dipole(NULL), v0z_brick_dipole(NULL), v1z_brick_dipole(NULL), 
-  v2z_brick_dipole(NULL), v3z_brick_dipole(NULL), v4z_brick_dipole(NULL), 
-  v5z_brick_dipole(NULL), work3(NULL), work4(NULL), 
-  densityx_fft_dipole(NULL), densityy_fft_dipole(NULL), 
+  densityx_brick_dipole(NULL), densityy_brick_dipole(NULL),
+  densityz_brick_dipole(NULL),
+  vdxx_brick_dipole(NULL), vdyy_brick_dipole(NULL), vdzz_brick_dipole(NULL),
+  vdxy_brick_dipole(NULL), vdxz_brick_dipole(NULL), vdyz_brick_dipole(NULL),
+  ux_brick_dipole(NULL), uy_brick_dipole(NULL), uz_brick_dipole(NULL),
+  v0x_brick_dipole(NULL), v1x_brick_dipole(NULL),
+  v2x_brick_dipole(NULL), v3x_brick_dipole(NULL), v4x_brick_dipole(NULL),
+  v5x_brick_dipole(NULL), v0y_brick_dipole(NULL), v1y_brick_dipole(NULL),
+  v2y_brick_dipole(NULL), v3y_brick_dipole(NULL), v4y_brick_dipole(NULL),
+  v5y_brick_dipole(NULL), v0z_brick_dipole(NULL), v1z_brick_dipole(NULL),
+  v2z_brick_dipole(NULL), v3z_brick_dipole(NULL), v4z_brick_dipole(NULL),
+  v5z_brick_dipole(NULL), work3(NULL), work4(NULL),
+  densityx_fft_dipole(NULL), densityy_fft_dipole(NULL),
   densityz_fft_dipole(NULL)
 {
   dipoleflag = 1;
@@ -534,10 +534,8 @@ void PPPMDipole::compute(int eflag, int vflag)
   // energy includes self-energy correction
 
   if (evflag_atom) {
-    double *q = atom->q;
     double **mu = atom->mu;
     int nlocal = atom->nlocal;
-    int ntotal = nlocal;
 
     if (eflag_atom) {
       for (i = 0; i < nlocal; i++) {
@@ -836,7 +834,7 @@ void PPPMDipole::set_grid_global()
     while (1) {
 
       // set grid dimension
-      
+
       nx_pppm = static_cast<int> (xprd/h_x);
       ny_pppm = static_cast<int> (yprd/h_y);
       nz_pppm = static_cast<int> (zprd_slab/h_z);
@@ -846,7 +844,7 @@ void PPPMDipole::set_grid_global()
       if (nz_pppm <= 1) nz_pppm = 2;
 
       // set local grid dimension
-      
+
       int npey_fft,npez_fft;
       if (nz_pppm >= nprocs) {
         npey_fft = 1;
@@ -926,11 +924,10 @@ double PPPMDipole::compute_qopt_dipole()
   const double unitkz = (MY_2PI/zprd_slab);
 
   double snx,sny,snz;
-  double cnx,cny,cnz;
   double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
   double sum1,sum2,dot1,dot2;
-  double numerator,denominator;
-  double u1,u2,u3,sqk;
+  double denominator;
+  double u1,sqk;
 
   int k,l,m,nx,ny,nz,kper,lper,mper;
 
@@ -943,22 +940,18 @@ double PPPMDipole::compute_qopt_dipole()
   for (m = nzlo_fft; m <= nzhi_fft; m++) {
     mper = m - nz_pppm*(2*m/nz_pppm);
     snz = square(sin(0.5*unitkz*mper*zprd_slab/nz_pppm));
-    cnz = cos(0.5*unitkz*mper*zprd_slab/nz_pppm);
 
     for (l = nylo_fft; l <= nyhi_fft; l++) {
       lper = l - ny_pppm*(2*l/ny_pppm);
       sny = square(sin(0.5*unitky*lper*yprd/ny_pppm));
-      cny = cos(0.5*unitky*lper*yprd/ny_pppm);
 
       for (k = nxlo_fft; k <= nxhi_fft; k++) {
         kper = k - nx_pppm*(2*k/nx_pppm);
         snx = square(sin(0.5*unitkx*kper*xprd/nx_pppm));
-        cnx = cos(0.5*unitkx*kper*xprd/nx_pppm);
 
         sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper);
 
         if (sqk != 0.0) {
-          numerator = MY_4PI/sqk;
           denominator = gf_denom(snx,sny,snz);
           sum1 = 0.0;
           sum2 = 0.0;
@@ -1021,10 +1014,9 @@ void PPPMDipole::compute_gf_dipole()
   const double unitkz = (MY_2PI/zprd_slab);
 
   double snx,sny,snz;
-  double cnx,cny,cnz;
   double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
   double sum1,dot1,dot2;
-  double numerator,denominator;
+  double denominator;
   double sqk;
 
   int k,l,m,n,nx,ny,nz,kper,lper,mper;
@@ -1044,22 +1036,18 @@ void PPPMDipole::compute_gf_dipole()
   for (m = nzlo_fft; m <= nzhi_fft; m++) {
     mper = m - nz_pppm*(2*m/nz_pppm);
     snz = square(sin(0.5*unitkz*mper*zprd_slab/nz_pppm));
-    cnz = cos(0.5*unitkz*mper*zprd_slab/nz_pppm);
 
     for (l = nylo_fft; l <= nyhi_fft; l++) {
       lper = l - ny_pppm*(2*l/ny_pppm);
       sny = square(sin(0.5*unitky*lper*yprd/ny_pppm));
-      cny = cos(0.5*unitky*lper*yprd/ny_pppm);
 
       for (k = nxlo_fft; k <= nxhi_fft; k++) {
         kper = k - nx_pppm*(2*k/nx_pppm);
         snx = square(sin(0.5*unitkx*kper*xprd/nx_pppm));
-        cnx = cos(0.5*unitkx*kper*xprd/nx_pppm);
 
         sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper);
 
         if (sqk != 0.0) {
-          numerator = MY_4PI/sqk;
           denominator = gf_denom(snx,sny,snz);
           sum1 = 0.0;
 
@@ -2389,12 +2377,10 @@ void PPPMDipole::slabcorr()
 {
   // compute local contribution to global dipole moment
 
-  double **x = atom->x;
-  double zprd = domain->zprd;
-  int nlocal = atom->nlocal;
-
   double dipole = 0.0;
   double **mu = atom->mu;
+  int nlocal = atom->nlocal;
+
   for (int i = 0; i < nlocal; i++) dipole += mu[i][2];
 
   // sum local contributions to get global dipole moment
@@ -2519,7 +2505,7 @@ double PPPMDipole::memory_usage()
   int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
     (nzhi_out-nzlo_out+1);
   bytes += 6 * nfft_both * sizeof(double);   // vg
-  bytes += nfft_both * sizeof(double); 	     // greensfn
+  bytes += nfft_both * sizeof(double);       // greensfn
   bytes += nfft_both*5 * sizeof(FFT_SCALAR); // work*2*2
   bytes += 9 * nbrick * sizeof(FFT_SCALAR);  // ubrick*3 + vdbrick*6
   bytes += nfft_both*7 * sizeof(FFT_SCALAR); // density_ffx*3 + work*2*2
diff --git a/src/KSPACE/pppm_dipole.h b/src/KSPACE/pppm_dipole.h
index d06919644b..a767f8b4c2 100644
--- a/src/KSPACE/pppm_dipole.h
+++ b/src/KSPACE/pppm_dipole.h
@@ -38,7 +38,7 @@ class PPPMDipole : public PPPM {
 
  protected:
   void set_grid_global();
-  double newton_raphson_f(); 
+  double newton_raphson_f();
 
   void allocate();
   void allocate_peratom();
diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp
index 9e9f07322c..7f7745eb3e 100644
--- a/src/KSPACE/pppm_dipole_spin.cpp
+++ b/src/KSPACE/pppm_dipole_spin.cpp
@@ -52,17 +52,17 @@ enum{FORWARD_MU,FORWARD_MU_PERATOM};
 
 /* ---------------------------------------------------------------------- */
 
-PPPMDipoleSpin::PPPMDipoleSpin(LAMMPS *lmp) : 
+PPPMDipoleSpin::PPPMDipoleSpin(LAMMPS *lmp) :
   PPPMDipole(lmp)
 {
   dipoleflag = 0;
   spinflag = 1;
-  
-  hbar = force->hplanck/MY_2PI;         	// eV/(rad.THz)
-  mub = 9.274e-4;                     		// in A.Ang^2
-  mu_0 = 785.15;               			// in eV/Ang/A^2
-  mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);	// in eV.Ang^3
-  mub2mu0hbinv = mub2mu0 / hbar;        	// in rad.THz
+
+  hbar = force->hplanck/MY_2PI;                 // eV/(rad.THz)
+  mub = 9.274e-4;                               // in A.Ang^2
+  mu_0 = 785.15;                                // in eV/Ang/A^2
+  mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);     // in eV.Ang^3
+  mub2mu0hbinv = mub2mu0 / hbar;                // in rad.THz
 }
 
 /* ----------------------------------------------------------------------
@@ -95,7 +95,7 @@ void PPPMDipoleSpin::init()
   // error check
 
   spinflag = atom->sp?1:0;
-  
+
   triclinic_check();
 
   if (triclinic != domain->triclinic)
@@ -146,8 +146,8 @@ void PPPMDipoleSpin::init()
 
   // kspace TIP4P not yet supported
   // qdist = offset only for TIP4P fictitious charge
-  
-  qdist = 0.0; 
+
+  qdist = 0.0;
   if (tip4pflag)
     error->all(FLERR,"Cannot yet use TIP4P with PPPMDipoleSpin");
 
@@ -177,7 +177,7 @@ void PPPMDipoleSpin::init()
 
   GridComm *cgtmp = NULL;
   int iteration = 0;
-    
+
   while (order >= minorder) {
     if (iteration && me == 0)
       error->warning(FLERR,"Reducing PPPMDipoleSpin order b/c stencil extends "
@@ -390,9 +390,9 @@ void PPPMDipoleSpin::compute(int eflag, int vflag)
 
     if (eflag_atom) {
       for (i = 0; i < nlocal; i++) {
-	spx = sp[i][0]*sp[i][3];
-	spy = sp[i][1]*sp[i][3];
-	spz = sp[i][2]*sp[i][3];
+        spx = sp[i][0]*sp[i][3];
+        spy = sp[i][1]*sp[i][3];
+        spz = sp[i][2]*sp[i][3];
         eatom[i] *= 0.5;
         eatom[i] -= (spx*spx + spy*spy + spz*spz)*2.0*g3/3.0/MY_PIS;
         eatom[i] *= spscale;
@@ -552,7 +552,7 @@ void PPPMDipoleSpin::fieldforce_ik_spin()
     f[i][2] += spfactor*(vxz*spx + vyz*spy + vzz*spz);
 
     // store long-range mag. precessions
-    
+
     const double spfactorh = mub2mu0hbinv * scale;
     fm_long[i][0] += spfactorh*ex;
     fm_long[i][1] += spfactorh*ey;
@@ -663,14 +663,12 @@ void PPPMDipoleSpin::slabcorr()
 {
   // compute local contribution to global spin moment
 
-  double **x = atom->x;
-  double zprd = domain->zprd;
-  int nlocal = atom->nlocal;
-
   double spin = 0.0;
   double **sp = atom->sp;
-  double spx,spy,spz;
-  for (int i = 0; i < nlocal; i++) { 
+  double spz;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++) {
     spz = sp[i][2]*sp[i][3];
     spin += spz;
   }
@@ -731,7 +729,7 @@ void PPPMDipoleSpin::spsum_spsq()
       spsqsum_local += spx*spx + spy*spy + spz*spz;
     }
 
-    // store results into pppm_dipole quantities 
+    // store results into pppm_dipole quantities
 
     MPI_Allreduce(&spsum_local,&musum,1,MPI_DOUBLE,MPI_SUM,world);
     MPI_Allreduce(&spsqsum_local,&musqsum,1,MPI_DOUBLE,MPI_SUM,world);
diff --git a/src/KSPACE/pppm_dipole_spin.h b/src/KSPACE/pppm_dipole_spin.h
index 2b4a989d5c..fe88fc75ce 100644
--- a/src/KSPACE/pppm_dipole_spin.h
+++ b/src/KSPACE/pppm_dipole_spin.h
@@ -32,8 +32,8 @@ class PPPMDipoleSpin : public PPPMDipole {
   void compute(int, int);
 
  protected:
-  double hbar;                  // reduced Planck's constant      
-  double mub;                   // Bohr's magneton                
+  double hbar;                  // reduced Planck's constant
+  double mub;                   // Bohr's magneton
   double mu_0;                  // vacuum permeability
   double mub2mu0;               // prefactor for mech force
   double mub2mu0hbinv;          // prefactor for mag force
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index c30d55dd68..0d0d4c7eb2 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -320,6 +320,8 @@ void PPPMDisp::init()
                mixflag == 1) && mixflag!= 2) { k = 1; break; }
           else if (ewald_mix==Pair::ARITHMETIC && mixflag!=2) { k = 2; break; }
           else if (mixflag == 2) { k = 3; break; }
+          else error->all(FLERR,"Unsupported mixing rule in kspace_style pppm/disp");
+          break;
         default:
           sprintf(str, "Unsupported order in kspace_style "
                   "pppm/disp, pair_style %s", force->pair_style);
diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp
index f664a0dca3..5a0ced3674 100644
--- a/src/KSPACE/pppm_tip4p.cpp
+++ b/src/KSPACE/pppm_tip4p.cpp
@@ -500,11 +500,18 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
     // since local atoms are in lambda coordinates, but ghosts are not.
 
     int *sametag = atom->sametag;
-    double xo[3],xh1[3],xh2[3];
+    double xo[3],xh1[3],xh2[3],xm[3];
+    const int nlocal = atom->nlocal;
 
-    domain->lamda2x(x[i],xo);
-    domain->lamda2x(x[iH1],xh1);
-    domain->lamda2x(x[iH2],xh2);
+    for (int ii = 0; ii < 3; ++ii) {
+      xo[ii] = x[i][ii];
+      xh1[ii] = x[iH1][ii];
+      xh2[ii] = x[iH2][ii];
+    }
+
+    if (i < nlocal) domain->lamda2x(x[i],xo);
+    if (iH1 < nlocal) domain->lamda2x(x[iH1],xh1);
+    if (iH2 < nlocal) domain->lamda2x(x[iH2],xh2);
 
     double delx = xo[0] - xh1[0];
     double dely = xo[1] - xh1[1];
@@ -513,6 +520,8 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
     double rsq;
     int closest = iH1;
 
+    // no need to run lamda2x() here -> ghost atoms
+
     while (sametag[iH1] >= 0) {
       iH1 = sametag[iH1];
       delx = xo[0] - x[iH1][0];
@@ -561,13 +570,13 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
     double dely2 = xh2[1] - xo[1];
     double delz2 = xh2[2] - xo[2];
 
-    xM[0] = xo[0] + alpha * 0.5 * (delx1 + delx2);
-    xM[1] = xo[1] + alpha * 0.5 * (dely1 + dely2);
-    xM[2] = xo[2] + alpha * 0.5 * (delz1 + delz2);
+    xm[0] = xo[0] + alpha * 0.5 * (delx1 + delx2);
+    xm[1] = xo[1] + alpha * 0.5 * (dely1 + dely2);
+    xm[2] = xo[2] + alpha * 0.5 * (delz1 + delz2);
 
     // ... and convert M to lamda space for PPPM
 
-    domain->x2lamda(xM,xM);
+    domain->x2lamda(xm,xM);
 
   } else {
 
diff --git a/src/MAKE/MACHINES/Makefile.stampede b/src/MAKE/MACHINES/Makefile.stampede
index 69da22c9c9..ecd0810d1d 100644
--- a/src/MAKE/MACHINES/Makefile.stampede
+++ b/src/MAKE/MACHINES/Makefile.stampede
@@ -6,13 +6,13 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		mpicc -openmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64
-MIC_OPT =       -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
-CCFLAGS =	-O3 -xhost -fp-model precise -restrict -override-limits $(MIC_OPT)
+CC =		mpicc -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64
+MIC_OPT =       -qoffload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
+CCFLAGS =	-O3 -xhost -fp-model precise -restrict -qoverride-limits $(MIC_OPT)
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpicc -openmp
+LINK =		mpicc -qopenmp
 LINKFLAGS =	-O3 -xhost
 LIB =           -ltbbmalloc
 SIZE =		size
diff --git a/src/MAKE/Makefile.mpi b/src/MAKE/Makefile.mpi
index f30220da3d..3be2e20f95 100644
--- a/src/MAKE/Makefile.mpi
+++ b/src/MAKE/Makefile.mpi
@@ -26,12 +26,12 @@ SHLIBFLAGS =	-shared
 # if you change any -D setting, do full re-compile after "make clean"
 
 # LAMMPS ifdef settings
-# see possible settings in Section 2.2 (step 4) of manual
+# see possible settings in Section 3.5 of the manual
 
-LMP_INC =	-DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64
+LMP_INC =	-DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64  # -DLAMMPS_CXX98
 
 # MPI library
-# see discussion in Section 2.2 (step 5) of manual
+# see discussion in Section 3.4 of the manual
 # MPI wrapper compiler/linker can provide this info
 # can point to dummy MPI library in src/STUBS as in Makefile.serial
 # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
diff --git a/src/MAKE/Makefile.serial b/src/MAKE/Makefile.serial
index 5954d97761..86ddd05053 100644
--- a/src/MAKE/Makefile.serial
+++ b/src/MAKE/Makefile.serial
@@ -26,12 +26,12 @@ SHLIBFLAGS =	-shared
 # if you change any -D setting, do full re-compile after "make clean"
 
 # LAMMPS ifdef settings
-# see possible settings in Section 2.2 (step 4) of manual
+# see possible settings in Section 3.5 of the manual
 
-LMP_INC =	-DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64
+LMP_INC =	-DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64  # -DLAMMPS_CXX98
 
 # MPI library
-# see discussion in Section 2.2 (step 5) of manual
+# see discussion in Section 3.4 of the manual
 # MPI wrapper compiler/linker can provide this info
 # can point to dummy MPI library in src/STUBS as in Makefile.serial
 # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
diff --git a/src/MAKE/OPTIONS/Makefile.intel_coprocessor b/src/MAKE/OPTIONS/Makefile.intel_coprocessor
index 75e4d89170..44f5c99f70 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_coprocessor
+++ b/src/MAKE/OPTIONS/Makefile.intel_coprocessor
@@ -6,7 +6,7 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		mpiicpc 
+CC =		mpiicpc -std=c++11
 MIC_OPT =       -qoffload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
 CCFLAGS =	-g -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \
                 -xHost -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT \
@@ -14,7 +14,7 @@ CCFLAGS =	-g -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpiicpc
+LINK =		mpiicpc -std=c++11
 LINKFLAGS =	-g -O3 -xHost -qopenmp -qoffload
 LIB =           -ltbbmalloc
 SIZE =		size
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu b/src/MAKE/OPTIONS/Makefile.intel_cpu
index f8e5eb3797..f52b4f3029 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu
@@ -6,16 +6,16 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		mpiicpc 
+CC =		mpiicpc -std=c++11
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
                 -qopt-zmm-usage=high
-CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
+CCFLAGS =	-qopenmp -qno-offload -ansi-alias -restrict \
                 -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
                 -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpiicpc
+LINK =		mpiicpc -std=c++11
 LINKFLAGS =	-qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
 LIB =           -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
 SIZE =		size
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
index 2c363cb2bf..07d720a592 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
@@ -6,16 +6,16 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		mpiicpc 
+CC =		mpiicpc -std=c++11
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
                 -qopt-zmm-usage=high
-CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
+CCFLAGS =	-qopenmp -qno-offload -ansi-alias -restrict \
                 -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
                 -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpiicpc
+LINK =		mpiicpc -std=c++11
 LINKFLAGS =	-qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
 LIB =           -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core	
 SIZE =		size
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
index a0730f3402..51cf975e5c 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
@@ -6,16 +6,16 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		mpicxx -cxx=icc
+CC =		mpicxx -cxx=icc -std=c++11
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
                 -qopt-zmm-usage=high
-CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
+CCFLAGS =	-qopenmp -qno-offload -ansi-alias -restrict \
                 -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
                 -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpicxx -cxx=icc
+LINK =		mpicxx -cxx=icc -std=c++11
 LINKFLAGS =	-qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
 LIB =           -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
 SIZE =		size
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
index 2e73bb2890..342637a460 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
@@ -7,16 +7,16 @@ SHELL = /bin/sh
 # specify flags and libraries needed for your compiler
 
 export OMPI_CXX = icc
-CC =		mpicxx
+CC =		mpicxx -std=c++11
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
                 -qopt-zmm-usage=high
-CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
+CCFLAGS =	-qopenmp -qno-offload -ansi-alias -restrict \
                 -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
                 -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpicxx
+LINK =		mpicxx -std=c++11
 LINKFLAGS =	-qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
 LIB =           -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
 SIZE =		size
diff --git a/src/MAKE/OPTIONS/Makefile.knl b/src/MAKE/OPTIONS/Makefile.knl
index cf7a3f8103..ab1b756a67 100644
--- a/src/MAKE/OPTIONS/Makefile.knl
+++ b/src/MAKE/OPTIONS/Makefile.knl
@@ -6,17 +6,17 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		mpiicpc
+CC =		mpiicpc -std=c++11
 OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
+CCFLAGS =	-qopenmp -qno-offload -ansi-alias -restrict \
                 -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
                 -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpiicpc
-LINKFLAGS =	-qopenmp $(OPTFLAGS)
-LIB =           -ltbbmalloc
+LINK =		mpiicpc -std=c++11
+LINKFLAGS =	-qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
+LIB =           -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
 SIZE =		size
 
 ARCHIVE =	ar
@@ -55,8 +55,7 @@ MPI_LIB =
 
 FFT_INC =       -DFFT_MKL -DFFT_SINGLE
 FFT_PATH = 
-FFT_LIB =       -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \
-                -lmkl_sequential -lmkl_core	
+FFT_LIB =
 
 # JPEG and/or PNG library
 # see discussion in Section 2.2 (step 7) of manual
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index fcc3a3efd2..1d9dd18887 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -3391,8 +3391,8 @@ void PairAIREBO::read_file(char *filename)
 
     // skip initial comment line and check for potential file style identifier comment
 
-    fgets(s,MAXLINE,fp);
-    fgets(s,MAXLINE,fp);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
 
     if (((variant == AIREBO) && (strncmp(s,"# AIREBO ",9) != 0))
         || ((variant == REBO_2) && (strncmp(s,"# REBO2 ",8) != 0))
@@ -3638,9 +3638,9 @@ void PairAIREBO::read_file(char *filename)
       utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       if (1 != sscanf(s,"%lg",&reqM_HH)) ++cerror;
     }
-    
+
   }
-  
+
   // check for errors parsing global parameters
 
   MPI_Bcast(&cerror,1,MPI_INT,0,world);
@@ -3654,7 +3654,7 @@ void PairAIREBO::read_file(char *filename)
   cerror = numpar = 0;
 
   if (me == 0) {
-    
+
     // gC spline
 
     utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
@@ -3899,7 +3899,7 @@ void PairAIREBO::read_file(char *filename)
 
     fclose(fp);
   }
-  
+
   // check for errors parsing spline data
 
   MPI_Bcast(&cerror,1,MPI_INT,0,world);
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index e604f44003..e943b6bfdd 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -27,6 +27,7 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "neighbor.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -310,10 +311,10 @@ void PairATM::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) for (k = j; k <= atom->ntypes; k++) {
-        if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp);
+          if (me == 0) utils::sfread(FLERR,&nu[i][j][k],sizeof(double),1,fp,NULL,error);
         MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world);
       }
     }
@@ -338,8 +339,8 @@ void PairATM::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&cut_triple,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_triple,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_triple,1,MPI_DOUBLE,0,world);
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 6b7468558e..1b08e4b88d 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -45,6 +45,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -61,6 +62,10 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
   manybody_flag = 1;
   ghostneigh = 1;
 
+  BOP_index = NULL;
+  BOP_index3 = NULL;
+  BOP_total = NULL;
+  BOP_total3 = NULL;
   map = NULL;
   pi_a = NULL;
   pro_delta = NULL;
@@ -102,6 +107,8 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
   rij = NULL;
   neigh_index = NULL;
   neigh_index3 = NULL;
+  neigh_flag = NULL;
+  neigh_flag3 = NULL;
   cosAng = NULL;
   betaS = NULL;
   dBetaS = NULL;
@@ -4976,13 +4983,13 @@ void PairBOP::read_table(char *filename)
       snprintf(str,128,"Cannot open BOP potential file %s",filename);
       error->one(FLERR,str);
     }
-    fgets(s,MAXLINE,fp);  // skip first comment line
-    fgets(s,MAXLINE,fp);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);  // skip first comment line
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
     sscanf(s,"%d",&bop_types);
     elements = new char*[bop_types];
     for(i=0;i<bop_types;i++) elements[i]=NULL;
     for(i=0;i<bop_types;i++) {
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       nws=0;
       ws=1;
       for(j=0;j<(int)strlen(s);j++) {
@@ -5011,7 +5018,7 @@ void PairBOP::read_table(char *filename)
     }
     nws=0;
     ws=1;
-    fgets(s,MAXLINE,fp);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
     for(j=0;j<(int)strlen(s);j++) {
       if(ws==1) {
         if(isspace(s[j])) {
@@ -5079,28 +5086,28 @@ void PairBOP::read_table(char *filename)
       snprintf(str,128,"Cannot open BOP potential file %s",filename);
       error->one(FLERR,str);
     }
-    fgets(s,MAXLINE,fp);  // skip first comment line
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);  // skip first comment line
     for(i=0;i<bop_types+2;i++) {
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
     }
-    fgets(s,MAXLINE,fp);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
     sscanf(s,"%lf%lf%lf%lf%lf%lf%lf",&small1,&small2,&small3g
         ,&small4,&small5,&small6,&small7);
     for(i=0;i<bop_types;i++) {
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       sscanf(s,"%lf",&pi_p[i]);
     }
     cutmax=0;
     for(i=0;i<npairs;i++) {
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       sscanf(s,"%lf",&rcut[i]);
       if(rcut[i]>cutmax)
         cutmax=rcut[i];
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       sscanf(s,"%lf%lf%lf%lf",&sigma_c[i],&sigma_a[i],&pi_c[i],&pi_a[i]);
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]);
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
     }
     if(nws==3) {
@@ -5109,56 +5116,56 @@ void PairBOP::read_table(char *filename)
           for(k=j;k<bop_types;k++) {
             if(npower<=2) {
               for(m=0;m<ntheta;m++) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gfunc[j][i][k][n],&gfunc[j][i][k][n+1]
                     ,&gfunc[j][i][k][n+2],&gfunc[j][i][k][n+3],&gfunc[j][i][k][n+4]);
                 n+=4;
               }
             } else {
               if(npower==3) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3]);
               }
               else if(npower==4) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
               }
               else if(npower==5) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf",&gpara[j][i][k][5]);
               }
               else if(npower==6) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6]);
               }
               else if(npower==7) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7]);
               }
               else if(npower==8) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8]);
               }
               else if(npower==9) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
               }
               else if(npower==10) {
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
-                fgets(s,MAXLINE,fp);
+                utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
                 sscanf(s,"%lf",&gpara[j][i][k][10]);
               }
             }
@@ -5167,14 +5174,14 @@ void PairBOP::read_table(char *filename)
       for(i=0;i<bop_types;i++)
         for(j=0;j<bop_types;j++)
           for(k=0;k<bop_types;k++) {
-            fgets(s,MAXLINE,fp);
+            utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
             sscanf(s,"%lf%lf%lf",&gpara[i][j][k][0],&gpara[i][j][k][1],&gpara[i][j][k][2]);
             gpara[j][i][k][3]=0;
           }
     }
     for(i=0;i<npairs;i++) {
       for(j=0;j<nr;j++) {
-        fgets(s,MAXLINE,fp);
+        utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
         sscanf(s,"%lf%lf%lf%lf%lf",&pRepul[i][j],&pRepul[i][j+1]
             ,&pRepul[i][j+2],&pRepul[i][j+3],&pRepul[i][j+4]);
         j+=4;
@@ -5182,7 +5189,7 @@ void PairBOP::read_table(char *filename)
     }
     for(i=0;i<npairs;i++) {
       for(j=0;j<nr;j++) {
-        fgets(s,MAXLINE,fp);
+        utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
         sscanf(s,"%lf%lf%lf%lf%lf",&pBetaS[i][j],&pBetaS[i][j+1]
             ,&pBetaS[i][j+2],&pBetaS[i][j+3],&pBetaS[i][j+4]);
         j+=4;
@@ -5190,7 +5197,7 @@ void PairBOP::read_table(char *filename)
     }
     for(i=0;i<npairs;i++) {
       for(j=0;j<nr;j++) {
-        fgets(s,MAXLINE,fp);
+        utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
         sscanf(s,"%lf%lf%lf%lf%lf",&pBetaP[i][j],&pBetaP[i][j+1]
             ,&pBetaP[i][j+2],&pBetaP[i][j+3],&pBetaP[i][j+4]);
         j+=4;
@@ -5198,18 +5205,18 @@ void PairBOP::read_table(char *filename)
     }
     for(i=0;i<npairs;i++) {
       for(j=0;j<nBOt;j++) {
-        fgets(s,MAXLINE,fp);
+        utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
         sscanf(s,"%lf%lf%lf%lf%lf",&FsigBO[i][j],&FsigBO[i][j+1]
             ,&FsigBO[i][j+2],&FsigBO[i][j+3],&FsigBO[i][j+4]);
         j+=4;
       }
     }
     for(i=0;i<bop_types;i++) {
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       sscanf(s,"%lf",&pro_delta[i]);
     }
     for(i=0;i<bop_types;i++) {
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       sscanf(s,"%lf",&pro[i]);
     }
     for(i=0;i<npairs;i++) {
@@ -5226,7 +5233,7 @@ void PairBOP::read_table(char *filename)
       if(pass==1) {
         for(i=0;i<npairs;i++) {
           for(j=0;j<nr;j++) {
-            fgets(s,MAXLINE,fp);
+            utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
             sscanf(s,"%lf%lf%lf%lf%lf",&pLong[i][j],&pLong[i][j+1]
                 ,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
             j+=4;
@@ -5798,6 +5805,12 @@ void PairBOP::memory_theta_destroy()
   memory->destroy(neigh_flag3);
   memory->destroy(neigh_index);
   memory->destroy(neigh_index3);
+  itypeSigBk = NULL;
+  itypePiBk = NULL;
+  neigh_flag = NULL;
+  neigh_flag3 = NULL;
+  neigh_index = NULL;
+  neigh_index3 = NULL;
   if(otfly==0) {
     memory->destroy(cosAng);
     memory->destroy(dcAng);
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 6f1732dbb7..bf66ea550a 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -33,6 +33,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -319,12 +320,13 @@ void PairComb3::read_lib()
   // open libraray file on proc 0
 
   if (comm->me == 0) {
-    FILE *fp = force->open_potential("lib.comb3");
+    const char filename[] = "lib.comb3";
+    FILE *fp = force->open_potential(filename);
     if (fp == NULL) error->one(FLERR,"Cannot open COMB3 lib.comb3 file");
 
     // read and store at the same time
-    fgets(s,MAXLIB,fp);
-    fgets(s,MAXLIB,fp);
+    utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
+    utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
     nwords = 0;
     words[nwords++] = strtok(s," \t\n\r\f");
     while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -335,7 +337,7 @@ void PairComb3::read_lib()
     ccutoff[4] = atof(words[4]);
     ccutoff[5] = atof(words[5]);
 
-    fgets(s,MAXLIB,fp);
+    utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
     nwords = 0;
     words[nwords++] = strtok(s," \t\n\r\f");
     while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -347,7 +349,7 @@ void PairComb3::read_lib()
     ch_a[5] = atof(words[5]);
     ch_a[6] = atof(words[6]);
 
-    fgets(s,MAXLIB,fp);
+    utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
     nwords = 0;
     words[nwords++] = strtok(s," \t\n\r\f");
     while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -355,7 +357,7 @@ void PairComb3::read_lib()
     nsplrad = atoi(words[1]);
     nspltor = atoi(words[2]);
 
-    fgets(s,MAXLIB,fp);
+    utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
     nwords = 0;
     words[nwords++] = strtok(s," \t\n\r\f");
     while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -363,7 +365,7 @@ void PairComb3::read_lib()
     maxy = atoi(words[1]);
     maxz = atoi(words[2]);
 
-    fgets(s,MAXLIB,fp);
+    utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
     nwords = 0;
     words[nwords++] = strtok(s," \t\n\r\f");
     while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -372,7 +374,7 @@ void PairComb3::read_lib()
     maxconj = atoi(words[2]);
 
     for (l=0; l<nsplpcn; l++) {
-      fgets(s,MAXLIB,fp);
+      utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
       nwords = 0;
       words[nwords++] = strtok(s," \t\n\r\f");
       while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -381,14 +383,14 @@ void PairComb3::read_lib()
       dvmaxxcn[l] = atof(words[3]);
     }
 
-    fgets(s,MAXLIB,fp);
+    utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
     nwords = 0;
     words[nwords++] = strtok(s," \t\n\r\f");
     while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
     ntab = atoi(words[0]);
 
     for (i=0; i<ntab+1; i++){
-      fgets(s,MAXLIB,fp);
+      utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
       nwords = 0;
       words[nwords++] = strtok(s," \t\n\r\f");
       while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -401,7 +403,7 @@ void PairComb3::read_lib()
       for (i=0; i<maxx+1; i++)
         for (j=0; j<maxy+1; j++)
           for (k=0; k<maxz+1; k++) {
-            fgets(s,MAXLIB,fp);
+            utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
             nwords = 0;
             words[nwords++] = strtok(s," \t\n\r\f");
             while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -419,7 +421,7 @@ void PairComb3::read_lib()
       for (i=0; i<maxx; i++)
         for (j=0; j<maxy; j++)
           for (k=0; k<maxz; k++) {
-            fgets(s,MAXLIB,fp);
+            utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
             nwords = 0;
             words[nwords++] = strtok(s," \t\n\r\f");
             while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -428,7 +430,7 @@ void PairComb3::read_lib()
            jj = atoi(words[2]);
            kk = atoi(words[3]);
            for(iii=0; iii<2; iii++) {
-             fgets(s,MAXLIB,fp);
+             utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
              nwords = 0;
              words[nwords++] = strtok(s," \t\n\r\f");
              while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -443,7 +445,7 @@ void PairComb3::read_lib()
       for (i=0; i<maxxc+1; i++)
         for (j=0; j<maxyc+1; j++)
           for (k=0; k<maxconj; k++) {
-            fgets(s,MAXLIB,fp);
+            utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
             nwords = 0;
             words[nwords++] = strtok(s," \t\n\r\f");
             while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -461,7 +463,7 @@ void PairComb3::read_lib()
       for (i=0; i<maxxc; i++)
         for (j=0; j<maxyc; j++)
           for (k=0; k<maxconj-1; k++) {
-            fgets(s,MAXLIB,fp);
+            utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
             nwords = 0;
             words[nwords++] = strtok(s," \t\n\r\f");
             while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -470,7 +472,7 @@ void PairComb3::read_lib()
             jj = atoi(words[2]);
             kk = atoi(words[3])-1;
             for (iii=0; iii<2; iii++) {
-              fgets(s,MAXLIB,fp);
+              utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
               nwords = 0;
               words[nwords++] = strtok(s," \t\n\r\f");
               while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -485,7 +487,7 @@ void PairComb3::read_lib()
       for (i=0; i<maxxc+1; i++)
         for (j=0; j<maxyc+1; j++)
           for (k=0; k<maxconj; k++) {
-            fgets(s,MAXLIB,fp);
+            utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
             nwords = 0;
             words[nwords++] = strtok(s," \t\n\r\f");
             while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -503,7 +505,7 @@ void PairComb3::read_lib()
       for (i=0; i<maxxc; i++)
         for (j=0; j<maxyc; j++)
           for (k=0; k<maxconj-1; k++) {
-            fgets(s,MAXLIB,fp);
+            utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
             nwords = 0;
             words[nwords++] = strtok(s," \t\n\r\f");
             while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -512,7 +514,7 @@ void PairComb3::read_lib()
             jj = atoi(words[2]);
             kk = atoi(words[3])-1;
             for(iii=0; iii<2; iii++) {
-              fgets(s,MAXLIB,fp);
+              utils::sfgets(FLERR,s,MAXLIB,fp,filename,error);
               nwords = 0;
               words[nwords++] = strtok(s," \t\n\r\f");
               while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index acb0e654d8..5459a92b69 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -27,6 +27,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -42,6 +43,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
   nmax = 0;
   rho = NULL;
   fp = NULL;
+  numforce = NULL;
   map = NULL;
   type2frho = NULL;
 
@@ -76,6 +78,7 @@ PairEAM::~PairEAM()
 
   memory->destroy(rho);
   memory->destroy(fp);
+  memory->destroy(numforce);
 
   if (allocated) {
     memory->destroy(setflag);
@@ -150,9 +153,11 @@ void PairEAM::compute(int eflag, int vflag)
   if (atom->nmax > nmax) {
     memory->destroy(rho);
     memory->destroy(fp);
+    memory->destroy(numforce);
     nmax = atom->nmax;
     memory->create(rho,nmax,"pair:rho");
     memory->create(fp,nmax,"pair:fp");
+    memory->create(numforce,nmax,"pair:numforce");
   }
 
   double **x = atom->x;
@@ -254,6 +259,7 @@ void PairEAM::compute(int eflag, int vflag)
 
     jlist = firstneigh[i];
     jnum = numneigh[i];
+    numforce[i] = 0;
 
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
@@ -265,6 +271,7 @@ void PairEAM::compute(int eflag, int vflag)
       rsq = delx*delx + dely*dely + delz*delz;
 
       if (rsq < cutforcesq) {
+        ++numforce[i];
         jtype = type[j];
         r = sqrt(rsq);
         p = r*rdr + 1.0;
@@ -466,10 +473,10 @@ void PairEAM::read_file(char *filename)
 
   int tmp,nwords;
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     sscanf(line,"%d %lg",&tmp,&file->mass);
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     nwords = sscanf(line,"%d %lg %d %lg %lg",
            &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
@@ -784,7 +791,7 @@ void PairEAM::grab(FILE *fptr, int n, double *list)
 
   int i = 0;
   while (i < n) {
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
     ptr = strtok(line," \t\n\r\f");
     list[i++] = atof(ptr);
     while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr);
@@ -801,6 +808,18 @@ double PairEAM::single(int i, int j, int itype, int jtype,
   double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
   double *coeff;
 
+  if (numforce[i] > 0) {
+    p = rho[i]*rdrho + 1.0;
+    m = static_cast<int> (p);
+    m = MAX(1,MIN(m,nrho-1));
+    p -= m;
+    p = MIN(p,1.0);
+    coeff = frho_spline[type2frho[itype]][m];
+    phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
+    if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
+    phi *= 1.0/static_cast<double>(numforce[i]);
+  } else phi = 0.0;
+
   r = sqrt(rsq);
   p = r*rdr + 1.0;
   m = static_cast<int> (p);
@@ -817,7 +836,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
   z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
 
   recip = 1.0/r;
-  phi = z2*recip;
+  phi += z2*recip;
   phip = z2p*recip - phi*recip;
   psip = fp[i]*rhojp + fp[j]*rhoip + phip;
   fforce = -psip*recip;
diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h
index 8bcb44c347..add33ab3f0 100644
--- a/src/MANYBODY/pair_eam.h
+++ b/src/MANYBODY/pair_eam.h
@@ -70,6 +70,7 @@ class PairEAM : public Pair {
   // per-atom arrays
 
   double *rho,*fp;
+  int *numforce;
 
   // potentials as file data
 
diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp
index 5b7f9877d7..a9622f9e07 100644
--- a/src/MANYBODY/pair_eam_alloy.cpp
+++ b/src/MANYBODY/pair_eam_alloy.cpp
@@ -23,6 +23,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -136,10 +137,10 @@ void PairEAMAlloy::read_file(char *filename)
 
   int n;
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     n = strlen(line) + 1;
   }
   MPI_Bcast(&n,1,MPI_INT,0,world);
@@ -164,7 +165,7 @@ void PairEAMAlloy::read_file(char *filename)
   delete [] words;
 
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     nwords = sscanf(line,"%d %lg %d %lg %lg",
            &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
@@ -188,7 +189,7 @@ void PairEAMAlloy::read_file(char *filename)
   int i,j,tmp;
   for (i = 0; i < file->nelements; i++) {
     if (me == 0) {
-      fgets(line,MAXLINE,fptr);
+      utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
       sscanf(line,"%d %lg",&tmp,&file->mass[i]);
     }
     MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp
index 7e00783922..c91e7b5298 100644
--- a/src/MANYBODY/pair_eam_fs.cpp
+++ b/src/MANYBODY/pair_eam_fs.cpp
@@ -23,6 +23,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -136,10 +137,10 @@ void PairEAMFS::read_file(char *filename)
 
   int n;
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     n = strlen(line) + 1;
   }
   MPI_Bcast(&n,1,MPI_INT,0,world);
@@ -164,7 +165,7 @@ void PairEAMFS::read_file(char *filename)
   delete [] words;
 
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     nwords = sscanf(line,"%d %lg %d %lg %lg",
            &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
@@ -190,7 +191,7 @@ void PairEAMFS::read_file(char *filename)
   int i,j,tmp;
   for (i = 0; i < file->nelements; i++) {
     if (me == 0) {
-      fgets(line,MAXLINE,fptr);
+      utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
       sscanf(line,"%d %lg",&tmp,&file->mass[i]);
     }
     MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index dd65d92cdd..dc1c7fa019 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -26,6 +26,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -966,11 +967,11 @@ int PairEIM::grabpair(FILE *fptr, int i, int j)
           sscanf(data,"%lg %lg %lg %lg %lg",
             &setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
             &setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
-          fgets(line,MAXLINE,fptr);
+          utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
           sscanf(line,"%lg %lg %lg %lg %lg",
             &setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
             &setfl->rq[ij],&setfl->rcutsigma[ij]);
-          fgets(line,MAXLINE,fptr);
+          utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
           sscanf(line,"%lg %lg %lg %d",
             &setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
             &setfl->tp[ij]);
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index 873a675cd9..cc97fd9e9b 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -29,6 +29,7 @@
 #include "my_page.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -978,43 +979,43 @@ void PairLCBOP::read_file(char *filename)
     // skip initial comment lines
 
     while (1) {
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       if (s[0] != '#') break;
     }
 
     // read parameters
 
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&r_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&r_2);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&gamma_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&A);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&B_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&B_2);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&alpha);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&beta_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&beta_2);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&d);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&C_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&C_4);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&C_6);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&L);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&kappa);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&R_0);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&R_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&r_0);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&r_1_LR);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&r_2_LR);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&v_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&v_2);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&eps_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&eps_2);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&lambda_1);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&lambda_2);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&eps);
-    fgets(s,MAXLINE,fp);    sscanf(s,"%lg",&delta);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&r_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&r_2);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&gamma_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&A);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&B_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&B_2);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&alpha);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&beta_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&beta_2);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&d);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&C_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&C_4);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&C_6);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&L);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&kappa);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&R_0);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&R_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&r_0);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&r_1_LR);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&r_2_LR);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&v_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&v_2);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&eps_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&eps_2);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&lambda_1);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&lambda_2);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&eps);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);    sscanf(s,"%lg",&delta);
 
     while (1) {
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       if (s[0] != '#') break;
     }
 
@@ -1023,27 +1024,27 @@ void PairLCBOP::read_file(char *filename)
     for (k = 0; k < 2; k++) { // 2 values of N_ij_conj
       for (l = 0; l < 3; l++) { // 3 types of data: f, dfdx, dfdy
         for (i = 0; i < 4; i++) { // 4x4 matrix
-          fgets(s,MAXLINE,fp);
+          utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
           sscanf(s,"%lg %lg %lg %lg",
             &F_conj_data[i][0][k][l],
             &F_conj_data[i][1][k][l],
             &F_conj_data[i][2][k][l],
             &F_conj_data[i][3][k][l]);
         }
-        while (1) { fgets(s,MAXLINE,fp); if (s[0] != '#') break; }
+        while (1) { utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (s[0] != '#') break; }
       }
     }
 
     // G spline
 
     // x coordinates of mesh points
-    fgets(s,MAXLINE,fp);
+    utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
     sscanf( s,"%lg %lg %lg %lg %lg %lg",
       &gX[0], &gX[1], &gX[2],
       &gX[3], &gX[4], &gX[5] );
 
     for (i = 0; i < 6; i++) { // for each power in polynomial
-      fgets(s,MAXLINE,fp);
+      utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
       sscanf( s,"%lg %lg %lg %lg %lg",
         &gC[i][0], &gC[i][1], &gC[i][2],
         &gC[i][3], &gC[i][4] );
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index d3964b292c..8db4d63d4c 100644
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -29,6 +29,7 @@
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -573,8 +574,8 @@ void PairPolymorphic::read_file(char *file)
       error->one(FLERR,str);
     }
     // move past comments to first data line
-    fgets(line,MAXLINE,fp);
-    while (line == strchr(line,'#')) fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
+    while (line == strchr(line,'#')) utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
     n = strlen(line) + 1;
   }
   MPI_Bcast(&n,1,MPI_INT,0,world);
@@ -590,7 +591,7 @@ void PairPolymorphic::read_file(char *file)
   // map the elements in the potential file to LAMMPS atom types
   for (int i = 0; i < nelements; i++) {
     if (comm->me == 0) {
-      fgets(line,MAXLINE,fp);
+      utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
       n = strlen(line) + 1;
     }
     MPI_Bcast(&n,1,MPI_INT,0,world);
@@ -608,7 +609,7 @@ void PairPolymorphic::read_file(char *file)
   }
   // sizes
   if (comm->me == 0) {
-    fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
     n = strlen(line) + 1;
   }
 
@@ -644,7 +645,7 @@ void PairPolymorphic::read_file(char *file)
   for (int i = 0; i < npair; i++) {
     PairParameters & p = pairParameters[i];
     if (comm->me == 0) {
-      fgets(line,MAXLINE,fp);
+      utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
       n = strlen(line) + 1;
     }
     MPI_Bcast(&n,1,MPI_INT,0,world);
@@ -875,7 +876,7 @@ void PairPolymorphic::grab(FILE *fp, int n, double *list)
 
   int i = 0;
   while (i < n) {
-    fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
     ptr = strtok(line," \t\n\r\f");
     list[i++] = atof(ptr);
     while ((ptr = strtok(NULL," \t\n\r\f")))
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 2ff0e4126f..2e8200f751 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -33,7 +33,8 @@ using namespace FixConst;
 
 FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL), broken(NULL), copy(NULL), random(NULL)
+  partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL),
+  broken(NULL), copy(NULL), random(NULL)
 {
   if (narg < 6) error->all(FLERR,"Illegal fix bond/break command");
 
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 3f63a22d60..629e6defff 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -18,6 +18,7 @@
 #include "respa.h"
 #include "atom.h"
 #include "force.h"
+#include "modify.h"
 #include "pair.h"
 #include "comm.h"
 #include "neighbor.h"
@@ -216,6 +217,19 @@ void FixBondCreate::init()
   if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
     error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
 
+  // warn if more than one fix bond/create or also a fix bond/break
+  // because this fix stores per-atom state in bondcount
+  //   if other fixes create/break bonds, this fix will not know about it
+
+  int count = 0;
+  for (int i = 0; i < modify->nfix; i++) {
+    if (strcmp(modify->fix[i]->style,"bond/create") == 0) count++;
+    if (strcmp(modify->fix[i]->style,"bond/break") == 0) count++;
+  }
+  if (count > 1 && me == 0)
+    error->warning(FLERR,"Fix bond/create is used multiple times "
+                   " or with fix bond/break - may not work as expected");
+
   // enable angle/dihedral/improper creation if atype/dtype/itype
   //   option was used and a force field has been specified
 
diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h
index 403b1ae340..1e4b9a11c1 100644
--- a/src/MC/fix_bond_create.h
+++ b/src/MC/fix_bond_create.h
@@ -170,4 +170,11 @@ See the read_data command for info on setting the "extra special per
 atom" header value to allow for additional special values to be
 stored.
 
+W: Fix bond/create is used multiple times or with fix bond/break - may not work as expected
+
+When using fix bond/create multiple times or in combination with
+fix bond/break, the individual fix instances do not share information
+about changes they made at the same time step and thus it may result
+in unexpected behavior.
+
 */
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 1050fd4712..732e76b77e 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -268,6 +268,8 @@ void FixGCMC::options(int narg, char **arg)
   tfac_insert = 1.0;
   overlap_cutoffsq = 0.0;
   overlap_flag = 0;
+  min_ngas = -1;
+  max_ngas = INT_MAX;
 
   int iarg = 0;
   while (iarg < narg) {
@@ -387,6 +389,14 @@ void FixGCMC::options(int narg, char **arg)
       overlap_cutoffsq = rtmp*rtmp;
       overlap_flag = 1;
       iarg += 2;
+    } else if (strcmp(arg[iarg],"min") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
+      min_ngas = force->numeric(FLERR,arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"max") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
+      max_ngas = force->numeric(FLERR,arg[iarg+1]);
+      iarg += 2;
     } else error->all(FLERR,"Illegal fix gcmc command");
   }
 }
@@ -893,7 +903,7 @@ void FixGCMC::attempt_atomic_deletion()
 {
   ndeletion_attempts += 1.0;
 
-  if (ngas == 0) return;
+  if (ngas == 0 || ngas <= min_ngas) return;
 
   int i = pick_random_gas_atom();
 
@@ -934,6 +944,8 @@ void FixGCMC::attempt_atomic_insertion()
 
   ninsertion_attempts += 1.0;
 
+  if (ngas >= max_ngas) return;
+
   // pick coordinates for insertion point
 
   double coord[3];
@@ -1248,7 +1260,7 @@ void FixGCMC::attempt_molecule_deletion()
 {
   ndeletion_attempts += 1.0;
 
-  if (ngas == 0) return;
+  if (ngas == 0 || ngas <= min_ngas) return;
 
   // work-around to avoid n=0 problem with fix rigid/nvt/small
 
@@ -1287,6 +1299,8 @@ void FixGCMC::attempt_molecule_insertion()
   double lamda[3];
   ninsertion_attempts += 1.0;
 
+  if (ngas >= max_ngas) return;
+
   double com_coord[3];
   if (regionflag) {
     int region_attempt = 0;
@@ -1570,7 +1584,7 @@ void FixGCMC::attempt_atomic_deletion_full()
 
   ndeletion_attempts += 1.0;
 
-  if (ngas == 0) return;
+  if (ngas == 0 || ngas <= min_ngas) return;
 
   double energy_before = energy_stored;
 
@@ -1619,6 +1633,8 @@ void FixGCMC::attempt_atomic_insertion_full()
   double lamda[3];
   ninsertion_attempts += 1.0;
 
+  if (ngas >= max_ngas) return;
+
   double energy_before = energy_stored;
 
   double coord[3];
@@ -1914,7 +1930,7 @@ void FixGCMC::attempt_molecule_deletion_full()
 {
   ndeletion_attempts += 1.0;
 
-  if (ngas == 0) return;
+  if (ngas == 0 || ngas <= min_ngas) return;
 
   // work-around to avoid n=0 problem with fix rigid/nvt/small
 
@@ -1997,6 +2013,8 @@ void FixGCMC::attempt_molecule_insertion_full()
   double lamda[3];
   ninsertion_attempts += 1.0;
 
+  if (ngas >= max_ngas) return;
+
   double energy_before = energy_stored;
 
   tagint maxmol = 0;
diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h
index da4232d19b..e111642548 100644
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@@ -119,6 +119,8 @@ class FixGCMC : public Fix {
   imageint imagezero;
   double overlap_cutoffsq; // square distance cutoff for overlap
   int overlap_flag;
+  int max_ngas;
+  int min_ngas;
 
   double energy_intra;
 
diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp
index 43bffa7e8d..dbb68b56f7 100644
--- a/src/MC/pair_dsmc.cpp
+++ b/src/MC/pair_dsmc.cpp
@@ -27,6 +27,7 @@
 #include "domain.h"
 #include "update.h"
 #include "random_mars.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -345,12 +346,12 @@ void PairDSMC::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -378,11 +379,11 @@ void PairDSMC::write_restart_settings(FILE *fp)
 void PairDSMC::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&max_cell_size,sizeof(double),1,fp);
-    fread(&seed,sizeof(int),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&max_cell_size,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
 
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
index f8fc349746..214025be63 100644
--- a/src/MESSAGE/message.cpp
+++ b/src/MESSAGE/message.cpp
@@ -28,7 +28,7 @@ void Message::command(int narg, char **arg)
 {
   if (narg < 3) error->all(FLERR,"Illegal message command");
 
-  int clientserver;
+  int clientserver=0;
   if (strcmp(arg[0],"client") == 0) clientserver = 1;
   else if (strcmp(arg[0],"server") == 0) clientserver = 2;
   else error->all(FLERR,"Illegal message command");
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index 267bce9a02..c8736840e4 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -184,8 +184,11 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
   if (idnext) find_maxid();
 
   // random number generator, same for all procs
+  // warm up the generator 30x to avoid correlations in first-particle
+  // positions if runs are repeated with consecutive seeds
 
   random = new RanPark(lmp,seed);
+  for (int ii=0; ii < 30; ii++) random->uniform();
 
   // set up reneighboring
 
diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp
index d868254c50..c7e7af9057 100644
--- a/src/MISC/fix_evaporate.cpp
+++ b/src/MISC/fix_evaporate.cpp
@@ -56,8 +56,11 @@ FixEvaporate::FixEvaporate(LAMMPS *lmp, int narg, char **arg) :
   if (seed <= 0) error->all(FLERR,"Illegal fix evaporate command");
 
   // random number generator, same for all procs
+  // warm up the generator 30x to avoid correlations in first-particle
+  // positions if runs are repeated with consecutive seeds
 
   random = new RanPark(lmp,seed);
+  for (int ii=0; ii < 30; ii++) random->uniform();
 
   // optional args
 
diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp
index a084491a78..07731fe93b 100644
--- a/src/MISC/pair_nm_cut.cpp
+++ b/src/MISC/pair_nm_cut.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -318,15 +319,15 @@ void PairNMCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&e0[i][j],sizeof(double),1,fp);
-          fread(&r0[i][j],sizeof(double),1,fp);
-          fread(&nn[i][j],sizeof(double),1,fp);
-          fread(&mm[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
@@ -356,10 +357,10 @@ void PairNMCut::write_restart_settings(FILE *fp)
 void PairNMCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp
index df8a34062a..270f4080ee 100644
--- a/src/MISC/pair_nm_cut_coul_cut.cpp
+++ b/src/MISC/pair_nm_cut_coul_cut.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -369,16 +370,16 @@ void PairNMCutCoulCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&e0[i][j],sizeof(double),1,fp);
-          fread(&r0[i][j],sizeof(double),1,fp);
-          fread(&nn[i][j],sizeof(double),1,fp);
-          fread(&mm[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
-          fread(&cut_coul[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
@@ -410,11 +411,11 @@ void PairNMCutCoulCut::write_restart_settings(FILE *fp)
 void PairNMCutCoulCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp
index 4109fb0d9e..b63ede2b63 100644
--- a/src/MISC/pair_nm_cut_coul_long.cpp
+++ b/src/MISC/pair_nm_cut_coul_long.cpp
@@ -28,6 +28,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -413,15 +414,15 @@ void PairNMCutCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&e0[i][j],sizeof(double),1,fp);
-          fread(&r0[i][j],sizeof(double),1,fp);
-          fread(&nn[i][j],sizeof(double),1,fp);
-          fread(&mm[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
@@ -454,13 +455,13 @@ void PairNMCutCoulLong::write_restart_settings(FILE *fp)
 void PairNMCutCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp
index 8a45f29368..161ad90ea3 100644
--- a/src/MOLECULE/angle_charmm.cpp
+++ b/src/MOLECULE/angle_charmm.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -245,10 +246,10 @@ void AngleCharmm::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k_ub[1],sizeof(double),atom->nangletypes,fp);
-    fread(&r_ub[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k_ub[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&r_ub[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp
index 645cf66ff2..59593d2448 100644
--- a/src/MOLECULE/angle_cosine.cpp
+++ b/src/MOLECULE/angle_cosine.cpp
@@ -22,6 +22,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -193,7 +194,7 @@ void AngleCosine::read_restart(FILE *fp)
 {
   allocate();
 
-  if (comm->me == 0) fread(&k[1],sizeof(double),atom->nangletypes,fp);
+  if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
 
   for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp
index 22c2f7ce8b..95f299683e 100644
--- a/src/MOLECULE/angle_cosine_periodic.cpp
+++ b/src/MOLECULE/angle_cosine_periodic.cpp
@@ -27,6 +27,7 @@
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -246,9 +247,9 @@ void AngleCosinePeriodic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&b[1],sizeof(int),atom->nangletypes,fp);
-    fread(&multiplicity[1],sizeof(int),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&b[1],sizeof(int),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->nangletypes,fp,NULL,error);
   }
 
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp
index 56b3ee58cf..9056600c3f 100644
--- a/src/MOLECULE/angle_cosine_squared.cpp
+++ b/src/MOLECULE/angle_cosine_squared.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -215,8 +216,8 @@ void AngleCosineSquared::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp
index 2e96884c9d..baeb9a8ed8 100644
--- a/src/MOLECULE/angle_harmonic.cpp
+++ b/src/MOLECULE/angle_harmonic.cpp
@@ -22,6 +22,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -215,8 +216,8 @@ void AngleHarmonic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp
index 54046c2ba8..b6439084a6 100644
--- a/src/MOLECULE/angle_table.cpp
+++ b/src/MOLECULE/angle_table.cpp
@@ -29,6 +29,7 @@
 #include "memory.h"
 #include "error.h"
 #include "utils.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -309,8 +310,8 @@ void AngleTable::write_restart_settings(FILE *fp)
 void AngleTable::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&tabstyle,sizeof(int),1,fp);
-    fread(&tablength,sizeof(int),1,fp);
+    utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
   MPI_Bcast(&tablength,1,MPI_INT,0,world);
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index 776291701b..b8e197a344 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -21,6 +21,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -215,10 +216,10 @@ void BondFENE::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&sigma[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&sigma[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index d03dfd9125..9cdc2639a5 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -21,6 +21,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -224,11 +225,11 @@ void BondFENEExpand::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&sigma[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&shift[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&sigma[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&shift[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp
index 284c9202fd..6732cc4457 100644
--- a/src/MOLECULE/bond_gromos.cpp
+++ b/src/MOLECULE/bond_gromos.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -166,8 +167,8 @@ void BondGromos::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp
index 7b19034629..569c92f99d 100644
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@@ -21,6 +21,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -167,8 +168,8 @@ void BondHarmonic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp
index 6e16070cae..249f92928f 100644
--- a/src/MOLECULE/bond_morse.cpp
+++ b/src/MOLECULE/bond_morse.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -171,9 +172,9 @@ void BondMorse::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&d0[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&alpha[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&d0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&alpha[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&d0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&alpha[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp
index e06b1b9aac..ee943ad28f 100644
--- a/src/MOLECULE/bond_nonlinear.cpp
+++ b/src/MOLECULE/bond_nonlinear.cpp
@@ -20,6 +20,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -166,9 +167,9 @@ void BondNonlinear::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&lamda[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&lamda[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp
index 352b642bbe..813e322473 100644
--- a/src/MOLECULE/bond_quartic.cpp
+++ b/src/MOLECULE/bond_quartic.cpp
@@ -25,6 +25,7 @@
 #include "pair.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -275,11 +276,11 @@ void BondQuartic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&b1[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&b2[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&rc[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&u0[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&b1[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&b2[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&rc[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&u0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&b1[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp
index ce41303a7d..20e4e311c8 100644
--- a/src/MOLECULE/bond_table.cpp
+++ b/src/MOLECULE/bond_table.cpp
@@ -252,8 +252,8 @@ void BondTable::write_restart_settings(FILE *fp)
 void BondTable::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&tabstyle,sizeof(int),1,fp);
-    fread(&tablength,sizeof(int),1,fp);
+    utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
   MPI_Bcast(&tablength,1,MPI_INT,0,world);
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index 8cc0713024..e66165efd7 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -29,6 +29,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -423,11 +424,11 @@ void DihedralCharmm::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
-    fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
-    fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&weightflag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&shift[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&weight[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&weightflag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp
index f384c4cd36..efff35d9c5 100644
--- a/src/MOLECULE/dihedral_charmmfsw.cpp
+++ b/src/MOLECULE/dihedral_charmmfsw.cpp
@@ -32,6 +32,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -466,11 +467,11 @@ void DihedralCharmmfsw::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
-    fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
-    fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&weightflag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&shift[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&weight[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&weightflag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp
index 4f6a88eca5..48adf07903 100644
--- a/src/MOLECULE/dihedral_harmonic.cpp
+++ b/src/MOLECULE/dihedral_harmonic.cpp
@@ -25,6 +25,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -327,9 +328,9 @@ void DihedralHarmonic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
-    fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&sign[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&sign[1],atom->ndihedraltypes,MPI_INT,0,world);
diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp
index 56f7a3b5e8..26461883c6 100644
--- a/src/MOLECULE/dihedral_helix.cpp
+++ b/src/MOLECULE/dihedral_helix.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -322,9 +323,9 @@ void DihedralHelix::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&aphi[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&bphi[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&cphi[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&aphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&bphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&cphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
   }
   MPI_Bcast(&aphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&bphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp
index eda7cede3e..b5db685247 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.cpp
+++ b/src/MOLECULE/dihedral_multi_harmonic.cpp
@@ -25,6 +25,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -318,11 +319,11 @@ void DihedralMultiHarmonic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&a1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&a2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&a3[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&a4[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&a5[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&a1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&a2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&a3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&a4[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&a5[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
   }
   MPI_Bcast(&a1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&a2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp
index 556efd850a..5dd268b39f 100644
--- a/src/MOLECULE/dihedral_opls.cpp
+++ b/src/MOLECULE/dihedral_opls.cpp
@@ -25,6 +25,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -330,10 +331,10 @@ void DihedralOPLS::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&k4[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&k1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&k2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&k3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&k4[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
   }
   MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp
index abd2d4e11e..0ffb3f3c31 100644
--- a/src/MOLECULE/improper_cvff.cpp
+++ b/src/MOLECULE/improper_cvff.cpp
@@ -21,6 +21,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -333,9 +334,9 @@ void ImproperCvff::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&sign[1],sizeof(int),atom->nimpropertypes,fp);
-    fread(&multiplicity[1],sizeof(int),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&sign[1],sizeof(int),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&sign[1],atom->nimpropertypes,MPI_INT,0,world);
diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp
index 778fe646e1..e90bc04c90 100644
--- a/src/MOLECULE/improper_harmonic.cpp
+++ b/src/MOLECULE/improper_harmonic.cpp
@@ -22,6 +22,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -274,8 +275,8 @@ void ImproperHarmonic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp
index d3adf19993..5259b6baf4 100644
--- a/src/MOLECULE/improper_umbrella.cpp
+++ b/src/MOLECULE/improper_umbrella.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -315,9 +316,9 @@ void ImproperUmbrella::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&kw[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&w0[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&C[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&kw[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&w0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&C[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&kw[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&w0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
index 5ebfe0a110..0712f6be73 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
@@ -26,6 +26,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -374,14 +375,14 @@ void PairLJCharmmCoulCharmm::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&eps14[i][j],sizeof(double),1,fp);
-          fread(&sigma14[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -435,12 +436,12 @@ void PairLJCharmmCoulCharmm::write_restart_settings(FILE *fp)
 void PairLJCharmmCoulCharmm::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_inner,sizeof(double),1,fp);
-    fread(&cut_lj,sizeof(double),1,fp);
-    fread(&cut_coul_inner,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_inner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
index 4fb7cc5229..026b96c00c 100644
--- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
+++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
@@ -31,6 +31,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -432,14 +433,14 @@ void PairLJCharmmfswCoulCharmmfsh::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&eps14[i][j],sizeof(double),1,fp);
-          fread(&sigma14[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -469,11 +470,11 @@ void PairLJCharmmfswCoulCharmmfsh::write_restart_settings(FILE *fp)
 void PairLJCharmmfswCoulCharmmfsh::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_inner,sizeof(double),1,fp);
-    fread(&cut_lj,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);
diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
index e5f25a511b..673fb83066 100644
--- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
@@ -30,6 +30,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -617,13 +618,13 @@ void PairLJCutTIP4PCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -659,17 +660,17 @@ void PairLJCutTIP4PCut::write_restart_settings(FILE *fp)
 void PairLJCutTIP4PCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&typeO,sizeof(int),1,fp);
-    fread(&typeH,sizeof(int),1,fp);
-    fread(&typeB,sizeof(int),1,fp);
-    fread(&typeA,sizeof(int),1,fp);
-    fread(&qdist,sizeof(double),1,fp);
+    utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
 
   MPI_Bcast(&typeO,1,MPI_INT,0,world);
diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp
index 3a6702c9b2..334dbf89c8 100644
--- a/src/MOLECULE/pair_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_tip4p_cut.cpp
@@ -28,6 +28,7 @@
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -474,7 +475,7 @@ void PairTIP4PCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
     }
 }
@@ -501,13 +502,13 @@ void PairTIP4PCut::write_restart_settings(FILE *fp)
 void PairTIP4PCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&typeO,sizeof(int),1,fp);
-    fread(&typeH,sizeof(int),1,fp);
-    fread(&typeB,sizeof(int),1,fp);
-    fread(&typeA,sizeof(int),1,fp);
-    fread(&qdist,sizeof(double),1,fp);
+    utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_coul,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
   }
 
   MPI_Bcast(&typeO,1,MPI_INT,0,world);
diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp
index ad24aaee63..7dff5cff4b 100644
--- a/src/OPT/pair_eam_opt.cpp
+++ b/src/OPT/pair_eam_opt.cpp
@@ -80,11 +80,13 @@ void PairEAMOpt::eval()
   // grow energy array if necessary
 
   if (atom->nmax > nmax) {
-    memory->sfree(rho);
-    memory->sfree(fp);
+    memory->destroy(rho);
+    memory->destroy(fp);
+    memory->destroy(numforce);
     nmax = atom->nmax;
-    rho = (double *) memory->smalloc(nmax*sizeof(double),"pair:rho");
-    fp = (double *) memory->smalloc(nmax*sizeof(double),"pair:fp");
+    memory->create(rho,nmax,"pair:rho");
+    memory->create(fp,nmax,"pair:fp");
+    memory->create(numforce,nmax,"pair:numforce");
   }
 
   double** _noalias x = atom->x;
@@ -269,6 +271,7 @@ void PairEAMOpt::eval()
 
     fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr];
     double* _noalias scale_i = scale[itype1+1]+1;
+    numforce[i] = 0;
 
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
@@ -280,6 +283,7 @@ void PairEAMOpt::eval()
       double rsq = delx*delx + dely*dely + delz*delz;
 
       if (rsq < tmp_cutforcesq) {
+        ++numforce[i];
         jtype = type[j] - 1;
         double r = sqrt(rsq);
         double rhoip,rhojp,z2,z2p;
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp
index 230b766725..8bea52f1cf 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_damage_atom.cpp
@@ -59,11 +59,9 @@ void ComputeDamageAtom::init()
 
   // find associated PERI_NEIGH fix that must exist
 
-  ifix_peri = -1;
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
+  ifix_peri = modify->find_fix_by_style("PERI_NEIGH");
   if (ifix_peri == -1)
-    error->all(FLERR,"Compute damage/atom requires peridynamic potential");
+    error->all(FLERR,"Compute damage/atom requires a peridynamic potential");
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp
index 095f619838..65a25cda03 100644
--- a/src/PERI/compute_dilatation_atom.cpp
+++ b/src/PERI/compute_dilatation_atom.cpp
@@ -66,10 +66,10 @@ void ComputeDilatationAtom::init()
   // check PD pair style
 
   isPMB = isLPS = isVES = isEPS = 0;
-  if (force->pair_match("peri/pmb",1)) isPMB = 1;
-  if (force->pair_match("peri/lps",1)) isLPS = 1;
-  if (force->pair_match("peri/ves",1)) isVES = 1;
-  if (force->pair_match("peri/eps",1)) isEPS = 1;
+  if (force->pair_match("^peri/pmb",0)) isPMB = 1;
+  if (force->pair_match("^peri/lps",0)) isLPS = 1;
+  if (force->pair_match("^peri/ves",0)) isVES = 1;
+  if (force->pair_match("^peri/eps",0)) isEPS = 1;
 
   if (isPMB)
     error->all(FLERR,"Compute dilatation/atom cannot be used "
@@ -77,10 +77,7 @@ void ComputeDilatationAtom::init()
 
   // find associated PERI_NEIGH fix that must exist
 
-  int ifix_peri = -1;
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
-  if (ifix_peri == -1)
+  if (modify->find_fix_by_style("^PERI_NEIGH") == -1)
     error->all(FLERR,"Compute dilatation/atom requires Peridynamic pair style");
 }
 
diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp
index e312630b62..d90e211506 100644
--- a/src/PERI/compute_plasticity_atom.cpp
+++ b/src/PERI/compute_plasticity_atom.cpp
@@ -66,11 +66,9 @@ void ComputePlasticityAtom::init()
 
   // find associated PERI_NEIGH fix that must exist
 
-  ifix_peri = -1;
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
+  ifix_peri = modify->find_fix_by_style("^PERI_NEIGH");
   if (ifix_peri == -1)
-    error->all(FLERR,"Compute plasticity/atom requires Peridynamic pair style");
+    error->all(FLERR,"Compute plasticity/atom requires a Peridynamics pair style");
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp
index 2579a9b75a..cd2ab3a2d0 100644
--- a/src/PERI/pair_peri_eps.cpp
+++ b/src/PERI/pair_peri_eps.cpp
@@ -31,6 +31,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -524,9 +525,9 @@ void PairPeriEPS::init_style()
   // find associated PERI_NEIGH fix that must exist
   // could have changed locations in fix list since created
 
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
-  if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
+  ifix_peri = modify->find_fix_by_style("^PERI_NEIGH");
+  if (ifix_peri == -1)
+    error->all(FLERR,"Fix peri neigh does not exist");
 
   neighbor->request(this,instance_me);
 }
@@ -564,16 +565,16 @@ void PairPeriEPS::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&bulkmodulus[i][j],sizeof(double),1,fp);
-          fread(&shearmodulus[i][j],sizeof(double),1,fp);
-          fread(&s00[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
-          fread(&m_yieldstress[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&m_yieldstress[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index f32ce5fb1c..0ad6a7b0d2 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -31,6 +31,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "math_const.h"
 
 using namespace LAMMPS_NS;
@@ -450,9 +451,9 @@ void PairPeriLPS::init_style()
   // find associated PERI_NEIGH fix that must exist
   // could have changed locations in fix list since created
 
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
-  if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
+  ifix_peri = modify->find_fix_by_style("^PERI_NEIGH");
+  if (ifix_peri == -1)
+    error->all(FLERR,"Fix peri neigh does not exist");
 
   neighbor->request(this,instance_me);
 }
@@ -489,15 +490,15 @@ void PairPeriLPS::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&bulkmodulus[i][j],sizeof(double),1,fp);
-          fread(&shearmodulus[i][j],sizeof(double),1,fp);
-          fread(&s00[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp
index ceab40d88d..88aca99efb 100644
--- a/src/PERI/pair_peri_pmb.cpp
+++ b/src/PERI/pair_peri_pmb.cpp
@@ -32,6 +32,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -380,9 +381,9 @@ void PairPeriPMB::init_style()
   // find associated PERI_NEIGH fix that must exist
   // could have changed locations in fix list since created
 
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
-  if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
+  ifix_peri = modify->find_fix_by_style("^PERI_NEIGH");
+  if (ifix_peri == -1)
+    error->all(FLERR,"Fix peri neigh does not exist");
 
   neighbor->request(this,instance_me);
 }
@@ -418,14 +419,14 @@ void PairPeriPMB::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&kspring[i][j],sizeof(double),1,fp);
-          fread(&s00[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&kspring[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&kspring[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index bd1eaa5fd2..1cef9635a9 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -31,6 +31,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
@@ -506,9 +507,9 @@ void PairPeriVES::init_style()
   // find associated PERI_NEIGH fix that must exist
   // could have changed locations in fix list since created
 
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
-  if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
+  ifix_peri = modify->find_fix_by_style("^PERI_NEIGH");
+  if (ifix_peri == -1)
+    error->all(FLERR,"Fix peri neigh does not exist");
 
   neighbor->request(this,instance_me);
 }
@@ -547,17 +548,17 @@ void PairPeriVES::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&bulkmodulus[i][j],sizeof(double),1,fp);
-          fread(&shearmodulus[i][j],sizeof(double),1,fp);
-          fread(&s00[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
-          fread(&m_lambdai[i][j],sizeof(double),1,fp);
-          fread(&m_taubi[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&m_lambdai[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&m_taubi[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp
index 0d79a31946..8fbb3e6f8b 100644
--- a/src/PYTHON/pair_python.cpp
+++ b/src/PYTHON/pair_python.cpp
@@ -40,6 +40,7 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
   one_coeff = 1;
   reinitflag = 0;
   cut_global = 0.0;
+  centroidstressflag = 1;
 
   py_potential = NULL;
   skip_types = NULL;
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index 7768c01a41..84ba33e28a 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -476,6 +476,7 @@ int FixQEq::pack_forward_comm(int n, int *list, double *buf,
     for(m = 0; m < n; m++) buf[m] = t[list[m]];
   else if( pack_flag == 4 )
     for(m = 0; m < n; m++) buf[m] = atom->q[list[m]];
+  else m = 0;
 
   return m;
 }
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 3e6130ac7c..101b94c2a4 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -52,8 +52,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),
   tflag(NULL), langextra(NULL), sum(NULL), all(NULL),
   remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),
-  dorient(NULL), id_dilate(NULL), random(NULL), avec_ellipsoid(NULL),
-  avec_line(NULL), avec_tri(NULL)
+  dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL),
+  avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL)
 {
   int i,ibody;
 
@@ -124,14 +124,17 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
     if (custom_flag) {
       if (narg < 5) error->all(FLERR,"Illegal fix rigid command");
 
-      // determine whether atom-style variable or atom property is used.
+      // determine whether atom-style variable or atom property is used
+
       if (strstr(arg[4],"i_") == arg[4]) {
         int is_double=0;
         int custom_index = atom->find_custom(arg[4]+2,is_double);
         if (custom_index == -1)
-          error->all(FLERR,"Fix rigid custom requires previously defined property/atom");
+          error->all(FLERR,"Fix rigid custom requires "
+                     "previously defined property/atom");
         else if (is_double)
-          error->all(FLERR,"Fix rigid custom requires integer-valued property/atom");
+          error->all(FLERR,"Fix rigid custom requires "
+                     "integer-valued property/atom");
         int minval = INT_MAX;
         int *value = atom->ivector[custom_index];
         for (i = 0; i < nlocal; i++)
@@ -163,12 +166,15 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
           if (mask[i] & groupbit)
             molecule[i] = (tagint)((tagint)value[i] - minval + 1);
         delete[] value;
+
       } else error->all(FLERR,"Unsupported fix rigid custom property");
+
     } else {
       if (atom->molecule_flag == 0)
         error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");
       molecule = atom->molecule;
     }
+
     iarg = 4 + custom_flag;
 
     tagint maxmol_tag = -1;
@@ -297,6 +303,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   }
 
   // number of linear rigid bodies is counted later
+
   nlinear = 0;
 
   // parse optional args
@@ -308,12 +315,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   tstat_flag = 0;
   pstat_flag = 0;
   allremap = 1;
-  id_dilate = NULL;
   t_chain = 10;
   t_iter = 1;
   t_order = 3;
   p_chain = 10;
+
   inpfile = NULL;
+  id_gravity = NULL;
+  id_dilate = NULL;
 
   pcouple = NONE;
   pstyle = ANISO;
@@ -543,12 +552,20 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
 
     } else if (strcmp(arg[iarg],"reinit") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
       if (strcmp("yes",arg[iarg+1]) == 0) reinitflag = 1;
       else if  (strcmp("no",arg[iarg+1]) == 0) reinitflag = 0;
       else error->all(FLERR,"Illegal fix rigid command");
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"gravity") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
+      delete [] id_gravity;
+      int n = strlen(arg[iarg+1]) + 1;
+      id_gravity = new char[n];
+      strcpy(id_gravity,arg[iarg+1]);
+      iarg += 2;
+
     } else error->all(FLERR,"Illegal fix rigid command");
   }
 
@@ -621,6 +638,9 @@ FixRigid::~FixRigid()
 
   delete random;
   delete [] inpfile;
+  delete [] id_dilate;
+  delete [] id_gravity;
+
   memory->destroy(mol2body);
   memory->destroy(body2mol);
 
@@ -687,7 +707,7 @@ void FixRigid::init()
   avec_tri = (AtomVecTri *) atom->style_match("tri");
 
   // warn if more than one rigid fix
-  // if earlyflag, warn if any post-force fixes come after POEMS fix
+  // if earlyflag, warn if any post-force fixes come after a rigid fix
 
   int count = 0;
   for (i = 0; i < modify->nfix; i++)
@@ -701,24 +721,54 @@ void FixRigid::init()
       if (rflag && (modify->fmask[i] & POST_FORCE) &&
           !modify->fix[i]->rigid_flag) {
         char str[128];
-        snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
+        snprintf(str,128,"Fix %s alters forces after fix rigid",
+                 modify->fix[i]->id);
         error->warning(FLERR,str);
       }
     }
   }
 
+  // warn if body properties are read from inpfile
+  //   and the gravity keyword is not set and a gravity fix exists
+  // this could mean body particles are overlapped
+  //   and gravity is not applied correctly
+
+  if (inpfile && !id_gravity) {
+    for (i = 0; i < modify->nfix; i++) {
+      if (strcmp(modify->fix[i]->style,"gravity") == 0) {
+        if (comm->me == 0)
+          error->warning(FLERR,"Gravity may not be correctly applied "
+                         "to rigid bodies if they consist of "
+                         "overlapped particles");
+        break;
+      }
+    }
+  }
+
   // error if npt,nph fix comes before rigid fix
 
   for (i = 0; i < modify->nfix; i++) {
     if (strcmp(modify->fix[i]->style,"npt") == 0) break;
     if (strcmp(modify->fix[i]->style,"nph") == 0) break;
   }
+
   if (i < modify->nfix) {
     for (int j = i; j < modify->nfix; j++)
       if (strcmp(modify->fix[j]->style,"rigid") == 0)
         error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
   }
 
+  // add gravity forces based on gravity vector from fix
+
+  if (id_gravity) {
+    int ifix = modify->find_fix(id_gravity);
+    if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
+      error->all(FLERR,"Fix rigid gravity fix is invalid");
+    int tmp;
+    gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
+  }
+
   // timestep info
 
   dtv = update->dt;
@@ -1061,8 +1111,17 @@ void FixRigid::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
-}
 
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+    for (ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
+}
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h
index 8c4ab9ed49..c261d89cce 100644
--- a/src/RIGID/fix_rigid.h
+++ b/src/RIGID/fix_rigid.h
@@ -66,7 +66,8 @@ class FixRigid : public Fix {
   double *step_respa;
   int triclinic;
 
-  char *inpfile;             // file to read rigid body attributes from
+  char *inpfile;            // file to read rigid body attributes from
+
   int rstyle;               // SINGLE,MOLECULE,GROUP
   int setupflag;            // 1 if body properties are setup, else 0
   int earlyflag;            // 1 if forces/torques computed at post_force()
@@ -131,6 +132,9 @@ class FixRigid : public Fix {
   int dilate_group_bit;      // mask for dilation group
   char *id_dilate;           // group name to dilate
 
+  char *id_gravity;         // ID of fix gravity command to add gravity forces
+  double *gvec;             // ptr to gravity vector inside the fix
+
   class RanMars *random;
   class AtomVecEllipsoid *avec_ellipsoid;
   class AtomVecLine *avec_line;
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index ba570d5840..33105418ff 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -57,7 +57,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
   xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
   avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
   itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL),
-  id_dilate(NULL), onemols(NULL)
+  id_dilate(NULL), id_gravity(NULL), onemols(NULL)
 {
   int i;
 
@@ -107,7 +107,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       bodyID = new tagint[nlocal];
       customflag = 1;
 
-      // determine whether atom-style variable or atom property is used.
+      // determine whether atom-style variable or atom property is used
+
       if (strstr(arg[4],"i_") == arg[4]) {
         int is_double=0;
         int custom_index = atom->find_custom(arg[4]+2,is_double);
@@ -356,6 +357,13 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       p_chain = force->numeric(FLERR,arg[iarg+1]);
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"gravity") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
+      delete [] id_gravity;
+      int n = strlen(arg[iarg+1]) + 1;
+      id_gravity = new char[n];
+      strcpy(id_gravity,arg[iarg+1]);
+      iarg += 2;
 
     } else error->all(FLERR,"Illegal fix rigid/small command");
   }
@@ -515,6 +523,8 @@ FixRigidSmall::~FixRigidSmall()
 
   delete random;
   delete [] inpfile;
+  delete [] id_dilate;
+  delete [] id_gravity;
 
   memory->destroy(langextra);
   memory->destroy(mass_body);
@@ -543,6 +553,7 @@ void FixRigidSmall::init()
   triclinic = domain->triclinic;
 
   // warn if more than one rigid fix
+  // if earlyflag, warn if any post-force fixes come after a rigid fix
 
   int count = 0;
   for (i = 0; i < modify->nfix; i++)
@@ -563,6 +574,23 @@ void FixRigidSmall::init()
     }
   }
 
+  // warn if body properties are read from inpfile or a mol template file
+  //   and the gravity keyword is not set and a gravity fix exists
+  // this could mean body particles are overlapped
+  //   and gravity is not applied correctly
+
+  if ((inpfile || onemols) && !id_gravity) {
+    for (i = 0; i < modify->nfix; i++) {
+      if (strcmp(modify->fix[i]->style,"gravity") == 0) {
+        if (comm->me == 0)
+          error->warning(FLERR,"Gravity may not be correctly applied "
+                         "to rigid bodies if they consist of "
+                         "overlapped particles");
+        break;
+      }
+    }
+  }
+
   // error if npt,nph fix comes before rigid fix
 
   for (i = 0; i < modify->nfix; i++) {
@@ -575,6 +603,17 @@ void FixRigidSmall::init()
         error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
   }
 
+  // add gravity forces based on gravity vector from fix
+
+  if (id_gravity) {
+    int ifix = modify->find_fix(id_gravity);
+    if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
+      error->all(FLERR,"Fix rigid/small gravity fix is invalid");
+    int tmp;
+    gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
+  }
+
   // timestep info
 
   dtv = update->dt;
@@ -954,8 +993,20 @@ void FixRigidSmall::compute_forces_and_torques()
       tcm[2] += langextra[ibody][5];
     }
   }
-}
 
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+    double mass;
+    for (ibody = 0; ibody < nlocal_body; ibody++) {
+      mass = body[ibody].mass;
+      fcm = body[ibody].fcm;
+      fcm[0] += gvec[0]*mass;
+      fcm[1] += gvec[1]*mass;
+      fcm[2] += gvec[2]*mass;
+    }
+  }
+}
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index 0d1cdb5963..974f5711e2 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -164,6 +164,9 @@ class FixRigidSmall : public Fix {
   int dilate_group_bit;      // mask for dilation group
   char *id_dilate;           // group name to dilate
 
+  char *id_gravity;         // ID of fix gravity command to add gravity forces
+  double *gvec;             // ptr to gravity vector inside the fix
+
   double p_current[3],p_target[3];
 
   // molecules added on-the-fly as rigid bodies
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 48a08118c5..054985ba72 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -32,6 +32,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -360,9 +361,8 @@ void FixShake::init()
   // could have changed locations in fix list since created
   // set ptrs to rRESPA variables
 
-  if (strstr(update->integrate_style,"respa")) {
-    for (i = 0; i < modify->nfix; i++)
-      if (strcmp(modify->fix[i]->style,"RESPA") == 0) ifix_respa = i;
+  if (utils::strmatch(update->integrate_style,"^respa")) {
+    ifix_respa = modify->find_fix_by_style("^RESPA");
     nlevels_respa = ((Respa *) update->integrate)->nlevels;
     loop_respa = ((Respa *) update->integrate)->loop;
     step_respa = ((Respa *) update->integrate)->step;
diff --git a/src/RIGID/rigid_const.h b/src/RIGID/rigid_const.h
index 14db517fcd..3aae988197 100644
--- a/src/RIGID/rigid_const.h
+++ b/src/RIGID/rigid_const.h
@@ -32,7 +32,7 @@ namespace LAMMPS_NS {
           ANGMOM    = 1<<7,
           TORQUE    = 1<<8
     };
-    
+
     static const double TOLERANCE = 1.0e-6;
     static const double EPSILON   = 1.0e-7;
     static const double BIG       = 1.0e20;
diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp
new file mode 100644
index 0000000000..43b6a419da
--- /dev/null
+++ b/src/SNAP/compute_snap.cpp
@@ -0,0 +1,515 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "compute_snap.h"
+#include <cstring>
+#include <cstdlib>
+#include "sna.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "force.h"
+#include "pair.h"
+#include "comm.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+enum{SCALAR,VECTOR,ARRAY};
+
+ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snap(NULL),
+  radelem(NULL), wjelem(NULL), snap_peratom(NULL), snapall(NULL)
+{
+
+  array_flag = 1;
+  extarray = 0;
+
+  double rfac0, rmin0;
+  int twojmax, switchflag, bzeroflag;
+  radelem = NULL;
+  wjelem = NULL;
+
+  int ntypes = atom->ntypes;
+  int nargmin = 6+2*ntypes;
+
+  if (narg < nargmin) error->all(FLERR,"Illegal compute snap command");
+
+  // default values
+
+  rmin0 = 0.0;
+  switchflag = 1;
+  bzeroflag = 1;
+  quadraticflag = 0;
+
+  // process required arguments
+
+  memory->create(radelem,ntypes+1,"snap:radelem"); // offset by 1 to match up with types
+  memory->create(wjelem,ntypes+1,"snap:wjelem");
+  rcutfac = atof(arg[3]);
+  rfac0 = atof(arg[4]);
+  twojmax = atoi(arg[5]);
+  for(int i = 0; i < ntypes; i++)
+    radelem[i+1] = atof(arg[6+i]);
+  for(int i = 0; i < ntypes; i++)
+    wjelem[i+1] = atof(arg[6+ntypes+i]);
+
+  // construct cutsq
+
+  double cut;
+  cutmax = 0.0;
+  memory->create(cutsq,ntypes+1,ntypes+1,"snap:cutsq");
+  for(int i = 1; i <= ntypes; i++) {
+    cut = 2.0*radelem[i]*rcutfac;
+    if (cut > cutmax) cutmax = cut;
+    cutsq[i][i] = cut*cut;
+    for(int j = i+1; j <= ntypes; j++) {
+      cut = (radelem[i]+radelem[j])*rcutfac;
+      cutsq[i][j] = cutsq[j][i] = cut*cut;
+    }
+  }
+
+  // process optional args
+
+  int iarg = nargmin;
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"rmin0") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      rmin0 = atof(arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"bzeroflag") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      bzeroflag = atoi(arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"switchflag") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      switchflag = atoi(arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      quadraticflag = atoi(arg[iarg+1]);
+      iarg += 2;
+    } else error->all(FLERR,"Illegal compute snap command");
+  }
+
+  snaptr = new SNA(lmp,rfac0,twojmax,
+                   rmin0,switchflag,bzeroflag);
+
+  ncoeff = snaptr->ncoeff;
+  nperdim = ncoeff;
+  if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
+  ndims_force = 3;
+  ndims_virial = 6;
+  yoffset = nperdim;
+  zoffset = 2*nperdim;
+  natoms = atom->natoms;
+  size_array_rows = 1+ndims_force*natoms+ndims_virial;
+  size_array_cols = nperdim*atom->ntypes+1;
+  lastcol = size_array_cols-1;
+
+  ndims_peratom = ndims_force;
+  size_peratom = ndims_peratom*nperdim*atom->ntypes;
+
+  nmax = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeSnap::~ComputeSnap()
+{
+  memory->destroy(snap);
+  memory->destroy(snapall);
+  memory->destroy(snap_peratom);
+  memory->destroy(radelem);
+  memory->destroy(wjelem);
+  memory->destroy(cutsq);
+  delete snaptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeSnap::init()
+{
+  if (force->pair == NULL)
+    error->all(FLERR,"Compute snap requires a pair style be defined");
+
+  if (cutmax > force->pair->cutforce)
+    error->all(FLERR,"Compute snap cutoff is longer than pairwise cutoff");
+
+  // need an occasional full neighbor list
+
+  int irequest = neighbor->request(this,instance_me);
+  neighbor->requests[irequest]->pair = 0;
+  neighbor->requests[irequest]->compute = 1;
+  neighbor->requests[irequest]->half = 0;
+  neighbor->requests[irequest]->full = 1;
+  neighbor->requests[irequest]->occasional = 1;
+
+  int count = 0;
+  for (int i = 0; i < modify->ncompute; i++)
+    if (strcmp(modify->compute[i]->style,"snap") == 0) count++;
+  if (count > 1 && comm->me == 0)
+    error->warning(FLERR,"More than one compute snap");
+  snaptr->init();
+
+  // allocate memory for global array
+
+  memory->create(snap,size_array_rows,size_array_cols,
+                 "snap:snap");
+  memory->create(snapall,size_array_rows,size_array_cols,
+                 "snap:snapall");
+  array = snapall;
+
+  // INCOMPLETE: modify->find_compute()
+  // was called 223960 times by snappy Ta example
+  // that is over 600 times per config?
+  // how is this possible???
+
+  // find compute for reference energy
+
+  char *id_pe = (char *) "thermo_pe";
+  int ipe = modify->find_compute(id_pe);
+  if (ipe == -1)
+    error->all(FLERR,"compute thermo_pe does not exist.");
+  c_pe = modify->compute[ipe];
+
+  // add compute for reference virial tensor
+
+  char *id_virial = (char *) "snap_press";
+  char **newarg = new char*[5];
+  newarg[0] = id_virial;
+  newarg[1] = (char *) "all";
+  newarg[2] = (char *) "pressure";
+  newarg[3] = (char *) "NULL";
+  newarg[4] = (char *) "virial";
+  modify->add_compute(5,newarg);
+  delete [] newarg;
+
+  int ivirial = modify->find_compute(id_virial);
+  if (ivirial == -1)
+    error->all(FLERR,"compute snap_press does not exist.");
+  c_virial = modify->compute[ivirial];
+
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeSnap::init_list(int /*id*/, NeighList *ptr)
+{
+  list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeSnap::compute_array()
+{
+  int ntotal = atom->nlocal + atom->nghost;
+
+  invoked_array = update->ntimestep;
+
+  // grow snap_peratom array if necessary
+
+  if (atom->nmax > nmax) {
+    memory->destroy(snap_peratom);
+    nmax = atom->nmax;
+    memory->create(snap_peratom,nmax,size_peratom,
+                   "snap:snap_peratom");
+  }
+
+  // clear global array
+
+  for (int irow = 0; irow < size_array_rows; irow++)
+    for (int icoeff = 0; icoeff < size_array_cols; icoeff++)
+      snap[irow][icoeff] = 0.0;
+
+  // clear local peratom array
+
+  for (int i = 0; i < ntotal; i++)
+    for (int icoeff = 0; icoeff < size_peratom; icoeff++) {
+      snap_peratom[i][icoeff] = 0.0;
+    }
+
+  // invoke full neighbor list (will copy or build if necessary)
+
+  neighbor->build_one(list);
+
+  const int inum = list->inum;
+  const int* const ilist = list->ilist;
+  const int* const numneigh = list->numneigh;
+  int** const firstneigh = list->firstneigh;
+  int * const type = atom->type;
+
+  // compute sna derivatives for each atom in group
+  // use full neighbor list to count atoms less than cutoff
+
+  double** const x = atom->x;
+  const int* const mask = atom->mask;
+
+  for (int ii = 0; ii < inum; ii++) {
+    const int i = ilist[ii];
+    if (mask[i] & groupbit) {
+
+      const double xtmp = x[i][0];
+      const double ytmp = x[i][1];
+      const double ztmp = x[i][2];
+      const int itype = type[i];
+      const double radi = radelem[itype];
+      const int* const jlist = firstneigh[i];
+      const int jnum = numneigh[i];
+      const int typeoffset_local = ndims_peratom*nperdim*(itype-1);
+      const int typeoffset_global = nperdim*(itype-1);
+
+      // insure rij, inside, and typej  are of size jnum
+
+      snaptr->grow_rij(jnum);
+
+      // rij[][3] = displacements between atom I and those neighbors
+      // inside = indices of neighbors of I within cutoff
+      // typej = types of neighbors of I within cutoff
+      // note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi
+
+      int ninside = 0;
+      for (int jj = 0; jj < jnum; jj++) {
+        int j = jlist[jj];
+        j &= NEIGHMASK;
+
+        const double delx = x[j][0] - xtmp;
+        const double dely = x[j][1] - ytmp;
+        const double delz = x[j][2] - ztmp;
+        const double rsq = delx*delx + dely*dely + delz*delz;
+        int jtype = type[j];
+        if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
+          snaptr->rij[ninside][0] = delx;
+          snaptr->rij[ninside][1] = dely;
+          snaptr->rij[ninside][2] = delz;
+          snaptr->inside[ninside] = j;
+          snaptr->wj[ninside] = wjelem[jtype];
+          snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
+          ninside++;
+        }
+      }
+
+      snaptr->compute_ui(ninside);
+      snaptr->compute_zi();
+      snaptr->compute_bi();
+
+      for (int jj = 0; jj < ninside; jj++) {
+        const int j = snaptr->inside[jj];
+        snaptr->compute_duidrj(snaptr->rij[jj],
+                                    snaptr->wj[jj],
+                                    snaptr->rcutij[jj],jj);
+        snaptr->compute_dbidrj();
+
+        // Accumulate dBi/dRi, -dBi/dRj
+
+        double *snadi = snap_peratom[i]+typeoffset_local;
+        double *snadj = snap_peratom[j]+typeoffset_local;
+
+        for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+          snadi[icoeff] += snaptr->dblist[icoeff][0];
+          snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
+          snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
+          snadj[icoeff] -= snaptr->dblist[icoeff][0];
+          snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
+          snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
+        }
+
+        if (quadraticflag) {
+          const int quadraticoffset = ncoeff;
+          snadi += quadraticoffset;
+          snadj += quadraticoffset;
+          int ncount = 0;
+          for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+            double bi = snaptr->blist[icoeff];
+            double bix = snaptr->dblist[icoeff][0];
+            double biy = snaptr->dblist[icoeff][1];
+            double biz = snaptr->dblist[icoeff][2];
+
+            // diagonal elements of quadratic matrix
+
+            double dbxtmp = bi*bix;
+            double dbytmp = bi*biy;
+            double dbztmp = bi*biz;
+
+            snadi[ncount] +=         dbxtmp;
+            snadi[ncount+yoffset] += dbytmp;
+            snadi[ncount+zoffset] += dbztmp;
+            snadj[ncount] -=         dbxtmp;
+            snadj[ncount+yoffset] -= dbytmp;
+            snadj[ncount+zoffset] -= dbztmp;
+
+            ncount++;
+
+            // upper-triangular elements of quadratic matrix
+
+            for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
+              double dbxtmp = bi*snaptr->dblist[jcoeff][0]
+                + bix*snaptr->blist[jcoeff];
+              double dbytmp = bi*snaptr->dblist[jcoeff][1]
+                + biy*snaptr->blist[jcoeff];
+              double dbztmp = bi*snaptr->dblist[jcoeff][2]
+                + biz*snaptr->blist[jcoeff];
+
+              snadi[ncount] +=         dbxtmp;
+              snadi[ncount+yoffset] += dbytmp;
+              snadi[ncount+zoffset] += dbztmp;
+              snadj[ncount] -=         dbxtmp;
+              snadj[ncount+yoffset] -= dbytmp;
+              snadj[ncount+zoffset] -= dbztmp;
+
+              ncount++;
+            }
+          }
+
+        }
+      }
+
+      // Accumulate Bi
+
+      // linear contributions
+
+      int k = typeoffset_global;
+      for (int icoeff = 0; icoeff < ncoeff; icoeff++)
+        snap[0][k++] += snaptr->blist[icoeff];
+
+      // quadratic contributions
+
+      if (quadraticflag) {
+        for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+          double bveci = snaptr->blist[icoeff];
+          snap[0][k++] += 0.5*bveci*bveci;
+          for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
+            double bvecj = snaptr->blist[jcoeff];
+            snap[0][k++] += bveci*bvecj;
+          }
+        }
+      }
+    }
+  }
+
+  // accumulate bispectrum force contributions to global array
+
+  for (int itype = 0; itype < atom->ntypes; itype++) {
+    const int typeoffset_local = ndims_peratom*nperdim*itype;
+    const int typeoffset_global = nperdim*itype;
+    for (int icoeff = 0; icoeff < nperdim; icoeff++) {
+      int irow = 1;
+      for (int i = 0; i < ntotal; i++) {
+        double *snadi = snap_peratom[i]+typeoffset_local;
+        int iglobal = atom->tag[i];
+        int irow = 3*(iglobal-1)+1;
+        snap[irow][icoeff+typeoffset_global] += snadi[icoeff];
+        snap[irow+1][icoeff+typeoffset_global] += snadi[icoeff+yoffset];
+        snap[irow+2][icoeff+typeoffset_global] += snadi[icoeff+zoffset];
+      }
+    }
+  }
+
+ // accumulate forces to global array
+
+  for (int i = 0; i < atom->nlocal; i++) {
+    int iglobal = atom->tag[i];
+    int irow = 3*(iglobal-1)+1;
+    snap[irow][lastcol] = atom->f[i][0];
+    snap[irow+1][lastcol] = atom->f[i][1];
+    snap[irow+2][lastcol] = atom->f[i][2];
+  }
+
+  // accumulate bispectrum virial contributions to global array
+
+  dbdotr_compute();
+
+  // sum up over all processes
+
+  MPI_Allreduce(&snap[0][0],&snapall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
+
+  // assign energy to last column
+
+  int irow = 0;
+  double reference_energy = c_pe->compute_scalar();
+  snapall[irow++][lastcol] = reference_energy;
+
+  // assign virial stress to last column
+  // switch to Voigt notation
+
+  c_virial->compute_vector();
+  irow += 3*natoms;
+  snapall[irow++][lastcol] = c_virial->vector[0];
+  snapall[irow++][lastcol] = c_virial->vector[1];
+  snapall[irow++][lastcol] = c_virial->vector[2];
+  snapall[irow++][lastcol] = c_virial->vector[5];
+  snapall[irow++][lastcol] = c_virial->vector[4];
+  snapall[irow++][lastcol] = c_virial->vector[3];
+
+}
+
+/* ----------------------------------------------------------------------
+   compute global virial contributions via summing r_i.dB^j/dr_i over
+   own & ghost atoms
+------------------------------------------------------------------------- */
+
+void ComputeSnap::dbdotr_compute()
+{
+  double **x = atom->x;
+  int irow0 = 1+ndims_force*natoms;
+
+  // sum over bispectrum contributions to forces
+  // on all particles including ghosts
+
+  int nall = atom->nlocal + atom->nghost;
+  for (int i = 0; i < nall; i++)
+    for (int itype = 0; itype < atom->ntypes; itype++) {
+      const int typeoffset_local = ndims_peratom*nperdim*itype;
+      const int typeoffset_global = nperdim*itype;
+      double *snadi = snap_peratom[i]+typeoffset_local;
+      for (int icoeff = 0; icoeff < nperdim; icoeff++) {
+        double dbdx = snadi[icoeff];
+        double dbdy = snadi[icoeff+yoffset];
+        double dbdz = snadi[icoeff+zoffset];
+        int irow = irow0;
+        snap[irow++][icoeff+typeoffset_global] += dbdx*x[i][0];
+        snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][1];
+        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][2];
+        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][1];
+        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][0];
+        snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][0];
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   memory usage
+------------------------------------------------------------------------- */
+
+double ComputeSnap::memory_usage()
+{
+
+  double bytes = size_array_rows*size_array_cols *
+    sizeof(double);                                     // snap
+  bytes += size_array_rows*size_array_cols *
+    sizeof(double);                                     // snapall
+  bytes += nmax*size_peratom * sizeof(double);          // snap_peratom
+  bytes += snaptr->memory_usage();                      // SNA object
+
+  return bytes;
+}
diff --git a/src/SNAP/compute_snap.h b/src/SNAP/compute_snap.h
new file mode 100644
index 0000000000..4f30b7c507
--- /dev/null
+++ b/src/SNAP/compute_snap.h
@@ -0,0 +1,82 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(snap,ComputeSnap)
+
+#else
+
+#ifndef LMP_COMPUTE_SNAP_H
+#define LMP_COMPUTE_SNAP_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeSnap : public Compute {
+ public:
+  ComputeSnap(class LAMMPS *, int, char **);
+  ~ComputeSnap();
+  void init();
+  void init_list(int, class NeighList *);
+  void compute_array();
+  double memory_usage();
+
+ private:
+  int natoms, nmax, size_peratom, lastcol;
+  int ncoeff, nperdim, yoffset, zoffset;
+  int ndims_peratom, ndims_force, ndims_virial;
+  double **cutsq;
+  class NeighList *list;
+  double **snap, **snapall;
+  double **snap_peratom;
+  double rcutfac;
+  double *radelem;
+  double *wjelem;
+  class SNA* snaptr;
+  double cutmax;
+  int quadraticflag;
+
+  Compute *c_pe;
+  Compute *c_virial;
+
+  void dbdotr_compute();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Compute snap requires a pair style be defined
+
+Self-explanatory.
+
+E: Compute snap cutoff is longer than pairwise cutoff
+
+UNDOCUMENTED
+
+W: More than one compute snad/atom
+
+Self-explanatory.
+
+*/
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index 59b333fa31..6f7cf54659 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -108,7 +108,7 @@ void PairSNAP::compute(int eflag, int vflag)
 
   // compute dE_i/dB_i = beta_i for all i in list
 
-  if (quadraticflag || eflag) 
+  if (quadraticflag || eflag)
     compute_bispectrum();
   compute_beta();
 
@@ -165,7 +165,7 @@ void PairSNAP::compute(int eflag, int vflag)
     snaptr->compute_ui(ninside);
 
     // for neighbors of I within cutoff:
-    // compute Fij = dEi/dRj = -dEi/dRi 
+    // compute Fij = dEi/dRj = -dEi/dRi
     // add to Fi, subtract from Fj
 
     snaptr->compute_yi(beta[ii]);
@@ -273,7 +273,7 @@ void PairSNAP::compute_bispectrum()
 {
   int i,j,jnum,ninside;
   double delx,dely,delz,rsq;
-  int *jlist,*numneigh,**firstneigh;
+  int *jlist;
 
   double **x = atom->x;
   int *type = atom->type;
@@ -350,9 +350,9 @@ void PairSNAP::allocate()
    global settings
 ------------------------------------------------------------------------- */
 
-void PairSNAP::settings(int narg, char **arg)
+void PairSNAP::settings(int narg, char ** /* arg */)
 {
-  for (int i=0; i < narg; i++)
+  if (narg > 0)
     error->all(FLERR,"Illegal pair_style command");
 }
 
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index 01d2d12b8f..99834635b7 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -20,6 +20,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "comm.h"
 
 using namespace std;
 using namespace LAMMPS_NS;
@@ -170,7 +171,7 @@ void SNA::build_indexlist()
   for(int j1 = 0; j1 <= twojmax; j1++)
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) {
-        idxcg_block[j1][j2][j] = idxcg_count; 
+        idxcg_block[j1][j2][j] = idxcg_count;
         for (int m1 = 0; m1 <= j1; m1++)
           for (int m2 = 0; m2 <= j2; m2++)
             idxcg_count++;
@@ -184,9 +185,9 @@ void SNA::build_indexlist()
                  "sna:idxu_block");
 
   int idxu_count = 0;
-  
+
   for(int j = 0; j <= twojmax; j++) {
-    idxu_block[j] = idxu_count; 
+    idxu_block[j] = idxu_count;
     for(int mb = 0; mb <= j; mb++)
       for(int ma = 0; ma <= j; ma++)
         idxu_count++;
@@ -195,15 +196,15 @@ void SNA::build_indexlist()
 
   // index list for beta and B
 
-  int idxb_count = 0;  
+  int idxb_count = 0;
   for(int j1 = 0; j1 <= twojmax; j1++)
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2)
         if (j >= j1) idxb_count++;
-  
+
   idxb_max = idxb_count;
   idxb = new SNA_BINDICES[idxb_max];
-  
+
   idxb_count = 0;
   for(int j1 = 0; j1 <= twojmax; j1++)
     for(int j2 = 0; j2 <= j1; j2++)
@@ -224,7 +225,7 @@ void SNA::build_indexlist()
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) {
         if (j >= j1) {
-          idxb_block[j1][j2][j] = idxb_count; 
+          idxb_block[j1][j2][j] = idxb_count;
           idxb_count++;
         }
       }
@@ -239,18 +240,18 @@ void SNA::build_indexlist()
         for (int mb = 0; 2*mb <= j; mb++)
           for (int ma = 0; ma <= j; ma++)
             idxz_count++;
-  
+
   idxz_max = idxz_count;
   idxz = new SNA_ZINDICES[idxz_max];
-  
+
   memory->create(idxz_block, jdim, jdim, jdim,
                  "sna:idxz_block");
-  
+
   idxz_count = 0;
   for(int j1 = 0; j1 <= twojmax; j1++)
     for(int j2 = 0; j2 <= j1; j2++)
       for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) {
-        idxz_block[j1][j2][j] = idxz_count; 
+        idxz_block[j1][j2][j] = idxz_count;
 
         // find right beta[jjb] entry
         // multiply and divide by j+1 factors
@@ -283,6 +284,7 @@ void SNA::build_indexlist()
 void SNA::init()
 {
   init_clebsch_gordan();
+  //   print_clebsch_gordan();
   init_rootpqarray();
 }
 
@@ -348,7 +350,6 @@ void SNA::compute_ui(int jnum)
 void SNA::compute_zi()
 {
 
-  int ma2, mb2;
   for(int jjz = 0; jjz < idxz_max; jjz++) {
     const int j1 = idxz[jjz].j1;
     const int j2 = idxz[jjz].j2;
@@ -405,8 +406,6 @@ void SNA::compute_zi()
 
 void SNA::compute_yi(const double* beta)
 {
-  int j;
-  int jjz;
   int jju;
   double betaj;
 
@@ -420,7 +419,6 @@ void SNA::compute_yi(const double* beta)
       } // end loop over ma, mb
   } // end loop over j
 
-  int ma2, mb2;
   for(int jjz = 0; jjz < idxz_max; jjz++) {
     const int j1 = idxz[jjz].j1;
     const int j2 = idxz[jjz].j2;
@@ -433,8 +431,6 @@ void SNA::compute_yi(const double* beta)
     const int nb = idxz[jjz].nb;
 
     const double* cgblock = cglist + idxcg_block[j1][j2][j];
-    int mb = (2 * (mb1min+mb2max) - j1 - j2 + j) / 2;
-    int ma = (2 * (ma1min+ma2max) - j1 - j2 + j) / 2;
 
     double ztmp_r = 0.0;
     double ztmp_i = 0.0;
@@ -485,7 +481,7 @@ void SNA::compute_yi(const double* beta)
       if (j1 == j) {
         if (j2 == j) betaj = 3*beta[jjb];
         else betaj = 2*beta[jjb];
-      } else betaj = beta[jjb]; 
+      } else betaj = beta[jjb];
     } else if (j >= j2) {
       const int jjb = idxb_block[j][j2][j1];
       if (j2 == j) betaj = 2*beta[jjb]*(j1+1)/(j+1.0);
@@ -547,14 +543,13 @@ void SNA::compute_deidrj(double* dedr)
         jju++;
       }
 
-      int ma = mb;
       double* dudr_r = dulist_r[jju];
       double* dudr_i = dulist_i[jju];
       double jjjmambyarray_r = ylist_r[jju];
       double jjjmambyarray_i = ylist_i[jju];
 
       for(int k = 0; k < 3; k++)
-        dedr[k] += 
+        dedr[k] +=
           (dudr_r[k] * jjjmambyarray_r +
            dudr_i[k] * jjjmambyarray_i)*0.5;
       jju++;
@@ -593,24 +588,24 @@ void SNA::compute_bi()
     double sumzu = 0.0;
     for (int mb = 0; 2*mb < j; mb++)
       for (int ma = 0; ma <= j; ma++) {
-        sumzu += ulisttot_r[jju]*zlist_r[jjz] + 
+        sumzu += ulisttot_r[jju]*zlist_r[jjz] +
           ulisttot_i[jju]*zlist_i[jjz];
         jjz++;
         jju++;
-      } // end loop over ma, mb                                                                                                   
+      } // end loop over ma, mb
 
     // For j even, handle middle column
 
     if (j%2 == 0) {
       int mb = j/2;
       for(int ma = 0; ma < mb; ma++) {
-        sumzu += ulisttot_r[jju]*zlist_r[jjz] + 
+        sumzu += ulisttot_r[jju]*zlist_r[jjz] +
           ulisttot_i[jju]*zlist_i[jjz];
         jjz++;
         jju++;
       }
 
-      sumzu += 0.5*(ulisttot_r[jju]*zlist_r[jjz] + 
+      sumzu += 0.5*(ulisttot_r[jju]*zlist_r[jjz] +
                    ulisttot_i[jju]*zlist_i[jjz]);
     } // end if jeven
 
@@ -656,10 +651,6 @@ void SNA::compute_dbidrj()
   double* dbdr;
   double* dudr_r, *dudr_i;
   double sumzdu_r[3];
-  double** jjjzarray_r;
-  double** jjjzarray_i;
-  double jjjmambzarray_r;
-  double jjjmambzarray_i;
   int jjz, jju;
 
   for(int jjb = 0; jjb < idxb_max; jjb++) {
@@ -706,7 +697,6 @@ void SNA::compute_dbidrj()
         jjz++;
         jju++;
       }
-      int ma = mb;
       dudr_r = dulist_r[jju];
       dudr_i = dulist_i[jju];
       for(int k = 0; k < 3; k++)
@@ -756,7 +746,6 @@ void SNA::compute_dbidrj()
         jjz++;
         jju++;
       }
-      int ma = mb;
       dudr_r = dulist_r[jju];
       dudr_i = dulist_i[jju];
       for(int k = 0; k < 3; k++)
@@ -806,7 +795,6 @@ void SNA::compute_dbidrj()
         jjz++;
         jju++;
       }
-      int ma = mb;
       dudr_r = dulist_r[jju];
       dudr_i = dulist_i[jju];
       for(int k = 0; k < 3; k++)
@@ -1497,7 +1485,7 @@ void SNA::init_clebsch_gordan()
                  factorial((j - j2 + aa2) / 2 + z) *
                  factorial((j - j1 - bb2) / 2 + z));
             }
-            
+
             cc2 = 2 * m - j;
             dcg = deltacg(j1, j2, j);
             sfaccg = sqrt(factorial((j1 + aa2) / 2) *
@@ -1507,7 +1495,7 @@ void SNA::init_clebsch_gordan()
                           factorial((j  + cc2) / 2) *
                           factorial((j  - cc2) / 2) *
                           (j + 1));
-            
+
             cglist[idxcg_count] = sum * dcg * sfaccg;
             idxcg_count++;
           }
@@ -1515,6 +1503,40 @@ void SNA::init_clebsch_gordan()
       }
 }
 
+/* ----------------------------------------------------------------------
+   print out values of Clebsch-Gordan coefficients
+   format and notation follows VMK Table 8.11
+------------------------------------------------------------------------- */
+
+void SNA::print_clebsch_gordan()
+{
+  if (comm->me) return;
+
+  int aa2, bb2, cc2;
+  for (int j = 0; j <= twojmax; j += 1) {
+    printf("c = %g\n",j/2.0);
+    printf("a alpha b beta C_{a alpha b beta}^{c alpha+beta}\n");
+    for (int j1 = 0; j1 <= twojmax; j1++)
+      for (int j2 = 0; j2 <= j1; j2++)
+        if (j1-j2 <= j && j1+j2 >= j && (j1+j2+j)%2 == 0) {
+          int idxcg_count = idxcg_block[j1][j2][j];
+          for (int m1 = 0; m1 <= j1; m1++) {
+            aa2 = 2*m1-j1;
+            for (int m2 = 0; m2 <= j2; m2++) {
+              bb2 = 2*m2-j2;
+              double cgtmp = cglist[idxcg_count];
+              cc2 = aa2+bb2;
+              if (cc2 >= -j && cc2 <= j)
+                if (j1 != j2 || (aa2 > bb2 && aa2 >= -bb2) || (aa2 == bb2 && aa2 >= 0))
+                  printf("%4g %4g %4g %4g %10.6g\n",
+                         j1/2.0,aa2/2.0,j2/2.0,bb2/2.0,cgtmp);
+              idxcg_count++;
+            }
+          }
+        }
+  }
+}
+
 /* ----------------------------------------------------------------------
    pre-compute table of sqrt[p/m2], p, q = 1,twojmax
    the p = 0, q = 0 entries are allocated and skipped for convenience.
diff --git a/src/SNAP/sna.h b/src/SNAP/sna.h
index e6bf4e3f9e..16d3338277 100644
--- a/src/SNAP/sna.h
+++ b/src/SNAP/sna.h
@@ -81,8 +81,8 @@ private:
   int idxcg_max, idxu_max, idxz_max, idxb_max;
 
   double** rootpqarray;
-  double* cglist;  
-  int*** idxcg_block; 
+  double* cglist;
+  int*** idxcg_block;
 
   double* ulisttot_r, * ulisttot_i;
   double** ulist_r_ij, ** ulist_i_ij;
@@ -103,6 +103,7 @@ private:
   void create_twojmax_arrays();
   void destroy_twojmax_arrays();
   void init_clebsch_gordan();
+  void print_clebsch_gordan();
   void init_rootpqarray();
   void zero_uarraytot();
   void addself_uarraytot(double);
diff --git a/src/SPIN/README b/src/SPIN/README
index a4eb4ff22b..ad296c69b7 100644
--- a/src/SPIN/README
+++ b/src/SPIN/README
@@ -8,7 +8,6 @@ atom in the system
 * integrating the equations of motion for the coupled spin-lattice system
 * implementing magnetic pair interactions and magnetic forces
 * thermostating and applying a transverse damping to the magnetic spins
-* minimizing spin configurations with an adaptive timestep scheme
 * performing geodesic NEB calculations
 * computing and outputing magnetic quantities
 * minimizing the energy or total torque of a magnetic system
diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp
index ad1384ffd2..28c52bb39d 100644
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@@ -848,17 +848,16 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values)
 
 int AtomVecSpin::data_atom_hybrid(int nlocal, char **values)
 {
-
-  sp[nlocal][0] = utils::numeric(FLERR,values[0],true,lmp);
-  sp[nlocal][1] = utils::numeric(FLERR,values[1],true,lmp);
-  sp[nlocal][2] = utils::numeric(FLERR,values[2],true,lmp);
+  sp[nlocal][3] = utils::numeric(FLERR,values[0],true,lmp);
+  sp[nlocal][0] = utils::numeric(FLERR,values[1],true,lmp);
+  sp[nlocal][1] = utils::numeric(FLERR,values[2],true,lmp);
+  sp[nlocal][2] = utils::numeric(FLERR,values[3],true,lmp);
   double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] +
                           sp[nlocal][1]*sp[nlocal][1] +
                           sp[nlocal][2]*sp[nlocal][2]);
   sp[nlocal][0] *= inorm;
   sp[nlocal][1] *= inorm;
   sp[nlocal][2] *= inorm;
-  sp[nlocal][3] = utils::numeric(FLERR,values[3],true,lmp);
 
   return 4;
 }
diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h
index 1f1c34df52..6ce2c9dc7d 100644
--- a/src/SPIN/atom_vec_spin.h
+++ b/src/SPIN/atom_vec_spin.h
@@ -67,13 +67,13 @@ class AtomVecSpin : public AtomVec {
   tagint *tag;
   int *type,*mask;
   imageint *image;
-  double **x,**v,**f;		// lattice quantities
-  
-  				// spin quantities
-  double **sp;			// sp[i][0-2] direction of the spin i
-				// sp[i][3] atomic magnetic moment of the spin i
-  double **fm;			// fm[i][0-2] direction of magnetic precession
-  double **fm_long;		// storage of long-range spin prec. components
+  double **x,**v,**f;           // lattice quantities
+
+                                // spin quantities
+  double **sp;                  // sp[i][0-2] direction of the spin i
+                                // sp[i][3] atomic magnetic moment of the spin i
+  double **fm;                  // fm[i][0-2] direction of magnetic precession
+  double **fm_long;             // storage of long-range spin prec. components
 };
 
 }
diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index 1f808eb1bd..7ee2b5bcfc 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -128,7 +128,7 @@ void ComputeSpin::compute_vector()
   magtot[2] *= scale;
   magtot[3] = sqrt((magtot[0]*magtot[0])+(magtot[1]*magtot[1])+(magtot[2]*magtot[2]));
   spintemperature = hbar*tempnumtot;
-  spintemperature /= (kb*tempdenomtot);
+  spintemperature /= (2.0*kb*tempdenomtot);
 
   vector[0] = magtot[0];
   vector[1] = magtot[1];
diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp
index ec9c98c4f8..6b9ad517bb 100644
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@@ -30,7 +30,8 @@
 #include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "random_park.h"
+// #include "random_park.h"
+#include "random_mars.h"
 #include "respa.h"
 #include "update.h"
 #include "utils.h"
@@ -74,7 +75,8 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
 
   // initialize Marsaglia RNG with processor-unique seed
 
-  random = new RanPark(lmp,seed + comm->me);
+  // random = new RanPark(lmp,seed + comm->me);
+  random = new RanMars(lmp,seed + comm->me);
 
 }
 
@@ -82,8 +84,6 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
 
 FixLangevinSpin::~FixLangevinSpin()
 {
-  memory->destroy(spi);
-  memory->destroy(fmi);
   delete random;
 }
 
@@ -113,15 +113,15 @@ void FixLangevinSpin::init()
   }
   if (flag_force >= flag_lang) error->all(FLERR,"Fix langevin/spin has to come after all other spin fixes");
 
-  memory->create(spi,3,"langevin:spi");
-  memory->create(fmi,3,"langevin:fmi");
-
   gil_factor = 1.0/(1.0+(alpha_t)*(alpha_t));
-  dts = update->dt;
+  dts = 0.25 * update->dt;
 
   double hbar = force->hplanck/MY_2PI;  // eV/(rad.THz)
   double kb = force->boltz;             // eV/K
-  D = (MY_2PI*alpha_t*gil_factor*kb*temp);
+  // D = (MY_2PI*alpha_t*gil_factor*kb*temp);
+
+  D = (alpha_t*gil_factor*kb*temp);
+  // D = (12.0/MY_2PI)*(MY_2PI*alpha_t*gil_factor*kb*temp);
   D /= (hbar*dts);
   sigma = sqrt(2.0*D);
 }
@@ -157,9 +157,12 @@ void FixLangevinSpin::add_tdamping(double spi[3], double fmi[3])
 void FixLangevinSpin::add_temperature(double fmi[3])
 {
 
-  double rx = sigma*(2.0*random->uniform() - 1.0);
-  double ry = sigma*(2.0*random->uniform() - 1.0);
-  double rz = sigma*(2.0*random->uniform() - 1.0);
+  // double rx = sigma*(2.0*random->uniform() - 1.0);
+  // double ry = sigma*(2.0*random->uniform() - 1.0);
+  // double rz = sigma*(2.0*random->uniform() - 1.0);
+  double rx = sigma*random->gaussian();
+  double ry = sigma*random->gaussian();
+  double rz = sigma*random->gaussian();
 
   // adding the random field
 
diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h
index 5358438396..0e4fc69f92 100644
--- a/src/SPIN/fix_langevin_spin.h
+++ b/src/SPIN/fix_langevin_spin.h
@@ -32,23 +32,22 @@ class FixLangevinSpin : public Fix {
   void init();
   void setup(int);
   void post_force_respa(int, int, int);
-  void add_tdamping(double spi[3], double fmi[3]);	// add transverse damping
-  void add_temperature(double fmi[3]);			// add temperature
-  int tdamp_flag, ldamp_flag, temp_flag;		// damping and temperature flags
+  void add_tdamping(double *, double *);                 // add transverse damping
+  void add_temperature(double *);                        // add temperature
+  int tdamp_flag, ldamp_flag, temp_flag;                 // damping and temperature flags
 
  protected:
-  double *spi, *fmi;
-  double alpha_t;		// transverse mag. damping
-  double dts;        		// magnetic timestep
-  double temp;       		// spin bath temperature
-  double D,sigma;    		// bath intensity var.
-  double gil_factor; 		// gilbert's prefactor
+  double alpha_t;               // transverse mag. damping
+  double dts;                   // magnetic timestep
+  double temp;                  // spin bath temperature
+  double D,sigma;               // bath intensity var.
+  double gil_factor;            // gilbert's prefactor
 
   char *id_temp;
   class Compute *temperature;
 
   int nlevels_respa;
-  class RanPark *random;
+  class RanMars *random;
   int seed;
 
 };
diff --git a/src/SPIN/fix_neb_spin.h b/src/SPIN/fix_neb_spin.h
index 7ac83ddce7..9646684a3a 100644
--- a/src/SPIN/fix_neb_spin.h
+++ b/src/SPIN/fix_neb_spin.h
@@ -60,20 +60,20 @@ class FixNEBSpin : public Fix {
   double **spprev,**spnext,**fmnext;
   double **springF;
   double **tangent;
-  double **xsend,**xrecv;      	// coords to send/recv to/from other replica
-  double **fsend,**frecv;	// coords to send/recv to/from other replica
-  double **spsend,**sprecv;	// sp to send/recv to/from other replica
-  double **fmsend,**fmrecv;	// fm to send/recv to/from other replica
-  tagint *tagsend,*tagrecv;	// ditto for atom IDs
+  double **xsend,**xrecv;       // coords to send/recv to/from other replica
+  double **fsend,**frecv;       // coords to send/recv to/from other replica
+  double **spsend,**sprecv;     // sp to send/recv to/from other replica
+  double **fmsend,**fmrecv;     // fm to send/recv to/from other replica
+  tagint *tagsend,*tagrecv;     // ditto for atom IDs
 
-  				// info gathered from all procs in my replica
-  double **xsendall,**xrecvall;		// coords to send/recv to/from other replica
-  double **fsendall,**frecvall;		// force to send/recv to/from other replica
-  double **spsendall,**sprecvall;	// sp to send/recv to/from other replica
-  double **fmsendall,**fmrecvall;	// fm to send/recv to/from other replica
-  tagint *tagsendall,*tagrecvall;	// ditto for atom IDs
+                                // info gathered from all procs in my replica
+  double **xsendall,**xrecvall;         // coords to send/recv to/from other replica
+  double **fsendall,**frecvall;         // force to send/recv to/from other replica
+  double **spsendall,**sprecvall;       // sp to send/recv to/from other replica
+  double **fmsendall,**fmrecvall;       // fm to send/recv to/from other replica
+  tagint *tagsendall,*tagrecvall;       // ditto for atom IDs
 
-  int *counts,*displacements;		// used for MPI_Gather
+  int *counts,*displacements;           // used for MPI_Gather
 
   double geodesic_distance(double *, double *);
   void inter_replica_comm();
diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp
index b1b466b5a4..462a359d99 100644
--- a/src/SPIN/fix_nve_spin.cpp
+++ b/src/SPIN/fix_nve_spin.cpp
@@ -91,12 +91,17 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) :
 
   // defining lattice_flag
 
+  // changing the lattice option, from (yes,no) -> (moving,frozen)
+  // for now, (yes,no) still works (to avoid user's confusions).
+
   int iarg = 3;
   while (iarg < narg) {
     if (strcmp(arg[iarg],"lattice") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix/NVE/spin command");
       if (strcmp(arg[iarg+1],"no") == 0) lattice_flag = 0;
+      else if (strcmp(arg[iarg+1],"frozen") == 0) lattice_flag = 0;
       else if (strcmp(arg[iarg+1],"yes") == 0) lattice_flag = 1;
+      else if (strcmp(arg[iarg+1],"moving") == 0) lattice_flag = 1;
       else error->all(FLERR,"Illegal fix/NVE/spin command");
       iarg += 2;
     } else error->all(FLERR,"Illegal fix/NVE/spin command");
@@ -242,7 +247,7 @@ void FixNVESpin::init()
       locksetforcespin = (FixSetForceSpin *) modify->fix[iforce];
     }
   }
-  
+
   // setting the sector variables/lists
 
   nsectors = 0;
@@ -302,7 +307,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/)
           ComputeInteractionsSpin(i);
           AdvanceSingleSpin(i);
           i = forward_stacks[i];
-	}
+        }
       }
     }
     for (int j = nsectors-1; j >= 0; j--) {     // advance quarter s for nlocal
@@ -313,7 +318,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/)
           ComputeInteractionsSpin(i);
           AdvanceSingleSpin(i);
           i = backward_stacks[i];
-	}
+        }
       }
     }
   } else if (sector_flag == 0) {                // serial seq. update
@@ -355,7 +360,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/)
           ComputeInteractionsSpin(i);
           AdvanceSingleSpin(i);
           i = forward_stacks[i];
-	}
+        }
       }
     }
     for (int j = nsectors-1; j >= 0; j--) {     // advance quarter s for nlocal
@@ -366,7 +371,7 @@ void FixNVESpin::initial_integrate(int /*vflag*/)
           ComputeInteractionsSpin(i);
           AdvanceSingleSpin(i);
           i = backward_stacks[i];
-	}
+        }
       }
     }
   } else if (sector_flag == 0) {                // serial seq. update
diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h
index 1e3b87c1fb..5aa6b8e4e4 100644
--- a/src/SPIN/fix_nve_spin.h
+++ b/src/SPIN/fix_nve_spin.h
@@ -34,30 +34,30 @@ friend class PairSpin;
   virtual void initial_integrate(int);
   virtual void final_integrate();
 
-  void ComputeInteractionsSpin(int);	// compute and advance single spin functions
+  void ComputeInteractionsSpin(int);    // compute and advance single spin functions
   void AdvanceSingleSpin(int);
 
-  void sectoring();			// sectoring operation functions
+  void sectoring();                     // sectoring operation functions
   int coords2sector(double *);
 
   void setup_pre_neighbor();
   void pre_neighbor();
 
-  int lattice_flag; 			// lattice_flag = 0 if spins only
-  					// lattice_flag = 1 if spin-lattice calc.
+  int lattice_flag;                     // lattice_flag = 0 if spins only
+                                        // lattice_flag = 1 if spin-lattice calc.
 
  protected:
-  int sector_flag;			// sector_flag = 0  if serial algorithm
-  					// sector_flag = 1  if parallel algorithm
+  int sector_flag;                      // sector_flag = 0  if serial algorithm
+                                        // sector_flag = 1  if parallel algorithm
 
-  double dtv, dtf, dts;			// velocity, force, and spin timesteps
+  double dtv, dtf, dts;                 // velocity, force, and spin timesteps
 
-  int nlocal_max;			// max value of nlocal (for lists size)
+  int nlocal_max;                       // max value of nlocal (for size of lists)
 
-  int pair_spin_flag;			// magnetic pair flags
-  int long_spin_flag;			// magnetic long-range flag
-  int precession_spin_flag;		// magnetic precession flags
-  int maglangevin_flag;			// magnetic langevin flags
+  int pair_spin_flag;                   // magnetic pair flags
+  int long_spin_flag;                   // magnetic long-range flag
+  int precession_spin_flag;             // magnetic precession flags
+  int maglangevin_flag;                 // magnetic langevin flags
   int tdamp_flag, temp_flag;
   int setforce_spin_flag;
 
@@ -69,9 +69,9 @@ friend class PairSpin;
 
   // pointers to magnetic pair styles
 
-  int npairs, npairspin;		// # of pairs, and # of spin pairs
+  int npairs, npairspin;                // # of pairs, and # of spin pairs
   class Pair *pair;
-  class PairSpin **spin_pairs;		// vector of spin pairs
+  class PairSpin **spin_pairs;          // vector of spin pairs
 
   // sectoring variables
 
@@ -80,10 +80,10 @@ friend class PairSpin;
 
   // stacking variables for sectoring algorithm
 
-  int *stack_head;			// index of first atom in backward_stacks
-  int *stack_foot;			// index of first atom in forward_stacks
-  int *backward_stacks;			// index of next atom in backward stack
-  int *forward_stacks;			// index of next atom in forward stack
+  int *stack_head;                      // index of first atom in backward_stacks
+  int *stack_foot;                      // index of first atom in forward_stacks
+  int *backward_stacks;                 // index of next atom in backward stack
+  int *forward_stacks;                  // index of next atom in forward stack
 
 };
 
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index 3296b28228..2d55de33ea 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -126,7 +126,7 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lm
     nay *= inorm;
     naz *= inorm;
   }
-  
+
   if (cubic_flag) {
     inorm = 1.0/sqrt(nc1x*nc1x + nc1y*nc1y + nc1z*nc1z);
     nc1x *= inorm;
@@ -175,7 +175,7 @@ void FixPrecessionSpin::init()
 {
   const double hbar = force->hplanck/MY_2PI;    // eV/(rad.THz)
   const double mub = 5.78901e-5;                // in eV/T
-  const double gyro = mub/hbar;                 // in rad.THz/T
+  const double gyro = 2.0*mub/hbar;             // in rad.THz/T
 
   // convert field quantities to rad.THz
 
@@ -236,7 +236,7 @@ void FixPrecessionSpin::post_force(int /* vflag */)
   if (varflag != CONSTANT) {
     modify->clearstep_compute();
     modify->addstep_compute(update->ntimestep + 1);
-    set_magneticprecession();		// update mag. field if time-dep.
+    set_magneticprecession();           // update mag. field if time-dep.
   }
 
   int *mask = atom->mask;
@@ -244,7 +244,7 @@ void FixPrecessionSpin::post_force(int /* vflag */)
   double **sp = atom->sp;
   const int nlocal = atom->nlocal;
   double spi[3], fmi[3], epreci;
-  
+
   eflag = 0;
   eprec = 0.0;
   for (int i = 0; i < nlocal; i++) {
@@ -265,9 +265,9 @@ void FixPrecessionSpin::post_force(int /* vflag */)
         epreci -= compute_anisotropy_energy(spi);
       }
 
-      if (cubic_flag) {		// compute cubic anisotropy
-	compute_cubic(spi,fmi);
-	epreci -= compute_cubic_energy(spi);
+      if (cubic_flag) {         // compute cubic anisotropy
+        compute_cubic(spi,fmi);
+        epreci -= compute_cubic_energy(spi);
       }
 
       eprec += epreci;
@@ -317,48 +317,6 @@ double FixPrecessionSpin::compute_anisotropy_energy(double spi[3])
   double energy = 0.0;
   double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2];
   energy = Ka*scalar*scalar;
-  return energy; 
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
-{
-  if (ilevel == ilevel_respa) post_force(vflag);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPrecessionSpin::set_magneticprecession()
-{
-  if (zeeman_flag) {
-    hx = H_field*nhx;
-    hy = H_field*nhy;
-    hz = H_field*nhz;
-  }
-  if (aniso_flag) {
-    Kax = 2.0*Kah*nax;
-    Kay = 2.0*Kah*nay;
-    Kaz = 2.0*Kah*naz;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   compute cubic aniso energy of spin i
-------------------------------------------------------------------------- */
-
-double FixPrecessionSpin::compute_cubic_energy(double spi[3])
-{
-  double energy = 0.0;
-  double skx,sky,skz;
-
-  skx = spi[0]*nc1x+spi[1]*nc1y+spi[2]*nc1z;
-  sky = spi[0]*nc2x+spi[1]*nc2y+spi[2]*nc2z;
-  skz = spi[0]*nc3x+spi[1]*nc3y+spi[2]*nc3z;
-
-  energy = k1c*(skx*skx*sky*sky + sky*sky*skz*skz + skx*skx*skz*skz);
-  energy += k2c*skx*skx*sky*sky*skz*skz;
-
   return energy;
 }
 
@@ -391,14 +349,49 @@ void FixPrecessionSpin::compute_cubic(double spi[3], double fmi[3])
   six1 = 2.0*skx*sky2*skz2;
   six2 = 2.0*sky*skx2*skz2;
   six3 = 2.0*skz*skx2*sky2;
-  
+
   sixx = k2ch*(nc1x*six1 + nc2x*six2 + nc3x*six3);
   sixy = k2ch*(nc1y*six1 + nc2y*six2 + nc3y*six3);
   sixz = k2ch*(nc1z*six1 + nc2z*six2 + nc3z*six3);
-  
-  fmi[0] += fourx + sixx;
-  fmi[1] += foury + sixy;
-  fmi[2] += fourz + sixz;
+
+  fmi[0] += (fourx + sixx);
+  fmi[1] += (foury + sixy);
+  fmi[2] += (fourz + sixz);
+}
+
+/* ----------------------------------------------------------------------
+   compute cubic aniso energy of spin i
+------------------------------------------------------------------------- */
+
+double FixPrecessionSpin::compute_cubic_energy(double spi[3])
+{
+  double energy = 0.0;
+  double skx,sky,skz;
+
+  skx = spi[0]*nc1x+spi[1]*nc1y+spi[2]*nc1z;
+  sky = spi[0]*nc2x+spi[1]*nc2y+spi[2]*nc2z;
+  skz = spi[0]*nc3x+spi[1]*nc3y+spi[2]*nc3z;
+
+  energy = k1c*(skx*skx*sky*sky + sky*sky*skz*skz + skx*skx*skz*skz);
+  energy += k2c*skx*skx*sky*sky*skz*skz;
+
+  return energy;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPrecessionSpin::set_magneticprecession()
+{
+  if (zeeman_flag) {
+    hx = H_field*nhx;
+    hy = H_field*nhy;
+    hz = H_field*nhz;
+  }
+  if (aniso_flag) {
+    Kax = 2.0*Kah*nax;
+    Kay = 2.0*Kah*nay;
+    Kaz = 2.0*Kah*naz;
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -422,3 +415,10 @@ void FixPrecessionSpin::min_post_force(int vflag)
 {
   post_force(vflag);
 }
+
+/* ---------------------------------------------------------------------- */
+
+void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
+{
+  if (ilevel == ilevel_respa) post_force(vflag);
+}
diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h
index 0037784a48..6ece653ca7 100644
--- a/src/SPIN/fix_precession_spin.h
+++ b/src/SPIN/fix_precession_spin.h
@@ -42,7 +42,7 @@ class FixPrecessionSpin : public Fix {
   int zeeman_flag, aniso_flag, cubic_flag;
   void compute_single_precession(int, double *, double *);
   void compute_zeeman(int, double *);
-  
+
   // uniaxial aniso calculations
 
   void compute_anisotropy(double *, double *);
@@ -52,9 +52,9 @@ class FixPrecessionSpin : public Fix {
 
   void compute_cubic(double *, double *);
   double compute_cubic_energy(double *);
- 
+
  protected:
-  int style; 			// style of the magnetic precession
+  int style;                    // style of the magnetic precession
 
   double degree2rad;
   double hbar;
@@ -72,19 +72,19 @@ class FixPrecessionSpin : public Fix {
 
   double H_field;
   double nhx, nhy, nhz;
-  double hx, hy, hz; 		// temp. force variables
+  double hx, hy, hz;            // temp. force variables
 
   // magnetic anisotropy intensity and direction
 
-  double Ka;			// aniso const. in eV
-  double Kah;			// aniso const. in rad.THz
+  double Ka;                    // aniso const. in eV
+  double Kah;                   // aniso const. in rad.THz
   double nax, nay, naz;
-  double Kax, Kay, Kaz; 	// temp. force variables
+  double Kax, Kay, Kaz;         // temp. force variables
 
   // cubic anisotropy intensity
 
-  double k1c,k2c;		// cubic const. in eV
-  double k1ch,k2ch;		// cubic const. in rad.THz
+  double k1c,k2c;               // cubic const. in eV
+  double k1ch,k2ch;             // cubic const. in rad.THz
   double nc1x,nc1y,nc1z;
   double nc2x,nc2y,nc2z;
   double nc3x,nc3y,nc3z;
diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp
index e36a9d260d..ec738b7522 100644
--- a/src/SPIN/fix_setforce_spin.cpp
+++ b/src/SPIN/fix_setforce_spin.cpp
@@ -140,7 +140,7 @@ void FixSetForceSpin::single_setforce_spin(int i, double fmi[3])
 
   foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
   force_flag = 0;
- 
+
   // constant force
 
   if (varflag == CONSTANT) {
diff --git a/src/SPIN/fix_setforce_spin.h b/src/SPIN/fix_setforce_spin.h
index a836911d85..1c5ce54dd3 100644
--- a/src/SPIN/fix_setforce_spin.h
+++ b/src/SPIN/fix_setforce_spin.h
@@ -29,7 +29,7 @@ class FixSetForceSpin : public FixSetForce {
   FixSetForceSpin(class LAMMPS *, int, char **);
   virtual void post_force(int);
   void post_force_respa(int, int, int);
-  void single_setforce_spin(int, double *); 
+  void single_setforce_spin(int, double *);
 };
 
 }
diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp
index 553526ea8e..e39eb18744 100644
--- a/src/SPIN/min_spin.cpp
+++ b/src/SPIN/min_spin.cpp
@@ -41,15 +41,15 @@ using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-MinSpin::MinSpin(LAMMPS *lmp) : Min(lmp) {}
+MinSpin::MinSpin(LAMMPS *lmp) : Min(lmp) {
+  alpha_damp = 1.0;
+  discrete_factor = 10.0;
+}
 
 /* ---------------------------------------------------------------------- */
 
 void MinSpin::init()
 {
-  alpha_damp = 1.0;
-  discrete_factor = 10.0;
-
   Min::init();
 
   dts = dt = update->dt;
@@ -77,12 +77,12 @@ void MinSpin::setup_style()
 int MinSpin::modify_param(int narg, char **arg)
 {
   if (strcmp(arg[0],"alpha_damp") == 0) {
-    if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+    if (narg < 2) error->all(FLERR,"Illegal min_modify command");
     alpha_damp = force->numeric(FLERR,arg[1]);
     return 2;
   }
   if (strcmp(arg[0],"discrete_factor") == 0) {
-    if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+    if (narg < 2) error->all(FLERR,"Illegal min_modify command");
     discrete_factor = force->numeric(FLERR,arg[1]);
     return 2;
   }
@@ -116,7 +116,7 @@ void MinSpin::reset_vectors()
 int MinSpin::iterate(int maxiter)
 {
   bigint ntimestep;
-  double fmdotfm;
+  double fmdotfm,fmsq;
   int flag,flagall;
 
   for (int iter = 0; iter < maxiter; iter++) {
@@ -130,7 +130,7 @@ int MinSpin::iterate(int maxiter)
     // optimize timestep accross processes / replicas
     // need a force calculation for timestep optimization
 
-    energy_force(0);
+    if (iter == 0) energy_force(0);
     dts = evaluate_dt();
 
     // apply damped precessional dynamics to the spins
@@ -163,8 +163,13 @@ int MinSpin::iterate(int maxiter)
     // magnetic torque tolerance criterion
     // sync across replicas if running multi-replica minimization
 
+    fmdotfm = fmsq = 0.0;
     if (update->ftol > 0.0) {
-      fmdotfm = fmnorm_sqr();
+      if (normstyle == MAX) fmsq = max_torque();        // max torque norm
+      else if (normstyle == INF) fmsq = inf_torque();   // inf torque norm
+      else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm
+      else error->all(FLERR,"Illegal min_modify command");
+      fmdotfm = fmsq*fmsq;
       if (update->multireplica == 0) {
         if (fmdotfm < update->ftol*update->ftol) return FTOL;
       } else {
@@ -242,7 +247,7 @@ void MinSpin::advance_spins(double dts)
   double **sp = atom->sp;
   double **fm = atom->fm;
   double tdampx,tdampy,tdampz;
-  double msq,scale,fm2,energy,dts2;
+  double fm2,energy,dts2;
   double cp[3],g[3];
 
   dts2 = dts*dts;
@@ -288,37 +293,3 @@ void MinSpin::advance_spins(double dts)
     // because no need for simplecticity
   }
 }
-
-/* ----------------------------------------------------------------------
-   compute and return ||mag. torque||_2^2
-------------------------------------------------------------------------- */
-
-double MinSpin::fmnorm_sqr()
-{
-  int nlocal = atom->nlocal;
-  double tx,ty,tz;
-  double **sp = atom->sp;
-  double **fm = atom->fm;
-
-  // calc. magnetic torques
-
-  double local_norm2_sqr = 0.0;
-  for (int i = 0; i < nlocal; i++) {
-    tx = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]);
-    ty = (fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]);
-    tz = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]);
-
-    local_norm2_sqr += tx*tx + ty*ty + tz*tz;
-  }
-
-  // no extra atom calc. for spins
-
-  if (nextra_atom)
-    error->all(FLERR,"extra atom option not available yet");
-
-  double norm2_sqr = 0.0;
-  MPI_Allreduce(&local_norm2_sqr,&norm2_sqr,1,MPI_DOUBLE,MPI_SUM,world);
-
-  return norm2_sqr;
-}
-
diff --git a/src/SPIN/min_spin.h b/src/SPIN/min_spin.h
index fbc624a9cc..f2df81e58c 100644
--- a/src/SPIN/min_spin.h
+++ b/src/SPIN/min_spin.h
@@ -35,7 +35,6 @@ class MinSpin : public Min {
   int iterate(int);
   double evaluate_dt();
   void advance_spins(double);
-  double fmnorm_sqr();
 
  private:
 
diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp
new file mode 100644
index 0000000000..8815ad89db
--- /dev/null
+++ b/src/SPIN/min_spin_cg.cpp
@@ -0,0 +1,649 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ------------------------------------------------------------------------
+   Contributing authors: Aleksei Ivanov (University of Iceland)
+                         Julien Tranchida (SNL)
+
+   Please cite the related publication:
+   Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust
+   Algorithm for the Minimisation of the Energy of Spin Systems. arXiv
+   preprint arXiv:1904.02669.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include "min_spin_cg.h"
+#include "universe.h"
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "force.h"
+#include "update.h"
+#include "output.h"
+#include "timer.h"
+#include "error.h"
+#include "memory.h"
+#include "modify.h"
+#include "math_special.h"
+#include "math_const.h"
+#include "universe.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+static const char cite_minstyle_spin_cg[] =
+  "min_style spin/cg command:\n\n"
+  "@article{ivanov2019fast,\n"
+  "title={Fast and Robust Algorithm for the Minimisation of the Energy of "
+  "Spin Systems},\n"
+  "author={Ivanov, A. V and Uzdin, V. M. and J{\'o}nsson, H.},\n"
+  "journal={arXiv preprint arXiv:1904.02669},\n"
+  "year={2019}\n"
+  "}\n\n";
+
+// EPS_ENERGY = minimum normalization for energy tolerance
+
+#define EPS_ENERGY 1.0e-8
+
+#define DELAYSTEP 5
+
+/* ---------------------------------------------------------------------- */
+
+MinSpinCG::MinSpinCG(LAMMPS *lmp) :
+  Min(lmp), g_old(NULL), g_cur(NULL), p_s(NULL), sp_copy(NULL)
+{
+  if (lmp->citeme) lmp->citeme->add(cite_minstyle_spin_cg);
+  nlocal_max = 0;
+
+  // nreplica = number of partitions
+  // ireplica = which world I am in universe
+
+  nreplica = universe->nworlds;
+  ireplica = universe->iworld;
+  use_line_search = 0;  // no line search as default option for CG
+
+  discrete_factor = 10.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+MinSpinCG::~MinSpinCG()
+{
+  memory->destroy(g_old);
+  memory->destroy(g_cur);
+  memory->destroy(p_s);
+  if (use_line_search)
+    memory->destroy(sp_copy);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MinSpinCG::init()
+{
+  local_iter = 0;
+  der_e_cur = 0.0;
+  der_e_pr = 0.0;
+
+  Min::init();
+
+  // warning if line_search combined to gneb
+
+  if ((nreplica >= 1) && (linestyle != 4) && (comm->me == 0))
+    error->warning(FLERR,"Line search incompatible gneb");
+
+  // set back use_line_search to 0 if more than one replica
+
+  if (linestyle == 3 && nreplica == 1){
+    use_line_search = 1;
+  }
+  else{
+    use_line_search = 0;
+  }
+
+  dts = dt = update->dt;
+  last_negative = update->ntimestep;
+
+  // allocate tables
+
+  nlocal_max = atom->nlocal;
+  memory->grow(g_old,3*nlocal_max,"min/spin/cg:g_old");
+  memory->grow(g_cur,3*nlocal_max,"min/spin/cg:g_cur");
+  memory->grow(p_s,3*nlocal_max,"min/spin/cg:p_s");
+  if (use_line_search)
+    memory->grow(sp_copy,nlocal_max,3,"min/spin/cg:sp_copy");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MinSpinCG::setup_style()
+{
+  double **v = atom->v;
+  int nlocal = atom->nlocal;
+
+  // check if the atom/spin style is defined
+
+  if (!atom->sp_flag)
+    error->all(FLERR,"min spin/cg requires atom/spin style");
+
+  for (int i = 0; i < nlocal; i++)
+    v[i][0] = v[i][1] = v[i][2] = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int MinSpinCG::modify_param(int narg, char **arg)
+{
+  if (strcmp(arg[0],"discrete_factor") == 0) {
+    if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+    discrete_factor = force->numeric(FLERR,arg[1]);
+    return 2;
+  }
+  return 0;
+}
+
+/* ----------------------------------------------------------------------
+   set current vector lengths and pointers
+   called after atoms have migrated
+------------------------------------------------------------------------- */
+
+void MinSpinCG::reset_vectors()
+{
+  // atomic dof
+
+  // size sp is 4N vector
+  nvec = 4 * atom->nlocal;
+  if (nvec) spvec = atom->sp[0];
+
+  nvec = 3 * atom->nlocal;
+  if (nvec) fmvec = atom->fm[0];
+
+  if (nvec) xvec = atom->x[0];
+  if (nvec) fvec = atom->f[0];
+}
+
+/* ----------------------------------------------------------------------
+   minimization via orthogonal spin optimisation
+------------------------------------------------------------------------- */
+
+int MinSpinCG::iterate(int maxiter)
+{
+  int nlocal = atom->nlocal;
+  bigint ntimestep;
+  double fmdotfm,fmsq;
+  int flag, flagall;
+  double **sp = atom->sp;
+  double der_e_cur_tmp = 0.0;
+
+  if (nlocal_max < nlocal) {
+    local_iter = 0;
+    nlocal_max = nlocal;
+    memory->grow(g_old,3*nlocal_max,"min/spin/cg:g_old");
+    memory->grow(g_cur,3*nlocal_max,"min/spin/cg:g_cur");
+    memory->grow(p_s,3*nlocal_max,"min/spin/cg:p_s");
+    if (use_line_search)
+      memory->grow(sp_copy,nlocal_max,3,"min/spin/cg:sp_copy");
+  }
+
+  for (int iter = 0; iter < maxiter; iter++) {
+
+    if (timer->check_timeout(niter))
+      return TIMEOUT;
+
+    ntimestep = ++update->ntimestep;
+    niter++;
+
+    // optimize timestep accross processes / replicas
+    // need a force calculation for timestep optimization
+
+    if (use_line_search) {
+
+      // here we need to do line search
+      if (local_iter == 0){
+        calc_gradient();
+      }
+
+      calc_search_direction();
+      der_e_cur = 0.0;
+      for (int i = 0; i < 3 * nlocal; i++)
+        der_e_cur += g_cur[i] * p_s[i];
+      MPI_Allreduce(&der_e_cur,&der_e_cur_tmp,1,MPI_DOUBLE,MPI_SUM,world);
+      der_e_cur = der_e_cur_tmp;
+      if (update->multireplica == 1) {
+        MPI_Allreduce(&der_e_cur_tmp,&der_e_cur,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+      }
+      for (int i = 0; i < nlocal; i++)
+        for (int j = 0; j < 3; j++)
+          sp_copy[i][j] = sp[i][j];
+
+      eprevious = ecurrent;
+      der_e_pr = der_e_cur;
+      calc_and_make_step(0.0, 1.0, 0);
+    }
+    else{
+
+      // here we don't do line search
+      // if gneb calc., nreplica > 1
+      // then calculate gradients and advance spins
+      // of intermediate replicas only
+      calc_gradient();
+      calc_search_direction();
+      advance_spins();
+      neval++;
+      eprevious = ecurrent;
+      ecurrent = energy_force(0);
+    }
+
+    // energy tolerance criterion
+    // only check after DELAYSTEP elapsed since velocties reset to 0
+    // sync across replicas if running multi-replica minimization
+
+    if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) {
+      if (update->multireplica == 0) {
+        if (fabs(ecurrent-eprevious) <
+            update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+          return ETOL;
+      } else {
+        if (fabs(ecurrent-eprevious) <
+            update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+          flag = 0;
+        else flag = 1;
+        MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
+        if (flagall == 0) return ETOL;
+      }
+    }
+
+    // magnetic torque tolerance criterion
+    // sync across replicas if running multi-replica minimization
+
+    fmdotfm = fmsq = 0.0;
+    if (update->ftol > 0.0) {
+      if (normstyle == MAX) fmsq = max_torque();        // max torque norm
+      else if (normstyle == INF) fmsq = inf_torque();   // inf torque norm
+      else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm
+      else error->all(FLERR,"Illegal min_modify command");
+      fmdotfm = fmsq*fmsq;
+      if (update->multireplica == 0) {
+        if (fmdotfm < update->ftol*update->ftol) return FTOL;
+      } else {
+        if (fmdotfm < update->ftol*update->ftol) flag = 0;
+        else flag = 1;
+        MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
+        if (flagall == 0) return FTOL;
+      }
+    }
+
+    // output for thermo, dump, restart files
+
+    if (output->next == ntimestep) {
+      timer->stamp();
+      output->write(ntimestep);
+      timer->stamp(Timer::OUTPUT);
+    }
+  }
+
+  return MAXITER;
+}
+
+/* ----------------------------------------------------------------------
+   calculate gradients
+---------------------------------------------------------------------- */
+
+void MinSpinCG::calc_gradient()
+{
+  int nlocal = atom->nlocal;
+  double **sp = atom->sp;
+  double **fm = atom->fm;
+  double hbar = force->hplanck/MY_2PI;
+  double factor;
+
+  if (use_line_search)
+    factor = hbar;
+  else factor = evaluate_dt();
+
+  // loop on all spins on proc.
+
+  for (int i = 0; i < nlocal; i++) {
+    g_cur[3 * i + 0] = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]) * factor;
+    g_cur[3 * i + 1] = -(fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]) * factor;
+    g_cur[3 * i + 2] = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]) * factor;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   search direction:
+   The Fletcher-Reeves conj. grad. method
+   See Jorge Nocedal and Stephen J. Wright 'Numerical
+   Optimization' Second Edition, 2006 (p. 121)
+---------------------------------------------------------------------- */
+
+void MinSpinCG::calc_search_direction()
+{
+  int nlocal = atom->nlocal;
+  double g2old = 0.0;
+  double g2 = 0.0;
+  double beta = 0.0;
+
+  double g2_global = 0.0;
+  double g2old_global = 0.0;
+
+  double factor = 1.0;
+
+  // for multiple replica do not move end points
+  if (nreplica > 1)
+    if (ireplica == 0 || ireplica == nreplica - 1)
+      factor = 0.0;
+
+
+  if (local_iter == 0 || local_iter % 5 == 0){  // steepest descent direction
+    for (int i = 0; i < 3 * nlocal; i++) {
+      p_s[i] = -g_cur[i] * factor;
+      g_old[i] = g_cur[i] * factor;
+    }
+  } else {                              // conjugate direction
+    for (int i = 0; i < 3 * nlocal; i++) {
+      g2old += g_old[i] * g_old[i];
+      g2 += g_cur[i] * g_cur[i];
+    }
+
+    // now we need to collect/broadcast beta on this replica
+    // need to check what is beta for GNEB
+
+    MPI_Allreduce(&g2,&g2_global,1,MPI_DOUBLE,MPI_SUM,world);
+    MPI_Allreduce(&g2old,&g2old_global,1,MPI_DOUBLE,MPI_SUM,world);
+
+    // Sum over all replicas. Good for GNEB.
+
+    if (nreplica > 1) {
+      g2 = g2_global * factor;
+      g2old = g2old_global * factor;
+      MPI_Allreduce(&g2,&g2_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+      MPI_Allreduce(&g2old,&g2old_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+    }
+    if (fabs(g2_global) < 1.0e-60) beta = 0.0;
+    else beta = g2_global / g2old_global;
+
+    // calculate conjugate direction
+
+    for (int i = 0; i < 3 * nlocal; i++) {
+      p_s[i] = (beta * p_s[i] - g_cur[i]) * factor;
+      g_old[i] = g_cur[i] * factor;
+    }
+  }
+
+  local_iter++;
+}
+
+/* ----------------------------------------------------------------------
+   rotation of spins along the search direction
+---------------------------------------------------------------------- */
+
+void MinSpinCG::advance_spins()
+{
+  int nlocal = atom->nlocal;
+  double **sp = atom->sp;
+  double rot_mat[9];    // exponential of matrix made of search direction
+  double s_new[3];
+
+  // loop on all spins on proc.
+
+  for (int i = 0; i < nlocal; i++) {
+    rodrigues_rotation(p_s + 3 * i, rot_mat);
+
+    // rotate spins
+
+    vm3(rot_mat, sp[i], s_new);
+    for (int j = 0; j < 3; j++) sp[i][j] = s_new[j];
+  }
+}
+
+/* ----------------------------------------------------------------------
+  calculate 3x3 matrix exponential using Rodrigues' formula
+  (R. Murray, Z. Li, and S. Shankar Sastry,
+  A Mathematical Introduction to
+  Robotic Manipulation (1994), p. 28 and 30).
+
+  upp_tr - vector x, y, z so that one calculate
+  U = exp(A) with A= [[0, x, y],
+                      [-x, 0, z],
+                      [-y, -z, 0]]
+------------------------------------------------------------------------- */
+
+void MinSpinCG::rodrigues_rotation(const double *upp_tr, double *out)
+{
+  double theta,A,B,D,x,y,z;
+  double s1,s2,s3,a1,a2,a3;
+
+  if (fabs(upp_tr[0]) < 1.0e-40 &&
+      fabs(upp_tr[1]) < 1.0e-40 &&
+      fabs(upp_tr[2]) < 1.0e-40){
+
+    // if upp_tr is zero, return unity matrix
+
+    for(int k = 0; k < 3; k++){
+      for(int m = 0; m < 3; m++){
+        if (m == k) out[3 * k + m] = 1.0;
+        else out[3 * k + m] = 0.0;
+      }
+    }
+    return;
+  }
+
+  theta = sqrt(upp_tr[0] * upp_tr[0] +
+               upp_tr[1] * upp_tr[1] +
+               upp_tr[2] * upp_tr[2]);
+
+  A = cos(theta);
+  B = sin(theta);
+  D = 1.0 - A;
+  x = upp_tr[0]/theta;
+  y = upp_tr[1]/theta;
+  z = upp_tr[2]/theta;
+
+  // diagonal elements of U
+
+  out[0] = A + z * z * D;
+  out[4] = A + y * y * D;
+  out[8] = A + x * x * D;
+
+  // off diagonal of U
+
+  s1 = -y * z *D;
+  s2 = x * z * D;
+  s3 = -x * y * D;
+
+  a1 = x * B;
+  a2 = y * B;
+  a3 = z * B;
+
+  out[1] = s1 + a1;
+  out[3] = s1 - a1;
+  out[2] = s2 + a2;
+  out[6] = s2 - a2;
+  out[5] = s3 + a3;
+  out[7] = s3 - a3;
+
+}
+
+/* ----------------------------------------------------------------------
+  out = vector^T x m,
+  m -- 3x3 matrix , v -- 3-d vector
+------------------------------------------------------------------------- */
+
+void MinSpinCG::vm3(const double *m, const double *v, double *out)
+{
+  for(int i = 0; i < 3; i++){
+    out[i] = 0.0;
+    for(int j = 0; j < 3; j++) out[i] += *(m + 3 * j + i) * v[j];
+  }
+}
+
+/* ----------------------------------------------------------------------
+  advance spins
+------------------------------------------------------------------------- */
+
+void MinSpinCG::make_step(double c, double *energy_and_der)
+{
+  double p_scaled[3];
+  int nlocal = atom->nlocal;
+  double rot_mat[9]; // exponential of matrix made of search direction
+  double s_new[3];
+  double **sp = atom->sp;
+  double der_e_cur_tmp = 0.0;
+
+  for (int i = 0; i < nlocal; i++) {
+
+    // scale the search direction
+
+    for (int j = 0; j < 3; j++) p_scaled[j] = c * p_s[3 * i + j];
+
+    // calculate rotation matrix
+
+    rodrigues_rotation(p_scaled, rot_mat);
+
+    // rotate spins
+
+    vm3(rot_mat, sp[i], s_new);
+    for (int j = 0; j < 3; j++) sp[i][j] = s_new[j];
+  }
+
+  ecurrent = energy_force(0);
+  calc_gradient();
+  neval++;
+  der_e_cur = 0.0;
+  for (int i = 0; i < 3 * nlocal; i++) {
+    der_e_cur += g_cur[i] * p_s[i];
+  }
+  MPI_Allreduce(&der_e_cur,&der_e_cur_tmp,1,MPI_DOUBLE,MPI_SUM,world);
+  der_e_cur = der_e_cur_tmp;
+  if (update->multireplica == 1) {
+    MPI_Allreduce(&der_e_cur_tmp,&der_e_cur,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+  }
+
+  energy_and_der[0] = ecurrent;
+  energy_and_der[1] = der_e_cur;
+}
+
+/* ----------------------------------------------------------------------
+  Calculate step length which satisfies approximate Wolfe conditions
+  using the cubic interpolation
+------------------------------------------------------------------------- */
+
+int MinSpinCG::calc_and_make_step(double a, double b, int index)
+{
+  double e_and_d[2] = {0.0,0.0};
+  double alpha,c1,c2,c3;
+  double **sp = atom->sp;
+  int nlocal = atom->nlocal;
+
+  make_step(b,e_and_d);
+  ecurrent = e_and_d[0];
+  der_e_cur = e_and_d[1];
+  index++;
+
+  if (adescent(eprevious,e_and_d[0]) || index == 5){
+    MPI_Bcast(&b,1,MPI_DOUBLE,0,world);
+    for (int i = 0; i < 3 * nlocal; i++) {
+      p_s[i] = b * p_s[i];
+    }
+    return 1;
+  }
+  else {
+    double r,f0,f1,df0,df1;
+    r = b - a;
+    f0 = eprevious;
+    f1 = ecurrent;
+    df0 = der_e_pr;
+    df1 = der_e_cur;
+
+    c1 = -2.0*(f1-f0)/(r*r*r)+(df1+df0)/(r*r);
+    c2 = 3.0*(f1-f0)/(r*r)-(df1+2.0*df0)/(r);
+    c3 = df0;
+
+    // f(x) = c1 x^3 + c2 x^2 + c3 x^1 + c4
+    // has minimum at alpha below. We do not check boundaries.
+
+    alpha = (-c2 + sqrt(c2*c2 - 3.0*c1*c3))/(3.0*c1);
+    MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world);
+
+    if (alpha < 0.0) alpha = r/2.0;
+
+    for (int i = 0; i < nlocal; i++) {
+      for (int j = 0; j < 3; j++) sp[i][j] = sp_copy[i][j];
+    }
+    calc_and_make_step(0.0, alpha, index);
+   }
+
+  return 0;
+}
+
+/* ----------------------------------------------------------------------
+  Approximate descent
+------------------------------------------------------------------------- */
+
+int MinSpinCG::adescent(double phi_0, double phi_j){
+
+  double eps = 1.0e-6;
+
+  if (phi_j<=phi_0+eps*fabs(phi_0))
+    return 1;
+  else
+    return 0;
+}
+
+/* ----------------------------------------------------------------------
+   evaluate max timestep
+---------------------------------------------------------------------- */
+
+double MinSpinCG::evaluate_dt()
+{
+  double dtmax;
+  double fmsq;
+  double fmaxsqone,fmaxsqloc,fmaxsqall;
+  int nlocal = atom->nlocal;
+  double **fm = atom->fm;
+
+  // finding max fm on this proc.
+
+  fmsq = fmaxsqone = fmaxsqloc = fmaxsqall = 0.0;
+  for (int i = 0; i < nlocal; i++) {
+    fmsq = fm[i][0]*fm[i][0]+fm[i][1]*fm[i][1]+fm[i][2]*fm[i][2];
+    fmaxsqone = MAX(fmaxsqone,fmsq);
+  }
+
+  // finding max fm on this replica
+
+  fmaxsqloc = fmaxsqone;
+  MPI_Allreduce(&fmaxsqone,&fmaxsqloc,1,MPI_DOUBLE,MPI_MAX,world);
+
+  // finding max fm over all replicas, if necessary
+  // this communicator would be invalid for multiprocess replicas
+
+  fmaxsqall = fmaxsqloc;
+  if (update->multireplica == 1) {
+    fmaxsqall = fmaxsqloc;
+    MPI_Allreduce(&fmaxsqloc,&fmaxsqall,1,MPI_DOUBLE,MPI_MAX,universe->uworld);
+  }
+
+  if (fmaxsqall == 0.0)
+    error->all(FLERR,"Incorrect fmaxsqall calculation");
+
+  // define max timestep by dividing by the
+  // inverse of max frequency by discrete_factor
+
+  dtmax = MY_2PI/(discrete_factor*sqrt(fmaxsqall));
+
+  return dtmax;
+}
diff --git a/src/SPIN/min_spin_cg.h b/src/SPIN/min_spin_cg.h
new file mode 100644
index 0000000000..640721b8ef
--- /dev/null
+++ b/src/SPIN/min_spin_cg.h
@@ -0,0 +1,71 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef MINIMIZE_CLASS
+
+MinimizeStyle(spin/cg, MinSpinCG)
+
+#else
+
+#ifndef LMP_MIN_SPIN_CG_H
+#define LMP_MIN_SPIN_CG_H
+
+#include "min.h"
+
+namespace LAMMPS_NS {
+
+class MinSpinCG: public Min {
+ public:
+  MinSpinCG(class LAMMPS *);
+  virtual ~MinSpinCG();
+  void init();
+  void setup_style();
+  void reset_vectors();
+  int modify_param(int, char **);
+  int iterate(int);
+
+ private:
+  int local_iter;               // for neb
+  int nlocal_max;               // max value of nlocal (for size of lists)
+  int use_line_search;          // use line search or not.
+  int ireplica,nreplica;        // for neb
+  double dt;                    // global timestep
+  double dts;                   // spin timestep
+  double discrete_factor;       // factor for spin timestep evaluation
+  double der_e_cur;             // current derivative along search dir.
+  double der_e_pr;              // previous derivative along search dir.
+  double *spvec;                // variables for atomic dof, as 1d vector
+  double *fmvec;                // variables for atomic dof, as 1d vector
+  double *g_old;                // gradient vector at previous step
+  double *g_cur;                // current gradient vector
+  double *p_s;                  // search direction vector
+  double **sp_copy;             // copy of the spins
+
+  void advance_spins();
+  void calc_gradient();
+  void calc_search_direction();
+  void vm3(const double *, const double *, double *);
+  void rodrigues_rotation(const double *, double *);
+  void make_step(double, double *);
+  int calc_and_make_step(double, double, int);
+  int adescent(double, double);
+  double evaluate_dt();
+  double maximum_rotation(double *);
+
+  bigint last_negative;
+};
+
+}
+
+#endif
+#endif
diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp
new file mode 100644
index 0000000000..7f6d7692cd
--- /dev/null
+++ b/src/SPIN/min_spin_lbfgs.cpp
@@ -0,0 +1,754 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ------------------------------------------------------------------------
+   Contributing authors: Aleksei Ivanov (University of Iceland)
+                         Julien Tranchida (SNL)
+
+   Please cite the related publication:
+   Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust
+   Algorithm for the Minimisation of the Energy of Spin Systems. arXiv
+   preprint arXiv:1904.02669.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include "min_spin_lbfgs.h"
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "force.h"
+#include "update.h"
+#include "output.h"
+#include "timer.h"
+#include "error.h"
+#include "memory.h"
+#include "modify.h"
+#include "math_special.h"
+#include "math_const.h"
+#include "universe.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+static const char cite_minstyle_spin_lbfgs[] =
+  "min_style spin/lbfgs command:\n\n"
+  "@article{ivanov2019fast,\n"
+  "title={Fast and Robust Algorithm for the Minimisation of the Energy of "
+  "Spin Systems},\n"
+  "author={Ivanov, A. V and Uzdin, V. M. and J{\'o}nsson, H.},\n"
+  "journal={arXiv preprint arXiv:1904.02669},\n"
+  "year={2019}\n"
+  "}\n\n";
+
+// EPS_ENERGY = minimum normalization for energy tolerance
+
+#define EPS_ENERGY 1.0e-8
+
+#define DELAYSTEP 5
+
+/* ---------------------------------------------------------------------- */
+
+MinSpinLBFGS::MinSpinLBFGS(LAMMPS *lmp) :
+  Min(lmp), g_old(NULL), g_cur(NULL), p_s(NULL), rho(NULL), ds(NULL), dy(NULL), sp_copy(NULL)
+{
+  if (lmp->citeme) lmp->citeme->add(cite_minstyle_spin_lbfgs);
+  nlocal_max = 0;
+
+  // nreplica = number of partitions
+  // ireplica = which world I am in universe
+
+  nreplica = universe->nworlds;
+  ireplica = universe->iworld;
+  use_line_search = 0;  // no line search as default option for LBFGS
+
+  maxepsrot = MY_2PI / (100.0);
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+MinSpinLBFGS::~MinSpinLBFGS()
+{
+    memory->destroy(g_old);
+    memory->destroy(g_cur);
+    memory->destroy(p_s);
+    memory->destroy(ds);
+    memory->destroy(dy);
+    memory->destroy(rho);
+    if (use_line_search)
+      memory->destroy(sp_copy);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MinSpinLBFGS::init()
+{
+  num_mem = 3;
+  local_iter = 0;
+  der_e_cur = 0.0;
+  der_e_pr = 0.0;
+
+  Min::init();
+
+  // warning if line_search combined to gneb
+
+  if ((nreplica >= 1) && (linestyle != 4) && (comm->me == 0))
+    error->warning(FLERR,"Line search incompatible gneb");
+
+  // set back use_line_search to 0 if more than one replica
+
+  if (linestyle == 3 && nreplica == 1){
+    use_line_search = 1;
+  }
+  else{
+    use_line_search = 0;
+  }
+
+  last_negative = update->ntimestep;
+
+  // allocate tables
+
+  nlocal_max = atom->nlocal;
+  memory->grow(g_old,3*nlocal_max,"min/spin/lbfgs:g_old");
+  memory->grow(g_cur,3*nlocal_max,"min/spin/lbfgs:g_cur");
+  memory->grow(p_s,3*nlocal_max,"min/spin/lbfgs:p_s");
+  memory->grow(rho,num_mem,"min/spin/lbfgs:rho");
+  memory->grow(ds,num_mem,3*nlocal_max,"min/spin/lbfgs:ds");
+  memory->grow(dy,num_mem,3*nlocal_max,"min/spin/lbfgs:dy");
+  if (use_line_search)
+    memory->grow(sp_copy,nlocal_max,3,"min/spin/lbfgs:sp_copy");
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MinSpinLBFGS::setup_style()
+{
+  double **v = atom->v;
+  int nlocal = atom->nlocal;
+
+  // check if the atom/spin style is defined
+
+  if (!atom->sp_flag)
+    error->all(FLERR,"min spin/lbfgs requires atom/spin style");
+
+  for (int i = 0; i < nlocal; i++)
+    v[i][0] = v[i][1] = v[i][2] = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int MinSpinLBFGS::modify_param(int narg, char **arg)
+{
+  if (strcmp(arg[0],"discrete_factor") == 0) {
+    if (narg < 2) error->all(FLERR,"Illegal min_modify command");
+    double discrete_factor;
+    discrete_factor = force->numeric(FLERR,arg[1]);
+    maxepsrot = MY_2PI / (10 * discrete_factor);
+    return 2;
+  }
+  return 0;
+}
+
+/* ----------------------------------------------------------------------
+   set current vector lengths and pointers
+   called after atoms have migrated
+------------------------------------------------------------------------- */
+
+void MinSpinLBFGS::reset_vectors()
+{
+  // atomic dof
+
+  // size sp is 4N vector
+  nvec = 4 * atom->nlocal;
+  if (nvec) spvec = atom->sp[0];
+
+  nvec = 3 * atom->nlocal;
+  if (nvec) fmvec = atom->fm[0];
+
+  if (nvec) xvec = atom->x[0];
+  if (nvec) fvec = atom->f[0];
+}
+
+/* ----------------------------------------------------------------------
+   minimization via damped spin dynamics
+------------------------------------------------------------------------- */
+
+int MinSpinLBFGS::iterate(int maxiter)
+{
+  int nlocal = atom->nlocal;
+  bigint ntimestep;
+  double fmdotfm,fmsq;
+  int flag, flagall;
+  double **sp = atom->sp;
+  double der_e_cur_tmp = 0.0;
+
+  if (nlocal_max < nlocal) {
+    nlocal_max = nlocal;
+    local_iter = 0;
+    memory->grow(g_old,3*nlocal_max,"min/spin/lbfgs:g_old");
+    memory->grow(g_cur,3*nlocal_max,"min/spin/lbfgs:g_cur");
+    memory->grow(p_s,3*nlocal_max,"min/spin/lbfgs:p_s");
+    memory->grow(rho,num_mem,"min/spin/lbfgs:rho");
+    memory->grow(ds,num_mem,3*nlocal_max,"min/spin/lbfgs:ds");
+    memory->grow(dy,num_mem,3*nlocal_max,"min/spin/lbfgs:dy");
+    if (use_line_search)
+      memory->grow(sp_copy,nlocal_max,3,"min/spin/lbfgs:sp_copy");
+  }
+
+  for (int iter = 0; iter < maxiter; iter++) {
+
+    if (timer->check_timeout(niter))
+      return TIMEOUT;
+
+    ntimestep = ++update->ntimestep;
+    niter++;
+
+    // optimize timestep accross processes / replicas
+    // need a force calculation for timestep optimization
+
+    if (use_line_search) {
+
+      // here we need to do line search
+      if (local_iter == 0){
+        eprevious = ecurrent;
+        ecurrent = energy_force(0);
+        calc_gradient();
+      }
+
+      calc_search_direction();
+      der_e_cur = 0.0;
+      for (int i = 0; i < 3 * nlocal; i++)
+        der_e_cur += g_cur[i] * p_s[i];
+      MPI_Allreduce(&der_e_cur,&der_e_cur_tmp,1,MPI_DOUBLE,MPI_SUM,world);
+      der_e_cur = der_e_cur_tmp;
+      if (update->multireplica == 1) {
+        MPI_Allreduce(&der_e_cur_tmp,&der_e_cur,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+      }
+      for (int i = 0; i < nlocal; i++)
+        for (int j = 0; j < 3; j++)
+      sp_copy[i][j] = sp[i][j];
+
+      eprevious = ecurrent;
+      der_e_pr = der_e_cur;
+      calc_and_make_step(0.0, 1.0, 0);
+    }
+    else{
+
+      // here we don't do line search
+      // but use cutoff rotation angle
+      // if gneb calc., nreplica > 1
+      // then calculate gradients and advance spins
+      // of intermediate replicas only
+      eprevious = ecurrent;
+      ecurrent = energy_force(0);
+      calc_gradient();
+      calc_search_direction();
+      advance_spins();
+      neval++;
+    }
+
+    // energy tolerance criterion
+    // only check after DELAYSTEP elapsed since velocties reset to 0
+    // sync across replicas if running multi-replica minimization
+
+    if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) {
+      if (update->multireplica == 0) {
+        if (fabs(ecurrent-eprevious) <
+            update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+          return ETOL;
+      } else {
+        if (fabs(ecurrent-eprevious) <
+            update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+          flag = 0;
+        else flag = 1;
+        MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
+        if (flagall == 0) return ETOL;
+      }
+    }
+
+    // magnetic torque tolerance criterion
+    // sync across replicas if running multi-replica minimization
+
+    fmdotfm = fmsq = 0.0;
+    if (update->ftol > 0.0) {
+      if (normstyle == MAX) fmsq = max_torque();        // max torque norm
+      else if (normstyle == INF) fmsq = inf_torque();   // inf torque norm
+      else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm
+      else error->all(FLERR,"Illegal min_modify command");
+      fmdotfm = fmsq*fmsq;
+      if (update->multireplica == 0) {
+        if (fmdotfm < update->ftol*update->ftol) return FTOL;
+      } else {
+        if (fmdotfm < update->ftol*update->ftol) flag = 0;
+        else flag = 1;
+        MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
+        if (flagall == 0) return FTOL;
+      }
+    }
+
+    // output for thermo, dump, restart files
+
+    if (output->next == ntimestep) {
+      timer->stamp();
+      output->write(ntimestep);
+      timer->stamp(Timer::OUTPUT);
+    }
+  }
+
+  return MAXITER;
+}
+
+/* ----------------------------------------------------------------------
+   calculate gradients
+---------------------------------------------------------------------- */
+
+void MinSpinLBFGS::calc_gradient()
+{
+  int nlocal = atom->nlocal;
+  double **sp = atom->sp;
+  double **fm = atom->fm;
+  double hbar = force->hplanck/MY_2PI;
+
+  // loop on all spins on proc.
+
+  for (int i = 0; i < nlocal; i++) {
+    g_cur[3 * i + 0] = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]) * hbar;
+    g_cur[3 * i + 1] = -(fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]) * hbar;
+    g_cur[3 * i + 2] = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]) * hbar;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   search direction:
+   Limited-memory BFGS.
+   See Jorge Nocedal and Stephen J. Wright 'Numerical
+   Optimization' Second Edition, 2006 (p. 177)
+---------------------------------------------------------------------- */
+
+void MinSpinLBFGS::calc_search_direction()
+{
+  int nlocal = atom->nlocal;
+
+  double dyds = 0.0;
+  double sq = 0.0;
+  double yy = 0.0;
+  double yr = 0.0;
+  double beta = 0.0;
+
+  double dyds_global = 0.0;
+  double sq_global = 0.0;
+  double yy_global = 0.0;
+  double yr_global = 0.0;
+
+  int m_index = local_iter % num_mem; // memory index
+  int c_ind = 0;
+  double *q;
+  double *alpha;
+
+  double factor;
+  double scaling = 1.0;
+
+  // for multiple replica do not move end points
+  if (nreplica > 1) {
+    if (ireplica == 0 || ireplica == nreplica - 1) {
+      factor = 0.0;
+    }
+    else factor = 1.0;
+  }else{
+    factor = 1.0;
+  }
+
+  if (local_iter == 0){         // steepest descent direction
+
+    //if no line search then calculate maximum rotation
+    if (use_line_search == 0)
+      scaling = maximum_rotation(g_cur);
+
+    for (int i = 0; i < 3 * nlocal; i++) {
+      p_s[i] = -g_cur[i] * factor * scaling;;
+      g_old[i] = g_cur[i]  * factor;
+      for (int k = 0; k < num_mem; k++){
+        ds[k][i] = 0.0;
+        dy[k][i] = 0.0;
+      }
+    }
+    for (int k = 0; k < num_mem; k++)
+      rho[k] = 0.0;
+
+    } else {
+    dyds = 0.0;
+    for (int i = 0; i < 3 * nlocal; i++) {
+      ds[m_index][i] = p_s[i];
+      dy[m_index][i] = g_cur[i] - g_old[i];
+      dyds += ds[m_index][i] * dy[m_index][i];
+    }
+    MPI_Allreduce(&dyds, &dyds_global, 1, MPI_DOUBLE, MPI_SUM, world);
+
+    if (nreplica > 1) {
+      dyds_global *= factor;
+      dyds = dyds_global;
+      MPI_Allreduce(&dyds, &dyds_global, 1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+    }
+
+    if (fabs(dyds_global) > 1.0e-60) rho[m_index] = 1.0 / dyds_global;
+    else rho[m_index] = 1.0e60;
+
+    if (rho[m_index] < 0.0){
+      local_iter = 0;
+      return calc_search_direction();
+    }
+    q = (double *) calloc(3*nlocal, sizeof(double));
+    alpha = (double *) calloc(num_mem, sizeof(double));
+    // set the q vector
+
+    for (int i = 0; i < 3 * nlocal; i++) {
+      q[i] = g_cur[i];
+    }
+
+    // loop over last m indecies
+    for(int k = num_mem - 1; k > -1; k--) {
+      // this loop should run from the newest memory to the oldest one.
+
+      c_ind = (k + m_index + 1) % num_mem;
+
+      // dot product between dg and q
+
+      sq = 0.0;
+      for (int i = 0; i < 3 * nlocal; i++) {
+        sq += ds[c_ind][i] * q[i];
+      }
+      MPI_Allreduce(&sq,&sq_global,1,MPI_DOUBLE,MPI_SUM,world);
+      if (nreplica > 1) {
+        sq_global *= factor;
+        sq = sq_global;
+        MPI_Allreduce(&sq,&sq_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+      }
+
+      // update alpha
+
+      alpha[c_ind] = rho[c_ind] * sq_global;
+
+      // update q
+
+      for (int i = 0; i < 3 * nlocal; i++) {
+        q[i] -= alpha[c_ind] * dy[c_ind][i];
+      }
+    }
+
+    // dot product between dg with itself
+    yy = 0.0;
+    for (int i = 0; i < 3 * nlocal; i++) {
+      yy += dy[m_index][i] * dy[m_index][i];
+    }
+    MPI_Allreduce(&yy,&yy_global,1,MPI_DOUBLE,MPI_SUM,world);
+    if (nreplica > 1) {
+      yy_global *= factor;
+      yy = yy_global;
+      MPI_Allreduce(&yy,&yy_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+    }
+
+    // calculate now search direction
+
+    double devis = rho[m_index] * yy_global;
+
+    if (fabs(devis) > 1.0e-60) {
+      for (int i = 0; i < 3 * nlocal; i++) {
+        p_s[i] = factor * q[i] / devis;
+      }
+    }else{
+      for (int i = 0; i < 3 * nlocal; i++) {
+        p_s[i] = factor * q[i] * 1.0e60;
+      }
+    }
+
+    for (int k = 0; k < num_mem; k++){
+      // this loop should run from the oldest memory to the newest one.
+
+      if (local_iter < num_mem) c_ind = k;
+      else c_ind = (k + m_index + 1) % num_mem;
+
+      // dot product between p and da
+      yr = 0.0;
+      for (int i = 0; i < 3 * nlocal; i++) {
+        yr += dy[c_ind][i] * p_s[i];
+      }
+
+      MPI_Allreduce(&yr,&yr_global,1,MPI_DOUBLE,MPI_SUM,world);
+      if (nreplica > 1) {
+        yr_global *= factor;
+        yr = yr_global;
+        MPI_Allreduce(&yr,&yr_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+      }
+
+      beta = rho[c_ind] * yr_global;
+      for (int i = 0; i < 3 * nlocal; i++) {
+        p_s[i] += ds[c_ind][i] * (alpha[c_ind] - beta);
+      }
+    }
+    if (use_line_search == 0)
+      scaling = maximum_rotation(p_s);
+    for (int i = 0; i < 3 * nlocal; i++) {
+      p_s[i] = - factor * p_s[i] * scaling;
+      g_old[i] = g_cur[i] * factor;
+    }
+    free(q);
+    free(alpha);
+  }
+  local_iter++;
+}
+
+/* ----------------------------------------------------------------------
+   rotation of spins along the search direction
+---------------------------------------------------------------------- */
+
+void MinSpinLBFGS::advance_spins()
+{
+  int nlocal = atom->nlocal;
+  double **sp = atom->sp;
+  double rot_mat[9]; // exponential of matrix made of search direction
+  double s_new[3];
+
+  // loop on all spins on proc.
+
+  for (int i = 0; i < nlocal; i++) {
+    rodrigues_rotation(p_s + 3 * i, rot_mat);
+
+    // rotate spins
+
+    vm3(rot_mat, sp[i], s_new);
+    for (int j = 0; j < 3; j++) sp[i][j] = s_new[j];
+  }
+}
+
+/* ----------------------------------------------------------------------
+  calculate 3x3 matrix exponential using Rodrigues' formula
+  (R. Murray, Z. Li, and S. Shankar Sastry,
+  A Mathematical Introduction to
+  Robotic Manipulation (1994), p. 28 and 30).
+
+  upp_tr - vector x, y, z so that one calculate
+  U = exp(A) with A= [[0, x, y],
+                      [-x, 0, z],
+                      [-y, -z, 0]]
+------------------------------------------------------------------------- */
+
+void MinSpinLBFGS::rodrigues_rotation(const double *upp_tr, double *out)
+{
+  double theta,A,B,D,x,y,z;
+  double s1,s2,s3,a1,a2,a3;
+
+  if (fabs(upp_tr[0]) < 1.0e-40 &&
+      fabs(upp_tr[1]) < 1.0e-40 &&
+      fabs(upp_tr[2]) < 1.0e-40){
+
+    // if upp_tr is zero, return unity matrix
+    for(int k = 0; k < 3; k++){
+      for(int m = 0; m < 3; m++){
+    if (m == k) out[3 * k + m] = 1.0;
+    else out[3 * k + m] = 0.0;
+        }
+    }
+    return;
+  }
+
+  theta = sqrt(upp_tr[0] * upp_tr[0] +
+               upp_tr[1] * upp_tr[1] +
+               upp_tr[2] * upp_tr[2]);
+
+  A = cos(theta);
+  B = sin(theta);
+  D = 1 - A;
+  x = upp_tr[0]/theta;
+  y = upp_tr[1]/theta;
+  z = upp_tr[2]/theta;
+
+  // diagonal elements of U
+
+  out[0] = A + z * z * D;
+  out[4] = A + y * y * D;
+  out[8] = A + x * x * D;
+
+  // off diagonal of U
+
+  s1 = -y * z *D;
+  s2 = x * z * D;
+  s3 = -x * y * D;
+
+  a1 = x * B;
+  a2 = y * B;
+  a3 = z * B;
+
+  out[1] = s1 + a1;
+  out[3] = s1 - a1;
+  out[2] = s2 + a2;
+  out[6] = s2 - a2;
+  out[5] = s3 + a3;
+  out[7] = s3 - a3;
+
+}
+
+/* ----------------------------------------------------------------------
+  out = vector^T x m,
+  m -- 3x3 matrix , v -- 3-d vector
+------------------------------------------------------------------------- */
+
+void MinSpinLBFGS::vm3(const double *m, const double *v, double *out)
+{
+  for(int i = 0; i < 3; i++){
+    out[i] = 0.0;
+    for(int j = 0; j < 3; j++)
+    out[i] += *(m + 3 * j + i) * v[j];
+  }
+}
+
+
+void MinSpinLBFGS::make_step(double c, double *energy_and_der)
+{
+  double p_scaled[3];
+  int nlocal = atom->nlocal;
+  double rot_mat[9]; // exponential of matrix made of search direction
+  double s_new[3];
+  double **sp = atom->sp;
+  double der_e_cur_tmp = 0.0;
+
+  for (int i = 0; i < nlocal; i++) {
+
+    // scale the search direction
+
+    for (int j = 0; j < 3; j++) p_scaled[j] = c * p_s[3 * i + j];
+
+    // calculate rotation matrix
+
+    rodrigues_rotation(p_scaled, rot_mat);
+
+    // rotate spins
+
+    vm3(rot_mat, sp[i], s_new);
+    for (int j = 0; j < 3; j++) sp[i][j] = s_new[j];
+  }
+
+  ecurrent = energy_force(0);
+  calc_gradient();
+  neval++;
+  der_e_cur = 0.0;
+  for (int i = 0; i < 3 * nlocal; i++) {
+    der_e_cur += g_cur[i] * p_s[i];
+  }
+  MPI_Allreduce(&der_e_cur,&der_e_cur_tmp, 1, MPI_DOUBLE, MPI_SUM, world);
+  der_e_cur = der_e_cur_tmp;
+  if (update->multireplica == 1) {
+    MPI_Allreduce(&der_e_cur_tmp,&der_e_cur,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+  }
+
+  energy_and_der[0] = ecurrent;
+  energy_and_der[1] = der_e_cur;
+}
+
+/* ----------------------------------------------------------------------
+  Calculate step length which satisfies approximate Wolfe conditions
+  using the cubic interpolation
+------------------------------------------------------------------------- */
+
+int MinSpinLBFGS::calc_and_make_step(double a, double b, int index)
+{
+  double e_and_d[2] = {0.0,0.0};
+  double alpha,c1,c2,c3;
+  double **sp = atom->sp;
+  int nlocal = atom->nlocal;
+
+  make_step(b,e_and_d);
+  ecurrent = e_and_d[0];
+  der_e_cur = e_and_d[1];
+  index++;
+
+  if (adescent(eprevious,e_and_d[0]) || index == 5){
+    MPI_Bcast(&b,1,MPI_DOUBLE,0,world);
+    for (int i = 0; i < 3 * nlocal; i++) {
+      p_s[i] = b * p_s[i];
+    }
+    return 1;
+  }
+  else{
+    double r,f0,f1,df0,df1;
+    r = b - a;
+    f0 = eprevious;
+    f1 = ecurrent;
+    df0 = der_e_pr;
+    df1 = der_e_cur;
+
+    c1 = -2.0*(f1-f0)/(r*r*r)+(df1+df0)/(r*r);
+    c2 = 3.0*(f1-f0)/(r*r)-(df1+2.0*df0)/(r);
+    c3 = df0;
+
+    // f(x) = c1 x^3 + c2 x^2 + c3 x^1 + c4
+    // has minimum at alpha below. We do not check boundaries.
+
+    alpha = (-c2 + sqrt(c2*c2 - 3.0*c1*c3))/(3.0*c1);
+    MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world);
+
+    if (alpha < 0.0) alpha = r/2.0;
+
+    for (int i = 0; i < nlocal; i++) {
+      for (int j = 0; j < 3; j++) sp[i][j] = sp_copy[i][j];
+    }
+    calc_and_make_step(0.0, alpha, index);
+   }
+
+  return 0;
+}
+
+/* ----------------------------------------------------------------------
+  Approximate descent
+------------------------------------------------------------------------- */
+
+int MinSpinLBFGS::adescent(double phi_0, double phi_j){
+
+  double eps = 1.0e-6;
+
+  if (phi_j<=phi_0+eps*fabs(phi_0))
+    return 1;
+  else
+    return 0;
+}
+
+double MinSpinLBFGS::maximum_rotation(double *p)
+{
+  double norm2,norm2_global,scaling,alpha;
+  int nlocal = atom->nlocal;
+  int ntotal = 0;
+
+  norm2 = 0.0;
+  for (int i = 0; i < 3 * nlocal; i++) norm2 += p[i] * p[i];
+
+  MPI_Allreduce(&norm2,&norm2_global,1,MPI_DOUBLE,MPI_SUM,world);
+  if (nreplica > 1) {
+    norm2 = norm2_global;
+    MPI_Allreduce(&norm2,&norm2_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
+  }
+  MPI_Allreduce(&nlocal,&ntotal,1,MPI_INT,MPI_SUM,world);
+  if (nreplica > 1) {
+    nlocal = ntotal;
+    MPI_Allreduce(&nlocal,&ntotal,1,MPI_INT,MPI_SUM,universe->uworld);
+  }
+
+  scaling = (maxepsrot * sqrt((double) ntotal / norm2_global));
+
+  if (scaling < 1.0) alpha = scaling;
+  else alpha = 1.0;
+
+  return alpha;
+}
diff --git a/src/SPIN/min_spin_lbfgs.h b/src/SPIN/min_spin_lbfgs.h
new file mode 100644
index 0000000000..8b470b5d23
--- /dev/null
+++ b/src/SPIN/min_spin_lbfgs.h
@@ -0,0 +1,72 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef MINIMIZE_CLASS
+
+MinimizeStyle(spin/lbfgs, MinSpinLBFGS)
+
+#else
+
+#ifndef LMP_MIN_SPIN_LBFGS_H
+#define LMP_MIN_SPIN_LBFGS_H
+
+#include "min.h"
+
+namespace LAMMPS_NS {
+
+class MinSpinLBFGS: public Min {
+ public:
+  MinSpinLBFGS(class LAMMPS *);
+  virtual ~MinSpinLBFGS();
+  void init();
+  void setup_style();
+  int modify_param(int, char **);
+  void reset_vectors();
+  int iterate(int);
+
+ private:
+  int local_iter;               // for neb
+  int use_line_search;          // use line search or not.
+  int nlocal_max;               // max value of nlocal (for size of lists)
+  int ireplica,nreplica;        // for neb
+  double der_e_cur;             // current derivative along search dir.
+  double der_e_pr;              // previous derivative along search dir.
+  double maxepsrot;
+  double *spvec;                // variables for atomic dof, as 1d vector
+  double *fmvec;                // variables for atomic dof, as 1d vector
+  double *g_old;                // gradient vector at previous step
+  double *g_cur;                // current gradient vector
+  double *p_s;                  // search direction vector
+
+  void advance_spins();
+  void calc_gradient();
+  void calc_search_direction();
+  void vm3(const double *, const double *, double *);
+  void rodrigues_rotation(const double *, double *);
+  void make_step(double, double *);
+  int calc_and_make_step(double, double, int);
+  int adescent(double, double);
+  double maximum_rotation(double *);
+
+  double *rho;          // estimation of curvature
+  double **ds;          // change in rotation matrix between two iterations, da
+  double **dy;          // change in gradients between two iterations, dg
+  double **sp_copy;     // copy of the spins
+  int num_mem;          // number of stored steps
+  bigint last_negative;
+};
+
+}
+
+#endif
+#endif
diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp
index 2bcfe6573a..075850d1af 100644
--- a/src/SPIN/neb_spin.cpp
+++ b/src/SPIN/neb_spin.cpp
@@ -43,6 +43,8 @@
 #include "timer.h"
 #include "memory.h"
 #include "error.h"
+#include "math_const.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -177,7 +179,7 @@ void NEBSpin::run()
 
   update->whichflag = 2;
   update->etol = etol;
-  update->ftol = ttol;		// update->ftol is a torque tolerance
+  update->ftol = ttol;          // update->ftol is a torque tolerance
   update->multireplica = 1;
 
   lmp->init();
@@ -186,8 +188,8 @@ void NEBSpin::run()
 
   if (update->minimize->searchflag)
     error->all(FLERR,"NEBSpin requires damped dynamics minimizer");
-  if (strcmp(update->minimize_style,"spin") != 0)
-    error->all(FLERR,"NEBSpin requires spin minimizer");
+  if (!utils::strmatch(update->minimize_style,"^spin"))
+    error->all(FLERR,"NEBSpin requires a spin minimizer");
 
   // setup regular NEBSpin minimization
 
@@ -212,7 +214,7 @@ void NEBSpin::run()
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT "
                 "RD1 PE1 RD2 PE2 ... RDN PEN "
-		"GradV0dottan DN0 ... GradVNdottan DNN\n");
+                "GradV0dottan DN0 ... GradVNdottan DNN\n");
       } else {
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
@@ -222,10 +224,10 @@ void NEBSpin::run()
 
     if (ulogfile) {
       if (verbose) {
-	fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
-	    "GradV0 GradV1 GradVc EBF EBR RDT "
-	    "RD1 PE1 RD2 PE2 ... RDN PEN "
-	    "GradV0dottan DN0 ... GradVNdottan DNN\n");
+        fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
+            "GradV0 GradV1 GradVc EBF EBR RDT "
+            "RD1 PE1 RD2 PE2 ... RDN PEN "
+            "GradV0dottan DN0 ... GradVNdottan DNN\n");
       } else {
         fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
@@ -243,6 +245,8 @@ void NEBSpin::run()
   timer->init();
   timer->barrier_start();
 
+  // if(ireplica != 0 && ireplica != nreplica -1)
+
   while (update->minimize->niter < n1steps) {
     update->minimize->run(nevery);
     print_status();
@@ -297,7 +301,7 @@ void NEBSpin::run()
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT "
                 "RD1 PE1 RD2 PE2 ... RDN PEN "
-		"GradV0dottan DN0... GradVNdottan DNN\n");
+                "GradV0dottan DN0... GradVNdottan DNN\n");
       } else {
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc "
@@ -307,10 +311,10 @@ void NEBSpin::run()
     }
     if (ulogfile) {
       if (verbose) {
-	fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
-	    "GradV0 GradV1 GradVc EBF EBR RDT "
-	    "RD1 PE1 RD2 PE2 ... RDN PEN "
-	    "GradV0dottan DN0 ... GradVNdottan DNN\n");
+        fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
+            "GradV0 GradV1 GradVc EBF EBR RDT "
+            "RD1 PE1 RD2 PE2 ... RDN PEN "
+            "GradV0dottan DN0 ... GradVNdottan DNN\n");
       } else {
         fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc "
@@ -468,8 +472,8 @@ void NEBSpin::readfile(char *file, int flag)
       m = atom->map(tag);
       if (m >= 0 && m < nlocal) {
         ncount++;
-	musp = atof(values[1]);
-	xx = atof(values[2]);
+        musp = atof(values[1]);
+        xx = atof(values[2]);
         yy = atof(values[3]);
         zz = atof(values[4]);
         spx = atof(values[5]);
@@ -478,39 +482,39 @@ void NEBSpin::readfile(char *file, int flag)
 
         if (flag == 0) {
 
-	  spinit[0] = sp[m][0];
-	  spinit[1] = sp[m][1];
-	  spinit[2] = sp[m][2];
-	  spfinal[0] = spx;
-	  spfinal[1] = spy;
-	  spfinal[2] = spz;
+          spinit[0] = sp[m][0];
+          spinit[1] = sp[m][1];
+          spinit[2] = sp[m][2];
+          spfinal[0] = spx;
+          spfinal[1] = spy;
+          spfinal[2] = spz;
 
-	  // interpolate intermediate spin states
+          // interpolate intermediate spin states
 
-	  sp[m][3] = musp;
-	  if (fraction == 0.0) {
-	    sp[m][0] = spinit[0];
-	    sp[m][1] = spinit[1];
-	    sp[m][2] = spinit[2];
-	  } else if (fraction == 1.0) {
-	    sp[m][0] = spfinal[0];
-	    sp[m][1] = spfinal[1];
-	    sp[m][2] = spfinal[2];
-	  } else {
+          sp[m][3] = musp;
+          if (fraction == 0.0) {
+            sp[m][0] = spinit[0];
+            sp[m][1] = spinit[1];
+            sp[m][2] = spinit[2];
+          } else if (fraction == 1.0) {
+            sp[m][0] = spfinal[0];
+            sp[m][1] = spfinal[1];
+            sp[m][2] = spfinal[2];
+          } else {
             temp_flag = initial_rotation(spinit,spfinal,fraction);
             rot_flag = MAX(temp_flag,rot_flag);
-	    sp[m][0] = spfinal[0];
-	    sp[m][1] = spfinal[1];
-	    sp[m][2] = spfinal[2];
-	  }
+            sp[m][0] = spfinal[0];
+            sp[m][1] = spfinal[1];
+            sp[m][2] = spfinal[2];
+          }
         } else {
           sp[m][3] = musp;
-	  x[m][0] = xx;
+          x[m][0] = xx;
           x[m][1] = yy;
           x[m][2] = zz;
-	  sp[m][0] = spx;
-	  sp[m][1] = spy;
-	  sp[m][2] = spz;
+          sp[m][0] = spx;
+          sp[m][1] = spy;
+          sp[m][2] = spz;
         }
       }
 
@@ -598,24 +602,24 @@ int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction)
   // Rodrigues' formula breaks, needs to define another axis k
 
   if (knormsq == 0.0) {
-    if (sidotsf > 0.0) { 	// spins aligned and in same direction
+    if (sidotsf > 0.0) {        // spins aligned and in same direction
       return 0;
-    } else if (sidotsf < 0.0) {	// spins aligned and in opposite directions
+    } else if (sidotsf < 0.0) { // spins aligned and in opposite directions
 
       // defining a rotation axis
       // first guess, k = spi x [100]
       // second guess, k = spi x [010]
 
       if (spiy*spiy + spiz*spiz != 0.0) { // spin not along [100]
-	kx = 0.0;
-	ky = spiz;
-	kz = -spiy;
-	knormsq = ky*ky + kz*kz;
+        kx = 0.0;
+        ky = spiz;
+        kz = -spiy;
+        knormsq = ky*ky + kz*kz;
       } else if (spix*spix + spiz*spiz != 0.0) { // spin not along [010]
-	kx = -spiz;
-	ky = 0.0;
-	kz = spix;
-	knormsq = kx*kx + kz*kz;
+        kx = -spiz;
+        ky = 0.0;
+        kz = spix;
+        knormsq = kx*kx + kz*kz;
       } else error->all(FLERR,"Incorrect initial rotation operation");
       rot_flag = 1;
     }
@@ -639,7 +643,7 @@ int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction)
   kcrossy = kz*spix - kx*spiz;
   kcrossz = kx*spiy - ky*spix;
 
-  kdots = kx*spix + ky*spiz + kz*spiz;
+  kdots = kx*spix + ky*spiy + kz*spiz;
 
   omega = acos(sidotsf);
   omega *= fraction;
@@ -818,9 +822,9 @@ void NEBSpin::print_status()
       for (int i = 0; i < nreplica; i++)
         fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
       if (verbose) {
-	for (int i = 0; i < nreplica-1; i++)
-	  fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]);
-	fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
+        for (int i = 0; i < nreplica-1; i++)
+          fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]);
+        fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
       }
       fprintf(uscreen,"\n");
     }
@@ -834,9 +838,9 @@ void NEBSpin::print_status()
       for (int i = 0; i < nreplica; i++)
         fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
       if (verbose) {
-	for (int i = 0; i < nreplica-1; i++)
-	  fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]);
-	fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
+        for (int i = 0; i < nreplica-1; i++)
+          fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]);
+        fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
       }
       fprintf(ulogfile,"\n");
       fflush(ulogfile);
diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp
index fef247c09b..f167e3455c 100644
--- a/src/SPIN/pair_spin.cpp
+++ b/src/SPIN/pair_spin.cpp
@@ -24,13 +24,17 @@
 #include "pair_spin.h"
 #include <cstring>
 #include "atom.h"
+#include "comm.h"
 #include "error.h"
 #include "fix.h"
 #include "force.h"
 #include "math_const.h"
 #include "modify.h"
+#include "neighbor.h"
+#include "neigh_request.h"
 #include "pair.h"
 #include "update.h"
+#include "fix_nve_spin.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -41,7 +45,9 @@ PairSpin::PairSpin(LAMMPS *lmp) : Pair(lmp)
 {
   hbar = force->hplanck/MY_2PI;
   single_enable = 0;
+  respa_enable = 0;
   no_virial_fdotr_compute = 1;
+  lattice_flag = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -57,11 +63,10 @@ void PairSpin::settings(int narg, char **/*arg*/)
   if (narg < 1 || narg > 2)
     error->all(FLERR,"Incorrect number of args in pair_style pair/spin command");
 
-  // pair/spin need the metal unit style
+  // pair spin/* need the metal unit style
 
   if (strcmp(update->unit_style,"metal") != 0)
-    error->all(FLERR,"pair/spin style requires metal units");
-
+    error->all(FLERR,"Spin pair styles require metal units");
 }
 
 /* ----------------------------------------------------------------------
@@ -73,13 +78,24 @@ void PairSpin::init_style()
   if (!atom->sp_flag)
     error->all(FLERR,"Pair spin requires atom/spin style");
 
-  // checking if nve/spin is a listed fix
+  // checking if nve/spin or neb/spin is a listed fix
+
+  bool have_fix = ((modify->find_fix_by_style("^nve/spin") != -1)
+                   || (modify->find_fix_by_style("^neb/spin") != -1));
+
+  if (!have_fix && (comm->me == 0))
+    error->warning(FLERR,"Using spin pair style without nve/spin or neb/spin");
+
+  // need a full neighbor list
+
+  int irequest = neighbor->request(this,instance_me);
+  neighbor->requests[irequest]->half = 0;
+  neighbor->requests[irequest]->full = 1;
+
+  // get the lattice_flag from nve/spin
+
+  int ifix = modify->find_fix_by_style("^nve/spin");
+  if (ifix >=0)
+    lattice_flag = ((FixNVESpin *) modify->fix[ifix])->lattice_flag;
 
-  int ifix = 0;
-  while (ifix < modify->nfix) {
-    if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
-    ifix++;
-  }
-  if (ifix == modify->nfix)
-    error->all(FLERR,"pair/spin style requires nve/spin");
 }
diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h
index 3a909e1d13..34f12d8d59 100644
--- a/src/SPIN/pair_spin.h
+++ b/src/SPIN/pair_spin.h
@@ -33,7 +33,8 @@ friend class FixNVESpin;
   virtual void compute_single_pair(int, double *) {}
 
  protected:
-  double hbar;				// Planck constant (eV.ps.rad-1)
+  double hbar;                          // Planck constant (eV.ps.rad-1)
+  int lattice_flag;                     // flag for mech force computation
 
   virtual void allocate() {}
 };
diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp
index fb0ec8bb20..a7372b480d 100644
--- a/src/SPIN/pair_spin_dipole_cut.cpp
+++ b/src/SPIN/pair_spin_dipole_cut.cpp
@@ -27,40 +27,31 @@
 #include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "fix.h"
-#include "fix_nve_spin.h"
 #include "force.h"
 #include "math_const.h"
 #include "memory.h"
 #include "modify.h"
 #include "error.h"
 #include "update.h"
-
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-PairSpinDipoleCut::PairSpinDipoleCut(LAMMPS *lmp) : PairSpin(lmp),
-lockfixnvespin(NULL)
+PairSpinDipoleCut::PairSpinDipoleCut(LAMMPS *lmp) : PairSpin(lmp)
 {
-  single_enable = 0;
   spinflag = 1;
-  respa_enable = 0;
-  no_virial_fdotr_compute = 1;
-  lattice_flag = 0;
-
-  hbar = force->hplanck/MY_2PI;			// eV/(rad.THz)
-  mub = 9.274e-4;                               // in A.Ang^2
-  mu_0 = 785.15;                                // in eV/Ang/A^2
-  mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);     // in eV.Ang^3
-  //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);	// in eV
-  mub2mu0hbinv = mub2mu0 / hbar;		// in rad.THz
 
+  hbar = force->hplanck/MY_2PI;                       // eV/(rad.THz)
+  mub = 9.274e-4;                             // in A.Ang^2
+  mu_0 = 785.15;                              // in eV/Ang/A^2
+  mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);   // in eV.Ang^3
+  //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);   // in eV
+  mub2mu0hbinv = mub2mu0 / hbar;              // in rad.THz
 }
 
 /* ----------------------------------------------------------------------
@@ -82,19 +73,12 @@ PairSpinDipoleCut::~PairSpinDipoleCut()
 
 void PairSpinDipoleCut::settings(int narg, char **arg)
 {
-  if (narg < 1 || narg > 2)
-    error->all(FLERR,"Incorrect args in pair_style command");
-
-  if (strcmp(update->unit_style,"metal") != 0)
-    error->all(FLERR,"Spin simulations require metal unit style");
-
-  if (!atom->sp) 
-    error->all(FLERR,"Pair/spin style requires atom attribute sp");
+  PairSpin::settings(narg,arg);
 
   cut_spin_long_global = force->numeric(FLERR,arg[0]);
-  
+
   // reset cutoffs that have been explicitly set
-  
+
   if (allocated) {
     int i,j;
     for (i = 1; i <= atom->ntypes; i++) {
@@ -115,10 +99,10 @@ void PairSpinDipoleCut::settings(int narg, char **arg)
 void PairSpinDipoleCut::coeff(int narg, char **arg)
 {
   if (!allocated) allocate();
- 
-  if (narg != 3) 
+
+  if (narg != 3)
     error->all(FLERR,"Incorrect args in pair_style command");
-  
+
   int ilo,ihi,jlo,jhi;
   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
@@ -137,43 +121,6 @@ void PairSpinDipoleCut::coeff(int narg, char **arg)
   if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairSpinDipoleCut::init_style()
-{
-  if (!atom->sp_flag)
-    error->all(FLERR,"Pair spin requires atom/spin style");
-  
-  // need a full neighbor list
-
-  int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->half = 0;
-  neighbor->requests[irequest]->full = 1;
-  
-  // checking if nve/spin or neb/spin are a listed fix
-
-  int ifix = 0;
-  while (ifix < modify->nfix) {
-    if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
-    if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
-    ifix++;
-  }
-  if ((ifix == modify->nfix) && (comm->me == 0))
-    error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
-
-  // get the lattice_flag from nve/spin
-
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"nve/spin") == 0) {
-      lockfixnvespin = (FixNVESpin *) modify->fix[i];
-      lattice_flag = lockfixnvespin->lattice_flag;
-    }
-  }
-
-}
-
 /* ----------------------------------------------------------------------
    init for one type pair i,j and corresponding j,i
 ------------------------------------------------------------------------- */
@@ -181,9 +128,9 @@ void PairSpinDipoleCut::init_style()
 double PairSpinDipoleCut::init_one(int i, int j)
 {
   if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
-  
+
   cut_spin_long[j][i] = cut_spin_long[i][j];
-  
+
   return cut_spin_long_global;
 }
 
@@ -216,8 +163,8 @@ void *PairSpinDipoleCut::extract(const char *str, int &dim)
 
 void PairSpinDipoleCut::compute(int eflag, int vflag)
 {
-  int i,j,ii,jj,inum,jnum,itype,jtype;  
-  int *ilist,*jlist,*numneigh,**firstneigh;  
+  int i,j,ii,jj,inum,jnum,itype,jtype;
+  int *ilist,*jlist,*numneigh,**firstneigh;
   double rinv,r2inv,r3inv,rsq,local_cut2,evdwl,ecoul;
   double xi[3],rij[3],eij[3],spi[4],spj[4],fi[3],fmi[3];
 
@@ -225,13 +172,13 @@ void PairSpinDipoleCut::compute(int eflag, int vflag)
   if (eflag || vflag) ev_setup(eflag,vflag);
   else evflag = vflag_fdotr = 0;
 
-  int *type = atom->type;  
-  int nlocal = atom->nlocal;  
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
   double **x = atom->x;
   double **f = atom->f;
   double **fm = atom->fm;
-  double **sp = atom->sp;	
+  double **sp = atom->sp;
 
   inum = list->inum;
   ilist = list->ilist;
@@ -247,9 +194,9 @@ void PairSpinDipoleCut::compute(int eflag, int vflag)
     xi[1] = x[i][1];
     xi[2] = x[i][2];
     jlist = firstneigh[i];
-    jnum = numneigh[i]; 
-    spi[0] = sp[i][0]; 
-    spi[1] = sp[i][1]; 
+    jnum = numneigh[i];
+    spi[0] = sp[i][0];
+    spi[1] = sp[i][1];
     spi[2] = sp[i][2];
     spi[3] = sp[i][3];
     itype = type[i];
@@ -259,15 +206,15 @@ void PairSpinDipoleCut::compute(int eflag, int vflag)
       j &= NEIGHMASK;
       jtype = type[j];
 
-      spj[0] = sp[j][0]; 
-      spj[1] = sp[j][1]; 
-      spj[2] = sp[j][2]; 
-      spj[3] = sp[j][3]; 
+      spj[0] = sp[j][0];
+      spj[1] = sp[j][1];
+      spj[2] = sp[j][2];
+      spj[3] = sp[j][3];
 
       evdwl = 0.0;
       fi[0] = fi[1] = fi[2] = 0.0;
       fmi[0] = fmi[1] = fmi[2] = 0.0;
-     
+
       rij[0] = x[j][0] - xi[0];
       rij[1] = x[j][1] - xi[1];
       rij[2] = x[j][2] - xi[2];
@@ -281,36 +228,36 @@ void PairSpinDipoleCut::compute(int eflag, int vflag)
 
       if (rsq < local_cut2) {
         r2inv = 1.0/rsq;
-	r3inv = r2inv*rinv;
-	
-	compute_dipolar(i,j,eij,fmi,spi,spj,r3inv);
-	if (lattice_flag) compute_dipolar_mech(i,j,eij,fi,spi,spj,r2inv);
+        r3inv = r2inv*rinv;
+
+        compute_dipolar(i,j,eij,fmi,spi,spj,r3inv);
+        if (lattice_flag) compute_dipolar_mech(i,j,eij,fi,spi,spj,r2inv);
       }
 
       // force accumulation
 
-      f[i][0] += fi[0]; 
-      f[i][1] += fi[1];  	  
+      f[i][0] += fi[0];
+      f[i][1] += fi[1];
       f[i][2] += fi[2];
       fm[i][0] += fmi[0];
       fm[i][1] += fmi[1];
       fm[i][2] += fmi[2];
 
       if (newton_pair || j < nlocal) {
-	f[j][0] -= fi[0];	 
-        f[j][1] -= fi[1];	  	  
+        f[j][0] -= fi[0];
+        f[j][1] -= fi[1];
         f[j][2] -= fi[2];
       }
 
       if (eflag) {
-	if (rsq <= local_cut2) {
-	  evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-	  evdwl *= hbar;
-	}
+        if (rsq <= local_cut2) {
+          evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
+          evdwl *= 0.5*hbar;
+        }
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
-	  evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+          evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
 
     }
   }
@@ -322,21 +269,21 @@ void PairSpinDipoleCut::compute(int eflag, int vflag)
 
 void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3])
 {
-  int j,jnum,itype,jtype,ntypes; 
-  int *ilist,*jlist,*numneigh,**firstneigh;  
+  int j,jnum,itype,jtype,ntypes;
+  int *jlist,*numneigh,**firstneigh;
   double rsq,rinv,r2inv,r3inv,local_cut2;
   double xi[3],rij[3],eij[3],spi[4],spj[4];
 
   int k,locflag;
-  int *type = atom->type;  
+  int *type = atom->type;
   double **x = atom->x;
-  double **sp = atom->sp;	
+  double **sp = atom->sp;
 
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
   // check if interaction applies to type of ii
-  
+
   itype = type[ii];
   ntypes = atom->ntypes;
   locflag = 0;
@@ -360,28 +307,28 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3])
 
   // if interaction applies to type ii,
   // locflag = 1 and compute pair interaction
- 
+
   if (locflag == 1) {
 
     xi[0] = x[ii][0];
     xi[1] = x[ii][1];
     xi[2] = x[ii][2];
-    spi[0] = sp[ii][0]; 
-    spi[1] = sp[ii][1]; 
+    spi[0] = sp[ii][0];
+    spi[1] = sp[ii][1];
     spi[2] = sp[ii][2];
     spi[3] = sp[ii][3];
     jlist = firstneigh[ii];
-    jnum = numneigh[ii]; 
-    
+    jnum = numneigh[ii];
+
     for (int jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
       j &= NEIGHMASK;
       jtype = type[j];
 
-      spj[0] = sp[j][0]; 
-      spj[1] = sp[j][1]; 
-      spj[2] = sp[j][2]; 
-      spj[3] = sp[j][3]; 
+      spj[0] = sp[j][0];
+      spj[1] = sp[j][1];
+      spj[2] = sp[j][2];
+      spj[3] = sp[j][3];
 
       rij[0] = x[j][0] - xi[0];
       rij[1] = x[j][1] - xi[1];
@@ -397,9 +344,9 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3])
       if (rsq < local_cut2) {
         r2inv = 1.0/rsq;
         r3inv = r2inv*rinv;
-        
+
         // compute dipolar interaction
-        
+
         compute_dipolar(ii,j,eij,fmi,spi,spj,r3inv);
       }
     }
@@ -410,7 +357,7 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3])
    compute dipolar interaction between spins i and j
 ------------------------------------------------------------------------- */
 
-void PairSpinDipoleCut::compute_dipolar(int i, int j, double eij[3], 
+void PairSpinDipoleCut::compute_dipolar(int /* i */, int /* j */, double eij[3],
     double fmi[3], double spi[4], double spj[4], double r3inv)
 {
   double sjdotr;
@@ -426,11 +373,11 @@ void PairSpinDipoleCut::compute_dipolar(int i, int j, double eij[3],
 }
 
 /* ----------------------------------------------------------------------
-   compute the mechanical force due to the dipolar interaction between 
+   compute the mechanical force due to the dipolar interaction between
    atom i and atom j
 ------------------------------------------------------------------------- */
 
-void PairSpinDipoleCut::compute_dipolar_mech(int i, int j, double eij[3],
+void PairSpinDipoleCut::compute_dipolar_mech(int /* i */, int /* j */, double eij[3],
     double fi[3], double spi[3], double spj[3], double r2inv)
 {
   double sisj,sieij,sjeij;
@@ -440,7 +387,7 @@ void PairSpinDipoleCut::compute_dipolar_mech(int i, int j, double eij[3],
   sisj = spi[0]*spj[0] + spi[1]*spj[1] + spi[2]*spj[2];
   sieij = spi[0]*eij[0] + spi[1]*eij[1] + spi[2]*eij[2];
   sjeij = spj[0]*eij[0] + spj[1]*eij[1] + spj[2]*eij[2];
-  
+
   bij = sisj - 5.0*sieij*sjeij;
   pre = 3.0*mub2mu0*gigjri4;
 
@@ -480,7 +427,7 @@ void PairSpinDipoleCut::write_restart(FILE *fp)
     for (j = i; j <= atom->ntypes; j++) {
       fwrite(&setflag[i][j],sizeof(int),1,fp);
       if (setflag[i][j]) {
-	fwrite(&cut_spin_long[i][j],sizeof(int),1,fp);
+        fwrite(&cut_spin_long[i][j],sizeof(int),1,fp);
       }
     }
   }
@@ -500,13 +447,13 @@ void PairSpinDipoleCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
-	if (me == 0) {
-	  fread(&cut_spin_long[i][j],sizeof(int),1,fp);
-	}
-	MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world);
+        if (me == 0) {
+          utils::sfread(FLERR,&cut_spin_long[i][j],sizeof(int),1,fp,NULL,error);
+        }
+        MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world);
       }
     }
   }
@@ -529,8 +476,8 @@ void PairSpinDipoleCut::write_restart_settings(FILE *fp)
 void PairSpinDipoleCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_spin_long_global,sizeof(double),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_spin_long_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_spin_long_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/SPIN/pair_spin_dipole_cut.h b/src/SPIN/pair_spin_dipole_cut.h
index 77e452b179..3adceaf1c7 100644
--- a/src/SPIN/pair_spin_dipole_cut.h
+++ b/src/SPIN/pair_spin_dipole_cut.h
@@ -29,44 +29,40 @@ class PairSpinDipoleCut : public PairSpin {
   double cut_coul;
   double **sigma;
 
-  PairSpinDipoleCut(class LAMMPS *);
-  ~PairSpinDipoleCut();
+  PairSpinDipoleCut(LAMMPS *);
+  virtual ~PairSpinDipoleCut();
   void settings(int, char **);
   void coeff(int, char **);
   double init_one(int, int);
-  void init_style();
-  void *extract(const char *, int &); 
-  
+  void *extract(const char *, int &);
+
   void compute(int, int);
   void compute_single_pair(int, double *);
 
-  void compute_dipolar(int, int, double *, double *, double *, 
+  void compute_dipolar(int, int, double *, double *, double *,
       double *, double);
-  void compute_dipolar_mech(int, int, double *, double *, double *, 
+  void compute_dipolar_mech(int, int, double *, double *, double *,
       double *, double);
 
   void write_restart(FILE *);
   void read_restart(FILE *);
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
-  
-  double cut_spin_long_global;	// global long cutoff distance 
+
+  double cut_spin_long_global;  // global long cutoff distance
 
  protected:
-  double hbar;	 		// reduced Planck's constant
-  double mub;			// Bohr's magneton
-  double mu_0;			// vacuum permeability
-  double mub2mu0;		// prefactor for mech force
-  double mub2mu0hbinv;		// prefactor for mag force
+  double hbar;                  // reduced Planck's constant
+  double mub;                   // Bohr's magneton
+  double mu_0;                  // vacuum permeability
+  double mub2mu0;               // prefactor for mech force
+  double mub2mu0hbinv;          // prefactor for mag force
 
-  double **cut_spin_long;	// cutoff distance long
+  double **cut_spin_long;       // cutoff distance long
 
   double g_ewald;
   int ewald_order;
 
-  int lattice_flag;			// flag for mech force computation
-  class FixNVESpin *lockfixnvespin;	// ptr for setups
-
   void allocate();
 };
 
diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp
index 670fccfce2..124522a9b9 100644
--- a/src/SPIN/pair_spin_dipole_long.cpp
+++ b/src/SPIN/pair_spin_dipole_long.cpp
@@ -22,11 +22,8 @@
 #include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "fix.h"
-#include "fix_nve_spin.h"
 #include "force.h"
 #include "kspace.h"
 #include "math_const.h"
@@ -34,7 +31,7 @@
 #include "modify.h"
 #include "error.h"
 #include "update.h"
-
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -49,14 +46,9 @@ using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-PairSpinDipoleLong::PairSpinDipoleLong(LAMMPS *lmp) : PairSpin(lmp),
-lockfixnvespin(NULL)
+PairSpinDipoleLong::PairSpinDipoleLong(LAMMPS *lmp) : PairSpin(lmp)
 {
-  single_enable = 0;
   ewaldflag = pppmflag = spinflag = 1;
-  respa_enable = 0;
-  no_virial_fdotr_compute = 1;
-  lattice_flag = 0;
 
   hbar = force->hplanck/MY_2PI;                 // eV/(rad.THz)
   mub = 9.274e-4;                               // in A.Ang^2
@@ -86,16 +78,12 @@ PairSpinDipoleLong::~PairSpinDipoleLong()
 
 void PairSpinDipoleLong::settings(int narg, char **arg)
 {
-  if (narg < 1 || narg > 2)
-    error->all(FLERR,"Incorrect args in pair_style command");
-
-  if (strcmp(update->unit_style,"metal") != 0)
-    error->all(FLERR,"Spin simulations require metal unit style");
+  PairSpin::settings(narg,arg);
 
   cut_spin_long_global = force->numeric(FLERR,arg[0]);
-  
+
   // reset cutoffs that have been explicitly set
-  
+
   if (allocated) {
     int i,j;
     for (i = 1; i <= atom->ntypes; i++) {
@@ -106,7 +94,6 @@ void PairSpinDipoleLong::settings(int narg, char **arg)
       }
     }
   }
-
 }
 
 /* ----------------------------------------------------------------------
@@ -116,10 +103,10 @@ void PairSpinDipoleLong::settings(int narg, char **arg)
 void PairSpinDipoleLong::coeff(int narg, char **arg)
 {
   if (!allocated) allocate();
-  
+
   if (narg != 3)
     error->all(FLERR,"Incorrect args in pair_style command");
-  
+
   int ilo,ihi,jlo,jhi;
   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
@@ -144,34 +131,7 @@ void PairSpinDipoleLong::coeff(int narg, char **arg)
 
 void PairSpinDipoleLong::init_style()
 {
-  if (!atom->sp_flag)
-    error->all(FLERR,"Pair spin requires atom/spin style");
-  
-  // need a full neighbor list
-
-  int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->half = 0;
-  neighbor->requests[irequest]->full = 1;
-  
-  // checking if nve/spin or neb/spin are a listed fix
-
-  int ifix = 0;
-  while (ifix < modify->nfix) {
-    if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
-    if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
-    ifix++;
-  }
-  if ((ifix == modify->nfix) && (comm->me == 0))
-    error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
-
-  // get the lattice_flag from nve/spin
-
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"nve/spin") == 0) {
-      lockfixnvespin = (FixNVESpin *) modify->fix[i];
-      lattice_flag = lockfixnvespin->lattice_flag;
-    }
-  }
+  PairSpin::init_style();
 
   // insure use of KSpace long-range solver, set g_ewald
 
@@ -188,9 +148,9 @@ void PairSpinDipoleLong::init_style()
 double PairSpinDipoleLong::init_one(int i, int j)
 {
   if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
-  
+
   cut_spin_long[j][i] = cut_spin_long[i][j];
-  
+
   return cut_spin_long_global;
 }
 
@@ -223,7 +183,7 @@ void *PairSpinDipoleLong::extract(const char *str, int &dim)
 
 void PairSpinDipoleLong::compute(int eflag, int vflag)
 {
-  int i,j,ii,jj,inum,jnum,itype,jtype;  
+  int i,j,ii,jj,inum,jnum,itype,jtype;
   double r,rinv,r2inv,rsq;
   double grij,expm2,t,erfc;
   double evdwl,ecoul;
@@ -233,7 +193,7 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
   double fi[3],fmi[3];
   double local_cut2;
   double pre1,pre2,pre3;
-  int *ilist,*jlist,*numneigh,**firstneigh;  
+  int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = ecoul = 0.0;
   if (eflag || vflag) ev_setup(eflag,vflag);
@@ -242,9 +202,9 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
   double **x = atom->x;
   double **f = atom->f;
   double **fm = atom->fm;
-  double **sp = atom->sp;       
-  int *type = atom->type;  
-  int nlocal = atom->nlocal;  
+  double **sp = atom->sp;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
 
   inum = list->inum;
@@ -265,9 +225,9 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
     xi[1] = x[i][1];
     xi[2] = x[i][2];
     jlist = firstneigh[i];
-    jnum = numneigh[i]; 
-    spi[0] = sp[i][0]; 
-    spi[1] = sp[i][1]; 
+    jnum = numneigh[i];
+    spi[0] = sp[i][0];
+    spi[1] = sp[i][1];
     spi[2] = sp[i][2];
     spi[3] = sp[i][3];
     itype = type[i];
@@ -277,17 +237,17 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
       j &= NEIGHMASK;
       jtype = type[j];
 
-      spj[0] = sp[j][0]; 
-      spj[1] = sp[j][1]; 
-      spj[2] = sp[j][2]; 
-      spj[3] = sp[j][3]; 
+      spj[0] = sp[j][0];
+      spj[1] = sp[j][1];
+      spj[2] = sp[j][2];
+      spj[3] = sp[j][3];
 
       evdwl = 0.0;
 
       fi[0] = fi[1] = fi[2] = 0.0;
       fmi[0] = fmi[1] = fmi[2] = 0.0;
       bij[0] = bij[1] = bij[2] = bij[3] = 0.0;
-     
+
       rij[0] = x[j][0] - xi[0];
       rij[1] = x[j][1] - xi[1];
       rij[2] = x[j][2] - xi[2];
@@ -319,24 +279,24 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
 
       // force accumulation
 
-      f[i][0] += fi[0];  
-      f[i][1] += fi[1];           
+      f[i][0] += fi[0];
+      f[i][1] += fi[1];
       f[i][2] += fi[2];
-      fm[i][0] += fmi[0];        
-      fm[i][1] += fmi[1];                 
+      fm[i][0] += fmi[0];
+      fm[i][1] += fmi[1];
       fm[i][2] += fmi[2];
 
       if (newton_pair || j < nlocal) {
-        f[j][0] -= fi[0];        
-        f[j][1] -= fi[1];                 
+        f[j][0] -= fi[0];
+        f[j][1] -= fi[1];
         f[j][2] -= fi[2];
       }
 
       if (eflag) {
         if (rsq <= local_cut2) {
-          evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + 
+          evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] +
             spi[2]*fmi[2];
-          evdwl *= hbar;
+          evdwl *= 0.5*hbar;
         }
       } else evdwl = 0.0;
 
@@ -354,23 +314,21 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
 
 void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3])
 {
-  //int i,j,jj,jnum,itype,jtype;  
-  int j,jj,jnum,itype,jtype,ntypes; 
+  int j,jj,jnum,itype,jtype,ntypes;
   int k,locflag;
-  int *ilist,*jlist,*numneigh,**firstneigh;  
+  int *jlist,*numneigh,**firstneigh;
   double r,rinv,r2inv,rsq,grij,expm2,t,erfc;
   double local_cut2,pre1,pre2,pre3;
   double bij[4],xi[3],rij[3],eij[3],spi[4],spj[4];
 
-  int *type = atom->type;  
+  int *type = atom->type;
   double **x = atom->x;
-  double **sp = atom->sp;       
+  double **sp = atom->sp;
   double **fm_long = atom->fm_long;
 
-  ilist = list->ilist;
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
-  
+
   // check if interaction applies to type of ii
 
   itype = type[ii];
@@ -404,17 +362,16 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3])
 
     // computation of the exchange interaction
     // loop over neighbors of atom i
-      
-    //i = ilist[ii];
+
     xi[0] = x[ii][0];
     xi[1] = x[ii][1];
     xi[2] = x[ii][2];
-    spi[0] = sp[ii][0]; 
-    spi[1] = sp[ii][1]; 
+    spi[0] = sp[ii][0];
+    spi[1] = sp[ii][1];
     spi[2] = sp[ii][2];
     spi[3] = sp[ii][3];
     jlist = firstneigh[ii];
-    jnum = numneigh[ii]; 
+    jnum = numneigh[ii];
     //itype = type[i];
 
     for (jj = 0; jj < jnum; jj++) {
@@ -422,14 +379,14 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3])
       j &= NEIGHMASK;
       jtype = type[j];
 
-      spj[0] = sp[j][0]; 
-      spj[1] = sp[j][1]; 
-      spj[2] = sp[j][2]; 
-      spj[3] = sp[j][3]; 
+      spj[0] = sp[j][0];
+      spj[1] = sp[j][1];
+      spj[2] = sp[j][2];
+      spj[3] = sp[j][3];
 
       fmi[0] = fmi[1] = fmi[2] = 0.0;
       bij[0] = bij[1] = bij[2] = bij[3] = 0.0;
-     
+
       rij[0] = x[j][0] - xi[0];
       rij[1] = x[j][1] - xi[1];
       rij[2] = x[j][2] - xi[2];
@@ -460,7 +417,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3])
     }
 
     // adding the kspace components to fm
-    
+
     fmi[0] += fm_long[ii][0];
     fmi[1] += fm_long[ii][1];
     fmi[2] += fm_long[ii][2];
@@ -471,7 +428,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3])
    compute dipolar interaction between spins i and j
 ------------------------------------------------------------------------- */
 
-void PairSpinDipoleLong::compute_long(int i, int j, double eij[3], 
+void PairSpinDipoleLong::compute_long(int /* i */, int /* j */, double eij[3],
     double bij[4], double fmi[3], double spi[4], double spj[4])
 {
   double sjeij,pre;
@@ -490,11 +447,11 @@ void PairSpinDipoleLong::compute_long(int i, int j, double eij[3],
 }
 
 /* ----------------------------------------------------------------------
-   compute the mechanical force due to the dipolar interaction between 
+   compute the mechanical force due to the dipolar interaction between
    atom i and atom j
 ------------------------------------------------------------------------- */
 
-void PairSpinDipoleLong::compute_long_mech(int i, int j, double eij[3],
+void PairSpinDipoleLong::compute_long_mech(int /* i */, int /* j */, double eij[3],
     double bij[4], double fi[3], double spi[3], double spj[3])
 {
   double sisj,sieij,sjeij,b2,b3;
@@ -569,11 +526,11 @@ void PairSpinDipoleLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&cut_spin_long[i][j],sizeof(int),1,fp);
+          utils::sfread(FLERR,&cut_spin_long[i][j],sizeof(int),1,fp,NULL,error);
         }
         MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world);
       }
@@ -598,8 +555,8 @@ void PairSpinDipoleLong::write_restart_settings(FILE *fp)
 void PairSpinDipoleLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_spin_long_global,sizeof(double),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_spin_long_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_spin_long_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/SPIN/pair_spin_dipole_long.h b/src/SPIN/pair_spin_dipole_long.h
index 6a05f56032..1ec30cdb93 100644
--- a/src/SPIN/pair_spin_dipole_long.h
+++ b/src/SPIN/pair_spin_dipole_long.h
@@ -29,44 +29,41 @@ class PairSpinDipoleLong : public PairSpin {
   double cut_coul;
   double **sigma;
 
-  PairSpinDipoleLong(class LAMMPS *);
-  ~PairSpinDipoleLong();
+  PairSpinDipoleLong(LAMMPS *);
+  virtual ~PairSpinDipoleLong();
   void settings(int, char **);
   void coeff(int, char **);
-  double init_one(int, int);
   void init_style();
-  void *extract(const char *, int &); 
-  
+  double init_one(int, int);
+  void *extract(const char *, int &);
+
   void compute(int, int);
   void compute_single_pair(int, double *);
 
-  void compute_long(int, int, double *, double *, double *, 
+  void compute_long(int, int, double *, double *, double *,
       double *, double *);
-  void compute_long_mech(int, int, double *, double *, double *, 
+  void compute_long_mech(int, int, double *, double *, double *,
       double *, double *);
 
   void write_restart(FILE *);
   void read_restart(FILE *);
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
-  
-  double cut_spin_long_global;	// global long cutoff distance 
+
+  double cut_spin_long_global;  // global long cutoff distance
 
  protected:
-  double hbar;	 		// reduced Planck's constant
-  double mub;			// Bohr's magneton
-  double mu_0;			// vacuum permeability
-  double mub2mu0;		// prefactor for mech force
-  double mub2mu0hbinv;		// prefactor for mag force
+  double hbar;                  // reduced Planck's constant
+  double mub;                   // Bohr's magneton
+  double mu_0;                  // vacuum permeability
+  double mub2mu0;               // prefactor for mech force
+  double mub2mu0hbinv;          // prefactor for mag force
 
-  double **cut_spin_long;	// cutoff distance long
+  double **cut_spin_long;       // cutoff distance long
 
   double g_ewald;
   int ewald_order;
 
-  int lattice_flag;			// flag for mech force computation
-  class FixNVESpin *lockfixnvespin;	// ptr for setups
-
   void allocate();
 };
 
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index afd2deaa6a..04c2dc408d 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -30,28 +30,16 @@
 #include "error.h"
 #include "force.h"
 #include "fix.h"
-#include "fix_nve_spin.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "modify.h"
 #include "update.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairSpinDmi::PairSpinDmi(LAMMPS *lmp) : PairSpin(lmp),
-lockfixnvespin(NULL)
-{
-  single_enable = 0;
-  no_virial_fdotr_compute = 1;
-  lattice_flag = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
 PairSpinDmi::~PairSpinDmi()
 {
   if (allocated) {
@@ -74,11 +62,7 @@ PairSpinDmi::~PairSpinDmi()
 
 void PairSpinDmi::settings(int narg, char **arg)
 {
-  if (narg < 1 || narg > 2)
-    error->all(FLERR,"Incorrect number of args in pair/spin/dmi command");
-
-  if (strcmp(update->unit_style,"metal") != 0)
-    error->all(FLERR,"Spin simulations require metal unit style");
+  PairSpin::settings(narg,arg);
 
   cut_spin_dmi_global = force->numeric(FLERR,arg[0]);
 
@@ -144,44 +128,6 @@ void PairSpinDmi::coeff(int narg, char **arg)
   }
   if (count == 0)
     error->all(FLERR,"Incorrect args in pair_style command");
-
-}
-
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairSpinDmi::init_style()
-{
-  if (!atom->sp_flag)
-    error->all(FLERR,"Pair spin requires atom/spin style");
-
-  // need a full neighbor list
-
-  int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->half = 0;
-  neighbor->requests[irequest]->full = 1;
-
-  // checking if nve/spin is a listed fix
-
-  int ifix = 0;
-  while (ifix < modify->nfix) {
-    if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
-    if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
-    ifix++;
-  }
-  if ((ifix == modify->nfix) && (comm->me == 0))
-    error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
-
-  // get the lattice_flag from nve/spin
-
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"nve/spin") == 0) {
-      lockfixnvespin = (FixNVESpin *) modify->fix[i];
-      lattice_flag = lockfixnvespin->lattice_flag;
-    }
-  }
-
 }
 
 /* ----------------------------------------------------------------------
@@ -313,7 +259,7 @@ void PairSpinDmi::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        evdwl *= hbar;
+        evdwl *= 0.5*hbar;
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
@@ -373,7 +319,6 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
   // if interaction applies to type ii,
   // locflag = 1 and compute pair interaction
 
-  //i = ilist[ii];
   if (locflag == 1) {
 
     xi[0] = x[ii][0];
@@ -532,18 +477,18 @@ void PairSpinDmi::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&DM[i][j],sizeof(double),1,fp);
-          fread(&v_dmx[i][j],sizeof(double),1,fp);
-          fread(&v_dmy[i][j],sizeof(double),1,fp);
-          fread(&v_dmz[i][j],sizeof(double),1,fp);
-          fread(&vmech_dmx[i][j],sizeof(double),1,fp);
-          fread(&vmech_dmy[i][j],sizeof(double),1,fp);
-          fread(&vmech_dmz[i][j],sizeof(double),1,fp);
-          fread(&cut_spin_dmi[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&DM[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&v_dmx[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&v_dmy[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&v_dmz[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&vmech_dmx[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&vmech_dmy[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&vmech_dmz[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_spin_dmi[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&DM[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&v_dmx[i][j],1,MPI_DOUBLE,0,world);
@@ -577,9 +522,9 @@ void PairSpinDmi::write_restart_settings(FILE *fp)
 void PairSpinDmi::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_spin_dmi_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_spin_dmi_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_spin_dmi_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h
index 68e42e879d..01022623ec 100644
--- a/src/SPIN/pair_spin_dmi.h
+++ b/src/SPIN/pair_spin_dmi.h
@@ -26,11 +26,10 @@ namespace LAMMPS_NS {
 
 class PairSpinDmi : public PairSpin {
  public:
-  PairSpinDmi(class LAMMPS *);
+  PairSpinDmi(LAMMPS *lmp) : PairSpin(lmp) {}
   virtual ~PairSpinDmi();
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   double init_one(int, int);
   void *extract(const char *, int &);
 
@@ -45,16 +44,13 @@ class PairSpinDmi : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
-  double cut_spin_dmi_global;			// short range pair cutoff
+  double cut_spin_dmi_global;                   // short range pair cutoff
 
  protected:
-  double **DM;                     		// dmi coeff in eV
-  double **v_dmx, **v_dmy, **v_dmz;		// dmi direction
-  double **vmech_dmx, **vmech_dmy, **vmech_dmz;	// dmi mech direction
-  double **cut_spin_dmi;      			// cutoff distance dmi
-
-  int lattice_flag;             	        // flag for mech force computation
-  class FixNVESpin *lockfixnvespin;     	// ptr to FixNVESpin for setups
+  double **DM;                                  // dmi coeff in eV
+  double **v_dmx, **v_dmy, **v_dmz;             // dmi direction
+  double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction
+  double **cut_spin_dmi;                        // cutoff distance dmi
 
   void allocate();
 };
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index cc28018ad0..6eacb04ee3 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -29,29 +29,17 @@
 #include "comm.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_nve_spin.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "modify.h"
 #include "update.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairSpinExchange::PairSpinExchange(LAMMPS *lmp) : PairSpin(lmp),
-lockfixnvespin(NULL)
-{
-  single_enable = 0;
-  no_virial_fdotr_compute = 1;
-  lattice_flag = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
 PairSpinExchange::~PairSpinExchange()
 {
   if (allocated) {
@@ -71,11 +59,7 @@ PairSpinExchange::~PairSpinExchange()
 
 void PairSpinExchange::settings(int narg, char **arg)
 {
-  if (narg < 1 || narg > 7) 
-    error->all(FLERR,"Incorrect number of args in pair_style pair/spin command");
-
-  if (strcmp(update->unit_style,"metal") != 0)
-    error->all(FLERR,"Spin simulations require metal unit style");
+  PairSpin::settings(narg,arg);
 
   cut_spin_exchange_global = force->numeric(FLERR,arg[0]);
 
@@ -89,7 +73,6 @@ void PairSpinExchange::settings(int narg, char **arg)
           cut_spin_exchange[i][j] = cut_spin_exchange_global;
         }
   }
-
 }
 
 /* ----------------------------------------------------------------------
@@ -134,43 +117,6 @@ void PairSpinExchange::coeff(int narg, char **arg)
   if (count == 0) error->all(FLERR,"Incorrect args in pair_style command");
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairSpinExchange::init_style()
-{
-  if (!atom->sp_flag)
-    error->all(FLERR,"Pair spin requires atom/spin style");
-
-  // need a full neighbor list
-
-  int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->half = 0;
-  neighbor->requests[irequest]->full = 1;
-
-  // checking if nve/spin or neb/spin are a listed fix
-
-  int ifix = 0;
-  while (ifix < modify->nfix) {
-    if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
-    if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
-    ifix++;
-  }
-  if ((ifix == modify->nfix) && (comm->me == 0))
-    error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
-
-  // get the lattice_flag from nve/spin
-
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"nve/spin") == 0) {
-      lockfixnvespin = (FixNVESpin *) modify->fix[i];
-      lattice_flag = lockfixnvespin->lattice_flag;
-    }
-  }
-
-}
-
 /* ----------------------------------------------------------------------
    init for one type pair i,j and corresponding j,i
 ------------------------------------------------------------------------- */
@@ -296,7 +242,8 @@ void PairSpinExchange::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        evdwl *= hbar;
+        evdwl *= 0.5*hbar;
+        // evdwl *= hbar;
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
@@ -497,15 +444,15 @@ void PairSpinExchange::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&J1_mag[i][j],sizeof(double),1,fp);
-          fread(&J1_mech[i][j],sizeof(double),1,fp);
-          fread(&J2[i][j],sizeof(double),1,fp);
-          fread(&J2[i][j],sizeof(double),1,fp);
-          fread(&cut_spin_exchange[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&J1_mag[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&J1_mech[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&J2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&J3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_spin_exchange[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&J1_mag[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&J1_mech[i][j],1,MPI_DOUBLE,0,world);
@@ -536,9 +483,9 @@ void PairSpinExchange::write_restart_settings(FILE *fp)
 void PairSpinExchange::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_spin_exchange_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_spin_exchange_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_spin_exchange_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h
index b524a513eb..19eafeb5ca 100644
--- a/src/SPIN/pair_spin_exchange.h
+++ b/src/SPIN/pair_spin_exchange.h
@@ -26,11 +26,10 @@ namespace LAMMPS_NS {
 
 class PairSpinExchange : public PairSpin {
  public:
-  PairSpinExchange(class LAMMPS *);
+  PairSpinExchange(LAMMPS *lmp) : PairSpin(lmp) {}
   virtual ~PairSpinExchange();
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   double init_one(int, int);
   void *extract(const char *, int &);
 
@@ -45,16 +44,13 @@ class PairSpinExchange : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
-  double cut_spin_exchange_global;	// global exchange cutoff distance
+  double cut_spin_exchange_global;      // global exchange cutoff distance
 
  protected:
-  double **J1_mag;			// exchange coeffs in eV
-  double **J1_mech;			// mech exchange coeffs in
+  double **J1_mag;                      // exchange coeffs in eV
+  double **J1_mech;                     // mech exchange coeffs in
   double **J2, **J3;                    // J1 in eV, J2 adim, J3 in Ang
-  double **cut_spin_exchange;		// cutoff distance exchange
-
-  int lattice_flag; 			// flag for mech force computation
-  class FixNVESpin *lockfixnvespin;	// ptr to FixNVESpin for setups
+  double **cut_spin_exchange;           // cutoff distance exchange
 
   void allocate();
 };
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
index 6756ebc3cc..fabad4ae4d 100644
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@@ -29,29 +29,17 @@
 #include "comm.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_nve_spin.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "modify.h"
 #include "update.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairSpinMagelec::PairSpinMagelec(LAMMPS *lmp) : PairSpin(lmp),
-lockfixnvespin(NULL)
-{
-  single_enable = 0;
-  no_virial_fdotr_compute = 1;
-  lattice_flag = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
 PairSpinMagelec::~PairSpinMagelec()
 {
   if (allocated) {
@@ -72,11 +60,8 @@ PairSpinMagelec::~PairSpinMagelec()
 
 void PairSpinMagelec::settings(int narg, char **arg)
 {
-  if (narg < 1 || narg > 2)
-    error->all(FLERR,"Incorrect number of args in pair_style pair/spin command");
 
-  if (strcmp(update->unit_style,"metal") != 0)
-    error->all(FLERR,"Spin simulations require metal unit style");
+  PairSpin::settings(narg,arg);
 
   cut_spin_magelec_global = force->numeric(FLERR,arg[0]);
 
@@ -140,43 +125,6 @@ void PairSpinMagelec::coeff(int narg, char **arg)
     error->all(FLERR,"Incorrect args in pair_style command");
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairSpinMagelec::init_style()
-{
-  if (!atom->sp_flag)
-    error->all(FLERR,"Pair spin requires atom/spin style");
-
-  // need a full neighbor list
-
-  int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->half = 0;
-  neighbor->requests[irequest]->full = 1;
-
-  // checking if nve/spin is a listed fix
-
-  int ifix = 0;
-  while (ifix < modify->nfix) {
-    if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
-    if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
-    ifix++;
-  }
-  if ((ifix == modify->nfix) && (comm->me == 0))
-    error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
-
-  // get the lattice_flag from nve/spin
-
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"nve/spin") == 0) {
-      lockfixnvespin = (FixNVESpin *) modify->fix[i];
-      lattice_flag = lockfixnvespin->lattice_flag;
-    }
-  }
-
-}
-
 /* ----------------------------------------------------------------------
    init for one type pair i,j and corresponding j,i
 ------------------------------------------------------------------------- */
@@ -303,7 +251,7 @@ void PairSpinMagelec::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        evdwl *= hbar;
+        evdwl *= 0.5*hbar;
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
@@ -414,17 +362,17 @@ void PairSpinMagelec::compute_magelec(int i, int j, double eij[3], double fmi[3]
   vy = v_mey[itype][jtype];
   vz = v_mez[itype][jtype];
 
-  meix = vy*eij[2] - vz*eij[1];
-  meiy = vz*eij[0] - vx*eij[2];
-  meiz = vx*eij[1] - vy*eij[0];
+  meix = (vy*eij[2] - vz*eij[1]);
+  meiy = (vz*eij[0] - vx*eij[2]);
+  meiz = (vx*eij[1] - vy*eij[0]);
 
   meix *= ME[itype][jtype];
   meiy *= ME[itype][jtype];
   meiz *= ME[itype][jtype];
 
-  fmi[0] += spj[1]*meiz - spj[2]*meiy;
-  fmi[1] += spj[2]*meix - spj[0]*meiz;
-  fmi[2] += spj[0]*meiy - spj[1]*meix;
+  fmi[0] += (spj[1]*meiz - spj[2]*meiy);
+  fmi[1] += (spj[2]*meix - spj[0]*meiz);
+  fmi[2] += (spj[0]*meiy - spj[1]*meix);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -443,17 +391,17 @@ void PairSpinMagelec::compute_magelec_mech(int i, int j, double fi[3], double sp
   vy = v_mey[itype][jtype];
   vz = v_mez[itype][jtype];
 
-  meix = spi[1]*spi[2] - spi[2]*spj[1];
-  meiy = spi[2]*spi[0] - spi[0]*spj[2];
-  meiz = spi[0]*spi[1] - spi[1]*spj[0];
+  meix = (spi[1]*spi[2] - spi[2]*spj[1]);
+  meiy = (spi[2]*spi[0] - spi[0]*spj[2]);
+  meiz = (spi[0]*spi[1] - spi[1]*spj[0]);
 
   meix *= ME_mech[itype][jtype];
   meiy *= ME_mech[itype][jtype];
   meiz *= ME_mech[itype][jtype];
 
-  fi[0] += meiy*vz - meiz*vy;
-  fi[1] += meiz*vx - meix*vz;
-  fi[2] += meix*vy - meiy*vx;
+  fi[0] += (meiy*vz - meiz*vy);
+  fi[1] += (meiz*vx - meix*vz);
+  fi[2] += (meix*vy - meiy*vx);
 
 }
 
@@ -516,15 +464,15 @@ void PairSpinMagelec::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&ME[i][j],sizeof(double),1,fp);
-          fread(&v_mex[i][j],sizeof(double),1,fp);
-          fread(&v_mey[i][j],sizeof(double),1,fp);
-          fread(&v_mez[i][j],sizeof(double),1,fp);
-          fread(&cut_spin_magelec[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&ME[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&v_mex[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&v_mey[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&v_mez[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_spin_magelec[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&ME[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&v_mex[i][j],1,MPI_DOUBLE,0,world);
@@ -554,9 +502,9 @@ void PairSpinMagelec::write_restart_settings(FILE *fp)
 void PairSpinMagelec::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_spin_magelec_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_spin_magelec_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_spin_magelec_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h
index 5e72a4c35e..4df0078bea 100644
--- a/src/SPIN/pair_spin_magelec.h
+++ b/src/SPIN/pair_spin_magelec.h
@@ -26,11 +26,10 @@ namespace LAMMPS_NS {
 
 class PairSpinMagelec : public PairSpin {
  public:
-  PairSpinMagelec(class LAMMPS *);
+  PairSpinMagelec(LAMMPS *lmp) : PairSpin(lmp) {}
   virtual ~PairSpinMagelec();
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   double init_one(int, int);
   void *extract(const char *, int &);
 
@@ -45,15 +44,12 @@ class PairSpinMagelec : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
-  double cut_spin_magelec_global;	// global me cutoff
+  double cut_spin_magelec_global;       // global me cutoff
 
  protected:
-  double **ME, **ME_mech;		// magelec coeff in eV
-  double **v_mex, **v_mey, **v_mez;	// magelec direction
-  double **cut_spin_magelec;		// magelec cutoff distance
-
-  int lattice_flag;                     // flag for mech force computation
-  class FixNVESpin *lockfixnvespin;     // ptr to FixNVESpin for setups
+  double **ME, **ME_mech;               // magelec coeff in eV
+  double **v_mex, **v_mey, **v_mez;     // magelec direction
+  double **cut_spin_magelec;            // magelec cutoff distance
 
   void allocate();
 };
diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp
index 355ba20f39..4a5d453de2 100644
--- a/src/SPIN/pair_spin_neel.cpp
+++ b/src/SPIN/pair_spin_neel.cpp
@@ -29,29 +29,17 @@
 #include "comm.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_nve_spin.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "modify.h"
 #include "update.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairSpinNeel::PairSpinNeel(LAMMPS *lmp) : PairSpin(lmp),
-lockfixnvespin(NULL)
-{
-  single_enable = 0;
-  no_virial_fdotr_compute = 1;
-  lattice_flag = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
 PairSpinNeel::~PairSpinNeel()
 {
   if (allocated) {
@@ -75,11 +63,7 @@ PairSpinNeel::~PairSpinNeel()
 
 void PairSpinNeel::settings(int narg, char **arg)
 {
-  if (narg < 1 || narg > 2)
-    error->all(FLERR,"Incorrect number of args in pair_style pair/spin command");
-
-  if (strcmp(update->unit_style,"metal") != 0)
-    error->all(FLERR,"Spin simulations require metal unit style");
+  PairSpin::settings(narg,arg);
 
   cut_spin_neel_global = force->numeric(FLERR,arg[0]);
 
@@ -146,43 +130,6 @@ void PairSpinNeel::coeff(int narg, char **arg)
 
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairSpinNeel::init_style()
-{
-  if (!atom->sp_flag)
-    error->all(FLERR,"Pair spin requires atom/spin style");
-
-  // need a full neighbor list
-
-  int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->half = 0;
-  neighbor->requests[irequest]->full = 1;
-
-  // checking if nve/spin is a listed fix
-
-  int ifix = 0;
-  while (ifix < modify->nfix) {
-    if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
-    if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
-    ifix++;
-  }
-  if ((ifix == modify->nfix) && (comm->me == 0))
-    error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
-
-  // get the lattice_flag from nve/spin
-
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"nve/spin") == 0) {
-      lockfixnvespin = (FixNVESpin *) modify->fix[i];
-      lattice_flag = lockfixnvespin->lattice_flag;
-    }
-  }
-
-}
-
 /* ----------------------------------------------------------------------
    init for one type pair i,j and corresponding j,i
 ------------------------------------------------------------------------- */
@@ -313,7 +260,7 @@ void PairSpinNeel::compute(int eflag, int vflag)
 
       if (eflag) {
         evdwl = (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
-        evdwl *= hbar;
+        evdwl *= 0.5*hbar;
       } else evdwl = 0.0;
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
@@ -643,10 +590,8 @@ void PairSpinNeel::allocate()
   memory->create(q3,n+1,n+1,"pair/spin/soc/neel:q3");
 
   memory->create(cutsq,n+1,n+1,"pair/spin/soc/neel:cutsq");
-
 }
 
-
 /* ----------------------------------------------------------------------
    proc 0 writes to restart file
 ------------------------------------------------------------------------- */
@@ -687,19 +632,19 @@ void PairSpinNeel::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&g1[i][j],sizeof(double),1,fp);
-          fread(&g1_mech[i][j],sizeof(double),1,fp);
-          fread(&g2[i][j],sizeof(double),1,fp);
-          fread(&g2[i][j],sizeof(double),1,fp);
-          fread(&q1[i][j],sizeof(double),1,fp);
-          fread(&q1_mech[i][j],sizeof(double),1,fp);
-          fread(&q2[i][j],sizeof(double),1,fp);
-          fread(&q2[i][j],sizeof(double),1,fp);
-          fread(&cut_spin_neel[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&g1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&g1_mech[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&g2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&g3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&q1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&q1_mech[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&q2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&q3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_spin_neel[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&g1[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&g1_mech[i][j],1,MPI_DOUBLE,0,world);
@@ -733,9 +678,9 @@ void PairSpinNeel::write_restart_settings(FILE *fp)
 void PairSpinNeel::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_spin_neel_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_spin_neel_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_spin_neel_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h
index f60d7d2dca..5261a7f746 100644
--- a/src/SPIN/pair_spin_neel.h
+++ b/src/SPIN/pair_spin_neel.h
@@ -26,11 +26,10 @@ namespace LAMMPS_NS {
 
 class PairSpinNeel : public PairSpin {
  public:
-  PairSpinNeel(class LAMMPS *);
+  PairSpinNeel(LAMMPS *lmp) : PairSpin(lmp) {}
   virtual ~PairSpinNeel();
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   double init_one(int, int);
   void *extract(const char *, int &);
 
@@ -45,21 +44,17 @@ class PairSpinNeel : public PairSpin {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
-  double cut_spin_neel_global;		// global neel cutoff distance
+  double cut_spin_neel_global;          // global neel cutoff distance
 
  protected:
 
   // pseudo-dipolar and pseudo-quadrupolar coeff.
 
-  double **g1, **g1_mech; 		// neel coeffs gij
-  double **g2, **g3; 			// g1 in eV, g2 adim, g3 in Ang
-  double **q1, **q1_mech; 		// neel coeffs qij
-  double **q2, **q3; 			// q1 in eV, q2 adim, q3 in Ang
-  double **cut_spin_neel;		// cutoff distance exchange
-
-  int lattice_flag;			// flag for mech force computation
-  class FixNVESpin *lockfixnvespin;	// ptr to FixNVESpin for setups
-
+  double **g1, **g1_mech;               // neel coeffs gij
+  double **g2, **g3;                    // g1 in eV, g2 adim, g3 in Ang
+  double **q1, **q1_mech;               // neel coeffs qij
+  double **q2, **q3;                    // q1 in eV, q2 adim, q3 in Ang
+  double **cut_spin_neel;               // cutoff distance exchange
 
   void allocate();
 };
diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c
index f56d3616c8..a5a00f86a5 100644
--- a/src/STUBS/mpi.c
+++ b/src/STUBS/mpi.c
@@ -12,14 +12,13 @@
 ------------------------------------------------------------------------ */
 
 /* Single-processor "stub" versions of MPI routines */
-/* -I. in Makefile insures dummy mpi.h in this dir is included */
 
 #include <stdlib.h>
 #include <string.h>
 #include <stdio.h>
 #include <stdint.h>
 #include <sys/time.h>
-#include <mpi.h>
+#include "mpi.h"
 #include "../version.h"
 
 /* data structure for double/int */
diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp
index e2a1768f55..0e9cd02ad6 100644
--- a/src/USER-ATC/fix_atc.cpp
+++ b/src/USER-ATC/fix_atc.cpp
@@ -581,7 +581,7 @@ void FixATC::min_setup(int vflag)
   setup(vflag);
 }
 
-void FixATC::setup(int vflag)
+void FixATC::setup(int /* vflag */)
 {
   comm->forward_comm_fix(this);
 
@@ -642,7 +642,7 @@ void FixATC::grow_arrays(int nmax)
   atc_->grow_arrays(nmax);
 }
 
-void FixATC::copy_arrays(int i, int j, int delflag)
+void FixATC::copy_arrays(int i, int j, int /* delflag */)
 {
   atc_->copy_arrays(i,j);
 }
@@ -675,7 +675,7 @@ void FixATC::unpack_forward_comm(int n, int first, double *buf)
    pack values in local atom-based arrays for restart file
    ------------------------------------------------------------------------- */
 
-int FixATC::pack_restart(int i, double *buf){
+int FixATC::pack_restart(int /* i */, double * /* buf */){
   return 0;
 }
 
@@ -683,7 +683,7 @@ int FixATC::pack_restart(int i, double *buf){
    unpack values from atom->extra array to restart the fix
    ------------------------------------------------------------------------- */
 
-void FixATC::unpack_restart(int nlocal, int nth){
+void FixATC::unpack_restart(int /* nlocal */, int /* nth */){
 }
 
 /* ----------------------------------------------------------------------
@@ -698,7 +698,7 @@ int FixATC::maxsize_restart(){
    size of atom nlocal's restart data
    ------------------------------------------------------------------------- */
 
-int FixATC::size_restart(int nlocal){
+int FixATC::size_restart(int /* nlocal */){
   return 0;
 }
 
@@ -706,7 +706,7 @@ int FixATC::size_restart(int nlocal){
    pack entire state of Fix into one write
    ------------------------------------------------------------------------- */
 
-void FixATC::write_restart(FILE *fp){
+void FixATC::write_restart(FILE * /* fp */){
 
   char ** args = new char*[2];
   args[0] = new char[50];
@@ -728,7 +728,7 @@ void FixATC::write_restart(FILE *fp){
    use state info from restart file to restart the Fix
    ------------------------------------------------------------------------- */
 
-void FixATC::restart(char *buf){
+void FixATC::restart(char * /* buf */){
 
   char ** args = new char*[2];
   args[0] = new char[50];
@@ -750,7 +750,7 @@ void FixATC::restart(char *buf){
    allow for both per-type and per-atom mass
    ------------------------------------------------------------------------- */
 
-void FixATC::initial_integrate(int vflag)
+void FixATC::initial_integrate(int /* vflag */)
 {
   try {
     atc_->pre_init_integrate();
@@ -836,7 +836,7 @@ void FixATC::pre_neighbor()
   }
 }
 /* ---------------------------------------------------------------------- */
-void FixATC::pre_force(int vflag)
+void FixATC::pre_force(int /* vflag */)
 {
 
   try {
@@ -848,7 +848,7 @@ void FixATC::pre_force(int vflag)
   }
 }
 /* ---------------------------------------------------------------------- */
-void FixATC::post_force(int vflag)
+void FixATC::post_force(int /* vflag */)
 {
 
   try {
@@ -884,7 +884,7 @@ void FixATC::setup_pre_neighbor()
   }
 }
 /* ---------------------------------------------------------------------- */
-void FixATC::min_pre_force(int vflag)
+void FixATC::min_pre_force(int /* vflag */)
 {
   try {
     atc_->min_pre_force();
@@ -896,7 +896,7 @@ void FixATC::min_pre_force(int vflag)
 }
 
 /* ---------------------------------------------------------------------- */
-void FixATC::min_post_force(int vflag)
+void FixATC::min_post_force(int /* vflag */)
 {
   try {
     atc_->min_post_force();
diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp
index a147a11081..b4a1cbf72a 100644
--- a/src/USER-AWPMD/fix_nve_awpmd.cpp
+++ b/src/USER-AWPMD/fix_nve_awpmd.cpp
@@ -72,7 +72,7 @@ void FixNVEAwpmd::init()
    allow for only per-type  mass
 ------------------------------------------------------------------------- */
 
-void FixNVEAwpmd::initial_integrate(int vflag)
+void FixNVEAwpmd::initial_integrate(int /* vflag */)
 {
 
 
@@ -117,7 +117,7 @@ void FixNVEAwpmd::final_integrate(){}
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVEAwpmd::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVEAwpmd::initial_integrate_respa(int vflag, int ilevel, int /* iloop */)
 {
   dtv = step_respa[ilevel];
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -131,7 +131,7 @@ void FixNVEAwpmd::initial_integrate_respa(int vflag, int ilevel, int iloop)
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVEAwpmd::final_integrate_respa(int ilevel, int iloop)
+void FixNVEAwpmd::final_integrate_respa(int ilevel, int /* iloop */)
 {
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
   final_integrate();
diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp
index 75ebb0e251..092327c367 100644
--- a/src/USER-AWPMD/pair_awpmd_cut.cpp
+++ b/src/USER-AWPMD/pair_awpmd_cut.cpp
@@ -32,6 +32,7 @@
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 #include "logexc.h"
 #include "vector_3.h"
@@ -600,10 +601,10 @@ void PairAWPMDCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
-        if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
+        if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
       }
     }
@@ -627,9 +628,9 @@ void PairAWPMDCut::write_restart_settings(FILE *fp)
 void PairAWPMDCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
@@ -642,7 +643,7 @@ void PairAWPMDCut::read_restart_settings(FILE *fp)
    these arrays are stored locally by pair style
 ------------------------------------------------------------------------- */
 
-void PairAWPMDCut::min_xf_pointers(int ignore, double **xextra, double **fextra)
+void PairAWPMDCut::min_xf_pointers(int /* ignore */, double **xextra, double **fextra)
 {
   // grow arrays if necessary
   // need to be atom->nmax in length
@@ -665,7 +666,7 @@ void PairAWPMDCut::min_xf_pointers(int ignore, double **xextra, double **fextra)
    calculate and store in min_eradius and min_erforce
 ------------------------------------------------------------------------- */
 
-void PairAWPMDCut::min_xf_get(int ignore)
+void PairAWPMDCut::min_xf_get(int /* ignore */)
 {
   double *eradius = atom->eradius;
   double *erforce = atom->erforce;
@@ -704,7 +705,7 @@ void PairAWPMDCut::min_xf_get(int ignore)
    propagate the minimizer values to the atom values
 ------------------------------------------------------------------------- */
 
-void PairAWPMDCut::min_x_set(int ignore)
+void PairAWPMDCut::min_x_set(int /* ignore */)
 {
   double *eradius = atom->eradius;
   double **v=atom->v;
diff --git a/src/USER-CGDNA/Install.sh b/src/USER-CGDNA/Install.sh
index fa62b0daf2..9ef10d3f62 100755
--- a/src/USER-CGDNA/Install.sh
+++ b/src/USER-CGDNA/Install.sh
@@ -30,8 +30,10 @@ action () {
 
 action  bond_oxdna_fene.cpp bond_fene.h
 action  bond_oxdna2_fene.cpp bond_fene.h
+action  bond_oxrna2_fene.cpp bond_fene.h
 action  bond_oxdna_fene.h bond_fene.h
 action  bond_oxdna2_fene.h bond_fene.h
+action  bond_oxrna2_fene.h bond_fene.h
 action  fix_nve_dotc_langevin.cpp atom_vec_ellipsoid.h
 action  fix_nve_dotc_langevin.h atom_vec_ellipsoid.h
 action  fix_nve_dot.cpp atom_vec_ellipsoid.h
@@ -43,13 +45,23 @@ action  pair_oxdna_coaxstk.h atom_vec_ellipsoid.h
 action  pair_oxdna2_coaxstk.h atom_vec_ellipsoid.h
 action  pair_oxdna_excv.cpp atom_vec_ellipsoid.h
 action  pair_oxdna2_excv.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_excv.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_excv.h atom_vec_ellipsoid.h
 action  pair_oxdna2_excv.h atom_vec_ellipsoid.h
+action  pair_oxrna2_excv.h atom_vec_ellipsoid.h
 action  pair_oxdna_hbond.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_hbond.h atom_vec_ellipsoid.h
+action  pair_oxrna2_hbond.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_hbond.h atom_vec_ellipsoid.h
 action  pair_oxdna_stk.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_stk.h atom_vec_ellipsoid.h
+action  pair_oxrna2_stk.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_stk.h atom_vec_ellipsoid.h
 action  pair_oxdna_xstk.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_xstk.h atom_vec_ellipsoid.h
+action  pair_oxrna2_xstk.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_xstk.h atom_vec_ellipsoid.h
 action  pair_oxdna2_dh.cpp atom_vec_ellipsoid.h
 action  pair_oxdna2_dh.h atom_vec_ellipsoid.h
+action  pair_oxrna2_dh.cpp atom_vec_ellipsoid.h
+action  pair_oxrna2_dh.h atom_vec_ellipsoid.h
diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README
deleted file mode 100644
index 48d6178d13..0000000000
--- a/src/USER-CGDNA/README
+++ /dev/null
@@ -1,87 +0,0 @@
-This package contains a LAMMPS implementation of coarse-grained
-models of DNA, which can be used to model sequence-specific
-DNA strands.
-
-Please cite [1] and the relevant oxDNA articles in any publication 
-that uses this package.
-
-See the doc pages and [2,3,4] for the individual bond and pair styles. 
-The packages contains also a new Langevin-type rigid-body integrator,
-which has also its own doc page and is explained in [5].
-
-[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
-"Coarse-grained simulation of DNA using LAMMPS", 
-Eur. Phys. J. E 41, 57 (2018).
-
-[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, 
-and thermodynamic properties of a coarse-grained DNA model",
-J. Chem. Phys. 134, 085101 (2011).
-
-[3] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA 
-self-assembly, DPhil. University of Oxford (2011).
-
-[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
-Improved Structural Properties and Salt Dependence into a Coarse-Grained
-Model of DNA, J. Chem. Phys. 142, 234901 (2015).
-
-[5] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and 
-gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 
-144114 (2015).
-
-Example input and data files can be found in
-/examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. Python setup 
-tools which create single straight or helical DNA strands as
-well as DNA duplexes or arrays of duplexes can be found in
-/examples/USER/cgdna/util/. A technical report with more information
-on the models, the structure of the input and data file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA can be found
-in /doc/src/PDF/USER-CGDNA.pdf.
-
-IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
-with the MOLECULE and ASPHERE packages.  These should be included in
-the LAMMPS build by typing "make yes-asphere yes-molecule" prior to
-the usual compilation (see the "Including/excluding packages" section
-of the LAMMPS manual).
-
-The creator of this package is:
-
-Dr Oliver Henrich
-University of Strathclyde, Glasgow, UK
-oliver d o t henrich a t strath d o t ac d o t uk
-
-
---------------------------------------------------------------------------
-
-** Bond styles provided by this package:
-
-bond_oxdna_fene.cpp:  backbone connectivity, a modified FENE potential
-
-bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3])
-
-** Pair styles provided by this package:
-
-pair_oxdna_excv.cpp:  excluded volume interaction between the nucleotides
-
-pair_oxdna_stk.cpp:  stacking interaction between consecutive nucleotides
-                     on the same strand
-
-pair_oxdna_hbond.cpp:  hydrogen-bonding interaction between complementary
-                       nucleotides on different strands, e.g. A-T and C-G
-
-pair_oxdna_xstk.cpp:  cross-stacking interaction between nucleotides
-
-pair_oxdna_coaxstk.cpp:  coaxial stacking interaction between nucleotides
-
-
-pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp:
-                     corresponding pair styles in oxDNA2 (see [3])
-
-pair_oxdna2_dh.cpp:  Debye-Hueckel electrostatic interaction between backbone
-                     sites
-
-** Fixes provided by this package:
-
-fix_nve_dotc_langevin.cpp:  fix for Langevin-type rigid body integrator "C"
-                            in above Ref. [3] 
-
-fix_nve_dot.cpp:  NVE-type rigid body integrator without noise
diff --git a/src/USER-CGDNA/README.md b/src/USER-CGDNA/README.md
new file mode 100644
index 0000000000..138638525e
--- /dev/null
+++ b/src/USER-CGDNA/README.md
@@ -0,0 +1,105 @@
+This package contains a LAMMPS implementation of coarse-grained
+models of DNA, which can be used to model sequence-specific
+DNA strands.
+
+Please cite 
+
+[![DOI](https://zenodo.org/badge/132764768.svg)](https://zenodo.org/badge/latestdoi/132764768)
+
+as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles 
+in any publication that uses this package.
+
+See the doc pages and [2,3,4,5,6] for the individual bond and pair styles. 
+The packages contains also a new Langevin-type rigid-body integrator,
+which has also its own doc page and is explained in [7].
+
+[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
+"Coarse-grained simulation of DNA using LAMMPS", 
+Eur. Phys. J. E 41, 57 (2018).
+
+[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, 
+and thermodynamic properties of a coarse-grained DNA model",
+J. Chem. Phys. 134, 085101 (2011).
+
+[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA 
+self-assembly", DPhil. University of Oxford (2011).
+
+[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., "Introducing
+Improved structural properties and salt dependence into a coarse-grained
+model of DNA", J. Chem. Phys. 142, 234901 (2015).
+
+[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level 
+coarse-grained model of RNA", J. Chem. Phys. 140, 235102 (2014).
+
+[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent 
+thermodynamics of a coarse-grained DNA model",
+J. Chem. Phys. 137, 135101 (2012). 
+
+[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and 
+gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 
+144114 (2015).
+
+Example input and data files can be found in
+/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. 
+Python setup tools which create single straight or helical DNA or RNA 
+strands as well as DNA or RNA duplexes or arrays of duplexes can be 
+found in /examples/USER/cgdna/util/. A technical report with more 
+general information on the model, its implementation and performance 
+as well as the structure of the data and input file can be found
+in /doc/src/PDF/USER-CGDNA.pdf.
+
+IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
+with the MOLECULE and ASPHERE packages.  These should be included in
+the LAMMPS build by typing "make yes-asphere yes-molecule" prior to
+the usual compilation (see the "Including/excluding packages" section
+of the LAMMPS manual).
+
+The creator of this package is:
+
+Dr Oliver Henrich
+University of Strathclyde, Glasgow, UK
+oliver d o t henrich a t strath d o t ac d o t uk
+
+
+--------------------------------------------------------------------------
+
+** Bond styles provided by this package:
+
+bond_oxdna_fene.cpp:    backbone connectivity, 
+                        a modified FENE potential (see [2,3])
+
+bond_oxdna2_fene.cpp:   corresponding bond style in oxDNA2 (see [4])
+
+bond_oxrna2_fene.cpp:   corresponding bond style in oxRNA2 (see [5])
+
+** Pair styles provided by this package:
+
+pair_oxdna_excv.cpp:    excluded volume interaction between the nucleotides
+
+pair_oxdna_stk.cpp:     stacking interaction between consecutive nucleotides
+                        on the same strand
+
+pair_oxdna_hbond.cpp:   hydrogen-bonding interaction between complementary
+                        nucleotides on different strands, e.g. A-T and C-G
+
+pair_oxdna_xstk.cpp:    cross-stacking interaction between nucleotides
+
+pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
+
+pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: 
+                        corresponding pair styles in oxDNA2 (see [4])
+
+pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp, 
+pair_oxrna2_xstk.cpp: 
+                        corresponding pair styles in oxDNA2 (see [5])
+
+pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp:  
+               Debye-Hueckel electrostatic interaction between backbone sites
+
+
+** Fixes provided by this package:
+
+fix_nve_dotc_langevin.cpp:  fix for Langevin-type rigid body integrator "C"
+                            in above Ref. [7] 
+
+fix_nve_dot.cpp:  NVE-type rigid body integrator without noise
diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp
index f549fc423d..1cb332df8f 100644
--- a/src/USER-CGDNA/bond_oxdna_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna_fene.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
@@ -379,9 +380,9 @@ void BondOxdnaFene::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&Delta[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&Delta[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&Delta[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/USER-CGDNA/bond_oxrna2_fene.cpp
new file mode 100644
index 0000000000..bdddccda87
--- /dev/null
+++ b/src/USER-CGDNA/bond_oxrna2_fene.cpp
@@ -0,0 +1,49 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdlib>
+#include "bond_oxrna2_fene.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+BondOxrna2Fene::BondOxrna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp)
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+BondOxrna2Fene::~BondOxrna2Fene()
+{
+
+}
+
+/* ----------------------------------------------------------------------
+    compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
+------------------------------------------------------------------------- */
+void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3],
+  double e3[3], double r[3])
+{
+  double d_cs_x=-0.4, d_cs_z=+0.2;
+
+  r[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
+  r[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
+  r[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
+
+}
diff --git a/src/USER-CGDNA/bond_oxrna2_fene.h b/src/USER-CGDNA/bond_oxrna2_fene.h
new file mode 100644
index 0000000000..585a253eb5
--- /dev/null
+++ b/src/USER-CGDNA/bond_oxrna2_fene.h
@@ -0,0 +1,65 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef BOND_CLASS
+
+BondStyle(oxrna2/fene,BondOxrna2Fene)
+
+#else
+
+#ifndef LMP_BOND_OXRNA2_FENE_H
+#define LMP_BOND_OXRNA2_FENE_H
+
+#include "bond_oxdna_fene.h"
+
+namespace LAMMPS_NS {
+
+class BondOxrna2Fene : public BondOxdnaFene {
+ public:
+  BondOxrna2Fene(class LAMMPS *);
+  virtual ~BondOxrna2Fene();
+  virtual void compute_interaction_sites(double *, double *, double *,
+    double *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+W: FENE bond too long: %ld %d %d %g
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up.
+
+E: Bad FENE bond
+
+Two atoms in a FENE bond have become so far apart that the bond cannot
+be computed.
+
+E: Incorrect args for bond coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+W: Use special bonds = 0,1,1 with bond style oxrna
+
+Most FENE models need this setting for the special_bonds command.
+
+W: FENE bond too long: %ld %g
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index 609b63e27f..51ff26cc6e 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
@@ -676,20 +677,6 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg)
 
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairOxdna2Coaxstk::init_style()
-{
-  int irequest;
-
-  // request regular neighbor lists
-
-  irequest = neighbor->request(this,instance_me);
-
-}
-
 /* ----------------------------------------------------------------------
    neighbor callback to inform pair style of neighbor list to use regular
 ------------------------------------------------------------------------- */
@@ -829,47 +816,47 @@ void PairOxdna2Coaxstk::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
 
-          fread(&k_cxst[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_0[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_c[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_lo[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_hi[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_lc[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_hc[i][j],sizeof(double),1,fp);
-          fread(&b_cxst_lo[i][j],sizeof(double),1,fp);
-          fread(&b_cxst_hi[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&k_cxst[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst_hi[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst1[i][j],sizeof(double),1,fp);
-          fread(&theta_cxst1_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst1_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst1[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst1_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_cxst1_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst1_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst4[i][j],sizeof(double),1,fp);
-          fread(&theta_cxst4_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst4_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst4[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst4_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_cxst4_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst4_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst4_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst5[i][j],sizeof(double),1,fp);
-          fread(&theta_cxst5_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst5_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst5[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst5_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_cxst5_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst5_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst5_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst6[i][j],sizeof(double),1,fp);
-          fread(&theta_cxst6_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst6_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst6[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst6_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_cxst6_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst6_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst6_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&AA_cxst1[i][j],sizeof(double),1,fp);
-          fread(&BB_cxst1[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&AA_cxst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&BB_cxst1[i][j],sizeof(double),1,fp,NULL,error);
 
         }
 
@@ -933,9 +920,9 @@ void PairOxdna2Coaxstk::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.h b/src/USER-CGDNA/pair_oxdna2_coaxstk.h
index be8d6d6b37..e20d1b3fdc 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.h
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.h
@@ -31,7 +31,6 @@ class PairOxdna2Coaxstk : public Pair {
   virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
   void write_restart(FILE *);
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index 630dd7a559..e698d8d906 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -25,6 +25,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
@@ -63,7 +64,7 @@ PairOxdna2Dh::~PairOxdna2Dh()
     compute vector COM-sugar-phosphate backbone interaction site in oxDNA2
 ------------------------------------------------------------------------- */
 void PairOxdna2Dh::compute_interaction_sites(double e1[3],
-  double e2[3], double r[3])
+  double e2[3], double /*e3*/[3], double r[3])
 {
   double d_cs_x=-0.34, d_cs_y=+0.3408;
 
@@ -124,7 +125,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
     MathExtra::q_to_exyz(qa,ax,ay,az);
 
     // vector COM-backbone site a
-    compute_interaction_sites(ax,ay,ra_cs);
+    compute_interaction_sites(ax,ay,az,ra_cs);
 
     rtmp_s[0] = x[a][0] + ra_cs[0];
     rtmp_s[1] = x[a][1] + ra_cs[1];
@@ -144,7 +145,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
       MathExtra::q_to_exyz(qb,bx,by,bz);
 
       // vector COM-backbone site b
-      compute_interaction_sites(bx,by,rb_cs);
+      compute_interaction_sites(bx,by,bz,rb_cs);
 
       // vector backbone site b to a
       delr[0] = rtmp_s[0] - x[b][0] - rb_cs[0];
@@ -358,19 +359,6 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
   if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/dh");
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairOxdna2Dh::init_style()
-{
-  int irequest;
-
-  // request regular neighbor lists
-
-  irequest = neighbor->request(this,instance_me);
-}
-
 /* ----------------------------------------------------------------------
    neighbor callback to inform pair style of neighbor list to use regular
 ------------------------------------------------------------------------- */
@@ -450,16 +438,16 @@ void PairOxdna2Dh::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
 
-          fread(&kappa_dh[i][j],sizeof(double),1,fp);
-          fread(&qeff_dh_pf[i][j],sizeof(double),1,fp);
-          fread(&b_dh[i][j],sizeof(double),1,fp);
-          fread(&cut_dh_ast[i][j],sizeof(double),1,fp);
-          fread(&cut_dh_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&kappa_dh[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&qeff_dh_pf[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_dh[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_dh_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_dh_c[i][j],sizeof(double),1,fp,NULL,error);
 
         }
 
@@ -492,9 +480,9 @@ void PairOxdna2Dh::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/USER-CGDNA/pair_oxdna2_dh.h
index b40346e1cf..da72060927 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.h
+++ b/src/USER-CGDNA/pair_oxdna2_dh.h
@@ -28,11 +28,11 @@ class PairOxdna2Dh : public Pair {
  public:
   PairOxdna2Dh(class LAMMPS *);
   virtual ~PairOxdna2Dh();
-  virtual void compute_interaction_sites(double *, double *, double *);
+  virtual void compute_interaction_sites(double *, double *, double *,
+    double *);
   virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
   void write_restart(FILE *);
diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp
index d8a263676f..dd0f6c9d68 100644
--- a/src/USER-CGDNA/pair_oxdna2_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp
@@ -35,7 +35,7 @@ PairOxdna2Excv::~PairOxdna2Excv()
 /* ----------------------------------------------------------------------
     compute vector COM-excluded volume interaction sites in oxDNA2
 ------------------------------------------------------------------------- */
-void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], 
+void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3],
     double /*e3*/[3], double rs[3], double rb[3])
 {
   double d_cs_x=-0.34, d_cs_y=+0.3408, d_cb=+0.4;
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
index d71acc2029..750c6c022d 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
@@ -58,7 +59,7 @@ PairOxdnaCoaxstk::~PairOxdnaCoaxstk()
     memory->destroy(cut_cxst_hi);
     memory->destroy(cut_cxst_lc);
     memory->destroy(cut_cxst_hc);
-    memory->destroy(cutsq_cxst_hc); 
+    memory->destroy(cutsq_cxst_hc);
     memory->destroy(b_cxst_lo);
     memory->destroy(b_cxst_hi);
 
@@ -822,20 +823,6 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg)
 
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairOxdnaCoaxstk::init_style()
-{
-  int irequest;
-
-  // request regular neighbor lists
-
-  irequest = neighbor->request(this,instance_me);
-
-}
-
 /* ----------------------------------------------------------------------
    neighbor callback to inform pair style of neighbor list to use regular
 ------------------------------------------------------------------------- */
@@ -988,53 +975,53 @@ void PairOxdnaCoaxstk::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
 
-          fread(&k_cxst[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_0[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_c[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_lo[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_hi[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_lc[i][j],sizeof(double),1,fp);
-          fread(&cut_cxst_hc[i][j],sizeof(double),1,fp);
-          fread(&b_cxst_lo[i][j],sizeof(double),1,fp);
-          fread(&b_cxst_hi[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&k_cxst[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_cxst_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst_hi[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst1[i][j],sizeof(double),1,fp);
-          fread(&theta_cxst1_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst1_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst1[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst1_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_cxst1_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst1_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst4[i][j],sizeof(double),1,fp);
-          fread(&theta_cxst4_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst4_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst4[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst4_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_cxst4_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst4_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst4_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst5[i][j],sizeof(double),1,fp);
-          fread(&theta_cxst5_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst5_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst5[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst5_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_cxst5_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst5_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst5_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst6[i][j],sizeof(double),1,fp);
-          fread(&theta_cxst6_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst6_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst6[i][j],sizeof(double),1,fp);
-          fread(&dtheta_cxst6_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_cxst6_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst6_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_cxst6_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_cxst3p[i][j],sizeof(double),1,fp);
-          fread(&cosphi_cxst3p_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst3p[i][j],sizeof(double),1,fp);
-          fread(&cosphi_cxst3p_c[i][j],sizeof(double),1,fp);
-          fread(&a_cxst4p[i][j],sizeof(double),1,fp);
-          fread(&cosphi_cxst4p_ast[i][j],sizeof(double),1,fp);
-          fread(&b_cxst4p[i][j],sizeof(double),1,fp);
-          fread(&cosphi_cxst4p_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_cxst3p[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_cxst3p_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst3p[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_cxst3p_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&a_cxst4p[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_cxst4p_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_cxst4p[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_cxst4p_c[i][j],sizeof(double),1,fp,NULL,error);
 
         }
 
@@ -1104,9 +1091,9 @@ void PairOxdnaCoaxstk::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/USER-CGDNA/pair_oxdna_coaxstk.h
index f9228c94a2..79c8fa24ed 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.h
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.h
@@ -14,6 +14,7 @@
 #ifdef PAIR_CLASS
 
 PairStyle(oxdna/coaxstk,PairOxdnaCoaxstk)
+PairStyle(oxrna2/coaxstk,PairOxdnaCoaxstk)
 
 #else
 
@@ -31,7 +32,6 @@ class PairOxdnaCoaxstk : public Pair {
   virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
   void write_restart(FILE *);
diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp
index f187fc7403..e8e2fad020 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna_excv.cpp
@@ -26,6 +26,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
@@ -85,7 +86,7 @@ PairOxdnaExcv::~PairOxdnaExcv()
 /* ----------------------------------------------------------------------
     compute vector COM-excluded volume interaction sites in oxDNA
 ------------------------------------------------------------------------- */
-void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3], 
+void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3],
     double /*e3*/[3], double rs[3], double rb[3])
 {
   double d_cs=-0.4, d_cb=+0.4;
@@ -562,20 +563,6 @@ void PairOxdnaExcv::coeff(int narg, char **arg)
 
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairOxdnaExcv::init_style()
-{
-  int irequest;
-
-  // request regular neighbor lists
-
-  irequest = neighbor->request(this,instance_me);
-
-}
-
 /* ----------------------------------------------------------------------
    neighbor callback to inform pair style of neighbor list to use regular
 ------------------------------------------------------------------------- */
@@ -710,26 +697,26 @@ void PairOxdnaExcv::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
 
-          fread(&epsilon_ss[i][j],sizeof(double),1,fp);
-          fread(&sigma_ss[i][j],sizeof(double),1,fp);
-          fread(&cut_ss_ast[i][j],sizeof(double),1,fp);
-          fread(&b_ss[i][j],sizeof(double),1,fp);
-          fread(&cut_ss_c[i][j],sizeof(double),1,fp);
-          fread(&epsilon_sb[i][j],sizeof(double),1,fp);
-          fread(&sigma_sb[i][j],sizeof(double),1,fp);
-          fread(&cut_sb_ast[i][j],sizeof(double),1,fp);
-          fread(&b_sb[i][j],sizeof(double),1,fp);
-          fread(&cut_sb_c[i][j],sizeof(double),1,fp);
-          fread(&epsilon_bb[i][j],sizeof(double),1,fp);
-          fread(&sigma_bb[i][j],sizeof(double),1,fp);
-          fread(&cut_bb_ast[i][j],sizeof(double),1,fp);
-          fread(&b_bb[i][j],sizeof(double),1,fp);
-          fread(&cut_bb_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon_ss[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma_ss[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_ss_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_ss[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_ss_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&epsilon_sb[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma_sb[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_sb_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_sb[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_sb_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&epsilon_bb[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma_bb[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_bb_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_bb[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_bb_c[i][j],sizeof(double),1,fp,NULL,error);
 
          }
 
@@ -772,9 +759,9 @@ void PairOxdnaExcv::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/USER-CGDNA/pair_oxdna_excv.h b/src/USER-CGDNA/pair_oxdna_excv.h
index c80a112fec..34fd323ec1 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.h
+++ b/src/USER-CGDNA/pair_oxdna_excv.h
@@ -33,7 +33,6 @@ class PairOxdnaExcv : public Pair {
   virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
   void write_restart(FILE *);
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp
index e9852d0e38..26042339ea 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp
@@ -26,26 +26,43 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace MFOxdna;
 
-// sequence-specific base-pairing strength
-// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
-static const double alpha_hb[4][4] = 
-{{1.00000,1.00000,1.00000,0.82915},
- {1.00000,1.00000,1.15413,1.00000},
- {1.00000,1.15413,1.00000,1.00000},
- {0.82915,1.00000,1.00000,1.00000}};
-
 /* ---------------------------------------------------------------------- */
 
 PairOxdnaHbond::PairOxdnaHbond(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 0;
   writedata = 1;
+
+  // sequence-specific base-pairing strength
+  // A:0 C:1 G:2 T:3, 5'- [i][j] -3'
+
+  alpha_hb[0][0] = 1.00000;
+  alpha_hb[0][1] = 1.00000;
+  alpha_hb[0][2] = 1.00000;
+  alpha_hb[0][3] = 0.82915;
+
+  alpha_hb[1][0] = 1.00000;
+  alpha_hb[1][1] = 1.00000;
+  alpha_hb[1][2] = 1.15413;
+  alpha_hb[1][3] = 1.00000;
+
+  alpha_hb[2][0] = 1.00000;
+  alpha_hb[2][1] = 1.15413;
+  alpha_hb[2][2] = 1.00000;
+  alpha_hb[2][3] = 1.00000;
+
+  alpha_hb[3][0] = 0.82915;
+  alpha_hb[3][1] = 1.00000;
+  alpha_hb[3][2] = 1.00000;
+  alpha_hb[3][3] = 1.00000;
+
 }
 
 /* ---------------------------------------------------------------------- */
@@ -616,7 +633,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
   if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond");
   if (!allocated) allocate();
 
-  int ilo,ihi,jlo,jhi;
+  int ilo,ihi,jlo,jhi,imod4,jmod4;
   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
 
@@ -729,8 +746,13 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
   for (int i = ilo; i <= ihi; i++) {
     for (int j = MAX(jlo,i); j <= jhi; j++) {
 
+      imod4 = i%4;
+      if (imod4 == 0) imod4 = 4;
+      jmod4 = j%4;
+      if (jmod4 == 0) jmod4 = 4;
+
       epsilon_hb[i][j] = epsilon_hb_one;
-      if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[i-1][j-1];
+      if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[imod4-1][jmod4-1];
       a_hb[i][j] = a_hb_one;
       cut_hb_0[i][j] = cut_hb_0_one;
       cut_hb_c[i][j] = cut_hb_c_one;
@@ -741,7 +763,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
       b_hb_lo[i][j] = b_hb_lo_one;
       b_hb_hi[i][j] = b_hb_hi_one;
       shift_hb[i][j] = shift_hb_one;
-      if (seqdepflag) shift_hb[i][j] *= alpha_hb[i-1][j-1];
+      if (seqdepflag) shift_hb[i][j] *= alpha_hb[imod4-1][jmod4-1];
 
       a_hb1[i][j] = a_hb1_one;
       theta_hb1_0[i][j] = theta_hb1_0_one;
@@ -788,20 +810,6 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
 
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairOxdnaHbond::init_style()
-{
-  int irequest;
-
-  // request regular neighbor lists
-
-  irequest = neighbor->request(this,instance_me);
-
-}
-
 /* ----------------------------------------------------------------------
    neighbor callback to inform pair style of neighbor list to use regular
 ------------------------------------------------------------------------- */
@@ -820,6 +828,7 @@ void PairOxdnaHbond::init_list(int id, NeighList *ptr)
 
 double PairOxdnaHbond::init_one(int i, int j)
 {
+  int imod4,jmod4;
 
   if (setflag[i][j] == 0) {
     error->all(FLERR,"Coefficient mixing not defined in oxDNA");
@@ -828,8 +837,13 @@ double PairOxdnaHbond::init_one(int i, int j)
     error->all(FLERR,"Offset not supported in oxDNA");
   }
 
+  imod4 = i%4;
+  if (imod4 == 0) imod4 = 4;
+  jmod4 = j%4;
+  if (jmod4 == 0) jmod4 = 4;
+
   if (seqdepflag) {
-    epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1];
+    epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[imod4-1][jmod4-1] * alpha_hb[jmod4-1][imod4-1];
   }
   else {
     epsilon_hb[j][i] = epsilon_hb[i][j];
@@ -844,7 +858,7 @@ double PairOxdnaHbond::init_one(int i, int j)
   cut_hb_lc[j][i] = cut_hb_lc[i][j];
   cut_hb_hc[j][i] = cut_hb_hc[i][j];
   if (seqdepflag) {
-    shift_hb[j][i] = shift_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1];
+    shift_hb[j][i] = shift_hb[i][j] / alpha_hb[imod4-1][jmod4-1] * alpha_hb[jmod4-1][imod4-1];
   }
   else {
     shift_hb[j][i] = shift_hb[i][j];
@@ -973,58 +987,58 @@ void PairOxdnaHbond::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
 
-          fread(&epsilon_hb[i][j],sizeof(double),1,fp);
-          fread(&a_hb[i][j],sizeof(double),1,fp);
-          fread(&cut_hb_0[i][j],sizeof(double),1,fp);
-          fread(&cut_hb_c[i][j],sizeof(double),1,fp);
-          fread(&cut_hb_lo[i][j],sizeof(double),1,fp);
-          fread(&cut_hb_hi[i][j],sizeof(double),1,fp);
-          fread(&cut_hb_lc[i][j],sizeof(double),1,fp);
-          fread(&cut_hb_hc[i][j],sizeof(double),1,fp);
-          fread(&b_hb_lo[i][j],sizeof(double),1,fp);
-          fread(&b_hb_hi[i][j],sizeof(double),1,fp);
-          fread(&shift_hb[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon_hb[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&a_hb[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_hb_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_hb_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_hb_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_hb_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_hb_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_hb_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_hb_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_hb_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shift_hb[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_hb1[i][j],sizeof(double),1,fp);
-          fread(&theta_hb1_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb1_ast[i][j],sizeof(double),1,fp);
-          fread(&b_hb1[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb1_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_hb1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_hb1_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_hb1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb1_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_hb2[i][j],sizeof(double),1,fp);
-          fread(&theta_hb2_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb2_ast[i][j],sizeof(double),1,fp);
-          fread(&b_hb2[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb2_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_hb2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_hb2_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb2_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_hb2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb2_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_hb3[i][j],sizeof(double),1,fp);
-          fread(&theta_hb3_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb3_ast[i][j],sizeof(double),1,fp);
-          fread(&b_hb3[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb3_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_hb3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_hb3_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb3_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_hb3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb3_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_hb4[i][j],sizeof(double),1,fp);
-          fread(&theta_hb4_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb4_ast[i][j],sizeof(double),1,fp);
-          fread(&b_hb4[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb4_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_hb4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_hb4_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb4_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_hb4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb4_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_hb7[i][j],sizeof(double),1,fp);
-          fread(&theta_hb7_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb7_ast[i][j],sizeof(double),1,fp);
-          fread(&b_hb7[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb7_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_hb7[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_hb7_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb7_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_hb7[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb7_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_hb8[i][j],sizeof(double),1,fp);
-          fread(&theta_hb8_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb8_ast[i][j],sizeof(double),1,fp);
-          fread(&b_hb8[i][j],sizeof(double),1,fp);
-          fread(&dtheta_hb8_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_hb8[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_hb8_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb8_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_hb8[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_hb8_c[i][j],sizeof(double),1,fp,NULL,error);
 
         }
 
@@ -1099,9 +1113,9 @@ void PairOxdnaHbond::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.h b/src/USER-CGDNA/pair_oxdna_hbond.h
index 028853a087..fe451480a8 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.h
+++ b/src/USER-CGDNA/pair_oxdna_hbond.h
@@ -32,7 +32,6 @@ class PairOxdnaHbond : public Pair {
   virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
   void write_restart(FILE *);
@@ -45,6 +44,7 @@ class PairOxdnaHbond : public Pair {
 
  protected:
   // h-bonding interaction
+  double alpha_hb[4][4];
   double **epsilon_hb, **a_hb, **cut_hb_0, **cut_hb_c, **cut_hb_lo, **cut_hb_hi;
   double **cut_hb_lc, **cut_hb_hc, **b_hb_lo, **b_hb_hi, **shift_hb;
   double **cutsq_hb_hc;
diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp
index 3d0c4e9136..4d1c4a7101 100644
--- a/src/USER-CGDNA/pair_oxdna_stk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_stk.cpp
@@ -26,26 +26,43 @@
 #include "neighbor.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace MFOxdna;
 
-// sequence-specific stacking strength
-// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
-static const double eta_st[4][4] =
-{{1.11960,1.00852,0.96950,0.99632},
- {1.01889,0.97804,1.02681,0.96950},
- {0.98169,1.05913,0.97804,1.00852},
- {0.94694,0.98169,1.01889,0.96383}};
-
 /* ---------------------------------------------------------------------- */
 
 PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 0;
   writedata = 1;
+
+  // sequence-specific stacking strength
+  // A:0 C:1 G:2 T:3, 5'- [i][j] -3'
+
+  eta_st[0][0] = 1.11960;
+  eta_st[0][1] = 1.00852;
+  eta_st[0][2] = 0.96950;
+  eta_st[0][3] = 0.99632;
+
+  eta_st[1][0] = 1.01889;
+  eta_st[1][1] = 0.97804;
+  eta_st[1][2] = 1.02681;
+  eta_st[1][3] = 0.96950;
+
+  eta_st[2][0] = 0.98169;
+  eta_st[2][1] = 1.05913;
+  eta_st[2][2] = 0.97804;
+  eta_st[2][3] = 1.00852;
+
+  eta_st[3][0] = 0.94694;
+  eta_st[3][1] = 0.98169;
+  eta_st[3][2] = 1.01889;
+  eta_st[3][3] = 0.96383;
+
 }
 
 /* ---------------------------------------------------------------------- */
@@ -104,7 +121,7 @@ PairOxdnaStk::~PairOxdnaStk()
    tally energy and virial into global and per-atom accumulators
 
    NOTE: Although this is a pair style interaction, the algorithm below
-   follows the virial incrementation of the bond style. This is because 
+   follows the virial incrementation of the bond style. This is because
    the bond topology is used in the main compute loop.
 ------------------------------------------------------------------------- */
 
@@ -761,7 +778,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
   if (narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
   if (!allocated) allocate();
 
-  int ilo,ihi,jlo,jhi;
+  int ilo,ihi,jlo,jhi,imod4,jmod4;
   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
 
@@ -852,16 +869,21 @@ void PairOxdnaStk::coeff(int narg, char **arg)
   dtheta_st6_c_one = 1/(a_st6_one*dtheta_st6_ast_one);
 
   b_st1_one = a_st1_one*a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one/(1-a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one);
-  cosphi_st1_c_one=1/(a_st1_one*cosphi_st1_ast_one);
+  cosphi_st1_c_one = 1/(a_st1_one*cosphi_st1_ast_one);
 
   b_st2_one = a_st2_one*a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one/(1-a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one);
-  cosphi_st2_c_one=1/(a_st2_one*cosphi_st2_ast_one);
+  cosphi_st2_c_one = 1/(a_st2_one*cosphi_st2_ast_one);
 
   for (int i = ilo; i <= ihi; i++) {
     for (int j = MAX(jlo,i); j <= jhi; j++) {
 
+      imod4 = i%4;
+      if (imod4 == 0) imod4 = 4;
+      jmod4 = j%4;
+      if (jmod4 == 0) jmod4 = 4;
+
       epsilon_st[i][j] = epsilon_st_one;
-      if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1];
+      if (seqdepflag) epsilon_st[i][j] *= eta_st[imod4-1][jmod4-1];
       a_st[i][j] = a_st_one;
       cut_st_0[i][j] = cut_st_0_one;
       cut_st_c[i][j] = cut_st_c_one;
@@ -872,7 +894,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
       b_st_lo[i][j] = b_st_lo_one;
       b_st_hi[i][j] = b_st_hi_one;
       shift_st[i][j] = shift_st_one;
-      if (seqdepflag) shift_st[i][j] *= eta_st[i-1][j-1];
+      if (seqdepflag) shift_st[i][j] *= eta_st[imod4-1][jmod4-1];
 
       a_st4[i][j] = a_st4_one;
       theta_st4_0[i][j] = theta_st4_0_one;
@@ -911,20 +933,6 @@ void PairOxdnaStk::coeff(int narg, char **arg)
 
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairOxdnaStk::init_style()
-{
-  int irequest;
-
-  // request regular neighbor lists
-
-  irequest = neighbor->request(this,instance_me);
-
-}
-
 /* ----------------------------------------------------------------------
    neighbor callback to inform pair style of neighbor list to use regular
 ------------------------------------------------------------------------- */
@@ -944,6 +952,8 @@ void PairOxdnaStk::init_list(int id, NeighList *ptr)
 double PairOxdnaStk::init_one(int i, int j)
 {
 
+  int imod4,jmod4;
+
   if (setflag[i][j] == 0) {
     error->all(FLERR,"Coefficient mixing not defined in oxDNA");
   }
@@ -951,8 +961,13 @@ double PairOxdnaStk::init_one(int i, int j)
     error->all(FLERR,"Offset not supported in oxDNA");
   }
 
+  imod4 = i%4;
+  if (imod4 == 0) imod4 = 4;
+  jmod4 = j%4;
+  if (jmod4 == 0) jmod4 = 4;
+
   if (seqdepflag) {
-    epsilon_st[j][i] = epsilon_st[i][j]  / eta_st[i-1][j-1] * eta_st[j-1][i-1];
+    epsilon_st[j][i] = epsilon_st[i][j]  / eta_st[imod4-1][jmod4-1] * eta_st[jmod4-1][imod4-1];
   }
   else {
     epsilon_st[j][i] = epsilon_st[i][j];
@@ -967,7 +982,7 @@ double PairOxdnaStk::init_one(int i, int j)
   cut_st_lc[j][i] = cut_st_lc[i][j];
   cut_st_hc[j][i] = cut_st_hc[i][j];
   if (seqdepflag) {
-    shift_st[j][i] = shift_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1];
+    shift_st[j][i] = shift_st[i][j] / eta_st[imod4-1][jmod4-1] * eta_st[jmod4-1][imod4-1];
   }
   else {
     shift_st[j][i] = shift_st[i][j];
@@ -1079,49 +1094,49 @@ void PairOxdnaStk::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
 
-          fread(&epsilon_st[i][j],sizeof(double),1,fp);
-          fread(&a_st[i][j],sizeof(double),1,fp);
-          fread(&cut_st_0[i][j],sizeof(double),1,fp);
-          fread(&cut_st_c[i][j],sizeof(double),1,fp);
-          fread(&cut_st_lo[i][j],sizeof(double),1,fp);
-          fread(&cut_st_hi[i][j],sizeof(double),1,fp);
-          fread(&cut_st_lc[i][j],sizeof(double),1,fp);
-          fread(&cut_st_hc[i][j],sizeof(double),1,fp);
-          fread(&b_st_lo[i][j],sizeof(double),1,fp);
-          fread(&b_st_hi[i][j],sizeof(double),1,fp);
-          fread(&shift_st[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon_st[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&a_st[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shift_st[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_st4[i][j],sizeof(double),1,fp);
-          fread(&theta_st4_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_st4_ast[i][j],sizeof(double),1,fp);
-          fread(&b_st4[i][j],sizeof(double),1,fp);
-          fread(&dtheta_st4_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_st4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st4_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st4_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st4_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_st5[i][j],sizeof(double),1,fp);
-          fread(&theta_st5_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_st5_ast[i][j],sizeof(double),1,fp);
-          fread(&b_st5[i][j],sizeof(double),1,fp);
-          fread(&dtheta_st5_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_st5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st5_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st5_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st5_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_st6[i][j],sizeof(double),1,fp);
-          fread(&theta_st6_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_st6_ast[i][j],sizeof(double),1,fp);
-          fread(&b_st6[i][j],sizeof(double),1,fp);
-          fread(&dtheta_st6_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_st6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st6_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st6_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st6_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_st1[i][j],sizeof(double),1,fp);
-          fread(&cosphi_st1_ast[i][j],sizeof(double),1,fp);
-          fread(&b_st1[i][j],sizeof(double),1,fp);
-          fread(&cosphi_st1_c[i][j],sizeof(double),1,fp);
-          fread(&a_st2[i][j],sizeof(double),1,fp);
-          fread(&cosphi_st2_ast[i][j],sizeof(double),1,fp);
-          fread(&b_st2[i][j],sizeof(double),1,fp);
-          fread(&cosphi_st2_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_st1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st1_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&a_st2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st2_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st2_c[i][j],sizeof(double),1,fp,NULL,error);
 
         }
 
@@ -1187,9 +1202,9 @@ void PairOxdnaStk::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/USER-CGDNA/pair_oxdna_stk.h b/src/USER-CGDNA/pair_oxdna_stk.h
index 581e87f4b2..29ed168ca3 100644
--- a/src/USER-CGDNA/pair_oxdna_stk.h
+++ b/src/USER-CGDNA/pair_oxdna_stk.h
@@ -32,7 +32,6 @@ class PairOxdnaStk : public Pair {
   virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
   void write_restart(FILE *);
@@ -45,6 +44,7 @@ class PairOxdnaStk : public Pair {
 
  protected:
   // stacking interaction
+  double eta_st[4][4];
   double stacking_strength(double, double, double);
   double **epsilon_st, **a_st, **cut_st_0, **cut_st_c;
   double **cut_st_lo, **cut_st_hi;
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp
index 95f5694818..a1fc86bd4d 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
@@ -776,20 +777,6 @@ void PairOxdnaXstk::coeff(int narg, char **arg)
 
 }
 
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairOxdnaXstk::init_style()
-{
-  int irequest;
-
-  // request regular neighbor lists
-
-  irequest = neighbor->request(this,instance_me);
-
-}
-
 /* ----------------------------------------------------------------------
    neighbor callback to inform pair style of neighbor list to use regular
 ------------------------------------------------------------------------- */
@@ -947,56 +934,56 @@ void PairOxdnaXstk::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
 
-          fread(&k_xst[i][j],sizeof(double),1,fp);
-          fread(&cut_xst_0[i][j],sizeof(double),1,fp);
-          fread(&cut_xst_c[i][j],sizeof(double),1,fp);
-          fread(&cut_xst_lo[i][j],sizeof(double),1,fp);
-          fread(&cut_xst_hi[i][j],sizeof(double),1,fp);
-          fread(&cut_xst_lc[i][j],sizeof(double),1,fp);
-          fread(&cut_xst_hc[i][j],sizeof(double),1,fp);
-          fread(&b_xst_lo[i][j],sizeof(double),1,fp);
-          fread(&b_xst_hi[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&k_xst[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst_hi[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_xst1[i][j],sizeof(double),1,fp);
-          fread(&theta_xst1_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst1_ast[i][j],sizeof(double),1,fp);
-          fread(&b_xst1[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst1_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_xst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst1_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst1_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_xst2[i][j],sizeof(double),1,fp);
-          fread(&theta_xst2_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst2_ast[i][j],sizeof(double),1,fp);
-          fread(&b_xst2[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst2_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_xst2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst2_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst2_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst2_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_xst3[i][j],sizeof(double),1,fp);
-          fread(&theta_xst3_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst3_ast[i][j],sizeof(double),1,fp);
-          fread(&b_xst3[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst3_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_xst3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst3_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst3_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst3_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_xst4[i][j],sizeof(double),1,fp);
-          fread(&theta_xst4_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst4_ast[i][j],sizeof(double),1,fp);
-          fread(&b_xst4[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst4_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_xst4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst4_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst4_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst4_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_xst7[i][j],sizeof(double),1,fp);
-          fread(&theta_xst7_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst7_ast[i][j],sizeof(double),1,fp);
-          fread(&b_xst7[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst7_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_xst7[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst7_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst7_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst7[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst7_c[i][j],sizeof(double),1,fp,NULL,error);
 
-          fread(&a_xst8[i][j],sizeof(double),1,fp);
-          fread(&theta_xst8_0[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst8_ast[i][j],sizeof(double),1,fp);
-          fread(&b_xst8[i][j],sizeof(double),1,fp);
-          fread(&dtheta_xst8_c[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a_xst8[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst8_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst8_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst8[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst8_c[i][j],sizeof(double),1,fp,NULL,error);
 
         }
 
@@ -1069,9 +1056,9 @@ void PairOxdnaXstk::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.h b/src/USER-CGDNA/pair_oxdna_xstk.h
index 5c443a4dac..d2fc7fde89 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.h
+++ b/src/USER-CGDNA/pair_oxdna_xstk.h
@@ -32,7 +32,6 @@ class PairOxdnaXstk : public Pair {
   virtual void compute(int, int);
   void settings(int, char **);
   void coeff(int, char **);
-  void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
   void write_restart(FILE *);
diff --git a/src/USER-CGDNA/pair_oxrna2_dh.cpp b/src/USER-CGDNA/pair_oxrna2_dh.cpp
new file mode 100644
index 0000000000..7cc785ad39
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_dh.cpp
@@ -0,0 +1,47 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include "pair_oxrna2_dh.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Dh::PairOxrna2Dh(LAMMPS *lmp) : PairOxdna2Dh(lmp)
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Dh::~PairOxrna2Dh()
+{
+
+}
+
+/* ----------------------------------------------------------------------
+    compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
+------------------------------------------------------------------------- */
+void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3],
+  double e3[3], double r[3])
+{
+  double d_cs_x=-0.4, d_cs_z=+0.2;
+
+  r[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
+  r[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
+  r[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
+
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_dh.h b/src/USER-CGDNA/pair_oxrna2_dh.h
new file mode 100644
index 0000000000..8ff4010113
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_dh.h
@@ -0,0 +1,53 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/dh,PairOxrna2Dh)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_DH_H
+#define LMP_PAIR_OXRNA2_DH_H
+
+#include "pair_oxdna2_dh.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Dh : public PairOxdna2Dh {
+ public:
+  PairOxrna2Dh(class LAMMPS *);
+  virtual ~PairOxrna2Dh();
+  virtual void compute_interaction_sites(double *, double *, double *,
+    double *);
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/USER-CGDNA/pair_oxrna2_excv.cpp
new file mode 100644
index 0000000000..3c0194d636
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_excv.cpp
@@ -0,0 +1,55 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_oxrna2_excv.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Excv::PairOxrna2Excv(LAMMPS *lmp) : PairOxdnaExcv(lmp)
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Excv::~PairOxrna2Excv()
+{
+
+}
+
+/* ----------------------------------------------------------------------
+    compute vector COM-excluded volume interaction sites in oxRNA2
+------------------------------------------------------------------------- */
+void PairOxrna2Excv::compute_interaction_sites(double e1[3], double /*e2*/[3],
+  double e3[3], double rs[3], double rb[3])
+{
+  double d_cs_x=-0.4, d_cs_z=+0.2, d_cb=+0.4;
+
+  rs[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
+  rs[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
+  rs[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
+
+  rb[0] = d_cb*e1[0];
+  rb[1] = d_cb*e1[1];
+  rb[2] = d_cb*e1[2];
+
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_excv.h b/src/USER-CGDNA/pair_oxrna2_excv.h
new file mode 100644
index 0000000000..2dfb356203
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_excv.h
@@ -0,0 +1,52 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/excv,PairOxrna2Excv)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_EXCV_H
+#define LMP_PAIR_OXRNA2_EXCV_H
+
+#include "pair_oxdna_excv.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Excv : public PairOxdnaExcv {
+ public:
+  PairOxrna2Excv(class LAMMPS *);
+  virtual ~PairOxrna2Excv();
+  virtual void compute_interaction_sites(double *, double *,
+    double *, double *, double *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.cpp b/src/USER-CGDNA/pair_oxrna2_hbond.cpp
new file mode 100644
index 0000000000..08e1b1d737
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_hbond.cpp
@@ -0,0 +1,58 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include "pair_oxrna2_hbond.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp)
+{
+  single_enable = 0;
+  writedata = 1;
+
+  // sequence-specific base-pairing strength
+  // A:0 C:1 G:2 U:3, 5'- [i][j] -3'
+
+  alpha_hb[0][0] = 1.00000;
+  alpha_hb[0][1] = 1.00000;
+  alpha_hb[0][2] = 1.00000;
+  alpha_hb[0][3] = 0.94253;
+
+  alpha_hb[1][0] = 1.00000;
+  alpha_hb[1][1] = 1.00000;
+  alpha_hb[1][2] = 1.22288;
+  alpha_hb[1][3] = 1.00000;
+
+  alpha_hb[2][0] = 1.00000;
+  alpha_hb[2][1] = 1.22288;
+  alpha_hb[2][2] = 1.00000;
+  alpha_hb[2][3] = 0.58655;
+
+  alpha_hb[3][0] = 0.94253;
+  alpha_hb[3][1] = 1.00000;
+  alpha_hb[3][2] = 0.58655;
+  alpha_hb[3][3] = 1.00000;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Hbond::~PairOxrna2Hbond()
+{
+
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.h b/src/USER-CGDNA/pair_oxrna2_hbond.h
new file mode 100644
index 0000000000..3386cc23ec
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_hbond.h
@@ -0,0 +1,50 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/hbond,PairOxrna2Hbond)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_HBOND_H
+#define LMP_PAIR_OXRNA2_HBOND_H
+
+#include "pair_oxdna_hbond.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Hbond : public PairOxdnaHbond {
+ public:
+  PairOxrna2Hbond(class LAMMPS *);
+  virtual ~PairOxrna2Hbond();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp
new file mode 100644
index 0000000000..de2cd63799
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp
@@ -0,0 +1,1435 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_oxrna2_stk.h"
+#include "mf_oxdna.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "utils.h"
+#include "atom_vec_ellipsoid.h"
+#include "math_extra.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+using namespace MFOxdna;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp)
+{
+  single_enable = 0;
+  writedata = 1;
+
+  // sequence-specific stacking strength
+  // A:0 C:1 G:2 U:3, 5'- [i][j] -3'
+
+  eta_st[0][0] = 0.93851;
+  eta_st[0][1] = 1.12901;
+  eta_st[0][2] = 1.15626;
+  eta_st[0][3] = 0.88850;
+
+  eta_st[1][0] = 0.86331;
+  eta_st[1][1] = 1.05060;
+  eta_st[1][2] = 0.90982;
+  eta_st[1][3] = 0.83252;
+
+  eta_st[2][0] = 0.99407;
+  eta_st[2][1] = 1.14333;
+  eta_st[2][2] = 1.06573;
+  eta_st[2][3] = 0.91705;
+
+  eta_st[3][0] = 0.98804;
+  eta_st[3][1] = 1.04949;
+  eta_st[3][2] = 1.12063;
+  eta_st[3][3] = 0.83818;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Stk::~PairOxrna2Stk()
+{
+  if (allocated) {
+
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(epsilon_st);
+    memory->destroy(a_st);
+    memory->destroy(cut_st_0);
+    memory->destroy(cut_st_c);
+    memory->destroy(cut_st_lo);
+    memory->destroy(cut_st_hi);
+    memory->destroy(cut_st_lc);
+    memory->destroy(cut_st_hc);
+    memory->destroy(b_st_lo);
+    memory->destroy(b_st_hi);
+    memory->destroy(shift_st);
+    memory->destroy(cutsq_st_hc);
+
+    memory->destroy(a_st5);
+    memory->destroy(theta_st5_0);
+    memory->destroy(dtheta_st5_ast);
+    memory->destroy(b_st5);
+    memory->destroy(dtheta_st5_c);
+
+    memory->destroy(a_st6);
+    memory->destroy(theta_st6_0);
+    memory->destroy(dtheta_st6_ast);
+    memory->destroy(b_st6);
+    memory->destroy(dtheta_st6_c);
+
+    memory->destroy(a_st9);
+    memory->destroy(theta_st9_0);
+    memory->destroy(dtheta_st9_ast);
+    memory->destroy(b_st9);
+    memory->destroy(dtheta_st9_c);
+
+    memory->destroy(a_st10);
+    memory->destroy(theta_st10_0);
+    memory->destroy(dtheta_st10_ast);
+    memory->destroy(b_st10);
+    memory->destroy(dtheta_st10_c);
+
+    memory->destroy(a_st1);
+    memory->destroy(cosphi_st1_ast);
+    memory->destroy(b_st1);
+    memory->destroy(cosphi_st1_c);
+    memory->destroy(a_st2);
+    memory->destroy(cosphi_st2_ast);
+    memory->destroy(b_st2);
+    memory->destroy(cosphi_st2_c);
+
+  }
+}
+
+/* ----------------------------------------------------------------------
+   tally energy and virial into global and per-atom accumulators
+
+   NOTE: Although this is a pair style interaction, the algorithm below
+   follows the virial incrementation of the bond style. This is because
+   the bond topology is used in the main compute loop.
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::ev_tally_xyz(int i, int j, int nlocal, int newton_bond,
+                    double evdwl,
+                    double fx, double fy, double fz,
+                    double delx, double dely, double delz)
+{
+  double evdwlhalf,v[6];
+
+  if (eflag_either) {
+    if (eflag_global) {
+      if (newton_bond) eng_vdwl += evdwl;
+      else {
+        evdwlhalf = 0.5*evdwl;
+        if (i < nlocal) eng_vdwl += evdwlhalf;
+        if (j < nlocal) eng_vdwl += evdwlhalf;
+      }
+    }
+    if (eflag_atom) {
+      evdwlhalf = 0.5*evdwl;
+      if (newton_bond || i < nlocal) eatom[i] += evdwlhalf;
+      if (newton_bond || j < nlocal) eatom[j] += evdwlhalf;
+    }
+  }
+
+  if (vflag_either) {
+    v[0] = delx*fx;
+    v[1] = dely*fy;
+    v[2] = delz*fz;
+    v[3] = delx*fy;
+    v[4] = delx*fz;
+    v[5] = dely*fz;
+
+    if (vflag_global) {
+      if (newton_bond) {
+        virial[0] += v[0];
+        virial[1] += v[1];
+        virial[2] += v[2];
+        virial[3] += v[3];
+        virial[4] += v[4];
+        virial[5] += v[5];
+      } else {
+        if (i < nlocal) {
+          virial[0] += 0.5*v[0];
+          virial[1] += 0.5*v[1];
+          virial[2] += 0.5*v[2];
+          virial[3] += 0.5*v[3];
+          virial[4] += 0.5*v[4];
+          virial[5] += 0.5*v[5];
+        }
+        if (j < nlocal) {
+          virial[0] += 0.5*v[0];
+          virial[1] += 0.5*v[1];
+          virial[2] += 0.5*v[2];
+          virial[3] += 0.5*v[3];
+          virial[4] += 0.5*v[4];
+          virial[5] += 0.5*v[5];
+        }
+      }
+    }
+
+    if (vflag_atom) {
+      if (newton_bond || i < nlocal) {
+        vatom[i][0] += 0.5*v[0];
+        vatom[i][1] += 0.5*v[1];
+        vatom[i][2] += 0.5*v[2];
+        vatom[i][3] += 0.5*v[3];
+        vatom[i][4] += 0.5*v[4];
+        vatom[i][5] += 0.5*v[5];
+      }
+      if (newton_bond || j < nlocal) {
+        vatom[j][0] += 0.5*v[0];
+        vatom[j][1] += 0.5*v[1];
+        vatom[j][2] += 0.5*v[2];
+        vatom[j][3] += 0.5*v[3];
+        vatom[j][4] += 0.5*v[4];
+        vatom[j][5] += 0.5*v[5];
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   compute function for oxRNA2 pair interactions
+   s=sugar-phosphate backbone site, b=base site, st=stacking site
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::compute(int eflag, int vflag)
+{
+
+  double delf[3],delta[3],deltb[3]; // force, torque increment;
+  double evdwl,fpair,finc,tpair;
+  double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
+  double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
+  double theta5p,t5pdir[3],cost5p;
+  double theta6p,t6pdir[3],cost6p;
+  double theta9,t9dir[3],cost9;
+  double theta10,t10dir[3],cost10;
+  double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3];
+
+  // distances COM-backbone site, COM-3' and COM-5' stacking site
+  double d_cs_x=-0.4, d_cs_z=+0.2;
+  double d_cst_x_3p=+0.4, d_cst_y_3p=+0.1;
+  double d_cst_x_5p=+0.124906078525, d_cst_y_5p=-0.00866274917473;
+
+  // 3' and p5' auxiliary vectors
+  double  d3p_x=-0.462510,d3p_y=-0.528218,d3p_z=+0.712089;
+  double  d5p_x=-0.104402,d5p_y=-0.841783,d5p_z=+0.529624;
+  double aux3p[3], aux5p[3];
+
+  // vectors COM-backbone site, COM-stacking site in lab frame
+  double ra_cs[3],ra_cst[3];
+  double rb_cs[3],rb_cst[3];
+
+  // quaternions and Cartesian unit vectors in lab frame
+  double *qa,ax[3],ay[3],az[3];
+  double *qb,bx[3],by[3],bz[3];
+
+  double **x = atom->x;
+  double **f = atom->f;
+  double **torque = atom->torque;
+  int *type = atom->type;
+
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+
+  int **bondlist = neighbor->bondlist;
+  int nbondlist = neighbor->nbondlist;
+
+  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
+  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
+
+  int a,b,in,atype,btype;
+
+  double f1,f4t5,f4t6,f4t9,f4t10,f5c1,f5c2;
+  double df1,df4t5,df4t6,df4t9,df4t10,df5c1,df5c2;
+  double tptofp;
+
+  evdwl = 0.0;
+  ev_init(eflag,vflag);
+
+  // loop over stacking interaction neighbors using bond topology
+
+  for (in = 0; in < nbondlist; in++) {
+
+    a = bondlist[in][1];
+    b = bondlist[in][0];
+
+    qa=bonus[a].quat;
+    MathExtra::q_to_exyz(qa,ax,ay,az);
+    qb=bonus[b].quat;
+    MathExtra::q_to_exyz(qb,bx,by,bz);
+
+    // vector COM a - 3'-stacking site a
+    ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0];
+    ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1];
+    ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2];
+
+    // vector COM b - 5'-stacking site b
+    rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0];
+    rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1];
+    rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2];
+
+    // vector 5'-stacking site b to 3'-stacking site a
+    delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
+    delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
+    delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
+
+    // test for directionality of vector b to a
+    tptofp = MFOxdna::is_3pto5p(delr_st,bz);
+
+    // if b to a is 5' to 3' we need to swap roles of a and b
+    if (tptofp == -1) {
+
+      std::swap(a,b);
+      std::swap(ax,bx);
+      std::swap(ay,by);
+      std::swap(az,bz);
+
+    }
+
+    // a now in 5' direction, b in 3' direction
+    atype = type[a];
+    btype = type[b];
+
+    // calculate again
+    // vector COM a - 3'-stacking site a
+    ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0];
+    ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1];
+    ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2];
+
+    // vector COM b - 5'-stacking site b
+    rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0];
+    rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1];
+    rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2];
+
+    // vector 5'-stacking site b to 3'-stacking site a
+    delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
+    delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
+    delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
+
+    rsq_st = delr_st[0]*delr_st[0] + delr_st[1]*delr_st[1] + delr_st[2]*delr_st[2];
+    r_st = sqrt(rsq_st);
+    rinv_st = 1.0/r_st;
+
+    delr_st_norm[0] = delr_st[0] * rinv_st;
+    delr_st_norm[1] = delr_st[1] * rinv_st;
+    delr_st_norm[2] = delr_st[2] * rinv_st;
+
+    // vector COM a - backbone site a
+    ra_cs[0] = d_cs_x*ax[0] + d_cs_z*az[0];
+    ra_cs[1] = d_cs_x*ax[1] + d_cs_z*az[1];
+    ra_cs[2] = d_cs_x*ax[2] + d_cs_z*az[2];
+
+    // vector COM b - backbone site b
+    rb_cs[0] = d_cs_x*bx[0] + d_cs_z*bz[0];
+    rb_cs[1] = d_cs_x*bx[1] + d_cs_z*bz[1];
+    rb_cs[2] = d_cs_x*bx[2] + d_cs_z*bz[2];
+
+    // vector backbone site b to a
+    delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]);
+    delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]);
+    delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]);
+
+    rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2];
+    r_ss = sqrt(rsq_ss);
+    rinv_ss = 1.0/r_ss;
+
+    delr_ss_norm[0] = delr_ss[0] * rinv_ss;
+    delr_ss_norm[1] = delr_ss[1] * rinv_ss;
+    delr_ss_norm[2] = delr_ss[2] * rinv_ss;
+
+    f1 = F1(r_st, epsilon_st[atype][btype], a_st[atype][btype], cut_st_0[atype][btype],
+        cut_st_lc[atype][btype], cut_st_hc[atype][btype], cut_st_lo[atype][btype], cut_st_hi[atype][btype],
+        b_st_lo[atype][btype], b_st_hi[atype][btype], shift_st[atype][btype]);
+
+    // early rejection criterium
+    if (f1) {
+
+    // theta5 angle and correction
+    cost5p  = MathExtra::dot3(delr_st_norm,az);
+    if (cost5p >  1.0) cost5p =  1.0;
+    if (cost5p < -1.0) cost5p = -1.0;
+    theta5p = acos(cost5p);
+
+    f4t5 = F4(theta5p, a_st5[atype][btype], theta_st5_0[atype][btype], dtheta_st5_ast[atype][btype],
+        b_st5[atype][btype], dtheta_st5_c[atype][btype]);
+
+    // early rejection criterium
+    if (f4t5) {
+
+    cost6p = MathExtra::dot3(delr_st_norm,bz);
+    if (cost6p >  1.0) cost6p =  1.0;
+    if (cost6p < -1.0) cost6p = -1.0;
+    theta6p = acos(cost6p);
+
+    aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0];
+    aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1];
+    aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2];
+
+    aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0];
+    aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1];
+    aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2];
+
+    cost9 = MathExtra::dot3(delr_ss_norm,aux3p);
+    if (cost9 >  1.0) cost9 =  1.0;
+    if (cost9 < -1.0) cost9 = -1.0;
+    theta9 = acos(cost9);
+
+    cost10 = MathExtra::dot3(delr_ss_norm,aux5p);
+    if (cost10 >  1.0) cost10 =  1.0;
+    if (cost10 < -1.0) cost10 = -1.0;
+    theta10 = acos(cost10);
+
+    cosphi1 = MathExtra::dot3(delr_ss_norm,ay);
+    if (cosphi1 >  1.0) cosphi1 =  1.0;
+    if (cosphi1 < -1.0) cosphi1 = -1.0;
+
+    cosphi2 = MathExtra::dot3(delr_ss_norm,by);
+    if (cosphi2 >  1.0) cosphi2 =  1.0;
+    if (cosphi2 < -1.0) cosphi2 = -1.0;
+
+    f4t6 = F4(theta6p, a_st6[atype][btype], theta_st6_0[atype][btype], dtheta_st6_ast[atype][btype],
+        b_st6[atype][btype], dtheta_st6_c[atype][btype]);
+
+    f4t9 = F4(theta9, a_st9[atype][btype], theta_st9_0[atype][btype], dtheta_st9_ast[atype][btype],
+        b_st9[atype][btype], dtheta_st9_c[atype][btype]);
+
+    f4t10 = F4(theta10, a_st10[atype][btype], theta_st10_0[atype][btype], dtheta_st10_ast[atype][btype],
+        b_st10[atype][btype], dtheta_st10_c[atype][btype]);
+
+    f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
+        cosphi_st1_c[atype][btype]);
+
+    f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
+        cosphi_st2_c[atype][btype]);
+
+
+    evdwl = f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
+
+    // early rejection criterium
+    if (evdwl) {
+
+    df1 = DF1(r_st, epsilon_st[atype][btype], a_st[atype][btype], cut_st_0[atype][btype],
+        cut_st_lc[atype][btype], cut_st_hc[atype][btype], cut_st_lo[atype][btype], cut_st_hi[atype][btype],
+        b_st_lo[atype][btype], b_st_hi[atype][btype]);
+
+    df4t5 = DF4(theta5p, a_st5[atype][btype], theta_st5_0[atype][btype], dtheta_st5_ast[atype][btype],
+        b_st5[atype][btype], dtheta_st5_c[atype][btype])/sin(theta5p);
+
+    df4t6 = DF4(theta6p, a_st6[atype][btype], theta_st6_0[atype][btype], dtheta_st6_ast[atype][btype],
+        b_st6[atype][btype], dtheta_st6_c[atype][btype])/sin(theta6p);
+
+    df4t9 = DF4(theta9, a_st9[atype][btype], theta_st9_0[atype][btype], dtheta_st9_ast[atype][btype],
+        b_st9[atype][btype], dtheta_st9_c[atype][btype])/sin(theta9);
+
+    df4t10 = DF4(theta10, a_st10[atype][btype], theta_st10_0[atype][btype], dtheta_st10_ast[atype][btype],
+        b_st10[atype][btype], dtheta_st10_c[atype][btype])/sin(theta10);
+
+    df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
+        cosphi_st1_c[atype][btype]);
+
+    df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
+        cosphi_st2_c[atype][btype]);
+
+
+    // force, torque and virial contribution for forces between stacking sites
+
+    fpair = 0.0;
+
+    delf[0] = 0.0;
+    delf[1] = 0.0;
+    delf[2] = 0.0;
+
+    delta[0] = 0.0;
+    delta[1] = 0.0;
+    delta[2] = 0.0;
+
+    deltb[0] = 0.0;
+    deltb[1] = 0.0;
+    deltb[2] = 0.0;
+
+    // radial force
+    finc  = -df1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
+    fpair += finc;
+
+    delf[0] += delr_st[0] * finc;
+    delf[1] += delr_st[1] * finc;
+    delf[2] += delr_st[2] * finc;
+
+    // theta5p force
+    if (theta5p) {
+
+      finc   = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
+      fpair += finc;
+
+      delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc;
+      delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc;
+      delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc;
+
+    }
+
+    // theta6p force
+    if (theta6p) {
+
+      finc   = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
+      fpair += finc;
+
+      delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc;
+      delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc;
+      delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc;
+
+    }
+
+    // increment forces and torques
+
+    if (newton_bond || a < nlocal) {
+
+      f[a][0] += delf[0];
+      f[a][1] += delf[1];
+      f[a][2] += delf[2];
+
+      MathExtra::cross3(ra_cst,delf,delta);
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      f[b][0] -= delf[0];
+      f[b][1] -= delf[1];
+      f[b][2] -= delf[2];
+
+      MathExtra::cross3(rb_cst,delf,deltb);
+
+    }
+
+    if (newton_bond || a < nlocal) {
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      torque[b][0] -= deltb[0];
+      torque[b][1] -= deltb[1];
+      torque[b][2] -= deltb[2];
+
+    }
+
+    // increment energy and virial
+    // NOTE: The virial is calculated on the 'molecular' basis.
+    // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
+
+    if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl,
+        delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
+
+    // force, torque and virial contribution for forces between backbone sites
+
+    fpair = 0.0;
+
+    delf[0] = 0.0;
+    delf[1] = 0.0;
+    delf[2] = 0.0;
+
+    delta[0] = 0.0;
+    delta[1] = 0.0;
+    delta[2] = 0.0;
+
+    deltb[0] = 0.0;
+    deltb[1] = 0.0;
+    deltb[2] = 0.0;
+
+    // theta9 force
+    if (theta9) {
+
+      finc   = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2 * rinv_ss;
+      fpair += finc;
+
+      delf[0] += (delr_ss_norm[0]*cost9 - aux3p[0]) * finc;
+      delf[1] += (delr_ss_norm[1]*cost9 - aux3p[1]) * finc;
+      delf[2] += (delr_ss_norm[2]*cost9 - aux3p[2]) * finc;
+
+    }
+
+    // theta10 force
+    if (theta10) {
+
+      finc   = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2 * rinv_ss;
+      fpair += finc;
+
+      delf[0] += (delr_ss_norm[0]*cost10 - aux5p[0]) * finc;
+      delf[1] += (delr_ss_norm[1]*cost10 - aux5p[1]) * finc;
+      delf[2] += (delr_ss_norm[2]*cost10 - aux5p[2]) * finc;
+
+    }
+
+    // cosphi1 force
+    if (cosphi1) {
+
+      finc   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2 * rinv_ss;
+      fpair += finc;
+
+      delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc;
+      delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc;
+      delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc;
+
+    }
+
+    // cosphi2 force
+    if (cosphi2) {
+
+      finc   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2 * rinv_ss;
+      fpair += finc;
+
+      delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc;
+      delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc;
+      delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc;
+
+    }
+
+    // increment forces and torques
+
+    if (newton_bond || a < nlocal) {
+
+      f[a][0] += delf[0];
+      f[a][1] += delf[1];
+      f[a][2] += delf[2];
+
+      MathExtra::cross3(ra_cs,delf,delta);
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      f[b][0] -= delf[0];
+      f[b][1] -= delf[1];
+      f[b][2] -= delf[2];
+
+      MathExtra::cross3(rb_cs,delf,deltb);
+
+    }
+
+    if (newton_bond || a < nlocal) {
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      torque[b][0] -= deltb[0];
+      torque[b][1] -= deltb[1];
+      torque[b][2] -= deltb[2];
+
+    }
+
+    // increment virial only
+    if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0,
+        delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
+
+    // pure torques not expressible as r x f
+
+    delta[0] = 0.0;
+    delta[1] = 0.0;
+    delta[2] = 0.0;
+    deltb[0] = 0.0;
+    deltb[1] = 0.0;
+    deltb[2] = 0.0;
+
+    // theta5p torque
+    if (theta5p) {
+
+      tpair = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
+      MathExtra::cross3(delr_st_norm,az,t5pdir);
+
+      delta[0] += t5pdir[0] * tpair;
+      delta[1] += t5pdir[1] * tpair;
+      delta[2] += t5pdir[2] * tpair;
+
+    }
+
+    // theta6p torque
+    if (theta6p) {
+
+      tpair = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2;
+      MathExtra::cross3(delr_st_norm,bz,t6pdir);
+
+      deltb[0] -= t6pdir[0] * tpair;
+      deltb[1] -= t6pdir[1] * tpair;
+      deltb[2] -= t6pdir[2] * tpair;
+
+    }
+
+    // theta9 torque
+    if (theta9) {
+
+      tpair = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2;
+      MathExtra::cross3(delr_ss_norm,aux3p,t9dir);
+
+      delta[0] += t9dir[0] * tpair;
+      delta[1] += t9dir[1] * tpair;
+      delta[2] += t9dir[2] * tpair;
+
+    }
+
+    // theta10 torque
+    if (theta10) {
+
+      tpair = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2;
+      MathExtra::cross3(delr_ss_norm,aux5p,t10dir);
+
+      deltb[0] -= t10dir[0] * tpair;
+      deltb[1] -= t10dir[1] * tpair;
+      deltb[2] -= t10dir[2] * tpair;
+
+    }
+
+    // cosphi1 torque
+    if (cosphi1) {
+
+      tpair   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2;
+      MathExtra::cross3(delr_ss_norm,ay,cosphi1dir);
+
+      delta[0] += cosphi1dir[0] * tpair;
+      delta[1] += cosphi1dir[1] * tpair;
+      delta[2] += cosphi1dir[2] * tpair;
+
+    }
+
+    // cosphi2 torque
+    if (cosphi2) {
+
+      tpair   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2;
+      MathExtra::cross3(delr_ss_norm,by,cosphi2dir);
+
+      deltb[0] -= cosphi2dir[0] * tpair;
+      deltb[1] -= cosphi2dir[1] * tpair;
+      deltb[2] -= cosphi2dir[2] * tpair;
+
+    }
+
+    // increment torques
+    if (newton_bond || a < nlocal) {
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+    }
+    if (newton_bond || b < nlocal) {
+
+      torque[b][0] -= deltb[0];
+      torque[b][1] -= deltb[1];
+      torque[b][2] -= deltb[2];
+
+    }
+
+    }
+    }
+    }
+    // end early rejection criteria
+
+  }
+  // end stacking interaction
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+  memory->create(epsilon_st,n+1,n+1,"pair:epsilon_st");
+  memory->create(a_st,n+1,n+1,"pair:a_st");
+  memory->create(cut_st_0,n+1,n+1,"pair:cut_st_0");
+  memory->create(cut_st_c,n+1,n+1,"pair:cut_st_c");
+  memory->create(cut_st_lo,n+1,n+1,"pair:cut_st_lo");
+  memory->create(cut_st_hi,n+1,n+1,"pair:cut_st_hi");
+  memory->create(cut_st_lc,n+1,n+1,"pair:cut_st_lc");
+  memory->create(cut_st_hc,n+1,n+1,"pair:cut_st_hc");
+  memory->create(b_st_lo,n+1,n+1,"pair:b_st_lo");
+  memory->create(b_st_hi,n+1,n+1,"pair:b_st_hi");
+  memory->create(shift_st,n+1,n+1,"pair:shift_st");
+  memory->create(cutsq_st_hc,n+1,n+1,"pair:cutsq_st_hc");
+
+  memory->create(a_st5,n+1,n+1,"pair:a_st5");
+  memory->create(theta_st5_0,n+1,n+1,"pair:theta_st5_0");
+  memory->create(dtheta_st5_ast,n+1,n+1,"pair:dtheta_st5_ast");
+  memory->create(b_st5,n+1,n+1,"pair:b_st5");
+  memory->create(dtheta_st5_c,n+1,n+1,"pair:dtheta_st5_c");
+
+  memory->create(a_st6,n+1,n+1,"pair:a_st6");
+  memory->create(theta_st6_0,n+1,n+1,"pair:theta_st6_0");
+  memory->create(dtheta_st6_ast,n+1,n+1,"pair:dtheta_st6_ast");
+  memory->create(b_st6,n+1,n+1,"pair:b_st6");
+  memory->create(dtheta_st6_c,n+1,n+1,"pair:dtheta_st6_c");
+
+  memory->create(a_st9,n+1,n+1,"pair:a_st9");
+  memory->create(theta_st9_0,n+1,n+1,"pair:theta_st9_0");
+  memory->create(dtheta_st9_ast,n+1,n+1,"pair:dtheta_st9_ast");
+  memory->create(b_st9,n+1,n+1,"pair:b_st9");
+  memory->create(dtheta_st9_c,n+1,n+1,"pair:dtheta_st9_c");
+
+  memory->create(a_st10,n+1,n+1,"pair:a_st10");
+  memory->create(theta_st10_0,n+1,n+1,"pair:theta_st10_0");
+  memory->create(dtheta_st10_ast,n+1,n+1,"pair:dtheta_st10_ast");
+  memory->create(b_st10,n+1,n+1,"pair:b_st10");
+  memory->create(dtheta_st10_c,n+1,n+1,"pair:dtheta_st10_c");
+
+  memory->create(a_st1,n+1,n+1,"pair:a_st1");
+  memory->create(cosphi_st1_ast,n+1,n+1,"pair:cosphi_st1_ast");
+  memory->create(b_st1,n+1,n+1,"pair:b_st1");
+  memory->create(cosphi_st1_c,n+1,n+1,"pair:cosphi_st1_c");
+  memory->create(a_st2,n+1,n+1,"pair:a_st2");
+  memory->create(cosphi_st2_ast,n+1,n+1,"pair:cosphi_st2_ast");
+  memory->create(b_st2,n+1,n+1,"pair:b_st2");
+  memory->create(cosphi_st2_c,n+1,n+1,"pair:cosphi_st2_c");
+
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::settings(int narg, char **/*arg*/)
+{
+  if (narg != 0) error->all(FLERR,"Illegal pair_style command");
+
+}
+
+/* ----------------------------------------------------------------------
+   return temperature dependent oxRNA stacking strength
+------------------------------------------------------------------------- */
+
+double PairOxrna2Stk::stacking_strength(double xi_st, double kappa_st, double T)
+{
+  double eps;
+
+  eps = xi_st + kappa_st * T;
+
+  return eps;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::coeff(int narg, char **arg)
+{
+  int count;
+
+  if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+  // stacking interaction
+  count = 0;
+
+  double T, epsilon_st_one, xi_st_one, kappa_st_one, a_st_one, b_st_lo_one, b_st_hi_one;
+  double cut_st_0_one, cut_st_c_one, cut_st_lo_one, cut_st_hi_one;
+  double cut_st_lc_one, cut_st_hc_one, tmp, shift_st_one;
+
+  double a_st5_one, theta_st5_0_one, dtheta_st5_ast_one;
+  double b_st5_one, dtheta_st5_c_one;
+
+  double a_st6_one, theta_st6_0_one, dtheta_st6_ast_one;
+  double b_st6_one, dtheta_st6_c_one;
+
+  double a_st9_one, theta_st9_0_one, dtheta_st9_ast_one;
+  double b_st9_one, dtheta_st9_c_one;
+
+  double a_st10_one, theta_st10_0_one, dtheta_st10_ast_one;
+  double b_st10_one, dtheta_st10_c_one;
+
+  double a_st1_one, cosphi_st1_ast_one, b_st1_one, cosphi_st1_c_one;
+  double a_st2_one, cosphi_st2_ast_one, b_st2_one, cosphi_st2_c_one;
+
+  if (strcmp(arg[2], "seqav") != 0 && strcmp(arg[2], "seqdep") != 0) {
+    error->all(FLERR,"Incorrect setting, select seqav or seqdep in oxrna2/stk");
+  }
+  if (strcmp(arg[2],"seqav")  == 0) seqdepflag = 0;
+  if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1;
+
+  T = force->numeric(FLERR,arg[3]);
+  xi_st_one = force->numeric(FLERR,arg[4]);
+  kappa_st_one = force->numeric(FLERR,arg[5]);
+  epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T);
+
+  a_st_one = force->numeric(FLERR,arg[6]);
+  cut_st_0_one = force->numeric(FLERR,arg[7]);
+  cut_st_c_one = force->numeric(FLERR,arg[8]);
+  cut_st_lo_one = force->numeric(FLERR,arg[9]);
+  cut_st_hi_one = force->numeric(FLERR,arg[10]);
+
+  a_st5_one = force->numeric(FLERR,arg[11]);
+  theta_st5_0_one = force->numeric(FLERR,arg[12]);
+  dtheta_st5_ast_one = force->numeric(FLERR,arg[13]);
+  a_st6_one = force->numeric(FLERR,arg[14]);
+  theta_st6_0_one = force->numeric(FLERR,arg[15]);
+  dtheta_st6_ast_one = force->numeric(FLERR,arg[16]);
+
+  a_st9_one = force->numeric(FLERR,arg[17]);
+  theta_st9_0_one = force->numeric(FLERR,arg[18]);
+  dtheta_st9_ast_one = force->numeric(FLERR,arg[19]);
+  a_st10_one = force->numeric(FLERR,arg[20]);
+  theta_st10_0_one = force->numeric(FLERR,arg[21]);
+  dtheta_st10_ast_one = force->numeric(FLERR,arg[22]);
+
+  a_st1_one = force->numeric(FLERR,arg[23]);
+  cosphi_st1_ast_one = force->numeric(FLERR,arg[24]);
+  a_st2_one = force->numeric(FLERR,arg[25]);
+  cosphi_st2_ast_one = force->numeric(FLERR,arg[26]);
+
+  b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
+        2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
+        (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))/
+        (4*((1-exp(-a_st_one*(cut_st_lo_one -cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))-
+        (1-exp(-a_st_one*(cut_st_c_one -cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_c_one-cut_st_0_one)))));
+
+  cut_st_lc_one = cut_st_lo_one - a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
+        (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))/b_st_lo_one;
+
+  b_st_hi_one = 2*a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))*
+        2*a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))*
+        (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))/
+        (4*((1-exp(-a_st_one*(cut_st_hi_one -cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))-
+        (1-exp(-a_st_one*(cut_st_c_one -cut_st_0_one)))*
+        (1-exp(-a_st_one*(cut_st_c_one-cut_st_0_one)))));
+
+  cut_st_hc_one = cut_st_hi_one - a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))*
+        (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))/b_st_hi_one;
+
+  tmp = 1 - exp(-(cut_st_c_one-cut_st_0_one) * a_st_one);
+  shift_st_one = epsilon_st_one * tmp * tmp;
+
+  b_st5_one = a_st5_one*a_st5_one*dtheta_st5_ast_one*dtheta_st5_ast_one/(1-a_st5_one*dtheta_st5_ast_one*dtheta_st5_ast_one);
+  dtheta_st5_c_one = 1/(a_st5_one*dtheta_st5_ast_one);
+
+  b_st6_one = a_st6_one*a_st6_one*dtheta_st6_ast_one*dtheta_st6_ast_one/(1-a_st6_one*dtheta_st6_ast_one*dtheta_st6_ast_one);
+  dtheta_st6_c_one = 1/(a_st6_one*dtheta_st6_ast_one);
+
+  b_st9_one = a_st9_one*a_st9_one*dtheta_st9_ast_one*dtheta_st9_ast_one/(1-a_st9_one*dtheta_st9_ast_one*dtheta_st9_ast_one);
+  dtheta_st9_c_one = 1/(a_st9_one*dtheta_st9_ast_one);
+
+  b_st10_one = a_st10_one*a_st10_one*dtheta_st10_ast_one*dtheta_st10_ast_one/(1-a_st10_one*dtheta_st10_ast_one*dtheta_st10_ast_one);
+  dtheta_st10_c_one = 1/(a_st10_one*dtheta_st10_ast_one);
+
+  b_st1_one = a_st1_one*a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one/(1-a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one);
+  cosphi_st1_c_one=1/(a_st1_one*cosphi_st1_ast_one);
+
+  b_st2_one = a_st2_one*a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one/(1-a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one);
+  cosphi_st2_c_one=1/(a_st2_one*cosphi_st2_ast_one);
+
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+
+      epsilon_st[i][j] = epsilon_st_one;
+      if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1];
+      a_st[i][j] = a_st_one;
+      cut_st_0[i][j] = cut_st_0_one;
+      cut_st_c[i][j] = cut_st_c_one;
+      cut_st_lo[i][j] = cut_st_lo_one;
+      cut_st_hi[i][j] = cut_st_hi_one;
+      cut_st_lc[i][j] = cut_st_lc_one;
+      cut_st_hc[i][j] = cut_st_hc_one;
+      b_st_lo[i][j] = b_st_lo_one;
+      b_st_hi[i][j] = b_st_hi_one;
+      shift_st[i][j] = shift_st_one;
+      if (seqdepflag) shift_st[i][j] *= eta_st[i-1][j-1];
+
+      a_st5[i][j] = a_st5_one;
+      theta_st5_0[i][j] = theta_st5_0_one;
+      dtheta_st5_ast[i][j] = dtheta_st5_ast_one;
+      b_st5[i][j] = b_st5_one;
+      dtheta_st5_c[i][j] = dtheta_st5_c_one;
+
+      a_st6[i][j] = a_st6_one;
+      theta_st6_0[i][j] = theta_st6_0_one;
+      dtheta_st6_ast[i][j] = dtheta_st6_ast_one;
+      b_st6[i][j] = b_st6_one;
+      dtheta_st6_c[i][j] = dtheta_st6_c_one;
+
+      a_st9[i][j] = a_st9_one;
+      theta_st9_0[i][j] = theta_st9_0_one;
+      dtheta_st9_ast[i][j] = dtheta_st9_ast_one;
+      b_st9[i][j] = b_st9_one;
+      dtheta_st9_c[i][j] = dtheta_st9_c_one;
+
+      a_st10[i][j] = a_st10_one;
+      theta_st10_0[i][j] = theta_st10_0_one;
+      dtheta_st10_ast[i][j] = dtheta_st10_ast_one;
+      b_st10[i][j] = b_st10_one;
+      dtheta_st10_c[i][j] = dtheta_st10_c_one;
+
+      a_st1[i][j] = a_st1_one;
+      cosphi_st1_ast[i][j] = cosphi_st1_ast_one;
+      b_st1[i][j] = b_st1_one;
+      cosphi_st1_c[i][j] = cosphi_st1_c_one;
+
+      a_st2[i][j] = a_st2_one;
+      cosphi_st2_ast[i][j] = cosphi_st2_ast_one;
+      b_st2[i][j] = b_st2_one;
+      cosphi_st2_c[i][j] = cosphi_st2_c_one;
+
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
+
+}
+
+/* ----------------------------------------------------------------------
+   neighbor callback to inform pair style of neighbor list to use regular
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::init_list(int id, NeighList *ptr)
+{
+  if (id == 0) list = ptr;
+  if (id  > 0) error->all(FLERR,"Respa not supported");
+
+}
+
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairOxrna2Stk::init_one(int i, int j)
+{
+
+  if (setflag[i][j] == 0) {
+    error->all(FLERR,"Coefficient mixing not defined in oxRNA");
+  }
+  if (offset_flag) {
+    error->all(FLERR,"Offset not supported in oxRNA");
+  }
+
+  if (seqdepflag) {
+    epsilon_st[j][i] = epsilon_st[i][j]  / eta_st[i-1][j-1] * eta_st[j-1][i-1];
+  }
+  else {
+    epsilon_st[j][i] = epsilon_st[i][j];
+  }
+  a_st[j][i] = a_st[i][j];
+  b_st_lo[j][i] = b_st_lo[i][j];
+  b_st_hi[j][i] = b_st_hi[i][j];
+  cut_st_0[j][i] = cut_st_0[i][j];
+  cut_st_c[j][i] = cut_st_c[i][j];
+  cut_st_lo[j][i] = cut_st_lo[i][j];
+  cut_st_hi[j][i] = cut_st_hi[i][j];
+  cut_st_lc[j][i] = cut_st_lc[i][j];
+  cut_st_hc[j][i] = cut_st_hc[i][j];
+  if (seqdepflag) {
+    shift_st[j][i] = shift_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1];
+  }
+  else {
+    shift_st[j][i] = shift_st[i][j];
+  }
+
+  a_st5[j][i] = a_st5[i][j];
+  theta_st5_0[j][i] = theta_st5_0[i][j];
+  dtheta_st5_ast[j][i] = dtheta_st5_ast[i][j];
+  b_st5[j][i] = b_st5[i][j];
+  dtheta_st5_c[j][i] = dtheta_st5_c[i][j];
+
+  a_st6[j][i] = a_st6[i][j];
+  theta_st6_0[j][i] = theta_st6_0[i][j];
+  dtheta_st6_ast[j][i] = dtheta_st6_ast[i][j];
+  b_st6[j][i] = b_st6[i][j];
+  dtheta_st6_c[j][i] = dtheta_st6_c[i][j];
+
+  a_st9[j][i] = a_st9[i][j];
+  theta_st9_0[j][i] = theta_st9_0[i][j];
+  dtheta_st9_ast[j][i] = dtheta_st9_ast[i][j];
+  b_st9[j][i] = b_st9[i][j];
+  dtheta_st9_c[j][i] = dtheta_st9_c[i][j];
+
+  a_st10[j][i] = a_st10[i][j];
+  theta_st10_0[j][i] = theta_st10_0[i][j];
+  dtheta_st10_ast[j][i] = dtheta_st10_ast[i][j];
+  b_st10[j][i] = b_st10[i][j];
+  dtheta_st10_c[j][i] = dtheta_st10_c[i][j];
+
+  a_st1[j][i] = a_st1[i][j];
+  cosphi_st1_ast[j][i] = cosphi_st1_ast[i][j];
+  b_st1[j][i] = b_st1[i][j];
+  cosphi_st1_c[j][i] = cosphi_st1_c[i][j];
+
+  a_st2[j][i] = a_st2[i][j];
+  cosphi_st2_ast[j][i] = cosphi_st2_ast[i][j];
+  b_st2[j][i] = b_st2[i][j];
+  cosphi_st2_c[j][i] = cosphi_st2_c[i][j];
+
+  cutsq_st_hc[i][j] = cut_st_hc[i][j]*cut_st_hc[i][j];
+  cutsq_st_hc[j][i] = cutsq_st_hc[i][j];
+
+  // set the master list distance cutoff
+  return cut_st_hc[i][j];
+
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+      if (setflag[i][j]) {
+
+        fwrite(&epsilon_st[i][j],sizeof(double),1,fp);
+        fwrite(&a_st[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_0[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_c[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_lo[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_hi[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_lc[i][j],sizeof(double),1,fp);
+        fwrite(&cut_st_hc[i][j],sizeof(double),1,fp);
+        fwrite(&b_st_lo[i][j],sizeof(double),1,fp);
+        fwrite(&b_st_hi[i][j],sizeof(double),1,fp);
+        fwrite(&shift_st[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st5[i][j],sizeof(double),1,fp);
+        fwrite(&theta_st5_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st5_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st5[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st5_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st6[i][j],sizeof(double),1,fp);
+        fwrite(&theta_st6_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st6_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st6[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st6_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st9[i][j],sizeof(double),1,fp);
+        fwrite(&theta_st9_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st9_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st9[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st9_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st10[i][j],sizeof(double),1,fp);
+        fwrite(&theta_st10_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st10_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st10[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_st10_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_st1[i][j],sizeof(double),1,fp);
+        fwrite(&cosphi_st1_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st1[i][j],sizeof(double),1,fp);
+        fwrite(&cosphi_st1_c[i][j],sizeof(double),1,fp);
+        fwrite(&a_st2[i][j],sizeof(double),1,fp);
+        fwrite(&cosphi_st2_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_st2[i][j],sizeof(double),1,fp);
+        fwrite(&cosphi_st2_c[i][j],sizeof(double),1,fp);
+
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+
+          utils::sfread(FLERR,&epsilon_st[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&a_st[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_st_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shift_st[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st5_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st5_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st5[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st5_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st6_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st6_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st6[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st6_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st9[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st9_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st9_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st9[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st9_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st10[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_st10_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st10_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st10[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_st10_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_st1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st1_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&a_st2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st2_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_st2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cosphi_st2_c[i][j],sizeof(double),1,fp,NULL,error);
+
+        }
+
+        MPI_Bcast(&epsilon_st[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&a_st[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_c[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_lo[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_hi[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_lc[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_st_hc[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st_lo[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st_hi[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&shift_st[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st5[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_st5_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st5_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st5[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st5_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st6[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_st6_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st6_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st6[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st6_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st9[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_st9_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st9_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st9[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st9_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st10[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_st10_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st10_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st10[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_st10_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_st1[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cosphi_st1_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st1[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cosphi_st1_c[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&a_st2[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cosphi_st2_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_st2[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cosphi_st2_c[i][j],1,MPI_DOUBLE,0,world);
+
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::write_restart_settings(FILE *fp)
+{
+  fwrite(&offset_flag,sizeof(int),1,fp);
+  fwrite(&mix_flag,sizeof(int),1,fp);
+  fwrite(&tail_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::read_restart_settings(FILE *fp)
+{
+  int me = comm->me;
+  if (me == 0) {
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+  }
+  MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d\
+         %g %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g\
+         %g %g %g %g\
+         \n",i,
+        epsilon_st[i][i],a_st[i][i],cut_st_0[i][i],cut_st_c[i][i],cut_st_lo[i][i],cut_st_hi[i][i],
+        cut_st_lc[i][i],cut_st_hc[i][i],b_st_lo[i][i],b_st_hi[i][i],shift_st[i][i],
+        a_st5[i][i],theta_st5_0[i][i],dtheta_st5_ast[i][i],b_st5[i][i],dtheta_st5_c[i][i],
+        a_st6[i][i],theta_st6_0[i][i],dtheta_st6_ast[i][i],b_st6[i][i],dtheta_st6_c[i][i],
+        a_st9[i][i],theta_st9_0[i][i],dtheta_st9_ast[i][i],b_st9[i][i],dtheta_st9_c[i][i],
+        a_st10[i][i],theta_st10_0[i][i],dtheta_st10_ast[i][i],b_st10[i][i],dtheta_st10_c[i][i],
+        a_st1[i][i],cosphi_st1_ast[i][i],b_st1[i][i], cosphi_st1_c[i][i],
+        a_st2[i][i],cosphi_st2_ast[i][i],b_st2[i][i], cosphi_st2_c[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Stk::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d\
+         %g %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g\
+         %g %g %g %g\
+         \n",i,j,
+        epsilon_st[i][j],a_st[i][j],cut_st_0[i][j],cut_st_c[i][j],cut_st_lo[i][j],cut_st_hi[i][j],
+        cut_st_lc[i][j],cut_st_hc[i][j],b_st_lo[i][j],b_st_hi[i][j],shift_st[i][j],
+        a_st5[i][j],theta_st5_0[i][j],dtheta_st5_ast[i][j],b_st5[i][j],dtheta_st5_c[i][j],
+        a_st6[i][j],theta_st6_0[i][j],dtheta_st6_ast[i][j],b_st6[i][j],dtheta_st6_c[i][j],
+        a_st9[i][j],theta_st9_0[i][j],dtheta_st9_ast[i][j],b_st9[i][j],dtheta_st9_c[i][j],
+        a_st10[i][j],theta_st10_0[i][j],dtheta_st10_ast[i][j],b_st10[i][j],dtheta_st10_c[i][j],
+        a_st1[i][j],cosphi_st1_ast[i][j],b_st1[i][j],cosphi_st1_c[i][j],
+        a_st2[i][j],cosphi_st2_ast[i][j],b_st2[i][j],cosphi_st2_c[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairOxrna2Stk::extract(const char *str, int &dim)
+{
+  dim = 2;
+
+  if (strcmp(str,"epsilon_st") == 0) return (void *) epsilon_st;
+  if (strcmp(str,"a_st") == 0) return (void *) a_st;
+  if (strcmp(str,"cut_st_0") == 0) return (void *) cut_st_0;
+  if (strcmp(str,"cut_st_c") == 0) return (void *) cut_st_c;
+  if (strcmp(str,"cut_st_lo") == 0) return (void *) cut_st_lo;
+  if (strcmp(str,"cut_st_hi") == 0) return (void *) cut_st_hi;
+  if (strcmp(str,"cut_st_lc") == 0) return (void *) cut_st_lc;
+  if (strcmp(str,"cut_st_hc") == 0) return (void *) cut_st_hc;
+  if (strcmp(str,"b_st_lo") == 0) return (void *) b_st_lo;
+  if (strcmp(str,"b_st_hi") == 0) return (void *) b_st_hi;
+  if (strcmp(str,"shift_st") == 0) return (void *) shift_st;
+
+  if (strcmp(str,"a_st5") == 0) return (void *) a_st5;
+  if (strcmp(str,"theta_st5_0") == 0) return (void *) theta_st5_0;
+  if (strcmp(str,"dtheta_st5_ast") == 0) return (void *) dtheta_st5_ast;
+  if (strcmp(str,"b_st5") == 0) return (void *) b_st5;
+  if (strcmp(str,"dtheta_st5_c") == 0) return (void *) dtheta_st5_c;
+
+  if (strcmp(str,"a_st6") == 0) return (void *) a_st6;
+  if (strcmp(str,"theta_st6_0") == 0) return (void *) theta_st6_0;
+  if (strcmp(str,"dtheta_st6_ast") == 0) return (void *) dtheta_st6_ast;
+  if (strcmp(str,"b_st6") == 0) return (void *) b_st6;
+  if (strcmp(str,"dtheta_st6_c") == 0) return (void *) dtheta_st6_c;
+
+  if (strcmp(str,"a_st9") == 0) return (void *) a_st9;
+  if (strcmp(str,"theta_st9_0") == 0) return (void *) theta_st9_0;
+  if (strcmp(str,"dtheta_st9_ast") == 0) return (void *) dtheta_st9_ast;
+  if (strcmp(str,"b_st9") == 0) return (void *) b_st9;
+  if (strcmp(str,"dtheta_st9_c") == 0) return (void *) dtheta_st9_c;
+
+  if (strcmp(str,"a_st10") == 0) return (void *) a_st10;
+  if (strcmp(str,"theta_st10_0") == 0) return (void *) theta_st10_0;
+  if (strcmp(str,"dtheta_st10_ast") == 0) return (void *) dtheta_st10_ast;
+  if (strcmp(str,"b_st10") == 0) return (void *) b_st10;
+  if (strcmp(str,"dtheta_st10_c") == 0) return (void *) dtheta_st10_c;
+
+  if (strcmp(str,"a_st1") == 0) return (void *) a_st1;
+  if (strcmp(str,"cosphi_st1_ast") == 0) return (void *) cosphi_st1_ast;
+  if (strcmp(str,"b_st1") == 0) return (void *) b_st1;
+  if (strcmp(str,"cosphi_st1_c") == 0) return (void *) cosphi_st1_c;
+
+  if (strcmp(str,"a_st2") == 0) return (void *) a_st2;
+  if (strcmp(str,"cosphi_st2_ast") == 0) return (void *) cosphi_st2_ast;
+  if (strcmp(str,"b_st2") == 0) return (void *) b_st2;
+  if (strcmp(str,"cosphi_st2_c") == 0) return (void *) cosphi_st2_c;
+
+  return NULL;
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_stk.h b/src/USER-CGDNA/pair_oxrna2_stk.h
new file mode 100644
index 0000000000..519f7c0707
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_stk.h
@@ -0,0 +1,86 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/stk,PairOxrna2Stk)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_STK_H
+#define LMP_PAIR_OXRNA2_STK_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Stk : public Pair {
+ public:
+  PairOxrna2Stk(class LAMMPS *);
+  virtual ~PairOxrna2Stk();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  void init_list(int, class NeighList *);
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
+  void *extract(const char *, int &);
+
+ protected:
+  // stacking interaction
+  double eta_st[4][4];
+  double stacking_strength(double, double, double);
+  double **epsilon_st, **a_st, **cut_st_0, **cut_st_c;
+  double **cut_st_lo, **cut_st_hi;
+  double **cut_st_lc, **cut_st_hc, **b_st_lo, **b_st_hi, **shift_st;
+  double **cutsq_st_hc;
+  double **a_st5, **theta_st5_0, **dtheta_st5_ast;
+  double **b_st5, **dtheta_st5_c;
+  double **a_st6, **theta_st6_0, **dtheta_st6_ast;
+  double **b_st6, **dtheta_st6_c;
+  double **a_st9, **theta_st9_0, **dtheta_st9_ast;
+  double **b_st9, **dtheta_st9_c;
+  double **a_st10, **theta_st10_0, **dtheta_st10_ast;
+  double **b_st10, **dtheta_st10_c;
+  double **a_st1, **cosphi_st1_ast, **b_st1, **cosphi_st1_c;
+  double **a_st2, **cosphi_st2_ast, **b_st2, **cosphi_st2_c;
+
+  int seqdepflag;
+
+  virtual void allocate();
+  void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp
new file mode 100644
index 0000000000..f5207c53e7
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp
@@ -0,0 +1,1079 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+
+#include "pair_oxrna2_xstk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include "mf_oxdna.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "utils.h"
+#include "atom_vec_ellipsoid.h"
+#include "math_extra.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+using namespace MFOxdna;
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Xstk::PairOxrna2Xstk(LAMMPS *lmp) : Pair(lmp)
+{
+  single_enable = 0;
+  writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairOxrna2Xstk::~PairOxrna2Xstk()
+{
+  if (allocated) {
+
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(k_xst);
+    memory->destroy(cut_xst_0);
+    memory->destroy(cut_xst_c);
+    memory->destroy(cut_xst_lo);
+    memory->destroy(cut_xst_hi);
+    memory->destroy(cut_xst_lc);
+    memory->destroy(cut_xst_hc);
+    memory->destroy(cutsq_xst_hc);
+    memory->destroy(b_xst_lo);
+    memory->destroy(b_xst_hi);
+
+    memory->destroy(a_xst1);
+    memory->destroy(theta_xst1_0);
+    memory->destroy(dtheta_xst1_ast);
+    memory->destroy(b_xst1);
+    memory->destroy(dtheta_xst1_c);
+
+    memory->destroy(a_xst2);
+    memory->destroy(theta_xst2_0);
+    memory->destroy(dtheta_xst2_ast);
+    memory->destroy(b_xst2);
+    memory->destroy(dtheta_xst2_c);
+
+    memory->destroy(a_xst3);
+    memory->destroy(theta_xst3_0);
+    memory->destroy(dtheta_xst3_ast);
+    memory->destroy(b_xst3);
+    memory->destroy(dtheta_xst3_c);
+
+    memory->destroy(a_xst7);
+    memory->destroy(theta_xst7_0);
+    memory->destroy(dtheta_xst7_ast);
+    memory->destroy(b_xst7);
+    memory->destroy(dtheta_xst7_c);
+
+    memory->destroy(a_xst8);
+    memory->destroy(theta_xst8_0);
+    memory->destroy(dtheta_xst8_ast);
+    memory->destroy(b_xst8);
+    memory->destroy(dtheta_xst8_c);
+
+  }
+}
+
+/* ----------------------------------------------------------------------
+   compute function for oxDNA pair interactions
+   hb=hydrogen bonding site
+
+   NOTE: The cross-stacking interaction takes place between hb sites
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::compute(int eflag, int vflag)
+{
+
+  double delf[3],delta[3],deltb[3]; // force, torque increment;
+  double evdwl,fpair,finc,tpair,factor_lj;
+  double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
+  double theta1,t1dir[3],cost1;
+  double theta2,t2dir[3],cost2;
+  double theta3,t3dir[3],cost3;
+  double theta4,theta4p,t4dir[3],cost4;
+  double theta7,theta7p,t7dir[3],cost7;
+  double theta8,theta8p,t8dir[3],cost8;
+
+  // distance COM-h-bonding site
+  double d_chb=+0.4;
+  // vectors COM-h-bonding site in lab frame
+  double ra_chb[3],rb_chb[3];
+
+  // quaternions and Cartesian unit vectors in lab frame
+  double *qa,ax[3],ay[3],az[3];
+  double *qb,bx[3],by[3],bz[3];
+
+  double **x = atom->x;
+  double **f = atom->f;
+  double **torque = atom->torque;
+  int *type = atom->type;
+
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+  int *alist,*blist,*numneigh,**firstneigh;
+  double *special_lj = force->special_lj;
+
+  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
+  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
+
+  int a,b,ia,ib,anum,bnum,atype,btype;
+
+  double f2,f4t1,f4t2,f4t3,f4t7,f4t8;
+  double df2,df4t1,df4t2,df4t3,df4t7,df4t8,rsint;
+
+  evdwl = 0.0;
+  ev_init(eflag,vflag);
+
+  anum = list->inum;
+  alist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over pair interaction neighbors of my atoms
+
+  for (ia = 0; ia < anum; ia++) {
+
+    a = alist[ia];
+    atype = type[a];
+
+    qa=bonus[a].quat;
+    MathExtra::q_to_exyz(qa,ax,ay,az);
+
+    ra_chb[0] = d_chb*ax[0];
+    ra_chb[1] = d_chb*ax[1];
+    ra_chb[2] = d_chb*ax[2];
+
+    blist = firstneigh[a];
+    bnum = numneigh[a];
+
+    for (ib = 0; ib < bnum; ib++) {
+
+      b = blist[ib];
+      factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
+      b &= NEIGHMASK;
+
+      btype = type[b];
+
+      qb=bonus[b].quat;
+      MathExtra::q_to_exyz(qb,bx,by,bz);
+
+      rb_chb[0] = d_chb*bx[0];
+      rb_chb[1] = d_chb*bx[1];
+      rb_chb[2] = d_chb*bx[2];
+
+      // vector h-bonding site b to a
+      delr_hb[0] = x[a][0] + ra_chb[0] - x[b][0] - rb_chb[0];
+      delr_hb[1] = x[a][1] + ra_chb[1] - x[b][1] - rb_chb[1];
+      delr_hb[2] = x[a][2] + ra_chb[2] - x[b][2] - rb_chb[2];
+
+      rsq_hb = delr_hb[0]*delr_hb[0] + delr_hb[1]*delr_hb[1] + delr_hb[2]*delr_hb[2];
+      r_hb = sqrt(rsq_hb);
+      rinv_hb = 1.0/r_hb;
+
+      delr_hb_norm[0] = delr_hb[0] * rinv_hb;
+      delr_hb_norm[1] = delr_hb[1] * rinv_hb;
+      delr_hb_norm[2] = delr_hb[2] * rinv_hb;
+
+      f2 = F2(r_hb, k_xst[atype][btype], cut_xst_0[atype][btype],
+           cut_xst_lc[atype][btype], cut_xst_hc[atype][btype], cut_xst_lo[atype][btype], cut_xst_hi[atype][btype],
+           b_xst_lo[atype][btype], b_xst_hi[atype][btype], cut_xst_c[atype][btype]);
+
+      // early rejection criterium
+      if (f2) {
+
+      cost1 = -1.0*MathExtra::dot3(ax,bx);
+      if (cost1 >  1.0) cost1 =  1.0;
+      if (cost1 < -1.0) cost1 = -1.0;
+      theta1 = acos(cost1);
+
+      f4t1 = F4(theta1, a_xst1[atype][btype], theta_xst1_0[atype][btype], dtheta_xst1_ast[atype][btype],
+             b_xst1[atype][btype], dtheta_xst1_c[atype][btype]);
+
+      // early rejection criterium
+      if (f4t1) {
+
+      cost2 = -1.0*MathExtra::dot3(ax,delr_hb_norm);
+      if (cost2 >  1.0) cost2 =  1.0;
+      if (cost2 < -1.0) cost2 = -1.0;
+      theta2 = acos(cost2);
+
+      f4t2 = F4(theta2, a_xst2[atype][btype], theta_xst2_0[atype][btype], dtheta_xst2_ast[atype][btype],
+             b_xst2[atype][btype], dtheta_xst2_c[atype][btype]);
+
+      // early rejection criterium
+      if (f4t2) {
+
+      cost3 = MathExtra::dot3(bx,delr_hb_norm);
+      if (cost3 >  1.0) cost3 =  1.0;
+      if (cost3 < -1.0) cost3 = -1.0;
+      theta3 = acos(cost3);
+
+      f4t3 = F4(theta3, a_xst3[atype][btype], theta_xst3_0[atype][btype], dtheta_xst3_ast[atype][btype],
+             b_xst3[atype][btype], dtheta_xst3_c[atype][btype]);
+
+      // early rejection criterium
+      if (f4t3) {
+
+      cost7 = -1.0*MathExtra::dot3(az,delr_hb_norm);
+      if (cost7 >  1.0) cost7 =  1.0;
+      if (cost7 < -1.0) cost7 = -1.0;
+      theta7 = acos(cost7);
+      theta7p = MY_PI - theta7;
+
+      f4t7 = F4(theta7, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype],
+             b_xst7[atype][btype], dtheta_xst7_c[atype][btype]) +
+             F4(theta7p, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype],
+             b_xst7[atype][btype], dtheta_xst7_c[atype][btype]);
+
+      // early rejection criterium
+      if (f4t7) {
+
+      cost8 = MathExtra::dot3(bz,delr_hb_norm);
+      if (cost8 >  1.0) cost8 =  1.0;
+      if (cost8 < -1.0) cost8 = -1.0;
+      theta8 = acos(cost8);
+      theta8p = MY_PI -theta8;
+
+      f4t8 = F4(theta8, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype],
+             b_xst8[atype][btype], dtheta_xst8_c[atype][btype]) +
+             F4(theta8p, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype],
+             b_xst8[atype][btype], dtheta_xst8_c[atype][btype]);
+
+
+      evdwl = f2 * f4t1 * f4t2 * f4t3 * f4t7 * f4t8 * factor_lj;
+
+
+      // early rejection criterium
+      if (evdwl) {
+
+      df2 = DF2(r_hb, k_xst[atype][btype], cut_xst_0[atype][btype],
+            cut_xst_lc[atype][btype], cut_xst_hc[atype][btype], cut_xst_lo[atype][btype], cut_xst_hi[atype][btype],
+            b_xst_lo[atype][btype], b_xst_hi[atype][btype]);
+
+      df4t1 = DF4(theta1, a_xst1[atype][btype], theta_xst1_0[atype][btype], dtheta_xst1_ast[atype][btype],
+              b_xst1[atype][btype], dtheta_xst1_c[atype][btype])/sin(theta1);
+
+      df4t2 = DF4(theta2, a_xst2[atype][btype], theta_xst2_0[atype][btype], dtheta_xst2_ast[atype][btype],
+              b_xst2[atype][btype], dtheta_xst2_c[atype][btype])/sin(theta2);
+
+      df4t3 = DF4(theta3, a_xst3[atype][btype], theta_xst3_0[atype][btype], dtheta_xst3_ast[atype][btype],
+              b_xst3[atype][btype], dtheta_xst3_c[atype][btype])/sin(theta3);
+
+      rsint = 1.0/sin(theta7);
+      df4t7 = DF4(theta7, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype],
+              b_xst7[atype][btype], dtheta_xst7_c[atype][btype])*rsint -
+              DF4(theta7p, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype],
+              b_xst7[atype][btype], dtheta_xst7_c[atype][btype])*rsint;
+
+      rsint = 1.0/sin(theta8);
+      df4t8 = DF4(theta8, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype],
+              b_xst8[atype][btype], dtheta_xst8_c[atype][btype])*rsint -
+              DF4(theta8p, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype],
+              b_xst8[atype][btype], dtheta_xst8_c[atype][btype])*rsint;
+
+      // force, torque and virial contribution for forces between h-bonding sites
+
+      fpair = 0.0;
+
+      delf[0] = 0.0;
+      delf[1] = 0.0;
+      delf[2] = 0.0;
+
+      delta[0] = 0.0;
+      delta[1] = 0.0;
+      delta[2] = 0.0;
+
+      deltb[0] = 0.0;
+      deltb[1] = 0.0;
+      deltb[2] = 0.0;
+
+      // radial force
+      finc  = -df2 * f4t1 * f4t2 * f4t3 * f4t7 * f4t8 * rinv_hb *factor_lj;
+      fpair += finc;
+
+      delf[0] += delr_hb[0] * finc;
+      delf[1] += delr_hb[1] * finc;
+      delf[2] += delr_hb[2] * finc;
+
+      // theta2 force
+      if (theta2) {
+
+        finc  = -f2 * f4t1 * df4t2 * f4t3 * f4t7 * f4t8 * rinv_hb * factor_lj;
+        fpair += finc;
+
+        delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc;
+        delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc;
+        delf[2] += (delr_hb_norm[2]*cost2 + ax[2]) * finc;
+
+      }
+
+      // theta3 force
+      if (theta3) {
+
+        finc  = -f2 * f4t1 * f4t2 * df4t3 * f4t7 * f4t8 * rinv_hb * factor_lj;
+        fpair += finc;
+
+        delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc;
+        delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc;
+        delf[2] += (delr_hb_norm[2]*cost3 - bx[2]) * finc;
+
+      }
+
+      // theta7 force
+      if (theta7) {
+
+        finc  = -f2 * f4t1 * f4t2 * f4t3 * df4t7 * f4t8 * rinv_hb * factor_lj;
+        fpair += finc;
+
+        delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc;
+        delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc;
+        delf[2] += (delr_hb_norm[2]*cost7 + az[2]) * finc;
+
+      }
+
+      // theta8 force
+      if (theta8) {
+
+        finc  = -f2 * f4t1 * f4t2 * f4t3 * f4t7 * df4t8 * rinv_hb * factor_lj;
+        fpair += finc;
+
+        delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc;
+        delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc;
+        delf[2] += (delr_hb_norm[2]*cost8 - bz[2]) * finc;
+
+      }
+
+      // increment forces and torques
+
+      f[a][0] += delf[0];
+      f[a][1] += delf[1];
+      f[a][2] += delf[2];
+
+      MathExtra::cross3(ra_chb,delf,delta);
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+      if (newton_pair || b < nlocal) {
+
+        f[b][0] -= delf[0];
+        f[b][1] -= delf[1];
+        f[b][2] -= delf[2];
+
+
+        MathExtra::cross3(rb_chb,delf,deltb);
+
+        torque[b][0] -= deltb[0];
+        torque[b][1] -= deltb[1];
+        torque[b][2] -= deltb[2];
+
+      }
+
+      // increment energy and virial
+      // NOTE: The virial is calculated on the 'molecular' basis.
+      // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
+
+      if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
+          delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
+
+      // pure torques not expressible as r x f
+
+      delta[0] = 0.0;
+      delta[1] = 0.0;
+      delta[2] = 0.0;
+      deltb[0] = 0.0;
+      deltb[1] = 0.0;
+      deltb[2] = 0.0;
+
+      // theta1 torque
+      if (theta1) {
+
+        tpair = -f2 * df4t1 * f4t2 * f4t3 * f4t7 * f4t8 * factor_lj;
+        MathExtra::cross3(ax,bx,t1dir);
+
+        delta[0] += t1dir[0]*tpair;
+        delta[1] += t1dir[1]*tpair;
+        delta[2] += t1dir[2]*tpair;
+
+        deltb[0] += t1dir[0]*tpair;
+        deltb[1] += t1dir[1]*tpair;
+        deltb[2] += t1dir[2]*tpair;
+
+      }
+
+      // theta2 torque
+      if (theta2) {
+
+        tpair = -f2 * f4t1 * df4t2 * f4t3 * f4t7 * f4t8 * factor_lj;
+        MathExtra::cross3(ax,delr_hb_norm,t2dir);
+
+        delta[0] += t2dir[0]*tpair;
+        delta[1] += t2dir[1]*tpair;
+        delta[2] += t2dir[2]*tpair;
+
+      }
+
+      // theta3 torque
+      if (theta3) {
+
+        tpair = -f2 * f4t1 * f4t2 * df4t3 * f4t7 * f4t8 * factor_lj;
+        MathExtra::cross3(bx,delr_hb_norm,t3dir);
+
+        deltb[0] += t3dir[0]*tpair;
+        deltb[1] += t3dir[1]*tpair;
+        deltb[2] += t3dir[2]*tpair;
+
+      }
+
+      // theta7 torque
+      if (theta7) {
+
+        tpair = -f2 * f4t1 * f4t2 * f4t3 * df4t7 * f4t8 * factor_lj;
+        MathExtra::cross3(az,delr_hb_norm,t7dir);
+
+        delta[0] += t7dir[0]*tpair;
+        delta[1] += t7dir[1]*tpair;
+        delta[2] += t7dir[2]*tpair;
+
+      }
+
+      // theta8 torque
+      if (theta8) {
+
+        tpair = -f2 * f4t1 * f4t2 * f4t3 * f4t7 * df4t8 * factor_lj;
+        MathExtra::cross3(bz,delr_hb_norm,t8dir);
+
+        deltb[0] += t8dir[0]*tpair;
+        deltb[1] += t8dir[1]*tpair;
+        deltb[2] += t8dir[2]*tpair;
+
+      }
+
+      // increment torques
+
+      torque[a][0] += delta[0];
+      torque[a][1] += delta[1];
+      torque[a][2] += delta[2];
+
+      if (newton_pair || b < nlocal) {
+
+        torque[b][0] -= deltb[0];
+        torque[b][1] -= deltb[1];
+        torque[b][2] -= deltb[2];
+
+      }
+
+
+      }
+      }
+      }
+      }
+      }
+      }// end early rejection criteria
+
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+  memory->create(k_xst,n+1,n+1,"pair:k_xst");
+  memory->create(cut_xst_0,n+1,n+1,"pair:cut_xst_0");
+  memory->create(cut_xst_c,n+1,n+1,"pair:cut_xst_c");
+  memory->create(cut_xst_lo,n+1,n+1,"pair:cut_xst_lo");
+  memory->create(cut_xst_hi,n+1,n+1,"pair:cut_xst_hi");
+  memory->create(cut_xst_lc,n+1,n+1,"pair:cut_xst_lc");
+  memory->create(cut_xst_hc,n+1,n+1,"pair:cut_xst_hc");
+  memory->create(b_xst_lo,n+1,n+1,"pair:b_xst_lo");
+  memory->create(b_xst_hi,n+1,n+1,"pair:b_xst_hi");
+  memory->create(cutsq_xst_hc,n+1,n+1,"pair:cutsq_xst_hc");
+
+  memory->create(a_xst1,n+1,n+1,"pair:a_xst1");
+  memory->create(theta_xst1_0,n+1,n+1,"pair:theta_xst1_0");
+  memory->create(dtheta_xst1_ast,n+1,n+1,"pair:dtheta_xst1_ast");
+  memory->create(b_xst1,n+1,n+1,"pair:b_xst1");
+  memory->create(dtheta_xst1_c,n+1,n+1,"pair:dtheta_xst1_c");
+
+  memory->create(a_xst2,n+1,n+1,"pair:a_xst2");
+  memory->create(theta_xst2_0,n+1,n+1,"pair:theta_xst2_0");
+  memory->create(dtheta_xst2_ast,n+1,n+1,"pair:dtheta_xst2_ast");
+  memory->create(b_xst2,n+1,n+1,"pair:b_xst2");
+  memory->create(dtheta_xst2_c,n+1,n+1,"pair:dtheta_xst2_c");
+
+  memory->create(a_xst3,n+1,n+1,"pair:a_xst3");
+  memory->create(theta_xst3_0,n+1,n+1,"pair:theta_xst3_0");
+  memory->create(dtheta_xst3_ast,n+1,n+1,"pair:dtheta_xst3_ast");
+  memory->create(b_xst3,n+1,n+1,"pair:b_xst3");
+  memory->create(dtheta_xst3_c,n+1,n+1,"pair:dtheta_xst3_c");
+
+  memory->create(a_xst7,n+1,n+1,"pair:a_xst7");
+  memory->create(theta_xst7_0,n+1,n+1,"pair:theta_xst7_0");
+  memory->create(dtheta_xst7_ast,n+1,n+1,"pair:dtheta_xst7_ast");
+  memory->create(b_xst7,n+1,n+1,"pair:b_xst7");
+  memory->create(dtheta_xst7_c,n+1,n+1,"pair:dtheta_xst7_c");
+
+  memory->create(a_xst8,n+1,n+1,"pair:a_xst8");
+  memory->create(theta_xst8_0,n+1,n+1,"pair:theta_xst8_0");
+  memory->create(dtheta_xst8_ast,n+1,n+1,"pair:dtheta_xst8_ast");
+  memory->create(b_xst8,n+1,n+1,"pair:b_xst8");
+  memory->create(dtheta_xst8_c,n+1,n+1,"pair:dtheta_xst8_c");
+
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::settings(int narg, char **/*arg*/)
+{
+  if (narg != 0) error->all(FLERR,"Illegal pair_style command");
+
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::coeff(int narg, char **arg)
+{
+  int count;
+
+  if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+  // cross-stacking interaction
+  count = 0;
+
+  double k_xst_one, cut_xst_0_one, cut_xst_c_one, cut_xst_lo_one, cut_xst_hi_one;
+  double b_xst_lo_one, b_xst_hi_one, cut_xst_lc_one, cut_xst_hc_one;
+
+  double a_xst1_one, theta_xst1_0_one, dtheta_xst1_ast_one;
+  double b_xst1_one, dtheta_xst1_c_one;
+
+  double a_xst2_one, theta_xst2_0_one, dtheta_xst2_ast_one;
+  double b_xst2_one, dtheta_xst2_c_one;
+
+  double a_xst3_one, theta_xst3_0_one, dtheta_xst3_ast_one;
+  double b_xst3_one, dtheta_xst3_c_one;
+
+  double a_xst7_one, theta_xst7_0_one, dtheta_xst7_ast_one;
+  double b_xst7_one, dtheta_xst7_c_one;
+
+  double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one;
+  double b_xst8_one, dtheta_xst8_c_one;
+
+  k_xst_one = force->numeric(FLERR,arg[2]);
+  cut_xst_0_one = force->numeric(FLERR,arg[3]);
+  cut_xst_c_one = force->numeric(FLERR,arg[4]);
+  cut_xst_lo_one = force->numeric(FLERR,arg[5]);
+  cut_xst_hi_one = force->numeric(FLERR,arg[6]);
+
+  a_xst1_one = force->numeric(FLERR,arg[7]);
+  theta_xst1_0_one = force->numeric(FLERR,arg[8]);
+  dtheta_xst1_ast_one = force->numeric(FLERR,arg[9]);
+
+  a_xst2_one = force->numeric(FLERR,arg[10]);
+  theta_xst2_0_one = force->numeric(FLERR,arg[11]);
+  dtheta_xst2_ast_one = force->numeric(FLERR,arg[12]);
+
+  a_xst3_one = force->numeric(FLERR,arg[13]);
+  theta_xst3_0_one = force->numeric(FLERR,arg[14]);
+  dtheta_xst3_ast_one = force->numeric(FLERR,arg[15]);
+
+  a_xst7_one = force->numeric(FLERR,arg[16]);
+  theta_xst7_0_one = force->numeric(FLERR,arg[17]);
+  dtheta_xst7_ast_one = force->numeric(FLERR,arg[18]);
+
+  a_xst8_one = force->numeric(FLERR,arg[19]);
+  theta_xst8_0_one = force->numeric(FLERR,arg[20]);
+  dtheta_xst8_ast_one = force->numeric(FLERR,arg[21]);
+
+
+  b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/
+        (0.5 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one) -
+        k_xst_one * 0.5 * (cut_xst_0_one -cut_xst_c_one) * (cut_xst_0_one - cut_xst_c_one)/k_xst_one);
+
+  cut_xst_lc_one = cut_xst_lo_one - 0.5 * (cut_xst_lo_one - cut_xst_0_one)/b_xst_lo_one;;
+
+  b_xst_hi_one = 0.25 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one)/
+        (0.5 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one) -
+        k_xst_one * 0.5 * (cut_xst_0_one -cut_xst_c_one) * (cut_xst_0_one - cut_xst_c_one)/k_xst_one);
+
+  cut_xst_hc_one = cut_xst_hi_one - 0.5* (cut_xst_hi_one - cut_xst_0_one)/b_xst_hi_one;
+
+
+  b_xst1_one = a_xst1_one*a_xst1_one*dtheta_xst1_ast_one*dtheta_xst1_ast_one/(1-a_xst1_one*dtheta_xst1_ast_one*dtheta_xst1_ast_one);
+  dtheta_xst1_c_one = 1/(a_xst1_one*dtheta_xst1_ast_one);
+
+  b_xst2_one = a_xst2_one*a_xst2_one*dtheta_xst2_ast_one*dtheta_xst2_ast_one/(1-a_xst2_one*dtheta_xst2_ast_one*dtheta_xst2_ast_one);
+  dtheta_xst2_c_one = 1/(a_xst2_one*dtheta_xst2_ast_one);
+
+  b_xst3_one = a_xst3_one*a_xst3_one*dtheta_xst3_ast_one*dtheta_xst3_ast_one/(1-a_xst3_one*dtheta_xst3_ast_one*dtheta_xst3_ast_one);
+  dtheta_xst3_c_one = 1/(a_xst3_one*dtheta_xst3_ast_one);
+
+  b_xst7_one = a_xst7_one*a_xst7_one*dtheta_xst7_ast_one*dtheta_xst7_ast_one/(1-a_xst7_one*dtheta_xst7_ast_one*dtheta_xst7_ast_one);
+  dtheta_xst7_c_one = 1/(a_xst7_one*dtheta_xst7_ast_one);
+
+  b_xst8_one = a_xst8_one*a_xst8_one*dtheta_xst8_ast_one*dtheta_xst8_ast_one/(1-a_xst8_one*dtheta_xst8_ast_one*dtheta_xst8_ast_one);
+  dtheta_xst8_c_one = 1/(a_xst8_one*dtheta_xst8_ast_one);
+
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+
+      k_xst[i][j] = k_xst_one;
+      cut_xst_0[i][j] = cut_xst_0_one;
+      cut_xst_c[i][j] = cut_xst_c_one;
+      cut_xst_lo[i][j] = cut_xst_lo_one;
+      cut_xst_hi[i][j] = cut_xst_hi_one;
+      cut_xst_lc[i][j] = cut_xst_lc_one;
+      cut_xst_hc[i][j] = cut_xst_hc_one;
+      b_xst_lo[i][j] = b_xst_lo_one;
+      b_xst_hi[i][j] = b_xst_hi_one;
+
+      a_xst1[i][j] = a_xst1_one;
+      theta_xst1_0[i][j] = theta_xst1_0_one;
+      dtheta_xst1_ast[i][j] = dtheta_xst1_ast_one;
+      b_xst1[i][j] = b_xst1_one;
+      dtheta_xst1_c[i][j] = dtheta_xst1_c_one;
+
+      a_xst2[i][j] = a_xst2_one;
+      theta_xst2_0[i][j] = theta_xst2_0_one;
+      dtheta_xst2_ast[i][j] = dtheta_xst2_ast_one;
+      b_xst2[i][j] = b_xst2_one;
+      dtheta_xst2_c[i][j] = dtheta_xst2_c_one;
+
+      a_xst3[i][j] = a_xst3_one;
+      theta_xst3_0[i][j] = theta_xst3_0_one;
+      dtheta_xst3_ast[i][j] = dtheta_xst3_ast_one;
+      b_xst3[i][j] = b_xst3_one;
+      dtheta_xst3_c[i][j] = dtheta_xst3_c_one;
+
+      a_xst7[i][j] = a_xst7_one;
+      theta_xst7_0[i][j] = theta_xst7_0_one;
+      dtheta_xst7_ast[i][j] = dtheta_xst7_ast_one;
+      b_xst7[i][j] = b_xst7_one;
+      dtheta_xst7_c[i][j] = dtheta_xst7_c_one;
+
+      a_xst8[i][j] = a_xst8_one;
+      theta_xst8_0[i][j] = theta_xst8_0_one;
+      dtheta_xst8_ast[i][j] = dtheta_xst8_ast_one;
+      b_xst8[i][j] = b_xst8_one;
+      dtheta_xst8_c[i][j] = dtheta_xst8_c_one;
+
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk");
+
+}
+
+/* ----------------------------------------------------------------------
+   neighbor callback to inform pair style of neighbor list to use regular
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::init_list(int id, NeighList *ptr)
+{
+  if (id == 0) list = ptr;
+  if (id  > 0) error->all(FLERR,"Respa not supported");
+
+}
+
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairOxrna2Xstk::init_one(int i, int j)
+{
+
+  if (setflag[i][j] == 0) {
+    error->all(FLERR,"Coefficient mixing not defined in oxDNA");
+  }
+  if (offset_flag) {
+    error->all(FLERR,"Offset not supported in oxDNA");
+  }
+
+  k_xst[j][i] = k_xst[i][j];
+  cut_xst_0[j][i] = cut_xst_0[i][j];
+  cut_xst_c[j][i] = cut_xst_c[i][j];
+  cut_xst_lo[j][i] = cut_xst_lo[i][j];
+  cut_xst_hi[j][i] = cut_xst_hi[i][j];
+  b_xst_lo[j][i] = b_xst_lo[i][j];
+  b_xst_hi[j][i] = b_xst_hi[i][j];
+  cut_xst_lc[j][i] = cut_xst_lc[i][j];
+  cut_xst_hc[j][i] = cut_xst_hc[i][j];
+
+  a_xst1[j][i] = a_xst1[i][j];
+  theta_xst1_0[j][i] = theta_xst1_0[i][j];
+  dtheta_xst1_ast[j][i] = dtheta_xst1_ast[i][j];
+  b_xst1[j][i] = b_xst1[i][j];
+  dtheta_xst1_c[j][i] = dtheta_xst1_c[i][j];
+
+  a_xst2[j][i] = a_xst2[i][j];
+  theta_xst2_0[j][i] = theta_xst2_0[i][j];
+  dtheta_xst2_ast[j][i] = dtheta_xst2_ast[i][j];
+  b_xst2[j][i] = b_xst2[i][j];
+  dtheta_xst2_c[j][i] = dtheta_xst2_c[i][j];
+
+  a_xst3[j][i] = a_xst3[i][j];
+  theta_xst3_0[j][i] = theta_xst3_0[i][j];
+  dtheta_xst3_ast[j][i] = dtheta_xst3_ast[i][j];
+  b_xst3[j][i] = b_xst3[i][j];
+  dtheta_xst3_c[j][i] = dtheta_xst3_c[i][j];
+
+  a_xst7[j][i] = a_xst7[i][j];
+  theta_xst7_0[j][i] = theta_xst7_0[i][j];
+  dtheta_xst7_ast[j][i] = dtheta_xst7_ast[i][j];
+  b_xst7[j][i] = b_xst7[i][j];
+  dtheta_xst7_c[j][i] = dtheta_xst7_c[i][j];
+
+  a_xst8[j][i] = a_xst8[i][j];
+  theta_xst8_0[j][i] = theta_xst8_0[i][j];
+  dtheta_xst8_ast[j][i] = dtheta_xst8_ast[i][j];
+  b_xst8[j][i] = b_xst8[i][j];
+  dtheta_xst8_c[j][i] = dtheta_xst8_c[i][j];
+
+  cutsq_xst_hc[i][j] = cut_xst_hc[i][j]*cut_xst_hc[i][j];
+  cutsq_xst_hc[j][i] = cutsq_xst_hc[i][j];
+
+  // set the master list distance cutoff
+  return cut_xst_hc[i][j];
+
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+      if (setflag[i][j]) {
+
+        fwrite(&k_xst[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_0[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_c[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_lo[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_hi[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_lc[i][j],sizeof(double),1,fp);
+        fwrite(&cut_xst_hc[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst_lo[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst_hi[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst1[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst1_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst1_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst1[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst1_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst2[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst2_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst2_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst2[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst2_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst3[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst3_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst3_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst3[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst3_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst7[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst7_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst7_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst7[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst7_c[i][j],sizeof(double),1,fp);
+
+        fwrite(&a_xst8[i][j],sizeof(double),1,fp);
+        fwrite(&theta_xst8_0[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst8_ast[i][j],sizeof(double),1,fp);
+        fwrite(&b_xst8[i][j],sizeof(double),1,fp);
+        fwrite(&dtheta_xst8_c[i][j],sizeof(double),1,fp);
+
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+
+          utils::sfread(FLERR,&k_xst[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_hi[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_lc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_xst_hc[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst_lo[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst_hi[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst1_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst1_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst1_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst2_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst2_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst2_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst3_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst3_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst3_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst7[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst7_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst7_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst7[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst7_c[i][j],sizeof(double),1,fp,NULL,error);
+
+          utils::sfread(FLERR,&a_xst8[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&theta_xst8_0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst8_ast[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b_xst8[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&dtheta_xst8_c[i][j],sizeof(double),1,fp,NULL,error);
+
+        }
+
+        MPI_Bcast(&k_xst[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_c[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_lo[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_hi[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_lc[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_xst_hc[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst_lo[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst_hi[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst1[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst1_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst1_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst1[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst1_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst2[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst2_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst2_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst2[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst2_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst3[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst3_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst3_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst3[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst3_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst7[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst7_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst7_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst7[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst7_c[i][j],1,MPI_DOUBLE,0,world);
+
+        MPI_Bcast(&a_xst8[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&theta_xst8_0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst8_ast[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&b_xst8[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&dtheta_xst8_c[i][j],1,MPI_DOUBLE,0,world);
+
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::write_restart_settings(FILE *fp)
+{
+  fwrite(&offset_flag,sizeof(int),1,fp);
+  fwrite(&mix_flag,sizeof(int),1,fp);
+  fwrite(&tail_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::read_restart_settings(FILE *fp)
+{
+  int me = comm->me;
+  if (me == 0) {
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+  }
+  MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d\
+         %g %g %g %g %g\
+         %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         \n",i,
+        k_xst[i][i],cut_xst_0[i][i],cut_xst_c[i][i],cut_xst_lo[i][i],cut_xst_hi[i][i],
+        cut_xst_lc[i][i],cut_xst_hc[i][i],b_xst_lo[i][i],b_xst_hi[i][i],
+        a_xst1[i][i],theta_xst1_0[i][i],dtheta_xst1_ast[i][i],b_xst1[i][i],dtheta_xst1_c[i][i],
+        a_xst2[i][i],theta_xst2_0[i][i],dtheta_xst2_ast[i][i],b_xst2[i][i],dtheta_xst2_c[i][i],
+        a_xst3[i][i],theta_xst3_0[i][i],dtheta_xst3_ast[i][i],b_xst3[i][i],dtheta_xst3_c[i][i],
+        a_xst7[i][i],theta_xst7_0[i][i],dtheta_xst7_ast[i][i],b_xst7[i][i],dtheta_xst7_c[i][i],
+        a_xst8[i][i],theta_xst8_0[i][i],dtheta_xst8_ast[i][i],b_xst8[i][i],dtheta_xst8_c[i][i]);
+
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairOxrna2Xstk::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d\
+         %g %g %g %g %g\
+         %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         %g %g %g %g %g\
+         \n",i,j,
+        k_xst[i][j],cut_xst_0[i][j],cut_xst_c[i][j],cut_xst_lo[i][j],cut_xst_hi[i][j],
+        cut_xst_lc[i][j],cut_xst_hc[i][j],b_xst_lo[i][j],b_xst_hi[i][j],
+        a_xst1[i][j],theta_xst1_0[i][j],dtheta_xst1_ast[i][j],b_xst1[i][j],dtheta_xst1_c[i][j],
+        a_xst2[i][j],theta_xst2_0[i][j],dtheta_xst2_ast[i][j],b_xst2[i][j],dtheta_xst2_c[i][j],
+        a_xst3[i][j],theta_xst3_0[i][j],dtheta_xst3_ast[i][j],b_xst3[i][j],dtheta_xst3_c[i][j],
+        a_xst7[i][j],theta_xst7_0[i][j],dtheta_xst7_ast[i][j],b_xst7[i][j],dtheta_xst7_c[i][j],
+        a_xst8[i][j],theta_xst8_0[i][j],dtheta_xst8_ast[i][j],b_xst8[i][j],dtheta_xst8_c[i][j]);
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairOxrna2Xstk::extract(const char *str, int &dim)
+{
+  dim = 2;
+
+  if (strcmp(str,"k_xst") == 0) return (void *) k_xst;
+  if (strcmp(str,"cut_xst_0") == 0) return (void *) cut_xst_0;
+  if (strcmp(str,"cut_xst_c") == 0) return (void *) cut_xst_c;
+  if (strcmp(str,"cut_xst_lo") == 0) return (void *) cut_xst_lo;
+  if (strcmp(str,"cut_xst_hi") == 0) return (void *) cut_xst_hi;
+  if (strcmp(str,"cut_xst_lc") == 0) return (void *) cut_xst_lc;
+  if (strcmp(str,"cut_xst_hc") == 0) return (void *) cut_xst_hc;
+  if (strcmp(str,"b_xst_lo") == 0) return (void *) b_xst_lo;
+  if (strcmp(str,"b_xst_hi") == 0) return (void *) b_xst_hi;
+
+  if (strcmp(str,"a_xst1") == 0) return (void *) a_xst1;
+  if (strcmp(str,"theta_xst1_0") == 0) return (void *) theta_xst1_0;
+  if (strcmp(str,"dtheta_xst1_ast") == 0) return (void *) dtheta_xst1_ast;
+  if (strcmp(str,"b_xst1") == 0) return (void *) b_xst1;
+  if (strcmp(str,"dtheta_xst1_c") == 0) return (void *) dtheta_xst1_c;
+
+  if (strcmp(str,"a_xst2") == 0) return (void *) a_xst2;
+  if (strcmp(str,"theta_xst2_0") == 0) return (void *) theta_xst2_0;
+  if (strcmp(str,"dtheta_xst2_ast") == 0) return (void *) dtheta_xst2_ast;
+  if (strcmp(str,"b_xst2") == 0) return (void *) b_xst2;
+  if (strcmp(str,"dtheta_xst2_c") == 0) return (void *) dtheta_xst2_c;
+
+  if (strcmp(str,"a_xst3") == 0) return (void *) a_xst3;
+  if (strcmp(str,"theta_xst3_0") == 0) return (void *) theta_xst3_0;
+  if (strcmp(str,"dtheta_xst3_ast") == 0) return (void *) dtheta_xst3_ast;
+  if (strcmp(str,"b_xst3") == 0) return (void *) b_xst3;
+  if (strcmp(str,"dtheta_xst3_c") == 0) return (void *) dtheta_xst3_c;
+
+  if (strcmp(str,"a_xst7") == 0) return (void *) a_xst7;
+  if (strcmp(str,"theta_xst7_0") == 0) return (void *) theta_xst7_0;
+  if (strcmp(str,"dtheta_xst7_ast") == 0) return (void *) dtheta_xst7_ast;
+  if (strcmp(str,"b_xst7") == 0) return (void *) b_xst7;
+  if (strcmp(str,"dtheta_xst7_c") == 0) return (void *) dtheta_xst7_c;
+
+  if (strcmp(str,"a_xst8") == 0) return (void *) a_xst8;
+  if (strcmp(str,"theta_xst8_0") == 0) return (void *) theta_xst8_0;
+  if (strcmp(str,"dtheta_xst8_ast") == 0) return (void *) dtheta_xst8_ast;
+  if (strcmp(str,"b_xst8") == 0) return (void *) b_xst8;
+  if (strcmp(str,"dtheta_xst8_c") == 0) return (void *) dtheta_xst8_c;
+
+  return NULL;
+}
diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.h b/src/USER-CGDNA/pair_oxrna2_xstk.h
new file mode 100644
index 0000000000..97e878c342
--- /dev/null
+++ b/src/USER-CGDNA/pair_oxrna2_xstk.h
@@ -0,0 +1,85 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(oxrna2/xstk,PairOxrna2Xstk)
+
+#else
+
+#ifndef LMP_PAIR_OXRNA2_XSTK_H
+#define LMP_PAIR_OXRNA2_XSTK_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairOxrna2Xstk : public Pair {
+ public:
+  PairOxrna2Xstk(class LAMMPS *);
+  virtual ~PairOxrna2Xstk();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  void init_list(int, class NeighList *);
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
+  void *extract(const char *, int &);
+
+ protected:
+  // cross-stacking interaction
+  double **k_xst, **cut_xst_0, **cut_xst_c, **cut_xst_lo, **cut_xst_hi;
+  double **cut_xst_lc, **cut_xst_hc, **b_xst_lo, **b_xst_hi;
+  double **cutsq_xst_hc;
+
+  double **a_xst1, **theta_xst1_0, **dtheta_xst1_ast;
+  double **b_xst1, **dtheta_xst1_c;
+
+  double **a_xst2, **theta_xst2_0, **dtheta_xst2_ast;
+  double **b_xst2, **dtheta_xst2_c;
+
+  double **a_xst3, **theta_xst3_0, **dtheta_xst3_ast;
+  double **b_xst3, **dtheta_xst3_c;
+
+  double **a_xst7, **theta_xst7_0, **dtheta_xst7_ast;
+  double **b_xst7, **dtheta_xst7_c;
+
+  double **a_xst8, **theta_xst8_0, **dtheta_xst8_ast;
+  double **b_xst8, **dtheta_xst8_c;
+
+  virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/
diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp
index 862c165bbd..11b3a8308c 100644
--- a/src/USER-CGSDK/angle_sdk.cpp
+++ b/src/USER-CGSDK/angle_sdk.cpp
@@ -30,6 +30,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 #include "lj_sdk_common.h"
 
@@ -332,9 +333,9 @@ void AngleSDK::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
-    fread(&repscale[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&repscale[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp
index 1301dc4155..3e4f8deee8 100644
--- a/src/USER-CGSDK/pair_lj_sdk.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk.cpp
@@ -26,6 +26,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 #define LMP_NEED_SDK_FIND_LJ_TYPE 1
 #include "lj_sdk_common.h"
@@ -373,14 +374,14 @@ void PairLJSDK::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&lj_type[i][j],sizeof(int),1,fp);
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&lj_type[i][j],sizeof(int),1,fp,NULL,error);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world);
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
@@ -410,10 +411,10 @@ void PairLJSDK::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
index 62acf00d27..5721e72d08 100644
--- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
@@ -28,6 +28,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 #define LMP_NEED_SDK_FIND_LJ_TYPE 1
 #include "lj_sdk_common.h"
@@ -465,14 +466,14 @@ void PairLJSDKCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&lj_type[i][j],sizeof(int),1,fp);
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&lj_type[i][j],sizeof(int),1,fp,NULL,error);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world);
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
@@ -504,13 +505,13 @@ void PairLJSDKCoulLong::write_restart_settings(FILE *fp)
 void PairLJSDKCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp
index a1369df2fb..3756208212 100644
--- a/src/USER-COLVARS/ndx_group.cpp
+++ b/src/USER-COLVARS/ndx_group.cpp
@@ -126,7 +126,7 @@ void Ndx2Group::command(int narg, char **arg)
         }
         name = find_section(fp,NULL);
         if (name != NULL) {
-          len=strlen(name);
+          len=strlen(name)+1;
 
           // skip over group "all", which is called "System" in gromacs
           if (strcmp(name,"System") == 0) continue;
@@ -152,8 +152,8 @@ void Ndx2Group::command(int narg, char **arg)
         MPI_Bcast(&len,1,MPI_INT,0,world);
         if (len > 0) {
           delete[] name;
-          name = new char[len+1];
-          MPI_Bcast(name,len+1,MPI_CHAR,0,world);
+          name = new char[len];
+          MPI_Bcast(name,len,MPI_CHAR,0,world);
 
           MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
           tags = (tagint *)malloc(sizeof(tagint)*(num ? num : 1));
@@ -174,7 +174,7 @@ void Ndx2Group::command(int narg, char **arg)
         if (name != NULL) delete[] name;
         rewind(fp);
         name = find_section(fp,arg[idx]);
-        if (name != NULL) len=strlen(name);
+        if (name != NULL) len=strlen(name)+1;
 
         if (screen)
           fprintf(screen," %s group '%s'\n",
@@ -185,7 +185,7 @@ void Ndx2Group::command(int narg, char **arg)
 
         MPI_Bcast(&len,1,MPI_INT,0,world);
         if (len > 0) {
-          MPI_Bcast(name,len+1,MPI_CHAR,0,world);
+          MPI_Bcast(name,len,MPI_CHAR,0,world);
           // read tags for atoms in group and broadcast
           num = 0;
           tags = read_section(fp,num);
@@ -199,8 +199,8 @@ void Ndx2Group::command(int narg, char **arg)
         MPI_Bcast(&len,1,MPI_INT,0,world);
         if (len > 0) {
           delete[] name;
-          name = new char[len+1];
-          MPI_Bcast(name,len+1,MPI_CHAR,0,world);
+          name = new char[len];
+          MPI_Bcast(name,len,MPI_CHAR,0,world);
 
           MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
           tags = (tagint *)malloc(sizeof(tagint)*(num ? num : 1));
diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp
index 971d9bd380..3ae25f223c 100644
--- a/src/USER-DIFFRACTION/compute_saed.cpp
+++ b/src/USER-DIFFRACTION/compute_saed.cpp
@@ -510,7 +510,7 @@ void ComputeSAED::compute_vector()
 
   if (me == 0 && echo) {
     if (screen)
-      fprintf(screen," 100%% \nTime ellapsed during compute_saed = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0,  bytes/1024.0/1024.0);
+      fprintf(screen," 100%% \nTime elapsed during compute_saed = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0,  bytes/1024.0/1024.0);
   }
 
   delete [] xlocal;
diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp
index f48951f1ff..7f69449282 100644
--- a/src/USER-DIFFRACTION/compute_xrd.cpp
+++ b/src/USER-DIFFRACTION/compute_xrd.cpp
@@ -513,7 +513,7 @@ void ComputeXRD::compute_array()
 
   if (me == 0 && echo) {
     if (screen)
-      fprintf(screen," 100%% \nTime ellapsed during compute_xrd = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0);
+      fprintf(screen," 100%% \nTime elapsed during compute_xrd = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0);
   }
 
   delete [] scratch;
diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp
index ff9a186c47..dc6310ae42 100644
--- a/src/USER-DPD/fix_eos_table.cpp
+++ b/src/USER-DPD/fix_eos_table.cpp
@@ -23,6 +23,7 @@
 #include "error.h"
 #include "force.h"
 #include "memory.h"
+#include "utils.h"
 
 #define MAXLINE 1024
 
@@ -214,16 +215,16 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
     if (line[0] == '#') continue;                          // comment
     char *word = strtok(line," \t\n\r");
     if (strcmp(word,keyword) == 0) break;           // matching keyword
-    fgets(line,MAXLINE,fp);                         // no match, skip section
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);                         // no match, skip section
     param_extract(tb,tb2,line);
-    fgets(line,MAXLINE,fp);
-    for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
+    for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   }
 
   // read args on 2nd line of section
   // allocate table arrays for file values
 
-  fgets(line,MAXLINE,fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   param_extract(tb,tb2,line);
   memory->create(tb->rfile,tb->ninput,"eos:rfile");
   memory->create(tb->efile,tb->ninput,"eos:efile");
@@ -233,9 +234,9 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
   // read r,e table values from file
 
   int itmp;
-  fgets(line,MAXLINE,fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   for (int i = 0; i < tb->ninput; i++) {
-    fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
     sscanf(line,"%d %lg %lg",&itmp,&tb->rfile[i],&tb->efile[i]);
     sscanf(line,"%d %lg %lg",&itmp,&tb2->efile[i],&tb2->rfile[i]);
   }
diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp
index 9f1bd6a3bb..152b58dbb7 100644
--- a/src/USER-DPD/fix_eos_table_rx.cpp
+++ b/src/USER-DPD/fix_eos_table_rx.cpp
@@ -26,6 +26,7 @@
 #include "memory.h"
 #include "comm.h"
 #include "modify.h"
+#include "utils.h"
 
 #define MAXLINE 1024
 
@@ -433,16 +434,16 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
     if (line[0] == '#') continue;                          // comment
     char *word = strtok(line," \t\n\r");
     if (strcmp(word,keyword) == 0) break;           // matching keyword
-    fgets(line,MAXLINE,fp);                         // no match, skip section
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);                         // no match, skip section
     param_extract(tb,line);
-    fgets(line,MAXLINE,fp);
-    for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
+    for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   }
 
   // read args on 2nd line of section
   // allocate table arrays for file values
 
-  fgets(line,MAXLINE,fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   param_extract(tb,line);
   tb2->ninput = tb->ninput;
   memory->create(tb->rfile,tb->ninput,"eos:rfile");
@@ -470,9 +471,9 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
   int ispecies;
   int ninputs = tb->ninput;
 
-  fgets(line,MAXLINE,fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   for (int i = 0; i < ninputs; i++) {
-    fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
 
     nwords = atom->count_words(line);
     if(nwords != nspecies+2){
diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp
index 1cb9d68d06..5b62972d1b 100644
--- a/src/USER-DPD/pair_dpd_fdt.cpp
+++ b/src/USER-DPD/pair_dpd_fdt.cpp
@@ -30,6 +30,7 @@
 #include "memory.h"
 #include "modify.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -313,7 +314,7 @@ void PairDPDfdt::init_style()
     error->all(FLERR,"Pair dpd/fdt requires ghost atoms store velocity");
 
   splitFDT_flag = false;
-  int irequest = neighbor->request(this,instance_me);
+  neighbor->request(this,instance_me);
   for (int i = 0; i < modify->nfix; i++)
     if (strncmp(modify->fix[i]->style,"shardlow", 8) == 0){
       splitFDT_flag = true;
@@ -375,13 +376,13 @@ void PairDPDfdt::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a0[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -410,10 +411,10 @@ void PairDPDfdt::write_restart_settings(FILE *fp)
 void PairDPDfdt::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&temperature,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&seed,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&temperature,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp
index 22741a055d..5ea8d2e9e1 100644
--- a/src/USER-DPD/pair_dpd_fdt_energy.cpp
+++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp
@@ -30,6 +30,7 @@
 #include "memory.h"
 #include "modify.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -406,7 +407,7 @@ void PairDPDfdtEnergy::init_style()
     error->all(FLERR,"Pair dpd/fdt/energy requires ghost atoms store velocity");
 
   splitFDT_flag = false;
-  int irequest = neighbor->request(this,instance_me);
+  neighbor->request(this,instance_me);
   for (int i = 0; i < modify->nfix; i++)
     if (strncmp(modify->fix[i]->style,"shardlow", 8) == 0){
       splitFDT_flag = true;
@@ -476,14 +477,14 @@ void PairDPDfdtEnergy::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a0[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&kappa[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&kappa[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -513,9 +514,9 @@ void PairDPDfdtEnergy::write_restart_settings(FILE *fp)
 void PairDPDfdtEnergy::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&seed,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&seed,1,MPI_INT,0,world);
diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp
index 5cf2859ae3..5e23113feb 100644
--- a/src/USER-DPD/pair_exp6_rx.cpp
+++ b/src/USER-DPD/pair_exp6_rx.cpp
@@ -24,6 +24,7 @@
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "modify.h"
 #include "fix.h"
 
@@ -968,11 +969,11 @@ void PairExp6rx::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
       }
@@ -998,10 +999,10 @@ void PairExp6rx::write_restart_settings(FILE *fp)
 void PairExp6rx::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp
index ffc1562f88..1cbb29a93c 100644
--- a/src/USER-DPD/pair_multi_lucy.cpp
+++ b/src/USER-DPD/pair_multi_lucy.cpp
@@ -33,7 +33,9 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "citeme.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -362,16 +364,16 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword)
     if (line[0] == '#') continue;                          // comment
     char *word = strtok(line," \t\n\r");
     if (strcmp(word,keyword) == 0) break;           // matching keyword
-    fgets(line,MAXLINE,fp);                         // no match, skip section
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);                         // no match, skip section
     param_extract(tb,line);
-    fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
     for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
   }
 
   // read args on 2nd line of section
-  // allocate table arrays for file values
+  // allocate table arrays for file valuesutils::s
 
-  fgets(line,MAXLINE,fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   param_extract(tb,line);
   memory->create(tb->rfile,tb->ninput,"pair:rfile");
   memory->create(tb->efile,tb->ninput,"pair:efile");
@@ -384,9 +386,9 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword)
   int itmp;
   double rtmp;
 
-  fgets(line,MAXLINE,fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   for (int i = 0; i < tb->ninput; i++) {
-    fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
     sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]);
 
     if (tb->rflag == RLINEAR)
@@ -705,8 +707,8 @@ void PairMultiLucy::write_restart_settings(FILE *fp)
 void PairMultiLucy::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&tabstyle,sizeof(int),1,fp);
-    fread(&tablength,sizeof(int),1,fp);
+    utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
   MPI_Bcast(&tablength,1,MPI_INT,0,world);
diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp
index 801e8ff039..36ca7e0321 100644
--- a/src/USER-DPD/pair_multi_lucy_rx.cpp
+++ b/src/USER-DPD/pair_multi_lucy_rx.cpp
@@ -33,9 +33,11 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "citeme.h"
 #include "modify.h"
 #include "fix.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -507,16 +509,16 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword)
     if (line[0] == '#') continue;                          // comment
     char *word = strtok(line," \t\n\r");
     if (strcmp(word,keyword) == 0) break;           // matching keyword
-    fgets(line,MAXLINE,fp);                         // no match, skip section
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);                         // no match, skip section
     param_extract(tb,line);
-    fgets(line,MAXLINE,fp);
-    for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
+    for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   }
 
   // read args on 2nd line of section
   // allocate table arrays for file values
 
-  fgets(line,MAXLINE,fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   param_extract(tb,line);
   memory->create(tb->rfile,tb->ninput,"pair:rfile");
   memory->create(tb->efile,tb->ninput,"pair:efile");
@@ -529,9 +531,9 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword)
   int itmp;
   double rtmp;
 
-  fgets(line,MAXLINE,fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
   for (int i = 0; i < tb->ninput; i++) {
-    fgets(line,MAXLINE,fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
     sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]);
 
     if (tb->rflag == RLINEAR)
@@ -850,8 +852,8 @@ void PairMultiLucyRX::write_restart_settings(FILE *fp)
 void PairMultiLucyRX::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&tabstyle,sizeof(int),1,fp);
-    fread(&tablength,sizeof(int),1,fp);
+    utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
   MPI_Bcast(&tablength,1,MPI_INT,0,world);
diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
index 851effd89c..98c2ff196a 100644
--- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
+++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
@@ -29,6 +29,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "modify.h"
 #include "domain.h"
 
@@ -357,7 +358,7 @@ void PairLJCutTholeLong::init_style()
       error->all(FLERR, "Pair style lj/cut/thole/long requires fix drude");
   fix_drude = (FixDrude *) modify->fix[ifix];
 
-  int irequest = neighbor->request(this,instance_me);
+  neighbor->request(this,instance_me);
 
   cut_coulsq = cut_coul * cut_coul;
 
@@ -488,16 +489,16 @@ void PairLJCutTholeLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&polar[i][j],sizeof(double),1,fp);
-          fread(&thole[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&polar[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&thole[i][j],sizeof(double),1,fp,NULL,error);
           ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -533,15 +534,15 @@ void PairLJCutTholeLong::write_restart_settings(FILE *fp)
 void PairLJCutTholeLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&thole_global,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&thole_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp
index 1f81263e95..6eadfa8bf6 100644
--- a/src/USER-DRUDE/pair_thole.cpp
+++ b/src/USER-DRUDE/pair_thole.cpp
@@ -22,6 +22,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "fix.h"
 #include "fix_drude.h"
 #include "domain.h"
@@ -311,13 +312,13 @@ void PairThole::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&polar[i][j],sizeof(double),1,fp);
-          fread(&thole[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&polar[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&thole[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
           ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
           }
         MPI_Bcast(&polar[i][j],1,MPI_DOUBLE,0,world);
@@ -347,10 +348,10 @@ void PairThole::write_restart_settings(FILE *fp)
 void PairThole::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&thole_global,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&thole_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&thole_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp
index a4c0557620..e7aed14030 100644
--- a/src/USER-EFF/pair_eff_cut.cpp
+++ b/src/USER-EFF/pair_eff_cut.cpp
@@ -31,6 +31,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -965,10 +966,10 @@ void PairEffCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
-        if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
+        if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
       }
     }
@@ -992,9 +993,9 @@ void PairEffCut::write_restart_settings(FILE *fp)
 void PairEffCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp
index a4ff3ca846..eb872ab8b9 100644
--- a/src/USER-FEP/pair_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_coul_cut_soft.cpp
@@ -26,12 +26,15 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairCoulCutSoft::PairCoulCutSoft(LAMMPS *lmp) : Pair(lmp) {}
+PairCoulCutSoft::PairCoulCutSoft(LAMMPS *lmp) : Pair(lmp) {
+  centroidstressflag = 1;
+}
 
 /* ---------------------------------------------------------------------- */
 
@@ -272,12 +275,12 @@ void PairCoulCutSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -306,12 +309,12 @@ void PairCoulCutSoft::write_restart_settings(FILE *fp)
 void PairCoulCutSoft::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphac,sizeof(double),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp
index c0030f8935..a631dca1b7 100644
--- a/src/USER-FEP/pair_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_coul_long_soft.cpp
@@ -28,6 +28,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -294,11 +295,11 @@ void PairCoulLongSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0)
-          fread(&lambda[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
         MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
       }
     }
@@ -325,12 +326,12 @@ void PairCoulLongSoft::write_restart_settings(FILE *fp)
 void PairCoulLongSoft::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphac,sizeof(double),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
index 4c3be6addb..f20d351d1c 100644
--- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
@@ -31,6 +31,7 @@
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -836,15 +837,15 @@ void PairLJCharmmCoulLongSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&eps14[i][j],sizeof(double),1,fp);
-          fread(&sigma14[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -879,15 +880,15 @@ void PairLJCharmmCoulLongSoft::write_restart_settings(FILE *fp)
 void PairLJCharmmCoulLongSoft::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphalj,sizeof(double),1,fp);
-    fread(&alphac,sizeof(double),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_inner,sizeof(double),1,fp);
-    fread(&cut_lj,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
 
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp
index bbe67e4ff3..255bdf6a07 100644
--- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp
@@ -23,6 +23,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -32,6 +33,7 @@ using namespace MathConst;
 PairLJClass2CoulCutSoft::PairLJClass2CoulCutSoft(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -380,15 +382,15 @@ void PairLJClass2CoulCutSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
-          fread(&cut_coul[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -423,15 +425,15 @@ void PairLJClass2CoulCutSoft::write_restart_settings(FILE *fp)
 void PairLJClass2CoulCutSoft::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphalj,sizeof(double),1,fp);
-    fread(&alphac,sizeof(double),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp
index a3e0f732a2..dda10ed9e0 100644
--- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp
@@ -24,6 +24,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -396,14 +397,14 @@ void PairLJClass2CoulLongSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -437,15 +438,15 @@ void PairLJClass2CoulLongSoft::write_restart_settings(FILE *fp)
 void PairLJClass2CoulLongSoft::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphalj,sizeof(double),1,fp);
-    fread(&alphac,sizeof(double),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp
index d98a5db5f3..957fc0f8ab 100644
--- a/src/USER-FEP/pair_lj_class2_soft.cpp
+++ b/src/USER-FEP/pair_lj_class2_soft.cpp
@@ -22,6 +22,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -31,6 +32,7 @@ using namespace MathConst;
 PairLJClass2Soft::PairLJClass2Soft(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -319,14 +321,14 @@ void PairLJClass2Soft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -358,12 +360,12 @@ void PairLJClass2Soft::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphalj,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
index 38fcb6fc07..3f85a2c8aa 100644
--- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -36,6 +37,7 @@ using namespace MathConst;
 PairLJCutCoulCutSoft::PairLJCutCoulCutSoft(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -376,15 +378,15 @@ void PairLJCutCoulCutSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
-          fread(&cut_coul[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -419,15 +421,15 @@ void PairLJCutCoulCutSoft::write_restart_settings(FILE *fp)
 void PairLJCutCoulCutSoft::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphalj,sizeof(double),1,fp);
-    fread(&alphac,sizeof(double),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
 
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
index 740daabf62..cf80a3e405 100644
--- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
@@ -32,6 +32,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -792,14 +793,14 @@ void PairLJCutCoulLongSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -833,15 +834,15 @@ void PairLJCutCoulLongSoft::write_restart_settings(FILE *fp)
 void PairLJCutCoulLongSoft::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphalj,sizeof(double),1,fp);
-    fread(&alphac,sizeof(double),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
 
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp
index 5e9a77877e..9d03b4e1e2 100644
--- a/src/USER-FEP/pair_lj_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_soft.cpp
@@ -31,6 +31,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -42,6 +43,7 @@ PairLJCutSoft::PairLJCutSoft(LAMMPS *lmp) : Pair(lmp)
   respa_enable = 1;
   writedata = 1;
   allocated = 0;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -653,14 +655,14 @@ void PairLJCutSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -693,13 +695,13 @@ void PairLJCutSoft::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&nlambda,sizeof(double),1,fp);
-    fread(&alphalj,sizeof(double),1,fp);
+    utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
index d4f6dcb910..0601a641ac 100644
--- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
@@ -31,6 +31,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -516,17 +517,17 @@ void PairLJCutTIP4PLongSoft::read_restart_settings(FILE *fp)
   PairLJCutCoulLongSoft::read_restart_settings(fp);
 
   if (comm->me == 0) {
-    fread(&typeO,sizeof(int),1,fp);
-    fread(&typeH,sizeof(int),1,fp);
-    fread(&typeB,sizeof(int),1,fp);
-    fread(&typeA,sizeof(int),1,fp);
-    fread(&qdist,sizeof(double),1,fp);
+    utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
 
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
 
   MPI_Bcast(&typeO,1,MPI_INT,0,world);
diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp
index 2803e7df49..54123bf3cd 100644
--- a/src/USER-FEP/pair_morse_soft.cpp
+++ b/src/USER-FEP/pair_morse_soft.cpp
@@ -22,6 +22,7 @@
 #include "memory.h"
 #include "math_special.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;
@@ -312,15 +313,15 @@ void PairMorseSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&d0[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&r0[i][j],sizeof(double),1,fp);
-          fread(&lambda[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp
index 9cea5b54c5..d5e1ae116c 100644
--- a/src/USER-FEP/pair_tip4p_long_soft.cpp
+++ b/src/USER-FEP/pair_tip4p_long_soft.cpp
@@ -31,6 +31,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -453,11 +454,11 @@ void PairTIP4PLongSoft::read_restart_settings(FILE *fp)
   PairCoulLongSoft::read_restart_settings(fp);
 
   if (comm->me == 0) {
-    fread(&typeO,sizeof(int),1,fp);
-    fread(&typeH,sizeof(int),1,fp);
-    fread(&typeB,sizeof(int),1,fp);
-    fread(&typeA,sizeof(int),1,fp);
-    fread(&qdist,sizeof(double),1,fp);
+    utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&typeO,1,MPI_INT,0,world);
   MPI_Bcast(&typeH,1,MPI_INT,0,world);
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 83a22f0562..5ecae79b30 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -16,6 +16,7 @@
                         Anupama Kurpad (Intel) - Host Affinitization
 ------------------------------------------------------------------------- */
 
+#include "fix_intel.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -27,7 +28,7 @@
 #include "timer.h"
 #include "universe.h"
 #include "update.h"
-#include "fix_intel.h"
+#include "utils.h"
 
 #include <cstring>
 #include <cstdlib>
@@ -63,6 +64,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) :  Fix(lmp, narg, arg)
   _three_body_neighbor = 0;
   _pair_intel_count = 0;
   _hybrid_nonpair = 0;
+  _print_pkg_info = 1;
 
   _precision_mode = PREC_MODE_MIXED;
   _offload_balance = -1.0;
@@ -290,6 +292,7 @@ int FixIntel::setmask()
   mask |= POST_FORCE;
   mask |= MIN_POST_FORCE;
   #endif
+  mask |= POST_RUN;
   return mask;
 }
 
@@ -310,12 +313,7 @@ void FixIntel::init()
   #endif
 
   const int nstyles = _pair_intel_count;
-  if (force->pair_match("hybrid", 1) != NULL) {
-    _pair_hybrid_flag = 1;
-    if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute)
-      error->all(FLERR,
-                 "Intel package requires fdotr virial with newton on.");
-  } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
+  if (force->pair_match("^hybrid", 0) != NULL) {
     _pair_hybrid_flag = 1;
     if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute)
       error->all(FLERR,
@@ -394,6 +392,20 @@ void FixIntel::setup_pre_reverse(int eflag, int vflag)
 
 /* ---------------------------------------------------------------------- */
 
+bool FixIntel::pair_hybrid_check()
+{
+  PairHybrid *ph = (PairHybrid *)force->pair;
+  bool has_intel = false;
+  int nstyles = ph->nstyles;
+
+  for (int i = 0; i < nstyles; ++i)
+    if (ph->styles[i]->suffix_flag & Suffix::INTEL) has_intel = true;
+
+  return has_intel;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void FixIntel::pair_init_check(const bool cdmessage)
 {
   #ifdef INTEL_VMASK
@@ -475,7 +487,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
   set_offload_affinity();
   #endif
 
-  if (comm->me == 0) {
+  if (_print_pkg_info && comm->me == 0) {
     if (screen) {
       fprintf(screen,
               "----------------------------------------------------------\n");
@@ -498,6 +510,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
               "----------------------------------------------------------\n");
     }
   }
+  _print_pkg_info = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -510,14 +523,11 @@ void FixIntel::bond_init_check()
       "USER-INTEL package requires same setting for newton bond and non-bond.");
 
   int intel_pair = 0;
-  if (force->pair_match("/intel", 0) != NULL)
+  if (force->pair_match("/intel$", 0) != NULL)
     intel_pair = 1;
-  else if (force->pair_match("hybrid", 1) != NULL) {
+  else if (force->pair_match("^hybrid", 0) != NULL) {
     _hybrid_nonpair = 1;
-    if (_pair_intel_count) intel_pair = 1;
-  } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
-    _hybrid_nonpair = 1;
-    if (_pair_intel_count) intel_pair = 1;
+    if (pair_hybrid_check()) intel_pair = 1;
   }
 
   if (intel_pair == 0)
@@ -530,14 +540,11 @@ void FixIntel::bond_init_check()
 void FixIntel::kspace_init_check()
 {
   int intel_pair = 0;
-  if (force->pair_match("/intel", 0) != NULL)
+  if (force->pair_match("/intel$", 0) != NULL)
     intel_pair = 1;
-  else if (force->pair_match("hybrid", 1) != NULL) {
+  else if (force->pair_match("^hybrid", 0) != NULL) {
     _hybrid_nonpair = 1;
-    if (_pair_intel_count) intel_pair = 1;
-  } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
-    _hybrid_nonpair = 1;
-    if (_pair_intel_count) intel_pair = 1;
+    if (pair_hybrid_check()) intel_pair = 1;
   }
 
   if (intel_pair == 0)
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index f23e305ca7..4c50164d31 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -46,6 +46,7 @@ class FixIntel : public Fix {
   inline void min_setup(int in) { setup(in); }
   void setup_pre_reverse(int eflag = 0, int vflag = 0);
 
+  bool pair_hybrid_check();
   void pair_init_check(const bool cdmessage=false);
   void bond_init_check();
   void kspace_init_check();
@@ -54,6 +55,8 @@ class FixIntel : public Fix {
   inline void min_pre_reverse(int eflag = 0, int vflag = 0)
     { pre_reverse(eflag, vflag); }
 
+  void post_run() { _print_pkg_info = 1; }
+
   // Get all forces, calculation results from coprocesser
   void sync_coprocessor();
 
@@ -83,13 +86,12 @@ class FixIntel : public Fix {
   }
   inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; }
   inline int lrt() {
-    if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1)
+    if (force->kspace_match("^pppm/.*intel$", 0) && update->whichflag == 1)
       return _lrt;
     else return 0;
   }
   inline int pppm_table() {
-    if (force->kspace_match("pppm/intel", 0) ||
-        force->kspace_match("pppm/disp/intel",0))
+    if (force->kspace_match("^pppm/.*intel$", 0))
       return INTEL_P3M_TABLE;
     else return 0;
   }
@@ -101,7 +103,7 @@ class FixIntel : public Fix {
   IntelBuffers<double,double> *_double_buffers;
 
   int _precision_mode, _nthreads, _nbor_pack_width, _three_body_neighbor;
-  int _pair_intel_count, _pair_hybrid_flag;
+  int _pair_intel_count, _pair_hybrid_flag, _print_pkg_info;
   // These should be removed in subsequent update w/ simpler hybrid arch
   int _pair_hybrid_zero, _hybrid_nonpair, _zero_master;
 
diff --git a/src/USER-INTEL/intel_intrinsics.h b/src/USER-INTEL/intel_intrinsics.h
index 069eb5bed5..ee20cd1119 100644
--- a/src/USER-INTEL/intel_intrinsics.h
+++ b/src/USER-INTEL/intel_intrinsics.h
@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing author: Markus Höhnerbach (RWTH)
+   Contributing author: Markus Hoehnerbach (RWTH)
 ------------------------------------------------------------------------- */
 
 // This file provides an intrinsics abstraction that allows access to the
diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp
index 8359587eb2..78c6246389 100644
--- a/src/USER-INTEL/nbin_intel.cpp
+++ b/src/USER-INTEL/nbin_intel.cpp
@@ -56,6 +56,8 @@ NBinIntel::~NBinIntel() {
       nocopy(binhead,bins,_atombin,_binpacked:alloc_if(0) free_if(1))
   }
   #endif
+  memory->destroy(_atombin);
+  memory->destroy(_binpacked);
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
index e1e09fd3da..00b032d495 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
@@ -150,8 +150,8 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
   const int nlocal = atom->nlocal;
 
   #ifndef _LMP_INTEL_OFFLOAD
-  int * const mask = atom->mask;
-  tagint * const molecule = atom->molecule;
+  int * _noalias const mask = atom->mask;
+  tagint * _noalias const molecule = atom->molecule;
   #endif
 
   int moltemplate;
@@ -162,7 +162,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
                "Can't use moltemplate with npair style full/bin/ghost/intel.");
 
   int tnum;
-  int *overflow;
+  int * _noalias overflow;
   #ifdef _LMP_INTEL_OFFLOAD
   double *timer_compute;
   if (offload) {
@@ -200,7 +200,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
   const int mbinx = this->mbinx;
   const int mbiny = this->mbiny;
   const int mbinz = this->mbinz;
-  const int * const stencilxyz = &this->stencilxyz[0][0];
+  const int * _noalias const stencilxyz = &this->stencilxyz[0][0];
 
   int sb = 1;
   if (special_flag[1] == 0) {
@@ -295,7 +295,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
 
       int pack_offset = maxnbors;
       int ct = (ifrom + tid * 2) * maxnbors;
-      int *neighptr = intel_list + ct;
+      int * _noalias neighptr = intel_list + ct;
       const int obound = pack_offset + maxnbors * 2;
 
       const int toffs = tid * ncache_stride;
@@ -370,7 +370,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
 
         int n = maxnbors;
         int n2 = n * 2;
-        int *neighptr2 = neighptr;
+        int * _noalias neighptr2 = neighptr;
         const flt_t * _noalias cutsq;
         if (i < nlocal) cutsq = cutneighsq;
         else cutsq = cutneighghostsq;
diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
index ad9ec6e7d3..4256e03b3c 100644
--- a/src/USER-INTEL/npair_intel.cpp
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -154,12 +154,12 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
   const int nlocal = atom->nlocal;
 
   #ifndef _LMP_INTEL_OFFLOAD
-  int * const mask = atom->mask;
-  tagint * const molecule = atom->molecule;
+  int * _noalias const mask = atom->mask;
+  tagint * _noalias const molecule = atom->molecule;
   #endif
 
   int tnum;
-  int *overflow;
+  int * _noalias overflow;
   #ifdef _LMP_INTEL_OFFLOAD
   double *timer_compute;
   if (offload) {
@@ -298,8 +298,8 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
       const int obound = maxnbors * 3;
       #endif
       int ct = (ifrom + tid * 2) * maxnbors;
-      int *neighptr = intel_list + ct;
-      int *neighptr2;
+      int * _noalias neighptr = intel_list + ct;
+      int * _noalias neighptr2;
       if (THREE) neighptr2 = neighptr;
 
       const int toffs = tid * ncache_stride;
@@ -360,7 +360,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
             if (THREE) ttag[u] = tag[j];
           }
 
-          if (FULL == 0 || TRI == 1) {
+          if (FULL == 0 && TRI != 1) {
             icount = 0;
             istart = ncount;
             IP_PRE_edge_align(istart, sizeof(int));
@@ -392,7 +392,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
         // ---------------------- Loop over i bin
 
         int n = 0;
-        if (FULL == 0 || TRI == 1) {
+        if (FULL == 0 && TRI != 1) {
           #if defined(LMP_SIMD_COMPILER)
           #pragma vector aligned
           #pragma ivdep
diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp
index 4ebdce9a96..690496d546 100644
--- a/src/USER-INTEL/pair_dpd_intel.cpp
+++ b/src/USER-INTEL/pair_dpd_intel.cpp
@@ -283,7 +283,7 @@ void PairDPDIntel::eval(const int offload, const int vflag,
         }
 
         #if defined(LMP_SIMD_COMPILER)
-        #pragma vector aligned
+        #pragma vector aligned nog2s
         #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \
                                  sv0, sv1, sv2, sv3, sv4, sv5)
         #endif
diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp
index 32d7e74cbc..984823f07e 100644
--- a/src/USER-INTEL/pair_eam_intel.cpp
+++ b/src/USER-INTEL/pair_eam_intel.cpp
@@ -305,7 +305,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
         acc_t rhoi = (acc_t)0.0;
         int ej = 0;
         #if defined(LMP_SIMD_COMPILER)
-        #pragma vector aligned
+        #pragma vector aligned nog2s
         #pragma ivdep
         #endif
         for (int jj = 0; jj < jnum; jj++) {
@@ -324,7 +324,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
         }
 
         #if defined(LMP_SIMD_COMPILER)
-        #pragma vector aligned
+        #pragma vector aligned nog2s
         #pragma simd reduction(+:rhoi)
         #endif
         for (int jj = 0; jj < ej; jj++) {
@@ -411,7 +411,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
       if (EFLAG) tevdwl = (acc_t)0.0;
 
       #if defined(LMP_SIMD_COMPILER)
-      #pragma vector aligned
+      #pragma vector aligned nog2s
       #pragma simd reduction(+:tevdwl)
       #endif
       for (int ii = iifrom; ii < iito; ++ii) {
@@ -485,7 +485,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
 
         int ej = 0;
         #if defined(LMP_SIMD_COMPILER)
-        #pragma vector aligned
+        #pragma vector aligned nog2s
         #pragma ivdep
         #endif
         for (int jj = 0; jj < jnum; jj++) {
@@ -507,7 +507,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
         }
 
         #if defined(LMP_SIMD_COMPILER)
-        #pragma vector aligned
+        #pragma vector aligned nog2s
         #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \
                                  sv0, sv1, sv2, sv3, sv4, sv5)
         #endif
diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/USER-INTEL/pair_gayberne_intel.cpp
index 862dee2287..30e61f67b9 100644
--- a/src/USER-INTEL/pair_gayberne_intel.cpp
+++ b/src/USER-INTEL/pair_gayberne_intel.cpp
@@ -555,10 +555,10 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
           dchi_2 = temp2 * (iota_2 - temp1 * r12hat_2);
 
           temp1 = -eta * u_r;
-          temp2 = eta * chi;
-          fforce_0 = temp1 * dchi_0 - temp2 * dUr_0;
-          fforce_1 = temp1 * dchi_1 - temp2 * dUr_1;
-          fforce_2 = temp1 * dchi_2 - temp2 * dUr_2;
+          temp3 = eta * chi;
+          fforce_0 = temp1 * dchi_0 - temp3 * dUr_0;
+          fforce_1 = temp1 * dchi_1 - temp3 * dUr_1;
+          fforce_2 = temp1 * dchi_2 - temp3 * dUr_2;
 
           // torque for particle 1 and 2
           // compute dUr
@@ -579,18 +579,17 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
 
           ME_vecmat(iota, b1, tempv);
           ME_cross3(tempv, iota, dchi);
-          temp1 = (flt_t)-4.0 / rsq_form[jj];
-          dchi_0 *= temp1;
-          dchi_1 *= temp1;
-          dchi_2 *= temp1;
+          dchi_0 *= temp2;
+          dchi_1 *= temp2;
+          dchi_2 *= temp2;
           flt_t dchi2_0, dchi2_1, dchi2_2;
 
           if (NEWTON_PAIR) {
             ME_vecmat(iota, b2, tempv);
             ME_cross3(tempv, iota, dchi2);
-            dchi2_0 *= temp1;
-            dchi2_1 *= temp1;
-            dchi2_2 *= temp1;
+            dchi2_0 *= temp2;
+            dchi2_1 *= temp2;
+            dchi2_2 *= temp2;
           }
 
           // compute d_eta
diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
index 929ac2123f..243c7f577d 100644
--- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
@@ -525,8 +525,10 @@ void PairLJCutCoulLongIntel::pack_force_const(ForceConst<flt_t> &fc,
       double cut;
       if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0))
         cut = init_one(i, j);
-      else
+      else { // need to set cutsq and cut_ljsq for hybrid pair_style
         cut = 0.0;
+        cut_ljsq[i][j] = cut_ljsq[j][i] = 0.0;
+      }
       cutsq[i][j] = cutsq[j][i] = cut*cut;
     }
   }
diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp
index 39db9c7333..b484cb68d9 100644
--- a/src/USER-INTEL/pair_lj_cut_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_intel.cpp
@@ -236,7 +236,7 @@ void PairLJCutIntel::eval(const int offload, const int vflag,
           if (vflag==1) sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0;
 
         #if defined(LMP_SIMD_COMPILER)
-        #pragma vector aligned
+        #pragma vector aligned nog2s
         #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \
                                sv0, sv1, sv2, sv3, sv4, sv5)
         #endif
@@ -459,11 +459,8 @@ void PairLJCutIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
                                                    const int cop) {
   if (ntypes != _ntypes) {
     if (_ntypes > 0) {
-      fc_packed1 *oljc12o = ljc12o[0];
-      fc_packed2 *olj34 = lj34[0];
-
-      _memory->destroy(oljc12o);
-      _memory->destroy(olj34);
+      _memory->destroy(ljc12o);
+      _memory->destroy(lj34);
     }
     if (ntypes > 0) {
       _cop = cop;
diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 4e5b298ffb..719e1af6f0 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -2,13 +2,15 @@
 #define LMP_MEAM_H
 
 #include <cmath>
+#include <cstring>
+#include "math_const.h"
 
 #define maxelt 5
 
 namespace LAMMPS_NS {
 class Memory;
 
-typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t;
+typedef enum { FCC, BCC, HCP, DIM, DIA, DIA3, B1, C11, L12, B2, CH4, LIN, ZIG, TRI } lattice_t;
 
 class MEAM
 {
@@ -26,9 +28,7 @@ private:
 
   // Ec_meam = cohesive energy
   // re_meam = nearest-neighbor distance
-  // Omega_meam = atomic volume
   // B_meam = bulk modulus
-  // Z_meam = number of first neighbors for reference structure
   // ielt_meam = atomic number of element
   // A_meam = adjustable parameter
   // alpha_meam = sqrt(9*Omega*B/Ec)
@@ -64,8 +64,11 @@ private:
   // nr,dr = pair function discretization parameters
   // nrar,rdrar = spline coeff array parameters
 
+  // theta = angle between three atoms in line, zigzag, and trimer reference structures
+  // stheta_meam = sin(theta/2) in radian used in line, zigzag, and trimer reference structures
+  // ctheta_meam = cos(theta/2) in radian used in line, zigzag, and trimer reference structures
+
   double Ec_meam[maxelt][maxelt], re_meam[maxelt][maxelt];
-  double Omega_meam[maxelt], Z_meam[maxelt];
   double A_meam[maxelt], alpha_meam[maxelt][maxelt], rho0_meam[maxelt];
   double delta_meam[maxelt][maxelt];
   double beta0_meam[maxelt], beta1_meam[maxelt];
@@ -108,6 +111,10 @@ public:
   int maxneigh;
   double *scrfcn, *dscrfcn, *fcpair;
 
+  //angle for trimer, zigzag, line reference structures
+  double stheta_meam[maxelt][maxelt];
+  double ctheta_meam[maxelt][maxelt];
+
 protected:
   // meam_funcs.cpp
 
@@ -191,9 +198,12 @@ protected:
   double embedding(const double A, const double Ec, const double rhobar, double& dF) const;
   static double erose(const double r, const double re, const double alpha, const double Ec, const double repuls, const double attrac, const int form);
 
-  static void get_shpfcn(const lattice_t latt, double (&s)[3]);
-  static int get_Zij(const lattice_t latt);
-  static int get_Zij2(const lattice_t latt, const double cmin, const double cmax, double &a, double &S);
+  static void get_shpfcn(const lattice_t latt, const double sthe, const double cthe, double (&s)[3]);
+
+  static int get_Zij2(const lattice_t latt, const double cmin, const double cmax,
+                      const double sthe, double &a, double &S);
+  static int get_Zij2_b2nn(const lattice_t latt, const double cmin, const double cmax, double &S);
+
 protected:
   void meam_checkindex(int, int, int, int*, int*);
   void getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** x, int numneigh,
@@ -204,6 +214,7 @@ protected:
   void alloyparams();
   void compute_pair_meam();
   double phi_meam(double, int, int);
+  const double phi_meam_series(const double scrn, const int Z1, const int Z2, const int a, const int b, const double r, const double arat);
   void compute_reference_density();
   void get_tavref(double*, double*, double*, double*, double*, double*, double, double, double, double,
                   double, double, double, int, int, lattice_t);
@@ -212,7 +223,41 @@ protected:
   void interpolate_meam(int);
 
 public:
-  void meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt, double* alpha,
+  //-----------------------------------------------------------------------------
+  // convert lattice spec to lattice_t
+  // only use single-element lattices if single=true
+  // return false on failure
+  // return true and set lat on success
+  static bool str_to_lat(const char* str, bool single, lattice_t& lat)
+  {
+    if (strcmp(str,"fcc") == 0) lat = FCC;
+    else if (strcmp(str,"bcc") == 0) lat = BCC;
+    else if (strcmp(str,"hcp") == 0) lat = HCP;
+    else if (strcmp(str,"dim") == 0) lat = DIM;
+    else if (strcmp(str,"dia") == 0) lat = DIA;
+    else if (strcmp(str,"dia3") == 0) lat = DIA3;
+    else if (strcmp(str,"lin") == 0) lat = LIN;
+    else if (strcmp(str,"zig") == 0) lat = ZIG;
+    else if (strcmp(str,"tri") == 0) lat = TRI;
+    else {
+      if (single)
+        return false;
+
+      if (strcmp(str,"b1")  == 0) lat = B1;
+      else if (strcmp(str,"c11") == 0) lat = C11;
+      else if (strcmp(str,"l12") == 0) lat = L12;
+      else if (strcmp(str,"b2")  == 0) lat = B2;
+      else if (strcmp(str,"ch4")  == 0) lat = CH4;
+      else if (strcmp(str,"lin")  == 0) lat =LIN;
+      else if (strcmp(str,"zig")  == 0) lat = ZIG;
+      else if (strcmp(str,"tri")  == 0) lat = TRI;
+      else return false;
+    }
+    return true;
+  }
+
+  static int get_Zij(const lattice_t latt);
+  void meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* atwt, double* alpha,
                          double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
                          double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
                          int* ibar);
@@ -222,9 +267,9 @@ public:
   void meam_dens_init(int i, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
                       int numneigh_full, int* firstneigh_full, int fnoffset);
   void meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl,
-                       double* eatom, int ntype, int* type, int* fmap, int& errorflag);
+                       double* eatom, int ntype, int* type, int* fmap, double** scale, int& errorflag);
   void meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl,
-                  double* eatom, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
+                  double* eatom, int ntype, int* type, int* fmap, double** scale, double** x, int numneigh, int* firstneigh,
                   int numneigh_full, int* firstneigh_full, int fnoffset, double** f, double** vatom);
 };
 
@@ -234,6 +279,10 @@ static inline bool iszero(const double f) {
   return fabs(f) < 1e-20;
 }
 
+static inline bool isone(const double f) {
+  return fabs(f-1.0) < 1e-20;
+}
+
 // Helper functions
 
 static inline double fdiv_zero(const double n, const double d) {
diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp
index 867106df88..fe9e74ca7c 100644
--- a/src/USER-MEAMC/meam_dens_final.cpp
+++ b/src/USER-MEAMC/meam_dens_final.cpp
@@ -4,18 +4,20 @@ using namespace LAMMPS_NS;
 
 void
 MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl,
-                      double* eatom, int /*ntype*/, int* type, int* fmap, int& errorflag)
+                      double* eatom, int /*ntype*/, int* type, int* fmap, double** scale, int& errorflag)
 {
   int i, elti;
   int m;
   double rhob, G, dG, Gbar, dGbar, gam, shp[3], Z;
   double denom, rho_bkgd, Fl;
+  double scaleii;
 
   //     Complete the calculation of density
 
   for (i = 0; i < nlocal; i++) {
     elti = fmap[type[i]];
     if (elti >= 0) {
+      scaleii = scale[type[i]][type[i]];
       rho1[i] = 0.0;
       rho2[i] = -1.0 / 3.0 * arho2b[i] * arho2b[i];
       rho3[i] = 0.0;
@@ -52,12 +54,14 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
         gamma[i] = gamma[i] / (rho0[i] * rho0[i]);
       }
 
-      Z = this->Z_meam[elti];
+      Z = get_Zij(this->lattce_meam[elti][elti]);
 
       G = G_gam(gamma[i], this->ibar_meam[elti], errorflag);
       if (errorflag != 0)
         return;
-      get_shpfcn(this->lattce_meam[elti][elti], shp);
+
+      get_shpfcn(this->lattce_meam[elti][elti], this->stheta_meam[elti][elti], this->ctheta_meam[elti][elti], shp);
+
       if (this->ibar_meam[elti] <= 0) {
         Gbar = 1.0;
         dGbar = 0.0;
@@ -113,6 +117,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
       Fl = embedding(this->A_meam[elti], this->Ec_meam[elti][elti], rhob, frhop[i]);
 
       if (eflag_either != 0) {
+        Fl *= scaleii;
         if (eflag_global != 0) {
           *eng_vdwl = *eng_vdwl + Fl;
         }
diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp
index 155941422c..39e3ff9467 100644
--- a/src/USER-MEAMC/meam_dens_init.cpp
+++ b/src/USER-MEAMC/meam_dens_init.cpp
@@ -197,7 +197,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
     //     Now compute derivatives
     dscrfcn[jn] = 0.0;
     sfcij = sij * fcij;
-    if (!iszero(sfcij) && !iszero(sfcij - 1.0)) {
+    if (!iszero(sfcij) && !isone(sfcij)) {
       for (kn = 0; kn < numneigh_full; kn++) {
         k = firstneigh_full[kn];
         if (k == j) continue;
diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp
index 09aad90111..2b6832e155 100644
--- a/src/USER-MEAMC/meam_force.cpp
+++ b/src/USER-MEAMC/meam_force.cpp
@@ -8,7 +8,7 @@ using namespace LAMMPS_NS;
 
 void
 MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl,
-                 double* eatom, int /*ntype*/, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
+                 double* eatom, int /*ntype*/, int* type, int* fmap, double** scale, double** x, int numneigh, int* firstneigh,
                  int numneigh_full, int* firstneigh_full, int fnoffset, double** f, double** vatom)
 {
   int j, jn, k, kn, kk, m, n, p, q;
@@ -17,7 +17,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
   double v[6], fi[3], fj[3];
   double third, sixth;
   double pp, dUdrij, dUdsij, dUdrijm[3], force, forcem;
-  double r, recip, phi, phip;
+  double recip, phi, phip;
   double sij;
   double a1, a1i, a1j, a2, a2i, a2j;
   double a3i, a3j;
@@ -42,6 +42,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
   double arg1i1, arg1j1, arg1i2, arg1j2, arg1i3, arg1j3, arg3i3, arg3j3;
   double dsij1, dsij2, force1, force2;
   double t1i, t2i, t3i, t1j, t2j, t3j;
+  double scaleij;
 
   third = 1.0 / 3.0;
   sixth = 1.0 / 6.0;
@@ -59,6 +60,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
   for (jn = 0; jn < numneigh; jn++) {
     j = firstneigh[jn];
     eltj = fmap[type[j]];
+    scaleij = scale[type[i]][type[j]];
 
     if (!iszero(scrfcn[fnoffset + jn]) && eltj >= 0) {
 
@@ -69,7 +71,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
       rij2 = delij[0] * delij[0] + delij[1] * delij[1] + delij[2] * delij[2];
       if (rij2 < this->cutforcesq) {
         rij = sqrt(rij2);
-        r = rij;
+        recip = 1.0 / rij;
 
         //     Compute phi and phip
         ind = this->eltind[elti][eltj];
@@ -78,17 +80,16 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
         kk = std::min(kk, this->nrar - 2);
         pp = pp - kk;
         pp = std::min(pp, 1.0);
-        phi = ((this->phirar3[ind][kk] * pp + this->phirar2[ind][kk]) * pp + this->phirar1[ind][kk]) * pp +
-          this->phirar[ind][kk];
+        phi = ((this->phirar3[ind][kk] * pp + this->phirar2[ind][kk]) * pp + this->phirar1[ind][kk]) * pp + this->phirar[ind][kk];
         phip = (this->phirar6[ind][kk] * pp + this->phirar5[ind][kk]) * pp + this->phirar4[ind][kk];
-        recip = 1.0 / r;
 
         if (eflag_either != 0) {
+          double phi_sc = phi * scaleij;
           if (eflag_global != 0)
-            *eng_vdwl = *eng_vdwl + phi * sij;
+            *eng_vdwl = *eng_vdwl + phi_sc * sij;
           if (eflag_atom != 0) {
-            eatom[i] = eatom[i] + 0.5 * phi * sij;
-            eatom[j] = eatom[j] + 0.5 * phi * sij;
+            eatom[i] = eatom[i] + 0.5 * phi_sc * sij;
+            eatom[j] = eatom[j] + 0.5 * phi_sc * sij;
           }
         }
 
@@ -287,8 +288,9 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
         }
 
         //     Compute derivatives of total density wrt rij, sij and rij(3)
-        get_shpfcn(this->lattce_meam[elti][elti], shpi);
-        get_shpfcn(this->lattce_meam[eltj][eltj], shpj);
+        get_shpfcn(this->lattce_meam[elti][elti], this->stheta_meam[elti][elti], this->ctheta_meam[elti][elti], shpi);
+        get_shpfcn(this->lattce_meam[eltj][eltj], this->stheta_meam[elti][elti], this->ctheta_meam[elti][elti], shpj);
+
         drhodr1 = dgamma1[i] * drho0dr1 +
           dgamma2[i] * (dt1dr1 * rho1[i] + t1i * drho1dr1 + dt2dr1 * rho2[i] + t2i * drho2dr1 +
                         dt3dr1 * rho3[i] + t3i * drho3dr1) -
@@ -379,6 +381,13 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
         for (m = 0; m < 3; m++) {
           dUdrijm[m] = frhop[i] * drhodrm1[m] + frhop[j] * drhodrm2[m];
         }
+        if (!isone(scaleij)) {
+          dUdrij *= scaleij;
+          dUdsij *= scaleij;
+          dUdrijm[0] *= scaleij;
+          dUdrijm[1] *= scaleij;
+          dUdrijm[2] *= scaleij;
+        }
 
         //     Add the part of the force due to dUdrij and dUdsij
 
@@ -410,7 +419,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
 
         //     Now compute forces on other atoms k due to change in sij
 
-        if (iszero(sij) || iszero(sij - 1.0)) continue; //: cont jn loop
+        if (iszero(sij) || isone(sij)) continue; //: cont jn loop
 
         double dxik(0), dyik(0), dzik(0);
         double dxjk(0), dyjk(0), dzjk(0);
@@ -429,7 +438,7 @@ MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int
 
             dsij1 = 0.0;
             dsij2 = 0.0;
-            if (!iszero(sij) && !iszero(sij - 1.0)) {
+            if (!iszero(sij) && !isone(sij)) {
               const double rbound = rij2 * this->ebound_meam[elti][eltj];
               delc = Cmax - Cmin;
               dxjk = x[k][0] - x[j][0];
diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp
index 312caff686..da984cfeb7 100644
--- a/src/USER-MEAMC/meam_funcs.cpp
+++ b/src/USER-MEAMC/meam_funcs.cpp
@@ -198,7 +198,7 @@ MEAM::erose(const double r, const double re, const double alpha, const double Ec
 // Shape factors for various configurations
 //
 void
-MEAM::get_shpfcn(const lattice_t latt, double (&s)[3])
+MEAM::get_shpfcn(const lattice_t latt, const double sthe, const double cthe, double (&s)[3])
 {
   switch (latt) {
     case FCC:
@@ -214,7 +214,9 @@ MEAM::get_shpfcn(const lattice_t latt, double (&s)[3])
       s[1] = 0.0;
       s[2] = 1.0 / 3.0;
       break;
+    case CH4: // CH4 actually needs shape factor for diamond for C, dimer for H
     case DIA:
+    case DIA3:
       s[0] = 0.0;
       s[1] = 0.0;
       s[2] = 32.0 / 9.0;
@@ -222,8 +224,20 @@ MEAM::get_shpfcn(const lattice_t latt, double (&s)[3])
     case DIM:
       s[0] = 1.0;
       s[1] = 2.0 / 3.0;
-      //        s(3) = 1.d0
-      s[2] = 0.40;
+      //        s(3) = 1.d0 // this should be 0.4 unless (1-legendre) is multiplied in the density calc.
+      s[2] = 0.40; // this is (1-legendre) where legendre = 0.6 in dynamo is accounted.
+      break;
+    case LIN: //linear, theta being 180
+      s[0] = 0.0;
+      s[1] = 8.0 / 3.0; // 4*(co**4 + si**4 - 1.0/3.0) in zig become 4*(1-1/3)
+      s[2] = 0.0;
+      break;
+    case ZIG: //zig-zag
+    case TRI: //trimer e.g. H2O
+      s[0] = 4.0*pow(cthe,2);
+      s[1] = 4.0*(pow(cthe,4) + pow(sthe,4) - 1.0/3.0);
+      s[2] = 4.0*(pow(cthe,2) * (3*pow(sthe,4) + pow(cthe,4)));
+      s[2] = s[2] - 0.6*s[0]; //legend in dyn, 0.6 is default value.
       break;
     default:
       s[0] = 0.0;
@@ -232,7 +246,7 @@ MEAM::get_shpfcn(const lattice_t latt, double (&s)[3])
 }
 
 //-----------------------------------------------------------------------------
-// Number of neighbors for the reference structure
+// Number of first neighbors for reference structure
 //
 int
 MEAM::get_Zij(const lattice_t latt)
@@ -244,18 +258,25 @@ MEAM::get_Zij(const lattice_t latt)
       return 8;
     case HCP:
       return 12;
-    case B1:
-      return 6;
     case DIA:
+    case DIA3:
       return 4;
     case DIM:
       return 1;
+    case B1:
+      return 6;
     case C11:
       return 10;
     case L12:
       return 12;
     case B2:
       return 8;
+    case CH4: // DYNAMO currenly implemented this way while it needs two Z values, 4 and 1
+      return 4;
+    case LIN:
+    case ZIG:
+    case TRI:
+      return 2;
       //        call error('Lattice not defined in get_Zij.')
   }
   return 0;
@@ -263,11 +284,13 @@ MEAM::get_Zij(const lattice_t latt)
 
 //-----------------------------------------------------------------------------
 // Number of second neighbors for the reference structure
-//   a = distance ratio R1/R2
-//   S = second neighbor screening function
+//   a = distance ratio R1/R2 (a2nn in dynamo)
+//   numscr = number of atoms that screen the 2NN bond
+//   S = second neighbor screening function (xfac, a part of b2nn in dynamo)
 //
 int
-MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, double& a, double& S)
+MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax,
+                const double stheta, double& a, double& S)
 {
 
   double C, x, sijk;
@@ -299,7 +322,7 @@ MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, doubl
     numscr = 2;
     break;
 
-  case DIA:
+  case DIA: // 2NN
     Zij2 = 12;
     a = sqrt(8.0 / 3.0);
     numscr = 1;
@@ -308,12 +331,35 @@ MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, doubl
     }
     break;
 
+  case DIA3: // 3NN
+    Zij2 = 12;
+    a = sqrt(11.0 / 3.0);
+    numscr = 4;
+    if (cmin < 0.500001) {
+        //          call error('can not do 2NN MEAM for dia')
+    }
+    break;
+
+  case CH4: //does not have 2nn structure so it returns 0
+  case LIN: //line
   case DIM:
     //        this really shouldn't be allowed; make sure screening is zero
     a = 1.0;
     S = 0.0;
     return 0;
 
+  case TRI: //TRI
+    Zij2 = 1;
+    a = 2.0*stheta;
+    numscr=2;
+    break;
+
+  case ZIG: //zig-zag
+    Zij2 = 2;
+    a = 2.0*stheta;
+    numscr=1;
+    break;
+
   case L12:
     Zij2 = 6;
     a = sqrt(2.0);
@@ -335,10 +381,38 @@ MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, doubl
   }
 
   // Compute screening for each first neighbor
-  C = 4.0 / (a * a) - 1.0;
+  if (latt==DIA3){ // special case for 3NN diamond structure
+	C = 1.0;
+  } else {
+	C = 4.0 / (a * a) - 1.0;
+  }
   x = (C - cmin) / (cmax - cmin);
   sijk = fcut(x);
   // There are numscr first neighbors screening the second neighbors
   S = MathSpecial::powint(sijk, numscr);
   return Zij2;
 }
+
+int
+MEAM::get_Zij2_b2nn(const lattice_t latt, const double cmin, const double cmax, double &S)
+{
+
+  double x, sijk, C;
+  int numscr = 0, Zij2 = 0;
+  switch (latt) {
+  case ZIG: //zig-zag for b11s and b22s term
+  case TRI: //trimer for b11s
+    Zij2 = 2;
+    numscr=1;
+    break;
+  default:
+    // unknown lattic flag in get Zij
+    //        call error('Lattice not defined in get_Zij.')
+    break;
+  }
+  C = 1.0;
+  x = (C - cmin) / (cmax - cmin);
+  sijk = fcut(x);
+  S = MathSpecial::powint(sijk, numscr);
+  return Zij2;
+}
\ No newline at end of file
diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp
index 74e8af1cde..0a0b95e14a 100644
--- a/src/USER-MEAMC/meam_impl.cpp
+++ b/src/USER-MEAMC/meam_impl.cpp
@@ -38,7 +38,7 @@ MEAM::MEAM(Memory* mem)
 
   neltypes = 0;
   for (int i = 0; i < maxelt; i++) {
-    Omega_meam[i] = Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] =
+    A_meam[i] = rho0_meam[i] = beta0_meam[i] =
       beta1_meam[i]= beta2_meam[i] = beta3_meam[i] =
       t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] =
       rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0;
diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp
index 7000eac6ae..99b330a83a 100644
--- a/src/USER-MEAMC/meam_setup_done.cpp
+++ b/src/USER-MEAMC/meam_setup_done.cpp
@@ -103,6 +103,9 @@ MEAM::alloyparams(void)
         this->alpha_meam[i][j] = this->alpha_meam[j][i];
         this->lattce_meam[i][j] = this->lattce_meam[j][i];
         this->nn2_meam[i][j] = this->nn2_meam[j][i];
+	    // theta for lin,tri,zig references
+        this->stheta_meam[i][j] = this->stheta_meam[j][i];
+        this->ctheta_meam[i][j] = this->ctheta_meam[j][i];
         // If i<j and term is unset, use default values (e.g. mean of i-i and
         // j-j)
       } else if (j > i) {
@@ -161,10 +164,10 @@ void
 MEAM::compute_pair_meam(void)
 {
 
-  double r /*ununsed:, temp*/;
+  double r, b2nn, phi_val;
   int j, a, b, nv2;
   double astar, frac, phizbl;
-  int n, nmax, Z1, Z2;
+  int n, Z1, Z2;
   double arat, rarat, scrn, scrn2;
   double phiaa, phibb /*unused:,phitmp*/;
   double C, s111, s112, s221, S11, S22;
@@ -215,7 +218,7 @@ MEAM::compute_pair_meam(void)
         if (this->nn2_meam[a][b] == 1) {
           Z1 = get_Zij(this->lattce_meam[a][b]);
           Z2 = get_Zij2(this->lattce_meam[a][b], this->Cmin_meam[a][a][b],
-                   this->Cmax_meam[a][a][b], arat, scrn);
+                     this->Cmax_meam[a][a][b], this->stheta_meam[a][b], arat, scrn);
 
           //     The B1, B2,  and L12 cases with NN2 have a trick to them; we need to
           //     compute the contributions from second nearest neighbors, like a-a
@@ -229,35 +232,26 @@ MEAM::compute_pair_meam(void)
             phiaa = phi_meam(rarat, a, a);
             Z1 = get_Zij(this->lattce_meam[a][a]);
             Z2 = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
-                     this->Cmax_meam[a][a][a], arat, scrn);
-            nmax = 10;
-            if (scrn > 0.0) {
-              for (n = 1; n <= nmax; n++) {
-                phiaa = phiaa + pow((-Z2 * scrn / Z1), n) * phi_meam(rarat * pow(arat, n), a, a);
-              }
-            }
+                     this->Cmax_meam[a][a][a], this->stheta_meam[a][a], arat, scrn);
+            phiaa+= phi_meam_series(scrn, Z1, Z2, a, a, rarat, arat);
 
             //               phi_bb
             phibb = phi_meam(rarat, b, b);
             Z1 = get_Zij(this->lattce_meam[b][b]);
             Z2 = get_Zij2(this->lattce_meam[b][b], this->Cmin_meam[b][b][b],
-                     this->Cmax_meam[b][b][b], arat, scrn);
-            nmax = 10;
-            if (scrn > 0.0) {
-              for (n = 1; n <= nmax; n++) {
-                phibb = phibb + pow((-Z2 * scrn / Z1), n) * phi_meam(rarat * pow(arat, n), b, b);
-              }
-            }
+                     this->Cmax_meam[b][b][b], this->stheta_meam[b][b], arat, scrn);
+            phibb+= phi_meam_series(scrn, Z1, Z2, b, b, rarat, arat);
 
             if (this->lattce_meam[a][b] == B1 || this->lattce_meam[a][b] == B2 ||
                 this->lattce_meam[a][b] == DIA) {
               //     Add contributions to the B1 or B2 potential
               Z1 = get_Zij(this->lattce_meam[a][b]);
               Z2 = get_Zij2(this->lattce_meam[a][b], this->Cmin_meam[a][a][b],
-                       this->Cmax_meam[a][a][b], arat, scrn);
+                       this->Cmax_meam[a][a][b], this->stheta_meam[a][b],  arat, scrn);
               this->phir[nv2][j] = this->phir[nv2][j] - Z2 * scrn / (2 * Z1) * phiaa;
               Z2 = get_Zij2(this->lattce_meam[a][b], this->Cmin_meam[b][b][a],
-                       this->Cmax_meam[b][b][a], arat, scrn2);
+                       this->Cmax_meam[b][b][a], this->stheta_meam[a][b], arat, scrn2);
+
               this->phir[nv2][j] = this->phir[nv2][j] - Z2 * scrn2 / (2 * Z1) * phibb;
 
             } else if (this->lattce_meam[a][b] == L12) {
@@ -279,11 +273,7 @@ MEAM::compute_pair_meam(void)
             }
 
           } else {
-            nmax = 10;
-            for (n = 1; n <= nmax; n++) {
-              this->phir[nv2][j] =
-                this->phir[nv2][j] + pow((-Z2 * scrn / Z1), n) * phi_meam(r * pow(arat, n), a, b);
-            }
+            this->phir[nv2][j]+= phi_meam_series(scrn, Z1, Z2, a, b, r, arat);
           }
         }
 
@@ -328,11 +318,12 @@ MEAM::phi_meam(double r, int a, int b)
   double rho02, rho12, rho22, rho32;
   double scalfac, phiaa, phibb;
   double Eu;
-  double arat, scrn /*unused:,scrn2*/;
+  double arat, scrn, scrn2;
   int Z12, errorflag;
-  int n, nmax, Z1nn, Z2nn;
+  int n, Z1nn, Z2nn;
   lattice_t latta /*unused:,lattb*/;
   double rho_bkgd1, rho_bkgd2;
+  double b11s, b22s;
 
   double phi_m = 0.0;
 
@@ -341,6 +332,8 @@ MEAM::phi_meam(double r, int a, int b)
 
   // get number of neighbors in the reference structure
   //   Nref[i][j] = # of i's neighbors of type j
+  Z1 = get_Zij(this->lattce_meam[a][a]);
+  Z2 = get_Zij(this->lattce_meam[b][b]);
   Z12 = get_Zij(this->lattce_meam[a][b]);
 
   get_densref(r, a, b, &rho01, &rho11, &rho21, &rho31, &rho02, &rho12, &rho22, &rho32);
@@ -401,19 +394,17 @@ MEAM::phi_meam(double r, int a, int b)
     //     If using mixing rule for t, apply to reference structure; else
     //     use precomputed values
     if (this->mix_ref_t == 1) {
-      Z1 = this->Z_meam[a];
-      Z2 = this->Z_meam[b];
       if (this->ibar_meam[a] <= 0)
         G1 = 1.0;
       else {
-        get_shpfcn(this->lattce_meam[a][a], s1);
+        get_shpfcn(this->lattce_meam[a][a], this->stheta_meam[a][a], this->ctheta_meam[a][a], s1);
         Gam1 = (s1[0] * t11av + s1[1] * t21av + s1[2] * t31av) / (Z1 * Z1);
         G1 = G_gam(Gam1, this->ibar_meam[a], errorflag);
       }
       if (this->ibar_meam[b] <= 0)
         G2 = 1.0;
       else {
-        get_shpfcn(this->lattce_meam[b][b], s2);
+        get_shpfcn(this->lattce_meam[b][b], this->stheta_meam[b][b], this->ctheta_meam[b][b],  s2);
         Gam2 = (s2[0] * t12av + s2[1] * t22av + s2[2] * t32av) / (Z2 * Z2);
         G2 = G_gam(Gam2, this->ibar_meam[b], errorflag);
       }
@@ -439,8 +430,8 @@ MEAM::phi_meam(double r, int a, int b)
       rho_bkgd2 = rho0_2;
     } else {
       if (this->bkgd_dyn == 1) {
-        rho_bkgd1 = this->rho0_meam[a] * this->Z_meam[a];
-        rho_bkgd2 = this->rho0_meam[b] * this->Z_meam[b];
+        rho_bkgd1 = this->rho0_meam[a] * Z1;
+        rho_bkgd2 = this->rho0_meam[b] * Z2;
       } else {
         rho_bkgd1 = this->rho_ref_meam[a];
         rho_bkgd2 = this->rho_ref_meam[b];
@@ -454,7 +445,7 @@ MEAM::phi_meam(double r, int a, int b)
 
   F1 = embedding(this->A_meam[a], this->Ec_meam[a][a], rhobar1, dF);
   F2 = embedding(this->A_meam[b], this->Ec_meam[b][b], rhobar2, dF);
-  
+
 
   // compute Rose function, I.16
   Eu = erose(r, this->re_meam[a][b], this->alpha_meam[a][b], this->Ec_meam[a][b], this->repuls_meam[a][b],
@@ -475,20 +466,44 @@ MEAM::phi_meam(double r, int a, int b)
     //       account for second neighbor a-a potential here...
     Z1nn = get_Zij(this->lattce_meam[a][a]);
     Z2nn = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
-             this->Cmax_meam[a][a][a], arat, scrn);
-    nmax = 10;
-    if (scrn > 0.0) {
-      for (n = 1; n <= nmax; n++) {
-        phiaa = phiaa + pow((-Z2nn * scrn / Z1nn), n) * phi_meam(r * pow(arat, n), a, a);
-      }
-    }
+             this->Cmax_meam[a][a][a], this->stheta_meam[a][b], arat, scrn);
+
+
+    phiaa += phi_meam_series(scrn, Z1nn, Z2nn, a, a, r, arat);
     phi_m = Eu / 3.0 - F1 / 4.0 - F2 / 12.0 - phiaa;
 
+  } else if (this->lattce_meam[a][b] == CH4) {
+    phi_m = (5 * Eu - F1 - 4*F2)/4;
+
+  } else if (this->lattce_meam[a][b] == ZIG){
+      if (a==b){
+        phi_m = (2 * Eu - F1 - F2) / Z12;
+      } else{
+        Z1 = get_Zij(this->lattce_meam[a][b]);
+        Z2 = get_Zij2_b2nn(this->lattce_meam[a][b], this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b], scrn);
+        b11s = -Z2/Z1*scrn;
+        Z2 = get_Zij2_b2nn(this->lattce_meam[a][b], this->Cmin_meam[b][b][a], this->Cmax_meam[b][b][a], scrn2);
+        b22s = -Z2/Z1*scrn2;
+
+        phiaa = phi_meam(2.0*this->stheta_meam[a][b]*r, a, a);
+        phibb = phi_meam(2.0*this->stheta_meam[a][b]*r, b, b);
+        phi_m = (2.0*Eu - F1 - F2 + phiaa*b11s + phibb*b22s) / Z12;
+      }
+
+  } else if (this->lattce_meam[a][b] == TRI) {
+      if (a==b){
+        phi_m = (3.0*Eu - 2.0*F1 - F2) / Z12;
+     } else {
+        Z1 = get_Zij(this->lattce_meam[a][b]);
+        Z2 = get_Zij2_b2nn(this->lattce_meam[a][b], this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b], scrn);
+        b11s = -Z2/Z1*scrn;
+        phiaa = phi_meam(2.0*this->stheta_meam[a][b]*r, a, a);
+        phi_m = (3.0*Eu - 2.0*F1 - F2 + phiaa*b11s) / Z12;
+      }
+
   } else {
-    //
     // potential is computed from Rose function and embedding energy
     phi_m = (2 * Eu - F1 - F2) / Z12;
-    //
   }
 
   // if r = 0, just return 0
@@ -499,6 +514,31 @@ MEAM::phi_meam(double r, int a, int b)
   return phi_m;
 }
 
+//----------------------------------------------------------------------c
+// Compute 2NN series terms for phi
+//   To avoid nan values of phir due to rapid decrease of b2nn^n or/and
+//   argument of phi_meam, i.e. r*arat^n, in some cases (3NN dia with low Cmin value)
+//
+const double
+MEAM::phi_meam_series(const double scrn, const int Z1, const int Z2, const int a, const int b, const double r, const double arat)
+{
+  double phi_sum = 0.0;
+  double b2nn, phi_val;
+  if (scrn > 0.0) {
+    b2nn = -Z2*scrn/Z1;
+    for (int n = 1; n <= 10; n++) {
+      phi_val = MathSpecial::powint(b2nn,n) * phi_meam(r * MathSpecial::powint(arat, n), a, b);
+      if (iszero(phi_val)) {
+        // once either term becomes zero at some point, all folliwng will also be zero
+        // necessary to avoid numerical error (nan or infty) due to exponential decay in phi_meam
+        break;
+      }
+      phi_sum += phi_val;
+    }
+  }
+  return phi_sum;
+}
+
 //----------------------------------------------------------------------c
 // Compute background density for reference structure of each element
 void
@@ -510,11 +550,11 @@ MEAM::compute_reference_density(void)
 
   // loop over element types
   for (a = 0; a < this->neltypes; a++) {
-    Z = (int)this->Z_meam[a];
+    Z = get_Zij(this->lattce_meam[a][a]);
     if (this->ibar_meam[a] <= 0)
       Gbar = 1.0;
     else {
-      get_shpfcn(this->lattce_meam[a][a], shp);
+      get_shpfcn(this->lattce_meam[a][a], this->stheta_meam[a][a], this->ctheta_meam[a][a], shp);
       gam = (this->t1_meam[a] * shp[0] + this->t2_meam[a] * shp[1] + this->t3_meam[a] * shp[2]) / (Z * Z);
       Gbar = G_gam(gam, this->ibar_meam[a], errorflag);
     }
@@ -529,7 +569,7 @@ MEAM::compute_reference_density(void)
     //     screening)
     if (this->nn2_meam[a][a] == 1) {
       Z2 = get_Zij2(this->lattce_meam[a][a], this->Cmin_meam[a][a][a],
-               this->Cmax_meam[a][a][a], arat, scrn);
+               this->Cmax_meam[a][a][a], this->stheta_meam[a][a], arat, scrn);
       rho0_2nn = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * (arat - 1));
       rho0 = rho0 + Z2 * rho0_2nn * scrn;
     }
@@ -555,30 +595,43 @@ MEAM::get_tavref(double* t11av, double* t21av, double* t31av, double* t12av, dou
     *t12av = t12;
     *t22av = t22;
     *t32av = t32;
-  } else if (latt == FCC || latt == BCC || latt == DIA || latt == HCP || latt == B1 || latt == DIM || latt == B2) {
-    //     all neighbors are of the opposite type
-    *t11av = t12;
-    *t21av = t22;
-    *t31av = t32;
-    *t12av = t11;
-    *t22av = t21;
-    *t32av = t31;
-  } else {
-    a1 = r / this->re_meam[a][a] - 1.0;
-    a2 = r / this->re_meam[b][b] - 1.0;
-    rhoa01 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * a1);
-    rhoa02 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
-    if (latt == L12) {
-      rho01 = 8 * rhoa01 + 4 * rhoa02;
-      *t11av = (8 * t11 * rhoa01 + 4 * t12 * rhoa02) / rho01;
+  } else switch (latt)  {
+    case FCC:
+    case BCC:
+    case DIA:
+    case DIA3:
+    case HCP:
+    case B1:
+    case DIM:
+    case B2:
+    case CH4:
+    case LIN:
+    case ZIG:
+    case TRI:
+      //     all neighbors are of the opposite type
+      *t11av = t12;
+      *t21av = t22;
+      *t31av = t32;
       *t12av = t11;
-      *t21av = (8 * t21 * rhoa01 + 4 * t22 * rhoa02) / rho01;
       *t22av = t21;
-      *t31av = (8 * t31 * rhoa01 + 4 * t32 * rhoa02) / rho01;
       *t32av = t31;
-    } else {
-      //      call error('Lattice not defined in get_tavref.')
-    }
+      break;
+    default:
+      a1 = r / this->re_meam[a][a] - 1.0;
+      a2 = r / this->re_meam[b][b] - 1.0;
+      rhoa01 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * a1);
+      rhoa02 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
+      if (latt == L12) {
+        rho01 = 8 * rhoa01 + 4 * rhoa02;
+        *t11av = (8 * t11 * rhoa01 + 4 * t12 * rhoa02) / rho01;
+        *t12av = t11;
+        *t21av = (8 * t21 * rhoa01 + 4 * t22 * rhoa02) / rho01;
+        *t22av = t21;
+        *t31av = (8 * t31 * rhoa01 + 4 * t32 * rhoa02) / rho01;
+        *t32av = t31;
+      } else {
+        //      call error('Lattice not defined in get_tavref.')
+      }
   }
 }
 
@@ -600,7 +653,7 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
   double a1, a2;
   double s[3];
   lattice_t lat;
-  int Zij2nn;
+  int Zij,Zij2nn;
   double rhoa01nn, rhoa02nn;
   double rhoa01, rhoa11, rhoa21, rhoa31;
   double rhoa02, rhoa12, rhoa22, rhoa32;
@@ -621,6 +674,8 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
 
   lat = this->lattce_meam[a][b];
 
+  Zij = get_Zij(lat);
+
   *rho11 = 0.0;
   *rho21 = 0.0;
   *rho31 = 0.0;
@@ -628,64 +683,133 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
   *rho22 = 0.0;
   *rho32 = 0.0;
 
-  if (lat == FCC) {
-    *rho01 = 12.0 * rhoa02;
-    *rho02 = 12.0 * rhoa01;
-  } else if (lat == BCC) {
-    *rho01 = 8.0 * rhoa02;
-    *rho02 = 8.0 * rhoa01;
-  } else if (lat == B1) {
-    *rho01 = 6.0 * rhoa02;
-    *rho02 = 6.0 * rhoa01;
-  } else if (lat == DIA) {
-    *rho01 = 4.0 * rhoa02;
-    *rho02 = 4.0 * rhoa01;
-    *rho31 = 32.0 / 9.0 * rhoa32 * rhoa32;
-    *rho32 = 32.0 / 9.0 * rhoa31 * rhoa31;
-  } else if (lat == HCP) {
-    *rho01 = 12 * rhoa02;
-    *rho02 = 12 * rhoa01;
-    *rho31 = 1.0 / 3.0 * rhoa32 * rhoa32;
-    *rho32 = 1.0 / 3.0 * rhoa31 * rhoa31;
-  } else if (lat == DIM) {
-    get_shpfcn(DIM, s);
-    *rho01 = rhoa02;
-    *rho02 = rhoa01;
-    *rho11 = s[0] * rhoa12 * rhoa12;
-    *rho12 = s[0] * rhoa11 * rhoa11;
-    *rho21 = s[1] * rhoa22 * rhoa22;
-    *rho22 = s[1] * rhoa21 * rhoa21;
-    *rho31 = s[2] * rhoa32 * rhoa32;
-    *rho32 = s[2] * rhoa31 * rhoa31;
-  } else if (lat == C11) {
-    *rho01 = rhoa01;
-    *rho02 = rhoa02;
-    *rho11 = rhoa11;
-    *rho12 = rhoa12;
-    *rho21 = rhoa21;
-    *rho22 = rhoa22;
-    *rho31 = rhoa31;
-    *rho32 = rhoa32;
-  } else if (lat == L12) {
-    *rho01 = 8 * rhoa01 + 4 * rhoa02;
-    *rho02 = 12 * rhoa01;
-    if (this->ialloy == 1) {
-      *rho21 = 8. / 3. * MathSpecial::square(rhoa21 * this->t2_meam[a] - rhoa22 * this->t2_meam[b]);
-      denom = 8 * rhoa01 * MathSpecial::square(this->t2_meam[a]) + 4 * rhoa02 * MathSpecial::square(this->t2_meam[b]);
-      if (denom > 0.)
-        *rho21 = *rho21 / denom * *rho01;
-    } else
-      *rho21 = 8. / 3. * (rhoa21 - rhoa22) * (rhoa21 - rhoa22);
-  } else if (lat == B2) {
-    *rho01 = 8.0 * rhoa02;
-    *rho02 = 8.0 * rhoa01;
-  } else {
+  switch (lat) {
+    case FCC:
+      *rho01 = 12.0 * rhoa02;
+      *rho02 = 12.0 * rhoa01;
+      break;
+    case BCC:
+      *rho01 = 8.0 * rhoa02;
+      *rho02 = 8.0 * rhoa01;
+      break;
+    case B1:
+      *rho01 = 6.0 * rhoa02;
+      *rho02 = 6.0 * rhoa01;
+      break;
+    case DIA:
+    case DIA3:
+      *rho01 = 4.0 * rhoa02;
+      *rho02 = 4.0 * rhoa01;
+      *rho31 = 32.0 / 9.0 * rhoa32 * rhoa32;
+      *rho32 = 32.0 / 9.0 * rhoa31 * rhoa31;
+      break;
+    case HCP:
+      *rho01 = 12 * rhoa02;
+      *rho02 = 12 * rhoa01;
+      *rho31 = 1.0 / 3.0 * rhoa32 * rhoa32;
+      *rho32 = 1.0 / 3.0 * rhoa31 * rhoa31;
+      break;
+    case DIM:
+      get_shpfcn(DIM, 0, 0, s);
+      *rho01 = rhoa02;
+      *rho02 = rhoa01;
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+      break;
+    case C11:
+      *rho01 = rhoa01;
+      *rho02 = rhoa02;
+      *rho11 = rhoa11;
+      *rho12 = rhoa12;
+      *rho21 = rhoa21;
+      *rho22 = rhoa22;
+      *rho31 = rhoa31;
+      *rho32 = rhoa32;
+      break;
+    case L12:
+      *rho01 = 8 * rhoa01 + 4 * rhoa02;
+      *rho02 = 12 * rhoa01;
+      if (this->ialloy == 1) {
+        *rho21 = 8. / 3. * MathSpecial::square(rhoa21 * this->t2_meam[a] - rhoa22 * this->t2_meam[b]);
+        denom = 8 * rhoa01 * MathSpecial::square(this->t2_meam[a]) + 4 * rhoa02 * MathSpecial::square(this->t2_meam[b]);
+        if (denom > 0.)
+          *rho21 = *rho21 / denom * *rho01;
+      } else
+        *rho21 = 8. / 3. * (rhoa21 - rhoa22) * (rhoa21 - rhoa22);
+      break;
+    case B2:
+      *rho01 = 8.0 * rhoa02;
+      *rho02 = 8.0 * rhoa01;
+      break;
+    case CH4:
+      *rho01 = 4.0 * rhoa02; //in assumption that 'a' represent carbon
+      *rho02 = rhoa01;	//in assumption that 'b' represent hydrogen
+
+      get_shpfcn(DIM, 0, 0, s);	//H
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+
+      get_shpfcn(CH4, 0, 0, s); //C
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      break;
+    case LIN:
+      *rho01 = rhoa02*Zij;
+      *rho02 = rhoa01*Zij;
+
+      get_shpfcn(LIN, this->stheta_meam[a][b], this->ctheta_meam[a][b], s);
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      break;
+    case ZIG:
+      *rho01 = rhoa02*Zij;
+      *rho02 = rhoa01*Zij;
+
+      get_shpfcn(ZIG, this->stheta_meam[a][b], this->ctheta_meam[a][b], s);
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      break;
+    case TRI:
+      *rho01 = rhoa02;
+      *rho02 = rhoa01*Zij;
+
+      get_shpfcn(TRI, this->stheta_meam[a][b], this->ctheta_meam[a][b], s);
+      *rho12 = s[0] * rhoa11 * rhoa11;
+      *rho22 = s[1] * rhoa21 * rhoa21;
+      *rho32 = s[2] * rhoa31 * rhoa31;
+      s[0] = 1.0;
+      s[1] = 2.0/3.0;
+      s[2] = 1.0 - 0.6*s[0];
+
+      *rho11 = s[0] * rhoa12 * rhoa12;
+      *rho21 = s[1] * rhoa22 * rhoa22;
+      *rho31 = s[2] * rhoa32 * rhoa32;
+      break;
+
+
+    // default:
     //        call error('Lattice not defined in get_densref.')
   }
 
   if (this->nn2_meam[a][b] == 1) {
 
-    Zij2nn = get_Zij2(lat, this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b], arat, scrn);
+
+    Zij2nn = get_Zij2(lat, this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b],
+                      this->stheta_meam[a][b], arat, scrn);
 
     a1 = arat * r / this->re_meam[a][a] - 1.0;
     a2 = arat * r / this->re_meam[b][b] - 1.0;
@@ -712,7 +836,8 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
       *rho01 = *rho01 + Zij2nn * scrn * rhoa01nn;
 
       //     Assume Zij2nn and arat don't depend on order, but scrn might
-      Zij2nn = get_Zij2(lat, this->Cmin_meam[b][b][a], this->Cmax_meam[b][b][a], arat, scrn);
+      Zij2nn = get_Zij2(lat, this->Cmin_meam[b][b][a], this->Cmax_meam[b][b][a],
+                        this->stheta_meam[a][b], arat, scrn);
       *rho02 = *rho02 + Zij2nn * scrn * rhoa02nn;
     }
   }
diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp
index b66aafa06c..ac5718914c 100644
--- a/src/USER-MEAMC/meam_setup_global.cpp
+++ b/src/USER-MEAMC/meam_setup_global.cpp
@@ -18,7 +18,7 @@ static inline void setall3d(TYPE (&arr)[maxi][maxj][maxk], const TYPE v) {
 }
 
 void
-MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* /*atwt*/, double* alpha,
+MEAM::meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* /*atwt*/, double* alpha,
                         double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
                         double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
                         int* ibar)
@@ -32,7 +32,6 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, doub
   for (i = 0; i < nelt; i++) {
     this->lattce_meam[i][i] = lat[i];
 
-    this->Z_meam[i] = z[i];
     this->ielt_meam[i] = ielement[i];
     this->alpha_meam[i][i] = alpha[i];
     this->beta0_meam[i] = b0[i];
@@ -49,17 +48,26 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, doub
     this->rho0_meam[i] = rozero[i];
     this->ibar_meam[i] = ibar[i];
 
-    if (this->lattce_meam[i][i] == FCC)
-      this->re_meam[i][i] = tmplat[i] / sqrt(2.0);
-    else if (this->lattce_meam[i][i] == BCC)
-      this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 2.0;
-    else if (this->lattce_meam[i][i] == HCP)
-      this->re_meam[i][i] = tmplat[i];
-    else if (this->lattce_meam[i][i] == DIM)
-      this->re_meam[i][i] = tmplat[i];
-    else if (this->lattce_meam[i][i] == DIA)
-      this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 4.0;
-    else {
+    switch(this->lattce_meam[i][i]) {
+      case FCC:
+        this->re_meam[i][i] = tmplat[i] / sqrt(2.0);
+        break;
+      case BCC:
+        this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 2.0;
+        break;
+      case HCP:
+      case DIM:
+      case CH4:
+      case LIN:
+      case ZIG:
+      case TRI:
+        this->re_meam[i][i] = tmplat[i];
+        break;
+      case DIA:
+      case DIA3:
+        this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 4.0;
+        break;
+      //default:
       //           error
     }
   }
@@ -82,4 +90,7 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, doub
   this->emb_lin_neg = 0;
   this->bkgd_dyn = 0;
   this->erose_form = 0;
+  // for trimer, zigzag, line refernece structure, sungkwang
+  setall2d(this->stheta_meam, 1.0); // stheta = sin(theta/2*pi/180) where theta is 180, so 1.0
+  setall2d(this->ctheta_meam, 0.0); // stheta = cos(theta/2*pi/180) where theta is 180, so 0
 }
diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/USER-MEAMC/meam_setup_param.cpp
index 585b5b5712..70d8b63598 100644
--- a/src/USER-MEAMC/meam_setup_param.cpp
+++ b/src/USER-MEAMC/meam_setup_param.cpp
@@ -1,6 +1,7 @@
 #include "meam.h"
 #include <algorithm>
 using namespace LAMMPS_NS;
+using namespace MathConst;
 
 //
 //     do a sanity check on index parameters
@@ -46,6 +47,8 @@ MEAM::meam_checkindex(int num, int lim, int nidx, int* idx /*idx(3)*/, int* ierr
 //     18 = zbl_meam
 //     19 = emb_lin_neg
 //     20 = bkgd_dyn
+//     21 = theta
+
 
 void
 MEAM::meam_setup_param(int which, double value, int nindex, int* index /*index(3)*/, int* errorflag)
@@ -203,6 +206,20 @@ MEAM::meam_setup_param(int which, double value, int nindex, int* index /*index(3
       this->bkgd_dyn = (int)value;
       break;
 
+    //     21 = theta
+    // see alloyparams(void) in meam_setup_done.cpp
+    case 21:
+      // const double PI = 3.141592653589793238463;
+      meam_checkindex(2, neltypes, nindex, index, errorflag);
+      if (*errorflag != 0)
+        return;
+      i1 = std::min(index[0], index[1]);
+      i2 = std::max(index[0], index[1]);
+      // we don't use theta, instead stheta and ctheta
+      this->stheta_meam[i1][i2] = sin(value/2*MY_PI/180.0);
+      this->ctheta_meam[i1][i2] = cos(value/2*MY_PI/180.0);
+      break;
+
     default:
       *errorflag = 1;
   }
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index a9034a1af3..3d7d0b2a17 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -33,13 +33,13 @@ using namespace LAMMPS_NS;
 
 #define MAXLINE 1024
 
-static const int nkeywords = 21;
+static const int nkeywords = 22;
 static const char *keywords[] = {
   "Ec","alpha","rho0","delta","lattce",
   "attrac","repuls","nn2","Cmin","Cmax","rc","delr",
   "augt1","gsmooth_factor","re","ialloy",
   "mixture_ref_t","erose_form","zbl",
-  "emb_lin_neg","bkgd_dyn"};
+  "emb_lin_neg","bkgd_dyn", "theta"};
 
 /* ---------------------------------------------------------------------- */
 
@@ -56,6 +56,7 @@ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp)
   elements = NULL;
   mass = NULL;
   meam_inst = new MEAM(memory);
+  scale = NULL;
 
   // set comm size needed by this Pair
 
@@ -79,6 +80,7 @@ PairMEAMC::~PairMEAMC()
   if (allocated) {
     memory->destroy(setflag);
     memory->destroy(cutsq);
+    memory->destroy(scale);
     delete [] map;
   }
 }
@@ -143,7 +145,7 @@ void PairMEAMC::compute(int eflag, int vflag)
   comm->reverse_comm_pair(this);
 
   meam_inst->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom,
-                   &eng_vdwl,eatom,ntype,type,map,errorflag);
+                   &eng_vdwl,eatom,ntype,type,map,scale,errorflag);
   if (errorflag) {
     char str[128];
     sprintf(str,"MEAM library error %d",errorflag);
@@ -164,7 +166,7 @@ void PairMEAMC::compute(int eflag, int vflag)
   for (ii = 0; ii < inum_half; ii++) {
     i = ilist_half[ii];
     meam_inst->meam_force(i,eflag_either,eflag_global,eflag_atom,
-                vflag_atom,&eng_vdwl,eatom,ntype,type,map,x,
+                vflag_atom,&eng_vdwl,eatom,ntype,type,map,scale,x,
                 numneigh_half[i],firstneigh_half[i],
                 numneigh_full[i],firstneigh_full[i],
                 offset,f,vptr);
@@ -183,6 +185,7 @@ void PairMEAMC::allocate()
 
   memory->create(setflag,n+1,n+1,"pair:setflag");
   memory->create(cutsq,n+1,n+1,"pair:cutsq");
+  memory->create(scale,n+1,n+1,"pair:scale");
 
   map = new int[n+1];
 }
@@ -267,13 +270,16 @@ void PairMEAMC::coeff(int narg, char **arg)
   // set mass for i,i in atom class
 
   int count = 0;
-  for (int i = 1; i <= n; i++)
-    for (int j = i; j <= n; j++)
+  for (int i = 1; i <= n; i++) {
+    for (int j = i; j <= n; j++) {
       if (map[i] >= 0 && map[j] >= 0) {
         setflag[i][j] = 1;
         if (i == j) atom->set_mass(FLERR,i,mass[map[i]]);
         count++;
       }
+      scale[i][j] = 1.0;
+    }
+  }
 
   if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
 }
@@ -312,8 +318,10 @@ void PairMEAMC::init_list(int id, NeighList *ptr)
    init for one type pair i,j and corresponding j,i
 ------------------------------------------------------------------------- */
 
-double PairMEAMC::init_one(int /*i*/, int /*j*/)
+double PairMEAMC::init_one(int i, int j)
 {
+  if (setflag[i][j] == 0) scale[i][j] = 1.0;
+  scale[j][i] = scale[i][j];
   return cutmax;
 }
 
@@ -431,12 +439,8 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
 
     // map lat string to an integer
 
-    if (strcmp(words[1],"fcc") == 0) lat[i] = FCC;
-    else if (strcmp(words[1],"bcc") == 0) lat[i] = BCC;
-    else if (strcmp(words[1],"hcp") == 0) lat[i] = HCP;
-    else if (strcmp(words[1],"dim") == 0) lat[i] = DIM;
-    else if (strcmp(words[1],"dia") == 0) lat[i] = DIA;
-    else error->all(FLERR,"Unrecognized lattice type in MEAM file 1");
+    if (!MEAM::str_to_lat(words[1], true, lat[i]))
+      error->all(FLERR,"Unrecognized lattice type in MEAM file 1");
 
     // store parameters
 
@@ -458,8 +462,12 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
     rozero[i] = atof(words[17]);
     ibar[i] = atoi(words[18]);
 
-    if (!iszero(t0[i]-1.0))
-      error->all(FLERR,"Unsupported parameter in MEAM potential file");
+    if (!isone(t0[i]))
+      error->all(FLERR,"Unsupported parameter in MEAM potential file: t0!=1");
+
+    // z given is ignored: if this is mismatched, we definitely won't do what the user said -> fatal error
+    if (z[i] != MEAM::get_Zij(lat[i]))
+      error->all(FLERR,"Mismatched parameter in MEAM potential file: z!=lat");
 
     nset++;
   }
@@ -471,7 +479,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
 
   // pass element parameters to MEAM package
 
-  meam_inst->meam_setup_global(nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3,
+  meam_inst->meam_setup_global(nelements,lat,ielement,atwt,alpha,b0,b1,b2,b3,
                        alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
 
   // set element masses
@@ -523,6 +531,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
 
   int which;
   double value;
+  lattice_t latt;
   int nindex,index[3];
   int maxparams = 6;
   char **params = new char*[maxparams];
@@ -571,16 +580,9 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
     // map lattce_meam value to an integer
 
     if (which == 4) {
-      if (strcmp(params[nparams-1],"fcc") == 0) value = FCC;
-      else if (strcmp(params[nparams-1],"bcc") == 0) value = BCC;
-      else if (strcmp(params[nparams-1],"hcp") == 0) value = HCP;
-      else if (strcmp(params[nparams-1],"dim") == 0) value = DIM;
-      else if (strcmp(params[nparams-1],"dia") == 0) value = DIA;
-      else if (strcmp(params[nparams-1],"b1")  == 0) value = B1;
-      else if (strcmp(params[nparams-1],"c11") == 0) value = C11;
-      else if (strcmp(params[nparams-1],"l12") == 0) value = L12;
-      else if (strcmp(params[nparams-1],"b2")  == 0) value = B2;
-      else error->all(FLERR,"Unrecognized lattice type in MEAM file 2");
+      if (!MEAM::str_to_lat(params[nparams-1], false, latt))
+        error->all(FLERR,"Unrecognized lattice type in MEAM file 2");
+      value = latt;
     }
     else value = atof(params[nparams-1]);
 
@@ -783,3 +785,12 @@ void PairMEAMC::neigh_strip(int inum, int *ilist,
     for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK;
   }
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *PairMEAMC::extract(const char *str, int &dim)
+{
+  dim = 2;
+  if (strcmp(str,"scale") == 0) return (void *) scale;
+  return NULL;
+}
diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h
index 31dd8ba022..102985f0ca 100644
--- a/src/USER-MEAMC/pair_meamc.h
+++ b/src/USER-MEAMC/pair_meamc.h
@@ -35,6 +35,7 @@ class PairMEAMC : public Pair {
   void init_style();
   void init_list(int, class NeighList *);
   double init_one(int, int);
+  virtual void *extract(const char *, int &);
 
   int pack_forward_comm(int, int *, double *, int, int *);
   void unpack_forward_comm(int, int, double *);
@@ -50,6 +51,7 @@ class PairMEAMC : public Pair {
   double *mass;                 // mass of each element
 
   int *map;                     // mapping from atom types (1-indexed) to elements (1-indexed)
+  double **scale;               // scaling factor for adapt
 
   void allocate();
   void read_files(char *, char *);
diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp
index f72b6d6b93..c32477513d 100644
--- a/src/USER-MESO/pair_edpd.cpp
+++ b/src/USER-MESO/pair_edpd.cpp
@@ -31,6 +31,7 @@
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -452,24 +453,24 @@ void PairEDPD::read_restart(FILE *fp)
   int me = comm->me;
   for (int i = 1; i <= atom->ntypes; i++)
     for (int j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a0[i][j],sizeof(double),1,fp);
-          fread(&gamma[i][j],sizeof(double),1,fp);
-          fread(&power[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
-          fread(&kappa[i][j],sizeof(double),1,fp);
-          fread(&powerT[i][j],sizeof(double),1,fp);
-          fread(&cutT[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&power[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&kappa[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&powerT[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cutT[i][j],sizeof(double),1,fp,NULL,error);
           if(power_flag)
           for (int k = 0; k < 4; k++)
-            fread(&sc[i][j][k],sizeof(double),1,fp);
+            utils::sfread(FLERR,&sc[i][j][k],sizeof(double),1,fp,NULL,error);
 
           if(kappa_flag)
           for (int k = 0; k < 4; k++)
-            fread(&kc[i][j][k],sizeof(double),1,fp);
+            utils::sfread(FLERR,&kc[i][j][k],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
@@ -507,9 +508,9 @@ void PairEDPD::write_restart_settings(FILE *fp)
 void PairEDPD::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&seed,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&seed,1,MPI_INT,0,world);
diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp
index 56adad26ce..7f98e6da79 100644
--- a/src/USER-MESO/pair_mdpd.cpp
+++ b/src/USER-MESO/pair_mdpd.cpp
@@ -30,6 +30,7 @@
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -347,15 +348,15 @@ void PairMDPD::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&A_att[i][j],sizeof(double),1,fp);
-          fread(&B_rep[i][j],sizeof(double),1,fp);
-          fread(&gamma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
-          fread(&cut_r[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&A_att[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&B_rep[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_r[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&A_att[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&B_rep[i][j],1,MPI_DOUBLE,0,world);
@@ -385,10 +386,10 @@ void PairMDPD::write_restart_settings(FILE *fp)
 void PairMDPD::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&temperature,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&seed,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&temperature,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index 346401b1ba..f5350de53d 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -29,6 +29,7 @@
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -394,19 +395,19 @@ void PairTDPD::read_restart(FILE *fp)
   int me = comm->me;
   for (int i = 1; i <= atom->ntypes; i++)
     for (int j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a0[i][j],sizeof(double),1,fp);
-          fread(&gamma[i][j],sizeof(double),1,fp);
-          fread(&power[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
-          fread(&cutcc[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&power[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cutcc[i][j],sizeof(double),1,fp,NULL,error);
           for(int k=0; k<cc_species; k++) {
-            fread(&kappa[i][j][k],sizeof(double),1,fp);
-            fread(&epsilon[i][j][k],sizeof(double),1,fp);
-            fread(&powercc[i][j][k],sizeof(double),1,fp);
+            utils::sfread(FLERR,&kappa[i][j][k],sizeof(double),1,fp,NULL,error);
+            utils::sfread(FLERR,&epsilon[i][j][k],sizeof(double),1,fp,NULL,error);
+            utils::sfread(FLERR,&powercc[i][j][k],sizeof(double),1,fp,NULL,error);
           }
         }
         MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
@@ -442,10 +443,10 @@ void PairTDPD::write_restart_settings(FILE *fp)
 void PairTDPD::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&temperature,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&seed,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&temperature,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 442feedf87..18b8cfb58d 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -31,6 +31,7 @@ compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
 compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
 compute gyration/shape, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 July 2019
+compute gyration/shape/chunk, Evangelos Voyiatzis, evoyiatzis at gmail.com, 22 October 2019
 compute hma, Andrew Schultz & David Kofke (UB), ajs42 at buffalo.edu & kofke at buffalo.edu, 1 Jul 2019
 compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018
 compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019
@@ -84,6 +85,7 @@ pair_style lebedeva/z, Zbigniew Koziol (National Center for Nuclear Research), s
 pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
 pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
 pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
+pair_style local/density, Tanmoy Sanyal (tanmoy dot 7989 at gmail.com) and M. Scott Shell (UCSB), and David Rosenberger (TU Darmstadt), 9 Sept 19
 pair_style kolmogorov/crespi/full, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
 pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17
 pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp
index b18ddc79d3..d403b61c42 100644
--- a/src/USER-MISC/angle_cosine_shift.cpp
+++ b/src/USER-MISC/angle_cosine_shift.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -224,10 +225,10 @@ void AngleCosineShift::read_restart(FILE *fp)
 
   if (comm->me == 0)
     {
-       fread(&k[1],sizeof(double),atom->nangletypes,fp);
-       fread(&kcost[1],sizeof(double),atom->nangletypes,fp);
-       fread(&ksint[1],sizeof(double),atom->nangletypes,fp);
-       fread(&theta[1],sizeof(double),atom->nangletypes,fp);
+      utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+      utils::sfread(FLERR,&kcost[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+      utils::sfread(FLERR,&ksint[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+      utils::sfread(FLERR,&theta[1],sizeof(double),atom->nangletypes,fp,NULL,error);
     }
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&kcost[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp
index 79cb0fea7c..ef5a2824b9 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.cpp
+++ b/src/USER-MISC/angle_cosine_shift_exp.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -256,11 +257,11 @@ void AngleCosineShiftExp::read_restart(FILE *fp)
 
   if (comm->me == 0)
       {
-         fread(&umin[1],sizeof(double),atom->nangletypes,fp);
-         fread(&a[1],sizeof(double),atom->nangletypes,fp);
-         fread(&cost[1],sizeof(double),atom->nangletypes,fp);
-         fread(&sint[1],sizeof(double),atom->nangletypes,fp);
-         fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+        utils::sfread(FLERR,&umin[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+        utils::sfread(FLERR,&a[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+        utils::sfread(FLERR,&cost[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+        utils::sfread(FLERR,&sint[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+        utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
       }
   MPI_Bcast(&umin[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&a[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index 0956ba3b8f..e2fd7e618f 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -205,8 +206,8 @@ void AngleDipole::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&gamma0[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&gamma0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&gamma0[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp
index dcf5080431..f83c9c4f88 100644
--- a/src/USER-MISC/angle_fourier.cpp
+++ b/src/USER-MISC/angle_fourier.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -231,10 +232,10 @@ void AngleFourier::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&C0[1],sizeof(double),atom->nangletypes,fp);
-    fread(&C1[1],sizeof(double),atom->nangletypes,fp);
-    fread(&C2[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&C0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&C1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&C2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&C0[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp
index bbe3f8520b..baf4953760 100644
--- a/src/USER-MISC/angle_fourier_simple.cpp
+++ b/src/USER-MISC/angle_fourier_simple.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -237,9 +238,9 @@ void AngleFourierSimple::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&C[1],sizeof(double),atom->nangletypes,fp);
-    fread(&N[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&C[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&N[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&C[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp
index 5c5f3411e4..097e774f17 100644
--- a/src/USER-MISC/angle_quartic.cpp
+++ b/src/USER-MISC/angle_quartic.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -232,10 +233,10 @@ void AngleQuartic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k2[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k3[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k4[1],sizeof(double),atom->nangletypes,fp);
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&k3[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp
index fdd3111783..79e401eddb 100644
--- a/src/USER-MISC/bond_harmonic_shift.cpp
+++ b/src/USER-MISC/bond_harmonic_shift.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -176,9 +177,9 @@ void BondHarmonicShift::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r1[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r1[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp
index 0688cb428a..aa051f4bec 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.cpp
+++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -178,9 +179,9 @@ void BondHarmonicShiftCut::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r1[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r1[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp
index a0ee6089b7..aef5ef91a3 100644
--- a/src/USER-MISC/compute_gyration_shape.cpp
+++ b/src/USER-MISC/compute_gyration_shape.cpp
@@ -39,7 +39,7 @@ ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 0;
   extvector = 0;
 
-  // ID of compute gyration 
+  // ID of compute gyration
   int n = strlen(arg[3]) + 1;
   id_gyration = new char[n];
   strcpy(id_gyration,arg[3]);
@@ -112,19 +112,15 @@ void ComputeGyrationShape::compute_vector()
   }
 
   // compute the shape parameters of the gyration tensor
-  double sq_eigen_x = MathSpecial::square(evalues[0]);
-  double sq_eigen_y = MathSpecial::square(evalues[1]);
-  double sq_eigen_z = MathSpecial::square(evalues[2]);
-
-  double nominator = MathSpecial::square(sq_eigen_x)
-    + MathSpecial::square(sq_eigen_y)
-    + MathSpecial::square(sq_eigen_z);
-  double denominator = MathSpecial::square(sq_eigen_x+sq_eigen_y+sq_eigen_z);
+  double nominator = MathSpecial::square(evalues[0])
+    + MathSpecial::square(evalues[1])
+    + MathSpecial::square(evalues[2]);
+  double denominator = MathSpecial::square(evalues[0]+evalues[1]+evalues[2]);
 
   vector[0] = evalues[0];
   vector[1] = evalues[1];
   vector[2] = evalues[2];
-  vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y);
-  vector[4] = sq_eigen_y - sq_eigen_x;
-  vector[5] = 0.5*(3*nominator/denominator - 1.0);
+  vector[3] = evalues[0] - 0.5*(evalues[1] + evalues[2]);
+  vector[4] = evalues[1] - evalues[2];
+  vector[5] = 1.5*nominator/denominator - 0.5;
 }
diff --git a/src/USER-MISC/compute_gyration_shape_chunk.cpp b/src/USER-MISC/compute_gyration_shape_chunk.cpp
new file mode 100644
index 0000000000..b493455ebf
--- /dev/null
+++ b/src/USER-MISC/compute_gyration_shape_chunk.cpp
@@ -0,0 +1,191 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ *    Contributing author:  Evangelos Voyiatzis (Royal DSM)
+ * ------------------------------------------------------------------------- */
+
+
+#include "compute_gyration_shape_chunk.h"
+#include <cmath>
+#include <cstring>
+#include "error.h"
+#include "math_extra.h"
+#include "math_special.h"
+#include "modify.h"
+#include "memory.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg), id_gyration_chunk(NULL), shape_parameters(NULL)
+{
+  if (narg != 4) error->all(FLERR,"Illegal compute gyration/shape/chunk command");
+
+  // ID of compute gyration
+  int n = strlen(arg[3]) + 1;
+  id_gyration_chunk = new char[n];
+  strcpy(id_gyration_chunk,arg[3]);
+
+  init();
+
+  array_flag = 1;
+  size_array_cols = 6;
+  size_array_rows = 0;
+  size_array_rows_variable = 1;
+  extarray = 0;
+
+  firstflag = 1;
+  former_nchunks = 0;
+  current_nchunks = 1;
+  allocate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyrationShapeChunk::~ComputeGyrationShapeChunk()
+{
+  delete [] id_gyration_chunk;
+  memory->destroy(shape_parameters);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGyrationShapeChunk::init()
+{
+  // check that the compute gyration command exist
+  int icompute = modify->find_compute(id_gyration_chunk);
+  if (icompute < 0)
+    error->all(FLERR,"Compute gyration/chunk ID does not exist for "
+               "compute gyration/shape/chunk");
+
+  // check the id_gyration_chunk corresponds really to a compute gyration/chunk command
+  c_gyration_chunk = (Compute *) modify->compute[icompute];
+  if (strcmp(c_gyration_chunk->style,"gyration/chunk") != 0)
+    error->all(FLERR,"Compute gyration/shape/chunk does not point to "
+               "gyration compute/chunk");
+
+  // check the compute gyration/chunk command computes the whole gyration tensor
+  if (c_gyration_chunk->array_flag == 0)
+    error->all(FLERR,"Compute gyration/chunk where gyration/shape/chunk points to "
+               "does not calculate the gyration tensor");
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGyrationShapeChunk::setup()
+{
+  // one-time calculation of per-chunk mass
+  // done in setup, so that ComputeChunkAtom::setup() is already called
+
+  if (firstflag) {
+    compute_array();
+    firstflag = 0;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   compute shape parameters based on the eigenvalues of the
+   gyration tensor of group of atoms
+------------------------------------------------------------------------- */
+
+void ComputeGyrationShapeChunk::compute_array()
+{
+  invoked_array = update->ntimestep;
+  c_gyration_chunk->compute_array();
+
+  current_nchunks = c_gyration_chunk->size_array_rows; // how to check for the number of chunks in the gyration/chunk?
+  if (former_nchunks != current_nchunks) allocate();
+
+  double **gyration_tensor = c_gyration_chunk->array;
+
+  // call the function for the calculation of the eigenvalues
+  double ione[3][3], evalues[3], evectors[3][3];
+
+  for (int ichunk = 0; ichunk < current_nchunks; ichunk++) {
+
+    ione[0][0] = gyration_tensor[ichunk][0];
+    ione[1][1] = gyration_tensor[ichunk][1];
+    ione[2][2] = gyration_tensor[ichunk][2];
+    ione[0][1] = ione[1][0] = gyration_tensor[ichunk][3];
+    ione[0][2] = ione[2][0] = gyration_tensor[ichunk][4];
+    ione[1][2] = ione[2][1] = gyration_tensor[ichunk][5];
+
+    int ierror = MathExtra::jacobi(ione,evalues,evectors);
+    if (ierror) error->all(FLERR, "Insufficient Jacobi rotations "
+                         "for gyration/shape");
+
+    // sort the eigenvalues according to their size with bubble sort
+    double t;
+    for (int i = 0; i < 3; i++) {
+      for (int j = 0; j < 2-i; j++) {
+        if (fabs(evalues[j]) < fabs(evalues[j+1])) {
+          t = evalues[j];
+          evalues[j] = evalues[j+1];
+          evalues[j+1] = t;
+        }
+      }
+    }
+
+    // compute the shape parameters of the gyration tensor
+    double sq_eigen_x = MathSpecial::square(evalues[0]);
+    double sq_eigen_y = MathSpecial::square(evalues[1]);
+    double sq_eigen_z = MathSpecial::square(evalues[2]);
+
+    double nominator = sq_eigen_x + sq_eigen_y + sq_eigen_z;
+    double denominator = MathSpecial::square(evalues[0]+evalues[1]+evalues[2]);
+
+    shape_parameters[ichunk][0] = evalues[0];
+    shape_parameters[ichunk][1] = evalues[1];
+    shape_parameters[ichunk][2] = evalues[2];
+    shape_parameters[ichunk][3] = evalues[0] - 0.5*(evalues[1] + evalues[2]);
+    shape_parameters[ichunk][4] = evalues[1] - evalues[2];
+    shape_parameters[ichunk][5] = 1.5*nominator/denominator - 0.5;
+  }
+}
+
+/* ----------------------------------------------------------------------
+ *    calculate and return # of chunks = length of vector/array
+ *    ------------------------------------------------------------------------- */
+
+int ComputeGyrationShapeChunk::lock_length()
+{
+  int number_of_chunks = c_gyration_chunk->size_array_rows;
+  return number_of_chunks;
+}
+
+/* ----------------------------------------------------------------------
+ *    free and reallocate per-chunk arrays
+ * ---------------------------------------------------------------------- */
+
+void ComputeGyrationShapeChunk::allocate()
+{
+  memory->destroy(shape_parameters);
+  former_nchunks = current_nchunks;
+  memory->create(shape_parameters,current_nchunks,6,"gyration/shape/chunk:shape_parameters");
+  array = shape_parameters;
+}
+
+/* ----------------------------------------------------------------------
+ *    memory usage of local data
+ * ---------------------------------------------------------------------- */
+
+double ComputeGyrationShapeChunk::memory_usage()
+{
+  double bytes = (bigint) current_nchunks * 6 * sizeof(double);
+  return bytes;
+}
diff --git a/src/USER-MISC/compute_gyration_shape_chunk.h b/src/USER-MISC/compute_gyration_shape_chunk.h
new file mode 100644
index 0000000000..1ce4b9f758
--- /dev/null
+++ b/src/USER-MISC/compute_gyration_shape_chunk.h
@@ -0,0 +1,75 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(gyration/shape/chunk,ComputeGyrationShapeChunk)
+
+#else
+
+#ifndef LMP_COMPUTE_GYRATION_SHAPE_CHUNK_H
+#define LMP_COMPUTE_GYRATION_SHAPE_CHUNK_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeGyrationShapeChunk : public Compute {
+ public:
+  char *id_gyration_chunk;              // fields accessed by other classes
+
+  ComputeGyrationShapeChunk(class LAMMPS *, int, char **);
+  ~ComputeGyrationShapeChunk();
+  void init();
+  void setup();
+  void compute_array();
+
+  int lock_length();
+
+  double memory_usage();
+
+ private:
+  int current_nchunks, former_nchunks;
+  int firstflag;
+  double **shape_parameters;
+  class Compute *c_gyration_chunk;
+
+  void allocate();
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Compute gyration/chunk ID does not exist for compute gyration/shape/chunk
+
+Self-explanatory.  Provide a valid compute ID
+
+E: Compute gyration/shape/chunk ID does not point to a gyration/chunk compute
+
+Self-explanatory.  Provide an ID of a compute gyration/chunk command.
+
+E: Compute gyration/chunk does not compute gyration tensor
+
+Self-explanatory. Use keyword tensor in compute gyration/chunk command
+*/
diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp
index a14084b9ca..f552126f4f 100644
--- a/src/USER-MISC/compute_hma.cpp
+++ b/src/USER-MISC/compute_hma.cpp
@@ -78,21 +78,21 @@ using namespace LAMMPS_NS;
 ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg), id_temp(NULL), deltaR(NULL)
 {
-  if (narg < 4) error->all(FLERR,"Illegal compute hma command");                    
+  if (narg < 4) error->all(FLERR,"Illegal compute hma command");
   if (igroup) error->all(FLERR,"Compute hma must use group all");
-  if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");}       
+  if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");}
   else {
-    int n = strlen(arg[3]) + 1;                  
-    id_temp = new char[n];   
-    strcpy(id_temp,arg[3]);                         
+    int n = strlen(arg[3]) + 1;
+    id_temp = new char[n];
+    strcpy(id_temp,arg[3]);
   }
- 
-  create_attribute = 1;                  
-  extscalar = 1;                         
-  timeflag = 1;                         
 
-  // (from compute displace/atom) create a new fix STORE style  
-  // our new fix's id (id_fix)= compute-ID + COMPUTE_STORE 
+  create_attribute = 1;
+  extscalar = 1;
+  timeflag = 1;
+
+  // (from compute displace/atom) create a new fix STORE style
+  // our new fix's id (id_fix)= compute-ID + COMPUTE_STORE
   // our new fix's group = same as compute group
 
   int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
@@ -100,30 +100,30 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
   strcpy(id_fix,id);
   strcat(id_fix,"_COMPUTE_STORE");
 
-  char **newarg = new char*[6];     
+  char **newarg = new char*[6];
   newarg[0] = id_fix;
   newarg[1] = group->names[igroup];
-  newarg[2] = (char *) "STORE";              
+  newarg[2] = (char *) "STORE";
   newarg[3] = (char *) "peratom";
   newarg[4] = (char *) "1";
   newarg[5] = (char *) "3";
-  modify->add_fix(6,newarg);        
-  fix = (FixStore *) modify->fix[modify->nfix-1];    
- 
-  delete [] newarg;                               
+  modify->add_fix(6,newarg);
+  fix = (FixStore *) modify->fix[modify->nfix-1];
+
+  delete [] newarg;
 
   // calculate xu,yu,zu for fix store array
   // skip if reset from restart file
 
-  if (fix->restart_reset) fix->restart_reset = 0;   
+  if (fix->restart_reset) fix->restart_reset = 0;
   else {
-    double **xoriginal = fix->astore;            
+    double **xoriginal = fix->astore;
     double **x = atom->x;
     imageint *image = atom->image;
     int nlocal = atom->nlocal;
 
     for (int i = 0; i < nlocal; i++)
-      domain->unmap(x[i],image[i],xoriginal[i]);          
+      domain->unmap(x[i],image[i],xoriginal[i]);
   }
 
   vector_flag = 1;
@@ -175,7 +175,7 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
   memory->create(vector, size_vector, "hma:vector");
 
   if (computeU>-1 || computeCv>-1) {
-    peflag = 1;                             
+    peflag = 1;
   }
   if (computeP>-1) {
     pressflag = 1;
@@ -209,12 +209,12 @@ void ComputeHMA::init() {
   }
 
   int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->pair = 0; 
-  neighbor->requests[irequest]->compute = 1; 
-  neighbor->requests[irequest]->occasional = 1; 
+  neighbor->requests[irequest]->pair = 0;
+  neighbor->requests[irequest]->compute = 1;
+  neighbor->requests[irequest]->occasional = 1;
 }
 
-void ComputeHMA::init_list(int id, NeighList *ptr)
+void ComputeHMA::init_list(int /* id */, NeighList *ptr)
 {
   list = ptr;
 }
@@ -224,22 +224,22 @@ void ComputeHMA::setup()
   int dummy=0;
   int ifix = modify->find_fix(id_temp);
   if (ifix < 0) error->all(FLERR,"Could not find compute hma temperature ID");
-  double * temperat = (double *) modify->fix[ifix]->extract("t_target",dummy);      
+  double * temperat = (double *) modify->fix[ifix]->extract("t_target",dummy);
   if (temperat==NULL) error->all(FLERR,"Could not find compute hma temperature ID");
-  finaltemp = * temperat;       
+  finaltemp = * temperat;
 
   // set fix which stores original atom coords
 
   int ifix2 = modify->find_fix(id_fix);
   if (ifix2 < 0) error->all(FLERR,"Could not find hma store fix ID");
-  fix = (FixStore *) modify->fix[ifix2];             
+  fix = (FixStore *) modify->fix[ifix2];
 }
 
 /* ---------------------------------------------------------------------- */
 
 void ComputeHMA::compute_vector()
 {
-  invoked_vector = update->ntimestep;         
+  invoked_vector = update->ntimestep;
 
   // grow deltaR array if necessary
   if (comm_forward>0 && atom->nmax > nmax) {
@@ -257,7 +257,7 @@ void ComputeHMA::compute_vector()
   int nlocal = atom->nlocal;
 
   double *h = domain->h;
-  double xprd = domain->xprd;   
+  double xprd = domain->xprd;
   double yprd = domain->yprd;
   double zprd = domain->zprd;
 
@@ -318,11 +318,9 @@ void ComputeHMA::compute_vector()
   double phiSum = 0.0;
   if (computeCv>-1) {
     comm->forward_comm_compute(this);
-    int *type = atom->type;
     double** cutsq = force->pair->cutsq;
     if (force->pair) {
       double **x = atom->x;
-      double **f = atom->f;
       int *type = atom->type;
       int nlocal = atom->nlocal;
       double *special_lj = force->special_lj;
@@ -459,16 +457,8 @@ double ComputeHMA::virial_compute(int n)
 /* ---------------------------------------------------------------------- */
 
 int ComputeHMA::pack_forward_comm(int n, int *list, double *buf,
-                                        int pbc_flag, int *pbc)
+                                  int /* pbc_flag */, int * /* pbc */)
 {
-  double **xoriginal = fix->astore;
-  imageint *image = atom->image;
-  double **x = atom->x;
-  double *h = domain->h;
-  double xprd = domain->xprd;   
-  double yprd = domain->yprd;
-  double zprd = domain->zprd;
-
   int m = 0;
   for (int ii = 0; ii < n; ii++) {
     int i = list[ii];
@@ -483,7 +473,6 @@ int ComputeHMA::pack_forward_comm(int n, int *list, double *buf,
 
 void ComputeHMA::unpack_forward_comm(int n, int first, double *buf)
 {
-  double **xoriginal = fix->astore;
   int i,m,last;
 
   m = 0;
diff --git a/src/USER-MISC/compute_hma.h b/src/USER-MISC/compute_hma.h
index 233e8bbe57..5fc1130c8b 100644
--- a/src/USER-MISC/compute_hma.h
+++ b/src/USER-MISC/compute_hma.h
@@ -64,4 +64,4 @@ class ComputeHMA : public Compute {
 #endif
 #endif
 
- 
+
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
index 820dfabdeb..0537e555a2 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
@@ -26,6 +26,7 @@
 #include "memory.h"
 #include "math_const.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -321,11 +322,11 @@ void DihedralCosineShiftExp::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&umin[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&a[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&cost[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&sint[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&theta[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&umin[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&a[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&cost[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&sint[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&theta[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
   }
   MPI_Bcast(&umin[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&a[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp
index 7cc250b1a8..f30a5e1eab 100644
--- a/src/USER-MISC/dihedral_fourier.cpp
+++ b/src/USER-MISC/dihedral_fourier.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -364,7 +365,7 @@ void DihedralFourier::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0)
-    fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&nterms[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
 
   MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
 
@@ -379,9 +380,9 @@ void DihedralFourier::read_restart(FILE *fp)
 
   if (comm->me == 0) {
     for (int i=1; i<=atom->ndihedraltypes; i++) {
-      fread(k[i],sizeof(double),nterms[i],fp);
-      fread(multiplicity[i],sizeof(int),nterms[i],fp);
-      fread(shift[i],sizeof(double),nterms[i],fp);
+      utils::sfread(FLERR,k[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,multiplicity[i],sizeof(int),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,shift[i],sizeof(double),nterms[i],fp,NULL,error);
     }
   }
 
diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp
index f1e0018689..56254a5c03 100644
--- a/src/USER-MISC/dihedral_nharmonic.cpp
+++ b/src/USER-MISC/dihedral_nharmonic.cpp
@@ -26,6 +26,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -318,7 +319,7 @@ void DihedralNHarmonic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0)
-    fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&nterms[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
 
   MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
 
@@ -328,7 +329,7 @@ void DihedralNHarmonic::read_restart(FILE *fp)
 
   if (comm->me == 0) {
     for(int i = 1; i <= atom->ndihedraltypes; i++)
-      fread(a[i],sizeof(double),nterms[i],fp);
+      utils::sfread(FLERR,a[i],sizeof(double),nterms[i],fp,NULL,error);
   }
 
   for (int i = 1; i <= atom->ndihedraltypes; i++ )
diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp
index 02effc2f4f..28efad65b7 100644
--- a/src/USER-MISC/dihedral_quadratic.cpp
+++ b/src/USER-MISC/dihedral_quadratic.cpp
@@ -27,6 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -325,8 +326,8 @@ void DihedralQuadratic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
-    fread(&phi0[1],sizeof(double),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
+    utils::sfread(FLERR,&phi0[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&phi0[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp
index 78d45f923d..c72570c494 100644
--- a/src/USER-MISC/dihedral_spherical.cpp
+++ b/src/USER-MISC/dihedral_spherical.cpp
@@ -30,6 +30,7 @@
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace std;
 using namespace LAMMPS_NS;
@@ -755,7 +756,7 @@ void DihedralSpherical::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0)
-    fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
+    utils::sfread(FLERR,&nterms[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error);
 
   MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
 
@@ -775,16 +776,16 @@ void DihedralSpherical::read_restart(FILE *fp)
 
   if (comm->me == 0) {
     for (int i=1; i<=atom->ndihedraltypes; i++) {
-      fread(Ccoeff[i],sizeof(double),nterms[i],fp);
-      fread(phi_mult[i],sizeof(double),nterms[i],fp);
-      fread(phi_shift[i],sizeof(double),nterms[i],fp);
-      fread(phi_offset[i],sizeof(double),nterms[i],fp);
-      fread(theta1_mult[i],sizeof(double),nterms[i],fp);
-      fread(theta1_shift[i],sizeof(double),nterms[i],fp);
-      fread(theta1_offset[i],sizeof(double),nterms[i],fp);
-      fread(theta2_mult[i],sizeof(double),nterms[i],fp);
-      fread(theta2_shift[i],sizeof(double),nterms[i],fp);
-      fread(theta2_offset[i],sizeof(double),nterms[i],fp);
+      utils::sfread(FLERR,Ccoeff[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,phi_mult[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,phi_shift[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,phi_offset[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,theta1_mult[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,theta1_shift[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,theta1_offset[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,theta2_mult[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,theta2_shift[i],sizeof(double),nterms[i],fp,NULL,error);
+      utils::sfread(FLERR,theta2_offset[i],sizeof(double),nterms[i],fp,NULL,error);
     }
   }
 
diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp
index 59a16f376f..a14c3d9d79 100644
--- a/src/USER-MISC/dihedral_table.cpp
+++ b/src/USER-MISC/dihedral_table.cpp
@@ -33,6 +33,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "dihedral_table.h"
 #include "utils.h"
 
@@ -1042,8 +1043,8 @@ void DihedralTable::write_restart_settings(FILE *fp)
 void DihedralTable::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&tabstyle,sizeof(int),1,fp);
-    fread(&tablength,sizeof(int),1,fp);
+    utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
   }
 
   MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp
index 87f0c9bf66..8d530253c2 100644
--- a/src/USER-MISC/dihedral_table_cut.cpp
+++ b/src/USER-MISC/dihedral_table_cut.cpp
@@ -1029,8 +1029,8 @@ void DihedralTableCut::write_restart_settings(FILE *fp)
 void DihedralTableCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&tabstyle,sizeof(int),1,fp);
-    fread(&tablength,sizeof(int),1,fp);
+    utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
   }
 
   MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
index b1bcc07fa7..3a28e47cda 100644
--- a/src/USER-MISC/fix_ave_correlate_long.cpp
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -504,7 +504,8 @@ void FixAveCorrelateLong::end_of_step()
     fflush(fp);
     if (overwrite) {
       long fileend = ftell(fp);
-      if (fileend > 0) ftruncate(fileno(fp),fileend);
+      if ((fileend > 0) && (ftruncate(fileno(fp),fileend)))
+        perror("Error while tuncating output");
     }
   }
 
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 05dc54c57e..2995a596a5 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -35,6 +35,8 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
 #include "molecule.h"
 #include "group.h"
 #include "citeme.h"
+#include "math_const.h"
+#include "math_extra.h"
 #include "memory.h"
 #include "error.h"
 
@@ -42,6 +44,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
+using namespace MathConst;
 
 static const char cite_fix_bond_react[] =
   "fix bond/react:\n\n"
@@ -56,9 +59,8 @@ static const char cite_fix_bond_react[] =
 
 #define BIG 1.0e20
 #define DELTA 16
-#define MAXLINE 256
 #define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm
-#define MAXCONARGS 5 // max # of arguments for any type of constraint
+#define MAXCONARGS 7 // max # of arguments for any type of constraint + rxnID
 
 // various statuses of superimpose algorithm:
 // ACCEPT: site successfully matched to pre-reacted template
@@ -69,6 +71,9 @@ static const char cite_fix_bond_react[] =
 // RESTORE: restore mode, load most recent restore point
 enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};
 
+// types of available reaction constraints
+enum{DISTANCE,ANGLE,ARRHENIUS};
+
 /* ---------------------------------------------------------------------- */
 
 FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
@@ -87,6 +92,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   MPI_Comm_size(world,&nprocs);
   newton_bond = force->newton_bond;
 
+  restart_global = 1;
   attempted_rxn = 0;
   force_reneighbor = 1;
   next_reneighbor = -1;
@@ -94,6 +100,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   global_freq = 1;
   extvector = 0;
   rxnID = 0;
+  nconstraints = 0;
+  narrhenius = 0;
   status = PROCEED;
 
   nxspecial = NULL;
@@ -107,7 +115,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   master_group = (char *) "bond_react_MASTER_group";
 
   // by using fixed group names, only one instance of fix bond/react is allowed.
-  if (modify->find_fix_by_style("bond/react") != -1)
+  if (modify->find_fix_by_style("^bond/react") != -1)
     error->all(FLERR,"Only one instance of fix bond/react allowed at a time");
 
   // let's find number of reactions specified
@@ -169,8 +177,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   memory->create(limit_duration,nreacts,"bond/react:limit_duration");
   memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
   memory->create(update_edges_flag,nreacts,"bond/react:update_edges_flag");
-  memory->create(nconstraints,nreacts,"bond/react:nconstraints");
-  memory->create(constraints,nreacts,MAXCONARGS,"bond/react:constraints");
+  memory->create(constraints,1,MAXCONARGS,"bond/react:constraints");
   memory->create(iatomtype,nreacts,"bond/react:iatomtype");
   memory->create(jatomtype,nreacts,"bond/react:jatomtype");
   memory->create(ibonding,nreacts,"bond/react:ibonding");
@@ -188,7 +195,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     max_rxn[i] = INT_MAX;
     stabilize_steps_flag[i] = 0;
     update_edges_flag[i] = 0;
-    nconstraints[i] = 0;
     // set default limit duration to 60 timesteps
     limit_duration[i] = 60;
     reaction_count[i] = 0;
@@ -207,7 +213,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
 
     iarg++;
 
-    rxn_name[rxn] = arg[iarg++];
+    int n = strlen(arg[iarg]) + 1;
+    if (n > MAXLINE) error->all(FLERR,"Reaction name (react-ID) is too long (limit: 256 characters)");
+    strncpy(rxn_name[rxn],arg[iarg++],n);
 
     int igroup = group->find(arg[iarg++]);
     if (igroup == -1) error->all(FLERR,"Could not find fix group ID");
@@ -252,12 +260,12 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
                                        "probability seed must be positive");
         iarg += 3;
       } else if (strcmp(arg[iarg],"max_rxn") == 0) {
-	      if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
-	      			                        "'max_rxn' has too few arguments");
-	      max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]);
-	      if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: "
-	      				                         "'max_rxn' cannot be negative");
-	      iarg += 2;
+              if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
+                                                        "'max_rxn' has too few arguments");
+              max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]);
+              if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: "
+                                                                 "'max_rxn' cannot be negative");
+              iarg += 2;
       } else if (strcmp(arg[iarg],"stabilize_steps") == 0) {
         if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword "
                                                 "used without stabilization keyword");
@@ -290,6 +298,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
   memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges");
   memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
+  memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms");
 
   for (int j = 0; j < nreacts; j++)
     for (int i = 0; i < max_natoms; i++) {
@@ -297,6 +306,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
       if (update_edges_flag[j] == 1) custom_edges[i][j] = 1;
       else custom_edges[i][j] = 0;
       delete_atoms[i][j] = 0;
+      for (int k = 0; k < 6; k++) {
+        chiral_atoms[i][k][j] = 0;
+      }
     }
 
   // read all map files afterward
@@ -316,6 +328,16 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     find_landlocked_atoms(i);
   }
 
+  // initialize Marsaglia RNG with processor-unique seed (Arrhenius prob)
+
+  rrhandom = new class RanMars*[narrhenius];
+  int tmp = 0;
+  for (int i = 0; i < nconstraints; i++) {
+    if (constraints[i][1] == ARRHENIUS) {
+      rrhandom[tmp++] = new RanMars(lmp,(int) constraints[i][6] + me);
+    }
+  }
+
   for (int i = 0; i < nreacts; i++) {
     delete [] files[i];
   }
@@ -342,7 +364,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     }
   }
 
-  // initialize Marsaglia RNG with processor-unique seed
+  // initialize Marsaglia RNG with processor-unique seed ('prob' keyword)
 
   random = new class RanMars*[nreacts];
   for (int i = 0; i < nreacts; i++) {
@@ -386,6 +408,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   id_fix3 = NULL;
   statted_id = NULL;
   custom_exclude_flag = 0;
+
+  // used to store restart info
+  set = new Set[nreacts];
+  memset(set,0,nreacts*sizeof(Set));
 }
 
 /* ---------------------------------------------------------------------- */
@@ -409,6 +435,7 @@ FixBondReact::~FixBondReact()
   memory->destroy(landlocked_atoms);
   memory->destroy(custom_edges);
   memory->destroy(delete_atoms);
+  memory->destroy(chiral_atoms);
 
   memory->destroy(nevery);
   memory->destroy(cutsq);
@@ -469,6 +496,7 @@ FixBondReact::~FixBondReact()
   delete [] statted_id;
   delete [] guess_branch;
   delete [] pioneer_count;
+  delete [] set;
 
   if (group) {
     char **newarg;
@@ -1131,6 +1159,22 @@ void FixBondReact::superimpose_algorithm()
       glove[myjbonding-1][1] = created[lcl_inst][1][rxnID];
       glove_counter++;
 
+      // special case, only two atoms in reaction templates
+      // then: bonding onemol_nxspecials guaranteed to be equal, and either 0 or 1
+      if (glove_counter == onemol->natoms) {
+        tagint local_atom1 = atom->map(glove[myibonding-1][1]);
+        tagint local_atom2 = atom->map(glove[myjbonding-1][1]);
+        if ( (nxspecial[local_atom1][0] == onemol_nxspecial[myibonding-1][0] &&
+              nxspecial[local_atom2][0] == nxspecial[local_atom1][0]) &&
+             (nxspecial[local_atom1][0] == 0 ||
+              xspecial[local_atom1][0] == atom->tag[local_atom2]) &&
+             check_constraints() ) {
+          status = ACCEPT;
+          glove_ghostcheck();
+        } else
+          status = REJECT;
+      }
+
       avail_guesses = 0;
 
       for (int i = 0; i < max_natoms; i++)
@@ -1209,7 +1253,7 @@ void FixBondReact::superimpose_algorithm()
           rxn_by_proc[j] = -1; // corresponds to ghostly
         int itemp = 0;
         for (int j = 0; j < nprocs; j++)
-          for (int k = 0; k < local_rxn_count[j]; k++)
+          for (int k = 0; k < local_rxncounts[j]; k++)
             rxn_by_proc[itemp++] = j;
         std::random_shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn]);
         for (int j = 0; j < nprocs; j++)
@@ -1610,26 +1654,150 @@ evaluate constraints: return 0 if any aren't satisfied
 
 int FixBondReact::check_constraints()
 {
-  tagint atom1,atom2;
+  tagint atom1,atom2,atom3;
   double delx,dely,delz,rsq;
+  double delx1,dely1,delz1,delx2,dely2,delz2;
+  double rsq1,rsq2,r1,r2,c,t,prrhob;
 
   double **x = atom->x;
 
-  for (int i = 0; i < nconstraints[rxnID]; i++) {
-    if (constraints[rxnID][0] == 0) { // 'distance' type
-      atom1 = atom->map(glove[(int) constraints[rxnID][1]-1][1]);
-      atom2 = atom->map(glove[(int) constraints[rxnID][2]-1][1]);
-      delx = x[atom1][0] - x[atom2][0];
-      dely = x[atom1][1] - x[atom2][1];
-      delz = x[atom1][2] - x[atom2][2];
-      domain->minimum_image(delx,dely,delz); // ghost location fix
-      rsq = delx*delx + dely*dely + delz*delz;
-      if (rsq < constraints[rxnID][3] || rsq > constraints[rxnID][4]) return 0;
+  for (int i = 0; i < nconstraints; i++) {
+    if (constraints[i][0] == rxnID) {
+      if (constraints[i][1] == DISTANCE) {
+        atom1 = atom->map(glove[(int) constraints[i][2]-1][1]);
+        atom2 = atom->map(glove[(int) constraints[i][3]-1][1]);
+        delx = x[atom1][0] - x[atom2][0];
+        dely = x[atom1][1] - x[atom2][1];
+        delz = x[atom1][2] - x[atom2][2];
+        domain->minimum_image(delx,dely,delz); // ghost location fix
+        rsq = delx*delx + dely*dely + delz*delz;
+        if (rsq < constraints[i][4] || rsq > constraints[i][5]) return 0;
+      } else if (constraints[i][1] == ANGLE) {
+        atom1 = atom->map(glove[(int) constraints[i][2]-1][1]);
+        atom2 = atom->map(glove[(int) constraints[i][3]-1][1]);
+        atom3 = atom->map(glove[(int) constraints[i][4]-1][1]);
+
+        // 1st bond
+        delx1 = x[atom1][0] - x[atom2][0];
+        dely1 = x[atom1][1] - x[atom2][1];
+        delz1 = x[atom1][2] - x[atom2][2];
+        domain->minimum_image(delx1,dely1,delz1); // ghost location fix
+        rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
+        r1 = sqrt(rsq1);
+
+        // 2nd bond
+        delx2 = x[atom3][0] - x[atom2][0];
+        dely2 = x[atom3][1] - x[atom2][1];
+        delz2 = x[atom3][2] - x[atom2][2];
+        domain->minimum_image(delx2,dely2,delz2); // ghost location fix
+        rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
+        r2 = sqrt(rsq2);
+
+        // angle (cos and sin)
+        c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+        c /= r1*r2;
+        if (c > 1.0) c = 1.0;
+        if (c < -1.0) c = -1.0;
+        if (acos(c) < constraints[i][5] || acos(c) > constraints[i][6]) return 0;
+      } else if (constraints[i][1] == ARRHENIUS) {
+        t = get_temperature();
+        prrhob = constraints[i][3]*pow(t,constraints[i][4])*
+               exp(-constraints[i][5]/(force->boltz*t));
+        if (prrhob < rrhandom[(int) constraints[i][2]]->uniform()) return 0;
+      }
     }
   }
+
+  // let's also check chirality within 'check_constraint'
+  for (int i = 0; i < onemol->natoms; i++) {
+    if (chiral_atoms[i][0][rxnID] == 1) {
+      double my4coords[12];
+      // already ensured, by transitive property, that chiral simulation atom has four neighs
+      for (int j = 0; j < 4; j++) {
+        atom1 = atom->map(glove[i][1]);
+        // loop over known types involved in chiral center
+        for (int jj = 0; jj < 4; jj++) {
+          if (atom->type[atom->map(xspecial[atom1][j])] == chiral_atoms[i][jj+2][rxnID]) {
+            atom2 = atom->map(xspecial[atom1][j]);
+            atom2 = domain->closest_image(atom1,atom2);
+            for (int k = 0; k < 3; k++) {
+              my4coords[3*jj+k] = x[atom2][k];
+            }
+            break;
+          }
+        }
+      }
+      if (get_chirality(my4coords) != chiral_atoms[i][1][rxnID]) return 0;
+    }
+  }
+
   return 1;
 }
 
+/* ----------------------------------------------------------------------
+compute local temperature: average over all atoms in reaction template
+------------------------------------------------------------------------- */
+
+double FixBondReact::get_temperature()
+{
+  int i,ilocal;
+  double adof = domain->dimension;
+
+  double **v = atom->v;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int *type = atom->type;
+
+  double t = 0.0;
+
+  if (rmass) {
+    for (i = 0; i < onemol->natoms; i++) {
+      ilocal = atom->map(glove[i][1]);
+      t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +
+        v[ilocal][2]*v[ilocal][2]) * rmass[ilocal];
+    }
+  } else {
+    for (i = 0; i < onemol->natoms; i++) {
+      ilocal = atom->map(glove[i][1]);
+      t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +
+        v[ilocal][2]*v[ilocal][2]) * mass[type[ilocal]];
+    }
+  }
+
+  // final temperature
+  double dof = adof*onemol->natoms;
+  double tfactor = force->mvv2e / (dof * force->boltz);
+  t *= tfactor;
+  return t;
+}
+
+/* ----------------------------------------------------------------------
+return handedness (1 or -1) of a chiral center, given ordered set of coordinates
+------------------------------------------------------------------------- */
+
+int FixBondReact::get_chirality(double four_coords[12])
+{
+  // define oriented plane with first three coordinates
+  double vec1[3],vec2[3],vec3[3],vec4[3],mean3[3],dot;
+
+  for (int i = 0; i < 3; i++) {
+    vec1[i] = four_coords[i]-four_coords[i+3];
+    vec2[i] = four_coords[i+3]-four_coords[i+6];
+  }
+
+  MathExtra::cross3(vec1,vec2,vec3);
+
+  for (int i = 0; i < 3; i++) {
+    mean3[i] = (four_coords[i] + four_coords[i+3] +
+                                 four_coords[i+6])/3;
+    vec4[i] = four_coords[i+9] - mean3[i];
+  }
+
+  dot = MathExtra::dot3(vec3,vec4);
+  dot = dot/fabs(dot);
+  return (int) dot;
+}
+
 /* ----------------------------------------------------------------------
   Get xspecials for current molecule templates
 ------------------------------------------------------------------------- */
@@ -1801,7 +1969,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
     if (dedup_mode == 1) ghostly_rxn_count[i] = 0;
   }
 
-  int dedup_size;
+  int dedup_size = 0;
   if (dedup_mode == 0) {
     dedup_size = local_num_mega;
   } else if (dedup_mode == 1) {
@@ -2750,15 +2918,21 @@ void FixBondReact::read(int myrxn)
     if (strspn(line," \t\n\r") == strlen(line)) continue;
 
     if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge);
-    else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent);
+    else if (strstr(line,"equivalences")) {
+      sscanf(line,"%d",&nequivalent);
+      if (nequivalent != onemol->natoms)
+        error->one(FLERR,"Bond/react: Number of equivalences in map file must "
+                                  "equal number of atoms in reaction templates");
+    }
     else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
     else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
-    else if (strstr(line,"constraints")) sscanf(line,"%d",&nconstraints[myrxn]);
-    else break;
+    else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral);
+    else if (strstr(line,"constraints")) {
+      sscanf(line,"%d",&nconstr);
+      memory->grow(constraints,nconstraints+nconstr,MAXCONARGS,"bond/react:constraints");
+    } else break;
   }
 
-  //count = NULL;
-
   // grab keyword and skip next line
 
   parse_keyword(0,line,keyword);
@@ -2766,7 +2940,7 @@ void FixBondReact::read(int myrxn)
 
   // loop over sections of superimpose file
 
-  int equivflag = 0, edgeflag = 0, bondflag = 0, customedgesflag = 0;
+  int equivflag = 0, bondflag = 0, customedgesflag = 0;
   while (strlen(keyword)) {
     if (strcmp(keyword,"BondingIDs") == 0) {
       bondflag = 1;
@@ -2775,7 +2949,6 @@ void FixBondReact::read(int myrxn)
       readline(line);
       sscanf(line,"%d",&jbonding[myrxn]);
     } else if (strcmp(keyword,"EdgeIDs") == 0) {
-      edgeflag = 1;
       EdgeIDs(line, myrxn);
     } else if (strcmp(keyword,"Equivalences") == 0) {
       equivflag = 1;
@@ -2785,6 +2958,8 @@ void FixBondReact::read(int myrxn)
       CustomEdges(line, myrxn);
     } else if (strcmp(keyword,"DeleteIDs") == 0) {
       DeleteAtoms(line, myrxn);
+    } else if (strcmp(keyword,"ChiralIDs") == 0) {
+      ChiralCenters(line, myrxn);
     } else if (strcmp(keyword,"Constraints") == 0) {
       Constraints(line, myrxn);
     } else error->one(FLERR,"Bond/react: Unknown section in map file");
@@ -2862,23 +3037,72 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn)
   }
 }
 
+void FixBondReact::ChiralCenters(char *line, int myrxn)
+{
+  int tmp;
+  for (int i = 0; i < nchiral; i++) {
+    readline(line);
+    sscanf(line,"%d",&tmp);
+    chiral_atoms[tmp-1][0][myrxn] = 1;
+    if (onemol->xflag == 0)
+      error->one(FLERR,"Bond/react: Molecule template 'Coords' section required for chiralIDs keyword");
+    if ((int) onemol_nxspecial[tmp-1][0] != 4)
+      error->one(FLERR,"Bond/react: Chiral atoms must have exactly four first neighbors");
+    for (int j = 0; j < 4; j++) {
+      for (int k = j+1; k < 4; k++) {
+        if (onemol->type[onemol_xspecial[tmp-1][j]-1] ==
+            onemol->type[onemol_xspecial[tmp-1][k]-1])
+          error->one(FLERR,"Bond/react: First neighbors of chiral atoms must be of mutually different types");
+      }
+    }
+    // record order of atom types, and coords
+    double my4coords[12];
+    for (int j = 0; j < 4; j++) {
+      chiral_atoms[tmp-1][j+2][myrxn] = onemol->type[onemol_xspecial[tmp-1][j]-1];
+      for (int k = 0; k < 3; k++) {
+        my4coords[3*j+k] = onemol->x[onemol_xspecial[tmp-1][j]-1][k];
+      }
+    }
+    // get orientation
+    chiral_atoms[tmp-1][1][myrxn] = get_chirality(my4coords);
+  }
+}
+
 void FixBondReact::Constraints(char *line, int myrxn)
 {
   double tmp[MAXCONARGS];
   int n = strlen("distance") + 1;
   char *constraint_type = new char[n];
-  for (int i = 0; i < nconstraints[myrxn]; i++) {
+  for (int i = 0; i < nconstr; i++) {
     readline(line);
     sscanf(line,"%s",constraint_type);
+    constraints[nconstraints][0] = myrxn;
     if (strcmp(constraint_type,"distance") == 0) {
-      constraints[myrxn][0] = 0; // 0 = 'distance' ...maybe use another enum eventually
+      constraints[nconstraints][1] = DISTANCE;
       sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]);
-      constraints[myrxn][1] = tmp[0];
-      constraints[myrxn][2] = tmp[1];
-      constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance
-      constraints[myrxn][4] = tmp[3]*tmp[3];
+      constraints[nconstraints][2] = tmp[0];
+      constraints[nconstraints][3] = tmp[1];
+      constraints[nconstraints][4] = tmp[2]*tmp[2]; // using square of distance
+      constraints[nconstraints][5] = tmp[3]*tmp[3];
+    } else if (strcmp(constraint_type,"angle") == 0) {
+      constraints[nconstraints][1] = ANGLE;
+      sscanf(line,"%*s %lg %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3],&tmp[4]);
+      constraints[nconstraints][2] = tmp[0];
+      constraints[nconstraints][3] = tmp[1];
+      constraints[nconstraints][4] = tmp[2];
+      constraints[nconstraints][5] = tmp[3]/180.0 * MY_PI;
+      constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI;
+    } else if (strcmp(constraint_type,"arrhenius") == 0) {
+      constraints[nconstraints][1] = ARRHENIUS;
+      constraints[nconstraints][2] = narrhenius++;
+      sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]);
+      constraints[nconstraints][3] = tmp[0];
+      constraints[nconstraints][4] = tmp[1];
+      constraints[nconstraints][5] = tmp[2];
+      constraints[nconstraints][6] = tmp[3];
     } else
       error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file");
+    nconstraints++;
   }
   delete [] constraint_type;
 }
@@ -3098,6 +3322,42 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf)
   }
 }
 
+/* ----------------------------------------------------------------------
+   write Set data to restart file
+------------------------------------------------------------------------- */
+
+void FixBondReact::write_restart(FILE *fp)
+{
+  set[0].nreacts = nreacts;
+  for (int i = 0; i < nreacts; i++) {
+    set[i].reaction_count_total = reaction_count_total[i];
+    strncpy(set[i].rxn_name,rxn_name[i],MAXLINE);
+    set[i].rxn_name[MAXLINE-1] = '\0';
+  }
+
+  if (me == 0) {
+    int size = nreacts*sizeof(Set);
+    fwrite(&size,sizeof(int),1,fp);
+    fwrite(set,sizeof(Set),nreacts,fp);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   use selected state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixBondReact::restart(char *buf)
+{
+  Set *set_restart = (Set *) buf;
+  for (int i = 0; i < set_restart[0].nreacts; i++) {
+    for (int j = 0; j < nreacts; j++) {
+      if (strcmp(set_restart[i].rxn_name,rxn_name[j]) == 0) {
+        reaction_count_total[j] = set_restart[i].reaction_count_total;
+      }
+    }
+  }
+}
+
 /* ----------------------------------------------------------------------
 memory usage of local atom-based arrays
 ------------------------------------------------------------------------- */
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
index 1ac8d624a9..a5bf2bc587 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-MISC/fix_bond_react.h
@@ -30,6 +30,9 @@ namespace LAMMPS_NS {
 
 class FixBondReact : public Fix {
  public:
+
+  enum {MAXLINE=256};
+
   FixBondReact(class LAMMPS *, int, char **);
   ~FixBondReact();
   int setmask();
@@ -61,7 +64,8 @@ class FixBondReact : public Fix {
   int custom_exclude_flag;
   int *stabilize_steps_flag;
   int *update_edges_flag;
-  int *nconstraints;
+  int nconstraints;
+  int narrhenius;
   double **constraints;
   int status;
   int *groupbits;
@@ -85,7 +89,8 @@ class FixBondReact : public Fix {
   Fix *fix2;              // properties/atom used to indicate 1) relaxing atoms
                           //                                  2) to which 'react' atom belongs
   Fix *fix3;              // property/atom used for system-wide thermostat
-  class RanMars **random;
+  class RanMars **random; // random number for 'prob' keyword
+  class RanMars **rrhandom; // random number for Arrhenius constraint
   class NeighList *list;
 
   int *reacted_mol,*unreacted_mol;
@@ -105,7 +110,7 @@ class FixBondReact : public Fix {
 
   int *ibonding,*jbonding;
   int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
-  int nedge,nequivalent,ncustom,ndelete; // number of edge, equivalent, custom atoms in mapping file
+  int nedge,nequivalent,ncustom,ndelete,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file
   int attempted_rxn; // there was an attempt!
   int *local_rxn_count;
   int *ghostly_rxn_count;
@@ -121,6 +126,7 @@ class FixBondReact : public Fix {
   int **landlocked_atoms; // all atoms at least three bonds away from edge atoms
   int **custom_edges; // atoms in molecule templates with incorrect valences
   int **delete_atoms; // atoms in pre-reacted templates to delete
+  int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types
 
   int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors
   tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list
@@ -144,6 +150,7 @@ class FixBondReact : public Fix {
   void Equivalences(char *,int);
   void CustomEdges(char *,int);
   void DeleteAtoms(char *,int);
+  void ChiralCenters(char *,int);
   void Constraints(char *,int);
 
   void make_a_guess ();
@@ -153,6 +160,8 @@ class FixBondReact : public Fix {
   void inner_crosscheck_loop();
   void ring_check();
   int check_constraints();
+  double get_temperature();
+  int get_chirality(double[12]); // get handedness given an ordered set of coordinates
 
   void open(char *);
   void readline(char *);
@@ -170,6 +179,15 @@ class FixBondReact : public Fix {
   void unlimit_bond();
   void limit_bond(int);
   void dedup_mega_gloves(int); //dedup global mega_glove
+  virtual void write_restart(FILE *);
+  virtual void restart(char *buf);
+
+  struct Set {
+    int nreacts;
+    char rxn_name[MAXLINE];
+    int reaction_count_total;
+  };
+  Set *set;
 
   // DEBUG
 
@@ -234,6 +252,18 @@ E: Bond/react: A deleted atom cannot remain bonded to an atom that is not delete
 
 Self-explanatory.
 
+E: Bond/react: First neighbors of chiral atoms must be of mutually different types
+
+Self-explanatory.
+
+E: Bond/react: Chiral atoms must have exactly four first neighbors
+
+Self-explanatory.
+
+E: Bond/react: Molecule template 'Coords' section required for chiralIDs keyword
+
+The coordinates of atoms in the pre-reacted template are used to determine chirality.
+
 E: Bond/react special bond generation overflow
 
 The number of special bonds per-atom created by a reaction exceeds the
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index 55526a9149..49e9cc02a6 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "citeme.h"
 #include "math_const.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -93,10 +94,11 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
   if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
     error->all(FLERR,"Fix ttm/mod number of nodes must be > 0");
 
-  FILE *fpr = force->open_potential(arg[8]);
+  const char *filename = arg[8];
+  FILE *fpr = force->open_potential(filename);
   if (fpr == NULL) {
     char str[128];
-    snprintf(str,128,"Cannot open file %s",arg[8]);
+    snprintf(str,128,"Cannot open file %s",filename);
     error->all(FLERR,str);
   }
 
@@ -117,113 +119,113 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
   double tresh_d;
   int tresh_i;
   // C0 (metal)
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   esheat_0 = tresh_d;
   // C1 (metal*10^3)
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   esheat_1 = tresh_d;
   // C2 (metal*10^6)
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   esheat_2 = tresh_d;
   // C3 (metal*10^9)
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   esheat_3 = tresh_d;
   // C4 (metal*10^12)
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   esheat_4 = tresh_d;
   // C_limit
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   C_limit = tresh_d;
   //Temperature damping factor
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   T_damp = tresh_d;
   // rho_e
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   electronic_density = tresh_d;
   //thermal_diffusion
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   el_th_diff = tresh_d;
   // gamma_p
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   gamma_p = tresh_d;
   // gamma_s
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   gamma_s = tresh_d;
   // v0
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   v_0 = tresh_d;
   // average intensity of pulse (source of energy) (metal units)
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   intensity = tresh_d;
   // coordinate of 1st surface in x-direction (in box units) - constant
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%d",&tresh_i);
   surface_l = tresh_i;
   // coordinate of 2nd surface in x-direction (in box units) - constant
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%d",&tresh_i);
   surface_r = tresh_i;
   // skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%d",&tresh_i);
   skin_layer = tresh_i;
   // width of pulse (picoseconds)
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   width = tresh_d;
   // factor of electronic pressure (PF) Pe = PF*Ce*Te
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   pres_factor = tresh_d;
   // effective free path of electrons (angstrom)
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   free_path = tresh_d;
   // ionic density (ions*angstrom^{-3})
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   ionic_density = tresh_d;
   // if movsur = 0: surface is freezed
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%d",&tresh_i);
   movsur = tresh_i;
   // electron_temperature_min
-  fgets(linee,MAXLINE,fpr_2);
-  fgets(linee,MAXLINE,fpr_2);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
+  utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error);
   sscanf(linee,"%lg",&tresh_d);
   electron_temperature_min = tresh_d;
   fclose(fpr_2);
diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp
index 2ea804b95d..c5556b746d 100644
--- a/src/USER-MISC/improper_cossq.cpp
+++ b/src/USER-MISC/improper_cossq.cpp
@@ -26,6 +26,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "math_const.h"
 
 using namespace LAMMPS_NS;
@@ -301,8 +302,8 @@ void ImproperCossq::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp
index 2efab8b5f8..146bd344f1 100644
--- a/src/USER-MISC/improper_distance.cpp
+++ b/src/USER-MISC/improper_distance.cpp
@@ -25,6 +25,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -247,8 +248,8 @@ void ImproperDistance::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp
index a0ef3a2058..beb473d78c 100644
--- a/src/USER-MISC/improper_fourier.cpp
+++ b/src/USER-MISC/improper_fourier.cpp
@@ -26,6 +26,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -325,11 +326,11 @@ void ImproperFourier::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&C0[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&C1[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&C2[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&all[1],sizeof(int),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&C0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&C1[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&C2[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&all[1],sizeof(int),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&C0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp
index 48db5a41e9..7f818595a2 100644
--- a/src/USER-MISC/improper_ring.cpp
+++ b/src/USER-MISC/improper_ring.cpp
@@ -47,6 +47,7 @@
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -325,8 +326,8 @@ void ImproperRing::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index b3abc647ef..a03e24ed35 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -243,7 +243,7 @@ void PairAGNI::allocate()
    global settings
 ------------------------------------------------------------------------- */
 
-void PairAGNI::settings(int narg, char **/*arg*/)
+void PairAGNI::settings(int narg, char ** /* arg */)
 {
   if (narg != 0) error->all(FLERR,"Illegal pair_style command");
 }
diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp
index e977197522..6339f7d135 100644
--- a/src/USER-MISC/pair_buck_mdf.cpp
+++ b/src/USER-MISC/pair_buck_mdf.cpp
@@ -25,6 +25,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -302,14 +303,14 @@ void PairBuckMDF::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&rho[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@@ -338,10 +339,10 @@ void PairBuckMDF::write_restart_settings(FILE *fp)
 void PairBuckMDF::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp
index 4544a6db43..7c0cb3372d 100644
--- a/src/USER-MISC/pair_cosine_squared.cpp
+++ b/src/USER-MISC/pair_cosine_squared.cpp
@@ -30,6 +30,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -124,7 +125,7 @@ void PairCosineSquared::coeff(int narg, char **arg)
 {
   if (narg < 4 || narg > 6)
     error->all(FLERR, "Incorrect args for pair coefficients (too few or too many)");
-  
+
   if (!allocated)
     allocate();
 
@@ -275,14 +276,14 @@ void PairCosineSquared::read_restart(FILE *fp)
   for (i = 1; i <= atom->ntypes; i++) {
     for (j = i; j <= atom->ntypes; j++) {
       if (me == 0)
-        fread(&setflag[i][j], sizeof(int), 1, fp);
+        utils::sfread(FLERR,&setflag[i][j], sizeof(int), 1, fp,NULL,error);
       MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j], sizeof(double), 1, fp);
-          fread(&sigma[i][j], sizeof(double), 1, fp);
-          fread(&cut[i][j], sizeof(double), 1, fp);
-          fread(&wcaflag[i][j], sizeof(int), 1, fp);
+          utils::sfread(FLERR,&epsilon[i][j], sizeof(double), 1, fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j], sizeof(double), 1, fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j], sizeof(double), 1, fp,NULL,error);
+          utils::sfread(FLERR,&wcaflag[i][j], sizeof(int), 1, fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
         MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world);
@@ -310,7 +311,7 @@ void PairCosineSquared::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global, sizeof(double), 1, fp);
+    utils::sfread(FLERR,&cut_global, sizeof(double), 1, fp,NULL,error);
   }
   MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
 }
@@ -458,7 +459,7 @@ double PairCosineSquared::single(int /* i */, int /* j */, int itype, int jtype,
                          double &fforce)
 {
   double r, r2inv, r6inv, cosone, force, energy;
-  
+
   r = sqrt(rsq);
 
   if (r <= sigma[itype][jtype]) {
@@ -477,7 +478,7 @@ double PairCosineSquared::single(int /* i */, int /* j */, int itype, int jtype,
     }
   } else {
     cosone = cos(MY_PI*(r-sigma[itype][jtype]) / (2.0*w[itype][jtype]));
-    force = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) * 
+    force = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) *
                  sin(MY_PI*(r-sigma[itype][jtype]) / w[itype][jtype]) / r;
     energy = -epsilon[itype][jtype]*cosone*cosone;
   }
diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp
index a375901ecd..bdb605f547 100644
--- a/src/USER-MISC/pair_coul_diel.cpp
+++ b/src/USER-MISC/pair_coul_diel.cpp
@@ -24,6 +24,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -282,9 +283,9 @@ void PairCoulDiel::read_restart(FILE *fp)
     for (j = i; j <= atom->ntypes; j++) {
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&rme[i][j],sizeof(double),1,fp);
-          fread(&sigmae[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&rme[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigmae[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&rme[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world);
@@ -311,9 +312,9 @@ void PairCoulDiel::write_restart_settings(FILE *fp)
 void PairCoulDiel::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp
index 9264e51287..980b4a71d5 100644
--- a/src/USER-MISC/pair_coul_shield.cpp
+++ b/src/USER-MISC/pair_coul_shield.cpp
@@ -28,6 +28,7 @@
 #include "memory.h"
 #include "math_special.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -298,8 +299,8 @@ void PairCoulShield::read_restart(FILE *fp)
     for (j = i; j <= atom->ntypes; j++) {
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&sigmae[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&sigmae[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -325,9 +326,9 @@ void PairCoulShield::write_restart_settings(FILE *fp)
 void PairCoulShield::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp
index 8507fd49f6..f7670d30b5 100644
--- a/src/USER-MISC/pair_extep.cpp
+++ b/src/USER-MISC/pair_extep.cpp
@@ -757,7 +757,7 @@ void PairExTeP::read_file(char *file)
     // skip line if it is a leftover from the previous section,
     // which can be identified by having 3 elements (instead of 2)
     // as first words.
-     
+
     if (isupper(words[0][0]) && isupper(words[1][0]) && isupper(words[2][0]))
       continue;
 
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index e6cfc02f63..2a4f61cce3 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -24,6 +24,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "math_const.h"
 
 using namespace LAMMPS_NS;
@@ -300,14 +301,14 @@ void PairGaussCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&hgauss[i][j],sizeof(double),1,fp);
-          fread(&rmh[i][j],sizeof(double),1,fp);
-          fread(&sigmah[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&hgauss[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rmh[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigmah[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&hgauss[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rmh[i][j],1,MPI_DOUBLE,0,world);
@@ -336,9 +337,9 @@ void PairGaussCut::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index 4741263603..e998abf005 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -442,13 +442,13 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
   if (vflag_fdotr) virial_fdotr_compute();
 }
 
-/* ---------------------------------------------------------------------- 
+/* ----------------------------------------------------------------------
    van der Waals forces and energy
 ------------------------------------------------------------------------- */
 
-void PairILPGrapheneHBN::calc_FvdW(int eflag, int vflag)
+void PairILPGrapheneHBN::calc_FvdW(int eflag, int /* vflag */)
 {
-  int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
+  int i,j,ii,jj,inum,jnum,itype,jtype;
   tagint itag,jtag;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,r,Rcut,r2inv,r6inv,r8inv,Tap,dTap,Vilp,TSvdw,TSvdw2inv,fsum;
@@ -523,7 +523,7 @@ void PairILPGrapheneHBN::calc_FvdW(int eflag, int vflag)
 
         // derivatives
         fpair = -6.0*p.C6*r8inv/TSvdw + p.C6*p.d/p.seff*(TSvdw-1.0)*TSvdw2inv*r8inv*r;
-	fsum = fpair*Tap - Vilp*dTap/r;
+        fsum = fpair*Tap - Vilp*dTap/r;
 
         f[i][0] += fsum*delx;
         f[i][1] += fsum*dely;
@@ -540,19 +540,19 @@ void PairILPGrapheneHBN::calc_FvdW(int eflag, int vflag)
   }
 }
 
-/* ---------------------------------------------------------------------- 
+/* ----------------------------------------------------------------------
    Repulsive forces and energy
 ------------------------------------------------------------------------- */
 
-void PairILPGrapheneHBN::calc_FRep(int eflag, int vflag)
+void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
 {
   int i,j,ii,jj,inum,jnum,itype,jtype,k,kk;
   double prodnorm1,fkcx,fkcy,fkcz;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1;
-  double rsq,r,Rcut,rhosq1,exp0,exp1,r2inv,r6inv,r8inv,Tap,dTap,Vilp;
-  double frho1,TSvdw,TSvdw2inv,Erep,fsum,rdsq1;
+  double rsq,r,Rcut,rhosq1,exp0,exp1,Tap,dTap,Vilp;
+  double frho1,Erep,fsum,rdsq1;
   int *ilist,*jlist,*numneigh,**firstneigh;
-  int *ILP_neighs_i,*ILP_neighs_j;
+  int *ILP_neighs_i;
 
   evdwl = 0.0;
 
@@ -634,12 +634,12 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int vflag)
         dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz;
         dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz;
         dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz;
-  	fp1[0] = prodnorm1*normal[i][0]*fpair1;
-  	fp1[1] = prodnorm1*normal[i][1]*fpair1;
-  	fp1[2] = prodnorm1*normal[i][2]*fpair1;
-  	fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1;
-  	fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1;
-  	fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1;
+        fp1[0] = prodnorm1*normal[i][0]*fpair1;
+        fp1[1] = prodnorm1*normal[i][1]*fpair1;
+        fp1[2] = prodnorm1*normal[i][2]*fpair1;
+        fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1;
+        fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1;
+        fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1;
 
         fkcx = (delx*fsum - fp1[0])*Tap - Vilp*dTap*delx/r;
         fkcy = (dely*fsum - fp1[1])*Tap - Vilp*dTap*dely/r;
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h
index ec6146fa33..5ca8eb64a7 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.h
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.h
@@ -48,7 +48,7 @@ class PairILPGrapheneHBN : public Pair {
   MyPage<int> *ipage;              // neighbor list pages
   int *ILP_numneigh;                // # of pair neighbors for each atom
   int **ILP_firstneigh;             // ptr to 1st neighbor of each atom
-  int tap_flag;			   // flag to turn on/off taper function
+  int tap_flag;                    // flag to turn on/off taper function
 
   struct Param {
     double z0,alpha,epsilon,C,delta,d,sR,reff,C6,S;
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index 7bfbedfa1c..eea0b1261c 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -444,13 +444,13 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
   if (vflag_fdotr) virial_fdotr_compute();
 }
 
-/* ---------------------------------------------------------------------- 
+/* ----------------------------------------------------------------------
    van der Waals forces and energy
 ------------------------------------------------------------------------- */
 
-void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int vflag)
+void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int /* vflag */)
 {
-  int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
+  int i,j,ii,jj,inum,jnum,itype,jtype;
   tagint itag,jtag;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,r,Rcut,r2inv,r6inv,r8inv,Tap,dTap,Vkc,fsum;
@@ -519,11 +519,11 @@ void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int vflag)
           dTap = calc_dTap(r,Rcut);
         } else {Tap = 1.0; dTap = 0.0;}
 
-	Vkc = -p.A*p.z06*r6inv;
+        Vkc = -p.A*p.z06*r6inv;
 
         // derivatives
         fpair = -6.0*p.A*p.z06*r8inv;
-	fsum = fpair*Tap - Vkc*dTap/r;
+        fsum = fpair*Tap - Vkc*dTap/r;
 
         f[i][0] += fsum*delx;
         f[i][1] += fsum*dely;
@@ -540,19 +540,19 @@ void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int vflag)
   }
 }
 
-/* ---------------------------------------------------------------------- 
+/* ----------------------------------------------------------------------
    Repulsive forces and energy
 ------------------------------------------------------------------------- */
 
-void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag)
+void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */)
 {
   int i,j,ii,jj,inum,jnum,itype,jtype,k,kk;
   double prodnorm1,fkcx,fkcy,fkcz;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1;
-  double rsq,r,rhosq1,exp0,exp1,r2inv,r6inv,r8inv,Tap,dTap,Vkc;
+  double rsq,r,rhosq1,exp0,exp1,Tap,dTap,Vkc;
   double frho_ij,sumC1,sumC11,sumCff,fsum,rho_ij;
   int *ilist,*jlist,*numneigh,**firstneigh;
-  int *KC_neighs_i,*KC_neighs_j;
+  int *KC_neighs_i;
 
   evdwl = 0.0;
 
@@ -606,14 +606,12 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag)
         Param& p = params[iparam_ij];
 
         r = sqrt(rsq);
-        r2inv = 1.0/rsq;
-        r6inv = r2inv*r2inv*r2inv;
-        r8inv = r2inv*r6inv;
-	// turn on/off taper function
-	if (tap_flag) {
-	  Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
-	  dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
-	} else {Tap = 1.0; dTap = 0.0;}
+
+        // turn on/off taper function
+        if (tap_flag) {
+          Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
+          dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
+        } else {Tap = 1.0; dTap = 0.0;}
 
         // Calculate the transverse distance
         prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz;
@@ -628,7 +626,7 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag)
         sumC11 = (p.C2 + 2.0*p.C4*rho_ij)*p.delta2inv;
         frho_ij = exp1*sumC1;
         sumCff = 0.5*p.C + frho_ij;
-	Vkc = exp0*sumCff;
+        Vkc = exp0*sumCff;
 
         // derivatives
         fpair =  p.lambda*exp0/r*sumCff;
@@ -655,10 +653,10 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag)
         f[j][1] -= fkcy;
         f[j][2] -= fkcz;
 
-	// calculate the forces acted on the neighbors of atom i from atom j
-	KC_neighs_i = KC_firstneigh[i];
-	for (kk = 0; kk < KC_numneigh[i]; kk++) {
-	  k = KC_neighs_i[kk];
+        // calculate the forces acted on the neighbors of atom i from atom j
+        KC_neighs_i = KC_firstneigh[i];
+        for (kk = 0; kk < KC_numneigh[i]; kk++) {
+          k = KC_neighs_i[kk];
           if (k == i) continue;
           // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i
           dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz;
@@ -674,7 +672,7 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag)
           delkj[1] = x[k][1] - x[j][1];
           delkj[2] = x[k][2] - x[j][2];
           if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]);
-	}
+        }
 
         if (eflag) {
           if (tap_flag) pvector[1] += evdwl = Tap*Vkc;
@@ -792,7 +790,7 @@ void PairKolmogorovCrespiFull::calc_normal()
     memory->create(dnormal,3,3,3,nmax,"KolmogorovCrespiFull:dnormal");
   }
 
-  inum = list->inum;	
+  inum = list->inum;
   ilist = list->ilist;
   //Calculate normals
   for (ii = 0; ii < inum; ii++) {
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h
index d2971e3fbc..c579788110 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.h
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h
@@ -48,7 +48,7 @@ class PairKolmogorovCrespiFull : public Pair {
   MyPage<int> *ipage;              // neighbor list pages
   int *KC_numneigh;                // # of pair neighbors for each atom
   int **KC_firstneigh;             // ptr to 1st neighbor of each atom
-  int tap_flag;			   // flag to turn on/off taper function
+  int tap_flag;                    // flag to turn on/off taper function
 
 
   struct Param {
diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp
index 50f59107a0..c539bb30e2 100644
--- a/src/USER-MISC/pair_lennard_mdf.cpp
+++ b/src/USER-MISC/pair_lennard_mdf.cpp
@@ -26,6 +26,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -302,14 +303,14 @@ void PairLJ_AB_MDF::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&aparm[i][j],sizeof(double),1,fp);
-          fread(&bparm[i][j],sizeof(double),1,fp);
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&aparm[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&bparm[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&aparm[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&bparm[i][j],1,MPI_DOUBLE,0,world);
@@ -336,7 +337,7 @@ void PairLJ_AB_MDF::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
 }
diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp
index ffa828826f..f52e427c18 100644
--- a/src/USER-MISC/pair_lj_expand_coul_long.cpp
+++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp
@@ -31,6 +31,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -785,9 +786,9 @@ double PairLJExpandCoulLong::init_one(int i, int j)
        (1.0/3.0 + 2.0*shift1/(4.0*rc1) + shift2/(5.0*rc2))/rc3);
     ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 *
       ((1.0/9.0 + 3.0*shift1/(10.0*rc1) +
-	3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 -
+        3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 -
        (1.0/3.0 + 3.0*shift1/(4.0*rc1) +
-	3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3);
+        3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3);
   }
 
   return cut;
@@ -828,14 +829,14 @@ void PairLJExpandCoulLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&shift[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shift[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -867,13 +868,13 @@ void PairLJExpandCoulLong::write_restart_settings(FILE *fp)
 void PairLJExpandCoulLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp
index 3fe0fa6bf9..51e24639b9 100644
--- a/src/USER-MISC/pair_lj_mdf.cpp
+++ b/src/USER-MISC/pair_lj_mdf.cpp
@@ -26,6 +26,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -310,14 +311,14 @@ void PairLJMDF::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -344,7 +345,7 @@ void PairLJMDF::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
 }
diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index 758962ce29..19bc66bdcb 100644
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -27,6 +27,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
@@ -486,15 +487,15 @@ void PairLJSFDipoleSF::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
-          fread(&cut_coul[i][j],sizeof(double),1,fp);
-          fread(&scale[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&scale[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -523,9 +524,9 @@ void PairLJSFDipoleSF::write_restart_settings(FILE *fp)
 void PairLJSFDipoleSF::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp
new file mode 100644
index 0000000000..8ad9793f98
--- /dev/null
+++ b/src/USER-MISC/pair_local_density.cpp
@@ -0,0 +1,894 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors:
+   Tanmoy Sanyal, M.Scott Shell, UC Santa Barbara
+   David Rosenberger, TU Darmstadt
+------------------------------------------------------------------------- */
+
+#include "pair_local_density.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <string>
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "memory.h"
+#include "error.h"
+#include "domain.h"
+#include "citeme.h"
+#include "utils.h"
+
+using namespace LAMMPS_NS;
+
+#define MAXLINE 1024
+
+static const char cite_pair_local_density[] =
+  "pair_style  local/density  command:\n\n"
+  "@Article{Sanyal16,\n"
+  " author =  {T.Sanyal and M.Scott Shell},\n"
+  " title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},\n"
+  " journal = {J.~Chem.~Phys.},\n"
+  " year =    2016,\n"
+  " DOI = doi.org/10.1063/1.4958629"
+  "}\n\n"
+  "@Article{Sanyal18,\n"
+  " author =  {T.Sanyal and M.Scott Shell},\n"
+  " title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},\n"
+  " journal = {J.~Phys.~Chem. B},\n"
+  " year =    2018,\n"
+  " DOI = doi.org/10.1021/acs.jpcb.7b12446"
+  "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+PairLocalDensity::PairLocalDensity(LAMMPS *lmp) : Pair(lmp)
+{
+  restartinfo = 0;
+  one_coeff = 1;
+  single_enable = 1;
+
+  // stuff read from tabulated file
+  nLD = 0;
+  nrho = 0;
+  rho_min = NULL;
+  rho_max = NULL;
+  a = NULL;
+  b = NULL;
+  c0 = NULL;
+  c2 = NULL;
+  c4 = NULL;
+  c6 = NULL;
+  uppercut = NULL;
+  lowercut = NULL;
+  uppercutsq = NULL;
+  lowercutsq = NULL;
+  frho = NULL;
+  rho = NULL;
+
+  // splined arrays
+  frho_spline = NULL;
+
+  // per-atom arrays
+  nmax = 0;
+  fp = NULL;
+  localrho = NULL;
+
+  // set comm size needed by this pair
+  comm_forward = 1;
+  comm_reverse = 1;
+
+  // cite publication
+  if (lmp->citeme) lmp->citeme->add(cite_pair_local_density);
+}
+
+/* ----------------------------------------------------------------------
+   check if allocated, since class can be destructed when incomplete
+------------------------------------------------------------------------- */
+
+PairLocalDensity::~PairLocalDensity()
+{
+
+  memory->destroy(localrho);
+  memory->destroy(fp);
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+  }
+
+  memory->destroy(frho_spline);
+
+  memory->destroy(rho_min);
+  memory->destroy(rho_max);
+  memory->destroy(delta_rho);
+  memory->destroy(c0);
+  memory->destroy(c2);
+  memory->destroy(c4);
+  memory->destroy(c6);
+  memory->destroy(uppercut);
+  memory->destroy(lowercut);
+  memory->destroy(uppercutsq);
+  memory->destroy(lowercutsq);
+  memory->destroy(frho);
+  memory->destroy(rho);
+
+  memory->destroy(a);
+  memory->destroy(b);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLocalDensity::compute(int eflag, int vflag)
+{
+
+  int i,j,ii,jj,m,k,inum,jnum,itype,jtype;
+  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+  double rsqinv, phi, uLD, dphi, evdwl,fpair;
+  double p, *coeff;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  phi = uLD = evdwl = fpair = rsqinv = 0.0;
+
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
+
+  /* localrho = LD at each atom
+     fp = derivative of embedding energy at each atom for each LD potential
+     uLD = embedding energy of each atom due to each LD potential*/
+
+  // grow LD and fp arrays if necessary
+  // need to be atom->nmax in length
+
+  if (atom->nmax > nmax) {
+    memory->destroy(localrho);
+    memory->destroy(fp);
+    nmax = atom->nmax;
+    memory->create(localrho, nLD, nmax, "pairLD:localrho");
+    memory->create(fp, nLD, nmax, "pairLD:fp");
+  }
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // zero out LD and fp
+
+  if (newton_pair) {
+    m = nlocal + atom->nghost;
+    for (k = 0; k < nLD; k++) {
+        for (i = 0; i < m; i++) {
+            localrho[k][i] = 0.0;
+            fp[k][i] = 0.0;
+        }
+    }
+  }
+  else {
+    for (k = 0; k < nLD; k++){
+        for (i = 0; i < nlocal; i++) {
+            localrho[k][i] = 0.0;
+            fp[k][i] = 0.0;
+        }
+    }
+   }
+
+  // loop over neighs of central atoms and types of LDs
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      jtype = type[j];
+
+      // calculate distance-squared between i,j atom-types
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+
+      // calculating LDs based on central and neigh filters
+
+      for (k = 0; k < nLD; k++) {
+        if (rsq < lowercutsq[k]) {
+             phi = 1.0;
+        }
+          else if (rsq > uppercutsq[k]) {
+             phi = 0.0;
+        }
+          else {
+             phi = c0[k] + rsq * (c2[k] + rsq * (c4[k] + c6[k]*rsq));
+        }
+        localrho[k][i] += (phi * b[k][jtype]);
+
+        /*checking for both i,j is necessary
+        since a half neighbor list is processed.*/
+
+        if (newton_pair || j<nlocal) {
+            localrho[k][j] += (phi * b[k][itype]);
+        }
+      }
+    }
+  }
+
+  // communicate and sum LDs over all procs
+  if (newton_pair) comm->reverse_comm_pair(this);
+
+  //
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    itype = type[i];
+    uLD = 0.0;
+
+    for (k = 0; k < nLD; k++) {
+
+        /*skip over this loop if the LD potential
+          is not intendend for central atomtype <itype>*/
+        if (!(a[k][itype])) continue;
+
+        // linear extrapolation at rho_min and rho_max
+
+        if (localrho[k][i] <= rho_min[k]) {
+            coeff = frho_spline[k][0];
+            fp[k][i] = coeff[2];
+            uLD +=  a[k][itype] * ( coeff[6] + fp[k][i]*(localrho[k][i] - rho_min[k]) );
+        }
+        else if (localrho[k][i] >= rho_max[k]) {
+            coeff = frho_spline[k][nrho-2];
+            fp[k][i] = coeff[0] + coeff[1]  + coeff[2];
+            uLD +=  a[k][itype] * ( (coeff[3] + coeff[4] + coeff[5] + coeff[6]) + fp[k][i]*(localrho[k][i] - rho_max[k]) );
+        }
+        else {
+            p = (localrho[k][i] - rho_min[k]) / delta_rho[k];
+            m = static_cast<int> (p);
+            m = MAX(0, MIN(m, nrho-2));
+            p -= m;
+            p = MIN(p, 1.0);
+            coeff = frho_spline[k][m];
+            fp[k][i] = (coeff[0]*p + coeff[1])*p + coeff[2];
+            uLD +=  a[k][itype] * (((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]);
+        }
+    }
+
+    if (eflag) {
+        if (eflag_global) eng_vdwl += uLD;
+        if (eflag_atom) eatom[i] += uLD;
+    }
+ }
+
+  // communicate LD and fp to all procs
+
+  comm->forward_comm_pair(this);
+
+  // compute forces on each atom
+  // loop over neighbors of my atoms
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      jtype = type[j];
+
+      // calculate square of distance between i,j atoms
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+
+      // calculate force between two atoms
+      fpair = 0.0;
+      if (rsq < cutforcesq) {   // global cutoff check
+        rsqinv = 1.0/rsq;
+        for (k = 0; k < nLD; k++) {
+            if (rsq >= lowercutsq[k] && rsq < uppercutsq[k]) {
+               dphi = rsq * (2.0*c2[k] + rsq * (4.0*c4[k] + 6.0*c6[k]*rsq));
+               fpair += -(a[k][itype]*b[k][jtype]*fp[k][i] + a[k][jtype]*b[k][itype]*fp[k][j]) * dphi;
+            }
+        }
+        fpair *= rsqinv;
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+        if (newton_pair || j < nlocal) {
+            f[j][0] -= delx*fpair;
+            f[j][1] -= dely*fpair;
+            f[j][2] -= delz*fpair;
+        }
+
+      /*eng_vdwl has already been completely built,
+        so no need to add anything here*/
+
+      if (eflag) evdwl = 0.0;
+
+      if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             evdwl,0.0,fpair,delx,dely,delz);
+      }
+
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairLocalDensity::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairLocalDensity::settings(int narg, char ** /* arg */)
+{
+  if (narg > 0) error->all(FLERR,"Illegal pair_style command");
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for all type pairs
+   read tabulated LD input file
+------------------------------------------------------------------------- */
+
+void PairLocalDensity::coeff(int narg, char **arg)
+{
+  int i, j;
+  if (!allocated) allocate();
+
+  if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients");
+
+  // insure I,J args are * *
+
+  if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  // parse LD file
+
+  parse_file(arg[2]);
+
+
+ // clear setflag since coeff() called once with I,J = * *
+
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++)
+      setflag[i][j] = 0;
+
+  // set setflag for all i,j type pairs
+
+  int count = 0;
+  for (i = 1; i <= atom->ntypes; i++) {
+    for (j = i; j <= atom->ntypes; j++) {
+        setflag[i][j] = 1;
+        count++;
+      }
+    }
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLocalDensity::init_style()
+{
+  // spline rho and frho arrays
+  // request half neighbor list
+
+  array2spline();
+
+  // half neighbor request
+  neighbor->request(this);
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairLocalDensity::init_one(int /* i */, int /* j */)
+{
+  // single global cutoff = max of all uppercuts read in from LD file
+
+  cutmax = 0.0;
+  for (int k = 0; k < nLD; k++)
+    cutmax = MAX(cutmax,uppercut[k]);
+
+  cutforcesq = cutmax*cutmax;
+
+  return cutmax;
+}
+
+
+/*--------------------------------------------------------------------------
+  pair_write functionality for this pair style that gives just a snap-shot
+  of the LD potential without doing an actual MD run
+ ---------------------------------------------------------------------------*/
+
+double PairLocalDensity::single(int /* i */, int /* j */, int itype, int jtype,
+                                double rsq, double /* factor_coul */,
+                                double /* factor_lj */, double &fforce)
+{
+    int m, k, index;
+    double rsqinv, p, uLD;
+    double *coeff, **LD;
+    double dFdrho, phi, dphi;
+
+    uLD = dFdrho = dphi = 0.0;
+
+    memory->create(LD, nLD, 3, "pairLD:LD");
+    for (k = 0; k < nLD; k++) {
+        LD[k][1] = 0.0; // itype:- 1
+        LD[k][2] = 0.0; // jtype:- 2
+        }
+
+    rsqinv = 1.0/rsq;
+    for (k = 0; k < nLD; k++) {
+        if (rsq < lowercutsq[k]) {
+             phi = 1.0;
+        }
+        else if (rsq > uppercutsq[k]) {
+             phi = 0.0;
+        }
+        else {
+             phi = c0[k] + rsq * (c2[k] + rsq * (c4[k] + c6[k]*rsq));
+        }
+        LD[k][1] += (phi * b[k][jtype]);
+        LD[k][2] += (phi * b[k][itype]);
+    }
+
+    for (k = 0; k < nLD; k++) {
+        if (a[k][itype]) index = 1;
+        if (a[k][jtype]) index = 2;
+
+        if (LD[k][index] <= rho_min[k]) {
+            coeff = frho_spline[k][0];
+            dFdrho = coeff[2];
+            uLD +=  a[k][itype] * ( coeff[6] + dFdrho*(LD[k][index] - rho_min[k]) );
+        }
+        else if (LD[k][index] >= rho_max[k]) {
+            coeff = frho_spline[k][nrho-1];
+            dFdrho = coeff[0] + coeff[1]  + coeff[2];
+            uLD +=  a[k][itype] * ( (coeff[3] + coeff[4] + coeff[5] + coeff[6]) + dFdrho*(LD[k][index] - rho_max[k]) );
+        }
+        else {
+            p = (LD[k][index] - rho_min[k]) / delta_rho[k];
+            m = static_cast<int> (p);
+            m = MAX(0, MIN(m, nrho-2));
+            p -= m;
+            p = MIN(p, 1.0);
+            coeff = frho_spline[k][m];
+            dFdrho = (coeff[0]*p + coeff[1])*p + coeff[2];
+            uLD +=  a[k][itype] * (((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]);
+        }
+
+        if (rsq < lowercutsq[k]) {
+           dphi = 0.0;
+        }
+        else if (rsq > uppercutsq[k]) {
+           dphi = 0.0;
+        }
+        else {
+           dphi = rsq * (2.0*c2[k] + rsq * (4.0*c4[k] + 6.0*c6[k]*rsq));
+        }
+        fforce +=  -(a[k][itype]*b[k][jtype]*dFdrho + a[k][jtype]*b[k][itype]*dFdrho) * dphi *rsqinv;
+    }
+    memory->destroy(LD);
+
+    return uLD;
+}
+
+/*--------------------------------------------------------------------
+   spline the array frho read in from the file to create
+   frho_spline
+---------------------------------------------------------------------- */
+
+void PairLocalDensity::array2spline() {
+  memory->destroy(frho_spline);
+  memory->create(frho_spline, nLD, nrho, 7, "pairLD:frho_spline");
+
+  for (int k = 0; k < nLD; k++)
+    interpolate_cbspl(nrho, delta_rho[k], frho[k], frho_spline[k]);
+
+}
+
+/* ----------------------------------------------------------------------
+  (one-dimensional) cubic spline interpolation sub-routine,
+  which determines the coeffs for a clamped cubic spline
+  given tabulated data
+ ------------------------------------------------------------------------*/
+
+void PairLocalDensity::interpolate_cbspl(int n, double delta,
+                                         double *f, double **spline)
+{
+/*   inputs:
+          n         number of interpolating points
+
+          f                 array containing function values to
+                                be interpolated;  f[i] is the function
+                                value corresponding to x[i]
+                                    ('x' refers to the independent var)
+
+              delta     difference in tabulated values of x
+
+         outputs: (packaged as columns of the coeff matrix)
+          coeff_b       coeffs of linear terms
+              coeff_c   coeffs of quadratic terms
+              coeff_d   coeffs of cubic terms
+          spline    matrix that collects b,c,d
+
+
+         other parameters:
+          fpa           derivative of function at x=a
+          fpb           derivative of function at x=b
+*/
+
+     double *dl, *dd, *du;
+     double *coeff_b, *coeff_c, *coeff_d;
+     double fpa, fpb;
+
+     int i;
+
+     coeff_b = new double [n];
+     coeff_c = new double [n];
+     coeff_d = new double [n];
+     dl = new double [n];
+     dd = new double [n];
+     du = new double [n];
+
+     // initialize values
+     for ( i = 0; i<n; i++) {
+         coeff_b[i] = coeff_c[i] = coeff_d[i] = 0.;
+         dl[i] = dd[i] = du[i] = 0.;
+     }
+
+     // set slopes at beginning and end
+     fpa = 0.;
+     fpb = 0.;
+
+     for ( i = 0; i < n-1; i++ ) {
+         dl[i] = du[i] = delta;
+     }
+
+     dd[0] = 2.0 * delta;
+     dd[n-1] = 2.0 * delta;
+     coeff_c[0] = ( 3.0 / delta ) * ( f[1] - f[0] ) - 3.0 * fpa;
+     coeff_c[n-1] = 3.0 * fpb - ( 3.0 / delta ) * ( f[n-1] - f[n-2] );
+     for ( i = 0; i < n-2; i++ ) {
+         dd[i+1] = 4.0 * delta;
+         coeff_c[i+1] = ( 3.0 / delta ) * ( f[i+2] - f[i+1] ) -
+                        ( 3.0 / delta ) * ( f[i+1] - f[i] );
+     }
+
+     // tridiagonal solver
+     for ( i = 0; i < n-1; i++ ) {
+         du[i] /= dd[i];
+         dd[i+1] -= dl[i]*du[i];
+     }
+
+     coeff_c[0] /= dd[0];
+     for ( i = 1; i < n; i++ )
+         coeff_c[i] = ( coeff_c[i] - dl[i-1] * coeff_c[i-1] ) / dd[i];
+
+     for ( i = n-2; i >= 0; i-- )
+         coeff_c[i] -= coeff_c[i+1] * du[i];
+
+     for ( i = 0; i < n-1; i++ ) {
+         coeff_d[i] = ( coeff_c[i+1] - coeff_c[i] ) / ( 3.0 * delta );
+         coeff_b[i] = ( f[i+1] - f[i] ) / delta - delta * ( coeff_c[i+1] + 2.0*coeff_c[i] ) / 3.0;
+     }
+
+     // normalize
+     for ( i = 0; i < n-1; i++ ) {
+         coeff_b[i] = coeff_b[i] * delta ;
+         coeff_c[i] = coeff_c[i] * delta*delta ;
+         coeff_d[i] = coeff_d[i] * delta*delta*delta;
+     }
+
+     //copy to coefficient matrix
+     for ( i = 0; i < n; i++) {
+         spline[i][3] = coeff_d[i];
+         spline[i][4] = coeff_c[i];
+         spline[i][5] = coeff_b[i];
+         spline[i][6] = f[i];
+         spline[i][2] = spline[i][5]/delta;
+         spline[i][1] = 2.0*spline[i][4]/delta;
+         spline[i][0] = 3.0*spline[i][3]/delta;
+     }
+
+     delete [] coeff_b;
+     delete [] coeff_c;
+     delete [] coeff_d;
+     delete [] du;
+     delete [] dd;
+     delete [] dl;
+}
+
+/* ----------------------------------------------------------------------
+   read potential values from tabulated LD input file
+------------------------------------------------------------------------- */
+
+void PairLocalDensity::parse_file(char *filename) {
+
+  int k, n;
+  int me = comm->me;
+  FILE *fptr;
+  char line[MAXLINE];
+  double ratio, lc2, uc2, denom;
+
+
+  if (me == 0) {
+    fptr = fopen(filename, "r");
+    if (fptr == NULL) {
+      char str[128];
+      sprintf(str,"Cannot open Local Density potential file %s",filename);
+      error->one(FLERR,str);
+    }
+  }
+
+ double *ftmp; // tmp var to extract the complete 2D frho array from file
+
+ // broadcast number of LD potentials and number of (rho,frho) pairs
+ if (me == 0) {
+
+   // first 2 comment lines ignored
+   utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+   utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+
+   // extract number of potentials and number of (frho, rho) points
+   utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+   sscanf(line, "%d %d", &nLD, &nrho);
+   utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+  }
+
+  MPI_Bcast(&nLD,1,MPI_INT,0,world);
+  MPI_Bcast(&nrho,1,MPI_INT,0,world);
+
+  // setting up all arrays to be read from files and broadcasted
+  memory->create(uppercut, nLD, "pairLD:uppercut");
+  memory->create(lowercut, nLD, "pairLD:lowercut");
+  memory->create(uppercutsq, nLD, "pairLD:uppercutsq");
+  memory->create(lowercutsq, nLD, "pairLD:lowercutsq");
+  memory->create(c0, nLD, "pairLD:c0");
+  memory->create(c2, nLD, "pairLD:c2");
+  memory->create(c4, nLD, "pairLD:c4");
+  memory->create(c6, nLD, "pairLD:c6");
+  memory->create(rho_min,  nLD, "pairLD:rho_min");
+  memory->create(rho_max,  nLD, "pairLD:rho_max");
+  memory->create(delta_rho, nLD,"pairLD:delta_rho");
+  memory->create(ftmp, nrho*nLD, "pairLD:ftmp");
+
+  // setting up central and neighbor atom filters
+  memory->create(a, nLD, atom->ntypes+1 , "pairLD:a");
+  memory->create(b, nLD, atom->ntypes+1, "pairLD:b");
+  if (me == 0) {
+    for (n = 1; n <= atom->ntypes; n++){
+        for (k = 0; k < nLD; k++) {
+            a[k][n] = 0;
+            b[k][n] = 0;
+        }
+    }
+  }
+
+ // read file block by block
+
+  if (me == 0) {
+    for (k = 0; k < nLD; k++) {
+
+        // parse upper and lower cut values
+        if (fgets(line,MAXLINE,fptr)==NULL) break;
+        sscanf(line, "%lf %lf", &lowercut[k], &uppercut[k]);
+
+        // parse and broadcast central atom filter
+        utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error);
+        char *tmp = strtok(line, " /t/n/r/f");
+        while (tmp != NULL) {
+            a[k][atoi(tmp)] = 1;
+            tmp = strtok(NULL, " /t/n/r/f");
+        }
+
+        // parse neighbor atom filter
+        utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error);
+        tmp = strtok(line, " /t/n/r/f");
+        while (tmp != NULL) {
+            b[k][atoi(tmp)] = 1;
+            tmp = strtok(NULL, " /t/n/r/f");
+        }
+
+        // parse min, max and delta rho values
+        utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error);
+        sscanf(line, "%lf %lf %lf", &rho_min[k], &rho_max[k], &delta_rho[k]);
+        // recompute delta_rho from scratch for precision
+        delta_rho[k] = (rho_max[k] - rho_min[k]) / (nrho - 1);
+
+        // parse tabulated frho values from each line into temporary array
+        for (n = 0; n < nrho; n++) {
+          utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+            sscanf(line, "%lf", &ftmp[k*nrho + n]);
+        }
+
+        // ignore blank line at the end of every block
+        utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+
+        // set coefficients for local density indicator function
+        uc2 = uppercut[k] * uppercut[k];
+        uppercutsq[k] = uc2;
+        lc2 = lowercut[k] * lowercut[k];
+        lowercutsq[k] = lc2;
+        ratio = lc2/uc2;
+        denom = 1.0 - ratio;
+        denom = denom*denom*denom;
+        c0[k] = (1 - 3.0 * ratio) / denom;
+        c2[k] = (6.0 * ratio) / (uc2 * denom);
+        c4[k] = -(3.0 + 3.0*ratio) / (uc2*uc2 * denom);
+        c6[k] = 2.0 / (uc2*uc2*uc2 * denom);
+      }
+  }
+
+  // Broadcast all parsed arrays
+  MPI_Bcast(&lowercut[0], nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&uppercut[0], nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&lowercutsq[0], nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&uppercutsq[0], nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&c0[0], nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&c2[0], nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&c4[0], nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&c6[0], nLD, MPI_DOUBLE, 0, world);
+  for (k = 0; k < nLD; k++) {
+      MPI_Bcast(&a[k][1], atom->ntypes, MPI_INT, 0, world);
+      MPI_Bcast(&b[k][1], atom->ntypes, MPI_INT, 0, world);
+  }
+  MPI_Bcast(&rho_min[0],  nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&rho_max[0],  nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&delta_rho[0], nLD, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&ftmp[0], nLD*nrho, MPI_DOUBLE, 0, world);
+
+  if (me == 0) fclose(fptr);
+
+  // set up rho and frho arrays
+  memory->create(rho, nLD, nrho, "pairLD:rho");
+  memory->create(frho, nLD, nrho, "pairLD:frho");
+
+  for (k = 0; k < nLD; k++) {
+    for (n = 0; n < nrho; n++) {
+        rho[k][n] = rho_min[k] + n*delta_rho[k];
+        frho[k][n] = ftmp[k*nrho + n];
+    }
+ }
+
+  // delete temporary array
+  memory->destroy(ftmp);
+}
+
+/* ----------------------------------------------------------------------
+   communication routines
+------------------------------------------------------------------------- */
+
+int PairLocalDensity::pack_comm(int n, int *list, double *buf,
+                                int /* pbc_flag */, int * /* pbc */) {
+  int i,j,k;
+  int m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    for (k = 0; k < nLD; k++) {
+      buf[m++] = fp[k][j];
+    }
+  }
+
+  return nLD;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLocalDensity::unpack_comm(int n, int first, double *buf) {
+
+  int i,k,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    for (k = 0; k < nLD; k++) {
+      fp[k][i] = buf[m++];
+    }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int PairLocalDensity::pack_reverse_comm(int n, int first, double *buf) {
+
+  int i,k,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    for (k = 0; k < nLD; k++) {
+      buf[m++] = localrho[k][i];
+    }
+  }
+  return nLD;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLocalDensity::unpack_reverse_comm(int n, int *list, double *buf) {
+
+  int i,j,k;
+  int m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    for (k = 0; k < nLD; k++) {
+      localrho[k][j] += buf[m++];
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
+
+double PairLocalDensity::memory_usage()
+{
+  double bytes = maxeatom * sizeof(double);
+  bytes += maxvatom*6 * sizeof(double);
+  bytes += 2 * (nmax*nLD) * sizeof(double);
+  return bytes;
+}
+
diff --git a/src/USER-MISC/pair_local_density.h b/src/USER-MISC/pair_local_density.h
new file mode 100644
index 0000000000..e999352680
--- /dev/null
+++ b/src/USER-MISC/pair_local_density.h
@@ -0,0 +1,88 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+-------------------------------------------------------------------------
+   pair_LocalDensity written by:
+   Tanmoy Sanyal and M. Scott Shell from UC Santa Barbara
+   David Rosenberger: TU Darmstadt
+-------------------------------------------------------------------------*/
+
+
+#ifdef PAIR_CLASS
+
+PairStyle(local/density,PairLocalDensity)
+
+#else
+
+#ifndef LMP_PAIR_LOCAL_DENSITY_H
+#define LMP_PAIR_LOCAL_DENSITY_H
+
+#include "pair.h"
+
+
+namespace LAMMPS_NS {
+
+class PairLocalDensity : public Pair {
+  public:
+    PairLocalDensity(class LAMMPS *);
+    virtual ~PairLocalDensity();
+    virtual void compute(int, int);
+    void settings(int, char **);
+    virtual void coeff(int, char **);
+    void init_style();
+    double init_one(int, int);
+    double single(int, int, int, int, double, double, double, double &);
+
+    virtual int pack_comm(int, int *, double *, int, int *);
+    virtual void unpack_comm(int, int, double *);
+    int pack_reverse_comm(int, int, double *);
+    void unpack_reverse_comm(int, int *, double *);
+    double memory_usage();
+
+
+  protected:
+    //------------------------------------------------------------------------
+    //This information is read from the tabulated input file
+
+    int nLD, nrho;                          // number of LD types
+    int **a, **b;                           // central and neigh atom filters
+    double *uppercut, *lowercut;            // upper and lower cutoffs
+    double *uppercutsq, *lowercutsq;        // square of above cutoffs
+    double *c0, *c2, *c4, *c6;              // coeffs for indicator function
+    double *rho_min, *rho_max, *delta_rho;  // min, max & grid-size for LDs
+    double **rho, **frho;                   // LD and LD function tables
+
+    //------------------------------------------------------------------------
+
+    double ***frho_spline; // splined LD potentials
+    double cutmax;          // max cutoff for all elements
+    double cutforcesq;      // square of global upper cutoff
+
+    int nmax;               // max size of per-atom arrays
+    double **localrho;     // per-atom LD
+    double **fp;           // per-atom LD potential function derivative
+
+    void allocate();
+
+        // read tabulated input file
+        void parse_file(char *);
+
+        // convert array to spline
+        void array2spline();
+
+        // cubic spline interpolation
+    void interpolate_cbspl(int, double, double *, double **);
+};
+
+}
+
+#endif
+#endif
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 79e7ac7e09..27deff9a6e 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -43,6 +43,7 @@
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -439,13 +440,13 @@ void PairMEAMSpline::read_file(const char* filename)
     // Skip first line of file. It's a comment.
     char line[MAXLINE];
     char *ptr;
-    fgets(line, MAXLINE, fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
 
     // Second line holds potential type ("meam/spline")
     // in new potential format.
 
     bool isNewFormat = false;
-    fgets(line, MAXLINE, fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
     ptr = strtok(line, " \t\n\r\f");
 
     if (strcmp(ptr, "meam/spline") == 0) {
@@ -475,7 +476,7 @@ void PairMEAMSpline::read_file(const char* filename)
       elements[0] = new char[1];
       strcpy(elements[0], "");
       rewind(fp);
-      fgets(line, MAXLINE, fp);
+      utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
     }
 
     nmultichoose2 = ((nelements+1)*nelements)/2;
@@ -639,27 +640,27 @@ void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error,
 
   // If new format, read the spline format.  Should always be "spline3eq" for now.
   if (isNewFormat)
-    fgets(line, MAXLINE, fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
 
   // Parse number of spline knots.
-  fgets(line, MAXLINE, fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
   int n = atoi(line);
   if(n < 2)
     error->one(FLERR,"Invalid number of spline knots in MEAM potential file");
 
   // Parse first derivatives at beginning and end of spline.
-  fgets(line, MAXLINE, fp);
+  utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
   double d0 = atof(strtok(line, " \t\n\r\f"));
   double dN = atof(strtok(NULL, " \t\n\r\f"));
   init(n, d0, dN);
 
   // Skip line in old format
   if (!isNewFormat)
-    fgets(line, MAXLINE, fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
 
   // Parse knot coordinates.
   for(int i=0; i<n; i++) {
-    fgets(line, MAXLINE, fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
     double x, y, y2;
     if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) {
       error->one(FLERR,"Invalid knot line in MEAM potential file");
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index eeadacf33a..73d6c81004 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -35,6 +35,7 @@
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -468,7 +469,7 @@ void PairMEAMSWSpline::read_file(const char* filename)
 
     // Skip first line of file.
     char line[MAXLINE];
-    fgets(line, MAXLINE, fp);
+    utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
 
     // Parse spline functions.
     phi.parse(fp, error);
@@ -600,23 +601,23 @@ void PairMEAMSWSpline::SplineFunction::parse(FILE* fp, Error* error)
         char line[MAXLINE];
 
         // Parse number of spline knots.
-        fgets(line, MAXLINE, fp);
+        utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
         int n = atoi(line);
         if(n < 2)
                 error->one(FLERR,"Invalid number of spline knots in MEAM potential file");
 
         // Parse first derivatives at beginning and end of spline.
-        fgets(line, MAXLINE, fp);
+        utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
         double d0 = atof(strtok(line, " \t\n\r\f"));
         double dN = atof(strtok(NULL, " \t\n\r\f"));
         init(n, d0, dN);
 
         // Skip line.
-        fgets(line, MAXLINE, fp);
+        utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
 
         // Parse knot coordinates.
         for(int i=0; i<n; i++) {
-                fgets(line, MAXLINE, fp);
+          utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error);
                 double x, y, y2;
                 if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) {
                         error->one(FLERR,"Invalid knot line in MEAM potential file");
diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp
index 29d5715302..8786394221 100644
--- a/src/USER-MISC/pair_momb.cpp
+++ b/src/USER-MISC/pair_momb.cpp
@@ -25,6 +25,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "citeme.h"
 
 using namespace LAMMPS_NS;
@@ -307,16 +308,16 @@ void PairMomb::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&d0[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&r0[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&rr[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rr[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
@@ -348,11 +349,11 @@ void PairMomb::write_restart_settings(FILE *fp)
 void PairMomb::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&sscale,sizeof(double),1,fp);
-    fread(&dscale,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&sscale,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&dscale,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&sscale,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index c3cbe39db7..bbdae231f8 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -21,6 +21,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -273,14 +274,14 @@ void PairMorseSmoothLinear::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&d0[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&r0[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
@@ -307,8 +308,8 @@ void PairMorseSmoothLinear::write_restart_settings(FILE *fp)
 void PairMorseSmoothLinear::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp
index 416ace8132..606fdc9fc5 100644
--- a/src/USER-MISC/pair_srp.cpp
+++ b/src/USER-MISC/pair_srp.cpp
@@ -44,6 +44,7 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil).
 #include "thermo.h"
 #include "output.h"
 #include "citeme.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -698,13 +699,12 @@ void PairSRP::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          printf(" i %d j %d \n",i,j);
-          fread(&a0[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -732,12 +732,12 @@ void PairSRP::write_restart_settings(FILE *fp)
 void PairSRP::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&bptype,sizeof(int),1,fp);
-    fread(&btype,sizeof(int),1,fp);
-    fread(&min,sizeof(int),1,fp);
-    fread(&midpoint,sizeof(int),1,fp);
-    fread(&exclude,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&bptype,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&btype,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&min,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&midpoint,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&exclude,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
 }
diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp
index bb0a01d546..839148bc13 100644
--- a/src/USER-MOFFF/angle_class2_p6.cpp
+++ b/src/USER-MOFFF/angle_class2_p6.cpp
@@ -28,6 +28,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -385,21 +386,21 @@ void AngleClass2P6::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k2[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k3[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k4[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k5[1],sizeof(double),atom->nangletypes,fp);
-    fread(&k6[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k5[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&k6[1],sizeof(double),atom->nangletypes,fp,NULL,error);
 
-    fread(&bb_k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp);
-    fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&bb_k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&bb_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&bb_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
 
-    fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp);
-    fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp);
-    fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp);
-    fread(&ba_r2[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&ba_k1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&ba_k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&ba_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&ba_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
 
   MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index c17b2a1dba..a6643601c1 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -28,6 +28,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -331,9 +332,9 @@ void AngleCosineBuck6d::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nangletypes,fp);
-    fread(&multiplicity[1],sizeof(int),atom->nangletypes,fp);
-    fread(&th0[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&th0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
 
   MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 12f7062ccc..e38b82067d 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -29,6 +29,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -312,8 +313,8 @@ void ImproperInversionHarmonic::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&kw[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&w0[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&kw[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&w0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&kw[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&w0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
index 9c917d1c19..57a935a0b3 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
@@ -29,6 +29,7 @@
 #include "memory.h"
 #include "math_const.h"
 #include "error.h"
+#include "utils.h"
 #include "math_special.h"
 
 using namespace LAMMPS_NS;
@@ -414,16 +415,16 @@ void PairBuck6dCoulGaussDSF::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&buck6d1[i][j],sizeof(double),1,fp);
-          fread(&buck6d2[i][j],sizeof(double),1,fp);
-          fread(&buck6d3[i][j],sizeof(double),1,fp);
-          fread(&buck6d4[i][j],sizeof(double),1,fp);
-          fread(&alpha_ij[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&buck6d1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&buck6d2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&buck6d3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&buck6d4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha_ij[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&buck6d1[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&buck6d2[i][j],1,MPI_DOUBLE,0,world);
@@ -456,12 +457,12 @@ void PairBuck6dCoulGaussDSF::write_restart_settings(FILE *fp)
 void PairBuck6dCoulGaussDSF::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&vdwl_smooth,sizeof(double),1,fp);
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&vdwl_smooth,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&vdwl_smooth,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
index 953507ce21..d3ccec3a55 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
@@ -29,6 +29,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "math_special.h"
 
 using namespace LAMMPS_NS;
@@ -446,16 +447,16 @@ void PairBuck6dCoulGaussLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&buck6d1[i][j],sizeof(double),1,fp);
-          fread(&buck6d2[i][j],sizeof(double),1,fp);
-          fread(&buck6d3[i][j],sizeof(double),1,fp);
-          fread(&buck6d4[i][j],sizeof(double),1,fp);
-          fread(&alpha_ij[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&buck6d1[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&buck6d2[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&buck6d3[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&buck6d4[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha_ij[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&buck6d1[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&buck6d2[i][j],1,MPI_DOUBLE,0,world);
@@ -489,13 +490,13 @@ void PairBuck6dCoulGaussLong::write_restart_settings(FILE *fp)
 void PairBuck6dCoulGaussLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&vdwl_smooth,sizeof(double),1,fp);
-    fread(&coul_smooth,sizeof(double),1,fp);
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&vdwl_smooth,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&coul_smooth,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&vdwl_smooth,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&coul_smooth,1,MPI_DOUBLE,0,world);
diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp
index 5cff56753b..292a451a87 100644
--- a/src/USER-MOLFILE/reader_molfile.cpp
+++ b/src/USER-MOLFILE/reader_molfile.cpp
@@ -282,7 +282,7 @@ bigint ReaderMolfile::read_header(double box[3][3], int &boxinfo, int &triclinic
   }
 
   // if no field info requested, just return
- 
+
  if (!fieldinfo) return natoms;
 
   memory->create(fieldindex,nfield,"read_dump:fieldindex");
diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp
index f135446915..116c937788 100644
--- a/src/USER-OMP/angle_charmm_omp.cpp
+++ b/src/USER-OMP/angle_charmm_omp.cpp
@@ -55,7 +55,7 @@ void AngleCharmmOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp
index 0cf5489663..9aab1d73b3 100644
--- a/src/USER-OMP/angle_class2_omp.cpp
+++ b/src/USER-OMP/angle_class2_omp.cpp
@@ -55,7 +55,7 @@ void AngleClass2OMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp
index 7f4d994c4f..44326c124e 100644
--- a/src/USER-OMP/angle_cosine_delta_omp.cpp
+++ b/src/USER-OMP/angle_cosine_delta_omp.cpp
@@ -55,7 +55,7 @@ void AngleCosineDeltaOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp
index 0543c94799..3bfa2aa39c 100644
--- a/src/USER-OMP/angle_cosine_omp.cpp
+++ b/src/USER-OMP/angle_cosine_omp.cpp
@@ -55,7 +55,7 @@ void AngleCosineOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp
index 907315f83b..700179119c 100644
--- a/src/USER-OMP/angle_cosine_periodic_omp.cpp
+++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp
@@ -57,7 +57,7 @@ void AngleCosinePeriodicOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
index 6c42319905..1e37688425 100644
--- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
@@ -55,7 +55,7 @@ void AngleCosineShiftExpOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp
index 5c0afcf316..35b409edf1 100644
--- a/src/USER-OMP/angle_cosine_shift_omp.cpp
+++ b/src/USER-OMP/angle_cosine_shift_omp.cpp
@@ -55,7 +55,7 @@ void AngleCosineShiftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp
index 27c47b90d8..9da5a0fce3 100644
--- a/src/USER-OMP/angle_cosine_squared_omp.cpp
+++ b/src/USER-OMP/angle_cosine_squared_omp.cpp
@@ -55,7 +55,7 @@ void AngleCosineSquaredOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp
index 6af5b44a03..33ec216f6a 100644
--- a/src/USER-OMP/angle_dipole_omp.cpp
+++ b/src/USER-OMP/angle_dipole_omp.cpp
@@ -59,7 +59,7 @@ void AngleDipoleOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag)
diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp
index 98527c2028..64ff99e6c6 100644
--- a/src/USER-OMP/angle_fourier_omp.cpp
+++ b/src/USER-OMP/angle_fourier_omp.cpp
@@ -55,7 +55,7 @@ void AngleFourierOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp
index 71d0197b72..2ae8c5561d 100644
--- a/src/USER-OMP/angle_fourier_simple_omp.cpp
+++ b/src/USER-OMP/angle_fourier_simple_omp.cpp
@@ -55,7 +55,7 @@ void AngleFourierSimpleOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp
index ee08bbd8ad..66c0602396 100644
--- a/src/USER-OMP/angle_harmonic_omp.cpp
+++ b/src/USER-OMP/angle_harmonic_omp.cpp
@@ -55,7 +55,7 @@ void AngleHarmonicOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp
index 5745948222..903b0e4225 100644
--- a/src/USER-OMP/angle_quartic_omp.cpp
+++ b/src/USER-OMP/angle_quartic_omp.cpp
@@ -55,7 +55,7 @@ void AngleQuarticOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp
index e0b1da0baf..3c8ee9cde8 100644
--- a/src/USER-OMP/angle_sdk_omp.cpp
+++ b/src/USER-OMP/angle_sdk_omp.cpp
@@ -57,7 +57,7 @@ void AngleSDKOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp
index 4f6edf2073..de36d09980 100644
--- a/src/USER-OMP/angle_table_omp.cpp
+++ b/src/USER-OMP/angle_table_omp.cpp
@@ -55,7 +55,7 @@ void AngleTableOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp
index 7d1b693faf..9da50d1aa0 100644
--- a/src/USER-OMP/bond_class2_omp.cpp
+++ b/src/USER-OMP/bond_class2_omp.cpp
@@ -55,7 +55,7 @@ void BondClass2OMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp
index aefae6dcf7..a937cb6c34 100644
--- a/src/USER-OMP/bond_fene_expand_omp.cpp
+++ b/src/USER-OMP/bond_fene_expand_omp.cpp
@@ -56,7 +56,7 @@ void BondFENEExpandOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp
index 2b579114ba..3c653fedae 100644
--- a/src/USER-OMP/bond_fene_omp.cpp
+++ b/src/USER-OMP/bond_fene_omp.cpp
@@ -56,7 +56,7 @@ void BondFENEOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp
index ba23217a1f..cedd5f96b7 100644
--- a/src/USER-OMP/bond_gromos_omp.cpp
+++ b/src/USER-OMP/bond_gromos_omp.cpp
@@ -52,7 +52,7 @@ void BondGromosOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp
index 5515284f9a..4144f02a39 100644
--- a/src/USER-OMP/bond_harmonic_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_omp.cpp
@@ -54,7 +54,7 @@ void BondHarmonicOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
index a871fa8c04..10e4cdcd1c 100644
--- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
@@ -54,7 +54,7 @@ void BondHarmonicShiftCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp
index 4117da9159..a0a7750890 100644
--- a/src/USER-OMP/bond_harmonic_shift_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp
@@ -54,7 +54,7 @@ void BondHarmonicShiftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp
index e6526dc8dc..32361cb5de 100644
--- a/src/USER-OMP/bond_morse_omp.cpp
+++ b/src/USER-OMP/bond_morse_omp.cpp
@@ -54,7 +54,7 @@ void BondMorseOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp
index 0d1a648415..f21772435f 100644
--- a/src/USER-OMP/bond_nonlinear_omp.cpp
+++ b/src/USER-OMP/bond_nonlinear_omp.cpp
@@ -54,7 +54,7 @@ void BondNonlinearOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp
index 60d3a5601c..46ee4ab96b 100644
--- a/src/USER-OMP/bond_quartic_omp.cpp
+++ b/src/USER-OMP/bond_quartic_omp.cpp
@@ -60,7 +60,7 @@ void BondQuarticOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp
index 8e1e792c73..db1599fbcc 100644
--- a/src/USER-OMP/bond_table_omp.cpp
+++ b/src/USER-OMP/bond_table_omp.cpp
@@ -54,7 +54,7 @@ void BondTableOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp
index 95ad9af6a6..242a0a1d86 100644
--- a/src/USER-OMP/dihedral_charmm_omp.cpp
+++ b/src/USER-OMP/dihedral_charmm_omp.cpp
@@ -64,7 +64,7 @@ void DihedralCharmmOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp
index 6c2bc02ff4..215677612b 100644
--- a/src/USER-OMP/dihedral_class2_omp.cpp
+++ b/src/USER-OMP/dihedral_class2_omp.cpp
@@ -58,7 +58,7 @@ void DihedralClass2OMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
@@ -159,6 +159,11 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
     costh13 = c0;
     costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
 
+    costh12 = MAX(MIN(costh12, 1.0), -1.0);
+    costh13 = MAX(MIN(costh13, 1.0), -1.0);
+    costh23 = MAX(MIN(costh23, 1.0), -1.0);
+    c0 = costh13;
+
     // cos and sin of 2 angles and final c
 
     sin2 = MAX(1.0 - costh12*costh12,0.0);
diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
index d77e9d6b3e..f42121f8a9 100644
--- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
@@ -58,7 +58,7 @@ void DihedralCosineShiftExpOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp
index 93dbd773ca..cd12b3630e 100644
--- a/src/USER-OMP/dihedral_fourier_omp.cpp
+++ b/src/USER-OMP/dihedral_fourier_omp.cpp
@@ -57,7 +57,7 @@ void DihedralFourierOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp
index 84aa584d9e..c3adb113e2 100644
--- a/src/USER-OMP/dihedral_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_harmonic_omp.cpp
@@ -58,7 +58,7 @@ void DihedralHarmonicOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp
index 51b07754e2..b38ff2739a 100644
--- a/src/USER-OMP/dihedral_helix_omp.cpp
+++ b/src/USER-OMP/dihedral_helix_omp.cpp
@@ -61,7 +61,7 @@ void DihedralHelixOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
index 4cb6919a96..7b79a63722 100644
--- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
@@ -58,7 +58,7 @@ void DihedralMultiHarmonicOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp
index 203884531b..f3d8471c95 100644
--- a/src/USER-OMP/dihedral_nharmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp
@@ -58,7 +58,7 @@ void DihedralNHarmonicOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp
index af12bb866e..24cc4cd064 100644
--- a/src/USER-OMP/dihedral_opls_omp.cpp
+++ b/src/USER-OMP/dihedral_opls_omp.cpp
@@ -59,7 +59,7 @@ void DihedralOPLSOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp
index 8cea62aaea..6f82c1e6b0 100644
--- a/src/USER-OMP/dihedral_quadratic_omp.cpp
+++ b/src/USER-OMP/dihedral_quadratic_omp.cpp
@@ -59,7 +59,7 @@ void DihedralQuadraticOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp
index 6b10027b9d..a760fc6094 100644
--- a/src/USER-OMP/dihedral_table_omp.cpp
+++ b/src/USER-OMP/dihedral_table_omp.cpp
@@ -121,7 +121,7 @@ void DihedralTableOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/domain_omp.cpp b/src/USER-OMP/domain_omp.cpp
index a18931c551..18d2a587ca 100644
--- a/src/USER-OMP/domain_omp.cpp
+++ b/src/USER-OMP/domain_omp.cpp
@@ -44,11 +44,10 @@ void DomainOMP::pbc()
   imageint    * _noalias const image = atom->image;
   const int nlocal = atom->nlocal;
 
-  int i;
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     imageint idim,otherdims;
 
     if (xperiodic) {
@@ -142,12 +141,11 @@ void DomainOMP::lamda2x(int n)
 {
   dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
   const int num = n;
-  int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (i = 0; i < num; i++) {
+  for (int i = 0; i < num; i++) {
     x[i].x = h[0]*x[i].x + h[5]*x[i].y + h[4]*x[i].z + boxlo[0];
     x[i].y = h[1]*x[i].y + h[3]*x[i].z + boxlo[1];
     x[i].z = h[2]*x[i].z + boxlo[2];
@@ -163,12 +161,11 @@ void DomainOMP::x2lamda(int n)
 {
   dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
   const int num = n;
-  int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (i = 0; i < num; i++) {
+  for (int i = 0; i < num; i++) {
     double delta0 = x[i].x - boxlo[0];
     double delta1 = x[i].y - boxlo[1];
     double delta2 = x[i].z - boxlo[2];
diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp
index aadf63741d..a539394f69 100644
--- a/src/USER-OMP/ewald_omp.cpp
+++ b/src/USER-OMP/ewald_omp.cpp
@@ -115,7 +115,7 @@ void EwaldOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, nlocal, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, 0, NULL, NULL, thr);
+    ev_setup_thr(eflag, vflag, 0, NULL, NULL, NULL, thr);
 
     for (i = ifrom; i < ito; i++) {
       ek[i][0] = 0.0;
diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp
index fa6b698821..5bc1085f34 100644
--- a/src/USER-OMP/fix_gravity_omp.cpp
+++ b/src/USER-OMP/fix_gravity_omp.cpp
@@ -63,19 +63,17 @@ void FixGravityOMP::post_force(int /* vflag */)
   const double xacc_thr = xacc;
   const double yacc_thr = yacc;
   const double zacc_thr = zacc;
-  double massone;
 
-  int i;
   eflag = 0;
   double grav = 0.0;
 
   if (rmass) {
 #if defined(_OPENMP)
-#pragma omp parallel for private(i,massone) default(none) reduction(-:grav)
+#pragma omp parallel for default(none) reduction(-:grav)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
-        massone = rmass[i];
+        const double massone = rmass[i];
         f[i][0] += massone*xacc_thr;
         f[i][1] += massone*yacc_thr;
         f[i][2] += massone*zacc_thr;
@@ -83,11 +81,11 @@ void FixGravityOMP::post_force(int /* vflag */)
       }
   } else {
 #if defined(_OPENMP)
-#pragma omp parallel for private(i,massone) default(none) reduction(-:grav)
+#pragma omp parallel for default(none) reduction(-:grav)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
-        massone = mass[type[i]];
+        const double massone = mass[type[i]];
         f[i][0] += massone*xacc_thr;
         f[i][1] += massone*yacc_thr;
         f[i][2] += massone*zacc_thr;
diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp
index b0967bf7f7..185eab5f47 100644
--- a/src/USER-OMP/fix_nh_asphere_omp.cpp
+++ b/src/USER-OMP/fix_nh_asphere_omp.cpp
@@ -77,15 +77,14 @@ void FixNHAsphereOMP::nve_v()
   const double * _noalias const rmass = atom->rmass;
   const int * _noalias const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   // standard nve_v velocity update. for efficiency the loop is
   // merged with FixNHOMP instead of calling it for the COM update.
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
       const double dtfm = dtf / rmass[i];
       v[i].x += dtfm*f[i].x;
@@ -112,7 +111,6 @@ void FixNHAsphereOMP::nve_x()
   AtomVecEllipsoid::Bonus * _noalias const bonus = avec->bonus;
   const int * _noalias const ellipsoid = atom->ellipsoid;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   // set timestep here since dt may have changed or come via rRESPA
 
@@ -124,9 +122,9 @@ void FixNHAsphereOMP::nve_x()
   // principal moments of inertia
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++)
+  for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
       double omega[3], inertia[3];
 
@@ -162,13 +160,12 @@ void FixNHAsphereOMP::nh_v_temp()
   dbl3_t * _noalias const angmom = (dbl3_t *) atom->angmom[0];
   const int * _noalias const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   if (which == NOBIAS) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         v[i].x *= factor_eta;
         v[i].y *= factor_eta;
@@ -180,9 +177,9 @@ void FixNHAsphereOMP::nh_v_temp()
     }
   } else if (which == BIAS) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       double buf[3];
       if (mask[i] & groupbit) {
         temperature->remove_bias_thr(i,&v[i].x,buf);
diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp
index 2abd739f71..d584bcd11f 100644
--- a/src/USER-OMP/fix_nh_omp.cpp
+++ b/src/USER-OMP/fix_nh_omp.cpp
@@ -56,11 +56,10 @@ void FixNHOMP::remap()
 
   if (allremap) domain->x2lamda(nlocal);
   else {
-    int i;
 #if defined (_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & dilate_group_bit)
         domain->x2lamda(x[i],x[i]);
   }
@@ -207,11 +206,10 @@ void FixNHOMP::remap()
 
   if (allremap) domain->lamda2x(nlocal);
   else {
-    int i;
 #if defined (_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & dilate_group_bit)
         domain->lamda2x(x[i],x[i]);
   }
@@ -234,13 +232,12 @@ void FixNHOMP::nh_v_press()
   dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
   const int * _noalias const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   if (which == NOBIAS) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         v[i].x *= factor0;
         v[i].y *= factor1;
@@ -256,9 +253,9 @@ void FixNHOMP::nh_v_press()
     }
   } else if (which == BIAS) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       double buf[3];
       if (mask[i] & groupbit) {
         temperature->remove_bias_thr(i,&v[i].x,buf);
@@ -288,14 +285,13 @@ void FixNHOMP::nve_v()
   const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
   const int * _noalias const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   if (atom->rmass) {
     const double * _noalias const rmass = atom->rmass;
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         const double dtfm = dtf / rmass[i];
         v[i].x += dtfm*f[i].x;
@@ -307,9 +303,9 @@ void FixNHOMP::nve_v()
     const double *_noalias const mass = atom->mass;
     const int * _noalias const type = atom->type;
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         const double dtfm = dtf / mass[type[i]];
         v[i].x += dtfm*f[i].x;
@@ -330,14 +326,13 @@ void FixNHOMP::nve_x()
   const dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
   const int * _noalias const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   // x update by full step only for atoms in group
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
       x[i].x += dtv * v[i].x;
       x[i].y += dtv * v[i].y;
@@ -354,13 +349,12 @@ void FixNHOMP::nh_v_temp()
   dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
   const int * _noalias const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   if (which == NOBIAS) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         v[i].x *= factor_eta;
         v[i].y *= factor_eta;
@@ -369,9 +363,9 @@ void FixNHOMP::nh_v_temp()
     }
   } else if (which == BIAS) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       double buf[3];
       if (mask[i] & groupbit) {
         temperature->remove_bias_thr(i,&v[i].x,buf);
diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp
index 64bc536bb0..0048ae7ff7 100644
--- a/src/USER-OMP/fix_nh_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nh_sphere_omp.cpp
@@ -76,7 +76,6 @@ void FixNHSphereOMP::nve_v()
   const double dtfrotate = dtf / INERTIA;
 
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   // standard nve_v velocity update. for efficiency the loop is
   // merged with FixNHOMP instead of calling it for the COM update.
@@ -86,9 +85,9 @@ void FixNHSphereOMP::nve_v()
   // 4 cases depending on radius vs shape and rmass vs mass
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
       const double dtfm = dtf / rmass[i];
       v[i].x += dtfm*f[i].x;
@@ -113,13 +112,12 @@ void FixNHSphereOMP::nh_v_temp()
   dbl3_t * _noalias const omega = (dbl3_t *) atom->omega[0];
   const int * _noalias const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   if (which == NOBIAS) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         v[i].x *= factor_eta;
         v[i].y *= factor_eta;
@@ -131,9 +129,9 @@ void FixNHSphereOMP::nh_v_temp()
     }
   } else if (which == BIAS) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++) {
+    for (int i = 0; i < nlocal; i++) {
       double buf[3];
       if (mask[i] & groupbit) {
         temperature->remove_bias_thr(i,&v[i].x,buf);
diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/USER-OMP/fix_nve_omp.cpp
index 61ed82b16f..f693c2fa20 100644
--- a/src/USER-OMP/fix_nve_omp.cpp
+++ b/src/USER-OMP/fix_nve_omp.cpp
@@ -37,14 +37,13 @@ void FixNVEOMP::initial_integrate(int /* vflag */)
   const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
   const int * const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   if (atom->rmass) {
     const double * const rmass = atom->rmass;
 #if defined (_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
         const double dtfm = dtf / rmass[i];
         v[i].x += dtfm * f[i].x;
@@ -59,9 +58,9 @@ void FixNVEOMP::initial_integrate(int /* vflag */)
     const double * const mass = atom->mass;
     const int * const type = atom->type;
 #if defined (_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
         const double dtfm = dtf / mass[type[i]];
         v[i].x += dtfm * f[i].x;
@@ -84,14 +83,13 @@ void FixNVEOMP::final_integrate()
   const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
   const int * const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   if (atom->rmass) {
     const double * const rmass = atom->rmass;
 #if defined (_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
         const double dtfm = dtf / rmass[i];
         v[i].x += dtfm * f[i].x;
@@ -103,9 +101,9 @@ void FixNVEOMP::final_integrate()
     const double * const mass = atom->mass;
     const int * const type = atom->type;
 #if defined (_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
         const double dtfm = dtf / mass[type[i]];
         v[i].x += dtfm * f[i].x;
diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp
index ccdd654874..bc7be4019c 100644
--- a/src/USER-OMP/fix_nve_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nve_sphere_omp.cpp
@@ -42,7 +42,6 @@ void FixNVESphereOMP::initial_integrate(int /* vflag */)
   const double * const rmass = atom->rmass;
   const int * const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   // set timestep here since dt may have changed or come via rRESPA
   const double dtfrotate = dtf / INERTIA;
@@ -50,9 +49,9 @@ void FixNVESphereOMP::initial_integrate(int /* vflag */)
   // update v,x,omega for all particles
   // d_omega/dt = torque / inertia
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none)
+#pragma omp parallel for default(none)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
       const double dtfm = dtf / rmass[i];
       v[i][0] += dtfm * f[i][0];
@@ -77,9 +76,9 @@ void FixNVESphereOMP::initial_integrate(int /* vflag */)
     double * const * const mu = atom->mu;
     if (dlm == NODLM) {
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none)
+#pragma omp parallel for default(none)
 #endif
-      for (i = 0; i < nlocal; i++) {
+      for (int i = 0; i < nlocal; i++) {
         double g0,g1,g2,msq,scale;
         if (mask[i] & groupbit) {
           if (mu[i][3] > 0.0) {
@@ -96,10 +95,10 @@ void FixNVESphereOMP::initial_integrate(int /* vflag */)
       }
     } else {
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none)
+#pragma omp parallel for default(none)
 #endif
       // Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
-      for (i = 0; i < nlocal; i++) {
+      for (int i = 0; i < nlocal; i++) {
         vector w, w_temp, a;
         matrix Q, Q_temp, R;
 
@@ -215,7 +214,6 @@ void FixNVESphereOMP::final_integrate()
   const double * const radius = atom->radius;
   const int * const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   // set timestep here since dt may have changed or come via rRESPA
 
@@ -225,9 +223,9 @@ void FixNVESphereOMP::final_integrate()
   // d_omega/dt = torque / inertia
 
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none)
+#pragma omp parallel for default(none)
 #endif
-  for (i = 0; i < nlocal; i++)
+  for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
       const double dtfm = dtf / rmass[i];
       v[i][0] += dtfm * f[i][0];
diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp
index 208dfb9432..9b3b515415 100644
--- a/src/USER-OMP/fix_nvt_sllod_omp.cpp
+++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp
@@ -107,7 +107,6 @@ void FixNVTSllodOMP::nh_v_temp()
   dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
   const int * _noalias const mask = atom->mask;
   const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
-  int i;
 
   if (nondeformbias) temperature->compute_scalar();
 
@@ -115,9 +114,9 @@ void FixNVTSllodOMP::nh_v_temp()
   MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) shared(h_two) schedule(static)
+#pragma omp parallel for default(none) shared(h_two) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     double vdelu0,vdelu1,vdelu2,buf[3];
     if (mask[i] & groupbit) {
       vdelu0 = h_two[0]*v[i].x + h_two[5]*v[i].y + h_two[4]*v[i].z;
diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp
index f7945b5579..a10d3127a9 100644
--- a/src/USER-OMP/fix_qeq_reax_omp.cpp
+++ b/src/USER-OMP/fix_qeq_reax_omp.cpp
@@ -188,7 +188,7 @@ void FixQEqReaxOMP::compute_H()
 #pragma omp parallel default(shared)
 #endif
   {
-    int i, j, ii, jj, mfill, jnum, flag;
+    int  mfill, jnum, flag;
     int *jlist;
     double dx, dy, dz, r_sqr;
 
@@ -197,15 +197,15 @@ void FixQEqReaxOMP::compute_H()
 #if defined(_OPENMP)
 #pragma omp for schedule(guided)
 #endif
-    for (ii = 0; ii < inum; ii++) {
-      i = ilist[ii];
+    for (int ii = 0; ii < inum; ii++) {
+      int i = ilist[ii];
       if (mask[i] & groupbit) {
         jlist = firstneigh[i];
         jnum = numneigh[i];
         mfill = H.firstnbr[i];
 
-        for (jj = 0; jj < jnum; jj++) {
-          j = jlist[jj];
+        for (int jj = 0; jj < jnum; jj++) {
+          int j = jlist[jj];
 
           dx = x[j][0] - x[i][0];
           dy = x[j][1] - x[i][1];
@@ -450,13 +450,13 @@ void FixQEqReaxOMP::init_matvec()
 
 int FixQEqReaxOMP::CG( double *b, double *x)
 {
-  int  i, ii, imax;
+  int  i, imax;
   double alpha, beta, b_norm;
   double sig_old, sig_new;
 
   double my_buf[2], buf[2];
 
-  int nn, jj;
+  int nn;
   int *ilist;
   if (reaxc) {
     nn = reaxc->list->inum;
@@ -476,16 +476,16 @@ int FixQEqReaxOMP::CG( double *b, double *x)
   tmp1 = tmp2 = 0.0;
 
 #if defined(_OPENMP)
-#pragma omp parallel for schedule(dynamic,50) private(i) reduction(+:tmp1,tmp2)
+#pragma omp parallel for schedule(dynamic,50) reduction(+:tmp1,tmp2)
 #endif
-  for (jj = 0; jj < nn; ++jj) {
-    i = ilist[jj];
-    if (atom->mask[i] & groupbit) {
-      r[i] = b[i] - q[i];
-      d[i] = r[i] * Hdia_inv[i]; //pre-condition
+  for (int jj = 0; jj < nn; ++jj) {
+    int ii = ilist[jj];
+    if (atom->mask[ii] & groupbit) {
+      r[ii] = b[ii] - q[ii];
+      d[ii] = r[ii] * Hdia_inv[ii]; //pre-condition
 
-      tmp1 += b[i] * b[i];
-      tmp2 += r[i] * d[i];
+      tmp1 += b[ii] * b[ii];
+      tmp2 += r[ii] * d[ii];
     }
   }
 
@@ -509,10 +509,10 @@ int FixQEqReaxOMP::CG( double *b, double *x)
     {
 
 #if defined(_OPENMP)
-#pragma omp for schedule(dynamic,50) private(ii) reduction(+:tmp1)
+#pragma omp for schedule(dynamic,50) reduction(+:tmp1)
 #endif
-      for (jj = 0; jj < nn; jj++) {
-        ii = ilist[jj];
+      for (int jj = 0; jj < nn; jj++) {
+        int ii = ilist[jj];
         if (atom->mask[ii] & groupbit) tmp1 += d[ii] * q[ii];
       }
 
@@ -529,10 +529,10 @@ int FixQEqReaxOMP::CG( double *b, double *x)
 
 #if defined(_OPENMP)
 #pragma omp barrier
-#pragma omp for schedule(dynamic,50) private(ii) reduction(+:tmp1)
+#pragma omp for schedule(dynamic,50) reduction(+:tmp1)
 #endif
-      for (jj = 0; jj < nn; jj++) {
-        ii = ilist[jj];
+      for (int jj = 0; jj < nn; jj++) {
+        int ii = ilist[jj];
         if (atom->mask[ii] & groupbit) {
           x[ii] += alpha * d[ii];
           r[ii] -= alpha * q[ii];
@@ -552,10 +552,10 @@ int FixQEqReaxOMP::CG( double *b, double *x)
     beta = sig_new / sig_old;
 
 #if defined(_OPENMP)
-#pragma omp for schedule(dynamic,50) private(ii)
+#pragma omp for schedule(dynamic,50)
 #endif
-    for (jj = 0; jj < nn; jj++) {
-      ii = ilist[jj];
+    for (int jj = 0; jj < nn; jj++) {
+      int ii = ilist[jj];
       if (atom->mask[ii] & groupbit) d[ii] = p[ii] + beta * d[ii];
     }
   }
@@ -765,13 +765,13 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
   startTimeBase = MPI_Wtime();
 #endif
 
-  int  i, imax;
+  int i, imax;
   double alpha_s, alpha_t, beta_s, beta_t, b_norm_s, b_norm_t;
   double sig_old_s, sig_old_t, sig_new_s, sig_new_t;
 
   double my_buf[4], buf[4];
 
-  int nn, ii, jj;
+  int nn;
   int *ilist;
   if (reaxc) {
     nn = reaxc->list->inum;
@@ -785,26 +785,26 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
 
   pack_flag = 5; // forward 2x d and reverse 2x q
   dual_sparse_matvec( &H, x1, x2, q );
-  comm->reverse_comm_fix( this); //Coll_Vector( q );
+  comm->reverse_comm_fix(this); //Coll_Vector( q );
 
   double tmp1, tmp2, tmp3, tmp4;
   tmp1 = tmp2 = tmp3 = tmp4 = 0.0;
 
 #if defined(_OPENMP)
-#pragma omp parallel for schedule(dynamic,50) private(i) reduction(+:tmp1,tmp2,tmp3,tmp4)
+#pragma omp parallel for schedule(dynamic,50) reduction(+:tmp1,tmp2,tmp3,tmp4)
 #endif
-  for (jj = 0; jj < nn; ++jj) {
-    i = ilist[jj];
-    if (atom->mask[i] & groupbit) {
-      int indxI = 2 * i;
-      r[indxI  ] = b1[i] - q[indxI  ];
-      r[indxI+1] = b2[i] - q[indxI+1];
+  for (int jj = 0; jj < nn; ++jj) {
+    int ii = ilist[jj];
+    if (atom->mask[ii] & groupbit) {
+      int indxI = 2 * ii;
+      r[indxI  ] = b1[ii] - q[indxI  ];
+      r[indxI+1] = b2[ii] - q[indxI+1];
 
-      d[indxI  ] = r[indxI  ] * Hdia_inv[i]; //pre-condition
-      d[indxI+1] = r[indxI+1] * Hdia_inv[i];
+      d[indxI  ] = r[indxI  ] * Hdia_inv[ii]; //pre-condition
+      d[indxI+1] = r[indxI+1] * Hdia_inv[ii];
 
-      tmp1 += b1[i] * b1[i];
-      tmp2 += b2[i] * b2[i];
+      tmp1 += b1[ii] * b1[ii];
+      tmp2 += b2[ii] * b2[ii];
 
       tmp3 += r[indxI  ] * d[indxI  ];
       tmp4 += r[indxI+1] * d[indxI+1];
@@ -836,10 +836,10 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
     {
 
 #if defined(_OPENMP)
-#pragma omp for schedule(dynamic,50) private(ii) reduction(+:tmp1,tmp2)
+#pragma omp for schedule(dynamic,50) reduction(+:tmp1,tmp2)
 #endif
-      for (jj = 0; jj < nn; jj++) {
-        ii = ilist[jj];
+      for (int jj = 0; jj < nn; jj++) {
+        int ii = ilist[jj];
         if (atom->mask[ii] & groupbit) {
           int indxI = 2 * ii;
           tmp1 += d[indxI  ] * q[indxI  ];
@@ -865,10 +865,10 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
 
 #if defined(_OPENMP)
 #pragma omp barrier
-#pragma omp for schedule(dynamic,50) private(ii) reduction(+:tmp1,tmp2)
+#pragma omp for schedule(dynamic,50) reduction(+:tmp1,tmp2)
 #endif
-      for (jj = 0; jj < nn; jj++) {
-        ii = ilist[jj];
+      for (int jj = 0; jj < nn; jj++) {
+        int ii = ilist[jj];
         if (atom->mask[ii] & groupbit) {
           int indxI = 2 * ii;
           x1[ii] += alpha_s * d[indxI  ];
@@ -905,10 +905,10 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
     beta_t = sig_new_t / sig_old_t;
 
 #if defined(_OPENMP)
-#pragma omp for schedule(dynamic,50) private(ii)
+#pragma omp for schedule(dynamic,50)
 #endif
-    for (jj = 0; jj < nn; jj++) {
-      ii = ilist[jj];
+    for (int jj = 0; jj < nn; jj++) {
+      int ii = ilist[jj];
       if (atom->mask[ii] & groupbit) {
         int indxI = 2 * ii;
 
diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp
index 866021b3f4..da512cb428 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nh_omp.cpp
@@ -87,12 +87,11 @@ void FixRigidNHOMP::initial_integrate(int vflag)
 
   // update xcm, vcm, quat, conjqm and angmom
   double akt=0.0, akr=0.0;
-  int ibody;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) shared(scale_r,scale_t,scale_v) schedule(static) reduction(+:akt,akr)
+#pragma omp parallel for default(none) shared(scale_r,scale_t,scale_v) schedule(static) reduction(+:akt,akr)
 #endif
-  for (ibody = 0; ibody < nbody; ibody++) {
+  for (int ibody = 0; ibody < nbody; ibody++) {
     double mbody[3],tbody[3],fquat[4];
     const double dtf2 = dtf * 2.0;
 
@@ -384,13 +383,25 @@ void FixRigidNHOMP::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+    for (ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixRigidNHOMP::final_integrate()
 {
-  int ibody;
   double scale_t[3],scale_r;
 
   // compute scale variables
@@ -422,9 +433,9 @@ void FixRigidNHOMP::final_integrate()
   const double dtf2 = dtf * 2.0;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr)
+#pragma omp parallel for default(none) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr)
 #endif
-  for (ibody = 0; ibody < nbody; ibody++) {
+  for (int ibody = 0; ibody < nbody; ibody++) {
     double mbody[3],tbody[3],fquat[4];
 
     // update vcm by 1/2 step
@@ -542,11 +553,10 @@ void FixRigidNHOMP::remap()
 
   if (allremap) domain->x2lamda(nlocal);
   else {
-    int i;
 #if defined (_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & dilate_group_bit)
         domain->x2lamda(x[i],x[i]);
   }
@@ -575,11 +585,10 @@ void FixRigidNHOMP::remap()
 
   if (allremap) domain->lamda2x(nlocal);
   else {
-    int i;
 #if defined (_OPENMP)
-#pragma omp parallel for private(i) default(none) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & dilate_group_bit)
         domain->lamda2x(x[i],x[i]);
   }
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 3baa9de20a..770361d557 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -46,12 +46,10 @@ typedef struct { double x,y,z; } dbl3_t;
 
 void FixRigidOMP::initial_integrate(int vflag)
 {
-  int ibody;
-
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (ibody = 0; ibody < nbody; ibody++) {
+  for (int ibody = 0; ibody < nbody; ibody++) {
 
     // update vcm by 1/2 step
 
@@ -120,12 +118,11 @@ void FixRigidOMP::compute_forces_and_torques()
    if (rstyle == SINGLE) {
      // we have just one rigid body. use OpenMP reduction to get sum[]
      double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0;
-     int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) reduction(+:s0,s1,s2,s3,s4,s5)
+#pragma omp parallel for default(none) reduction(+:s0,s1,s2,s3,s4,s5)
 #endif
-     for (i = 0; i < nlocal; i++) {
+     for (int i = 0; i < nlocal; i++) {
        const int ibody = body[i];
        if (ibody < 0) continue;
 
@@ -159,12 +156,11 @@ void FixRigidOMP::compute_forces_and_torques()
 
      for (int ib = 0; ib < nbody; ++ib) {
        double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0;
-       int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5)
+#pragma omp parallel for default(none) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5)
 #endif
-       for (i = 0; i < nlocal; i++) {
+       for (int i = 0; i < nlocal; i++) {
          const int ibody = body[i];
          if (ibody != ib) continue;
 
@@ -248,12 +244,11 @@ void FixRigidOMP::compute_forces_and_torques()
   // update vcm and angmom
   // include Langevin thermostat forces
   // fflag,tflag = 0 for some dimensions in 2d
-  int ibody;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (ibody = 0; ibody < nbody; ibody++) {
+  for (int ibody = 0; ibody < nbody; ibody++) {
     fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
     fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
     fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
@@ -261,22 +256,33 @@ void FixRigidOMP::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) schedule(static)
+#endif
+    for (int ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixRigidOMP::final_integrate()
 {
-  int ibody;
-
   if (!earlyflag) compute_forces_and_torques();
 
   // update vcm and angmom
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (ibody = 0; ibody < nbody; ibody++) {
+  for (int ibody = 0; ibody < nbody; ibody++) {
 
     // update vcm by 1/2 step
 
@@ -338,12 +344,11 @@ void FixRigidOMP::set_xv_thr()
   // set x and v of each atom
 
   const int nlocal = atom->nlocal;
-  int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5)
+#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     const int ibody = body[i];
     if (ibody < 0) continue;
 
@@ -539,12 +544,11 @@ void FixRigidOMP::set_v_thr()
   // set v of each atom
 
   const int nlocal = atom->nlocal;
-  int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5)
+#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     const int ibody = body[i];
     if (ibody < 0) continue;
 
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index 523bd4df07..fc6b6fa57a 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -44,12 +44,11 @@ typedef struct { double x,y,z; } dbl3_t;
 
 void FixRigidSmallOMP::initial_integrate(int vflag)
 {
-  int ibody;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (ibody = 0; ibody < nlocal_body; ibody++) {
+  for (int ibody = 0; ibody < nlocal_body; ibody++) {
 
     Body &b = body[ibody];
 
@@ -116,12 +115,11 @@ void FixRigidSmallOMP::compute_forces_and_torques()
   const double * const * const torque_one = atom->torque;
   const int nlocal = atom->nlocal;
   const int nthreads=comm->nthreads;
-  int i, ibody;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
+  for (int ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
     double * _noalias const fcm = body[ibody].fcm;
     fcm[0] = fcm[1] = fcm[2] = 0.0;
     double * _noalias const tcm = body[ibody].torque;
@@ -134,7 +132,7 @@ void FixRigidSmallOMP::compute_forces_and_torques()
   // and then each thread only processes some bodies.
 
 #if defined(_OPENMP)
-#pragma omp parallel default(none) private(i,ibody)
+#pragma omp parallel default(none)
 #endif
   {
 #if defined(_OPENMP)
@@ -143,8 +141,8 @@ void FixRigidSmallOMP::compute_forces_and_torques()
     const int tid = 0;
 #endif
 
-    for (i = 0; i < nlocal; i++) {
-      ibody = atom2body[i];
+    for (int i = 0; i < nlocal; i++) {
+      int ibody = atom2body[i];
       if ((ibody < 0) || (ibody % nthreads != tid)) continue;
 
       Body &b = body[ibody];
@@ -185,9 +183,9 @@ void FixRigidSmallOMP::compute_forces_and_torques()
 
   if (langflag) {
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-    for (ibody = 0; ibody < nlocal_body; ibody++) {
+    for (int ibody = 0; ibody < nlocal_body; ibody++) {
       double * _noalias const fcm = body[ibody].fcm;
       fcm[0] += langextra[ibody][0];
       fcm[1] += langextra[ibody][1];
@@ -198,22 +196,35 @@ void FixRigidSmallOMP::compute_forces_and_torques()
       tcm[2] += langextra[ibody][5];
     }
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) schedule(static)
+#endif
+    for (int ibody = 0; ibody < nbody; ibody++) {
+      double * _noalias const fcm = body[ibody].fcm;
+      const double mass = body[ibody].mass;
+      fcm[0] += gvec[0]*mass;
+      fcm[1] += gvec[1]*mass;
+      fcm[2] += gvec[2]*mass;
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixRigidSmallOMP::final_integrate()
 {
-  int ibody;
-
   if (!earlyflag) compute_forces_and_torques();
 
   // update vcm and angmom, recompute omega
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
 #endif
-  for (ibody = 0; ibody < nlocal_body; ibody++) {
+  for (int ibody = 0; ibody < nlocal_body; ibody++) {
     Body &b = body[ibody];
 
     // update vcm by 1/2 step
@@ -281,12 +292,11 @@ void FixRigidSmallOMP::set_xv_thr()
   // set x and v of each atom
 
   const int nlocal = atom->nlocal;
-  int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5)
+#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     const int ibody = atom2body[i];
     if (ibody  < 0) continue;
 
@@ -477,12 +487,11 @@ void FixRigidSmallOMP::set_v_thr()
   // set v of each atom
 
   const int nlocal = atom->nlocal;
-  int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5)
+#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     const int ibody = atom2body[i];
     if (ibody < 0) continue;
 
diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp
index 3bff179b44..32c7406ada 100644
--- a/src/USER-OMP/improper_class2_omp.cpp
+++ b/src/USER-OMP/improper_class2_omp.cpp
@@ -58,7 +58,7 @@ void ImproperClass2OMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp
index 0f99f2732f..230f13eac7 100644
--- a/src/USER-OMP/improper_cossq_omp.cpp
+++ b/src/USER-OMP/improper_cossq_omp.cpp
@@ -58,7 +58,7 @@ void ImproperCossqOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp
index fdc29c74b1..f5ff590775 100644
--- a/src/USER-OMP/improper_cvff_omp.cpp
+++ b/src/USER-OMP/improper_cvff_omp.cpp
@@ -58,7 +58,7 @@ void ImproperCvffOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp
index b49b895c78..4e83c025d0 100644
--- a/src/USER-OMP/improper_fourier_omp.cpp
+++ b/src/USER-OMP/improper_fourier_omp.cpp
@@ -58,7 +58,7 @@ void ImproperFourierOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp
index 32e837fdfe..f2f19557d9 100644
--- a/src/USER-OMP/improper_harmonic_omp.cpp
+++ b/src/USER-OMP/improper_harmonic_omp.cpp
@@ -58,7 +58,7 @@ void ImproperHarmonicOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp
index c8fe685faa..1d0cc6cc46 100644
--- a/src/USER-OMP/improper_ring_omp.cpp
+++ b/src/USER-OMP/improper_ring_omp.cpp
@@ -58,7 +58,7 @@ void ImproperRingOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp
index f3fdf4570f..4cea8a4b63 100644
--- a/src/USER-OMP/improper_umbrella_omp.cpp
+++ b/src/USER-OMP/improper_umbrella_omp.cpp
@@ -58,7 +58,7 @@ void ImproperUmbrellaOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
 
     if (inum > 0) {
       if (evflag) {
diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp
index 645d697994..0a48de453e 100644
--- a/src/USER-OMP/pair_adp_omp.cpp
+++ b/src/USER-OMP/pair_adp_omp.cpp
@@ -70,7 +70,7 @@ void PairADPOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (force->newton_pair)
       thr->init_adp(nall, rho, mu, lambda);
diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp
index 854bcbebf3..1580256e35 100644
--- a/src/USER-OMP/pair_agni_omp.cpp
+++ b/src/USER-OMP/pair_agni_omp.cpp
@@ -57,7 +57,7 @@ void PairAGNIOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) eval<1>(ifrom, ito, thr);
     else eval<0>(ifrom, ito, thr);
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index bed6c81ee4..7890c8aed3 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -66,7 +66,7 @@ void PairAIREBOOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     FREBO_thr(ifrom,ito,evflag,eflag,vflag_atom,&pv0,thr);
     if (ljflag) FLJ_thr(ifrom,ito,evflag,eflag,vflag_atom,&pv1,thr);
diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp
index 8d0605fae9..72e41f074c 100644
--- a/src/USER-OMP/pair_beck_omp.cpp
+++ b/src/USER-OMP/pair_beck_omp.cpp
@@ -53,7 +53,7 @@ void PairBeckOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp
index a5df8f8182..f7e3fced46 100644
--- a/src/USER-OMP/pair_born_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_long_omp.cpp
@@ -59,7 +59,7 @@ void PairBornCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp
index ad1e5e63cd..b057cbc706 100644
--- a/src/USER-OMP/pair_born_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp
@@ -56,7 +56,7 @@ void PairBornCoulMSMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
index 55da972c4e..bac38ae43a 100644
--- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
@@ -53,7 +53,7 @@ void PairBornCoulWolfOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp
index 35ad4fcb48..6cacd5625b 100644
--- a/src/USER-OMP/pair_born_omp.cpp
+++ b/src/USER-OMP/pair_born_omp.cpp
@@ -51,7 +51,7 @@ void PairBornOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp
index 6367976c7d..907a447332 100644
--- a/src/USER-OMP/pair_brownian_omp.cpp
+++ b/src/USER-OMP/pair_brownian_omp.cpp
@@ -143,7 +143,7 @@ void PairBrownianOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     // generate a random number generator instance for
     // all threads != 0. make sure we use unique seeds.
diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp
index dcb4124634..f6f5f269a5 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.cpp
+++ b/src/USER-OMP/pair_brownian_poly_omp.cpp
@@ -143,7 +143,7 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     // generate a random number generator instance for
     // all threads != 0. make sure we use unique seeds.
diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp
index b9b77dc2b6..c9ccb12447 100644
--- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp
@@ -51,7 +51,7 @@ void PairBuckCoulCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp
index 951ba0688c..0929157895 100644
--- a/src/USER-OMP/pair_buck_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp
@@ -59,7 +59,7 @@ void PairBuckCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp
index 6226191627..a4d322890a 100644
--- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp
@@ -56,7 +56,7 @@ void PairBuckCoulMSMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
index 20d380a464..d30e8949b3 100644
--- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
@@ -64,7 +64,7 @@ void PairBuckLongCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (order6) {
       if (order1) {
@@ -328,7 +328,7 @@ void PairBuckLongCoulLongOMP::compute_inner()
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(0, 0, nall, 0, 0, thr);
+    ev_setup_thr(0, 0, nall, 0, 0, NULL, thr);
     eval_inner(ifrom, ito, thr);
     thr->timer(Timer::PAIR);
 
@@ -353,7 +353,7 @@ void PairBuckLongCoulLongOMP::compute_middle()
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(0, 0, nall, 0, 0, thr);
+    ev_setup_thr(0, 0, nall, 0, 0, NULL, thr);
     eval_middle(ifrom, ito, thr);
     thr->timer(Timer::PAIR);
 
@@ -383,7 +383,7 @@ void PairBuckLongCoulLongOMP::compute_outer(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (order6) {
       if (order1) {
diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp
index 8d5c80513a..563133e1cd 100644
--- a/src/USER-OMP/pair_buck_omp.cpp
+++ b/src/USER-OMP/pair_buck_omp.cpp
@@ -51,7 +51,7 @@ void PairBuckOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp
index 64613cb31d..0fc4b1bdf2 100644
--- a/src/USER-OMP/pair_colloid_omp.cpp
+++ b/src/USER-OMP/pair_colloid_omp.cpp
@@ -54,7 +54,7 @@ void PairColloidOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp
index be641dd0b9..4b5f0ea6c7 100644
--- a/src/USER-OMP/pair_comb_omp.cpp
+++ b/src/USER-OMP/pair_comb_omp.cpp
@@ -60,7 +60,7 @@ void PairCombOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp
index 267beeecbd..ce858666cb 100644
--- a/src/USER-OMP/pair_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_coul_cut_omp.cpp
@@ -51,7 +51,7 @@ void PairCoulCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp
index 70997da62b..7b6ed22f0c 100644
--- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp
@@ -51,7 +51,7 @@ void PairCoulCutSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp
index 4d3f92c495..270770ee5d 100644
--- a/src/USER-OMP/pair_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_coul_debye_omp.cpp
@@ -51,7 +51,7 @@ void PairCoulDebyeOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp
index f2bb6a46bf..67e09690de 100644
--- a/src/USER-OMP/pair_coul_diel_omp.cpp
+++ b/src/USER-OMP/pair_coul_diel_omp.cpp
@@ -51,7 +51,7 @@ void PairCoulDielOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp
index bd7f5cfed2..40e285e7c8 100644
--- a/src/USER-OMP/pair_coul_dsf_omp.cpp
+++ b/src/USER-OMP/pair_coul_dsf_omp.cpp
@@ -60,7 +60,7 @@ void PairCoulDSFOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp
index 1e3170c73c..b135ffa7e6 100644
--- a/src/USER-OMP/pair_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_coul_long_omp.cpp
@@ -60,7 +60,7 @@ void PairCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp
index dd1fc1030d..891123b8b3 100644
--- a/src/USER-OMP/pair_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp
@@ -59,7 +59,7 @@ void PairCoulLongSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp
index 9b50b86954..9417df7ac6 100644
--- a/src/USER-OMP/pair_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_coul_msm_omp.cpp
@@ -57,7 +57,7 @@ void PairCoulMSMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp
index 92d5bd7b15..9163eff086 100644
--- a/src/USER-OMP/pair_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_coul_wolf_omp.cpp
@@ -53,7 +53,7 @@ void PairCoulWolfOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp
index b7f3a7f4d4..7c265b2b7b 100644
--- a/src/USER-OMP/pair_dpd_omp.cpp
+++ b/src/USER-OMP/pair_dpd_omp.cpp
@@ -88,7 +88,7 @@ void PairDPDOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     // generate a random number generator instance for
     // all threads != 0. make sure we use unique seeds.
diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp
index d7233a16c5..076e27a299 100644
--- a/src/USER-OMP/pair_dpd_tstat_omp.cpp
+++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp
@@ -87,7 +87,7 @@ void PairDPDTstatOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     // generate a random number generator instance for
     // all threads != 0. make sure we use unique seeds.
diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp
index 78b4735863..d36574713f 100644
--- a/src/USER-OMP/pair_eam_alloy_omp.cpp
+++ b/src/USER-OMP/pair_eam_alloy_omp.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -136,10 +137,10 @@ void PairEAMAlloyOMP::read_file(char *filename)
 
   int n;
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     n = strlen(line) + 1;
   }
   MPI_Bcast(&n,1,MPI_INT,0,world);
@@ -164,7 +165,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
   delete [] words;
 
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     sscanf(line,"%d %lg %d %lg %lg",
            &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
@@ -184,7 +185,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
   int i,j,tmp;
   for (i = 0; i < file->nelements; i++) {
     if (me == 0) {
-      fgets(line,MAXLINE,fptr);
+      utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
       sscanf(line,"%d %lg",&tmp,&file->mass[i]);
     }
     MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
diff --git a/src/USER-OMP/pair_eam_cd_omp.cpp b/src/USER-OMP/pair_eam_cd_omp.cpp
index 51b83f3bf5..1d945e06a8 100644
--- a/src/USER-OMP/pair_eam_cd_omp.cpp
+++ b/src/USER-OMP/pair_eam_cd_omp.cpp
@@ -85,7 +85,7 @@ void PairEAMCDOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (force->newton_pair)
       thr->init_cdeam(nall, rho, rhoB, D_values);
diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp
index 17fecf9b4f..d1014c5a14 100644
--- a/src/USER-OMP/pair_eam_fs_omp.cpp
+++ b/src/USER-OMP/pair_eam_fs_omp.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -136,10 +137,10 @@ void PairEAMFSOMP::read_file(char *filename)
 
   int n;
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     n = strlen(line) + 1;
   }
   MPI_Bcast(&n,1,MPI_INT,0,world);
@@ -164,7 +165,7 @@ void PairEAMFSOMP::read_file(char *filename)
   delete [] words;
 
   if (me == 0) {
-    fgets(line,MAXLINE,fptr);
+    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
     sscanf(line,"%d %lg %d %lg %lg",
            &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
@@ -186,7 +187,7 @@ void PairEAMFSOMP::read_file(char *filename)
   int i,j,tmp;
   for (i = 0; i < file->nelements; i++) {
     if (me == 0) {
-      fgets(line,MAXLINE,fptr);
+      utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
       sscanf(line,"%d %lg",&tmp,&file->mass[i]);
     }
     MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp
index 99417f27da..899323a680 100644
--- a/src/USER-OMP/pair_eam_omp.cpp
+++ b/src/USER-OMP/pair_eam_omp.cpp
@@ -51,9 +51,11 @@ void PairEAMOMP::compute(int eflag, int vflag)
   if (atom->nmax > nmax) {
     memory->destroy(rho);
     memory->destroy(fp);
+    memory->destroy(numforce);
     nmax = atom->nmax;
     memory->create(rho,nthreads*nmax,"pair:rho");
     memory->create(fp,nmax,"pair:fp");
+    memory->create(numforce,nmax,"pair:numforce");
   }
 
 #if defined(_OPENMP)
@@ -65,7 +67,7 @@ void PairEAMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (force->newton_pair)
       thr->init_eam(nall, rho);
@@ -232,6 +234,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
 
     jlist = firstneigh[i];
     jnum = numneigh[i];
+    numforce[i] = 0;
 
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
@@ -243,6 +246,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
       rsq = delx*delx + dely*dely + delz*delz;
 
       if (rsq < cutforcesq) {
+        ++numforce[i];
         jtype = type[j];
         r = sqrt(rsq);
         p = r*rdr + 1.0;
diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp
index 144d893c1c..d1fa4c1c7a 100644
--- a/src/USER-OMP/pair_edip_omp.cpp
+++ b/src/USER-OMP/pair_edip_omp.cpp
@@ -58,7 +58,7 @@ void PairEDIPOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp
index 2ecd6f8ec7..dd590b75e2 100644
--- a/src/USER-OMP/pair_eim_omp.cpp
+++ b/src/USER-OMP/pair_eim_omp.cpp
@@ -65,7 +65,7 @@ void PairEIMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (force->newton_pair)
       thr->init_eim(nall, rho, fp);
diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp
index 928312240b..e14a85fc95 100644
--- a/src/USER-OMP/pair_gauss_cut_omp.cpp
+++ b/src/USER-OMP/pair_gauss_cut_omp.cpp
@@ -51,7 +51,7 @@ void PairGaussCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp
index 159f1c3e31..de212c9213 100644
--- a/src/USER-OMP/pair_gauss_omp.cpp
+++ b/src/USER-OMP/pair_gauss_omp.cpp
@@ -53,7 +53,7 @@ void PairGaussOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp
index cfa05745ff..a58c16eafc 100644
--- a/src/USER-OMP/pair_gayberne_omp.cpp
+++ b/src/USER-OMP/pair_gayberne_omp.cpp
@@ -53,7 +53,7 @@ void PairGayBerneOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
index 271c70e9b9..1e3d86a1a5 100644
--- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
@@ -77,7 +77,7 @@ void PairGranHertzHistoryOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (shearupdate) {
diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
index 9a0e8aab76..d0e44cc430 100644
--- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
@@ -78,7 +78,7 @@ void PairGranHookeHistoryOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (shearupdate) {
diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/USER-OMP/pair_gran_hooke_omp.cpp
index d226ceaa14..33296e22fa 100644
--- a/src/USER-OMP/pair_gran_hooke_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_omp.cpp
@@ -73,7 +73,7 @@ void PairGranHookeOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag)
       if (force->newton_pair) eval<1,1>(ifrom, ito, thr);
diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
index ea56ff51b5..77cc60e437 100644
--- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
+++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
@@ -82,7 +82,7 @@ void PairHbondDreidingLJOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
index 1cff2de3b2..47b2818be8 100644
--- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
+++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
@@ -82,7 +82,7 @@ void PairHbondDreidingMorseOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp
index 9ba8e09a54..b48946b3f9 100644
--- a/src/USER-OMP/pair_lj96_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj96_cut_omp.cpp
@@ -52,7 +52,7 @@ void PairLJ96CutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
index 3dc9b77c0f..10a253de6c 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
@@ -51,7 +51,7 @@ void PairLJCharmmCoulCharmmImplicitOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
index f9230996f0..c4c5a9650e 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
@@ -51,7 +51,7 @@ void PairLJCharmmCoulCharmmOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
index 4bdaa3519f..949ea3ded7 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
@@ -52,7 +52,7 @@ void PairLJCharmmCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
index 1f6daf052c..2a41b0690b 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
@@ -52,7 +52,7 @@ void PairLJCharmmCoulLongSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
index eab62d919e..cecd27bfdc 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
@@ -57,7 +57,7 @@ void PairLJCharmmCoulMSMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
index b9ffad134b..9e4dc08fd5 100644
--- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
@@ -51,7 +51,7 @@ void PairLJClass2CoulCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
index e5995363ad..4fd371e2eb 100644
--- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
@@ -59,7 +59,7 @@ void PairLJClass2CoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp
index 67715572ae..fa9b6ae703 100644
--- a/src/USER-OMP/pair_lj_class2_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_omp.cpp
@@ -51,7 +51,7 @@ void PairLJClass2OMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp
index 5fa4f92f45..3fe6fab5de 100644
--- a/src/USER-OMP/pair_lj_cubic_omp.cpp
+++ b/src/USER-OMP/pair_lj_cubic_omp.cpp
@@ -52,7 +52,7 @@ void PairLJCubicOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
index 69cc2d3042..6c0a3706f7 100644
--- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
@@ -51,7 +51,7 @@ void PairLJCutCoulCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
index 5dfa414bd4..742565d19c 100644
--- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
@@ -51,7 +51,7 @@ void PairLJCutCoulCutSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
index 4644e565a7..413758cc4a 100644
--- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
@@ -51,7 +51,7 @@ void PairLJCutCoulDebyeOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
index 13d877ec07..3295ede132 100644
--- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
@@ -61,7 +61,7 @@ void PairLJCutCoulDSFOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
index d4fe5fd2a7..d32ec58607 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
@@ -60,7 +60,7 @@ void PairLJCutCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
index 4a0ef73f60..d1f97941f5 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
@@ -60,7 +60,7 @@ void PairLJCutCoulLongSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
index 4c34b73622..9c48e03a13 100644
--- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
@@ -57,7 +57,7 @@ void PairLJCutCoulMSMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp
index 052be0a2fa..09403b893c 100644
--- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp
@@ -53,7 +53,7 @@ void PairLJCutCoulWolfOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
index 55359db3be..c259b006c5 100644
--- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
@@ -51,7 +51,7 @@ void PairLJCutDipoleCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp
index 34068185d2..f8670b7c28 100644
--- a/src/USER-OMP/pair_lj_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_omp.cpp
@@ -52,7 +52,7 @@ void PairLJCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp
index 9bbe58146c..988af13938 100644
--- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp
@@ -52,7 +52,7 @@ void PairLJCutSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
index 87d637e80d..63c5d9601a 100644
--- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
@@ -74,7 +74,7 @@ void PairLJCutTholeLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
index 288724cd77..40cfcb6bc2 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
@@ -101,7 +101,7 @@ void PairLJCutTIP4PCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
index 18fc207015..d51382c0f1 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
@@ -101,7 +101,7 @@ void PairLJCutTIP4PLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
   if (ncoultablebits) {
     if (evflag) {
@@ -145,7 +145,7 @@ void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
   dbl3_t x1,x2,xH1,xH2;
 
   int *ilist,*jlist,*numneigh,**firstneigh;
-  int i,j,ii,jj,jnum,itype,jtype,itable, key;
+  int i,j,ii,jj,jnum,itype,jtype,itable, key=0;
   int n,vlist[6];
   int iH1,iH2,jH1,jH2;
 
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
index 6baba8aec4..350bea884d 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
@@ -101,7 +101,7 @@ void PairLJCutTIP4PLongSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp
index 6c6ddb045e..d3d1da263c 100644
--- a/src/USER-OMP/pair_lj_expand_omp.cpp
+++ b/src/USER-OMP/pair_lj_expand_omp.cpp
@@ -51,7 +51,7 @@ void PairLJExpandOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
index 77c5bc0da0..2fe7c39afe 100644
--- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
+++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
@@ -51,7 +51,7 @@ void PairLJGromacsCoulGromacsOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp
index 15bcb08eed..4a4e68ec6e 100644
--- a/src/USER-OMP/pair_lj_gromacs_omp.cpp
+++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp
@@ -51,7 +51,7 @@ void PairLJGromacsOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
index c9edc087b6..7286771c26 100644
--- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
@@ -64,7 +64,7 @@ void PairLJLongCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (order6) {
       if (order1) {
@@ -326,7 +326,7 @@ void PairLJLongCoulLongOMP::compute_inner()
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(0, 0, nall, 0, 0, thr);
+    ev_setup_thr(0, 0, nall, 0, 0, NULL, thr);
     eval_inner(ifrom, ito, thr);
     thr->timer(Timer::PAIR);
 
@@ -351,7 +351,7 @@ void PairLJLongCoulLongOMP::compute_middle()
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(0, 0, nall, 0, 0, thr);
+    ev_setup_thr(0, 0, nall, 0, 0, NULL, thr);
     eval_middle(ifrom, ito, thr);
     thr->timer(Timer::PAIR);
 
@@ -381,7 +381,7 @@ void PairLJLongCoulLongOMP::compute_outer(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (order6) {
       if (order1) {
diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
index 6d7c5b5638..7735d6fde4 100644
--- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
@@ -104,7 +104,7 @@ void PairLJLongTIP4PLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (order6) {
       if (order1) {
@@ -387,7 +387,7 @@ void PairLJLongTIP4PLongOMP::compute_inner()
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(0, 0, nall, 0, 0, thr);
+    ev_setup_thr(0, 0, nall, 0, 0, NULL, thr);
     eval_inner(ifrom, ito, thr);
     thr->timer(Timer::PAIR);
 
@@ -412,7 +412,7 @@ void PairLJLongTIP4PLongOMP::compute_middle()
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(0, 0, nall, 0, 0, thr);
+    ev_setup_thr(0, 0, nall, 0, 0, NULL, thr);
     eval_middle(ifrom, ito, thr);
     thr->timer(Timer::PAIR);
 
@@ -466,7 +466,7 @@ void PairLJLongTIP4PLongOMP::compute_outer(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (order6) {
       if (order1) {
diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
index 16c87d5ed4..15fea32f53 100644
--- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
@@ -53,7 +53,7 @@ void PairLJSDKCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
index 1002cc193e..3326034da8 100644
--- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
@@ -59,7 +59,7 @@ void PairLJSDKCoulMSMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp
index 1e64973cbb..9ba90a2937 100644
--- a/src/USER-OMP/pair_lj_sdk_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_omp.cpp
@@ -55,7 +55,7 @@ void PairLJSDKOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
index aea22fc4df..ca08f817dc 100644
--- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
+++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
@@ -51,7 +51,7 @@ void PairLJSFDipoleSFOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
index 420c55b0ed..0b29a8fc30 100644
--- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
+++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
@@ -51,7 +51,7 @@ void PairLJSmoothLinearOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp
index d61dc19ff1..fe3d64cbf6 100644
--- a/src/USER-OMP/pair_lj_smooth_omp.cpp
+++ b/src/USER-OMP/pair_lj_smooth_omp.cpp
@@ -51,7 +51,7 @@ void PairLJSmoothOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp
index 132dbc575e..dc6be0b96a 100644
--- a/src/USER-OMP/pair_lubricate_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_omp.cpp
@@ -117,7 +117,7 @@ void PairLubricateOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (flaglog) {
       if (evflag) {
diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp
index 04ac59b121..648b10b114 100644
--- a/src/USER-OMP/pair_lubricate_poly_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp
@@ -114,7 +114,7 @@ void PairLubricatePolyOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (flaglog) {
       if (shearing) {
diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp
index e9307c8666..f4aff69881 100644
--- a/src/USER-OMP/pair_meam_spline_omp.cpp
+++ b/src/USER-OMP/pair_meam_spline_omp.cpp
@@ -65,7 +65,7 @@ void PairMEAMSplineOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     thr->init_eam(nall,Uprime_values);
 
diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp
index bf57019f11..c77196d1c5 100644
--- a/src/USER-OMP/pair_morse_omp.cpp
+++ b/src/USER-OMP/pair_morse_omp.cpp
@@ -51,7 +51,7 @@ void PairMorseOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
index 5ba6acb439..e30a774bf2 100644
--- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
+++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
@@ -55,7 +55,7 @@ void PairMorseSmoothLinearOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
index d62b4e5c62..7ffd189a5b 100644
--- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
@@ -51,7 +51,7 @@ void PairNMCutCoulCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
index a8696c74a1..0a0a861b6f 100644
--- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
@@ -59,7 +59,7 @@ void PairNMCutCoulLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp
index 9304b10ef0..cb74eed3f1 100644
--- a/src/USER-OMP/pair_nm_cut_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_omp.cpp
@@ -51,7 +51,7 @@ void PairNMCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp
index 61db45363e..3ea41321a7 100644
--- a/src/USER-OMP/pair_peri_lps_omp.cpp
+++ b/src/USER-OMP/pair_peri_lps_omp.cpp
@@ -70,7 +70,7 @@ void PairPeriLPSOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp
index b1816e4052..95e50df50d 100644
--- a/src/USER-OMP/pair_peri_pmb_omp.cpp
+++ b/src/USER-OMP/pair_peri_pmb_omp.cpp
@@ -66,7 +66,7 @@ void PairPeriPMBOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp
index aedd438066..8743fb8e4a 100644
--- a/src/USER-OMP/pair_reaxc_omp.cpp
+++ b/src/USER-OMP/pair_reaxc_omp.cpp
@@ -285,14 +285,13 @@ void PairReaxCOMP::compute(int eflag, int vflag)
 
   if (vflag_fdotr) virial_fdotr_compute();
 
-// Set internal timestep counter to that of LAMMPS
+  // Set internal timestep counter to that of LAMMPS
 
   data->step = update->ntimestep;
 
   Output_Results( system, control, data, &lists, out_control, mpi_data );
 
   // populate tmpid and tmpbo arrays for fix reax/c/species
-  int i, j;
 
   if(fixspecies_flag) {
     if (system->N > nmax) {
@@ -306,8 +305,8 @@ void PairReaxCOMP::compute(int eflag, int vflag)
 #if defined(_OPENMP)
 #pragma omp parallel for collapse(2) schedule(static) default(shared)
 #endif
-    for (i = 0; i < system->N; i ++)
-      for (j = 0; j < MAXSPECBOND; j ++) {
+    for (int i = 0; i < system->N; i++)
+      for (int j = 0; j < MAXSPECBOND; j++) {
         tmpbo[i][j] = 0.0;
         tmpid[i][j] = 0;
       }
@@ -325,9 +324,10 @@ void PairReaxCOMP::init_style( )
 
   // firstwarn = 1;
 
-  int iqeq = modify->find_fix_by_style("qeq/reax/omp");
-  if (iqeq < 0 && qeqflag == 1)
-    error->all(FLERR,"Pair reax/c/omp requires use of fix qeq/reax/omp");
+  bool have_qeq = ((modify->find_fix_by_style("^qeq/reax") != -1)
+                   || (modify->find_fix_by_style("^qeq/shielded") != -1));
+  if (!have_qeq && qeqflag == 1)
+    error->all(FLERR,"Pair reax/c requires use of fix qeq/reax or qeq/shielded");
 
   system->n = atom->nlocal; // my atoms
   system->N = atom->nlocal + atom->nghost; // mine + ghosts
@@ -612,13 +612,11 @@ void PairReaxCOMP::read_reax_forces(int /* vflag */)
 void PairReaxCOMP::FindBond()
 {
   const double bo_cut = 0.10;
-  int i;
 
 #if defined(_OPENMP)
-#pragma omp parallel for schedule(static) default(shared)   \
-  private(i)
+#pragma omp parallel for schedule(static) default(shared)
 #endif
-  for (i = 0; i < system->n; i++) {
+  for (int i = 0; i < system->n; i++) {
     int j, pj, nj;
     double bo_tmp;
     bond_data *bo_ij;
diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h
index 0cae28f56b..38994c5264 100644
--- a/src/USER-OMP/pair_reaxc_omp.h
+++ b/src/USER-OMP/pair_reaxc_omp.h
@@ -37,8 +37,10 @@ class PairReaxCOMP : public PairReaxC, public ThrOMP {
   };
 
   inline void ev_setup_thr_proxy(int eflagparm, int vflagparm, int nallparm,
-                                 double *eatomparm, double **vatomparm, ThrData *thrparm) {
-    ev_setup_thr(eflagparm, vflagparm, nallparm, eatomparm, vatomparm, thrparm);
+                                 double *eatomparm, double **vatomparm,
+                                 double **cvatomparm, ThrData *thrparm) {
+    ev_setup_thr(eflagparm, vflagparm, nallparm, eatomparm, vatomparm,
+                 cvatomparm, thrparm);
   };
 
   // reduce per thread data as needed
diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp
index d9e0059a9f..65f1c7289f 100644
--- a/src/USER-OMP/pair_resquared_omp.cpp
+++ b/src/USER-OMP/pair_resquared_omp.cpp
@@ -53,7 +53,7 @@ void PairRESquaredOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp
index eb151bc0df..7de94a2cd1 100644
--- a/src/USER-OMP/pair_soft_omp.cpp
+++ b/src/USER-OMP/pair_soft_omp.cpp
@@ -55,7 +55,7 @@ void PairSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp
index 745b3a1f04..9812cf06ba 100644
--- a/src/USER-OMP/pair_sw_omp.cpp
+++ b/src/USER-OMP/pair_sw_omp.cpp
@@ -52,7 +52,7 @@ void PairSWOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp
index b55817e75c..bf18d53d2e 100644
--- a/src/USER-OMP/pair_table_omp.cpp
+++ b/src/USER-OMP/pair_table_omp.cpp
@@ -52,7 +52,7 @@ void PairTableOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
index a11bd87640..6b6b130c65 100644
--- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
@@ -51,7 +51,7 @@ void PairTersoffMODCOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp
index da22110c1c..634676ee49 100644
--- a/src/USER-OMP/pair_tersoff_mod_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp
@@ -51,7 +51,7 @@ void PairTersoffMODOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp
index 661f15d64d..9735ccaa1f 100644
--- a/src/USER-OMP/pair_tersoff_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_omp.cpp
@@ -52,7 +52,7 @@ void PairTersoffOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp
index 7e83814f95..fa9512bf71 100644
--- a/src/USER-OMP/pair_tersoff_table_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_table_omp.cpp
@@ -76,7 +76,7 @@ void PairTersoffTableOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag)
       if (vflag_atom) eval<1,1>(ifrom, ito, thr);
diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/USER-OMP/pair_tip4p_cut_omp.cpp
index 1900ed4394..c8584b4fe3 100644
--- a/src/USER-OMP/pair_tip4p_cut_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_cut_omp.cpp
@@ -100,7 +100,7 @@ void PairTIP4PCutOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_tip4p_long_omp.cpp b/src/USER-OMP/pair_tip4p_long_omp.cpp
index ee65937c46..89c3c17684 100644
--- a/src/USER-OMP/pair_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_long_omp.cpp
@@ -101,7 +101,7 @@ void PairTIP4PLongOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
   if (!ncoultablebits) {
     if (evflag) {
diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
index adb984a2cd..88da3d02a8 100644
--- a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
@@ -101,7 +101,7 @@ void PairTIP4PLongSoftOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/USER-OMP/pair_ufm_omp.cpp
index 08d8cc15f9..23e76186c0 100644
--- a/src/USER-OMP/pair_ufm_omp.cpp
+++ b/src/USER-OMP/pair_ufm_omp.cpp
@@ -53,7 +53,7 @@ void PairUFMOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp
index 28104013f0..a218ddf3ed 100644
--- a/src/USER-OMP/pair_vashishta_omp.cpp
+++ b/src/USER-OMP/pair_vashishta_omp.cpp
@@ -52,7 +52,7 @@ void PairVashishtaOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp
index b044902ebe..0986128bf6 100644
--- a/src/USER-OMP/pair_vashishta_table_omp.cpp
+++ b/src/USER-OMP/pair_vashishta_table_omp.cpp
@@ -52,7 +52,7 @@ void PairVashishtaTableOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp
index 86314ce7b8..9b8428c648 100644
--- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp
+++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp
@@ -51,7 +51,7 @@ void PairYukawaColloidOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp
index add81e9b04..20d557e605 100644
--- a/src/USER-OMP/pair_yukawa_omp.cpp
+++ b/src/USER-OMP/pair_yukawa_omp.cpp
@@ -51,7 +51,7 @@ void PairYukawaOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp
index f6856c4fa0..3a300ce477 100644
--- a/src/USER-OMP/pair_zbl_omp.cpp
+++ b/src/USER-OMP/pair_zbl_omp.cpp
@@ -52,7 +52,7 @@ void PairZBLOMP::compute(int eflag, int vflag)
     loop_setup_thr(ifrom, ito, tid, inum, nthreads);
     ThrData *thr = fix->get_thr(tid);
     thr->timer(Timer::START);
-    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, NULL, thr);
 
     if (evflag) {
       if (eflag) {
diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp
index de902b1a57..6b2c180a3f 100644
--- a/src/USER-OMP/pppm_disp_omp.cpp
+++ b/src/USER-OMP/pppm_disp_omp.cpp
@@ -364,11 +364,11 @@ void PPPMDispOMP::particle_map(double dxinv, double dyinv,
   if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
     error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
 
-  int i, flag = 0;
+  int flag = 0;
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static)
+#pragma omp parallel for default(none) reduction(+:flag) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
 
     // (nx,ny,nz) = global coords of grid pt to "lower left" of charge
     // current particle coord can be outside global and local box
diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp
index fc9466e395..bdd8f23ee4 100644
--- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp
@@ -356,11 +356,11 @@ void PPPMDispTIP4POMP::particle_map_c(double dxinv, double dyinv,
   if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
     error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
 
-  int i, flag = 0;
+  int flag = 0;
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static)
+#pragma omp parallel for default(none) reduction(+:flag) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     dbl3_t xM;
     int iH1,iH2;
 
@@ -432,11 +432,11 @@ void PPPMDispTIP4POMP::particle_map(double dxinv, double dyinv,
   const int nyhi_out = nyhi_o;
   const int nzhi_out = nzhi_o;
 
-  int i, flag = 0;
+  int flag = 0;
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static)
+#pragma omp parallel for default(none) reduction(+:flag) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
 
     // (nx,ny,nz) = global coords of grid pt to "lower left" of charge
     // current particle coord can be outside global and local box
diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp
index 3ef3de1ab7..c6aaafaa31 100644
--- a/src/USER-OMP/pppm_omp.cpp
+++ b/src/USER-OMP/pppm_omp.cpp
@@ -48,7 +48,7 @@ using namespace MathSpecial;
 
 PPPMOMP::PPPMOMP(LAMMPS *lmp) : PPPM(lmp), ThrOMP(lmp, THR_KSPACE)
 {
-  triclinic_support = 0;
+  triclinic_support = 1;
   suffix_flag |= Suffix::OMP;
 }
 
diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp
index d7c12613d9..322730b573 100644
--- a/src/USER-OMP/pppm_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_tip4p_omp.cpp
@@ -353,11 +353,11 @@ void PPPMTIP4POMP::particle_map()
   if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
     error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
 
-  int i, flag = 0;
+  int flag = 0;
 #if defined(_OPENMP)
-#pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static)
+#pragma omp parallel for default(none) reduction(+:flag) schedule(static)
 #endif
-  for (i = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     dbl3_t xM;
     int iH1,iH2;
 
@@ -750,11 +750,18 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM)
     // since local atoms are in lambda coordinates, but ghosts are not.
 
     int *sametag = atom->sametag;
-    double xo[3],xh1[3],xh2[3];
+    double xo[3],xh1[3],xh2[3],xm[3];
+    const int nlocal = atom->nlocal;
 
-    domain->lamda2x(x[i],xo);
-    domain->lamda2x(x[iH1],xh1);
-    domain->lamda2x(x[iH2],xh2);
+    for (int ii = 0; ii < 3; ++ii) {
+      xo[ii] = x[i][ii];
+      xh1[ii] = x[iH1][ii];
+      xh2[ii] = x[iH2][ii];
+    }
+
+    if (i < nlocal) domain->lamda2x(x[i],xo);
+    if (iH1 < nlocal) domain->lamda2x(x[iH1],xh1);
+    if (iH2 < nlocal) domain->lamda2x(x[iH2],xh2);
 
     double delx = xo[0] - xh1[0];
     double dely = xo[1] - xh1[1];
@@ -763,6 +770,7 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM)
     double rsq;
     int closest = iH1;
 
+    // no need to run lamda2x here -> ghost atoms
     while (sametag[iH1] >= 0) {
       iH1 = sametag[iH1];
       delx = xo[0] - x[iH1][0];
@@ -811,13 +819,13 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM)
     double dely2 = xh2[1] - xo[1];
     double delz2 = xh2[2] - xo[2];
 
-    xM.x = xo[0] + alpha * 0.5 * (delx1 + delx2);
-    xM.y = xo[1] + alpha * 0.5 * (dely1 + dely2);
-    xM.z = xo[2] + alpha * 0.5 * (delz1 + delz2);
+    xm[0] = xo[0] + alpha * 0.5 * (delx1 + delx2);
+    xm[1] = xo[1] + alpha * 0.5 * (dely1 + dely2);
+    xm[2] = xo[2] + alpha * 0.5 * (delz1 + delz2);
 
     // ... and convert M to lamda space for PPPM
 
-    domain->x2lamda((double *)&xM,(double *)&xM);
+    domain->x2lamda(xm,(double *)&xM);
 
   } else {
 
diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp
index b6a76b3f3a..80e9b90ecc 100644
--- a/src/USER-OMP/reaxc_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_bonds_omp.cpp
@@ -87,7 +87,8 @@ void BondsOMP( reax_system *system, control_params * /* control */,
 
   pair_reax_ptr->ev_setup_thr_proxy(system->pair_ptr->eflag_either,
                                     system->pair_ptr->vflag_either, system->N,
-                                    system->pair_ptr->eatom, system->pair_ptr->vatom, thr);
+                                    system->pair_ptr->eatom,
+                                    system->pair_ptr->vatom, NULL, thr);
 
 #if defined(_OPENMP)
 #pragma omp for schedule(guided)
diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp
index 971667cc2d..e48a5c11d4 100644
--- a/src/USER-OMP/reaxc_forces_omp.cpp
+++ b/src/USER-OMP/reaxc_forces_omp.cpp
@@ -162,7 +162,7 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control,
     class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);
 
     pair_reax_ptr->ev_setup_thr_proxy(0, 1, natoms, system->pair_ptr->eatom,
-                                      system->pair_ptr->vatom, thr);
+                                      system->pair_ptr->vatom, NULL, thr);
 
 #if defined(_OPENMP)
 #pragma omp for schedule(guided)
@@ -265,12 +265,12 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control,
 void Validate_ListsOMP(reax_system *system, storage * /*workspace*/, reax_list **lists,
                        int step, int n, int N, int numH, MPI_Comm /*comm*/)
 {
-  int i, comp, Hindex;
+  int comp, Hindex;
   reax_list *bonds, *hbonds;
   double saferzone = system->saferzone;
 
 #if defined(_OPENMP)
-#pragma omp parallel default(shared) private(i, comp, Hindex)
+#pragma omp parallel default(shared) private(comp,Hindex)
 #endif
   {
 
@@ -281,7 +281,7 @@ void Validate_ListsOMP(reax_system *system, storage * /*workspace*/, reax_list *
 #if defined(_OPENMP)
 #pragma omp for schedule(guided)
 #endif
-    for( i = 0; i < N; ++i ) {
+    for(int i = 0; i < N; ++i ) {
       system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS);
 
       if (i < N-1)
@@ -305,7 +305,7 @@ void Validate_ListsOMP(reax_system *system, storage * /*workspace*/, reax_list *
 #if defined(_OPENMP)
 #pragma omp for schedule(guided)
 #endif
-    for( i = 0; i < n; ++i ) {
+    for(int i = 0; i < n; ++i ) {
       Hindex = system->my_atoms[i].Hindex;
       if (Hindex > -1) {
         system->my_atoms[i].num_hbonds =
@@ -338,7 +338,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
   startTimeBase = MPI_Wtime();
 #endif
 
-  int i, j, pj;
+  int j, pj;
   int start_i, end_i;
   int type_i, type_j;
   int ihb, jhb, ihb_top, jhb_top;
@@ -367,8 +367,8 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
 
 #if defined(_OPENMP)
 #pragma omp parallel default(shared) \
-  private(i, atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \
-          j, atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp)
+  private(atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \
+          atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp)
 #endif
   {
 
@@ -382,9 +382,9 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
     long totalReductionSize = system->N * nthreads;
 
 #if defined(_OPENMP)
-#pragma omp for schedule(dynamic,50) reduction(+ : num_bonds)
+#pragma omp for schedule(dynamic,50) reduction(+:num_bonds)
 #endif
-  for (i = 0; i < system->N; ++i) {
+  for (int i = 0; i < system->N; ++i) {
     atom_i = &(system->my_atoms[i]);
     type_i  = atom_i->type;
     sbp_i = &(system->reax_param.sbp[type_i]);
@@ -395,7 +395,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
     for( pj = start_i; pj < end_i; ++pj ) {
       nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
       if (nbr_pj->d <= cutoff) {
-        j = nbr_pj->nbr;
+        int j = nbr_pj->nbr;
         atom_j = &(system->my_atoms[j]);
         type_j = atom_j->type;
         sbp_j = &(system->reax_param.sbp[type_j]);
@@ -490,7 +490,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
 #if defined(_OPENMP)
 #pragma omp for schedule(dynamic,50)
 #endif
-  for(i=0; i<system->N; i++)
+  for(int i=0; i<system->N; i++)
     for(int t=0; t<nthreads; t++) {
       const int indx = t*system->N + i;
       workspace->dDeltap_self[i][0]  += tmp_ddelta[indx][0];
@@ -506,7 +506,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
 #if defined(_OPENMP)
 #pragma omp for schedule(dynamic,50) reduction(+ : num_hbonds)
 #endif
-     for (i = 0; i < system->n; ++i) {
+     for (int i = 0; i < system->n; ++i) {
        atom_i = &(system->my_atoms[i]);
        type_i  = atom_i->type;
        sbp_i = &(system->reax_param.sbp[type_i]);
@@ -572,7 +572,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
 #if defined(_OPENMP)
 #pragma omp for schedule(guided)
 #endif
-  for(i=0; i<totalReductionSize; i++) {
+  for(int i=0; i<totalReductionSize; i++) {
     tmp_ddelta[i][0]  = 0.0;
     tmp_ddelta[i][1]  = 0.0;
     tmp_ddelta[i][2]  = 0.0;
diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp
index 9d40479ddf..66f1acf91c 100644
--- a/src/USER-OMP/reaxc_init_md_omp.cpp
+++ b/src/USER-OMP/reaxc_init_md_omp.cpp
@@ -45,19 +45,17 @@ extern int Init_Workspace(reax_system*, control_params*, storage*, char*);
 
 /* ---------------------------------------------------------------------- */
 
-int Init_ListsOMP( reax_system *system, control_params *control,
-                 simulation_data * /* data */, storage * /* workspace */,
-                 reax_list **lists, mpi_datatypes *mpi_data, char * /* msg */)
+int Init_ListsOMP(reax_system *system, control_params *control,
+                  simulation_data * /* data */, storage * /* workspace */,
+                  reax_list **lists, mpi_datatypes * /* mpi_data */, char * /* msg */)
 {
   int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
   int *hb_top, *bond_top;
-  MPI_Comm comm;
 
   int mincap = system->mincap;
   double safezone = system->safezone;
   double saferzone = system->saferzone;
 
-  comm = mpi_data->world;
   bond_top = (int*) calloc( system->total_cap, sizeof(int) );
   hb_top = (int*) calloc( system->local_cap, sizeof(int) );
   Estimate_Storages( system, control, lists,
diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h
index 68673e7503..2c1e42a3a3 100644
--- a/src/USER-OMP/thr_data.h
+++ b/src/USER-OMP/thr_data.h
@@ -97,6 +97,10 @@ class ThrData {
   double **vatom_dihed;
   double **vatom_imprp;
   double **vatom_kspce;
+  double **cvatom_pair;
+  double **cvatom_angle;
+  double **cvatom_dihed;
+  double **cvatom_imprp;
 
   // per thread segments of various force or similar arrays
 
diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp
index 51030358d3..c086f6d6b5 100644
--- a/src/USER-OMP/thr_omp.cpp
+++ b/src/USER-OMP/thr_omp.cpp
@@ -64,7 +64,7 @@ ThrOMP::~ThrOMP()
    ---------------------------------------------------------------------- */
 
 void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
-                          double **vatom, ThrData *thr)
+                          double **vatom, double **cvatom, ThrData *thr)
 {
   const int tid = thr->get_tid();
   if (tid == 0) thr_error = 0;
@@ -75,11 +75,22 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
       if (nall > 0)
         memset(&(thr->eatom_pair[0]),0,nall*sizeof(double));
     }
-    if (vflag & 4) {
+    // per-atom virial and per-atom centroid virial are the same for two-body
+    // many-body pair styles not yet implemented
+    if (vflag & 12) {
       thr->vatom_pair = vatom + tid*nall;
       if (nall > 0)
         memset(&(thr->vatom_pair[0][0]),0,nall*6*sizeof(double));
     }
+    // check cvatom_pair, because can't access centroidstressflag
+    if ((vflag & 8) && cvatom) {
+      thr->cvatom_pair = cvatom + tid*nall;
+      if (nall > 0)
+        memset(&(thr->cvatom_pair[0][0]),0,nall*9*sizeof(double));
+    } else {
+      thr->cvatom_pair = NULL;
+    }
+
   }
 
   if (thr_style & THR_BOND) {
@@ -88,7 +99,8 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
       if (nall > 0)
         memset(&(thr->eatom_bond[0]),0,nall*sizeof(double));
     }
-    if (vflag & 4) {
+    // per-atom virial and per-atom centroid virial are the same for bonds
+    if (vflag & 12) {
       thr->vatom_bond = vatom + tid*nall;
       if (nall > 0)
         memset(&(thr->vatom_bond[0][0]),0,nall*6*sizeof(double));
@@ -106,6 +118,11 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
       if (nall > 0)
         memset(&(thr->vatom_angle[0][0]),0,nall*6*sizeof(double));
     }
+    if (vflag & 8) {
+      thr->cvatom_angle = cvatom + tid*nall;
+      if (nall > 0)
+        memset(&(thr->cvatom_angle[0][0]),0,nall*9*sizeof(double));
+    }
   }
 
   if (thr_style & THR_DIHEDRAL) {
@@ -119,6 +136,11 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
       if (nall > 0)
         memset(&(thr->vatom_dihed[0][0]),0,nall*6*sizeof(double));
     }
+    if (vflag & 8) {
+      thr->cvatom_dihed = cvatom + tid*nall;
+      if (nall > 0)
+        memset(&(thr->cvatom_dihed[0][0]),0,nall*9*sizeof(double));
+    }
   }
 
   if (thr_style & THR_IMPROPER) {
@@ -132,6 +154,11 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
       if (nall > 0)
         memset(&(thr->vatom_imprp[0][0]),0,nall*6*sizeof(double));
     }
+    if (vflag & 8) {
+      thr->cvatom_imprp = cvatom + tid*nall;
+      if (nall > 0)
+        memset(&(thr->cvatom_imprp[0][0]),0,nall*9*sizeof(double));
+    }
   }
 
   // nothing to do for THR_KSPACE
@@ -211,9 +238,15 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
       if (eflag & 2) {
         data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
       }
-      if (vflag & 4) {
+      // per-atom virial and per-atom centroid virial are the same for two-body
+      // many-body pair styles not yet implemented
+      if (vflag & 12) {
         data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
       }
+      // check cvatom_pair, because can't access centroidstressflag
+      if ((vflag & 8) && thr->cvatom_pair) {
+        data_reduce_thr(&(pair->cvatom[0][0]), nall, nthreads, 9, tid);
+      }
     }
   }
     break;
@@ -242,7 +275,8 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
       if (eflag & 2) {
         data_reduce_thr(&(bond->eatom[0]), nall, nthreads, 1, tid);
       }
-      if (vflag & 4) {
+      // per-atom virial and per-atom centroid virial are the same for bonds
+      if (vflag & 12) {
         data_reduce_thr(&(bond->vatom[0][0]), nall, nthreads, 6, tid);
       }
 
@@ -276,6 +310,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
       if (vflag & 4) {
         data_reduce_thr(&(angle->vatom[0][0]), nall, nthreads, 6, tid);
       }
+      if (vflag & 8) {
+        data_reduce_thr(&(angle->cvatom[0][0]), nall, nthreads, 9, tid);
+      }
 
     }
     break;
@@ -307,6 +344,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
       if (vflag & 4) {
         data_reduce_thr(&(dihedral->vatom[0][0]), nall, nthreads, 6, tid);
       }
+      if (vflag & 8) {
+        data_reduce_thr(&(dihedral->cvatom[0][0]), nall, nthreads, 9, tid);
+      }
 
     }
     break;
@@ -345,8 +385,19 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
       }
       if (vflag & 4) {
         data_reduce_thr(&(dihedral->vatom[0][0]), nall, nthreads, 6, tid);
+      }
+      if (vflag & 8) {
+        data_reduce_thr(&(dihedral->cvatom[0][0]), nall, nthreads, 9, tid);
+      }
+      // per-atom virial and per-atom centroid virial are the same for two-body
+      // many-body pair styles not yet implemented
+      if (vflag & 12) {
         data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
       }
+      // check cvatom_pair, because can't access centroidstressflag
+      if ((vflag & 8) && thr->cvatom_pair) {
+        data_reduce_thr(&(pair->cvatom[0][0]), nall, nthreads, 9, tid);
+      }
     }
     break;
 
@@ -377,6 +428,9 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
       if (vflag & 4) {
         data_reduce_thr(&(improper->vatom[0][0]), nall, nthreads, 6, tid);
       }
+      if (vflag & 8) {
+        data_reduce_thr(&(improper->cvatom[0][0]), nall, nthreads, 9, tid);
+      }
 
     }
     break;
@@ -449,6 +503,19 @@ static void v_tally(double * const vout, const double * const vin)
   vout[5] += vin[5];
 }
 
+static void v_tally9(double * const vout, const double * const vin)
+{
+  vout[0] += vin[0];
+  vout[1] += vin[1];
+  vout[2] += vin[2];
+  vout[3] += vin[3];
+  vout[4] += vin[4];
+  vout[5] += vin[5];
+  vout[6] += vin[6];
+  vout[7] += vin[7];
+  vout[8] += vin[8];
+}
+
 static void v_tally(double * const vout, const double scale, const double * const vin)
 {
   vout[0] += scale*vin[0];
@@ -898,6 +965,77 @@ void ThrOMP::ev_tally_thr(Angle * const angle, const int i, const int j, const i
       }
     }
   }
+
+  // per-atom centroid virial
+  if (angle->cvflag_atom) {
+    double f2[3], v1[9], v2[9], v3[9];
+    double a1[3], a2[3], a3[3];
+
+    // r0 = (r1+r2+r3)/3
+    // rij = ri-rj
+    // total virial = r10*f1 + r20*f2 + r30*f3
+    // del1: r12
+    // del2: r32
+
+    // a1 = r10 = (2*r12 -   r32)/3
+    a1[0] = THIRD*(2*delx1-delx2);
+    a1[1] = THIRD*(2*dely1-dely2);
+    a1[2] = THIRD*(2*delz1-delz2);
+
+    // a2 = r20 = ( -r12 -   r32)/3
+    a2[0] = THIRD*(-delx1-delx2);
+    a2[1] = THIRD*(-dely1-dely2);
+    a2[2] = THIRD*(-delz1-delz2);
+
+    // a3 = r30 = ( -r12 + 2*r32)/3
+    a3[0] = THIRD*(-delx1+2*delx2);
+    a3[1] = THIRD*(-dely1+2*dely2);
+    a3[2] = THIRD*(-delz1+2*delz2);
+
+    f2[0] = - f1[0] - f3[0];
+    f2[1] = - f1[1] - f3[1];
+    f2[2] = - f1[2] - f3[2];
+
+    v1[0] = a1[0]*f1[0];
+    v1[1] = a1[1]*f1[1];
+    v1[2] = a1[2]*f1[2];
+    v1[3] = a1[0]*f1[1];
+    v1[4] = a1[0]*f1[2];
+    v1[5] = a1[1]*f1[2];
+    v1[6] = a1[1]*f1[0];
+    v1[7] = a1[2]*f1[0];
+    v1[8] = a1[2]*f1[1];
+
+    v2[0] = a2[0]*f2[0];
+    v2[1] = a2[1]*f2[1];
+    v2[2] = a2[2]*f2[2];
+    v2[3] = a2[0]*f2[1];
+    v2[4] = a2[0]*f2[2];
+    v2[5] = a2[1]*f2[2];
+    v2[6] = a2[1]*f2[0];
+    v2[7] = a2[2]*f2[0];
+    v2[8] = a2[2]*f2[1];
+
+    v3[0] = a3[0]*f3[0];
+    v3[1] = a3[1]*f3[1];
+    v3[2] = a3[2]*f3[2];
+    v3[3] = a3[0]*f3[1];
+    v3[4] = a3[0]*f3[2];
+    v3[5] = a3[1]*f3[2];
+    v3[6] = a3[1]*f3[0];
+    v3[7] = a3[2]*f3[0];
+    v3[8] = a3[2]*f3[1];
+
+    if (newton_bond) {
+      v_tally9(thr->cvatom_angle[i],v1);
+      v_tally9(thr->cvatom_angle[j],v2);
+      v_tally9(thr->cvatom_angle[k],v3);
+    } else {
+      if (i < nlocal) v_tally9(thr->cvatom_angle[i],v1);
+      if (j < nlocal) v_tally9(thr->cvatom_angle[j],v2);
+      if (k < nlocal) v_tally9(thr->cvatom_angle[k],v3);
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -1046,6 +1184,96 @@ void ThrOMP::ev_tally_thr(Dihedral * const dihed, const int i1, const int i2,
       }
     }
   }
+
+  // per-atom centroid virial
+  if (dihed->cvflag_atom) {
+    double f2[3], v1[9], v2[9], v3[9], v4[9];
+    double a1[3], a2[3], a3[3], a4[3];
+
+    // r0 = (r1+r2+r3+r4)/4
+    // rij = ri-rj
+    // total virial = r10*f1 + r20*f2 + r30*f3 + r40*f4
+    // vb1: r12
+    // vb2: r32
+    // vb3: r43
+
+    // a1 = r10 = (3*r12 - 2*r32 -   r43)/4
+    a1[0] = 0.25*(3*vb1x - 2*vb2x - vb3x);
+    a1[1] = 0.25*(3*vb1y - 2*vb2y - vb3y);
+    a1[2] = 0.25*(3*vb1z - 2*vb2z - vb3z);
+
+    // a2 = r20 = ( -r12 - 2*r32 -   r43)/4
+    a2[0] = 0.25*(-vb1x - 2*vb2x - vb3x);
+    a2[1] = 0.25*(-vb1y - 2*vb2y - vb3y);
+    a2[2] = 0.25*(-vb1z - 2*vb2z - vb3z);
+
+    // a3 = r30 = ( -r12 + 2*r32 -   r43)/4
+    a3[0] = 0.25*(-vb1x + 2*vb2x - vb3x);
+    a3[1] = 0.25*(-vb1y + 2*vb2y - vb3y);
+    a3[2] = 0.25*(-vb1z + 2*vb2z - vb3z);
+
+    // a4 = r40 = ( -r12 + 2*r32 + 3*r43)/4
+    a4[0] = 0.25*(-vb1x + 2*vb2x + 3*vb3x);
+    a4[1] = 0.25*(-vb1y + 2*vb2y + 3*vb3y);
+    a4[2] = 0.25*(-vb1z + 2*vb2z + 3*vb3z);
+
+    f2[0] = - f1[0] - f3[0] - f4[0];
+    f2[1] = - f1[1] - f3[1] - f4[1];
+    f2[2] = - f1[2] - f3[2] - f4[2];
+
+    v1[0] = a1[0]*f1[0];
+    v1[1] = a1[1]*f1[1];
+    v1[2] = a1[2]*f1[2];
+    v1[3] = a1[0]*f1[1];
+    v1[4] = a1[0]*f1[2];
+    v1[5] = a1[1]*f1[2];
+    v1[6] = a1[1]*f1[0];
+    v1[7] = a1[2]*f1[0];
+    v1[8] = a1[2]*f1[1];
+
+    v2[0] = a2[0]*f2[0];
+    v2[1] = a2[1]*f2[1];
+    v2[2] = a2[2]*f2[2];
+    v2[3] = a2[0]*f2[1];
+    v2[4] = a2[0]*f2[2];
+    v2[5] = a2[1]*f2[2];
+    v2[6] = a2[1]*f2[0];
+    v2[7] = a2[2]*f2[0];
+    v2[8] = a2[2]*f2[1];
+
+    v3[0] = a3[0]*f3[0];
+    v3[1] = a3[1]*f3[1];
+    v3[2] = a3[2]*f3[2];
+    v3[3] = a3[0]*f3[1];
+    v3[4] = a3[0]*f3[2];
+    v3[5] = a3[1]*f3[2];
+    v3[6] = a3[1]*f3[0];
+    v3[7] = a3[2]*f3[0];
+    v3[8] = a3[2]*f3[1];
+
+    v4[0] = a4[0]*f4[0];
+    v4[1] = a4[1]*f4[1];
+    v4[2] = a4[2]*f4[2];
+    v4[3] = a4[0]*f4[1];
+    v4[4] = a4[0]*f4[2];
+    v4[5] = a4[1]*f4[2];
+    v4[6] = a4[1]*f4[0];
+    v4[7] = a4[2]*f4[0];
+    v4[8] = a4[2]*f4[1];
+
+    if (newton_bond) {
+      v_tally9(thr->cvatom_dihed[i1],v1);
+      v_tally9(thr->cvatom_dihed[i2],v2);
+      v_tally9(thr->cvatom_dihed[i3],v3);
+      v_tally9(thr->cvatom_dihed[i4],v4);
+    } else {
+      if (i1 < nlocal) v_tally9(thr->cvatom_dihed[i1],v1);
+      if (i2 < nlocal) v_tally9(thr->cvatom_dihed[i2],v2);
+      if (i3 < nlocal) v_tally9(thr->cvatom_dihed[i3],v3);
+      if (i4 < nlocal) v_tally9(thr->cvatom_dihed[i4],v4);
+    }
+  }
+
 }
 
 /* ----------------------------------------------------------------------
@@ -1138,6 +1366,96 @@ void ThrOMP::ev_tally_thr(Improper * const imprp, const int i1, const int i2,
       }
     }
   }
+
+  // per-atom centroid virial
+  if (imprp->cvflag_atom) {
+    double f2[3], v1[9], v2[9], v3[9], v4[9];
+    double a1[3], a2[3], a3[3], a4[3];
+
+    // r0 = (r1+r2+r3+r4)/4
+    // rij = ri-rj
+    // total virial = r10*f1 + r20*f2 + r30*f3 + r40*f4
+    // vb1: r12
+    // vb2: r32
+    // vb3: r43
+
+    // a1 = r10 = (3*r12 - 2*r32 -   r43)/4
+    a1[0] = 0.25*(3*vb1x - 2*vb2x - vb3x);
+    a1[1] = 0.25*(3*vb1y - 2*vb2y - vb3y);
+    a1[2] = 0.25*(3*vb1z - 2*vb2z - vb3z);
+
+    // a2 = r20 = ( -r12 - 2*r32 -   r43)/4
+    a2[0] = 0.25*(-vb1x - 2*vb2x - vb3x);
+    a2[1] = 0.25*(-vb1y - 2*vb2y - vb3y);
+    a2[2] = 0.25*(-vb1z - 2*vb2z - vb3z);
+
+    // a3 = r30 = ( -r12 + 2*r32 -   r43)/4
+    a3[0] = 0.25*(-vb1x + 2*vb2x - vb3x);
+    a3[1] = 0.25*(-vb1y + 2*vb2y - vb3y);
+    a3[2] = 0.25*(-vb1z + 2*vb2z - vb3z);
+
+    // a4 = r40 = ( -r12 + 2*r32 + 3*r43)/4
+    a4[0] = 0.25*(-vb1x + 2*vb2x + 3*vb3x);
+    a4[1] = 0.25*(-vb1y + 2*vb2y + 3*vb3y);
+    a4[2] = 0.25*(-vb1z + 2*vb2z + 3*vb3z);
+
+    f2[0] = - f1[0] - f3[0] - f4[0];
+    f2[1] = - f1[1] - f3[1] - f4[1];
+    f2[2] = - f1[2] - f3[2] - f4[2];
+
+    v1[0] = a1[0]*f1[0];
+    v1[1] = a1[1]*f1[1];
+    v1[2] = a1[2]*f1[2];
+    v1[3] = a1[0]*f1[1];
+    v1[4] = a1[0]*f1[2];
+    v1[5] = a1[1]*f1[2];
+    v1[6] = a1[1]*f1[0];
+    v1[7] = a1[2]*f1[0];
+    v1[8] = a1[2]*f1[1];
+
+    v2[0] = a2[0]*f2[0];
+    v2[1] = a2[1]*f2[1];
+    v2[2] = a2[2]*f2[2];
+    v2[3] = a2[0]*f2[1];
+    v2[4] = a2[0]*f2[2];
+    v2[5] = a2[1]*f2[2];
+    v2[6] = a2[1]*f2[0];
+    v2[7] = a2[2]*f2[0];
+    v2[8] = a2[2]*f2[1];
+
+    v3[0] = a3[0]*f3[0];
+    v3[1] = a3[1]*f3[1];
+    v3[2] = a3[2]*f3[2];
+    v3[3] = a3[0]*f3[1];
+    v3[4] = a3[0]*f3[2];
+    v3[5] = a3[1]*f3[2];
+    v3[6] = a3[1]*f3[0];
+    v3[7] = a3[2]*f3[0];
+    v3[8] = a3[2]*f3[1];
+
+    v4[0] = a4[0]*f4[0];
+    v4[1] = a4[1]*f4[1];
+    v4[2] = a4[2]*f4[2];
+    v4[3] = a4[0]*f4[1];
+    v4[4] = a4[0]*f4[2];
+    v4[5] = a4[1]*f4[2];
+    v4[6] = a4[1]*f4[0];
+    v4[7] = a4[2]*f4[0];
+    v4[8] = a4[2]*f4[1];
+
+    if (newton_bond) {
+      v_tally9(thr->cvatom_imprp[i1],v1);
+      v_tally9(thr->cvatom_imprp[i2],v2);
+      v_tally9(thr->cvatom_imprp[i3],v3);
+      v_tally9(thr->cvatom_imprp[i4],v4);
+    } else {
+      if (i1 < nlocal) v_tally9(thr->cvatom_imprp[i1],v1);
+      if (i2 < nlocal) v_tally9(thr->cvatom_imprp[i2],v2);
+      if (i3 < nlocal) v_tally9(thr->cvatom_imprp[i3],v3);
+      if (i4 < nlocal) v_tally9(thr->cvatom_imprp[i4],v4);
+    }
+  }
+
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h
index 062d77bc0e..2db6e6f54f 100644
--- a/src/USER-OMP/thr_omp.h
+++ b/src/USER-OMP/thr_omp.h
@@ -64,7 +64,7 @@ class ThrOMP {
 
  protected:
   // extra ev_tally setup work for threaded styles
-  void ev_setup_thr(int, int, int, double *, double **, ThrData *);
+  void ev_setup_thr(int, int, int, double *, double **, double **, ThrData *);
 
   // compute global per thread virial contribution from per-thread force
   void virial_fdotr_compute_thr(double * const, const double * const * const,
diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh
index 26104b45cf..a73f529cfa 100755
--- a/src/USER-PHONON/Install.sh
+++ b/src/USER-PHONON/Install.sh
@@ -42,3 +42,5 @@ action fix_phonon.cpp fft3d_wrap.h
 action fix_phonon.h fft3d_wrap.h
 action dynamical_matrix.cpp
 action dynamical_matrix.h
+action third_order.cpp
+action third_order.h
diff --git a/src/USER-PHONON/README b/src/USER-PHONON/README
index b554eacd5e..d5ed666c0c 100644
--- a/src/USER-PHONON/README
+++ b/src/USER-PHONON/README
@@ -3,11 +3,11 @@ matrices from finite temperature MD simulations, which can then be
 used to compute phonon dispersion relations, directly from molecular
 dynamics simulations.
 
-It also contains a command to compute the dynamical matrix at
-pre-optimized positions through finite differences.
+It also contains commands to compute the dynamical matrix and third
+order tensor at pre-optimized positions through finite differences.
 
 See the doc page for the fix phonon command or the dynamical_matrix
-command for detailed usage instructions.
+or third_order commands for detailed usage instructions.
 
 Use of this package requires building LAMMPS with FFT suppport, as
 described in doc/Section_start.html.
diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp
index 559ef4c36f..d03a8d3ab0 100644
--- a/src/USER-PHONON/dynamical_matrix.cpp
+++ b/src/USER-PHONON/dynamical_matrix.cpp
@@ -19,6 +19,7 @@
 #include "improper.h"
 #include "kspace.h"
 #include "update.h"
+#include "modify.h"
 #include "neighbor.h"
 #include "pair.h"
 #include "timer.h"
@@ -66,11 +67,6 @@ void DynamicalMatrix::setup()
     domain->image_check();
     domain->box_too_small_check();
     neighbor->build(1);
-    neighbor->ncalls = 0;
-    neighbor->every = 2;                       // build every this many steps
-    neighbor->delay = 1;
-    neighbor->ago = 0;
-    neighbor->ndanger = 0;
 
     // compute all forces
     external_force_clear = 0;
@@ -264,7 +260,7 @@ void DynamicalMatrix::calculateMatrix()
         fprintf(screen,"  Atoms in group = " BIGINT_FORMAT "\n", gcount);
         fprintf(screen,"  Total dynamical matrix elements = " BIGINT_FORMAT "\n", (dynlen*dynlen) );
     }
-    
+
     // emit dynlen rows of dimalpha*dynlen*dimbeta elements
 
     update->nsteps = 0;
@@ -273,7 +269,7 @@ void DynamicalMatrix::calculateMatrix()
         local_idx = atom->map(i);
         if (gm[i-1] < 0)
             continue;
-        for (bigint alpha=0; alpha<3; alpha++){
+        for (int alpha=0; alpha<3; alpha++){
             displace_atom(local_idx, alpha, 1);
             update_force();
             for (bigint j=1; j<=natoms; j++){
@@ -291,7 +287,7 @@ void DynamicalMatrix::calculateMatrix()
                 local_jdx = atom->map(j);
                 if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
                     && gm[j-1] >= 0){
-                    for (bigint beta=0; beta<3; beta++){
+                    for (int beta=0; beta<3; beta++){
                         if (atom->rmass_flag == 1)
                             imass = sqrt(m[local_idx] * m[local_jdx]);
                         else
@@ -390,6 +386,7 @@ void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude)
 void DynamicalMatrix::update_force()
 {
     force_clear();
+    int n_post_force = modify->n_post_force;
 
     if (pair_compute_flag) {
         force->pair->compute(eflag,vflag);
@@ -410,6 +407,12 @@ void DynamicalMatrix::update_force()
         comm->reverse_comm();
         timer->stamp(Timer::COMM);
     }
+
+    // force modifications
+
+    if (n_post_force) modify->post_force(vflag);
+    timer->stamp(Timer::MODIFY);
+
     ++ update->nsteps;
 }
 
diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp
new file mode 100644
index 0000000000..7764287337
--- /dev/null
+++ b/src/USER-PHONON/third_order.cpp
@@ -0,0 +1,575 @@
+//
+// Created by charlie sievers on 7/5/18.
+//
+
+#include "third_order.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include "atom.h"
+#include "domain.h"
+#include "comm.h"
+#include "error.h"
+#include "group.h"
+#include "force.h"
+#include "memory.h"
+#include "bond.h"
+#include "angle.h"
+#include "dihedral.h"
+#include "improper.h"
+#include "kspace.h"
+#include "update.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "timer.h"
+#include "finish.h"
+#include "math_special.h"
+#include <algorithm>
+#include <complex>
+
+using namespace LAMMPS_NS;
+using namespace MathSpecial;
+enum{REGULAR,BALLISTICO};
+
+/* ---------------------------------------------------------------------- */
+
+ThirdOrder::ThirdOrder(LAMMPS *lmp) : Pointers(lmp), fp(NULL)
+{
+  external_force_clear = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ThirdOrder::~ThirdOrder()
+{
+  if (fp && me == 0) fclose(fp);
+  fp = NULL;
+  memory->destroy(groupmap);
+}
+
+/* ----------------------------------------------------------------------
+   setup without output or one-time post-init setup
+   flag = 0 = just force calculation
+   flag = 1 = reneighbor and force calculation
+------------------------------------------------------------------------- */
+
+void ThirdOrder::setup()
+{
+  // setup domain, communication and neighboring
+  // acquire ghosts
+  // build neighbor lists
+  if (triclinic) domain->x2lamda(atom->nlocal);
+  domain->pbc();
+  domain->reset_box();
+  comm->setup();
+  if (neighbor->style) neighbor->setup_bins();
+  comm->exchange();
+  comm->borders();
+  if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+  domain->image_check();
+  domain->box_too_small_check();
+  neighbor->build(1);
+
+  // compute all forces
+  external_force_clear = 0;
+  eflag=0;
+  vflag=0;
+  update_force();
+
+  if (gcount == atom->natoms)
+    for (bigint i=0; i<atom->natoms; i++)
+      groupmap[i] = i;
+  else
+    create_groupmap();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ThirdOrder::command(int narg, char **arg)
+{
+  MPI_Comm_rank(world,&me);
+
+  if (domain->box_exist == 0)
+    error->all(FLERR,"third_order command before simulation box is defined");
+  if (narg < 2) error->all(FLERR,"Illegal third_order command");
+
+  lmp->init();
+
+  // orthogonal vs triclinic simulation box
+
+  triclinic = domain->triclinic;
+
+  if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
+  else pair_compute_flag = 0;
+  if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
+  else kspace_compute_flag = 0;
+
+  // group and style
+
+  igroup = group->find(arg[0]);
+  if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID");
+  groupbit = group->bitmask[igroup];
+  gcount = group->count(igroup);
+  dynlen = (gcount)*3;
+  memory->create(groupmap,atom->natoms,"total_group_map:totalgm");
+  update->setupflag = 1;
+
+  int style = -1;
+  if (strcmp(arg[1],"regular") == 0) style = REGULAR;
+  else if (strcmp(arg[1],"eskm") == 0) style = BALLISTICO;
+  else error->all(FLERR,"Illegal Dynamical Matrix command");
+
+  // set option defaults
+
+  binaryflag = 0;
+  scaleflag = 0;
+  compressed = 0;
+  file_flag = 0;
+  file_opened = 0;
+  conversion = 1;
+
+  // read options from end of input line
+  if (style == REGULAR) options(narg-3,&arg[3]);  //COME BACK
+  else if (style == BALLISTICO) options(narg-3,&arg[3]); //COME BACK
+  else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n");
+  del = force->numeric(FLERR, arg[2]);
+
+  if (atom->map_style == 0)
+    error->all(FLERR,"third_order command requires an atom map, see atom_modify");
+
+  // move atoms by 3-vector or specified variable(s)
+
+  if (style == REGULAR) {
+    setup();
+    timer->init();
+    timer->barrier_start();
+    calculateMatrix();
+    timer->barrier_stop();
+  }
+
+  if (style == BALLISTICO) {
+    setup();
+    convert_units(update->unit_style);
+    conversion = conv_energy/conv_distance/conv_distance;
+    timer->init();
+    timer->barrier_start();
+    calculateMatrix();
+    timer->barrier_stop();
+  }
+
+  Finish finish(lmp);
+  finish.end(1);
+}
+
+/* ----------------------------------------------------------------------
+   parse optional parameters
+------------------------------------------------------------------------- */
+
+void ThirdOrder::options(int narg, char **arg)
+{
+  if (narg < 0) error->all(FLERR,"Illegal third_order command");
+  int iarg = 0;
+  const char *filename = "third_order.dat";
+  std::stringstream fss;
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"file") == 0) {
+      if (iarg+2 > narg) error->all(FLERR, "Illegal third_order command");
+      fss << arg[iarg + 1];
+      filename = fss.str().c_str();
+      file_flag = 1;
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"binary") == 0) {
+      if (iarg + 2 > narg) error->all(FLERR, "Illegal third_order command");
+      if (strcmp(arg[iarg+1],"gzip") == 0) {
+        compressed = 1;
+      } else if (strcmp(arg[iarg+1],"yes") == 0) {
+        binaryflag = 1;
+      }
+      iarg += 2;
+    } else error->all(FLERR,"Illegal third_order command");
+  }
+  if (file_flag == 1 and me == 0) {
+    openfile(filename);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   generic opening of a file
+   ASCII or binary or gzipped
+   some derived classes override this function
+------------------------------------------------------------------------- */
+
+void ThirdOrder::openfile(const char* filename)
+{
+  // if file already opened, return
+  if (file_opened) return;
+
+  if (compressed) {
+#ifdef LAMMPS_GZIP
+    char gzip[128];
+    sprintf(gzip,"gzip -6 > %s",filename);
+#ifdef _WIN32
+    fp = _popen(gzip,"wb");
+#else
+    fp = popen(gzip,"w");
+#endif
+#else
+    error->one(FLERR,"Cannot open gzipped file");
+#endif
+  } else if (binaryflag) {
+    fp = fopen(filename,"wb");
+  } else {
+    fp = fopen(filename,"w");
+  }
+
+  if (fp == NULL) error->one(FLERR,"Cannot open dump file");
+
+  file_opened = 1;
+}
+
+/* ----------------------------------------------------------------------
+   create dynamical matrix
+------------------------------------------------------------------------- */
+
+void ThirdOrder::calculateMatrix()
+{
+  int local_idx; // local index
+  int local_jdx; // second local index
+  int local_kdx; // third local index
+  int nlocal = atom->nlocal;
+  bigint natoms = atom->natoms;
+  bigint *gm = groupmap;
+  double **f = atom->f;
+
+  double *dynmat = new double[3*dynlen];
+  double *fdynmat = new double[3*dynlen];
+  memset(&dynmat[0],0,dynlen*sizeof(double));
+  memset(&fdynmat[0],0,dynlen*sizeof(double));
+
+  if (comm->me == 0 && screen) {
+    fprintf(screen,"Calculating Third Order ...\n");
+    fprintf(screen,"  Total # of atoms = " BIGINT_FORMAT "\n", natoms);
+    fprintf(screen,"  Atoms in group = " BIGINT_FORMAT "\n", gcount);
+    fprintf(screen,"  Total third order elements = "
+            BIGINT_FORMAT "\n", (dynlen*dynlen*dynlen) );
+  }
+
+  update->nsteps = 0;
+  int prog = 0;
+  for (bigint i=1; i<=natoms; i++){
+    local_idx = atom->map(i);
+    for (int alpha=0; alpha<3; alpha++){
+      for (bigint j=1; j<=natoms; j++){
+        local_jdx = atom->map(j);
+        for (int beta=0; beta<3; beta++){
+          displace_atom(local_idx, alpha, 1);
+          displace_atom(local_jdx, beta, 1);
+          update_force();
+          for (bigint k=1; k<=natoms; k++){
+            local_kdx = atom->map(k);
+            for (int gamma=0; gamma<3; gamma++){
+              if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
+                  && gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
+                  && local_kdx < nlocal) {
+                dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma];
+              }
+            }
+          }
+          displace_atom(local_jdx, beta, -2);
+          update_force();
+          for (bigint k=1; k<=natoms; k++){
+            local_kdx = atom->map(k);
+            for (int gamma=0; gamma<3; gamma++){
+              if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
+                  && gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
+                  && local_kdx < nlocal) {
+                dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma];
+              }
+            }
+          }
+          displace_atom(local_jdx, beta, 1);
+          displace_atom(local_idx,alpha,-2);
+          displace_atom(local_jdx, beta, 1);
+          update_force();
+          for (bigint k=1; k<=natoms; k++){
+            local_kdx = atom->map(k);
+            for (int gamma=0; gamma<3; gamma++){
+              if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
+                  && gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
+                  && local_kdx < nlocal) {
+                dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma];
+              }
+            }
+          }
+          displace_atom(local_jdx, beta, -2);
+          update_force();
+          for (bigint k=1; k<=natoms; k++){
+            local_kdx = atom->map(k);
+            for (int gamma=0; gamma<3; gamma++){
+              if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
+                  && gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
+                  && local_kdx < nlocal) {
+                dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma];
+                dynmat[gm[k-1]*3+gamma] /= (4 * del * del);
+              }
+            }
+          }
+          displace_atom(local_jdx, beta, 1);
+          displace_atom(local_idx, alpha, 1);
+          MPI_Reduce(dynmat,fdynmat,3*dynlen,MPI_DOUBLE,MPI_SUM,0,world);
+          if (me == 0){
+            writeMatrix(fdynmat, gm[i-1], alpha, gm[j-1], beta);
+          }
+          memset(&dynmat[0],0,dynlen*sizeof(double));
+        }
+      }
+    }
+    if (comm->me == 0 && screen) {
+      int p = 10 * gm[i-1] / gcount;
+      if (p > prog) {
+        prog = p;
+        fprintf(screen," %d%%",p*10);
+        fflush(screen);
+      }
+    }
+  }
+
+  delete [] dynmat;
+  delete [] fdynmat;
+
+  if (screen && me ==0 )
+    fprintf(screen,"Finished Calculating Third Order Tensor\n");
+}
+
+/* ----------------------------------------------------------------------
+   write dynamical matrix
+------------------------------------------------------------------------- */
+
+void ThirdOrder::writeMatrix(double *dynmat, bigint i, int a, bigint j, int b)
+{
+  if (me != 0)
+    return;
+
+  double norm;
+  if (!binaryflag && fp) {
+    clearerr(fp);
+    for (int k = 0; k < gcount; k++){
+      norm = square(dynmat[k*3])+
+        square(dynmat[k*3+1])+
+        square(dynmat[k*3+2]);
+      if (norm > 1.0e-16)
+        fprintf(fp,
+                BIGINT_FORMAT " %d " BIGINT_FORMAT " %d " BIGINT_FORMAT
+                " %7.8f %7.8f %7.8f\n",
+                i+1, a + 1, j+1, b + 1, groupmap[k]+1,
+                dynmat[k*3] * conversion,
+                dynmat[k*3+1] * conversion,
+                dynmat[k*3+2] * conversion);
+    }
+  } else if (binaryflag && fp){
+    clearerr(fp);
+    fwrite(&dynmat[0], sizeof(double), dynlen, fp);
+  }
+  if (ferror(fp)) error->one(FLERR,"Error writing to file");
+
+}
+
+/* ----------------------------------------------------------------------
+  Displace atoms
+   ---------------------------------------------------------------------- */
+
+void ThirdOrder::displace_atom(int local_idx, int direction, int magnitude)
+{
+  if (local_idx < 0) return;
+
+  double **x = atom->x;
+  int *sametag = atom->sametag;
+  int j = local_idx;
+
+  x[local_idx][direction] += del*magnitude;
+
+  while (sametag[j] >= 0){
+    j = sametag[j];
+    x[j][direction] += del*magnitude;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   evaluate potential energy and forces
+   may migrate atoms due to reneighboring
+   return new energy, which should include nextra_global dof
+   return negative gradient stored in atom->f
+   return negative gradient for nextra_global dof in fextra
+------------------------------------------------------------------------- */
+
+void ThirdOrder::update_force()
+{
+  force_clear();
+
+  if (pair_compute_flag) {
+    force->pair->compute(eflag,vflag);
+    timer->stamp(Timer::PAIR);
+  }
+  if (atom->molecular) {
+    if (force->bond) force->bond->compute(eflag,vflag);
+    if (force->angle) force->angle->compute(eflag,vflag);
+    if (force->dihedral) force->dihedral->compute(eflag,vflag);
+    if (force->improper) force->improper->compute(eflag,vflag);
+    timer->stamp(Timer::BOND);
+  }
+  if (kspace_compute_flag) {
+    force->kspace->compute(eflag,vflag);
+    timer->stamp(Timer::KSPACE);
+  }
+  if (force->newton) {
+    comm->reverse_comm();
+    timer->stamp(Timer::COMM);
+  }
+  ++ update->nsteps;
+}
+
+/* ----------------------------------------------------------------------
+   clear force on own & ghost atoms
+   clear other arrays as needed
+------------------------------------------------------------------------- */
+
+void ThirdOrder::force_clear()
+{
+  if (external_force_clear) return;
+
+  // clear global force array
+  // if either newton flag is set, also include ghosts
+
+  size_t nbytes = sizeof(double) * atom->nlocal;
+  if (force->newton) nbytes += sizeof(double) * atom->nghost;
+
+  if (nbytes) {
+    memset(&atom->f[0][0],0,3*nbytes);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ThirdOrder::convert_units(const char *style)
+{
+  // physical constants from:
+  // http://physics.nist.gov/cuu/Constants/Table/allascii.txt
+  // using thermochemical calorie = 4.184 J
+
+  if (strcmp(style,"lj") == 0) {
+    error->all(FLERR,"Conversion Not Set");
+    //conversion = 1; // lj -> 10 J/mol
+
+  } else if (strcmp(style,"real") == 0) {
+    conv_energy = 418.4; // kcal/mol -> 10 J/mol
+    conv_mass = 1; // g/mol -> g/mol
+    conv_distance = 1; // angstrom -> angstrom
+
+  } else if (strcmp(style,"metal") == 0) {
+    conv_energy = 9648.5; // eV -> 10 J/mol
+    conv_mass = 1; // g/mol -> g/mol
+    conv_distance = 1; // angstrom -> angstrom
+
+  } else if (strcmp(style,"si") == 0) {
+    if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
+    conv_energy = 6.022E22; // J -> 10 J/mol
+    conv_mass = 6.022E26; // kg -> g/mol
+    conv_distance = 1E-10; // meter -> angstrom
+
+  } else if (strcmp(style,"cgs") == 0) {
+    if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
+    conv_energy = 6.022E12; // Erg -> 10 J/mol
+    conv_mass = 6.022E23; // g -> g/mol
+    conv_distance = 1E-7; // centimeter -> angstrom
+
+  } else if (strcmp(style,"electron") == 0) {
+    conv_energy = 262550; // Hartree -> 10 J/mol
+    conv_mass = 1; // amu -> g/mol
+    conv_distance = 0.529177249; // bohr -> angstrom
+
+  } else if (strcmp(style,"micro") == 0) {
+    if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
+    conv_energy = 6.022E10; // picogram-micrometer^2/microsecond^2 -> 10 J/mol
+    conv_mass = 6.022E11; // pg -> g/mol
+    conv_distance = 1E-4; // micrometer -> angstrom
+
+  } else if (strcmp(style,"nano") == 0) {
+    if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
+    conv_energy = 6.022E4; // attogram-nanometer^2/nanosecond^2 -> 10 J/mol
+    conv_mass = 6.022E5; // ag -> g/mol
+    conv_distance = 0.1; // angstrom -> angstrom
+
+  } else error->all(FLERR,"Units Type Conversion Not Found");
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ThirdOrder::create_groupmap()
+{
+  //Create a group map which maps atom order onto group
+  // groupmap[global atom index-1] = output column/row
+
+  int local_idx; // local index
+  int gid = 0; //group index
+  int nlocal = atom->nlocal;
+  int *mask = atom->mask;
+  bigint natoms = atom->natoms;
+  int *recv = new int[comm->nprocs];
+  int *displs = new int[comm->nprocs];
+  bigint *temp_groupmap = new bigint[natoms];
+
+  //find number of local atoms in the group (final_gid)
+  for (bigint i=1; i<=natoms; i++){
+    local_idx = atom->map(i);
+    if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit)
+      gid += 1; // gid at the end of loop is final_Gid
+  }
+  //create an array of length final_gid
+  bigint *sub_groupmap = new bigint[gid];
+
+  gid = 0;
+  //create a map between global atom id and group atom id for each proc
+  for (bigint i=1; i<=natoms; i++){
+    local_idx = atom->map(i);
+    if ((local_idx >= 0) && (local_idx < nlocal)
+        && (mask[local_idx] & groupbit)){
+      sub_groupmap[gid] = i;
+      gid += 1;
+    }
+  }
+
+  //populate arrays for Allgatherv
+  for (int i=0; i<comm->nprocs; i++){
+    recv[i] = 0;
+  }
+  recv[comm->me] = gid;
+  MPI_Allreduce(recv,displs,comm->nprocs,MPI_INT,MPI_SUM,world);
+  for (int i=0; i<comm->nprocs; i++){
+    recv[i]=displs[i];
+    if (i>0) displs[i] = displs[i-1]+recv[i-1];
+    else displs[i] = 0;
+  }
+
+  //combine subgroup maps into total temporary groupmap
+  MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,
+                 temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);
+  std::sort(temp_groupmap,temp_groupmap+gcount);
+
+  //populate member groupmap based on temp groupmap
+  bigint j = 0;
+  for (bigint i=1; i<=natoms; i++){
+    // flag groupmap contents that are in temp_groupmap
+    if (j < gcount && i == temp_groupmap[j])
+      groupmap[i-1] = j++;
+    else
+      groupmap[i-1] = -1;
+  }
+
+  //free that memory!
+  delete[] recv;
+  delete[] displs;
+  delete[] sub_groupmap;
+  delete[] temp_groupmap;
+}
diff --git a/src/USER-PHONON/third_order.h b/src/USER-PHONON/third_order.h
new file mode 100644
index 0000000000..83062b6b1f
--- /dev/null
+++ b/src/USER-PHONON/third_order.h
@@ -0,0 +1,76 @@
+//
+// Created by charlie sievers on 7/5/18.
+//
+
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(third_order,ThirdOrder)
+
+#else
+
+#ifndef LMP_THIRD_ORDER_H
+#define LMP_THIRD_ORDER_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+  class ThirdOrder : protected Pointers {
+   public:
+    ThirdOrder(class LAMMPS *);
+    virtual ~ThirdOrder();
+    void command(int, char **);
+    void setup();
+
+   protected:
+    int eflag,vflag;            // flags for energy/virial computation
+    int external_force_clear;   // clear forces locally or externally
+
+
+    int triclinic;              // 0 if domain is orthog, 1 if triclinic
+    int pairflag;
+
+    int pair_compute_flag;            // 0 if pair->compute is skipped
+    int kspace_compute_flag;          // 0 if kspace->compute is skipped
+
+    int nvec;                   // local atomic dof = length of xvec
+
+    void update_force();
+    void force_clear();
+    virtual void openfile(const char* filename);
+
+
+   private:
+    void options(int, char **);
+    void create_groupmap();
+    void calculateMatrix();
+    void convert_units(const char *style);
+    void displace_atom(int local_idx, int direction, int magnitude);
+    void writeMatrix(double *, bigint, int, bigint, int);
+
+    double conversion;
+    double conv_energy;
+    double conv_distance;
+    double conv_mass;
+    double del;
+    int igroup,groupbit;
+    bigint dynlen;
+    int scaleflag;
+    int me;
+    bigint gcount;  // number of atoms in group
+    bigint *groupmap;
+
+    int compressed;            // 1 if dump file is written compressed, 0 no
+    int binaryflag;            // 1 if dump file is written binary, 0 no
+    int file_opened;           // 1 if openfile method has been called, 0 no
+    int file_flag;             // 1 custom file name, 0 dynmat.dat
+
+    FILE *fp;
+  };
+}
+
+
+#endif //LMP_THIRD_ORDER_H
+#endif
+
diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp
index c75a48f9b4..b02de2af0d 100644
--- a/src/USER-PLUMED/fix_plumed.cpp
+++ b/src/USER-PLUMED/fix_plumed.cpp
@@ -411,7 +411,7 @@ void FixPlumed::post_force(int /* vflag */)
 
   // pass all pointers to plumed:
   p->cmd("setStep",&step);
-  int plumedStopCondition=0; 
+  int plumedStopCondition=0;
   p->cmd("setStopFlag",&plumedStopCondition);
   p->cmd("setPositions",&atom->x[0][0]);
   p->cmd("setBox",&box[0][0]);
diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp
index ad3d3facdb..3a2c8daac4 100644
--- a/src/USER-PTM/compute_ptm_atom.cpp
+++ b/src/USER-PTM/compute_ptm_atom.cpp
@@ -23,6 +23,7 @@ under
 #include <vector>
 
 #include "atom.h"
+#include "citeme.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -82,6 +83,9 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
       PTM_CHECK_ALL,
       PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO};
 
+  if (lmp->citeme)
+    lmp->citeme->add(cite_user_ptm_package);
+
   input_flags = 0;
   while (*ptr != '\0') {
 
diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp
index dc4ce4e747..60ef4cf87b 100644
--- a/src/USER-PTM/ptm_voronoi_cell.cpp
+++ b/src/USER-PTM/ptm_voronoi_cell.cpp
@@ -210,13 +210,15 @@ void voronoicell_base::add_memory_vorder(vc_class &vc) {
         fprintf(stderr,"Vertex order memory scaled up to %d\n",i);
 #endif
         p1=new int[i];
-        for(j=0;j<current_vertex_order;j++) p1[j]=mem[j];while(j<i) p1[j++]=0;
+        for(j=0;j<current_vertex_order;j++) p1[j]=mem[j];
+        while(j<i) p1[j++]=0;
         delete [] mem;mem=p1;
         p2=new int*[i];
         for(j=0;j<current_vertex_order;j++) p2[j]=mep[j];
         delete [] mep;mep=p2;
         p1=new int[i];
-        for(j=0;j<current_vertex_order;j++) p1[j]=mec[j];while(j<i) p1[j++]=0;
+        for(j=0;j<current_vertex_order;j++) p1[j]=mec[j];
+        while(j<i) p1[j++]=0;
         delete [] mec;mec=p1;
         vc.n_add_memory_vorder(i);
         current_vertex_order=i;
@@ -257,8 +259,8 @@ void voronoicell_base::add_memory_ds2(int *&stackp2) {
  * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
  * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
 void voronoicell_base::init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
-        for(int i=0;i<current_vertex_order;i++) mec[i]=0;up=0;
-        mec[3]=p=8;xmin*=2;xmax*=2;ymin*=2;ymax*=2;zmin*=2;zmax*=2;
+        for(int i=0;i<current_vertex_order;i++) mec[i]=0;
+        up=0;mec[3]=p=8;xmin*=2;xmax*=2;ymin*=2;ymax*=2;zmin*=2;zmax*=2;
         *pts=xmin;pts[1]=ymin;pts[2]=zmin;
         pts[3]=xmax;pts[4]=ymin;pts[5]=zmin;
         pts[6]=xmin;pts[7]=ymax;pts[8]=zmin;
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 959405576e..28f9a193c4 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -39,6 +39,7 @@
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 #include "reaxc_defs.h"
 #include "reaxc_types.h"
@@ -372,12 +373,10 @@ void PairReaxC::init_style( )
 
   // firstwarn = 1;
 
-  int iqeq;
-  for (iqeq = 0; iqeq < modify->nfix; iqeq++)
-    if (strstr(modify->fix[iqeq]->style,"qeq/reax")
-       || strstr(modify->fix[iqeq]->style,"qeq/shielded")) break;
-  if (iqeq == modify->nfix && qeqflag == 1)
-    error->all(FLERR,"Pair reax/c requires use of fix qeq/reax");
+  bool have_qeq = ((modify->find_fix_by_style("^qeq/reax") != -1)
+                   || (modify->find_fix_by_style("^qeq/shielded") != -1));
+  if (!have_qeq && qeqflag == 1)
+    error->all(FLERR,"Pair reax/c requires use of fix qeq/reax or qeq/shielded");
 
   system->n = atom->nlocal; // my atoms
   system->N = atom->nlocal + atom->nghost; // mine + ghosts
diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp
index e3a6645fc2..c8e097eb1c 100644
--- a/src/USER-REAXC/reaxc_ffield.cpp
+++ b/src/USER-REAXC/reaxc_ffield.cpp
@@ -154,7 +154,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
 
     /* Sanity checks */
     if (c == 2 && !lgflag)
-        control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'");	
+        control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'");
 
     if (c < 9) {
       snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s);
diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp
index 88e95dd338..7f1443c654 100644
--- a/src/USER-VTK/dump_vtk.cpp
+++ b/src/USER-VTK/dump_vtk.cpp
@@ -166,13 +166,6 @@ DumpVTK::DumpVTK(LAMMPS *lmp, int narg, char **arg) :
   header_choice = NULL;
   write_choice = NULL;
   boxcorners = NULL;
-
-  // unsupported feature by dump vtk
-  delete [] vformat;
-  vformat = NULL;
-
-  delete [] format_column_user;
-  format_column_user = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp
index 0f8861cdf5..3d5715c23e 100644
--- a/src/USER-YAFF/angle_cross.cpp
+++ b/src/USER-YAFF/angle_cross.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -278,12 +279,12 @@ void AngleCross::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&kss[1],sizeof(double),atom->nangletypes,fp);
-    fread(&kbs0[1],sizeof(double),atom->nangletypes,fp);
-    fread(&kbs1[1],sizeof(double),atom->nangletypes,fp);
-    fread(&r00[1],sizeof(double),atom->nangletypes,fp);
-    fread(&r01[1],sizeof(double),atom->nangletypes,fp);
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&kss[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&kbs0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&kbs1[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&r00[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&r01[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
 
   MPI_Bcast(&kss[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp
index b90db37afa..cb3010e97c 100644
--- a/src/USER-YAFF/angle_mm3.cpp
+++ b/src/USER-YAFF/angle_mm3.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -225,8 +226,8 @@ void AngleMM3::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k2[1],sizeof(double),atom->nangletypes,fp);
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
 
   MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp
index 2a7d5d1843..8001e35d74 100644
--- a/src/USER-YAFF/bond_mm3.cpp
+++ b/src/USER-YAFF/bond_mm3.cpp
@@ -24,6 +24,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -178,8 +179,8 @@ void BondMM3::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k2[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&k2[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp
index 2b62f827e7..751e6e19c2 100644
--- a/src/USER-YAFF/improper_distharm.cpp
+++ b/src/USER-YAFF/improper_distharm.cpp
@@ -26,6 +26,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -256,8 +257,8 @@ void ImproperDistHarm::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp
index bcc0549f7e..82bf4a1755 100644
--- a/src/USER-YAFF/improper_sqdistharm.cpp
+++ b/src/USER-YAFF/improper_sqdistharm.cpp
@@ -26,6 +26,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -256,8 +257,8 @@ void ImproperSQDistHarm::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
-    fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
+    utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error);
   }
   MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
index ab983a78bc..022b93a0d2 100644
--- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
+++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
@@ -31,6 +31,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -132,7 +133,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
 
       if (rsq < cutsq[itype][jtype]) {
         r2inv = 1.0/rsq;
- 
+
         if (rsq < cut_coulsq) {
           if (!ncoultablebits || rsq <= tabinnersq) {
             r = sqrt(rsq);
@@ -201,7 +202,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
             if (r>cut_lj[itype][jtype]-truncw) {
               trx = (cut_lj[itype][jtype]-r)*truncwi;
               tr = trx*trx*(3.0-2.0*trx);
-              ftr = 6.0*trx*(1.0-trx)*r*truncwi;    
+              ftr = 6.0*trx*(1.0-trx)*r*truncwi;
               forcelj = forcelj*tr + evdwl*ftr;
               evdwl *= tr;
             }
@@ -520,14 +521,14 @@ void PairLJSwitch3CoulGaussLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&gamma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -560,14 +561,14 @@ void PairLJSwitch3CoulGaussLong::write_restart_settings(FILE *fp)
 void PairLJSwitch3CoulGaussLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&truncw,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&truncw,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
@@ -682,7 +683,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
       if (r>cut_lj[itype][jtype]-truncw) {
         trx = (cut_lj[itype][jtype]-r)*truncwi;
         tr = trx*trx*(3.0-2.0*trx);
-        ftr = 6.0*trx*(1.0-trx)*r*truncwi;    
+        ftr = 6.0*trx*(1.0-trx)*r*truncwi;
         forcelj = forcelj*tr + evdwl*ftr;
         evdwl *= tr;
       }
diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
index 4175ef915d..6b0466cd6d 100644
--- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
+++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
@@ -31,6 +31,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -132,7 +133,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
 
       if (rsq < cutsq[itype][jtype]) {
         r2inv = 1.0/rsq;
- 
+
         if (rsq < cut_coulsq) {
           if (!ncoultablebits || rsq <= tabinnersq) {
             r = sqrt(rsq);
@@ -203,7 +204,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
             if (r>cut_lj[itype][jtype]-truncw) {
               trx = (cut_lj[itype][jtype]-r)*truncwi;
               tr = trx*trx*(3.0-2.0*trx);
-              ftr = 6.0*trx*(1.0-trx)*r*truncwi;    
+              ftr = 6.0*trx*(1.0-trx)*r*truncwi;
               forcelj = forcelj*tr + evdwl*ftr;
               evdwl *= tr;
             }
@@ -520,14 +521,14 @@ void PairMM3Switch3CoulGaussLong::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&gamma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -560,16 +561,15 @@ void PairMM3Switch3CoulGaussLong::write_restart_settings(FILE *fp)
 void PairMM3Switch3CoulGaussLong::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&truncw,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
-    fread(&ncoultablebits,sizeof(int),1,fp);
-    fread(&tabinner,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&truncw,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error);
   }
-  printf("Reading from restart, trunc = %f\n",truncw);
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&truncw,1,MPI_DOUBLE,0,world);
@@ -683,7 +683,7 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype,
       if (r>cut_lj[itype][jtype]-truncw) {
         trx = (cut_lj[itype][jtype]-r)*truncwi;
         tr = trx*trx*(3.0-2.0*trx);
-        ftr = 6.0*trx*(1.0-trx)*r*truncwi;    
+        ftr = 6.0*trx*(1.0-trx)*r*truncwi;
         forcelj = forcelj*tr + evdwl*ftr;
         evdwl *= tr;
       }
diff --git a/src/angle.cpp b/src/angle.cpp
index 1b9532ea32..ee7e855782 100644
--- a/src/angle.cpp
+++ b/src/angle.cpp
@@ -34,9 +34,10 @@ Angle::Angle(LAMMPS *lmp) : Pointers(lmp)
   allocated = 0;
   suffix_flag = Suffix::NONE;
 
-  maxeatom = maxvatom = 0;
+  maxeatom = maxvatom = maxcvatom = 0;
   eatom = NULL;
   vatom = NULL;
+  cvatom = NULL;
   setflag = NULL;
 
   execution_space = Host;
@@ -54,6 +55,7 @@ Angle::~Angle()
 
   memory->destroy(eatom);
   memory->destroy(vatom);
+  memory->destroy(cvatom);
 }
 
 /* ----------------------------------------------------------------------
@@ -85,9 +87,10 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
   eflag_global = eflag % 2;
   eflag_atom = eflag / 2;
 
-  vflag_either = vflag;
   vflag_global = vflag % 4;
-  vflag_atom = vflag / 4;
+  vflag_atom = vflag & 4;
+  cvflag_atom = vflag & 8;
+  vflag_either = vflag_global || vflag_atom;
 
   // reallocate per-atom arrays if necessary
 
@@ -105,6 +108,13 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
       memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom");
     }
   }
+  if (cvflag_atom && atom->nmax > maxcvatom) {
+    maxcvatom = atom->nmax;
+    if (alloc) {
+      memory->destroy(cvatom);
+      memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom");
+    }
+  }
 
   // zero accumulators
 
@@ -127,6 +137,22 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
       vatom[i][5] = 0.0;
     }
   }
+  if (cvflag_atom && alloc) {
+    n = atom->nlocal;
+    if (force->newton_bond) n += atom->nghost;
+    for (i = 0; i < n; i++) {
+      cvatom[i][0] = 0.0;
+      cvatom[i][1] = 0.0;
+      cvatom[i][2] = 0.0;
+      cvatom[i][3] = 0.0;
+      cvatom[i][4] = 0.0;
+      cvatom[i][5] = 0.0;
+      cvatom[i][6] = 0.0;
+      cvatom[i][7] = 0.0;
+      cvatom[i][8] = 0.0;
+      cvatom[i][9] = 0.0;
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -230,6 +256,76 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
       }
     }
   }
+
+  // per-atom centroid virial
+  if (cvflag_atom) {
+
+    // r0 = (r1+r2+r3)/3
+    // rij = ri-rj
+    // total virial = r10*f1 + r20*f2 + r30*f3
+    // del1: r12
+    // del2: r32
+
+    if (newton_bond || i < nlocal) {
+      double a1[3];
+
+      // a1 = r10 = (2*r12 -   r32)/3
+      a1[0] = THIRD*(2*delx1-delx2);
+      a1[1] = THIRD*(2*dely1-dely2);
+      a1[2] = THIRD*(2*delz1-delz2);
+
+      cvatom[i][0] += a1[0]*f1[0];
+      cvatom[i][1] += a1[1]*f1[1];
+      cvatom[i][2] += a1[2]*f1[2];
+      cvatom[i][3] += a1[0]*f1[1];
+      cvatom[i][4] += a1[0]*f1[2];
+      cvatom[i][5] += a1[1]*f1[2];
+      cvatom[i][6] += a1[1]*f1[0];
+      cvatom[i][7] += a1[2]*f1[0];
+      cvatom[i][8] += a1[2]*f1[1];
+    }
+    if (newton_bond || j < nlocal) {
+      double a2[3];
+      double f2[3];
+
+      // a2 = r20 = ( -r12 -   r32)/3
+      a2[0] = THIRD*(-delx1-delx2);
+      a2[1] = THIRD*(-dely1-dely2);
+      a2[2] = THIRD*(-delz1-delz2);
+
+      f2[0] = - f1[0] - f3[0];
+      f2[1] = - f1[1] - f3[1];
+      f2[2] = - f1[2] - f3[2];
+
+      cvatom[j][0] += a2[0]*f2[0];
+      cvatom[j][1] += a2[1]*f2[1];
+      cvatom[j][2] += a2[2]*f2[2];
+      cvatom[j][3] += a2[0]*f2[1];
+      cvatom[j][4] += a2[0]*f2[2];
+      cvatom[j][5] += a2[1]*f2[2];
+      cvatom[j][6] += a2[1]*f2[0];
+      cvatom[j][7] += a2[2]*f2[0];
+      cvatom[j][8] += a2[2]*f2[1];
+    }
+    if (newton_bond || k < nlocal) {
+      double a3[3];
+
+      // a3 = r30 = ( -r12 + 2*r32)/3
+      a3[0] = THIRD*(-delx1+2*delx2);
+      a3[1] = THIRD*(-dely1+2*dely2);
+      a3[2] = THIRD*(-delz1+2*delz2);
+
+      cvatom[k][0] += a3[0]*f3[0];
+      cvatom[k][1] += a3[1]*f3[1];
+      cvatom[k][2] += a3[2]*f3[2];
+      cvatom[k][3] += a3[0]*f3[1];
+      cvatom[k][4] += a3[0]*f3[2];
+      cvatom[k][5] += a3[1]*f3[2];
+      cvatom[k][6] += a3[1]*f3[0];
+      cvatom[k][7] += a3[2]*f3[0];
+      cvatom[k][8] += a3[2]*f3[1];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -238,5 +334,6 @@ double Angle::memory_usage()
 {
   double bytes = comm->nthreads*maxeatom * sizeof(double);
   bytes += comm->nthreads*maxvatom*6 * sizeof(double);
+  bytes += comm->nthreads*maxcvatom*9 * sizeof(double);
   return bytes;
 }
diff --git a/src/angle.h b/src/angle.h
index c0d1199dcd..139380ff39 100644
--- a/src/angle.h
+++ b/src/angle.h
@@ -28,6 +28,7 @@ class Angle : protected Pointers {
   double energy;                  // accumulated energies
   double virial[6];               // accumulated virial
   double *eatom,**vatom;          // accumulated per-atom energy/virial
+  double **cvatom;                // accumulated per-atom centroid virial
 
   // KOKKOS host/device flag and data masks
 
@@ -56,12 +57,12 @@ class Angle : protected Pointers {
 
   int evflag;
   int eflag_either,eflag_global,eflag_atom;
-  int vflag_either,vflag_global,vflag_atom;
-  int maxeatom,maxvatom;
+  int vflag_either,vflag_global,vflag_atom,cvflag_atom;
+  int maxeatom,maxvatom,maxcvatom;
 
   void ev_init(int eflag, int vflag, int alloc = 1) {
     if (eflag||vflag) ev_setup(eflag, vflag, alloc);
-    else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0;
+    else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = cvflag_atom = 0;
   }
   void ev_setup(int, int, int alloc = 1);
   void ev_tally(int, int, int, int, int, double, double *, double *,
diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp
index 6ffbc19d08..7c0cbd3008 100644
--- a/src/angle_hybrid.cpp
+++ b/src/angle_hybrid.cpp
@@ -21,6 +21,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -127,6 +128,14 @@ void AngleHybrid::compute(int eflag, int vflag)
         for (j = 0; j < 6; j++)
           vatom[i][j] += vatom_substyle[i][j];
     }
+    if (cvflag_atom) {
+      n = atom->nlocal;
+      if (force->newton_bond) n += atom->nghost;
+      double **cvatom_substyle = styles[m]->cvatom;
+      for (i = 0; i < n; i++)
+        for (j = 0; j < 9; j++)
+          cvatom[i][j] += cvatom_substyle[i][j];
+    }
   }
 
   // restore ptrs to original anglelist
@@ -334,7 +343,7 @@ void AngleHybrid::write_restart(FILE *fp)
 void AngleHybrid::read_restart(FILE *fp)
 {
   int me = comm->me;
-  if (me == 0) fread(&nstyles,sizeof(int),1,fp);
+  if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error);
   MPI_Bcast(&nstyles,1,MPI_INT,0,world);
   styles = new Angle*[nstyles];
   keywords = new char*[nstyles];
@@ -343,10 +352,10 @@ void AngleHybrid::read_restart(FILE *fp)
 
   int n,dummy;
   for (int m = 0; m < nstyles; m++) {
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     keywords[m] = new char[n];
-    if (me == 0) fread(keywords[m],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
     styles[m] = force->new_angle(keywords[m],0,dummy);
     styles[m]->read_restart_settings(fp);
@@ -369,6 +378,7 @@ double AngleHybrid::memory_usage()
 {
   double bytes = maxeatom * sizeof(double);
   bytes += maxvatom*6 * sizeof(double);
+  bytes += maxcvatom*9 * sizeof(double);
   for (int m = 0; m < nstyles; m++) bytes += maxangle[m]*4 * sizeof(int);
   for (int m = 0; m < nstyles; m++)
     if (styles[m]) bytes += styles[m]->memory_usage();
diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp
index 3c92b852b3..5da8e9d5bc 100644
--- a/src/angle_zero.cpp
+++ b/src/angle_zero.cpp
@@ -24,6 +24,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -128,7 +129,7 @@ void AngleZero::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error);
   }
   MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
 
diff --git a/src/atom.cpp b/src/atom.cpp
index 24ad2d40da..de5d30930a 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -211,7 +211,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   tag_enable = 1;
   map_style = map_user = 0;
   map_tag_max = -1;
-  map_maxarray = map_nhash = -1;
+  map_maxarray = map_nhash = map_nbucket = -1;
 
   max_same = 0;
   sametag = NULL;
diff --git a/src/atom.h b/src/atom.h
index 81f643c007..4c640f3252 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -287,6 +287,7 @@ class Atom : protected Pointers {
 
   inline int* get_map_array() {return map_array;};
   inline int get_map_size() {return map_tag_max+1;};
+  inline int get_max_same() {return max_same;};
   inline int get_map_maxarray() {return map_maxarray+1;};
 
   bigint memory_usage();
diff --git a/src/atom_map.cpp b/src/atom_map.cpp
index 7949e327a9..c23aeec83c 100644
--- a/src/atom_map.cpp
+++ b/src/atom_map.cpp
@@ -335,7 +335,7 @@ void Atom::map_delete()
       map_bucket = NULL;
       map_hash = NULL;
     }
-    map_nhash = 0;
+    map_nhash = map_nbucket = 0;
   }
 }
 
diff --git a/src/bond.cpp b/src/bond.cpp
index bb54306280..d16ce5fe0f 100644
--- a/src/bond.cpp
+++ b/src/bond.cpp
@@ -91,6 +91,7 @@ void Bond::ev_setup(int eflag, int vflag, int alloc)
 
   vflag_either = vflag;
   vflag_global = vflag % 4;
+  // per-atom virial and per-atom centroid virial are the same for bonds
   vflag_atom = vflag / 4;
 
   // reallocate per-atom arrays if necessary
diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp
index 2b365014cf..c66d2c1425 100644
--- a/src/bond_hybrid.cpp
+++ b/src/bond_hybrid.cpp
@@ -21,6 +21,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -335,7 +336,7 @@ void BondHybrid::write_restart(FILE *fp)
 void BondHybrid::read_restart(FILE *fp)
 {
   int me = comm->me;
-  if (me == 0) fread(&nstyles,sizeof(int),1,fp);
+  if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error);
   MPI_Bcast(&nstyles,1,MPI_INT,0,world);
   styles = new Bond*[nstyles];
   keywords = new char*[nstyles];
@@ -344,10 +345,10 @@ void BondHybrid::read_restart(FILE *fp)
 
   int n,dummy;
   for (int m = 0; m < nstyles; m++) {
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     keywords[m] = new char[n];
-    if (me == 0) fread(keywords[m],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
     styles[m] = force->new_bond(keywords[m],0,dummy);
     styles[m]->read_restart_settings(fp);
diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp
index 9be37c13be..428fd0ace2 100644
--- a/src/bond_zero.cpp
+++ b/src/bond_zero.cpp
@@ -23,6 +23,7 @@
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -126,7 +127,7 @@ void BondZero::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error);
   }
   MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
 
diff --git a/src/comm.cpp b/src/comm.cpp
index fa6790e0ec..9a577c0e4f 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -673,7 +673,7 @@ double Comm::get_comm_cutoff()
   // cutoff was given and no pair style present. Otherwise print a
   // warning, if the estimated bond based cutoff is larger than what
   // is currently used.
-  
+
   if (!force->pair && (cutghostuser == 0.0)) {
     maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff);
   } else {
diff --git a/src/compute.h b/src/compute.h
index 38d001db6f..c28af32c26 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -59,6 +59,8 @@ class Compute : protected Pointers {
   int pressflag;      // 1 if Compute can be used as pressure (uses virial)
                       // must have both compute_scalar, compute_vector
   int pressatomflag;  // 1 if Compute calculates per-atom virial
+                      // 2 if Compute calculates per-atom centroid virial
+                      // 3 if Compute calculates both
   int peflag;         // 1 if Compute calculates PE (uses Force energies)
   int peatomflag;     // 1 if Compute calculates per-atom PE
   int create_attribute;    // 1 if compute stores attributes that need
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index e14f188e62..010e8db627 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -130,7 +130,7 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
   singleflag = 0;
   velflag = 0;
   for (int i = 0; i < nvalues; i++) {
-    if (bstyle[i] == ENGPOT || bstyle[i] == FORCE || bstyle[i] == FX       || 
+    if (bstyle[i] == ENGPOT || bstyle[i] == FORCE || bstyle[i] == FX       ||
         bstyle[i] == FY     || bstyle[i] == FZ) singleflag = 1;
     if (bstyle[i] == VELVIB || bstyle[i] == OMEGA || bstyle[i] == ENGTRANS ||
         bstyle[i] == ENGVIB || bstyle[i] == ENGROT) velflag = 1;
diff --git a/src/compute_centroid_stress_atom.cpp b/src/compute_centroid_stress_atom.cpp
new file mode 100644
index 0000000000..3f5b2cba81
--- /dev/null
+++ b/src/compute_centroid_stress_atom.cpp
@@ -0,0 +1,438 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "compute_centroid_stress_atom.h"
+#include <cstring>
+#include "atom.h"
+#include "update.h"
+#include "comm.h"
+#include "force.h"
+#include "pair.h"
+#include "bond.h"
+#include "angle.h"
+#include "dihedral.h"
+#include "improper.h"
+#include "kspace.h"
+#include "modify.h"
+#include "fix.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+enum{NOBIAS,BIAS};
+
+/* ---------------------------------------------------------------------- */
+
+ComputeCentroidStressAtom::ComputeCentroidStressAtom(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg),
+  id_temp(NULL), stress(NULL)
+{
+  if (narg < 4) error->all(FLERR,"Illegal compute centroid/stress/atom command");
+
+  peratom_flag = 1;
+  size_peratom_cols = 9;
+  pressatomflag = 2;
+  timeflag = 1;
+  comm_reverse = 9;
+
+  // store temperature ID used by stress computation
+  // insure it is valid for temperature computation
+
+  if (strcmp(arg[3],"NULL") == 0) id_temp = NULL;
+  else {
+    int n = strlen(arg[3]) + 1;
+    id_temp = new char[n];
+    strcpy(id_temp,arg[3]);
+
+    int icompute = modify->find_compute(id_temp);
+    if (icompute < 0)
+      error->all(FLERR,"Could not find compute centroid/stress/atom temperature ID");
+    if (modify->compute[icompute]->tempflag == 0)
+      error->all(FLERR,
+                 "Compute centroid/stress/atom temperature ID does not "
+                 "compute temperature");
+  }
+
+  // process optional args
+
+  if (narg == 4) {
+    keflag = 1;
+    pairflag = 1;
+    bondflag = angleflag = dihedralflag = improperflag = 1;
+    kspaceflag = 1;
+    fixflag = 1;
+  } else {
+    keflag = 0;
+    pairflag = 0;
+    bondflag = angleflag = dihedralflag = improperflag = 0;
+    kspaceflag = 0;
+    fixflag = 0;
+    int iarg = 4;
+    while (iarg < narg) {
+      if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
+      else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
+      else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
+      else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
+      else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
+      else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
+      else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
+      else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
+      else if (strcmp(arg[iarg],"virial") == 0) {
+        pairflag = 1;
+        bondflag = angleflag = dihedralflag = improperflag = 1;
+        kspaceflag = fixflag = 1;
+      } else error->all(FLERR,"Illegal compute centroid/stress/atom command");
+      iarg++;
+    }
+  }
+
+  nmax = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeCentroidStressAtom::~ComputeCentroidStressAtom()
+{
+  delete [] id_temp;
+  memory->destroy(stress);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCentroidStressAtom::init()
+{
+  // set temperature compute, must be done in init()
+  // fixes could have changed or compute_modify could have changed it
+
+  if (id_temp) {
+    int icompute = modify->find_compute(id_temp);
+    if (icompute < 0)
+      error->all(FLERR,"Could not find compute centroid/stress/atom temperature ID");
+    temperature = modify->compute[icompute];
+    if (temperature->tempbias) biasflag = BIAS;
+    else biasflag = NOBIAS;
+  } else biasflag = NOBIAS;
+
+  // check if pair styles support centroid atom stress
+  if (pairflag && force->pair)
+    if (force->pair->centroidstressflag & 4)
+      error->all(FLERR, "Pair style does not support compute centroid/stress/atom");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCentroidStressAtom::compute_peratom()
+{
+  int i,j;
+  double onemass;
+
+  invoked_peratom = update->ntimestep;
+  if (update->vflag_atom != invoked_peratom)
+    error->all(FLERR,"Per-atom virial was not tallied on needed timestep");
+
+  // grow local stress array if necessary
+  // needs to be atom->nmax in length
+
+  if (atom->nmax > nmax) {
+    memory->destroy(stress);
+    nmax = atom->nmax;
+    memory->create(stress,nmax,9,"centroid/stress/atom:stress");
+    array_atom = stress;
+  }
+
+  // npair includes ghosts if either newton flag is set
+  //   b/c some bonds/dihedrals call pair::ev_tally with pairwise info
+  // nbond includes ghosts if newton_bond is set
+  // ntotal includes ghosts if either newton flag is set
+  // KSpace includes ghosts if tip4pflag is set
+
+  int nlocal = atom->nlocal;
+  int npair = nlocal;
+  int nbond = nlocal;
+  int ntotal = nlocal;
+  int nkspace = nlocal;
+  if (force->newton) npair += atom->nghost;
+  if (force->newton_bond) nbond += atom->nghost;
+  if (force->newton) ntotal += atom->nghost;
+  if (force->kspace && force->kspace->tip4pflag) nkspace += atom->nghost;
+
+  // clear local stress array
+
+  for (i = 0; i < ntotal; i++)
+    for (j = 0; j < 9; j++)
+      stress[i][j] = 0.0;
+
+  // add in per-atom contributions from each force
+
+  // per-atom virial and per-atom centroid virial are the same for two-body
+  // many-body pair styles not yet implemented
+  if (pairflag && force->pair) {
+    if (force->pair->centroidstressflag & 2) {
+      double **cvatom = force->pair->cvatom;
+      for (i = 0; i < npair; i++)
+        for (j = 0; j < 9; j++)
+          stress[i][j] += cvatom[i][j];
+    } else {
+      double **vatom = force->pair->vatom;
+      for (i = 0; i < npair; i++) {
+        for (j = 0; j < 6; j++)
+          stress[i][j] += vatom[i][j];
+        for (j = 6; j < 9; j++)
+          stress[i][j] += vatom[i][j-3];
+      }
+    }
+  }
+
+  // per-atom virial and per-atom centroid virial are the same for bonds
+  if (bondflag && force->bond) {
+    double **vatom = force->bond->vatom;
+    for (i = 0; i < nbond; i++) {
+      for (j = 0; j < 6; j++)
+        stress[i][j] += vatom[i][j];
+      for (j = 6; j < 9; j++)
+        stress[i][j] += vatom[i][j-3];
+    }
+  }
+
+  if (angleflag && force->angle) {
+    double **cvatom = force->angle->cvatom;
+    for (i = 0; i < nbond; i++)
+      for (j = 0; j < 9; j++)
+        stress[i][j] += cvatom[i][j];
+  }
+
+  if (dihedralflag && force->dihedral) {
+    double **cvatom = force->dihedral->cvatom;
+    for (i = 0; i < nbond; i++)
+      for (j = 0; j < 9; j++)
+        stress[i][j] += cvatom[i][j];
+  }
+
+  if (improperflag && force->improper) {
+    double **cvatom = force->improper->cvatom;
+    for (i = 0; i < nbond; i++)
+      for (j = 0; j < 9; j++)
+        stress[i][j] += cvatom[i][j];
+  }
+
+  if (kspaceflag && force->kspace) {
+    double **vatom = force->kspace->vatom;
+    for (i = 0; i < nkspace; i++) {
+      for (j = 0; j < 6; j++)
+        stress[i][j] += vatom[i][j];
+      for (j = 6; j < 9; j++)
+        stress[i][j] += vatom[i][j-3];
+    }
+  }
+
+  // add in per-atom contributions from relevant fixes
+  // skip if vatom = NULL
+  // possible during setup phase if fix has not initialized its vatom yet
+  // e.g. fix ave/spatial defined before fix shake,
+  //   and fix ave/spatial uses a per-atom stress from this compute as input
+
+  if (fixflag) {
+    for (int ifix = 0; ifix < modify->nfix; ifix++)
+      if (modify->fix[ifix]->virial_flag) {
+        double **vatom = modify->fix[ifix]->vatom;
+        if (vatom)
+          for (i = 0; i < nlocal; i++) {
+            for (j = 0; j < 6; j++)
+              stress[i][j] += vatom[i][j];
+            for (j = 6; j < 9; j++)
+              stress[i][j] += vatom[i][j-3];
+          }
+      }
+  }
+
+  // communicate ghost virials between neighbor procs
+
+  if (force->newton || (force->kspace && force->kspace->tip4pflag))
+    comm->reverse_comm_compute(this);
+
+  // zero virial of atoms not in group
+  // only do this after comm since ghost contributions must be included
+
+  int *mask = atom->mask;
+
+  for (i = 0; i < nlocal; i++)
+    if (!(mask[i] & groupbit)) {
+      stress[i][0] = 0.0;
+      stress[i][1] = 0.0;
+      stress[i][2] = 0.0;
+      stress[i][3] = 0.0;
+      stress[i][4] = 0.0;
+      stress[i][5] = 0.0;
+      stress[i][6] = 0.0;
+      stress[i][7] = 0.0;
+      stress[i][8] = 0.0;
+    }
+
+  // include kinetic energy term for each atom in group
+  // apply temperature bias is applicable
+  // mvv2e converts mv^2 to energy
+
+  if (keflag) {
+    double **v = atom->v;
+    double *mass = atom->mass;
+    double *rmass = atom->rmass;
+    int *type = atom->type;
+    double mvv2e = force->mvv2e;
+
+    if (biasflag == NOBIAS) {
+      if (rmass) {
+        for (i = 0; i < nlocal; i++)
+          if (mask[i] & groupbit) {
+            onemass = mvv2e * rmass[i];
+            stress[i][0] += onemass*v[i][0]*v[i][0];
+            stress[i][1] += onemass*v[i][1]*v[i][1];
+            stress[i][2] += onemass*v[i][2]*v[i][2];
+            stress[i][3] += onemass*v[i][0]*v[i][1];
+            stress[i][4] += onemass*v[i][0]*v[i][2];
+            stress[i][5] += onemass*v[i][1]*v[i][2];
+            stress[i][6] += onemass*v[i][1]*v[i][0];
+            stress[i][7] += onemass*v[i][2]*v[i][0];
+            stress[i][8] += onemass*v[i][2]*v[i][1];
+          }
+
+      } else {
+        for (i = 0; i < nlocal; i++)
+          if (mask[i] & groupbit) {
+            onemass = mvv2e * mass[type[i]];
+            stress[i][0] += onemass*v[i][0]*v[i][0];
+            stress[i][1] += onemass*v[i][1]*v[i][1];
+            stress[i][2] += onemass*v[i][2]*v[i][2];
+            stress[i][3] += onemass*v[i][0]*v[i][1];
+            stress[i][4] += onemass*v[i][0]*v[i][2];
+            stress[i][5] += onemass*v[i][1]*v[i][2];
+            stress[i][6] += onemass*v[i][1]*v[i][0];
+            stress[i][7] += onemass*v[i][2]*v[i][0];
+            stress[i][8] += onemass*v[i][2]*v[i][1];
+          }
+      }
+
+    } else {
+
+      // invoke temperature if it hasn't been already
+      // this insures bias factor is pre-computed
+
+      if (keflag && temperature->invoked_scalar != update->ntimestep)
+        temperature->compute_scalar();
+
+      if (rmass) {
+        for (i = 0; i < nlocal; i++)
+          if (mask[i] & groupbit) {
+            temperature->remove_bias(i,v[i]);
+            onemass = mvv2e * rmass[i];
+            stress[i][0] += onemass*v[i][0]*v[i][0];
+            stress[i][1] += onemass*v[i][1]*v[i][1];
+            stress[i][2] += onemass*v[i][2]*v[i][2];
+            stress[i][3] += onemass*v[i][0]*v[i][1];
+            stress[i][4] += onemass*v[i][0]*v[i][2];
+            stress[i][5] += onemass*v[i][1]*v[i][2];
+            stress[i][6] += onemass*v[i][1]*v[i][0];
+            stress[i][7] += onemass*v[i][2]*v[i][0];
+            stress[i][8] += onemass*v[i][2]*v[i][1];
+            temperature->restore_bias(i,v[i]);
+          }
+
+      } else {
+        for (i = 0; i < nlocal; i++)
+          if (mask[i] & groupbit) {
+            temperature->remove_bias(i,v[i]);
+            onemass = mvv2e * mass[type[i]];
+            stress[i][0] += onemass*v[i][0]*v[i][0];
+            stress[i][1] += onemass*v[i][1]*v[i][1];
+            stress[i][2] += onemass*v[i][2]*v[i][2];
+            stress[i][3] += onemass*v[i][0]*v[i][1];
+            stress[i][4] += onemass*v[i][0]*v[i][2];
+            stress[i][5] += onemass*v[i][1]*v[i][2];
+            stress[i][6] += onemass*v[i][1]*v[i][0];
+            stress[i][7] += onemass*v[i][2]*v[i][0];
+            stress[i][8] += onemass*v[i][2]*v[i][1];
+            temperature->restore_bias(i,v[i]);
+          }
+      }
+    }
+  }
+
+  // convert to stress*volume units = -pressure*volume
+
+  double nktv2p = -force->nktv2p;
+  for (i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      stress[i][0] *= nktv2p;
+      stress[i][1] *= nktv2p;
+      stress[i][2] *= nktv2p;
+      stress[i][3] *= nktv2p;
+      stress[i][4] *= nktv2p;
+      stress[i][5] *= nktv2p;
+      stress[i][6] *= nktv2p;
+      stress[i][7] *= nktv2p;
+      stress[i][8] *= nktv2p;
+    }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int ComputeCentroidStressAtom::pack_reverse_comm(int n, int first, double *buf)
+{
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    buf[m++] = stress[i][0];
+    buf[m++] = stress[i][1];
+    buf[m++] = stress[i][2];
+    buf[m++] = stress[i][3];
+    buf[m++] = stress[i][4];
+    buf[m++] = stress[i][5];
+    buf[m++] = stress[i][6];
+    buf[m++] = stress[i][7];
+    buf[m++] = stress[i][8];
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCentroidStressAtom::unpack_reverse_comm(int n, int *list, double *buf)
+{
+  int i,j,m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    stress[j][0] += buf[m++];
+    stress[j][1] += buf[m++];
+    stress[j][2] += buf[m++];
+    stress[j][3] += buf[m++];
+    stress[j][4] += buf[m++];
+    stress[j][5] += buf[m++];
+    stress[j][6] += buf[m++];
+    stress[j][7] += buf[m++];
+    stress[j][8] += buf[m++];
+  }
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputeCentroidStressAtom::memory_usage()
+{
+  double bytes = nmax*9 * sizeof(double);
+  return bytes;
+}
diff --git a/src/compute_centroid_stress_atom.h b/src/compute_centroid_stress_atom.h
new file mode 100644
index 0000000000..8d931c179c
--- /dev/null
+++ b/src/compute_centroid_stress_atom.h
@@ -0,0 +1,74 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(centroid/stress/atom,ComputeCentroidStressAtom)
+
+#else
+
+#ifndef LMP_COMPUTE_CENTROID_STRESS_ATOM_H
+#define LMP_COMPUTE_CENTROID_STRESS_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeCentroidStressAtom : public Compute {
+ public:
+  ComputeCentroidStressAtom(class LAMMPS *, int, char **);
+  ~ComputeCentroidStressAtom();
+  void init();
+  void compute_peratom();
+  int pack_reverse_comm(int, int, double *);
+  void unpack_reverse_comm(int, int *, double *);
+  double memory_usage();
+
+ private:
+  int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;
+  int kspaceflag,fixflag,biasflag;
+  Compute *temperature;
+  char *id_temp;
+
+  int nmax;
+  double **stress;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Could not find compute centroid/stress/atom temperature ID
+
+Self-explanatory.
+
+E: Compute centroid/stress/atom temperature ID does not compute temperature
+
+The specified compute must compute temperature.
+
+E: Per-atom virial was not tallied on needed timestep
+
+You are using a thermo keyword that requires potentials to have
+tallied the virial, but they didn't on this timestep.  See the
+variable doc page for ideas on how to make this work.
+
+*/
diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp
index c465a2ab02..7b607bd4db 100644
--- a/src/compute_heat_flux.cpp
+++ b/src/compute_heat_flux.cpp
@@ -65,9 +65,10 @@ ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
     error->all(FLERR,"Compute heat/flux compute ID does not compute ke/atom");
   if (modify->compute[ipe]->peatomflag == 0)
     error->all(FLERR,"Compute heat/flux compute ID does not compute pe/atom");
-  if (modify->compute[istress]->pressatomflag == 0)
+  if (modify->compute[istress]->pressatomflag != 1
+      && modify->compute[istress]->pressatomflag != 2)
     error->all(FLERR,
-               "Compute heat/flux compute ID does not compute stress/atom");
+               "Compute heat/flux compute ID does not compute stress/atom or centroid/stress/atom");
 
   vector = new double[size_vector];
 }
@@ -137,18 +138,48 @@ void ComputeHeatFlux::compute_vector()
   double jv[3] = {0.0,0.0,0.0};
   double eng;
 
-  for (int i = 0; i < nlocal; i++) {
-    if (mask[i] & groupbit) {
-      eng = pe[i] + ke[i];
-      jc[0] += eng*v[i][0];
-      jc[1] += eng*v[i][1];
-      jc[2] += eng*v[i][2];
-      jv[0] -= stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
-        stress[i][4]*v[i][2];
-      jv[1] -= stress[i][3]*v[i][0] + stress[i][1]*v[i][1] +
-        stress[i][5]*v[i][2];
-      jv[2] -= stress[i][4]*v[i][0] + stress[i][5]*v[i][1] +
-        stress[i][2]*v[i][2];
+  // heat flux via centroid atomic stress
+  if (c_stress->pressatomflag == 2) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        eng = pe[i] + ke[i];
+        jc[0] += eng*v[i][0];
+        jc[1] += eng*v[i][1];
+        jc[2] += eng*v[i][2];
+        // stress[0]: rijx*fijx
+        // stress[1]: rijy*fijy
+        // stress[2]: rijz*fijz
+        // stress[3]: rijx*fijy
+        // stress[4]: rijx*fijz
+        // stress[5]: rijy*fijz
+        // stress[6]: rijy*fijx
+        // stress[7]: rijz*fijx
+        // stress[8]: rijz*fijy
+        // jv[0]  = rijx fijx vjx + rijx fijy vjy + rijx fijz vjz
+        jv[0] -= stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
+          stress[i][4]*v[i][2];
+        // jv[1]  = rijy fijx vjx + rijy fijy vjy + rijy fijz vjz
+        jv[1] -= stress[i][6]*v[i][0] + stress[i][1]*v[i][1] +
+          stress[i][5]*v[i][2];
+        // jv[2]  = rijz fijx vjx + rijz fijy vjy + rijz fijz vjz
+        jv[2] -= stress[i][7]*v[i][0] + stress[i][8]*v[i][1] +
+          stress[i][2]*v[i][2];
+      }
+    }
+  } else {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        eng = pe[i] + ke[i];
+        jc[0] += eng*v[i][0];
+        jc[1] += eng*v[i][1];
+        jc[2] += eng*v[i][2];
+        jv[0] -= stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
+          stress[i][4]*v[i][2];
+        jv[1] -= stress[i][3]*v[i][0] + stress[i][1]*v[i][1] +
+          stress[i][5]*v[i][2];
+        jv[2] -= stress[i][4]*v[i][0] + stress[i][5]*v[i][1] +
+          stress[i][2]*v[i][2];
+      }
     }
   }
 
diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp
index 0a78356127..dcb104fc3a 100644
--- a/src/compute_orientorder_atom.cpp
+++ b/src/compute_orientorder_atom.cpp
@@ -493,7 +493,7 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
   }
 
   // calculate Q_l
-  // NOTE: optional W_l_hat and components of Q_qlcomp use these stored Q_l values 
+  // NOTE: optional W_l_hat and components of Q_qlcomp use these stored Q_l values
 
   int jj = 0;
   for (int il = 0; il < nqlist; il++) {
@@ -505,7 +505,7 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
     qn[jj++] = qnormfac * sqrt(qm_sum);
   }
 
-  // TODO: 
+  // TODO:
   // 1. [done]Need to allocate extra memory in qnarray[] for this option
   // 2. [done]Need to add keyword option
   // 3. [done]Need to caclulate Clebsch-Gordan/Wigner 3j coefficients
@@ -673,7 +673,7 @@ void ComputeOrientOrderAtom::init_clebsch_gordan()
         for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) {
           bb2 = m2 - l;
           m = aa2 + bb2 + l;
-          
+
           sum = 0.0;
           for (int z = MAX(0, MAX(-aa2, bb2));
                z <= MIN(l, MIN(l - aa2, l + bb2)); z++) {
@@ -686,7 +686,7 @@ void ComputeOrientOrderAtom::init_clebsch_gordan()
                factorial(aa2 + z) *
                factorial(-bb2 + z));
           }
-          
+
           cc2 = m - l;
           sfaccg = sqrt(factorial(l + aa2) *
                         factorial(l - aa2) *
@@ -695,7 +695,7 @@ void ComputeOrientOrderAtom::init_clebsch_gordan()
                         factorial(l + cc2) *
                         factorial(l - cc2) *
                         (2*l + 1));
-          
+
           sfac1 = factorial(3*l + 1);
           sfac2 = factorial(l);
           dcg = sqrt(sfac2*sfac2*sfac2 / sfac1);
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 8a091ef2ef..c7df5ac264 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -606,8 +606,11 @@ void CreateAtoms::add_random()
   double *boxlo,*boxhi;
 
   // random number generator, same for all procs
+  // warm up the generator 30x to avoid correlations in first-particle
+  // positions if runs are repeated with consecutive seeds
 
   RanPark *random = new RanPark(lmp,seed);
+  for (int ii=0; ii < 30; ii++) random->uniform();
 
   // bounding box for atom creation
   // in real units, even if triclinic
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index 5b7c354595..437f5959db 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -12,7 +12,9 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing authors: Mike Salerno (NRL) added single methods
+   Contributing authors:
+     Mike Salerno (NRL) added single methods
+     Thomas Farmer (ISIS) added single/improper
 ------------------------------------------------------------------------- */
 
 #include "create_bonds.h"
@@ -31,7 +33,7 @@
 
 using namespace LAMMPS_NS;
 
-enum{MANY,SBOND,SANGLE,SDIHEDRAL};
+enum{MANY,SBOND,SANGLE,SDIHEDRAL,SIMPROPER};
 
 /* ---------------------------------------------------------------------- */
 
@@ -100,6 +102,18 @@ void CreateBonds::command(int narg, char **arg)
         (datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4))
       error->all(FLERR,"Illegal create_bonds command");
     iarg = 6;
+  } else if (strcmp(arg[0],"single/improper") == 0) {
+    style = SIMPROPER;
+    if (narg < 6) error->all(FLERR,"Illegal create_bonds command");
+    dtype = force->inumeric(FLERR,arg[1]);
+    datom1 = force->tnumeric(FLERR,arg[2]);
+    datom2 = force->tnumeric(FLERR,arg[3]);
+    datom3 = force->tnumeric(FLERR,arg[4]);
+    datom4 = force->tnumeric(FLERR,arg[5]);
+    if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) ||
+        (datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4))
+      error->all(FLERR,"Illegal create_bonds command");
+    iarg = 6;
   } else error->all(FLERR,"Illegal create_bonds command");
 
   // optional args
@@ -132,6 +146,9 @@ void CreateBonds::command(int narg, char **arg)
   } else if (style == SDIHEDRAL) {
     if (dtype <= 0 || dtype > atom->ndihedraltypes)
       error->all(FLERR,"Invalid dihedral type in create_bonds command");
+  } else if (style == SIMPROPER) {
+    if (dtype <= 0 || dtype > atom->nimpropertypes)
+      error->all(FLERR,"Invalid improper type in create_bonds command");
   }
 
   // invoke creation method
@@ -140,6 +157,7 @@ void CreateBonds::command(int narg, char **arg)
   else if (style == SBOND) single_bond();
   else if (style == SANGLE) single_angle();
   else if (style == SDIHEDRAL) single_dihedral();
+  else if (style == SIMPROPER) single_improper();
 
   // trigger special list build
 
@@ -512,3 +530,89 @@ void CreateBonds::single_dihedral()
     num_dihedral[m]++;
   }
 }
+
+/* ---------------------------------------------------------------------- */
+
+void CreateBonds::single_improper()
+{
+  int m;
+
+  // check that 4 atoms exist
+
+  const int nlocal = atom->nlocal;
+  const int idx1 = atom->map(datom1);
+  const int idx2 = atom->map(datom2);
+  const int idx3 = atom->map(datom3);
+  const int idx4 = atom->map(datom4);
+
+  int count = 0;
+  if ((idx1 >= 0) && (idx1 < nlocal)) count++;
+  if ((idx2 >= 0) && (idx2 < nlocal)) count++;
+  if ((idx3 >= 0) && (idx3 < nlocal)) count++;
+  if ((idx4 >= 0) && (idx4 < nlocal)) count++;
+
+  int allcount;
+  MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
+  if (allcount != 4)
+    error->all(FLERR,"Create_bonds single/improper atoms do not exist");
+
+  // create bond once or 4x if newton_bond set
+
+  int *num_improper = atom->num_improper;
+  int **improper_type = atom->improper_type;
+  tagint **improper_atom1 = atom->improper_atom1;
+  tagint **improper_atom2 = atom->improper_atom2;
+  tagint **improper_atom3 = atom->improper_atom3;
+  tagint **improper_atom4 = atom->improper_atom4;
+
+  if ((m = idx2) >= 0) {
+    if (num_improper[m] == atom->improper_per_atom)
+      error->one(FLERR,
+                 "New improper exceeded impropers per atom in create_bonds");
+    improper_type[m][num_improper[m]] = dtype;
+    improper_atom1[m][num_improper[m]] = datom1;
+    improper_atom2[m][num_improper[m]] = datom2;
+    improper_atom3[m][num_improper[m]] = datom3;
+    improper_atom4[m][num_improper[m]] = datom4;
+    num_improper[m]++;
+  }
+  atom->nimpropers++;
+
+  if (force->newton_bond) return;
+
+  if ((m = idx1) >= 0) {
+    if (num_improper[m] == atom->improper_per_atom)
+      error->one(FLERR,
+                 "New improper exceeded impropers per atom in create_bonds");
+    improper_type[m][num_improper[m]] = dtype;
+    improper_atom1[m][num_improper[m]] = datom1;
+    improper_atom2[m][num_improper[m]] = datom2;
+    improper_atom3[m][num_improper[m]] = datom3;
+    improper_atom4[m][num_improper[m]] = datom4;
+    num_improper[m]++;
+  }
+
+  if ((m = idx3) >= 0) {
+    if (num_improper[m] == atom->improper_per_atom)
+      error->one(FLERR,
+                 "New improper exceeded impropers per atom in create_bonds");
+    improper_type[m][num_improper[m]] = dtype;
+    improper_atom1[m][num_improper[m]] = datom1;
+    improper_atom2[m][num_improper[m]] = datom2;
+    improper_atom3[m][num_improper[m]] = datom3;
+    improper_atom4[m][num_improper[m]] = datom4;
+    num_improper[m]++;
+  }
+
+  if ((m = idx4) >= 0) {
+    if (num_improper[m] == atom->improper_per_atom)
+      error->one(FLERR,
+                 "New improper exceeded impropers per atom in create_bonds");
+    improper_type[m][num_improper[m]] = dtype;
+    improper_atom1[m][num_improper[m]] = datom1;
+    improper_atom2[m][num_improper[m]] = datom2;
+    improper_atom3[m][num_improper[m]] = datom3;
+    improper_atom4[m][num_improper[m]] = datom4;
+    num_improper[m]++;
+  }
+}
diff --git a/src/create_bonds.h b/src/create_bonds.h
index 0c71242ed9..eea99b0113 100644
--- a/src/create_bonds.h
+++ b/src/create_bonds.h
@@ -39,6 +39,7 @@ class CreateBonds : protected Pointers {
   void single_bond();
   void single_angle();
   void single_dihedral();
+  void single_improper();
 };
 
 }
@@ -87,6 +88,10 @@ E: Invalid dihedral type in create_bonds command
 
 UNDOCUMENTED
 
+E: Invalid improper type in create_bonds command
+
+UNDOCUMENTED
+
 E: Create_bonds requires a pair style be defined
 
 Self-explanatory.
@@ -135,4 +140,12 @@ E: New dihedral exceeded dihedrals per atom in create_bonds
 
 UNDOCUMENTED
 
+E: Create_bonds single/improper atoms do not exist
+
+UNDOCUMENTED
+
+E: New improper exceeded impropers per atom in create_bonds
+
+UNDOCUMENTED
+
 */
diff --git a/src/dihedral.cpp b/src/dihedral.cpp
index d2de841dd0..7c6f6aad5e 100644
--- a/src/dihedral.cpp
+++ b/src/dihedral.cpp
@@ -33,9 +33,10 @@ Dihedral::Dihedral(LAMMPS *lmp) : Pointers(lmp)
 
   allocated = 0;
 
-  maxeatom = maxvatom = 0;
+  maxeatom = maxvatom = maxcvatom = 0;
   eatom = NULL;
   vatom = NULL;
+  cvatom = NULL;
   setflag = NULL;
 
   execution_space = Host;
@@ -53,6 +54,7 @@ Dihedral::~Dihedral()
 
   memory->destroy(eatom);
   memory->destroy(vatom);
+  memory->destroy(cvatom);
 }
 
 /* ----------------------------------------------------------------------
@@ -83,9 +85,10 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc)
   eflag_global = eflag % 2;
   eflag_atom = eflag / 2;
 
-  vflag_either = vflag;
   vflag_global = vflag % 4;
-  vflag_atom = vflag / 4;
+  vflag_atom = vflag & 4;
+  cvflag_atom = vflag & 8;
+  vflag_either = vflag_global || vflag_atom;
 
   // reallocate per-atom arrays if necessary
 
@@ -103,6 +106,13 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc)
       memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom");
     }
   }
+  if (cvflag_atom && atom->nmax > maxcvatom) {
+    maxcvatom = atom->nmax;
+    if (alloc) {
+      memory->destroy(cvatom);
+      memory->create(cvatom,comm->nthreads*maxcvatom,9,"dihedral:cvatom");
+    }
+  }
 
   // zero accumulators
 
@@ -125,6 +135,22 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc)
       vatom[i][5] = 0.0;
     }
   }
+  if (cvflag_atom && alloc) {
+    n = atom->nlocal;
+    if (force->newton_bond) n += atom->nghost;
+    for (i = 0; i < n; i++) {
+      cvatom[i][0] = 0.0;
+      cvatom[i][1] = 0.0;
+      cvatom[i][2] = 0.0;
+      cvatom[i][3] = 0.0;
+      cvatom[i][4] = 0.0;
+      cvatom[i][5] = 0.0;
+      cvatom[i][6] = 0.0;
+      cvatom[i][7] = 0.0;
+      cvatom[i][8] = 0.0;
+      cvatom[i][9] = 0.0;
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -250,6 +276,95 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
       }
     }
   }
+
+  // per-atom centroid virial
+  if (cvflag_atom) {
+
+    // r0 = (r1+r2+r3+r4)/4
+    // rij = ri-rj
+    // total virial = r10*f1 + r20*f2 + r30*f3 + r40*f4
+    // vb1: r12
+    // vb2: r32
+    // vb3: r43
+
+    if (newton_bond || i1 < nlocal) {
+      double a1[3];
+
+      // a1 = r10 = (3*r12 - 2*r32 -   r43)/4
+      a1[0] = 0.25*(3*vb1x - 2*vb2x - vb3x);
+      a1[1] = 0.25*(3*vb1y - 2*vb2y - vb3y);
+      a1[2] = 0.25*(3*vb1z - 2*vb2z - vb3z);
+
+      cvatom[i1][0] += a1[0]*f1[0];
+      cvatom[i1][1] += a1[1]*f1[1];
+      cvatom[i1][2] += a1[2]*f1[2];
+      cvatom[i1][3] += a1[0]*f1[1];
+      cvatom[i1][4] += a1[0]*f1[2];
+      cvatom[i1][5] += a1[1]*f1[2];
+      cvatom[i1][6] += a1[1]*f1[0];
+      cvatom[i1][7] += a1[2]*f1[0];
+      cvatom[i1][8] += a1[2]*f1[1];
+    }
+    if (newton_bond || i2 < nlocal) {
+      double a2[3];
+      double f2[3];
+
+      // a2 = r20 = ( -r12 - 2*r32 -   r43)/4
+      a2[0] = 0.25*(-vb1x - 2*vb2x - vb3x);
+      a2[1] = 0.25*(-vb1y - 2*vb2y - vb3y);
+      a2[2] = 0.25*(-vb1z - 2*vb2z - vb3z);
+
+      f2[0] = - f1[0] - f3[0] - f4[0];
+      f2[1] = - f1[1] - f3[1] - f4[1];
+      f2[2] = - f1[2] - f3[2] - f4[2];
+
+      cvatom[i2][0] += a2[0]*f2[0];
+      cvatom[i2][1] += a2[1]*f2[1];
+      cvatom[i2][2] += a2[2]*f2[2];
+      cvatom[i2][3] += a2[0]*f2[1];
+      cvatom[i2][4] += a2[0]*f2[2];
+      cvatom[i2][5] += a2[1]*f2[2];
+      cvatom[i2][6] += a2[1]*f2[0];
+      cvatom[i2][7] += a2[2]*f2[0];
+      cvatom[i2][8] += a2[2]*f2[1];
+    }
+    if (newton_bond || i3 < nlocal) {
+      double a3[3];
+
+      // a3 = r30 = ( -r12 + 2*r32 -   r43)/4
+      a3[0] = 0.25*(-vb1x + 2*vb2x - vb3x);
+      a3[1] = 0.25*(-vb1y + 2*vb2y - vb3y);
+      a3[2] = 0.25*(-vb1z + 2*vb2z - vb3z);
+
+      cvatom[i3][0] += a3[0]*f3[0];
+      cvatom[i3][1] += a3[1]*f3[1];
+      cvatom[i3][2] += a3[2]*f3[2];
+      cvatom[i3][3] += a3[0]*f3[1];
+      cvatom[i3][4] += a3[0]*f3[2];
+      cvatom[i3][5] += a3[1]*f3[2];
+      cvatom[i3][6] += a3[1]*f3[0];
+      cvatom[i3][7] += a3[2]*f3[0];
+      cvatom[i3][8] += a3[2]*f3[1];
+    }
+    if (newton_bond || i4 < nlocal) {
+      double a4[3];
+
+      // a4 = r40 = ( -r12 + 2*r32 + 3*r43)/4
+      a4[0] = 0.25*(-vb1x + 2*vb2x + 3*vb3x);
+      a4[1] = 0.25*(-vb1y + 2*vb2y + 3*vb3y);
+      a4[2] = 0.25*(-vb1z + 2*vb2z + 3*vb3z);
+
+      cvatom[i4][0] += a4[0]*f4[0];
+      cvatom[i4][1] += a4[1]*f4[1];
+      cvatom[i4][2] += a4[2]*f4[2];
+      cvatom[i4][3] += a4[0]*f4[1];
+      cvatom[i4][4] += a4[0]*f4[2];
+      cvatom[i4][5] += a4[1]*f4[2];
+      cvatom[i4][6] += a4[1]*f4[0];
+      cvatom[i4][7] += a4[2]*f4[0];
+      cvatom[i4][8] += a4[2]*f4[1];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -258,5 +373,6 @@ double Dihedral::memory_usage()
 {
   double bytes = comm->nthreads*maxeatom * sizeof(double);
   bytes += comm->nthreads*maxvatom*6 * sizeof(double);
+  bytes += comm->nthreads*maxcvatom*9 * sizeof(double);
   return bytes;
 }
diff --git a/src/dihedral.h b/src/dihedral.h
index f7b0ad1c71..c96891b1c4 100644
--- a/src/dihedral.h
+++ b/src/dihedral.h
@@ -28,6 +28,7 @@ class Dihedral : protected Pointers {
   double energy;                     // accumulated energy
   double virial[6];                  // accumulated virial
   double *eatom,**vatom;             // accumulated per-atom energy/virial
+  double **cvatom;                   // accumulated per-atom centroid virial
 
   // KOKKOS host/device flag and data masks
 
@@ -54,12 +55,12 @@ class Dihedral : protected Pointers {
 
   int evflag;
   int eflag_either,eflag_global,eflag_atom;
-  int vflag_either,vflag_global,vflag_atom;
-  int maxeatom,maxvatom;
+  int vflag_either,vflag_global,vflag_atom,cvflag_atom;
+  int maxeatom,maxvatom,maxcvatom;
 
   void ev_init(int eflag, int vflag, int alloc = 1) {
     if (eflag||vflag) ev_setup(eflag, vflag, alloc);
-    else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0;
+    else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = cvflag_atom = 0;
   }
   void ev_setup(int, int, int alloc = 1);
   void ev_tally(int, int, int, int, int, int, double,
diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp
index 6c0a4338ae..ca5c90093c 100644
--- a/src/dihedral_hybrid.cpp
+++ b/src/dihedral_hybrid.cpp
@@ -21,9 +21,11 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
+
 #define EXTRA 1000
 
 /* ---------------------------------------------------------------------- */
@@ -128,6 +130,14 @@ void DihedralHybrid::compute(int eflag, int vflag)
         for (j = 0; j < 6; j++)
           vatom[i][j] += vatom_substyle[i][j];
     }
+    if (cvflag_atom) {
+      n = atom->nlocal;
+      if (force->newton_bond) n += atom->nghost;
+      double **cvatom_substyle = styles[m]->cvatom;
+      for (i = 0; i < n; i++)
+        for (j = 0; j < 9; j++)
+          cvatom[i][j] += cvatom_substyle[i][j];
+    }
   }
 
   // restore ptrs to original dihedrallist
@@ -319,7 +329,7 @@ void DihedralHybrid::write_restart(FILE *fp)
 void DihedralHybrid::read_restart(FILE *fp)
 {
   int me = comm->me;
-  if (me == 0) fread(&nstyles,sizeof(int),1,fp);
+  if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error);
   MPI_Bcast(&nstyles,1,MPI_INT,0,world);
   styles = new Dihedral*[nstyles];
   keywords = new char*[nstyles];
@@ -328,10 +338,10 @@ void DihedralHybrid::read_restart(FILE *fp)
 
   int n,dummy;
   for (int m = 0; m < nstyles; m++) {
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     keywords[m] = new char[n];
-    if (me == 0) fread(keywords[m],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
     styles[m] = force->new_dihedral(keywords[m],0,dummy);
     styles[m]->read_restart_settings(fp);
@@ -346,6 +356,7 @@ double DihedralHybrid::memory_usage()
 {
   double bytes = maxeatom * sizeof(double);
   bytes += maxvatom*6 * sizeof(double);
+  bytes += maxcvatom*9 * sizeof(double);
   for (int m = 0; m < nstyles; m++) bytes += maxdihedral[m]*5 * sizeof(int);
   for (int m = 0; m < nstyles; m++)
     if (styles[m]) bytes += styles[m]->memory_usage();
diff --git a/src/domain.cpp b/src/domain.cpp
index 372b264013..e894682556 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -352,6 +352,11 @@ void Domain::set_local_box()
 void Domain::reset_box()
 {
   // perform shrink-wrapping
+
+  // nothing to do for empty systems
+
+  if (atom->natoms == 0) return;
+
   // compute extent of atoms on this proc
   // for triclinic, this is done in lamda space
 
diff --git a/src/dump.cpp b/src/dump.cpp
index 57a8decbb0..83b74f1bbc 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -87,6 +87,9 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   buffer_flag = 0;
   padflag = 0;
   pbcflag = 0;
+  time_flag = 0;
+  unit_flag = 0;
+  unit_count = 0;
   delay_flag = 0;
 
   maxfiles = -1;
@@ -545,6 +548,8 @@ void Dump::openfile()
   if (singlefile_opened) return;
   if (multifile == 0) singlefile_opened = 1;
 
+  unit_count = 0;
+
   // if one file per timestep, replace '*' with current timestep
 
   char *filecurrent = filename;
@@ -1119,6 +1124,20 @@ void Dump::modify_params(int narg, char **arg)
       }
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"time") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      if (strcmp(arg[iarg+1],"yes") == 0) time_flag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) time_flag = 0;
+      else error->all(FLERR,"Illegal dump_modify command");
+      iarg += 2;
+
+    } else if (strcmp(arg[iarg],"units") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      if (strcmp(arg[iarg+1],"yes") == 0) unit_flag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) unit_flag = 0;
+      else error->all(FLERR,"Illegal dump_modify command");
+      iarg += 2;
+
     } else {
       int n = modify_param(narg-iarg,&arg[iarg]);
       if (n == 0) error->all(FLERR,"Illegal dump_modify command");
@@ -1127,6 +1146,12 @@ void Dump::modify_params(int narg, char **arg)
   }
 }
 
+/* ---------------------------------------------------------------------- */
+
+double Dump::compute_time()
+{
+  return update->atime + (update->ntimestep - update->atimestep)*update->dt;
+}
 /* ----------------------------------------------------------------------
    return # of bytes of allocated memory
 ------------------------------------------------------------------------- */
diff --git a/src/dump.h b/src/dump.h
index bc7fd2d5a5..17e9434faa 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -75,6 +75,9 @@ class Dump : protected Pointers {
   int sortcol;               // 0 to sort on ID, 1-N on columns
   int sortcolm1;             // sortcol - 1
   int sortorder;             // ASCEND or DESCEND
+  int time_flag;             // 1 if output accumulated time
+  int unit_flag;             // 1 if dump should contain unit information
+  int unit_count;            // # of times the unit information was written
   int delay_flag;            // 1 if delay output until delaystep
   bigint delaystep;
 
@@ -143,6 +146,7 @@ class Dump : protected Pointers {
   virtual int convert_string(int, double *) {return 0;}
   virtual void write_data(int, double *) = 0;
   void pbc_allocate();
+  double compute_time();
 
   void sort();
 #if defined(LMP_QSORT)
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index e2e77cfb77..401b47051d 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -15,9 +15,9 @@
 #include <cstring>
 #include "domain.h"
 #include "atom.h"
-#include "update.h"
 #include "memory.h"
 #include "error.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 
@@ -209,6 +209,12 @@ void DumpAtom::header_binary_triclinic(bigint ndump)
 
 void DumpAtom::header_item(bigint ndump)
 {
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+  }
+  if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time());
+
   fprintf(fp,"ITEM: TIMESTEP\n");
   fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
   fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
@@ -224,6 +230,12 @@ void DumpAtom::header_item(bigint ndump)
 
 void DumpAtom::header_item_triclinic(bigint ndump)
 {
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+  }
+  if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time());
+
   fprintf(fp,"ITEM: TIMESTEP\n");
   fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
   fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index ce83e442c9..4b25896d79 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -20,14 +20,14 @@
 #include "region.h"
 #include "group.h"
 #include "input.h"
-#include "variable.h"
-#include "update.h"
 #include "modify.h"
 #include "compute.h"
 #include "fix.h"
 #include "fix_store.h"
 #include "memory.h"
 #include "error.h"
+#include "update.h"
+#include "variable.h"
 
 using namespace LAMMPS_NS;
 
@@ -248,8 +248,10 @@ DumpCustom::~DumpCustom()
     delete [] vformat;
   }
 
-  for (int i = 0; i < size_one; i++) delete [] format_column_user[i];
-  delete [] format_column_user;
+  if (format_column_user) {
+    for (int i = 0; i < size_one; i++) delete [] format_column_user[i];
+    delete [] format_column_user;
+  }
 
   delete [] columns;
 }
@@ -420,6 +422,12 @@ void DumpCustom::header_binary_triclinic(bigint ndump)
 
 void DumpCustom::header_item(bigint ndump)
 {
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+  }
+  if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time());
+
   fprintf(fp,"ITEM: TIMESTEP\n");
   fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
   fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
@@ -435,6 +443,12 @@ void DumpCustom::header_item(bigint ndump)
 
 void DumpCustom::header_item_triclinic(bigint ndump)
 {
+  if (unit_flag && !unit_count) {
+    ++unit_count;
+    fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+  }
+  if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time());
+
   fprintf(fp,"ITEM: TIMESTEP\n");
   fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
   fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index 9f021a7b6a..21a96d1e8a 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -256,6 +256,12 @@ int DumpLocal::modify_param(int narg, char **arg)
 void DumpLocal::write_header(bigint ndump)
 {
   if (me == 0) {
+    if (unit_flag && !unit_count) {
+      ++unit_count;
+      fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
+    }
+    if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time());
+
     fprintf(fp,"ITEM: TIMESTEP\n");
     fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
     fprintf(fp,"ITEM: NUMBER OF %s\n",label);
diff --git a/src/dump_local.h b/src/dump_local.h
index 91381ba1ec..9b15082995 100644
--- a/src/dump_local.h
+++ b/src/dump_local.h
@@ -29,7 +29,7 @@ class DumpLocal : public Dump {
   DumpLocal(LAMMPS *, int, char **);
   virtual ~DumpLocal();
 
- private:
+ protected:
   int nevery;                // dump frequency to check Fix against
   char *label;               // string for dump file header
 
@@ -55,11 +55,11 @@ class DumpLocal : public Dump {
 
   void init_style();
   int modify_param(int, char **);
-  void write_header(bigint);
+  virtual void write_header(bigint);
   int count();
   void pack(tagint *);
   int convert_string(int, double *);
-  void write_data(int, double *);
+  virtual void write_data(int, double *);
 
   void parse_fields(int, char **);
   int add_compute(char *);
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 45eb38f5c2..0ebdddb9df 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -1055,7 +1055,8 @@ void FixAveChunk::end_of_step()
 
     if (overwrite) {
       long fileend = ftell(fp);
-      if (fileend > 0) ftruncate(fileno(fp),fileend);
+      if ((fileend > 0) && (ftruncate(fileno(fp),fileend)))
+        perror("Error while tuncating output");
     }
   }
 }
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index f65b53efc8..0a8a4cd17f 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -535,7 +535,8 @@ void FixAveCorrelate::end_of_step()
 
     if (overwrite) {
       long fileend = ftell(fp);
-      if (fileend > 0) ftruncate(fileno(fp),fileend);
+      if ((fileend > 0) && (ftruncate(fileno(fp),fileend)))
+        perror("Error while tuncating output");
     }
   }
 
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index 5a5de6d0b6..1a292bf8d2 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -851,7 +851,8 @@ void FixAveHisto::end_of_step()
     fflush(fp);
     if (overwrite) {
       long fileend = ftell(fp);
-      if (fileend > 0) ftruncate(fileno(fp),fileend);
+      if ((fileend > 0) && (ftruncate(fileno(fp),fileend)))
+        perror("Error while tuncating output");
     }
   }
 }
diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp
index f4ff0ae55f..4b86681153 100644
--- a/src/fix_ave_histo_weight.cpp
+++ b/src/fix_ave_histo_weight.cpp
@@ -493,7 +493,8 @@ void FixAveHistoWeight::end_of_step()
     fflush(fp);
     if (overwrite) {
       long fileend = ftell(fp);
-      if (fileend > 0) ftruncate(fileno(fp),fileend);
+      if ((fileend > 0) && (ftruncate(fileno(fp),fileend)))
+        perror("Error while tuncating output");
     }
   }
 }
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 05d556d0c8..9b8dd13f05 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -698,7 +698,8 @@ void FixAveTime::invoke_scalar(bigint ntimestep)
 
     if (overwrite) {
       long fileend = ftell(fp);
-      if (fileend > 0) ftruncate(fileno(fp),fileend);
+      if ((fileend > 0) && (ftruncate(fileno(fp),fileend)))
+        perror("Error while tuncating output");
     }
   }
 }
@@ -909,7 +910,8 @@ void FixAveTime::invoke_vector(bigint ntimestep)
     fflush(fp);
     if (overwrite) {
       long fileend = ftell(fp);
-      if (fileend > 0) ftruncate(fileno(fp),fileend);
+      if ((fileend > 0) && (ftruncate(fileno(fp),fileend)))
+        perror("Error while tuncating output");
     }
   }
 }
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 14ba913c01..d130717470 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -37,7 +37,8 @@ enum{CONSTANT,EQUAL};
 
 FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), xstr(NULL), ystr(NULL), zstr(NULL)
+  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL),
+  xstr(NULL), ystr(NULL), zstr(NULL)
 {
   if (narg < 5) error->all(FLERR,"Illegal fix gravity command");
 
@@ -61,8 +62,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
     mstyle = CONSTANT;
   }
 
+  int iarg;
+
   if (strcmp(arg[4],"chute") == 0) {
-    if (narg != 6) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 6) error->all(FLERR,"Illegal fix gravity command");
     style = CHUTE;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -73,9 +76,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       vert = force->numeric(FLERR,arg[5]);
       vstyle = CONSTANT;
     }
+    iarg = 6;
 
   } else if (strcmp(arg[4],"spherical") == 0) {
-    if (narg != 7) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 7) error->all(FLERR,"Illegal fix gravity command");
     style = SPHERICAL;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -95,9 +99,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       theta = force->numeric(FLERR,arg[6]);
       tstyle = CONSTANT;
     }
+    iarg = 7;
 
   } else if (strcmp(arg[4],"vector") == 0) {
-    if (narg != 8) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 8) error->all(FLERR,"Illegal fix gravity command");
     style = VECTOR;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -126,9 +131,23 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       zdir = force->numeric(FLERR,arg[7]);
       zstyle = CONSTANT;
     }
+    iarg = 8;
 
   } else error->all(FLERR,"Illegal fix gravity command");
 
+  // optional keywords
+
+  disable = 0;
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"disable") == 0) {
+      disable = 1;
+      iarg++;
+    } else error->all(FLERR,"Illegal fix gravity command");
+  }
+
+  // initializations
+
   degree2rad = MY_PI/180.0;
   time_origin = update->ntimestep;
 
@@ -266,6 +285,12 @@ void FixGravity::post_force(int /*vflag*/)
     set_acceleration();
   }
 
+  // just exit if application of force is disabled
+
+  if (disable) return;
+
+  // apply gravity force to each particle
+
   double **x = atom->x;
   double **f = atom->f;
   double *rmass = atom->rmass;
@@ -338,9 +363,9 @@ void FixGravity::set_acceleration()
     }
   }
 
-  xacc = magnitude*xgrav;
-  yacc = magnitude*ygrav;
-  zacc = magnitude*zgrav;
+  gvec[0] = xacc = magnitude*xgrav;
+  gvec[1] = yacc = magnitude*ygrav;
+  gvec[2] = zacc = magnitude*zgrav;
 }
 
 /* ----------------------------------------------------------------------
@@ -357,3 +382,16 @@ double FixGravity::compute_scalar()
   }
   return egrav_all;
 }
+
+/* ----------------------------------------------------------------------
+   extract current gravity direction vector
+------------------------------------------------------------------------- */
+
+void *FixGravity::extract(const char *name, int &dim)
+{
+  if (strcmp(name,"gvec") == 0) {
+    dim = 1;
+    return (void *) gvec;
+  }
+  return NULL;
+}
diff --git a/src/fix_gravity.h b/src/fix_gravity.h
index 1f18ee274b..ba6a61ee0d 100644
--- a/src/fix_gravity.h
+++ b/src/fix_gravity.h
@@ -36,9 +36,10 @@ class FixGravity : public Fix {
   virtual void post_force(int);
   virtual void post_force_respa(int, int, int);
   double compute_scalar();
+  void *extract(const char *, int &);
 
  protected:
-  int style;
+  int style,disable;
   double magnitude;
   double vert,phi,theta;
   double xdir,ydir,zdir;
@@ -46,6 +47,8 @@ class FixGravity : public Fix {
   double degree2rad;
   int ilevel_respa;
   int time_origin;
+  double gvec[3];
+
   int eflag;
   double egrav,egrav_all;
 
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index 1e86a90218..f8f85fcf30 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -14,6 +14,9 @@
 /* ----------------------------------------------------------------------
    Contributing authors: Carolyn Phillips (U Mich), reservoir energy tally
                          Aidan Thompson (SNL) GJF formulation
+                         Charles Sievers & Niels Gronbech-Jensen (UC Davis)
+                             updated GJF formulation and included
+                             statistically correct 2GJ velocity
 ------------------------------------------------------------------------- */
 
 #include "fix_langevin.h"
@@ -35,6 +38,7 @@
 #include "memory.h"
 #include "error.h"
 #include "group.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -50,7 +54,7 @@ enum{CONSTANT,EQUAL,ATOM};
 FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
   gjfflag(0), gfactor1(NULL), gfactor2(NULL), ratio(NULL), tstr(NULL),
-  flangevin(NULL), tforce(NULL), franprev(NULL), id_temp(NULL), random(NULL)
+  flangevin(NULL), tforce(NULL), franprev(NULL), lv(NULL), id_temp(NULL), random(NULL)
 {
   if (narg < 7) error->all(FLERR,"Illegal fix langevin command");
 
@@ -96,6 +100,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
   oflag = 0;
   tallyflag = 0;
   zeroflag = 0;
+  osflag = 0;
 
   int iarg = 7;
   while (iarg < narg) {
@@ -106,8 +111,18 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
     } else if (strcmp(arg[iarg],"gjf") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command");
-      if (strcmp(arg[iarg+1],"no") == 0) gjfflag = 0;
-      else if (strcmp(arg[iarg+1],"yes") == 0) gjfflag = 1;
+      if (strcmp(arg[iarg+1],"no") == 0) {
+        gjfflag = 0;
+        osflag = 0;
+      }
+      else if (strcmp(arg[iarg+1],"vfull") == 0) {
+        gjfflag = 1;
+        osflag = 1;
+      }
+      else if (strcmp(arg[iarg+1],"vhalf") == 0) {
+        gjfflag = 1;
+        osflag = 0;
+      }
       else error->all(FLERR,"Illegal fix langevin command");
       iarg += 2;
     } else if (strcmp(arg[iarg],"omega") == 0) {
@@ -153,6 +168,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
   flangevin = NULL;
   flangevin_allocated = 0;
   franprev = NULL;
+  lv = NULL;
   tforce = NULL;
   maxatom1 = maxatom2 = 0;
 
@@ -161,7 +177,6 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
   // no need to set peratom_flag, b/c data is for internal use only
 
   if (gjfflag) {
-    nvalues = 3;
     grow_arrays(atom->nmax);
     atom->add_callback(0);
 
@@ -172,6 +187,9 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
       franprev[i][0] = 0.0;
       franprev[i][1] = 0.0;
       franprev[i][2] = 0.0;
+      lv[i][0] = 0.0;
+      lv[i][1] = 0.0;
+      lv[i][2] = 0.0;
     }
   }
 
@@ -192,6 +210,7 @@ FixLangevin::~FixLangevin()
 
   if (gjfflag) {
     memory->destroy(franprev);
+    memory->destroy(lv);
     atom->delete_callback(id,0);
   }
 }
@@ -201,6 +220,7 @@ FixLangevin::~FixLangevin()
 int FixLangevin::setmask()
 {
   int mask = 0;
+  if (gjfflag) mask |= INITIAL_INTEGRATE;
   mask |= POST_FORCE;
   mask |= POST_FORCE_RESPA;
   mask |= END_OF_STEP;
@@ -212,6 +232,21 @@ int FixLangevin::setmask()
 
 void FixLangevin::init()
 {
+  if (gjfflag) {
+    if (t_period*2 == update->dt)
+      error->all(FLERR,"Fix langevin gjf cannot have t_period equal to dt/2");
+
+    // warn if any integrate fix comes after this one
+    int before = 1;
+    int flag = 0;
+    for (int i = 0; i < modify->nfix; i++) {
+      if (strcmp(id,modify->fix[i]->id) == 0) before = 0;
+      else if ((modify->fmask[i] && utils::strmatch(modify->fix[i]->style,"^nve")) && before) flag = 1;
+    }
+    if (flag)
+      error->all(FLERR,"Fix langevin gjf should come before fix nve");
+  }
+
   if (oflag && !atom->sphere_flag)
     error->all(FLERR,"Fix langevin omega requires atom style sphere");
   if (ascale && !atom->ellipsoid_flag)
@@ -261,9 +296,14 @@ void FixLangevin::init()
   if (!atom->rmass) {
     for (int i = 1; i <= atom->ntypes; i++) {
       gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
-      gfactor2[i] = sqrt(atom->mass[i]) *
-        sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
-        force->ftm2v;
+      if (gjfflag)
+        gfactor2[i] = sqrt(atom->mass[i]) *
+          sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) /
+          force->ftm2v;
+      else
+        gfactor2[i] = sqrt(atom->mass[i]) *
+          sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
+          force->ftm2v;
       gfactor1[i] *= 1.0/ratio[i];
       gfactor2[i] *= 1.0/sqrt(ratio[i]);
     }
@@ -275,14 +315,60 @@ void FixLangevin::init()
   if (strstr(update->integrate_style,"respa"))
     nlevels_respa = ((Respa *) update->integrate)->nlevels;
 
-  if (gjfflag) gjffac = 1.0/(1.0+update->dt/2.0/t_period);
+  if (utils::strmatch(update->integrate_style,"^respa") && gjfflag)
+    error->all(FLERR,"Fix langevin gjf and respa are not compatible");
 
+  if (gjfflag) gjfa = (1.0-update->dt/2.0/t_period)/(1.0+update->dt/2.0/t_period);
+  if (gjfflag) gjfsib = sqrt(1.0+update->dt/2.0/t_period);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixLangevin::setup(int vflag)
 {
+  if (gjfflag) {
+    double dtfm;
+    double dt = update->dt;
+    double **v = atom->v;
+    double **f = atom->f;
+    int *mask = atom->mask;
+    int nlocal = atom->nlocal;
+    double *rmass = atom->rmass;
+    double *mass = atom->mass;
+    int *type = atom->type;
+    if (rmass) {
+      for (int i = 0; i < nlocal; i++)
+        if (mask[i] & groupbit) {
+          dtfm = 0.5 * dt / rmass[i];
+          v[i][0] -= dtfm * f[i][0];
+          v[i][1] -= dtfm * f[i][1];
+          v[i][2] -= dtfm * f[i][2];
+          if (tbiasflag)
+            temperature->remove_bias(i,v[i]);
+          v[i][0] /= gjfa*gjfsib*gjfsib;
+          v[i][1] /= gjfa*gjfsib*gjfsib;
+          v[i][2] /= gjfa*gjfsib*gjfsib;
+          if (tbiasflag)
+            temperature->restore_bias(i,v[i]);
+        }
+
+    } else {
+      for (int i = 0; i < nlocal; i++)
+        if (mask[i] & groupbit) {
+          dtfm = 0.5 * dt / mass[type[i]];
+          v[i][0] -= dtfm * f[i][0];
+          v[i][1] -= dtfm * f[i][1];
+          v[i][2] -= dtfm * f[i][2];
+          if (tbiasflag)
+            temperature->remove_bias(i,v[i]);
+          v[i][0] /= gjfa*gjfsib*gjfsib;
+          v[i][1] /= gjfa*gjfsib*gjfsib;
+          v[i][2] /= gjfa*gjfsib*gjfsib;
+          if (tbiasflag)
+            temperature->restore_bias(i,v[i]);
+        }
+    }
+  }
   if (strstr(update->integrate_style,"verlet"))
     post_force(vflag);
   else {
@@ -290,6 +376,61 @@ void FixLangevin::setup(int vflag)
     post_force_respa(vflag,nlevels_respa-1,0);
     ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
   }
+  if (gjfflag) {
+    double dtfm;
+    double dt = update->dt;
+    double **f = atom->f;
+    double **v = atom->v;
+    int *mask = atom->mask;
+    int nlocal = atom->nlocal;
+    double *rmass = atom->rmass;
+    double *mass = atom->mass;
+    int *type = atom->type;
+    if (rmass) {
+      for (int i = 0; i < nlocal; i++)
+        if (mask[i] & groupbit) {
+          dtfm = 0.5 * dt / rmass[i];
+          v[i][0] += dtfm * f[i][0];
+          v[i][1] += dtfm * f[i][1];
+          v[i][2] += dtfm * f[i][2];
+          lv[i][0] = v[i][0];
+          lv[i][1] = v[i][1];
+          lv[i][2] = v[i][2];
+        }
+//
+    } else {
+      for (int i = 0; i < nlocal; i++)
+        if (mask[i] & groupbit) {
+          dtfm = 0.5 * dt / mass[type[i]];
+          v[i][0] += dtfm * f[i][0];
+          v[i][1] += dtfm * f[i][1];
+          v[i][2] += dtfm * f[i][2];
+          lv[i][0] = v[i][0];
+          lv[i][1] = v[i][1];
+          lv[i][2] = v[i][2];
+        }
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixLangevin::initial_integrate(int /* vflag */)
+{
+  double **v = atom->v;
+  double **f = atom->f;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      f[i][0] /= gjfa;
+      f[i][1] /= gjfa;
+      f[i][2] /= gjfa;
+      v[i][0] = lv[i][0];
+      v[i][1] = lv[i][1];
+      v[i][2] = lv[i][2];
+    }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -304,7 +445,7 @@ void FixLangevin::post_force(int /*vflag*/)
 
   if (tstyle == ATOM)
     if (gjfflag)
-      if (tallyflag)
+      if (tallyflag || osflag)
         if (tbiasflag == BIAS)
           if (rmass)
             if (zeroflag) post_force_templated<1,1,1,1,1,1>();
@@ -335,7 +476,7 @@ void FixLangevin::post_force(int /*vflag*/)
             if (zeroflag) post_force_templated<1,1,0,0,0,1>();
             else          post_force_templated<1,1,0,0,0,0>();
     else
-      if (tallyflag)
+      if (tallyflag || osflag)
         if (tbiasflag == BIAS)
           if (rmass)
             if (zeroflag) post_force_templated<1,0,1,1,1,1>();
@@ -367,7 +508,7 @@ void FixLangevin::post_force(int /*vflag*/)
             else          post_force_templated<1,0,0,0,0,0>();
   else
     if (gjfflag)
-      if (tallyflag)
+      if (tallyflag  || osflag)
         if (tbiasflag == BIAS)
           if (rmass)
             if (zeroflag) post_force_templated<0,1,1,1,1,1>();
@@ -398,7 +539,7 @@ void FixLangevin::post_force(int /*vflag*/)
             if (zeroflag) post_force_templated<0,1,0,0,0,1>();
             else          post_force_templated<0,1,0,0,0,0>();
     else
-      if (tallyflag)
+      if (tallyflag || osflag)
         if (tbiasflag == BIAS)
           if (rmass)
             if (zeroflag) post_force_templated<0,0,1,1,1,1>();
@@ -511,7 +652,10 @@ void FixLangevin::post_force_templated()
       if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]);
       if (Tp_RMASS) {
         gamma1 = -rmass[i] / t_period / ftm2v;
-        gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
+        if (Tp_GJF)
+          gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v;
+        else
+          gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
         gamma1 *= 1.0/ratio[type[i]];
         gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
       } else {
@@ -519,9 +663,15 @@ void FixLangevin::post_force_templated()
         gamma2 = gfactor2[type[i]] * tsqrt;
       }
 
-      fran[0] = gamma2*(random->uniform()-0.5);
-      fran[1] = gamma2*(random->uniform()-0.5);
-      fran[2] = gamma2*(random->uniform()-0.5);
+      if (Tp_GJF) {
+        fran[0] = gamma2*random->gaussian();
+        fran[1] = gamma2*random->gaussian();
+        fran[2] = gamma2*random->gaussian();
+      } else {
+        fran[0] = gamma2*(random->uniform()-0.5);
+        fran[1] = gamma2*(random->uniform()-0.5);
+        fran[2] = gamma2*(random->uniform()-0.5);
+      }
 
       if (Tp_BIAS) {
         temperature->remove_bias(i,v[i]);
@@ -539,6 +689,16 @@ void FixLangevin::post_force_templated()
       }
 
       if (Tp_GJF) {
+        if (Tp_BIAS)
+          temperature->remove_bias(i,v[i]);
+        lv[i][0] = gjfsib*v[i][0];
+        lv[i][1] = gjfsib*v[i][1];
+        lv[i][2] = gjfsib*v[i][2];
+        if (Tp_BIAS)
+          temperature->restore_bias(i,v[i]);
+        if (Tp_BIAS)
+          temperature->restore_bias(i,lv[i]);
+
         fswap = 0.5*(fran[0]+franprev[i][0]);
         franprev[i][0] = fran[0];
         fran[0] = fswap;
@@ -549,32 +709,44 @@ void FixLangevin::post_force_templated()
         franprev[i][2] = fran[2];
         fran[2] = fswap;
 
-        fdrag[0] *= gjffac;
-        fdrag[1] *= gjffac;
-        fdrag[2] *= gjffac;
-        fran[0] *= gjffac;
-        fran[1] *= gjffac;
-        fran[2] *= gjffac;
-        f[i][0] *= gjffac;
-        f[i][1] *= gjffac;
-        f[i][2] *= gjffac;
+        fdrag[0] *= gjfa;
+        fdrag[1] *= gjfa;
+        fdrag[2] *= gjfa;
+        fran[0] *= gjfa;
+        fran[1] *= gjfa;
+        fran[2] *= gjfa;
+        f[i][0] *= gjfa;
+        f[i][1] *= gjfa;
+        f[i][2] *= gjfa;
       }
 
       f[i][0] += fdrag[0] + fran[0];
       f[i][1] += fdrag[1] + fran[1];
       f[i][2] += fdrag[2] + fran[2];
 
-      if (Tp_TALLY) {
-        flangevin[i][0] = fdrag[0] + fran[0];
-        flangevin[i][1] = fdrag[1] + fran[1];
-        flangevin[i][2] = fdrag[2] + fran[2];
-      }
-
       if (Tp_ZERO) {
         fsum[0] += fran[0];
         fsum[1] += fran[1];
         fsum[2] += fran[2];
       }
+
+      if (Tp_TALLY) {
+        if (Tp_GJF) {
+          fdrag[0] = gamma1*lv[i][0]/gjfsib/gjfsib;
+          fdrag[1] = gamma1*lv[i][1]/gjfsib/gjfsib;
+          fdrag[2] = gamma1*lv[i][2]/gjfsib/gjfsib;
+          fswap = (2*fran[0]/gjfa - franprev[i][0])/gjfsib;
+          fran[0] = fswap;
+          fswap = (2*fran[1]/gjfa - franprev[i][1])/gjfsib;
+          fran[1] = fswap;
+          fswap = (2*fran[2]/gjfa - franprev[i][2])/gjfsib;
+          fran[2] = fswap;
+        }
+        flangevin[i][0] = fdrag[0] + fran[0];
+        flangevin[i][1] = fdrag[1] + fran[1];
+        flangevin[i][2] = fdrag[2] + fran[2];
+
+      }
     }
   }
 
@@ -754,18 +926,71 @@ void FixLangevin::angmom_thermostat()
 
 void FixLangevin::end_of_step()
 {
-  if (!tallyflag) return;
+  if (!tallyflag && !gjfflag) return;
 
   double **v = atom->v;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
+  double dtfm;
+  double dt = update->dt;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  double **f = atom->f;
+  int *type = atom->type;
 
   energy_onestep = 0.0;
 
-  for (int i = 0; i < nlocal; i++)
-    if (mask[i] & groupbit)
-      energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
-        flangevin[i][2]*v[i][2];
+  if (tallyflag) {
+    if (gjfflag) {
+      for (int i = 0; i < nlocal; i++)
+        if (mask[i] & groupbit) {
+          if (tbiasflag)
+            temperature->remove_bias(i, lv[i]);
+          energy_onestep += flangevin[i][0]*lv[i][0] + flangevin[i][1]*lv[i][1] +
+                            flangevin[i][2]*lv[i][2];
+          if (tbiasflag)
+            temperature->restore_bias(i, lv[i]);
+        }
+    }
+    else
+      for (int i = 0; i < nlocal; i++)
+        if (mask[i] & groupbit)
+          energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
+                            flangevin[i][2]*v[i][2];
+  }
+
+  if (gjfflag) {
+    double tmp[3];
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        tmp[0] = v[i][0];
+        tmp[1] = v[i][1];
+        tmp[2] = v[i][2];
+        if (!osflag) {
+          v[i][0] = lv[i][0];
+          v[i][1] = lv[i][1];
+          v[i][2] = lv[i][2];
+        } else {
+          if (atom->rmass) {
+            dtfm = force->ftm2v * 0.5 * dt / rmass[i];
+          } else {
+            dtfm = force->ftm2v * 0.5 * dt / mass[type[i]];
+          }
+          v[i][0] = 0.5 * gjfsib*gjfsib*(v[i][0] + dtfm * f[i][0] / gjfa) +
+                    dtfm * 0.5 * (gjfsib * flangevin[i][0] - franprev[i][0]) +
+                    (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][0];
+          v[i][1] = 0.5 * gjfsib*gjfsib*(v[i][1] + dtfm * f[i][1] / gjfa) +
+                    dtfm * 0.5 * (gjfsib * flangevin[i][1] - franprev[i][1]) +
+                    (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][1];
+          v[i][2] = 0.5 * gjfsib*gjfsib*(v[i][2] + dtfm * f[i][2] / gjfa) +
+                    dtfm * 0.5 * (gjfsib * flangevin[i][2] - franprev[i][2]) +
+                    (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][2];
+        }
+        lv[i][0] = tmp[0];
+        lv[i][1] = tmp[1];
+        lv[i][2] = tmp[2];
+      }
+  }
 
   energy += energy_onestep*update->dt;
 }
@@ -783,12 +1008,21 @@ void FixLangevin::reset_dt()
 {
   if (atom->mass) {
     for (int i = 1; i <= atom->ntypes; i++) {
-      gfactor2[i] = sqrt(atom->mass[i]) *
-        sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
-        force->ftm2v;
+      if (gjfflag)
+        gfactor2[i] = sqrt(atom->mass[i]) *
+          sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) /
+          force->ftm2v;
+      else
+        gfactor2[i] = sqrt(atom->mass[i]) *
+          sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
+          force->ftm2v;
       gfactor2[i] *= 1.0/sqrt(ratio[i]);
     }
   }
+  if (gjfflag) {
+    gjfa = (1.0-update->dt/2.0/t_period)/(1.0+update->dt/2.0/t_period);
+    gjfsib = sqrt(1.0+update->dt/2.0/t_period);
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -831,11 +1065,24 @@ double FixLangevin::compute_scalar()
 
   if (update->ntimestep == update->beginstep) {
     energy_onestep = 0.0;
-    for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit)
-        energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
-          flangevin[i][2]*v[i][2];
-    energy = 0.5*energy_onestep*update->dt;
+    if (!gjfflag) {
+      for (int i = 0; i < nlocal; i++)
+        if (mask[i] & groupbit)
+          energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
+                            flangevin[i][2]*v[i][2];
+      energy = 0.5*energy_onestep*update->dt;
+    } else {
+      for (int i = 0; i < nlocal; i++)
+        if (mask[i] & groupbit) {
+          if (tbiasflag)
+            temperature->remove_bias(i, lv[i]);
+          energy_onestep += flangevin[i][0]*lv[i][0] + flangevin[i][1]*lv[i][1] +
+                            flangevin[i][2]*lv[i][2];
+          if (tbiasflag)
+            temperature->restore_bias(i, lv[i]);
+        }
+      energy = -0.5*energy_onestep*update->dt;
+    }
   }
 
   // convert midstep energy back to previous fullstep energy
@@ -867,8 +1114,8 @@ void *FixLangevin::extract(const char *str, int &dim)
 double FixLangevin::memory_usage()
 {
   double bytes = 0.0;
-  if (gjfflag) bytes += atom->nmax*3 * sizeof(double);
-  if (tallyflag) bytes += atom->nmax*3 * sizeof(double);
+  if (gjfflag) bytes += atom->nmax*6 * sizeof(double);
+  if (tallyflag || osflag) bytes += atom->nmax*3 * sizeof(double);
   if (tforce) bytes += atom->nmax * sizeof(double);
   return bytes;
 }
@@ -880,6 +1127,7 @@ double FixLangevin::memory_usage()
 void FixLangevin::grow_arrays(int nmax)
 {
   memory->grow(franprev,nmax,3,"fix_langevin:franprev");
+  memory->grow(lv,nmax,3,"fix_langevin:lv");
 }
 
 /* ----------------------------------------------------------------------
@@ -888,8 +1136,12 @@ void FixLangevin::grow_arrays(int nmax)
 
 void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
 {
-  for (int m = 0; m < nvalues; m++)
-    franprev[j][m] = franprev[i][m];
+  franprev[j][0] = franprev[i][0];
+  franprev[j][1] = franprev[i][1];
+  franprev[j][2] = franprev[i][2];
+  lv[j][0] = lv[i][0];
+  lv[j][1] = lv[i][1];
+  lv[j][2] = lv[i][2];
 }
 
 /* ----------------------------------------------------------------------
@@ -898,8 +1150,14 @@ void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
 
 int FixLangevin::pack_exchange(int i, double *buf)
 {
-  for (int m = 0; m < nvalues; m++) buf[m] = franprev[i][m];
-  return nvalues;
+  int n = 0;
+  buf[n++] = franprev[i][0];
+  buf[n++] = franprev[i][1];
+  buf[n++] = franprev[i][2];
+  buf[n++] = lv[i][0];
+  buf[n++] = lv[i][1];
+  buf[n++] = lv[i][2];
+  return n;
 }
 
 /* ----------------------------------------------------------------------
@@ -908,6 +1166,12 @@ int FixLangevin::pack_exchange(int i, double *buf)
 
 int FixLangevin::unpack_exchange(int nlocal, double *buf)
 {
-  for (int m = 0; m < nvalues; m++) franprev[nlocal][m] = buf[m];
-  return nvalues;
+  int n = 0;
+  franprev[nlocal][0] = buf[n++];
+  franprev[nlocal][1] = buf[n++];
+  franprev[nlocal][2] = buf[n++];
+  lv[nlocal][0] = buf[n++];
+  lv[nlocal][1] = buf[n++];
+  lv[nlocal][2] = buf[n++];
+  return n;
 }
diff --git a/src/fix_langevin.h b/src/fix_langevin.h
index 4b5570ac2e..868b71a44d 100644
--- a/src/fix_langevin.h
+++ b/src/fix_langevin.h
@@ -31,6 +31,7 @@ class FixLangevin : public Fix {
   int setmask();
   void init();
   void setup(int);
+  virtual void initial_integrate(int);
   virtual void post_force(int);
   void post_force_respa(int, int, int);
   virtual void end_of_step();
@@ -46,7 +47,7 @@ class FixLangevin : public Fix {
   int unpack_exchange(int, double *);
 
  protected:
-  int gjfflag,oflag,tallyflag,zeroflag,tbiasflag;
+  int gjfflag,nvalues,osflag,oflag,tallyflag,zeroflag,tbiasflag;
   int flangevin_allocated;
   double ascale;
   double t_start,t_stop,t_period,t_target;
@@ -54,7 +55,7 @@ class FixLangevin : public Fix {
   double energy,energy_onestep;
   double tsqrt;
   int tstyle,tvar;
-  double gjffac;
+  double gjfa, gjfsib; //gjf a and gjf sqrt inverse b
   char *tstr;
 
   class AtomVecEllipsoid *avec;
@@ -63,7 +64,7 @@ class FixLangevin : public Fix {
   double **flangevin;
   double *tforce;
   double **franprev;
-  int nvalues;
+  double **lv; //half step velocity
 
   char *id_temp;
   class Compute *temperature;
@@ -139,6 +140,18 @@ E: Fix_modify temperature ID does not compute temperature
 
 The compute ID assigned to the fix must compute temperature.
 
+E: Fix langevin gjf cannot have period equal to dt/2
+
+If the period is equal to dt/2 then division by zero will happen.
+
+E: Fix langevin gjf should come before fix nve
+
+Self-explanatory
+
+E: Fix langevin gjf and respa are not compatible
+
+Self-explanatory
+
 W: Group for fix_modify temp != fix group
 
 The fix_modify command is specifying a temperature computation that
diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp
index 673e2b1c06..86865ba316 100644
--- a/src/fix_neigh_history.cpp
+++ b/src/fix_neigh_history.cpp
@@ -407,7 +407,7 @@ void FixNeighHistory::pre_exchange_newton()
         m = npartner[j]++;
         partner[j][m] = tag[i];
         jvalues = &valuepartner[j][dnum*m];
-        if (pair->nondefault_history_transfer) 
+        if (pair->nondefault_history_transfer)
           pair->transfer_history(onevalues,jvalues);
         else for (n = 0; n < dnum; n++) jvalues[n] = -onevalues[n];
       }
@@ -521,7 +521,7 @@ void FixNeighHistory::pre_exchange_no_newton()
           m = npartner[j]++;
           partner[j][m] = tag[i];
           jvalues = &valuepartner[j][dnum*m];
-          if (pair->nondefault_history_transfer) 
+          if (pair->nondefault_history_transfer)
             pair->transfer_history(onevalues, jvalues);
           else for (n = 0; n < dnum; n++) jvalues[n] = -onevalues[n];
         }
diff --git a/src/fix_print.cpp b/src/fix_print.cpp
index dc76fc39f9..54a706d24b 100644
--- a/src/fix_print.cpp
+++ b/src/fix_print.cpp
@@ -134,7 +134,10 @@ void FixPrint::init()
     if (next_print <= update->ntimestep)
       error->all(FLERR,"Fix print timestep variable returned a bad timestep");
   } else {
-     next_print = (update->ntimestep/nevery)*nevery + nevery;
+    if (update->ntimestep % nevery)
+      next_print = (update->ntimestep/nevery)*nevery + nevery;
+    else
+      next_print = update->ntimestep;
   }
 
   // add next_print to all computes that store invocation times
@@ -146,6 +149,13 @@ void FixPrint::init()
 
 /* ---------------------------------------------------------------------- */
 
+void FixPrint::setup(int /* vflag */)
+{
+  end_of_step();
+}
+
+/* ---------------------------------------------------------------------- */
+
 void FixPrint::end_of_step()
 {
   if (update->ntimestep != next_print) return;
@@ -168,6 +178,7 @@ void FixPrint::end_of_step()
   } else {
     next_print = (update->ntimestep/nevery)*nevery + nevery;
   }
+
   modify->addstep_compute(next_print);
 
   if (me == 0) {
diff --git a/src/fix_print.h b/src/fix_print.h
index 5644160220..6ee39318e8 100644
--- a/src/fix_print.h
+++ b/src/fix_print.h
@@ -29,6 +29,7 @@ class FixPrint : public Fix {
   FixPrint(class LAMMPS *, int, char **);
   ~FixPrint();
   void init();
+  void setup(int);
   int setmask();
   void end_of_step();
 
diff --git a/src/force.cpp b/src/force.cpp
index 1a826b2843..63d1fcbe31 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -21,6 +21,7 @@
 #include "style_improper.h"
 #include "style_pair.h"
 #include "style_kspace.h"
+#include "atom.h"
 #include "comm.h"
 #include "pair.h"
 #include "pair_hybrid.h"
@@ -196,6 +197,28 @@ void Force::init()
   if (angle) angle->init();
   if (dihedral) dihedral->init();
   if (improper) improper->init();
+
+  // print warnings if topology and force field are inconsistent
+
+  if (comm->me == 0) {
+    if (!bond && (atom->nbonds > 0)) {
+      error->warning(FLERR,"Bonds are defined but no bond style is set");
+      if ((special_lj[1] != 1.0) || (special_coul[1] != 1.0))
+        error->warning(FLERR,"Likewise 1-2 special neighbor interactions != 1.0");
+    }
+    if (!angle && (atom->nangles > 0)) {
+      error->warning(FLERR,"Angles are defined but no angle style is set");
+      if ((special_lj[2] != 1.0) || (special_coul[2] != 1.0))
+        error->warning(FLERR,"Likewise 1-3 special neighbor interactions != 1.0");
+    }
+    if (!dihedral && (atom->ndihedrals > 0)) {
+      error->warning(FLERR,"Dihedrals are defined but no dihedral style is set");
+      if ((special_lj[3] != 1.0) || (special_coul[3] != 1.0))
+        error->warning(FLERR,"Likewise 1-4 special neighbor interactions != 1.0");
+    }
+    if (!improper && (atom->nimpropers > 0))
+      error->warning(FLERR,"Impropers are defined but no improper style is set");
+  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/force.h b/src/force.h
index 26a3ecdfb8..2dcbdbdd75 100644
--- a/src/force.h
+++ b/src/force.h
@@ -226,4 +226,48 @@ A command with an argument that specifies an integer or range of
 integers is using a value that is less than 1 or greater than the
 maximum allowed limit.
 
+W: Bonds are defined but no bond style is set
+
+The topology contains bonds, but there are no bond forces computed
+since there was no bond_style command.
+
+W: Angles are defined but no angle style is set
+
+The topology contains angles, but there are no angle forces computed
+since there was no angle_style command.
+
+W: Dihedrals are defined but no dihedral style is set
+
+The topology contains dihedrals, but there are no dihedral forces computed
+since there was no dihedral_style command.
+
+W: Impropers are defined but no improper style is set
+
+The topology contains impropers, but there are no improper forces computed
+since there was no improper_style command.
+
+W: Likewise 1-2 special neighbor interactions != 1.0
+
+The topology contains bonds, but there is no bond style defined
+and a 1-2 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the bond style.
+
+W: Likewise 1-3 special neighbor interactions != 1.0
+
+The topology contains angles, but there is no angle style defined
+and a 1-3 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the angle style.
+
+W: Likewise 1-4 special neighbor interactions != 1.0
+
+The topology contains dihedrals, but there is no dihedral style defined
+and a 1-4 special neighbor scaling factor was not 1.0. This
+means that pair style interactions may have scaled or missing
+pairs in the neighbor list in expectation of interactions for
+those pairs being computed from the dihedral style.
+
 */
diff --git a/src/group.cpp b/src/group.cpp
index d119964ea1..93cd668194 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -31,6 +31,7 @@
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 #include <map>
 
@@ -735,7 +736,7 @@ void Group::read_restart(FILE *fp)
 
   for (i = 0; i < MAX_GROUP; i++) delete [] names[i];
 
-  if (me == 0) fread(&ngroup,sizeof(int),1,fp);
+  if (me == 0) utils::sfread(FLERR,&ngroup,sizeof(int),1,fp,NULL,error);
   MPI_Bcast(&ngroup,1,MPI_INT,0,world);
 
   // use count to not change restart format with deleted groups
@@ -747,11 +748,11 @@ void Group::read_restart(FILE *fp)
       names[i] = NULL;
       continue;
     }
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     if (n) {
       names[i] = new char[n];
-      if (me == 0) fread(names[i],sizeof(char),n,fp);
+      if (me == 0) utils::sfread(FLERR,names[i],sizeof(char),n,fp,NULL,error);
       MPI_Bcast(names[i],n,MPI_CHAR,0,world);
       count++;
     } else names[i] = NULL;
diff --git a/src/improper.cpp b/src/improper.cpp
index eefe3222ee..ad79a1a972 100644
--- a/src/improper.cpp
+++ b/src/improper.cpp
@@ -32,9 +32,10 @@ Improper::Improper(LAMMPS *lmp) : Pointers(lmp)
   allocated = 0;
   suffix_flag = Suffix::NONE;
 
-  maxeatom = maxvatom = 0;
+  maxeatom = maxvatom = maxcvatom = 0;
   eatom = NULL;
   vatom = NULL;
+  cvatom = NULL;
   setflag = NULL;
 
   execution_space = Host;
@@ -52,6 +53,7 @@ Improper::~Improper()
 
   memory->destroy(eatom);
   memory->destroy(vatom);
+  memory->destroy(cvatom);
 }
 
 /* ----------------------------------------------------------------------
@@ -83,9 +85,10 @@ void Improper::ev_setup(int eflag, int vflag, int alloc)
   eflag_global = eflag % 2;
   eflag_atom = eflag / 2;
 
-  vflag_either = vflag;
   vflag_global = vflag % 4;
-  vflag_atom = vflag / 4;
+  vflag_atom = vflag & 4;
+  cvflag_atom = vflag & 8;
+  vflag_either = vflag_global || vflag_atom;
 
   // reallocate per-atom arrays if necessary
 
@@ -103,6 +106,13 @@ void Improper::ev_setup(int eflag, int vflag, int alloc)
       memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom");
     }
   }
+  if (cvflag_atom && atom->nmax > maxcvatom) {
+    maxcvatom = atom->nmax;
+    if (alloc) {
+      memory->destroy(cvatom);
+      memory->create(cvatom,comm->nthreads*maxcvatom,9,"improper:cvatom");
+    }
+  }
 
   // zero accumulators
 
@@ -125,6 +135,22 @@ void Improper::ev_setup(int eflag, int vflag, int alloc)
       vatom[i][5] = 0.0;
     }
   }
+  if (cvflag_atom && alloc) {
+    n = atom->nlocal;
+    if (force->newton_bond) n += atom->nghost;
+    for (i = 0; i < n; i++) {
+      cvatom[i][0] = 0.0;
+      cvatom[i][1] = 0.0;
+      cvatom[i][2] = 0.0;
+      cvatom[i][3] = 0.0;
+      cvatom[i][4] = 0.0;
+      cvatom[i][5] = 0.0;
+      cvatom[i][6] = 0.0;
+      cvatom[i][7] = 0.0;
+      cvatom[i][8] = 0.0;
+      cvatom[i][9] = 0.0;
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -250,6 +276,95 @@ void Improper::ev_tally(int i1, int i2, int i3, int i4,
       }
     }
   }
+
+  // per-atom centroid virial
+  if (cvflag_atom) {
+
+    // r0 = (r1+r2+r3+r4)/4
+    // rij = ri-rj
+    // total virial = r10*f1 + r20*f2 + r30*f3 + r40*f4
+    // vb1: r12
+    // vb2: r32
+    // vb3: r43
+
+    if (newton_bond || i1 < nlocal) {
+      double a1[3];
+
+      // a1 = r10 = (3*r12 - 2*r32 -   r43)/4
+      a1[0] = 0.25*(3*vb1x - 2*vb2x - vb3x);
+      a1[1] = 0.25*(3*vb1y - 2*vb2y - vb3y);
+      a1[2] = 0.25*(3*vb1z - 2*vb2z - vb3z);
+
+      cvatom[i1][0] += a1[0]*f1[0];
+      cvatom[i1][1] += a1[1]*f1[1];
+      cvatom[i1][2] += a1[2]*f1[2];
+      cvatom[i1][3] += a1[0]*f1[1];
+      cvatom[i1][4] += a1[0]*f1[2];
+      cvatom[i1][5] += a1[1]*f1[2];
+      cvatom[i1][6] += a1[1]*f1[0];
+      cvatom[i1][7] += a1[2]*f1[0];
+      cvatom[i1][8] += a1[2]*f1[1];
+    }
+    if (newton_bond || i2 < nlocal) {
+      double a2[3];
+      double f2[3];
+
+      // a2 = r20 = ( -r12 - 2*r32 -   r43)/4
+      a2[0] = 0.25*(-vb1x - 2*vb2x - vb3x);
+      a2[1] = 0.25*(-vb1y - 2*vb2y - vb3y);
+      a2[2] = 0.25*(-vb1z - 2*vb2z - vb3z);
+
+      f2[0] = - f1[0] - f3[0] - f4[0];
+      f2[1] = - f1[1] - f3[1] - f4[1];
+      f2[2] = - f1[2] - f3[2] - f4[2];
+
+      cvatom[i2][0] += a2[0]*f2[0];
+      cvatom[i2][1] += a2[1]*f2[1];
+      cvatom[i2][2] += a2[2]*f2[2];
+      cvatom[i2][3] += a2[0]*f2[1];
+      cvatom[i2][4] += a2[0]*f2[2];
+      cvatom[i2][5] += a2[1]*f2[2];
+      cvatom[i2][6] += a2[1]*f2[0];
+      cvatom[i2][7] += a2[2]*f2[0];
+      cvatom[i2][8] += a2[2]*f2[1];
+    }
+    if (newton_bond || i3 < nlocal) {
+      double a3[3];
+
+      // a3 = r30 = ( -r12 + 2*r32 -   r43)/4
+      a3[0] = 0.25*(-vb1x + 2*vb2x - vb3x);
+      a3[1] = 0.25*(-vb1y + 2*vb2y - vb3y);
+      a3[2] = 0.25*(-vb1z + 2*vb2z - vb3z);
+
+      cvatom[i3][0] += a3[0]*f3[0];
+      cvatom[i3][1] += a3[1]*f3[1];
+      cvatom[i3][2] += a3[2]*f3[2];
+      cvatom[i3][3] += a3[0]*f3[1];
+      cvatom[i3][4] += a3[0]*f3[2];
+      cvatom[i3][5] += a3[1]*f3[2];
+      cvatom[i3][6] += a3[1]*f3[0];
+      cvatom[i3][7] += a3[2]*f3[0];
+      cvatom[i3][8] += a3[2]*f3[1];
+    }
+    if (newton_bond || i4 < nlocal) {
+      double a4[3];
+
+      // a4 = r40 = ( -r12 + 2*r32 + 3*r43)/4
+      a4[0] = 0.25*(-vb1x + 2*vb2x + 3*vb3x);
+      a4[1] = 0.25*(-vb1y + 2*vb2y + 3*vb3y);
+      a4[2] = 0.25*(-vb1z + 2*vb2z + 3*vb3z);
+
+      cvatom[i4][0] += a4[0]*f4[0];
+      cvatom[i4][1] += a4[1]*f4[1];
+      cvatom[i4][2] += a4[2]*f4[2];
+      cvatom[i4][3] += a4[0]*f4[1];
+      cvatom[i4][4] += a4[0]*f4[2];
+      cvatom[i4][5] += a4[1]*f4[2];
+      cvatom[i4][6] += a4[1]*f4[0];
+      cvatom[i4][7] += a4[2]*f4[0];
+      cvatom[i4][8] += a4[2]*f4[1];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/improper.h b/src/improper.h
index c30079bb5e..f3bed2607c 100644
--- a/src/improper.h
+++ b/src/improper.h
@@ -28,6 +28,7 @@ class Improper : protected Pointers {
   double energy;                  // accumulated energies
   double virial[6];               // accumulated virial
   double *eatom,**vatom;          // accumulated per-atom energy/virial
+  double **cvatom;                // accumulated per-atom centroid virial
 
   // KOKKOS host/device flag and data masks
 
@@ -54,12 +55,12 @@ class Improper : protected Pointers {
 
   int evflag;
   int eflag_either,eflag_global,eflag_atom;
-  int vflag_either,vflag_global,vflag_atom;
-  int maxeatom,maxvatom;
+  int vflag_either,vflag_global,vflag_atom,cvflag_atom;
+  int maxeatom,maxvatom,maxcvatom;
 
   void ev_init(int eflag, int vflag, int alloc = 1) {
     if (eflag||vflag) ev_setup(eflag, vflag, alloc);
-    else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0;
+    else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = cvflag_atom = 0;
   }
   void ev_setup(int, int, int alloc = 1);
   void ev_tally(int, int, int, int, int, int, double,
diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp
index 730a75766c..69dfc2d9cd 100644
--- a/src/improper_hybrid.cpp
+++ b/src/improper_hybrid.cpp
@@ -21,6 +21,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -128,6 +129,14 @@ void ImproperHybrid::compute(int eflag, int vflag)
         for (j = 0; j < 6; j++)
           vatom[i][j] += vatom_substyle[i][j];
     }
+    if (cvflag_atom) {
+      n = atom->nlocal;
+      if (force->newton_bond) n += atom->nghost;
+      double **cvatom_substyle = styles[m]->cvatom;
+      for (i = 0; i < n; i++)
+        for (j = 0; j < 9; j++)
+          cvatom[i][j] += cvatom_substyle[i][j];
+    }
   }
 
   // restore ptrs to original improperlist
@@ -316,7 +325,7 @@ void ImproperHybrid::write_restart(FILE *fp)
 void ImproperHybrid::read_restart(FILE *fp)
 {
   int me = comm->me;
-  if (me == 0) fread(&nstyles,sizeof(int),1,fp);
+  if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error);
   MPI_Bcast(&nstyles,1,MPI_INT,0,world);
   styles = new Improper*[nstyles];
   keywords = new char*[nstyles];
@@ -325,10 +334,10 @@ void ImproperHybrid::read_restart(FILE *fp)
 
   int n,dummy;
   for (int m = 0; m < nstyles; m++) {
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     keywords[m] = new char[n];
-    if (me == 0) fread(keywords[m],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
     styles[m] = force->new_improper(keywords[m],0,dummy);
     styles[m]->read_restart_settings(fp);
@@ -343,6 +352,7 @@ double ImproperHybrid::memory_usage()
 {
   double bytes = maxeatom * sizeof(double);
   bytes += maxvatom*6 * sizeof(double);
+  bytes += maxcvatom*9 * sizeof(double);
   for (int m = 0; m < nstyles; m++) bytes += maximproper[m]*5 * sizeof(int);
   for (int m = 0; m < nstyles; m++)
     if (styles[m]) bytes += styles[m]->memory_usage();
diff --git a/src/info.cpp b/src/info.cpp
index caa2d6fdd0..ca90a6cc2f 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -281,6 +281,7 @@ void Info::command(int narg, char **arg)
     infobuf = get_compiler_info();
     fprintf(out,"\nCompiler: %s with %s\n",infobuf,get_openmp_info());
     delete[] infobuf;
+    fprintf(out,"C++ standard: %s\n",get_cxx_info());
 
     fputs("\nActive compile time flags:\n\n",out);
     if (has_gzip_support()) fputs("-DLAMMPS_GZIP\n",out);
@@ -353,20 +354,8 @@ void Info::command(int narg, char **arg)
   }
 
   if (flags & COMM) {
-    int major,minor,len;
-#if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS)
-    char version[MPI_MAX_LIBRARY_VERSION_STRING];
-    MPI_Get_library_version(version,&len);
-#else
-    char version[] = "Undetected MPI implementation";
-    len = strlen(version);
-#endif
-
-    MPI_Get_version(&major,&minor);
-    if (len > 80) {
-      char *ptr = strchr(version+80,'\n');
-      if (ptr) *ptr = '\0';
-    }
+    int major,minor;
+    const char *version = get_mpi_info(major,minor);
 
     fprintf(out,"\nCommunication information:\n");
     fprintf(out,"MPI library level: MPI v%d.%d\n",major,minor);
@@ -1208,6 +1197,42 @@ const char *Info::get_openmp_info()
 #endif
 }
 
+const char *Info::get_mpi_info(int &major, int &minor)
+{
+  int len;
+  #if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS)
+  static char version[MPI_MAX_LIBRARY_VERSION_STRING];
+  MPI_Get_library_version(version,&len);
+#else
+  static char version[] = "Undetected MPI implementation";
+  len = strlen(version);
+#endif
+
+  MPI_Get_version(&major,&minor);
+  if (len > 80) {
+    char *ptr = strchr(version+80,'\n');
+    if (ptr) *ptr = '\0';
+  }
+  return version;
+}
+
+const char *Info::get_cxx_info()
+{
+#if __cplusplus > 201703L
+  return (const char *)"newer than C++17";
+#elif __cplusplus == 201703L
+  return (const char *)"C++17";
+#elif __cplusplus == 201402L
+  return (const char *)"C++14";
+#elif __cplusplus == 201103L
+  return (const char *)"C++11";
+#elif __cplusplus == 199711L
+  return (const char *)"C++98";
+#else
+  return (const char *)"unknown";
+#endif
+}
+
 /* ---------------------------------------------------------------------- */
 
 char **Info::get_variable_names(int &num) {
diff --git a/src/info.h b/src/info.h
index ff8f15676d..01d6105ff2 100644
--- a/src/info.h
+++ b/src/info.h
@@ -43,6 +43,8 @@ class Info : protected Pointers {
   static char *get_os_info();
   static char *get_compiler_info();
   static const char *get_openmp_info();
+  static const char *get_mpi_info(int &, int &);
+  static const char *get_cxx_info();
 
   char **get_variable_names(int &num);
 
diff --git a/src/input.h b/src/input.h
index 4b274c17a9..b4df0f0160 100644
--- a/src/input.h
+++ b/src/input.h
@@ -39,7 +39,7 @@ class Input : protected Pointers {
                                  // substitute for variables in a string
   int expand_args(int, char **, int, char **&);  // expand args due to wildcard
   void write_echo(const char *); // send text to active echo file pointers
-  
+
  protected:
   char *command;               // ptr to current command
   int echo_screen;             // 0 = no, 1 = yes
diff --git a/src/integrate.cpp b/src/integrate.cpp
index 545de849d5..1f50ff76c5 100644
--- a/src/integrate.cpp
+++ b/src/integrate.cpp
@@ -26,7 +26,7 @@ using namespace LAMMPS_NS;
 Integrate::Integrate(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp)
 {
   elist_global = elist_atom = NULL;
-  vlist_global = vlist_atom = NULL;
+  vlist_global = vlist_atom = cvlist_atom = NULL;
   external_force_clear = 0;
 }
 
@@ -38,6 +38,7 @@ Integrate::~Integrate()
   delete [] elist_atom;
   delete [] vlist_global;
   delete [] vlist_atom;
+  delete [] cvlist_atom;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -72,25 +73,28 @@ void Integrate::ev_setup()
   delete [] elist_atom;
   delete [] vlist_global;
   delete [] vlist_atom;
+  delete [] cvlist_atom;
   elist_global = elist_atom = NULL;
-  vlist_global = vlist_atom = NULL;
+  vlist_global = vlist_atom = cvlist_atom = NULL;
 
   nelist_global = nelist_atom = 0;
-  nvlist_global = nvlist_atom = 0;
+  nvlist_global = nvlist_atom = ncvlist_atom = 0;
   for (int i = 0; i < modify->ncompute; i++) {
     if (modify->compute[i]->peflag) nelist_global++;
     if (modify->compute[i]->peatomflag) nelist_atom++;
     if (modify->compute[i]->pressflag) nvlist_global++;
-    if (modify->compute[i]->pressatomflag) nvlist_atom++;
+    if (modify->compute[i]->pressatomflag & 1) nvlist_atom++;
+    if (modify->compute[i]->pressatomflag & 2) ncvlist_atom++;
   }
 
   if (nelist_global) elist_global = new Compute*[nelist_global];
   if (nelist_atom) elist_atom = new Compute*[nelist_atom];
   if (nvlist_global) vlist_global = new Compute*[nvlist_global];
   if (nvlist_atom) vlist_atom = new Compute*[nvlist_atom];
+  if (ncvlist_atom) cvlist_atom = new Compute*[ncvlist_atom];
 
   nelist_global = nelist_atom = 0;
-  nvlist_global = nvlist_atom = 0;
+  nvlist_global = nvlist_atom = ncvlist_atom = 0;
   for (int i = 0; i < modify->ncompute; i++) {
     if (modify->compute[i]->peflag)
       elist_global[nelist_global++] = modify->compute[i];
@@ -98,8 +102,10 @@ void Integrate::ev_setup()
       elist_atom[nelist_atom++] = modify->compute[i];
     if (modify->compute[i]->pressflag)
       vlist_global[nvlist_global++] = modify->compute[i];
-    if (modify->compute[i]->pressatomflag)
+    if (modify->compute[i]->pressatomflag & 1)
       vlist_atom[nvlist_atom++] = modify->compute[i];
+    if (modify->compute[i]->pressatomflag & 2)
+      cvlist_atom[ncvlist_atom++] = modify->compute[i];
   }
 }
 
@@ -116,6 +122,10 @@ void Integrate::ev_setup()
    vflag = 2 = global virial with pair portion via F dot r including ghosts
    vflag = 4 = per-atom virial only
    vflag = 5 or 6 = both global and per-atom virial
+   vflag = 8 = per-atom centroid virial only
+   vflag = 9 or 10 = both global and per-atom centroid virial
+   vflag = 12 = both per-atom virial and per-atom centroid virial
+   vflag = 13 or 15 = global, per-atom virial and per-atom centroid virial
 ------------------------------------------------------------------------- */
 
 void Integrate::ev_set(bigint ntimestep)
@@ -150,7 +160,13 @@ void Integrate::ev_set(bigint ntimestep)
     if (vlist_atom[i]->matchstep(ntimestep)) flag = 1;
   if (flag) vflag_atom = 4;
 
+  flag = 0;
+  int cvflag_atom = 0;
+  for (i = 0; i < ncvlist_atom; i++)
+    if (cvlist_atom[i]->matchstep(ntimestep)) flag = 1;
+  if (flag) cvflag_atom = 8;
+
   if (vflag_global) update->vflag_global = ntimestep;
-  if (vflag_atom) update->vflag_atom = ntimestep;
-  vflag = vflag_global + vflag_atom;
+  if (vflag_atom || cvflag_atom) update->vflag_atom = ntimestep;
+  vflag = vflag_global + vflag_atom + cvflag_atom;
 }
diff --git a/src/integrate.h b/src/integrate.h
index 9a50fad1f7..f07faacbfa 100644
--- a/src/integrate.h
+++ b/src/integrate.h
@@ -36,11 +36,12 @@ class Integrate : protected Pointers {
   int external_force_clear;         // clear forces locally or externally
 
   int nelist_global,nelist_atom;    // # of PE,virial computes to check
-  int nvlist_global,nvlist_atom;
+  int nvlist_global,nvlist_atom,ncvlist_atom;
   class Compute **elist_global;     // lists of PE,virial Computes
   class Compute **elist_atom;
   class Compute **vlist_global;
   class Compute **vlist_atom;
+  class Compute **cvlist_atom;
 
   int pair_compute_flag;            // 0 if pair->compute is skipped
   int kspace_compute_flag;          // 0 if kspace->compute is skipped
diff --git a/src/kspace.h b/src/kspace.h
index c04a0db989..60df2345fd 100644
--- a/src/kspace.h
+++ b/src/kspace.h
@@ -44,7 +44,7 @@ class KSpace : protected Pointers {
   int dispersionflag;            // 1 if a LJ/dispersion solver
   int tip4pflag;                 // 1 if a TIP4P solver
   int dipoleflag;                // 1 if a dipole solver
-  int spinflag;			 // 1 if a spin solver
+  int spinflag;                  // 1 if a spin solver
   int differentiation_flag;
   int neighrequest_flag;         // used to avoid obsolete construction
                                  // of neighbor lists
diff --git a/src/lammps.cpp b/src/lammps.cpp
index 5ddc1600a4..4b09429b52 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -444,6 +444,19 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
     if ((universe->me == 0) && !helpflag) {
       if (screen) fprintf(screen,"LAMMPS (%s)\n",universe->version);
       if (logfile) fprintf(logfile,"LAMMPS (%s)\n",universe->version);
+#if defined(LAMMPS_CXX98)
+      const char warning[] = "\nWARNING-WARNING-WARNING-WARNING-WARNING\n"
+        "This LAMMPS executable was compiled using C++98 compatibility.\n"
+        "Please report the compiler info below at https://github.com/lammps/lammps/issues/1659\n";
+      const char *infobuf = Info::get_compiler_info();
+      if (screen)
+         fprintf(screen,"%s%s\nWARNING-WARNING-WARNING-WARNING-WARNING\n\n",
+                 warning,infobuf);
+      if (logfile)
+         fprintf(logfile,"%s%s\nWARNING-WARNING-WARNING-WARNING-WARNING\n\n",
+                 warning,infobuf);
+      delete[] infobuf;
+#endif
     }
 
   // universe is one or more worlds, as setup by partition switch
@@ -1000,7 +1013,7 @@ void _noopt LAMMPS::init_pkg_lists()
 #undef REGION_CLASS
 }
 
-bool LAMMPS::is_installed_pkg(const char *pkg) 
+bool LAMMPS::is_installed_pkg(const char *pkg)
 {
   for (int i=0; installed_packages[i] != NULL; ++i)
     if (strcmp(installed_packages[i],pkg) == 0) return true;
@@ -1258,13 +1271,18 @@ void LAMMPS::print_config(FILE *fp)
   const char *pkg;
   int ncword, ncline = 0;
 
-  char *infobuf = Info::get_os_info();
+  const char *infobuf = Info::get_os_info();
   fprintf(fp,"OS: %s\n\n",infobuf);
   delete[] infobuf;
 
   infobuf = Info::get_compiler_info();
-  fprintf(fp,"Compiler: %s with %s\n\n",infobuf,Info::get_openmp_info());
+  fprintf(fp,"Compiler: %s with %s\n",infobuf,Info::get_openmp_info());
   delete[] infobuf;
+  fprintf(fp,"C++ standard: %s\n",Info::get_cxx_info());
+
+  int major,minor;
+  infobuf = Info::get_mpi_info(major,minor);
+  fprintf(fp,"MPI v%d.%d: %s\n\n",major,minor,infobuf);
 
   fputs("Active compile time flags:\n\n",fp);
   if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp);
diff --git a/src/library.cpp b/src/library.cpp
index 6f283ea4da..ee98e47aaa 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -38,6 +38,9 @@
 #include "force.h"
 #include "info.h"
 #include "fix_external.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
 
 #if defined(LAMMPS_EXCEPTIONS)
 #include "exceptions.h"
@@ -1727,3 +1730,171 @@ int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
 }
 
 #endif
+
+/*******************************************************************************
+ * Find neighbor list index of pair style neighbor list
+ *
+ * Try finding pair instance that matches style. If exact is set, the pair must
+ * match style exactly. If exact is 0, style must only be contained. If pair is
+ * of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style.
+ *
+ * Once the pair instance has been identified, multiple neighbor list requests
+ * may be found. Every neighbor list is uniquely identified by its request
+ * index. Thus, providing this request index ensures that the correct neighbor
+ * list index is returned.
+ *
+ * @param ptr      Pointer to LAMMPS instance
+ * @param style    String used to search for pair style instance
+ * @param exact    Flag to control whether style should match exactly or only
+ *                 must be contained in pair style name
+ * @param nsub     match nsub-th hybrid sub-style
+ * @param request  request index that specifies which neighbor list should be
+ *                 returned, in case there are multiple neighbor lists requests
+ *                 for the found pair style
+ * @return         return neighbor list index if found, otherwise -1
+ ******************************************************************************/
+int lammps_find_pair_neighlist(void* ptr, char * style, int exact, int nsub, int request) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Pair* pair = lmp->force->pair_match(style, exact, nsub);
+
+  if (pair != NULL) {
+    // find neigh list
+    for (int i = 0; i < lmp->neighbor->nlist; i++) {
+      NeighList * list = lmp->neighbor->lists[i];
+      if (list->requestor_type != NeighList::PAIR || pair != list->requestor) continue;
+
+      if (list->index == request) {
+          return i;
+      }
+    }
+  }
+  return -1;
+}
+
+/*******************************************************************************
+ * Find neighbor list index of fix neighbor list
+ *
+ * @param ptr      Pointer to LAMMPS instance
+ * @param id       Identifier of fix instance
+ * @param request  request index that specifies which request should be returned,
+ *                 in case there are multiple neighbor lists for this fix
+ * @return         return neighbor list index if found, otherwise -1
+ ******************************************************************************/
+int lammps_find_fix_neighlist(void* ptr, char * id, int request) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Fix* fix = NULL;
+  const int nfix = lmp->modify->nfix;
+
+  // find fix with name
+  for (int ifix = 0; ifix < nfix; ifix++) {
+    if (strcmp(lmp->modify->fix[ifix]->id, id) == 0) {
+        fix = lmp->modify->fix[ifix];
+        break;
+    }
+  }
+
+  if (fix != NULL) {
+    // find neigh list
+    for (int i = 0; i < lmp->neighbor->nlist; i++) {
+      NeighList * list = lmp->neighbor->lists[i];
+      if (list->requestor_type != NeighList::FIX || fix != list->requestor) continue;
+
+      if (list->index == request) {
+          return i;
+      }
+    }
+  }
+  return -1;
+}
+
+/*******************************************************************************
+ * Find neighbor list index of compute neighbor list
+ *
+ * @param ptr      Pointer to LAMMPS instance
+ * @param id       Identifier of fix instance
+ * @param request  request index that specifies which request should be returned,
+ *                 in case there are multiple neighbor lists for this fix
+ * @return         return neighbor list index if found, otherwise -1
+ ******************************************************************************/
+int lammps_find_compute_neighlist(void* ptr, char * id, int request) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Compute* compute = NULL;
+  const int ncompute = lmp->modify->ncompute;
+
+  // find compute with name
+  for (int icompute = 0; icompute < ncompute; icompute++) {
+    if (strcmp(lmp->modify->compute[icompute]->id, id) == 0) {
+        compute = lmp->modify->compute[icompute];
+        break;
+    }
+  }
+
+  if (compute == NULL) {
+    // find neigh list
+    for (int i = 0; i < lmp->neighbor->nlist; i++) {
+      NeighList * list = lmp->neighbor->lists[i];
+      if (list->requestor_type != NeighList::COMPUTE || compute != list->requestor) continue;
+
+      if (list->index == request) {
+          return i;
+      }
+    }
+  }
+  return -1;
+}
+
+/*******************************************************************************
+ * Return the number of entries in the neighbor list with given index
+ *
+ * @param ptr      Pointer to LAMMPS instance
+ * @param idx      neighbor list index
+ * @return         return number of entries in neighbor list, -1 if idx is
+ *                 not a valid index
+ ******************************************************************************/
+int lammps_neighlist_num_elements(void * ptr, int idx) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Neighbor * neighbor = lmp->neighbor;
+
+  if(idx < 0 || idx >= neighbor->nlist) {
+    return -1;
+  }
+
+  NeighList * list = neighbor->lists[idx];
+  return list->inum;
+}
+
+/*******************************************************************************
+ * Return atom local index, number of neighbors, and array of neighbor local
+ * atom indices of neighbor list entry
+ *
+ * @param ptr             Pointer to LAMMPS instance
+ * @param idx             neighbor list index
+ * @param element         neighbor list element index
+ * @param[out] iatom      atom local index in range [0, nlocal + nghost), -1 if
+                          invalid idx or element index
+ * @param[out] numneigh   number of neighbors of atom i or 0
+ * @param[out] neighbors  pointer to array of neighbor atom local indices or
+ *                        NULL
+ ******************************************************************************/
+void lammps_neighlist_element_neighbors(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors) {
+  LAMMPS *  lmp = (LAMMPS *) ptr;
+  Neighbor * neighbor = lmp->neighbor;
+  *iatom = -1;
+  *numneigh = 0;
+  *neighbors = NULL;
+
+  if(idx < 0 || idx >= neighbor->nlist) {
+    return;
+  }
+
+  NeighList * list = neighbor->lists[idx];
+
+  if(element < 0 || element >= list->inum) {
+    return;
+  }
+
+  int i = list->ilist[element];
+  *iatom     = i;
+  *numneigh  = list->numneigh[i];
+  *neighbors = list->firstneigh[i];
+}
diff --git a/src/library.h b/src/library.h
index 59b68b9502..9e6c4f45f8 100644
--- a/src/library.h
+++ b/src/library.h
@@ -16,8 +16,16 @@
    new LAMMPS-specific functions can be added
 */
 
+/*
+ * Follow the behavior of regular LAMMPS compilation and assume
+ * -DLAMMPS_SMALLBIG when no define is set.
+ */
+#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)
+#define LAMMPS_SMALLBIG
+#endif
+
 #include <mpi.h>
-#ifdef LAMMPS_BIGBIG
+#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
 #include <inttypes.h>  /* for int64_t */
 #endif
 
@@ -58,9 +66,12 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
 void lammps_scatter_atoms(void *, char *, int, int, void *);
 void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
 
-#ifdef LAMMPS_BIGBIG
+#if defined(LAMMPS_BIGBIG)
 typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
 void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
+#elif defined(LAMMPS_SMALLBIG)
+typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
+void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
 #else
 typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
 void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
@@ -75,6 +86,12 @@ int lammps_config_has_jpeg_support();
 int lammps_config_has_ffmpeg_support();
 int lammps_config_has_exceptions();
 
+int lammps_find_pair_neighlist(void* ptr, char * style, int exact, int nsub, int request);
+int lammps_find_fix_neighlist(void* ptr, char * id, int request);
+int lammps_find_compute_neighlist(void* ptr, char * id, int request);
+int lammps_neighlist_num_elements(void* ptr, int idx);
+void lammps_neighlist_element_neighbors(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);
+
 // lammps_create_atoms() takes tagint and imageint as args
 // ifdef insures they are compatible with rest of LAMMPS
 // caller must match to how LAMMPS library is built
diff --git a/src/lmptype.h b/src/lmptype.h
index 65e46535fc..c1902e7ebe 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -28,6 +28,13 @@
 #ifndef LMP_LMPTYPE_H
 #define LMP_LMPTYPE_H
 
+// C++11 check
+#ifndef LAMMPS_CXX98
+#if __cplusplus <= 199711L
+  #error LAMMPS is planning to transition to C++11. To disable this error please use a C++11 compliant compiler, enable C++11 (or later) compliance, or define LAMMPS_CXX98 in your makefile
+#endif
+#endif
+
 #ifndef __STDC_LIMIT_MACROS
 #define __STDC_LIMIT_MACROS
 #endif
diff --git a/src/math_special.cpp b/src/math_special.cpp
index bf11a1ad45..d4abc36f25 100644
--- a/src/math_special.cpp
+++ b/src/math_special.cpp
@@ -538,6 +538,8 @@ double MathSpecial::exp2_x86(double x)
 double MathSpecial::fm_exp(double x)
 {
 #if defined(__BYTE_ORDER__) && (__BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__)
+    if (x < -1022.0/FM_DOUBLE_LOG2OFE) return 0;
+    if (x > 1023.0/FM_DOUBLE_LOG2OFE) return INFINITY;
     return exp2_x86(FM_DOUBLE_LOG2OFE * x);
 #else
     return ::exp(x);
diff --git a/src/min.cpp b/src/min.cpp
index b6bed01c75..003fd18b81 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -42,10 +42,12 @@
 #include "output.h"
 #include "thermo.h"
 #include "timer.h"
+#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
+using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
@@ -54,9 +56,10 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp)
   dmax = 0.1;
   searchflag = 0;
   linestyle = 1;
+  normstyle = TWO;
 
   elist_global = elist_atom = NULL;
-  vlist_global = vlist_atom = NULL;
+  vlist_global = vlist_atom = cvlist_atom = NULL;
 
   nextra_global = 0;
   fextra = NULL;
@@ -80,6 +83,7 @@ Min::~Min()
   delete [] elist_atom;
   delete [] vlist_global;
   delete [] vlist_atom;
+  delete [] cvlist_atom;
 
   delete [] fextra;
 
@@ -659,6 +663,15 @@ void Min::modify_params(int narg, char **arg)
       if (strcmp(arg[iarg+1],"backtrack") == 0) linestyle = 0;
       else if (strcmp(arg[iarg+1],"quadratic") == 0) linestyle = 1;
       else if (strcmp(arg[iarg+1],"forcezero") == 0) linestyle = 2;
+      else if (strcmp(arg[iarg+1],"spin_cubic") == 0) linestyle = 3;
+      else if (strcmp(arg[iarg+1],"spin_none") == 0) linestyle = 4;
+      else error->all(FLERR,"Illegal min_modify command");
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"norm") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
+      if (strcmp(arg[iarg+1],"two") == 0) normstyle = TWO;
+      else if (strcmp(arg[iarg+1],"max") == 0) normstyle = MAX;
+      else if (strcmp(arg[iarg+1],"inf") == 0) normstyle = INF;
       else error->all(FLERR,"Illegal min_modify command");
       iarg += 2;
     } else {
@@ -679,25 +692,28 @@ void Min::ev_setup()
   delete [] elist_atom;
   delete [] vlist_global;
   delete [] vlist_atom;
+  delete [] cvlist_atom;
   elist_global = elist_atom = NULL;
-  vlist_global = vlist_atom = NULL;
+  vlist_global = vlist_atom = cvlist_atom = NULL;
 
   nelist_global = nelist_atom = 0;
-  nvlist_global = nvlist_atom = 0;
+  nvlist_global = nvlist_atom = ncvlist_atom = 0;
   for (int i = 0; i < modify->ncompute; i++) {
     if (modify->compute[i]->peflag) nelist_global++;
     if (modify->compute[i]->peatomflag) nelist_atom++;
     if (modify->compute[i]->pressflag) nvlist_global++;
-    if (modify->compute[i]->pressatomflag) nvlist_atom++;
+    if (modify->compute[i]->pressatomflag & 1) nvlist_atom++;
+    if (modify->compute[i]->pressatomflag & 2) ncvlist_atom++;
   }
 
   if (nelist_global) elist_global = new Compute*[nelist_global];
   if (nelist_atom) elist_atom = new Compute*[nelist_atom];
   if (nvlist_global) vlist_global = new Compute*[nvlist_global];
   if (nvlist_atom) vlist_atom = new Compute*[nvlist_atom];
+  if (ncvlist_atom) cvlist_atom = new Compute*[ncvlist_atom];
 
   nelist_global = nelist_atom = 0;
-  nvlist_global = nvlist_atom = 0;
+  nvlist_global = nvlist_atom = ncvlist_atom = 0;
   for (int i = 0; i < modify->ncompute; i++) {
     if (modify->compute[i]->peflag)
       elist_global[nelist_global++] = modify->compute[i];
@@ -705,8 +721,10 @@ void Min::ev_setup()
       elist_atom[nelist_atom++] = modify->compute[i];
     if (modify->compute[i]->pressflag)
       vlist_global[nvlist_global++] = modify->compute[i];
-    if (modify->compute[i]->pressatomflag)
+    if (modify->compute[i]->pressatomflag & 1)
       vlist_atom[nvlist_atom++] = modify->compute[i];
+    if (modify->compute[i]->pressatomflag & 2)
+      cvlist_atom[ncvlist_atom++] = modify->compute[i];
   }
 }
 
@@ -724,6 +742,10 @@ void Min::ev_setup()
    vflag = 2 = global virial with pair portion via F dot r including ghosts
    vflag = 4 = per-atom virial only
    vflag = 5 or 6 = both global and per-atom virial
+   vflag = 8 = per-atom centroid virial only
+   vflag = 9 or 10 = both global and per-atom centroid virial
+   vflag = 12 = both per-atom virial and per-atom centroid virial
+   vflag = 13 or 15 = global, per-atom virial and per-atom centroid virial
 ------------------------------------------------------------------------- */
 
 void Min::ev_set(bigint ntimestep)
@@ -756,9 +778,15 @@ void Min::ev_set(bigint ntimestep)
     if (vlist_atom[i]->matchstep(ntimestep)) flag = 1;
   if (flag) vflag_atom = 4;
 
+  flag = 0;
+  int cvflag_atom = 0;
+  for (i = 0; i < ncvlist_atom; i++)
+    if (cvlist_atom[i]->matchstep(ntimestep)) flag = 1;
+  if (flag) cvflag_atom = 8;
+
   if (vflag_global) update->vflag_global = update->ntimestep;
-  if (vflag_atom) update->vflag_atom = update->ntimestep;
-  vflag = vflag_global + vflag_atom;
+  if (vflag_atom || cvflag_atom) update->vflag_atom = update->ntimestep;
+  vflag = vflag_global + vflag_atom + cvflag_atom;
 }
 
 /* ----------------------------------------------------------------------
@@ -822,6 +850,139 @@ double Min::fnorm_inf()
   return norm_inf;
 }
 
+/* ----------------------------------------------------------------------
+   compute and return ||force||_max (inf norm per-vector)
+------------------------------------------------------------------------- */
+
+double Min::fnorm_max()
+{
+  int i,n;
+  double fdotf,*fatom;
+
+  double local_norm_max = 0.0;
+  for (i = 0; i < nvec; i+=3) {
+    fdotf = fvec[i]*fvec[i]+fvec[i+1]*fvec[i+1]+fvec[i+2]*fvec[i+2];
+    local_norm_max = MAX(fdotf,local_norm_max);
+  }
+  if (nextra_atom) {
+    for (int m = 0; m < nextra_atom; m++) {
+      fatom = fextra_atom[m];
+      n = extra_nlen[m];
+      for (i = 0; i < n; i+=3) {
+        fdotf = fatom[i]*fatom[i]+fatom[i+1]*fatom[i+1]+fatom[i+2]*fatom[i+2];
+        local_norm_max = MAX(fdotf,local_norm_max);
+      }
+    }
+  }
+
+  double norm_max = 0.0;
+  MPI_Allreduce(&local_norm_max,&norm_max,1,MPI_DOUBLE,MPI_MAX,world);
+
+  if (nextra_global) {
+    for (i = 0; i < nextra_global; i+=3) {
+      fdotf = fextra[i]*fextra[i];
+      norm_max = MAX(fdotf,norm_max);
+    }
+  }
+  return norm_max;
+}
+
+/* ----------------------------------------------------------------------
+   compute and return  sum_i||mag. torque_i||_2 (in eV)
+------------------------------------------------------------------------- */
+
+double Min::total_torque()
+{
+  double fmsq,ftotsqone,ftotsqall;
+  int nlocal = atom->nlocal;
+  double hbar = force->hplanck/MY_2PI;
+  double tx,ty,tz;
+  double **sp = atom->sp;
+  double **fm = atom->fm;
+
+  fmsq = ftotsqone = ftotsqall = 0.0;
+  for (int i = 0; i < nlocal; i++) {
+    tx = fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1];
+    ty = fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2];
+    tz = fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0];
+    fmsq = tx*tx + ty*ty + tz*tz;
+    ftotsqone += fmsq;
+  }
+
+  // summing all fmsqtot on this replica
+
+  MPI_Allreduce(&ftotsqone,&ftotsqall,1,MPI_DOUBLE,MPI_SUM,world);
+
+  // multiply it by hbar so that units are in eV
+
+  return sqrt(ftotsqall) * hbar;
+}
+
+/* ----------------------------------------------------------------------
+   compute and return max_i ||mag. torque components|| (in eV)
+------------------------------------------------------------------------- */
+
+double Min::inf_torque()
+{
+  double fmaxsqone,fmaxsqall;
+  int nlocal = atom->nlocal;
+  double hbar = force->hplanck/MY_2PI;
+  double tx,ty,tz;
+  double **sp = atom->sp;
+  double **fm = atom->fm;
+
+  fmaxsqone = fmaxsqall = 0.0;
+  for (int i = 0; i < nlocal; i++) {
+    tx = fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1];
+    ty = fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2];
+    tz = fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0];
+    fmaxsqone = MAX(fmaxsqone,tx*tx);
+    fmaxsqone = MAX(fmaxsqone,ty*ty);
+    fmaxsqone = MAX(fmaxsqone,tz*tz);
+  }
+
+  // finding max fm on this replica
+
+  fmaxsqall = fmaxsqone;
+  MPI_Allreduce(&fmaxsqone,&fmaxsqall,1,MPI_DOUBLE,MPI_MAX,world);
+
+  // multiply it by hbar so that units are in eV
+
+  return sqrt(fmaxsqall) * hbar;
+}
+
+/* ----------------------------------------------------------------------
+   compute and return max_i ||mag. torque_i|| (in eV)
+------------------------------------------------------------------------- */
+
+double Min::max_torque()
+{
+  double fmsq,fmaxsqone,fmaxsqall;
+  int nlocal = atom->nlocal;
+  double hbar = force->hplanck/MY_2PI;
+  double tx,ty,tz;
+  double **sp = atom->sp;
+  double **fm = atom->fm;
+
+  fmsq = fmaxsqone = fmaxsqall = 0.0;
+  for (int i = 0; i < nlocal; i++) {
+    tx = fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1];
+    ty = fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2];
+    tz = fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0];
+    fmsq = tx*tx + ty*ty + tz*tz;
+    fmaxsqone = MAX(fmaxsqone,fmsq);
+  }
+
+  // finding max fm on this replica
+
+  fmaxsqall = fmaxsqone;
+  MPI_Allreduce(&fmaxsqone,&fmaxsqall,1,MPI_DOUBLE,MPI_MAX,world);
+
+  // multiply it by hbar so that units are in eV
+
+  return sqrt(fmaxsqall) * hbar;
+}
+
 /* ----------------------------------------------------------------------
    possible stop conditions
 ------------------------------------------------------------------------- */
diff --git a/src/min.h b/src/min.h
index 835e6b3ed5..ba47f95410 100644
--- a/src/min.h
+++ b/src/min.h
@@ -41,6 +41,14 @@ class Min : protected Pointers {
   virtual int modify_param(int, char **) {return 0;}
   virtual double fnorm_sqr();
   virtual double fnorm_inf();
+  virtual double fnorm_max();
+
+  enum{TWO,MAX,INF};
+
+  // methods for spin minimizers
+  double total_torque();
+  double inf_torque();
+  double max_torque();
 
   virtual void init_style() {}
   virtual void setup_style() = 0;
@@ -56,15 +64,19 @@ class Min : protected Pointers {
   int virial_style;           // compute virial explicitly or implicitly
   int external_force_clear;   // clear forces locally or externally
 
-  double dmax;                // max dist to move any atom in one step
-  int linestyle;              // 0 = backtrack, 1 = quadratic, 2 = forcezero
+  double dmax;                  // max dist to move any atom in one step
+  int linestyle;                // 0 = backtrack, 1 = quadratic, 2 = forcezero
+                                // 3 = spin_cubic, 4 = spin_none
+
+  int normstyle;                // TWO, MAX or INF flag for force norm evaluation
 
   int nelist_global,nelist_atom;    // # of PE,virial computes to check
-  int nvlist_global,nvlist_atom;
+  int nvlist_global,nvlist_atom,ncvlist_atom;
   class Compute **elist_global;     // lists of PE,virial Computes
   class Compute **elist_atom;
   class Compute **vlist_global;
   class Compute **vlist_atom;
+  class Compute **cvlist_atom;
 
   int triclinic;              // 0 if domain is orthog, 1 if triclinic
   int pairflag;
@@ -104,9 +116,6 @@ class Min : protected Pointers {
   virtual double energy_force(int);
   virtual void force_clear();
 
-  double compute_force_norm_sqr();
-  double compute_force_norm_inf();
-
   void ev_setup();
   void ev_set(bigint);
 
diff --git a/src/min_cg.cpp b/src/min_cg.cpp
index ff318d23da..9db1fd9799 100644
--- a/src/min_cg.cpp
+++ b/src/min_cg.cpp
@@ -14,6 +14,7 @@
 #include "min_cg.h"
 #include <mpi.h>
 #include <cmath>
+#include "error.h"
 #include "update.h"
 #include "output.h"
 #include "timer.h"
@@ -35,7 +36,7 @@ MinCG::MinCG(LAMMPS *lmp) : MinLineSearch(lmp) {}
 int MinCG::iterate(int maxiter)
 {
   int i,m,n,fail,ntimestep;
-  double beta,gg,dot[2],dotall[2];
+  double beta,gg,dot[2],dotall[2],fdotf;
   double *fatom,*gatom,*hatom;
 
   // nlimit = max # of CG iterations before restarting
@@ -90,6 +91,7 @@ int MinCG::iterate(int maxiter)
       dot[0] += fvec[i]*fvec[i];
       dot[1] += fvec[i]*g[i];
     }
+
     if (nextra_atom)
       for (m = 0; m < nextra_atom; m++) {
         fatom = fextra_atom[m];
@@ -107,7 +109,14 @@ int MinCG::iterate(int maxiter)
         dotall[1] += fextra[i]*gextra[i];
       }
 
-    if (dotall[0] < update->ftol*update->ftol) return FTOL;
+    fdotf = 0.0;
+    if (update->ftol > 0.0) {
+      if (normstyle == MAX) fdotf = fnorm_max();        // max force norm
+      else if (normstyle == INF) fdotf = fnorm_inf();   // infinite force norm
+      else if (normstyle == TWO) fdotf = fnorm_sqr();   // Euclidean force 2-norm
+      else error->all(FLERR,"Illegal min_modify command");
+      if (fdotf < update->ftol*update->ftol) return FTOL;
+    }
 
     // update new search direction h from new f = -Grad(x) and old g
     // this is Polak-Ribieri formulation
diff --git a/src/min_fire.cpp b/src/min_fire.cpp
index b7f853afd2..ca37e410b8 100644
--- a/src/min_fire.cpp
+++ b/src/min_fire.cpp
@@ -16,6 +16,7 @@
 #include <cmath>
 #include "universe.h"
 #include "atom.h"
+#include "error.h"
 #include "force.h"
 #include "update.h"
 #include "output.h"
@@ -249,8 +250,12 @@ int MinFire::iterate(int maxiter)
     // force tolerance criterion
     // sync across replicas if running multi-replica minimization
 
+    fdotf = 0.0;
     if (update->ftol > 0.0) {
-      fdotf = fnorm_sqr();
+      if (normstyle == MAX) fdotf = fnorm_max();        // max force norm
+      else if (normstyle == INF) fdotf = fnorm_inf();   // inf force norm
+      else if (normstyle == TWO) fdotf = fnorm_sqr();   // Euclidean force 2-norm
+      else error->all(FLERR,"Illegal min_modify command");
       if (update->multireplica == 0) {
         if (fdotf < update->ftol*update->ftol) return FTOL;
       } else {
diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp
index dcfed10fef..63432aab63 100644
--- a/src/min_hftn.cpp
+++ b/src/min_hftn.cpp
@@ -22,6 +22,7 @@
 #include <cmath>
 #include <cstring>
 #include "atom.h"
+#include "error.h"
 #include "fix_minimize.h"
 #include "modify.h"
 #include "output.h"
@@ -112,6 +113,9 @@ void MinHFTN::init()
 {
   Min::init();
 
+  if (normstyle == MAX)
+    error->all(FLERR,"Incorrect min_modify option");
+
   for (int  i = 1; i < NUM_HFTN_ATOM_BASED_VECTORS; i++) {
     if (_daExtraGlobal[i] != NULL)
       delete [] _daExtraGlobal[i];
diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp
index 04e72b046d..5e7643bf3b 100644
--- a/src/min_quickmin.cpp
+++ b/src/min_quickmin.cpp
@@ -16,6 +16,7 @@
 #include <cmath>
 #include "universe.h"
 #include "atom.h"
+#include "error.h"
 #include "force.h"
 #include "update.h"
 #include "output.h"
@@ -214,8 +215,12 @@ int MinQuickMin::iterate(int maxiter)
     // force tolerance criterion
     // sync across replicas if running multi-replica minimization
 
+    fdotf = 0.0;
     if (update->ftol > 0.0) {
-      fdotf = fnorm_sqr();
+      if (normstyle == MAX) fdotf = fnorm_max();       // max force norm
+      else if (normstyle == INF) fdotf = fnorm_inf();  // inf force norm
+      else if (normstyle == TWO) fdotf = fnorm_sqr();  // Euclidean force 2-norm
+      else error->all(FLERR,"Illegal min_modify command");
       if (update->multireplica == 0) {
         if (fdotf < update->ftol*update->ftol) return FTOL;
       } else {
diff --git a/src/min_sd.cpp b/src/min_sd.cpp
index e4e159003f..d973ec1c82 100644
--- a/src/min_sd.cpp
+++ b/src/min_sd.cpp
@@ -13,6 +13,7 @@
 
 #include "min_sd.h"
 #include <cmath>
+#include "error.h"
 #include "update.h"
 #include "output.h"
 #include "timer.h"
@@ -77,8 +78,14 @@ int MinSD::iterate(int maxiter)
 
     // force tolerance criterion
 
-    fdotf = fnorm_sqr();
-    if (fdotf < update->ftol*update->ftol) return FTOL;
+    fdotf = 0.0;
+    if (update->ftol > 0.0) {
+      if (normstyle == MAX) fdotf = fnorm_max();        // max force norm
+      else if (normstyle == INF) fdotf = fnorm_inf();   // infinite force norm
+      else if (normstyle == TWO) fdotf = fnorm_sqr();   // Euclidean force 2-norm
+      else error->all(FLERR,"Illegal min_modify command");
+      if (fdotf < update->ftol*update->ftol) return FTOL;
+    }
 
     // set new search direction h to f = -Grad(x)
 
diff --git a/src/modify.cpp b/src/modify.cpp
index 109571d531..101540f786 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -1029,7 +1029,7 @@ int Modify::find_fix_by_style(const char *style)
 {
   int ifix;
   for (ifix = 0; ifix < nfix; ifix++)
-    if (strcmp(style,fix[ifix]->style) == 0) break;
+    if (utils::strmatch(fix[ifix]->style,style)) break;
   if (ifix == nfix) return -1;
   return ifix;
 }
@@ -1364,7 +1364,7 @@ int Modify::read_restart(FILE *fp)
   // nfix_restart_global = # of restart entries with global state info
 
   int me = comm->me;
-  if (me == 0) fread(&nfix_restart_global,sizeof(int),1,fp);
+  if (me == 0) utils::sfread(FLERR,&nfix_restart_global,sizeof(int),1,fp,NULL,error);
   MPI_Bcast(&nfix_restart_global,1,MPI_INT,0,world);
 
   // allocate space for each entry
@@ -1381,22 +1381,22 @@ int Modify::read_restart(FILE *fp)
 
   int n;
   for (int i = 0; i < nfix_restart_global; i++) {
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     id_restart_global[i] = new char[n];
-    if (me == 0) fread(id_restart_global[i],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,id_restart_global[i],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(id_restart_global[i],n,MPI_CHAR,0,world);
 
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     style_restart_global[i] = new char[n];
-    if (me == 0) fread(style_restart_global[i],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,style_restart_global[i],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(style_restart_global[i],n,MPI_CHAR,0,world);
 
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     state_restart_global[i] = new char[n];
-    if (me == 0) fread(state_restart_global[i],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,state_restart_global[i],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(state_restart_global[i],n,MPI_CHAR,0,world);
 
     used_restart_global[i] = 0;
@@ -1406,7 +1406,7 @@ int Modify::read_restart(FILE *fp)
 
   int maxsize = 0;
 
-  if (me == 0) fread(&nfix_restart_peratom,sizeof(int),1,fp);
+  if (me == 0) utils::sfread(FLERR,&nfix_restart_peratom,sizeof(int),1,fp,NULL,error);
   MPI_Bcast(&nfix_restart_peratom,1,MPI_INT,0,world);
 
   // allocate space for each entry
@@ -1423,19 +1423,19 @@ int Modify::read_restart(FILE *fp)
   // set index = which set of extra data this fix represents
 
   for (int i = 0; i < nfix_restart_peratom; i++) {
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     id_restart_peratom[i] = new char[n];
-    if (me == 0) fread(id_restart_peratom[i],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,id_restart_peratom[i],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(id_restart_peratom[i],n,MPI_CHAR,0,world);
 
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     style_restart_peratom[i] = new char[n];
-    if (me == 0) fread(style_restart_peratom[i],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,style_restart_peratom[i],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(style_restart_peratom[i],n,MPI_CHAR,0,world);
 
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     maxsize += n;
 
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 31720cc78c..1c53b2f7a4 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -85,6 +85,9 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
   // USER-DPD package
 
   np = NULL;
+
+  requestor = NULL;
+  requestor_type = NeighList::NONE;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/neigh_list.h b/src/neigh_list.h
index aca11cd921..146a01e7b5 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -20,6 +20,10 @@ namespace LAMMPS_NS {
 
 class NeighList : protected Pointers {
  public:
+  enum RequestorType { NONE, PAIR, FIX, COMPUTE };
+  void *         requestor;        // object that made request
+  RequestorType  requestor_type;   // type of requestor
+
   int index;                   // index of which neigh list this is
                                // also indexes the request it came from
                                // and the npair list of NPair classes
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index d38aed08c0..b62945f116 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -34,6 +34,7 @@
 #include "comm.h"
 #include "force.h"
 #include "pair.h"
+#include "pair_hybrid.h"
 #include "domain.h"
 #include "group.h"
 #include "modify.h"
@@ -374,9 +375,32 @@ void Neighbor::init()
     special_flag[3] = 1;
   else special_flag[3] = 2;
 
-  if (force->kspace || force->pair_match("coul/wolf",0) ||
-      force->pair_match("coul/dsf",0) || force->pair_match("thole",0))
-     special_flag[1] = special_flag[2] = special_flag[3] = 2;
+  // We cannot remove special neighbors with kspace or kspace-like pair styles
+  // as the exclusion needs to remove the full coulomb and not the damped interaction.
+  // Special treatment is required for hybrid pair styles since Force::pair_match()
+  // will only return a non-NULL pointer if there is only one substyle of the kind.
+
+  if (force->kspace) {
+    special_flag[1] = special_flag[2] = special_flag[3] = 2;
+  } else {
+    PairHybrid *ph = reinterpret_cast<PairHybrid *>(force->pair_match("^hybrid",0));
+    if (ph) {
+      int flag=0;
+      for (int isub=0; isub < ph->nstyles; ++isub) {
+        if (force->pair_match("coul/wolf",0,isub)
+            || force->pair_match("coul/dsf",0,isub)
+            || force->pair_match("thole",0,isub))
+          ++flag;
+      }
+      if (flag)
+        special_flag[1] = special_flag[2] = special_flag[3] = 2;
+    } else {
+      if (force->pair_match("coul/wolf",0)
+          || force->pair_match("coul/dsf",0)
+          || force->pair_match("thole",0))
+        special_flag[1] = special_flag[2] = special_flag[3] = 2;
+    }
+  }
 
   // maxwt = max multiplicative factor on atom indices stored in neigh list
 
@@ -701,6 +725,15 @@ int Neighbor::init_pair()
       create_kokkos_list(i);
     else lists[i] = new NeighList(lmp);
     lists[i]->index = i;
+    lists[i]->requestor = requests[i]->requestor;
+
+    if(requests[i]->pair) {
+        lists[i]->requestor_type = NeighList::PAIR;
+    } else if(requests[i]->fix) {
+        lists[i]->requestor_type = NeighList::FIX;
+    } else if(requests[i]->compute) {
+        lists[i]->requestor_type = NeighList::COMPUTE;
+    }
 
     if (requests[i]->pair && i < nrequest_original) {
       Pair *pair = (Pair *) requests[i]->requestor;
@@ -1941,6 +1974,7 @@ int Neighbor::decide()
    conservative shrink procedure:
      compute distance each of 8 corners of box has moved since last reneighbor
      reduce skin distance by sum of 2 largest of the 8 values
+     if reduced skin distance is negative, set to zero
      new trigger = 1/2 of reduced skin distance
    for orthogonal box, only need 2 lo/hi corners
    for triclinic, need all 8 corners since deformations can displace all 8
@@ -1962,6 +1996,7 @@ int Neighbor::check_distance()
       delz = bboxhi[2] - boxhi_hold[2];
       delta2 = sqrt(delx*delx + dely*dely + delz*delz);
       delta = 0.5 * (skin - (delta1+delta2));
+      if (delta < 0.0) delta = 0.0;
       deltasq = delta*delta;
     } else {
       domain->box_corners();
@@ -1975,6 +2010,7 @@ int Neighbor::check_distance()
         else if (delta > delta2) delta2 = delta;
       }
       delta = 0.5 * (skin - (delta1+delta2));
+      if (delta < 0.0) delta = 0.0;
       deltasq = delta*delta;
     }
   } else deltasq = triggersq;
diff --git a/src/pair.cpp b/src/pair.cpp
index 7c8424ce18..0cedc18620 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -72,6 +72,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
 
   ewaldflag = pppmflag = msmflag = dispersionflag = tip4pflag = dipoleflag = spinflag = 0;
   reinitflag = 1;
+  centroidstressflag = 4;
 
   // pair_modify settings
 
@@ -91,9 +92,10 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
   allocated = 0;
   suffix_flag = Suffix::NONE;
 
-  maxeatom = maxvatom = 0;
+  maxeatom = maxvatom = maxcvatom = 0;
   eatom = NULL;
   vatom = NULL;
+  cvatom = NULL;
 
   num_tally_compute = 0;
   list_tally_compute = NULL;
@@ -122,6 +124,7 @@ Pair::~Pair()
 
   memory->destroy(eatom);
   memory->destroy(vatom);
+  memory->destroy(cvatom);
 }
 
 /* ----------------------------------------------------------------------
@@ -779,9 +782,21 @@ void Pair::ev_setup(int eflag, int vflag, int alloc)
   eflag_global = eflag % 2;
   eflag_atom = eflag / 2;
 
-  vflag_either = vflag;
   vflag_global = vflag % 4;
-  vflag_atom = vflag / 4;
+  vflag_atom = vflag & 4;
+  cvflag_atom = 0;
+
+  if (vflag & 8) {
+    if (centroidstressflag & 2) {
+      cvflag_atom = 1;
+    } else {
+      vflag_atom = 1;
+    }
+    // extra check, because both bits might be set
+    if (centroidstressflag & 1) vflag_atom = 1;
+  }
+
+  vflag_either = vflag_global || vflag_atom;
 
   // reallocate per-atom arrays if necessary
 
@@ -799,6 +814,13 @@ void Pair::ev_setup(int eflag, int vflag, int alloc)
       memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom");
     }
   }
+  if (cvflag_atom && atom->nmax > maxcvatom) {
+    maxcvatom = atom->nmax;
+    if (alloc) {
+      memory->destroy(cvatom);
+      memory->create(cvatom,comm->nthreads*maxcvatom,9,"pair:cvatom");
+    }
+  }
 
   // zero accumulators
   // use force->newton instead of newton_pair
@@ -823,6 +845,22 @@ void Pair::ev_setup(int eflag, int vflag, int alloc)
       vatom[i][5] = 0.0;
     }
   }
+  if (cvflag_atom && alloc) {
+    n = atom->nlocal;
+    if (force->newton) n += atom->nghost;
+    for (i = 0; i < n; i++) {
+      cvatom[i][0] = 0.0;
+      cvatom[i][1] = 0.0;
+      cvatom[i][2] = 0.0;
+      cvatom[i][3] = 0.0;
+      cvatom[i][4] = 0.0;
+      cvatom[i][5] = 0.0;
+      cvatom[i][6] = 0.0;
+      cvatom[i][7] = 0.0;
+      cvatom[i][8] = 0.0;
+      cvatom[i][9] = 0.0;
+    }
+  }
 
   // if vflag_global = 2 and pair::compute() calls virial_fdotr_compute()
   // compute global virial via (F dot r) instead of via pairwise summation
@@ -831,7 +869,7 @@ void Pair::ev_setup(int eflag, int vflag, int alloc)
   if (vflag_global == 2 && no_virial_fdotr_compute == 0) {
     vflag_fdotr = 1;
     vflag_global = 0;
-    if (vflag_atom == 0) vflag_either = 0;
+    if (vflag_atom == 0 && cvflag_atom == 0) vflag_either = 0;
     if (vflag_either == 0 && eflag_either == 0) evflag = 0;
   } else vflag_fdotr = 0;
 
@@ -863,6 +901,7 @@ void Pair::ev_unset()
   vflag_either = 0;
   vflag_global = 0;
   vflag_atom = 0;
+  cvflag_atom = 0;
   vflag_fdotr = 0;
 }
 
@@ -1760,6 +1799,7 @@ double Pair::memory_usage()
 {
   double bytes = comm->nthreads*maxeatom * sizeof(double);
   bytes += comm->nthreads*maxvatom*6 * sizeof(double);
+  bytes += comm->nthreads*maxcvatom*9 * sizeof(double);
   return bytes;
 }
 
diff --git a/src/pair.h b/src/pair.h
index a0269bd5b2..d578908b20 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -26,6 +26,7 @@ class Pair : protected Pointers {
   friend class DihedralCharmm;
   friend class DihedralCharmmOMP;
   friend class FixGPU;
+  friend class FixIntel;
   friend class FixOMP;
   friend class ThrOMP;
   friend class Info;
@@ -36,6 +37,7 @@ class Pair : protected Pointers {
   double eng_vdwl,eng_coul;      // accumulated energies
   double virial[6];              // accumulated virial
   double *eatom,**vatom;         // accumulated per-atom energy/virial
+  double **cvatom;               // accumulated per-atom centroid virial
 
   double cutforce;               // max cutoff for all atom pairs
   double **cutsq;                // cutoff sq for each atom pair
@@ -65,13 +67,18 @@ class Pair : protected Pointers {
   int spinflag;                  // 1 if compatible with spin solver
   int reinitflag;                // 1 if compatible with fix adapt and alike
 
+  int centroidstressflag;        // compatibility with centroid atomic stress
+                                 // 1 if same as two-body atomic stress
+                                 // 2 if implemented and different from two-body
+                                 // 4 if not compatible/implemented
+
   int tail_flag;                 // pair_modify flag for LJ tail correction
   double etail,ptail;            // energy/pressure tail corrections
   double etail_ij,ptail_ij;
 
   int evflag;                    // energy,virial settings
   int eflag_either,eflag_global,eflag_atom;
-  int vflag_either,vflag_global,vflag_atom;
+  int vflag_either,vflag_global,vflag_atom,cvflag_atom;
 
   int ncoultablebits;            // size of Coulomb table, accessed by KSpace
   int ndisptablebits;            // size of dispersion table
@@ -229,7 +236,7 @@ class Pair : protected Pointers {
 
  protected:
   int vflag_fdotr;
-  int maxeatom,maxvatom;
+  int maxeatom,maxvatom,maxcvatom;
 
   int copymode;   // if set, do not deallocate during destruction
                   // required when classes are used as functors by Kokkos
diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp
index b94436b696..31dd2ef62f 100644
--- a/src/pair_beck.cpp
+++ b/src/pair_beck.cpp
@@ -25,13 +25,16 @@
 #include "memory.h"
 #include "error.h"
 #include "math_special.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;
 
 /* ---------------------------------------------------------------------- */
 
-PairBeck::PairBeck(LAMMPS *lmp) : Pair(lmp) {}
+PairBeck::PairBeck(LAMMPS *lmp) : Pair(lmp) {
+  centroidstressflag = 1;
+}
 
 /* ---------------------------------------------------------------------- */
 
@@ -277,16 +280,16 @@ void PairBeck::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&AA[i][j],sizeof(double),1,fp);
-          fread(&BB[i][j],sizeof(double),1,fp);
-          fread(&aa[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&beta[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&AA[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&BB[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&aa[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&beta[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&AA[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&BB[i][j],1,MPI_DOUBLE,0,world);
@@ -316,8 +319,8 @@ void PairBeck::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/pair_born.cpp b/src/pair_born.cpp
index bd993acb56..b0aba57df5 100644
--- a/src/pair_born.cpp
+++ b/src/pair_born.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -329,16 +330,16 @@ void PairBorn::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&rho[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&d[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@@ -369,10 +370,10 @@ void PairBorn::write_restart_settings(FILE *fp)
 void PairBorn::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp
index f7e139c750..3e8c76696b 100644
--- a/src/pair_born_coul_dsf.cpp
+++ b/src/pair_born_coul_dsf.cpp
@@ -28,6 +28,7 @@
 #include "memory.h"
 #include "error.h"
 #include "math_special.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -360,16 +361,16 @@ void PairBornCoulDSF::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&rho[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&d[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@@ -401,11 +402,11 @@ void PairBornCoulDSF::write_restart_settings(FILE *fp)
 void PairBornCoulDSF::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&alpha,sizeof(double),1,fp);
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&alpha,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp
index f4d533bdb0..dc4e4b8e3f 100644
--- a/src/pair_born_coul_wolf.cpp
+++ b/src/pair_born_coul_wolf.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -359,16 +360,16 @@ void PairBornCoulWolf::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&rho[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&d[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@@ -400,11 +401,11 @@ void PairBornCoulWolf::write_restart_settings(FILE *fp)
 void PairBornCoulWolf::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&alf,sizeof(double),1,fp);
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&alf,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&alf,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index a94ce87891..6fc1c782e0 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -22,6 +22,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -31,6 +32,7 @@ using namespace MathConst;
 PairBuck::PairBuck(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -307,14 +309,14 @@ void PairBuck::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&rho[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@@ -343,10 +345,10 @@ void PairBuck::write_restart_settings(FILE *fp)
 void PairBuck::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp
index d05c139f71..ed0fb1fef8 100644
--- a/src/pair_buck_coul_cut.cpp
+++ b/src/pair_buck_coul_cut.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -35,6 +36,7 @@ using namespace MathConst;
 PairBuckCoulCut::PairBuckCoulCut(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -363,15 +365,15 @@ void PairBuckCoulCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&rho[i][j],sizeof(double),1,fp);
-          fread(&c[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
-          fread(&cut_coul[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
@@ -402,11 +404,11 @@ void PairBuckCoulCut::write_restart_settings(FILE *fp)
 void PairBuckCoulCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp
index 9e6f238eba..a197955085 100644
--- a/src/pair_coul_cut.cpp
+++ b/src/pair_coul_cut.cpp
@@ -22,12 +22,15 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairCoulCut::PairCoulCut(LAMMPS *lmp) : Pair(lmp) {}
+PairCoulCut::PairCoulCut(LAMMPS *lmp) : Pair(lmp) {
+  centroidstressflag = 1;
+}
 
 /* ---------------------------------------------------------------------- */
 
@@ -244,10 +247,10 @@ void PairCoulCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
-        if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
+        if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
       }
     }
@@ -271,9 +274,9 @@ void PairCoulCut::write_restart_settings(FILE *fp)
 void PairCoulCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp
index 1b87a93701..b45353837a 100644
--- a/src/pair_coul_debye.cpp
+++ b/src/pair_coul_debye.cpp
@@ -19,6 +19,7 @@
 #include "force.h"
 #include "neigh_list.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -145,10 +146,10 @@ void PairCoulDebye::write_restart_settings(FILE *fp)
 void PairCoulDebye::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&kappa,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&kappa,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&kappa,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp
index 22230182b0..a21bf61afb 100644
--- a/src/pair_coul_dsf.cpp
+++ b/src/pair_coul_dsf.cpp
@@ -28,6 +28,7 @@
 #include "memory.h"
 #include "math_const.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -42,7 +43,9 @@ using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-PairCoulDSF::PairCoulDSF(LAMMPS *lmp) : Pair(lmp) {}
+PairCoulDSF::PairCoulDSF(LAMMPS *lmp) : Pair(lmp) {
+  centroidstressflag = 1;
+}
 
 /* ---------------------------------------------------------------------- */
 
@@ -252,7 +255,7 @@ void PairCoulDSF::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
     }
 }
@@ -276,10 +279,10 @@ void PairCoulDSF::write_restart_settings(FILE *fp)
 void PairCoulDSF::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&alpha,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&alpha,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp
index 15c7839fc6..b34877f508 100644
--- a/src/pair_coul_wolf.cpp
+++ b/src/pair_coul_wolf.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -35,6 +36,7 @@ using namespace MathConst;
 PairCoulWolf::PairCoulWolf(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 0;        // NOTE: single() method below is not yet correct
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -248,7 +250,7 @@ void PairCoulWolf::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
     }
 }
@@ -272,10 +274,10 @@ void PairCoulWolf::write_restart_settings(FILE *fp)
 void PairCoulWolf::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&alf,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&alf,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&alf,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp
index ec65eaafd6..ef0b7dd21d 100644
--- a/src/pair_dpd.cpp
+++ b/src/pair_dpd.cpp
@@ -27,6 +27,7 @@
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -313,13 +314,13 @@ void PairDPD::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a0[i][j],sizeof(double),1,fp);
-          fread(&gamma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
@@ -347,10 +348,10 @@ void PairDPD::write_restart_settings(FILE *fp)
 void PairDPD::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&temperature,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&seed,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&temperature,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp
index 15d7c90b27..8366ff459f 100644
--- a/src/pair_dpd_tstat.cpp
+++ b/src/pair_dpd_tstat.cpp
@@ -21,6 +21,7 @@
 #include "comm.h"
 #include "random_mars.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -231,12 +232,12 @@ void PairDPDTstat::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&gamma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -264,11 +265,11 @@ void PairDPDTstat::write_restart_settings(FILE *fp)
 void PairDPDTstat::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&t_start,sizeof(double),1,fp);
-    fread(&t_stop,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&seed,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&t_start,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&t_stop,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&t_start,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&t_stop,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp
index 7fd3233f4c..dcc3ac5f51 100644
--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@@ -25,6 +25,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -279,13 +280,13 @@ void PairGauss::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&b[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&b[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&b[i][j],1,MPI_DOUBLE,0,world);
@@ -312,9 +313,9 @@ void PairGauss::write_restart_settings(FILE *fp)
 void PairGauss::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index 3c619b6c95..b88fa49a85 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -26,6 +26,8 @@
 #include "memory.h"
 #include "error.h"
 #include "respa.h"
+#include "utils.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -39,6 +41,10 @@ PairHybrid::PairHybrid(LAMMPS *lmp) : Pair(lmp),
 
   outerflag = 0;
   respaflag = 0;
+
+  // assume pair hybrid always supports centroid atomic stress,
+  // so that cflag_atom gets set when needed
+  centroidstressflag = 2;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -158,6 +164,27 @@ void PairHybrid::compute(int eflag, int vflag)
         for (j = 0; j < 6; j++)
           vatom[i][j] += vatom_substyle[i][j];
     }
+    if (cvflag_atom) {
+      n = atom->nlocal;
+      if (force->newton_pair) n += atom->nghost;
+      if (styles[m]->centroidstressflag & 2) {
+        double **cvatom_substyle = styles[m]->cvatom;
+        for (i = 0; i < n; i++)
+          for (j = 0; j < 9; j++)
+            cvatom[i][j] += cvatom_substyle[i][j];
+      } else {
+        double **vatom_substyle = styles[m]->vatom;
+        for (i = 0; i < n; i++) {
+          for (j = 0; j < 6; j++) {
+            cvatom[i][j] += vatom_substyle[i][j];
+          }
+          for (j = 6; j < 9; j++) {
+            cvatom[i][j] += vatom_substyle[i][j-3];
+          }
+        }
+      }
+    }
+
   }
 
   delete [] saved_special;
@@ -361,6 +388,7 @@ void PairHybrid::flags()
     if (styles[m]->dispersionflag) dispersionflag = 1;
     if (styles[m]->tip4pflag) tip4pflag = 1;
     if (styles[m]->compute_flag) compute_flag = 1;
+    if (styles[m]->centroidstressflag & 4) centroidstressflag |= 4;
   }
   init_svector();
 }
@@ -681,7 +709,7 @@ void PairHybrid::write_restart(FILE *fp)
 void PairHybrid::read_restart(FILE *fp)
 {
   int me = comm->me;
-  if (me == 0) fread(&nstyles,sizeof(int),1,fp);
+  if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error);
   MPI_Bcast(&nstyles,1,MPI_INT,0,world);
 
   // allocate list of sub-styles
@@ -704,32 +732,32 @@ void PairHybrid::read_restart(FILE *fp)
   // each sub-style is created via new_pair()
   // each reads its settings, but no coeff info
 
-  if (me == 0) fread(compute_tally,sizeof(int),nstyles,fp);
+  if (me == 0) utils::sfread(FLERR,compute_tally,sizeof(int),nstyles,fp,NULL,error);
   MPI_Bcast(compute_tally,nstyles,MPI_INT,0,world);
 
   int n,dummy;
   for (int m = 0; m < nstyles; m++) {
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     keywords[m] = new char[n];
-    if (me == 0) fread(keywords[m],sizeof(char),n,fp);
+    if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
     styles[m] = force->new_pair(keywords[m],0,dummy);
     styles[m]->read_restart_settings(fp);
     // read back per style special settings, if present
     special_lj[m] = special_coul[m] = NULL;
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     if (n > 0 ) {
       special_lj[m] = new double[4];
-      if (me == 0) fread(special_lj[m],sizeof(double),4,fp);
+      if (me == 0) utils::sfread(FLERR,special_lj[m],sizeof(double),4,fp,NULL,error);
       MPI_Bcast(special_lj[m],4,MPI_DOUBLE,0,world);
     }
-    if (me == 0) fread(&n,sizeof(int),1,fp);
+    if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
     MPI_Bcast(&n,1,MPI_INT,0,world);
     if (n > 0 ) {
       special_coul[m] = new double[4];
-      if (me == 0) fread(special_coul[m],sizeof(double),4,fp);
+      if (me == 0) utils::sfread(FLERR,special_coul[m],sizeof(double),4,fp,NULL,error);
       MPI_Bcast(special_coul[m],4,MPI_DOUBLE,0,world);
     }
   }
@@ -766,7 +794,6 @@ double PairHybrid::single(int i, int j, int itype, int jtype,
   double fone;
   fforce = 0.0;
   double esum = 0.0;
-  int n = 0;
 
   for (int m = 0; m < nmap[itype][jtype]; m++) {
     if (rsq < styles[map[itype][jtype][m]]->cutsq[itype][jtype]) {
@@ -893,6 +920,12 @@ void PairHybrid::modify_special(int m, int /*narg*/, char **arg)
   special[2] = force->numeric(FLERR,arg[2]);
   special[3] = force->numeric(FLERR,arg[3]);
 
+  // have to cast to PairHybrid to work around C++ access restriction
+
+  if (((PairHybrid *)styles[m])->suffix_flag & (Suffix::INTEL|Suffix::GPU))
+    error->all(FLERR,"Pair_modify special is not compatible with "
+                     "suffix version of hybrid substyle");
+
   if (strcmp(arg[0],"lj/coul") == 0) {
     if (!special_lj[m]) special_lj[m] = new double[4];
     if (!special_coul[m]) special_coul[m] = new double[4];
@@ -1015,6 +1048,7 @@ double PairHybrid::memory_usage()
 {
   double bytes = maxeatom * sizeof(double);
   bytes += maxvatom*6 * sizeof(double);
+  bytes += maxcvatom*9 * sizeof(double);
   for (int m = 0; m < nstyles; m++) bytes += styles[m]->memory_usage();
   return bytes;
 }
diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h
index 61e961ddcb..7717d1fd51 100644
--- a/src/pair_hybrid.h
+++ b/src/pair_hybrid.h
@@ -29,6 +29,7 @@ class PairHybrid : public Pair {
   friend class FixIntel;
   friend class FixOMP;
   friend class Force;
+  friend class Neighbor;
   friend class Respa;
   friend class Info;
   friend class PairDeprecated;
diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp
index c27038900d..f554872965 100644
--- a/src/pair_lj96_cut.cpp
+++ b/src/pair_lj96_cut.cpp
@@ -30,6 +30,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -605,13 +606,13 @@ void PairLJ96Cut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -640,10 +641,10 @@ void PairLJ96Cut::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp
index 7990952494..2af308b2f0 100644
--- a/src/pair_lj_cubic.cpp
+++ b/src/pair_lj_cubic.cpp
@@ -25,13 +25,16 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace PairLJCubicConstants;
 
 /* ---------------------------------------------------------------------- */
 
-PairLJCubic::PairLJCubic(LAMMPS *lmp) : Pair(lmp) {}
+PairLJCubic::PairLJCubic(LAMMPS *lmp) : Pair(lmp) {
+  centroidstressflag = 1;
+}
 
 /* ---------------------------------------------------------------------- */
 
@@ -276,14 +279,14 @@ void PairLJCubic::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -310,7 +313,7 @@ void PairLJCubic::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
 }
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index 0302858adb..e31e275a7d 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -30,6 +30,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -40,6 +41,7 @@ PairLJCut::PairLJCut(LAMMPS *lmp) : Pair(lmp)
 {
   respa_enable = 1;
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -599,13 +601,13 @@ void PairLJCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -634,10 +636,10 @@ void PairLJCut::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp
index d4640bee3a..7f0f89a5bf 100644
--- a/src/pair_lj_cut_coul_cut.cpp
+++ b/src/pair_lj_cut_coul_cut.cpp
@@ -23,6 +23,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -32,6 +33,7 @@ using namespace MathConst;
 PairLJCutCoulCut::PairLJCutCoulCut(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -352,14 +354,14 @@ void PairLJCutCoulCut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
-          fread(&cut_coul[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -389,11 +391,11 @@ void PairLJCutCoulCut::write_restart_settings(FILE *fp)
 void PairLJCutCoulCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp
index 4ef533a743..a65d7aa50f 100644
--- a/src/pair_lj_cut_coul_debye.cpp
+++ b/src/pair_lj_cut_coul_debye.cpp
@@ -19,6 +19,7 @@
 #include "force.h"
 #include "comm.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -170,11 +171,11 @@ void PairLJCutCoulDebye::write_restart_settings(FILE *fp)
 void PairLJCutCoulDebye::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul_global,sizeof(double),1,fp);
-    fread(&kappa,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&kappa,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp
index 778f9f2fb4..9dc6c001f4 100644
--- a/src/pair_lj_cut_coul_dsf.cpp
+++ b/src/pair_lj_cut_coul_dsf.cpp
@@ -28,6 +28,7 @@
 #include "memory.h"
 #include "math_const.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -45,6 +46,7 @@ using namespace MathConst;
 PairLJCutCoulDSF::PairLJCutCoulDSF(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 0;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -375,13 +377,13 @@ void PairLJCutCoulDSF::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -411,12 +413,12 @@ void PairLJCutCoulDSF::write_restart_settings(FILE *fp)
 void PairLJCutCoulDSF::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&alpha,sizeof(double),1,fp);
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&alpha,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp
index 00a5832529..c69e90f28b 100644
--- a/src/pair_lj_cut_coul_wolf.cpp
+++ b/src/pair_lj_cut_coul_wolf.cpp
@@ -26,6 +26,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -36,6 +37,7 @@ PairLJCutCoulWolf::PairLJCutCoulWolf(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 0;
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -367,13 +369,13 @@ void PairLJCutCoulWolf::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_lj[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -404,12 +406,12 @@ void PairLJCutCoulWolf::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&alf,sizeof(double),1,fp);
-    fread(&cut_lj_global,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&alf,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&alf,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index a5184bc2f5..98c8a808e2 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -22,6 +22,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -31,6 +32,7 @@ using namespace MathConst;
 PairLJExpand::PairLJExpand(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -323,14 +325,14 @@ void PairLJExpand::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&shift[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&shift[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -359,10 +361,10 @@ void PairLJExpand::write_restart_settings(FILE *fp)
 void PairLJExpand::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp
index baef482ef9..73f4307d62 100644
--- a/src/pair_lj_gromacs.cpp
+++ b/src/pair_lj_gromacs.cpp
@@ -24,6 +24,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -338,14 +339,14 @@ void PairLJGromacs::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -375,10 +376,10 @@ void PairLJGromacs::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_inner_global,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp
index c62944b6a1..a5663ecfd8 100644
--- a/src/pair_lj_gromacs_coul_gromacs.cpp
+++ b/src/pair_lj_gromacs_coul_gromacs.cpp
@@ -25,6 +25,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -33,6 +34,7 @@ using namespace LAMMPS_NS;
 PairLJGromacsCoulGromacs::PairLJGromacsCoulGromacs(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -377,12 +379,12 @@ void PairLJGromacsCoulGromacs::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -411,12 +413,12 @@ void PairLJGromacsCoulGromacs::write_restart_settings(FILE *fp)
 void PairLJGromacsCoulGromacs::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_lj_inner,sizeof(double),1,fp);
-    fread(&cut_lj,sizeof(double),1,fp);
-    fread(&cut_coul_inner,sizeof(double),1,fp);
-    fread(&cut_coul,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul_inner,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp
index 7c7eb51b53..bf97a44732 100644
--- a/src/pair_lj_smooth.cpp
+++ b/src/pair_lj_smooth.cpp
@@ -24,6 +24,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -32,6 +33,7 @@ using namespace LAMMPS_NS;
 PairLJSmooth::PairLJSmooth(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -351,14 +353,14 @@ void PairLJSmooth::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -388,10 +390,10 @@ void PairLJSmooth::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_inner_global,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp
index bc2904c262..19e84f971d 100644
--- a/src/pair_lj_smooth_linear.cpp
+++ b/src/pair_lj_smooth_linear.cpp
@@ -24,6 +24,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -31,6 +32,7 @@ using namespace LAMMPS_NS;
 
 PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) {
   single_hessian_enable = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -284,13 +286,13 @@ void PairLJSmoothLinear::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -317,8 +319,8 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp
index 46657687f6..4ce82381f3 100644
--- a/src/pair_mie_cut.cpp
+++ b/src/pair_mie_cut.cpp
@@ -30,6 +30,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -626,15 +627,15 @@ void PairMIECut::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&gamR[i][j],sizeof(double),1,fp);
-          fread(&gamA[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&gamR[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&gamA[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -665,10 +666,10 @@ void PairMIECut::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
-    fread(&tail_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index d088f98bf4..b883036c18 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -21,6 +21,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -29,6 +30,7 @@ using namespace LAMMPS_NS;
 PairMorse::PairMorse(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -264,14 +266,14 @@ void PairMorse::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&d0[i][j],sizeof(double),1,fp);
-          fread(&alpha[i][j],sizeof(double),1,fp);
-          fread(&r0[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
@@ -299,9 +301,9 @@ void PairMorse::write_restart_settings(FILE *fp)
 void PairMorse::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index 6f821e684b..ddfc4476dc 100644
--- a/src/pair_soft.cpp
+++ b/src/pair_soft.cpp
@@ -22,6 +22,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -244,12 +245,12 @@ void PairSoft::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&prefactor[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&prefactor[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -274,8 +275,8 @@ void PairSoft::write_restart_settings(FILE *fp)
 void PairSoft::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 9fcbc3ee9f..9cb86b4123 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -976,13 +976,13 @@ void PairTable::write_restart_settings(FILE *fp)
 void PairTable::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&tabstyle,sizeof(int),1,fp);
-    fread(&tablength,sizeof(int),1,fp);
-    fread(&ewaldflag,sizeof(int),1,fp);
-    fread(&pppmflag,sizeof(int),1,fp);
-    fread(&msmflag,sizeof(int),1,fp);
-    fread(&dispersionflag,sizeof(int),1,fp);
-    fread(&tip4pflag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&ewaldflag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&pppmflag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&msmflag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&dispersionflag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&tip4pflag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
   MPI_Bcast(&tablength,1,MPI_INT,0,world);
diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp
index 8cc4d2796f..dd5bd078a3 100644
--- a/src/pair_ufm.cpp
+++ b/src/pair_ufm.cpp
@@ -27,6 +27,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -35,6 +36,7 @@ using namespace LAMMPS_NS;
 PairUFM::PairUFM(LAMMPS *lmp) : Pair(lmp)
 {
   writedata = 1;
+  centroidstressflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -278,13 +280,13 @@ void PairUFM::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilon[i][j],sizeof(double),1,fp);
-          fread(&sigma[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@@ -312,9 +314,9 @@ void PairUFM::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index e8775c9668..d1e06fdb84 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -20,6 +20,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -252,12 +253,12 @@ void PairYukawa::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&a[i][j],sizeof(double),1,fp);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
@@ -284,10 +285,10 @@ void PairYukawa::write_restart_settings(FILE *fp)
 void PairYukawa::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&kappa,sizeof(double),1,fp);
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&kappa,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&kappa,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp
index 403bd73944..6ab108ff4f 100644
--- a/src/pair_zero.cpp
+++ b/src/pair_zero.cpp
@@ -23,6 +23,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -31,6 +32,8 @@ using namespace LAMMPS_NS;
 PairZero::PairZero(LAMMPS *lmp) : Pair(lmp) {
   coeffflag=1;
   writedata=1;
+  single_enable=1;
+  respa_enable=1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -49,10 +52,16 @@ PairZero::~PairZero()
 void PairZero::compute(int eflag, int vflag)
 {
  ev_init(eflag,vflag);
-
  if (vflag_fdotr) virial_fdotr_compute();
 }
 
+/* ---------------------------------------------------------------------- */
+
+void PairZero::compute_outer(int eflag, int vflag)
+{
+ ev_init(eflag,vflag);
+}
+
 /* ----------------------------------------------------------------------
    allocate all arrays
 ------------------------------------------------------------------------- */
@@ -170,11 +179,11 @@ void PairZero::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
         }
         MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
       }
@@ -199,8 +208,8 @@ void PairZero::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&coeffflag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
+    utils::sfread(FLERR,&coeffflag,sizeof(int),1,fp,NULL,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&coeffflag,1,MPI_INT,0,world);
@@ -227,4 +236,13 @@ void PairZero::write_data_all(FILE *fp)
       fprintf(fp,"%d %d %g\n",i,j,cut[i][j]);
 }
 
+/* ---------------------------------------------------------------------- */
+
+double PairZero::single(int /*i*/, int /*j*/, int /* itype */, int /* jtype */,
+                        double /* rsq */, double /*factor_coul*/,
+                        double /* factor_lj */, double &fforce)
+{
+  fforce = 0.0;
+  return 0.0;
+}
 
diff --git a/src/pair_zero.h b/src/pair_zero.h
index b980ed89d1..058edbd053 100644
--- a/src/pair_zero.h
+++ b/src/pair_zero.h
@@ -39,6 +39,7 @@ class PairZero : public Pair {
   PairZero(class LAMMPS *);
   virtual ~PairZero();
   virtual void compute(int, int);
+  virtual void compute_outer(int, int);
   void settings(int, char **);
   void coeff(int, char **);
   double init_one(int, int);
@@ -48,6 +49,7 @@ class PairZero : public Pair {
   void read_restart_settings(FILE *);
   void write_data(FILE *);
   void write_data_all(FILE *);
+  double single(int, int, int, int, double, double, double, double &);
 
  protected:
   double cut_global;
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 1208ab4b43..d558b87633 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -2151,7 +2151,7 @@ void ReadData::parse_coeffs(char *line, const char *addstr,
   // to avoid segfaults on empty lines
 
   if (narg == 0) return;
-  
+
   if (noffset) {
     int value = force->inumeric(FLERR,arg[0]);
     sprintf(argoffset1,"%d",value+offset);
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index 7316a2f5cd..c61c467a59 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -434,8 +434,9 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip)
   // all filereader procs close all their files and return
 
   if (ntimestep < 0) {
-    for (int i = 0; i < nreader; i++)
-      readers[i]->close_file();
+    if (filereader)
+      for (int i = 0; i < nreader; i++)
+        readers[i]->close_file();
     return ntimestep;
   }
 
@@ -503,7 +504,7 @@ void ReadDump::header(int fieldinfo)
     yhi = box[1][1];
     zlo = box[2][0];
     zhi = box[2][1];
-    
+
     if (triclinic_snap) {
       xy = box[0][2];
       xz = box[1][2];
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 3d2e2b6592..a31700990d 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -35,6 +35,7 @@
 #include "mpiio.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -302,24 +303,24 @@ void ReadRestart::command(int narg, char **arg)
         error->one(FLERR,str);
       }
 
-      fread(&flag,sizeof(int),1,fp);
+      utils::sfread(FLERR,&flag,sizeof(int),1,fp,NULL,error);
       if (flag != PROCSPERFILE)
         error->one(FLERR,"Invalid flag in peratom section of restart file");
       int procsperfile;
-      fread(&procsperfile,sizeof(int),1,fp);
+      utils::sfread(FLERR,&procsperfile,sizeof(int),1,fp,NULL,error);
 
       for (int i = 0; i < procsperfile; i++) {
-        fread(&flag,sizeof(int),1,fp);
+        utils::sfread(FLERR,&flag,sizeof(int),1,fp,NULL,error);
         if (flag != PERPROC)
           error->one(FLERR,"Invalid flag in peratom section of restart file");
 
-        fread(&n,sizeof(int),1,fp);
+        utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
         if (n > maxbuf) {
           maxbuf = n;
           memory->destroy(buf);
           memory->create(buf,maxbuf,"read_restart:buf");
         }
-        fread(buf,sizeof(double),n,fp);
+        utils::sfread(FLERR,buf,sizeof(double),n,fp,NULL,error);
 
         m = 0;
         while (m < n) m += avec->unpack_restart(&buf[m]);
@@ -379,10 +380,10 @@ void ReadRestart::command(int narg, char **arg)
     int flag,procsperfile;
 
     if (filereader) {
-      fread(&flag,sizeof(int),1,fp);
+      utils::sfread(FLERR,&flag,sizeof(int),1,fp,NULL,error);
       if (flag != PROCSPERFILE)
         error->one(FLERR,"Invalid flag in peratom section of restart file");
-      fread(&procsperfile,sizeof(int),1,fp);
+      utils::sfread(FLERR,&procsperfile,sizeof(int),1,fp,NULL,error);
     }
     MPI_Bcast(&procsperfile,1,MPI_INT,0,clustercomm);
 
@@ -391,17 +392,17 @@ void ReadRestart::command(int narg, char **arg)
 
     for (int i = 0; i < procsperfile; i++) {
       if (filereader) {
-        fread(&flag,sizeof(int),1,fp);
+        utils::sfread(FLERR,&flag,sizeof(int),1,fp,NULL,error);
         if (flag != PERPROC)
           error->one(FLERR,"Invalid flag in peratom section of restart file");
 
-        fread(&n,sizeof(int),1,fp);
+        utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error);
         if (n > maxbuf) {
           maxbuf = n;
           memory->destroy(buf);
           memory->create(buf,maxbuf,"read_restart:buf");
         }
-        fread(buf,sizeof(double),n,fp);
+        utils::sfread(FLERR,buf,sizeof(double),n,fp,NULL,error);
 
         if (i % nclusterprocs) {
           iproc = me + (i % nclusterprocs);
@@ -734,8 +735,12 @@ void ReadRestart::header(int incompatible)
 
     } else if (flag == NPROCS) {
       nprocs_file = read_int();
-      if (nprocs_file != comm->nprocs && me == 0)
-        error->warning(FLERR,"Restart file used different # of processors");
+      if (nprocs_file != comm->nprocs && me == 0) {
+        char msg[128];
+        snprintf(msg,128,"Restart file used different # of processors: %d vs. %d",
+                 nprocs_file,comm->nprocs);
+        error->warning(FLERR,msg);
+      }
 
     // don't set procgrid, warn if different
 
@@ -1101,7 +1106,7 @@ void ReadRestart::file_layout()
           memory->create(nproc_chunk_number,nprocs,
                          "write_restart:nproc_chunk_number");
 
-          fread(all_written_send_sizes,sizeof(int),nprocs_file,fp);
+          utils::sfread(FLERR,all_written_send_sizes,sizeof(int),nprocs_file,fp,NULL,error);
 
           if ((nprocs != nprocs_file) && !(atom->nextra_store)) {
             // nprocs differ, but atom sizes are fixed length, yeah!
@@ -1283,7 +1288,7 @@ char *ReadRestart::read_string()
   int n = read_int();
   if (n < 0) error->all(FLERR,"Illegal size string or corrupt restart");
   char *value = new char[n];
-  if (me == 0) fread(value,sizeof(char),n,fp);
+  if (me == 0) utils::sfread(FLERR,value,sizeof(char),n,fp,NULL,error);
   MPI_Bcast(value,n,MPI_CHAR,0,world);
   return value;
 }
@@ -1295,7 +1300,7 @@ char *ReadRestart::read_string()
 void ReadRestart::read_int_vec(int n, int *vec)
 {
   if (n < 0) error->all(FLERR,"Illegal size integer vector read requested");
-  if (me == 0) fread(vec,sizeof(int),n,fp);
+  if (me == 0) utils::sfread(FLERR,vec,sizeof(int),n,fp,NULL,error);
   MPI_Bcast(vec,n,MPI_INT,0,world);
 }
 
@@ -1306,6 +1311,6 @@ void ReadRestart::read_int_vec(int n, int *vec)
 void ReadRestart::read_double_vec(int n, double *vec)
 {
   if (n < 0) error->all(FLERR,"Illegal size double vector read requested");
-  if (me == 0) fread(vec,sizeof(double),n,fp);
+  if (me == 0) utils::sfread(FLERR,vec,sizeof(double),n,fp,NULL,error);
   MPI_Bcast(vec,n,MPI_DOUBLE,0,world);
 }
diff --git a/src/reader_native.cpp b/src/reader_native.cpp
index fba613bdd3..da2c97bbe5 100644
--- a/src/reader_native.cpp
+++ b/src/reader_native.cpp
@@ -56,12 +56,19 @@ int ReaderNative::read_time(bigint &ntimestep)
   char *eof = fgets(line,MAXLINE,fp);
   if (eof == NULL) return 1;
 
+  // skip over unit information, if present.
+
+  if (strstr(line,"ITEM: UNITS") == line)
+    read_lines(2);
+
   if (strstr(line,"ITEM: TIMESTEP") != line)
     error->one(FLERR,"Dump file is incorrectly formatted");
+
   read_lines(1);
   int rv = sscanf(line,BIGINT_FORMAT,&ntimestep);
   if (rv != 1)
     error->one(FLERR,"Dump file is incorrectly formatted");
+
   return 0;
 }
 
@@ -106,7 +113,7 @@ void ReaderNative::skip()
    only called by proc 0
 ------------------------------------------------------------------------- */
 
-bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic, 
+bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
                                  int fieldinfo, int nfield,
                                  int *fieldtype, char **fieldlabel,
                                  int scaleflag, int wrapflag, int &fieldflag,
diff --git a/src/suffix.h b/src/suffix.h
index 817600dfd5..88629aa796 100644
--- a/src/suffix.h
+++ b/src/suffix.h
@@ -16,13 +16,14 @@
 
 namespace LAMMPS_NS {
 
-namespace Suffix {
-  static const int NONE = 0;
-  static const int OPT  = 1<<0;
-  static const int GPU  = 1<<1;
-  static const int OMP  = 1<<2;
-  static const int INTEL  = 1<<3;
-}
+enum Suffix {
+  NONE   = 0,
+  OPT    = 1<<0,
+  GPU    = 1<<1,
+  OMP    = 1<<2,
+  INTEL  = 1<<3,
+  KOKKOS = 1<<4
+};
 
 }
 
diff --git a/src/update.cpp b/src/update.cpp
index 68a6a1a057..c82e2bcf96 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -404,7 +404,7 @@ void Update::create_minimize(int narg, char **arg, int trysuffix)
    create the Minimize style, first with suffix appended
 ------------------------------------------------------------------------- */
 
-void Update::new_minimize(char *style, int narg, char **arg,
+void Update::new_minimize(char *style, int /* narg */, char ** /* arg */,
                            int trysuffix, int &sflag)
 {
   if (trysuffix && lmp->suffix_enable) {
diff --git a/src/utils.cpp b/src/utils.cpp
index 5e53a3a09d..f6556a3ac8 100644
--- a/src/utils.cpp
+++ b/src/utils.cpp
@@ -17,6 +17,10 @@
 #include "lammps.h"
 #include "error.h"
 
+#if defined(__linux)
+#include <unistd.h>  // for readlink
+#endif
+
 /*! \file utils.cpp */
 
 /*
@@ -103,14 +107,43 @@ int utils::cfvarg(std::string mode, const char *arg, char *&cfv_id)
   return rv;
 }
 
+/** \brief try to detect pathname from FILE pointer. Currently only supported on Linux, otherwise will report "(unknown)".
+ *
+ *  \param buf  storage buffer for pathname. output will be truncated if not large enough
+ *  \param len  size of storage buffer. output will be truncated to this length - 1
+ *  \param fp   FILE pointer structe from STDIO library for which we want to detect the name
+ *  \return pointer to the storage buffer, i.e. buf
+ */
+static const char *guesspath(char *buf, int len, FILE *fp)
+{
+  memset(buf,0,len);
+
+#if defined(__linux)
+  char procpath[32];
+  int fd = fileno(fp);
+  snprintf(procpath,32,"/proc/self/fd/%d",fd);
+  // get pathname from /proc or copy (unknown)
+  if (readlink(procpath,buf,len-1) <= 0) strcpy(buf,"(unknown)");
+#else
+  strcpy(buf,"(unknown)");
+#endif
+  return buf;
+}
+
+#define MAXPATHLENBUF 1024
 /* like fgets() but aborts with an error or EOF is encountered */
 void utils::sfgets(const char *srcname, int srcline, char *s, int size,
                    FILE *fp, const char *filename, Error *error)
 {
   char *rv = fgets(s,size,fp);
   if (rv == NULL) { // something went wrong
+    char buf[MAXPATHLENBUF];
     std::string errmsg;
 
+    // try to figure out the file name from the file pointer
+    if (!filename)
+      filename = guesspath(buf,MAXPATHLENBUF,fp);
+
     if (feof(fp)) {
       errmsg = "Unexpected end of file while reading file '";
     } else if (ferror(fp)) {
@@ -127,6 +160,34 @@ void utils::sfgets(const char *srcname, int srcline, char *s, int size,
   return;
 }
 
+/* like fread() but aborts with an error or EOF is encountered */
+void utils::sfread(const char *srcname, int srcline, void *s, size_t size,
+                   size_t num, FILE *fp, const char *filename, Error *error)
+{
+  size_t rv = fread(s,size,num,fp);
+  if (rv != num) { // something went wrong
+    char buf[MAXPATHLENBUF];
+    std::string errmsg;
+
+    // try to figure out the file name from the file pointer
+    if (!filename)
+      filename = guesspath(buf,MAXPATHLENBUF,fp);
+
+    if (feof(fp)) {
+      errmsg = "Unexpected end of file while reading file '";
+    } else if (ferror(fp)) {
+      errmsg = "Unexpected error while reading file '";
+    } else {
+      errmsg = "Unexpected short read while reading file '";
+    }
+    errmsg += filename;
+    errmsg += "'";
+
+    if (error) error->one(srcname,srcline,errmsg.c_str());
+  }
+  return;
+}
+
 /* ------------------------------------------------------------------ */
 
 std::string utils::check_packages_for_style(std::string style,
diff --git a/src/utils.h b/src/utils.h
index 5f71bfae76..e87aa4bb91 100644
--- a/src/utils.h
+++ b/src/utils.h
@@ -63,12 +63,27 @@ namespace LAMMPS_NS {
      *  \param s        buffer for storing the result of fgets()
      *  \param size     size of buffer s (max number of bytes read by fgets())
      *  \param fp       file pointer used by fgets()
-     *  \param filename file name associated with fp (for error message)
+     *  \param filename file name associated with fp (may be NULL; then LAMMPS will try to detect)
      *  \param error    pointer to Error class instance (for abort)
      */
     void sfgets(const char *srcname, int srcline, char *s, int size,
                 FILE *fp, const char *filename, Error *error);
 
+    /** \brief safe wrapper around fread() which aborts on errors
+     *  or EOF and prints a suitable error message to help debugging
+     *
+     *  \param srcname  name of the calling source file (from FLERR macro)
+     *  \param srcline  line in the calling source file (from FLERR macro)
+     *  \param s        buffer for storing the result of fread()
+     *  \param size     size of data elements read by fread()
+     *  \param num      number of data elements read by fread()
+     *  \param fp       file pointer used by fread()
+     *  \param filename file name associated with fp (may be NULL; then LAMMPS will try to detect)
+     *  \param error    pointer to Error class instance (for abort)
+     */
+    void sfread(const char *srcname, int srcline, void *s, size_t size,
+                size_t num, FILE *fp, const char *filename, Error *error);
+
     /** \brief Report if a requested style is in a package or may have a typo
      *
      *  \param style type of style that is to be checked for
diff --git a/src/version.h b/src/version.h
index 7387a3a1a4..1c5c4c6206 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "7 Aug 2019"
+#define LAMMPS_VERSION "09 Jan 2020"
diff --git a/tools/binary2txt.cpp b/tools/binary2txt.cpp
index e0778fbf3c..119e9e3574 100644
--- a/tools/binary2txt.cpp
+++ b/tools/binary2txt.cpp
@@ -99,9 +99,9 @@ int main(int narg, char **arg)
       // detect end-of-file
 
       if (feof(fp)) {
-	fclose(fp);
-	fclose(fptxt);
-	break;
+        fclose(fp);
+        fclose(fptxt);
+        break;
       }
 
       fread(&natoms,sizeof(bigint),1,fp);
@@ -114,13 +114,13 @@ int main(int narg, char **arg)
       fread(&zlo,sizeof(double),1,fp);
       fread(&zhi,sizeof(double),1,fp);
       if (triclinic) {
-	fread(&xy,sizeof(double),1,fp);
-	fread(&xz,sizeof(double),1,fp);
-	fread(&yz,sizeof(double),1,fp);
+        fread(&xy,sizeof(double),1,fp);
+        fread(&xz,sizeof(double),1,fp);
+        fread(&yz,sizeof(double),1,fp);
       }
       fread(&size_one,sizeof(int),1,fp);
       fread(&nchunk,sizeof(int),1,fp);
-      
+
       fprintf(fptxt,"ITEM: TIMESTEP\n");
       fprintf(fptxt,BIGINT_FORMAT "\n",ntimestep);
       fprintf(fptxt,"ITEM: NUMBER OF ATOMS\n");
@@ -128,26 +128,26 @@ int main(int narg, char **arg)
 
       m = 0;
       for (int idim = 0; idim < 3; idim++) {
-	for (int iside = 0; iside < 2; iside++) {
-	  if (boundary[idim][iside] == 0) boundstr[m++] = 'p';
-	  else if (boundary[idim][iside] == 1) boundstr[m++] = 'f';
-	  else if (boundary[idim][iside] == 2) boundstr[m++] = 's';
-	  else if (boundary[idim][iside] == 3) boundstr[m++] = 'm';
-	}
-	boundstr[m++] = ' ';
+        for (int iside = 0; iside < 2; iside++) {
+          if (boundary[idim][iside] == 0) boundstr[m++] = 'p';
+          else if (boundary[idim][iside] == 1) boundstr[m++] = 'f';
+          else if (boundary[idim][iside] == 2) boundstr[m++] = 's';
+          else if (boundary[idim][iside] == 3) boundstr[m++] = 'm';
+        }
+        boundstr[m++] = ' ';
       }
       boundstr[8] = '\0';
-      
+
       if (!triclinic) {
-	fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr);
-	fprintf(fptxt,"%g %g\n",xlo,xhi);
-	fprintf(fptxt,"%g %g\n",ylo,yhi);
-	fprintf(fptxt,"%g %g\n",zlo,zhi);
+        fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr);
+        fprintf(fptxt,"%g %g\n",xlo,xhi);
+        fprintf(fptxt,"%g %g\n",ylo,yhi);
+        fprintf(fptxt,"%g %g\n",zlo,zhi);
       } else {
-	fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr);
-	fprintf(fptxt,"%g %g %g\n",xlo,xhi,xy);
-	fprintf(fptxt,"%g %g %g\n",ylo,yhi,xz);
-	fprintf(fptxt,"%g %g %g\n",zlo,zhi,yz);
+        fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr);
+        fprintf(fptxt,"%g %g %g\n",xlo,xhi,xy);
+        fprintf(fptxt,"%g %g %g\n",ylo,yhi,xz);
+        fprintf(fptxt,"%g %g %g\n",zlo,zhi,yz);
       }
       fprintf(fptxt,"ITEM: ATOMS\n");
 
@@ -156,25 +156,25 @@ int main(int narg, char **arg)
       // loop over processor chunks in file
 
       for (i = 0; i < nchunk; i++) {
-	fread(&n,sizeof(int),1,fp);
+        fread(&n,sizeof(int),1,fp);
 
-	// extend buffer to fit chunk size
-	
-	if (n > maxbuf) {
-	  if (buf) delete [] buf;
-	  buf = new double[n];
-	  maxbuf = n;
-	}
+        // extend buffer to fit chunk size
 
-	// read chunk and write as size_one values per line
+        if (n > maxbuf) {
+          if (buf) delete [] buf;
+          buf = new double[n];
+          maxbuf = n;
+        }
 
-	fread(buf,sizeof(double),n,fp);
-	n /= size_one;
-	m = 0;
-	for (j = 0; j < n; j++) {
-	  for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]);
-	  fprintf(fptxt,"\n");
-	}
+        // read chunk and write as size_one values per line
+
+        fread(buf,sizeof(double),n,fp);
+        n /= size_one;
+        m = 0;
+        for (j = 0; j < n; j++) {
+          for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]);
+          fprintf(fptxt,"\n");
+        }
       }
 
       printf(" " BIGINT_FORMAT,ntimestep);
diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl
index bda9ace2bc..b53bd00541 100755
--- a/tools/ch2lmp/charmm2lammps.pl
+++ b/tools/ch2lmp/charmm2lammps.pl
@@ -39,6 +39,7 @@
 #    20161001   Added instructions in CMAP section to fix problem if 'ter'
 #                 is not designated in the .pdb file to identify last amino acid
 #    20161005   Added tweak to embed command line in generated LAMMPS input
+#    20181120   Fix topology parsing bug
 #
 #    General    Many thanks to Paul S. Crozier for checking script validity
 #               against his projects.
@@ -86,8 +87,8 @@
     my $notes;
 
     $program            = "charmm2lammps";
-    $version            = "1.9.1";
-    $year               = "2016";
+    $version            = "1.9.2";
+    $year               = "2018";
     $add                = 1;
     $water_dens         = 0;
     $ions               = 0;
diff --git a/tools/eam_database/create.f b/tools/eam_database/create.f
index 2bdf49dd0d..528b4251db 100644
--- a/tools/eam_database/create.f
+++ b/tools/eam_database/create.f
@@ -73,8 +73,9 @@ ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
          rhoin(ntypes)=rhol(ntypes)*rhoe(ntypes)
          rhoout(ntypes)=rhoh(ntypes)*rhoe(ntypes)
       else
-         do 1 i=1,27
-1        read(10,*)vtmp
+         do i=1,27
+           read(10,*)vtmp
+         end do
          goto 11
       endif
       close(10)
@@ -94,28 +95,29 @@ ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
       rst=0.5
       dr=rc/(nr-1.0)
       fmax=-1.0
-      do 3 i1=1,ntypes
-      do 3 i2=1,i1
-      if ( i1 .eq. i2) then
-         do 4 i=1,nr
-            r=(i-1.0)*dr
-            if (r .lt. rst) r=rst
-            call prof(i1,r,fvalue)
-            if (fmax .lt. fvalue) fmax=fvalue
-            rhor(i,i1)=fvalue
-            call pair(i1,i2,r,psi)
-            z2r(i,i1,i2)=r*psi
-4        continue
-      else
-         do 5 i=1,nr
-            r=(i-1.0)*dr
-            if (r .lt. rst) r=rst
-            call pair(i1,i2,r,psi)
-            z2r(i,i1,i2)=r*psi
-            z2r(i,i2,i1)=z2r(i,i1,i2)
-5        continue
-      endif
-3     continue
+      do i1=1,ntypes
+         do i2=1,i1
+         if ( i1 .eq. i2) then
+            do i=1,nr
+               r=(i-1.0)*dr
+               if (r .lt. rst) r=rst
+               call prof(i1,r,fvalue)
+               if (fmax .lt. fvalue) fmax=fvalue
+               rhor(i,i1)=fvalue
+               call pair(i1,i2,r,psi)
+               z2r(i,i1,i2)=r*psi
+            end do
+         else
+            do i=1,nr
+               r=(i-1.0)*dr
+               if (r .lt. rst) r=rst
+               call pair(i1,i2,r,psi)
+               z2r(i,i1,i2)=r*psi
+               z2r(i,i2,i1)=z2r(i,i1,i2)
+            end do
+         endif
+         end do
+      end do
       rhom=fmax
       if (rhom .lt. 2.0*rhoemax) rhom=2.0*rhoemax
       if (rhom .lt. 100.0) rhom=100.0
@@ -239,10 +241,11 @@ ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
 10    continue
 11    format(i5,2g15.5,a8)
 12    format(5e24.16)
-      do 13 i1=1,ntypes
-      do 13 i2=1,i1
-      write(1,12)(z2r(i,i1,i2),i=1,nr)
-13    continue
+      do i1=1,ntypes
+         do i2=1,i1
+            write(1,12)(z2r(i,i1,i2),i=1,nr)
+         end do
+      end do
       close(1)
       return
       end
diff --git a/tools/python/pizza/cfg.py b/tools/python/pizza/cfg.py
index 8cefd38acd..bbd930ea3c 100644
--- a/tools/python/pizza/cfg.py
+++ b/tools/python/pizza/cfg.py
@@ -3,7 +3,7 @@
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-# certain rights in this software.  This software is distributed under 
+# certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
 # cfg tool
@@ -11,14 +11,14 @@
 oneline = "Convert LAMMPS snapshots to AtomEye CFG format"
 
 docstr = """
-c = cfg(d)		d = object containing atom coords (dump, data)
+c = cfg(d)              d = object containing atom coords (dump, data)
 
 c.one()                 write all snapshots to tmp.cfg
 c.one("new")            write all snapshots to new.cfg
 c.many()                write snapshots to tmp0000.cfg, tmp0001.cfg, etc
 c.many("new")           write snapshots to new0000.cfg, new0001.cfg, etc
-c.single(N)             write snapshot for timestep N to tmp.cfg 
-c.single(N,"file")      write snapshot for timestep N to file.cfg 
+c.single(N)             write snapshot for timestep N to tmp.cfg
+c.single(N,"file")      write snapshot for timestep N to file.cfg
 """
 
 # History
@@ -46,7 +46,7 @@ class cfg:
 
   def __init__(self,data):
     self.data = data
-   
+
   # --------------------------------------------------------------------
 
   def one(self,*args):
@@ -68,16 +68,16 @@ class cfg:
       print >>f,"Number of particles = %d " % len(atoms)
       print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
       print >>f,"H0(1,1) = %20.10f A " % xlen
-      print >>f,"H0(1,2) = 0.0 A " 
-      print >>f,"H0(1,3) = 0.0 A " 
-      print >>f,"H0(2,1) = 0.0 A " 
+      print >>f,"H0(1,2) = 0.0 A "
+      print >>f,"H0(1,3) = 0.0 A "
+      print >>f,"H0(2,1) = 0.0 A "
       print >>f,"H0(2,2) = %20.10f A " % ylen
-      print >>f,"H0(2,3) = 0.0 A " 
-      print >>f,"H0(3,1) = 0.0 A " 
-      print >>f,"H0(3,2) = 0.0 A " 
+      print >>f,"H0(2,3) = 0.0 A "
+      print >>f,"H0(3,1) = 0.0 A "
+      print >>f,"H0(3,2) = 0.0 A "
       print >>f,"H0(3,3) = %20.10f A " % zlen
       print >>f,"#"
-      
+
       for atom in atoms:
         itype = int(atom[1])
         xfrac = (atom[2]-box[0])/xlen
@@ -85,14 +85,14 @@ class cfg:
         zfrac = (atom[4]-box[2])/zlen
 #        print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  %15.10f  %15.10f  %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
         print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
-      
+
       print time,
       sys.stdout.flush()
       n += 1
-      
+
     f.close()
     print "\nwrote %d snapshots to %s in CFG format" % (n,file)
-      
+
   # --------------------------------------------------------------------
 
   def many(self,*args):
@@ -104,7 +104,7 @@ class cfg:
       which,time,flag = self.data.iterator(flag)
       if flag == -1: break
       time,box,atoms,bonds,tris,lines = self.data.viz(which)
-      
+
       if n < 10:
         file = root + "000" + str(n)
       elif n < 100:
@@ -112,7 +112,7 @@ class cfg:
       elif n < 1000:
         file = root + "0" + str(n)
       else:
-        file = root + str(n)  
+        file = root + str(n)
       file += ".cfg"
       f = open(file,"w")
 
@@ -123,16 +123,16 @@ class cfg:
       print >>f,"Number of particles = %d " % len(atoms)
       print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
       print >>f,"H0(1,1) = %20.10f A " % xlen
-      print >>f,"H0(1,2) = 0.0 A " 
-      print >>f,"H0(1,3) = 0.0 A " 
-      print >>f,"H0(2,1) = 0.0 A " 
+      print >>f,"H0(1,2) = 0.0 A "
+      print >>f,"H0(1,3) = 0.0 A "
+      print >>f,"H0(2,1) = 0.0 A "
       print >>f,"H0(2,2) = %20.10f A " % ylen
-      print >>f,"H0(2,3) = 0.0 A " 
-      print >>f,"H0(3,1) = 0.0 A " 
-      print >>f,"H0(3,2) = 0.0 A " 
+      print >>f,"H0(2,3) = 0.0 A "
+      print >>f,"H0(3,1) = 0.0 A "
+      print >>f,"H0(3,2) = 0.0 A "
       print >>f,"H0(3,3) = %20.10f A " % zlen
       print >>f,"#"
-      
+
       for atom in atoms:
         itype = int(atom[1])
         xfrac = (atom[2]-box[0])/xlen
@@ -140,14 +140,14 @@ class cfg:
         zfrac = (atom[4]-box[2])/zlen
 #        print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  %15.10f  %15.10f  %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
         print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
-      
+
       print time,
       sys.stdout.flush()
       f.close()
       n += 1
-  
+
     print "\nwrote %s snapshots in CFG format" % n
-  
+
   # --------------------------------------------------------------------
 
   def single(self,time,*args):
@@ -166,16 +166,16 @@ class cfg:
     print >>f,"Number of particles = %d " % len(atoms)
     print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
     print >>f,"H0(1,1) = %20.10f A " % xlen
-    print >>f,"H0(1,2) = 0.0 A " 
-    print >>f,"H0(1,3) = 0.0 A " 
-    print >>f,"H0(2,1) = 0.0 A " 
+    print >>f,"H0(1,2) = 0.0 A "
+    print >>f,"H0(1,3) = 0.0 A "
+    print >>f,"H0(2,1) = 0.0 A "
     print >>f,"H0(2,2) = %20.10f A " % ylen
-    print >>f,"H0(2,3) = 0.0 A " 
-    print >>f,"H0(3,1) = 0.0 A " 
-    print >>f,"H0(3,2) = 0.0 A " 
+    print >>f,"H0(2,3) = 0.0 A "
+    print >>f,"H0(3,1) = 0.0 A "
+    print >>f,"H0(3,2) = 0.0 A "
     print >>f,"H0(3,3) = %20.10f A " % zlen
     print >>f,"#"
-      
+
     for atom in atoms:
       itype = int(atom[1])
       xfrac = (atom[2]-box[0])/xlen
@@ -183,5 +183,5 @@ class cfg:
       zfrac = (atom[4]-box[2])/zlen
 #        print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  %15.10f  %15.10f  %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
       print >>f,"1.0  %d   %15.10f  %15.10f  %15.10f  0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
-      
+
     f.close()
diff --git a/tools/python/pizza/dump.py b/tools/python/pizza/dump.py
index 8098a2c4b7..1c6eb5edfd 100644
--- a/tools/python/pizza/dump.py
+++ b/tools/python/pizza/dump.py
@@ -3,7 +3,7 @@
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-# certain rights in this software.  This software is distributed under 
+# certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
 # dump tool
@@ -12,15 +12,15 @@ oneline = "Read, write, manipulate dump files and particle attributes"
 
 docstr = """
 d = dump("dump.one")              read in one or more dump files
-d = dump("dump.1 dump.2.gz")	  can be gzipped
-d = dump("dump.*")		  wildcard expands to multiple files
-d = dump("dump.*",0)		  two args = store filenames, but don't read
+d = dump("dump.1 dump.2.gz")      can be gzipped
+d = dump("dump.*")                wildcard expands to multiple files
+d = dump("dump.*",0)              two args = store filenames, but don't read
 
   incomplete and duplicate snapshots are deleted
   atoms will be unscaled if stored in files as scaled
-  self-describing column names assigned 
+  self-describing column names assigned
 
-time = d.next()             	  read next snapshot from dump files
+time = d.next()                   read next snapshot from dump files
 
   used with 2-argument constructor to allow reading snapshots one-at-a-time
   snapshot will be skipped only if another snapshot has same time stamp
@@ -31,21 +31,21 @@ time = d.next()             	  read next snapshot from dump files
 d.map(1,"id",3,"x")               assign names to columns (1-N)
 
   not needed if dump file is self-describing
-  
-d.tselect.all()			  select all timesteps
-d.tselect.one(N)		  select only timestep N
-d.tselect.none()		  deselect all timesteps
-d.tselect.skip(M)		  select every Mth step
+
+d.tselect.all()                   select all timesteps
+d.tselect.one(N)                  select only timestep N
+d.tselect.none()                  deselect all timesteps
+d.tselect.skip(M)                 select every Mth step
 d.tselect.test("$t >= 100 and $t < 10000")      select matching timesteps
-d.delete()	      	      	  delete non-selected timesteps
+d.delete()                        delete non-selected timesteps
 
   selecting a timestep also selects all atoms in the timestep
   skip() and test() only select from currently selected timesteps
   test() uses a Python Boolean expression with $t for timestep value
     Python comparison syntax: == != < > <= >= and or
 
-d.aselect.all()	      	                      select all atoms in all steps
-d.aselect.all(N)      	                      select all atoms in one step
+d.aselect.all()                               select all atoms in all steps
+d.aselect.all(N)                              select all atoms in one step
 d.aselect.test("$id > 100 and $type == 2")    select match atoms in all steps
 d.aselect.test("$id > 100 and $type == 2",N)  select matching atoms in one step
 
@@ -56,24 +56,24 @@ d.aselect.test("$id > 100 and $type == 2",N)  select matching atoms in one step
     Python comparison syntax: == != < > <= >= and or
     $name must end with a space
 
-d.write("file")	   	           write selected steps/atoms to dump file
-d.write("file",head,app)	   write selected steps/atoms to dump file
-d.scatter("tmp")		   write selected steps/atoms to multiple files
+d.write("file")                    write selected steps/atoms to dump file
+d.write("file",head,app)           write selected steps/atoms to dump file
+d.scatter("tmp")                   write selected steps/atoms to multiple files
 
   write() can be specified with 2 additional flags
     head = 0/1 for no/yes snapshot header, app = 0/1 for write vs append
   scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc
 
-d.scale() 	    	  	   scale x,y,z to 0-1 for all timesteps
-d.scale(100)			   scale atom coords for timestep N
-d.unscale()			   unscale x,y,z to box size to all timesteps
-d.unscale(1000)			   unscale atom coords for timestep N
-d.wrap()			   wrap x,y,z into periodic box via ix,iy,iz
-d.unwrap()			   unwrap x,y,z out of box via ix,iy,iz
-d.owrap("other")		   wrap x,y,z to same image as another atom
-d.sort()              	  	   sort atoms by atom ID in all selected steps
-d.sort("x")            	  	   sort atoms by column value in all steps
-d.sort(1000)			   sort atoms in timestep N
+d.scale()                          scale x,y,z to 0-1 for all timesteps
+d.scale(100)                       scale atom coords for timestep N
+d.unscale()                        unscale x,y,z to box size to all timesteps
+d.unscale(1000)                    unscale atom coords for timestep N
+d.wrap()                           wrap x,y,z into periodic box via ix,iy,iz
+d.unwrap()                         unwrap x,y,z out of box via ix,iy,iz
+d.owrap("other")                   wrap x,y,z to same image as another atom
+d.sort()                           sort atoms by atom ID in all selected steps
+d.sort("x")                        sort atoms by column value in all steps
+d.sort(1000)                       sort atoms in timestep N
 
   scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms
   wrap(), unwrap(), owrap() require ix,iy,iz be defined
@@ -85,8 +85,8 @@ d.sort(1000)			   sort atoms in timestep N
 m1,m2 = d.minmax("type")               find min/max values for a column
 d.set("$ke = $vx * $vx + $vy * $vy")   set a column to a computed value
 d.setv("type",vector)                  set a column to a vector of values
-d.spread("ke",N,"color")	       2nd col = N ints spread over 1st col
-d.clone(1000,"color")	       	       clone timestep N values to other steps
+d.spread("ke",N,"color")               2nd col = N ints spread over 1st col
+d.clone(1000,"color")                  clone timestep N values to other steps
 
   minmax() operates on selected timesteps and atoms
   set() operates on selected timesteps and atoms
@@ -107,17 +107,17 @@ d.clone(1000,"color")	       	       clone timestep N values to other steps
     values at every timestep are set to value at timestep N for that atom ID
     useful for propagating a color map
 
-t = d.time()  	     	       	   return vector of selected timestep values
+t = d.time()                            return vector of selected timestep values
 fx,fy,... = d.atom(100,"fx","fy",...)   return vector(s) for atom ID N
 fx,fy,... = d.vecs(1000,"fx","fy",...)  return vector(s) for timestep N
 
   atom() returns vectors with one value for each selected timestep
   vecs() returns vectors with one value for each selected atom in the timestep
 
-index,time,flag = d.iterator(0/1)          loop over dump snapshots
+index,time,flag = d.iterator(0/1)       loop over dump snapshots
 time,box,atoms,bonds,tris,lines = d.viz(index)   return list of viz objects
-d.atype = "color"                          set column returned as "type" by viz
-d.extra(obj)				   extract bond/tri/line info from obj
+d.atype = "color"                       set column returned as "type" by viz
+d.extra(obj)                            extract bond/tri/line info from obj
 
   iterator() loops over selected timesteps
   iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
@@ -137,7 +137,7 @@ d.extra(obj)				   extract bond/tri/line info from obj
       if extra() used to define lines, else NULL
   atype is column name viz() will return as atom type (def = "type")
   extra() extracts bonds/tris/lines from obj each time viz() is called
-    obj can be data object for bonds, cdata object for tris and lines, 
+    obj can be data object for bonds, cdata object for tris and lines,
       bdump object for bonds, tdump object for tris, ldump object for lines.
       mdump object for tris
 """
@@ -227,7 +227,7 @@ class dump:
     for word in words: self.flist += glob.glob(word)
     if len(self.flist) == 0 and len(list) == 1:
       raise StandardError,"no dump file specified"
-    
+
     if len(list) == 1:
       self.increment = 0
       self.read_all()
@@ -270,7 +270,7 @@ class dump:
     self.tselect.all()
 
     # print column assignments
-    
+
     if len(self.names):
       print "assigned columns:",self.names2str()
     else:
@@ -304,15 +304,15 @@ class dump:
       snap = self.read_snapshot(f)
       if not snap:
         self.nextfile += 1
-	if self.nextfile == len(self.flist): return -1
+        if self.nextfile == len(self.flist): return -1
         f.close()
-	self.eof = 0
-	continue
+        self.eof = 0
+        continue
       self.eof = f.tell()
       f.close()
       try:
         self.findtime(snap.time)
-	continue
+        continue
       except: break
 
     # select the new snapshot with all its atoms
@@ -334,7 +334,7 @@ class dump:
   #   assign column names (file must be self-describing)
   #   set scale_original to 0/1/-1 for unscaled/scaled/unknown
   #   convert xs,xu to x in names
-  
+
   def read_snapshot(self,f):
     try:
       snap = Snap()
@@ -351,7 +351,7 @@ class dump:
       else: snap.boxstr = words[1].strip()
       if "xy" in snap.boxstr: snap.triclinic = 1
       else: snap.triclinic = 0
-      
+
       words = f.readline().split()
       if len(words) == 2:
         snap.xlo,snap.xhi,snap.xy = float(words[0]),float(words[1]),0.0
@@ -372,7 +372,7 @@ class dump:
       else:
         snap.zlo,snap.zhi,snap.yz = \
             float(words[0]),float(words[1]),float(words[2])
-          
+
       item = f.readline()
       if len(self.names) == 0:
         self.scale_original = -1
@@ -401,7 +401,7 @@ class dump:
             else: self.names[words[i]] = i
           if xflag == 0 and yflag == 0 and zflag == 0: self.scale_original = 0
           if xflag == 1 and yflag == 1 and zflag == 1: self.scale_original = 1
-          
+
       if snap.natoms:
         words = f.readline().split()
         ncol = len(words)
@@ -424,7 +424,7 @@ class dump:
 
   # --------------------------------------------------------------------
   # map atom column names
-  
+
   def map(self,*pairs):
     if len(pairs) % 2 != 0:
       raise StandardError, "dump map() requires pairs of mappings"
@@ -509,7 +509,7 @@ class dump:
         atoms[:,y] = (atoms[:,y] - snap.ylo)*h1inv + \
             (atoms[:,z] - snap.zlo)*h3inv
         atoms[:,z] = (atoms[:,z] - snap.zlo)*h2inv
-        
+
   # --------------------------------------------------------------------
   # unscale coords from 0-1 to box size for all snapshots or just one
   # use 6 params as h-matrix to treat orthogonal or triclinic boxes
@@ -564,7 +564,7 @@ class dump:
         atoms[:,x] = snap.xlo + atoms[:,x]*h0 + atoms[:,y]*h5 + atoms[:,z]*h4
         atoms[:,y] = snap.ylo + atoms[:,y]*h1 + atoms[:,z]*h3
         atoms[:,z] = snap.zlo + atoms[:,z]*h2
-        
+
   # --------------------------------------------------------------------
   # wrap coords from outside box to inside
 
@@ -577,7 +577,7 @@ class dump:
     ix = self.names["ix"]
     iy = self.names["iy"]
     iz = self.names["iz"]
-    
+
     for snap in self.snaps:
       xprd = snap.xhi - snap.xlo
       yprd = snap.yhi - snap.ylo
@@ -599,7 +599,7 @@ class dump:
     ix = self.names["ix"]
     iy = self.names["iy"]
     iz = self.names["iz"]
-    
+
     for snap in self.snaps:
       xprd = snap.xhi - snap.xlo
       yprd = snap.yhi - snap.ylo
@@ -612,10 +612,10 @@ class dump:
   # --------------------------------------------------------------------
   # wrap coords to same image as atom ID stored in "other" column
   # if dynamic extra lines or triangles defined, owrap them as well
-      
+
   def owrap(self,other):
     print "Wrapping to other ..."
-    
+
     id = self.names["id"]
     x = self.names["x"]
     y = self.names["y"]
@@ -641,10 +641,10 @@ class dump:
       # should bonds also be owrapped ?
       if self.lineflag == 2 or self.triflag == 2:
         self.objextra.owrap(snap.time,xprd,yprd,zprd,ids,atoms,iother,ix,iy,iz)
-          
+
   # --------------------------------------------------------------------
   # convert column names assignment to a string, in column order
-  
+
   def names2str(self):
     pairs = self.names.items()
     values = self.names.values()
@@ -697,7 +697,7 @@ class dump:
     else: id = -1
     if "type" in self.names: type = self.names["type"]
     else: type = -1
-    
+
     for snap in self.snaps:
       if not snap.tselect: continue
       print snap.time,
@@ -719,7 +719,7 @@ class dump:
           print >>f,snap.ylo,snap.yhi
           print >>f,snap.zlo,snap.zhi
         print >>f,"ITEM: ATOMS",namestr
-      
+
       atoms = snap.atoms
       nvalues = len(atoms[0])
       for i in xrange(snap.natoms):
@@ -743,7 +743,7 @@ class dump:
       if not snap.tselect: continue
       print snap.time,
       sys.stdout.flush()
-      
+
       file = root + "." + str(snap.time)
       f = open(file,"w")
       print >>f,"ITEM: TIMESTEP"
@@ -761,7 +761,7 @@ class dump:
         print >>f,snap.ylo,snap.yhi
         print >>f,snap.zlo,snap.zhi
       print >>f,"ITEM: ATOMS",namestr
-      
+
       atoms = snap.atoms
       nvalues = len(atoms[0])
       for i in xrange(snap.natoms):
@@ -803,7 +803,7 @@ class dump:
     lhs = list[0][1:]
     if not self.names.has_key(lhs):
       self.newcolumn(lhs)
-      
+
     for item in list:
       name = item[1:]
       column = self.names[name]
@@ -815,7 +815,7 @@ class dump:
       if not snap.tselect: continue
       for i in xrange(snap.natoms):
         if snap.aselect[i]: exec ceq
-          
+
   # --------------------------------------------------------------------
   # set a column value via an input vec for all selected snapshots/atoms
 
@@ -835,7 +835,7 @@ class dump:
         if snap.aselect[i]:
           atoms[i][icol] = vec[m]
           m += 1
-          
+
   # --------------------------------------------------------------------
   # clone value in col across selected timesteps for atoms with same ID
 
@@ -901,7 +901,7 @@ class dump:
       columns.append(self.names[name])
       values.append(self.nselect * [0])
     ncol = len(columns)
-    
+
     id = self.names["id"]
     m = 0
     for snap in self.snaps:
@@ -917,13 +917,13 @@ class dump:
 
     if len(list) == 1: return values[0]
     else: return values
-  
+
   # --------------------------------------------------------------------
   # extract vector(s) of values for selected atoms at chosen timestep
 
   def vecs(self,n,*list):
     snap = self.snaps[self.findtime(n)]
-    
+
     if len(list) == 0:
       raise StandardError, "no columns specified"
     columns = []
@@ -978,7 +978,7 @@ class dump:
         del self.snaps[i]
       else:
         i += 1
-  
+
   # --------------------------------------------------------------------
   # iterate over selected snapshots
 
@@ -990,12 +990,12 @@ class dump:
         self.iterate = i
         return i,self.snaps[i].time,1
     return 0,0,-1
-  
+
   # --------------------------------------------------------------------
   # return list of atoms to viz for snapshot isnap
   # if called with flag, then index is timestep, so convert to snapshot index
   # augment with bonds, tris, lines if extra() was invoked
-  
+
   def viz(self,index,flag=0):
     if not flag: isnap = index
     else:
@@ -1019,7 +1019,7 @@ class dump:
 
     # create atom list needed by viz from id,type,x,y,z
     # need Numeric/Numpy mode here
-    
+
     atoms = []
     for i in xrange(snap.natoms):
       if not snap.aselect[i]: continue
@@ -1059,7 +1059,7 @@ class dump:
       if self.triflag == 1: tris = self.trilist
       elif self.triflag == 2:
         tmp1,tmp2,tmp3,tmp4,tris,tmp5 = self.objextra.viz(time,1)
-      
+
     # create list of lines from static or dynamic tri list
     # if dynamic, could eliminate lines for unselected atoms
 
@@ -1070,7 +1070,7 @@ class dump:
         tmp1,tmp2,tmp3,tmp4,tmp5,lines = self.objextra.viz(time,1)
 
     return time,box,atoms,bonds,tris,lines
-  
+
   # --------------------------------------------------------------------
 
   def findtime(self,n):
@@ -1115,7 +1115,7 @@ class dump:
   def extra(self,arg):
 
     # data object, grab bonds statically
-    
+
     if type(arg) is types.InstanceType and ".data" in str(arg.__class__):
       self.bondflag = 0
       try:
@@ -1132,7 +1132,7 @@ class dump:
         raise StandardError,"could not extract bonds from data object"
 
     # cdata object, grab tris and lines statically
-    
+
     elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__):
       self.triflag = self.lineflag = 0
       try:
@@ -1147,32 +1147,32 @@ class dump:
         raise StandardError,"could not extract tris/lines from cdata object"
 
     # mdump object, grab tris dynamically
-    
+
     elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__):
       self.triflag = 2
       self.objextra = arg
 
     # bdump object, grab bonds dynamically
-    
+
     elif type(arg) is types.InstanceType and ".bdump" in str(arg.__class__):
       self.bondflag = 2
       self.objextra = arg
 
     # ldump object, grab lines dynamically
-    
+
     elif type(arg) is types.InstanceType and ".ldump" in str(arg.__class__):
       self.lineflag = 2
       self.objextra = arg
 
     # tdump object, grab tris dynamically
-    
+
     elif type(arg) is types.InstanceType and ".tdump" in str(arg.__class__):
       self.triflag = 2
       self.objextra = arg
 
     else:
       raise StandardError,"unrecognized argument to dump.extra()"
-      
+
   # --------------------------------------------------------------------
 
   def compare_atom(self,a,b):
@@ -1181,7 +1181,7 @@ class dump:
     elif a[0] > b[0]:
       return 1
     else:
-      return 0  
+      return 0
 
 # --------------------------------------------------------------------
 # one snapshot
@@ -1196,7 +1196,7 @@ class tselect:
 
   def __init__(self,data):
     self.data = data
-    
+
   # --------------------------------------------------------------------
 
   def all(self):
@@ -1243,7 +1243,7 @@ class tselect:
       data.nselect -= 1
     data.aselect.all()
     print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
-  
+
   # --------------------------------------------------------------------
 
   def test(self,teststr):
@@ -1289,7 +1289,7 @@ class aselect:
     data = self.data
 
     # replace all $var with snap.atoms references and compile test string
-    
+
     pattern = "\$\w*"
     list = re.findall(pattern,teststr)
     for item in list:
diff --git a/tools/python/pizza/gnu.py b/tools/python/pizza/gnu.py
index f6f0167330..d99ab3811d 100644
--- a/tools/python/pizza/gnu.py
+++ b/tools/python/pizza/gnu.py
@@ -3,7 +3,7 @@
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-# certain rights in this software.  This software is distributed under 
+# certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
 # gnu tool
@@ -11,12 +11,12 @@
 oneline = "Create plots via GnuPlot plotting program"
 
 docstr = """
-g = gnu()		       start up GnuPlot
-g.stop()		       shut down GnuPlot process
-    
+g = gnu()                      start up GnuPlot
+g.stop()                       shut down GnuPlot process
+
 g.plot(a)                      plot vector A against linear index
-g.plot(a,b)	 	       plot B against A
-g.plot(a,b,c,d,...)	       plot B against A, D against C, etc
+g.plot(a,b)                    plot B against A
+g.plot(a,b,c,d,...)            plot B against A, D against C, etc
 g.mplot(M,N,S,"file",a,b,...)  multiple plots saved to file0000.eps, etc
 
   each plot argument can be a tuple, list, or Numeric/NumPy vector
@@ -29,21 +29,21 @@ g.mplot(M,N,S,"file",a,b,...)  multiple plots saved to file0000.eps, etc
 
 g("plot 'file.dat' using 2:3 with lines")      execute string in GnuPlot
 
-g.enter()	   	                enter GnuPlot shell
+g.enter()                               enter GnuPlot shell
 gnuplot> plot sin(x) with lines         type commands directly to GnuPlot
-gnuplot> exit, quit	      	        exit GnuPlot shell
-    
+gnuplot> exit, quit                     exit GnuPlot shell
+
 g.export("data",range(100),a,...)       create file with columns of numbers
 
   all vectors must be of equal length
   could plot from file with GnuPlot command: plot 'data' using 1:2 with lines
 
-g.select(N)  	               figure N becomes the current plot
-  
+g.select(N)                    figure N becomes the current plot
+
   subsequent commands apply to this plot
 
-g.hide(N)  	               delete window for figure N
-g.save("file")	               save current plot as file.eps
+g.hide(N)                      delete window for figure N
+g.save("file")                 save current plot as file.eps
 
 Set attributes for current plot:
 
@@ -94,7 +94,7 @@ except: PIZZA_GNUTERM = "x11"
 # Class definition
 
 class gnu:
-  
+
   # --------------------------------------------------------------------
 
   def __init__(self):
@@ -102,7 +102,7 @@ class gnu:
     self.file = "tmp.gnu"
     self.figures = []
     self.select(1)
-              
+
   # --------------------------------------------------------------------
 
   def stop(self):
@@ -114,7 +114,7 @@ class gnu:
   def __call__(self,command):
     self.GNUPLOT.write(command + '\n')
     self.GNUPLOT.flush()
-    
+
   # --------------------------------------------------------------------
 
   def enter(self):
@@ -152,7 +152,7 @@ class gnu:
         if i: partial_vecs.append(vec[:i])
         else: partial_vecs.append([0])
       self.plot(*partial_vecs)
-      
+
       if n < 10:     newfile = file + "000" + str(n)
       elif n < 100:  newfile = file + "00" + str(n)
       elif n < 1000: newfile = file + "0" + str(n)
@@ -160,7 +160,7 @@ class gnu:
 
       self.save(newfile)
       n += 1
-  
+
   # --------------------------------------------------------------------
   # write list of equal-length vectors to filename
 
@@ -201,7 +201,7 @@ class gnu:
   # do not continue until plot file is written out
   #   else script could go forward and change data file
   #   use tmp.done as semaphore to indicate plot is finished
-  
+
   def save(self,file):
     self.__call__("set terminal postscript enhanced solid lw 2 color portrait")
     cmd = "set output '%s.eps'" % file
@@ -212,7 +212,7 @@ class gnu:
     while not os.path.exists("tmp.done"): continue
     self.__call__("set output")
     self.select(self.current)
-  
+
   # --------------------------------------------------------------------
   # restore default attributes by creating a new fig object
 
@@ -221,7 +221,7 @@ class gnu:
     fig.ncurves = self.figures[self.current-1].ncurves
     self.figures[self.current-1] = fig
     self.draw()
-  
+
   # --------------------------------------------------------------------
 
   def aspect(self,value):
@@ -245,12 +245,12 @@ class gnu:
     else:
       self.figures[self.current-1].ylimit = (values[0],values[1])
     self.draw()
-    	    
+
   # --------------------------------------------------------------------
 
   def label(self,x,y,text):
     self.figures[self.current-1].labels.append((x,y,text))
-    self.figures[self.current-1].nlabels += 1  	    
+    self.figures[self.current-1].nlabels += 1
     self.draw()
 
   # --------------------------------------------------------------------
@@ -259,7 +259,7 @@ class gnu:
     self.figures[self.current-1].nlabel = 0
     self.figures[self.current-1].labels = []
     self.draw()
-      
+
   # --------------------------------------------------------------------
 
   def title(self,*strings):
@@ -276,13 +276,13 @@ class gnu:
   def xtitle(self,label):
     self.figures[self.current-1].xtitle = label
     self.draw()
-    
+
   # --------------------------------------------------------------------
 
   def ytitle(self,label):
     self.figures[self.current-1].ytitle = label
     self.draw()
-    
+
   # --------------------------------------------------------------------
 
   def xlog(self):
@@ -291,7 +291,7 @@ class gnu:
     else:
       self.figures[self.current-1].xlog = 1
     self.draw()
- 
+
   # --------------------------------------------------------------------
 
   def ylog(self):
@@ -300,7 +300,7 @@ class gnu:
     else:
       self.figures[self.current-1].ylog = 1
     self.draw()
-  
+
   # --------------------------------------------------------------------
 
   def curve(self,num,color):
@@ -316,10 +316,10 @@ class gnu:
   def draw(self):
     fig = self.figures[self.current-1]
     if not fig.ncurves: return
-    
+
     cmd = 'set size ratio ' + str(1.0/float(fig.aspect))
     self.__call__(cmd)
-      
+
     cmd = 'set title ' + '"' + fig.title + '"'
     self.__call__(cmd)
     cmd = 'set xlabel ' + '"' + fig.xtitle + '"'
@@ -331,11 +331,11 @@ class gnu:
     else: self.__call__("unset logscale x")
     if fig.ylog: self.__call__("set logscale y")
     else: self.__call__("unset logscale y")
-    if fig.xlimit: 
+    if fig.xlimit:
       cmd = 'set xr [' + str(fig.xlimit[0]) + ':' + str(fig.xlimit[1]) + ']'
       self.__call__(cmd)
     else: self.__call__("set xr [*:*]")
-    if fig.ylimit: 
+    if fig.ylimit:
       cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']'
       self.__call__(cmd)
     else: self.__call__("set yr [*:*]")
@@ -365,7 +365,7 @@ class figure:
 
   def __init__(self):
     self.ncurves = 0
-    self.colors  = []    
+    self.colors  = []
     self.title   = ""
     self.xtitle  = ""
     self.ytitle  = ""
diff --git a/tools/python/pizza/log.py b/tools/python/pizza/log.py
index aeca1d8d82..a255af2030 100644
--- a/tools/python/pizza/log.py
+++ b/tools/python/pizza/log.py
@@ -3,7 +3,7 @@
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-# certain rights in this software.  This software is distributed under 
+# certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
 # log tool
@@ -28,7 +28,7 @@ nvec = l.nvec                        # of vectors of thermo info
 nlen = l.nlen                        length of each vectors
 names = l.names                      list of vector names
 t,pe,... = l.get("Time","KE",...)    return one or more vectors of values
-l.write("file.txt")	 	     write all vectors to a file
+l.write("file.txt")                  write all vectors to a file
 l.write("file.txt","Time","PE",...)  write listed vectors to a file
 
   get and write allow abbreviated (uniquely) vector names
@@ -89,7 +89,7 @@ class log:
 
   # --------------------------------------------------------------------
   # read all thermo from all files
-  
+
   def read_all(self):
     self.read_header(self.flist[0])
     if self.nvec == 0: raise StandardError,"log file has no values"
@@ -100,7 +100,7 @@ class log:
     print
 
     # sort entries by timestep, cull duplicates
-    
+
     self.data.sort(self.compare)
     self.cull()
     self.nlen = len(self.data)
@@ -133,9 +133,9 @@ class log:
       else:
         count = 0
         for i in range(self.nvec):
-	  if self.names[i].find(key) == 0:
-	    count += 1
-	    index = i
+          if self.names[i].find(key) == 0:
+            count += 1
+            index = i
         if count == 1:
           map.append(index)
         else:
@@ -161,9 +161,9 @@ class log:
         else:
           count = 0
           for i in range(self.nvec):
-	    if self.names[i].find(key) == 0:
-	      count += 1
-	      index = i
+            if self.names[i].find(key) == 0:
+              count += 1
+              index = i
           if count == 1:
             map.append(index)
           else:
@@ -226,7 +226,7 @@ class log:
       keywords.insert(0,"Step")
       i = 0
       for keyword in keywords:
-	self.names.append(keyword)
+        self.names.append(keyword)
         self.ptr[keyword] = i
         i += 1
 
@@ -236,7 +236,7 @@ class log:
       line = txt[s1:s2]
       words = line.split()
       for i in range(len(words)):
-	self.names.append(words[i])
+        self.names.append(words[i])
         self.ptr[words[i]] = i
 
     self.nvec = len(self.names)
@@ -275,43 +275,43 @@ class log:
 
       if s1 >= 0 and s2 >= 0 and s1 < s2:    # found s1,s2 with s1 before s2
         if self.style == 2:
-	  s1 = txt.find("\n",s1) + 1
+          s1 = txt.find("\n",s1) + 1
       elif s1 >= 0 and s2 >= 0 and s2 < s1:  # found s1,s2 with s2 before s1
         s1 = 0
       elif s1 == -1 and s2 >= 0:             # found s2, but no s1
-	last = 1
+        last = 1
         s1 = 0
       elif s1 >= 0 and s2 == -1:             # found s1, but no s2
         last = 1
         if self.style == 1:
           s2 = txt.rfind("\n--",s1) + 1
         else:
-	  s1 = txt.find("\n",s1) + 1
+          s1 = txt.find("\n",s1) + 1
           s2 = txt.rfind("\n",s1) + 1
-	eof -= len(txt) - s2
+        eof -= len(txt) - s2
       elif s1 == -1 and s2 == -1:            # found neither
                                              # could be end-of-file section
-					     # or entire read was one chunk
+                                             # or entire read was one chunk
 
         if txt.find("Loop time of",start) == start:   # end of file, so exit
-	  eof -= len(txt) - start                     # reset eof to "Loop"
-	  break
+          eof -= len(txt) - start                     # reset eof to "Loop"
+          break
 
-	last = 1                                      # entire read is a chunk
+        last = 1                                      # entire read is a chunk
         s1 = 0
         if self.style == 1:
           s2 = txt.rfind("\n--",s1) + 1
         else:
           s2 = txt.rfind("\n",s1) + 1
-	eof -= len(txt) - s2
-	if s1 == s2: break
+        eof -= len(txt) - s2
+        if s1 == s2: break
 
       chunk = txt[s1:s2-1]
       start = s2
 
       # split chunk into entries
       # parse each entry for numeric fields, append to data
-  
+
       if self.style == 1:
         sections = chunk.split("\n--")
         pat1 = re.compile("Step\s*(\S*)\s")
diff --git a/tools/python/pizza/pdbfile.py b/tools/python/pizza/pdbfile.py
index 1713ada043..9b2238cbd6 100644
--- a/tools/python/pizza/pdbfile.py
+++ b/tools/python/pizza/pdbfile.py
@@ -3,7 +3,7 @@
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-# certain rights in this software.  This software is distributed under 
+# certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
 # pdb tool
@@ -22,7 +22,7 @@ p = pdbfile("3CRO",d)       read in single PDB file with snapshot data
     if only one 4-char file specified and it is not found,
       it will be downloaded from http://www.rcsb.org as 3CRO.pdb
   d arg is object with atom coordinates (dump, data)
-  
+
 p.one()                     write all output as one big PDB file to tmp.pdb
 p.one("mine")               write to mine.pdb
 p.many()                    write one PDB file per snapshot: tmp0000.pdb, ...
@@ -36,7 +36,7 @@ p.single(N,"new")           write as new.pdb
     if one file in str arg and d: one new PDB file per snapshot
       using input PDB file as template
     multiple input PDB files with a d is not allowed
-    
+
 index,time,flag = p.iterator(0)
 index,time,flag = p.iterator(1)
 
@@ -87,7 +87,7 @@ class pdbfile:
 
     # flist = full list of all PDB input file names
     # append .pdb if needed
-    
+
     if filestr:
       list = filestr.split()
       flist = []
@@ -107,7 +107,7 @@ class pdbfile:
       raise StandardError, "no input PDB file(s)"
 
     # grab PDB file from http://rcsb.org if not a local file
-    
+
     if len(self.files) == 1 and len(self.files[0]) == 8:
       try:
         open(self.files[0],'r').close()
@@ -117,7 +117,7 @@ class pdbfile:
         urllib.urlretrieve(fetchstr,self.files[0])
 
     if self.data and len(self.files): self.read_template(self.files[0])
-      
+
   # --------------------------------------------------------------------
   # write a single large PDB file for concatenating all input data or files
   # if data exists:
@@ -135,7 +135,7 @@ class pdbfile:
     f = open(file,'w')
 
     # use template PDB file with each snapshot
-    
+
     if self.data:
       n = flag = 0
       while 1:
@@ -153,7 +153,7 @@ class pdbfile:
         print >>f,"END"
         print file,
         sys.stdout.flush()
-        
+
     f.close()
     print "\nwrote %d datasets to %s in PDB format" % (n,file)
 
@@ -189,7 +189,7 @@ class pdbfile:
         f = open(file,'w')
         self.convert(f,which)
         f.close()
-        
+
         print time,
         sys.stdout.flush()
         n += 1
@@ -206,13 +206,13 @@ class pdbfile:
         else:
           file = root + str(n)
         file += ".pdb"
-        
+
         f = open(file,'w')
         f.write(open(infile,'r').read())
         f.close()
         print file,
         sys.stdout.flush()
-        
+
         n += 1
 
     print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root)
@@ -239,7 +239,7 @@ class pdbfile:
       self.convert(f,which)
     else:
       f.write(open(self.files[time],'r').read())
-      
+
     f.close()
 
   # --------------------------------------------------------------------
@@ -258,8 +258,8 @@ class pdbfile:
 
   # --------------------------------------------------------------------
   # read a PDB file and store ATOM lines
-  
-  def read_template(self,file):  
+
+  def read_template(self,file):
     lines = open(file,'r').readlines()
     self.atomlines = {}
     for line in lines:
diff --git a/tools/python/pizza/xyz.py b/tools/python/pizza/xyz.py
index 66699ab5fa..92b681540a 100644
--- a/tools/python/pizza/xyz.py
+++ b/tools/python/pizza/xyz.py
@@ -3,7 +3,7 @@
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-# certain rights in this software.  This software is distributed under 
+# certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
 # xyz tool
@@ -11,14 +11,14 @@
 oneline = "Convert LAMMPS snapshots to XYZ format"
 
 docstr = """
-x = xyz(d)		d = object containing atom coords (dump, data)
+x = xyz(d)              d = object containing atom coords (dump, data)
 
 x.one()                 write all snapshots to tmp.xyz
 x.one("new")            write all snapshots to new.xyz
 x.many()                write snapshots to tmp0000.xyz, tmp0001.xyz, etc
 x.many("new")           write snapshots to new0000.xyz, new0001.xyz, etc
-x.single(N)             write snapshot for timestep N to tmp.xyz 
-x.single(N,"file")      write snapshot for timestep N to file.xyz 
+x.single(N)             write snapshot for timestep N to tmp.xyz
+x.single(N,"file")      write snapshot for timestep N to file.xyz
 """
 
 # History
@@ -41,7 +41,7 @@ class xyz:
 
   def __init__(self,data):
     self.data = data
-   
+
   # --------------------------------------------------------------------
 
   def one(self,*args):
@@ -61,14 +61,14 @@ class xyz:
       for atom in atoms:
         itype = int(atom[1])
         print >>f,itype,atom[2],atom[3],atom[4]
-      
+
       print time,
       sys.stdout.flush()
       n += 1
-      
+
     f.close()
     print "\nwrote %d snapshots to %s in XYZ format" % (n,file)
-      
+
   # --------------------------------------------------------------------
 
   def many(self,*args):
@@ -80,7 +80,7 @@ class xyz:
       which,time,flag = self.data.iterator(flag)
       if flag == -1: break
       time,box,atoms,bonds,tris,lines = self.data.viz(which)
-      
+
       if n < 10:
         file = root + "000" + str(n)
       elif n < 100:
@@ -88,7 +88,7 @@ class xyz:
       elif n < 1000:
         file = root + "0" + str(n)
       else:
-        file = root + str(n)  
+        file = root + str(n)
       file += ".xyz"
       f = open(file,"w")
       print >>f,len(atoms)
@@ -100,9 +100,9 @@ class xyz:
       sys.stdout.flush()
       f.close()
       n += 1
-  
+
     print "\nwrote %s snapshots in XYZ format" % n
-  
+
   # --------------------------------------------------------------------
 
   def single(self,time,*args):
diff --git a/tools/singularity/README.md b/tools/singularity/README.md
new file mode 100644
index 0000000000..d316e629f3
--- /dev/null
+++ b/tools/singularity/README.md
@@ -0,0 +1,50 @@
+# Singularity container definitions for compiling/testing LAMMPS
+
+The *.def files in this folder can be used to build container images
+for [Singularity](https://sylabs.io) suitable for compiling and testing
+LAMMPS on a variety of OS variants with support for most standard packages
+and building/spellchecking the manual. This allows to test and debug
+LAMMPS code on different OS variants than what is locally installed on
+your development workstation, e.g. when bugs are reported that can only
+be reproduced on a specific OS or with specific (mostly older) versions
+of tools, compilers, or libraries.
+
+Ready-to-use container images built from these definition files are
+occasionally uploaded to the container library at sylabs.io. They
+can be found here: https://cloud.sylabs.io/library/lammps/default/lammps_development#
+and will be signed with the key fingerprint: EEA103764C6C633EDC8AC428D9B44E93BF0C375A
+
+Here is a workflow for testing a compilation of LAMMPS with a locally
+built CentOS 7.x singularity container.
+
+```
+cd some/work/directory
+git clone --depth 500  git://github.com/lammps/lammps.git lammps
+mkdir build-centos7
+cd build-centos7
+sudo singularity build centos7.sif ../tools/singularity/centos7.def
+singularity shell centos7.sif
+cmake -C ../cmake/presets/most.cmake -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -std=c++11" ../cmake
+make
+```
+
+And here is the equivalent workflow for testing a compilation of LAMMPS
+using a pre-built Ubuntu 18.04LTS singularity container.
+
+```
+cd some/work/directory
+git clone --depth 500  git://github.com/lammps/lammps.git lammps
+mkdir build-ubuntu18
+cd build-ubuntu18
+singularity pull library://lammps/default/lammps_development:ubuntu18.04
+singularity shell lammps_development_ubuntu18.04.sif
+cmake -C ../cmake/presets/most.cmake ../cmake
+make
+```
+
+| Currently available: |     |
+| --- | --- |
+| centos7.def | CentOS 7.x with EPEL enabled |
+| centos8.def | CentOS 8.x with EPEL enabled |
+| ubuntu16.04.def | Ubuntu 16.04LTS with default MPI == OpenMPI |
+| ubuntu18.04.def | Ubuntu 18.04LTS with default MPI == OpenMPI |
diff --git a/tools/singularity/centos7.def b/tools/singularity/centos7.def
new file mode 100644
index 0000000000..8160105524
--- /dev/null
+++ b/tools/singularity/centos7.def
@@ -0,0 +1,10 @@
+BootStrap: library
+From: centos:7
+
+%post
+	yum -y install epel-release
+        yum -y update
+	yum -y install vim-enhanced ccache gcc-c++ gcc-gfortran clang gdb valgrind-openmpi make cmake cmake3 ninja-build patch which file git libpng-devel libjpeg-devel openmpi-devel mpich-devel python-devel python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant
+
+%labels
+	Author akohlmey
diff --git a/tools/singularity/centos8.def b/tools/singularity/centos8.def
new file mode 100644
index 0000000000..b48979cab1
--- /dev/null
+++ b/tools/singularity/centos8.def
@@ -0,0 +1,13 @@
+BootStrap: docker
+From: centos:8
+
+%post
+	dnf -y install epel-release dnf-utils
+        dnf config-manager --set-enabled PowerTools
+        dnf -y update
+	dnf -y install vim-enhanced ccache gcc-c++ gcc-gfortran clang gdb make cmake patch which file git libpng-devel libjpeg-devel openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel enchant platform-python-devel python3-virtualenv valgrind openblas ninja-build eigen3-devel
+
+#No match for argument: valgrind-openmpi
+
+%labels
+	Author akohlmey
diff --git a/tools/singularity/ubuntu16.04.def b/tools/singularity/ubuntu16.04.def
new file mode 100644
index 0000000000..2f7841bd4a
--- /dev/null
+++ b/tools/singularity/ubuntu16.04.def
@@ -0,0 +1,9 @@
+BootStrap: docker
+From: ubuntu:16.04
+
+%post
+	apt-get update -y
+	env DEBIAN_FRONTEND=noninteractive apt-get install -y make cmake cmake-curses-gui ninja-build git ccache gcc g++ gfortran libfftw3-dev libjpeg-dev libpng12-dev libblas-dev liblapack-dev mpi-default-bin mpi-default-dev libeigen3-dev libgsl-dev libopenblas-dev virtualenv python-dev enchant vim-nox
+
+%labels
+	Author akohlmey
diff --git a/tools/singularity/ubuntu18.04.def b/tools/singularity/ubuntu18.04.def
new file mode 100644
index 0000000000..c87daa8de5
--- /dev/null
+++ b/tools/singularity/ubuntu18.04.def
@@ -0,0 +1,9 @@
+BootStrap: docker
+From: ubuntu:18.04
+
+%post
+	apt-get update -y
+	env DEBIAN_FRONTEND=noninteractive apt-get install -y make cmake cmake-curses-gui ninja-build git ccache gcc g++ gfortran libfftw3-dev libjpeg-dev libpng-dev libblas-dev liblapack-dev mpi-default-bin mpi-default-dev libeigen3-dev libgsl-dev libopenblas-dev virtualenv python-dev enchant vim-nox voro++-dev
+
+%labels
+	Author akohlmey

From 9ed987c25508a6ffac344ac72d358d00afdf26d4 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Mon, 13 Jan 2020 13:15:17 -0700
Subject: [PATCH 196/199] minor changes to syntax and documentation of fix
 deposit orient

---
 doc/src/fix_deposit.rst  |   9 ++
 doc/txt/fix_deposit.txt  | 299 ---------------------------------------
 src/MISC/fix_deposit.cpp |   8 +-
 src/MISC/fix_deposit.h   |   4 +-
 4 files changed, 17 insertions(+), 303 deletions(-)
 delete mode 100644 doc/txt/fix_deposit.txt

diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst
index 45ae785f89..29b4381441 100644
--- a/doc/src/fix_deposit.rst
+++ b/doc/src/fix_deposit.rst
@@ -57,6 +57,8 @@ Syntax
          fix-ID = ID of :doc:`fix rigid/small <fix_rigid>` command
        *shake* value = fix-ID
          fix-ID = ID of :doc:`fix shake <fix_shake>` command
+       *orient* values = rx ry rz
+         rx,ry,rz = vector to randomly rotate an inserted molecule around
        *units* value = *lattice* or *box*
          lattice = the geometry is defined in lattice units
          box = the geometry is defined in simulation box units
@@ -236,6 +238,13 @@ sputtering process.  E.g. the target point can be far away, so that
 all incident particles strike the surface as if they are in an
 incident beam of particles at a prescribed angle.
 
+The *orient* keyword is only used when molecules are deposited.  By
+default, each molecule is inserted at a random orientation.  If this
+keyword is specified, then (rx,ry,rz) is used as an orientation
+vector, and each inserted molecule is rotated around that vector with
+a random value from zero to 2*PI.  For a 2d simulation, rx = ry = 0.0
+is required, since rotations can only be performed around the z axis.
+
 The *id* keyword determines how atom IDs and molecule IDs are assigned
 to newly deposited particles.  Molecule IDs are only assigned if
 molecules are being inserted.  For the *max* setting, the atom and
diff --git a/doc/txt/fix_deposit.txt b/doc/txt/fix_deposit.txt
deleted file mode 100644
index 45ef7d655e..0000000000
--- a/doc/txt/fix_deposit.txt
+++ /dev/null
@@ -1,299 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix deposit command :h3
-
-[Syntax:]
-
-fix ID group-ID deposit N type M seed keyword values ... :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-deposit = style name of this fix command :l
-N = # of atoms or molecules to insert :l
-type = atom type to assign to inserted atoms (offset for molecule insertion) :l
-M = insert a single atom or molecule every M steps :l
-seed = random # seed (positive integer) :l
-one or more keyword/value pairs may be appended to args :l
-keyword = {region} or {id} or {global} or {local} or {near} or {gaussian} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} or {orientation} :l
-  {region} value = region-ID
-    region-ID = ID of region to use as insertion volume
-  {id} value = {max} or {next}
-    max = atom ID for new atom(s) is max ID of all current atoms plus one
-    next = atom ID for new atom(s) increments by one for every deposition
-  {global} values = lo hi
-    lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
-  {local} values = lo hi delta
-    lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
-    delta = lateral distance within which a neighbor is considered "nearby" (distance units)
-  {near} value = R
-    R = only insert atom/molecule if further than R from existing particles (distance units)
-  {gaussian} values = xmid ymid zmid sigma
-    xmid,ymid,zmid = center of the gaussian distribution (distance units)
-    sigma = width of gaussian distribution (distance units)
-  {attempt} value = Q
-    Q = attempt a single insertion up to Q times
-  {rate} value = V
-    V = z velocity (y in 2d) at which insertion volume moves (velocity units)
-  {vx} values = vxlo vxhi
-    vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
-  {vy} values = vylo vyhi
-    vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
-  {vz} values = vzlo vzhi
-    vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
-  {target} values = tx ty tz
-    tx,ty,tz = location of target point (distance units)
-  {mol} value = template-ID
-    template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
-  {molfrac} values = f1 f2 ... fN
-    f1 to fN = relative probability of creating each of N molecules in template-ID
-  {rigid} value = fix-ID
-    fix-ID = ID of "fix rigid/small"_fix_rigid.html command
-  {shake} value = fix-ID
-    fix-ID = ID of "fix shake"_fix_shake.html command
-  {units} value = {lattice} or {box}
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units 
-  {orientation} value = rx ry rz
-    rx,ry,rz = axis of orientation vector :pre
-:ule
-
-[Examples:]
-
-fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
-fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
-fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
-fix 5 insert deposit 200 2 100 777 region disk gaussian 5.0 5.0 9.0 1.0 units box :pre
-
-[Description:]
-
-Insert a single atom or molecule into the simulation domain every M
-timesteps until N atoms or molecules have been inserted.  This is
-useful for simulating deposition onto a surface.  For the remainder of
-this doc page, a single inserted atom or molecule is referred to as a
-"particle".
-
-If inserted particles are individual atoms, they are assigned the
-specified atom type.  If they are molecules, the type of each atom in
-the inserted molecule is specified in the file read by the
-"molecule"_molecule.html command, and those values are added to the
-specified atom type.  E.g. if the file specifies atom types 1,2,3, and
-those are the atom types you want for inserted molecules, then specify
-{type} = 0.  If you specify {type} = 2, the in the inserted molecule
-will have atom types 3,4,5.
-
-All atoms in the inserted particle are assigned to two groups: the
-default group "all" and the group specified in the fix deposit command
-(which can also be "all").
-
-If you are computing temperature values which include inserted
-particles, you will want to use the
-"compute_modify"_compute_modify.html dynamic option, which insures the
-current number of atoms is used as a normalizing factor each time the
-temperature is computed.
-
-Care must be taken that inserted particles are not too near existing
-atoms, using the options described below.  When inserting particles
-above a surface in a non-periodic box (see the
-"boundary"_boundary.html command), the possibility of a particle
-escaping the surface and flying upward should be considered, since the
-particle may be lost or the box size may grow infinitely large.  A
-"fix wall/reflect"_fix_wall_reflect.html command can be used to
-prevent this behavior.  Note that if a shrink-wrap boundary is used,
-it is OK to insert the new particle outside the box, however the box
-will immediately be expanded to include the new particle. When
-simulating a sputtering experiment it is probably more realistic to
-ignore those atoms using the "thermo_modify"_thermo_modify.html
-command with the {lost ignore} option and a fixed
-"boundary"_boundary.html.
-
-The fix deposit command must use the {region} keyword to define an
-insertion volume.  The specified region must have been previously
-defined with a "region"_region.html command.  It must be defined with
-side = {in}.
-
-NOTE: LAMMPS checks that the specified region is wholly inside the
-simulation box.  It can do this correctly for orthonormal simulation
-boxes.  However for "triclinic boxes"_Howto_triclinic.html, it only
-tests against the larger orthonormal box that bounds the tilted
-simulation box.  If the specified region includes volume outside the
-tilted box, then an insertion will likely fail, leading to a "lost
-atoms" error.  Thus for triclinic boxes you should insure the
-specified region is wholly inside the simulation box.
-
-The locations of inserted particles are taken from uniform distributed
-random numbers, unless the {gaussian} keyword is used. Then the
-individual coordinates are taken from a gaussian distribution of
-width {sigma} centered on {xmid,ymid,zmid}.
-
-Individual atoms are inserted, unless the {mol} keyword is used.  It
-specifies a {template-ID} previously defined using the
-"molecule"_molecule.html command, which reads files that define one or
-more molecules.  The coordinates, atom types, charges, etc, as well as
-any bond/angle/etc and special neighbor information for the molecule
-can be specified in the molecule file.  See the
-"molecule"_molecule.html command for details.  The only settings
-required to be in each file are the coordinates and types of atoms in
-the molecule.
-
-If the molecule template contains more than one molecule, the relative
-probability of depositing each molecule can be specified by the
-{molfrac} keyword.  N relative probabilities, each from 0.0 to 1.0, are
-specified, where N is the number of molecules in the template.  Each
-time a molecule is deposited, a random number is used to sample from
-the list of relative probabilities.  The N values must sum to 1.0.
-
-If you wish to insert molecules via the {mol} keyword, that will be
-treated as rigid bodies, use the {rigid} keyword, specifying as its
-value the ID of a separate "fix rigid/small"_fix_rigid.html
-command which also appears in your input script.
-
-NOTE: If you wish the new rigid molecules (and other rigid molecules)
-to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
-or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
-"fix_modify dynamic/dof yes" command for the rigid fix.  This is to
-inform that fix that the molecule count will vary dynamically.
-
-If you wish to insert molecules via the {mol} keyword, that will have
-their bonds or angles constrained via SHAKE, use the {shake} keyword,
-specifying as its value the ID of a separate "fix
-shake"_fix_shake.html command which also appears in your input script.
-
-Each timestep a particle is inserted, the coordinates for its atoms
-are chosen as follows.  For insertion of individual atoms, the
-"position" referred to in the following description is the coordinate
-of the atom.  For insertion of molecule, the "position" is the
-geometric center of the molecule; see the "molecule"_molecule.html doc
-page for details.  A random rotation of the molecule around its center
-point is performed, which determines the coordinates all the
-individual atoms.
-
-A random position within the region insertion volume is generated.  If
-neither the {global} or {local} keyword is used, the random position
-is the trial position.  If the {global} keyword is used, the random
-x,y values are used, but the z position of the new particle is set
-above the highest current atom in the simulation by a distance
-randomly chosen between lo/hi.  (For a 2d simulation, this is done for
-the y position.)  If the {local} keyword is used, the z position is
-set a distance between lo/hi above the highest current atom in the
-simulation that is "nearby" the chosen x,y position.  In this context,
-"nearby" means the lateral distance (in x,y) between the new and old
-particles is less than the {delta} setting.
-
-Once a trial x,y,z position has been selected, the insertion is only
-performed if no current atom in the simulation is within a distance R
-of any atom in the new particle, including the effect of periodic
-boundary conditions if applicable.  R is defined by the {near}
-keyword.  Note that the default value for R is 0.0, which will allow
-atoms to strongly overlap if you are inserting where other atoms are
-present.  This distance test is performed independently for each atom
-in an inserted molecule, based on the randomly rotated configuration
-of the molecule.  If this test fails, a new random position within the
-insertion volume is chosen and another trial is made.  Up to Q
-attempts are made.  If the particle is not successfully inserted,
-LAMMPS prints a warning message.
-
-NOTE: If you are inserting finite size particles or a molecule or
-rigid body consisting of finite-size particles, then you should
-typically set R larger than the distance at which any inserted
-particle may overlap with either a previously inserted particle or an
-existing particle.  LAMMPS will issue a warning if R is smaller than
-this value, based on the radii of existing and inserted particles.
-
-The {rate} option moves the insertion volume in the z direction (3d)
-or y direction (2d).  This enables particles to be inserted from a
-successively higher height over time.  Note that this parameter is
-ignored if the {global} or {local} keywords are used, since those
-options choose a z-coordinate for insertion independently.
-
-The vx, vy, and vz components of velocity for the inserted particle
-are set using the values specified for the {vx}, {vy}, and {vz}
-keywords.  Note that normally, new particles should be a assigned a
-negative vertical velocity so that they move towards the surface.  For
-molecules, the same velocity is given to every particle (no rotation
-or bond vibration).
-
-If the {target} option is used, the velocity vector of the inserted
-particle is changed so that it points from the insertion position
-towards the specified target point.  The magnitude of the velocity is
-unchanged.  This can be useful, for example, for simulating a
-sputtering process.  E.g. the target point can be far away, so that
-all incident particles strike the surface as if they are in an
-incident beam of particles at a prescribed angle.
-
-The {id} keyword determines how atom IDs and molecule IDs are assigned
-to newly deposited particles.  Molecule IDs are only assigned if
-molecules are being inserted.  For the {max} setting, the atom and
-molecule IDs of all current atoms are checked.  Atoms in the new
-particle are assigned IDs starting with the current maximum plus one.
-If a molecule is inserted it is assigned an ID = current maximum plus
-one.  This means that if particles leave the system, the new IDs may
-replace the lost ones.  For the {next} setting, the maximum ID of any
-atom and molecule is stored at the time the fix is defined.  Each time
-a new particle is added, this value is incremented to assign IDs to
-the new atom(s) or molecule.  Thus atom and molecule IDs for deposited
-particles will be consecutive even if particles leave the system over
-time.
-
-The {units} keyword determines the meaning of the distance units used
-for the other deposition parameters.  A {box} value selects standard
-distance units as defined by the "units"_units.html command,
-e.g. Angstroms for units = real or metal.  A {lattice} value means the
-distance units are in lattice spacings.  The "lattice"_lattice.html
-command must have been previously used to define the lattice spacing.
-Note that the units choice affects all the keyword values that have
-units of distance or velocity.
-
-The {orientation} keyword determines the fixed rotation axis r = (rx,ry,rz) for randomly rotated of any inserted molecules. Note that the for a 2d simulation, (rx,ry,rz) should equal to (0,0,1).
-
-NOTE: If you are monitoring the temperature of a system where the atom
-count is changing due to adding particles, you typically should use
-the "compute_modify dynamic yes"_compute_modify.html command for the
-temperature compute you are using.
-
-[Restart, fix_modify, output, run start/stop, minimize info:]
-
-This fix writes the state of the deposition to "binary restart
-files"_restart.html.  This includes information about how many
-particles have been deposited, the random number generator seed, the
-next timestep for deposition, etc.  See the
-"read_restart"_read_restart.html command for info on how to re-specify
-a fix in an input script that reads a restart file, so that the
-operation of the fix continues in an uninterrupted fashion.
-
-NOTE: For this to work correctly, the timestep must [not] be changed
-after reading the restart with "reset_timestep"_reset_timestep.html.
-The fix will try to detect it and stop with an error.
-
-None of the "fix_modify"_fix_modify.html options are relevant to this
-fix.  No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Howto_output.html.  No parameter
-of this fix can be used with the {start/stop} keywords of the
-"run"_run.html command.  This fix is not invoked during "energy
-minimization"_minimize.html.
-
-[Restrictions:]
-
-This fix is part of the MISC package.  It is only enabled if LAMMPS
-was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-The specified insertion region cannot be a "dynamic" region, as
-defined by the "region"_region.html command.
-
-[Related commands:]
-
-"fix pour"_fix_pour.html, "region"_region.html
-
-[Default:]
-
-Insertions are performed for individual atoms, i.e. no {mol} setting
-is defined.  If the {mol} keyword is used, the default for {molfrac}
-is an equal probabilities for all molecules in the template.
-Additional option defaults are id = max, delta = 0.0, near = 0.0,
-attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0,
-and units = lattice.
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index c8736840e4..5279b2df36 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -421,7 +421,7 @@ void FixDeposit::pre_exchange()
       while (rng > molfrac[imol]) imol++;
       natom = onemols[imol]->natoms;
       if (dimension == 3) {
-        if (orientflag == 1) {
+        if (orientflag) {
           r[0] = rx;
           r[1] = ry;
           r[2] = rz;
@@ -779,12 +779,16 @@ void FixDeposit::options(int narg, char **arg)
       vzlo = force->numeric(FLERR,arg[iarg+1]);
       vzhi = force->numeric(FLERR,arg[iarg+2]);
       iarg += 3;
-    } else if (strcmp(arg[iarg],"orientation") == 0) {
+    } else if (strcmp(arg[iarg],"orient") == 0) {
       if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
       orientflag = 1;
       rx = force->numeric(FLERR,arg[iarg+1]);
       ry = force->numeric(FLERR,arg[iarg+2]);
       rz = force->numeric(FLERR,arg[iarg+3]);
+      if (domain->dimension == 2 && (rx != 0.0 || ry != 0.0))
+        error->all(FLERR,"Illegal fix deposit orient settings");
+      if (rx == 0.0 && ry == 0.0 && rz == 0.0)
+        error->all(FLERR,"Illegal fix deposit orient settings");
       iarg += 4;
     } else if (strcmp(arg[iarg],"units") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index 92598862d2..92ecdd9efd 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -40,9 +40,9 @@ class FixDeposit : public Fix {
   int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag;
   int mode,rigidflag,shakeflag,idnext,distflag,orientflag;
   double lo,hi,deltasq,nearsq,rate,sigma;
-  double vxlo,vxhi,vylo,vyhi,vzlo,vzhi,rx,ry,rz;
+  double vxlo,vxhi,vylo,vyhi,vzlo,vzhi;
   double xlo,xhi,ylo,yhi,zlo,zhi,xmid,ymid,zmid;
-  double tx,ty,tz;
+  double rx,ry,rz,tx,ty,tz;
   char *idregion;
   char *idrigid,*idshake;
 

From 8258d0cb5910d33144cd14f8166b6f70d81446f7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 13 Jan 2020 22:28:02 -0500
Subject: [PATCH 197/199] remove obsolete .txt file

---
 doc/txt/pair_lj_switch3_coulgauss.txt | 86 ---------------------------
 1 file changed, 86 deletions(-)
 delete mode 100644 doc/txt/pair_lj_switch3_coulgauss.txt

diff --git a/doc/txt/pair_lj_switch3_coulgauss.txt b/doc/txt/pair_lj_switch3_coulgauss.txt
deleted file mode 100644
index 1277cff9aa..0000000000
--- a/doc/txt/pair_lj_switch3_coulgauss.txt
+++ /dev/null
@@ -1,86 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style lj/switch3/coulgauss/long command :h3
-
-[Syntax:]
-
-pair_style style args :pre
-
-style = {lj/switch3/coulgauss/long}
-args = list of arguments for a particular style :ul
-  {lj/switch3/coulgauss/long} args = cutoff (cutoff2) width
-    cutoff  = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-    width  = width parameter of the smoothing function (distance units) :pre
-
-[Examples:]
-
-pair_style lj/switch3/coulgauss/long    12.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-pair_style lj/switch3/coulgauss/long   12.0 10.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-[Description:]
-
-The {lj/switch3/coulgauss} style evaluates the LJ
-vdW potential
-
-:c,image(Eqs/pair_lj_switch3.jpg)
-
-, which goes smoothly to zero at the cutoff r_c as defined
-by the switching function
-
-:c,image(Eqs/pair_switch3.jpg)
-
-where w is the width defined in the arguments. This potential
-is combined with Coulomb interaction between Gaussian charge densities:
-
-:c,image(Eqs/pair_coulgauss.jpg)
-
-where qi and qj are the
-charges on the 2 atoms, epsilon is the dielectric constant which
-can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
-are the widths of the Gaussian charge distribution and erf() is the error-function.
-This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
-
-If one cutoff is specified it is used for both the vdW and Coulomb
-terms.  If two cutoffs are specified, the first is used as the cutoff
-for the vdW terms, and the second is the cutoff for the Coulombic term.
-
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-epsilon (energy)
-sigma (distance)
-gamma (distance) :ul
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-Shifting the potential energy is not necessary because the switching
-function ensures that the potential is zero at the cut-off.
-
-
-[Restrictions:]
-
-These styles are part of the USER-YAFF package.  They are only
-enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html
-
-[Default:] none
-

From bd5a97e07e0b2ad41a3ce171ef5ff392e0c763c5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 13 Jan 2020 22:41:08 -0500
Subject: [PATCH 198/199] add false positives

---
 doc/utils/sphinx-config/false_positives.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 3182c8605e..b0e80b485a 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -1141,6 +1141,7 @@ ico
 icosahedral
 idealgas
 IDR
+idx
 ielement
 ieni
 ifdefs
@@ -2475,6 +2476,8 @@ Runge
 runtime
 Rutuparna
 rx
+ry
+rz
 Ryckaert
 Rycroft
 Rydbergs

From f095aacad7483543cd64130eed5fd3bb5bf20cdf Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 13 Jan 2020 23:08:20 -0500
Subject: [PATCH 199/199] remove outdated .txt files

---
 doc/txt/Packages_details.txt | 2157 ----------------------------------
 doc/txt/fix.txt              |  392 ------
 2 files changed, 2549 deletions(-)
 delete mode 100644 doc/txt/Packages_details.txt
 delete mode 100644 doc/txt/fix.txt

diff --git a/doc/txt/Packages_details.txt b/doc/txt/Packages_details.txt
deleted file mode 100644
index fc30c045cf..0000000000
--- a/doc/txt/Packages_details.txt
+++ /dev/null
@@ -1,2157 +0,0 @@
-"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Package details :h3
-
-Here is a brief description of all the standard and user packages in
-LAMMPS.  It lists authors (if applicable) and summarizes the package
-contents.  It has specific instructions on how to install the package,
-including, if necessary, info on how to download or build any extra
-library it requires.  It also gives links to documentation, example
-scripts, and pictures/movies (if available) that illustrate use of the
-package.
-
-The majority of packages can be included in a LAMMPS build with a
-single setting (-D PGK_NAME for CMake) or command ("make yes-name" for
-make).  See the "Build package"_Build_package.html doc page for more
-info.  A few packages may require additional steps; this is indicated
-in the descriptions below.  The "Build extras"_Build_extras.html doc
-page gives those details.
-
-NOTE: To see the complete list of commands a package adds to LAMMPS,
-you can examine the files in its src directory, e.g. "ls
-src/GRANULAR".  Files with names that start with fix, compute, atom,
-pair, bond, angle, etc correspond to commands with the same style name
-as contained in the file name.
-
-"ASPHERE"_#PKG-ASPHERE,
-"BODY"_#PKG-BODY,
-"CLASS2"_#PKG-CLASS2,
-"COLLOID"_#PKG-COLLOID,
-"COMPRESS"_#PKG-COMPRESS,
-"CORESHELL"_#PKG-CORESHELL,
-"DIPOLE"_#PKG-DIPOLE,
-"GPU"_#PKG-GPU,
-"GRANULAR"_#PKG-GRANULAR,
-"KIM"_#PKG-KIM,
-"KOKKOS"_#PKG-KOKKOS,
-"KSPACE"_#PKG-KSPACE,
-"LATTE"_#PKG-LATTE,
-"MANYBODY"_#PKG-MANYBODY,
-"MC"_#PKG-MC,
-"MESSAGE"_#PKG-MESSAGE,
-"MISC"_#PKG-MISC,
-"MOLECULE"_#PKG-MOLECULE,
-"MPIIO"_#PKG-MPIIO,
-"MSCG"_#PKG-MSCG,
-"OPT"_#PKG-OPT,
-"PERI"_#PKG-PERI,
-"POEMS"_#PKG-POEMS,
-"PYTHON"_#PKG-PYTHON,
-"QEQ"_#PKG-QEQ,
-"REPLICA"_#PKG-REPLICA2,
-"RIGID"_#PKG-RIGID,
-"SHOCK"_#PKG-SHOCK,
-"SNAP"_#PKG-SNAP,
-"SPIN"_#PKG-SPIN,
-"SRD"_#PKG-SRD,
-"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
-
-"USER-ADIOS"_#PKG-USER-ADIOS,
-"USER-ATC"_#PKG-USER-ATC,
-"USER-AWPMD"_#PKG-USER-AWPMD,
-"USER-BOCS"_#PKG-USER-BOCS,
-"USER-CGDNA"_#PKG-USER-CGDNA,
-"USER-CGSDK"_#PKG-USER-CGSDK,
-"USER-COLVARS"_#PKG-USER-COLVARS,
-"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION,
-"USER-DPD"_#PKG-USER-DPD,
-"USER-DRUDE"_#PKG-USER-DRUDE,
-"USER-EFF"_#PKG-USER-EFF,
-"USER-FEP"_#PKG-USER-FEP,
-"USER-H5MD"_#PKG-USER-H5MD,
-"USER-INTEL"_#PKG-USER-INTEL,
-"USER-LB"_#PKG-USER-LB,
-"USER-MANIFOLD"_#PKG-USER-MANIFOLD,
-"USER-MEAMC"_#PKG-USER-MEAMC,
-"USER-MESO"_#PKG-USER-MESO,
-"USER-MGPT"_#PKG-USER-MGPT,
-"USER-MISC"_#PKG-USER-MISC,
-"USER-MOFFF"_#PKG-USER-MOFFF,
-"USER-MOLFILE"_#PKG-USER-MOLFILE,
-"USER-NETCDF"_#PKG-USER-NETCDF,
-"USER-OMP"_#PKG-USER-OMP,
-"USER-PHONON"_#PKG-USER-PHONON,
-"USER-PLUMED"_#PKG-USER-PLUMED,
-"USER-PTM"_#PKG-USER-PTM,
-"USER-QMMM"_#PKG-USER-QMMM,
-"USER-QTB"_#PKG-USER-QTB,
-"USER-QUIP"_#PKG-USER-QUIP,
-"USER-REAXC"_#PKG-USER-REAXC,
-"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
-"USER-SDPD"_#PKG-USER-SDPD,
-"USER-SMD"_#PKG-USER-SMD,
-"USER-SMTBQ"_#PKG-USER-SMTBQ,
-"USER-SPH"_#PKG-USER-SPH,
-"USER-TALLY"_#PKG-USER-TALLY,
-"USER-UEF"_#PKG-USER-UEF,
-"USER-VTK"_#PKG-USER-VTK,
-"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c)
-
-:line
-
-ASPHERE package :link(PKG-ASPHERE),h4
-
-[Contents:]
-
-Computes, time-integration fixes, and pair styles for aspherical
-particle models including ellipsoids, 2d lines, and 3d triangles.
-
-[Supporting info:]
-
-src/ASPHERE: filenames -> commands
-"Howto spherical"_Howto_spherical.html
-"pair_style gayberne"_pair_gayberne.html
-"pair_style resquared"_pair_resquared.html
-"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf
-"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf
-examples/ASPHERE
-examples/ellipse
-http://lammps.sandia.gov/movies.html#line
-http://lammps.sandia.gov/movies.html#tri :ul
-
-:line
-
-BODY package :link(PKG-BODY),h4
-
-[Contents:]
-
-Body-style particles with internal structure.  Computes,
-time-integration fixes, pair styles, as well as the body styles
-themselves.  See the "Howto body"_Howto_body.html doc page for an
-overview.
-
-[Supporting info:]
-
-src/BODY filenames -> commands
-"Howto_body"_Howto_body.html
-"atom_style body"_atom_style.html
-"fix nve/body"_fix_nve_body.html
-"pair_style body/nparticle"_pair_body_nparticle.html
-examples/body :ul
-
-:line
-
-CLASS2 package :link(PKG-CLASS2),h4
-
-[Contents:]
-
-Bond, angle, dihedral, improper, and pair styles for the COMPASS
-CLASS2 molecular force field.
-
-[Supporting info:]
-
-src/CLASS2: filenames -> commands
-"bond_style class2"_bond_class2.html
-"angle_style class2"_angle_class2.html
-"dihedral_style class2"_dihedral_class2.html
-"improper_style class2"_improper_class2.html
-"pair_style lj/class2"_pair_class2.html :ul
-
-:line
-
-COLLOID package :link(PKG-COLLOID),h4
-
-[Contents:]
-
-Coarse-grained finite-size colloidal particles.  Pair styles and fix
-wall styles for colloidal interactions.  Includes the Fast Lubrication
-Dynamics (FLD) method for hydrodynamic interactions, which is a
-simplified approximation to Stokesian dynamics.
-
-[Authors:] This package includes Fast Lubrication Dynamics pair styles
-which were created by Amit Kumar and Michael Bybee from Jonathan
-Higdon's group at UIUC.
-
-[Supporting info:]
-
-src/COLLOID: filenames -> commands
-"fix wall/colloid"_fix_wall.html
-"pair_style colloid"_pair_colloid.html
-"pair_style yukawa/colloid"_pair_yukawa_colloid.html
-"pair_style brownian"_pair_brownian.html
-"pair_style lubricate"_pair_lubricate.html
-"pair_style lubricateU"_pair_lubricateU.html
-examples/colloid
-examples/srd :ul
-
-:line
-
-COMPRESS package :link(PKG-COMPRESS),h4
-
-[Contents:]
-
-Compressed output of dump files via the zlib compression library,
-using dump styles with a "gz" in their style name.
-
-To use this package you must have the zlib compression library
-available on your system.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#compress on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/COMPRESS: filenames -> commands
-src/COMPRESS/README
-lib/compress/README
-"dump atom/gz"_dump.html
-"dump cfg/gz"_dump.html
-"dump custom/gz"_dump.html
-"dump xyz/gz"_dump.html :ul
-
-:line
-
-CORESHELL package :link(PKG-CORESHELL),h4
-
-[Contents:]
-
-Compute and pair styles that implement the adiabatic core/shell model
-for polarizability.  The pair styles augment Born, Buckingham, and
-Lennard-Jones styles with core/shell capabilities.  The "compute
-temp/cs"_compute_temp_cs.html command calculates the temperature of a
-system with core/shell particles.  See the "Howto
-coreshell"_Howto_coreshell.html doc page for an overview of how to use
-this package.
-
-[Author:] Hendrik Heenen (Technical U of Munich).
-
-[Supporting info:]
-
-src/CORESHELL: filenames -> commands
-"Howto coreshell"_Howto_coreshell.html
-"Howto polarizable"_Howto_polarizable.html
-"compute temp/cs"_compute_temp_cs.html
-"pair_style born/coul/long/cs"_pair_cs.html
-"pair_style buck/coul/long/cs"_pair_cs.html
-"pair_style lj/cut/coul/long/cs"_pair_lj.html
-examples/coreshell :ul
-
-:line
-
-DIPOLE package :link(PKG-DIPOLE),h4
-
-[Contents:]
-
-An atom style and several pair styles for point dipole models with
-short-range or long-range interactions.
-
-[Supporting info:]
-
-src/DIPOLE: filenames -> commands
-"atom_style dipole"_atom_style.html
-"pair_style lj/cut/dipole/cut"_pair_dipole.html
-"pair_style lj/cut/dipole/long"_pair_dipole.html
-"pair_style lj/long/dipole/long"_pair_dipole.html
-examples/dipole :ul
-
-:line
-
-GPU package :link(PKG-GPU),h4
-
-[Contents:]
-
-Dozens of pair styles and a version of the PPPM long-range Coulombic
-solver optimized for GPUs.  All such styles have a "gpu" as a suffix
-in their style name. The GPU code can be compiled with either CUDA or
-OpenCL, however the OpenCL variants are no longer actively maintained
-and only the CUDA versions are regularly tested.  The "Speed
-gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
-software is required on your system, and details on how to build and
-use this package.  Its styles can be invoked at run time via the "-sf
-gpu" or "-suffix gpu" "command-line switches"_Run_options.html.  See
-also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
-
-[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
-(Northwestern U) while at ORNL.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/GPU: filenames -> commands
-src/GPU/README
-lib/gpu/README
-"Speed packages"_Speed_packages.html
-"Speed gpu"_Speed_gpu.html
-"Section 2.6 -sf gpu"_Run_options.html
-"Section 2.6 -pk gpu"_Run_options.html
-"package gpu"_package.html
-"Commands all"_lc pages (pair,kspace) for styles followed by (g)
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-GRANULAR package :link(PKG-GRANULAR),h4
-
-[Contents:]
-
-Pair styles and fixes for finite-size granular particles, which
-interact with each other and boundaries via frictional and dissipative
-potentials.
-
-[Supporting info:]
-
-src/GRANULAR: filenames -> commands
-"Howto granular"_Howto_granular.html
-"fix pour"_fix_pour.html
-"fix wall/gran"_fix_wall_gran.html
-"pair_style gran/hooke"_pair_gran.html
-"pair_style gran/hertz/history"_pair_gran.html
-examples/granregion
-examples/pour
-bench/in.chute
-http://lammps.sandia.gov/pictures.html#jamming
-http://lammps.sandia.gov/movies.html#hopper
-http://lammps.sandia.gov/movies.html#dem
-http://lammps.sandia.gov/movies.html#brazil
-http://lammps.sandia.gov/movies.html#granregion :ul
-
-:line
-
-KIM package :link(PKG-KIM),h4
-
-[Contents:]
-
-This package contains a set of commands that serve as a wrapper on the
-"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
-repository of interatomic models (IMs)
-enabling compatible ones to be used in LAMMPS simulations.
-This includes "kim_init and kim_interactions"_kim_commands.html
-commands to select, initialize and instantiate the IM, and a
-"kim_query"_kim_commands.html command to perform web queries
-for material property predictions of OpenKIM IMs.
-Support for KIM IMs that conform to the
-"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/
-is provided by the "pair_style kim"_pair_kim.html command.
-
-NOTE: The command {pair_style kim} is called by {kim_interactions} and
-is not recommended to be directly used in input scripts.
-
-To use this package you must have the KIM API library available on your
-system. The KIM API is available for download on the
-"OpenKIM website"_https://openkim.org/kim-api/.
-When installing LAMMPS from binary, the kim-api package
-is a dependency that is automatically downloaded and installed.
-
-Information about the KIM project can be found at its website:
-"https://openkim.org"_https://openkim.org.
-The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota)
-and is funded by the "National Science Foundation"_https://www.nsf.gov/.
-
-[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
-API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and
-Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html
-interface in close collaboration with Ryan Elliott.
-
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#kim on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-"kim_commands"_kim_commands.html
-"pair_style kim"_pair_kim.html
-src/KIM: filenames -> commands
-src/KIM/README
-lib/kim/README
-examples/kim :ul
-
-:line
-
-KOKKOS package :link(PKG-KOKKOS),h4
-
-[Contents:]
-
-Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
-styles adapted to compile using the Kokkos library which can convert
-them to OpenMP or CUDA code so that they run efficiently on multicore
-CPUs, KNLs, or GPUs.  All the styles have a "kk" as a suffix in their
-style name.  The "Speed kokkos"_Speed_kokkos.html doc page gives
-details of what hardware and software is required on your system, and
-how to build and use this package.  Its styles can be invoked at run
-time via the "-sf kk" or "-suffix kk" "command-line
-switches"_Run_options.html.  Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
-"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
-have styles optimized for CPUs, KNLs, and GPUs.
-
-You must have a C++11 compatible compiler to use this package.
-KOKKOS makes extensive use of advanced C++ features, which can
-expose compiler bugs, especially when compiling for maximum
-performance at high optimization levels. Please see the file
-lib/kokkos/README for a list of compilers and their respective
-platforms, that are known to work.
-
-[Authors:] The KOKKOS package was created primarily by Christian Trott
-and Stan Moore (Sandia), with contributions from other folks as well.
-It uses the open-source "Kokkos library"_https://github.com/kokkos
-which was developed by Carter Edwards, Christian Trott, and others at
-Sandia, and which is included in the LAMMPS distribution in
-lib/kokkos.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#kokkos on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/KOKKOS: filenames -> commands
-src/KOKKOS/README
-lib/kokkos/README
-"Speed packages"_Speed_packages.html
-"Speed kokkos"_Speed_kokkos.html
-"Section 2.6 -k on ..."_Run_options.html
-"Section 2.6 -sf kk"_Run_options.html
-"Section 2.6 -pk kokkos"_Run_options.html
-"package kokkos"_package.html
-"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k)
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-KSPACE package :link(PKG-KSPACE),h4
-
-[Contents:]
-
-A variety of long-range Coulombic solvers, as well as pair styles
-which compute the corresponding short-range pairwise Coulombic
-interactions.  These include Ewald, particle-particle particle-mesh
-(PPPM), and multilevel summation method (MSM) solvers.
-
-[Install:]
-
-Building with this package requires a 1d FFT library be present on
-your system for use by the PPPM solvers.  This can be the KISS FFT
-library provided with LAMMPS, 3rd party libraries like FFTW, or a
-vendor-supplied FFT library.  See the "Build
-settings"_Build_settings.html doc page for details on how to select
-different FFT options for your LAMPMS build.
-
-[Supporting info:]
-
-src/KSPACE: filenames -> commands
-"kspace_style"_kspace_style.html
-"doc/PDF/kspace.pdf"_PDF/kspace.pdf
-"Howto tip3p"_Howto_tip3p.html
-"Howto tip4p"_Howto_tip4p.html
-"Howto spc"_Howto_spc.html
-"pair_style coul"_pair_coul.html
-"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name
-examples/peptide
-bench/in.rhodo :ul
-
-:line
-
-LATTE package :link(PKG-LATTE),h4
-
-[Contents:]
-
-A fix command which wraps the LATTE DFTB code, so that molecular
-dynamics can be run with LAMMPS using density-functional tight-binding
-quantum forces calculated by LATTE.
-
-More information on LATTE can be found at this web site:
-"https://github.com/lanl/LATTE"_latte-home.  A brief technical
-description is given with the "fix latte"_fix_latte.html command.
-
-:link(latte-home,https://github.com/lanl/LATTE)
-
-[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia).  LATTE
-itself is developed at Los Alamos National Laboratory by Marc
-Cawkwell, Anders Niklasson, and Christian Negre.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#latte on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/LATTE: filenames -> commands
-src/LATTE/README
-lib/latte/README
-"fix latte"_fix_latte.html
-examples/latte
-"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul
-
-:line
-
-MANYBODY package :link(PKG-MANYBODY),h4
-
-[Contents:]
-
-A variety of many-body and bond-order potentials.  These include
-(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
-
-[Supporting info:]
-
-src/MANYBODY: filenames -> commands
-"Commands pair"_Commands_pair.html page
-examples/comb
-examples/eim
-examples/nb3d
-examples/shear
-examples/streitz
-examples/vashishta
-bench/in.eam :ul
-
-:line
-
-MC package :link(PKG-MC),h4
-
-[Contents:]
-
-Several fixes and a pair style that have Monte Carlo (MC) or MC-like
-attributes.  These include fixes for creating, breaking, and swapping
-bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) in conjunction with dynamics.
-
-[Supporting info:]
-
-src/MC: filenames -> commands
-"fix atom/swap"_fix_atom_swap.html
-"fix bond/break"_fix_bond_break.html
-"fix bond/create"_fix_bond_create.html
-"fix bond/swap"_fix_bond_swap.html
-"fix gcmc"_fix_gcmc.html
-"pair_style dsmc"_pair_dsmc.html
-http://lammps.sandia.gov/movies.html#gcmc :ul
-
-:line
-
-MESSAGE package :link(PKG-MESSAGE),h4
-
-[Contents:]
-
-Commands to use LAMMPS as either a client or server and couple it to
-another application.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#message on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/MESSAGE: filenames -> commands
-lib/message/README
-"message"_message.html
-"fix client/md"_fix_client_md.html
-"server md"_server_md.html
-"server mc"_server_mc.html
-examples/message :ul
-
-:line
-
-MISC package :link(PKG-MISC),h4
-
-[Contents:]
-
-A variety of compute, fix, pair, dump styles with specialized
-capabilities that don't align with other packages.  Do a directory
-listing, "ls src/MISC", to see the list of commands.
-
-NOTE: the MISC package contains styles that require using the
--restrict flag, when compiling with Intel compilers.
-
-[Supporting info:]
-
-src/MISC: filenames -> commands
-"compute ti"_compute_ti.html
-"fix evaporate"_fix_evaporate.html
-"fix orient/fcc"_fix_orient.html
-"fix ttm"_fix_ttm.html
-"fix thermal/conductivity"_fix_thermal_conductivity.html
-"fix viscosity"_fix_viscosity.html
-examples/KAPPA
-examples/VISCOSITY
-http://lammps.sandia.gov/pictures.html#ttm
-http://lammps.sandia.gov/movies.html#evaporation :ul
-
-:line
-
-MOLECULE package :link(PKG-MOLECULE),h4
-
-[Contents:]
-
-A large number of atom, pair, bond, angle, dihedral, improper styles
-that are used to model molecular systems with fixed covalent bonds.
-The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
-force fields, and a TIP4P water model.
-
-[Supporting info:]
-
-src/MOLECULE: filenames -> commands
-"atom_style"_atom_style.html
-"bond_style"_bond_style.html
-"angle_style"_angle_style.html
-"dihedral_style"_dihedral_style.html
-"improper_style"_improper_style.html
-"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html
-"pair_style lj/charmm/coul/charmm"_pair_charmm.html
-"Howto bioFF"_Howto_bioFF.html
-examples/cmap
-examples/dreiding
-examples/micelle,
-examples/peptide
-bench/in.chain
-bench/in.rhodo :ul
-
-:line
-
-MPIIO package :link(PKG-MPIIO),h4
-
-[Contents:]
-
-Support for parallel output/input of dump and restart files via the
-MPIIO library.  It adds "dump styles"_dump.html with a "mpiio" in
-their style name.  Restart files with an ".mpiio" suffix are also
-written and read in parallel.
-
-[Supporting info:]
-
-src/MPIIO: filenames -> commands
-"dump"_dump.html
-"restart"_restart.html
-"write_restart"_write_restart.html
-"read_restart"_read_restart.html :ul
-
-:line
-
-MSCG package :link(PKG-mscg),h4
-
-[Contents:]
-
-A "fix mscg"_fix_mscg.html command which can parameterize a
-Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
-library"_mscg-home.
-
-:link(mscg-home,https://github.com/uchicago-voth/MSCG-release)
-
-To use this package you must have the MS-CG library available on your
-system.
-
-[Authors:] The fix was written by Lauren Abbott (Sandia).  The MS-CG
-library was developed by Jacob Wagner in Greg Voth's group at the
-University of Chicago.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#mscg on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/MSCG: filenames -> commands
-src/MSCG/README
-lib/mscg/README
-examples/mscg :ul
-
-:line
-
-OPT package :link(PKG-OPT),h4
-
-[Contents:]
-
-A handful of pair styles which are optimized for improved CPU
-performance on single or multiple cores.  These include EAM, LJ,
-CHARMM, and Morse potentials.  The styles have an "opt" suffix in
-their style name.  The "Speed opt"_Speed_opt.html doc page gives
-details of how to build and use this package.  Its styles can be
-invoked at run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Run_options.html.  See also the "KOKKOS"_#PKG-KOKKOS,
-"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
-have styles optimized for CPU performance.
-
-[Authors:] James Fischer (High Performance Technologies), David Richie,
-and Vincent Natoli (Stone Ridge Technolgy).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#opt on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/OPT: filenames -> commands
-"Speed packages"_Speed_packages.html
-"Speed opt"_Speed_opt.html
-"Section 2.6 -sf opt"_Run_options.html
-"Commands pair"_Commands_pair.html for styles followed by (t)
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-PERI package :link(PKG-PERI),h4
-
-[Contents:]
-
-An atom style, several pair styles which implement different
-Peridynamics materials models, and several computes which calculate
-diagnostics.  Peridynamics is a particle-based meshless continuum
-model.
-
-[Authors:] The original package was created by Mike Parks (Sandia).
-Additional Peridynamics models were added by Rezwanur Rahman and John
-Foster (UTSA).
-
-[Supporting info:]
-
-src/PERI: filenames -> commands
-"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf
-"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf
-"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf
-"atom_style peri"_atom_style.html
-"pair_style peri/*"_pair_peri.html
-"compute damage/atom"_compute_damage_atom.html
-"compute plasticity/atom"_compute_plasticity_atom.html
-examples/peri
-http://lammps.sandia.gov/movies.html#peri :ul
-
-:line
-
-POEMS package :link(PKG-POEMS),h4
-
-[Contents:]
-
-A fix that wraps the Parallelizable Open source Efficient Multibody
-Software (POEMS) library, which is able to simulate the dynamics of
-articulated body systems.  These are systems with multiple rigid
-bodies (collections of particles) whose motion is coupled by
-connections at hinge points.
-
-[Author:] Rudra Mukherjee (JPL) while at RPI.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#poems on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/POEMS: filenames -> commands
-src/POEMS/README
-lib/poems/README
-"fix poems"_fix_poems.html
-examples/rigid :ul
-
-:line
-
-PYTHON package :link(PKG-PYTHON),h4
-
-[Contents:]
-
-A "python"_python.html command which allow you to execute Python code
-from a LAMMPS input script.  The code can be in a separate file or
-embedded in the input script itself.  See the "Python
-call"_Python_call.html doc page for an overview of using Python from
-LAMMPS in this manner and all the "Python"_Python_head.html doc pages
-for other ways to use LAMMPS and Python together.
-
-NOTE: Building with the PYTHON package assumes you have a Python
-shared library available on your system, which needs to be a Python 2
-version, 2.6 or later.  Python 3 is not yet supported.  See the
-lib/python/README for more details.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#python on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/PYTHON: filenames -> commands
-"Python call"_Python_head.html
-lib/python/README
-examples/python :ul
-
-:line
-
-QEQ package :link(PKG-QEQ),h4
-
-[Contents:]
-
-Several fixes for performing charge equilibration (QEq) via different
-algorithms.  These can be used with pair styles that perform QEq as
-part of their formulation.
-
-[Supporting info:]
-
-src/QEQ: filenames -> commands
-"fix qeq/*"_fix_qeq.html
-examples/qeq
-examples/streitz :ul
-
-:line
-
-REPLICA package :link(PKG-REPLICA2),h4
-
-[Contents:]
-
-A collection of multi-replica methods which can be used when running
-multiple LAMMPS simulations (replicas).  See the "Howto
-replica"_Howto_replica.html doc page for an overview of how to run
-multi-replica simulations in LAMMPS.  Methods in the package include
-nudged elastic band (NEB), parallel replica dynamics (PRD),
-temperature accelerated dynamics (TAD), parallel tempering, and a
-verlet/split algorithm for performing long-range Coulombics on one set
-of processors, and the remainder of the force field calculation on
-another set.
-
-[Supporting info:]
-
-src/REPLICA: filenames -> commands
-"Howto replica"_Howto_replica.html
-"neb"_neb.html
-"prd"_prd.html
-"tad"_tad.html
-"temper"_temper.html,
-"run_style verlet/split"_run_style.html
-examples/neb
-examples/prd
-examples/tad :ul
-
-:line
-
-RIGID package :link(PKG-RIGID),h4
-
-[Contents:]
-
-Fixes which enforce rigid constraints on collections of atoms or
-particles.  This includes SHAKE and RATTLE, as well as various
-rigid-body integrators for a few large bodies or many small bodies.
-Also several computes which calculate properties of rigid bodies.
-
-[Supporting info:]
-
-src/RIGID: filenames -> commands
-"compute erotate/rigid"_compute_erotate_rigid.html
-fix shake"_fix_shake.html
-"fix rattle"_fix_shake.html
-"fix rigid/*"_fix_rigid.html
-examples/ASPHERE
-examples/rigid
-bench/in.rhodo
-http://lammps.sandia.gov/movies.html#box
-http://lammps.sandia.gov/movies.html#star :ul
-
-:line
-
-SHOCK package :link(PKG-SHOCK),h4
-
-[Contents:]
-
-Fixes for running impact simulations where a shock-wave passes through
-a material.
-
-[Supporting info:]
-
-src/SHOCK: filenames -> commands
-"fix append/atoms"_fix_append_atoms.html
-"fix msst"_fix_msst.html
-"fix nphug"_fix_nphug.html
-"fix wall/piston"_fix_wall_piston.html
-examples/hugoniostat
-examples/msst :ul
-
-:line
-
-SNAP package :link(PKG-SNAP),h4
-
-[Contents:]
-
-A pair style for the spectral neighbor analysis potential (SNAP).
-SNAP is methodology for deriving a highly accurate classical potential
-fit to a large archive of quantum mechanical (DFT) data. Also several
-computes which analyze attributes of the potential.
-
-[Author:] Aidan Thompson (Sandia).
-
-[Supporting info:]
-
-src/SNAP: filenames -> commands
-"pair_style snap"_pair_snap.html
-"compute sna/atom"_compute_sna_atom.html
-"compute snad/atom"_compute_sna_atom.html
-"compute snav/atom"_compute_sna_atom.html
-examples/snap :ul
-
-:line
-
-SPIN package :link(PKG-SPIN),h4
-
-[Contents:]
-
-Model atomic magnetic spins classically, coupled to atoms moving in
-the usual manner via MD.  Various pair, fix, and compute styles.
-
-[Author:] Julien Tranchida (Sandia).
-
-[Supporting info:]
-
-src/SPIN: filenames -> commands
-"Howto spins"_Howto_spins.html
-"pair_style spin/dipole/cut"_pair_spin_dipole.html
-"pair_style spin/dipole/long"_pair_spin_dipole.html
-"pair_style spin/dmi"_pair_spin_dmi.html
-"pair_style spin/exchange"_pair_spin_exchange.html
-"pair_style spin/magelec"_pair_spin_magelec.html
-"pair_style spin/neel"_pair_spin_neel.html
-"fix nve/spin"_fix_nve_spin.html
-"fix precession/spin"_fix_precession_spin.html
-"compute spin"_compute_spin.html
-"neb/spin"_neb_spin.html
-examples/SPIN :ul
-
-:line
-
-SRD package :link(PKG-SRD),h4
-
-[Contents:]
-
-A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
-method for coarse-graining of a solvent, typically around large
-colloidal particles.
-
-[Supporting info:]
-
-src/SRD: filenames -> commands
-"fix srd"_fix_srd.html
-"fix wall/srd"_fix_wall_srd.html
-examples/srd
-examples/ASPHERE
-http://lammps.sandia.gov/movies.html#tri
-http://lammps.sandia.gov/movies.html#line
-http://lammps.sandia.gov/movies.html#poly :ul
-
-:line
-
-VORONOI package :link(PKG-VORONOI),h4
-
-[Contents:]
-
-A compute command which calculates the Voronoi tesselation of a
-collection of atoms by wrapping the "Voro++ library"_voro-home.  This
-can be used to calculate the local volume or each atoms or its near
-neighbors.
-
-:link(voro-home,http://math.lbl.gov/voro++)
-
-To use this package you must have the Voro++ library available on your
-system.
-
-[Author:] Daniel Schwen (INL) while at LANL.  The open-source Voro++
-library was written by Chris Rycroft (Harvard U) while at UC Berkeley
-and LBNL.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#voronoi on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/VORONOI: filenames -> commands
-src/VORONOI/README
-lib/voronoi/README
-"compute voronoi/atom"_compute_voronoi_atom.html
-examples/voronoi :ul
-
-:line
-
-USER-ADIOS package :link(PKG-USER-ADIOS),h4
-
-[Contents:]
-
-ADIOS is a high-performance I/O library. This package implements the
-dump "atom/adios" and dump "custom/adios" commands to write data using
-the ADIOS library.
-
-[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-adios on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-ADIOS: filenames -> commands
-src/USER-ADIOS/README
-examples/USER/adios
-https://github.com/ornladios/ADIOS2 :ul
-
-:line
-
-USER-ATC package :link(PKG-USER-ATC),h4
-
-[Contents:]
-
-ATC stands for atoms-to-continuum.  This package implements a "fix
-atc"_fix_atc.html command to either couple molecular dynamics with
-continuum finite element equations or perform on-the-fly conversion of
-atomic information to continuum fields.
-
-[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-atc on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-ATC: filenames -> commands
-src/USER-ATC/README
-"fix atc"_fix_atc.html
-examples/USER/atc
-http://lammps.sandia.gov/pictures.html#atc :ul
-
-:line
-
-USER-AWPMD package :link(PKG-USER-AWPMD),h4
-
-[Contents:]
-
-AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics.  This
-package implements an atom, pair, and fix style which allows electrons
-to be treated as explicit particles in a classical molecular dynamics
-model.
-
-[Author:] Ilya Valuev (JIHT, Russia).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-awpmd on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-AWPMD: filenames -> commands
-src/USER-AWPMD/README
-"pair_style awpmd/cut"_pair_awpmd.html
-examples/USER/awpmd :ul
-
-:line
-
-USER-BOCS package :link(PKG-USER-BOCS),h4
-
-[Contents:]
-
-This package provides "fix bocs"_fix_bocs.html, a modified version
-of "fix npt"_fix_nh.html which includes the pressure correction to
-the barostat as outlined in:
-
-N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
-accurately describe the structure, pressure, and compressibility of
-molecular liquids," J. Chem. Phys. 143, 243148 (2015).
-
-[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The
-Pennsylvania State University)
-
-[Supporting info:]
-
-The USER-BOCS user package for LAMMPS is part of the BOCS software package:
-"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
-
-See the following reference for information about the entire package:
-
-Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
-"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
-J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
-
-Example inputs are in the examples/USER/bocs folder.
-
-:line
-
-USER-CGDNA package :link(PKG-USER-CGDNA),h4
-
-[Contents:]
-
-Several pair styles, a bond style, and integration fixes for
-coarse-grained models of single- and double-stranded DNA based on the
-oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
-This includes Langevin-type rigid-body integrators with improved
-stability.
-
-[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
-
-[Supporting info:]
-
-src/USER-CGDNA: filenames -> commands
-/src/USER-CGDNA/README
-"pair_style oxdna/*"_pair_oxdna.html
-"pair_style oxdna2/*"_pair_oxdna2.html
-"bond_style oxdna/*"_bond_oxdna.html
-"bond_style oxdna2/*"_bond_oxdna.html
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
-
-:line
-
-USER-CGSDK package :link(PKG-USER-CGSDK),h4
-
-[Contents:]
-
-Several pair styles and an angle style which implement the
-coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
-simulation of ionic liquids, electrolytes, lipids and charged amino
-acids.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Supporting info:]
-
-src/USER-CGSDK: filenames -> commands
-src/USER-CGSDK/README
-"pair_style lj/sdk/*"_pair_sdk.html
-"angle_style sdk"_angle_sdk.html
-examples/USER/cgsdk
-http://lammps.sandia.gov/pictures.html#cg :ul
-
-:line
-
-USER-COLVARS package :link(PKG-USER-COLVARS),h4
-
-[Contents:]
-
-COLVARS stands for collective variables, which can be used to
-implement various enhanced sampling methods, including Adaptive
-Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and
-Restraints.  A "fix colvars"_fix_colvars.html command is implemented
-which wraps a COLVARS library, which implements these methods.
-simulations.
-
-[Authors:] The COLVARS library is written and maintained by
-Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
-and Jerome Henin (LISM, CNRS, Marseille, France), originally for
-the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
-(Temple U) provided the interface to LAMMPS.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-colvars on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-COLVARS: filenames -> commands
-"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf
-src/USER-COLVARS/README
-lib/colvars/README
-"fix colvars"_fix_colvars.html
-examples/USER/colvars :ul
-
-:line
-
-USER-PLUMED package :link(PKG-USER-PLUMED),h4
-
-[Contents:]
-
-The fix plumed command allows you to use the PLUMED free energy plugin
-for molecular dynamics to analyze and bias your LAMMPS trajectory on
-the fly.  The PLUMED library is called from within the LAMMPS input
-script by using the "fix plumed"_fix_plumed.html command.
-
-[Authors:] The "PLUMED library"_#PLUMED is written and maintained by
-Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth
-Tribello.
-
-:link(PLUMED,http://www.plumed.org)
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-plumed on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-PLUMED/README
-lib/plumed/README
-"fix plumed"_fix_plumed.html
-examples/USER/plumed :ul
-
-:line
-
-USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
-
-[Contents:]
-
-Two computes and a fix for calculating x-ray and electron diffraction
-intensities based on kinematic diffraction theory.
-
-[Author:] Shawn Coleman while at the U Arkansas.
-
-[Supporting info:]
-
-src/USER-DIFFRACTION: filenames -> commands
-"compute saed"_compute_saed.html
-"compute xrd"_compute_xrd.html
-"fix saed/vtk"_fix_saed_vtk.html
-examples/USER/diffraction :ul
-
-:line
-
-USER-DPD package :link(PKG-USER-DPD),h4
-
-[Contents:]
-
-DPD stands for dissipative particle dynamics.  This package implements
-coarse-grained DPD-based models for energetic, reactive molecular
-crystalline materials.  It includes many pair styles specific to these
-systems, including for reactive DPD, where each particle has internal
-state for multiple species and a coupled set of chemical reaction ODEs
-are integrated each timestep.  Highly accurate time integrators for
-isothermal, isoenergetic, isobaric and isenthalpic conditions are
-included.  These enable long timesteps via the Shardlow splitting
-algorithm.
-
-[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John
-Brennan (ARL).
-
-[Supporting info:]
-
-src/USER-DPD: filenames -> commands
-/src/USER-DPD/README
-"compute dpd"_compute_dpd.html
-"compute dpd/atom"_compute_dpd_atom.html
-"fix eos/cv"_fix_eos_table.html
-"fix eos/table"_fix_eos_table.html
-"fix eos/table/rx"_fix_eos_table_rx.html
-"fix shardlow"_fix_shardlow.html
-"fix rx"_fix_rx.html
-"pair_style table/rx"_pair_table_rx.html
-"pair_style dpd/fdt"_pair_dpd_fdt.html
-"pair_style dpd/fdt/energy"_pair_dpd_fdt.html
-"pair_style exp6/rx"_pair_exp6_rx.html
-"pair_style multi/lucy"_pair_multi_lucy.html
-"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html
-examples/USER/dpd :ul
-
-:line
-
-USER-DRUDE package :link(PKG-USER-DRUDE),h4
-
-[Contents:]
-
-Fixes, pair styles, and a compute to simulate thermalized Drude
-oscillators as a model of polarization.  See the "Howto
-drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages
-for an overview of how to use the package.  There are auxiliary tools
-for using this package in tools/drude.
-
-[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
-Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
-
-[Supporting info:]
-
-src/USER-DRUDE: filenames -> commands
-"Howto drude"_Howto_drude.html
-"Howto drude2"_Howto_drude2.html
-"Howto polarizable"_Howto_polarizable.html
-src/USER-DRUDE/README
-"fix drude"_fix_drude.html
-"fix drude/transform/*"_fix_drude_transform.html
-"compute temp/drude"_compute_temp_drude.html
-"pair_style thole"_pair_thole.html
-"pair_style lj/cut/thole/long"_pair_thole.html
-examples/USER/drude
-tools/drude :ul
-
-:line
-
-USER-EFF package :link(PKG-USER-EFF),h4
-
-[Contents:]
-
-EFF stands for electron force field which allows a classical MD code
-to model electrons as particles of variable radius.  This package
-contains atom, pair, fix and compute styles which implement the eFF as
-described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
-JCC, 2010.  The eFF potential was first introduced by Su and Goddard,
-in 2007.  There are auxiliary tools for using this package in
-tools/eff; see its README file.
-
-[Author:] Andres Jaramillo-Botero (CalTech).
-
-[Supporting info:]
-
-src/USER-EFF: filenames -> commands
-src/USER-EFF/README
-"atom_style electron"_atom_style.html
-"fix nve/eff"_fix_nve_eff.html
-"fix nvt/eff"_fix_nh_eff.html
-"fix npt/eff"_fix_nh_eff.html
-"fix langevin/eff"_fix_langevin_eff.html
-"compute temp/eff"_compute_temp_eff.html
-"pair_style eff/cut"_pair_eff.html
-"pair_style eff/inline"_pair_eff.html
-examples/USER/eff
-tools/eff/README
-tools/eff
-http://lammps.sandia.gov/movies.html#eff :ul
-
-:line
-
-USER-FEP package :link(PKG-USER-FEP),h4
-
-[Contents:]
-
-FEP stands for free energy perturbation.  This package provides
-methods for performing FEP simulations by using a "fix
-adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials,
-which have a "soft" in their style name.  There are auxiliary tools
-for using this package in tools/fep; see its README file.
-
-[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
-
-[Supporting info:]
-
-src/USER-FEP: filenames -> commands
-src/USER-FEP/README
-"fix adapt/fep"_fix_adapt_fep.html
-"compute fep"_compute_fep.html
-"pair_style */soft"_pair_fep_soft.html
-examples/USER/fep
-tools/fep/README
-tools/fep :ul
-
-:line
-
-USER-H5MD package :link(PKG-USER-H5MD),h4
-
-[Contents:]
-
-H5MD stands for HDF5 for MD.  "HDF5"_HDF5 is a portable, binary,
-self-describing file format, used by many scientific simulations.
-H5MD is a format for molecular simulations, built on top of HDF5.
-This package implements a "dump h5md"_dump_h5md.html command to output
-LAMMPS snapshots in this format.
-
-:link(HDF5,http://www.hdfgroup.org/HDF5)
-
-To use this package you must have the HDF5 library available on your
-system.
-
-[Author:] Pierre de Buyl (KU Leuven) created both the package and the
-H5MD format.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-h5md on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-H5MD: filenames -> commands
-src/USER-H5MD/README
-lib/h5md/README
-"dump h5md"_dump_h5md.html :ul
-
-:line
-
-USER-INTEL package :link(PKG-USER-INTEL),h4
-
-[Contents:]
-
-Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
-styles which are optimized for Intel CPUs and KNLs (Knights Landing).
-All of them have an "intel" in their style name.  The "Speed
-intel"_Speed_intel.html doc page gives details of what hardware and
-compilers are required on your system, and how to build and use this
-package.  Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Run_options.html.  Also see
-the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages,
-which have styles optimized for CPUs and KNLs.
-
-You need to have an Intel compiler, version 14 or higher to take full
-advantage of this package. While compilation with GNU compilers is
-supported, performance will be sub-optimal.
-
-NOTE: the USER-INTEL package contains styles that require using the
--restrict flag, when compiling with Intel compilers.
-
-[Author:] Mike Brown (Intel).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-intel on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-INTEL: filenames -> commands
-src/USER-INTEL/README
-"Speed packages"_Speed_packages.html
-"Speed intel"_Speed_intel.html
-"Section 2.6 -sf intel"_Run_options.html
-"Section 2.6 -pk intel"_Run_options.html
-"package intel"_package.html
-"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i)
-src/USER-INTEL/TEST
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-USER-LB package :link(PKG-USER-LB),h4
-
-[Contents:]
-
-Fixes which implement a background Lattice-Boltzmann (LB) fluid, which
-can be used to model MD particles influenced by hydrodynamic forces.
-
-[Authors:] Frances Mackay and Colin Denniston (University of Western
-Ontario).
-
-[Supporting info:]
-
-src/USER-LB: filenames -> commands
-src/USER-LB/README
-"fix lb/fluid"_fix_lb_fluid.html
-"fix lb/momentum"_fix_lb_momentum.html
-"fix lb/viscous"_fix_lb_viscous.html
-examples/USER/lb :ul
-
-:line
-
-USER-MGPT package :link(PKG-USER-MGPT),h4
-
-[Contents:]
-
-A pair style which provides a fast implementation of the quantum-based
-MGPT multi-ion potentials.  The MGPT or model GPT method derives from
-first-principles DFT-based generalized pseudopotential theory (GPT)
-through a series of systematic approximations valid for mid-period
-transition metals with nearly half-filled d bands.  The MGPT method
-was originally developed by John Moriarty at LLNL.  The pair style in
-this package calculates forces and energies using an optimized
-matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
-
-[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
-
-[Supporting info:]
-
-src/USER-MGPT: filenames -> commands
-src/USER-MGPT/README
-"pair_style mgpt"_pair_mgpt.html
-examples/USER/mgpt :ul
-
-:line
-
-USER-MISC package :link(PKG-USER-MISC),h4
-
-[Contents:]
-
-A potpourri of (mostly) unrelated features contributed to LAMMPS by
-users.  Each feature is a single fix, compute, pair, bond, angle,
-dihedral, improper, or command style.
-
-[Authors:] The author for each style in the package is listed in the
-src/USER-MISC/README file.
-
-[Supporting info:]
-
-src/USER-MISC: filenames -> commands
-src/USER-MISC/README
-one doc page per individual command listed in src/USER-MISC/README
-examples/USER/misc :ul
-
-:line
-
-USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4
-
-[Contents:]
-
-Several fixes and a "manifold" class which enable simulations of
-particles constrained to a manifold (a 2D surface within the 3D
-simulation box).  This is done by applying the RATTLE constraint
-algorithm to formulate single-particle constraint functions
-g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
-n = grad(g).
-
-[Author:] Stefan Paquay (until 2017: Eindhoven University of
-Technology (TU/e), The Netherlands; since 2017: Brandeis University,
-Waltham, MA, USA)
-
-[Supporting info:]
-
-src/USER-MANIFOLD: filenames -> commands
-src/USER-MANIFOLD/README
-"Howto manifold"_Howto_manifold.html
-"fix manifoldforce"_fix_manifoldforce.html
-"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
-"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
-examples/USER/manifold
-http://lammps.sandia.gov/movies.html#manifold :ul
-
-:line
-
-USER-MEAMC package :link(PKG-USER-MEAMC),h4
-
-[Contents:]
-
-A pair style for the modified embedded atom (MEAM) potential
-translated from the Fortran version in the (obsolete) "MEAM" package
-to plain C++. The USER-MEAMC fully replaces the MEAM package, which
-has been removed from LAMMPS after the 12 December 2018 version.
-
-[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
-based on the Fortran version of Greg Wagner (Northwestern U) while at
-Sandia.
-
-[Supporting info:]
-
-src/USER-MEAMC: filenames -> commands
-src/USER-MEAMC/README
-"pair_style meam/c"_pair_meamc.html
-examples/meamc :ul
-
-:line
-
-USER-MESO package :link(PKG-USER-MESO),h4
-
-[Contents:]
-
-Several extensions of the dissipative particle dynamics (DPD)
-method.  Specifically, energy-conserving DPD (eDPD) that can model
-non-isothermal processes, many-body DPD (mDPD) for simulating
-vapor-liquid coexistence, and transport DPD (tDPD) for modeling
-advection-diffusion-reaction systems. The equations of motion of these
-DPD extensions are integrated through a modified velocity-Verlet (MVV)
-algorithm.
-
-[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
-
-[Supporting info:]
-
-src/USER-MESO: filenames -> commands
-src/USER-MESO/README
-"atom_style edpd"_atom_style.html
-"pair_style edpd"_pair_meso.html
-"pair_style mdpd"_pair_meso.html
-"pair_style tdpd"_pair_meso.html
-"fix mvv/dpd"_fix_mvv_dpd.html
-examples/USER/meso
-http://lammps.sandia.gov/movies.html#mesodpd :ul
-
-:line
-
-USER-MOFFF package :link(PKG-USER-MOFFF),h4
-
-[Contents:]
-
-Pair, angle and improper styles needed to employ the MOF-FF
-force field by Schmid and coworkers with LAMMPS.
-MOF-FF is a first principles derived force field with the primary aim
-to simulate MOFs and related porous framework materials, using spherical
-Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
-2013, 250, 1128-1141.
-For the usage of MOF-FF see the example in the example directory as
-well as the "MOF+"_MOFplus website.
-
-:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
-
-[Author:] Hendrik Heenen (Technical U of Munich),
-Rochus Schmid (Ruhr-University Bochum).
-
-[Supporting info:]
-
-src/USER-MOFFF: filenames -> commands
-src/USER-MOFFF/README
-"pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html
-"angle_style class2"_angle_class2.html
-"angle_style cosine/buck6d"_angle_cosine_buck6d.html
-"improper_style inversion/harmonic"_improper_inversion_harmonic.html
-examples/USER/mofff :ul
-
-:line
-
-USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
-
-[Contents:]
-
-A "dump molfile"_dump_molfile.html command which uses molfile plugins
-that are bundled with the "VMD"_vmd-home
-molecular visualization and analysis program, to enable LAMMPS to dump
-snapshots in formats compatible with various molecular simulation
-tools.
-
-To use this package you must have the desired VMD plugins available on
-your system.
-
-Note that this package only provides the interface code, not the
-plugins themselves, which will be accessed when requesting a specific
-plugin via the "dump molfile"_dump_molfile.html command.  Plugins can
-be obtained from a VMD installation which has to match the platform
-that you are using to compile LAMMPS for. By adding plugins to VMD,
-support for new file formats can be added to LAMMPS (or VMD or other
-programs that use them) without having to re-compile the application
-itself.  More information about the VMD molfile plugins can be found
-at
-"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-molfile on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-MOLFILE: filenames -> commands
-src/USER-MOLFILE/README
-lib/molfile/README
-"dump molfile"_dump_molfile.html :ul
-
-:line
-
-USER-NETCDF package :link(PKG-USER-NETCDF),h4
-
-[Contents:]
-
-Dump styles for writing NetCDF formatted dump files.  NetCDF is a
-portable, binary, self-describing file format developed on top of
-HDF5. The file contents follow the AMBER NetCDF trajectory conventions
-(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
-
-To use this package you must have the NetCDF library available on your
-system.
-
-Note that NetCDF files can be directly visualized with the following
-tools:
-
-"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
-"VMD"_vmd-home
-"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
-
-:link(ovito,http://www.ovito.org)
-:link(vmd-home,https://www.ks.uiuc.edu/Research/vmd/)
-:link(atomeye,http://www.libatoms.org)
-
-[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-netcdf on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-NETCDF: filenames -> commands
-src/USER-NETCDF/README
-lib/netcdf/README
-"dump netcdf"_dump_netcdf.html :ul
-
-:line
-
-USER-OMP package :link(PKG-USER-OMP),h4
-
-[Contents:]
-
-Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
-kspace styles which are altered to enable threading on many-core CPUs
-via OpenMP directives.  All of them have an "omp" in their style name.
-The "Speed omp"_Speed_omp.html doc page gives details of what hardware
-and compilers are required on your system, and how to build and use
-this package.  Its styles can be invoked at run time via the "-sf omp"
-or "-suffix omp" "command-line switches"_Run_options.html.  Also see
-the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL
-packages, which have styles optimized for CPUs.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-NOTE: To enable multi-threading support the compile flag "-fopenmp"
-and the link flag "-fopenmp" (for GNU compilers, you have to look up
-the equivalent flags for other compilers) must be used to build LAMMPS.
-When using Intel compilers, also the "-restrict" flag is required.
-The USER-OMP package can be compiled without enabling OpenMP; then
-all code will be compiled as serial and the only improvement over the
-regular styles are some data access optimization. These flags should
-be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
-See src/MAKE/OPTIONS/Makefile.omp for an example.
-
-Once you have an appropriate Makefile.machine, you can
-install/un-install the package and build LAMMPS in the usual manner:
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-omp on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-OMP: filenames -> commands
-src/USER-OMP/README
-"Speed packages"_Speed_packages.html
-"Speed omp"_Speed_omp.html
-"Section 2.6 -sf omp"_Run_options.html
-"Section 2.6 -pk omp"_Run_options.html
-"package omp"_package.html
-"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o)
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-USER-PHONON package :link(PKG-USER-PHONON),h4
-
-[Contents:]
-
-A "fix phonon"_fix_phonon.html command that calculates dynamical
-matrices, which can then be used to compute phonon dispersion
-relations, directly from molecular dynamics simulations.
-And a "dynamical_matrix"_dynamical_matrix.html as well as a
-"third_order"_third_order.html command to compute the dynamical matrix
-and third order tensor from finite differences.
-
-[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
-and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
-
-
-[Supporting info:]
-
-src/USER-PHONON: filenames -> commands
-src/USER-PHONON/README
-"fix phonon"_fix_phonon.html
-"dynamical_matrix"_dynamical_matrix.html
-"third_order"_third_order.html
-examples/USER/phonon :ul
-
-:line
-
-USER-PTM package :link(PKG-USER-PTM),h4
-
-[Contents:]
-
-A "compute ptm/atom"_compute_ptm_atom.html command that calculates
-local structure characterization using the Polyhedral Template
-Matching methodology.
-
-[Author:] Peter Mahler Larsen (MIT).
-
-[Supporting info:]
-
-src/USER-PTM: filenames not starting with ptm_ -> commands
-src/USER-PTM: filenames starting with ptm_ -> supporting code
-src/USER-PTM/LICENSE
-"compute ptm/atom"_compute_ptm_atom.html :ul
-
-:line
-
-USER-QMMM package :link(PKG-USER-QMMM),h4
-
-[Contents:]
-
-A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
-QM/MM simulation, currently only in combination with the "Quantum
-ESPRESSO"_espresso package.
-
-:link(espresso,http://www.quantum-espresso.org)
-
-To use this package you must have Quantum ESPRESSO available on your
-system.
-
-The current implementation only supports an ONIOM style mechanical
-coupling to the Quantum ESPRESSO plane wave DFT package.
-Electrostatic coupling is in preparation and the interface has been
-written in a manner that coupling to other QM codes should be possible
-without changes to LAMMPS itself.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-qmmm on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-QMMM: filenames -> commands
-src/USER-QMMM/README
-lib/qmmm/README
-"fix phonon"_fix_phonon.html
-lib/qmmm/example-ec/README
-lib/qmmm/example-mc/README :ul
-
-:line
-
-USER-QTB package :link(PKG-USER-QTB),h4
-
-[Contents:]
-
-Two fixes which provide a self-consistent quantum treatment of
-vibrational modes in a classical molecular dynamics simulation.  By
-coupling the MD simulation to a colored thermostat, it introduces zero
-point energy into the system, altering the energy power spectrum and
-the heat capacity to account for their quantum nature. This is useful
-when modeling systems at temperatures lower than their classical
-limits or when temperatures ramp across the classical limits in a
-simulation.
-
-[Author:] Yuan Shen (Stanford U).
-
-[Supporting info:]
-
-src/USER-QTB: filenames -> commands
-src/USER-QTB/README
-"fix qtb"_fix_qtb.html
-"fix qbmsst"_fix_qbmsst.html
-examples/USER/qtb :ul
-
-:line
-
-USER-QUIP package :link(PKG-USER-QUIP),h4
-
-[Contents:]
-
-A "pair_style quip"_pair_quip.html command which wraps the "QUIP
-libAtoms library"_quip, which includes a variety of interatomic
-potentials, including Gaussian Approximation Potential (GAP) models
-developed by the Cambridge University group.
-
-:link(quip,https://github.com/libAtoms/QUIP)
-
-To use this package you must have the QUIP libAtoms library available
-on your system.
-
-[Author:] Albert Bartok (Cambridge University)
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-quip on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-QUIP: filenames -> commands
-src/USER-QUIP/README
-"pair_style quip"_pair_quip.html
-examples/USER/quip :ul
-
-:line
-
-USER-REAXC package :link(PKG-USER-REAXC),h4
-
-[Contents:]
-
-A pair style which implements the ReaxFF potential in C/C++.  ReaxFF
-is a universal reactive force field.  See the src/USER-REAXC/README file
-for more info on differences between the two packages.  Also two fixes
-for monitoring molecules as bonds are created and destroyed.
-
-[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
-
-[Supporting info:]
-
-src/USER-REAXC: filenames -> commands
-src/USER-REAXC/README
-"pair_style reax/c"_pair_reaxc.html
-"fix reax/c/bonds"_fix_reaxc_bonds.html
-"fix reax/c/species"_fix_reaxc_species.html
-examples/reax :ul
-
-:line
-
-USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
-
-[Contents:]
-
-A KSpace style which wraps the "ScaFaCoS Coulomb solver
-library"_http://www.scafacos.de to compute long-range Coulombic
-interactions.
-
-To use this package you must have the ScaFaCoS library available on
-your system.
-
-[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
-
-ScaFaCoS itself was developed by a consortium of German research
-facilities with a BMBF (German Ministry of Science and Education)
-funded project in 2009-2012. Participants of the consortium were the
-Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
-the Forschungszentrum Juelich.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-scafacos on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-SCAFACOS: filenames -> commands
-src/USER-SCAFACOS/README
-"kspace_style scafacos"_kspace_style.html
-"kspace_modify"_kspace_modify.html
-examples/USER/scafacos :ul
-
-:line
-
-USER-SDPD package :link(PKG-USER-SDPD),h4
-
-[Contents:]
-
-A pair style for smoothed dissipative particle dynamics (SDPD), which
-is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
-where thermal fluctuations are important (see the
-"USER-SPH package"_#PKG-USER-SPH).
-Also two fixes for moving and rigid body integration of SPH/SDPD particles
-(particles of atom_style meso).
-
-[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic
-Sciences, Iran).
-
-[Supporting info:]
-
-src/USER-SDPD: filenames -> commands
-src/USER-SDPD/README
-"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html
-"fix meso/move"_fix_meso_move.html
-"fix rigid/meso"_fix_rigid_meso.html
-examples/USER/sdpd :ul
-
-:line
-
-USER-SMD package :link(PKG-USER-SMD),h4
-
-[Contents:]
-
-An atom style, fixes, computes, and several pair styles which
-implements smoothed Mach dynamics (SMD) for solids, which is a model
-related to smoothed particle hydrodynamics (SPH) for liquids (see the
-"USER-SPH package"_#PKG-USER-SPH).
-
-This package solves solids mechanics problems via a state of the art
-stabilized meshless method with hourglass control.  It can specify
-hydrostatic interactions independently from material strength models,
-i.e. pressure and deviatoric stresses are separated.  It provides many
-material models (Johnson-Cook, plasticity with hardening,
-Mie-Grueneisen, Polynomial EOS) and allows new material models to be
-added.  It implements rigid boundary conditions (walls) which can be
-specified as surface geometries from *.STL files.
-
-[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
-Dynamics, Ernst Mach Institute, Germany).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-smd on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-SMD: filenames -> commands
-src/USER-SMD/README
-doc/PDF/SMD_LAMMPS_userguide.pdf
-examples/USER/smd
-http://lammps.sandia.gov/movies.html#smd :ul
-
-:line
-
-USER-SMTBQ package :link(PKG-USER-SMTBQ),h4
-
-[Contents:]
-
-A pair style which implements a Second Moment Tight Binding model with
-QEq charge equilibration (SMTBQ) potential for the description of
-ionocovalent bonds in oxides.
-
-[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
-Tetot (LAAS-CNRS, France).
-
-[Supporting info:]
-
-src/USER-SMTBQ: filenames -> commands
-src/USER-SMTBQ/README
-"pair_style smtbq"_pair_smtbq.html
-examples/USER/smtbq :ul
-
-:line
-
-USER-SPH package :link(PKG-USER-SPH),h4
-
-[Contents:]
-
-An atom style, fixes, computes, and several pair styles which
-implements smoothed particle hydrodynamics (SPH) for liquids.  See the
-related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics
-(SMD) for solids.
-
-This package contains ideal gas, Lennard-Jones equation of states,
-Tait, and full support for complete (i.e. internal-energy dependent)
-equations of state.  It allows for plain or Monaghans XSPH integration
-of the equations of motion.  It has options for density continuity or
-density summation to propagate the density field.  It has
-"set"_set.html command options to set the internal energy and density
-of particles from the input script and allows the same quantities to
-be output with thermodynamic output or to dump files via the "compute
-property/atom"_compute_property_atom.html command.
-
-[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
-Dynamics, Ernst Mach Institute, Germany).
-
-[Supporting info:]
-
-src/USER-SPH: filenames -> commands
-src/USER-SPH/README
-doc/PDF/SPH_LAMMPS_userguide.pdf
-examples/USER/sph
-http://lammps.sandia.gov/movies.html#sph :ul
-
-:line
-
-USER-TALLY package :link(PKG-USER-TALLY),h4
-
-[Contents:]
-
-Several compute styles that can be called when pairwise interactions
-are calculated to tally information (forces, heat flux, energy,
-stress, etc) about individual interactions.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Supporting info:]
-
-src/USER-TALLY: filenames -> commands
-src/USER-TALLY/README
-"compute */tally"_compute_tally.html
-examples/USER/tally :ul
-
-:line
-
-USER-UEF package :link(PKG-USER-UEF),h4
-
-[Contents:]
-
-A fix style for the integration of the equations of motion under
-extensional flow with proper boundary conditions, as well as several
-supporting compute styles and an output option.
-
-[Author:] David Nicholson (MIT).
-
-[Supporting info:]
-
-src/USER-UEF: filenames -> commands
-src/USER-UEF/README
-"fix nvt/uef"_fix_nh_uef.html
-"fix npt/uef"_fix_nh_uef.html
-"compute pressure/uef"_compute_pressure_uef.html
-"compute temp/uef"_compute_temp_uef.html
-"dump cfg/uef"_dump_cfg_uef.html
-examples/uef :ul
-
-:line
-
-USER-VTK package :link(PKG-USER-VTK),h4
-
-[Contents:]
-
-A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
-"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
-other visualization packages.
-
-:link(vtk,http://www.vtk.org)
-:link(paraview,http://www.paraview.org)
-
-To use this package you must have VTK library available on your
-system.
-
-[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-vtk on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-VTK: filenames -> commands
-src/USER-VTK/README
-lib/vtk/README
-"dump vtk"_dump_vtk.html :ul
-
-
-:line
-
-USER-YAFF package :link(PKG-USER-YAFF),h4
-
-[Contents:]
-
-Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code.
-The expressions and their use are discussed in the following papers
-
-Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015
-Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul
-
-which discuss the "QuickFF"_quickff methodology.
-
-
-:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877)
-:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173)
-:link(quickff,http://molmod.github.io/QuickFF)
-:link(yaff,https://github.com/molmod/yaff)
-
-
-[Author:] Steven Vandenbrande.
-
-[Supporting info:]
-
-src/USER-YAFF/README
-"angle_style cross"_angle_cross.html
-"angle_style mm3"_angle_mm3.html
-"bond_style mm3"_bond_mm3.html
-"improper_style distharm"_improper_distharm.html
-"improper_style sqdistharm"_improper_sqdistharm.html
-"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
-"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
-examples/USER/yaff :ul
diff --git a/doc/txt/fix.txt b/doc/txt/fix.txt
deleted file mode 100644
index fd281bce83..0000000000
--- a/doc/txt/fix.txt
+++ /dev/null
@@ -1,392 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix command :h3
-
-[Syntax:]
-
-fix ID group-ID style args :pre
-
-ID = user-assigned name for the fix
-group-ID = ID of the group of atoms to apply the fix to
-style = one of a long list of possible style names (see below)
-args = arguments used by a particular style :ul
-
-[Examples:]
-
-fix 1 all nve
-fix 3 all nvt temp 300.0 300.0 0.01
-fix mine top setforce 0.0 NULL 0.0 :pre
-
-[Description:]
-
-Set a fix that will be applied to a group of atoms.  In LAMMPS, a
-"fix" is any operation that is applied to the system during
-timestepping or minimization.  Examples include updating of atom
-positions and velocities due to time integration, controlling
-temperature, applying constraint forces to atoms, enforcing boundary
-conditions, computing diagnostics, etc.  There are hundreds of fixes
-defined in LAMMPS and new ones can be added; see the
-"Modify"_Modify.html doc page for details.
-
-Fixes perform their operations at different stages of the timestep.
-If 2 or more fixes operate at the same stage of the timestep, they are
-invoked in the order they were specified in the input script.
-
-The ID of a fix can only contain alphanumeric characters and
-underscores.
-
-Fixes can be deleted with the "unfix"_unfix.html command.
-
-NOTE: The "unfix"_unfix.html command is the only way to turn off a
-fix; simply specifying a new fix with a similar style will not turn
-off the first one.  This is especially important to realize for
-integration fixes.  For example, using a "fix nve"_fix_nve.html
-command for a second run after using a "fix nvt"_fix_nh.html command
-for the first run, will not cancel out the NVT time integration
-invoked by the "fix nvt" command.  Thus two time integrators would be
-in place!
-
-If you specify a new fix with the same ID and style as an existing
-fix, the old fix is deleted and the new one is created (presumably
-with new settings).  This is the same as if an "unfix" command were
-first performed on the old fix, except that the new fix is kept in the
-same order relative to the existing fixes as the old one originally
-was.  Note that this operation also wipes out any additional changes
-made to the old fix via the "fix_modify"_fix_modify.html command.
-
-The "fix modify"_fix_modify.html command allows settings for some
-fixes to be reset.  See the doc page for individual fixes for details.
-
-Some fixes store an internal "state" which is written to binary
-restart files via the "restart"_restart.html or
-"write_restart"_write_restart.html commands.  This allows the fix to
-continue on with its calculations in a restarted simulation.  See the
-"read_restart"_read_restart.html command for info on how to re-specify
-a fix in an input script that reads a restart file.  See the doc pages
-for individual fixes for info on which ones can be restarted.
-
-:line
-
-Some fixes calculate one of three styles of quantities: global,
-per-atom, or local, which can be used by other commands or output as
-described below.  A global quantity is one or more system-wide values,
-e.g. the energy of a wall interacting with particles.  A per-atom
-quantity is one or more values per atom, e.g. the displacement vector
-for each atom since time 0.  Per-atom values are set to 0.0 for atoms
-not in the specified fix group.  Local quantities are calculated by
-each processor based on the atoms it owns, but there may be zero or
-more per atoms.
-
-Note that a single fix can produce either global or per-atom or local
-quantities (or none at all), but not both global and per-atom.  It can
-produce local quantities in tandem with global or per-atom quantities.
-The fix doc page will explain.
-
-Global, per-atom, and local quantities each come in three kinds: a
-single scalar value, a vector of values, or a 2d array of values.  The
-doc page for each fix describes the style and kind of values it
-produces, e.g. a per-atom vector.  Some fixes produce more than one
-kind of a single style, e.g. a global scalar and a global vector.
-
-When a fix quantity is accessed, as in many of the output commands
-discussed below, it can be referenced via the following bracket
-notation, where ID is the ID of the fix:
-
-f_ID | entire scalar, vector, or array
-f_ID\[I\] | one element of vector, one column of array
-f_ID\[I\]\[J\] | one element of array :tb(s=|)
-
-In other words, using one bracket reduces the dimension of the
-quantity once (vector -> scalar, array -> vector).  Using two brackets
-reduces the dimension twice (array -> scalar).  Thus a command that
-uses scalar fix values as input can also process elements of a vector
-or array.
-
-Note that commands and "variables"_variable.html which use fix
-quantities typically do not allow for all kinds, e.g. a command may
-require a vector of values, not a scalar.  This means there is no
-ambiguity about referring to a fix quantity as f_ID even if it
-produces, for example, both a scalar and vector.  The doc pages for
-various commands explain the details.
-
-:line
-
-In LAMMPS, the values generated by a fix can be used in several ways:
-
-Global values can be output via the "thermo_style
-custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
-Or the values can be referenced in a "variable equal"_variable.html or
-"variable atom"_variable.html command. :ulb,l
-
-Per-atom values can be output via the "dump custom"_dump.html command.
-Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html
-command or reduced by the "compute reduce"_compute_reduce.html
-command.  Or the per-atom values can be referenced in an "atom-style
-variable"_variable.html. :l
-
-Local values can be reduced by the "compute
-reduce"_compute_reduce.html command, or histogrammed by the "fix
-ave/histo"_fix_ave_histo.html command. :l
-:ule
-
-See the "Howto output"_Howto_output.html doc page for a summary of
-various LAMMPS output options, many of which involve fixes.
-
-The results of fixes that calculate global quantities can be either
-"intensive" or "extensive" values.  Intensive means the value is
-independent of the number of atoms in the simulation,
-e.g. temperature.  Extensive means the value scales with the number of
-atoms in the simulation, e.g. total rotational kinetic energy.
-"Thermodynamic output"_thermo_style.html will normalize extensive
-values by the number of atoms in the system, depending on the
-"thermo_modify norm" setting.  It will not normalize intensive values.
-If a fix value is accessed in another way, e.g. by a
-"variable"_variable.html, you may want to know whether it is an
-intensive or extensive value.  See the doc page for individual fixes
-for further info.
-
-:line
-
-Each fix style has its own doc page which describes its arguments and
-what it does, as listed below.  Here is an alphabetic list of fix
-styles available in LAMMPS.  They are also listed in more compact form
-on the "Commands fix"_Commands_fix.html doc page.
-
-There are also additional accelerated fix styles included in the
-LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
-The individual style names on the "Commands fix"_Commands_fix.html doc
-page are followed by one or more of (g,i,k,o,t) to indicate which
-accelerated styles exist.
-
-"adapt"_fix_adapt.html - change a simulation parameter over time
-"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt
-"addforce"_fix_addforce.html - add a force to each atom
-"addtorque"_fix_addtorque.html - add a torque to a group of atoms
-"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
-"atc"_fix_atc.html - initiates a coupled MD/FE simulation
-"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
-"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
-"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
-"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
-"ave/correlate/long"_fix_ave_correlate_long.html -
-"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
-"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo
-"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
-"aveforce"_fix_aveforce.html - add an averaged force to each atom
-"balance"_fix_balance.html - perform dynamic load-balancing
-"bocs"_fix_bocs.html - NPT style time integration with pressure correction
-"bond/break"_fix_bond_break.html - break bonds on the fly
-"bond/create"_fix_bond_create.html - create bonds on the fly
-"bond/react"_fix_bond_react.html - apply topology changes to model reactions
-"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
-"box/relax"_fix_box_relax.html - relax box size during energy minimization
-"client/md"_fix_client_md.html - MD client for client/server simulations
-"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
-"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library
-"controller"_fix_controller.html - apply control loop feedback mechanism
-"deform"_fix_deform.html - change the simulation box size/shape
-"deposit"_fix_deposit.html - add new atoms above a surface
-"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics
-"drag"_fix_drag.html - drag atoms towards a defined coordinate
-"drude"_fix_drude.html - part of Drude oscillator polarization model
-"drude/transform/direct"_fix_drude_transform.html -  part of Drude oscillator polarization model
-"drude/transform/inverse"_fix_drude_transform.html -  part of Drude oscillator polarization model
-"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
-"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations
-"efield"_fix_efield.html - impose electric field on system
-"ehex"_fix_ehex.html - enhanced heat exchange algorithm
-"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
-"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
-"eos/cv"_fix_eos_cv.html -
-"eos/table"_fix_eos_table.html -
-"eos/table/rx"_fix_eos_table_rx.html -
-"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
-"external"_fix_external.html - callback to an external driver program
-"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat
-"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA
-"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux
-"freeze"_fix_freeze.html - freeze atoms in a granular simulation
-"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
-"gld"_fix_gld.html - generalized Langevin dynamics integrator
-"gle"_fix_gle.html - generalized Langevin equation thermostat
-"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
-"grem"_fix_grem.html - implements the generalized replica exchange method
-"halt"_fix_halt.html - terminate a dynamics run or minimization
-"heat"_fix_heat.html - add/subtract momentum-conserving heat
-"hyper/global"_fix_hyper_global.html - global hyperdynamics
-"hyper/local"_fix_hyper_local.html - local hyperdynamics
-"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol
-"indent"_fix_indent.html - impose force due to an indenter
-"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
-"langevin"_fix_langevin.html - Langevin temperature control
-"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators
-"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model
-"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system
-"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
-"lb/fluid"_fix_lb_fluid.html -
-"lb/momentum"_fix_lb_momentum.html -
-"lb/pc"_fix_lb_pc.html -
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
-"lb/viscous"_fix_lb_viscous.html -
-"lineforce"_fix_lineforce.html - constrain atoms to move in a line
-"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization
-"meso"_fix_meso.html - time integration for SPH/DPDE particles
-"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
-"meso/stationary"_fix_meso_stationary.html -
-"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
-"move"_fix_move.html - move atoms in a prescribed fashion
-"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
-"msst"_fix_msst.html - multi-scale shock technique (MSST) integration
-"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
-"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
-"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
-"neb"_fix_neb.html - nudged elastic band (NEB) spring forces
-"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
-"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
-"nph/body"_fix_nph_body.html - NPH for body particles
-"nph/eff"_fix_nh_eff.html - NPH for  nuclei and electrons in the electron force field model
-"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
-"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
-"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
-"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
-"npt/body"_fix_npt_body.html - NPT for body particles
-"npt/eff"_fix_nh_eff.html - NPT for  nuclei and electrons in the electron force field model
-"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
-"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow
-"nve"_fix_nve.html - constant NVE time integration
-"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces
-"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
-"nve/body"_fix_nve_body.html - NVE for body particles
-"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models
-"nve/eff"_fix_nve_eff.html - NVE for  nuclei and electrons in the electron force field model
-"nve/limit"_fix_nve_limit.html - NVE with limited step length
-"nve/line"_fix_nve_line.html - NVE for line segments
-"nve/manifold/rattle"_fix_nve_manifold_rattle.html -
-"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
-"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
-"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system
-"nve/tri"_fix_nve_tri.html - NVE for triangles
-"nvk"_fix_nvk.html - constant kinetic energy time integration
-"nvt"_fix_nh.html - NVT time integration via Nose/Hoover
-"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
-"nvt/body"_fix_nvt_body.html - NVT for body particles
-"nvt/eff"_fix_nh_eff.html - NVE for  nuclei and electrons in the electron force field model
-"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
-"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model
-"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
-"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow
-"oneway"_fix_oneway.html - constrain particles on move in one direction
-"orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
-"orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
-"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations
-"pimd"_fix_pimd.html - Feynman path integral molecular dynamics
-"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
-"plumed"_fix_plumed.html - wrapper on PLUMED free energy library
-"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
-"pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain
-"precession/spin"_fix_precession_spin.html -
-"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
-"print"_fix_print.html - print text and variables during a simulation
-"property/atom"_fix_property_atom.html - add customized per-atom values
-"python/invoke"_fix_python_invoke.html - call a Python function during a simulation
-"python/move"_fix_python_move.html -  call a Python function during a simulation run
-"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator
-"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
-"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
-"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
-"qeq/point"_fix_qeq.html - charge equilibration via point method
-"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential
-"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
-"qeq/slater"_fix_qeq.html - charge equilibration via Slater method
-"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling
-"qtb"_fix_qtb.html - implement quantum thermal bath scheme
-"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
-"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
-"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
-"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
-"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
-"rhok"_fix_rhok.html - add bias potential for long-range ordered systems
-"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
-"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
-"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
-"rigid/nph/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
-"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
-"rigid/npt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
-"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
-"rigid/nve/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
-"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
-"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
-"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
-"rx"_fix_rx.html -
-"saed/vtk"_fix_saed_vtk.html -
-"setforce"_fix_setforce.html - set the force on each atom
-"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
-"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
-"smd"_fix_smd.html - applied a steered MD force to a group
-"smd/adjust_dt"_fix_smd_adjust_dt.html -
-"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
-"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
-"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html -
-"smd/setvel"_fix_smd_setvel.html -
-"smd/wall_surface"_fix_smd_wall_surface.html -
-"spring"_fix_spring.html - apply harmonic spring force to group of atoms
-"spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms
-"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms
-"spring/self"_fix_spring_self.html - spring from each atom to its origin
-"srd"_fix_srd.html - stochastic rotation dynamics (SRD)
-"store/force"_fix_store_force.html - store force on each atom
-"store/state"_fix_store_state.html - store attributes for each atom
-"tdpd/source"_fix_dpd_source.html -
-"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat
-"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
-"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
-"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
-"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model
-"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
-"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
-"ti/spring"_fix_ti_spring.html -
-"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
-"ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
-"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options
-"tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
-"vector"_fix_vector.html - accumulate a global vector every N timesteps
-"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
-"viscous"_fix_viscous.html - viscous damping for granular simulations
-"wall/body/polygon"_fix_wall_body_polygon.html -
-"wall/body/polyhedron"_fix_wall_body_polyhedron.html -
-"wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
-"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles
-"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
-"wall/gran/region"_fix_wall_gran_region.html -
-"wall/harmonic"_fix_wall.html - harmonic spring wall
-"wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
-"wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
-"wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
-"wall/morse"_fix_wall.html - Morse potential wall
-"wall/piston"_fix_wall_piston.html - moving reflective piston wall
-"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
-"wall/region"_fix_wall_region.html - use region surface as wall
-"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles
-"wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
-
-[Restrictions:]
-
-Some fix styles are part of specific packages.  They are only enabled
-if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  The doc pages for
-individual fixes tell if it is part of a package.
-
-[Related commands:]
-
-"unfix"_unfix.html, "fix_modify"_fix_modify.html
-
-[Default:] none